# hmmscan :: search sequence(s) against a profile database
# HMMER 3.2.1 (June 2018); http://hmmer.org/
# Copyright (C) 2018 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query sequence file:             /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Thaumarchaeota/Candidatus_Nitrosoarchaeum_limnia_BG20-ASM24114v2/GCA_000241145.2_ASM24114v2_protein.faa
# target HMM database:             /oak/stanford/groups/akundaje/marinovg/genomes/PFam/PFam32.0/Pfam-A.hmm
# output directed to file:         /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Thaumarchaeota/Candidatus_Nitrosoarchaeum_limnia_BG20-ASM24114v2/GCA_000241145.2_ASM24114v2_protein.PFam32-A
# per-seq hits tabular output:     /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Thaumarchaeota/Candidatus_Nitrosoarchaeum_limnia_BG20-ASM24114v2/GCA_000241145.2_ASM24114v2_protein.PFam32-A.tblout
# number of worker threads:        20
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       EPA04243.1  [L=436]
Description: phosphomethylpyrimidine kinase, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-72  244.2   0.7    2.2e-72  243.4   0.7    1.4  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase
    3.5e-55  186.1   0.0    7.4e-55  185.0   0.0    1.6  1  ThiP_synth    Thiamine-phosphate synthase
    3.1e-10   39.9   0.0    4.9e-10   39.2   0.0    1.2  1  PfkB          pfkB family carbohydrate kinase
    5.2e-05   23.3   7.5     0.0017   18.4   0.5    3.4  3  HTH_56        Cch helix turn helix domain
     0.0021   17.6   0.1     0.0033   16.9   0.1    1.4  1  Carb_kinase   Carbohydrate kinase
  ------ inclusion threshold ------
       0.07   12.5   0.3       0.31   10.4   0.3    1.9  1  HK            Hydroxyethylthiazole kinase family
       0.68   10.1   5.0        1.3    9.2   0.5    3.0  3  KH_5          NusA-like KH domain


Domain annotation for each model (and alignments):
>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  243.4   0.7   8.8e-76   2.2e-72       1     242 [.      10     247 ..      10     251 .. 0.98

  Alignments for each domain:
  == domain 1  score: 243.4 bits;  conditional E-value: 8.8e-76
                   ETTSSSHHHHHHHHHHHTTEEEEEEEEEEEEEETTCEEEEEE--HHHHHHHHHHHHHTS--SEEEE-S--SHHHHHHHHHHHHHTTSSEEEE---SS CS
  Phos_pyr_kin   1 DssGGAGiqADlktfsalgvygmsvitaltaqntkgvkevhplpaelveaqleavledvkvdavKiGmlasaeiievvaeklkkykvpvVlDPVmva 97 
                   D+s+GAGiq D+ktf +l++yg++vita+t qnt +   v+p++++++++ql+++++d+k+d +KiGm++++eii+++ ++lk++k+p+V+DPV+ +
    EPA04243.1  10 DPSSGAGIQSDVKTFDSLNAYGLTVITAITGQNTSNFGMVEPVSQKILKNQLDSIMTDFKIDGIKIGMVYNSEIIKTISKELKNKKIPIVIDPVIKS 106
                   9************************************************************************************************ PP

                   CTSSSBSSHHHHHHHHHHTGGG-SEEE-BHHHHHHHHT---SSHHHHHHHHHHHHHTT-SEEEEEEGGS-SSSEEEEEEEETSSEEEEEEEE----S CS
  Phos_pyr_kin  98 ksgselleeeavealkeeLlplatvitPNlpEaeaLlgekikteedmkeaakkllklgakaVlikGghlegeeavvtdvlydgeeveeleaerietk 194
                   ++g +l+++ a+  +k+ L+platvitPN +Eae L++ ki+t++++++aa k++++g+++V+i+G +    + ++ d+++++++++++++++i+ k
    EPA04243.1 107 TTGGQLIDKAAIVDFKKFLIPLATVITPNKFEAEFLSEIKIRTKKSLHKAALKIQAMGVENVIITGLKS---DGQISDYILEQKNEYTISSKKIS-K 199
                   *******************************************************************95...56679******************.* PP

                   --BTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHHHHHHHCG-BSTSSS CS
  Phos_pyr_kin 195 nthGtGCtlssaiaaelakgesleeAvkkAkeyvteaikealelgkga 242
                   ++hG+GC +s+++  +l +g +l++Avk +ke+++++ik+a ++g g+
    EPA04243.1 200 TNHGSGCNYSASLLFSLVNGAPLKDAVKFSKEFTYNSIKNAKNIGYGI 247
                   ********************************************9876 PP

>> ThiP_synth  Thiamine-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.0   0.0   2.9e-58   7.4e-55       1     164 [.     261     429 ..     261     430 .. 0.98

  Alignments for each domain:
  == domain 1  score: 185.0 bits;  conditional E-value: 2.9e-58
                 HHHHHHHHHHCC--.GCC--TT-B-EEEE-ST--SGGGEEEETT-EEE-TSSEEE-S-EEETS-CHHHHHHHHHHCC-TT--EEEEEE--HHHHHHHCC CS
  ThiP_synth   1 eleralelleeeeefakliPevgsNiayalpdAksieDvaavpGRIvrvkgrvkvvgepefgasshvarvllaamkfdpevraainirydekilealee 99 
                 el++a++++ ++++++k iPe+++N++++++++ksi+++++++GRIv++++ v+v+g+ ++g+s+hvar+l+ ++k++p++ +ain+ry+e+i+++l++
  EPA04243.1 261 ELTNAINKFLQIKNIHKNIPECQTNFVFSKKNPKSIKEILGISGRIVKTGNAVTVAGDLAYGGSKHVARALIIMNKKFPDMCSAINLRYSEEIISKLRK 359
                 6899*********************************************************************************************** PP

                 TTSEEEE--CCCS-CCC....T-HHHHHHHHHHHCC.S-ECEEEE--BCTB--EEEEEESSHHHHHHHHH CS
  ThiP_synth 100 lglkvvefdreeepeev....gstmewgvaeaieel.evpdviydeGgvGkEpmiyvlgkdaeevvekvl 164
                 + l ++++dr++ep++v    gst+ewg+++ai++l ++pdviy++G++GkEpmi++++++++ +++k+ 
  EPA04243.1 360 KRLVIASYDRSKEPKNVkskdGSTVEWGIKQAIRNLkKPPDVIYHTGDFGKEPMIIIFAETPTLILKKIS 429
                 ************************************99**************************999986 PP

>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   0.0   1.9e-13   4.9e-10     151     282 ..      87     229 ..      74     240 .. 0.80

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 1.9e-13
                 HHHHHHHTTEEEEEECESSSHH..........HHHHHHHHH.CTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSEEEEEEGGGEEEEEE.. CS
        PfkB 151 laeaaknggtfdpnlldplgaq..........fkeallell.aladllkpneeElealtgekledieealaalhklkakgaktvvvtlGkeGalvve.. 236
                 +++  kn++  +p++ dp +++          +  +++++l +la++++pn  E+e+l++ k+ + +++ +a+ k++a g+++v++t  k   ++++  
  EPA04243.1  87 ISKELKNKK--IPIVIDPVIKSttggqlidkaAIVDFKKFLiPLATVITPNKFEAEFLSEIKIRTKKSLHKAALKIQAMGVENVIITGLKSDGQISDyi 183
                 555556666..4444444444444444888898899999999*********************************************888888888887 PP

                 ..TTEEEEEEE.SSSS-SBGT.THHHHHHHHHHHHHHTTHHHHHHHHHH CS
        PfkB 237 ..kdgelkvpavpkvkvvDtt.GAGDsfvggflaallegksleealrfa 282
                   +++e+ +    ++k+  t+ G G  + +++l +l++g++l++a++f 
  EPA04243.1 184 leQKNEYTI---SSKKISKTNhGSGCNYSASLLFSLVNGAPLKDAVKFS 229
                 534444444...4577788877*************************96 PP

>> HTH_56  Cch helix turn helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.2    0.0038       9.6      31      65 ..      42      71 ..      35      96 .. 0.85
   2 ?    1.0   0.1      0.17   4.3e+02      66      98 ..     166     199 ..     131     213 .. 0.79
   3 !   18.4   0.5   6.7e-07    0.0017      17      96 ..     282     380 ..     271     394 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0038
      HTH_56 31 pneiwGkiekkkektevyIlknvfdkileeagFed 65
                ++ ++G++e+ ++     Ilkn++d+i+++++  d
  EPA04243.1 42 NTSNFGMVEPVSQ----KILKNQLDSIMTDFKI-D 71
                45789*****995....8***********9987.4 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.17
      HTH_56  66 tkvvlkelkekGllesekdrntkkrtv.kkkseg 98 
                 ++v+++ lk+ G +      +++ +t+ +kk+ +
  EPA04243.1 166 ENVIITGLKSDGQISDYILEQKNEYTIsSKKISK 199
                 6788999999999988888888888885555544 PP

  == domain 3  score: 18.4 bits;  conditional E-value: 6.7e-07
      HTH_56  17 nqskFkeegkeasnpn...eiwGkiekkkekte................vyIlknvfdkileeagFedtkvvlkelkekGllesekdrntkkrtvkkks 96 
                  q +F  ++k+ +  +    i G+i k+++  +                ++I++++f +++   + + ++ ++++l++k l+ ++ dr++  ++vk+k 
  EPA04243.1 282 CQTNFVFSKKNPKSIKeilGISGRIVKTGNAVTvagdlayggskhvaraLIIMNKKFPDMCSAINLRYSEEIISKLRKKRLVIASYDRSKEPKNVKSKD 380
                 5666666666544333367899999999988879999999*******************************************************6553 PP

>> Carb_kinase  Carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   1.3e-06    0.0033       4     159 ..       6     170 ..       3     255 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.3e-06
                  EE-BTTCHHHHHHHHHHHHCTT..-SEEEEEESSTTTCCCCTTTTTCEECCTTHTTTS...--SSS-SEEEE-TT-SSSHCHHHHCHHHCCCCS-EEE CS
  Carb_kinase   4 igGsedytGAallaalaalrlg..aglvsvateseaiavlksylpevivhplledeqakileklerldavviGpGLgrdekikklleevlekdeplvi 99 
                  igGs+  +GA++ +   +  +    gl+ + +   + +++   ++  + +++l+++  +i+ +  ++d + iG+   + e ik + +e  +k+ p+vi
   EPA04243.1   6 IGGSDPSSGAGIQSDVKTFDSLnaYGLTVITAITGQNTSNFGMVEP-VSQKILKNQLDSIMTDF-KIDGIKIGMV-YNSEIIKTISKELKNKKIPIVI 100
                  9*************99999876547777666655555555555555.55555534444677776.9********5.56677899************** PP

                  E.......GGGGGSGGGG.....TTTTSSEEEE--HHHHHHHCTTTCHHCCSHHHHHHHHHHHH.TTEEE CS
  Carb_kinase 100 D.......AdgLnllaqkne..lserkaeviLTPhkkEfkrLlkaivkkeddrlelarelaqkl.navvl 159
                  D       ++ L  +a   +  ++    ++++TP+k E + L++  +  +++  ++a +++++  + v++
   EPA04243.1 101 DpviksttGGQLIDKAAIVDfkKFLIPLATVITPNKFEAEFLSEIKIRTKKSLHKAALKIQAMGvENVII 170
                  *5555543344444444334666777789**************999965555555554444432123333 PP

>> HK  Hydroxyethylthiazole kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.3   0.00012      0.31      55     194 ..      73     212 ..      69     260 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00012
                 EE-TT--HHHHHHHHHHHHHHHHTT--EEEE-TTBTTBHHHHHHHHHHHHHS--.....SEEEEEHHHHHHHHTSSCCSCSSSSSS-SHHHHHHHHHHH CS
          HK  55 lNiGtleekaiealkaAvksakevnrPvvlDPVgvgAtelRrelalellkevkl.....avikGNasEilslaglelkvkGvDskeaataavaavqkvA 148
                 + iG + +   e++k+  k+ k++++P+v+DPV  + t         ++   k+      vi  N+ E   l++++ ++k   s +      aa ++ A
  EPA04243.1  73 IKIGMVYN--SEIIKTISKELKNKKIPIVIDPVIKSTTGGQLIDKAAIVDFKKFliplaTVITPNKFEAEFLSEIKIRTK--KSLH-----KAALKIQA 162
                 67899988..88999999***************99998776666666665444322222567777777666666654443..1222.....22333334 PP

                 HHHTSEEEE....ESSS.EEEEESSEEEEEE-S-GGGGGSTTHHHHHHHHH CS
          HK 149 qklrvvvvv....tGev.DvvsdgkkvyklknGtellgkitasGCllgsvv 194
                 + ++ v++      G++ D++ + k++y++++ +++     +sGC +++ +
  EPA04243.1 163 MGVENVIITglksDGQIsDYILEQKNEYTISS-KKISKTNHGSGCNYSASL 212
                 44444333211113443377777777777765.556666677777777654 PP

>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.5   0.00049       1.3      27      45 ..      81      99 ..      68     102 .. 0.89
   2 ?   -2.9   0.0       2.9   7.5e+03      18      31 ..     295     308 ..     286     309 .. 0.74
   3 ?    1.2   0.1      0.16     4e+02      29      48 ..     349     368 ..     346     376 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00049
        KH_5 27 GsrikavsseLkgekidvv 45
                 ++ik++s+eLk++ki +v
  EPA04243.1 81 SEIIKTISKELKNKKIPIV 99
                679*************998 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.9
        KH_5  18 pvGaivgkkGsrik 31 
                  + +i+g +G+++k
  EPA04243.1 295 SIKEILGISGRIVK 308
                 57789999999987 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.16
        KH_5  29 rikavsseLkgekidvvews 48 
                 ++++++s+L++++  +  ++
  EPA04243.1 349 YSEEIISKLRKKRLVIASYD 368
                 6789*********9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       767  (0.0427799); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.62u 0.35s 00:00:00.97 Elapsed: 00:00:00.54
# Mc/sec: 2447.39
//
Query:       EPA04244.1  [L=52]
Description: hypothetical protein BG20_I2366, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.074   13.0   0.8       0.13   12.2   0.1    1.7  2  HalOD2    Halobacterial output domain 2


Domain annotation for each model (and alignments):
>> HalOD2  Halobacterial output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1       0.1   1.8e+03      34      37 ..      18      21 ..      15      25 .. 0.69
   2 ?   12.2   0.1     7e-06      0.13      29      39 ..      34      44 ..      27      50 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.1
      HalOD2 34 CtrC 37
                Ct C
  EPA04244.1 18 CTSC 21
                5555 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 7e-06
      HalOD2 29 ayvWkCtrCGe 39
                ay W+C +CG+
  EPA04244.1 34 AYLWQCFKCGK 44
                8*********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.28s 00:00:00.64 Elapsed: 00:00:00.45
# Mc/sec: 346.42
//
Query:       EPA04245.1  [L=165]
Description: hypothetical protein BG20_I2336 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.1e-38  129.4   0.0    8.5e-38  129.0   0.0    1.1  1  Ribo_biogen_C  Ribosome biogenesis protein, C-terminal
    8.6e-07   28.7   0.1    1.3e-06   28.1   0.1    1.3  1  RLI            Possible Fer4-like domain in RNase L inhibitor


Domain annotation for each model (and alignments):
>> Ribo_biogen_C  Ribosome biogenesis protein, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.0   0.0   9.5e-42   8.5e-38       1     125 [.      38     159 ..      38     160 .. 0.95

  Alignments for each domain:
  == domain 1  score: 129.0 bits;  conditional E-value: 9.5e-42
                    EEE-TT-SSB--GGGHHHHHHT-EEEE---TTT--GGGTTT-E....EB--S-B--STTTTT-BS---HHHHHHHHHHHTT-HHHHHHHHTSSTTH CS
  Ribo_biogen_C   1 ivlspkakkvlspaDreiveksgiavvdcsWarleevkfkklkakeerlLPyLvAaNpvnYgkplkLscvEAlaaalyilglkeeaeellskfkwg 96 
                    +vl+p+++k+l p+D+++++  +i+ +dcsW+ ++++  kk+    +r+LP L+A+Np+nY+k  kL+++EAl+a+l+ilg++++a ++l+kfkwg
     EPA04245.1  38 LVLDPFSEKTLLPSDKSLIN--SIIGIDCSWTLADQAFSKKF-NGIKRKLPPLLAGNPINYSKLNKLTTAEALSASLFILGFRDDALAILDKFKWG 130
                    69*************99976..6***********99998888.679************************************************** PP

                    HHHHHHCHHHHHHH.TT--HHHHHHHHHH CS
  Ribo_biogen_C  97 eeFlelnkelleeYakckdseevvevqke 125
                    ++F+eln++ll+eY+k ++++++  + ke
     EPA04245.1 131 HTFYELNQNLLDEYSKLESEDQIDIILKE 159
                    *********************99877766 PP

>> RLI  Possible Fer4-like domain in RNase L inhibitor, RLI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.1   1.4e-10   1.3e-06       9      31 ..       9      31 ..       1      36 [. 0.84

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 1.4e-10
                --------TTHHHHHTTSEEEES CS
         RLI  9 dqCdPKKCtgkkcarfcpvrlvr 31
                 q+dPKKCt+ k+++f+++++++
  EPA04245.1  9 YQDDPKKCTAAKMVKFGIAKNIK 31
                59*****************9855 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.35s 00:00:00.96 Elapsed: 00:00:00.57
# Mc/sec: 870.89
//
Query:       EPA04246.1  [L=324]
Description: hypothetical protein BG20_I2335, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       770  (0.0429472); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 1942.18
//
Query:       EPA04247.1  [L=104]
Description: hypothetical protein BG20_I2334, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 671.14
//
Query:       EPA04248.1  [L=299]
Description: fibronectin type III domain protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.5e-37  125.2  24.3      5e-14   52.4   5.0    4.2  4  fn3              Fibronectin type III domain
    3.8e-06   27.4  26.5      0.012   16.2   0.7    4.8  4  Pur_ac_phosph_N  Purple acid Phosphatase, N-terminal domain
    6.8e-06   26.0   0.2        2.6    8.0   0.0    4.1  5  fn3_4            Fibronectin-III type domain
      0.002   18.4  26.5     0.0039   17.4   9.0    4.1  4  SusE             SusE outer membrane protein
  ------ inclusion threshold ------
      0.088   13.1   1.5        3.9    7.8   0.1    2.8  3  Interfer-bind    Interferon-alpha/beta receptor, fibronectin 
       0.12   12.8   0.3         21    5.6   0.0    2.5  2  Fimbrillin_C     Major fimbrial subunit protein type IV, Fimb
       0.27   11.1  25.0       0.22   11.4   0.7    4.6  4  PKD              PKD domain
       0.28   12.2   5.8       0.97   10.5   0.7    3.2  3  CopC             CopC domain
          2    9.0   7.9        1.4    9.4   0.6    2.4  2  EspB_PE          ESX-1 secreted protein B PE domain


Domain annotation for each model (and alignments):
>> fn3  Fibronectin type III domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.8   5.6e-05      0.11      56      84 ..       2      30 ..       1      32 [. 0.87
   2 !   52.4   5.0   2.5e-17     5e-14       1      83 [.      52     132 ..      52     134 .. 0.90
   3 !   38.8   0.6   4.5e-13     9e-10       6      83 ..     149     224 ..     146     226 .. 0.87
   4 !   34.0   0.1   1.4e-11   2.8e-08       2      41 ..     248     288 ..     247     298 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.6e-05
                SEEEEESSSTTEEEEEEEEEEETSEEEEE CS
         fn3 56 tsvtltgLkpgteYevrVqavngggegpe 84
                t++  tgL+ gt Y+ +V a+n +g++  
  EPA04248.1  2 TTYSHTGLTTGTVYTYKVSAINSVGTSSA 30
                47999*******************97655 PP

  == domain 2  score: 52.4 bits;  conditional E-value: 2.5e-17
                 TCECEEEEEEESSSEEEEEEE-CS.SSSSTEEEEEEEEEETTSTSTEEEEEECSTSSEEEEESSSTTEEEEEEEEEEETSEEEE CS
         fn3   1 saPsnlsvsevtstsltvsWeppk.dgggpitgYeveyrekgseeewneftvprtttsvtltgLkpgteYevrVqavngggegp 83 
                 ++P+nl++ + ++t++++sW++p  +gg+pit+Y+ve+++ +++    + t + +t ++  tgL+ gt Y+ +V a+n +g++ 
  EPA04248.1  52 DSPTNLTAVSSSPTQINLSWSAPAnNGGAPITSYKVEFKSGSGT--YSTLTTTQST-TYSHTGLTTGTSYTYKVSAINSVGTSY 132
                 57************************************999666..4677777777.8**********************8775 PP

  == domain 3  score: 38.8 bits;  conditional E-value: 4.5e-13
                 EEEEEESSSEEEEEEE-CS.SSSSTEEEEEEEEEETTSTSTEEEEEECSTSSEEEEESSSTTEEEEEEEEEEETSEEEE CS
         fn3   6 lsvsevtstsltvsWeppk.dgggpitgYeveyrekgseeewneftvprtttsvtltgLkpgteYevrVqavngggegp 83 
                 l++++v++t+++++W +p+ + g++i++Y++e + ++++   +e++  ++t s+ ++gL+ g++Y++ V a  g g ++
  EPA04248.1 149 LTATDVSPTQIRLTWIAPSqTYGQHISSYKIEEKLSSGT--FIEVDSESST-SFLVSGLTTGKTYTFVVSANFGLGSSQ 224
                 89*****************************87766444..7888888888.*****************9977666665 PP

  == domain 4  score: 34.0 bits;  conditional E-value: 1.4e-11
                 CECEEEEEEESSSEEEEEEE-CS.SSSSTEEEEEEEEEETT CS
         fn3   2 aPsnlsvsevtstsltvsWeppk.dgggpitgYeveyrekg 41 
                 aP+nl++ + ++t++++sW+ p+ +gg+pitgY++ey++ +
  EPA04248.1 248 APTNLTAVSSSATQINLSWNIPSsNGGAPITGYKIEYKSGS 288
                 8************************************8765 PP

>> Pur_ac_phosph_N  Purple acid Phosphatase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.4    0.0026       5.2      66      87 ..       6      28 ..       1      38 [. 0.75
   2 !   10.6   8.6   0.00032      0.63       6      84 ..      57     127 ..      53     146 .. 0.63
   3 !   16.2   0.7   5.9e-06     0.012       5      83 ..     148     219 ..     144     232 .. 0.79
   4 ?    3.3   0.1     0.064   1.3e+02       6      39 ..     252     290 ..     249     299 .] 0.64

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0026
  Pur_ac_phosph_N 66 ltgLepgttYyYrvgddeg.gwS 87
                      tgL+ gt Y Y+v + ++ g+S
       EPA04248.1  6 HTGLTTGTVYTYKVSAINSvGTS 28
                     69************887665444 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00032
  Pur_ac_phosph_N   6 lsltedtstsmtvsWitpektkksvvrygtssdalestaeatsstyettnyksgyshkatltgLepgttYyYrvgddeg 84 
                      l+  ++++t+++ sW  p++++ + +   + + ++     +t+st      ++  s+++  tgL+ gt Y Y+v + ++
       EPA04248.1  57 LTAVSSSPTQINLSWSAPANNGGAPITSYKVEFKSG---SGTYST-----LTTTQSTTYSHTGLTTGTSYTYKVSAINS 127
                      55556689999****999977655444444433332...233333.....34444444455899999999999976654 PP

  == domain 3  score: 16.2 bits;  conditional E-value: 5.9e-06
  Pur_ac_phosph_N   5 hlsltedtstsmtvsWitpektkksvvrygtssdalestaeatsstyettnyksgyshkatltgLepgttYyYrvgdd.e 83 
                      +l+ t+ ++t+++ +Wi p++       yg+  ++++ + + +s t+   + +s+ s++ +++gL+ g+tY + v ++ +
       EPA04248.1 148 TLTATDVSPTQIRLTWIAPSQ------TYGQHISSYKIEEKLSSGTF--IEVDSESSTSFLVSGLTTGKTYTFVVSANfG 219
                      68899999************9......57777777777777777766..67899*********************87743 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.064
  Pur_ac_phosph_N   6 lsltedtstsmtvsWitpektkks.....vvrygtssda 39 
                      l+  ++++t+++ sW+ p++++ +     +++y   s+ 
       EPA04248.1 252 LTAVSSSATQINLSWNIPSSNGGApitgyKIEYKSGSGT 290
                      55555689********99855443333336666666655 PP

>> fn3_4  Fibronectin-III type domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       3.1   6.1e+03      77      99 ..      10      32 ..       7      35 .. 0.70
   2 !    8.0   0.0    0.0013       2.6       7      39 ..      56      87 ..      49     105 .. 0.84
   3 !    5.3   0.0     0.009        18       4      39 ..     145     179 ..     140     182 .. 0.89
   4 ?   -2.3   0.0       2.2   4.3e+03      75      88 ..     203     216 ..     198     218 .. 0.82
   5 !    7.4   0.0    0.0021       4.2       7      39 ..     251     282 ..     244     293 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.1
       fn3_4 77 kegkkyyFavravDvygRvgpfs 99
                + g++y + v a++  g  ++ s
  EPA04248.1 10 TTGTVYTYKVSAINSVGTSSASS 32
                56788888888888777666655 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0013
       fn3_4  7 qlkiaksvpkgivlsWnveeldkkaaevesYel 39
                +l++ +s+p++i lsW++   ++  a++ sY++
  EPA04248.1 56 NLTAVSSSPTQINLSWSAP-ANNGGAPITSYKV 87
                5777777************.9999*******97 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.009
       fn3_4   4 qkpqlkiaksvpkgivlsWnveeldkkaaevesYel 39 
                 ++p+l+++ ++p++i l+W +  +++  ++++sY++
  EPA04248.1 145 TTPTLTATDVSPTQIRLTWIAP-SQTYGQHISSYKI 179
                 5799***************999.7788889999986 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 2.2
       fn3_4  75 qfkegkkyyFavra 88 
                  ++ gk+y F+v a
  EPA04248.1 203 GLTTGKTYTFVVSA 216
                 567899*****987 PP

  == domain 5  score: 7.4 bits;  conditional E-value: 0.0021
       fn3_4   7 qlkiaksvpkgivlsWnveeldkkaaevesYel 39 
                 +l++ +s++++i lsWn+  +++  a++  Y++
  EPA04248.1 251 NLTAVSSSATQINLSWNIP-SSNGGAPITGYKI 282
                 57777779***********.8889999999987 PP

>> SusE  SusE outer membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.2      0.22   4.4e+02      72      93 ..      10      32 ..       1      42 [. 0.69
   2 !   17.4   9.0     2e-06    0.0039      17      90 ..      49     131 ..      35     140 .. 0.73
   3 ?    4.9   0.9     0.015        30      12      82 ..     136     202 ..     129     216 .. 0.68
   4 !    6.3   0.5    0.0055        11      13      55 ..     238     283 ..     226     298 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.22
        SusE 72 ttetslsitvkeLNtalld.lgl 93
                tt+t ++++v+ +N++ ++ +  
  EPA04248.1 10 TTGTVYTYKVSAINSVGTSsASS 32
                77888999999999888774443 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 2e-06
        SusE  17 tapasevvldednasnealtftWtaa.dygvpaavtYtvqfdkkgedFskp.......vdatg.ttetslsitvkeLNtalld 90 
                  ap s  +l+  ++s ++++++W+a+ + g    ++Y+v+f +  + +s+        ++ tg tt+ts++++v+ +N++ ++
  EPA04248.1  49 VAPDSPTNLTAVSSSPTQINLSWSAPaNNGGAPITSYKVEFKSGSGTYSTLtttqsttYSHTGlTTGTSYTYKVSAINSVGTS 131
                 34444556777777************888888899******9999666666665665544444799************99877 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.015
        SusE  12 daseLtapasevvldednasnealtftWtaadygvpa.avtYtvqfdkkgedFskpvdatgttetslsitvk 82 
                 +as++   +++ +l+    s +++++tW a+   ++    +Y+++  ++ + F +       +e+s+s+ v+
  EPA04248.1 136 EASSIPRETTTPTLTATDVSPTQIRLTWIAPSQTYGQhISSYKIEEKLSSGTFIEV-----DSESSTSFLVS 202
                 4455555556778999999************6666663667888866666555555.....44555555554 PP

  == domain 4  score: 6.3 bits;  conditional E-value: 0.0055
        SusE  13 a..seLtapasevvldednasnealtftWtaadygvpaavt.Ytvq 55 
                 a  ++ t p    +l+  ++s+++++++W+ +  + +a++t Y+++
  EPA04248.1 238 AppPTTTVPGAPTNLTAVSSSATQINLSWNIPSSNGGAPITgYKIE 283
                 13477777877778888888**********9977777766536665 PP

>> Interfer-bind  Interferon-alpha/beta receptor, fibronectin type III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       2.9   5.7e+03      67      93 ..       4      29 ..       1      35 [. 0.61
   2 ?    7.8   0.1     0.002       3.9      43      85 ..      84     127 ..      60     145 .. 0.84
   3 ?    3.7   0.0     0.039        78      43      85 ..     176     219 ..     154     234 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.9
                   EEEES--TT-EEEEEEEEEESSSTEEE CS
  Interfer-bind 67 vvledLepettYCvsVqaesrksnkks 93
                   + +  L  +t Y  +V a   +   +s
     EPA04248.1  4 YSHTGLTTGTVYTYKVSA-INSVGTSS 29
                   566778888888888887.44444444 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.002
                    EEEEEEEETTTCEEEEEEEESSSEEEEES--TT-EEEEEEEE..E CS
  Interfer-bind  43 sYkvsywknssneekkelestnslvvledLepettYCvsVqa..e 85 
                    sYkv++ + s +   + ++++++++ +  L  +t+Y  +V a  +
     EPA04248.1  84 SYKVEFKSGSGT-YSTLTTTQSTTYSHTGLTTGTSYTYKVSAinS 127
                    799998888888.999999999999***********999999431 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.039
                    EEEEEEEETTTCEEEEEEEESSSEEEEES--TT-EEEEEEEE..E CS
  Interfer-bind  43 sYkvsywknssneekkelestnslvvledLepettYCvsVqa..e 85 
                    sYk++   +s +   ++ +++++++ ++ L  ++tY + V a   
     EPA04248.1 176 SYKIEEKLSSGT-FIEVDSESSTSFLVSGLTTGKTYTFVVSAnfG 219
                    566665555555.44444556667799*************99531 PP

>> Fimbrillin_C  Major fimbrial subunit protein type IV, Fimbrillin, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0      0.01        21      36      51 ..      13      41 ..       3      67 .. 0.67
   2 ?    4.7   0.1     0.021        41      31      58 ..     111     144 ..      84     163 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.01
  Fimbrillin_C 36 niYklnvtsiseiG.............dp 51
                  ++Y+ +v++i+++G             +p
    EPA04248.1 13 TVYTYKVSAINSVGtssasseatatpaTP 41
                  69************444444444433322 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.021
  Fimbrillin_C  31 gvvRNniYklnvtsiseiGdpede......pevt 58 
                   g    + Y+ +v++i+++G+++ +      p +t
    EPA04248.1 111 GLTTGTSYTYKVSAINSVGTSYSSneassiPRET 144
                   5555578************888874444443333 PP

>> PKD  PKD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   1.1     0.051     1e+02      21      53 ..      10      41 ..       2      43 .. 0.85
   2 ?    7.3   6.4     0.002         4       2      68 ..      43     130 ..      42     132 .. 0.86
   3 ?   -0.0   0.1      0.41   8.2e+02      44      44 ..     193     193 ..     136     237 .. 0.55
   4 ?   11.4   0.7   0.00011      0.22       4      37 ..     239     272 ..     229     291 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.051
                .-SS-SEEEEE--SS--EEEEETTEEEEEE-SS CS
         PKD 21 pdganvtysWdfgdgsvvqvlseptvthtYlsp 53
                 +g+ +ty     + sv++++ ++++t t+++p
  EPA04248.1 10 TTGTVYTYKVSAIN-SVGTSSASSEATATPATP 41
                47888999999999.**************9987 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.002
                 E---S--BSSEEEEEEEES.-SS-SEEEEE--SS....................--EEEEETTEEEEEE-SSEE.EEEEEEEE-SS-E CS
         PKD   2 sasptvlvpgatvaftaavpdganvtysWdfgdg....................svvqvlseptvthtYlspGe.YeVtvtasnavgs 68 
                 s+  t+++p  + ++ta++ +++ ++ sW                         s+ +++ + t +ht l++G+ Y+ +v a n+vg 
  EPA04248.1  43 STPTTPVAPDSPTNLTAVSSSPTQINLSWSAPANnggapitsykvefksgsgtySTLTTTQSTTYSHTGLTTGTsYTYKVSAINSVGT 130
                 5667899************9988888888887777788888888888888***999999999999***99999559999999999985 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.41
                 T CS
         PKD  44 p 44 
                 +
  EPA04248.1 193 S 193
                 1 PP

  == domain 4  score: 11.4 bits;  conditional E-value: 0.00011
                 -.-S--BSSEEEEEEEES.-SS-SEEEEE--SS-- CS
         PKD   4 s.ptvlvpgatvaftaavpdganvtysWdfgdgsv 37 
                   pt  vpga+ ++ta++ +++ ++ sW+    s+
  EPA04248.1 239 PpPTTTVPGAPTNLTAVSSSATQINLSWNIPS-SN 272
                 258999***********************988.54 PP

>> CopC  CopC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.7   0.00048      0.97       8      72 ..      53     122 ..      23     126 .. 0.83
   2 ?    2.0   0.1      0.22   4.4e+02       7      63 ..     145     205 ..     141     217 .. 0.63
   3 ?    0.4   0.0      0.72   1.4e+03       9      25 ..     249     265 ..     224     290 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00048
        CopC   8 tPaagatvaaapeevtLtFsepvel.....skvkvtdpdgkeevetvdaktveaelkvplpelaaGtYtV 72 
                 +P++ ++v+++p++++L+ s p ++     ++ kv  ++g+ + +t + +++++  ++ l+++++ tY+V
  EPA04248.1  53 SPTNLTAVSSSPTQINLSWSAPANNggapiTSYKVEFKSGSGTYSTLTTTQSTTYSHTGLTTGTSYTYKV 122
                 79999******************99998888888887777666666666666667777777666667776 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.22
        CopC   7 stPaagatvaaapeevtLtFsepvel.....skvkvtdpdgkeevetvdaktveaelkvplp 63 
                 +tP+  at   +p++++Lt   p ++     s+ k+ ++ ++ +  +vd+++++  l   l+
  EPA04248.1 145 TTPTLTATD-VSPTQIRLTWIAPSQTygqhiSSYKIEEKLSSGTFIEVDSESSTSFLVSGLT 205
                 566655554.89*******9999988885555555544444335555565555555555555 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.72
        CopC   9 PaagatvaaapeevtLt 25 
                 P++ ++v+++ ++++L+
  EPA04248.1 249 PTNLTAVSSSATQINLS 265
                 33333344444444444 PP

>> EspB_PE  ESX-1 secreted protein B PE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   1.4     0.078   1.6e+02       7      41 ..      39      70 ..      32      75 .. 0.78
   2 ?    9.4   0.6   0.00071       1.4       9      41 ..     233     265 ..     224     267 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.078
                HHHCTS----------.-SSSSHHHHHHHHHHHHH CS
     EspB_PE  7 AaeleaplpeppsavpqaPdgLelakaaveqLnas 41
                A+ +++  p++p a++ +P +L++++++ +q+n+s
  EPA04248.1 39 ATPVST--PTTPVAPD-SPTNLTAVSSSPTQINLS 70
                444555..55777777.999************987 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00071
                 HCTS----------.-SSSSHHHHHHHHHHHHH CS
     EspB_PE   9 eleaplpeppsavpqaPdgLelakaaveqLnas 41 
                    + +p+p+++vp aP +L++++++++q+n+s
  EPA04248.1 233 PTANSAPPPTTTVPGAPTNLTAVSSSATQINLS 265
                 444555668888888***************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 1896.03
//
Query:       EPA04249.1  [L=181]
Description: porphobilinogen synthase, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-66  224.4   0.4    2.2e-66  224.2   0.4    1.0  1  ALAD      Delta-aminolevulinic acid dehydratase


Domain annotation for each model (and alignments):
>> ALAD  Delta-aminolevulinic acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  224.2   0.4   1.2e-70   2.2e-66       2     176 ..       6     181 .]       5     181 .] 0.99

  Alignments for each domain:
  == domain 1  score: 224.2 bits;  conditional E-value: 1.2e-70
                 --GGGGGSSHHHHHHC-S----GGGEEEEEEEESS-SS-EE-TTSTT-EEEEGGGHHHHHHHHHHTT--EEEEEEE-SS-BSS-GGGGSTTSHHHHHHH CS
        ALAD   2 krlrrlrksealrelvretrlsasdlilplfvkegeeekeeiksmpgvyrlsvdelvkeveelvklgikavllFgvpeekdeegsealnedglvqrair 100
                 +rlrrlr+se++rel++et+ls +dli+p+fv+e+ +++ +++sm +++rl++d++ +ev ++ +lgi+a++lFg+p++kde+g++a++++g+vq+ai+
  EPA04249.1   6 RRLRRLRTSEKMRELIQETTLSSRDLICPVFVQEDLKTRIKVESMSEIERLPIDDINDEVGTISDLGIPAIMLFGIPAKKDENGTSAFDDNGIVQKAIS 104
                 79************************************************************************************************* PP

                 HHHHH-.TTSEEEEEE-STTTBSS-SSSEEESS.EEHHHHHHHHHHHHHHHHHCT-SEEEE-S--TTHHHHHHHHHH CS
        ALAD 101 aikeev.pelvvitDvclceytshGhcgileekevdndetlellakvavsqaeaGadivapSdmmDgrvaaireaLd 176
                 +i++++ +++v+++Dvclc++ts+Ghcgi++ ++vdnd++le+lak+avsqa+aG+d+v+pS mmDg+va+ir+aLd
  EPA04249.1 105 QIRKNFgDKIVIMADVCLCQFTSTGHCGIIKGNKVDNDTSLETLAKIAVSQAKAGVDTVSPSAMMDGQVATIRKALD 181
                 ******777******************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1227.77
//
Query:       EPA04250.1  [L=48]
Description: hypothetical protein BG20_I2610, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.7e-05   24.5   0.0    3.1e-05   24.4   0.0    1.1  1  GlutR_dimer  Glutamyl-tRNAGlu reductase, dimerisation domain


Domain annotation for each model (and alignments):
>> GlutR_dimer  Glutamyl-tRNAGlu reductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   1.7e-09   3.1e-05      58      96 ..       1      40 [.       1      41 [. 0.93

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.7e-09
                 -TTHHHHHHHHHHHHHHHHHHSS-TTTT.HHHHHHHHH.. CS
  GlutR_dimer 58 lekltrslvnkllheptarLkeaedeee.ellealrrlFn 96
                 +e+lt+++v  ++ +p++++++a+++++ ++++++++lF+
   EPA04250.1  1 IEELTKAVVESIVSTPMNNIRKASEQGNpDIIKMASKLFD 40
                 79*********************777778**********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.29s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 343.04
//
Query:       EPA04251.1  [L=124]
Description: hypothetical protein BG20_I2119 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       882  (0.049194); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 886.61
//
Query:       EPA04252.1  [L=210]
Description: methyltransferase, FkbM family, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-11   45.0   0.5    1.9e-11   44.3   0.5    1.4  1  Methyltransf_21  Methyltransferase FkbM domain


Domain annotation for each model (and alignments):
>> Methyltransf_21  Methyltransferase FkbM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   0.5   1.1e-15   1.9e-11      18     157 ..       6     148 ..       1     171 [. 0.72

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 1.1e-15
  Methyltransf_21  18 rlcggggevlaiEPvpns.....lpkfeklranll..tlavgndvglyelivegksggkyfpfavgdtngfstssvlggedaryievpvvtlds 104
                       + g+ g+++++EP +++     ++  e+   n++   +av++++g +el++         pf+ ++++ f   +++g++ ++ +++  + +ds
       EPA04252.1   6 SKVGPNGKIFSFEPSKENislfkKSIVENSFTNIIvvDAAVSDHDGHSELFL--------SPFYKSEHSLFEYNYSSGEHKGSKQKIKIISIDS 91 
                      478999***********88777655555555554467777777777777665........46667777777777777789999*********** PP

  Methyltransf_21 105 fleeikksridllkiDvEGaElevLeGaqkglkr.cqpnlivvEvhkfkefet.....e 157
                      fle+    ++d++k+DvEG+E   L G +k++++  + +li  E+     f++     +
       EPA04252.1  92 FLEKTEDLKVDIIKMDVEGSEKKSLDGMKKTIQFnKKLTLI-TEFWPQ-GFVNagiepK 148
                      *****9**************************983334443.565433.3444454442 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       866  (0.0483016); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1373.34
//
Query:       EPA04253.1  [L=244]
Description: hypothetical protein BG20_I2121 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00032   20.8   1.2    0.00049   20.2   1.2    1.2  1  Spore_III_AF     Stage III sporulation protein AF (Spore_III_
  ------ inclusion threshold ------
      0.055   12.8   1.2      0.075   12.4   1.2    1.1  1  Phlebovirus_NSM  Phlebovirus nonstructural protein NS-M
       0.17   11.8   0.2       0.23   11.3   0.2    1.2  1  BAAT_C           BAAT / Acyl-CoA thioester hydrolase C termin


Domain annotation for each model (and alignments):
>> Spore_III_AF  Stage III sporulation protein AF (Spore_III_AF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   1.2   8.2e-08   0.00049      21     110 ..       2      93 ..       1     105 [. 0.74

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 8.2e-08
  Spore_III_AF  21 kYvklvlGLllilai.lsPvlsll.nkdldlelaaesesleeeleeikeegeelkeenkkealeeyeqrlekqikeelke.egyevkdvevei 110
                   kYvkl+  L +i+a+ + P   ++ ++d++ +++a  + + + +e  k++  + ++++ ++ ++e +q++++q++++ ++ +    ++++v++
    EPA04253.1   2 KYVKLFSALAIIMAVaMAPASTVFaQSDVNADVNADVSVNANTAE-TKDKQIYKEQKQVRDQIKEQRQNIKTQLNDLRDLrNDRLAEKTDVNV 93 
                   9********999987699999999888999999775555555555.555555555555555666679******99988777766666666665 PP

>> Phlebovirus_NSM  Phlebovirus nonstructural protein NS-M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.2   1.3e-05     0.075     147     201 ..      42      92 ..      17     100 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.3e-05
  Phlebovirus_NSM 147 kkkaeekdktisrktkesEediknqvlhseieqlknelqkkRndikrgqekrdak 201
                       + ae kdk i ++ k+  + ik+q   ++i+   n+l+ +Rnd  r  ek d++
       EPA04253.1  42 ANTAETKDKQIYKEQKQVRDQIKEQ--RQNIKTQLNDLRDLRND--RLAEKTDVN 92 
                      5778****************99999..67899999*********..988888875 PP

>> BAAT_C  BAAT / Acyl-CoA thioester hydrolase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   3.9e-05      0.23      44      95 ..      32      83 ..      14     103 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.9e-05
                SSEEEEEEES--SB--SSEEEETTE..EE----B-GGG-EE-TTS-EE-TT- CS
      BAAT_C 44 kkisavvlingsavvvegklvykdeskvlpelklsmeklkvnknglldivdv 95
                 +++a v++n+ ++ +++k++yk++++v  ++k++ +++k++ n+l d ++ 
  EPA04253.1 32 ADVNADVSVNANTAETKDKQIYKEQKQVRDQIKEQRQNIKTQLNDLRDLRND 83
                4899***********************************8877776655543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2196  (0.122483); expected 358.6 (0.02)
Passed bias filter:                     1131  (0.0630822); expected 358.6 (0.02)
Passed Vit filter:                       144  (0.00803168); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.68u 0.33s 00:00:01.01 Elapsed: 00:00:00.50
# Mc/sec: 1469.69
//
Query:       EPA04254.1  [L=452]
Description: aminotransferase, class I/II [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.5e-41  141.2   0.0    5.7e-41  140.9   0.0    1.1  1  Aminotran_1_2  Aminotransferase class I and II
  ------ inclusion threshold ------
      0.039   13.0   0.1      0.079   12.0   0.1    1.5  1  S-layer        S-layer protein


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.9   0.0   6.3e-45   5.7e-41      19     338 ..      51     372 ..      37     387 .. 0.85

  Alignments for each domain:
  == domain 1  score: 140.9 bits;  conditional E-value: 6.3e-45
                    HHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTT CS
  Aminotran_1_2  19 tlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilrlsg 114
                    ++p+ ++ e   + ++ +   y    g pel++a+ k+ +    ++++++ ++ vg+G+++li  l  +l+   g  +++p+p +  y + +rl +
     EPA04254.1  51 PVPKLIQNE---LVKNASKGAYAAVPGIPELRSAISKYNKYYFDIDVDPQ-RIYVGPGTKELIFNLLEILH---G-TVILPTPAWLGYLPQIRLLK 138
                    444445444...45777778899999**********888844489999**.*******************5...5.8999***************9 PP

                    SEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTS CS
  Aminotran_1_2 115 gevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveee 210
                       +  p+   +++++  ++l ++  +++ ++   k++++++phNPtG ++++ ele+++d++k++n+l+++De+Ya + ++ +++v+     + +
     EPA04254.1 139 KNYHMLPTG--ANRKISPNSLRKLGLRLQDRQ---KILILNNPHNPTGLLYDRLELEEIADVCKEQNILIISDEIYAQTTYDFSKFVS---MGKIY 226
                    999999955..99**********877776555...5*********************************************9556655...44445 PP

                    TT.EEEEEESSSTTSSGGG-EEEEEEEH...HHHHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS.TEEE CS
  Aminotran_1_2 211 pn.llivgslsKafGlaGeRvGyilgna...avvsqlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLael.glkv 299
                    p+ ++++++lsK+ ++ G R+Gy++  +   ++  q +k+ ++ +   s++ q+a++a  + +++++++++ +r+ ++ + ++ +++Lae+ g+k+
     EPA04254.1 227 PEgTFVTNGLSKSHAAGGYRLGYVIFPQnasDLQLQFKKILATEYTavSTPIQHAAVAGFEISDEMNEYFTITRSIHEIMGEYTYNKLAEIeGVKI 322
                    5567**********************776777888888887777777************************************************* PP

                    ECCSCSSEEEEEETHH..........CHHHHHHHHHHT.CTEEEEEGGGG CS
  Aminotran_1_2 300 lasqsgmflltdlsae..........takelskkLlee.vgvyvtpgtsf 338
                    ++++++++ll+ ++++          t ++ls++L+ + ++ +++ g s 
     EPA04254.1 323 TKPEATFYLLVNFNHYslelqtakitTSQKLSEALIVHpYHTAIVGGDSL 372
                    ****************9999988888888888887776677777766665 PP

>> S-layer  S-layer protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   8.8e-06     0.079      88     141 ..     340     394 ..     301     401 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.8e-06
     S-layer  88 etsddvsllsdekLskvlidedeektlksgssleLe.egYeleikqiDvdgdkvw 141
                  + +++++ +++kLs+ li +  ++ +  g+sl Le  +Y+ +i  +D dg kv+
  EPA04254.1 340 LELQTAKITTSQKLSEALIVHPYHTAIVGGDSLVLErTDYSARIAYVDYDGGKVY 394
                 45567889999************************9459***************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 2874.26
//
Query:       EPA04255.1  [L=168]
Description: hypothetical protein BG20_I2410 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-07   31.9   0.1    4.9e-06   26.9   0.0    2.7  3  HEAT_2    HEAT repeats
  ------ inclusion threshold ------
      0.065   13.5   0.1         21    5.7   0.0    3.2  4  HEAT      HEAT repeat
       0.12   12.2   0.0       0.21   11.4   0.0    1.5  1  COQ9      COQ9


Domain annotation for each model (and alignments):
>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.12   7.1e+02       7      25 ..      28      46 ..      12      57 .. 0.57
   2 !   26.9   0.0   8.2e-10   4.9e-06       2      76 ..      64     139 ..      63     150 .. 0.84
   3 ?    2.4   0.0     0.035   2.1e+02       6      28 ..     131     153 ..     126     159 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.12
      HEAT_2  7 alendpdpevrraairaLg 25
                +l+n  d+  r+ a++  g
  EPA04255.1 28 ILKNERDESRRWDAVWLAG 46
                3333333333444444333 PP

  == domain 2  score: 26.9 bits;  conditional E-value: 8.2e-10
      HEAT_2   2 daLlqalendpdpevrraairaLgrignpealpaLvell.ededpavRraaaeaLgaigdpealpaLkellddddd 76 
                 d+++ +lend +  v+++a+ +++  + ++ +p Lv+ +  d+++ v ++a+e+Lg ++  e+ +  k +l+d++ 
  EPA04255.1  64 DLMVWILENDDNGVVKHEACFQIAARNMRKKIPNLVNSAfYDKSALVKHEAIESLGLMRAFEVENEIKVALNDPSP 139
                 567889*******************************9989***************99877677777766655444 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.035
      HEAT_2   6 qalendpdpevrraairaLgrig 28 
                 +++ ndp+p+v  +a  +L r+ 
  EPA04255.1 131 KVALNDPSPDVSETARFVLKRLE 153
                 55558999999888888887665 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.3   7.5e+03      17      17 ..      38      38 ..      25      51 .. 0.50
   2 ?   -2.1   0.0       1.1   6.7e+03      10      23 ..      72      85 ..      67      88 .. 0.72
   3 ?    3.9   0.0     0.014        81       3      25 ..      96     119 ..      95     121 .. 0.83
   4 ?    5.7   0.0    0.0035        21       8      21 ..     133     146 ..     128     152 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.3
                H CS
        HEAT 17 R 17
                R
  EPA04255.1 38 R 38
                3 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.1
                T-SSHHHHHHHHHH CS
        HEAT 10 sDpspeVReaAaka 23
                +D++  V   A+  
  EPA04255.1 72 NDDNGVVKHEACFQ 85
                88888888777765 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.014
                 HHHHHHH.T-SSHHHHHHHHHHHH CS
        HEAT   3 Plllkll.sDpspeVReaAakaLg 25 
                 P l++    D+s+ V   A+++Lg
  EPA04255.1  96 PNLVNSAfYDKSALVKHEAIESLG 119
                 777777559**************9 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.0035
                 HHT-SSHHHHHHHH CS
        HEAT   8 llsDpspeVReaAa 21 
                 +l+Dpsp+V e+A 
  EPA04255.1 133 ALNDPSPDVSETAR 146
                 79*******99985 PP

>> COQ9  COQ9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   3.4e-05      0.21      49      76 ..     133     160 ..     100     161 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.4e-05
        COQ9  49 mlqdksedfedtwaFldrriddvmalek 76 
                  l+d s+d ++t +F+ +r+++ ++++k
  EPA04255.1 133 ALNDPSPDVSETARFVLKRLERTRNITK 160
                 599*******************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1030.11
//
Query:       EPA04256.1  [L=51]
Description: hypothetical protein BG20_I2411 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       219  (0.0122148); expected 358.6 (0.02)
Passed bias filter:                      131  (0.0073066); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 318.66
//
Query:       EPA04257.1  [L=190]
Description: hypothetical protein BG20_I2412, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.026   14.4   0.0      0.097   12.6   0.0    1.9  2  TrmB      Sugar-specific transcriptional regulator TrmB
       0.17   12.5   2.0        1.2    9.8   0.1    2.6  3  Mga       Mga helix-turn-helix domain


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.32   2.8e+03       4      43 ..      36      44 ..      32      56 .. 0.57
   2 ?   12.6   0.0   1.1e-05     0.097      18      55 ..     115     152 ..     112     169 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.32
                CHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHH CS
        TrmB  4 lGLseyEakvYlaLlklgpatadeiaeelgvprskvYevL 43
                +G+                                 Ye+L
  EPA04257.1 36 FGIGI-------------------------------YESL 44
                55554...............................5555 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 1.1e-05
                 HHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
        TrmB  18 lklgpatadeiaeelgvprskvYevLrsLedkGlVere 55 
                 ++ +++t++ei ++ ++p+++ Y+ +++L++  + +++
  EPA04257.1 115 VTDKSMTIYEILQKCDIPQTSGYRKIKQLIENNFLTIQ 152
                 56789**************************9998766 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1     0.041   3.6e+02      39      65 ..      13      40 ..       7      60 .. 0.83
   2 ?    9.8   0.1   0.00013       1.2      21      55 ..     111     144 ..      86     151 .. 0.81
   3 ?   -3.3   0.0       1.6   1.4e+04      54      68 ..     166     180 ..     158     184 .. 0.61

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.041
                HCT--HHHHHHHHHHHHHHCH.CCT-EE CS
         Mga 39 elyiSestlkrkikelnklLk.efdlel 65
                e  iSe      + +++ +L+ +f++ +
  EPA04257.1 13 ESIISENLGHSALSKIKSRLSeKFGIGI 40
                56788888888999******98999988 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00013
                 HHHHHHHHSEEEHHHHHHHCT--HHHHHHHHHHHH CS
         Mga  21 llkflfeeeevsieelaqelyiSestlkrkikeln 55 
                 ++ ++ ++++++i+e+ q+  i +++ +rkik+l 
  EPA04257.1 111 MINCV-TDKSMTIYEILQKCDIPQTSGYRKIKQLI 144
                 44444.599***********************986 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 1.6
                 HHHHCHCCT-EEETT CS
         Mga  54 lnklLkefdleltkk 68 
                    + +++++ ++k+
  EPA04257.1 166 YTSVFENIKIDIEKN 180
                 555566667777444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1196.28
//
Query:       EPA04258.1  [L=77]
Description: hypothetical protein BG20_I2567, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.012   15.5   0.4       0.85    9.6   0.0    2.2  2  zf-trcl          Probable zinc-ribbon domain
      0.042   13.7   1.1       0.81    9.6   0.1    2.3  2  zf-FPG_IleRS     Zinc finger found in FPG and IleRS
       0.05   13.7   0.9      0.068   13.3   0.9    1.3  1  zf-RRPl_C4       Putative ribonucleoprotein zinc-finger pf C4
      0.066   13.6   0.2      0.089   13.2   0.2    1.3  1  Lar_restr_allev  Restriction alleviation protein Lar


Domain annotation for each model (and alignments):
>> zf-trcl  Probable zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00019      0.85      30      45 ..      14      29 ..       6      32 .. 0.81
   2 ?    4.5   0.1    0.0075        33       3      15 ..      42      54 ..      40      59 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00019
     zf-trcl 30 dnepkRCkaCRkarkq 45
                  epk C++C k ++ 
  EPA04258.1 14 LKEPKLCPTCQKGDRL 29
                579*******998775 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0075
     zf-trcl  3 ktltCkdCgaefv 15
                +tl C++C+a  v
  EPA04258.1 42 QTLLCTRCEALTV 54
                6899****98666 PP

>> zf-FPG_IleRS  Zinc finger found in FPG and IleRS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1   0.00018      0.81      21      29 ..      17      25 ..      14      26 .. 0.85
   2 ?    2.8   0.1     0.024   1.1e+02      23      27 ..      45      49 ..      36      51 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00018
                  EEE-TTTT. CS
  zf-FPG_IleRS 21 tyfCprCqk 29
                  + +Cp+Cqk
    EPA04258.1 17 PKLCPTCQK 25
                  679*****7 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.024
                  E-TTT CS
  zf-FPG_IleRS 23 fCprC 27
                  +C rC
    EPA04258.1 45 LCTRC 49
                  79999 PP

>> zf-RRPl_C4  Putative ribonucleoprotein zinc-finger pf C4 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.9   1.5e-05     0.068      40     100 ..       5      61 ..       1      69 [. 0.76

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.5e-05
  zf-RRPl_C4  40 vpikelekislrdkLCtkCkeknekekeircetfeeylkklklCkeCkervekvlkndfvk 100
                 + i+e+ +i  + kLC +C++  + ek+i  e  ++   +  lC++C +   +v+ n+  k
  EPA04258.1   5 IYIREIITILKEPKLCPTCQKGDRLEKNIVFE--RKTDGQTLLCTRCEAL--TVITNHNLK 61 
                 56777777777789**************9999..777788899****864..455555555 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2     2e-05     0.089       4      45 ..      18      58 ..      15      74 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2e-05
  Lar_restr_allev  4 kpCPfCggravlersqrvva.eigqcvyCadCga....stpwfkiae 45
                     k CP C + + le++        gq+  C+ C+a            +
       EPA04258.1 18 KLCPTCQKGDRLEKNIVFERkTDGQTLLCTRCEAltviT------NH 58
                     78******99999986544303455*********44432......22 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       692  (0.0385967); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 501.40
//
Query:       EPA04259.1  [L=39]
Description: hypothetical protein BG20_I2565, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.4e-12   45.2   0.1    7.7e-12   45.1   0.1    1.0  1  DUF1297   Domain of unknown function (DUF1297)


Domain annotation for each model (and alignments):
>> DUF1297  Domain of unknown function (DUF1297)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.1   0.1   4.3e-16   7.7e-12     152     188 .]       3      39 .]       1      39 [] 0.97

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 4.3e-16
                 --CCHHHTTSS---HHHHHHHHHHHHHHCT-GGGCEE CS
     DUF1297 152 gspyskllfgeplsmGrrialEikeaiekdrleeivt 188
                 +spy+k+++g+++ +Grria+Eik+a e+drl+eivt
  EPA04259.1   3 TSPYTKYQYGKTFGIGRRIAMEIKQAQEEDRLDEIVT 39 
                 89**********************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 290.08
//
Query:       EPA04260.1  [L=66]
Description: hypothetical protein BG20_I2566 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 479.79
//
Query:       EPA04261.1  [L=348]
Description: peptidase, M50 family, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.4e-19   68.7   1.1    9.4e-17   61.1   1.1    2.3  1  Peptidase_M50  Peptidase family M50
    3.7e-09   36.8   0.0    6.5e-09   36.0   0.0    1.4  1  PDZ_2          PDZ domain
    6.7e-08   32.3   0.0    1.1e-07   31.6   0.0    1.4  1  PDZ_6          PDZ domain
    0.00074   19.8   0.1     0.0016   18.8   0.1    1.5  1  PDZ            PDZ domain


Domain annotation for each model (and alignments):
>> Peptidase_M50  Peptidase family M50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.1   1.1   2.1e-20   9.4e-17       1     232 [.      68     313 ..      68     331 .. 0.78

  Alignments for each domain:
  == domain 1  score: 61.1 bits;  conditional E-value: 2.1e-20
                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXX CS
                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Peptidase_M50   1 afilllgilvvvHElGHflvAklcgvkveefsigfGpkllsfkkgeteYaiallpLGGyVkmageepeeelseeeakaflkkspwqrllivlAGpl 96 
                    +f+l + +++v+HE +H++vA l+++k++                   +ai +  + G+V+ ++ee            f+k++ +++l+++ AG  
     EPA04261.1  68 YFLLSIPVVLVIHEGAHGIVATLEKIKIKT----------------GGFAIFIAMFAGFVEPDEEE------------FNKAKKISKLRVIGAGAT 135
                    699999**********************76................44678888888*********............****************** PP

                    XXXXXXXXXXXX................................-EEECE.....CTTTSCEE-SEEEC-XXXXXXXXXXXXXXXXXXXXX.XXXX CS
                    xxxxxxxxxxxx................................xxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
  Peptidase_M50  97 anfilailvfvv................................pkkske.....seeekrgviGvspkpvkkegllealkegvektlkvv.vltv 154
                     n+i+a+++ ++                                p++ +e      +   +++ Gv+  ++ + + ++ + + + ++  +   +++
     EPA04261.1 136 SNVIFAFALGLIlltnpffamivpepllsvfydlpdgvtvlsiiPDSGAEkagllANDIITSINGVQILSPLDFQKTDLIPGDIAQVSILRdGQIL 231
                    *******9999999***********99999999999999999994444444566666666667788888877777777777777776554415666 PP

                    XXXXXXXXX.XXXXXXXXXXXXXXXXX.......XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                    xxxxxxxxx.xxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Peptidase_M50 155 kalgklitg.klslktlggpisiaqla.......seaaeaglssflqllalisvnLgilNLlPipvLDGghllfalleairrkpls 232
                    +  +++i   + + k l g i   ++a        e  + g+s+fl +l +is+ +gi+N+lP+p+LDGg+++  ++++      s
     EPA04261.1 232 QFPVEVIPSpDDPQKGLIGIIRDNSFAykpvlnfIEWKDPGVSMFLLWLWMISFFIGIINMLPLPILDGGKFIHTIIDKKI----S 313
                    6667777774555557777777777775555555445556666******************************99987543....4 PP

>> PDZ_2  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.0   1.5e-12   6.5e-09      12      82 .]     171     237 ..     162     237 .. 0.89

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 1.5e-12
                 -..-EEEEEE-TTSGGGGT.--TT-EEEEETTB--SSHHHHHHHHHTS-TT-EEEEEEEETTEEEEEEEE- CS
       PDZ_2  12 dtggvlvvsVkeggPaakaglkagDvilkvdgkkvksledlislllkkkpGdtVkltvlRdgkkktvevkl 82 
                 d  gv+v s+ +++ a+kagl a+D+i++++g+++ s  d+  +     pGd  ++++lRdg+ +++ v++
  EPA04261.1 171 D--GVTVLSIIPDSGAEKAGLLANDIITSINGVQILSPLDF--QKTDLIPGDIAQVSILRDGQILQFPVEV 237
                 4..9*******************************555555..557999****************999986 PP

>> PDZ_6  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0   2.5e-11   1.1e-07       2      39 ..     175     210 ..     174     212 .. 0.93

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 2.5e-11
       PDZ_6   2 VtaVdpgsPAdrAGlrvGDiilsvNGqpveglsladva 39 
                 V +++p+s A++AGl ++Dii+s+NG+ +  ls+ d++
  EPA04261.1 175 VLSIIPDSGAEKAGLLANDIITSINGVQI--LSPLDFQ 210
                 7899*************************..9999987 PP

>> PDZ  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   3.5e-07    0.0016      27      58 ..     172     203 ..     167     208 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 3.5e-07
                 SEEEEEECTTSHHHHHTSSTTEEEEEETTEET CS
         PDZ  27 gifvsevlpggaaeadglkvGDkIlsvNgvdv 58 
                 g+ v ++ p++ ae++gl ++D+I+s+Ngv +
  EPA04261.1 172 GVTVLSIIPDSGAEKAGLLANDIITSINGVQI 203
                 89999*****7788888************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2186.82
//
Query:       EPA04262.1  [L=192]
Description: PP-loop family protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-17   63.2   0.0      4e-17   62.6   0.0    1.2  1  ATP_bind_3     PP-loop family
    1.3e-05   24.2   0.0    1.7e-05   23.8   0.0    1.1  1  tRNA_Me_trans  tRNA methyl transferase
     0.0079   15.7   0.1      0.021   14.3   0.0    1.8  2  QueC           Queuosine biosynthesis protein QueC
  ------ inclusion threshold ------
      0.032   14.3   0.0      0.044   13.8   0.0    1.3  1  PAPS_reduct    Phosphoadenosine phosphosulfate reductase fami
      0.065   13.3   1.1        1.3    9.1   0.0    2.1  2  QueH           Epoxyqueuosine reductase QueH


Domain annotation for each model (and alignments):
>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.6   0.0   1.1e-20     4e-17       2     121 ..      50     181 ..      49     189 .. 0.92

  Alignments for each domain:
  == domain 1  score: 62.6 bits;  conditional E-value: 1.1e-20
                 EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--H............HHCTTSTCCCHHHHHHHHHH CS
  ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklnikleiekvdv............akkkgknleeaARelRYevl 88 
                 v+vAvSgG DS+aLl+++++++++ ++++ ai++d g+    +e  e+v+e+c+kln+++++ + +               +++++      +lR +++
  EPA04262.1  50 VAVAVSGGKDSLALLNVINQMRSTHNFRIKAITIDEGIPGYRNEALEIVQEFCAKLNVEHKVFSYKElfdltldealdlRGNEKTSSCSICGTLRRRAI 148
                 689***********************************************************999999999999998884445677778999******* PP

                 HHCHHCCT.CEEE---BHHHHHHHHHHHHCCT- CS
  ATP_bind_3  89 kealkkegievlllAhhadDqaEtfllrlargs 121
                 ++a++  +++v++++h+ dD + tf++++  g 
  EPA04262.1 149 DHAANDINADVIATGHNLDDTLQTFVINMLSGD 181
                 **************************9988775 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   4.8e-09   1.7e-05       3     125 ..      50     165 ..      48     182 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 4.8e-09
  tRNA_Me_trans   3 vvvalSgGVDSsvaaallkeqgyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfekeykekvfeefleeyeeGrTPnPdvlC 98 
                    v+va+SgG DS +a++ + +q +++  + +k ++ ++        +e l+ +++ + kl+++++v+++++ +    ++e l+   + +T   +  C
     EPA04262.1  50 VAVAVSGGKDS-LALLNVINQMRSTHNFRIKAITIDEGI--PGYRNEALEIVQEFCAKLNVEHKVFSYKELFDL-TLDEALDLRGNEKTS-SCSIC 140
                    99********7.78999999***********99983333..4688899*********************99975.578899988888885.69999 PP

  tRNA_Me_trans  99 NkeiKfgallekakeelgadalatGHY 125
                     +  + +a +++a ++ +ad +atGH 
     EPA04262.1 141 GTL-RRRA-IDHAANDINADVIATGHN 165
                    875.4454.5666666**********5 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   5.9e-06     0.021       4      67 ..      52     120 ..      49     136 .. 0.79
   2 ?   -2.2   0.1      0.67   2.4e+03     186     203 ..     130     147 ..     123     154 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.9e-06
                 EE--SSHHHHHHHHHHHHH-....SEEEEEEEESS-T..TSHHHHHHHHHHHHT--.-EEEEE-GGGGGG CS
        QueC   4 vllSGGlDSttvlalakkeg....kevealtfdYgqr..hkkeleaakkiakelgveehkildldllkel 67 
                 v +SGG DS ++l + ++       +++a+t+d g    +++ le++++++++l+v ehk+++ + l +l
  EPA04262.1  52 VAVSGGKDSLALLNVINQMRsthnFRIKAITIDEGIPgyRNEALEIVQEFCAKLNV-EHKVFSYKELFDL 120
                 679******99987766543222279********9877567779************.***9998876655 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.67
                 S.-BTTTTSSSHHHHHHH CS
        QueC 186 geeegkaCgeCdaCalRk 203
                 g+e++++C  C + ++R+
  EPA04262.1 130 GNEKTSSCSICGTLRRRA 147
                 567778888888766664 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.2e-05     0.044       3     106 ..      51     163 ..      49     185 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.2e-05
                  EEE--SSCTCHHHHHHHHHHCTTH....EEEEEE-ST..B-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH-S-THHHC...HHHHHHTHHHH CS
  PAPS_reduct   3 vvsvsgGkdslVllhLalkafkpv....pvvfvdtgh..efpetiefvdeleeryglrlkvyepeeevaekinaekhgsslyee...aaeriaKvepl 91 
                  +v+vsgGkdsl+ll  + ++        + + +d g     +e +e v+e+  +++++ kv++ +e ++  + ++     + ++    ++   + +++
   EPA04262.1  51 AVAVSGGKDSLALLNVINQMRSTHnfriKAITIDEGIpgYRNEALEIVQEFCAKLNVEHKVFSYKELFDLTLDEALDLRGNEKTsscSICGTLRRRAI 148
                  799**************999988445668999999973346899999999999999998888877766555544433222222233455555555566 PP

                  HHHHHCTTECEEE-- CS
  PAPS_reduct  92 kkaLekldedalltG 106
                    a +++++d++ tG
   EPA04262.1 149 DHAANDINADVIATG 163
                  666666666666666 PP

>> QueH  Epoxyqueuosine reductase QueH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.3     0.017        60      75     105 ..      12      43 ..       4      84 .. 0.63
   2 ?    9.1   0.0   0.00035       1.3      45     114 ..      96     166 ..      57     186 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.017
        QueH  75 lekekekgeRCekCyelr.LektaelAkengf 105
                 ++++  +++ C++C++   L+kta++ ++ ++
  EPA04262.1  12 YTRKYSGEKLCSNCFSNSiLRKTAKTISKYNM 43 
                 5666678889*****86537889988766554 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00035
        QueH  45 eelkrlieelkielieedydleefleav.kgl.ekekekgeRCekCyelrLektaelAkengfdaftttlti 114
                 e +++++++l++e    +y++  f  ++ + l  + +ek++ C+ C +lr ++  + A++ ++d+++t   +
  EPA04262.1  96 EIVQEFCAKLNVEHKVFSYKE-LFDLTLdEALdLRGNEKTSSCSICGTLRRRAIDHAANDINADVIATGHNL 166
                 445666666666666666653.3332331222134567899**************************97655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       878  (0.0489709); expected 358.6 (0.02)
Passed bias filter:                      568  (0.0316805); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1200.91
//
Query:       EPA04263.1  [L=118]
Description: putative chemotaxis protein Chey [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-25   89.1   3.1    2.2e-25   89.0   3.1    1.0  1  Response_reg  Response regulator receiver domain
  ------ inclusion threshold ------
      0.015   15.7   0.2      0.035   14.5   0.2    1.8  1  FleQ          Flagellar regulatory protein FleQ
      0.028   14.7   1.7      0.051   13.8   1.7    1.5  1  TrkA_N        TrkA-N domain


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.0   3.1   3.7e-29   2.2e-25       1     112 []       6     117 ..       6     117 .. 0.99

  Alignments for each domain:
  == domain 1  score: 89.0 bits;  conditional E-value: 3.7e-29
                   EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEESSTSHHHHHHHHHCTESEE CS
  Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviiltahseeedavealkagaddf 97 
                   v++vdDd+++r++++++l+ +g+++va+a +g++a+e++ + ++d++l+Di+mp+ dG+  + +i++ +++ ++i++ta +++e++++  ++  + +
    EPA04263.1   6 VVVVDDDEDNRNAMTDILQFKGVSVVATAVNGSDAVEKFSKYAPDVVLMDIMMPDFDGFYGIMNIKNINSDAKIIAVTADQSDETIQKLRDIKHELI 102
                   79*********************************************************************************************** PP

                   EESSG-HHHHHHHHH CS
  Response_reg  98 lsKpfdpeeLlkale 112
                   + Kpfd + L+++++
    EPA04263.1 103 IYKPFDVNVLVQMIN 117
                   ************986 PP

>> FleQ  Flagellar regulatory protein FleQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.2   5.9e-06     0.035       1      34 [.       5      38 ..       5     103 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.9e-06
        FleQ  1 kiLvidddaerrrdletiLeFlgeeveavsseel 34
                k+ v+ddd+++r++++ iL+F g +v+a++ +  
  EPA04263.1  5 KVVVVDDDEDNRNAMTDILQFKGVSVVATAVNGS 38
                789********************99777665443 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   1.7   8.5e-06     0.051      23     109 ..       5      98 ..       2     105 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.5e-06
                 EEEEEESSHHHHHHHHHTT....SEEEES-TTSHHHHHHTTGGGESEEEE-SSSH.HHHHHHHHHHHHHTSSSEEEEEESSGGG..HHHHHHHT CS
      TrkA_N  23 dvvvidkdeerveelreeg....levvvgdatdeevLeeagiekadaviaatgdd.eanilavllakelnpkkkiiaraqdpeh..aellkklg 109
                 +vvv+d+de++ + +++      + vv   +   +++e+      d+v+  +     +  + ++++k++n+++kiia + d+++  +++l+++ 
  EPA04263.1   5 KVVVVDDDEDNRNAMTDILqfkgVSVVATAVNGSDAVEKFSKYAPDVVLMDIMMPdFDGFYGIMNIKNINSDAKIIAVTADQSDetIQKLRDIK 98 
                 6********998777665553337799999999*************99999876537778889999**********998777662366666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       754  (0.0420548); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 707.24
//
Query:       EPA04264.1  [L=70]
Description: hypothetical protein BG20_I2447, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1060  (0.0591221); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 486.92
//
Query:       EPA04265.1  [L=163]
Description: hypothetical protein BG20_I1896 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.03   14.2   2.2        1.3    8.8   0.5    2.3  2  DUF1944        Domain of unknown function (DUF1944)
       0.13   12.3   0.0       0.17   11.9   0.0    1.2  1  SpoVT_C        Stage V sporulation protein T C-terminal, tran
       0.23   11.7   5.5       0.57   10.4   0.4    2.3  2  HEPN_RES_NTD1  HEPN/RES N-terminal domain 1


Domain annotation for each model (and alignments):
>> DUF1944  Domain of unknown function (DUF1944)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0    0.0034        20      40      70 ..      23      53 ..      13      63 .. 0.85
   2 ?    8.8   0.5   0.00022       1.3      71     107 ..     121     158 ..      71     162 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0034
     DUF1944 40 elaeesnwkicaDavvlskhkakaklkwGae 70
                +++ ++ + i +D  ++  hk++ak+kw + 
  EPA04265.1 23 SIGGKEGMLILTDRHLMFIHKTQAKMKWWQA 53
                677778888999****************766 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00022
     DUF1944  71 ckqYkvsvtaetgql.askPalrlklewekvPsslkev 107
                  ++Y+ s+     +  a++P+  +k++we   +++k+ 
  EPA04265.1 121 LQKYQYSIAQDWVKYpAKEPTKYMKVDWEPFVQYIKDR 158
                 489**************************999999876 PP

>> SpoVT_C  Stage V sporulation protein T C-terminal, transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.9e-05      0.17      46     115 ..      56     130 ..      27     139 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.9e-05
     SpoVT_C  46 skeleklmeerktvlakk..eekklv...veeekeeysaqviaPIiaeGdviGaVillskeekkklgelekklae 115
                 ++++ +++++++t++ ++  +e++l+    +e+++++s   i  I  e+   G++++l+ e++ kl++ +  +a+
  EPA04265.1  56 QRQVINFLKSKNTMIRHDgyNESNLIedmENEKNTQLSFDDILNITHEEKEWGSILVLEYEKEGKLQKYQYSIAQ 130
                 456889999999999998865555555532555567777889*******************99999999999987 PP

>> HEPN_RES_NTD1  HEPN/RES N-terminal domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   2.6     0.035   2.1e+02      52      99 ..      70     117 ..      48     135 .. 0.71
   2 ?   10.4   0.4   9.6e-05      0.57      87     121 ..     130     162 ..     124     163 .] 0.90

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.035
  HEPN_RES_NTD1  52 lvgetydtedlleevieleaendeLiediadal.edkaWverdpyglse 99 
                    + ++ y+  +l+e++ e+e++++  ++di +   e+k+W ++ ++  ++
     EPA04265.1  70 IRHDGYNESNLIEDM-ENEKNTQLSFDDILNIThEEKEWGSILVLEYEK 117
                    4455589999****9.455555555899999997899998885554444 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 9.6e-05
  HEPN_RES_NTD1  87 kaWverdpyglsedealkysWeaFkelvkhksRyv 121
                    + Wv++   ++++++ +k +We F++++k +++++
     EPA04265.1 130 QDWVKY--PAKEPTKYMKVDWEPFVQYIKDRQKFT 162
                    679998..7889999****************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       986  (0.0549947); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1126.69
//
Query:       EPA04266.1  [L=355]
Description: nucleic acid-binding domain protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.1e-11   41.5   0.0    1.7e-10   40.6   0.0    1.4  1  DNA_pol_E_B      DNA polymerase alpha/epsilon subunit B
    1.1e-10   42.3   0.0    2.1e-10   41.5   0.0    1.3  1  Metallophos      Calcineurin-like phosphoesterase
  ------ inclusion threshold ------
      0.064   13.2   0.1       0.15   12.1   0.1    1.6  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
      0.072   13.2   0.3       0.73    9.9   0.2    2.3  2  DUF1877          Domain of unknown function (DUF1877)
        0.1   12.3   0.9       0.38   10.5   0.7    1.9  2  DUF2326          Uncharacterised protein conserved in bacteri
       0.11   12.6   0.2       0.26   11.4   0.0    1.9  2  DNA_pol_D_N      DNA polymerase delta subunit OB-fold domain


Domain annotation for each model (and alignments):
>> DNA_pol_E_B  DNA polymerase alpha/epsilon subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.0   5.8e-14   1.7e-10       2     148 ..     207     352 ..     206     354 .. 0.72

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 5.8e-14
                  EEEES--S-TT---...-HHHHHHHHHHH.HTT--SEEEEES-SSBTTSHHHHHT---S--SSHHHHHHHHTHHHHTTS-TTSEEEEE--TTBTT-S- CS
  DNA_pol_E_B   2 vivsglnldndnrs...leaLrkiLqgyapeesppdvlilaGnfvdaahkaiasskvstdekkenfdalalllsilesllekttvvlvPgpnDpanst 96 
                  v++s+l++ ++ +    ++ +  +L++ +p + ++  +++ G +vd      ++ k      ++ ++ l+++ + ++++ + ++++++Pg  Dp  + 
   EPA04266.1 207 VFLSDLHIGSKYFMeeeFTEFVSWLSSPDPIARKIRFVLIGGDLVDGVGIYPNQDKE--LVCQTIEEQLKKVEELIDRVPNYIKIFIMPGNHDPGRR- 301
                  567777777554444445555555555556677777777777777754333332221..234444556666666666666778**************. PP

                  SBSB----TTTTT--TTT...EEE--BSEEEEETTEEEEE--S-HHHH---E CS
  DNA_pol_E_B  97 vlPqqPlprlllsrikrvfkelklvtNPsrielnsvevvltsddivkdlkre 148
                  +lPq+++p+++ s + +  +++ +v NP  ++ln+v+v+++ ++ ++d+ ++
   EPA04266.1 302 ALPQPAIPKKYNSGLWER-ENVFMVGNPAVVSLNGVKVMMFHGQSIDDIVKT 352
                  **********99999887.67**************************99876 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5   0.0     7e-14   2.1e-10       4     126 ..     207     347 ..     206     354 .. 0.73

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 7e-14
                  EEEESBTB...TTCCTHHHHHHHHHHHH.HHHTTESEEEEESTSSSSS.................HHHHHHHHHHHHHHHHTSEEEEEC-TTSCHHH. CS
  Metallophos   4 lvigDlHl...algggqlddllkllddl.lreekpdlvllaGDlvdrg.................dlekellellaalvkypipvylllGNHegfee. 79 
                  ++++DlH+      ++ + +++ +l+   +   k+ +vl+ GDlvd+                  +l k ++el++++ +y i++++++GNH+     
   EPA04266.1 207 VFLSDLHIgskYFMEEEFTEFVSWLSSPdPIARKIRFVLIGGDLVDGVgiypnqdkelvcqtieeQLKK-VEELIDRVPNY-IKIFIMPGNHD-PGRr 301
                  689****9666555555555556552224333689************779**99999999876644444.66666666665.***********.6676 PP

                  HHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESECEE CS
  Metallophos  80 ellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGgspe 126
                   l+++   ++++s++w++++ ++ + p ++  +g +kv   hG s++
   EPA04266.1 302 ALPQPAIPKKYNSGLWERENVFMVGNPAVVSLNG-VKVMMFHGQSID 347
                  777777777777*******988888888886666.688888888544 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1     5e-05      0.15       3      56 ..     123     175 ..     121     185 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5e-05
                      EEEEEEEEEEEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEE.E CS
  tRNA_anti-codon   3 vaGrvtsisdrsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvt.G 56 
                      v+G vts+    ++++  ++l+D +g ++ ++f++e +k+a +l +++++ ++ G
       EPA04266.1 123 VCGLVTSR--ITERNITKLVLEDPSGLFEGIVFDTELQKVAGSLLNDQFIMARiG 175
                      89******..**********************************99999998866 PP

>> DUF1877  Domain of unknown function (DUF1877)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.2   0.00024      0.73      87     135 ..      13      61 ..       9      69 .. 0.88
   2 ?    0.3   0.0      0.22   6.5e+02      69     103 ..     244     282 ..     231     286 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00024
     DUF1877  87 rlltpeqVkevaeaLaeldfeelrerfdaeeleeaeiYpniweeeeeed 135
                 ++l++ +Vk++ + ++e+ +e+ ++++++ + +  e+Y +i e+++ ++
  EPA04266.1  13 KFLENVDVKKLEKIIKEIVREKTKQKLFQINQDDLEVYLGIKEDQTLQN 61 
                 578999***********************************99955444 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.22
     DUF1877  69 vvlGgeelge....edegygparlltpeqVkevaeaLae 103
                 v++Gg+ ++     ++++ + +  +  eq k+v e +++
  EPA04266.1 244 VLIGGDLVDGvgiyPNQDKELVCQTIEEQLKKVEELIDR 282
                 555666555555555566666666666666666665555 PP

>> DUF2326  Uncharacterised protein conserved in bacteria (DUF2326)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.7   0.00013      0.38      69     123 ..      15      65 ..       4      73 .. 0.73
   2 ?   -1.1   0.0      0.48   1.4e+03      82     136 ..      95     148 ..      82     150 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00013
     DUF2326  69 fegvderqlaklleliaevaeklgiQyivtlnkdklpkeeeees..klekdveknev 123
                 +e+vd ++l+k+++ i    +++ +Q    +n+d+l   e + +  +++  ++++++
  EPA04266.1  15 LENVDVKKLEKIIKEI---VREKTKQKLFQINQDDL---EVYLGikEDQTLQNDHKI 65 
                 6777777777777777...78899************...444445455566666666 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.48
     DUF2326  82 eliaevaeklgiQyivtlnkdklpkeeeeesklekdveknev.klsltDekdekLF 136
                 ++i++  e++ + +i ++ + k ++++   + +++ +++ ++ kl l+D  +++LF
  EPA04266.1  95 RIISDRPESRMLKTITSVKSAKSDDDMYVCGLVTSRITERNItKLVLED--PSGLF 148
                 5555555566666677777777755555555555555555565888888..55777 PP

>> DNA_pol_D_N  DNA polymerase delta subunit OB-fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       1.7     5e+03      56      71 ..      22      37 ..      17      59 .. 0.47
   2 ?   11.4   0.0   8.7e-05      0.26       2      57 ..      82     134 ..      81     223 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.7
  DNA_pol_D_N 56 lkpsvlkeiakedesa 71
                 +  +++kei +e++++
   EPA04266.1 22 KLEKIIKEIVREKTKQ 37
                 3344444444322221 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 8.7e-05
  DNA_pol_D_N   2 YaniYfaRleqlkprlleaakekwskeelkvnrildlkegeecivvGtiykemklk 57 
                  Y++++ +R+ +lk+++ ++ ++++ k   ++ +++  k++++++v+G +  ++ ++
   EPA04266.1  82 YNALFASRFSKLKRIISDRPESRMLK---TITSVKSAKSDDDMYVCGLVTSRITER 134
                  9999********************44...899****************99888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       875  (0.0488036); expected 358.6 (0.02)
Passed bias filter:                      633  (0.0353059); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 2130.85
//
Query:       EPA04267.1  [L=238]
Description: precorrin-6y C5,15-methyltransferase (decarboxylating), CbiE subunit [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-34  119.2   0.0    2.6e-34  119.0   0.0    1.0  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.0   0.0   1.4e-38   2.6e-34       1     212 [.       3     208 ..       3     209 .. 0.89

  Alignments for each domain:
  == domain 1  score: 119.0 bits;  conditional E-value: 1.4e-38
  TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaeal.aealragkd.VvllvsGDPlvy.. 93 
                   k+y VGvGpG+p ++T  ++++++++dvv+g++ ++l+ ++dlla            ke +e ++++++e + + +l+ g +  v+ ++GD +++  
    EPA04267.1   3 KIYAVGVGPGSPRYVTRIVREVIQDCDVVIGYK-YTLKTIEDLLAG-----------KEIHEITMNNQEESYqKILLELGDRsLVIPFTGDVNFSes 87 
                   79*******************************.*********965...........7888888888888887555555544399999*******99 PP

  TP_methylase  94 gtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvllpglakeeereleallangdtlvllkapr.k.......laelaelLke 182
                    ++++l+e++ +      ve+iPG+ss+q  a+++++pl++++ +++++++++++++ ++ +al++ g++++l+ +p+ k       ++e+a  Lk 
    EPA04267.1  88 EVVDRLIEIFGE------VEIIPGISSIQVTASKARVPLDKSKIITMHVTTSIEEKKLELQKALID-GYSVILVPRPWpKqpdkhfmPSEIAIYLKN 177
                   999999999999......*******************************77777666666666665.*******9999868999**88888888888 PP

  TP_methylase 183 a.lyddttpvavveragtedervvrgtleel 212
                     +  ++ +v+v+e+++te+e+ ++gt+++l
    EPA04267.1 178 NgFNTKNMKVHVFEALTTENETNFVGTVKDL 208
                   8***************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       680  (0.0379274); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 1355.72
//
Query:       EPA04268.1  [L=166]
Description: integral membrane protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-08   34.1   8.0      3e-08   33.9   8.0    1.1  1  SpoIIM    Stage II sporulation protein M


Domain annotation for each model (and alignments):
>> SpoIIM  Stage II sporulation protein M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   8.0   1.7e-12     3e-08      36     151 ..      36     149 ..       2     153 .. 0.78

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 1.7e-12
      SpoIIM  36 lflaifanNlrvalllfllGllllgiptilvl.linGfvlGavaalvaef.gglllflllilPhgilelpaiiiagaaglrlgkalrsrrkalkeakre 132
                  ++ if++Nl+v+l +f+ G+   g++  l+  + +Gf   a++++  e  +   l ll++ P gi+el+a+ ia++ ++ l ka++++ +    +k  
  EPA04268.1  36 DAIGIFIHNLSVSLPMFIPGF---GVVWGLFSaWSTGFAFSAITTISPEIaKIPPLTLLFLSPFGIMELTAYSIATSRSFMLIKAIYKKTNLIPFLKPT 131
                 4789****************5...888888888********99777777764468899****************************8666666667777 PP

      SpoIIM 133 llklllllvpllliAaliE 151
                 ++++ +++  lll ++ +E
  EPA04268.1 132 AIEISIVTG-LLLTGGYLE 149
                 777666666.556666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1000.27
//
Query:       EPA04269.1  [L=300]
Description: hypothetical protein BG20_I1897 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.069   13.6   0.0       0.14   12.6   0.0    1.5  1  Copper-bind  Copper binding proteins, plastocyanin/azurin fam
       0.18   11.2   0.0       0.26   10.7   0.0    1.2  1  DUF1571      Protein of unknown function (DUF1571)


Domain annotation for each model (and alignments):
>> Copper-bind  Copper binding proteins, plastocyanin/azurin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.6e-05      0.14      13      80 ..     200     266 ..     189     277 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.6e-05
                  EEESSEEEEETTEEEEEEEESSSSBEEEEETTSSTTTGGGTTSCTTC.EEEEBSTTEEEEEEEESSEEE CS
  Copper-bind  13 qFetkeitvkkgekvtfvnlavmgHNvvldkdgvpagvdkdkvkaed.etkliggGekdsvtfdeagtY 80 
                   F++ +i++k+g+++t vn + + H +   kd  +   ++  v+ ++ +t  i + ++ ++tf++ag Y
   EPA04269.1 200 LFSQDRISIKPGTTITIVNDDTVTHSIQSGKDTGDR-YNR-FVSDGRiSTGDILPNKSVNITFENAGFY 266
                  3999***************************77422.222.2222222343455556666666666666 PP

>> DUF1571  Protein of unknown function (DUF1571)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   2.9e-05      0.26      79     154 ..     132     208 ..     117     218 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 2.9e-05
     DUF1571  79 dgplAmaesrypv.tdlGlenlieklieereldleaeeaevelkreerldgrrvtalevehpskeeqvefskaelll 154
                 +g+ Am +++y +   + l++l++  i+  e++++++++ +++ +++ ++g+  t+ ++  ++++e + fs+ ++ +
  EPA04269.1 132 TGRIAMDNNNYKIiYTAKLSELTKINITPTESKTTDQKTIIHILKGASTQGVGSTIGQYGSSQGTELKLFSQDRISI 208
                 7999*******9726899*****************************************999999999999887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1975.19
//
Query:       EPA04270.1  [L=447]
Description: peptidyl-prolyl cis-trans isomerase, cyclophilin-type, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-50  171.4   0.3    3.4e-50  170.4   0.3    1.5  1  Pro_isomerase  Cyclophilin type peptidyl-prolyl cis-trans iso
  ------ inclusion threshold ------
       0.04   13.4   0.1       0.14   11.6   0.1    1.9  1  Lpp-LpqN       Probable lipoprotein LpqN


Domain annotation for each model (and alignments):
>> Pro_isomerase  Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.4   0.3   3.8e-54   3.4e-50       2     157 ..      30     186 ..      29     187 .. 0.90

  Alignments for each domain:
  == domain 1  score: 170.4 bits;  conditional E-value: 3.8e-54
  Pro_isomerase   2 vdietsskGrivieLfadkaPktvenFlklvkegfYdgttFhRvikgfmvqgGdptgktsageqe.kkggesiraipdEitsklkhkrGalamart 96 
                    v ++t+ +G+ivie f+++aPk+venF+kl+++gfYdgt+FhR+i+gfm+qgGdp++k+ + + +   gg   + +++E+ +++kh+rG+++mar+
     EPA04270.1  30 VILHTN-LGKIVIEFFPNDAPKHVENFIKLAESGFYDGTVFHRIIPGFMIQGGDPNTKSGDPT-TwGIGG-PNYSVNAEF-NTIKHNRGIVSMARS 121
                    678997.************************************************99977444.436666.46899****.9************** PP

  Pro_isomerase  97 gkepnsagsqFfItlkeaphldgkytvFGkVv..eGmdvvekiekvetde...erpkknvkivsae 157
                     ++pnsagsqFfI+ k+ ++ld++ytvFG++v  e++d+++ki++v+t +       ++vki++ae
     EPA04270.1 122 -ADPNSAGSQFFIVHKDSNFLDEQYTVFGRIVtqESFDTLDKIASVQTGDrdiPVNIEQVKITKAE 186
                    .69*****************************9*************99998554455669999887 PP

>> Lpp-LpqN  Probable lipoprotein LpqN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   1.5e-05      0.14      24     145 ..     220     342 ..     215     369 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.5e-05
                 --SEEEE----TT-EE-SS---TTEEEEEEETT.SSSSS-EEEEEEEEEEES---HHHHHCCTTH...HHHTSTT-EEEEEE---BTTB-EEE..EEEE CS
    Lpp-LpqN  24 lgaltvdlplPegWedagdpnledayaviaktqpesgedtptavllvskLtGdvDpaealehapv...daqnlpgfkatdgstadlsGfpssq..ieGt 117
                  +al++++++P+gW  +++++ +++   i+   p  g+  p + l+vs  +G    +++++  ++   +a ++ + +  +++++ +++ ++++   +G 
  EPA04270.1 220 NKALDISFNVPTGWLLQEPEKTDENAPDIVAVGPRVGTINPVISLTVSDSKGRS-LDDLIKEKDEflkNALKTGNLEIISQEKSIINEKQAYVtnAKGF 317
                 689************88888888888888888****************999873.44566654440113444566777777777777777776225799 PP

                 EECTTEEEEEEEEEEEEEETT...EEEE CS
    Lpp-LpqN 118 YdkdgkrlavaqrtViitgappdaqrYl 145
                 ++++g+ ++v  r  ii++  p++  Y+
  EPA04270.1 318 FSNNGTSYNVQFRETIIST--PEK-FYV 342
                 9999999999999999988..555.676 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 3204.55
//
Query:       EPA04271.1  [L=200]
Description: hypothetical protein BG20_I2647, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1349.29
//
Query:       EPA04272.1  [L=81]
Description: hypothetical protein BG20_I2659, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 542.74
//
Query:       EPA04273.1  [L=101]
Description: hypothetical protein BG20_I2660, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.3e-12   45.7   0.4    1.1e-11   45.1   0.4    1.2  1  HHH_5            Helix-hairpin-helix domain
    2.2e-06   27.4   0.0    6.8e-06   25.8   0.0    1.8  2  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
      6e-06   26.3   0.0    2.3e-05   24.4   0.0    1.9  2  HHH_2            Helix-hairpin-helix motif
     0.0018   18.6   0.1       0.11   12.8   0.1    2.3  2  HHH_8            Helix-hairpin-helix domain
     0.0068   16.2   0.0      0.077   12.9   0.0    2.8  3  HHH              Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.024   14.9   0.1       0.22   11.8   0.0    2.1  2  Cdd1             Pathogenicity locus
      0.033   14.4   0.0      0.066   13.5   0.0    1.3  1  DUF4332          Domain of unknown function (DUF4332)
       0.05   13.4   1.0       0.14   12.0   0.1    2.1  3  RNA_pol_A_CTD    Bacterial RNA polymerase, alpha chain C term


Domain annotation for each model (and alignments):
>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.1   0.4   4.9e-15   1.1e-11       3      57 .]      45      99 ..      42      99 .. 0.97

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 4.9e-15
                HHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHHHH CS
       HHH_5  3 eLlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriilelkd 57
                +L +v+GiG+ +A+ l+++Gi  ++dla+  v++La+i  iG   A++i+ el++
  EPA04273.1 45 DLVKVKGIGRIRARMLYKHGIQNLDDLANIPVNKLADIDKIGSTIADNIKSELRK 99
                899**************************************************97 PP

>> DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.98   2.2e+03      30      43 ..      26      39 ..      16      40 .. 0.62
   2 !   25.8   0.0   3.1e-09   6.8e-06       3      42 ..      46      86 ..      45      93 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.98
  DNA_pol_lambd_f 30 akrakLtreqqiGl 43
                      + ++L r   +G+
       EPA04273.1 26 DELDNLRRRITYGI 39
                     33466777777666 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 3.1e-09
  DNA_pol_lambd_f  3 FtkvyGVGpktAkkwyakGirtledlra.krakLtreqqiG 42
                     + kv G+G+ +A+++y+ Gi +l+dl +   +kL    +iG
       EPA04273.1 46 LVKVKGIGRIRARMLYKHGIQNLDDLANiPVNKLADIDKIG 86
                     6799***********************97557888777777 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.029        65      34      50 ..      43      59 ..      38      63 .. 0.81
   2 !   24.4   0.0     1e-08   2.3e-05       9      53 ..      50      95 ..      46     100 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.029
       HHH_2 34 leeLlevddiGeeiAqs 50
                l +L++v++iG + A+ 
  EPA04273.1 43 LLDLVKVKGIGRIRARM 59
                56899******998875 PP

  == domain 2  score: 24.4 bits;  conditional E-value: 1e-08
       HHH_2  9 rhVGektAklLakr.FksldaLkkasleeLlevddiGeeiAqsive 53
                + +G   A+ L k+  ++ld L++  +++L+ +d iG +iA++i++
  EPA04273.1 50 KGIGRIRARMLYKHgIQNLDDLANIPVNKLADIDKIGSTIADNIKS 95
                6799999*****99567**************************986 PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.0    0.0044       9.9      34      57 ..      27      54 ..      25      60 .. 0.84
   2 !   12.8   0.1   5.1e-05      0.11       9      64 ..      41      94 ..      41      98 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0044
                CCCC-SS-HHHH.TT...HCTTSTT--H CS
       HHH_8 34 aiealpeeitsl.ee...eltklpgiGk 57
                 +++l ++it + +e   +l k++giG 
  EPA04273.1 27 ELDNLRRRITYGiREellDLVKVKGIGR 54
                68999******995559999*******5 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 5.1e-05
                HHHHHHHHHCT--CCCHHH.HHHHHCCCCC-SS.-HHHHTTHCTTSTT--HHHHHHHH CS
       HHH_8  9 eeladllelkgedpfrvra.YrrAaraiealpe.eitsleeeltklpgiGkkiaakie 64
                eel dl ++kg    r+r  Y+  ++++++l   +++     l +++ iG  ia+ i+
  EPA04273.1 41 EELLDLVKVKGIGRIRARMlYKHGIQNLDDLANiPVNK----LADIDKIGSTIADNIK 94
                57888888888556666657************999999....999**********995 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   3.5e-05     0.077      12      28 ..      45      61 ..      40      63 .. 0.90
   2 ?   -1.2   0.0         1   2.3e+03       9      17 ..      67      75 ..      66      75 .. 0.84
   3 ?   -1.2   0.0         1   2.3e+03      19      29 ..      85      95 ..      78      96 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.5e-05
                HHHTSTT-SHHHHHHHH CS
         HHH 12 eLlalPGVGpktAeaIl 28
                +L++++G+G+ +A+  +
  EPA04273.1 45 DLVKVKGIGRIRARMLY 61
                79***********9765 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1
                SHHHHHTST CS
         HHH  9 sreeLlalP 17
                ++++L+ +P
  EPA04273.1 67 NLDDLANIP 75
                5799*9998 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1
                -SHHHHHHHHH CS
         HHH 19 VGpktAeaIls 29
                +G   A+ I s
  EPA04273.1 85 IGSTIADNIKS 95
                88889998875 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0    0.0001      0.22       2      35 ..      40      73 ..      39      82 .. 0.89
   2 ?    1.5   0.0      0.16   3.5e+02       6      22 ..      77      93 ..      74      97 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0001
        Cdd1  2 rkalkelqdiPniGkalaedlvelGirsveelkg 35
                r++l +l ++ +iG+  a++l++ Gi+++++l++
  EPA04273.1 40 REELLDLVKVKGIGRIRARMLYKHGIQNLDDLAN 73
                57889999************************97 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.16
        Cdd1  6 kelqdiPniGkalaedl 22
                ++l di  iG  +a+++
  EPA04273.1 77 NKLADIDKIGSTIADNI 93
                7899*********9876 PP

>> DUF4332  Domain of unknown function (DUF4332)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.9e-05     0.066      52      89 ..      43      80 ..      39      87 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.9e-05
     DUF4332 52 lAdLarikgigeeyaeLLeaaGvdsvaeLaqrnpanLh 89
                l dL+++kgig+  a +L + G++   +La+ ++++L 
  EPA04273.1 43 LLDLVKVKGIGRIRARMLYKHGIQNLDDLANIPVNKLA 80
                569****************************9999986 PP

>> RNA_pol_A_CTD  Bacterial RNA polymerase, alpha chain C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.7   3.8e+03      11      17 ..      15      21 ..      11      31 .. 0.57
   2 ?   -1.0   0.0      0.68   1.5e+03      46      55 ..      45      54 ..      39      55 .. 0.81
   3 ?   12.0   0.1   6.1e-05      0.14      28      66 ..      60      98 ..      56      99 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.7
                   X--BHHH CS
  RNA_pol_A_CTD 11 lsisIee 17
                   +s+++e 
     EPA04273.1 15 ISKHVER 21
                   3444444 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.68
                   HHTTSSS-SS CS
  RNA_pol_A_CTD 46 eLlkikNlGk 55
                   +L k+k +G+
     EPA04273.1 45 DLVKVKGIGR 54
                   8999999997 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 6.1e-05
                   HHHTT--BHHHHHHS-HHHHTTSSS-SSHHHHHHHHHHH CS
  RNA_pol_A_CTD 28 LkragiktvgeLvklseeeLlkikNlGkKSleEIkekLe 66
                   L + gi+ +++L+++  ++L  i  +G    + Ik+ L 
     EPA04273.1 60 LYKHGIQNLDDLANIPVNKLADIDKIGSTIADNIKSELR 98
                   7789*******************************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 652.43
//
Query:       EPA04274.1  [L=349]
Description: hypothetical protein BG20_I2497, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.6e-06   26.4   1.4    1.4e-05   24.9   1.1    2.1  1  DUF2334          Uncharacterized protein conserved in bacteri
     0.0011   18.8   0.0     0.0025   17.7   0.0    1.6  2  Polysacc_deac_1  Polysaccharide deacetylase


Domain annotation for each model (and alignments):
>> DUF2334  Uncharacterized protein conserved in bacteria (DUF2334)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   1.1   1.6e-09   1.4e-05      88     166 ..     123     208 ..      96     284 .. 0.72

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.6e-09
     DUF2334  88 sgegfeflseseakeriekGi.eilkklgikpkgFeaPhyaaseetykalkky.fsiiyerykeyk..gq...kegltyipenlgy 166
                   + f   s++e+ + ++++i eil+++g++p++F++P+ +++e+t+++l ++ f+ ++ +  +++  +    +e l+  pe++  
  EPA04274.1 123 GSAPFTNYSKQEQDKLLKQSIvEILNNAGVRPHIFVPPQNQYNEDTKQVLIENkFTHVSGSVSQEEvvKFplkDETLYKFPETATT 208
                 333444488999999999998799**************************9888*****885555444225554444444444333 PP

>> Polysacc_deac_1  Polysaccharide deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   2.8e-07    0.0025      25     122 ..      77     178 ..      51     180 .. 0.84
   2 ?   -3.7   0.0       1.2     1e+04      23      33 ..     229     239 ..     221     242 .. 0.61

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.8e-07
                      HHHHHHCT--EEEEE-HHHHCH-...HHHHHHHHHTT.EEEEE--SS--EGGGSHHHHHHHHHHHHHHHHHHHHS----EEE-GGGEE-HHHHH CS
  Polysacc_deac_1  25 lpvLkkykvkatffvigglvedy...pdevremaasG.veignHtinhsnlkrlseeevrreierakdalrkalgreprlfryPygsasatvle 114
                      ++++ +++++ t+ +i    ++      +v+    +  +ei++ +i    +++ s++e+++ ++++   + +  g +p+ f +P  ++++++ +
       EPA04274.1  77 INTFVEKNIPLTVGIIADSFGNDqkiTAIVKDASSKNkIEIASEGIGSAPFTNYSKQEQDKLLKQSIVEILNNAGVRPHIFVPPQNQYNEDTKQ 170
                      55666777777777777764333345788999999999******************************************************** PP

                      HHHHTT.E CS
  Polysacc_deac_1 115 varelgfa 122
                      v+ e  f+
       EPA04274.1 171 VLIENKFT 178
                      *9988876 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 1.2
                      HHHHHHHHCT- CS
  Polysacc_deac_1  23 eilpvLkkykv 33 
                        +++Lkky++
       EPA04274.1 229 DTVDALKKYGF 239
                      34556666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 2060.14
//
Query:       EPA04275.1  [L=421]
Description: 3-phosphoshikimate 1-carboxyvinyltransferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   2.8e-103  345.8   0.0   3.5e-103  345.5   0.0    1.0  1  EPSP_synthase  EPSP synthase (3-phosphoshikimate 1-carboxyvin


Domain annotation for each model (and alignments):
>> EPSP_synthase  EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  345.5   0.0    2e-107  3.5e-103       4     415 ..       7     410 ..       5     412 .. 0.94

  Alignments for each domain:
  == domain 1  score: 345.5 bits;  conditional E-value: 2e-107
                    SS--EEEEE--B-HHHHHHHHHHHGGGBSSEEEES---SHHHHHHHHHHHHTT.EEEEEECTSEEEEEGTT..--EE-HHHHTT-GGGGGGHHHHH CS
  EPSP_synthase   4 gkrlegevkvpGsksisnralllAaLaegestitnlLdseDvrsmlealreLgaeiikldeekevviveglggsfeapeelvldlgnsgtalrlLt 99 
                    +++l+g v+ p++ks+s+ra+ lA+La ++s+i+n+L s+D+ +++ea++++gaei++   + ++++ ++      +p    +d++nsgt++r+  
     EPA04275.1   7 KSKLSGHVTCPPNKSYSHRAIFLASLAGNNSKIDNVLFSADTIATIEACKNFGAEIEQK--NTSIIVKKPIKIDKIVP---EIDAKNSGTTIRIAS 97 
                    579**************************************************877555..55666666654445555...59************* PP

                    HHHSEESSEEEEE-SBTTCGS--HHHHHHHHHTT-EEEEETTEEEEEESEET.SS-BEEEEETSSTTHHHHHHHHHHHTTSBS.EEEEES.-TTHH CS
  EPSP_synthase 100 allalasgevvLtGdesirkRPidrlldaLrqlGaeieveegenkaplkvkg.lklkgveikaevsSqqvtsllllaallaeg.ttelee.lasep 192
                    ++++l s++++LtGd s++kRP+++lldaL+++Ga++ + +g   +p+++ g   +++v+i +++sSq++++ll++a+l+  g ++++e+ l+s+p
     EPA04275.1  98 GIASLFSKPITLTGDSSLQKRPMQPLLDALESIGAKCSSTNG--MPPIRITGkILGGDVSIPGNFSSQFISALLICAPLTERGiNLTIEGnLVSKP 191
                    *****99*******************************6666..********9999**************************************** PP

                    HHHHHHHHHHHTT-EEEETTSSEEEEEE--SSB--EEEE--B-HHHHHHHHHHHHHTT-EEEEES--GGGGHHH..HHHHHHHHTTEEEEEESTSE CS
  EPSP_synthase 193 siddtlkmlkkfgikietsgteesitvkGkeklpgteyvvegDassAayflvaAaitggevtvenvginslqGdiealdeilekmgaeitqeedas 288
                    + d t+  +++fg+ ++t   +++  ++++  + + e++v+ D ss a +l aA++ g evt+++   n  qGd +++d i+e+mg++i  +ed+ 
     EPA04275.1 192 YLDATIATMRNFGVSVQTLIPYKKYHITPQIYKAS-EFTVPMDFSSLALLLSAAILNGDEVTIHGKMGNLPQGDEAFID-IIEQMGVKIIIKEDQM 285
                    ******************999999*****655666.**************************************99999.**********999999 PP

                    EEEEETTS--BEEEEEBGSTTSBHGGGHHHHHHHHHTSBSEEEEEGSSSTTCCHHHHHHHTTT-EEEEETTEEEEEEEEE.EB-EEEE-TTSTTTT CS
  EPSP_synthase 289 ivvgpsglklkdvdietlpdeaptlavlaafaegttviegiaelrvketdrlaamateLrklGaeveeeedgliiipaekqlkgaevesydDhRia 384
                    +++++ +l++ + d+++ pd +p+la+la+ a++  +i ++++ r ketdr+  +a eL+klG++++e+edgli +p++ +l+ga ++s +DhR+ 
     EPA04275.1 286 TIESTEKLDGGKFDLSNSPDILPPLAILALKAKNPIEIINVKHARLKETDRILILARELKKLGMHIQEKEDGLILEPPK-ELHGALLNSENDHRLF 380
                    999999*******************************************************************988886.6*************** PP

                    HHHHHHHHHSBSEEEEETTHHHHHHSSSHHH CS
  EPSP_synthase 385 malalaglvaegeveiddiectdksfpefee 415
                    ma+ +ag +  g+ +++d e +++s+p+f+ 
     EPA04275.1 381 MAFCIAG-MYIGNCIVTDHESVAVSYPDFIS 410
                    *******.66677****************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2633.41
//
Query:       EPA04276.1  [L=179]
Description: ATPase/histidine kinase/DNA gyrase B/HSP90 domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.8e-15   57.4   0.6      3e-15   56.7   0.1    1.6  2  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    4.1e-07   29.8   0.2    9.7e-07   28.6   0.0    1.7  2  HATPase_c_5  GHKL domain
     0.0052   16.7   0.0     0.0085   16.0   0.0    1.3  1  HATPase_c_2  Histidine kinase-like ATPase domain
  ------ inclusion threshold ------
       0.15   12.7   2.2       0.23   12.1   2.2    1.2  1  DUF3800      Protein of unknown function (DUF3800)


Domain annotation for each model (and alignments):
>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.88     4e+03      25      31 ..      42      48 ..      14      70 .. 0.54
   2 !   56.7   0.1   6.7e-19     3e-15       5     110 ..      79     176 ..      75     178 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.88
                TEEEEEE CS
   HATPase_c 25 geievei 31
                +++  ei
  EPA04276.1 42 KHLLHEI 48
                2222222 PP

  == domain 2  score: 56.7 bits;  conditional E-value: 6.7e-19
                 HHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHHHHHHHHHTTTEEEEEEETTTEEE CS
   HATPase_c   5 rLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsivkklvelmgGeiwvesepgrGtt 103
                 ++  ++ nl+ Nav+   ++g+i+++ + ++    i+v D+G+ i+ + l+k+fe++ +     ++++gtGlGl  +k++ve ++G ++v+++p    t
  EPA04276.1  79 QMIIVFTNLIYNAVQKFEDDGKISIQYSDDDTSHIIQVVDSGKPISDDVLPKIFEPLFT-----TKQKGTGLGLVSCKAIVEIHNGVLSVKNNP---VT 169
                 5566899********633555555555545589999*******************6666.....699***********************9888...78 PP

                 EEEEEES CS
   HATPase_c 104 ftftlpl 110
                 ft+ lp+
  EPA04276.1 170 FTIVLPK 176
                 8887775 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1      0.66     3e+03      21      36 ..      12      27 ..       3      48 .. 0.50
   2 !   28.6   0.0   2.2e-10   9.7e-07       3      96 ..      77     172 ..      75     175 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.66
  HATPase_c_5 21 cskieeekrfIrltvr 36
                 c+ki+++   I  +++
   EPA04276.1 12 CNKIKHSLDQILRQIN 27
                 4444433333333333 PP

  == domain 2  score: 28.6 bits;  conditional E-value: 2.2e-10
  HATPase_c_5   3 dldlcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg...ek.kkle..sskskkeehGiGlksireivkkykgnlsieaedglF 94 
                  d  +++++ nl+ NA++  ++    + +I+++ + ++ s ii++  s +    +   k++    ++k++  G+Gl s + iv+ ++g ls++++  +F
   EPA04276.1  77 DSQMIIVFTNLIYNAVQKFED----DGKISIQYSDDDTSHIIQVVDSGKPisdDVlPKIFepLFTTKQKGTGLGLVSCKAIVEIHNGVLSVKNNPVTF 170
                  67899*********9865554....779****************99966633222434333434667799***********************99999 PP

  HATPase_c_5  95 tl 96 
                  t 
   EPA04276.1 171 TI 172
                  85 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.9e-06    0.0085      40     105 ..      84     150 ..      83     171 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.9e-06
  HATPase_c_2  40 ctNavehayleap.egpvevrlesdeealtvevaDsGpgfdpetlpdpteeepkeslkegGrGlali 105
                  +tN +  a ++ + +g++++++++d+++  ++v DsG++     lp+  e+  ++++k  G+Gl   
   EPA04276.1  84 FTNLIYNAVQKFEdDGKISIQYSDDDTSHIIQVVDSGKPISDDVLPKIFEPLFTTKQKGTGLGLVSC 150
                  677776666666669************************6666666666666667777777777655 PP

>> DUF3800  Protein of unknown function (DUF3800)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   2.2   5.1e-05      0.23      27     111 ..      15     118 ..       2     119 .. 0.51

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.1e-05
     DUF3800  27 ie.eikkleekikelkkky...............krlleriakflkkndlik...............sdeesdesilivldk......kkkkekakkel 88 
                 i+   +++ ++                       k+ll++i k++++                    +   +d++++iv+ +      +          
  EPA04276.1  15 IKhSLDQILRQ-------IndvtnfvrihptkfqKHLLHEIIKDALEL---MiipnnivielpkgnpEIICDDSQMIIVFTNliynavQ---------- 93 
                 22333333334.......244445556666666655666655555553...02233444334445442223344444444443322220.......... PP

     DUF3800  89 eilld......esvkfvdSkesrglQlAD 111
                     +      +s+++ d ++s  +Q++D
  EPA04276.1  94 ----KfeddgkISIQYSDDDTSHIIQVVD 118
                 ....1334455*****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 1434.93
//
Query:       EPA04277.1  [L=57]
Description: hypothetical protein BG20_I2084, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-15   56.6   0.0    1.8e-15   56.5   0.0    1.0  1  Chorismate_synt  Chorismate synthase


Domain annotation for each model (and alignments):
>> Chorismate_synt  Chorismate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.5   0.0     1e-19   1.8e-15       3      48 ..      12      57 .]      10      57 .] 0.94

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 1e-19
                     EEEE-SCCSSEEEEEEE---BT-B--HHHHHHHHHHHTCTSSSSSS CS
  Chorismate_synt  3 vttfGeShgkalgavidgvpagleldeediqkeLdrRrpgqskltt 48
                     +t+fGeShgk++gav+dg+pagle+de++iqk Ld R+pgqs ++t
       EPA04277.1 12 LTSFGESHGKSIGAVLDGCPAGLEIDEKEIQKMLDYRKPGQSLIST 57
                     799**************************************88765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 414.34
//
Query:       EPA04278.1  [L=158]
Description: PAS domain S-box [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-12   45.9   0.0    6.9e-12   45.5   0.0    1.2  1  PAS_9     PAS domain
    9.9e-09   35.4   0.0    1.5e-08   34.8   0.0    1.2  1  PAS_3     PAS fold
    3.2e-08   33.8   0.0      4e-08   33.5   0.0    1.1  1  PAS_4     PAS fold
      2e-07   31.0   0.0    2.7e-07   30.6   0.0    1.2  1  PAS       PAS fold
    7.9e-07   29.0   0.0    1.3e-06   28.2   0.0    1.4  1  PAS_8     PAS domain
  ------ inclusion threshold ------
      0.018   15.2   0.0      0.026   14.6   0.0    1.3  1  PAS_11    PAS domain


Domain annotation for each model (and alignments):
>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   0.0   2.3e-15   6.9e-12       2     103 ..      11     113 ..      10     114 .. 0.87

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 2.3e-15
       PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgks.itdlf..vtdpeanerlraaleqgrkkerevevvlirkngetfwvlltaspvkdddgelvgiiv 97 
                 d+ ++ ++dg+i+++N++ ++ lGy+++e++g     d++  ++ p+a + + ++++ g     +v  ++ rk+++tf+   + + ++d+ g+l g++v
  EPA04278.1  11 DMLALFDKDGKIIDCNDHCAKNLGYDKNEMIGMIgPVDFIveKDRPKAVDAFTQVVKKGI--NLNVSFDMLRKDQSTFPSIWSGTVLYDEFGNLEGYLV 107
                 5566656**********************9998754444468888888888888888888..************************************* PP

       PAS_9  98 ilrDit 103
                 + +D++
  EPA04278.1 108 TGKDLS 113
                 ****97 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.0   4.9e-12   1.5e-08       1      85 [.      22     105 ..      22     108 .. 0.95

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 4.9e-12
       PAS_3   1 iiyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirdengkpvrv 85 
                 ii +++ + + lGy+++e++g      d++   Dr+++ +a+ +++kkg  +++ + ++rkd +++   ++++v++de g+   +
  EPA04278.1  22 IIDCNDHCAKNLGYDKNEMIGM-IGPVDFIVEKDRPKAVDAFTQVVKKGINLNVSFDMLRKDQSTFPSIWSGTVLYDEFGNLEGY 105
                 589*******************.8899***************************************************9998766 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.0   1.3e-11     4e-08       1     109 [.       6     116 ..       6     117 .. 0.97

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 1.3e-11
       PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktla.ellpeedaarleralrrvlegeepiefleelll.pgeerhyelrllPlrdesGevig 97 
                 ++s+pd+la +d+dg+++++N   a+ +g++  e++G+    ++  e d++   +a ++v++ +  +     +l+ ++++ +  ++ + l de G   g
  EPA04278.1   6 FESTPDMLALFDKDGKIIDCNDHCAKNLGYDKNEMIGMIGPvDFIVEKDRPKAVDAFTQVVKKGINLNVSFDMLRkDQSTFPSIWSGTVLYDEFGNLEG 104
                 79*************************************************************************99********************** PP

       PAS_4  98 vlvisrDiTerr 109
                 +lv++ D+++++
  EPA04278.1 105 YLVTGKDLSNLK 116
                 *******98865 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.0   9.1e-11   2.7e-07       6     112 ..       5     111 ..       1     112 [. 0.86

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 9.1e-11
                 HHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSB.GGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEEC..TTSSEEEEEEEEEEEEETTE CS
         PAS   6 ileslpdpifvvDedgrilyvNaaaeellGlsreevlgks.lldliheeddaelaelleqlleqgeesrageisfkl..rdgrpihlevraspvrdagg 101
                 ++es+pd+  + D+dg+i+ +N+  ++ lG++ +e++g    +d+i+e+d   +++++    ++ +++ + ++sf+   +d+++++     + ++d+ g
  EPA04278.1   5 LFESTPDMLALFDKDGKIIDCNDHCAKNLGYDKNEMIGMIgPVDFIVEKD---RPKAVDAFTQVVKKGINLNVSFDMlrKDQSTFPSIWSGTVLYDEFG 100
                 789***********************************984667777766...6777777777777888888888888899****************** PP

                 EEEEEEEEEEE CS
         PAS 102 eilgflgvlrd 112
                 ++ g+l++++d
  EPA04278.1 101 NLEGYLVTGKD 111
                 *******9998 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   4.5e-10   1.3e-06       4      51 ..       3      53 ..       1      69 [. 0.78

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 4.5e-10
       PAS_8  4 ralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellg..qllpv 51
                + lfes pd +a++d +++i+d+N+  ++ lGy+ ++++g+      +++ 
  EPA04278.1  3 KILFESTPDMLALFDKDGKIIDCNDHCAKNLGYDkNEMIGMIGPvdFIVEK 53
                559************6666********************988753344444 PP

>> PAS_11  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   8.9e-06     0.026       9      75 ..      17      80 ..      11      92 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8.9e-06
      PAS_11  9 didgkIisvDtsaLrasfslglekeelvgrs.iydLchpqdlstlkshlrevissngeatsslyRLrl 75
                d dgkIi+++         lg+ k+e++g++   d++ ++d+ ++ +++ +v+ ++g +   ++ +  
  EPA04278.1 17 DKDGKIIDCND---HCAKNLGYDKNEMIGMIgPVDFIVEKDRPKAVDAFTQVV-KKGINLNVSFDMLR 80
                789********...99*************87589******************9.88877666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1081.35
//
Query:       EPA04279.1  [L=207]
Description: putative shikimate kinase, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-09   38.4   0.2    1.8e-09   37.7   0.2    1.3  1  GHMP_kinases_N  GHMP kinases N terminal domain


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.2     1e-13   1.8e-09       2      66 .]      37     105 ..      36     105 .. 0.74

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 1e-13
                     EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHH.HH......HHHHHHHHHHHHHHHHHSHHH.HHHHHSS CS
  GHMP_kinases_N   2 ivikseiPvgaGLGSSAAlavalvaAllallglsl.ee......aklaleaerlaqggngsggDv.aasvyGg 66 
                     i+++s iP+g GL SS+A++ a+++A  + +  +l ++      ++ ++e+     +  ++  D+ + ++yGg
      EPA04279.1  37 ITLESQIPTGYGLKSSSAISSAVALACSKIFKPKLtDKqillsgVEASIESK----VSITGAYDDaCSCYYGG 105
                     899****************************766853366554455555555....45556666637777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1272.96
//
Query:       EPA04280.1  [L=182]
Description: hypothetical protein BG20_I1586 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.9e-20   71.5   0.1    9.2e-20   71.1   0.1    1.1  1  Aminotran_1_2    Aminotransferase class I and II
     0.0064   15.8   0.0     0.0084   15.4   0.0    1.2  1  Beta_elim_lyase  Beta-eliminating lyase
     0.0085   14.7   0.0      0.011   14.3   0.0    1.1  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.1   0.1   1.5e-23   9.2e-20       2     156 ..      47     172 ..      46     173 .. 0.90

  Alignments for each domain:
  == domain 1  score: 71.1 bits;  conditional E-value: 1.5e-23
                    EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEE CS
  Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeil 97 
                    +++nL+sn+ylg     ++++   + ++   +++++  +g+ + +++lee+lak  +        ++ ++++ +G+ a++  ++++ k  +gd il
     EPA04280.1  47 KLLNLCSNDYLGI----QVTK--TKINQ--MQSSSRLVSGNDEAYKKLEEKLAKHKS--------HQNSLIYPTGYMANLGSITAISK--KGDLIL 124
                    789********98....4443..44444..77999**********************........8889******************9..****** PP

                    EEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEES CS
  Aminotran_1_2  98 vpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilves 156
                    ++++++as+++ ++lsg++++ y+       h+d+++l ++lk+      k+k++++e+
     EPA04280.1 125 SDELNHASIIESCKLSGAKIIIYK-------HNDIDDLNKKLKQKG----KNKFVVTEG 172
                    ************************.......************933....568***986 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.4e-06    0.0084      27     123 ..      76     164 ..      60     172 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.4e-06
                      CCT--HHHHHHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHHHHHHS-- CS
  Beta_elim_lyase  27 sYgedktvnrLedavaelfgkeaalfvpqGtaAnsillkillqrgeevivtepahihfdetgaiaelagvklrdlknkeaGkmdlekleaaike 120
                      + g+d+ +++Le+++a+   ++  l  p+G +An  +++++ ++g+ ++ +e +h    e   +   +g+k + +++ +    d+++l++++k+
       EPA04280.1  76 VSGNDEAYKKLEEKLAKHKSHQNSLIYPTGYMANLGSITAISKKGDLILSDELNHASIIESCKL---SGAKII-IYKHN----DIDDLNKKLKQ 161
                      5699***************************************************998887544...555333.33333....56666666666 PP

                      S-T CS
  Beta_elim_lyase 121 vga 123
                      +g+
       EPA04280.1 162 KGK 164
                      554 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   1.8e-06     0.011      55     142 ..      84     167 ..      62     177 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.8e-06
                      HHHHHHHHHHHT-SEEEEESSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEESTTSHHHHHHHCCTTEEEEE CS
  Cys_Met_Meta_PP  55 svleeriaaLeggeaalavssGmaAiaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdtsdleelekaikentklvy 142
                      + lee++a+ ++ +++l++++G  A   +i+a+ k+Gd i++++  + +      + +k +g ++ ++  +d+++l+k++k++ k  +
       EPA04280.1  84 KKLEEKLAKHKSHQNSLIYPTGYMANLGSITAISKKGDLILSDELNHASII----ESCKLSGAKIIIYKHNDIDDLNKKLKQKGKNKF 167
                      68************************************9988876555444....455566777777777778888888887655444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1110  (0.0619109); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1223.18
//
Query:       EPA04281.1  [L=203]
Description: LemA family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-48  164.5   0.1    1.9e-48  164.1   0.1    1.1  1  LemA            LemA family
     0.0011   19.2   0.3     0.0017   18.6   0.3    1.3  1  DUF4330         Domain of unknown function (DUF4330)
     0.0022   17.4   1.1     0.0028   17.0   1.1    1.2  1  ALIX_LYPXL_bnd  ALIX V-shaped domain binding to HIV
     0.0039   17.6   0.3     0.0056   17.1   0.3    1.3  1  ACP_PD          Acyl carrier protein phosphodiesterase
  ------ inclusion threshold ------
      0.025   14.8   0.8      0.053   13.7   0.8    1.6  1  Chordopox_A13L  Chordopoxvirus A13L protein
       0.26   11.6   3.9       0.49   10.7   3.9    1.7  1  MacB_PCD        MacB-like periplasmic core domain
        1.2    9.0   7.2        1.9    8.3   3.0    2.1  2  SurA_N_2        SurA N-terminal domain


Domain annotation for each model (and alignments):
>> LemA  LemA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.1   0.1   7.4e-52   1.9e-48       3     148 ..      46     199 ..      44     200 .. 0.89

  Alignments for each domain:
  == domain 1  score: 164.1 bits;  conditional E-value: 7.4e-52
        LemA   3 sqidvqlkrRaDlipnLvetvkgyakhEketleevteaRakaaeaesveekaeaenqlssalsrllavaEnYPdLkanenfleLqeelegtEnriavaR 101
                 +++dvql+rR+DlipnL+++vkgy+++Ek++le+vt++R++ ++ +++ e+ e +nq+++als+++++ EnYP+Lka++++++L++el+gtEnri+vaR
  EPA04281.1  46 ADVDVQLQRRYDLIPNLIQSVKGYMQFEKDVLEQVTKLRSQWQATSNTGERVELSNQIEQALSKIILTYENYPELKADSTVTRLMDELAGTENRISVAR 144
                 79************************************************************************************************* PP

        LemA 102 rrYneavreyntkiesfpsnivak..lf.....gfkekelfea.eeaereapkVk 148
                 ++Yn+ vr++n +i++fp+n++ +  ++     g+++ + +ea + a++++pkV+
  EPA04281.1 145 TYYNDGVRDFNVNIRTFPNNVFNQsgFLgmspwGLQPYPAYEAtSMAQTTVPKVD 199
                 *********************9873333111224666777888444667778775 PP

>> DUF4330  Domain of unknown function (DUF4330)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.3   6.7e-07    0.0017      16     129 ..       6     117 ..       4     148 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 6.7e-07
     DUF4330  16 ilDllailvilavivgiflkpgts.gsvaqaeaaatkpvevdvvvrglev...peelakvkegektniiirnqPagdveikdvkvlprkvvvpqpdGkv 110
                 i+ +++ +vi+a+i+ i++ +  s  ++aq+++++ k+  +dv v+  +     ++l++  +++ +++ +         +++v+ l+++ ++++ +G+ 
  EPA04281.1   6 IIGIIIGVVIVALIFSILYGMYFSgYNAAQIKDEQIKKYAADVDVQLQRRydlIPNLIQ-SVKGYMQFEK-------DVLEQVTKLRSQWQATSNTGER 96 
                 88899****************9997778*****9999999*****97777444333444.3344443333.......2477888888899999999999 PP

     DUF4330 111 kaled..epylkdllvtlegk 129
                 ++l++  e+ l+ +++t e  
  EPA04281.1  97 VELSNqiEQALSKIILTYENY 117
                 999887557788888776655 PP

>> ALIX_LYPXL_bnd  ALIX V-shaped domain binding to HIV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   1.1   1.1e-06    0.0028     194     273 ..      53     149 ..      32     161 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.1e-06
  ALIX_LYPXL_bnd 194 eeelekydplqeqleqslakqeellkeiqeaneefeqskksdseq.sqrqreevlqkleaaydkykelksnlee................glkFY 271
                     +++ + +  l++ ++  ++ ++++l++++++ +++++++++ +    ++q e++l+k+ + y+ y elk++                   ++++Y
      EPA04281.1  53 QRRYDLIPNLIQSVKGYMQFEKDVLEQVTKLRSQWQATSNTGERVeLSNQIEQALSKIILTYENYPELKADSTVtrlmdelagtenrisvARTYY 147
                     55555666788889999999*******************999877769*********************99884344444444444444466666 PP

  ALIX_LYPXL_bnd 272 nd 273
                     nd
      EPA04281.1 148 ND 149
                     65 PP

>> ACP_PD  Acyl carrier protein phosphodiesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.3   2.2e-06    0.0056      10      91 ..      34     116 ..      27     134 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.2e-06
      ACP_PD  10 seysaepLeefvqrvyaqlekneealPerlqrllprmi.eedwLesYaelegieralqrmarrlkrasklaeaieeleenyae 91 
                 ++ ++e++++++++v  ql+++++ +P+ +q++  +m  e+d Le+  +l    +a ++  +r++ ++++++a++++   y++
  EPA04281.1  34 AQIKDEQIKKYAADVDVQLQRRYDLIPNLIQSVKGYMQfEKDVLEQVTKLRSQWQATSNTGERVELSNQIEQALSKIILTYEN 116
                 677899*******************************64889*******************************9998776654 PP

>> Chordopox_A13L  Chordopoxvirus A13L protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.8   2.1e-05     0.053       5      42 ..       6      46 ..       1      67 [. 0.74

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.1e-05
  Chordopox_A13L  5 lllliiCvaivgl...ivYgiYnrkketqttnpstveeyee 42
                    ++ +ii v+iv+l   i+Yg+Y  + +  + + + +++y  
      EPA04281.1  6 IIGIIIGVVIVALifsILYGMYFSGYNAAQIKDEQIKKYAA 46
                    555899999999844459****9998888888777788765 PP

>> MacB_PCD  MacB-like periplasmic core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   3.9   0.00019      0.49       5      28 ..       6      29 ..       6     195 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00019
    MacB_PCD  5 vLGiaiGvaaviaivslgeglqas 28
                ++Gi+iGv  v +i+s+  g+  s
  EPA04281.1  6 IIGIIIGVVIVALIFSILYGMYFS 29
                79***************9999733 PP

>> SurA_N_2  SurA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   3.0   0.00075       1.9       9      65 ..       4      55 ..       2      80 .. 0.63
   2 ?    3.4   0.6     0.025        63      53     121 ..      69     135 ..      66     157 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00075
    SurA_N_2  9 qgllviiiglallaFilgdlfgvgsylfssssnevaeVnGekIslqefqqaveearq 65
                + ++ iiig++++a i + l g+    f  s  ++a++ +e+I+  + +  v+ +r+
  EPA04281.1  4 KKIIGIIIGVVIVALIFSILYGMY---F--SGYNAAQIKDEQIKKYAADVDVQLQRR 55
                44778889********55555543...3..5899********987555555544444 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.025
    SurA_N_2  53 lqefqqaveearqqlqqqlgenfdeseedeaqlreqvldqlvseklleqeaeklGltvsdeelqdaiqg 121
                 + +f++ v e+  +l++q + + ++ e    +l +q+ ++l + +l  +++ +l+   +   l d + g
  EPA04281.1  69 YMQFEKDVLEQVTKLRSQWQATSNTGER--VELSNQIEQALSKIILTYENYPELKADSTVTRLMDELAG 135
                 6789999999999999998777666554..778888777776666777777777666666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1533  (0.0855039); expected 358.6 (0.02)
Passed bias filter:                     1089  (0.0607396); expected 358.6 (0.02)
Passed Vit filter:                       123  (0.00686039); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 1337.46
//
Query:       EPA04282.1  [L=318]
Description: response regulator receiver domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.2e-38  130.9  13.1    7.1e-38  130.2  13.1    1.3  1  TackOD1         Thaumarchaeal output domain 1
    1.6e-18   66.9   0.1    3.3e-18   65.9   0.1    1.6  1  Response_reg    Response regulator receiver domain
     0.0016   18.3  13.4      0.087   12.8   2.8    2.8  3  zinc-ribbons_6  zinc-ribbons
     0.0081   16.2  10.8        0.4   10.8   4.3    2.6  2  DZR             Double zinc ribbon
  ------ inclusion threshold ------
       0.03   14.6   4.5      0.079   13.3   4.1    2.0  1  zf-Di19         Drought induced 19 protein (Di19), zinc-bindi
      0.037   12.7   1.5      0.055   12.1   1.5    1.1  1  HCV_NS1         Hepatitis C virus non-structural protein E2/N
      0.053   13.5  16.5          1    9.4   3.2    4.0  3  HypA            Hydrogenase/urease nickel incorporation, meta
       0.61   10.5  12.4        2.2    8.7   4.5    2.7  2  DnaJ_CXXCXGXG   DnaJ central domain
        7.5    6.7  19.2       0.63   10.2   0.2    3.8  4  Spt4            Spt4/RpoE2 zinc finger


Domain annotation for each model (and alignments):
>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.2  13.1   3.6e-41   7.1e-38       4     187 .]     132     315 ..     129     315 .. 0.94

  Alignments for each domain:
  == domain 1  score: 130.2 bits;  conditional E-value: 3.6e-41
     TackOD1   4 rskeeteekllayllsrdeeklepvldp..kskelysypllealskeke.eseelleelvkrglleeelvdrirlCpsCksghlnvrevCpkCkSidie 99 
                  ++e+++ k+l+  + +d++k ++ +d   +s++++s +lle+++++++ +++++l+el++++ + +   ++   C++C+s +++ + +Cp+CkS++++
  EPA04282.1 132 FENESEQIKTLNQEKREDKKKTHELIDLilRSSKQISLNLLEQMIGFSDdSVTSYLKELEDNRKIIQIGDKKELGCNQCDSVKITQTFYCPSCKSSNFK 230
                 67888899999999999999999998862245669***********8887************************************************* PP

     TackOD1 100 eqelihhftCgnvgpeeeflkegkleCpkCktkLrhiGvDYdrplevykCnsCkslfsepevkarClsCekesesddlkvreiysykl 187
                   +li+h++Cgn+++e+++++++   Cp+C++ +r++GvDY+ ++++y+Cn+Ck +fse +  + Cl+Ce++++ ++ ++++  ++k+
  EPA04282.1 231 LGKLIEHYDCGNISEENTYVDDK---CPSCNKLIRALGVDYRVMQNHYICNNCKGFFSEISSDYLCLKCENKFKLEEGRWKTSKNFKV 315
                 *********************99...*******************************************************9999986 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.9   0.1   1.7e-21   3.3e-18       1     110 [.       7     121 ..       7     123 .. 0.91

  Alignments for each domain:
  == domain 1  score: 65.9 bits;  conditional E-value: 1.7e-21
                   EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHH....ESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEESSTS.HHHHHHHHHC CS
  Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeek....vdlillDinmpgmdGlellkeireedpelpviiltahse.eedavealka 92 
                   vliv+D+p++ +ll+++le+ gy++++++++g+ a+e +ke +      ++llD ++p+md   +l+++ + +p+ +v++ ta+++ +e ++e +++
    EPA04282.1   7 VLIVEDSPAIGMLLKNYLEKLGYSKIHTCTNGSTAIETFKELAnqdrHPIVLLDYMLPDMDARSILTQLLAIQPNARVVMETATEKdDEGIKELIRL 103
                   8************************************996665555588*********************************6665388899999** PP

                   TESEEEESSG-HHHHHHH CS
  Response_reg  93 gaddflsKpfdpeeLlka 110
                   g++++l Kp++ e+L ++
    EPA04282.1 104 GVYQYLEKPVRFENLQSI 121
                   ************999865 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   3.1   0.00037      0.75      14      38 ..     202     227 ..     188     244 .. 0.81
   2 !   11.1   0.5   0.00015       0.3      15      60 ..     236     285 ..     227     290 .. 0.72
   3 !   12.8   2.8   4.4e-05     0.087       2      39 ..     253     300 ..     252     305 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00037
                     SSEEE-TTT--.EEEEEEE-SSS-S- CS
  zinc-ribbons_6  14 geqyhCeaCqe.dlkkealCpeCeqe 38 
                     ++++ C++C++ +++++ +Cp C+++
      EPA04282.1 202 KKELGCNQCDSvKITQTFYCPSCKSS 227
                     47899*****9899999******975 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00015
                     SEEE-TTT--.EEEEEEE-SSS-S---EE...EETTEEEE--TTTT---- CS
  zinc-ribbons_6  15 eqyhCeaCqe.dlkkealCpeCeqelevl...kaCgavdyfCnkcneLiS 60 
                     e+y C + +e +  +   Cp C++ +  l          y+Cn+c+++ S
      EPA04282.1 236 EHYDCGNISEeNTYVDDKCPSCNKLIRALgvdYRVMQNHYICNNCKGFFS 285
                     67888766553666778999999988777222356677899999999877 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 4.4e-05
                     --SSS-S--EE-S.......SEEE-TTT--...EEEEEEE-SSS-S-- CS
  zinc-ribbons_6   2 kCpeCqqelekrg.......eqyhCeaCqe...dlkkealCpeCeqel 39 
                     kCp+C++ ++  g       ++y C++C+    +++   lC +Ce++ 
      EPA04282.1 253 KCPSCNKLIRALGvdyrvmqNHYICNNCKGffsEISSDYLCLKCENKF 300
                     7******99988889999999********988899999******9986 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   4.3    0.0002       0.4       1      36 [.     207     259 ..     207     265 .. 0.78
   2 !    9.1   3.9   0.00064       1.3       1      41 [.     254     303 ..     254     305 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0002
         DZR   1 CpqCgeelppdarfCseCgtk...lkavaa.................edrCpsCge 36 
                 C qC +    +  +C+ C+++   l    +                  d+CpsC++
  EPA04282.1 207 CNQCDSVKITQTFYCPSCKSSnfkL---GKliehydcgniseentyvDDKCPSCNK 259
                 9*******************95552...4455556678888888888888888876 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00064
         DZR   1 CpqCgee.........lppdarfCseCgtklkavaaedrCpsCgekvdpe 41 
                 Cp+C++          + ++   C++C+   ++ ++ + C +C+ k ++e
  EPA04282.1 254 CPSCNKLiralgvdyrVMQNHYICNNCKGFFSEISSDYLCLKCENKFKLE 303
                 9999999999999998889999**********************987765 PP

>> zf-Di19  Drought induced 19 protein (Di19), zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   4.1     4e-05     0.079       1      42 [.     217     262 ..     217     293 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4e-05
     zf-Di19   1 esftCPyCgk.eltvkeLveHvedeHrveskevv...CPvCaekvt 42 
                 ++f CP C+  +++  +L+eH +    +e++ +v   CP C + ++
  EPA04282.1 217 QTFYCPSCKSsNFKLGKLIEHYDCGNISEENTYVddkCPSCNKLIR 262
                 68********89***********98888777665555****98765 PP

>> HCV_NS1  Hepatitis C virus non-structural protein E2/NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.5   2.8e-05     0.055     165     236 ..     205     278 ..     197     286 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.8e-05
                 SEEEEEBTTSXEEEEEXXGGGGSXTTTTXSSSXSXXXXXXXXXXXX..XXXSSXECCTTEEEXXTTHHHHXGGG CS
     HCV_NS1 165 fgctwmnstgftktcgappcriggdgnatllcptdcfrkhpeatyl..kcgsgpwltprclvdypyrlwhypct 236
                 +gc   +s   t+t  +p c+ ++     l+   dc     e ty+  kc s  +l     vdy     hy c 
  EPA04282.1 205 LGCNQCDSVKITQTFYCPSCKSSNFKLGKLIEHYDCGNISEENTYVddKCPSCNKLIRALGVDYRVMQNHYICN 278
                 79********************9999999****************7669********9999**********996 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   3.2   0.00051         1      67      99 ..     201     231 ..      78     237 .. 0.79
   2 ?    3.4   0.5     0.039        77      75      94 ..     239     259 ..     235     267 .. 0.82
   3 ?    8.1   0.4    0.0013       2.7      67     103 ..     271     306 ..     262     315 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00051
                 E--EEEETTTS-EEECHHHHHS-TTTSSS-EEE CS
        HypA  67 vpvkvrCreCgkefeleekalrCpkCgsadvei 99 
                  + ++ C++C+ ++++++ ++ Cp+C+s+++++
  EPA04282.1 201 DKKELGCNQCD-SVKITQ-TFYCPSCKSSNFKL 231
                 566889*****.566553.478******99886 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.039
                 TTS-EEECHHH.HHS-TTTSS CS
        HypA  75 eCgkefeleek.alrCpkCgs 94 
                 +Cg+  e++++ + +Cp+C++
  EPA04282.1 239 DCGNISEENTYvDDKCPSCNK 259
                 799888877756779****87 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0013
                 E--EEEETTTS-EEECHHHHHS-TTTSSS-EEEEESS CS
        HypA  67 vpvkvrCreCgkefeleekalrCpkCgsadveivsGe 103
                 ++ ++ C++C+  f++ ++++ C kC++ ++++ +G+
  EPA04282.1 271 MQNHYICNNCKGFFSEISSDYLCLKCEN-KFKLEEGR 306
                 5667889999999886655688999987.57777776 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   6.4     0.033        65       1      64 [.     207     258 ..     200     260 .. 0.79
   2 ?    8.7   4.5    0.0011       2.2      13      65 ..     248     298 ..     238     299 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.033
  DnaJ_CXXCXGXG   1 CkkCkGsgakkgkkktCktCkGsGvvreeqktlgpfvqqsqstCpeCeGtGkvikekdkCkkCk 64 
                    C++C+  +   +++  C++Ck s      +  lg+++   + +C + + + +++  +dkC++C+
     EPA04282.1 207 CNQCDSVKI--TQTFYCPSCKSSNF----K--LGKLI--EHYDCGNISEENTYV--DDKCPSCN 258
                    999999887..44556****99982....2..55555..457999999999999..77899997 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0011
  DnaJ_CXXCXGXG  13 k..kktCktCkGsGvvreeqktlgpfvqqsqstCpeCeGtGkvikekdkCkkCkG 65 
                    +   ++C++C+   +      ++   v+q++  C++C+G  + i+++  C kC++
     EPA04282.1 248 TyvDDKCPSCNKLIRA--L--GVDYRVMQNHYICNNCKGFFSEISSDYLCLKCEN 298
                    3346789999865521..1..233345567899***********88889****97 PP

>> Spt4  Spt4/RpoE2 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.2       2.5     5e+03       9      35 ..     124     150 ..     123     156 .. 0.68
   2 ?    6.5   1.2    0.0045         9       3      25 ..     206     225 ..     204     233 .. 0.77
   3 ?   10.2   0.2   0.00031      0.63       6      27 ..     239     261 ..     238     274 .. 0.84
   4 ?    1.7   1.2      0.14   2.9e+02       4      44 ..     277     313 ..     274     316 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.5
        Spt4   9 lvktedqFeeegCpnCeilelkgdkek 35 
                 ++++e++F e+  +  ++l+ ++ ++k
  EPA04282.1 124 TIEKEQSFFENESEQIKTLNQEKREDK 150
                 577888888888888888876544444 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0045
        Spt4   3 ACllCklvktedqFeeegCpnCe 25 
                  C +C  vk +++F+   Cp C+
  EPA04282.1 206 GCNQCDSVKITQTFY---CPSCK 225
                 5************76...77773 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.00031
        Spt4   6 lCklvktedqFeeegCpnC.eil 27 
                 +C+ + +e+++ +++Cp C +++
  EPA04282.1 239 DCGNISEENTYVDDKCPSCnKLI 261
                 6******************5554 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.14
        Spt4   4 CllCklvktedqFeeegCpnC.eilelkgdkekvsectseef 44 
                 C +Ck   +e +  +  C  C + ++l++    +  +ts++f
  EPA04282.1 277 CNNCKGFFSEIS-SDYLCLKCeNKFKLEE----GRWKTSKNF 313
                 899998888887.7899999955566555....445555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1964  (0.109543); expected 358.6 (0.02)
Passed bias filter:                      765  (0.0426683); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); expected 17.9 (0.001)
Passed Fwd filter:                        29  (0.00161749); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 1965.54
//
Query:       EPA04283.1  [L=356]
Description: aminotransferase, class III [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-82  277.5   0.1    1.8e-82  277.2   0.1    1.0  1  Aminotran_3      Aminotransferase class-III
     0.0001   21.7   0.0    0.00015   21.1   0.0    1.2  1  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
      0.056   12.6   0.0       0.11   11.6   0.0    1.4  1  Aminotran_1_2    Aminotransferase class I and II


Domain annotation for each model (and alignments):
>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  277.2   0.1     3e-86   1.8e-82       8     332 ..      16     349 ..      10     354 .. 0.95

  Alignments for each domain:
  == domain 1  score: 277.2 bits;  conditional E-value: 3e-86
                  -SCEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT-..SEEEEESSHHHHHHHHHH CS
  Aminotran_3   8 nlllvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapkgldkvflansGseAvetAlK 105
                    +  i ka+G++ltd dg+++lD v+s++ +  Gh+ P++++a+ +q +k++h+s+ +ltnepa++la  l+k+ p+ + kvf+ ++Gs+A+e A+K
   EPA04283.1  16 DSFTKIVKAKGMWLTDSDGNNLLDGVASMWCNVWGHSKPELINAITKQSKKTQHTSMFNLTNEPAEDLATNLIKISPG-MHKVFYSDNGSSAMEIAFK 112
                  457889************************************************************************.******************* PP

                  HHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE-TTBGGGTB-HH...HHHHHHHHHHHHHHCHTCCCEEEEEE-S CS
  Aminotran_3 106 larkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrlkypdeevlkene...eeeaalleelealekkkkdevaAvivEp 200
                  +  +y  + ++++ktki+++++++HG+t+g+++v+   ++  ++f+  l  +++++ p +++++      + ++ ++ ++e++   k++++a +++E 
   EPA04283.1 113 MGLQYWNNIGEKKKTKIMTLENGYHGDTFGSMAVGYI-PEFFNKFKRQLFATIQIPVPNKYRIPKGFsyqDYQNFCIDKIEDIF-SKDEKIAMFVMES 208
                  ************************************9.99*******************9999876523367777788888877.899********** PP

                  .CETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TTTTTTTTSSSSGGGGCTS--SEEEE-GGGGTT.SS-EEEEEEHHHHTTS-TTS........B- CS
  Aminotran_3 201 .iqgegGvvvaspeflaklrelckkhdvllivDEvqtGfGrTGklfAlehagvspDlmtlaKaltgG.lplsavlataevmqalapgs........hg 288
                    q +gGv++ +++f +k+ +lckk+++ll+ DE++tGfGr G +  + +    pD+ + +K+ltgG ++++a+la++++++ +  g+        hg
   EPA04283.1 209 gAQVAGGVNIFPEGFQKKISKLCKKYNILLVLDEIATGFGRLGSMLQYTEQKSIPDIAVYGKMLTGGyITMAATLANKKIYDSF-LGEfddwkhlfHG 305
                  *******************************************************************99***************.777899******* PP

                  -TTTT-HHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHC CS
  Aminotran_3 289 sTfgGnplacavalavleiieeekllenaqelgaalkegLeelq 332
                  +Tf+Gnpla++va++ l++ e+  l++++++ +++l++ ++e q
   EPA04283.1 306 HTFTGNPLAASVANENLKLYEKYSLIKKIKKHQKYLRNIMKEYQ 349
                  ************************************99888776 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   2.6e-08   0.00015      46     167 ..      93     241 ..      60     243 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.6e-08
                      T-SEEEEES-HHHHHHHHHHHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTT..............................TBE CS
  Beta_elim_lyase  46 gkeaalfvpqGtaAnsillkillqrgeevivtepahihfdetgaiaelagvklrdlknkea..............................Gkm 109
                      g+ ++++  +G  A +i++k+ lq ++++  +++  i++ e+g +    g++++    +                                 ++
       EPA04283.1  93 GMHKVFYSDNGSSAMEIAFKMGLQYWNNIGEKKKTKIMTLENGYHGDTFGSMAVGYIPEFFnkfkrqlfatiqipvpnkyripkgfsyqdyQNF 186
                      5556667779***********************************999888777765554478999**************************** PP

                      -HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB.---HHHHHHHHHHHHHCT-EEEEE CS
  Beta_elim_lyase 110 dlekleaaikevgaheekiklisltvTnntagGq.vvsleelrevaaiakkygiplhlD 167
                       ++k+e++  +  +  eki++ +++   ++agG  + +    +++++++kky+i l+lD
       EPA04283.1 187 CIDKIEDIFSK--D--EKIAMFVMESGAQVAGGVnIFPEGFQKKISKLCKKYNILLVLD 241
                      ***********..6..89***************72556667789**************9 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   1.8e-05      0.11     171     295 ..     225     348 ..     215     355 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.8e-05
                    HHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHH.HGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEH.........HHHHHHHHHHHHHTSSHHH CS
  Aminotran_1_2 171 eklldlakkynlllfvDeaYagfvfgsldavat.ranveeepnllivgslsKafGlaGeRvGyilgna.........avvsqlrklsrpflsssll 256
                    +k+ +l+kkyn+ll++De+  gf    +        + ++ + ++ v++  K   l+G   Gyi+  a          ++    +++  f   + +
     EPA04283.1 225 KKISKLCKKYNILLVLDEIATGFGRLGS----MlQYTEQKSIPDIAVYG--K--MLTG---GYITMAAtlankkiydSFLGEFDDWKHLFHGHTFT 309
                    789999************9777776533....22788888888888875..5..4788...88888777888899998999999999999999999 PP

                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS CS
  Aminotran_1_2 257 qaavaaalsdallkqseleemrqrlqkrrkelrdeLael 295
                       +aa++ +++lk  e     ++++k+ k+lr+ ++e 
     EPA04283.1 310 GNPLAASVANENLKLYEKYSLIKKIKKHQKYLRNIMKEY 348
                    999999999999988888899999999999999999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       821  (0.0457917); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2385.42
//
Query:       EPA04284.1  [L=35]
Description: hypothetical protein BG20_I1574, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (35 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       267  (0.0148921); expected 358.6 (0.02)
Passed bias filter:                      188  (0.0104858); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.43
# Mc/sec: 244.66
//
Query:       EPA04285.1  [L=75]
Description: hypothetical protein BG20_I1584 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-06   27.1   0.0    1.6e-06   27.0   0.0    1.0  1  Aminotran_3  Aminotransferase class-III


Domain annotation for each model (and alignments):
>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0     9e-11   1.6e-06     349     406 .]       2      67 ..       1      67 [. 0.91

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 9e-11
                  EEEEBCCCETTC.........HHHHHHHHHCTEE-EEETTTEEEE---TT--HHHHHHHHHHHHHHH CS
  Aminotran_3 349 aielkeeaevke.........keilkkakekGvlilsaGdnvirllppliitdeeidelleilkkal 406
                  +iel+++++ k          k +++++k++G++++++G n++ ++ppl i+++e+d ll+++ k++
   EPA04285.1   2 GIELVKNKQSKVsihpkksinKIFFEEGKKHGIYLRTLG-NIVMIVPPLAISENELDTLLNRTIKTI 67 
                  799999999777999999998889***************.*********************998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 491.63
//
Query:       EPA04286.1  [L=229]
Description: DSBA-like thioredoxin domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-35  122.9   0.0      2e-35  122.4   0.0    1.1  1  Thioredoxin_4  Thioredoxin
    4.5e-18   65.7   0.1    5.7e-17   62.1   0.1    2.0  1  DSBA           DSBA-like thioredoxin domain
      3e-07   30.8   0.5      6e-07   29.9   0.5    1.5  1  Thioredoxin_2  Thioredoxin-like domain
    0.00072   19.3   0.0     0.0011   18.7   0.0    1.2  1  Thioredoxin_5  Thioredoxin
  ------ inclusion threshold ------
      0.028   14.1   0.0      0.053   13.2   0.0    1.4  1  DUF5314        Family of unknown function (DUF5314)
      0.045   14.1   0.2        4.9    7.6   0.0    2.3  2  Thioredoxin_8  Thioredoxin-like
      0.048   13.5   0.0       0.11   12.3   0.0    1.5  2  TraF           F plasmid transfer operon protein
        1.1    9.3   2.9         11    6.2   3.0    2.1  1  OTT_1508_deam  OTT_1508-like deaminase


Domain annotation for each model (and alignments):
>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.4   0.0     9e-39     2e-35       4     162 ..      54     221 ..      52     224 .. 0.88

  Alignments for each domain:
  == domain 1  score: 122.4 bits;  conditional E-value: 9e-39
                    SSEEES-TT-SEEEEEEE-TT-HHHHHHHHHHH.HHHHHHHHTTSEEEEEEE-..---STTTHHHHHHHTT--TTHHHHHHHHHHHHTH....HHH CS
  Thioredoxin_4   4 tdiviGnpdApvtvieyedlrCphCakfeeeve.klleeyidtGkvkfiirdfpldkekeslkaamaarcageespeaflaikallysq....qee 94 
                    +++v+G+p+Ap+t+ie+ d++C  C +f+ ++e +l++ y++tGkvk+i++df + +   s++aa aa+ca +++  +f+++++ ly++       
     EPA04286.1  54 GSPVLGDPNAPITLIEFGDYQCYFCNQFFHKTEdELFKNYVETGKVKVIFKDFTIIGAD-SISAAHAAHCADDQG--FFWEYHDTLYNNwtgeNNG 146
                    6799***********************9999999*******************888887.9*************9..***********96665444 PP

                    TTS-..HHHHH.....HHHHHTS-------HHHHHHHHHHHHHHT--SS-EEEE...TTEE..E-TT--HHHHHH CS
  Thioredoxin_4  95 waes..lkelaaealdkdekfeacleeekldalveaeskeakkagiestPtfii...ngek..veepqtyeelka 162
                    wa s  l ++a++ + +  +f++c++++k+++++++  k+ak +g+++tP f++   + ++  + ++q+y+ +++
     EPA04286.1 147 WASSknLLQFARDVGLNIDEFSKCMTDSKYSTKIANSNKDAKDLGLTGTPAFFVispDNKVtkIGGAQPYDVFER 221
                    44445677788999999************************************9888444435788888887765 PP

>> DSBA  DSBA-like thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.1   0.1   2.6e-20   5.7e-17       1     190 [.      66     221 ..      66     224 .. 0.94

  Alignments for each domain:
  == domain 1  score: 62.1 bits;  conditional E-value: 2.6e-20
                 EEEEEEBTTBHHHHHHHHHHHHHHHHC....CTEEEEEEE-SSSCHHHHCT.S.GGGSHHHHHHHHHHHHHHHHHHT....GGSSHHHHHHHHHHHHHH CS
        DSBA   1 tvdeffDvlCPyCylgkerleklaars....pdvkvvlrpfelagakkasgnvgpselpeklkylledlkrlaeaegiplrfpkdklknstraarllla 95 
                 t++ef D++C +C +++++ e  + ++     +vkv +++f + ga                                          +s +aa++++ 
  EPA04286.1  66 TLIEFGDYQCYFCNQFFHKTEDELFKNyvetGKVKVIFKDFTIIGA------------------------------------------DSISAAHAAHC 122
                 6899*************9998655555599667*************..........................................*********** PP

                 HHHHHGHHHHHHHHHHHHHTSSS-TSSHHHHHHHHHHTTS.HHHHHHHHTSHHHHHHHHHHHHHHHHTT-SSSSEEEE...TTC.EEEESSSSHHHHHH CS
        DSBA  96 agaeglaekvvrelfealwsegqaitddqellevaekaGldaeeldealeseavkeavrentaaaqslgvtGvPtvvv...dgk.rmvfGadrldtlad 190
                 a  +g   ++  +l++   +e+    ++++ll++a+++Gl+ +e+ + + ++++  +++ + + a++lg+tG+P+++v   d+k   + Ga+++d +++
  EPA04286.1 123 ADDQGFFWEYHDTLYNNWTGENNGWASSKNLLQFARDVGLNIDEFSKCMTDSKYSTKIANSNKDAKDLGLTGTPAFFVispDNKvTKIGGAQPYDVFER 221
                 *****999************************************************************************9888799********9987 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.5   2.7e-10     6e-07       7     107 ..      65     221 ..      60     223 .. 0.84

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 2.7e-10
  Thioredoxin_2   7 pvlvvftdpdCpyCkklkkelkel........ddvtvrvllfp.lkpsfepkavaiwcakekk..........kafkd.................. 65 
                     +l+ f d +C++C ++  ++++          +v+v+  +f  +++++  +a a  ca+++            ++++                  
     EPA04286.1  65 ITLIEFGDYQCYFCNQFFHKTEDElfknyvetGKVKVIFKDFTiIGADSISAAHAAHCADDQGffweyhdtlyNNWTGenngwassknllqfardv 160
                    67888*********88755444444555997777777777777*******************96666666555444449999999*********** PP

  Thioredoxin_2  66 ...................ieenvelarkygvrgtPtivfldgkeivarlpGyvpaeelea 107
                                       i+ +++ a+ +g++gtP+++++ ++++v+++ G+ p + +e 
     EPA04286.1 161 glnidefskcmtdskystkIANSNKDAKDLGLTGTPAFFVISPDNKVTKIGGAQPYDVFER 221
                    *************************************999999999*********999886 PP

>> Thioredoxin_5  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   4.7e-07    0.0011     108     185 ..     145     220 ..     134     221 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 4.7e-07
  Thioredoxin_5 108 kniskeellleiaekaglDveefkeDlesklakkafqcDlklakemgvtevPtlvffneneeeeglkveglksyevye 185
                    +  ++ + ll+ a+++gl+++ef + +  +  +++  +  k ak++g t +P++++     +++  k+ g ++y+v+e
     EPA04286.1 145 NGWASSKNLLQFARDVGLNIDEFSKCMTDSKYSTKIANSNKDAKDLGLTGTPAFFVIS--PDNKVTKIGGAQPYDVFE 220
                    555667999****************99988899999999*****************99..889999*********987 PP

>> DUF5314  Family of unknown function (DUF5314)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.4e-05     0.053       9      62 ..      55     107 ..      50     118 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.4e-05
     DUF5314   9 sPvassklipikLsgvqnfdiWl.eklenvvsetsliwaeYvetGdissirveag 62 
                 sPv+ +   pi L + ++++  + +++ ++  + + ++++YvetG+++ i+  + 
  EPA04286.1  55 SPVLGDPNAPITLIEFGDYQCYFcNQFFHK--TEDELFKNYVETGKVKVIFKDFT 107
                 8999****************9984566664..5578999*******999987665 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1     0.018        40       3      40 ..      65     103 ..      63     141 .. 0.85
   2 ?    7.6   0.0    0.0022       4.9      65      95 .]     177     207 ..     149     207 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.018
                    EEEEEE--SSSHHHHHHHHHHHH.HHHHHHHTTSEEEEE CS
  Thioredoxin_8   3 vvlLyfgaswcppckaftpklke.lyeklkkkkkveivy 40 
                    ++l+ fg+++c  c +f  k  + l++++ +  kv++++
     EPA04286.1  65 ITLIEFGDYQCYFCNQFFHKTEDeLFKNYVETGKVKVIF 103
                    68999***********98887744899998888888886 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0022
                    EE-TT-HHHHTT-S--TT-SEEEEE-TT-BE CS
  Thioredoxin_8  65 pfddkkrnklkkkynvkaiPtlvvldkngev 95 
                     ++  ++nk +k +++++ P ++v++++++v
     EPA04286.1 177 STKIANSNKDAKDLGLTGTPAFFVISPDNKV 207
                    3334457888******************987 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0         2   4.4e+03     110     147 ..      44      81 ..      24      83 .. 0.51
   2 ?   12.3   0.0   4.8e-05      0.11     151     209 ..     153     210 ..     148     213 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2
        TraF 110 kvlndarkeekeaalkklakeygLlfFyrgkcpyceaq 147
                 +v+ d   e+ + +l +      L+ F + +c +c ++
  EPA04286.1  44 QVTADTFMENGSPVLGDPNAPITLIEFGDYQCYFCNQF 81 
                 44444444444444445555556666667777777665 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 4.8e-05
        TraF 151 lqafadkyglevraVs...vdgrplpelpnarvdkgqaarlgvkrtPalvlvdpksqkvvpv 209
                 l +fa++ gl +   s   +d + +++++n   +++ a+ lg++ tPa+++++p+ +kv+ +
  EPA04286.1 153 LLQFARDVGLNIDEFSkcmTDSKYSTKIAN---SNKDAKDLGLTGTPAFFVISPD-NKVTKI 210
                 566777777766655522256677766666...9999******************.555555 PP

>> OTT_1508_deam  OTT_1508-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   3.0    0.0047        11      31      60 ..      74     140 ..      63     143 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0047
  OTT_1508_deam  31 aCylCelylrahg...............................katl........kvreshgklydkW 60 
                     Cy+C+++++ ++                               +  +         + e h +ly++W
     EPA04286.1  74 QCYFCNQFFHKTEdelfknyvetgkvkvifkdftiigadsisaaH--AahcaddqgFFWEYHDTLYNNW 140
                    6********877777766666666555555555444444444330..1333444445556666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1468.96
//
Query:       EPA04287.1  [L=113]
Description: hypothetical protein BG20_I1578 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-16   59.0   0.0      6e-16   58.9   0.0    1.0  1  AAA_26    AAA domain
    0.00012   22.1   0.0    0.00017   21.6   0.0    1.3  1  CbiA      CobQ/CobB/MinD/ParA nucleotide binding domain


Domain annotation for each model (and alignments):
>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.9   0.0   6.6e-20     6e-16     108     197 ..       2      96 ..       1      97 [. 0.90

  Alignments for each domain:
  == domain 1  score: 58.9 bits;  conditional E-value: 6.6e-20
      AAA_26 108 gglgvpiteellnadiaknlgapvilVargglgtinqllltiealrqknvrvlGvilNkvrnp.....envetlekksgipvlGvvPylpdleap 197
                 gg+++pi+++ +++d++k++ +++i+V+r++ gt+n++++t +++ + ++ v+G+i+N++        e  + le  +++pvlG++P ++d++++
  EPA04287.1   2 GGIMTPILKNYFVTDLIKSMSLETIIVTRTKVGTVNHTIMTCKMCENYKISVKGIIINNFDINgykvkELKRDLEDLTNYPVLGSIPFIDDMSDA 96 
                 789********************************************************754445555577888888999*********998875 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   1.9e-08   0.00017      73     124 ..      47      99 ..      16     102 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.9e-08
                 H.....EEEEEEEEESS...-.TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHH CS
                 x...xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        CbiA  73 l...lkiagvvlnrvdgenee.tllkealeelkqrygvpvlgviprdeavaeapar 124
                 +   + ++g+++n +d + ++ ++lk +le+l    + pvlg+ip+ ++ ++a   
  EPA04287.1  47 EnykISVKGIIINNFDINGYKvKELKRDLEDLT---NYPVLGSIPFIDDMSDASLY 99 
                 1445889*********99765267888899988...*************9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       693  (0.0386525); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 831.90
//
Query:       EPA04288.1  [L=159]
Description: hypothetical protein BG20_I1588, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.2e-21   75.2   0.0    5.7e-21   75.1   0.0    1.0  1  Aminotran_1_2  Aminotransferase class I and II
  ------ inclusion threshold ------
      0.024   13.8   0.1        3.3    6.8   0.0    2.1  2  RuvC_1         RuvC nuclease domain


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.1   0.0   6.3e-25   5.7e-21     160     325 ..       1     157 [.       1     159 [] 0.88

  Alignments for each domain:
  == domain 1  score: 75.1 bits;  conditional E-value: 6.3e-25
                    TT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSS.HTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHHHTSSH CS
  Aminotran_1_2 160 PtGtvatleeleklldlakkynlllfvDeaYagfvfgsl.davatranveeepnllivgslsKafGlaGeRvGyilgnaavvsqlrklsrpflsss 254
                    ++G++ +l+e++++   ++k n+++++D+a+++fv g+  + ++++ nve++++ l v+slsK +G+ G   Gy++++ ++++   + s +f+++s
     EPA04288.1   1 MDGDISKLKEITEI---TEKSNAITILDDAHGDFVIGEDgKGTPNYQNVEKKID-LYVSSLSKGLGSFG---GYVSSSNNIIDLCINKSKSFIYTS 89 
                    78999999999999...********************76655555*********.**************...*****9988888888888888888 PP

                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSEEEEEETHHCHHHHHHHHH CS
  Aminotran_1_2 255 llqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmflltdlsaetakelskkLl 325
                    +l+ ++++   +  +  s+ e+ r++l+++  +l  +L+++g ++ + ++++++l  ++++ta+e+ + L 
     EPA04288.1  90 ALPSFLVEYSLKRFE--SNREKQRRKLESNKIQLIRGLKQIGYQINS-KTHIIPLIIGNEKTAMEFGDYLF 157
                    888888887777664..499********************9999655.6****************988775 PP

>> RuvC_1  RuvC nuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0   0.00037       3.3      95     137 ..       8      50 ..       2      59 .. 0.89
   2 ?    5.3   0.0     0.001       9.4      57     106 ..      96     146 ..      66     157 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.00037
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
      RuvC_1  95 vhkiaklaikynaivvlEdLnlgFkrgrqkvekqvyqkfEkaL 137
                 +++i+++  k nai +l+d    F  g        yq+ Ek++
  EPA04288.1   8 LKEITEITEKSNAITILDDAHGDFVIGEDGKGTPNYQNVEKKI 50 
                 5799*********************999999999999999975 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.001
                 xxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
      RuvC_1  57 vdYrelLderekerekarknW..qkiekikelKe.gYlsqvvhkiaklaikyn 106
                 v+Y   L++ e++rek+r++   +ki+ i+ lK+ gY  +  ++i  l+i ++
  EPA04288.1  96 VEY--SLKRFESNREKQRRKLesNKIQLIRGLKQiGYQINSKTHIIPLIIGNE 146
                 455..46777777777776542278********87897777777777776554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       734  (0.0409393); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1129.81
//
Query:       EPA04289.1  [L=84]
Description: hypothetical protein BG20_I1579 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      8e-13   48.7   0.0    8.4e-13   48.6   0.0    1.0  1  AAA_26    AAA domain
    6.7e-05   22.9   0.0    6.7e-05   22.9   0.0    1.2  1  CbiA      CobQ/CobB/MinD/ParA nucleotide binding domain
  ------ inclusion threshold ------
      0.062   12.6   0.1      0.062   12.6   0.1    1.1  1  DUF1611   Domain of unknown function (DUF1611_C) P-loop domai
      0.073   12.5   0.0      0.073   12.5   0.0    1.1  1  ParA      NUBPL iron-transfer P-loop NTPase


Domain annotation for each model (and alignments):
>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.6   0.0   1.9e-16   8.4e-13       1      75 [.       2      81 ..       2      84 .] 0.89

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 1.9e-16
      AAA_26  1 rtifvtgtdtgvGKTvvslgLvralkrkgvkvgyfKPiqtgie.....ededselikellgldqtyelpeplalsaplsp 75
                +++f++gtdt+vGKT +++gL+ ++++ +v vg++KP+++gi      + ed+e ++++++++++++l++p  +  p+sp
  EPA04289.1  2 KSFFIAGTDTDVGKTYITAGLAVSFRKMNVDVGVMKPFAAGIPqktgfKSEDVEILANAAHVNDPEDLLNPQFFPIPASP 81
                579****************************************55554455*******************9999888776 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   1.5e-08   6.7e-05       2      34 ..       5      37 ..       4      71 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.5e-08
                EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEE CS
                xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        CbiA  2 aiastkGGvGKTtlaanLaralarrglrVllvD 34
                +ia+t  +vGKT ++a+La+++ + + +V + +
  EPA04289.1  5 FIAGTDTDVGKTYITAGLAVSFRKMNVDVGVMK 37
                79**********************777775554 PP

>> DUF1611  Domain of unknown function (DUF1611_C) P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   1.4e-05     0.062      15      47 ..       4      36 ..       1      63 [. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.4e-05
     DUF1611 15 vlvvGTdcavGKrttaleleealeerGlkaafv 47
                 ++ GTd +vGK + +  l+  +++  ++++++
  EPA04289.1  4 FFIAGTDTDVGKTYITAGLAVSFRKMNVDVGVM 36
                689****************99999998888776 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.6e-05     0.073      14      39 ..      12      37 ..       2      68 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.6e-05
        ParA 14 GVGKStvavnlAlaLakkglkvgllD 39
                 VGK+ +++ lA++++k++++vg++ 
  EPA04289.1 12 DVGKTYITAGLAVSFRKMNVDVGVMK 37
                59**********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       201  (0.0112109); expected 358.6 (0.02)
Passed bias filter:                      193  (0.0107647); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 644.56
//
Query:       EPA04290.1  [L=175]
Description: hypothetical protein BG20_I1582 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-18   65.9   0.3      6e-18   65.2   0.3    1.3  1  TPM_phosphatase  TPM domain
  ------ inclusion threshold ------
      0.076   13.1   0.0        0.1   12.6   0.0    1.3  1  ETRAMP           Malarial early transcribed membrane protein 


Domain annotation for each model (and alignments):
>> TPM_phosphatase  TPM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.2   0.3   6.7e-22     6e-18       1     108 [.      34     161 ..      34     169 .. 0.81

  Alignments for each domain:
  == domain 1  score: 65.2 bits;  conditional E-value: 6.7e-22
                      EEE-SS-S-HHHHHHHHHHHHHHHHTT--EEEEEEESB-TT--HHHHHHHH................HHHHSTTTTS-SSEEEEEEETT.T... CS
  TPM_phosphatase   1 vvDeaglLsdeeeaeleeklaalekktgvqivvvtvdsldgediedyadel................fdkwglgkkkkdngvllliavd.d... 74 
                      v+D+a+++s+e e+ l+++l+++ + t+v+iv+ t++s+ g+ i++  +e+                    g+gk++kdng+l+l++++ d   
       EPA04290.1  34 VYDNADVISSEYESLLDNYLRKVDDATSVEIVIWTTSSFYGHGIKKDNQEIhdrdllahyifndvslNSIKGIGKADKDNGILILLSKErDssg 127
                      89*************************************7777764444444444455555555552334567999999*******97653333 PP

                      TEEEEEE-STTTTT--HHHHHHHHHHTHHHHHHH CS
  TPM_phosphatase  75 rkvrietgyglegaltdaraesildetilpalkd 108
                        +r+e g+gleg +td+ a  ild++++pa+++
       EPA04290.1 128 GSMRLEIGRGLEGDITDGTAGAILDAYLVPAMQS 161
                      55****************************9984 PP

>> ETRAMP  Malarial early transcribed membrane protein (ETRAMP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.2e-05       0.1       5      38 ..       3      83 ..       1     114 [. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.2e-05
      ETRAMP  5 kv.llffafLlavnlltpeslcdevnkkk..............................................ekakka 38
                kv ++f++fL+av+l+++++++++    +                                              +k++++
  EPA04290.1  3 KVlMVFLVFLVAVSLVSQGYSQNAKGSRPayvydnadvisseyeslldnylrkvddatsveiviwttssfyghgiKKDNQE 83
                67799*****************99988888888888888777777777777777777777777777776666666444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1093.39
//
Query:       EPA04291.1  [L=464]
Description: putative hydroxymethylglutaryl-CoA synthase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.9e-32  112.4   0.1    6.6e-32  111.2   0.1    1.5  1  HMG_CoA_synt_C  Hydroxymethylglutaryl-coenzyme A synthase C t
    2.5e-30  105.6   0.2      4e-30  105.0   0.2    1.3  1  HMG_CoA_synt_N  Hydroxymethylglutaryl-coenzyme A synthase N t


Domain annotation for each model (and alignments):
>> HMG_CoA_synt_C  Hydroxymethylglutaryl-coenzyme A synthase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.2   0.1   7.4e-36   6.6e-32       2     236 ..     180     424 ..     179     443 .. 0.82

  Alignments for each domain:
  == domain 1  score: 111.2 bits;  conditional E-value: 7.4e-36
                     EE-TT--EEEE----SEE---TT-S--EE-HHHHHHHHHHHHHHHHHHHHHH..HHHHHHH------GGG-SEEEE--SSHHHHHHHHHHHHHHH CS
  HMG_CoA_synt_C   2 vfdrklrashmehayDFykPdlaseYPvvDGklslscYlkaldrcYksyskk..vkkitkdadkeftlddfdyvifhsPfcklvqkslarllynD 94 
                     +fd+k+ a+ +++ yDFy+P +  e P+v G++s   Y+  ++++ ++y+kk  +  + k +  e+ ld++dy+ +h P++ + +k+la l+  +
      EPA04291.1 180 AFDPKVTATSIKDEYDFYRP-FGKETPIVHGQYSNLLYMIQVRKALETYKKKalSSGLIKLEPGETILDHMDYLNMHLPYSNMGKKALAYLVRHE 273
                     79*****************9.99*****************************54455565579999**************************999 PP

                     HHH.S-HHH...HHHH-GGGGGG.....TT--GGGGGT-HHHH..HHHHHHH..HHHHHHHTGGGGHHHHHH---GGGHHHHHHHHHHH..HS-H CS
  HMG_CoA_synt_C  95 flanassdk...eeevkekleek.....ddlkldesltdkdle..kallkia..kelfkkkvkpsllvptevGnmYtaslyaalaslls..kvsa 175
                     +++ ++ +k   e ++ e + +      +++  d  ++ kd e  k + k    +e+++ k ++sl++++ +Gn+Ytasly  + s l+  +++ 
      EPA04291.1 274 WRQLPRWKKiiqEIGIPEPIPKDprgtiESVLGDGEFMAKDHEftKLFTKTKefQEVYESKLASSLVASKMIGNLYTASLYLGFRSCLEfeYQKG 368
                     998766433111334555554432222355555666666655421555554322689******************************96225566 PP

                     HHHTT-EEEEEEEETTTEEEEEEEEE-S--STTSHHHHHTTTTHHHHHHTSEEE-HHHHHH CS
  HMG_CoA_synt_C 176 delagkriglfsYGsGlaaslfslrvkqdvsedsildiakvldlkkkLdsRkevtPeefee 236
                      +l+gkr+g+ sYGsG++a +fs  ++ + +e     i k ++l+ +L+ R+++t ee+e 
      EPA04291.1 369 IDLNGKRVGFGSYGSGSSAMVFSGLIQPQYEE-----IVKDMNLEAELAPRRKLTLEEYEI 424
                     79************************999998.....*********************974 PP

>> HMG_CoA_synt_N  Hydroxymethylglutaryl-coenzyme A synthase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.0   0.2   4.4e-34     4e-30       5     170 ..       3     173 ..       1     176 [. 0.92

  Alignments for each domain:
  == domain 1  score: 105.0 bits;  conditional E-value: 4.4e-34
  HMG_CoA_synt_N   5 vgilaleiylpaqyvdqaelekfdgveagkytiglgqtrmgfvsdredinslsltvvqkllertkldydaigrlevgtetiidksksvksvlm.. 97 
                      gi  + iy+p  y+d +++ k  g++  k   glg ++m++v+ ++d   l+     ++++++kl+ + igrl v te+  d sk+++s ++  
      EPA04291.1   3 AGIDDIAIYIPRLYIDASDFAKARGLDPEKLQKGLGVSQMAIVDTNQDPACLAANACLQIMKKNKLSPEDIGRLYVSTESSFDESKAMNSYVIgm 97 
                     5999***********************************************************************************99976511 PP

  HMG_CoA_synt_N  98 ..qlfeesgntdiegidtlnacyggtaalfnavnwiessawdgryalvvagdiaiydsgna.rptggagavallig 170
                       q++++ +     g++t  ac  g+ al++  nwi +   +g++alvv+ dia yd g++   t gagav +l+ 
      EPA04291.1  98 leQVYGQGAFEHCGGVETKFACVSGSYALYDNTNWIRAGEAEGKQALVVVSDIAKYDMGSSgEMTQGAGAVVMLLN 173
                     22566666667888*********************************************873679********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 3119.15
//
Query:       EPA04292.1  [L=181]
Description: hypothetical protein BG20_I1577 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1063  (0.0592894); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1292.34
//
Query:       EPA04293.1  [L=54]
Description: hypothetical protein BG20_I1581 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        3.2    7.4   3.5          3    7.5   3.5    1.0  1  TraT      Enterobacterial TraT complement resistance protein


Domain annotation for each model (and alignments):
>> TraT  Enterobacterial TraT complement resistance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   3.5   0.00017         3      78     110 ..      20      52 ..       3      54 .] 0.62

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00017
        TraT  78 kaaaegalkaGfggalagaaagaaigaanggsa 110
                      g++ +Gfgg++ g+++g + g++ gg+a
  EPA04293.1  20 RGFYGGFIGGGFGGGGGGGGFGGGGGGSGGGGA 52 
                 333456778888888888888888888766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.31s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 342.61
//
Query:       EPA04294.1  [L=326]
Description: biotin synthase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-17   64.6   0.4    3.2e-17   63.4   0.3    1.6  2  Radical_SAM  Radical SAM superfamily
    1.6e-12   47.4   0.0    3.2e-12   46.4   0.0    1.5  1  BATS         Biotin and Thiamin Synthesis associated domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.4   0.3   3.6e-21   3.2e-17       5     164 ..      67     223 ..      64     226 .. 0.88
   2 ?   -2.2   0.0      0.53   4.7e+03      52      84 ..     276     306 ..     254     323 .. 0.54

  Alignments for each domain:
  == domain 1  score: 63.4 bits;  conditional E-value: 3.6e-21
                  SEESS--TTTSCCTT.HHHHHHHHHHHHHHHHHHHHHHHHHTT..SEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHH CS
                  xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM   5 rgCnlrCsfCarpet.vrregrgrslsveeileevkelkaekg..vkevilgggepllypdfvellerlaklavpgiritvetngtlpdeeklerlle 99 
                  ++C+ +CsfC ++       ++++  + ee++ +++++k + g     ++    ep+  +df++    + ++ ++++ i+ve++ + +++ ++++l+e
   EPA04294.1  67 NACSEDCSFCGQSAFfNTGIDTYQLPPAEEVVIKAEKAK-KEGaeSYCLVAAWREPSP-RDFEKVCNIIQEI-NDKVGISVECSLGFLTPVQAKKLKE 161
                  68***********9999999******************6.666234444444677777.6677777777777.7************************ PP

                  TT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHHH CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM 100 lgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGendeeleell 164
                  l v r++++le+  ++ + +++  +ht+e++l++l ++r+ag++  +++ +++ Ge+++++ el+
   EPA04294.1 162 LKVKRYNHNLETSKSK-FSEIC-TTHTYEDRLKTLYIARDAGLE-LCTGGIIGLGETRKQRLELA 223
                  ****************.*****.9********************.9999999999**99988876 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.53
                  EESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEE CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM  52 lgggepllypdfvellerlaklavpgiritvet 84 
                  ++gg  +   d  e+l++  ++    i+  + t
   EPA04294.1 276 ISGGRETNLNDSGEELLQSGAN--GIITSGYLT 306
                  4444444334444444444444..344444444 PP

>> BATS  Biotin and Thiamin Synthesis associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4   0.0   3.5e-16   3.2e-12       2      86 .]     236     325 ..     235     325 .. 0.94

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 3.5e-16
                 --B----TCCCC...........HHHHHHHHHHSTTSE.CCCTCHH-HHHHHH.HHHCCT--EEE-C---TTTGGGSESSTT-TCCCCHHHHHHTT-E CS
        BATS   2 iprlrpikdtpl...........lkiiaalRlllPkag.illsgResaefrdq.lllklGansisagsktevggyaflttdgrsleedvkmleelGle 86 
                 i++l+p+++tpl           +++  ++R+llP++   +++gRe++ ++    ll+ Gan i++          +lt  g++ ++d++m+++ Gle
  EPA04294.1 236 INILVPVPGTPLelqtklenteiVRMFSVVRFLLPESViKISGGRETNLNDSGeELLQSGANGIITSG--------YLTMGGNDSQKDMNMIKKIGLE 325
                 8*************************************99******99988777666***********........*******************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       764  (0.0426125); expected 358.6 (0.02)
Passed bias filter:                      599  (0.0334096); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2343.57
//
Query:       EPA04295.1  [L=58]
Description: hypothetical protein BG20_I2583, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.9e-12   45.0   0.0    1.1e-11   44.8   0.0    1.0  1  DUF1743   Domain of unknown function (DUF1743)


Domain annotation for each model (and alignments):
>> DUF1743  Domain of unknown function (DUF1743)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8   0.0   6.1e-16   1.1e-11      67     116 .]       2      50 ..       1      50 [. 0.96

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 6.1e-16
                 CS-STTSSEEEEEEES-HHHHHHHHHCSEE..S-EECEEEEEESTTS-TT CS
     DUF1743  67 lvPhtpdpvlfGirgedpeallkaakeilskeeeseemavfrtnqgtdah 116
                 ++Ph+pdpv++Girge+ +all+a k +++ +e+    ++f++nqgt +h
  EPA04295.1   2 ITPHGPDPVFYGIRGENMDALLHATKILKT-DEKLAGHLIFKSNQGTGDH 50 
                 89***************************9.999999**********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       181  (0.0100954); expected 358.6 (0.02)
Passed bias filter:                      168  (0.00937029); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.29s 00:00:00.68 Elapsed: 00:00:00.46
# Mc/sec: 378.30
//
Query:       EPA04296.1  [L=87]
Description: hypothetical protein BG20_I2580 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 645.20
//
Query:       EPA04297.1  [L=45]
Description: hypothetical protein BG20_I2581 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.6e-09   35.6   0.1    8.5e-09   35.5   0.1    1.0  1  DUF1743   Domain of unknown function (DUF1743)


Domain annotation for each model (and alignments):
>> DUF1743  Domain of unknown function (DUF1743)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.1   4.8e-13   8.5e-09      23      61 ..       2      41 ..       1      44 [. 0.94

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 4.8e-13
                EEEEEE-GGGTT.---EEHHHHHHHHHHHTTCECTSEBTT CS
     DUF1743 23 EllaYreperwg.erevdeesvieadektypetfdnvDls 61
                Ell+Yr+++++g +r++++ sv++++ekt p+tf+++D +
  EPA04297.1  2 ELLSYRKNSQFGkDRKLSATSVKTMQEKTQPNTFNSFDNK 41
                9*************************************44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      206  (0.0114898); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 308.70
//
Query:       EPA04298.1  [L=89]
Description: hypothetical protein BG20_I2006 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-31  106.6   2.1    5.6e-31  106.4   2.1    1.0  1  UPF0147          Uncharacterised protein family (UPF0147)
     0.0028   17.9   0.0       0.64   10.3   0.0    2.3  2  UPF0253          Uncharacterised protein family (UPF0253)
  ------ inclusion threshold ------
      0.055   12.7   0.2      0.067   12.5   0.2    1.3  1  PPDK_N           Pyruvate phosphate dikinase, PEP/pyruvate bi
      0.081   13.7   0.4      0.096   13.5   0.4    1.1  1  Glyco_hydro_20b  Glycosyl hydrolase family 20, domain 2
       0.14   12.3   0.3       0.84    9.9   0.1    2.1  2  CUTL             CUT1-like DNA-binding domain of SATB


Domain annotation for each model (and alignments):
>> UPF0147  Uncharacterised protein family (UPF0147)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.4   2.1   1.6e-34   5.6e-31       1      81 []       7      87 ..       7      87 .. 0.98

  Alignments for each domain:
  == domain 1  score: 106.4 bits;  conditional E-value: 1.6e-34
                HHHHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHHHH CS
     UPF0147  1 neekikevielLeeiiedtsvPrniRraakeakekLkdekeslavraataisiLdeisnDpnmPlhaRtliwevvskLEti 81
                n+e++ke+ie+L++i++++s+P++i++a+++ +++L++e+ sl+vra+++is+Ld++++DpnmP+++Rt++w+ vskLE+i
  EPA04298.1  7 NKETMKEAIETLNQIATNHSTPKTIKKAITDLITDLNNEEYSLSVRANNTISLLDDVTQDPNMPSYVRTQLWQAVSKLESI 87
                5899***************************************************************************98 PP

>> UPF0253  Uncharacterised protein family (UPF0253)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   0.00018      0.64      27      49 ..      11      33 ..       7      37 .. 0.87
   2 !    5.5   0.0    0.0059        21      30      50 ..      56      76 ..      51      84 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00018
     UPF0253 27 iscalktLdevaanealpeevre 49
                ++ a++tL+++a n++ p+ ++ 
  EPA04298.1 11 MKEAIETLNQIATNHSTPKTIKK 33
                5679***************9985 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0059
     UPF0253 30 alktLdevaanealpeevrek 50
                ++  Ld+v ++ ++p+ vr +
  EPA04298.1 56 TISLLDDVTQDPNMPSYVRTQ 76
                6889**************987 PP

>> PPDK_N  Pyruvate phosphate dikinase, PEP/pyruvate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   1.9e-05     0.067      54     108 ..       4      54 ..       1      83 [. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.9e-05
      PPDK_N  54 dvddvdelrkaskeirelilsaelPeeleeaikeayeelgkkfgdeelpvaVRSS 108
                 d ++ +++++a ++++++ ++ + P+ +++ai++++ +l++    ee +++VR  
  EPA04298.1   4 DKQNKETMKEAIETLNQIATNHSTPKTIKKAITDLITDLNN----EEYSLSVRAN 54 
                 567889999******************************87....5688999965 PP

>> Glyco_hydro_20b  Glycosyl hydrolase family 20, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.4   2.7e-05     0.096      32      87 ..       3      57 ..       1      65 [. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.7e-05
  Glyco_hydro_20b 32 adeatadllaevlkaatgirlt.eakepgkgdirllalkdaelgaEgYrLavded.ti 87
                      d++ +++++e +++  +i ++ ++ +  k++i  l    ++l++E Y L+v+++ ti
       EPA04298.1  3 DDKQNKETMKEAIETLNQIATNhSTPKTIKKAITDLI---TDLNNEEYSLSVRANnTI 57
                     5788899999999999999999666777788888543...78**********986455 PP

>> CUTL  CUT1-like DNA-binding domain of SATB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.11   3.9e+02       6      21 ..       3      18 ..       1      24 [. 0.80
   2 ?    9.9   0.1   0.00023      0.84       3      30 ..      20      47 ..      18      64 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.11
        CUTL  6 pdkwssttvrkavkel 21
                 dk++++t+++a+  l
  EPA04298.1  3 DDKQNKETMKEAIETL 18
                58999*****999854 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00023
        CUTL  3 elppdkwssttvrkavkellkemlqstl 30
                ++++++++ +t++ka+++l+ + +++  
  EPA04298.1 20 QIATNHSTPKTIKKAITDLITDLNNEEY 47
                6788999*************99887755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1699  (0.0947627); expected 358.6 (0.02)
Passed bias filter:                      879  (0.0490267); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 502.92
//
Query:       EPA04299.1  [L=102]
Description: Rieske [2Fe-2S] domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-18   65.6   0.1    3.6e-18   65.3   0.1    1.0  1  Rieske    Rieske [2Fe-2S] domain
    6.8e-08   32.4   0.0    8.2e-08   32.1   0.0    1.1  1  Rieske_2  Rieske-like [2Fe-2S] domain


Domain annotation for each model (and alignments):
>> Rieske  Rieske [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.3   0.1     4e-22   3.6e-18       5      83 ..       6      83 ..       3      90 .. 0.91

  Alignments for each domain:
  == domain 1  score: 65.3 bits;  conditional E-value: 4e-22
                EEEGGGC-TTCEEEEEETTEEEEEEE-TTS-EEEEESC-TTTT-BCGGSEEETT.EEE-TTT--EEE.TTSBEEE-TTHH CS
      Rieske  5 vakesdvpegdpltvkvggeplvvlrdedgevyAlsdvCtHrgaplsegkidekgvleCpcHgwayd.adGkvikgPapr 83
                + k+sd+ +g++ +v+v g++++v +  dg++ A++d CtH g +lsegk+ ++ +++C +Hg+++d ++Gk+ k Pa+ 
  EPA04299.1  6 AGKTSDITPGKMIKVSVDGKEIMVAN-IDGTYCAVDDACTHSGSSLSEGKL-DGCNVICGWHGAQFDcKTGKLFKFPAKI 83
                5789**********************.6***********************.677**********************974 PP

>> Rieske_2  Rieske-like [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.0   9.2e-12   8.2e-08       7     102 ..       8      99 ..       4     101 .. 0.91

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 9.2e-12
                 ECCCS-TTB-EEEEETTEEEEEEE-TTS-EEEEESS-TTTSSSTCCCSEEEECTTCEEEE-TTT--EEETTT-BBSS-TT..SB-BEE-EEESTSEEE CS
    Rieske_2   7 kledlvketgvaalvdgkqvalfrlekeevyAidnldpaseanvlsrGlvgdkkgelvvasPlykqkfdLktGecledee..vslkvypvrvedgkve 102
                 k++d+++++ + + vdgk+++++ + +++  A+d+ ++ s  + ls+G+++       v +  ++ +fd ktG+ +++++  + l+ y+v ve ++v 
  EPA04299.1   8 KTSDITPGKMIKVSVDGKEIMVANI-DGTYCAVDDACTHS-GSSLSEGKLDGC----NVICGWHGAQFDCKTGKLFKFPAkiRDLASYNVSVEADNVF 99 
                 789**********************.9999*********6.889****99765....899*****************7665589***********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 656.40
//
Query:       EPA04300.1  [L=569]
Description: glutamate--tRNA ligase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-78  263.8   0.0    2.9e-78  262.9   0.0    1.4  1  tRNA-synt_1c    tRNA synthetases class I (E and Q), catalytic
      3e-22   79.3   0.1    6.4e-22   78.3   0.1    1.6  1  tRNA-synt_1c_C  tRNA synthetases class I (E and Q), anti-codo


Domain annotation for each model (and alignments):
>> tRNA-synt_1c  tRNA synthetases class I (E and Q), catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  262.9   0.0   3.2e-82   2.9e-78       2     310 ..     101     400 ..     100     404 .. 0.96

  Alignments for each domain:
  == domain 1  score: 262.9 bits;  conditional E-value: 3.2e-82
                   -EEEE---SSSS-BHHHHHHHHHHHHHHHHTT-EEEEEE--SSCCC--HHHHHHHHHHHHHTT---SSEEEEGGGGHHHHHHHHHHHHHTTSEEEE- CS
  tRNA-synt_1c   2 VrtRfaPePtGyLHiGhakaallnylfAknnnGkfilRieDTdperekeeaeesiledlkwlgikwdekptyqsdrfdelkkyaeeLikkGkAYvce 98 
                   V tRf+PeP+Gy+HiGhakaa++n  +Ak ++GkfilR++DT+pe e  e+ ++i+  l+wlgik  + +  +sd ++++++   eLi++GkAYvc 
    EPA04300.1 101 VITRFPPEPNGYPHIGHAKAAIINSEYAKMYGGKFILRMDDTNPEAERMEYHAAIKVGLDWLGIKF-DIIKNTSDDMEIFYEKGIELINSGKAYVCT 196
                   89****************************************************************.569*************************** PP

                   STHHHHHHHHCCSSHSS-TTTTS-HHHHHHHHHHHHHTTHSTTTS-EEEESSBTTSS.GGGSSTEEEEEEESGGGSBTTTBTSTSEEE-HHHHHHHH CS
  tRNA-synt_1c  99 ctkeeleeereeqeklgskerdrydeenlklfeeemkkgkaegekavvRlkideess.vefrDlvrgriklepqeihdlvivksdiyPtYdfavvid 194
                   c+ e + ++r+e ++ +   +   +++n + + e+m   k++ + a+vR++ d++++  ++rD+v  ri  e+   h   ++k+++ P+Yd+av+i 
    EPA04300.1 197 CKREDISKNRKELKACK--CSRGDIKQNVQGW-EKMF-DKFKPGDAIVRFRGDMKADnAVMRDPVLFRIIDEK---HYTLGNKYRVWPSYDLAVAIE 286
                   **********9966655..67788999*****.7887.689999*************9************999...********************* PP

                   HHHTT-SEEEEEGGGGCCHHHHHHHHHHTT-S.-EEEEEE--EEETTSB-SHHHHHHHHHTTSSSSTT-TTSCBHHHHHHCTB-HHHHHHHHHHHCC CS
  tRNA-synt_1c 195 DaleeithvlrteefldntpkyiwllealglevppfiheylrlnlekkklSKRklsllvdekqvkewddlreallnflrrlGwtpekerelftreel 291
                   D++ ++th++r +ef+ +++  +++l+al+++ +p++  ++rl +++  +SKR l+ l++e +v   dd+r+++l+ l r+G++pe++++++ + +l
    EPA04300.1 287 DSIDGVTHAFRSKEFELRKELIDAILDALNMR-KPYQDFFSRLEFKGMPISKRILKPLIEEGKVSWYDDPRLPTLESLKRRGIKPEAIKKFILSLGL 382
                   ********************************.**************************************************************** PP

                   CSSS.EEEEHHHHHHHHHH CS
  tRNA-synt_1c 292 iksfdlnresksleafdrk 310
                   +k+  + +  ++le+f+rk
    EPA04300.1 383 TKAN-TLAPFDALESFNRK 400
                   ***9.88899999999988 PP

>> tRNA-synt_1c_C  tRNA synthetases class I (E and Q), anti-codon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.3   0.1   7.1e-26   6.4e-22       3     174 .]     408     559 ..     406     559 .. 0.86

  Alignments for each domain:
  == domain 1  score: 78.3 bits;  conditional E-value: 7.1e-26
  tRNA-synt_1c_C   3 RymaVldpvkvtienlpegkeeelevplhpknpelgtrkvpfskeiyiereDakrlkpgeevrLkelynikveevekde.sgevtelkleydges 96 
                     R+++V +p k++i+ lp    +++e+++hp  +++g+rk+ ++++i+i+ eDa+ +k+g ++rL +l+ + +++ + de +ge  e         
      EPA04300.1 408 RLFMVSKPKKLKIKKLP---FTSVEISNHPI-KNMGKRKINLNENIFISGEDADVIKEGTQIRLLGLGDVMISKRN-DEfEGEFLE--------- 488
                     99************766...789********.7***************************************9874.322433333......... PP

  tRNA-synt_1c_C  97 leearkkkg.iihWvsaeeaveaevrlYdrLfkeeededfllnpdslkvleeglaepalanlkkgdivQfeRiGyfrvd 174
                       + +++ + +i+Wvs+++a  +++    +Lf +     + +n++sl++l e++ ep+  +lk g+ +Qf R+Gy+r d
      EPA04300.1 489 --NVKSPSQqKIQWVSQKDAHMIKILIPKQLFID-----DEFNENSLEEL-EVYTEPHYLQLKDGEEIQFVRFGYCRKD 559
                     ..333555559******99999988888888764.....6799*****97.*************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (569 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.23s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 4154.32
//
Query:       EPA04301.1  [L=289]
Description: FAH family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-69  234.2   0.0    1.7e-69  233.8   0.0    1.1  1  FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family
     0.0021   18.9   0.0     0.0056   17.5   0.0    1.7  1  DUF2437        Domain of unknown function (DUF2437)


Domain annotation for each model (and alignments):
>> FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  233.8   0.0   1.9e-73   1.7e-69       1     218 []      79     284 ..      79     284 .. 0.97

  Alignments for each domain:
  == domain 1  score: 233.8 bits;  conditional E-value: 1.9e-73
                    .EEEEEEE--SHHHHHTTT.-SS-EEEEEEGGGE.EETTE..EE-TTSSSS-EE......EEEEEEEESS-B--T--HHHHHTTEEEEEEEEEEE- CS
  FAA_hydrolase   1 kivcdglnyaehvreagkaaeeppdrhiplepvfflkrasslvgpgdpirrPagsekldyEvELavvigkplrevlsveeAedaiaGytllnDvsa 96 
                    ki+c ++ny +h++e +     pp+      p++ lk++++l g +++i  P+++++ldyEvELa++igk ++++ + ++A++ai+Gy++lnDvsa
     EPA04301.1  79 KIICLAFNYIDHAKEQN---LLPPE-----DPAIVLKPRTALNGTDTDIICPDFVTQLDYEVELALIIGKNCKNI-DEKQAKEAIFGYMILNDVSA 165
                    699************86...45666.....677******************************************.9******************* PP

                    SBGGG---.HHHHHHTGGGEEEEEE-B--B-.STT---SS-EEEEEETTEEEEEEEGGGTTTSHHHHHHHHHHHH-B-TT-EEEEEES.......S CS
  FAA_hydrolase  97 RdlqaeekaplgwflgksfdtftpiGpwivtpdeledpedlelrlrvngeevqdsntkdmifspaeliahlsagltLepGdliltGTpsgvgaeee 192
                    Rd+q+++k   ++++gksfdtf+p Gpwi+t+de+edp++l+l++ vng+ +q+s+t++m  +++e+++ ls+++tLe Gd+i+tGTp+gv  ++ 
     EPA04301.1 166 RDIQFKDK---QFTRGKSFDTFAPSGPWITTVDEIEDPQNLKLTTKVNGDLRQNSSTNNMFIKIPEIVSKLSKVMTLEKGDIISTGTPAGVMLNKP 258
                    ********...9*******************************************************************************8889* PP

                    --EE--TT-EEEEEETTTEEEEEEE. CS
  FAA_hydrolase 193 slkflkdgDeveveieglGelrnrVa 218
                    +++flk gD +e+eie+lG l+n+++
     EPA04301.1 259 NAVFLKNGDKIEMEIEKLGILKNTIR 284
                    ***********************985 PP

>> DUF2437  Domain of unknown function (DUF2437)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   6.3e-07    0.0056       1      23 [.       1      23 [.       1      37 [. 0.92

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 6.3e-07
                -EEEEEEETTEEEEEEEE.EEEE CS
     DUF2437  1 MriaRFshgggpryGvlegdtvv 23
                M+iaR+ h+++  yG ++gd++ 
  EPA04301.1  1 MKIARIVHENTETYGFVKGDKIS 23
                ******************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1921.43
//
Query:       EPA04302.1  [L=120]
Description: hypothetical protein BG20_I2004, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-06   28.7   0.0    2.4e-06   28.1   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
    2.4e-05   24.2   0.1    4.4e-05   23.3   0.1    1.4  1  Methyltransf_31  Methyltransferase domain
    3.9e-05   23.3   0.0    5.7e-05   22.7   0.0    1.2  1  DOT1             Histone methylation protein DOT1
    5.4e-05   23.8   0.0    0.00013   22.6   0.0    1.5  2  Methyltransf_11  Methyltransferase domain
     0.0016   18.0   0.0      0.002   17.7   0.0    1.1  1  Methyltransf_5   MraW methylase family
     0.0044   17.7   0.0     0.0065   17.2   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
     0.0083   15.6   0.2     0.0093   15.4   0.2    1.2  1  TehB             Tellurite resistance protein TehB
     0.0092   15.3   0.0      0.011   15.1   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
  ------ inclusion threshold ------
      0.023   14.2   0.0      0.026   14.1   0.0    1.1  1  MTS              Methyltransferase small domain
      0.046   14.0   0.1      0.047   14.0   0.1    1.2  1  PA-IIL           Fucose-binding lectin II (PA-IIL)
      0.073   13.3   0.0        0.1   12.9   0.0    1.2  1  TrkA_N           TrkA-N domain
      0.074   13.0   0.0      0.095   12.6   0.0    1.2  1  Methyltransf_18  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   1.6e-09   2.4e-06       4      64 ..      45     105 ..      42     118 .. 0.89

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 1.6e-09
                      ET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTT CS
  Methyltransf_25   4 lGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgs 64 
                      lGcG+G+ + +++k+++ +k +g+D ++e +++a+e +++e++  e+++ d+++ +  d++
       EPA04302.1  45 LGCGNGKGVSMALKEYNVKKAVGIDNNPEKIRQAKEILNKENILGELICEDIQNSNILDAT 105
                      8******99999999999**********************************998776655 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.1   2.9e-08   4.4e-05       8      52 ..      43      86 ..      36     100 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 2.9e-08
  Methyltransf_31  8 lDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklg 52
                     + lGCG+G+ +  +  + +  ++ vGiD+++e i++A+e++ k +
       EPA04302.1 43 YHLGCGNGKGVSMAL-KEYNVKKAVGIDNNPEKIRQAKEILNKEN 86
                     569*****9888888.55667899***************988765 PP

>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   3.8e-08   5.7e-05      29      78 ..      25      74 ..       9      91 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 3.8e-08
                HHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHH--SEEEEEE--HHH CS
        DOT1 29 eflsevldkvnlkkedvFvDLGSGvGnvvlqaalevgcklsvGvEimdna 78
                + l e+++ +nl+++d+F+ LG G G+ v +a  e+++k++vG++   + 
  EPA04302.1 25 KSLREIFNFLNLGENDIFYHLGCGNGKGVSMALKEYNVKKAVGIDNNPEK 74
                568899*************************************9865444 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       3.7   5.6e+03      74      88 ..      20      34 ..      15      37 .. 0.65
   2 !   22.6   0.0   8.5e-08   0.00013       2      61 ..      44     105 ..      43     114 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.7
                     -CCHHHHHHHHHHHE CS
  Methyltransf_11 74 vedpekalkeiaRvL 88
                     v+ p+k l+ei   L
       EPA04302.1 20 VQLPDKSLREIFNFL 34
                     455677777776655 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 8.5e-08
                      EET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT- CS
  Methyltransf_11   2 dvGcGtGrlaealakrg..arvvgvDlskemlklakekaseeglkvefvvadaeklpfedns 61 
                      ++GcG+G+ +    k +  ++ vg+D ++e +++ake  ++e++  e++++d+++ ++ d++
       EPA04302.1  44 HLGCGNGKGVSMALKEYnvKKAVGIDNNPEKIRQAKEILNKENILGELICEDIQNSNILDAT 105
                      58*******9999988889**********************9997789*****997777765 PP

>> Methyltransf_5  MraW methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.3e-06     0.002       9      66 ..      27      84 ..      26     102 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.3e-06
                    THHHHHHT---TT-EEEES--TTSHHHHHHHTT--TTEEEEEES-HHHHHHHTT.... CS
  Methyltransf_5  9 lqevvellepkedgvyiDaTlGaggHsealLeqlselrligidrDksalarakerLke 66
                    l+e++++l+ +e+ ++     G+g    + L++++ ++++gid+ ++ + +ake L++
      EPA04302.1 27 LREIFNFLNLGENDIFYHLGCGNGKGVSMALKEYNVKKAVGIDNNPEKIRQAKEILNK 84
                    6899**************************************************9986 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   4.3e-06    0.0065       2      45 ..      44      87 ..      43     107 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.3e-06
  Methyltransf_12  2 eiGcGtGsllralleklpdieytgvDispsaiedakeklakren 45
                     ++GcG+G  +++ l++   ++ +g+D +p+ i +ake l+k++ 
       EPA04302.1 44 HLGCGNGKGVSMALKEYNVKKAVGIDNNPEKIRQAKEILNKENI 87
                     58******************************999999888765 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.2   6.2e-06    0.0093      36      92 ..      44     101 ..      29     120 .] 0.75

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 6.2e-06
                 EES-TTSHHHHHHHHTT-EEE...EEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG--- CS
        TehB  36 dlgcgqgrnslylsllgydvt...awdknensiafleeikekenlknistalydineakl 92 
                  lgcg+g+  + ++l+ y+v+    +d+n + i   +ei +ken+ + +    di++ ++
  EPA04302.1  44 HLGCGNGKG-VSMALKEYNVKkavGIDNNPEKIRQAKEILNKENILG-ELICEDIQNSNI 101
                 69*****85.6789999**973224799***************9863.444455555554 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   7.1e-06     0.011      51     109 ..      27      86 ..      18      98 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 7.1e-06
                 HHHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--E.EEEEES-HHHHHHHHHHHHTS- CS
        CMAS  51 ldlileklelkpGmtlLdiGcGWGslvrraverydvk.vvglTlSkeqaklakkrvdeld 109
                 l+ i++ l+l + +    +GcG G+ v  a ++y+vk  vg+    e+ ++ak+ +++++
  EPA04302.1  27 LREIFNFLNLGENDIFYHLGCGNGKGVSMALKEYNVKkAVGIDNNPEKIRQAKEILNKEN 86 
                 67789999****************************637999999999999999998876 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.7e-05     0.026      37      91 ..      44      98 ..      24     108 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.7e-05
                EET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTT CS
         MTS 37 DlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvle 91
                 lGcG+G    +++ke++  + + +d++ + ++ ake l+++++ +e++ +d+ +
  EPA04302.1 44 HLGCGNGKGVSMALKEYNVKKAVGIDNNPEKIRQAKEILNKENILGELICEDIQN 98
                69*****97777778888889**********************999999888765 PP

>> PA-IIL  Fucose-binding lectin II (PA-IIL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   3.1e-05     0.047      56     105 ..      61     110 ..      10     112 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.1e-05
                 EEEEEEEETTEE-EEEEEEEEETTTEEEEEEEEESSSSSSSBSEEEEEEE CS
      PA-IIL  56 kvrvevsanGkpsklrsaqvtlekklnfaivgsedgtdndYnDsivvlnW 105
                 +v+  v  +  p k+r+a+ +l+k+  ++ +  ed ++++  D+ v+l W
  EPA04302.1  61 NVKKAVGIDNNPEKIRQAKEILNKENILGELICEDIQNSNILDATVILFW 110
                 67778889999**************************************9 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   6.8e-05       0.1      10      55 ..      50     102 ..      45     109 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.8e-05
                 HHHHHHHHHHTT.EEEEEEESSHHHHHHHHHTT....SE..EEES-TTSHHHH CS
      TrkA_N  10 GrslaeeLsegg.kdvvvidkdeerveelreeg....le..vvvgdatdeevL 55 
                 G+ +   L+e++ k+ v+id+++e++++++e      +    ++ d  + ++L
  EPA04302.1  50 GKGVSMALKEYNvKKAVGIDNNPEKIRQAKEILnkenILgeLICEDIQNSNIL 102
                 8999999***55588*************9876532221133666666665555 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   6.4e-05     0.095       5      63 ..      27      87 ..      24     106 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.4e-05
  Methyltransf_18  5 Lkaiaslvekgs..rvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagl 63
                     L++i+++++ g+  ++   G+  g    +++ke ++kk++ +D n++ +++ake ++k+++
       EPA04302.1 27 LREIFNFLNLGEndIFYHLGCGNGKGVSMALKEYNVKKAVGIDNNPEKIRQAKEILNKENI 87
                     7777777774433388999*****9999999************************999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 811.53
//
Query:       EPA04303.1  [L=262]
Description: acetyltransferase, GNAT family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-06   28.3   0.0    3.4e-06   27.3   0.0    1.5  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    5.3e-05   23.2   0.0    0.00021   21.2   0.0    1.9  2  Acetyltransf_10  Acetyltransferase (GNAT) domain
    8.7e-05   22.4   0.0    0.00019   21.3   0.0    1.6  1  FR47             FR47-like protein
    0.00062   20.1   0.0     0.0013   19.1   0.0    1.5  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
     0.0019   17.8   1.2      0.033   13.8   0.1    2.2  2  GNAT_acetyltran  GNAT acetyltransferase
     0.0033   18.1   0.0     0.0057   17.3   0.0    1.4  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
       0.02   15.1   0.3      0.098   12.9   0.0    2.2  2  PABP             Poly-adenylate binding protein, unique domai
      0.073   13.2   0.0       0.49   10.5   0.0    2.3  2  Acetyltransf_9   Acetyltransferase (GNAT) domain
      0.077   13.2   0.7       0.26   11.6   0.1    2.1  2  Gly_acyl_tr_C    Aralkyl acyl-CoA:amino acid N-acyltransferas


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   1.7e-09   3.4e-06      14     111 ..      25     115 ..      11     121 .. 0.72

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 1.7e-09
                     HHHHHHHHHHHHHHHHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTEHHH CS
  Acetyltransf_1  14 ppnedaseeefeesfsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlaveedndaa 108
                     + ++d  ++++  +    aeg l++ e  +++G + +       ++ +++e++ ++p+ +++Gl+s+L+ ++e +a+e++i   +  ++  n  +
      EPA04303.1  25 FSWGDYIQYVWNYW---LAEGNLFVIEKKQPVGICHAIFS----KNQVWVEGIRINPDNHRQGLASKLVHHVESIAKEKQISFSYMLIDIENSSS 112
                     45677777776666...55544554555689999944444....4579999****************************8866544355556555 PP

                     HHH CS
  Acetyltransf_1 109 irl 111
                      ++
      EPA04303.1 113 LEM 115
                     555 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   1.1e-07   0.00021      34      86 ..      45      99 ..      26     122 .. 0.83
   2 ?   -0.9   0.0      0.73   1.4e+03      71      87 ..     217     233 ..     166     242 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.1e-07
  Acetyltransf_10 34 lvaeeggkivGvi.el.rdgs.hisllfVdpeyrgqGigkaLleaveeeaekdgik 86
                     +v  e++++vG++ ++ ++++  ++ + ++p+ ++qG++++L+++ve+ a++++i+
       EPA04303.1 45 FVI-EKKQPVGIChAIfSKNQvWVEGIRINPDNHRQGLASKLVHHVESIAKEKQIS 99
                     444.5679*****7776555569***************************998876 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.73
  Acetyltransf_10  71 aLleaveeeaekdgikl 87 
                      +L+ ++++++ ++++++
       EPA04303.1 217 ELISYIQNYCAEKKYHK 233
                      68888888888888774 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   9.8e-08   0.00019      10      81 ..      53     125 ..      46     130 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 9.8e-08
                 --EEEEEEE-TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EE..EEEETT-HHHHHHHHHHT-EEEE CS
        FR47  10 gelaawilrkdggelgalqvlpehrrrGlgsrlvkalakeiaergktvl..lvvvasNtpsirlyeklGfekie 81 
                 + ++  i+ k+   + ++ ++p+  r+Gl+s+lv+ + + ia++ ++++  +++ ++N+ s ++ + l+++ +e
  EPA04303.1  53 VGICHAIFSKNQVWVEGIRINPDNHRQGLASKLVHHV-ESIAKEKQISFsyMLIDIENSSSLEMAKNLNYKIYE 125
                 5566677777777888999*****************8.568886666552367899**************9884 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   6.5e-07    0.0013       3      55 ..      42     107 ..      36     131 .. 0.61

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 6.5e-07
                     EEEEEEEETTEEEEEEEEEEES..TCTEEEEE-GGGTTSSHHHHHHHH........TTSEEE........E CS
  Acetyltransf_7   3 gevfVaeddgkivGfialslld..aeitrlaVdpeyrgkGiGraLlea........aekgii........l 55 
                     g++fV+e ++++vG + +  ++   + +++ ++p+ +++G++++L+ +        +    i        +
      EPA04303.1  42 GNLFVIE-KKQPVGICHAIFSKnqVWVEGIRINPDNHRQGLASKLVHHvesiakekQ----IsfsymlidI 107
                     4567764.49999*888777776666666*****************98555433220....1233333332 PP

>> GNAT_acetyltran  GNAT acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.1   1.7e-05     0.033     161     243 .]      45     130 ..      24     130 .. 0.88
   2 ?    3.1   0.1     0.031        61     167     191 ..     217     241 ..     177     245 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.7e-05
  GNAT_acetyltran 161 vilkngeivsgasSysvyekgieieidTkedyrrkgLAtivaaalileclkrglyPsW...DaaneaSvaLaekLGYefekeYkvy 243
                      +++++++ v  + ++++ ++     i  ++d  r+gLA+++ ++  + + ++++  s+   D +n +S+++a++L Y+  ++++ y
       EPA04303.1  45 FVIEKKQPVGICHAIFSKNQVWVEGIRINPDNHRQGLASKLVHHVESIAKEKQISFSYmliDIENSSSLEMAKNLNYKIYETWNFY 130
                      46678899**********9999999******************998888888886555333888**************99999877 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.031
  GNAT_acetyltran 167 eivsgasSysvyekgieieidTked 191
                      e++s +  y+  +k + i+i T+e+
       EPA04303.1 217 ELISYIQNYCAEKKYHKIQILTREK 241
                      79999*****************997 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   2.9e-06    0.0057      45     135 ..      38     119 ..       9     122 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.9e-06
  Acetyltransf_3  45 waeeseeegygwaivlkdtgviGsvglrdleeedeeaelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvlekl 135
                     w +    eg  ++i +k++  +G++     + + + +  g++++p+ +++G+a+  v+ +  +a +e +++  +  id eN+ S   ++ l
      EPA04303.1  38 WLA----EGNLFVI-EKKQ-PVGICHAIFSK-N-QVWVEGIRINPDNHRQGLASKLVHHVESIA-KEKQISFSYMLIDIENSSSLEMAKNL 119
                     433....5555788.5555.58888443222.2.22777*******88****************.7777****************999887 PP

>> PABP  Poly-adenylate binding protein, unique domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   4.9e-05     0.098       7      53 ..      72     118 ..      70     129 .. 0.88
   2 ?   -1.6   0.1       1.6   3.3e+03      21      36 ..     231     253 ..     227     258 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.9e-05
        PABP   7 aspeqqkqiLGerLypkiqklnpelAgKITGMLLemdnsellelles 53 
                 ++p++++q L ++L + ++++ +e+      ML++++ns  le+ ++
  EPA04303.1  72 INPDNHRQGLASKLVHHVESIAKEKQISFSYMLIDIENSSSLEMAKN 118
                 67899***********************************9999844 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.6
        PABP  21 ypkiqklnpelAg.......KIT 36 
                 y+kiq l  e+         KIT
  EPA04303.1 231 YHKIQILTREKISftnsiehKIT 253
                 89999886655544455555777 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00025      0.49      75     112 ..      66     103 ..       5     123 .. 0.91
   2 ?   -3.9   0.0       6.8   1.4e+04      37      51 ..     172     186 ..     167     189 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00025
                     EEEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE CS
  Acetyltransf_9  75 gvtgVavapehrgrgvlskLlaraleemreegqplsll 112
                     +v g+  +p++ ++g++skL++++   ++e+++++s+ 
      EPA04303.1  66 WVEGIRINPDNHRQGLASKLVHHVESIAKEKQISFSYM 103
                     67888899***************************985 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 6.8
                     HHHTTSEEEEEEETT CS
  Acetyltransf_9  37 klleesrvlgaedng 51 
                     +l++++++++a + g
      EPA04303.1 172 QLYKQNKIIVANNSG 186
                     578888888888755 PP

>> Gly_acyl_tr_C  Aralkyl acyl-CoA:amino acid N-acyltransferase, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00013      0.26      30      89 .]      75     134 ..      71     134 .. 0.87
   2 ?   -1.4   0.1       1.4   2.7e+03      37      61 ..     226     250 ..     218     260 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00013
  Gly_acyl_tr_C  30 kYrrqglvahvivkqakalekkgiPv.YshvdkenekvqklseslghveipceWnqWncvP 89 
                    +  rqgl ++++ + + + ++k+i + Y+ +d en+++  + ++l++++   +Wn +   P
     EPA04303.1  75 DNHRQGLASKLVHHVESIAKEKQISFsYMLIDIENSSSLEMAKNLNYKI-YETWNFYSILP 134
                    557899******************9879*****************9975.57899877665 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.4
  Gly_acyl_tr_C  37 vahvivkqakalekkgiPvYshvdk 61 
                     a+  ++++++l++ +i + +++++
     EPA04303.1 226 CAEKKYHKIQILTREKISFTNSIEH 250
                    5566788899999998888777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       905  (0.0504769); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1726.91
//
Query:       EPA04304.1  [L=144]
Description: porphobilinogen synthase, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.8e-64  216.0   1.0    7.5e-64  215.9   1.0    1.0  1  ALAD      Delta-aminolevulinic acid dehydratase
  ------ inclusion threshold ------
      0.053   13.1   0.0       0.11   12.1   0.0    1.5  1  DUF2674   Protein of unknown function (DUF2674)
      0.084   11.6   0.0       0.12   11.1   0.0    1.1  1  AtuA      Acyclic terpene utilisation family protein AtuA
      0.097   12.2   0.1       0.24   11.0   0.1    1.7  1  SH3_6     SH3 domain (SH3b1 type)


Domain annotation for each model (and alignments):
>> ALAD  Delta-aminolevulinic acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  215.9   1.0   1.7e-67   7.5e-64     178     316 ..       2     140 ..       1     141 [. 0.99

  Alignments for each domain:
  == domain 1  score: 215.9 bits;  conditional E-value: 1.7e-67
                 TT-TT-EEB---EEB--CGGHHHHHHHT---S.S--TTTSB-TT-HHHHHHHHHHHHHTT-SBEEEES-TTGHHHHHHHHTT-SS-EEEEE-HHHHHHH CS
        ALAD 178 agfeevailsYsaKyaSafYgPFrdaaesapsfgdrktYqmdpansrealreveldleeGADivmvKPalaylDiirevkeefdlpvaayqvSGEYami 276
                 +gf++v+i+s+saK+ S+fY PFrdaae+ap+fgdrktYq++++n+rea+ eve+d++eG Divm+KPal+ylD+i+e++++f++pvaay+vSGEYa++
  EPA04304.1   2 EGFTDVSIMSHSAKHRSSFYSPFRDAAECAPKFGDRKTYQVPFTNAREAMMEVETDINEGVDIVMIKPALSYLDLIAETRRRFNVPVAAYSVSGEYALV 100
                 89************************************************************************************************* PP

                 HHHHHTTSS-HHHHHHHHHHHHHHTT-SEEEETTHHHHHH CS
        ALAD 277 kaaaengwldekkvvlEsllsikRAGadliltYfakevak 316
                 k aa++gw++ek+++ E l sikRAGad+i+tYfak++ak
  EPA04304.1 101 KGAAKQGWVNEKDITEEILYSIKRAGADMIVTYFAKSAAK 140
                 *************************************997 PP

>> DUF2674  Protein of unknown function (DUF2674)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.4e-05      0.11       9      36 ..      42      69 ..      37      74 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.4e-05
     DUF2674  9 vsfderkkDikkIekeleeGWvIvnlvP 36
                v+f + +  + ++e +++eG  Iv ++P
  EPA04304.1 42 VPFTNAREAMMEVETDINEGVDIVMIKP 69
                89*************************9 PP

>> AtuA  Acyclic terpene utilisation family protein AtuA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   2.6e-05      0.12     216     258 ..      82     124 ..      71     133 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.6e-05
        AtuA 216 anlgfPiaeisadGevvitkeegtgGlvtvdtvkeqllYEiqg 258
                  ++++P+a  s +Ge  + k + ++G v+++ ++e +lY i+ 
  EPA04304.1  82 RRFNVPVAAYSVSGEYALVKGAAKQGWVNEKDITEEILYSIKR 124
                 46789**********************************9976 PP

>> SH3_6  SH3 domain (SH3b1 type)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   5.4e-05      0.24      29      52 ..      86     109 ..      83     110 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5.4e-05
                 EEEEEE-TTSSEEEEE-SS-EEEE CS
       SH3_6  29 VlilhaSkDgaWlfVetsfasGWv 52 
                 V ++ +S  g++++V+  +  GWv
  EPA04304.1  86 VPVAAYSVSGEYALVKGAAKQGWV 109
                 557889999**************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 992.24
//
Query:       EPA04305.1  [L=103]
Description: hypothetical protein BG20_I2553 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.021   14.9   0.6      0.026   14.6   0.6    1.4  1  DUF1896   Domain of unknown function (DUF1896)
      0.027   14.8   2.2      0.034   14.5   0.6    1.8  2  DUF2833   Protein of unknown function (DUF2833)
       0.03   14.3   0.1       0.03   14.3   0.1    1.1  1  IMS       impB/mucB/samB family
       0.17   11.8   2.7          1    9.4   0.2    2.4  2  JmjN      jmjN domain


Domain annotation for each model (and alignments):
>> DUF1896  Domain of unknown function (DUF1896)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.6   5.9e-06     0.026      86     126 ..      33      76 ..      12      99 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.9e-06
                 TS-TTHHHHH...HHHHHT-HHHHHTTS---TTGGGSTHHHHHH CS
     DUF1896  86 eipeekreel...alkllpevkevFkkydlsddFaespeydkLy 126
                 +i +++ree    +l+ l+ +++vF+ y+ +++F+e  +y +++
  EPA04305.1  33 KIQKPTREEYrkkVLEYLKMMEPVFESYKTDENFSEIVKYINIR 76 
                 45555555550005555666****************99997765 PP

>> DUF2833  Protein of unknown function (DUF2833)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.6   7.5e-06     0.034      23      63 ..      24      67 ..      15      77 .. 0.73
   2 ?    0.4   0.1      0.19   8.4e+02      27      60 ..      67     100 ..      65     102 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7.5e-06
     DUF2833 23 Wfvtsdvvqkltkkekrefrklileyrdlll...dqyetlwnyv 63
                W v      k++k+ + e+rk++ley++++    ++y+t  n+ 
  EPA04305.1 24 WAVIWFRLNKIQKPTREEYRKKVLEYLKMMEpvfESYKTDENFS 67
                444444678999*****************962225666666665 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.19
     DUF2833  27 sdvvqkltkkekrefrklileyrdllldqyetlw 60 
                 s+ v+ ++ +++ e+ k+ ++  + + ++ye   
  EPA04305.1  67 SEIVKYINIRKQEEYEKISSGLNKEVEKRYERYI 100
                 5667777778888888888888888888888655 PP

>> IMS  impB/mucB/samB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   6.8e-06      0.03      67     130 ..      33      96 ..       5     103 .] 0.72

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.8e-06
                 EEE-HHHHHHHHHHHHHHHHH-S..EEEEETTEEEEE-HH.HHHHHH-SHHHHHHHHHHHHHHHH CS
         IMS  67 kvdlekyrraskkileilkrfispkvekasiDEayldltg.leelaesegaalakelrkaikeel 130
                 k++ +  +++ kk+le+lk +  p  e+++ DE + ++ + ++ ++++e +++ + l k+++++ 
  EPA04305.1  33 KIQKPTREEYRKKVLEYLKMM-EPVFESYKTDENFSEIVKyINIRKQEEYEKISSGLNKEVEKRY 96 
                 666666677789999999999.889***************6444444457999999999999876 PP

>> JmjN  jmjN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.2   0.00022         1       4      26 ..      36      59 ..      35      61 .. 0.86
   2 ?    2.9   0.6     0.024   1.1e+02       6      18 ..      62      74 ..      55      90 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00022
                ---HHHHC.-HHHHHHHHHHHHCC CS
        JmjN  4 yPTeeEFk.dplkYiekieplgek 26
                +PT eE++   l+Y++ +ep  e 
  EPA04305.1 36 KPTREEYRkKVLEYLKMMEPVFES 59
                6******65**********97665 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.024
                -HHHHC-HHHHHH CS
        JmjN  6 TeeEFkdplkYie 18
                T e F+   kYi+
  EPA04305.1 62 TDENFSEIVKYIN 74
                8999*******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1516  (0.0845557); expected 358.6 (0.02)
Passed bias filter:                      710  (0.0396006); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 681.10
//
Query:       EPA04306.1  [L=323]
Description: putative replication factor C small subunit [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-16   61.2   0.2    8.2e-13   48.4   0.2    2.5  2  DNA_pol3_delta2  DNA polymerase III, delta subunit
    7.7e-13   49.0   1.0    1.4e-12   48.2   0.1    1.8  2  AAA              ATPase family associated with various cellul
    7.6e-11   42.3   1.5    1.3e-10   41.6   0.5    1.9  1  Rep_fac_C        Replication factor C C-terminal domain
    5.3e-05   23.1   0.2    0.00014   21.7   0.2    1.7  1  DNA_pol3_delta   DNA polymerase III, delta subunit
    6.2e-05   23.4   0.1    0.00026   21.4   0.1    2.2  1  AAA_16           AAA ATPase domain
    0.00012   21.9   0.0    0.00033   20.4   0.0    1.8  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00032   21.0   1.1       0.11   12.7   0.0    2.6  2  AAA_22           AAA domain
    0.00036   20.5   0.1     0.0035   17.3   0.0    2.4  2  Rad17            Rad17 P-loop domain
     0.0004   20.7   0.1    0.00099   19.4   0.1    1.7  1  AAA_assoc_2      AAA C-terminal domain
    0.00042   20.2   0.0     0.0008   19.3   0.0    1.4  1  AAA_3            ATPase family associated with various cellul
     0.0041   16.6   0.0       0.55    9.6   0.0    2.5  2  TniB             Bacterial TniB protein
     0.0055   16.7   0.2       0.19   11.7   0.0    2.4  2  ResIII           Type III restriction enzyme, res subunit
     0.0072   15.7   0.0       0.55    9.6   0.0    2.6  3  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0079   16.3   0.2      0.066   13.3   0.0    2.2  2  PTPlike_phytase  Inositol hexakisphosphate
  ------ inclusion threshold ------
       0.02   14.3   0.2        2.6    7.4   0.0    2.3  2  PhoH             PhoH-like protein
      0.026   14.3   0.9        1.4    8.7   0.1    2.7  2  DEAD             DEAD/DEAH box helicase
      0.044   13.5   2.0        1.1    8.9   2.0    2.4  1  AAA_24           AAA domain
      0.063   12.3   0.1       0.82    8.7   0.0    2.1  2  T2SSE            Type II/IV secretion system protein
       0.12   12.4   0.6        1.2    9.1   0.6    2.4  1  AAA_5            AAA domain (dynein-related subfamily)
       0.17   12.2   1.1        2.6    8.4   0.5    2.7  2  AAA_19           AAA domain
       0.64   10.1   4.9         14    5.7   4.8    2.2  1  DUF87            Helicase HerA, central domain


Domain annotation for each model (and alignments):
>> DNA_pol3_delta2  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   0.00047       0.4       2      50 ..      30      78 ..      29      89 .. 0.84
   2 !   48.4   0.2   9.6e-16   8.2e-13      87     161 ..      93     169 ..      81     171 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00047
  DNA_pol3_delta2  2 qeealkilskalksgrlahayLfeGdegigkkelalnlakallceekne 50
                     q+e++  l+  +k  +    ++f+G++g+gk ++al++a+++l e +++
       EPA04306.1 30 QTEIIGSLEALIKDPTDMPHLMFSGSAGVGKTTTALCIARQILGEYAKD 78
                     677777788888888888889*********************9987765 PP

  == domain 2  score: 48.4 bits;  conditional E-value: 9.6e-16
  DNA_pol3_delta2  87 qirelieelsrkpre..skkkiiiiedaekmtksAaNalLktlEEPsenaifiLitsdtnklLktirSRcqelkfsp 161
                       +re  +++sr +       kiii+++a++mt+ A+ al +++E+  ++  fiLi+++ +k++++i+SRc ++kf +
       EPA04306.1  93 MVREKVKKFSRFAGMaeVPFKIIILDEADEMTADAQTALRRIIEDTAKYCRFILIANNISKIIDPIQSRCATFKFTS 169
                      56666666666554312678*******************************************************86 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.2   0.1   1.7e-15   1.4e-12       2     126 ..      51     164 ..      50     169 .. 0.85
   2 ?   -1.9   0.1       4.9   4.2e+03      10      53 ..     234     279 ..     229     297 .. 0.49

  Alignments for each domain:
  == domain 1  score: 48.2 bits;  conditional E-value: 1.7e-15
                 EEESSTTSSHHHHHHHHHHHH.....THEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTS.EEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHH CS
         AAA   2 llyGppGtGKTllakavakel.....gvefleisgsellskyvgesekkirelfkeakekakp.silfiDEidalaksrsgseseeeervvnqLlteld 94 
                 +++G  G+GKT++a  +a+++     + + le+++s+ +   +g   +k++++ + a   + p +i+++DE+d+++ +            + +L + ++
  EPA04306.1  51 MFSGSAGVGKTTTALCIARQIlgeyaKDYTLELNASDER--GIGMVREKVKKFSRFAGMAEVPfKIIILDEADEMTADA-----------QTALRRIIE 136
                 899*****************5554447889*********..77777777777776665444567***********9888...........********* PP

                 HTTTSSSTEEEEEEESSGGGSTHHHHSTTSSE CS
         AAA  95 gvkkkeskvivigatnrpdkldpallrgRfdr 126
                 +  k+   + +i+++n+++k+ +++  +R+  
  EPA04306.1 137 DTAKY---CRFILIANNISKIIDPIQ-SRCAT 164
                 ****5...99****************.99975 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.9
                 SHHHHHHHHHHHH.THEEEEEETTTCS.SSSTTHHHHHHHHHHHHH CS
         AAA  10 GKTllakavakel.gvefleisgsell.skyvgesekkirelfkea 53 
                  KT+ +  v k +   ++le   + +   k+ g se+++ +++++a
  EPA04306.1 234 TKTSDVDEVLKMAlAGKVLEAREKMIElIKVYGMSESDFLKYINSA 279
                 5666666666664322222222222222245555555555554444 PP

>> Rep_fac_C  Replication factor C C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   0.5   1.5e-13   1.3e-10       4      87 ..     237     317 ..     234     318 .. 0.94

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 1.5e-13
                 HHHHHHHHHHHHT-HHHHHHHHHHHHHHC---HHHHHHHHHHHGCCS..S-HHHHHHHHHHHHHHHHHHHCTH-HHHHHHHHHH CS
   Rep_fac_C   4 teieeileaclngdfeeaykklrellvekGysaediltqlhrvvkeqeelpeaqkleilellgeiekrlveGasehlqlsalla 87 
                 ++++e+l+ +l+g++ ea++k+ el+  +G+s +d l+ +   v++    + +   +il++++ +++r+++Ga++++qlsalla
  EPA04306.1 237 SDVDEVLKMALAGKVLEAREKMIELIKVYGMSESDFLKYINSAVFKT---KHEKLSDILKVIAKYDFRILSGANSEIQLSALLA 317
                 799******************99899999*************99985...479999**************************98 PP

>> DNA_pol3_delta  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.2   1.7e-07   0.00014      59     170 ..     113     214 ..     110     216 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.7e-07
                     EEEEEE--.....TT-S-TTHHHHHHHHTTT--SSEEEEEEES.S--HHHHHHHHHTTTEEEEEE----TTTHHHHHHHHHHHTT-EE-HHHHHH CS
  DNA_pol3_delta  59 rivvlknpklltkesklnekllkeLeeylsnlpedtlLiliapkklderkklvklLkkkatvveaktlkeeelkkwiqkraqelglkiekealel 153
                     +i++l+ +      +  +++ +++L ++++++ +++ +ilia+ +++   k+++ ++++   ++++   +e++++ ++++++++++k +k+ l+ 
      EPA04306.1 113 KIIILDEA------DEMTADAQTALRRIIEDTAKYCRFILIAN-NIS---KIIDPIQSRCATFKFTSIPQEDVINHLESISKKEKIKSDKKGLKA 197
                     66777776......6789*************************.777...89******************************************* PP

                     HHHHHTT-HHHHHHHHH CS
  DNA_pol3_delta 154 Llelvennlsaikqele 170
                     +++++e++l+ + + l+
      EPA04306.1 198 IYDYSEGDLRHAINLLQ 214
                     *********99988765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.1   3.1e-07   0.00026       8     107 ..      33     154 ..      27     287 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 3.1e-07
      AAA_16   8 eleqLlsalervrsgrpelvllsGesGvGKsslvrellralekd...............ggiflrgkcdqlesaipysalaqalareellrqlldeaes 91 
                  +  L++++++  +   + +++sG +GvGK++ + +++r++ ++               g+  +r+k +++    +++  a++ ++  ++ +++de   
  EPA04306.1  33 IIGSLEALIKDPTDM--PHLMFSGSAGVGKTTTALCIARQILGEyakdytlelnasderGIGMVREKVKKF---SRFAGMAEVPFK-IIILDEADE--- 122
                 566677777755433..899***********************9998888888888886677788888888...333444444433.444444444... PP

      AAA_16  92 aeleawrekleeala.................a 107
                    ++++++l++ ++                 +
  EPA04306.1 123 -MTADAQTALRRIIEdtakycrfilianniskI 154
                 .44444444444433222366666655554441 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   3.8e-07   0.00033       2      57 ..      20      71 ..      19      85 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 3.8e-07
      RuvB_N  2 rPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakel 57
                rP++l+e + q+++  +l+ +i+      + + h++++G+ G+Gktt a  ia+++
  EPA04306.1 20 RPTKLSEIVNQTEIIGSLEALIKDP----TDMPHLMFSGSAGVGKTTTALCIARQI 71
                9*****************9999765....5789********************986 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.3    0.0036       3.1       7      30 ..      49      72 ..      45      98 .. 0.79
   2 !   12.7   0.0   0.00013      0.11      54     129 ..      69     148 ..      67     153 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0036
      AAA_22  7 ilvvtGesGtGKTtllrrlleqld 30
                +l+  G +G+GKTt++  +++q  
  EPA04306.1 49 HLMFSGSAGVGKTTTALCIARQIL 72
                67889***********99999864 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00013
      AAA_22  54 kdllrellralglelkaerlsseellealeqalrarav........ielliiDEaqhlrseealeeLrsllnlsrkgvqliLvG 129
                 +++l e +++++lel+a   s e+ + ++++ +++ ++         +++i+DEa+ + +++a + Lr++ ++  k +++iL+ 
  EPA04306.1  69 RQILGEYAKDYTLELNA---SDERGIGMVREKVKKFSRfagmaevpFKIIILDEADEM-TADAQTALRRIIEDTAKYCRFILIA 148
                 67788888888888888...7777777777777777777777999999**********.9999999988888788888888875 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   4.1e-06    0.0035       8     119 ..      14     122 ..      10     166 .. 0.71
   2 ?    0.3   0.1      0.64   5.5e+02      73      99 ..     272     298 ..     234     316 .. 0.54

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.1e-06
       Rad17   8 lWfekykPekaeelavhkkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLsk.elgiklrewlnpvslkepdnqksdfkgltekesrflsq 105
                  W+eky+P k+ e+    + i  ++  +k    +      L+ sG +G gk+t+   +++ +lg   +++   ++  + +     ++ +++k+srf  +
  EPA04306.1  14 MWVEKYRPTKLSEIVNQTEIIGSLEALIK----DPTDMPHLMFSGSAGVGKTTTALCIARqILGEYAKDYTLELN-ASDERGIGMVREKVKKFSRFAGM 107
                 7************9766665655555444....34444469**********998777766156666666665555.44444667789999999999887 PP

       Rad17 106 ies.fkeleLkdaky 119
                  e+ fk + L +a  
  EPA04306.1 108 AEVpFKIIILDEADE 122
                 776567666666655 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.64
       Rad17  73 lrewlnpvslkepdnqksdfkglteke 99 
                 + +++n+  +k  + + sd++ ++ k 
  EPA04306.1 272 FLKYINSAVFKTKHEKLSDILKVIAKY 298
                 234455555555555555555555544 PP

>> AAA_assoc_2  AAA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   1.2e-06   0.00099       2      52 ..     185     228 ..     184     257 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.2e-06
                  XX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXX CS
  AAA_assoc_2   2 ekklkleddalealaeladGDaRkaLnlLElaaeaaeakegkieitledle 52 
                  ++k+k +++ l+a+ ++++GD R a+nlL++ a+  e +       +e+++
   EPA04306.1 185 KEKIKSDKKGLKAIYDYSEGDLRHAINLLQATASLGEIT-------EEHVK 228
                  578999************************998877643.......33332 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   9.3e-07    0.0008       1      88 [.      49     137 ..      49     143 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 9.3e-07
       AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkG..pvfanllladeinrappktqsalleamee 88 
                 h+++ g  G++kt+++  +a+++  e+ +  +t +l  sd  G+ +++ek k+f+  +G   v  ++++ de +  ++ +q+al  ++e+
  EPA04306.1  49 HLMFSGSAGVGKTTTALCIARQILGEYAK-DYTLELNASDERGIGMVREKVKKFSRFAGmaEVPFKIIILDEADEMTADAQTALRRIIED 137
                 8999***********************98.8***********************988883357889*****************9887765 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0   0.00064      0.55      16      51 ..      30      63 ..      20      80 .. 0.88
   2 ?    4.2   0.0     0.029        25     114     141 ..     106     133 ..      92     146 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00064
        TniB 16 akeilerLeeLleypkrkrmpnlllvGdsnnGKtmi 51
                 +ei+ +Le+L++ p  ++mp+l++ G   +GKt+ 
  EPA04306.1 30 QTEIIGSLEALIKDP--TDMPHLMFSGSAGVGKTTT 63
                578999******988..58***************96 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.029
        TniB 114 llrelkvrvLiiDEihnllagsarkqre 141
                  + e+  +++i+DE +++ a  +++ r+
  EPA04306.1 106 GMAEVPFKIIILDEADEMTADAQTALRR 133
                 5889999**********99766665555 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   0.00022      0.19       8      54 ..      30      77 ..      23      86 .. 0.83
   2 ?    2.6   0.1      0.14   1.2e+02     133     162 ..     112     143 ..      83     173 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00022
                HHHHHHHHT.......TTSEEEEEESTTSTHHHHHHHHHHHH-S.... CS
      ResIII  8 Qeeaienlleklks.krdkrglikmaTGtGKTlvaaklierllkkgke 54
                Q+e+i +l++ +k+ ++  ++++    G+GKT +a+ +++++l ++ +
  EPA04306.1 30 QTEIIGSLEALIKDpTDMPHLMFSGSAGVGKTTTALCIARQILGEYAK 77
                8899999999998844445999******************99987655 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.14
                 -SEEEEETGGGTTS...TTTHHHHHT---SEE CS
      ResIII 133 fdviiiDEaHrlgak..kswreilekfkeavl 162
                 f++ii DEa  ++a+  ++ r+i+e   ++++
  EPA04306.1 112 FKIIILDEADEMTADaqTALRRIIEDTAKYCR 143
                 669*********99855377776555444433 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0   0.00065      0.55      24      59 ..      49      85 ..      25     103 .. 0.88
   2 ?    3.2   0.0     0.057        49     109     133 ..     114     138 ..     110     148 .. 0.92
   3 ?   -2.6   0.0       3.4   2.9e+03      51      87 ..     255     290 ..     246     292 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00065
  Mg_chelatase 24 nlllvGppGsGKtmlakrlp.sllpplseeealevak 59
                  +l++ G++G GKt  a +++ ++l +  ++ +le ++
    EPA04306.1 49 HLMFSGSAGVGKTTTALCIArQILGEYAKDYTLELNA 85
                  89**************998537999999999988765 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.057
  Mg_chelatase 109 vLfLDElpefkrkvlevLRePledg 133
                   +++LDE+ e+++++  +LR+ +ed+
    EPA04306.1 114 IIILDEADEMTADAQTALRRIIEDT 138
                   689*****************99985 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 3.4
  Mg_chelatase  51 eeealevakiasvagkkeeekllkrrpfraphhsask 87 
                   +e+++e  k++ +++ ++  k+++++ f++ h+  s+
    EPA04306.1 255 REKMIELIKVYGMSE-SDFLKYINSAVFKTKHEKLSD 290
                   467889999998888.777888999999999988775 PP

>> PTPlike_phytase  Inositol hexakisphosphate
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   7.7e-05     0.066     118     153 ..      34      69 ..      11      72 .. 0.86
   2 ?    0.4   0.1      0.74   6.3e+02      36      72 ..     173     211 ..     163     246 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.7e-05
                      HHHHHHHHHTS-TT-EEEEE-SSSSHHHHHHHHHHH CS
  PTPlike_phytase 118 fdalvsilkeapektalvfnCqmGrgRTTtamviat 153
                      + +l  ++k+  + + l+f+ ++G+g+TTta++ia 
       EPA04306.1  34 IGSLEALIKDPTDMPHLMFSGSAGVGKTTTALCIAR 69 
                      55677788888889*******************985 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.74
                      HHHHHHHHHHHHT-SEEEEEEEHHHHHTT-CCG-EE..E CS
  PTPlike_phytase  36 aeeleklearlkeevlaeakksegrvlvhdeteegk..d 72 
                      ++ +  le+  k+e +++ kk+ + ++ + e + +   +
       EPA04306.1 173 EDVINHLESISKKEKIKSDKKGLKAIYDYSEGDLRHaiN 211
                      678889999999999999999999999888887765331 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0031       2.6      22      44 ..      50      72 ..      27      80 .. 0.78
   2 ?    4.7   0.0     0.021        18     122     146 ..     114     137 ..     110     195 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0031
                EEEE--TTSSTTHHHHHHHHHHH CS
        PhoH 22 vfaiGpaGtGKtylavalaveal 44
                ++  G+aG GKt  a+++a ++l
  EPA04306.1 50 LMFSGSAGVGKTTTALCIARQIL 72
                6778**************98876 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.021
                 EEEE-SGGG--HHHHHHHHTTB-TT CS
        PhoH 122 fvilDEAQnttkeqmkmfltRlGen 146
                 ++ilDEA ++t    ++ l R+ e+
  EPA04306.1 114 IIILDEADEMTAD-AQTALRRIIED 137
                 8*********975.56777777544 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1     0.066        56      17      41 ..      50      74 ..      30      99 .. 0.83
   2 ?    8.7   0.1    0.0016       1.4     123     150 ..     113     139 ..      93     148 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.066
                EEEEESTTSSHHHHHHHHHHHHHHH CS
                xxxxxxxxxxxxxxxxxxxxxxxxx RF
        DEAD 17 vlvaaeTGsGKTlaflipvlqivye 41
                ++ ++  G GKT+ +l  + qi+ e
  EPA04306.1 50 LMFSGSAGVGKTTTALCIARQILGE 74
                6678899*********999999865 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0016
                 EEEEEETHHHHHHTTTHHHHHHHHHHSH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        DEAD 123 rflVlDEadrlldqgfsdfinrilnqlp 150
                 ++++lDEad++  +  +  ++ri++ ++
  EPA04306.1 113 KIIILDEADEMTAD-AQTALRRIIEDTA 139
                 78**********98.9999999998874 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   2.0    0.0013       1.1       7      85 ..      52     131 ..      48     290 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0013
      AAA_24   7 iyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdieswedfldevvel....aaeladyktlviDtideleelclaev 85 
                   G++g+GKTt+a+ +  + ++    k  + +   +  d +++ +++++v+++      ++ ++k++++D +de+   +   +
  EPA04306.1  52 FSGSAGVGKTTTALCI-ARQILGEYAK--DYTLELNASDERGIGMVREKVKKFsrfaGMAEVPFKIIILDEADEMTADAQTAL 131
                 5699************.4444443333..333344444455778888888888777767777899999999999877665554 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0   0.00096      0.82     103     151 ..      22      69 ..      14      88 .. 0.81
   2 ?    1.4   0.1      0.16   1.4e+02      32     123 ..     191     293 ..     173     321 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00096
       T2SSE 103 ltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallk 151
                  +l++++ + +    ++++++ + +    +++sG  g GKtt++  +  
  EPA04306.1  22 TKLSEIVNQTEIIGSLEALIKDP-TDMPHLMFSGSAGVGKTTTALCIAR 69 
                 56788888888889999999999.88899*************9855544 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.16
       T2SSE  32 dgielreveelekaalerlisriaalakl.diseerplqdarlpekgvrlrvvllPvvagealviRkksakeltlddlgaeealk...........eki 118
                 d+  l+++ + ++  l+  i+ ++a+a+l +i ee++  +a l+ k  ++  vl  ++ag+ l  R+k  + +++  ++ +  lk           ek+
  EPA04306.1 191 DKKGLKAIYDYSEGDLRHAINLLQATASLgEITEEHVKASAGLT-KTSDVDEVLKMALAGKVLEAREKMIELIKVYGMSESDFLKyinsavfktkhEKL 288
                 44457777778888888888888887775489999999999999.899998888888888888888766666544433333333355555555554555 PP

       T2SSE 119 aevlr 123
                 +++l+
  EPA04306.1 289 SDILK 293
                 55555 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.6    0.0014       1.2       1      91 [.      49     137 ..      49     142 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0014
                 EEEEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT--HHHHH--B--.........--------.G-SEEEEESGGG--HHHHHHHHHHHHS CS
       AAA_5   1 dvlLvGppGtgKselaerlaaal.nreveyvqltrdtteedlkgrreikngttslvdsplvraar.egeilvlDEveraesevlnsLlsllee 91 
                 +++  G  G+gK++ a  +a+ + +     + l  + + e  +g ++  ++ ++++  + + a +   +i++lDE +++  +++ +L +++e+
  EPA04306.1  49 HLMFSGSAGVGKTTTALCIARQIlGEYAKDYTLELNASDERGIGMVR--EKVKKFSRFAGM-A-EvPFKIIILDEADEMTADAQTALRRIIED 137
                 67889999999999999999999744444444444444444444444..355555555555.3.248899*****************999997 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.5     0.003       2.6      11      62 ..      48      98 ..      38     148 .. 0.73
   2 ?   -0.6   0.0       1.8   1.5e+03      16      40 ..     228     252 ..     175     292 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.003
      AAA_19 11 kvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerl 62
                ++l+  + +G GKT++  +i + ++ +   +  ++ l a  +r    +re++
  EPA04306.1 48 PHLMFSGSAGVGKTTTALCIARQILGEYAKD-YTLELNASDERGIGMVREKV 98
                6678899*********999998877666443.55555666666666666655 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.8
      AAA_19  16 taGpGtGKTrvlkhivallvelggv 40 
                  a +G  KT  + ++++++++ + +
  EPA04306.1 228 KASAGLTKTSDVDEVLKMALAGKVL 252
                 4555555555555555544444433 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   4.8     0.017        14      29     201 ..      53     284 ..      47     306 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.017
       DUF87  29 lgsTGsGKSntvavLleelle...................................kkgatililDpHGEYgkal.......ekllsekvkvitpspsa 85 
                  gs+G+GK++t+  + +++l                                    +   +i+ilD   E  +             ++++        +
  EPA04306.1  53 SGSAGVGKTTTALCIARQILGeyakdytlelnasdergigmvrekvkkfsrfagmaEVPFKIIILDEADEMTADAqtalrriI---EDTA--------K 140
                 58999999999999999999777777777777777777777777777776666544444577777777777666645553331...2222........1 PP

       DUF87  86 ..................kdkelkinpwsldpeelldllee.ddkpaaavqrsvleealdqaka..keekeklssdepveklleelk.......kekee 156
                                   + +  ++++ s+  e++++ le  ++k++ +  ++ l+ ++d+ +   ++ ++ l++ +++ ++ ee         k+++ 
  EPA04306.1 141 ycrfilianniskiidpiQSRCATFKFTSIPQEDVINHLESiSKKEKIKSDKKGLKAIYDYSEGdlRHAINLLQATASLGEITEEHVkasagltKTSDV 239
                 223344445556677777778889999999999999999998888887788888888888776566555555555555555555444577777656667 PP

       DUF87 157 lrklknqaiarlldkledllrkggsfsnsstdliallleklekeg 201
                  + lk+ ++ ++l+++e++++  +  + s++d+++ +     k++
  EPA04306.1 240 DEVLKMALAGKVLEAREKMIELIKVYGMSESDFLKYINSAVFKTK 284
                 777777778888888888888888888888888877766655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       918  (0.051202); expected 358.6 (0.02)
Passed bias filter:                      595  (0.0331865); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.44
# Mc/sec: 2190.01
//
Query:       EPA04307.1  [L=109]
Description: hypothetical protein BG20_I1723 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.6e-14   51.7   0.0      1e-13   51.5   0.0    1.1  1  DEAD      DEAD/DEAH box helicase
    1.9e-05   24.8   0.0    2.3e-05   24.5   0.0    1.1  1  ResIII    Type III restriction enzyme, res subunit
      0.001   18.2   0.0     0.0011   18.1   0.0    1.1  1  T2SSE     Type II/IV secretion system protein
  ------ inclusion threshold ------
      0.036   14.0   0.0      0.048   13.6   0.0    1.1  1  ATPase_2  ATPase domain predominantly from Archaea
      0.054   13.1   0.0      0.065   12.8   0.0    1.1  1  AAA_25    AAA domain
       0.17   11.3   0.0       0.19   11.1   0.0    1.1  1  PhoH      PhoH-like protein


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.5   0.0   3.4e-17     1e-13       2      75 ..      26      95 ..      25     106 .. 0.89

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 3.4e-17
                HHHHHHHHHHH.TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST CS
                xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        DEAD  2 diQaeaiplil.gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyid 75
                + Qa +i++ l +g+++lv+a+T+sGKTl +++++++ +    +k++ k+++++P+r+La + ++++kk+ k id
  EPA04307.1 26 PPQADCIDNGLlDGKSILVSAPTASGKTLTAILAMINYL----SKNNGKIIYLSPLRALAAEKFTEFKKLEK-ID 95
                6799999998879***********************999....57888*********************998.45 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   7.7e-09   2.3e-05       3      80 ..      23      94 ..      21     105 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 7.7e-09
                EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG CS
      ResIII  3 elreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflse 80
                +l++ Q+++i+n l      + k +l+ ++T +GKTl+a+ ++ ++l+k++  k++ l p ++l     +efkk+ + 
  EPA04307.1 23 KLYPPQADCIDNGL-----LDGKSILVSAPTASGKTLTAILAMINYLSKNN-GKIIYLSPLRALAAEKFTEFKKLEKI 94
                57778888888887.....45789***************666666666533.4*************999999998765 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   3.8e-07    0.0011     119     162 ..      29      73 ..       7      81 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.8e-07
       T2SSE 119 aevlrkavrerglilvsGgTgsGKttll.yallkeinksderivt 162
                 a+ + + +   ++ilvs +T sGKt ++  a+++++ k++ +i+ 
  EPA04307.1  29 ADCIDNGLLDGKSILVSAPTASGKTLTAiLAMINYLSKNNGKIIY 73 
                 5666666777799************77658999999999999985 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.6e-05     0.048      27      75 ..      46      93 ..      39     105 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.6e-05
    ATPase_2 27 GpegsGKt.aLlkeiienledkdkyviyyialreesiskldefieeeeek 75
                 p  sGKt + +  +i+ l++ + ++iy+++lr  + +k++ef  ++ ek
  EPA04307.1 46 APTASGKTlTAILAMINYLSKNNGKIIYLSPLRALAAEKFTEF--KKLEK 93
                5889****778999*****99999*******************..33333 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.2e-05     0.065      16      58 ..      22      64 ..       8      78 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.2e-05
      AAA_25 16 aapppprrwlvk.gllpagelallaGapgtGKttlaldlalava 58
                 +  pp+ + ++ gll  g+ +l+ +++++GKt  a+  ++ ++
  EPA04307.1 22 SKLYPPQADCIDnGLL-DGKSILVSAPTASGKTLTAILAMINYL 64
                4444556666662665.8****************9998877766 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   6.4e-05      0.19      20      59 ..      40      78 ..      26     101 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 6.4e-05
                SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S- CS
        PhoH 20 divfaiGpaGtGKtylavalavealkkkkvkriiltrpav 59
                + + + +p+ +GKt+ a+ + +++l+k++  +ii++ p  
  EPA04307.1 40 KSILVSAPTASGKTLTAILAMINYLSKNN-GKIIYLSPLR 78
                4567789**********999999887655.7899988865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.42u 0.32s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 701.64
//
Query:       EPA04308.1  [L=513]
Description: hypothetical protein BG20_I1722, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    8.4e-12   45.4   0.6    2.5e-10   40.7   0.2    2.8  2  Helicase_C  Helicase conserved C-terminal domain
    1.3e-07   31.5   0.1    3.5e-07   30.2   0.1    1.6  1  DEAD        DEAD/DEAH box helicase


Domain annotation for each model (and alignments):
>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   0.2   2.8e-14   2.5e-10      11     109 ..     191     296 ..     144     298 .. 0.64
   2 ?   -3.7   0.0       1.7   1.5e+04      13      35 ..     429     449 ..     421     475 .. 0.60

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 2.8e-14
                 HHTTTTSEEEEEESSHHHHHHHHHHHHHT......TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEE....ESSSS..... CS
  Helicase_C  11 kleeeggkilifvntidrlekvklllekk......gikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVi....nfdlp..... 94 
                 +le++ +kil   + ++ +         k      +  va +h+ l+qn r+ i ++f+kg++++L +t  ++ G+++p  ++Vi    +++++     
  EPA04308.1 191 ELEKISKKILSDNEHTELV---------KtlamliKKGVAFHHAGLNQNCRQTIETEFRKGTIKLLSSTPTLAAGVNLPARRVVIsninRYNAKvganr 280
                 2333333333333333333.........0334445778999**************************************99888865554444455443 PP

                 .SSHHHHHHHHTTSSS CS
  Helicase_C  95 .rnvtsyiqriGRtgR 109
                   ++ +y+q  GR+gR
  EPA04308.1 281 pISILEYKQLCGRAGR 296
                 3446************ PP

  == domain 2  score: -3.7 bits;  conditional E-value: 1.7
                 TTTTSEEEEEESSHHHHHHHHHH CS
  Helicase_C  13 eeeggkilifvntidrlekvkll 35 
                 ++e++ +  f++ i+++e  +++
  EPA04308.1 429 SQERKHSFGFLHLITNCE--EFF 449
                 466677777888888886..333 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.1   3.9e-11   3.5e-07      88     171 ..      17      96 ..       4     100 .. 0.80

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 3.9e-11
                 HHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEEEEEESSBS.H CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
        DEAD  88 rdqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrqvivlSATlp.k 171
                 ++  ++l ++ +++v t +++d++++     ++++ +++ DE++ + d++++++++ +l++l+    + k   q++ lSAT++ +
  EPA04308.1  17 ENIEKNL-EKNNVLVLTNEKMDSIIRHSAEWIDEIGLVIADEIHLIGDESRGPTLEMVLTKLKLL--ESK--PQIVGLSATITnS 96 
                 4455666.7789************9555545*******************************433..223..35*******9944 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (513 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       833  (0.046461); expected 358.6 (0.02)
Passed bias filter:                      649  (0.0361983); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.50
# Mc/sec: 3092.57
//
Query:       EPA04309.1  [L=695]
Description: ATPase, AAA family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.3e-94  313.8   0.0    6.2e-94  313.3   0.0    1.2  1  MCM           MCM P-loop domain
    1.6e-35  121.7   0.1    2.8e-35  120.9   0.1    1.3  1  MCM_OB        MCM OB domain
    1.8e-23   82.8   1.3    3.7e-23   81.8   1.3    1.6  1  MCM_lid       MCM AAA-lid domain
    7.4e-10   39.4   2.0    1.1e-09   38.8   0.3    2.1  2  MCM_N         MCM N-terminal domain
    1.6e-06   28.2   0.0    2.3e-05   24.4   0.0    2.7  2  AAA_5         AAA domain (dynein-related subfamily)
    2.8e-06   26.9   0.0     0.0002   20.8   0.0    2.5  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
    0.00081   19.3   0.0     0.0026   17.6   0.0    1.8  1  AAA_3         ATPase family associated with various cellular 
  ------ inclusion threshold ------
      0.075   12.7   0.2       0.18   11.5   0.2    1.6  1  AAA_30        AAA domain
       0.17   12.3   0.7        4.8    7.5   0.0    3.0  4  AAA_16        AAA ATPase domain


Domain annotation for each model (and alignments):
>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  313.3   0.0   3.1e-97   6.2e-94       2     224 .]     288     509 ..     287     509 .. 0.98

  Alignments for each domain:
  == domain 1  score: 313.3 bits;  conditional E-value: 3.1e-97
                 HHHHHHHHTSSTHHHHHHHHSSTTSSS-HHHHHHHHHHHH---EBBBSSSSBBCSS-EEEEEESSTSTHHHHHHHHHHHSSSEEEEESSSSSSSHSSSE CS
         MCM   2 veeikelakekdiieklvksiapsiyghedvkkaillqlfggvkkkledktklrgdinvllvgdpgtaKsqlLkyveklapravytsgkgssaagLtaa 100
                 +++ik+l+++++++++l++s+ap+i g++ +k+aill+++g++++ l d++k+rgdinv lvgdpgtaKs++Lk+++++apr+ ytsg+gs+aagLtaa
  EPA04309.1 288 EKMIKTLSQSPNVYQRLIDSFAPHIQGQSLIKEAILLLIVGSTQRLLGDGSKIRGDINVFLVGDPGTAKSEMLKFCARIAPRGLYTSGRGSTAAGLTAA 386
                 789************************************************************************************************ PP

                 EEEESSSSSEEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE--EEEEEEE--SSSSCCTTS-HHHHSSSSHHHHHHSS CS
         MCM 101 vvrdeetgefvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaKaGivatLnartsvlaAanpkagrydkkksvaeninlsaalLsrFD 199
                 vvrd+ tg ++leaGa+vl d+G++ciDefdkmk edrsalhE+mEqq+ siaK+GivatLnarts+laAanp++g+yd+ k+++en+nl+ +lL+rFD
  EPA04309.1 387 VVRDK-TGIMMLEAGAVVLGDQGLVCIDEFDKMKPEDRSALHEVMEQQSASIAKGGIVATLNARTSILAAANPMYGKYDPFKNITENVNLPIPLLTRFD 484
                 ***98.567****************************************************************************************** PP

                 EEEEE-SSTTHHHHHHHHHHHHHHH CS
         MCM 200 lifvllDkvdeekDeelaehivslh 224
                 lifv++D + +ekDe++a+hi++lh
  EPA04309.1 485 LIFVVRDIPGREKDEKIARHIIELH 509
                 **********************987 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.9   0.1   1.4e-38   2.8e-35       2     125 ..     113     240 ..     112     241 .. 0.94

  Alignments for each domain:
  == domain 1  score: 120.9 bits;  conditional E-value: 1.4e-38
                 XGG--GGGTTSEEEEEEEEEEE---EEEEEEEEEEETTT-.-EEES---.....-SB-..TTT-HHH-EEE-GGGSEEEEEEEEEEE------------ CS
      MCM_OB   2 lRdlrsehigklvkveGivtrasevkpklkkavfeckkcgktvevelee.....PrkCeekeCeskdpfkletekskfvdfqklklQEspeevpaGelP 95 
                 lR++++e+ig++ +v+G+v+rasevkp +k++vf c++ ++t+ ++l+      P  C++++C+ ++ f+l++e skf+dfq l+lQE pe++p+G+lP
  EPA04309.1 113 LRQINAETIGNITSVSGMVVRASEVKPLAKELVFICPDEHQTKVIQLKGmdvkiPIVCDNPSCK-HRDFELKPEASKFIDFQILRLQELPEDLPPGQLP 210
                 8************************************99998878555556666**********.89******************************** PP

                 -EEEEEEEGGGTT---TT-EEEEEEEEEEE CS
      MCM_OB  96 rslevileddlvdkvkPGdrvevtGiyral 125
                 + ++v++++dlvd+++PGdr+ +tGi+r+ 
  EPA04309.1 211 HYIDVTIRQDLVDNARPGDRIILTGIVRVE 240
                 ***************************985 PP

>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.8   1.3   1.8e-26   3.7e-23       2      86 ..     524     604 ..     523     605 .. 0.95

  Alignments for each domain:
  == domain 1  score: 81.8 bits;  conditional E-value: 1.8e-26
                 HHHHHHHHHHHTT--BETCHHHHHHHHHHHHHHHHHTSSTSSSST--HHHHHHHHHHHHHHHHHHTSSSE-HHHHHHHHHHHHHH CS
     MCM_lid   2 llrkYiayarekikPklseeakeklseaYvelRkeeedskrksipitvRqLesliRLseAlAklrlsevvteedveeairllkes 86 
                 +l+kY++ya+ + +P l++ea+ek+ e+Y+++R+ e+   ++ i++t+RqLe +iRLs+A+A+l +++ v+eed+e+ai l++++
  EPA04309.1 524 ILTKYLSYAK-RSSPDLTKEAEEKILEYYLQMRNVES---EEMITVTPRQLEGIIRLSTARARLLMKDKVEEEDAERAIFLIQSM 604
                 79********.***********************873...689*************************************99875 PP

>> MCM_N  MCM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.3   5.5e-13   1.1e-09       3     102 ..      17     104 ..      15     122 .. 0.89
   2 ?   -2.2   0.1       3.2   6.3e+03      50      82 ..     536     568 ..     516     598 .. 0.66

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 5.5e-13
       MCM_N   3 kFedFLeefkddsededgekkYrdqlqemaerekttLevdlddLaafdeeLaeailenpkeylplleealkevvkklepsykddakefpaeltrrfqvr 101
                 k +dFL  f    +d+ g++kY++q+ em  ++ + + vd++dL  +++e+    +++p ++l+++++a+ke +++ +p+y+++        + +++vr
  EPA04309.1  17 KVKDFLTRF----KDKFGSYKYVEQIDEMMPKGAKFILVDYNDLV-VEPEIEIIFSTDPDRILNAFSRAIKEALQTRFPDYAEK-------IKDEVRVR 103
                 789******....678899*************************5.79999999*************************99987.......44555554 PP

       MCM_N 102 f 102
                 +
  EPA04309.1 104 L 104
                 4 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.2
       MCM_N  50 deeLaeailenpkeylplleealkevvkkleps 82 
                 +++L ++ +e+  ey+  ++++  e + +++p+
  EPA04309.1 536 SPDLTKEAEEKILEYYLQMRNVESEEMITVTPR 568
                 447777777777777777777777777776665 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.46   9.2e+02      56      81 ..     218     243 ..     201     249 .. 0.85
   2 !   24.4   0.0   1.1e-08   2.3e-05       1     124 [.     345     460 ..     345     471 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.46
                 .--------G-SEEEEESGGG--HHH CS
       AAA_5  56 dsplvraaregeilvlDEveraesev 81 
                  + lv++ar g+ ++l ++ r+e+e 
  EPA04309.1 218 RQDLVDNARPGDRIILTGIVRVEQES 243
                 6889******************9554 PP

  == domain 2  score: 24.4 bits;  conditional E-value: 1.1e-08
                 EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--..........--------G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..- CS
       AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik.ngttslvdsplvraaregeilvlDEveraesevlnsLlslleerrlllee 98 
                 +v+LvG+pGt+Kse+ +  a+   r +      r+ t++ l+  +  +  g   l+ +++v       ++++DE++++++e  ++L+ ++e++  ++++
  EPA04309.1 345 NVFLVGDPGTAKSEMLKFCARIAPRGLY--TSGRGSTAAGLTAAVVRDkTGIMMLEAGAVV--LGDQGLVCIDEFDKMKPEDRSALHEVMEQQSASIAK 439
                 69*************9877777666544..4567889999999988666677777778777..77888999*************************999 PP

                 SSSEEE---......-EEEEEESS-- CS
       AAA_5  99 ggelvkaknddllerfrviatanpld 124
                 gg +   ++      ++++a+anp +
  EPA04309.1 440 GGIVATLNAR-----TSILAAANPMY 460
                 9999988886.....89******987 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.024        49      21      47 ..     342     368 ..     338     375 .. 0.85
   2 !   20.8   0.0   9.9e-08    0.0002      96     160 ..     396     460 ..     384     496 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.024
  Mg_chelatase  21 GgHnlllvGppGsGKtmlakrlpsllp 47 
                   G  n++lvG pG+ K+ + k  + + p
    EPA04309.1 342 GDINVFLVGDPGTAKSEMLKFCARIAP 368
                   8889************99887777766 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 9.9e-08
  Mg_chelatase  96 kpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpcp 160
                     + G++ l  +G++ +DE+ ++k +   +L e +e+++ +i++    ++  ar+ ++aa+Np  
    EPA04309.1 396 MLEAGAVVLGDQGLVCIDEFDKMKPEDRSALHEVMEQQSASIAKGGIVATLNARTSILAAANPMY 460
                   5688***********************************************************74 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.3e-06    0.0026       5     113 ..     349     459 ..     345     465 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.3e-06
       AAA_3   5 egvPGlaktllvkalakaldlefkriqftpdl.lPsdilGtevfeekekefefkkGpvf...anllladeinrappktqsalleameerqvtv..eget 97 
                  g PG+ak  + k  a++    +    +t+     +  l + v+++k+  + +++G+v+   + l+  de ++ +p  +sal e+me++  ++  +g  
  EPA04309.1 349 VGDPGTAKSEMLKFCARIAPRGL----YTSGRgSTAAGLTAAVVRDKTGIMMLEAGAVVlgdQGLVCIDEFDKMKPEDRSALHEVMEQQSASIakGGIV 443
                 55666666666666665543332....22221012222345678889999999999998444469*********************9987666115678 PP

       AAA_3  98 hklpepflvlatqnPi 113
                  +l+    +la+ nP+
  EPA04309.1 444 ATLNARTSILAAANPM 459
                 99*************7 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   9.3e-05      0.18      20     119 ..     345     437 ..     331     449 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.3e-05
      AAA_30  20 vavltGpAGtGKttalkalreaweaa.ggrviglAptgkaAkvLaeelgieastiakllkrlkgrarlepgtllivDEagmvdtkqlaallkaaekaga 117
                  ++l+G +Gt K+ +lk  ++++ +    +  g +  g  A+v+++++gi       ++        l ++ l+ +DE   +  ++  al + +e+++a
  EPA04309.1 345 NVFLVGDPGTAKSEMLKFCARIAPRGlYTSGRGSTAAGLTAAVVRDKTGIMMLEAGAVV--------LGDQGLVCIDEFDKMKPEDRSALHEVMEQQSA 435
                 5789*****************99988556677888888899999999997555544444........45678**********99999999999999888 PP

      AAA_30 118 kv 119
                 ++
  EPA04309.1 436 SI 437
                 77 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.7   3.3e+03      40      85 ..      73     105 ..      68     148 .. 0.60
   2 ?    7.5   0.0    0.0024       4.8      26      59 ..     345     376 ..     331     392 .. 0.75
   3 ?    0.6   0.0      0.32   6.4e+02     138     163 ..     409     434 ..     401     443 .. 0.86
   4 ?   -2.9   0.0         4     8e+03      97     145 ..     543     590 ..     503     609 .. 0.57

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.7
      AAA_16  40 lvrellralekdggiflrgkcdqlesaipysalaqalareellrql 85 
                 +++++ ra++++    l++++ ++         a+ ++ e  +r +
  EPA04309.1  73 ILNAFSRAIKEA----LQTRFPDY---------AEKIKDEVRVRLV 105
                 567777777777....77777777.........5555333333333 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0024
      AAA_16  26 lvllsGesGvGKsslvrellralekdggiflrgk 59 
                 +v+l+G++G+ Ks +++ ++r +  + g++++g+
  EPA04309.1 345 NVFLVGDPGTAKSEMLKFCAR-IAPR-GLYTSGR 376
                 89**************99995.6666.4545544 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.32
      AAA_16 138 vlvlDdlqwadeaslqllaaLlrlle 163
                 ++++D++++ +++++++l + ++ ++
  EPA04309.1 409 LVCIDEFDKMKPEDRSALHEVMEQQS 434
                 689**************999888766 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 4
      AAA_16  97 wrekleealaavpelagaea.srllellkrllallsrderplvlvlDdlq 145
                 + ek++e + + ++++++e  +   ++l  +++l++ ++   +l  D ++
  EPA04309.1 543 AEEKILEYYLQMRNVESEEMiTVTPRQLEGIIRLSTARA--RLLMKDKVE 590
                 444444444444444444445555555555554444322..344444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (695 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.75u 0.33s 00:00:01.08 Elapsed: 00:00:00.52
# Mc/sec: 4046.95
//
Query:       EPA04310.1  [L=468]
Description: ATPase/histidine kinase/DNA gyrase B/HSP90 domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.2e-22   78.2   0.4    4.3e-21   75.5   0.1    2.3  2  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
      1e-10   41.4   0.0    1.6e-10   40.8   0.0    1.3  1  PorA         Porin PorA
    1.4e-09   37.8   0.1    3.4e-09   36.6   0.1    1.6  1  HisKA        His Kinase A (phospho-acceptor) domain
    1.8e-08   34.2   0.6    1.1e-07   31.7   0.0    2.4  2  HATPase_c_5  GHKL domain
    2.8e-05   23.9   0.3    7.2e-05   22.6   0.0    1.8  2  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like
     0.0067   16.4   0.0      0.013   15.5   0.0    1.4  1  HATPase_c_2  Histidine kinase-like ATPase domain
  ------ inclusion threshold ------
       0.28   11.3   1.4       0.34   11.0   0.1    1.8  2  PspB         Phage shock protein B


Domain annotation for each model (and alignments):
>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0      0.47   1.2e+03      36      63 ..     190     217 ..     158     261 .. 0.74
   2 !   75.5   0.1   1.7e-24   4.3e-21       2     109 ..     369     467 ..     368     468 .] 0.90

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.47
                 TEEEEEEEESSSSSTTHHHTGTCSTTCH CS
   HATPase_c  36 ddlvisveDnGiGipkedlkklfekfsq 63 
                 + +++ + D G   + e  +++ ++f q
  EPA04310.1 190 NGKRVNIIDVGEKHTTEFTELVLTHFAQ 217
                 6789999999999999999999999999 PP

  == domain 2  score: 75.5 bits;  conditional E-value: 1.7e-24
                 HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHHHHHHHHHTTTEEEEEEETTT CS
   HATPase_c   2 dekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsivkklvelmgGeiwvesepgr 100
                 d+ ++ +++ n+++N+v++  k g+i+++ k++ ++++i+  D+G+Gipk++++k+f+++ +     ++++gtGlGl+ +k+l+e++gG+i+v+++p  
  EPA04310.1 369 DKNQIIKVFLNILKNSVEA-MKHGKITITAKTRTKTVEIEFADSGPGIPKDKIDKIFDPLFT-----TKTKGTGLGLASCKSLIEKHGGSISVKNNP-- 459
                 5678899***********8.899999999997557***********************6666.....5999**********************9999.. PP

                 EEEEEEEEE CS
   HATPase_c 101 Gttftftlp 109
                  t+ft+ lp
  EPA04310.1 460 -TRFTVILP 467
                 .89998877 PP

>> PorA  Porin PorA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   0.0   6.2e-14   1.6e-10     143     290 ..      98     237 ..      52     246 .. 0.85

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 6.2e-14
        PorA 143 FPf..dtekksYqyFDptlrkavpadfvgeeevdGlevyrFeqevpptklaaklrltvPaslwvtmtryysatrtlwVepeTGviVkgeekirqylard 239
                 F f  ++ek++Y +F p++   +p++f +++ v+ levy+Fe e++ ++ +     ++P+ +    t   ++   l+Vep TG ++k e++ + yl ++
  EPA04310.1  98 FGFlpGVEKTDYFFFHPAVFYGAPMKFLKTDYVNELEVYVFETEIKGEDAS----NSFPQFS--GHTILTDNISRLYVEPITGSVIKFEKEWNNYLVEN 190
                 444449***************************************999999....7899985..889999999***********************999 PP

        PorA 240 gdeaeeaavtlldadlawdeetveaqveqakegrdklkllgrtlpivllvl 290
                 g++       +  ++ +++e t   + + a+e+ +  ++ + ++pi l+vl
  EPA04310.1 191 GKRV----NIIDVGEKHTTEFTELVLTHFAQEKIENEEFSKIIMPIFLIVL 237
                 8766....4555566666777777777777777777777777777776665 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.1   1.3e-12   3.4e-09       3      64 ..     268     328 ..     266     330 .. 0.89

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 1.3e-12
                 HHHHHHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCH CS
       HisKA   3 grflagvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedlLdlsri 64 
                 g+++a ++H+Lr+PL+ ++  +e+ +    + e+ +e+ ++i++ ++r++  +e ++d+ r 
  EPA04310.1 268 GDMTAKLSHDLRNPLTIMKNGLELFQMG-LAEEKKEENMRRIQNAVERISYEIESIMDFVRD 328
                 799************************5.44566666*********************9886 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.46   1.2e+03      33      53 ..      64      84 ..      44     101 .. 0.59
   2 !   31.7   0.0   4.3e-11   1.1e-07       2      96 ..     369     464 ..     368     467 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.46
  HATPase_c_5 33 ltvrekkksliisieNsyege 53
                  + r++ +  i+++eN y+ +
   EPA04310.1 64 TSKRTDTHEEIFHVENIYHVD 84
                 333445566788888877665 PP

  == domain 2  score: 31.7 bits;  conditional E-value: 4.3e-11
  HATPase_c_5   2 kdldlcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg....ekkkle..sskskkeehGiGlksireivkkykgnlsieaedgl 93 
                  +++ ++ ++ n+L N++ea+++ +     I++t++++ k++ i++  s  g    +++k++    ++k++  G+Gl s +++++k++g++s++++ ++
   EPA04310.1 369 DKNQIIKVFLNILKNSVEAMKHGK-----ITITAKTRTKTVEIEFADSGPGipkdKIDKIFdpLFTTKTKGTGLGLASCKSLIEKHGGSISVKNNPTR 461
                  5788999************99877.....******************977766555566664444677899*************************** PP

  HATPase_c_5  94 Ftl 96 
                  Ft+
   EPA04310.1 462 FTV 464
                  *97 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.1         4     1e+04      92     107 ..      51      66 ..      47      89 .. 0.46
   2 !   22.6   0.0   2.8e-08   7.2e-05       6      80 ..     376     440 ..     372     451 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 4
  HATPase_c_3  92 tkkegesstltldvdk 107
                  + +++e +  ++ ++k
   EPA04310.1  51 SQNNNEITIKSVITSK 66 
                  5544444422222222 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 2.8e-08
  HATPase_c_3   6 AlaelvdNsldAdae.nvkievnknrgktgeivieDdGkGmseeelknalrlatsskeakrkstslGkkGiGlklA 80 
                  + + +++Ns++A  + +++i+++++ +kt ei + D G G++++++++ + +  ++k+          kG Gl lA
   EPA04310.1 376 VFLNILKNSVEAMKHgKITITAKTR-TKTVEIEFADSGPGIPKDKIDKIFDPLFTTKT----------KGTGLGLA 440
                  56789*******76637******96.68**********************99999888..........34444455 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0     5e-06     0.013      43     111 ..     380     448 ..     376     465 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 5e-06
  HATPase_c_2  43 avehayleapegpvevrlesdeealtvevaDsGpgfdpetlpdpteeepkeslkegGrGlalikglvDe 111
                  + +   +  ++g+++++++ +++++++e+aDsGpg +  ++++   +  +++ k  G+Gla  k+l ++
   EPA04310.1 380 ILKNSVEAMKHGKITITAKTRTKTVEIEFADSGPGIPKDKIDKIFDPLFTTKTKGTGLGLASCKSLIEK 448
                  5555555556899**********************8888888888777789999999999988888766 PP

>> PspB  Phage shock protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00013      0.34       5      34 ..     230     259 ..     225     278 .. 0.74
   2 ?   -3.6   0.1       4.8   1.2e+04      55      63 ..     313     322 ..     298     325 .. 0.46

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00013
        PspB   5 lavpliifvlfVapiWLiLHYrskkkrskg 34 
                 + + li++v+ +  iW++L Y +k kr++ 
  EPA04310.1 230 MPIFLIVLVFGIGTIWILLTYLEKIKRESA 259
                 3344566666699***********998764 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 4.8
        PspB  55 eRie.tLEri 63 
                 eRi+  +E+i
  EPA04310.1 313 ERISyEIESI 322
                 3333134555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (468 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1119  (0.0624129); expected 358.6 (0.02)
Passed bias filter:                      594  (0.0331307); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.49
# Mc/sec: 2887.13
//
Query:       EPA04311.1  [L=170]
Description: 4Fe-4S binding domain protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-09   36.6   8.2    0.00023   20.8   2.7    2.3  2  Fer4      4Fe-4S binding domain
      3e-08   33.7   5.2    1.8e-07   31.2   5.8    1.9  2  Fer4_10   4Fe-4S dicluster domain
    4.2e-08   33.7  15.7    5.8e-06   26.8   9.8    2.1  2  Fer4_7    4Fe-4S dicluster domain
    5.3e-08   32.9   4.5     0.0016   18.6   0.8    2.2  2  Fer4_21   4Fe-4S dicluster domain
    7.1e-08   32.8  12.1    5.8e-07   29.9   5.9    1.7  2  Fer4_8    4Fe-4S dicluster domain
    1.1e-06   29.5   5.5    2.5e-06   28.3   5.6    1.6  1  Fer4_16   4Fe-4S double cluster binding domain
    2.2e-06   27.7   7.2      2e-05   24.7   7.5    2.1  2  Fer4_9    4Fe-4S dicluster domain
    6.9e-06   25.9   9.6      0.019   15.0   0.4    2.3  2  Fer4_6    4Fe-4S binding domain
      5e-05   23.8   4.2    0.00014   22.3   4.5    1.6  1  Fer4_17   4Fe-4S dicluster domain
    0.00013   21.8  11.0     0.0034   17.4   0.9    2.3  2  Fer4_2    4Fe-4S binding domain
     0.0014   18.8   8.8      0.011   15.9   6.5    2.2  2  Fer4_18   4Fe-4S dicluster domain
     0.0015   18.9   8.3       0.27   11.9   0.3    2.4  2  Fer4_4    4Fe-4S binding domain
      0.003   18.1   9.3       0.12   13.0   0.3    2.6  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
     0.0047   17.7   0.5        3.6    8.5   0.1    2.3  2  Fer4_22   4Fe-4S dicluster domain
  ------ inclusion threshold ------
       0.28   12.2  13.7        3.2    8.9   5.1    2.5  2  Fer4_3    4Fe-4S binding domain
        2.7    8.8  12.3       0.34   11.7   1.3    2.7  2  Fer4_15   4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.3     8e-07    0.0009       2      21 ..      59      78 ..      58      81 .. 0.91
   2 !   20.8   2.7   2.1e-07   0.00023       3      24 .]     120     141 ..     119     141 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 8e-07
                EEETTTSSS-THHHHHSTTT CS
        Fer4  2 videekCigCGaCvevCPvg 21
                 +d++ Ci+ G C++vCPv 
  EPA04311.1 59 AVDWDSCIAAGSCMSVCPVQ 78
                69****************96 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 2.1e-07
                 EETTTSSS-THHHHHSTTTEEE CS
        Fer4   3 ideekCigCGaCvevCPvgAIt 24 
                 i e +C+ C+aC e+CP+g I+
  EPA04311.1 120 IREHDCTVCMACQEICPTGSIR 141
                 56779**************985 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   5.8   1.6e-10   1.8e-07       3      56 .]      59     136 ..      57     136 .. 0.90
   2 !   13.5   3.1   5.1e-05     0.057       6      22 ..     122     138 ..     117     162 .. 0.76

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 1.6e-10
     Fer4_10   3 vidddtCirCgkCvkaCPadl........................tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                  +d d+Ci  g C+++CP++                         ++ + +  +  ++ + +   +Ct c aC+e+CP
  EPA04311.1  59 AVDWDSCIAAGSCMSVCPVQTfqwyrteqdipakdvvgkvfegtgKTEQDERLDYTDKSQPIREHDCTVCMACQEICP 136
                 56889**************99**********************997777777777777788888*************9 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 5.1e-05
     Fer4_10   6 ddtCirCgkCvkaCPad 22 
                 +  C+ C +C++ CP+ 
  EPA04311.1 122 EHDCTVCMACQEICPTG 138
                 56799999999999993 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.3     6e-06    0.0067      29      51 ..      56      78 ..      27      79 .. 0.71
   2 !   26.8   9.8   5.1e-09   5.8e-06       1      51 [.      64     138 ..      64     139 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6e-06
      Fer4_7 29 ekveidpekClgCgaCvavCPtg 51
                 +v++d ++C+  g+C++vCP++
  EPA04311.1 56 TTVAVDWDSCIAAGSCMSVCPVQ 78
                6679999**************96 PP

  == domain 2  score: 26.8 bits;  conditional E-value: 5.1e-09
      Fer4_7   1 rCigCgaCvaaCpvkaieldeeenek...........gtekv................eidpekClgCgaCvavCPtg 51 
                 +Ci  g C+++Cpv+++++   e++            g   +                 i++ +C+ C aC++ CPtg
  EPA04311.1  64 SCIAAGSCMSVCPVQTFQWYRTEQDIpakdvvgkvfeG---TgkteqderldytdksqPIREHDCTVCMACQEICPTG 138
                 5*****************97643333344444444441...03334455555555554677889************98 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.2     1e-05     0.011      32      54 ..      56      78 ..      42      81 .. 0.84
   2 !   18.6   0.8   1.4e-06    0.0016      31      58 ..     115     141 ..     104     142 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1e-05
     Fer4_21 32 tvlkvvedeCvGCnlCssvCPve 54
                t+++v  d+C++   C+svCPv+
  EPA04311.1 56 TTVAVDWDSCIAAGSCMSVCPVQ 78
                55678889*************95 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 1.4e-06
     Fer4_21  31 ktvlkvvedeCvGCnlCssvCPvedcie 58 
                 ++  +++e++C+ C  C ++CP+ + i+
  EPA04311.1 115 DKSQPIREHDCTVCMACQEICPT-GSIR 141
                 4567899***************6.7775 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.4   7.6e-05     0.085      46      63 ..      60      77 ..      31      79 .. 0.63
   2 !   29.9   5.9   5.1e-10   5.8e-07       3      64 ..      63     138 ..      61     139 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.6e-05
      Fer4_8 46 ealwsCttcgaCtevCpv 63
                  ++sC + g+C +vCpv
  EPA04311.1 60 VDWDSCIAAGSCMSVCPV 77
                456777777777777776 PP

  == domain 2  score: 29.9 bits;  conditional E-value: 5.1e-10
      Fer4_8   3 ekCieCgaCqsaCp.....................vlrrtkkhlldargeaaedvqeeqvlee..eealwsCttcgaCtevCpvg 64 
                 ++Ci  g C+s Cp                     v++ t+k  +d r + ++         +      + Ct c+aC+e Cp+g
  EPA04311.1  63 DSCIAAGSCMSVCPvqtfqwyrteqdipakdvvgkVFEGTGKTEQDERLDYTD---------KsqPIREHDCTVCMACQEICPTG 138
                 78***********9877765555555544444444444444444444444333.........133344699************86 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   5.6   2.2e-09   2.5e-06       2      66 ..      65     137 ..      64     138 .. 0.71

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 2.2e-09
     Fer4_16   2 CgtCgkCaevCPtnaikek.kekeiearecisy......ntaekkd.laedeekckkqeaitgCdiCqdvCPa 66 
                 C+  g C++vCP++ ++   +e+ i a++ + +      +t+++++  ++d+ +  ++ ++t C +Cq++CP 
  EPA04311.1  65 CIAAGSCMSVCPVQTFQWYrTEQDIPAKDVVGKvfegtgKTEQDERlDYTDKSQPIREHDCTVCMACQEICPT 137
                 9999*************7735666666665555777777444443303444455556899************7 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.3   0.00061      0.69      33      49 ..      56      78 ..      31      80 .. 0.68
   2 !   24.7   7.5   1.8e-08     2e-05       2      50 ..      65     139 ..      64     140 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00061
      Fer4_9 33 e......eaCigCgaCveaCpkg 49
                       ++Ci  g+C+ +Cp +
  EPA04311.1 56 TtvavdwDSCIAAGSCMSVCPVQ 78
                04444446899999999999986 PP

  == domain 2  score: 24.7 bits;  conditional E-value: 1.8e-08
      Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraase..........................eaCigCgaCveaCpkga 50 
                 C+  g+C+++Cp ++++  + e+ +  +                               +C+ C+aC e+Cp+g 
  EPA04311.1  65 CIAAGSCMSVCPVQTFQWYRTEQDIPAKDVVGkvfegtgkteqderldytdksqpireHDCTVCMACQEICPTGS 139
                 88899******9999999999999998665448999999999****************99************985 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.4   1.7e-05     0.019       2      22 ..      58      78 ..      57      80 .. 0.90
   2 !   14.7   3.3   2.2e-05     0.024       9      24 .]     125     140 ..     120     140 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.7e-05
      Fer4_6  2 veidpdkCigCgdCvrvCPeg 22
                v++d d+Ci  g C++vCP +
  EPA04311.1 58 VAVDWDSCIAAGSCMSVCPVQ 78
                77888**************87 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 2.2e-05
      Fer4_6   9 CigCgdCvrvCPegai 24 
                 C+ C++C  +CP+g i
  EPA04311.1 125 CTVCMACQEICPTGSI 140
                 *************965 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   4.5   1.2e-07   0.00014       2      59 ..      65     138 ..      64     139 .. 0.71

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.2e-07
     Fer4_17   2 CiqCgyClpeCps..yeaydnepkkllraakl............glleeaekee..kaslCieCgeCerkCPqg 59 
                 Ci  g C+ +Cp   +++y++e++ +++++              ++l+++ k++  + ++C+ C  C++ CP g
  EPA04311.1  65 CIAAGSCMSVCPVqtFQWYRTEQDIPAKDVVGkvfegtgkteqdERLDYTDKSQpiREHDCTVCMACQEICPTG 138
                 ************64488899998867766633335566555544455555554423779*************75 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.9     3e-06    0.0034       3      21 ..      58      76 ..      57      77 .. 0.92
   2 !    9.0   3.4    0.0015       1.6      10      22 .]     125     137 ..     120     137 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3e-06
      Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                v+vd d+Ci+ g+C s+CP
  EPA04311.1 58 VAVDWDSCIAAGSCMSVCP 76
                57999************** PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0015
      Fer4_2  10 CigCgaCvsaCPa 22 
                 C+ C aC+  CP+
  EPA04311.1 125 CTVCMACQEICPT 137
                 999*********7 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.9    0.0029       3.2      57      74 ..      61      78 ..      29      83 .. 0.83
   2 !   15.9   6.5   9.8e-06     0.011       6      74 ..      71     138 ..      69     146 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0029
     Fer4_18 57 gagdcidcescvkvcPtg 74
                +   ci+ +sc++vcP++
  EPA04311.1 61 DWDSCIAAGSCMSVCPVQ 78
                5578************85 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 9.8e-06
     Fer4_18   6 cvyvcPyarvqsvlydee..tllvvydakrGekiagrkkekkalkekeerkekgagdcidcescvkvcPtg 74 
                 c+ vcP   +q    +++  ++ vv ++  G +++++    + l  +++ +   + dc+ c +c ++cPtg
  EPA04311.1  71 CMSVCPVQTFQWYRTEQDipAKDVVGKVFEGTGKTEQ---DERLDYTDKSQPIREHDCTVCMACQEICPTG 138
                 99*********87766652245566666666555444...4455566777788899**************8 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.3   0.00024      0.27       2      17 .]      63      78 ..      62      84 .. 0.91
   2 !    9.7   2.8    0.0011       1.3       4      17 .]     125     138 ..     116     138 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00024
      Fer4_4  2 erCigCgsCvaaCPqg 17
                ++Ci  gsC+++CP++
  EPA04311.1 63 DSCIAAGSCMSVCPVQ 78
                899999********75 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0011
      Fer4_4   4 CigCgsCvaaCPqg 17 
                 C+ C++C  +CP+g
  EPA04311.1 125 CTVCMACQEICPTG 138
                 999*********86 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.3   0.00011      0.12       1      17 [.      60      76 ..      60      87 .. 0.93
   2 !    8.1   3.5    0.0034       3.8       4      17 ..     123     136 ..     120     138 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00011
     Fer4_13  1 VDrdtCiacgaCvelaP 17
                VD d+Cia g+C +++P
  EPA04311.1 60 VDWDSCIAAGSCMSVCP 76
                899************** PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0034
     Fer4_13   4 dtCiacgaCvelaP 17 
                 + C+ c+aC e++P
  EPA04311.1 123 HDCTVCMACQEICP 136
                 67************ PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0     0.005       5.6       2      94 ..      65      77 ..      31      98 .. 0.72
   2 !    8.5   0.1    0.0032       3.6       2      15 ..     125     138 ..     103     160 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.005
     Fer4_22  2 ClsCgaCtlvCptCsCfdvedetkeeskegervrvwdsClleeftkvaggenvrkekkerlrqrllhklsefkekfgesgCvGCgRCieacpv 94
                C++ g+C  vCp                                                                                v
  EPA04311.1 65 CIAAGSCMSVCP--------------------------------------------------------------------------------V 77
                555555555555................................................................................4 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0032
     Fer4_22   2 ClsCgaCtlvCptC 15 
                 C  C aC+ +Cpt 
  EPA04311.1 125 CTVCMACQEICPTG 138
                 78888888888875 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   1.3    0.0052       5.9       5      13 ..      69      77 ..      63      78 .. 0.75
   2 ?    8.9   5.1    0.0029       3.2       1      14 [.     125     138 ..     125     139 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0052
      Fer4_3  5 gaCvevCPv 13
                g C+ vCPv
  EPA04311.1 69 GSCMSVCPV 77
                57******7 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0029
      Fer4_3   1 CtgCgaCvevCPvg 14 
                 Ct C+aC e CP+g
  EPA04311.1 125 CTVCMACQEICPTG 138
                 777*********98 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.3   0.00031      0.34       1      19 [.      58      76 ..      58     116 .. 0.88
   2 ?    4.0   1.5     0.075        85       7      20 ..     124     137 ..     120     143 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00031
     Fer4_15  1 VvvDrdaCigcglCvaeap 19
                V vD+d Ci  g C+ ++p
  EPA04311.1 58 VAVDWDSCIAAGSCMSVCP 76
                89****************7 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.075
     Fer4_15   7 aCigcglCvaeape 20 
                  C+ c +C + +p+
  EPA04311.1 124 DCTVCMACQEICPT 137
                 7**********995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1074.12
//
Query:       EPA04312.1  [L=176]
Description: hypothetical protein BG20_I1725 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-09   36.8   1.1    6.3e-09   36.3   1.1    1.2  1  Sld5      GINS complex protein
  ------ inclusion threshold ------
      0.025   14.0   0.2       0.07   12.5   0.1    1.7  2  DUF620    Protein of unknown function (DUF620)


Domain annotation for each model (and alignments):
>> Sld5  GINS complex protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   1.1   7.1e-13   6.3e-09       2     108 ..      45     148 ..      44     149 .. 0.86

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 7.1e-13
                 EEEHHHHHHHHHTTSCCCHHCHHHCHHHHHHCCCHHTTS..SSSTTTTTTHH.HHHHHHHHHHT..HCHHHHHHHHHHHHHHHHHHHTHCHHHHHHHTS CS
        Sld5   2 eLPlWlaelLkrqrrveieppewlspesleailedetks..sdlpslpphfl.elavkllelard.ldelkrllrdllevRlakirkfaenledaaggg 96 
                 +LP W  ++L+++  ++++ p+++   +l++ l++e+ +   + ++l phf+ +l + + +l rd  + + +++++l++ R  k+ k+a++ + ++   
  EPA04312.1  45 NLPQWIGKILSQNKLATMDTPDMI--TELKQALSKEKMVgeYQMSTLDPHFYiKLKESMKNLNRDdFNHVESIMLELFRMRRGKLVKLADSTKLNS--- 138
                 8*********************97..88999999999999956666666665166666******99***********************9999999... PP

                 -TCCHCCS-HHH CS
        Sld5  97 ggellsglseeE 108
                   el ++l+ eE
  EPA04312.1 139 --ELYNKLTVEE 148
                 ..8888888887 PP

>> DUF620  Protein of unknown function (DUF620)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.13   1.1e+03     226     237 ..      25      36 ..      18      38 .. 0.80
   2 ?   12.5   0.1   7.9e-06      0.07     100     179 ..      75     156 ..      64     168 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.13
      DUF620 226 eevdfnvvglsl 237
                  +++fnv+gl +
  EPA04312.1  25 HDIKFNVAGLKV 36 
                 589******976 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 7.9e-06
      DUF620 100 fseaacvgekkinded.cfvLkleadkealkarseseaevirhtvfgyfsqrtGllvkleDskLlrik..ae..eeeavyWetti 179
                  s+ ++vge +++  d  f +kl+ + ++l+     +++ ++  ++  f  r G lvkl Ds+ l+ +  ++   ee+++++t  
  EPA04312.1  75 LSKEKMVGEYQMSTLDpHFYIKLKESMKNLNRD---DFNHVESIMLELFRMRRGKLVKLADSTKLNSElyNKltVEENIFFKTIH 156
                 577889999999987736999999877777655...5556666688999************986665533334347788877755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       705  (0.0393218); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1251.01
//
Query:       EPA04313.1  [L=56]
Description: hypothetical protein BG20_I2511, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       193  (0.0107647); expected 358.6 (0.02)
Passed bias filter:                      173  (0.00964917); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 341.05
//
Query:       EPA04314.1  [L=129]
Description: hypothetical protein BG20_I2509 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-15   57.1  14.4    2.3e-15   56.9  14.4    1.0  1  EamA             EamA-like transporter family
     0.0045   16.4   4.7     0.0052   16.2   4.7    1.0  1  TPT              Triose-phosphate Transporter family
  ------ inclusion threshold ------
      0.055   13.3   0.0      0.074   12.8   0.0    1.2  1  ATP_bind_1       Conserved hypothetical ATP binding protein
       0.19   11.9   1.5        1.9    8.8   0.2    2.9  2  Ery_res_leader1  Erythromycin resistance leader peptide


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.9  14.4   5.2e-19   2.3e-15      12     135 ..       1     123 [.       1     125 [. 0.98

  Alignments for each domain:
  == domain 1  score: 56.9 bits;  conditional E-value: 5.2e-19
        EamA  12 lfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafllffyalkktsasnaslitslePvftlilsv 110
                 +f+a+ + +sk+++ ++++ ++t ++++++g++ l i++  ++++  +s +++  +ll gllgt +a ++f+ +lk +++ + +l+ s+  +f +++s+
  EPA04314.1   1 MFFAADINISKYVSDRIDSKRITQITSFVSGLVALGIMFTLDIPF-DISFTHIPGILLSGLLGTGIATFFFVLSLKFIGSVRTTLLYSTGTAFGVMFSW 98 
                 58999999*************************************.***************************************************** PP

        EamA 111 lllgekltlkqllgivlillGvlli 135
                 ++lge ++++ +l +++i+ G++++
  EPA04314.1  99 AILGEVISIINILTVIMIISGIFFL 123
                 **********************997 PP

>> TPT  Triose-phosphate Transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   4.7   1.2e-06    0.0052      33     133 ..      22     121 ..       4     124 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.2e-06
         TPT  33 tvsavqllvgsvlilvlwalglkkrpkisseflkailplalvkt.lghvlavvslskvaVSfthtvKasePiFtvilsrlllgeklsllvylsLlpivg 130
                 ++   ++++g v + ++++l++    +is + +  il  +l+ t ++ ++ v+sl+ +    t  + ++  +F v++s  +lge++s+  +l+++ i+ 
  EPA04314.1  22 ITQITSFVSGLVALGIMFTLDIPF--DISFTHIPGILLSGLLGTgIATFFFVLSLKFIGSVRTTLLYSTGTAFGVMFSWAILGEVISIINILTVIMIIS 118
                 455678999***********9987..999999999999998765389999*******99999************************************* PP

         TPT 131 Gva 133
                 G+ 
  EPA04314.1 119 GIF 121
                 *85 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.7e-05     0.074     130     166 ..      17      52 ..       9      61 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.7e-05
  ATP_bind_1 130 vDsqrltdptkfisgllsalsamlrlelPhvvvlnkf 166
                 +Ds+r+t+ t+f+sg l+al +m++l++P+ + ++++
  EPA04314.1  17 IDSKRITQITSFVSG-LVALGIMFTLDIPFDISFTHI 52 
                 7**************.*************98888776 PP

>> Ery_res_leader1  Erythromycin resistance leader peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.27   1.2e+03       4       8 ..      88      92 ..      84      94 .. 0.82
   2 ?    8.8   0.2   0.00043       1.9       1      12 [.     115     126 ..     115     128 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.27
  Ery_res_leader1  4 sGtAF 8 
                      GtAF
       EPA04314.1 88 TGTAF 92
                     59**9 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00043
  Ery_res_leader1   1 mLisGtAFLRLR 12 
                      m+isG  FLR R
       EPA04314.1 115 MIISGIFFLRKR 126
                      9*********88 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       943  (0.0525964); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 841.04
//
Query:       EPA04315.1  [L=124]
Description: putative chemotaxis protein Chey [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-25   88.8   0.8    2.8e-25   88.7   0.8    1.0  1  Response_reg  Response regulator receiver domain
     0.0037   16.7   0.0     0.0044   16.4   0.0    1.1  1  2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, 
  ------ inclusion threshold ------
       0.07   13.5   0.1        1.8    8.9   0.0    2.2  2  DUF2183       Uncharacterized conserved protein (DUF2183)
       0.12   12.1   0.1       0.16   11.7   0.1    1.3  1  DUF1647       Protein of unknown function (DUF1647)


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.7   0.8   6.3e-29   2.8e-25       2     111 ..       6     115 ..       5     116 .. 0.96

  Alignments for each domain:
  == domain 1  score: 88.7 bits;  conditional E-value: 6.3e-29
                   EEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEESSTSHHHHHHHHHCTESEEE CS
  Response_reg   2 livdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviiltahseeedavealkagaddfl 98 
                   +i++Dd  ++e+ ++lle +++ + a  ++g+ea+el+++ k+d++l+D++mp+ dG+  +++ir+ dp+ ++i++ta+s+++++++  ++ a+  +
    EPA04315.1   6 IIIEDDYELCEVEKELLELNEIVVLAIGNNGQEAVELYQKFKPDIVLMDVRMPNYDGIYGIENIRKFDPKSKIIMITAESNDDTIQKINELKASALI 102
                   79****************88885888999******************************************************************** PP

                   ESSG-HHHHHHHH CS
  Response_reg  99 sKpfdpeeLlkal 111
                    Kpfd ++L k +
    EPA04315.1 103 LKPFDAAKLFKTI 115
                   *********9987 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   9.9e-07    0.0044      34     111 ..      22      95 ..       9     102 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 9.9e-07
                   GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE-S--STTTTTSBSH CS
  2-Hacid_dh_C  34 lsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelvsleellaesDivslhlpltpetrhlina 111
                   l+  ++ ++ +G+ Gq++ ++ ++f+ +++ +d++  + +      +  +++ ++  +s i+++++  +++t + in+
    EPA04315.1  22 LELNEIVVLAIGNNGQEAVELYQKFKPDIVLMDVRMPNYD----GIYGIENIRKFDPKSKIIMITAESNDDTIQKINE 95 
                   55678999***************************77444....334678***********************99997 PP

>> DUF2183  Uncharacterized conserved protein (DUF2183)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   0.00041       1.8      54      84 ..      16      46 ..       4      51 .. 0.83
   2 ?    2.5   0.0     0.042   1.9e+02      55      78 ..      66      89 ..      63      99 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00041
     DUF2183 54 eiekiletfperkfiliGDsgqkdpeiYaei 84
                e+ek l ++ e  ++ iG++gq+ +e+Y+++
  EPA04315.1 16 EVEKELLELNEIVVLAIGNNGQEAVELYQKF 46
                566666778888999*************987 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.042
     DUF2183 55 iekiletfperkfiliGDsgqkdp 78
                ie+i +  p++k+i+i  ++++d 
  EPA04315.1 66 IENIRKFDPKSKIIMITAESNDDT 89
                88999999********99999885 PP

>> DUF1647  Protein of unknown function (DUF1647)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   3.5e-05      0.16      60     122 ..      48     110 ..      15     119 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.5e-05
     DUF1647  60 edvvFvsatsddhlkeakksiksirkyypkkklilysldlseeeieklk..kdknlevrkFntsk 122
                 +d+v +     ++       i+ irk+ pk+k+i+   + ++++i+k++  k++ l ++ F+++k
  EPA04315.1  48 PDIVLMDVRMPNY--DGIYGIENIRKFDPKSKIIMITAESNDDTIQKINelKASALILKPFDAAK 110
                 5555555554444..33456899*************************98888999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 922.53
//
Query:       EPA04316.1  [L=39]
Description: hypothetical protein BG20_I1942 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.50
# Mc/sec: 235.75
//
Query:       EPA04317.1  [L=131]
Description: hypothetical protein BG20_I1948 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       777  (0.0433376); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.30s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 902.98
//
Query:       EPA04318.1  [L=274]
Description: signal peptidase I [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-09   37.2   0.4    3.8e-09   36.4   0.4    1.4  1  Peptidase_S24  Peptidase S24-like
  ------ inclusion threshold ------
      0.013   14.8   0.8      0.013   14.8   0.8    1.9  2  Pho88          Phosphate transport (Pho88)
       0.12   12.8   4.4        4.6    7.8   0.9    2.5  2  DUF202         Domain of unknown function (DUF202)
       0.14   11.7  11.1       0.72    9.3   0.3    2.4  2  DUF1129        Protein of unknown function (DUF1129)
       0.47   10.7  12.5        1.5    9.1   3.4    3.0  3  TctB           Tripartite tricarboxylate transporter TctB fam


Domain annotation for each model (and alignments):
>> Peptidase_S24  Peptidase S24-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.4   1.1e-12   3.8e-09       4      67 ..      36     100 ..      35     103 .. 0.92

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 1.1e-12
                    SSTTCCTXXTTXEEEEECTS---TTSEEEEEETTCE-EEEEEEEEETTEEEEE.SST.T.STEEEE CS
  Peptidase_S24   4 GdSMeptlldGdlilVdkfsepkrGdivvfrlpgeeeayiKrviglpgdrvllasnn.e.ypplyi 67 
                    G SM  t+++G +i+ ++++++  Gdi++f  ++++   ++r++++++d + ++ +n + ++p  i
     EPA04318.1  36 GQSMHGTIESGTFIIAKPDPQYYIGDIIAFVNEHDR-SVVHRIVEQTDDGFITKGDNnPrNDPKVI 100
                    89*********************************8.*****************988766777665 PP

>> Pho88  Phosphate transport (Pho88)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.3     0.014        49       9      55 ..     136     182 ..     130     185 .. 0.82
   2 ?   14.8   0.8   3.6e-06     0.013       5      65 ..     171     235 ..     167     243 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.014
       Pho88   9 viilvlmqvskkidfedpevllyvRilYvvsqliillvylyikskik 55 
                 ++++++   skk ++++ + +++ +i++++s +  +l +++i ++i+
  EPA04318.1 136 ILTVFASKKSKKKKLTNFSSVIVFKIAFIASVVNYVLTLMIIGTNIQ 182
                 45556666788889999999************999999999988886 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 3.6e-06
       Pho88   5 vtnlviilvlmqvskk..idfedpevllyvRilYvvsqliillvylyikskikkkn..Dlttlky 65 
                 v  l+ii + +q++k   i+f+d     ++ +lY++s  i++ v+++i ++ +kk+  D++ lk 
  EPA04318.1 171 VLTLMIIGTNIQIAKTinIPFSDYFEPSIANTLYFCSISIVIFVLYLIDHSLDKKKteDTKYLKL 235
                 78899**********955699999999*************************9999889888885 PP

>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.9    0.0013       4.6      13      55 ..     122     166 ..     119     182 .. 0.58
   2 ?    5.8   0.1    0.0053        19      17      62 ..     207     252 ..     202     256 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0013
      DUF202  13 WlRtslalialglallrffl.....tgepsalgkilglilivlgiltl 55 
                 +l ts+++ ++g+++l +f      +   ++l+   ++i + +++++ 
  EPA04318.1 122 FLQTSVGMSIFGILILTVFAskkskK---KKLTNFSSVIVFKIAFIAS 166
                 689**************998654331...2222222222222222222 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0053
      DUF202  17 slalialglallrffltgepsalgkilglilivlgiltllvglvry 62 
                 s++++++ l l+   l++ ++  +k l li+ ++gi++ll+ l++ 
  EPA04318.1 207 SISIVIFVLYLIDHSLDKKKTEDTKYLKLIFSLAGIMVLLLQLISI 252
                 66777777777766566666666799**************999876 PP

>> DUF1129  Protein of unknown function (DUF1129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   5.6    0.0034        12     110     171 ..     115     177 ..     112     206 .. 0.68
   2 ?    9.3   0.3    0.0002      0.72     125     175 ..     213     261 ..     193     269 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0034
     DUF1129 110 siGlitlllvalvgGlamvlv.yrlltrekkkkkrpplwkrllilllllvvwlvlftlvallp 171
                 ++G++tl+l + vg  ++ ++  +++  +k+kkk+   + ++++  +++++ +v ++l+ ++ 
  EPA04318.1 115 YVGFTTLFLQTSVGMSIFGILiLTVFASKKSKKKKLTNFSSVIVFKIAFIASVVNYVLTLMII 177
                 579****99877777777665155666557777777666666666666666666666666633 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0002
     DUF1129 125 lamvlvyrlltrekkkkkrpplwkrllilllllvvwlvlftlvallpaviN 175
                 ++++l+ + l+  kkk++ ++ +k ++ l++++v++l l+++v+ +p + N
  EPA04318.1 213 FVLYLIDHSLD--KKKTEDTKYLKLIFSLAGIMVLLLQLISIVNTIPFFSN 261
                 23333444443..799999*************************9996655 PP

>> TctB  Tripartite tricarboxylate transporter TctB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.1      0.27   9.7e+02     109     124 ..       5      20 ..       1      48 [. 0.72
   2 ?    9.1   3.4   0.00042       1.5      35      89 ..     123     179 ..     105     192 .. 0.70
   3 ?    6.1   0.3    0.0035        12      36      95 ..     207     257 ..     190     273 .. 0.47

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.27
        TctB 109 lkalilavvlallvyl 124
                 +k++il +++++l+yl
  EPA04318.1   5 IKIIILLLLIPVLIYL 20 
                 4555555555555554 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00042
        TctB  35 l..gvllallgllllv..aadgekeekearedwrkllklvlallaalllyallleplGf 89 
                 l  +v++ ++g+l+l   a   +k++k++ ++  +++ + +a++a+++ y+l+l ++G 
  EPA04318.1 123 LqtSVGMSIFGILILTvfA--SKKSKKKKLTNFSSVIVFKIAFIASVVNYVLTLMIIGT 179
                 2448999999955555332..4444555555666666688888899999****999996 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0035
        TctB  36 gvllallgllllvaadgekeekearedwrkllklvlallaalllyallleplGfilatal 95 
                 ++ ++++ +l+l+ ++  +++k++ ++  k   l++    +  + +lll+ +  i+ t+ 
  EPA04318.1 207 SISIVIF-VLYLI-DHSLDKKKTEDTKYLK---LIFS---LAGIMVLLLQLIS-IVNTIP 257
                 4555555.55666.3333333334333333...4444...2222334455444.333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1036  (0.0577835); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1725.07
//
Query:       EPA04319.1  [L=86]
Description: hypothetical protein BG20_I1940 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0036   17.5   0.1     0.0041   17.3   0.1    1.1  1  EamA      EamA-like transporter family


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   2.3e-07    0.0041       2      49 ..      17      68 ..      16      84 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.3e-07
        EamA  2 lgillallaalfwaiyfvlskil....lrkvspltltfvrfliagillliia 49
                +g++lal++a++ +++ v+ k l    +++vsp+tl+fv +++ g+++  ++
  EPA04319.1 17 IGYVLALASAVLASLMHVVPKELldngINDVSPITLAFVIYIVNGLFFTSVS 68
                79********************966666677**************9996554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 579.35
//
Query:       EPA04320.1  [L=133]
Description: hypothetical protein BG20_I1943 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 848.33
//
Query:       EPA04321.1  [L=146]
Description: hypothetical protein BG20_I1946 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.067   13.8   0.0        0.1   13.1   0.0    1.4  1  Sar8_2    Sar8.2 family
        0.2   12.0   0.0       0.31   11.4   0.0    1.3  1  DciA      Dna[CI] antecedent, DciA


Domain annotation for each model (and alignments):
>> Sar8_2  Sar8.2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.2e-05       0.1      13      46 ..      13      46 ..       2      66 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.2e-05
      Sar8_2 13 lailllvissqadaremskaaapitqamnsnnis 46
                +ail++ ++s + a e s aa pi  +m s+  +
  EPA04321.1 13 FAILVIAVTSGIFAEEFSFAAKPILDDMSSEFFT 46
                69***************************98776 PP

>> DciA  Dna[CI] antecedent, DciA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   3.5e-05      0.31      50      85 ..      15      50 ..       5      57 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.5e-05
        DciA 50 tLvvevesgawateLryqkpqllerlneelgeeavr 85
                 Lv++v+sg  a e +++++ +l+ +++e+  + v+
  EPA04321.1 15 ILVIAVTSGIFAEEFSFAAKPILDDMSSEFFTPTVG 50
                59************************9999776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 865.43
//
Query:       EPA04322.1  [L=138]
Description: hypothetical protein BG20_I1947 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.032   14.5   0.3      0.045   14.0   0.3    1.2  1  DUF4352    Domain of unknown function (DUF4352)
      0.073   12.2   0.2       0.08   12.1   0.2    1.1  1  Tmemb_cc2  Predicted transmembrane and coiled-coil 2 protein


Domain annotation for each model (and alignments):
>> DUF4352  Domain of unknown function (DUF4352)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.3     5e-06     0.045      29     111 ..      52     128 ..      29     134 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5e-06
                 -CEETT-.SEEEEEEEEEEE-SSS-EEEEGGGEEEEETTEEE-BEEESCCCCTTB--EEEE-TT-EEEEEEEEEESTT-CGEE CS
     DUF4352  29 eylqpdaggeflivdvtvkNkgkealtvnssqfkLkdgdgkeydadlsasskaddlflgtlnpGkkvtGklvFdvpkgkkkle 111
                 + l+  +g     ++vtvkN++  + t+   +  ++++    +d+++s+ ++ +     ++++ ++ + +++F +p+ + +l+
  EPA04322.1  52 TVLN-TSGVNAISATVTVKNIDTISHTYRICM--IVKAGALISDTSGSGADCSN---TASISASNTGSTTITFAIPRTTNNLS 128
                 4443.366777889**************6554..455677999*****999997...59******************999765 PP

>> Tmemb_cc2  Predicted transmembrane and coiled-coil 2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   8.9e-06      0.08     139     201 ..      32     114 ..      22     137 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.9e-06
   Tmemb_cc2 139 nkfGSADninslksseees...eeesgskslssstallvsks....................kytsddesssssvesssadsnsns 201
                 nk+GSADni+ +k + + +    ++sg +++s +   ++ k+                    + ts   +++s+++s+sa++++++
  EPA04322.1  32 NKIGSADNIAVSKPTVDVTntvLNTSGVNAISAT---VTVKNidtishtyricmivkagaliSDTSGSGADCSNTASISASNTGST 114
                 9************777777333444444444444...3333334466677777777777666455555555555556666555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       753  (0.041999); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.55
# Mc/sec: 757.67
//
Query:       EPA04323.1  [L=230]
Description: DSBA-like thioredoxin domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-34  119.0   0.0    2.8e-34  118.7   0.0    1.1  1  Thioredoxin_4  Thioredoxin
    2.4e-12   47.0   0.1    4.7e-11   42.8   0.1    2.1  1  DSBA           DSBA-like thioredoxin domain
      7e-09   36.1   0.0      1e-08   35.6   0.0    1.2  1  Thioredoxin_2  Thioredoxin-like domain
      0.009   15.7   0.0      0.014   15.0   0.0    1.3  1  Thioredoxin_5  Thioredoxin
  ------ inclusion threshold ------
       0.03   14.6   0.1        8.3    6.8   0.0    2.4  2  Thioredoxin_8  Thioredoxin-like
       0.17   11.1   0.0       0.17   11.1   0.0    1.1  1  Voltage_CLC    Voltage gated chloride channel


Domain annotation for each model (and alignments):
>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.7   0.0   9.5e-38   2.8e-34       2     166 .]      53     227 ..      52     227 .. 0.91

  Alignments for each domain:
  == domain 1  score: 118.7 bits;  conditional E-value: 9.5e-38
                    SSSSEEES-TT-SEEEEEEE-TT-HHHHHHHHHHH.HHHHHHHHTTSEEEEEEE-..---STTTHHHHHHHTT--TTHHHHHHHHHHHHTHHHHTT CS
  Thioredoxin_4   2 tetdiviGnpdApvtvieyedlrCphCakfeeeve.klleeyidtGkvkfiirdfpldkekeslkaamaarcageespeaflaikallysqqeewa 96 
                    t++++v+G+++Ap+t+ie+ d++Cp C k++++++  + ++yi+tGkvk+i+ dfp+ +   s++a   + ca e++   ++ ++++ly++q + +
     EPA04323.1  53 TKGSPVLGESSAPITIIEFGDYQCPFCQKWNQNTKpLIDRDYISTGKVKLIYVDFPIVGPD-SINAHAGSYCADEQG--LYWQYHDFLYKNQGHEN 145
                    67899******************************56889******************998.**************9..****************9 PP

                    S-...HHHHH..........HHHHHTS-------HHHHHHHHHHHHHHT--SS-EEEE...TTEE..E-TT--HHHHHHHHT- CS
  Thioredoxin_4  97 es...lkelaae.....aldkdekfeacleeekldalveaeskeakkagiestPtfii...ngek..veepqtyeelkalida 166
                         +++l+ +     ++++   f++c++++k+ + v+++++ a k+g +stP+fi+   ng+   ++++q+y+ +k+ id+
     EPA04323.1 146 SGwvsMNNLK-NivsgmEGMDVNLFSNCIDSGKYNDRVKENKNIAVKNGAKSTPSFIVigpNGHGvaISGAQPYSVFKQTIDE 227
                    9976633333.2455569999999**********************************9**88874579************95 PP

>> DSBA  DSBA-like thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.8   0.1   1.6e-14   4.7e-11       1     192 [.      67     225 ..      67     226 .. 0.88

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 1.6e-14
                 EEEEEEBTTBHHHHHHHHHHHHHHHHC....CTEEEEEEE-SSSCHHHHCT.S.GGGSHHHHHHHHHHHHHHHHHHT....GGSSHHHHHHHHHHHHHH CS
        DSBA   1 tvdeffDvlCPyCylgkerleklaars....pdvkvvlrpfelagakkasgnvgpselpeklkylledlkrlaeaegiplrfpkdklknstraarllla 95 
                 t++ef D++CP+C   +++ + l+ r+     +vk+ + +f++ g                                           +s +a++  + 
  EPA04323.1  67 TIIEFGDYQCPFCQKWNQNTKPLIDRDyistGKVKLIYVDFPIVGP------------------------------------------DSINAHAGSYC 123
                 799**********************999**777*************..........................................*********** PP

                 HHHHHGHHHHHHHHHHHHHTSSS-TSSHHHHHHHHH.HTTS.HHHHHHHHTSHHHHHHHHHHHHHHHHTT-SSSSEEEE...TTC.EEEESSSSHHHHH CS
        DSBA  96 agaeglaekvvrelfealwsegqaitddqellevae.kaGldaeeldealeseavkeavrentaaaqslgvtGvPtvvv...dgk.rmvfGadrldtla 189
                 a ++gl+ ++   l++    e+    + ++l+ +++   G+d++ +   ++s+++++ v+en + a++ g+  +P ++v   +g+ ++++Ga+++  ++
  EPA04323.1 124 ADEQGLYWQYHDFLYKNQGHENSGWVSMNNLKNIVSgMEGMDVNLFSNCIDSGKYNDRVKENKNIAVKNGAKSTPSFIVigpNGHgVAISGAQPYSVFK 222
                 ****97666666666655555555555566888876256****************************************99877789*********999 PP

                 HHH CS
        DSBA 190 dal 192
                 + +
  EPA04323.1 223 QTI 225
                 877 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.0   3.5e-12     1e-08       8     107 ..      67     223 ..      61     225 .. 0.92

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 3.5e-12
  Thioredoxin_2   8 vlvvftdpdCpyCkklkkelkel........ddvtvrvllfp.lkpsfepkavaiwcakekkkafkd............................. 65 
                    +++ f d +Cp+C+k ++++k+l         +v+ ++++fp ++p++  +++  +ca+e+   ++                              
     EPA04323.1  67 TIIEFGDYQCPFCQKWNQNTKPLidrdyistGKVKLIYVDFPiVGPDSINAHAGSYCADEQGLYWQYhdflyknqghensgwvsmnnlknivsgme 162
                    78889************************9999*****************************9999999999************************ PP

  Thioredoxin_2  66 ...................ieenvelarkygvrgtPtivfldgk.eivarlpGyvpaeelea 107
                                       ++en+  a k g ++tP+++++ ++   v  + G+ p   +++
     EPA04323.1 163 gmdvnlfsncidsgkyndrVKENKNIAVKNGAKSTPSFIVIGPNgHGV-AISGAQPYSVFKQ 223
                    *************************************99988885444.6699988777766 PP

>> Thioredoxin_5  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   4.8e-06     0.014     114     186 .]     152     223 ..     135     223 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.8e-06
  Thioredoxin_5 114 ellleiaeka.glDveefkeDlesklakkafqcDlklakemgvtevPtlvffneneeeeglkveglksyevyee 186
                    + l++i++ + g+Dv+ f + + s   ++  ++  ++a   g +++P++++     +++g+ ++g ++y+v+++
     EPA04323.1 152 NNLKNIVSGMeGMDVNLFSNCIDSGKYNDRVKENKNIAVKNGAKSTPSFIVIG--PNGHGVAISGAQPYSVFKQ 223
                    5566666655499***************************************9..999************9986 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0    0.0028       8.3       3      42 ..      66     106 ..      65     142 .. 0.85
   2 ?    5.6   0.1    0.0068        20      69      93 ..     183     207 ..     152     208 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0028
                    EEEEEE--SSSHHHHHHHHHHHHHHHHHHH.TTSEEEEEEE CS
  Thioredoxin_8   3 vvlLyfgaswcppckaftpklkelyeklkk.kkkveivyvs 42 
                    ++++ fg+++cp c++ +++ k l ++      kv+++yv 
     EPA04323.1  66 ITIIEFGDYQCPFCQKWNQNTKPLIDRDYIsTGKVKLIYVD 106
                    68899***************998754443348999999997 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0068
                    T-HHHHTT-S--TT-SEEEEE-TT- CS
  Thioredoxin_8  69 kkrnklkkkynvkaiPtlvvldkng 93 
                    k+++ ++ k + k+ P+++v+++ng
     EPA04323.1 183 KENKNIAVKNGAKSTPSFIVIGPNG 207
                    45777888889999**********9 PP

>> Voltage_CLC  Voltage gated chloride channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   5.7e-05      0.17     164     221 ..      17      77 ..       4     171 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.7e-05
                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHH.CHHHH.HHH.HHHHHHHHHHHHCCCSC CS
  Voltage_CLC 164 lilfvllGilgGllgalfvrlllkverlfrkle.klkik.krl.epalvgllvgllglllp 221
                     f+++G++++++ga+ + +++++e++ +kl   + +  ++l e  + ++++ +  +  p
   EPA04323.1  17 TTKFIIIGVIIAIAGAVLISTNYNSESQSNKLSiDTTKGsPVLgESSAPITIIEFGDYQCP 77 
                  5679**************************9976554445777777666666665555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       781  (0.0435607); expected 358.6 (0.02)
Passed bias filter:                      610  (0.0340231); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1414.01
//
Query:       EPA04324.1  [L=144]
Description: hypothetical protein BG20_I1944 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 957.32
//
Query:       EPA04325.1  [L=136]
Description: translation initiation factor eIF-5A [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-07   30.4   0.8    4.3e-07   29.9   0.8    1.2  1  eIF-5a    Eukaryotic elongation factor 5A hypusine, DNA-bindi
    5.8e-05   23.0   0.1     0.0089   16.0   0.0    2.3  2  EFP_N     Elongation factor P (EF-P) KOW-like domain


Domain annotation for each model (and alignments):
>> eIF-5a  Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.8   4.8e-11   4.3e-07       2      69 .]      75     135 ..      74     135 .. 0.89

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 4.8e-11
                 -EEEEEEEEEE-SS.EEEEEE.TT--EEE.EEGG..GB-HHHHTT--TT-E..EEEEEETTEEEEEEE- CS
      eIF-5a   2 VkrkeyqLidIqdDgflsLmd.ddgetkeDlklpegelgkqikekfeegkdvlVtVlsamGeekiiavK 69 
                 +++++ q+i+I ++ ++++md ++ et + +      ++++i++   +g++  V+++++mG+ ki+++K
  EPA04325.1  75 IDKRTGQVISIIGE-TIQIMDsETFETID-VT----LIDEEINGTVANGQN--VEYWNVMGRIKIMRIK 135
                 89**********99.*****966667755.55....5699***********..**************98 PP

>> EFP_N  Elongation factor P (EF-P) KOW-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0     1e-06    0.0089      14      33 ..      25      44 ..      23      48 .. 0.94
   2 !    4.7   0.0    0.0035        31       6      24 ..      78      96 ..      75     100 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1e-06
                TTEEEEEEEEEEEEETTS-- CS
       EFP_N 14 dgklyvVlefehvkpGkGqa 33
                dg++++++e++ +kpGk +a
  EPA04325.1 25 DGEPCRIVEYDTSKPGKHGA 44
                9****************998 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0035
                -TT-EEEETTEEEEEEEEE CS
       EFP_N  6 kkGlvieidgklyvVlefe 24
                ++G+vi i g+++++++ e
  EPA04325.1 78 RTGQVISIIGETIQIMDSE 96
                89**************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.31s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 874.22
//
Query:       EPA04326.1  [L=271]
Description: hypothetical protein BG20_I1395 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-08   33.6   1.0      0.078   13.4   0.0    4.3  4  CBS       CBS domain
  ------ inclusion threshold ------
      0.056   13.1   0.1       0.55    9.9   0.0    2.2  2  DHFR_1    Dihydrofolate reductase
       0.11   12.5   0.1       0.28   11.1   0.1    1.7  1  DUF5049   Domain of unknown function (DUF5049)


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.0    0.0021        13      30      52 ..      45      67 ..      15      72 .. 0.65
   2 !    8.3   0.0   0.00051         3       1      29 [.      84     112 ..      84     122 .. 0.79
   3 !   13.4   0.0   1.3e-05     0.078       2      36 ..     147     180 ..     142     187 .. 0.88
   4 ?    0.6   0.0      0.13     8e+02      11      33 ..     224     245 ..     213     263 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0021
                SSEEEEEETTTBEEEEEEHHHHH CS
         CBS 30 vsrlPVVdedgklvGivtlrDll 52
                 ++l V+++d+k++G++  + ++
  EPA04326.1 45 TDSLVVTEKDEKPIGVIGGKEII 67
                46895559899*****9666665 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00051
                 HHHHSBSSCEEEETTSBHHHHHHHHHHHT CS
         CBS   1 Vgdimtrdvvtvppdttleealelmrekg 29 
                 V+++  +++v +++dt l e+le+ +e++
  EPA04326.1  84 VEEVVDKNLVILSEDTKLVELLEKWKETR 112
                 789999*****************985533 PP

  == domain 3  score: 13.4 bits;  conditional E-value: 1.3e-05
                 HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEE CS
         CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVV 36 
                 ++++ ++ +t++ ++t+++++ lm +++ + l V+
  EPA04326.1 147 SELPKKETITFSRNDTIKDIISLMLQNNTRKL-VL 180
                 68899999****************99999999.87 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 0.13
                 EEETTSBHHHHHHHHHHHT.SSEE CS
         CBS  11 tvppdttleealelmrekg.vsrl 33 
                  v+ d +l+e+ ++m  +g v+ +
  EPA04326.1 224 KVSKDVNLSEISKIM--YGmVHPY 245
                 677788888888888..7766644 PP

>> DHFR_1  Dihydrofolate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   9.2e-05      0.55      54     108 ..      13      72 ..       5     122 .. 0.62
   2 ?    0.9   0.0     0.053   3.2e+02      38      71 ..     132     165 ..     115     194 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 9.2e-05
                 --TTCEEEEE-S-TT---..TTEEEESSHHHHCC...CCTTS.SEEEEEE-HHHHHHCGG CS
      DHFR_1  54 pLpnrkniVltrnedlkv..egvevvssleeala...lakeekeevfviGGaeiYkqalp 108
                 pL  r++  ++ +++ k+  + + +++ le++++   +++++++ + viGG+ei  ++++
  EPA04326.1  13 PLSLRTTPAVSIRKENKMwtATCMLMHYLESFTDslvVTEKDEKPIGVIGGKEIITNIFE 72 
                 78888888888666655543467777777777743314444478999*****99776653 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.053
                 CEEEEEHHHHHCC-.S--TTCEEEEE-S-TT--- CS
      DHFR_1  38 kpvimGrkTfeslgkrpLpnrkniVltrnedlkv 71 
                 k + +G +    l    Lp++++i  +rn+++k 
  EPA04326.1 132 KLLEIGANCVTDLTISELPKKETITFSRNDTIKD 165
                 55556666666677779***********988653 PP

>> DUF5049  Domain of unknown function (DUF5049)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   4.6e-05      0.28      17      47 ..     182     214 ..     180     219 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.6e-05
     DUF5049  17 ltNMf..dvaaVqriAeergfyeLvvyleehkk 47 
                 +tNMf  d  ++q+iA++ +f+  v +l++  +
  EPA04326.1 182 NTNMFisDRLIIQSIAQKFDFFRNVKFLDQRVA 214
                 59***888999*****************97655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1672.09
//
Query:       EPA04327.1  [L=90]
Description: hypothetical protein BG20_I1412, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-11   45.5   0.0    1.1e-11   45.5   0.0    1.1  1  ABC_tran        ABC transporter
    0.00012   21.8   0.1    0.00017   21.3   0.1    1.4  1  AAA_29          P-loop containing region of AAA domain
    0.00071   19.8   0.0    0.00082   19.5   0.0    1.1  1  AAA_33          AAA domain
     0.0024   17.5   0.0     0.0024   17.5   0.0    1.1  1  AAA_25          AAA domain
     0.0027   17.4   0.0     0.0034   17.0   0.0    1.1  1  AAA_27          AAA domain
     0.0036   16.8   0.1     0.0045   16.5   0.1    1.1  1  SMC_N           RecF/RecN/SMC N terminal domain
     0.0045   16.8   0.0     0.0047   16.8   0.0    1.1  1  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
     0.0084   16.6   0.2      0.011   16.3   0.2    1.2  1  AAA_23          AAA domain
  ------ inclusion threshold ------
      0.015   15.0   0.0      0.016   14.9   0.0    1.1  1  AAA_24          AAA domain
      0.021   14.7   0.0      0.024   14.6   0.0    1.1  1  RsgA_GTPase     RsgA GTPase
      0.029   14.9   0.0      0.039   14.5   0.0    1.2  1  AAA_18          AAA domain
      0.041   13.9   0.0      0.052   13.6   0.0    1.2  1  AAA_14          AAA domain
      0.043   14.2   0.0      0.043   14.2   0.0    1.1  1  AAA_16          AAA ATPase domain
      0.047   13.9   0.0      0.051   13.8   0.0    1.1  1  AAA_28          AAA domain
      0.053   13.4   0.0      0.063   13.2   0.0    1.1  1  ATPase_2        ATPase domain predominantly from Archaea
      0.054   13.8   0.0      0.061   13.6   0.0    1.2  1  AAA_22          AAA domain
      0.064   13.7   0.0      0.081   13.3   0.0    1.2  1  RNA_helicase    RNA helicase
      0.069   12.2   0.0      0.075   12.1   0.0    1.2  1  T2SSE           Type II/IV secretion system protein
      0.073   13.5   0.0      0.097   13.1   0.0    1.2  1  AAA_17          AAA domain
      0.093   12.4   0.0       0.13   12.0   0.0    1.2  1  Cytidylate_kin  Cytidylate kinase
      0.098   11.6   0.0       0.11   11.5   0.0    1.1  1  MeaB            Methylmalonyl Co-A mutase-associated GTPase M
       0.15   11.8   0.0       0.15   11.8   0.0    1.1  1  AAA_15          AAA ATPase domain
       0.19   10.9   0.1        0.2   10.8   0.1    1.1  1  NB-ARC          NB-ARC domain
       0.19   11.7   0.0       0.23   11.3   0.0    1.2  1  NACHT           NACHT domain
       0.24   10.1   0.1       0.27   10.0   0.1    1.0  1  ABC_ATPase      Predicted ATPase of the ABC class
       0.29    9.7   0.0       0.29    9.7   0.0    1.0  1  AAA_13          AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   0.0   1.5e-14   1.1e-11       1      58 [.      19      79 ..      19      90 .] 0.84

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 1.5e-14
                EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--..SEEEEEETTCEGGG.B-HHHCC CS
                xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx.xxxxxxx RF
    ABC_tran  1 lknvslklkegekvaivGenGaGKStLlkllagllkp..teGeilldgkdlke.qeleslr 58
                lk v+lk  +ge++ai+G+nG+GKStL+ +l+ + k   t+G+illdg+++ +    e+++
  EPA04327.1 19 LKGVNLKTGPGEVHAIMGPNGSGKSTLAYTLLAHPKYevTQGDILLDGESILDlSADERAK 79
                799****************************99866666***********99964444444 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.1   2.5e-07   0.00017      16      46 ..      23      51 ..      14      61 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2.5e-07
      AAA_29 16 tieidlkgatlltGpsGsGKSTllDAiqalL 46
                 ++  + +++ ++Gp+GsGKSTl  A++ l 
  EPA04327.1 23 NLKTGPGEVHAIMGPNGSGKSTL--AYTLLA 51
                5566666799************9..455555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   1.2e-06   0.00082       3      34 ..      33      64 ..      31      81 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.2e-06
      AAA_33  3 llvGlpGsGKstlaerllkklgavllssdtlr 34
                 + G++GsGKstla  ll++ ++++   d+l+
  EPA04327.1 33 AIMGPNGSGKSTLAYTLLAHPKYEVTQGDILL 64
                678***************99999999888876 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   3.5e-06    0.0024      32      56 ..      28      52 ..       5      79 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.5e-06
      AAA_25 32 agelallaGapgtGKttlaldlala 56
                 ge+++++G+ g+GK+tla+ l ++
  EPA04327.1 28 PGEVHAIMGPNGSGKSTLAYTLLAH 52
                599*****************99886 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0     5e-06    0.0034       3      44 ..       6      47 ..       4      52 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5e-06
      AAA_27  3 lerLdLeryGkftdrsldfsaeeadlhliyGpNEAGKstalr 44
                ++ L+++r Gk   + ++++++  ++h i+GpN +GKst+  
  EPA04327.1  6 IRDLHVKREGKEILKGVNLKTGPGEVHAIMGPNGSGKSTLAY 47
                7788888888888899999999*****************865 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   6.5e-06    0.0045      25      43 ..      30      48 ..      15      52 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.5e-06
                SEEEEEESTTSSHHHHHHH CS
                xxxxxxxxxxxxxxxxxxx RF
       SMC_N 25 sftaivGpNGSGKsnlldA 43
                ++ ai+GpNGSGKs l   
  EPA04327.1 30 EVHAIMGPNGSGKSTLAYT 48
                5789**********99765 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   6.8e-06    0.0047       2      19 ..      32      49 ..      31      80 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 6.8e-06
      AAA_21  2 nvliGpNgsGKSnLLdal 19
                 ++ GpNgsGKS+L ++l
  EPA04327.1 32 HAIMGPNGSGKSTLAYTL 49
                6899**********9999 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.2   1.6e-05     0.011      21      36 ..      31      46 ..      14      50 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.6e-05
      AAA_23 21 ltlItGpNGaGKTTil 36
                + +I GpNG+GK+T+ 
  EPA04327.1 31 VHAIMGPNGSGKSTLA 46
                668***********95 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   2.3e-05     0.016       6      23 ..      33      52 ..      29      76 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.3e-05
      AAA_24  6 liyGpsgiGKTtlakel..g 23
                +i+Gp+g+GK+tla++l   
  EPA04327.1 33 AIMGPNGSGKSTLAYTLlaH 52
                79**************9542 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   3.5e-05     0.024      99     127 ..      29      57 ..       4      64 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.5e-05
                  TSEEEEECSTTSSHHHHHHHHCTT----- CS
  RsgA_GTPase  99 dktsvlvGqSGvGKStLinallpelelkt 127
                  +++ +++G+ G GKStL  +ll + + ++
   EPA04327.1  29 GEVHAIMGPNGSGKSTLAYTLLAHPKYEV 57 
                  4899**************99998776665 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   5.7e-05     0.039       3      44 ..      34      75 ..      33      82 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.7e-05
      AAA_18  3 ltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpe 44
                ++G+ G+GK+tla  L  + ++ v  +d++ ++++ l+  ++
  EPA04327.1 34 IMGPNGSGKSTLAYTLLAHPKYEVTQGDILLDGESILDLSAD 75
                89*************988778888888888877776666555 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   7.5e-05     0.052       3      40 ..      30      76 ..      28      86 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.5e-05
      AAA_14  3 kilvitGaRrvGKTtllkqlikell.........vkkesilyinldd 40
                ++ +i+G+  +GK+tl+++l+ +            + esil ++ d+
  EPA04327.1 30 EVHAIMGPNGSGKSTLAYTLLAHPKyevtqgdilLDGESILDLSADE 76
                5779***************9877666755555555555555555555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   6.3e-05     0.043      22      49 ..      27      54 ..       7      79 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.3e-05
      AAA_16 22 grpelvllsGesGvGKsslvrellrale 49
                g +e+  + G+ G+GKs+l+ +ll + +
  EPA04327.1 27 GPGEVHAIMGPNGSGKSTLAYTLLAHPK 54
                33378889************88887655 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   7.3e-05     0.051       3      26 ..      33      57 ..      31      81 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.3e-05
      AAA_28  3 vitGgestGKTtlleaLaar.gypv 26
                +i+G+ ++GK+tl+  L a+ +y+v
  EPA04327.1 33 AIMGPNGSGKSTLAYTLLAHpKYEV 57
                89**************999988876 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   9.2e-05     0.063      15      39 ..      24      48 ..      12      58 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.2e-05
    ATPase_2 15 lerepneiyfiYGpegsGKtaLlke 39
                l+++p e+  i Gp gsGK++L   
  EPA04327.1 24 LKTGPGEVHAIMGPNGSGKSTLAYT 48
                67899****************9765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   8.8e-05     0.061       9      29 ..      33      53 ..      26      80 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.8e-05
      AAA_22  9 vvtGesGtGKTtllrrlleql 29
                +++G+ G+GK+tl+ +ll   
  EPA04327.1 33 AIMGPNGSGKSTLAYTLLAHP 53
                79************9998765 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   0.00012     0.081       3      20 ..      34      51 ..      32      67 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00012
  RNA_helicase  3 lyGpsgeGKStlakeLak 20
                  + Gp+g GKStla++L +
    EPA04327.1 34 IMGPNGSGKSTLAYTLLA 51
                  79*************765 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00011     0.075     134     152 ..      34      52 ..       2      63 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00011
       T2SSE 134 vsGgTgsGKttllyallke 152
                 + G+ gsGK+tl+y+ll+ 
  EPA04327.1  34 IMGPNGSGKSTLAYTLLAH 52 
                 67*************9975 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00014     0.097       1      31 [.      35      64 ..      35      81 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00014
                EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHH CS
      AAA_17  1 lGgPGsGKgtqceklvekygfthlsaGdllr 31
                +G+ GsGK+t++ +l  + ++++ + Gd+l 
  EPA04327.1 35 MGPNGSGKSTLAYTLLAHPKYEVTQ-GDILL 64
                599*******************998.99987 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00018      0.13       2      23 ..      33      54 ..      32      63 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00018
                    EEE-STTSSHHHHHHHHHHHHT CS
  Cytidylate_kin  2 aiDGPagsGKssvaralaeklg 23
                    ai GP gsGKs++a +l  + +
      EPA04327.1 33 AIMGPNGSGKSTLAYTLLAHPK 54
                    799***********99866555 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00015      0.11      14      50 ..      14      50 ..       2      65 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00015
                HHHHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHH CS
        MeaB 14 eakellerllakaGraqvvGltGvPGaGkstlvealg 50
                e ke+l+ +  k+G  +v  + G  G+Gkstl   l 
  EPA04327.1 14 EGKEILKGVNLKTGPGEVHAIMGPNGSGKSTLAYTLL 50
                789****************************987765 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00021      0.15      25      43 ..      31      49 ..      19      88 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00021
      AAA_15 25 ltvliGkNnsGKSsileal 43
                +  + G+N+sGKS++++ l
  EPA04327.1 31 VHAIMGPNGSGKSTLAYTL 49
                66899**********9988 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00029       0.2      17      43 ..      27      52 ..      12      61 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00029
                TSCSEEEEEEESTTSSHHHHHHHHCCS CS
      NB-ARC 17 elqslvvalvGmgGvGKttlakqilnk 43
                +++  v a++G  G+GK+tla   l +
  EPA04327.1 27 GPG-EVHAIMGPNGSGKSTLAYTLLAH 52
                555.5779************9887765 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00034      0.23       3      21 ..      32      50 ..      30      62 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00034
                EEEEC-TTTCHHHHHHHHH CS
       NACHT  3 vilqGeaGsGKTtLlqkla 21
                 ++ G++GsGK+tL+  l 
  EPA04327.1 32 HAIMGPNGSGKSTLAYTLL 50
                5799**********98775 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00039      0.27     232     264 ..      14      49 ..       4      62 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00039
                 TTTEEEEEEEE-SS...EEEEEE-TTSSHHHHHHHH CS
  ABC_ATPase 232 pngkkvsGmgipkG...vtlIvGggfhGKsTLLeAl 264
                   ++ ++G+ +++G   v +I+G++  GKsTL   l
  EPA04327.1  14 EGKEILKGVNLKTGpgeVHAIMGPNGSGKSTLAYTL 49 
                 34556799999998889***************8765 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00042      0.29      17      37 ..      30      50 ..      19      74 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00042
      AAA_13 17 riNliYGwNGaGKTtLSrllr 37
                ++  i G NG+GK+tL+  l 
  EPA04327.1 30 EVHAIMGPNGSGKSTLAYTLL 50
                556799**********97664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 584.34
//
Query:       EPA04328.1  [L=58]
Description: hypothetical protein BG20_I1392, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.056   13.0   2.8      0.058   13.0   2.8    1.0  1  APG5      Autophagy protein Apg5
      0.065   13.5   3.0      0.091   13.1   3.0    1.3  1  FCH       Fes/CIP4, and EFC/F-BAR homology domain


Domain annotation for each model (and alignments):
>> APG5  Autophagy protein Apg5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   2.8   6.5e-06     0.058      55     111 ..       3      57 ..       1      58 [] 0.89

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.5e-06
        APG5  55 geeslkdsfinslKeAdfirngsakkvmnLskedqeqLWqsvknhdldkfwsinskl 111
                 +++s+++ f  slK+A+  ++ +  k  +  k+++e+L++s +++++ ++ +i++kl
  EPA04328.1   3 QVNSIHKKFADSLKKAKTRQSLN--KAYSTHKKEHEKLLKSHLAEEMRQIKKIKAKL 57 
                 67899************855555..77899************************998 PP

>> FCH  Fes/CIP4, and EFC/F-BAR homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   3.0     1e-05     0.091      37      76 ..       4      43 ..       1      44 [. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1e-05
                HHHHCT----TT-.....HHHHHHHHHHHHHHHHHHHHHH CS
         FCH 37 LqkLakkylkrrkkkseestlvtawtvlleeteklaqshl 76
                 + + kk++++ kk + +++l++a+++ ++e+ekl +shl
  EPA04328.1  4 VNSIHKKFADSLKKAKTRQSLNKAYSTHKKEHEKLLKSHL 43
                578899***976444599*********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2562  (0.142897); expected 358.6 (0.02)
Passed bias filter:                      697  (0.0388756); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 371.84
//
Query:       EPA04329.1  [L=511]
Description: hypothetical protein BG20_I1402 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (511 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.68u 0.29s 00:00:00.97 Elapsed: 00:00:00.51
# Mc/sec: 3012.44
//
Query:       EPA04330.1  [L=63]
Description: cold-shock DNA-binding domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-21   75.6   3.4    2.5e-21   75.3   3.4    1.1  1  CSD       'Cold-shock' DNA-binding domain
    2.2e-06   27.3   0.7    2.2e-06   27.2   0.7    1.1  1  OB_RNB    Ribonuclease B OB domain


Domain annotation for each model (and alignments):
>> CSD  'Cold-shock' DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.3   3.4   2.8e-25   2.5e-21       2      65 ..       3      61 ..       2      62 .. 0.96

  Alignments for each domain:
  == domain 1  score: 75.3 bits;  conditional E-value: 2.8e-25
                EEEEEEEETTTTEEEEEETTSS-EEEEETTTS-STT.TS--STSEEEEEEEECSSCEEEEEEEE CS
         CSD  2 tGtVkwfnakkgfGFItredgdkdvFvHvsaiqgdgfrsLqegqeVeFevvegkkgpeAanVtk 65
                +GtVkwfn+ kgfGFI+re+gd d+FvH s++ g      +eg++VeFev +g+kgp A++V+k
  EPA04330.1  3 QGTVKWFNRTKGFGFIERESGD-DLFVHKSDVDGFI----NEGDKVEFEVGQGQKGPAAQKVKK 61
                8*********************.********98877....**********************87 PP

>> OB_RNB  Ribonuclease B OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.7   2.5e-10   2.2e-06       7      47 ..      12      52 ..       4      61 .. 0.86

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 2.5e-10
                SSS-EEEEECT.TEEEEE-HHHHTTS-T.T-EEEEEEEESSS CS
      OB_RNB  7 kkGFGFlipdegkeDifippeqmkkamh.GDrVlvritkgdr 47
                 kGFGF++ ++ ++D+f++++++ + ++ GD+V+ ++ +g++
  EPA04330.1 12 TKGFGFIERES-GDDLFVHKSDVDGFINeGDKVEFEVGQGQK 52
                59********8.***************889****99977554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 407.20
//
Query:       EPA04331.1  [L=69]
Description: hypothetical protein BG20_I1410 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-05   23.6   0.0    3.9e-05   23.5   0.0    1.1  1  Gar1      Gar1/Naf1 RNA binding region
  ------ inclusion threshold ------
      0.099   13.0   0.0       0.11   13.0   0.0    1.1  1  DUF782    Circovirus protein of unknown function (DUF782)


Domain annotation for each model (and alignments):
>> Gar1  Gar1/Naf1 RNA binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   4.4e-09   3.9e-05      47      98 ..       5      52 ..       2      67 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 4.4e-09
                -BTT-EEEETT--EEEE--EEES-SSS-EEEEE--GGHHHHHHHTTTTSEEE CS
        Gar1 47 ldfnsilflenktqiGkVdEifGpvnepyysVklnsseeikaksfkvgdkvy 98
                l +++il++e +t++ kV E +Gp++ p+ s  +  +++ik+    +g+ v+
  EPA04331.1  5 LAEGQILCDETGTKVAKVMELIGPIKRPFASATPL-TNNIKK---YIGKSVF 52
                6799*************************998777.556665...4555555 PP

>> DUF782  Circovirus protein of unknown function (DUF782)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.2e-05      0.11      21      58 ..      28      66 ..      15      69 .] 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.2e-05
      DUF782 21 kisspfafatprwphndvyirlpi.tllhfpahfqkfsq 58
                 i  pfa atp       yi+  + t+ h pa  qkf +
  EPA04331.1 28 PIKRPFASATPLTNNIKKYIGKSVfTFDHSPANTQKFRR 66
                5889****************98764899*********75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 466.95
//
Query:       EPA04332.1  [L=103]
Description: translation initiation factor eIF-1A [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-19   68.2   1.7    5.3e-19   67.8   1.7    1.2  1  eIF-1a    Translation initiation factor 1A / IF-1
      0.009   15.8   1.2       0.57   10.1   0.1    2.5  2  Myosin_N  Myosin N-terminal SH3-like domain


Domain annotation for each model (and alignments):
>> eIF-1a  Translation initiation factor 1A / IF-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.8   1.7   5.9e-23   5.3e-19       2      64 .]      22      84 ..      21      84 .. 0.95

  Alignments for each domain:
  == domain 1  score: 67.8 bits;  conditional E-value: 5.9e-23
                EEEEEEEEEETTTEEEEEE.SSSSBEEEEE-HHHHCT----TT-EEEEEE-TT-TT.EEEEES- CS
      eIF-1a  2 evigkViealgnnlfrVelpdngkevlaeipgkfRnkiwikrGdyVlVelspydlt.kGrIvyr 64
                e  g+V+++lg+ ++ V+++d g+++ ++i+gk+++++wi+ +d+V++ ++++  + +G+Iv+r
  EPA04332.1 22 ELFGRVLKMLGGENVMVKCTD-GVTRRGRIRGKLKRRVWIRDNDIVIIAPWDFKENeRGDIVWR 84
                789****************96.*******************************9778*****98 PP

>> Myosin_N  Myosin N-terminal SH3-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.1   6.4e-05      0.57      22      36 ..      32      46 ..      18      47 .. 0.78
   2 !    4.4   0.2    0.0037        34       1       8 [.      55      62 ..      55      64 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 6.4e-05
                ESSEEEEEETTSEEE CS
    Myosin_N 22 eGdkvtVetedGktv 36
                 G++v V+++dG t+
  EPA04332.1 32 GGENVMVKCTDGVTR 46
                4677********998 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0037
                SEEEEETT CS
    Myosin_N  1 KklVWVpD 8 
                K++VW++D
  EPA04332.1 55 KRRVWIRD 62
                9*****99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.34s 00:00:00.86 Elapsed: 00:00:00.53
# Mc/sec: 580.70
//
Query:       EPA04333.1  [L=187]
Description: hypothetical protein BG20_I1400 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-10   41.5   0.3    3.5e-10   40.4   0.3    1.6  1  CxxCxxCC  Putative zinc- or iron-chelating domain


Domain annotation for each model (and alignments):
>> CxxCxxCC  Putative zinc- or iron-chelating domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   0.3   1.9e-14   3.5e-10       2      84 ..       5     129 ..       4     133 .. 0.88

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 1.9e-14
    CxxCxxCC   2 Cke.CgaCCkelkvklteedlerlkaaevaeeeeeskkiak...................................adgrCvfldeetk........lC 56 
                 C + C +CC  ++ + + +++ ++      ee+e  +++ak                                   +++ C+fld et          C
  EPA04333.1   5 CIQdCSQCCI-EREYYPTKKFGKIGVLILPEEKERIENLAKvnklkiiilprigvsekgesgpskilayqlmgiekNGNTCPFLDTETStksphggfPC 102
                 9888******.77788888888888888877777777777799999*****************************9999********9999*****99* PP

    CxxCxxCC  57 kiYeeRpkicrlfpasekeellaraetC 84 
                 kiY+eRp++c+++p   ++e  ++++ C
  EPA04333.1 103 KIYNERPLACMTYPLL-ESEPIKLDQKC 129
                 ***************5.67777777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1285.67
//
Query:       EPA04334.1  [L=216]
Description: hypothetical protein BG20_I1403 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      0.001   19.4   0.1     0.0025   18.1   0.1    1.6  2  fn3       Fibronectin type III domain
  ------ inclusion threshold ------
      0.077   12.6   0.1       0.15   11.7   0.1    1.6  1  DUF1411   Protein of unknown function (DUF1411)


Domain annotation for each model (and alignments):
>> fn3  Fibronectin type III domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   2.8e-07    0.0025       6      64 ..      51     110 ..      50     114 .. 0.83
   2 ?   -3.4   0.0       1.5   1.3e+04      41      72 ..     186     194 ..     173     198 .. 0.55

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.8e-07
                 EEEEEESSSEEEEEEE-CS.SSSSTEEEEEEEEEETTSTS.TEEEEEECSTSSEEEEESSS CS
         fn3   6 lsvsevtstsltvsWeppk.dgggpitgYeveyrekgsee.ewneftvprtttsvtltgLk 64 
                 +++++ + +sl + W++p+  +g+++ gYe++ +  +s   + + +++p+++ s+  ++L+
  EPA04334.1  51 VKITTHSKNSLKLDWQKPNsVQGQDLIGYEIQRKILNSDYvDLIKISNPKQA-SYIDSNLQ 110
                 788999***************************9998776666666677766.77777776 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.5
                 TSTSTEEEEEECSTSSEEEEESSSTTEEEEEE CS
         fn3  41 gseeewneftvprtttsvtltgLkpgteYevr 72 
                 +                        g++Y+++
  EPA04334.1 186 R-----------------------TGSDYQLK 194
                 3.......................34455544 PP

>> DUF1411  Protein of unknown function (DUF1411)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   1.6e-05      0.15      20      95 ..      11     110 ..       3     167 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.6e-05
     DUF1411  20 mlasvvvlsalsgnvla.................deaevskkpvekkkegglfsk....ewnead.ivkedkkkl..kalsdltktentektslsdisv 94 
                 m+asv+vls++ + v+a                  + e++ k + ++k++ ++ +      +  d i +e ++k+  +++ dl+k +n +++s  d  +
  EPA04334.1  11 MIASVLVLSSIGNFVFAqevtwksdyhvgilnadMNSEIPVKITTHSKNSLKLDWqkpnSVQGQDlIGYEIQRKIlnSDYVDLIKISNPKQASYIDSNL 109
                 9****************6666666665555555444555555555555555555533332222231334444454556667777777766666666555 PP

     DUF1411  95 k 95 
                 +
  EPA04334.1 110 Q 110
                 4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1475.46
//
Query:       EPA04335.1  [L=166]
Description: HTH domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.6e-10   38.2   2.0    4.4e-05   23.0   0.2    2.4  2  HTH_24           Winged helix-turn-helix DNA-binding
    1.9e-09   37.2   1.5    1.4e-08   34.4   0.9    2.5  2  HTH_AsnC-type    AsnC-type helix-turn-helix domain
    1.9e-07   30.9   0.9    2.9e-07   30.3   0.3    1.6  2  HTH_12           Ribonuclease R winged-helix domain
    1.4e-06   28.2   0.6    5.8e-06   26.1   0.6    2.1  1  HTH_11           HTH domain
    6.8e-05   23.2   0.3    0.00036   20.8   0.0    2.0  2  Penicillinase_R  Penicillinase repressor
    0.00013   22.1   1.5    0.00021   21.5   0.1    2.0  3  HTH_Tnp_Tc3_2    Transposase
    0.00017   21.6   0.0    0.00025   21.0   0.0    1.2  1  HTH_20           Helix-turn-helix domain
      0.003   17.3   0.1      0.011   15.5   0.1    2.0  1  HTH_DeoR         DeoR-like helix-turn-helix domain
  ------ inclusion threshold ------
      0.011   16.0   0.1      0.028   14.8   0.0    1.7  2  Myb_DNA-bind_4   Myb/SANT-like DNA-binding domain
      0.016   15.1   0.3      0.047   13.6   0.0    1.8  2  DUF3658          Protein of unknown function
      0.021   15.4   0.0       0.04   14.5   0.0    1.4  1  HTH_32           Homeodomain-like domain
      0.026   14.7   0.1      0.056   13.6   0.0    1.5  2  FUR              Ferric uptake regulator family
       0.04   13.7   0.3        0.1   12.4   0.3    1.7  1  Arg_repressor    Arginine repressor, DNA binding domain
      0.042   14.1   2.0      0.084   13.2   0.4    1.9  2  RNA_binding      RNA binding
      0.049   13.5   0.1       0.11   12.4   0.1    1.6  1  Nuc_N            Nuclease N terminal
      0.053   13.5   0.0       0.26   11.3   0.0    2.2  2  DUF3783          Domain of unknown function (DUF3783)
      0.067   13.2   2.4       0.23   11.4   0.1    2.2  2  HU-DNA_bdg       DNA-binding domain
       0.08   12.6   0.1       0.16   11.7   0.1    1.5  1  Sigma70_r4_2     Sigma-70, region 4
        9.5    6.8   8.3        4.8    7.8   1.0    2.9  3  PepSY_like       Putative beta-lactamase-inhibitor-like, PepS


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.2   4.6e-08   4.4e-05       1      30 [.       9      38 ..       9      40 .. 0.95
   2 !   14.6   0.1   1.9e-05     0.018      29      48 .]      42      61 ..      41      61 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 4.6e-08
      HTH_24  1 ldetdrkILelLqknprisqreLAerlglS 30
                ld+ d kI+e+L  n+r++ +e+A++l  S
  EPA04335.1  9 LDKVDQKIIEILNSNARTPSKEIADELKKS 38
                79************************9877 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 1.9e-05
      HTH_24 29 lSpstvnrrlkrLeeeGlIk 48
                +S  t+++r++rLe++G+Ik
  EPA04335.1 42 VSDRTIRKRIERLEKSGIIK 61
                6888***************8 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.9   1.5e-11   1.4e-08       1      42 []       9      55 ..       9      55 .. 0.85
   2 ?   -2.1   0.0       3.9   3.7e+03       9      21 ..     119     131 ..     117     132 .. 0.81

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 1.5e-11
  HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervG.....lSestvlrRvrrLe 42
                   LD++D+kI+e+L  +aR++ +e+A+++      +S  t+++R++rLe
     EPA04335.1  9 LDKVDQKIIEILNSNARTPSKEIADELKksghdVSDRTIRKRIERLE 55
                   8************************9963333377888888888887 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.9
  HTH_AsnC-type   9 LeaLqedaRisya 21 
                    L ++q d+  s++
     EPA04335.1 119 LVIIQIDSAKSNT 131
                    7789999998886 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.3   3.1e-10   2.9e-07       3      49 ..      16      61 ..      14      74 .. 0.86
   2 ?   -2.8   0.0         7   6.6e+03      24      24 ..     140     140 ..     124     152 .. 0.48

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 3.1e-10
      HTH_12  3 ILkilaesdkpigakeiaeeLkkrgydigeravRyrLrkleergltr 49
                I++il+ + +   +keia+eLkk g d+++r++R r+  le+ g+++
  EPA04335.1 16 IIEILNSNAR-TPSKEIADELKKSGHDVSDRTIRKRIERLEKSGIIK 61
                7888877776.789******************************997 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 7
      HTH_12  24 k 24 
                  
  EPA04335.1 140 S 140
                 1 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.6   6.2e-09   5.8e-06       3      44 ..      14      59 ..      13      66 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 6.2e-09
      HTH_11  3 lqilelLleargpisgeeLAeeL.....nvSrrtvrrdIkaLeelgv 44
                ++i+e+L +++   +++e+A+eL     +vS rt+r++I++Le++g+
  EPA04335.1 14 QKIIEIL-NSNARTPSKEIADELkksghDVSDRTIRKRIERLEKSGI 59
                699****.666669*********666666****************94 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   3.9e-07   0.00036       4      55 ..      12      64 ..       9      68 .. 0.93
   2 ?    0.0   0.0       1.1   1.1e+03      10      30 ..     122     142 ..     113     150 .. 0.68

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3.9e-07
                     S-SHHHHHHHHHS-EEHHHHHHT--GG.G---HHHHHHHHHHHHHTTS-EEEE CS
  Penicillinase_R  4 lEaevmeilwekgeatvkevveeleee.kelaysTVktllrrLvkKgllsrek 55
                      +++++eil ++ ++ +ke+ +el++  +++++ T++  ++rL+k g+++ +k
       EPA04335.1 12 VDQKIIEILNSNARTPSKEIADELKKSgHDVSDRTIRKRIERLEKSGIIKGYK 64
                     5789**********************99********************99776 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.1
                      HHHHHHS-EEHHHHHHT--GG CS
  Penicillinase_R  10 eilwekgeatvkevveeleee 30 
                        + ++++ t++++ve+++ee
       EPA04335.1 122 IQIDSAKSNTSQKIVEKFSEE 142
                      445566678888888888877 PP

>> HTH_Tnp_Tc3_2  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.1   2.2e-07   0.00021       2      40 ..      14      52 ..      13      67 .. 0.87
   2 ?   -2.1   0.0         5   4.7e+03      10      23 ..      83      96 ..      78      98 .. 0.73
   3 ?   -2.6   0.0       7.5     7e+03       8      25 ..     124     141 ..     120     144 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2.2e-07
  HTH_Tnp_Tc3_2  2 rrIvrlvrkdPritlreLanelkeeGksvsreTirrrLr 40
                    +I+++ + + r+ ++e+a elk++G+ vs++Tir+r+ 
     EPA04335.1 14 QKIIEILNSNARTPSKEIADELKKSGHDVSDRTIRKRIE 52
                   689********************************9864 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 5
  HTH_Tnp_Tc3_2 10 kdPritlreLanel 23
                    +P+++l++++n++
     EPA04335.1 83 IKPSKSLEMVKNSI 96
                   56888888888887 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 7.5
  HTH_Tnp_Tc3_2   8 vrkdPritlreLanelke 25 
                    ++   + t+++++++++e
     EPA04335.1 124 IDSAKSNTSQKIVEKFSE 141
                    556667788888888765 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   2.7e-07   0.00025       9      56 ..      10      62 ..       9      65 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.7e-07
                -HHHHHHHHHHSTCTTB-HHHHHHHH.....TS-HHHHHHHHHHHHHCTTEEE CS
      HTH_20  9 hPvRrrilraLaraegltaselaerl.....dlskntlsyHLrvLeeagLvev 56
                ++v  +i   L++++    +e+a++l     d+s+ t++++++ Le+ g++++
  EPA04335.1 10 DKVDQKIIEILNSNARTPSKEIADELkksghDVSDRTIRKRIERLEKSGIIKG 62
                56778999******************998888*******************87 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   1.2e-05     0.011       3      45 ..      14      61 ..      13      66 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.2e-05
    HTH_DeoR  3 eqilellkqqgklsveelvell.....gvSeaTiRRDLneLeeqgllt 45
                ++i+e l++      +e++++l     +vS+ TiR+ ++ Le++g+++
  EPA04335.1 14 QKIIEILNSNARTPSKEIADELkksghDVSDRTIRKRIERLEKSGIIK 61
                7899999999999999999988555557*****************974 PP

>> Myb_DNA-bind_4  Myb/SANT-like DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0     3e-05     0.028      15      65 ..       5      56 ..       4      72 .. 0.79
   2 ?   -2.8   0.0       9.2   8.7e+03      52      68 ..     131     147 ..     124     153 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3e-05
                    HHHH...HHHHHHH..SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHHH CS
  Myb_DNA-bind_4 15 awge.rilelrfqergkkrnkklWeevaeamaergykrspeqCkeKienLkk 65
                    aw++ + +++++ e  ++ ++   +e+a+++++ g+++s+  ++++ie L+k
      EPA04335.1  5 AWSNlDKVDQKIIEILNSNARTPSKEIADELKKSGHDVSDRTIRKRIERLEK 56
                    6766655555565544444444579*************************98 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 9.2
                     -HHHHHHHHHHHHHHHH CS
  Myb_DNA-bind_4  52 speqCkeKienLkkrYk 68 
                     + +++ eK+ +   +Y+
      EPA04335.1 131 TSQKIVEKFSEELTDYR 147
                     55556666655555555 PP

>> DUF3658  Protein of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0     5e-05     0.047      43      95 ..       9      61 ..       6      66 .. 0.94
   2 ?   -1.3   0.1       2.2     2e+03      73      87 ..     136     150 ..     100     153 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5e-05
     DUF3658 43 edyfDdlileaakkewqkaarligevlghldqfisDefleyRireLikaGvle 95
                 d++D+ i+e ++++ ++ ++ i++ l+++  ++sD  +  Ri+ L k+G+++
  EPA04335.1  9 LDKVDQKIIEILNSNARTPSKEIADELKKSGHDVSDRTIRKRIERLEKSGIIK 61
                6899**********************************************986 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.2
     DUF3658  73 dqfisDefleyRire 87 
                  ++ s+e+  yRi+e
  EPA04335.1 136 VEKFSEELTDYRINE 150
                 233445666667665 PP

>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   4.2e-05      0.04      32      71 ..      11      49 ..      10      51 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.2e-05
      HTH_32 32 evrariiallreeprWsprqlaarlaeregvkvShstvyr 71
                 v ++ii++l ++ r   +++a++l ++ g +vS +t+++
  EPA04335.1 11 KVDQKIIEILNSNARTPSKEIADEL-KKSGHDVSDRTIRK 49
                6789******6677888889*****.777799******97 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0     6e-05     0.056      11      61 ..      14      63 ..      11      74 .. 0.91
   2 ?   -3.2   0.0       9.2   8.7e+03     111     111 ..     142     142 ..     125     160 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6e-05
                HHHHHHHHHHSSSBEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEE CS
         FUR 11 ekilevlekseehlsaeevykelkeedpeislaTVYrtLklleeaglvkel 61
                +ki+e+l+++   +s +e+ +elk+ ++++s  T+ + ++ le++g++k  
  EPA04335.1 14 QKIIEILNSNARTPS-KEIADELKKSGHDVSDRTIRKRIERLEKSGIIKGY 63
                589999999988776.79******************************966 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 9.2
                 E CS
         FUR 111 k 111
                 +
  EPA04335.1 142 E 142
                 1 PP

>> Arg_repressor  Arginine repressor, DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.3   0.00011       0.1       7      47 ..      13      53 ..       8      61 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                   HHHHHHHHHHS---SHHHHHHHHHTTT----HHHHHHHHHH CS
  Arg_repressor  7 qklikkiikeekissQkelvelLkeeGidvtQatvSRdLke 47
                    ++i +i++++  +  ke++++Lk+ G dv   t+   ++ 
     EPA04335.1 13 DQKIIEILNSNARTPSKEIADELKKSGHDVSDRTIRKRIER 53
                   58999*************************99988766665 PP

>> RNA_binding  RNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.82   7.8e+02      22      71 ..      17      38 ..       5      71 .. 0.50
   2 ?   13.2   0.4   8.8e-05     0.084       9      76 ..      84     151 ..      78     163 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.82
                 HTTSTTS....E---EEEEEE-CCC-EEEEEEEEESSHHHHHHHHHHHHHHCCC CS
  RNA_binding 22 snllpee....eveieeeeaeGhygnpitileaelekkkakkvlkkllellree 71
                  ++l+++    +                                k+++++l+++
   EPA04335.1 17 IEILNSNartpS--------------------------------KEIADELKKS 38
                 333333333332................................2222222222 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 8.8e-05
                  -TTC-HHHHHHHHHTTSTTSE---EEEEEE-CCC-EEEEEEEEESSHHH.HHHHHHHHHHHCCCCHHHH CS
  RNA_binding   9 haTEdeekVlealsnllpeeeveieeeeaeGhygnpitileaelekkka.kkvlkkllellreeeikeL 76 
                  +++   e V+++++ ++ + +  + ++++eG ++   +i+++   k++  +k+++k+ e+l++ +i+e+
   EPA04335.1  84 KPSKSLEMVKNSIKDFIIKLDNYLMVSNMEGEWN-MLVIIQIDSAKSNTsQKIVEKFSEELTDYRINEI 151
                  56667789*********9998899*********8.9**********9999***********99998765 PP

>> Nuc_N  Nuclease N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00011      0.11      32      56 ..      38      63 ..      34      65 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
       Nuc_N 32 eaHkaSKAkiQsrIsklEkeG.vkgt 56
                  H+ S   i  rI++lEk G +kg 
  EPA04335.1 38 SGHDVSDRTIRKRIERLEKSGiIKGY 63
                67*******************88885 PP

>> DUF3783  Domain of unknown function (DUF3783)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       3.5   3.3e+03      37      51 ..      23      37 ..      21      37 .. 0.81
   2 ?   11.3   0.0   0.00028      0.26       6      36 ..      40      70 ..      40      72 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.5
     DUF3783 37 NinWtlkeLleElek 51
                N+   +ke  +El+k
  EPA04335.1 23 NARTPSKEIADELKK 37
                788889999999987 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00028
     DUF3783  6 sgfsseeldklldalkkaglpiplkAvlTpt 36
                ++ s++ + k ++ l k g+   +kAvlT  
  EPA04335.1 40 HDVSDRTIRKRIERLEKSGIIKGYKAVLTDV 70
                7899*************************86 PP

>> HU-DNA_bdg  DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00025      0.23      14      59 ..      10      56 ..       4      72 .. 0.79
   2 ?    1.4   0.4      0.32     3e+02       6      49 ..     107     150 ..     102     161 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00025
                -----EEEEE----E.E-HHHHHHHHHHH-TTS-HHHHHHHHHHHHH CS
  HU-DNA_bdg 14 dkksdyiaqvessgs.ltledIidemvkegtevrketienilnlykr 59
                dk +++i ++ +s + +  ++I+de++k g +v+  ti + ++++++
  EPA04335.1 10 DKVDQKIIEILNSNArTPSKEIADELKKSGHDVSDRTIRKRIERLEK 56
                66666777766554415689*******************99998876 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.32
                 EEE----------EEEEE----EE-HHHHHHHHHHH-TTS-HHH CS
  HU-DNA_bdg   6 LrdNkltkdkksdyiaqvessgsltledIidemvkegtevrket 49 
                 L+++ +  + +   i q+ s++s t ++I+++  +e t++r   
  EPA04335.1 107 LMVSNMEGEWNMLVIIQIDSAKSNTSQKIVEKFSEELTDYRINE 150
                 555555666666678899999999********999999998655 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00017      0.16      28      49 ..      27      53 ..      24      57 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00017
                  -HHHHHHHH.....T--HHHHHHHHHH CS
  Sigma70_r4_2 28 sykEIAell.....gisegtVksrlsR 49
                  + kEIA +l     ++s++t+++r+ R
    EPA04335.1 27 PSKEIADELkksghDVSDRTIRKRIER 53
                  689**********************98 PP

>> PepSY_like  Putative beta-lactamase-inhibitor-like, PepSY-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.2       1.5   1.4e+03      47      47 ..      38      38 ..       5      84 .. 0.56
   2 ?    2.5   0.1      0.23   2.1e+02      48      70 ..      84     106 ..      74     112 .. 0.78
   3 ?    7.8   1.0    0.0051       4.8      17      60 ..     112     155 ..     111     163 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.5
                H CS
  PepSY_like 47 s 47
                s
  EPA04335.1 38 S 38
                2 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.23
                 TTTEEEEEEEECSSEEEEEETTS CS
  PepSY_like  48 ypdekvtkierkkkeyeielene 70 
                  p+++ +++++  k+++i+l+n 
  EPA04335.1  84 KPSKSLEMVKNSIKDFIIKLDNY 106
                 4667889999999*******995 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0051
                 TTS-EEEEE-TTSEESGGGS-HHHHHHHHHHTTTEEEEEEEECS CS
  PepSY_like  17 kkGeWkeiegkkteiplsilpkavlkaiknsypdekvtkierkk 60 
                  +GeW ++ + +++   s+ ++++++ ++++ +d  +++i+ k+
  EPA04335.1 112 MEGEWNMLVIIQIDSAKSNTSQKIVEKFSEELTDYRINEIDIKN 155
                 58******99999999999***************9999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1456  (0.0812092); expected 358.6 (0.02)
Passed bias filter:                      675  (0.0376485); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1108.53
//
Query:       EPA04336.1  [L=350]
Description: oxidoreductase, zinc-binding dehydrogenase family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-33  115.4   0.9    1.7e-33  114.7   0.9    1.3  1  ADH_N         Alcohol dehydrogenase GroES-like domain
    1.3e-27   96.4   0.2    2.1e-27   95.7   0.2    1.4  1  ADH_zinc_N    Zinc-binding dehydrogenase
    5.2e-13   50.2   0.0    7.8e-13   49.6   0.0    1.3  1  ADH_zinc_N_2  Zinc-binding dehydrogenase
    5.3e-08   32.6   0.1    1.3e-07   31.4   0.1    1.5  1  Glu_dehyd_C   Glucose dehydrogenase C-terminus
      0.002   18.8   2.1     0.0042   17.7   2.1    1.6  1  PglD_N        PglD N-terminal domain
     0.0075   15.6   0.2      0.012   14.9   0.2    1.2  1  AlaDh_PNT_C   Alanine dehydrogenase/PNT, C-terminal domain
  ------ inclusion threshold ------
      0.018   15.3   0.2      0.039   14.2   0.1    1.6  2  TrkA_N        TrkA-N domain
      0.032   14.4   0.3       0.06   13.5   0.3    1.4  1  DapB_N        Dihydrodipicolinate reductase, N-terminus


Domain annotation for each model (and alignments):
>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.7   0.9   7.8e-37   1.7e-33       2     105 ..      26     140 ..      25     145 .. 0.96

  Alignments for each domain:
  == domain 1  score: 114.7 bits;  conditional E-value: 7.8e-37
                 TEEEEEEEEEEE-HHHHHHHTTS...........TTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHTT-GGG-TTBEETTT CS
       ADH_N   2 gevlikvkaagiCgsDlhilkgg...........kelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCkegeenlCeeakllgv 89 
                 ++v++kvk++g+C+sDlh+++gg           ++  vk+p+++GHEivG+v+e+g++v+++++Gd+V+v+p+i cg+C+aCk g+enlC++ k lgv
  EPA04336.1  26 NQVMVKVKSVGVCHSDLHLWEGGydlgdgkfmkvTDRGVKYPVTPGHEIVGTVQELGDNVQGISKGDQVLVYPWIGCGQCPACKVGNENLCDTPKSLGV 124
                 79********************************9**************************************************************** PP

                 SS-SSSBSEEEECGGG CS
       ADH_N  90 sldGgfaeyvvvpekk 105
                  +dGg+++y +vp+ k
  EPA04336.1 125 FQDGGYSDYSLVPHYK 140
                 ************9543 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.7   0.2   9.4e-31   2.1e-27       1     128 [.     185     312 ..     185     314 .. 0.94

  Alignments for each domain:
  == domain 1  score: 95.7 bits;  conditional E-value: 9.4e-31
                 HHHHHHHHHHH.HTT-EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHHCEEEEEEEEECSCTSSEEEEE CS
  ADH_zinc_N   1 gvGlaavqlAk.alGaeviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvGsgatleaalkllkpgGrlvvvGggkgeeefd 98 
                 g+Gl++vq+Ak + + ++i+vd +++kle+ak++Gad+vin+k+ +  ++i ++++g+g+d v+++v+++ t ++ l++l+++G lv+vG+++g  e++
  EPA04336.1 185 GLGLMGVQIAKsITKSKIICVDLDDQKLEIAKEMGADFVINSKDSEATQKIIAICNGKGADSVVDFVNAPPTAKMGLAVLRKRGNLVLVGLFGGSMELS 283
                 89*********55555**************************7769*********************************************8888889* PP

                 HHHHHHTT-EEEEE-SSCHHHHHHHHHHHH CS
  ADH_zinc_N  99 lrnlllkeksilGsllgslreefkealdll 128
                 l  + lk++ i+G   g+  +++ e+ldl+
  EPA04336.1 284 LVTIPLKSIIIQGAYTGN-YHDMVELLDLA 312
                 ******************.89999999985 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6   0.0   3.5e-16   7.8e-13       1     133 []     218     348 ..     218     348 .. 0.79

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 3.5e-16
                   TT-SEEEETTSTTHH....HHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE----.S-EEE-CHHHCTTT-EEEE--GGG...-.-HHHHHHH CS
  ADH_zinc_N_2   1 lGAdevidyrtedfe....aatggegvDvvldtvggealleaslkvlpggGrlvsiggpplsaallkpakkrkgrsvkyeflfsmkasaqadileel 93 
                   +GAd vi++++ +++    a  +g+g D v+d v+ + +++  l+vl+++G lv +g    + + +++++     +  +      + +  +d + el
    EPA04336.1 218 MGADFVINSKDSEATqkiiAICNGKGADSVVDFVNAPPTAKMGLAVLRKRGNLVLVGL---FGGSMELSLVTIPLKSIIIQGA-YTGN-YHD-MVEL 308
                   59*****9995555558889999************888879999999999***99994...3344444443322233333333.2445.999.**** PP

                   HHHHHHHH----EEEEEEGGGHHHHHHHHHSS--SSEEEE CS
  ADH_zinc_N_2  94 aalieeGklrpvvdrvfpleeaaeAhrylesgrarGKiVl 133
                   ++l  +G+++p ++++++l++a+ A+++l++++ +G+ V+
    EPA04336.1 309 LDLARKGTINPMISKRYSLDNANSALEDLKARKIVGRAVI 348
                   ************************************9996 PP

>> Glu_dehyd_C  Glucose dehydrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.1   5.6e-11   1.3e-07      15     201 ..     159     336 ..     148     343 .. 0.78

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 5.6e-11
  Glu_dehyd_C  15 KaielaeasrsafewepesalvlGaGslGLLalalleaeerglervyvlgrrdrpdptidlveelGatYv.dsre.tpvdeipea..seemdlvvEaT 108
                   ++    a++++ +  pe  +++GaG lGL+ + + ++   + +++ +++    +d+++++ +e+Ga +v +s+  +  ++i ++   +  d vv+  
   EPA04336.1 159 SGLTAYSAIKKSNQNAPEFLVIIGAGGLGLMGVQIAKS--ITKSKIICVD---LDDQKLEIAKEMGADFViNSKDsEATQKIIAIcnGKGADSVVDFV 251
                  455566678999999*****************766654..4456788998...5788***********98433321334555554115789******* PP

  Glu_dehyd_C 109 GsakhafeaiealapnGvaaLlGvpedsevevdggelhrelvleNkalvGsvNanrrhfeaavdtLaalpeslldelvtkvvdldeleeAfed 201
                   +++ a   +  l+  G  +L+G+  +s +e+       ++ l+  ++ G+    + +++  v+ L+ + +  ++ +++k++ ld++++A ed
   EPA04336.1 252 NAPPTAKMGLAVLRKRGNLVLVGLFGGS-MELSLV----TIPLKSIIIQGA---YTGNYHDMVELLDLARKGTINPMISKRYSLDNANSALED 336
                  ************************9887.555443....445666677775...567799999999999999**************9999987 PP

>> PglD_N  PglD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   2.1   1.9e-06    0.0042       2      67 ..     178     240 ..     177     249 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.9e-06
      PglD_N   2 ivIiGaGGhgkvvadiieangeyeiigf.lDdnkktevegypvlgkaiellkslseeeyevviAIGn 67 
                 +vIiGaGG g +  +i++++ + +ii++ lDd+k   +e  + +g +   ++s   e+++ +iAI n
  EPA04336.1 178 LVIIGAGGLGLMGVQIAKSITKSKIICVdLDDQK---LEIAKEMGAD-FVINSKDSEATQKIIAICN 240
                 79*******************9988874377777...3334445543.3455555667778888877 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.2   5.2e-06     0.012      31      88 ..     178     235 ..     161     252 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.2e-06
                  EEEESTSHHHHHHHHHHHHT.T-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHHHHHH CS
  AlaDh_PNT_C  31 vlviGgGvaGlqAiatakgl.gakVtvlDvrparleqleslgakfvevlksqeellaea 88 
                   ++iG+G  Gl  +++ak++ + k+  +D++ ++le  +++ga fv + ++++e+ ++ 
   EPA04336.1 178 LVIIGAGGLGLMGVQIAKSItKSKIICVDLDDQKLEIAKEMGADFV-INSKDSEATQKI 235
                  69****************98357899******************65.444444444444 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   1.7e-05     0.039       5      56 ..     185     234 ..     178     266 .. 0.84
   2 ?   -3.5   0.0       5.5   1.2e+04      71     113 ..     300     342 ..     296     343 .. 0.48

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.7e-05
                 S-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHH CS
      TrkA_N   5 GlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdatdeevLe 56 
                 GlG +G ++a+ +++++  ++ +d d++++e ++e g+++v+ +  +e++ +
  EPA04336.1 185 GLGLMGVQIAKSITKSK--IICVDLDDQKLEIAKEMGADFVINSKDSEATQK 234
                 57778889999998866..9*******************9999888888765 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 5.5
                 SSHHHHHHHHHHHHHHTSSSEEEEEESSGGGHHHHHHHTTSEE CS
      TrkA_N  71 gddeanilavllakelnpkkkiiaraqdpehaellkklgadvv 113
                 g++ + + ++ la++   ++ i  r + +    +l++l a ++
  EPA04336.1 300 GNYHDMVELLDLARKGTINPMISKRYSLDNANSALEDLKARKI 342
                 5555666666666653332333334444444444566666655 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.3   2.7e-05      0.06       6      91 ..     183     267 ..     178     282 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.7e-05
                 ETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEBSSHHHHHHH..-SEEEE-S-HHHHHHHHHHHHHTT CS
      DapB_N   6 vGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavtddleevlek..advliDFTtpeavlenlklalekg 91 
                 +G  G mG +++k +++ +++  v   d+k    ++k++g    +++ + + t+++ ++++   ad ++DF +   + ++  ++l+k+
  EPA04336.1 183 AGGLGLMGVQIAKSITK-SKIICVDLDDQKL--EIAKEMGADFVINSKDSEATQKIIAICNGkgADSVVDFVNAPPTAKMGLAVLRKR 267
                 566789**********9.5565555555544..588999999999999999999999988888********87655555544444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2267.07
//
Query:       EPA04337.1  [L=318]
Description: transcription factor TFIIB repeat protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.1e-25   86.5   2.3    2.1e-12   46.9   0.1    2.5  2  TFIIB           Transcription factor TFIIB repeat
    6.5e-09   35.2   1.2    6.5e-09   35.2   1.2    1.8  2  TF_Zn_Ribbon    TFIIB zinc-binding
  ------ inclusion threshold ------
      0.014   15.9   2.2        1.1    9.9   2.2    2.8  1  RPA_interact_C  Replication protein A interacting C-terminal
       0.05   13.8   0.4       0.05   13.8   0.4    2.1  2  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 
        0.1   12.7   4.1        6.1    7.0   0.2    2.5  2  DUF2318         Predicted membrane protein (DUF2318)
       0.33   11.0   3.8          1    9.4   0.2    2.5  2  zinc-ribbons_6  zinc-ribbons
       0.54   10.3   4.1       0.31   11.1   0.3    2.2  2  DZR             Double zinc ribbon


Domain annotation for each model (and alignments):
>> TFIIB  Transcription factor TFIIB repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.9   0.1     8e-16   2.1e-12       4      61 ..     126     183 ..     123     187 .. 0.96
   2 !   39.1   0.2   2.3e-13   5.8e-10       4      71 .]     227     294 ..     224     294 .. 0.91

  Alignments for each domain:
  == domain 1  score: 46.9 bits;  conditional E-value: 8e-16
                 HHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHH CS
       TFIIB   4 fadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeis 61 
                  +d l+L++ V + A  ++++      +kG+s a+i AA +y+Ac+++ v r+++ei+
  EPA04337.1 126 TCDGLNLSKNVLETASMIYRNLDGHVEVKGKSVASITAATIYMACKQCDVVRSLEEIC 183
                 59*******************************************************8 PP

  == domain 2  score: 39.1 bits;  conditional E-value: 2.3e-13
                 HHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
       TFIIB   4 fadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                 +a+  +    V++ A e+a++++   +  G+ p+giaAA ly+A+ + + +  q+++ss++ V+e+ti
  EPA04337.1 227 IANMTQTEVRVERLALEIAEKTKGSSIADGKAPNGIAAAYLYVASVLLGQNVLQRDVSSIAGVTEVTI 294
                 55555556689*******************************************************98 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   1.2   2.5e-12   6.5e-09       3      39 ..       9      44 ..       7      47 .. 0.94
   2 ?   -1.9   0.1      0.99   2.5e+03       2       9 ..     169     176 ..     168     181 .. 0.63

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 2.5e-12
                  ETTTTCEECHEETSTTCEEESSSSBEEEECCCCCCCH CS
  TF_Zn_Ribbon  3 CPnCgstnlveDpergelvCtdCGlVlednsidegpe 39
                  CP+C  + lv D  +ge++C+ CG+V+ ++ +d+gpe
    EPA04337.1  9 CPECQAS-LVDDIQNGEIICSGCGVVVAEQMVDYGPE 44
                  *****75.9***************************9 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.99
                   EETTTTCE CS
  TF_Zn_Ribbon   2 kCPnCgst 9  
                    C+ C   
    EPA04337.1 169 ACKQCDVV 176
                   58888664 PP

>> RPA_interact_C  Replication protein A interacting C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   2.2   0.00043       1.1       2      28 ..       9      52 ..       8     178 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00043
  RPA_interact_C  2 CPvCkkrklkets.evifCe.Cglrlet...............s 28
                    CP C+ + +   +   i+C+ Cg+ ++                 
      EPA04337.1  9 CPECQASLVDDIQnGEIICSgCGVVVAEqmvdygpetksanleD 52
                    *********9966589***99**999984444444333333220 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.4     2e-05      0.05      15      40 .]       6      31 ..       3      31 .. 0.91
   2 ?   -2.1   0.5       1.8   4.7e+03      18      24 ..     170     176 ..     168     183 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2e-05
  Auto_anti-p27 15 aetCpvCgvPLmrdrkggkvyCvaCd 40
                    ++Cp+C++ L+ d ++g+++C  C+
     EPA04337.1  6 TQSCPECQASLVDDIQNGEIICSGCG 31
                   689***********999********6 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.8
  Auto_anti-p27  18 CpvCgvP 24 
                    C++C v+
     EPA04337.1 170 CKQCDVV 176
                    8889775 PP

>> DUF2318  Predicted membrane protein (DUF2318)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.6    0.0037       9.4      36      67 ..       8      40 ..       3      47 .. 0.83
   2 ?    7.0   0.2    0.0024       6.1      51      82 ..     167     196 ..     161     207 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0037
     DUF2318 36 aCevCekkgYv.qegeelvCknCgvrfaldsig 67
                 C  C+ +    +++ e++C  Cgv++a + ++
  EPA04337.1  8 SCPECQASLVDdIQNGEIICSGCGVVVAEQMVD 40
                688887666666999**********99988876 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0024
     DUF2318  51 elvCknCgvrfaldsigekkGGCnpipleytv 82 
                  + Ck+C+v+ +l++i   +G C p  +++++
  EPA04337.1 167 YMACKQCDVVRSLEEIC--RGICAPKDVKSKT 196
                 589*************9..9*****9997765 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.2   0.00039         1       2      28 ..       8      36 ..       7      65 .. 0.82
   2 ?    2.2   0.3     0.072   1.9e+02      16      33 ..     167     184 ..     156     202 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00039
                    --SSS-S--E..E-SSEEE-TTT--EEEE CS
  zinc-ribbons_6  2 kCpeCqqele..krgeqyhCeaCqedlkk 28
                    +CpeCq+ l+   ++ ++ C+ C   + +
      EPA04337.1  8 SCPECQASLVddIQNGEIICSGCGVVVAE 36
                    6********96556799******985544 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.072
                     EEE-TTT--EEEEEEE-S CS
  zinc-ribbons_6  16 qyhCeaCqedlkkealCp 33 
                      + C++C+   + e +C 
      EPA04337.1 167 YMACKQCDVVRSLEEICR 184
                     568999998888888885 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.3   0.00012      0.31      15      37 ..       9      33 ..       3      41 .. 0.59
   2 ?   -0.4   0.4      0.49   1.2e+03      30      35 ..     169     174 ..     155     187 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00012
         DZR 15 CseCgtklkavaa..edrCpsCgek 37
                C+eC+++l    +  e+ C+ Cg  
  EPA04337.1  9 CPECQASLVDDIQngEIICSGCGVV 33
                6666666543333556666666544 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.49
         DZR  30 rCpsCg 35 
                 +C +C+
  EPA04337.1 169 ACKQCD 174
                 455554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1055  (0.0588432); expected 358.6 (0.02)
Passed bias filter:                      680  (0.0379274); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2096.46
//
Query:       EPA04338.1  [L=224]
Description: ScpA/B protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-06   27.2   0.8       0.02   14.8   0.0    2.1  2  SMC_ScpA  Segregation and condensation protein ScpA


Domain annotation for each model (and alignments):
>> SMC_ScpA  Segregation and condensation protein ScpA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.2   1.5e-05      0.27       8      68 ..      28      87 ..      24     105 .. 0.87
   2 !   14.8   0.0   1.1e-06      0.02     184     232 ..     164     211 ..     125     218 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 1.5e-05
                HHTSSSSXXXXHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHSXXXXXXXXXXXXX CS
    SMC_ScpA  8 dvtdvavakvtdqflayiktllnkleleesteylviastlvelKaasLlpleqveeeedee 68
                dv+d++++++ +  ++ ++    k +l  ++ + + +s + ++K +s++ l++ + e  + 
  EPA04338.1 28 DVWDIDLIQILNLLIKILEKS-GKKDLRVAGMAALSSSLIYRMKVESIFALQRAAMERKPI 87
                9******************99.899**************************9998877665 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 1.1e-06
                 ..HHH..TS-EEGGGSSTT...--HHHHHHHHHHHHHHHHTT-EEEEESST CS
    SMC_ScpA 184 vLldl..rswvdlseLladnkledkkelvgvFlAlLeLiknqavaleQeef 232
                 +++++   ++  l+e+++d    d  + + +F+A+L L ++++v+leQ + 
  EPA04338.1 164 IIKKIseTGYGMLQEIIKD---LDAVDSIRCFFAILFLARDEKVDLEQIND 211
                 5555643345566777777...8999**********************764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1508.59
//
Query:       EPA04339.1  [L=89]
Description: hypothetical protein BG20_I1409 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-12   46.8   0.1    5.3e-12   46.5   0.1    1.1  1  SRP19     SRP19 protein


Domain annotation for each model (and alignments):
>> SRP19  SRP19 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   0.1     3e-16   5.3e-12       6      91 ..       3      80 ..       1      85 [. 0.84

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 3e-16
                CCBTTS-CCCT--S-CCCSBSS--HHHHHHHHHHCTSCEE.EEEEECTTSS.TTCCEEEEEC-..........SS-CHHHHHHHHHHH CS
       SRP19  6 YldskktrkeGRrvpkelavenPtaqeiaealkalglevv.vepeksyPrd.wanpGrVrvklkedgkevnekiknkkellkkiaell 91
                Y++++  r++GR+++ke++v +P+++e+ ea++a g++++  +++ ++P++ ++++G++ + ++          ++k+++l+ki+e+l
  EPA04339.1  3 YFNKTLPRAKGRKLEKEKCVFDPSLKELTEAAQAAGFQITeTDEKVRFPKRpYVRSGYIVLPKE----------STKTKILNKISEKL 80
                **************************************995666678****77789****9986..........45555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 516.96
//
Query:       EPA04340.1  [L=87]
Description: hypothetical protein BG20_I1393 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.032   14.2   0.0      0.032   14.2   0.0    1.2  1  PX        PX domain


Domain annotation for each model (and alignments):
>> PX  PX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.8e-06     0.032      16      54 ..       4      41 ..       1      79 [. 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.8e-06
                TSSEEEEEEEEEETTSSSEEEEEEEHHHHHHHHHHHHHH CS
          PX 16 skkhsyylyevelktgakewtvkRrYsdFeeLhskLlrk 54
                ++ +  +++e+++ ++  + ++ R+Y+dF +L ++L ++
  EPA04340.1  4 ESFYLATVIEFTTWDN-GKEKIIRKYKDFGDLPTQLHDE 41
                5556678899999888.999*********9887777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 560.82
//
Query:       EPA04341.1  [L=192]
Description: segregation and condensation protein B [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.5e-36  123.0   0.6      1e-35  122.7   0.6    1.1  1  SMC_ScpB  Segregation and condensation complex subunit ScpB
  ------ inclusion threshold ------
      0.027   14.4   0.4       0.91    9.5   0.1    2.3  2  PadR      Transcriptional regulator PadR-like family
      0.041   14.1   0.0      0.095   13.0   0.0    1.6  1  HHH_3     Helix-hairpin-helix motif
       0.11   12.6   0.0       0.36   10.9   0.0    1.9  2  HTH_20    Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> SMC_ScpB  Segregation and condensation complex subunit ScpB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.7   0.6   2.3e-39     1e-35       1     158 [.      12     165 ..      12     167 .. 0.96

  Alignments for each domain:
  == domain 1  score: 122.7 bits;  conditional E-value: 2.3e-39
    SMC_ScpB   1 aiiEAiLfvageplsleeLakilels.keeveealeeLkeeyeeedrglelvev.aggyrlvtkpelaevvkklvkekkktrLsqaaletLaiIaykqp 97 
                 a+iEA+L++ag+pl++eeL ++ +++ ++++ e+l+e++++ +++ ++le+v + +g y +++kpe+++ +k+++++   + L +a+l+tL++Iay qp
  EPA04341.1  12 ARIEAALYSAGRPLKIEELIRASGTEsRTKTYELLNEIMKKTKSAFKALEVVTLpDGSYVFQLKPEYSSTIKRYASK---PILPNATLKTLSYIAYMQP 107
                 58*********************9778***************************999********************...99***************** PP

    SMC_ScpB  98 vtraeieeiRGvnsdsvvrtLlerglieekgrkeepgrpilYgtTekFleyfglks.leeLp 158
                 ++++++ e RG+ +++++++L + ++i++++    +gr  +Y+tTekF +yfg++  +e+L+
  EPA04341.1 108 ISSKQLVETRGSGVYEHLKELRQLDFITHQN----VGRLKIYNTTEKFQKYFGIQGdVENLK 165
                 *******************************....9******************98788776 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.022        98      31      65 ..      15      45 ..       1      53 [. 0.79
   2 ?    9.5   0.1    0.0002      0.91      27      71 ..     114     153 ..     105     156 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.022
                HHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEE CS
        PadR 31 eGslYpaLkrLekeglveseweesgegpprkyYrl 65
                e+ lY a + L+ e+l+ ++ +es    ++k+Y+l
  EPA04341.1 15 EAALYSAGRPLKIEELIRASGTES----RTKTYEL 45
                788999999999999999997775....9999987 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0002
                 CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCH CS
        PadR  27 lelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrr 71 
                 +e   + +Y  Lk+L++ ++++++++      + k+Y+ T++ ++
  EPA04341.1 114 VETRGSGVYEHLKELRQLDFITHQNVG-----RLKIYNTTEKFQK 153
                 55666779****************884.....7999999998655 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.1e-05     0.095      10      56 ..      93     138 ..      91     145 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.1e-05
       HHH_3  10 tAsaeeLqklpGlgpklAknIvayReknGpfksreeLlkvkglgpkt 56 
                  A+++ L++++ + p  +k++v+ R   G +++++eL +   ++ + 
  EPA04341.1  93 NATLKTLSYIAYMQPISSKQLVETR-GSGVYEHLKELRQLDFITHQN 138
                 599**********************.889********9877776665 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.71   3.2e+03      12      29 ..      11      29 ..       7      40 .. 0.66
   2 ?   10.9   0.0   7.9e-05      0.36      33      61 .]     113     141 ..      99     141 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.71
                HHHHHHHH.STCTTB-HHH CS
      HTH_20 12 RrrilraL.araegltase 29
                 +ri++aL + +++l  +e
  EPA04341.1 11 TARIEAALySAGRPLKIEE 29
                5789999955555555555 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 7.9e-05
                 HHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
      HTH_20  33 rldlskntlsyHLrvLeeagLvevvregr 61 
                 +++++ + ++ HL++L++ ++++ + +gr
  EPA04341.1 113 LVETRGSGVYEHLKELRQLDFITHQNVGR 141
                 44678899***************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       723  (0.0403257); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1241.71
//
Query:       EPA04342.1  [L=548]
Description: magnesium and cobalt transport protein CorA [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-69  234.7   5.3    1.3e-69  234.7   5.3    1.9  2  CorA         CorA-like Mg2+ transporter protein
  ------ inclusion threshold ------
      0.014   15.2   1.2      0.014   15.2   1.2    2.4  2  Tetraspanin  Tetraspanin family
      0.029   14.2   2.6      0.035   13.9   0.3    2.3  2  Herpes_UL92  UL92 family
       0.58   10.1   0.0       0.58   10.1   0.0    3.3  3  T2SSF        Type II secretion system (T2SS), protein F


Domain annotation for each model (and alignments):
>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   1.2      0.53   2.4e+03     272     291 ..      61      78 ..      52      79 .. 0.75
   2 !  234.7   5.3   2.9e-73   1.3e-69       4     292 .]     254     542 ..     251     542 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.53
        CorA 272 fvlllglmallailllfwfk 291
                 ++  ++++++++i++l+ +k
  EPA04342.1  61 WW--VISTVIITIISLIIVK 78 
                 35..7888888888888876 PP

  == domain 2  score: 234.7 bits;  conditional E-value: 2.9e-73
        CorA   4 fvWldlssptee.eleeLaeelgldelaledlldseerprvedyddylllvlpsveldkseeeeeevplsillgdnflitvrreplealdevikrlk.. 99 
                 + W+++  ++++ ++e++   +g+++l   +++++e rp++e+y+dy++l+l+ ++ +++  + e  ++s++++++ l+t+++ + +++d+++krl+  
  EPA04342.1 254 VSWINIIGVHDPhTIEKFGNAFGVHPLHQANIMNTELRPSIEFYEDYIFLMLKMPHFNEQTGKIELEQISFFISEHHLLTFQEIEADFFDQIRKRLRen 352
                 78****9999999***************888******************************************************************75 PP

        CorA 100 deggkpkspgellyrlldeivdrlfellekleeeldeledeledstkkeilrelaqlrrrlvklrralapnrevlkrllakaddkllddedkeylrdll 198
                   + +++    l y lld+i+d++f +lek+++  + ledel+ + + + l +l  l+r+++ lr++++p revl ++l+++ ++l+ de k ylrd++
  EPA04342.1 353 IGKIRKSETDYLGYVLLDAIIDSYFLVLEKISDISENLEDELMVNPTPKTLHTLQFLKRQMILLRKSIWPAREVL-DNLQRNQTPLIHDETKTYLRDVY 450
                 4445666666788**************************************************************.88888****************** PP

        CorA 199 delerllemlealrerleslqdtyssllserlNrvmkvLTvltaiflPlTlitGiyGmNfkglPelewsygypfvlllglmallailllfwfkr 292
                 +++ ++++++e lr+++ sl dty s ls+++N+vmk+LTv++ if+P T+i+G+yG Nf+++Pel ws  y+    +g+ma ++i++l wfk+
  EPA04342.1 451 NHVIQVIDTTEGLRDVVGSLLDTYLSSLSNKMNEVMKTLTVIASIFIPITFIAGVYGTNFDYIPELSWSGSYFVM--IGVMATIVIIMLGWFKK 542
                 **********************************************************************88888..***************97 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   1.2     3e-06     0.014      10     125 ..      59     185 ..      55     246 .. 0.68
   2 ?    1.8   0.8     0.036   1.6e+02      41     105 ..     478     543 ..     466     546 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3e-06
                  XXXXXXXXXXXXXXXXXXX.XXX......................XXXXXXXXXXXXXXX..XXXXXXXXX..........XXXXXXX.XXXXXXXXX CS
                  xxxxxxxxxxxxxxxxxxx.xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxx..........xxxxxxx.xxxxxxxxx RF
  Tetraspanin  10 llfwligivllavGvwlrl.khaea.alacllsesaedpailaillivvGvllfllgflG..cigalkenk..........cllltfs.llllvlfll 92 
                  + +w+i+ v++ +   l++ kh+++ + ++++++   +p+i  i++ivvG+++ ++ fl   +ig +  n+           l + f+ l+l +lf +
   EPA04342.1  59 ISWWVISTVIITII-SLIIvKHKQYfSIYKNEKHIEIPPKISLITIIVVGSVISFMFFLMdsVIGLFATNTasdvqaiyesALTGNFVpLYLSILFSI 155
                  45899999999884.33334555440455556667778889999*******65555544333555555555555888898878888887888888888 PP

                  XXXXXXXXX--HHH........HHHHHHHHHHH CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Tetraspanin  93 elaagilgfvfsdkargkvseiinnaievkyrd 125
                  + +++i+g+  + ++ +k+    ++   +++++
   EPA04342.1 156 LTGFIIVGVSAKTSSVSKI---TKDFRVDNIHH 185
                  8888888888777744444...33333333333 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.036
                  ............XXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXX--HH CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Tetraspanin  41 esaedpailaillivvGvllfllgflGcigalkenk.cllltfsllllvlfllelaagilgfvfsd 105
                   s++ + ++++l +++++++ ++ ++G++g+  + +  l ++ s ++++ +++ +++++lg++ + 
   EPA04342.1 478 LSNKMNEVMKTLTVIASIFIPITFIAGVYGTNFDYIpELSWSGSYFVMIGVMATIVIIMLGWFKKR 543
                  344555556566777777888888899999887777456666666666666667776777777665 PP

>> Herpes_UL92  UL92 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1      0.71   3.2e+03     144     180 ..     150     183 ..     117     199 .. 0.71
   2 ?   13.9   0.3   7.8e-06     0.035      88     161 ..     437     509 ..     402     514 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.71
  Herpes_UL92 144 dvicslyiqviisiyskktvYdallfkvtknKryDsv 180
                  +++ s+    ii   s kt   + + k+tk  r D +
   EPA04342.1 150 SILFSILTGFIIVGVSAKT---SSVSKITKDFRVDNI 183
                  5555666666666667776...567777777777766 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 7.8e-06
  Herpes_UL92  88 avkkdvysylikekeklaevseeileedglkkevedlikvtfneclkvfreaqsgydvicslyiqv..iisiyskk 161
                   ++ +  +yl   ++ +++v++ i +++gl++ v  l+++ ++   + ++e+ ++++vi+s++i +  i ++y ++
   EPA04342.1 437 LIHDETKTYL---RDVYNHVIQVIDTTEGLRDVVGSLLDTYLSSLSNKMNEVMKTLTVIASIFIPItfIAGVYGTN 509
                  5667778888...78899*************************9999999999**********8654488899876 PP

>> T2SSF  Type II secretion system (T2SS), protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.2      0.14   6.3e+02     103     120 ..      98     115 ..      87     117 .. 0.58
   2 ?   10.1   0.0   0.00013      0.58      56     117 ..     443     503 ..     412     507 .. 0.86
   3 ?   -4.5   3.3         4   1.8e+04     107     120 ..     524     537 ..     520     540 .. 0.55

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.14
                 HTTXXXXXXXXXXXXXXX CS
       T2SSF 103 lepllllvvallvllill 120
                 ++ + ++vv+++++++++
  EPA04342.1  98 ISLITIIVVGSVISFMFF 115
                 334445555555555555 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00013
                 TT.TS-HHHHHHHHHHHHHT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXX CS
       T2SSF  56 pssefpelvvqlirageeggnLaevLerlaeyleeerelrrkllaallepllllvvallvll 117
                 + + +++++  +i++++++  L +v   l +++   + ++ ++  ++l +++++++ + +++
  EPA04342.1 443 K-TYLRDVYNHVIQVIDTTEGLRDVVGSLLDTYLSSLSNKMNEVMKTLTVIASIFIPITFIA 503
                 3.4789******************************************99999998766665 PP

  == domain 3  score: -4.5 bits;  conditional E-value: 4
                 XXXXXXXXXXXXXX CS
       T2SSF 107 lllvvallvllill 120
                 +++ v++ +++i+l
  EPA04342.1 524 VMIGVMATIVIIML 537
                 45555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (548 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1002  (0.0558871); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.69u 0.31s 00:00:01.00 Elapsed: 00:00:00.50
# Mc/sec: 3291.04
//
Query:       EPA04343.1  [L=126]
Description: ribosomal protEin S8.e [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      5e-23   81.8   5.4    5.8e-23   81.6   5.4    1.1  1  Ribosomal_S8e  Ribosomal protein S8e


Domain annotation for each model (and alignments):
>> Ribosomal_S8e  Ribosomal protein S8e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.6   5.4   3.2e-27   5.8e-23       6     137 .]       6     125 ..       1     125 [. 0.94

  Alignments for each domain:
  == domain 1  score: 81.6 bits;  conditional E-value: 3.2e-27
                    XCCCSEESSTEEXXXSSXXXCCSBXXXXXXXEESSHEEEEEEETTCEEEEEEESESEEEEEETTTTEEEEEEEEEEECSSSTCHHHHTTC--TTEE CS
  Ribosomal_S8e   6 dskhkrkltGgkakllrkkrkielgrkekatklgaervkvvrvrgGkrkkralrlkkanvthpeekvtkklkIlgVkknpsnneyvrlgvltKgai 101
                    ++  + k+tGg++k+ r +rk e  r +++  +ga++  + rvrg+++k+++  ++  nv+ +  kv kklkIl+V+ n++nn+y r+g++tKgai
     EPA04343.1   6 ENLATSKITGGRRKPARIRRKSEIDRYPNEPVVGAQVTITRRVRGNNTKTALKTIDFVNVSSGDSKV-KKLKILKVISNATNNDYQRRGIITKGAI 100
                    5566789*******************************************************87765.78************************** PP

                    EEEESHHHHHHHHTTEEEEEEESEHHHHSSEEEEEE CS
  Ribosomal_S8e 102 ievdvseLgevtqsgkvvAqvtsrPgqdGcvnavlL 137
                    +e++ ++            +v s+Pgq+G vnavl+
     EPA04343.1 101 LETEQGN-----------CRVVSKPGQSGTVNAVLI 125
                    *******...........9***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.77
# Mc/sec: 496.33
//
Query:       EPA04344.1  [L=203]
Description: hypothetical protein BG20_I1397 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       764  (0.0426125); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1256.00
//
Query:       EPA04345.1  [L=249]
Description: response regulator receiver domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-18   66.4   0.4    3.6e-18   65.7   0.4    1.3  1  Response_reg  Response regulator receiver domain
     0.0041   17.1   0.1        0.2   11.8   0.0    2.7  2  TPR_2         Tetratricopeptide repeat
  ------ inclusion threshold ------
       0.01   16.4   0.0      0.057   14.0   0.0    2.2  2  Rhodanese     Rhodanese-like domain
      0.032   14.1   0.0      0.097   12.5   0.0    1.9  1  TPR_1         Tetratricopeptide repeat
      0.039   14.2   0.0        0.1   12.8   0.0    1.6  1  PK_C          Pyruvate kinase, alpha/beta domain
       0.07   13.4   1.4       0.33   11.3   0.1    2.8  3  TPR_8         Tetratricopeptide repeat
       0.13   12.5   0.9       0.86    9.8   0.1    2.4  3  NFACT-R_2     NFACT protein RNA binding domain
       0.14   12.9   0.2        5.6    7.8   0.0    3.1  2  TPR_6         Tetratricopeptide repeat
       0.19   12.5   1.7       0.41   11.4   0.1    2.1  2  DUF4829       Domain of unknown function (DUF4829)
       0.19   11.1   1.0       0.35   10.3   0.5    2.0  2  SMC_N         RecF/RecN/SMC N terminal domain


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.7   0.4     2e-21   3.6e-18       1     111 [.     123     238 ..     123     239 .. 0.92

  Alignments for each domain:
  == domain 1  score: 65.7 bits;  conditional E-value: 2e-21
                   EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHH....HHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEESSTS.HHHHHHHHHC CS
  Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealell....keekvdlillDinmpgmdGlellkeireedpelpviiltahse.eedavealka 92 
                   ++i+dD++++ + l++++e+ gy e+  +e+gk+ ++ +     e+k  +++lD+++p+ dG  +  ++ +e+++l++i++ta ++  + +++ ++ 
    EPA04345.1 123 IVIIDDSKAISMKLQTYIEKLGYGEIFLFENGKSGMKGCqklfSENKQPIVFLDMELPDFDGDVISAKLLKEKNDLQIIVITADEKtTKRVNKTISS 219
                   79********************************999884444666799********************99999********88775889999**** PP

                   TESEEEESSG-HHHHHHHH CS
  Response_reg  93 gaddflsKpfdpeeLlkal 111
                   g+  f++Kpf+ +e++ka+
    EPA04345.1 220 GVIAFIQKPFTLDEIKKAV 238
                   ****************998 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.11     2e+02       3      24 ..      25      46 ..      23      49 .. 0.87
   2 !   11.8   0.0   0.00011       0.2       4      30 ..      86     112 ..      83     116 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.11
       TPR_2  3 alynlGlayyklgdyeeAleaf 24
                +l n++++++k ++++ Al ++
  EPA04345.1 25 LLLNQAESLRKTDHLKSALLYM 46
                68899*************9886 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00011
       TPR_2   4 lynlGlayyklgdyeeAleafekAlel 30 
                 l +  ++ + lg++++A+  ++kA  +
  EPA04345.1  86 LLCASKCFLSLGEFDKAKISYQKAKTI 112
                 667788999**************9655 PP

>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   3.2e-05     0.057      29     103 ..      81     157 ..      47     161 .. 0.72
   2 ?   -0.4   0.0      0.91   1.6e+03      56      84 ..     189     215 ..     166     230 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.2e-05
   Rhodanese  29 hIpgAvnv.skdtlsrakkseapllelpeellel.gidnkktvvvycdgggraaaaaallkklGyknvsvldGGfka 103
                  I+gA+   sk  ls +++++a+  ++ ++ +    i n +++v+++d++  ++ +++ ++klGy ++++ ++G ++
  EPA04345.1  81 NIQGALLCaSKCFLSLGEFDKAKISYQKAKTIFStSIENSRPIVIIDDSKAISMKLQTYIEKLGYGEIFLFENGKSG 157
                 4555555575556666666666666666665555789***************9999998888**988***9999765 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.91
   Rhodanese  56 eellelgidnkktvvvycdgggraaaaaa 84 
                 ++ll++  +n+ +++v+ ++ + ++++ +
  EPA04345.1 189 AKLLKE--KNDLQIIVITADEKTTKRVNK 215
                 455555..788999998888777666655 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.4e-05     0.097      10      30 ..      92     112 ..      91     116 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.4e-05
                 HHHHTT-HHHHHHHHHHHHHH CS
       TPR_1  10 ayfklgkydeAleyyekALel 30 
                 ++++lg++d+A   y+kA ++
  EPA04345.1  92 CFLSLGEFDKAKISYQKAKTI 112
                 899***************776 PP

>> PK_C  Pyruvate kinase, alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   5.7e-05       0.1      31      86 ..     190     242 ..     186     247 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.7e-05
                 HHHHT-TSSEEEEEESHHHHHHHHH..HCTTEEHHH.HHHHH...TTSHHHHHHHHHH CS
        PK_C  31 liskyrpkvpiiavtpneltarqla..lyrGvypvlvekaktaestdellreavkvak 86 
                 ++ k + +++ii++t +e+t ++++  ++ Gv+++  +k     ++de +++av++a 
  EPA04345.1 190 KLLKEKNDLQIIVITADEKTTKRVNktISSGVIAFI-QK---PFTLDE-IKKAVDIAE 242
                 67788999****************99999******5.55...455788.888988886 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       2.1   3.7e+03       3       8 ..      43      48 ..      25      57 .. 0.61
   2 ?   11.3   0.1   0.00019      0.33      10      30 ..      92     112 ..      89     115 .. 0.87
   3 ?   -3.3   0.0       8.9   1.6e+04      25      32 ..     235     242 ..     233     243 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2.1
                HHHHHH CS
       TPR_8  3 ayynlg 8 
                ++y+l+
  EPA04345.1 43 LLYMLA 48
                345555 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00019
                 HHHHTT-HHHHHHHHHHHHHH CS
       TPR_8  10 iylklgdyeeAkeyyekalel 30 
                 + l+lg++++Ak +y+ka ++
  EPA04345.1  92 CFLSLGEFDKAKISYQKAKTI 112
                 6789*************9765 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 8.9
                 HHHHHHHH CS
       TPR_8  25 ekaleldp 32 
                 +ka+++++
  EPA04345.1 235 KKAVDIAE 242
                 79999876 PP

>> NFACT-R_2  NFACT protein RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00048      0.86      48      76 ..      55      83 ..      45      91 .. 0.92
   2 ?   -2.4   0.0       3.1   5.5e+03      30      49 ..     109     128 ..      97     138 .. 0.57
   3 ?   -0.0   0.0      0.56     1e+03      28      63 ..     205     241 ..     183     246 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00048
   NFACT-R_2 48 dgelseedlelaarivarYskgkeeeeve 76
                +g+ s++++e +a++ + Ysk+k+ ++++
  EPA04345.1 55 QGKESKDEIEKTADLFLEYSKAKNSKNIQ 83
                68999*******************99875 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.1
   NFACT-R_2  30 kdfvslrakshkGplvlidg 49 
                  +++  +  + + p+v+id+
  EPA04345.1 109 AKTIFSTSIENSRPIVIIDD 128
                 33332344455567777764 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.56
   NFACT-R_2  28 l.kkdfvslrakshkGplvlidgelseedlelaariv 63 
                 + +k + +++ +  +G ++ i+  ++ ++++ a +i+
  EPA04345.1 205 AdEKTTKRVNKTISSGVIAFIQKPFTLDEIKKAVDIA 241
                 2233344455555566666677777777777777765 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1      0.35   6.2e+02       4      15 ..      27      38 ..      25      70 .. 0.63
   2 ?    7.8   0.0    0.0031       5.6       8      33 .]      91     116 ..      85     116 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.35
                HHHHHHHHHHHH CS
       TPR_6  4 yklalsyrklgd 15
                +++a+s+rk++ 
  EPA04345.1 27 LNQAESLRKTDH 38
                566666666522 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0031
                 HHHHHHHHHHHHHHHHHHHHHH-TT- CS
       TPR_6   8 lsyrklgdtdkAlealerlikeYPdS 33 
                 +++++lg+ dkA+  +++  + + +S
  EPA04345.1  91 KCFLSLGEFDKAKISYQKAKTIFSTS 116
                 7999999***********98887665 PP

>> DUF4829  Domain of unknown function (DUF4829)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.2       1.2   2.2e+03      36      59 ..      18      45 ..       3      66 .. 0.51
   2 ?   11.4   0.1   0.00023      0.41       6      62 ..      72     136 ..      69     148 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.2
     DUF4829 36 fenlensklinisees....eekqklky 59
                ++ + ++ l+n+ e      + k  l+y
  EPA04345.1 18 QFITAHNLLLNQAESLrktdHLKSALLY 45
                3456666777777766333333333333 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00023
     DUF4829   6 eYFkalnkkdaeaakallsk..eslkkslnidfenlensklinisees......eekqklkyiky 62 
                 eY ka n k+++ a+ + sk   sl+++ +++ ++ + ++++++s+e+      +++ k +++k+
  EPA04345.1  72 EYSKAKNSKNIQGALLCASKcfLSLGEFDKAKISYQKAKTIFSTSIENsrpiviIDDSKAISMKL 136
                 6889****************88899*********************9878887766666666665 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.5    0.0002      0.35     160     209 ..     171     217 ..      38     227 .. 0.77
   2 ?   -2.2   0.0       1.3   2.3e+03     162     174 ..     229     241 ..     221     244 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0002
                 SEEEECTTTTTS.-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEE CS
                 xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       SMC_N 160 plyllDeidaaL.DeknvkkvaellkeksknaQfivislreemlekadklv 209
                 p+++lD   ++L D+    + a+llkek+ + Q+ivi+ +e+++++++k++
  EPA04345.1 171 PIVFLD---MELpDFDGDVISAKLLKEKN-DLQIIVITADEKTTKRVNKTI 217
                 555554...55523334444567777766.9**************998876 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.3
                 EEECTTTTTS-HH CS
                 xxxxxxxxxxxxx RF
       SMC_N 162 yllDeidaaLDek 174
                 + lDei  a D +
  EPA04345.1 229 FTLDEIKKAVDIA 241
                 579*****99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       959  (0.0534888); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 1503.50
//
Query:       EPA04346.1  [L=318]
Description: protein CbiG, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-33  113.3   0.2    6.4e-33  112.6   0.2    1.3  1  CbiG_N    Cobalamin synthesis G N-terminal
    4.4e-25   88.5   0.1    3.4e-24   85.7   0.0    2.0  2  CbiG_C    Cobalamin synthesis G C-terminus
    2.3e-14   53.3   0.0    5.5e-14   52.1   0.0    1.7  1  CbiG_mid  Cobalamin biosynthesis central region


Domain annotation for each model (and alignments):
>> CbiG_N  Cobalamin synthesis G N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.6   0.2   1.1e-36   6.4e-33       4      82 .]      22     100 ..      19     100 .. 0.97

  Alignments for each domain:
  == domain 1  score: 112.6 bits;  conditional E-value: 1.1e-36
                 HHHCCC-SEEEEES-HHHHHHHHHHH---TTT--EEEEE-TT--EEEEEE-TT.TTHHHHHHHHHHHTT-EE-XXXXX. CS
      CbiG_N   4 relfkeydalvfilaaGivvRliapllkdKktDpaVvvvdeagrfvisllsGhlggAnelAeeiaallgaepviTtatd 82 
                  elfk++ al++++++G+v+Rliap+lkdKktDpaV+v+d+++ fvis+lsGhlggAnel++ +a+ l+a+pviTta d
  EPA04346.1  22 VELFKNNTALICLFSLGAVIRLIAPYLKDKKTDPAVIVIDDKADFVISMLSGHLGGANELTQIVAQKLNATPVITTAAD 100
                 589**************************************************************************97 PP

>> CbiG_C  Cobalamin synthesis G C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.14   8.5e+02      59      89 ..      80     110 ..      44     113 .. 0.75
   2 !   85.7   0.0   5.6e-28   3.4e-24       1     116 []     197     314 ..     197     314 .. 0.97

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.14
                 TEEEE-HHHHHCHHCSCT-CHHHCCCSSS-H CS
      CbiG_C  59 plktfsaeeLaavevpnpsefvkkevGvpsV 89 
                 +l+ + a++L+a +v ++ + v+k++ v+ V
  EPA04346.1  80 ELTQIVAQKLNATPVITTAADVNKTIAVDLV 110
                 4777889999999999999999999988766 PP

  == domain 2  score: 85.7 bits;  conditional E-value: 5.6e-28
                 EEEEEEE-SS--HHHHHHHHHHHHHHCT--GGGEEEEEESSCCSHHHHHHHHHHHCTSTEEEE-HHHHHCHHCSCT-CHHHCCCSSS-HHHHHHHHHC. CS
      CbiG_C   1 lvvGiGcrrgtsaeeieeaieealeeaglseeavaalatidlKadepgllelaeklglplktfsaeeLaavevpnpsefvkkevGvpsVaEaaAllaa. 98 
                 lv+GiG + +t++++i++ i+ +l++ +lse+++a+l +i++ +d +gl+++ +++g+ ++++++eeLa+++ pnps++vk+  G+ sV+EaaA+  + 
  EPA04346.1 197 LVIGIGLHWDTPKQTIKKGIDFCLQKFKLSEKSIAKLVSIKKPEDIKGLVDIGKEMGIIVEYIEREELAEISAPNPSDTVKAFEGTSSVSEAAAIKVSr 295
                 79*********************************************************************************************8764 PP

                 .EECSCEEEE.TTEEEEEE CS
      CbiG_C  99 arllvpKqak.ggvTvAia 116
                 ++l+v+Kq+   + T+Aia
  EPA04346.1 296 GKLIVEKQKFpPNLTIAIA 314
                 7******87799******8 PP

>> CbiG_mid  Cobalamin biosynthesis central region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.1   0.0   9.2e-18   5.5e-14       1      84 []     105     194 ..     105     194 .. 0.93

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 9.2e-18
    CbiG_mid   1 palDilgrpfGwriegegaltevsaalvngepvavlqdvrlegterlertlpehvdveyk.e.......kaliwitprqlrfseesd.lqlhP 84 
                 +a+D++g++fGw+i++++ +t+vsa +vn+e ++v+q     g ++  ++lp+ v+++ + e       k  ++i+++ ++++  ++ ++++P
  EPA04346.1 105 IAVDLVGKDFGWKIDDDSTVTKVSAYMVNEENIGVYQ---EIGRKDWVKELPKNVKIYSSlEeminsnsKGYLIISDKIVEGDFLKNsVVYRP 194
                 69***********************************...577888888899999999998799*****************9999888***99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 1969.77
//
Query:       EPA04347.1  [L=101]
Description: sirohydrochlorin cobaltochelatase, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-16   59.9   0.0    2.7e-16   59.8   0.0    1.0  1  CbiX      CbiX


Domain annotation for each model (and alignments):
>> CbiX  CbiX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.8   0.0   1.5e-20   2.7e-16       1      94 [.      10     100 ..      10     101 .] 0.89

  Alignments for each domain:
  == domain 1  score: 59.8 bits;  conditional E-value: 1.5e-20
                 -STSSCCHHHHHHHHHHHHHHHCCSCCCEECESCCCECCSCCSSHHHHC-SBSEEEEEEESSSSSHHHHTHHHHHCT--SSSS-TTEEEEE--- CS
        CbiX   1 HGSrdpesneeveklaeelrekgpfkpvelgfleleepsleealrelaeqgvkrivvvPlflfaGvhvkeDIpeeleeaeeahpkdveieytep 94 
                 +GSr++e++ee+e +++++++k++++  e++fle+e p++e++++++ +q +++ ++vP+fl +G  vk+ +++    ++ +++ +v++++t+p
  EPA04347.1  10 RGSREREASEELEIICDAIKAKRDYVFAEYCFLEVEPPYIEDGIEKCLKQDIDHLTIVPYFLYPGKKVKNAVTD---VMKFQKDTKVKFVVTKP 100
                 7*********************************************************************5544...44444444568888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 639.18
//
Query:       EPA04348.1  [L=290]
Description: hypothetical protein BG20_I2552, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-06   27.1   0.0    6.7e-06   25.2   0.0    1.7  1  Trp_halogenase  Tryptophan halogenase


Domain annotation for each model (and alignments):
>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   3.7e-10   6.7e-06     197     362 ..      72     232 ..      63     257 .. 0.73

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 3.7e-10
                     EEE-SEEEE-SGGG-IIIIIIT---EEE-TTT----EEEEEEEE--H.---SSEEEEE-SSEEEEEEEETTEEEE.EEE.E-TTTS-HHHHHHHH CS
  Trp_halogenase 197 eveadlfiDcsGfrgllieqaLktgfedwsdvLltdrAlavqvesee.lvepytrataekaGWtWkiPLqhrlgn.Gyv.yssahadddeAlael 288
                     e e+d+++Dc+Gf++  + + L++ f   +           +v++++  +ep+       +G +W+ PL ++    G+  y+++h+   +A++++
      EPA04348.1  72 EKEYDMIVDCTGFARAYLPK-LEEDFFLPTYEY--KVEYPDKVPFDDfYIEPF----PGMSGYFWYFPLGEKWAHiGAGdYRKNHI---KATDDF 156
                     5689***********99999.566664443333..233333455555555555....5679*********9988878754999999...9***** PP

                     HHHCT--TTTS-.EEEE-.--EEES-SEETTEEE-CCCTEE--CCCS-HHHHHHHHHHHHHHT--BTT--HHHHHH CS
  Trp_halogenase 289 laeldgkleaep.rkirf.ttGrrkqawvknvvalGlasgfvePlestsihliqaalrrLlallpdksdepaaiae 362
                     l++++gk+ +++ r ir+ t G+ k +++  vv +G++ g v +l + +i   ++ ++  +  + d    + a++e
      EPA04348.1 157 LKKYGGKVLQTKgRPIRLaTPGKCKPFYKGKVVGVGESIGTVYALLGEGIIPSMQCVDIFIDNMNDFAAYEKAVDE 232
                     ********99999****9456**********************999999877666655555555544444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 1730.31
//
Query:       EPA04349.1  [L=69]
Description: hypothetical protein BG20_I2644, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.8e-11   42.0   0.0      8e-11   41.9   0.0    1.0  1  Transket_pyr  Transketolase, pyrimidine binding domain


Domain annotation for each model (and alignments):
>> Transket_pyr  Transketolase, pyrimidine binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   0.0   4.5e-15     8e-11       6      72 ..       2      65 ..       1      69 [] 0.93

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 4.5e-15
                  HHHHHHHHHHHHCTTTTEEEEESSTHHHHTTCHCCHHEGGTTEGEEE--S-HHHHHHHHHHHHHHCT CS
  Transket_pyr  6 rkaeaealaellkedpevvligaDvaggtfsvrkgllhdqgegrvidsgisEqavlgfavGaalagp 72
                  r  + ++l el+ke+p++v++gaD++ +  +  +g+++++   r++++gi+E++++ + +G+a++g+
    EPA04349.1  2 RSEYSKTLIELGKENPNIVVLGADTTDSLKTSGFGKMFPN---RFFNVGIAEANLVSTSAGLAASGK 65
                  6667899*********************************...**********************94 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       169  (0.00942607); expected 358.6 (0.02)
Passed bias filter:                      148  (0.00825478); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 481.96
//
Query:       EPA04350.1  [L=127]
Description: hypothetical protein BG20_I2643, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.4e-12   46.2   0.0    5.2e-12   45.6   0.0    1.3  1  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
  ------ inclusion threshold ------
       0.17   11.9   0.0       0.24   11.5   0.0    1.3  1  DUF3939         Protein of unknown function (DUF3939)


Domain annotation for each model (and alignments):
>> Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.0   5.8e-16   5.2e-12     135     198 .]       1      64 [.       1      64 [. 0.98

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 5.8e-16
                     SS-TT-SS----CCHHHHHHHHHHHHHHHT---EEEEESS--TTTCHHHHHHT--EEEESHHHH CS
  Ribul_P_3_epim 135 svePgfgGQkFipevlekikkvrklidekeldlkievDGGvkldnieqiaeagadvlVagsavf 198
                     sv Pg++GQk+i+e+  k+ k+ +++ e++++  ie+DGGv+ldni     +ga ++V gsa++
      EPA04350.1   1 SVIPGKSGQKYIEETHGKMTKLNTILREQKFSGCIEADGGVTLDNIGSCFLDGARAFVGGSAII 64 
                     799***********************************************************95 PP

>> DUF3939  Protein of unknown function (DUF3939)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   2.6e-05      0.24       6      44 ..      64     101 ..      61     118 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.6e-05
     DUF3939   6 vtldevrkAvrkfeeklpkginrtvlvnddkeidlerLa 44 
                 + +++vr+A+r+f +++  +++r++l+++ +e+  + L 
  EPA04350.1  64 IGKQDVRTAIRDFRNQV-LKTKRKILIDKANELGGSDLV 101
                 6789***********95.5699*******9999877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 865.92
//
Query:       EPA04351.1  [L=442]
Description: putative ATP synthase F1, delta subunit [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.9e-23   81.3   1.1    1.6e-22   80.1   1.1    1.7  1  HATPase_c        Histidine kinase-, DNA gyrase B-, and HSP90-
      1e-12   48.2   0.0    1.7e-12   47.5   0.0    1.4  1  MEDS             MEDS: MEthanogen/methylotroph, DcmR Sensory 
    4.4e-12   45.9   0.0    1.3e-11   44.4   0.0    1.8  1  HisKA            His Kinase A (phospho-acceptor) domain
    2.4e-07   30.6   1.1    2.4e-07   30.6   1.1    1.9  2  HATPase_c_5      GHKL domain
     0.0083   16.2   6.6      0.017   15.1   0.8    3.2  3  Cdc13_OB2        Cell division control protein 13, OB2 domain
  ------ inclusion threshold ------
      0.014   15.4   0.2      0.049   13.7   0.2    2.0  1  Sigma70_r1_1     Sigma-70 factor, region 1.1
      0.015   15.3   0.0      0.027   14.4   0.0    1.4  1  HATPase_c_2      Histidine kinase-like ATPase domain
      0.094   12.0   0.1       0.16   11.2   0.1    1.3  1  tRNA-synt_His    Histidyl-tRNA synthetase
        0.1   12.9   1.1         18    5.7   0.1    3.0  3  Cyc-maltodext_N  Cyclomaltodextrinase, N-terminal
       0.11   12.3   1.9       0.53   10.1   1.9    2.2  1  HATPase_c_3      Histidine kinase-, DNA gyrase B-, and HSP90-
       0.12   12.2   0.2        0.2   11.6   0.2    1.4  1  MLIP             Muscular LMNA-interacting protein
       0.64   10.4   4.4          2    8.9   0.1    3.2  3  BRCT             BRCA1 C Terminus (BRCT) domain
        2.6    8.7   8.7      0.095   13.3   1.1    2.3  2  DUF3800          Protein of unknown function (DUF3800)


Domain annotation for each model (and alignments):
>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.1   1.1   1.2e-25   1.6e-22       2     111 ..     141     245 ..     140     246 .. 0.91

  Alignments for each domain:
  == domain 1  score: 80.1 bits;  conditional E-value: 1.2e-25
                 HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHHHHHHHHHTTTEEEEEEETTT CS
   HATPase_c   2 dekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsivkklvelmgGeiwvesepgr 100
                 d+++L+ +++n+++Na  + t+++ i+++ + +++++ i+++D+G Gi+ ++l+k+fe++ +     ++++gtGlGl+ +k++++ +gG+i+v+se g+
  EPA04351.1 141 DKEKLKVVFNNMITNANHAITDGDIISIQTSEDKNNIIIQISDSGHGISADILPKIFEPLFT-----TKQKGTGLGLTSCKSIIQEHGGTINVSSEIGK 234
                 7789999***********97788888999887779***********************6666.....699************8888************* PP

                 EEEEEEEEESS CS
   HATPase_c 101 Gttftftlple 111
                 Gttft+ lp++
  EPA04351.1 235 GTTFTIILPKD 245
                 ******99986 PP

>> MEDS  MEDS: MEthanogen/methylotroph, DcmR Sensory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.5   0.0   1.2e-15   1.7e-12       1     160 [.     270     431 ..     270     432 .. 0.87

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 1.2e-15
        MEDS   1 dHvclfyedeeellealvpfikaglargekvlyvasastldelrealrkagldvdaalesgqleildaeety...lrgggfdpermlealrralakala 96 
                 dH+++ ++d +el e +++f   g++ +   ++v+s+++ d+ +++l ++g+ + ++++s++l i++++e+y     g +f  e ++++l+++ + a +
  EPA04351.1 270 DHLAFEFSDNDELSEYISEFMMLGMRMNCLNVLVISKEEIDDYYNMLTSNGISIKDLVNSEDLIICSHDEMYqnvKVGSSF--EPVIKYLNKVHKIAKK 366
                 8****************************99999999***********************************844444444..5577777777777779 PP

        MEDS  97 dgyaglrvigemtwalrspaereelleyEallnelia..depvtalClYdrrrfsaevladvlrtH 160
                 ++ +gl +ig     l+++ + +++++ E+ ++e+i+  ++p+ ++C+Y  +  ++++++ ++  H
  EPA04351.1 367 KKKTGLCIIGIIAGNLENNGNHKDCIRIEKAWHEIIPnyEMPIRLICPYK-SLSDSKTIESLVLYH 431
                 99***********7666666*****************5566889*****9.777888888888777 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.4   0.0   9.4e-15   1.3e-11       3      64 ..      42     103 ..      40     105 .. 0.94

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 9.4e-15
                 HHHHHHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCH CS
       HisKA   3 grflagvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedlLdlsri 64 
                 g++ a +aH+Lr+PL++i+  +ea+k ++k +e+  + le++++ + r++h+++++Ld+++ 
  EPA04351.1  42 GELSARIAHDLRNPLAVIQCGVEAIKQDVKCDEKTIARLERMQRAVGRMTHQINEVLDFTKP 103
                 899**********************888999999999**********************985 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   1.1   1.8e-10   2.4e-07       3      90 ..     142     231 ..     140     242 .. 0.81
   2 ?   -2.6   0.1       3.7   5.1e+03      55      68 ..     358     371 ..     321     388 .. 0.61

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 1.8e-10
  HATPase_c_5   3 dldlcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg...ek.kkle..sskskkeehGiGlksireivkkykgnlsieae 90 
                  +  l v++ n++ NA  a ++ +    +I+++ +e+k+++ii+i+ s +g   ++  k++    ++k++  G+Gl+s ++i+++++g+++++ e
   EPA04351.1 142 KEKLKVVFNNMITNANHAITDGD----IISIQTSEDKNNIIIQISDSGHGisaDIlPKIFepLFTTKQKGTGLGLTSCKSIIQEHGGTINVSSE 231
                  567899**********9998866....9*******************88854422533333333566799*****************9998765 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.7
  HATPase_c_5  55 kklesskskkeehG 68 
                  +k+++  +kk++ G
   EPA04351.1 358 NKVHKIAKKKKKTG 371
                  33333334444444 PP

>> Cdc13_OB2  Cell division control protein 13, OB2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.13   1.8e+02      45      77 ..      66      98 ..      59     132 .. 0.81
   2 ?   -0.4   0.4      0.84   1.2e+03      40      74 ..     124     157 ..     108     180 .. 0.69
   3 !   15.1   0.8   1.3e-05     0.017      45      98 ..     292     345 ..     259     358 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.13
   Cdc13_OB2 45 liPninCiEililtaeeikelFGtlvedskslk 77
                ++ ++ C E  i   e++++  G++ ++ +++ 
  EPA04351.1 66 IKQDVKCDEKTIARLERMQRAVGRMTHQINEVL 98
                5667899******************98876654 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.84
   Cdc13_OB2  40 kedivliPninCiEililtaeeikelFGtlvedsk 74 
                 + + +++  ++ i i i ++e++k +F +++++++
  EPA04351.1 124 SSNVEIKSLSENIKI-ICDKEKLKVVFNNMITNAN 157
                 445555555555655.4667778888877776654 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 1.3e-05
   Cdc13_OB2  45 liPninCiEililtaeeikelFGtlvedskslkeilfsseisvelerikyklnk 98 
                 l   +nC+++l+ ++eei + +  l  +  s+k+++ s+ + +  +  +y++ k
  EPA04351.1 292 LGMRMNCLNVLVISKEEIDDYYNMLTSNGISIKDLVNSEDLIICSHDEMYQNVK 345
                 45568********************************99999988888888765 PP

>> Sigma70_r1_1  Sigma-70 factor, region 1.1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   3.6e-05     0.049      33      64 ..     303     334 ..     296     345 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.6e-05
                   S--HHHHHHHHHHHHCCT-EEE-SS-...... CS
  Sigma70_r1_1  33 eldseqiediiemLedmgIdvveeaededell 64 
                   ++++e+i+d + mL  +gI++ +  ++ed ++
    EPA04351.1 303 VISKEEIDDYYNMLTSNGISIKDLVNSEDLII 334
                   6899******************9999776655 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0     2e-05     0.027      40     108 ..     149     218 ..     129     241 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2e-05
  HATPase_c_2  40 ctNavehayleap.egpvevrlesdeealtvevaDsGpgfdpetlpdpteeepkeslkegGrGlalikgl 108
                  ++N ++ a++  +  + ++++ + d++ + ++++DsG+g  +  lp+  e+  ++++k  G+Gl   k++
   EPA04351.1 149 FNNMITNANHAITdGDIISIQTSEDKNNIIIQISDSGHGISADILPKIFEPLFTTKQKGTGLGLTSCKSI 218
                  678888899998867888*********************9999999988888788888888888765555 PP

>> tRNA-synt_His  Histidyl-tRNA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00012      0.16      69     122 ..      17      69 ..      15     109 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00012
                    SSSHHHHHHHHHHHHHTSS-EEEEEEEEEEESS-SSTT--CCEEEEEEEEESS- CS
  tRNA-synt_His  69 aDiTpqvaRiaahrlnrerplRlcYaGsvlrtrpdglgrsreplQvGaEliGae 122
                     D+T q+   + h +n ++  Rl  +G++  + + +l++   ++Q+G+E i ++
     EPA04351.1  17 NDTTRQIIQSTKH-VNSPGSERLEAIGELSARIAHDLRNPLAVIQCGVEAIKQD 69 
                    599*****99998.69*********************************99776 PP

>> Cyc-maltodext_N  Cyclomaltodextrinase, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       3.1   4.3e+03      25      56 ..     153     182 ..     141     189 .. 0.64
   2 ?    4.5   0.0     0.031        43      23      56 ..     244     277 ..     236     289 .. 0.85
   3 ?    5.7   0.1     0.013        18       9      46 ..     292     330 ..     288     334 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.1
  Cyc-maltodext_N  25 iakaevslsypgvklkkveklenpnYlfvdLd 56 
                      i++a+  ++  +  + +++++e++n ++++++
       EPA04351.1 153 ITNANHAIT--DGDIISIQTSEDKNNIIIQIS 182
                      444444444..335667777777777777665 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.031
  Cyc-maltodext_N  23 kniakaevslsypgvklkkveklenpnYlfvdLd 56 
                      k+i+    ++++pg  l+k++k++n ++l  +++
       EPA04351.1 244 KDITRLGSRVNEPGTILEKISKMKNHDHLAFEFS 277
                      788889999*******************987765 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.013
  Cyc-maltodext_N   9 vgmknpelqllvyg.kniakaevslsypgvklkkvekle 46 
                       gm+ + l++lv + ++i ++   l+++g+++k+++++e
       EPA04351.1 292 LGMRMNCLNVLVISkEEIDDYYNMLTSNGISIKDLVNSE 330
                      59*******99876489999999999*******998876 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   1.9   0.00038      0.53       9      63 ..     151     206 ..     115     241 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00038
  HATPase_c_3   9 elvdNsldAdaen..vkievnknrgktgeivieDdGkGmseeelknalrlatsskea 63 
                   ++ N+  A      ++i+ ++++ ++  i+i D G+G+s + l + +++  ++k++
   EPA04351.1 151 NMITNANHAITDGdiISIQTSEDK-NNIIIQISDSGHGISADILPKIFEPLFTTKQK 206
                  445555554333366899999886.68999************999999988888874 PP

>> MLIP  Muscular LMNA-interacting protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   0.00014       0.2     123     197 ..      20      95 ..      11     135 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00014
        MLIP 123 egtvldthselcspaqlrqq.teelcavidqvlqdpltmvtsessadepkvllssetvkvsttlqraaGretryan 197
                   +++++   + sp   r     el a i + l++pl++++  ++a ++ v++ ++t      +qra Gr t+  n
  EPA04351.1  20 TRQIIQSTKHVNSPGSERLEaIGELSARIAHDLRNPLAVIQCGVEAIKQDVKCDEKTIARLERMQRAVGRMTHQIN 95 
                 45667777788888887754168*************************************************9877 PP

>> BRCT  BRCA1 C Terminus (BRCT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       2.7   3.7e+03      11      27 ..       8      26 ..       4      28 .. 0.76
   2 ?    8.9   0.1    0.0014         2      26      51 ..     216     243 ..     202     287 .. 0.80
   3 ?    1.6   0.1      0.26   3.6e+02      16      52 ..     303     338 ..     297     370 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.7
                EEE..EESTSSHHHHHHHH CS
        BRCT 11 fvi..tgvldnftrdelee 27
                f+i  +++++++tr+ +++
  EPA04351.1  8 FFIckKTTKNDTTRQIIQS 26
                7777888888899988876 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0014
                 HHHHHHTTCEE..ESSCSTTSSEEEESS CS
        BRCT  26 eelikehGGkv..ttevskktthlvvge 51 
                 +++i+ehGG++  ++e+ k tt+ ++  
  EPA04351.1 216 KSIIQEHGGTInvSSEIGKGTTFTIILP 243
                 89*********9999999*999999644 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.26
                 STSSHHHHHHHHHHHHTTCEEESSCSTTSSEEEESSS CS
        BRCT  16 vldnftrdeleelikehGGkvttevskktthlvvgep 52 
                 v + ++ d++ +++ ++G ++ + v+++ ++++++++
  EPA04351.1 303 VISKEEIDDYYNMLTSNGISIKDLVNSE-DLIICSHD 338
                 4588899999***********6655555.44444444 PP

>> DUF3800  Protein of unknown function (DUF3800)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   1.1   6.9e-05     0.095      44     111 ..      87     183 ..       3     188 .. 0.59
   2 ?   -1.0   1.3       1.9   2.6e+03      44      57 ..     327     366 ..     235     424 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.9e-05
     DUF3800  44 y.......................krlleriakflkkndlik.........sdeesdesilivldkkkkkekakkel.eilld.......esvkfvdSk 102
                 +                       +++l+ i          k         + ++ +e+i+i++dk+k k + ++++ + + +       +s++  + k
  EPA04351.1  87 VgrmthqinevldftkprslvlsqCHILDII----------KevisnssnvEIKSLSENIKIICDKEKLKVVFNNMItNAN-HaitdgdiISIQTSEDK 174
                 0333333333333333333333332233332..........1344444555445678899999999554444333334222.13555889********* PP

     DUF3800 103 esrglQlAD 111
                 +++ +Q+ D
  EPA04351.1 175 NNIIIQISD 183
                 *******99 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.9
     DUF3800  44 y..........................krlleriakflkk 57 
                 +                           + l++++k +kk
  EPA04351.1 327 VnsedliicshdemyqnvkvgssfepvIKYLNKVHKIAKK 366
                 2333333333333344444433333333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (442 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       897  (0.0500307); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.66u 0.29s 00:00:00.95 Elapsed: 00:00:00.48
# Mc/sec: 2747.55
//
Query:       EPA04352.1  [L=40]
Description: hypothetical protein BG20_I1834 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.47
# Mc/sec: 255.05
//
Query:       EPA04353.1  [L=128]
Description: hypothetical protein BG20_I1839 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00031   20.9   0.5    0.00043   20.5   0.5    1.2  1  Yippee-Mis18  Yippee zinc-binding/DNA-binding /Mis18, centrom
     0.0034   17.6   0.3     0.0061   16.8   0.3    1.4  1  RIG-I_C-RD    C-terminal domain of RIG-I
  ------ inclusion threshold ------
       0.08   12.6   0.1       0.11   12.2   0.1    1.1  1  DUF4371       Domain of unknown function (DUF4371)


Domain annotation for each model (and alignments):
>> Yippee-Mis18  Yippee zinc-binding/DNA-binding /Mis18, centromere assembly
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.5   7.2e-08   0.00043      25      69 ..      15      60 ..       2      70 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 7.2e-08
                  CEEEES---CCCEEEECEEEETTS.TTEEEEEEEETTT--EEEEEE CS
  Yippee-Mis18 25 lnivvlkkvtrnvvvgkelvtdee.gkctystlsCkgCnsvlGwkY 69
                   ++++++k tr+++v+++++++e+ ++ +++++ C++Cn+ +G   
    EPA04353.1 15 VQTLIIEKGTRRIRVRSHPIQKEStQTDKIQKIVCESCNNDIGSNI 60
                  689999****************774669***************865 PP

>> RIG-I_C-RD  C-terminal domain of RIG-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.3     1e-06    0.0061      35      70 ..      25      59 ..       3      66 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1e-06
  RIG-I_C-RD 35 elvkvkekkkkekkfedfekkgkikCkkCkkdwGim 70
                ++++v+ +++ +k+  ++ k +ki C++C++d+G+ 
  EPA04353.1 25 RRIRVR-SHPIQKESTQTDKIQKIVCESCNNDIGSN 59
                455555.99999999*******************86 PP

>> DUF4371  Domain of unknown function (DUF4371)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   1.8e-05      0.11     105     156 ..      10      63 ..       3      76 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.8e-05
     DUF4371 105 sqneaikkvvlknaPknnkltspdiqkdivhv..fakevtssiikelddalfsl 156
                 ++ e+++ +++++  ++ ++ s++iqk+ +++  + k v +s  ++++ ++  +
  EPA04353.1  10 TNYETVQTLIIEKGTRRIRVRSHPIQKESTQTdkIQKIVCESCNNDIGSNICKV 63 
                 56799***********************98862245666677777776666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       883  (0.0492498); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 874.82
//
Query:       EPA04354.1  [L=89]
Description: hypothetical protein TIGR00725 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-26   92.1   0.8    2.9e-26   91.9   0.8    1.0  1  LDcluster4      SLOG cluster4 family
    0.00075   18.8   0.1    0.00083   18.7   0.1    1.1  1  DNA_processg_A  DNA recombination-mediator protein A


Domain annotation for each model (and alignments):
>> LDcluster4  SLOG cluster4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.9   0.8   3.3e-30   2.9e-26       1      86 [.       4      88 ..       4      89 .] 0.94

  Alignments for each domain:
  == domain 1  score: 91.9 bits;  conditional E-value: 3.3e-30
  LDcluster4  1 klkigVmGsaeteakeealelaeelGrliAkegavlltGgrtGvmeaaskGakeagGltvGilpassekehsnkyvdiiiyTGlgl 86
                k++i V+G+++++++++++++a+e+G ++Ak+ +vl+tGg +Gvm+aas+Ga++++GltvGi+p+ ++ + +n+++d++i++G+g 
  EPA04354.1  4 KVQILVIGHNDNGCTPTHEKIAYEIGCEVAKASCVLITGGLGGVMKAASQGAHDENGLTVGIIPQ-DDASFANEFCDVVIPSGMGI 88
                689********88****************************************************.556667777*********96 PP

>> DNA_processg_A  DNA recombination-mediator protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   9.2e-08   0.00083      53     104 ..      17      68 ..       2      76 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 9.2e-08
  DNA_processg_A  53 aseygkevakklakelaeagitivSGlAlGiDaaahraaleaggktvavlgt 104
                     +++ ++++a ++  e+a+a+++ + G+  G+ +aa ++a +++g tv+++++
      EPA04354.1  17 CTPTHEKIAYEIGCEVAKASCVLITGGLGGVMKAASQGAHDENGLTVGIIPQ 68 
                     789999*******************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 580.04
//
Query:       EPA04355.1  [L=135]
Description: histidine triad domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-22   80.3   0.6    1.7e-22   80.0   0.6    1.1  1  HIT            HIT domain
    1.8e-12   47.7   0.1    2.4e-12   47.3   0.1    1.1  1  DcpS_C         Scavenger mRNA decapping enzyme C-term binding
     0.0011   18.8   0.2     0.0015   18.4   0.2    1.3  1  CwfJ_C_1       Protein similar to CwfJ C-terminus 1
     0.0088   15.8   0.1      0.011   15.4   0.1    1.2  1  GalP_UDP_tr_C  Galactose-1-phosphate uridyl transferase, C-te


Domain annotation for each model (and alignments):
>> HIT  HIT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.0   0.6   3.8e-26   1.7e-22       2      97 ..      11     104 ..      10     105 .. 0.95

  Alignments for each domain:
  == domain 1  score: 80.0 bits;  conditional E-value: 3.8e-26
                 GCC-CCEEEE-SSEEEEE-SS-SSSSEEEEEESSTGCSGGGCCHHHHHHHHHHHHHHHHHHHTCTTCCCEEEEEEESGGGT-SSSS-EEEEEEC-T CS
         HIT   2 keipstvvyeddlvlafldidpkapghlLvipkkhlselhdlteeelakllsavkkvakalqkkfknkglrvvinngahagqsvahlHiHviprre 97 
                 ++ip++++ ++ +++afld +p a+gh+Lvipk h+++++d++ ee ++l+s+v  v  ++ +     ++ v++ ng++agq+++h+H+H++pr++
  EPA04355.1  11 GQIPTKIIGQTSHSIAFLDAFPLAKGHTLVIPKYHYAKIQDMNTEENSDLFSLVHDVLPKVDELT--GSTLVAVHNGKEAGQEIQHVHVHLVPRSK 104
                 689***********************************************************943..4788999*******************986 PP

>> DcpS_C  Scavenger mRNA decapping enzyme C-term binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   0.1   5.4e-16   2.4e-12       2     103 ..       3     103 ..       2     110 .. 0.88

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 5.4e-16
                 -HHHHHHTTSS-B-EEEE-SSEEEEE-SS-SSSEEEEEEESS---SGGG--TTTTTHHHHHHHHHHHHHHHTT-T-EEEEE--SCCCT--S-S--EEEE CS
      DcpS_C   2 wvfnilakgkepervvyedekfvvlkDikpkaklhllvipkrdikslrdLtkehlpllkemrekakkvieekynevdaeelrvgvhyqPsvyhlHlHvi 100
                 ++f++++ g++p++++ ++++ +++ D+ p ak h lvipk + ++++d+++e+ + l ++++++   ++e   +     +  g ++ + ++h+H+H++
  EPA04355.1   3 CIFCKIVAGQIPTKIIGQTSHSIAFLDAFPLAKGHTLVIPKYHYAKIQDMNTEENSDLFSLVHDVLPKVDELT-GSTLVAVHNGKEAGQEIQHVHVHLV 100
                 9*************************************************88877777777777777776666.5688899****************99 PP

                 E.. CS
      DcpS_C 101 sld 103
                   +
  EPA04355.1 101 PRS 103
                 754 PP

>> CwfJ_C_1  Protein similar to CwfJ C-terminus 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.2   3.3e-07    0.0015      14     113 ..       3     106 ..       1     116 [. 0.77

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 3.3e-07
                 -S----SS---SS--S-B-SSEEEE---S-SSTT-EEEEESS--SSTTSS-HHHHHHH.HHHHHHHHHHHHHTT--EEEEEE-...SSS-----EEEEE CS
    CwfJ_C_1  14 ClfClsnpklekhlivsignkvYlalpkgpLssgHvliipieHisallsldeevldei.rkfrkalvkmykkqdkdavvfEis...sersvHlaiqvip 108
                 C fC   + +    i+   ++  + l   pL++gH l+ip  H ++ + ++ e+ +++ +  +  l k+ + +++ +v   +     ++ +H++++++p
  EPA04355.1   3 CIFCKIVAGQIPTKIIGQTSHSIAFLDAFPLAKGHTLVIPKYHYAKIQDMNTEENSDLfSLVHDVLPKVDELTGSTLVAVHNGkeaGQEIQHVHVHLVP 101
                 77776666666666777666666777889******************99998777665266778888998888998887776656678899******99 PP

                 --HHH CS
    CwfJ_C_1 109 vpksi 113
                  +k  
  EPA04355.1 102 RSKDD 106
                 87765 PP

>> GalP_UDP_tr_C  Galactose-1-phosphate uridyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   2.5e-06     0.011      52     118 ..      37      99 ..      24     129 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.5e-06
                    -EEEEESS--SSGGG--HHHHHHHHHHHHHHHHHHHHHCT............S---EEEEEE---SCCCTTTT--EEEE CS
  GalP_UDP_tr_C  52 evlllrkaevkslaeladeekedlaailkklarkydnlfe............tsfeysmGlhqaplnaeednswlHaHf 118
                    ++l+++k + +++++++ ee++dl + +++++ k d+l                              +e ++ +H+H+
     EPA04355.1  37 HTLVIPKYHYAKIQDMNTEENSDLFSLVHDVLPKVDELTGstlvavhngkeaG---------------QEIQH-VHVHL 99 
                    59***********************************9774333333333322...............22222.34443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.33s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 791.88
//
Query:       EPA04356.1  [L=100]
Description: hypothetical protein BG20_I1833, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.021   15.3   7.2       0.75   10.3   0.8    2.2  2  zf-C4pol        C4-type zinc-finger of DNA polymerase delta
      0.076   12.9  11.4        1.5    8.7   0.1    3.5  4  HNH_5           HNH endonuclease
       0.31   11.1  10.5       0.81    9.7   5.0    2.2  2  Cytochrome_C7   Cytochrome c7 and related cytochrome c
          2    8.4  15.9        2.3    8.2   0.7    3.5  3  DUF4428         Domain of unknown function (DUF4428)
        3.6    7.5  12.2       0.87    9.5   0.5    3.5  4  Prok-RING_4     Prokaryotic RING finger family 4
        4.7    7.8  11.3    1.7e+02    2.8  11.3    2.7  1  Cytochrom_c3_2  Cytochrome c3


Domain annotation for each model (and alignments):
>> zf-C4pol  C4-type zinc-finger of DNA polymerase delta
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.8   0.00085       2.5       1      26 [.      11      48 ..      11      53 .. 0.75
   2 ?   10.3   0.8   0.00025      0.75       1      25 [.      55      92 ..      55      99 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00085
    zf-C4pol  1 ClvCkeklk............kalCkkCrsdkqesllk 26
                C +C+++l+             +lC +C+ +k++++++
  EPA04356.1 11 CAICNKELThkhkpkrewnvkGSLCGDCHFEKSKEYYE 48
                999*9544455566677778799*****9888888775 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00025
    zf-C4pol  1 ClvCk......eklk..........kalCkkCrsdkqesll 25
                C+vC+      e               lCk+C ++k+es +
  EPA04356.1 55 CVVCGttkiisE--LweprwqwdmeGLLCKECFDKKEES-F 92
                9****6655550..0455555666699*****9666554.3 PP

>> HNH_5  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.4   0.00062       1.9      34      50 ..       9      25 ..       3      30 .. 0.83
   2 ?    5.2   3.5    0.0066        20       1      28 [.      11      39 ..      11      53 .. 0.74
   3 ?   -0.8   0.1      0.48   1.4e+03       1       8 [.      55      62 ..      55      67 .. 0.79
   4 ?    8.7   0.1    0.0005       1.5      28      50 ..      73      95 ..      71      98 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00062
       HNH_5 34 tlCkkCNqkkgqkvdaa 50
                t+C  CN+++++k++++
  EPA04356.1  9 TYCAICNKELTHKHKPK 25
                68999****99998765 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0066
       HNH_5  1 CiyCgke.iaekelseeHIiPeslGGklt 28
                C++C+ke +++++ ++e  +  sl+G  +
  EPA04356.1 11 CAICNKElTHKHKPKREWNVKGSLCGDCH 39
                88888885555555888888888887655 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.48
       HNH_5  1 CiyCgkei 8 
                C++Cg ++
  EPA04356.1 55 CVVCGTTK 62
                99999874 PP

  == domain 4  score: 8.7 bits;  conditional E-value: 0.0005
       HNH_5 28 tisnlvtlCkkCNqkkgqkvdaa 50
                +++  + lCk+C +kk +++d++
  EPA04356.1 73 QWDMEGLLCKECFDKKEESFDSK 95
                5555566************9987 PP

>> Cytochrome_C7  Cytochrome c7 and related cytochrome c
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   5.0   0.00027      0.81      16      71 ..      11      58 ..       4      60 .. 0.61
   2 ?    4.8   0.2    0.0095        28      45      68 ..      76      99 ..      61     100 .] 0.70

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00027
  Cytochrome_C7 16 CtdCHsklfeskakkkmaemekgkskkaeves.lt.CgaCHdgknaf..svakkaeCakC 71
                   C+ C ++l            ++++  k+e++   + Cg+CH +k ++  + + ++ C  C
     EPA04356.1 11 CAICNKEL------------THKHKPKREWNVkGSlCGDCHFEKSKEyyEGKVRQPCVVC 58
                   44454444............2333334455554336*****8888875555668888888 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0095
  Cytochrome_C7 45 vesltCgaCHdgknafsvakkaeC 68
                   +e l C++C d+k+++   kk+ C
     EPA04356.1 76 MEGLLCKECFDKKEESFDSKKKFC 99
                   233459999999998866667766 PP

>> DUF4428  Domain of unknown function (DUF4428)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   3.1    0.0023       6.9       2      26 ..      11      38 ..      10      46 .. 0.68
   2 ?    0.7   0.2      0.17     5e+02       1       7 [.      54      60 ..      54      65 .. 0.85
   3 ?    8.2   0.7   0.00076       2.3      19      35 ..      77      93 ..      76      98 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0023
     DUF4428  2 CaiCgkKigllkr...lkleDgyvCkdC 26
                CaiC+k+++  ++        g +C dC
  EPA04356.1 11 CAICNKELTHKHKpkrEWNVKGSLCGDC 38
                *******998755321222235677777 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.17
     DUF4428  1 iCaiCgk 7 
                +C +Cg+
  EPA04356.1 54 PCVVCGT 60
                5****96 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.00076
     DUF4428 19 DgyvCkdClkKlsefls 35
                +g +Ck+C+ K  e+++
  EPA04356.1 77 EGLLCKECFDKKEESFD 93
                589********544443 PP

>> Prok-RING_4  Prokaryotic RING finger family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.2     0.022        66      31      42 ..       9      20 ..       4      24 .. 0.75
   2 ?   -1.0   0.1      0.55   1.6e+03      20      26 ..      34      40 ..      33      49 .. 0.73
   3 ?    0.7   0.1      0.16   4.9e+02       1       7 [.      55      61 ..      53      67 .. 0.84
   4 ?    9.5   0.5   0.00029      0.87      19      31 ..      79      91 ..      77      99 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.022
  Prok-RING_4 31 ssCPlCqrrisk 42
                 + C +C++++ +
   EPA04356.1  9 TYCAICNKELTH 20
                 569999999865 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.55
  Prok-RING_4 20 vCkeCfd 26
                 +C +C  
   EPA04356.1 34 LCGDCHF 40
                 6999954 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.16
  Prok-RING_4  1 CvlCgeq 7 
                 Cv+Cg+ 
   EPA04356.1 55 CVVCGTT 61
                 9999986 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.00029
  Prok-RING_4 19 lvCkeCfdskdls 31
                 l+CkeCfd+k+ s
   EPA04356.1 79 LLCKECFDKKEES 91
                 79*******9866 PP

>> Cytochrom_c3_2  Cytochrome c3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8  11.3     0.057   1.7e+02       5      71 ..      31      91 ..       5     100 .] 0.48

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.057
                    CT.TGGGTSSSST-SSTTHHHHHHHHHHH--HHHCHTTSST............TSSBTTSSC.TSSS-GGGTS-TTTSB CS
  Cytochrom_c3_2  5 egvkCadCHtkekpkkdkaveeekClsCHgkleelakktkea...........keanphksh.ekeleCteCHkeHkks 71
                    +g  C dCH +++++  +    +                              +  +p  +  ++ l C+eC  + ++s
      EPA04356.1 31 KGSLCGDCHFEKSKEYYEGKVRQ------------------PcvvcgttkiisELWEPRWQWdMEGLLCKECFDKKEES 91
                    33345555555554444444444..................14444444443322333333324666677777666644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       811  (0.045234); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 595.50
//
Query:       EPA04357.1  [L=379]
Description: 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.4e-66  221.7   0.6    6.4e-66  221.7   0.6    1.6  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
      9e-34  116.0   0.2    1.4e-26   93.0   0.1    2.8  3  3HCDH           3-hydroxyacyl-CoA dehydrogenase, C-terminal d
    4.2e-05   23.6   0.1    7.4e-05   22.8   0.1    1.5  1  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
    0.00013   22.2   0.1    0.00023   21.4   0.1    1.5  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
  ------ inclusion threshold ------
      0.054   14.1   1.3        0.2   12.2   1.3    2.1  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
        0.3   10.7   3.4         20    4.7   3.4    2.3  1  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
        1.4    9.6   6.9       0.41   11.3   0.6    2.9  4  DUF643          Protein of unknown function (DUF643)


Domain annotation for each model (and alignments):
>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  221.7   0.6   2.5e-69   6.4e-66       1     179 [.       5     185 ..       5     186 .. 0.99
   2 ?   -3.1   0.1       2.4   6.1e+03      88     115 ..     295     322 ..     292     333 .. 0.72

  Alignments for each domain:
  == domain 1  score: 221.7 bits;  conditional E-value: 2.5e-69
                 EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES-HHHHH.C-SEEEE-S-SSHHHHHHHHH CS
     3HCDH_N   1 kvaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalarisfttdleeav.dadlviEavvEnlelKrkvfa 98 
                 +++v+G+G+mG+gia+v a ag++Vvl di++ +l+ka+eki+ sl+klv k+k+++++++++ +ri++  +l+eav da+lviE v+E +elK+kv+a
  EPA04357.1   5 NITVLGSGIMGHGIAQVSATAGYNVVLRDIEQGFLDKAMEKIKWSLDKLVTKEKISQQDADSIYSRIKPVVNLSEAVkDAQLVIEVVPEIMELKKKVYA 103
                 69************************************************************************************************* PP

                 HHHCCS-TTSEEEE--SSS-HHHHCCCSSSGGGEEEEEE-SSTTT--EEEEEE-TT--HHHHHHHHHHHHHTT-EEEEE.CS CS
     3HCDH_N  99 elekiakpdailasnTSslsiselaealkrperviglHFfnPpplmkLvEvvrgekTseetvatvvelakkigktpvvv.kd 179
                 el+++a +++i+asnTS+l+i+e+a++++rpe++ig+HFfnPp+lmkLvEv++gekTs+e+++ + +++k+++k+pv + kd
  EPA04357.1 104 ELDSVAGKNVIFASNTSTLPITEIANTTTRPEKFIGIHFFNPPQLMKLVEVIPGEKTSNEIIDLTLDYVKSVKKEPVICrKD 185
                 ******************************************************************************9777 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.4
                 SSHHHHHHHHHHHHCCS-TTSEEEE--S CS
     3HCDH_N  88 EnlelKrkvfaelekiakpdailasnTS 115
                 E+l+ K + ++ +++i+++ a l++n  
  EPA04357.1 295 EELAKKCNPIQLVANILNNAAWLITNKA 322
                 7777788888888888888888888854 PP

>> 3HCDH  3-hydroxyacyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       1.3   3.4e+03      42      95 ..      17      68 ..      10      69 .. 0.56
   2 !   93.0   0.1   5.3e-30   1.4e-26       1      97 []     188     283 ..     188     283 .. 0.95
   3 !   19.8   0.0   3.7e-07   0.00094       7      78 ..     306     376 ..     305     379 .] 0.88

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.3
                CHHHHHHHHHHHHHHHHHHHHHHHTTTHGGHH-.HHHHHHHHTT--BGGGTBSSS CS
       3HCDH 42 Gpfelldlvgldvakkilevlaeelgerayaps.plleklveagrlgrktgkgfy 95
                G+ +++ ++g +v+++ +e   +++ ++a ++    l+klv +++++++  + +y
  EPA04357.1 17 GIAQVSATAGYNVVLRDIE---QGFLDKAMEKIkWSLDKLVTKEKISQQDADSIY 68
                6666666666666655444...333344222220236777777777777666665 PP

  == domain 2  score: 93.0 bits;  conditional E-value: 5.3e-30
                 TTTHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHTTTHGGHH-HHHHHHHHTT--BGGGTBSSSBC CS
       3HCDH   1 GFvvnRvlapllneavrlveegvaspediDaamrlglGlpmGpfelldlvgldvakkilevlaeelgerayapsplleklveagrlgrktgkgfyky 97 
                 GF+ nR+++p++ ea+ ++++  a++ +iD+a++ +lG+pmG+fel+d +g+dv +k++  ++ + ++    p+p +ek+++a++lg+k+g+gfyky
  EPA04357.1 188 GFIINRLFIPMVHEACYMMDRTGATMSEIDSAVKFKLGFPMGIFELADFTGMDVIHKATVEMHLRDKKV-ILPHPTIEKMFDAKKLGQKSGEGFYKY 283
                 9**********************************************************9888886666.5569**********************9 PP

  == domain 3  score: 19.8 bits;  conditional E-value: 3.7e-07
                 HHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHTTTHGGHH-HHHH CS
       3HCDH   7 vlapllneavrlveegvaspediDaamrlglGlpmGpfelldlvgldvakkilevlaeelgerayapsplle 78 
                 ++a +ln+a +l+ ++  ++++i++a++lglGl+   f+++ ++g+    + l+ la ++g+  y+p pll 
  EPA04357.1 306 LVANILNNAAWLITNKASDIAEIEKAAQLGLGLKKPLFQTAKEIGIKNIVNELNQLATKYGKF-YEPDPLLV 376
                 57889*****************************************99999888899988876.55666665 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.1   2.9e-08   7.4e-05       1      98 [.       5     114 ..       5     165 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 2.9e-08
                     -EEEE--SHHHHHHHHHHHTTT--EEEE-S-H....HHHHHHH......HHSSBTTTBTT----TTEEEES-HHHHHTT--EEEE---HHH..HH CS
  NAD_Gly3P_dh_N   1 kiavlGaGswGtalAkvlaenghevrlwvree....elieein......eehenvkyLpgiklpenlvattdlaealkgadiivlvvPsqa..lr 83 
                     +i+vlG+G  G  +A+v a +g +v+l   e+    + +e+i+       ++e     +  ++ + ++ + +l ea+k+a++++ vvP  +   +
      EPA04357.1   5 NITVLGSGIMGHGIAQVSATAGYNVVLRDIEQgfldKAMEKIKwsldklVTKEKISQQDADSIYSRIKPVVNLSEAVKDAQLVIEVVPEIMelKK 99 
                     59**************************99999999555555422211112333333344578899**********************7431145 PP

                     HHHHHHCCC--TT-E CS
  NAD_Gly3P_dh_N  84 evlkklkgllkkkai 98 
                     +v ++l+ +  k++i
      EPA04357.1 100 KVYAELDSVAGKNVI 114
                     666666666555555 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.1     9e-08   0.00023       1      92 [.       5     121 ..       5     146 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 9e-08
                    EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT........................EEE-SSHHHHHHHCSEEEE-SSSHHHHHH. CS
  NAD_binding_2   1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg........................akaaesieelvasldvvitmvkagkavde. 71 
                    +i ++G G+MG+ +a+  + agy+v++ + ++  +++++++                         +k++ +++e+v+++++vi +v++  + ++ 
     EPA04357.1   5 NITVLGSGIMGHGIAQVSATAGYNVVLRDIEQGFLDKAMEKIkwsldklvtkekisqqdadsiysrIKPVVNLSEAVKDAQLVIEVVPEIMELKKk 100
                    6899********************************99999779999999**************************************98888651 PP

                    HHHSHCCC--TT-EEEE-S-- CS
  NAD_binding_2  72 viegllealkkgdilidgsts 92 
                    v+ +l + + k+ i+   +++
     EPA04357.1 101 VYAELDSVAGKNVIFASNTST 121
                    555565555555444443333 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.3     8e-05       0.2       2      65 ..       6      87 ..       5     119 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8e-05
                   EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.......................-EEECECHHHHHHH-SEE CS
  F420_oxidored  2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg.......................vkvtavdneeaaeeadvv 65
                   i ++G+G mg+++a+  ++ag   +++v   + ++  ++++ e+++                       +k    + +ea+++a  v
     EPA04357.1  6 ITVLGSGIMGHGIAQVSATAG---YNVV-LRDIEQGFLDKAMEKIKwsldklvtkekisqqdadsiysrIKPVV-NLSEAVKDAQLV 87
                   89*******************...**99.436666667777777776666666665555555555554444444.455555555555 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   3.4    0.0077        20      49      78 ..      72     103 ..       1     120 [. 0.57

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0077
                 -EEEEHHHHHHT-SEEEE-S-H..HHHHHHHH CS
        IlvN  49 fevltvaeavkkadvvmiliPD..elqkevye 78 
                   v++++eavk+a++v+ ++P+  el+k+vy 
  EPA04357.1  72 KPVVNLSEAVKDAQLVIEVVPEimELKKKVYA 103
                 34778888888888888888874455677774 PP

>> DUF643  Protein of unknown function (DUF643)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.6   0.00016      0.41       7      69 ..      38     102 ..      32     120 .. 0.83
   2 ?    0.1   0.1      0.48   1.2e+03      57      81 ..     160     184 ..     153     187 .. 0.79
   3 ?   -1.3   0.0       1.3   3.4e+03      19      39 ..     263     283 ..     249     320 .. 0.77
   4 ?   -3.0   0.0       4.2   1.1e+04      16      42 ..     322     348 ..     304     356 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00016
      DUF643   7 fydnlskdtkkeinklyeteqltleqkkqlysavkkiqey..kiktGksveeiindiiepekefi 69 
                 f d   +++k +++kl + e+++++    +ys +k + +    +k  + v e++ +i+e +k++ 
  EPA04357.1  38 FLDKAMEKIKWSLDKLVTKEKISQQDADSIYSRIKPVVNLseAVKDAQLVIEVVPEIMELKKKVY 102
                 89999****************************998876522578888899********999975 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.48
      DUF643  57 iindiiepekefikdvlkdknlikk 81 
                   n+ii+ + +++k v k+  + +k
  EPA04357.1 160 TSNEIIDLTLDYVKSVKKEPVICRK 184
                 4688999999999999888777665 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.3
      DUF643  19 inklyeteqltleqkkqlysa 39 
                 i+k++++++l ++  + +y+ 
  EPA04357.1 263 IEKMFDAKKLGQKSGEGFYKY 283
                 888888888888888888864 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 4.2
      DUF643  16 kkeinklyeteqltleqkkqlysavkk 42 
                   +i+ + ++ ql l  kk l+++ k+
  EPA04357.1 322 ASDIAEIEKAAQLGLGLKKPLFQTAKE 348
                 445777777777777777777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 2402.46
//
Query:       EPA04358.1  [L=95]
Description: hypothetical protein BG20_I1842 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.11   12.4   0.1       0.17   11.7   0.1    1.3  1  Microcin  Colicin E1 (microcin) immunity protein


Domain annotation for each model (and alignments):
>> Microcin  Colicin E1 (microcin) immunity protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   9.7e-06      0.17      10      31 ..      22      43 ..      19      45 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.7e-06
    Microcin 10 LyaiviSTILcPySkyaiEhia 31
                 ++iv+ST+ +P+   + E+++
  EPA04358.1 22 VVVIVMSTMVFPFWNLIREDVF 43
                69***********887777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       798  (0.0445089); expected 358.6 (0.02)
Passed bias filter:                      564  (0.0314574); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 674.50
//
Query:       EPA04359.1  [L=47]
Description: hypothetical protein BG20_I1838 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.029   14.3   0.4       0.04   13.9   0.4    1.3  1  RHH_1           Ribbon-helix-helix protein, copG family
      0.048   14.4   1.3       0.13   13.1   1.3    1.7  1  VAPB_antitox    Putative antitoxin
      0.057   13.4   0.1      0.079   12.9   0.1    1.2  1  VapB_antitoxin  Bacterial antitoxin of type II TA system, Vap
      0.065   13.7   0.2       0.11   13.1   0.2    1.3  1  BrnA_antitoxin  BrnA antitoxin of type II toxin-antitoxin sys


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.4   8.9e-06      0.04       1      28 [.       4      31 ..       4      32 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.9e-06
                EEEEEEEHHHHHHHHHHHHHHTSSHHHH CS
       RHH_1  1 rvsirldeellerLdelarrrgrSrSel 28
                r++i ld++++++L+++ +++ +  Se+
  EPA04359.1  4 RITIMLDDDVVKKLRAIQAKQIKESSEA 31
                8****************99999888876 PP

>> VAPB_antitox  Putative antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.3   2.8e-05      0.13       2      32 ..       6      43 ..       5      47 .] 0.75

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.8e-05
  VAPB_antitox  2 tIsIsdevYekL.....kklKr..egeSFsdvIerLle 32
                  tI+++d+v +kL     k++K+  e  SFs vI+  + 
    EPA04359.1  6 TIMLDDDVVKKLraiqaKQIKEssEAVSFSKVINDHIA 43
                  8***********4444445676667889*****97665 PP

>> VapB_antitoxin  Bacterial antitoxin of type II TA system, VapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   1.8e-05     0.079       2      28 ..       4      32 ..       3      34 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.8e-05
                    XXXXXXXXXXXXX..XXXXXXXXXXXXXX CS
  VapB_antitoxin  2 rtnIeiDDeLlae..AirltglktKrEaV 28
                    r +I +DD+ +++  Ai+   +k+ +EaV
      EPA04359.1  4 RITIMLDDDVVKKlrAIQAKQIKESSEAV 32
                    89**********76699999********9 PP

>> BrnA_antitoxin  BrnA antitoxin of type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.2   2.4e-05      0.11      38      53 ..       4      19 ..       2      24 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.4e-05
  BrnA_antitoxin 38 kvtlRLDadVleaFka 53
                    ++t+ LD dV+++++a
      EPA04359.1  4 RITIMLDDDVVKKLRA 19
                    79*************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 322.51
//
Query:       EPA04360.1  [L=234]
Description: DnaJ domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-15   56.9   1.1      4e-15   55.7   1.1    1.6  1  DnaJ             DnaJ domain
    5.7e-10   39.6   1.3    1.6e-09   38.2   1.3    1.8  1  Fer4_13          4Fe-4S single cluster domain of Ferredoxin I
      9e-06   26.3   3.2    6.5e-05   23.6   3.2    2.3  1  Fer4_15          4Fe-4S single cluster domain
     0.0045   17.0   1.3      0.011   15.7   1.3    1.6  1  Fer4_19          Divergent 4Fe-4S mono-cluster
  ------ inclusion threshold ------
      0.095   12.5   9.9       0.93    9.4   5.9    2.3  2  Fer4             4Fe-4S binding domain
        6.4    7.6   5.9        4.3    8.2   0.1    3.2  3  SRR              Seven Residue Repeat


Domain annotation for each model (and alignments):
>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.7   1.1   1.3e-18     4e-15       4      56 ..      19      70 ..      15      75 .. 0.90

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 1.3e-18
                HHHTSSTTG-HHHHHHHHHHHHHHHSTTTSCCHHHHHHHHHHHHHHHHHHTSH CS
        DnaJ  4 eiLgvskdasedeIkkaYrklalkyHPDknpkdpeaeekFkeineAyevLsdp 56
                + L+v++d+s deIk+aYrklal++HPDkn++++e  e Fk+++eAy+ L+++
  EPA04360.1 19 KALNVKPDSSWDEIKAAYRKLALEFHPDKNTSQKEGIE-FKKVTEAYNHLKKN 70
                679***************************77776665.***********875 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   1.3   5.2e-13   1.6e-09       1      58 []     164     222 ..     164     222 .. 0.86

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 5.2e-13
     Fer4_13   1 VDrdtCiacgaCvelaPdvFeeddeggasvvaeqpts..eeekadaeeAadaCPvesIgv 58 
                 VD++ Ci+c +C  +aPdvF ++++ ++s  +    +   +  +++++Aa++CP+++I+v
  EPA04360.1 164 VDKSLCIGCCSCEIIAPDVFLINKN-SKSNPKSSVINpkGAGVNKIMNAAETCPTKAITV 222
                 9**********************98.889888764442244589**************97 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   3.2   2.2e-08   6.5e-05       1      66 []     162     222 ..     162     222 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 2.2e-08
     Fer4_15   1 VvvDrdaCigcglCvaeapevfeldedglasvllddgeiaegevpddeeeaaqeAaraCPvdAIrv 66 
                 V vD+++Cigc  C   ap+vf ++++ ++  + +         +   + ++  Aa++CP++AI+v
  EPA04360.1 162 VDVDKSLCIGCCSCEIIAPDVFLINKNSKSNPKSS-----VINPKGAGVNKIMNAAETCPTKAITV 222
                 679************************99977732.....22445667899*************97 PP

>> Fer4_19  Divergent 4Fe-4S mono-cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   1.3   3.8e-06     0.011       5      60 ..     159     221 ..     156     224 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.8e-06
     Fer4_19   5 eitiednrelCihsgnCvkglpevFdpkrk.......pwikpdeasteeiievverCPSGALs 60 
                 ++ +  +++lCi+  +C   +p+vF  +++         i+p +a +++i++++e+CP  A++
  EPA04360.1 159 NLFVDVDKSLCIGCCSCEIIAPDVFLINKNsksnpksSVINPKGAGVNKIMNAAETCPTKAIT 221
                 56688899*****************544321122112478******************88876 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   5.9   0.00031      0.93       2      15 ..     163     176 ..     162     178 .. 0.88
   2 ?    5.0   0.1    0.0078        23      15      24 .]     212     221 ..     212     221 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00031
                 EEETTTSSS-THHH CS
        Fer4   2 videekCigCGaCv 15 
                  +d+++CigC  C+
  EPA04360.1 163 DVDKSLCIGCCSCE 176
                 69***********8 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0078
                 HHHSTTTEEE CS
        Fer4  15 vevCPvgAIt 24 
                 +e CP+ AIt
  EPA04360.1 212 AETCPTKAIT 221
                 578******7 PP

>> SRR  Seven Residue Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       3.8   1.1e+04       8      14 .]      13      19 ..      12      19 .. 0.78
   2 ?    8.2   0.1    0.0014       4.3       3      14 .]      57      68 ..      56      68 .. 0.90
   3 ?    0.6   0.5      0.46   1.4e+03       7      12 ..      87      92 ..      87      92 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3.8
         SRR  8 naYeqLs 14
                n Y++L+
  EPA04360.1 13 NTYQALK 19
                7799996 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0014
         SRR  3 fekVknaYeqLs 14
                f+kV++aY+ L+
  EPA04360.1 57 FKKVTEAYNHLK 68
                9********986 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.46
         SRR  7 knaYeq 12
                kn+Ye+
  EPA04360.1 87 KNNYEK 92
                79**95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1505  (0.0839422); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 1662.69
//
Query:       EPA04361.1  [L=55]
Description: hypothetical protein BG20_I1841 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.028   14.9   3.0      0.044   14.3   3.0    1.3  1  zf-C2H2    Zinc finger, C2H2 type
      0.047   14.6   2.5      0.065   14.1   2.5    1.2  1  zf-C2H2_4  C2H2-type zinc finger


Domain annotation for each model (and alignments):
>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   3.0   4.9e-06     0.044       2      23 .]      15      37 ..      14      37 .. 0.97

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.9e-06
                EETTTTEEESSHHHHHHHHHC.C CS
     zf-C2H2  2 kCpdCgksFkrksnLkrHirt.H 23
                kC++Cg  + +++ LkrH ++ H
  EPA04361.1 15 KCDECGLECHDPERLKRHTKKaH 37
                8*******************999 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   2.5   7.3e-06     0.065       2      24 .]      15      37 ..      14      37 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.3e-06
   zf-C2H2_4  2 kCpiCgksFsskkaLlrHlkthH 24
                kC+ Cg  ++++++L+rH k+ H
  EPA04361.1 15 KCDECGLECHDPERLKRHTKKAH 37
                8******************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 395.06
//
Query:       EPA04362.1  [L=86]
Description: hypothetical protein BG20_I1837 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-15   55.4   0.0    5.8e-15   55.2   0.0    1.0  1  LDcluster4       SLOG cluster4 family
    0.00014   21.1   0.1    0.00015   21.0   0.1    1.1  1  LSDAT_prok       SLOG in TRPM, prokaryote
  ------ inclusion threshold ------
      0.011   15.8   0.3      0.027   14.6   0.3    1.7  1  Lysine_decarbox  Possible lysine decarboxylase
       0.04   13.5   0.2      0.046   13.3   0.2    1.3  1  DAGK_cat         Diacylglycerol kinase catalytic domain


Domain annotation for each model (and alignments):
>> LDcluster4  SLOG cluster4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.2   0.0   1.3e-18   5.8e-15      85     157 .]       4      77 ..       2      77 .. 0.81

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 1.3e-18
  LDcluster4  85 glagRnlilvlssdvviaiggrsGTlsEialaleegkpvivlkgtdellseiiekkekder..kvivaespkelv 157
                 gl+ R+++++ls+d vi++gg+sGTlsEi+ a+ ++kp++++++t    ++ i++  ++ +  k+i ++++k++v
  EPA04362.1   4 GLT-RDFLNALSADGVIIVGGGSGTLSEICAAYMYKKPMVAIRNTGGAADKFIDGYVDHRKnvKIIGVDTAKDAV 77 
                 556.***************************************99545555555543333345899999888875 PP

>> LSDAT_prok  SLOG in TRPM, prokaryote
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.1   3.4e-08   0.00015     127     170 ..      18      62 ..       8      85 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3.4e-08
  LSDAT_prok 127 tvlvnGgeitlkdiresvkagrpilvvaGsgrladeiaaal.rgd 170
                 +++v+Gg+ tl++i ++   ++p++ ++ +g++ad+ +++  + +
  EPA04362.1  18 VIIVGGGSGTLSEICAAYMYKKPMVAIRNTGGAADKFIDGYvDHR 62 
                 799*********************************988775322 PP

>> Lysine_decarbox  Possible lysine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.3     6e-06     0.027      52      74 ..      14      36 ..       6      80 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6e-06
                     HESEEEE-S-SHHHHHHHHHHHH CS
  Lysine_decarbox 52 ladafvilPGGiGTleElleilt 74
                      ad+++i+ GG GTl E+  ++ 
       EPA04362.1 14 SADGVIIVGGGSGTLSEICAAYM 36
                     69***************976554 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2     1e-05     0.046      50      88 ..      12      45 ..       4      82 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1e-05
                HHHHCC-SEEEEEESHHHHHHHHHHHCTHHCTTSEEEEE CS
    DAGK_cat 50 eakeegvdlivvaGGDGtvsevlnglleelatkpplgii 88
                 ++++   +i+v GG Gt+se++ + +    +kp ++i 
  EPA04362.1 12 ALSAD--GVIIVGGGSGTLSEICAAYMY---KKPMVAIR 45
                44444..789999***********9999...78877775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 545.64
//
Query:       EPA04363.1  [L=217]
Description: siroheme synthase domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-20   73.4   0.7      5e-20   71.9   0.1    1.8  2  NAD_binding_7   Putative NAD(P)-binding
    0.00042   19.7   0.0     0.0012   18.3   0.0    1.7  1  Sirohm_synth_M  Sirohaem biosynthesis protein central
     0.0023   18.2   4.3          1    9.7   0.8    2.5  2  ATP-synt_F      ATP synthase (F/14-kDa) subunit
     0.0054   16.8   1.4     0.0054   16.8   1.4    2.1  2  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
  ------ inclusion threshold ------
      0.029   13.6   0.1      0.064   12.5   0.1    1.6  2  LSDAT_prok      SLOG in TRPM, prokaryote


Domain annotation for each model (and alignments):
>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.9   0.1   1.4e-23     5e-20       3     104 .]       5     115 ..       3     115 .. 0.89
   2 ?   -0.4   0.1      0.43   1.5e+03      47      66 ..     166     174 ..     129     209 .. 0.49

  Alignments for each domain:
  == domain 1  score: 71.9 bits;  conditional E-value: 1.4e-23
  NAD_binding_7   3 ldlkgkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvklaeeele.kdlegad........lviaatddrelneriaeaakarrilv 89 
                    l+l+++ v+v+GgG+ A++++++ll++++++ v++ +++++++ lvk ++ +++ ++++++         ++i++t+d++ln++i ++ak+++i  
     EPA04363.1   5 LNLHDRLVIVIGGGNEALKRINSLLRENCQILVISSAINNQIKTLVKNKKIKFKkQKIQNMNiflthtpyMIITTTNDKKLNQKIINYAKKKKIIA 100
                    7899***************************************999988888852556664444555677************************** PP

  NAD_binding_7  90 nvadkpelcdfifpa 104
                      +d+pel+df  pa
     EPA04363.1 101 YSSDNPELSDFSNPA 115
                    ***********9997 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.43
  NAD_binding_7  47 lvklaeeelekdlegadlvi 66 
                      +la+            vi
     EPA04363.1 166 ARELAR-----------KVI 174
                    111222...........222 PP

>> Sirohm_synth_M  Sirohaem biosynthesis protein central
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   3.3e-07    0.0012       5      24 ..     124     143 ..     123     144 .. 0.96

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.3e-07
  Sirohm_synth_M   5 QIaiSTnGksPrLAaliRre 24 
                     QIai T+G sP++++++++e
      EPA04363.1 124 QIAIFTGGRSPAMSKKLKEE 143
                     ******************98 PP

>> ATP-synt_F  ATP synthase (F/14-kDa) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.1   0.00036       1.3      27      63 ..      19      54 ..      13      62 .. 0.87
   2 !    9.7   0.8   0.00029         1      23      65 ..     138     180 ..     113     195 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00036
                HHHHHHHHHHHHHTTEEEEEEEHHHHCCCHHHHHHCT CS
  ATP-synt_F 27 eeieealkelleredigiilitekiaeeirelideyk 63
                +e+ + +++ll re+++i++i+ +i ++i++l+++ k
  EPA04363.1 19 NEALKRINSLL-RENCQILVISSAINNQIKTLVKNKK 54
                57788899999.******************9998755 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00029
                 CSSHHHHHHHHHHHHHHTTEEEEEEEHHHHCCCHHHHHHCTCS CS
  ATP-synt_F  23 vtdeeeieealkelleredigiilitekiaeeirelideykee 65 
                 ++ +ee e+++k+++++edi+ i i++k  e  r+ i + +e+
  EPA04363.1 138 KKLKEESEKIFKKIITKEDINQIKIQNKARELARKVIATQNER 180
                 45589*******************************9998886 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   1.4   1.5e-06    0.0054       9     115 ..       6     115 ..       1     129 [. 0.75
   2 ?    1.7   0.4      0.07   2.5e+02      25      61 ..     145     182 ..     142     200 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.5e-06
                   ..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-S.SSS...S-SB-HHHHHCCHHH CS
  Shikimate_DH   9 slkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisat.ase...epilekeeveealkk 101
                   +l+++ v++iG G+ a + ++ Ll+++++ +v+     ++ k+l+++  + +++ +k+++++  l +   +i+ t + +   + i++ ++ +++ + 
    EPA04363.1   6 NLHDRLVIVIGGGNEALKRINSLLRENCQILVISSAINNQIKTLVKNK-KIKFKKQKIQNMNIFLTHTPYMIITTtNDKklnQKIINYAKKKKIIAY 101
                   689999***********************7777777888899999887.5559***********998876555550443111356666666666666 PP

                   .S..EEEEE--SS- CS
  Shikimate_DH 102 rkkplllvDiavPR 115
                   ++++  l D ++P 
    EPA04363.1 102 SSDNPELSDFSNPA 115
                   55666667777775 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.07
                   HHHHHHHHCC.T-CEEEEEESSHHHHHHHHHHHT.ET- CS
  Shikimate_DH  25 elvakhLlak.gvkkvvvaNRtlerakelaeelkgeei 61 
                   e+++k++++k  ++++ + N  +e a+++    ++ ++
    EPA04363.1 145 EKIFKKIITKeDINQIKIQNKARELARKVIATQNERKM 182
                   66666666554899999999988888887766655544 PP

>> LSDAT_prok  SLOG in TRPM, prokaryote
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   1.8e-05     0.064     124     173 ..       9      56 ..       4      87 .. 0.73
   2 ?   -2.9   0.0      0.93   3.3e+03       8      30 ..     130     153 ..     125     171 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.8e-05
  LSDAT_prok 124 psvtvlvnGgeitlkdiresvkagrpilvvaGsgrladeiaaalrgdsee 173
                  +++++++Gg+ +lk i+  ++++ +ilv+  s  ++++i + +++++ +
  EPA04363.1   9 DRLVIVIGGGNEALKRINSLLRENCQILVI--SSAINNQIKTLVKNKKIK 56 
                 5799**************************..678899987666555444 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.93
  LSDAT_prok   8 Ggas.gldeeeaarlrkllravla 30 
                 Gg+s  ++++  ++ +k++++++ 
  EPA04363.1 130 GGRSpAMSKKLKEESEKIFKKIIT 153
                 555523555556666666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2147  (0.11975); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1609.80
//
Query:       EPA04364.1  [L=372]
Description: glutamyl-tRNA reductase, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-37  127.8   0.1    6.6e-37  126.5   0.1    1.6  1  GlutR_N          Glutamyl-tRNAGlu reductase, N-terminal domai
      8e-30  103.7   0.1    1.5e-29  102.8   0.1    1.5  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    2.9e-08   34.1   1.4    8.7e-08   32.5   1.4    1.9  1  GlutR_dimer      Glutamyl-tRNAGlu reductase, dimerisation dom
    4.3e-05   24.0   0.0    0.00011   22.7   0.0    1.8  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    0.00083   18.8   0.0     0.0041   16.5   0.0    1.9  2  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
  ------ inclusion threshold ------
      0.028   14.7   0.0      0.082   13.2   0.0    1.8  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
       0.03   13.6   0.1        0.2   10.9   0.0    2.0  2  Malic_M          Malic enzyme, NAD binding domain
       0.12   12.8   0.0        0.3   11.6   0.0    1.6  1  NAD_binding_7    Putative NAD(P)-binding
        1.1    9.0   0.0        1.1    9.0   0.0    2.5  3  DUF4535          Domain of unknown function (DUF4535)


Domain annotation for each model (and alignments):
>> GlutR_N  Glutamyl-tRNAGlu reductase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.5   0.1   3.3e-40   6.6e-37       3     146 .]      10     154 ..       9     154 .. 0.87

  Alignments for each domain:
  == domain 1  score: 126.5 bits;  conditional E-value: 3.3e-40
     GlutR_N   3 inhktapvelreklafseeelkellkel.ee.kvkeaviLsTCNRtEiylsaeeeeeaseellellaevs...leelkeklyvlegeeavrHlfrVasG 96 
                 +++++ p++++e++++   +l+++++++ e+ +++e+vi++TCNR+E++   ++++   +++++++a+ +   +e +ke++++ e+ ea++Hl++++sG
  EPA04364.1  10 VTFRNSPIHILERFTIR--DLENAYDQFkEHsGLDECVIIQTCNRIELFG--KAQNYDINKIKKTWASLTgleEEAFKENIEFVENGEALHHLLKLTSG 104
                 68999**********96..5667777775455899**************5..44445666666666555445599999********************* PP

     GlutR_N  97 LdSlvlGEdqIlgQvkeayelakeagtlgkvLerlfqkaikvakrvrtet 146
                 LdS+v+GE+qIlgQ+k+++++a++a+++g+ L+ lf+kai+++ r+r++t
  EPA04364.1 105 LDSMVVGEEQILGQIKNSITAARNAKASGQHLNNLFDKAIRIGTRIRNST 154
                 ***********************************************987 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.8   0.1   7.7e-33   1.5e-29       1     137 [.     169     301 ..     169     302 .. 0.98

  Alignments for each domain:
  == domain 1  score: 102.8 bits;  conditional E-value: 7.7e-33
                   HHHHHHHS..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSSSS-SB-HHHHHC CS
  Shikimate_DH   1 elakkkleslkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisataseepilekeevee 97 
                   +la++++++lk kk+lliG+Ge+++lvak L ++g++  vv+ Rtl+r ++++e ++g+    +k+ee+ +  +++dv+++at ++ +++++e++ +
    EPA04364.1 169 KLAEENIDELKLKKILLIGTGEVSTLVAKSLGRRGYD-FVVTSRTLQRSQAFCETMGGK---PIKFEEVLSGFEKYDVLFVATTAPYFLVTQERIIK 261
                   589*********************************9.********************9...*********************************** PP

                   CHHH.S..EEEEE--SS-SB-TTGGGSTTCCCEEHHHHHH CS
  Shikimate_DH  98 alkkrkkplllvDiavPRdvepevaeledvrlytvDdLke 137
                   a+k+rk+ ++++D+++PR v+++va++  v+l+++D + e
    EPA04364.1 262 AMKERKNGMMILDLSNPRTVDEKVATVGRVKLMNLDQIAE 301
                   ************************************9976 PP

>> GlutR_dimer  Glutamyl-tRNAGlu reductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   1.4   4.4e-11   8.7e-08       2      58 ..     317     371 ..     316     372 .] 0.93

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 4.4e-11
                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-S..-------- CS
  GlutR_dimer   2 AeaiIeeeveefeawlkslevvptIkalrekaeeireeeleralkklaldgedreel 58 
                  +e+iI+ee++ +ea +k+l+++p++k++ ++++++re+el++al+ l  +++d++++
   EPA04364.1 317 VENIISEELSVLEASMKRLDAEPLVKDVFKNIDSLREKELQKALQML--NEKDEKKI 371
                  79********************************************9..57777665 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   5.7e-08   0.00011       1      96 [.     182     277 ..     182     278 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 5.7e-08
                    EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECE.CHHHHHHH-SEEEE-S-HHHHHHHHHHC...GHHHHTTSEEE CS
  F420_oxidored   1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtav.dneeaaeeadvvvlavkpedveevlsel...akdalkgklvi 92 
                    ki +iG+G++   +a+ l ++g   +++vv+ sr+ ++ +++ e++g k ++  +     e+ dv+++a    ++  + + +   +k+ ++g +++
     EPA04364.1 182 KILLIGTGEVSTLVAKSLGRRG---YDFVVT-SRTLQRSQAFCETMGGKPIKFeEVLSGFEKYDVLFVATTAPYFLVTQERIikaMKERKNGMMIL 273
                    6789******************...****55.***************7766630244456699******988777655555544446666666666 PP

                    EESS CS
  F420_oxidored  93 svla 96 
                    + ++
     EPA04364.1 274 DLSN 277
                    6665 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   2.1e-06    0.0041      28     134 ..     172     283 ..     155     285 .. 0.72
   2 ?    1.5   0.0     0.082   1.6e+02     131     160 ..     253     282 ..     241     301 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.1e-06
                   CGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH.CHHHHTCEECSHHHHHHH-SEEEE-S--STTTTTSBSHHH....HHCSTT CS
  2-Hacid_dh_C  28 allgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkee.eeeelgvelvsleellaesDivslhlpltpetrhlinaee....lakmkk 119
                   +  + el+ k++ +iG+G++ + vak l   g + ++++r+ ++++  +e++g +  ++ee+l+  +   +   +t + + l+++e+    +++ k+
    EPA04364.1 172 EENIDELKLKKILLIGTGEVSTLVAKSLGRRGYDFVVTSRTLQRSQaFCETMGGKPIKFEEVLSGFEKYDVLFVATTAPYFLVTQERiikaMKERKN 268
                   5667899**********************************99998777888889999999987554444444444444444444431000344455 PP

                   TEEEEESS-GGGB-H CS
  2-Hacid_dh_C 120 gailiNtaRGglvde 134
                   g++++  +   +vde
    EPA04364.1 269 GMMILDLSNPRTVDE 283
                   566666666666665 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.082
                   GB-HHHHHHHHHTTSCCEEEES--SSSSSG CS
  2-Hacid_dh_C 131 lvdeeaLleaLksgkiagaalDvfeeeplp 160
                   lv +e +++a+k++k +++ lD  ++  ++
    EPA04364.1 253 LVTQERIIKAMKERKNGMMILDLSNPRTVD 282
                   688999****************87776655 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.1e-05     0.082       1      54 [.     183     233 ..     183     239 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.1e-05
                      EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE- CS
  Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaial 54 
                      +l+iG G v+  va+ l r++ +  +++v +r++++ +a ++++ g+ ++++++
       EPA04364.1 183 ILLIGTGEVSTLVAKSLGRRG-Y--DFVVTSRTLQRSQAFCETMGGKPIKFEEV 233
                      89*****************98.5..7****************998888877765 PP

>> Malic_M  Malic enzyme, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.21   4.2e+02      17      44 ..     171     199 ..     157     219 .. 0.73
   2 ?   10.9   0.0   9.8e-05       0.2      99     151 ..     228     283 ..     205     290 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.21
                 HHH-S-.GGG--EEEEC-SHHHHHHHHHH CS
     Malic_M  17 kitgkk.lseqkivvlGaGsagiGiaeqi 44 
                   ++   l+ +ki+++G+G+ ++ +a+ +
  EPA04364.1 171 AEENIDeLKLKKILLIGTGEVSTLVAKSL 199
                 333222488899********999888876 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 9.8e-05
                 .SHHHHHHHH.--SEEEE-SSSSS-S..-HHHHHHHHHHSSS-EEEE--SSGGGSS CS
     Malic_M  99 ltLeevvkkv.kptvliGlsgvagaf..teeivremaksterPiilplSNPtskaE 151
                 +++eev++ + k +vl  +++++  +  +e i+++m++ ++  +il lSNP +  E
  EPA04364.1 228 IKFEEVLSGFeKYDVLFVATTAPYFLvtQERIIKAMKERKNGMMILDLSNPRTVDE 283
                 5666776665245666655555543233688********************98766 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00015       0.3       5      86 ..     178     267 ..     176     284 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00015
  NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklleagakvtvvapev...keeleelvklaeeelekd...legadlviaatddr...elneriaeaakarr 86 
                    lk kk+l++G Gev +  +++l + g + +v + ++   ++++e ++  ++ ++e+    +e++d++++at+ +     +eri +a+k+r+
     EPA04364.1 178 LKLKKILLIGTGEVSTLVAKSLGRRGYDFVVTSRTLqrsQAFCE-TMGGKPIKFEEVlsgFEKYDVLFVATTAPyflVTQERIIKAMKERK 267
                    6779*******************************743333333.3333444444442226667777777776522245777877776643 PP

>> DUF4535  Domain of unknown function (DUF4535)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00056       1.1      16      31 ..      59      74 ..      58      83 .. 0.88
   2 ?   -1.5   0.2       1.1   2.2e+03      24      39 ..     303     318 ..     290     319 .. 0.68
   3 ?   -2.9   0.2         3     6e+03      24      41 ..     348     365 ..     347     370 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00056
     DUF4535 16 AQNYeVPnvkklaakg 31
                AQNY++  +kk++a++
  EPA04364.1 59 AQNYDINKIKKTWASL 74
                9**********99865 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.1
     DUF4535  24 vkklaakglekakele 39 
                 v+k +++ l k+k +e
  EPA04364.1 303 VEKNMKTRLNKVKSVE 318
                 3566777777777665 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 3
     DUF4535  24 vkklaakglekakeleea 41 
                 +  l +k l+ka +++ +
  EPA04364.1 348 IDSLREKELQKALQMLNE 365
                 555666777777776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1171  (0.0653132); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.51
# Mc/sec: 2198.52
//
Query:       EPA04365.1  [L=36]
Description: hypothetical protein BG20_I2191, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (36 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      197  (0.0109878); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.22s 00:00:00.54 Elapsed: 00:00:00.37
# Mc/sec: 291.19
//
Query:       EPA04366.1  [L=350]
Description: hypothetical protein BG20_I2190 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-53  177.5   0.0    2.9e-29  101.0   0.0    3.0  3  AsnC_trans_reg2  AsnC-like ligand binding domain
    0.00063   19.5   0.0       0.51   10.2   0.0    2.4  2  HTH_AsnC-type    AsnC-type helix-turn-helix domain
    0.00067   19.6   0.1          8    6.5   0.0    4.6  4  AsnC_trans_reg   Lrp/AsnC ligand binding domain


Domain annotation for each model (and alignments):
>> AsnC_trans_reg2  AsnC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.6   0.0   3.7e-24   2.2e-20       1      82 []      73     153 ..      73     153 .. 0.99
   2 ?   -0.5   0.0      0.24   1.5e+03      54      80 ..     186     212 ..     180     213 .. 0.81
   3 !  101.0   0.0   4.9e-33   2.9e-29       1      82 []     244     329 ..     244     329 .. 0.98

  Alignments for each domain:
  == domain 1  score: 72.6 bits;  conditional E-value: 3.7e-24
  AsnC_trans_reg2   1 klGfkanalvawkvpeerveevaevvaelpevtHcYeRewpynlyfmvharseeeveevlaeiaaatgledyevLpstrefK 82 
                      +lG+k ++lva++++ +++e va++++++p+v+H+YeR++++nl+f+++++  +++++ +++ +   g++++++Lp+++ fK
       EPA04366.1  73 RLGYK-SSLVAMEIEPSQLEHVANQINRHPGVSHNYERDHQFNLWFTLAVPPGSDLKTEVDKFSVLKGIKKVRMLPTIQLFK 153
                      59***.*************************************************************************999 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.24
  AsnC_trans_reg2  54 eeveevlaeiaaatgledyevLpstre 80 
                      ee +e+++e+++ ++++d   L s ++
       EPA04366.1 186 EEDKEFIRELQKDMEITDRPFLNSAKK 212
                      556789999999999999998888876 PP

  == domain 3  score: 101.0 bits;  conditional E-value: 4.9e-33
  AsnC_trans_reg2   1 klGfkanalvawkvpeerveevaevvaelpevtHcYeR....ewpynlyfmvharseeeveevlaeiaaatgledyevLpstrefK 82 
                      ++Gf+an++++w+vp++++ ev++++ ++p+v+HcY+R    +wpy ++ m+h++se+e ee+++ i+++++++dy++L+strefK
       EPA04366.1 244 EVGFTANGMIVWNVPNNKILEVGTKLGAFPQVSHCYQRptypDWPYSVFSMIHCKSEDEAEEMAKTIQNQIHVDDYKILFSTREFK 329
                      58************************************88888******************************************9 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0   8.5e-05      0.51       1      28 [.      13      43 ..      13      57 .. 0.72
   2 !    7.0   0.0   0.00084         5       5      36 ..     188     222 ..     186     228 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 8.5e-05
  HTH_AsnC-type  1 LDeiDrkILeaLqed...aRisyaeLAervG 28
                   +De+D+ IL+++q        ++ ++A +  
     EPA04366.1 13 MDELDKEILNEIQWTfplTPKPFDDIATKFA 43
                   9***********9766666666666666655 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.00084
  HTH_AsnC-type   5 DrkILeaLqed...aRisyaeLAervGlSestvlr 36 
                    D+  +++Lq+d     +++   A+++Gl+e++  +
     EPA04366.1 188 DKEFIRELQKDmeiTDRPFLNSAKKLGLTEEQLFE 222
                    67779************************987655 PP

>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.027   1.6e+02      37      58 ..       3      24 ..       2      28 .. 0.86
   2 ?    0.4   0.0      0.11   6.4e+02      11      27 ..      33      49 ..      26      51 .. 0.85
   3 !    6.5   0.0    0.0013         8       3      69 ..      83     145 ..      81     150 .. 0.79
   4 ?    3.5   0.0     0.012        71      14      31 ..     263     280 ..     256     327 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.027
                    SEEEEEEESSHHHHHHHHHHTT CS
  AsnC_trans_reg 37 dyllkvvvrdlealerflrekl 58
                    d+++++ ++++++l++ + +++
      EPA04366.1  3 DIVIEILAQSMDELDKEILNEI 24
                    899***********99777766 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.11
                    THHHHHHHHHHTSTTEE CS
  AsnC_trans_reg 11 eqleefeealaelpeVv 27
                    +++++++ ++a+ pe++
      EPA04366.1 33 KPFDDIATKFATTPEII 49
                    4699***********97 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.0013
                     EEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEE CS
  AsnC_trans_reg   3 vslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartet 69 
                     +++ep++   le ++ ++ ++p V + y     +++ +  +v+   +l + +++ ++ l+g+++++ 
      EPA04366.1  83 MEIEPSQ---LEHVANQINRHPGVSHNYERDHQFNLWFTLAVPPGSDLKTEVDK-FSVLKGIKKVRM 145
                     6778777...***************99998888888888888888888777666.777777777765 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.012
                     HHHHHHHHTSTTEEEEEE CS
  AsnC_trans_reg  14 eefeealaelpeVvecyr 31 
                      e+  +l ++p+V +cy+
      EPA04366.1 263 LEVGTKLGAFPQVSHCYQ 280
                     578889999999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       720  (0.0401584); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2617.65
//
Query:       EPA04367.1  [L=1167]
Description: hypothetical protein BG20_I1695, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.78u 0.31s 00:00:01.09 Elapsed: 00:00:00.51
# Mc/sec: 6941.12
//
Query:       EPA04368.1  [L=109]
Description: phosphoribosyl-AMP cyclohydrolase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-33  112.9   0.1    5.5e-33  112.6   0.1    1.1  1  PRA-CH    Phosphoribosyl-AMP cyclohydrolase


Domain annotation for each model (and alignments):
>> PRA-CH  Phosphoribosyl-AMP cyclohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.6   0.1   3.1e-37   5.5e-33       2      74 .]      32     104 ..      31     104 .. 0.99

  Alignments for each domain:
  == domain 1  score: 112.6 bits;  conditional E-value: 3.1e-37
                 EEEE-HHHHHHHHHHSB-EEEETTTTEEEETTTTTS--EEEEEEEE-TTSSEEEEEEEESS-SSTTSBSSS-- CS
      PRA-CH   2 laymnkealektletgkavyySrsrkklWkKGetSgnvqkvkeirlDcDqDalllkveqkgaaCHtgkesCFy 74 
                 lay+nke+le t +tg+ +++Srsr+klW+KGe+Sgn+qk+kei +DcD+Da+++ ve++g+aCHtg++ CF+
  EPA04368.1  32 LAYTNKESLELTKKTGNSWFWSRSRNKLWMKGEESGNTQKIKEILVDCDSDAIIYLVEPSGPACHTGERVCFH 104
                 79**********************************************************************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 701.95
//
Query:       EPA04369.1  [L=447]
Description: bacteriocin biosynthesis cyclodehydratase, SagC family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-64  216.2   0.3    7.2e-64  215.5   0.3    1.3  1  ThiF             ThiF family
    1.9e-05   25.2   0.0    5.4e-05   23.7   0.0    1.8  1  ThiS             ThiS family
    0.00016   22.0   1.4    0.00064   20.0   1.4    2.0  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0067   16.5   0.1       0.02   14.9   0.1    1.8  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
  ------ inclusion threshold ------
      0.014   14.7   0.0      0.028   13.8   0.0    1.4  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas


Domain annotation for each model (and alignments):
>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  215.5   0.3     2e-67   7.2e-64       2     240 ..     105     336 ..     104     345 .. 0.95

  Alignments for each domain:
  == domain 1  score: 215.5 bits;  conditional E-value: 2e-67
                 HHHHHH..HHHHHHHHHHTSEEEEE--SHHHHHHHHHHHHHTTTEEEEEESSB--GGGGGTBTTS-GGGTTSBHHHHHHHHHHHT-TTSEEEEEES-CC CS
                 xxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        ThiF   2 srqlal..lgedgqekLrdskvllvGaGglGsellknLalsGvgkltlvDnDkielsNlnRqflfreediGkpKaevaaealqeinpdveveavterit 98 
                 srq++l  +g +gq kL++skv++vG+GglG+++   La++Gvg l++vD D+ielsNl+Rq +f e+d+G+ K+e a ++lq++npd+++ea+  +i+
  EPA04369.1 105 SRQVMLeeIGYQGQLKLKNSKVCVVGVGGLGNPITSRLAAMGVGTLRIVDRDVIELSNLHRQTMFDESDVGQVKVEIASKKLQKLNPDCKIEALAISIN 203
                 68888888999**************************************************************************************** PP

                 GCCS-HHHHTT-SEEEEESSSHHHHHHHHHHHHHHT-EEEEEEEETTEEEEEEEEECCS-ECTSS-TGGS.EECCCCEEHHHHHHCTE-B-HHHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        ThiF  99 detvleellesvDlVvdalDniearrlvnracvkkgiplieagtlgfegqvvviipgktgcyeCldpsstedptekkvplctsiagnipaiatttavva 197
                 d t + ++++++D+V+dalD++ ar+++n+acvk gip+++++++g++gqv++i+p++++cy C++p      +e++ p+c si g   +  +++++v+
  EPA04369.1 204 DYT-ALDVVQGCDVVIDALDSVNARYALNNACVKFGIPFVTGAAVGVSGQVFTILPKESACYYCMFP----ELNEDTMPTC-SIEG---VHPSILSIVG 293
                 *55.45************************************************************9....8999******.****...88888***** PP

                 HHHHHHHHHHHTTBCGGGCCEEEECCTTTTEEEEECCEEEEEE CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        ThiF 198 glaalellkllsgkeklenslltqvdllesrfenvelerakks 240
                 g+ ++e++k++ gk+++  ++   +dl++  f++++  ra+++
  EPA04369.1 294 GIEVAEAVKIIIGKKPSLSQRILHIDLENLDFTSTRTFRAEEC 336
                 ***********999889999999***********999998855 PP

>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   1.5e-08   5.4e-05      39      77 .]      44      92 ..      14      92 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.5e-08
                G.........TTTTEEEEETTEEEGC.CTTTSB--TTCEEEEEESTTC- CS
        ThiS 39 a.........lerrvavavNgeivpr.lwldtelkdgDevailppVaGG 77
                +          +  +++++Ng+++++  + +t+l dg  + ilp+VaGG
  EPA04369.1 44 KrrvlesdgtPRSLINIYINGKNAKFsGGMETILVDGNDIYILPAVAGG 92
                14455555666699************88********************9 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   1.4   1.8e-07   0.00064       1     102 [.     126     258 ..     126     275 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.8e-07
                      EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH.......................TTTCEEEEE--TTTHHHHHHHHHTTSS CS
  Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka.......................lgvrfeaialdaenyeavLaallkegd 71 
                      v ++G G+ G +++  la+ +    ++ ++dr+  +l +l  ++                          ++ea a+ +++y+a L+  +++ d
       EPA04369.1 126 VCVVGVGGLGNPITSRLAAMGVG--TLRIVDRDVIELSNLHRQTmfdesdvgqvkveiaskklqklnPDCKIEALAISINDYTA-LDV-VQGCD 215
                      6799***************9976..99*********9999999999*****************998888999999999999999.776.8999* PP

                      EEEE-SSGG.GHHHHHHHHHHHT-EEEESS-...........B CS
  Sacchrp_dh_NADP  72 lvvnlsppi.ssldvlkaCietgvhyvdtsi...........s 102
                      +v++++ ++    ++  aC++ g+ +v+ +            +
       EPA04369.1 216 VVIDALDSVnARYALNNACVKFGIPFVTGAAvgvsgqvftilP 258
                      *********7777999***********9444344555555544 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   5.6e-06      0.02       9      56 ..     120     167 ..     112     190 .. 0.84
   2 ?   -2.3   0.0       1.2   4.2e+03      61      85 ..     197     223 ..     182     229 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.6e-06
                   ..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHH CS
  Shikimate_DH   9 slkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeel 56 
                   +lk++kv+++G G +++ +++ L+a gv  + ++ R++   ++l ++ 
    EPA04369.1 120 KLKNSKVCVVGVGGLGNPITSRLAAMGVGTLRIVDRDVIELSNLHRQT 167
                   699**********************************99988887775 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.2
                   -EEEEGCGHH..HHHHT-SEEEE-SSS CS
  Shikimate_DH  61 iealkleelk..ellaeadvvisatas 85 
                   + a+++++++  ++++ +dvvi a  s
    EPA04369.1 197 ALAISINDYTalDVVQGCDVVIDALDS 223
                   455555555411478999999988776 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   7.9e-06     0.028      30      68 ..     117     156 ..      97     184 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.9e-06
                   SBS-GTTSEEEEES-SHHHHHHHHHHHHTT-.EEEEESSS CS
  2-Hacid_dh_C  30 lgkelsgktvGiiGlGrIGqavakrlkafgm.kviaydrs 68 
                    + +l++++v+++G+G +G+ +  rl+a+g+  + ++dr 
    EPA04369.1 117 GQLKLKNSKVCVVGVGGLGNPITSRLAAMGVgTLRIVDRD 156
                   34589*************************9444455554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 2597.59
//
Query:       EPA04370.1  [L=206]
Description: hypothetical protein BG20_I1699 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.16   11.9   0.0       0.24   11.3   0.0    1.2  1  MgsA_C    MgsA AAA+ ATPase C terminal


Domain annotation for each model (and alignments):
>> MgsA_C  MgsA AAA+ ATPase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   1.3e-05      0.24      57     123 ..       7      73 ..       2      92 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.3e-05
                 H-TTTTHHHHHHHHHHHHCS----GG.GHHHHHHHHH--.-------GGGST...........T-T-- CS
      MgsA_C  57 iGlpEariaLaqavvylalapKSnaaykAikkaledvke.kkslevPlhLrnaptklakklgygkgYk 123
                 iG+   ++++  a + l ++pKSn +    k+  + vk  k++ +v + L+n + + +++ + +k+Y+
  EPA04370.1   7 IGITSISVIVVIASILLVTSPKSNVIE-TDKTLDNIVKPeKEEIQVENVLNNLKNTETNSSEIQKKYD 73 
                 7888888999999***********874.3334444444313344555555555444444444555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1554  (0.0866752); expected 358.6 (0.02)
Passed bias filter:                      903  (0.0503653); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 1229.72
//
Query:       EPA04371.1  [L=209]
Description: putative imidazoleglycerol phosphate synthase, cyclase subunit, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.9e-59  198.7   0.5      1e-58  198.5   0.5    1.0  1  His_biosynth  Histidine biosynthesis protein
    4.4e-08   32.6   0.4    0.00059   19.0   0.1    2.1  2  Dus           Dihydrouridine synthase (Dus)
    1.8e-05   24.3   0.4      0.027   13.8   0.1    2.2  2  NMO           Nitronate monooxygenase
    7.8e-05   22.0   0.1      0.024   13.9   0.0    2.2  2  DHO_dh        Dihydroorotate dehydrogenase
    0.00013   21.3   0.2      0.014   14.8   0.0    2.3  2  TMP-TENI      Thiamine monophosphate synthase
    0.00074   18.9   0.3       0.48    9.7   0.1    2.3  2  ThiG          Thiazole biosynthesis protein ThiG
  ------ inclusion threshold ------
      0.014   14.8   0.1        1.9    7.9   0.0    2.3  2  G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
      0.061   12.2   0.0      0.088   11.6   0.0    1.3  1  Trp_syntA     Tryptophan synthase alpha chain


Domain annotation for each model (and alignments):
>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.5   0.5   4.5e-62     1e-58      57     227 ..       1     190 [.       1     192 [. 0.94

  Alignments for each domain:
  == domain 1  score: 198.5 bits;  conditional E-value: 4.5e-62
                   THHHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEE.....C.............EE CS
  His_biosynth  57 greanldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarr.....g.............yk 135
                   +r++ ++lv+++a+ ++ip++vGGG++sl+d++++l +gadkv i+t a++np +i+el+e fg+q++vvaiDa+r     +             ++
    EPA04371.1   1 QRKTLKELVRNVASVIDIPFTVGGGVKSLDDARNILLNGADKVGINTGAINNPAVITELMELFGRQCVVVAIDAKRnfdiqNeknifsengkqfwFE 97 
                   588999**********************************************************************66665156677778899*9** PP

                   EEETTTTEEEEEEHHHHHHHHHHTT-SEEEEEETTTTTTSS---HHHHHHHHHHHSSEEEEESS--SHHHHHHHHHTTC.SEEEESHHHHTTS CS
  His_biosynth 136 vaikgwreetgldavelakkleelgageilltdidrdGtlsGpdleltkelaeavkipviasGGvgsledlkelksegv.davivgsalyege 227
                   v+i g+++ tg+da+e+akk+++lgageillt+id+dGt++G+d+ lt+e+ ++v+ipviasGG+g+++d+ ++++e   da++++s++++++
    EPA04371.1  98 VFIFGGKQGTGIDAIEWAKKADDLGAGEILLTSIDKDGTRDGYDILLTREIVNSVSIPVIASGGCGTPDDMVNVFKESNaDAALAASIFHYQT 190
                   ***************************************************************************66666**********975 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   2.6e-07   0.00059     175     233 ..       9      67 ..       3      92 .. 0.81
   2 !   12.1   0.0   3.3e-05     0.074     175     213 ..     145     183 ..     106     204 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.6e-07
                 HHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTHHHH.HHHHHHSC CS
         Dus 175 IkevkqavsipviaNGdIkdaedaqaileetGadgvmigrgalgnPwlfae.stavktge 233
                 +++v   + ip+ + G++k+++da++il + Gad v i  ga +nP+++ e ++ + +++
  EPA04371.1   9 VRNVASVIDIPFTVGGGVKSLDDARNILLN-GADKVGINTGAINNPAVITElMELFGRQC 67 
                 567777788*******************99.******************98766655555 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 3.3e-05
                 HHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEES CS
         Dus 175 IkevkqavsipviaNGdIkdaedaqaileetGadgvmig 213
                  +e+ ++vsipvia G++ +++d+ ++ +e+ ad+ +++
  EPA04371.1 145 TREIVNSVSIPVIASGGCGTPDDMVNVFKESNADAALAA 183
                 5789999***************************98765 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0    0.0004      0.89     180     223 ..       4      47 ..       1      52 [. 0.91
   2 !   13.8   0.1   1.2e-05     0.027     145     214 ..     111     174 ..     105     203 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0004
         NMO 180 glfaLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigt 223
                  l +Lv +v++++diP    GG+    +   +L  GA  v i t
  EPA04371.1   4 TLKELVRNVASVIDIPFTVGGGVKSLDDARNILLNGADKVGINT 47 
                 56789*********************************999887 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1.2e-05
         NMO 145 svkearkvearGaDalivqGpeaGGhqGtpevgdkglfaLvpqvldavdiPviAaGGiidrrgvaaaLal 214
                 +++ a+k+  +Ga  + ++  ++ G +    +     + L  ++++ v+iPviA GG  +  ++  ++  
  EPA04371.1 111 AIEWAKKADDLGAGEILLTSIDKDGTRD--GY----DILLTREIVNSVSIPVIASGGCGTPDDMVNVFKE 174
                 5666666666776666666666666555..33....478999****************999998887765 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   1.1e-05     0.024     232     286 ..       7      58 ..       2      64 .. 0.84
   2 !    6.2   0.0    0.0023       5.1     235     263 ..     146     172 ..     141     201 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.1e-05
                 HHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHHHH CS
      DHO_dh 232 kvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegpkiakk 286
                 +++r+++++++  ip    GG++s +Da + +  GA  v + t+   ++p+++ +
  EPA04371.1   7 ELVRNVASVID--IPFTVGGGVKSLDDARNILLNGADKVGINTGA-INNPAVITE 58 
                 57888888888..999999*************************9.566666555 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0023
                 HHHHHHTTT.S-EEEESS--SHHHHHHHH CS
      DHO_dh 235 relykrlkkeipiIgvGGiesgeDaleki 263
                 re+ + ++  ip+I++GG  + +D ++ +
  EPA04371.1 146 REIVNSVS--IPVIASGGCGTPDDMVNVF 172
                 67778888..*************987654 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.5   0.0    0.0087        19     140     175 ..       7      43 ..       3      48 .. 0.80
   2 !   14.8   0.0   6.1e-06     0.014     114     170 ..     115     174 ..     107     198 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0087
    TMP-TENI 140 eglkelaealeiPvvaiGGit.lenvaevleagadgv 175
                 e+++++a+ + iP+ + GG++ l+++ ++l  gad v
  EPA04371.1   7 ELVRNVASVIDIPFTVGGGVKsLDDARNILLNGADKV 43 
                 45677788888********973588999999999887 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 6.1e-06
    TMP-TENI 114 algadYigvGpifpTdtKkdaeplglegl..kelaealeiPvvaiGGi.tlenvaevlea 170
                 a++ad +g+G i  T+  kd +  g + l  +e++++++iPv+a GG  t++++ +v++ 
  EPA04371.1 115 AKKADDLGAGEILLTSIDKDGTRDGYDILltREIVNSVSIPVIASGGCgTPDDMVNVFKE 174
                 568999***********99997776666555****************8456777777743 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0   0.00091         2     165     208 ..       7      51 ..       2      89 .. 0.83
   2 !    9.7   0.1   0.00021      0.48     166     205 ..     144     184 ..     108     197 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00091
                 HHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESH.HHH CS
        ThiG 165 ealkiiieeakvPvivDAGigspsdaaqamelGadavllnt.ava 208
                 e ++ + + +++P  v  G+ s  da + +  Gad v +nt a++
  EPA04371.1   7 ELVRNVASVIDIPFTVGGGVKSLDDARNILLNGADKVGINTgAIN 51 
                 5677788889******************************94444 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00021
                 HHHHHHHH-SS-BEEES---SHHHHHHHH.HTT-SEEEESH CS
        ThiG 166 alkiiieeakvPvivDAGigspsdaaqam.elGadavllnt 205
                   + i++++++Pvi   G g+p d ++++ e  ada l ++
  EPA04371.1 144 LTREIVNSVSIPVIASGGCGTPDDMVNVFkESNADAALAAS 184
                 4567999******************9997466788877665 PP

>> G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0   0.00083       1.9     128     166 ..       6      44 ..       3      50 .. 0.90
   2 ?    4.6   0.0    0.0083        19     131     160 ..     145     174 ..     140     184 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00083
                   HHHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEE CS
  G3P_antiterm 128 pkvikeikkelkipiiaGGLietkedveealkaGaiavs 166
                   +++++++ + ++ip+  GG +++ +d +++l +Ga+ v 
    EPA04371.1   6 KELVRNVASVIDIPFTVGGGVKSLDDARNILLNGADKVG 44 
                   67899999***************************9885 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0083
                   HCTSTTS...EEEEESS--SHHHHHHHCTT CS
  G3P_antiterm 131 ikeikkelkipiiaGGLietkedveealka 160
                   ++ei ++++ip+ia+G   t +d+ +++k+
    EPA04371.1 145 TREIVNSVSIPVIASGGCGTPDDMVNVFKE 174
                   6789999*********99999999888765 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   3.9e-05     0.088     184     223 ..       3      43 ..       1      71 [. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.9e-05
                 TTHHHHHHHHHHCTSS-EEEESSS-SHHHHHHHH.TT-SEE CS
   Trp_syntA 184 aevdelverlkkltavPvavGFGistkeqvkqva.kvadGv 223
                 ++++elv+++ ++ + P  vG G+++ ++++++  ++ad v
  EPA04371.1   3 KTLKELVRNVASVIDIPFTVGGGVKSLDDARNILlNGADKV 43 
                 6799*****************************99999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1295.46
//
Query:       EPA04372.1  [L=404]
Description: threonine synthase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.9e-72  242.0   0.6      1e-71  241.8   0.6    1.0  1  PALP           Pyridoxal-phosphate dependent enzyme
  ------ inclusion threshold ------
      0.047   13.9   0.7       0.18   12.0   0.0    2.4  3  ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthas
      0.093   13.1   1.9       0.17   12.2   1.9    1.4  1  C1_2           C1 domain
       0.28   11.0   0.6       0.56   10.0   0.6    1.4  1  zf-C2H2_11     zinc-finger C2H2-type


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  241.8   0.6   2.3e-75     1e-71       2     294 .]      68     373 ..      67     373 .. 0.97

  Alignments for each domain:
  == domain 1  score: 241.8 bits;  conditional E-value: 2.3e-75
                 GGCSSS--EEEECCTCCCCCCE.EEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-EEEEEEETTS-HHHHHHHHH CS
        PALP   2 tlgigpTPlvrlprlskelgvp.lflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallGlkvtivvpadaspekvallrl 99 
                 + g+g TPl+++++l k+lg + l++K++s npt SfKdR a  +++++ke  g   v +as+GN + a+Aa aa++Gl+++++ p++   +k+a+  +
  EPA04372.1  68 SIGAGMTPLIKADNLGKKLGLNnLYIKNDSVNPTFSFKDRPAGVAISKAKEF-GLSAVGCASTGNLASATAAHAAKAGLPCHVFAPSNIEMAKIAQALS 165
                 67899***********************************************.********************************************** PP

                 TT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHHTT.TTEEEEEEE-SSSHHHHHHHHHHHH........HSTT-EEEE CS
        PALP 100 lGaevvevggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEileqlg.gkpdavvvpvGgGgliaGiaaglke........rrpdvrvig 189
                 +Ga+ + v+g+yd+a ++aa++  + +g+ +v+    ++ +eg +t+++E++eql+ ++pd ++vpvG+G+++ +i++g+ e        +  + ++i+
  EPA04372.1 166 YGANYIAVDGTYDDANRIAAQIGDS-KGIGVVNINMRSHYVEGSKTLAYEVAEQLDwQVPDQLIVPVGSGAMLNAICKGFEElqqvsllnNVANMHMIA 263
                 *************************.********************************************************888887654445***** PP

                 EEECTTCGGTTCCS..S.SS..B...SSS.CCSTCS..CGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHH.HHHHHHCCT CS
        PALP 190 vepegsdalarslragrrvtvpvs..dtiadglavg..spselafelldrlvdeivtvsdeealeamrllarregivvepssaaalaal.klreagelk 283
                 ++p g++++ +++++++ + +pv+  dtia++la+g   +++++++ l+++++ + + +++e+l+a+ lla++egi++ep++++++a+l k++e+g+++
  EPA04372.1 264 AQPHGCAPIVDAFKKNSKEVIPVEnpDTIAKSLAIGdpGDGRYVLKRLKQYNGFAEECNNQEILDAILLLAKTEGIFTEPAGGVSVAVLqKMVEQGKID 362
                 *************9999999988899**********9999*********************************************************** PP

                 TCEEEEEEE-B CS
        PALP 284 egdrvvviltg 294
                 ++d+vv+ +tg
  EPA04372.1 363 KNDSVVCYVTG 373
                 ********998 PP

>> ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       2.8   1.2e+04      73      82 ..      65      74 ..      61      74 .. 0.75
   2 ?   -2.2   0.1       1.1   4.9e+03      44      56 ..     128     140 ..     123     171 .. 0.75
   3 ?   12.0   0.0     4e-05      0.18      54      88 ..     349     383 ..     344     385 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.8
                   EEEEEETTTE CS
  ACP_syn_III_C 73 llvgfGaGlt 82
                    +v++GaG+t
     EPA04372.1 65 NIVSIGAGMT 74
                   5789999987 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.1
                    HH-B-GGGHHHHH CS
  ACP_syn_III_C  44 eyGntsaasipla 56 
                     +Gn+++a+   a
     EPA04372.1 128 STGNLASATAAHA 140
                    6788888876554 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 4e-05
                    HHHHHHHHHTTSS-TT-EEEEEEEETTTEEEEEEE CS
  ACP_syn_III_C  54 plaLdeaveegklkpgdlvllvgfGaGltwgaall 88 
                    +  L+++ve+gk++++d v+   +G Gl  + a++
     EPA04372.1 349 VAVLQKMVEQGKIDKNDSVVCYVTGNGLKATEAIM 383
                    5689************************9887776 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.9   3.8e-05      0.17      18      38 ..       5      26 ..       2      33 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.8e-05
        C1_2 18 sfnCsaCgrk.idgffYsCseC 38
                s +C+ C+++ ++ f+Y+C+eC
  EPA04372.1  5 SLQCRECKKEySTAFKYICDEC 26
                679*******888888****** PP

>> zf-C2H2_11  zinc-finger C2H2-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.6   0.00013      0.56       3      15 ..       4      16 ..       3      19 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00013
  zf-C2H2_11  3 stcqCleCGlcft 15
                +++qC+eC+  ++
  EPA04372.1  4 TSLQCRECKKEYS 16
                799******9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       752  (0.0419432); expected 358.6 (0.02)
Passed bias filter:                      617  (0.0344135); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 2831.57
//
Query:       EPA04373.1  [L=201]
Description: hypothetical protein TIGR01213, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-06   27.0   0.1    5.7e-06   26.5   0.1    1.2  1  THUMP     THUMP domain
  ------ inclusion threshold ------
      0.074   13.2   0.2       0.17   12.0   0.2    1.6  1  Tox-PL-2  Papain fold toxin 2


Domain annotation for each model (and alignments):
>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.1   6.3e-10   5.7e-06      39     140 ..      46     154 ..      25     157 .. 0.77

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 6.3e-10
                 HHHHHHHTSTTECEEEEEEEEEESSHHHHHHHHHHHHHHHHHHCT-EEEEEEEESSSTS...............SSHHHHHHHHHHHHHHCCTT-EE-S CS
       THUMP  39 llkealekargiqrvipvcevceadledileaakeivkkkfeeeketFaVrvkrrgkhf...............eftsreinrevGkaivektglkVdl 122
                 ++  ++++ +        c +c + l+ +  + k + +   +    +  V++  + + +               +  + +i +e+Gk + +kt++  d+
  EPA04373.1  46 KIHAKHSFKK--------CFICKNLLDNLTSYLKLMLEYSAKYDFSSIVVGALIKPSIIdrddyirskyklrgiDSVKTDITKELGKQFIKKTKKIIDF 136
                 4544445544........77777777777777777777777777777777777777777888888888888888999********************** PP

                 SS-SEEEEEEEETTEEEE CS
       THUMP 123 enPdivvrveiikdkayi 140
                  nPd+++ v + ++ + i
  EPA04373.1 137 QNPDLTFTVNFKDESCQI 154
                 **********99998876 PP

>> Tox-PL-2  Papain fold toxin 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   1.9e-05      0.17      18      60 ..      21      65 ..       5      71 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.9e-05
    Tox-PL-2 18 CveCAaal...ekyLkeqgisGkrlklktksaedaasfilserlek 60
                C++C   l   +  L +++i Gk+lk+++k++ + ++fi ++ l++
  EPA04373.1 21 CDSCLGRLfskQMNLSSNKILGKKLKIHAKHSFK-KCFICKNLLDN 65
                8888776644355799***************996.9***9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       900  (0.050198); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1306.74
//
Query:       EPA04374.1  [L=242]
Description: signal peptide binding domain protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-30  105.1   0.0    5.5e-30  104.5   0.0    1.3  1  SRP54     SRP54-type protein, GTPase domain
    4.3e-26   91.4   1.0    7.9e-26   90.6   0.5    1.7  2  SRP_SPB   Signal peptide binding domain
  ------ inclusion threshold ------
      0.046   11.7   0.2       0.06   11.3   0.2    1.1  1  TssR      Type VI secretion system, TssR


Domain annotation for each model (and alignments):
>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.5   0.0   9.1e-34   5.5e-30     103     196 .]       2      95 ..       1      95 [. 0.98

  Alignments for each domain:
  == domain 1  score: 104.5 bits;  conditional E-value: 9.1e-34
                 HHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEESTTSSSSTTHHHHHHHHHTS-EEEEE-SSSTTGEEE--HHHHHHHHHT CS
       SRP54 103 eelkkikkvvkpdevllvldattgqeavkqakaFkeavgitgviltklDgdakgGaalsiaaelklPikfigvGekiedleefdperlvsrllg 196
                 +e+++i+kv +pd  +lv+d+t+gq+ ++qa+aF++++ ++g+i+tklD++akgG+a++++a+++  i+++g+Ge+i+dle+f+p+r+v rllg
  EPA04374.1   2 SEMEQINKVSDPDLAILVIDGTIGQQCFNQAEAFHKTIPVGGIIITKLDSSAKGGGAIAASAATGAQIMYVGTGERIDDLEKFSPTRFVGRLLG 95 
                 79******************************************************************************************95 PP

>> SRP_SPB  Signal peptide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.5     9e+03      31      31 ..     110     110 ..      91     124 .. 0.45
   2 !   90.6   0.5   1.3e-29   7.9e-26       2      99 .]     126     224 ..     125     224 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.5
                 . CS
     SRP_SPB  31 s 31 
                  
  EPA04374.1 110 E 110
                 1 PP

  == domain 2  score: 90.6 bits;  conditional E-value: 1.3e-29
                 SCTHHHHHHHHHHHCCCCCCHHHHCCC.......H.....CCCCCHHHHHHHHHTTSBHHHHHSGCG-..HHHHHHHHHHTTS-HHHHHHHHHHHHHHH CS
     SRP_SPB   2 ftlrdlleqlqqikkmGplskllsmiPgmsae..akae..eeaekklkrieaiidSMTkeErdspekllkesRkrRiArGsGtsvqevnellkqfeqmk 96 
                 ++++d+  ql++++k+G+l+ +l+++Pg+s +     +  ++ e +++++ +ii+SMTkeE+++p+ ll++sR++Ri+rGsG   +ev+ellk++++ k
  EPA04374.1 126 MNMDDFFYQLEEVTKVGSLKGFLDNMPGLSGMvkD--DqlDQMEGRVSKWRFIIQSMTKEEKADPD-LLNSSRIKRISRGSGWPEHEVKELLKNYKNSK 221
                 799*************************9999642..33588899*********************.899***************************** PP

                 HHT CS
     SRP_SPB  97 kmm 99 
                 +mm
  EPA04374.1 222 SMM 224
                 **8 PP

>> TssR  Type VI secretion system, TssR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2     1e-05      0.06     679     733 ..     177     232 ..     158     238 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1e-05
        TssR 679 lelitglpsss.ellkkykvkdlkkkkvipdeelekllkyfkekkekleeakkeek 733
                 ++  t+ + ++ +ll++ ++k + + +  p++e+++llk++k++k+ ++++k  + 
  EPA04374.1 177 IQSMTKEEKADpDLLNSSRIKRISRGSGWPEHEVKELLKNYKNSKSMMKASKGRQM 232
                 5566666777789************************************9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1573.97
//
Query:       EPA04375.1  [L=194]
Description: chlorite O(2)-lyase, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-54  184.7   0.1    1.4e-54  184.6   0.1    1.0  1  Chlor_dismutase  Chlorite dismutase


Domain annotation for each model (and alignments):
>> Chlor_dismutase  Chlorite dismutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.6   0.1     8e-59   1.4e-54       8     193 ..       6     183 ..       1     184 [. 0.92

  Alignments for each domain:
  == domain 1  score: 184.6 bits;  conditional E-value: 8e-59
                      HHHHHHHTTSCEEEEEEEETSTTTT-SEEEEEEESSHHHHHHHHHHHHHSTGGGGEEEEEEEEEEEEEESSSSS-GGGHHHCHHHHS----SSS CS
  Chlor_dismutase   8 lealleeaeegvlralysvlGlradaDlmlwllretleelqeaerelrrtalgkvlepaysyvsvtelseYkeedeenkshvearlapelpkkk 101
                      +e +l  +++g+  ++ys+lGlr+daD+++w++++t+ee+q+a ++l +t +gk++ p+ +y+s+t++s Y      +k++   ++ + +  kk
       EPA04375.1   6 VEIVL--KNSGIKFRTYSTLGLRDDADFLFWFAAKTVEEIQNAIAKLYTTVFGKYIIPSRTYLSCTRPSIY-----VEKGKPLGFVSDAE-MKK 91 
                      44444..3456789*********************************************************.....45555566666666.99* PP

                      EEEEEEEEE-EEGGGS-HHHHHHHHHHHHHHHHGCTTEEEEEEE-TTTSSSSEEEEEEESSTHHHHHHHHHHCTSHHHHHHEEE-S-EEEEE CS
  Chlor_dismutase 102 yvcvYPmsksreWYllpeeeRrelmaeHgeigrkYgkVrqiitgsfGldDyEwgvaleaddleefkdlvyelRfdeasakvaeegpfyvGrr 193
                      +v+vYP++k+reWYllp+eeR+++m+eH+e+++kY+++  ++t+sfG++D ++++a+e d++ +f+dl+++lR++++s++v++++p++v+ +
       EPA04375.1  92 HVIVYPFTKTREWYLLPKEERQSIMDEHIEVSKKYPQIILNTTYSFGIHDEDFMLAFEVDEIRDFQDLIMDLRETRVSRYVKNDIPMIVCVK 183
                      *****************************************************************************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1370.13
//
Query:       EPA04376.1  [L=331]
Description: oxidoreductase, aldo/keto reductase family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-56  192.2   0.1    1.2e-56  192.0   0.1    1.0  1  Aldo_ket_red  Aldo/keto reductase family


Domain annotation for each model (and alignments):
>> Aldo_ket_red  Aldo/keto reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.0   0.1   6.9e-61   1.2e-56       1     293 [.      15     317 ..      15     318 .. 0.96

  Alignments for each domain:
  == domain 1  score: 192.0 bits;  conditional E-value: 6.9e-61
                   .EEEE-SSS-ST....TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE........--SSSTTSSSS-HHHH CS
  Aldo_ket_red   1 elglGtwqlgsk...eeiskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKv........dlrdaeiksglskeni 86 
                   e+g+G+w++g +   ++i+++ea ++l++a++ Ginff tA++Ygkg se+l+G+++k    +r+ev+i+tK         + + ae ++++++e  
    EPA04376.1  15 EIGFGAWTIGLDwwgKKIEEDEAKRMLKKAYDLGINFFETADMYGKGISEKLIGQVFKG---MRDEVVISTKYgydfanveQIGHAELPQSFEPEFT 108
                   69*********************************************************...*********************************** PP

                   HHHHHHHHHHHT-S-EEEEEE-S--TTS-.HHHHHHHHHHHHHTTSEEEEEEE.....S--HHHHHHHHHTTT--EEEEE-B-BTT-HHHHTTHHHH CS
  Aldo_ket_red  87 resleeslkrLgtdyvDllllHrpdpslpsieevldaleelvkeGkiraiGvS.....nfsveqlekakkkkkvkivavqveynllreleeegllel 178
                   +++l++slkrL+tdy+D + +H+p+ ++ +   +++++++l++eGki+   v+     +++ e le++   +   ++ vq  yn+l++   ++l++ 
    EPA04376.1 109 QKALNASLKRLQTDYIDSYGMHNPKLNHIRNDATFEMFDKLIDEGKIKTSQVAlgpaiGWTKEGLEAM---ERKSVSGVQTVYNILEQTPGNELIQK 202
                   *****************************99*********************9878788888888877...99999********************* PP

                   HHHTT-EEEEBSTTGGGTTGTTTSS---SSSCCC-------TS-HHHHHHHHHHHHHHHHTT--HHHHHHHHHTTSTT-SEEEE--SSHHHHHHHHG CS
  Aldo_ket_red 179 ckkkgvpliaysplggGlltgkyqseedkedkeprkdlkrdertsknldaaeelselakehgvslaqlalryalsqpavgivipgasnieqlednld 275
                   ++k++v++ +  p ++G+ltgk++ e+  ++ ++rkd k+ e+ +++l+++e+++ +a+ +g ++++ a++++ls++a  +v+p + ++e++e+ ++
    EPA04376.1 203 AEKQNVGILVRVPDASGILTGKVKAETVIPSNDHRKDRKQ-EWRQEALKKVEQFRPIAERNGLNITEFAIKFILSKKAIASVLPTVVSVEEIETFAA 298
                   ***********************************99655.999***************************************************** PP

                   GGG-.---HHHHHHHHHHH CS
  Aldo_ket_red 276 alel.klseeevaeldell 293
                     +   l++++++e+d l+
    EPA04376.1 299 ISDGkYLNSSDMKEIDDLY 317
                   **88799********9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       741  (0.0413297); expected 358.6 (0.02)
Passed bias filter:                      568  (0.0316805); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 2252.64
//
Query:       EPA04377.1  [L=37]
Description: hypothetical protein BG20_I2290, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.42
# Mc/sec: 267.20
//
Query:       EPA04378.1  [L=181]
Description: hypothetical protein BG20_I2292 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-45  155.6   0.1    1.2e-45  155.5   0.1    1.0  1  DUF1802   Domain of unknown function (DUF1802)


Domain annotation for each model (and alignments):
>> DUF1802  Domain of unknown function (DUF1802)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.5   0.1   6.8e-50   1.2e-45       2     170 ..       4     171 ..       3     175 .. 0.94

  Alignments for each domain:
  == domain 1  score: 155.5 bits;  conditional E-value: 6.8e-50
     DUF1802   2 LkewavaveaLeeGrqivllrKggireergkFeveeeeflLYPtvehqkaellkpeyaallepvasestpe.kveikawAeveeavevsdeealealsk 99 
                 Lkewa++v aLe+G q+vllrKggi +   +F++e ++f L+Pt+ehq+ +++kpe++++le+v+ +  +    +i+++Ae+     +s  e++++lsk
  EPA04378.1   4 LKEWATVVAALEDGVQTVLLRKGGILDVASGFKIETKKFPLFPTQEHQDYNHIKPEFHKYLEQVKINPPKTgFNRITSYAEILSEADISLDETIKKLSK 102
                 9***************************************************************7777666888************************* PP

     DUF1802 100 lhiwteeavedrlkykpkqpltvlllRvyrleepvelpetpeyagckswvdlpeseaeeakPVlsdeefee 170
                 +hiw+++++++r ++kp++p+++++l+vy++++ v+ p ++ey+gcksw++++e+    +k+Vlsd+e e+
  EPA04378.1 103 FHIWSDSYINERKNWKPENPIKAVFLKVYKIPK-VNTPLKSEYQGCKSWININEE-IPVGKAVLSDKETES 171
                 *******************************87.56678999************9.9999******98665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1200.47
//
Query:       EPA04379.1  [L=263]
Description: hypothetical protein BG20_I2582, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-34  117.5   0.0    1.9e-32  111.8   0.0    2.2  2  DUF1743   Domain of unknown function (DUF1743)


Domain annotation for each model (and alignments):
>> DUF1743  Domain of unknown function (DUF1743)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.7   0.0    0.0034        60      66     112 ..      48     104 ..      41     108 .. 0.80
   2 !  111.8   0.0     1e-36   1.9e-32       1     116 []     142     255 ..     142     255 .. 0.97

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.0034
                 CCS-STTSS......EEEEEEES-HHHHHHHHHCSEE..S-EEC....EEEEEESTT CS
     DUF1743  66 vlvPhtpdp......vlfGirgedpeallkaakeilskeeesee....mavfrtnqg 112
                   +P+ p +      v + ir ++p +++  +k + +k++ +++     +vf +n+ 
  EPA04379.1  48 RFNPNIPWKtrgngaVSMKIRTKNPSKIKGKIKHLVKKYSDINNganpGLVFYENEI 104
                 5667777777788889999********************999887666666666665 PP

  == domain 2  score: 111.8 bits;  conditional E-value: 1e-36
                 TTHHHHHHHHHH-..-TTS-EEEEEEEE-GGGTT.---EEHHHHHHHHHHHTTCECTSEBTTTTCECCS-STTSSEEEEEEES-HHHHHHHHHCSEE.. CS
     DUF1743   1 grgiiGAtaalganialedstyEllaYreperwg.erevdeesvieadektypetfdnvDlshklvvlvPhtpdpvlfGirgedpeallkaakeilske 98 
                 g+g++GA+ a+g+++  +d+t Ell+Yr+++++g +r++++ sv++++ekt p+tf+++D ++++v+++Ph+pdpv++Girge+ ++ll+a k +++ +
  EPA04379.1 142 GQGLVGAIGAIGYDF--KDHTLELLSYRKNSKFGkDRKLSATSVKTMQEKTQPNTFNSFDNKKNRVLITPHGPDPVFYGIRGENIDTLLHATKILKT-D 237
                 789**********55..58*****************************************************************************9.9 PP

                 S-EECEEEEEESTTS-TT CS
     DUF1743  99 eeseemavfrtnqgtdah 116
                 e+    ++f++nqgt +h
  EPA04379.1 238 EKLAGHLIFKSNQGTGDH 255
                 99999**********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       701  (0.0390987); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1725.47
//
Query:       EPA04380.1  [L=252]
Description: putative glutamate racemase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.3e-14   52.1   0.0      1e-13   51.7   0.0    1.1  1  Asp_Glu_race  Asp/Glu/Hydantoin racemase


Domain annotation for each model (and alignments):
>> Asp_Glu_race  Asp/Glu/Hydantoin racemase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.7   0.0   5.6e-18     1e-13       3     222 ..       6     209 ..       4     210 .. 0.77

  Alignments for each domain:
  == domain 1  score: 51.7 bits;  conditional E-value: 5.6e-18
                   EC.SCCCCHHHHHHHHHHBTTSSGGGS..EEEEE-CC.S-TCHHHHHCH.T..THH.HHHHHHHHHHC.TTESEEEE--CHHHHHHHHHHHH-SSEE CS
  Asp_Glu_race   3 gm.gpeatlsvlrklveatpaesdqehlplivlndsa.ipdrteaieeesgddpvl.klleaakkLek.agadaiviaCnTahavadelqkkikiPv 95 
                   ++ ++ ++lsv+++++++++ +        i+++ds+ +p  +++i+       ++  +l+ +  L++  ++ +i++  nT  ++  + +   +  +
    EPA04380.1   6 VFdSGLGSLSVIKQIQKQFKCSI-------IYFADSKnYPYGKKSIK------LLNeITLQTIMTLQNsFKPNLIIVGSNTL-SLTLNSR---PRNI 85 
                   778999*********99888776.......99999999997777883......44458888888888758************.4444444...6689 PP

                   EECHHHHHHHHHHHSS-EEEEEE-HHHHHCTH...HHHHHHHHGT.EE.E....T-CCCHHCCHCHHHH.TT-TTSH...HHHHHHHHHHHHH.TTT CS
  Asp_Glu_race  96 lgiveataealkatgvkkvglLgTrgtlksgl...yqkeleanqgiev.vvpseelqssvnqaiyeelk.aGevtee...arrailkllerla.erg 183
                   ++++++  ea k t+ k++++L+T+  +ks+l   y + +  n g+++ ++  ++l+         el+ +G++ +     +  i+k l+ +  +++
    EPA04380.1  86 ISVLPPISEAKKITKSKTIAILATESIVKSKLlekYLDLFNTN-GLKIfKINASALV---------ELVeSGKFYSNpesCKTIIEKTLSSMLiKNN 172
                   9988887776666*****************8733366667775.8866444444444.........4444555433333458888899998988*** PP

                   -SEEEE-STTHHHHHHHHHHCC-TT.SEEEEHHHHHHHH CS
  Asp_Glu_race 184 adaviLGCTelplllekaealekeksvpvidptdilare 222
                   +d+viL  T+lp+ll+ ++ + +   v+++dp  +la++
    EPA04380.1 173 IDVVILSSTHLPFLLKFLKDVFPT--VTFLDPSILLAKK 209
                   ******************999995..9*****9999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       821  (0.0457917); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 1455.74
//
Query:       EPA04381.1  [L=77]
Description: hypothetical protein BG20_I2474, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.017   15.3   0.1      0.021   15.1   0.1    1.1  1  ATG16     Autophagy protein 16 (ATG16)


Domain annotation for each model (and alignments):
>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.1   1.1e-06     0.021     140     194 ..      18      72 ..       9      74 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.1e-06
       ATG16 140 kdreeelrekeklvqdlqDElsaLqlqlnqaEeklrklekENkeLveRWmkrkaq 194
                 ++++e+++ + +l   +q +++ Lq+q +++++ l kl++  ++L +R +  ++q
  EPA04381.1  18 EKLRETIKPQGALKPRIQTAVNKLQVQISKMDSMLGKLHERDAQLFQRVVTAMQQ 72 
                 56778888888888999************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1072  (0.0597914); expected 358.6 (0.02)
Passed bias filter:                      612  (0.0341346); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 485.02
//
Query:       EPA04382.1  [L=80]
Description: hypothetical protein BG20_I2636, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.011   15.2   0.0      0.012   15.1   0.0    1.1  1  SMC_N     RecF/RecN/SMC N terminal domain
      0.016   15.0   0.0       0.02   14.7   0.0    1.1  1  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
      0.065   13.2   0.0       0.12   12.4   0.0    1.4  2  FR47      FR47-like protein


Domain annotation for each model (and alignments):
>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0     2e-06     0.012     168     211 ..       3      47 ..       1      57 [. 0.83

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2e-06
                 TTTS-HHHHHHHHHHHHHHC.TTSEEEEE-SSHHHCCC-SCEEEE CS
                 xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
       SMC_N 168 daaLDeknvkkvaellkeks.knaQfivislreemlekadklvgv 211
                 d+ LD   v++va+ + + s k+a +ivi++ +++l+  dkl  v
  EPA04382.1   3 DSGLDIDAVQAVAKAISQVSgKDATVIVITHYARILKFLDKLDFV 47 
                 899*************9765277************9999887544 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   3.4e-06      0.02     265     302 ..       1      38 [.       1      39 [. 0.95

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.4e-06
      AAA_21 265 EpEngLHPkllrrllellkelsrngaQviltTHSplll 302
                 Ep++gL+  ++  +++ +++ s ++a vi+ TH   +l
  EPA04382.1   1 EPDSGLDIDAVQAVAKAISQVSGKDATVIVITHYARIL 38 
                 9********************************87766 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0     2e-05      0.12      37      79 ..       5      48 ..       3      54 .. 0.90
   2 ?   -3.2   0.0       1.4   8.3e+03      47      56 ..      64      73 ..      61      78 .. 0.47

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2e-05
                SHHHHHHHHHHHHHHH.S-S-EEEEEETT-HHHHHHHHHHT-EE CS
        FR47 37 Glgsrlvkalakeiae.rgktvllvvvasNtpsirlyeklGfek 79
                Gl +  v+a+ak+i++  gk+++++v ++  +  +++ kl f  
  EPA04382.1  5 GLDIDAVQAVAKAISQvSGKDATVIVITHYARILKFLDKLDFVH 48
                888889**********************9999999999999966 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.4
                HHHHHHS-S- CS
        FR47 47 akeiaergkt 56
                a ++  +g++
  EPA04382.1 64 ADKLESEGYD 73
                4444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 494.97
//
Query:       EPA04383.1  [L=92]
Description: NHL repeat protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.3e-06   26.0   0.0    1.2e-05   25.1   0.0    1.5  1  NHL       NHL repeat
    0.00022   20.9   0.0    0.00024   20.8   0.0    1.1  1  SGL       SMP-30/Gluconolactonase/LRE-like region
     0.0024   17.8   2.1     0.0048   16.9   2.1    1.7  1  SBBP      Beta-propeller repeat


Domain annotation for each model (and alignments):
>> NHL  NHL repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   1.9e-09   1.2e-05       1      28 []      50      77 ..      50      77 .. 0.94

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.9e-09
                BSSEEEEEEETTTEEEEEECCCTEEEEE CS
         NHL  1 fnyPhGvavdsnGdiyVaDsenhrvqvF 28
                ++yP G+avds ++iyVaD  n r+q+F
  EPA04383.1 50 LSYPDGIAVDSADNIYVADIFNYRIQIF 77
                78*****************889999998 PP

>> SGL  SMP-30/Gluconolactonase/LRE-like region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0     4e-08   0.00024     183     214 ..      48      81 ..      19      87 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 4e-08
         SGL 183 e..gepDGlavDaeGnvwvAvwgggkvvrfdpdG 214
                 +  ++pDG+avD+ +n++vA + + +++ f+ +G
  EPA04383.1  48 DhlSYPDGIAVDSADNIYVADIFNYRIQIFNAAG 81 
                 24589*************************9998 PP

>> SBBP  Beta-propeller repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   2.1   8.1e-07    0.0048      10      29 ..      47      67 ..      32      67 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 8.1e-07
        SBBP 10 gast.ygngIavDsnGNiYvt 29
                ++++ y+ gIavDs  NiYv+
  EPA04383.1 47 NDHLsYPDGIAVDSADNIYVA 67
                44555999************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 567.12
//
Query:       EPA04384.1  [L=274]
Description: 3-dehydroquinate synthase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   8.7e-101  337.3   0.9   9.6e-101  337.2   0.9    1.0  1  DHQS             3-dehydroquinate synthase II
  ------ inclusion threshold ------
      0.019   15.0   0.2      0.071   13.2   0.0    1.9  2  CppA_N           CppA N-terminal
      0.093   11.1   0.0       0.14   10.6   0.0    1.2  1  Glyco_transf_41  Glycosyl transferase family 41
       0.11   12.5   0.2       0.76    9.8   0.0    2.2  2  Prot_ATP_ID_OB   Proteasomal ATPase OB C-terminal domain


Domain annotation for each model (and alignments):
>> DHQS  3-dehydroquinate synthase II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  337.2   0.9  2.1e-104  9.6e-101      81     352 .]       4     274 .]       1     274 [] 0.95

  Alignments for each domain:
  == domain 1  score: 337.2 bits;  conditional E-value: 2.1e-104
        DHQS  81 skeeeeeaaeaakeadyvivelkdwtvIPlEnliAalqgeetkiiaavksaeeAklaletLEkGadgvllktedveeikelaelleeaeeekleLkeae 179
                 +k+ e+ ++ a+k  d+vive+kdw++IPlEn+iA+l++ +tki+a++++ ee + ++++LE G+dgv+++t +++e++e + +l +++    eLk+a+
  EPA04384.1   4 NKDIENILTLAKKGLDFVIVEVKDWKIIPLENIIAKLHKINTKIFAIANTPEEVRKMFSILEVGVDGVIFNTASINEVREAMLYLGTRN---FELKPAK 99 
                 455566666677779*****************************************************************999996665...99***** PP

        DHQS 180 vtkveevgmgdRvcvDtcslmkegeGmLvGsssrglfLvhsEtlespYvasRPFRVNAGavhaYvlvpggkTkYLseLkaGdevlvvdkkGktreavvG 278
                 + +++evg g+RvcvDt+s++++geGmL+Gs s+ lfLvh E++ s++ ++RPFRVNAGavh+Y+l p+g T+YLse+++G evl++++kG++r+a+vG
  EPA04384.1 100 IIEIKEVGDGERVCVDTASILHKGEGMLIGSRSNFLFLVHNESVGSSFTSPRPFRVNAGAVHCYTLSPDGTTNYLSEVETGAEVLIINSKGNARRATVG 198
                 *************************************************************************************************** PP

        DHQS 279 RvKiEkRPlllveaeaegkkvstilQnaetirlvtedgkaisvteLkeGdevlvylee.kaRHfGikie.EtiiEk 352
                 R KiE+RP+l+++a + ++   +i Q+aetir v+++g+ +svt+Lk+Gd v+v+ ++ ++RHfG+++  E i+Ek
  EPA04384.1 199 RSKIERRPMLMIKAVVGDEIGGIIAQDAETIRFVRPNGQLVSVTHLKKGDIVMVHAKSaTGRHFGMEVSdEYILEK 274
                 *******************************************************986489*******54999998 PP

>> CppA_N  CppA N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1      0.61   2.7e+03      68      88 ..      21      43 ..       7      64 .. 0.54
   2 ?   13.2   0.0   1.6e-05     0.071      33     115 ..     171     255 ..     159     260 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.61
      CppA_N 68 iiikvenpkei..ekllakgaqa 88
                +i+ v++ k i  e+++ak  ++
  EPA04384.1 21 VIVEVKDWKIIplENIIAKLHKI 43
                44444444332224455444433 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 1.6e-05
      CppA_N  33 lavfsdwaeaeelfvieespslrtraveGtkklak...iiikvenpkeiekllakgaqakklfkGqnGyafetispeddlillhae 115
                    +s+ +++ e+++i+   + r ra  G+ k+++   ++ik+    ei  ++a++a++ +  + +      t   ++d +++ha+
  EPA04384.1 171 TNYLSEVETGAEVLIINSKGNAR-RATVGRSKIERrpmLMIKAVVGDEIGGIIAQDAETIRFVRPNGQLVSVTHLKKGDIVMVHAK 255
                 56688898999999998888877.788899999876669*******************9998876555555666778999999996 PP

>> Glyco_transf_41  Glycosyl transferase family 41
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   3.1e-05      0.14      32      61 ..     159     188 ..     150     202 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 3.1e-05
  Glyco_transf_41  32 evfcyalspddgttfrkkiakeaehfvdls 61 
                       v+cy+lspd +t++ +++ + ae ++  s
       EPA04384.1 159 AVHCYTLSPDGTTNYLSEVETGAEVLIINS 188
                      599*******************99887655 PP

>> Prot_ATP_ID_OB  Proteasomal ATPase OB C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.24   1.1e+03       4      18 ..     103     116 ..      98     134 .. 0.60
   2 ?    9.8   0.0   0.00017      0.76       7      49 ..     213     256 ..     208     258 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.24
                     EEEE-TTSSEEEEE- CS
  Prot_ATP_ID_OB   4 VsEvlddteraiVkt 18 
                     ++Ev d  er+ V t
      EPA04384.1 103 IKEVGDG-ERVCVDT 116
                     5555555.6666665 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00017
                     E-TTSSEEEEE-TTS-EEEEEE-G.GGSSST--TTEEEEEETTT CS
  Prot_ATP_ID_OB   7 vlddteraiVktssdeevvvslag.avpremLrpgDlVavdkdt 49 
                     v++d  + i+ + + + ++v+  g +v  + L+ gD V+v+ ++
      EPA04384.1 213 VVGDEIGGIIAQDAETIRFVRPNGqLVSVTHLKKGDIVMVHAKS 256
                     6666667889999999999999995777999**********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1886.21
//
Query:       EPA04385.1  [L=260]
Description: putative 3-deoxy-7-phosphoheptulonate synthase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-49  169.3   0.0    1.2e-49  169.0   0.0    1.1  1  DeoC      DeoC/LacD family aldolase


Domain annotation for each model (and alignments):
>> DeoC  DeoC/LacD family aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.0   0.0   6.8e-54   1.2e-49       3     235 .]      20     232 ..      18     232 .. 0.97

  Alignments for each domain:
  == domain 1  score: 169.0 bits;  conditional E-value: 6.8e-54
                 EEEECCSHHHHHHHHCTSSHHHHHHHHHHHHHHGGGSSEEEEETTTHHHHHHCSCTTSEEEEETECSSCCTTSTTEEEETTCHHHHHHHTT-SEEEEEE CS
        DeoC   3 ilavDqrvankddtasaqneqledlkalvkealtpgasavlldpgviasaskeyakdiallvkldkgtyllkskqrdvdevasveeakalGAdavkvvv 101
                  +++D++++n+++++       +d+++++ +  t g  ++ +++g++       +  i++lv+++++t l+ s++r+++   +veea+++GAd v++++
  EPA04385.1  20 CIPMDHGISNGPIEGL------TDPASIIYKCETRGLTSIIINKGILKTLPNPTK--IGVLVHFSSSTSLSMSPNRKML-TGTVEEAVRMGADGVSLHI 109
                 689*************......9************************99988777..**********************.9****************** PP

                 EEHTTTTCHHHHHHHHHHHHHHHHHHHTEEEEEEEEE-CTTBSSTTCHHHHHHHHHHHHTCCT-SEEEE--SSCC.B.HHHHHHHHHHHHHCHSSTEEE CS
        DeoC 102 yyradgseeeqqklaeikrvkeacheeglplilelylrdeaikdekvdpdlvaeAarvsaelGaDiiKvevpkevvnateedaevfkdvikaapvpgvv 200
                 ++   g +ee ++l+++++ +e+ch++++pl++++y+r+e+ik+ + dp+ v++ ar++ae+GaDi+K+ ++        +d+++f + +k++pvp +v
  EPA04385.1 110 NI---GGKEEPEMLEQLGMTAEQCHKWDMPLLAMMYPRGENIKNPH-DPEMVGHVARIGAECGADIVKTLYT--------GDIDSFAKIVKSTPVP-IV 195
                 **...*****************************************.*************************........****************.** PP

                 EETTS...SHHHHHHHHHHHHHHHTHCEEEESHHHHTT CS
        DeoC 201 lsGGv...seedfletvedAvkeagasGvlsGRaifqk 235
                 ++GG+   ++ d+l++ edA+ +aga Gv +GR+if++
  EPA04385.1 196 IAGGPkskTDLDILQMTEDAM-AAGAKGVTYGRNIFAH 232
                 *****976677889*******.**************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1683.27
//
Query:       EPA04386.1  [L=103]
Description: hypothetical protein BG20_I2289, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      2e-15   57.7   0.1    2.1e-15   57.6   0.1    1.0  1  DHquinase_I  Type I 3-dehydroquinase


Domain annotation for each model (and alignments):
>> DHquinase_I  Type I 3-dehydroquinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.6   0.1   1.2e-19   2.1e-15       1     101 [.       6      99 ..       6     103 .] 0.91

  Alignments for each domain:
  == domain 1  score: 57.6 bits;  conditional E-value: 1.2e-19
                  EEEE--SSHHHHHHHHHHHTTS-SEEEEEGGG-.TT.THHHHHHHHHHHHHHTTS-EEEE---GGGT-S.SSS-HHHHHHHHHHHHHCT-SEEEEEGG CS
  DHquinase_I   1 cvpitgktleeilaelesgkekaDlvElRlDllketseaedvseeleelrstsdlpliftlrtkaeggrfkrkseeeylellrtaielgadyvDvElt 98 
                  cv+i +++  +i + l+++ +++D +E+R D+lk    ++++ ++le +++   +++++tlr+k+egg+f ++se+e++++l+ ++e ++ ++DvE+ 
   EPA04386.1   6 CVSIAEDSPIKIKKNLKETLRRSDYAEVRFDFLK----INEIPKTLEIIKK-DLKKIVCTLRPKSEGGKF-EGSEKERISILKLIAEYNPFLLDVEY- 96 
                  9******************99************5....4678899998877.6778**************.9*************************. PP

                  -.H CS
  DHquinase_I  99 eap 101
                  +++
   EPA04386.1  97 NTI 99 
                  444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.35s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 615.84
//
Query:       EPA04387.1  [L=46]
Description: hypothetical protein BG20_I2287 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.28s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 324.07
//
Query:       EPA04388.1  [L=163]
Description: CBS domain protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.2e-21   75.1   2.3    2.4e-10   40.7   0.5    2.4  2  CBS            CBS domain
    1.4e-12   47.3   0.0    1.9e-12   46.9   0.0    1.2  1  IMPDH          IMP dehydrogenase / GMP reductase domain
  ------ inclusion threshold ------
      0.037   13.7   0.0      0.056   13.2   0.0    1.2  1  FAD_binding_4  FAD binding domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.0   5.4e-12   3.2e-08       2      52 ..      34      84 ..      13      87 .. 0.95
   2 !   40.7   0.5   4.1e-14   2.4e-10       1      52 [.      93     144 ..      93     148 .. 0.93

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 5.4e-12
                HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHH CS
         CBS  2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDll 52
                g++m +++  ++ d t+  a++  +ek++s+l+V+d++ klvGivt+rDll
  EPA04388.1 34 GSVMIENPYAISFDKTVQYAINYAEEKEISGLLVIDSNSKLVGIVTDRDLL 84
                5799********************9999*******9999***********9 PP

  == domain 2  score: 40.7 bits;  conditional E-value: 4.1e-14
                 HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHH CS
         CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDll 52 
                 ++d+mt+dvvt++   +l ea +++ ++++  lP+Vd++g + G++t +D+ 
  EPA04388.1  93 IKDVMTKDVVTAKLGVSLDEAKKILHKHRIEKLPIVDDSGFIKGLITSKDIT 144
                 68***********************8888***********777*******96 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.9   0.0   3.2e-16   1.9e-12      50      96 ..       1     163 []       1     163 [] 0.93

  Alignments for each domain:
  == domain 1  score: 46.9 bits;  conditional E-value: 3.2e-16
                 HHHHHHHTTSEEEE-SSS-HHHHHHHHHHHHTS.................................................................. CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................................................................. RF
       IMPDH  50 mAialareGgigvihknlsieeqaeevkkvkrs.................................................................. 82 
                 mA+a+ar+Ggig+ih+ l+i+eqa+ev kvkrs                                                                  
  EPA04388.1   1 MAVAMARAGGIGIIHRFLTIKEQANEVLKVKRSgsvmienpyaisfdktvqyainyaeekeisgllvidsnsklvgivtdrdllfetdstrlikdvmtk 99 
                 9****************************************************************************************9999999999 PP

                 ..................................................TTSXBXTTSXB-EE CS
                 ..................................................xxxxxxxxxxxxxx RF
       IMPDH  83 ..................................................pnaakdekgrllvg 96 
                                                                   p+a+kd+kgr lvg
  EPA04388.1 100 dvvtaklgvsldeakkilhkhrieklpivddsgfikglitskditniedyPSASKDKKGRPLVG 163
                 9999999999999999999999999999999999999999999999999999999999988886 PP

>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   9.4e-06     0.056      12      84 ..      49     120 ..      46     138 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.4e-06
                    HHHHHHHHHHHCTSC.EEEESSSTTEESTTCSCCEEEEEETTS--EEEEETTTTEEEEETTSBHHHHHHHHHHH CS
  FAD_binding_4  12 evaaalrlaneaglp.vlvrGgGssllgqavatggvvldlsrlnrileideeegtatveaGvtlgdlvealaak 84 
                     v+ a+++a+e+++  +lv+ + s+l+g ++ +++++  ++  + i ++  ++ ++t++ Gv l+++ + l+++
     EPA04388.1  49 TVQYAINYAEEKEISgLLVIDSNSKLVGIVT-DRDLLFETDSTRLIKDVM-TKDVVTAKLGVSLDEAKKILHKH 120
                    6999**********999*************8.********6555566666.6*******************776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1099.48
//
Query:       EPA04389.1  [L=313]
Description: oxidoreductase, aldo/keto reductase family protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-53  181.6   0.2    2.2e-53  181.4   0.2    1.0  1  Aldo_ket_red  Aldo/keto reductase family


Domain annotation for each model (and alignments):
>> Aldo_ket_red  Aldo/keto reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.4   0.2   1.2e-57   2.2e-53       5     293 ..       1     299 [.       1     300 [. 0.96

  Alignments for each domain:
  == domain 1  score: 181.4 bits;  conditional E-value: 1.2e-57
                   E-SSS-ST....TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE........--SSSTTSSSS-HHHHHHHH CS
  Aldo_ket_red   5 Gtwqlgsk...eeiskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKv........dlrdaeiksglskeniresl 90 
                   G+w++g +   ++i+++ea ++l++a++ Ginff tA++Ygkg se+l+G+++k    +r ev+i+tK         + + ae ++++++e  +++l
    EPA04389.1   1 GAWTIGLDwwgKKIEEDEAKRMLKKAYDLGINFFETADMYGKGISEKLIGQVFKG---MRNEVVISTKYgydfanveQIGHAELPQRFEPEFTQKAL 94 
                   889999989999*******************************************...*************************************** PP

                   HHHHHHHT-S-EEEEEE-S--TTS-.HHHHHHHHHHHHHTTSEEEEEEE.....S--HHHHHHHHHTTT--EEEEE-B-BTT-HHHHTTHHHHHHHT CS
  Aldo_ket_red  91 eeslkrLgtdyvDllllHrpdpslpsieevldaleelvkeGkiraiGvS.....nfsveqlekakkkkkvkivavqveynllreleeegllelckkk 182
                   ++sl+rL+tdy+D + +H+p+ ++ +   +++++++l++eGki+   v+     +++ e le++   +   ++ vq  yn+l++   ++l + ++k+
    EPA04389.1  95 NASLERLQTDYIDSYGMHNPKLNHIRNDATFEMFDKLIDEGKIKTSQVAlgpaiGWTKEGLEAM---ERKSVSGVQTVYNILEQTPGNELMQKAEKQ 188
                   *************************99*********************9878788888888877...99999************************* PP

                   T-EEEEBSTTGGGTTGTTTSS---SSSCCC-------TS-HHHHHHHHHHHHHHHHTT--HHHHHHHHHTTSTT-SEEEE--SSHHHHHHHHGGGG- CS
  Aldo_ket_red 183 gvpliaysplggGlltgkyqseedkedkeprkdlkrdertsknldaaeelselakehgvslaqlalryalsqpavgivipgasnieqlednldalel 279
                   +v++ +  p ++G+ltgk++ e+  ++ ++rkd k+ e+ +++l+++e+++ +a+ +g ++++ a++++ls++a  +v+p + ++e++e+ ++  + 
    EPA04389.1 189 NVGILVRVPDASGILTGKVKAETVIPSNDHRKDRKQ-EWRQEALKKVEQFRPIAERNGLNITEFAIKFILSKKAIASVLPTVVSVEEIETFAAISDG 284
                   *******************************99655.999*******************************************************88 PP

                   .---HHHHHHHHHHH CS
  Aldo_ket_red 280 .klseeevaeldell 293
                     l++++++e+d l+
    EPA04389.1 285 kYLNSSDMKEIDDLY 299
                   799********9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       680  (0.0379274); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 1846.10
//
Query:       EPA04390.1  [L=37]
Description: hypothetical protein BG20_I2492, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.28s 00:00:00.59 Elapsed: 00:00:00.42
# Mc/sec: 265.20
//
Query:       EPA04391.1  [L=248]
Description: hypothetical protein BG20_I2117 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00054   20.0   1.1    0.00089   19.3   1.1    1.3  1  Spore_III_AF  Stage III sporulation protein AF (Spore_III_AF)
  ------ inclusion threshold ------
      0.023   15.1   0.1      0.031   14.7   0.1    1.1  1  RNA_pol_Rpc4  RNA polymerase III RPC4
       0.42   10.1   4.1         23    4.5   0.0    2.7  3  DUF2140       Uncharacterized protein conserved in bacteria (


Domain annotation for each model (and alignments):
>> Spore_III_AF  Stage III sporulation protein AF (Spore_III_AF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   1.1   1.5e-07   0.00089      21     109 ..       2      96 ..       1     109 [. 0.68

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.5e-07
  Spore_III_AF  21 kYvklvlGLllilai.lsPvlsll.nkdldlelaaesesleeeleeikeegeelkeenkke...aleeyeqrlekqikeelke.egyevkdveve 109
                   kYvkl+  L +i+a+ + P   ++ ++d++ +++a  ++    +++  e  +++  +++k+    ++e +q++++q+ ++ ++ +    ++++v+
    EPA04391.1   2 KYVKLFSALTIIMAVaMAPASTVFaQSDVNADVNADVNADVSVNANTAETKDKQIYKEQKQvrdQIKEQRQNIKTQLDDLRDLrNDRLAEKTDVN 96 
                   9********99998769999999998888888866444433333333333334434444442337777799999999988777666666666666 PP

>> RNA_pol_Rpc4  RNA polymerase III RPC4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   5.2e-06     0.031      25     124 ..      28     181 ..      17     213 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.2e-06
  RNA_pol_Rpc4  25 eddkseaesqsaekakaeeeskaekasgaeaeekkskkksskkkkkkkskalklkslpe...................................... 83 
                   +d++ + +++ +++ + +++++++k+++  +e+k+  ++ +++ ++ k++  +l++l++                                      
    EPA04391.1  28 SDVNADVNADVNADVSVNANTAETKDKQIYKEQKQVRDQIKEQRQNIKTQLDDLRDLRNdrlaektdvnvvpslefsgkvtgwaviggkavpatfdl 124
                   4444444444455555555555555555555555444444444444444445555555577888999999*************************** PP

  RNA_pol_Rpc4  84 ....GviGkLlvhkSGkvelrlGg..illevs..........pGaqpsFlqevvvve 124
                       G+iG+     SG +  ++G+  ++++++          +G++ +F   vv+++
    EPA04391.1 125 sgeaGKIGQRGWKISGTADAEIGDrnVTFDLQgfargnhvvlKGTTSEFDSVVVHLN 181
                   ***********************999************************9999995 PP

>> DUF2140  Uncharacterized protein conserved in bacteria (DUF2140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   2.6    0.0072        43       8      79 ..       7      78 ..       3      85 .. 0.66
   2 ?    2.5   0.8     0.015        92      34      68 ..      58      93 ..      43     126 .. 0.72
   3 ?    4.5   0.0    0.0039        23      80     118 ..     161     200 ..     143     220 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.0072
     DUF2140  8 liLlalllllvavvlvrvfapseeste.kssekekkseaeftitttkkqlnalinkylkkkqkdeklkykvel 79
                ++ l++++++++  +++vfa+s+ +   +++ + + s +  t +t+ kq+ +  + +++++ k++  + k +l
  EPA04391.1  7 FSALTIIMAVAMAPASTVFAQSDVNADvNADVNADVSVNANTAETKDKQIYKEQK-QVRDQIKEQRQNIKTQL 78
                67789999999999*********99874555555555555556666666655444.44455555555555555 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.015
     DUF2140 34 e.kssekekkseaeftitttkkqlnalinkylkkkq 68
                + +++ +++ +e+  +i+t+ ++l +l n+ l++k+
  EPA04391.1 58 KeQKQVRDQIKEQRQNIKTQLDDLRDLRNDRLAEKT 93
                2356666666778999***********999995543 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.0039
     DUF2140  80 ddevvlegeikvlgq.kvplkltfePevlenGnvvLkaks 118
                  ++vvl+g+++ + +  v+l+ +f P ++e+G+  L  ++
  EPA04391.1 161 GNHVVLKGTTSEFDSvVVHLNGYFAPIADESGSFALAFHR 200
                 6899******9997625799*************9997665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2161  (0.120531); expected 358.6 (0.02)
Passed bias filter:                     1093  (0.0609627); expected 358.6 (0.02)
Passed Vit filter:                       155  (0.00864521); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 1702.41
//
Query:       EPA04392.1  [L=124]
Description: hypothetical protein BG20_I2115 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       814  (0.0454013); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 829.13
//
Query:       EPA04393.1  [L=454]
Description: aminotransferase, class I/II [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.6e-41  141.2   0.0    5.9e-41  140.8   0.0    1.1  1  Aminotran_1_2  Aminotransferase class I and II
  ------ inclusion threshold ------
      0.045   12.8   0.1      0.091   11.8   0.1    1.5  1  S-layer        S-layer protein


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.8   0.0   6.6e-45   5.9e-41      19     339 ..      53     375 ..      39     391 .. 0.85

  Alignments for each domain:
  == domain 1  score: 140.8 bits;  conditional E-value: 6.6e-45
                    HHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTT CS
  Aminotran_1_2  19 tlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilrlsg 114
                    ++p+ ++ e   + ++ +   y    g pel+ a+ k+ +    ++++++ ++ vg+G+++li  l  +l+   g  +++p+p +  y + +rl +
     EPA04393.1  53 PVPKLIQNE---LVKNASKGAYAAVPGIPELRRAISKYNKYYFDIDVDPQ-RIYVGPGTKELIFNLLEILH---G-TVILPTPAWLGYLPQIRLLK 140
                    444445444...4577777889999***********888844489999**.*******************5...5.8999***************9 PP

                    SEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTS CS
  Aminotran_1_2 115 gevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveee 210
                       +  p+   +++++  ++l ++  +++ ++   k++++++phNPtG ++++ ele+++d++k++n+l+++De+Ya + ++ +++v+     + +
     EPA04393.1 141 KNYHMLPTG--ANRKISPNSLRKLGLRLQDRQ---KILILNNPHNPTGLLYDRLELEEIADVCKEQNILIISDEIYAQTTYDFSKFVS---MGKIY 228
                    999999955..99**********877776555...5*********************************************9556655...44445 PP

                    TT.EEEEEESSSTTSSGGG-EEEEEEEH...HHHHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS.TEEE CS
  Aminotran_1_2 211 pn.llivgslsKafGlaGeRvGyilgna...avvsqlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLael.glkv 299
                    p+ ++++++lsK+ ++ G R+Gy++  +   ++  q +k+ ++ +   s++ q+a++a  + +++++++++ +r+ ++ + ++ +++Lae+ g+k+
     EPA04393.1 229 PEgTFVTNGLSKSHAAGGYRLGYVIFPQnasDLQLQFKKILATEYTavSTPIQHAAVAGFEISDEMNEYFTITRSIHEIMGEYTYNKLAEIeGVKI 324
                    5567**********************776777888888887777777************************************************* PP

                    ECCSCSSEEEEEETHH..........CHHHHHHHHHHT.CTEEEEEGGGGT CS
  Aminotran_1_2 300 lasqsgmflltdlsae..........takelskkLlee.vgvyvtpgtsft 339
                    ++++++++ll+ ++++          t ++ls++L+ + ++ +++ g s  
     EPA04393.1 325 TKPEATFYLLVNFNHYslelqtakitTSQKLSEALIVHpYHTAIVGGDSLV 375
                    ****************99999988888888888887766777777766655 PP

>> S-layer  S-layer protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1     1e-05     0.091      88     141 ..     342     396 ..     303     403 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1e-05
     S-layer  88 etsddvsllsdekLskvlidedeektlksgssleLe.egYeleikqiDvdgdkvw 141
                  + +++++ +++kLs+ li +  ++ +  g+sl Le  +Y+ +i  +D dg kv+
  EPA04393.1 342 LELQTAKITTSQKLSEALIVHPYHTAIVGGDSLVLErTDYSARIAYVDYDGAKVY 396
                 45567889999************************9459***************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3274.54
//
Query:       EPA04394.1  [L=210]
Description: methyltransferase, FkbM family, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.6e-11   42.8   0.6    9.3e-11   42.0   0.5    1.4  2  Methyltransf_21  Methyltransferase FkbM domain


Domain annotation for each model (and alignments):
>> Methyltransf_21  Methyltransferase FkbM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0   0.5   5.2e-15   9.3e-11      18     149 ..       6     136 ..       1     170 [. 0.74
   2 ?   -2.3   0.0      0.21   3.8e+03      99     113 ..     161     176 ..     153     182 .. 0.70

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 5.2e-15
  Methyltransf_21  18 rlcggggevlaiEPvpns.....lpkfeklranll..tlavgndvglyelivegksggkyfpfavgdtngfstssvlggedaryievpvvtlds 104
                       + g+ g+++++EP +++     ++  e+   n++   +av++++g +el++         pf+ ++++ f   +++g++ ++ +++  + +ds
       EPA04394.1   6 SKVGPNGKIFSFEPSKENislfkKSIVENSFTNIIvvDAAVSDHDGHSELFL--------SPFYKSEHSLFEYNYSSGEHKGSKQKIKIISIDS 91 
                      478999***********88777655555555554467777777777777665........46667777777777777789999*********** PP

  Methyltransf_21 105 fleeikksridllkiDvEGaElevLeGaqkglkr.cqpnlivvEvh 149
                      fle+ +  + d++k+DvEG+E   L G +k++++  + +li  E+ 
       EPA04394.1  92 FLEKTGNLKADIIKMDVEGSEKKSLDGMKKTIEFnKKLTLI-TEFW 136
                      ********************************983333333.5544 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.21
  Methyltransf_21  99 vvtldsfleei.kksr 113
                        ++d+fl++    ++
       EPA04394.1 161 LYHIDEFLQKTyHVTV 176
                      5799999887645554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       890  (0.0496402); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1322.84
//
Query:       EPA04395.1  [L=273]
Description: S1 RNA binding domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.7e-19   67.6   0.6    9.7e-19   67.6   0.6    1.8  2  EIF_2_alpha  Eukaryotic translation initiation factor 2 alpha
    1.8e-12   47.4   0.2    8.7e-12   45.2   0.1    2.1  2  S1           S1 RNA binding domain
  ------ inclusion threshold ------
      0.024   15.2   0.3      0.087   13.4   0.1    2.1  2  EXOSC1       Exosome component EXOSC1/CSL4
       0.11   13.3   0.1       0.37   11.5   0.0    2.0  1  PCB_OB       Penicillin-binding protein OB-like domain


Domain annotation for each model (and alignments):
>> EIF_2_alpha  Eukaryotic translation initiation factor 2 alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.6   0.6   2.2e-22   9.7e-19       4     115 ..     131     234 ..     129     235 .. 0.90
   2 ?   -3.3   0.2       2.1   9.5e+03      47      63 ..     238     254 ..     236     257 .. 0.70

  Alignments for each domain:
  == domain 1  score: 67.6 bits;  conditional E-value: 2.2e-22
                  CTHHHHTTTTS-HHHHH.HHHHSTTHHHHHTTS-TTTHHHHHHCTHHHHHHT-EEEEEEEEEEE-STTHHHHHHHHHHHHST.S..TTSSSEEEEEEE CS
  EIF_2_alpha   4 evgwklyekyghaydaF.klaitdeevldkleipeeveeaLveiikkklkpqkvkiradieltcftkdGveaIkeaLkageeasneeeveeeeevkik 100
                  ++   +y k++++ydaF ++  ++ e +++l+ip++++ ++ e+i  k+k + v+ir+ +e+t  ++dGve Ik+aL  +        ++++ +++i+
   EPA04395.1 131 KLEDMIYSKFDSVYDAFiEIGRNGIESIKELKIPKKTATVI-EEICSKIKLPSVEIRGIMEITNNKSDGVEIIKKALLDA--------TKKDPTIDIT 219
                  667789****************************9998776.667778******************************33........345699**** PP

                  ESSSSEEEEEEEES. CS
  EIF_2_alpha 101 liapPeYvltvetld 115
                  + ++P+Y+l+++++d
   EPA04395.1 220 YLGAPKYRLSITSED 234
                  ***********9987 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.1
                  THHHHHHT-EEEEEEEE CS
  EIF_2_alpha  47 ikkklkpqkvkiradie 63 
                  ++k lkp  ++i+  ie
   EPA04395.1 238 AEKTLKPILIEIQENIE 254
                  56777777777777776 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   0.1     2e-15   8.7e-12       2      75 .]      17      91 ..      16      91 .. 0.97
   2 ?   -1.3   0.0      0.62   2.8e+03      19      29 ..     145     156 ..     141     161 .. 0.86

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 2e-15
                STTTCEEEEEEEEEETTEEEEEET..TTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTTEEEEEEC CS
          S1  2 pekgevveGeVtsvtkgGafVelg..ngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrrriilsik 75
                pe ge+v +++t+v+++Ga+V l+  ng++gf+++se++    +++ ++ +k G++  + v kv+ dr+ i+ls+k
  EPA04395.1 17 PEQGEIVLATITKVMDHGAYVTLDeyNGIQGFLHISEIAPG-WIRSVSRFVKDGEKKVLLVKKVNQDRGDIDLSLK 91
                789************************************99.9*******************************86 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.62
                 EEEEEET.TTEE CS
          S1  19 GafVelg.ngve 29 
                  af+e+g ng+e
  EPA04395.1 145 DAFIEIGrNGIE 156
                 69*****99987 PP

>> EXOSC1  Exosome component EXOSC1/CSL4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   1.9e-05     0.087       1      74 [.      16      91 ..      16     136 .. 0.76
   2 ?   -1.4   0.0      0.79   3.6e+03      38      52 ..     190     205 ..     156     249 .. 0.51

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.9e-05
                -S-TT-EEEEEEEEEESSEEEEEEEEECTBSBCCCEEECCCTTSS--STS.TTSSCCHCTE.EETTS...STTTT.SEE CS
      EXOSC1  1 lPkegdvVLarvtrlrkkqalveilsvegennvlsdsgvgangegavkei.eagggldsll.svatv...ssdlgetfk 74
                +P++g++VLa +t++  + a+v +      n + + +++++   g ++++ + + ++++++  v++v     d+++++k
  EPA04395.1 16 MPEQGEIVLATITKVMDHGAYVTLDEY---NGIQGFLHISEIAPGWIRSVsRFVKDGEKKVlLVKKVnqdRGDIDLSLK 91
                6********************998777...5567788888888888888876665555544044444444455556665 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.79
                 ECCCTTSS--STS.TT CS
      EXOSC1  38 gvgangegavkei.ea 52 
                  + +n++  v+ i +a
  EPA04395.1 190 EITNNKSDGVEIIkKA 205
                 4444444444433222 PP

>> PCB_OB  Penicillin-binding protein OB-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   8.3e-05      0.37      17      69 ..       5      61 ..       1      93 [. 0.71

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.3e-05
                .HHHHHHHCCTSSTCTTEEEEEEEEEETTEEEEEETTS..-EEEEEGGGGT..TTGC CS
      PCB_OB 17 deealeealkklpdsgelrpAvVlsvseksarvglrdg..etgtipleglk..wark 69
                + e++++++++ p++ge+++A +++v + +a v l++    +g++ +++++  w r 
  EPA04395.1  5 NLEEMSTEVQEMPEQGEIVLATITKVMDHGAYVTLDEYngIQGFLHISEIApgWIRS 61
                578999*****************************6432345555555443334444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1401  (0.0781416); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1939.72
//
Query:       EPA04396.1  [L=234]
Description: CobQ/CobB/MinD/ParA nucleotide binding domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-18   66.7   0.0      3e-18   66.1   0.0    1.3  1  CbiA          CobQ/CobB/MinD/ParA nucleotide binding domain
    5.4e-13   49.2   0.5    1.5e-06   28.1   0.0    2.2  2  AAA_26        AAA domain
     0.0094   15.3   0.6      0.024   14.0   0.1    1.8  2  CTP_synth_N   CTP synthase N-terminus
  ------ inclusion threshold ------
      0.018   14.6   0.5       0.21   11.2   0.1    2.1  2  SRP54         SRP54-type protein, GTPase domain
       0.07   12.6   0.5       0.28   10.6   0.0    1.9  2  ParA          NUBPL iron-transfer P-loop NTPase
      0.095   13.3   0.0       0.16   12.5   0.0    1.3  1  AAA_18        AAA domain
      0.098   12.6   0.2       0.35   10.9   0.2    1.9  1  DUF3217       Protein of unknown function (DUF3217)
       0.11   12.2   0.0       0.23   11.2   0.0    1.5  1  Beta_helix_2  Beta helix repeat of Inulin fructotransferase
       0.13   11.7   0.0       0.23   10.9   0.0    1.3  1  CBP_BcsQ      Cellulose biosynthesis protein BcsQ
       0.15   11.8   0.2       0.58    9.9   0.0    1.9  2  IstB_IS21     IstB-like ATP binding protein


Domain annotation for each model (and alignments):
>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.1   0.0   1.7e-21     3e-18       1     119 [.       6     184 ..       6     193 .. 0.92

  Alignments for each domain:
  == domain 1  score: 66.1 bits;  conditional E-value: 1.7e-21
                 EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH............................................. CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................................. RF
        CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep............................................. 54 
                 i+ia+ ++GvGKT+++++++ al+++g+ V++++++p+    ++l   +  +                                               
  EPA04396.1   6 ITIAGATSGVGKTSITCAIIYALQKKGFSVQPFKVGPDYIDPSYLSSISDHE-Afnldvwlmgrnqllnsfvsnsnsdisiiegvmgyydgfggdsnya 103
                 79************************************88877533333333.2589999999999********************************* PP

                 .................CCHCCCHHHHHHCHCHHHH.....EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHC CS
                 .................xxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        CbiA  55 .................dlkrllellealgkkkall...lkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeava 119
                                  d+++ +++++a  ++++++    +i g++ln+++++++e l +eale +    ++p++g+i ++ +++
  EPA04396.1 104 sthhvasitkspvililDASKTSRSIAATAIGFQKFhknSRISGIILNKIGSKKHEILCREALEIT----KLPIIGIIYKNLELN 184
                 **********************************99***************************998....8*******9998884 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.4   4.6e-07   0.00083       3      36 ..       6      39 ..       4      45 .. 0.93
   2 !   28.1   0.0   8.6e-10   1.5e-06      84     194 ..      68     183 ..      43     187 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 4.6e-07
      AAA_26  3 ifvtgtdtgvGKTvvslgLvralkrkgvkvgyfK 36
                i ++g + gvGKT+++ ++++al++kg++v+ fK
  EPA04396.1  6 ITIAGATSGVGKTSITCAIIYALQKKGFSVQPFK 39
                88**************************998777 PP

  == domain 2  score: 28.1 bits;  conditional E-value: 8.6e-10
      AAA_26  84 edidlekivkelekdadivvVEGagglgvpi...teellnadiaknlgapvilVarg..glgtinqllltiealrqknvrvlGvilNkvrnpe...nve 174
                 + + l+++    + ++di ++EG+ g+ ++    ++ +++  +a   ++pvil++ +  ++++i+++++  + +++ n r+ G+ilNk+ +++     +
  EPA04396.1  68 RNQLLNSF--VSNSNSDISIIEGVMGYYDGFggdSNYASTHHVASITKSPVILILDAskTSRSIAATAIGFQKFHK-NSRISGIILNKIGSKKheiLCR 163
                 55556666..456789********999988522144489999************9994344679999999998887.89*********87775445667 PP

      AAA_26 175 tlekksgipvlGvvPylpdl 194
                 ++ + +++p++G++  + +l
  EPA04396.1 164 EALEITKLPIIGIIYKNLEL 183
                 77778889****99777666 PP

>> CTP_synth_N  CTP synthase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.1   1.3e-05     0.024       7      60 ..       9      61 ..       6      63 .. 0.89
   2 ?   -2.0   0.1         1   1.8e+03     116     130 ..     196     210 ..     175     229 .. 0.50

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.3e-05
                 E--STTTTHHHHHHHHHHHHHCTT--EEEEEEE-SSSSSSTT--CCCC--EEE- CS
  CTP_synth_N  7 GGvvSglGkGiiaaslgallksrglkvtlikiDPYlnvdagtlsplehGEvfvl 60
                  G +Sg+Gk  i+ ++   l+++g++v+  k+ P   +d++ ls++   E f l
   EPA04396.1  9 AGATSGVGKTSITCAIIYALQKKGFSVQPFKVGPD-YIDPSYLSSISDHEAFNL 61
                 5889******************************4.479*****9999999865 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1
                  HHHHHHHHHHHHH.H CS
  CTP_synth_N 116 vtdeikeriekvakk 130
                    +++k++i+k +k 
   EPA04396.1 196 KEKNLKSKIKKNSKV 210
                  333333333333332 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.11   2.1e+02       9      32 ..      12      35 ..       4      37 .. 0.80
   2 ?   11.2   0.1   0.00012      0.21     113     170 ..     112     173 ..     102     179 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.11
                STTSSHHHHHHHHHHHHHHTTS-E CS
       SRP54  9 lqGaGKTttlaKLaallkkegkkv 32
                + G+GKT+ +  +   l+k+g +v
  EPA04396.1 12 TSGVGKTSITCAIIYALQKKGFSV 35
                46******9999999999998876 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00012
                 SSSEEEEEEETTBHTHHHH.HH...HHHHHHSSCSEEEEESTTSSSSTTHHHHHHHHHTS-E CS
       SRP54 113 kpdevllvldattgqeavk.qa...kaFkeavgitgviltklDgdakgGaalsiaaelklPi 170
                 ++  v+l+lda+  +  ++ +a   ++F+++  i+g+il k+ ++ +      + + +klPi
  EPA04396.1 112 TKSPVILILDASKTSRSIAaTAigfQKFHKNSRISGIILNKIGSKKHEILCREALEITKLPI 173
                 5677999**998777665522234489***************98887766666677777776 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00016      0.28       6      35 ..       6      35 ..       4      39 .. 0.92
   2 ?   -0.1   0.1      0.28   5.1e+02     164     226 ..     142     210 ..     104     228 .. 0.51

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00016
        ParA  6 iavlSgKGGVGKStvavnlAlaLakkglkv 35
                i+++ +  GVGK+++++ + +aL+kkg++v
  EPA04396.1  6 ITIAGATSGVGKTSITCAIIYALQKKGFSV 35
                77888899*******************988 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.28
        ParA 164 kvkvlGvveNmsgfvcpk..cgekteifgk....gggeklaeelgvpllgeipldpeireasdegkplv 226
                 + ++ G++ N  g + ++  c+e  ei +        ++l  +++ + lg ip++++  ++  ++++ v
  EPA04396.1 142 NSRISGIILNKIGSKKHEilCREALEITKLpiigIIYKNLELNFESRHLGLIPVKEKNLKSKIKKNSKV 210
                 455666666654443332224444444433111122344444555577777777765544444444333 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   9.1e-05      0.16       3      83 ..       8      90 ..       6      97 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.1e-05
      AAA_18  3 ltG.tpGvGKttlakeL....skrlgf....gvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleegknlvidghl 83
                ++G t+GvGKt+++ ++    +k+ gf      +  d++  ++l+   d+e    ++ +  + +++ll+ +  ns+     +  +i+g++
  EPA04396.1  8 IAGaTSGVGKTSITCAIiyalQKK-GFsvqpFKVGPDYIDPSYLSSISDHE--AFNLDVWLMGRNQLLNSFVSNSN----SDISIIEGVM 90
                555489*******99988887888.56779999999***************..********************987....7888999987 PP

>> DUF3217  Protein of unknown function (DUF3217)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.2   0.00019      0.35      52      95 ..     181     226 ..     175     233 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00019
     DUF3217  52 lelekytkevkvlsvk.Gvlktylekkskivktsilvekilk.nkn 95 
                 lel+  +++   + vk   lk +++k+sk++  si veki++  kn
  EPA04396.1 181 LELNFESRHLGLIPVKeKNLKSKIKKNSKVISDSIDVEKIIQiIKN 226
                 4566666777778886257*********************984444 PP

>> Beta_helix_2  Beta helix repeat of Inulin fructotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00013      0.23      15      46 ..      97     129 ..      96     145 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00013
  Beta_helix_2  15 sGasNviatnhvvsnvavkhv.VLDasttktkv 46 
                   +G+sN+ +t hv+s  ++  + +LDas t+  +
    EPA04396.1  97 GGDSNYASTHHVASITKSPVIlILDASKTSRSI 129
                   8*****988888877666554478***997655 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00013      0.23       3      33 ..       5      35 ..       3      45 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00013
    CBP_BcsQ  3 vlalqGvRGGvGttsllaaLawalhelgesv 33
                 +++ G   GvG+ts++ a+ +al++ g sv
  EPA04396.1  5 RITIAGATSGVGKTSITCAIIYALQKKGFSV 35
                68999*********************99887 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00032      0.58      52      79 ..       8      36 ..       4      43 .. 0.83
   2 ?   -1.0   0.0      0.69   1.2e+03      44      78 ..     111     145 ..     103     156 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00032
   IstB_IS21 52 llG.psGvGKshlaialgveavraglsvl 79
                + G  sGvGK+ +++a+ ++  ++g+sv 
  EPA04396.1  8 IAGaTSGVGKTSITCAIIYALQKKGFSVQ 36
                556247********************996 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.69
   IstB_IS21  44 iekkenivllGpsGvGKshlaialgveavraglsv 78 
                 i+k+  i++l  s + +s  a+a+g +  +++ ++
  EPA04396.1 111 ITKSPVILILDASKTSRSIAATAIGFQKFHKNSRI 145
                 55666677778888888888999998888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1374.47
//
Query:       EPA04397.1  [L=118]
Description: hypothetical protein BG20_I2018, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.19   11.7   0.2       0.48   10.4   0.0    1.6  2  VIT_2     Vault protein inter-alpha-trypsin domain


Domain annotation for each model (and alignments):
>> VIT_2  Vault protein inter-alpha-trypsin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1      0.16   2.9e+03      34      43 ..      49      58 ..      47      64 .. 0.75
   2 ?   10.4   0.0   2.7e-05      0.48      10      52 ..      68     110 ..      65     115 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.16
       VIT_2 34 ltYyNdqeqp 43
                l+Y+N q+q+
  EPA04397.1 49 LAYVNLQTQQ 58
                7899999886 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 2.7e-05
       VIT_2  10 tplplkaskvsacvlgaslgvtasltYyNdqeqpvegvFvyPl 52 
                 tp+  k++k ++  +g    v as ++  ++ qpv gvFvy +
  EPA04397.1  68 TPIYVKDIKYTSDGNGPLQLVHASPSFNAEKGQPVIGVFVYKV 110
                 67889999999******************************66 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       245  (0.013665); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 854.65
//
Query:       EPA04398.1  [L=213]
Description: precorrin-8X methylmutase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-73  246.1   1.0    2.6e-73  245.9   1.0    1.0  1  CbiC      Precorrin-8X methylmutase


Domain annotation for each model (and alignments):
>> CbiC  Precorrin-8X methylmutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  245.9   1.0   1.4e-77   2.6e-73       2     195 ..       9     205 ..       8     206 .. 0.97

  Alignments for each domain:
  == domain 1  score: 245.9 bits;  conditional E-value: 1.4e-77
                 HHHHHHHHHHCHC-TT.S-CHHHHHHHHHHHHHT-CCHH..HHEEE-TTHHHHHHHHHHCT-EEEESSHHHHCCS-HHHHHTTC-EEEECTC-HHHHHH CS
        CbiC   2 IeaeSfaiideelgeeelseeeeevvrRvihatadfela..ellrfspdaveaglealkagapivtDvemvkaGitkkrleklgnevlclladpevael 98 
                 Ie+ S+++id+e+g+++++e+e+++vrR+ih+tadf++a  + + f+++a+e+g++alk+g++iv+Dv+ v  G++k+  + ++n+++c ++dp+v+e+
  EPA04398.1   9 IEDASMQMIDKEIGTHQYNEKEWPIVRRIIHSTADFDFAreNRVIFHKKAIESGIKALKNGCSIVVDVNGVIGGLNKQNPKDFQNKIVCNISDPKVMEM 107
                 99************************************9556799****************************************************** PP

                 HHHHTS-HHHHHHHHHHHCTTTCEEEESS-HHHHHHHHHHHHHS..HTSEEEE----SCCHHHHHHHHHCSS.S-EEEESSS---HHHHHHHHHHHHH CS
        CbiC  99 akekgitrsaaamekaaeelegaivviGnAPtALlellelieegkvkpalvigvPvGFvgaaesKealaese.vpyitveGrkGGsavAaaivnaLle 195
                 ak++++trs+++m+ a ++ +g+iv+iGnAPtALle++++++eg vkpal+ig+PvGF+ aaesKe+l+++e +p+it+ GrkGGs+ A ai+naL++
  EPA04398.1 108 AKKENKTRSQVSMRVASSDIDGGIVAIGNAPTALLEVIHMVKEGIVKPALIIGIPVGFICAAESKEELSKLEeTPFITNIGRKGGSSSASAIINALYK 205
                 *********************************************************************9656***********************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1523.58
//
Query:       EPA04399.1  [L=148]
Description: sirohydrochlorin cobaltochelatase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.9e-16   59.3   0.0    5.1e-16   58.9   0.0    1.2  1  CbiX            CbiX
    1.5e-05   24.5   0.2    1.8e-05   24.2   0.2    1.0  1  CbiK            Cobalt chelatase (CbiK)
  ------ inclusion threshold ------
      0.087   11.9   0.1       0.91    8.5   0.0    1.9  2  Ferrochelatase  Ferrochelatase


Domain annotation for each model (and alignments):
>> CbiX  CbiX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.9   0.0   8.6e-20   5.1e-16       1     106 [.      36     138 ..      36     139 .. 0.92

  Alignments for each domain:
  == domain 1  score: 58.9 bits;  conditional E-value: 8.6e-20
                 -STSSCCHHHHHHHHHHHHHHHCCSCCCEECESCCCECCSCCSSHHHHC-SBSEEEEEEESSSSSHHHHTHHHHHCT--SSSS-TTEEEEE---CCCSC CS
        CbiX   1 HGSrdpesneeveklaeelrekgpfkpvelgfleleepsleealrelaeqgvkrivvvPlflfaGvhvkeDIpeeleeaeeahpkdveieytepLGthp 99 
                 HGS+dp+++  +  +++ l++  +++ v  ++le+e+p++ ++++++++++ +  v+v +fl +G hvk+DI + l  a e+     + ++t++LG ++
  EPA04399.1  36 HGSKDPNAQLSLDYVVDGLKN--NYRNVNRCWLEIEQPDIVQGIKTCEKNNPQVLVIVFYFLHEGAHVKTDINNDLIPALENSS-IKKAYITKHLGVDE 131
                 *********************..556**********************************************996665555555.4799********** PP

                 CHHHHHH CS
        CbiX 100 lvaevlk 106
                 +++++++
  EPA04399.1 132 KMIDLII 138
                 ****997 PP

>> CbiK  Cobalt chelatase (CbiK)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.2     3e-09   1.8e-05     132     260 ..      19     144 ..       9     146 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 3e-09
                 HTTS----TTEEEEEEE---SCHHHHHHHHHHHHHHH..CT-S.EEEEETT.SSS-HHHHHHHHHHHT--EEEEEE-SSS--HHHHCCCCSSSTTSHHH CS
        CbiK 132 kdeierarkdealvfvgHGtehesnavyaeldkvlke..kdfkqvvvgtve.gyPeveevieelkkkgikevkliPlmlvAGdHaknDmasdeedswke 227
                 +++++  +kd  ++ +gHG++ + ++    ld+v++   +++++v  + +e  +P++ + i++ +k++ +   ++ ++l  G H+k D+    +++   
  EPA04399.1  19 ENKVTISKKDVDVLIIGHGSKDPNAQ--LSLDYVVDGlkNNYRNVNRCWLEiEQPDIVQGIKTCEKNNPQVLVIVFYFLHEGAHVKTDI----NNDLIP 111
                 34555567999999******998776..467777764447799*****999558***************99999999************....568999 PP

                 HHHHTT--EEE----GGGSHHHHHHHHHHHHHH CS
        CbiK 228 aleaaGikveiilkgLGeieeirsifikhikea 260
                 ale+  ik   i k LG +e++ ++ i++ ke+
  EPA04399.1 112 ALENSSIKKAYITKHLGVDEKMIDLIIERAKEV 144
                 ****************************99986 PP

>> Ferrochelatase  Ferrochelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.017     1e+02     160     193 ..       2      38 ..       1      63 [. 0.85
   2 ?    8.5   0.0   0.00015      0.91     241     314 ..      70     142 ..      59     145 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.017
                     -HHHHHHHHHHHHHHHTTS-...HC.C-EEEEEEE-- CS
  Ferrochelatase 160 hpgyiealaesikealeelp...eekkakllfsaHgl 193
                     h+++i+ + ++i+ +l+e++   ++k +++l+  Hg 
      EPA04399.1   2 HKTLINLVENRIFSTLQENKvtiSKKDVDVLIIGHGS 38 
                     8999**************9999844469999999995 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00015
                     SSBHHHHHHHHCCC.-S-EEEE-TT-SS--HHHHIIIIIIIITTSTT..CCCEEE----TT-HHHHHHHHHHHH CS
  Ferrochelatase 241 ePdtddtleelaekgvkaivvvpigFvsDhlEtleeldiearelaeeaggekfvrvptlndspafiealadlve 314
                     +Pd+ + ++ +++++  +++v+   F  +   ++ +++  +  ++e+++++k    + l+ ++++i+++ + ++
      EPA04399.1  70 QPDIVQGIKTCEKNN-PQVLVIVFYFLHEGAHVKTDINNDLIPALENSSIKKAYITKHLGVDEKMIDLIIERAK 142
                     6999999*9999998.9**************************************************9988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1048.76
//
Query:       EPA04400.1  [L=144]
Description: CobB/CobQ-like glutamine amidotransferase domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.4e-24   85.2   0.4    4.9e-24   85.0   0.4    1.0  1  GATase_3    CobB/CobQ-like glutamine amidotransferase domain
     0.0032   17.5   0.3     0.0053   16.8   0.3    1.3  1  DUF1836     Domain of unknown function (DUF1836)
  ------ inclusion threshold ------
      0.062   14.0   0.0      0.086   13.6   0.0    1.3  1  Sec23_BS    Sec23/Sec24 beta-sandwich domain
      0.062   13.1   0.4      0.081   12.8   0.4    1.4  1  Beta_helix  Right handed beta helix region


Domain annotation for each model (and alignments):
>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.0   0.4   1.1e-27   4.9e-24      64     195 ..       2     129 ..       1     130 [. 0.83

  Alignments for each domain:
  == domain 1  score: 85.0 bits;  conditional E-value: 1.1e-27
    GATase_3  64 ldeaikeaaeaggpvlgiCGGlqmLGeeiedpegvegeageveglglLdietefekekltgqvegevel....aaegeevkGyEiHsGrtilkekakpl 158
                 +++ ik+++e+++p++++CGGl++L ++i   + +     + +++g++d+et+++k+  ++ ++g+v      + ++ +++G+E+H+++     + +  
  EPA04400.1   2 MKNTIKKLSEDNTPIYAECGGLMYLTKSIDYGN-K-----KFKMIGIFDAETKMTKKMKLNYTKGKVISkniiTDKTHALRGHEFHYSELDA-VSSDSK 93 
                 8999************************97654.3.....8***************777778888855589987788***********6654.445555 PP

    GATase_3 159 lkvkv..ggnng.ekdGavkksedgnvlGtYlHglfdnrn 195
                 ++++   g +++ +kdG+++     n+l++Y H+ fd+++
  EPA04400.1  94 FAYELdiGLGIKnQKDGLIQY----NTLASYGHLYFDSSD 129
                 5555545666667******99....************976 PP

>> DUF1836  Domain of unknown function (DUF1836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.3   1.2e-06    0.0053      11      51 ..      24      65 ..      17      73 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.2e-06
     DUF1836 11 Lyldqvvelvnqvleslkrned.kvltktminNYvKkkllek 51
                +yl + +++ n++++ +   +  +++tk m  NY+K k+++k
  EPA04400.1 24 MYLTKSIDYGNKKFKMIGIFDAeTKMTKKMKLNYTKGKVISK 65
                799999**********9998888*****************97 PP

>> Sec23_BS  Sec23/Sec24 beta-sandwich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.9e-05     0.086       7      76 ..      46     117 ..      43     138 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.9e-05
                 EEEE-TTEEEEEEESSSEECSTBESSEESECSE..SEEEEEEEETT--EEEEEEESSBTCTTSEEEEEEEEE CS
    Sec23_BS   7 evrtSkelkvsgliGncvslsnvsekeiGeggt..sewklcsldpdstlavyfdideklksgkqayiQfatl 76 
                 e +++k++k++   G+++s++ +++k+    g      +l ++++ds +a ++di   +k++k+ +iQ+ tl
  EPA04400.1  46 ETKMTKKMKLNYTKGKVISKNIITDKTHALRGHefHYSELDAVSSDSKFAYELDIGLGIKNQKDGLIQYNTL 117
                 67899***************877777444433300467899999***********989**********9875 PP

>> Beta_helix  Right handed beta helix region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.4   1.8e-05     0.081      71     133 ..      52     139 ..       2     144 .] 0.58

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.8e-05
                 EE-TT--S--EEES-EEES-.....SS-......................SEE-TT-S--EEES-EEESTT--SEE---TT.---EEES-E CS
  Beta_helix  71 gialfgasnnlienneitdn.....ggs......................GiylnyssnntienNiidnnagsGividdss.snvtvtnNt 133
                  ++l+++++ +i++n itd      g +                      G+ ++++++  i++N++ + +   +++d+s+ ++v v+n++
  EPA04400.1  52 KMKLNYTKGKVISKNIITDKthalrG-HefhyseldavssdskfayeldiGLGIKNQKDGLIQYNTLASYG--HLYFDSSDyARVFVKNCI 139
                 45666667777777777777444430.03333333334444444444444777777888888888884444..444444445555444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1097.01
//
Query:       EPA04401.1  [L=51]
Description: H/ACA RNA-protein complex component Nop10p [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.1e-23   81.2   3.5    4.2e-23   81.1   3.5    1.0  1  Nop10p       Nucleolar RNA-binding protein, Nop10p family
     0.0014   18.1   1.8     0.0018   17.8   1.8    1.2  1  RecR         RecR protein
     0.0074   14.2   0.2     0.0074   14.2   0.2    1.0  1  PolC_DP2     DNA polymerase II large subunit DP2
  ------ inclusion threshold ------
      0.044   13.7   1.8      0.054   13.4   1.8    1.1  1  Prok-RING_4  Prokaryotic RING finger family 4


Domain annotation for each model (and alignments):
>> Nop10p  Nucleolar RNA-binding protein, Nop10p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.1   3.5   9.5e-27   4.2e-23       1      48 [.       1      48 [.       1      51 [] 0.96

  Alignments for each domain:
  == domain 1  score: 81.1 bits;  conditional E-value: 9.5e-27
                .----EE-TTT--EESSSB-TTT-SB-B-SS--S--TT-TTCHHHHHC CS
      Nop10p  1 mksylrkcgkcrvYTLkkvcpecggptksahPaRFSPdDkyskyRral 48
                m++ lr+c+kc++Y Lk++cp c+++t+sahPa+FSPdDky +yR a 
  EPA04401.1  1 MRFLLRRCSKCNRYSLKERCPLCNEETVSAHPAKFSPDDKYMRYRLAE 48
                99*******************************************985 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   1.8     4e-07    0.0018      16      37 ..       5      26 ..       2      27 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4e-07
                -EE-TTT--EESSSS-CCCCST CS
        RecR 16 vrhCsrCgnlteedlCaICsdp 37
                +r+Cs+C+ ++ ++ C+ C+ +
  EPA04401.1  5 LRRCSKCNRYSLKERCPLCNEE 26
                589****************865 PP

>> PolC_DP2  DNA polymerase II large subunit DP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.2   1.7e-06    0.0074     617     642 ..       4      29 ..       1      47 [. 0.86

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.7e-06
    PolC_DP2 617 arrkCkkCgketlearCeeCgektee 642
                   r+C+kC++ +l+ rC+ C+e+t +
  EPA04401.1   4 LLRRCSKCNRYSLKERCPLCNEETVS 29 
                 679*******************9986 PP

>> Prok-RING_4  Prokaryotic RING finger family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   1.8   1.2e-05     0.054      21      41 ..       8      28 ..       5      35 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.2e-05
  Prok-RING_4 21 CkeCfdskdlssCPlCqrris 41
                 C +C   +  ++CPlC+++  
   EPA04401.1  8 CSKCNRYSLKERCPLCNEETV 28
                 77887777777******9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 356.46
//
Query:       EPA04402.1  [L=176]
Description: cob(I)yrinic acid a,c-diamide adenosyltransferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      7e-60  202.2   0.5    7.7e-60  202.1   0.5    1.0  1  CobA_CobO_BtuR  ATP:corrinoid adenosyltransferase BtuR/CobO/C
     0.0026   17.8   0.4     0.0043   17.1   0.1    1.5  2  AAA_14          AAA domain


Domain annotation for each model (and alignments):
>> CobA_CobO_BtuR  ATP:corrinoid adenosyltransferase BtuR/CobO/CobP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.1   0.5   8.6e-64   7.7e-60       2     172 .]       3     176 .]       2     176 .] 0.97

  Alignments for each domain:
  == domain 1  score: 202.1 bits;  conditional E-value: 8.6e-64
  CobA_CobO_BtuR   2 kglihvytGdGKGKttAAlGlalRalgaglkvlvvqFlKgekesgElaalkkl..eielerlgkegfv..kmeeeekeedaaaakealekakeal 92 
                     +gl +vytG+GKGKttAAlG+alRa+g  +k +++qF+Kg++++gE  + k+l  e+e++ +g +gfv    +++ k+e+++ a+ea++  +e++
      EPA04402.1   3 EGLTIVYTGKGKGKTTAALGIALRATGYAKKTCMIQFIKGSWHYGEMYSSKRLepEFEMVAIG-KGFVgiIDDKSPKTEHERVAAEAIKISTEKI 96 
                     6999*************************************************766*******.9***9877788899***************** PP

  CobA_CobO_BtuR  93 aseeydlvvlDEinyalklglldeeevlellkkkpeklelvlTGrnapeelleaADlvtemkkvkHpydkgikarkGiey 172
                     +s++yd+v+lDEinya++lgl+++e+v++l+k+kp+kl+l+lTG +a+++++e+ADlvtemk++kHp++ g+ka+kGi++
      EPA04402.1  97 QSGKYDIVILDEINYAINLGLVEIEDVINLIKTKPPKLDLILTGNYAKDKIIELADLVTEMKEIKHPFQYGVKAKKGIDF 176
                     ******************************************************************************98 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1      0.45   4.1e+03      14      23 ..      15      24 ..       8      55 .. 0.71
   2 !   17.1   0.1   4.8e-07    0.0043      47     113 ..      83     154 ..      63     165 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.45
      AAA_14 14 GKTtllkqli 23
                GKTt +  ++
  EPA04402.1 15 GKTTAALGIA 24
                8888766554 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 4.8e-07
      AAA_14  47 adpekllelileklkeekktylflDEiqev.....pewekalkslvdegknldvivtGSnskllskeiatsl 113
                 +  ++ +++  ek+++ k  +++lDEi ++      e+e++++ +  + ++ld+i+tG  +k++  e+a+ +
  EPA04402.1  83 RVAAEAIKISTEKIQSGKYDIVILDEINYAinlglVEIEDVINLIKTKPPKLDLILTGNYAKDKIIELADLV 154
                 323356677777765557788*********88888899********************99999877776554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1147.12
//
Query:       EPA04403.1  [L=201]
Description: hypothetical protein BG20_I2444 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.06   13.5   0.8       0.06   13.5   0.8    1.9  2  YtpI      YtpI-like protein
      0.098   12.9   0.3       0.37   11.1   0.0    1.8  2  DUF3040   Protein of unknown function (DUF3040)
       0.14   12.6   0.8       0.62   10.5   0.0    2.1  2  DUF202    Domain of unknown function (DUF202)
       0.18   12.0   0.3       0.18   12.0   0.3    1.7  2  DUF2371   Uncharacterised conserved protein (DUF2371)


Domain annotation for each model (and alignments):
>> YtpI  YtpI-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1      0.58   2.6e+03      36      44 ..      18      26 ..      10      33 .. 0.52
   2 ?   13.5   0.8   1.3e-05      0.06      53      80 ..     160     187 ..     154     189 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.58
        YtpI 36 ialGlflil 44
                i++++++++
  EPA04403.1 18 ISISIMVSV 26
                344444444 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 1.3e-05
        YtpI  53 lestvalvvgavflvlGlanlfaGiray 80 
                  ++ v lv++a++l++G++ l+ Gi+ y
  EPA04403.1 160 RNTIVPLVISAILLIFGIIILIVGIIMY 187
                 678999******************9876 PP

>> DUF3040  Protein of unknown function (DUF3040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.3      0.49   2.2e+03      53      62 ..      10      19 ..       3      29 .. 0.49
   2 ?   11.1   0.0   8.2e-05      0.37      19      64 ..     142     185 ..     140     190 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.49
     DUF3040 53 vaGllllvlG 62
                v+Gl+l+ + 
  EPA04403.1 10 VSGLVLVAIS 19
                3344444333 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 8.2e-05
     DUF3040  19 aaeDPklaaalrggaararrrslrrlavlavllfvaGllllvlGva 64 
                  +eDP+  +a+  ++++++ r++   +v++++l+++G+++l++G++
  EPA04403.1 142 ISEDPDNSDAF--TNPNSPLRNTIVPLVISAILLIFGIIILIVGII 185
                 579********..55554444445557888999999********65 PP

>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.4      0.26   1.1e+03      42      56 ..      10      24 ..       4      28 .. 0.75
   2 ?   10.5   0.0   0.00014      0.62      39      63 ..     164     188 ..     111     193 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.26
      DUF202 42 ilglilivlgiltll 56
                + gl+l++++i +++
  EPA04403.1 10 VSGLVLVAISISIMV 24
                568888888887775 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00014
      DUF202  39 lgkilglilivlgiltllvglvryl 63 
                 +  ++++il+++gi++l+vg++ yl
  EPA04403.1 164 VPLVISAILLIFGIIILIVGIIMYL 188
                 457889****************997 PP

>> DUF2371  Uncharacterised conserved protein (DUF2371)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.2       1.2   5.6e+03      45      58 ..      10      23 ..       5      36 .. 0.56
   2 ?   12.0   0.3   4.1e-05      0.18      38      63 ..     167     192 ..     159     200 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.2
     DUF2371 45 llGllvllvGiama 58
                + Gl+++++ i++ 
  EPA04403.1 10 VSGLVLVAISISIM 23
                34444444444433 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 4.1e-05
     DUF2371  38 svsglvlllGllvllvGiamavlgyw 63 
                  +s+++l++G+++l+vGi m ++ + 
  EPA04403.1 167 VISAILLIFGIIILIVGIIMYLIDWK 192
                 57899***************988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1158  (0.0645881); expected 358.6 (0.02)
Passed bias filter:                      729  (0.0406604); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1411.59
//
Query:       EPA04404.1  [L=101]
Description: nucleic acid-binding domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-06   26.1   0.3    7.8e-06   25.8   0.3    1.2  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
    6.4e-05   22.8   0.8    7.2e-05   22.6   0.8    1.1  1  REPA_OB_2        Replication protein A OB domain
  ------ inclusion threshold ------
      0.032   14.4   0.7        4.3    7.6   0.4    2.1  2  HupF_HypC        HupF/HypC family


Domain annotation for each model (and alignments):
>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.3   1.3e-09   7.8e-06       3      69 ..      19      89 ..      17      99 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 1.3e-09
                     EEEEEEEEE........EEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEE.EEEEECTTSSEEEE CS
  tRNA_anti-codon  3 vaGrvtsis........drsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvt.Grvkrrpggelelk 69
                     ++++v+s+         ++++  v+++++ D++++i+++l+     +  + + +Gdvv +t G+ ++++g+ ++l+
       EPA04404.1 19 LKAEVKSKGdprtvnlkTGGTVDVCDAVIADESDEIKLTLWG----DDIKAVNVGDVVVITnGYTNEFKGE-VSLT 89
                     677888888888888888889999******************....999*******************998.8875 PP

>> REPA_OB_2  Replication protein A OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.8   1.2e-08   7.2e-05      17      97 ..      21      98 ..       5      99 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.2e-08
   REPA_OB_2 17 gvvksveevseitskstekelkkreltlvDesgasvevtlWgkeaekfesseepvvalkgvkvsdFgg.rslsllssstlkv 97
                + vks ++ ++++ k+++ +++ ++  + Des  ++++tlWg++ + +  +  +vv++ ++  ++F+g  sl+  + +++++
  EPA04404.1 21 AEVKSKGDPRTVNLKTGG-TVDVCDAVIADESD-EIKLTLWGDDIKAV--NVGDVVVITNGYTNEFKGeVSLTKGKFGKMEI 98
                5689999999*****999.9***********97.7********98885..5889**************66776666666665 PP

>> HupF_HypC  HupF/HypC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0014       8.5       8      43 ..       9      47 ..       6      49 .. 0.82
   2 ?    7.6   0.4   0.00072       4.3      22      48 ..      48      78 ..      39      82 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0014
                EEEEEET...TEEEEECTTEEEEEEGTTCTTB-TT-EEE CS
   HupF_HypC  8 kvveied...elAlvdvgGvrrevslalveevkvGdyVL 43
                +v ++       A v+ +G  r+v+l+  + v v d V+
  EPA04404.1  9 QVKKMRSginLKAEVKSKGDPRTVNLKTGGTVDVCDAVI 47
                566666655458***************999999999998 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00072
                TTEEEEEEGTTC....TTB-TT-EEEEETTE CS
   HupF_HypC 22 gGvrrevslalv....eevkvGdyVLvhvGf 48
                 +++ e++l l     + v+vGd V++  G+
  EPA04404.1 48 ADESDEIKLTLWgddiKAVNVGDVVVITNGY 78
                478899999999877777*********9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 702.29
//
Query:       EPA04405.1  [L=159]
Description: hypothetical protein BG20_I2353, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-20   72.1   0.0    6.2e-20   71.8   0.0    1.1  1  GSDH      Glucose / Sorbosone dehydrogenase


Domain annotation for each model (and alignments):
>> GSDH  Glucose / Sorbosone dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.8   0.0   3.5e-24   6.2e-20     250     329 ..       3      83 ..       1      93 [. 0.90

  Alignments for each domain:
  == domain 1  score: 71.8 bits;  conditional E-value: 3.5e-24
                 TT---EEEEEEE........TTEEEEEETTTTEEEEEEEEEE.EEEEEEEEEE.ESS-.-EEEEEE-TTS-EEEEE-TTTTT CS
        GSDH 250 tpsiapsglafytgdafpewkgdllvggLksqsllrleldeg.ekvveeerll.eelgeriRdVeqgpdGalyvltdeedgk 329
                 + ++apsg+ fy+ d++p+w+g+l+v++L+ ++l  l++d++ +k+ +++ ++ +e+g r+Rd+  gpdG+ly+lt+++dg+
  EPA04405.1   3 DDTWAPSGISFYNNDKIPSWNGKLFVATLRGSHLKILDIDSSqDKIISQQDIFvNEFG-RLRDIVSGPDGYLYLLTSNNDGR 83 
                 5689***********************************6542667777777768898.*********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.32s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1008.34
//
Query:       EPA04406.1  [L=353]
Description: PAS domain S-box, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-22   80.2   0.2    3.3e-22   79.1   0.2    1.6  1  HATPase_c      Histidine kinase-, DNA gyrase B-, and HSP90-li
    4.5e-13   49.2   0.0    8.9e-12   45.0   0.0    2.4  2  PAS            PAS fold
    1.7e-11   44.3   0.1    3.9e-11   43.1   0.1    1.7  1  PAS_9          PAS domain
      2e-09   37.4   0.2      5e-09   36.1   0.2    1.7  1  HisKA          His Kinase A (phospho-acceptor) domain
    5.2e-07   29.9   0.0    7.5e-07   29.4   0.0    1.2  1  PAS_4          PAS fold
    2.1e-06   27.9   0.0    5.6e-06   26.6   0.0    1.7  1  PAS_3          PAS fold
    0.00018   21.5   0.0    0.00037   20.4   0.0    1.5  1  PAS_8          PAS domain
     0.0003   20.6   0.1     0.0011   18.8   0.0    2.0  2  HATPase_c_5    GHKL domain
  ------ inclusion threshold ------
      0.018   14.9   0.0      0.038   13.8   0.0    1.5  1  HATPase_c_3    Histidine kinase-, DNA gyrase B-, and HSP90-li
       0.14   12.1   0.0       0.23   11.4   0.0    1.4  1  HATPase_c_2    Histidine kinase-like ATPase domain
       0.55    9.9   3.9         11    5.7   0.3    3.2  3  CRM1_repeat_2  CRM1 / Exportin repeat 2


Domain annotation for each model (and alignments):
>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.1   0.2     2e-25   3.3e-22       2     109 ..     251     353 .]     250     353 .] 0.93

  Alignments for each domain:
  == domain 1  score: 79.1 bits;  conditional E-value: 2e-25
                 HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHHHHHHHHHTTTEEEEEEETTT CS
   HATPase_c   2 dekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsivkklvelmgGeiwvesepgr 100
                 d+++++ i++nlv Na+++ +++g+i ++ + +e +++i v+D+G+Gip + + k+f+++ +     +++ gtGlGl i+k ++e++gG+i++e+e ++
  EPA04406.1 251 DQRKIEIILRNLVLNAIQAMGEKGSIIITTNETESHVKILVKDTGPGIPHKLRFKIFDPLFT-----TRQIGTGLGLPICKTVIEQHGGSISFETELEK 344
                 7889999************889**99999997779***********************6666.....5889***********9999************* PP

                 EEEEEEEEE CS
   HATPase_c 101 Gttftftlp 109
                 Gttft++lp
  EPA04406.1 345 GTTFTISLP 353
                 ******997 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.0   0.0   5.4e-15   8.9e-12       2     113 .]      16     126 ..      15     126 .. 0.89
   2 ?    1.5   0.0      0.18   2.9e+02      50      92 ..     216     260 ..     205     276 .. 0.84

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 5.4e-15
                 HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEECTTSSEEEEEEEEEEEEETT CS
         PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfklrdgrpihlevraspvrdag 100
                 ++r+i e++pd    ++ +g+i+ +N+++ e lG+  +ev+gk+++d  +ee+ ++++e +e+  + g + ++ ei++k+++g ++ +++ a+ ++d+ 
  EPA04406.1  16 MYRSIYENSPDLFRTININGEIINCNKSYFETLGYLKSEVIGKTIFDHTSEESLSQMRETFEEW-KKGGCVSNSEIWLKKKNGDKFLALLSANNLFDKY 113
                 89**************************************************888777777765.556777788***********************99 PP

                 EEEEEEEEEEEES CS
         PAS 101 geilgflgvlrdi 113
                 g+++g    +rdi
  EPA04406.1 114 GTLIGSNTSIRDI 126
                 9888876666665 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.18
                 BSTTHHHHHHHHHHHHHHHTT-ECCCCEEEEC......TTSSEEEEEEE CS
         PAS  50 iheeddaelaelleqlleqgeesrageisfkl......rdgrpihlevr 92 
                   +     l+++le++++++  ++ + +++++      +d+r+i++ +r
  EPA04406.1 216 QQNS----LKKILENVINEMPIPEEFIVTIPTndiminCDQRKIEIILR 260
                 4333....999*********************99999999999998765 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   0.1   2.4e-14   3.9e-11       7     104 .]      31     128 ..      25     128 .. 0.95

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 2.4e-14
       PAS_9   7 dnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk..kerevevvlirkngetfwvlltaspvkdddgelvgiivilrDit 103
                 +n +g+i+ +N++  + lGy + ev+gk i+d    ++e+ + +r+ +e+ +k   + + e+ l +kng +f++ll+a  ++d+ g+l+g    +rDit
  EPA04406.1  31 ININGEIINCNKSYFETLGYLKSEVIGKTIFDHT--SEESLSQMRETFEEWKKggCVSNSEIWLKKKNGDKFLALLSANNLFDKYGTLIGSNTSIRDIT 127
                 5689******************************..999999999999999999************************************99******* PP

       PAS_9 104 e 104
                 e
  EPA04406.1 128 E 128
                 8 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.2     3e-12     5e-09       5      61 ..     150     207 ..     146     209 .. 0.88

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 3e-12
                 HHHHHHHHHHHHHHHHHHHHHHH...HC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHH CS
       HisKA   5 flagvaHELrtPLsailgnaeaL...kregklteelkeyletiesearrldhlvedlLdl 61 
                 +   vaH+L++PL++i+  ++++   k  ++ te+    l +ie  + r+dh+++++L++
  EPA04406.1 150 LSIRVAHDLKNPLNVIKNSVQLIqfrK--EPSTENYSNTLTRIEHAVIRMDHQINEVLEF 207
                 55579******************6533..5899*************************98 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   4.6e-10   7.5e-07       2     107 ..      22     128 ..      21     131 .. 0.98

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 4.6e-10
       PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.pgeerhyelrllPlrdesGevigvl 99 
                 +++pd++  ++ +g ++ +N+++ e +g+   e++Gkt ++  +ee+  + ++  +++ +g+ +  +++ l+  +g+    +l+++ l+d  G+ ig  
  EPA04406.1  22 ENSPDLFRTININGEIINCNKSYFETLGYLKSEVIGKTIFDHTSEESLSQMRETFEEWKKGGCVSNSEIWLKKkNGDKFLALLSANNLFDKYGTLIGSN 120
                 89***********************************************************************9************************* PP

       PAS_4 100 visrDiTe 107
                   +rDiTe
  EPA04406.1 121 TSIRDITE 128
                 *******9 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   3.4e-09   5.6e-06       1      80 [.      37     114 ..      37     119 .. 0.90

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 3.4e-09
       PAS_3   1 iiyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirdeng 80 
                 ii +++++ e+lGy ++e++gk  ++ d+   e ++++re+++e+ k+g++ + e+ +++k+G+ +    +a+ ++d+ g
  EPA04406.1  37 IINCNKSYFETLGYLKSEVIGK--TIFDHTSEESLSQMRETFEEWKKGGCVSNSEIWLKKKNGDKFLALLSANNLFDKYG 114
                 589*******************..**************************99***********97777777666666665 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   2.3e-07   0.00037       3      66 ..      17      79 ..      15      80 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.3e-07
       PAS_8  3 lralfesspdgiavvd.lgdrivdvNqaalellGysadlkgellg.qllpvlrplle.daeqlldlv 66
                +r+++e+spd    ++ +g+ i+ +N+++ e lGy   lk e++g +++++  ++    ++++++++
  EPA04406.1 17 YRSIYENSPDLFRTINiNGE-IINCNKSYFETLGY---LKSEVIGkTIFDHTSEESLsQMRETFEEW 79
                9***************9999.*************5...56666664444444444445555555555 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       2.4     4e+03      31      52 ..      90     112 ..      82     157 .. 0.53
   2 !   18.8   0.0   6.7e-07    0.0011       4      91 ..     253     342 ..     250     352 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.4
  HATPase_c_5  31 IrltvrekkksliisieNs.yeg 52 
                  I l+ ++ +k+l +   N+ +++
   EPA04406.1  90 IWLKKKNGDKFLALLSANNlFDK 112
                  55555555555444433331332 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 6.7e-07
  HATPase_c_5   4 ldlcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyegekkkle......sskskkeehGiGlksireivkkykgnlsieaed 91 
                    + +il nl  NAi+a+ +      +I +t +e+++++ i ++ +  g  +kl+        ++++   G+Gl   + ++++++g++s+e+e 
   EPA04406.1 253 RKIEIILRNLVLNAIQAMGEK----GSIIITTNETESHVKILVKDTGPGIPHKLRfkifdpLFTTRQIGTGLGLPICKTVIEQHGGSISFETEL 342
                  66889************9874....5899*****************88855444433444444677899*******************998864 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.3e-05     0.038       5      48 ..     257     301 ..     253     315 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.3e-05
  HATPase_c_3   5 kAlaelvdNsldAdaenvkievnknr.gktgeivieDdGkGmsee 48 
                  + l  lv N+++A  e+ +i + +n+ +++ +i ++D G G++ +
   EPA04406.1 257 IILRNLVLNAIQAMGEKGSIIITTNEtESHVKILVKDTGPGIPHK 301
                  56778*********99988887777745679***********876 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00014      0.23      30     112 ..     251     332 ..     215     352 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00014
  HATPase_c_2  30 d..eirlaveEactNavehayleapegpvevrlesdeealtvevaDsGpgfdpetlpdpteeepkeslkegGrGlalikglvDev 112
                  d  +i++ +  ++ Na+++  +   +g++ ++   +e  +++ v+D Gpg + + + +   +  ++ +   G+Gl + k++ ++ 
   EPA04406.1 251 DqrKIEIILRNLVLNAIQAMGE---KGSIIITTNETESHVKILVKDTGPGIPHKLRFKIFDPLFTTRQIGTGLGLPICKTVIEQH 332
                  055899999999*****99987...577999*999***************88877777666666788888899998888877665 PP

>> CRM1_repeat_2  CRM1 / Exportin repeat 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.2   1.9e+03       3      19 ..     181     197 ..     179     208 .. 0.77
   2 ?    5.7   0.3     0.007        11       7      29 ..     218     240 ..     214     248 .. 0.86
   3 ?    3.7   0.1      0.03        49       8      44 ..     258     294 ..     251     296 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.2
  CRM1_repeat_2   3 qlYkeiLsqlrlvlier 19 
                    ++Y++ L+++ + +i+ 
     EPA04406.1 181 ENYSNTLTRIEHAVIRM 197
                    7899****999999865 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.007
  CRM1_repeat_2   7 eiLsqlrlvlierMakPeEVliv 29 
                    + L+++   +i+ M+ PeE ++ 
     EPA04406.1 218 NSLKKILENVINEMPIPEEFIVT 240
                    679999999**********9986 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.03
  CRM1_repeat_2   8 iLsqlrlvlierMakPeEVliveneeGeivretvkdt 44 
                    iL +l l  i+ M     ++i +ne    v+  vkdt
     EPA04406.1 258 ILRNLVLNAIQAMGEKGSIIITTNETESHVKILVKDT 294
                    899999999999*9999*****************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       771  (0.043003); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2416.86
//
Query:       EPA04407.1  [L=540]
Description: hypothetical protein BG20_I2337, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.01   16.0   0.0      0.036   14.3   0.0    1.9  1  ASH       Abnormal spindle-like microcephaly-assoc'd, ASPM-SP
      0.068   13.0   0.0         60    3.6   0.0    3.4  3  eIF-1a    Translation initiation factor 1A / IF-1


Domain annotation for each model (and alignments):
>> ASH  Abnormal spindle-like microcephaly-assoc'd, ASPM-SPD-2-Hydin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0     4e-06     0.036      18      85 ..     447     516 ..     443     522 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4e-06
                 ----EEEEEEE-EEESS-SS--EEEEEEEE--XXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXX CS
         ASH  18 dvkvGssaerlLtveNpseepaevkvskvpaaekgfsveete..levqpgesvtltvtwtPteegavrev 85 
                  v+v +  + + ++ N+++++++ ++   +++ +g++v+ ++    +++g+s++  ++w Pte+g+ +++
  EPA04407.1 447 AVNVDQQVQITADLANGQDKKQVFAYLVQIQDGNGVTVSLAWitGALSAGQSFSPALSWIPTEAGTYTAT 516
                 57888888889999*******99999999***********99999********************99876 PP

>> eIF-1a  Translation initiation factor 1A / IF-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.017   1.5e+02      41      61 ..       4      24 ..       1      26 [. 0.91
   2 ?    3.6   0.0    0.0067        60      37      54 ..     383     400 ..     371     414 .. 0.88
   3 ?    2.5   0.0     0.014   1.2e+02       6      33 ..     436     462 ..     434     487 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.017
                --TT-EEEEEE-TT-TTEEEE CS
      eIF-1a 41 ikrGdyVlVelspydltkGrI 61
                i++Gd+  Ve ++ +++ G+I
  EPA04407.1  4 ILQGDILQVEYTDPADASGDI 24
                99*********999999**99 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.0067
                 CT----TT-EEEEEE-TT CS
      eIF-1a  37 nkiwikrGdyVlVelspy 54 
                 ++ ++++Gd V+ e  ++
  EPA04407.1 383 HRLRVAEGDTVTAEYEDN 400
                 6899*********98665 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.014
                 EEEEEETTTEEEEEE.SSSSBEEEEE-H CS
      eIF-1a   6 kViealgnnlfrVelpdngkevlaeipg 33 
                 +V+ a gn+l  V   d++++++a ++ 
  EPA04407.1 436 RVVDAFGNSLSAVNV-DQQVQITADLAN 462
                 799************.799999998864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (540 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 3318.31
//
Query:       EPA04408.1  [L=132]
Description: hypothetical protein BG20_I2101 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.6e-07   31.6   0.0      2e-07   31.3   0.0    1.1  1  SnoaL_3    SnoaL-like domain
    1.1e-05   25.6   0.0    2.9e-05   24.2   0.0    1.7  1  CaMKII_AD  Calcium/calmodulin dependent protein kinase II ass
    0.00015   22.1   0.0     0.0002   21.7   0.0    1.2  1  DUF4440    Domain of unknown function (DUF4440)


Domain annotation for each model (and alignments):
>> SnoaL_3  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.0   3.3e-11     2e-07       3     117 ..       9     130 ..       7     132 .] 0.83

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 3.3e-11
     SnoaL_3   3 alldafyeaaaegdfdalfalwa..ddivfigtgadelltgreevrrslkqifakgegisfeltdvrvtesgdvawvtelldvtaa.edgteg...... 92 
                 ++++ ++e  +++df  l ++++   +++ +   ++  l +++   +  +  f  +   ++++++ ++++ gd a+v+ +l+ +     ++++      
  EPA04408.1   9 KIIETLFESGKSKDFSSLRDIHLndSKFSSFSDLPPYDLKNYQTTIELEELRFVSISDYEYQIKNPKISVFGDAAVVALELKQKGMlV-DNKAftgehi 106
                 5677777788899999999999977778888877878899*****************************************9965422.2222346666 PP

     SnoaL_3  93 egqlrlTgvlrrtdggWkivhhhlS 117
                 + + r+T+vl+++   Wki+h+hlS
  EPA04408.1 107 SIEGRATFVLVKQP-TWKIAHIHLS 130
                 7778*******987.6********9 PP

>> CaMKII_AD  Calcium/calmodulin dependent protein kinase II association domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   4.8e-09   2.9e-05       2     125 ..       4     130 ..       3     132 .] 0.73

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 4.8e-09
                 HHHHHHHHHHHHHHHHTT-HHHHHHHE..EEEEEEE-...GGGTT-EEESSHHHHGGGS...SSSS-SEEEEEESEEEEEESTTEEEEEEEEEEE..EE CS
   CaMKII_AD   2 kqeiiklletlleaisegdfetytklc..dpeltvfe...pevlgnlveglefhrfyfekllakrkkavrttilnkrvrllgddsAviayvrllt..ll 93 
                 ++eiik++etl e+ +++df +  ++   d +++ f    p  l n    +e  +  f          ++ +i n+++ ++gd +Av+a  +  +  l+
  EPA04408.1   4 NEEIIKIIETLFESGKSKDFSSLRDIHlnDSKFSSFSdlpPYDLKNYQTTIELEELRFV-----SISDYEYQIKNPKISVFGD-AAVVALELKQKgmLV 96 
                 68*********************987611555555432226667777777777666665.....566777799**********.999996432212244 PP

                 -TT...S-EEEEEEEEEEEEEEETTEEEEEEEEEE CS
   CaMKII_AD  94 dkn...GkkhtrqseetrVwekrdgkWkivhvHrS 125
                 d++   G++   + + t+V +k++  Wki h+H S
  EPA04408.1  97 DNKaftGEHISIEGRATFVLVKQP-TWKIAHIHLS 130
                 443233999999999******987.7*******88 PP

>> DUF4440  Domain of unknown function (DUF4440)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   3.3e-08    0.0002       1     107 []       7     124 ..       7     124 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 3.3e-08
                 HHHHHHHHHHHHHCT-HHHHHHCEEEEEEEE.-TTS-EEEHHHHHHHHHC...CHCEEEEE..EEEEEEEEEETTEEEEEEEEEEEECC.T.....TEE CS
     DUF4440   1 iaaleealeeafvagdaealaallapdavlv.gpsgtvldkeellealea...gfaagrsl..elteeevrvlgdlAvvtgrytfegrg.d.....gep 87 
                 i +++e+l+e  +++d+  l +++ +d  +   ++ + +d +++   +e     f+  +++  ++ +++++v gd Avv+ + + +g+  d     ge+
  EPA04408.1   7 IIKIIETLFESGKSKDFSSLRDIHLNDSKFSsFSDLPPYDLKNYQTTIELeelRFVSISDYeyQIKNPKISVFGDAAVVALELKQKGMLvDnkaftGEH 105
                 7789999999999999999999999999999666677787666666555511144444555335666*****************999665556666899 PP

                 EEEEEEEEEEEEEETTEEEE CS
     DUF4440  88 vegrgrftsvwrkegggWri 107
                 ++ +gr t+v++k++ +W+i
  EPA04408.1 106 ISIEGRATFVLVKQP-TWKI 124
                 99************9.6987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 822.98
//
Query:       EPA04409.1  [L=160]
Description: acetolactate synthase, small subunit [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-22   79.3   0.8    5.4e-21   74.6   0.0    2.2  2  ALS_ss_C        Small subunit of acetolactate synthase
    9.2e-15   54.2   0.0      2e-14   53.2   0.0    1.6  1  ACT_5           ACT domain
    9.9e-13   47.6   0.0      2e-12   46.7   0.0    1.5  1  ACT             ACT domain
     0.0032   18.0   0.1     0.0081   16.7   0.1    1.7  1  ACT_4           ACT domain
  ------ inclusion threshold ------
       0.04   13.3   0.5      0.058   12.7   0.5    1.2  1  ADPrib_exo_Tox  ADP-ribosyltransferase exoenzyme
      0.043   13.6   0.2      0.046   13.6   0.2    1.1  1  SLS             Mitochondrial inner-membrane-bound regulator


Domain annotation for each model (and alignments):
>> ALS_ss_C  Small subunit of acetolactate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.2     0.031        93      36      58 ..      45      67 ..      16      74 .. 0.84
   2 !   74.6   0.0   1.8e-24   5.4e-21       1      73 [.      84     157 ..      84     158 .. 0.98

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.031
                EEEEEEEE-HHHHHHHHHHS-GG CS
    ALS_ss_C 36 sliieltgteekidaliellkpf 58
                 ++i   g+e++++++++ l+++
  EPA04409.1 45 RMTITTYGDEKQVEQIVKQLDKM 67
                5899999**********999743 PP

  == domain 2  score: 74.6 bits;  conditional E-value: 1.8e-24
                 EEEEEEEEE.-SC.HHHHHHHHHHHTT-EEEEEETTEEEEEEEE-HHHHHHHHHHS-GGGEEEEEEEEEEEEES CS
    ALS_ss_C   1 RElaLiKVkaeke.erseileiaeifrakivdvspdsliieltgteekidaliellkpfgilevvRtGrvAleR 73 
                 REl ++K+k +++ +  e++++a+++ +ki dv +ds+++elt t+++i a+ el kpfgil+v+RtG++Al+R
  EPA04409.1  84 RELSIFKIKLSNAnDSMEVNKLANAYGGKIHDVRKDSIMVELTATPDQIRAFEELAKPFGILDVARTGVAALQR 157
                 9**********976999********************************************************9 PP

>> ACT_5  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.2   0.0   6.5e-18     2e-14       2      62 .]      12      73 ..      11      73 .. 0.97

  Alignments for each domain:
  == domain 1  score: 53.2 bits;  conditional E-value: 6.5e-18
       ACT_5  2 apgvLeRvlrvvrrrgFevkslnmsttedggtvrieltVes.ersvelLsnQleKLidVlkV 62
                +pg+L +v+ ++r r F+++s+++  te+ +++r+++t ++ e+ ve++++Ql+K+id ++V
  EPA04409.1 12 KPGILFKVTHLFRSRNFNIDSISVGVTENPEYSRMTITTYGdEKQVEQIVKQLDKMIDTIEV 73
                79********************************************************8876 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   0.0   6.6e-16     2e-12       2      64 ..       4      66 ..       3      69 .. 0.94

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 6.6e-16
                EEEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHT CS
         ACT  2 vlrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkk 64
                +l ++v+++PG+L++v+ ++  r++Nidsi+++ +e    ++++++  +de+++e+++++l k
  EPA04409.1  4 ILTLLVENKPGILFKVTHLFRSRNFNIDSISVGVTENPEYSRMTITTYGDEKQVEQIVKQLDK 66
                57789********************************************************88 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   2.7e-06    0.0081       9      78 ..       5      73 ..       3      84 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.7e-06
       ACT_4  9 leveaedrkglLaditqviseekanivsvnaktrkkdglaeikitveVkdvehLsrviakLraipgVisV 78
                l++ +e+++g+L ++t ++ + + ni s+++  +++ ++ +++it    d +++++++++L ++ + i+V
  EPA04409.1  5 LTLLVENKPGILFKVTHLFRSRNFNIDSISVGVTENPEYSRMTITTY-GDEKQVEQIVKQLDKMIDTIEV 73
                67889****************************98877898888865.8999********9999888887 PP

>> ADPrib_exo_Tox  ADP-ribosyltransferase exoenzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.5   1.9e-05     0.058      48     109 ..      56     114 ..      43     118 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.9e-05
                     GS-SCHHHHHHHHHHHHCCT-B-SS-EEEEEEE-GGGG-HHHHTT.-HHHHHHHHHHHTT-EE CS
  ADPrib_exo_Tox  48 dldkselekkiknldsaleksripeniivYRrvdeaelgleldsk.neekvsefeakvkgkvf 109
                     ++  +++ k+ +++ +++e + + e  +vYR  +   ++ +l++  ++++v+++ + + gk+ 
      EPA04409.1  56 QV--EQIVKQLDKMIDTIEVKHLDEHKTVYRELS--IFKIKLSNAnDSMEVNKLANAYGGKIH 114
                     22..4555555555567889999*********85..55555555436********99999975 PP

>> SLS  Mitochondrial inner-membrane-bound regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   1.5e-05     0.046      62     128 ..      40     108 ..       6     138 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.5e-05
         SLS  62 nrsenklrit..Atkstaeyieasineilknittetvd.lsellkl..skvdklkdllseelleelgrltnt 128
                 n++ +++ it  ++++++e+i +++++++  i+++++d  ++       + +k+k+  ++ +  e+ +l n+
  EPA04409.1  40 NPEYSRMTITtyGDEKQVEQIVKQLDKMIDTIEVKHLDeHKTV--YreLSIFKIKLS-NANDSMEVNKLANA 108
                 455555666555**************************42222..133444555555.55555566666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1432  (0.0798706); expected 358.6 (0.02)
Passed bias filter:                      905  (0.0504769); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1051.10
//
Query:       EPA04410.1  [L=562]
Description: acetolactate synthase, large subunit, biosynthetic type [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.1e-61  204.6   0.2    2.5e-58  196.5   0.1    2.5  2  TPP_enzyme_N    Thiamine pyrophosphate enzyme, N-terminal TPP
    9.9e-48  161.4   0.1    2.1e-47  160.3   0.1    1.6  1  TPP_enzyme_M    Thiamine pyrophosphate enzyme, central domain
    1.9e-47  160.9   0.3    3.6e-46  156.7   0.1    2.8  4  TPP_enzyme_C    Thiamine pyrophosphate enzyme, C-terminal TPP
  ------ inclusion threshold ------
      0.039   13.6   0.0      0.081   12.6   0.0    1.5  1  TPP_enzyme_M_2  Middle domain of thiamine pyrophosphate


Domain annotation for each model (and alignments):
>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.5   0.1   5.5e-62   2.5e-58       3     168 ..       6     169 ..       4     171 .. 0.98
   2 !    5.6   0.0    0.0025        11      81     151 ..     451     529 ..     405     543 .. 0.78

  Alignments for each domain:
  == domain 1  score: 196.5 bits;  conditional E-value: 5.5e-62
                   HHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHHHHHHHHHHT--EEEEEEE CS
  TPP_enzyme_N   3 vaealvraLkalgvehvfgvpGsrilplldalseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnaltalaeAkvdriPllvlsgd 99 
                   +a+al  a++++gv++vfg+pG+ +lp++d++++ + ir++l+rhEq+aa++Adg+ r+++kpgv+++tsgpGatn+lt++a+A+ d++P+++++g+
    EPA04410.1   6 GARALMVAMEKEGVKEVFGLPGGANLPMYDEFARCD-IRHILVRHEQSAAHMADGFGRVSRKPGVCFATSGPGATNILTGIATAQADSSPMIAVTGQ 101
                   7899*******************************6.************************************************************ PP

                   --CCCHHS..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--EEEEEEEHHHCC-EE CS
  TPP_enzyme_N 100 rptslrgqgvlqqeldqlalfrpvtkyaervtspeelpealrrAirtalsgrpgPvylelpkdvlleev 168
                   +p++++g++++q e d+ ++++pv+kya+++++p e+pe++r+ + +a +grpgPv++++pkdv+++e+
    EPA04410.1 102 VPVAMIGRDAFQ-ESDIIGMANPVVKYAFQPRTPGEIPEVVRKGFYIAETGRPGPVLIDIPKDVQQKEA 169
                   ************.****************************************************9986 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0025
                   HHHHHHHHHT--EEEEEEE--CCCHH............S..TC--T.-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS CS
  TPP_enzyme_N  81 talaeAkvdriPllvlsgdrptslrg............qgvlqqel.dqlalfrpvtkyaervtspeelpealrrAirtalsgr 151
                   ++la+A ++ iP++v+  +++t                 gv q+ + d ++l++++     r +s +el    ++Ai+ta  + 
    EPA04410.1 451 NSLATAVLEDIPVIVFLLNNFTLGMVaqwqrtfydrrmIGVDQGKCpDYVKLAESYGAQGIRAQSMDEL----DKAIKTA-LKS 529
                   68999999******9999999887777888888888888888888889999999999777777777765....5555555.444 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.3   0.1   4.6e-51   2.1e-47       1     135 [.     193     326 ..     193     328 .. 0.98

  Alignments for each domain:
  == domain 1  score: 160.3 bits;  conditional E-value: 4.6e-51
                   HHHHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGGTTSS-TTSTTEEEESGGGSCHHHHHHHHH-SEEEEES-SSSTCCCTTTT CS
  TPP_enzyme_M   1 iekaaellkaakrpvilvGggvarsgaseelrelaeklgiPvvttlmgkgvipedhplylgmlglhgskaanealeeaDlvlalGarfddirttgse 97 
                   +e+a+e+l +a++p+il+Ggg++ s a +el+  ae l iPvvtt++gkg++pe+hpl+lg +g+hg+++an+++ eaD+vla+G+rf+d r++g++
    EPA04410.1 193 VERAIEMLLSAEKPIILAGGGTIISSAFAELQTIAELLMIPVVTTFKGKGAFPENHPLSLGPIGMHGHAEANKMMTEADCVLAIGTRFSD-RSVGTF 288
                   689***************************************************************************************.999*** PP

                   TTTTTT-EEEEEESSCCCCTTCC--SEEEECTHHHHHH CS
  TPP_enzyme_M  98 pefapeakiihididpaeigknyqvdlaivgdvketle 135
                   ++f ++ kiih d+dpaeigkn ++++a+vgdv+++l+
    EPA04410.1 289 EAFEKRLKIIHMDVDPAEIGKNQTTSVAVVGDVRASLR 326
                   ***9988****************************997 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       1.6   7.2e+03      38      60 ..      83     106 ..      77     115 .. 0.71
   2 ?   -2.1   0.0      0.66     3e+03     127     153 .]     129     160 ..     107     160 .. 0.74
   3 ?    0.4   0.0      0.11   5.1e+02      47      72 ..     204     230 ..     195     238 .. 0.77
   4 !  156.7   0.1   8.1e-50   3.6e-46       2     153 .]     390     537 ..     389     537 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.6
                   HHHHHHST.TSEEEEEEEHHHHHH CS
  TPP_enzyme_C  38 iGaklakp.drevvaivGDGgflm 60 
                   +G++ a+  +++++a++G    +m
    EPA04410.1  83 TGIATAQAdSSPMIAVTGQVPVAM 106
                   688887652579999998655555 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.66
                   ESSH.HHHHHHHHHHHH.....CSSSEEEEEE CS
  TPP_enzyme_C 127 vekadveeleealkeal.....ekkgpaliev 153
                    +++++ e+ e++++ +      + gp+li++
    EPA04410.1 129 FQPRTPGEIPEVVRKGFyiaetGRPGPVLIDI 160
                   34667799999999999999888999999986 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.11
                   SEEEEEEEHHHHHHT.GGGHHHHHHTT CS
  TPP_enzyme_C  47 revvaivGDGgflmi.lqelatavrrn 72 
                   ++ + ++G G+++ + + el t+++  
    EPA04410.1 204 EKPIILAGGGTIISSaFAELQTIAELL 230
                   577899*****************9974 PP

  == domain 4  score: 156.7 bits;  conditional E-value: 8.1e-50
                   SSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHTGGGHHHHHHTT-SEEEEEEE-SBCCCHHHHHHHHTCC CS
  TPP_enzyme_C   2 iGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmilqelatavrrnlpitvvvlnNegygmtggqqepfggk 98 
                   +G++++wa+ +++v +p+++++s+glgtmG+g+paAiGak+a+pd +vv i+GDG+f m+ + latav +++p++v++lnN ++gm+ ++q+ f+++
    EPA04410.1 390 VGQHQMWASLFYDVIQPGTFFSSTGLGTMGWGFPAAIGAKVARPDVPVVDIAGDGSFSMTENSLATAVLEDIPVIVFLLNNFTLGMVAQWQRTFYDR 486
                   9************************************************************************************************ PP

                   TTTTSBB.BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHHCSSSEEEEEE CS
  TPP_enzyme_C  99 rksgpagkdlkpvdfaklaealGakgarvekadveeleealkealekkgpaliev 153
                   r  g+++  +k +d++klae++Ga+g+r ++   +el++a+k+al+++  ++i++
    EPA04410.1 487 RMIGVDQ--GKCPDYVKLAESYGAQGIRAQSM--DELDKAIKTALKSDVATVIDI 537
                   ****995..9999***************6566..*******************97 PP

>> TPP_enzyme_M_2  Middle domain of thiamine pyrophosphate
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.8e-05     0.081      88     204 ..     260     384 ..     184     386 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.8e-05
                     SHHHHHHHTT-SEEEEESB---SHHHHHHHHH---SEEEEEESS-SB--TT--SEEEEES-HHHHHH........HS-----.----SHHHHHHH CS
  TPP_enzyme_M_2  88 npkvkeeLaqadiviqfGsrlvsKrllqflaelkpeeyWlvdesqgrldpahhrkrrfvakveewlr........ahpaesq.kpWalellalse 173
                     ++++++ +++ad v+ +G+r+  + +  f a  k  +  ++d  +  +  ++ ++  +v +v++ lr        +   ++q + W++++++++ 
      EPA04410.1 260 HAEANKMMTEADCVLAIGTRFSDRSVGTFEAFEKRLKIIHMDVDPAEIGKNQTTSVAVVGDVRASLRimvkmllqKTAKRTQdTVWIKHVKETKA 354
                     8899*************************99999888888777777777777666666666655444111011004444444455********** PP

                     HHHHHHHTT.TTSSSHHHHHHTGGGGS-TT- CS
  TPP_enzyme_M_2 174 klaelveqqldeefgEaqlahqlaellpeqg 204
                       +e+++ +  +e+g a++ ++l+e+lp+++
      EPA04410.1 355 YWKEHLKLH-PGEMGAAKILRKLREILPHES 384
                     999999976.889***************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (562 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 4004.13
//
Query:       EPA04411.1  [L=266]
Description: HMGL-like protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.8e-88  294.3   0.3    9.8e-88  294.1   0.3    1.0  1  HMGL-like       HMGL-like
      0.003   16.9   0.0     0.0043   16.4   0.0    1.2  1  Glyco_hydro_97  Glycoside hydrolase 97
  ------ inclusion threshold ------
      0.037   13.5   0.0          1    8.8   0.0    2.1  2  AP_endonuc_2    Xylose isomerase-like TIM barrel


Domain annotation for each model (and alignments):
>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  294.1   0.3   1.6e-91   9.8e-88       1     264 []       2     263 ..       2     263 .. 0.99

  Alignments for each domain:
  == domain 1  score: 294.1 bits;  conditional E-value: 1.6e-91
                 B-EEEE-TTTHHHHTSSS---HHHHHHHHHHHHHHT-SEE--TSGGGT.THHHHHHHS---TT-B..--EE-SSHHHHHHHHH....TT-SEEEEEEES CS
   HMGL-like   1 kvkivdttLRDGeqalkaalsveeklaiakaLdeagvdeiEvgfpaaseddfevvraiakavkkarilalvrarekdikaavealkgagakrvhvfiat 99 
                 kv+i+dttLRDGeq+++++ls ++klaiak+Ld++gvd+iE+gfp+ s ++f++v+ ia+++ + +i +l r  ++di+ av+    ag + +h+fiat
  EPA04411.1   2 KVRIFDTTLRDGEQTIGVSLSPDQKLAIAKKLDDLGVDAIEAGFPVISSGEFKAVKMIAAEGLSCEIAGLTRTIKNDIDSAVN----AGLNYIHTFIAT 96 
                 699********************************************************************************....************ PP

                 -HHHHHHHHSSTHHHHHHHHHHHHHHHHHTT-ETTT-BTTTBS--HHHHHHHHHHHHHHT-SEEEEEETTS---HHHHHHHHHHHHHHS-.GGGEEEEE CS
   HMGL-like 100 selhlkaklkkdreevakkaeeavkaarslgkdvelsledasrtdleflaevveaaeeaGatriniaDtvGvltPneaaelisalkervkdkvilsvHc 198
                 s++hl++klk++re++++ka eav++ +s+g +ve+s+eda+rtd efl +v   +++aGa+r+ni+DtvG+ tP+ +ael +  ++ ++  +++svHc
  EPA04411.1  97 SDIHLQYKLKMTREQALEKAIEAVEYGKSRGLQVEFSAEDATRTDREFLKKVFADVAKAGADRVNIPDTVGYSTPEYMAELTRDTVKATN--LPVSVHC 193
                 ******************************************************************************************..******* PP

                 B-TTS-HHHHHHHHHHTT--EEEEBTTS--SSBBB-BHHHHHHHHHHTT....-B----HHHHHHHHHHH CS
   HMGL-like 199 HndlGlAvantlaAveaGadrvdgtvnGlGeraGnaaleelvaalealg....vdtgldlqklrsiaalv 264
                 Hnd+GlAvan+la+++aGa+   +t+nG+GeraGna+lee+ +al+ l+    ++t+++ + ++++++++
  EPA04411.1 194 HNDFGLAVANSLAGIHAGASCAHVTINGIGERAGNASLEEFSMALKCLPfeqkYETNIKSELIYETSRFI 263
                 ***********************************************99888899999999999999876 PP

>> Glyco_hydro_97  Glycoside hydrolase 97
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   7.2e-07    0.0043      34     163 ..      72     194 ..      56     198 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 7.2e-07
  Glyco_hydro_97  34 tetvkryiDfAaengleyvlvegwdegWeekkkkekefdftkpypdfdleelvaYakekgvgvelwlhsetsgnvanlekq.ldkafklyeklGv 127
                     t+t+k+ iD A + gl+y+    + +  +   + +++ ++t++ +  +  e v+Y+k++g +ve+ +++ t     + +++ l+k+f+ ++k G 
      EPA04411.1  72 TRTIKNDIDSAVNAGLNYIHT--FIATSD--IHLQYKLKMTREQALEKAIEAVEYGKSRGLQVEFSAEDAT-----RTDREfLKKVFADVAKAGA 157
                     7899999**********9988..455555..456788999999999999999********99999999998.....7888857************ PP

  Glyco_hydro_97 128 kgvKv.dfvgrddqemvnhyekvlekAakyklmvdfH 163
                     + v + d vg +  e +    + + kA +  + v+ H
      EPA04411.1 158 DRVNIpDTVGYSTPEYMAELTRDTVKATNLPVSVHCH 194
                     *998756666655444444444444555555555555 PP

>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00017         1      26     140 ..      22     145 ..       5     162 .. 0.62
   2 ?    3.9   0.0    0.0052        31       2      59 ..     150     203 ..     149     239 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00017
                   HHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHC...........HTTCSHHHHHHHHHHHHHHHHHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHH CS
  AP_endonuc_2  26 sdeelrelrkaldelglriaslslftrfgypded...........erearreesvdalkraielaaaLGapllvlhpGtagagpkgseeeawerlae 111
                   s+++  +++k ld+lg+      ++  +++ +             e     +   + +k+ i+ a   G  ++++++ t + +     + ++e++ e
    EPA04411.1  22 SPDQKLAIAKKLDDLGVDAIEAGFPVISSGEFKAvkmiaaeglscE----IAGLTRTIKNDIDSAVNAGLNYIHTFIATSDIHLQYKLKMTREQALE 114
                   5556667777777777775555555555554444666666553332....2344789*********************9555555555566666666 PP

                   HHHHHHHHHHHHT..SEEEEE--TTTTSSST CS
  AP_endonuc_2 112 slneladyaekeg..vklalEtlagsgvelg 140
                   +  e+++y++ +g  v++ +E  ++++ e++
    EPA04411.1 115 KAIEAVEYGKSRGlqVEFSAEDATRTDREFL 145
                   6666666666666445555555555555444 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.0052
                   HHHHHCT-SEEEEECCTCSHHHHCHHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHC CS
  AP_endonuc_2   2 aaaaeaGfdgvElfgrdlvpvselsdeelrelrkaldelglriaslslftrfgypded 59 
                   a +a+aG+d v +    +++  e    +++  r  +++++l  +s++++++fg  + +
    EPA04411.1 150 ADVAKAGADRVNIPDTVGYSTPE---YMAELTRDTVKATNLP-VSVHCHNDFGLAVAN 203
                   67899999999999999999986...599999**********.677777777665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 1757.63
//
Query:       EPA04412.1  [L=174]
Description: hypothetical protein BG20_I1721, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 997.55
//
Query:       EPA04413.1  [L=141]
Description: hypothetical protein BG20_I1715 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0076   16.1   1.9     0.0097   15.7   1.5    1.4  1  RIH_assoc  RyR and IP3R Homology associated
  ------ inclusion threshold ------
       0.52   10.9   5.1       0.83   10.2   1.5    2.5  3  DUF4473    Domain of unknown function (DUF4473)


Domain annotation for each model (and alignments):
>> RIH_assoc  RyR and IP3R Homology associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   1.5   1.1e-06    0.0097      17      94 ..      31     107 ..      16     115 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.1e-06
   RIH_assoc  17 lceghnselqnylreQkdnktsynlvseivdllenlskatelnskslelmlqvl.dtLtefvqgpCpeNqeaiinskfl 94 
                  + + ++ + n   +Q+  +   n+v  ++ + +++ k+  +  +  + +l+v+ dt  efv+   ++Nq+++++++  
  EPA04413.1  31 SVPQYHQSITNV--QQEYLQAYENIVDSTITIQKEYAKKAGIAANIPQATLKVIhDTTEEFVKAASIQNQITLATIDAT 107
                 555555555553..666667777****************999999999999988579999*************988765 PP

>> DUF4473  Domain of unknown function (DUF4473)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1      0.03   2.7e+02      42      74 ..      18      50 ..       2      56 .. 0.70
   2 ?   10.2   1.5   9.2e-05      0.83      18      69 ..      51      99 ..      50     107 .. 0.82
   3 ?   -2.1   0.0      0.68   6.1e+03      47      50 ..     112     115 ..      99     134 .. 0.53

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.03
     DUF4473 42 keaakkafeklkaevdafiktqseeDqaaykaf 74
                +e+ +k+f  +   v ++ ++ +  +q+  +a+
  EPA04413.1 18 QENVDKLFSGIRHSVPQYHQSITNVQQEYLQAY 50
                567777777777777777777777777755554 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 9.2e-05
     DUF4473 18 ekaadglvkiaekfksefakakgdkeaakkafeklkaevdafiktqseeDqa 69
                e+ +d  + i+++++++   a++ ++a+ k++   ++ +++f+k  s + q 
  EPA04413.1 51 ENIVDSTITIQKEYAKKAGIAANIPQATLKVI---HDTTEEFVKAASIQNQI 99
                56788888999998888888899999988888...78889999999998886 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.68
     DUF4473  47 kafe 50 
                 k+f+
  EPA04413.1 112 KTFN 115
                 2222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1415  (0.0789224); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.35s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 837.22
//
Query:       EPA04414.1  [L=128]
Description: hypothetical protein BG20_I1720 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 831.43
//
Query:       EPA04415.1  [L=130]
Description: hypothetical protein BG20_I1712 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 773.12
//
Query:       EPA04416.1  [L=97]
Description: hypothetical protein BG20_I1710 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.13   12.7   0.4       0.21   12.0   0.4    1.3  1  DUF1599   Nucleotide modification associated domain 1


Domain annotation for each model (and alignments):
>> DUF1599  Nucleotide modification associated domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.4   1.2e-05      0.21      20      49 ..      57      86 ..      46      87 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.2e-05
     DUF1599 20 qiliKakRirsleekgeakvdEgiadeyid 49
                q + Ka Rir +++   +kv E++ ++y+d
  EPA04416.1 57 QCISKATRIRYMQTPSYEKVAEDLIKDYQD 86
                7789************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 599.97
//
Query:       EPA04417.1  [L=303]
Description: putative transcription initiation factor IIB [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-32  110.6   6.1    3.3e-16   59.1   0.2    2.3  2  TFIIB           Transcription factor TFIIB repeat
    3.6e-11   42.4   1.4    6.2e-11   41.6   1.4    1.4  1  TF_Zn_Ribbon    TFIIB zinc-binding
    5.9e-05   22.8   0.5    0.00047   19.9   0.1    2.0  2  Cyclin_N        Cyclin, N-terminal domain
     0.0023   17.9   0.6     0.0062   16.5   0.6    1.7  1  TFIIB_C_1       Transcription factor IIB C-terminal module 1
  ------ inclusion threshold ------
      0.064   13.0   0.4       0.15   11.8   0.4    1.5  1  Ribosomal_S27e  Ribosomal protein S27
      0.072   13.1   0.3       0.16   12.0   0.3    1.5  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
      0.079   13.0   0.1       0.13   12.3   0.1    1.3  1  RB_B            Retinoblastoma-associated protein B domain
       0.11   12.5   0.9       0.26   11.2   0.9    1.6  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
        1.6    8.5   4.2        2.5    7.9   0.2    2.5  2  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
        3.9    7.3   6.3         17    5.3   0.3    2.5  2  zinc_ribbon_2   zinc-ribbon domain


Domain annotation for each model (and alignments):
>> TFIIB  Transcription factor TFIIB repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.1   0.2   1.9e-19   3.3e-16       3      70 ..     128     195 ..     126     196 .. 0.94
   2 !   54.1   1.3   6.6e-18   1.2e-14       1      71 []     220     290 ..     220     290 .. 0.98

  Alignments for each domain:
  == domain 1  score: 59.1 bits;  conditional E-value: 1.9e-19
                 HHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHH CS
       TFIIB   3 rfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekt 70 
                 ++ d+l L + V ++A +++++a+e+k++ Grs +g++AAcly  cr  e+ rt+ ++++ ++++ k 
  EPA04417.1 128 KLKDKLALTDAVVEKAAYIYRKAMEKKLVRGRSIQGLVAACLYASCRNTETPRTLDDVAKGINIRRKD 195
                 6779*******************************************************999998875 PP

  == domain 2  score: 54.1 bits;  conditional E-value: 6.6e-18
                 HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
       TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                 ++r+a+ +eL+ek +++A+ ++++a++ ++++G+ p giaAA+ly+Ac   ++ ++qk+is  + V+e+ti
  EPA04417.1 220 VSRIASIAELSEKSKRKAVVILEQAKKIGMVAGKDPMGIAAAALYLACISTGEIKSQKDISIASGVTEVTI 290
                 6799*****************************************************************98 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   1.4   3.4e-14   6.2e-11       2      43 .]      11      52 ..      10      52 .. 0.98

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 3.4e-14
                  EETTTTCEECHEETSTTCEEESSSSBEEEECCCCCCCHHHHH CS
  TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGlVlednsidegpewref 43
                  kCP Cg +++++D+ +gel+C++CG V+ + + d g ewr f
    EPA04417.1 11 KCPSCGDKKMITDETTGELFCGRCGFVMSEKISDTGAEWRSF 52
                  8***************************************87 PP

>> Cyclin_N  Cyclin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.1   2.6e-07   0.00047      29     125 ..     118     210 ..      92     212 .. 0.83
   2 ?    1.1   0.0      0.18   3.2e+02      55      85 ..     237     267 ..     222     287 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.6e-07
                 HHHHHHHHHHHHHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHHHSSS---HHHHHHHTTTSS-HHHHHHHHHHHHHHTTT- CS
    Cyclin_N  29 emRailidwlvevaekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAaKveeisppkledlvyitdeafteeeilemErliLetLnfd 125
                 + R+ +++ + ++  k+ lt  ++  a+ ++ + ++kk v+ + +q ++a+cL+ +++  e+ p +l+d++  ++  ++++++ +  rli+++L+ +
  EPA04417.1 118 NLRQ-ALNEMDKLKDKLALTDAVVEKAAYIYRKAMEKKLVRGRSIQGLVAACLYASCRNTET-PRTLDDVAKGIN--IRRKDVARCYRLIFRELELK 210
                 4444.56668899999*********************************************9.999**9988765..99999999999999999866 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.18
                 HHHHHHHHHHHS---CCCHHHHHHHHHHHHH CS
    Cyclin_N  55 avnyldRflskksvpkdklqlvgatcLllAa 85 
                 av++l++  +   v  ++   ++a++L+lA+
  EPA04417.1 237 AVVILEQAKKIGMVAGKDPMGIAAAALYLAC 267
                 56666666666666777777899*******9 PP

>> TFIIB_C_1  Transcription factor IIB C-terminal module 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.6   3.4e-06    0.0062       5      93 ..     122     201 ..     119     206 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.4e-06
   TFIIB_C_1   5 mrnalevllklsrrdeavleealelakrfvGkrrergervekqeevaaaclmlaaerlrqPvPLaelrvldpslkdvelrrkevvrevk 93 
                  +n ++ l ++ +  +av e+a  + ++ + k+  rg+ +   +  +aacl  ++ ++++P      r+ld   k ++ rrk+v r  +
  EPA04417.1 122 ALNEMDKLKDKLALTDAVVEKAAYIYRKAMEKKLVRGRSI---QGLVAACLYASCRNTETP------RTLDDVAKGINIRRKDVARCYR 201
                 57899**************************999999987...5679*****999999999......99***************98665 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.4   8.2e-05      0.15       9      37 ..      11      39 ..       9      42 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.2e-05
                    E-TTTS-EEEEESS-SS-EEESSSTCEEE CS
  Ribosomal_S27e  9 kCpdCenetvvFshaatvvkCisCgkvLv 37
                    kCp C++++++ +       C  Cg v+ 
      EPA04417.1 11 KCPSCGDKKMITDETTGELFCGRCGFVMS 39
                    9************************9886 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.3   8.8e-05      0.16      18      44 ..       9      35 ..       7      37 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.8e-05
  Zn_Tnp_IS1595 18 gfvCPhCgsrkayriktrglfqCkeCr 44
                   g+ CP Cg +k ++ +t g + C +C+
     EPA04417.1  9 GPKCPSCGDKKMITDETTGELFCGRCG 35
                   899*******99999999********8 PP

>> RB_B  Retinoblastoma-associated protein B domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   7.3e-05      0.13      12      93 ..     121     200 ..     115     213 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.3e-05
        RB_B  12 laavrlrdLcerLklsselrekiwtlfehvlveetellkdRhlDqillcavYvvakvtkeelsFkeiikaYrkqpqasskvy 93 
                  a   + +L ++L l++ + ek+  + ++++  e++l++ R +  ++ +++Y+ ++ t++ +++ ++ k  + + +  ++ y
  EPA04417.1 121 QALNEMDKLKDKLALTDAVVEKAAYIYRKAM--EKKLVRGRSIQGLVAACLYASCRNTETPRTLDDVAKGINIRRKDVARCY 200
                 6777888999999999988888766666654..679**********************999999999876665555555544 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.9   0.00014      0.26      27      56 ..       8      38 ..       3      41 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00014
  OrfB_Zn_ribbon 27 TSktCseCgsknke.alsgrtfkCpnCgfea 56
                    +  +C+ Cg k+   + ++ ++ C +Cgf++
      EPA04417.1  8 SGPKCPSCGDKKMItDETTGELFCGRCGFVM 38
                    5679*****99988899***********986 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.7      0.19   3.4e+02      24      28 ..      12      16 ..      11      18 .. 0.64
   2 ?    7.9   0.2    0.0014       2.5       5      10 ..      30      35 ..      29      45 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.19
  zf-NADH-PPase 24 CpaCg 28
                   Cp+Cg
     EPA04417.1 12 CPSCG 16
                   66665 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0014
  zf-NADH-PPase  5 FCgrCG 10
                   FCgrCG
     EPA04417.1 30 FCGRCG 35
                   *****9 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   1.2      0.02        36       1       7 [.      11      17 ..      11      19 .. 0.82
   2 ?    5.3   0.3    0.0092        17      12      21 ..      27      36 ..      25      38 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.02
  zinc_ribbon_2  1 fCpnCGa 7 
                   +Cp+CG 
     EPA04417.1 11 KCPSCGD 17
                   7999995 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0092
  zinc_ribbon_2 12 nakFCpyCGt 21
                   ++ FC +CG+
     EPA04417.1 27 GELFCGRCGF 36
                   5679****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       931  (0.051927); expected 358.6 (0.02)
Passed bias filter:                      656  (0.0365888); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2038.78
//
Query:       EPA04418.1  [L=141]
Description: SpoVT/AbrB-like protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00082   19.2   0.4     0.0013   18.6   0.1    1.5  2  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
  ------ inclusion threshold ------
      0.014   15.6   0.9      0.022   15.1   0.9    1.3  1  GAT             GAT domain
      0.026   14.6   0.0      0.062   13.4   0.0    1.6  2  AbrB-like       AbrB-like transcriptional regulator


Domain annotation for each model (and alignments):
>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       1.6   9.3e+03       1       8 [.      19      26 ..      16      26 .. 0.75
   2 !   18.6   0.1   2.2e-07    0.0013       2      32 ..      98     128 ..      97     138 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.6
                    EEETTEEE CS
  MazE_antitoxin  1 fkvGnsga 8 
                    +k+G+ +a
      EPA04418.1 19 QKNGRAQA 26
                    57888776 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 2.2e-07
                     EETTEEEEEE-CCCHHHCCEECTCEEEEEEC CS
  MazE_antitoxin   2 kvGnsgavriPkevrfelgireGdevelevd 32 
                     +v+++g+++iP + r +lg+ eGd v +++ 
      EPA04418.1  98 TVSSNGRISIPEAERTALGLGEGDLVQVIIL 128
                     89************************99875 PP

>> GAT  GAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.9   3.6e-06     0.022      10      60 ..      34      82 ..      26      91 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.6e-06
         GAT 10 mLsstepdeellenellkeLyetckamqpriqklieetadeedllaelLql 60
                mL++ ++ +++   e+l e  ++ +++q  ++k ++++++++  ++++ q+
  EPA04418.1 34 MLMTNQNTQTFNPLETLREVSDNTRNAQSDLMKNMSSMQNKS--METMFQI 82
                6666654569999************************76666..6666665 PP

>> AbrB-like  AbrB-like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       2.5   1.5e+04      34      40 ..      17      23 ..      13      24 .. 0.70
   2 ?   13.4   0.0     1e-05     0.062      30      61 ..      94     125 ..      92     133 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 2.5
   AbrB-like 34 sVqknGn 40
                 +qknG+
  EPA04418.1 17 WIQKNGR 23
                5788885 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 1e-05
   AbrB-like  30 sYrvsVqknGnLliGsaYTkklgLkpGdefeI 61 
                  Y+++V +nG++ i +a  ++lgL  Gd  ++
  EPA04418.1  94 AYKTTVSSNGRISIPEAERTALGLGEGDLVQV 125
                 5***************************8776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1108  (0.0617993); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 966.50
//
Query:       EPA04419.1  [L=151]
Description: peptide-methionine (S)-S-oxide reductase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.4e-67  224.5   1.0      7e-67  224.4   1.0    1.0  1  PMSR      Peptide methionine sulfoxide reductase


Domain annotation for each model (and alignments):
>> PMSR  Peptide methionine sulfoxide reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  224.4   1.0   3.9e-71     7e-67       1     147 [.       2     148 ..       2     151 .] 0.99

  Alignments for each domain:
  == domain 1  score: 224.4 bits;  conditional E-value: 3.9e-71
                 EEEEE-S-HHHHHHHHCTSTTEEEEEEEEESSS-SS--HHHHHTTTT--EEEEEEEEETTTS-HHHHHHHHHHTS-TT-SSEETTEESGGG--EEEESS CS
        PMSR   1 eavlagGCFWgveklfeklkGvlstevGYagGktenptYeevcsgktghaEavevvydpekvsleellelffeihDptqlnrqgnDvGtqYrsaiyytn 99 
                 +a++++GCFW ve+l++k+kGv st+vGY+gGk +nptYeevc+++tghaEav+v+ydp+++s++ell++f+++hDpt+lnrqg D+G+qYrsai++++
  EPA04419.1   2 KATFGAGCFWHVEDLLRKTKGVKSTQVGYIGGKLSNPTYEEVCTDTTGHAEAVQVEYDPNEISYDELLQVFWNNHDPTTLNRQGLDIGNQYRSAIFFHD 100
                 589************************************************************************************************ PP

                 CCHHHHHHHHHHHHHTTHTTSSS---EEEEG-SEEE--CCCTTHHHH- CS
        PMSR 100 eeqkevaeevleelqkkkalkkkivteieplkefykaeeyHqqYlekn 147
                 eeqk++a++++eel+k+ +l+k+ivtei p+ +fykaeeyHq+Y++k+
  EPA04419.1 101 EEQKKIAQKSKEELEKSGKLHKPIVTEIVPAPTFYKAEEYHQKYFQKH 148
                 **********************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       770  (0.0429472); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1055.22
//
Query:       EPA04420.1  [L=262]
Description: hydrolase, alpha/beta domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.2e-29  100.9   0.0    6.8e-23   81.6   0.0    2.0  2  Abhydrolase_1  alpha/beta hydrolase fold
      6e-21   76.1   0.0    8.4e-21   75.6   0.0    1.1  1  Abhydrolase_6  Alpha/beta hydrolase family
    2.3e-16   59.8   0.0    3.5e-16   59.2   0.0    1.3  1  Hydrolase_4    Serine aminopeptidase, S33
    4.4e-06   26.6   0.1       0.15   11.9   0.0    3.2  4  Abhydrolase_2  Phospholipase/Carboxylesterase
    1.3e-05   24.1   0.0      2e-05   23.5   0.0    1.3  1  Ndr            Ndr family
     0.0002   21.3   0.0      0.043   13.7   0.0    2.8  1  Ser_hydrolase  Serine hydrolase
  ------ inclusion threshold ------
      0.021   14.2   0.0       0.12   11.8   0.0    1.9  2  DUF3530        Protein of unknown function (DUF3530)
      0.047   13.4   0.0        2.6    7.8   0.0    2.6  2  Abhydrolase_5  Alpha/beta hydrolase family
       0.13   11.9   0.0       0.23   11.1   0.0    1.6  1  FSH1           Serine hydrolase (FSH1)
       0.14   12.1   0.0       0.21   11.5   0.0    1.3  1  UPF0227        Uncharacterised protein family (UPF0227)
       0.16   11.6   0.0       0.28   10.8   0.0    1.3  1  MOZART2        Mitotic-spindle organizing gamma-tubulin ring 
       0.19   11.9   0.0       0.35   11.0   0.0    1.5  1  Abhydrolase_4  TAP-like protein


Domain annotation for each model (and alignments):
>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.6   0.0   4.6e-26   6.8e-23       1     125 [.      23     142 ..      23     147 .. 0.89
   2 !   17.6   0.0   1.6e-06    0.0023     206     257 .]     186     249 ..     143     249 .. 0.81

  Alignments for each domain:
  == domain 1  score: 81.6 bits;  conditional E-value: 4.6e-26
                    SEEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEEEETHHHHHHHHHHHHHGG CS
  Abhydrolase_1   1 pvlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltlvGhSmGGmialayaaeype 96 
                    ++lv++hGl++s++ w    ++p++ak +++vi++Dl G+gyS++++     dy+  ++ ++l ++ldal ++ ++++G S+GG+i+++y + +p+
     EPA04420.1  23 NTLVLVHGLGASAERWNL--VIPTFAK-HYRVIVPDLIGYGYSDKPIL----DYSPEMFVNFLGKFLDALQIKCPIIIGSSLGGQISAEYTSANPK 111
                    689**********98777..*******.*******************8....69999*************************************** PP

                    GEEEEEEESE..CSSCCHHHHHHHHHHHHHH CS
  Abhydrolase_1  97 rVkalvllga..idpaaslieaqrqqaksfp 125
                    +V +lvl+++   +  + +  +++  a+ +p
     EPA04420.1 112 NVEKLVLVSPagAMKQSTPALDAYIMAALYP 142
                    **********875555555555555555555 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 1.6e-06
                    C............THHHHSEEEEEEETTCSSSCHHHHHHHHHCHTSEEEEEEETCSSSHHHHSH CS
  Abhydrolase_1 206 e............lknvlaptlvisgtsDplvppkaledlaqllpkkrlvvisdagHlaflegp 257
                    +            l+ + +ptlvi+g +Dp+vp +  + + + +++ + ++ +++gH+ + ++p
     EPA04420.1 186 IlgmknseiispkLHTIQCPTLVIWGVNDPVVPVEFADGFVSFIRDCKFHKMEKCGHTPYVQDP 249
                    14445567777889********************8888888888998***********998875 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.6   0.0   5.6e-24   8.4e-21       1     217 [.      25     252 ..      25     254 .. 0.68

  Alignments for each domain:
  == domain 1  score: 75.6 bits;  conditional E-value: 5.6e-24
                    EEEE--GC.....GCHHHHHHHHCCTCEEEEE--TTSTS-GGCS--HHHCHHHHHHHCCTT....TTSEEEEEETCHHHHHHHHHHCC.......E CS
  Abhydrolase_6   1 vlllHGagssassWlvapLaallaagvhvlapDlpGhGrsdpppldledladlaalldelaa..gggpvvlvGHSlGGalalaaapla.....lvv 89 
                    ++l+HG+g+sa+ W    + + +a++++v++pDl G+G sd p ld+++ + ++++l ++ +  + + ++++G SlGG ++++   ++      v+
     EPA04420.1  25 LVLVHGLGASAERWN--LVIPTFAKHYRVIVPDLIGYGYSDKPILDYSP-EMFVNFLGKFLDalQIKCPIIIGSSLGGQISAE---YTsanpkNVE 114
                    79************6..56888899**********************99.5556666666655569999**************...5555586445 PP

                    E.EEES-..----TTT....S----TTHHHHHHTT-CCCCHCCHS-HSCCCCHHHCCCCHCHCCCGHHHHCCHHC...........HTTCCHHTT- CS
  Abhydrolase_6  90 g.vlldppptalpagl....laaalelllallallrllawlsreplprlfladedadaawrarlarlaallaglg...........llpaaawadl 169
                    + vl++p   a+ +      l+a++  +l ++   ++ a++ +e+ + +  +      ++     r++   ++l            +   + + ++
     EPA04420.1 115 KlVLVSP---AGAMKQstpaLDAYIMAALYPNEQSAKNAFDLMEASGNTVDE-----KIVKGFIERMQLPNSKLAfmstilgmknsEIISPKLHTI 202
                    58*****...555555532233333333333334444688855422224444.....4444444444433332221111112323344588***** PP

                    TTGCEEEC.TT-CHHH.HCHHCCCH..STTEEETCE...SSS-HHHHSHHHH CS
  Abhydrolase_6 170 pvpllvlg.geDplvp.rllerlla..qagarlpvvlpgaGHlphleepdev 217
                     +p+lv++  +Dp+vp +++ +  +  ++++++ + ++ +GH p+ ++p+ +
     EPA04420.1 203 QCPTLVIWgVNDPVVPvEFA-DGFVsfIRDCKF-HKMEKCGHTPYVQDPETF 252
                    ****9996699**9994444.55555*******.**********99999755 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.2   0.0   2.3e-19   3.5e-16       3     234 ..      21     244 ..      19     250 .. 0.81

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 2.3e-19
  Hydrolase_4   3 pkavvvlvHGlaehsgryaelaeaLaaqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpelplfllGhSmGGliallyllrypdk 100
                   k ++vlvHGl+ +++r + ++  +a++ + v+  D  G+G s+       s + +v+ l +f+++++     +  +++G S+GG i+++y+  +p++
   EPA04420.1  21 SKNTLVLVHGLGASAERWNLVIPTFAKH-YRVIVPDLIGYGYSDKPIL-DYSPEMFVNFLGKFLDALQ----IKCPIIIGSSLGGQISAEYTSANPKN 112
                  6899*********************987.**************76666.4567899999999999998....555589******************** PP

  Hydrolase_4 101 vaglilsaPalkikaklkappllklllkllgkllpklqv....snnlkadslsrdpevvaayeadplv.hgkitvrlllelldamkrleeraakitlP 193
                  v++l+l++Pa ++k++++a  +      +++ l+p+ q      + ++a+  + d++ v+ + +   +   k+        ++  + +  + + i+ P
   EPA04420.1 113 VEKLVLVSPAGAMKQSTPALDA-----YIMAALYPNEQSaknaFDLMEASGNTVDEKIVKGFIERMQLpNSKLAFMSTILGMKNSEIISPKLHTIQCP 205
                  ***********99987543222.....4555555555552222245667777777888886666666657777766666667888999********** PP

  Hydrolase_4 194 llllhGeaDkvvdpeasrelyerlgskdktlklypglyHel 234
                  +l++ G +D+vv+ e +  ++  ++  d++++ ++++ H  
   EPA04420.1 206 TLVIWGVNDPVVPVEFADGFVSFIR--DCKFHKMEKCGHTP 244
                  **************99999999998..89999999999976 PP

>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   9.8e-05      0.15      13      40 ..      21      48 ..      15      57 .. 0.82
   2 ?    1.3   0.0      0.17   2.5e+02     108     147 ..      91     130 ..      73     139 .. 0.86
   3 ?   -2.9   0.0       3.2   4.9e+03      83     101 ..     150     168 ..     135     183 .. 0.57
   4 !    9.3   0.0   0.00061      0.91     151     201 ..     198     244 ..     182     262 .] 0.72

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.8e-05
                   --EEEEEE--TT--SHHHHHHHH.TT-- CS
  Abhydrolase_2 13 aqavviflHGlGdsghawaeaakteaal 40
                    +++++++HGlG+s++ w ++  t+a++
     EPA04420.1 21 SKNTLVLVHGLGASAERWNLVIPTFAKH 48
                   689***************9998877765 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.17
                    EEEEETHHHHHHHHHHHT-SS--SEEEEES---TTGGGTT CS
  Abhydrolase_2 108 iigGFSqGaalalylaltlpkklggivafsgalplsqkle 147
                    ii+G S G+ ++ + + + pk +   v +s a +++q+++
     EPA04420.1  91 IIIGSSLGGQISAEYTSANPKNVEKLVLVSPAGAMKQSTP 130
                    89******************99999999998888777766 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 3.2
                    HHHHHHHHHHHHHHHHHTT CS
  Abhydrolase_2  83 ikksaekleelidaelkkg 101
                      + +e   +++d+++ kg
     EPA04420.1 150 AFDLMEASGNTVDEKIVKG 168
                    3344555556666666665 PP

  == domain 4  score: 9.3 bits;  conditional E-value: 0.00061
                    -GGGGG-EEEEEEETT-SSS-HHHHHHHHHHHHTTS-GEEEEEETT--SS- CS
  Abhydrolase_2 151 tavtkklpilqiHgeeDpvvplalgkaakevlkkllkkvelksyeglaHsi 201
                     + t + p l i+g  Dpvvp+ ++  +  ++++    ++++++e+ +H  
     EPA04420.1 198 KLHTIQCPTLVIWGVNDPVVPVEFADGFVSFIRD----CKFHKMEKCGHTP 244
                    445568899**************99998877665....5677777777753 PP

>> Ndr  Ndr family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   1.3e-08     2e-05      89     276 ..      78     260 ..      69     262 .] 0.82

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.3e-08
                 HHHHHHHHT---EEEEEETHHHHHHHHHHHHSGGGEEEEEEES---S---HHHHHHHHHH.......TTTS-HHHHHHHHHS-HHHHHHT-HHHHHHHH CS
         Ndr  89 llavldhfklksviglGvgaGAyilarfalkhperveglvLinitskaagwvewakeKlsskllkkvgltdllkdlllahkFgkeeksensdlvreyrk 187
                 l + ld +++k  i +G   G  i a ++ ++p+ ve lvL+++ +  +  +      +++ l+ + + ++++ dl+ a   g+  +   + +v+ + +
  EPA04420.1  78 LGKFLDALQIKCPIIIGSSLGGQISAEYTSANPKNVEKLVLVSPAGAMKQSTPALDAYIMAALYPNEQSAKNAFDLMEAS--GNTVD---EKIVKGFIE 171
                 567899********************************************9*999999**99999999999999987553..33333...459999988 PP

                 HHHT-TTHHHHHHHHHHHHT-------TTSSSS-EEEEEETTSTTHHHHHHHHHHS-TTTEEEEEETT-TT-HHHH-HHHHHHHHHHHH CS
         Ndr 188 llkerlnsknlelyleaynkRrdleierkklevkvllvvGdkspfvdevvevnskldkkkttllkvadsgglvleeqPdklaeslklfl 276
                 +++   ++   +  +  +++ + ++ ++++ ++++l++ G + p v            +  ++ k++++g  +  + P+  +  + +fl
  EPA04420.1 172 RMQLPNSKLAFMSTILGMKNSEIISPKLHTIQCPTLVIWGVNDPVVPVEFADGFVSFIRDCKFHKMEKCGHTPYVQDPETFLSIVLNFL 260
                 88888887788888888888888999999999************98543332222234667899******9**9999999877666654 PP

>> Ser_hydrolase  Serine hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   2.9e-05     0.043      51      94 ..      83     144 ..      25     247 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.9e-05
                    HC-STT.EEEEEETCHHHHHHHHHHHTTSSSEEEEEEET--SGG..................S CS
  Ser_hydrolase  51 eaaeek.vvlvAHSlgclavlhaaelqlakkvagalLVapadve..................e 94 
                    +a++ k  +++  Slg  +++++   + +k+v++ +LV+pa  +                  e
     EPA04420.1  83 DALQIKcPIIIGSSLGGQISAEYT-SANPKNVEKLVLVSPAGAMkqstpaldayimaalypnE 144
                    55544424899************9.99**************9874444444444444444430 PP

>> DUF3530  Protein of unknown function (DUF3530)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.35   5.2e+02     188     209 ..      13      34 ..      10      36 .. 0.90
   2 ?   11.8   0.0   7.8e-05      0.12     190     246 ..      81     136 ..      80     142 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.35
     DUF3530 188 iaflnqrgaenivllghgtgAy 209
                 i +l++  ++n ++l hg gA+
  EPA04420.1  13 IRYLESGDSKNTLVLVHGLGAS 34 
                 7899999999**********96 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 7.8e-05
     DUF3530 190 flnqrgaenivllghgtgAywaarylaekksakvdaLvlvdarepaeaaekqLaeql 246
                 fl+  + +  +++g+  g +  a+y +  ++++v++Lvlv++   ++++ ++L+ ++
  EPA04420.1  81 FLDALQIKCPIIIGSSLGGQISAEYTSA-NPKNVEKLVLVSPAGAMKQSTPALDAYI 136
                 566667777799****************.******************9999998876 PP

>> Abhydrolase_5  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0    0.0017       2.6      60      89 ..      91     121 ..      81     166 .. 0.78
   2 ?    2.8   0.0     0.061        91      96     140 ..     199     242 ..     193     247 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0017
  Abhydrolase_5  60 vvgGhslGGvvasrfaaee.ekiegvvflas 89 
                    ++ G slGG +++++++ + +++e +v+++ 
     EPA04420.1  91 IIIGSSLGGQISAEYTSANpKNVEKLVLVSP 121
                    788*************999679999998764 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.061
  Abhydrolase_5  96 lselskkvlsivgteDgvlnvkslekakkflpkdtkvvsieGgnh 140
                    l++ + ++l i+g +D v++v+ ++    f+ +d k++++e   h
     EPA04420.1 199 LHTIQCPTLVIWGVNDPVVPVEFADGFVSFI-RDCKFHKMEKCGH 242
                    6778899************998766555544.6677777766666 PP

>> FSH1  Serine hydrolase (FSH1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00015      0.23     154     192 ..     194     233 ..      63     245 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00015
        FSH1 154 yy..eedkiqtptLhvlGelDtvvdeerseaLaeafknssk 192
                     + + iq+ptL + G +D vv+ e +  ++  +++  k
  EPA04420.1 194 IIspKLHTIQCPTLVIWGVNDPVVPVEFADGFVSFIRD-CK 233
                 223456789****************8888777777666.54 PP

>> UPF0227  Uncharacterised protein family (UPF0227)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00014      0.21      42      93 ..      71     125 ..      54     154 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00014
     UPF0227  42 pqqalkeleklvaelgddnillvGssLGGyy.atrlgerfglrq..vllnPalkp 93 
                 p+  ++ l k + +l+ + ++++GssLGG   a++ ++  + +   vl+ Pa + 
  EPA04420.1  71 PEMFVNFLGKFLDALQIKCPIIIGSSLGGQIsAEYTSANPKNVEklVLVSPAGAM 125
                 55666667777778887889*********87256666655544456888888655 PP

>> MOZART2  Mitotic-spindle organizing gamma-tubulin ring associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00018      0.28      32      79 ..     149     196 ..     133     203 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00018
     MOZART2  32 eLyeLtqaaGiviDqevfkiivDLLklnvaPlavfqvLksmcagqria 79 
                 + ++L +a+G ++D+++ k  ++ ++l  + la + ++  m ++++i+
  EPA04420.1 149 NAFDLMEASGNTVDEKIVKGFIERMQLPNSKLAFMSTILGMKNSEIIS 196
                 679*****************************************9998 PP

>> Abhydrolase_4  TAP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00023      0.35      34      82 ..     203     251 ..     189     262 .] 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00023
  Abhydrolase_4  34 aapvLllqnerDpaTPyegakklakalggavlvtvegeGHgalaagntC 82 
                    + p+L++ + +Dp++P e a  + + +++ +    e+ GH+ + +  + 
     EPA04420.1 203 QCPTLVIWGVNDPVVPVEFADGFVSFIRDCKFHKMEKCGHTPYVQDPET 251
                    479**********************999999999999999998755554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 1644.12
//
Query:       EPA04421.1  [L=354]
Description: poly(R)-hydroxyalkanoic acid synthase, class III, PhaC subunit [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-13   50.5   0.0    4.4e-12   45.8   0.0    2.3  1  Hydrolase_4    Serine aminopeptidase, S33
    2.6e-13   50.2   0.0    3.9e-13   49.6   0.0    1.5  1  Abhydrolase_1  alpha/beta hydrolase fold
    2.2e-12   47.0   0.1    4.3e-12   46.0   0.1    1.4  1  PhaC_N         Poly-beta-hydroxybutyrate polymerase (PhaC) N-
      1e-06   27.5   0.0    1.5e-06   26.9   0.0    1.2  1  DUF3141        Protein of unknown function (DUF3141)
    0.00028   20.5   0.0      0.002   17.7   0.0    2.0  2  DLH            Dienelactone hydrolase family
     0.0066   16.4   0.0      0.013   15.4   0.0    1.5  1  BAAT_C         BAAT / Acyl-CoA thioester hydrolase C terminal
  ------ inclusion threshold ------
      0.012   15.1   0.0      0.083   12.3   0.0    2.2  2  PHB_depo_C     PHB de-polymerase C-terminus


Domain annotation for each model (and alignments):
>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   0.0   1.7e-15   4.4e-12      24     230 ..      90     328 ..      87     329 .. 0.79

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 1.7e-15
  Hydrolase_4  24 aeaLaaqGfavyalDhrGhGrsegkrghvpsfddyvdD.laafvekvkeehpelplfllGhSmGGliallyllrypdkvaglilsaPalkikaklk.a 119
                  +++L  qGf+vy+lD+ G   s     +  +fddyv+  l++ ve +k+e++++++ l G  +G++ia++y++ +p++v+  i +aP+++ + ++  +
   EPA04421.1  90 VRNLLLQGFDVYMLDW-GSPTSMD---KYLDFDDYVNGyLDSSVEYIKNESSTEKISLQGYCTGATIATAYTALHPESVKNYIATAPVIDGWRDTTvI 183
                  678999*********8.5555544...4559999999746778***************************************************9777 PP

  Hydrolase_4 120 ppllkl.....llkllgkllpklqv....................snnlkadslsrdpevva.ayeadplvhgkitvrlllelldamkrleeraakit 191
                  + l+k      + +++g++ p++                      + n+++++  ++  +v+  + + p + g++  +++ ++++    ++++     
   EPA04421.1 184 SNLAKHmdvdkMVEIIGNMPPEFMYycfsvlkpfeqgiekyvnffK-NIENKKFVDNFLRVEkWLGDTPPIPGELFRQWIKDIYQENLLIQNKMY--V 278
                  77777677788888999988888889999*********77777744.455555555544444155666666777777888777776666665542..0 PP

  Hydrolase_4 192 ...........lPllllhGeaDkvvdpeasrelyerlgskdktlklypgl 230
                             +Pl+   +  D++v+pe s  l+ ++gs+dktlk+yp +
   EPA04421.1 279 ggslidlkkinMPLFTQVAVGDHLVSPECSMPLHYAVGSEDKTLKIYPTG 328
                  23444455555************************************975 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6   0.0   1.5e-16   3.9e-13       4     128 ..      69     207 ..      66     331 .. 0.86

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 1.5e-16
                    EEE-STTT...CGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEEEETHHHHHHHHHHHHHGG CS
  Abhydrolase_1   4 vilhGlpg...ssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltlvGhSmGGmialayaaeype 96 
                    +i  +l +    +d++ e++++++L  +gfdv++lD+  + + ++ ++   ddy +  +  ++++i++    +k+ l G++ G +ia+ay a++pe
     EPA04421.1  69 LISYALINryhILDIQPEKSWVRNLLLQGFDVYMLDWGSPTSMDKYLDF--DDYVNGYLDSSVEYIKNESSTEKISLQGYCTGATIATAYTALHPE 162
                    55555555444678899********************888888888887..9******************************************** PP

                    GEEEEEEESE.............CSSCCHHHHHHHHHHHHHHCHH CS
  Abhydrolase_1  97 rVkalvllga.............idpaaslieaqrqqaksfpdff 128
                    +Vk+ +++++             ++ +++ ++  + + + +p+f+
     EPA04421.1 163 SVKNYIATAPvidgwrdttvisnLAKHMDVDKMVEIIGNMPPEFM 207
                    **********87777766666666666666666666666666655 PP

>> PhaC_N  Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.0   0.1   1.7e-15   4.3e-12     118     171 ..      38      91 ..      34      93 .. 0.95

  Alignments for each domain:
  == domain 1  score: 46.0 bits;  conditional E-value: 1.7e-15
      PhaC_N 118 attpGkvvfrnelleliqykpttekvlkrPllivPplinkfYilDLkpenslvr 171
                  +tp ++v + + + l++y+p+t+k++k+Plli  +lin++ ilD++pe+s vr
  EPA04421.1  38 EITPHDIVQEIDKTRLLHYRPLTDKQHKTPLLISYALINRYHILDIQPEKSWVR 91 
                 67999**********************************************998 PP

>> DUF3141  Protein of unknown function (DUF3141)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0     6e-10   1.5e-06     220     316 ..     211     308 ..     202     334 .. 0.90

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 6e-10
     DUF3141 220 feklnPantlwskqynlyakvdtea..erylefekwWGghvllnkeeieyivdnLfvGnrlatgelvtsdgvriDlrnirsPivvfaskgDnitPPqqa 316
                 f  l P ++  +k++n ++++++++  + +l +ekw G+   + +e  +  +++++  n l +++++   g+ iDl++i  P+    + gD +  P+ +
  EPA04421.1 211 FSVLKPFEQGIEKYVNFFKNIENKKfvDNFLRVEKWLGDTPPIPGELFRQWIKDIYQENLLIQNKMY-VGGSLIDLKKINMPLFTQVAVGDHLVSPECS 308
                 88999****************99864489*****************99999999**99999999885.5799********************9999866 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   7.6e-07     0.002      78     125 ..     121     167 ..     108     198 .. 0.82
   2 ?    0.1   0.0      0.19     5e+02     138     187 ..     283     329 ..     279     341 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 7.6e-07
         DLH  78 vlddlkaavaylksvpevstkkvgvvGfCmGGalalllaaev.pevdaa 125
                 v   l+ +v+y+k+ +  st+k+ + G+C G+++a ++ a   + v+  
  EPA04421.1 121 VNGYLDSSVEYIKNES--STEKISLQGYCTGATIATAYTALHpESVKNY 167
                 55667899*****999..899***************9998885666655 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.19
         DLH 138 eeaakikapilalfgeeDefipadevekleealkaanvdlelkvYpgagH 187
                 ++ +ki+ p++  ++  D+ +  +    l+ a+     d  lk+Yp  gH
  EPA04421.1 283 IDLKKINMPLFTQVAVGDHLVSPECSMPLHYAVGS--EDKTLKIYP-TGH 329
                 5678999**************99998888888844..455677788.666 PP

>> BAAT_C  BAAT / Acyl-CoA thioester hydrolase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   5.2e-06     0.013       5      59 ..     124     177 ..     122     250 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.2e-06
                 HHHHHHHHHHCSTTB--SSEEEEEETHHHHHHHHHHHHSS.SEEEEEEES--SB-- CS
      BAAT_C   5 YFeeainyllrhpkvkkdkigllGiSkGgelalllasflk.kisavvlingsavvv 59 
                 Y +  ++y+++++ ++  ki l+G + G+++a + ++ ++ ++++ ++ ++     
  EPA04421.1 124 YLDSSVEYIKNESSTE--KISLQGYCTGATIATAYTALHPeSVKNYIATAPVIDGW 177
                 7788999***997776..*********************999**999988865444 PP

>> PHB_depo_C  PHB de-polymerase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.18   4.6e+02       4      37 ..     174     206 ..     171     246 .. 0.76
   2 ?   12.3   0.0   3.2e-05     0.083      97     200 ..     253     351 ..     229     354 .] 0.74

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.18
  PHB_depo_C   4 iDarksptavnelakekslewfeenviqkvpvky 37 
                 iD  +++t++++lak+  ++++ e +i ++p+++
  EPA04421.1 174 IDGWRDTTVISNLAKHMDVDKMVE-IIGNMPPEF 206
                 8999999********999999865.556666655 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 3.2e-05
  PHB_depo_C  97 ltaefylqtveevfqefalakgklkvegkrvdlkkikrvalltveGenDDisglGqtkaaldlctgipesrkahylqegvGhyGvfsGsrfreeivPrv 195
                 ++ e + q +++++qe  l ++k+ v g  +dlkki+ + l+t     D + ++   + +  l  ++  + k+  + + +Gh G+ + s  ++++ P +
  EPA04421.1 253 IPGELFRQWIKDIYQENLLIQNKMYVGGSLIDLKKIN-MPLFTQVAVGDHLVSP---ECSMPLHYAVGSEDKTLKIYP-TGHVGMIASSLSQNKVLPEL 346
                 57799999****************************6.6677766666776665...334445555555555555544.58888888888888888887 PP

  PHB_depo_C 196 rdfir 200
                  ++++
  EPA04421.1 347 GKWLE 351
                 77665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 2018.06
//
Query:       EPA04422.1  [L=144]
Description: hypothetical protein BG20_I1711 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-06   27.7   0.0      0.043   13.3   0.0    2.1  2  Pribosyltran  Phosphoribosyl transferase domain
  ------ inclusion threshold ------
      0.031   14.5   0.2        6.4    7.0   0.1    2.4  2  FF            FF domain
      0.036   13.8   0.5        2.9    7.6   0.1    2.2  2  DUF956        Domain of unknown function (DUF956)


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   1.1e-05     0.066       3      62 ..      15      67 ..       9      72 .. 0.80
   2 !   13.3   0.0   7.2e-06     0.043      91     133 ..      73     113 ..      70     136 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.1e-05
                  HHTTT---EEEEEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEE CS
  Pribosyltran  3 sellenpaildavarlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvk 62
                  +      +i++++++l+++ l         + +i rgG+++a  lad++++ +  v+k k
    EPA04422.1 15 K------EIEKIIEELSKKVLLL-HKDFSSISTISRGGLVPARLLADHMGIDVILVDKNK 67
                  3......4444888888888888.66667999*****************88888777765 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 7.2e-06
                   EEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHHHHHH CS
  Pribosyltran  91 liVDDildtGgTllaalelLkekgpeevriavlvdkpateeev 133
                   l VDDi d+G+T +++l   k  +p  +  a+l++++ ++ ++
    EPA04422.1  73 LFVDDIYDSGSTFKKILP--KISNPSDFVYATLFARRGKKYPK 113
                   78*************987..44567777777777777777666 PP

>> FF  FF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1    0.0011       6.4      20      31 ..       8      23 ..       2      34 .. 0.79
   2 ?    5.4   0.0    0.0035        21      17      31 ..      80      94 ..      62     115 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0011
                S....SHHHHHHHCTT CS
          FF 20 s....tWseikkilen 31
                s    +W+ei+ki+e+
  EPA04422.1  8 SyqniSWKEIEKIIEE 23
                444559********97 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0035
                -TTSSHHHHHHHCTT CS
          FF 17 tpkstWseikkilen 31
                ++ st+++i+++++n
  EPA04422.1 80 DSGSTFKKILPKISN 94
                6789*********98 PP

>> DUF956  Domain of unknown function (DUF956)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.1   0.00049       2.9      41      64 ..       5      28 ..       2      42 .. 0.86
   2 ?    4.4   0.0    0.0048        28      38      55 ..     119     136 ..     112     140 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00049
      DUF956 41 nvedyiqipWeevdsvvasvlfkg 64
                n++ y +i W+e+++++ +++ k 
  EPA04422.1  5 NMNSYQNISWKEIEKIIEELSKKV 28
                7899*************9998774 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0048
      DUF956  38 ndknvedyiqipWeevds 55 
                 ++++ ++yi +pW+++++
  EPA04422.1 119 KKTHGNEYIVFPWDKLEY 136
                 4566799*******9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 901.09
//
Query:       EPA04423.1  [L=193]
Description: hypothetical protein BG20_I1713 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-12   46.7   0.1    2.8e-12   46.4   0.1    1.2  1  PHA_synth_III_E  Poly(R)-hydroxyalkanoic acid synthase subuni
     0.0014   19.0   5.7       0.14   12.6   0.0    2.4  2  DUF4200          Domain of unknown function (DUF4200)
  ------ inclusion threshold ------
      0.011   15.9   3.8       0.66   10.2   3.0    2.3  2  Cnn_1N           Centrosomin N-terminal motif 1
      0.017   15.0   4.5        0.8    9.5   0.2    2.3  2  Bacillus_HBL     Bacillus haemolytic enterotoxin (HBL)
       0.04   14.2   3.2        1.1    9.7   0.3    2.9  3  GAT              GAT domain
      0.078   13.2   6.4      0.048   13.9   2.3    2.2  2  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
        0.1   12.9   5.1       0.54   10.6   0.1    2.5  2  KxDL             Uncharacterized conserved protein
       0.17   12.0   6.0        2.4    8.3   2.0    2.2  2  ApoLp-III        Apolipophorin-III precursor (apoLp-III)
       0.19   12.2   1.8        0.7   10.4   1.1    2.2  2  DUF4094          Domain of unknown function (DUF4094)
       0.23   11.8   2.7        5.6    7.3   0.4    3.3  3  Retrotrans_gag   Retrotransposon gag protein
       0.25   11.5   8.7       0.42   10.8   2.1    2.9  3  Lge1             Transcriptional regulatory protein LGE1
       0.55   10.4   5.0        1.3    9.2   2.9    2.1  2  Uds1             Up-regulated During Septation
       0.64   10.1  12.9        0.3   11.2   5.7    2.7  3  IFP_35_N         Interferon-induced 35 kDa protein (IFP 35) N


Domain annotation for each model (and alignments):
>> PHA_synth_III_E  Poly(R)-hydroxyalkanoic acid synthase subunit (PHA_synth_III_E)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4   0.1     2e-15   2.8e-12     191     313 ..      59     178 ..      35     179 .. 0.90

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 2e-15
  PHA_synth_III_E 191 ravvdyqqasqeYqallaavgvksverlreklqeaaekgkqiksaralfdlWveaaeevyaevvaseeyakiygrlvnaqmalkaemqrlveev 284
                      + ++++++ + eY ++l++   ++ +++  k  ++ +  +q++s++    +W++  ++ + e + se++ + yg+lv+   +l ++ +++ + +
       EPA04423.1  59 ESLLEFNKFVTEYYKQLSETWTDAQKKVNLKSPDVPHDVEQMESFK---RIWIDIFDNDFTELFDSEKFGENYGKLVSKELELTKHWNNISNVI 149
                      5678999999999999999999999999998888888866666655...68******************************************* PP

  PHA_synth_III_E 285 lealnlPtRsEldtlhkriqelrrevrrl 313
                      l+++nlP++ E+d+++k+++ l++++ +l
       EPA04423.1 150 LQSVNLPSKEEIDEVYKEMHSLKKRITKL 178
                      ************************99877 PP

>> DUF4200  Domain of unknown function (DUF4200)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   9.9e-05      0.14      26      74 ..      40      88 ..      37      92 .. 0.88
   2 !    6.5   3.1    0.0078        11      79     108 ..     158     187 ..     151     190 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.9e-05
     DUF4200 26 eealkqreeelekkeqeleedllkfdkflkendakraralkkaeeerkl 74
                ++a+++  +++  +  +++e+ll+f+kf+ e  ++ ++    a+++ +l
  EPA04423.1 40 MRAFASNAKKISTELIQINESLLEFNKFVTEYYKQLSETWTDAQKKVNL 88
                78999999************************99998888877777665 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0078
     DUF4200  79 eaeikklkaeietlkseiekleekleeykk 108
                 ++ei +  +e+  lk++i+kle +l++ k+
  EPA04423.1 158 KEEIDEVYKEMHSLKKRITKLEIELKKKKE 187
                 6899********************999886 PP

>> Cnn_1N  Centrosomin N-terminal motif 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.029        40      30      71 ..      34      80 ..      24      82 .. 0.82
   2 ?   10.2   3.0   0.00048      0.66      36      64 ..     159     187 ..     135     193 .] 0.69

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.029
      Cnn_1N 30 leklse.....eqkeellkenielkveveslqkelkekkkllreaek 71
                l+ l++     ++ +++  e+i++ + + +  k + e+ k+l e ++
  EPA04423.1 34 LTSLGPmrafaSNAKKISTELIQINESLLEFNKFVTEYYKQLSETWT 80
                4555557777789999**************************99987 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00048
      Cnn_1N  36 eqkeellkenielkveveslqkelkekkk 64 
                 e+++e+ ke   lk ++ +l+ elk+kk+
  EPA04423.1 159 EEIDEVYKEMHSLKKRITKLEIELKKKKE 187
                 66777777777777777777777776665 PP

>> Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.2   0.00058       0.8      65     104 ..      49      89 ..      41      93 .. 0.87
   2 ?    6.9   0.6    0.0036         5      81     122 ..     139     183 ..     130     190 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00058
  Bacillus_HBL  65 evkPqliktiqdiigYstkFqsyyktlveav.dkkdkaell 104
                   +++ +li++++ ++++++   +yyk+l+e+  d+++k +l+
    EPA04423.1  49 KISTELIQINESLLEFNKFVTEYYKQLSETWtDAQKKVNLK 89 
                   68889************************986777776665 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0036
  Bacillus_HBL  81 stkFqsyyktlveavdkkdkaellellek...Lqeeiqqnqkevk 122
                    + ++++ + + ++v+   k+e+ e++++   L++ i++ + e k
    EPA04423.1 139 TKHWNNISNVILQSVNLPSKEEIDEVYKEmhsLKKRITKLEIELK 183
                   6789***********777777666555541116667777766655 PP

>> GAT  GAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.42   5.9e+02      55      64 ..      52      61 ..      41      71 .. 0.79
   2 ?    3.0   0.1     0.094   1.3e+02      23      55 ..      69     101 ..      57     106 .. 0.81
   3 ?    9.7   0.3   0.00077       1.1      10      46 ..     149     181 ..     145     192 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.42
         GAT 55 aelLqlNDeL 64
                 el+q+N++L
  EPA04423.1 52 TELIQINESL 61
                5899999988 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.094
         GAT  23 nellkeLyetckamqpriqklieetadeedlla 55 
                  e +k+L et   +q+++     +++++ + ++
  EPA04423.1  69 TEYYKQLSETWTDAQKKVNLKSPDVPHDVEQME 101
                 5889**************988888877766665 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.00077
         GAT  10 mLsste.pdeellenellkeLyetckamqpriqkliee 46 
                 +L+s++ p+     +e ++e y++ +++++ri+kl  e
  EPA04423.1 149 ILQSVNlPS-----KEEIDEVYKEMHSLKKRITKLEIE 181
                 677777444.....9******************99655 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.46   6.4e+02      75      96 ..      46      67 ..      22      79 .. 0.57
   2 ?   13.9   2.3   3.5e-05     0.048      40      95 ..     130     187 ..     112     191 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.46
                  CCHHHHHHHHHHHHHHHHHHHH CS
  Seryl_tRNA_N 75 evkelkeelkaleaelkeleae 96
                   +k++++el ++++ l e ++ 
    EPA04423.1 46 NAKKISTELIQINESLLEFNKF 67
                  3444555555555555444444 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 3.5e-05
                   HHHHHHHHHHHHHHHHHHHCCCCCCTT..S-TCCCCCCCHHHHHHHHHHHHHHHHHHH CS
  Seryl_tRNA_N  40 elqveleelqaerNelskeIgkakkkk..edaeeliaevkelkeelkaleaelkelea 95 
                   +l ++  el +  N++s+ I +  +    e+++e+ +e+ +lk+++ +le elk+ ++
    EPA04423.1 130 KLVSKELELTKHWNNISNVILQSVNLPskEEIDEVYKEMHSLKKRITKLEIELKKKKE 187
                   56666678899999999999998754445************************99765 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00039      0.54      16      56 ..      45      85 ..      32     106 .. 0.82
   2 ?    3.6   1.6      0.06        83      55      81 ..     159     185 ..     126     187 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00039
        KxDL 16 alQaqtsgrlnkknreLlelnalsqerlaklrarfkqgtkl 56
                +  +++s++l + n+ Lle+n+++ e +++l++   + +k 
  EPA04423.1 45 SNAKKISTELIQINESLLEFNKFVTEYYKQLSETWTDAQKK 85
                556899**************************998877765 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.06
        KxDL  55 kllkevkkdLesifkkirslkaklakk 81 
                 + + ev k++ s++k+i++l+ +l+kk
  EPA04423.1 159 EEIDEVYKEMHSLKKRITKLEIELKKK 185
                 457788899999999999999888876 PP

>> ApoLp-III  Apolipophorin-III precursor (apoLp-III)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1     0.011        15      56      86 ..      57      87 ..      34     102 .. 0.51
   2 ?    8.3   2.0    0.0017       2.4       2      52 ..     140     185 ..     139     192 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.011
   ApoLp-III 56 leealkevkkkieetadklseenPevkkkaq 86
                ++e+l e++k ++e  ++lse   +++kk++
  EPA04423.1 57 INESLLEFNKFVTEYYKQLSETWTDAQKKVN 87
                2334444444444444444444444444433 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0017
   ApoLp-III   2 kaieelqksvkkqlnlpsqeevvetiKensenlvdqlkqvikslqeelkkk 52 
                 k+ +++++ + +++nlps+ee+ e+ Ke       +lk+ i +l+ elkkk
  EPA04423.1 140 KHWNNISNVILQSVNLPSKEEIDEVYKEM-----HSLKKRITKLEIELKKK 185
                 6889********************99985.....45566666666666655 PP

>> DUF4094  Domain of unknown function (DUF4094)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       1.1   1.5e+03      56      77 ..      22      52 ..       7      58 .. 0.84
   2 ?   10.4   1.1    0.0005       0.7      54      86 ..     157     186 ..     103     188 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.1
     DUF4094 56 dilgevskthkaiqtL.........dktiss 77
                di++ +s +++a+++L          k+is+
  EPA04423.1 22 DIIHLMSSKPQALTSLgpmrafasnAKKIST 52
                7888889999999999888888888888875 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0005
     DUF4094  54 skdilgevskthkaiqtLdktissLemeLaaar 86 
                 sk++++ev k   +  +L+k+i +Le+eL  ++
  EPA04423.1 157 SKEEIDEVYK---EMHSLKKRITKLEIELKKKK 186
                 3444444444...4469************9887 PP

>> Retrotrans_gag  Retrotransposon gag protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0       0.2   2.7e+02      60      85 ..       6      32 ..       3      38 .. 0.74
   2 ?    7.3   0.4    0.0041       5.6      59      79 ..      64      84 ..      40     107 .. 0.77
   3 ?    0.9   0.1      0.41   5.6e+02      53      78 ..     150     176 ..      99     189 .. 0.68

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.2
  Retrotrans_gag 60 tesvreYvtrfktladqlde.vlteea 85
                    +   +eY++ ++ +++++ + ++++ +
      EPA04423.1  6 STNPTEYYKHLSLFWTDIIHlMSSKPQ 32
                    55568************9997555544 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0041
  Retrotrans_gag 59 gtesvreYvtrfktladqlde 79
                     ++ v+eY+++++++++++++
      EPA04423.1 64 FNKFVTEYYKQLSETWTDAQK 84
                    467899999999999999986 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.41
  Retrotrans_gag  53 lsslrQ.gtesvreYvtrfktladqld 78 
                     l+s++   +e ++e ++++++l  ++ 
      EPA04423.1 150 LQSVNLpSKEEIDEVYKEMHSLKKRIT 176
                     444444455666666666666666655 PP

>> Lge1  Transcriptional regulatory protein LGE1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1     0.051        71      17      55 ..      46      84 ..      21     102 .. 0.84
   2 ?   -0.3   0.1      0.89   1.2e+03      34      58 ..     126     150 ..     122     159 .. 0.78
   3 ?   10.8   2.1   0.00031      0.42      23      53 ..     159     189 ..     156     193 .] 0.88

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.051
        Lge1 17 kiesklkeiesldkqleelklkvlkleleldlleeqier 55
                  +++ +e+ ++++ l e ++ v   + +l+ +++ +++
  EPA04423.1 46 NAKKISTELIQINESLLEFNKFVTEYYKQLSETWTDAQK 84
                6678889999*******9999999999999999998876 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.89
        Lge1  34 elklkvlkleleldlleeqierdaL 58 
                 e  +k++  elel   ++ i   +L
  EPA04423.1 126 ENYGKLVSKELELTKHWNNISNVIL 150
                 5678999999999999988877766 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00031
        Lge1  23 keiesldkqleelklkvlkleleldlleeqi 53 
                 +ei++++k+ + lk+ + kle+el   +e  
  EPA04423.1 159 EEIDEVYKEMHSLKKRITKLEIELKKKKEIK 189
                 79*********************99877765 PP

>> Uds1  Up-regulated During Septation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.39   5.4e+02      73     107 ..      43      77 ..      21      88 .. 0.66
   2 ?    9.2   2.9   0.00091       1.3      19      51 ..     157     189 ..     151     192 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.39
        Uds1  73 arsnskssreslakaeeelaeserkvdelaselek 107
                   sn+k+++++l + +e+l e ++ v e  ++l +
  EPA04423.1  43 FASNAKKISTELIQINESLLEFNKFVTEYYKQLSE 77 
                 44666666677777777777777777776666654 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00091
        Uds1  19 sleeVeelkkelkaLeerlealrkkLaletklr 51 
                 s ee++e+ ke+++L++r+++l+ +L+ ++ ++
  EPA04423.1 157 SKEEIDEVYKEMHSLKKRITKLEIELKKKKEIK 189
                 789*******************99998877765 PP

>> IFP_35_N  Interferon-induced 35 kDa protein (IFP 35) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.3     0.074     1e+02      38      55 ..      83     100 ..      47     105 .. 0.79
   2 ?   -2.9   0.0       5.3   7.4e+03      50      62 ..     137     149 ..     130     156 .. 0.65
   3 ?   11.2   5.7   0.00021       0.3       2      32 ..     161     190 ..     160     193 .] 0.83

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.074
    IFP_35_N  38 etKikftsvEtPeddsql 55 
                 ++K+ + s+++P+d  q+
  EPA04423.1  83 QKKVNLKSPDVPHDVEQM 100
                 68**********988776 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.3
    IFP_35_N  50 eddsqlsniskSl 62 
                 e++++  nis  +
  EPA04423.1 137 ELTKHWNNISNVI 149
                 6777778877655 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.00021
    IFP_35_N   2 iaeitkeniqLkeeiqkLeaELQettrefqi 32 
                 i+e+ ke   Lk++i kLe EL ++ +e + 
  EPA04423.1 161 IDEVYKEMHSLKKRITKLEIELKKK-KEIKT 190
                 799*******************864.55454 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1763  (0.0983323); expected 358.6 (0.02)
Passed bias filter:                      611  (0.0340789); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.62u 0.34s 00:00:00.96 Elapsed: 00:00:00.52
# Mc/sec: 1118.33
//
Query:       EPA04424.1  [L=144]
Description: universal stress family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.1e-28   97.9   0.0    8.1e-28   97.7   0.0    1.0  1  Usp       Universal stress protein family
  ------ inclusion threshold ------
      0.063   13.8   0.3      0.079   13.5   0.3    1.2  1  s48_45    Sexual stage antigen s48/45 domain


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.7   0.0   9.1e-32   8.1e-28       3     141 .]       7     144 .]       5     144 .] 0.95

  Alignments for each domain:
  == domain 1  score: 97.7 bits;  conditional E-value: 9.1e-32
                 SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTCEEEEEEEESSHHHHHHHHH.. CS
         Usp   3 krIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggvkvevvveegdpaeeileva.. 99 
                  +IlV++Dgs++s +Ale+A+  a++++a++++ ++i +++ ++     + ++e  +e ++  + a+   ++ ++  v+ + ++ +gd +  ++++a  
  EPA04424.1   7 TKILVPMDGSKNSFRALEMAISIARQFEATITCTYAINMQPHSEFQGITSITKEINKEIKKIMNTAK---ELSDKNNVSFKEKTMVGDIGYNLVKLAhd 102
                 79***********************************************999999999999999875...899*****************999988766 PP

                 HHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
         Usp 100 eeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                 ++e+ dliV+Gsrgrs +++++lGSvs+yv++++++pVl+V+
  EPA04424.1 103 KKEKFDLIVMGSRGRSVVKEVFLGSVSNYVIHSSKIPVLIVK 144
                 999**************************************8 PP

>> s48_45  Sexual stage antigen s48/45 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.3   8.8e-06     0.079      26      86 ..      24      84 ..       6     110 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.8e-06
                EEEEEE-TT-EEEEE--TT-EEESTTCTTEEEEEETTEEEEGCCCCC-T-EEE--SCTTTT CS
      s48_45 26 eCnvkikkndivGlkCpkgfklePenCFenvlekkeeekvkleellkkkielekdsnkknt 86
                e  ++i  +  + ++C + ++++P++ F+ +++ ++e +++++++++++ el +++n +++
  EPA04424.1 24 EMAISIARQFEATITCTYAINMQPHSEFQGITSITKEINKEIKKIMNTAKELSDKNNVSFK 84
                5667777788899*******************88899999999999944444444443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1393  (0.0776954); expected 358.6 (0.02)
Passed bias filter:                      696  (0.0388198); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 874.57
//
Query:       EPA04425.1  [L=103]
Description: divalent cation tolerance protein, CutA1 family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.2e-31  108.5   3.4    1.3e-31  108.3   3.4    1.0  1  CutA1      CutA1 divalent ion tolerance protein
  ------ inclusion threshold ------
       0.29   10.8   1.9        1.2    8.9   0.0    2.5  3  GGA_N-GAT  GGA N-GAT domain


Domain annotation for each model (and alignments):
>> CutA1  CutA1 divalent ion tolerance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.3   3.4   1.5e-35   1.3e-31       1      98 [.       4     100 ..       4     101 .. 0.97

  Alignments for each domain:
  == domain 1  score: 108.3 bits;  conditional E-value: 1.5e-35
                 EEEEEEESSHHHHHHHHHHHHHTTS-SEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEGGGHHHHHHHHHHHSSSSS-EEEEEEESEEEHHHHHHHHH CS
       CutA1   1 vlvlvtapseeeakklaralveeklaACvnilpkieSvYrWkgkieedkEvllliktreekveelekrvkelhpyevpeiialpieagseaYlkWiee 98 
                 ++++ t+p++++  k+a++lv++k++ACvni++ i+S+Y Wk+kie+++E+l ++kt++++ ++l++++k+ hpy+vpeii+++i +++++Yl+W+ +
  EPA04425.1   4 IMIISTYPNKNSITKIANELVKDKIVACVNITK-ISSIYSWKEKIENTSEYLAFFKTTQKNKKHLKEKIKSTHPYDVPEIIEIDIISINKSYLQWLIK 100
                 58999**************************99.*************************************************************975 PP

>> GGA_N-GAT  GGA N-GAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1      0.15   1.4e+03      25      31 ..      20      26 ..      18      29 .. 0.83
   2 ?    8.9   0.0   0.00013       1.2       5      22 ..      62      79 ..      58      81 .. 0.90
   3 ?   -0.1   0.0      0.08   7.2e+02      12      32 ..      97     102 ..      91     103 .] 0.62

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.15
   GGA_N-GAT 25 ANrLIKs 31
                AN L K 
  EPA04425.1 20 ANELVKD 26
                9**9995 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00013
   GGA_N-GAT  5 eksklLarLLkSknpeDL 22
                +++k+L++ +kS++p D+
  EPA04425.1 62 KNKKHLKEKIKSTHPYDV 79
                689**************7 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.08
   GGA_N-GAT  12 rLLkSknpeDLqaANrLIKsm 32 
                                 LIKs+
  EPA04425.1  97 W---------------LIKST 102
                 4...............66654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1669  (0.0930894); expected 358.6 (0.02)
Passed bias filter:                      613  (0.0341904); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 696.46
//
Query:       EPA04426.1  [L=187]
Description: eRF1 domain 3, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.1e-11   43.1   0.8    3.6e-10   40.3   0.3    2.3  2  eRF1_3          eRF1 domain 3
      1e-05   25.8   0.2    3.5e-05   24.1   0.1    1.9  1  eRF1_2          eRF1 domain 2
     0.0049   16.6   0.0     0.0082   15.8   0.0    1.3  1  Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 famil


Domain annotation for each model (and alignments):
>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.13     8e+02       8      31 ..      16      40 ..       4      44 .. 0.52
   2 !   40.3   0.3     6e-14   3.6e-10       3     113 .]      91     185 ..      89     185 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.13
                HHHHHHHHHC.TCSSEEESHHHHHH CS
      eRF1_3  8 leefleelak.dtgkavYGveevlk 31
                +++ l ++ +  +  +++G  e++k
  EPA04426.1 16 IQQALISIIReTDSIIIFGPGETKK 40
                3333333333133445677777766 PP

  == domain 2  score: 40.3 bits;  conditional E-value: 6e-14
                 HHHHHHHHHHHHHHCTCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSHHHHHS-HHH-HHHHHHHHHHHHHHHHHTT-EEEEE-TTSHHHHHHHHH CS
      eRF1_3   3 qekklleefleelakdtgkavYGveevlkalemgAvetLLvseelersrdtlkekvketgeelelvelieelvenveesgakveiisseseeGeqlvka 101
                 + +++++e + + +k ++k + G+ee+lka+++gAve L+ s++  +++d+            +    + el++++e+ g k + + s+++ G ++ ++
  EPA04426.1  91 KVSSIIDEIMLRANKKSRKFTMGFEETLKANQYGAVELLVFSDKAIQTNDEK-----------Q----VIELLNDAESKGVKTFSVDSSTDIGLRV-TG 173
                 6678999******************************999999998886432...........2....678*************************.** PP

                 TTTEEEEESS-- CS
      eRF1_3 102 fgGiaaiLRykv 113
                 +gGi+ +LRy +
  EPA04426.1 174 LGGIVSLLRYAI 185
                 **********75 PP

>> eRF1_2  eRF1 domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.1   5.8e-09   3.5e-05      57     123 ..       8      74 ..       1      86 [. 0.84

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 5.8e-09
                 HHHHHHHHHHHHHHHCHTTTESEEEEEESSTHHHHHHHHHHHHHHHHTCCEEEEE.-S-TSCHHHHHH CS
      eRF1_2  57 flkkvaeaankafllvdkdklkgiilagpgfvkeefldkdlldaelkkkviklvd.vsyggesglnev 123
                  ++k++e++++a+++  + + + ii+ gpg++k+ f + +l  ++++k +i++++ + +gge g+  +
  EPA04426.1   8 NIEKFFEQIQQALIS-IIRETDSIIIFGPGETKKRFSNFLLRSQNAQKYKIQIAEgIDSGGEDGFTHL 74 
                 479*********994.68999***************************99886543888999998765 PP

>> Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.4e-06    0.0082       7      71 ..     101     168 ..      98     181 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.4e-06
                     HHHHHHHTEEEESHHHHHHHHHTTTESEEEEETTSSSGGHHH.HHHHHHH..HTTEEEEEESCHHHHH CS
  Ribosomal_L7Ae   7 lkkakkagklvlGlkevtkalergeaklvilAedvepeekkk.llealck..ekevpyvkvkskkeLG 71 
                     l++ kk++k ++G +e++ka + g ++l + ++ + + +++k  +e l     k+v+ ++v+s  ++G
      EPA04426.1 101 LRANKKSRKFTMGFEETLKANQYGAVELLVFSDKAIQTNDEKqVIELLNDaeSKGVKTFSVDSSTDIG 168
                     778899**************************99877766664677775566***********99999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       850  (0.0474092); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1201.32
//
Query:       EPA04427.1  [L=51]
Description: hypothetical protein BG20_I2484, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.33s 00:00:00.82 Elapsed: 00:00:00.53
# Mc/sec: 288.23
//
Query:       EPA04428.1  [L=257]
Description: hypothetical protein BG20_I1832 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.09   12.7   0.0       0.16   11.9   0.0    1.4  1  TrmB      Sugar-specific transcriptional regulator TrmB
       0.11   12.1   0.1        0.2   11.2   0.1    1.4  1  RecR      RecR protein


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.8e-05      0.16      12      62 ..      48     102 ..      42     107 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.8e-05
                 CHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST....TTEE CS
        TrmB  12 kvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr....pklY 62 
                 kv laL ++++++++ i  ++g+  ++ Y v+  L+++ ++  ++ r     k+Y
  EPA04428.1  48 KVLLALDNHKKLNVSGILDKSGIHTNTLYHVMPILLKRKIISEKRIRhinnQKFY 102
                 7899999*****************************9999988776655555555 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   2.3e-05       0.2      12      29 ..     217     234 ..     210     235 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.3e-05
                 HHHH-EE-TTT--EESSS CS
        RecR  12 akekvrhCsrCgnlteed 29 
                 +k+++++C +Cg+ t ed
  EPA04428.1 217 VKDGISYCAECGHETKED 234
                 79***********99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       921  (0.0513693); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1546.29
//
Query:       EPA04429.1  [L=184]
Description: hypothetical protein BG20_I1824 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.55    9.8   7.8       0.75    9.4   7.8    1.2  1  SUR7      SUR7/PalI family


Domain annotation for each model (and alignments):
>> SUR7  SUR7/PalI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   7.8   4.2e-05      0.75     116     202 ..      55     166 ..      35     168 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 4.2e-05
        SUR7 116 filhiialvlsfislvvgllaic.......................vspdnsrl..........lsflnlllsvlsflatllaalldtllfvfvrkkin 181
                 f +++i +++sf  +v +l+a++                       v      +          ++++  +++++++++++l a+ ++ll ++    + 
  EPA04429.1  55 FGFLFIMTIFSFAGIVSSLIANSwfvrnmgiisniekeflkfdadeV------IpkswtlgkvpFLNVENWWTIVALFSAILIAIHVVLLSTVSEADL- 146
                 78888999999999999999887666666666555555555555551......04444555633666666*******************999443333. PP

        SUR7 182 lkefgikaslglkflafaWla 202
                  k++  +++ g+ f++f W++
  EPA04429.1 147 PKQILLDVFGGI-FVGFYWIV 166
                 455555555555.66666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1244.50
//
Query:       EPA04430.1  [L=476]
Description: hypothetical protein BG20_I1829 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.9e-05   22.6   0.1    6.9e-05   22.6   0.1    1.7  2  AAA_lid_2  AAA lid domain
  ------ inclusion threshold ------
      0.047   14.3   0.4       0.29   11.7   0.1    2.3  2  Mga        Mga helix-turn-helix domain
      0.077   12.0   0.1       0.13   11.3   0.1    1.3  1  PAD        Protein-arginine deiminase (PAD)
       0.11   12.5   0.1       0.21   11.5   0.1    1.5  1  TrmB       Sugar-specific transcriptional regulator TrmB


Domain annotation for each model (and alignments):
>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.2         3   1.3e+04      12      18 ..     162     168 ..     160     169 .. 0.87
   2 !   22.6   0.1   1.5e-08   6.9e-05      15      51 ..     310     346 ..     309     351 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 3
   AAA_lid_2  12 gvsgrRa 18 
                 gv+grR+
  EPA04430.1 162 GVHGRRG 168
                 9*****9 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 1.5e-08
   AAA_lid_2  15 grRadlallraArAlAalegrdyVtpeDvkeaaplVL 51 
                 + Ra+ al++ Ar +A l gr+y+t++D+  ++   L
  EPA04430.1 310 PNRASNALYNLARGHAVLCGRNYITDDDLAVVVAVTL 346
                 899**************************98887665 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   6.6e-05      0.29      14      71 ..     349     409 ..     337     415 .. 0.83
   2 ?   -0.9   0.0      0.57   2.6e+03      53      73 ..     424     444 ..     422     448 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.6e-05
                 HHSHHHHHHHHHH.HHSEEEHHHHHHHCT--HHHHHHHHHHHH..HHCHCCT-EEETTCCE CS
         Mga  14 keslkyqllkflf.eeeevsieelaqelyiSestlkrkikeln..klLkefdleltkknlk 71 
                 ++++  +l k l+ ++ ++++e++ ++  +S+st+ +++k l   +l   +d +l++k++k
  EPA04430.1 349 ASRDRVELFKRLLdCNGKQNTEQFMESAKVSRSTALKEMKSLVilELVDMYDEQLETKPVK 409
                 67888999999999999***********************975226677888888777765 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.57
                 HHHHHCHCCT-EEETTCCEEE CS
         Mga  53 elnklLkefdleltkknlklr 73 
                 e++k+++efd +l+ +n kl+
  EPA04430.1 424 EFKKYMREFDATLNPENSKLS 444
                 6799*******9977777765 PP

>> PAD  Protein-arginine deiminase (PAD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   2.8e-05      0.13     242     290 ..     209     257 ..     182     258 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.8e-05
                 ..TTS--EECHHHHC-CCHHHHHHHHHHHHHHHHHHHHHHHT--CCCEE CS
         PAD 242 aekevekvtinelLadeslikenayvqkkidknreilkeelglseedii 290
                  +++++k++i+++L+des +k+ + +++ i++  ++++++ +l+e +ii
  EPA04430.1 209 DSTTEKKRKIKQILKDESYTKKVESAKTAITRFWNVIEKNPQLNEGKII 257
                 56778999*************************************9998 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   4.7e-05      0.21      11      55 ..     354     399 ..     350     414 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.7e-05
                 CCHCHHHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
        TrmB  11 akvYlaLl.klgpatadeiaeelgvprskvYevLrsLedkGlVere 55 
                 ++ ++ Ll ++g+ ++++  e ++v+rs++ + ++sL+   lV+  
  EPA04430.1 354 VELFKRLLdCNGKQNTEQFMESAKVSRSTALKEMKSLVILELVDMY 399
                 578999********************************99999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (476 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       775  (0.0432261); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.25s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 3140.67
//
Query:       EPA04431.1  [L=70]
Description: hypothetical protein BG20_I1823, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.33s 00:00:00.86 Elapsed: 00:00:00.53
# Mc/sec: 396.12
//
Query:       EPA04432.1  [L=52]
Description: toxin-antitoxin system, antitoxin component, ribbon-helix-helix domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      0.009   16.8   0.3      0.011   16.5   0.3    1.2  1  VAPB_antitox  Putative antitoxin


Domain annotation for each model (and alignments):
>> VAPB_antitox  Putative antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.3   6.2e-07     0.011       2      36 ..      12      46 ..      11      51 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.2e-07
  VAPB_antitox  2 tIsIsdevYekLkklKregeSFsdvIerLlekkkk 36
                  tI ++  + ++L +l ++++ F++v++ L+e+k+ 
    EPA04432.1 12 TIVLQKQTRDRLASLAKKDQTFDEVVRLLIEEKEG 46
                  89999999******9999************96653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       641  (0.0357521); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.47
# Mc/sec: 329.99
//
Query:       EPA04433.1  [L=74]
Description: hypothetical protein BG20_I1828 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0055   16.6   0.1     0.0067   16.4   0.1    1.2  1  Sugarporin_N  Maltoporin periplasmic N-terminal extension


Domain annotation for each model (and alignments):
>> Sugarporin_N  Maltoporin periplasmic N-terminal extension
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   3.7e-07    0.0067       6      39 ..      38      72 ..      32      74 .] 0.79

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.7e-07
  Sugarporin_N  6 lalaialllstaasv.aaaasltiEaRLaaLEkrL 39
                  ++  i++l  + + +  +a+++t+E R++ LE r+
    EPA04433.1 38 ISQNIGYLVQVQSGLiKDAEASTLEKRIEELERRM 72
                  555677777777777789***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1010  (0.0563333); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 487.09
//
Query:       EPA04434.1  [L=95]
Description: hypothetical protein BG20_I1825 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.12   12.7   0.1       0.14   12.4   0.1    1.1  1  Type_III_YscX  Type III secretion system YscX (type_III_YscX)


Domain annotation for each model (and alignments):
>> Type_III_YscX  Type III secretion system YscX (type_III_YscX)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1     8e-06      0.14      54     111 ..      12      69 ..       5      79 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8e-06
  Type_III_YscX  54 qaLlelarPelgfheLlrpedfrqaldelrsllqesrsaalqaaaellestqeDerlL 111
                     +L+ l  P ++++ L  p d++  +++ r+llq+    +  ++ e l+ +q++++l 
     EPA04434.1  12 DFLETLTFPTVNNRVLSYPADHKMLINNFRKLLQQNVYYNPDRLKEWLHFHQQENQLQ 69 
                    68999999***************************99998888888888888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       832  (0.0464053); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 630.93
//
Query:       EPA04435.1  [L=222]
Description: hypothetical protein BG20_I1826 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-08   35.2   0.7    6.2e-08   32.9   0.7    1.9  1  Terminase_6C  Terminase RNaseH-like domain


Domain annotation for each model (and alignments):
>> Terminase_6C  Terminase RNaseH-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.7   3.5e-12   6.2e-08       2     152 ..       5     163 ..       4     164 .. 0.84

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 3.5e-12
                   EEE--SSCTTBEEEEEEE.ETTTTCEEEEEEEEESSS-CCCHHHHHHHHHHCTTCEEEEECCSC..HHHHHHHHHHCCT--S-SCEESSH..HHHHH CS
  Terminase_6C   2 gvDpaegrggDyaalvvi.dvkddkfellavlherglspalqaaaikklaerynviyvyieits..aGesvaellkrdlesealavkpepaskdkat 95 
                   g+D a   ++D  alv+i +  ddk++l    ++r+++ +l++++ k+   ++n +++y++ t+  +  ++ ++l ++ +    +v +++   +k++
    EPA04435.1   5 GLDVA--FSNDFMALVIIeQGGDDKIRLRSLDTWRKMDWHLWKESMKEKQSKFNIDEIYVDHTNnqSVVMELQELGMKVQ----GVSFSN--SSKND 93 
                   89***..***********9999***************************************9997788888888888885....899998..***** PP

                   HHHHHHHHHHTTSEEEETHH.....CECCCCCCHCC-EEHCC........HHCHCSGCCTCHHHHHHHHH CS
  Terminase_6C  96 rvskvkdliesgrlkvdkga.....ecaksfealegfhtdlg........aerstsaehdDlvdAlsyal 152
                   ++     l+  g l  +++         k+ ++l  +                  + +hdDl++Al+ al
    EPA04435.1  94 MIRNATKLMVIGELIMPEITrihskKQQKLASELLLQLQEQEikhdsvhpKLMHPKGRHDDLLWALCLAL 163
                   **************99999888888444555555444444445555577433455779********9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       837  (0.0466841); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.51
# Mc/sec: 1318.65
//
Query:       EPA04436.1  [L=282]
Description: hypothetical protein BG20_I1827 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.03   14.0   0.2       0.18   11.4   0.2    2.4  1  Terminase_6  Terminase-like family


Domain annotation for each model (and alignments):
>> Terminase_6  Terminase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2     1e-05      0.18       3     109 ..      69     170 ..      67     266 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1e-05
                  EE-SSS-HHHHHHHHHHHHHHSSSS...-EEEEEESSHHHHHHHHHHHHHHHHTS-T...TTS--EEEE-SSEEEETTS-EEEEES....SHHHHHT. CS
  Terminase_6   3 lggrqsGKTfagarellrhalgrgp..rnqvflsasktqareeggqfekgigelake...ildiefeesaknlvvlsnGaslhflslesetaggiqG. 94 
                   ++r++G+T +++r++l++a++++   r+  ++ + +  + +      ++i++++     i +i++  s++ ++++ n ++++  +++    ++i+G 
   EPA04436.1  69 NKARGIGATEIILRWILFRAVQNKIpgRKFLIVTGIRLGLAR------DHIKRMINLcynIPGIIKQ-SSQYNITI-NNSEVIAIPANP---AAIRGy 155
                  689*******************99876555555544444444......3344443332013444444.44444444.555566666555...677776 PP

                  S--SEEEEESGGGST CS
  Terminase_6  95 aqidliyfDElteip 109
                   ++ +i+ DE+++++
   EPA04436.1 156 ENVEVIFADEAAHWD 170
                  778899999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1816.96
//
Query:       EPA04437.1  [L=363]
Description: site-specific recombinase, phage integrase family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-10   39.9   0.2    3.5e-10   39.9   0.2    1.9  2  Phage_integrase  Phage integrase family
  ------ inclusion threshold ------
       0.14   12.2   1.5       0.37   10.9   0.0    2.4  2  F-112            F-112 protein


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   0.2   3.9e-14   3.5e-10       3     135 ..     129     255 ..     127     260 .. 0.93
   2 ?   -2.4   0.1      0.39   3.5e+03      52      84 ..     317     351 ..     309     357 .. 0.52

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 3.9e-14
                      HHHHHHHHHHHCCGCHHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEE..EEECSSSSEEEEECTHHHHHHHHHHHHHHCHCCTTT CS
  Phage_integrase   3 ltedeverllaaleeslkirdklllellyetGlRisEllsLrvkdldlengvilvh..eregKgskeravplseealellkellskaleeaeks 94 
                      lt +e+++++a +      r+  +   l +tG+R +Ell+ r kd+d+ ++++++   +++ K++  r v l++ea +ll + l++     +++
       EPA04437.1 129 LTLEEIQKIFAVSLP----RRTGFYLALISTGARPGELLQVRKKDIDTTQKRVKIRieAENVKTRSGRSVWLTREASKLLLTRLKDL----SDN 214
                      788999999999999....99999****************************99988799***************************....999 PP

                      SBSSBETTSSB--HHHHHHHHHHHHHHCT-SSC--TTHHHH CS
  Phage_integrase  95 ellfaskrgkplsrqtvrkafkraveeagiekpltpHtlRh 135
                      +l+ a  ++    +++ +++f+++  eag +++ +++ +R 
       EPA04437.1 215 DLIWATNENPAHAEKAESTMFNKYTTEAGFTQKYKSNGFRM 255
                      999999988888899999********************995 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.39
                      TTEEEEE.EEECSSSSEEEEE.CTHHHHHHHHHHH CS
  Phage_integrase  52 ngvilvh.eregKgskeravp.lseealellkell 84 
                      ++ i++h  ++ K + + ++p l +ea+e lk+ +
       EPA04437.1 317 RQKIMIHqLEQEKLEMKKQIPsLVNEAVERLKKEM 351
                      44555554344444444444424466666666554 PP

>> F-112  F-112 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1      0.56   5.1e+03      59      80 ..       7      29 ..       5      45 .. 0.49
   2 ?   10.9   0.0   4.1e-05      0.37      17      78 ..     124     185 ..     117     195 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.56
                EE-SS-EEE.EE--XXXXXXXXX CS
       F-112 59 qkknrktvf.kwikqeqkeeqkq 80
                 kknrk+   k  k   k  q+ 
  EPA04437.1  7 EKKNRKSFEdKVSKLSIKTRQNI 29
                45666654212223333333333 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 4.1e-05
                 HHHSEE-HHHHHHHH---HHHHHHHHHHHHHHHHH-TTTEEEEE-SS-EEEEE--XXXXXXX CS
       F-112  17 ekkkeltledilaqfeisvssayaiqralkaicerhqdecevqkknrktvfkwikqeqkeeq 78 
                 e+  eltle+i  +f +s +     + al     r  +  +v kk+  t+ k +k   + e+
  EPA04437.1 124 EELHELTLEEIQKIFAVSLPRRTGFYLALISTGARPGELLQVRKKDIDTTQKRVKIRIEAEN 185
                 5678**************************9999999999**********999997655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1053  (0.0587317); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 2300.36
//
Query:       EPA04438.1  [L=53]
Description: hypothetical protein BG20_I2614, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.042   13.7   0.6        7.7    6.5   0.1    2.3  2  HSBP1      Heat shock factor binding protein 1
      0.068   13.3   5.2          7    7.2   0.1    3.4  2  KID        KID repeat
        0.1   12.9   0.7        3.4    8.0   0.1    2.0  2  DUF1922    Domain of unknown function (DUF1922)
       0.17   12.5   5.8       0.27   11.9   0.8    2.0  2  GTP-bdg_M  GTP-binding GTPase Middle Region
       0.54    9.7   7.1       0.51    9.7   1.2    2.0  2  HNOBA      Heme NO binding associated


Domain annotation for each model (and alignments):
>> HSBP1  Heat shock factor binding protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1    0.0022       7.7      35      46 ..      13      24 ..       4      29 .. 0.81
   2 ?    6.0   0.1     0.003        11      35      46 ..      34      45 ..      30      49 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0022
       HSBP1 35 riDdLEksiadl 46
                + D+LEk++a++
  EPA04438.1 13 KTDELEKNLATV 24
                569999999875 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.003
       HSBP1 35 riDdLEksiadl 46
                + D+LEk++a++
  EPA04438.1 34 KTDELEKNLATV 45
                569*****9975 PP

>> KID  KID repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1     0.002         7       1       9 [.      13      21 ..      13      23 .. 0.86
   2 ?    7.2   0.1     0.002       7.1       1       9 [.      34      42 ..      34      44 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.002
         KID  1 KIDsVEKNL 9 
                K D  EKNL
  EPA04438.1 13 KTDELEKNL 21
                77999***9 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.002
         KID  1 KIDsVEKNL 9 
                K D  EKNL
  EPA04438.1 34 KTDELEKNL 42
                77999***9 PP

>> DUF1922  Domain of unknown function (DUF1922)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1     0.011        38      29      46 ..       3      20 ..       1      25 [. 0.81
   2 ?    8.0   0.1   0.00094       3.4      28      48 ..      23      43 ..      21      49 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.011
                EE--SSS-BS--SSHHHH CS
     DUF1922 29 ikvkerrilkkaedaeeA 46
                i++++++i++k+++ e+ 
  EPA04438.1  3 IELEKKKIFEKTDELEKN 20
                8999********998875 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00094
                EEE--SSS-BS--SSHHHHHH CS
     DUF1922 28 tikvkerrilkkaedaeeAse 48
                t+++++rri++k+++ e+   
  EPA04438.1 23 TVELEKRRIFEKTDELEKNLA 43
                6899*********99887655 PP

>> GTP-bdg_M  GTP-binding GTPase Middle Region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.7    0.0046        16      47      69 ..       3      25 ..       1      28 [. 0.91
   2 ?   11.9   0.8   7.5e-05      0.27      47      74 ..      24      51 ..      22      53 .] 0.91

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0046
                XHHHHHHHHHHHHHHHHHHHHHH CS
   GTP-bdg_M 47 leldrrlireriaklkkeLekvk 69
                +el++++i e+ ++l+k+L+ v+
  EPA04438.1  3 IELEKKKIFEKTDELEKNLATVE 25
                799****************9997 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 7.5e-05
                XHHHHHHHHHHHHHHHHHHHHHHHHHH. CS
   GTP-bdg_M 47 leldrrlireriaklkkeLekvkkkrel 74
                +el++r+i e+ ++l+k+L+ v+ +r+ 
  EPA04438.1 24 VELEKRRIFEKTDELEKNLATVELERKS 51
                79********************999975 PP

>> HNOBA  Heme NO binding associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   1.2   0.00014      0.51     178     205 ..       4      31 ..       1      33 [. 0.88
   2 ?    4.5   0.5    0.0055        20     186     204 ..      33      51 ..      30      53 .] 0.87

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00014
       HNOBA 178 elaldqleeksaeLeesmkeleeekkrt 205
                 el +++  ek++eLe++++ +e ek+r+
  EPA04438.1   4 ELEKKKIFEKTDELEKNLATVELEKRRI 31 
                 67778899******************96 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0055
       HNOBA 186 eksaeLeesmkeleeekkr 204
                 ek++eLe++++ +e e+k 
  EPA04438.1  33 EKTDELEKNLATVELERKS 51 
                 79************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       894  (0.0498633); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 346.92
//
Query:       EPA04439.1  [L=142]
Description: hypothetical protein BG20_I2613, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
        3.4    8.3  23.8        1.6    9.4   1.4    3.9  4  GTP-bdg_M     GTP-binding GTPase Middle Region


Domain annotation for each model (and alignments):
>> GTP-bdg_M  GTP-binding GTPase Middle Region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   1.5    0.0017        30      45      74 ..       6      35 ..       5      39 .. 0.92
   2 ?    5.1   1.8    0.0019        34      50      75 ..      50      75 ..      45      78 .. 0.87
   3 ?    6.4   1.9   0.00074        13      47      73 ..      68      94 ..      66      99 .. 0.91
   4 ?    9.4   1.4     9e-05       1.6      44      69 ..     113     138 ..      98     142 .] 0.85

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0017
                XXXHHHHHHHHHHHHHHHHHHHHHHHHHH. CS
   GTP-bdg_M 45 tkleldrrlireriaklkkeLekvkkkrel 74
                t++e +r+ + ++ ++l+k+L+ v+ +r++
  EPA04439.1  6 TEVEQERKNVVQKSDELEKNLATVELERKH 35
                789*********************999986 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0019
                HHHHHHHHHHHHHHHHHHHHHHHH.. CS
   GTP-bdg_M 50 drrlireriaklkkeLekvkkkrelq 75
                +r  i++++++l+++L++++ +re  
  EPA04439.1 50 ERTNISKKEKELQENLAAIEIEREKI 75
                6889****************999865 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.00074
                XHHHHHHHHHHHHHHHHHHHHHHHHHH CS
   GTP-bdg_M 47 leldrrlireriaklkkeLekvkkkre 73
                +e++r +i++++++l++++++v+ +r+
  EPA04439.1 68 IEIEREKISQKEEELESRIAAVELERR 94
                89********************98886 PP

  == domain 4  score: 9.4 bits;  conditional E-value: 9e-05
                 XXXXHHHHHHHHHHHHHHHHHHHHHH CS
   GTP-bdg_M  44 etkleldrrlireriaklkkeLekvk 69 
                 e+ +el+r+ i++++++lk+ +++v+
  EPA04439.1 113 ESMIELERKNISQKEEELKNSIAAVE 138
                 899*******************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2247  (0.125328); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.68u 0.33s 00:00:01.01 Elapsed: 00:00:00.51
# Mc/sec: 833.14
//
Query:       EPA04440.1  [L=246]
Description: transketolase, C-terminal domain protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.2e-31  106.6   0.0    9.7e-31  106.2   0.0    1.2  1  Transketolase_C  Transketolase, C-terminal domain
    1.2e-13   51.1   0.0    1.8e-13   50.6   0.0    1.2  1  Transket_pyr     Transketolase, pyrimidine binding domain
      0.003   17.8   0.0     0.0056   17.0   0.0    1.4  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma


Domain annotation for each model (and alignments):
>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.2   0.0   1.6e-34   9.7e-31       1     111 [.     111     218 ..     111     234 .. 0.93

  Alignments for each domain:
  == domain 1  score: 106.2 bits;  conditional E-value: 1.6e-34
                      TEEEEEETTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSHHHHHHHHHHHCCCTTCSS CS
  Transketolase_C   1 gkaeilregkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavkrgGigsevaaalaeeafdglda 94 
                      gk+ +lr+g+d t+ a G +v++aleAa+ L++egis++V+d++++kp+D e++++++++tg +v+ e+++++gG+gs+va+ ++e    + ++
       EPA04440.1 111 GKGITLRDGSDCTIAACGITVRMALEAADSLNQEGISCRVLDMFSIKPIDAELLEKAARETGGIVTCEDHNIMGGMGSAVAESVSE----RYPV 200
                      78899*********************************************************************************....99** PP

                      EEEEEEE-SS.SSSSGHH CS
  Transketolase_C  95 pvkrvggpdv.iepgsae 111
                      p+kr+g+ d+ +e++   
       EPA04440.1 201 PIKRIGAQDMfGESARDN 218
                      **********99999844 PP

>> Transket_pyr  Transketolase, pyrimidine binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.6   0.0     3e-17   1.8e-13      88     176 ..      10      99 ..       1     100 [. 0.89

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 3e-17
                   G..HHGGHHHHHCHHHHHT--EE.EEESBSGGGSTTGTTTSBSSHHHHHHTSTTEEEE--SSHHHHHHHHHHHHHSSS.SEEEEEE-SSEEC CS
  Transket_pyr  88 A..qiyadqairsgeakgklkvg.vvtrlpigvgedGpehqsaeleaflrlipglkvvrPsdpaetkhllrrairredrkPvvlrlpksllr 176
                   A  qi++  a  s   k++l+v+ vv + +++vg dG +hq +e++a++r+ip+++v+ P+d   + +l r  ++  + +P ++r+ +s+++
    EPA04440.1  10 AvdQIRNGIAYPSSGNKKGLNVKlVVSHGGLSVGPDGGSHQQIEDIAIMRAIPNFRVFIPADTFAVSKLTRLMAN--EYGPFYMRMARSNTP 99 
                   36688888888888899**********************************************************..569*********986 PP

>> PFOR_II  Pyruvate:ferredoxin oxidoreductase core domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   9.3e-07    0.0056       2      81 ..     121     197 ..     120     214 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 9.3e-07
                 SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHHTGGG CS
     PFOR_II   2 evvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaalkks 81 
                 +  i a G++++ a +a+d+l +egi+  +l + ++ P  +e l+++++++  +v+ +  + +g    +++ v+++++++
  EPA04440.1 121 DCTIAACGITVRMALEAADSLNQEGISCRVLDMFSIKPIDAELLEKAARETGGIVTCEDHNIMGG---MGSAVAESVSER 197
                 678999**************************************************998885555...555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1561.43
//
Query:       EPA04441.1  [L=55]
Description: hypothetical protein BG20_I2547, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-09   37.0   0.0    2.5e-09   36.9   0.0    1.0  1  TAL_FSA   Transaldolase/Fructose-6-phosphate aldolase


Domain annotation for each model (and alignments):
>> TAL_FSA  Transaldolase/Fructose-6-phosphate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.0   1.4e-13   2.5e-09       1      49 [.       3      51 ..       3      54 .. 0.90

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 1.4e-13
                EEEE---HHHHHHHHHTT---EEE--HHHHHH..TTS.-HHHHHHHHHH CS
     TAL_FSA  1 lvlDtadrelikklleekgiqgvTtNPsliekaikykalydeaieeikk 49
                ++lDta++e+i+k+ + + ++g+TtNPsl++k+  + +++ e+i++i k
  EPA04441.1  3 IFLDTANLEAIRKFNDMGLLDGITTNPSLLSKEGGNPKDVMEEIANIIK 51
                79******************************88888888888887764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       234  (0.0130515); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 349.86
//
Query:       EPA04442.1  [L=193]
Description: protein-L-isoaspartate O-methyltransferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.4e-57  192.1   0.0    1.1e-56  191.9   0.0    1.0  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    3.6e-09   36.6   0.0      7e-09   35.7   0.0    1.5  2  Methyltransf_31  Methyltransferase domain
    2.4e-08   33.8   0.0    5.8e-08   32.6   0.0    1.5  2  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
    3.4e-08   32.9   0.0    5.7e-08   32.1   0.0    1.3  1  RrnaAD           Ribosomal RNA adenine dimethylase
    6.2e-07   30.0   0.0    2.2e-06   28.3   0.0    1.7  2  Methyltransf_25  Methyltransferase domain
    3.1e-05   24.5   0.0    5.2e-05   23.8   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    6.8e-05   22.7   0.0    0.00013   21.7   0.0    1.4  1  GCD14            tRNA methyltransferase complex GCD14 subunit
      7e-05   22.2   0.1    0.00031   20.1   0.0    1.8  2  GidB             rRNA small subunit methyltransferase G
    0.00025   20.5   0.0    0.00048   19.7   0.0    1.5  2  Methyltransf_4   Putative methyltransferase
    0.00042   19.9   0.0    0.00081   19.0   0.0    1.4  1  MTS              Methyltransferase small domain
     0.0022   17.3   0.0     0.0033   16.7   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
      0.003   16.9   0.0     0.0043   16.4   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
     0.0095   15.1   0.0      0.014   14.5   0.0    1.2  1  Fibrillarin      Fibrillarin
  ------ inclusion threshold ------
      0.023   14.7   0.0      0.037   14.0   0.0    1.3  1  Methyltransf_32  Methyltransferase domain
      0.036   13.8   0.0      0.054   13.2   0.0    1.2  1  DUF938           Protein of unknown function (DUF938)
      0.062   12.8   0.0       0.11   12.0   0.0    1.3  1  DOT1             Histone methylation protein DOT1
      0.084   12.6   0.0       0.13   12.0   0.0    1.3  1  Methyltransf_16  Lysine methyltransferase
      0.089   13.8   0.0       0.15   13.1   0.0    1.4  1  Methyltransf_24  Methyltransferase domain
       0.17   11.6   0.0       0.23   11.2   0.0    1.2  1  Met_10           Met-10+ like-protein


Domain annotation for each model (and alignments):
>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.9   0.0   1.2e-59   1.1e-56       4     186 ..      12     192 ..       9     193 .] 0.98

  Alignments for each domain:
  == domain 1  score: 191.9 bits;  conditional E-value: 1.2e-59
                 HHHHHHHHHTTS---HHHHHHHHHS-GGGGSSCGGGGGTTSSS-EEEETTEEE--HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEE CS
        PCMT   4 ealieelkkkgviksdkvaealeevdReefvpesfkekaYedaplsigynatiSaphmvalalellelkkgarvLevGsGsGyltavlarlvgekgrvv 102
                 ++li+ +kk+g+++++k+  a+++ +R+efvp+s+ ek+Y+d+p++i  n+tiS+p++v++++e+l++k+g+++Le+GsGsG++ta+la lvg+   v 
  EPA04442.1  12 DHLISVMKKSGFLNDKKIELAIRNAPRHEFVPSSLIEKTYDDSPIQIMKNQTISQPSVVSRMTEWLDVKEGQKILEIGSGSGWQTAILAYLVGHGI-VY 109
                 799******************************************************************************************977.** PP

                 EEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTTGGG-SEEEEEESSBBSS--HHHHHTEEEEEEEEEEESBSSSEEEEEEEE CS
        PCMT 103 sierikelveeakrnlkkldlenvivvvgDGrkGyeekaPYdaihvgaaapeiPealidQLkeGGrlvvPvgeeeeQvlklvdk 186
                 sier +el+e ak+nl kl+++nv+v+ gDG  G++e++P+d+i+++aa ++iP++l++QL   G l++Pvg  + Q + l++k
  EPA04442.1 110 SIERHAELAEFAKKNLDKLGIHNVKVISGDGSFGFPEESPFDRIIITAACKKIPDSLLEQLSINGLLIAPVG-GYPQSMILLKK 192
                 ************************************************************************.9***9999988 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       8.8   8.3e+03      38      53 ..      26      41 ..      24      48 .. 0.78
   2 !   35.7   0.0   7.4e-12     7e-09       3      89 ..      81     164 ..      79     178 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 8.8
  Methyltransf_31 38 eeaielArenaqklgl 53
                      + ielA  na ++++
       EPA04442.1 26 DKKIELAIRNAPRHEF 41
                     5678889888888876 PP

  == domain 2  score: 35.7 bits;  conditional E-value: 7.4e-12
  Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDlilsnevlnalad 89 
                      +g ++l++G+G+G  t  la +   ++ v++i++ +e  e+A++n++klg+ nv++  gd    +++    ++fD i+  +++  ++d
       EPA04442.1  81 EGQKILEIGSGSGWQTAILAYL-VGHGIVYSIERHAELAEFAKKNLDKLGIHNVKVISGDGSFgFPEE---SPFDRIIITAACKKIPD 164
                      6789****************55.55799********************************9999**54...99****99776655555 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0         3   2.8e+03     117     134 ..       7      24 ..       2      46 .. 0.77
   2 !   32.6   0.0   6.2e-11   5.8e-08       3      89 ..      76     159 ..      74     162 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3
                      HHHHHHHHCCCEEEEEEE CS
  Methyltr_RsmB-F 117 qkellsaaidllkkgGvl 134
                       ++ l+ +i ++kk G+l
       EPA04442.1   7 YQQKLDHLISVMKKSGFL 24 
                      455577777777777776 PP

  == domain 2  score: 32.6 bits;  conditional E-value: 6.2e-11
                      HH---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC..EEEEEEEE-- CS
  Methyltr_RsmB-F   3 lLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggelfDriLlDaPC 89 
                      +L+ +e+++il++ ++ G +T+ +a l   +g v+ +++++e ++  ++nl +Lg++n++v+++D++    +  ++ fDri++ a C
       EPA04442.1  76 WLDVKEGQKILEIGSGSGWQTAILAYL-VGHGIVYSIERHAELAEFAKKNLDKLGIHNVKVISGDGSFG--FPEESPFDRIIITAAC 159
                      899***********************9.6789**********************************976..666777********99 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.0     6e-11   5.7e-08      14      85 ..      65     140 ..      56     159 .. 0.88

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 6e-11
                 --HHHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-..SEEEEE-S-HHHHHHHHCHTT..TCCCEEEE-S-C CS
      RrnaAD  14 knkkvineIldklnleekltvleigpGkGilTeeLakra..kqvvvlElderLakllqkkls..kdeklkvvhqDf 85 
                   ++v+ +  + l+++e +++leig+G G +T++La  +    v ++E   +La++ +k+l     +++kv+  D+
  EPA04442.1  65 SQPSVVSRMTEWLDVKEGQKILEIGSGSGWQTAILAYLVghGIVYSIERHAELAEFAKKNLDklGIHNVKVISGDG 140
                 568899999999***************************8777889*************9998889*******997 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       3.8   3.6e+03      63      91 ..       9      38 ..       3      39 .. 0.74
   2 !   28.3   0.0   2.3e-09   2.2e-06       1      79 [.      85     164 ..      85     171 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 3.8
                     TTEEEEEEEST.GGGSSHHHHHHHHHHHHH CS
  Methyltransf_25 63 gsfDlvvssga.lhhlsdedlekalkeiar 91
                     ++ D  +s++    +l+d+++e a++++ r
       EPA04442.1  9 QKLDHLISVMKkSGFLNDKKIELAIRNAPR 38
                     567888887777778888888888888765 PP

  == domain 2  score: 28.3 bits;  conditional E-value: 2.3e-09
                      EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCG.BSSSTTTEEEEEEESTGGGSSH CS
  Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaed.lpfedgsfDlvvssgalhhlsd 79 
                      +L++G G+G  t+ la  +g++ v+ ++  +e+ e a++++++ g+ nv+++ gd +  +p e++ fD ++++ a   ++d
       EPA04442.1  85 ILEIGSGSGWQTAILAYLVGHGIVYSIERHAELAEFAKKNLDKLGIhNVKVISGDGSFgFP-EESPFDRIIITAACKKIPD 164
                      8***************99999*********************9999*********966255.566******9755655554 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   5.5e-08   5.2e-05       1      74 [.      86     162 ..      86     170 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 5.5e-08
                      EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT-.EEEEEEES-CCC- CS
  Methyltransf_11   1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseegl.kvefvvadaeklpfedns.fDlvvssevlhhv 74 
                      L++G+G+G  ++ la  +  + v+ ++  +e+ + ak++  + g+ +v+++ +d + + f+++s fD ++++ +   +
       EPA04442.1  86 LEIGSGSGWQTAILAYLVghGIVYSIERHAELAEFAKKNLDKLGIhNVKVISGDGS-FGFPEESpFDRIIITAACKKI 162
                      89*************555699**********************************9.89999744***9999987766 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   1.4e-07   0.00013      29      95 ..      70     134 ..      56     148 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.4e-07
       GCD14  29 isliimkLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvt 95 
                 +s ++  L++k+G +++e G Gsg   +ai+  +   G ++++e h++ ae+a++++ + ++++ v+
  EPA04442.1  70 VSRMTEWLDVKEGQKILEIGSGSGWQ-TAILAYLVGHGIVYSIERHAELAEFAKKNLDKLGIHN-VK 134
                 5778889****************975.6677777789********************9999864.44 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0      0.49   4.7e+02      78      99 ..      14      35 ..       5      52 .. 0.82
   2 !   20.1   0.0   3.2e-07   0.00031      42     125 ..      76     159 ..      56     186 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.49
                EES-HHHHHHHHHHHHHCT-SS CS
        GidB 78 leslekkiaFLeevkeelklen 99
                l s  kk  FL+  k el++ n
  EPA04442.1 14 LISVMKKSGFLNDKKIELAIRN 35
                557889999**99999999887 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 3.2e-07
                 GGCS-CCC-.EEEETSTTTTTHHHHHHH-TTSEEEEEES-HHHHHHHHHHHHHCT-SSEEEEES-CCC.TTTTT-EEEEEEC-SS CS
        GidB  42 lellkekrdkviDvGsGaGlPGipLaiarpelkltLleslekkiaFLeevkeelklenveivearaee.kqeeekydvvtsRAla 125
                 +  +ke + k++ +GsG G    +La +  +  ++ +e++   ++F ++   +l+++nv+++  +    + ee+++d +++ A +
  EPA04442.1  76 WLDVKEGQ-KILEIGSGSGWQTAILAYLVGHGIVYSIERHAELAEFAKKNLDKLGIHNVKVISGDGSFgFPEESPFDRIIITAAC 159
                 44566666.7*****************************************************9988789999999999998766 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       5.6   5.2e+03      99     113 ..      10      24 ..       5      37 .. 0.63
   2 !   19.7   0.0     5e-07   0.00048       4      60 ..      84     140 ..      81     162 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 5.6
                     HHHHHHHHEEEEEEE CS
  Methyltransf_4  99 llkelarvLkkgGvl 113
                      l++l +v+kk+G+l
      EPA04442.1  10 KLDHLISVMKKSGFL 24 
                     445555555555554 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 5e-07
                     EEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-C CS
  Methyltransf_4   4 vvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgda 60 
                      +leiG+G+G+ +  lA    +  +  iE + ++ + + k+ ++l+++N++++ gd 
      EPA04442.1  84 KILEIGSGSGWQTAILAYLVGHGIVYSIERHAELAEFAKKNLDKLGIHNVKVISGDG 140
                     589***************************************************997 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   8.6e-07   0.00081      24     102 ..      74     154 ..      69     156 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 8.6e-07
                 HHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTST.TS-EEEEE CS
         MTS  24 letlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleeve.ekkfdliv 102
                  e l+ ++ +k+l +G+G G  +a la    +  v  ++ +a+  e+ak+nl + +++ v+v+  d+   ++ e  fd i+
  EPA04442.1  74 TEWLDVKEGQKILEIGSGSGWQTAILAYLVGHGIVYSIERHAELAEFAKKNLDKLGIHnVKVISGDGSFGFPeESPFDRII 154
                 5678888999***********************************************99*******999887355688887 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   3.5e-06    0.0033      49     133 ..      68     155 ..      59     168 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.5e-06
                 HHHHHHHTTTT--TT-EEEEES-TTS..HHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG---..--SEEEE CS
        CMAS  49 aKldlileklelkpGmtlLdiGcGWG..slvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedlde..kvdrvvs 133
                 + + ++ e l++k+G+++L+iG G G  + +      +   v ++   +e a+ akk++d+l++++ + ++  +   ++e  ++dr++ 
  EPA04442.1  68 SVVSRMTEWLDVKEGQKILEIGSGSGwqTAILAYLVGH-GIVYSIERHAELAEFAKKNLDKLGIHNVKVISGDGSFGFPEesPFDRIII 155
                 556788899************98755104444333332.347888889999999**********9999999999999998889999975 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   4.5e-06    0.0043      42     132 ..      76     165 ..      48     176 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4.5e-06
                      H--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES-GGG-S-H CS
  Ubie_methyltran  42 lvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtvsfGlrnvtDk 132
                         vk+g+k+l++ +G+g  ++ l+  vg +g v  ++  +++ + ++k l + g  n++ + +++     e+  fD + ++   + ++D 
       EPA04442.1  76 WLDVKEGQKILEIGSGSGWQTAILAYLVG-HGIVYSIERHAELAEFAKKNLDKLGIHNVKVISGDGSFGFPEESPFDRIIITAACKKIPDS 165
                      55689*************88888888777.68999*****************************997655556789*99999999998886 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   1.5e-05     0.014      64     104 ..      75     114 ..      65     130 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.5e-05
                  S--S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESS CS
  Fibrillarin  64 kelpikkgskvLYlGaasGttvsHvsDivgeegvvyavefs 104
                  + l +k+g+k+L +G++sG   + ++ +vg +g+vy++e  
   EPA04442.1  75 EWLDVKEGQKILEIGSGSGWQTAILAYLVG-HGIVYSIERH 114
                  44679*************************.9******964 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   3.9e-05     0.037      12      75 ..      69     129 ..      60     142 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.9e-05
  Methyltransf_32  12 lvakllkelakesgaltvvDvGaGkgYLsfvlalkeke.yklkvvgidakeelvekaekraeklg 75 
                      +v+++++   + ++ ++++++G+G g+ + +la+      +  v++i+ ++el+e a+k  +klg
       EPA04442.1  69 VVSRMTEW-LDVKEGQKILEIGSGSGWQTAILAY---LvGHGIVYSIERHAELAEFAKKNLDKLG 129
                      55665555.57788899*****************...5368889**************9999998 PP

>> DUF938  Protein of unknown function (DUF938)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   5.7e-05     0.054      24      78 ..      80     134 ..      61     137 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.7e-05
      DUF938  24 kttervLEiasGtGqHAvffApalpnlkwqpsdqdeelresiaawadelalsnlk 78 
                 k+++++LEi+sG+G   + +A ++ +    + + + el e  ++ +d+l+++n+k
  EPA04442.1  80 KEGQKILEIGSGSGWQTAILAYLVGHGIVYSIERHAELAEFAKKNLDKLGIHNVK 134
                 34458******************99999999999999999999999999999987 PP

>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00012      0.11      28      88 ..      67     127 ..      64     136 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
                 HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHH--SEEEEEE--HHHHHHHHHHHHH CS
        DOT1  28 peflsevldkvnlkkedvFvDLGSGvGnvvlqaalevgcklsvGvEimdnaselaekqkee 88 
                 p+++s++ + +++k+ +  +++GSG G  +   a  vg    + +E   + +e+a+k+ + 
  EPA04442.1  67 PSVVSRMTEWLDVKEGQKILEIGSGSGWQTAILAYLVGHGIVYSIERHAELAEFAKKNLDK 127
                 78999**************************************************998765 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00014      0.13      45      91 ..      80     127 ..      57     138 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
  Methyltransf_16  45 lsklsvlELGsGtGlvGlavaellpeakvi.ltDleellellkkniel 91 
                       +++++lE+GsG+G    ++a l+++  v+ +    el e+ kkn++ 
       EPA04442.1  80 KEGQKILEIGSGSGWQTAILAYLVGHGIVYsIERHAELAEFAKKNLDK 127
                      57899************99**9996555552777888********987 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00016      0.15       1      58 [.      86     140 ..      86     170 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00016
  Methyltransf_24   1 vEiGvysGvstlwllralrrngagrlvavdhdpgaeeaaalare...aglddrvrlikads 58 
                      +EiG+ sG+ t++l++++ + g   +++++ ++   e a++a++   +   ++v++i++d 
       EPA04442.1  86 LEIGSGSGWQTAILAYLVGH-G--IVYSIERHA---ELAEFAKKnldKLGIHNVKVISGDG 140
                      7*************977654.4..49*******...7777777655333334588888775 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00025      0.23      98     176 ..      79     157 ..      61     170 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00025
                 --TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG.---TT-EEEEEE-- CS
      Met_10  98 veegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgre.vireqladrvvmnl 176
                 v+eg+ ++++  G G  +  +a +    +v++i+   e  ++ k+n+    +++ vk+i +Dg   + +e+ +dr+++ +
  EPA04442.1  79 VKEGQKILEIGSGSGWQTAILAYLVGHGIVYSIERHAELAEFAKKNLDKLGIHN-VKVISGDGSFgFPEESPFDRIIITA 157
                 99**************99999999999*******************98887765.78*****99725559999**99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1508.18
//
Query:       EPA04443.1  [L=58]
Description: hypothetical protein BG20_I2459 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0073   16.3   0.2     0.0077   16.2   0.2    1.1  1  FlpD         Methyl-viologen-reducing hydrogenase, delta subu
  ------ inclusion threshold ------
      0.099   13.4   0.0       0.12   13.1   0.0    1.1  1  LZ_Tnp_IS66  Transposase C of IS166 homeodomain


Domain annotation for each model (and alignments):
>> FlpD  Methyl-viologen-reducing hydrogenase, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.2   8.6e-07    0.0077      71     114 ..      13      56 ..       4      58 .] 0.92

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 8.6e-07
        FlpD  71 nekaerrveklkelleelgiepeRvrleevsaaegekfaevike 114
                 ne  + r++k++e  ++l+ ++ R+++e+v ++e ek+++v+ke
  EPA04443.1  13 NEIRDIRFSKMSESEKQLKCDNLRLEFEHVMIEEEEKVVKVMKE 56 
                 66677899**********************************98 PP

>> LZ_Tnp_IS66  Transposase C of IS166 homeodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.4e-05      0.12       5      44 ..      11      51 ..       8      56 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.4e-05
  LZ_Tnp_IS66  5 qlallkrklFGrsSE.ltardpeQleLaleeleaeeaevea 44
                  ++  +  +F ++SE  ++   + l L++e +  ee+e   
   EPA04443.1 11 IVNEIRDIRFSKMSEsEKQLKCDNLRLEFEHVMIEEEEKVV 51
                 67888999*******86677778888899999988888655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1003  (0.0559429); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 399.73
//
Query:       EPA04444.1  [L=37]
Description: hypothetical protein BG20_I2460, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       249  (0.0138881); expected 358.6 (0.02)
Passed bias filter:                      206  (0.0114898); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 277.98
//
Query:       EPA04445.1  [L=40]
Description: hypothetical protein BG20_I2457 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 301.72
//
Query:       EPA04446.1  [L=184]
Description: hypothetical protein BG20_I2219, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      0.004   17.5   1.7     0.0069   16.7   1.7    1.4  1  Calycin_like  Calycin-like beta-barrel domain


Domain annotation for each model (and alignments):
>> Calycin_like  Calycin-like beta-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   1.7   3.8e-07    0.0069      10     115 ..      20     132 ..      17     140 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.8e-07
                   EEEETTEE---B-S-EEEEEE-SSS-EE.....EEEE-GG..G------EEEEEEEEE-SSSSSBEEEEEEEEE-TT--E.....EEEEEE.EEE.E CS
  Calycin_like  10 svsvggeespsdadakvtitknedgtvn.....lsLknfs.fgelplGditvdnvkvtkeggsyttfsgsqkltlagggdaee..atvsls.Gti.s 96 
                    v++++e++++d+++++ i+ +++g++        +++f  ++++++Gdi vd++ vt++  +y  f g+ +    ++g +++  + v+ + G + s
    EPA04446.1  20 GVQITSEKNTKDKKETIEISFDNNGSIIadkkcCVIEKFMyLTPIKIGDILVDDLIVTSDA-TY-EFDGKSRRVWIAQGVKKQdtLIVDKQtGLVlS 114
                   5899999999999999999999998886111114556666666****************97.77.88887766655555555557556555576666 PP

                   TTEEEEEEEEE..ETT-SS CS
  Calycin_like  97 gkklnltitikvkdgamtm 115
                   ++  ++ ++ik+ d+++ m
    EPA04446.1 115 DSHKETGLNIKW-DKTELM 132
                   666666666666.444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       781  (0.0435607); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1168.37
//
Query:       EPA04447.1  [L=160]
Description: RDD family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-17   64.1   2.0      2e-17   63.7   2.0    1.1  1  RDD       RDD family


Domain annotation for each model (and alignments):
>> RDD  RDD family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.7   2.0   1.1e-21     2e-17       2     139 ..      13     137 ..      12     139 .. 0.86

  Alignments for each domain:
  == domain 1  score: 63.7 bits;  conditional E-value: 1.1e-21
         RDD   2 aslgrRllAfliDlvllliislllallivallnakasaneavagslllllllvlllvllvyqllllskkgqTlGklllglkvvdedgrklglaqaliRa 100
                 a+++ R++A+liD+v++++is +++  i+    ++  ++ +      +  ++   ++++ y+++l++ kgqT+Gk++l lk+++  g+k++l+  li +
  EPA04447.1  13 AKWSERFFAWLIDFVIISVISTIAISSIFG---SIDYDFNEKFFWAEMTQFIPTSVIFFGYWVILEYLKGQTIGKKILNLKITNMYGKKPDLKGILISS 108
                 89***********************99999...67889999999999999999999****************************************998 PP

         RDD 101 lllllllvlglslvlllllligflfvlfsrkrqalhDkl 139
                 +          +  +ll + +g+ +++ ++ rq++  k+
  EPA04447.1 109 F----------GKTFLLPIDVGLGWIFTNEMRQRIFNKI 137
                 7..........4555555555666666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       794  (0.0442858); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.33s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 976.11
//
Query:       EPA04448.1  [L=277]
Description: methyltransferase domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-10   41.9   0.0    2.2e-10   41.1   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    4.2e-05   24.2   0.0    6.8e-05   23.5   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    0.00028   20.7   0.0    0.00046   20.0   0.0    1.4  1  Methyltransf_31  Methyltransferase domain
      0.003   17.5   0.0     0.0084   16.0   0.0    1.9  1  Methyltransf_8   Hypothetical methyltransferase
     0.0035   18.1   0.0      0.006   17.3   0.0    1.4  1  Methyltransf_12  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   0.0   6.1e-14   2.2e-10       1      95 [.      77     168 ..      77     169 .. 0.87

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 6.1e-14
                      EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHHHHHHHHHHEEEEE CS
  Methyltransf_11   1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedpekalkeiaRvLkpgG 92 
                      +dvG+G  + a  + +++   ++++++++  +l  +     +++ ++ f  ++ +klpf+dns+D v++ e+ +h++ +++++ e +R+Lk +G
       EPA04448.1  77 VDVGSGLSAPAIFWRDKYekLDLFCININYDQLSFS-----GPQKNIHFFNSTSTKLPFADNSVDRVLALESSQHFKPLKDFILESKRILKSNG 165
                      599999999999999888778888888888888333.....4444599********************************************** PP

                      EEE CS
  Methyltransf_11  93 llv 95 
                      +l 
       EPA04448.1 166 ILT 168
                      985 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   1.9e-08   6.8e-05       2      97 .]      77     165 ..      76     165 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.9e-08
                      EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHHHHHHHHHHHHHEEE CS
  Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsdedlekalkeiarvLkp 95 
                      +d+G G    ++ + ++++k ++ ++ i+ ++l     +      n++f +   ++lpf+d+s+D v++  + +h++   l++++ e +r+Lk 
       EPA04448.1  77 VDVGSGLSAPAIFWRDKYEKLDLFCININYDQLSFSGPQK-----NIHFFNSTSTKLPFADNSVDRVLALESSQHFK--PLKDFILESKRILKS 163
                      5888888888888888887788888888888888766655.....9***********************88899998..5889**********9 PP

                      EE CS
  Methyltransf_25  96 gG 97 
                      +G
       EPA04448.1 164 NG 165
                      98 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   1.3e-07   0.00046       2     117 ..      71     177 ..      70     219 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.3e-07
  Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnevlnaladpdkile 95 
                      +k+++++D+G+G ++ ++ +    ++k +++ i i+ + ++++         +n++F  +  ++l+  ++d+++D +l+ e  ++++ +++++ 
       EPA04448.1  71 EKAKNLVDVGSGLSAPAIFWR-DKYEKLDLFCININYDQLSFSGPQ------KNIHFFNSTSTKLP--FADNSVDRVLALESSQHFKPLKDFIL 155
                      689999***************.558899999999999999999885......89************..************************** PP

  Methyltransf_31  96 eiervlkpggilliedprllae 117
                      e +r lk++gil ++ p ++++
       EPA04448.1 156 ESKRILKSNGILTLAIPVTMQN 177
                      *************999986655 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   2.3e-06    0.0084     114     157 ..     126     170 ..     103     226 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.3e-06
                     TS-S--TT-EEEEEEES.---SS-HHHHHHHHHHHEEEEEEEEEE CS
  Methyltransf_8 114 akvPledesvdvavfcl.slmgtnladflkeanrvlkvGGllkva 157
                     +k+P +d+svd ++    s   + l+df+ e +r+lk  G+l +a
      EPA04448.1 126 TKLPFADNSVDRVLALEsSQHFKPLKDFILESKRILKSNGILTLA 170
                     79*********7765541667899******************998 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.7e-06     0.006       1      99 []      77     167 ..      77     167 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.7e-06
  Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.ssfDlvvasnvlhhlkdirevldnirklL 93 
                      +++G+G ++ +  +++k + +++ ++ i+ +++      ++  ++    n+++++  + +l+   +s+D v+a++  +h+k++++++ + ++ L
       EPA04448.1  77 VDVGSGLSAPAIFWRDKYEKLDLFCININYDQL-----SFSGPQK----NIHFFNSTSTKLPFAdNSVDRVLALESSQHFKPLKDFILESKRIL 161
                      589999999999999999999999999999999.....5555553....44444444443333356**************************** PP

  Methyltransf_12  94 kpgGrl 99 
                      k +G+l
       EPA04448.1 162 KSNGIL 167
                      ****87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1792.09
//
Query:       EPA04449.1  [L=54]
Description: hypothetical protein BG20_I2222 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       254  (0.014167); expected 358.6 (0.02)
Passed bias filter:                      182  (0.0101512); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 357.81
//
Query:       EPA04450.1  [L=142]
Description: hypothetical protein BG20_I2223 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 930.45
//
Query:       EPA04451.1  [L=212]
Description: putative 2-phospho-L-lactate guanylyltransferase CofC [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.2e-21   74.6   4.1      8e-21   74.2   4.1    1.0  1  CofC          Guanylyl transferase CofC like
    7.9e-05   23.1   0.0    8.9e-05   22.9   0.0    1.2  1  NTP_transf_3  MobA-like NTP transferase domain


Domain annotation for each model (and alignments):
>> CofC  Guanylyl transferase CofC like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.2   4.1   8.9e-25     8e-21       2     183 ..       4     193 ..       3     210 .. 0.84

  Alignments for each domain:
  == domain 1  score: 74.2 bits;  conditional E-value: 8.9e-25
        CofC   2 kviiPvsainsaktrlseilseeerkellkamlldvidalkr...ld.vlvvsedeevleyaldelgvevvkek.ekdlntaveka...feeieekevi 92 
                  +iiPv++++ aktrl   ls ++++el k ml +++ +l+    ++ +++v+++e+ +e  + + +v ++ ++ ek +n av  a   + e +++  i
  EPA04451.1   4 AAIIPVKTFSLAKTRLN--LSSHQKEELCKIMLEEIVYTLSIspqIEkIIIVTKEEKAIEIGK-KYKVIIIPDDeEKSVNHAVALAdkyLLENQFDASI 99 
                 58**************6..9****************998763336888**************9.667777765549*******8777768899****** PP

        CofC  93 iipsdiPlikkedvkdllelek..radvviaPargGGtnllllr.ksalevkyedfsflkhleearkrglkvkiydsfylsvdinteedlgeil 183
                 + p diP+ik +d++ +l  ++  ++ +v+   r  Gtn l+    +++  +y++ s+  h++ a++   +v +  +  +  d+++ edl  +l
  EPA04451.1 100 VFPQDIPFIKTQDIDFMLTYKTppNFAIVVPSRRFDGTNALVRMpINLMITHYDEDSYKIHMNTAKEHTRNVALVFAKRIMWDVDNMEDLKFLL 193
                 ***************999766522566666555679****987746777889*****************999998899999********98665 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   9.9e-09   8.9e-05      26     128 ..      33     137 ..      16     195 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 9.9e-09
                   HHHHHHHHHCTT..-CEEEEECSHCHHHHHHTTCTS-EEE-TTSS-SHHHHHHHHHHH.H..SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEE CS
  NTP_transf_3  26 llervldalraa.gvdevvvvggdeevlaalarlgvrvvededpgkgplaslaaalra.aa.dadavlvlacDmPlltpelverllaaaaasgadvv 119
                   +le ++ +l+ + +++++++v+++e+  +  ++++v +++d++ +k   +++a a +  ++ + da +v++ D+P+++++ ++ +l   ++ + ++v
    EPA04451.1  33 MLEEIVYTLSISpQIEKIIIVTKEEKAIEIGKKYKVIIIPDDE-EKSVNHAVALADKYlLEnQFDASIVFPQDIPFIKTQDIDFMLTYKTPPNFAIV 128
                   788888888777449*********9999999**********85.78888888888888522599************************999999999 PP

                   EEESSSEEE CS
  NTP_transf_3 120 vptyegerg 128
                   vp+++ +  
    EPA04451.1 129 VPSRRFDGT 137
                   999986654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       888  (0.0495287); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1523.11
//
Query:       EPA04452.1  [L=130]
Description: hypothetical protein BG20_I1010 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.13   11.3   1.4       0.16   11.1   1.4    1.1  1  RP853     Uncharacterized RP853


Domain annotation for each model (and alignments):
>> RP853  Uncharacterized RP853
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.4   8.8e-06      0.16     197     256 ..      45     110 ..      32     122 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 8.8e-06
       RP853 197 ksnifkqatgkivgavcallvgaisvatag.....aafsii.vvpalifavryapelgekigelil 256
                 + ni+k++ gki g++ + +vg+i+ a +      aa+s    v a+ f+     el  +ig +il
  EPA04452.1  45 RINILKKSKGKISGSLFSSFVGSIAGACSCgpigfAAISTFgSVGATAFSFLTNFELPIRIGAIIL 110
                 68*********************9988754132223333322466677777777788888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       676  (0.0377043); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 877.25
//
Query:       EPA04453.1  [L=39]
Description: hypothetical protein BG20_I1033 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00045   20.2   1.1     0.0005   20.0   1.1    1.1  1  zinc_ribbon_6  Zinc-ribbon
     0.0017   18.3   0.9     0.0017   18.3   0.9    1.0  1  Cytochrome_C7  Cytochrome c7 and related cytochrome c
  ------ inclusion threshold ------
      0.015   15.3   1.1      0.015   15.3   1.1    1.0  1  HypA           Hydrogenase/urease nickel incorporation, metal
      0.024   14.7   2.6      0.025   14.6   2.6    1.0  1  DUF1451        Zinc-ribbon containing domain
       0.05   13.5   1.3       0.05   13.5   1.3    1.1  1  DYW_deaminase  DYW family of nucleic acid deaminases


Domain annotation for each model (and alignments):
>> zinc_ribbon_6  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   1.1   1.4e-07    0.0005      27      54 ..      10      37 ..       5      38 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.4e-07
  zinc_ribbon_6 27 kvkilCnDCekksevkfhvlglkCkeCg 54
                   + +i+C DC+++ e++      kC+ C+
     EPA04453.1 10 RNRIICMDCHQELETRSERSMKKCEGCQ 37
                   678************************7 PP

>> Cytochrome_C7  Cytochrome c7 and related cytochrome c
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.9   4.7e-07    0.0017      45      71 ..       9      36 ..       1      37 [. 0.80

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 4.7e-07
  Cytochrome_C7 45 ves.ltCgaCHdgknafsvakkaeCakC 71
                   +++   C++CH++ ++ s+++ ++C+ C
     EPA04453.1  9 MRNrIICMDCHQELETRSERSMKKCEGC 36
                   334445***********99*******99 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   1.1   4.3e-06     0.015      64      93 ..       6      37 ..       2      39 .] 0.80

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.3e-06
                EEEE--EEEETTTS-EEECHH.H.HHS-TTTS CS
        HypA 64 ieevpvkvrCreCgkefelee.k.alrCpkCg 93
                i+ ++ ++ C +C++e e+++ +   +C+ C+
  EPA04453.1  6 IDIMRNRIICMDCHQELETRSeRsMKKCEGCQ 37
                7778899***********77744566999997 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   2.6   6.9e-06     0.025     114     139 ..      12      37 ..       8      39 .] 0.92

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6.9e-06
     DUF1451 114 tlvCekCgkelalkkteeippCpkCg 139
                 +++C+ C++el+ ++ + +++C+ C+
  EPA04453.1  12 RIICMDCHQELETRSERSMKKCEGCQ 37 
                 579**********************8 PP

>> DYW_deaminase  DYW family of nucleic acid deaminases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.3   1.4e-05      0.05      87     109 ..       5      27 ..       2      37 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.4e-05
  DYW_deaminase  87 qiriiknlrvCeDChsafklisk 109
                     i+i+ n  +C DCh+ ++  s+
     EPA04453.1   5 RIDIMRNRIICMDCHQELETRSE 27 
                    6899************9998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       844  (0.0470746); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 272.72
//
Query:       EPA04454.1  [L=408]
Description: hypothetical protein BG20_I1032 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-98  330.8   0.1    1.4e-98  330.6   0.1    1.0  1  DUF2070   Predicted membrane protein (DUF2070)
  ------ inclusion threshold ------
      0.081   13.2   0.0       0.22   11.8   0.0    1.7  1  MapZ_C2   MapZ extracellular C-terminal domain 2


Domain annotation for each model (and alignments):
>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  330.6   0.1  1.6e-102   1.4e-98     159     563 ..       4     405 ..       1     406 [. 0.97

  Alignments for each domain:
  == domain 1  score: 330.6 bits;  conditional E-value: 1.6e-102
     DUF2070 159 llslifalavylfivvvdrplkrnlgvsaldllsaFlahilegskelEeffeeigeeadvpvkvlsfrredg.ekallvvPniHPGPlgeiGGsnLpki 256
                  +  +f++++ ++ v+ dr +++ +  s+++ ++a+la+  +  +e Ee+ e+ + + +v+++ +++   +   ++++v+P+iHPGP++ +GGsn+p++
  EPA04454.1   4 GFGTVFLIIASVWSVLTDRAGRPGM-ESTHRTIQAYLASQGNDFSEAEEIIEQRSYKTKVSTSQIRLYSSNSnSEFRMVLPEIHPGPYHPVGGSNIPYL 101
                 56789******************88.9****************7778********************999998************************** PP

     DUF2070 257 laerldelvlvlHgtatHdfNlvserevekiveavkealeeleysskaskpvrvesgdvkllgqrfgdslllvitrapegiDDiplsvglsimaeakae 355
                 +++++d++++++H++++H++Nl+s++eve+++++++++  + e    +++pv+v++++++++g+ fg++ ll+++ +p+g++Dip ++  +i+++ak++
  EPA04454.1 102 MYKNFDSSAMIMHSISDHSLNLPSKNEVENYLKNLDKSVVKEE-GLVCTEPVTVQINKARVTGLLFGKNPLLFLSLSPHGMEDIPDYMKTEIEQYAKNR 199
                 ***************************************9976.999**************************************************** PP

     DUF2070 356 gfedvllVDaHNsfseeagevlpgsedaeeliraaekalekleaaeeselkvgvarsetpkltpeeglGdlgiqvlvlevdgqktayvliDgNNmepgl 454
                 ++ + l+VD+HN+++ee +     +ed e++++aa+++l++l ++e +++++g+a+s+ ++++  e+l  +g+ +++l+++++k+++ ++D+NNme+g+
  EPA04454.1 200 NYVRTLIVDCHNAMGEEIS-----KEDGEDMLKAAKSCLDSLITKESYPIEFGYANSDNMDVWT-EDLAMGGLGIVCLKINNKKFFLGWADANNMENGI 292
                 **************99977.....8********************************9999887.7********************************* PP

     DUF2070 455 reeirealke.vdlevevmTTDtHvvngvsl...gynpvGekvskdelielvlelvekAiadlepvevgyatervevkvfgedrfeelvstvnsvvsva 549
                 re+i+e++ + + + +e++T+DtH++    +   gy+++G  +s+++l +++le+  +A ++++ +++++ ++++ vkv+g+ ++e+++++++++++++
  EPA04454.1 293 REKIVENFAKlGHTLLEICTSDTHFAPVKARnrnGYYQLGLITSAEKLSKWFLEIAYHAESKMTAAKFEILENETDVKVMGRGIYEDYSKALDNSLKIT 391
                 *********98888***********99988899****************************************************************** PP

     DUF2070 550 kilaaallllaill 563
                 k +++  ++l+i++
  EPA04454.1 392 KGFMIGSVILFIIT 405
                 *********99987 PP

>> MapZ_C2  MapZ extracellular C-terminal domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.5e-05      0.22      17      66 ..     285     338 ..     273     350 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.5e-05
     MapZ_C2  17 awtwapgvkekviatsierGy....iveggyilervriengegyYnlyatdnks 66 
                 a +  +g++ek++++  + G+    i   +  + +v+ +n +gyY l   ++ +
  EPA04454.1 285 ANNMENGIREKIVENFAKLGHtlleICTSDTHFAPVKARNRNGYYQLGLITSAE 338
                 667899**************86666789999**************996665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       852  (0.0475208); expected 358.6 (0.02)
Passed bias filter:                      672  (0.0374812); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.35s 00:00:00.92 Elapsed: 00:00:00.47
# Mc/sec: 2591.51
//
Query:       EPA04455.1  [L=102]
Description: translation initiation factor Sui1 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-18   66.7   0.0    2.8e-18   66.2   0.0    1.2  1  SUI1      Translation initiation factor SUI1
  ------ inclusion threshold ------
      0.015   15.0   0.1      0.015   15.0   0.1    1.1  1  DTW       DTW domain


Domain annotation for each model (and alignments):
>> SUI1  Translation initiation factor SUI1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.2   0.0   3.1e-22   2.8e-18       3      77 .]      25      95 ..      23      95 .. 0.95

  Alignments for each domain:
  == domain 1  score: 66.2 bits;  conditional E-value: 3.1e-22
        SUI1  3 pkihirleqrggrKkvTtvsgleafgidlkklakelkkkfacsgsvvkdggeeiqvQGdqrkkvaelLtekygvp 77
                 ki irle+r+ +Kk T ++gl+++  +l+++akelk+k ac+g+  k+g   i +QGd+r+ +++ L+   g+p
  EPA04455.1 25 TKIIIRLETRRFKKKGTMIEGLDPKLNNLETVAKELKNKYACGGTA-KEG--YIFLQGDHRDTIKDTLIHL-GFP 95
                699******************************************6.888..8***************997.876 PP

>> DTW  DTW domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   1.6e-06     0.015       3      56 ..       4      54 ..       2      90 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.6e-06
         DTW  3 lCerCllpaevclcsslppleklpikvlilqhpkEkkkstntarllalslanlr 56
                +C++C lp+ +c c +l + + + +k++i    + +kk+    + l ++l+nl+
  EPA04455.1  4 ICNTCGLPEDLCACGELAK-D-S-TKIIIRLETRRFKKKGTMIEGLDPKLNNLE 54
                6*****************9.5.5.899987777776666555555666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       680  (0.0379274); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.33s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 601.57
//
Query:       EPA04456.1  [L=302]
Description: putative transcription initiation factor IIB [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.3e-36  121.7   5.5    2.8e-18   65.7   1.3    2.2  2  TFIIB          Transcription factor TFIIB repeat
    2.6e-09   36.4   1.5    4.5e-09   35.7   1.5    1.4  1  TF_Zn_Ribbon   TFIIB zinc-binding
    0.00052   19.5   0.0       0.27   10.8   0.0    2.8  2  Sigma70_r4     Sigma-70, region 4
     0.0014   18.7   0.0       0.74    9.9   0.0    2.2  2  Cyclin_C       Cyclin, C-terminal domain
     0.0025   17.5   0.1      0.064   13.0   0.0    2.1  2  Cyclin_N       Cyclin, N-terminal domain
     0.0049   16.7   0.1       0.21   11.4   0.0    2.8  3  HTH_AsnC-type  AsnC-type helix-turn-helix domain
     0.0092   16.1   0.9      0.022   14.9   0.9    1.6  1  Ribosomal_S27  Ribosomal protein S27a
  ------ inclusion threshold ------
       0.02   14.6   0.0      0.035   13.8   0.0    1.3  1  RPW8           Arabidopsis broad-spectrum mildew resistance p
      0.058   12.8   4.5       0.46   10.0   4.5    2.2  1  zf-ribbon_3    zinc-ribbon domain
      0.059   13.4   0.0       0.13   12.3   0.0    1.5  1  RB_B           Retinoblastoma-associated protein B domain
      0.063   13.3   0.8       0.16   12.0   0.8    1.7  1  DZR            Double zinc ribbon
      0.072   12.8   0.5      0.072   12.8   0.5    2.2  2  zf-CCHC_5      GAG-polyprotein viral zinc-finger
       0.19   11.2   0.6        3.5    7.1   0.0    3.1  4  HTH_Tnp_ISL3   Helix-turn-helix domain of transposase family 
       0.35   10.7   1.3        2.6    7.9   0.0    2.7  3  MerR           MerR family regulatory protein
       0.35   10.7   1.5        1.7    8.5   0.2    2.7  2  LacI           Bacterial regulatory proteins, lacI family
       0.47   10.2   5.3          3    7.7   0.5    2.4  2  zinc_ribbon_2  zinc-ribbon domain
        1.4    8.6   9.9        0.9    9.3   0.7    2.4  2  zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
        1.7    8.9   4.0         12    6.2   0.1    2.5  2  NOB1_Zn_bind   Nin one binding (NOB1) Zn-ribbon like


Domain annotation for each model (and alignments):
>> TFIIB  Transcription factor TFIIB repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.2   0.2   6.4e-19   6.4e-16       3      71 .]     127     195 ..     125     195 .. 0.96
   2 !   65.7   1.3   2.8e-21   2.8e-18       1      71 []     219     289 ..     219     289 .. 0.99

  Alignments for each domain:
  == domain 1  score: 58.2 bits;  conditional E-value: 6.4e-19
                 HHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
       TFIIB   3 rfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                 r+ d+l   + V ++A +++++ale++++ Grs  +++A++ly Acr  e+ rt+k+i + ++++ k i
  EPA04456.1 127 RLKDKLAVGDAVIEKAAYIYRKALEKGLVRGRSISALIASALYAACRDTETPRTLKDIGQASNIKRKDI 195
                 67899***********************************************************99876 PP

  == domain 2  score: 65.7 bits;  conditional E-value: 2.8e-21
                 HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
       TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                 i+r+a++++L+ek ++aA++++++a e+k+ +G+ p g+aAA+ly+Ac  +++ +tq+++++ + V+e+ti
  EPA04456.1 219 ISRIASKAGLSEKTKRAATKILQTAEEQKISAGKDPMGLAAAALYVACVTNGESKTQRDVAEAAGVTEVTI 289
                 89*******************************************************************98 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   1.5   4.6e-12   4.5e-09       2      43 .]      10      51 ..      10      51 .. 0.97

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 4.6e-12
                  EETTTTCEECHEETSTTCEEESSSSBEEEECCCCCCCHHHHH CS
  TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGlVlednsidegpewref 43
                  +CP Cg  +lv+D+ ++e +C++CG V+ +   ++gpewr f
    EPA04456.1 10 RCPRCGQGTLVTDATTAENFCGKCGFVITEKVDESGPEWRSF 51
                  5******99*******************************87 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.013        13      18      37 ..     176     195 ..     168     206 .. 0.79
   2 !   10.8   0.0   0.00027      0.27      18      42 ..     270     294 ..     261     298 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.013
                 TTT--HHHHHHHHTS-HHHH CS
  Sigma70_r4  18 geglTleEIgerlgiSrerV 37 
                 + ++Tl++Ig+  +i r  +
  EPA04456.1 176 ETPRTLKDIGQASNIKRKDI 195
                 789*********99998765 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00027
                 TTT--HHHHHHHHTS-HHHHHHHHH CS
  Sigma70_r4  18 geglTleEIgerlgiSrerVrqiek 42 
                 ge  T+ +++e  g+++ ++r + k
  EPA04456.1 270 GESKTQRDVAEAAGVTEVTIRNRYK 294
                 8999*****************9976 PP

>> Cyclin_C  Cyclin, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.0    0.0079       7.9      48      89 ..     164     205 ..     158     211 .. 0.85
   2 !    9.9   0.0   0.00074      0.74       3      84 ..     215     294 ..     213     301 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0079
                 HHHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHHHHHHH CS
    Cyclin_C  48 Aaaalllarstlnspewtetlehytgyskedlkpcvelilel 89 
                  a+al++a++  ++p   + + + + ++ +d+  c++l+l  
  EPA04456.1 164 IASALYAACRDTETPRTLKDIGQASNIKRKDIARCYRLLLRE 205
                 4778888888889999999*******************9875 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00074
                 HHHHHHHH.HCCSSHT.-HCCHHCHHCHHHHHHCSCCHCCS-HHHHHHHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHH CS
    Cyclin_C   3 plsFlrrf.lkaadasedselrtlakylleltlldydflsyppSliAaaalllarstlnspewtetlehytgyskedlkpcve 84 
                 p+ +++r+ +ka    ++ +++  a  +l ++  +  +++ +p  +Aaaal++a+ t ++++ ++ + +  g+++  +++ ++
  EPA04456.1 215 PVKCISRIaSKA--GLSE-KTKRAATKILQTAEEQKISAGKDPMGLAAAALYVACVTNGESKTQRDVAEAAGVTEVTIRNRYK 294
                 778888987777..3335.66667777777777777799999***************99999999999999999998887776 PP

>> Cyclin_N  Cyclin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   6.4e-05     0.064      38     126 ..     125     210 ..      93     211 .. 0.87
   2 ?    2.5   0.0      0.11   1.1e+02      38      87 ..     219     268 ..     215     292 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.4e-05
                 HHHHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHHHSSS---HHHHHHHTTTSS-HHHHHHHHHHHHHHTTT-- CS
    Cyclin_N  38 lvevaekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAaKveeisppkledlvyitdeafteeeilemErliLetLnfdl 126
                 l ++  k+ +   ++  a+ ++ + l+k  v+ + +  + a++L+ A++  e+ p +l+d+  ++   +++++i +  rl+L++Ln ++
  EPA04456.1 125 LDRLKDKLAVGDAVIEKAAYIYRKALEKGLVRGRSISALIASALYAACRDTET-PRTLKDIGQAS--NIKRKDIARCYRLLLRELNLKM 210
                 5567778888888999999*********************************9.9*****99995..5*****************9876 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.11
                 HHHHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHH CS
    Cyclin_N  38 lvevaekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAaKv 87 
                 + ++a+k  l+++t   a ++l    ++k+   ++   ++a++L++A+ +
  EPA04456.1 219 ISRIASKAGLSEKTKRAATKILQTAEEQKISAGKDPMGLAAAALYVACVT 268
                 677888888899999999999999888888888899999********976 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0         7     7e+03      18      32 ..     179     193 ..     174     197 .. 0.68
   2 ?    1.9   0.0       0.2   1.9e+02      21      33 ..     220     232 ..     214     240 .. 0.88
   3 !   11.4   0.0   0.00021      0.21      19      41 ..     274     296 ..     268     297 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 7
  HTH_AsnC-type  18 isyaeLAervGlSes 32 
                    ++ ++++++ ++ + 
     EPA04456.1 179 RTLKDIGQASNIKRK 193
                    678888887666555 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.2
  HTH_AsnC-type  21 aeLAervGlSest 33 
                    +++A + GlSe t
     EPA04456.1 220 SRIASKAGLSEKT 232
                    689*******987 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00021
  HTH_AsnC-type  19 syaeLAervGlSestvlrRvrrL 41 
                    + +++Ae+ G++e t+++R++ L
     EPA04456.1 274 TQRDVAEAAGVTEVTIRNRYKGL 296
                    789****************9976 PP

>> Ribosomal_S27  Ribosomal protein S27a
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.9   2.2e-05     0.022      17      43 ..       8      34 ..       3      36 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.2e-05
                   S-B-SS-S-TTSBEEECTT.EEEESSTT CS
  Ribosomal_S27 17 rkeCpreCGaGvfMAehkd.RkyCGkCg 43
                   +++Cpr CG+G+   +     + CGkCg
     EPA04456.1  8 KDRCPR-CGQGTLVTDATTaENFCGKCG 34
                   789***.********9988799*****9 PP

>> RPW8  Arabidopsis broad-spectrum mildew resistance protein RPW8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.5e-05     0.035      14     103 ..      71     163 ..      66     172 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.5e-05
        RPW8  14 gellkaileakkksldfksilkrLestleritP..vvkeiek.lnkeldrpreeieeLkklLekaekLVekcsklkrynvlkkyrYkkklkeL 103
                 ++ l  +++ +++ ++ k+    ++st+er+++  ++ ++ + +  ++ +  +e+++Lk++L  +   +ek + + r ++ k     + + +L
  EPA04456.1  71 DMGLATVINPQNRDATGKPLTSAMKSTIERLRTwdSRSQVHEpVDRNFRQAFSELDRLKDKLAVGDAVIEKAAYIYRKALEKGLVRGRSISAL 163
                 567889*************************9844567776515555588888********************99988887777666666665 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   4.5   0.00046      0.46       2      26 .]       8      37 ..       7      37 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00046
  zf-ribbon_3  2 tvrCPnCGa.plssdd....nvCpyCGtkl 26
                 + rCP+CG+  l +d+    n+C +CG ++
   EPA04456.1  8 KDRCPRCGQgTLVTDAttaeNFCGKCGFVI 37
                 579******9876665333379*****986 PP

>> RB_B  Retinoblastoma-associated protein B domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00013      0.13      11      93 ..     119     199 ..     114     210 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
        RB_B  11 klaavrlrdLcerLklsselrekiwtlfehvlveetellkdRhlDqillcavYvvakvtkeelsFkeiikaYrkqpqasskvy 93 
                 + a + l +L ++L + + + ek+  + +++l  e+ l++ R +  ++ +a+Y+ ++ t++ +++k+i +a + + +  ++ y
  EPA04456.1 119 RQAFSELDRLKDKLAVGDAVIEKAAYIYRKAL--EKGLVRGRSISALIASALYAACRDTETPRTLKDIGQASNIKRKDIARCY 199
                 56778899999999999988888877777777..578**********************999999999887666665555555 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.8   0.00016      0.16      27      49 .]       7      34 ..       1      38 [. 0.68

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00016
         DZR 27 aedrCpsCge.....kvdpearfCpeCG 49
                 +drCp+Cg+     +++  ++fC++CG
  EPA04456.1  7 PKDRCPRCGQgtlvtDATTAENFCGKCG 34
                4789999986333224566778899998 PP

>> zf-CCHC_5  GAG-polyprotein viral zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.5   7.3e-05     0.072       1      12 [.       7      18 ..       7      22 .. 0.89
   2 ?   -1.3   0.2       1.9   1.8e+03       2       9 ..      27      34 ..      26      34 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.3e-05
                ---B-TTT-SSB CS
   zf-CCHC_5  1 ppglCpRCkkgk 12
                p ++CpRC++g+
  EPA04456.1  7 PKDRCPRCGQGT 18
                689*******98 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.9
                --B-TTT- CS
   zf-CCHC_5  2 pglCpRCk 9 
                ++ C +C+
  EPA04456.1 27 ENFCGKCG 34
                789****8 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       4.2   4.2e+03       7      27 ..     155     175 ..     153     183 .. 0.71
   2 ?   -1.3   0.0       1.5   1.5e+03      31      39 ..     193     201 ..     192     201 .. 0.87
   3 ?    0.0   0.0      0.58   5.7e+02      12      26 ..     231     245 ..     220     249 .. 0.83
   4 ?    7.1   0.0    0.0035       3.5      26      49 ..     271     294 ..     267     296 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 4.2
  HTH_Tnp_ISL3   7 rrrsriTlrleayilellles 27 
                    r+++i+ + + + +++++++
    EPA04456.1 155 VRGRSISALIASALYAACRDT 175
                   577777777777777777766 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.5
  HTH_Tnp_ISL3  31 kavArqlgv 39 
                   k++Ar++++
    EPA04456.1 193 KDIARCYRL 201
                   89****996 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.58
  HTH_Tnp_ISL3  12 iTlrleayilellle 26 
                    T+r++ +il+ + e
    EPA04456.1 231 KTKRAATKILQTAEE 245
                   589999999998765 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.0035
  HTH_Tnp_ISL3  26 esrsvkavArqlgvSwtTVwrild 49 
                   es++ ++vA+  gv++ T++++++
    EPA04456.1 271 ESKTQRDVAEAAGVTEVTIRNRYK 294
                   5689****************9976 PP

>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0      0.77   7.7e+02      12      30 ..      97     115 ..      96     117 .. 0.81
   2 ?   -2.3   0.1         4     4e+03       2      15 ..     219     232 ..     219     232 .. 0.84
   3 ?    7.9   0.0    0.0026       2.6       4      17 ..     277     290 ..     276     291 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.77
                 THHHHHHHHHTTSSTSEEE CS
        MerR  12 sprtLRyYEreGLipppeR 30 
                 ++  LR ++++  + +p++
  EPA04456.1  97 TIERLRTWDSRSQVHEPVD 115
                 67779*****999888775 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4
                 HHHHHHHHTTTHHH CS
        MerR   2 IgevAeltGvsprt 15 
                 I+ +A ++G+s +t
  EPA04456.1 219 ISRIASKAGLSEKT 232
                 67789999**9988 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0026
                 HHHHHHTTTHHHHH CS
        MerR   4 evAeltGvsprtLR 17 
                 +vAe++Gv+  t+R
  EPA04456.1 277 DVAEAAGVTEVTIR 290
                 8************9 PP

>> LacI  Bacterial regulatory proteins, lacI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1         1     1e+03       5      30 ..     222     232 ..     219     247 .. 0.57
   2 ?    8.5   0.2    0.0017       1.7       3      15 ..     276     288 ..     274     290 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1
                 HHHHCTS-HHHHHHHCTTSSSSTHHH CS
        LacI   5 VArlAGVSkaTVSrvLnnkerVseet 30 
                 +A +AG S               e+t
  EPA04456.1 222 IASKAGLS---------------EKT 232
                 45555555...............444 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0017
                 HHHHHHCTS-HHH CS
        LacI   3 kDVArlAGVSkaT 15 
                 +DVA++AGV+  T
  EPA04456.1 276 RDVAEAAGVTEVT 288
                 7********9888 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.4     0.031        31       2       6 ..      11      15 ..       3      17 .. 0.75
   2 ?    7.7   0.5     0.003         3      13      21 ..      27      35 ..      25      37 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.031
  zinc_ribbon_2  2 CpnCG 6 
                   Cp+CG
     EPA04456.1 11 CPRCG 15
                   66666 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.003
  zinc_ribbon_2 13 akFCpyCGt 21
                   ++FC +CG+
     EPA04456.1 27 ENFCGKCGF 35
                   69******7 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.7   0.00091       0.9       6      20 ..      11      25 ..      10      26 .. 0.86
   2 ?    3.1   2.9     0.075        75       5      10 ..      29      34 ..      28      35 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00091
  zf-NADH-PPase  6 CgrCGaptepaeggw 20
                   C+rCG+ t + ++ +
     EPA04456.1 11 CPRCGQGTLVTDATT 25
                   ********9988865 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.075
  zf-NADH-PPase  5 FCgrCG 10
                   FCg+CG
     EPA04456.1 29 FCGKCG 34
                   *****9 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1     0.012        12      21      35 ..       6      20 ..       1      27 [. 0.79
   2 ?    3.8   4.1     0.066        66      11      31 ..      11      35 ..      10      44 .. 0.58

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.012
  NOB1_Zn_bind 21 mtkkFCpkCGnktLk 35
                  + k  Cp+CG+ tL 
    EPA04456.1  6 NPKDRCPRCGQGTLV 20
                  56778********95 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.066
  NOB1_Zn_bind 11 ChaCfkvt....kdmtkkFCpkCGn 31
                  C  C + t     ++  +FC kCG 
    EPA04456.1 11 CPRCGQGTlvtdATTAENFCGKCGF 35
                  6666653323223477788888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       809  (0.0451224); expected 358.6 (0.02)
Passed bias filter:                      654  (0.0364772); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2034.63
//
Query:       EPA04457.1  [L=439]
Description: hypothetical protein BG20_I1023 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 2620.52
//
Query:       EPA04458.1  [L=205]
Description: hypothetical protein BG20_I1034 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0037   17.3   0.0      0.006   16.6   0.0    1.3  1  Mrr_cat   Restriction endonuclease
  ------ inclusion threshold ------
      0.031   14.8   0.0      0.055   13.9   0.0    1.5  1  NERD      Nuclease-related domain
      0.086   13.1   0.0       0.12   12.6   0.0    1.3  1  UPF0102   Uncharacterised protein family UPF0102


Domain annotation for each model (and alignments):
>> Mrr_cat  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0     1e-06     0.006       4      75 ..      77     149 ..      76     177 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1e-06
                 T-TTCHHHHHHHHHHHHSSS...EEE---B-TTSSB--EEEETTEEEEEEEEEEE--T...S-B-HHHHHHHHHHCTT CS
     Mrr_cat   4 mspkeFeklvaellealGyk...eveltgrsgDggiDliakkdplgserilvqaKryk...nkvgvkeVqeligalkk 75 
                 +++k+Fe lvae+l ++ +    ++ lt+      iD+i  +  lg   +l+ +K++k   ++  + +V++ i++ k+
  EPA04458.1  77 LDWKDFEGLVAEILLSKNFAiikNLILTK--PRMEIDVIGIR--LG-VAMLIDCKHWKrynSSALSTAVKKQIARTKH 149
                 69******************876666665..7899****765..56.89********866445666666666665555 PP

>> NERD  Nuclease-related domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   9.1e-06     0.055      11      59 ..      88     131 ..      79     165 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9.1e-06
        NERD  11 keLkelkedeylvlhdvrlrpgtgeiDhlvispkgifviEvKnwsGwif 59 
                 + L   +++++ +++++ l++ + eiD++ i  +  ++i++K+w+   +
  EPA04458.1  88 EIL---LSKNFAIIKNLILTKPRMEIDVIGIRLGVAMLIDCKHWKR--Y 131
                 433...4568999******66655**********99********95..2 PP

>> UPF0102  Uncharacterised protein family UPF0102
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.1e-05      0.12       2      59 ..      83     143 ..      82     175 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.1e-05
                 HHHHHHHHHHTT-EEEEEEEEETT.EEEEEEE..TTEEEEEEEEE-......-------HH CS
     UPF0102   2 EelaaeyLekkgyeilernwrcra.gEiDiia..tevlvfvEVKtRssekfgspaeavtpr 59 
                 E l+ae+L +k++ i+++ + ++   EiD+i     v + ++ K  ++ ++ +   av+++
  EPA04458.1  83 EGLVAEILLSKNFAIIKNLILTKPrMEIDVIGirLGVAMLIDCKHWKRYNSSALSTAVKKQ 143
                 889*************9999774449*******955899*****97544444444444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.33s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1250.83
//
Query:       EPA04459.1  [L=47]
Description: hypothetical protein BG20_I1011 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.30s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 310.95
//
Query:       EPA04460.1  [L=364]
Description: putative DNA polymerase IV [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.2e-41  140.8   0.1    2.3e-40  138.1   0.1    2.0  2  IMS        impB/mucB/samB family
    1.4e-10   41.9   0.3    2.9e-10   40.9   0.3    1.5  1  IMS_C      impB/mucB/samB family C-terminal domain
      7e-07   29.2   0.0    1.8e-06   28.0   0.0    1.7  1  IMS_HHH    IMS family HHH motif
     0.0089   16.2   0.1      0.049   13.9   0.0    2.3  3  Cdd1       Pathogenicity locus
  ------ inclusion threshold ------
      0.014   15.5   3.4      0.024   14.8   3.4    1.3  1  UPF0242    Uncharacterised protein family (UPF0242) N-terminu
      0.045   13.9   1.6       0.19   11.8   1.6    2.0  1  7TMR-HDED  7TM-HD extracellular
      0.054   13.8   3.1      0.062   13.6   0.8    2.1  2  DUF2524    Protein of unknown function (DUF2524)
        1.9    9.0   5.0         25    5.4   1.6    2.6  2  NPV_P10    Nucleopolyhedrovirus P10 protein


Domain annotation for each model (and alignments):
>> IMS  impB/mucB/samB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.1   0.1     1e-43   2.3e-40       1     150 []       9     163 ..       9     163 .. 0.95
   2 ?    0.4   0.0      0.27   5.9e+02     112     138 ..     264     296 ..     213     300 .. 0.73

  Alignments for each domain:
  == domain 1  score: 138.1 bits;  conditional E-value: 1e-43
                 EEETTHHHHHHHHHT.T-TTS-EEEEET.......TEEEEE-HHHHTTT--TTSBHHHHHTTH...TT-EEEEEE-HHHHHHHHHHHHHHHHH-S..EE CS
         IMS   1 iDmdaFyasverardpeLkgkPvvvaqgsek...rgiviavsyeArayGvkrgmrikeakklc...pdlivvkvdlekyrraskkileilkrfispkve 93 
                 iD+d F+a++e++r+p+Lk+kPv+v+ +s++   +g +++++y Ar++Gvk+g +i+ akk     +d+++++vd+++y ++s++ ++++k+  ++  e
  EPA04460.1   9 IDFDYFFAQCEELRNPDLKSKPVCVCVYSDRggdSGAIATANYIARKFGVKSGIPISFAKKRLedrKDAVFLPVDFDYYLEISENAMSVIKES-ADIFE 106
                 8***************************9999999***************************9443469************************.779** PP

                 EEETTEEEEE-HHHHHHHH-SHHHHHHHHHHHHHHHH---EEEEEESSHHHHHHHHH CS
         IMS  94 kasiDEayldltgleelaesegaalakelrkaikeelgltvsiGiasnkllAKlase 150
                  ++ DEayld+++++e   +++++la+++++a+ ++++l++siG+++nkl+AK+as+
  EPA04460.1 107 YVGKDEAYLDVSNRVEGDFNKASHLAQQIKNAVRDKVKLSCSIGVSTNKLIAKIASD 163
                 *************777777778*********************************96 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.27
                 H-S......HHHHHHHHHHHHHHHH---EEEEE CS
         IMS 112 ese......gaalakelrkaikeelgltvsiGi 138
                 ++       +++l+ el + +k++ ++  siGi
  EPA04460.1 264 KDFdflaenINQLCVELHEVVKKNNRMFKSIGI 296
                 333445445799999999999999999999998 PP

>> IMS_C  impB/mucB/samB family C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   0.3   1.3e-13   2.9e-10       1     113 [.     243     357 ..     243     360 .. 0.91

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 1.3e-13
       IMS_C   1 vvearpepksissektfpepydesk....lkkelreLaeelarrLrdkglvartitlklrysdfh.asrsatLprptsdtreileaalkLlrrlidepg 94 
                 +v++r+++ ++s+ +t+++   +sk    l + +++L+ el++  ++++++ ++i ++   sd + +++s+ L++pt + +e+ + a +Ll++   +++
  EPA04460.1 243 PVKERDPSVQYSKITTLKK---DSKdfdfLAENINQLCVELHEVVKKNNRMFKSIGIQFIQSDLTnKTKSRMLKNPTANLEELQKNANQLLKEALEDQK 338
                 6899**************9...4444568888999************************8777778*************************999998** PP

       IMS_C  95 lpirligvsasnlvekaes 113
                   ir++gv +s+l+e +++
  EPA04460.1 339 NTIRRLGVKVSELSELRGQ 357
                 **************88877 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   7.9e-10   1.8e-06       1      31 [.     175     205 ..     175     206 .. 0.93

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 7.9e-10
     IMS_HHH   1 pddvkefLwplpitkipGiGgklgekLeklG 31 
                 p+ ++efL+ l+i+ ipGiG+k+++++ +++
  EPA04460.1 175 PEKIEEFLGQLKIRAIPGIGKKTEDRFTQMN 205
                 7899**********************88876 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   2.2e-05     0.049       7      51 ..     186     230 ..     182     233 .. 0.89
   2 ?   -3.6   0.0         6   1.3e+04      33      51 ..     244     262 ..     241     265 .. 0.72
   3 ?   -2.2   0.0       2.3   5.1e+03      28      45 ..     317     334 ..     282     341 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.2e-05
        Cdd1   7 elqdiPniGkalaedlvelGirsveelkgedpeelyeklekltga 51 
                 +++ iP+iGk++ + ++++ ++ +++lk+ d   l +++ +++g+
  EPA04460.1 186 KIRAIPGIGKKTEDRFTQMNFEIIDDLKKLDVFTLNKEFGRKHGT 230
                 5789*************************9999998888777775 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 6
        Cdd1  33 lkgedpeelyeklekltga 51 
                 +k++dp   y+k+ +l++ 
  EPA04460.1 244 VKERDPSVQYSKITTLKKD 262
                 6888898888888777665 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 2.3
        Cdd1  28 rsveelkgedpeelyekl 45 
                  ++eel+++  + l e+l
  EPA04460.1 317 ANLEELQKNANQLLKEAL 334
                 345555555555555555 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   3.4   1.1e-05     0.024      74     183 ..     241     352 ..     212     355 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.1e-05
     UPF0242  74 eaklteldeglktkee.aleelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelkleleeqLaekqellqeyqetieeq.rsvlekrqd 170
                  + ++e d++++  +  +l++  ++ + L+e++++   el++  ++n+ + +       + +   +     L++ +  l+e+q++ +++ ++ le +++
  EPA04460.1 241 TEPVKERDPSVQYSKItTLKKDSKDFDFLAENINQLCVELHEVVKKNNRMFKSIGIQFIQSDLTNKTKSRMLKNPTANLEELQKNANQLlKEALEDQKN 339
                 45566777666554433999999999***************9999888776444443344555566667899**************995499******* PP

     UPF0242 171 qieqLeskVrDln 183
                  i +L  kV+ l+
  EPA04460.1 340 TIRRLGVKVSELS 352
                 *********9986 PP

>> 7TMR-HDED  7TM-HD extracellular
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.6   8.6e-05      0.19      35     126 ..     241     340 ..       7     360 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.6e-05
   7TMR-HDED  35 vppvydldpevteqvrqelenlleeleelratseenlselieqlkqarekyaqa.........gaelsdeelrallelsdeeleelqqgieqilerils 124
                 ++pv ++dp+v  + +++l++  ++ + l     en ++l  +l +  +k+++          +++l++ + +++l+   ++leelq+++ q+l+++l+
  EPA04460.1 241 TEPVKERDPSVQYSKITTLKKDSKDFDFLA----ENINQLCVELHEVVKKNNRMfksigiqfiQSDLTNKTKSRMLKNPTANLEELQKNANQLLKEALE 335
                 455556666666666666666666655555....5555555666666555544488889999988899999999999999******************5 PP

   7TMR-HDED 125 q...g 126
                 +    
  EPA04460.1 336 DqknT 340
                 52331 PP

>> DUF2524  Protein of unknown function (DUF2524)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1       0.8   1.8e+03      35      59 ..     110     134 ..      85     145 .. 0.56
   2 ?   13.6   0.8   2.8e-05     0.062       7      78 ..     280     351 ..     277     354 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.8
     DUF2524  35 ndeeYteAqlkLEeavneLeklaks 59 
                 +de+Y +  +++E  +n+ ++la++
  EPA04460.1 110 KDEAYLDVSNRVEGDFNKASHLAQQ 134
                 3455555556666555555555555 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 2.8e-05
     DUF2524   7 veellqkceqaieeaeeqfeeakrqehyndeeYteAqlkLEeavneLeklaksandqQreqLeRarlqlqqL 78 
                 ++e+++k +   ++   qf ++   ++ +    +++  +LEe+ ++ ++l+k a ++Q++ + R+ +++ +L
  EPA04460.1 280 LHEVVKKNNRMFKSIGIQFIQSDLTNKTKSRMLKNPTANLEELQKNANQLLKEALEDQKNTIRRLGVKVSEL 351
                 67888888888888889999999999999999999*****************************99888776 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.3      0.03        68      25      57 ..     254     295 ..     241     316 .. 0.79
   2 ?    5.4   1.6     0.011        25      26      63 ..     318     353 ..     299     357 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.03
     NPV_P10  25 qqvddvqenlpdvtelnekLdaqsaqLaelet.........k 57 
                 ++++ ++++++d++ l e+++++  +L+e+ +          
  EPA04460.1 254 SKITTLKKDSKDFDFLAENINQLCVELHEVVKknnrmfksiG 295
                 57899*******************999999874455554444 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.011
     NPV_P10  26 qvddvqenlpdvtelnekLdaqsaqLaeletkvenIqd 63 
                 +++++q+n ++   l+e L++q +++  l  kv++ ++
  EPA04460.1 318 NLEELQKNANQ--LLKEALEDQKNTIRRLGVKVSELSE 353
                 57888999888..89******************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1205  (0.0672095); expected 358.6 (0.02)
Passed bias filter:                      610  (0.0340231); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 2259.65
//
Query:       EPA04461.1  [L=69]
Description: hypothetical protein BG20_I1017 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.055   13.4   0.1      0.088   12.7   0.1    1.3  1  DUF3797        Domain of unknown function (DUF3797)
      0.099   13.3   0.1       0.15   12.8   0.1    1.6  1  zinc-ribbon_6  zinc-ribbon domain
       0.17   11.5   0.4       0.34   10.5   0.1    1.7  2  zf_UBZ         Ubiquitin-Binding Zinc Finger


Domain annotation for each model (and alignments):
>> DUF3797  Domain of unknown function (DUF3797)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   1.5e-05     0.088      15      42 ..       5      32 ..       4      35 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.5e-05
     DUF3797 15 qCPeCgNnkvlNsegkviieddtfyreC 42
                 CP+Cg      +e ++ ie+  + + C
  EPA04461.1  5 TCPDCGKRLFHENEVTLKIEETIHGKFC 32
                6********************9988888 PP

>> zinc-ribbon_6  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   2.5e-05      0.15       2      25 ..       4      27 ..       3      62 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.5e-05
  zinc-ribbon_6  2 feCeqCgqllffenssClkCgaal 25
                   f+C  Cg++lf+en+  lk ++++
     EPA04461.1  4 FTCPDCGKRLFHENEVTLKIEETI 27
                   9*************9988877765 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   5.7e-05      0.34       3      12 ..       4      13 ..       2      19 .. 0.86
   2 ?   -2.1   0.0       0.5     3e+03       8      17 ..      32      41 ..      32      46 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 5.7e-05
      zf_UBZ  3 ylCerCgkei 12
                ++C++Cgk++
  EPA04461.1  4 FTCPDCGKRL 13
                9*******85 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.5
      zf_UBZ  8 Cgkeipesel 17
                C k++ e++ 
  EPA04461.1 32 CRKKVGETQS 41
                8888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.28s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 494.61
//
Query:       EPA04462.1  [L=82]
Description: hypothetical protein BG20_I1004 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1204  (0.0671538); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 533.98
//
Query:       EPA04463.1  [L=179]
Description: hypothetical protein BG20_I1031 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-13   49.2  11.2    2.9e-13   49.0  11.2    1.0  1  DUF2070   Predicted membrane protein (DUF2070)
  ------ inclusion threshold ------
        0.4   10.8   2.9       0.24   11.5   1.0    1.6  2  DUF1230   Conserved in the green lineage and diatoms 27
       0.65    9.8   3.9       0.59    9.9   2.1    1.9  1  IncD      Inclusion membrane protein D


Domain annotation for each model (and alignments):
>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0  11.2   4.8e-17   2.9e-13      10     148 ..      17     160 ..       9     173 .. 0.83

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 4.8e-17
     DUF2070  10 r..lPswk.vsllliillalligllaflssklfgillfglpalvafllt.lpvlrilggrltykrslflalltelivviisllaillsall.qalvlla 103
                 +  +P+ + +sl+ ++++a++i++ ++  ++    ++f +p+++ +l++ + +++ + ++ +y++sl+ +l+ ++++++++l+++l+s++l ++ +l++
  EPA04463.1  17 TliNPASHyFSLVGSLIIAAVITATVHFGYHELDNIWFRIPIVIGVLALsQIIDKQFTRKKEYSKSLHASLFGNMLWIAVLLMGLLASWVLvKEASLFF 115
                 444677777999999999999888887777767778888887776655505555666666********************************9999*** PP

     DUF2070 104 lvlslalvfalrllvlvavsdesllkavlpaliqpllailllvly 148
                 +  +++l +++r+ +++++ ++s++ka++++++qpl+++l++++y
  EPA04463.1 116 VTYGMFLFASFRIGIFTTTLGASIKKAWAICMVQPLAMFLAIIPY 160
                 ********************************************9 PP

>> DUF1230  Conserved in the green lineage and diatoms 27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.0   3.9e-05      0.24       9      92 ..      21     110 ..      19     118 .. 0.78
   2 ?   -1.7   0.0      0.48   2.8e+03      49      68 ..     127     146 ..     110     167 .. 0.45

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.9e-05
     DUF1230   9 PvneyeeLkesllfswatlesaeyl.rrlllvwlvlllvvgpvaaa.....sfspekellelllssalgalvlvalvllrlylgWsYvgd 92 
                 P + y +L  sl+   + + ++++  ++l  +w+ + +v+g +a +      f+ +ke  + l +s +g ++ +a++l+ l  +W  v++
  EPA04463.1  21 PASHYFSLVGSLIIAAVITATVHFGyHELDNIWFRIPIVIGVLALSqiidkQFTRKKEYSKSLHASLFGNMLWIAVLLMGLLASWVLVKE 110
                 6777777777777777777776665145777777766666666665444448899******************************99975 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.48
     DUF1230  49 pvaaasfspekellelllss 68 
                 ++ +++++   ++ ++ ++ 
  EPA04463.1 127 RIGIFTTTLGASIKKAWAIC 146
                 44444444433333322222 PP

>> IncD  Inclusion membrane protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   2.1   9.9e-05      0.59      50      93 ..      91     134 ..      59     142 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 9.9e-05
        IncD  50 llvvagllfsgvlcspvsvlaaslffgv.gafllggalvggvltt 93 
                 +l +a +l+ g+l+s v v  aslff   g fl+    +g   tt
  EPA04463.1  91 MLWIA-VLLMGLLASWVLVKEASLFFVTyGMFLFASFRIGIFTTT 134
                 45555.55679*************996527777776666544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       741  (0.0413297); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1429.05
//
Query:       EPA04464.1  [L=253]
Description: oxidoreductase, short chain dehydrogenase/reductase family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-68  230.5   0.4    2.2e-68  230.3   0.4    1.0  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    7.5e-61  205.0   1.1    8.8e-61  204.8   1.1    1.1  1  adh_short        short chain dehydrogenase
    3.3e-09   36.9   0.3    4.6e-09   36.4   0.3    1.1  1  KR               KR domain
    2.7e-05   23.8   1.2    6.1e-05   22.6   1.2    1.8  1  Epimerase        NAD dependent epimerase/dehydratase family
    0.00023   21.7   1.3    0.00036   21.0   0.6    1.7  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
     0.0019   18.1   0.3     0.0033   17.4   0.3    1.4  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
     0.0031   17.4   0.2     0.0059   16.5   0.2    1.4  1  DFP              DNA / pantothenate metabolism flavoprotein
     0.0059   16.0   1.7      0.024   14.1   1.7    1.9  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
      0.009   15.2   2.3      0.012   14.8   2.3    1.1  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
  ------ inclusion threshold ------
      0.058   13.5   1.0       0.15   12.2   1.0    1.8  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
      0.096   12.9   0.1       0.16   12.2   0.1    1.3  1  5_nucleotid_C    5'-nucleotidase, C-terminal domain
       0.15   12.6   0.0       0.43   11.1   0.0    1.9  2  DUF2660          Protein of unknown function (DUF2660)


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  230.3   0.4   1.4e-71   2.2e-68       1     233 [.      12     248 ..      12     249 .. 0.96

  Alignments for each domain:
  == domain 1  score: 230.3 bits;  conditional E-value: 1.4e-71
                   TTTTSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSEEEE--TTSHHHHHHHHHHHHHHHSSEEEEEE-----EGCSS-GGGH-HHHHH CS
  adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgaevlecDVtdeeqvealveevvekfgklDilvnnagiapklkgpfletsreefd 96 
                   Ga s IG+++Ak++ eeGa+v+l  +n e+ +k+ +e+ +e +++ + cD tde+qv ++++++++++gk+Dil+nnag  ++   +f+e+s++e++
    EPA04464.1  12 GASSDIGKGVAKRFVEEGAQVILIARNLEGlEKARKEIGNEKSTASMSCDLTDESQVIQTINQIMNTYGKIDILINNAGAIND-PVHFHEMSDSEIK 107
                   89999*************************7777777777766667************************************9.9************ PP

                   HHHHHHTHHHHHHHHHHHHHCTSC..CEEEEEEEGGGTSBSTTTT..HHHHHHHHHHHHHHHHHHHHGGGTEEEEEEEE--BHCTGGGGSTTHHHHH CS
  adh_short_C2  97 raldvnlyslfllakaalplmkeg..gsivnlssvgaervvpnyn..aygaaKaalealtrylAvelgpkgiRvNavspgpikTlaasgikgfdell 189
                   + +d+nl ++f+++ka+l+ m e+  gsivn+ s+++er++p  +  ay+a+Kaa+  +t+++Ave++++ iR+N+v pg+i+  + + + + ++ +
    EPA04464.1 108 KLIDINLFGVFHITKAVLNKMSETknGSIVNIGSISSERAIPRVHlaAYSATKAAITMFTKSIAVEYARRHIRCNCVNPGIINSGMIKPYLDDPQAR 204
                   *******************8877668****************99999************************************************** PP

                   HHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEEEESTTG CS
  adh_short_C2 190 eelearaplgrlgtpeevaeaalfLasdeasyitGqtlvvDgGl 233
                   + le+r pl r+g+p++va+a+lfLasdea++itG++l vDgG 
    EPA04464.1 205 KVLEERLPLARIGEPSDVANAVLFLASDEANWITGAILNVDGGK 248
                   *******************************************6 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  204.8   1.1   5.9e-64   8.8e-61       1     191 [.       6     198 ..       6     202 .. 0.95

  Alignments for each domain:
  == domain 1  score: 204.8 bits;  conditional E-value: 5.9e-64
                 SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEEE---S.S--SSGGGCSH CS
   adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldvLvnNAGi.tgsgpfselse 98 
                 kv+++tGass IG+ +ak++++eGa+v++++r+ e le++ ke+++e ++   +++D+td+++v ++++++++ +gk+d+L+nNAG  + ++ f+e+s+
  EPA04464.1   6 KVAIITGASSDIGKGVAKRFVEEGAQVILIARNLEGLEKARKEIGNE-KSTASMSCDLTDESQVIQTINQIMNTYGKIDILINNAGAiNDPVHFHEMSD 103
                 89*******************************************96.789999********************************98999******** PP

                 HHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGG..TSB-TTBHHHHHHHHHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHHC CS
   adh_short  99 eewervievNltgvflltravlpamlkqssGrIvnvsSvag..kvpvagvaaYsAsKaavagltrslakelaptgirvnavaPGlvdTdmakelr 191
                 +e++++i++Nl+gvf++t+avl++m + ++G+Ivn++S+ +    p  ++aaYsA+Kaa++++t+s+a e+a++ ir+n+v+PG+++++m k+  
  EPA04464.1 104 SEIKKLIDINLFGVFHITKAVLNKMSETKNGSIVNIGSISSerAIPRVHLAAYSATKAAITMFTKSIAVEYARRHIRCNCVNPGIINSGMIKPYL 198
                 *****************************************434566789***************************************988765 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.3   3.1e-12   4.6e-09       4     159 ..       9     166 ..       7     185 .. 0.82

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 3.1e-12
                 EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS---EEEE-------.--TTT-- CS
          KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppikGvihaAgvlrd.klleemt 101
                 +itG+   +G+ +a+  +e+ga+ ++l++R+ +  e++++   e+ + + +   +++D++d+++v +++++i ++ ++i   i+ Ag+++d   + em+
  EPA04464.1   9 IITGASSDIGKGVAKRFVEEGAQ-VILIARNLEGLEKARK---EIGN-EKSTASMSCDLTDESQVIQTINQIMNTYGKIDILINNAGAINDpVHFHEMS 102
                 8********************96.6788999555555554...4444.4456789********************************99983579**** PP

                 HHHHHHHHTTTTHHHHHHHHHTTT....S--SEEEEEEEHHH..HH--TT-HHHHHHHHHHHHH CS
          KR 102 aedleqvlapKvkGawnLhelled....esldffvlfSSiag..llgsagqanYaaaNaflDal 159
                 ++++++++   + G+ ++ +++ +    ++   +v + Si++   +   + a+Y+a+ a +  +
  EPA04464.1 103 DSEIKKLIDINLFGVFHITKAVLNkmseTKNGSIVNIGSISSerAIPRVHLAAYSATKAAITMF 166
                 ***************9999998875555666678888888885566677778888887776655 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   1.2   4.1e-08   6.1e-05       2     171 ..       9     185 ..       8     244 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 4.1e-08
                 EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC......EEEE--TT-HH....HHHHHHHHH.T-SEEEE--S---HHHHHHSHHHHHH CS
   Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl......elveldltdrs....alerlfkee.qpdavihlAavggvaassedpadfie 89 
                 ++tGa+  iG+ ++k++ e+g +vi ++r+ ++ ++ar+e +        + +dltd+s     ++++++++ ++d+ i+ A+  + ++ + + +d  e
  EPA04464.1   9 IITGASSDIGKGVAKRFVEEGAQVILIARNLEGLEKARKE-IgnekstASMSCDLTDESqviqTINQIMNTYgKIDILINNAGAINDPVHFHEMSD-SE 105
                 89***************************96666665554.358999999*********555455566667789*******996665555555544.34 PP

                 HHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSS...BSTCSTTS----SSHHHHHHHHHHHHHHHHHHHHT-EEEEEEESE CS
   Epimerase  90 knlqgtlnlleaarkagvkrllflsSsevYGkdaeqp...keettltgplkpnspYaaaKlageklveayaaqyglnaiilrlfn 171
                 +   +  nl+ + + +++  +l+  S +  G   ++     e  +   p     +Y+a+K+a+   ++++a +y  + i  ++ n
  EPA04464.1 106 IKKLIDINLFGVFHITKA--VLNKMSETKNGSIVNIGsisSERAI---PRVHLAAYSATKAAITMFTKSIAVEYARRHIRCNCVN 185
                 444444455555444433..3333333333333332211033334...6688899999999999999999999977666655555 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.6   2.4e-07   0.00036       1      64 [.       6      68 ..       6      72 .. 0.81
   2 ?   -3.0   0.0       7.9   1.2e+04      15      28 ..     125     136 ..     114     164 .. 0.57

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.4e-07
                   EEEEE..TTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.-EEECECHHHHHHH-SE CS
  F420_oxidored  1 kigii..GaGnmgealasgllaagaqpheivvansrnpekaeelaeelg.vkvtavdneeaaeeadv 64
                   k++ii  ++ ++g+++a++++++g    +++++  rn e +e++++e+g  k ta+   ++ +e+ v
     EPA04464.1  6 KVAIItgASSDIGKGVAKRFVEEG---AQVILI-ARNLEGLEKARKEIGnEKSTASMSCDLTDESQV 68
                   68999944579*************...999988.9************99655555566666666665 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 7.9
                    HHHHHHTTS-GGCE CS
  F420_oxidored  15 asgllaagaqphei 28 
                    +++++++   + +i
     EPA04464.1 125 LNKMSETK--NGSI 136
                    33333332..2222 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.3   2.2e-06    0.0033       9      66 ..      16      74 ..       6      89 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.2e-06
                CCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-.HHHHCCCHHC CS
     3HCDH_N  9 tmGagiaavfasagleVvlvdiseealekalekieksleklvekgklk.eeeveaalar 66
                 +G+g+a+ f+++g +V l+ ++ e leka+++i ++ + +  +  l+ e++v +++++
  EPA04464.1 16 DIGKGVAKRFVEEGAQVILIARNLEGLEKARKEIGNEKSTASMSCDLTdESQVIQTINQ 74
                59********************************9944444333333314444444443 PP

>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.2   3.9e-06    0.0059      18     135 ..       5     135 ..       3     162 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.9e-06
                 CTTEEEEE----HHHHHHHHHHHHTT-EEEEEE-S-.SS--.........-TT-EEEE--SHHHHHHHHHHHH...TT-SEEEE--.-S--.EEES--- CS
         DFP  18 DpVRfisNrSSGkmGyalAeaaaarGaeVtlvsgpv.slet.........pegvevvkvesaeemleaveeal...keadivimaA.AvaD.yrpkeaa 101
                 D+V +i+  SS   G  +A++++++Ga+V l++ +   le+          ++    + ++ ++  +++++ +    + di+i  A A+ D  + +e +
  EPA04464.1   5 DKVAIITGASS-DIGKGVAKRFVEEGAQVILIARNLeGLEKarkeignekSTASMSCDLTDESQVIQTINQIMntyGKIDILINNAgAINDpVHFHEMS 102
                 88999999998.79*******************996245533333333221111233344444444444433322266699998665899944558888 PP

                 ----------..----EEE---HHHHHHHC-S.S CS
         DFP 102 eeKikkeeeeeeltleleknpdilaelaekkkkk 135
                 ++ ikk   + +l   ++ ++ +l++++e+k+ +
  EPA04464.1 103 DSEIKK-LIDINLFGVFHITKAVLNKMSETKNGS 135
                 899998.444456666777777777776655544 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   1.7   1.6e-05     0.024       1      78 [.       9      84 ..       9     195 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.6e-05
                   EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHH.....T-SE CS
  GDP_Man_Dehyd  1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaev.....qpde 78
                   +iTG +  iG  +a++++e+g +v+ i r+ + ++ +r e         +e++   +++DltD+s++++ ++++     ++d 
     EPA04464.1  9 IITGASSDIGKGVAKRFVEEGAQVILIARNLEGLEKARKEIG-------NEKSTASMSCDLTDESQVIQTINQImntygKIDI 84
                   59***********************99988777776665542.......23456789************99998444445555 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   2.3   7.9e-06     0.012       2     161 ..       9     179 ..       8     191 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 7.9e-06
                      EEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT...T-SEEEE------HH... CS
  Polysacc_synt_2   2 lvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleel.kvdvvfhaAAlKhVP... 91 
                      ++tGa+  iG+ + ++++++ ++ i++  +    l + +ke+ +e+++ +++++   +  + +  ++++++++++ k+d++++ A   + P   
       EPA04464.1   9 IITGASSDIGKGVAKRFVEEGAQVILIARN-LEGLEKARKEIGNEKSTASMSCD---LTDESQVIQTINQIMNTYgKIDILINNAGAINDPvhf 98 
                      69****************999876666555.55788888888777777667665...2223344466677777764789988877554444111 PP

                      ..HHHHSHHHHHHHHHHHHHHHHHHH....HHTT-SEEE...EEEEGGGSS--..SHHHHHHHHHHHHHHHGGG--SSS-- CS
  Polysacc_synt_2  92 ..lveenpleaiktNvlgtenvieaa....ieagvkkvv...liStDKAvnPt..nvmGatKrlaekllqalakeseekkt 161
                        + ++++ + i+ N +g  ++ +a      e++  ++v    iS+ +A+  +   ++ atK++  +++ ++a e ++++ 
       EPA04464.1  99 heMSDSEIKKLIDINLFGVFHITKAVlnkmSETKNGSIVnigSISSERAIPRVhlAAYSATKAAITMFTKSIAVEYARRHI 179
                      113345667789999999655555541000444444455222578899987662245788888888877777766655555 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.0   9.8e-05      0.15      10      90 ..       3      86 ..       1     114 [. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.8e-05
                  .TT-EEEEES-S.HHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EE...EEGCGHHHHHHT-SEEEE-SSSSS-SB CS
  Shikimate_DH 10 lkekkvlliGaG.emaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiea...lkleelkellaeadvvisataseepil 90
                  lk+k +++ Ga   +++ vak ++++g++ v+ + R+le  ++ ++e+++e+++a   ++l++ +++++ ++ ++   +  ++++
    EPA04464.1  3 LKDKVAIITGASsDIGKGVAKRFVEEGAQ-VILIARNLEGLEKARKEIGNEKSTAsmsCDLTDESQVIQTINQIMNTYGKIDILI 86
                  7788889999963699************9.77778**********9998776654222667777777777776666555555555 PP

>> 5_nucleotid_C  5'-nucleotidase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00011      0.16      13      51 ..      57      96 ..      44     124 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
                   ---HH.TS--HHHHHHHHHHTGSTT--EEEEEGGG----B CS
  5_nucleotid_C 13 dlalr.tgetnlgnliadalraaagadialangggiradl 51
                    ++++ t e+++++ i++ ++++ + di + n+g+i++ +
     EPA04464.1 57 SMSCDlTDESQVIQTINQIMNTYGKIDILINNAGAINDPV 96
                   4566689*****************************9955 PP

>> DUF2660  Protein of unknown function (DUF2660)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       4.1   6.2e+03      53      68 ..      15      30 ..       2      39 .. 0.68
   2 ?   11.1   0.0   0.00029      0.43      40      82 ..     105     147 ..      65     152 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 4.1
     DUF2660 53 ydltkiilkkfskedv 68
                 d+ k + k+f  e  
  EPA04464.1 15 SDIGKGVAKRFVEEGA 30
                5888888999987653 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00029
     DUF2660  40 slkekielswqflydltkiilkkfskedvvevnkiGsklfenG 82 
                  +k++i++    ++ +tk +l+k+s      +  iGs+  e  
  EPA04464.1 105 EIKKLIDINLFGVFHITKAVLNKMSETKNGSIVNIGSISSERA 147
                 5788999999999************************988865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       749  (0.0417759); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 1570.10
//
Query:       EPA04465.1  [L=128]
Description: hypothetical protein BG20_I1013 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 860.01
//
Query:       EPA04466.1  [L=193]
Description: hypothetical protein BG20_I1015 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-54  184.0   0.0    1.9e-54  183.9   0.0    1.0  1  DUF99           Protein of unknown function DUF99
  ------ inclusion threshold ------
      0.078   12.9   0.2       0.12   12.3   0.2    1.3  1  Kinase-PolyVal  Serine/Threonine/Tyrosine Kinase found in pol


Domain annotation for each model (and alignments):
>> DUF99  Protein of unknown function DUF99
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.9   0.0   2.1e-58   1.9e-54       2     182 ..      10     186 ..       9     187 .. 0.98

  Alignments for each domain:
  == domain 1  score: 183.9 bits;  conditional E-value: 2.1e-58
                 GSEEEEEEEEE.....-SS-EEEEEEEEETT.EEEEEEEEEE-TT-S-HHHHHHHHHCC-TTTTEEEEEESSSEETTTEE--HHHHHHHH---EEEEES CS
       DUF99   2 eirvlGiddsfferkkkdgksvlvGvvmradrvvdgvafgrvtvdGtDateaiielvkrleredirvvlldGitiagFNvvDlerlheetglPviavtr 100
                 ++r l+i++sf  + ++++ks+l G vmr+d v+dgv+fg++t  G Date+i++++ +l+r+di+++ll+G++++++N++D+++l++++++Pvi +++
  EPA04466.1  10 GLRCLAIAESF--K-QNSEKSILTGLVMRKDFVIDGVVFGSATLKGNDATEQILQMYYDLNRSDINYLLLSGLIVSMYNIIDIKKLFSSLKIPVIGIAY 105
                 79*********..4.459********************************************************************************* PP

                 S---HHHHHHCCT.TSTTH.HHHHHHHHHC.---EEETT....EEEEEESS-HHHHHHHHHHC-SSSSS-HHHHHHHHHHHHH CS
       DUF99 101 eepdlgklekaLrkhfpde.eeRlelieklgerieevektgeelyvravGieleeaaklvrkltlegriPEPlRvAhliAsal 182
                 +e++ g +e+aL++hfp++ e++++ ++klg+r++++ +t+++l+vr+ G+ l+++ +l++ ltl+g +PEP+R+++liA+al
  EPA04466.1 106 HESQ-G-IENALKQHFPKSfETKINEYKKLGKRETITLHTNHNLFVRYEGCMLSDVHHLLNDLTLHGSVPEPVRISQLIANAL 186
                 ****.8.*************************************************************************986 PP

>> Kinase-PolyVal  Serine/Threonine/Tyrosine Kinase found in polyvalent proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   1.3e-05      0.12      65     139 ..      87     161 ..      71     169 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.3e-05
  Kinase-PolyVal  65 llhNllFpntayellGfa.kseeklvavvkQpfikadeevdleevkeflekngfentrnndyinkelgliledlhd 139
                     +    lF++ ++ ++G+a ++++++   +kQ+f k+  e++ +e k++ ++     + n++ + +  g +l+d+h 
      EPA04466.1  87 IDIKKLFSSLKIPVIGIAyHESQGIENALKQHFPKS-FETKINEYKKLGKRETITLHTNHNLFVRYEGCMLSDVHH 161
                     545579************9999***********988.999**********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1267.36
//
Query:       EPA04467.1  [L=298]
Description: NAD binding domain of 6-phosphogluconate dehydrogenase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.3e-37  126.8   0.6    1.5e-36  126.0   0.6    1.4  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
    1.6e-19   70.3   0.0    2.8e-19   69.6   0.0    1.4  1  NAD_binding_11  NAD-binding of NADP-dependent 3-hydroxyisobut
    6.2e-07   29.6   0.2    1.1e-06   28.7   0.2    1.6  1  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
    1.4e-06   28.8   1.2    2.8e-06   27.8   0.6    1.8  2  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
    3.5e-05   23.2   0.1    6.6e-05   22.3   0.1    1.4  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
    3.5e-05   23.5   0.1    6.1e-05   22.7   0.1    1.4  1  ApbA            Ketopantoate reductase PanE/ApbA
    5.5e-05   23.1   0.5     0.0014   18.6   0.5    2.4  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
    8.9e-05   22.3   0.1     0.0041   17.0   0.1    2.3  2  Rossmann-like   Rossmann-like domain
     0.0003   20.4   0.2    0.00071   19.2   0.2    1.7  1  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
    0.00031   20.4   1.7      0.067   12.8   0.1    2.3  2  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
      0.001   19.1   0.1     0.0046   16.9   0.1    2.1  2  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
  ------ inclusion threshold ------
      0.062   12.5   0.1      0.092   12.0   0.1    1.2  1  FAD_binding_3   FAD binding domain


Domain annotation for each model (and alignments):
>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.0   0.6     1e-39   1.5e-36       1     156 [.       3     160 ..       3     162 .. 0.98

  Alignments for each domain:
  == domain 1  score: 126.0 bits;  conditional E-value: 1e-39
                    EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS...HCCC--TT-EEEE-S--- CS
  NAD_binding_2   1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdevieg...llealkkgdilidgstss 93 
                    k+g+iG G++G+    +ll++g++++v+nrtkek++el ++gak+a+s++ ++++ ++vit+vk+ +av+++ +g   ++e +++g ++ d+st++
     EPA04467.1   3 KVGIIGAGMLGNAVGIHLLESGFDLIVFNRTKEKTNELKNKGAKIADSPKIVAENSELVITIVKDAEAVKQISFGkngIIEGYHEGLVVADMSTIN 98 
                    69********************************************************************************************** PP

                    HHHHHHHHHHHHHTT-EEEEEEEESHHHHHHHT-EEEEEEE-HHHHHHHHHHHHHHEEEEEEE CS
  NAD_binding_2  94 pedtrelakelkekglkfldaPVSGGeegAekGtLsimvGGseeafervkpvleaigakvthv 156
                    p ++++++k+  e ++  +d+PV GG + A++G+L +m++G+e++f++ k+v+e+i++k++ +
     EPA04467.1  99 PIESKNISKKFLEFNIIKIDIPVMGGPNVAKTGELVLMASGDEKTFNKFKNVFEKIANKTF-F 160
                    *********************************************************9988.4 PP

>> NAD_binding_11  NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.6   0.0   1.8e-22   2.8e-19       1     121 [.     165     284 ..     165     285 .. 0.97

  Alignments for each domain:
  == domain 1  score: 69.6 bits;  conditional E-value: 1.8e-22
  NAD_binding_11   1 GaGqavKlvnnlllainlaaasEalvlaekaGldpekvlevinassgrsnalenklpqrvlsrdfdpgFaldlmlKDlglalelareagaplpll 95 
                     G+++ vKl  nl +++  + +sE+++la+ a +dp+ +l+++n+   +  ++enk   ++++++f p+F+l+ + KD+++++++a+++g++lp++
      EPA04467.1 165 GTAHLVKLSMNLQITMLALSLSEGITLARNANVDPKIFLDILNSTYFKTGMSENKAY-KMIQDEFSPTFTLANLKKDISIITDTADSLGIKLPMI 258
                     899****************************************************98.699********************************** PP

  NAD_binding_11  96 alaeqlyaaaaaegggdaDhsaivrl 121
                     + ae+++ +a ++g g+ D++ i+ +
      EPA04467.1 259 KKAEEVFTEAVKQGFGEIDYTGILAY 284
                     *********************99875 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.2   7.7e-10   1.1e-06      13      57 ..       2      45 ..       1     118 [. 0.76

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 7.7e-10
                  -EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT CS
  Shikimate_DH 13 kkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelk 57
                   kv +iGaG++++ v  hLl++g++ ++v+NRt e+ +el ++  
    EPA04467.1  2 TKVGIIGAGMLGNAVGIHLLESGFD-LIVFNRTKEKTNELKNKGA 45
                  5899********************9.**************87752 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.6   1.8e-09   2.8e-06       1      72 [.       3      68 ..       3      79 .. 0.89
   2 ?   -3.2   0.0       9.1   1.4e+04      21      47 ..     130     152 ..     126     159 .. 0.59

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 1.8e-09
                   EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HH CS
  F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpe 72
                   k+giiGaG +g a+   ll++g    +++v  +r++ek +el+++ g+k+   + + +ae+++ v+  vk +
     EPA04467.1  3 KVGIIGAGMLGNAVGIHLLESG---FDLIVF-NRTKEKTNELKNK-GAKIAD-SPKIVAENSELVITIVKDA 68
                   79********************...9***67.**********888.568888.8999999******999865 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 9.1
                    TTS-GGCEEEEEESSCCCHHHHHHHHC CS
  F420_oxidored  21 agaqpheivvansrnpekaeelaeelg 47 
                    +g   + +++a s ++++ +++++ ++
     EPA04467.1 130 TG---ELVLMA-SGDEKTFNKFKNVFE 152
                    44...444434.777777777766554 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.1   4.4e-08   6.6e-05      38      99 ..       3      65 ..       1      75 [. 0.82

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 4.4e-08
                  EEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHH.HH-SEEEE-S CS
  2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelvsleell.aesDivslhl 99
                  +vGiiG+G +G+av   l + g+++i+++r+k+k++e +++g++ ++  +++ ++s+ v+  +
    EPA04467.1  3 KVGIIGAGMLGNAVGIHLLESGFDLIVFNRTKEKTNELKNKGAKIADSPKIVaENSELVITIV 65
                  89*******************************999*******99866665505566665554 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.1   4.1e-08   6.1e-05       1      50 [.       4      52 ..       4      77 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 4.1e-08
                EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETTCEE CS
        ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseggee 50
                + i+GaG +G  ++ +L + g d ++ +r++ + ++lk++G ++ ++   +
  EPA04467.1  4 VGIIGAGMLGNAVGIHLLESGFDLIVFNRTKeKTNELKNKGAKIADSP--K 52
                57******************************************9988..2 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.5     9e-07    0.0014       1      87 [.       3      86 ..       3      92 .. 0.78
   2 ?    1.7   0.0      0.13     2e+02     141     172 ..     125     157 ..     122     163 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 9e-07
                EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES-HHHHH.C-SEEEE-S- CS
     3HCDH_N  1 kvaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalarisfttdleeav.dadlviEavv 87
                kv++iGaG++G+ +   ++++g++  ++++++e+ ++ ++k +k     + + k+ +e+ e +++ ++ ++ ++++  + + +iE   
  EPA04467.1  3 KVGIIGAGMLGNAVGIHLLESGFDLIVFNRTKEKTNELKNKGAK----IADSPKIVAENSELVITIVKDAEAVKQISfGKNGIIEGYH 86
                79****************************99998887777665....5566677777777777777777777777777777777655 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.13
                 TTT--EEEEEE-TT--HHHHHHHHHHHHHT.T- CS
     3HCDH_N 141 pplmkLvEvvrgekTseetvatvvelakki.gk 172
                 p++ k+ E+v  ++ +e+t+++++++++ki +k
  EPA04467.1 125 PNVAKTGELVLMASGDEKTFNKFKNVFEKIaNK 157
                 677888899********************9555 PP

>> Rossmann-like  Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   2.7e-06    0.0041      12     108 ..       3      99 ..       1     105 [. 0.73
   2 ?    2.8   0.0     0.066        98      56      81 ..     118     143 ..     104     168 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.7e-06
  Rossmann-like  12 svGiisaGrvGtalgaaleraghvvvgisaisaasreraer..rlPdvpvlevedvaaraellllavPdaelpglvk..glaatgavraGtivaht 103
                    +vGii+aG +G a+g  l  +g  ++  +   + ++e+ ++  ++ d+p +    va+++el++  v dae  + ++  +    +  ++G +va +
     EPA04467.1   3 KVGIIGAGMLGNAVGIHLLESGFDLIVFNRTKEKTNELKNKgaKIADSPKI----VAENSELVITIVKDAEAVKQISfgKNGIIEGYHEGLVVADM 94 
                    7******************99999888777776666655431155555544....6799***********97665542122334567788888887 PP

  Rossmann-like 104 sganG 108
                    s+ n 
     EPA04467.1  95 STINP 99 
                    77665 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.066
  Rossmann-like  56 dvpvlevedvaaraellllavPdael 81 
                    d+pv+  ++va+  el+l+a  d + 
     EPA04467.1 118 DIPVMGGPNVAKTGELVLMASGDEKT 143
                    78999999************999865 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.2   4.8e-07   0.00071       6      72 ..       3      69 ..       1      92 [. 0.85

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 4.8e-07
                -EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHH.HHHT-SEEEE-S-HHH CS
        IlvN  6 kiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvae.avkkadvvmiliPDel 72
                k+ +iG G  G+a +  l +sg+d++v +r+++ ++++ k++g ++++  + +++++++v++++ D  
  EPA04467.1  3 KVGIIGAGMLGNAVGIHLLESGFDLIVFNRTKE-KTNELKNKGAKIADSPKiVAENSELVITIVKDAE 69
                89*************************999988.6677888999988776615678999999998864 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.1   4.5e-05     0.067       2      48 ..       3      49 ..       2      57 .. 0.93
   2 !    7.0   0.2    0.0027         4      19      84 ..      54     119 ..      50     132 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.5e-05
                    EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS-- CS
  UDPG_MGDP_dh_N  2 kisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiye 48
                    k+ +iG+G +G   ++ l e g+++i+    +ek ++l+++  +i +
      EPA04467.1  3 KVGIIGAGMLGNAVGIHLLESGFDLIVFNRTKEKTNELKNKGAKIAD 49
                    899************************************99998875 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0027
                     HHHCTSEEEEE-S-HHHHHHHCTTS-SS--TTHHHHHHHHCHTTTEEEES-HHHHHHC-SEEEE-- CS
  UDPG_MGDP_dh_N  19 laeighevigvDideekvdklnsgkipiyepgLeelvkkavesgrlsfttdvekaveeadvifiaV 84 
                     +ae    vi + +d+e+v+++  gk  i+e   e lv + +++ +   + +++k++ e ++i i +
      EPA04467.1  54 VAENSELVITIVKDAEAVKQISFGKNGIIEGYHEGLVVADMSTINPIESKNISKKFLEFNIIKIDI 119
                     67888889*********************************999999999****999999998765 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   3.1e-06    0.0046       1      52 [.       3      54 ..       3      76 .. 0.84
   2 ?   -1.2   0.0       1.2   1.7e+03     121     137 ..     114     129 ..      93     134 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.1e-06
                    -EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHHSSBTTTBTT-- CS
  NAD_Gly3P_dh_N  1 kiavlGaGswGtalAkvlaenghevrlwvreeelieeineehenvkyLpgik 52
                    k++++GaG+ G a+ ++l e g +  ++ r +e ++e++++    +  p+i 
      EPA04467.1  3 KVGIIGAGMLGNAVGIHLLESGFDLIVFNRTKEKTNELKNKGAKIADSPKIV 54
                    79*************************************9987777666655 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.2
                     HH-S--EEEEESS--HH CS
  NAD_Gly3P_dh_N 121 elkeekvavlsGpslAe 137
                     ++k++ + v+ Gp++A+
      EPA04467.1 114 IIKID-IPVMGGPNVAK 129
                     34444.99999999996 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   6.1e-05     0.092       2      43 ..       2      43 ..       1      48 [. 0.91

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.1e-05
                   EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS-- CS
  FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlprad 43
                   t+V I+GaG  G   +  L e G + ++ ++ ++++++ + +
     EPA04467.1  2 TKVGIIGAGMLGNAVGIHLLESGFDLIVFNRTKEKTNELKNK 43
                   79*********************************9987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1985.40
//
Query:       EPA04468.1  [L=39]
Description: hypothetical protein BG20_I1021 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      148  (0.00825478); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.29s 00:00:00.65 Elapsed: 00:00:00.45
# Mc/sec: 259.21
//
Query:       EPA04469.1  [L=405]
Description: geranylgeranyl reductase family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-17   63.9   0.6      1e-07   31.9   0.1    2.3  2  DAO             FAD dependent oxidoreductase
    3.5e-16   59.4   0.0    5.3e-16   58.8   0.0    1.3  1  FAD_binding_3   FAD binding domain
    6.5e-14   52.1   0.1    9.1e-14   51.6   0.1    1.2  1  FAD_oxidored    FAD dependent oxidoreductase
    1.9e-12   46.8   0.2    2.8e-07   29.8   0.0    2.2  2  Trp_halogenase  Tryptophan halogenase
    3.6e-11   42.8   0.5    4.4e-07   29.3   0.1    2.1  2  FAD_binding_2   FAD binding domain
    1.8e-09   37.3   1.9    1.1e-06   28.2   0.3    2.2  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    3.4e-08   32.6   0.4    3.6e-06   26.0   0.1    2.1  2  HI0933_like     HI0933-like protein
    7.4e-08   31.8   0.1    1.1e-07   31.3   0.1    1.2  1  Lycopene_cycl   Lycopene cyclase protein
    8.5e-07   28.4   0.8    5.5e-05   22.5   0.1    2.2  2  Thi4            Thi4 family
    1.6e-06   28.2   0.1    6.4e-06   26.3   0.1    2.0  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
      3e-06   26.6   0.6      1e-05   24.8   0.3    1.8  2  GIDA            Glucose inhibited division protein A
      8e-05   23.1   1.1      0.058   14.0   0.2    2.4  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    0.00012   21.5   1.1    0.00031   20.1   1.1    1.7  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.024   14.5   0.2      0.063   13.2   0.1    1.6  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
       0.13   12.6   0.1       0.29   11.4   0.1    1.6  1  TrkA_N          TrkA-N domain
       0.15   11.4   0.2        1.2    8.4   0.0    2.0  2  GMC_oxred_N     GMC oxidoreductase


Domain annotation for each model (and alignments):
>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.1   9.4e-11     1e-07       1      44 [.       8      51 ..       8      59 .. 0.89
   2 !   30.6   0.0   2.3e-10   2.6e-07     138     206 ..      88     159 ..      81     309 .. 0.72

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 9.4e-11
                EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEE CS
         DAO  1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgll 44
                d+v++GGG +G+s+Aye+a+ g  V+llek++ ++   S r+sg+ 
  EPA04469.1  8 DLVVVGGGPAGSSVAYEAAKNGikVALLEKEETIA--YSVRTSGVT 51
                89*****************************7776..777777765 PP

  == domain 2  score: 30.6 bits;  conditional E-value: 2.3e-10
                 TTEEEEEHHHHHHHHHHHHHHTT-EEEESECEEE.EEEEETCEEEEEEECT.EEE.EEEEEEEE--GGGHHH CS
         DAO 138 pdtgqvdpakltaalaraaealGveilegtevtg.leeedgkvwgverttp.gen.daadavVnaaGawsdl 206
                 p+++++d +k  ++la++ae++G++i+++t++++ ++++dg+++gv  t++ ge+ ++ + v+ a G  s  
  EPA04469.1  88 PHAAVLDVRKTYRWLAQQAEKHGADIFLKTNIKDvIKNKDGDIAGVSGTSKeGEViFHSKVVIDASGFSSVV 159
                 89999*****************************669999******955555877655588*****977633 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   0.0   4.8e-19   5.3e-16       3     338 ..       8     327 ..       6     338 .. 0.75

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 4.8e-19
                    EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEEEEEEECCCCCEEEEEHHCHHCST- CS
  FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradglnqrtmellrqlGledrilaegapnelmgealynelsdtpkaradlelessper 98 
                    d ++VG+GpaG + a + ++ G++v l+ek +t ++  r +g++   +e++++ G+ d +++  +  +                + ++++  + ++
     EPA04469.1   8 DLVVVGGGPAGSSVAYEAAKNGIKVALLEKEETIAYSVRTSGVT--WIESIKEFGIPDDCYNPIKNYSF---CSP---------NNEVTITDTIPH 89 
                    779*************************************9985..69************987733332...222.........3355567999** PP

                    CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEEEE--GTT-HHHHHHTGGEEEEEEEEEEEEEEEEEEC CS
  FAD_binding_3  99 vtvypqteleriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvrakYlvGaDGgrStvrktlgiefegeetvyeagvldvlfda 194
                     +v+ + ++ r L+++ae++g+++  kt+++ + ++++g  a v + +++ e  +++k ++ a G+ S v k++g+  + e+        ++  ++
     EPA04469.1  90 AAVLDVRKTYRWLAQQAEKHGADIFLKTNIKDVIKNKDGDIAGVSGTSKEGEVIFHSKVVIDASGFSSVVSKSMGFVTQWER-FGA----GAEYEV 180
                    *********************************************99999999**********************9744333.212....222222 PP

                    -SCCCTTC..CEEEEECCTTEE..EEEECCETEEEEEEEEECCE-GGGSCCCHHHHHHHHHHHHHHTTSSCEEEEEEEE.EEEE..EEEEESSSEE CS
  FAD_binding_3 195 dlsdivep..lvlilsaesrgv..mviPlentlerfyvqvearaekeersekfteeevkarlreivgektldveieevs.awtv..aqrvaekyrk 283
                    + +++ e+  + +++++ s+     + P+ n     +v + ++  k e+  +  +e++k+ +++ +g+     +i+ ++ ++++  ++ +++k   
     EPA04469.1 181 KAENVDEEtwWLMVGQKYSPAGyaWIFPVGN----NIVRIGVGVGKPESAVDP-TERLKELIDSKTGPISKLGKITPIEfHYGLipNDGLTRKTVY 271
                    3333333344444444443333458999999....334444444333333333.356888888888887777777776623333337889999999 PP

                    TTEEE-GGGTEEE-STTSHHHHHHHHHHHHHHHHHHHHHT.TSS-GGGGHHHHHHH CS
  FAD_binding_3 284 grvflaGDAaHihpPtgGqGlNtaiqDavnLawkLaavlk.GeAkeelLdtYeeer 338
                    +++ l+GD+a    P    G+  ai+     ++   +++k G+ +e+ L +Yee+ 
     EPA04469.1 272 NNLILVGDSAGQANPLVLEGIRYAIKFGRIAGKIASEAIKfGKTDEDALYAYEENW 327
                    99999999999999998888888888777777777777766778888888887765 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.6   0.1   8.1e-17   9.1e-14       1     149 [.       8     159 ..       8     194 .. 0.84

  Alignments for each domain:
  == domain 1  score: 51.6 bits;  conditional E-value: 8.1e-17
  FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaeeqvvtgiareflerlrqrgga....rlkkrskwn.......tfep 86 
                   D+vVvGGgpaG   A+ Aa++G kv+L+e+++ +   +   +v++++  k       gi ++ ++ +++   +    +     + +       + ++
    EPA04469.1   8 DLVVVGGGPAGSSVAYEAAKNGIKVALLEKEETIAYSVRTSGVTWIESIK-----EFGIPDDCYNPIKNYSFCspnnE----VTITdtiphaaVLDV 95 
                   99******************************998888888888888866.....89**********77333333221....111123445669999 PP

  FAD_oxidored  87 evakavleemlaeagvtvllntrlveveke.gkriesvtveskegrktirAkvfiDATgdGdla 149
                   +   + l +  +++g +++l+t +++v+k+ +++i +v   skeg+  +++kv+iDA+g   ++
    EPA04469.1  96 RKTYRWLAQQAEKHGADIFLKTNIKDVIKNkDGDIAGVSGTSKEGEVIFHSKVVIDASGFSSVV 159
                   99999999999******************74677******9999**************976665 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.3   7.7e-06    0.0086       2      60 ..       9      63 ..       8      68 .. 0.86
   2 !   29.8   0.0   2.5e-10   2.8e-07     136     338 ..      76     294 ..      65     330 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 7.7e-06
                    EEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS---SS-EE--THHHHTHHHHT--H CS
  Trp_halogenase  2 ivivGGGtaGwlaAaalakalkgklevtlveseeigtvgvGeatipsirkllrlLgide 60
                    +v+vGGG+aG+ +A   ak +   ++v l+e+ee+  + v  + ++ i+ +   +gi++
      EPA04469.1  9 LVVVGGGPAGSSVAYEAAKNG---IKVALLEKEETIAYSVRTSGVTWIESIK-EFGIPD 63
                    79************9999998...9**************9999998887654.456665 PP

  == domain 2  score: 29.8 bits;  conditional E-value: 2.5e-10
                     SB-TT..S-B-S--EEEE-HHHHHHHHHHHHHHCT-EE.EE--EEEEEE-TTS-EEEEEETT..S-E.EE-SEEEE-SGGG-IIIIIIT---EEE CS
  Trp_halogenase 136 prekd..glsalsyAyhldaalyakfLrrvaearGvtr.vegkvvevqldedgrveslrled..gre.veadlfiDcsGfrgllieqaLktgfed 224
                     +++++   + ++ +A  ld ++  ++L + ae++G ++ +++++++v  ++dg+++++  ++  g++ +    +iD+sGf + + ++    gf +
      EPA04469.1  76 SPNNEvtITDTIPHAAVLDVRKTYRWLAQQAEKHGADIfLKTNIKDVIKNKDGDIAGVSGTSkeGEViFHSKVVIDASGFSSVVSKSM---GFVT 167
                     4455556778999***********************973688999999999*******87666566526899**********999996...6666 PP

                     -TTT----EEEEEEEE--H..---SSEEEEE-SSEEEEEEEETTEEEE...EEEE-TTTS-HHHHHHHHHHHCT--TTTS-..EEEE---EE... CS
  Trp_halogenase 225 wsdvLltdrAlavqvesee..lvepytrataekaGWtWkiPLqhrlgn...GyvyssahadddeAlaellaeldgkleaep..rkirfttGr... 309
                       + +       v+ e+++  +   + +     aG  W  P  +++     G+   ++ +d  e l+el+    g   +      i+f+ G    
      EPA04469.1 168 QWERFGAGAEYEVKAENVDeeTWWLMVGQKYSPAGYAWIFPVGNNIVRigvGVGKPESAVDPTERLKELIDSKTGPISKLGkiTPIEFHYGLipn 262
                     6677767777777777777544444555778899********98765551155556777899999999998766655444327899999999999 PP

                     ...ES-SEETTEEE-CCCTEE--CCCS-HHHH CS
  Trp_halogenase 310 ...rkqawvknvvalGlasgfvePlestsihl 338
                         +++  +n++++G+++g  +Pl   +i  
      EPA04469.1 263 dglTRKTVYNNLILVGDSAGQANPLVLEGIRY 294
                     9998888889**************98777765 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.1   3.9e-10   4.4e-07       1      45 [.       8      51 ..       8      64 .. 0.83
   2 !   11.9   0.0   7.8e-05     0.087     140     200 ..      95     154 ..      80     188 .. 0.83

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 3.9e-10
                   SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-E CS
  FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgi 45
                   D++V+G+G AG + A+eaa++G kva++eke+     ++  +G  
     EPA04469.1  8 DLVVVGGGPAGSSVAYEAAKNGIKVALLEKEET-IAYSVRTSGVT 51
                   89*****************************96.22344445555 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 7.8e-05
                    HHHHHHHHHHHHHTCTEEEEESEEEEEEEEC.TTEEEEEEEEETTTTCEEEEEESEEEE--- CS
  FAD_binding_2 140 ghallarlvesarkagvdfqerteadeLive.dgrvtGavvenpesgrevrirakavvlatg 200
                     ++    l+++a+k+g d++ +t+++++i + dg++ G+  +  ++++ev +++k v++a+g
     EPA04469.1  95 VRKTYRWLAQQAEKHGADIFLKTNIKDVIKNkDGDIAGVSGT--SKEGEVIFHSKVVIDASG 154
                    566677899*********************6488*****999..999999888888888776 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.3   9.5e-10   1.1e-06       1      37 [.       7      43 ..       7      58 .. 0.93
   2 !    8.7   0.1   0.00083      0.93     167     237 ..      80     155 ..      49     178 .. 0.77

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 9.5e-10
                 CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtcln 37
                 +d+vv+GgGpAG ++a ++a++g+kv+l+e+e+t+ +
   EPA04469.1  7 YDLVVVGGGPAGSSVAYEAAKNGIKVALLEKEETIAY 43
                 689***************************9999887 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00083
                  EEEEEESSSSSSTTS-.HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE....EEEEEETTSCE.EEESEEEE-S-E CS
                  xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxx.xxxxxxxxxxxx RF
  Pyr_redox_2 167 evtlveardrllrald.kelsaaleealekeGvevklgtsvkeidgnge....klevvledgee.idadlvvvavGv 237
                  evt+ +  ++    ld ++  ++l+++ ek+G ++ l+t++k++++n++     ++ + ++ge+ +  + v+ a G+
   EPA04469.1  80 EVTITDTIPHAA-VLDvRKTYRWLAQQAEKHGADIFLKTNIKDVIKNKDgdiaGVSGTSKEGEViFHSKVVIDASGF 155
                  677777777776.455467778999************************9554444555555554555555556565 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.1   3.2e-09   3.6e-06       2      43 ..       8      49 ..       7      52 .. 0.96
   2 !    4.7   0.0    0.0091        10     113     167 ..     100     157 ..      94     180 .. 0.73

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 3.2e-09
                 SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHHHCG CS
  HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrKilisG 43
                 d++v+GgG+AG   A +aak+g +V+llek+++++  +++sG
   EPA04469.1  8 DLVVVGGGPAGSSVAYEAAKNGIKVALLEKEETIAYSVRTSG 49
                 89***********************************99999 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0091
                  HHHHHHHHHHT-EEE-S--EEEEECETTE.EE.EEE...TTEEEEESEEEE----SS- CS
  HI0933_like 113 dallkelkeagvklrletevksvekeedgkfr.vkt..kseeeleadklvlAtGGlSi 167
                  + l +++++ g ++ l+t++k+v k++dg +  v+   k++e +  +k+v+   G S 
   EPA04469.1 100 RWLAQQAEKHGADIFLKTNIKDVIKNKDGDIAgVSGtsKEGEVIFHSKVVIDASGFSS 157
                  67999******************99998865414433456677777777775555554 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.1   9.5e-11   1.1e-07       1     175 [.       8     193 ..       8     212 .. 0.72

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 9.5e-11
  Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieaspsllfpnny...vWsdefedlgaleecvehsWsgtivylddgkkillgraYgrvss.krlkee 92 
                    D+vv+G+GpAg s+A +   ak g+kv l+e  + + ++ +    +W    ++ g  ++c +   +      +++ +i+ + + + v   ++  + 
     EPA04469.1   8 DLVVVGGGPAGSSVAYEA--AKNGIKVALLEKEETIAYSVRTsgvTWIESIKEFGIPDDCYNPIKNYSFCSPNNEVTITDTIPHAAVLDvRKTYRW 101
                    9*****************..************9998765544333999999999988899988877777777888888888888887541455566 PP

  Lycopene_cycl  93 llerlv.engvklleakvesveeeeage...slvvleggr.kirarlvvdarglaslkkarrlgl..Qt..f.yGvevevdnppfdldkmvlM 175
                    l+++   +++ ++l+  ++ v ++++g+   ++ + ++g+   ++++v+da+g +s+  ++ +g+  Q   f  G e ev+++  d ++  lM
     EPA04469.1 102 LAQQAEkHGADIFLKTNIKDVIKNKDGDiagVSGTSKEGEvIFHSKVVIDASG-FSSVVSKSMGFvtQWerFgAGAEYEVKAENVDEETWWLM 193
                    6666664666799********9999855111344445555266899*******.777755554441132112246666666666666665555 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.1   4.9e-08   5.5e-05      18      50 ..       7      38 ..       2      56 .. 0.87
   2 ?    4.2   0.0      0.02        22     104     153 ..     102     151 ..      78     173 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 4.9e-08
                EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESS CS
        Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailers 50
                 D+v+vG+G++G + ay  ak+ ++kva+le++
  EPA04469.1  7 YDLVVVGGGPAGSSVAYEAAKN-GIKVALLEKE 38
                69********************.********86 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.02
                 HHHHHTSTTEEEEESEEEEEEEEETBTEEEEEEEEEHHHHTCTTTSS.-B CS
        Thi4 104 lskvlqlanvkllnavaveDlivregegvaGvvinwtlvelahdtqscvD 153
                 l++  ++ ++ ++  + + D+i  ++  +aGv   ++  e+  +++ ++D
  EPA04469.1 102 LAQQAEKHGADIFLKTNIKDVIKNKDGDIAGVSGTSKEGEVIFHSKVVID 151
                 45555668999***********999999***9877776666644556665 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.1   5.7e-09   6.4e-06       1      32 [.      11      42 ..      11      57 .. 0.88
   2 ?   -2.2   0.0       4.4   4.9e+03      43      60 ..     105     118 ..      97     124 .. 0.69

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 5.7e-09
                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSS CS
  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlG 32
                   +vG+G +G++ Ay++ak+g++v llek + + 
     EPA04469.1 11 VVGGGPAGSSVAYEAAKNGIKVALLEKEETIA 42
                   8**************************99884 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4.4
                    CEECTS---EEETTHHHH CS
  NAD_binding_8  43 vrvdygahifhgsgyypn 60 
                    ++ ++ga if ++    n
     EPA04469.1 105 QAEKHGADIFLKT----N 118
                    5568999999884....4 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.3     9e-09     1e-05       1      36 [.       8      42 ..       8      51 .. 0.88
   2 ?   -0.8   0.0      0.54     6e+02      95     149 ..      97     154 ..      88     178 .. 0.57

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 9e-09
                CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT CS
        GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithkldtia 36
                d++V+GgG AG+  A++aa+ G+kv+L+ +k +tia
  EPA04469.1  8 DLVVVGGGPAGSSVAYEAAKNGIKVALL-EKEETIA 42
                689************************9.6666665 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.54
                 HHHHHHHHHHHHTSTTEEEEES-EEEEEECTTEEEEEE..ETTS-EEEECEEEE.--T CS
        GIDA  95 elyskevteklenepnleiieeeveeliveekkvkgvv..tedgetikakavvi.atG 149
                 ++y+   +++ ++  ++ + ++  + ++ +++ ++gv    ++ge+i  ++vvi a+G
  EPA04469.1  97 KTYRWLAQQAEKHGADIFLKTNIKDVIKNKDGDIAGVSgtSKEGEVIFHSKVVIdASG 154
                 3344444444444455555555555555555788887521345556555555541555 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.2   5.2e-05     0.058       2      35 ..       9      42 ..       8      58 .. 0.92
   2 !    7.7   0.1    0.0047       5.2      44      77 ..     100     134 ..      78     139 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.2e-05
                EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
   Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35
                +vvvGgG  g  +A ++a+ g kV ++e ++++ 
  EPA04469.1  9 LVVVGGGPAGSSVAYEAAKNGIKVALLEKEETIA 42
                79**************************998875 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0047
                 HHHHHHHHHTTEEEECSEEEEEEEEETTS.EEEEE CS
   Pyr_redox  44 kilqeklekngievllntkveeiegsedg.vesvk 77 
                 ++l+++ ek+g ++ l+t+++ + +++dg + +v 
  EPA04469.1 100 RWLAQQAEKHGADIFLKTNIKDVIKNKDGdIAGVS 134
                 78999***********************9888885 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   1.1   2.8e-07   0.00031       1     113 [.      10     128 ..      10     163 .. 0.56

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.8e-07
  Pyr_redox_3   1 iIiGaGPaGlaaaielkkagledylilEkg.nignsiy....rypkemtfispsftsekleipdlnaiseetspafs...lkeeklsrkealeYlrev 90 
                  +++G+GPaG ++a+e+ k+g+ ++  lEk+ +i  s++     + ++ + +          i++  + s++++ +++    +   l  ++  ++l++ 
   EPA04469.1  10 VVVGGGPAGSSVAYEAAKNGI-KVALLEKEeTIAYSVRtsgvTWIESIKEFGIPD-DCYNPIKNYSFCSPNNEVTITdtiPHAAVLDVRKTYRWLAQQ 105
                  79*******************.79*****95555555411113444444444321.111223333444444433222111123344555566666677 PP

  Pyr_redox_3  91 aksfelpiklfeeVesvkkedeg 113
                  a+++  +i l++++++v k+++g
   EPA04469.1 106 AEKHGADIFLKTNIKDVIKNKDG 128
                  77777777777777777775544 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   5.6e-05     0.063       3      38 ..      10      45 ..       8      60 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.6e-05
                EEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHH CS
     3HCDH_N  3 aviGaGtmGagiaavfasagleVvlvdiseealeka 38
                 v+G G  G+++a+ +a++g++V l++ +e ++ ++
  EPA04469.1 10 VVVGGGPAGSSVAYEAAKNGIKVALLEKEETIAYSV 45
                69*************************999877655 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00026      0.29       2      45 ..      10      53 ..       9      55 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00026
                EEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEE CS
      TrkA_N  2 iiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeglevv 45
                +++G G  G+s+a e  ++g++v + +k+e  + ++r  g++++
  EPA04469.1 10 VVVGGGPAGSSVAYEAAKNGIKVALLEKEETIAYSVRTSGVTWI 53
                8*****************9989*********9999999998877 PP

>> GMC_oxred_N  GMC oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.23   2.6e+02       1      33 [.       7      38 ..       7      55 .. 0.80
   2 ?    8.4   0.0    0.0011       1.2     197     255 ..     100     154 ..      93     159 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.23
  GMC_oxred_N  1 vdelveggGsagsvvAaRLsedpstsvlvleag 33
                 +d +v+ggG ags vA+  +++  ++v +le +
   EPA04469.1  7 YDLVVVGGGPAGSSVAYEAAKN-GIKVALLEKE 38
                 6889**********99976554.4667777755 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0011
  GMC_oxred_N 197 awLrpalerpnleiltgakaekiilegrkkravGVeasdkkgtvkrlvvaakevvvaaG 255
                   wL +  e+++++i  +++ + + ++++++ + GV+ ++k+g+   ++  +k+v+ a+G
   EPA04469.1 100 RWLAQQAEKHGADIFLKTNIKDV-IKNKDGDIAGVSGTSKEGE---VIFHSKVVIDASG 154
                  69*********************.677*********9999999...7777788887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.60u 0.25s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 2713.17
//
Query:       EPA04470.1  [L=114]
Description: sjogren'S syndrome/scleroderma autoantigen 1 (Autoantigen p27) [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-09   38.1   2.4    1.9e-09   37.5   2.4    1.3  1  Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (
  ------ inclusion threshold ------
       0.01   15.6   3.4      0.012   15.4   3.4    1.1  1  TIP120         TATA-binding protein interacting (TIP20)
      0.024   15.0   0.5      0.032   14.6   0.5    1.2  1  DUF1178        Protein of unknown function (DUF1178)
        0.2   10.7   1.7       0.23   10.5   1.7    1.1  1  DUF3422        Protein of unknown function (DUF3422)
       0.23   10.5   1.5       0.27   10.3   1.5    1.1  1  FUSC-like      FUSC-like inner membrane protein yccS
       0.83    9.2   3.6        1.1    8.9   1.5    2.2  2  TF_Zn_Ribbon   TFIIB zinc-binding
        1.5    8.8   5.9        3.1    7.9   5.9    1.6  1  Holin_BhlA     BhlA holin family


Domain annotation for each model (and alignments):
>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.5   2.4   7.5e-13   1.9e-09       1      40 []       7      44 ..       7      44 .. 0.92

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 7.5e-13
  Auto_anti-p27  1 kkmgelLlkGwtMLaetCpvC.gvPLmrdrkggkvyCvaCd 40
                   kk++++Ll G t+L+e Cp C gv  m+  k g  +C++C+
     EPA04470.1  7 KKAADMLLSGGTLLSEPCPYCsGVRVMK--K-GHALCINCG 44
                   799******************9999999..4.788*****6 PP

>> TIP120  TATA-binding protein interacting (TIP20)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   3.4   4.6e-06     0.012     108     156 ..      63     111 ..      44     114 .] 0.86

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 4.6e-06
      TIP120 108 ealrktlskklkekavkqelEkqeelkrsvlrvvaalnsklesaevaks 156
                 + l++tl+kkl+e + + e E+++e ++ +lr ++++ +++e+ + +++
  EPA04470.1  63 TGLETTLEKKLSELSKELEQETNHEKQQEILRSINSIMETIEKIKNKQE 111
                 56899********************************999999885444 PP

>> DUF1178  Protein of unknown function (DUF1178)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.5   1.3e-05     0.032      35     100 ..      24      85 ..      15     110 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.3e-05
     DUF1178  35 CpvCgstevekalmaprvakskkkaaeaaeaeaaaaaakaaaa...............aekekeleaalaelrrkveknse 100
                 Cp+C   +v k+  a  ++ +++ ++++ + +++++++++  +               +                   +++
  EPA04470.1  24 CPYCSGVRVMKKGHALCINCGREPEKKDIPITKEHNSKQTGLEttlekklselskeleQ-------------------ETN 85 
                 ********************999998877766655554444433444445444444442...................332 PP

>> DUF3422  Protein of unknown function (DUF3422)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.7   9.1e-05      0.23     218     259 ..      68     109 ..      53     112 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 9.1e-05
     DUF3422 218 eleerLaaltsalaeseeeedeqelleeLtelaaevealaar 259
                 +le++L++l ++l++++++e++qe+l+++ ++ + +e++ ++
  EPA04470.1  68 TLEKKLSELSKELEQETNHEKQQEILRSINSIMETIEKIKNK 109
                 689*********************************998765 PP

>> FUSC-like  FUSC-like inner membrane protein yccS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.5   0.00011      0.27     239     283 ..      67     109 ..      53     110 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00011
   FUSC-like 239 erleraleeleqslellakqnnekekellaalrallrnLrtierq 283
                 + le+ l+el ++le+  ++n+ek++e+l++++++++ +++i+++
  EPA04470.1  67 TTLEKKLSELSKELEQ--ETNHEKQQEILRSINSIMETIEKIKNK 109
                 4567777777777777..4479*******************9875 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   1.5   0.00042       1.1       3      34 ..      24      52 ..      22      59 .. 0.80
   2 ?   -0.6   0.0      0.37   9.5e+02      32      42 ..      97     107 ..      94     108 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00042
                  ETTTTCEECHEETSTTCEEESSSSBEEEECCC CS
  TF_Zn_Ribbon  3 CPnCgstnlveDpergelvCtdCGlVlednsi 34
                  CP+C++   v+  + g  +C +CG   e  +i
    EPA04470.1 24 CPYCSG---VRVMKKGHALCINCGREPEKKDI 52
                  ******...555789999******87776666 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.37
                   CCCCCCCHHHH CS
  TF_Zn_Ribbon  32 nsidegpewre 42 
                   nsi+e +e+++
    EPA04470.1  97 NSIMETIEKIK 107
                   89*****9986 PP

>> Holin_BhlA  BhlA holin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   5.9    0.0012       3.1      33      64 ..      78     109 ..      54     112 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0012
  Holin_BhlA  33 reekqeerekkyqeiikkltekfeiveeikkd 64 
                 +e+ qe   +k+qei+  +    e++e+ik++
  EPA04470.1  78 KELEQETNHEKQQEILRSINSIMETIEKIKNK 109
                 578899999********************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3029  (0.168944); expected 358.6 (0.02)
Passed bias filter:                     1145  (0.063863); expected 358.6 (0.02)
Passed Vit filter:                       152  (0.00847788); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 725.50
//
Query:       EPA04471.1  [L=319]
Description: LPPG:FO 2-phospho-L-lactate transferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-58  197.3   0.1    3.7e-58  197.1   0.1    1.0  1  UPF0052   Uncharacterised protein family UPF0052


Domain annotation for each model (and alignments):
>> UPF0052  Uncharacterised protein family UPF0052
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.1   0.1     2e-62   3.7e-58       1     259 [.      15     279 ..      15     311 .. 0.88

  Alignments for each domain:
  == domain 1  score: 197.1 bits;  conditional E-value: 2e-62
                 EEEEE-CHHHHHHHHHHCCSSCEEEEEE-----SHHHHHHHHHHTS---HHHHHHHHHH...--S-C...HHHHHCH-B-SS.............SSSS CS
     UPF0052   1 vvvlgGGtGlskllrglkevtaeltavvtvaDdggssGelrrelgllaigDirnvlval...idder...lleeLfqyRfkg.............dgdl 80 
                 ++vl+GGtG  kl+rgl + ++++ ++ +v+D+ ++ G       l++++Di+++++ l   +d+er   ++++ f++ +++             d+d 
  EPA04471.1  15 ITVLAGGTGSVKLVRGLVAQESKVNVISNVGDNYWLYG-------LYVCPDIDTIVYGLadlLDQERgwgIKKDTFNF-LRQmevfgeetwfrvgDRDA 105
                 89************************************.......************9988788888***88888888.5556788899999999**** PP

                 TT-BHHHHHHHHHHHHHS.-HHHHHHHHHHHTT-SSEEEES-SS--EEEEEETTS-EEESTTTGGGG-S...-EEE.EEEESTT----HHHHHHHHH-S CS
     UPF0052  81 aghslgnllLaalaeltg.sleeaiealskilkvrgrvlPatddpvelsaeledGeeitgeskisearklkapikr.vflepegaeaapevleaikeAd 177
                 a+h++++ +L++     g +l+++++ +++ ++v+++++P+td+++e+++++++Ge   +e++++++   + p++   ++++++a+++pe+++ai++Ad
  EPA04471.1 106 ATHLIRTNMLKN-----GkNLSDITKWMCEKFAVSANIIPVTDNSIETRITTDKGELHLQEYWVKHR--GRDPVEGiQYIGADKARPNPEAVNAIHDAD 197
                 ************.....99*************************************555*****444..568*************************** PP

                 EEEE-SS-IIIIIHHHHTSCCHHHHHHH-SSEEEEE--SB--TTTSTT-BHHHHHHHHHHCH-.....SS....S...-SEEEEE-S--- CS
     UPF0052 178 livlgpGslytSiiPiLlvpgiaealreskakkvlvsnimtqkGetdgfsvsdhvkaieravg.....kgvakay...vdavlvntsevp 259
                 +++l+pG+++tSi+P+L+++gi+++l++ k+k+v+vs++++      +++vs++++++++a+g     +g ak+y   ++ ++++t+  +
  EPA04471.1 198 MVILAPGNPLTSIGPMLQIKGIRKELSKIKKKVVAVSPLIG------DKAVSGPAAKYMEAAGietnaYGLAKMYsdvCSNIVIDTK--D 279
                 ****************************************9......****************888875555555666777778777..2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2380.16
//
Query:       EPA04472.1  [L=125]
Description: zinc finger, C2H2 type [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.1e-05   23.6   0.7    4.6e-05   23.1   0.7    1.3  1  zf-H2C2_5  C2H2-type zinc-finger domain
     0.0005   20.4   1.3    0.00082   19.7   1.3    1.4  1  zf-C2H2    Zinc finger, C2H2 type
     0.0016   19.1   1.4      0.003   18.3   1.4    1.5  1  zf-C2H2_4  C2H2-type zinc finger
  ------ inclusion threshold ------
       0.06   13.8   0.0       0.07   13.6   0.0    1.2  1  OrsD       Orsellinic acid/F9775 biosynthesis cluster protein
      0.093   12.3   0.5       0.13   11.7   0.5    1.2  1  LIM_bind   LIM-domain binding protein


Domain annotation for each model (and alignments):
>> zf-H2C2_5  C2H2-type zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.7   1.3e-08   4.6e-05       1      24 [.     101     123 ..     101     124 .. 0.97

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.3e-08
   zf-H2C2_5   1 YKCsqCDYstawksnLkRHlrrkH 24 
                 + C++C ++t++  +L+ H++ +H
  EPA04472.1 101 FSCTHCGFVTSYEVELQNHMK-IH 123
                 89*******************.*9 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   1.3   2.3e-07   0.00082       1      23 []     101     123 ..     101     123 .. 0.98

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 2.3e-07
                 EEETTTTEEESSHHHHHHHHHCC CS
     zf-C2H2   1 ykCpdCgksFkrksnLkrHirtH 23 
                 + C++Cg + +   +L++H+++H
  EPA04472.1 101 FSCTHCGFVTSYEVELQNHMKIH 123
                 89*******************99 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   1.4   8.4e-07     0.003       1      23 [.     101     123 ..     101     124 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 8.4e-07
   zf-C2H2_4   1 fkCpiCgksFsskka..LlrHlkth 23 
                 f C++C   F ++++  L++H+k h
  EPA04472.1 101 FSCTHC--GFVTSYEveLQNHMKIH 123
                 89****..999999989******99 PP

>> OrsD  Orsellinic acid/F9775 biosynthesis cluster protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.9e-05      0.07      44     110 ..      57     121 ..      27     124 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.9e-05
        OrsD  44 elletvehemslrqldelareaeavslpsaesepipgLpvy.eGy.rCrakakCkyltrslktlrkHlq 110
                 +++e ++   + r+++ +  +++ +s++s   ++i+  p++ +G+  C    +C ++t  + +l++H++
  EPA04472.1  57 AIKEFLDSIGESRNFA-VISNNNVISIKSVTGKVIERNPTMsTGFfSC---THCGFVTSYEVELQNHMK 121
                 4444444447778888.88999999**************998997256...8***************97 PP

>> LIM_bind  LIM-domain binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.5   3.8e-05      0.13      62     112 ..      69     119 ..      68     124 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.8e-05
    LIM_bind  62 ryfrtlfesgvkslqlildgareqvlsngsivlecdkatfvytyedgsrvv 112
                 r f ++ +++v+s++ ++ ++ e+     + ++ c+++ fv+ ye +++ +
  EPA04472.1  69 RNFAVISNNNVISIKSVTGKVIERNPTMSTGFFSCTHCGFVTSYEVELQNH 119
                 66999*********************999999************9776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       775  (0.0432261); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 870.24
//
Query:       EPA04473.1  [L=56]
Description: hypothetical protein BG20_I1019 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0043   17.0   2.3     0.0057   16.6   2.3    1.4  1  ADD_DNMT3  Cysteine rich ADD domain in DNMT3
  ------ inclusion threshold ------
       0.17    9.7   3.3       0.15    9.9   3.3    1.0  1  PolC_DP2   DNA polymerase II large subunit DP2


Domain annotation for each model (and alignments):
>> ADD_DNMT3  Cysteine rich ADD domain in DNMT3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   2.3   6.4e-07    0.0057       8      32 ..       7      31 ..       4      46 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6.4e-07
   ADD_DNMT3  8 evkenkrniEdiClsCGslevetqH 32
                + ++ +++i  iC+sCG+  +e +H
  EPA04473.1  7 KCTQCNKTIKMICISCGNRTTEQFH 31
                5678899*****************9 PP

>> PolC_DP2  DNA polymerase II large subunit DP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   3.3   1.7e-05      0.15     616     646 ..       3      32 ..       1      54 [. 0.73

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 1.7e-05
    PolC_DP2 616 iarrkCkkCgketlearCeeCgekteeklvC 646
                 i  +kC++C+k t+++ C +Cg++t+e+++ 
  EPA04473.1   3 IDYCKCTQCNK-TIKMICISCGNRTTEQFHS 32 
                 56789****85.89***********996543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       988  (0.0551063); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 421.37
//
Query:       EPA04474.1  [L=213]
Description: methyltransferase domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.5e-19   68.2   0.0    1.4e-18   67.3   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
      1e-17   64.4   0.0    1.3e-17   64.1   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    9.1e-17   61.6   0.0    3.1e-16   59.9   0.0    1.8  2  Methyltransf_12  Methyltransferase domain
    2.8e-16   60.0   0.0    6.2e-16   58.9   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
    7.8e-15   55.0   0.1    1.1e-14   54.5   0.1    1.3  1  Methyltransf_31  Methyltransferase domain
    2.5e-10   39.8   0.1      6e-10   38.5   0.0    1.6  2  Methyltransf_9   Protein of unknown function (DUF1698)
    4.8e-10   39.4   0.0    5.8e-10   39.1   0.0    1.1  1  NodS             Nodulation protein S (NodS)
    1.8e-09   37.3   1.2    2.5e-09   36.8   1.2    1.3  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    5.9e-09   35.6   0.2    9.7e-06   25.2   0.0    2.2  2  Methyltransf_4   Putative methyltransferase
    2.1e-06   27.4   0.1    1.4e-05   24.8   0.0    1.9  2  MetW             Methionine biosynthesis protein MetW
    1.6e-05   24.5   0.1    0.00027   20.5   0.0    2.1  2  DOT1             Histone methylation protein DOT1
    7.2e-05   22.2   0.7    9.5e-05   21.8   0.7    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
    9.6e-05   22.7   1.4    0.00019   21.7   0.0    2.0  2  AdoMet_MTase     Predicted AdoMet-dependent methyltransferase
    0.00073   19.6   0.1     0.0032   17.5   0.0    1.8  2  Methyltransf_32  Methyltransferase domain
    0.00096   18.3   0.2     0.0014   17.8   0.2    1.3  1  DREV             DREV methyltransferase
     0.0014   18.6   0.0     0.0025   17.8   0.0    1.4  1  Methyltransf_18  Methyltransferase domain
     0.0022   17.3   0.0     0.0055   16.1   0.0    1.7  1  GidB             rRNA small subunit methyltransferase G
     0.0032   17.0   0.0     0.0051   16.4   0.0    1.4  1  MTS              Methyltransferase small domain
  ------ inclusion threshold ------
      0.013   13.8   0.3      0.021   13.2   0.3    1.3  1  ActA             ActA Protein
      0.032   14.0   0.0      0.067   12.9   0.0    1.5  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.3   0.0   1.6e-21   1.4e-18       1      96 []      44     138 ..      44     138 .. 0.92

  Alignments for each domain:
  == domain 1  score: 67.3 bits;  conditional E-value: 1.6e-21
                      EEET-TTSHHHHHHH..HTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT.-EEEEEEES-CCC-CCHHHHHHHHHHHEEEE CS
  Methyltransf_11   1 LdvGcGtGrlaeala..krgarvvgvDlskemlklakekaseeglkvefvvadaeklpfedn.sfDlvvssevlhhvedpekalkeiaRvLkpg 91 
                      LdvGcG+G +++++   +++++ +g+D sk+m+ +a++k++++    +++  d+e+  ++d+ +fD+v+s e+l +v+  + alk+i+++Lkpg
       EPA04474.1  44 LDVGCGNGWVVRKISesNHCKKAIGIDKSKNMILQANTKKKNKT--EKYINTDIES--LNDKvKFDFVFSMESLYYVDSIDVALKKIYKLLKPG 133
                      8**************66666*************99999999988..58*******9..56655******************************* PP

                      EEEEE CS
  Methyltransf_11  92 Gllvi 96 
                      G++++
       EPA04474.1 134 GKFFC 138
                      **986 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.1   0.0   1.5e-20   1.3e-17      20     162 ..      37     179 ..       8     195 .. 0.82

  Alignments for each domain:
  == domain 1  score: 64.1 bits;  conditional E-value: 1.5e-20
  Methyltransf_23  20 lraggrvLdiGcGtGillevlrengf..svtgvDlspeaveiaekakkaqkdqfdeqeaaepqg..kfdlIvlrevlehvpdppellrqiatll 109
                       +++ + Ld+GcG G + + ++e  +  + +g+D s +++  a ++kk++ +++   +++  ++  kfd++ ++e+l+ v++   +l++i++ll
       EPA04474.1  37 FDKPFSFLDVGCGNGWVVRKISESNHckKAIGIDKSKNMILQANTKKKNKTEKYINTDIESLNDkvKFDFVFSMESLYYVDSIDVALKKIYKLL 130
                      4566699**************88866689**************99999999999888888888888**************************** PP

  Methyltransf_23 110 kpgGylllseplaslkedrllldwlylvpagrhisffsarslkelleeaGlev 162
                      kpgG +++ +     ++d+++  +++ + +   +++ s +++ e +++ G+ev
       EPA04474.1 131 KPGGKFFCGTDF---YSDNKAT-IKWSNMMKVQMHLLSKKEWVEKFKNTGFEV 179
                      ********9984...5555533.344444444578999999999999999997 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.9   0.0   3.5e-19   3.1e-16       1      99 []      44     136 ..      44     136 .. 0.89
   2 ?   -1.2   0.0       3.8   3.4e+03      19      41 ..     170     192 ..     156     210 .. 0.67

  Alignments for each domain:
  == domain 1  score: 59.9 bits;  conditional E-value: 3.5e-19
  Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlkdirevldnirklLk 94 
                      L++GcG+G ++r + e+++ ++ +g+D s+++i      l+++ +++n+  ++ ++d+++l ++ +fD v++ + l +++ i+ +l++i+klLk
       EPA04474.1  44 LDVGCGNGWVVRKISESNHCKKAIGIDKSKNMI------LQANTKKKNKTEKYINTDIESLNDKVKFDFVFSMESLYYVDSIDVALKKIYKLLK 131
                      8********************************......66666666666777777777777778***************************** PP

  Methyltransf_12  95 pgGrl 99 
                      pgG++
       EPA04474.1 132 PGGKF 136
                      ***86 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3.8
  Methyltransf_12  19 pdieytgvDispsaiedakekla 41 
                      +  + tg ++ ++ i+d k+k +
       EPA04474.1 170 EKFKNTGFEVKTKHIKDLKNKKK 192
                      55677888888888866666655 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.9   0.0   6.9e-19   6.2e-16       2      97 .]      44     134 ..      43     134 .. 0.91

  Alignments for each domain:
  == domain 1  score: 58.9 bits;  conditional E-value: 6.9e-19
                      EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHHHHHHHHHHHHHEEE CS
  Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsdedlekalkeiarvLkp 95 
                      Ld+GcG+G +++++++  + +k +g+D s++m+ +a+++ ++     ++++ d+e+l+ +  +fD+v+s+ +l +++   ++ alk+i+++Lkp
       EPA04474.1  44 LDVGCGNGWVVRKISESNHCKKAIGIDKSKNMILQANTKKKN--KTEKYINTDIESLNDK-VKFDFVFSMESLYYVD--SIDVALKKIYKLLKP 132
                      9****************779****************999954..4789*********966.5*******88899998..67899********** PP

                      EE CS
  Methyltransf_25  96 gG 97 
                      gG
       EPA04474.1 133 GG 134
                      *9 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.5   0.1   1.2e-17   1.1e-14       4     111 ..      40     140 ..      37     204 .. 0.73

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 1.2e-17
  Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnevlnaladpdkileei 97 
                        ++lD+GCG+G  + ++  e +  ++ +GiD s+++i +A+++ +k++ +  +    die+l+ +    kfD+++s e l+++ + d +l++i
       EPA04474.1  40 PFSFLDVGCGNGWVVRKIS-ESNHCKKAIGIDKSKNMILQANTK-KKNKTE--KYINTDIESLNDK---VKFDFVFSMESLYYVDSIDVALKKI 126
                      5679***************.8899999****************5.555555..7899*****9954...78*********************** PP

  Methyltransf_31  98 ervlkpggillied 111
                       ++lkpgg + + +
       EPA04474.1 127 YKLLKPGGKFFCGT 140
                      *********98643 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   0.0   6.7e-13     6e-10     104     220 ..      25     141 ..      16     163 .. 0.77
   2 ?   -2.7   0.0       2.4   2.1e+03      97     117 ..     167     190 ..     164     192 .. 0.59

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 6.7e-13
                     HHHHGGGS.--...TT-EEEEET-TTSHHHHHHH.HCT-SEEEEE---HHHHHHHHHHHCCTTTTSSEEEE---GGGS-T---EEEEEEES-GGG CS
  Methyltransf_9 104 Wdrvlphlsdl...kgrtildvGcgnGyhlwrmv.gegaklvvGidPselfliqfeavrkllgedqrahllplgieqlpeleafdtvfsmGvlyh 194
                     W+ v + l  +   k  + ldvGcgnG+ + ++  +++ k ++Gid s+  ++q ++ +k    ++ +  +   ie l+    fd vfsm  ly+
      EPA04474.1  25 WKNVIKFLKTVsfdKPFSFLDVGCGNGWVVRKISeSNHCKKAIGIDKSKNMILQANTKKK----NKTEKYINTDIESLNDKVKFDFVFSMESLYY 115
                     6666655554421155679********98766542346789*********9999776554....45666777899******************** PP

                     -S-HHHHHHHHHCTEEEEEEEEEEEE CS
  Methyltransf_9 195 rrsPldhllqlkdqlvkgGelvletl 220
                       s    l ++ + l+ gG++   t 
      EPA04474.1 116 VDSIDVALKKIYKLLKPGGKFFCGTD 141
                     *9987789999999999999877665 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.4
                     SEEHHHH...HHHHGGGS.--TT- CS
  Methyltransf_9  97 eWrsdwk...Wdrvlphlsdlkgr 117
                     eW   +k   ++  ++h+ dlk++
      EPA04474.1 167 EWVEKFKntgFEVKTKHIKDLKNK 190
                     555555522233446889998887 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   0.0   6.4e-13   5.8e-10      44     147 ..      40     141 ..       7     174 .. 0.82

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 6.4e-13
        NodS  44 iadalevGcaaGalterla..pyckrltvvdvveeaiararervkesshiswivsdvqqfstdekfdlivvaevlyyiedvaelraavrnlvsllapdg 140
                   + l+vGc  G +  +++   +ck+   +d  ++ i +a+++ k+    ++i +d++ ++ + kfd +   e lyy++    +  a++ + +ll+p+g
  EPA04474.1  40 PFSFLDVGCGNGWVVRKISesNHCKKAIGIDKSKNMILQANTKKKN-KTEKYINTDIESLNDKVKFDFVFSMESLYYVDS---IDVALKKIYKLLKPGG 134
                 45789***********9963379******************99999.55699*************************975...678************* PP

        NodS 141 qlvfGsa 147
                 ++  G+ 
  EPA04474.1 135 KFFCGTD 141
                 **99864 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   1.2   2.7e-12   2.5e-09      31     151 ..      21     138 ..       2     173 .. 0.85

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 2.7e-12
                      THHHHHH..HHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEE CS
  Ubie_methyltran  31 ihrlWkk..fveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtv 122
                        + Wk+  +  k+v+  ++ ++lDv +G g +  k+s+s + k k +++D ++nm+ +++ k k+++    ++++++ e L+ ++  fD+v  
       EPA04474.1  21 EKEHWKNviKFLKTVSFDKPFSFLDVGCGNGWVVRKISESNHCK-KAIGIDKSKNMILQANTKKKNKTE---KYINTDIESLN-DKVKFDFVFS 109
                      567899955556777778999**********9999999987655.77899*******999999999877...57788999987.56789*9999 PP

                      ES-GGG-S-HHHHHHHHHHHEEEEEEEEE CS
  Ubie_methyltran 123 sfGlrnvtDklkaLkeayrvlkpGGrlvv 151
                         l  v  ++ aLk++y+ lkpGG++++
       EPA04474.1 110 MESLYYVDSIDVALKKIYKLLKPGGKFFC 138
                      999************************99 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   1.1e-08   9.7e-06       4      59 ..      42      99 ..      39     116 .. 0.84
   2 !    8.6   0.1    0.0013       1.2     100     167 ..     123     191 ..     119     200 .. 0.72

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1.1e-08
                    EEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHC..TTSSEEEEES- CS
  Methyltransf_4  4 vvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkieal..elkNlrilrgd 59
                     +l++GcG+G+++ ++++ n  k+ +Gi+++++++ +++ k +++  ++ N  i   +
      EPA04474.1 42 SFLDVGCGNGWVVRKISESNHCKKAIGIDKSKNMILQANTKKKNKteKYINTDIESLN 99
                    699************************************9998886677776665555 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0013
                     HHHHHHHEEEEEEEEEEESHHHHHHHHHHHHHC.STTEEESSCCCSCCTCHCHHCCCSSTTCCCCCCTT CS
  Methyltransf_4 100 lkelarvLkkgGvlelaTDveeyaeemlkvlee.eplferlskeeeleeeplsvlriatkyeqkvqskg 167
                     lk++ + Lk+gG +   TD++   +  +k  +  + +++ lsk+e++e   ++ +++ tk  +  ++k+
      EPA04474.1 123 LKKIYKLLKPGGKFFCGTDFYSDNKATIKWSNMmKVQMHLLSKKEWVEKFKNTGFEVKTKHIKDLKNKK 191
                     89999**************77777666665443133677888888888777777788887555554444 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   1.6e-08   1.4e-05      17      98 ..      43     126 ..      25     133 .. 0.87
   2 ?    0.6   0.1      0.41   3.7e+02     141     181 ..     158     198 ..     142     207 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.6e-08
        MetW  17 vldlGcGdGellellkeekqv.dgrGleldeegvaecvakGlsviqgdldkdlenfedk.sfdyvvlsqtlqatrnpkevldel 98 
                  ld+GcG+G +++ + e+++  ++ G++++++ + ++ +k  +  ++ +++d+e  +dk +fd+v    +l  +   +  l+++
  EPA04474.1  43 FLDVGCGNGWVVRKISESNHCkKAIGIDKSKNMILQANTKKKNKTEKYINTDIESLNDKvKFDFVFSMESLYYVDSIDVALKKI 126
                 69***********999988773689********************************9967****9988888887777777665 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.41
        MetW 141 pnihlltikdfvelceelnlkvedrvaldekgrkvpavklv 181
                   +hll+ k++ve  ++++++v+ + + d k++k+++ ++ 
  EPA04474.1 158 VQMHLLSKKEWVEKFKNTGFEVKTKHIKDLKNKKKWKREFG 198
                 35799999999999999999999999999998888876665 PP

>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0     3e-07   0.00027      29      88 ..      26      85 ..      13      95 .. 0.85
   2 ?    1.6   0.0      0.19   1.7e+02     135     176 ..     117     159 ..     105     177 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 3e-07
                HHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHH--SEEEEEE--HHHHHHHHHHHHH CS
        DOT1 29 eflsevldkvnlkkedvFvDLGSGvGnvvlqaalevgcklsvGvEimdnaselaekqkee 88
                + ++++l+ v ++k   F+D G G G vv +++ + +ck+++G+++++n    a+++k+ 
  EPA04474.1 26 KNVIKFLKTVSFDKPFSFLDVGCGNGWVVRKISESNHCKKAIGIDKSKNMILQANTKKKN 85
                6688999****************************************9988777665543 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.19
                 HHHHHHHHHHHTT--TT-EEEESS-SS-TT--.--SSSTT-GG CS
        DOT1 135 aelnkqlkellqdlkegtkiislkslvpskyk.insrnlediv 176
                  +++ +lk++ + lk g+k     ++ ++++  i+ +n+ ++ 
  EPA04474.1 117 DSIDVALKKIYKLLKPGGKFFCGTDFYSDNKAtIKWSNMMKVQ 159
                 56788999************99999998877646666665554 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.7   1.1e-07   9.5e-05      54     179 ..      31     153 ..      12     196 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.1e-07
                 HHTTTT--TT-EEEEES-TTSHHHHHHHHHH--.EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG---..--SEEEEES-GGGTSGGGHHHHH CS
        CMAS  54 ileklelkpGmtlLdiGcGWGslvrraverydv.kvvglTlSkeqaklakkrvdeldlerkvevklldyedlde..kvdrvvsvgafehvgkenydtff 149
                  l+ ++ ++    Ld+GcG G +vr+  e     k +g+  Sk+   +a+ + ++     +++   +d e l++  k+d v s++ +  v  ++ d   
  EPA04474.1  31 FLKTVSFDKPFSFLDVGCGNGWVVRKISESNHCkKAIGIDKSKNMILQANTKKKNK----TEKYINTDIESLNDkvKFDFVFSMESLYYV--DSIDVAL 123
                 5666777777889***********99888744416788888887766655443332....23344567888888789********99887..5788889 PP

                 HHHHHHS-TT-EEEEEEEEE--HHHHHCTT CS
        CMAS 150 kklkkllkedGllllhtitslhkkelaerg 179
                 kk++kllk++G +   t +  ++k + +  
  EPA04474.1 124 KKIYKLLKPGGKFFCGTDFYSDNKATIKWS 153
                 **************9999888888776433 PP

>> AdoMet_MTase  Predicted AdoMet-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   2.1e-07   0.00019      50     105 ..      31      86 ..      24      93 .. 0.73
   2 ?   -1.0   0.3       2.5   2.3e+03       4      24 ..     169     189 ..     166     198 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2.1e-07
  AdoMet_MTase  50 wkktrseeketsfvdvgcgngllvyvlaaegykgygidlrkrklwelypaevkvdl 105
                   + kt s +k++sf dvgcgng +v  ++   +    i + k k   l   + k++ 
    EPA04474.1  31 FLKTVSFDKPFSFLDVGCGNGWVVRKISESNHCKKAIGIDKSKNMILQANTKKKNK 86 
                   55788899****************99988777666666666666555555555544 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.5
  AdoMet_MTase   4 lekyndlykelkqkyakrlve 24 
                   +ek++++  e+k k+ k l +
    EPA04474.1 169 VEKFKNTGFEVKTKHIKDLKN 189
                   577777777888888777754 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   3.6e-06    0.0032      15      87 ..      30     100 ..      21     113 .. 0.76
   2 ?   -0.4   0.0       1.1   9.9e+02      49      74 ..     169     193 ..     156     212 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.6e-06
  Methyltransf_32  15 kllkelakesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekra.eklgkkfnkrlsfael 87 
                      k+lk+  + +++++ +DvG+G+g+  + ++   +++  k +gid +++++ +a++ + +k +k++n++++  + 
       EPA04474.1  30 KFLKT-VSFDKPFSFLDVGCGNGWVVRKISE--SNHCKKAIGIDKSKNMILQANTKKkNKTEKYINTDIESLND 100
                      44555.35577999***************99..4477899*****99999888766515667777776666555 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.1
  Methyltransf_32  49 eyklkvvgidakeelvekaekraekl 74 
                        k+k +g+++k++++++ ++ + k 
       EPA04474.1 169 VEKFKNTGFEVKTKHIKDLKNKK-KW 193
                      46788899999999998876543.33 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.2   1.5e-06    0.0014      88     184 ..      33     136 ..      12     183 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.5e-06
        DREV  88 spasdqedkklldlGaGdGeitkrva..ptfeevyatelsetmrdrlkkkkyn.....vlsalelqetdvkldlilclnlldrcfdplklledirsale 179
                 +  s  ++   ld+G G+G + ++++  ++ ++    + s++m+ + + kk n     + + +e  + +vk+d + +++ l   ++    l+ i++ l+
  EPA04474.1  33 KTVSFDKPFSFLDVGCGNGWVVRKISesNHCKKAIGIDKSKNMILQANTKKKNktekyINTDIESLNDKVKFDFVFSMESLYYVDSIDVALKKIYKLLK 131
                 3445568899************999633799999*********9887655444222325678898899*************9999999999***99999 PP

        DREV 180 pngrv 184
                 p g+ 
  EPA04474.1 132 PGGKF 136
                 98875 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.8e-06    0.0025      17      70 ..      42      94 ..      28     106 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.8e-06
  Methyltransf_18 17 rvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievr 70
                     +++D+G+  g +  ++ +++++kk+i +D +++ + +a+++ ++ ++e+ i++ 
       EPA04474.1 42 SFLDVGCGNGWVVRKISESNHCKKAIGIDKSKNMILQANTKKKN-KTEKYINTD 94
                     689**********************************9987654.667777765 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   6.1e-06    0.0055      30     146 ..      20     138 ..      12     174 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 6.1e-06
                 HHHHCHHHHHHHGGCS-CCC-..EEEETSTTTTTHHHHHHH-TTSEEEEEES-HHHHHHHHHHHHHCT-SSEEEEES-CCCTTTTT-EEEEEEC-.... CS
        GidB  30 llerhlldslsvlellkekrd.kviDvGsGaGlPGipLaiarpelkltLleslekkiaFLeevkeelklenveivearaeekqeeekydvvtsRA.... 123
                 + + h  + ++ l++++ ++  +++DvG G+G   ++ +i  ++     +  ++ k   L ++ ++ k++  +++++++e+ + + k+d+v s      
  EPA04474.1  20 MEKEHWKNVIKFLKTVSFDKPfSFLDVGCGNGW--VVRKISESNHCKKAIGIDKSKNMIL-QANTKKKNKTEKYINTDIESLNDKVKFDFVFSMEslyy 115
                 55679999************967*********8..7777776655445555444444444.44444455556*******************98532333 PP

                 SSSHHHHHHHHCCCEEEEEEEEE CS
        GidB 124 laslnelteillkllkegglila 146
                 + s++   + + kllk+gg+++ 
  EPA04474.1 116 VDSIDVALKKIYKLLKPGGKFFC 138
                 77888888888899999999985 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   5.7e-06    0.0051      34     102 ..      42     108 ..      28     140 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5.7e-06
                 EEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEEE CS
         MTS  34 kvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdliv 102
                 + lD+GcG+G +  ++ + +   +   +d++++ +  a+   ++++   +++++d+ +  ++ kfd++ 
  EPA04474.1  42 SFLDVGCGNGWVVRKISESNHCKKAIGIDKSKNMILQAN--TKKKNKTEKYINTDIESLNDKVKFDFVF 108
                 589***************9999999999*9999886654..4444444677778887777777899986 PP

>> ActA  ActA Protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.3   2.4e-05     0.021     214     252 ..      47      86 ..      27      98 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.4e-05
        ActA 214 kdagkwvrdkidenpevkkai.vdksaglidqlltkkkse 252
                      wv  ki e    kkai +dks  +i q  tkkk +
  EPA04474.1  47 GCGNGWVVRKISESNHCKKAIgIDKSKNMILQANTKKKNK 86 
                 44557***************989*************9975 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   7.4e-05     0.067      65     123 ..      31      88 ..      22     109 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.4e-05
                 HHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTT CS
        PCMT  65 alellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldl 123
                 +l+ ++++k  + L+vG+G G+    +++  + k ++++i+++k+++ +a+ + k++  
  EPA04474.1  31 FLKTVSFDKPFSFLDVGCGNGWVVRKISESNHCK-KAIGIDKSKNMILQANTKKKNKTE 88 
                 556666899999**********988888875555.59*********9999877666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1233  (0.0687713); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 1343.74
//
Query:       EPA04475.1  [L=65]
Description: Sec61beta family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.4e-13   48.7   0.4    6.4e-13   48.5   0.4    1.1  1  Sec61_beta  Sec61beta family


Domain annotation for each model (and alignments):
>> Sec61_beta  Sec61beta family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.5   0.4   3.5e-17   6.4e-13       1      40 [.      23      62 ..      23      63 .. 0.97

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 3.5e-17
                XXXXXXXXXX----SS-B-THHHHHHHHHHHHHHHHHTSS CS
  Sec61_beta  1 SsaGLlryyeedapgikidPkvVlvlsvafiasVilLhil 40
                Ss GL+r++e++++g+k+dPk+V+ + + +i++ +l  i+
  EPA04475.1 23 SSGGLMRFFEDETKGFKVDPKIVVSVPISLIVVSWLIDIF 62
                8***********************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       204  (0.0113782); expected 358.6 (0.02)
Passed bias filter:                      151  (0.00842211); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 434.56
//
Query:       EPA04476.1  [L=330]
Description: CAAX amino terminal protease family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.4e-13   48.4   7.3    9.4e-13   48.4   7.3    2.5  2  CPBP      CPBP intramembrane metalloprotease
  ------ inclusion threshold ------
        3.5    7.5   8.8         14    5.6   1.0    3.2  2  CoxIIa    Cytochrome c oxidase subunit IIa family


Domain annotation for each model (and alignments):
>> CPBP  CPBP intramembrane metalloprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   4.8         2   1.8e+04      26      26 ..      66      66 ..       9     132 .. 0.59
   2 !   48.4   7.3     1e-16   9.4e-13       9      91 ..     157     270 ..     122     271 .. 0.81

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 2
                C CS
        CPBP 26 l 26
                 
  EPA04476.1 66 P 66
                1 PP

  == domain 2  score: 48.4 bits;  conditional E-value: 1e-16
                 HHHHHHHHHHHHHHHTTCHHHH...................HHHH.S-.............HHHHHHHHHHHHHCSGGG.....HHHHHHHHHHHHHHH CS
        CPBP   9 llalllapllEEllfRglllql...................lqergss.............tlailissilFglaHlpn.....gpsvllaalaGlvlg 70 
                 +l++ l p++EE++fR++l+ l                   +     s             +l i++ +++Fg+ H+++        +l a++ G++lg
  EPA04476.1 157 FLYVSLSPIVEEFGFRVILIGLplfvfyshklsfshflkslW-----SpnrnlhiydskkpLLLIVLVGVFFGISHIITgepwsEGKLLQASVSGIILG 250
                 5678899************77777777777777666644430.....34444555555566******************995543239*********** PP

                 HHHHHTT-HHHHHHHHHHHHH CS
        CPBP  71 ylylktgsllaaillHallnl 91 
                 +ly + g l+aail+H+++n+
  EPA04476.1 251 WLYFRFG-LIAAILVHWATNY 270
                 *******.************8 PP

>> CoxIIa  Cytochrome c oxidase subunit IIa family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   1.5    0.0038        34      13      29 ..      22      38 ..      15      39 .. 0.76
   2 ?    5.6   1.0    0.0016        14      14      29 ..     258     273 ..     256     274 .. 0.94

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0038
                HHHHHHHHHHHHHHHHH CS
      CoxIIa 13 vLtatILvFWfgvFyvF 29
                +  +  L F fgvF vF
  EPA04476.1 22 IFAMMLLSFPFGVFVVF 38
                34556788********9 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0016
                 HHHHHHHHHHHHHHHH CS
      CoxIIa  14 LtatILvFWfgvFyvF 29 
                 L+a ILv W   +++F
  EPA04476.1 258 LIAAILVHWATNYFIF 273
                 8899**********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       920  (0.0513135); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2142.81
//
Query:       EPA04477.1  [L=315]
Description: putative membrane protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.24   11.6   3.1       0.29   11.3   0.0    2.5  3  SRTM1     Serine-rich and transmembrane domain-containing pro


Domain annotation for each model (and alignments):
>> SRTM1  Serine-rich and transmembrane domain-containing protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1     0.067   1.2e+03      51      69 ..      42      60 ..      26      75 .. 0.68
   2 ?   -3.1   0.2       0.5     9e+03      41      56 ..     105     120 ..      90     125 .. 0.50
   3 ?   11.3   0.0   1.6e-05      0.29      44      75 ..     281     313 ..     263     315 .] 0.86

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.067
       SRTM1 51 flllllvialqrlkniiss 69
                f l+++v  l  lk iis 
  EPA04477.1 42 FALVFVVAELIGLKIIISK 60
                4455555556666666654 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.5
       SRTM1  41 yvsiflsllaflllll 56 
                 +++ f+ + +f+++ l
  EPA04477.1 105 WMWDFIVMAIFVVVAL 120
                 3333444444544443 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 1.6e-05
       SRTM1  44 ifls.llaflllllvialqrlkniisssssype 75 
                 +fl  l+afll++++i  +rlk + s   s p+
  EPA04477.1 281 MFLPwLFAFLLIVILIETKRLKKLESQGKSTPK 313
                 4554278*******************9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       850  (0.0474092); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.35s 00:00:00.97 Elapsed: 00:00:00.55
# Mc/sec: 1722.21
//
Query:       EPA04478.1  [L=39]
Description: hypothetical protein BG20_I1007 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       262  (0.0146132); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.28s 00:00:00.59 Elapsed: 00:00:00.41
# Mc/sec: 285.50
//
Query:       EPA04479.1  [L=306]
Description: ABC transporter, substrate-binding protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.7e-23   82.3   0.0    5.4e-23   81.8   0.0    1.2  1  Peripla_BP_2  Periplasmic binding protein


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.8   0.0     3e-27   5.4e-23       1     236 [.       6     266 ..       6     268 .. 0.89

  Alignments for each domain:
  == domain 1  score: 81.8 bits;  conditional E-value: 3e-27
                   EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT.....TS..-BSBESSSB-H.................HHHHHH--SEEEE-GGG...... CS
  Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdtttsdpldadklee...ai..vevgadgeidv.................EklaalkPDlvilskgl...... 69 
                   i+sl ps te+l++lG++d + gv + +++p+da+ ++    ++   +  +++eid+                   ++++ PDl+i++ +       
    EPA04479.1   6 IVSLLPSATELLYELGVEDLLYGVTHECKYPEDAKTKPRvikSVidSDSLSSKEIDTktcqllsegkeiftlneKNMIEANPDLIISQDTCeacaah 102
                   89*********************************99987773322333444455557777777777777899566**************99****9 PP

                   ....GGGHHHHHHHS-EEE----TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT.-EEEEEEEETTE..EEEE-TTSTTTHHHH CS
  Peripla_BP_2  70 .gltdedeellksgiptvivessntgeslkeqiralgellgledeaeklvaeidsklaaaksaidsekpkpvlvfggadeggyvvagsnsyigdlld 165
                     ++++++++l ++  ++ +++ n  +++ e++  +g++  +ed+a+++ +++++++  +++   +    p ++ +++ e    +++ +++i +++ 
    EPA04479.1 103 nNHVTQAIKILPKKPTVYSMDPHNL-QEIVETVNNIGKIITREDKAKEITEFLNKRINVIRDTKFKV--NPKVLAIEWIE---PFFTAGHWIPEMIM 193
                   9999********************7.***********************************999999..44455556666...7************* PP

                   TS--EESTTT--STT-EEE-HHHHHHH--SEEEEEEH...HHHT-S--HHHHT-SHHHHTSHHHHTT-EEEE-H CS
  Peripla_BP_2 166 algieniaaeskkseyeeisaEqilasdpdvifvsgr...aeadnktgleflkenpllaelpAvkngrVyalds 236
                    +g+en+++   ++++ ++ +++i++sdpd+i+ +++        ++  + lk n+++++l A k+++++a+d+
    EPA04479.1 194 YAGGENMISKV-GEYSRKLTMDEIKKSDPDIIILMPCgfdTFRTISEYNKILKDNEEWKHLRATKSNNIFAVDA 266
                   *******9999.*************************997777788888899999***************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       878  (0.0489709); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.34s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 1739.45
//
Query:       EPA04480.1  [L=385]
Description: hypothetical protein BG20_I1008 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-91  305.9   0.0    4.7e-91  305.4   0.0    1.1  1  Nre_N     Archaeal Nre, N-terminal
    4.3e-32  110.3   0.0    6.8e-32  109.7   0.0    1.3  1  Nre_C     Archaeal Nre, C-terminal


Domain annotation for each model (and alignments):
>> Nre_N  Archaeal Nre, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  305.4   0.0   5.2e-95   4.7e-91       8     267 ..      11     267 ..       7     269 .. 0.96

  Alignments for each domain:
  == domain 1  score: 305.4 bits;  conditional E-value: 5.2e-95
       Nre_N   8 pileklravekakkki.sskeleGsspPsvfVGrygYPkVsvgplvppvegdasvldspekwlglslediiklrlslvrgekkvkvkkakedklleeiq 105
                 +il k+++  ++  +  ss++++GsspPsvfVG+y+YPkV vgp+vpp++gd+s ld+pe+w g+sledi+++rl+l+rg +kv++++++  +++e++q
  EPA04480.1  11 AILAKWHENLSKYGNLfSSDSISGSSPPSVFVGSYNYPKVFVGPMVPPIHGDTSLLDNPERWTGKSLEDIVNFRLNLIRGIQKVSIHQTE-GRYIENLQ 108
                 577888777777776679**********************************************************************98.******** PP

       Nre_N 106 elalsekpvdvevelekkpkaklkfdevlaPvGpsaeleklkvaenpkvprkveklveDtdlkAeeavveLyrsgvdvykiqrlLSvGlLGekkkrrlV 204
                 e+++s+kp ++++e++k++++++ +d+++aP+Gp +el+++k   n ++ +++ek+++D+dl+A++av++Ly+sg++++kiq+++S+G+LG+  kr+lV
  EPA04480.1 109 EITMSSKPTESDLEFTKNTTPNVFLDGESAPFGPIGELKSAKF-YNTSTTKSIEKIFYDKDLNASDAVLHLYNSGINISKIQKCFSIGMLGQ--KRKLV 204
                 *******************************************.899999*****************************************9..***** PP

       Nre_N 205 PTrWsITAvddivgkelkkeikdlpeidevevfsgeylgNrflviLaPgkwsfelvEawapgs 267
                 PT+WsITA+ddi++k+l+kei +++ id+++vf++e+lgN f viL+P++w +e++Eaw+ + 
  EPA04480.1 205 PTKWSITATDDIISKSLTKEILNYSLIDTYKVFTYEHLGNLFSVILFPHRWIYEMIEAWYSNG 267
                 ***********************************************************9875 PP

>> Nre_C  Archaeal Nre, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.7   0.0   7.6e-36   6.8e-32       2     110 .]     277     384 ..     276     384 .. 0.96

  Alignments for each domain:
  == domain 1  score: 109.7 bits;  conditional E-value: 7.6e-36
       Nre_C   2 gyegrkeyseiaGaYyaarlavleaLekikrqakvivlreitpeYwaPvGvWqvReavrkalekkpkefesleealeevseklklplkkllkkskllke 100
                 +++g ++ ++iaGaY+aa+l+v e+L+k k q++vi+lrei+peY +PvGvWqvRe++r+a+ k+p   +++++al+ +s+k+++ ++++l+k +++k 
  EPA04480.1 277 DARGIDHPPQIAGAYFAAKLGVSEYLAKNKIQSGVIILREIRPEYAIPVGVWQVREGIRSAMMKTPLIGDNFDDALTLASKKMSIAKHEWLSKGNMMKL 375
                 5677788899****************************************************************************************9 PP

       Nre_C 101 lkkqktLddF 110
                 + +qkt+ dF
  EPA04480.1 376 I-RQKTIADF 384
                 9.8****998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 2252.39
//
Query:       EPA04481.1  [L=254]
Description: oxidoreductase, zinc-binding dehydrogenase family protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      4e-25   88.3   0.0    6.4e-25   87.6   0.0    1.3  1  ADH_zinc_N     Zinc-binding dehydrogenase
    2.3e-17   64.3   0.0    3.6e-17   63.7   0.0    1.3  1  ADH_zinc_N_2   Zinc-binding dehydrogenase
  ------ inclusion threshold ------
      0.019   15.1   0.2      0.062   13.5   0.0    1.9  2  ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthas


Domain annotation for each model (and alignments):
>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.6   0.0   1.1e-28   6.4e-25       1     129 [.      82     216 ..      82     217 .. 0.90

  Alignments for each domain:
  == domain 1  score: 87.6 bits;  conditional E-value: 1.1e-28
                 HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHT........TTSSEEEEEESSCSHHHHHHHHHCEEEEEEEEECSC. CS
  ADH_zinc_N   1 gvGlaavqlAkalGaeviavdsseeklelakklGadevinykeadlverikelt........ggegvdvvfecvGsgatleaalkllkpgGrlvvvGg. 90 
                 gvG +++q+Ak +G++via++s + kl+++ +lG d++i+++++d+ ++++++         ++ gvdv+fe++G g+ ++  l+llk+g ++v+ G+ 
  EPA04481.1  82 GVGNYGIQIAKLFGCTVIATASPD-KLDKLLELGSDYAIDHRKDDWHKQVRDISkkipkpfgDTPGVDVIFEHIG-GSHWNKELTLLKYGATIVTTGAt 178
                 8******************98765.8***************444899999999989999996588**********.**********************7 PP

                 .TSSEEEEEHHHHHHTT-EEEEE-SSCHHHHHHHHHHHHH CS
  ADH_zinc_N  91 .gkgeeefdlrnlllkeksilGsllgslreefkealdlla 129
                  g++ +  dlr++++k ++ilGs+ g+ r+e+++al +++
  EPA04481.1 179 tGYDAK-TDLRHIFFKGINILGSTQGT-RSELEQALYWMS 216
                 444444.********************.*******99875 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.7   0.0   6.1e-21   3.6e-17       1     131 [.     113     250 ..     113     252 .. 0.78

  Alignments for each domain:
  == domain 1  score: 63.7 bits;  conditional E-value: 6.1e-21
                   TT-SEEEETTSTTHH..............HHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE----.S-EEE-CHHHCTTT-EEEE--GGG... CS
  ADH_zinc_N_2   1 lGAdevidyrtedfe..............aatggegvDvvldtvggealleaslkvlpggGrlvsiggpplsaallkpakkrkgrsvkyeflfsmka 83 
                   lG d +id+r++d++               +t   gvDv+++ +gg ++  + l++l+ g+++v+ g++   ++  +++   +   +k   ++  ++
    EPA04481.1 113 LGSDYAIDHRKDDWHkqvrdiskkipkpfGDT--PGVDVIFEHIGGSHW-NKELTLLKYGATIVTTGAT---TGYDAKTD-LRHIFFKGINILGSTQ 202
                   899************9*****99998666554..57*************.8888899777889999963...22223323.3344444444443455 PP

                   -.-HHHHHHHHHHHHHHH----EEEEEEGGGHHHHHHHHHSS--S.SEE CS
  ADH_zinc_N_2  84 saqadileelaalieeGklrpvvdrvfpleeaaeAhrylesgrar.GKi 131
                   + + + le+ + ++++Gk++ v+d+v+++e+aaeAh ++ +g+   GKi
    EPA04481.1 203 GTRSE-LEQALYWMSQGKIKSVIDSVYSFEQAAEAHTKMLTGKGLfGKI 250
                   53566.*********************************8887544887 PP

>> ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0     1e-05     0.062      35      81 ..      33      83 ..      21      92 .. 0.68
   2 ?   -1.9   0.0      0.64   3.8e+03      66      81 ..     166     181 ..     161     185 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1e-05
                   GGGB--THHHH-B-GGGHHHHHH....HHHHHTTSS-TT-EEEEEEEETTT CS
  ACP_syn_III_C 35 eekvvvnldeyGntsaasiplaL....deaveegklkpgdlvllvgfGaGl 81
                   e  vv++ d++ + saa   ++L    + +v + k++pg+lvl++g G G+
     EPA04481.1 33 EVNVVKIPDNVSYDSAAAASMTLltswHMLVGRAKIQPGQLVLIMGGGSGV 83
                   4444444455555554444333323338999999**************997 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.64
                    S-TT-EEEEEEEETTT CS
  ACP_syn_III_C  66 lkpgdlvllvgfGaGl 81 
                    lk g +++++g+  G+
     EPA04481.1 166 LKYGATIVTTGATTGY 181
                    6889999999999888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1791.94
//
Query:       EPA04482.1  [L=59]
Description: hypothetical protein BG20_I2526, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-08   32.4   3.7    0.00014   21.6   0.1    2.1  2  TPR_1     Tetratricopeptide repeat
    9.4e-05   22.2   1.6     0.0012   18.8   0.1    2.1  2  TPR_2     Tetratricopeptide repeat
     0.0007   19.6   1.3        1.1    9.6   0.0    2.2  2  TPR_8     Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.017   15.0   0.1      0.017   15.0   0.1    1.0  1  DUF4919   Domain of unknown function (DUF4919)
      0.021   14.5   0.7      0.038   13.7   0.6    1.6  1  TPR_11    TPR repeat
      0.022   14.6   0.2        6.7    6.7   0.0    2.2  2  TPR_10    Tetratricopeptide repeat
      0.027   14.9   1.1      0.074   13.5   0.5    1.9  2  TPR_17    Tetratricopeptide repeat
       0.03   14.8   0.0      0.039   14.5   0.0    1.2  1  TPR_19    Tetratricopeptide repeat
      0.033   14.8   0.1      0.086   13.5   0.0    1.7  2  TPR_6     Tetratricopeptide repeat
       0.04   13.9   0.7      0.062   13.3   0.1    1.7  2  TPR_3     Tetratricopeptide repeat
      0.054   14.2   0.0      0.062   14.0   0.0    1.1  1  TPR_16    Tetratricopeptide repeat
       0.11   12.9   0.3        1.4    9.2   0.3    2.0  1  TPR_12    Tetratricopeptide repeat
       0.11   13.3   0.0       0.15   12.9   0.0    1.3  1  TPR_14    Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.1   9.9e-08   0.00014      11      34 .]      17      40 ..      17      40 .. 0.94
   2 !   12.0   0.6    0.0001      0.14       4      18 ..      44      58 ..      42      59 .] 0.94

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 9.9e-08
                HHHTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1 11 yfklgkydeAleyyekALelnPnn 34
                +f +gk+deA++yy+  L  nPn+
  EPA04482.1 17 LFLKGKLDEAIKYYDMILHENPNH 40
                5889******************97 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.0001
                HHHHHHHHHHTT-HH CS
       TPR_1  4 lynlGnayfklgkyd 18
                l+n+G+a+ kl++yd
  EPA04482.1 44 LNNKGYALNKLKDYD 58
                8*************8 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   8.5e-07    0.0012       8      34 .]      14      40 ..      10      40 .. 0.93
   2 ?    3.0   0.2       0.1   1.4e+02       4      18 ..      44      58 ..      42      59 .] 0.89

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 8.5e-07
       TPR_2  8 GlayyklgdyeeAleafekAleldPnn 34
                ++ ++ +g+++eA+++++  l  +Pn+
  EPA04482.1 14 ANRLFLKGKLDEAIKYYDMILHENPNH 40
                8899*********************97 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.1
       TPR_2  4 lynlGlayyklgdye 18
                l+n G+a+ kl+dy+
  EPA04482.1 44 LNNKGYALNKLKDYD 58
                8999****9****98 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0   0.00082       1.1      13      25 ..      19      31 ..      12      40 .. 0.86
   2 !    9.5   0.3   0.00088       1.2       3      18 ..      43      58 ..      41      59 .] 0.92

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00082
                HTT-HHHHHHHHH CS
       TPR_8 13 klgdyeeAkeyye 25
                 +g+++eA++yy 
  EPA04482.1 19 LKGKLDEAIKYYD 31
                68*********95 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00088
                HHHHHHHHHHHTT-HH CS
       TPR_8  3 ayynlgsiylklgdye 18
                +++n+g+++ kl+dy+
  EPA04482.1 43 SLNNKGYALNKLKDYD 58
                799************8 PP

>> DUF4919  Domain of unknown function (DUF4919)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   1.3e-05     0.017      58     107 ..       7      57 ..       1      59 [] 0.84

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.3e-05
     DUF4919  58 leel.kldkkelseeelkeiislaeealkknPfdlkqlnllayaykalgkk 107
                 ++++  ++++   + +l+e+i++   +l++nP  +  ln+  ya+++l++ 
  EPA04482.1   7 IDSIlDEANRLFLKGKLDEAIKYYDMILHENPNHIGSLNNKGYALNKLKDY 57 
                 443336778888999********************************9986 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.6   2.8e-05     0.038       2      38 ..      15      51 ..      14      55 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.8e-05
      TPR_11  2 dayyeqGkyeeAieaYkkAlkldPdnaeayynLGlay 38
                + ++ +Gk++eAi+ Y   l  +P+    ++n G+a+
  EPA04482.1 15 NRLFLKGKLDEAIKYYDMILHENPNHIGSLNNKGYAL 51
                899***********99877777777766666666665 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0049       6.7       9      26 ..      14      31 ..      14      35 .. 0.90
   2 ?    6.2   0.1    0.0072        10       3      19 ..      42      58 ..      41      59 .] 0.91

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0049
      TPR_10  9 analrqrgrydeAealle 26
                an+l+  g++deA ++++
  EPA04482.1 14 ANRLFLKGKLDEAIKYYD 31
                899999*********996 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0072
      TPR_10  3 sslnNLanalrqrgryd 19
                 slnN + al ++++yd
  EPA04482.1 42 GSLNNKGYALNKLKDYD 58
                69*************98 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       1.2   1.7e+03      25      34 .]      19      28 ..      13      28 .. 0.79
   2 ?   13.5   0.5   5.4e-05     0.074       6      30 ..      34      58 ..      29      59 .] 0.86

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.2
      TPR_17 25 knGdlmtArq 34
                 +G+l++A++
  EPA04482.1 19 LKGKLDEAIK 28
                5799999975 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 5.4e-05
      TPR_17  6 leldPnnadaynnLAelllknGdlm 30
                l  +Pn+  ++nn++++l k++d++
  EPA04482.1 34 LHENPNHIGSLNNKGYALNKLKDYD 58
                5569******************997 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   2.8e-05     0.039       2      42 ..      18      58 ..      17      59 .] 0.86

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.8e-05
      TPR_19  2 laegdyaeAlalleqalqedpknaearllLAeallalgqld 42
                +  g+++eA++++  +l e+p++   + +   al +l+++d
  EPA04482.1 18 FLKGKLDEAIKYYDMILHENPNHIGSLNNKGYALNKLKDYD 58
                56799*****************9998888888888888876 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   6.2e-05     0.086       9      33 .]      17      40 ..      11      40 .. 0.86
   2 ?   -1.3   0.0       3.3   4.5e+03       7      17 ..      48      58 ..      46      59 .] 0.67

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.2e-05
                HHHHHHHHHHHHHHHHHHHHH-TT- CS
       TPR_6  9 syrklgdtdkAlealerlikeYPdS 33
                +++k+ + d+A+++++ ++ e P++
  EPA04482.1 17 LFLKG-KLDEAIKYYDMILHENPNH 40
                44555.*****************96 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 3.3
                HHHHHHHHHHH CS
       TPR_6  7 alsyrklgdtd 17
                ++++ kl+d+d
  EPA04482.1 48 GYALNKLKDYD 58
                66667777776 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   4.5e-05     0.062      11      25 ..      17      31 ..      14      37 .. 0.82
   2 ?   -1.7   0.1       2.2     3e+03      14      17 ..      54      57 ..      47      59 .] 0.52

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.5e-05
                HHHTT-HHHHHHH.. CS
       TPR_3 11 fynkkkyqeArelfs 25
                +++k+k++eA+ +++
  EPA04482.1 17 LFLKGKLDEAIKYYD 31
                789**********98 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.2
                TT-H CS
       TPR_3 14 kkky 17
                 k+y
  EPA04482.1 54 LKDY 57
                3455 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   4.5e-05     0.062       1      51 [.      11      58 ..      11      59 .] 0.92

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.5e-05
      TPR_16  1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrla 51
                l++a+ ++  g+ d+A+++++  l  +   P +  +l+++g a+ ++++++
  EPA04482.1 11 LDEANRLFLKGKLDEAIKYYDMILHEN---PNHIGSLNNKGYALNKLKDYD 58
                6789999999*****************...99999**********999998 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.3     0.001       1.4      13      61 ..      17      57 ..       6      59 .] 0.64

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.001
      TPR_12 13 lrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgry 61
                l+  g++deA+++++        l  +++p+ + +l+n g ++ +l++y
  EPA04482.1 17 LFLKGKLDEAIKYYDMI------L--HENPNHIGSLNNKGYALNKLKDY 57
                56678888888888877......2..33444455566666666665555 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00011      0.15       8      34 ..      14      40 ..       8      50 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
      TPR_14  8 aeallalGdpdeAiallrralalaPdd 34
                a  l+  G++deAi++++ +l  +P++
  EPA04482.1 14 ANRLFLKGKLDEAIKYYDMILHENPNH 40
                5667788**************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 405.60
//
Query:       EPA04483.1  [L=194]
Description: chlorite O(2)-lyase, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-54  184.4   0.1    1.8e-54  184.3   0.1    1.0  1  Chlor_dismutase  Chlorite dismutase


Domain annotation for each model (and alignments):
>> Chlor_dismutase  Chlorite dismutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.3   0.1   9.9e-59   1.8e-54       8     193 ..       6     183 ..       1     184 [. 0.92

  Alignments for each domain:
  == domain 1  score: 184.3 bits;  conditional E-value: 9.9e-59
                      HHHHHHHTTSCEEEEEEEETSTTTT-SEEEEEEESSHHHHHHHHHHHHHSTGGGGEEEEEEEEEEEEEESSSSS-GGGHHHCHHHHS----SSS CS
  Chlor_dismutase   8 lealleeaeegvlralysvlGlradaDlmlwllretleelqeaerelrrtalgkvlepaysyvsvtelseYkeedeenkshvearlapelpkkk 101
                      +e +l  +++g+  ++ys+lGlr+daD+++w++++t+ee+q+a ++l +t +gk++ p+ +y+s+t++s Y      +k++   ++ + +  kk
       EPA04483.1   6 VEIVL--KNSGIKFRTYSTLGLRDDADFLFWFAAKTVEEIQSAIAKLYTTVFGKYIIPSRTYLSCTRPSIY-----VEKGKPLGFVSDAE-MKK 91 
                      44444..3456789*********************************************************.....45555566666666.99* PP

                      EEEEEEEEE-EEGGGS-HHHHHHHHHHHHHHHHGCTTEEEEEEE-TTTSSSSEEEEEEESSTHHHHHHHHHHCTSHHHHHHEEE-S-EEEEE CS
  Chlor_dismutase 102 yvcvYPmsksreWYllpeeeRrelmaeHgeigrkYgkVrqiitgsfGldDyEwgvaleaddleefkdlvyelRfdeasakvaeegpfyvGrr 193
                      +v+vYP++k+reWYllp+eeR+++m+eH+e+++kY+++  ++t+sfG++D ++++a+e d++ +f+dl+++lR++++s++v++++p++v+ +
       EPA04483.1  92 HVIVYPFTKTREWYLLPKEERQSIMDEHIEVSKKYPQIILNTTYSFGIHDEDFMLAFEVDEIRDFQDLIMDLRETRVSRYVKNDIPMIVCVK 183
                      *****************************************************************************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1304.17
//
Query:       EPA04484.1  [L=181]
Description: hypothetical protein BG20_I2471 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.7e-48  163.0   0.4    6.4e-48  162.9   0.4    1.0  1  DUF1802   Domain of unknown function (DUF1802)


Domain annotation for each model (and alignments):
>> DUF1802  Domain of unknown function (DUF1802)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.9   0.4   3.6e-52   6.4e-48       2     170 ..       4     171 ..       3     175 .. 0.95

  Alignments for each domain:
  == domain 1  score: 162.9 bits;  conditional E-value: 3.6e-52
     DUF1802   2 LkewavaveaLeeGrqivllrKggireergkFeveeeeflLYPtvehqkaellkpeyaallepvasestpe.kveikawAeveeavevsdeealealsk 99 
                 Lkewa++v aLe+G q+vllrKggi +   +F++e+++flL+Pt+ehq+ +++kpe++++le+v+s+  ++   +i+++Ae+     +s  e++++lsk
  EPA04484.1   4 LKEWATVVAALEDGVQTVLLRKGGILDVASGFKIEAKKFLLFPTHEHQEHHHIKPEFHKYLEQVKSNPPKAgFNRITSYAEILSEADISLDETIKKLSK 102
                 9***************************************************************9988777988************************* PP

     DUF1802 100 lhiwteeavedrlkykpkqpltvlllRvyrleepvelpetpeyagckswvdlpeseaeeakPVlsdeefee 170
                 +hiw+++++++r ++kp++p+++++l+vy+++e  + p ++ey+gcksw++++e+    +k+Vlsd+e e+
  EPA04484.1 103 FHIWSDSYINERKNWKPENPIKAVFLKVYKIPEV-NTPLKSEYQGCKSWININEE-IPVRKAVLSDKETES 171
                 *******************************885.6678899************9.9999******98665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.53
# Mc/sec: 1035.08
//
Query:       EPA04485.1  [L=367]
Description: copper binding protein, plastocyanin/azurin family, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.7e-17   63.0   1.9    5.2e-09   36.5   0.2    2.5  2  Copper-bind   Copper binding proteins, plastocyanin/azurin fa
    1.2e-13   51.1   0.0    9.6e-06   25.7   0.0    2.6  2  Cupredoxin_1  Cupredoxin-like domain
  ------ inclusion threshold ------
        1.2    9.6  29.3       0.14   12.7  15.9    2.3  2  TonB_N        TonB polyproline region
        7.1    6.6  26.5       0.62   10.1  16.3    2.9  2  Trypan_PARP   Procyclic acidic repetitive protein (PARP)


Domain annotation for each model (and alignments):
>> Copper-bind  Copper binding proteins, plastocyanin/azurin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.2   1.2e-12   5.2e-09       9      98 ..     136     215 ..     130     216 .. 0.92
   2 !   25.6   0.1   2.7e-09   1.2e-05      14      99 .]     292     367 .]     282     367 .] 0.84

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 1.2e-12
                  TETSEEESSEEEEETTEEEEEEEESSSSBEEEEETTSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEESSEEEEEEETTTTTTTSEEEEEE CS
  Copper-bind   9 sgdlqFetkeitvkkgekvtfvnlavmgHNvvldkdgvpagvdkdkvkaedetkliggGekdsvtfdeagtYkffCsPHaaagMkgkvtv 98 
                   ++  +++ +i+++  ++v++ n +  +H v   kd  p+g+ ++ + ++        G++++ tfd++gtY +fC  H    M g+v+v
   EPA04485.1 136 TTSTCYSPDSIEIQVDDTVMWSNDDTAAHTVTSGKDVTPDGIFDSSLFMS--------GNTFEYTFDKTGTYPYFCMVHP--WMTGQVIV 215
                  555679***********************************999998885........**********************..69****98 PP

  == domain 2  score: 25.6 bits;  conditional E-value: 2.7e-09
                  EESSEEEEETTEEEEEEEESSSSBEEEEETTSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEESSEEEEEEETTTTTTTSEEEEEEE CS
  Copper-bind  14 FetkeitvkkgekvtfvnlavmgHNvvldkdgvpagvdkdkvkaedetkliggGekdsvtfdeagtYkffCsPHaaagMkgkvtve 99 
                  + + +  +++ge++ ++n+++ +H v   kd+ ++g  ++ + +        + ++ +  fd++g+Y++fC  H    M gkv+v+
   EPA04485.1 292 YLPYQAVINSGESIIWTNTDSAAHTVTSGKDATSDGNFDSGMMI--------PKNTWEHMFDKPGEYDYFCMLHP--WMTGKVVVN 367
                  67778899************************977755554444........34689******************..69****996 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   2.1e-09   9.6e-06      28     104 .]     137     215 ..     116     215 .. 0.89
   2 !   22.8   0.0   1.7e-08   7.5e-05      29     104 .]     289     366 ..     265     366 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 2.1e-09
  Cupredoxin_1  28 kdggfePskievkagekvklkiknkdktpeefesed......lgeekvlapgktttitiaplkpGeYeftcdmhmdakGkliV 104
                   +++ ++P++ie++ +   ++++ n+d+ +++++s +      +  +   ++g+t++ t+  +k G+Y+++c  h+ + G++iV
    EPA04485.1 137 TSTCYSPDSIEIQVDD--TVMWSNDDTAAHTVTSGKdvtpdgIFDSSLFMSGNTFEYTF--DKTGTYPYFCMVHPWMTGQVIV 215
                   4568***********9..99**************99999996445567799********..**************99*****9 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 1.7e-08
  Cupredoxin_1  29 dggfePskievkagekvklkiknkdktpeefesed.......lgeekvlapgktttitiaplkpGeYeftcdmhmdakGkliV 104
                   ++ + P +  +++ge  ++ ++n+d+ +++++s +       ++      p++t +  +  +kpGeY+++c +h+ + Gk++V
    EPA04485.1 289 NECYLPYQAVINSGE--SIIWTNTDSAAHTVTSGKdatsdgnFDS-GMMIPKNTWEHMF--DKPGEYDYFCMLHPWMTGKVVV 366
                   5578999999****9..89**************999999944443.3444555666666..**************99*****9 PP

>> TonB_N  TonB polyproline region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   5.5     0.043   1.9e+02      42      65 ..      99     126 ..      74     135 .. 0.45
   2 ?   12.7  15.9   3.1e-05      0.14      37      80 ..     231     267 ..     211     283 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.043
                 X..XXXXXXX..X..XXXXXXXXXXXXX CS
      TonB_N  42 vepePePePE..v..vPePpapvviekP 65 
                  +peP P+PE  v  +P  p+ v++++P
  EPA04485.1  99 KSPEPVPVPEkpVmaMPVAPQTVTVSIP 126
                 2244444444221112333334445555 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 3.1e-05
                 XXXXXX..XXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXX CS
      TonB_N  37 apePavepePePePEvvPePpapvviekPkPePkPkPkPkpvkk 80 
                 +p+P ++ ePeP  E++PeP        P PeP P P P p +k
  EPA04485.1 231 EPNPSAPVEPEPTNEPAPEPI-------PSPEPTPAPVPEPTEK 267
                 456777778888888888884.......6666666666666655 PP

>> Trypan_PARP  Procyclic acidic repetitive protein (PARP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   2.5      0.11   4.9e+02      13      49 ..      10      46 ..       1     136 [. 0.45
   2 ?   10.1  16.3   0.00014      0.62      76     109 ..     231     264 ..     216     283 .. 0.48

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.11
  Trypan_PARP 13 lfsanlfagvgfaaaaegpedkgltkggkgk.ekgtkv 49
                   s+n+++g+    +a +p + +  kg  g  ++ +k 
   EPA04485.1 10 APSSNMYSGIVSY-SASEPIQLVALKGPIGPdDHPAKT 46
                 4566666666433.334455555555555543333332 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00014
  Trypan_PARP  76 epepetepeeepepepepepepepepepepepep 109
                  ep+p +  e+ep +ep pep p pep p p pep
   EPA04485.1 231 EPNPSAPVEPEPTNEPAPEPIPSPEPTPAPVPEP 264
                  2222222222222222222222222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2375.67
//
Query:       EPA04486.1  [L=287]
Description: hypothetical protein BG20_I2303 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.7e-06   27.7   0.2    1.2e-05   25.7   0.1    2.0  1  Hint_2        Hint domain
  ------ inclusion threshold ------
       0.08   12.7   0.0       0.14   12.0   0.0    1.3  1  Vint          Hint-domain
      0.084   12.4   0.4       0.16   11.5   0.4    1.5  1  TF_Zn_Ribbon  TFIIB zinc-binding


Domain annotation for each model (and alignments):
>> Hint_2  Hint domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.1     2e-09   1.2e-05       1      47 [.     157     207 ..     157     235 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 2e-09
      Hint_2   1 pCflagtliatpeGevaveeLrvGdlVvtad....gglqpvrwigsrtlsa 47 
                 +C+ ++t i+tp+G+v + ++++G++V t+d    +++ ++++ g++ +s+
  EPA04486.1 157 ICLSEDTVIDTPNGNVNIKDVNQGMRVFTQDtsgnKQTVEILKTGKTLVSP 207
                 6******************************55444477778888877743 PP

>> Vint  Hint-domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.3e-05      0.14       2      64 ..     158     230 ..     156     237 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.3e-05
        Vint   2 Cfagesrvklaegktvkiselrkgmkvqtpk..garkvaavlkt...kvee.eelcrl.....gellvTpwHPv 64 
                 C++ ++ ++  +g  v+i+++ +gm+v t++  g ++ + +lkt    v+  ++++++     +el+  p HP 
  EPA04486.1 158 CLSEDTVIDTPNG-NVNIKDVNQGMRVFTQDtsGNKQTVEILKTgktLVSPdHKMVHIvlvdnRELYGSPNHPT 230
                 8888888887776.79*************998878888888876221455479999998998779999999995 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.4   2.7e-05      0.16       3      19 ..     155     171 ..     153     173 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.7e-05
                   ETTTTCEECHEETSTTC CS
  TF_Zn_Ribbon   3 CPnCgstnlveDperge 19 
                   CP+C s+++v D+ +g+
    EPA04486.1 155 CPICLSEDTVIDTPNGN 171
                   **************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2050.08
//
Query:       EPA04487.1  [L=536]
Description: hypothetical protein BG20_I1555 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      0.004   17.1   0.2      0.095   12.7   0.2    2.5  1  PDDEXK_7    PD-(D/E)XK nuclease superfamily
  ------ inclusion threshold ------
      0.019   14.3   0.0       0.03   13.7   0.0    1.2  1  Microvir_H  Microvirus H protein (pilot protein)


Domain annotation for each model (and alignments):
>> PDDEXK_7  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.2   1.1e-05     0.095      16     105 ..     322     387 ..     307     411 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.1e-05
    PDDEXK_7  16 kellglevkeqnllkvkekglrvqlekgraakllferlsdgeeielaynprfsrkeekqssytvtqkPDivleitkkekkkvlivfDAKY 105
                 +                ekgl ++l+ g++a+ +fe   +g+ ++ +y+++fs+  ++ +++     PD    ++ +    +l +fDAK 
  EPA04487.1 322 H----------------EKGLLINLKLGDKAHCQFEY--RGLIVTFWYEKSFSQ--KEGHAWILLHVPDFTAMVNDE----ILAIFDAKN 387
                 3................45778888888887777766..789***********5..44479********98777654....667999994 PP

>> Microvir_H  Microvirus H protein (pilot protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   3.4e-06      0.03     155     239 ..     375     460 ..     365     474 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.4e-06
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
  Microvir_H 155 tqkeiagiqsatsrqntkdqvyaqnemlayqqkestarvasimentnlskqq.qvseimrqmltqaqtagqyftndqikemtrkvs 239
                  + ei  i  a    nt     +qn+mlay ++  t+  a i  n     ++    e m+q++   +t     tn++ik+ +rk+ 
  EPA04487.1 375 VNDEILAIFDAKNYSNTGYYSESQNKMLAYMNNLDTSFGALIYPNYPKNWDDfTRDERMQQLVLFLDTKNSEATNNEIKNHARKLV 460
                 5679999************************************99866654416689**************************974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (536 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       923  (0.0514808); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.66u 0.36s 00:00:01.02 Elapsed: 00:00:00.53
# Mc/sec: 3037.24
//
Query:       EPA04488.1  [L=142]
Description: hypothetical protein BG20_I1553 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.054   13.6   0.0      0.069   13.2   0.0    1.2  1  DUF4513   Domain of unknown function (DUF4513)


Domain annotation for each model (and alignments):
>> DUF4513  Domain of unknown function (DUF4513)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   3.9e-06     0.069      50     125 ..      33     113 ..      15     120 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.9e-06
     DUF4513  50 pwkenmkfrnvnlkkaevsgiya..gpledslflnyserlchged...rkvvlkkgpleikiadmplhsplsryqstvish 125
                  wk  ++ rn+  +   ++gi      + + + +n++e + + +d   +k+ +k+gp e+k + +     lsr++s +i  
  EPA04488.1  33 SWKYWVRHRNITKNLITICGIEIpfHKVGNKICVNKQELIKKIQDdikKKIEIKNGPIEVKGTVIGDFVELSRWDSGMIGS 113
                 69999*******999*****9872246789999**99977655443337899************************99965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1038  (0.057895); expected 358.6 (0.02)
Passed bias filter:                      624  (0.0348039); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 880.33
//
Query:       EPA04489.1  [L=953]
Description: ATPase, AAA family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.2e-13   49.5   0.0    9.9e-13   48.3   0.0    1.7  1  AAA_5         AAA domain (dynein-related subfamily)
      3e-06   27.6   1.0    0.00012   22.4   0.2    2.9  2  Copper-bind   Copper binding proteins, plastocyanin/azurin fa
     0.0013   19.3   0.1      0.067   13.7   0.0    3.3  2  AAA_18        AAA domain
     0.0039   17.0   0.0        3.5    7.5   0.0    3.5  3  AAA_3         ATPase family associated with various cellular 
     0.0044   16.4   0.0      0.015   14.7   0.0    1.8  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
     0.0066   16.2   0.0      0.013   15.2   0.0    1.4  1  AAA_30        AAA domain
       0.01   16.3   0.1      0.053   13.9   0.1    2.3  1  AAA_16        AAA ATPase domain
  ------ inclusion threshold ------
      0.013   15.8   0.0        0.4   11.0   0.0    2.6  1  AAA_19        AAA domain
      0.019   15.1   0.0      0.047   13.8   0.0    1.7  1  Cupredoxin_1  Cupredoxin-like domain
      0.026   14.3   0.0      0.074   12.8   0.0    1.7  1  RuvB_N        Holliday junction DNA helicase RuvB P-loop doma
      0.051   13.6   0.0        0.1   12.6   0.0    1.5  1  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
      0.068   12.4   0.0       0.13   11.5   0.0    1.4  1  TIP49         TIP49 P-loop domain
       0.09   12.3   0.3       0.42   10.1   0.0    2.2  2  AAA_7         P-loop containing dynein motor region
      0.091   12.8   0.0       0.19   11.7   0.0    1.5  1  HOIP-UBA      HOIP UBA domain pair


Domain annotation for each model (and alignments):
>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   0.0   7.7e-16   9.9e-13       1     138 []     565     735 ..     565     735 .. 0.92

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 7.7e-16
                 EEEEE--SSSSHHHHHHHGGGGB.....S--EEEEE--TT--HHHHH--B--.............--------......................G-SE CS
       AAA_5   1 dvlLvGppGtgKselaerlaaal.....nreveyvqltrdtteedlkgrreik....ngttslvdsplvraar......................egei 68 
                 +vlL Gp GtgK++la+ + +++     +   e +  t+d++++d++ ++ +k    +  ++ +++++v+ +                       +g  
  EPA04489.1 565 HVLLAGPIGTGKTRLAQIIPKVFwesigGYYSEDYTATADWSTQDVIAGIFPKmsneKPLYEIQNGCVVETVAknwenginggnrsysnptpsasRGTW 663
                 79*************************99999*******************99765555578999****99999************************* PP

                 EEEESGGG--.HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--..-TT-TTHHHHTT- CS
       AAA_5  69 lvlDEverae.sevlnsLlslleerrllleeggelvkaknddllerfrviatanpld.rslnelspalrsRf 138
                 l++DE++ra+ +++++ L + l +r l ++  ++  + k  ++ e+ r+i+t n++d + l +ls al+sRf
  EPA04489.1 664 LIIDEFNRADiDKAFGQLFTALRTRSLKIPTDQKGLSYKHLKIPEDYRIIGTLNTADkHFLFQLSDALKSRF 735
                 ****************************998877776666336666***********9999**********9 PP

>> Copper-bind  Copper binding proteins, plastocyanin/azurin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.16   2.1e+02      18      64 ..      52      97 ..      34     111 .. 0.78
   2 !   22.4   0.2   9.4e-08   0.00012      10      98 ..     304     383 ..     297     384 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.16
                 EEEEETTEEEEEEEESSSSBEEEEETTSSTTTGGGTTSCTTCEEEEB CS
  Copper-bind 18 eitvkkgekvtfvnlavmgHNvvldkdgvpagvdkdkvkaedetkli 64
                 +i+++k ++ t    +   HN+  d+d   + +d d +++ed++kl+
   EPA04489.1 52 DIDIAKNSHLTARD-TLLKHNIIADNDDSYSLIDYDDLTIEDRNKLV 97
                 55565555544444.8899*********99*********99988876 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 9.4e-08
                  ETSEEESSEEEEETTEEEEEEEESSSSBEEEEETTSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEESSEEEEEEETTTTTTTSEEEEEE CS
  Copper-bind  10 gdlqFetkeitvkkgekvtfvnlavmgHNvvldkdgvpagvdkdkvkaedetkliggGekdsvtfdeagtYkffCsPHaaagMkgkvtv 98 
                  ++  F ++e++vkkg+ vt++n++  +H +   ++ v++g d +  +      l+ +  ++  +fde+g+  ++C  H    M+gk++v
   EPA04489.1 304 THSCFIPEELHVKKGDIVTWINTDNAAHTIT--SGTVSDGPDGKFDSS-----LMVSRAQFMYKFDESGEHPYHCMVHP--WMVGKIMV 383
                  556799**********************765..566766666655444.....6667789*******************..69****98 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1      0.34   4.3e+02      25      93 ..      60     134 ..      36     188 .. 0.76
   2 !   13.7   0.0   5.2e-05     0.067       1      51 [.     566     623 ..     566     688 .. 0.67

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.34
      AAA_18  25 gvnlrdvakenglllevdpe.aldeskrldedkldklldaleenss.....aleegknlvidghlaeleseaakd 93 
                 +   rd++ ++++  ++d+   l +++ l ++ ++kl+++    +s     a+     lv+ ++ ++  +e +kd
  EPA04489.1  60 HLTARDTLLKHNIIADNDDSySLIDYDDLTIEDRNKLVNLCTDKISeaatyASKISRRLVLFSVSGDASFEHFKD 134
                 778888888888888888888777777777777777777776666667777777777778877777777666665 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 5.2e-05
      AAA_18   1 IlltGtpGvGKttlakeLskrl.gf..gvnlrdvakenglllevdpe....aldeskr 51 
                 +ll+G++G+GKt la+ + k   ++  g+ + d+ +  ++++ +  +    + +++k 
  EPA04489.1 566 VLLAGPIGTGKTRLAQIIPKVFwESigGYYSEDYTATADWSTQDVIAgifpKMSNEKP 623
                 79****************8886655899999999999999988877766664444443 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1      0.17   2.2e+02      49      94 ..      13      58 ..       6      75 .. 0.80
   2 ?    3.1   0.0      0.06        77       1      43 [.     565     612 ..     565     641 .. 0.60
   3 !    7.5   0.0    0.0027       3.5      66     130 ..     664     736 ..     659     737 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.17
       AAA_3 49 ekekefefkkGpvfanllladeinrappktqsalleameerqvtve 94
                + + e e +  pvf   ll +    ++++++ al+ea  + +++ +
  EPA04489.1 13 KMKMEQEHNYQPVFIRTLLQNSGTATKAQIKQALIEANPDIDIAKN 58
                44566677788*************************9877666654 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.06
       AAA_3   1 hvllegvPGlaktllvkalakaldlef.....kriqftpdllPsdilG 43 
                 hvll g  G++kt+l++ + k++  ++     +    t+d    d++ 
  EPA04489.1 565 HVLLAGPIGTGKTRLAQIIPKVFWESIggyysEDYTATADWSTQDVIA 612
                 9***************98877653332111113345566666666654 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0027
       AAA_3  66 lladeinrap.pktqsalleameerqvtveg.......ethklpepflvlatqnPieqeGtyplpeaqldrfl 130
                 l+ de nra   k+   l+ a++ r + +         +  k+pe + ++ t n  +++  ++l +a   rf 
  EPA04489.1 664 LIIDEFNRADiDKAFGQLFTALRTRSLKIPTdqkglsyKHLKIPEDYRIIGTLNTADKHFLFQLSDALKSRFA 736
                 78899999973689999999999987765431111111456899*************************9995 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       4.4   5.7e+03     170     189 ..      99     118 ..      95     119 .. 0.84
   2 !   14.7   0.0   1.1e-05     0.015      17      46 ..     558     587 ..     548     601 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 4.4
  Mg_chelatase 170 ectcsekeierYlsklsgpl 189
                    ct + +e ++Y sk+s+ l
    EPA04489.1  99 LCTDKISEAATYASKISRRL 118
                   588889999*******9876 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1.1e-05
  Mg_chelatase  17 iaaaGgHnlllvGppGsGKtmlakrlpsll 46 
                    a a g ++ll+Gp G+GKt la+ +p+++
    EPA04489.1 558 TALASGRHVLLAGPIGTGKTRLAQIIPKVF 587
                   3667777899**************999876 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0     1e-05     0.013      12     118 ..     558     691 ..     554     694 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1e-05
      AAA_30  12 alltsgdrvavltGpAGtGKttalkal.reaweaag...............grvi.glAptgkaAkvLae.elgieastiakllkrlk..........g 82 
                 ++l+sg+  ++l Gp GtGKt + + + +  we+ g               ++vi g+ p+    k L e + g   +t+ak + +++           
  EPA04489.1 558 TALASGR-HVLLAGPIGTGKTRLAQIIpKVFWESIGgyysedytatadwstQDVIaGIFPKMSNEKPLYEiQNGCVVETVAKNW-ENGinggnrsysnP 654
                 4556664.89*****************777888886687666666666665333325555555555555456677888888877.333789******95 PP

      AAA_30  83 rarlepgtllivDEagmvdtkql.aallkaaekagak 118
                 + + ++gt li+DE   +d++++  +l++a+++++ k
  EPA04489.1 655 TPSASRGTWLIIDEFNRADIDKAfGQLFTALRTRSLK 691
                 5677889***********9976527888887776665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.1   4.1e-05     0.053      21      50 ..     562     589 ..     553     691 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.1e-05
      AAA_16  21 sgrpelvllsGesGvGKsslvrellralek 50 
                 sg  + vll G+ G+GK++l++ +++ + +
  EPA04489.1 562 SG--RHVLLAGPIGTGKTRLAQIIPKVFWE 589
                 33..89***************988875444 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00031       0.4       4     127 ..     556     687 ..     554     694 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00031
      AAA_19   4 avealkekvllvtaGp.GtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae...........atTiHrlalldfddlltealel 90 
                 +v+al+++  +++aGp GtGKTr+ + i +++ e  g    e + ++      + ++    ++  e            +T+ +     +++ +      
  EPA04489.1 556 IVTALASGRHVLLAGPiGTGKTRLAQIIPKVFWESIGGYYSEDYTATADWSTQDVIAGIFPKMSNEkplyeiqngcvVETVAKN----WENGI------ 644
                 66655555555555555******9999999887776655555555555555555555544444444555555555444555443....33333...... PP

      AAA_19  91 le.....eaeeekklqeeellivDEfq..dvdelqyrLlkallg 127
                  +     +++ +    ++++li+DEf   d+d+   +L+ al +
  EPA04489.1 645 -NggnrsYSNPTPSASRGTWLIIDEFNraDIDKAFGQLFTALRT 687
                 .2333335566666667778888888633566777788887765 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.7e-05     0.047      31     104 .]     307     383 ..     293     383 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.7e-05
  Cupredoxin_1  31 gfePskievkagekvklkiknkdktpeefesed......lgeekvlapgktttitiaplkpGeYeftcdmhmdakGkliV 104
                    f P++++vk+g    +++ n+d+ +++++s         +++  l+   ++ +  + ++ Ge++++c  h+ + Gk+ V
    EPA04489.1 307 CFIPEELHVKKGDI--VTWINTDNAAHTITSGTvsdgpdGKFDSSLMVSRAQFMY-KFDESGEHPYHCMVHPWMVGKIMV 383
                   589*********94..6788888888888887777788899*****999999988.88**************99***987 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   5.8e-05     0.074      34      55 ..     564     585 ..     538     593 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.8e-05
      RuvB_N  34 dhvllyGpPGlGkttlakiiak 55 
                  hvll+Gp G Gkt la+ii k
  EPA04489.1 564 RHVLLAGPIGTGKTRLAQIIPK 585
                 5******************976 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   8.1e-05       0.1       7      41 ..     553     585 ..     547     607 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.1e-05
                 HHHHHHHHHHCHTEEEEEEESTTSSHHHHHHHHHH CS
        TsaE   7 tealgkklakalgdvilLeGdLGaGKTtlvrglak 41 
                 + ++ ++la+  g+ +lL G++G+GKT l++ + k
  EPA04489.1 553 VIEIVTALAS--GRHVLLAGPIGTGKTRLAQIIPK 585
                 5566666766..899***************98765 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   9.9e-05      0.13      48      73 ..     561     586 ..     551     647 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.9e-05
                 XXXXXXXXXXXXXXXXXXXXXXXXXX CS
       TIP49  48 laGravLlaGpsgtGktalaiaiske 73 
                  +Gr vLlaGp gtGkt la  i k 
  EPA04489.1 561 ASGRHVLLAGPIGTGKTRLAQIIPKV 586
                 48******************888775 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.2       1.4   1.7e+03      50      85 ..      10      45 ..       4      49 .. 0.73
   2 ?   10.1   0.0   0.00033      0.42      28      51 ..     558     581 ..     544     596 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.4
       AAA_7 50 ikdllkkldkekylsltinfsaqtsanqlqdiiesk 85
                i++ +k  ++ +y++++i    q s + ++  i++ 
  EPA04489.1 10 IQNKMKMEQEHNYQPVFIRTLLQNSGTATKAQIKQA 45
                677777777788888888888887777777777765 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00033
       AAA_7  28 lllknkkpvllvGptGtGKtviik 51 
                 + l+++++vll Gp GtGKt +++
  EPA04489.1 558 TALASGRHVLLAGPIGTGKTRLAQ 581
                 467889**************8876 PP

>> HOIP-UBA  HOIP UBA domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00015      0.19      47     105 ..       3      69 ..       1      81 [. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00015
    HOIP-UBA  47 lpelldevaalaaseqkekke........nevgklsraEakealleagGdvekAvkqclreRrkKvk 105
                 ++el++ ++   + eq+++ +        ++ g+ ++a +k+al+ea+ d++ A ++ l+ R + +k
  EPA04489.1   3 FNELVNFIQNKMKMEQEHNYQpvfirtllQNSGTATKAQIKQALIEANPDIDIAKNSHLTARDTLLK 69 
                 5667777777666666554446999999999*******************************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (953 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       777  (0.0433376); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.83u 0.30s 00:00:01.12 Elapsed: 00:00:00.49
# Mc/sec: 5826.09
//
Query:       EPA04490.1  [L=166]
Description: zinc finger, C2H2 type [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0023   17.8   0.6        0.8    9.7   0.1    2.3  2  zf-LYAR    LYAR-type C2HC zinc finger
     0.0068   17.1   4.9        1.4   10.0   0.8    2.6  2  zf-C2H2_4  C2H2-type zinc finger
  ------ inclusion threshold ------
      0.011   16.1   5.9      0.059   13.8   0.1    2.5  2  zf-C2H2    Zinc finger, C2H2 type
       0.36   11.2   6.9        5.1    7.5   0.4    2.2  2  zf-C2H2_2  C2H2 type zinc-finger (2 copies)
       0.57   10.5   3.1       0.87    9.9   3.1    1.2  1  zf-C2H2_8  C2H2-type zinc ribbon
        2.5    8.7   8.8        3.5    8.2   0.0    2.8  3  zf-H2C2_2  Zinc-finger double domain
        7.1    6.8   7.8        1.7    8.7   2.6    2.1  2  zf-C2H2_6  C2H2-type zinc finger


Domain annotation for each model (and alignments):
>> zf-LYAR  LYAR-type C2HC zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.1   0.00031       0.8       1      14 [.      10      24 ..      10      30 .. 0.79
   2 !    6.5   0.0     0.003       7.8       2      19 ..      39      57 ..      38      58 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00031
     zf-LYAR  1 fsCiDCsktFdg.de 14
                + C+DC ++F++ de
  EPA04490.1 10 YECLDCEENFQKrDE 24
                67********98555 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.003
     zf-LYAR  2 sCiDCsktFdg.deykaHt 19
                 C  C+ +F   +++kaHt
  EPA04490.1 39 KCTLCNMKFLYlKSIKAHT 57
                5999*****999******9 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.2    0.0015       3.9       1      19 [.      10      28 ..      10      33 .. 0.90
   2 !   10.0   0.8   0.00055       1.4       2      24 .]      39      61 ..      38      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0015
   zf-C2H2_4  1 fkCpiCgksFsskkaLlrH 19
                ++C  C ++F  +++Ll H
  EPA04490.1 10 YECLDCEENFQKRDELLVH 28
                89********99999**99 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00055
   zf-C2H2_4  2 kCpiCgksFsskkaLlrHlkthH 24
                kC++C+  F   k+++ H +  H
  EPA04490.1 39 KCTLCNMKFLYLKSIKAHTEYSH 61
                8*****************77666 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   2.3e-05     0.059       1      23 []      10      33 ..      10      33 .. 0.97
   2 ?    4.1   1.6     0.029        74       2      23 .]      39      61 ..      38      62 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.3e-05
                EEETTTTEEESSHHHHHHHHHC.C CS
     zf-C2H2  1 ykCpdCgksFkrksnLkrHirt.H 23
                y+C dC + F  +++L +H +t H
  EPA04490.1 10 YECLDCEENFQKRDELLVHGQTkH 33
                99*****************99988 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.029
                EETTTTEEESSHHHHHHHHHC.C CS
     zf-C2H2  2 kCpdCgksFkrksnLkrHirt.H 23
                kC+ C+++F    + k+H    H
  EPA04490.1 39 KCTLCNMKFLYLKSIKAHTEYsH 61
                8******9988887777776554 PP

>> zf-C2H2_2  C2H2 type zinc-finger (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.4     0.002       5.1       2      23 ..      12      33 ..       5      37 .. 0.55
   2 ?    7.0   1.2    0.0028       7.3      51      76 ..      38      63 ..      34      69 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.002
   zf-C2H2_2  2 Clfcekkskeveellehmskkh 23
                Cl ce+++++++ell h ++kh
  EPA04490.1 12 CLDCEENFQKRDELLVHGQTKH 33
                5555555555555555555555 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0028
   zf-C2H2_2 51 leClyCekefkslealreHmkkkgHc 76
                l+C +C+ +f  l+++++H +  +H+
  EPA04490.1 38 LKCTLCNMKFLYLKSIKAHTEYSHHK 63
                58*******99********9988887 PP

>> zf-C2H2_8  C2H2-type zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   3.1   0.00034      0.87      36      86 ..      10      57 ..       3      65 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00034
   zf-C2H2_8 36 frcstascaetfpsmqelvahtklhykpnry.fkcencllrfrthrslfkhl 86
                ++  ++ c e f   +el+ h +   k nr  +kc  c ++f   +s+  h 
  EPA04490.1 10 YE--CLDCEENFQKRDELLVHGQT--KHNRIiLKCTLCNMKFLYLKSIKAHT 57
                44..478**************975..6677527*********9999987775 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.8     0.011        29       7      24 ..       2      19 ..       1      21 [. 0.81
   2 ?    8.2   0.0    0.0014       3.5      10      25 ..      28      48 ..      26      49 .. 0.67
   3 ?   -2.1   0.4       2.5   6.3e+03       5      11 ..      56      63 ..      53      66 .. 0.63

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.011
   zf-H2C2_2  7 rkHtgekpyeCplCdkaF 24
                r+  ++k yeC  C   F
  EPA04490.1  2 RFFSKKKNYECLDCEENF 19
                56668899******9887 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0014
   zf-H2C2_2 10 tgekpy.....eCplCdkaFk 25
                +g++++     +C lC+ +F 
  EPA04490.1 28 HGQTKHnriilKCTLCNMKFL 48
                45554333334********96 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 2.5
   zf-H2C2_2  5 Hi.rkHtg 11
                H+ ++H++
  EPA04490.1 56 HTeYSHHK 63
                75256886 PP

>> zf-C2H2_6  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.2      0.23     6e+02       2      17 ..      10      25 ..      10      34 .. 0.83
   2 ?    8.7   2.6   0.00066       1.7       3      26 ..      39      63 ..      39      64 .. 0.96

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.23
   zf-C2H2_6  2 heCsvCsksFpslqaL 17
                +eC  C + F++ ++L
  EPA04490.1 10 YECLDCEENFQKRDEL 25
                89999***99987766 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00066
   zf-C2H2_6  3 eCsvCsksFpslqaLggHk.ksHrk 26
                +C+ C+  F +l++   H  +sH+k
  EPA04490.1 39 KCTLCNMKFLYLKSIKAHTeYSHHK 63
                7***********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       990  (0.0552178); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 975.36
//
Query:       EPA04491.1  [L=37]
Description: hypothetical protein BG20_I1551 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       169  (0.00942607); expected 358.6 (0.02)
Passed bias filter:                      155  (0.00864521); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 260.82
//
Query:       EPA04492.1  [L=59]
Description: hypothetical protein BG20_I1547 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0046   17.0   3.4     0.0055   16.8   3.4    1.1  1  DUF2107    Predicted membrane protein (DUF2107)
  ------ inclusion threshold ------
      0.014   15.4   5.7      0.016   15.2   5.7    1.0  1  CRPA       Chlamydia 15 kDa cysteine-rich outer membrane prot
      0.034   14.4   1.5       0.04   14.1   1.5    1.1  1  TrbC       TrbC/VIRB2 family
       0.28   10.8   1.7       0.56    9.8   0.1    1.9  2  Saf_2TM    SAVED-fused 2TM effector domain
        1.3    9.0  10.9        0.4   10.7   4.0    2.2  2  Fst_toxin  Toxin Fst, type I toxin-antitoxin system


Domain annotation for each model (and alignments):
>> DUF2107  Predicted membrane protein (DUF2107)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   3.4   1.5e-06    0.0055       1      44 [.       2      45 ..       2      54 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.5e-06
     DUF2107  1 lyvGlilliiGtlaaaiGPrekdplvrllnlEvpa.vGvllilLa 44
                +++G+il i+Gtl+     + kdp+  ll + +p  vGv+l+l +
  EPA04492.1  2 FVIGVILTIAGTLMIFS-DMIKDPVNNLLPMMLPMvVGVVLLLVS 45
                799**********9777.9***************73699999875 PP

>> CRPA  Chlamydia 15 kDa cysteine-rich outer membrane protein (CRPA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   5.7   4.5e-06     0.016      68     111 ..       1      45 [.       1      54 [. 0.78

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.5e-06
        CRPA  68 lvvlGilLviaglallfilqa.qlganafylliPaviGlvkllvt 111
                 + v+G++L iag  ++f        +n + +++P v+G+v llv+
  EPA04492.1   1 MFVIGVILTIAGTLMIFSDMIkDPVNNLLPMMLPMVVGVVLLLVS 45 
                 78**********9999975540556666678*********99984 PP

>> TrbC  TrbC/VIRB2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   1.5   1.1e-05      0.04      57      96 ..       3      49 ..       1      52 [. 0.87

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.1e-05
        TrbC 57 iatiaiivaGimlafgrls.......wrtlvmvviGiviifgAssiv 96
                ++ +++ +aG  ++f ++        +++++++v+G+v++ +++si 
  EPA04492.1  3 VIGVILTIAGTLMIFSDMIkdpvnnlLPMMLPMVVGVVLLLVSGSIG 49
                566778889999999998789**********************9996 PP

>> Saf_2TM  SAVED-fused 2TM effector domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00016      0.56      72      93 ..       2      23 ..       1      27 [. 0.90
   2 ?    0.6   0.2       0.1   3.7e+02      72      83 ..      35      46 ..      29      57 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00016
     Saf_2TM 72 lvigvllivvGavllilryvne 93
                +vigv+l+++G ++++++++++
  EPA04492.1  2 FVIGVILTIAGTLMIFSDMIKD 23
                89****************9876 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.1
     Saf_2TM 72 lvigvllivvGa 83
                +v+gv+l++v+ 
  EPA04492.1 35 MVVGVVLLLVSG 46
                455555555554 PP

>> Fst_toxin  Toxin Fst, type I toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.6     0.041   1.5e+02       9      15 ..       3       9 ..       2      10 .. 0.89
   2 ?   10.7   4.0   0.00011       0.4       7      18 ..      34      45 ..      34      45 .. 0.95

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.041
   Fst_toxin  9 vVGVilt 15
                v GVilt
  EPA04492.1  3 VIGVILT 9 
                89***98 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00011
   Fst_toxin  7 PivVGViltLvd 18
                P vVGV+l+Lv+
  EPA04492.1 34 PMVVGVVLLLVS 45
                99********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       791  (0.0441185); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.41u 0.30s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 399.60
//
Query:       EPA04493.1  [L=57]
Description: hypothetical protein BG20_I1550 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.025   14.6   0.3      0.026   14.5   0.3    1.0  1  Phage_Gp15  Bacteriophage Gp15 protein


Domain annotation for each model (and alignments):
>> Phage_Gp15  Bacteriophage Gp15 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.3   1.4e-06     0.026      15      56 ..       3      44 ..       1      55 [. 0.80

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.4e-06
  Phage_Gp15 15 eykidldFrtvlrfedmledeelseeeKinlalellldeepe 56
                e++i+l  +++l+f ++ +++ ls +eKi+ +++++l  e++
  EPA04493.1  3 EITIKLKDKEYLDFQKISNESGLSPDEKIQEIIQYYLIIEKN 44
                7789999999************************99973332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 413.74
//
Query:       EPA04494.1  [L=284]
Description: hypothetical protein BG20_I1552 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-11   44.6   0.0    1.6e-11   44.3   0.0    1.1  1  Peripla_BP_4  Periplasmic binding protein domain
     0.0055   17.2   0.0      0.016   15.7   0.0    1.7  2  NYN           NYN domain
  ------ inclusion threshold ------
      0.075   13.7   0.0        3.9    8.2   0.0    2.6  2  PGM_PMM_II    Phosphoglucomutase/phosphomannomutase, alpha/be


Domain annotation for each model (and alignments):
>> Peripla_BP_4  Periplasmic binding protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   0.0   2.6e-15   1.6e-11      47     229 ..      81     270 ..      30     282 .. 0.79

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 2.6e-15
                   HHHHHHHTT-SEEEE--SSHHHHHHHHHHHHHTT-EEEEESTT.GCTTT-CEEEEEC-HHHHHHHHHHHHHHHCTTH...EEEEEETSCCCHHHHHH CS
  Peripla_BP_4  47 qiedaiakgvdgiivapvdstalapalkkakaaGIpVvafdsd.dapsgerlayvgfdneaaGelqaeylaeklggk..kgkvvilaGspgdpnaee 140
                   ++  a++ ++  +i++++ +++ +p ++++k++G+++  +  + +  ++  +  vgf +e + ++  e l++  + +  k  ++++ G  +++ + +
    EPA04494.1  81 ALILALNLNASSVIISSNTVSEFTPLFEELKENGVYIGIITDPnTDSNDLADNAVGFSQENVHAQTIEKLLQRPNLDskKLRIAYFPGPKSNNFTLK 177
                   5555677788889**********************876655556778899999*********88888888887776678****************** PP

                   HHHHHHHHHHH-TTCEECC...EEE.STTTCHHHHHHHHHHHHHTTT....ECEEEESSCCHHHCHHHHHHHTTTTSTEEEEEES-HHHHHHHHHTT CS
  Peripla_BP_4 141 riegfrkvlkeypgikiva...eva.ganwdaekaqqalealltanp....ldgilaandgmaegalealeaaglagkvvvtgqDatpealeaikdG 229
                   ri gf + lk+   +ki +    ++ g+n +++++ + +e++ ++n+     ++i+  ndgm +g  ++l+++g+   +  +g+D+ +e ++ i + 
    EPA04494.1 178 RISGFYDLLKK---FKISEeqvCIYpGGNFSPNETHDLAEKVVAENKldenFVAIF-QNDGMLLGFKTYLSENGILQNFPMIGVDGIDEVKKKISEN 270
                   ***********...444443232225888999999999999999665445577887.99****************77777***********999543 PP

>> NYN  NYN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.7e-06     0.016      79     140 ..      73     134 ..      40     140 .. 0.74
   2 ?   -2.5   0.0       1.1   6.6e+03      24      61 ..     211     248 ..     197     267 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.7e-06
         NYN  79 vDvelavdalelaydnkydtivLvsgD.gDFaplveklrergkrVevllaeeastsseLisaa 140
                 +D + +  al la + + + +++ s   ++F+pl+e+l+e+g+ + ++   +++ s++L + a
  EPA04494.1  73 TDLNGCKKALILALNLNASSVIISSNTvSEFTPLFEELKENGVYIGIIT-DPNTDSNDLADNA 134
                 5555566677777655455555555559**************9888887.7678888887766 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.1
         NYN  24 klleeirskgelvraraygn.wedeeqnkfqdalsstgi 61 
                  l+e+++  ++l   ++++  ++d+ + +f++ ls++gi
  EPA04494.1 211 DLAEKVVAENKL-DENFVAIfQNDGMLLGFKTYLSENGI 248
                 556666666666.44555554556667777888888877 PP

>> PGM_PMM_II  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0   0.00065       3.9      70     100 ..     102     132 ..      87     134 .. 0.85
   2 ?    2.5   0.0     0.038   2.3e+02       7      92 ..     147     233 ..     142     237 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00065
                 TTTTHHHHGGGGG-SEEEEE-TTS-BEEEEE CS
  PGM_PMM_II  70 alkllielvkkegadlglafDgDaDRlgvvd 100
                 ++  l+e  k++g  +g+++D++ D   ++d
  EPA04494.1 102 EFTPLFEELKENGVYIGIITDPNTDSNDLAD 132
                 57789999****************9765555 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.038
                 GGGTS-HHHHHHHT-EEEEE-TT-TTHHHHHHHHHHTT-.EEEES-----TT-TTSS----TT-TTTTHHHHGGGGG-..SEEEEE-TT CS
  PGM_PMM_II   7 lkekvdseaikksglkvvidplhGaggeilkellkelgv.dvvelnaepdpdfptkapnpeekealkllielvkkega..dlglafDgD 92 
                 +++ +++  + +++l++++ p+  +   +lk++ + +++ +  ++ +e+    p+++  p+e  + +l+ ++v +++   +++++f  D
  EPA04494.1 147 IEKLLQRPNLDSKKLRIAYFPGPKSNNFTLKRISGFYDLlKKFKISEEQVCIYPGGNFSPNE--THDLAEKVVAENKLdeNFVAIFQND 233
                 55556666678888999999999999999999999999987777888888888888888888..4444444555554422555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1824.47
//
Query:       EPA04495.1  [L=263]
Description: hypothetical protein BG20_I1549 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-46  158.5   0.0    3.1e-46  158.2   0.0    1.0  1  DUF72     Protein of unknown function DUF72


Domain annotation for each model (and alignments):
>> DUF72  Protein of unknown function DUF72
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.2   0.0   1.7e-50   3.1e-46       1     216 [.      20     243 ..      20     244 .. 0.89

  Alignments for each domain:
  == domain 1  score: 158.2 bits;  conditional E-value: 1.7e-50
                 B.TT..CCCHHHHHCCT-SEEEE-HHCCSSS-HHHHHHHHCTS-TT-EEEEE--CCCCCS.G-.SCHHHHHHHHHH.CHHHCT-EEEEEEE--TT--S. CS
       DUF72   1 YpeglkkkerLeyYarhfntVEinstFYalpspetvakwaaqtpedFrFavKapraitherne.daeealerflesalepLgeklgpllfQlppsfkfd 98 
                 Yp+ l+k ++L+yY++ f++ Einst+Y++p+++  +kw+a tp++FrF+ K+p+ ithe++  +++e +++fl s l p+++k+ +l++Qlpps++fd
  EPA04495.1  20 YPKRLEKTNWLKYYSSIFDITEINSTYYKIPDQSITKKWNADTPDSFRFTAKFPSIITHEHRLkNVQEHIHKFLSS-LIPIHHKVLALVLQLPPSLSFD 117
                 9**********************************************************852348**********9.*******************998 PP

                 HHHHHHHHHHTTTS-..S.EEEE--BGGGH..HHHHHHHHTT-EEEEE--SSC--------SSTEEEEEE--SHHTTB----H......HHHHHHHHHH CS
       DUF72  99 eenlerLeaflaalp..l.lavEvRhrswf..ellellrehgvavvldepkkpklpledvttadfvyvRlhgreeryayrYse......eelaewaeri 186
                 e    rLe++++ lp    + +E Rh+swf  e ++ l e++  +v+   +   +      t+d vyvRl+g+++  ++++ +      e +++w ++i
  EPA04495.1 118 E-AKPRLEELFSLLPndFkYPIEGRHESWFtdEAIDYLTEKNHCLVWN--EIVGVNNPYPITSDYVYVRLIGDRSIPENQFGKviidrkELIKKWSDKI 213
                 6.79***********9956***********955*********778886..3444444556669**********5556667775555565999******* PP

                 HHHHTCSSEEEEEE-SBCCCHHHHHHHHHH CS
       DUF72 187 kawaaegrevyvffnndaegqaplnaraLa 216
                 ++++++   + v+ nn++eg  p++a+ L+
  EPA04495.1 214 NHLENKVSLALVMGNNHFEGFGPATANSLR 243
                 **************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       701  (0.0390987); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1590.58
//
Query:       EPA04496.1  [L=95]
Description: early transcribed membrane protein (ETRAMP) family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0008   19.2   0.3     0.0008   19.2   0.3    2.2  2  LapA_dom         Lipopolysaccharide assembly protein A domain
     0.0013   18.3   0.9     0.0015   18.0   0.9    1.1  1  SieB             Super-infection exclusion protein B
     0.0013   17.6   0.1     0.0014   17.5   0.1    1.0  1  DUF2207          Predicted membrane protein (DUF2207)
     0.0016   18.2   0.2     0.0016   18.2   0.2    1.6  1  DivIC            Septum formation initiator
     0.0018   18.0   0.8     0.0018   18.0   0.8    2.0  2  Vpu              Vpu protein
     0.0052   17.2   0.7     0.0066   16.9   0.7    1.2  1  DUF4199          Protein of unknown function (DUF4199)
  ------ inclusion threshold ------
      0.016   15.0   0.0      0.021   14.6   0.0    1.2  1  OPA3             Optic atrophy 3 protein (OPA3)
      0.018   15.3   0.4      0.036   14.3   0.4    1.5  1  Chordopox_A13L   Chordopoxvirus A13L protein
      0.025   13.4   1.6      0.027   13.3   1.6    1.0  1  7TM_GPCR_Sra     Serpentine type 7TM GPCR chemoreceptor Sra
      0.028   14.2   0.2      0.037   13.8   0.1    1.3  1  Connexin         Connexin
      0.028   14.8   0.1      0.028   14.8   0.1    1.5  2  Ly49             Ly49-like protein, N-terminal region
      0.034   15.0   1.1      0.075   13.9   0.0    1.9  2  EphA2_TM         Ephrin type-A receptor 2 transmembrane domai
      0.038   14.0   0.0      0.047   13.7   0.0    1.1  1  THEG4            Testis highly expressed protein 4
      0.045   13.4   2.4      0.051   13.2   2.4    1.0  1  Virul_fac_BrkB   Virulence factor BrkB
      0.053   12.2   0.0      0.059   12.1   0.0    1.0  1  DUF2298          Uncharacterized membrane protein (DUF2298)
       0.06   13.2   0.1       0.06   13.2   0.1    1.6  2  ECSCR            Endothelial cell-specific chemotaxis regulat
       0.11   11.8   0.0       0.16   11.3   0.0    1.3  1  CcmH             Cytochrome C biogenesis protein
       0.12   12.6   0.2       0.12   12.6   0.2    1.5  1  Glycophorin_A    Glycophorin A
       0.13   12.5   0.1        0.2   11.9   0.0    1.4  1  DUF4381          Domain of unknown function (DUF4381)
       0.16   11.8   0.3        0.3   11.0   0.0    1.7  1  COX14            Cytochrome oxidase c assembly
       0.17   11.1   6.3        1.1    8.5   0.1    2.0  2  7tm_1            7 transmembrane receptor (rhodopsin family)
        0.2   10.7   7.3        4.7    6.2   9.1    1.8  2  EIIC-GAT         PTS system sugar-specific permease component
       0.67    9.4   7.5       0.11   12.1   0.3    1.8  2  DUF3169          Protein of unknown function (DUF3169)
       0.77    9.7  10.9      0.061   13.3   1.4    2.1  2  DUF4083          Domain of unknown function (DUF4083)
        1.1    8.4   3.8       0.22   10.7   0.9    1.4  2  TipE             Na+ channel auxiliary subunit TipE
        1.2    9.1   8.2       0.25   11.3   1.1    2.5  2  TNFR_16_TM       Tumor necrosis factor receptor member 16 tra
        1.8    8.9  10.2      0.036   14.4   2.4    1.9  2  Phage_Gp23       Protein gp23 (Bacteriophage A118)
        4.2    7.3   7.9        0.1   12.5   0.4    1.9  2  TMEM154          TMEM154 protein family
        4.6    7.6  10.0          2    8.8   0.2    2.2  2  Sigma_reg_N      Sigma factor regulator N-terminal
          5    7.5  11.2       0.33   11.3   6.0    1.8  1  RIC3             Resistance to inhibitors of cholinesterase h
        5.8    6.9   9.3       0.14   12.1   0.9    2.4  2  YajC             Preprotein translocase subunit
        6.4    7.4   9.5        9.2    6.9   9.5    1.3  1  TcpE             TcpE family


Domain annotation for each model (and alignments):
>> LapA_dom  Lipopolysaccharide assembly protein A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   1.3         5   2.8e+03      17      28 ..       3      14 ..       1      16 [. 0.67
   2 !   19.2   0.3   1.4e-06    0.0008      16      63 ..      36      84 ..      25      92 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 5
    LapA_dom 17 lpLsllllvafg 28
                + L++++l++++
  EPA04496.1  3 ITLITIILFVLL 14
                567777777765 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 1.4e-06
    LapA_dom 16 elpLsllllvafgiGallgwllsl.wsylrlrrelrrlkkkikklekel 63
                +l++++ l+++ +  +++g+ +++ ++y +++r+ ++++++ikkl++++
  EPA04496.1 36 TLNIVMYLIIFGLPSLIIGVTVFViYRYRKNKRKEKQQDNEIKKLKNRI 84
                5788899999999999999999984577777777777767776666654 PP

>> SieB  Super-infection exclusion protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.9   2.7e-06    0.0015       3      82 ..       5      88 ..       3      92 .. 0.62

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.7e-06
        SieB  3 aLiiasglllllPdsllekln....lgkfleeyglwiglvflis.iayllaqvvskllaeikekikkkreqkkvekklknLteee 82
                +++i+  +ll++P+ ++++      ++ ++ ++  ++ + +++   ++++   v+ ++ + k+k k+k++ ++++k  ++ +e e
  EPA04496.1  5 LITIILFVLLFIPNFVFAAHTpfdaID-VIFNTLNIVMYLIIFGlPSLIIGVTVFVIYRYRKNKRKEKQQDNEIKKLKNRIDELE 88
                689999********8888877666444.444444444444444425666666677777666666665555555555555566555 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   2.4e-06    0.0014     385     453 ..       5      82 ..       1      93 [. 0.61

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.4e-06
     DUF2207 385 alglgliilglilillallllvll.............lvfllilllillliaiivlllfsrllgrrteeGaellakwkgFkk 453
                 ++ ++l++l++i +++++    ++             ++ +++++++l+ ++i+v+++  ++ ++ +++ ++  +++k +k+
  EPA04496.1   5 LITIILFVLLFIPNFVFA----AHtpfdaidvifntlNIVMYLIIFGLPSLIIGVTVFVIYRYRKNKRKEKQQDNEIKKLKN 82 
                 333333333333333332....225678*********555555555555555555555556777777888888888888887 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.2   2.8e-06    0.0016      14      47 ..      58      91 ..      40      94 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.8e-06
                XXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
       DivIC 14 kgllaykqlkqeiaalqaelaklkaeneeLeaev 47
                  +++y++ k++ +++ +e++klk++++eLe+  
  EPA04496.1 58 FVIYRYRKNKRKEKQQDNEIKKLKNRIDELEKDK 91
                4567888888888899999999999999998865 PP

>> Vpu  Vpu protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   1.1       1.1   5.9e+02       4      21 ..       3      20 ..       1      23 [. 0.68
   2 !   18.0   0.8   3.2e-06    0.0018       9      52 ..      43      90 ..      32      94 .. 0.63

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.1
         Vpu  4 leliglialivaliiaiv 21
                ++li++i++++++i + v
  EPA04496.1  3 ITLITIILFVLLFIPNFV 20
                456788888877776765 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 3.2e-06
         Vpu  9 lialiv.aliiaivvWtivyreykkikkq.....keierlikrireraed 52
                li++++  lii + v  i   +y+k+k++     +ei++l +ri e + d
  EPA04496.1 43 LIIFGLpSLIIGVTVFVI--YRYRKNKRKekqqdNEIKKLKNRIDELEKD 90
                444433156666666544..445554444444899*********998876 PP

>> DUF4199  Protein of unknown function (DUF4199)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.7   1.2e-05    0.0066       8      59 ..       5      67 ..       2      86 .. 0.59

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.2e-05
     DUF4199  8 lvwilifllilyllglh...qi.lstg.pllgllallllllv...........pflvylalkkyrkkn 59
                l++i++f+l l++ ++    ++ ++   ++++ l+++++l++           +    + + +yrk++
  EPA04496.1  5 LITIILFVL-LFIPNFVfaaHTpFDAIdVIFNTLNIVMYLIIfglpsliigvtV----FVIYRYRKNK 67
                455555553.3333332102222333379999999999999999****744433....3333666655 PP

>> OPA3  Optic atrophy 3 protein (OPA3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   3.7e-05     0.021      83     125 .]      43      87 ..      28      91 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.7e-05
        OPA3  83 afifsv...agglilyEywrssrkeakkeeevkeeleeleerieel 125
                 ++if+     +g+ ++ ++r + k+++ke+++++e+++l++ri+el
  EPA04496.1  43 LIIFGLpslIIGVTVFVIYRYR-KNKRKEKQQDNEIKKLKNRIDEL 87 
                 6666541114566667677665.555799999999*****999986 PP

>> Chordopox_A13L  Chordopoxvirus A13L protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.4   6.5e-05     0.036       5      57 ..      43      90 ..      39      93 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.5e-05
  Chordopox_A13L  5 lllliiCvaivglivYgiYnrkketqttnpstveeyeeedniKtgfvdkLksd 57
                    l+++ +   i+g+ v+ iY+ +k++ +++++  +e ++ +n     +d+L++d
      EPA04496.1 43 LIIFGLPSLIIGVTVFVIYRYRKNKRKEKQQD-NEIKKLKNR----IDELEKD 90
                    677888889**********9888887776665.666666644....7999887 PP

>> 7TM_GPCR_Sra  Serpentine type 7TM GPCR chemoreceptor Sra
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   1.6   4.8e-05     0.027     238     320 ..       3      87 ..       1      93 [. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.8e-05
  7TM_GPCR_Sra 238 icflalsqFialliySvgvlvlrlir..eiisleqyyllvvwlYtvpfialllPllliyrirstksnRvekikeitsekqtqeeh 320
                   i+ +++  F++l+i  +++ +   +   + i  +   ++   ++ +p   + + +++iyr r+ k + +++ +ei++ k+  +e 
    EPA04496.1   3 ITLITIILFVLLFIPNFVFAAHTPFDaiDVIFNTLNIVMYLIIFGLPSLIIGVTVFVIYRYRKNKRKEKQQDNEIKKLKNRIDEL 87 
                   8899**********9998888777663233444434444456799999*****************99999999999999888875 PP

>> Connexin  Connexin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   6.5e-05     0.037      65     127 ..      28      91 ..      18      95 .] 0.61

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.5e-05
    Connexin  65 daffpishvrfwvlqiilvstPsll..ylvyvlhkiakeekekekeeeekeeeekeeekkkkkek 127
                 da+  i ++   v+ +i++ +Psl+  + v+v+++++k++++++ ++++++++ k++ ++ +k+k
  EPA04496.1  28 DAIDVIFNTLNIVMYLIIFGLPSLIigVTVFVIYRYRKNKRKEK-QQDNEIKKLKNRIDELEKDK 91 
                 5555555566678899999****973356788888888877555.44444444444444433322 PP

>> Ly49  Ly49-like protein, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.3       9.4   5.3e+03      10      19 ..       6      15 ..       2      24 .. 0.50
   2 ?   14.8   0.1     5e-05     0.028       7      60 ..      39      95 .]      33      95 .] 0.73

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 9.4
                XXXXXXXXXX CS
        Ly49 10 algILclllL 19
                +  IL +ll 
  EPA04496.1  6 ITIILFVLLF 15
                2233333333 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 5e-05
                XXXXXXXXXXX.XXXXXXXXXXXXXXXXX..XXXX.XXXXXXXXXXXXXXXXXXXXX CS
        Ly49  7 ivvalgILcll.lLvtvavLvtkifqysq..ekheleetlnlsqnysimqndinlke 60
                iv+ l I+ l  l++ v+v+v+  ++ ++  ek++ +e+ +l+++ + +++d + k+
  EPA04496.1 39 IVMYLIIFGLPsLIIGVTVFVIYRYRKNKrkEKQQDNEIKKLKNRIDELEKDKEKKD 95
                7777778776514556899998888776511566667788***********998775 PP

>> EphA2_TM  Ephrin type-A receptor 2 transmembrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.6       3.7   2.1e+03       8      15 ..       7      14 ..       1      25 [. 0.46
   2 ?   13.9   0.0   0.00013     0.075       2      37 ..      41      81 ..      39      95 .] 0.56

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 3.7
    EphA2_TM  8 glvllvil 15
                 ++l+v+l
  EPA04496.1  7 TIILFVLL 14
                11222211 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 0.00013
    EphA2_TM  2 iaaavaglvllvilvilvlvlvrrrsknrkqksdl.....k 37
                +  +++gl  l+i v+++++ + r++k++++++d+     k
  EPA04496.1 41 MYLIIFGLPSLIIGVTVFVIYRYRKNKRKEKQQDNeikklK 81
                55688888888887777766666666666655554333220 PP

>> THEG4  Testis highly expressed protein 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   8.3e-05     0.047       3      40 ..      39      77 ..      37      83 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.3e-05
       THEG4  3 vslyfGllGlcsvvtGgci.lflhwrknlrreeraqewv 40
                + +y+ ++Gl s+++G  + ++  +rkn r+e++  + +
  EPA04496.1 39 IVMYLIIFGLPSLIIGVTVfVIYRYRKNKRKEKQQDNEI 77
                678999**********76526678999999999876655 PP

>> Virul_fac_BrkB  Virulence factor BrkB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   2.4     9e-05     0.051     120     188 ..       4      70 ..       1      73 [. 0.65

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9e-05
  Virul_fac_BrkB 120 llllvllllslvlsvflqslllasapllglglelsell.llqllrwlvallllvlafallYrvlpnvkvr 188
                     +l+ ++l++ l+++ f+ ++    +p+ ++   + +l  ++ l+ + ++ l++ ++++++Yr+  n++++
      EPA04496.1   4 TLITIILFVLLFIPNFVFAAH---TPFDAIDVIFNTLNiVMYLIIFGLPSLIIGVTVFVIYRYRKNKRKE 70 
                     344445555555555554422...255565555656666777888888999************9998765 PP

>> DUF2298  Uncharacterized membrane protein (DUF2298)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00011     0.059     341     396 ..       6      68 ..       2      87 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00011
     DUF2298 341 vavlvlalllalPFllsfaasvggiallpersslselllvhGlflvlllaylvll.......r 396
                 ++++++ ll++  F+  + ++   i ++ +  +++ +l+++Gl+ +++ + +++        r
  EPA04496.1   6 ITIILFVLLFIPNFVFAAHTPFDAIDVIFNTLNIVMYLIIFGLPSLIIGVTVFVIyryrknkR 68 
                 34444445555558999999***************************9999987755543321 PP

>> ECSCR  Endothelial cell-specific chemotaxis regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.2       3.6     2e+03      29      39 ..       4      14 ..       2      29 .. 0.58
   2 ?   13.2   0.1   0.00011      0.06      24      71 ..      36      83 ..      23      93 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 3.6
       ECSCR 29 sfivilvvvvi 39
                ++i i++ v++
  EPA04496.1  4 TLITIILFVLL 14
                44443333332 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00011
       ECSCR 24 afgvisfivilvvvviilvsvvslrfkcrknkesedpqkpeisglses 71
                ++ ++ +++i+ +  +i+   v + ++ rknk  e  q  ei  l + 
  EPA04496.1 36 TLNIVMYLIIFGLPSLIIGVTVFVIYRYRKNKRKEKQQDNEIKKLKNR 83
                56778888888877777777778889*************999888765 PP

>> CcmH  Cytochrome C biogenesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00028      0.16      97     130 ..      43      83 ..      34      94 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00028
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.......X CS
        CcmH  97 llLWlgPllllllgllvlllllrrrkkkkaeee.......e 130
                 l+++ +P l++ + ++v++++ ++++k+k++++       +
  EPA04496.1  43 LIIFGLPSLIIGVTVFVIYRYRKNKRKEKQQDNeikklknR 83 
                 56777888888888777777777777666665544433331 PP

>> Glycophorin_A  Glycophorin A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   0.00021      0.12      58      90 ..      39      71 ..      29      83 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00021
                   TTHHHHHHHHHHHHHHHHHHHHHHHHTHSXXXX CS
  Glycophorin_A 58 lvitliifgvmAgvigtillisYlirRliKKss 90
                    v+ liifg    +ig+ +++ Y  r+ ++K +
     EPA04496.1 39 IVMYLIIFGLPSLIIGVTVFVIYRYRKNKRKEK 71
                   6899*******************9998777654 PP

>> DUF4381  Domain of unknown function (DUF4381)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00036       0.2      22      60 ..      42      85 ..      28      94 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00036
     DUF4381 22 wlllaalll..llllvlalwllrrrkrnrreAlreLaalr...a 60
                +l++++l    +++ v++++++r++kr+ ++  +e+++l+   +
  EPA04496.1 42 YLIIFGLPSliIGVTVFVIYRYRKNKRKEKQQDNEIKKLKnriD 85
                45554432234777777778888888888888888888885432 PP

>> COX14  Cytochrome oxidase c assembly
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00054       0.3      28      57 ..      52      81 ..      40      94 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00054
       COX14 28 aggllvytvysygkynrkqkaeliereklk 57
                  g++v+ +y+y k  rk+k++  e +klk
  EPA04496.1 52 IIGVTVFVIYRYRKNKRKEKQQDNEIKKLK 81
                57899999*************777777765 PP

>> 7tm_1  7 transmembrane receptor (rhodopsin family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   3.2     0.035        20     205     230 ..       2      27 ..       1      36 [. 0.87
   2 ?    8.5   0.1     0.002       1.1     146     185 ..      36      75 ..      28      94 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.035
                 HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxx RF
       7tm_1 205 rtlgivvavfivcwlPftiiyllqal 230
                 ++++i +++f++ ++P+++++  + +
  EPA04496.1   2 KITLITIILFVLLFIPNFVFAAHTPF 27 
                 7899****************998877 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.002
                 HHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHCHHHHSH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       7tm_1 146 vyiifsavlsfilPllvivilyarifrtvlktsrtktsks 185
                 +++i++ ++ f lP l+i ++ + i+r  ++++++k++ +
  EPA04496.1  36 TLNIVMYLIIFGLPSLIIGVTVFVIYRYRKNKRKEKQQDN 75 
                 6899999******************998777766666533 PP

>> EIIC-GAT  PTS system sugar-specific permease component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   9.1    0.0084       4.7      90     128 ..       7      45 ..       2      61 .. 0.82
   2 ?    2.0   0.1      0.16        88       2      24 ..      45      67 ..      44      71 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0084
    EIIC-GAT  90 valilllglivniilarfkktttlkyifltghvmlqqal 128
                 ++++++l +i n ++a+ ++++ +++if+t +++++  +
  EPA04496.1   7 TIILFVLLFIPNFVFAAHTPFDAIDVIFNTLNIVMYLII 45 
                 67899999************************9987654 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.16
    EIIC-GAT  2 ilggpaillglivligllllkkk 24
                i+g p++++g+ v++++   k k
  EPA04496.1 45 IFGLPSLIIGVTVFVIYRYRKNK 67
                7889************9877766 PP

>> DUF3169  Protein of unknown function (DUF3169)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   2.4      0.67   3.7e+02     139     156 ..       4      21 ..       1      33 [. 0.62
   2 ?   12.1   0.3   0.00019      0.11      44      98 ..      32      86 ..      24      93 .. 0.53

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.67
     DUF3169 139 fliaivlfliilflkiii 156
                  li+i+lf++ ++ ++++
  EPA04496.1   4 TLITIILFVLLFIPNFVF 21 
                 355555555555555544 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00019
     DUF3169 44 lllligskilpllli..iavlvviisvvflrkakkllkkwde.eddeeseeeyeqiek 98
                +++ + + i+++l+i  +  l++ ++v+++++ +k + k ++ +++ +   ++++i++
  EPA04496.1 32 VIFNTLN-IVMYLIIfgLPSLIIGVTVFVIYRYRKNKRKEKQqDNEIKK--LKNRIDE 86
                4555445.44555555866666666655555555555554440444444..4444443 PP

>> DUF4083  Domain of unknown function (DUF4083)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   2.4      0.47   2.6e+02       6      19 ..       5      16 ..       1      23 [. 0.46
   2 ?   13.3   1.4   0.00011     0.061       5      57 .]      39      90 ..      33      91 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.47
     DUF4083  6 iyliivivLilllv 19
                +++ii++v  ll++
  EPA04496.1  5 LITIILFV--LLFI 16
                33333333..3333 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00011
     DUF4083  5 liyliivivLilllvfsftlfiRrvvsrsaakkkkskeleqKLDkiIeLLeKd 57
                ++ ++i+++L  l+ +++t f+ +   ++  k+k++++  +KL   I  LeKd
  EPA04496.1 39 IVMYLIIFGLPSLI-IGVTVFVIYRYRKNKRKEKQQDNEIKKLKNRIDELEKD 90
                46788888887766.56666666667777888888888889999999999996 PP

>> TipE  Na+ channel auxiliary subunit TipE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.2       3.1   1.7e+03      24      41 ..       4      21 ..       2      29 .. 0.79
   2 ?   10.7   0.9   0.00039      0.22     283     317 ..      30      66 ..      17      95 .] 0.68

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3.1
        TipE 24 llGtfslfaflflvpfvi 41
                 l t+ lf +lf+  fv 
  EPA04496.1  4 TLITIILFVLLFIPNFVF 21
                577889999999988886 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00039
        TipE 283 ldmwqntlnlvfamai.pipsfiisv.iylafayfvi 317
                 +d+  ntln+v+ + i  +ps+ii v +++ + y + 
  EPA04496.1  30 IDVIFNTLNIVMYLIIfGLPSLIIGVtVFVIYRYRKN 66 
                 78999*****97665538******9856778888654 PP

>> TNFR_16_TM  Tumor necrosis factor receptor member 16 trans-membrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   1.1      0.62   3.5e+02      16      25 ..       7      16 ..       4      21 .. 0.77
   2 ?   11.3   1.1   0.00045      0.25      14      38 .]      48      72 ..      39      73 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.62
  TNFR_16_TM 16 aVvvgLlaYv 25
                +++++ l+++
  EPA04496.1  7 TIILFVLLFI 16
                6788888887 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00045
  TNFR_16_TM 14 LaaVvvgLlaYvifKrwksckqnkq 38
                L+  ++g  ++vi++  k+ ++ kq
  EPA04496.1 48 LPSLIIGVTVFVIYRYRKNKRKEKQ 72
                7789***********9998777444 PP

>> Phage_Gp23  Protein gp23 (Bacteriophage A118)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   1.4       3.4   1.9e+03      22      32 ..       6      16 ..       1      25 [. 0.52
   2 ?   14.4   2.4   6.4e-05     0.036      14      72 ..      29      91 ..      20      95 .] 0.78

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 3.4
  Phage_Gp23 22 lsvvlflilli 32
                + ++lf++l+i
  EPA04496.1  6 ITIILFVLLFI 16
                33444444433 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 6.4e-05
  Phage_Gp23 14 akevlfaalsvvlflil.....livtkriwddrkilkiemkeerekkeekrekkekeskeekdk 72
                a +v+f  l +v++li+     li++  ++   +  k + ke ++  e k+  k++  + ekdk
  EPA04496.1 29 AIDVIFNTLNIVMYLIIfglpsLIIGVTVFVIYRYRKNKRKEKQQDNEIKK-LKNRIDELEKDK 91
                5689***********976666689999999999999988888776666554.567777777776 PP

>> TMEM154  TMEM154 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   1.9       3.1   1.7e+03      62      74 ..       4      16 ..       1      26 [. 0.54
   2 ?   12.5   0.4   0.00018       0.1      58     100 ..      38      86 ..      22      94 .. 0.64

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 3.1
     TMEM154 62 iiiPlvllillll 74
                 +i  +l++ll++
  EPA04496.1  4 TLITIILFVLLFI 16
                3444445555544 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00018
     TMEM154  58 lvlmiiiPlvllillllvviiliqkkkrkrsKddekseaesd......e 100
                 +++m++i   l  l++ v +++i +++++++K++++++  +       e
  EPA04496.1  38 NIVMYLIIFGLPSLIIGVTVFVIYRYRKNKRKEKQQDNEIKKlknridE 86 
                 4556666666666677777788888888888888555433334454443 PP

>> Sigma_reg_N  Sigma factor regulator N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   6.9       1.2   6.7e+02      14      33 ..       2      21 ..       1      40 [. 0.61
   2 ?    8.8   0.2    0.0036         2      12      45 ..      36      72 ..      32      85 .. 0.58

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 1.2
  Sigma_reg_N 14 rivlislivlllifvilvvt 33
                 +i+li++i+++l+f+  +v 
   EPA04496.1  2 KITLITIILFVLLFIPNFVF 21
                 66777777666666544433 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0036
  Sigma_reg_N 12 ilrivlislivll..lifvil.vvtllylaekegnkl 45
                 +l iv+  +i+ l  li+ ++ +v+++y ++k+++k 
   EPA04496.1 36 TLNIVMYLIIFGLpsLIIGVTvFVIYRYRKNKRKEKQ 72
                 5566666666544113444444777777777776665 PP

>> RIC3  Resistance to inhibitors of cholinesterase homologue 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   6.0   0.00059      0.33      76     120 ..      48      92 ..      38      95 .] 0.71

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00059
        RIC3  76 lPlYtiGilvfilYtllKikskkkkekskeakakkkakenakkkt 120
                 lP   iG+ vf++Y   K k+k+k+++++ +k k++  e  k k+
  EPA04496.1  48 LPSLIIGVTVFVIYRYRKNKRKEKQQDNEIKKLKNRIDELEKDKE 92 
                 677779************999998885555555555555443333 PP

>> YajC  Preprotein translocase subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   1.6       3.2   1.8e+03       5      13 ..       7      15 ..       2      23 .. 0.46
   2 ?   12.1   0.9   0.00025      0.14       7      36 ..      50      81 ..      36      85 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 3.2
        YajC  5 plvlifvif 13
                 ++l++++f
  EPA04496.1  7 TIILFVLLF 15
                222222222 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00025
        YajC  7 vlifvifyfll..irpqqkkqkehkemlasLk 36
                 li+++ +f++  +r++++k+k++++ +++Lk
  EPA04496.1 50 SLIIGVTVFVIyrYRKNKRKEKQQDNEIKKLK 81
                46777777777335666666666667676666 PP

>> TcpE  TcpE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   9.5     0.017       9.2      24      65 ..       3      51 ..       1      72 [. 0.75

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.017
        TcpE 24 islsqiivfvlvlvlllllaslipv..ikgvl.....pfl.llyivipvv 65
                i+l +ii fvl++++ +++a  +p+  i+ ++     + + l+++++p  
  EPA04496.1  3 ITLITIILFVLLFIPNFVFAAHTPFdaIDVIFntlniV-MyLIIFGLPSL 51
                99*********************999988777764432.14666666643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3080  (0.171789); expected 358.6 (0.02)
Passed bias filter:                     1294  (0.0721736); expected 358.6 (0.02)
Passed Vit filter:                       194  (0.0108205); expected 17.9 (0.001)
Passed Fwd filter:                        39  (0.00217525); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              32  [number of targets reported over threshold]
# CPU time: 0.68u 0.40s 00:00:01.08 Elapsed: 00:00:00.54
# Mc/sec: 532.84
//
Query:       EPA04497.1  [L=239]
Description: hypothetical protein BG20_I1556, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1458.59
//
Query:       EPA04498.1  [L=71]
Description: hypothetical protein BG20_I1545 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.15   12.4   0.3       0.15   12.4   0.3    1.5  2  DUF2839   Protein of unknown function (DUF2839)
       0.55    8.9   3.1       0.57    8.9   3.1    1.0  1  DUF2207   Predicted membrane protein (DUF2207)


Domain annotation for each model (and alignments):
>> DUF2839  Protein of unknown function (DUF2839)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.3   1.7e-05      0.15      28      58 ..       2      32 ..       1      40 [. 0.91
   2 ?   -1.8   0.1      0.48   4.3e+03      44      56 ..      44      56 ..      36      62 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.7e-05
     DUF2839 28 tkkqaeqfvklttrgawiGigllvvlWvvvr 58
                tk ++++++++ ++  ++++g++v++ +++ 
  EPA04498.1  2 TKMKRSKILQICVNLGFVCVGIIVIANIIIS 32
                899**********************999886 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.48
     DUF2839 44 wiGigllvvlWvv 56
                + G g+l ++  +
  EPA04498.1 44 FWGFGILPIVFGI 56
                5566666555444 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   3.1   6.4e-05      0.57     381     430 ..      14      60 ..       1      69 [. 0.38

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 6.4e-05
     DUF2207 381 kklsalglgliilglilillallllvll.......lvfllilllillliaiivlllf 430
                   l+++ +g+i+++ i+i +++     +       + +++il +++++i+     l+
  EPA04498.1  14 VNLGFVCVGIIVIANIIISYGN-----AnpltlyeFWGFGILPIVFGIIF-----LL 60 
                 2233333444444444444443.....34432233333333333333333.....32 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 479.76
//
Query:       EPA04499.1  [L=118]
Description: putative chemotaxis protein Chey [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-25   89.1   3.1    2.2e-25   89.0   3.1    1.0  1  Response_reg  Response regulator receiver domain
  ------ inclusion threshold ------
      0.015   15.7   0.2      0.035   14.5   0.2    1.8  1  FleQ          Flagellar regulatory protein FleQ
      0.028   14.7   1.7      0.051   13.8   1.7    1.5  1  TrkA_N        TrkA-N domain


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.0   3.1   3.7e-29   2.2e-25       1     112 []       6     117 ..       6     117 .. 0.99

  Alignments for each domain:
  == domain 1  score: 89.0 bits;  conditional E-value: 3.7e-29
                   EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEESSTSHHHHHHHHHCTESEE CS
  Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviiltahseeedavealkagaddf 97 
                   v++vdDd+++r++++++l+ +g+++va+a +g++a+e++ + ++d++l+Di+mp+ dG+  + +i++ +++ ++i++ta +++e++++  ++  + +
    EPA04499.1   6 VVVVDDDEDNRNAMTDILQFKGVSVVATAVNGSDAVEKFSKYAPDVVLMDIMMPDFDGFYGIMNIKNINSDAKIIAVTADQSDETIQKLRDIKHELI 102
                   79*********************************************************************************************** PP

                   EESSG-HHHHHHHHH CS
  Response_reg  98 lsKpfdpeeLlkale 112
                   + Kpfd + L+++++
    EPA04499.1 103 IYKPFDVNVLVQMIN 117
                   ************986 PP

>> FleQ  Flagellar regulatory protein FleQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.2   5.9e-06     0.035       1      34 [.       5      38 ..       5     103 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.9e-06
        FleQ  1 kiLvidddaerrrdletiLeFlgeeveavsseel 34
                k+ v+ddd+++r++++ iL+F g +v+a++ +  
  EPA04499.1  5 KVVVVDDDEDNRNAMTDILQFKGVSVVATAVNGS 38
                789********************99777665443 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   1.7   8.5e-06     0.051      23     109 ..       5      98 ..       2     105 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.5e-06
                 EEEEEESSHHHHHHHHHTT....SEEEES-TTSHHHHHHTTGGGESEEEE-SSSH.HHHHHHHHHHHHHTSSSEEEEEESSGGG..HHHHHHHT CS
      TrkA_N  23 dvvvidkdeerveelreeg....levvvgdatdeevLeeagiekadaviaatgdd.eanilavllakelnpkkkiiaraqdpeh..aellkklg 109
                 +vvv+d+de++ + +++      + vv   +   +++e+      d+v+  +     +  + ++++k++n+++kiia + d+++  +++l+++ 
  EPA04499.1   5 KVVVVDDDEDNRNAMTDILqfkgVSVVATAVNGSDAVEKFSKYAPDVVLMDIMMPdFDGFYGIMNIKNINSDAKIIAVTADQSDetIQKLRDIK 98 
                 6********998777665553337799999999*************99999876537778889999**********998777662366666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       754  (0.0420548); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 771.27
//
Query:       EPA04500.1  [L=70]
Description: hypothetical protein BG20_I2445, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1060  (0.0591221); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.31s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 480.45
//
Query:       EPA04501.1  [L=341]
Description: radical SAM domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-20   74.2   0.0    5.2e-20   72.5   0.0    1.8  1  Radical_SAM   Radical SAM superfamily
    2.4e-20   72.6   0.1    1.8e-19   69.9   0.1    2.3  2  Wyosine_form  Wyosine base formation
  ------ inclusion threshold ------
      0.036   14.2   1.5       0.75    9.9   0.8    2.9  2  Fer4_14       4Fe-4S single cluster domain
      0.044   13.9   0.6      0.099   12.7   0.3    1.8  1  SAS4          Something about silencing, SAS, complex subunit
       0.09   12.5   0.1       0.17   11.5   0.0    1.5  1  AAT           Acyl-coenzyme A:6-aminopenicillanic acid acyl-t


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.5   0.0   1.4e-23   5.2e-20       7     159 ..      76     251 ..      71     257 .. 0.83

  Alignments for each domain:
  == domain 1  score: 72.5 bits;  conditional E-value: 1.4e-23
                  ESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEE.........................SSTGGGSTTHHHHHHHHHHTCCCTE CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx.........................xxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM   7 CnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilg.........................ggepllypdfvellerlaklavpgi 78 
                  C +rC++C+rp      +++  +++e+++e  ++l + +   k +i g                         +gep++yp++ el++ l+ l+ +  
   EPA04501.1  76 CENRCVYCWRPME---FYDSLKMDPEKVAEPKEILTKLMAeRKKLINGyygdsrndkqrldesllpshyaislSGEPTMYPKLPELIKYLKSLE-ETK 169
                  ***********85...666666666666665555554443355555555667777777777777777777777********************7.*** PP

                  EEEEEECSSCHGHHHHHHHHHTT..-SEEEEEEBSSSHHHHHHHHT..CTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHH CS
                  xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM  79 ritvetngtlpdeeklerllelg..vdrvslgleaaddekvlklmn..rghtfeevlealeklreagikrvvdrivglpGendee 159
                  +i+++tng    +++++rl +    +++++l+ +aad+e +lk+++    ++++++ ++le+l++++ + +v ri++++++nd+e
   EPA04501.1 170 SIFLVTNGQE--PDMIQRLQDEDalPTQLYLSTNAADYESFLKINKprYDDSWQRWNRTLEMLKKLDTR-TVLRITLIRNYNDQE 251
                  **********..69*******99****************777777776999******************.*************97 PP

>> Wyosine_form  Wyosine base formation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       0.5   1.8e+03      14      32 ..     121     142 ..     118     145 .. 0.84
   2 !   69.9   0.1   4.9e-23   1.8e-19       2      63 .]     264     325 ..     263     325 .. 0.97

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.5
                   ------...----------HHH CS
  Wyosine_form  14 yvGssr...srLtmknvPwhee 32 
                   y G+sr   +rL+ +  P+h+ 
    EPA04501.1 121 YYGDSRndkQRLDESLLPSHYA 142
                   5699999999999999999976 PP

  == domain 2  score: 69.9 bits;  conditional E-value: 4.9e-23
                   HT-SEEEEEE------------------HHHHHHHHHHHHTSSS.EEEEEEETTTTEEEEEE CS
  Wyosine_form   2 aepdFvEvKaytyvGssrsrLtmknvPwheevadfakrlegsaedYellaehrhSrvvllar 63 
                   a p+F+E+K+y+++G s++rL+ +n++++eev++f++ ++++++ +++++e+  Sr+v l++
    EPA04501.1 264 ASPHFIEIKSYMHIGRSTNRLEHSNMLEMEEVRKFSESVAEHSQIFSVMDESLVSRIVILQN 325
                   79********************************************************9985 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.8   0.00021      0.75      32      92 ..     126     180 ..      73     202 .. 0.60
   2 ?   -1.3   0.0      0.65   2.3e+03      67      95 ..     226     253 ..     219     266 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00021
     Fer4_14  32 elleqilk.dlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekkiwletngtle 92 
                 +  +q+l+ +l  s++    ++l+ GeP +y + +el+k +k l e   +k+i l tng   
  EPA04501.1 126 RNDKQRLDeSLLPSHY---AISLS-GEPTMYPKLPELIKYLKSLEE---TKSIFLVTNGQEP 180
                 4444455434455555...25555.7*****666666666666554...46*******9865 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.65
     Fer4_14  67 llklvkrlkeeypekkiwletngtleiel 95 
                  l+++k+l +++  ++i+l  n+  + e+
  EPA04501.1 226 TLEMLKKLDTRT-VLRITLIRNYNDQEEM 253
                 567777777777.7888888888777544 PP

>> SAS4  Something about silencing, SAS, complex subunit 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.3   2.8e-05     0.099      21      77 ..     207     262 ..     190     285 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.8e-05
        SAS4  21 rmrniekeraesEadrlerllekLqgqdwlrvlgkitkindpkdkkelerkreltik 77 
                 ++ +i+k r     +r +r le L++ d  +vl  it i++ +d++e+ ++   + k
  EPA04501.1 207 SFLKINKPRYDDSWQRWNRTLEMLKKLDTRTVLR-ITLIRNYNDQEEMIPAFAAMLK 262
                 56788899999999**************999998.999**********998876665 PP

>> AAT  Acyl-coenzyme A:6-aminopenicillanic acid acyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   4.8e-05      0.17     134     187 ..     195     252 ..     165     267 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.8e-05
                 EEEEE-SS-S-GGGSSS-----HHHHHHHHHHHHHHCSSSSB....HHHHHHHT---S CS
         AAT 134 ealahtNHfvnetleaenqnilesSisRlerlqellsqkesa....eeaiellkDred 187
                 + +++tN ++ e++ + n+  +++S++R +r  e l++ ++      + i+  +D+e+
  EPA04501.1 195 QLYLSTNAADYESFLKINKPRYDDSWQRWNRTLEMLKKLDTRtvlrITLIRNYNDQEE 252
                 57899********************************999987887788888888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 1996.70
//
Query:       EPA04502.1  [L=327]
Description: metallohydrolase, glycoprotease/Kae1 family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-75  254.5   0.0    1.7e-75  254.2   0.0    1.0  1  Peptidase_M22  Glycoprotease family


Domain annotation for each model (and alignments):
>> Peptidase_M22  Glycoprotease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  254.2   0.0   9.4e-80   1.7e-75       9     271 .]      34     295 ..      26     295 .. 0.95

  Alignments for each domain:
  == domain 1  score: 254.2 bits;  conditional E-value: 9.4e-80
                    EEEEE....S.SSSHHHHHHHHHHHHHHHHHHHHHHHTSTGGGEEEEEEEEESS-HHHHHHHHHHHHHHHHHCT--EEEEEHHHHHHHCCHCTSEC CS
  Peptidase_M22   9 sqkelhakyG.GvvPelasraHserllplieealaeaglsledldaIavtkgPGlftgLrvGvsfAkglalalnkPlvgVnhleahalaarleeke 103
                     +    ++ G G++P++asr+H e+   ++ e+l+e+g++++dld I +++gPGl+++LrvG+ +A+ la  +++P+++Vnh ++h++ ++l ++ 
     EPA04502.1  34 IY---RPPEGeGIHPREASRHHIENSATVLSECLQESGITIKDLDIISYAAGPGLGPCLRVGAVVARSLASYYDIPIYPVNHAIGHIELGKLLTGA 126
                    33...367788********************************************************************************99999 PP

                    SSCEEEEESSSTEEEEEECTTEEEEEEEESSSEHHHHHHHHHHHHT..SSCCHHHHHHHCTC.S.......EETTEEE.CHHHHHHHHHHSTTHHH CS
  Peptidase_M22 104 efPvvllvsGghtqvylvkegryeilgetlddaagealdkvarllglpypggpkieklakeg.kkiefprplkgldfsfsGlktavlkelekeved 198
                    ++P+vllvsGght++++  +++ +++getld+ +g+ ld+++r lg+  p g++ie+la +  +++ +p+ +kg+d+sfsGl +a+ + + ++++d
     EPA04502.1 127 KNPLVLLVSGGHTMLLAFLNKQWRVFGETLDITLGQLLDQFGRSLGFASPCGKNIESLATSTsNYVLLPYSVKGNDVSFSGLLSATKSIIPQNKAD 222
                    ******************99****************************************9988899***************999999995579** PP

                    HHHHHHHHHHHHHHHHHHHHHHHCTBSEEEEESGGGGXHHHHHCHCCHHHHTTSEEEXXXHHHHSSXCHHHHH CS
  Peptidase_M22 199 laasfqeavvdhlvekteralklpkakelvilGGvaankrLrealeeeaeelglkliiPplkyctdnaamiaw 271
                     ++s+qe++++++ e++eral+ +++kel+i+GGvaankrL e+l+++++++++++++ p+ky  d + +i w
     EPA04502.1 223 ACFSLQETAFAMISEVVERALSFTNKKELLIVGGVAANKRLSEMLQDVCKRHHCRFFVAPQKYAGDCGSQICW 295
                    ***************************************************99************99888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2016.67
//
Query:       EPA04503.1  [L=70]
Description: hypothetical protein BG20_I1173 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 446.07
//
Query:       EPA04504.1  [L=290]
Description: metallo-beta-lactamase domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-11   43.6   0.0    3.2e-11   43.1   0.0    1.2  1  Lactamase_B_2  Beta-lactamase superfamily domain
    5.9e-11   42.7   1.2      1e-09   38.7   1.3    2.1  1  Lactamase_B    Metallo-beta-lactamase superfamily
    1.9e-08   34.0   0.0    2.7e-08   33.5   0.0    1.3  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
    3.6e-06   27.0   0.0    1.4e-05   25.1   0.0    1.8  1  Lactamase_B_3  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   0.0   7.1e-15   3.2e-11      17     171 ..      41     195 ..      24     220 .. 0.68

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 7.1e-15
                    CGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHH..........HCCTTCGHHHCHTT............TTEEEEEE CS
  Lactamase_B_2  17 ralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvla..........vleanfvylaleee............pavnvhel 90 
                    +   P +   +++++da+++thaH DH  ++++l      + ++ya++ + +          +++          +               n++e+
     EPA04504.1  41 PE-YPLH--VKPKDLDAIIITHAHLDHSGNVPSLFVSG--NTDVYATPPTFDltrlliedmlKIT----------KdaqpfglpelnnMMRNAKEI 121
                    22.3554..34568********************9943..478****999985554444444222..........233345544454444555555 PP

                    -TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---....HHHHHHHCT-SEEEEE-S-SSTTH CS
  Lactamase_B_2  91 dwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyip....eeigerlggadllllditayedde 171
                       e+++ g  + ++++ +  h  g           ++++e+++kr++y+gD ++       e++  +g++dll+++ t+ + ++
     EPA04504.1 122 GFREKVTKG--NATFELRETGHVVGG---------GSVLVESQKKRLFYTGDIKTNGsrmlREADLDVGDIDLLIIESTYSQTEQ 195
                    555555555..678888888888888.........99*****************7766555667789**********99776655 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7   1.3   2.3e-13     1e-09      35     159 ..      42     171 ..      12     185 .. 0.76

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 2.3e-13
                  HHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHHHHCCHH......TTCHCGCCEEEEETTTEECCCTEEEEEHE CS
  Lactamase_B  35 laalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmeeaddaasrkgll......lagvsadkpdvdeeeldgnaggrralyvt 126
                   + l++kpkd+da+i+TH+HlDH G+++ l    +  v+a + +    +   +d     k +       l    ++++++   e  ++ g   +    
   EPA04504.1  42 EYPLHVKPKDLDAIIITHAHLDHSGNVPSLFVSGNTDVYATPPTFDLTRLLIEDMLKITKDAQpfglpeLNNMMRNAKEIGFREK-VTKGNATFELRE 138
                  5779****************************************99999999988888887779999753333333333333333.333333444445 PP

                  CTTSTSCCEEEEEETTCCEEEECTTTSSHHCCC CS
  Lactamase_B 127 ggpghghghgvveygggkvlftGDallagetgr 159
                   g++ g+g++ ve++ +++ +tGD   +g++ +
   EPA04504.1 139 TGHVVGGGSVLVESQKKRLFYTGDIKTNGSRML 171
                  67888999999*************987777665 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.0   6.1e-12   2.7e-08       1     175 [.      18     176 ..      18     192 .. 0.83

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 6.1e-12
  Lactamase_B_6   1 lLeldnvkiLlDvGwdeskvslesalkelekviptvdliLLshatlehlGayallyakfksklllnipvyatlpvvkLGrvslldlyaskgllgpe 96 
                    l++ d++++LlD G+   k   +    +l+   +++d+i+++ha l+h G  + l+++       n  vyat p++ L r+++ d  +      ++
     EPA04504.1  18 LVNCDGTNLLLDYGVLFGKRG-SPPEYPLHVKPKDLDAIIITHAHLDHSGNVPSLFVS------GNTDVYATPPTFDLTRLLIEDMLK-----ITK 101
                    678899999999999854332.2233344444589***************97777754......589**************9999865.....456 PP

  Lactamase_B_6  97 dseeleledideafdkiktlkYsQklelkskldgltitaynaGhtlGGtiWkiskesekivYavdwnhakeshLngaal 175
                    d + + l + ++++ + k++ +  k++      + t+   + Gh++GG    ++++ +++ Y  d+  +  ++L+ a+l
     EPA04504.1 102 DAQPFGLPELNNMMRNAKEIGFREKVTKG----NATFELRETGHVVGGGSVLVESQKKRLFYTGDIKTNGSRMLREADL 176
                    77889999****************98655....4688889***************************999999999886 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0     3e-09   1.4e-05       6     120 ..      13     169 ..      11     193 .. 0.63

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 3e-09
  Lactamase_B_3   6 ghnsflletagarilvDPf........kanlgyeppaeeaDlvlisqaledHahletlkqlaenvkvlee.......................... 67 
                    g + fl++ +g+++l+D++         ++  +  ++++ D+++i++a+ dH    +   +  n++v ++                          
     EPA04504.1  13 GRSGFLVNCDGTNLLLDYGvlfgkrgsPPEYPLHVKPKDLDAIIITHAHLDHSGNVPSLFVSGNTDVYATpptfdltrlliedmlkitkdaqpfgl 108
                    7899***************888776632266777777***************98776666656666666633333333333333333333333333 PP

  Lactamase_B_3  68 .........geslevggleiravatshdavggsergenngflleqdgltiyhlGhlahelss 120
                              +++ +++   ++ at + ++ g++ g++++  +e+++ ++++ G++ ++ s 
     EPA04504.1 109 pelnnmmrnAKEIGFREKVTKGNATFELRETGHVVGGGSVL-VESQKKRLFYTGDIKTNGSR 169
                    33333332244455555566666666688888888887775.56678899999999885332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.34s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1791.72
//
Query:       EPA04505.1  [L=88]
Description: thrombospondin type 3 repeat protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.1e-07   28.8  10.1    0.00016   21.3   2.6    3.5  3  TSP_3        Thrombospondin type 3 repeat
     0.0021   17.9   0.4        2.8    7.9   0.1    2.6  2  DUF282       Caenorhabditis protein of unknown function, DUF2
  ------ inclusion threshold ------
      0.074   13.7   0.0      0.093   13.4   0.0    1.1  1  FOXP-CC      FOXP coiled-coil domain
      0.083   12.8   0.0        1.3    9.0   0.0    2.1  2  U71          Tegument protein UL11 homolog
       0.12   13.0   9.1       0.71   10.5   0.7    3.1  3  Excalibur    Excalibur calcium-binding domain
       0.91   10.2   5.3          7    7.3   0.1    3.1  3  VCBS         Repeat domain in Vibrio, Colwellia, Bradyrhizobi


Domain annotation for each model (and alignments):
>> TSP_3  Thrombospondin type 3 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   2.6   5.3e-08   0.00016      15      33 ..       8      26 ..       7      29 .. 0.92
   2 ?   -0.0   0.1      0.25   7.4e+02      17      24 ..      33      40 ..      32      41 .. 0.63
   3 !   17.8   0.9   6.6e-07     0.002      15      30 ..      52      67 ..      51      74 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 5.3e-08
       TSP_3 15 DfDnDgvqddlDNCprnan 33
                D+D+Dg++d+ D Cp+ ++
  EPA04505.1  8 DADGDGIPDVKDACPNEPE 26
                9***************997 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.25
       TSP_3 17 DnDgvqdd 24
                D Dg +d+
  EPA04505.1 33 DWDGCPDV 40
                66777665 PP

  == domain 3  score: 17.8 bits;  conditional E-value: 6.6e-07
       TSP_3 15 DfDnDgvqddlDNCpr 30
                D D Dg++d+ D Cp+
  EPA04505.1 52 DSDHDGIPDSIDQCPT 67
                99*************8 PP

>> DUF282  Caenorhabditis protein of unknown function, DUF282
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.1   0.00094       2.8      15      28 ..      11      24 ..       7      27 .. 0.87
   2 !    7.5   0.0    0.0013       3.8      17      30 ..      57      70 ..      56      72 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00094
      DUF282 15 GvgiPslsdwCata 28
                G giP+ +d C+ +
  EPA04505.1 11 GDGIPDVKDACPNE 24
                99*********987 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0013
      DUF282 17 giPslsdwCataae 30
                giP++ d C+t+ e
  EPA04505.1 57 GIPDSIDQCPTERE 70
                9**********976 PP

>> FOXP-CC  FOXP coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   3.1e-05     0.093       7      50 ..      32      75 ..      28      78 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.1e-05
     FOXP-CC  7 CkWPgCekvledveeflkhlnseHalddkstaqlrvqmqvvqql 50
                 +W gC +vl   ++  + l+s+H+    s+ q+    ++v++ 
  EPA04505.1 32 LDWDGCPDVLAAESTIPSYLDSDHDGIPDSIDQCPTERENVNNF 75
                58**********************************99999876 PP

>> U71  Tegument protein UL11 homolog
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00044       1.3      19      50 ..      29      60 ..      21      62 .. 0.91
   2 ?    2.0   0.0     0.069   2.1e+02      18      31 ..      72      85 ..      64      88 .] 0.78

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00044
         U71 19 ntlidykGnPillateftvltdteseeeGmad 50
                n  +d+ G P +la+e t+    +s+ +G+ d
  EPA04505.1 29 NGYLDWDGCPDVLAAESTIPSYLDSDHDGIPD 60
                7789****************999999999877 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.069
         U71 18 entlidykGnPill 31
                 n + d  G Pill
  EPA04505.1 72 VNNFQDDDGCPILL 85
                47788999*****9 PP

>> Excalibur  Excalibur calcium-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.1    0.0022       6.5      27      36 ..       6      15 ..       2      15 .. 0.83
   2 ?   10.5   0.7   0.00024      0.71      26      36 ..      49      59 ..      24      59 .. 0.90
   3 ?   -2.8   0.2       3.5     1e+04      31      35 ..      77      81 ..      76      82 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0022
   Excalibur 27 klDrDkDGiA 36
                + D D+DGi+
  EPA04505.1  6 APDADGDGIP 15
                66*******8 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00024
   Excalibur 26 kklDrDkDGiA 36
                ++lD D+DGi+
  EPA04505.1 49 SYLDSDHDGIP 59
                79********8 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 3.5
   Excalibur 31 DkDGi 35
                D DG 
  EPA04505.1 77 DDDGC 81
                88986 PP

>> VCBS  Repeat domain in Vibrio, Colwellia, Bradyrhizobium and Shewanella
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.1    0.0023         7      48      59 ..       6      17 ..       1      17 [. 0.79
   2 ?    1.9   0.1      0.11   3.4e+02      51      60 ..      32      41 ..      30      42 .. 0.84
   3 ?    2.0   0.2      0.11   3.2e+02      49      58 ..      51      60 ..      43      62 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0023
        VCBS 48 vgDlDgDGdlDl 59
                + D DgDG +D+
  EPA04505.1  6 APDADGDGIPDV 17
                669999999996 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.11
        VCBS 51 lDgDGdlDll 60
                lD DG +D+l
  EPA04505.1 32 LDWDGCPDVL 41
                6899999997 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.11
        VCBS 49 gDlDgDGdlD 58
                 D D+DG +D
  EPA04505.1 51 LDSDHDGIPD 60
                5889999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       185  (0.0103185); expected 358.6 (0.02)
Passed bias filter:                      167  (0.00931452); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 576.94
//
Query:       EPA04506.1  [L=116]
Description: hypothetical protein BG20_I1166 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 829.45
//
Query:       EPA04507.1  [L=46]
Description: hypothetical protein BG20_I1162, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.011   15.2   0.1      0.011   15.2   0.1    1.1  1  Rax2      Cortical protein marker for cell polarity
       0.11   12.9   0.0       0.11   12.9   0.0    1.1  1  DUF2834   Protein of unknown function (DUF2834)
       0.15   11.9   0.2       0.15   11.9   0.2    1.1  1  Mid2      Mid2 like cell wall stress sensor


Domain annotation for each model (and alignments):
>> Rax2  Cortical protein marker for cell polarity
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.1   1.8e-06     0.011     155     182 ..      13      40 ..       1      42 [. 0.79

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.8e-06
        Rax2 155 kkkkklsrgfVVlIgLAlALgtvallgl 182
                 k++   + g++V+Ig ++A+g+v++l l
  EPA04507.1  13 KSDYSFHIGLIVGIGVGIAIGIVLFLIL 40 
                 56667788***************99976 PP

>> DUF2834  Protein of unknown function (DUF2834)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.8e-05      0.11      75      95 ..      22      42 ..       8      43 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.8e-05
     DUF2834 75 illtllvgvsfalPlfLalre 95
                ++++++vg+++++ lfL+lr+
  EPA04507.1 22 LIVGIGVGIAIGIVLFLILRQ 42
                667899**************8 PP

>> Mid2  Mid2 like cell wall stress sensor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   2.5e-05      0.15      41      68 ..      10      38 ..       1      43 [. 0.68

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.5e-05
        Mid2 41 Lskk.nrniviGcvvGigvPlllvillll 68
                +s+k +    iG +vGigv + + i+l+l
  EPA04507.1 10 ISDKsDYSFHIGLIVGIGVGIAIGIVLFL 38
                55552567789********9987665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.30s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 313.39
//
Query:       EPA04508.1  [L=399]
Description: translation-associated GTPase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-29  102.6   0.8    5.6e-29  101.0   0.2    2.0  2  MMR_HSR1_C     GTPase of unknown function C-terminal
    2.9e-20   72.5   0.0    8.7e-19   67.7   0.0    2.8  3  MMR_HSR1       50S ribosome-binding GTPase
    1.4e-12   47.5   0.2    3.4e-12   46.2   0.2    1.7  1  TGS            TGS domain
      4e-06   26.4   0.1    1.6e-05   24.5   0.0    2.0  2  FeoB_N         Ferrous iron transport protein B
     0.0023   18.1   0.3      0.012   15.8   0.2    2.2  1  YchF-GTPase_C  Protein of unknown function (DUF933)
  ------ inclusion threshold ------
      0.087   12.9   0.1       0.21   11.6   0.1    1.6  1  MMR_HSR1_Xtn   C-terminal region of MMR_HSR1 domain


Domain annotation for each model (and alignments):
>> MMR_HSR1_C  GTPase of unknown function C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.67     2e+03      56      92 ..     146     182 ..     131     194 .. 0.70
   2 !  101.0   0.2   1.9e-32   5.6e-29       1     112 []     224     327 ..     224     327 .. 0.97

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.67
  MMR_HSR1_C  56 feikedklkeldekqkkaLekirdlvlkrygsTGVqe 92 
                 ++i   + ++l+++ +++  k++d + kr+++ G+++
  EPA04508.1 146 IDILRREWEKLTKEIEQKRTKLTDGIAKRFTGLGIKD 182
                 4554445667889999999999999999998888665 PP

  == domain 2  score: 101.0 bits;  conditional E-value: 1.9e-32
  MMR_HSR1_C   1 alNKaDlpaadenieklkekypkdkkvvpvsAaaElaLrkaakqglikYepgdedfeikedklkeldekqkkaLekirdlvlkrygsTGVqealnaavf 99 
                 a+NKaDl ++ e i+k+ ++      v+p+sA++El Lrka+k+gl++Y++gde f++ e+  ke+  +qkkaL+ +++ vl++++sTG+q++ln avf
  EPA04508.1 224 AANKADLCKDLEIIKKISDT-----IVIPCSAETELLLRKASKAGLVNYKSGDEGFSVMEN--KEILPEQKKALDLVNT-VLSKIQSTGIQKILNIAVF 314
                 89***************998.....69*********************************9..77**************.******************* PP

  MMR_HSR1_C 100 elldlivVYPVed 112
                 +ll++ivV+PVed
  EPA04508.1 315 DLLKFIVVFPVED 327
                 ***********97 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.7   0.0   2.9e-22   8.7e-19       1      87 [.       5     116 ..       5     151 .. 0.82
   2 ?    0.8   0.1      0.16   4.8e+02      77     114 .]     186     227 ..     153     227 .. 0.59
   3 ?   -1.6   0.0       0.9   2.7e+03      75      87 ..     361     374 ..     344     393 .. 0.59

  Alignments for each domain:
  == domain 1  score: 67.7 bits;  conditional E-value: 2.9e-22
                 EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEE.......................EEEEECGGCSSHHHHHHHHHHHHHHHHC. CS
    MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgke.......................ielvDtpGliegaseekglgkaflalee. 75 
                 +++++G+ NvGKSt+++a t++ + ++++p+tT+++n g   +k  +                       ++l+D++Gl+ ga+e+kglg++fl+  + 
  EPA04508.1   5 QIGLLGKANVGKSTFFSAATETPVPIGNFPFTTIQPNVGVAYVKS-DcackhfaikhqnplcvngtrfipVKLIDVAGLVPGAHEGKGLGNRFLDDARq 102
                 589************************************877442.235555556666677777777777********999*************97776 PP

                 TSEEEEEEETT..T CS
    MMR_HSR1  76 adlillvvdas..e 87 
                 a+++++vvd++  +
  EPA04508.1 103 AEVLIHVVDIAgtT 116
                 9********88541 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.16
                 SEEEEEEETT....TTCSHHHH.HHHHHHHHHTTSEEEEEEES CS
    MMR_HSR1  77 dlillvvdas....eeklkpld.eeleelleeakkplilvlnk 114
                 + +l+ +++s    + ++++ d +++ + l++++kp+++++nk
  EPA04508.1 186 QDVLHKLELSsknpK-EWTDSDiQTFVKELRKNTKPILIAANK 227
                 445565655543422.343322133344445699999999998 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.9
                 C.TSEEEEEEETTT CS
    MMR_HSR1  75 e.adlillvvdase 87 
                 + a+ +l+ +d+++
  EPA04508.1 361 DiAKGFLHAIDCKT 374
                 23466666666663 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   0.2   1.1e-15   3.4e-12       4      59 ..     338     393 ..     332     394 .. 0.94

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 1.1e-15
                 EETTSSEEEEETTB-HHHHHHHHSTTHHHHEEEEEECS..EEEETTSBB-SSEEEEEE CS
         TGS   4 ytPdGkvpdlprgatveDfAykIhrslakkfiyAlVnG..qrvgldhvLedgdvveIv 59 
                 ++Pd+k+  lp  +t++D+A  Ih ++ak f++A+  +  qr g dh+L++gdv++Iv
  EPA04508.1 338 VLPDAKL--LPADSTAKDLAGLIHADIAKGFLHAIDCKtkQRIGADHKLKNGDVIKIV 393
                 4688888..******************************9*****************9 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   5.3e-09   1.6e-05       2      43 ..       5      46 ..       4      53 .. 0.90
   2 ?   -2.5   0.0       1.1   3.2e+03     100     123 ..     213     236 ..     209     253 .. 0.67

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 5.3e-09
                EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEE CS
      FeoB_N  2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklk 43
                ++ l+G+ nvGk+t+f a t++   +gN+p +t++ + g   
  EPA04508.1  5 QIGLLGKANVGKSTFFSAATETPVPIGNFPFTTIQPNVGVAY 46
                6889******************************99888765 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.1
                 HHHHTTSSEEEEEETHHHHHHTTE CS
      FeoB_N 100 qllelgvpvvlalnmideaekkgi 123
                 +l   ++p+++a n+ d  ++ +i
  EPA04508.1 213 ELRKNTKPILIAANKADLCKDLEI 236
                 566667888888888887766544 PP

>> YchF-GTPase_C  Protein of unknown function (DUF933)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.2   4.1e-06     0.012      19      48 ..     347     376 ..     342     392 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.1e-06
  YchF-GTPase_C  19 kgttapqaAgviHsDfekgFiraevikyed 48 
                     ++ta++ Ag iH D+ kgF++a  +k ++
     EPA04508.1 347 ADSTAKDLAGLIHADIAKGFLHAIDCKTKQ 376
                    6799*****************997777665 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1     7e-05      0.21      18      91 ..     183     254 ..     170     261 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7e-05
  MMR_HSR1_Xtn  18 etvkkilkeykihnaevliredvtvDdlidviegnrvYipclyvlNKiDlisleel.delarepnsvviSaekel 91 
                    +v+++l++  + + + +   d +++ ++  + +n+  +p l++ NK+Dl+++ e+ ++++    ++++Sae+el
    EPA04508.1 183 YQVQDVLHKLELSSKNPKEWTDSDIQTFVKELRKNT--KPILIAANKADLCKDLEIiKKISD-TIVIPCSAETEL 254
                   566666666666666665556666666666666666..699*********655444044433.466667777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       905  (0.0504769); expected 358.6 (0.02)
Passed bias filter:                      708  (0.0394891); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.51
# Mc/sec: 2341.23
//
Query:       EPA04509.1  [L=309]
Description: cation diffusion facilitator family transporter [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-33  115.0  11.8    4.3e-33  114.7  11.8    1.1  1  Cation_efflux    Cation efflux family
    0.00024   21.2   2.6    0.00038   20.5   2.6    1.3  1  ZT_dimer         Dimerisation domain of Zinc Transporter
  ------ inclusion threshold ------
       0.11   12.6   0.3       0.17   11.9   0.3    1.2  1  Spore_YhcN_YlaJ  Sporulation lipoprotein YhcN/YlaJ (Spore_Yhc
       0.96    8.8   7.2          2    7.7   0.5    2.9  3  ThrE             Putative threonine/serine exporter


Domain annotation for each model (and alignments):
>> Cation_efflux  Cation efflux family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.7  11.8   9.6e-37   4.3e-33       2     198 ..      10     224 ..       9     225 .. 0.97

  Alignments for each domain:
  == domain 1  score: 114.7 bits;  conditional E-value: 9.6e-37
  Cation_efflux   2 ilsllanlilalvelivglltnSlalladafhslsdlvsllllllalklsrkppderfpfGygrlevlgalvsgllllglavfllleaiqkli.ke 96 
                    +++l+ nl++a+ ++i+++ t+S++++a+++hs+sd+v++llll+++k s++  +  ++fG+ r ++++++++++l++g+   l le+ +++i ++
     EPA04509.1  10 YAALFGNLGIAITKFIAAISTGSVSMWAESYHSVSDTVNQLLLLFGIKRSKRAYSFSHQFGHSREQFFWSFIVASLIFGISGTLSLENGISAIlHG 105
                    6899******************************************************************************999999999888** PP

  Cation_efflux  97 gereihaglalvvalvslvvnlalllilrragrkl....................rsaalkaaalhvlgDaltslgvlvsalvillfnlksgplaD 172
                    g+++++a + ++v++++++++ + l+i  ++ r +                    +++al ++  +   D+++  g+ v+al+i+l + +++p++D
     EPA04509.1 106 GHNLENATINFIVLIIAAGFEGYALRIALKQLRMVikergeeptfkamiaefkdsKDPALLTVITE---DTAALSGIGVAALGIFLSMITGNPIYD 198
                    ******************************99988*******************************...*********************99**** PP

  Cation_efflux 173 pvaslligliilysalkllkeslseL 198
                    +++s++ig+i+++ al l+ke+   L
     EPA04509.1 199 AIGSIVIGAILMVLALFLAKENKDLL 224
                    *********************97665 PP

>> ZT_dimer  Dimerisation domain of Zinc Transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   2.6   8.5e-08   0.00038       3      72 ..     231     301 ..     229     308 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 8.5e-08
                 ..HHHHHHHHHTT-SS-EEEEEEEEE-S-.---EEEEEEEE-TTS-HHHHHHHHHHHHHHHHHH-TT--EE CS
    ZT_dimer   3 eeeeeeireiiksvpgvkgvhdlrtrksG.skifvdlhievdgdlsvkeaHeiadevekrikeefpgvadv 72 
                 + e+++i ++i++++++ +v  l+t + G +++++ +++ + + l   +   ++d+vek+i+e +p++ + 
  EPA04509.1 231 KREYKKIVDVIRDIEEINRVVTLKTMHLGpEDVLIGVQVNLIDGLDTDKIELVTDKVEKAIMEIIPNLNRQ 301
                 5689*************************66***********************************98654 PP

>> Spore_YhcN_YlaJ  Sporulation lipoprotein YhcN/YlaJ (Spore_YhcN_YlaJ)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.3   3.8e-05      0.17      60     117 ..     232     299 ..     221     304 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.8e-05
  Spore_YhcN_YlaJ  60 etaqniaqrverlegVedarvlvtgn....dvlVavqtde......sdnekvkkkVketVekvvddik 117
                      +  ++i++ ++++e+++++ +l t +    dvl++vq++       ++ e v +kV++++ ++ ++ +
       EPA04509.1 232 REYKKIVDVIRDIEEINRVVTLKTMHlgpeDVLIGVQVNLidgldtDKIELVTDKVEKAIMEIIPNLN 299
                      55689*****************99643334********999999999999999*******99998865 PP

>> ThrE  Putative threonine/serine exporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.31   1.4e+03     129     153 ..      16      40 ..       6      55 .. 0.55
   2 ?    3.7   0.3    0.0076        34     120     150 ..      63      93 ..      61     125 .. 0.82
   3 ?    7.7   0.5   0.00045         2     110     159 ..     176     225 ..     167     230 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.31
        ThrE 129 dwidflvaflagllggllrlllakr 153
                 ++  ++  f+a++ +g ++++ + +
  EPA04509.1  16 NLGIAITKFIAAISTGSVSMWAESY 40 
                 3444444455555555555544444 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.0076
        ThrE 120 aafallfggdwidflvaflagllggllrlll 150
                  +f++ fg +  +f+++f+++ l++ ++  l
  EPA04509.1  63 YSFSHQFGHSREQFFWSFIVASLIFGISGTL 93 
                 6899999999999999999999998877665 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.00045
        ThrE 110 lvvlaaglaaaafallfggdwidflvaflagllggllrlllakrglnsfv 159
                 l  ++++ ++ +++++ g  + d++ + ++g+++++l l+lak +   ++
  EPA04509.1 176 LSGIGVAALGIFLSMITGNPIYDAIGSIVIGAILMVLALFLAKENKDLLI 225
                 566778888888899999999********************998776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       913  (0.0509231); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.35s 00:00:00.95 Elapsed: 00:00:00.52
# Mc/sec: 1800.29
//
Query:       EPA04510.1  [L=528]
Description: cytochrome b/b6 family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-29  103.4   9.9    1.3e-29  103.4   9.9    2.4  3  Cytochrome_B     Cytochrome b/b6/petB
      2e-25   89.8   6.3      2e-25   89.8   6.3    3.1  3  Cytochrom_B_N_2  Cytochrome b(N-terminal)/b6/petB
    1.5e-09   38.1   1.3    1.5e-09   38.1   1.3    3.1  3  Cytochrom_B_C    Cytochrome b(C-terminal)/b6/petD
    7.3e-05   23.2   3.5    7.3e-05   23.2   3.5    3.4  3  DUF4405          Domain of unknown function (DUF4405)
     0.0053   16.6   0.2     0.0053   16.6   0.2    2.2  2  UPF0542          Uncharacterised protein family UPF0542
  ------ inclusion threshold ------
       0.26   11.8   0.0       0.26   11.8   0.0    3.6  4  DUF3899          Domain of unknown function (DUF3899)
        7.6    6.3  11.4        1.8    8.2   0.4    3.2  3  PTPLA            Protein tyrosine phosphatase-like protein, P


Domain annotation for each model (and alignments):
>> Cytochrome_B  Cytochrome b/b6/petB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.4   9.9   5.1e-33   1.3e-29      13     182 ..      42     210 ..      30     215 .. 0.94
   2 ?   -3.1   0.6       2.2   5.6e+03     141     151 ..     314     324 ..     262     354 .. 0.56
   3 ?   -0.7   0.8      0.42   1.1e+03      95     118 ..     425     448 ..     395     452 .. 0.64

  Alignments for each domain:
  == domain 1  score: 103.4 bits;  conditional E-value: 5.1e-33
  Cytochrome_B  13 iynlGsllllvlvlqiltGvalafyytptvtlaflsvqyilrdvnfGwlirsvhangasllflllylhifrglllgglkktrelvWviGvillllvi 109
                   +  lG l+++v+v+  ++G +l fyy+p ++ a+ svq+i  +v fG+ ir++h  g+  ++ll +lh+   ++ g +k + e  W +Gvil  ++i
    EPA04510.1  42 FGFLGMLTFVVFVILGISGALLMFYYQPMLDRAWDSVQFINDEVPFGFHIRNIHYHGSNAMVLLAILHMYYQYFSGRYKIRNEILWATGVILGTVTI 138
                   44579999999999999******************************************************************************** PP

  Cytochrome_B 110 vtafiGyvLpwdqmsyWavtvitnllsaiPviGstlvellwgsvsvddatLtrffslh.fllPflllillllhl 182
                    +af+Gy + ++  +  a+ + ++l  +iPv G t+ + ++gs +  d+ + rf++ h fllP+++l l+ +h+
    EPA04510.1 139 LEAFTGYDVIFSERAELAISIAASLTTSIPVAGPTIRDAMFGSGFS-DF-VLRFYAQHvFLLPLVMLGLMAVHF 210
                   ******************************************9874.45.569********************8 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.2
  Cytochrome_B 141 iGstlvellwg 151
                   + +++v+  wg
    EPA04510.1 314 LAQIMVTTYWG 324
                   22333333333 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.42
  Cytochrome_B  95 elvWviGvillllvivtafiGyvL 118
                      ++iG+il+++   + +  y L
    EPA04510.1 425 ISLFFIGIILIVFAGFFHVYRYGL 448
                   345677777777766666665555 PP

>> Cytochrom_B_N_2  Cytochrome b(N-terminal)/b6/petB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.6       3.2   8.2e+03      30      49 ..      45      64 ..      37      69 .. 0.70
   2 !   89.8   6.3   7.7e-29     2e-25       1     113 [.     100     210 ..     100     216 .. 0.97
   3 ?   -0.8   3.9      0.53   1.3e+03      73     158 ..     316     412 ..     303     445 .. 0.44

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 3.2
  Cytochrom_B_N_2 30 iGvllllltllegflGysLp 49
                     +G+l +++ ++ g+ G +L+
       EPA04510.1 45 LGMLTFVVFVILGISGALLM 64
                     56666666666666666664 PP

  == domain 2  score: 89.8 bits;  conditional E-value: 7.7e-29
  Cytochrom_B_N_2   1 yimiiliyvHmlrvfftGaYkkpRelnWiiGvllllltllegflGysLpddllsvtalrvgagiissvPvvgtwlvellfGgelpgeallsrly 94 
                      ++m+ l+++Hm  ++f G Yk + e+ W +Gv+l ++t+le+f+Gy  ++   +  a++++a++++s+Pv g+++  ++fG  +   + + r+y
       EPA04510.1 100 NAMVLLAILHMYYQYFSGRYKIRNEILWATGVILGTVTILEAFTGYDVIFSERAELAISIAASLTTSIPVAGPTIRDAMFGSGFS--DFVLRFY 191
                      58**********************************************************************************7..8899*** PP

  Cytochrom_B_N_2  95 alHilllpalllalivahl 113
                      a H++llp ++l l+++h+
       EPA04510.1 192 AQHVFLLPLVMLGLMAVHF 210
                      ******************9 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.53
  Cytochrom_B_N_2  73 twlvellfGgelpgealls...rlyalHilllpalllalivahlll....v..ekkgqtpsr.rkek..nvvg.....eplvpvnavkmlllfl 149
                      +++v+  +G ++p++ +++   rl +  + +l +++++l+ + + +    +   k+   + + +kek  ++v+     +       ++++++ l
       EPA04510.1 316 QIMVTTYWGFYIPSDTTIPlvqRLVIDPV-FLYTVMILLVPLGFGFsymmIklAKESERKAKlAKEKgpKKVAtinlsQ-----KWINWIIVGL 403
                      66666667766666654431115555555.4444444444444333111021122222222212222222222222221.....2222222222 PP

  Cytochrom_B_N_2 150 vlvallial 158
                      + + +++ +
       EPA04510.1 404 LAFQVFLNI 412
                      222222222 PP

>> Cytochrom_B_C  Cytochrome b(C-terminal)/b6/petD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.2      0.66   1.7e+03      70      84 ..      47      61 ..      10      75 .. 0.63
   2 !   38.1   1.3   5.8e-13   1.5e-09       8      94 ..     248     335 ..     243     342 .. 0.85
   3 ?   -2.1   0.1       1.8   4.7e+03      55      91 ..     386     422 ..     382     441 .. 0.60

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.66
                   HHHHHHHHHHHHHHT CS
  Cytochrom_B_C 70 allvvsfvvLgylGv 84
                   +l +v fv+Lg+ G+
     EPA04510.1 47 MLTFVVFVILGISGA 61
                   344556666666665 PP

  == domain 2  score: 38.1 bits;  conditional E-value: 5.8e-13
                    -TT-.---GGGHHHHHHHHCSSSHH.HHHHHHHHHHHGGGCHHHH---SSSSSTT-.HHHHHHHHHHHHHHHHHHHHHTS-SSCCHHHH CS
  Cytochrom_B_C   8 PahI.aPeWYflpfYaiLraipakl.lGvvamgaaivilfllpwldrskvksiryrkplakvllallvvsfvvLgylGvqppeevavll 94 
                    P+ I +PeWY++  Ya Lr+  +k+  Gv+  g  i+ ++l+p++dr k  s + r p+ +++ ++ +++++v +y G   p+++++ l
     EPA04510.1 248 PPGItVPEWYLTGLYAFLRTQYDKFvTGVLWPGLFIASFLLIPFIDRYKKFSWKDR-PIITAFGITGLAQIMVTTYWGFYIPSDTTIPL 335
                    444449**************98876269****************************.999999999999*********98887766554 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.8
                    SSSSTT-.HHHHHHHHHHHHHHHHHHHHHTS-SSCCH CS
  Cytochrom_B_C  55 vksiryrkplakvllallvvsfvvLgylGvqppeeva 91 
                    v  i+  +++ +++++ l++  v+L +++ + + + +
     EPA04510.1 386 VATINLSQKWINWIIVGLLAFQVFLNIAAYNAALSGF 422
                    5555666666666666666666666666655554444 PP

>> DUF4405  Domain of unknown function (DUF4405)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   3.5   2.8e-08   7.3e-05       2      64 ..      45     112 ..      44     114 .. 0.87
   2 ?   -1.1   0.8       1.1   2.9e+03      52      61 ..     200     209 ..     177     210 .. 0.80
   3 ?   -2.8   0.9       3.8   9.8e+03      52      62 ..     433     443 ..     424     445 .. 0.50

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 2.8e-08
     DUF4405   2 idlllllsflvlaiSGillsfavlpsgrgaywa...........flglskhqwrdiHeilgllflilvvlHlgl 64 
                 + +l++++f++l iSG ll f + p    a+             f       +r+iH   + ++++l++lH+++
  EPA04510.1  45 LGMLTFVVFVILGISGALLMFYYQPMLDRAWDSvqfindevpfgF------HIRNIHYHGSNAMVLLAILHMYY 112
                 66899*****************99977777777998888887543......7********************97 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.1
     DUF4405  52 llflilvvlH 61 
                 l++l+l+++H
  EPA04510.1 200 LVMLGLMAVH 209
                 6888888888 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 3.8
     DUF4405  52 llflilvvlHl 62 
                 +l +++  +H+
  EPA04510.1 433 ILIVFAGFFHV 443
                 23333444565 PP

>> UPF0542  Uncharacterised protein family UPF0542
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.6       3.5   8.9e+03      23      31 ..      50      58 ..      39      65 .. 0.50
   2 !   16.6   0.2   2.1e-06    0.0053      23      70 ..     345     393 ..     329     395 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3.5
     UPF0542 23 Flttvllil 31
                F+  v+l++
  EPA04510.1 50 FVVFVILGI 58
                344444444 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 2.1e-06
     UPF0542  23 FlttvlliltPllllsaflsyKLakelkkqekekklka.krkaniaksr 70 
                 Fl+tv++ l Pl +   ++  KLake +++ k  k k  k+ a i+ s+
  EPA04510.1 345 FLYTVMILLVPLGFGFSYMMIKLAKESERKAKLAKEKGpKKVATINLSQ 393
                 ********************************99998636667777665 PP

>> DUF3899  Domain of unknown function (DUF3899)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   1.8         7   1.8e+04      72      82 ..      46      56 ..      37      67 .. 0.54
   2 ?   -1.9   0.2         2     5e+03       3      12 ..     280     289 ..     270     291 .. 0.64
   3 ?    3.3   0.1     0.047   1.2e+02      28      74 ..     359     404 ..     345     412 .. 0.75
   4 ?   11.8   0.0    0.0001      0.26       4      37 ..     427     452 ..     425     487 .. 0.64

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 7
     DUF3899 72 Glllivlsivl 82
                G l +v+ ++l
  EPA04510.1 46 GMLTFVVFVIL 56
                44444444333 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2
     DUF3899   3 ilFllgllll 12 
                 +lF++++ll+
  EPA04510.1 280 GLFIASFLLI 289
                 3555555554 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.047
     DUF3899  28 gfsygfrklkklflkkskkddsyyeykekkkes....skkstrplliiGll 74 
                 gfsy++ kl k     s++++++ ++k +kk      s k+   ++i+Gll
  EPA04510.1 359 GFSYMMIKLAKE----SERKAKLAKEKGPKKVAtinlSQKW-INWIIVGLL 404
                 788888888888....9***********9998887744444.455555554 PP

  == domain 4  score: 11.8 bits;  conditional E-value: 0.0001
     DUF3899   4 lFllglllliigillivlnsGfFdgfsygfrklk 37 
                 lF +g+        ++++ +GfF +++yg ++ k
  EPA04510.1 427 LFFIGI--------ILIVFAGFFHVYRYGLNQAK 452
                 344444........44444566666666666665 PP

>> PTPLA  Protein tyrosine phosphatase-like protein, PTPLA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   2.7     0.057   1.4e+02      55     158 ..      14     118 ..       6     124 .. 0.64
   2 ?   -1.3   0.0      0.63   1.6e+03      92     140 ..     125     206 ..     115     224 .. 0.56
   3 ?    8.2   0.4   0.00072       1.8      87     158 ..     347     451 ..     324     454 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.057
       PTPLA  55 llaWsvtEviRYsfyalklsl.gkvpklltwlRYtlfivLYPlGvasElvliyaalpvlkeskklsielpnklnfsfsykyflll.llllyvpglyvly 151
                 ++ W    + R  f a+k s   +  ++  +l   +f+v  +lG+++ l+++y +  +l++       ++ ++ f f+++ + +    +++++ ++ +y
  EPA04510.1  14 FFYWLWDGLDRTIFTAIKFSFpARFVSPFGFLGMLTFVVFVILGISGALLMFYYQP-MLDRAWDSVQFINDEVPFGFHIRNIHYHgSNAMVLLAILHMY 111
                 566666666677777777732366677778888889999999***99888887764.444444444455566667777666666655555555555555 PP

       PTPLA 152 thmlkqR 158
                  + ++ R
  EPA04510.1 112 YQYFSGR 118
                 5555555 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.63
       PTPLA  92 vLYPlGvasElvliyaal....pvlkeskklsielpnklnfs.............................fsykyflllll 140
                 +L+ +Gv+   v+i++a+     +++e+++l+i++ ++l++s                             f +++++l l+
  EPA04510.1 125 ILWATGVILGTVTILEAFtgydVIFSERAELAISIAASLTTSipvagptirdamfgsgfsdfvlrfyaqhvFLLPLVMLGLM 206
                 6777777777777777775554334444455555555555445555555555555555555444444333344444444444 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.00072
       PTPLA  87 YtlfivLYPlGvasElvliyaalpvlkeskklsielpnklnfs.................................fsykyflllllllyvpglyvlyt 152
                 Yt+ i L PlG+   +++i  a ++ ++ k ++ + p+k+ +                                   ++++f++ ++l+++ g++ +y+
  EPA04510.1 347 YTVMILLVPLGFGFSYMMIKLAKESERKAKLAKEKGPKKVATInlsqkwinwiivgllafqvflniaaynaalsgfKNISLFFIGIILIVFAGFFHVYR 445
                 9***************99999997766666666666655443344466666677788888888888888888888667777777788888888888888 PP

       PTPLA 153 hmlkqR 158
                 + l+q 
  EPA04510.1 446 YGLNQA 451
                 877775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (528 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       928  (0.0517597); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.44
# Mc/sec: 3624.70
//
Query:       EPA04511.1  [L=792]
Description: thrombospondin type 3 repeat protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-56  186.7 232.0    1.4e-05   24.6   1.5   25.8 25  TSP_3            Thrombospondin type 3 repeat
    3.9e-08   33.1  33.6          7    6.7   0.1   14.1 15  DUF282           Caenorhabditis protein of unknown function, 
    0.00085   19.3   0.2         12    6.1   0.0    6.4  8  AKAP7_RIRII_bdg  PKA-RI-RII subunit binding domain of A-kinas
  ------ inclusion threshold ------
        9.1    6.6  19.7    1.7e+02    2.5   0.1    9.9 12  NOPS             NOPS (NUC059) domain


Domain annotation for each model (and alignments):
>> TSP_3  Thrombospondin type 3 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   4.6   2.8e-05      0.12      14      30 ..      28      44 ..      27      50 .. 0.91
   2 !    9.7   4.4   0.00015      0.69      15      30 ..      65      80 ..      47      83 .. 0.87
   3 ?   -0.9   0.2      0.31   1.4e+03      16      24 ..      89      97 ..      86      98 .. 0.70
   4 !   18.6   0.4   2.4e-07    0.0011      15      34 ..     108     127 ..     107     129 .. 0.93
   5 !   24.6   1.5   3.2e-09   1.4e-05      10      34 ..     135     165 ..     132     167 .. 0.83
   6 !    4.0   1.1    0.0092        41      16      27 ..     170     181 ..     167     185 .. 0.89
   7 !   15.0   0.9   3.3e-06     0.015      15      34 ..     186     205 ..     184     207 .. 0.92
   8 !   12.4   5.6   2.2e-05     0.097      14      31 ..     225     242 ..     210     247 .. 0.79
   9 ?   -3.6   0.2       2.1   9.4e+03      17      23 ..     251     257 ..     250     258 .. 0.56
  10 !   15.1   1.0     3e-06     0.013      13      30 ..     289     306 ..     288     310 .. 0.91
  11 ?   -0.3   0.3       0.2     9e+02      16      24 ..     315     323 ..     312     330 .. 0.80
  12 !   16.0   6.6   1.6e-06    0.0072      14      34 ..     331     351 ..     316     353 .. 0.88
  13 !   13.7   2.1   8.2e-06     0.037      13      31 ..     367     385 ..     357     389 .. 0.81
  14 !   22.3   1.8   1.7e-08   7.8e-05      14      34 ..     408     428 ..     393     430 .. 0.85
  15 !   15.8   4.6   1.9e-06    0.0085      14      33 ..     444     463 ..     433     465 .. 0.81
  16 !   17.8   3.4   4.5e-07     0.002       6      33 ..     472     500 ..     469     502 .. 0.82
  17 !   13.3   4.8   1.1e-05      0.05      10      31 ..     513     538 ..     506     542 .. 0.76
  18 ?   -2.2   0.6      0.79   3.5e+03      16      24 ..     546     554 ..     544     557 .. 0.81
  19 !   20.5   0.8   6.3e-08   0.00028      15      34 ..     563     582 ..     558     584 .. 0.93
  20 !   19.0   3.8   1.9e-07   0.00083      12      34 ..     592     620 ..     587     622 .. 0.81
  21 ?   -3.1   0.8       1.5   6.8e+03      17      24 ..     626     633 ..     625     634 .. 0.69
  22 !   17.3   1.8   6.3e-07    0.0028      15      34 ..     641     660 ..     640     662 .. 0.92
  23 !   19.4   4.2   1.4e-07   0.00063      12      33 ..     670     697 ..     665     699 .. 0.81
  24 !   15.1   5.6   3.1e-06     0.014      14      34 ..     719     739 ..     704     741 .. 0.89
  25 !   12.3   5.0   2.4e-05      0.11      13      33 ..     760     780 ..     747     783 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.8e-05
       TSP_3 14 kDfDnDgvqddlDNCpr 30
                +D D Dgv dd+D Cp+
  EPA04511.1 28 DDLDRDGVTDDVDKCPN 44
                69**************8 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00015
       TSP_3 15 DfDnDgvqddlDNCpr 30
                D+D Dg++dd D Cp 
  EPA04511.1 65 DADFDGIPDDIDQCPS 80
                99*************5 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.31
       TSP_3 16 fDnDgvqdd 24
                +D+Dg +d+
  EPA04511.1 89 QDQDGCPDT 97
                577777775 PP

  == domain 4  score: 18.6 bits;  conditional E-value: 2.4e-07
       TSP_3  15 DfDnDgvqddlDNCprnani 34 
                 D D+Dg+ d++D Cp+ +++
  EPA04511.1 108 DSDGDGISDLVDSCPTQPET 127
                 99***************987 PP

  == domain 5  score: 24.6 bits;  conditional E-value: 3.2e-09
       TSP_3  10 DaC......dkDfDnDgvqddlDNCprnani 34 
                 D C      ++D+D Dg++d+lD Cp na++
  EPA04511.1 135 DGCpdtfssNTDTDRDGIPDYLDACPLNAET 165
                 4455555789******************986 PP

  == domain 6  score: 4.0 bits;  conditional E-value: 0.0092
       TSP_3  16 fDnDgvqddlDN 27 
                 +D Dg +d++DN
  EPA04511.1 170 QDTDGCPDTVDN 181
                 69*********9 PP

  == domain 7  score: 15.0 bits;  conditional E-value: 3.3e-06
       TSP_3  15 DfDnDgvqddlDNCprnani 34 
                 D+DnDg++d lD C +++++
  EPA04511.1 186 DTDNDGIPDALDLCINKPET 205
                 9*************999975 PP

  == domain 8  score: 12.4 bits;  conditional E-value: 2.2e-05
       TSP_3  14 kDfDnDgvqddlDNCprn 31 
                  D+D+Dg++d++D Cp+ 
  EPA04511.1 225 GDADGDGIGDKSDLCPYQ 242
                 6***************97 PP

  == domain 9  score: -3.6 bits;  conditional E-value: 2.1
       TSP_3  17 DnDgvqd 23 
                 D Dg +d
  EPA04511.1 251 DYDGCPD 257
                 5566655 PP

  == domain 10  score: 15.1 bits;  conditional E-value: 3e-06
       TSP_3  13 dkDfDnDgvqddlDNCpr 30 
                 + D D Dg+ dd+D Cp+
  EPA04511.1 289 NLDSDADGIRDDVDQCPY 306
                 67***************8 PP

  == domain 11  score: -0.3 bits;  conditional E-value: 0.2
       TSP_3  16 fDnDgvqdd 24 
                 +D+Dg +d+
  EPA04511.1 315 QDEDGCPDY 323
                 699999997 PP

  == domain 12  score: 16.0 bits;  conditional E-value: 1.6e-06
       TSP_3  14 kDfDnDgvqddlDNCprnani 34 
                 +D+D+Dg++d+lD Cp+ +++
  EPA04511.1 331 ADTDGDGIPDNLDLCPTQPET 351
                 6****************9985 PP

  == domain 13  score: 13.7 bits;  conditional E-value: 8.2e-06
       TSP_3  13 dkDfDnDgvqddlDNCprn 31 
                  +D D+Dg++d  D Cp +
  EPA04511.1 367 TTDSDKDGIPDAIDACPLS 385
                 68***************75 PP

  == domain 14  score: 22.3 bits;  conditional E-value: 1.7e-08
       TSP_3  14 kDfDnDgvqddlDNCprnani 34 
                  DfD+Dg++d++D Cp++a++
  EPA04511.1 408 SDFDGDGIPDLSDKCPQIAET 428
                 7******************97 PP

  == domain 15  score: 15.8 bits;  conditional E-value: 1.9e-06
       TSP_3  14 kDfDnDgvqddlDNCprnan 33 
                  D DnDgv d+lD Cp+ ++
  EPA04511.1 444 MDSDNDGVRDSLDFCPTQPE 463
                 69***************997 PP

  == domain 16  score: 17.8 bits;  conditional E-value: 4.5e-07
       TSP_3   6 DgvGDaC.....dkDfDnDgvqddlDNCprnan 33 
                 Dg    C     + D+D Dg++d+ D Cp +a+
  EPA04511.1 472 DG----CpdnpsELDADRDGIPDTIDKCPLVAE 500
                 44....44444899***************9996 PP

  == domain 17  score: 13.3 bits;  conditional E-value: 1.1e-05
       TSP_3  10 DaC....dkDfDnDgvqddlDNCprn 31 
                 D+     + D D+Dg++d+ D Cp +
  EPA04511.1 513 DIPlvsnEVDSDGDGIPDSTDQCPSV 538
                 444666688***************86 PP

  == domain 18  score: -2.2 bits;  conditional E-value: 0.79
       TSP_3  16 fDnDgvqdd 24 
                 +D Dg +d+
  EPA04511.1 546 QDDDGCPDY 554
                 588999887 PP

  == domain 19  score: 20.5 bits;  conditional E-value: 6.3e-08
       TSP_3  15 DfDnDgvqddlDNCprnani 34 
                 D+D+Dg++d+ D Cp+ +++
  EPA04511.1 563 DTDGDGIPDKFDSCPTQPET 582
                 9****************987 PP

  == domain 20  score: 19.0 bits;  conditional E-value: 1.9e-07
       TSP_3  12 C......dkDfDnDgvqddlDNCprnani 34 
                 C      + D+D Dg++d  D+Cp na++
  EPA04511.1 592 CpdkilsNIDTDRDGIPDAIDTCPLNAET 620
                 444447788*****************986 PP

  == domain 21  score: -3.1 bits;  conditional E-value: 1.5
       TSP_3  17 DnDgvqdd 24 
                 D Dg +d+
  EPA04511.1 626 DDDGCPDT 633
                 77887775 PP

  == domain 22  score: 17.3 bits;  conditional E-value: 6.3e-07
       TSP_3  15 DfDnDgvqddlDNCprnani 34 
                 D DnDg++d++D Cp  a++
  EPA04511.1 641 DSDNDGIPDVNDKCPKLAET 660
                 99*************99975 PP

  == domain 23  score: 19.4 bits;  conditional E-value: 1.4e-07
       TSP_3  12 C......dkDfDnDgvqddlDNCprnan 33 
                 C      + D+D+Dgv+d++D Cp++++
  EPA04511.1 670 CpdskisQPDADGDGVPDTMDLCPTKPE 697
                 444445578*****************98 PP

  == domain 24  score: 15.1 bits;  conditional E-value: 3.1e-06
       TSP_3  14 kDfDnDgvqddlDNCprnani 34 
                 kD+D+Dg++d++D Cp  +++
  EPA04511.1 719 KDTDGDGINDNVDQCPMYPET 739
                 8***************98875 PP

  == domain 25  score: 12.3 bits;  conditional E-value: 2.4e-05
       TSP_3  13 dkDfDnDgvqddlDNCprnan 33 
                 + D D Dg+ +d D Cp +++
  EPA04511.1 760 NHDDDLDGILNDTDLCPMVPE 780
                 78****************997 PP

>> DUF282  Caenorhabditis protein of unknown function, DUF282
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.36   1.6e+03      17      27 ..      70      80 ..      68      83 .. 0.88
   2 ?    1.2   0.0     0.079   3.5e+02      15      29 ..     111     125 ..     105     127 .. 0.88
   3 ?    1.9   0.0     0.047   2.1e+02      17      30 ..     151     164 ..     149     166 .. 0.90
   4 ?    0.4   0.0      0.14   6.2e+02      17      28 ..     191     202 ..     190     205 .. 0.85
   5 ?    0.9   0.0     0.096   4.3e+02      15      30 ..     229     244 ..     226     246 .. 0.89
   6 !    6.7   0.1    0.0016         7      15      30 ..     335     350 ..     331     352 .. 0.88
   7 ?    2.1   0.0     0.043   1.9e+02      17      31 ..     374     388 ..     373     393 .. 0.85
   8 !    5.9   0.0    0.0027        12      15      30 ..     412     427 ..     409     428 .. 0.89
   9 ?   -2.4   0.0       1.1   4.9e+03      19      29 ..     452     462 ..     449     464 .. 0.75
  10 ?   -0.4   0.0      0.25   1.1e+03      17      27 ..     487     497 ..     486     500 .. 0.84
  11 !    5.0   0.1    0.0052        23      15      29 ..     525     539 ..     522     542 .. 0.87
  12 !    6.1   0.1    0.0023        10      15      30 ..     566     581 ..     563     582 .. 0.89
  13 ?    2.2   0.0     0.038   1.7e+02      17      30 ..     606     619 ..     605     621 .. 0.89
  14 ?    1.5   0.0     0.062   2.8e+02      17      30 ..     646     659 ..     645     660 .. 0.89
  15 !    6.2   0.3    0.0023        10      12      30 ..     679     697 ..     670     702 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.36
      DUF282 17 giPslsdwCat 27
                giP+  d C+ 
  EPA04511.1 70 GIPDDIDQCPS 80
                9********85 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.079
      DUF282  15 GvgiPslsdwCataa 29 
                 G gi +l d C+t+ 
  EPA04511.1 111 GDGISDLVDSCPTQP 125
                 99**********986 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.047
      DUF282  17 giPslsdwCataae 30 
                 giP+++d C+  ae
  EPA04511.1 151 GIPDYLDACPLNAE 164
                 9*********9887 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 0.14
      DUF282  17 giPslsdwCata 28 
                 giP+++d C+ +
  EPA04511.1 191 GIPDALDLCINK 202
                 9********875 PP

  == domain 5  score: 0.9 bits;  conditional E-value: 0.096
      DUF282  15 GvgiPslsdwCataae 30 
                 G gi + sd C+ ++e
  EPA04511.1 229 GDGIGDKSDLCPYQKE 244
                 99*********98876 PP

  == domain 6  score: 6.7 bits;  conditional E-value: 0.0016
      DUF282  15 GvgiPslsdwCataae 30 
                 G giP+++d C+t+ e
  EPA04511.1 335 GDGIPDNLDLCPTQPE 350
                 99**********9865 PP

  == domain 7  score: 2.1 bits;  conditional E-value: 0.043
      DUF282  17 giPslsdwCataaev 31 
                 giP++ d C+ ++e+
  EPA04511.1 374 GIPDAIDACPLSKET 388
                 9*********98875 PP

  == domain 8  score: 5.9 bits;  conditional E-value: 0.0027
      DUF282  15 GvgiPslsdwCataae 30 
                 G giP+lsd C++ ae
  EPA04511.1 412 GDGIPDLSDKCPQIAE 427
                 99**********9776 PP

  == domain 9  score: -2.4 bits;  conditional E-value: 1.1
      DUF282  19 PslsdwCataa 29 
                  +++d+C+t+ 
  EPA04511.1 452 RDSLDFCPTQP 462
                 57899***986 PP

  == domain 10  score: -0.4 bits;  conditional E-value: 0.25
      DUF282  17 giPslsdwCat 27 
                 giP++ d C+ 
  EPA04511.1 487 GIPDTIDKCPL 497
                 9********96 PP

  == domain 11  score: 5.0 bits;  conditional E-value: 0.0052
      DUF282  15 GvgiPslsdwCataa 29 
                 G giP+++d C+  +
  EPA04511.1 525 GDGIPDSTDQCPSVK 539
                 99*********9765 PP

  == domain 12  score: 6.1 bits;  conditional E-value: 0.0023
      DUF282  15 GvgiPslsdwCataae 30 
                 G giP+  d C+t+ e
  EPA04511.1 566 GDGIPDKFDSCPTQPE 581
                 99**********9865 PP

  == domain 13  score: 2.2 bits;  conditional E-value: 0.038
      DUF282  17 giPslsdwCataae 30 
                 giP++ d C+  ae
  EPA04511.1 606 GIPDAIDTCPLNAE 619
                 9*********9887 PP

  == domain 14  score: 1.5 bits;  conditional E-value: 0.062
      DUF282  17 giPslsdwCataae 30 
                 giP+ +d C++ ae
  EPA04511.1 646 GIPDVNDKCPKLAE 659
                 9*********9877 PP

  == domain 15  score: 6.2 bits;  conditional E-value: 0.0023
      DUF282  12 tCqGvgiPslsdwCataae 30 
                 +  G g+P++ d C+t+ e
  EPA04511.1 679 DADGDGVPDTMDLCPTKPE 697
                 5579***********9865 PP

>> AKAP7_RIRII_bdg  PKA-RI-RII subunit binding domain of A-kinase anchor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.078   3.5e+02      30      51 ..     164     185 ..     161     191 .. 0.77
   2 !    6.1   0.0    0.0026        12      27      44 ..     306     323 ..     300     337 .. 0.75
   3 ?    0.8   0.0      0.12   5.3e+02      30      42 ..     387     399 ..     385     411 .. 0.90
   4 ?   -3.7   0.0       2.9   1.3e+04      30      49 ..     463     482 ..     463     486 .. 0.79
   5 ?   -1.4   0.0      0.56   2.5e+03      29      42 ..     539     552 ..     538     562 .. 0.87
   6 ?   -1.9   0.0      0.79   3.5e+03      30      44 ..     581     595 ..     580     605 .. 0.87
   7 ?   -1.2   0.0       0.5   2.2e+03      30      47 ..     619     636 ..     618     645 .. 0.76
   8 ?   -1.6   0.0      0.67     3e+03      30      54 ..     738     762 ..     736     765 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.078
  AKAP7_RIRII_bdg  30 ETqnkarqadGssvKaeeadrg 51 
                      ET nk + +dG +   ++++  
       EPA04511.1 164 ETYNKFQDTDGCPDTVDNTKFI 185
                      9**********99776666555 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0026
  AKAP7_RIRII_bdg  27 YLEETqnkarqadGssvK 44 
                      YL ET nk +  dG +  
       EPA04511.1 306 YLKETYNKFQDEDGCPDY 323
                      **************9964 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.12
  AKAP7_RIRII_bdg  30 ETqnkarqadGss 42 
                      ET nk + +dG +
       EPA04511.1 387 ETYNKYQDTDGCP 399
                      9**********98 PP

  == domain 4  score: -3.7 bits;  conditional E-value: 2.9
  AKAP7_RIRII_bdg  30 ETqnkarqadGssvKaeead 49 
                      ET n+    dG +  + e d
       EPA04511.1 463 ETWNRYLDNDGCPDNPSELD 482
                      88999999999998877755 PP

  == domain 5  score: -1.4 bits;  conditional E-value: 0.56
  AKAP7_RIRII_bdg  29 EETqnkarqadGss 42 
                       ET nk +  dG +
       EPA04511.1 539 KETYNKFQDDDGCP 552
                      59**********98 PP

  == domain 6  score: -1.9 bits;  conditional E-value: 0.79
  AKAP7_RIRII_bdg  30 ETqnkarqadGssvK 44 
                      ET nk   +dG + K
       EPA04511.1 581 ETFNKFLDTDGCPDK 595
                      899*********988 PP

  == domain 7  score: -1.2 bits;  conditional E-value: 0.5
  AKAP7_RIRII_bdg  30 ETqnkarqadGssvKaee 47 
                      ET nk +  dG +    e
       EPA04511.1 619 ETYNKFQDDDGCPDTIFE 636
                      9**********9976555 PP

  == domain 8  score: -1.6 bits;  conditional E-value: 0.67
  AKAP7_RIRII_bdg  30 ETqnkarqadGssvKaeeadrggkn 54 
                      ET nk    dG +  + e +r +++
       EPA04511.1 738 ETYNKYLDWDGCPDTSPEQSRYNHD 762
                      999********99887777666544 PP

>> NOPS  NOPS (NUC059) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.84   3.8e+03       5      18 ..      83      96 ..      79      98 .. 0.82
   2 ?   -3.2   0.0       2.3     1e+04      10      23 ..     131     144 ..     126     147 .. 0.71
   3 ?    0.5   0.0      0.16   7.1e+02       1      19 [.     160     178 ..     160     185 .. 0.87
   4 ?    0.8   0.0      0.12   5.6e+02       4      23 ..     308     327 ..     305     331 .. 0.79
   5 ?   -2.0   0.0      0.96   4.3e+03       1      18 [.     383     400 ..     383     402 .. 0.80
   6 ?    2.5   0.1     0.037   1.7e+02       1      21 [.     423     443 ..     423     448 .. 0.87
   7 ?    1.6   0.1     0.071   3.2e+02       1      18 [.     496     513 ..     496     519 .. 0.93
   8 ?   -0.4   0.1       0.3   1.4e+03       2      18 ..     537     553 ..     536     560 .. 0.82
   9 ?   -3.6   0.0         3   1.3e+04      12      20 ..     565     573 ..     561     573 .. 0.75
  10 ?    0.1   0.0      0.21   9.2e+02       7      23 ..     583     599 ..     577     602 .. 0.77
  11 ?    1.5   0.0     0.076   3.4e+02       1      20 [.     615     634 ..     615     638 .. 0.86
  12 ?    0.5   0.0      0.16   7.2e+02       3      20 ..     657     674 ..     655     680 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.84
        NOPS  5 epleqkDdeDGlpE 18
                e+++++ d+DG p+
  EPA04511.1 83 ENYNKFQDQDGCPD 96
                889999999**997 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.3
        NOPS  10 kDdeDGlpEkllnk 23 
                 + d+DG p+ + ++
  EPA04511.1 131 FKDTDGCPDTFSSN 144
                 5678**99987665 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.16
        NOPS   1 PvvVepleqkDdeDGlpEk 19 
                 P+ +e+++++ d+DG p+ 
  EPA04511.1 160 PLNAETYNKFQDTDGCPDT 178
                 77899***********985 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 0.12
        NOPS   4 VepleqkDdeDGlpEkllnk 23 
                  e+++++ deDG p+ +  +
  EPA04511.1 308 KETYNKFQDEDGCPDYIADN 327
                 5899999*******977665 PP

  == domain 5  score: -2.0 bits;  conditional E-value: 0.96
        NOPS   1 PvvVepleqkDdeDGlpE 18 
                 P+  e++++  d+DG p+
  EPA04511.1 383 PLSKETYNKYQDTDGCPD 400
                 5666889999999**997 PP

  == domain 6  score: 2.5 bits;  conditional E-value: 0.037
        NOPS   1 PvvVepleqkDdeDGlpEkll 21 
                 P ++e+++ ++d+DG p++++
  EPA04511.1 423 PQIAETFNGFNDDDGCPDEIV 443
                 678999***********9987 PP

  == domain 7  score: 1.6 bits;  conditional E-value: 0.071
        NOPS   1 PvvVepleqkDdeDGlpE 18 
                 P+v+e ++ ++d+DG p+
  EPA04511.1 496 PLVAERYNGFEDDDGCPD 513
                 999************997 PP

  == domain 8  score: -0.4 bits;  conditional E-value: 0.3
        NOPS   2 vvVepleqkDdeDGlpE 18 
                  v e+++++ d+DG p+
  EPA04511.1 537 SVKETYNKFQDDDGCPD 553
                 5679999999****998 PP

  == domain 9  score: -3.6 bits;  conditional E-value: 3
        NOPS  12 deDGlpEkl 20 
                 d DG+p+k+
  EPA04511.1 565 DGDGIPDKF 573
                 34****996 PP

  == domain 10  score: 0.1 bits;  conditional E-value: 0.21
        NOPS   7 leqkDdeDGlpEkllnk 23 
                 ++++ d+DG p+k+l++
  EPA04511.1 583 FNKFLDTDGCPDKILSN 599
                 5556688******9975 PP

  == domain 11  score: 1.5 bits;  conditional E-value: 0.076
        NOPS   1 PvvVepleqkDdeDGlpEkl 20 
                 P+ +e+++++ d+DG p+ +
  EPA04511.1 615 PLNAETYNKFQDDDGCPDTI 634
                 77899***********9876 PP

  == domain 12  score: 0.5 bits;  conditional E-value: 0.16
        NOPS   3 vVepleqkDdeDGlpEkl 20 
                 ++e+++ ++d+DG p+  
  EPA04511.1 657 LAETYNGFEDDDGCPDSK 674
                 6899999*******9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (792 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       233  (0.0129957); expected 358.6 (0.02)
Passed bias filter:                      177  (0.00987227); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.73u 0.32s 00:00:01.05 Elapsed: 00:00:00.54
# Mc/sec: 4417.41
//
Query:       EPA04512.1  [L=167]
Description: hypothetical protein BG20_I1169 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-08   34.3   0.0    3.3e-08   33.9   0.0    1.1  1  HhH-GPD   HhH-GPD superfamily base excision DNA repair protei
  ------ inclusion threshold ------
      0.084   12.8   0.0        0.6   10.1   0.0    2.1  2  HHH       Helix-hairpin-helix motif


Domain annotation for each model (and alignments):
>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.0   3.7e-12   3.3e-08      22     100 ..       9     130 ..       3     137 .. 0.88

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 3.7e-12
                 HHHHS........HCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH........................................S-SSS- CS
                 xxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................................xxxxxx RF
     HhH-GPD  22 ferfg........fptpedladadeekLrelirelGfyrrKakyikelArilv........................................gkpdvl 72 
                  ++++        fp+p+++ada+ ++++++    G++ ++ak i+++A+++                                         +k + +
  EPA04512.1   9 EKKVEfddkefylFPEPKKIADASIQEIQNC----GVG-YRAKFIIDAAKMVEseqidfeymkksnyqdakkvilttpgignkvadcillfslDKLE-A 101
                 5555566667777******************....***.*****************************************************97776.8 PP

                 -TTSHHHHHHHHHHTTSSSS.TTHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
     HhH-GPD  73 ivvDvhvrrilkrlrsikek.ktkkkvek 100
                 ++ D ++ ril+++++ k    tk+ +ek
  EPA04512.1 102 FPLDRWMIRILGKYYLEKFElRTKSITEK 130
                 889************99987666666655 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0       0.1   9.2e+02       4      15 ..      27      38 ..      24      39 .. 0.81
   2 ?   10.1   0.0   6.6e-05       0.6      17      30 .]      81      94 ..      77      94 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.1
                HHHTSSHHHHHT CS
         HHH  4 glipasreeLla 15
                 + +as+ e++ 
  EPA04512.1 27 KIADASIQEIQN 38
                6899****9986 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 6.6e-05
                TT-SHHHHHHHHHH CS
         HHH 17 PGVGpktAeaIlsy 30
                PG+G k+A++Il +
  EPA04512.1 81 PGIGNKVADCILLF 94
                9**********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       753  (0.041999); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1167.39
//
Query:       EPA04513.1  [L=125]
Description: 8-oxoguanine DNA glycosylase, N-terminal domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      7e-12   45.5   0.2    4.7e-09   36.4   0.2    2.1  1  OGG_N         8-oxoguanine DNA glycosylase, N-terminal domain
     0.0061   16.9   0.2     0.0096   16.3   0.2    1.4  1  RNA_helicase  RNA helicase


Domain annotation for each model (and alignments):
>> OGG_N  8-oxoguanine DNA glycosylase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.2   5.2e-13   4.7e-09       7     120 ..       5      95 ..       1      96 [. 0.90

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 5.2e-13
                 SS--HHHHHCSSS-SSEEE-TTS-EEEEETTEEEEEEEETTEEEEET--.............HHHHHHTHHHHTTTTS-HHHHHHHHTT.SHHHHHHHC CS
       OGG_N   7 eeldlkktLkcGQsFrWkktekteyvgvlgdrvveLkqeeddllyrtlesesstkasseeakeeeteeilrdYfnLdvdleelykewskkdplfkksad 105
                   ++l++t+++GQ F Wkk+++  ++g+ g+ v++++   + + y++ +                     +d+f+   ++e+++k+ sk d+  k +++
  EPA04513.1   5 DSINLENTINSGQVFLWKKHKEF-WYGINGQDVLKINDSGKITTYSNKK---------------------YDFFRTGDNIEKIIKSISK-DKTTKIAVK 80 
                 4599*******************.*************777777777766.....................89************99988.999****** PP

                 CTTT-------HHHH CS
       OGG_N 106 kftGiRllrqdpwEc 120
                 k+ G+Rllrqdp+ c
  EPA04513.1  81 KYLGLRLLRQDPFQC 95 
                 *************99 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.2   1.1e-06    0.0096      29      71 ..      13      56 ..       4      80 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.1e-06
  RNA_helicase 29 kkkdsvysrnpeddfwdgYtgqevvvidDfgqvkdeenps.dla 71
                  +++++v+  ++ ++fw+g +gq+v+ i D g++++ +n++ d++
    EPA04513.1 13 INSGQVFLWKKHKEFWYGINGQDVLKINDSGKITTYSNKKyDFF 56
                  4667888899**********************986545554544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1048  (0.0584528); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 858.09
//
Query:       EPA04514.1  [L=107]
Description: hypothetical protein BG20_I1178 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.042   13.6   0.0      0.064   13.0   0.0    1.3  1  GP57             Phage Tail fiber assembly helper gene produc
      0.065   13.3   0.3        0.1   12.7   0.3    1.4  1  7kD_DNA_binding  7kD DNA-binding domain
      0.083   13.3   0.2       0.13   12.6   0.2    1.3  1  PH_2             Plant pleckstrin homology-like region


Domain annotation for each model (and alignments):
>> GP57  Phage Tail fiber assembly helper gene product 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.1e-05     0.064       3      45 ..      11      53 ..       9      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.1e-05
        GP57  3 eqtveqklsaeivtlksrildtqdqaarlmeeskilqGtlaei 45
                e   e k+ a i+tl  + l      ar+m+ sk +  t+ +i
  EPA04514.1 11 EDCNEDKIGAGILTLTNKRLAFDKTQARMMDFSKRFGDTVLDI 53
                67789*****************************988887766 PP

>> 7kD_DNA_binding  7kD DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.3   1.7e-05       0.1      12      57 ..      52     103 ..      39     104 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.7e-05
                      EEETTTEEEEEESSSS...EEEEEE-..SSSEEE.EEEETTTS-CHHHHHHT CS
  7kD_DNA_binding  12 evdiskikkvWrvGkm...vsftydd..nGktGr.GavsekdaPkelldmle 57 
                      ++ +s + kvW+ G++   v ft     + +t + G    kd  k++ +ml+
       EPA04514.1  52 DIPLSDVTKVWKEGRLikkVCFTAKTkeGEQTFKfGVFNTKDWLKNIENMLG 103
                      566799******9976222679876542445654477788999999888886 PP

>> PH_2  Plant pleckstrin homology-like region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   2.1e-05      0.13      39     102 ..      42     103 ..      33     106 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.1e-05
        PH_2  39 fskkkksvVldvskdipawpreeeese.eeryyfglkTaeglvefeckskaekkvWvegiknlLs 102
                 fsk    +Vld+   ++++++  +e++  ++++f  kT+eg   f++    + k+W++ i+n+L 
  EPA04514.1  42 FSKRFGDTVLDIP--LSDVTKVWKEGRlIKKVCFTAKTKEGEQTFKFG-VFNTKDWLKNIENMLG 103
                 5555556666654..22222222444445569*********9999996.78999*********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.30s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 713.76
//
Query:       EPA04515.1  [L=179]
Description: thrombospondin type 3 repeat protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.3e-14   53.6  47.6    0.00082   19.0   3.0    6.7  5  TSP_3      Thrombospondin type 3 repeat
  ------ inclusion threshold ------
      0.086   13.4   5.2        8.4    7.0   0.0    4.0  3  Fer4_13    4Fe-4S single cluster domain of Ferredoxin I
       0.25   11.6   1.4         64    3.8   0.0    3.7  3  NOPS       NOPS (NUC059) domain
       0.25   11.3   3.7         11    6.1   0.1    3.7  4  DUF282     Caenorhabditis protein of unknown function, DUF282
        0.3   10.3   0.8       0.64    9.2   0.6    1.8  2  DUF2709    Protein of unknown function (DUF2709)
        1.5    8.4   8.9         19    5.0   0.2    3.9  3  EF-hand_5  EF hand


Domain annotation for each model (and alignments):
>> TSP_3  Thrombospondin type 3 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   3.0   2.7e-07   0.00082      14      30 ..      28      44 ..      28      46 .. 0.95
   2 !   18.0   2.1   5.6e-07    0.0017      15      31 ..      65      81 ..      54      85 .. 0.91
   3 !   16.4   7.5   1.8e-06    0.0054      13      34 ..     105     126 ..      89     128 .. 0.76
   4 !   18.8   4.5   3.2e-07   0.00096      15      34 ..     145     164 ..     131     169 .. 0.86
   5 ?   -0.4   0.7      0.31   9.3e+02      16      24 ..     169     177 ..     165     178 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.7e-07
       TSP_3 14 kDfDnDgvqddlDNCpr 30
                +D+D+Dgv++d D Cp+
  EPA04515.1 28 QDTDGDGVPNDKDECPN 44
                7***************8 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 5.6e-07
       TSP_3 15 DfDnDgvqddlDNCprn 31
                D+D Dg++d+lD Cp++
  EPA04515.1 65 DADYDGIPDNLDSCPTV 81
                9**************97 PP

  == domain 3  score: 16.4 bits;  conditional E-value: 1.8e-06
       TSP_3  13 dkDfDnDgvqddlDNCprnani 34 
                  +D+D+Dg+ d++D Cp+ +++
  EPA04515.1 105 TADTDGDGIFDNVDKCPNQPET 126
                 57*****************987 PP

  == domain 4  score: 18.8 bits;  conditional E-value: 3.2e-07
       TSP_3  15 DfDnDgvqddlDNCprnani 34 
                 D+D Dg+ d+lD Cp n+++
  EPA04515.1 145 DTDHDGISDSLDACPLNPEV 164
                 9****************986 PP

  == domain 5  score: -0.4 bits;  conditional E-value: 0.31
       TSP_3  16 fDnDgvqdd 24 
                 +D Dg +d+
  EPA04515.1 169 QDDDGCPDV 177
                 588888885 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0    0.0028       8.4      18      54 ..      23      59 ..      18      63 .. 0.91
   2 ?    1.2   0.0      0.19   5.7e+02      40      53 ..      67      80 ..      61      81 .. 0.78
   3 ?    3.9   1.4     0.027        79      17      53 ..     124     160 ..      86     161 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0028
     Fer4_13 18 dvFeeddeggasvvaeqptseeekadaeeAadaCPve 54
                +v+ ++d +g  v  ++++ + + +d +  +d+CP +
  EPA04515.1 23 NVYSIQDTDGDGVPNDKDECPNLLEDYKGVIDGCPSS 59
                7999******9999999******************76 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.19
     Fer4_13 40 ekadaeeAadaCPv 53
                +++ + + +d+CP+
  EPA04515.1 67 DYDGIPDNLDSCPT 80
                566677889****8 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.027
     Fer4_13  17 PdvFeeddeggasvvaeqpts..eeekadaeeAadaCPv 53 
                 P++F   d++     ++q ts  +++++ + + +daCP 
  EPA04515.1 124 PETFNGVDDK--DGCPDQITSsiDTDHDGISDSLDACPL 160
                 6666655553..2346776667788899999******96 PP

>> NOPS  NOPS (NUC059) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.022        64       1      19 [.      79      97 ..      79     106 .. 0.87
   2 ?    3.2   0.0     0.034     1e+02       5      20 ..     125     140 ..     121     143 .. 0.84
   3 ?    1.0   0.1      0.17     5e+02       5      18 ..     163     176 ..     159     179 .] 0.79

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.022
        NOPS  1 PvvVepleqkDdeDGlpEk 19
                P v e+++++ deDG p+ 
  EPA04515.1 79 PTVRETYNKFQDEDGCPDA 97
                778899**********986 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.034
        NOPS   5 epleqkDdeDGlpEkl 20 
                 e+++ +Dd+DG p+++
  EPA04515.1 125 ETFNGVDDKDGCPDQI 140
                 677889*******975 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.17
        NOPS   5 epleqkDdeDGlpE 18 
                 e ++++ d+DG p+
  EPA04515.1 163 EVYNKFQDDDGCPD 176
                 889999999**997 PP

>> DUF282  Caenorhabditis protein of unknown function, DUF282
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.018        53      15      26 ..      32      43 ..      26      47 .. 0.90
   2 ?    6.1   0.1    0.0036        11      17      30 ..      70      83 ..      62      85 .. 0.87
   3 ?   -2.0   0.0       1.2   3.6e+03      15      28 ..     110     123 ..     109     126 .. 0.79
   4 ?   -1.9   0.0       1.1   3.2e+03      18      30 ..     151     163 ..     149     167 .. 0.59

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.018
      DUF282 15 GvgiPslsdwCa 26
                G g+P+ +d C+
  EPA04515.1 32 GDGVPNDKDECP 43
                99*********8 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0036
      DUF282 17 giPslsdwCataae 30
                giP+++d C+t  e
  EPA04515.1 70 GIPDNLDSCPTVRE 83
                9*********9665 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.2
      DUF282  15 GvgiPslsdwCata 28 
                 G gi ++ d C+ +
  EPA04515.1 110 GDGIFDNVDKCPNQ 123
                 78888999999976 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 1.1
      DUF282  18 iPslsdwCataae 30 
                 i +++d C+   e
  EPA04515.1 151 ISDSLDACPLNPE 163
                 5566677765544 PP

>> DUF2709  Protein of unknown function (DUF2709)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.78   2.3e+03     106     123 ..      68      85 ..      64      93 .. 0.78
   2 ?    9.2   0.6   0.00021      0.64      90     129 ..      94     133 ..      77     166 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.78
     DUF2709 106 qdaiydwvskcpenteri 123
                  d i d + +cp  +e  
  EPA04515.1  68 YDGIPDNLDSCPTVRETY 85 
                 578889999999988865 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00021
     DUF2709  90 cpftGkvfgdnthpnpqdaiydwvskcpenterigGlrvk 129
                 cp +    g +t     d i+d v kcp++ e  +G+  k
  EPA04515.1  94 CPDASPNVGKETADTDGDGIFDNVDKCPNQPETFNGVDDK 133
                 77777777888889999*****************999766 PP

>> EF-hand_5  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   1.2     0.053   1.6e+02       9      14 ..      29      34 ..      29      35 .. 0.92
   2 ?    5.0   0.2    0.0064        19       8      14 ..     106     112 ..     104     113 .. 0.87
   3 ?    4.1   0.1     0.012        36       8      14 ..     144     150 ..     142     151 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.053
                -SS-SS CS
   EF-hand_5  9 DlNgDG 14
                D++gDG
  EPA04515.1 29 DTDGDG 34
                9***** PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0064
                 H-SS-SS CS
   EF-hand_5   8 iDlNgDG 14 
                 +D++gDG
  EPA04515.1 106 ADTDGDG 112
                 8****** PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.012
                 H-SS-SS CS
   EF-hand_5   8 iDlNgDG 14 
                 iD+++DG
  EPA04515.1 144 IDTDHDG 150
                 9****** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.46u 0.33s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 1102.01
//
Query:       EPA04516.1  [L=119]
Description: RNA-metabolizing metallo-beta-lactamase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.6e-17   62.5   0.1    3.5e-17   62.1   0.1    1.2  1  RMMBL      Zn-dependent metallo-hydrolase RNA specificity dom
    2.1e-06   28.0   0.0    3.5e-06   27.3   0.0    1.4  1  Beta-Casp  Beta-Casp domain
  ------ inclusion threshold ------
      0.026   13.7   0.0      0.032   13.4   0.0    1.1  1  NB-ARC     NB-ARC domain


Domain annotation for each model (and alignments):
>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.1   0.1   5.8e-21   3.5e-17       2      62 .]      50     111 ..      49     111 .. 0.97

  Alignments for each domain:
  == domain 1  score: 62.1 bits;  conditional E-value: 5.8e-21
       RMMBL   2 ipvkarieeidfSgHadknellelirklkprn.vilvHGeeeatsalarllkeeegidvfiP 62 
                 ++v a++++++fSgHad+nel e+++k+k  + v  vHG+ e+++++a+ ++e++g d+++P
  EPA04516.1  50 LNVAAEVKQFEFSGHADRNELFEVVNKIKGNPkVLTVHGDMESCKKFAQEIHEKFGLDAHAP 111
                 5799***************************99***************************98 PP

>> Beta-Casp  Beta-Casp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   5.9e-10   3.5e-06      74     110 .]       1      37 [.       1      37 [. 0.98

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 5.9e-10
                 TSSSSHHHHHHHHHTTSTTSEEEESS---TTSHHHHH CS
   Beta-Casp  74 mlegGrsrellkklledprntvilvgyqaegTlgrkl 110
                 ml gG + ++l++l  +++n + lv+yq egT+grkl
  EPA04516.1   1 MLVGGNATYYLQELSFNKNNGIALVSYQGEGTPGRKL 37 
                 999********************************97 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   5.4e-06     0.032     187     218 ..      70     101 ..      52     109 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.4e-06
                 HHHHHHHCTT-HHHHHHHHHHHC-TCSCCHHH CS
      NB-ARC 187 akeivekckGlPlalkvlggllstkktveewk 218
                 + e+v+k kG+P +l v g++ s+kk+ +e +
  EPA04516.1  70 LFEVVNKIKGNPKVLTVHGDMESCKKFAQEIH 101
                 679*************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.53
# Mc/sec: 675.76
//
Query:       EPA04517.1  [L=508]
Description: putative archaeosine tRNA-ribosyltransferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-68  231.3   0.0    2.3e-68  230.9   0.0    1.1  1  TGT       Queuine tRNA-ribosyltransferase
    1.4e-10   41.2   0.2    2.7e-10   40.3   0.2    1.4  1  DUF5591   Domain of unknown function (DUF5591)


Domain annotation for each model (and alignments):
>> TGT  Queuine tRNA-ribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  230.9   0.0   2.6e-72   2.3e-68       3     349 ..      16     338 ..      12     339 .. 0.96

  Alignments for each domain:
  == domain 1  score: 230.9 bits;  conditional E-value: 2.6e-72
                 EEEEEEEETTEEEEESEEEEBETTSSBTTB-HHHHH.HTTES-EEEEHHHHHHTTTHHHHHHTTHHHHHHT--S-EEEE-SHHHHHHHEEEESSEEEEE CS
         TGT   3 aRlGklelphgtietPafmpvgtqgtvkgltpdelkeelgaqiilsntyhlelrpgeelvakagglhkflgwdkpiltdsggfqvfslkkiteegvsfq 101
                 +R+G ++++hg+ietPa++pv  ++  +++ +++++ e+g +++++n+y+++++ g+e   + +g+hk++++d++i+tdsgg+qv++            
  EPA04517.1  16 GRIGIIHTNHGKIETPAYVPV-IHPVKQTIPSKKIR-EIGFDLVITNAYITRNNYGDEA--EKKGIHKIIDFDGAIMTDSGGYQVLE------------ 98 
                 8********************.9999999******5.9**************9999988..788********************886............ PP

                 -TTTS-EEEE-HHHHHHHHHHHT-SEEE-------SS--HHHHHHHHHHHHHHHHHHHHHH....SEEEEEE--TT-HHHHHHHHHHHHHH--SEEEE- CS
         TGT 102 sridGskvlltpeesieiqeklgsDiimalddvvpspaskkrveksverTlrwldrcleah....qalfgivqGglyedlreesaeelakrdfdgyaig 196
                   + G+ v++ p e+ ++ +k+  D +++ld+++ +    k++e  v+ Tl+  ++  e      q+++g++qGg + dl ++s + l++++f+++a+g
  EPA04517.1  99 --Y-GD-VKVLPPEMADFEKKILTDFAIPLDKPTGYGLPWKKAESYVNHTLKVSKKTFEDRddngQIWIGPIQGGEHFDLVAKSTKSLVDMGFQMLALG 193
                 ..4.99.***************************************************888999899******************************** PP

                 S.SSSSS..HHHHHHHHHHHHGGGS-TTS-EEETTB-SHHHHHHHHHTT--EEEESHHHHHHHTTEEEETTEEEETTSGGGTT--SBSSSS--SHHHHH CS
         TGT 197 G.lsvge..ekeellevveavtellpedkprylmGvgtPedlleavalGvDmfdcvyptrtarngraltsegelnlknakyaedfspldegCsCytCkn 292
                 + ++++e  e++ l +++ a+++++p + p +l+G+g+P ++  avalG+D fd++ ++++a++gr++t++g+ nl++ ++     p    C+C +C++
  EPA04517.1 194 SpVEFMEsyEYKLLAQMIIAAKKQIPYSIPLHLFGAGHPLTIPFAVALGCDTFDSASYMLYAKQGRYITDDGTRNLEEISVF----P----CNCEVCSK 284
                 *9*****88899****************************************************************988777....9....******99 PP

                 -BHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHT CS
         TGT 293 ytraylhhllktkemlgaiLltiHNlhyylelfkriReaIkegtfeefveefarkye 349
                 yt+ +l++l  +++    + +++HNl+ ++ +++++++aI+eg+++e+v + ar+++
  EPA04517.1 285 YTPDELRQLESNEK---INEIALHNLYAIKLEVDKVKQAIHEGRLWEYVLKKARAHP 338
                 *********87777...9999****************************99999887 PP

>> DUF5591  Domain of unknown function (DUF5591)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.2   3.1e-14   2.7e-10       4     117 ..     382     490 ..     379     505 .. 0.89

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 3.1e-14
                 HHHHHHHH---S..SSEEEEEE--SSSSGGGSHHHHHHHHHS---...SEEEEE-SS-.EEEGGGTT----------------HHHHHHHHHHHHHHHH CS
     DUF5591   4 frervlerYeppeekkvlvLlPcsakkPyseskshrkfaeaikkrkakvheviltsPlGvvPreleevYPaaqYdiavtgewseeeiefvaellakyle 102
                 +++ v++ ++++  kk+l++  +s +kP   s++++ ++++ k+  ++++++ ++  lG++P e+  ++Paa+++     +++ +   + ++++ak+++
  EPA04517.1 382 YHKMVRN-FKSK--KKTLIITKESNTKPAYLSHEYSSLKRKFKDI-ESIQVCQYSPHLGLIPLEISDIFPAAHHESSRL-NFKPNDFPIFENTFAKFFK 475
                 5555555.8777..799***************************9.89*****************************99.8****************** PP

                 HHT-SEEEE---THH CS
     DUF5591 103 ktkyekviahleeey 117
                 ++++++v    ++++
  EPA04517.1 476 NNQFSQVYYDKSDNF 490
                 *****9988777664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (508 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       791  (0.0441185); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 3345.08
//
Query:       EPA04518.1  [L=100]
Description: 4Fe-4S binding domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-11   43.2  10.3    7.8e-06   25.5   0.4    2.2  2  Fer4      4Fe-4S binding domain
    4.5e-09   36.7   3.2    6.5e-09   36.2   3.2    1.2  1  Fer4_7    4Fe-4S dicluster domain
    8.1e-09   35.2   7.3    7.8e-05   22.6   1.6    2.2  2  Fer4_6    4Fe-4S binding domain
    1.2e-08   34.9   1.5    1.7e-08   34.4   1.5    1.2  1  Fer4_21   4Fe-4S dicluster domain
    1.2e-06   28.2   8.3     0.0014   18.6   2.0    2.3  2  Fer4_2    4Fe-4S binding domain
    2.7e-06   27.8   4.5     0.0042   17.6   0.8    2.3  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
    1.2e-05   25.3   8.0    0.00027   21.0   8.6    2.0  2  Fer4_10   4Fe-4S dicluster domain
    1.5e-05   25.0   4.6    8.9e-05   22.6   4.9    1.9  2  Fer4_9    4Fe-4S dicluster domain
    8.6e-05   22.7   7.5      0.022   15.2   2.3    2.2  2  Fer4_4    4Fe-4S binding domain
    0.00016   22.5   3.4       0.28   12.1   0.0    2.2  2  Fer4_16   4Fe-4S double cluster binding domain
    0.00092   20.0   2.4       0.43   11.4   0.5    2.1  2  Fer4_22   4Fe-4S dicluster domain
     0.0019   18.9  10.5     0.0072   17.0   2.6    2.3  2  Fer4_15   4Fe-4S single cluster domain
     0.0023   18.3   5.7      0.025   15.0   5.9    2.0  1  Fer4_8    4Fe-4S dicluster domain
     0.0032   18.3  10.4      0.098   13.6   3.6    2.3  2  Fer4_3    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.028   15.0   7.5        1.2    9.7   7.6    2.1  2  Fer4_17   4Fe-4S dicluster domain
       0.59   10.4   9.7        1.4    9.2   2.5    2.1  2  Fer4_18   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   4.0     1e-07   0.00012       2      18 ..       8      24 ..       7      26 .. 0.92
   2 !   25.5   0.4     7e-09   7.8e-06       2      23 ..      47      68 ..      46      69 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1e-07
                EEETTTSSS-THHHHHS CS
        Fer4  2 videekCigCGaCvevC 18
                 ide +CigC +Cve+C
  EPA04518.1  8 DIDEQRCIGCALCVEIC 24
                69*************** PP

  == domain 2  score: 25.5 bits;  conditional E-value: 7e-09
                EEETTTSSS-THHHHHSTTTEE CS
        Fer4  2 videekCigCGaCvevCPvgAI 23
                v+ +e+Ci  GaC+ vCP+  I
  EPA04518.1 47 VFYPERCISDGACIGVCPTKSI 68
                688****************877 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   3.2   5.8e-12   6.5e-09       1      51 [.      13      66 ..      13      67 .. 0.93

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 5.8e-12
      Fer4_7  1 rCigCgaCvaaCp...vkaieldeeenekgtekveidpekClgCgaCvavCPtg 51
                rCigC  Cv+ C     ++++++++e  k+ +  ++ pe+C++ gaC+ vCPt+
  EPA04518.1 13 RCIGCALCVEICTtlgPDVLRVKPVEGWKRGKAFVFYPERCISDGACIGVCPTK 66
                8***********877789*******999999999******************96 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   1.6     7e-08   7.8e-05       2      19 ..       7      24 ..       6      28 .. 0.92
   2 !   16.0   0.4   8.6e-06    0.0097       6      23 ..      50      67 ..      45      68 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 7e-08
      Fer4_6  2 veidpdkCigCgdCvrvC 19
                + id+++CigC  Cv +C
  EPA04518.1  7 PDIDEQRCIGCALCVEIC 24
                569*************** PP

  == domain 2  score: 16.0 bits;  conditional E-value: 8.6e-06
      Fer4_6  6 pdkCigCgdCvrvCPega 23
                p++Ci+ g+C+ vCP++ 
  EPA04518.1 50 PERCISDGACIGVCPTKS 67
                89*************975 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   1.5   1.6e-11   1.7e-08       3      55 ..       9      67 ..       7      71 .. 0.81

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 1.6e-11
     Fer4_21  3 idedkCigCgkCliaCedtshqaieidaktvl......kvvedeCvGCnlCssvCPved 55
                ide++CigC +C+  C + + + +++++ + +          ++C+    C+ vCP++ 
  EPA04518.1  9 IDEQRCIGCALCVEICTTLGPDVLRVKPVEGWkrgkafVFYPERCISDGACIGVCPTKS 67
                9***********************888776443333225569**************854 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   2.0   1.2e-06    0.0014       5      22 .]       9      26 ..       5      26 .. 0.90
   2 !   13.2   0.5   6.7e-05     0.075       3      22 .]      46      65 ..      44      65 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.2e-06
      Fer4_2  5 vdtdrCigCgaCvsaCPa 22
                +d++rCigC  Cv  C +
  EPA04518.1  9 IDEQRCIGCALCVEICTT 26
                8***************75 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 6.7e-05
      Fer4_2  3 vvvdtdrCigCgaCvsaCPa 22
                +v+ ++rCi+ gaC+ +CP+
  EPA04518.1 46 FVFYPERCISDGACIGVCPT 65
                78999***988********7 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.8   3.7e-06    0.0042       1      17 [.       9      25 ..       9      39 .. 0.89
   2 !   11.9   0.2   0.00023      0.26       4      18 ..      51      65 ..      50      83 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.7e-06
     Fer4_13  1 VDrdtCiacgaCvelaP 17
                +D+++Ci+c++Cve++ 
  EPA04518.1  9 IDEQRCIGCALCVEICT 25
                89*************94 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00023
     Fer4_13  4 dtCiacgaCvelaPd 18
                ++Ci++gaC  ++P 
  EPA04518.1 51 ERCISDGACIGVCPT 65
                79************5 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   8.6   2.4e-07   0.00027       4      56 .]       9      64 ..       6      64 .. 0.83
   2 !   13.2   0.4   6.3e-05     0.071       5      22 ..      49      66 ..      45      82 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.4e-07
     Fer4_10  4 idddtCirCgkCvkaCPadl....tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                id+++Ci+C+ Cv+ C ++l     +v+  +  ++++a    +e+C+  gaC+ +CP
  EPA04518.1  9 IDEQRCIGCALCVEIC-TTLgpdvLRVKPVEGWKRGKAFVFYPERCISDGACIGVCP 64
                89**************.5569997666666666666666779**************9 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 6.3e-05
     Fer4_10  5 dddtCirCgkCvkaCPad 22
                 +++Ci  g+C  +CP++
  EPA04518.1 49 YPERCISDGACIGVCPTK 66
                5799************94 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   2.5   5.7e-05     0.064      33      48 ..      11      26 ..       3      29 .. 0.79
   2 !   22.6   4.9   7.9e-08   8.9e-05       1      50 [.      13      67 ..      13      68 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.7e-05
      Fer4_9 33 eeaCigCgaCveaCpk 48
                e++CigC  Cve+C +
  EPA04518.1 11 EQRCIGCALCVEICTT 26
                358999*999999975 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 7.9e-08
      Fer4_9  1 kCtgCgaCveaC...pagvvvedaaerkarlraase..eaCigCgaCveaCpkga 50
                +C+gC  Cve C     +v + + +e+  r +a+    e+Ci+ gaC+ +Cp++ 
  EPA04518.1 13 RCIGCALCVEICttlGPDVLRVKPVEGWKRGKAFVFypERCISDGACIGVCPTKS 67
                6***********6665566677777777777665559999************985 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   2.3     2e-05     0.022       2      15 ..      12      25 ..      11      28 .. 0.92
   2 !   10.5   0.2   0.00065      0.72       1      16 [.      50      65 ..      50      72 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2e-05
      Fer4_4  2 erCigCgsCvaaCP 15
                +rCigC  Cv +C 
  EPA04518.1 12 QRCIGCALCVEICT 25
                79***********5 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00065
      Fer4_4  1 qerCigCgsCvaaCPq 16
                +erCi  g+C+ +CP+
  EPA04518.1 50 PERCISDGACIGVCPT 65
                69*************7 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   1.2   0.00064      0.72      52      65 ..      12      25 ..       5      27 .. 0.74
   2 !   12.1   0.0   0.00025      0.28       1      17 [.      52      68 ..      52      98 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00064
     Fer4_16 52 eaitgCdiCqdvCP 65
                ++++gC+ C+++C 
  EPA04518.1 12 QRCIGCALCVEICT 25
                56788888888885 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00025
     Fer4_16  1 rCgtCgkCaevCPtnai 17
                rC++ g+C+ vCPt+ i
  EPA04518.1 52 RCISDGACIGVCPTKSI 68
                69999*********998 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.5   0.00039      0.43      76      93 ..       8      25 ..       3      27 .. 0.83
   2 !    8.7   0.1    0.0027       3.1       1      21 [.      52      72 ..      52      86 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00039
     Fer4_22 76 kfgesgCvGCgRCieacp 93
                 ++e+ C+GC  C+e c+
  EPA04518.1  8 DIDEQRCIGCALCVEICT 25
                568899999999999997 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0027
     Fer4_22  1 rClsCgaCtlvCptCsCfdve 21
                rC+s gaC  vCpt s f ++
  EPA04518.1 52 RCISDGACIGVCPTKSIFWMR 72
                7*************8877665 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   2.6   6.4e-06    0.0072       3      20 ..       9      26 ..       8      47 .. 0.83
   2 ?    6.7   1.1     0.011        12       6      20 ..      51      65 ..      46      69 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.4e-06
     Fer4_15  3 vDrdaCigcglCvaeape 20
                +D+++Cigc+lCv+ +++
  EPA04518.1  9 IDEQRCIGCALCVEICTT 26
                8**************954 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.011
     Fer4_15  6 daCigcglCvaeape 20
                ++Ci++g+C+ ++p+
  EPA04518.1 51 ERCISDGACIGVCPT 65
                79**********985 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   5.9   2.2e-05     0.025       3      64 ..      12      66 ..      10      68 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.2e-05
      Fer4_8  3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64
                ++Ci+C +C + C +l     + +  +g + + +    +       ++C + gaC  vCp++
  EPA04518.1 12 QRCIGCALCVEICTTLGPDVLRVKPVEGWKRG-KAFVFY------PERCISDGACIGVCPTK 66
                58***********7776666666666666555.333333......799************86 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   3.6   8.8e-05     0.098       1      12 [.      14      25 ..      14      28 .. 0.92
   2 !    8.9   0.6    0.0028       3.2       1      14 [.      53      66 ..      52      67 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.8e-05
      Fer4_3  1 CtgCgaCvevCP 12
                C+gC +Cve C 
  EPA04518.1 14 CIGCALCVEICT 25
                ***********6 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0028
      Fer4_3  1 CtgCgaCvevCPvg 14
                C+  gaC  vCP++
  EPA04518.1 53 CISDGACIGVCPTK 66
                55558*******87 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   7.6    0.0011       1.2       1      58 [.      13      65 ..      13      67 .. 0.72
   2 ?    6.9   0.4    0.0082       9.1       1      15 [.      52      66 ..      52      82 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0011
     Fer4_17  1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPq 58
                rCi+C+ C++ C ++      + k+++      +++     + ++Ci+ g C  +CP 
  EPA04518.1 13 RCIGCALCVEICTTLGPDVL-RVKPVEG----WKRGKAFVFYPERCISDGACIGVCPT 65
                7*********8877655433.3344444....44444456899*************96 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0082
     Fer4_17  1 rCiqCgyClpeCpsy 15
                rCi+ g+C+ +Cp+ 
  EPA04518.1 52 RCISDGACIGVCPTK 66
                466666666666654 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   2.5    0.0012       1.4      84      98 ..      13      27 ..       8      43 .. 0.73
   2 ?    5.9   0.8     0.012        14      60      74 ..      52      66 ..      41      69 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0012
     Fer4_18 84 eciscllcidacdkv 98
                 ci c+lc++ c+++
  EPA04518.1 13 RCIGCALCVEICTTL 27
                477777777777654 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.012
     Fer4_18 60 dcidcescvkvcPtg 74
                 ci+ ++c+ vcPt+
  EPA04518.1 52 RCISDGACIGVCPTK 66
                699999*******95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 675.42
//
Query:       EPA04519.1  [L=310]
Description: thrombospondin type 3 repeat protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-29  100.3  96.6    2.8e-05   23.7   2.8   12.5 12  TSP_3            Thrombospondin type 3 repeat
     0.0076   16.2  14.8         14    5.7   0.1    7.5  8  DUF282           Caenorhabditis protein of unknown function, 
     0.0091   15.7   2.7       0.61    9.7   0.2    2.8  2  ChitinaseA_N     Chitinase A, N-terminal domain
  ------ inclusion threshold ------
        0.2   11.8   0.4         39    4.4   0.0    3.5  4  AKAP7_RIRII_bdg  PKA-RI-RII subunit binding domain of A-kinas


Domain annotation for each model (and alignments):
>> TSP_3  Thrombospondin type 3 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   2.8   6.3e-09   2.8e-05      14      34 ..      11      31 ..      10      33 .. 0.93
   2 ?   -0.5   0.2      0.22   9.9e+02      16      24 ..      36      44 ..      32      46 .. 0.75
   3 !   18.6   2.9   2.5e-07    0.0011      14      34 ..      52      72 ..      39      74 .. 0.89
   4 !   19.1   4.1   1.8e-07   0.00079      14      34 ..      90     110 ..      77     112 .. 0.84
   5 ?   -1.0   0.3      0.32   1.4e+03      17      24 ..     116     123 ..     113     125 .. 0.75
   6 !   19.3   2.1   1.5e-07   0.00067      15      33 ..     135     153 ..     133     156 .. 0.92
   7 ?   -1.2   0.1      0.38   1.7e+03      25      32 ..     161     168 ..     160     171 .. 0.71
   8 !   21.3   1.0   3.5e-08   0.00016      15      33 ..     177     195 ..     176     198 .. 0.92
   9 ?   -2.1   1.9       0.7   3.2e+03      17      24 ..     202     209 ..     201     211 .. 0.79
  10 !   19.9   0.9   9.9e-08   0.00044      15      31 ..     217     233 ..     212     237 .. 0.90
  11 !   18.7   4.1   2.3e-07     0.001      14      34 ..     257     277 ..     241     279 .. 0.87
  12 !   12.2   5.2   2.5e-05      0.11      13      29 ..     294     310 .]     282     310 .] 0.78

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 6.3e-09
       TSP_3 14 kDfDnDgvqddlDNCprnani 34
                +D+D+Dg++dd D Cp+n+++
  EPA04519.1 11 TDIDGDGIPDDKDACPYNPET 31
                6*****************986 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.22
       TSP_3 16 fDnDgvqdd 24
                +D Dg +d+
  EPA04519.1 36 QDTDGCPDS 44
                578888775 PP

  == domain 3  score: 18.6 bits;  conditional E-value: 2.5e-07
       TSP_3 14 kDfDnDgvqddlDNCprnani 34
                +D D+Dg+ d++D Cp+ +++
  EPA04519.1 52 ADSDGDGILDKVDKCPTQPET 72
                79****************987 PP

  == domain 4  score: 19.1 bits;  conditional E-value: 1.8e-07
       TSP_3  14 kDfDnDgvqddlDNCprnani 34 
                  D+D Dg++d++D Cp n+++
  EPA04519.1  90 LDTDRDGIPDVVDACPLNPEV 110
                 6*****************986 PP

  == domain 5  score: -1.0 bits;  conditional E-value: 0.32
       TSP_3  17 DnDgvqdd 24 
                 D Dg +d+
  EPA04519.1 116 DDDGCPDV 123
                 78888875 PP

  == domain 6  score: 19.3 bits;  conditional E-value: 1.5e-07
       TSP_3  15 DfDnDgvqddlDNCprnan 33 
                 D+D+Dg++d  D Cp+ ++
  EPA04519.1 135 DADGDGIPDIKDACPNEPE 153
                 9***************997 PP

  == domain 7  score: -1.2 bits;  conditional E-value: 0.38
       TSP_3  25 lDNCprna 32 
                  D Cp ++
  EPA04519.1 161 WDGCPDTP 168
                 47888877 PP

  == domain 8  score: 21.3 bits;  conditional E-value: 3.5e-08
       TSP_3  15 DfDnDgvqddlDNCprnan 33 
                 D+D Dg++d++D Cp++a+
  EPA04519.1 177 DADHDGIPDNVDQCPTVAE 195
                 9****************97 PP

  == domain 9  score: -2.1 bits;  conditional E-value: 0.7
       TSP_3  17 DnDgvqdd 24 
                 D Dg +dd
  EPA04519.1 202 DDDGCPDD 209
                 88999987 PP

  == domain 10  score: 19.9 bits;  conditional E-value: 9.9e-08
       TSP_3  15 DfDnDgvqddlDNCprn 31 
                 D+DnDg++d++D Cp +
  EPA04519.1 217 DADNDGIPDNVDKCPLV 233
                 99*************76 PP

  == domain 11  score: 18.7 bits;  conditional E-value: 2.3e-07
       TSP_3  14 kDfDnDgvqddlDNCprnani 34 
                 +D+D+Dg+ d+lD Cp+ +++
  EPA04519.1 257 ADTDGDGITDSLDLCPTQPET 277
                 7*****************987 PP

  == domain 12  score: 12.2 bits;  conditional E-value: 2.5e-05
       TSP_3  13 dkDfDnDgvqddlDNCp 29 
                   D+D Dg++d++D Cp
  EPA04519.1 294 TLDTDRDGIPDVVDACP 310
                 57**************9 PP

>> DUF282  Caenorhabditis protein of unknown function, DUF282
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.7   0.1    0.0064        29      15      28 ..      15      28 ..      11      36 .. 0.85
   2 ?   -1.8   0.0       0.7   3.1e+03      15      29 ..      56      70 ..      55      72 .. 0.81
   3 ?    1.1   0.0     0.088     4e+02      17      31 ..      96     110 ..      95     113 .. 0.84
   4 !    5.7   0.1    0.0032        14      15      28 ..     138     151 ..     134     154 .. 0.88
   5 ?    4.1   0.0      0.01        45      17      30 ..     182     195 ..     181     196 .. 0.90
   6 ?    0.9   0.0       0.1   4.6e+02      17      27 ..     222     232 ..     221     240 .. 0.83
   7 ?    1.8   0.0     0.053   2.4e+02      15      30 ..     261     276 ..     258     278 .. 0.88
   8 ?   -1.0   0.1      0.38   1.7e+03      17      26 ..     301     310 .]     300     310 .] 0.90

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0064
      DUF282 15 GvgiPslsdwCata 28
                G giP+ +d C+  
  EPA04519.1 15 GDGIPDDKDACPYN 28
                99*********976 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.7
      DUF282 15 GvgiPslsdwCataa 29
                G gi +  d C+t+ 
  EPA04519.1 56 GDGILDKVDKCPTQP 70
                7888899999**975 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.088
      DUF282  17 giPslsdwCataaev 31 
                 giP+  d C+   ev
  EPA04519.1  96 GIPDVVDACPLNPEV 110
                 99*******977665 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.0032
      DUF282  15 GvgiPslsdwCata 28 
                 G giP+ +d C+ +
  EPA04519.1 138 GDGIPDIKDACPNE 151
                 99*********987 PP

  == domain 5  score: 4.1 bits;  conditional E-value: 0.01
      DUF282  17 giPslsdwCataae 30 
                 giP++ d C+t ae
  EPA04519.1 182 GIPDNVDQCPTVAE 195
                 9*********9876 PP

  == domain 6  score: 0.9 bits;  conditional E-value: 0.1
      DUF282  17 giPslsdwCat 27 
                 giP++ d C+ 
  EPA04519.1 222 GIPDNVDKCPL 232
                 9********96 PP

  == domain 7  score: 1.8 bits;  conditional E-value: 0.053
      DUF282  15 GvgiPslsdwCataae 30 
                 G gi +++d C+t+ e
  EPA04519.1 261 GDGITDSLDLCPTQPE 276
                 99**********9865 PP

  == domain 8  score: -1.0 bits;  conditional E-value: 0.38
      DUF282  17 giPslsdwCa 26 
                 giP+  d C+
  EPA04519.1 301 GIPDVVDACP 310
                 9********7 PP

>> ChitinaseA_N  Chitinase A, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.0   0.2     0.004        18      93     113 ..      37      57 ..      30      71 .. 0.88
   2 !    9.7   0.2   0.00014      0.61      93     114 ..     242     263 ..     232     273 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.004
  ChitinaseA_N  93 daeGCsksapkeivvaDtDGs 113
                   d++GC +s p+    aD DG 
    EPA04519.1  37 DTDGCPDSIPADKSAADSDGD 57 
                   89*****************96 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00014
  ChitinaseA_N  93 daeGCsksapkeivvaDtDGsh 114
                   d++GC +s p+    aDtDG  
    EPA04519.1 242 DTDGCPDSVPSDKLTADTDGDG 263
                   89******************75 PP

>> AKAP7_RIRII_bdg  PKA-RI-RII subunit binding domain of A-kinase anchor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0    0.0088        39      27      45 ..      27      45 ..      23      58 .. 0.73
   2 ?   -3.7   0.0       3.1   1.4e+04      30      42 ..      71      83 ..      71      84 .. 0.85
   3 ?    3.2   0.0     0.021        95      29      43 ..     234     248 ..     232     262 .. 0.82
   4 ?   -1.8   0.0      0.78   3.5e+03      30      45 ..     276     291 ..     275     301 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0088
  AKAP7_RIRII_bdg 27 YLEETqnkarqadGssvKa 45
                     Y  ET nk + +dG +   
       EPA04519.1 27 YNPETYNKYQDTDGCPDSI 45
                     6679**********98654 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 3.1
  AKAP7_RIRII_bdg 30 ETqnkarqadGss 42
                     ET n  + +dG +
       EPA04519.1 71 ETFNGYQDTDGCP 83
                     7889999999987 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.021
  AKAP7_RIRII_bdg  29 EETqnkarqadGssv 43 
                       ET nk + +dG + 
       EPA04519.1 234 KETYNKYQDTDGCPD 248
                      69**********984 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 0.78
  AKAP7_RIRII_bdg  30 ETqnkarqadGssvKa 45 
                      ET n  +  dG + K 
       EPA04519.1 276 ETFNGYQDKDGCPDKF 291
                      899999999**99885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       213  (0.0118802); expected 358.6 (0.02)
Passed bias filter:                      159  (0.00886831); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2237.01
//
Query:       EPA04520.1  [L=206]
Description: Kae1-associated kinase Bud32 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-10   41.0   0.0      2e-10   40.6   0.0    1.2  1  RIO1         RIO1 family
      1e-08   34.8   0.1    7.5e-08   32.0   0.1    2.0  1  Kdo          Lipopolysaccharide kinase (Kdo/WaaP) family
    2.4e-07   30.4   1.0    2.9e-07   30.1   1.0    1.2  1  Pkinase      Protein kinase domain
    7.6e-06   26.0   0.0      0.033   14.1   0.0    2.1  2  APH          Phosphotransferase enzyme family
    0.00038   19.8   0.5     0.0013   18.1   0.0    2.0  2  Pkinase_Tyr  Protein tyrosine kinase
     0.0011   18.6   1.5     0.0019   17.8   1.4    1.6  1  WaaY         Lipopolysaccharide core biosynthesis protein (Wa
     0.0061   15.5   0.1     0.0098   14.8   0.1    1.4  1  DUF1679      Protein of unknown function (DUF1679)
  ------ inclusion threshold ------
      0.092   12.9   0.1        1.8    8.7   0.0    2.5  3  PIF6         Per os infectivity factor 6


Domain annotation for each model (and alignments):
>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.0     9e-14     2e-10      47     162 ..      38     150 ..      17     167 .. 0.82

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 9e-14
                 HHHHHHHHHHHHHHHHHHHHHTT--S--EE..EEETTEEEEE--EETTEEGGBHHHCG-HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETTE CS
        RIO1  47 prklvklwaekEfrnLkrleeagvpvPkpi..elkrhvlvmefigedgvaapklkdveeeeeaeelyeevleemrklykeaglvHaDLSeyNvlvdedk 143
                   k+ k  + +E + ++++++ g+p P ++  +lk+ +++m+ i+  g ++ +l d +    + +l +e+ + +  +++++gl H+DL   N ++ +++
  EPA04520.1  38 DSKIRKQRTIRESQTISEVKSFGIPTPLVYnvDLKKSAIIMQEIQ--GKPIHDLPDSK----IIDLCKEIGR-LVGIMHKNGLMHGDLTTSNFIYFKNQ 129
                 45677788899****************98622579**********..99999999988....6778888888.566777******************** PP

                 EEE--G..TTEEETTSTTHHH CS
        RIO1 144 vviIDv..sQaveldhpnale 162
                 v++ID+  sQ + +++++a +
  EPA04520.1 130 VFVIDFglSQKTIKSEDHAVD 150
                 *****7447988888888876 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.1   3.3e-11   7.5e-08      53     207 .]      41     177 ..      14     177 .. 0.77

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 3.3e-11
         Kdo  53 lgrtravrEfrllkrLeeagvavpkpvaagavkvgleyrAlllterlegaqdLedllakwaelaeelkrallkavgrliaklhragvnHadlyaknill 151
                 + + r  rE + + + ++ g+++p    ++   v+l  ++++++ +++g   +        +l++++   l k++grl+  +h+ g++H+dl   n+  
  EPA04520.1  41 IRKQRTIRESQTISEVKSFGIPTPLV--YN---VDL-KKSAIIMQEIQGK-PIH-------DLPDSKIIDLCKEIGRLVGIMHKNGLMHGDLTTSNFIY 125
                 77788888888888888888877643..22...233.3566777777763.222.......24445667899************************888 PP

         Kdo 152 qqeeeeeaeiwliDldkarlrlradrwrekdLarLkrsfl..kielteadweallraY 207
                  +++     + +iD+  +++ + +  +   dL+ +k  ++  + ++ +  w+++l++Y
  EPA04520.1 126 FKNQ-----VFVIDFGLSQKTI-KSEDHAVDLRLIKEILNsaHAKIMKSCWKNFLSGY 177
                 7776.....9*********999.9999999**999998888888999999*****999 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   1.0   1.3e-10   2.9e-07      37     153 ..      38     146 ..       2     167 .. 0.78

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 1.3e-10
                 HCHHHHHHHHHHHHHHHHHSCTTB--EEEEEEESSEEEEEEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTT CS
     Pkinase  37 akkkkekkvlrEikilkklkhpnivrlyevfeekdelylvleyveggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekg 135
                 ++k ++++++rE + + ++k+  i + + +  + ++  ++++ ++g+ ++d       l+++++ +++k+i + +  +H++g++H Dl ++N+++  k+
  EPA04520.1  38 DSKIRKQRTIRESQTISEVKSFGIPTPLVYNVDLKKSAIIMQEIQGKPIHD-------LPDSKIIDLCKEIGRLVGIMHKNGLMHGDLTTSNFIYF-KN 128
                 334444899999999999999999988888888777777888888775555.......56799********************************9.99 PP

                 EEEE-SGTTSEESSSSCS CS
     Pkinase 136 elKitDFGlakelesssk 153
                 ++ ++DFGl+++  +s++
  EPA04520.1 129 QVFVIDFGLSQKTIKSED 146
                 9*********99888764 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0    0.0002      0.45       5     106 ..       4     109 ..       1     111 [. 0.62
   2 !   14.1   0.0   1.5e-05     0.033     166     196 ..     111     138 ..     108     151 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0002
                 E--.SSCEEEEEEETT--EEEEE......E-TTS-HHHHH.....HHHHHHHHHHHTT-B--B-CTTBS-EEETTEEEEEEE----EE-SSHHHHHHHH CS
         APH   5 lsggasnrtylvttpagryvlrr......npparaaeeir.....revallrlLakagvpvPevlagdtddeeigllfalieyvpgrsllrklsaaqlp 92 
                 l+ ga+ + yl++++++r +l++       +p  ++ +ir     re +    +   g+p+P v+  d         + +++ + g+++++ l ++ + 
  EPA04520.1   4 LKKGAEADIYLIQWEGTRAILKIrktkkyRNPV-LDSKIRkqrtiRESQTISEVKSFGIPTPLVYNVDL-----KKSAIIMQEIQGKPIHD-LPDSKII 95 
                 789********************6666663333.44444433333444455566777779999999433.....33344455555555555.3346677 PP

                 HHHHHHHHHHCCHH CS
         APH  93 ellealgeflaalh 106
                 +l+ ++g++ + +h
  EPA04520.1  96 DLCKEIGRLVGIMH 109
                 77777777766666 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 1.5e-05
                 EEEE-SS-SGGGEEEC..TTEEEEE---TT- CS
         APH 166 tvllHgDlhpgNllvdpddgrvtGviDfeda 196
                  +l+HgDl + N++    +++v  viDf+++
  EPA04520.1 111 NGLMHGDLTTSNFIYF--KNQV-FVIDFGLS 138
                 589*************..5555.5****986 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   5.6e-07    0.0013      98     158 ..      87     146 ..       4     155 .. 0.82
   2 ?   -0.2   0.1      0.22   4.8e+02     233     244 ..     161     172 ..     153     175 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 5.6e-07
                  TTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETTEEEE-STTTHEETTTSSE CS
  Pkinase_Tyr  98 ekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenkvvkisDfGLardiekdde 158
                  + l  +++++++ ++ + +  ++++ l+H dl++ N +   +++v + DfGL++++ k+++
   EPA04520.1  87 HDLPDSKIIDLCKEIGRLVGIMHKNGLMHGDLTTSNFIYF-KNQVFVIDFGLSQKTIKSED 146
                  5667788999**************************8887.6677888*****99865554 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.22
                  HHHHHHHHHT-S CS
  Pkinase_Tyr 233 elyelmkkcwee 244
                  + +++mk+cw++
   EPA04520.1 161 AHAKIMKSCWKN 172
                  5679******85 PP

>> WaaY  Lipopolysaccharide core biosynthesis protein (WaaY)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   1.4   8.6e-07    0.0019     119     191 ..      75     150 ..       1     174 [. 0.78

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 8.6e-07
        WaaY 119 imiieyiegielvdmpeid.devkakikqsieklhqlgmvsgdphrgnfivkkdevriid..lsgkrasaerkakd 191
                  +i++ i+g  + d+p+ +  ++ ++i + +  +h+ g++ gd    nfi  k++v +id  ls k+  +e +a d
  EPA04520.1  75 AIIMQEIQGKPIHDLPDSKiIDLCKEIGRLVGIMHKNGLMHGDLTTSNFIYFKNQVFVIDfgLSQKTIKSEDHAVD 150
                 4677889*********8652467889*********************************95567777777766665 PP

>> DUF1679  Protein of unknown function (DUF1679)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   4.4e-06    0.0098     249     299 ..      90     136 ..      77     181 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.4e-06
     DUF1679 249 keililekaskvskvlGi..kkvlvhgDlwsaNiLfseeeegklklkkviDyQ 299
                 ++ +i++  +++ +++Gi  k+ l+hgDl  +N+++ +++        viD+ 
  EPA04520.1  90 PDSKIIDLCKEIGRLVGImhKNGLMHGDLTTSNFIYFKNQV------FVIDFG 136
                 6778899999*******99999**************99543......455554 PP

>> PIF6  Per os infectivity factor 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0    0.0008       1.8      35      71 ..      43      79 ..      33     101 .. 0.80
   2 ?   -0.7   0.0       0.7   1.6e+03      59      79 ..     135     155 ..     107     167 .. 0.66
   3 ?    1.1   0.0      0.18   4.1e+02      15      31 ..     163     179 ..     149     197 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0008
        PIF6 35 ldrtfRtgltvadlenFDykqPlyvnlktktlsssde 71
                 +rt R   t +++++F   +Pl++n+  k+ ++  +
  EPA04520.1 43 KQRTIRESQTISEVKSFGIPTPLVYNVDLKKSAIIMQ 79
                47999********************987776555334 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.7
        PIF6  59 vnlktktlsssdesirealna 79 
                 + l +kt+ s+d+++ + l++
  EPA04520.1 135 FGLSQKTIKSEDHAVDLRLIK 155
                 247889999999988887765 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.18
        PIF6  15 pedRelaWkellielak 31 
                  +  +++Wk++l    +
  EPA04520.1 163 AKIMKSCWKNFLSGYKS 179
                 555689****9976655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1276.99
//
Query:       EPA04521.1  [L=41]
Description: hypothetical protein BG20_I1165 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       199  (0.0110993); expected 358.6 (0.02)
Passed bias filter:                      170  (0.00948185); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 286.83
//
Query:       EPA04522.1  [L=202]
Description: Tat pathway signal sequence domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.4e-06   27.4   0.0    3.4e-06   26.9   0.0    1.3  1  Rieske      Rieske [2Fe-2S] domain
    5.3e-05   22.9   1.0    5.3e-05   22.9   1.0    1.6  2  TAT_signal  TAT (twin-arginine translocation) pathway signal 
     0.0016   17.7   0.1     0.0034   16.7   0.1    1.5  1  UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit T


Domain annotation for each model (and alignments):
>> Rieske  Rieske [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   5.8e-10   3.4e-06      34      82 ..     109     158 ..      61     169 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 5.8e-10
                 S-EEEEESC-TTTT-BCGGSEEETT.EEE-TTT--EEE.TTSBEEE-TTH CS
      Rieske  34 gevyAlsdvCtHrgaplsegkidekgvleCpcHgwayd.adGkvikgPap 82 
                  +++A+s vC H+ +  +    +++++ eCpcHg+ yd ++G + +gPa 
  EPA04522.1 109 SSFRAYSMVCLHLWCLWKYWPEEGRKRGECPCHGSMYDaRTGLAFAGPAS 158
                 4678************855333345588**************99999986 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   1.0   8.8e-09   5.3e-05       2      21 ..      12      31 ..      11      35 .. 0.73
   2 ?   -3.0   0.4       1.3   7.8e+03      18      25 ..     151     158 ..     150     159 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 8.8e-09
  TAT_signal  2 lSRRdFLKgsAAaaAAaalg 21
                lSRRdFLK  +Aa+ ++a++
  EPA04522.1 12 LSRRDFLKLMGAAGTGLAFA 31
                8*******666666666665 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.3
  TAT_signal  18 aalggcaa 25 
                 +a++g+a+
  EPA04522.1 151 LAFAGPAS 158
                 68888876 PP

>> UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   5.7e-07    0.0034       4      35 ..       7      34 ..       5      38 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.7e-07
  UCR_Fe-S_N  4 aesdeptRRDFLyiATgavgaVGaaaaawPfi 35
                ++s++ +RRDFL      +ga G+++a+ Pf+
  EPA04522.1  7 KKSGGLSRRDFL----KLMGAAGTGLAFAPFV 34
                5678889*****....88*************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1263.17
//
Query:       EPA04523.1  [L=182]
Description: hypothetical protein BG20_I1176 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-10   41.9   0.3    2.9e-10   40.8   0.1    1.7  2  AAA_18           AAA domain
    0.00046   20.6   0.0     0.0014   19.1   0.0    1.8  2  AAA              ATPase family associated with various cellul
     0.0074   15.8   0.2      0.014   14.9   0.1    1.6  1  KTI12            Chromatin associated protein KTI12
     0.0082   16.1   1.7      0.016   15.1   0.1    2.2  2  NTPase_1         NTPase
  ------ inclusion threshold ------
      0.013   15.6   0.0       0.32   11.1   0.0    2.2  2  Cytidylate_kin2  Cytidylate kinase-like family
      0.029   13.8   0.0       0.03   13.8   0.0    1.1  1  Sulfotransfer_1  Sulfotransferase domain
      0.033   13.9   0.1       0.25   11.1   0.0    2.0  2  Cytidylate_kin   Cytidylate kinase
      0.044   13.5   0.1        0.1   12.3   0.0    1.7  2  CoaE             Dephospho-CoA kinase
       0.05   14.0   0.1      0.096   13.1   0.1    1.7  1  AAA_17           AAA domain
      0.071   13.5   0.0      0.071   13.5   0.0    1.5  1  AAA_16           AAA ATPase domain
       0.08   12.9   0.0       0.18   11.8   0.0    1.7  2  AAA_5            AAA domain (dynein-related subfamily)
       0.16   11.7   0.0       0.28   10.9   0.0    1.4  1  Sigma54_activat  Sigma-54 interaction domain
       0.16   12.2   0.0       0.91    9.8   0.0    2.0  2  AAA_22           AAA domain


Domain annotation for each model (and alignments):
>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   0.1   2.1e-13   2.9e-10       1     129 [.       3     119 ..       3     120 .. 0.87
   2 ?   -2.9   0.0       6.7   9.2e+03      16      32 ..     146     164 ..     140     175 .. 0.48

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 2.1e-13
      AAA_18   1 IlltGtpGvGKttlakeLskrlgf.gvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleegknlvidghlaeleseaakdikkvv 98 
                 I++tG pGvGK ++ ke+sk l++  + ++++ak+ +l +e+d+      + +d     kl ++++e +s     ++ +i ghla ++  ++k++k +v
  EPA04523.1   3 IVITGNPGVGKHSIVKEISKQLKLpIIDINSIAKDAELFEENDDT-----NDVDVS---KLKKIIKEKIS-----SPSLIVGHLAPYVISSDKINKVIV 88 
                 99********************88999999999998888888888.....444444...46667777765.....888**********999999999** PP

      AAA_18  99 LtaspeelleRlekRgyeeakikeneeaeil 129
                 L+ +p  l+   +kR+y++ k+++n  +eil
  EPA04523.1  89 LRRNPYDLISVYKKREYSDEKTRDNAGSEIL 119
                 **********************999998887 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6.7
      AAA_18  16 keLskrlgf..gvnlrdva 32 
                 + L+k l +  g n+++ +
  EPA04523.1 146 EVLKKVLSIinGKNSNEEV 164
                 4443333333444444333 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   9.8e-07    0.0014       2      37 ..       4      39 ..       3      94 .. 0.79
   2 ?   -0.9   0.0       1.5   2.1e+03      28      48 ..     133     153 ..      96     168 .. 0.57

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 9.8e-07
                EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS CS
         AAA  2 llyGppGtGKTllakavakelgvefleisgsellsk 37
                +++G+pG+GK +++k + k+l+ +++ i+      +
  EPA04523.1  4 VITGNPGVGKHSIVKEISKQLKLPIIDINSIAKDAE 39
                689***********************9998665555 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.5
                 EEETTTCSSSSTTHHHHHHHH CS
         AAA  28 eisgsellskyvgesekkire 48 
                 ++s  +++ k ++e  kk+  
  EPA04523.1 133 KVSQVDVTGKSISEVLKKVLS 153
                 333333333333333333333 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1     1e-05     0.014       4      63 ..       3      62 ..       1      94 [. 0.81

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1e-05
                EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH.TTSSS--GGGHHHHHHHHHHH CS
       KTI12  4 vvltGlPssGKstrakeLakaleeekrsvvviddeslgiekdsykdsakekalRsslrsa 63
                +v+tG P +GK +++ke++k+l+   +++  i +++  +e+++ ++  +  +l++ ++++
  EPA04523.1  3 IVITGNPGVGKHSIVKEISKQLKLPIIDINSIAKDAELFEENDDTNDVDVSKLKKIIKEK 62
                89**********************999999998888888887744444444444444444 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   1.1e-05     0.016       2      24 ..       3      25 ..       2      35 .. 0.92
   2 ?   -0.8   0.1      0.94   1.3e+03     116     128 ..     142     154 ..     116     179 .. 0.54

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.1e-05
                EEEE--TTSSHHHHHHHHHHHH. CS
    NTPase_1  2 vfiTGppGvGKtTlvkkvlellk 24
                ++iTG+pGvGK  +vk ++++lk
  EPA04523.1  3 IVITGNPGVGKHSIVKEISKQLK 25
                89******************996 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.94
                 HHHHHHHTTTSEE CS
    NTPase_1 116 eaveevLksekpv 128
                 +++ evLk+   +
  EPA04523.1 142 KSISEVLKKVLSI 154
                 3333334333333 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00023      0.32       2      40 ..       3      41 ..       2      48 .. 0.84
   2 ?    2.9   0.0     0.074     1e+02      79     116 ..      49      84 ..      36     114 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00023
  Cytidylate_kin2  2 ITIsreyGsgGetigeaLAekLglpfydreiieevakel 40
                     I I+++ G g++ i ++++++L+lp++d + i++ a+ +
       EPA04523.1  3 IVITGNPGVGKHSIVKEISKQLKLPIIDINSIAKDAELF 41
                     7799************************87776666555 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.074
  Cytidylate_kin2  79 delfeaqervirelaaeesvVivGRgadliLkdrpnvl 116
                      d  +   +++i+e  ++ +  ivG  a ++    + + 
       EPA04523.1  49 DVDVSKLKKIIKEKISS-PSLIVGHLAPYVISSDK-IN 84 
                      333445599*****988.99********9998754.44 PP

>> Sulfotransfer_1  Sulfotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.2e-05      0.03      66     136 ..      48     114 ..      11     161 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.2e-05
                      HHHTTTEEHHHHHHHSTSS.EEEE...GGGS.CHHHHTT-EEEEEE--HHHHHHHHHHHHHHBTTSTTT-S CS
  Sulfotransfer_1  66 rsyshvaekvvrlralesprllktHlplkllpkslldsnlKiiylvRnpkdvavSryhfsrslkklkepet 136
                      +  + ++ k+   ++ +sp l++ Hl  +++     d+  K+i+l Rnp d ++S y     +++   +++
       EPA04523.1  48 NDVDVSKLKKIIKEKISSPSLIVGHLAPYVI---SSDKINKVIVLRRNPYD-LISVYKKREYSDEKTRDNA 114
                      55566677777788999**************...447889***********.6799999888876555554 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00018      0.25       1      60 [.       3      62 ..       3      89 .. 0.86
   2 ?    0.8   0.0      0.25   3.5e+02     190     209 ..     136     155 ..     127     157 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00018
                    EEEE-STTSSHHHHHHHHHHHHT-EEEEHHHHHHHHHHHHHHTT--TT-HHHHHHHHHT- CS
  Cytidylate_kin  1 iaiDGPagsGKssvaralaeklglkyldtgalYRalalaalrrkvdlldeaalvelakev 60
                    i i G  g GK s+ ++++++l+l ++d  ++ +   l   + +++ +d+++l +++ke 
      EPA04523.1  3 IVITGNPGVGKHSIVKEISKQLKLPIIDINSIAKDAELFEENDDTNDVDVSKLKKIIKEK 62
                    6788999*******************************9999999999999999998764 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.25
                     EEETTTS-HHHHHHHHHHHH CS
  Cytidylate_kin 190 iidtskltieevvekileli 209
                      +d + ++i+ev++k+l+ i
      EPA04523.1 136 QVDVTGKSISEVLKKVLSII 155
                     69999***********9887 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   7.4e-05       0.1       3      37 ..       3      38 ..       1      64 [. 0.82
   2 ?   -2.3   0.0       2.1   2.9e+03      20      48 ..     127     155 ..     122     163 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.4e-05
                EEEEESTTSSHHHHHHHHHH.TT-EEEEHHHHHHHT CS
        CoaE  3 vgltGgiasGKstvanlfad.lgvpivDaDlvArqv 37
                + +tG+ + GK  + + +++ l++pi+D   +A+ +
  EPA04523.1  3 IVITGNPGVGKHSIVKEISKqLKLPIIDINSIAKDA 38
                789********6666555544************976 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.1
                 HHHTT-EEEEHHHHHHHTTCCTHHHHHHH CS
        CoaE  20 fadlgvpivDaDlvArqvvepgsealkki 48 
                 ++++gv++   D+  +++ e  +++l+ i
  EPA04523.1 127 INQFGVKVSQVDVTGKSISEVLKKVLSII 155
                 56778888888888888877777777655 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1     7e-05     0.096       1      66 [.       6      64 ..       6     116 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7e-05
                EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHH CS
      AAA_17  1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemrklpleekkelqkeaaekia 66
                +G PG+GK  +++++ ++++++++     + + ak+ +l +++d+ ++++     +l k+++eki 
  EPA04523.1  6 TGNPGVGKHSIVKEISKQLKLPIID----INSIAKDAELFEENDDTNDVD---VSKLKKIIKEKIS 64
                699*********************9....788888888855555444444...4444455555554 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   5.1e-05     0.071      26      50 ..       2      26 ..       1     171 [. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.1e-05
      AAA_16 26 lvllsGesGvGKsslvrellralek 50
                +++++G++GvGK s+v+e+ ++l+ 
  EPA04523.1  2 SIVITGNPGVGKHSIVKEISKQLKL 26
                689*****************99875 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00013      0.18       2      24 ..       3      25 ..       2      60 .. 0.89
   2 ?   -2.6   0.0       3.7   5.1e+03      79      92 ..     145     158 ..     139     174 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00013
                EEEE--SSSSHHHHHHHGGGGBS CS
       AAA_5  2 vlLvGppGtgKselaerlaaaln 24
                +++ G+pG+gK ++++++++ l+
  EPA04523.1  3 IVITGNPGVGKHSIVKEISKQLK 25
                6899***************9885 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.7
                 HHHHHHHHHHHHSS CS
       AAA_5  79 sevlnsLlslleer 92 
                 sevl+++ls+++ +
  EPA04523.1 145 SEVLKKVLSIINGK 158
                 56666666666654 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0    0.0002      0.28      24      67 ..       2      42 ..       1      44 [. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0002
                     -EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHH CS
  Sigma54_activat 24 svlitGesGtGKellaraiheaskrkekpfvavncaaipeelle 67
                     s++itG+ G+GK  + + i    k+ + p++ +n  a  +el+e
       EPA04523.1  2 SIVITGNPGVGKHSIVKEIS---KQLKLPIIDINSIAKDAELFE 42
                     799***********999885...555689999999999999987 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00066      0.91       7      30 ..       2      25 ..       1      73 [. 0.82
   2 ?    0.4   0.0      0.51     7e+02      40      72 ..     132     163 ..     102     180 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00066
      AAA_22  7 ilvvtGesGtGKTtllrrlleqld 30
                ++v+tG +G+GK   ++++ +ql+
  EPA04523.1  2 SIVITGNPGVGKHSIVKEISKQLK 25
                69***********99999999984 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.51
      AAA_22  40 pevvfvtlpsstsskdllrellralglelkaer 72 
                 ++v  v++++++  +++l+++l++++ ++++e+
  EPA04523.1 132 VKVSQVDVTGKS-ISEVLKKVLSIINGKNSNEE 163
                 444456666665.99999999999998777733 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       814  (0.0454013); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1126.48
//
Query:       EPA04524.1  [L=188]
Description: non-canonical purine NTP pyrophosphatase, RdgB/HAM1 family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.4e-41  142.5   0.0    1.6e-41  142.3   0.0    1.0  1  Ham1p_like  Ham1 family


Domain annotation for each model (and alignments):
>> Ham1p_like  Ham1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.3   0.0   8.8e-46   1.6e-41       1     187 []       7     178 ..       7     178 .. 0.87

  Alignments for each domain:
  == domain 1  score: 142.3 bits;  conditional E-value: 8.8e-46
                 EEEC-S-HHHHHHHHHHTTTECCCE.EECCCCEE----BS.SSHHHHHHHHHHHHHH.HTS-EEEEEEEEEEGGGTTTBGGGTTTTTHTTCHHHHHHHH CS
  Ham1p_like   1 ivfaTgNkgKlrevkeilaeellevkslkelelpeveEtq.gtfeenalkKaraaae.aglpvladDsgLevdaLnglPGvysarfagegaedeenlak 97 
                 ++f+++N++K++e+k il++ ++++       + e+eE+q ++++e+a+kKa +a++ +++p++++D gL+++ L+g+PG+ys+++ +     + +++ 
  EPA04524.1   7 LFFVSSNNHKYKEAKIILDSFGINLGF----FKYELEEIQsSSLKEIAIKKATNAFQkYKKPIIVEDDGLFINSLSGFPGPYSSYVFK-----TIGNKG 96 
                 68***************9876665542....455778***9*************99746888************************64.....457899 PP

                 HHHHCTHTTS--EEEEEEEEEEEETTTTEEEEEEEEEEEEE-SS.--SSSSTTGGGEEETT-SSBTTTS.CHHHHHHSHHHHHHHHHHHH CS
  Ham1p_like  98 lleeleeeeedrsArfvcvlaladpeeeeellfeGeveGeiveeprgeggfGyDpiFvpeegektfaelskeeknaiShRgkAlekllef 187
                 +l+ l+   ++r+A+f++++ ++d   ++ + fe +++G i + +++ +g GyDpiF+p++++ktf+e+s   kn++ShR+kAl+k+ ++
  EPA04524.1  97 ILNLLK---QNRQAKFISIISYCDD--KNSKSFEAQIDGVISK-KQNGKGWGYDPIFIPKNSKKTFSEIS--DKNSLSHRFKALKKFSNW 178
                 ****96...469***********95..55589*********75.7777899********87677****98..6**************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1280.54
//
Query:       EPA04525.1  [L=99]
Description: copper binding protein, plastocyanin/azurin family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-09   38.6   0.0    1.3e-09   38.4   0.0    1.0  1  Copper-bind   Copper binding proteins, plastocyanin/azurin fa
    1.2e-05   25.4   0.0    1.7e-05   24.9   0.0    1.2  1  Cupredoxin_1  Cupredoxin-like domain


Domain annotation for each model (and alignments):
>> Copper-bind  Copper binding proteins, plastocyanin/azurin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.0   1.4e-13   1.3e-09      13      98 ..      13      94 ..       5      95 .. 0.84

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 1.4e-13
                 EEESSEEEEETT..EEEEEEEESSSSBEEEEETTSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEESSEEEEEEETTTTTTTSEEEEEE CS
  Copper-bind 13 qFetkeitvkkg..ekvtfvnlavmgHNvvldkdgvpagvdkdkvkaedetkliggGekdsvtfdeagtYkffCsPHaaagMkgkvtv 98
                 +F +k ++++ g  +++ ++n+++ +H v  d +++++    +  +++    ++ +Ge+++ tf+e+ t++++C+PH    M gk+++
   EPA04525.1 13 NFVPKLVNIQLGidNHIIWTNKDSTPHTVTPDDESLEDSYSGKFGSPG----VVKPGETYEFTFTEPITFSYHCAPHP--WMTGKLEI 94
                 5888888888873356788899***********999777777777775....999***********************..68999876 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   1.9e-09   1.7e-05      29     102 ..      11      92 ..       9      94 .. 0.94

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.9e-09
  Cupredoxin_1  29 dggfePskievkagekvklkiknkdktpeefesed..........lgeekvlapgktttitiaplkpGeYeftcdmhmdakGkl 102
                   ++ f P+ ++++ g    + ++nkd+tp++++ +d          +g   v++pg+t+++t+   +p +++++c  h+ + Gkl
    EPA04525.1  11 QDNFVPKLVNIQLGIDNHIIWTNKDSTPHTVTPDDesledsysgkFGSPGVVKPGETYEFTF--TEPITFSYHCAPHPWMTGKL 92 
                   5789***************************999999999999999999*************..9**********999889987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 669.89
//
Query:       EPA04526.1  [L=133]
Description: DHHA1 domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      7e-12   45.9   0.1    7.6e-12   45.8   0.1    1.1  1  DHHA1     DHHA1 domain


Domain annotation for each model (and alignments):
>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   0.1   4.2e-16   7.6e-12      57     135 ..      41     120 ..       5     123 .. 0.80

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 4.2e-16
                 HHHHHHHHTHGBTTCEEEEEEEECTEEEEEEEESSH...SS-HHHHHHHHHHHTTCCEEEETCEEEEEEEHCHHHHHHHHHH CS
       DHHA1  57 giaadklksklkkpvivfvakeegdkvkvsarskkd...gvdagelakeaaaklgggGGGHdlAaGagipaekleealeale 135
                   +a+  k+    ++i++ ++ e++++k+s r + +    ++++el+k  a+k+ g GGGH+ AaGa+i ++kl+ +l+ le
  EPA04526.1  41 SLIAGSPKN--AGKIIILRTGGEENTIKFSSRKSFGcksEINLSELMKIGAEKFDGVGGGHNAAAGAKITKDKLDGFLDYLE 120
                 334555555..55777777777777*******9988999***************************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       244  (0.0136092); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 841.76
//
Query:       EPA04527.1  [L=124]
Description: hypothetical protein BG20_I0339 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 744.32
//
Query:       EPA04528.1  [L=101]
Description: hypothetical protein BG20_I0373 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-17   64.4   0.1    1.4e-17   64.3   0.1    1.0  1  MethyltransfD12  D12 class N6 adenine-specific DNA methyltran
  ------ inclusion threshold ------
       0.15   11.7   1.0        0.3   10.7   0.3    1.8  2  Cons_hypoth95    Conserved hypothetical protein 95


Domain annotation for each model (and alignments):
>> MethyltransfD12  D12 class N6 adenine-specific DNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.3   0.1   1.5e-21   1.4e-17     176     260 .]       3      83 ..       1      83 [. 0.95

  Alignments for each domain:
  == domain 1  score: 64.3 bits;  conditional E-value: 1.5e-21
                      TTE.EEEE--S-T.S...TS--GGGG.CS-HHHHHHHHHHHHHH.HHTT-EEEEEEESEESHHHHHHCTT...SEEEEECCCCHH CS
  MethyltransfD12 176 ieddivYlDPPYnprqytanytlyetlafsdedevrlaevlkslsskfgvkvllsnsfkdtklfrelyksYnnesileveelrai 260
                      +++d+vY+DPPY+p + tan+t+y+t +f+++d  rla+++ +l+ ++g +vllsns  ++k++ e++++ n  +il+++++r+i
       EPA04528.1   3 KKGDLVYFDPPYQPVSATANFTSYTTKNFTYDDLTRLADLCLKLD-SKGCNVLLSNS--NSKEVAEIFSK-NPWKILKINANRSI 83 
                      6788****************************************7.9999*******..***********.*********99987 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.3   3.3e-05       0.3     112     132 ..       3      22 ..       1      41 [. 0.76
   2 ?   -0.1   0.0     0.071   6.4e+02      71     103 ..      58      82 ..      36      97 .. 0.48

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 3.3e-05
                    -EEEEEEE--SSSTTCH.HHH CS
  Cons_hypoth95 112 eefdivflDPPyakellieev 132
                    ++ d+v++DPPy+ + +  + 
     EPA04528.1   3 KKGDLVYFDPPYQPVSA-TAN 22 
                    4569********98876.444 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.071
                    ES-HHHHHHHHHHHCCCT--TTTEEEEES-HHH CS
  Cons_hypoth95  71 ekdkeavkilkenleelkleeetaelkedalea 103
                     ++ke+++i ++n         +++lk +a ++
     EPA04528.1  58 SNSKEVAEIFSKN--------PWKILKINANRS 82 
                    3333444444333........333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 691.66
//
Query:       EPA04529.1  [L=141]
Description: hypothetical protein BG20_I0356 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      7e-27   94.1   4.6    8.6e-27   93.8   4.6    1.1  1  RNA_binding  RNA binding


Domain annotation for each model (and alignments):
>> RNA_binding  RNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.8   4.6   4.8e-31   8.6e-27       1     118 [.       6     120 ..       6     121 .. 0.96

  Alignments for each domain:
  == domain 1  score: 93.8 bits;  conditional E-value: 4.8e-31
                  EEEEEEEE-TTC-HHHHHHHHHTTSTTSE---EEEEEE-CCC-EEEEEEEEESSHHHHHHHHHHHHHHCCCCHHHHHHCCHCCB-TTSEEEEEEEHHH CS
  RNA_binding   1 kievrafvhaTEdeekVlealsnllpeeeveieeeeaeGhygnpitileaelekkkakkvlkkllellreeeikeLlkeleervdekgklylrldKQa 98 
                  ++++ +++haTEd +k l++++ +++ ++  +++++++Gh++npit+l+a++ k++a+ ++++++ +l++e++keL +++eer+  ++++++rldKQ+
   EPA04529.1   6 EVTIDVIIHATEDISKFLKSFEDMFELKD-IFTVNQTTGHFENPITVLNANFGKNQAQYFVERFVGSLSSEQKKELVEQIEERTV-DSRFHIRLDKQE 101
                  599***********************885.79***************************************************99.9*********** PP

                  HHTT---BESSSSEEEEEEE CS
  RNA_binding  99 aylgklslvegddvIkvkik 118
                  +++g+l+++e +d Ik+ki+
   EPA04529.1 102 FIKGNLAFKE-KDTIKIKIH 120
                  ********55.899***998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       944  (0.0526521); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 831.22
//
Query:       EPA04530.1  [L=108]
Description: hypothetical protein BG20_I0333 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.6e-06   25.5  10.1     0.0017   18.0   0.1    3.9  4  TSP_3     Thrombospondin type 3 repeat


Domain annotation for each model (and alignments):
>> TSP_3  Thrombospondin type 3 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1     0.011     2e+02      25      33 ..       3      11 ..       1      14 [. 0.67
   2 !   18.0   0.1   9.4e-08    0.0017      14      31 ..      20      37 ..      19      41 .. 0.89
   3 ?    0.7   0.5     0.024   4.2e+02      16      24 ..      45      53 ..      42      54 .. 0.74
   4 !    9.2   0.1   5.3e-05      0.95      15      30 ..      61      76 ..      60      81 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.011
       TSP_3 25 lDNCprnan 33
                 D Cp ++ 
  EPA04530.1  3 WDGCPDTPS 11
                477887775 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 9.4e-08
       TSP_3 14 kDfDnDgvqddlDNCprn 31
                +D D Dg++d+ D Cp+ 
  EPA04530.1 20 ADSDFDGIPDYIDQCPTQ 37
                599*************86 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.024
       TSP_3 16 fDnDgvqdd 24
                +D Dg +d+
  EPA04530.1 45 QDDDGCPDT 53
                588888875 PP

  == domain 4  score: 9.2 bits;  conditional E-value: 5.3e-05
       TSP_3 15 DfDnDgvqddlDNCpr 30
                D D Dg+  ++D Cp+
  EPA04530.1 61 DPDADGIFGSNDLCPY 76
                89*************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 744.89
//
Query:       EPA04531.1  [L=174]
Description: hypothetical protein BG20_I0365 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1173.91
//
Query:       EPA04532.1  [L=113]
Description: nitrogen regulatory protein P-II [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-12   47.3   3.7    2.8e-12   47.1   3.7    1.0  1  P-II      Nitrogen regulatory protein P-II


Domain annotation for each model (and alignments):
>> P-II  Nitrogen regulatory protein P-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   3.7   1.6e-16   2.8e-12       1     100 [.       4     104 ..       4     106 .. 0.87

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 1.6e-16
                 EEEEEEGGGHHHHHHHHHHTTGGCEEEEEEEEEESTCCE.EEECTTEEEEEE.EEEEEEEEEEEEGGGHHHHHHHHHHHH-SSSTTSEEEEEEEESEEE CS
        P-II   1 ieaiirpekleevkeaLekagvkgltvtevkGrGkqkgh.telyrgaeyeve.llpkvkleivvsdedvekvveaiikaaktgeiGDGkiFvlpveevi 97 
                 iea i+ +k+  v +a++++ v g+t+ e +GrG+   + +++ rg+ + v  + +   ++ +v+d++ve+v++ai ++a +g+ GDG i ++ v++v+
  EPA04532.1   4 IEATIQVDKIGPVSDAIKEI-VGGFTILEGNGRGSGTRQtMRAGRGTGTFVAeFNKVATVSTIVEDSKVEQVIKAISDSAFSGKAGDGIIVISTVDDVV 101
                 899**************998.89***********9875514556777665552777778**************************************** PP

                 ETT CS
        P-II  98 rir 100
                 +i 
  EPA04532.1 102 NIA 104
                 995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 787.19
//
Query:       EPA04533.1  [L=211]
Description: thrombospondin type 3 repeat protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.8e-16   58.2  46.5    0.00038   20.1   0.8    8.0  8  TSP_3      Thrombospondin type 3 repeat


Domain annotation for each model (and alignments):
>> TSP_3  Thrombospondin type 3 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   1.6   3.9e-08    0.0007      15      34 ..      18      37 ..      16      39 .. 0.92
   2 ?   -0.8   0.0      0.07   1.2e+03      25      32 ..      44      51 ..      42      54 .. 0.61
   3 !   13.6   0.3   2.2e-06     0.039      15      30 ..      60      75 ..      59      80 .. 0.92
   4 ?   -0.7   0.7     0.067   1.2e+03      16      23 ..      84      91 ..      81      94 .. 0.73
   5 !   12.9   0.1   3.6e-06     0.065      15      30 ..     100     115 ..      98     120 .. 0.91
   6 ?   -0.1   0.8     0.044   7.9e+02      16      24 ..     124     132 ..     121     136 .. 0.81
   7 !   20.1   0.8   2.1e-08   0.00038      14      34 ..     140     160 ..     135     162 .. 0.90
   8 !   18.2   3.9   7.9e-08    0.0014      13      34 ..     177     198 ..     165     200 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 3.9e-08
       TSP_3 15 DfDnDgvqddlDNCprnani 34
                D+D Dg++d+ D Cp+ +++
  EPA04533.1 18 DADSDGIEDNKDACPNESET 37
                9***************9986 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.07
       TSP_3 25 lDNCprna 32
                 D Cp ++
  EPA04533.1 44 WDGCPDIS 51
                46666655 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 2.2e-06
       TSP_3 15 DfDnDgvqddlDNCpr 30
                D D D+++d++D Cp 
  EPA04533.1 60 DSDYDSIPDKVDKCPL 75
                99*************6 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 0.067
       TSP_3 16 fDnDgvqd 23
                +D Dg +d
  EPA04533.1 84 QDDDGCPD 91
                57888877 PP

  == domain 5  score: 12.9 bits;  conditional E-value: 3.6e-06
       TSP_3  15 DfDnDgvqddlDNCpr 30 
                 D+D+Dg+  ++D Cp+
  EPA04533.1 100 DYDGDGIFGSNDLCPY 115
                 ***************8 PP

  == domain 6  score: -0.1 bits;  conditional E-value: 0.044
       TSP_3  16 fDnDgvqdd 24 
                 +D Dg +d+
  EPA04533.1 124 QDDDGCPDS 132
                 688999987 PP

  == domain 7  score: 20.1 bits;  conditional E-value: 2.1e-08
       TSP_3  14 kDfDnDgvqddlDNCprnani 34 
                 +D+D+Dg+ d+lD Cp  +++
  EPA04533.1 140 ADTDGDGILDNLDLCPGQPET 160
                 7***************99986 PP

  == domain 8  score: 18.2 bits;  conditional E-value: 7.9e-08
       TSP_3  13 dkDfDnDgvqddlDNCprnani 34 
                   D D Dg++d+ D Cp+n+++
  EPA04533.1 177 TLDSDFDGIPDVKDACPYNSET 198
                 5799***************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1539.12
//
Query:       EPA04534.1  [L=84]
Description: hypothetical protein BG20_I0340 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.056   13.3   0.2       0.06   13.2   0.2    1.3  1  Erv26     Transmembrane adaptor Erv26
       0.17   12.1   1.6       0.22   11.7   0.3    1.8  2  DUF5433   Family of unknown function (DUF5433)


Domain annotation for each model (and alignments):
>> Erv26  Transmembrane adaptor Erv26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   6.7e-06      0.06     145     176 ..       9      40 ..       6      82 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.7e-06
       Erv26 145 fglcvWlvPfalfvsLsAgdnvLPtmgsesas 176
                 +glcvW++P  +f  +  ++  + t+++  ++
  EPA04534.1   9 LGLCVWFIPTIIFQIIVTSEDSVKTAEEAVSE 40 
                 79***********8888888777777666555 PP

>> DUF5433  Family of unknown function (DUF5433)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   2.5e-05      0.22      13      32 ..       7      24 ..       3      33 .. 0.84
   2 ?   -0.5   0.1      0.17   1.5e+03      31      55 ..      56      81 ..      45      84 .] 0.49

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.5e-05
     DUF5433 13 filalciifvPtiklyiqii 32
                +il lc+ f+Pti +  qii
  EPA04534.1  7 LILGLCVWFIPTIIF--QII 24
                69**********975..444 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.17
     DUF5433 31 iimrcvyangin.krstplshnrnpk 55
                ii++ v +   + krs     ++n+k
  EPA04534.1 56 IIVKGVITIRKErKRSRVEDSKKNKK 81
                55555555444313333333344444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       824  (0.0459591); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 614.79
//
Query:       EPA04535.1  [L=175]
Description: transcriptional regulator, AsnC family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-20   72.0   0.3    8.2e-10   38.5   0.0    2.2  2  AsnC_trans_reg   Lrp/AsnC ligand binding domain
    1.9e-07   31.0   1.0     0.0013   18.8   0.1    3.0  2  NapD             NapD protein
    0.00041   20.2   0.0       0.44   10.5   0.0    2.3  2  GYD              GYD domain
  ------ inclusion threshold ------
      0.012   15.7   0.0      0.029   14.6   0.0    1.7  1  Tn916-Xis        Excisionase from transposon Tn916
      0.032   14.4   0.6       0.45   10.7   0.0    2.1  2  PMT2_N           Phosphoethanolamine N-methyltransferase 2 N-
      0.098   12.9   1.0        4.8    7.5   0.1    2.4  2  THF_DHG_CYH      Tetrahydrofolate dehydrogenase/cyclohydrolas
       0.11   12.6   0.1         22    5.2   0.0    2.9  3  DUF2129          Uncharacterized protein conserved in bacteri
       0.13   12.2   0.0       0.28   11.1   0.0    1.5  1  Ferritin         Ferritin-like domain
       0.17   12.3   0.0       0.58   10.5   0.0    1.9  2  Cytochrome_CBB3  Cytochrome C oxidase, cbb3-type, subunit III


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.0   5.1e-11     1e-07       1      70 [.       6      72 ..       6      74 .. 0.95
   2 !   38.5   0.0   4.1e-13   8.2e-10      13      72 ..     110     169 ..      90     172 .. 0.92

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 5.1e-11
                    EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEE CS
  AsnC_trans_reg  1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartets 70
                    vl++++ g+    ++++  l+ l  V e++ + G yd ++k+ + + e +++++ + ++++p + +t t+
      EPA04535.1  6 VLINCDLGS---EKNVISSLKSLNDVSEVHGTLGLYDVIVKIESDSEEKIQKIITNFIRKMPKIHSTMTL 72
                    678888888...999****************************************************996 PP

  == domain 2  score: 38.5 bits;  conditional E-value: 4.1e-13
                     HHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEE CS
  AsnC_trans_reg  13 leefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsiv 72 
                       ++ + l  +peV+e+ +v G yd+++k+ +   + le+++ + +++lp+v+ t t+ v
      EPA04535.1 110 EYNILKNLSHIPEVKEADVVFGYYDIICKIETSEHKLLENIITKAIRKLPHVRTTMTLNV 169
                     5678899************************************************99866 PP

>> NapD  NapD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   6.4e-07    0.0013       6      67 ..       6      69 ..       6      76 .. 0.93
   2 !    8.1   0.1    0.0014       2.8       7      65 ..     102     162 ..     101     167 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 6.4e-07
        NapD  6 lvVqarperlaavkaalaalpgv.EvhasdeegklVvviEaesedeladtiea.iealpgVlsa 67
                ++++++ ++ + v  +l++l +v Evh++ +   ++v iE++se+++ ++i++ i+++p+++s+
  EPA04535.1  6 VLINCDLGSEKNVISSLKSLNDVsEVHGTLGLYDVIVKIESDSEEKIQKIITNfIRKMPKIHST 69
                5899999999**********98879***************************999*****9997 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0014
        NapD   7 vVqarperlaavkaalaalpgvEvhasdee.gklVvviEaesedeladtiea.iealpgVl 65 
                 v++ + ++   ++++l  +p+v  + +      +++ iE+++++ l ++i++ i++lp+V 
  EPA04535.1 102 VIHSDKGEEYNILKNLSHIPEVKEADVVFGyYDIICKIETSEHKLLENIITKaIRKLPHVR 162
                 6666666666777777777766444444444788888888888888888865588888885 PP

>> GYD  GYD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0   0.00022      0.44      37      65 ..      28      56 ..      15      80 .. 0.89
   2 !    7.7   0.0    0.0017       3.5      36      86 ..     122     174 ..     119     175 .] 0.88

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00022
         GYD 37 leslyatlGeyDvvvivEapDdetaaals 65
                + +++ tlG yDv+v +E + +e+++++ 
  EPA04535.1 28 VSEVHGTLGLYDVIVKIESDSEEKIQKII 56
                7899********************99986 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0017
         GYD  36 kleslyatlGeyDvvvivEapDdetaaalsl.alaasGtvrt.etlrafteee 86 
                 ++++  +++G yD+++ +E  +++  + +   a+++  +vrt  tl +++e+e
  EPA04535.1 122 EVKEADVVFGYYDIICKIETSEHKLLENIITkAIRKLPHVRTtMTLNVIPEQE 174
                 588999***************99999997653799999999999999999876 PP

>> Tn916-Xis  Excisionase from transposon Tn916
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.5e-05     0.029       6      45 ..      62     101 ..      57     108 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.5e-05
   Tn916-Xis   6 ktvPvwkkysLnvkeAAeYygiGekkldsilgesegadFv 45 
                 k   ++  ++L+ +e  e +   ek + s+lg+++   +v
  EPA04535.1  62 KMPKIHSTMTLTRSEGKELFHASEKLIGSMLGRNDIQAYV 101
                 55569*****************************977666 PP

>> PMT2_N  Phosphoethanolamine N-methyltransferase 2 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.2      0.11   2.2e+02       6      49 ..      15      60 ..      11      72 .. 0.71
   2 ?   10.7   0.0   0.00023      0.45       7      52 ..     111     158 ..     105     165 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.11
      PMT2_N  6 sievvkevesleelknlD.vlvvnnvLdke.ikdekkLdkfvksal 49
                + +v+++++sl++++++   l + +v+ k+  + e+k++k++++ +
  EPA04535.1 15 EKNVISSLKSLNDVSEVHgTLGLYDVIVKIeSDSEEKIQKIITNFI 60
                5678888899999988753454444444443778888999998865 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00023
      PMT2_N   7 ievvkevesleelknlDvlv..vnnvLdkeikdekkLdkfvksalesl 52 
                  ++ k+++++ e+k++Dv++  ++ + + e  ++k+L++++++a++ l
  EPA04535.1 111 YNILKNLSHIPEVKEADVVFgyYDIICKIETSEHKLLENIITKAIRKL 158
                 678899************974245555555889999********9876 PP

>> THF_DHG_CYH  Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.1    0.0024       4.8      70     108 ..      14      55 ..       4      62 .. 0.71
   2 ?    4.1   0.1     0.027        54      30      69 ..      86     130 ..      65     165 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0024
                  -HHHHHHHHHHHHH-TT--EEEE-SS-STTS...-HHHHHCC CS
  THF_DHG_CYH  70 seeellklieelneddsvdGilvqlPlpkhi...dekailea 108
                  se+++++ +++ln+ ++v+G l  + +  +i   +e++i+++
   EPA04535.1  14 SEKNVISSLKSLNDVSEVHGTLGLYDVIVKIesdSEEKIQKI 55 
                  7899****************9988877444411135555554 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.027
                  EEEEEEES--HHHHHHHHHHHHHHHHTT-EEEEEEE-TT......- CS
  THF_DHG_CYH  30 kLavilvgddpasevYvrnkkkaceevGieseliklped......v 69 
                  kL + + g  ++ ++Yv   +++ ee++i  +l ++pe        
   EPA04535.1  86 KLIGSMLGR-NDIQAYVVIHSDKGEEYNILKNLSHIPEVkeadvvF 130
                  555555555.58999*******************999743344440 PP

>> DUF2129  Uncharacterized protein conserved in bacteria (DUF2129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.027        54      31      59 ..       4      32 ..       2      35 .. 0.92
   2 ?    5.2   0.0     0.011        22      31      59 ..      99     127 ..      95     136 .. 0.91
   3 ?   -2.6   0.0       3.1   6.1e+03      45      56 ..     151     162 ..     141     164 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.027
     DUF2129 31 kYvvlYvneedveeiveklkklkfVkkVe 59
                 Yv++ ++    +++++ lk+l+ V++V+
  EPA04535.1  4 AYVLINCDLGSEKNVISSLKSLNDVSEVH 32
                69***********************9996 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.011
     DUF2129  31 kYvvlYvneedveeiveklkklkfVkkVe 59 
                  Yvv+  ++ +  +i+++l++++ Vk+++
  EPA04535.1  99 AYVVIHSDKGEEYNILKNLSHIPEVKEAD 127
                 6************************9875 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 3.1
     DUF2129  45 iveklkklkfVk 56 
                 i++ ++kl+ V+
  EPA04535.1 151 ITKAIRKLPHVR 162
                 456688888776 PP

>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00014      0.28      85     139 ..       8      63 ..       4      66 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00014
                 HHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH.HHHHHHHHHHHHHHH CS
    Ferritin  85 leaalehekkvteslrelielaeeegDpatadfledflee.qeeheweleallekl 139
                 + ++l +ek+v++sl+ l ++ e +g  +++d + ++  + +e+ ++ + ++++k+
  EPA04535.1   8 INCDLGSEKNVISSLKSLNDVSEVHGTLGLYDVIVKIESDsEEKIQKIITNFIRKM 63 
                 6789******************************9999995666666666666665 PP

>> Cytochrome_CBB3  Cytochrome C oxidase, cbb3-type, subunit III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00029      0.58      33      55 ..      48      72 ..      32      82 .. 0.80
   2 ?   -2.2   0.0       2.7   5.3e+03      34      53 ..     144     163 ..     138     167 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00029
  Cytochrome_CBB3 33 epdalvdiiknGkgaMpafgg..ql 55
                     +++++++ii+n +++Mp +++  +l
       EPA04535.1 48 SEEKIQKIITNFIRKMPKIHStmTL 72
                     3699***************995555 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.7
  Cytochrome_CBB3  34 pdalvdiiknGkgaMpafgg 53 
                      ++ l++ii++ +++ p  ++
       EPA04535.1 144 HKLLENIITKAIRKLPHVRT 163
                      56678899999888887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1039.03
//
Query:       EPA04536.1  [L=593]
Description: pyridoxal-phosphate dependent protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-21   77.1   0.1    9.8e-20   71.1   0.0    3.1  2  PALP      Pyridoxal-phosphate dependent enzyme


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.1   0.0   5.5e-24   9.8e-20      21     292 ..     139     444 ..     109     446 .. 0.68
   2 ?   -0.3   0.0     0.033   5.8e+02      38      72 ..     514     557 ..     513     566 .. 0.67

  Alignments for each domain:
  == domain 1  score: 71.1 bits;  conditional E-value: 5.5e-24
                 CCEEEEEEGGGSTTSBTTHHHHHHHHHH.HHTT..TTTSEEEEEBSSHHHHHHHHHHHHHT-EEEEEEETTS-H........................H CS
        PALP  21 gvplflKlEslnptgSfKdRgaeyllar.lkeg..tgaktvveassGNhgralAaaaallGlkvtivvpadasp........................e 92 
                   ++f K +s   +gS+K+R a++++++ +  g  ++++tv+ea+sGN g+al   ++ lGl v+ +v+++  +                        +
  EPA04536.1 139 DLKVFGKFDSNLLSGSIKVRPAVHIIHDaILTGklKSGQTVIEATSGNFGIALGQLSK-LGLTVVSLVSRKLQEgvfkelrnenirimdldmdvcpapG 236
                 3349************************733347899******************999.********99999963333333333333333333333443 PP

                 HHHHHHHTT-EEEEE................CCHHHHHHHHHHHHHHH............STTCEE--TTTSHHHHHH.HHTHHHHHHHHTT......T CS
        PALP  93 kvallrllGaevvev................ggdydeavaaaaelaae............gegaylvsqfdnptvieg.ygtiglEileqlg......g 156
                 +++    l a+ + +                +++  e +++    +a             ++g++   q+dn++++++  + ++ Ei +ql       +
  EPA04536.1 237 MKDNPNVLAAKATAYnirsqlselgfdptifDKSISEIESL----LAAqdiinlakflakIYGCFCPEQYDNELNTDAhKSITAVEIDQQLHeqgyslE 331
                 33333333333333333333444433322223333333333....222344445555555******************888899***977766666644 PP

                 TEEEEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCS.CGTTCCHHHHSEEEEEEEEEEHHHHHHHHHH CS
        PALP 157 kpdavvvpvGgGgliaGiaaglkerrpdvrvigvepegsdalarslragrrvtvpvsdtiadglavg.spselafelldrlvdeivtvsdeealeamrl 254
                 ++  +v++ G+Gg+ +G++ ++ e+  +  v +v     ++ ++ +                g++++ ++s l +   d + +  ++++ ++a   ++ 
  EPA04536.1 332 NFG-IVCSFGTGGTSGGLSNYISEKYNKKSVHVV----FPPAGQDV---------------AGIRTKdKASGLKLYKPDTYAG-QYEIDFDQAKHLLKY 409
                 444.********************8888566666....44445555...............5566665666666666677777.788999999999999 PP

                 HHHHHSB-B-HHHHHHHHHHHHHHHHCCTTCEEEEEEE CS
        PALP 255 larregivvepssaaalaalklreagelkegdrvvvil 292
                 +  + g+ +++ssa  l a+   + ++++++++ v+i+
  EPA04536.1 410 FV-EKGYDIGESSALELYAA--MQMANFGAEKKFVIII 444
                 99.99999999999999999..5666666666888887 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.033
                 THHHHHHHHHH....HHTT.......TTTSEEEEEBSSHHHHHHHH CS
        PALP  38 KdRgaeyllar....lkeg.......tgaktvveassGNhgralAa 72 
                 K+R++  lla+    +  +       t++k ++++ +GN+ + +  
  EPA04536.1 514 KARTINQLLATqqipE--ElsndlkgTKGKSLLVCMAGNTSLMAVN 557
                 6666776666665330..244455669*************987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (593 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1147  (0.0639746); expected 358.6 (0.02)
Passed bias filter:                      591  (0.0329634); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.69u 0.33s 00:00:01.02 Elapsed: 00:00:00.50
# Mc/sec: 3573.91
//
Query:       EPA04537.1  [L=157]
Description: cytidyltransferase-like domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-14   53.7   0.0    3.2e-14   53.3   0.0    1.2  1  CTP_transf_like  Cytidylyltransferase-like
  ------ inclusion threshold ------
       0.02   14.8   0.0      0.048   13.5   0.0    1.7  2  FAD_syn          FAD synthetase
       0.04   13.1   0.1       0.62    9.2   0.0    2.0  2  Pantoate_ligase  Pantoate-beta-alanine ligase
      0.051   13.7   0.1       0.13   12.4   0.0    1.7  2  DpaA_N           Dipicolinate synthase subunit A N-terminal d


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.3   0.0   7.1e-18   3.2e-14       2     142 ..       9     144 ..       8     145 .. 0.86

  Alignments for each domain:
  == domain 1  score: 53.3 bits;  conditional E-value: 7.1e-18
                      EEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST.-SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHH......HHHHHTTTTEEEEE CS
  CTP_transf_like   2 agGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkk.kkplasaeeRlemlelakevdevisvdpweltr......evlkklkpdklylv 88 
                      +gGtFD+iH+GHl+ll +a++  ++ +i+g++sde + k  kk+l +++ R ++l +    +  ++   +++ +        + + +++  +l+
       EPA04537.1   9 MGGTFDIIHKGHLTLLSKAFSISSK-VIIGLTSDELAEKRgKKTLNKYSKRFKTLVRT--INTNFPNHLYQISKldndfgPAVLEENVE--ALI 97 
                      69***********************.**************55************9988..44446888888887777888667777789..*** PP

                      EEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHHHHH CS
  CTP_transf_like  89 igadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstkire 142
                      +++++  +    ++l+      ++ vv +p       +  +++ n iS+++i++
       EPA04537.1  98 VSDETGNQGAILNQLRAEKNLSPVKVVIVP-------MVLAQDGNRISTSRIKN 144
                      ****99997777877777777777777778.......99*************86 PP

>> FAD_syn  FAD synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.1e-05     0.048      11      35 ..       9      33 ..       2      67 .. 0.87
   2 ?   -1.9   0.0       0.6   2.7e+03     131     157 ..     113     140 ..     102     141 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.1e-05
     FAD_syn 11 tlGnFDGvHlGHqallkkaveaake 35
                  G FD +H+GH +ll+ka +++++
  EPA04537.1  9 MGGTFDIIHKGHLTLLSKAFSISSK 33
                3379***************998765 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.6
     FAD_syn 131 kelgaklgfevevvpkv.eleeekisst 157
                 ++ ++   ++v +vp v  +++++is++
  EPA04537.1 113 RAEKNLSPVKVVIVPMVlAQDGNRISTS 140
                 3333333478888888767778888876 PP

>> Pantoate_ligase  Pantoate-beta-alanine ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00014      0.62      24      73 ..       8      58 ..       2      76 .. 0.72
   2 ?    2.1   0.0     0.021        92     148     180 ..     105     138 ..      95     152 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00014
                     EEEEE-SS-GHHHHHHHHHHHHHSSEEEEEEEEEGGGS.STTSCTTTSEEE CS
  Pantoate_ligase 24 glVpTmGaLHeGHlsLvkaakeendvvvvSiFvNplqF.gpkedlekYPrt 73
                     ++  T   +H+GHl+L+++a + +++v++ +  + l     k+ l+kY ++
       EPA04537.1  8 AMGGTFDIIHKGHLTLLSKAFSISSKVIIGLTSDELAEkRGKKTLNKYSKR 58
                     444566789*************99999998766655431334556666655 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.021
                      HHHHHHHHHHHTT-.SSEEEEEEEEBETTSEBTT CS
  Pantoate_ligase 148 qlavirrlvkdlnl.pveivavpivReedgLAlS 180
                      q a++++l ++ nl pv++v+vp+v ++dg  +S
       EPA04537.1 105 QGAILNQLRAEKNLsPVKVVIVPMVLAQDGNRIS 138
                      7899999999988857*********999997666 PP

>> DpaA_N  Dipicolinate synthase subunit A N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.93   4.2e+03      89     104 ..      31      46 ..      18      55 .. 0.66
   2 ?   12.4   0.0   2.9e-05      0.13      35      71 ..     104     141 ..      87     155 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.93
                 T-EEEESS--HHHHHH CS
      DpaA_N  89 gqllfgGiippelkel 104
                 ++ +++G+ ++el e 
  EPA04537.1  31 SSKVIIGLTSDELAEK 46 
                 4557777777777665 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 2.9e-05
                 -BTTEEEE-GGGS-GGG-SEEE--TT-BETTTEE-B.S CS
      DpaA_N  35 kiegvekaesleealedadviilPvpgtkdggeint.p 71 
                 +   + ++   e+ l+ ++v+i+P+ + +dg++i+t  
  EPA04537.1 104 NQGAILNQLRAEKNLSPVKVVIVPMVLAQDGNRISTsR 141
                 444555566788999*******************9933 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.56
# Mc/sec: 844.56
//
Query:       EPA04538.1  [L=254]
Description: hypothetical protein BG20_I0376 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      6e-05   22.8   0.0    0.00026   20.7   0.0    2.0  2  HTH_IclR       IclR helix-turn-helix domain
    8.9e-05   22.8   0.0    0.00015   22.1   0.0    1.3  1  B12-binding_2  B12 binding domain
     0.0021   18.0   0.0     0.0053   16.7   0.0    1.7  1  HTH_29         Winged helix-turn helix
     0.0031   17.4   0.0     0.0067   16.3   0.0    1.6  1  HTH_11         HTH domain
     0.0062   16.1   0.0      0.028   14.0   0.0    2.1  2  HTH_24         Winged helix-turn-helix DNA-binding
     0.0075   16.0   0.0      0.022   14.6   0.0    1.7  2  HTH_23         Homeodomain-like domain
  ------ inclusion threshold ------
      0.042   13.8   0.0      0.091   12.7   0.0    1.5  1  MarR           MarR family
      0.082   13.0   0.1       0.26   11.5   0.0    1.9  2  CtsR_C         CtsR C-terminal dimerization domain
      0.097   12.6   0.0       0.18   11.7   0.0    1.4  1  MarR_2         MarR family
       0.15   12.2   0.0       0.54   10.4   0.0    1.9  2  HTH_28         Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   1.5e-07   0.00026       9      51 ..       2      44 ..       1      45 [. 0.93
   2 ?   -1.0   0.0      0.91   1.6e+03       3      13 ..     137     147 ..     136     154 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.5e-07
                HCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
    HTH_IclR  9 LdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveqd 51
                +d l     +++  e+++++g++++t   +L+ +  +G+++q 
  EPA04538.1  2 IDVLKDSKTGMSGVEISEKLGVNRTTMTKYLKVFAAEGFLRQK 44
                5788899999*******************************96 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.91
                 HHHHHHHCT-C CS
    HTH_IclR   3 dRalaiLdala 13 
                 ++ l+iL +++
  EPA04538.1 137 SKSLQILSQIS 147
                 789****9987 PP

>> B12-binding_2  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   8.4e-08   0.00015       6      74 ..      75     143 ..      72     144 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 8.4e-08
  B12-binding_2   6 hwaivhgdkegieelidealaqgsaavdvlndvllpamkeVGdlfgagelflpqvllsaevmkkavahL 74 
                    ++ +v+g++ ++  l++ ++++g ++ +++ +v+lp m+ + +l+  g++   ++ l  +++ k + +L
     EPA04538.1  75 LENLVKGNESQVYSLVKNCINSGASVRKLVAEVILPSMDSIQKLYNDGKIGKSEEKLLEHIISKSLQIL 143
                    5789*********************************************98888877777777777665 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0     3e-06    0.0053       4      62 ..       4      59 ..       2      60 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3e-06
      HTH_29  4 allllaeGvstvsqiAkllglsrrtvyrwlkrfeegGlaalldrrrsgrprn.rlseeqe 62
                +l  ++ G+s   +i + lg+ r+t  ++lk f ++G    l+++  g+ +  +l ++qe
  EPA04538.1  4 VLKDSKTGMS-GVEISEKLGVNRTTMTKYLKVFAAEG---FLRQKDIGNISLwLLEPGQE 59
                788999***8.**************************...88888888888888888887 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   3.7e-06    0.0067       7      38 ..       3      34 ..       1      41 [. 0.85

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.7e-06
      HTH_11  7 elLleargpisgeeLAeeLnvSrrtvrrdIka 38
                  L++++  +sg e++e+L+v r+t  +++k 
  EPA04538.1  3 DVLKDSKTGMSGVEISEKLGVNRTTMTKYLKV 34
                578888888*****************999985 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   1.5e-05     0.028      17      47 ..      11      41 ..       3      42 .. 0.90
   2 ?   -2.5   0.0       2.2   3.9e+03       6      16 ..     140     150 ..     138     151 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.5e-05
      HTH_24 17 risqreLAerlglSpstvnrrlkrLeeeGlI 47
                ++s  e++e+lg+ ++t +++lk +  eG++
  EPA04538.1 11 GMSGVEISEKLGVNRTTMTKYLKVFAAEGFL 41
                67889**********************9987 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.2
      HTH_24   6 rkILelLqknp 16 
                 ++IL+ +  +p
  EPA04538.1 140 LQILSQISVDP 150
                 79999998887 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   1.2e-05     0.022      11      46 ..       5      40 ..       2      42 .. 0.86
   2 ?   -3.0   0.0       4.1   7.4e+03      31      41 ..      83      93 ..      82      99 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.2e-05
      HTH_23 11 llllaeGlsvreIAreLgvsrrTvyrwlkryreeGl 46
                l+  + G+s  eI+++Lgv+r T  ++lk +++eG+
  EPA04538.1  5 LKDSKTGMSGVEISEKLGVNRTTMTKYLKVFAAEGF 40
                4455569**********************9998985 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.1
      HTH_23 31 rrTvyrwlkry 41
                +++vy  +k  
  EPA04538.1 83 ESQVYSLVKNC 93
                79999999986 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   5.1e-05     0.091      18      48 ..      12      42 ..       5      46 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.1e-05
                EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
        MarR 18 lsvseLakklgvskstvtrvldrLekkGlie 48
                +s  e+ +klgv+++t+t+ l+    +G+++
  EPA04538.1 12 MSGVEISEKLGVNRTTMTKYLKVFAAEGFLR 42
                45559************************97 PP

>> CtsR_C  CtsR C-terminal dimerization domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00014      0.26      24      53 ..     113     141 ..     111     157 .. 0.85
   2 ?   -4.0   0.0       9.5   1.7e+04       6      17 ..     235     246 ..     232     247 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00014
      CtsR_C  24 aiiqrLleegliterEakLmkaalsdrvLd 53 
                 + iq+L+++g i + E kL+++++s++ L+
  EPA04538.1 113 DSIQKLYNDGKIGKSEEKLLEHIISKS-LQ 141
                 689**********************54.43 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 9.5
      CtsR_C   6 leilinsigdsi 17 
                 ++++ +++g++i
  EPA04538.1 235 INSIKEKMGKKI 246
                 555666666655 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0    0.0001      0.18      22      54 ..      12      44 ..       2      46 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0001
                EEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
      MarR_2 22 ltvgelarrlglsksavsrilkrLvaaGLverr 54
                ++  e+ ++lg+ + ++++ lk + a G+++++
  EPA04538.1 12 MSGVEISEKLGVNRTTMTKYLKVFAAEGFLRQK 44
                56679************************9875 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0    0.0003      0.54       5      44 ..       4      41 ..       2      47 .. 0.86
   2 ?   -1.6   0.0       1.7   3.1e+03      25      34 ..      82      91 ..      79      97 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0003
      HTH_28  5 iikllaaGhsvreaArelgisrrtvyrWikryeegGiagL 44
                ++k  + G+s  e++++lg++r+t  + +k + ++G+  L
  EPA04538.1  4 VLKDSKTGMSGVEISEKLGVNRTTMTKYLKVFAAEGF--L 41
                666677799999*********************9998..4 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.7
      HTH_28 25 srrtvyrWik 34
                ++++vy+++k
  EPA04538.1 82 NESQVYSLVK 91
                579****998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       705  (0.0393218); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1610.24
//
Query:       EPA04539.1  [L=195]
Description: hypothetical protein BG20_I0343 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.023   15.2   2.7       0.24   11.9   0.3    2.2  2  NERD      Nuclease-related domain
      0.095   12.7   0.0       0.24   11.4   0.0    1.8  1  CHDNT     CHDNT (NUC034) domain


Domain annotation for each model (and alignments):
>> NERD  Nuclease-related domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.3   2.7e-05      0.24      20      66 ..      48      98 ..      24     120 .. 0.60
   2 ?    3.6   0.2    0.0098        88      45      61 ..     132     149 ..     117     189 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.7e-05
        NERD 20 eylvlhdvrlrpg..tg..eiDhlvispkgifviEvKnwsG.wifgdkegrw 66
                +  +l d+ +++   +g  +iD l+ +++g++++E K +   +i    +g+ 
  EPA04539.1 48 GREILGDLIVHGMiaSGgtDIDWLIEHNGGFVILEFKGFHNdKINIA-KGQI 98
                34444555553336522459******************987433333.3333 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.0098
        NERD  45 gifviEvKnws.Gwifgd 61 
                 +++++E K w+ G i ++
  EPA04539.1 132 TVWIFEMKQWKtGAIPKN 149
                 69********96544444 PP

>> CHDNT  CHDNT (NUC034) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   2.7e-05      0.24      33      54 .]     174     195 .]     167     195 .] 0.94

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.7e-05
       CHDNT  33 vavsklvmLvaakwrEFqehnp 54 
                 ++++kl ++++  w+EF + +p
  EPA04539.1 174 INIEKLREIIDSHWKEFERIMP 195
                 899***************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       751  (0.0418874); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1305.99
//
Query:       EPA04540.1  [L=80]
Description: hypothetical protein BG20_I0359 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00019   21.5   0.0    0.00024   21.2   0.0    1.1  1  Pcc1      Transcription factor Pcc1
  ------ inclusion threshold ------
      0.042   14.2   0.0      0.051   13.9   0.0    1.2  1  DUF4854   Domain of unknown function (DUF4854)


Domain annotation for each model (and alignments):
>> Pcc1  Transcription factor Pcc1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   2.7e-08   0.00024       6      74 .]      11      80 .]       5      80 .] 0.86

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 2.7e-08
                EE-SSHHHHHHHHHHHHHHCHC-TTECEEEEEEETTEEEEEEEESSH.HHHHHHHHHHHHHHHHHHHHHH CS
        Pcc1  6 vpfpterlAsialrtLqvDkelsplavkrslslegnvLqveykAttn.rmLRvavngfleslglvletme 74
                +   ++++A+++ ++L++D+   p+  + +++  +n L+ ++++++n ++L   ++ +le+++++l+++e
  EPA04540.1 11 LNNLSKEKAETVKKALEPDNVNFPEGLSLHVENIDNRLVFNFESKENmKKLIGVIDEVLEHVQVALKVIE 80
                5567899************8888877888888889*********76638899999*************97 PP

>> DUF4854  Domain of unknown function (DUF4854)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   5.7e-06     0.051       6      54 ..      18      60 ..      16      79 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.7e-06
     DUF4854  6 qseevqsqieaakssledsGislevtaegntLvyeytlskslddaalda 54
                ++e+v++++e ++  + + G+sl v   +n Lv++++ ++      +++
  EPA04540.1 18 KAETVKKALEPDNVNFPE-GLSLHVENIDNRLVFNFESKEN-----MKK 60
                6899*************9.9****************98887.....333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1028  (0.0573373); expected 358.6 (0.02)
Passed bias filter:                      612  (0.0341346); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.51
# Mc/sec: 469.09
//
Query:       EPA04541.1  [L=208]
Description: DNA adenine methylase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.6e-38  131.4   0.5    5.9e-38  131.0   0.5    1.0  1  MethyltransfD12  D12 class N6 adenine-specific DNA methyltran
     0.0016   18.5   0.2     0.0042   17.1   0.1    1.7  2  DUF2089          Protein of unknown function (DUF2089)


Domain annotation for each model (and alignments):
>> MethyltransfD12  D12 class N6 adenine-specific DNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.0   0.5   6.6e-42   5.9e-38       5     177 ..      35     203 ..      34     206 .. 0.93

  Alignments for each domain:
  == domain 1  score: 131.0 bits;  conditional E-value: 6.6e-42
                      SCTTHHHHHCCS-..--SEEEETT-TTSCCHHCS.....SSCEEEEES-HHHHHHHHHHCCHSHHHHHHHHH.TCTTGGC.TSHHHHHHHHHHH CS
  MethyltransfD12   5 KrkllpeIkelipkdkgktfvepFaGggaVffeakk..qgkkvlinDinedlinlykaliknnveelikelekllekeelenereyfyelreef 96 
                      Kr+l+p ++++ip+ +  t++epF Ggga+ f++++  +g+k+ i+D+n+dl+  y  +i++++++li  l++++ k+ +++++ y+y +r e 
       EPA04541.1  35 KRQLIPILNQNIPE-SFGTYYEPFLGGGALLFNILTgkNGQKCSISDLNSDLVLAYT-TIRDKIDALITSLKSHE-KNYQKDSQTYYYSIR-ES 124
                      9************9.7789****************999*******************.**************855.556668999999999.77 PP

                      H...HHH-HHHHHHHHHHHHCCBGGG---B-TTS-B---B-S-SS-....HHHHHHHHHHHHH..CCEEEC-CHHHHTT--TT CS
  MethyltransfD12  97 nkkidaireaeeaidflylnrllfsglervnkkgnfnvpygaykkpkkvaekelklrseklkn..akiecgdfdavllkakie 177
                      n      +e e+ +++++lnr++f+gl+rvn+kg+fnvp g+y +p++v+e++l+ +s+ l++    i c df avl++ak++
       EPA04541.1 125 N----PRSEIEKTSRLIFLNRTCFNGLYRVNSKGKFNVPLGKYSNPNIVNEENLRAVSSILRSnrISINCRDFAAVLRDAKKR 203
                      7....6677777899************************************************9999**********999765 PP

>> DUF2089  Protein of unknown function (DUF2089)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.49   4.4e+03      18      30 ..      14      26 ..       5      42 .. 0.68
   2 !   17.1   0.1   4.7e-07    0.0042      51      88 ..      77     115 ..      72     135 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.49
     DUF2089 18 cettiegeFelse 30
                ce t++ +F+ s+
  EPA04541.1 14 CEATVRSDFSNSK 26
                8888888887653 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 4.7e-07
     DUF2089  51 nlkevekelgisYpTvrnrldeileaLgyeeeeeee.ee 88 
                 +++++++ l ++Y+T+r ++d+++++L+ +e++ ++ ++
  EPA04541.1  77 SISDLNSDLVLAYTTIRDKIDALITSLKSHEKNYQKdSQ 115
                 7999************************99997755222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       843  (0.0470188); expected 358.6 (0.02)
Passed bias filter:                      626  (0.0349155); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1262.13
//
Query:       EPA04542.1  [L=321]
Description: TIM-barrel protein, nifR3 family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-73  247.4   0.0    2.1e-73  247.1   0.0    1.0  1  Dus           Dihydrouridine synthase (Dus)
    3.8e-08   32.9   0.1      5e-06   25.9   0.1    2.2  1  DHO_dh        Dihydroorotate dehydrogenase
    4.9e-05   22.6   0.1    0.00016   20.9   0.0    1.8  2  NanE          Putative N-acetylmannosamine-6-phosphate epimer
    0.00077   18.8   0.0     0.0013   18.1   0.0    1.4  1  Oxidored_FMN  NADH:flavin oxidoreductase / NADH oxidase famil
      0.005   15.9   0.0     0.0074   15.3   0.0    1.3  1  IMPDH         IMP dehydrogenase / GMP reductase domain
     0.0059   16.2   0.0      0.013   15.1   0.0    1.6  1  MR_MLE_C      Enolase C-terminal domain-like
     0.0073   15.8   0.0      0.011   15.2   0.0    1.3  1  His_biosynth  Histidine biosynthesis protein
  ------ inclusion threshold ------
      0.034   13.2   0.0      0.066   12.2   0.0    1.5  1  FMN_dh        FMN-dependent dehydrogenase


Domain annotation for each model (and alignments):
>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  247.1   0.0   9.4e-77   2.1e-73       2     297 ..      11     309 ..      10     319 .. 0.86

  Alignments for each domain:
  == domain 1  score: 247.1 bits;  conditional E-value: 9.4e-77
                 E---TTTS-HHHHHHHHHTT-SSEEEEEE......EE-SSS---HHHHHHH-GG.GGGTSCEEEEEE-S-HHHHHHHHHHHHHTT-SCEEEEESSTTEE CS
         Dus   2 laPmagvtdlpfRelvrefgataLvvtem......vtakaivreekvrirmlse.eeeetplavQlggsdpallaeaAklvadlgadeIdlNvGCPskk 93 
                 laPmagv+d ++R  ++++ga+ Lvvte+      ++ + +++e+k++i+++ e +e+e+pl+vQl+gsd   l +aAk+v++   d+Id N+GCP++ 
  EPA04542.1  11 LAPMAGVSDPALRLQCKKMGAG-LVVTEFtsihsiIAKEHQLKENKKTIQEFLEySEKERPLSVQLFGSDLLALEKAAKIVEP-FFDIIDYNMGCPAPH 107
                 8*********************.*****83333324555666777777776544145559***********************.*************** PP

                 ETTEEEGGGGGGSHHHHHHHHHHHHCCSSS-EEEEEESESSTTTC.HH.HHHHHHHHCT-SEEEEESSECCCTT-CG--CHHHHHHHHH-SS-EEEESS CS
         Dus  94 vtrggaGaaLlrkpdlvaqivkavvkaveiPvtvkirigiddeeenal.elakiveaaGaqaltvHgRtraqnyegtadweaIkevkqavsipviaNGd 191
                 +t+++aG aLl++ +l +qi +++v+av+ Pvt+kir g+ d+++ ++ ++a i+e++G+q++t+H Rt  q+y+g+adw+ Ike+k+  +ip+++NGd
  EPA04542.1 108 ITQQMAGGALLQEINLTQQIFSTLVNAVKKPVTLKIRSGVTDASRYLFkDIATIAEDEGIQMITLHPRTVSQGYSGNADWKMIKELKEISNIPIVGNGD 206
                 *****************************************9999887479************************************************ PP

                 --SHHHHHHHHHHH--SEEEESCHHCCSTTHHHH.HHHHHHSC------HHHHHHHHHHHHHHCHHTTCCCCCCHHHHHHHHHHHHHHTTTTCHHHHHH CS
         Dus 192 IkdaedaqaileetGadgvmigrgalgnPwlfae.stavktgeaepapplaeeaeiveehlkkleeelgedkglrkirkhlawylkglkkaaelrrele 289
                 I+++eda++++++tG+d vmigrga gnP+lf++ + ++ktg +++       ++++++  ++l    + + ++ +i  +     kg+k+ +++r +++
  EPA04542.1 207 ITTPEDAKNMIDQTGCDYVMIGRGAMGNPFLFEQiNDYLKTGTYKQYSL----KDKIDSFFEYLSLSTQYKIKFSNIKGQAMRFTKGIKGGSKIRPKIS 301
                 *********************************9999999988877665....5555555555555555567777777777788888888888888887 PP

                 HHHHHHCC CS
         Dus 290 evsdkeea 297
                 ++++ +e 
  EPA04542.1 302 TSKNITEL 309
                 77776665 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.1   2.2e-09     5e-06     115     292 ..      84     246 ..      41     248 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 2.2e-09
                 HHHHHHHGGGESEEEEES-SCTCCTSCCCG.....CHHHHHHHHHHHHHHHHSSEEEEEE-SSSSHHHH...HHHHHHHHHHTECEEEE...BSEE--C CS
      DHO_dh 115 vevvrkigpfadilelNvSsPntpglrdlq.....ekeelkaillkvvkevskvpvlvKlaPdltdeek...kdiadvllelkldgiivtNttvqrlai 205
                  + ++ ++pf di+  N+ +P     ++++     ++ +l++++ + + ++ k+pv  K+   +td      kdia  +   ++++i         +  
  EPA04542.1  84 EKAAKIVEPFFDIIDYNMGCPAPHITQQMAggallQEINLTQQIFSTLVNAVKKPVTLKIRSGVTDASRylfKDIATIAEDEGIQMIT------LHP-- 174
                 45566678************975544433311111567788888888888889********999998763336777777788888776......222.. PP

                 TTCCGCCCCTTSSEEEEEGGGHHHHHHHHHHHHHHTTT.S-EEEESS--SHHHHHHHH.HHTECEEEESHHHHHHGTCHHHHHHHHHH CS
      DHO_dh 206 dlkseknvkanktGGlsGkalkdialkvirelykrlkkeipiIgvGGiesgeDaleki.eaGAslvqvytalvfegpkiakkikkele 292
                      ++v++    G sG+a      k+i el++  +  ipi+g G i++ eDa ++i + G   v ++ +    +p+++++i + l+
  EPA04542.1 175 -----RTVSQ----GYSGNA----DWKMIKELKEISN--IPIVGNGDITTPEDAKNMIdQTGCDYVMIGRGA-MGNPFLFEQINDYLK 246
                 .....23444....689975....789********99..******************9679*********99.99********99886 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.57   1.3e+03      96     120 ..      14      38 ..       8      64 .. 0.77
   2 !   20.9   0.0   7.1e-08   0.00016     103     175 ..     157     231 ..     106     244 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.57
                 EEE-SSHHHHHHHHHTT-SEEE-TT CS
        NanE  96 maDistleeglvakklGvdivGttl 120
                 ma +s     l++kk+G+ +v t +
  EPA04542.1  14 MAGVSDPALRLQCKKMGAGLVVTEF 38 
                 8888888889999999998887654 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 7.1e-08
                 HHHHHHHHTT-SEEE-TTTTSSTTS-..SS--HHHHHHHHH.TT--EEEES---SHHHHHHHHT.T--SEEEE-.HH CS
        NanE 103 eeglvakklGvdivGttlsGytkeeek.aepDfalvkalse.aglkviaeGrintPekakkaie.iGvdavvvG.sa 175
                 + + +a++ G++++  tl   t ++    + D++++k+l+e +++ ++ +G i tPe ak++i+ +G d v++G +a
  EPA04542.1 157 DIATIAEDEGIQMI--TLHPRTVSQGYsGNADWKMIKELKEiSNIPIVGNGDITTPEDAKNMIDqTGCDYVMIGrGA 231
                 44667888888888..666666555443789********9957899***************997379******9445 PP

>> Oxidored_FMN  NADH:flavin oxidoreductase / NADH oxidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   5.7e-07    0.0013     276     339 ..     182     245 ..     146     248 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 5.7e-07
                   HHCCTT.HHHHHHCCCHSSEEEE-SS--SHHHHHHHHHTTS-SEEEESTHHHH-TTHHHHHHCCT CS
  Oxidored_FMN 276 vrteqe.kntefvkevwkkplitvgriadeekaaeivaegeadLvamgRefladpdlveklkkgl 339
                   +    + k  + +ke+++ p+++ g i+ +e+a+ +  +   d v +gR  + +p+l e+++  l
    EPA04542.1 182 SGNA-DwKMIKELKEISNIPIVGNGDITTPEDAKNMIDQTGCDYVMIGRGAMGNPFLFEQINDYL 245
                   3333.3367799*******************99999999********************998766 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   3.3e-06    0.0074      42     176 ..      14     231 ..       9     233 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.3e-06
                 STTT-SHHHHHHHHHTTSEEEE-SSS-HHHHHHHHHHHHTS.......................................................... CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......................................................... RF
       IMPDH  42 mdtvtesemAialareGgigvihknlsieeqaeevkkvkrs.......................................................... 82 
                 m  v++  +  +  ++G+  v+ + +si++ +++ +++k++                                                          
  EPA04542.1  14 MAGVSDPALRLQCKKMGAGLVVTEFTSIHSIIAKEHQLKENkktiqefleysekerplsvqlfgsdllalekaakivepffdiidynmgcpaphitqqm 112
                 555566666666666665555555555555555555555555556666666666666666666666666666666666666666666666666666666 PP

                 ...................TTSXBX.TTSXB-EEEEE-SSTTHHHHHHHHHHTT-SEEEEE...-STSSSHHH.HHHHHHHHHHTTTSEEE.EEEE-SH CS
                 ...................xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxx.xxxxxxxxxxxxxxxxx.xxxxxxx RF
       IMPDH  83 ...................pnaakd.ekgrllvgaavgvkedalervkalveagvdvlvvd...sahghsekv.leavkeikkkveevevi.aGnvata 156
                                     na+k+  + +++ g +   +   ++ ++   ++g+ ++++    +++g+s +   +++ke+k+   ++ ++  G+++t 
  EPA04542.1 113 aggallqeinltqqifstlVNAVKKpVTLKIRSGVTDASRYLFKDIATIAEDEGIQMITLHprtVSQGYSGNAdWKMIKELKEIS-NIPIVgNGDITTP 210
                 6666666666666666665333333123333333332233223333334445778888875333789998765379******877.8999977****** PP

                 HHHHHHHH.TT-SEEEE-SS- CS
                 xxxxxxxx.xxxxxxxxxxxx RF
       IMPDH 157 egakaLie.agadavkvGiGp 176
                 e ak++i+ +g d v +G G+
  EPA04542.1 211 EDAKNMIDqTGCDYVMIGRGA 231
                 *******6279******9885 PP

>> MR_MLE_C  Enolase C-terminal domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   5.9e-06     0.013      85     128 ..     185     228 ..     167     242 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.9e-06
                 THHHHHHHHHHHHSSEEEESTTSSSHHHHHHHHHHTSESEEEEB CS
    MR_MLE_C  85 ddleglaelrarasipiaagEslysradfrelleagavdivqpd 128
                 +d++ ++el+++++ipi+++ ++++++d+++++++ ++d+v++ 
  EPA04542.1 185 ADWKMIKELKEISNIPIVGNGDITTPEDAKNMIDQTGCDYVMIG 228
                 56788889997669***************************986 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   5.1e-06     0.011      58     117 ..     183     243 ..     135     249 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.1e-06
                   HHHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHH.CT-SEEEESHHHHH-THHHHHHHH CS
  His_biosynth  58 reanldlveeiaeevfipvqvGGGIrsledveelle.agadkviigtaavknpelikelae 117
                    +a+ ++++e+ e  +ip+   G I + ed++++++  g+d+v+ig  a+ np l++++ +
    EPA04542.1 183 GNADWKMIKELKEISNIPIVGNGDITTPEDAKNMIDqTGCDYVMIGRGAMGNPFLFEQIND 243
                   4567799***********988888*********997479**************99999876 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0     3e-05     0.066     193     243 ..     175     227 ..     113     229 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3e-05
                 HHCCCHB-TC--HHHHHHHHHHHSSEEEEEE.E-SHHHHHHHHH.TTESEEEE CS
      FMN_dh 193 efvgkqldpsltwddikwlreqtklplvvKG.vltaedakrave.aGvdgivv 243
                 + v++ ++ + +w+ ik+l+e  ++p+v  G + t+edak++++  G+d +++
  EPA04542.1 175 RTVSQGYSGNADWKMIKELKEISNIPIVGNGdITTPEDAKNMIDqTGCDYVMI 227
                 67777788999******************9989********996368998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       769  (0.0428914); expected 358.6 (0.02)
Passed bias filter:                      576  (0.0321267); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 2356.44
//
Query:       EPA04543.1  [L=56]
Description: hypothetical protein BG20_I0374 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 364.62
//
Query:       EPA04544.1  [L=175]
Description: hypothetical protein BG20_I0370 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-98  328.5  12.5    1.2e-98  328.3  12.5    1.0  1  Archaeal_AmoA  Archaeal ammonia monooxygenase subunit A (AmoA


Domain annotation for each model (and alignments):
>> Archaeal_AmoA  Archaeal ammonia monooxygenase subunit A (AmoA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  328.3  12.5  6.4e-103   1.2e-98      28     183 .]       2     157 ..       1     157 [. 0.99

  Alignments for each domain:
  == domain 1  score: 328.3 bits;  conditional E-value: 6.4e-103
  Archaeal_AmoA  28 vfsisqslmlvvgaiyyllftgvpgtatyyalimtvyvwvakgawfalgypydfivvpvwlpsamlldlaywatkrnkhaliliggvlvglslplf 123
                    vfsisq+lml vga+yyl+ftgvpgtatyyalimtvy+w+akgawfalgypydfiv+pvwlpsamlldlaywatk+nkh+lil+ggvlvg+slplf
     EPA04544.1   2 VFSISQTLMLAVGATYYLTFTGVPGTATYYALIMTVYTWIAKGAWFALGYPYDFIVTPVWLPSAMLLDLAYWATKKNKHSLILFGGVLVGMSLPLF 97 
                    9*********************************************************************************************** PP

  Archaeal_AmoA 124 nmvnlllvadplevafkyprptlpaymtpiepqvgkfynspvalgagagavlsvtiaalg 183
                    nmvnl++vadple+afkyprptlp+ymtpiepqvgkfynspvalgagagavlsvt++alg
     EPA04544.1  98 NMVNLITVADPLETAFKYPRPTLPPYMTPIEPQVGKFYNSPVALGAGAGAVLSVTFTALG 157
                    **********************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1239.30
//
Query:       EPA04545.1  [L=73]
Description: hypothetical protein BG20_I0337 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       797  (0.0444531); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.30s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 502.43
//
Query:       EPA04546.1  [L=40]
Description: hypothetical protein BG20_I0342 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.068   13.0   0.0      0.069   13.0   0.0    1.2  1  HTH_10    HTH DNA binding domain


Domain annotation for each model (and alignments):
>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.8e-06     0.069      31      47 ..      14      30 ..       3      36 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.8e-06
      HTH_10 31 kelGIskstlsehLrka 47
                k++G+s+st+++++r +
  EPA04546.1 14 KQMGVSESTAKDYIRTV 30
                89*************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      189  (0.0105416); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.32u 0.25s 00:00:00.57 Elapsed: 00:00:00.40
# Mc/sec: 297.16
//
Query:       EPA04547.1  [L=243]
Description: cytochrome C biogenesis protein transmembrane region [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.6e-49  166.7  21.5    7.8e-49  166.4  21.5    1.0  1  DsbD             Cytochrome C biogenesis protein transmembran
    3.9e-06   26.9  15.0      6e-06   26.3  15.0    1.3  1  DsbD_2           Cytochrome C biogenesis protein transmembran
    0.00052   19.5   7.8      0.017   14.6   3.0    2.5  2  SfLAP            Sap, sulfolipid-1-addressing protein
  ------ inclusion threshold ------
       0.55    9.8   0.0       0.55    9.8   0.0    2.7  4  Baculo_11_kDa    Baculovirus 11 kDa family
       0.58    9.6  15.7       0.92    8.9  13.3    1.9  2  DUF373           Domain of unknown function (DUF373)


Domain annotation for each model (and alignments):
>> DsbD  Cytochrome C biogenesis protein transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.4  21.5   2.2e-52   7.8e-49       2     213 .]      10     224 ..       9     224 .. 0.90

  Alignments for each domain:
  == domain 1  score: 166.4 bits;  conditional E-value: 2.2e-52
        DsbD   2 flaGllsflsPCilpliPaylsyisgvsvedvktekkkv......kvllkallFvlGlslvfvslglsaaf.lgqllkdvkevirrvaglivillGlhf 93 
                 + aG+ sf++PCilp+iPa+l+yisg++v++  ++++         ++l++++FvlG+s+vf++lg+ +   l ++ +++ + +++v+g+i+i +G+ +
  EPA04547.1  10 LIAGIGSFVAPCILPMIPAFLAYISGTTVTELSSKNNSTisinrtGIILNTVFFVLGFSIVFSALGVLINSvLSSVSGEIIQSLNYVGGVIIISFGIFL 108
                 89***************************9987764332255655789******************987650566677********************* PP

        DsbD  94 lgvfkievleklklllkikkkaelsvlgalllGltFalgwsPCigPvlasvlalaaskeslakgallllvyvlGlaipfllvglllellkkklkslkky 192
                 l   ki+ l+ +k+     k+++ s+  ++++Gl+Fa+gw+PC+gP+l+++l+laa++   + +  lll+y+lGl+ipf+l+g++++++ k +k ++k+
  EPA04547.1 109 LLSTKIKSLNIEKKYFP--KRTKSSYPLSFVFGLAFAAGWTPCVGPILGTILTLAATTP--SVSFHLLLAYSLGLGIPFVLIGIFFSRATKIIKGMSKH 203
                 99899********9955..555555788*******************************..78899********************************* PP

        DsbD 193 skaveiaggvllvllGvllll 213
                  k+ + + g  +++lG+l+++
  EPA04547.1 204 LKYYNLILGGFIIFLGILVFT 224
                 ******************975 PP

>> DsbD_2  Cytochrome C biogenesis protein transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3  15.0   1.7e-09     6e-06       2     198 ..       9     220 ..       8     228 .. 0.68

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 1.7e-09
      DsbD_2   2 afllgLlgsl.hClgmCggivlalslsk.........p.....kra...lalllynlGRilsYallGalvgllgsvlqlageleglrallgvllgllll 82 
                 a+++g+ + + +C++   +  la+ +           +     +r+   l+++++ lG  + +++lG+l+  + s+++    +++l+ + gv+++ +++
  EPA04547.1   9 ALIAGIGSFVaPCILPMIPAFLAYISGTtvtelssknNstisiNRTgiiLNTVFFVLGFSIVFSALGVLINSVLSSVSGEI-IQSLNYVGGVIIISFGI 106
                 677777777788888888888888555544445433212232323354347************************996654.68899999999999999 PP

      DsbD_2  83 llglklllkkkllklerlgkllsrllkklakklkslasalllG..llnGllpC..glvysalllalasgsaleGalvmlaFgLGTlpalllfglllgll 177
                 +l+l+     k   +++l+   ++++ k +k   s++ ++++G  ++ G+ pC  +++ ++l+la+++ s++    ++la++LG  ++++l+g++++++
  EPA04547.1 107 FLLLST----K---IKSLN-IEKKYFPKRTK--SSYPLSFVFGlaFAAGWTPCvgPILGTILTLAATTPSVS--FHLLLAYSLGLGIPFVLIGIFFSRA 193
                 966555....3...33333.33455666666..3566666666115679****9445556677777776665..6777777777778888888888888 PP

      DsbD_2 178 skklr......kkllrlagvllillgl 198
                 +k ++      k  + ++g+++i+lg+
  EPA04547.1 194 TKIIKgmskhlKYYNLILGGFIIFLGI 220
                 774444444434444588999999987 PP

>> SfLAP  Sap, sulfolipid-1-addressing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   3.0   4.7e-06     0.017      28     123 ..      57     146 ..      51     174 .. 0.74
   2 !    5.5   4.1    0.0029        10       4      89 ..     140     225 ..     137     234 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.7e-06
       SfLAP  28 vlnllaFlvgwlvvlvalglivlfvlrsllsgasaapssaikalqivlGvlllllaaveavrrpkassrselprllsrle.slleggalwvAlvlgl 123
                 +ln ++F++g  +v  alg+++  vl+s++       + +i+ l +v Gv+++ ++++ +++++ +s   e++  ++r++ s +++ ++++A+++g 
  EPA04547.1  57 ILNTVFFVLGFSIVFSALGVLINSVLSSVS-------GEIIQSLNYVGGVIIISFGIFLLLSTKIKSLNIEKKYFPKRTKsSYPLSFVFGLAFAAGW 146
                 678888999999998888888877777777.......668***********************8888888888888888865666666666666553 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0029
       SfLAP   4 lAlvvalsPl..rlgvavlllsrprpvlnllaFlvgwlvvlvalglivlfvlrsllsgasaapssaikalqivlGvlllllaaveavr 89 
                 lA+++   P   ++  ++l l +  p  +  + l+  l  +++ +li +f++r++   + ++ s+++k   ++lG+++++l+++++++
  EPA04547.1 140 LAFAAGWTPCvgPILGTILTLAATTPSVSFHLLLAYSLGLGIPFVLIGIFFSRATK--IIKGMSKHLKYYNLILGGFIIFLGILVFTN 225
                 44444444431246667777777777766666666666677788888888888777..446679999999999999999999988876 PP

>> Baculo_11_kDa  Baculovirus 11 kDa family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.1       2.9     1e+04      49      59 ..       4      14 ..       4      19 .. 0.62
   2 ?   -1.6   0.3      0.55     2e+03      51      60 ..      61      70 ..      37      91 .. 0.63
   3 ?   -1.4   0.0      0.51   1.8e+03      47      67 ..      99     118 ..      96     132 .. 0.45
   4 ?    9.8   0.0   0.00015      0.55      29      61 ..     200     232 ..     191     238 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 2.9
  Baculo_11_kDa 49 ivlfilLlvvi 59
                   i++f+ L+  i
     EPA04547.1  4 ITIFVALIAGI 14
                   55677777655 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.55
  Baculo_11_kDa 51 lfilLlvvil 60
                   +f++L ++i+
     EPA04547.1 61 VFFVLGFSIV 70
                   3333333332 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.51
  Baculo_11_kDa  47 vvivlfilLlvvilknaeaee 67 
                    v+i+ f ++l+ +++++++ +
     EPA04547.1  99 VIIISFGIFLL-LSTKIKSLN 118
                    44444422222.222233333 PP

  == domain 4  score: 9.8 bits;  conditional E-value: 0.00015
  Baculo_11_kDa  29 NrsflrdFvLvicglvvfvvivlfilLlvvilk 61 
                      + l+ + L+++g+++f+ i++f   l +i++
     EPA04547.1 200 MSKHLKYYNLILGGFIIFLGILVFTNQLAYIAN 232
                    56679999****************998888876 PP

>> DUF373  Domain of unknown function (DUF373)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   1.5    0.0046        17     258     317 ..      14      78 ..       3      86 .. 0.55
   2 ?    8.9  13.3   0.00026      0.92     155     318 ..      59     231 ..      56     242 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0046
      DUF373 258 ilafiygavewlalailtaslgkiideylkre.....ekdiarllllpflvlaiglvlygasayl 317
                 i +f++  +  ++ a+l+++ g+ + e+ +++      +++  +l+++f+vl + +v+ ++   +
  EPA04547.1  14 IGSFVAPCILPMIPAFLAYISGTTVTELSSKNnstisINRTGIILNTVFFVLGFSIVFSALGVLI 78 
                 55566666666666666666666666666555454433333344455555555555555444433 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00026
      DUF373 155 ktiLvplGlllliyallll............lglpelalaiillllGlylll....rGfgldelleelleklkesleegritfvtyvvallllligiis 237
                 +t++ +lG+ +++ al +l            +++ +++ ++i++ +G++lll    + +++++  ++++ k  +s +  +++f  +++a     +g i 
  EPA04547.1  59 NTVFFVLGFSIVFSALGVLinsvlssvsgeiIQSLNYVGGVIIISFGIFLLLstkiKSLNIEK--KYFP-KRTKSSYPLSFVFGLAFAAGWTPCVGPIL 154
                 68899999999999998888999999****99999***************9633337888888..4445.55555566666677777888888999999 PP

      DUF373 238 gyislesvssasvssglltlilafiygavewlalailtaslgkiideylkreekdiarllllpflvlaiglvlygasayll 318
                 g+i + ++++ svs +ll  ++  +   +++++++i+++ ++kii+ +  ++  + ++l+l  f+++   lv+++  ay+ 
  EPA04547.1 155 GTILTLAATTPSVSFHLL--LAYSLGLGIPFVLIGIFFSRATKIIKGMS-KH-LKYYNLILGGFIIFLGILVFTNQLAYIA 231
                 977766666634333333..333356789999999999********999.43.3555677777777777777799999984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       873  (0.0486921); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1506.52
//
Query:       EPA04548.1  [L=265]
Description: ATPase, AAA family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-23   83.0   0.1    2.7e-23   82.5   0.1    1.2  1  AAA_5            AAA domain (dynein-related subfamily)
    3.7e-13   49.5   0.0    5.2e-13   49.0   0.0    1.2  1  AAA_3            ATPase family associated with various cellul
    1.1e-07   32.4   0.0    1.8e-07   31.7   0.0    1.4  1  AAA              ATPase family associated with various cellul
    5.1e-06   26.3   0.0    9.3e-06   25.5   0.0    1.4  1  Sigma54_activat  Sigma-54 interaction domain
    5.6e-06   26.0   0.0    9.8e-06   25.2   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
    7.7e-06   26.0   0.1    1.2e-05   25.3   0.1    1.3  1  AAA_14           AAA domain
    2.2e-05   24.5   0.1    3.2e-05   24.0   0.1    1.3  1  ATPase_2         ATPase domain predominantly from Archaea
     0.0001   22.8   0.1    0.00027   21.4   0.0    1.9  2  AAA_16           AAA ATPase domain
    0.00057   19.0   0.0    0.00095   18.3   0.0    1.3  1  MCM              MCM P-loop domain
    0.00077   18.5   0.0     0.0044   16.0   0.0    1.9  1  AAA_6            Hydrolytic ATP binding site of dynein motor 
    0.00082   19.1   0.4       0.06   13.1   0.2    2.8  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
     0.0013   19.0   0.0     0.0023   18.2   0.0    1.5  1  AAA_22           AAA domain
     0.0014   18.8   0.0      0.011   15.9   0.0    2.0  2  Sigma54_activ_2  Sigma-54 interaction domain
      0.002   18.0   0.0      0.003   17.4   0.0    1.2  1  AAA_11           AAA domain
     0.0028   17.1   0.0       0.42   10.0   0.0    2.2  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0031   18.1   0.0     0.0062   17.1   0.0    1.5  1  AAA_18           AAA domain
      0.006   16.8   0.1      0.012   15.9   0.1    1.4  1  Roc              Ras of Complex, Roc, domain of DAPkinase
  ------ inclusion threshold ------
      0.013   15.7   0.0      0.025   14.8   0.0    1.4  1  AAA_28           AAA domain
      0.018   14.8   0.1      0.092   12.5   0.0    2.1  2  AAA_30           AAA domain
      0.018   15.2   0.5      0.054   13.6   0.5    1.8  1  AAA_2            AAA domain (Cdc48 subfamily)
      0.034   13.6   0.0      0.079   12.4   0.0    1.6  1  TniB             Bacterial TniB protein
      0.035   14.4   0.0      0.071   13.4   0.0    1.5  1  CbbQ_C           CbbQ/NirQ/NorQ C-terminal
      0.039   13.7   0.1       0.11   12.2   0.1    1.8  2  AAA_24           AAA domain
      0.041   13.8   0.0      0.076   12.9   0.0    1.5  1  RsgA_GTPase      RsgA GTPase
       0.07   13.1   0.0       0.14   12.1   0.0    1.4  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.073   11.8   0.0       0.12   11.1   0.0    1.2  1  RNA12            RNA12 protein
      0.079   12.5   0.1       0.14   11.8   0.1    1.4  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
      0.084   13.4   0.1       0.17   12.4   0.1    1.6  1  ABC_tran         ABC transporter
      0.092   11.9   0.0       0.37    9.9   0.0    1.8  2  DUF815           Protein of unknown function (DUF815)
        0.1   12.8   0.0       0.18   11.9   0.0    1.6  1  AAA_33           AAA domain


Domain annotation for each model (and alignments):
>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.5   0.1   4.5e-26   2.7e-23       2     138 .]      27     161 ..      26     161 .. 0.93

  Alignments for each domain:
  == domain 1  score: 82.5 bits;  conditional E-value: 4.5e-26
                 EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG--HHHHHHHHHHHHSSE.EE..-S CS
       AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEveraesevlnsLlslleerr.llleeg 99 
                 vl++Gp+GtgK++l++ +a+  n ++e ++++ +t+e++l+g   +++gt  ++++ l ++++eg++l+lDE++ ae +vl +L   l++rr + l e+
  EPA04548.1  27 VLIIGPKGTGKTSLVRDFAENKNMKLESINFSLRTRESHLIGTKTLTDGTVNFEEGLLIKSMKEGSMLYLDEINAAEADVLLRLDEALDDRRqIILKES 125
                 89**************************************************************************************99873555666 PP

                 SSEEE---......-EEEEEESS--..-TT-TTHHHHTT- CS
       AAA_5 100 gelvkaknddllerfrviatanpld.rslnelspalrsRf 138
                 ++++ +++++    + viat npl   + +el p+l+sRf
  EPA04548.1 126 TGETVKAKEG----WFVIATINPLThSGTKELPPQLLSRF 161
                 6666666656....***********999***********9 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0   0.0   8.7e-16   5.2e-13       2     129 ..      27     161 ..      26     163 .. 0.85

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 8.7e-16
       AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfa.....nllladeinrappktqsalleameer.qvtve 94 
                 vl+ g  G++kt lv+ +a+  +++++ i f      s ++Gt+ +++ +  ++f++G +++     ++l  dein a++ +   l ea+++r q+ ++
  EPA04548.1  27 VLIIGPKGTGKTSLVRDFAENKNMKLESINFSLRTRESHLIGTKTLTDGT--VNFEEGLLIKsmkegSMLYLDEINAAEADVLLRLDEALDDRrQIILK 123
                 899999**************************************998765..55667777652222257999******************986266654 PP

       AAA_3  95 ...gethklpepflvlatqnPieqeGtyplpeaqldrf 129
                    get k +e ++v+at nP+ ++Gt +lp   l rf
  EPA04548.1 124 estGETVKAKEGWFVIATINPLTHSGTKELPPQLLSRF 161
                 22267889999*********************999999 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.0     3e-10   1.8e-07       1     131 [.      27     168 ..      27     169 .. 0.69

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 3e-10
                 EEEESSTTSSHHHHHHHHHHHHT.....HEE.EEEETTTCS.SSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHH CS
         AAA   1 vllyGppGtGKTllakavakelg.....vef.leisgsell.skyvgesekkirelfkeakekakpsilfiDEidalaksrsgseseeeervvnqLlte 92 
                 vl++Gp+GtGKT+l++  a++ +     ++f l++  s l+  k++ ++  +++e +  +k++++ s l +DEi a   +   + +e  ++  + +l+e
  EPA04548.1  27 VLIIGPKGTGKTSLVRDFAENKNmklesINFsLRTRESHLIgTKTLTDGTVNFEEGL-LIKSMKEGSMLYLDEINAAEADVLLRLDEALDDRRQIILKE 124
                 799******************661122233334444445554557777777777776.346665459*********97777444555555555666666 PP

                 HHHTTTS.SSTEEEEEEESS.....GGGSTHHHHSTTSSEEEETT CS
         AAA  93 ldgvkkk.eskvivigatnr.....pdkldpallrgRfdrkieie 131
                   g++ k ++  +vi++ n       ++l+p+ll +Rf ++i +e
  EPA04548.1 125 STGETVKaKEGWFVIATINPlthsgTKELPPQLL-SRFPVRISLE 168
                 6666666355577777666577778999******.9****99876 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   1.5e-08   9.3e-06      10     131 ..      12     128 ..       5     164 .. 0.73

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1.5e-08
                      HHHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBSSSSSTTTSS-BEHHHHHT..TTSEEEEET CS
  Sigma54_activat  10 elleqikkvaktdlsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhekGaFtGAekekkGlfeka..dgGtlfLDe 101
                      + ++ ++k+ + dl vli G +GtGK+ l r   e+++    ++ ++n +    +  es+L G++     G+ + ++Gl+ k+  +g++l+LDe
       EPA04548.1  12 DSIRILNKAYEADLFVLIIGPKGTGKTSLVRDFAENKN---MKLESINFS---LRTRESHLIGTKTL-TDGTVNFEEGLLIKSmkEGSMLYLDE 98 
                      6678899999*****************99998765554...555566655...455689****8764.478888899998654337889***** PP

                      GGGS-HHHHHHHHHHHHHSEEESBTSSSEE CS
  Sigma54_activat 102 igelplelQekLlrvlqegevervGsskei 131
                      i+  ++++  +L ++l++++   + +s+  
       EPA04548.1  99 INAAEADVLLRLDEALDDRRQIILKESTGE 128
                      *******99999999999876555444433 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   1.6e-08   9.8e-06      25     115 ..      16     105 ..       9     109 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1.6e-08
       AAA_7  25 llelllknkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanql..qdiiesklekrrkgvygPpggkklvvFvDDlnmpake 115
                 +l++  +++  vl++Gp+GtGKt++++d+ ++ +   ++  +infs +t  ++l   +++ +     ++g++   +++  ++++D++n  + +
  EPA04548.1  16 ILNKAYEADLFVLIIGPKGTGKTSLVRDFAENKN---MKLESINFSLRTRESHLigTKTLTDGTVNFEEGLLIKSMKEGSMLYLDEINAAEAD 105
                 56777888889******************98877...88888899988887765224555555555556666666666666778888877666 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.1     2e-08   1.2e-05       4      97 ..      26     122 ..      23     134 .. 0.67

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 2e-08
      AAA_14   4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderd.....kkladpe....kllelileklkeekktylflDEiqevp.ewekalkslvdegkn 92 
                  ++i G++ +GKT l++++++++   k + + ++l + +      k   + +    +++e +l k + ++ ++l+lDEi  ++ ++   l + +d++  
  EPA04548.1  26 FVLIIGPKGTGKTSLVRDFAENKN-MKLESINFSLRTREShligtK---TLTdgtvNFEEGLLIKSM-KEGSMLYLDEINAAEaDVLLRLDEALDDR-- 117
                 689*****************9999.556666666666555343322...222233445555555544.58999******998525667777777766.. PP

      AAA_14  93 ldviv 97 
                  ++i+
  EPA04548.1 118 RQIIL 122
                 25555 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.1   5.4e-08   3.2e-05       7     121 ..      13     121 ..       7     124 .. 0.70

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 5.4e-08
    ATPase_2   7 elkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekalgiavpkaeleeilk.eksklvfk 104
                  ++ l++ +e   + +++i Gp+g GKt+L++ ++en++ k + + +    re+ +  +++    ++   ++e+ l+i+  k     +l  ++++ +++
  EPA04548.1  13 SIRILNKAYEA--DLFVLIIGPKGTGKTSLVRDFAENKNMKLESINFSLRTRESHLIGTKTL---TDGTVNFEEGLLIKSMKEGS--MLYlDEINAAEA 104
                 56667777666..99***********************999999999998888887777776...56666677777777666555..233355555555 PP

    ATPase_2 105 aielllekikkkgkkii 121
                  + l l++  +++++ii
  EPA04548.1 105 DVLLRLDEALDDRRQII 121
                 55555555545555555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   4.5e-07   0.00027      25      46 ..      25      46 ..      12     167 .. 0.75
   2 ?   -2.0   0.0       6.9   4.1e+03      56      88 ..     183     207 ..     175     234 .. 0.67

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 4.5e-07
      AAA_16 25 elvllsGesGvGKsslvrellr 46
                  vl++G++G+GK+slvr +++
  EPA04548.1 25 LFVLIIGPKGTGKTSLVRDFAE 46
                68******************97 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 6.9
      AAA_16  56 lrgkcdqlesaipysalaqalareellrqllde 88 
                 ++g+ d+         ++qa++   +lrq ++ 
  EPA04548.1 183 VSGNHDSE--------IIQAIKLANILRQAAAV 207
                 55556666........77777666666665554 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.6e-06   0.00095      54     205 ..      21     168 ..      13     187 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.6e-06
                 BCSS-EEEEEESSTSTHHHHHHHHHHHSSSEEEEESSS..SSSSHSSSEEEEESSSSSEEEEETHHHHT..TTSEEEEESGGGSTCHHHHHHHHHHHHS CS
         MCM  54 lrgdinvllvgdpgtaKsqlLkyveklapravytsgkg..ssaagLtaavvrdeetgefvleaGalvla..dkGvcciDefdkmkeedrsalhEamEqq 148
                 + +d  vl++g  gt+K+ l++  +++ +        +  + ++ L    ++  + g + +e G l+ +  ++ ++++De++  + +    l Ea+++ 
  EPA04548.1  21 YEADLFVLIIGPKGTGKTSLVRDFAENKNMKLESINFSlrTRESHLIG--TKTLTDGTVNFEEGLLIKSmkEGSMLYLDEINAAEADVLLRLDEALDDR 117
                 567899****************99876655544333330034444544..4677788899*******7632556899*********************9 PP

                 EEEEESSSCEEEEE--EE..EEEEE--SSSSCCTTS-HHHHSSSSHHHHHHSSEEEEE- CS
         MCM 149 tisiaKaGivatLnarts..vlaAanpkagrydkkksvaeninlsaalLsrFDlifvll 205
                    i K +   t++a+    v+a +np +         +   +l+++lLsrF + + l 
  EPA04548.1 118 RQIILKESTGETVKAKEGwfVIATINPLTH--------SGTKELPPQLLSRFPVRISLE 168
                 999****99******9755599*****872........223367888888887766555 PP

>> AAA_6  Hydrolytic ATP binding site of dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   7.3e-06    0.0044      24     159 ..      16     161 ..      11     192 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 7.3e-06
       AAA_6  24 tltqAlklklggapaGpagtGKtEtvkdLakalakqvvvfncsdqldyksl......g....kifkGl....aqsGaWgCfdeFnrielevLSvvaqqi 108
                  l +A++  l   + Gp gtGKt  v+d+a++  + +  +n s +   + l      +    ++ +Gl    ++ G+   +de+n  e++vL    + +
  EPA04548.1  16 ILNKAYEADLFVLIIGPKGTGKTSLVRDFAENKNMKLESINFSLRTRESHLigtktlTdgtvNFEEGLliksMKEGSMLYLDEINAAEADVLLRLDEAL 114
                 57899*************************988887777777654443332111111211114556763333366888888888888888876666666 PP

       AAA_6 109 ktiqqalkekkkkfvfegkeiklnksvgifitmnp.gyagrteLPdnLkalf 159
                    +q + +++     +g+++k ++   ++ t+np + +g +eLP  L + f
  EPA04548.1 115 DDRRQIILKES-----TGETVKAKEGWFVIATINPlTHSGTKELPPQLLSRF 161
                 65555555444.....477888888888888999977789999998887766 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.2    0.0001      0.06      34     116 ..      25     121 ..      13     166 .. 0.69
   2 ?    0.0   0.0       1.1   6.3e+02      91     124 ..     198     233 ..     189     241 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.0001
      RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvklkitsgPvlekagdlaa...............lltnleekdvlfideihrlsraveevlysamedfrldiv 116
                   vl++Gp G Gkt+l +  a++ ++kl++       +++ l++               l+++++e+ +l++dei   +  v   l  a++d r  i+
  EPA04548.1  25 LFVLIIGPKGTGKTSLVRDFAENKNMKLESINFSLRTRESHLIGtktltdgtvnfeeglLIKSMKEGSMLYLDEINAAEADVLLRLDEALDDRRQ-II 121
                 479***************99999888877666555555555543221111222222232456788888899999888888888888888888763.33 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.1
      RuvB_N  91 deihrlsraveevlysa..medfrldivigkGpsar 124
                  +i r + avee++ys    e +++  +++kG s++
  EPA04548.1 198 ANILRQAAAVEELFYSPslRETIAFGKLLEKGMSSK 233
                 5788999999***99741136666677777777665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   3.8e-06    0.0023       5      32 ..      24      51 ..      20     122 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.8e-06
      AAA_22  5 agilvvtGesGtGKTtllrrlleqldee 32
                + +++++G++GtGKT l+r ++e+++  
  EPA04548.1 24 DLFVLIIGPKGTGKTSLVRDFAENKNMK 51
                5689******************998544 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.8e-05     0.011      14      95 ..      17     116 ..      13     123 .. 0.73
   2 ?   -1.1   0.0         3   1.8e+03      67      91 ..     131     155 ..     121     167 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.8e-05
                      HHHHHT-SS-EEEEEETT--HHHHHHCC--TTS-EE--SSTTHHHH-H................HHHHHH....T..TTSEEEEEE-TT--HHH CS
  Sigma54_activ_2  14 LeqaaqsklpvfltGekGsgkelvArlLhknsgpwleifvverlaklp................ldlleq....a..kggtLylkdiadlskae 85 
                      L++a ++ l v+++G+kG+gk++  r +++n+  +le  ++     +                           +  +g +Lyl +i+  +++ 
       EPA04548.1  17 LNKAYEADLFVLIIGPKGTGKTSLVRDFAENKNMKLESINFSLRTREShligtktltdgtvnfeE----GllikSmkEGSMLYLDEINAAEADV 106
                      78899999******************999999988887777433332234566556655544442....0332214488899999999999999 PP

                      HHHHHHHHHH CS
  Sigma54_activ_2  86 qkeLlellak 95 
                      + +L e+l+ 
       EPA04548.1 107 LLRLDEALDD 116
                      9999988876 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 3
                      HTTTSEEEEEE-TT--HHHHHHHHH CS
  Sigma54_activ_2  67 qakggtLylkdiadlskaeqkeLle 91 
                      +ak+g +++  i+ l  +  keL+ 
       EPA04548.1 131 KAKEGWFVIATINPLTHSGTKELPP 155
                      5899999999999999999988875 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0     5e-06     0.003       7      76 ..      14     112 ..      10     127 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5e-06
      AAA_11   7 reaiksalseseitliqGPPGtgKTktivellsqll..............sr...............rkseeeksakpriLvCapSNaAvDellerllr 76 
                  + +++a++ + ++li GP GtgKT+ +  + ++ +              s+               +    + +++  +L+  + NaA  ++l+rl +
  EPA04548.1  14 IRILNKAYEADLFVLIIGPKGTGKTSLVRDFAENKNmklesinfslrtreSHligtktltdgtvnfeEGLLIKSMKEGSMLYLDEINAAEADVLLRLDE 112
                 5667999************************99997656555555555441144444455555444322555667777777777777777777777655 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0      0.02        12      25      41 ..      27      43 ..      12      53 .. 0.86
   2 !   10.0   0.0   0.00071      0.42      83     159 ..      65     145 ..      45     169 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.02
  Mg_chelatase 25 lllvGppGsGKtmlakr 41
                  +l++Gp G+GKt l + 
    EPA04548.1 27 VLIIGPKGTGKTSLVRD 43
                  799*********99875 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00071
  Mg_chelatase  83 hsaskaalvGggskpkpGeisla.hnG.vLfLDElpefkrkvlevLRePledgevtisrakakvefpar..fqlvaamNpc 159
                   h + + +l  g  + + G + ++ ++G +L+LDE+   +++vl  L e l+d++  i + ++  +  a+    ++a++Np 
    EPA04548.1  65 HLIGTKTLTDGTVNFEEGLLIKSmKEGsMLYLDEINAAEADVLLRLDEALDDRRQIILKESTGETVKAKegWFVIATINPL 145
                   555666677777777777654441334399*********************998888887776666665226788889985 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0     1e-05    0.0062       1      78 [.      27     138 ..      27     145 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1e-05
      AAA_18   1 IlltGtpGvGKttlakeLskrlgf...............................gvnlrdvakenglllevdpe.aldeskrldedkldklldaleen 67 
                 +l+ G+ G+GKt+l +  ++  ++                               g  ++++   ++l+l++ ++ + d  +rlde  +d+ + +l+e+
  EPA04548.1  27 VLIIGPKGTGKTSLVRDFAENKNMklesinfslrtreshligtktltdgtvnfeeGLLIKSMKEGSMLYLDEINAaEADVLLRLDEALDDRRQIILKES 125
                 79****************999777999999999999999999999999999999999999999999999999888888888888888888888888776 PP

      AAA_18  68 ss..aleegknlv 78 
                       +++++ v
  EPA04548.1 126 TGetVKAKEGWFV 138
                 6555445555555 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   1.9e-05     0.012       2      39 ..      27      64 ..      27      80 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.9e-05
                EEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEE CS
         Roc  2 vvlvGdsgvGKtsllkrfvedkfsekekstigvdfltk 39
                v+++G +g+GKtsl++ f e+k  + e+  +++ + ++
  EPA04548.1 27 VLIIGPKGTGKTSLVRDFAENKNMKLESINFSLRTRES 64
                689****************9998777666555555544 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   4.2e-05     0.025       2      23 ..      27      49 ..      26      62 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.2e-05
      AAA_28  2 ivitGgestGKTtlleaLaar.g 23
                + i+G+ +tGKT+l++ +a++ +
  EPA04548.1 27 VLIIGPKGTGKTSLVRDFAENkN 49
                78*****************8743 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00015     0.092      16     114 ..      22     116 ..      15     123 .. 0.62
   2 ?   -1.9   0.0       3.8   2.3e+03     146     159 ..     192     205 ..     184     221 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00015
      AAA_30  16 sgdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgieastiakllkrlk.grarlepgtllivDEagmvdtkqlaallkaae 113
                 + d+++++ Gp GtGKt +++  +e  + +  + i ++   + ++ +++++ +       +  + +   +++++g++l  DE+  + ++ l +l +a++
  EPA04548.1  22 EADLFVLIIGPKGTGKTSLVRDFAENKNMK-LESINFSLRTRESHLIGTKTLT----DGTVNFEEGlLIKSMKEGSMLYLDEINAAEADVLLRLDEALD 115
                 456899*************99998876655.4556666666666666544332....111111112222345666777777777777777777766666 PP

      AAA_30 114 k 114
                 +
  EPA04548.1 116 D 116
                 5 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.8
      AAA_30 146 igtaeLtevvRqke 159
                 i++++L ++ Rq+ 
  EPA04548.1 192 IQAIKLANILRQAA 205
                 56777777887754 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.5     9e-05     0.054       6     125 ..      27     139 ..      24     164 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9e-05
                 EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS.........EEEEETGGG-------------HHH CS
       AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG.........ivllDEidKihpkessgadvSregV 95 
                 +l++gp+g+Gkt l +  ae  ++    kl  ++ s  +     e+ +   +   +g v++eeg          +++lDEi  + +           +V
  EPA04548.1  27 VLIIGPKGTGKTSLVRDFAENKNM----KLESINFSLRTR----ESHLIGTKTLTDGTVNFEEGLliksmkegsMLYLDEINAAEA-----------DV 106
                 5899*******************9....677777666666....444445555667888888877888888888********9999...........77 PP

                 HHHHHHHHH--E...E-------EE-TT-EEEE CS
       AAA_2  96 qrdLLqileggt...ltdkqgrkvdtknilfIm 125
                 +  L   l++ +   l+++ g++v+ k+  f++
  EPA04548.1 107 LLRLDEALDDRRqiiLKESTGETVKAKEGWFVI 139
                 777777777655333456666666666666555 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00013     0.079      38      61 ..      27      50 ..      16      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
        TniB 38 lllvGdsnnGKtmivekFarlhpp 61
                +l++G+  +GKt++v+ Fa++++ 
  EPA04548.1 27 VLIIGPKGTGKTSLVRDFAENKNM 50
                79*****************99875 PP

>> CbbQ_C  CbbQ/NirQ/NorQ C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   0.00012     0.071       1      61 [.     175     237 ..     175     246 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00012
                 HHHHHHHHH.T--HHHHHHHHHHHHHHHTTBTT.TBSS---HHHHHHHHHHHTTT--HHHHHH CS
      CbbQ_C   1 Eaeivares.gldeevakkLVklAneiRnlkeg.gLeegvSTRlLvyaAkLiasglpareacr 61 
                 E eiv+r   g  ++ + + +klAn +R+     +L   +S R  ++ +kL ++g++ +e+++
  EPA04548.1 175 ELEIVKRHVsGNHDSEIIQAIKLANILRQAAAVeELFYSPSLRETIAFGKLLEKGMSSKESAK 237
                 678888776577777777789*******8877636**********************998876 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00019      0.11       5      23 ..      27      45 ..      24     112 .. 0.89
   2 ?   -1.2   0.0       2.4   1.4e+03     163     194 ..     103     133 ..      60     135 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00019
      AAA_24  5 iliyGpsgiGKTtlakelg 23
                +li+Gp g+GKT+l++ + 
  EPA04548.1 27 VLIIGPKGTGKTSLVRDFA 45
                79*************9993 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.4
      AAA_24 163 evDlvlranlkredkvgervlktsksesidaK 194
                 e+D++lr++    d+  + +lk+s+ e++ aK
  EPA04548.1 103 EADVLLRLDE-ALDDRRQIILKESTGETVKAK 133
                 5777888774.355666777777777777777 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00013     0.076      91     132 ..      15      57 ..       5      86 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00013
                  HHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S---- CS
  RsgA_GTPase  91 eelkellkd.ktsvlvGqSGvGKStLinallpelelktgevse 132
                  + l+++ +   +++++G+ G GK++L+  +++++++k +++  
   EPA04548.1  15 RILNKAYEAdLFVLIIGPKGTGKTSLVRDFAENKNMKLESINF 57 
                  5566666653567789*****************9999998865 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00024      0.14      19      52 ..      24      56 ..       8      63 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00024
                TEEEEEEESTTSSHHHHHHHHHHHTT------TT CS
        TsaE 19 gdvilLeGdLGaGKTtlvrglakalgveevkSPT 52
                  ++l+ G+ G+GKT lvr +a++ ++ + +S  
  EPA04548.1 24 DLFVLIIGPKGTGKTSLVRDFAENKNM-KLESIN 56
                446999****************99876.455555 PP

>> RNA12  RNA12 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0    0.0002      0.12      16      40 ..      23      45 ..      16      59 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0002
       RNA12 16 vntFivvkGPrGSGkkeLvldrvlk 40
                ++ F+++ GP+G Gk++Lv d   +
  EPA04548.1 23 ADLFVLIIGPKGTGKTSLVRD--FA 45
                577****************44..33 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00023      0.14       3      99 ..      27     135 ..      25     151 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00023
                 EEEEESTTCCHHHHHHHHHCT--SS-EEEEESS-SSCHCCCCCCHCC..CT.EEEETTTTECCHCTT-HHHHHHHHHHHH............TT-SEEE CS
        cobW   3 tvltGflGsGKTtLlnhllenraglklavivNefgevsiDaellret..gveivelenGciCctlredllkelealeere............erldvil 87 
                 +++ G+ G+GKT+L++   en +++kl  i   +     +++l+ ++  ++ +v++e+G +  +++e  +  l+++ + e            +r ++il
  EPA04548.1  27 VLIIGPKGTGKTSLVRDFAEN-KNMKLESINFSLR--TRESHLIGTKtlTDGTVNFEEGLLIKSMKEGSMLYLDEINAAEadvllrldealdDRRQIIL 122
                 6799**************977.6777777765555..55555664442444477777777777777777777777777777777777788887788888 PP

                 EEECT.TTTHHHH CS
        cobW  88 iEttG.laePapv 99 
                  E+tG  +++++ 
  EPA04548.1 123 KESTGeTVKAKEG 135
                 8999988877765 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00028      0.17      13      45 ..      26      58 ..      17     131 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00028
                EEEEEESTTSSHHHHHHHHTTSS--SEEEEEET CS
                xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran 13 kvaivGenGaGKStLlkllagllkpteGeilld 45
                 v i+G+ G+GK++L++ +a++ + + ++i++ 
  EPA04548.1 26 FVLIIGPKGTGKTSLVRDFAENKNMKLESINFS 58
                588**************9999998888888554 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00062      0.37      56      77 ..      27      48 ..      12      64 .. 0.82
   2 ?   -0.8   0.0       1.2     7e+02     182     210 ..     157     185 ..     117     209 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00062
      DUF815 56 vLLwGarGtGKSslvkallney 77
                vL++G +GtGK slv+   ++ 
  EPA04548.1 27 VLIIGPKGTGKTSLVRDFAENK 48
                89**************877654 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.2
      DUF815 182 LsdRFGlwlgFykldqeeYleiveklakk 210
                 L  RF + ++ + ++++  leiv++ ++ 
  EPA04548.1 157 LLSRFPVRISLEYPSENVELEIVKRHVSG 185
                 55799999999999999999999988743 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0    0.0003      0.18       2      24 ..      27      49 ..      26     141 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0003
      AAA_33  2 vllvGlpGsGKstlaerllkklg 24
                vl++G++G+GK+ l++  +++  
  EPA04548.1 27 VLIIGPKGTGKTSLVRDFAENKN 49
                799*************9987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       679  (0.0378716); expected 358.6 (0.02)
Passed bias filter:                      590  (0.0329076); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 1823.02
//
Query:       EPA04549.1  [L=420]
Description: serine--tRNA ligase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.8e-37  128.0   0.1    6.8e-37  127.2   0.1    1.4  1  tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, 
      3e-24   85.3  11.0    6.5e-24   84.2  11.0    1.6  1  Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
  ------ inclusion threshold ------
       0.43    9.8   5.4       0.23   10.7   3.4    1.5  2  TMPIT         TMPIT-like protein


Domain annotation for each model (and alignments):
>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.2   0.1   1.1e-40   6.8e-37       5     178 ..     219     397 ..     215     398 .. 0.94

  Alignments for each domain:
  == domain 1  score: 127.2 bits;  conditional E-value: 1.1e-40
                   ETTSEEEEE-SSSHHHHHHHHHHHEEEBGGSSEEEEEEEEEEBTTTS....TBCTTTB-SEEEEEEEEEEESGGGHHHHHHHHHHHHHHHHHHTT.S CS
                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  tRNA-synt_2b   5 drndreyiLkPtneetfvelirdevlrskrLPlklyqiqtkyRdEks....dsrGLlRvreFhqkdgyvfhaeaslddslrdlikaisriferlgle 97 
                    +n ++++++ t+e++++++++de++  k+LPl+++ +++++R+E+     d++G++Rv++F++ +++vf  +++++d+ ++++  +++++++l ++
    EPA04549.1 219 IEN-EDLYMIGTSEHAMAAMHSDEIIEGKDLPLRYAGVSPCFRKEAGahgrDQKGIFRVHQFDKIEQFVFTRPDESWDEHEKMLSNAEEFYQKLEIP 314
                   455.89******************9999******************77899********************************************** PP

                   CEEEEEEGTTSCBTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHTTEEEECTTS.SEEEEEEEEEE.EEHHHHHHHHHHH CS
                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx.xxxxxxxxxxxxx RF
  tRNA-synt_2b  98 fraiielmsaksadykdkkefeavsesltkgieigtiqklgtrlserlgatvldenn.reksvimicaa.igveRllsaileq 178
                   +++++++ +++    ++++++ea++  +++++ei++++++ +++++rl++++ d+ n   +  ++++ + i+++R+l  i+e+
    EPA04549.1 315 YKVLLLSSGDMGKVSAKTYDIEAWMAGQNAYREIVSCSNCLDYQARRLKIRFRDKTNeDTQYLHTLNSTlIATSRVLVSIMEN 397
                   9999998887878899**************************************9984667899****************997 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.2  11.0   1.1e-27   6.5e-24       1     107 [.       1     106 [.       1     107 [. 0.99

  Alignments for each domain:
  == domain 1  score: 84.2 bits;  conditional E-value: 1.1e-27
                   ---HHHHHH-HHHHHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHH CS
  Seryl_tRNA_N   1 MLDiklirenpeavkeklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleael 97 
                   MLD+k+i +n + ++e +k+R+  + d+del+++d+krre +++++el++++N+++ eI+++kk+++d+++ ++e+k++++el +le+ + e+e++ 
    EPA04549.1   1 MLDPKIIKDNHQMIREMIKARN-VEYDFDELIDVDQKRREFIIKTDELRKKKNQIAMEISQKKKAGQDISSTLDEMKNISAELTKLETLQIEIEKKY 96 
                   *********************5.99************************************************************************ PP

                   HHHHCTS--- CS
  Seryl_tRNA_N  98 eklllaiPNi 107
                    +l+l+iPN+
    EPA04549.1  97 SSLALSIPNL 106
                   *********8 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   3.4   3.9e-05      0.23      12      82 ..      31      99 ..      19     110 .. 0.85
   2 ?   -3.5   0.0       0.8   4.8e+03      60      88 ..     369     397 ..     343     405 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 3.9e-05
       TMPIT 12 keleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvl 82
                 ++ ++ +e++ k++el k +++++ ei+++kk  ++++s+l+++k+   + e +++e+l+ e++++ ++l
  EPA04549.1 31 IDVDQKRREFIIKTDELRKKKNQIAMEISQKKKAGQDISSTLDEMKNI--SAELTKLETLQIEIEKKYSSL 99
                467888999************************************998..578888999999888876655 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 0.8
       TMPIT  60 vkeeeeeeveelkeelkerkkvlkevesl 88 
                 +++e+ + +++l+++l  +++vl ++ + 
  EPA04549.1 369 KTNEDTQYLHTLNSTLIATSRVLVSIMEN 397
                 23566666666666666666666544443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1528  (0.0852251); expected 358.6 (0.02)
Passed bias filter:                      701  (0.0390987); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.69u 0.30s 00:00:00.99 Elapsed: 00:00:00.54
# Mc/sec: 2323.13
//
Query:       EPA04550.1  [L=353]
Description: hypothetical protein BG20_I0380 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.04   14.0   0.0       0.13   12.3   0.0    1.8  2  Wzt_C     Wzt C-terminal domain
      0.052   13.7   0.1       0.17   12.0   0.1    1.9  1  OapA      Opacity-associated protein A LysM-like domain


Domain annotation for each model (and alignments):
>> Wzt_C  Wzt C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.52   4.7e+03      36      47 ..      69      80 ..      58      95 .. 0.59
   2 ?   12.3   0.0   1.5e-05      0.13       7      43 ..     234     274 ..     232     296 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.52
       Wzt_C 36 lrikvkahedve 47
                +ri+v++  dv+
  EPA04550.1 69 VRIHVNFFDDVN 80
                445555555553 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 1.5e-05
       Wzt_C   7 sgeaeIedvelldaegeetstfesgeevtlr....ikvkah 43 
                 ++ ++I +v++ld+eg++ s++++g++v+++    i++ a+
  EPA04550.1 234 TKLVTISNVSVLDSEGKPLSEIKVGSTVKIQseswIQFSAD 274
                 56789************************994444444444 PP

>> OapA  Opacity-associated protein A LysM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   1.9e-05      0.17      27      54 ..     239     266 ..     233     308 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.9e-05
        OapA  27 vnalakveGadkplSnlksGqkvrikln 54 
                 ++ ++  + ++kplS++k G +v+i+ +
  EPA04550.1 239 ISNVSVLDSEGKPLSEIKVGSTVKIQSE 266
                 5567778899**************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.34s 00:00:00.94 Elapsed: 00:00:00.54
# Mc/sec: 1951.78
//
Query:       EPA04551.1  [L=485]
Description: hypothetical protein BG20_I0355 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-06   28.1   1.5      0.027   13.6   0.0    2.2  2  FAD_binding_2   FAD binding domain
    1.4e-05   24.6   0.1    2.5e-05   23.8   0.1    1.4  1  FAD_oxidored    FAD dependent oxidoreductase
    0.00016   21.0   0.6      0.023   13.9   0.0    2.7  2  Thi4            Thi4 family
    0.00027   19.9   0.0     0.0077   15.1   0.0    2.7  3  Trp_halogenase  Tryptophan halogenase
     0.0024   17.2   0.5      0.087   12.1   0.0    2.4  2  FAD_binding_3   FAD binding domain
     0.0038   16.3   0.1     0.0059   15.7   0.1    1.4  1  Lycopene_cycl   Lycopene cyclase protein
     0.0046   16.2   0.2      0.012   14.9   0.2    1.7  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.011   15.4   0.6        2.1    7.8   0.0    2.3  2  DAO             FAD dependent oxidoreductase
      0.033   14.4   0.1       0.15   12.3   0.1    2.1  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
      0.083   11.6   0.0       0.15   10.8   0.0    1.4  1  HI0933_like     HI0933-like protein
      0.097   12.9   0.0       0.23   11.7   0.0    1.6  1  TrkA_N          TrkA-N domain


Domain annotation for each model (and alignments):
>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.4   1.7e-05     0.027       1      33 [.       5      40 ..       5      62 .. 0.82
   2 !   13.6   0.0   1.6e-05     0.027     146     206 ..     113     172 ..      56     186 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.7e-05
                   SEEEE--SHHHHHHHHHHHH...TTT-EEEEESSSG CS
  FAD_binding_2  1 DviViGsGlAGLaAAleaae...aGlkvavvekeqe 33
                   Dvi+ G+GlAG  AA + ++   +Glk++v++  ++
     EPA04551.1  5 DVIIAGGGLAGTIAAQSVSHysnQGLKILVIDRSPS 40
                   9**************998766669*******99987 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 1.6e-05
                    HHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG.. CS
  FAD_binding_2 146 rlvesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgral 206
                    r  ++ +++gvdf ++++++ L++e+++v+G+   + ++++  + +ak vv+atg  +  l
     EPA04551.1 113 RQNQRTLAMGVDFDFEINLTGLVYEGNQVVGVQGIDNKTKTPYKKTAKVVVDATGMTSM-L 172
                    5567788999************************9667777667777777777776553.3 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.1   1.6e-08   2.5e-05       1     145 [.       5     168 ..       5     175 .. 0.67

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.6e-08
  FAD_oxidored   1 DvvVvGGgpaGvaAAiaAa...raGakvlLveergv.lGGlltsglvatdignkaeeqvvtgiareflerlrq.rggarlkkrskwn.......... 82 
                   Dv++ GGg+aG++AA +     ++G k l++++++  l Gl +  +  +++g      v +  ++ ++ r++   ++ +++ + k +          
    EPA04551.1   5 DVIIAGGGLAGTIAAQSVShysNQGLKILVIDRSPSnLPGLKSVSG--WICGDA----VSKEAVDYMTTRIKVnWTEPEIEHKVKGVmafspdrets 95 
                   9**************99853337*********88644677665433..677755....344444444444433211111221222112233344554 PP

  FAD_oxidored  83 ........tfepevakavleemlaeagvtvllntrlvevekegkriesvtveske.g.rktirAkvfiDATgd 145
                           + + +v+ +  ++     gv+  ++  l++ + eg+++ +v+  +++ +  ++ +Akv++DATg 
    EPA04551.1  96 ipfdgagyMLNRQVLPERQNQRTLAMGVDFDFEINLTGLVYEGNQVVGVQGIDNKtKtPYKKTAKVVVDATGM 168
                   555566667777777777766666678888888888**************999887889************96 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   1.4e-05     0.023      17      85 ..       3      74 ..       1      97 [. 0.72
   2 ?    4.5   0.1     0.011        17     153     205 ..     153     209 ..     126     214 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.4e-05
                EEEEEEE--SHHHHHHHHHHHHC..TTS-EEEEESSSS--TT.TTTTSTTBSEEEEETTTHHHHHHTT---E CS
        Thi4 17 esDvvivGaGssGLtaayylakk..pdlkvailersvspGGG.awlGGqlfsaivvrkpakelLdelgikye 85
                + Dv+i G+G +G  aa+ +++    +lk+++++rs s   G     G +    v ++  + +   + ++++
  EPA04551.1  3 DYDVIIAGGGLAGTIAAQSVSHYsnQGLKILVIDRSPSNLPGlKSVSGWICGDAVSKEAVDYMTTRIKVNWT 74
                57******************9865589********9875444134555555555555555555555555555 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.011
                 B-EEEEEEEEEE--GSSSTTTTHHHHHHHHCTTTS....-----ECB-HHHHHHHHH CS
        Thi4 153 DPlvirakvvvdatGhdgeivavvvkkikleakie....kvkgeksldaekaedaiv 205
                  P    akvvvdatG  + + + +    k e+k++    + +g + ++ e +e+++ 
  EPA04551.1 153 TPYKKTAKVVVDATGMTSMLRNQISNTTKMEKKVDrrdvESTGRHIMYFEDGEKDLT 209
                 5777789*********99988877665544444331111346788899999998875 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   4.7e-06    0.0077       1      33 [.       5      37 ..       5      43 .. 0.93
   2 ?    0.3   0.0      0.15   2.4e+02     199     220 ..     158     179 ..     131     188 .. 0.81
   3 ?   -0.1   0.0      0.19   3.1e+02     298     339 ..     291     334 ..     263     372 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.7e-06
                    EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE- CS
  Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlves 33
                    +++i+GGG aG +aA  ++++ ++ l++++++ 
      EPA04551.1  5 DVIIAGGGLAGTIAAQSVSHYSNQGLKILVIDR 37
                    699*******************999*****975 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.15
                     E-SEEEE-SGGG-IIIIIIT-- CS
  Trp_halogenase 199 eadlfiDcsGfrgllieqaLkt 220
                      a  ++D++G+ ++l +q  +t
      EPA04551.1 158 TAKVVVDATGMTSMLRNQISNT 179
                     57899**********9997443 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.19
                     TS-.EEEE---EEES-SEETT.EEE-CCCTEE--CCCS-HHHHH CS
  Trp_halogenase 298 aep.rkirfttGrrkqawvkn.vvalGlasgfvePlestsihli 339
                     +++  + ++ + r++  +v n +v++G+++    Pl++ +i  +
      EPA04551.1 291 NNAtGNFQVSVRRQNDCMVANgFVLVGDSAWMPKPLDAGGIGPA 334
                     333356667777777777655499*******99***99998644 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   5.3e-05     0.087       2      38 ..       4      43 ..       3      49 .. 0.80
   2 ?    3.3   0.1     0.025        40     118     182 ..     121     186 ..     107     335 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.3e-05
                   EEEEEE--SHHHHHHHHHHHHT...THHEEEEESSSSSCC CS
  FAD_binding_3  2 tdVlIVGaGpaGlmlallLsea...Gvrvvlvekrsttvv 38
                   +dV+I G+G+aG ++a+  s +   G + +++++  ++ +
     EPA04551.1  4 YDVIIAGGGLAGTIAAQSVSHYsnqGLKILVIDRSPSNLP 43
                   79**************998654333999*****9887665 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.025
                    HTEEETCSEEEECCEECCCCCCCEEE.ECCTTEEEEEEEEEEEE--GTT-HHHHHHTGGEEEEEEE CS
  FAD_binding_3 118 rglqvrfktevesleqdeegvtaevr.dketgeeetvrakYlvGaDGgrStvrktlgiefegeetv 182
                     g++++f+ ++++l  ++++v  +   d++t + ++ +ak +v a G+ S  r+++  + + e++v
     EPA04551.1 121 MGVDFDFEINLTGLVYEGNQVVGVQGiDNKTKTPYKKTAKVVVDATGMTSMLRNQISNTTKMEKKV 186
                    5788888888888888887776655448899999999******************99887777765 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   3.6e-06    0.0059       1      48 [.       5      55 ..       5     174 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.6e-06
  Lycopene_cycl  1 DvvviGaGpAglslAarl.teakpglkvvlieaspsllfpnny..vWsdef 48
                   Dv++ G+G+Ag   A+ +   +++glk+++i+ sps l + +    W + +
     EPA04551.1  5 DVIIAGGGLAGTIAAQSVsHYSNQGLKILVIDRSPSNLPGLKSvsGWICGD 55
                   9**********9999888456899***********9965555434476644 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.2   7.4e-06     0.012       1     111 [.       4     170 ..       4     197 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 7.4e-06
                  CSEEEE--SHHHHHHHHHHHH...HTS-EEEEE.TTHCHHHCSHHHHCHHHHHHHHHHHHH..................................... CS
                  xxxxxxxxxxxxxxxxxxxxx...xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx..................................... RF
  Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaq...agakvtlve.legtclnggcllskallgvaedaeias..................................... 57 
                  +dv++ GgG AG+ aa+ +++   +g+k+++++ +  ++++ + +   +++g a  +e +                                      
   EPA04551.1   4 YDVIIAGGGLAGTIAAQSVSHysnQGLKILVIDrSPSNLPGLKSVS-GWICGDAVSKEAVDymttrikvnwtepeiehkvkgvmafspdretsipfdg 100
                  69*******************8767*******87666666665554.333333333322224555566668887777777777777777777777777 PP

                  .............HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEECTCEEEEEE....SEEEE---EEE CS
                  .............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxx RF
  Pyr_redox_2  58 .............evvkklnqgielllgeevvkidpgkkkvklekkkegdeekiay....dklvlAtGssp 111
                               ++ + l  g+++  + + +++ ++  +v+  +   ++++k  y    + +v AtG ++
   EPA04551.1 101 agymlnrqvlperQNQRTLAMGVDFDFEINLTGLVYEGNQVVGVQGI-DNKTKTPYkktaKVVVDATGMTS 170
                  77777777666663335555556665666666666666666664444.44444444334355666777654 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.2    0.0041       6.7       1      30 [.       5      39 ..       5      61 .. 0.85
   2 ?    7.8   0.0    0.0013       2.1     157     227 ..     119     200 ..      69     347 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0041
                EEEEECTSHHHHHHHHHHHHT...T..EEEEESSS CS
         DAO  1 dvviiGGGiiGlstAyeLarr...g..Vtllekgd 30
                dv+i GGG +G  +A   +     g  ++++++++
  EPA04551.1  5 DVIIAGGGLAGTIAAQSVSHYsnqGlkILVIDRSP 39
                8*****************65433369******983 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0013
                 HHTT-EEEESECEEEEEEEETCEEEEE.....EECT.EEEEEEEEEEE--GGGHH...HHHTT.CTT.......TSEEEEEEEEEEEE CS
         DAO 157 ealGveilegtevtgleeedgkvwgve.....rttp.gendaadavVnaaGawsd...llgll.kel.......dlpispvrgqvlvl 227
                  a Gv++ ++ + tgl  e+++v+gv+     ++tp    ++a+ vV a+G  s    +   + ++        ++ ++   g ++++
  EPA04551.1 119 LAMGVDFDFEINLTGLVYEGNQVVGVQgidnkTKTPyK--KTAKVVVDATGMTSMlrnQ---IsNTTkmekkvdRRDVE-STGRHIMY 200
                 57899999999999996677899999888754444433..35699******88753332...22211233333224433.44444444 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   9.2e-05      0.15       1      30 [.       8      40 ..       8      68 .. 0.84
   2 ?   -2.2   0.0       3.2   5.2e+03      19      38 ..     245     264 ..     243     281 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.2e-05
                   EE--SHHHHHHHHHHHCC...TEEEEEE-SSSS CS
  NAD_binding_8  1 IvGaGlsGlvaAylLaka...gfdvlllekrdr 30
                   I G+Gl+G  aA+  + +   g+++l+++++++
     EPA04551.1  8 IAGGGLAGTIAAQSVSHYsnqGLKILVIDRSPS 40
                   67**********998874455********9875 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.2
                    TEEEEEE-SSSSSSGGG-EE CS
  NAD_binding_8  19 gfdvlllekrdrlGGraasy 38 
                    g++ +llekr++  G++ s+
     EPA04551.1 245 GVEKTLLEKRNQRLGKSDSV 264
                    56678999998855666655 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0     9e-05      0.15       1      34 [.       4      40 ..       4      50 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 9e-05
                 -SEEEE--SHHHHHHHHHH...HHTT--EEEE-SSSS CS
  HI0933_like  1 kdviviGgGaAGlmaAisa...akrgkrVlllekakk 34
                 +dvi+ GgG AG  aA s+   +++g ++l++++ ++
   EPA04551.1  4 YDVIIAGGGLAGTIAAQSVshySNQGLKILVIDRSPS 40
                 59***************997778999*******9865 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00014      0.23       1      55 [.       6      62 ..       6      66 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00014
                EEEES-SHHHHHHHHHHHH.TT...EEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHH CS
      TrkA_N  1 iiiiGlGrvGrslaeeLse.gg...kdvvvidkdeerveelreeglevvvgdatdeevL 55
                +ii+G G  G+  a+ +s+ ++   k ++vid++++++  l+     +++gda ++e++
  EPA04551.1  6 VIIAGGGLAGTIAAQSVSHySNqglK-ILVIDRSPSNLPGLK-SVSGWICGDAVSKEAV 62
                79*****************5559966.*************97.44569*****999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (485 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 3051.07
//
Query:       EPA04552.1  [L=149]
Description: ribosomal protein S15 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-26   92.4   0.1    2.3e-26   91.6   0.1    1.4  1  Ribosomal_S13_N  Ribosomal S13/S15 N-terminal domain
      1e-11   44.9   0.3    1.6e-11   44.2   0.3    1.3  1  Ribosomal_S15    Ribosomal protein S15
  ------ inclusion threshold ------
       0.12   12.8   0.1       0.24   11.8   0.1    1.5  1  Nnf1             Nnf1


Domain annotation for each model (and alignments):
>> Ribosomal_S13_N  Ribosomal S13/S15 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.6   0.1   3.9e-30   2.3e-26       1      60 []       1      60 [.       1      60 [. 0.99

  Alignments for each domain:
  == domain 1  score: 91.6 bits;  conditional E-value: 3.9e-30
                     X--SSSSSS--------S-SS--TTS---HHHHHHHHHHHHHTT--HHHHHHHHHHCCT- CS
  Ribosomal_S13_N  1 MarmhsrgkGkSgSarPyrreapsWlklskeeveelivklakkGltpSqIGviLRDqyGv 60
                     M+r+h++++GkS+S rP++ +apsW+++s++e+eel+vk+ak+GltpSqIG++LRDq+ +
       EPA04552.1  1 MGRLHTHRHGKSHSIRPATLRAPSWITISPKEIEELVVKYAKDGLTPSQIGLKLRDQHSI 60
                     **********************************************************87 PP

>> Ribosomal_S15  Ribosomal protein S15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.3   2.7e-15   1.6e-11       3      75 ..      73     143 ..      72     149 .] 0.90

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 2.7e-15
                    HHHHHHSSSTT-TSSHHHHHHHHHHHHHHHHHHHHCTTT-HHHHHHHHHHHHHHHHHHHHHHHH-H..HHHHHHH CS
  Ribosomal_S15   3 elikefqrhekDtGspevqiallterInnltehlkenkkDkhsrrgLlklvskRrkllkYLkrkdv..erYkkli 75 
                    ++++e+  ++    ++++++ +++++++ l++hlk+nk D+++ r+L ++++k ++l  Y+kr d+  +++k+  
     EPA04552.1  73 QILEENDLKP----EMPEDLDNIVRKAVGLQKHLKSNKGDNRNVRSLELIEAKVHRLSVYYKRIDRipQNWKYKS 143
                    5788888899....9***************************************************998887754 PP

>> Nnf1  Nnf1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   4.1e-05      0.24      18      77 ..      67     123 ..      63     134 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.1e-05
                 HHHHHHHHHHHTTHHHHHHH.HHHHHHHHHCCHH-.T..........TTSSTTTHHHHHHHH CS
        Nnf1  18 iraefeeIleerdvvekLne.LDdlieeAkerree.geeeasrpevpphtLpPeeliaahla 77 
                 +++ + +Ilee+d++ ++ e LD+++++A   ++  +++++++ +v+     + eli+a+++
  EPA04552.1  67 TKKSIGQILEENDLKPEMPEdLDNIVRKAVGLQKHlKSNKGDNRNVR-----SLELIEAKVH 123
                 57899*************655********944443133333333355.....6666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 874.67
//
Query:       EPA04553.1  [L=187]
Description: transcription factor [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-54  182.2   0.0    9.2e-28   96.0   0.0    2.0  2  TBP       Transcription factor TFIID (or TATA-binding protein
      8e-06   25.9   0.0       0.13   12.4   0.0    2.4  2  DUF3378   Domain of unknown function (DUF3378)


Domain annotation for each model (and alignments):
>> TBP  Transcription factor TFIID (or TATA-binding protein, TBP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.0   0.0     1e-31   9.2e-28       3      84 ..       9      88 ..       7      89 .. 0.96
   2 !   84.4   0.0   4.3e-28   3.9e-24       2      83 ..      99     178 ..      98     179 .. 0.96

  Alignments for each domain:
  == domain 1  score: 96.0 bits;  conditional E-value: 1e-31
                EEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHHHHHHHH CS
         TBP  3 kiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakkiapilkk 84
                 ++Nvvasa++++++dL+++ +k    ++eY pe+fpglv+rl++p+++ liF++Gk+v+tGakse+ + +a+++++++l+k
  EPA04553.1  9 SVENVVASASVDQKIDLNEITEKF--PDTEYHPEQFPGLVFRLQNPRTATLIFRTGKMVCTGAKSEDMAIKAVNTVVQKLRK 88
                79******************7665..******************************************************97 PP

  == domain 2  score: 84.4 bits;  conditional E-value: 4.3e-28
                 EEEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHHHHHHH CS
         TBP   2 fkiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakkiapilk 83 
                 +++qN+va +nlg +++Lek a+++    + Yepe+fpgl+ r+ +pk+++l+F+sGk+v+tGak+e+++++ ++++  +l+
  EPA04553.1  99 ITVQNIVAAINLGGKIHLEKAARTL--PRSMYEPEQFPGLIHRMLDPKTVILLFASGKLVCTGAKKESDVYRSVHNLHSLLE 178
                 68*******************9887..***********************************************99988886 PP

>> DUF3378  Domain of unknown function (DUF3378)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   1.4e-05      0.13      10      61 ..      24      76 ..      16      90 .. 0.86
   2 !   11.2   0.0   3.3e-05       0.3      24      59 ..     130     165 ..     117     176 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.4e-05
     DUF3378 10 tikkmkeyyksk.lrskkppyavfaakkndttItaYtSgKVlFQGknaeaeAs 61
                ++++++e++ +     ++ p+ vf+ +++ t   +++ gK +  G++ e  A 
  EPA04553.1 24 DLNEITEKFPDTeYHPEQFPGLVFRLQNPRTATLIFRTGKMVCTGAKSEDMAI 76
                678888888766467899*****************************999885 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 3.3e-05
     DUF3378  24 skkppyavfaakkndttItaYtSgKVlFQGknaeae 59 
                  ++ p+ + +  +++t+I ++ SgK++  G++ e++
  EPA04553.1 130 PEQFPGLIHRMLDPKTVILLFASGKLVCTGAKKESD 165
                 678899999999***************999887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1415.63
//
Query:       EPA04554.1  [L=63]
Description: hypothetical protein BG20_I0375 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.027   14.7   0.1       0.03   14.5   0.1    1.1  1  Lectin_like  Lectin like domain


Domain annotation for each model (and alignments):
>> Lectin_like  Lectin like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   1.7e-06      0.03      51      96 ..      14      56 ..       4      61 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.7e-06
  Lectin_like 51 yvykdfenekplsnklklaasgtlkyaGYytvdldkpvelkagkkf 96
                  vy++f++  + ++ + + ++g  + +GY+t  l++   ++++k+f
   EPA04554.1 14 TVYDKFQDVYQKNKDSLA-MKGVNSFSGYVTYMLEE--MMQKDKTF 56
                 689999999555555555.5***************9..66777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1097  (0.0611858); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 461.60
//
Query:       EPA04555.1  [L=151]
Description: ASCH domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-10   40.8   0.0    3.3e-10   40.5   0.0    1.2  1  ASCH      ASCH domain


Domain annotation for each model (and alignments):
>> ASCH  ASCH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.5   0.0   1.9e-14   3.3e-10       1     103 [.       4     107 ..       4     111 .. 0.89

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 1.9e-14
                 EEE-TTHHHHHHTTS--EEEESSTTTGGGT-CEEEEEECCC...............CTSEEEEEEEEEEEEEE.HHHHHHHHHCHCC---HCHHHHHHH CS
        ASCH   1 lsfhqelaslivsGkKtaeirvwdeelpkvrgdllilaalk...............ptgralgivevtkvevk.pfeevteehalkegesleewrevhe 83 
                 ls+ q++a+li+sGkK +e r w+++    rg++li+a lk                tg ++g++e+ +v+++ + +ev+++ +l           + +
  EPA04555.1   4 LSVSQPFADLIISGKKIIELRNWNTN---FRGEFLIHAPLKiriddvkrlkinkkfVTGAIIGKAELYDVKKYnSSKEVSNDKKL---------HYASR 90 
                 6899**********************...99******9999********************************999999888777.........77788 PP

                 CCHHHHHCCEEEEEEEEEEE CS
        ASCH  84 efyeeeseeyedelvvveef 103
                 +fy++ ++   ++l +++ +
  EPA04555.1  91 NFYSKSFG---FILKNAKPL 107
                 88888877...666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1149.00
//
Query:       EPA04556.1  [L=96]
Description: hypothetical protein BG20_I0383, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.022   14.8   3.7      0.053   13.5   3.5    1.8  2  zinc_ribbon_6   Zinc-ribbon
       0.44   10.3   3.5        1.6    8.5   3.5    1.9  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
        1.3    9.1  10.0        4.9    7.2  10.0    1.8  1  Eapp_C          E2F-associated phosphoprotein


Domain annotation for each model (and alignments):
>> zinc_ribbon_6  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   3.5   8.9e-06     0.053      21      48 ..      52      79 ..      33      89 .. 0.79
   2 ?    0.2   0.1      0.13   7.9e+02      29      39 ..      81      91 ..      75      94 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.9e-06
  zinc_ribbon_6 21 eeyknkkvkilCnDCekksevkfhvlgl 48
                   +e k+++ +++C DC+++++++f    +
     EPA04556.1 52 DERKSEMHTVTCADCGDECQIPFEPKFN 79
                   57789999**************986554 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.13
  zinc_ribbon_6 29 kilCnDCekks 39
                    ++C  C +k 
     EPA04556.1 81 PVYCSECFQKN 91
                   58899998775 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   3.5   0.00026       1.6       3      23 ..      63      87 ..      62      90 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00026
                    -SSS--B---....-SSS----SSS CS
  DNA_RNApol_7kD  3 CgeCgaevsl....kkgdpiRCkeC 23
                    C++Cg+e ++    k + p+ C eC
      EPA04556.1 63 CADCGDECQIpfepKFNRPVYCSEC 87
                    6666655555222277899999999 PP

>> Eapp_C  E2F-associated phosphoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2  10.0   0.00082       4.9      76     131 ..      15      69 ..       4      91 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00082
      Eapp_C  76 ykeaesekkkkkkkkskkkeekeeeaeaeeaeeeeeeeeeeeesyhpvkCseCste 131
                  + ++s+++++++ + ++ +++ ++++++++++++ +++e+++++h v+C+ C  e
  EPA04556.1  15 RH-SKSSQTSNRSFRDDEPSRSFRNSKEKRSSRDRYSRDERKSEMHTVTCADCGDE 69 
                 33.23333333333333334444444445555566677778999*********876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1303  (0.0726756); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 656.24
//
Query:       EPA04557.1  [L=120]
Description: hypothetical protein BG20_I0369 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 805.84
//
Query:       EPA04558.1  [L=189]
Description: hypothetical protein BG20_I0367 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.9e-09   35.0   0.0    1.6e-08   33.8   0.0    1.5  1  Monooxygenase_B  Monooxygenase subunit B protein


Domain annotation for each model (and alignments):
>> Monooxygenase_B  Monooxygenase subunit B protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.0   8.9e-13   1.6e-08       6     129 ..      38     155 ..      34     157 .. 0.91

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 8.9e-13
                      -HHHHHSSEEEEEEEES-SEEETT-EEEEEEEEEE-TT--TTS--SSSEEEEEESSSTTEEEEEEEETTEE-SS-B---TT-EEEEEEEEEE-S CS
  Monooxygenase_B   6 eaflrmrTiqfYDvkwskeevkvneeltitGkvhvledWPeavekpevsflnvgePgPvlvrkesvvngkfvprsvslelGedYefkvvlkaRr 99 
                      +a l+ r ++  D  + +++++ +e+lt++G++         ve+   ++l++++ +     + +++   +  + + +   +  ++++ +ka  
       EPA04558.1  38 QAQLQSRFVRIEDETFNRQSLQTGETLTVKGTLVS------LVERDLRGWLSIFSESTNAGNRWEMLARDPPGNVFDIAGNSVVDYELSAKALE 125
                      67788888888999999999999999999999874......488999999999999999999999999999999999999999*********** PP

                      -EEEEEEEEEEESSS-EEEEEEEEEEEES- CS
  Monooxygenase_B 100 pGtyhvhpmlnvedaGplvGpgkwvtiegd 129
                      +G yhvh++ln+   Gp +Gpg+ v +egd
       EPA04558.1 126 AGVYHVHTQLNIAKVGPGLGPGQTVVVEGD 155
                      ****************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1179.09
//
Query:       EPA04559.1  [L=520]
Description: von Willebrand factor type A domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-07   30.0   0.0    1.1e-06   29.0   0.0    1.6  1  VWA       von Willebrand factor type A domain
  ------ inclusion threshold ------
      0.011   16.3   0.0       0.03   15.0   0.0    1.7  1  VWA_2     von Willebrand factor type A domain
        0.1   13.0   0.0       0.34   11.3   0.0    1.9  2  DUF3828   Protein of unknown function (DUF3828)


Domain annotation for each model (and alignments):
>> VWA  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0   1.8e-10   1.1e-06       2     153 ..     349     491 ..     348     512 .. 0.76

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 1.8e-10
                 EEEEEE-STTSCHHHHHHHHHHHHHHHHHHTBTTTTEEEEEEEESSSEEEEEETTSHC.HHHHHHHHHHTG.SGGGGSSC-HHHHHHHHHHHHHHHHGT CS
         VWA   2 ivfvlDgSgsmgeenfekvkefikklveklevgpegtrvglvqfssevktefslndys.skeellsalnnl.kysgggttntgkalkyaleklfkssag 98 
                 iv++lD S+s+ +++  + k++   l e l     ++++++  f+++ + ++ ++ +  + ++ + + ++l ++  +g+t     l+++++k++   ++
  EPA04559.1 349 IVILLDHSSSI-ASDALEYKKATLALCEVLA--YLKVKFAIYAFNTHNRNVVCWSIKPdNMKWNNASAKRLaQIDANGST----PLAEVYDKMLPILQS 440
                 9**********.8888889999999999999..899***********888866666553557777777777344445555....455566655555555 PP

                 SSTTSEEEEEEEESS--CS.SHTHHHHHHHHGCTEEEEEEEESSSHHHHHHHHHSS CS
         VWA  99 aRenakkviilltdGksnd.gdpkeaaneakeqgikvfavGvgnadekelLnkias 153
                    + + +++ ltdG+++d + ++   +++k+ gik++a+G g+++ ++  + ia+
  EPA04559.1 441 ---KRPDIFLTLTDGEPSDpDAVRAITKSLKNLGIKMVALGLGSNTVRA--TIIAN 491
                 ...4468************55888888899999*********9988877..44554 PP

>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0     5e-06      0.03       1     107 []     349     453 ..     349     453 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5e-06
       VWA_2   1 lvfvlDtSgSmrngdygptrleaakdaveallkslp..gdrvglvtfsdgpevliplt...kdkakilnalrnleak..gggtnlaaaLqlarkalkkr 92 
                 +v++lD S S++++          k+a+ al++ l+  ++++++ +f+++ + ++ ++   ++ +  ++  ++l +   +g t la+  +++  +l+++
  EPA04559.1 349 IVILLDHSSSIASD------ALEYKKATLALCEVLAylKVKFAIYAFNTHNRNVVCWSikpDNMKWNNASAKRLAQIdaNGSTPLAEVYDKMLPILQSK 441
                 79***********9......45566667777775543378*********8888877764454433334444444433557*****************98 PP

       VWA_2  93 rkgekrvivlitDge 107
                 r   + + + +tDge
  EPA04559.1 442 R---PDIFLTLTDGE 453
                 8...99*******96 PP

>> DUF3828  Protein of unknown function (DUF3828)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.92   5.5e+03      28      49 ..      24      45 ..      20      81 .. 0.66
   2 ?   11.3   0.0   5.7e-05      0.34       2      56 ..     137     191 ..     136     225 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.92
     DUF3828 28 mreyiskellkrlksakiqqeg 49
                +re+i+ e+ ++++  ++ q  
  EPA04559.1 24 ERENITVEFSNKVETRTRLQDN 45
                6888888888888866666654 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 5.7e-05
     DUF3828   2 peqtvkqfYqqyv..qtfteivkqeatamreyiskellkrlksakiqqegeqevlda 56 
                 ++++v++fYq+++  + ++ei  +++  +r   +++++k++  ++i++++  e+l+ 
  EPA04559.1 137 KARIVEAFYQYFMfgTIRGEIQSSQF--ERIKNADKFAKKIVLESIEKNYDTEWLEK 191
                 7899*********9777777444444..577779********************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (520 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 3331.61
//
Query:       EPA04560.1  [L=104]
Description: hypothetical protein BG20_I0366 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 698.55
//
Query:       EPA04561.1  [L=373]
Description: redoxin family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-36  126.5   0.0    1.6e-36  125.9   0.0    1.3  1  Thioredoxin_10  Thioredoxin like C-terminal domain
    1.2e-08   35.0   0.1    1.9e-08   34.2   0.1    1.3  1  AhpC-TSA        AhpC/TSA family
    5.6e-08   32.6   0.0    9.7e-08   31.8   0.0    1.4  1  Redoxin         Redoxin
     0.0017   18.7   0.1     0.0033   17.7   0.1    1.5  1  Thioredoxin_8   Thioredoxin-like
  ------ inclusion threshold ------
      0.084   13.2   0.3          6    7.3   0.1    2.4  2  Gemini_AL1      Geminivirus Rep catalytic domain


Domain annotation for each model (and alignments):
>> Thioredoxin_10  Thioredoxin like C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.9   0.0   4.6e-40   1.6e-36       1     142 []     229     373 .]     229     373 .] 0.98

  Alignments for each domain:
  == domain 1  score: 125.9 bits;  conditional E-value: 4.6e-40
  Thioredoxin_10   1 tpEtYLGyara...enfaspeklkedkaatytlpeklalnefaLsGkWtveeesitaasegarirlrfkArdvhlVlgeggpgtvkvtldgka.. 90 
                     tpE+Y+Gy+     ++++spe++++++  ty++p++ + ++f+L+G+W++ e s+++ s++++i+l +++++v++V +  g++++k+++dgk+  
      EPA04561.1 229 TPELYFGYDFVtgrNQLGSPEGFQPNQDVTYSIPQSKQIHKFYLDGTWKNLEGSMKLVSNSGTIVLPYSGKEVNIVTA--GDANLKIKIDGKTid 321
                     8********98776889*************************************************************..*************98 PP

  Thioredoxin_10  91 gadagkdvdadgtitvsgprlyqlvrqeevgegtleiefldpGveaYaFTFG 142
                      a agkdvd +g+++v++prly++v++e+++++tlei +++pG+e+++FTFG
      EPA04561.1 322 PAFAGKDVDINGQVRVQEPRLYNIVQTETSEDHTLEILVESPGFEIFTFTFG 373
                     899************************************************9 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.1   5.4e-12   1.9e-08      26     123 ..      83     180 ..      61     181 .. 0.90

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 5.4e-12
                 SEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCH......HHHHHHHH-H.SSEEEE-TTSHHHHHTT-EETTTTECSCEEEEE-TT CS
    AhpC-TSA  26 kpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspe......shkkfiekeslnfpllsDeegkvakaygvlkeekglalratfvidke 118
                 + vvl+ + + +c  C + lp +   +e+++++g+ +ig+ + + e      ++k+ +ek+++++p+++D+++++ ka+g         ++  ++ d+e
  EPA04561.1  83 HSVVLYDIWTYSCINCIRTLPFITSWNEKYADQGLLIIGIHSPEFEfekdvtNVKNAVEKYGITYPVVLDNDKETWKAFGNN------YWPRKYIADSE 175
                 56777766666*****************************885555699999******************************......9********** PP

                 SBEEE CS
    AhpC-TSA 119 gkiry 123
                 g iry
  EPA04561.1 176 GYIRY 180
                 ***98 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.0   2.7e-11   9.7e-08      23     135 ..      77     186 ..      67     199 .. 0.86

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 2.7e-11
                 HHH.HTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHH......HHHHHHHTT-TSEEEE-TTSHHHHHTT-TTEEE.GGGEE CS
     Redoxin  23 lse.fkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndaf......vkefwgkeglkfpvlsDgsaaftkalGlrleedaseglr 114
                 l+e     +v+  +++   c  C + +p+++  +e++++ g  ++++ + + +f      vk++++k+g+++pv++D +++  ka+G +          
  EPA04561.1  77 LQEkIDHSVVLYDIWTY-SCINCIRTLPFITSWNEKYADQGLLIIGIHSPEFEFekdvtnVKNAVEKYGITYPVVLDNDKETWKAFGNN---------Y 165
                 55534444555566666.9********************************************************************99.........8 PP

                 E-EEEEEEETTEEEEEEESSS CS
     Redoxin 115 tpryavidedgkvvylevepe 135
                  pr  + d +g ++y + ++ 
  EPA04561.1 166 WPRKYIADSEGYIRYDHIGEG 186
                 9999999********998875 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   9.3e-07    0.0033       2      95 .]      84     178 ..      82     178 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 9.3e-07
                    SEEEEEE--SSSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-SS-HHHHHHHGGGS....-TTSEE.EE-TT-HHHHTT-S--TT-SEEEEE-TT- CS
  Thioredoxin_8   2 kvvlLyfgaswcppckaftpklkelyeklkkkkkveivyvsldkkeeefekylkkn....kkpwlsvpfddkkrnklkkkynvkaiPtlvvldkng 93 
                    +vvl  ++++ c +c + +p ++   ek+  ++++ i+ +++ +   efek +++     +k  + +p+  ++ ++ +k ++ + +P+ ++ d++g
     EPA04561.1  84 SVVLYDIWTYSCINCIRTLPFITSWNEKYA-DQGLLIIGIHSPEF--EFEKDVTNVknavEKYGITYPVVLDNDKETWKAFGNNYWPRKYIADSEG 176
                    589999***********************8.79999999999754..5555555543444667999999***********************9999 PP

                    BE CS
  Thioredoxin_8  94 ev 95 
                     +
     EPA04561.1 177 YI 178
                    76 PP

>> Gemini_AL1  Geminivirus Rep catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.1    0.0017         6      34     104 ..      66     146 ..      40     149 .. 0.84
   2 ?    3.5   0.0     0.025        90      57      78 ..     330     351 ..     327     362 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0017
  Gemini_AL1  34 nkkyikiareahedgekhlhvllqlekkfrirdlrlfdlvsnikek..........ffhPniqgaksssdvreyvkkdgdt 104
                 +  yi i  ++ +++  h  vl  +     i+ +r +   ++ +ek           ++P+ +  k++++v++ v+k g t
  EPA04561.1  66 ISEYINIQPDKLQEKIDHSVVLYDIWTYSCINCIRTLPFITSWNEKyadqglliigIHSPEFEFEKDVTNVKNAVEKYGIT 146
                 5689999999999999999999988887777777777777777777789999999999*******************9875 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.025
  Gemini_AL1  57 qlekkfrirdlrlfdlvsnike 78 
                  +++++r+++ rl+++v++  +
  EPA04561.1 330 DINGQVRVQEPRLYNIVQTETS 351
                 689*************997554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2477.62
//
Query:       EPA04562.1  [L=79]
Description: transcriptional regulator, AsnC family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-12   46.8   0.1    2.4e-12   46.6   0.1    1.0  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
  ------ inclusion threshold ------
      0.013   15.6   0.1      0.015   15.3   0.1    1.1  1  NapD            NapD protein


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.6   0.1   2.7e-16   2.4e-12       1      71 [.       6      73 ..       6      76 .. 0.95

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 2.7e-16
                    EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEE CS
  AsnC_trans_reg  1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsi 71
                    vl++++ g+    e+++ +l++++ V+e++ v G yd+l+kv ++ +e+l++ +  k++++  +++t t++
      EPA04562.1  6 VLINCDLGS---EESVISELKTIDGVKEVHGVFGAYDILAKVESKQVESLRETITWKIRKIQKIRSTLTLM 73
                    788999899...9******************************************************9987 PP

>> NapD  NapD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.1   1.7e-06     0.015       6      66 ..       6      68 ..       4      73 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.7e-06
        NapD  6 lvVqarperlaavkaalaalpgv.EvhasdeegklVvviEaesedeladtiea.iealpgVls 66
                ++++++ ++ ++v  +l++++gv Evh++ ++  +   +E++++++l +ti+  i++++++ s
  EPA04562.1  6 VLINCDLGSEESVISELKTIDGVkEVHGVFGAYDILAKVESKQVESLRETITWkIRKIQKIRS 68
                6899******************99**************************9976888887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       689  (0.0384294); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.34s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 458.15
//
Query:       EPA04563.1  [L=110]
Description: hypothetical protein BG20_I0363 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.048   13.9   0.4      0.086   13.1   0.4    1.4  1  COX7C     Cytochrome c oxidase subunit VIIc


Domain annotation for each model (and alignments):
>> COX7C  Cytochrome c oxidase subunit VIIc
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.4   4.8e-06     0.086      34      61 ..       2      29 ..       1      31 [. 0.94

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.8e-06
                SSHHHHHHHHHHHHHHHHHHHHHHHHHH CS
       COX7C 34 nnKipfavkywgflgvgFalPFlavrwQ 61
                n Ki +a+ +++++++g ++P ++++ Q
  EPA04563.1  2 NTKILLAASLIAVFAIGSFAPVMVAYAQ 29
                789***********************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 725.36
//
Query:       EPA04564.1  [L=109]
Description: hypothetical protein BG20_I0382 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.40
# Mc/sec: 817.90
//
Query:       EPA04565.1  [L=184]
Description: antioxidant, AhpC/TSA family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.7e-20   71.5   0.4    7.1e-20   71.2   0.4    1.1  1  AhpC-TSA       AhpC/TSA family
    4.2e-12   46.0   0.1    5.2e-12   45.7   0.1    1.1  1  Redoxin        Redoxin
    1.1e-06   28.9   0.7    1.9e-06   28.1   0.7    1.4  1  Thioredoxin_8  Thioredoxin-like
     0.0011   18.3   0.1      0.015   14.6   0.0    1.9  2  T4_deiodinase  Iodothyronine deiodinase
  ------ inclusion threshold ------
      0.012   16.1   0.1      0.019   15.4   0.1    1.3  1  Thioredoxin_2  Thioredoxin-like domain
      0.017   15.1   0.5       0.13   12.4   0.0    2.2  2  Thioredoxin_3  Thioredoxin domain
      0.071   13.1   0.2        0.6   10.1   0.1    2.1  2  Thioredoxin    Thioredoxin


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.2   0.4   2.8e-23   7.1e-20       2     121 ..      13     133 ..      12     136 .. 0.90

  Alignments for each domain:
  == domain 1  score: 71.2 bits;  conditional E-value: 2.8e-23
                 TSB----EEESTTCEEEECHHHTT.SEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCH........HHHHHHHH-H.SSEEEE-TT CS
    AhpC-TSA   2 gdkapdfelknadgetvslsdykg.kpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspe........shkkfiekeslnfpllsDee 91 
                 gd ap+f+l   d ++ +l+dy+  + +++ f+++ +cp+ ++++ al++lye+f   ++ +ig+++++ +        ++kk +++++++f++l D  
  EPA04565.1  13 GDIAPEFQLLGVDDKKHTLNDYSSyQGILVIFMCN-HCPYVKAKVDALNELYEKFG-DKIAIIGINSNDAKdypedsfeNMKKIVQEKNFKFDYLVDDI 109
                 99********************6646677777777.9*******************.5699******99888*************************** PP

                 SHHHHHTT-EETTTTECSCEEEEE-TTSBE CS
    AhpC-TSA  92 gkvakaygvlkeekglalratfvidkegki 121
                 +++ak+yg++      +++  f++++++ +
  EPA04565.1 110 QEIAKKYGAI------CTPDPFLFNNKKQL 133
                 **********......88888888888766 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.7   0.1     2e-15   5.2e-12       1     131 [.      11     137 ..      11     154 .. 0.88

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 2e-15
                 -TTSBB---ECCEETTCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHH........HHHHHHHTT-TSEEEE CS
     Redoxin   1 kagdkaPdftlplaatdgnsvslsefkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndaf........vkefwgkeglkfpvls 91 
                 k gd aP+f+l  +  d ++++l ++     +++++ +++cP+ +a++ +l++l+e++++k + ++++++++           +k+ + +++ kf +l+
  EPA04565.1  11 KTGDIAPEFQL--LGVDDKKHTLNDYSSYQGILVIFMCNHCPYVKAKVDALNELYEKFGDK-IAIIGINSNDAKDypedsfenMKKIVQEKNFKFDYLV 106
                 579999****8..67*********************************9999999998888.8888888887665789988999999999********* PP

                 -TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEEEEE CS
     Redoxin  92 DgsaaftkalGlrleedaseglrtpryavidedgkvvyle 131
                 D  ++++k++G+          +tp  ++++ ++++v  +
  EPA04565.1 107 DDIQEIAKKYGAI---------CTPDPFLFNNKKQLVFHG 137
                 ***********77.........999999999999887655 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.7   7.3e-10   1.9e-06       4      93 ..      40     131 ..      37     133 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 7.3e-10
                    EEEEE--SSSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-SS-HHHHHHHGGGS....-TTSEE.EE-TT-HHHHTT-S--TT-SEEEEE-TT- CS
  Thioredoxin_8   4 vlLyfgaswcppckaftpklkelyeklkkkkkveivyvsldkkeeefekylkkn....kkpwlsvpfddkkrnklkkkynvkaiPtlvvldkng 93 
                    +l+ f  ++cp  ka +  l+elyek+   +k+ i+ +++   ++  e+ ++++    +++   +++  +++++++kky+  + P  ++ ++++
     EPA04565.1  40 ILVIFMCNHCPYVKAKVDALNELYEKFG--DKIAIIGINSNDAKDYPEDSFENMkkivQEKNFKFDYLVDDIQEIAKKYGAICTPDPFLFNNKK 131
                    6899***********************9..**********7766777777777733333344555666688**************999999765 PP

>> T4_deiodinase  Iodothyronine deiodinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   5.9e-06     0.015      70     138 ..       7      73 ..       1      88 [. 0.82
   2 ?    1.9   0.0     0.043   1.1e+02     121     165 ..      88     132 ..      85     155 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.9e-06
  T4_deiodinase  70 ykqvkeGgdaPnsevvrvsgteschildfaqgnrPlvlnfGsatcPpflaklsafkrlveefssvadfl 138
                      + k+G+ aP+ +++ v+ ++   + d+ + +  lv+ f    cP   ak++a++ l e+f  ++  +
     EPA04565.1   7 QIKLKTGDIAPEFQLLGVDDKK-HTLNDYSSYQGILVI-FMCNHCPYVKAKVDALNELYEKFGDKIAII 73 
                    557799*************999.889999998877776.88899******************9877554 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.043
  T4_deiodinase 121 lsafkrlveefssvadfliiyieeahpsdGWaikddsfeikkhqs 165
                    ++++k++v+e + + d+l+  i+e     G + + d+f  ++ ++
     EPA04565.1  88 FENMKKIVQEKNFKFDYLVDDIQEIAKKYGAICTPDPFLFNNKKQ 132
                    67899*******************999999999999965544443 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.1   7.5e-06     0.019       7      99 ..      39     138 ..      35     150 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 7.5e-06
  Thioredoxin_2   7 pvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekk....kafkd............ieenvelarkygvrgtPtivf 86 
                     +lv+f  ++Cpy k+   +++ l+++ ++     +++++ ++ ++   ak+ +    +++k+            +++ +e a+kyg   tP+ ++
     EPA04565.1  39 GILVIFMCNHCPYVKA---KVDALNELYEK-----FGDKIAIIGINSNDAKDYPedsfENMKKivqeknfkfdylVDDIQEIAKKYGAICTPDPFL 126
                    68999999****9777...44444444444.....45554444444444444443333222225555555557799*****************665 PP

  Thioredoxin_2  87 ldgkeivarlpGy 99 
                    ++ k ++++  G 
     EPA04565.1 127 FNNK-KQLVFHGR 138
                    5555.34455554 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1       0.2   5.1e+02      10      20 ..      46      59 ..      40      86 .. 0.63
   2 ?   12.4   0.0   4.9e-05      0.13      18      56 ..      89     128 ..      82     148 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.2
                   STTCH...HHHHHH CS
  Thioredoxin_3 10 CakCp...klekav 20
                   C++Cp   + + a+
     EPA04565.1 46 CNHCPyvkAKVDAL 59
                   77777332333333 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 4.9e-05
                    HHHHHHCHCCTCECEEECCTTHHHH.HHCT-SSSSEE.ECT CS
  Thioredoxin_3  18 kavkeaaaekgikaevekvtdfeei.ekygVmsvPal.vid 56 
                    +++k++++ek++k+++  v d++ei +kyg + +P   + +
     EPA04565.1  89 ENMKKIVQEKNFKFDY-LVDDIQEIaKKYGAICTPDPfLFN 128
                    799***********96.69****************864444 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00024       0.6      18      67 ..      37      86 ..      21     103 .. 0.85
   2 ?    1.2   0.0      0.14   3.5e+02      58      84 ..     106     132 ..      86     151 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00024
                 SSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHH CS
  Thioredoxin 18 kklvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakk 67
                  + +lv F+ + C+  ka    l++l e++ dk+ ++ ++ ++ +d +++
   EPA04565.1 37 YQGILVIFMCNHCPYVKAKVDALNELYEKFGDKIAIIGINSNDAKDYPED 86
                 56789999999999999999999999999999********9999988765 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.14
                  TTTSHHHHHHTT-SSSSEEEEEETTEE CS
  Thioredoxin  58 vdenedlakkyevegiPtlklfkngke 84 
                  vd+ +++akky+  + P   lf+n k+
   EPA04565.1 106 VDDIQEIAKKYGAICTPDPFLFNNKKQ 132
                  678889999999999999988888773 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       866  (0.0483016); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1284.51
//
Query:       EPA04566.1  [L=73]
Description: hypothetical protein BG20_I0345 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 500.53
//
Query:       EPA04567.1  [L=113]
Description: hypothetical protein BG20_I0364 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.28   11.2   2.1       0.46   10.5   2.1    1.4  1  FixQ      Cbb3-type cytochrome oxidase component FixQ


Domain annotation for each model (and alignments):
>> FixQ  Cbb3-type cytochrome oxidase component FixQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   2.1   2.6e-05      0.46       8      30 ..      54      76 ..      51      87 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 2.6e-05
        FixQ  8 gfadswgllflvllfygvviyaf 30
                 +++++g++ + ++++g++ + +
  EPA04567.1 54 VMIYIFGTIMFSIFLLGIISFWL 76
                589***************97665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       633  (0.0353059); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 688.03
//
Query:       EPA04568.1  [L=124]
Description: thrombospondin type 3 repeat protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.3e-11   43.2  31.6    0.00019   21.0   2.2    5.2  6  TSP_3      Thrombospondin type 3 repeat
  ------ inclusion threshold ------
        1.6    9.4  13.3        1.3    9.7   0.4    3.9  4  Excalibur  Excalibur calcium-binding domain


Domain annotation for each model (and alignments):
>> TSP_3  Thrombospondin type 3 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   2.6   3.1e-08   0.00028      15      33 ..       8      26 ..       7      29 .. 0.92
   2 ?    0.7   0.1     0.047   4.2e+02      25      32 ..      34      41 ..      32      45 .. 0.70
   3 !   21.0   2.2   2.1e-08   0.00019      15      34 ..      52      71 ..      51      72 .. 0.94
   4 ?    0.5   0.1     0.057   5.1e+02      17      30 ..      77      83 ..      76      89 .. 0.57
   5 !   16.5   2.4   5.6e-07     0.005      15      33 ..      94     112 ..      92     114 .. 0.93
   6 ?   -1.7   0.0      0.28   2.5e+03      25      30 ..     118     123 ..     117     124 .] 0.77

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 3.1e-08
       TSP_3 15 DfDnDgvqddlDNCprnan 33
                D+D+Dg++d+ D Cp+ ++
  EPA04568.1  8 DADGDGIPDVKDACPNEPE 26
                9***************997 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.047
       TSP_3 25 lDNCprna 32
                 D Cp ++
  EPA04568.1 34 WDGCPDTP 41
                47788776 PP

  == domain 3  score: 21.0 bits;  conditional E-value: 2.1e-08
       TSP_3 15 DfDnDgvqddlDNCprnani 34
                D D+Dg++dd+D Cp n+++
  EPA04568.1 52 DSDKDGIPDDVDQCPSNPET 71
                99***************985 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.057
       TSP_3 17 DnDgvqddlDNCpr 30
                D        D Cp 
  EPA04568.1 77 DT-------DGCPD 83
                44.......45554 PP

  == domain 5  score: 16.5 bits;  conditional E-value: 5.6e-07
       TSP_3  15 DfDnDgvqddlDNCprnan 33 
                 D D Dg+ +d+D Cp +++
  EPA04568.1  94 DDDLDGIINDVDKCPLVPE 112
                 9**************9986 PP

  == domain 6  score: -1.7 bits;  conditional E-value: 0.28
       TSP_3  25 lDNCpr 30 
                  D Cp+
  EPA04568.1 118 IDGCPE 123
                 599997 PP

>> Excalibur  Excalibur calcium-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1    0.0012        10      27      36 ..       6      15 ..       2      15 .. 0.83
   2 ?    9.7   0.4   0.00014       1.3      24      36 ..      47      59 ..      25      59 .. 0.86
   3 ?   -1.1   0.0      0.34     3e+03      28      34 ..      76      80 ..      70      82 .. 0.60
   4 ?   -1.8   1.3      0.58   5.2e+03      29      35 ..      94     100 ..      92     100 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0012
   Excalibur 27 klDrDkDGiA 36
                + D D+DGi+
  EPA04568.1  6 APDADGDGIP 15
                66*******8 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00014
   Excalibur 24 ankklDrDkDGiA 36
                a+++ D DkDGi+
  EPA04568.1 47 APTRPDSDKDGIP 59
                5699********8 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.34
   Excalibur 28 lDrDkDG 34
                   D DG
  EPA04568.1 76 R--DTDG 80
                4..5555 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 0.58
   Excalibur  29 DrDkDGi 35 
                 D D DGi
  EPA04568.1  94 DDDLDGI 100
                 9999**8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 790.80
//
Query:       EPA04569.1  [L=126]
Description: hypothetical protein BG20_I0352 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1073  (0.0598472); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 825.53
//
Query:       EPA04570.1  [L=238]
Description: hypothetical protein BG20_I0344 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0043   17.5   2.0       0.01   16.3   1.1    2.2  2  DUF3899   Domain of unknown function (DUF3899)
     0.0048   16.5   1.0     0.0074   15.9   1.0    1.4  1  PIRT      Phosphoinositide-interacting protein family
  ------ inclusion threshold ------
      0.024   14.7   0.1      0.048   13.7   0.1    1.6  1  I-set     Immunoglobulin I-set domain
      0.044   13.7   0.9        0.2   11.5   0.8    2.1  1  FlgD_ig   FlgD Ig-like domain
      0.096   13.1   0.1       0.24   11.9   0.1    1.7  1  MG2       MG2 domain


Domain annotation for each model (and alignments):
>> DUF3899  Domain of unknown function (DUF3899)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   1.1   2.8e-06      0.01      40      83 ..      80     124 ..      39     125 .. 0.93
   2 ?   -1.9   0.0       1.4   4.9e+03      13      30 ..     189     206 ..     188     209 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.8e-06
     DUF3899  40 flkk.skkddsyyeykekkkesskkstrplliiGlllivlsivll 83 
                 f+k+ s+k++s+y    k k+s +k t++ll++G+  +v+ i+++
  EPA04570.1  80 FSKTsSQKVESLYSKSNKNKKSTSKNTKILLGAGGATFVMLIIIS 124
                 4444899***********9999*********************97 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.4
     DUF3899  13 iigillivlnsGfFdgfs 30 
                 i++ ++ v n+G F++++
  EPA04570.1 189 IWSEAISVKNNGRFSTLA 206
                 66667889999*999987 PP

>> PIRT  Phosphoinositide-interacting protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   1.0   2.1e-06    0.0074      14      91 ..      72     150 ..      59     176 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.1e-06
        PIRT  14 kdlltsqtastlcissrsesvwtngprskwdvykkpiivlsvGgavfllGvvit.tlsrnstlknkdkevf.klsGpafl 91 
                 k +++     +  +s + es++++++++k    k   i+l  Gga f++ ++i+ +l+   +l+++d+++  + s  a l
  EPA04570.1  72 KPIVPD-VIFSKTSSQKVESLYSKSNKNKKSTSKNTKILLGAGGATFVMLIIISmSLTGILNLESNDSQIIsEDSSSASL 150
                 444433.33344678899*****************************998887524555555555554443244455555 PP

>> I-set  Immunoglobulin I-set domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   1.4e-05     0.048      12      87 ..     159     235 ..     141     237 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.4e-05
                 EETTS-EEEEEEEECSSS-EEEEEETTCB-STSSSEEEEEETTEEEEEESSB-GGG.GEEEEEEEEETSEEEEEEEE CS
       I-set  12 vseGesvelectveGepepsvsWakdgselkssqrvkvtveeaeytLtIsnvevsD.eGkYtckatnsagkaeakae 87 
                  ++G+ ++++ t   +++ + s ++++ +l  s+ ++v++++  +tL I      D +G+Yt++++n++++++ +++
  EPA04570.1 159 YQKGDIISISGTSDTSGKVTLSIKNQDGKLIWSEAISVKNNGRFSTLAIAGGPGWDkSGTYTIQVNNNSETKSNTFS 235
                 5666666666666666666666666777777799***************988765538**********999998876 PP

>> FlgD_ig  FlgD Ig-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.8   5.6e-05       0.2      13      75 ..     164     225 ..     151     229 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.6e-05
                 EEEEE..ESSSEEEEEEEE-SS--EEEEEEEEESSSEEEE.EEE-SB-TTS-B--SEEEEEEEEE CS
     FlgD_ig  13 plgve.lpeaadevtvtikDasGevVrtidlgaqsaGvvs.ftWdGtdndGnkladGaYtvkvta 75 
                  ++++  ++ + +vt++ik++ G+++ +     ++ G +s ++  G    ++   +G+Yt++v+ 
  EPA04570.1 164 IISISgTSDTSGKVTLSIKNQDGKLIWSEAISVKNNGRFStLAIAGGPGWDK---SGTYTIQVNN 225
                 556666788999**************99988888888875266666665555...6777777765 PP

>> MG2  MG2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   6.7e-05      0.24      34      93 ..     175     235 ..     154     237 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.7e-05
                 EEEEEEEE-TTSSEEEEEEEEE-CTTEEEEEEE-...-TT--SEEEEEEEEECSTTT-EEEEE CS
         MG2  34 lplkltirdpdgkevkelplatdetggaesefal...peaaklGeysvelsadsaeeslssgs 93 
                  +++l+i+++dgk ++++ +  +++g ++ ++a+   p   k G+y++++ +++ e+++++ s
  EPA04570.1 175 GKVTLSIKNQDGKLIWSEAISVKNNGRFS-TLAIaggPGWDKSGTYTIQV-NNNSETKSNTFS 235
                 5799***************9777776654.555512255579********.444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1389  (0.0774723); expected 358.6 (0.02)
Passed bias filter:                      601  (0.0335211); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 1586.49
//
Query:       EPA04571.1  [L=203]
Description: ribosomal S3Ae family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-59  200.3   4.9    2.7e-59  200.1   4.9    1.0  1  Ribosomal_S3Ae  Ribosomal S3Ae family


Domain annotation for each model (and alignments):
>> Ribosomal_S3Ae  Ribosomal S3Ae family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.1   4.9   1.5e-63   2.7e-59       2     201 ..       4     193 ..       3     194 .. 0.97

  Alignments for each domain:
  == domain 1  score: 200.1 bits;  conditional E-value: 1.5e-63
                     S----S-TCCSEEEEEEEB-TTSSSSEEEEEEEE--BSSSESHHSHTT-EEEEESHH.HHTCSHTSSSEEEEEEEEEEESSEEEEEEEEEEE-HH CS
  Ribosomal_S3Ae   2 kkkkvvDkfkkKeWydvkaPslfgkreiGktlvnrtqgtkiaseklkgrvvevslaD.LtndekeqafrklklkieevqgknaltnFkgmeltrD 95 
                     +k++v+Dk+++K+W++v+aP+ f++++i+++++       ++ e+++grv+ev+l+D L++d+ +q+++k++++i++v+g++a+t Fk  e++++
      EPA04571.1   4 RKGRVKDKWREKKWVTVNAPDSFNNVPIAYVPI-------TDDENAVGRVLEVTLYDiLKGDP-SQHQYKIYFQINKVEGEKATTIFKRYEYSKE 90 
                     6899*****************************.......*****************889**9.556**************************** PP

                     HHHHH--SSB-EEEEEEEEEESSSEEEEEEEEEEE-STTB---HHHHHHHHHHHHHHHHHHHHHS-HHHHHHHHTTTHHHHHHHHHHTTTS-EEE CS
  Ribosomal_S3Ae  96 klrslvrkwsslIeaivdvktkDgyllrvfvvafTkkrnsYakssqkkaIrkkmveilteeaseldlkelvkklipeslgkeiekeakkIyplrn 190
                     +lrslvr++ss+I++++d+ktkDgy++r++++a+T+++   +++s+k+a+r ++++++++++++++++++v++ + ++++++i  + kk++ +r+
      EPA04571.1  91 FLRSLVRRGSSKINFVIDIKTKDGYVFRIKILALTHRQ---LNTSRKHALRLIARDVINNTVPQMTIDQFVQATCYSKINSDIMAAFKKVIRVRH 182
                     **************************************...***********************************88***************** PP

                     EEEEEEEEEE- CS
  Ribosomal_S3Ae 191 veirKvkvlkk 201
                     v  +Kvk++++
      EPA04571.1 183 VGLEKVKLIRT 193
                     ********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1326.86
//
Query:       EPA04572.1  [L=334]
Description: DHH family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0024   18.1   0.1     0.0047   17.1   0.1    1.5  1  DHH       DHH family


Domain annotation for each model (and alignments):
>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   2.6e-07    0.0047       7      65 ..      25     114 ..      21     156 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.6e-07
                 ECSSSHHHHHH.HHHHHH................................CECS--TCGGCGCCHHCCCSEEEEEEE-S---SS---SS--E CS
                 xxxxxxxxxxx.xxxxxx................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
         DHH   7 hknpDtDsigS.aialan................................llvDhneksqavegeakeeaedviiiDHHrlgeefetlapil 65 
                   + D+D+++S +i  ++                                ++ D      +  +  ++ +e+ i++DHH+++e+ +++++++
  EPA04572.1  25 TTHIDCDGLTSgSIITKAliragakctvrtskefskkvieslkkdsrefhVITDLAGGFSKNLD--ESLGENWIVLDHHQISEDEKENQNVI 114
                 6799*******98888886666666666666665555555555555555557776666555555..89*************98555554332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 2047.05
//
Query:       EPA04573.1  [L=187]
Description: ammonia monooxygenase/methane monooxygenase, subunit C [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-13   49.9   6.3      3e-13   49.6   6.3    1.1  1  AmoC      Ammonia monooxygenase/methane monooxygenase, subuni
     0.0059   16.2   0.2      0.009   15.6   0.2    1.2  1  RTA1      RTA1 like protein


Domain annotation for each model (and alignments):
>> AmoC  Ammonia monooxygenase/methane monooxygenase, subunit C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6   6.3   3.3e-17     3e-13      96     242 ..      13     156 ..       2     160 .. 0.72

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 3.3e-17
        AmoC  96 elkryltlllwlvvyalavyWGasffte..qdgtWhqtvirdtdftPshiiefylsyPiyiilgvaaflyaktrlPlf...akglslpylvlvagplmi 189
                 e++r+ +  +wl+v a++    as  ++   dg+ hqt ird  ftP+h      s+ i   lg+aa      ++P++   +++++  + +++ g l +
  EPA04573.1  13 EIQRLKK--IWLIVIAMGSTA-ASVEVDnfVDGSLHQTSIRDSAFTPAHWWL--YSHFITLPLGWAAAAIYDRKVPVLrgpNNSINTGLKMTILGYLAT 106
                 5555443..344444444333.2322221149*****************754..36668888999988888889999844457888899********** PP

        AmoC 190 lpnvglnewGhtfWfmeelfvaPLhwgfvvlgWaalavlGvalqvlarlsell 242
                 +  +g+ne  h fWf+ee+f+ P hw f +   + +a++G ++ v+  +++l+
  EPA04573.1 107 MFTIGVNEMWH-FWFVEEIFAVPNHWMFNMG--VVVAFMGALAYVVRVYARLV 156
                 *********99.9**************9763..45666676666666555555 PP

>> RTA1  RTA1 like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.2     1e-06     0.009     101     187 ..      91     181 ..      83     186 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1e-06
        RTA1 101 eaklGeniiiaGlalQvvvlvvFlllaldFllrvr...kskkfkkfllalyaavlliliRsiyRvvElaeGw.dgylithEvyfyvLdall 187
                 + ++G +++i G +  +++++v  + ++ F+ ++    +++ f++ +++ ++  l+ ++R   R+vEl     + +    E+y ++L++ l
  EPA04573.1  91 SINTGLKMTILGYLATMFTIGVNEMWHFWFVEEIFavpNHWMFNMGVVVAFMGALAYVVRVYARLVELGAETpGENPYVAEMYKMALEGKL 181
                 3799******************************9**98899**************************88773455677899999999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.36s 00:00:00.91 Elapsed: 00:00:00.55
# Mc/sec: 1018.02
//
Query:       EPA04574.1  [L=106]
Description: hypothetical protein BG20_I0351 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.23   11.5   0.8       0.38   10.8   0.8    1.3  1  ETRAMP    Malarial early transcribed membrane protein (ETRAMP


Domain annotation for each model (and alignments):
>> ETRAMP  Malarial early transcribed membrane protein (ETRAMP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.8   2.1e-05      0.38      42      69 ..       3      30 ..       1      33 [. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 2.1e-05
      ETRAMP 42 iddkiekkkkkkKliiistiatalallv 69
                ++++iekk    K i+i ++at+++l++
  EPA04574.1  3 KTKQIEKKAPVLKFILILAAATSVILVF 30
                689*********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.34s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 598.04
//
Query:       EPA04575.1  [L=63]
Description: AN1-like Zinc finger [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.7e-11   42.7   3.4    5.8e-11   42.4   3.4    1.2  1  zf-AN1    AN1-like Zinc finger


Domain annotation for each model (and alignments):
>> zf-AN1  AN1-like Zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   3.4   3.2e-15   5.8e-11      12      39 ..       4      31 ..       1      32 [. 0.92

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 3.2e-15
      zf-AN1 12 lpfkCryCgkvFClkHrlpedHdCkkla 39
                +pf+C+yC+  FC++Hrlpe+H C kl+
  EPA04575.1  4 MPFQCNYCKDPFCSEHRLPEEHRCVKLS 31
                69**********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.31s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 407.15
//
Query:       EPA04576.1  [L=382]
Description: pyridine nucleotide-disulfide oxidoreductase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.3e-19   68.9   0.0    5.9e-18   65.1   0.0    2.0  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    0.00016   22.1   3.9       0.22   12.1   0.0    3.8  4  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
     0.0013   18.7   0.0      0.025   14.6   0.0    2.7  3  NAD_binding_9   FAD-NAD(P)-binding
      0.002   18.3   0.0     0.0038   17.4   0.0    1.4  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
  ------ inclusion threshold ------
      0.033   13.3   0.0          1    8.4   0.0    2.6  3  FAD_binding_2   FAD binding domain
       0.04   12.8   0.0      0.057   12.3   0.0    1.2  1  Trp_halogenase  Tryptophan halogenase


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.1   0.0     2e-21   5.9e-18       2     279 ..       6     292 ..       5     307 .. 0.76

  Alignments for each domain:
  == domain 1  score: 65.1 bits;  conditional E-value: 2e-21
                  SEEEE--SHHHHHHHHHHHH....HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHHHHHHCHHHH.CCCCHCCTCEEEEESCEEEEETEEECTC CS
                  xxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Pyr_redox_2   2 dvvviGgGpAGlaaaltlaq....agakvtlvelegtclnggcllskallgvaedaeiasevvkklnqg.ielllgeevvkidpgkkkvklekkkegd 94 
                  +++++GgG++Glaaa ++++    +++k+t+v +++ ++ +g     ++ g++ +++ +   +++l+++ i ++++ e++ki   +k++++     g+
   EPA04576.1   6 HLLILGGGFGGLAAANEIRKnlpaSQIKITVV-DKKDWFMVGFAKLWIINGTRTFENSIG-SLNELRKKeINFIKE-EITKINLHNKNIEI-----GN 95 
                  679*****************99988*******.999999998887666666666666555.457777773666666.**************.....66 PP

                  EEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-TSEEEEES-SHHHHHHHHH.H....HHHT-.................EEEE CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x....xxxxx.................xxxx RF
  Pyr_redox_2  95 eekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllpkrivvvGgGyiGvElAaa.l....aklgk.................evtl 170
                  +  + yd l++A+G+     +ip + en+  l    ++  +++ k ++  i    +G i++ + ++ +    a + +                 e++l
   EPA04576.1  96 G-ILSYDFLIIAMGAVLAPEKIPWLSENGMNL-YDHNQLTEIHNKIKK--I---KSGKIAISIMGMpYkcppAPFEAsllidsmlrqeevrnsiEIHL 186
                  5.8***********977777889887788776.344444444444444..3...34444444444411112222222455556777888888989*** PP

                  EESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESS CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Pyr_redox_2 171 veardrllraldkelsaaleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvavGvrpstelleeklglelderggivvdeflrtnv 268
                     +++ l+  + e+s+++ + ++ e++ ++  +++k +++n+    ++ ++ge  + dl++ a+   + ++ +  ++gl+  e+g+i++d+ ++t  
   EPA04576.1 187 YSPAPITLPVAGIEISQQILNLINSENIIFHDSCKIKSVEKNK----LIFQNGEA-EFDLLL-AIPPHIAPKVI-YESGLAK-EGGFILIDRECKTPF 276
                  ****************************************999....78888885.888765.66677777777.99***98.*************** PP

                  TTEEE-GGGC.....T CS
                  xxxxxxxxxx.....x RF
  Pyr_redox_2 269 pgiyaiGDva.....g 279
                  +++ya+GDv+     +
   EPA04576.1 277 EDVYAVGDVTtlavnE 292
                  *********9544432 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   7.2e-05      0.22       1      35 [.       6      44 ..       6      50 .. 0.83
   2 ?   -1.3   0.2       1.1   3.4e+03      48      62 ..      67      81 ..      60      93 .. 0.76
   3 ?    1.9   0.0      0.11   3.2e+02      50      72 ..     119     141 ..     118     148 .. 0.84
   4 !    6.4   0.0    0.0045        13      26      70 ..     185     229 ..     176     233 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.2e-05
                EEEEECSSHHHHHHHHHHHH.TT...SEEEEEESSSSSS CS
   Pyr_redox  1 kvvvvGgGyiglElAgalae.lg...kkVtvversdkll 35
                +++++GgG+ gl +A+++++ l     k+tvv+ +d+++
  EPA04576.1  6 HLLILGGGFGGLAAANEIRKnLPasqIKITVVDKKDWFM 44
                789***************66455444699********99 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.1
                HHHHHTTEEEECSEE CS
   Pyr_redox 48 eklekngievllntk 62
                ++l+k+ i+++ ++ 
  EPA04576.1 67 NELRKKEINFIKEEI 81
                689999999998764 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.11
                 HHHTTEEEECSEEEEEEEEETTS CS
   Pyr_redox  50 lekngievllntkveeiegsedg 72 
                 l++ng++++ +++++ei+ + ++
  EPA04576.1 119 LSENGMNLYDHNQLTEIHNKIKK 141
                 789**************976665 PP

  == domain 4  score: 6.4 bits;  conditional E-value: 0.0045
                 EEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEET CS
   Pyr_redox  26 tvversdkllrllDeeaskilqeklekngievllntkveeiegse 70 
                 ++   ++  l++ + e+s+ + + +  ++i ++ + k++++e+++
  EPA04576.1 185 HLYSPAPITLPVAGIEISQQILNLINSENIIFHDSCKIKSVEKNK 229
                 555566667799999***************************985 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   8.4e-06     0.025       2      35 ..       9      41 ..       8      49 .. 0.90
   2 ?   -0.2   0.0      0.29   8.8e+02     114     154 ..      71     108 ..      60     110 .. 0.81
   3 ?   -0.5   0.0      0.38   1.1e+03      10      54 ..     166     208 ..     163     221 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8.4e-06
  NAD_binding_9  2 ivGaGprGlavlerLlarakkkspleitlfdpse 35
                   i G+G+ Gla+++++ ++  ++s+++it++d++ 
     EPA04576.1  9 ILGGGFGGLAAANEIRKNL-PASQIKITVVDKKD 41
                   89****************8.***********965 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.29
  NAD_binding_9 114 gvtvevhraevvdleeradgqavlladgaslaadaVvLAlG 154
                    + +++++++e+++++ ++++ ++   ++  l +d +++A+G
     EPA04576.1  71 KKEINFIKEEITKINLHNKNIEI---GNGILSYDFLIIAMG 108
                    45899*********999999777...777889999999988 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.38
  NAD_binding_9  10 lavlerLlarakkkspleitlfdpsepgagrvwrtdqseelllNv 54 
                     ++++ +l++++ ++++ei+l+ p+++    v+  + s + +lN+
     EPA04576.1 166 SLLIDSMLRQEEVRNSIEIHLYSPAPIT-LPVAGIEIS-QQILNL 208
                    5677788888888999******999986.444444433.334554 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.3e-06    0.0038       1      29 [.       9      41 ..       9      43 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.3e-06
                   EE--SHHHHHHHHHHHCC....TEEEEEE-SSS CS
  NAD_binding_8  1 IvGaGlsGlvaAylLaka....gfdvlllekrd 29
                   I+G+G++Gl+aA +++k+    ++++++++k d
     EPA04576.1  9 ILGGGFGGLAAANEIRKNlpasQIKITVVDKKD 41
                   89***************7666799******976 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0   0.00034         1       2      30 ..       7      39 ..       6      45 .. 0.75
   2 ?   -2.0   0.0      0.46   1.4e+03      84     105 ..     107     128 ..     103     146 .. 0.78
   3 ?    1.9   0.0     0.032        94     376     405 ..     266     289 ..     206     302 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00034
                   EEEE--SHHHHHHHHHHHH...TTT.-EEEEES CS
  FAD_binding_2  2 viViGsGlAGLaAAleaae...aGl.kvavvek 30
                   +++ G+G++GLaAA e+++   a + k++vv+k
     EPA04576.1  7 LLILGGGFGGLAAANEIRKnlpASQiKITVVDK 39
                   69*************999844433346666666 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.46
                    HHHHTHHHHHHHHHHTT----B CS
  FAD_binding_2  84 afveaapeavdeLeelgvpfsr 105
                    +++  ape++ +L e+g+ +  
     EPA04576.1 107 MGAVLAPEKIPWLSENGMNLYD 128
                    5556699*********998766 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.032
                    EEBETTSBESTTEEESSBTEEE-STCEESS CS
  FAD_binding_2 376 vetdengrvldadgqpipGLYAaGevaagg 405
                    + +d ++++      p ++ YA+G v+   
     EPA04576.1 266 ILIDRECKT------PFEDVYAVGDVTTLA 289
                    456666666......**********99554 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.9e-05     0.057       2      53 ..       7      60 ..       6      76 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.9e-05
                    EEEE--SHHHHHHHHHHHHHTTTS.SEEEEEE-SSS---SS-E.E--THHHHTH CS
  Trp_halogenase  2 ivivGGGtaGwlaAaalakalkgk.levtlveseeigtvgvGe.atipsirkll 53
                    ++i+GGG  G  aA+ ++k l  + +++t+v++++ ++vg  +   i+ +r++ 
      EPA04576.1  7 LLILGGGFGGLAAANEIRKNLPASqIKITVVDKKDWFMVGFAKlWIINGTRTFE 60
                    68*******************9999*********99999876644555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2364.36
//
Query:       EPA04577.1  [L=443]
Description: tRNA adenylyltransferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.3e-38  129.1   0.1    1.6e-37  128.2   0.1    1.5  1  tRNA_NucTransf2  tRNA nucleotidyltransferase, second domain
    1.1e-09   38.4   0.2    3.3e-09   36.9   0.2    1.8  1  NTP_transf_2     Nucleotidyltransferase domain
     0.0005   20.1   0.1     0.0018   18.3   0.1    2.0  1  Polbeta          Polymerase beta, Nucleotidyltransferase
     0.0008   19.6   1.5     0.0013   19.0   0.5    1.9  2  SMODS            Second Messenger Oligonucleotide or Dinucleo
  ------ inclusion threshold ------
      0.033   14.7   0.0       0.15   12.6   0.0    2.0  2  MCR_alpha        Methyl-coenzyme M reductase alpha subunit, C


Domain annotation for each model (and alignments):
>> tRNA_NucTransf2  tRNA nucleotidyltransferase, second domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.2   0.1   4.4e-41   1.6e-37       1     112 [.     152     258 ..     152     259 .. 0.97

  Alignments for each domain:
  == domain 1  score: 128.2 bits;  conditional E-value: 4.4e-41
                      HHHHHHHHHHHHTT-BSSSTTT-SB-HHHHHHHHHHHSSHHHHHHHHTT--TTEEEE......EEE..-SS-EEEETTEEEEETTTTS-HHHHH CS
  tRNA_NucTransf2   1 devrllKkflkgigvYGselkvkGfsGYlaEllvleygsfeevleaaakwkpkvvidleekeallkkfdeplvviDPvDpkRNvaaalslekla 94 
                      +evr+lK+flk++++YGse+  +GfsGY++E+l+l++gsfe+v++++ak++p+++i      +++k+f++p+v++DP+D++RN aaa+s+e++ 
       EPA04577.1 152 NEVRILKTFLKSTKIYGSEIAKQGFSGYVSEVLILNFGSFENVIKSIAKIQPNQIIG-----NASKTFETPIVIMDPIDNNRNLAAAISNENIG 240
                      79******************************************************5.....44689*************************** PP

                      HHHHHHHHHHHS--GGGG CS
  tRNA_NucTransf2  95 efilaareflkkpseeff 112
                      +f+l +r+f k+p+++ff
       EPA04577.1 241 KFVLVCRAFQKNPTLQFF 258
                      *****************9 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.2   9.1e-13   3.3e-09      13      80 ..      41     124 ..      31     141 .. 0.87

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 9.1e-13
                   T.TSEEEEEHHHHCTTSCTT.SSEEEEEEESTTCHHH..............HHHEHHHHHHHHCCCEEECTTEEEEEECEEECC CS
  NTP_transf_2  13 p.vakvvlfGSyarGtalkg.SDiDllvvlpeevsre..............kkeegleklaeiikfleellglevdlvtrekle 80 
                   p  + +   GSya++t+l++  D+D+++ +++   +e              kk++   +++e+++++ ++++ ++ +v+++ + 
    EPA04577.1  41 PeLVGLEFGGSYAKDTWLSNeADVDIFIKFKKTITDEkfvdiskkigfesmKKYKPYVRYSEHPYVEAKIKKTKINIVPCYDVN 124
                   456788999************************9999**************9999999**********************9987 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1     5e-07    0.0018       5      85 ..      35     115 ..      32     119 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 5e-07
                 TTHHHHHHHHSTTEEEEEE-S---.---EEEEEEEESS---HHHHHHHHHHHHHH.SSSEEEEEETTTS-HHHHHHHHHS-E CS
     Polbeta   5 eilekekeielaylFGSrakgkar.eeSDiDlavllkekldleeelelaaelediklgkkvDlvdlneapplllyeilkegk 85 
                 e +++++e+  +   GS+ak++   +e D+D+++ +k++ + e+ +++++++    + kk +  +  + +p++ ++i k+++
  EPA04577.1  35 EQVNNYPELVGLEFGGSYAKDTWLsNEADVDIFIKFKKTITDEKFVDISKKIGFE-SMKKYKPYVRYSEHPYVEAKIKKTKI 115
                 556667777777778****88865279************************9988.44444444433333666666666665 PP

>> SMODS  Second Messenger Oligonucleotide or Dinucleotide Synthetase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.5   3.5e-07    0.0013      26     139 ..      28     129 ..       7     145 .. 0.73
   2 ?   -3.0   0.0         2   7.1e+03       6      28 ..     411     433 ..     409     435 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 3.5e-07
       SMODS  26 srvkaitkrLnkdfrelkskiaesllvGSyardTaikpvsdkdmlfeldvdllvvvnevegd.epsdlleklkkalkktyksseirqdrqvvvvelnei 123
                 ++ + +++++n++      +++     GSya+dT +     +    e dvd++++++++  d +  d+ +k+     k+yk   +  +++ v  ++++ 
  EPA04577.1  28 EAFSLVKEQVNNYP-----ELVGLEFGGSYAKDTWLS----N----EADVDIFIKFKKTITDeKFVDISKKIGFESMKKYKPYVRYSEHPYVEAKIKKT 113
                 44444555555555.....45666678********98....4....6899*******987772444555555555599999999999************ PP

       SMODS 124 kidvvPavenkdgsye 139
                 ki +vP+   + g+++
  EPA04577.1 114 KINIVPCYDVNLGEWK 129
                 *******988877776 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2
       SMODS   6 qFkeflsnielsqttkdsissrv 28 
                  Fk f+ n +ls++ k+ is+ +
  EPA04577.1 411 GFKVFVGNRNLSKSIKEAISDLI 433
                 59999999999999999998765 PP

>> MCR_alpha  Methyl-coenzyme M reductase alpha subunit, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   4.1e-05      0.15      46      86 ..      12      52 ..       2      66 .. 0.88
   2 ?   -1.2   0.0      0.75   2.7e+03      51      75 ..      74      98 ..      54     106 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.1e-05
   MCR_alpha 46 lakvkatlevvkdiatevtlyaleqyekyptlledhfGGsq 86
                ++ +k+t+++ k+ia+e      eq ++yp l+  +fGGs 
  EPA04577.1 12 VNPSKNTIKIKKQIADEAFSLVKEQVNNYPELVGLEFGGSY 52
                456799*********************************96 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.75
   MCR_alpha 51 atlevvkdiatevtlyaleqyekyp 75
                 t e+  di++++ + ++++y+ y 
  EPA04577.1 74 ITDEKFVDISKKIGFESMKKYKPYV 98
                3567778999999999999998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 3214.63
//
Query:       EPA04578.1  [L=39]
Description: hypothetical protein BG20_I1808, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.30s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 257.64
//
Query:       EPA04579.1  [L=94]
Description: hypothetical protein BG20_I1805 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      0.003   16.9   0.3     0.0036   16.6   0.3    1.2  1  CLN6       Ceroid-lipofuscinosis neuronal protein 6
  ------ inclusion threshold ------
       0.06   13.1   0.9      0.089   12.6   0.0    1.7  2  B12D       NADH-ubiquinone reductase complex 1 MLRQ subunit
        5.9    5.6   8.1         11    4.8   0.2    2.0  2  LptF_LptG  Lipopolysaccharide export system permease LptF/Lpt


Domain annotation for each model (and alignments):
>> CLN6  Ceroid-lipofuscinosis neuronal protein 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.3     6e-07    0.0036     171     223 ..      32      85 ..       5      93 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6e-07
        CLN6 171 vkaeeklpl.sallllapsalyywylvtegqifilfiftffamlalvlhqkrkg 223
                 vk+ + + l s  ++    ++yyw+++   q f l  + +fa+   +++q r++
  EPA04579.1  32 VKTPKWIKLwSQAVVSIGFGIYYWFVLPAPQNFPLTAMVMFALAIALIYQGRRA 85 
                 44444333312333334569***********************99999997764 PP

>> B12D  NADH-ubiquinone reductase complex 1 MLRQ subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.2       2.1   1.2e+04       5      11 ..      16      22 ..      13      25 .. 0.70
   2 ?   12.6   0.0   1.5e-05     0.089       5      32 ..      63      90 ..      60      92 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 2.1
        B12D  5 liPLfvf 11
                ++P++++
  EPA04579.1 16 IYPVIGI 22
                6787765 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 1.5e-05
        B12D  5 liPLfvfigagvggavfylvRllltnPD 32
                 +PL + +++++++a+ y  R +  +PD
  EPA04579.1 63 NFPLTAMVMFALAIALIYQGRRAKISPD 90
                58*************************9 PP

>> LptF_LptG  Lipopolysaccharide export system permease LptF/LptG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   3.1    0.0032        19     308     351 ..      10      54 ..       4      58 .. 0.83
   2 ?    4.8   0.2    0.0018        11     278     299 ..      64      85 ..      62      88 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.0032
   LptF_LptG 308 aillfvlyyvl.lslgkalaengvlppilaawlpnilflllglfl 351
                  +l++++y v+ +++ +a++++ + p ++  w+  ++ +++g++ 
  EPA04579.1  10 DFLFYTIYPVIgIFIVEAISRAVKTPKWIKLWSQAVVSIGFGIYY 54 
                 578899977662567899999999999************999985 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0018
   LptF_LptG 278 lplaclvfaliaaplglvkrrg 299
                 +pl+++v++ +a++l +  rr 
  EPA04579.1  64 FPLTAMVMFALAIALIYQGRRA 85 
                 69**************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 617.12
//
Query:       EPA04580.1  [L=71]
Description: hypothetical protein BG20_I1802 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.011   15.8   2.0      0.014   15.5   1.4    1.6  1  His_Me_b4a2  His-Me finger endonuclease beta4-alpha2 domain


Domain annotation for each model (and alignments):
>> His_Me_b4a2  His-Me finger endonuclease beta4-alpha2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   1.4   7.6e-07     0.014      12      25 ..       2      15 ..       1      22 [. 0.88

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7.6e-07
  His_Me_b4a2 12 KiCNiCHiLkkted 25
                 KiCNiCH +  t++
   EPA04580.1  2 KICNICHRISGTDQ 15
                 9*******999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       679  (0.0378716); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.46
# Mc/sec: 460.30
//
Query:       EPA04581.1  [L=180]
Description: 2'-5' RNA ligase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-23   81.3   0.0    2.3e-12   46.9   0.0    2.1  2  LigT_PEase       LigT like Phosphoesterase
      6e-13   49.2   0.1    8.8e-13   48.6   0.1    1.2  1  AKAP7_NLS        AKAP7 2'5' RNA ligase-like domain
    3.8e-09   36.6   0.0    4.6e-09   36.4   0.0    1.1  1  2_5_RNA_ligase2  2'-5' RNA ligase superfamily


Domain annotation for each model (and alignments):
>> LigT_PEase  LigT like Phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.9   0.0   3.8e-16   2.3e-12       4      87 .]      11      87 ..       7      87 .. 0.92
   2 !   32.7   0.0     1e-11   6.1e-08       2      87 .]      89     170 ..      88     170 .. 0.80

  Alignments for each domain:
  == domain 1  score: 46.9 bits;  conditional E-value: 3.8e-16
                CHHHHHHHHHHHHHHHHHHCCTTEEETSGGGSEEEEEEEEEESHHHHHHHHHHHHHHHHTSBEEEEEEEEEEEEEECCSCCEEE CS
  LigT_PEase  4 peeiaeelarlaaeleralaklglkpvrpfnpHiTLaflgevdeekvpellealaeiasgaepfelkvdgvglfpsrlrprviy 87
                ++ i + ++++++e+       ++k  +p n+H TL+flge+++++++++ +al+++  ++ +f+++++ +g+fp ++ pr+i+
  EPA04581.1 11 SDKIIDSISKFQSEIN-----INAKSIEPHNLHFTLQFLGEISKDMLDHVSRALDSV--KFSKFSVNLKNIGVFPTQKFPRIIW 87
                6788899999999999.....788888******************************..8889************999999999 PP

  == domain 2  score: 32.7 bits;  conditional E-value: 1e-11
                 E-CHHHHHHHHHHHHHHHHHHCCTTEEETSGGGSEEEEEEEEEESHHHHHHHHHHHHHHHHTSBEEEE.EEEEEEEEEECC.SCCEEE CS
  LigT_PEase   2 gppeeiaeelarlaaeleralaklglkpvrpfnpHiTLaflgevdeekvpellealaeiasgaepfel.kvdgvglfpsrl.rprviy 87 
                 g +e+  + l +la+++e+al  lg+ +++pf+pHiT+ ++++    ++ ++ ++++++  +   f + +++g+ l +s l ++++ y
  EPA04581.1  89 GTDENGGKLLVELAKKVENALTPLGFTVDKPFKPHITVFRIKN----RIGDISKEMDKF--KLIDFGIqQISGFKLKQSVLsSKGPTY 170
                 5577888999*******************************87....555555555555..444444426999999999999999877 PP

>> AKAP7_NLS  AKAP7 2'5' RNA ligase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.6   0.1   1.5e-16   8.8e-13       4     190 ..       4     162 ..       2     176 .. 0.88

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 1.5e-16
                 EEEEE---HHHHHHHHHHHHHHHHH-GGGGGGB.--TT--EEEEEEE---SHHHHHHHHHHHHHHHHHHHHHHTTS--EEEEEEEEEE.....TTTEEE CS
   AKAP7_NLS   4 FlsiplnsnklrkklekfqesvlsklpgldeslfikpeklHlTllvlkLknkeeiaaakevLkevkeeikdaldnkplslrlkGletfnddpakarVlY 102
                 F++i ++s+k+++ ++kfq ++  + +       i+p +lH+Tl  l   +k+++++ +++L +vk          ++s++lk +++f   ++  r+++
  EPA04581.1   4 FVAIEISSDKIIDSISKFQSEININAK-----S-IEPHNLHFTLQFLGEISKDMLDHVSRALDSVK------F--SKFSVNLKNIGVF-PTQKFPRIIW 87 
                 9********************976555.....5.79999*********99************9995......3..799**********.455559**** PP

                 EEE--SHHHHHHHHHHHHHHHHHHTTT--B--SS-.---EEEEEEGGG-THHHHTT--S--GG.GGGGGTT-EEEEEE--EEEEEESS CS
   AKAP7_NLS 103 akveeesneekLqeladriikafeeaglvlekdkkkvklHaTlmnsrkrkkkqakskesfdareilkqfkdfefgeekineihLsqle 190
                 ++ +e++  + L ela+++ +a+   g++++k    +k+H+T++ +++r +  +k+          ++fk  +fg ++i+ ++L q  
  EPA04581.1  88 VGTDENG-GKLLVELAKKVENALTPLGFTVDKP---FKPHITVFRIKNRIGDISKEM---------DKFKLIDFGIQQISGFKLKQSV 162
                 ****998.999******************9988...77*********9999888777.........8899999999999999998765 PP

>> 2_5_RNA_ligase2  2'-5' RNA ligase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.0   7.6e-13   4.6e-09      17     114 ..      28     127 ..      10     153 .. 0.87

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 7.6e-13
  2_5_RNA_ligase2  17 ydkayprwppHitLlypfvededladlaellsrlaketepfevrldgfgvFeh.kks.vvylsv..sdsealqalraallealpeagdkedsge 106
                      + k+++ + +H tL +++++++d  d ++++ + +  +++f v l+++gvF++ k   ++++    ++ + l++l +++++al + g  +d ++
       EPA04581.1  28 NAKSIEPHNLHFTLQFLGEISKDMLDHVSRALDSV-KFSKFSVNLKNIGVFPTqKFPrIIWVGTdeNGGKLLVELAKKVENALTPLGFTVD-KP 119
                      56788999*************98766555555665.7899*************98889******99999********************99.** PP

  2_5_RNA_ligase2 107 ftPHlTia 114
                      f+PH+T+ 
       EPA04581.1 120 FKPHITVF 127
                      ******95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1140.96
//
Query:       EPA04582.1  [L=41]
Description: hypothetical protein BG20_I1807 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 287.74
//
Query:       EPA04583.1  [L=134]
Description: hypothetical protein BG20_I1796, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-13   50.3   0.1    3.8e-13   50.0   0.1    1.1  1  AAA_17           AAA domain
      1e-12   48.7   0.0    1.4e-12   48.3   0.0    1.2  1  AAA_18           AAA domain
      5e-05   23.5   0.0    8.4e-05   22.8   0.0    1.4  1  AAA_33           AAA domain
    0.00038   20.4   0.4       0.19   11.6   0.2    2.2  2  NTPase_1         NTPase
     0.0017   18.5   0.1      0.002   18.2   0.1    1.1  1  ADK              Adenylate kinase
     0.0023   18.2   0.0     0.0028   17.9   0.0    1.2  1  AAA_28           AAA domain
     0.0032   17.2   0.1     0.0053   16.4   0.1    1.3  1  CoaE             Dephospho-CoA kinase
     0.0037   17.2   0.0      0.015   15.2   0.0    1.8  2  APS_kinase       Adenylylsulphate kinase
     0.0037   16.5   0.1     0.0074   15.6   0.0    1.5  2  Zeta_toxin       Zeta toxin
     0.0039   17.2   0.0     0.0054   16.8   0.0    1.2  1  AAA_14           AAA domain
     0.0052   16.3   0.1      0.013   15.0   0.0    1.7  2  KTI12            Chromatin associated protein KTI12
     0.0066   15.5   0.0     0.0087   15.1   0.0    1.3  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
     0.0094   15.5   0.0      0.022   14.3   0.0    1.5  1  Hpr_kinase_C     HPr Serine kinase C-terminal domain
  ------ inclusion threshold ------
       0.01   15.0   0.0       0.01   15.0   0.0    1.2  1  NB-ARC           NB-ARC domain
      0.011   15.4   0.2       0.02   14.6   0.2    1.4  1  AAA_29           P-loop containing region of AAA domain
      0.017   15.5   0.2      0.028   14.9   0.2    1.4  1  AAA              ATPase family associated with various cellul
      0.025   14.7   0.0       0.18   12.0   0.0    2.0  2  UPF0180          Uncharacterised protein family (UPF0180)
       0.03   14.6   0.3       0.07   13.4   0.3    1.8  1  AAA_22           AAA domain
      0.046   14.2   0.5      0.065   13.7   0.5    1.6  1  AAA_23           AAA domain
      0.069   13.5   0.1       0.13   12.6   0.1    1.4  1  AAA_16           AAA ATPase domain
       0.09   12.7   0.0        0.1   12.5   0.0    1.3  1  Ploopntkinase3   P-loop Nucleotide Kinase3
      0.098   12.4   0.0       0.11   12.2   0.0    1.3  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
        0.1   12.3   0.2       0.12   12.1   0.2    1.5  1  AAA_30           AAA domain
        0.1   12.6   0.1        0.4   10.7   0.0    1.9  2  AAA_5            AAA domain (dynein-related subfamily)
       0.12   12.4   0.1       0.34   10.9   0.1    1.8  1  P-mevalo_kinase  Phosphomevalonate kinase


Domain annotation for each model (and alignments):
>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.0   0.1   5.3e-16   3.8e-13       1     131 [.       9     130 ..       9     134 .] 0.75

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 5.3e-16
                 EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHH....HHHHHSSEEEEEE-SEEEETTEEEESSHHH CS
      AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemrklpleekkelqkeaaeki....aeeakkkgvlvdghprikeqagfldglpke 95 
                 +G+PG+GK+t+++ l++k g+ ++++G ++r eak+++l+++  ++ kl le +++  + a +++      ++k++ +++dg  ++   a      + +
  EPA04583.1   9 TGMPGAGKSTIADGLKKK-GYDIINMGNIVRTEAKNRNLDPTGPNLGKLMLELREKNGQGAVAELvvpqITNSKSNVIIIDGIRSN---A------EID 97 
                 7***********888665.********************999999998866666655544444442222233578889****9974...3......346 PP

                 HHHHH..SEEEEEE--HHHHHHHHHHHTTST-TS-S CS
      AAA_17  96 vleelkpdaiilleadpeeilerrlkdrtrgrdddn 131
                 vl+++ + +++ ++a+  + +e  lk  +rgr+dd 
  EPA04583.1  98 VLRKYGTVKLLAIHASINTRFE-FLK--QRGRSDDP 130
                 788999999********97775.555..36776664 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   0.0   1.9e-15   1.4e-12       1     118 [.       6     129 ..       6     134 .] 0.74

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 1.9e-15
      AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpealdeskrldedkldklldaleenss............aleegknlvidghlaele 87 
                 ++ltG+pG+GK+t+a+ L+k++       d++  ++++ ++ ++   +++    ++l kl+ +l+e +             ++ + ++++idg++++ e
  EPA04583.1   6 VCLTGMPGAGKSTIADGLKKKG------YDIINMGNIVRTEAKN---RNLDPTGPNLGKLMLELREKNGqgavaelvvpqiTNSKSNVIIIDGIRSNAE 95 
                 89******************95......4444444444444444...44455555555555555555555555555555567899************** PP

      AAA_18  88 seaakdikk...vvLtaspeelleRlekRgyeea 118
                  + ++++++     ++as ++++e l++Rg++++
  EPA04583.1  96 IDVLRKYGTvklLAIHASINTRFEFLKQRGRSDD 129
                 ************9999********9999998764 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   1.2e-07   8.4e-05       2     125 ..       6     130 ..       5     134 .] 0.66

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.2e-07
      AAA_33   2 vllvGlpGsGKstlaerllkklgavllssdtlrrrlfgtdqqskt......dytrvl.drlyqilnela.rkalsagrnvildatnlsrrerarflkla 92 
                 v l G+pG+GKst a++l  k g+ +++  ++ r+ +++ + ++t         +++ ++  + ++el+  +   ++ nvi+  + +s++e + ++k  
  EPA04583.1   6 VCLTGMPGAGKSTIADGLK-KKGYDIINMGNIVRTEAKNRNLDPTgpnlgkLMLELReKNGQGAVAELVvPQITNSKSNVIIIDGIRSNAEIDVLRKY- 102
                 7889*************65.889888887776664444333333323344322332213333333343304455788889999999999998766655. PP

      AAA_33  93 rrlgvpvrivvvetdeetlkeRlakRaangddr 125
                    g  v++++++++  t  e l++R ++ dd+
  EPA04583.1 103 ---G-TVKLLAIHASINTRFEFLKQRGRS-DDP 130
                 ...5.699999999999999999999996.444 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.2   0.00027      0.19       2      17 ..       6      21 ..       5      30 .. 0.83
   2 !    7.9   0.0    0.0036       2.6      43     104 ..      24      90 ..      21      92 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00027
                EEEE--TTSSHHHHHH CS
    NTPase_1  2 vfiTGppGvGKtTlvk 17
                v++TG+pG GK+T+ +
  EPA04583.1  6 VCLTGMPGAGKSTIAD 21
                789**********976 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0036
                 ---EEEEEET.T--EEEEEETT.---SSEETTEEE-HHH......HHHHHHHHHHHHHHHH-EEEE--- CS
    NTPase_1  43 rrigFkivdlasgeegiLarve.akreprvgkyvvdves......feelalealrkalseadviviDEi 104
                 ++ g++i+++ +  +++  +++ ++ +p++gk ++++ +      + el+++++++  s+++vi+iD i
  EPA04583.1  24 KKKGYDIINMGNIVRTEAKNRNlDPTGPNLGKLMLELREkngqgaVAELVVPQITN--SKSNVIIIDGI 90 
                 57788888885555555555557899999999999998877777788889999987..89*******76 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   2.8e-06     0.002       1      86 [.       8      93 ..       8     132 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.8e-06
                EEESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHHCT-..HHHHHHHHHH.HTTSS--HHHHHHHHHHHHHCHGTTTEEEEESB-SSH CS
                xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
         ADK  1 llGaPgaGKGtqaeklvkkyglahlstGdllRaevksgt..elGkeakevm.dkgelvpdevvvklvkeelekedkkkgfllDGfPRtv 86
                l G PgaGK t a+ l+kk g+  +  G+++R e k+    ++G ++ ++m +  e   +  v +lv  +++++ k++  ++DG  R+ 
  EPA04583.1  8 LTGMPGAGKSTIADGLKKK-GYDIINMGNIVRTEAKNRNldPTGPNLGKLMlELREKNGQGAVAELVVPQITNS-KSNVIIIDGI-RSN 93
                679************9876.7788999*****999765422778777655426677788899999999999977.8889999996.443 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   3.9e-06    0.0028       2      33 ..       6      39 ..       5      89 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3.9e-06
      AAA_28  2 ivitGgestGKTtlleaLaargypvv..pEaare 33
                +++tG +++GK+t++  L+++gy ++    ++r+
  EPA04583.1  6 VCLTGMPGAGKSTIADGLKKKGYDIInmGNIVRT 39
                89*********************98854455544 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   7.4e-06    0.0053       1      36 [.       4      39 ..       4      49 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 7.4e-06
                EEEEEEESTTSSHHHHHHHHHHTT-EEEEHHHHHHH CS
        CoaE  1 livgltGgiasGKstvanlfadlgvpivDaDlvArq 36
                liv ltG  ++GKst+a+ +++ g++i+    + r 
  EPA04583.1  4 LIVCLTGMPGAGKSTIADGLKKKGYDIINMGNIVRT 39
                69**************************98877765 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   2.1e-05     0.015       3      25 ..       4      26 ..       2      47 .. 0.80
   2 ?   -0.5   0.0       1.4     1e+03      13      38 ..      64      89 ..      58     100 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.1e-05
                EEEEEESSTTSSHHHHHHHHHHH CS
  APS_kinase  3 vvvwltGlsgsGKstianalekk 25
                ++v ltG+ g+GKstia  l+kk
  EPA04583.1  4 LIVCLTGMPGAGKSTIADGLKKK 26
                6899*************998865 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.4
                SSHHHHHHHHHHHHHHTT--EEEEEH CS
  APS_kinase 13 sGKstianalekkLvekgisvylLdG 38
                 G+ ++a+ +  ++++++ +v+++dG
  EPA04583.1 64 NGQGAVAELVVPQITNSKSNVIIIDG 89
                58889999999999999999999998 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0     1e-05    0.0074      16      48 ..       3      38 ..       1      50 [. 0.82
   2 ?   -2.3   0.0       3.1   2.2e+03      31      50 ..      68      88 ..      62     103 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1e-05
  Zeta_toxin 16 PklillgGqpGAGKselaellkdele...rqgnvvr 48
                + ++ l G pGAGKs++a+ lk++     + gn+vr
  EPA04583.1  3 KLIVCLTGMPGAGKSTIADGLKKKGYdiiNMGNIVR 38
                56899*****************99755556666665 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.1
  Zeta_toxin 31 elaellkdele.rqgnvvrld 50
                ++ael+  +++ +++nv+ +d
  EPA04583.1 68 AVAELVVPQITnSKSNVIIID 88
                555555555554455555554 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   7.5e-06    0.0054       3      75 ..       4      92 ..       2     104 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 7.5e-06
      AAA_14  3 kilvitGaRrvGKTtllkqlikell..vkkesilyinldderd.............kkladpe...kllelileklkeekktylflDEiqe 75
                 i+++tG+  +GK+t++  l k+ +  ++  +i+  + ++ ++                ++++    + el+  +++++k +++++D i  
  EPA04583.1  4 LIVCLTGMPGAGKSTIADGLKKKGYdiINMGNIVRTEAKNRNLdptgpnlgklmleL--REKNgqgAVAELVVPQITNSKSNVIIIDGIRS 92
                689*****************9999999999999999999988877777776655331..222233466677777766689999****9876 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.8e-05     0.013       4      36 ..       6      38 ..       3      93 .. 0.60
   2 ?   -0.2   0.0      0.75   5.3e+02     128     128 ..     109     109 ..      56     132 .. 0.55

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.8e-05
                EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE- CS
       KTI12  4 vvltGlPssGKstrakeLakaleeekrsvvvid 36
                v ltG+P +GKst+a+ L+k+  +      +++
  EPA04583.1  6 VCLTGMPGAGKSTIADGLKKKGYDIINMGNIVR 38
                789***************998666433334444 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.75
                 H CS
       KTI12 128 e 128
                 +
  EPA04583.1 109 A 109
                 1 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.2e-05    0.0087      31      51 ..       5      25 ..       2      73 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.2e-05
                EEEEEE-TTSSHHHHHHHHHH CS
        MeaB 31 vvGltGvPGaGkstlvealgl 51
                 v ltG+PGaGkst+ + l  
  EPA04583.1  5 IVCLTGMPGAGKSTIADGLKK 25
                689************987754 PP

>> Hpr_kinase_C  HPr Serine kinase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   3.1e-05     0.022      21      76 ..       6      61 ..       2      70 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.1e-05
                  EEEEESTCHHHHHHHHHHHTTT-EEEEESSEEEEEETTE.EEEEE-TTTTTEEEET CS
  Hpr_kinase_C 21 vLitGesgvGKselaleLikrghrLvaDDaveikridektlvGrapellkhllevr 76
                  v +tG  g GKs +a  L k+g+ ++   ++  ++ ++++l  + p+l k +le+r
    EPA04583.1  6 VCLTGMPGAGKSTIADGLKKKGYDIINMGNIVRTEAKNRNLDPTGPNLGKLMLELR 61
                  779************************9999999999999**************99 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   1.4e-05      0.01      20      43 ..       3      26 ..       1     100 [. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.4e-05
                SEEEEEEESTTSSHHHHHHHHCCS CS
      NB-ARC 20 slvvalvGmgGvGKttlakqilnk 43
                +l+v l Gm+G GK+t+a    +k
  EPA04583.1  3 KLIVCLTGMPGAGKSTIADGLKKK 26
                589***************987776 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.2   2.8e-05      0.02      25      42 ..       6      23 ..       1      25 [. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.8e-05
      AAA_29 25 tlltGpsGsGKSTllDAi 42
                + ltG  G+GKST+ D +
  EPA04583.1  6 VCLTGMPGAGKSTIADGL 23
                679************987 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.2   3.9e-05     0.028       1      69 [.       6      92 ..       6     106 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.9e-05
                EEEESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSS............STTHHHHHHHHHHHHHHHTS....TSEEEEEETGGG CS
         AAA  1 vllyGppGtGKTllakavakelg..vefleisgsellsk............yvgesekkirelfkeakeka....kpsilfiDEida 69
                v+l+G pG GK+++a  + k+    +++ +i  +e  +             +++ +ek+ ++ ++e+   +    k  +++iD i +
  EPA04583.1  6 VCLTGMPGAGKSTIADGLKKKGYdiINMGNIVRTEAKNRnldptgpnlgklMLELREKNGQGAVAELVVPQitnsKSNVIIIDGIRS 92
                79****************999323344444444444433444444545555333333333333333322224443457888887755 PP

>> UPF0180  Uncharacterised protein family (UPF0180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00025      0.18      10      32 ..      17      43 ..      14      49 .. 0.79
   2 ?    0.7   0.0      0.84     6e+02      32      47 ..      79      94 ..      59     123 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00025
     UPF0180 10 snvkeaLrekGYeVvdlet....eeda 32
                s +++ L++kGY+++++++    e+++
  EPA04583.1 17 STIADGLKKKGYDIINMGNivrtEAKN 43
                6799**************976554444 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.84
     UPF0180 32 aqsvdaiVvtGqdtnv 47
                + + ++i+++G  +n+
  EPA04583.1 79 NSKSNVIIIDGIRSNA 94
                4556667777765554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.3   9.8e-05      0.07       4      28 ..       2      26 ..       1     112 [. 0.75

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.8e-05
      AAA_22  4 tagilvvtGesGtGKTtllrrlleq 28
                t+ i+++tG +G+GK+t +  l+++
  EPA04583.1  2 TKLIVCLTGMPGAGKSTIADGLKKK 26
                67899*************9988876 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.5     9e-05     0.065      21      40 ..       5      24 ..       2     132 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9e-05
      AAA_23 21 ltlItGpNGaGKTTildAik 40
                ++++tG+ GaGK+Ti d +k
  EPA04583.1  5 IVCLTGMPGAGKSTIADGLK 24
                789**************987 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00018      0.13      25      46 ..       4      25 ..       2      46 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00018
      AAA_16 25 elvllsGesGvGKsslvrellr 46
                 +v l+G++G GKs++++ l++
  EPA04583.1  4 LIVCLTGMPGAGKSTIADGLKK 25
                5899************987775 PP

>> Ploopntkinase3  P-loop Nucleotide Kinase3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00014       0.1       1      38 [.       1      39 [.       1      95 [. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
  Ploopntkinase3  1 mtarliylvGqPGaGkstlmaelt.kgfdrskveqeeet 38
                    mt+ ++ l G PGaGkst+   l  kg+d +++ +  +t
      EPA04583.1  1 MTKLIVCLTGMPGAGKSTIADGLKkKGYDIINMGNIVRT 39
                    6777889************99996257888777644444 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00015      0.11       4      51 ..       9      54 ..       6     110 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00015
  Viral_helicase1  4 hGvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvd 51
                      G+pG+GKSt i + l+++ ++  ++++ ++++te+k+++ ++++ ++ 
       EPA04583.1  9 TGMPGAGKST-IADGLKKKgYD--IINMGNIVRTEAKNRNLDPTGPNLG 54
                     7*********.66666665433..4777788888888666665555544 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   0.00017      0.12      19      39 ..       4      24 ..       1      89 [. 0.91

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00017
      AAA_30 19 rvavltGpAGtGKttalkalr 39
                ++++ltG +G+GK+t+  +l+
  EPA04583.1  4 LIVCLTGMPGAGKSTIADGLK 24
                6899***********998875 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00056       0.4       2      21 ..       6      25 ..       5      46 .. 0.92
   2 ?   -0.3   0.0       1.3   9.7e+02      64      75 ..      78      91 ..      53     101 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00056
                EEEE--SSSSHHHHHHHGGG CS
       AAA_5  2 vlLvGppGtgKselaerlaa 21
                v+L G pG gKs++a+ l++
  EPA04583.1  6 VCLTGMPGAGKSTIADGLKK 25
                8**************98765 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.3
                -..G-SEEEEESGG CS
       AAA_5 64 r..egeilvlDEve 75
                +  ++ ++++D++ 
  EPA04583.1 78 TnsKSNVIIIDGIR 91
                35688999999996 PP

>> P-mevalo_kinase  Phosphomevalonate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00047      0.34      75     110 ..      66     101 ..       8     104 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00047
  P-mevalo_kinase  75 pglFcraaiekieaakkdvliisDiRrktdleyfke 110
                      +g   + ++ +i+ +k++v+ii++iR +++++++++
       EPA04583.1  66 QGAVAELVVPQITNSKSNVIIIDGIRSNAEIDVLRK 101
                      55566777788888999***************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.47u 0.33s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 872.26
//
Query:       EPA04584.1  [L=246]
Description: oxidoreductase, short chain dehydrogenase/reductase family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-61  206.8   1.7    2.8e-61  206.4   1.7    1.2  1  adh_short        short chain dehydrogenase
    2.9e-48  164.5   1.8    3.6e-48  164.2   1.8    1.0  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
      1e-13   51.6   0.2    1.6e-13   50.9   0.1    1.3  1  KR               KR domain
     0.0056   16.2   0.6       0.38   10.2   0.6    2.5  1  Epimerase        NAD dependent epimerase/dehydratase family
  ------ inclusion threshold ------
      0.021   14.1   2.8       0.39   10.0   0.0    2.6  3  THF_DHG_CYH_C    Tetrahydrofolate dehydrogenase/cyclohydrolas
      0.028   13.1   0.1       0.04   12.5   0.1    1.2  1  Cullin           Cullin family
       0.11   12.2   1.0        0.3   10.9   1.0    1.7  1  Eno-Rase_NADH_b  NAD(P)H binding domain of trans-2-enoyl-CoA 
       0.14   12.6   0.0        0.3   11.5   0.0    1.6  1  BRCT_2           BRCT domain, a BRCA1 C-terminus domain
       0.21   12.2   2.5       0.66   10.6   0.2    2.3  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  206.4   1.7   1.4e-64   2.8e-61       1     193 [.       5     198 ..       5     200 .. 0.98

  Alignments for each domain:
  == domain 1  score: 206.4 bits;  conditional E-value: 1.4e-64
                 SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEEE---SS--SSGGGCSHH CS
   adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldvLvnNAGitgsgpfselsee 99 
                 kv+++tGassGIG a+a +l k+Gakv++ +r+ e l ++ k +ke+g +++  ++Dvt+++e++ +ve++ kk+ k+d+LvnNAG+   + f++l+ +
  EPA04584.1   5 KVAIITGASSGIGFATALALSKAGAKVAIGARRTEMLSKLEKIIKENGGEVYSQKLDVTKKNECDSFVENVLKKWNKVDILVNNAGLMPLSFFKNLKVD 103
                 89************************************************************************************************* PP

                 HHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHHHHHHHHHHGGGT.EEEEEEEESSBSSHHHHHHCTH CS
   adh_short 100 ewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaavagltrslakelaptg.irvnavaPGlvdTdmakelrek 193
                 ew+++i+vN++gv+ +t av+++ml+++ G+I+n+sSvag+  ++ +++Y+A+K+a++++++ l++el+ ++ irv+++ PG+v+T+++++++++
  EPA04584.1 104 EWDQMIDVNIKGVLYCTGAVVTHMLENKTGHIINISSVAGRIVFPAGSVYCATKHAITAFSEGLRQELSVRKnIRVTCIEPGVVATELTNTITDE 198
                 ********************************************************************98877****************998765 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.2   1.8   1.8e-51   3.6e-48       1     213 [.      11     224 ..      11     236 .. 0.93

  Alignments for each domain:
  == domain 1  score: 164.2 bits;  conditional E-value: 1.8e-51
                   TTTTSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEE..EE--TTSHHHHHHHHHHHHHHHSSEEEEEE-----EGCSS-GGGH-HHHH CS
  adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneeakkrveelaeelgaev..lecDVtdeeqvealveevvekfgklDilvnnagiapklkgpfletsreef 95 
                   Ga sgIG+a+A al ++Ga+v++  ++ e  +++e++ +e g ev   ++DVt++++++++ve+v +k++k+Dilvnnag +p   + f +++ +e+
    EPA04584.1  11 GASSGIGFATALALSKAGAKVAIGARRTEMLSKLEKIIKENGGEVysQKLDVTKKNECDSFVENVLKKWNKVDILVNNAGLMPL--SFFKNLKVDEW 105
                   899***************************************997689************************************..99999****** PP

                   HHHHHHHTHHHHHHHHHHHHHCTSC..CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHHHHHHGG.GTEEEEEEEE--BHCTGGGGSTTHHHHH CS
  adh_short_C2  96 draldvnlyslfllakaalplmkeg..gsivnlssvgaervvpnynaygaaKaalealtrylAvelgp.kgiRvNavspgpikTlaasgikgfdell 189
                   d+++dvn++++++++ a++ +m e+  g i+n+ssv++++v+p  ++y+a+K+a+ a++  l  el   k+iRv ++ pg+++T++++ i+  de l
    EPA04584.1 106 DQMIDVNIKGVLYCTGAVVTHMLENktGHIINISSVAGRIVFPAGSVYCATKHAITAFSEGLRQELSVrKNIRVTCIEPGVVATELTNTIT--DESL 200
                   ********************6655558***************************************8659********************8..5555 PP

                   HHHHHHSTTSS-B-HHHHHHHHHH CS
  adh_short_C2 190 eelearaplgrlgtpeevaeaalf 213
                   +++ ++a   +  ++e++a+a+++
    EPA04584.1 201 QAFVESAKKMESLQAEDIANAIVY 224
                   555556666666**********98 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.9   0.1   8.2e-17   1.6e-13       4     166 ..       8     170 ..       6     189 .. 0.86

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 8.2e-17
                 EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS---EEEE---------TTT--H CS
          KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppikGvihaAgvlrdklleemta 102
                 +itG+  g+G ++a  l + ga+ +++ +R+   +e  ++l + ++++g ev   ++Dv++k++  + +e++ ++ +++   ++ Ag++  + +++++ 
  EPA04584.1   8 IITGASSGIGFATALALSKAGAK-VAIGARR---TEMLSKLEKIIKENGGEVYSQKLDVTKKNECDSFVENVLKKWNKVDILVNNAGLMPLSFFKNLKV 102
                 8********************97.5666666...34444466677899*************************************************** PP

                 HHHHHHHTTTTHHHHHHHHHTTT....S--SEEEEEEEHHHHH--TT-HHHHHHHHHHHHHHHHHHHH CS
          KR 103 edleqvlapKvkGawnLhelled....esldffvlfSSiagllgsagqanYaaaNaflDalaeyrrsq 166
                 ++++q++   +kG+     ++      ++  +++ +SS+ag +  +  + Y a+ + + a+ e  r++
  EPA04584.1 103 DEWDQMIDVNIKGVLYCTGAVVThmleNKTGHIINISSVAGRIVFPAGSVYCATKHAITAFSEGLRQE 170
                 *************988766655434448899******************************9977664 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.6   0.00019      0.38       2      62 ..       8      74 ..       7     239 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00019
                EEETTTSHHHHHHHHHHHHCTSEEEEEES-.STTTTCHHCHHC........EEEE--TT-HHHHHHHHHH CS
   Epimerase  2 lVtGatGfiGsalvkallekgyevigldrl.ssasntarledl........elveldltdrsalerlfke 62
                ++tGa+  iG a++ al ++g +v   +r+ +  s+ ++   +           +ld+t++++++ ++++
  EPA04584.1  8 IITGASSGIGFATALALSKAGAKVAIGARRtEMLSKLEK---IikenggevYSQKLDVTKKNECDSFVEN 74
                79*******************996666666033333333...3456999998899999999988777764 PP

>> THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0    0.0002      0.39      34      76 ..       2      44 ..       1      51 [. 0.90
   2 ?    4.1   0.1     0.013        26      66     132 ..      68     134 ..      58     161 .. 0.81
   3 ?   -2.3   0.0       1.2   2.4e+03      78      94 ..     217     233 ..     171     238 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0002
                   -TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTSCCHHHH CS
  THF_DHG_CYH_C 34 legkkvvvvGrsnivgkplallLleknatVtvchsktkdlaei 76
                   +++k +++ G+s+ +g + al L++++a V +  ++t+ l+++
     EPA04584.1  2 IKDKVAIITGASSGIGFATALALSKAGAKVAIGARRTEMLSKL 44
                   5789999******************************888764 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.013
                    E-TTSCCHHHHHCCSSEEEE-SS-T..T-B-GGGS-TT-EEEE---EEC-TTEEE-SB-HHHHCTTSSE CS
  THF_DHG_CYH_C  66 chsktkdlaeitreadivvvavGkp..elikaemvkegavviDvGinrvekgklvGDvdfeevkevasa 132
                    c+s  +++ ++ ++ di+v  +G    ++ k+  v e   +iDv i+ v    ++G v ++ ++++ ++
     EPA04584.1  68 CDSFVENVLKKWNKVDILVNNAGLMplSFFKNLKVDEWDQMIDVNIKGV--LYCTGAVVTHMLENKTGH 134
                    888899999999*******999976336788888889999999999988..666777766666666554 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 1.2
                    CCSSEEEE-SS-TT-B- CS
  THF_DHG_CYH_C  78 readivvvavGkpelik 94 
                      a+ +v av  p+ ++
     EPA04584.1 217 DIANAIVYAVEAPKHVN 233
                    23555666666666665 PP

>> Cullin  Cullin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1     2e-05      0.04     276     328 ..      37      89 ..      26     119 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2e-05
      Cullin 276 leeLrkaleeyikeegkaivkdakekektedakkyveklLelkdkfdklvkea 328
                  +e+ ++le++ike+g ++ +++ + +k+++ +++ve++L+  +k+d lv++a
  EPA04584.1  37 RTEMLSKLEKIIKENGGEVYSQKLDVTKKNECDSFVENVLKKWNKVDILVNNA 89 
                 6799************7777666677999*********************987 PP

>> Eno-Rase_NADH_b  NAD(P)H binding domain of trans-2-enoyl-CoA reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   1.0   0.00015       0.3      41      66 ..       5      30 ..       1      37 [. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00015
                     SEEEEESTSSHHHHHHHHHHHHSS-- CS
  Eno-Rase_NADH_b 41 kkvLviGaStGYGLAsriaaafgaga 66
                     k +++ GaS+G G A+ +a++ +   
       EPA04584.1  5 KVAIITGASSGIGFATALALSKAGAK 30
                     788999************99877444 PP

>> BRCT_2  BRCT domain, a BRCA1 C-terminus domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00015       0.3      21      40 ..      41      66 ..      33     112 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00015
      BRCT_2 21 reklkklIeknGGevveti......t 40
                 +kl+k+I++nGGev+++       +
  EPA04584.1 41 LSKLEKIIKENGGEVYSQKldvtkkN 66
                589************66553333323 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.2   0.00033      0.66       1      47 [.       5      49 ..       5      73 .. 0.75
   2 ?    1.5   0.1      0.23   4.5e+02      37      81 ..     198     238 ..     174     246 .] 0.67

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00033
                   EEEEE.TTSH.HHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC CS
  F420_oxidored  1 kigii.GaGn.mgealasgllaagaqpheivvansrnpekaeelaeelg 47
                   k++ii Ga + +g+a a+ l++ag    ++ ++  r  e + +l++ ++
     EPA04584.1  5 KVAIItGASSgIGFATALALSKAG---AKVAIG-ARRTEMLSKLEKIIK 49
                   689998665449************...****88.777777888877665 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.23
                    CCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHHC CS
  F420_oxidored  37 ekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevlsel 81 
                    e+++    ++  ++++++  +a + a+ +v av   ++ +v + l
     EPA04584.1 198 ESLQ----AFVESAKKMESLQAEDIANAIVYAVEAPKHVNVNEIL 238
                    3333....3444555666666666777999999988888887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       960  (0.0535445); expected 358.6 (0.02)
Passed bias filter:                      636  (0.0354733); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 1590.02
//
Query:       EPA04585.1  [L=253]
Description: hypothetical protein BG20_I1800 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.6e-06   25.2   0.9    1.4e-05   24.6   0.4    1.5  1  Pkinase         Protein kinase domain
    8.3e-05   22.3   0.0    0.00015   21.5   0.0    1.4  1  RIO1            RIO1 family
    0.00036   20.2   0.0       0.12   12.0   0.0    2.6  2  Choline_kinase  Choline/ethanolamine kinase


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.4   2.3e-09   1.4e-05       4     124 ..      56     168 ..      53     208 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 2.3e-09
                 EEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHHHHHHHHHHHHHHHSCTTB--EEEEEEESSEEEEEEE--TTEBHHHHHH.HHSS--HHHHH CS
     Pkinase   4 leklGeGsfGkVykaveketgkivAvKkikkekakkkkekkvlrEikilkklkhpnivrlyevfeekdelylvleyveggeladlle.rkgslseeeak 101
                 l+ lG+G +G+V+ a+  ++++i+A+K+ + ++++++++    +E  +l      n v +   +++ ++ +lv+ey++g++++d++   kg+ s +++k
  EPA04585.1  56 LQILGKGYVGVVVLAK--KKNDIIALKIRRLDSQRSEMK----SEADLLS---IANTVSVGPKLYSVSKNFLVMEYLKGEKIEDWILsLKGVGSAKKLK 145
                 689************9..799***********9999776....8888776...556666666667777889*************987578889999*** PP

                 HHHHHHHHHHHHHHHTTEE-SS- CS
     Pkinase 102 kiakqilegleylHskgiiHrDl 124
                 ++++++le    l + g+ H  l
  EPA04585.1 146 SVIRTVLEDCYRLDQIGFDHGEL 168
                 *****998766666666666555 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   2.4e-08   0.00015      52     150 ..      88     188 ..      69     202 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2.4e-08
                 HHHHHHHHHHHHHHHHTT--S--EEEEETTEEEEE--EETTEE..GGBHHHCG-HHHHHHHHHHHHHHHHHHHHTSTEEESS-STT..SEEEETTEEEE CS
        RIO1  52 klwaekEfrnLkrleeagvpvPkpielkrhvlvmefigedgva..apklkdveeeeeaeelyeevleemrklykeaglvHaDLSey..Nvlvdedkvvi 146
                 +   + E + L+ +++     Pk + + ++ lvme+++ ++++  +  lk v + ++++++ ++vle   +l  + g  H+ LS     v+vd+ + ++
  EPA04585.1  88 RSEMKSEADLLSIANTV-SVGPKLYSVSKNFLVMEYLKGEKIEdwILSLKGVGSAKKLKSVIRTVLEDCYRL-DQIGFDHGELSSIskHVIVDKSRSTL 184
                 44555566655555555.445*****************666652266788888899***********86665.5**********87335999******* PP

                 --GT CS
        RIO1 147 IDvs 150
                 ID+ 
  EPA04585.1 185 IDFE 188
                 **94 PP

>> Choline_kinase  Choline/ethanolamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   1.9e-05      0.12      15      58 ..      86     129 ..      73     138 .. 0.88
   2 !    5.4   0.0     0.002        12     155     180 ..     173     196 ..     137     208 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.9e-05
                     TTCCHHHHHHHHHHHHHHTTSSS-EEEEETTEEEEE--TCEE-- CS
  Choline_kinase  15 eelidretElvvfallserglgpklygifenGrieefiesrtls 58 
                     ++ +++++E+  + + ++ ++gpkly + +n  + e++++++++
      EPA04585.1  86 SQRSEMKSEADLLSIANTVSVGPKLYSVSKNFLVMEYLKGEKIE 129
                     566899*********************************99865 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.002
                     GGEEE.-CTTEEEE--GTT-EEEEHH CS
  Choline_kinase 155 gNillnkeekklvlIDFEYagynyrg 180
                     + +++  ++++ +lIDFE +++n r+
      EPA04585.1 173 KHVIV--DKSRSTLIDFESSSVNRRV 196
                     55666..6677799*********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       908  (0.0506442); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1838.60
//
Query:       EPA04586.1  [L=158]
Description: hypothetical protein BG20_I1806 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00058   20.2   1.3    0.00094   19.5   0.8    1.7  1  Ca_bind_SSO6904  Calcium binding protein SSO6904
  ------ inclusion threshold ------
      0.037   14.3   0.6       0.38   11.0   0.2    2.1  2  Tox-PLDMTX       Dermonecrotoxin of the Papain-like fold


Domain annotation for each model (and alignments):
>> Ca_bind_SSO6904  Calcium binding protein SSO6904
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.8     1e-07   0.00094      21      79 ..      63     121 ..      46     125 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1e-07
                      HHHHHHHHHHHHHHHHHSS-HHHHHHHHHHHTHHHHHHTHHHHHHHHHHHHHHHTTT-H CS
  Ca_bind_SSO6904  21 veevekileeieedlrksnnikssiifvyanhveevkknkefydliskilekyakkiGv 79 
                       +e + il+  ee+ ++++ i s+ii   ++++e + +n+++  ++ + l+   + iG+
       EPA04586.1  63 LDEEKFILDAQEEQRERTEMILSAIINGKSKFLESISQNHKTKTVVIRFLQEVDEIIGA 121
                      4455679********************************************99999986 PP

>> Tox-PLDMTX  Dermonecrotoxin of the Papain-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.032   2.9e+02      59     100 ..      15      56 ..      10      63 .. 0.76
   2 ?   11.0   0.2   4.3e-05      0.38      52     134 ..      64     145 ..      57     156 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.032
                 ETTGGGGTTT-TT--S-EEEEHHHHHHHHHTT-SS-EEEEEE CS
  Tox-PLDMTX  59 DvsahqfsklkenlsseiidteeeWvkkyqaalktkLvkikd 100
                 D+  + f+ +++++++ iidt  e   ++ ++   k+ +++d
  EPA04586.1  15 DLKKQEFDGVESKIKEAIIDTSTELTSLLINIRLDKISRLED 56 
                 6667789999999********999888877776666655555 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 4.3e-05
                 TTEEEEEETTGGGGTTT-TT--S-EEEEHHHHHHHHHTT-SS-EEEEEEESS.HHHHHHHT-SS---GGGS--TT......-EE CS
  Tox-PLDMTX  52 ndeeyvlDvsahqfsklkenlsseiidteeeWvkkyqaalktkLvkikdfkn.dslaenatkasapvkendelaggrsikdakv 134
                 ++e+++lD   +q ++  e + s ii+ ++++   + ++ ktk v i+ ++  d+++    +   p+k +d+ a  ++ + + +
  EPA04586.1  64 DEEKFILDAQEEQRER-TEMILSAIINGKSKFLESISQNHKTKTVVIRFLQEvDEIIGADLEKYGPFKTEDI-ATIPYENAQAL 145
                 7899***********8.899999********************88888777624455555555567766654.44455554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1047  (0.058397); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 975.97
//
Query:       EPA04587.1  [L=92]
Description: 4a-hydroxytetrahydrobiopterin dehydratase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.5e-33  112.6   0.2    8.1e-33  112.5   0.2    1.0  1  Pterin_4a  Pterin 4 alpha carbinolamine dehydratase
  ------ inclusion threshold ------
      0.036   14.2   0.1      0.062   13.4   0.1    1.5  1  IF-2       Translation-initiation factor 2


Domain annotation for each model (and alignments):
>> Pterin_4a  Pterin 4 alpha carbinolamine dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.5   0.2     9e-37   8.1e-33       2      90 ..       3      90 ..       2      91 .. 0.95

  Alignments for each domain:
  == domain 1  score: 112.5 bits;  conditional E-value: 9e-37
   Pterin_4a  2 klseeeiqkllaelpgWrleeaeelerefkfkdfeeaiafvnrvaalaeeenHhpdilvsynkvtvrltThdaggltenDfklAakide 90
                +ls+++i+++l++lpgW+   +e+l++ef+f++f++a++f++r a+  e++nHhp+++++ynk+t++ltThdagg+t+nD++lA+ +++
  EPA04587.1  3 RLSQADIEEELKNLPGWKI-VNEKLHKEFQFESFNQAFGFMTRAAMEIEKMNHHPEWFNVYNKITIELTTHDAGGITKNDVNLAKILNS 90
                699********999****7.6679************************************************************98876 PP

>> IF-2  Translation-initiation factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   6.9e-06     0.062      40      67 ..      63      90 ..      48      92 .] 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.9e-06
                SSTEEEECEEEESSB-HHHHHHHHHSTE CS
        IF-2 40 eevkvkvihsgvGaitesDvelasasna 67
                ++++++   ++ G it++Dv+la+  n+
  EPA04587.1 63 NKITIELTTHDAGGITKNDVNLAKILNS 90
                689999*****************98665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 637.01
//
Query:       EPA04588.1  [L=373]
Description: hypothetical protein BG20_I1381 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.69   10.4   3.2       0.41   11.1   0.2    2.1  2  Usp       Universal stress protein family


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   2.3e-05      0.41      20     109 ..      46     130 ..      34     156 .. 0.70
   2 ?   -1.3   0.2      0.16   2.8e+03      80      97 ..     220     237 ..     179     278 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.3e-05
                 HHHHH.HHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTCEEEEEEEESSHHHHHHHHHHHTTSSEEEE CS
         Usp  20 ewAle.lakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggvkvevvveegdpaeeilevaeeedadliVv 109
                  wA+e ++ +++ael l+h+ +p a  ++s+ +e  e  ++ +++ e+ +     ++ + +v+++  ++  d a ei+++     a l+Vv
  EPA04588.1  46 FWAIEkNLDDNNAELALVHATHPIAELYSSMKPELKEANPEFDAKVEKTLMD-LGKKTGSDVTRQDAQKAIDDAKEIIKE-----ARLLVV 130
                 5999988888*************************99999999999888664.333333333333333333333333333.....445555 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.16
                 CEEEEEEEESSHHHHHHH CS
         Usp  80 vkvevvveegdpaeeile 97 
                 v++  +   ++ +e+  e
  EPA04588.1 220 VETFADGIIHEIGEAVGE 237
                 333333333333333322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1172  (0.065369); expected 358.6 (0.02)
Passed bias filter:                      632  (0.0352502); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2807.64
//
Query:       EPA04589.1  [L=453]
Description: adenylosuccinate lyase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-49  168.1   1.4    4.8e-49  167.4   1.4    1.2  1  Lyase_1   Lyase
    3.7e-14   53.0   0.0    8.7e-14   51.8   0.0    1.7  1  ADSL_C    Adenylosuccinate lyase C-terminus
     0.0072   16.4   0.0       0.02   15.0   0.0    1.7  1  ASL_C     Adenylosuccinate lyase C-terminal


Domain annotation for each model (and alignments):
>> Lyase_1  Lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.4   1.4     8e-53   4.8e-49       7     306 ..      13     293 ..       9     297 .. 0.94

  Alignments for each domain:
  == domain 1  score: 167.4 bits;  conditional E-value: 8e-53
                 TCHHHHHHHHHHHHHGGGHHHHHCHHHHHHHHHHHTTSSTHHHHHHHHHHHHHHHCHCHHCGGHHHBSSSSSHHHHHHHHHHHHHHHHTTHSSGIIIII CS
     Lyase_1   7 adklmgiftersrenfrlseedikalaalkkaaakanvdlkeeaaaiikaldevleegklddqfvlkviqegsgtavnmnlnevigellgekvepndkv 105
                 + ++m+if+e+ + +++l+     +++a++ +  + ++++k++ ++i +a+   ++ gk++ + ++k  + +s +++ + l e ++e+    ++++ ++
  EPA04589.1  13 TKEMMAIFSEQKKIDYQLE-----IEGAAALSQSEIGIIPKTVGKKIYNAA---IS-GKIN-AKRIKELESKSDHDTAA-LVESLSEKCT--KDARPWI 98 
                 6789***************.....8999999999******99999998875...66.8999.99************999.99****7777..69***** PP

                 TTT--HHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHTTT-EEEEEETTEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHTCEETTTTTTT CS
     Lyase_1 106 htgqSsnDqvpTalrlalkkalsekLlpaleqLidalkekakefkdvvkiGrThlqdAtPvtlgqelsayaealerdrerlkellkrllvellgggtav 204
                 h+g +snD v+T+ ++++++al + ++p++ +++++l+++a ++ +++ +GrTh+q+A  + +g +++ +a+++ +++er++e++kr+l  +  g +++
  EPA04589.1  99 HFGLTSNDLVDTSNSMQMRDAL-KIIEPKVAKMASILSKRAIQHGKIPAVGRTHGQHASIISFGLKFANWAAEMAKHIERIEEMKKRVLICKTLGVVGT 196
                 **********************.66************************************************************************** PP

                 SSTTTSCC.THHHHHHHHHHHHHCSTEESSSHHHHHHC-HHHHHHHHHHHHHHHHHHHHHHHHHHHTSTTTSSEEEEGCCTSSC-TTSTTTEBTHHHHH CS
     Lyase_1 205 gtglnadp.efaelvakelakvtglpvkapnsfeavsdrDavvellgalkllatsLskfaeDlrllssgeaglvelslaesepGSSiMPgKvNPvqlEl 302
                 g  ++a+  e++++vak+l+   +     ++ ++++ +r +++e+++ l+l+ + L k+a ++r l+ +e+g+v +++ +++ GSS  P K+NP+++E 
  EPA04589.1 197 GSLMGAKSlEVQKRVAKKLN---L---FPAEVTTQIIPRERYAEYVFELALIGATLEKIAVEIRNLQRTEIGEVAEQFKKGQMGSSAVPVKRNPIKSER 289
                 *******99***********...6...55677789***************************************************************9 PP

                 HHHH CS
     Lyase_1 303 ltgv 306
                 +t+ 
  EPA04589.1 290 VTSL 293
                 9876 PP

>> ADSL_C  Adenylosuccinate lyase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.8   0.0   1.4e-17   8.7e-14       1      73 []     363     441 ..     363     441 .. 0.95

  Alignments for each domain:
  == domain 1  score: 51.8 bits;  conditional E-value: 1.4e-17
                 TGGGHHHHHHHHH.HTH-HHHHHHHHHHHHHHHHHC...HHHHHHT-HHHH.C.HHCHHHHHT-GGGCCTTHHHHHHHH CS
      ADSL_C   1 GlifservllaLv.kglgReeAyelVqeaamkawee...llelLaadpevk.k.seeeldalfdpayylgsadeivdrv 73 
                 G if+e vl aL+ kg+ R  Ay+ Vq+ a +a ++   +++++++d++++   +++e+d +f+p+++lg++++i++ v
  EPA04589.1 363 GQIFAEFVLEALIkKGIPRFVAYKDVQRVAFEANDKgiqYIDAIKNDKAFTsNlTDKEIDSIFSPEKHLGASPVIINNV 441
                 789**********66********************9***************55*999******************9865 PP

>> ASL_C  Adenylosuccinate lyase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   3.3e-06      0.02       4      82 ..     313     392 ..     311     423 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.3e-06
                 T--TCHHHHHTTCHHHHHHHHH.HHHHHHHHHCCEEE-HHHHHHHHHT-.GGGGHHHHHHHHHHTT-TT..HHHHHHHHHTTS CS
       ASL_C   4 QRDLtdStvlRnlgvalahsli.alksllkglsklevneealaedLden.wevlaEaiqtvlrregiek..pYeklkeltrgk 82 
                  RDL++S+  R +  + a  +   l+ ++k +s+l vne+++ e+L  +  ++ aE +  +l ++gi++  +Y+ ++++   +
  EPA04589.1 313 ERDLSNSANERFVLPTAAILVDeMLETMIKIISNLIVNEKRIVENLYITkGQIFAEFVLEALIKKGIPRfvAYKDVQRV---A 392
                 6**********987666665542578999*****************865389**********99999863345444444...3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 3031.41
//
Query:       EPA04590.1  [L=120]
Description: hypothetical protein BG20_I1376 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.1e-10   39.1   0.0    7.4e-10   38.9   0.0    1.1  1  PTPS      6-pyruvoyl tetrahydropterin synthase


Domain annotation for each model (and alignments):
>> PTPS  6-pyruvoyl tetrahydropterin synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   0.0   4.1e-14   7.4e-10      41     116 ..       8     110 ..       1     115 [. 0.88

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 4.1e-14
                 TCTTBSS-HHHHHHHHHHHHHCTTTEEC.CCC-CCHHCCS..............................--HHHHHHHHHHHHHHHHGCCCGCEEEEE CS
        PTPS  41 detgmvvdfgelkealkeileelDhkfl.naddpeleell.............................spTaEnlaklifeelkerlqekevklskvr 109
                  +++ +vdfg +k+++k+++ e+Dhkf  n   + +++                               + T+Enl++ i++ l+++l +++v+   v 
  EPA04590.1   8 MKDNLLVDFGIAKKIIKDVITEFDHKFFiN--RKYMKNEDdshyqikfdgpkgmfdiqvpkntayllegEATVENLSSEIIKLLAPKL-PQNVEAVGVY 103
                 67899**********************966..55555544679999***********************99*****************.99******** PP

                 EEEETTE CS
        PTPS 110 vwEtpns 116
                 ++E  n+
  EPA04590.1 104 IYEGYNK 110
                 *998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 837.85
//
Query:       EPA04591.1  [L=105]
Description: hypothetical protein BG20_I1389 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.11   12.4   0.0       0.16   11.9   0.0    1.2  1  PIG-P     PIG-P


Domain annotation for each model (and alignments):
>> PIG-P  PIG-P
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   8.7e-06      0.16      50     121 .]       5      72 ..       2      78 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.7e-06
       PIG-P  50 ayllmlvlyiyvalaslnlevltppldsletivDeaakveeeeeeeelkeyaseetdavmDlpigeVnevlY 121
                 +++ m ++++  +l sl l++ltpp++s+ t+ ++ +k+     +e  + +as +  ++  lp g++n+++Y
  EPA04591.1   5 IWFAMGIVVASALLGSLVLGFLTPPISSVITLQEKCEKI-A---KEGFQIHASYPDLQLDQLPTGDMNRLMY 72 
                 6999******************************99973.2...2333333444444444567777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 675.29
//
Query:       EPA04592.1  [L=52]
Description: hypothetical protein BG20_I1384 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 366.39
//
Query:       EPA04593.1  [L=104]
Description: hypothetical protein BG20_I1383 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.067   13.6   0.0      0.097   13.1   0.0    1.5  1  FAA_hydro_N_2  Fumarylacetoacetase N-terminal domain 2


Domain annotation for each model (and alignments):
>> FAA_hydro_N_2  Fumarylacetoacetase N-terminal domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   5.4e-06     0.097      15      46 ..      13      44 ..       8      81 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.4e-06
  FAA_hydro_N_2 15 LvvVsrdlkkavdaseiaptlqaaLdnWdeve 46
                   L+ V +d+++  d+s+i p++q+++d+W+++ 
     EPA04593.1 13 LISVFKDNTNPDDVSRITPQIQEIIDEWQSTG 44
                   66788999999*****************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.32s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 658.85
//
Query:       EPA04594.1  [L=316]
Description: thiamine-phosphate kinase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-13   50.5   0.0    6.4e-13   49.2   0.0    1.7  2  AIRS      AIR synthase related protein, N-terminal domain
    0.00021   21.5   0.0    0.00042   20.5   0.0    1.5  1  AIRS_C    AIR synthase related protein, C-terminal domain


Domain annotation for each model (and alignments):
>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2   0.0   7.2e-17   6.4e-13       6      93 ..      38     134 ..      25     135 .. 0.88
   2 ?   -3.9   0.0         2   1.8e+04      58      74 ..     210     226 ..     206     233 .. 0.74

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 7.2e-17
                 EEEEEEEE.EECCTCCCC........HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC......HHHHHHHHHHHHHHHTT-EEEEEEEEEESSEEEEEEE CS
        AIRS   6 vvttdshnrpvlvepvhf........iGakavavnlsDlaamGArPlalllslalp......wleevvrglaeaaeelgvplvgGdtsfsneptisvta 90 
                 v ++d     ++v+ +++        +++k++ +++sD aa G rP++ + sl lp      ++ e+ +g+++a++e++++++gGdt++++e++i+v+ 
  EPA04594.1  38 VTKVD-----TFVQSTDMpskmkvgdAARKSIIACVSDFAAKGVRPRYGIISLVLPrkishkKIIEMSNGIKRAVDEFNIKILGGDTNEGKEIIINVSL 131
                 55666.....55655555666677888********************99************************************************** PP

                 EEE CS
        AIRS  91 vGl 93 
                 +G+
  EPA04594.1 132 FGT 134
                 996 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 2
                 HHHHHHHHHHHTT-EEE CS
        AIRS  58 vvrglaeaaeelgvplv 74 
                 + + l+e+a++ +++ v
  EPA04594.1 210 LSTTLNEMANQSKCKFV 226
                 56677888888888766 PP

>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   4.6e-08   0.00042       2     152 ..     146     296 ..     145     300 .. 0.64

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 4.6e-08
                 TTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHH...HTTECEEEE--TTHHHHHHHHHHHTTTEEEEEECG..... CS
      AIRS_C   2 pGdvliltgslGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaal...kglvkaahDvTgGGLlgalaemapasgvgaeidld..... 92 
                  Gd +++tg+ G  ++g ++  + ++++ +    +++         ++  ++l +    +   ++  D ++ GL+ +l+ema++s+++++i+       
  EPA04594.1 146 SGDIIFVTGPFGYTASG-LKMLEKNKKSNQF--VKKIIK-----SFVNPRPKLDFGvinRRYLSSSMDSSD-GLSTTLNEMANQSKCKFVINNIptgkd 235
                 68888888886666666.3333333333211..222333.....333333333333334457778888888.8******************99856665 PP

                 THHHHHHHH........HHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEESSSEE CS
      AIRS_C  93 kvpifdele........splemllsensGrllvavppeeadavlaileeeglpeaavIGevtakeels 152
                        +e        + + +++  ++   +++v+++ ++ +++ + + + p   +IG+vt+++++ 
  EPA04594.1 236 M------IEfvklnkmnLNELVFHGGEEYEFVFTVSKKYKAIIKKNALQLNTP-IIEIGHVTKGRGVF 296
                 3......3344343474555555666777777888888887777777788876.*********98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1864.62
//
Query:       EPA04595.1  [L=435]
Description: phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.7e-23   82.9   0.0    4.3e-23   81.5   0.0    1.7  1  PGM_PMM_I    Phosphoglucomutase/phosphomannomutase, alpha/bet
    5.6e-15   55.5   0.1    4.3e-14   52.7   0.0    2.2  2  PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/bet
    3.8e-12   46.7   0.0      1e-11   45.4   0.0    1.7  1  PGM_PMM_II   Phosphoglucomutase/phosphomannomutase, alpha/bet
    1.2e-06   28.6   0.1    3.8e-06   27.0   0.0    1.9  2  PGM_PMM_IV   Phosphoglucomutase/phosphomannomutase, C-termina


Domain annotation for each model (and alignments):
>> PGM_PMM_I  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.5   0.0   9.7e-27   4.3e-23       6     132 ..       8     126 ..       3     131 .. 0.92

  Alignments for each domain:
  == domain 1  score: 81.5 bits;  conditional E-value: 9.7e-27
                 TTCEEEECCHCTBSCCHHHHHHHHHHHHCHHCSTS-EEEEEE-S-TTHHHHHHHHHHHHHCCT-CEEEEEEB-HHHHHHHHHHCCECEEEEE--TTS-T CS
   PGM_PMM_I   6 tsGlRgkvgegeltpelveklgqaiaeylkaeakkkkvvvGrDtRvssrelaealaaglaanGvevillgllptPavsfairklkadagimitaSHnpp 104
                  sG+Rg++g + ++ + ++++ + + + +++    kk v+G+DtR s+ +++e + a l++nG+++++l+ +ptP+v    rk  + ag++it SHnp 
  EPA04595.1   8 ISGIRGIFG-DDFNLKDTLQFCNNFSSLIES----KKCVLGKDTRPSGIMIKEVASAALMKNGINTYNLETVPTPVVFRESRK--YGAGLVITSSHNPI 99 
                 59*******.669*****************9....7******************************************99999..789*********** PP

                 TCCCEEEEETTTCE--CHHHHHHHHHHC CS
   PGM_PMM_I 105 eyngiKvylsnGgpispeveekIeaiie 132
                 e ngiK++ + G  i++e+  +I ++ e
  EPA04595.1 100 EWNGIKFIIN-GRGINEEELPRIIENQE 126
                 *********9.99999998888776655 PP

>> PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0      0.21   9.6e+02      20      50 ..      48      78 ..      36      81 .. 0.83
   2 !   52.7   0.0   9.5e-18   4.3e-14      12     112 ..     248     343 ..     237     345 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.21
                 TTCEEEEETTS-THHHHHHHHTT-EEEEESS CS
  PGM_PMM_III 20 pgagvvktvmtslalervakklgiklvetkv 50
                 p++ ++k+v +  ++++ ++ +++++v t+v
   EPA04595.1 48 PSGIMIKEVASAALMKNGINTYNLETVPTPV 78
                 4445999******************999998 PP

  == domain 2  score: 52.7 bits;  conditional E-value: 9.5e-18
                  HHHCHCSTTTCEEEEETTS-THHHHHHHHTT-EEEEESSSCHHHHHHHHHTTECEEEETT.CEEEETTTBSS--HHHHHHHHHHHHHHHTS-HHHHHH CS
  PGM_PMM_III  12 ylleeklkpgagvvktvmtslalervakklgiklvetkvGdkyvleemkeegavlGgEeS.ghiifldeattkDGilaallvleilaetgkslselle 108
                  ++le  l ++++ v ++ ts  +e+++k++g+++ ++kvG  +v+++m +++a+ GgE S g++i++++++++ Gil++ l+ ++l ++  + +e+l 
   EPA04595.1 248 KALE--L-GYKQFVLSIDTSISVEKFIKEKGGRVQRSKVGEANVIDLMLKTDAQAGGEGSsGGFILPEFNYCREGILTSGLISSMLGNS--KFNEIL- 339
                  3444..3.4557999*********************************************9************************9886..677777. PP

                  HHHH CS
  PGM_PMM_III 109 ellk 112
                  ++++
   EPA04595.1 340 NFME 343
                  5555 PP

>> PGM_PMM_II  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   0.0   2.2e-15     1e-11       2     101 ..     141     232 ..     140     235 .. 0.82

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 2.2e-15
                 HHHHHGGGTS-HHHHHHHT-EEEEE-TT-TTHHHHHHHHHHTT-EEEES-----TT-TTSS----TT-TTTTHHHHGGGGG-SEEEEE-TTS-BEEEEE CS
  PGM_PMM_II   2 aYiealkekvdseaikksglkvvidplhGaggeilkellkelgvdvvelnaepdpdfptkapnpeekealkllielvkkegadlglafDgDaDRlgvvd 100
                 +Y+e+ ke +   +i +s+ k+vid ++Ga++++++ ll++lg+ v  +n++ +     + p+p+  ++l++li++   ++ ++g+afD D+DRl+vv 
  EPA04595.1 141 SYLEDAKELIG--KI-ESNPKIVIDIGGGAAKDFAPILLRQLGCTVSVINENLSNCT--RGPDPTS-DSLSDLINA--TSKKEIGFAFDLDGDRLVVVR 231
                 69999999998..33.44469***********************9999999999854..6699999.777777444..34559**************95 PP

                 T CS
  PGM_PMM_II 101 e 101
                 +
  EPA04595.1 232 N 232
                 4 PP

>> PGM_PMM_IV  Phosphoglucomutase/phosphomannomutase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       2.9   1.3e+04      22      40 ..     210     228 ..     200     231 .. 0.65
   2 !   27.0   0.0   8.4e-10   3.8e-06      25      72 ..     380     426 ..     350     428 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.9
                 THHCCCCCCCCGCCEEEE. CS
  PGM_PMM_IV  22 vasikeglkilledGrrla 40 
                 + s ke+   ++ dG rl+
  EPA04595.1 210 ATSKKEIGFAFDLDGDRLV 228
                 4456677777778888886 PP

  == domain 2  score: 27.0 bits;  conditional E-value: 8.4e-10
                 CCCCCCCCGCCEEEE.EEEETTCCEEEEEEEESSHHHHHHHHHHHHHH CS
  PGM_PMM_IV  25 ikeglkilledGrrlavRpSGTepllrvyvEaksdeelarlaeevael 72 
                 + ++  i +ed ++l +R S+Te+ +rv +E+ + ++++r+ +  +el
  EPA04595.1 380 QDGIKGIIDEDSWVL-IRKSNTEDIIRVSAESNNVDKCNRIMKNTLEL 426
                 344556899******.**********************9998887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 2613.62
//
Query:       EPA04596.1  [L=161]
Description: ribosomal protein S11P [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-41  141.6   1.9    1.5e-41  141.2   1.9    1.1  1  Ribosomal_S11  Ribosomal protein S11
  ------ inclusion threshold ------
      0.041   14.1   0.1       0.08   13.2   0.1    1.5  1  CBM_25         Carbohydrate binding domain (family 25)


Domain annotation for each model (and alignments):
>> Ribosomal_S11  Ribosomal protein S11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.2   1.9   1.7e-45   1.5e-41       1     110 []      39     157 ..      39     157 .. 0.99

  Alignments for each domain:
  == domain 1  score: 141.2 bits;  conditional E-value: 1.7e-45
  Ribosomal_S11   1 GvahiqasfnntiititdlkGaevlvksaGglgvkasr.kssPyaaqlaaekaaekvldkGikavevkvkg........pGpGreaalralaraGl 87 
                    G+ahi++s+nntii++tdl+G e+++ s+Gg+ v a+r +ssP+aa++aa++++e +  kG +  +++v++        pGpG++aa+ralar G+
     EPA04596.1  39 GIAHIYSSYNNTIIHMTDLTGGETVSISSGGVHVNADRyESSPFAAMKAANAVVEVAHTKGFTGFHIRVRAvggvgsrvPGPGAQAAIRALARGGF 134
                    9*********************************************************************************************** PP

  Ribosomal_S11  88 kigriedvtPiPhdgirrpkkrr 110
                    kigri+dvtPiPhd++r+++++r
     EPA04596.1 135 KIGRIDDVTPIPHDTTRKKGGKR 157
                    *******************9987 PP

>> CBM_25  Carbohydrate binding domain (family 25)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1     9e-06      0.08      11      55 ..      94     138 ..      85     150 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9e-06
      CBM_25  11 strkkGftsayihyrpaGGswtavpGvkmrdaeaGyakkdvdlGa 55 
                  +++kGft  +i  r  GG  + vpG + ++a    a+    +G 
  EPA04596.1  94 VAHTKGFTGFHIRVRAVGGVGSRVPGPGAQAAIRALARGGFKIGR 138
                 4789****************************9888777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1025.30
//
Query:       EPA04597.1  [L=232]
Description: hypothetical protein BG20_I1374 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 1330.53
//
Query:       EPA04598.1  [L=103]
Description: hypothetical protein BG20_I1388 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 634.20
//
Query:       EPA04599.1  [L=138]
Description: hypothetical protein BG20_I1386 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.9e-06   27.5   0.5    3.6e-06   27.2   0.5    1.1  1  dsDNA_bind      Double-stranded DNA-binding domain
     0.0031   17.9   1.7     0.0063   16.9   1.7    1.5  1  EF-1_beta_acid  Eukaryotic elongation factor 1 beta central a
  ------ inclusion threshold ------
        0.4   10.2   3.6        1.5    8.4   3.5    2.0  1  DDRGK           DDRGK domain


Domain annotation for each model (and alignments):
>> dsDNA_bind  Double-stranded DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.5     6e-10   3.6e-06       1     109 [.      11     116 ..      11     118 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 6e-10
                 XXXXXXXXXXXXXXXXXXXX...XXXX--SS..S--SSHHHHTTS--HHHHHHHHHHTTT-HHHHHHHHHHHHHHHH--SS-----HHHHHHHHHHHS- CS
  dsDNA_bind   1 irkarlaelqaqagsssgsggaseqqeqqqeaseeeakqaiLsqiLepeAreRLsrirlvkperaeavenrLiqlaqsGqlrskvteeqLkeLLeqvae 99 
                 ++++rlae+q++ +s+++ +  +  ++     +++++ ++++ + L  +  e L++ +   p+ +++v ++L +l+ sG++++ ++  +L  L++++  
  EPA04599.1  11 LKAKRLAEMQQNISSRKEIE--KPTNNL--SPKHTKQPRDVVVERLGYRGLEVLQNAESQFPNDTKMVIEKLAELITSGEISEILDGGKLLALFRSIGL 105
                 689********998776532..233333..3348999************************************************************99 PP

                 .--XXXXX..X CS
  dsDNA_bind 100 .kkketkivis 109
                   + etki+++
  EPA04599.1 106 yIRMETKINVE 116
                 88888999886 PP

>> EF-1_beta_acid  Eukaryotic elongation factor 1 beta central acidic region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   1.7   1.1e-06    0.0063       8      24 ..       3      19 ..       2      21 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.1e-06
  EF-1_beta_acid  8 EEDeEaerlreeRLaaY 24
                    +ED E erl+++RLa+ 
      EPA04599.1  3 DEDSELERLKAKRLAEM 19
                    459************95 PP

>> DDRGK  DDRGK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   3.5   0.00025       1.5      68     149 ..      13      93 ..       1     117 [. 0.71

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00025
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXHHHHHHHHHHH-SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EEE-T CS
       DDRGK  68 erkeqeeyeklksefvveeegtekesaeeeeklleefinyikekKvvlleelavkfklktqevierikeLeeqgsltGvlDd 149
                 +++  e  ++++s  ++e+  ++  s ++ ++  + +++ +  + +  l++  ++f  +t+ vie++ eL ++g+++ +lD 
  EPA04599.1  13 AKRLAEMQQNISSRKEIEKPTNN-LSPKHTKQPRDVVVERLGYRGLEVLQNAESQFPNDTKMVIEKLAELITSGEISEILDG 93 
                 44445555555555555554333.3333334455566666666777778888899*************************94 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 859.71
//
Query:       EPA04600.1  [L=773]
Description: valine--tRNA ligase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.3e-105  353.9   1.1   2.4e-104  349.8   1.1    2.2  1  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
    4.9e-31  107.8   2.9    4.9e-31  107.8   2.9    2.0  2  Anticodon_1    Anticodon-binding domain of tRNA
    4.4e-22   78.4   4.2    8.7e-12   44.5   0.0    3.2  2  tRNA-synt_1g   tRNA synthetases class I (M)
    0.00051   19.6   1.1        0.1   12.1   0.0    3.1  3  tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2


Domain annotation for each model (and alignments):
>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  349.8   1.1  5.4e-108  2.4e-104       2     592 ..      18     561 ..      17     571 .. 0.95

  Alignments for each domain:
  == domain 1  score: 349.8 bits;  conditional E-value: 5.4e-108
  tRNA-synt_1   2 lyekWeeedvfkkelekekekkefilvdgPPyvtGsl.HiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieakvekklgakekkerkklgre 98 
                  ++++W +e++++ +     ++++f++  +PPy  G++ HiG a + +  d++ r++rm Gk+v + +G+D  Gl++e   ekk  ++ +    +  r 
   EPA04600.1  18 ILKQWVNEKIYEFT----PKNDNFTIDTPPPYPSGRPwHIGAAAHYSQIDMIARTARMAGKNVYFPIGIDRNGLPVEIYTEKKHNIRMR----ETERG 107
                  78999999999988....67899************977*********************************************877766....88999 PP

  tRNA-synt_1  99 efrekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkgliyrgkklvnwstklktalselEveykdkkdalihvafplad 196
                  ef + +r   +   +e+   +k lG+s Df + y T ++e+   ++ +f  l +kg++y ++++ n+++ + t+++++E+ y+d    l++++f+++d
   EPA04600.1 108 EFLKLCRTALDDLEAEMILIMKSLGISGDFTNYYRTDSEEYRTLTQSTFIDLWKKGQVYLANRPNNYDWVSGTTIADAEITYEDLPTKLVYMKFQIKD 205
                  ************************************************************************************************** PP

  tRNA-synt_1 197 keevklviaTTtPeTllgdtavavnpeldyvitkeklilaeallkslvkkesekkiledergkeLegkevelplvnrkipiiaddyvdkeaGtGvVki 294
                   ++ +++ia T+Pe l + +++ vnpe                               der+++ +gk+v+ p++n ++ + +   + +e+G+G+V +
   EPA04600.1 206 TDK-EIIIASTRPELLCACKTIIVNPE-------------------------------DERYTNYVGKKVIVPITNVEVELRTHHSARQEFGSGAVMV 271
                  ***.***********************...............................9*************************************** PP

  tRNA-synt_1 295 aPahdedDyevgkkynlevinildedgtlteeaaefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkpiiyrateqWfvrvkeladaal 392
                    + d++D ++ ++ +l+ i+++  dg++te a+e+ glk ++ar k++e+l+++g   k+e+i h  p++ersk+pi+    e ++ ++ke  +++ 
   EPA04600.1 272 CSYGDQNDVALFRELELKEIVAIGLDGKMTEAAGEYVGLKPKQARTKIIEDLEKNGFVEKIEDIIHRTPVSERSKNPIEIIPMEEYYLKQKEAIEKMK 369
                  ************************************************************************************************** PP

  tRNA-synt_1 393 kavekvqfvpkskekryaswleniq.dWciSRqrwWGhriplfvsketeevvvreelkelvagreeeeaekkalekeakdkl.kkekgelekdedvlD 488
                  k  ++++f+p ++++  ++wle i+ dW iSR r++G+ ip+++ k+  e +v           e  +  k +lek  +++  k++  e+  +e ++D
   EPA04600.1 370 KLGQEITFYPAMHKQILMNWLESINiDWPISRRRYYGTEIPIWYCKSCSEPHV----------PEPGKYYKPWLEKCPINNCsKCKGTEFVGEERTFD 457
                  ***********************977***********************9999..........344556666777777777657778899******** PP

  tRNA-synt_1 489 vWFsSgswpfstlgypeedteelkkffpadmlleGlDiirgWvarlillslaltgsePfkevlvhglvrdeeGrKmSKslgNvidpldvikkygadal 586
                  +W +S+ +p  + +y +  +e ++k++p+++  +  Di+r W++  +l   +ltg++P+ e  v g  +de+G KmSKs+gN idpl vi++ gad  
   EPA04600.1 458 TWMDSSVSPLFVSKYNKD-QEFFNKVYPTSIRPQAKDIVRTWLYYTLLRCEQLTGKKPWSEAWVMGYGLDEKGMKMSKSKGNAIDPLPVIEQFGADTF 554
                  **************9877.999**************************************************************************** PP

  tRNA-synt_1 587 Rltli.l 592
                  R++ + +
   EPA04600.1 555 RFWSAsE 561
                  ***8744 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1      0.61   2.7e+03      82     109 ..       3      24 ..       2      75 .. 0.48
   2 !  107.8   2.9   1.1e-34   4.9e-31       1     149 [.     607     750 ..     607     753 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.61
  Anticodon_1  82 PfitEelwqr..eeeelgkkesimlaewpe 109
                  P i+E++w+   e       ++i l +w +
   EPA04600.1   3 PKIAEKAWNPelE-------KEI-LKQWVN 24 
                  7799999932321.......223.333432 PP

  == domain 2  score: 107.8 bits;  conditional E-value: 1.1e-34
  Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedk.ra.aqevllevletllrllaPfmPfitEelwqreeeel 96 
                  d+wil+el++l+ke+++ y+ey+f   a a+ ef+wn ++ +y+e+vk r y+   +d+ r  a ++l++ l+t+l+llaP++PfitE+lw    ++l
   EPA04600.1 607 DKWILAELDNLIKECKKGYDEYNFFIPAIAIREFTWNIFAAHYIEMVKARAYGIGFSDEeRDgAIYTLHKTLSTILKLLAPITPFITEHLW----KTL 700
                  9****************************************************9988889999****************************....9** PP

  Anticodon_1  97 gkkesimlaewpekaeelekeleeeevellkeivkairklrselkikpsselk 149
                   ++esi++++   ++e  e++   +  + + e ++ + + ++ ++++ +  +k
   EPA04600.1 701 YSSESIHKQKQV-TSESIENNN--KITKEITEFNSKVWNEKKAQNLSLKDSIK 750
                  *********965.444442222..23344444566666666777766666555 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.5   0.0   1.9e-15   8.7e-12       2     136 ..      38     188 ..      37     195 .. 0.82
   2 !   29.4   4.3   7.4e-11   3.3e-07     167     371 ..     340     575 ..     315     589 .. 0.79

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 1.9e-15
                   EEEE--B--SS--.-HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHT.TS-HHH........HH....HHHHHHHHHHHHHTT-- CS
  tRNA-synt_1g   2 lvttalpYangkl.HlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAeke.gvtpee........lv....ekvheeikelfkklnis 84 
                    + t+ pY++g++ H+G ++++ + D++aR  r+ g++v+f  g D  G p+e+  ek+ ++  +e        l+    ++ ++e+  ++k+l+is
    EPA04600.1  38 TIDTPPPYPSGRPwHIGAAAHYSQIDMIARTARMAGKNVYFPIGIDRNGLPVEIYTEKKhNIRMREtergeflkLCrtalDDLEAEMILIMKSLGIS 134
                   588999***99755***************************************9887642555443222222225511114456666678999**98 PP

                   ..-SEEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG-E CS
  tRNA-synt_1g  85 ..fdkygrttseehkelvqeifkklkekgliyekeieqlycpkderflpdryve 136
                     f++y+rt+see + l+q+ f  l +kg++y  +    y+   +++++d +++
    EPA04600.1 135 gdFTNYYRTDSEEYRTLTQSTFIDLWKKGQVYLANRPNNYDWVSGTTIADAEIT 188
                   6688**********************************************9986 PP

  == domain 2  score: 29.4 bits;  conditional E-value: 7.4e-11
                   ..........EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS-SSS-EET............TECCEEE-HHHH. CS
  tRNA-synt_1g 167 pksaisgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlaisrdldwGipvP............gaekkvlYVWld. 250
                   p+s  s++  e+   e++++k ++  +k+k+   +e +  +   k+i+ +wl++   d+ isr+  +G ++P             +++k+   Wl+ 
    EPA04600.1 340 PVSERSKNPIEIIPMEEYYLKQKEAIEKMKKLG-QEITFYPAMHKQILMNWLESINIDWPISRRRYYGTEIPiwyckscsephvPEPGKYYKPWLEk 435
                   6777777777888899***************99.6666799999**********999**************99999988888888999*******85 PP

                   HHHHHHHTTTTT-...TTSGGGG.G--S......EEEEEGGGHHHHHTHHHHHHHH...........TT--...........--S-EEEE--.EEE- CS
  tRNA-synt_1g 251 AligYisatkelakkkgeeekwkeyWakdkevelvhfigkdiikFHtifwPaillg...........aelk...........lpkkvvahey.ltve 324
                    +i+  s  k + +  gee++++++ ++      v    kd   F   ++P+ +                +             ++  + +y l  +
    EPA04600.1 436 CPINNCSKCKGT-EFVGEERTFDTWMDSSVSPLFVSKYNKDQEFFNK-VYPTSIRPqakdivrtwlyY--TllrceqltgkkPWSEAWVMGYgLDEK 528
                   79*****99986.5889999***999443333444455566655555.55555444355565555440..155555554553556777777767789 PP

                   -------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HHHH CS
  tRNA-synt_1g 325 gkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfswedf 371
                   g K+SkS+g+++++  ++e++ ad++R++ a+e ++  D+  +++++
    EPA04600.1 529 GMKMSKSKGNAIDPLPVIEQFGADTFRFWSASEINHGYDFRCNEQKI 575
                   9*******************************999999998887776 PP

>> tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.9   0.0    0.0036        16      11      45 ..     198     232 ..     195     239 .. 0.91
   2 !   12.1   0.0   2.3e-05       0.1      86     145 ..     240     299 ..     233     337 .. 0.79
   3 ?   -2.8   0.5      0.86   3.8e+03      52      70 ..     721     739 ..     702     751 .. 0.42

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0036
  tRNA-synt_1_2  11 eiefkveeseeklevfttrpdtlfGvtfvalapeh 45 
                     ++f+++++++++ +  trp+ l   + + + pe 
     EPA04600.1 198 YMKFQIKDTDKEIIIASTRPELLCACKTIIVNPED 232
                    689***********************999999986 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 2.3e-05
  tRNA-synt_1_2  86 glkaihPitgekipiwvanyvlmeygtgavmavPahdqrDfeFakkynlpikqvikpede 145
                    g k+i Pit+ ++++ +      e+g+gavm +   dq+D +  ++ +l+ +  i  +++
     EPA04600.1 240 GKKVIVPITNVEVELRTHHSARQEFGSGAVMVCSYGDQNDVALFRELELKEIVAIGLDGK 299
                    78999************************************9999988877777765443 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 0.86
  tRNA-synt_1_2  52 aekkkelaafieevkkkse 70 
                    ++ +ke+++f ++v ++++
     EPA04600.1 721 NKITKEITEFNSKVWNEKK 739
                    2222233333333332222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (773 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1024  (0.0571142); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.82u 0.35s 00:00:01.17 Elapsed: 00:00:00.57
# Mc/sec: 4049.96
//
Query:       EPA04601.1  [L=121]
Description: hypothetical protein BG20_I1377 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.1   12.8   0.0       0.17   12.1   0.0    1.4  1  PAS_7     PAS fold


Domain annotation for each model (and alignments):
>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   9.3e-06      0.17      45     113 ..      12      81 ..       4      83 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.3e-06
       PAS_7  45 lrynaergefgagdveaeverrlaaaragkphsfererpdgrvievrgnplpdgGfVtty...tDiTerrra 113
                 +ry+ ++g++ + ++e +v+++l+ + ++ +++ + + ++g+vi v  ++   +G++ +    +DiT+++r 
  EPA04601.1  12 FRYIDKKGNLLKTRTELTVAQMLSFLDQEYQYNHKITLKNGKVITVDFKTE--KGLIEVIdndDDITKYKRI 81 
                 58999999999999*******************************998764..4444433112578888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       902  (0.0503096); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.34s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 706.43
//
Query:       EPA04602.1  [L=251]
Description: asparagine synthase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-26   94.4   0.0    1.6e-20   74.1   0.0    2.0  2  Asn_synthase  Asparagine synthase
    1.8e-06   27.3   0.4    5.4e-06   25.7   0.1    1.9  2  NAD_synthase  NAD synthase
    0.00038   20.0   0.1    0.00092   18.8   0.1    1.7  1  QueC          Queuosine biosynthesis protein QueC
      0.009   15.5   0.2      0.021   14.2   0.0    1.7  2  RE_CfrBI      CfrBI restriction endonuclease
  ------ inclusion threshold ------
      0.051   13.4   0.1       0.25   11.1   0.0    2.1  2  PI31_Prot_N   PI31 proteasome regulator N-terminal


Domain annotation for each model (and alignments):
>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.1   0.0   4.6e-24   1.6e-20      11     162 ..      17     156 ..       7     179 .. 0.85
   2 !   18.6   0.0   3.3e-07    0.0012     239     295 ..     184     244 ..     168     250 .. 0.87

  Alignments for each domain:
  == domain 1  score: 74.1 bits;  conditional E-value: 4.6e-24
  Asn_synthase  11 krrlradvpvGalLSGGlDSSliaalaarqsksplktFsigfeekgsdeakyakevaehlgtehtelvlteeelldalpdviyhlee..pfadrsai 105
                      ++ + ++G+ +SGG+DS+l++ + + +s  +++  +igf  ++s ++ +akev + l+ +h+ l++++e + ++  +v + + +    +++  i
    EPA04602.1  17 S-ETVKEKKIGIAFSGGVDSTLVSTICSVMSY-DITLLTIGF--AESHDILFAKEVNAFLKYPHHILEIDPETFPQISSKVNQTINTenLSWNENCI 109
                   4.5678899********************996.*********..*********************************99999999999899****** PP

  Asn_synthase 106 plyllsrlakrkgvkvvLsGeGaDElfgGYpyfykaalsrsrefeklplarslrasl 162
                   + y++s+la++ ++  v + +G DElf+GY+  y++a s           +s+ ++ 
    EPA04602.1 110 AFYYVSKLANSLNLDTVVTANGIDELFCGYN-AYREAFSGG---------ESQITKV 156
                   *******************************.999886543.........3333344 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 3.3e-07
  Asn_synthase 239 vPflDhrlvevalrlppelklrg...gieKyiLRealegy.lPeeileRpKegfsapvgew 295
                    P+l  +++e+a ++p ++k+ +      K+i R+++  + +Pe  ++++K++ +++++ +
    EPA04602.1 184 QPLLSSQFIEYAKTIPLSEKIHDsedLYRKHIIRKLASTVgVPEISYTKRKKALQYGSKIH 244
                   69*********************998999**********9999999999999999876655 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.1   1.5e-09   5.4e-06       2     137 ..       5     139 ..       4     181 .. 0.80
   2 ?   -0.7   0.0      0.18   6.4e+02     156     176 ..     213     233 ..     203     239 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.5e-09
                   HHHHHHHHHHHHHHCTT.SEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE---HHHHHHHHHHHHHHH- CS
  NAD_synthase   2 ieelvdflkeyvkkaga.kgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievktidikpivrafeqelkeake 97 
                   +e+l + +k+ ++++   k++ +  SGGvDS+lv++++  +  +   l+      +++ +d+  a+++   l+   + ++i+p  ++f q  ++ ++
    EPA04602.1   5 YEKLLENIKNSISETVKeKKIGIAFSGGVDSTLVSTICSVMSYDITLLT----IGFAESHDILFAKEVNAFLKYPHHILEIDP--ETFPQISSKVNQ 95 
                   567777888888877664788899**************86653333333....367999***********************9..567777777778 PP

                   HHHHHHHHHHHHHHHHHHHHHHHTEEEB--....-BHHHHTTT- CS
  NAD_synthase  98 dlakgNlkaRiRmailyaianklnllvlgT....gnksElvvGy 137
                    ++++Nl   +  ++ y++++  n+l l T    +   El  Gy
    EPA04602.1  96 TINTENLSWNENCIAFYYVSKLANSLNLDTvvtaNGIDELFCGY 139
                   89****************99999988555411103345777777 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.18
                   HHHHHHHHHHTT--HHHHCS- CS
  NAD_synthase 156 KtevkeLakelnvPervlkkp 176
                   K  +++La +++vPe  ++k 
    EPA04602.1 213 KHIIRKLASTVGVPEISYTKR 233
                   566799********9988886 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   2.6e-07   0.00092       5      96 ..      28     116 ..      24     205 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.6e-07
                 E--SSHHHHHHHHHHHHH-SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-GGGGGGSCGGG-----------...--------TT CS
        QueC   5 llSGGlDSttvlalakkegkevealtfdYgqrhkkeleaakkiakelgveehkildldllkelggsaLtdeeievpkeeleeeelpntfVpa 96 
                  +SGG+DSt v ++ +   + +++lt+ + + h  ++  ak++ + l+   h+il++d  +  + s+ ++++i+ ++ + +e+ +   +V  
  EPA04602.1  28 AFSGGVDSTLVSTICSVMSYDITLLTIGFAESH--DILFAKEVNAFLKY-PHHILEIDPETFPQISSKVNQTINTENLSWNENCIAFYYVSK 116
                 69*************************998766..57889********9.*******94444456777888777777777777777777764 PP

>> RE_CfrBI  CfrBI restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   5.9e-06     0.021     176     241 ..       8      73 ..       3      76 .. 0.90
   2 ?   -2.9   0.1         1   3.6e+03      35      38 ..     166     169 ..     137     206 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.9e-06
    RE_CfrBI 176 llgvpeeknilsdlkrdkelvkeRevDakvletkreairvelkLlgsGnpevadviyardvklfie 241
                 ll+  ++    +  +++ ++     vD  ++ t    +  ++ Ll++G  e+ d ++a++v+ f++
  EPA04602.1   8 LLENIKNSISETVKEKKIGIAFSGGVDSTLVSTICSVMSYDITLLTIGFAESHDILFAKEVNAFLK 73 
                 555667778888889999*********************************************985 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1
    RE_CfrBI  35 llls 38 
                 ++++
  EPA04602.1 166 KMMK 169
                 2222 PP

>> PI31_Prot_N  PI31 proteasome regulator N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0     7e-05      0.25     120     159 ..     107     189 ..      77     193 .. 0.68
   2 ?   -0.4   0.0      0.25     9e+02     139     158 ..     202     221 ..     196     223 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 7e-05
  PI31_Prot_N 120 t.........................................g.edrsd.laeklkdvfiseerladLisllkvsivqklvpg 159
                  +                                         g ++ ++  ++kl +  +++++++ ++s++kv+ivq+l+++
   EPA04602.1 107 NciafyyvsklanslnldtvvtangidelfcgynayreafsgGeSQITKvMDAKLDNELKMMKAVNLVASEFKVKIVQPLLSS 189
                  45555555555555555566666666666666667777777634555556789999************************986 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.25
  PI31_Prot_N 139 erladLisllkvsivqklvp 158
                  e+++d  +l++++i+ kl++
   EPA04602.1 202 EKIHDSEDLYRKHIIRKLAS 221
                  678888999********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       793  (0.04423); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.51
# Mc/sec: 1474.16
//
Query:       EPA04603.1  [L=250]
Description: hypothetical protein BG20_I1373, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      0.001   18.9   1.9     0.0018   18.2   1.9    1.4  1  Apolipoprotein   Apolipoprotein A1/A4/E domain
  ------ inclusion threshold ------
      0.025   14.7   6.1      0.042   14.0   6.1    1.3  1  LicD             LicD family
      0.046   14.1   8.7      0.074   13.4   8.7    1.3  1  OmpH             Outer membrane protein (OmpH-like)
       0.49   10.5   3.7        5.3    7.1   0.0    2.3  2  Cytidylate_kin2  Cytidylate kinase-like family
        5.8    5.4  13.4        7.8    5.0  12.6    1.7  1  FapA             Flagellar Assembly Protein A
        8.4    5.5   6.9         11    5.1   6.9    1.2  1  TMPIT            TMPIT-like protein


Domain annotation for each model (and alignments):
>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   1.9     6e-07    0.0018      53     125 ..       3      84 ..       1     117 [. 0.81

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 6e-07
                     CCCCHHHHHHCCCHHHHHHHHHCCHHHHHHHH.........HHHHCHHCCHHCHCCHCHHHHHHHHHHHHHHHHHHCHHHHH CS
  Apolipoprotein  53 lepyrdevqeqlgqnleelrqrlapyteelre.........rlaadaeelqeqlavyaeelrerlerhvealkarlapyvee 125
                     le +r++++e+  ++l e++++l+++  +l++         +l+++++ ++e+l++ +ee++ +l++++++l  r   ++++
      EPA04603.1   3 LEIHRENFEEKQLKKLNEYQEKLKEIKAKLQAkmeknifddKLSQKSKIIEEKLTKSSEEIQLKLAAKADKLDLRTRNILDS 84 
                     6778888888888889999999999999998888888888888888888888888888888888888888776666666555 PP

>> LicD  LicD family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   6.1   1.4e-05     0.042     113     218 ..      18     119 ..       3     122 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.4e-05
        LicD 113 kkkekeklkkklalkkslskkdkkelkkkillkkksfklkklnkkkklkkleklekkkeydlkkseyiavlksgklrnkeilpleelsplkkvkFegve 211
                  ++ +eklk+ +a+ +++++k+++ + k  ++ k ++++++++ + ++ kl  + +k   dl +++ +  +++g  +++e ++ + +s+ ++++F  v 
  EPA04603.1  18 LNEYQEKLKEIKAKLQAKMEKNIF-DDKLSQKSKIIEEKLTKSSEEIQLKLAAKADK--LDLRTRNILDSINDGD-YMGEKITSDNYSETYELVFDSVD 112
                 111122222222222333444433.44455556666666666777777777777777..9999999999999988.5********************** PP

        LicD 212 vpipnny 218
                 ++ +n+ 
  EPA04603.1 113 ASLINDN 119
                 **99986 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   8.7   2.5e-05     0.074      29     121 ..      12     114 ..       2     126 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.5e-05
                 HHHHHHHHHHHHHHHHHHHHHHHHTTTS.........-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHHTT-SEEEE. CS
        OmpH  29 kklqaeleakekelqklqeelqkkakkl.e.......keekeqelqkkeqelqqkqqqkaqelqkkqqellkpil..dkinkaikevakekgydlvlds 117
                 +k  ++l++ +++l++ +++lq+k++k+         ++  e++l k  +e+q k+++ka +l  + + +l++i   d + + i+  +  + y lv+ds
  EPA04603.1  12 EKQLKKLNEYQEKLKEIKAKLQAKMEKNiFddklsqkSKIIEEKLTKSSEEIQLKLAAKADKLDLRTRNILDSINdgDYMGEKITSDNYSETYELVFDS 110
                 44445555555555555555555555543344433324444444***********************99999988667788888888888888888884 PP

                 GGG- CS
        OmpH 118 rgav 121
                  +a 
  EPA04603.1 111 VDAS 114
                 3444 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   1.9     0.044   1.3e+02      39      95 ..       7      70 ..       2      74 .. 0.59
   2 ?    7.1   0.0    0.0018       5.3      90     123 ..     172     203 ..     104     207 .. 0.59

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.044
  Cytidylate_kin2 39 elglseeeveevde.rsrlssflskllaarvagdtl.......deklddelfeaqervirelaae 95
                     + +++e+++++++e +++l+++ +k l+a++ ++ +       ++ ++++l ++ e++  +laa+
       EPA04603.1  7 RENFEEKQLKKLNEyQEKLKEIKAK-LQAKMEKNIFddklsqkSKIIEEKLTKSSEEIQLKLAAK 70
                     4556666665555533333222222.333344444445557889999999999999999999954 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0018
  Cytidylate_kin2  90 relaaeesvVivGRgadliLkdrpnvlrvfltap 123
                      +e+  ++s Vi+ +  d+ L++  ++l++fl ++
       EPA04603.1 172 TEI--KDSLVILAFLEDNALEEVHTTLKIFLNSD 203
                      333..569***********************987 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0  12.6    0.0026       7.8     343     447 ..      12     131 ..       2     138 .. 0.54

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0026
        FapA 343 eeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletk.....eklkeeleeleeelkelkeelesk...........keeakikvnkeiyp 425
                 e++l++l+e++eklk+  +kl++ k ek++  +k++q  k++e+k     e+++ +l++  ++l+    ++ ++           ++++  ++ + +++
  EPA04603.1  12 EKQLKKLNEYQEKLKEIKAKLQA-KMEKNIFDDKLSQKSKIIEEKltkssEEIQLKLAAKADKLDLRTRNILDSindgdymgekiTSDNYSETYELVFD 109
                 46677777777777777666777.556677777777777777766433333333333333333332222222223444555555544445555556666 PP

        FapA 426 gvkikigkkkliikreysnttf 447
                 +v+ ++ +++ +i+  ++++tf
  EPA04603.1 110 SVDASLINDNSKISSLIGKMTF 131
                 6666666666666666666665 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   6.9    0.0037        11      10     115 ..      11     122 ..       2     151 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0037
       TMPIT  10 efkeleetakeykqkleels.klqskcskei..kkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlk...evesllpkk.nglylklvl 101
                 e k+l++ + ey++kl+e++ klq k+ k+i  +k +++ k ++++l+k +++++ + + ++++l+ +++++  +++    + + ++++  +   +lv 
  EPA04603.1  11 EEKQLKKLN-EYQEKLKEIKaKLQAKMEKNIfdDKLSQKSKIIEEKLTKSSEEIQLKLAAKADKLDLRTRNILDSINdgdYMGEKITSDnYSETYELVF 108
                 445666666.89999988752788999999855678899999999999999999999999999999998888888885545777777775666778899 PP

       TMPIT 102 Gnvnvsllnkqdkf 115
                  +v+ sl+n+++k+
  EPA04603.1 109 DSVDASLINDNSKI 122
                 99999999988886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2455  (0.136929); expected 358.6 (0.02)
Passed bias filter:                      763  (0.0425568); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.63u 0.26s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 1624.71
//
Query:       EPA04604.1  [L=42]
Description: hypothetical protein BG20_I1382 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      187  (0.01043); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 277.69
//
Query:       EPA04605.1  [L=482]
Description: hypothetical protein BG20_I1385 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   3.9e-166  553.3   0.1   4.5e-166  553.1   0.1    1.0  1  RtcB          tRNA-splicing ligase RtcB
  ------ inclusion threshold ------
      0.022   14.8   0.1      0.061   13.4   0.1    1.7  1  Complex1_LYR  Complex 1 protein (LYR family)


Domain annotation for each model (and alignments):
>> RtcB  tRNA-splicing ligase RtcB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  553.1   0.1  5.1e-170  4.5e-166       1     412 []      48     482 .]      48     482 .] 0.99

  Alignments for each domain:
  == domain 1  score: 553.1 bits;  conditional E-value: 5.1e-170
                 HHHHHTTSTTB-S-EEEEEEEE--SSS-EEEEEEE-...-EE-HHHC-SST.-EEEEEEEEEEHHHHGGGHHHHHHHHHHHS-------------HHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        RtcB   1 qlknvaslpgivkhvaamPDvHlGkgapiGsViatk...gviiPaaVGvDI.CGvrllktnltaeeleeklkelvkelekavpvglgskkkvklskkel 95 
                 q+knva++pgiv h++++PD H G+g+p+G+V+a++   g+i+P++VG+DI CGvrll+tnlt+++++ klkelv++l++++p+g+gsk++vkls+++l
  EPA04605.1  48 QAKNVATIPGIVGHSVVLPDGHEGYGFPVGGVAAMDaeeGMISPGGVGYDInCGVRLLRTNLTENDVRLKLKELVTDLFSSIPSGVGSKGAVKLSHSQL 146
                 89************************************************************************************************* PP

                 HHHHHHTHHHHHHTTSS-GGGGGGBGGGG--TT--GGGS-HHHHHHHGGGTT---STT-EEEEEEEEEES-HHHHHHHT--TTEEEEEEEE--HHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        RtcB  96 eevleegakwaveeglgeeedlekieeegalkeadlekvskkakerarkqlGtlGsGNHFiEvqlveeildeeaakalgleegqvvvmlHsGSRglGhq 194
                 +evl +g++wa+++g+g+++d + +ee+g++k+ad++kvs+ka++r+++qlG+lGsGNHF+Evq v ei deeaa+++g++eg++++++H+GSRg+Ghq
  EPA04605.1 147 DEVLVRGVNWAIDNGYGSSDDANVCEENGQIKNADPNKVSDKARKRGAPQLGSLGSGNHFLEVQKVSEIHDEEAANRMGIKEGTITILIHCGSRGFGHQ 245
                 *************************************************************************************************** PP

                 HHHHHHHHHHCCHHHCT---SSGGG--EETTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT.T--HHHH--EEEEEEESEEEEEEEE...T.. CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..x.. RF
        RtcB 195 iaedylkiakkalkkkgiklpdrdLaylpagseegqaYlkamqaaanyAkaNRqvitervreilekvlkkekedlelelvvdvaHNiakkEehe..d.. 289
                 +++dyl++ +++++k++i+l dr+La++p +seeg++Y kam aa n+A+ NRq+it+++r+++e+v++++++dl+++lv+dvaHNiak E+h+  +  
  EPA04605.1 246 VCSDYLRVSEQSMEKYNIHLADRELACVPNTSEEGESYRKAMFAALNFAWSNRQMITHWTRKSFERVFNQTESDLDMNLVYDVAHNIAKVEKHKveGke 344
                 *********************************************************************9999*********************95377 PP

                 EEEEEEEES-EE-.............TT--EEEE--STTS-EEEEE--HHHH..SSSEE---S-----------------TTTTTCCCT-EEEE----- CS
                 xxxxxxxxxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        RtcB 290 ekvlVhRKGAtrA.............kvgqpviipGsmgtkSyivkGkgnae..sfgStsHGAGRlmsRakakkkfkleevkkdleeqgigvearkkeg 373
                 +k++VhRKGAtrA             + gqpv+ipGsmgt+S+i+ G+ n++  sfgSt+HGAGR+msR+ka++ ++ ++v+k+l+++gi ++a +++g
  EPA04605.1 345 RKLVVHRKGATRAfpsnreevplkyrDLGQPVLIPGSMGTSSWILLGQPNSMdlSFGSTAHGAGRTMSRSKARRDYTEDNVRKSLSDKGIFIKALTRDG 443
                 9************************************************************************************************** PP

                 -------------HHHHHHHHCTS-EEEEEEEEEEEEE- CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        RtcB 374 vleEapeaYKdideVveaqaeaglvevvarlkpvlvvkg 412
                 v+eE+p+aYKd+d+Vv++ ++ g++++va+l p++v+kg
  EPA04605.1 444 VVEETPQAYKDVDAVVNVSHNLGIATKVAKLVPIGVIKG 482
                 **************************************8 PP

>> Complex1_LYR  Complex 1 protein (LYR family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   6.8e-06     0.061       7      42 ..     283     319 ..     283     325 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.8e-06
  Complex1_LYR   7 YRalLRearkfpdyntreyfrrriRdeFrk..nkhvtD 42 
                   YR+ + +a  f + n r+ + +++R++F++  n+ ++D
    EPA04605.1 283 YRKAMFAALNFAWSN-RQMITHWTRKSFERvfNQTESD 319
                   9**************.**************66655655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (482 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 3317.76
//
Query:       EPA04606.1  [L=201]
Description: imidazole glycerol phosphate synthase, glutamine amidotransferase subunit [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.6e-25   88.0   0.0    7.4e-25   87.8   0.0    1.0  1  GATase         Glutamine amidotransferase class-I
    2.6e-05   24.1   0.1     0.0014   18.4   0.1    2.7  1  Peptidase_C26  Peptidase C26
    0.00013   21.9   0.0     0.0011   18.8   0.0    1.9  1  SNO            SNO glutamine amidotransferase family
     0.0011   18.6   0.0     0.0016   18.1   0.0    1.5  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.8   0.0   1.6e-28   7.4e-25       2     187 ..       6     196 ..       5     199 .. 0.85

  Alignments for each domain:
  == domain 1  score: 87.8 bits;  conditional E-value: 1.6e-28
                 EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT.....TTTHHHHHHHHCTSTS-EEEETHHHHHHHHHTTT..... CS
      GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg.....vegkieaikearenkiPiLGICLGmQllaiefgr..... 90 
                 + D++++++ +l+++l + g++v+v+  d ++ +i          l+ +G+g+       + ++ ++ +++ + ++P+LGICLGm + ++ + +     
  EPA04606.1   6 IFDYGAGNIFSLKNSLEKSGATVDVIT-DFDKPNI-------YSGLLLPGVGNFDpaiqsIAKSKTNFHNYVKDNTPVLGICLGMEMFFERSEEgkekg 96 
                 689*********************998.6555555.......45566688999888899955666666666666******************9988998 PP

                 ......EEE....EEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEEEEEEETTTEEEESSBTTSTTSTTH CS
      GATase  91 ......kvv....kekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeelmeiiekknpfvgvQFHPEststpeg 179
                       +v+    ++k  +h+g++    +++ ++l+g k+   +++ H+y v+p     ++ ++ta+s+ + ++ +++ek n f+g+QFHPE++ + + 
  EPA04606.1  97 lgiiegDVIilppSMK-VPHMGWNNLEIKKPGKILEGIKDNTWVYFVHSYRVKP----VDNSVITAESDYGIKVPAVVEKGN-FFGTQFHPEKSGKVG- 188
                 88777766699*7777.******999999899*********************9....6667899****************9.**********99988. PP

                 HHHHHHHH CS
      GATase 180 pellfnfl 187
                 + +++nfl
  EPA04606.1 189 KIMIQNFL 196
                 66666665 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   3.1e-07    0.0014      99     216 .]      66     182 ..      37     182 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 3.1e-07
  Peptidase_C26  99 raalergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhrehe.......q...saashavkvekgsllaellgseeievnslHhqaikelaee 184
                    ++ ++ ++P+lgiC+G++++            e +++     e +                +++++k + + e ++ +++ v  +H+  +k ++++
     EPA04606.1  66 HNYVKDNTPVLGICLGMEMFFERS-------EEGKEKGLGIIEGDviilppsMkvpHMGWNNLEIKKPGKILEGIK-DNTWVYFVHSYRVKPVDNS 153
                    567899************993322.......222222333333332323222234466678999997666666666.699***********99986 PP

  Peptidase_C26 185 lrveAvaeDgviEaieseeakafvlgvQwHPE 216
                    + ++A ++ g+     + e k  ++g Q+HPE
     EPA04606.1 154 V-ITAESDYGI-KVPAVVE-KGNFFGTQFHPE 182
                    4.666666554.4444444.4579*******9 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   2.5e-07    0.0011       9     184 ..      15     197 ..      10     201 .] 0.70

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.5e-07
                 HHHHHHHHHTTSEEEEE-SGGGGCC-SEEEE-S.S-.HHHHHHHHHHTT-HHHHHHHHHTT.--EEEETHHHHHHCCEETTBSS-SS--CCEEEETTTT CS
         SNO   9 eehveaikkclaenktvkrkedlaevdaliiPG.Ge.stamskliertglyedllefvknsekvvlGtCaGlillskelenelvktlellkvkvkrnaf 105
                     + ++k++a   ++ + ++ +   +l++PG G+   a++ +++      +++++vk++  +vlG C G+ ++ ++ e+ + k l++++ +v     
  EPA04606.1  15 FSLKNSLEKSGATVDVITDFDKPNIYSGLLLPGvGNfDPAIQSIAKSKT---NFHNYVKDN-TPVLGICLGMEMFFERSEEGKEKGLGIIEGDVIILPP 109
                 556678899999999999999999999*****94432469999998776...788899887.9*********99999999999999***9877765555 PP

                 -SCCGEE.EEEEEETTTC.......SEEEEEESS--EEEEE-.TTTCEEEEECT.T.EEEEEE.ETTEEEESS-GGGSTTHCHH.HHHHHH CS
         SNO 106 Grqvdsf.ekeldfknli.......ekftavfiraPvieeilddeavkvlyeld.g.eivvak.qkkilatsfhPelaeddirv.hdyfve 184
                   +v  +  ++l++k+ +       ++    f+ +  ++ +    + ++  e d g ++ ++  ++++++t fhPe + +  ++  + f++
  EPA04606.1 110 SMKVPHMgWNNLEIKKPGkilegikDNTWVYFVHSYRVKPVD---NSVITAESDyGiKVPAVVeKGNFFGTQFHPEKSGKVGKImIQNFLD 197
                 555544313455655543333333377777777777776664...666666666677887766467**********987644431455555 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   3.5e-07    0.0016      14     107 ..      10     102 ..       3     181 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.5e-07
    GATase_3  14 t..dldpLeaepevrvrfvplkdeslg..edadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmLGeeiedpegvegeageveg 107
                 +  ++  L++  e+ +  v+   ++++  + +  ++lpG  +   ++++ ++   + + ++++++++pvlgiC G+ m+ e+ e+  g+e+  g +eg
  EPA04606.1  10 GagNIFSLKNSLEKSGATVD-VITDFDkpNIYSGLLLPGVGNFDPAIQSIAK--SKTNFHNYVKDNTPVLGICLGMEMFFERSEE--GKEKGLGIIEG 102
                 35577777777777777776.3333332355788999999988777777766..7889*********************999654..55544444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1430.25
//
Query:       EPA04607.1  [L=113]
Description: putative imidazoleglycerol-phosphate dehydratase, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.8e-27   94.5   0.0    7.7e-27   94.4   0.0    1.0  1  IGPD          Imidazoleglycerol-phosphate dehydratase
  ------ inclusion threshold ------
      0.023   13.8   0.0      0.027   13.6   0.0    1.1  1  ANF_receptor  Receptor family ligand binding region


Domain annotation for each model (and alignments):
>> IGPD  Imidazoleglycerol-phosphate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.4   0.0   8.6e-31   7.7e-27      52     143 ..       1      92 [.       1      93 [. 0.98

  Alignments for each domain:
  == domain 1  score: 94.4 bits;  conditional E-value: 8.6e-31
                 S..-SSB--EEEEEEEETTEEEEEEEE--SS-EEE--..-SB--TT.--HHHHHHHHHHHHHHHT-EEEEEEEE--BHHHHHHHHHHHHHHH CS
        IGPD  52 lgdkrgikRfgsallpmDealaevaldlsgrpylvleaelkrekigeldtelveeffeslaeaagitlhvkvlrgenahhivealfKafara 143
                 lg+++gi+Rf  a +pmDe+lae+++dl +rp+++l  ++kr++i +++ e +e+ff+sl ++ + ++h++v++g+n+hh+vea++K++a a
  EPA04607.1   1 LGTRSGITRFSYASVPMDESLAEASIDLVKRPFWKLVLSIKRNTIEDISKEDLEHFFQSLLQNLNSCVHLTVKYGDNDHHKVEAAIKSLAVA 92 
                 7899*******************************999****************************************************98 PP

>> ANF_receptor  Receptor family ligand binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0     3e-06     0.027      97     170 ..      12      86 ..       4     101 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3e-06
                   EESS--CHHHHHHHHHHHHHTT--EEEEEEESS..HHHHHHHHHHHH.HHHHTT-EEEEEEEESTCHHHCHHHHHHH CS
  ANF_receptor  97 lrtvpsdtsqaqAivdilkhfgWkkvaliysdd..dygesglqalee.eleergicvalkekipessnddevvrkll 170
                      vp d+s+a+A +d++k+  Wk v  i  +   d  ++ l+ + +  l++ + cv l  k+    nd + v++  
    EPA04607.1  12 YASVPMDESLAEASIDLVKRPFWKLVLSIKRNTieDISKEDLEHFFQsLLQNLNSCVHLTVKYG--DNDHHKVEAAI 86 
                   6789****************************9986666655555555999999*********9..34445555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 796.61
//
Query:       EPA04608.1  [L=129]
Description: Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-38  132.6   0.1    1.6e-38  132.5   0.1    1.0  1  His_biosynth     Histidine biosynthesis protein
  ------ inclusion threshold ------
      0.096   11.8   0.0        0.1   11.8   0.0    1.1  1  Mitovir_RNA_pol  Mitovirus RNA-dependent RNA polymerase


Domain annotation for each model (and alignments):
>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.5   0.1   1.8e-42   1.6e-38       2     129 ..       3     128 ..       2     129 .] 0.98

  Alignments for each domain:
  == domain 1  score: 132.5 bits;  conditional E-value: 1.8e-42
                   EEEEEEEETTEEEEECTTCSTCEEEETTSHHHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SE CS
  His_biosynth   2 iipalDlkdGkvVrlvkGdrfqelryagdpvelakryeeegadelhvvDldaakegreanldlveeiaeevfipvqvGGGIrsledveelleagadk 98 
                   +ipa+Dl+dG+vVrl+kGd +q++ y+++pve+ak+++++gad+lh+vDlda+  +r+ nl ++++i+e+++ip+q+ GG r+ ++++++ ++ +++
    EPA04608.1   3 VIPAIDLMDGQVVRLYKGDPNQKTIYSNNPVEVAKKWQSNGADMLHLVDLDATL-SRGSNLLIIKKIVEQISIPIQIAGGLRDESTITDVSKI-CNR 97 
                   9**************************************************996.9*********************************9999.*** PP

                   EEESHHHHH-THHHHHHHHHHCGGGEEEEEE CS
  His_biosynth  99 viigtaavknpelikelaekfgsqkivvaiD 129
                   +++gt a+k++  +k+l+e+ g +kiv+++D
    EPA04608.1  98 IVLGTLAFKDKLTLKKLLEHLGPEKIVISVD 128
                   ******************************9 PP

>> Mitovir_RNA_pol  Mitovirus RNA-dependent RNA polymerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.1e-05       0.1     273     297 ..      24      48 ..      22     125 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.1e-05
  Mitovir_RNA_pol 273 sKslvSkdtyEFAKrwvknkkeisg 297
                      +K++ S++ +E AK+w +n++++  
       EPA04608.1  24 QKTIYSNNPVEVAKKWQSNGADMLH 48 
                      8******************999754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 780.31
//
Query:       EPA04609.1  [L=129]
Description: hypothetical protein BG20_I2264 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1378  (0.0768587); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 771.36
//
Query:       EPA04610.1  [L=83]
Description: hypothetical protein BG20_I2260 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.046   13.7   0.9        0.7    9.9   0.3    2.4  2  zinc_ribbon_4  zinc-ribbon domain
       0.94    9.7   7.0        9.2    6.5   2.2    2.6  2  zf-AN1         AN1-like Zinc finger


Domain annotation for each model (and alignments):
>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.023   2.1e+02       4       9 ..      10      15 ..       7      22 .. 0.73
   2 ?    9.9   0.3   7.8e-05       0.7      24      35 ..      34      45 ..      31      53 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.023
  zinc_ribbon_4  4 tCpsCk 9 
                    C sC+
     EPA04610.1 10 NCSSCN 15
                   466665 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 7.8e-05
  zinc_ribbon_4 24 vkvrCskCghvF 35
                   v ++C++C ++F
     EPA04610.1 34 VVIQCTNCEELF 45
                   667777777766 PP

>> zf-AN1  AN1-like Zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.2    0.0032        29       7      21 ..       2      16 ..       2      17 .. 0.85
   2 ?    6.5   2.2     0.001       9.2       6      30 ..      28      52 ..      25      55 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0032
      zf-AN1  7 kkkdflpfkCryCgk 21
                kk+d+l  +C++C+ 
  EPA04610.1  2 KKLDNLLLNCSSCNL 16
                6789999******95 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.001
      zf-AN1  6 CkkkdflpfkCryCgkvFClkHrlp 30
                C   ++++++C +C++ F  +H  p
  EPA04610.1 28 CDWGEHVVIQCTNCEELFSIDHKCP 52
                666677889********98888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 601.48
//
Query:       EPA04611.1  [L=42]
Description: hypothetical protein BG20_I2259, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 284.24
//
Query:       EPA04612.1  [L=66]
Description: hypothetical protein BG20_I2262 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 481.06
//
Query:       EPA04613.1  [L=180]
Description: hypothetical protein BG20_I2263 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1279.99
//
Query:       EPA04614.1  [L=50]
Description: hypothetical protein BG20_I2261 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1413  (0.0788109); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 370.39
//
Query:       EPA04615.1  [L=78]
Description: hypothetical protein BG20_I1968 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.024   15.1   2.8      0.024   15.1   2.8    1.8  2  Cep57_MT_bd   Centrosome microtubule-binding domain of Cep57
      0.057   14.0   3.9      0.071   13.6   3.9    1.1  1  APG6_N        Apg6 coiled-coil region
      0.069   13.1   7.6      0.082   12.8   7.6    1.0  1  eIF3_subunit  Translation initiation factor eIF3 subunit
       0.83    8.8   4.8          1    8.6   4.8    1.0  1  TMPIT         TMPIT-like protein
        1.3    9.2   0.0        1.3    9.2   0.0    3.1  4  ELK           ELK domain


Domain annotation for each model (and alignments):
>> Cep57_MT_bd  Centrosome microtubule-binding domain of Cep57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   2.8   6.8e-06     0.024      17      70 ..       6      56 ..       5      63 .. 0.92
   2 ?    0.6   0.1      0.22   7.7e+02      15      27 ..      63      75 ..      54      78 .] 0.62

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 6.8e-06
  Cep57_MT_bd 17 lkeLedEfehlklelqelaaqynaldpslgkrkRkdLaeeleelvkrlEaKadq 70
                 l+ L++Ef+ ++++l++l +++ +++   ++ +  ++ ++++ + k++E+ + q
   EPA04615.1  6 LNDLKKEFKGYSADLKRLKKKLLKSN---SSDEQSSIIKKIDTIAKEMEKNQRQ 56
                 6789**********************...9*******************98777 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.22
  Cep57_MT_bd 15 evlkeLedEfehl 27
                 + lke +++++h 
   EPA04615.1 63 SRLKEKQNQIRHF 75
                 4556666666665 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   3.9     2e-05     0.071      18      78 ..       6      65 ..       3      75 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2e-05
      APG6_N 18 leqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekere 78
                l++++ke + Y++ lk+lkk+  +++ + +e  ++ ++++++ ke e+ +++  ++ k r 
  EPA04615.1  6 LNDLKKEFKGYSADLKRLKKKLLKSN-SSDEQSSIIKKIDTIAKEMEKNQRQSVKVTKSRL 65
                7899*****************88877.688889999****999999998888777766654 PP

>> eIF3_subunit  Translation initiation factor eIF3 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   7.6   2.3e-05     0.082     157     220 ..       6      69 ..       4      76 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.3e-05
  eIF3_subunit 157 ltklekksphYssfleelirdlakslssedikkvassltvlaneKqkeeKaaekggKkkkkaka 220
                   l+ l+k+ + Ys+ l+ l ++l+ks ss++   ++++++++a+e +k ++++ k +K   k+k+
    EPA04615.1   6 LNDLKKEFKGYSADLKRLKKKLLKSNSSDEQSSIIKKIDTIAKEMEKNQRQSVKVTKSRLKEKQ 69 
                   6677777789*****************************************9777666655443 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   4.8   0.00028         1       6      67 ..       8      71 ..       4      77 .. 0.39

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00028
       TMPIT  6 elekefkeleetakeykqklee..lsklqskcskeikkqkkrlkelksslkklkksvkeeeeee 67
                +l+kefk  ++  k++k+kl +   s  qs++ k+i++  k++++ +++  k++ks  +e++++
  EPA04615.1  8 DLKKEFKGYSADLKRLKKKLLKsnSSDEQSSIIKKIDTIAKEMEKNQRQSVKVTKSRLKEKQNQ 71
                4444444444444444444422002333444444444444444444433333333322233332 PP

>> ELK  ELK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00035       1.3      13      21 ..       5      13 ..       5      13 .. 0.98
   2 ?   -3.2   0.2       2.8     1e+04       8      11 ..      14      17 ..      14      18 .. 0.72
   3 ?   -1.1   3.8      0.61   2.2e+03       1       8 [.      22      29 ..      22      29 .. 0.88
   4 ?   -1.2   0.2      0.65   2.3e+03       3       9 ..      62      68 ..      61      68 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00035
         ELK 13 yLssLRkEF 21
                yL++L+kEF
  EPA04615.1  5 YLNDLKKEF 13
                9*******9 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.8
         ELK  8 rKYs 11
                ++Ys
  EPA04615.1 14 KGYS 17
                5898 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.61
         ELK  1 ELKeqLLr 8 
                +LK++LL+
  EPA04615.1 22 RLKKKLLK 29
                79****97 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 0.65
         ELK  3 KeqLLrK 9 
                K +L+ K
  EPA04615.1 62 KSRLKEK 68
                6777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3543  (0.197613); expected 358.6 (0.02)
Passed bias filter:                      960  (0.0535445); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 583.86
//
Query:       EPA04616.1  [L=314]
Description: alcohol dehydrogenase, iron-dependent [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.4e-49  168.1   0.0    5.5e-49  166.9   0.0    1.6  1  Fe-ADH        Iron-containing alcohol dehydrogenase
    1.4e-17   64.3   0.0      2e-17   63.8   0.0    1.2  1  Fe-ADH_2      Iron-containing alcohol dehydrogenase
     0.0014   17.8   0.0       0.27   10.4   0.0    2.3  2  DHQ_synthase  3-dehydroquinate synthase


Domain annotation for each model (and alignments):
>> Fe-ADH  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.9   0.0   9.2e-53   5.5e-49       1     310 [.       7     281 ..       7     302 .. 0.88

  Alignments for each domain:
  == domain 1  score: 166.9 bits;  conditional E-value: 9.2e-53
                 -SEEEEETTGGGGHHHHHTTT-..EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEE.E.EEE-S---HHHHHHHHTTS-TT.--EEEEEESHHHHHHHH CS
      Fe-ADH   1 Ptrivfgkgaleelgellkklgakralivtdkgslkksglldkvlesleeagievt.vfdgvepnptleeveeaaalareegadvviavGGGsviDtAK 98 
                 P+ i fgk+al e+++       k+al+vt+       +l dk l ++   gi+   ++d+v+p+p++e+v++++++++++++ v+i++GGGs++D+ K
  EPA04616.1   7 PKIINFGKNALGETEY-----P-KNALVVTTVPP----ELSDKWLGKM---GIKDYmLYDQVKPEPSIEDVNKVISQFKDKNPSVLIGLGGGSSMDVVK 92 
                 5667777777755443.....3.68999998773....5899999999...766555****************************************** PP

                 HHHHHTT..................--EEEEESS-S-S-TT-SEEEEE.-TTSEEEEE-..SS--SEEEEEHHHHHHS-HHHHHHHHHHHHHHHHHHHH CS
      Fe-ADH  99 aialllanpevedylgegkakkkkalpliaiPTtaGtGsevtplavitdeeegeklsifdpellPdlaivDpeltltlPkrvtaatglDalahalEayv 197
                 ++a  ++                   + i iPTt GtG+e+t ++v+    +g+k+ ++++++l+d+a+vD  ++ ++P +v+ +++ Da a+a E y 
  EPA04616.1  93 YAAPEMK------------------KEKILIPTTFGTGAEMTTYCVLK--FDGKKKLLREDRFLADMAVVDSYFMDGTPEQVIKSSVCDACAQATEGYD 171
                 *******..................468********************..4447999999*************************************** PP

                 HHT---TTSSB--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSS---HHHHHHHHHHC.CGGGGGS-HHHHHHHHH..........HHHH CS
      Fe-ADH 198 skkanplsdalaleairliaknleravadgedleareqmllastlaglafsnaglgavHalahalgalfgiphglanaillpavlrfnaeaaperlaql 296
                 sk  n+++++++++a++++++++ +  +++      e+  ++s+l+g++f+n+++++ Hal++ ++   giphg++++ +   + + n++  ++r+++ 
  EPA04616.1 172 SKLGNDFTRTMCKQAFEILYDAIMN--NKP------ENYPYGSMLSGIGFGNCSTTLGHALSYVFSN-EGIPHGYSLSSCTTVAHKHNKSIFYDRFKEA 261
                 *********************9977..556......7888***************************.9****************99997779999999 PP

                 HHT.............T--H CS
      Fe-ADH 297 aralgge......sdeeaae 310
                   +lg +      + +eaa+
  EPA04616.1 262 MAKLGFDrltlkaDVSEAAD 281
                 99998887744433333333 PP

>> Fe-ADH_2  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.8   0.0   3.3e-21     2e-17      49     193 ..      49     194 ..      29     236 .. 0.91

  Alignments for each domain:
  == domain 1  score: 63.8 bits;  conditional E-value: 3.3e-21
    Fe-ADH_2  49 vevveeveeeadleeveklvealreketdlvvavGgGtiiDiakyvsaklnvpyvsvpTaaSvDGfaspgaslvvdgkkrtv.akaaaPlaviaDldvl 146
                  +++++v++e+++e+v+k++++++ k+  +++++GgG+ +D++ky++ + +++ + +pT+        +++ l+ dgkk+ +  +  ++   ++D  ++
  EPA04616.1  49 YMLYDQVKPEPSIEDVNKVISQFKDKNPSVLIGLGGGSSMDVVKYAAPEMKKEKILIPTTFGTGAEMTTYCVLKFDGKKKLLrEDRFLADMAVVDSYFM 147
                 4688999**********************************************************************99999777777777899***** PP

    Fe-ADH_2 147 aeAPrrllasGvGDllgkytaladwklanevseplaklsaamvqeaa 193
                    P++ + s v D+ ++ t  +d+kl+n++++ ++k++++++ +a+
  EPA04616.1 148 DGTPEQVIKSSVCDACAQATEGYDSKLGNDFTRTMCKQAFEILYDAI 194
                 ****************************************9986654 PP

>> DHQ_synthase  3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   4.5e-05      0.27      10      65 ..      55     108 ..      51     111 .. 0.81
   2 !    5.3   0.0    0.0016       9.4     183     239 ..     218     268 ..     146     289 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 4.5e-05
                   GCCHHHHHHHHHHHHHTT--TT-EEEEEESHHHHHHHHHHHHHBTT--EEEEEE-S CS
  DHQ_synthase  10 sKsletlekildalleakleRksllialGGGvvgDlaGfvAatylRGvrfvqvPtt 65 
                   +K   ++e++ +++ + k +  s+li lGGG  +D++ ++A  +++  + + +Ptt
    EPA04616.1  55 VKPEPSIEDVNKVISQFKDKNPSVLIGLGGGSSMDVVKYAAPEMKK--EKILIPTT 108
                   6666678888899999999999******************987765..55566665 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0016
                   HHHHHHHHHHHTTTTS-HHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHTT-- CS
  DHQ_synthase 183 HtigHaiEallgyekllHGeaVaiGmvlaaelseklgllkkeeverllkllkklglp 239
                    t+gHa+  +++ e + HG + +   ++a+++ +++       ++r ++ ++klg++
    EPA04616.1 218 TTLGHALSYVFSNEGIPHGYSLSSCTTVAHKHNKSIF------YDRFKEAMAKLGFD 268
                   599********************99999988875552......23444555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2068.38
//
Query:       EPA04617.1  [L=137]
Description: pyridoxamine 5'-phosphate oxidase family protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-22   80.6   0.0    1.2e-22   80.5   0.0    1.0  1  Pyridox_ox_2    Pyridoxamine 5'-phosphate oxidase
    6.9e-14   51.8   0.0      2e-13   50.3   0.0    1.7  1  Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
    8.1e-05   22.2   0.0       0.11   12.1   0.0    2.0  2  Pyrid_ox_like   Pyridoxamine 5'-phosphate oxidase like
      0.002   17.9   0.0     0.0023   17.6   0.0    1.1  1  FMN_bind_2      Putative FMN-binding domain


Domain annotation for each model (and alignments):
>> Pyridox_ox_2  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.5   0.0   2.6e-26   1.2e-22       3     114 ..      13     134 ..      11     137 .] 0.86

  Alignments for each domain:
  == domain 1  score: 80.5 bits;  conditional E-value: 2.6e-26
                   HHHHHHHHC-SEEEEEEEE.TTEEEEEEEEEEEETTEEEEEEETTSHCCHCCC.....T--ECEEEEEEEEEEE-SE.GG.EEE.EEEEEEEEEEEE CS
  Pyridox_ox_2   3 eeilalLdegevgrlafvd.dgepvilPvnyvvdgdslyfhgakgsrlaaalr.....gapvcvvvtevdglvlars.fn.sln.yrSVvvrGraee 90 
                   + i ++L++++vgr++  d +g+p i+P+n+v+ ++ +y+h+++++++++ +      g +v+ +++ + ++  + + ++ + + y SVv++G+a++
    EPA04617.1  13 RKIQEFLNQEHVGRISSIDdNGYPQIIPMNFVYIDNCIYMHSHTKGEKIENIHrnnkvGFEVDRELEFLPSYFEDPKdASlADTlYISVVIKGKASL 109
                   57899************995677*********************99999998875444444555555599999999999998889************ PP

                   E--HHHHHHHCCCHHHHHSTTT.GG CS
  Pyridox_ox_2  91 vtdeeekaealellvekivpgr.we 114
                   vtd+eek+ al++l+ek++p+  +e
    EPA04617.1 110 VTDKEEKTLALNGLMEKYQPEGrYE 134
                   ******************9987566 PP

>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.3   0.0   4.5e-17     2e-13       2      88 .]      12     114 ..      11     114 .. 0.96

  Alignments for each domain:
  == domain 1  score: 50.3 bits;  conditional E-value: 4.5e-17
                     HHHHHHHHHHSSEEEEEEEETTSEEEEEEEEEEEETTTTEEEEEEETTSHHHHHHHHH-EEEEEEEETT..................GSEEEEEE CS
  Putative_PNPOx   2 deelreflaeskavvlATvdedGrPnvspvllkagdgrdgivfatnadsrklrnleenprvallfldde..................lgrgvrie 78 
                     + +++efl+++++++++++d +G+P++ p+++++ d    i+++++++ +k +n+ +n++v++ ++ +                   l+++v i+
      EPA04617.1  12 TRKIQEFLNQEHVGRISSIDDNGYPQIIPMNFVYIDNC--IYMHSHTKGEKIENIHRNNKVGFEVDRELeflpsyfedpkdasladtLYISVVIK 104
                     679***********************************..*************************998899999********************* PP

                     EEEEEESCHH CS
  Putative_PNPOx  79 Gtaelvsdge 88 
                     G+a lv+d+e
      EPA04617.1 105 GKASLVTDKE 114
                     ******9986 PP

>> Pyrid_ox_like  Pyridoxamine 5'-phosphate oxidase like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   2.5e-05      0.11       3      67 ..      12      74 ..      10      81 .. 0.89
   2 !    8.4   0.0   0.00033       1.5      76     110 ..     101     135 ..      90     136 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.5e-05
  Pyrid_ox_like  3 vkklkelvkdiktamLttteadgklksrPMatqkveedgdlwfltkkdsdkvkeirkdsqvnlaf 67
                    +k++e +++ +++ +  ++++g  +  PM+   +  d++++  ++++ +k+++i+++++v + +
     EPA04617.1 12 TRKIQEFLNQEHVGRISSIDDNGYPQIIPMNFVYI--DNCIYMHSHTKGEKIENIHRNNKVGFEV 74
                   68999999999********999********99776..689********************98866 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00033
  Pyrid_ox_like  76 vsvsGtaevvedrakieelWspvvkawfpegkddp 110
                    v ++G+a++v+d++ +    + +++++ peg  +p
     EPA04617.1 101 VVIKGKASLVTDKEEKTLALNGLMEKYQPEGRYEP 135
                    4689**************************98765 PP

>> FMN_bind_2  Putative FMN-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   5.2e-07    0.0023       9     136 ..       9     129 ..       1     135 [. 0.86

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 5.2e-07
                 X--HCHHHHHHHHS-EEEEEEEETT.EEEEEEEE-EE...-TTSSEEEEEEETTSGGGGGT.TTS-EEEEEEEEEEEE-CCCSSTTS-....--EEEEE CS
  FMN_bind_2   9 eedleelrqlirenplgtLvtaies.glqashiPflldeeekgkgkLrgHlaraNpqakaleeeeevlvvfqgpdaYvsPswYtekkettkvvPTWnYa 106
                  ++++++++++++  +g + + +++  +q+  + f++       +++++H   + +++++++ +++v + +  + ++  Ps++++ k          Y 
  EPA04617.1   9 IKSTRKIQEFLNQEHVGRISSIDDNgYPQIIPMNFVY-----IDNCIYMHSHTKGEKIENIHRNNKVGFEVDRELEFL-PSYFEDPKD--ASLADTLYI 99 
                 5678899************999998678999999999.....55579**************99998888888888886.788888765..5666678** PP

                 EEEEEEEEEE---HHHHHHHHHHHHHHHS- CS
  FMN_bind_2 107 aVhvyGkakviedeeelrkqledltdqaEa 136
                 +V ++Gka++++d+ee++ +l+ l++++++
  EPA04617.1 100 SVVIKGKASLVTDKEEKTLALNGLMEKYQP 129
                 **************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 954.41
//
Query:       EPA04618.1  [L=375]
Description: MOFRL family protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-67  226.1   0.0    5.3e-67  225.7   0.0    1.2  1  DUF4147   Domain of unknown function (DUF4147)
    1.4e-18   67.1   0.9    1.4e-17   63.8   0.7    2.3  2  MOFRL     MOFRL family


Domain annotation for each model (and alignments):
>> DUF4147  Domain of unknown function (DUF4147)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  225.7   0.0   5.9e-71   5.3e-67       3     229 .]      19     251 ..      17     251 .. 0.93

  Alignments for each domain:
  == domain 1  score: 225.7 bits;  conditional E-value: 5.9e-71
                 HHHHHHHHHTTSHHHHHHTTHHH.....H--.......-SEEEEEESTTHHHHHHHHH..HHHGEEEEEEETT---..--TT-EEEEE-SSS--HHHHH CS
     DUF4147   3 raifeaaveavdpeklvkralsl.....keeeldlskkkrvvvvgaGKAaaamaaalee.ealksgvvvvkkghae..ekerievleaahplPdeesve 93 
                  +i+ea+++a+dpe+++ + +++     ++e l+++++++++ v++GKA  +m +al++   +ksg++v++kg+++  + +++++++++hp Pd+ sv+
  EPA04618.1  19 LDILEAGLRAADPENIIPKFVTAkeikiNDEVLKMEDFSNIYTVAFGKAGDSMTRALNAiIPIKSGIIVIPKGSKSkiKGKKFQIFNSGHPKPDQTSVK 117
                 689******************986555444478899**********************643466******989777556668***************** PP

                 HHHHHHHHHSS--TT-EEEEEE-TTHHHHS--B-TT--HHHHHHHHHHHHHCT--HHHHHHHHHTTBSSTTTHHHHHHTTSEEEEEEE--STT--TTTG CS
     DUF4147  94 aarkilelaeklkeddlvlvliSGGgSAllaaPaegitledkqaltkaLlasGasIqelNtVRkhlsaikGGrLaraaaparvvsLilSDVvgddldvI 192
                 aa+++ +++++ ++++l ++l+SGGgSAlla P  +itledk  +t++Ll+sGasIqe N++Rkhls+ikGG+L++ ++  + ++L++SDV gddl+ I
  EPA04618.1 118 AAKEVTKFLQNRRDGELTIFLVSGGGSALLAIPD-DITLEDKIYVTELLLKSGASIQEFNCIRKHLSKIKGGKLVENIKC-HGIALVMSDVEGDDLSSI 214
                 *********************************7.9******************************************99.999*************** PP

                 GG-TTS-----HHHHHHHHHHTT---..-HHHHHHH. CS
     DUF4147 193 ASGPtvpdsstfadalailekykleeklpesvrelLe 229
                 ASG t++d++tf dal+i++kykl++k+p ++++ Le
  EPA04618.1 215 ASGTTYKDDTTFLDALNIINKYKLKNKIPLEIMQRLE 251
                 ********************************99985 PP

>> MOFRL  MOFRL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0     0.066   5.9e+02      38      68 ..     195     225 ..     167     253 .. 0.78
   2 !   63.8   0.7   1.6e-21   1.4e-17       2      61 ..     319     375 .]     318     375 .] 0.94

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.066
                 T-TTEEEEEEETTS--SSSS--EEEEETTHH CS
       MOFRL  38 gaeevvllsagtDGiDGptdaaGaivdaetl 68 
                 + ++++l+  + +G D ++ a+G +++++t 
  EPA04618.1 195 KCHGIALVMSDVEGDDLSSIASGTTYKDDTT 225
                 5678899999999***999999999977664 PP

  == domain 2  score: 63.8 bits;  conditional E-value: 1.6e-21
                 EEEEEE--B----S-----HHHHHHHHHHH...HTTT-TTEEEEEEETTS--SSSS--EE CS
       MOFRL   2 vllsgGEttvtvkgkGkGGrnqelalalalelkelegaeevvllsagtDGiDGptdaaGa 61 
                 +l++gGEttv+v gkG GGrnqel+l+++++ ++    +++v++++gtDGiDG++  aGa
  EPA04618.1 319 CLIFGGETTVEVIGKGMGGRNQELVLRILKNSQN---LKKIVIAAIGTDGIDGNSLFAGA 375
                 89****************************5555...59********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2617.49
//
Query:       EPA04619.1  [L=367]
Description: luciferase-like monooxygenase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.3e-54  183.5   0.0    8.4e-54  183.1   0.0    1.1  1  Bac_luciferase  Luciferase-like monooxygenase


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.1   0.0   4.7e-58   8.4e-54      23     314 .]      25     336 ..      10     336 .. 0.91

  Alignments for each domain:
  == domain 1  score: 183.1 bits;  conditional E-value: 4.7e-58
  Bac_luciferase  23 rylvelaraaEelGfdavwvaehhggpgga....ldaftllaalaaaTerirlgtavtplytrhPavlAqqaatLdhlsgGRfglglgtggpave 113
                     ++++    +a++ G+d+++ ++h ++p+ +    ld++++l+a+aa+T++++lgt+vt + +rhP ++A +a tLd++s+GR++lg+g+g++++ 
      EPA04619.1  25 DQILTACMLADKTGYDSIFYMDHTNVPQWRnaivLDPWVMLSAIAAVTNNVELGTCVTDAIRRHPSNIALAAITLDRVSKGRAILGIGAGEAQNL 119
                     566666779****************9988899*************************************************************** PP

  Bac_luciferase 114 errfGvdhderyarlrEfvevlrrlwrg....eevdfeGeffsvkgalllprpgqgpiP.vyvaaaspaglelaarhadglllageppeeaaeli 203
                      + f +++++++   +E ++v++ l  g    ++v+++G++++++ga+l+ +p  +p+P  y+a+++ ++lel+++ ++g+l+ g +pe  ++++
      EPA04619.1 120 -KEFCIPFEKPVSKWEEQIQVIKTLY-GstpdNTVNYNGKYYKLEGACLQAPPIRKPHPpTYMASGGTRTLELTGKLGEGWLPIGYTPELFEDHA 212
                     .8889*********************.55786888******************9999666*********************************** PP

  Bac_luciferase 204 erlragaaeagrdpa...dirvgisltvivadteeeAraearaliagldfyaldsegagreaeaa..........eiqeeedanlwagaadavpd 285
                     ++++a   ++ r+++   +++ ++ + v+  +++ee +a++++ ++ + f+++  + +g ++               +++++  ++++aa+ +pd
      EPA04619.1 213 KQIQASMNKHNRTQQekdNFQYALDIDVYFSEDAEESWAKMKEAVKVSLFKPEVLRVHGIKEIEGfdfvkyfteySMSDQSWIVKMREAATKIPD 307
                     ************998999***********************99996666777777777777666656666655434477777788899******* PP

  Bac_luciferase 286 elvaatalvGtpeqvaerlaayaeagvde 314
                     ++ ++ ++vGtp++++  ++++ +agv++
      EPA04619.1 308 KIARSSTAVGTPDDIIPTFERFMKAGVNH 336
                     **************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.51
# Mc/sec: 2158.77
//
Query:       EPA04620.1  [L=143]
Description: hypothetical protein BG20_I1967 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.017   14.5   0.3      0.017   14.5   0.3    1.4  2  RNA_pol_Rpc34  RNA polymerase Rpc34 subunit


Domain annotation for each model (and alignments):
>> RNA_pol_Rpc34  RNA polymerase Rpc34 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.3   9.4e-07     0.017      79     141 ..       5      69 ..       2      80 .. 0.91
   2 ?   -3.1   0.3      0.21   3.8e+03     287     287 ..     124     124 ..      99     139 .. 0.47

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 9.4e-07
                    HHHHTSXHHHHHHHHHHHHHXSSX..EEHHHHHHTTGXXHHHHHHHHHHHHHTTXXEEEEXSSSS CS
  RNA_pol_Rpc34  79 kkktslsedeslVysiIeesGneG..IwsrtiksklnLhksvvkkcLksLeskkyiksvksvkap 141
                    +k +++s + +l +++ ee Gn+   Iw r++ +   ++k v+++++  L + k i++++  +++
     EPA04620.1   5 EKEEEMSRNTNLALKVLEEWGNNSrfIWFRELHRISDIEKGVLRNIINDLKKSKEIQEMHGTNNR 69 
                    78999*****************8666*********************************988776 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.21
                    T CS
  RNA_pol_Rpc34 287 r 287
                    r
     EPA04620.1 124 R 124
                    1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1350  (0.075297); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.33s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 948.14
//
Query:       EPA04621.1  [L=73]
Description: hypothetical protein BG20_I1966 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.047   13.1   1.4      0.057   12.8   1.4    1.3  1  Nop53     Nop53 (60S ribosomal biogenesis)
      0.065   13.3   2.9      0.081   12.9   2.1    1.5  1  LOH1CR12  Tumour suppressor protein
      0.071   13.4   1.4      0.086   13.1   1.4    1.1  1  FliS      Flagellar protein FliS


Domain annotation for each model (and alignments):
>> Nop53  Nop53 (60S ribosomal biogenesis)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.4   9.6e-06     0.057      11      40 ..      19      49 ..      14      72 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.6e-06
       Nop53 11 niDit.dveegLeevreeeritGgvlsekkd 40
                niDi  ++e+ Le+++e+e++tG  l+   d
  EPA04621.1 19 NIDILnNIEQTLEDQKEDEIVTGLELHHLYD 49
                9999779****************98887655 PP

>> LOH1CR12  Tumour suppressor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   2.1   1.4e-05     0.081      91     120 ..       4      33 ..       2      40 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.4e-05
    LOH1CR12  91 elsdqlsriqiiledivpllEtlnelLded 120
                 elsdq+ r+ +ile+++++l+++ + L+++
  EPA04621.1   4 ELSDQIERCLKILEENIDILNNIEQTLEDQ 33 
                 79**********************999875 PP

>> FliS  Flagellar protein FliS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.4   1.4e-05     0.086      40      97 ..       8      67 ..       2      71 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.4e-05
                THHHHHHHHHHHHHHHHHHHHTCCTTTSCHHHH..HHHHHHHHHHHHHHHHHHCT-HHHH CS
        FliS 40 diekkgeaiskaqdIiseLrasLdlekggeiak..nLaalYdyiirrlleanlkkdaekl 97
                +ie+  + ++  +dI+++ +++L+ +k+ ei+   +L++lYd+  +   +a+lk+ +++l
  EPA04621.1  8 QIERCLKILEENIDILNNIEQTLEDQKEDEIVTglELHHLYDMADEVAETAKLKRAESNL 67
                678888889999***********8888889998335789****99999999999887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1272  (0.0709465); expected 358.6 (0.02)
Passed bias filter:                      622  (0.0346924); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 506.47
//
Query:       EPA04622.1  [L=175]
Description: SNARE-like domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      3e-21   76.1   2.2    3.5e-21   75.9   1.6    1.4  1  SNARE_assoc  SNARE associated Golgi protein


Domain annotation for each model (and alignments):
>> SNARE_assoc  SNARE associated Golgi protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.9   1.6   1.9e-25   3.5e-21       1     119 [.      36     165 ..      33     166 .. 0.87

  Alignments for each domain:
  == domain 1  score: 75.9 bits;  conditional E-value: 1.9e-25
  SNARE_assoc   1 lPsevllvaaGvlf........glllgtlvtslgallGaslayllgrylgr....kalrrkllsekrvkalerlverygflallllrllpivPrdlvn 86 
                  +Pse++  +aG+ +        ++l + ++   ga+ Gas+ yl+++++gr    k+l+   ++ek++++++r++e+yg + +l++r++p++ r +v+
   EPA04622.1  36 IPSEAIFPLAGYSIlknnmnaiHVLGVGIAGGCGATTGASVIYLIAKKVGRigliKYLKYVKIKEKTLEKADRWFEKYGDKSVLVGRIIPGI-REIVS 132
                  56777776777766677666667778999999******************77777777777777777777**********************.***** PP

  SNARE_assoc  87 yvaGltrvsfkrFflatfiGsipwalvyaylGs 119
                  ++aG++++++ +F+++t+iGs +w++ ++ +G+
   EPA04622.1 133 IPAGIFNMNPIKFLIFTLIGSCIWSIALTSIGY 165
                  *******************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1291.39
//
Query:       EPA04623.1  [L=283]
Description: hypothetical protein BG20_I0962 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        2.2    8.6   9.4       0.26   11.6   1.8    2.7  3  MRP-S23   Mitochondrial ribosomal protein S23


Domain annotation for each model (and alignments):
>> MRP-S23  Mitochondrial ribosomal protein S23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.11   1.9e+03      80     106 ..      13      39 ..       8      56 .. 0.67
   2 ?    0.4   0.7     0.041   7.3e+02      39     106 ..      58     135 ..      22     156 .. 0.54
   3 ?   11.6   1.8   1.4e-05      0.26      55      82 ..     169     196 ..     152     223 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.11
     MRP-S23  80 seavdllkekkkstcqrfvekyqelkk 106
                 +e+++ l++k+    q f++k  +l k
  EPA04623.1  13 NEFIQYLNKKNDEIQQIFLSKIIDLIK 39 
                 555666666666666666666655544 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.041
     MRP-S23  39 fPPkreplyerpap.kl.edkvrei.lYeeDevrakfyk.qygkgseavdllkekkkst.........cqrfvekyqelkk 106
                 f Pkr   + +++  +l + +++++ + ++D +r  f k + ++g+  ++   +    +          qr +e ++el+ 
  EPA04623.1  58 FDPKRVNDFYQKIIkDLkDWSIQDVsISNNDDIRRIFTKfEIREGNYLISGHMSI---QyhvllyykpDQRVIEAQKELSD 135
                 5555544433333313333456666234567777777662222222222211111...11234444445555555555555 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 1.4e-05
     MRP-S23  55 edkvreilYeeDevrakfykqygkgsea 82 
                 ++k+ ei+Ye+De r+k yk+ ++++e+
  EPA04623.1 169 HQKLFEIFYENDEFREKIYKEIQNEIEV 196
                 567889**************88887664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1418  (0.0790897); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.54
# Mc/sec: 1591.68
//
Query:       EPA04624.1  [L=124]
Description: hypothetical protein BG20_I0945 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.031   14.7   0.6        9.2    6.8   0.0    2.4  2  Eno-Rase_FAD_bd  Enoyl reductase FAD binding domain
       0.11   12.6   0.1       0.15   12.2   0.1    1.2  1  7TMR-HDED        7TM-HD extracellular


Domain annotation for each model (and alignments):
>> Eno-Rase_FAD_bd  Enoyl reductase FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0     0.001       9.2      36      53 ..      28      45 ..       6      51 .. 0.79
   2 ?    6.3   0.4    0.0014        13      26      48 ..      50      71 ..      46      86 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.001
                     HHS-HHHHHHHHHHHTT- CS
  Eno-Rase_FAD_bd 36 eltDlegykeeFlklfGF 53
                     + +Dl+  k+e lk++GF
       EPA04624.1 28 NPGDLDLIKKEILKINGF 45
                     35899************9 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0014
                     HHTT-TTTHHHHS-HHHHHHHHH CS
  Eno-Rase_FAD_bd 26 wekvttenlkeltDlegykeeFl 48
                      +kvt+en + ltDl++ k+ F 
       EPA04624.1 50 INKVTNENYQ-LTDLSELKSKFE 71
                     689*****87.*******99883 PP

>> 7TMR-HDED  7TM-HD extracellular
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   1.6e-05      0.15      65     130 ..      24     116 ..       4     122 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.6e-05
   7TMR-HDED  65 a.............................tseenlselieqlkqarekyaqagael.sdeelrallelsdeeleelqqgieqilerilsqgiped 130
                 +                             t+e+++  ++++lk ++e y +       + e++++ +l ++++++l++   +ile+++++++ +d
  EPA04624.1  24 KlednpgdldlikkeilkingffhvfinkvTNENYQLTDLSELKSKFEYYLNT---YsFEKEIDTMSTLYSDDSDRLKNMRLKILESLMDKKLIDD 116
                 34445555555555666666666666666667777778888888888888442...123555557777777******************9987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1079  (0.0601818); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 844.12
//
Query:       EPA04625.1  [L=249]
Description: hypothetical protein BG20_I0941 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.036   13.8   0.0       0.07   12.9   0.0    1.4  1  DUF682    Protein of unknown function (DUF682)


Domain annotation for each model (and alignments):
>> DUF682  Protein of unknown function (DUF682)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   3.9e-06      0.07      77     104 ..     207     234 ..     193     240 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.9e-06
      DUF682  77 knhvlldalilyklykeevddtesafdi 104
                 +nh+ll+a+ + k y e +  tes f +
  EPA04625.1 207 ENHMLLQAMLFGKSYEEAFSHTESIFHM 234
                 7************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1780.73
//
Query:       EPA04626.1  [L=445]
Description: threonine synthase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.4e-47  161.7   0.0    3.1e-47  161.4   0.0    1.1  1  PALP       Pyridoxal-phosphate dependent enzyme
  ------ inclusion threshold ------
       0.35   10.6   2.0          2    8.2   0.1    2.6  3  4HPAD_g_N  4-Hydroxyphenylacetate decarboxylase subunit gamma


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.4   0.0   3.5e-51   3.1e-47      21     294 .]     116     420 ..     101     420 .. 0.92

  Alignments for each domain:
  == domain 1  score: 161.4 bits;  conditional E-value: 3.5e-51
                 CCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-EEEEEEETTS-.HHHHHHHHHTT-EEEEECCHHHHHHHHH CS
        PALP  21 gvplflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallGlkvtivvpadas.pekvallrllGaevvevggdydeavaaa 118
                 + +l+l  E+ np+gSfKd+g++ +++++k   gak +v+as+GN+ +++ + aa  G+ + +++p++   p+k+ +  ++Ga+++ev+g++d+a++  
  EPA04626.1 116 NSKLWLQPEGYNPSGSFKDNGMVTAVTHAKMV-GAKKIVCASTGNTSASAGMFAANEGIHCDVYIPSGQIaPGKLSQAYQFGAQIIEVDGNFDDALKQS 213
                 456*****************************.***********************************9978**************************9 PP

                 HHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHHTT.TTEEEEEEE-SSSHHHHHHHHHHHH....HSTT..-EEEEEEECTTCGGTTCC...S..S. CS
        PALP 119 aelaaegegaylvsqfdnptviegygtiglEileqlg.gkpdavvvpvGgGgliaGiaaglke....rrpd..vrvigvepegsdalarsl...ragrr 207
                  + a++ ++ y v++  np +ieg++ti +  le l  ++pd++v p G  g+ + ++++l+e    ++ +  +r+ ++++eg+++l + +    +g++
  EPA04626.1 214 LDDAKN-HNGYTVNSI-NPFRIEGQKTIPFRALEYLRwEAPDWIVYPGGALGNTSSCGKALMElyewGWIKkiPRIAVINSEGASTLSDLYngkFEGEE 310
                 999999.9********.9***************99999*************************9988666688*********99999999944434444 PP

                 SS..B..........................SSS.CCSTCS..CGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHH.HHHH CS
        PALP 208 vtvpvs.........................dtiadglavg..spselafelldrlvdeivtvsdeealeamrllarregivvepssaaalaal.klre 278
                 +                              +t a+++++g  ++  + +++l+ +++ + tvsd e+l++m  +   +g  +e +s+a++ ++ kl++
  EPA04626.1 311 L----RwnkgktntelitryyeyldkegirpKTKATAIQIGrpANILKGLRALEFTNGVATTVSDSEMLDGMSVVG-LNGFDCEMASGASVVGIkKLLN 404
                 4....3455589999999***********************877888889999***********************.********************** PP

                 HHCCTTCEEEEEEE-B CS
        PALP 279 agelkegdrvvviltg 294
                  + +k++d+vv iltg
  EPA04626.1 405 EEIIKKDDVVVGILTG 420
                 *******999999998 PP

>> 4HPAD_g_N  4-Hydroxyphenylacetate decarboxylase subunit gamma N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.04   3.6e+02      10      17 ..      23      30 ..      22      31 .. 0.93
   2 ?    8.2   0.1   0.00023         2       7      31 .]      72      95 ..      68      95 .. 0.91
   3 ?   -3.3   0.1       0.9   8.1e+03      24      31 .]     198     205 ..     198     205 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.04
   4HPAD_g_N 10 lalDceKG 17
                +++ ceKG
  EPA04626.1 23 INVECEKG 30
                799****9 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00023
   4HPAD_g_N  7 lnflalDceKGiCrltkeivpiDge 31
                lnf+ +D e  i+  +k +v +Dg+
  EPA04626.1 72 LNFCQIDTEN-IDECSKYLVSLDGA 95
                9******997.************95 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 0.9
   4HPAD_g_N  24 eivpiDge 31 
                 +i+ +Dg+
  EPA04626.1 198 QIIEVDGN 205
                 89****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (445 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 3177.69
//
Query:       EPA04627.1  [L=180]
Description: putative holliday junction resolvase Hjc [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00018   21.5   0.0    0.00029   20.8   0.0    1.5  1  Hjc       Archaeal holliday junction resolvase (hjc)
  ------ inclusion threshold ------
      0.044   13.2   0.2      0.063   12.7   0.2    1.2  1  R-HINP1I  R.HinP1I restriction endonuclease


Domain annotation for each model (and alignments):
>> Hjc  Archaeal holliday junction resolvase (hjc)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   3.2e-08   0.00029      15      84 ..      45     117 ..      10     127 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3.2e-08
                 -EEEEBSCSSSSSSSS-SEEEEETTE..EEEEEEEEESSSEEEEEHHHHHHHHHHHHHHTC....EEEEEEEETTT CS
         Hjc  15 favvRsagSggatkplpDviAirgdv..vlviEvKsskkeriylkkeqvekllefarkagg....elllavklqgk 84 
                 +++ R  +   a   lpDv+A++     +  iE Ks   + + + ++q+e+  ++ + + +    + +la+k+  k
  EPA04627.1  45 WKAFRLGSPSTA---LPDVLAVNTPNsiIFTIEAKSGTSTSLPVPADQIERCQKWIKTFDIyndrKVILAFKFLSK 117
                 677776555555...*******9755227789**************************965222267788887444 PP

>> R-HINP1I  R.HinP1I restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2     7e-06     0.063      41      93 ..     111     164 ..      90     177 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7e-06
    R-HINP1I  41 qvklvsnkk.gfnqidkrwlkkykelwdfskeilellkyfvgelepkienpkdk 93 
                   k++s k+ g+ + + r l+++ ++wd sk+i   +  + ge+  ki++ ++k
  EPA04627.1 111 AFKFLSKKRiGLGEYESRELREFYKVWDESKKITDCVCTYEGEIFAKIDGKREK 164
                 5688888776999************************************99988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1125.65
//
Query:       EPA04628.1  [L=79]
Description: transcriptional regulator, AsnC family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.01   15.7   0.3      0.013   15.4   0.3    1.2  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.3   7.3e-07     0.013       2      71 ..       6      71 ..       5      75 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 7.3e-07
                    EEEE-GGGTTHHHHHHHHHHT.STTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEE CS
  AsnC_trans_reg  2 lvslepghpeqleefeealae.lpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsi 71
                    l++++pg+   ++ ++e l++  + ++ + +vtG +d+ ++ +  +++++++ + + + +++++  tet+i
      EPA04628.1  6 LITVKPGK---VDGVIEILKKkRKIIKDVMVVTGRADITAILH-GSIDDINNTVID-FKKIKEIVTTETLI 71
                    799*****...********997888999**********99855.79**********.************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       802  (0.044732); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 509.94
//
Query:       EPA04629.1  [L=155]
Description: hypothetical protein BG20_I0966 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.031   14.0   0.3      0.055   13.2   0.3    1.4  1  DivIC     Septum formation initiator


Domain annotation for each model (and alignments):
>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.3   3.1e-06     0.055      18      51 ..     117     150 ..     103     154 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.1e-06
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-X CS
       DivIC  18 aykqlkqeiaalqaelaklkaeneeLeaevkdLk 51 
                  ++++++ ++ l++e++kl +en eL++++++ k
  EPA04629.1 117 PLFSQQNSVNSLKEENDKLLKENLELKKKLDNKK 150
                 5789999*********************999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1090  (0.0607954); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1132.71
//
Query:       EPA04630.1  [L=129]
Description: hypothetical protein BG20_I0958 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.34   11.4   3.2       0.13   12.8   0.7    1.6  2  DUF2085   Predicted membrane protein (DUF2085)


Domain annotation for each model (and alignments):
>> DUF2085  Predicted membrane protein (DUF2085)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1      0.36   6.4e+03      49      60 ..      11      22 ..       3      26 .. 0.59
   2 ?   12.8   0.7     7e-06      0.13      30      88 ..      52     113 ..      31     115 .. 0.64

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.36
     DUF2085 49 llvllllpmaiD 60
                + + ll++ +iD
  EPA04630.1 11 ISISLLVIYGID 22
                455566666666 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 7e-06
     DUF2085  30 llgllllllkaklsklslll.lvllllpmaiDgltqllglyestnllRlit..GllaGlala 88 
                 +l ++++++ +k +   l + l++  ++++i g +++ +  es+n  R+i   G l+G++++
  EPA04630.1  52 ILSFIAFFIAKKPPFKGLGImLIITGILIIIGGAMSMSSASESENAARMIGegGSLIGVGAI 113
                 3333333332333333333347777888999999***************9444888888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       761  (0.0424452); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 793.85
//
Query:       EPA04631.1  [L=47]
Description: hypothetical protein BG20_I0963 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.31s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 317.77
//
Query:       EPA04632.1  [L=48]
Description: hypothetical protein BG20_I0964 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       921  (0.0513693); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 315.73
//
Query:       EPA04633.1  [L=49]
Description: hypothetical protein BG20_I0954 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.066   12.1   0.1      0.068   12.1   0.1    1.0  1  NatB_MDM20       N-acetyltransferase B complex (NatB) non cat
      0.068   13.4   0.2      0.069   13.3   0.2    1.1  1  Ribonuc_red_2_N  Class II vitamin B12-dependent ribonucleotid


Domain annotation for each model (and alignments):
>> NatB_MDM20  N-acetyltransferase B complex (NatB) non catalytic subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   7.6e-06     0.068      78     114 ..       4      38 ..       2      47 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.6e-06
  NatB_MDM20  78 leYfekfgsKlccfeDLkkYleeLskeerkeflekvs 114
                 ++Y ++f +K+++ +D +kY ++  +++ ++f++++ 
  EPA04633.1   4 QSYADNFTQKSSFWDDASKYAAS--TSDDESFVSEIA 38 
                 68******************998..678888888876 PP

>> Ribonuc_red_2_N  Class II vitamin B12-dependent ribonucleotide reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   7.7e-06     0.069      64      97 ..       9      42 ..       1      44 [. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.7e-06
  Ribonuc_red_2_N 64 RlagtwtewgkkegyfdteedakafydElvymll 97
                      +++    w   ++y ++ +d + f+ E++ym++
       EPA04633.1  9 NFTQKSSFWDDASKYAASTSDDESFVSEIAYMMV 42
                     5555666788899*******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.30s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 326.67
//
Query:       EPA04634.1  [L=69]
Description: hypothetical protein BG20_I0938 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 405.84
//
Query:       EPA04635.1  [L=369]
Description: thiolase, C-terminal domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-12   47.6   1.0    2.4e-12   46.6   0.2    2.0  3  Thiolase_C       Thiolase, C-terminal domain
    1.2e-08   34.7   2.9      9e-08   31.8   0.5    2.6  2  Thiolase_N       Thiolase, N-terminal domain
    0.00011   21.9   0.1    0.00029   20.5   0.0    1.7  2  ketoacyl-synt    Beta-ketoacyl synthase, N-terminal domain
    0.00065   19.9   0.4     0.0014   18.8   0.4    1.5  1  Dodecin          Dodecin
    0.00067   19.7   0.7       0.37   10.8   0.2    2.5  2  Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
  ------ inclusion threshold ------
      0.012   15.5   0.0      0.034   14.0   0.0    1.8  1  ACP_syn_III      3-Oxoacyl-[acyl-carrier-protein (ACP)] synth


Domain annotation for each model (and alignments):
>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.5   4.6e+03      22      46 ..      23      48 ..      10      66 .. 0.65
   2 ?   -3.4   0.0       2.4   7.2e+03     102     116 ..      72      86 ..      52      88 .. 0.63
   3 !   46.6   0.2   8.1e-16   2.4e-12      25     107 ..     247     345 ..     227     368 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.5
                GHHHHHHHHHHHHH.T--GGGESEEE CS
  Thiolase_C 22 lgPayaikkvlkka.gltvedidlfE 46
                    + +kk+ +++  l+ +did++ 
  EPA04635.1 23 SVLLNSTKKLFDNTsNLNQNDIDAVL 48
                55556666776654267888888764 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.4
                 TSEEEEEEEETTTEE CS
  Thiolase_C 102 gklgvaalCigggqg 116
                    ++ +lC++g ++
  EPA04635.1  72 ISHSIESLCNSGTNA 86 
                 345678889888765 PP

  == domain 3  score: 46.6 bits;  conditional E-value: 8.1e-16
                 HHHHHHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--G................GGBSTT--HHHH-B-TTTHHHHHHHHHHHHHHHCTTSEEEE CS
  Thiolase_C  25 ayaikkvlkkagltvedidlfEinEAFaaqaLavakaldldl................ekvNvnGGaialGHPlGasGaRivvtllselkkeggklgva 107
                   a+ +++k    tv++id++E+++AF++   +++++++++                  k+N +GG i  GHPlGa+G  +++ ++++l+ + +k  + 
  EPA04635.1 247 QQAAANAIKMSKHTVKEIDVMEVHDAFSVCEPMALESIGFADkgkgldmikemhetnnLKINPRGGLIGAGHPLGATGIAQTIEITQQLQSRANKRQID 345
                 467888999*********************99999999999999************999******************************9987765554 PP

>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.5     3e-11     9e-08      19     189 ..      17     167 ..       4     193 .. 0.73
   2 ?   -3.3   0.1       1.5   4.5e+03      89     131 ..     251     255 ..     228     275 .. 0.43

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 3e-11
                 TTS-HHHHHHHHHHHHHHHHT.S-GGGCCEEEEEHSSCTTSTSCHHHHHHHHTTS-TTSEEEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEEST CS
  Thiolase_N  19 kdlsaeeLlaealkallekag.vdpeevdevivGnvlqagegqniarqaalkagipeevpavtvnkvcsSglkavalaaqsiaageadvvvagGvEsms 116
                  d ++e  l +  k+l ++++ ++++++d v v++   + + + +a  ++ +agi e+ +++ ++ +c Sg +a++ a   i +g advv++ G+E+  
  EPA04635.1  17 DDSKIESVLLNSTKKLFDNTSnLNQNDIDAVLVST---NDNSKYLAAVLSEMAGI-EPKISHSIESLCNSGTNAIVSAYSYITSGLADVVLVSGAERYD 111
                 56666677777777888777779999999998775...444556888999999**.9999************************************753 PP

                 TS-EEETCTTTTGGSSSSEEEEEHHHHHHTEETTTTSEHHHHHHHHHHHHT--HHHHHHHHHHHHHHHHHHHH CS
  Thiolase_N 117 naptaestdvrsglklgdekakdllipdgladafneehmGltaenlakkykisReeqdefAvkshqkaaaaqk 189
                         ++ +  +   e ++ +                + ++ + +++ i+ ee++   vk+h++a+++++
  EPA04635.1 112 SPG-----QILEWDNSRGEFKHPIFWA------------SIFTKSYKREFSITDEELAIIPVKNHKQAQNNPN 167
                 322.....2222333333444444433............3666666666666666666666666666666665 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.5
                 HHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTTTGGS CS
  Thiolase_N  89 lkavalaaqsiaageadvvvagGvEsmsnaptaestdvrsglk 131
                 +                                      + +k
  EPA04635.1 251 A--------------------------------------NAIK 255
                 1......................................1111 PP

>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   9.8e-08   0.00029     127     217 ..      34     122 ..       5     128 .. 0.74
   2 ?   -2.7   0.0       1.2   3.5e+03      59      84 ..     237     263 ..     204     289 .. 0.52

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 9.8e-08
                    HHHHHHHHHTTGGGSCTTHHHHHSTTHHHHHHHHHHT--S.SEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SHHHHHHHHHT CS
  ketoacyl-synt 127 aalaaldedgsevkaspkavgavlanviagrisyalglrG.psvtvdtACsSslvavhaavqslrsgeadvalaGGvellltpeavagfsaa 217
                    ++++ l++++ +  + +  ++  ++ ++a+ +s   g++   s+++++ C S+  a+  a++ + sg adv+l+ G+e   +p+++  +++ 
     EPA04635.1  34 DNTSNLNQND-IDAVLV-STND-NSKYLAAVLSEMAGIEPkISHSIESLCNSGTNAIVSAYSYITSGLADVVLVSGAERYDSPGQILEWDNS 122
                    4444555333.333344.5666.788999999999999873599*********88888888******************9999999888775 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.2
                    S.EEE..S.TTEGGTTSTHHHHHHHCT CS
  ketoacyl-synt  59 tklggfld.vddfdpeffgispreaea 84 
                    +     ++  ++  + + ++s++ +++
     EPA04635.1 237 NMTFSSMEsTQQAAANAIKMSKHTVKE 263
                    322233333444444444444444444 PP

>> Dodecin  Dodecin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.4   4.8e-07    0.0014      10      40 ..     241     271 ..     237     275 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 4.8e-07
                 EESS-HHHHHHHHHHHHHHH-SSEEEEEEEE CS
     Dodecin  10 sSpkSwedAiqnAiaeAsktlrnirwveVke 40 
                 sS +S ++A+ nAi+  + t+++i+++eV +
  EPA04635.1 241 SSMESTQQAAANAIKMSKHTVKEIDVMEVHD 271
                 89***************************86 PP

>> Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.2   0.00013      0.37       7      51 ..     227     271 ..     223     275 .. 0.92
   2 !    6.6   0.0    0.0025       7.5      88     109 ..     317     338 ..     313     345 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00013
                      EEEEE--STSSSTSTTHHHHHHHHHHHHHHHT--GGGEEEEE-SS CS
  Ketoacyl-synt_C   7 savnsdgahnsltapngeaqaraiekalaeagvdpedvdyveahg 51 
                       +++s g ++ +t  + e+ ++a ++a+++++ + +++d++e h+
       EPA04635.1 227 QKTTSAGFTKNMTFSSMESTQQAAANAIKMSKHTVKEIDVMEVHD 271
                      56788889999*********************************8 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0025
                      -B-GGGHHHHHHHHHHHHHHHT CS
  Ketoacyl-synt_C  88 GHleaAaGvaelikvvlalkhg 109
                      GH ++A G+a++i + ++l+ +
       EPA04635.1 317 GHPLGATGIAQTIEITQQLQSR 338
                      9*****************9976 PP

>> ACP_syn_III  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.2e-05     0.034       4      38 ..      77     111 ..      75     126 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.2e-05
                  E-GGGHHHHHHHHHHHHHHTTS-SEEEEEEEEEGG CS
  ACP_syn_III   4 naaCsgfvyalsvAdaliesgaakrvLvigaetls 38 
                  ++ C++ + a+  A ++i sg a  vLv gae++ 
   EPA04635.1  77 ESLCNSGTNAIVSAYSYITSGLADVVLVSGAERYD 111
                  677*****************************974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2285.56
//
Query:       EPA04636.1  [L=271]
Description: hypothetical protein BG20_I0965 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.9e-16   58.9   0.0    6.9e-16   58.4   0.0    1.1  1  Guanylate_cyc  Adenylate and Guanylate cyclase catalytic doma


Domain annotation for each model (and alignments):
>> Guanylate_cyc  Adenylate and Guanylate cyclase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.4   0.0   3.9e-20   6.9e-16       9     161 ..      82     242 ..      77     262 .. 0.85

  Alignments for each domain:
  == domain 1  score: 58.4 bits;  conditional E-value: 3.9e-20
  Guanylate_cyc   9 vtilFadIvgftalssahspie.vvklLnelyarfdelldekkvykvktiGda...ymvvsglpeekaahaaklaelaLdmleal.eevaves.ke 98 
                    + +l+ d+vg+t++  +  p++ +  ++ +  +++ ++++ +++y  k++Gda   y v+s+ p   a++a ++a+  L ++++  + + ++   +
     EPA04636.1  82 MIVLYVDLVGSTTMTLEL-PEDkLAIIISSFAQEMASVINLHGGYVLKFVGDAvigYFVASENPLLAADNAISCAKSMLTVIQKGiNPILNQYdYP 176
                    6699**************.665055566777789******************8777899999999999999999999999999986555444449* PP

  Guanylate_cyc  99 glkvrvGihtGpvvagviG..akkprydvwGntvnlAsrmestgkagkiqvseetyellk.eeqfe 161
                    +l+v++G + G+ ++   G  +   + d+ G + n+As+++s++k+++i + +++y+ l+ + q  
     EPA04636.1 177 DLMVKIGADFGQSIVVRYGsnQDSAHVDLMGPAMNIASKIQSHAKPNQILIGHDVYSKLHpSSQSM 242
                    ***********99888888778899*********************************99644443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1809.92
//
Query:       EPA04637.1  [L=49]
Description: hypothetical protein BG20_I0939 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.23s 00:00:00.55 Elapsed: 00:00:00.38
# Mc/sec: 382.26
//
Query:       EPA04638.1  [L=108]
Description: hypothetical protein BG20_I0940 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.2e-05   22.6   0.0    0.00016   21.8   0.0    1.4  1  DapB_N          Dihydrodipicolinate reductase, N-terminus
      0.004   17.8   0.0     0.0055   17.4   0.0    1.2  1  NAD_binding_3   Homoserine dehydrogenase, NAD binding domain
     0.0092   16.4   0.0      0.011   16.2   0.0    1.2  1  Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domai
  ------ inclusion threshold ------
      0.031   14.6   0.0      0.052   13.9   0.0    1.6  1  Gp_dh_N         Glyceraldehyde 3-phosphate dehydrogenase, NAD
       0.12   12.0   0.0        0.2   11.2   0.0    1.4  1  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin


Domain annotation for each model (and alignments):
>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   4.5e-08   0.00016       2      86 ..      11     102 ..      10     108 .] 0.77

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 4.5e-08
                 EEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHH........HHSSSS--S-BEBSSHHHHHHH-SEEEE-S-HHHHHHHHHH CS
      DapB_N   2 kvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdag........ellglgklgvavtddleevlekadvliDFTtpeavlenlkl 86 
                 kv v+G+ G +G+++++ +++++++ l ++ + ++ + ++  ++        e    +  ++++t ++e++l+++d +iD        +n k+
  EPA04638.1  11 KVFVNGY-GSIGSRITSFLQDDSEISLIGVGKYSPDDDVNLAISrgldvyvpERKLNDFKDFKITGTIESALDDCDLVIDAAPGGHGFKNKKI 102
                 89*****.**********************9999854444444477888775333333789*******************9854444555444 PP

>> NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.5e-06    0.0055       1      68 [.      16      92 ..      16      95 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.5e-06
                   --SHHHHHHHHHHHH---SSEEEEEEEEESSEEE-TT..............HHHHHT--CB---HHHHHHHHS-EEEEE-S- CS
  NAD_binding_3  1 GlGaiGsavleqlkrqqseielelvavadrdsllskd..............rkallasealtldlddliahldpdvvVEcas 68
                   G+G iGs++++ l+++ +   + l +v + ++  + +              +++++++ ++t  +++ ++  d d+v+++a+
     EPA04638.1 16 GYGSIGSRITSFLQDDSE---ISLIGVGKYSPDDDVNlaisrgldvyvperKLNDFKDFKITGTIESALD--DCDLVIDAAP 92
                   99**************95...88888888884445558899999999999999*****************..*******985 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0     3e-06     0.011       8      79 ..      17      96 ..      11     108 .] 0.82

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3e-06
                    TSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSG........GGTTTECEBEEEGGGGGCTT-SEEEE-SCHHHH CS
  Semialdhyde_dh  8 tGyvGqellrlLeehpevelvvllsssrsaGkklaeavk........aleegkdlkvedvdeeelkevdivflalpagvs 79
                     G +G+++   L+++ e++l+ +   s ++  +la   +        +l++ kd+k++ + e +l+++d+v+ a+p+g  
      EPA04638.1 17 YGSIGSRITSFLQDDSEISLIGVGKYSPDDDVNLAISRGldvyvperKLNDFKDFKITGTIESALDDCDLVIDAAPGGHG 96
                    6999******************9999985555554444455999999*****************************9865 PP

>> Gp_dh_N  Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.5e-05     0.052       2      35 ..      11      44 ..      10      94 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.5e-05
                EEEEESTSHHHHHHHHHHHHHTTCEEEEEE-TS- CS
     Gp_dh_N  2 kvainGfGRIGrlvlralleekelevvaindltd 35
                kv +nG+G IG  +   l +++e++++ + +   
  EPA04638.1 11 KVFVNGYGSIGSRITSFLQDDSEISLIGVGKYSP 44
                899************************9998543 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   5.5e-05       0.2       4      54 ..       9      61 ..       5      71 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.5e-05
                TS-EEEES-SHHHHHHHHHHHH.TT--.EEEEE-TT-HHHHHHHHTT-EEEEH CS
        IlvN  4 gkkiaviGyGsqGhaqalnlrd.sgld.vvvglregsksvkkAkeegfevltv 54
                 kk+ v GyGs G   +  l+d s +  + vg ++ +  v+ A ++g++v+  
  EPA04638.1  9 MKKVFVNGYGSIGSRITSFLQDdSEISlIGVGKYSPDDDVNLAISRGLDVYVP 61
                499*****************9725554144777777789*********99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       241  (0.0134419); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 705.20
//
Query:       EPA04639.1  [L=274]
Description: hypothetical protein BG20_I0950 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.036   13.4   0.0       0.16   11.2   0.0    1.8  2  CbiK      Cobalt chelatase (CbiK)


Domain annotation for each model (and alignments):
>> CbiK  Cobalt chelatase (CbiK)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0    0.0028        51      93     145 ..     166     218 ..     151     219 .. 0.71
   2 ?   11.2   0.0   9.1e-06      0.16     187     236 ..     201     248 ..     185     257 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.0028
                 HHHHHHGGGSSEEEEE--SCS......SHHHHHHHHHHHHTTS----.TTEEEE CS
        CbiK  93 reVkkfkkkfekiklgrPlldykGvedsteDykevvealkdeierar.kdealv 145
                 + V+ ++ +++++kl  P++ + G+ ++  D+    +++++  +++  k++ +v
  EPA04639.1 166 TCVDAIEFDYNSLKLKSPVFFIGGLPQMGGDILA-TNVIEKISTSNIkKNACIV 218
                 56899999**************999999999854.2333333333331555555 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 9.1e-06
                 HHHHHHHHHT--EEEEEE-SSS--HHHHCCCCSSSTT.SHHHHHHHTT--E CS
        CbiK 187 evieelkkkgikevkliPlmlvAGdHaknDmasdeed.swkealeaaGikv 236
                 +vie++  ++ik+      ++ AG H k+ + +d++d  w + +e++G+kv
  EPA04639.1 201 NVIEKISTSNIKKN---ACIVFAGTHSKRQLSGDQSDgGWSTLIEKHGLKV 248
                 67777777666665...56788**********9976528**********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1844.92
//
Query:       EPA04640.1  [L=219]
Description: phosphoribosylaminoimidazole carboxylase, catalytic subunit [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-58  196.4   0.1    2.4e-58  195.9   0.1    1.2  1  AIRC          AIR carboxylase
  ------ inclusion threshold ------
      0.014   15.0   0.3      0.092   12.3   0.0    2.3  3  PrpR_N        Propionate catabolism activator
      0.058   13.2   0.0       0.11   12.3   0.0    1.4  2  Asp_Glu_race  Asp/Glu/Hydantoin racemase


Domain annotation for each model (and alignments):
>> AIRC  AIR carboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.9   0.1     4e-62   2.4e-58       2     147 ..      37     196 ..      36     197 .. 0.95

  Alignments for each domain:
  == domain 1  score: 195.9 bits;  conditional E-value: 4e-62
                 EEEEESSGGGHHHHHHHHHHHHHTT-EEEEEE--TTTSHHHHHHHHHHCHTTTEEEEEEEEESS--HHHHHHHHSSS-EEEEEE-.............. CS
        AIRC   2 VgiimGSdsDlevmkkaaeilkelgveyevrvvSahrtpeelleyaeeaeerglkviIagAGgaahLpgvvaslttlPVigvPvk.............. 86 
                 +giimGS+sD ++m++aaeil+++++++e +++Sahrtp++l+eya++ae++g+k+iIagAGgaahLpg++as+t lPVigvP+               
  EPA04640.1  37 IGIIMGSSSDSKIMNDAAEILDKFKIKHEDQIISAHRTPSRLEEYAKHAENMGFKIIIAGAGGAAHLPGMIASHTILPVIGVPIMvyndkqskkpenmk 135
                 89**********************************************************************************988888877776554 PP

                 -STTCCHHHHHHHHT--TTS--EE-SSTHHHHHHHHHHHHHTTT-HHHHHHHHHHHHHHHH CS
        AIRC  87 skalkgldsllSivqmPsgvpvatvaigkaknAallAaqilalkdeelaekleeyreelke 147
                  +++ gldsllSi +mP+g pv++v+i+ka nA+++A++ila++ +el++kl++y+ ++++
  EPA04640.1 136 FSSFGGLDSLLSISEMPNGSPVVAVGINKAGNAGIYAMKILANEFPELKKKLKQYKLDQHD 196
                 249*****************************************************98876 PP

>> PrpR_N  Propionate catabolism activator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.15   8.9e+02      14      43 ..      50      79 ..      44      81 .. 0.82
   2 ?   12.3   0.0   1.5e-05     0.092      19      58 ..      80     123 ..      63     125 .. 0.83
   3 ?   -0.9   0.0      0.18   1.1e+03      93     120 ..     183     210 ..     170     214 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.15
      PrpR_N 14 leeavelakeleaegvdviiSrGgtaellr 43
                +++a+e++ + + ++ d iiS+  t + l+
  EPA04640.1 50 MNDAAEILDKFKIKHEDQIISAHRTPSRLE 79
                789999999998899999999988877776 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 1.5e-05
      PrpR_N  19 elakeleaegvdviiSrGgtae....llrkhvsvPVveikvsgy 58 
                 e+ak++e++g+++ii++ g a+    ++ +h+ +PV+ +++ +y
  EPA04640.1  80 EYAKHAENMGFKIIIAGAGGAAhlpgMIASHTILPVIGVPIMVY 123
                 789999*********9877776455579************9877 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.18
      PrpR_N  93 ldldieiytinseeeaeaavkelkaegv 120
                 l+ ++++y++++ +++ +  + lk++g 
  EPA04640.1 183 LKKKLKQYKLDQHDSVLKESESLKKQGL 210
                 5668899999999999999999999996 PP

>> Asp_Glu_race  Asp/Glu/Hydantoin racemase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.8e-05      0.11      49     108 ..      67     128 ..      39     140 .. 0.76
   2 ?   -3.0   0.0      0.87   5.2e+03      11      26 ..     171     186 ..     161     210 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.8e-05
                   H..T..THH.HHHHHHHHHHCTTESEEEE--CHHHHHHHHHHHH-SSEEEECHHHHHHHHHH CS
  Asp_Glu_race  49 e.sgddpvl.klleaakkLekagadaiviaCnTahavadelqkkikiPvlgiveataealka 108
                   +   +++++ +l+e ak+ e++g ++i+  +  a  +   +++++ +Pv+g++ ++ +  ++
    EPA04640.1  67 QiISAHRTPsRLEEYAKHAENMGFKIIIAGAGGAAHLPGMIASHTILPVIGVPIMVYNDKQS 128
                   23333467889***********************99999999*********99888655444 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.87
                   HHHHHHHHHBTTSSGG CS
  Asp_Glu_race  11 svlrklveatpaesdq 26 
                   + ++ l +++p+ +++
    EPA04640.1 171 YAMKILANEFPELKKK 186
                   4444444444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       693  (0.0386525); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1543.18
//
Query:       EPA04641.1  [L=221]
Description: nucleotidyl transferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-32  112.6   0.4    3.1e-32  112.1   0.4    1.2  1  NTP_transferase  Nucleotidyl transferase
    1.2e-11   45.3   0.0    1.7e-11   44.7   0.0    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
      0.001   18.9   0.0     0.0036   17.1   0.0    1.9  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
  ------ inclusion threshold ------
      0.089   12.8   2.3        1.2    9.2   0.1    2.3  2  CspB_prodomain   Csp protease B prodomain


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.1   0.4   6.9e-36   3.1e-32       1     246 [.       3     220 ..       3     221 .] 0.91

  Alignments for each domain:
  == domain 1  score: 112.1 bits;  conditional E-value: 6.9e-36
                      EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEESS--BGGHHHHHTH CS
  NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlialepegkgtAdAvalaa 94 
                      kavILaGG+G+RL+P+t  ++k+l+p  +  ++i+ +++ l ++gi+e i+++t +++++++++l+ +++fg++++i++e+ + gt +A+++a 
       EPA04641.1   3 KAVILAGGRGKRLRPITDYVPKPLIPLNNI-PIIEWQVKYLKKQGIKE-IIICTGYKAEMIKNYLEMKNNFGIKIKISVEKIPLGTGGAIKQAG 94 
                      79*************************999.*****************.********************************************* PP

                      HHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEECTTSBEEEEECS-SSHSHCSEECCSEEEEETTHHH CS
  NTP_transferase  95 elledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGvieadeegrverfvEKPkeakaselassGiYvfnsevll 188
                      + ++d++    ++vL+gD +++ +++++ kk  + a+           e +t++G++e+++ + v++f+EK +  +   ++++GiY  ++evl+
       EPA04641.1  95 LSIKDKS----FFVLNGDTITNINLKQLAKKQNAIAS----------IELKTKFGIMETQN-DIVTKFKEKKEISD--LWMNAGIYHLQNEVLK 171
                      ****999....8**********999998766555444..........8999********98.69*******88888..79************99 PP

                      HHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEEXSSHHHHHHHHHHHH CS
  NTP_transferase 189 flakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsDvGtldslleanekla 246
                       l       +++ d  + ++p + ++gk    + fk    W  + +++++ e +e+l+
       EPA04641.1 172 DL-------PKKGDIEKTVFPDYAKKGKLRT-VKFKNV-FWYSIDSFKDMEECSEELQ 220
                      98.......6677888899999999998884.566665.7999999999998888765 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7   0.0   3.8e-15   1.7e-11       1      97 [.       4     110 ..       4     129 .. 0.80

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 3.8e-15
                   EEEEEESS-TTTTT.....THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHHTTC...TS-E..EE-TTSS-SHHHHHHHHHHHH.S CS
  NTP_transf_3   1 aviLAGGrSsRmgg.....dKallplggkpllervldalraagvdevvvvggd..eevlaalarl...gvrv..vededpgkgplaslaaalraaad 85 
                   aviLAGGr++R+       +K+l+pl++ p++e++++ l+++g++e+++++g+  e ++++l+ +   g+++   +++    g++++++ a  ++ +
    EPA04641.1   4 AVILAGGRGKRLRPitdyvPKPLIPLNNIPIIEWQVKYLKKQGIKEIIICTGYkaEMIKNYLEMKnnfGIKIkiSVEK-IPLGTGGAIKQAGLSI-K 98 
                   79**********8444578********************************996567887776554445665213333.3689999999888888.8 PP

                   SSCEEEEETT-T CS
  NTP_transf_3  86 adavlvlacDmP 97 
                   ++ ++vl +D++
    EPA04641.1  99 DKSFFVLNGDTI 110
                   999999999985 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0     8e-07    0.0036       3      53 ..       4      56 ..       2     152 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 8e-07
                EEEECTTSSCTT-...SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-G CS
        IspD  3 vvipAAGsGkRmk...aglpKqflelkgqtllehtvdallaskavdkivvvvse 53
                +vi A G+GkR++     +pK ++ l++ +++e+ v+ l + + +++i++    
  EPA04641.1  4 AVILAGGRGKRLRpitDYVPKPLIPLNNIPIIEWQVKYLKK-QGIKEIIICTGY 56
                89*********86332679******************9987.889998887544 PP

>> CspB_prodomain  Csp protease B prodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.2     0.021        94      23      68 ..      36      77 ..      31      85 .. 0.76
   2 ?    9.2   0.1   0.00027       1.2      43      82 ..     113     153 ..     102     154 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.021
  CspB_prodomain 23 elsvgydeeentwelivkysgdleeleeelgieveeLlngYAi.vti 68
                    e +v+y ++++  e+i+  + + e ++     ++ e+ n+++i ++i
      EPA04641.1 36 EWQVKYLKKQGIKEIIICTGYKAEMIK-----NYLEMKNNFGIkIKI 77
                    5678999999999*****999999999.....555666666665555 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00027
  CspB_prodomain  43 gdleele.eelgieveeLlngYAivtipeskieelaalpei 82 
                      +l++l+ ++++i   eL  +++i++++++ + ++ + +ei
      EPA04641.1 113 INLKQLAkKQNAIASIELKTKFGIMETQNDIVTKFKEKKEI 153
                     456666689999*************************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       695  (0.038764); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1461.38
//
Query:       EPA04642.1  [L=128]
Description: hypothetical protein BG20_I0968 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       753  (0.041999); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 892.19
//
Query:       EPA04643.1  [L=40]
Description: hypothetical protein BG20_I0944 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       180  (0.0100396); expected 358.6 (0.02)
Passed bias filter:                      140  (0.00780858); expected 358.6 (0.02)
Passed Vit filter:                         3  (0.000167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 259.14
//
Query:       EPA04644.1  [L=417]
Description: CBS domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.5e-49  166.0   0.9      1e-48  165.4   0.9    1.3  1  DUF21      Cyclin M transmembrane N-terminal domain
    3.3e-17   62.3   0.5    3.3e-17   62.3   0.5    1.7  2  CorC_HlyC  Transporter associated domain
    5.6e-15   55.5   0.9    8.3e-06   26.2   0.1    3.3  3  CBS        CBS domain


Domain annotation for each model (and alignments):
>> DUF21  Cyclin M transmembrane N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.4   0.9   1.7e-52     1e-48       2     176 .]      10     186 ..       9     186 .. 0.98

  Alignments for each domain:
  == domain 1  score: 165.4 bits;  conditional E-value: 1.7e-52
       DUF21   2 iivlllllsaffsgaEtAlvslsrlrleelaekgkkkakrllkllknperlLstlligntlvnillsalatalfvellaegalavviatvivtllilvf 100
                 i+ +l++ls+ffsg+E+Alv ++++++++l++++ k+a++l k+ +np ++++++ +gn++vn+++sa+at+++ +++++   +++ia+ i+t+lilvf
  EPA04644.1  10 ILAILIGLSGFFSGLEVALVGTRKATVNQLVKQKVKGANALHKIKSNPAWMMASVNLGNNVVNVGSSAFATSVALRIFGN--DGLAIAVGIMTFLILVF 106
                 678999************************************************************************75..59*************** PP

       DUF21 101 gEilPkslalkyaekialalapplrvlmvllyPlvwllskllnlil....esesepavseeelkklveeseeegvieeee 176
                 gEi+Pk++++++a kial++ap+l ++ + ++P+v+ll+ ++++++    +s + p+++eee+k +v+++ +  ++e++e
  EPA04644.1 107 GEITPKTYCNANATKIALRFAPVLIIFGYAFWPVVKLLEIITKYMVkltgSSYQIPPITEEEIKGIVDQGLADKALEKDE 186
                 **************************************************9**********************9999987 PP

>> CorC_HlyC  Transporter associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.2       1.4   8.5e+03      10      30 ..     307     327 ..     304     330 .. 0.77
   2 !   62.3   0.5   5.5e-21   3.3e-17       2      80 ..     338     415 ..     337     416 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.4
                 EETT-BHHHHHHHHTSTTHHC CS
   CorC_HlyC  10 vdGslpldeleeelglelpee 30 
                 v+G ++ ++l ee+  ++++e
  EPA04644.1 307 VEGLVTFEDLIEEIVGDIEDE 327
                 788999999988887777664 PP

  == domain 2  score: 62.3 bits;  conditional E-value: 5.5e-21
                 EECTTEEEEETT-BHHHHHHHHTSTTHH.CT-SBHHHHHHHHH-S---TT-EEEEEETTEEEEEEEEETTCEEEEEEEE- CS
   CorC_HlyC   2 eldegsylvdGslpldeleeelglelpe.edyeTlgGlllellgriPkegesvevdleglrftVlemdgrrIkkvrvekl 80 
                 ++d+++++ +G++++  ++e+++ elpe +dy +l+Gll e+l++iPkeg+++e+d  ++++ V+++ +++ +++r+e++
  EPA04644.1 338 SIDKDTIITNGDIEIYRINEIFKSELPEgDDYASLNGLLHEKLQDIPKEGDKLEID--NIKIVVEKVIKNKPERIRIERI 415
                 67999***********************889********************99999..*******************986 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.063   3.8e+02      16      47 ..     138     174 ..     135     176 .. 0.63
   2 !   26.2   0.1   1.4e-09   8.3e-06       2      55 ..     202     258 ..     201     260 .. 0.83
   3 !   24.3   0.0   5.1e-09   3.1e-05       4      56 ..     270     321 ..     267     322 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.063
                 SBHHHHHHHHHH.....HT..SSEE.EEEETTTBEEEEEE CS
         CBS  16 ttleealelmre.....kg..vsrl.PVVdedgklvGivt 47 
                 +++ ++le++++     +g  + ++ P++ e++ + Giv 
  EPA04644.1 138 WPVVKLLEIITKymvklTGssY-QIpPIT-EEE-IKGIVD 174
                 5666777777542233333445.996799.677.99*996 PP

  == domain 2  score: 26.2 bits;  conditional E-value: 1.4e-09
                 HHHSBS..SCEEEETTSBHHHHHHHHHHHT.SSEEEEE.ETTTBEEEEEEHHHHHHHH CS
         CBS   2 gdimtr..dvvtvppdttleealelmrekg.vsrlPVV.dedgklvGivtlrDllral 55 
                 +++mt+  +++t+p  + l +al l+ +++ +sr+P+  + ++ +vG v+ rD+l  +
  EPA04644.1 202 RAVMTPrtKMFTLPSKMLLFDALPLI-NENpHSRIPIFgETNDDIVGFVHVRDILTHI 258
                 56766655999***************.6666*******755557***********987 PP

  == domain 3  score: 24.3 bits;  conditional E-value: 5.1e-09
                 HSBSSCEEEETTSBHHHHHHHHHHHT..SSEE.EEEETTTBEEEEEEHHHHHHHHH CS
         CBS   4 imtrdvvtvppdttleealelmrekg..vsrl.PVVdedgklvGivtlrDllrall 56 
                 i  r++v+++ +  ++ +l++m+  g    ++ +V+de g + G+vt +Dl++ ++
  EPA04644.1 270 I-ARKPVFASQEKMVSSLLKEMK--GrkT-HIaMVIDEHGGVEGLVTFEDLIEEIV 321
                 5.577889999999********4..3335.553699****************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       749  (0.0417759); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.24s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 2823.33
//
Query:       EPA04645.1  [L=37]
Description: hypothetical protein BG20_I0946 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      150  (0.00836633); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 262.39
//
Query:       EPA04646.1  [L=801]
Description: chitin synthase, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.8e-35  120.0   0.1    1.6e-34  119.1   0.1    1.5  1  Glycos_transf_2  Glycosyl transferase family 2
    1.4e-32  113.5   0.0    1.9e-32  113.0   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    8.1e-23   81.4   0.0    8.1e-23   81.4   0.0    1.8  1  Glyco_trans_2_3  Glycosyl transferase family group 2
    3.6e-12   45.7   0.2    1.3e-08   33.9   0.0    3.3  3  Chitin_synth_2   Chitin synthase
    2.2e-11   43.5   0.0    3.6e-11   42.8   0.0    1.3  1  Glyco_transf_21  Glycosyl transferase family 21
    2.4e-10   40.3   0.2    6.4e-10   39.0   0.1    1.8  2  Glyco_tranf_2_2  Glycosyltransferase like family 2
     0.0048   17.4   0.0      0.014   15.8   0.0    1.9  1  Glyco_tranf_2_4  Glycosyl transferase family 2
  ------ inclusion threshold ------
        0.1   12.9   0.7        1.2    9.5   0.1    2.9  2  SpaA             Prealbumin-like fold domain
       0.12   12.6   2.9       0.19   11.9   0.3    2.6  3  DUF4519          Domain of unknown function (DUF4519)
       0.43   10.9   5.4        0.3   11.4   0.5    2.7  2  Orf78            Orf78 (ac78)
        1.2    9.7   4.6        4.4    7.9   0.2    3.2  3  DUF3899          Domain of unknown function (DUF3899)


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.1   0.1     1e-37   1.6e-34       1     166 [.     188     348 ..     188     352 .. 0.97

  Alignments for each domain:
  == domain 1  score: 119.1 bits;  conditional E-value: 1e-37
                      EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--SSEEEEEESSEEE-T CS
  Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatgdyilflDaDdepdp 94 
                      sv+ip+yNeek ++ t+e+l++  +yp++eii+vDDgStD+t +i+ ++    ++++v+++e n Gka+aln gl +++g++i+++DaD+++ +
       EPA04646.1 188 SVIIPAYNEEKVIAHTIEALIET-KYPKKEIIFVDDGSTDKTLDIAMQYK---DKIKVLHKE-NGGKASALNYGLVYSKGEIIVIVDADTIIGR 276
                      8*********************9.*************************5...7********.55***************************** PP

                      THHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTCSTCCCEEEEHHH CS
  Glycos_transf_2  95 dwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfeigsaallrreal 166
                      + l+++++ ++ +++ +++++  + +   + i++ +  ++ + +++ +r + ++g+++++ g   ++r++ l
       EPA04646.1 277 NSLKEMMKGFQINEHVAAVAGNIKVRNRVNAITKCQALEYITGIQIVRRAFDIFGSITIVPGALGAFRKSFL 348
                      ***********************************999******************************9988 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.0   0.0   1.2e-35   1.9e-32       1     230 []     185     405 ..     185     405 .. 0.93

  Alignments for each domain:
  == domain 1  score: 113.0 bits;  conditional E-value: 1.2e-35
  Glyco_tranf_2_3   1 prdlavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnealravksdlvllv 94 
                      p+ ++v++p++nee+v+  ++e+l+  +yp  e+++v+d+s+++tl+ a++    ++d +++v+++++    +gk+ aln +l   k++++++v
       EPA04646.1 185 PT-VSVIIPAYNEEKVIAHTIEALIETKYPKKEIIFVDDGSTDKTLDIAMQ----YKD-KIKVLHKEN----GGKASALNYGLVYSKGEIIVIV 268
                      56.9*********************************************98....***.9****9988....489******************* PP

  Glyco_tranf_2_3  95 DdDtvvePdtlkrllqff.ltpkvgavgtpvfllnrstlvsalgalefaerhlrflaarralg.vltlnGsgslirrevlkelegldplflltd 186
                      D+Dt+++ ++lk +   f   + v+av ++  ++nr ++++  +ale+    + +++a + +g ++++ G++ ++r ++l+e +  ++   +++
       EPA04646.1 269 DADTIIGRNSLKEMMKGFqINEHVAAVAGNIKVRNRVNAITKCQALEYITGIQIVRRAFDIFGsITIVPGALGAFRKSFLTEAGAYGK-DTIVE 361
                      ******************9999************************96544444444446666368888**************98888.***** PP

  Glyco_tranf_2_3 187 DyelglrlrragfrtayvpgaavrevfpsslkayikqrnRwvyg 230
                      D++ +  l +ag  t+   +a+ +++ p +l ++i qr Rw++g
       EPA04646.1 362 DFDQTIKLLKAGLITQGSTKATAYTEAPNTLHDFISQRKRWYRG 405
                      ******************************************86 PP

>> Glyco_trans_2_3  Glycosyl transferase family group 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.4   0.0     5e-26   8.1e-23       1     190 [.     264     476 ..     264     483 .. 0.86

  Alignments for each domain:
  == domain 1  score: 81.4 bits;  conditional E-value: 5e-26
  Glyco_trans_2_3   1 iilllDaDtvlppdclreiaaela.spevaivqgpvlvmnvanwleelaalffaedhgkdilvrealgrvvpsvGsgaflrrsalqevggwdgd 93 
                      ii+++DaDt + +++l+e    ++ +  va+v g++ v+n+ n +++++al++   +   ++ ++ +g+ + ++G+  ++r s l+e+g +   
       EPA04646.1 264 IIVIVDADTIIGRNSLKEMMKGFQiNEHVAAVAGNIKVRNRVNAITKCQALEYITGIQIVRRAFDIFGSITIVPGALGAFRKSFLTEAGAYG-- 355
                      79**********************8899************************977888888999999**999*****************999.. PP

  Glyco_trans_2_3  94 essvsEDfdmglrlqrkGyrvrfvpeslvkekspltlraalrQrkRwayGceleklillvrll.........gylgsllwsalplhlallllfs 178
                       +++ EDfd  ++l+++G+++   + +  +++ p+tl +++ QrkRw++G+     i+ ++++         gyl +l + +l+l ++++++ +
       EPA04646.1 356 KDTIVEDFDQTIKLLKAGLITQGSTKATAYTEAPNTLHDFISQRKRWYRGN-----IQVLKRHgdaltnpryGYLQRLSFPYLVLGMLVTPIIG 444
                      89***********************9999*********************6.....44333333333333369*******************99 PP

  Glyco_trans_2_3 179 lla....................lalvlllll 190
                      ++a                    ++++++++l
       EPA04646.1 445 FVAtfnailgviqgdglyvlqvmTIFTIVHYL 476
                      99977777777777777766666555555554 PP

>> Chitin_synth_2  Chitin synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.048        79      27      64 ..     187     221 ..     161     230 .. 0.71
   2 !   33.9   0.0   8.2e-12   1.3e-08     200     287 ..     260     346 ..     233     367 .. 0.88
   3 !    6.0   0.0    0.0023       3.7     349     376 ..     381     408 ..     371     482 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.048
  Chitin_synth_2  27 ticlvtaysegeeglrttldslastdyddkrklllvvc 64 
                     + ++++ay e+ + + +t+++l +t+y++k+  ++ v 
      EPA04646.1 187 VSVIIPAYNEE-KVIAHTIEALIETKYPKKE--IIFVD 221
                     33568999885.6799***********9765..44445 PP

  == domain 2  score: 33.9 bits;  conditional E-value: 8.2e-12
  Chitin_synth_2 200 dfyeivlmvdadtkvapdsltrlvaalvkdpeilglcGetkiankkeswvtaiqvfeyyishhlskafesvfGsvtclPGcfslyrik 287
                     +  ei+++vdadt +  +sl++++  ++ ++++ ++ G+ k+ n+ ++ +t  q  ey    + ++    +fGs+t +PG + ++r  
      EPA04646.1 260 SKGEIIVIVDADTIIGRNSLKEMMKGFQINEHVAAVAGNIKVRNRVNA-ITKCQALEYITGIQIVRRAFDIFGSITIVPGALGAFRKS 346
                     55699***************************************9876.899*******99998876667************999954 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.0023
  Chitin_synth_2 349 qakcktvaPdtfkvllsqrrrwinstvh 376
                     +a++ t aP+t + ++sqr+rw    + 
      EPA04646.1 381 KATAYTEAPNTLHDFISQRKRWYRGNIQ 408
                     7999******************877665 PP

>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.8   0.0   2.2e-14   3.6e-11      17     173 .]     248     404 ..     239     404 .. 0.88

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 2.2e-14
  Glyco_transf_21  17 pKvnnllqaleaakydllvisDsdvrvkpdyLeellaaled.pkvglVtslpvgsdakglaaaleaafl....ntlagvlqaklsglgfavGks 105
                       K ++l+++l + k +++vi D+d+++ ++ L+e+++ ++  + v+ V + + + ++ ++ ++ +a+      +++ ++++  ++ + ++ G+ 
       EPA04646.1 248 GKASALNYGLVYSKGEIIVIVDADTIIGRNSLKEMMKGFQInEHVAAVAGNIKVRNRVNAITKCQALEYitgiQIVRRAFDI-FGSITIVPGAL 340
                      59999**********************************9757899999999999999998888777753223444444444.89********* PP

  Glyco_transf_21 106 malrreaLeaiGGfealadeLAeDyalgkllraaGlkvvlspapiaqtsvprrsslrallaRqlrWar 173
                       a+r++ L ++G + +  d++ eD+  +  l +aGl +  s+++ a t++p+  +l ++ ++  rW r
       EPA04646.1 341 GAFRKSFLTEAGAYGK--DTIVEDFDQTIKLLKAGLITQGSTKATAYTEAPN--TLHDFISQRKRWYR 404
                      ***************9..**************************99999996..9***********65 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.2   3.6e+03      61      77 ..     100     116 ..      90     118 .. 0.64
   2 !   39.0   0.1   3.9e-13   6.4e-10       1     108 [.     188     288 ..     188     399 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.2
  Glyco_tranf_2_2  61 deddkayslaaarNrGa 77 
                       ++ kays+ ++ NrG 
       EPA04646.1 100 SAQSKAYSKNKTGNRGP 116
                      34456777777777775 PP

  == domain 2  score: 39.0 bits;  conditional E-value: 3.9e-13
  Glyco_tranf_2_2   1 svviplraseerhyieerv..lqkakyydeeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrGaskaesdlvlFlDaDc 92 
                      sv+ip +++e+   i  ++  l ++ky  ++ e+i+vddgS++k+l+   + +d+ +    ++      ++a a N G  ++++++++ +DaD 
       EPA04646.1 188 SVIIPAYNEEKV--IAHTIeaLIETKY--PKKEIIFVDDGSTDKTLDIAMQYKDKIKVLHKEN-----GGKASALNYGLVYSKGEIIVIVDADT 272
                      89********99..*****98899999..***************9988777776655555333.....59************************ PP

  Glyco_tranf_2_2  93 fissDkfekilkliti 108
                       i  + ++ ++k  +i
       EPA04646.1 273 IIGRNSLKEMMKGFQI 288
                      **********995544 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   8.9e-06     0.014       1      53 [.     194     249 ..     194     283 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 8.9e-06
  Glyco_tranf_2_4   1 rneadiLpeflahhlalgf..drilvydndstDgtrailkelpe.vkllhvdksye 53 
                      +ne++++ ++++++ +  +  ++i+++d++stD+t +i  ++++ +k+lh ++  +
       EPA04646.1 194 YNEEKVIAHTIEALIETKYpkKEIIFVDDGSTDKTLDIAMQYKDkIKVLHKENGGK 249
                      69************999987679****************99866599998776544 PP

>> SpaA  Prealbumin-like fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.1      0.69   1.1e+03       8      45 ..     650     689 ..     646     723 .. 0.58
   2 ?    9.5   0.1   0.00076       1.2      13      58 ..     750     800 ..     740     801 .] 0.72

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.69
                 S-EEEEEETTTSCCCHCHHTT.......TTCCEESEEE-BTTSE CS
        SpaA   8 GaeFtlykvdtttdgkdalea......kktgtevttlttdenGk 45 
                 G++F ++ +d    gk+ +++       ++gt+    +t+++G 
  EPA04646.1 650 GIQFNVFYND----GKTPVKNalvaikSYDGTQLRIGKTNDQGD 689
                 6677777776....333333333445544555555555555554 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00076
                 EEETT....TSCCCHCHHTT.......TTCCEESEEE-BTTSEEEEEEEESEEEEE CS
        SpaA  13 lykvd....tttdgkdalea......kktgtevttlttdenGkatfegLplGtYll 58 
                 lyk++    t++dg     +      +  g+ +++  t++ G+a f++Lp  +Y+l
  EPA04646.1 750 LYKTEsekiTKNDG-----EfsillkDSLGNIIKKSQTNNRGEAYFSNLPSNEYFL 800
                 56665333333333.....145555666788889999*****************97 PP

>> DUF4519  Domain of unknown function (DUF4519)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.3   0.00011      0.19      12      51 ..      37      77 ..      28      81 .. 0.80
   2 ?   -1.6   0.0       1.9   3.1e+03      30      49 ..     539     558 ..     523     563 .. 0.63
   3 ?   -2.6   0.0       3.9   6.4e+03      32      50 ..     733     751 ..     730     753 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
     DUF4519 12 trkdKkeRr.kenkeaqekvttvVlPvlavlillivvfvYl 51
                 +k+Kke+  +  ke+q+k+ ++ +  ++++++++vv  Yl
  EPA04646.1 37 DQKNKKEKAiEHKKEIQKKFDSIQILLVVTILVFLVVSTYL 77
                357777776155789**********************9998 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.9
     DUF4519  30 vttvVlPvlavlillivvfv 49 
                 ++++++ vl++ +++ + +v
  EPA04646.1 539 ILKIAIIVLVLSLVIPINLV 558
                 55555555555555545555 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 3.9
     DUF4519  32 tvVlPvlavlillivvfvY 50 
                 ++++P+ a++  li v +Y
  EPA04646.1 733 KIIVPIPATVQDLITVSLY 751
                 8999*99999999999888 PP

>> Orf78  Orf78 (ac78)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.5   0.00018       0.3      28      84 ..      25      75 ..      14      85 .. 0.50
   2 ?    0.4   0.5       0.5   8.1e+02      49      84 ..     525     558 ..     512     572 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00018
       Orf78 28 nddndkaenkkekksaaeknditekesnaaekaqalnillisllavvcvlvllyviy 84
                ++ ++++ n++++++++++++i++k++  ++k  + +     +l vv++lv l v  
  EPA04646.1 25 TNIKNNPGNDNKDQKNKKEKAIEHKKEI-QKKFDSIQ-----ILLVVTILVFLVVST 75
                4445555566666555555555555554.23333333.....333333333333333 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.5
       Orf78  49 itekesnaaekaqalnillisllavvcvlvllyviy 84 
                 +++ ++   ++ ++ nil i+++++v  lv+ + ++
  EPA04646.1 525 LDKCKE--DRSLKNFNILKIAIIVLVLSLVIPINLV 558
                 222222..2344445666666666655555544444 PP

>> DUF3899  Domain of unknown function (DUF3899)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.2    0.0027       4.4      43      83 ..      37      78 ..      22      79 .. 0.76
   2 ?   -2.8   0.0         6   9.7e+03      53      81 ..     106     134 ..     102     136 .. 0.68
   3 ?    1.9   0.2      0.19   3.1e+02      31      82 ..     500     553 ..     497     557 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0027
     DUF3899 43 k.skkddsyyeykekkkesskkstrplliiGlllivlsivll 83
                  ++k+++ +e+k++ ++++     +l++++l+++v+s  l+
  EPA04646.1 37 DqKNKKEKAIEHKKEIQKKFDSIQILLVVTILVFLVVSTYLI 78
                148899999999999888677777777788899999998765 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 6
     DUF3899  53 ykekkkesskkstrplliiGlllivlsiv 81 
                 y ++k++++ +s+ +l++  + +i+ +i+
  EPA04646.1 106 YSKNKTGNRGPSVFLLFLLTSPFIIGAII 134
                 45556666777777777777777777777 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.19
     DUF3899  31 ygfrklkklflkk...skkddsyyeykekkkesskkstrplliiGlllivlsivl 82 
                 +gf+++ +++l k   + +++++    +k ke+++     +l i+++ +vls+v+
  EPA04646.1 500 FGFKQIVDFLLLKaiiE-QISNKKANLDKCKEDRSLKNFNILKIAIIVLVLSLVI 553
                 67777777777666742.3333333333334447777777888888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (801 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1600  (0.0892409); expected 358.6 (0.02)
Passed bias filter:                      756  (0.0421663); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.82u 0.34s 00:00:01.15 Elapsed: 00:00:00.50
# Mc/sec: 4833.11
//
Query:       EPA04647.1  [L=41]
Description: hypothetical protein BG20_I0957 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.021   14.8   5.3      0.087   12.9   5.3    1.8  1  DZR       Double zinc ribbon
       0.11   12.7   8.1       0.14   12.4   8.1    1.1  1  LIM       LIM domain
       0.41   10.7   4.5        1.1    9.2   0.1    2.0  2  Pox_A3L   Poxvirus A3L Protein


Domain annotation for each model (and alignments):
>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   5.3   1.5e-05     0.087       1      23 [.       4      34 ..       4      40 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.5e-05
         DZR  1 CpqCgee........lppdarfCseCgtklk 23
                C++C++e        +++d+++C eC t+l 
  EPA04647.1  4 CAKCNNEvskvydcdHTNDQEYCTECYTELH 34
                99****999****999************997 PP

>> LIM  LIM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   8.1   2.3e-05      0.14      28      57 ..       3      33 ..       3      34 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.3e-05
                B-TTT-SB-CTT..CEEETTEEEEHHHHHHH CS
         LIM 28 tCsdCqkeLkegs.fyekdgklyCkkdylkk 57
                tC++C++e ++ + +  ++++ yC ++y + 
  EPA04647.1  3 TCAKCNNEVSKVYdCDHTNDQEYCTECYTEL 33
                7************9**************875 PP

>> Pox_A3L  Poxvirus A3L Protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   1.4     0.012        70      12      27 ..       4      19 ..       2      24 .. 0.83
   2 ?    9.2   0.1   0.00019       1.1       9      26 ..      23      40 ..      19      41 .] 0.85

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.012
     Pox_A3L 12 CskCaanlveylkeDr 27
                C+kC +++ ++   D+
  EPA04647.1  4 CAKCNNEVSKVYDCDH 19
                *******999887775 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00019
     Pox_A3L  9 prrCskCaanlveylkeD 26
                   C++C ++l  yl+e 
  EPA04647.1 23 QEYCTECYTELHYYLTEE 40
                567************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       891  (0.049696); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 276.41
//
Query:       EPA04648.1  [L=105]
Description: hypothetical protein BG20_I0951 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-05   23.3   0.0    7.5e-05   22.5   0.0    1.3  1  DUF35_N   Rubredoxin-like zinc ribbon domain (DUF35_N)
  ------ inclusion threshold ------
      0.058   13.4   1.7       0.12   12.4   1.7    1.5  1  DZR       Double zinc ribbon


Domain annotation for each model (and alignments):
>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   8.3e-09   7.5e-05       4      32 ..       7      35 ..       5      39 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 8.3e-09
     DUF35_N  4 aaegrLvgqrCpdCGtvqfPPravCphCg 32
                ++ g ++++ C+ C   ++PP  +C +C+
  EPA04648.1  7 LKKGIFMISECTHCNETVWPPSEYCNRCF 35
                67899***********************8 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.7   1.3e-05      0.12       1      23 [.      17      39 ..      17      63 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.3e-05
         DZR  1 CpqCgeelppdarfCseCgtklk 23
                C +C+e + p +++C++C ++++
  EPA04648.1 17 CTHCNETVWPPSEYCNRCFKEVS 39
                99****************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 719.25
//
Query:       EPA04649.1  [L=322]
Description: luciferase-like monooxygenase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.5e-58  197.5   0.0    4.2e-58  197.2   0.0    1.0  1  Bac_luciferase  Luciferase-like monooxygenase


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.2   0.0   2.3e-62   4.2e-58      21     313 ..      12     295 ..       2     296 .. 0.96

  Alignments for each domain:
  == domain 1  score: 197.2 bits;  conditional E-value: 2.3e-62
  Bac_luciferase  21 slrylvelaraaEelGfdavwvaehhggpggaldaftllaalaaaTerirlgtavtplytrhPavlAqqaatLdhlsgGRfglglgtggpaveer 115
                     s+++++e+   + +   d++w++e++g     ++ f++l+++++ T + ++g+++ ++y+r+P  +A+ aat+d +s+GR++lglgt++ +++e+
      EPA04649.1  12 SIKQVLECSDIISHTSTDTIWIPETWG-----MENFSMLSMVSQKTLKQKIGSSIINIYSRSPSSIAMGAATVDTISNGRLVLGLGTSSLPIVED 101
                     67888888888888888**********.....9************************************************************** PP

  Bac_luciferase 116 rfGvdhderyarlrEfvevlrrlwrgeevdfeGeffsvkgalllprpgqgpiPvyvaaaspaglelaarhadglllageppeeaaelierlraga 210
                      +G  ++ ++ r++E+ve+++ +++g+ ++++G+ f++k++ ll +p+ + iP+y+aa++ ++++l++ +adg+++ + p  e++ +i++++   
      EPA04649.1 102 FHGYKFENPVLRMKEYVEIIKLILSGNQINYSGKIFNLKNFKLLIKPHREKIPIYMAAVNQKMVDLTWGIADGVIFYLRPINEMKNTIQKMQT-- 194
                     ************************99999******************9999*****************************************5.. PP

  Bac_luciferase 211 aeagrdpadirvgisltvivadteeeAraea...raliagld.fyaldsegagreaeaaeiqeeedanlwagaadavpdelvaatalvGtpeqva 301
                         r   +i+v++++ ++v +++e A  +a   +a+++++   y++  + +g++ e+ +i+ee+++ ++++  ++v+++++++++++Gtp+q++
      EPA04649.1 195 ---KR---KIDVTCQIITAVSHDAEIAITRAkqtLAFYISVGnIYREFLSKNGFQSETQNIFEEFKKSGFRSNYELVSEKMLNSLTIAGTPDQCI 283
                     ...89...***********************777777777769**************************************************** PP

  Bac_luciferase 302 erlaayaeagvd 313
                     ++l++++e+g+d
      EPA04649.1 284 KQLQRFRETGID 295
                     **********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       831  (0.0463495); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 1978.70
//
Query:       EPA04650.1  [L=154]
Description: hypothetical protein BG20_I0948 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       945  (0.0527079); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1162.12
//
Query:       EPA04651.1  [L=72]
Description: transcriptional regulator, AsnC family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.4e-07   29.5   0.0    5.9e-07   29.4   0.0    1.1  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   3.3e-11   5.9e-07      16      71 ..      15      69 ..       6      72 .] 0.93

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 3.3e-11
                    HHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEE CS
  AsnC_trans_reg 16 feealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsi 71
                    ++++l+++  V   + ++G +d ++++ v+ l  +++++++ +++++gv+rtet++
      EPA04651.1 15 IAARLRKVNSVYDSFPTSGQFDAVAIIEVEELGKIRDVTNQ-IQKINGVERTETMV 69
                    689999********************************999.************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 448.08
//
Query:       EPA04652.1  [L=416]
Description: threonine ammonia-lyase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-85  286.4   0.3      4e-85  285.8   0.3    1.2  1  PALP            Pyridoxal-phosphate dependent enzyme
    0.00023   20.9   0.1    0.00058   19.6   0.1    1.6  1  ACT             ACT domain
    0.00051   20.6   0.2     0.0014   19.2   0.2    1.7  1  ACT_4           ACT domain
     0.0012   18.6   0.0      0.012   15.4   0.0    2.4  2  Thr_dehydrat_C  C-terminal regulatory domain of Threonine deh
  ------ inclusion threshold ------
      0.028   14.0   0.5        4.8    6.7   0.2    2.5  2  Peripla_BP_4    Periplasmic binding protein domain


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  285.8   0.3   1.1e-88     4e-85       4     294 .]      32     317 ..      30     317 .. 0.98

  Alignments for each domain:
  == domain 1  score: 285.8 bits;  conditional E-value: 1.1e-88
                 CSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-EEEEEEETTS-HHHHHHHHHTT- CS
        PALP   4 gigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallGlkvtivvpadaspekvallrllGa 102
                 +i++TPlv +p +s+ +g +++lK E+ ++tgSfK+Rga+y ++ l  ++++++vv+as+GNh++++A+a++l ++++ti +p++asp+kv +++ +Ga
  EPA04652.1  32 EIRKTPLVYSPTFSDITGSQIYLKAEFQQKTGSFKIRGAYYKIKLLSSEEKKYGVVAASAGNHAQGVAFASSLEKIPCTIIMPKNASPSKVSATKGYGA 130
                 689******************************************99999************************************************* PP

                 EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHHTTTTEEEEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTC CS
        PALP 103 evvevggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEileqlggkpdavvvpvGgGgliaGiaaglkerrpdvrvigvepegsdalars 201
                 +v++ g +ydea a+a+e+ ++ +ga++++ fd++ vi+++g iglEile+l +++d ++vp+GgGgl+aG+  ++ke++p+++vigv+++  +++++s
  EPA04652.1 131 TVILEGVNYDEASAKAKEISQK-TGATMIHAFDDSEVIAAQGVIGLEILEEL-PDVDEIYVPIGGGGLAAGVLIAIKEKNPKIKVIGVQSKSFPSMYES 227
                 **********************.*****************************.6********************************************* PP

                 CS..S.SS..B.SSS.CCSTCSCGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHHHHHHHHCCTTCEEEEEEE-B CS
        PALP 202 lragrrvtvpvsdtiadglavgspselafelldrlvdeivtvsdeealeamrllarregivvepssaaalaalklreagelkegdrvvviltg 294
                 +++g+ +++  ++tiadg++v+ p+ ++f+++++l+de+v v+d e+++am ll +r + vvep++ ++la l     ++ ++g++vv+il+g
  EPA04652.1 228 IKNGSLTSCGGARTIADGISVKIPGQKTFSIIKELIDEVVLVDDSEIIKAMFLLMERSKFVVEPAGVVGLAYL---ISTKPAPGKKVVTILSG 317
                 *************************************************************************...8888888889*****98 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   1.6e-07   0.00058       3      64 ..     342     407 ..     341     408 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.6e-07
                 EEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTT....ECEEEEEEEEEEHHHHHHHHHHHHT CS
         ACT   3 lrvgvpDrPGlLarvfgaladrgiNidsieqrssedk....vagivfvvivvdeedleevlealkk 64 
                 +++++pDrPG++ ++   ++ ++ Ni+ + + +   +     ag + + ++ + e++++++e lkk
  EPA04652.1 342 ISILLPDRPGAFKEIVDEISAANANIVEVVHDRLSSNinagSAGVTLSLETQGKEQTDKLIEILKK 407
                 7899*************************9999988888888888888888888888888888887 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.2   3.9e-07    0.0014       8      71 ..     341     407 ..     337     409 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 3.9e-07
       ACT_4   8 rleveaedrkglLaditqviseekanivsvnaktrkk...dglaeikitveVkdvehLsrviakLra 71 
                 ++++   dr+g++++i++ is+++aniv+v  +  ++    g a +++++e +  e+ +++i+ L++
  EPA04652.1 341 KISILLPDRPGAFKEIVDEISAANANIVEVVHDRLSSninAGSAGVTLSLETQGKEQTDKLIEILKK 407
                 79999************************97666655555999*******************99986 PP

>> Thr_dehydrat_C  C-terminal regulatory domain of Threonine dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0       0.2   7.3e+02       8      25 ..      49      66 ..      47      67 .. 0.89
   2 !   15.4   0.0   3.4e-06     0.012      14      80 ..     343     414 ..     332     416 .] 0.77

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.2
                    XXXXXXXXXXXXXXXXXX CS
  Thr_dehydrat_C  8 gleallavefpeqpGaLk 25
                    g +++l  ef ++ G++k
      EPA04652.1 49 GSQIYLKAEFQQKTGSFK 66
                    578999***********8 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 3.4e-06
                     XXXXXXXXXXXXXXXXXXXXXX..XXX.XXXXXXXX.XXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
  Thr_dehydrat_C  14 avefpeqpGaLkkFlellggrnd.iTl.feYrkage.kngk..vLvgvevsqaeeldelierleklgykved 80 
                     ++ +p++pGa+k+ +++++  n  i + ++ r  ++ + g+  v    e++ +e+ d+lie l+k+++++  
      EPA04652.1 343 SILLPDRPGAFKEIVDEISAANAnIVEvVHDRLSSNiNAGSagVTLSLETQGKEQTDKLIEILKKKNIQFSL 414
                     6779***************9886666516778888866666115555666678889***********99865 PP

>> Peripla_BP_4  Periplasmic binding protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.2    0.0013       4.8     191     233 ..     193     235 ..      69     245 .. 0.75
   2 ?    5.1   0.0     0.004        14      63     126 ..     347     412 ..     343     416 .] 0.83

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0013
                   SCCHHHCHHHHHHHTTTTSTEEEEEES-HHHHHHHHHTTSSEE CS
  Peripla_BP_4 191 ndgmaegalealeaaglagkvvvtgqDatpealeaikdGtida 233
                   ++g a g+l a+++++ + kv+ +   + p + e+ik+G +++
    EPA04652.1 193 GGGLAAGVLIAIKEKNPKIKVIGVQSKSFPSMYESIKNGSLTS 235
                   4555569*******997777778888999**********9875 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.004
                   -SSHHHHHHHHHH..HHHTT-EEEEESTTGCTTT-CEEEEEC-HHHHHHHHHHHHHHHCTTH.EEE CS
  Peripla_BP_4  63 pvdstalapalkk..akaaGIpVvafdsddapsgerlayvgfdneaaGelqaeylaeklggkkgkv 126
                   p  + a ++++++  a++a+I+ v+ d++ ++ + ++a v+   e+ G+ q + l e l++k +++
    EPA04652.1 347 PDRPGAFKEIVDEisAANANIVEVVHDRLSSNINAGSAGVTLSLETQGKEQTDKLIEILKKKNIQF 412
                   566778888888855677778888899999999***************************986666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.34s 00:00:00.95 Elapsed: 00:00:00.51
# Mc/sec: 2439.35
//
Query:       EPA04653.1  [L=137]
Description: glyoxalase family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-08   35.1   0.0    1.3e-08   34.8   0.0    1.1  1  Glyoxalase_2  Glyoxalase-like domain
    5.3e-08   33.1   0.0    1.2e-07   31.9   0.0    1.6  1  Glyoxalase    Glyoxalase/Bleomycin resistance protein/Dioxyge
     0.0015   19.3   0.0     0.0018   19.0   0.0    1.1  1  Glyoxalase_6  Glyoxalase-like domain
     0.0036   17.6   0.0       0.11   12.7   0.0    2.1  1  Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxyge


Domain annotation for each model (and alignments):
>> Glyoxalase_2  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.0   2.9e-12   1.3e-08       3     114 ..       8     117 ..       6     120 .. 0.84

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 2.9e-12
                   ----EES-HHHHHHHHHHTT---EEEE-SSEEEETTS-EEEE.HHHHHH-------S--SS-EEEEEES-HHHHHHHH..GGGS-EEEEEEE-TTS- CS
  Glyoxalase_2   3 lillvvkdieeskkFYedvlelkikldfGenvsfetgfalke.dlkelinldesiaeqsnnfeLyFevedvdaflqklkeaeniellhelkekpWgq 98 
                   +++l+vkd+++s kFY++++ l+ik +  ++v   t  al + + ++l+  ++      n + ++F v dv +++++lk+++ +++  ++  ++ g+
    EPA04653.1   8 NVILAVKDLDKSVKFYNELIGLPIKRQRRSWVDLGTSGALLSlHPASLTA-QHIGSSIENGITIGFLVGDVTSAVEELKSKG-VKIYRDIVDREAGK 102
                   79********************************9988776515555554.4444446799*****************8877.*******9999998 PP

                   EEEEEE-TT--EEEEE CS
  Glyoxalase_2  99 rvirfyDpDkhiiEig 114
                     + + DpD  +i + 
    EPA04653.1 103 N-AMILDPDDYLISLF 117
                   7.5689***9999765 PP

>> Glyoxalase  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0   2.7e-11   1.2e-07       3     127 ..       7     115 ..       5     116 .. 0.74

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 2.7e-11
                 EEEEEEESHHHHHHHHHHHHHTSEEEEEEEEEESTEEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSCTSEEEEEEEEEHCHHHHHHHHHHHTTGEE CS
  Glyoxalase   3 dhvallvgdleksldFYtkvLGfklvkktdnteeteglriaffhaggghielvlneapsgaakhvkkieetvhhvafialdvedvgkaldrlkeagvkv 101
                 + v l+v+dl+ks++FY +  G+ + ++              +  +g  ++l  ++ +     +        +    i + v dv  a+++lk++gvk+
  EPA04653.1   7 GNVILAVKDLDKSVKFYNELIGLPIKRQRR--------SWVDLGTSGALLSLHPASLTAQHIGSS------IENGITIGFLVGDVTSAVEELKSKGVKI 91 
                 56789*************************........444444455444444444444444444......4456778888899999************ PP

                 EEEEECHHCTEEEEEEEEETTSEEEE CS
  Glyoxalase 102 vaepgrhyfgalysfyfrDpdGille 127
                  + + ++  g+     + Dpd +l+ 
  EPA04653.1  92 YRDIVDREAGKNAM--ILDPDDYLIS 115
                 98777766666663..9****99985 PP

>> Glyoxalase_6  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0     4e-07    0.0018       2     101 ..       9     111 ..       8     117 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 4e-07
  Glyoxalase_6   2 vvldaadpaalaaFwaaalgwevereeaaledpegvgpaaedaatllfqrvpe.......paknrvHldlavedldaevarlvalGArvlreprdgt 91 
                   v l+++d ++ ++F+ ++ g++ +r++      ++v + ++++a l+++++         + +n + + + v d+  +v++l + G +  r+  d++
    EPA04653.1   9 VILAVKDLDKSVKFYNELIGLPIKRQR-----RSWVDL-GTSGALLSLHPASLtaqhigsSIENGITIGFLVGDVTSAVEELKSKGVKIYRDIVDRE 99 
                   67999**********************.....233332.34555555555555555555577889***************************99999 PP

  Glyoxalase_6  92 hgr..vlaDPeG 101
                   +g+  ++ DP+ 
    EPA04653.1 100 AGKnaMILDPDD 111
                   999999999986 PP

>> Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   2.5e-05      0.11       5      94 ..      11      92 ..       8     107 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.5e-05
                  EE-S-HHHHHHHHHH.TT-EESS--E.EETTTTEEEEEEEETTEEEEEEEESSTT-THHHTS-EEEEEEEEES-HHHHHHHHCTTTEEEE CS
  Glyoxalase_4  5 ivVeDleaavarfsallGvgpwqryrdepqevdlafallgsgsvqieLieplegpeflaehgeglhhlaywvddldaavarleeqGfevv 94
                  ++V+Dl++ v+++ +l+G+  ++r  ++ ++vdl    +g     + L  ++ +++++    e    +++ v d+  av++l+++G+++ 
    EPA04653.1 11 LAVKDLDKSVKFYNELIGLP-IKR--QRRSWVDLGT--SGA---LLSLHPASLTAQHIGSSIENGITIGFLVGDVTSAVEELKSKGVKIY 92
                  7999***********99973.333..2344444422..222...2334334444466666666666799999999999999999999854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 968.68
//
Query:       EPA04654.1  [L=61]
Description: hypothetical protein BG20_I0971, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.044   12.7   0.2       0.05   12.5   0.2    1.0  1  Dak1       Dak1 domain
      0.073   13.7   0.0      0.073   13.7   0.0    1.2  1  CBFB_NFYA  CCAAT-binding transcription factor (CBF-B/NF-YA) s


Domain annotation for each model (and alignments):
>> Dak1  Dak1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   5.6e-06      0.05     109     133 ..      25      49 ..      12      52 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.6e-06
                 --EEEEEE--B-SSSSSTTCSSSB- CS
        Dak1 109 ikvetvvvdDDvavedseekagrRG 133
                  ++++v+vdDD+a+++++ +++rR+
  EPA04654.1  25 DDMSIVIVDDDIAIDQEKVNEERRA 49 
                 4899************999****97 PP

>> CBFB_NFYA  CCAAT-binding transcription factor (CBF-B/NF-YA) subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   8.2e-06     0.073      26      45 ..      40      59 ..      13      61 .] 0.88

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.2e-06
   CBFB_NFYA 26 elklrkarkkylheSRhkhA 45
                ++k++++r+ yl+eSR + A
  EPA04654.1 40 QEKVNEERRAYLEESRSQEA 59
                6788999**********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 426.81
//
Query:       EPA04655.1  [L=380]
Description: phosphoribosylaminoimidazole carboxylase, ATPase subunit [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-57  194.2   0.0    1.8e-57  193.6   0.0    1.2  1  ATP-grasp        ATP-grasp domain
    2.5e-12   46.3   0.0    5.3e-12   45.2   0.0    1.6  1  PurK_C           Phosphoribosylaminoimidazole carboxylase C-t
    5.9e-07   29.2   0.0    1.6e-06   27.8   0.0    1.8  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    0.00011   22.3   0.1    0.00024   21.2   0.1    1.6  1  ATP-grasp_3      ATP-grasp domain
     0.0025   17.2   0.0     0.0047   16.3   0.0    1.4  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
  ------ inclusion threshold ------
      0.022   14.3   0.0      0.035   13.6   0.0    1.3  1  DUF1297          Domain of unknown function (DUF1297)


Domain annotation for each model (and alignments):
>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.6   0.0   6.1e-61   1.8e-57       2     170 ..     112     280 ..     111     281 .. 0.99

  Alignments for each domain:
  == domain 1  score: 193.6 bits;  conditional E-value: 6.1e-61
                 HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHCGTTCEEEEE----SEEEEEEEEEETTC-EEE--EEEEEE CS
   ATP-grasp   2 eklglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqalealkeekvivEefvpfekElsvlvvrsaeGetafypvvetvq 100
                 +k+++p+p+f+ ++s  +lee ++++g+p+++Karr +ydG+G++ ++s++++++a ++++++k+++E+f+pf++E+sv+++r+++G++++yp+ve+++
  EPA04655.1 112 NKNNIPIPEFIKISSIFDLEEGLKKFGYPALLKARRDAYDGRGNFKINSPDQIKNAYDYFQGKKLMLEKFIPFKMEVSVIAARNTKGQIKTYPLVENIH 210
                 6899*********************************************************************************************** PP

                 ETTEEEEEEECEE-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEETTCTEEEEEEESS--GGGGGHHHH CS
   ATP-grasp 101 edgilrlsvapaevsekaqkkaeeiakkiveeLggvGvfavElFvledgellvnElapRpHnsGhvtlda 170
                 e++ilr+ +apa+vse++ kka++ia + +  L+g+Gvf++E+Fv++d+++++nE+apR+HnsGh tl++
  EPA04655.1 211 EENILRETIAPARVSETISKKANDIAIRTMTVLEGAGVFGIEMFVTHDDQIVINEIAPRVHNSGHHTLQS 280
                 ********************************************************************86 PP

>> PurK_C  Phosphoribosylaminoimidazole carboxylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   0.0   1.8e-15   5.3e-12       1      54 [.     307     362 ..     307     364 .. 0.87

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 1.8e-15
      PurK_C   1 avMvNlLGedaeeklee..llaipgahlHlYgKeearpgRKmGHitvvgdsaeele 54 
                 ++M+N+LG++++e+  +   l+  ++ l +YgKe ++p+RK+GH+++v+ + e +e
  EPA04655.1 307 TIMYNILGSKSFEGKYKpiSLSESDIFLKMYGKEISKPMRKLGHFNLVAYNGETIE 362
                 79*********9666666688889999999******************98877665 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0   5.5e-10   1.6e-06      32     173 ..     134     267 ..     110     270 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 5.5e-10
                      HHHC-SSEEEEESSSS.TTTTEEEESSGGGHHHHHHHHHTT-SCEEEEE--ESEEEEEEEEETSSCEEEEEEEEE-SSSSS-HHHHHC.TT-EE CS
  Dala_Dala_lig_C  32 eeelgypvfVKpareG.SSvGvskveseeelkeaieeafkydekvlvEeaiegreievavlgneklevsevgeivvkkgfydyeakysddkaql 124
                       +++gyp++ K+ r      G  k++s +++k+a +      +k + E++i  + +ev+v+        + g+i +   + +++++++    + 
       EPA04655.1 134 LKKFGYPALLKARRDAyDGRGNFKINSPDQIKNAYDYF--QGKKLMLEKFIPFK-MEVSVIA----ARNTKGQIKTYPLVENIHEENI--LRET 218
                      67889999999877652457999999999999988764..36789999999764.8999998....3344456666566666777775..5678 PP

                      ESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEEEEE CS
  Dala_Dala_lig_C 125 evpaklekeveekiqelalkaykaldlrGlaRvDfflteegeivlnEvN 173
                        pa++++ +++k +++a+++ ++l+++G+  + +f+t++++iv+nE+ 
       EPA04655.1 219 IAPARVSETISKKANDIAIRTMTVLEGAGVFGIEMFVTHDDQIVINEIA 267
                      89*********************************************95 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.1     8e-08   0.00024       2     159 ..     102     271 ..     101     273 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 8e-08
                  TSHHHHHHHHTTT.S---..........-EESS--.......SSSEEEEE.SS-------B--SS--TTE...........EEEE---SEEEEEEEEE CS
  ATP-grasp_3   2 sdKlktykkLkeagvkvP......tkleaeeleee.......ekklvvKp.rdGaggesvrvveekeeaeaaieeve....lvqefieGkplSvslls 81 
                  +dK+    +L+++++++P      +                  ++  +K  rd+ +g ++++++  ++ ++a ++ +    ++ +fi+ k + vs+++
   EPA04655.1 102 QDKFLQKTFLNKNNIPIPefikisSIFD------LeeglkkfGYPALLKArRDAYDGRGNFKINSPDQIKNAYDYFQgkklMLEKFIPFK-MEVSVIA 192
                  79****************5554432222......234455568999999626899************999999999899989999*9965.5666666 PP

                  .SSSEEEEEEEEEEEET....TEEEEEEES----H..HHHHHHHHHHHHTTSTT--EEEEEEEEESS..SEEEEEEESS-- CS
  ATP-grasp_3  82 dgekvlvlavnrqliekaekefvyaGnvtpietel..keevvelaeevvekleglaGyvGvDlvlkd.eepyviEvNPRlt 159
                    ++   + +   l+e+ ++e++ +  ++p+++++  ++++ ++a +++  l + aG++G+++ ++  +++++ E+ PR+ 
   EPA04655.1 193 ARNTKGQIKTY-PLVENIHEENILRETIAPARVSEtiSKKANDIAIRTMTVL-EGAGVFGIEMFVTHdDQIVINEIAPRVH 271
                  55444444444.355556677999999****9999889**************.99*******765542888888*****86 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.6e-06    0.0047      36      99 ..       2      74 ..       1      88 [. 0.77

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.6e-06
                  TSEEEEES-SHHHHHHHHHHHHTT-...EEEEESSSHHHHH......CHHHHTC.EECSHHHHHHH-SEEEE-S CS
  2-Hacid_dh_C 36 gktvGiiGlGrIGqavakrlkafgm...kviaydrskkkee......eeeelgv.elvsleellaesDivslhl 99
                  gk +GiiG G++G  +a+ +k++     k+i+ d++++  +      +  +  + +   ++el ++sDi++  +
    EPA04655.1  2 GKILGIIGGGQLGMMIAEAAKKMPEhisKIIVLDPTPNCPAsqvgadQITA-DFkDQNAIKELAEKSDIITYEI 74
                  7899*****************886433599******994444454422222.332566899*********9766 PP

>> DUF1297  Domain of unknown function (DUF1297)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.2e-05     0.035     118     157 ..     246     285 ..     191     297 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.2e-05
                 -EEEEEEEEE-TTS-EEEEEEESSB-GGGGGGTT--CCHH CS
     DUF1297 118 iGpFcLqsvvtkdlelvvfdvsaRivggtnvymegspysk 157
                  G F++++ vt+d ++v+ ++++R+  +   ++++s++s+
  EPA04655.1 246 AGVFGIEMFVTHDDQIVINEIAPRVHNSGHHTLQSSKTSQ 285
                 69***********************999988888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.37
# Mc/sec: 3089.41
//
Query:       EPA04656.1  [L=107]
Description: hypothetical protein BG20_I0947 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      0.002   18.2   0.3     0.0025   17.9   0.3    1.1  1  GIT1_C    G protein-coupled receptor kinase-interacting prote
  ------ inclusion threshold ------
      0.024   15.2   0.7        0.1   13.2   0.0    1.9  2  YtxH      YtxH-like protein
      0.047   13.9   1.6        1.2    9.3   0.1    2.1  2  IFT20     Intraflagellar transport complex B, subunit 20


Domain annotation for each model (and alignments):
>> GIT1_C  G protein-coupled receptor kinase-interacting protein 1 C term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.3   4.1e-07    0.0025      11      84 ..      17      96 ..      12     107 .] 0.74

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 4.1e-07
      GIT1_C 11 kteqitkriqeLlqaaqe..ekkesfvpcaerIqsaVqdlvalfpenlseetlrta....LkqLtssaerLqeeCeelqe 84
                 t+q++ ++++L ++ ++  e  esf +++  I s+++++++ + +++s+++l       +k + ++a+ +++e e  +e
  EPA04656.1 17 LTDQVINHVNNLKNLYNAayEDPESFEEVSAEISSTINEIATAVEPEASDSDLDGLiqeiIKVVDNKAAEMEQELEGKPE 96
                699999999888887775347889*********************99999999885223366666666677666666665 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.7e-05       0.1      23      73 ..      10      59 ..       8      61 .. 0.91
   2 ?    0.3   0.4      0.17     1e+03      58      72 ..      75      89 ..      62     107 .] 0.51

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.7e-05
        YtxH 23 GketRkdlkekaddlkekakelleeakekakekaedlkekvkekadelkek 73
                G e+R  l +++ +  +++k+l++ a+e   e++e+++ +++++++e++  
  EPA04656.1 10 GTEFRLTLTDQVINHVNNLKNLYNAAYED-PESFEEVSAEISSTINEIATA 59
                99************************999.999999999999999998865 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.17
        YtxH 58 dlkekvkekadelke 72
                ++ + v++ka e+ +
  EPA04656.1 75 EIIKVVDNKAAEMEQ 89
                333333333333332 PP

>> IFT20  Intraflagellar transport complex B, subunit 20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1   0.00021       1.2      15      59 ..      19      63 ..      12      67 .. 0.90
   2 ?    4.1   0.1    0.0082        49      37      59 ..      68      90 ..      64      93 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00021
       IFT20 15 pevaeeteelkeeckeFvkkinefqklvkelievleelakkveke 59
                 +v ++ ++lk+  +   ++ ++f+++  e++++++e+a++ve e
  EPA04656.1 19 DQVINHVNNLKNLYNAAYEDPESFEEVSAEISSTINEIATAVEPE 63
                57889999999999999999**********************976 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0082
       IFT20 37 efqklvkelievleelakkveke 59
                +++ l++e+i+v+++ a + e+e
  EPA04656.1 68 DLDGLIQEIIKVVDNKAAEMEQE 90
                7889999********99999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1238  (0.0690501); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 785.30
//
Query:       EPA04657.1  [L=645]
Description: hypothetical protein BG20_I2314, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-17   63.3   1.0    1.2e-16   60.9   0.0    2.1  2  Peptidase_S8  Subtilase family
    2.6e-05   24.9   0.3     0.0022   18.7   0.0    2.9  2  fn3_5         Fn3-like domain
  ------ inclusion threshold ------
      0.032   14.3   2.8        7.5    6.6   0.0    3.6  4  DUF916        Bacterial protein of unknown function (DUF916)


Domain annotation for each model (and alignments):
>> Peptidase_S8  Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.9   0.0     2e-20   1.2e-16     195     298 .]       8     112 ..       4     114 .. 0.86
   2 ?    0.5   0.3      0.05     3e+02      11     128 ..     489     635 ..     481     643 .. 0.56

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 2e-20
                   TTSSB-TT--B-TT.......-EEEE-S-.CCCCCCCCCHHHTTTHHEEEE-SHHHCHHHHHHHHHHHHHHHTT....--HHHHHHHHHCCS-EE.. CS
                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxx RF
  Peptidase_S8 195 tegkiapfSsrGpssdgklkpdivapGgn.ivstwsrqsnnsaglssyqsmsGTSmAsPnaagaaAlllsalpk....ltpetvraallntAqdlgk 286
                   + ++i +fSsrGp + g  kpd++  G+    ++   +++++ ++ s+ ++ GTSmA+P+++g+aA+l+++l k    + p t++ +l+ tA+dl  
    EPA04657.1   8 SSDEIVDFSSRGPGIIGDPKPDLMSIGAYgFTPSNVLKTTKNSKEESFSLFGGTSMAAPLVSGSAAVLMEGLHKqskeYDPFTIKNILMSTAKDL-- 102
                   678899***********************967777666666666666***********************6655599999999*********999.. PP

                   ....SSSSSSTT CS
                   xxxxxxxxxxxx RF
  Peptidase_S8 287 adniesfaqGaG 298
                     +  +f qG G
    EPA04657.1 103 --QNDPFTQGSG 112
                   ..3568888877 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.05
                   S-B-TT-TTTGGGEEE..EEEE---TTSG....................................GGEETT-SS-TT-SC-SSS....HHHHHHHHH CS
                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Peptidase_S8  11 tGvdpshpdlsvttdgerklvdvideegag...................................fngadsettstnwarddngnsieHGthvAGia 72 
                   + +++ + ++s +td ++ +v+v d +g+                                    + ++d+++t  ++  ++ g     +t +A   
    EPA04657.1 489 SSINSAAIEMSWKTDDTNLSVFVVDPKGKIvqsnmpsgvfghflgwpsldwlgnsvfsqgggffpVKNKDATSTVLYIPINQTG----TYTVMAHST 581
                   555555555555555555555555555554555555555555555555555555555555555443333333333333333333....455566555 PP

                   H-B..SSSSSB-SSTTSEEEEEE-SSTTSB-HH..HHHHHHHHHHHHCT-SEEEE- CS
                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Peptidase_S8  73 aanapeegekngvapgakilsvkvldtsggsmetgteliraieeaaedkvdvinms 128
                   + + +++ e   va + + +s +++  s++s+et+ + i++++e+++ +  + n s
    EPA04657.1 582 LFGGNSTTEPITVAAKFSNISSEII--SDQSNETNITSISNVTESNQINHTISNDS 635
                   5555677777777777777777777..44456667778888888888887788777 PP

>> fn3_5  Fn3-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1      0.03   1.8e+02       7      32 ..     182     209 ..     179     249 .. 0.70
   2 !   18.7   0.0   3.6e-07    0.0022      58     106 ..     382     427 ..     353     434 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.03
       fn3_5   7 gdkfsftltlkNtsnkaltykvsan..d 32 
                 gd  + t+t++N +nk+  ++v+ +  +
  EPA04657.1 182 GDHSKTTFTIENPTNKPINITVKPTtiS 209
                 5778899999999999999999988432 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 3.6e-07
       fn3_5  58 altfetskvtvpAnssktvtvtldlpsdakkkngyfveGfvtlkdsedk 106
                  +  e++++t+pAn+ + v++ l +p+d++      + Gf+t+++s+ +
  EPA04657.1 382 IIWPESETLTIPANGIASVDISLIAPNDLQT---GNYQGFITFEGSKHS 427
                 5666899********************9998...5579********987 PP

>> DUF916  Bacterial protein of unknown function (DUF916)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0013       7.5      17      50 ..     173     206 ..     166     217 .. 0.90
   2 ?   -0.4   0.0      0.19   1.2e+03      98     117 ..     327     346 ..     280     347 .. 0.82
   3 ?    5.2   0.0    0.0035        21      59     119 ..     365     422 ..     358     423 .. 0.83
   4 ?   -3.0   0.4       1.2   7.3e+03      35      35 ..     618     618 ..     586     638 .. 0.55

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0013
      DUF916  17 sYFdLkvkpgqeqelevkikNssdkeitveitvn 50 
                 s+F  ++ pg  ++ + +i+N ++k+i+++++ +
  EPA04657.1 173 SWFAGQLLPGDHSKTTFTIENPTNKPINITVKPT 206
                 67888899*********************99876 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.19
      DUF916  98 klkikmPkeefdGvilGGiy 117
                 +l i+ P+e+f+G+ l G+y
  EPA04657.1 327 ELRITEPNEKFKGTPLVGVY 346
                 678999*******9988876 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.0035
      DUF916  59 vidYskskekkdkslkvslselvkipkeitlpakesktvklkikmPkeefdGvilGGiyve 119
                  +dY+ +++ ++k   +++s +   ++++t+pa+    v++++ +P++  +G + G i++e
  EPA04657.1 365 SMDYTLTASYYHK---TKWSIIWPESETLTIPANGIASVDISLIAPNDLQTGNYQGFITFE 422
                 5677777777554...5788888888**************************999999886 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 1.2
      DUF916  35 i 35 
                 i
  EPA04657.1 618 I 618
                 2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (645 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 4349.18
//
Query:       EPA04658.1  [L=644]
Description: hypothetical protein BG20_I2315, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.1e-16   59.1   0.0    8.3e-16   58.1   0.0    1.4  1  Peptidase_S8  Subtilase family
    9.8e-06   26.2   0.6    0.00032   21.3   0.0    2.6  2  fn3_5         Fn3-like domain
    0.00018   21.5   0.1        1.6    8.8   0.0    3.2  3  DUF916        Bacterial protein of unknown function (DUF916)


Domain annotation for each model (and alignments):
>> Peptidase_S8  Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.1   0.0   1.4e-19   8.3e-16     196     298 .]       9     112 ..       4     115 .. 0.83

  Alignments for each domain:
  == domain 1  score: 58.1 bits;  conditional E-value: 1.4e-19
                   TSSB-TT--B-TT.......-EEEE-S-.CCCCCCCCCHHHTTTHHEEEE-SHHHCHHHHHHHHHHHHH.HHTT...--HHHHHHHHHCCS-EE... CS
                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx...xxxxxxxxxxxxxxxxxxxx RF
  Peptidase_S8 196 egkiapfSsrGpssdgklkpdivapGgn.ivstwsrqsnnsaglssyqsmsGTSmAsPnaagaaAllls.alpk...ltpetvraallntAqdlgka 287
                   +++i +fSsrGp + g  kpd++  G+    ++   +++++ ++ s+ ++ GTSmA+P+++g+aA+l++  +++   + p  ++ +l+ tAqdl+  
    EPA04658.1   9 NDEIVDFSSRGPGIIGDPKPDLMSIGAYgFTPSNVLKTTKNSKEESFSLFGGTSMAAPLVSGSAAILMEgLHKQskeYDPFIIKNILMSTAQDLQ-- 103
                   67899***********************967777666666666666***********************5555555555555**********993.. PP

                   ...SSSSSSTT CS
                   xxxxxxxxxxx RF
  Peptidase_S8 288 dniesfaqGaG 298
                       +f qG G
    EPA04658.1 104 --NDPFTQGSG 112
                   ..457888877 PP

>> fn3_5  Fn3-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1     0.042   2.5e+02       7      31 ..     182     206 ..     178     250 .. 0.70
   2 !   21.3   0.0   5.4e-08   0.00032      57     106 ..     381     427 ..     353     433 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.042
       fn3_5   7 gdkfsftltlkNtsnkaltykvsan 31 
                 gd  + t+t++N +nk+  ++++ +
  EPA04658.1 182 GDRSKATFTIENPTNKPINITIKPT 206
                 5677889999999999999988887 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 5.4e-08
       fn3_5  57 aaltfetskvtvpAnssktvtvtldlpsdakkkngyfveGfvtlkdsedk 106
                 + +  e++++tvpAn  ++v+v l +p+d++      + Gf+t+++++ +
  EPA04658.1 381 SLIWPESETITVPANDIAKVDVSLIAPNDLQT---GNYQGFITFEGQNHS 427
                 45666899********************9998...5579*******9987 PP

>> DUF916  Bacterial protein of unknown function (DUF916)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0003       1.8      16      50 ..     172     206 ..     164     219 .. 0.90
   2 ?   -1.6   0.0      0.44   2.7e+03      98     116 ..     327     345 ..     280     346 .. 0.76
   3 !    8.8   0.0   0.00026       1.6      58     119 ..     364     422 ..     358     423 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0003
      DUF916  16 ksYFdLkvkpgqeqelevkikNssdkeitveitvn 50 
                 +s+F  ++ pg +++ + +i+N ++k+i+++i+ +
  EPA04658.1 172 TSWFAGQLHPGDRSKATFTIENPTNKPINITIKPT 206
                 5789999***********************99976 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.44
      DUF916  98 klkikmPkeefdGvilGGi 116
                 +l i  P+e+f+G+ l G+
  EPA04658.1 327 ELRIAEPNEKFKGTPLVGV 345
                 5778889999999988776 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.00026
      DUF916  58 GvidYskskekkdkslkvslselvkipkeitlpakesktvklkikmPkeefdGvilGGiyve 119
                   +dY+ +++ ++k   +++s +   +++it+pa+   +v++++ +P++  +G + G i++e
  EPA04658.1 364 TSMDYTLTASYYQK---TKWSLIWPESETITVPANDIAKVDVSLIAPNDLQTGNYQGFITFE 422
                 56788887777555...6888888888**************************999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (644 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 4209.81
//
Query:       EPA04659.1  [L=39]
Description: hypothetical protein BG20_I2562, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.4e-12   45.2   0.1    7.7e-12   45.1   0.1    1.0  1  DUF1297   Domain of unknown function (DUF1297)


Domain annotation for each model (and alignments):
>> DUF1297  Domain of unknown function (DUF1297)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.1   0.1   4.3e-16   7.7e-12     152     188 .]       3      39 .]       1      39 [] 0.97

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 4.3e-16
                 --CCHHHTTSS---HHHHHHHHHHHHHHCT-GGGCEE CS
     DUF1297 152 gspyskllfgeplsmGrrialEikeaiekdrleeivt 188
                 +spy+k+++g+++ +Grria+Eik+a e+drl+eivt
  EPA04659.1   3 TSPYTKYQYGKTFGIGRRIAMEIKQAQEEDRLDEIVT 39 
                 89**********************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.28s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 270.92
//
Query:       EPA04660.1  [L=64]
Description: hypothetical protein BG20_I2564, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.024   14.5   1.0       0.54   10.2   0.1    2.2  2  zf-FPG_IleRS     Zinc finger found in FPG and IleRS
      0.033   14.1   2.0        1.2    9.0   0.4    2.2  2  zf-trcl          Probable zinc-ribbon domain
      0.034   14.5   0.1      0.044   14.2   0.1    1.2  1  Lar_restr_allev  Restriction alleviation protein Lar
       0.16   11.8   2.3       0.27   11.0   2.3    1.5  1  Cys_rich_KTR     Cysteine-rich KTR
       0.99    9.2   3.9        1.8    8.3   1.0    2.2  2  zf-CCHC_5        GAG-polyprotein viral zinc-finger


Domain annotation for each model (and alignments):
>> zf-FPG_IleRS  Zinc finger found in FPG and IleRS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00015      0.54      21      29 ..       4      12 ..       1      13 [. 0.84
   2 ?    3.2   0.1     0.023        81      23      27 ..      32      36 ..      23      38 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00015
                  EEE-TTTT. CS
  zf-FPG_IleRS 21 tyfCprCqk 29
                  + +Cp+Cqk
    EPA04660.1  4 PKLCPTCQK 12
                  679*****7 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.023
                  E-TTT CS
  zf-FPG_IleRS 23 fCprC 27
                  +C rC
    EPA04660.1 32 LCTRC 36
                  79999 PP

>> zf-trcl  Probable zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.4   0.00034       1.2      31      45 ..       2      16 ..       1      19 [. 0.81
   2 ?    4.9   0.1    0.0068        24       3      15 ..      29      41 ..      27      46 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00034
     zf-trcl 31 nepkRCkaCRkarkq 45
                 epk C++C k ++ 
  EPA04660.1  2 KEPKLCPTCQKGDRL 16
                69*******998775 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0068
     zf-trcl  3 ktltCkdCgaefv 15
                +tl C++C+a  v
  EPA04660.1 29 QTLLCTRCEALTV 41
                6899****98766 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   1.2e-05     0.044       4      42 ..       5      48 ..       2      61 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.2e-05
  Lar_restr_allev  4 kpCPfCggravlersqrvva.eigqcvyCadCga....stpwfk 42
                     k CP C + + le++        gq+  C+ C+a     ++  k
       EPA04660.1  5 KLCPTCQKGDRLEKNIVFERkTDGQTLLCTRCEAltviTNHNLK 48
                     78******99999986544303455*********5444333333 PP

>> Cys_rich_KTR  Cysteine-rich KTR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   2.3   7.6e-05      0.27       5      45 ..       6      48 ..       3      59 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 7.6e-05
  Cys_rich_KTR  5 lcPvCgnkTRl..kiredTvLknfpLfCPKCkqetlinvkqlk 45
                  lcP+C+   Rl   i  +     + L C +C   t+i  ++lk
    EPA04660.1  6 LCPTCQKGDRLekNIVFERKTDGQTLLCTRCEALTVITNHNLK 48
                  7****9999862257788888999*************999997 PP

>> zf-CCHC_5  GAG-polyprotein viral zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   1.0   0.00051       1.8       2      11 ..       4      13 ..       3      18 .. 0.89
   2 ?    1.6   0.1     0.063   2.3e+02       4       8 ..      32      36 ..      26      38 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00051
                --B-TTT-SS CS
   zf-CCHC_5  2 pglCpRCkkg 11
                p lCp C kg
  EPA04660.1  4 PKLCPTCQKG 13
                78*******9 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.063
                B-TTT CS
   zf-CCHC_5  4 lCpRC 8 
                lC RC
  EPA04660.1 32 LCTRC 36
                89**9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       784  (0.043728); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 460.54
//
Query:       EPA04661.1  [L=66]
Description: hypothetical protein BG20_I2563 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       697  (0.0388756); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.29s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 467.15
//
Query:       EPA04662.1  [L=175]
Description: putative endonuclease III [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-24   86.6   0.1      2e-24   86.1   0.1    1.2  1  HhH-GPD   HhH-GPD superfamily base excision DNA repair protei
    8.8e-09   34.8   0.0    2.4e-08   33.4   0.0    1.8  2  HHH       Helix-hairpin-helix motif
     0.0025   18.4   0.9       0.46   11.1   0.1    2.3  2  HHH_5     Helix-hairpin-helix domain
     0.0033   17.5   0.1      0.014   15.4   0.0    1.8  2  DUF2400   Protein of unknown function (DUF2400)
      0.005   16.2   1.7      0.017   14.4   1.7    1.8  1  AGOG      N-glycosylase/DNA lyase
  ------ inclusion threshold ------
      0.022   14.9   0.0        2.5    8.2   0.0    2.3  2  HHH_2     Helix-hairpin-helix motif


Domain annotation for each model (and alignments):
>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.1   0.1   6.7e-28     2e-24       5     107 ..       1     131 [.       1     132 [. 0.97

  Alignments for each domain:
  == domain 1  score: 86.1 bits;  conditional E-value: 6.7e-28
                 HHTTS-HHHHHHHHHHHHHHHSHCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH...............................S-SSS- CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...............................xxxxxx RF
     HhH-GPD   5 lsqqtsderanriierlferfgfptpedladadeekLrelirelGfyrrKakyikelArilv...............................gkpdvl 72 
                 +s++t+de+++++++ lf++++  ++++la+a  ++++++i+++Gfy+ K k+i+e+A+i+                                ++ +++
  EPA04662.1   1 MSARTKDETTTKAVKVLFSKYK--NAKELASAKTKDVEKIIKSIGFYHVKSKRIIEVAKIINskykgkvpdnleklvelpgvgrktancvlvyAFDKPA 97 
                 79******************99..*********************************************************************77789* PP

                 -TTSHHHHHHHHHHTTSSSSTTHHHHHHHHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
     HhH-GPD  73 ivvDvhvrrilkrlrsikekktkkkvekkleelle 107
                 i+vD+hv+ri +rl+++++ kt++++e++l+++++
  EPA04662.1  98 IPVDIHVHRISNRLGLVNT-KTPEETEQELMRIIP 131
                 *****************99.6*********99987 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.0   7.9e-12   2.4e-08       1      30 []      62      91 ..      62      91 .. 0.94
   2 ?   -3.6   0.0       4.4   1.3e+04       5      12 ..     114     121 ..     111     121 .. 0.77

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 7.9e-12
                SHHHHHTSSHHHHHTSTT-SHHHHHHHHHH CS
         HHH  1 sleglipasreeLlalPGVGpktAeaIlsy 30
                +++g +p+++e L++lPGVG+ktA+++l y
  EPA04662.1 62 KYKGKVPDNLEKLVELPGVGRKTANCVLVY 91
                589************************976 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 4.4
                 HHTSSHHH CS
         HHH   5 lipasree 12 
                 +++ ++ee
  EPA04662.1 114 VNTKTPEE 121
                 68899998 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.3    0.0049        15      13      56 ..      12      57 ..      10      58 .. 0.78
   2 !   11.1   0.1   0.00016      0.46      33      48 ..      70      85 ..      49      90 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0049
                HHHHHHHTTT--SHHHHHHS...-HHHHHTSTTS-HHHHHHHHHHHH CS
       HHH_5 13 ktAlallsaGiesvedlaaa...dveeLakipGiGkktAeriilelk 56
                k ++ l s+ ++   +la+a   dve++ k  G+   + +rii+ +k
  EPA04662.1 12 KAVKVLFSK-YKNAKELASAktkDVEKIIKSIGFYHVKSKRIIEVAK 57
                556667788.99999**998666788888878998999999998765 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00016
                -HHHHHTSTTS-HHHH CS
       HHH_5 33 dveeLakipGiGkktA 48
                + e+L ++pG+G ktA
  EPA04662.1 70 NLEKLVELPGVGRKTA 85
                568999*********9 PP

>> DUF2400  Protein of unknown function (DUF2400)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.31   9.2e+02     103     110 ..      33      40 ..       4      79 .. 0.42
   2 !   15.4   0.0   4.7e-06     0.014     172     195 ..      97     120 ..      92     137 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.31
     DUF2400 103 eeeeelee 110
                 ++ e++ +
  EPA04662.1  33 KDVEKIIK 40 
                 11111111 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 4.7e-06
     DUF2400 172 iiPlDvHvarvarklgllkrkqad 195
                  iP+D+Hv+r++++lgl+++k+ +
  EPA04662.1  97 AIPVDIHVHRISNRLGLVNTKTPE 120
                 59****************998754 PP

>> AGOG  N-glycosylase/DNA lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   1.7   5.8e-06     0.017     162     212 ..      89     139 ..       3     142 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.8e-06
                 ----TTS-.----HHHHHHHHHTTS-SS-HHHHHHTHCCHCS.HHHHHHHHH CS
        AGOG 162 iplpfeip.iPvDvRiakltktsglielknekklarkelvqeevieaWkevs 212
                   ++f+ p iPvD  +++++   gl+++k+ ++ +++el++ +++++W ++ 
  EPA04662.1  89 LVYAFDKPaIPVDIHVHRISNRLGLVNTKTPEE-TEQELMRIIPKKFWIDIN 139
                 5666666559******************99988.8899**********9885 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.016        49      15      40 ..      13      38 ..      11      44 .. 0.84
   2 ?    8.2   0.0   0.00085       2.5      34      54 ..      71      91 ..      68      98 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.016
       HHH_2 15 tAklLakrFksldaLkkasleeLlev 40
                + k L +++k+  +L++a++++  ++
  EPA04662.1 13 AVKVLFSKYKNAKELASAKTKDVEKI 38
                568999*************9998875 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00085
       HHH_2 34 leeLlevddiGeeiAqsivef 54
                le+L+e++++G ++A+ +  +
  EPA04662.1 71 LEKLVELPGVGRKTANCVLVY 91
                79**************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       874  (0.0487478); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1138.59
//
Query:       EPA04663.1  [L=175]
Description: putative endonuclease III, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.3e-25   87.2   0.1    1.3e-24   86.7   0.1    1.2  1  HhH-GPD        HhH-GPD superfamily base excision DNA repair p
    1.1e-08   34.5   0.0    2.4e-08   33.4   0.0    1.6  1  HHH            Helix-hairpin-helix motif
     0.0025   18.4   0.7       0.46   11.1   0.1    2.3  2  HHH_5          Helix-hairpin-helix domain
     0.0039   17.2   0.1      0.018   15.1   0.0    1.8  2  DUF2400        Protein of unknown function (DUF2400)
     0.0095   15.3   2.5      0.042   13.2   2.5    1.9  1  AGOG           N-glycosylase/DNA lyase
  ------ inclusion threshold ------
      0.014   15.5   0.0        2.5    8.2   0.0    2.3  2  HHH_2          Helix-hairpin-helix motif
        1.7    9.1   4.0        2.9    8.4   4.0    1.4  1  EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III


Domain annotation for each model (and alignments):
>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.7   0.1   5.2e-28   1.3e-24       5     107 ..       1     131 [.       1     132 [. 0.97

  Alignments for each domain:
  == domain 1  score: 86.7 bits;  conditional E-value: 5.2e-28
                 HHTTS-HHHHHHHHHHHHHHHSHCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH...............................S-SSS- CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...............................xxxxxx RF
     HhH-GPD   5 lsqqtsderanriierlferfgfptpedladadeekLrelirelGfyrrKakyikelArilv...............................gkpdvl 72 
                 ls++t+de+++++++ lf++++  ++++la+a  ++++++i+++Gfy+ K k+i+e+A+i+                                ++ +++
  EPA04663.1   1 LSARTKDETTTKAVKVLFSKYK--NAKELANAKTKDVEKIIKSIGFYHVKSKRIIEVAKIINskykgkvpdnleklvelpgvgrktancvlvyAFDKPA 97 
                 79******************99..*********************************************************************77789* PP

                 -TTSHHHHHHHHHHTTSSSSTTHHHHHHHHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
     HhH-GPD  73 ivvDvhvrrilkrlrsikekktkkkvekkleelle 107
                 i+vD+hv+ri +rl+++++ kt++++e++l+++++
  EPA04663.1  98 IPVDIHVHRISNRLGLVDT-KTPEETEQELMRIIP 131
                 *******************.6*********99987 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.0   9.2e-12   2.4e-08       1      30 []      62      91 ..      62      91 .. 0.94

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 9.2e-12
                SHHHHHTSSHHHHHTSTT-SHHHHHHHHHH CS
         HHH  1 sleglipasreeLlalPGVGpktAeaIlsy 30
                +++g +p+++e L++lPGVG+ktA+++l y
  EPA04663.1 62 KYKGKVPDNLEKLVELPGVGRKTANCVLVY 91
                589************************976 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.3    0.0064        16      13      56 ..      12      57 ..      10      58 .. 0.78
   2 !   11.1   0.1   0.00018      0.46      33      48 ..      70      85 ..      49      90 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0064
                HHHHHHHTTT--SHHHHHHS...-HHHHHTSTTS-HHHHHHHHHHHH CS
       HHH_5 13 ktAlallsaGiesvedlaaa...dveeLakipGiGkktAeriilelk 56
                k ++ l s+ ++   +la+a   dve++ k  G+   + +rii+ +k
  EPA04663.1 12 KAVKVLFSK-YKNAKELANAktkDVEKIIKSIGFYHVKSKRIIEVAK 57
                556667788.99999**998666788888878998999999998765 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00018
                -HHHHHTSTTS-HHHH CS
       HHH_5 33 dveeLakipGiGkktA 48
                + e+L ++pG+G ktA
  EPA04663.1 70 NLEKLVELPGVGRKTA 85
                568999*********9 PP

>> DUF2400  Protein of unknown function (DUF2400)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.32   8.3e+02      56      74 ..      31      49 ..       4      80 .. 0.42
   2 !   15.1   0.0   6.9e-06     0.018     172     195 ..      97     120 ..      92     137 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.32
     DUF2400 56 eeekdlkelekfkyRffns 74
                ++++  k ++++ +  ++s
  EPA04663.1 31 KTKDVEKIIKSIGFYHVKS 49
                1111111122222222233 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 6.9e-06
     DUF2400 172 iiPlDvHvarvarklgllkrkqad 195
                  iP+D+Hv+r++++lgl+++k+ +
  EPA04663.1  97 AIPVDIHVHRISNRLGLVDTKTPE 120
                 59****************988754 PP

>> AGOG  N-glycosylase/DNA lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   2.5   1.6e-05     0.042     159     212 ..      86     139 ..       3     142 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.6e-05
                 TS-----TTS-.----HHHHHHHHHTTS-SS-HHHHHHTHCCHCS.HHHHHHHHH CS
        AGOG 159 geeiplpfeip.iPvDvRiakltktsglielknekklarkelvqeevieaWkevs 212
                 +    ++f+ p iPvD  +++++   gl+++k+ ++ +++el++ +++++W ++ 
  EPA04663.1  86 NCVLVYAFDKPaIPVDIHVHRISNRLGLVDTKTPEE-TEQELMRIIPKKFWIDIN 139
                 4556677776669******************99988.8899**********9885 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.011        29      15      40 ..      13      38 ..      11      45 .. 0.84
   2 ?    8.2   0.0   0.00099       2.5      34      54 ..      71      91 ..      68      98 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.011
       HHH_2 15 tAklLakrFksldaLkkasleeLlev 40
                + k L +++k+  +L++a++++  ++
  EPA04663.1 13 AVKVLFSKYKNAKELANAKTKDVEKI 38
                568999*************9998875 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00099
       HHH_2 34 leeLlevddiGeeiAqsivef 54
                le+L+e++++G ++A+ +  +
  EPA04663.1 71 LEKLVELPGVGRKTANCVLVY 91
                79**************99765 PP

>> EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   4.0    0.0011       2.9       1      17 []     150     166 ..     150     166 .. 0.97

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0011
  EndIII_4Fe-2S   1 CTARkPkCeaCPLaDlC 17 
                    C++ +P C  C + + C
     EPA04663.1 150 CKPISPMCSVCKIKNDC 166
                    *************9999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       921  (0.0513693); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 1301.29
//
Query:       EPA04664.1  [L=369]
Description: copper binding protein, plastocyanin/azurin family, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.8e-18   64.4   2.1    3.6e-09   37.0   0.2    2.5  2  Copper-bind   Copper binding proteins, plastocyanin/azurin fa
    3.1e-14   52.9   0.0    6.7e-06   26.2   0.0    2.6  2  Cupredoxin_1  Cupredoxin-like domain
  ------ inclusion threshold ------
       0.59   10.6  29.4       0.06   13.9  16.1    2.4  2  TonB_N        TonB polyproline region
        1.8    8.5  27.2       0.19   11.7  17.2    2.9  2  Trypan_PARP   Procyclic acidic repetitive protein (PARP)


Domain annotation for each model (and alignments):
>> Copper-bind  Copper binding proteins, plastocyanin/azurin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.2   8.1e-13   3.6e-09       9      98 ..     136     215 ..     130     216 .. 0.92
   2 !   26.7   0.1   1.2e-09   5.5e-06      14      99 .]     294     369 .]     284     369 .] 0.85

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 8.1e-13
                  TETSEEESSEEEEETTEEEEEEEESSSSBEEEEETTSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEESSEEEEEEETTTTTTTSEEEEEE CS
  Copper-bind   9 sgdlqFetkeitvkkgekvtfvnlavmgHNvvldkdgvpagvdkdkvkaedetkliggGekdsvtfdeagtYkffCsPHaaagMkgkvtv 98 
                   ++  +++ +i+++  ++v++ n +  +H v   kd  p+gv ++ + ++        G++++ tfd++gtY +fC  H    M g+v+v
   EPA04664.1 136 TTSTCYSPDSIEIQVDDTVMWSNDDTAAHTVTSGKDVTPDGVFDSSLFMS--------GNTFEYTFDKTGTYPYFCMVHP--WMTGQVIV 215
                  555679***********************************999998885........**********************..69****98 PP

  == domain 2  score: 26.7 bits;  conditional E-value: 1.2e-09
                  EESSEEEEETTEEEEEEEESSSSBEEEEETTSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEESSEEEEEEETTTTTTTSEEEEEEE CS
  Copper-bind  14 FetkeitvkkgekvtfvnlavmgHNvvldkdgvpagvdkdkvkaedetkliggGekdsvtfdeagtYkffCsPHaaagMkgkvtve 99 
                  + + + ++++ge++ ++n+++ +H v   kd+ ++g  ++ + +        + ++ +  fd++g+Y++fC  H    M gkv+v+
   EPA04664.1 294 YLPYQAEINSGESIIWTNTDSAAHTVTSGKDATSDGNFDSGMMI--------PKNTWEHMFDKPGEYDYFCMLHP--WMTGKVVVN 369
                  7788899*************************977755554444........34689******************..69****996 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   1.5e-09   6.7e-06      28     104 .]     137     215 ..     117     215 .. 0.90
   2 !   24.2   0.0     6e-09   2.7e-05      29     104 .]     291     368 ..     268     368 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 1.5e-09
  Cupredoxin_1  28 kdggfePskievkagekvklkiknkdktpeefesed......lgeekvlapgktttitiaplkpGeYeftcdmhmdakGkliV 104
                   +++ ++P++ie++ +   ++++ n+d+ +++++s +      +  +   ++g+t++ t+  +k G+Y+++c  h+ + G++iV
    EPA04664.1 137 TSTCYSPDSIEIQVDD--TVMWSNDDTAAHTVTSGKdvtpdgVFDSSLFMSGNTFEYTF--DKTGTYPYFCMVHPWMTGQVIV 215
                   4568***********9..99**************99999997556677799********..**************99*****9 PP

  == domain 2  score: 24.2 bits;  conditional E-value: 6e-09
  Cupredoxin_1  29 dggfePskievkagekvklkiknkdktpeefesed.......lgeekvlapgktttitiaplkpGeYeftcdmhmdakGkliV 104
                   ++ + P + e+++ge  ++ ++n+d+ +++++s +       ++      p++t +  +  +kpGeY+++c +h+ + Gk++V
    EPA04664.1 291 NECYLPYQAEINSGE--SIIWTNTDSAAHTVTSGKdatsdgnFDS-GMMIPKNTWEHMF--DKPGEYDYFCMLHPWMTGKVVV 368
                   56799**********..99**************999999944443.3444555666666..**************99*****9 PP

>> TonB_N  TonB polyproline region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   5.2     0.052   2.3e+02      42      66 ..      99     127 ..      74     135 .. 0.48
   2 ?   13.9  16.1   1.3e-05      0.06      37      80 ..     231     269 ..     212     292 .. 0.67

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.052
                 X..XXXXXXX..X..XXXXXXXXXXXXXX CS
      TonB_N  42 vepePePePE..v..vPePpapvviekPk 66 
                  +peP P+PE  v  +P  p+ v++++P+
  EPA04664.1  99 KSPEPVPIPEkpVmaMPVAPQTVTVSIPQ 127
                 23555555553221133333445555555 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 1.3e-05
                 XXXXXX..XXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXX CS
      TonB_N  37 apePavepePePePEvvPePpapvviekPkPePkPkPkPkpvkk 80 
                 +p+P ++ eP P  E++PeP     i+ P+P P+P P P p +k
  EPA04664.1 231 EPNPSAPVEPAPTNEPAPEP-----IPAPEPTPEPAPVPEPTEK 269
                 34555555666666666666.....3556666666666666655 PP

>> Trypan_PARP  Procyclic acidic repetitive protein (PARP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   2.2     0.094   4.2e+02      11      49 ..       8      46 ..       1     134 [. 0.51
   2 ?   11.7  17.2   4.2e-05      0.19      76     112 ..     231     267 ..     216     283 .. 0.63

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.094
  Trypan_PARP 11 illfsanlfagvgfaaaaegpedkgltkggkgk.ekgtkv 49
                 il  s+n+++g+    +a +p + +  kg  g  +k  k 
   EPA04664.1  8 ILAPSSNMYSGIVSY-SASEPIQLVALKGPIGPdDKPEKT 46
                 444577777776433.344555566666655543444333 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 4.2e-05
  Trypan_PARP  76 epepetepeeepepepepepepepepepepepepepg 112
                  ep+p +  e+ p +ep pep p pep pep p pep 
   EPA04664.1 231 EPNPSAPVEPAPTNEPAPEPIPAPEPTPEPAPVPEPT 267
                  4555445555555666666666666666666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2336.58
//
Query:       EPA04665.1  [L=205]
Description: hypothetical protein BG20_I2442, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   12.7   0.3       0.45   10.8   0.0    1.9  2  DUF3040   Protein of unknown function (DUF3040)
       0.53   10.5   2.4        0.5   10.5   0.3    1.9  2  DUF2371   Uncharacterised conserved protein (DUF2371)
        1.3    9.2   7.6        0.2   11.8   1.4    2.2  2  YtpI      YtpI-like protein


Domain annotation for each model (and alignments):
>> DUF3040  Protein of unknown function (DUF3040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.2      0.37   2.2e+03      70      80 ..      12      22 ..       5      32 .. 0.52
   2 ?   10.8   0.0   7.6e-05      0.45      20      65 ..     147     190 ..     144     194 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.37
     DUF3040 70 lgvvGfvvmla 80
                +gv+G++++++
  EPA04665.1 12 IGVFGLMLVAI 22
                44444433332 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 7.6e-05
     DUF3040  20 aeDPklaaalrggaararrrslrrlavlavllfvaGllllvlGvaa 65 
                 +eDP+  +a+++ +   r+  +   +v+++ll+++G+++l++G+++
  EPA04665.1 147 SEDPDNSDAFTNPNFPLRN--TIVPLVISALLLIFGIIILIVGIIL 190
                 7999999999444444333..34448999999999********764 PP

>> DUF2371  Uncharacterised conserved protein (DUF2371)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       0.3   1.8e+03      44      57 ..      13      26 ..       3      41 .. 0.56
   2 ?   10.5   0.3   8.3e-05       0.5      38      63 ..     171     196 ..     163     204 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.3
     DUF2371 44 lllGllvllvGiam 57
                 ++Gl+++++ i++
  EPA04665.1 13 GVFGLMLVAISISI 26
                33444444443333 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 8.3e-05
     DUF2371  38 svsglvlllGllvllvGiamavlgyw 63 
                  +s+l+l++G+++l+vGi + ++ + 
  EPA04665.1 171 VISALLLIFGIIILIVGIILYLIDWK 196
                 5799**************99877655 PP

>> YtpI  YtpI-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.5      0.12   6.9e+02      38      52 ..      15      29 ..      12      36 .. 0.77
   2 ?   11.8   1.4   3.4e-05       0.2      50      79 ..     161     190 ..     155     193 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.12
        YtpI 38 lGlflilfginqlll 52
                +Gl+l++++i  +++
  EPA04665.1 15 FGLMLVAISISIMVS 29
                788999999887775 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 3.4e-05
        YtpI  50 llllestvalvvgavflvlGlanlfaGira 79 
                 + l ++ v lv++a++l++G++ l+ Gi+ 
  EPA04665.1 161 FPLRNTIVPLVISALLLIFGIIILIVGIIL 190
                 6678999********************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1184  (0.0660383); expected 358.6 (0.02)
Passed bias filter:                      721  (0.0402142); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1531.80
//
Query:       EPA04666.1  [L=101]
Description: nucleic acid-binding domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-06   26.1   0.3    7.8e-06   25.8   0.3    1.2  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
    6.4e-05   22.8   0.8    7.2e-05   22.6   0.8    1.1  1  REPA_OB_2        Replication protein A OB domain
  ------ inclusion threshold ------
      0.032   14.4   0.7        4.3    7.6   0.4    2.1  2  HupF_HypC        HupF/HypC family


Domain annotation for each model (and alignments):
>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.3   1.3e-09   7.8e-06       3      69 ..      19      89 ..      17      99 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 1.3e-09
                     EEEEEEEEE........EEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEE.EEEEECTTSSEEEE CS
  tRNA_anti-codon  3 vaGrvtsis........drsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvt.Grvkrrpggelelk 69
                     ++++v+s+         ++++  v+++++ D++++i+++l+     +  + + +Gdvv +t G+ ++++g+ ++l+
       EPA04666.1 19 LKAEVKSKGdprtvnlkTGGTVDVCDAVIADESDEIKLTLWG----DDIKAVNVGDVVVITnGYTNEFKGE-VSLT 89
                     677888888888888888889999******************....999*******************998.8875 PP

>> REPA_OB_2  Replication protein A OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.8   1.2e-08   7.2e-05      17      97 ..      21      98 ..       5      99 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.2e-08
   REPA_OB_2 17 gvvksveevseitskstekelkkreltlvDesgasvevtlWgkeaekfesseepvvalkgvkvsdFgg.rslsllssstlkv 97
                + vks ++ ++++ k+++ +++ ++  + Des  ++++tlWg++ + +  +  +vv++ ++  ++F+g  sl+  + +++++
  EPA04666.1 21 AEVKSKGDPRTVNLKTGG-TVDVCDAVIADESD-EIKLTLWGDDIKAV--NVGDVVVITNGYTNEFKGeVSLTKGKFGKMEI 98
                5689999999*****999.9***********97.7********98885..5889**************66776666666665 PP

>> HupF_HypC  HupF/HypC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0014       8.5       8      43 ..       9      47 ..       6      49 .. 0.82
   2 ?    7.6   0.4   0.00072       4.3      22      48 ..      48      78 ..      39      82 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0014
                EEEEEET...TEEEEECTTEEEEEEGTTCTTB-TT-EEE CS
   HupF_HypC  8 kvveied...elAlvdvgGvrrevslalveevkvGdyVL 43
                +v ++       A v+ +G  r+v+l+  + v v d V+
  EPA04666.1  9 QVKKMRSginLKAEVKSKGDPRTVNLKTGGTVDVCDAVI 47
                566666655458***************999999999998 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00072
                TTEEEEEEGTTC....TTB-TT-EEEEETTE CS
   HupF_HypC 22 gGvrrevslalv....eevkvGdyVLvhvGf 48
                 +++ e++l l     + v+vGd V++  G+
  EPA04666.1 48 ADESDEIKLTLWgddiKAVNVGDVVVITNGY 78
                478899999999877777*********9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 633.46
//
Query:       EPA04667.1  [L=298]
Description: CBS domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.4e-48  161.3  15.4    1.2e-12   48.1   0.4    4.1  4  CBS            CBS domain
  ------ inclusion threshold ------
      0.015   15.3   0.8      0.024   14.6   0.3    1.8  1  Peptidase_S55  SpoIVB peptidase S55
      0.041   13.5   2.6      0.075   12.7   2.4    1.6  1  EMC1_C         ER membrane protein complex subunit 1, C-termi
      0.042   13.6   9.5        2.3    7.9   0.6    3.8  4  PduV-EutP      Ethanolamine utilisation - propanediol utilisa
      0.054   12.6   1.6        0.1   11.7   1.1    1.7  2  Phytoreo_Pns   Phytoreovirus nonstructural protein Pns10/11
        0.1   12.7   0.0        3.4    7.7   0.0    2.3  2  DUF3641        Protein of unknown function (DUF3641)
       0.24   10.5   1.0       0.31   10.2   1.0    1.3  1  SPAN           Surface presentation of antigens protein


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.4     3e-12   7.7e-09       6      53 ..      21      67 ..      15      70 .. 0.87
   2 !   48.1   0.4   4.6e-16   1.2e-12       1      53 [.      82     134 ..      82     138 .. 0.94
   3 !   43.4   0.1   1.4e-14   3.5e-11       2      52 ..     147     196 ..     146     198 .. 0.92
   4 !   43.1   0.3   1.7e-14   4.4e-11       1      56 [.     238     292 ..     238     293 .. 0.94

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 3e-12
                BSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTT.BEEEEEEHHHHHH CS
         CBS  6 trdvvtvppdttleealelmrekgvsrlPVVdedg.klvGivtlrDllr 53
                t+ ++t++p+t++ +a +++ +++++rl VV   g k +Gi+t++D+++
  EPA04667.1 21 TKIPITISPNTSILDARDILLRYRIGRL-VVK-LGkKAIGIITEKDIAK 67
                66789**************99*******.**5.5538**********98 PP

  == domain 2  score: 48.1 bits;  conditional E-value: 4.6e-16
                 HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEE.ETTTBEEEEEEHHHHHH CS
         CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVV.dedgklvGivtlrDllr 53 
                 V+d+m++d+vtvp ++++ +++++m+ +++s++ ++ d+ ++lvGi+t++Dl++
  EPA04667.1  82 VKDVMSKDLVTVPSTSSIYDCAKQMITHNISSI-IIkDKRENLVGIITKTDLVS 134
                 89*******************************.99888889**********87 PP

  == domain 3  score: 43.4 bits;  conditional E-value: 1.4e-14
                 HHHSBSSCEEEETTSBHHHHHHH.HHHHTSSEEEEEETTTBEEEEEEHHHHH CS
         CBS   2 gdimtrdvvtvppdttleealel.mrekgvsrlPVVdedgklvGivtlrDll 52 
                 + imt++v+tv+p++++ e+    + ++++sr+ VV +++++vGi+t rD +
  EPA04667.1 147 SKIMTKKVITVSPEESVFEVQSVlF-NNKISRV-VVTKNKRPVGIITYRDFI 196
                 679********************77.777****.9889************86 PP

  == domain 4  score: 43.1 bits;  conditional E-value: 1.7e-14
                 HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
         CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                 ++dimt+++v  +pd +   a+ lm+++g+s++PV+  + +lvGi+t++D++++l+
  EPA04667.1 238 AKDIMTKELVITYPDNDAYTAAILMIRHGISGIPVI-LNQRLVGIITKSDIVNVLA 292
                 68*********************************9.5889***********9986 PP

>> Peptidase_S55  SpoIVB peptidase S55
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.3   9.5e-06     0.024     147     192 ..     238     284 ..     133     291 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9.5e-06
  Peptidase_S55 147 eskekeknlvikvtdeeLlektgG.ivqGmSGsPiiqngklvGavth 192
                     ++  +k+lvi+  d++  +++   i  G+SG P+i n++lvG +t+
     EPA04667.1 238 AKDIMTKELVITYPDNDAYTAAILmIRHGISGIPVILNQRLVGIITK 284
                    4455688888888888876665541557*****************97 PP

>> EMC1_C  ER membrane protein complex subunit 1, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   2.4   2.9e-05     0.075      49     148 ..     122     221 ..      84     242 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.9e-05
      EMC1_C  49 elpevlsqsfifpegikalavttTkkgItskslllalesgqivslprrlldpRrpvrkptaaekeeglipYepllpidpksvishkrevagvkkiltap 147
                 +l  +++++ ++++ +++ +++ +   I +k+++++  ++++++++  l++++ +    t++++  g+i Y  ++p ++++      +  + ++i ++p
  EPA04667.1 122 NLVGIITKTDLVSTFLAQSTASLSISKIMTKKVITVSPEESVFEVQSVLFNNKISRVVVTKNKRPVGIITYRDFIPAKTFDLQKEFTDPTEQDEISSNP 220
                 344457888888888889999999999**************************999778888888************9999888877777777777777 PP

      EMC1_C 148 t 148
                  
  EPA04667.1 221 Q 221
                 6 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.2     0.024        63      88     104 ..      52      68 ..      45      75 .. 0.82
   2 ?    7.9   0.6    0.0009       2.3      88     127 ..     119     158 ..      95     178 .. 0.66
   3 ?   -0.8   0.1      0.44   1.1e+03      87     101 ..     181     195 ..     148     206 .. 0.68
   4 ?    5.6   0.1    0.0048        12      86     102 ..     272     288 ..     257     294 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.024
   PduV-EutP  88 fnkeviGiitkidlaed 104
                 + k+ iGiit  d+a++
  EPA04667.1  52 LGKKAIGIITEKDIAKS 68 
                 67999********9954 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0009
   PduV-EutP  88 fnkeviGiitkidlaedeenieaveelLksaGaekifevs 127
                  + +++Giitk+dl+++  + +++   +++   +k+++vs
  EPA04667.1 119 KRENLVGIITKTDLVSTFLAQSTASLSISKIMTKKVITVS 158
                 34469*********96555555555555566666666665 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.44
   PduV-EutP  87 vfnkeviGiitkidl 101
                 + nk  +Giit  d 
  EPA04667.1 181 TKNKRPVGIITYRDF 195
                 336777899998776 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.0048
   PduV-EutP  86 svfnkeviGiitkidla 102
                  ++n+ ++Giitk d++
  EPA04667.1 272 VILNQRLVGIITKSDIV 288
                 6899***********87 PP

>> Phytoreo_Pns  Phytoreovirus nonstructural protein Pns10/11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.1   3.9e-05       0.1      86     143 ..      66     120 ..      48     183 .. 0.82
   2 ?   -3.1   0.0       1.3   3.3e+03     268     292 ..     254     279 ..     235     293 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.9e-05
  Phytoreo_Pns  86 tksv.llrgkllkdllpygvivaaivyvpetisvldsvrvyienqvkrplsvvllkdaa 143
                   +ksv +  gk +  +l   v+   +v vp t s+ d  + +i  +    +s +++kd  
    EPA04667.1  66 AKSVsIFSGKPIEKILVKDVMSKDLVTVPSTSSIYDCAKQMITHN----ISSIIIKDKR 120
                   45654789*******************************999887....4555666555 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.3
  Phytoreo_Pns 268 haysavil.wrgwastykellsqeql 292
                    ay+a il  r   s    +l+q  +
    EPA04667.1 254 DAYTAAILmIRHGISGIPVILNQRLV 279
                   45554333134444444444444433 PP

>> DUF3641  Protein of unknown function (DUF3641)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0013       3.4      63      94 ..      81     111 ..      72     133 .. 0.77
   2 ?    2.6   0.0     0.051   1.3e+02      52      85 ..     134     167 ..     111     194 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0013
     DUF3641  63 tveklmCrsllsvdwdGklydCdfnqmlelkl 94 
                  v+++m ++l+ v  + ++ydC  +qm+  ++
  EPA04667.1  81 LVKDVMSKDLVTVPSTSSIYDCA-KQMITHNI 111
                 5899******************7.45555444 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.051
     DUF3641  52 lellkeafneetveklmCrsllsvdwdGklydCd 85 
                  ++l+++  + +++k+m ++ + v+ + ++++ +
  EPA04667.1 134 STFLAQSTASLSISKIMTKKVITVSPEESVFEVQ 167
                 467888999999*************999999865 PP

>> SPAN  Surface presentation of antigens protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.0   0.00012      0.31      99     169 ..      49     116 ..      35     184 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00012
        SPAN  99 llkvtaeksvglisaeakvdksaallssknrplesvsgkk.lsadlkavesvsevtdnatgisddnikalpg 169
                 ++k   +k++g+i+ e  + ks +++s k  p+e +  k  +s dl +v s s + d a  +   ni ++  
  EPA04667.1  49 VVK-LGKKAIGIIT-EKDIAKSVSIFSGK--PIEKILVKDvMSKDLVTVPSTSSIYDCAKQMITHNISSIII 116
                 333.4579999885.889********986..9999988863799*****************99999987754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2034.12
//
Query:       EPA04668.1  [L=148]
Description: membrane protein, MgtC / SapB family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.7e-38  130.3  12.2    5.6e-38  130.0  12.2    1.0  1  MgtC      MgtC family
  ------ inclusion threshold ------
        0.1   12.3   0.6       0.11   12.1   0.6    1.2  1  DUF4956   Domain of unknown function (DUF4956)


Domain annotation for each model (and alignments):
>> MgtC  MgtC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.0  12.2   6.2e-42   5.6e-38       1     116 [.      18     133 ..      18     137 .. 0.95

  Alignments for each domain:
  == domain 1  score: 130.0 bits;  conditional E-value: 6.2e-42
        MgtC   1 LllAlllGlliGleRelrekaaGlRTfaLvalgaalfvllslelae..srvaaqvvsgigflgagvilkekegakvkglTTaaslwvtaaiGllvglgl 97 
                 LllA+ lG++iG+eRel++++aGlRT++Lv+lga++f+++sl++    +r+aa++v+gigflgag i++++   +++g+T+aa+lwv+a+iGl+vg+g+
  EPA04668.1  18 LLLAVGLGAIIGFERELKHRPAGLRTHMLVSLGATVFTVISLSFDVdpARIAAGIVTGIGFLGAGNIIAQRG--HIRGVTSAATLWVVAGIGLCVGVGQ 114
                 799*************************************88886699********************6665..8************************ PP

        MgtC  98 yllavvatvlvllllallr 116
                 y++av++++lv+++l+l r
  EPA04668.1 115 YAIAVISALLVFAILQLGR 133
                 ***************9865 PP

>> DUF4956  Domain of unknown function (DUF4956)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.6   1.3e-05      0.11      26     107 ..      46     132 ..      17     147 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.3e-05
     DUF4956  26 flllnvgvfavvlll.....asvevsiglglGLfgvlsilRlRseeisvrevtYlFvaialglinglaslslvellvlnvlivlvla 107
                 ++ l+++vf+v++l      a++ ++i +g+G +g   i+  R +   v   + l+v+  +gl+ g+++  ++ + +l v  +l l 
  EPA04668.1  46 LVSLGATVFTVISLSfdvdpARIAAGIVTGIGFLGAGNIIAQRGHIRGVTSAATLWVVAGIGLCVGVGQYAIAVISALLVFAILQLG 132
                 45566778888877667777777777779*************************************987777666666665555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 855.20
//
Query:       EPA04669.1  [L=37]
Description: hypothetical protein BG20_I1672, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       255  (0.0142228); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.28s 00:00:00.64 Elapsed: 00:00:00.44
# Mc/sec: 255.39
//
Query:       EPA04670.1  [L=219]
Description: protein-L-isoaspartate O-methyltransferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.8e-58  195.9   0.0    8.5e-58  195.6   0.0    1.0  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
      2e-08   34.1   0.0    3.4e-08   33.4   0.0    1.3  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
    5.5e-08   32.7   0.0    8.6e-08   32.1   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    2.5e-07   30.0   0.0    3.8e-07   29.4   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
    3.1e-06   27.8   0.0    5.2e-06   27.1   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
    8.6e-05   23.1   0.0    0.00014   22.5   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    0.00033   20.4   0.0    0.00049   19.8   0.0    1.2  1  GCD14            tRNA methyltransferase complex GCD14 subunit
     0.0017   18.0   0.0      0.003   17.1   0.0    1.3  1  DOT1             Histone methylation protein DOT1
     0.0029   16.9   0.0     0.0042   16.4   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
     0.0056   16.0   0.1      0.011   15.0   0.0    1.5  2  GidB             rRNA small subunit methyltransferase G
     0.0074   15.8   0.0      0.014   15.0   0.0    1.3  1  MTS              Methyltransferase small domain
     0.0094   16.0   0.0        7.3    6.7   0.0    3.0  3  Lambda_CIII      Lambda Phage CIII
  ------ inclusion threshold ------
      0.019   14.4   0.0      0.028   13.9   0.0    1.3  1  Methyltransf_4   Putative methyltransferase
      0.029   13.5   0.0      0.047   12.8   0.0    1.3  1  Fibrillarin      Fibrillarin
      0.049   13.0   0.0      0.058   12.7   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
      0.064   13.2   0.0       0.09   12.8   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
       0.08   12.9   0.0       0.15   12.0   0.0    1.5  1  Methyltransf_18  Methyltransferase domain
      0.088   12.6   0.0       0.12   12.2   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
       0.12   12.2   0.0       0.18   11.6   0.0    1.2  1  DUF938           Protein of unknown function (DUF938)


Domain annotation for each model (and alignments):
>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.6   0.0     9e-61   8.5e-58       4     208 ..      12     214 ..       9     216 .. 0.97

  Alignments for each domain:
  == domain 1  score: 195.6 bits;  conditional E-value: 9e-61
                 HHHHHHHHHTTS---HHHHHHHHHS-GGGGSSCGGGGGTTSSS-EEEETTEEE--HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEE CS
        PCMT   4 ealieelkkkgviksdkvaealeevdReefvpesfkekaYedaplsigynatiSaphmvalalellelkkgarvLevGsGsGyltavlarlvgekgrvv 102
                 ++li  +kk+g+++++kv  a+++++R+efvp ++ +kaY+d+p+ i  n+tiS+p++v++++e+l++++g+++Le+GsGsG++ta+la lvg  + v 
  EPA04670.1  12 DNLILVMKKSGFLNDKKVELAIRNTPRHEFVPITLIKKAYDDSPILIMKNQTISQPSVVSRMTEWLDVEEGQKILEIGSGSGWQTAILAYLVGCGM-VY 109
                 679999***************************************************************************************866.** PP

                 EEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTTGGG-SEEEEEESSBBSS--HHHHHTEEEEEEEEEEESBSSSEEEEEEEEETTTEEEEEEEEEE- CS
        PCMT 103 sierikelveeakrnlkkldlenvivvvgDGrkGyeekaPYdaihvgaaapeiPealidQLkeGGrlvvPvgeeeeQvlklvdkkadgkvvikkleevr 201
                 s+er  el+e ak+nl kl+++n +v+ gDG  G++e++P+d+i+++aa +++P++l++QL   G l++Pvg  + Q + l++k++ g ++ik++   +
  EPA04670.1 110 SVERHSELAEFAKKNLDKLGITNAKVISGDGSFGFPEESPFDRIIITAACKKVPDSLLEQLSINGLLIAPVG-GYPQSMVLLKKTSTGIIEIKNQPGYV 207
                 ************************************************************************.************************** PP

                 --B-BCC CS
        PCMT 202 fvpltdk 208
                 fvp  +k
  EPA04670.1 208 FVPFLGK 214
                 ***8766 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.0   3.6e-11   3.4e-08       3      90 ..      76     160 ..      74     163 .. 0.92

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 3.6e-11
                      HH---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC..EEEEEEEE--C CS
  Methyltr_RsmB-F   3 lLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggelfDriLlDaPCs 90 
                      +L+ +e+++il++ ++ G +T+ +a l+   g v+ v++++e ++  ++nl +Lg+tn++v+++D++    +  ++ fDri++ a C 
       EPA04670.1  76 WLDVEEGQKILEIGSGSGWQTAILAYLV-GCGMVYSVERHSELAEFAKKNLDKLGITNAKVISGDGSFG--FPEESPFDRIIITAACK 160
                      899************************5.5699*********************************976..666777********995 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.0   9.2e-11   8.6e-08       3      89 ..      81     164 ..      79     193 .. 0.86

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 9.2e-11
  Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDlilsnevlnalad 89 
                      +g ++l++G+G+G  t  la ++g  + v+++++  e  e+A++n++klg++n+++  gd    +++    ++fD i+  +++  ++d
       EPA04670.1  81 EGQKILEIGSGSGWQTAILAYLVG-CGMVYSVERHSELAEFAKKNLDKLGITNAKVISGDGSFgFPEE---SPFDRIIITAACKKVPD 164
                      5789****************6555.699********************************9999**54...99***999766655554 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0     4e-10   3.8e-07      14      85 ..      65     140 ..      59     162 .. 0.88

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 4e-10
                 --HHHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-..SEEEEE-S-HHHHHHHHCHTT..TCCCEEEE-S-C CS
      RrnaAD  14 knkkvineIldklnleekltvleigpGkGilTeeLakra..kqvvvlElderLakllqkkls..kdeklkvvhqDf 85 
                   ++v+ +  + l++ee +++leig+G G +T++La  +    v ++E  ++La++ +k+l     ++ kv+  D+
  EPA04670.1  65 SQPSVVSRMTEWLDVEEGQKILEIGSGSGWQTAILAYLVgcGMVYSVERHSELAEFAKKNLDklGITNAKVISGDG 140
                 568899999999***********************99998899****************99987788999998886 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   5.5e-09   5.2e-06       1      79 [.      85     164 ..      85     171 .. 0.86

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 5.5e-09
                      EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCG.BSSSTTTEEEEEEESTGGGSSH CS
  Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaed.lpfedgsfDlvvssgalhhlsd 79 
                      +L++G G+G  t+ la  +g + v+ v+  +e+ e a++++++ g+ n++++ gd +  +p e++ fD ++++ a   ++d
       EPA04670.1  85 ILEIGSGSGWQTAILAYLVGCGMVYSVERHSELAEFAKKNLDKLGItNAKVISGDGSFgFP-EESPFDRIIITAACKKVPD 164
                      8***************9999**********************9999*********966255.566******9755655554 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   1.4e-07   0.00014       1      76 [.      86     164 ..      86     171 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.4e-07
                      EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT.-EEEEEEES-CCC-CC CS
  Methyltransf_11   1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseegl.kvefvvadaeklpfedn.sfDlvvssevlhhved 76 
                      L++G+G+G  ++ la  +  + v+ v+   e+ + ak++  + g+ + +++ +d + + f+++  fD ++++ +   v+d
       EPA04670.1  86 LEIGSGSGWQTAILAYLVgcGMVYSVERHSELAEFAKKNLDKLGItNAKVISGDGS-FGFPEEsPFDRIIITAACKKVPD 164
                      89*************55569************************999999999999.89999726*****9999888854 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   5.2e-07   0.00049      29      92 ..      70     132 ..      56     146 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 5.2e-07
       GCD14  29 isliimkLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsq 92 
                 +s ++  L++++G +++e G Gsg   +ai+  +   G ++++e h + ae+a++++ + ++++
  EPA04670.1  70 VSRMTEWLDVEEGQKILEIGSGSGWQ-TAILAYLVGCGMVYSVERHSELAEFAKKNLDKLGITN 132
                 5778899****************975.5666677779*******************99988865 PP

>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   3.2e-06     0.003      28      88 ..      67     127 ..      64     136 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.2e-06
                 HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHH--SEEEEEE--HHHHHHHHHHHHH CS
        DOT1  28 peflsevldkvnlkkedvFvDLGSGvGnvvlqaalevgcklsvGvEimdnaselaekqkee 88 
                 p+++s++ + +++++ +  +++GSG G  +   a  vgc + + vE   + +e+a+k+ + 
  EPA04670.1  67 PSVVSRMTEWLDVEEGQKILEIGSGSGWQTAILAYLVGCGMVYSVERHSELAEFAKKNLDK 127
                 78999**************************************************998765 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   4.5e-06    0.0042      49     135 ..      68     157 ..      60     170 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4.5e-06
                 HHHHHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--.EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG---..--SEEEEES CS
        CMAS  49 aKldlileklelkpGmtlLdiGcGWGslvrraverydv.kvvglTlSkeqaklakkrvdeldlerkvevklldyedlde..kvdrvvsvg 135
                 + + ++ e l++++G+++L+iG G G  +   +   +   v ++   +e a+ akk++d+l++++ + ++  +   ++e  ++dr++   
  EPA04670.1  68 SVVSRMTEWLDVEEGQKILEIGSGSGWQTAILAYLVGCgMVYSVERHSELAEFAKKNLDKLGITNAKVISGDGSFGFPEesPFDRIIITA 157
                 556778899************99877544444433333257788888888999****************999999999988999998655 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       2.8   2.6e+03      82     100 ..      18      36 ..      13      37 .. 0.86
   2 !   15.0   0.0   1.2e-05     0.011      45     126 ..      79     160 ..      58     201 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.8
                 HHHHHHHHHHHHHCT-SSE CS
        GidB  82 ekkiaFLeevkeelklenv 100
                  kk  FL+  k el++ n+
  EPA04670.1  18 MKKSGFLNDKKVELAIRNT 36 
                 5999999999999999885 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.2e-05
                 S-CCC-.EEEETSTTTTTHHHHHHH-TTSEEEEEES-HHHHHHHHHHHHHCT-SSEEEEES-CCC.TTTTT-EEEEEEC-SSS CS
        GidB  45 lkekrdkviDvGsGaGlPGipLaiarpelkltLleslekkiaFLeevkeelklenveivearaee.kqeeekydvvtsRAlas 126
                 ++e + k++ +GsG G    +La +     ++ +e+++  ++F ++   +l+++n +++  +    + ee+++d +++ A ++
  EPA04670.1  79 VEEGQ-KILEIGSGSGWQTAILAYLVGCGMVYSVERHSELAEFAKKNLDKLGITNAKVISGDGSFgFPEESPFDRIIITAACK 160
                 55566.7*****************************************************99887899999999999988664 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.5e-05     0.014      25     102 ..      75     154 ..      70     156 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.5e-05
                 HHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTST.TS-EEEEE CS
         MTS  25 etlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleeve.ekkfdliv 102
                 e l+ e+ +k+l +G+G G  +a la       v  v+ + +  e+ak+nl + ++  ++v+  d+   ++ e  fd i+
  EPA04670.1  75 EWLDVEEGQKILEIGSGSGWQTAILAYLVGCGMVYSVERHSELAEFAKKNLDKLGITnAKVISGDGSFGFPeESPFDRII 154
                 678888999***********************************************99*******999887355688887 PP

>> Lambda_CIII  Lambda Phage CIII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       3.5   3.3e+03      13      25 ..      65      77 ..      63      88 .. 0.75
   2 !    6.7   0.0    0.0077       7.3       4      34 ..     136     164 ..     134     169 .. 0.82
   3 ?    5.7   0.0     0.016        15      32      40 ..     197     205 ..     178     207 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3.5
  Lambda_CIII 13 pqESlLdRitrkl 25
                 +q S  +R+t+ l
   EPA04670.1 65 SQPSVVSRMTEWL 77
                 6779999999755 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0077
  Lambda_CIII   4 iAGwpvaGvpqESlLdRitrklRegwkrlid 34 
                  i G    G p+ES  dRi   + + +k++ d
   EPA04670.1 136 ISGDGSFGFPEESPFDRII--ITAACKKVPD 164
                  6788889***********6..8899999876 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.016
  Lambda_CIII  32 lidiLNQPG 40 
                  +i+i NQPG
   EPA04670.1 197 IIEIKNQPG 205
                  9*******9 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0     3e-05     0.028       4      60 ..      84     140 ..      81     162 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3e-05
                     EEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-C CS
  Methyltransf_4   4 vvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgda 60 
                      +leiG+G+G+ +  lA       +  +E ++++ + + k+ ++l+++N +++ gd 
      EPA04670.1  84 KILEIGSGSGWQTAILAYLVGCGMVYSVERHSELAEFAKKNLDKLGITNAKVISGDG 140
                     589***************************************************997 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   4.9e-05     0.047      65     104 ..      76     114 ..      66     128 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.9e-05
                  --S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESS CS
  Fibrillarin  65 elpikkgskvLYlGaasGttvsHvsDivgeegvvyavefs 104
                   l +++g+k+L +G++sG   + ++ +vg  g+vy+ve  
   EPA04670.1  76 WLDVEEGQKILEIGSGSGWQTAILAYLVG-CGMVYSVERH 114
                  46799************************.9******965 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   6.2e-05     0.058      43     133 ..      77     166 ..      46     215 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.2e-05
                      --S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES-GGG-S-HH CS
  Ubie_methyltran  43 vavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtvsfGlrnvtDkl 133
                        v +g+k+l++ +G+g  ++ l+  vg  g v  ++  +++ + ++k l + g +n + + +++     e+  fD + ++   + v+D l
       EPA04670.1  77 LDVEEGQKILEIGSGSGWQTAILAYLVG-CGMVYSVERHSELAEFAKKNLDKLGITNAKVISGDGSFGFPEESPFDRIIITAACKKVPDSL 166
                      45789************88888887776.699*******************************99765555678*******9999999975 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   9.5e-05      0.09      12      78 ..      69     130 ..      60     148 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.5e-05
  Methyltransf_32  12 lvakllkelakesgaltvvDvGaGkgYLsfvlalkeke.yklkvvgidakeelvekaekraeklgkkf 78 
                      +v+++++   + ++ ++++++G+G g+ + +la+         v++++ ++el+e a+k  +klg  +
       EPA04670.1  69 VVSRMTEW-LDVEEGQKILEIGSGSGWQTAILAY---LvGCGMVYSVERHSELAEFAKKNLDKLG--I 130
                      55665555.57778899*****************...536789****************999999..3 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00016      0.15      12      89 ..      79     156 ..      70     196 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00016
  Methyltransf_18  12 vekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklkeee.vdtvvia 89 
                      ve+g++++ iG+  g  ++ l+    +  v+ ++ +++  e ak+n++k g++ + +v+ +dG   + ee+ +d ++i 
       EPA04670.1  79 VEEGQKILEIGSGSGWQTAILAYLVGCGMVYSVERHSELAEFAKKNLDKLGIT-NAKVISGDGSFGFPEESpFDRIIIT 156
                      78899*****************99***************************96.69*******9999988889999996 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00013      0.12      21     102 ..      80     170 ..      57     192 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
  Methyltransf_23  21 raggrvLdiGcGtG.illevlrengf.svtgvDlspeaveiae............kakkaqkdqfdeqeaaepqgkfdlIvlrevlehvpd.pp 99 
                      ++g+++L+iG G+G  ++ ++   g+  v+ v+  +e+ e a+             ++   +  f      +++  fd I+ +  +  vpd + 
       EPA04670.1  80 EEGQKILEIGSGSGwQTAILAYLVGCgMVYSVERHSELAEFAKknldklgitnakVISGDGSFGF------PEESPFDRIIITAACKKVPDsLL 167
                      57789*********5566666778**8888****8887776656666665554332222222223......55669999999999999987344 PP

  Methyltransf_23 100 ell 102
                      e l
       EPA04670.1 168 EQL 170
                      444 PP

>> DUF938  Protein of unknown function (DUF938)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00019      0.18      24      78 ..      80     134 ..      62     136 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00019
      DUF938  24 kttervLEiasGtGqHAvffApalpnlkwqpsdqdeelresiaawadelalsnlk 78 
                 ++++++LEi+sG+G   + +A ++   +  + + ++el e  ++ +d+l+++n k
  EPA04670.1  80 EEGQKILEIGSGSGWQTAILAYLVGCGMVYSVERHSELAEFAKKNLDKLGITNAK 134
                 23448*********99999999999888888888888888888888888888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1658.72
//
Query:       EPA04671.1  [L=55]
Description: hypothetical protein BG20_I1677 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.011   15.6   3.2      0.014   15.2   3.2    1.2  1  zf-C3HC4  Zinc finger, C3HC4 type (RING finger)


Domain annotation for each model (and alignments):
>> zf-C3HC4  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   3.2     8e-07     0.014       2      32 ..       7      34 ..       7      44 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 8e-07
                TTT-S--SS-E.E-TTS--B-CHHHHHHHHC CS
    zf-C3HC4  2 piCleeakepnelleCkHsfCskCirkilks 32
                +iCl++ k+++  ++C H +C +C++k+l+ 
  EPA04671.1  7 HICLTKSKIKK--SDCLH-LCIPCYDKVLEL 34
                7********99..*****.6********995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 354.39
//
Query:       EPA04672.1  [L=70]
Description: hypothetical protein BG20_I1673 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      0.008   16.2   1.4      0.012   15.7   0.8    1.5  2  FlpD         Methyl-viologen-reducing hydrogenase, delta subu
  ------ inclusion threshold ------
      0.018   15.4   2.1       0.02   15.3   2.1    1.1  1  Syntaxin_2   Syntaxin-like protein
      0.078   13.8   0.1      0.099   13.4   0.1    1.2  1  LZ_Tnp_IS66  Transposase C of IS166 homeodomain
       0.53   10.1   4.0        9.3    6.1   0.3    2.8  2  LacI         Bacterial regulatory proteins, lacI family


Domain annotation for each model (and alignments):
>> FlpD  Methyl-viologen-reducing hydrogenase, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.25   1.1e+03     105     121 ..       6      22 ..       1      30 [. 0.61
   2 !   15.7   0.8   2.6e-06     0.012      71     114 ..      25      68 ..      16      70 .] 0.92

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.25
        FlpD 105 gekfaevikefvekike 121
                 ++k+ e++ e +eki +
  EPA04672.1   6 QKKIDEIMYETNEKISA 22 
                 45556666666666554 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 2.6e-06
        FlpD  71 nekaerrveklkelleelgiepeRvrleevsaaegekfaevike 114
                 ne  + r++k++e  ++l+ ++ R+++e+v ++e ek+++v+ke
  EPA04672.1  25 NEIRDIRFSKMSESEKQLKCDKLRLEFEQVMIEEEEKVVKVMKE 68 
                 56667899**********************************98 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   2.1   4.4e-06      0.02      28      83 ..       2      55 ..       1      68 [. 0.90

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.4e-06
  Syntaxin_2 28 teelreklhelieeinelikktnellkklsqldnsssdsqqklqkekLkkdfkeal 83
                ++e+++k++e++ e+ne i+++ + ++++   + s+s   + l+ +kL+ +f++++
  EPA04672.1  2 NPETQKKIDEIMYETNEKISAIVNEIRDIRFSKMSES--EKQLKCDKLRLEFEQVM 55
                57899************************99999998..68899999999999887 PP

>> LZ_Tnp_IS66  Transposase C of IS166 homeodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   2.2e-05     0.099       4      44 ..      22      63 ..      19      68 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.2e-05
  LZ_Tnp_IS66  4 eqlallkrklFGrsSE.ltardpeQleLaleeleaeeaevea 44
                 + ++  +  +F ++SE  ++   + l L++e++  ee+e   
   EPA04672.1 22 AIVNEIRDIRFSKMSEsEKQLKCDKLRLEFEQVMIEEEEKVV 63
                 567888999*******86688888888899999988888655 PP

>> LacI  Bacterial regulatory proteins, lacI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.3    0.0021       9.3      25      40 ..      11      26 ..       1      28 [. 0.69
   2 ?    4.3   0.4    0.0076        34      25      40 ..      53      68 ..      46      69 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0021
                SSTHHHHHHHHHHHHH CS
        LacI 25 rVseetrerVeaamee 40
                 +  et e++ a+++e
  EPA04672.1 11 EIMYETNEKISAIVNE 26
                4556788888888887 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0076
                SSTHHHHHHHHHHHHH CS
        LacI 25 rVseetrerVeaamee 40
                +V  e  e+V ++m+e
  EPA04672.1 53 QVMIEEEEKVVKVMKE 68
                6667889*******99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1423  (0.0793686); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 499.05
//
Query:       EPA04673.1  [L=352]
Description: radical SAM domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-09   38.9   2.0    1.4e-09   38.5   0.2    2.0  3  Radical_SAM  Radical SAM superfamily
  ------ inclusion threshold ------
        6.3    6.7  11.2       0.14   11.9   0.9    2.8  3  HPIP_like    High potential iron-sulfur protein like


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   0.2   1.6e-13   1.4e-09       4     161 ..      80     229 ..      78     237 .. 0.91
   2 ?   -3.2   0.0       1.1   9.7e+03     129     153 ..     269     294 ..     256     297 .. 0.61
   3 ?   -2.1   0.1      0.48   4.3e+03       9      17 ..     324     332 ..     323     343 .. 0.85

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 1.6e-13
                  ESEESS--TTTSCCTT.HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHT CS
                  xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM   4 trgCnlrCsfCarpet.vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritvetngtlpdeeklerllel 100
                  t gCn  C++C++    +rr   g ++++e+++e++ e      ++++  +  ep+   +++++   la++  +g+ + +++ng+   +e +  + e 
   EPA04673.1  80 TTGCNWLCKYCINFDLsQRRKIEGVDITPEKVVEKALETG----CNGMAYTYNEPSIFLEYARDCGVLARK--NGLFNIFVSNGYGT-PESVSMMNEF 170
                  78************989*******************9997....***************************..8************8.*********7 PP

                  T-SEEEEEEBSSSHH.HHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHH CS
                  xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM 101 gvdrvslgleaadde.kvlklmnrghtfeevlealeklreagikrvvdrivglpGendeele 161
                    d ++++ +   +e  v+k++ + ++ + v ++l  +r++    v ++ +++p + d+ le
   EPA04673.1 171 L-DSITVDFKGNGEEkFVRKYI-GIPNSQPVFDTLLEIRDKTKIHVEITDLVVPEVGDD-LE 229
                  7.**********9997788888.99****************655588888888877776.44 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.1
                  HHHHHHHHHHHTTSET.EEEEEEEBT CS
                  xxxxxxxxxxxxxxxx.xxxxxxxxx RF
  Radical_SAM 129 evlealeklreagikr.vvdrivglp 153
                   + +  e++++ g++   v +++g+p
   EPA04673.1 269 TLEKHHEIAKKEGLRYaYVGNVPGHP 294
                  44455667777777767777777776 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.48
                  S--TTTSCC CS
                  xxxxxxxxx RF
  Radical_SAM   9 lrCsfCarp 17 
                  ++C++C  +
   EPA04673.1 324 NQCKYCGAK 332
                  68****876 PP

>> HPIP_like  High potential iron-sulfur protein like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.9   1.6e-05      0.14       2      20 ..      17      35 ..      16      42 .. 0.93
   2 ?    1.6   0.1     0.027   2.4e+02       2      10 ..      86      94 ..      85     101 .. 0.82
   3 ?   -4.3   0.6       1.9   1.7e+04       3       6 ..     326     329 ..     325     330 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.6e-05
                BGGGBTTEE---TTSEEEE CS
   HPIP_like  2 kCknCsnFknadeegiGtC 20
                 C  C+ +++ +e++iG+C
  EPA04673.1 17 RCLACARYCELGEDQIGLC 35
                599**************** PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.027
                BGGGBTTEE CS
   HPIP_like  2 kCknCsnFk 10
                 Ck C nF 
  EPA04673.1 86 LCKYCINFD 94
                5*******5 PP

  == domain 3  score: -4.3 bits;  conditional E-value: 1.9
                 GGGB CS
   HPIP_like   3 CknC 6  
                 Ck C
  EPA04673.1 326 CKYC 329
                 9999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.53
# Mc/sec: 1999.72
//
Query:       EPA04674.1  [L=548]
Description: thermosome, subunit [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
     1e-175  585.1  18.0   1.2e-175  584.9  18.0    1.0  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family
     0.0054   16.7   0.0      0.034   14.1   0.0    2.3  2  DUF3924     Protein of unknown function (DUF3924)


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  584.9  18.0  1.3e-179  1.2e-175       1     488 [.      39     527 ..      39     530 .. 0.99

  Alignments for each domain:
  == domain 1  score: 584.9 bits;  conditional E-value: 1.3e-179
                 HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHHHHHHHCTXXHHHHHHHHHHHHH CS
  Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleeaekliaagvhpttiiegyekale 99 
                 +a+i++t+lGP+GmdKmlv++ g++++TnDGatilke++++hPaak++ve+a+++d+evGDGTt++v+Lag+Lle+ae+li++++hp+ i +gy+ka  
  EPA04674.1  39 IAEIIQTSLGPRGMDKMLVDSLGDITITNDGATILKEIDVQHPAAKMMVEVAKATDSEVGDGTTSAVVLAGALLEKAESLIDDEIHPVIIADGYKKASR 137
                 79************************************************************************************************* PP

                 HHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHH.HCHCCCS..EECSCCCEECCCCEECECTTSEEESEEEESS--SSTTS CS
  Cpn60_TCP1 100 kaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAv.klieene..keldlgrikvvkieggsledselveGlvldkgvlspdm 195
                 ka+e+L+ei  +i+++ kdr++L k+a+ts+++kl+s +a  l+kl+v A  +++ee++   +++l++ikv+k++ggs++dselv G++ldk+++++ m
  EPA04674.1 138 KAIEFLSEI--AIKVDPKDRKILEKIAHTSMQTKLVSLDATDLAKLAVSAAlSVMEEKSgfFKVNLENIKVEKKTGGSVSDSELVSGIILDKEIVHSGM 234
                 *********..8888899*********************************88888888888899999******************************* PP

                 SCEEECEEEEEESS-BS--HHCCHHHCCCCSCCHHHHHHHHHHHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT CS
  Cpn60_TCP1 196 pkklenakvllldvsLeiektetkttvvlsdaeeleklekaeekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatG 294
                 p+k+enak++l++  Lei+kte ++++++s+++++++++++e ++l+e++++i++ ++nvv+cqkgidd+++h++ k+gila+rr+k++d+ +lakatG
  EPA04674.1 235 PRKIENAKIALVSEALEIKKTEFEAKLNISSPNQIKSFMEEESQILKEMVKSIKSINANVVLCQKGIDDIVQHYMSKEGILAVRRIKESDMSKLAKATG 333
                 *************************************************************************************************** PP

                 --EBSCGGGGGCGC-EEEEEEEECCETTCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHHHHHHHHCCCCT CS
  Cpn60_TCP1 295 atavssledltpeelGtakkveeekigsekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatelelakklkeyaks 393
                 +++v ++ dl++++lG+a++vee+++++++++++e++k++k+ +il+rg ++ v+de+ r+ +dAl vvk ++e++k+v+GGGa e  +a +l+++aks
  EPA04674.1 334 GRIVGNVNDLSNTDLGSAQNVEEKRVEEDNWVFVEGCKNPKAISILIRGGSQRVIDEADRSMHDALMVVKDVVENPKIVYGGGAPESFVALRLRDWAKS 432
                 *************************************************************************************************** PP

                 SXCCHHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTCEEECCCCTXEEEHHHHHHHHHHHHHHHHHHHCEEEEEX CS
  Cpn60_TCP1 394 vsgeeqlaieafakALevipktLaeNaGldpievlaklraahnkgekelgidvesgeiidlveagvvDplkvkrqalksAteaastiLrideiik 488
                 +sg+eqla+e+fa+A+e+ip +La+NaG++pi+ ++ lr+++n+gek +g+dv +g i d  + gv++plkvk+q++ksAte+a++iLrid ++ 
  EPA04674.1 433 LSGREQLAVEKFADAMESIPLALARNAGMNPIDSITLLRSKQNAGEKFTGVDVINGIIADFEKLGVIEPLKVKEQVIKSATETANMILRIDSVVA 527
                 *********************************************************************************************96 PP

>> DUF3924  Protein of unknown function (DUF3924)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   3.8e-06     0.034      16      47 ..     199     231 ..     187     240 .. 0.79
   2 ?   -1.6   0.0      0.29   2.6e+03      36      49 ..     304     317 ..     302     320 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.8e-06
     DUF3924  16 ldllkqayekktGasisestlvqtli.skefiq 47 
                 ++l     ekktG s+s+s lv  +i  ke + 
  EPA04674.1 199 VNLENIKVEKKTGGSVSDSELVSGIIlDKEIVH 231
                 55556668**************98873677765 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.29
     DUF3924  36 lvqtliskefiqai 49 
                 +vq  +ske i a+
  EPA04674.1 304 IVQHYMSKEGILAV 317
                 799******99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (548 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.66u 0.34s 00:00:01.00 Elapsed: 00:00:00.51
# Mc/sec: 3208.57
//
Query:       EPA04675.1  [L=399]
Description: methionine adenosyltransferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     2e-145  484.6   2.2   2.3e-145  484.4   2.2    1.0  1  AdoMet_Synthase  S-adenosylmethionine synthetase (AdoMet synt
  ------ inclusion threshold ------
      0.086   12.7   0.3        7.5    6.3   0.6    2.9  2  DUF4370          Domain of unknown function (DUF4370)
       0.15   12.7   0.2        1.2    9.8   0.0    2.5  2  S-AdoMet_synt_N  S-adenosylmethionine synthetase, N-terminal 


Domain annotation for each model (and alignments):
>> AdoMet_Synthase  S-adenosylmethionine synthetase (AdoMet synthetase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  484.4   2.2  3.8e-149  2.3e-145       2     396 .]       4     395 ..       3     395 .. 0.97

  Alignments for each domain:
  == domain 1  score: 484.4 bits;  conditional E-value: 3.8e-149
                      -EEEEE-TTS-GTTSSEEEEEEE-TTSHHHHHHHHHHHHHHHHHHHHHHHHSS---EEEEEEEEE--EEEEETTEEEEEE-EEEEEEEEEEEEE CS
  AdoMet_Synthase   2 nivveelkkkpveeqevEivErKGiGHPDsiaDgiaeavsralskeylekfgailhhniDkvllvaGesepkfgGGeviepieillsgratkev 95 
                      +i +e++++ p+ ++++EivErKGiGHPD+i+D +++++s++lsk yl+++gai hhn+Dk+llvaG+se++fgGG++i+pi+++l++rat +v
       EPA04675.1   4 QIFIESVNNIPTFKKRFEIVERKGIGHPDTICDLVMNQISVDLSKLYLKETGAIQHHNMDKALLVAGQSESNFGGGKIIKPIKMILGDRATFDV 97 
                      699******************************************************************************************* PP

                      .EEE--HHHHHHHHHHHHHHHH-SS--TTTSEEEEEEEEEEEEHHHHHHCH-SS..-BESSSEEEEEEES--HHHHHHHHHHHHHTSHHHHHH- CS
  AdoMet_Synthase  96 egekipveeialeaakeylkenlraldlekdvivdvklgkgsadLkdvferkkkevplaNDtSfgvgyaplseleklvleterllnskelkkkl 189
                      +g+++p++eia+++ak+++++n+r+++ e +v++++++g  s++L ++fe+ ++   +aNDtS+ vgyap++e+e++vl+te+++nsk++k+++
       EPA04675.1  98 DGKRLPIGEIAINSAKRWFEKNIRFVNEE-HVKYQIEIGVTSKELSSIFENPSS--FAANDTSVLVGYAPFTETESIVLNTEQHINSKQFKDDF 188
                      **************************966.*********************766..89************************************ PP

                      TTEEEEEEEEEEEETTEEEEEEEEEEEGGG--SHHHHHHHHHHHHHHHHHHHHHHSTTSEEEEEE-TT-BGG..GTB--EESSSSGGGTT--EE CS
  AdoMet_Synthase 190 pevGeDiKvmglRekkkielTvavalvdrlvkdleeYlevkeeikeeveelakkltkerevevevNtaDkke..eesvyltvtGtsaEegDdGs 281
                      pe+GeD+Kvmg+R+ ++++lT+a+a+vdr+v+++++Y+++kee+ +e++ ++kk+ +  +++ ++N++D+k+   +++yltv+GtsaE +D+G+
       EPA04675.1 189 PESGEDVKVMGFRDTNHVDLTIATAFVDRFVSSENQYFQKKEEMLQEIDGFLKKNYD-MKITAKMNCLDSKNkgLSGLYLTVLGTSAEGADSGQ 281
                      ******************************************************999.9**********99856689***************** PP

                      TTSS--TTSSB-TTS----S--TTS-TTT-HHHHHHHHHHHHHHHHHHH-TTEEEEEEEEEE-TTSBTTS-SEEEEEEEESSS---HHSHHHHH CS
  AdoMet_Synthase 282 vGRGNRvnGlitpnrpmslEAaaGKNPvsHvGKiYnvlaneiakeiveevegvkevyvrllsqiGkpidePlvasvqvilekgvsleevekeve 375
                      vGRGN +  +i+p+rp + EA+aGKNP+sH+GKiYn+l+ +ia+ei+++v+g++ev v++ + iG+p+++P+++ vq i + +   +e +++++
       EPA04675.1 282 VGRGNMASRVISPSRPAGSEATAGKNPISHIGKIYNALSFKIANEIHTKVSGLDEVCVWMYNVIGSPVNKPRAVIVQPIITGQLGNTE-KNQIN 374
                      *****************************************************************************98877655555.79*** PP

                      HHHHHHHT-HHHHHHHHTTT- CS
  AdoMet_Synthase 376 eiideelekieeiteeliegk 396
                      ei++++le+i+e+++eli+gk
       EPA04675.1 375 EIVEKNLENIQEFCNELISGK 395
                      ******************986 PP

>> DUF4370  Domain of unknown function (DUF4370)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.037   2.2e+02      25      77 ..      51     103 ..      34     119 .. 0.77
   2 ?    6.3   0.6    0.0013       7.5     183     226 ..     232     273 ..     181     279 .. 0.61

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.037
     DUF4370  25 aaasaalekhlssrslfavlsasskavlsdlrsplalslGsvrsfsedvshlP 77 
                 ++++ a+++h   + l+    ++s+    ++ +p+ + lG++ +f  d ++lP
  EPA04675.1  51 LKETGAIQHHNMDKALLVAGQSESNFGGGKIIKPIKMILGDRATFDVDGKRLP 103
                 456678889988888886666666666778899****************9999 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0013
     DUF4370 183 sfgpeevylrkkvemelGtkmihlkmrcsglgsewGkvtvlGts 226
                  ++  + +l+k  +m + +km  l  +  gl   +  +tvlGts
  EPA04675.1 232 MLQEIDGFLKKNYDMKITAKMNCLDSKNKGLSGLY--LTVLGTS 273
                 22333578888888888888888888888888765..8999998 PP

>> S-AdoMet_synt_N  S-adenosylmethionine synthetase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0    0.0002       1.2      11      28 ..      28      45 ..      21      89 .. 0.71
   2 ?   -1.6   0.1      0.75   4.5e+03      50      74 ..     360     384 ..     355     389 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0002
  S-AdoMet_synt_N 11 eGHPDkvadqisdailda 28
                      GHPD ++d + ++i   
       EPA04675.1 28 IGHPDTICDLVMNQISVD 45
                     6********999988444 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.75
  S-AdoMet_synt_N  50 vvageittkakvdiekivrevikei 74 
                      +++g++ ++ k +i++iv + +++i
       EPA04675.1 360 IITGQLGNTEKNQINEIVEKNLENI 384
                      6788888888899999999999888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       788  (0.0439511); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.37s 00:00:01.00 Elapsed: 00:00:00.52
# Mc/sec: 2305.69
//
Query:       EPA04676.1  [L=47]
Description: hypothetical protein BG20_I1675 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00071   19.6   0.4    0.00088   19.3   0.4    1.2  1  Zn-ribbon_8    Zinc ribbon domain
     0.0052   16.8   0.2     0.0053   16.8   0.2    1.0  1  HypA           Hydrogenase/urease nickel incorporation, metal
      0.009   15.4   0.3     0.0092   15.4   0.3    1.0  1  Rtf2           Rtf2 RING-finger
  ------ inclusion threshold ------
      0.016   14.7   1.0        2.2    7.8   0.1    2.2  2  TF_Zn_Ribbon   TFIIB zinc-binding
      0.017   15.9   0.6        1.9    9.5   0.0    2.2  2  zf-C2H2_4      C2H2-type zinc finger
      0.018   15.0   1.1      0.019   15.0   1.1    1.1  1  zf-C2HC5       Putative zinc finger motif, C2HC5-type
      0.023   15.0   0.1      0.023   14.9   0.1    1.0  1  DUF2072        Zn-ribbon containing protein
       0.04   14.3   0.2      0.045   14.1   0.2    1.1  1  DnaJ_CXXCXGXG  DnaJ central domain


Domain annotation for each model (and alignments):
>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.4   3.9e-07   0.00088       8      35 ..       2      28 ..       1      32 [. 0.82

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 3.9e-07
  Zn-ribbon_8  8 CeeCghefevlqsisdaplta.CPeCgs.e 35
                 C+ Cg++f + + ++    +  CP+C++  
   EPA04676.1  2 CKLCGNVFSKKAGVA---IISsCPQCHGtS 28
                 *********999888...5666*****944 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.2   2.4e-06    0.0053      72     103 ..       1      35 [.       1      46 [. 0.79

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.4e-06
                 EETTTS-EEECHH..H.HHS-TTTSSS-EEEEESS CS
        HypA  72 rCreCgkefelee..k.alrCpkCgsadveivsGe 103
                 +C+ Cg+ f++++  +   +Cp+C+++++e+++ +
  EPA04676.1   1 MCKLCGNVFSKKAgvAiISSCPQCHGTSLELITLN 35 
                 5*********8864335559********9998754 PP

>> Rtf2  Rtf2 RING-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.3   4.1e-06    0.0092     134     175 ..       3      41 ..       1      46 [. 0.86

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 4.1e-06
        Rtf2 134 rkCGcVfsekalkevksevClvCgkeykeedviplnptkeel 175
                 + CG Vfs+ka  ++ s+ C++C+ +  + ++i+ln + +e+
  EPA04676.1   3 KLCGNVFSKKAGVAIISS-CPQCHGT--SLELITLNENSDEV 41 
                 67**********999999.****985..56799999999987 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1    0.0035       7.8      22      29 ..       2       9 ..       1      17 [. 0.83
   2 ?    7.8   0.1     0.001       2.2       3      12 ..      21      33 ..      20      42 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0035
                  ESSSSBEE CS
  TF_Zn_Ribbon 22 CtdCGlVl 29
                  C+ CG+V 
    EPA04676.1  2 CKLCGNVF 9 
                  999*9996 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.001
                  ETTTTCEEC...H CS
  TF_Zn_Ribbon  3 CPnCgstnl...v 12
                  CP C++t+l   +
    EPA04676.1 21 CPQCHGTSLeliT 33
                  ******9984444 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00087       1.9       3      13 ..       2      12 ..       1      16 [. 0.81
   2 ?    5.2   0.1     0.021        46       3       9 ..      21      27 ..      19      34 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00087
   zf-C2H2_4  3 CpiCgksFssk 13
                C++Cg +Fs k
  EPA04676.1  2 CKLCGNVFSKK 12
                ********654 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.021
   zf-C2H2_4  3 CpiCgks 9 
                Cp+C+++
  EPA04676.1 21 CPQCHGT 27
                ****765 PP

>> zf-C2HC5  Putative zinc finger motif, C2HC5-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   1.1   8.4e-06     0.019      19      43 ..       1      28 [.       1      41 [. 0.81

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8.4e-06
    zf-C2HC5 19 nClnCGkiiCakegls..kpCsfCg.sp 43
                +C  CG++  +k g+   ++C+ C+ ++
  EPA04676.1  1 MCKLCGNVFSKKAGVAiiSSCPQCHgTS 28
                7**************999******8533 PP

>> DUF2072  Zn-ribbon containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.1     1e-05     0.023       3      41 ..       1      40 [.       1      46 [. 0.80

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1e-05
     DUF2072  3 kCtkCekvfedgs.keilkGCpsCGgkkFlyvkeeekked 41
                +C  C++vf+  +   i + Cp+C g   + +  +e++++
  EPA04676.1  1 MCKLCGNVFSKKAgVAIISSCPQCHGTSLELITLNENSDE 40
                599******8655267**********99999987776655 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.2     2e-05     0.045       1      24 [.       2      28 ..       2      43 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2e-05
  DnaJ_CXXCXGXG  1 CkkCkGsgakkgk...kktCktCkGsG 24
                   Ck C    +kk+     ++C++C+G+ 
     EPA04676.1  2 CKLCGNVFSKKAGvaiISSCPQCHGTS 28
                   8889888877643467889*****998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.44u 0.33s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 289.85
//
Query:       EPA04677.1  [L=50]
Description: hypothetical protein BG20_I1683 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 362.84
//
Query:       EPA04678.1  [L=52]
Description: hypothetical protein BG20_I1684, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      198  (0.0110436); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.47
# Mc/sec: 335.46
//
Query:       EPA04679.1  [L=128]
Description: hypothetical protein BG20_I1674 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-10   40.9   0.0    2.8e-10   40.5   0.0    1.2  1  AAA_33    AAA domain
     0.0022   17.5   0.5     0.0023   17.5   0.5    1.1  1  KTI12     Chromatin associated protein KTI12
  ------ inclusion threshold ------
       0.05   13.9   0.0       0.07   13.4   0.0    1.3  1  DPBB_1    Lytic transglycolase


Domain annotation for each model (and alignments):
>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.5   0.0   4.6e-14   2.8e-10      34     143 .]       8     107 ..       2     107 .. 0.83

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 4.6e-14
      AAA_33  34 rrrlfgtdqqsktdytrvldrlyqilnelarkalsagrnvildatnlsrrerarflklarrlgvpvrivvvetdeetlkeRlakRaangddrsevpeea 132
                 r++ f+ ++  +++ ++ +   ++ l e+++k+l+ gr++i+d tnl+ + r++ + la++++++vr ++++t+  +l++R ++R ++       p+++
  EPA04679.1   8 RKANFNYEVIALSYFNNNR---KKEL-EYIEKCLKDGRSIIVDDTNLTVSIRKQHIDLAKKFNAKVRGIFMNTSTVLLEQRQKRRRDS------IPLSV 96 
                 5555556666665544443...3444.889********************************************************97......88999 PP

      AAA_33 133 ldrqkarferp 143
                 + +q++ +e+p
  EPA04679.1  97 IYKQIKELEVP 107
                 88888888876 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.5   3.8e-07    0.0023      54     133 ..      23     100 ..       3     127 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.8e-07
                 HHHHHHHHHHHHHHHTT.SEEEE-S---SHHHHHHHHHHHHHTT-EEEEEEEE--HHHHHHHHHHTT-S..S-HHHHHHH CS
       KTI12  54 kalRsslrsavkrdLskekvVIvDslnyikgfRYeLyciakaakttlcvvyvvapldvlvkwneereekeeyekelldaL 133
                  + R++  + +++ L+  + +IvD++n + + R + + +ak+ + ++  +++ ++   l ++++ r ++  ++  ++ + 
  EPA04679.1  23 NNNRKKELEYIEKCLKDGRSIIVDDTNLTVSIRKQHIDLAKKFNAKVRGIFMNTSTVLLEQRQKRRRDS--IPLSVIYKQ 100
                 5678999999*****************************************999988888888888776..555554444 PP

>> DPBB_1  Lytic transglycolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.2e-05      0.07      35      66 ..      34      64 ..       7      70 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.2e-05
                -EEEETT--EEEEEEEE----STTECEEE-HH CS
      DPBB_1 35 tycrvlsgksvtVtitDrgpfppgrhiDLSka 66
                 +c++ +g+s++V  t+   +++++hiDL+k+
  EPA04679.1 34 EKCLK-DGRSIIVDDTNLTVSIRKQHIDLAKK 64
                33555.59*********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       901  (0.0502538); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 968.91
//
Query:       EPA04680.1  [L=98]
Description: hypothetical protein BG20_I1371 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-11   42.7   2.1    5.5e-11   41.8   2.1    1.5  1  SHOCT     Short C-terminal domain
  ------ inclusion threshold ------
      0.041   14.0   0.0       0.05   13.8   0.0    1.1  1  Popeye    Popeye protein conserved region
        0.1   12.4   0.0       0.15   12.0   0.0    1.2  1  VbhA      Antitoxin VbhA
       0.11   12.6   0.6       0.17   11.9   0.6    1.5  1  GvpG      Gas vesicle protein G
       0.15   12.2   0.0        0.2   11.7   0.0    1.2  1  DUF1707   Domain of unknown function (DUF1707)


Domain annotation for each model (and alignments):
>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   2.1   1.5e-14   5.5e-11       1      27 [.      70      96 ..      70      97 .. 0.96

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 1.5e-14
       SHOCT  1 daLekLkeLyarGeIteEEFeakKakL 27
                d Le+Lk++yarGeI++EEF++ Ka+L
  EPA04680.1 70 DSLEILKQRYARGEISKEEFDKIKADL 96
                67************************9 PP

>> Popeye  Popeye protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.4e-05      0.05      38     106 ..      24      93 ..       7      96 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.4e-05
                 xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
      Popeye  38 lllalwawlvv.CaldiflWnlllvlinlaqllyllyklrpvkfekeleelYkklFqplkvsrkeFkklv 106
                 +++a+ +++vv    d+f+ +   ++i +  ++++++ l++ k +++  e+ k+ +++ ++s++eF+k+ 
  EPA04680.1  24 IIFAVLSIIVVyLGADMFFHYPYRIIIQFGTIAIIIWILKRNKKKPDSLEILKQRYARGEISKEEFDKIK 93 
                 55555555544157899***************************************************95 PP

>> VbhA  Antitoxin VbhA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.1e-05      0.15      27      41 ..      76      90 ..      70      92 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.1e-05
        VbhA 27 leayvrGeIdadElv 41
                 ++y+rGeI+ +E  
  EPA04680.1 76 KQRYARGEISKEEFD 90
                69**********975 PP

>> GvpG  Gas vesicle protein G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.6   4.7e-05      0.17      36      58 ..      71      93 ..      51      98 .] 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.7e-05
        GvpG 36 eLaaLqqeLdaGeIdeeeFdrrE 58
                 L  L+q+  +GeI++eeFd+  
  EPA04680.1 71 SLEILKQRYARGEISKEEFDKIK 93
                57789***************865 PP

>> DUF1707  Domain of unknown function (DUF1707)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   5.6e-05       0.2      12      31 ..      72      91 ..      66      96 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.6e-05
     DUF1707 12 velLrealaeGrLtldEfde 31
                +e+L++ +a+G ++ +Efd+
  EPA04680.1 72 LEILKQRYARGEISKEEFDK 91
                799***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1016  (0.056668); expected 358.6 (0.02)
Passed bias filter:                      618  (0.0344693); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 698.80
//
Query:       EPA04681.1  [L=207]
Description: putative superoxide dismutase, Mn [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-36  123.1   1.5    7.7e-36  122.4   1.5    1.4  1  Sod_Fe_C  Iron/manganese superoxide dismutases, C-terminal do
      1e-25   90.0   0.1    2.3e-25   88.9   0.1    1.6  1  Sod_Fe_N  Iron/manganese superoxide dismutases, alpha-hairpin


Domain annotation for each model (and alignments):
>> Sod_Fe_C  Iron/manganese superoxide dismutases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.4   1.5   8.6e-40   7.7e-36       1     102 []      99     201 ..      99     201 .. 0.97

  Alignments for each domain:
  == domain 1  score: 122.4 bits;  conditional E-value: 8.6e-40
                 --HHHHHHHHHHHSSHHHHHHHHHHHHHHSSSSEEEEEEEETT.TEEEEEEEETTTBGGGGTTCEEEEEE-SGGGTHHHHTT-HHHHHHHHGGGBBHHH CS
    Sod_Fe_C   1 psgelaeaieedfgslekfkkefkaaalavfgsGwawLvldkk.kkLeivttknqdnplvkeakplLalDvwehAYyldyqnkradYieafwnvvnWke 98 
                 p g+l ++i+  f+++e+fkkef+++al+++gsGw+wLv++++ +k+e++tt nq++p + ++ plL+lD+weh+Yyl+yqnk++dY+e++wnvvnW+ 
  EPA04681.1  99 PCGKLSDSIDVYFENFENFKKEFSSKALSIEGSGWCWLVFNQTfNKIELITTLNQNSPWSIRKIPLLGLDMWEHSYYLKYQNKKSDYVESWWNVVNWDY 197
                 6799*************************************9989*****************************************************9 PP

                 HHHH CS
    Sod_Fe_C  99 veer 102
                 v +r
  EPA04681.1 198 VGNR 201
                 9775 PP

>> Sod_Fe_N  Iron/manganese superoxide dismutases, alpha-hairpin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.9   0.1   2.5e-29   2.3e-25       1      81 [.       3      91 ..       3      92 .. 0.91

  Alignments for each domain:
  == domain 1  score: 88.9 bits;  conditional E-value: 2.5e-29
                S------SS-TTTTTTTS-HHHHHHHHHTHHHHHHHHHHHHHHCH..HHHCHCCHHHHHH......HHHHHHHHHHHHHHHHHHHHHTB CS
    Sod_Fe_N  1 kyeLpeLpYaydaLePhisketlelHhdkHhktYvnnlNkalekl..eeakkkleelvlk......klekalrnnagghvnHslfwknl 81
                kyeLp LpY yd LeP+++k+t+e+Hh+kHh++Yv++lN++l+k+  e++ + + ++ +       + ++++ + +gg  nH+lfw+++
  EPA04681.1  3 KYELPRLPYGYDELEPYFDKRTMEIHHQKHHQAYVDGLNNTLAKIggEFHPQYITSVLSDlsvipeSVRNDIVFFGGGFENHKLFWETM 91
                6*******************************************9767777766666655778888999******************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1460.11
//
Query:       EPA04682.1  [L=455]
Description: ABC transporter, permease protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.7e-27   94.6   9.1    5.7e-27   94.6   9.1    2.3  3  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
      0.052   13.5   0.2      0.052   13.5   0.2    2.7  3  OppC_N        N-terminal TM domain of oligopeptide transport 


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.2     0.036   3.2e+02     157     174 ..      21      38 ..       4      50 .. 0.59
   2 ?   -4.7   1.3       1.9   1.7e+04     158     166 ..     254     262 ..     243     268 .. 0.39
   3 !   94.6   9.1   6.4e-31   5.7e-27       1     184 [.     269     454 ..     269     455 .] 0.95

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.036
  BPD_transp_1 157 gvlalviavlllnlvadi 174
                   + +a++++++ ++++++i
    EPA04682.1  21 AGIAILLILISISILVMI 38 
                   333333333333333333 PP

  == domain 2  score: -4.7 bits;  conditional E-value: 1.9
  BPD_transp_1 158 vlalviavl 166
                   +l+++++v+
    EPA04682.1 254 ALFIGLVVA 262
                   222222222 PP

  == domain 3  score: 94.6 bits;  conditional E-value: 6.4e-31
  BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrslpkdlveaaralGasrwqi 97 
                   g++ G++a+ +r+kk+d++++++ +v+++lP + ++i+l +     +i  + +  v +l+++++++++ + r++al++  +++veaa ++G ++ +i
    EPA04682.1 269 GLVYGVYAG-YRGKKTDEVMMRFNDVIYALPALPFLIILSV-----TISNSIFVLVGFLMVFGWVGIAKVSRSMALQIKTRGYVEAANMMGQKDSKI 359
                   7899*****.****************************995.....888888888****************************************** PP

  BPD_transp_1  98 frkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis.............nggvlalviavlllnlvadilqrlldp 181
                   + +++lP++lp+++++++++++++++  + l+flg    lg++ + +++g+ ++ ++             + + ++++i  l+++++ ++l ++++p
    EPA04682.1 360 VLRHILPQLLPYAFASIAISVPAAITTEAGLSFLG----LGDPSF-PTWGQILHDANvygaasrglwwwiMPPGVMIAITGLAFVFIGNALDAIVNP 451
                   ***********************************....998766.67888888888889999********************************** PP

  BPD_transp_1 182 rvr 184
                   +++
    EPA04682.1 452 KLK 454
                   *97 PP

>> OppC_N  N-terminal TM domain of oligopeptide transport permease C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   5.8e-06     0.052       8      41 ..      11      44 ..       7      57 .. 0.82
   2 ?   -1.5   0.1      0.29   2.6e+03      18      30 ..     257     269 ..     253     288 .. 0.60
   3 ?   -2.6   0.5      0.64   5.8e+03      16      34 ..     432     451 ..     429     453 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.8e-06
      OppC_N  8 rrFkrNklAvvglvilllllliaifaPliaPydp 41
                  F++ k+ ++g +ill+l+ i+i+   ++P d 
  EPA04682.1 11 NEFLKSKIGIAGIAILLILISISILVMIVIPVDT 44
                67***********************877778775 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.29
      OppC_N  18 vglvillllllia 30 
                 +glv+ ++ +++ 
  EPA04682.1 257 IGLVVAIASVVMG 269
                 4444444444443 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 0.64
      OppC_N  16 Avvglvilll.llliaifaP 34 
                 A+ gl+++ +  +l ai++P
  EPA04682.1 432 AITGLAFVFIgNALDAIVNP 451
                 55555555443556677777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (455 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       773  (0.0431145); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 3076.20
//
Query:       EPA04683.1  [L=187]
Description: transcription factor [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.3e-55  182.5   0.1    4.4e-27   93.9   0.0    2.0  2  TBP       Transcription factor TFIID (or TATA-binding protein
    6.1e-07   29.5   0.0       0.02   15.0   0.0    2.3  2  DUF3378   Domain of unknown function (DUF3378)


Domain annotation for each model (and alignments):
>> TBP  Transcription factor TFIID (or TATA-binding protein, TBP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.9   0.0   4.9e-31   4.4e-27       2      84 ..       8      88 ..       7      89 .. 0.96
   2 !   87.0   0.0   6.9e-29   6.2e-25       2      83 ..      99     178 ..      98     179 .. 0.95

  Alignments for each domain:
  == domain 1  score: 93.9 bits;  conditional E-value: 4.9e-31
                EEEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHHHHHHHH CS
         TBP  2 fkiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakkiapilkk 84
                + i+Nvvasa++++++dL+ + +k    ++eY p++fpglv+rl++pk++ liF++Gk+v+tG ksee +r a+k+++++l+k
  EPA04683.1  8 ISIVNVVASATVDQKFDLNDITKKF--PDTEYHPDQFPGLVFRLKNPKTATLIFRTGKMVCTGSKSEEMARSAVKTVVQKLRK 88
                68*******************7665..******************************************************97 PP

  == domain 2  score: 87.0 bits;  conditional E-value: 6.9e-29
                 EEEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHHHHHHH CS
         TBP   2 fkiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakkiapilk 83 
                 +++qN+vas+nlg +++Lek a+++    + Yepe+fpgl+ r+ +pk+++liFssGk+v+tGak+e+++ + ++++  +l+
  EPA04683.1  99 VTVQNIVASINLGGKVHLEKAARTL--PRSMYEPEQFPGLIHRMLDPKTVILIFSSGKLVCTGAKNESDVFRSVHNLHSLLE 178
                 68*******************9887..*********************************************9999988886 PP

>> DUF3378  Domain of unknown function (DUF3378)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.2e-06      0.02      14      61 ..      28      76 ..      18      89 .. 0.83
   2 !   12.3   0.0   1.6e-05      0.14      24      58 ..     130     164 ..     120     173 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.2e-06
     DUF3378 14 mkeyyksk.lrskkppyavfaakkndttItaYtSgKVlFQGknaeaeAs 61
                +++++ +      + p+ vf+ k+++t   +++ gK +  G++ e+ A 
  EPA04683.1 28 ITKKFPDTeYHPDQFPGLVFRLKNPKTATLIFRTGKMVCTGSKSEEMAR 76
                555554443567899******************************9996 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 1.6e-05
     DUF3378  24 skkppyavfaakkndttItaYtSgKVlFQGknaea 58 
                  ++ p+ + +  +++t+I ++ SgK++  G++ e+
  EPA04683.1 130 PEQFPGLIHRMLDPKTVILIFSSGKLVCTGAKNES 164
                 578899999999***************99988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       891  (0.049696); expected 358.6 (0.02)
Passed bias filter:                      680  (0.0379274); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1358.77
//
Query:       EPA04684.1  [L=570]
Description: SNF2 family N-terminal domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.1e-38  131.0   0.0    5.9e-38  130.5   0.0    1.2  1  SNF2_N         SNF2 family N-terminal domain
      4e-13   49.7   0.6    2.1e-12   47.3   0.0    2.3  2  Helicase_C     Helicase conserved C-terminal domain
    4.5e-09   36.6   0.1    4.5e-09   36.6   0.1    1.9  2  ResIII         Type III restriction enzyme, res subunit
    3.6e-06   26.9   0.3    1.1e-05   25.3   0.0    1.9  3  DEAD           DEAD/DEAH box helicase
  ------ inclusion threshold ------
      0.039   13.1   0.1       0.08   12.1   0.1    1.5  1  ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase


Domain annotation for each model (and alignments):
>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.5   0.0   1.6e-41   5.9e-38      54     287 ..     124     346 ..     114     400 .. 0.88

  Alignments for each domain:
  == domain 1  score: 130.5 bits;  conditional E-value: 1.6e-41
                 TT--EEE---TTS--HHHHHHHHH...HHTTTS---.......S-EEEE--HHHHHHHHHHHHHH-TTS-EEE--SSHHHH-----------------E CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
      SNF2_N  54 svrGGiLaDemGLGKTvqvlalilaqrakeekdkekkrkdtlagptLivvPaslldqWeneierhvsssalrvlvyggqkkmkkkntkvapklladydv 152
                 s+ + +LaDemGLGKTvq+l+ +++++                +p+L+v+P  +l++We+ei++++++++ +  + ++++++    ++ + k l  +d 
  EPA04684.1 124 SSGNALLADEMGLGKTVQTLSYVATEK--------------QTFPVLVVAPLVTLNNWEREIAKFMKKKSRNGRIIESESSTATIIRTGKSKELPVTDF 208
                 56688*******************322..............359************************9999988888888888888888999999999 PP

                 EEE-HHHHHHHT......TTS-S-S-SEEEES-GGGT--TTSHHHHHHHH--....-S-EEEE-S--SSS-HHHHHHHHHHH-TTTT--HHHHHHHTHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
      SNF2_N 153 vittYdvlsreaelqkkrsvlkqvewkrvvlDEghtlknstskaaeavskLs....tsnrwiltGTPiqnsledlygLlkfLreepfgekqtfdkllqr 247
                  i++Y+ l ++       s l++++++ +v+DE h+l+++t++ ++av+kL+     s+r+ l+GTPi n  ++++++++ L+++ +g+++ f + +  
  EPA04684.1 209 YIINYELLYKRL------SDLSKLNIRTIVCDEVHNLRSKTTQKYKAVKKLAalpsISYRIGLSGTPIYNRGSEIWPIVDILKPGLLGSFKEFCEYFCY 301
                 999999999777......*********************************8777789*******************************9999998877 PP

                 HHH....HHHHHHHHHHHTT-S.TTEE---GGGT--S---EEEEE CS
                 xxx....xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
      SNF2_N 248 pie....aqaekgrsrLlqllq.rlmlrrakkdveknlPpkteei 287
                   e       e++r+ L++ lq  +mlrr k+dv k+l +k+ + 
  EPA04684.1 302 VNEkgkaIVLENKRASLRNELQkHVMLRRKKSDVLKELKDKVRYK 346
                 6665566556788888988887469*********99999988765 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1       0.5   1.8e+03       7      32 ..     296     324 ..     291     347 .. 0.64
   2 !   47.3   0.0   5.9e-16   2.1e-12       5     111 .]     402     508 ..     398     508 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.5
                 HHHHHHTTTTSEEEEEESSHHHHHH...H CS
  Helicase_C   7 lellkleeeggkilifvntidrlek...v 32 
                 +e++   +e+gk+++  n++ +l +    
  EPA04684.1 296 CEYFCYVNEKGKAIVLENKRASLRNelqK 324
                 55555678999999999999977533332 PP

  == domain 2  score: 47.3 bits;  conditional E-value: 5.9e-16
                 HHHHHH.HHTTTTSEEEEEESSHHHHHHHHHHHHHT.TSTEEEESTTSTHHHHHHHHHHHHTTSSS.EEEESGGGTSSSTSTTESEEEESSSSSSHHHH CS
  Helicase_C   5 allell.kleeeggkilifvntidrlekvklllekk.gikvavlhgelpqnereeileqfnkgesd.vLiatdvaerGidipkvnlVinfdlprnvtsy 100
                 ++++++ +  e+++ +++f++ +      kll+ek  +++ + + g  + + r+e++++f+kges+ ++   +++  Gi+++++++Vi+ +l+++++  
  EPA04684.1 402 HVINFVkNIMEIEESVVVFCHHKVIH---KLLHEKLgEFSPVSIIGGQSDKMRQEAIDKFQKGESKlMIAGLRAGNVGINLTRAKYVIFAELDWSPAIH 497
                 55555544458899999999999966...899887778999999999*******************888889*************************** PP

                 HHHHTTSSSTT CS
  Helicase_C 101 iqriGRtgRag 111
                  q+ +R +R+g
  EPA04684.1 498 RQAEDRLHRIG 508
                 *********97 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.1   1.2e-12   4.5e-09      22     169 ..     123     269 ..      93     271 .. 0.78
   2 ?   -2.1   0.3      0.91   3.3e+03     113     113 ..     383     383 ..     306     460 .. 0.58

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 1.2e-12
                 .TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B--.............-SEEEEEHHHH CS
      ResIII  22 krdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseaykeigkkvsgdkkka......kekdstnkkilvttiqsl 114
                 k   ++l++ + G GKT+  ++ ++  ++      +l+++p  +l + +++e++kf++++   +g ++++++ +a      k+k+   +++++++++ l
  EPA04684.1 123 KSSGNALLADEMGLGKTVQTLSYVATEKQT---FPVLVVAPLVTL-NNWEREIAKFMKKKSR-NGRIIESESSTAtiirtgKSKELPVTDFYIINYELL 216
                 556688899999*****9988888776665...569999999987.579********99976.666666666666666788888888999********* PP

                 HHTH........HHHTTT-SEEEEETGGGTTS...TTTHHHHHT---....SEEEEEESS- CS
      ResIII 115 dadseeeeeeseellrdrfdviiiDEaHrlgak..kswreilekfke....avllglTATp 169
                 ++++        +l++ ++  i++DE+H+l++k  ++++++++   +    ++++gl++Tp
  EPA04684.1 217 YKRL-------SDLSKLNIRTIVCDEVHNLRSKttQKYKAVKKLA-AlpsiSYRIGLSGTP 269
                 ****.......899999999************7544888874433.223459********9 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.91
                 H CS
      ResIII 113 s 113
                 s
  EPA04684.1 383 S 383
                 1 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   3.1e-09   1.1e-05       3     144 ..     113     249 ..     111     273 .. 0.72
   2 ?   -3.1   0.0       1.6   5.7e+03     115     131 ..     475     491 ..     427     494 .. 0.52
   3 ?   -2.9   0.0       1.4     5e+03     105     149 ..     521     563 ..     479     568 .. 0.52

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 3.1e-09
                 HHHHHHHHHH.TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHHHHHH.HTT.. CS
                 xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx.. RF
        DEAD   3 iQaeaiplil.gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaardqlskl.dng.. 97 
                  Q+e ++ +l + g+ l+a e G GKT   l  v       ++k++  +l+v+P+  L  +  +++ kf+k+ + r   ii++++ +  + +  +++  
  EPA04684.1 113 FQKEGLDFLLkSSGNALLADEMGLGKTVQTLSYVA------TEKQTFPVLVVAPLVTLN-NWEREIAKFMKKKS-RNGRIIESESSTATIIRTgKSKel 203
                 57888888885668**************9998888......579*************95.67888888888643.555666655554444444232246 PP

                 ..CSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHH CS
                 ..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        DEAD  98 ..vdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinr 144
                   +d+++ + + l + ls   l+  ++r++V DE+++l ++   +++++
  EPA04684.1 204 pvTDFYIINYELLYKRLS--DLSKLNIRTIVCDEVHNLRSK-TTQKYKA 249
                 778999999999999665..444667899***********9.3333333 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.6
                 TSSHCTTEEEEEEETHH CS
                 xxxxxxxxxxxxxxxxx RF
        DEAD 115 gklnlsqvrflVlDEad 131
                   +nl + +++++ E d
  EPA04684.1 475 VGINLTRAKYVIFAELD 491
                 23566666666666655 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.4
                 HHHHHHHHHCTSSHCTTEEE.EEEET.HHHHHHTTTHHHHHHHHHHS CS
                 xxxxxxxxxxxxxxxxxxxx.xxxxx.xxxxxxxxxxxxxxxxxxxx RF
        DEAD 105 pgrlddllstgklnlsqvrf.lVlDE.adrlldqgfsdfinrilnql 149
                  g ldd++  + l  ++ ++  ++DE ad++ +   +d+ + il+q+
  EPA04684.1 521 NGTLDDHVA-NILVDKSYEIdSIMDEtADTYEN---KDKAELILAQI 563
                 455666653.22222333333566662333333...34444444444 PP

>> ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   2.2e-05      0.08      53     149 ..     407     508 ..     376     561 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.2e-05
  ERCC3_RAD25_C  53 ikyhekrgDkiivfsDnvfaLkeyakkl...kkpyiyGetseaerlkilqkfkknpkvntiflskvgDtsiDlPeanvliqissh..fgsrrqeaq 143
                    +k  ++ ++ ++vf+ +    k + +kl   +   i G  s++ r++ ++kf+k ++  +i   + g+  i+l +a+ +i  + +   +  rq   
     EPA04684.1 407 VKNIMEIEESVVVFCHHKVIHKLLHEKLgefSPVSIIGGQSDKMRQEAIDKFQKGESKLMIAGLRAGNVGINLTRAKYVIFAELDwsPAIHRQAED 502
                    44445567789999987665555555551115678***********************9***99*************99976655116789***** PP

  ERCC3_RAD25_C 144 rlGriL 149
                    rl ri 
     EPA04684.1 503 RLHRIG 508
                    **9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (570 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       755  (0.0421105); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 3888.40
//
Query:       EPA04685.1  [L=282]
Description: hypothetical protein BG20_I1362 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.035   14.6   0.6      0.077   13.5   0.6    1.7  1  DUF5400   Family of unknown function (DUF5400)
       0.15   11.9   1.3        1.2    9.1   0.1    2.6  3  FlgD_ig   FlgD Ig-like domain


Domain annotation for each model (and alignments):
>> DUF5400  Family of unknown function (DUF5400)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.6   8.6e-06     0.077      12      52 ..     236     277 ..     225     282 .] 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.6e-06
     DUF5400  12 lsGfitfrllGmrlaphfavl.ilaliltlaalltkntivvy 52 
                 +sG +tf ++G + +p f+++ +l li++++++l+ n+ + +
  EPA04685.1 236 SSGKVTFEIVGTHAIPEFGSIaVLILIVAITSILIVNKSISH 277
                 699***************9874788999******99998865 PP

>> FlgD_ig  FlgD Ig-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1   0.00013       1.2      26      75 ..      63     110 ..      37     113 .. 0.77
   2 ?   -3.5   0.0       1.1   9.6e+03      17      29 ..     166     178 ..     161     180 .. 0.72
   3 ?    0.5   0.0     0.063   5.7e+02      38      56 ..     228     246 ..     209     249 .. 0.55

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00013
                 EEEEE-SS--EEEEEEEEESSSEEEEEEE-SB-TTS-.B--SEEEEEEEEE CS
     FlgD_ig  26 tvtikDasGevVrtidlgaqsaGvvsftWdGtdndGn.kladGaYtvkvta 75 
                    +++  G+vV  +++ ++  G +sf+++    +G    ++G+Y +kv++
  EPA04685.1  63 LAVVTNPVGNVVTVQQFVSEGDGNFSFELN---TSGPlWSQNGEYVLKVQS 110
                 56799***********************99...444404578999888875 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.1
                 E.ESSSEEEEEEE CS
     FlgD_ig  17 elpeaadevtvti 29 
                 +l+++++++t+++
  EPA04685.1 166 TLNSDSKTLTLEL 178
                 5788888888876 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.063
                 EEEEEEESSSEEEEEEE-S CS
     FlgD_ig  38 rtidlgaqsaGvvsftWdG 56 
                 r i+    s+G v+f+  G
  EPA04685.1 228 RHIQIDYPSSGKVTFEIVG 246
                 5555566666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1777.68
//
Query:       EPA04686.1  [L=350]
Description: ABC transporter, permease protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.8e-37  127.0  18.2    6.8e-37  127.0  18.2    2.0  2  BPD_transp_1  Binding-protein-dependent transport system inne
     0.0051   17.3   3.1     0.0053   17.2   0.2    2.5  2  DUF5400       Family of unknown function (DUF5400)
  ------ inclusion threshold ------
        0.3   10.8   6.5        4.2    7.2   0.4    2.8  3  DUF3481       C-terminal domain of neuropilin glycoprotein


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.4       0.2   1.2e+03     160     171 ..      15      26 ..       3      42 .. 0.49
   2 !  127.0  18.2   1.1e-40   6.8e-37       1     184 [.     145     348 ..     145     349 .. 0.99

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.2
  BPD_transp_1 160 alviavlllnlv 171
                   ++v+++ ll+++
    EPA04686.1  15 FVVLMITLLITI 26 
                   222222222222 PP

  == domain 2  score: 127.0 bits;  conditional E-value: 1.1e-40
  BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf.....................vilsilghlilpviillllsaapyvrlirraal 76 
                   gi+lG++++ + ++++d++ + + i+ +s+P+ ++++l++++f                     +i s l+h+ lp+i++++++++ +++l+r+ ++
    EPA04686.1 145 GIFLGAFSGSKVGSIIDRITSSFAIISSSFPVWWIGMLMIFLFsfvyhifpsratplipssdpnYIGSLLYHMTLPLITIVIIGFGSWAYLVRNFIV 241
                   89**************************************999****************************************************** PP

  BPD_transp_1  77 rslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseisnggvlalviavlllnlvad 173
                    ++++d++ a ++ G   ++i+++++l+na+ppiit l+l++ g+lgga+++e ++ wpG+g+l +eai  +d++ i+ g++++l++++l+ ++vad
    EPA04686.1 242 GIMQEDFIIAKKTIGIDQRKIVYTHALKNAAPPIITILALSLSGSLGGAIITEAVFDWPGMGRLYFEAITVMDLPVII-GSTYILTVFFLISIFVAD 337
                   ******************************************************************************.****************** PP

  BPD_transp_1 174 ilqrlldprvr 184
                   +l+ ++dprvr
    EPA04686.1 338 LLYGYFDPRVR 348
                   **********8 PP

>> DUF5400  Family of unknown function (DUF5400)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.2   8.9e-07    0.0053      19      71 ..       5      57 ..       2      66 .. 0.91
   2 ?   -2.0   0.2      0.83     5e+03      28      53 ..     238     265 ..     211     284 .. 0.60

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 8.9e-07
     DUF5400 19 rllGmrlaphfavlilaliltlaalltkntivvylaillqvlaaltaytqiln 71
                r +  rl++ f+vl+++l++t+a + +++  +    +++qv   +t  ++i +
  EPA04686.1  5 RYVATRLITMFVVLMITLLITIALVGSNMDSILKQGVAFQVREEITKNPKIAE 57
                667789****************************************9988875 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.83
     DUF5400  28 hfavlil..aliltlaalltkntivvyl 53 
                  f+v i+   +i++  ++ +++  +vy 
  EPA04686.1 238 NFIVGIMqeDFIIAKKTIGIDQRKIVYT 265
                 4444333113556656666666666665 PP

>> DUF3481  C-terminal domain of neuropilin glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.4   0.00069       4.2      20      35 ..     138     153 ..     127     160 .. 0.83
   2 ?   -3.1   0.0       1.1   6.8e+03       8      23 ..     212     227 ..     208     233 .. 0.66
   3 ?    6.2   0.2    0.0014       8.2       9      34 ..     267     292 ..     261     297 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00069
     DUF3481  20 iiamsalGvllGaicG 35 
                  i++sa+G++lGa  G
  EPA04686.1 138 TIIISAIGIFLGAFSG 153
                 5789*********987 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.1
     DUF3481   8 sllktldPilitiiam 23 
                 sll+ +   liti+++
  EPA04686.1 212 SLLYHMTLPLITIVII 227
                 5666555557777654 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.0014
     DUF3481   9 llktldPilitiiamsalGvllGaic 34 
                  lk   P +iti+a+s  G l Gai 
  EPA04686.1 267 ALKNAAPPIITILALSLSGSLGGAII 292
                 578888999***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       864  (0.0481901); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 2484.58
//
Query:       EPA04687.1  [L=495]
Description: FAD binding domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.3e-42  143.7   0.0    1.1e-41  143.2   0.0    1.2  1  FAD-oxidase_C  FAD linked oxidases, C-terminal domain
    1.3e-32  112.4   0.0    2.3e-32  111.6   0.0    1.3  1  FAD_binding_4  FAD binding domain
  ------ inclusion threshold ------
      0.041   14.0   0.0       0.12   12.5   0.0    1.8  1  BBE            Berberine and berberine like
       0.12   12.3   0.1       0.33   10.9   0.1    1.7  1  MRP-S35        Mitochondrial ribosomal protein MRP-S35


Domain annotation for each model (and alignments):
>> FAD-oxidase_C  FAD linked oxidases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.2   0.0   2.3e-45   1.1e-41       2     250 .]     253     481 ..     252     481 .. 0.91

  Alignments for each domain:
  == domain 1  score: 143.2 bits;  conditional E-value: 2.3e-45
                    -SEEEEEEEEESSHHHHHHHHHHHHHHT---SEEEEE-HHHHHHHHHTS-SSTTS-TTT-EEEEEEEEE-HHHHHHHHHHHHHHHTTT-EEEEE.. CS
  FAD-oxidase_C   2 pearavalvafpsfeaavkavreiaqagiipaalelmdkkaldlveatkgakkglpdeeealllvefegddeeeaeeelealveaileatgaadvl 97 
                    p +r+++ v ++s ++a++  ++i+     p+a+e++dk+ ++ ++   ++      + ++ll+ve+++   ++++++++  v+ + ++++  +  
     EPA04687.1 253 PNNRVLLIVEYQSEKEAATNCSQIVNT--FPTAIEFVDKTIMKNINHRFDK------KSKCLLFVEYDSEI-KNIQKRIKKIVTGKISKIIENN-- 337
                    899************************..**********988766655555......9*************.5666666646666666666665.. PP

                    ........ETGGGGGGGGHHHHHHHHHCTTEEEEEEEEEEEHHHHHHHHHHHHHHHHHHHEEEEEEEEEETTEEEEEEEEEEE..--TT--THHHH CS
  FAD-oxidase_C  98 vaqdeaeaealwkaRkaalpylrdallkagvavlseDtsvPvsrladlvrdikalldkyglevvlfgHagdgnlhlyilfdladeaeeeraeklvd 193
                          +++++wk R + l y +++  k+++  ++eD +vPv+rl++l + ik++ +k+ ++ + +gHag gn+h++++++    ++   ++k++ 
     EPA04687.1 338 -----LDIQKWWKFRDSSLYYSSKV-IKSKTLHVIEDATVPVERLPELFSSIKKINQKFHTKSIAYGHAGNGNIHIRLILKK---KKISIIKKIAN 424
                    .....8899***********88887.9*****************************************************65...78888999999 PP

                    HHHHHHHHTT-----------------------THHHHHHHHHHHH-TT--BSTT-- CS
  FAD-oxidase_C 194 evvdlavelgGsisgEHGvGldkkaylerekgeeglalmrriKaalDPkgiLNPgkv 250
                    e +d+++++gG+i+gEHG Gl++++y+++++g + ++l+ ++K+ +DP+ iLNP k+
     EPA04687.1 425 EYFDIIIKMGGTITGEHGDGLARSEYVKKQYGSKNYKLFIELKNQFDPDSILNPEKI 481
                    99999*************************************************996 PP

>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.6   0.0   5.1e-36   2.3e-32       1     134 [.      52     181 ..      52     185 .. 0.96

  Alignments for each domain:
  == domain 1  score: 111.6 bits;  conditional E-value: 5.1e-36
                    EEEEEEESSHHHHHHHHHHHHHCTSCEEEESSSTTEESTTCSCCEEEEEETTS--EEEEETTTTEEEEETTSBHHHHHHHHHHHTTECSSGGGTTC CS
  FAD_binding_4   1 paavvrpeseeevaaalrlaneaglpvlvrGgGssllgqavatggvvldlsrlnrileideeegtatveaGvtlgdlvealaakglllglepgsgi 96 
                    p++vv p++e +v++++++a+++++pv+vrG+G++l+g+a+ ++g+++dl+++++ ++i+  ++ ++v+aG++ g+l++al+ k  ++++ p+ g 
     EPA04687.1  52 PDIVVIPKNERDVINIVKIARKYKVPVTVRGAGTGLVGSAL-NSGIIMDLKKFDS-IKIQ--KNNVKVGAGTIKGNLDKALENKRKFFPPSPSVGP 143
                    899*************************************8.********88999.6888..89******************************** PP

                    GSBHHHTTTTT-EETTEEGG--HHGTEEEEEEEETTSE CS
  FAD_binding_4  97 pgtvGGaiatnagGygsekyGlirdnvlglevvladGe 134
                    ++++GG+i +n++G++s kyG++ dn+++ ++v++ G+
     EPA04687.1 144 YCSIGGMIGNNSSGSRSLKYGSTIDNIEKITFVDGYGN 181
                    **********************************9886 PP

>> BBE  Berberine and berberine like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.6e-05      0.12      12      40 ..     447     477 ..     424     482 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.6e-05
                 H.HHHHHHHG.GGHHHHHHHHHHH-TT--S- CS
         BBE  12 k.ewgerYFg.gNferLvkvKtkyDPdNvFr 40 
                 + e++++ +g +N++   ++K+++DPd + +
  EPA04687.1 447 RsEYVKKQYGsKNYKLFIELKNQFDPDSILN 477
                 44899999999***************98765 PP

>> MRP-S35  Mitochondrial ribosomal protein MRP-S35
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   7.3e-05      0.33      14      48 ..     313     347 ..     301     352 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 7.3e-05
     MRP-S35  14 sklvqlGdaegklvvGkifhiveddlyidfGlkfh 48 
                 s++ ++ +   k+v+Gki +i+e++l i   +kf+
  EPA04687.1 313 SEIKNIQKRIKKIVTGKISKIIENNLDIQKWWKFR 347
                 66777778889**********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (495 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       976  (0.0544369); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.62u 0.34s 00:00:00.96 Elapsed: 00:00:00.51
# Mc/sec: 2947.87
//
Query:       EPA04688.1  [L=120]
Description: hypothetical protein BG20_I1369 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.32s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 747.60
//
Query:       EPA04689.1  [L=105]
Description: hypothetical protein BG20_I1353 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.067   13.4   0.1        0.1   12.8   0.1    1.3  1  CRISPR_Cas2  CRISPR associated protein Cas2


Domain annotation for each model (and alignments):
>> CRISPR_Cas2  CRISPR associated protein Cas2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   5.8e-06       0.1      12      70 ..      32      94 ..      26      99 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.8e-06
                 HHHHHHHHHHHHHHTTEEEEETTEEEEEESHHH.....HHHHHHHHHHHSHTTTCEEEEEEEET CS
  CRISPR_Cas2 12 drkrrrkvakilkkyGfqrvQySVFegelseaq.....leklkkrlkkiidpeedsiriyklte 70
                 d ++++k+  +l k+++++ Q S+ + e ++a       +  +++l  i d++ + ++ +kl++
   EPA04689.1 32 DTNNYQKFIAYLLKNNLNMKQMSICFDESDKASegghsKKVFANKLAAINDEN-SACYSIKLND 94
                 7899********************99999998888886666677777766655.7777666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 710.22
//
Query:       EPA04690.1  [L=99]
Description: hypothetical protein BG20_I1356 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.33s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 594.95
//
Query:       EPA04691.1  [L=146]
Description: hypothetical protein BG20_I1360 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.026   14.1   0.6       0.05   13.2   0.6    1.5  1  DEAD_2    DEAD_2
       0.13   13.0   2.2        0.2   12.4   2.2    1.5  1  RecG_N    RecG N-terminal helical domain
       0.13   12.3   1.9        0.3   11.2   0.7    2.0  2  AIDA      Adhesin of bacterial autotransporter system, probab
       0.17   11.7   2.2        3.3    7.6   0.6    2.2  2  DUF5362   Family of unknown function (DUF5362)


Domain annotation for each model (and alignments):
>> DEAD_2  DEAD_2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.6   1.1e-05      0.05     129     167 ..      21      58 ..      17      66 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.1e-05
                 HHHHTSCCCHHHHHT..GCGCEEEECTCCCHHHHHHHCC CS
      DEAD_2 129 YqyLldekireslkgislknsivilDEAhNiedvceeaa 167
                 Y  +++++ir+ ++  +++ +i i+DEA+ i+++++e  
  EPA04691.1  21 YLDVMEASIRNIVE-NQVNLTIKIFDEAKQIKNNIIEKG 58 
                 5557899******9.689999*************99865 PP

>> RecG_N  RecG N-terminal helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   2.2   4.6e-05       0.2       3      62 ..      19      75 ..      17      98 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.6e-05
                HHHHHHHHHHHTS---TTT........HHHHHHH---GGGG-HHHH.HHHHHHHHHHTTS CS
      RecG_N  3 EeFLeelekllkkvlsgkleteelieeikkkleliddplleneevlkeklskfldYikpi 62
                Ee+L+ +e+++ +++++++   +l   i +++++i+++++e+  ++++   + l+Yi+  
  EPA04691.1 19 EEYLDVMEASIRNIVENQV---NLTIKIFDEAKQIKNNIIEKGGSEEDANLAYLEYILIS 75
                9***************999...788888899***********999988888889998755 PP

>> AIDA  Adhesin of bacterial autotransporter system, probable stalk
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.31   1.4e+03      36      45 ..      51      60 ..      30      66 .. 0.55
   2 ?   11.2   0.7   6.7e-05       0.3       8      47 ..      81     120 ..      76     127 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.31
        AIDA 36 tdtivdsgGk 45
                ++ i+++gG 
  EPA04691.1 51 KNNIIEKGGS 60
                2345555554 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 6.7e-05
        AIDA   8 aFsisggvAnnvlLenGGsLtVlaggsAtdtivdsgGkli 47 
                  F +++ +++n + +nG   t+ ++ s  +tiv+ ++++i
  EPA04691.1  81 NFGVNNEESQNEITSNGEDITIQSKISGIKTIVSGNATMI 120
                 799*******************************999995 PP

>> DUF5362  Family of unknown function (DUF5362)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.012        55      36      59 ..      37      60 ..      29      74 .. 0.79
   2 ?    7.6   0.6   0.00073       3.3       4      26 ..     100     122 ..      98     133 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.012
     DUF5362 36 Iivglklfkaakaikealrsksee 59
                ++  +k+f+ ak+ik+ + +k + 
  EPA04691.1 37 VNLTIKIFDEAKQIKNNIIEKGGS 60
                56789**********998776555 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00073
     DUF5362   4 islwmkilGvlliilGaltcLsI 26 
                 i + +ki G+ +i++G  t++sI
  EPA04691.1 100 ITIQSKISGIKTIVSGNATMISI 122
                 67789************999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       924  (0.0515366); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 975.85
//
Query:       EPA04692.1  [L=157]
Description: Hsp20/alpha crystallin family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      2e-23   82.5   2.1    2.7e-23   82.0   2.1    1.2  1  HSP20       Hsp20/alpha crystallin family
    4.2e-06   26.2   0.0    6.2e-06   25.7   0.0    1.3  1  ArsA_HSP20  HSP20-like domain found in ArsA
    0.00022   22.2   0.7    0.00035   21.5   0.7    1.3  1  CS          CS domain
    0.00051   20.1   0.7       0.62   10.2   0.1    2.5  2  FKBP26_C    FKBP26_C-terminal
  ------ inclusion threshold ------
      0.015   15.7   0.1      0.021   15.2   0.1    1.4  1  PIH1_CS     PIH1 CS-like domain


Domain annotation for each model (and alignments):
>> HSP20  Hsp20/alpha crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.0   2.1   7.5e-27   2.7e-23       1     102 []      54     157 .]      54     157 .] 0.97

  Alignments for each domain:
  == domain 1  score: 82.0 bits;  conditional E-value: 7.5e-27
                 E--SSEEEEEEEEE-TT--CCCEEEEEETTEEEEEEE--....---TT----SS---EEEEEE--STTB-TTT-EEEEETTEEEEEEEBSS--..---- CS
       HSP20   1 dikeeeeefevkldvpglkkeelkvkvednrvlvkgehe..eeeedekglikerssrkFsrkftLPenvdadkvkaslkdGvLtvtvpkkepekkkker 97 
                 d+++e ++++vk+dvpg+kk+e+k++v++n+v v++eh+  +e++++++l+kers+ ++ r++ L   v ++kv a+l dGvL +t+pk++p + + ++
  EPA04692.1  54 DVIDEGKQYRVKMDVPGIKKNEIKLNVTENSVEVTAEHKesSEDKKKNYLRKERSQISYYRSLPLSGKVQPNKVIAKLTDGVLDITLPKSTPSETQMKK 152
                 5788999********************************9999999***********************************************999999 PP

                 ----- CS
       HSP20  98 kiqiq 102
                 +++i+
  EPA04692.1 153 SVSIS 157
                 99995 PP

>> ArsA_HSP20  HSP20-like domain found in ArsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   1.7e-09   6.2e-06       2      63 .]      60     140 ..      59     140 .. 0.98

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.7e-09
  ArsA_HSP20   2 deyvlkldLPfvdkeeidlsrsgdeLtIkig....................nfrRqitLPsvlarkevtsAkfedgvLeIrF 63 
                 ++y++k d+P+++k ei+l  +++   ++++                    ++ R+ +L  +++  +v  Ak+ dgvL I++
  EPA04692.1  60 KQYRVKMDVPGIKKNEIKLNVTENSVEVTAEhkessedkkknylrkersqiSYYRSLPLSGKVQPNKV-IAKLTDGVLDITL 140
                 78******************************************************************.***********96 PP

>> CS  CS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.7   9.8e-08   0.00035      14      76 .]      64     142 ..      59     142 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 9.8e-08
                 EEEE-TTCTTTTTCEEEEEETTEEEEEE.TSCEEEEECE..................BSS-BETTTEEEEEETTEEEEEEEB CS
          CS  14 vtiyvkkvnikkkdvkvefkerslkvki.gkeklliege..................LfgpIdpeesswtieskkveitLkK 76 
                 v+  v+++  kk+++k++ +e+s++v   +ke+  ++ +                  L g+++p++   ++++  ++itL K
  EPA04692.1  64 VKMDVPGI--KKNEIKLNVTENSVEVTAeHKESSEDK-KknylrkersqisyyrslpLSGKVQPNKVIAKLTDGVLDITLPK 142
                 55667777..*************99999555333333.369***************************************98 PP

>> FKBP26_C  FKBP26_C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.1   0.00017      0.62       9      33 ..      64      88 ..      57      94 .. 0.90
   2 !    7.9   0.0    0.0009       3.2      16      38 ..     122     144 ..     117     152 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00017
                HHHH-TT--..--EEEEETTEEEEE CS
    FKBP26_C  9 IkryiPnidlekfkieiedktvtIe 33
                +k+ +P i+++++k+++++++v+++
  EPA04692.1 64 VKMDVPGIKKNEIKLNVTENSVEVT 88
                8999******************998 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0009
                 --..--EEEEETTEEEEE--TTG CS
    FKBP26_C  16 idlekfkieiedktvtIelpeea 38 
                 ++ +k+  +++d+++ I+lp+++
  EPA04692.1 122 VQPNKVIAKLTDGVLDITLPKST 144
                 5668999*************987 PP

>> PIH1_CS  PIH1 CS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.1   5.8e-06     0.021      31      84 ..      60     130 ..      37     142 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.8e-06
     PIH1_CS  31 kelaieielPllksikevklrvgerrlel..................eskkakyfLslkLpYpvdedkveAk 84 
                 k++++++++P++   +e+kl+v+e+++e+                  e  + +y  sl+L  +v+ +kv Ak
  EPA04692.1  60 KQYRVKMDVPGI-KKNEIKLNVTENSVEVtaehkessedkkknylrkERSQISYYRSLPLSGKVQPNKVIAK 130
                 89**********.789*************9999999999988888754444788888888888888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1385  (0.0772491); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1078.78
//
Query:       EPA04693.1  [L=55]
Description: hypothetical protein BG20_I1359 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.051   14.0   5.4       0.07   13.5   5.4    1.3  1  Lar_restr_allev  Restriction alleviation protein Lar
      0.083   13.2   4.8       0.11   12.8   1.3    2.2  2  Prim_Zn_Ribbon   Zinc-binding domain of primase-helicase


Domain annotation for each model (and alignments):
>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   5.4   7.8e-06      0.07       5      38 ..       8      45 ..       6      54 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.8e-06
  Lar_restr_allev  5 pCPfCggravlersqrvvaeigq...cvyCadCga..st 38
                     pCP Cgg+   +  + + + i +   +  C++C+   ++
       EPA04693.1  8 PCPICGGKMCSISYETTLS-ILKkrsWQVCKECNFerNS 45
                     9***********9999987.555699********95433 PP

>> Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.3   1.2e-05      0.11       4      12 ..       7      15 ..       5      16 .. 0.90
   2 ?    1.6   0.1     0.038   3.4e+02      26      31 ..      34      39 ..      28      47 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.2e-05
                    E--TTTT-T CS
  Prim_Zn_Ribbon  4 spCPvCGGr 12
                    +pCP+CGG+
      EPA04693.1  7 IPCPICGGK 15
                    8*******8 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.038
                    EEETTT CS
  Prim_Zn_Ribbon 26 wfCrqC 31
                     +C++C
      EPA04693.1 34 QVCKEC 39
                    59*999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       777  (0.0433376); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 371.80
//
Query:       EPA04694.1  [L=202]
Description: hypothetical protein BG20_I1364 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00063   19.6   1.6     0.0022   17.8   0.6    2.4  2  HTH_5          Bacterial regulatory protein, arsR family
  ------ inclusion threshold ------
      0.014   15.5   0.2      0.039   14.1   0.2    1.7  1  HTH_34         Winged helix DNA-binding domain
      0.035   14.6   0.7          4    8.0   0.1    2.3  2  Baculo_LEF-11  Baculovirus LEF-11 protein
      0.054   13.6   0.0       0.47   10.6   0.0    2.2  2  HTH_20         Helix-turn-helix domain
       0.14   12.3   0.9       0.21   11.7   0.9    1.3  1  MRP-L20        Mitochondrial ribosomal protein subunit L20
       0.18   12.1   4.8       0.19   12.0   1.5    2.3  2  DUF4709        Domain of unknown function (DUF4709)
        0.2   11.6   1.3        1.1    9.2   0.1    2.6  3  TrmB           Sugar-specific transcriptional regulator TrmB
        3.4    7.7   6.3       0.45   10.5   0.4    2.6  4  HTH_11         HTH domain


Domain annotation for each model (and alignments):
>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.76   1.7e+03      11      11 ..      55      55 ..      36      70 .. 0.55
   2 !   17.8   0.6   9.9e-07    0.0022       2      45 ..      77     120 ..      77     120 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.76
                H CS
       HTH_5 11 L 11
                L
  EPA04694.1 55 L 55
                1 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 9.9e-07
                 HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
       HTH_5   2 ptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLV 45 
                 p ++kIL+lL+ ++++   +++ l++s+ ++S+   kLr++ +V
  EPA04694.1  77 PLQVKILRLLEIKSCSLETISDFLKISETKISEEIEKLRKSQFV 120
                 6689***********************************98665 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.2   1.7e-05     0.039      11      71 ..      87     147 ..      79     151 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.7e-05
      HTH_34  11 svdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkk 71 
                 + ++ + +++++ l++++ ++s +++kL k +++ ++   ++ k   +++i peG e+ k+
  EPA04694.1  87 EIKSCSLETISDFLKISETKISEEIEKLRKSQFVLMSPLRQESKIIKMYEILPEGIEKIKE 147
                 556778899**********************************************998775 PP

>> Baculo_LEF-11  Baculovirus LEF-11 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.017        38      25      61 ..      79     120 ..      72     148 .. 0.74
   2 ?    8.0   0.1    0.0018         4       4      25 ..     163     184 ..     162     198 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.017
  Baculo_LEF-11  25 edvtahhldtds..Fetirefirehadvivrknsk...rkav 61 
                    ++ ++  l+++s   eti +f++  +++i ++  k    ++v
     EPA04694.1  79 QVKILRLLEIKScsLETISDFLKISETKISEEIEKlrkSQFV 120
                    556677788887779********9999996654441004465 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0018
  Baculo_LEF-11   4 rseiialvrevintlkstndte 25 
                    + ei  lv evin+ k+  d++
     EPA04694.1 163 KEEIFDLVDEVINQIKESSDIH 184
                    679*************999985 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.34   7.6e+02      16      33 ..      41      69 ..      39      73 .. 0.69
   2 ?   10.6   0.0   0.00021      0.47      10      54 ..      77     120 ..      74     126 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.34
                HHHH...........STCTTB-HHHHHHH CS
      HTH_20 16 lraL...........araegltaselaer 33
                l+ L           + ++ +++++la++
  EPA04694.1 41 LDSLaslkdrklidlNKDGSFSVTDLARQ 69
                55555555555566688999999999986 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00021
                 HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTE CS
      HTH_20  10 PvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLv 54 
                 P + +ilr+L + +  +++ + + l +s + +s  +++L++  +v
  EPA04694.1  77 PLQVKILRLL-EIKSCSLETISDFLKISETKISEEIEKLRKSQFV 120
                 8899******.****************************998776 PP

>> MRP-L20  Mitochondrial ribosomal protein subunit L20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.9   9.5e-05      0.21      58     145 ..     110     198 ..      90     201 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.5e-05
     MRP-L20  58 akeskassksselPpvlkkksekekkyhltkedieeirrLraeDPekwsr.kkLakk.Fgcsklfvsmvteapkekkkeveaeleavker 145
                 + e+  +s+   + p++++ s+  k y++ +e ie+i++  +   + +s  kkL ++ F+     ++ + e ++ ++++v ++le++k++
  EPA04694.1 110 EIEKLRKSQFVLMSPLRQE-SKIIKMYEILPEGIEKIKEIEKLGLQDNSFeKKLKEEiFDLVDEVINQIKESSDIHREQVVSKLEEIKAK 198
                 4444444434445555544.444799*****999999888888888888625677657*****************************987 PP

>> DUF4709  Domain of unknown function (DUF4709)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.4       0.2   4.4e+02      63      86 ..     123     148 ..      73     155 .. 0.54
   2 ?   12.0   1.5   8.5e-05      0.19      58      92 ..     155     189 ..     128     200 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.2
     DUF4709  63 eklkeea..lelytrlndklkelekl 86 
                 + l++e+  +++y+ l + +++++++
  EPA04694.1 123 SPLRQESkiIKMYEILPEGIEKIKEI 148
                 33333332257777777666666554 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 8.5e-05
     DUF4709  58 qakyeeklkeealelytrlndklkeleklykekve 92 
                 + ++e+klkee ++l +++ +++ke  ++++e+v 
  EPA04694.1 155 DNSFEKKLKEEIFDLVDEVINQIKESSDIHREQVV 189
                 568***************************99875 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.51   1.1e+03      38      55 ..      39      56 ..      20      68 .. 0.81
   2 ?    9.2   0.1    0.0005       1.1      17      56 ..      85     124 ..      82     139 .. 0.81
   3 ?   -1.4   0.1      0.99   2.2e+03      26      44 ..     175     193 ..     171     198 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.51
                CHHHHHHHHHHCTSEEEE CS
        TrmB 38 kvYevLrsLedkGlVere 55
                ++ ++L sL+d+ l++ +
  EPA04694.1 39 RILDSLASLKDRKLIDLN 56
                677889999998888765 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0005
                 HHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
        TrmB  17 LlklgpatadeiaeelgvprskvYevLrsLedkGlVerek 56 
                 Ll+ ++ + ++i+  l+++++k+ e +++L +  +V  ++
  EPA04694.1  85 LLEIKSCSLETISDFLKISETKISEEIEKLRKSQFVLMSP 124
                 7888888999**********************99996555 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.99
                 CHHCCCTTSSCHCHHHHHH CS
        TrmB  26 deiaeelgvprskvYevLr 44 
                 ++i e +++ r +v + L+
  EPA04694.1 175 NQIKESSDIHREQVVSKLE 193
                 6789999999988866665 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.4   3.2e+03      11      24 ..      56      69 ..      51      70 .. 0.76
   2 ?   10.5   0.4    0.0002      0.45       4      44 ..      81     119 ..      79     124 .. 0.86
   3 ?   -3.2   0.1       3.8   8.6e+03      36      43 ..     145     152 ..     144     154 .. 0.80
   4 ?   -3.5   0.0       4.7   1.1e+04      26      41 ..     182     197 ..     175     199 .. 0.53

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.4
      HTH_11 11 eargpisgeeLAee 24
                +++g +s  +LA++
  EPA04694.1 56 NKDGSFSVTDLARQ 69
                56667999999987 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0002
      HTH_11   4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44 
                 +il+lL e ++  s e++++ L++S++ +   I++L+++ +
  EPA04694.1  81 KILRLL-EIKS-CSLETISDFLKISETKISEEIEKLRKSQF 119
                 688888.6666.9***********************99865 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 3.8
      HTH_11  36 IkaLeelg 43 
                 Ik++e+lg
  EPA04694.1 145 IKEIEKLG 152
                 89999998 PP

  == domain 4  score: -3.5 bits;  conditional E-value: 4.7
      HTH_11  26 nvSrrtvrrdIkaLee 41 
                 ++ r  v+  ++++++
  EPA04694.1 182 DIHREQVVSKLEEIKA 197
                 4555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1596  (0.0890178); expected 358.6 (0.02)
Passed bias filter:                      656  (0.0365888); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 1352.33
//
Query:       EPA04695.1  [L=176]
Description: OsmC-like protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-17   63.1   0.0    4.6e-17   62.3   0.0    1.3  1  OsmC      OsmC-like protein


Domain annotation for each model (and alignments):
>> OsmC  OsmC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.3   0.0   2.5e-21   4.6e-17       1      98 [.      70     172 ..      70     174 .. 0.91

  Alignments for each domain:
  == domain 1  score: 62.3 bits;  conditional E-value: 2.5e-21
                 TTXSSB-HHHHHHHHHHHHHHHHHHHHTCCCT---SCEEEEEEEEEECCECT......CEEEEEEEEEEE-SS-H..HHHHHHHHHHHHHSHHHHHHCT CS
        OsmC   1 gdgsgpsPeelllaalasCfaitlravakkkgikledleveveaerdpegak......giteirlkvevkipgadseeklkkllekaekrCpvsntlkn 93 
                 g+g+   P+ +++a++ sCf+ t+  +a+++gi+l++l v  e++ + ++++        ++i++k++v++ +ad ++kl+++l+ ae+rCp + ++++
  EPA04695.1  70 GQGNRLGPMAYCIAGITSCFIGTFVGIASQQGIQLTKLNVNTECNVNFAKTFdisnepITEGINFKIDVTSNNAD-KKKLEEILKMAEERCPAMYSMTH 167
                 6788899*******************************99999877777777888888789********988888.6********************** PP

                 -SSSE CS
        OsmC  94 gvkve 98 
                  ++v+
  EPA04695.1 168 KINVN 172
                 *9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1135.77
//
Query:       EPA04696.1  [L=40]
Description: hypothetical protein BG20_I1352, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00037   20.1   3.0      0.013   15.1   0.7    2.1  2  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
     0.0057   16.2   1.2     0.0057   16.2   1.2    1.0  1  Peptidase_C74    Pestivirus NS2 peptidase
     0.0085   16.0   0.1     0.0094   15.9   0.1    1.1  1  zinc-ribbons_6   zinc-ribbons
  ------ inclusion threshold ------
      0.012   15.5   0.8      0.013   15.3   0.8    1.1  1  Prok-RING_4      Prokaryotic RING finger family 4
      0.025   15.1   5.1       0.13   12.7   1.2    2.0  2  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
       0.03   13.9   1.5       0.14   11.8   0.1    2.0  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
      0.031   13.8   2.1       0.27   10.8   0.1    2.1  2  TF_Zn_Ribbon     TFIIB zinc-binding
      0.049   13.5   2.3        4.8    7.2   0.1    2.1  2  Zn_ribbon_SprT   SprT-like zinc ribbon domain
      0.057   13.5   3.9       0.45   10.7   3.9    1.9  1  Zn-ribbon_8      Zinc ribbon domain
      0.075   12.9   3.1        4.2    7.3   0.1    2.1  2  TFIIS_C          Transcription factor S-II (TFIIS)
        0.3   11.0   5.3       0.64    9.9   5.3    1.6  1  zf-HIT           HIT zinc finger


Domain annotation for each model (and alignments):
>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.7   0.1    0.0074        12      19      31 ..      11      23 ..       5      24 .. 0.87
   2 !   15.1   0.7   8.2e-06     0.013       6      16 ..      28      38 ..      28      39 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0074
  zf-NADH-PPase 19 gwarvCpaCgleh 31
                   g + vC  C++ h
     EPA04696.1 11 GIKYVCLVCNNKH 23
                   7889******988 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 8.2e-06
  zf-NADH-PPase  6 CgrCGaptepa 16
                   C+rCG+++++a
     EPA04696.1 28 CPRCGSKMQRA 38
                   *********98 PP

>> Peptidase_C74  Pestivirus NS2 peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   1.2   3.5e-06    0.0057     163     184 ..      14      34 ..       6      39 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.5e-06
  Peptidase_C74 163 iictvcegrewkggtcpkcgrh 184
                     +c vc+ +  kggtcp+cg +
     EPA04696.1  14 YVCLVCNNK-HKGGTCPRCGSK 34 
                    589***975.7*********76 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   5.8e-06    0.0094      15      41 ..      12      37 ..       4      39 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.8e-06
                    SEEE-TTT--EEEEEEE-SSS-S---E CS
  zinc-ribbons_6 15 eqyhCeaCqedlkkealCpeCeqelev 41
                     +y C  C+++  k  +Cp+C++++++
      EPA04696.1 12 IKYVCLVCNNKH-KGGTCPRCGSKMQR 37
                    6899****9875.6799*******997 PP

>> Prok-RING_4  Prokaryotic RING finger family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.8   8.1e-06     0.013      20      43 ..      15      38 ..      12      40 .] 0.90

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 8.1e-06
  Prok-RING_4 20 vCkeCfdskdlssCPlCqrrisks 43
                 vC  C ++ +  +CP C ++++++
   EPA04696.1 15 VCLVCNNKHKGGTCPRCGSKMQRA 38
                 9*****************998775 PP

>> Zn_ribbon_recom  Recombinase zinc beta ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.2   8.3e-05      0.13      23      40 ..      13      29 ..       2      30 .. 0.77
   2 ?    9.2   0.5    0.0011       1.7       8      17 ..      28      37 ..      27      39 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.3e-05
  Zn_ribbon_recom 23 krhyYrCstyrrkgkkCs 40
                     k+ + +C++++++g +C+
       EPA04696.1 13 KYVCLVCNNKHKGG-TCP 29
                     56899*********.**7 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0011
  Zn_ribbon_recom  8 CgeCGspmtr 17
                     C +CGs+m r
       EPA04696.1 28 CPRCGSKMQR 37
                     ********87 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.2      0.12   1.9e+02       3      10 ..      14      21 ..      13      23 .. 0.84
   2 ?   11.8   0.1   8.6e-05      0.14       4      16 ..      27      39 ..      24      40 .] 0.84

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.12
      zf_UBZ  3 ylCerCgk 10
                y+C  C+ 
  EPA04696.1 14 YVCLVCNN 21
                99**9*96 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 8.6e-05
      zf_UBZ  4 lCerCgkeipese 16
                +C+rCg++++ ++
  EPA04696.1 27 TCPRCGSKMQRAD 39
                8*******98765 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.3     0.042        69       1       9 [.      14      22 ..      14      23 .. 0.82
   2 ?   10.8   0.1   0.00017      0.27       2      12 ..      27      37 ..      26      40 .] 0.73

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.042
                  EEETTTTCE CS
  TF_Zn_Ribbon  1 ykCPnCgst 9 
                  y+C +C+++
    EPA04696.1 14 YVCLVCNNK 22
                  799999986 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00017
                  EETTTTCEECH CS
  TF_Zn_Ribbon  2 kCPnCgstnlv 12
                  +CP Cgs+++ 
    EPA04696.1 27 TCPRCGSKMQR 37
                  69999998765 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1    0.0029       4.8       4      12 ..      13      21 ..      10      24 .. 0.80
   2 ?    6.8   0.3     0.004       6.5       6      13 ..      27      34 ..      26      38 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0029
  Zn_ribbon_SprT  4 vYrCtgCgr 12
                    +Y+C  C +
      EPA04696.1 13 KYVCLVCNN 21
                    8******94 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.004
  Zn_ribbon_SprT  6 rCtgCgre 13
                    +C++Cg++
      EPA04696.1 27 TCPRCGSK 34
                    69999965 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   3.9   0.00028      0.45       6      38 ..      14      37 ..      13      38 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00028
  Zn-ribbon_8  6 YrCeeCghefevlqsisdapltaCPeCgsevrr 38
                 Y C  C++++            +CP+Cgs+++r
   EPA04696.1 14 YVCLVCNNKHK---------GGTCPRCGSKMQR 37
                 55555554333.........457*******999 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.1    0.0026       4.2      27      38 ..      12      23 ..       9      24 .. 0.83
   2 ?    6.7   0.4     0.004       6.5       2       9 ..      27      34 ..      26      37 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0026
     TFIIS_C 27 vfykCtkCghrW 38
                + y+C+ C+++ 
  EPA04696.1 12 IKYVCLVCNNKH 23
                679******985 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.004
     TFIIS_C  2 kCpkCgsr 9 
                +Cp+Cgs+
  EPA04696.1 27 TCPRCGSK 34
                6****997 PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   5.3   0.00039      0.64       4      21 ..      15      33 ..      12      35 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00039
                B-TTT-S.B-SEE-TTT-- CS
      zf-HIT  4 lCgvCgf.pakYkCpkCnt 21
                +C vC++  +  +Cp+C+ 
  EPA04696.1 15 VCLVCNNkHKGGTCPRCGS 33
                7******88889*****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 282.38
//
Query:       EPA04697.1  [L=79]
Description: hypothetical protein BG20_I1358 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.11   12.5   0.1       0.13   12.2   0.1    1.1  1  DUF3290   Protein of unknown function (DUF3290)


Domain annotation for each model (and alignments):
>> DUF3290  Protein of unknown function (DUF3290)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   7.3e-06      0.13      97     132 ..       4      40 ..       1      44 [. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.3e-06
     DUF3290  97 edvlvnstslkdglivkidkkyYrvtlnsdnn.sYtl 132
                 + +  +++ +++g +vkid++ Y+++ +sd + sY +
  EPA04697.1   4 NTIKKAKKLVETGGVVKIDDDLYQIKSSSDPEkSYFV 40 
                 566667788999******************7657765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 532.99
//
Query:       EPA04698.1  [L=219]
Description: hypothetical protein BG20_I1363 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1525.08
//
Query:       EPA04699.1  [L=113]
Description: ArsC family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      5e-13   48.9   0.2    6.1e-13   48.6   0.2    1.1  1  ArsC          ArsC family
    0.00057   20.1   1.9      0.071   13.3   0.3    2.1  2  Glutaredoxin  Glutaredoxin
  ------ inclusion threshold ------
       0.03   14.1   0.0      0.044   13.5   0.0    1.2  1  PriCT_1       Primase C terminal 1 (PriCT-1)


Domain annotation for each model (and alignments):
>> ArsC  ArsC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.6   0.2     1e-16   6.1e-13       1      55 [.       4     103 ..       4     105 .. 0.90

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 1e-16
                 EE-TT.............................................GCB-TTSHHHHHCTCCCTTSBHHHHHHHHHH-GGGB-S-EEEESSEEEE CS
                 xxxxx.............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        ArsC   1 Ygspn.............................................ellskrgttyreLnldkedlsedellelilenpsLirRPivvdgkrlqi 54 
                 Y+ p+                                             ell+kr++ y+ L l+k++ +++++++l+++np Li RPiv+ + ++ +
  EPA04699.1   4 YHKPScitckntiiemermkadiekrdffkepfseselrkiikmtgkkhvELLRKRDKMYKHLELEKNKKTDEQIIKLMVKNPGLILRPIVIVNNKAFV 102
                 77788888888888888888888888888889999999999999999999***************99999*************************9988 PP

                 S CS
                 x RF
        ArsC  55 G 55 
                 G
  EPA04699.1 103 G 103
                 8 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.3   1.2e-05     0.071       2      45 ..       2      45 ..       1      53 [. 0.80
   2 !    7.1   0.1     0.001       6.2      14      58 ..      51      99 ..      48     101 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.2e-05
                  EEEESTSSHHHHHHHHHHHHTTGGEEEEEGCCSHHHHHHHHHHH CS
  Glutaredoxin  2 vlftkptCpyCkkakrlLkelgvkfeeidvdkdeeireelkels 45
                   ++ kp C  Ck+++  ++++++++e +d  k++    el+++ 
    EPA04699.1  2 KVYHKPSCITCKNTIIEMERMKADIEKRDFFKEPFSESELRKII 45
                  59******************************995445544443 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.001
                  HHHHHHHHTTGGEEEEEGCCSHHHHHHHHHHH....TSSSSSEEEETTE CS
  Glutaredoxin 14 kakrlLkelgvkfeeidvdkdeeireelkels....gvrtvPqvfidgk 58
                  k ++lL+++   ++  +++k+++  e++ +l+    g    P v +++k
    EPA04699.1 51 KHVELLRKRDKMYKHLELEKNKKTDEQIIKLMvknpGLILRPIVIVNNK 99
                  5679**********************99999998888888888888876 PP

>> PriCT_1  Primase C terminal 1 (PriCT-1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   7.4e-06     0.044      29      59 ..      17      46 ..      14      52 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.4e-06
     PriCT_1 29 vdrerllalahaiNsrlepPLdesEvrktar 59
                ++ er++a +++ + ++++P++esE+rk+++
  EPA04699.1 17 IEMERMKADIEKRD-FFKEPFSESELRKIIK 46
                56788999999988.89************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1192  (0.0664845); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 701.44
//
Query:       EPA04700.1  [L=193]
Description: hypothetical protein BG20_I1361 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.6e-08   32.2   1.1    1.6e-07   31.5   1.1    1.3  1  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
    1.2e-05   25.2   1.2    1.2e-05   25.2   1.2    1.9  2  Big_1            Bacterial Ig-like domain (group 1)
    0.00014   21.8   1.1    0.00022   21.2   1.1    1.4  1  CarbopepD_reg_2  CarboxypepD_reg-like domain
    0.00015   21.9   0.6    0.00028   21.1   0.6    1.5  1  MetallophosN     N terminal of Calcineurin-like phosphoestera
     0.0075   16.5   0.7      0.013   15.7   0.7    1.4  1  SdrD_B           SdrD B-like domain
  ------ inclusion threshold ------
      0.038   14.3   0.5       0.07   13.4   0.5    1.4  1  Big_6            Bacterial Ig domain
      0.047   13.8   0.1       0.09   12.9   0.1    1.5  1  GBS_Bsp-like     GBS Bsp-like repeat


Domain annotation for each model (and alignments):
>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   1.1   6.2e-11   1.6e-07       2      68 ..      46     117 ..      45     125 .. 0.80

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 6.2e-11
  CarboxypepD_reg   2 isGrVtdasgapiagatVtvtnadtgtvastttdadGafrlrglpp.....gtysvtv...sapGyatatreevt 68 
                      isG Vtd+  +pi+ +tV+++   ++ ++ t td++G+f+++ l+      g+y v +   +a+G    t++e++
       EPA04700.1  46 ISGIVTDHASKPIKDVTVSIR--TGDGTTITSTDEEGKFTIE-LTNikritGNYIVNIiatTADGKTGITSTEFQ 117
                      9********************..455666789*********8.55557788999998866667776666666665 PP

>> Big_1  Bacterial Ig-like domain (group 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   1.2   4.8e-09   1.2e-05      10      56 ..      47      90 ..      43      98 .. 0.89
   2 ?   -1.5   0.1      0.98   2.5e+03      42      48 ..     103     109 ..      90     115 .. 0.57

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 4.8e-09
       Big_1 10 tatvkDangnpvagatVtfsvsggalsassgtTdanGkatvtltstk 56
                + +v+D   +p++++tV++++ +g++++    Td++Gk+t++lt+ k
  EPA04700.1 47 SGIVTDHASKPIKDVTVSIRTGDGTTIT---STDEEGKFTIELTNIK 90
                568********************99964...7************976 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.98
       Big_1  42 TdanGka 48 
                 T a+Gk+
  EPA04700.1 103 TTADGKT 109
                 3444443 PP

>> CarbopepD_reg_2  CarboxypepD_reg-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   1.1   8.5e-08   0.00022       1      40 [.      46      86 ..      46     122 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 8.5e-08
  CarbopepD_reg_2  1 isGtVvdketkeplpgatVyvkg..tkkgtvTdenGnFelkn 40
                     isG V+d  + +p+  +tV++     ++ t+Tde+G+F+++ 
       EPA04700.1 46 ISGIVTDHAS-KPIKDVTVSIRTgdGTTITSTDEEGKFTIEL 86
                     89*****988.7*********6522478899********973 PP

>> MetallophosN  N terminal of Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.6   1.1e-07   0.00028       1      35 [.      48      87 ..      48     114 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.1e-07
  MetallophosN  1 GkVt.skgkgvagVvVs....DGvnvtkTdakGrYeLksd 35
                  G Vt ++ k++++V+Vs    DG+++t Td++G+++++ +
    EPA04700.1 48 GIVTdHASKPIKDVTVSirtgDGTTITSTDEEGKFTIELT 87
                  7899999*********99999***************9844 PP

>> SdrD_B  SdrD B-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.7     5e-06     0.013      17      68 ..      51     104 ..      47     125 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5e-06
      SdrD_B  17 qdagekgisgvtVtLkdakgevvatttTdasGkYkFt..nlt..pGeYkVeftapa 68 
                  d+  k i++vtV++ + +g+++  t Td++Gk++ +  n++   G+Y V+++a++
  EPA04700.1  51 TDHASKPIKDVTVSIRTGDGTTI--TSTDEEGKFTIEltNIKriTGNYIVNIIATT 104
                 58999**********99999988..99******98652254433699*99997744 PP

>> Big_6  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.5   2.7e-05      0.07      26      76 ..      62     112 ..      56     119 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.7e-05
       Big_6  26 tVtvkdadgtvlgtgtadadGeFsvtlepaq..angetlsvvatDaagntSda 76 
                 tV +++ dgt++ +   d++G+F+++l++ +  + +  ++++at a+g+t+ +
  EPA04700.1  62 TVSIRTGDGTTITS--TDEEGKFTIELTNIKriTGNYIVNIIATTADGKTGIT 112
                 78899999999766..79*********98776667777899999999988655 PP

>> GBS_Bsp-like  GBS Bsp-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   3.5e-05      0.09      50      88 ..      75     113 ..      52     116 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.5e-05
  GBS_Bsp-like  50 qsdgtykvtvniknhkneaGkYnvhvYvtdkngkqkglg 88 
                   ++d++ k t++++n k  +G+Y v + +t+++gk+ +++
    EPA04700.1  75 STDEEGKFTIELTNIKRITGNYIVNIIATTADGKTGITS 113
                   56788899***********************99987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 1104.66
//
Query:       EPA04701.1  [L=134]
Description: hypothetical protein BG20_I2514, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-29  102.8   0.0    1.3e-15   57.3   0.0    2.0  2  Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd s
  ------ inclusion threshold ------
      0.039   13.4   0.1      0.063   12.7   0.1    1.3  1  Ribosomal_S5_C  Ribosomal protein S5, C-terminal domain


Domain annotation for each model (and alignments):
>> Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   0.0   1.8e-15   1.6e-11     115     166 ..       1      53 [.       1      62 [. 0.91
   2 !   57.3   0.0   1.4e-19   1.3e-15     203     271 .]      66     134 .]      60     134 .] 0.97

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 1.8e-15
                     S-SSGGGS-------SSBSHHHHHHHHHHHHHHHHHHHHHHHHT--..S-SB- CS
  Complex1_49kDa 115 pYeaYdeldfdvpvgeegDvydRylvrveEmrqSlkIieqaleklpe.gpvla 166
                     pY++Ydeld +  v +egD+y+R  v    m +S++Ii+qal+k+p+ g+v +
      EPA04701.1   1 PYDVYDELDVHTNVMKEGDSYARSKVPWLDMLESCNIIRQALQKMPKsGSVRV 53 
                     9********************************************98677665 PP

  == domain 2  score: 57.3 bits;  conditional E-value: 1.4e-19
                     EEEEEEEETTEEEEEEEEEESSSS-SEEEEE-HHHHTTTTHHHHTTTS-SGGGTHHHHTT---HHHHH- CS
  Complex1_49kDa 203 evyaavEapkGelgvylvsdgsskpyrlkirapsfvnlqaleellkgellaDvvailgsldivlgevDR 271
                      vy++vE+++G lg+y+vsdg+ +pyr+k+   sf nl al++llkge+l  ++ ++ sl++   e+DR
      EPA04701.1  66 TVYKRVESGRGSLGCYIVSDGKPEPYRVKMSVGSFRNLIALPYLLKGEKLGNMPSVYWSLNYWPVEADR 134
                     79****************************************************************998 PP

>> Ribosomal_S5_C  Ribosomal protein S5, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1     7e-06     0.063       3      20 ..      47      64 ..      45      67 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7e-06
                    EETTEEEEEEE--TT--E CS
  Ribosomal_S5_C  3 kfgavkvllkpaprGtGi 20
                    k g+v+v+lkp p+G+G+
      EPA04701.1 47 KSGSVRVKLKPNPKGKGL 64
                    78***************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       243  (0.0135535); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.36s 00:00:00.84 Elapsed: 00:00:00.53
# Mc/sec: 766.09
//
Query:       EPA04702.1  [L=195]
Description: hypothetical protein BG20_I2515, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.8e-26   90.7   4.4    9.8e-26   90.7   4.4    1.4  2  NADHdh    NADH dehydrogenase
  ------ inclusion threshold ------
       0.12   12.4   0.3       0.12   12.4   0.3    2.3  3  NDUF_B12  NADH-ubiquinone oxidoreductase B12 subunit family


Domain annotation for each model (and alignments):
>> NADHdh  NADH dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.3      0.42   3.7e+03     243     243 ..      31      31 ..       7      58 .. 0.53
   2 !   90.7   4.4   1.1e-29   9.8e-26       9     107 ..      91     192 ..      83     195 .] 0.94

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.42
                 S CS
      NADHdh 243 w 243
                 +
  EPA04702.1  31 I 31 
                 1 PP

  == domain 2  score: 90.7 bits;  conditional E-value: 1.1e-29
                 HHHHHHHHHHHHHHHHHHHHTTS--S-SSTTT.TTTHHHHHHHHHCCS-----TTS-HHHHHHHHHHHHHHHHCTTTTS-SSS..SSS--TTHHHHHHH CS
      NADHdh   9 vlllvvalltlleRkvlAriqdRlGPnrvGpl.GllqplaDalKlllKediipkkadkllfllapvlalilallafaviPfge..vladlnvglllila 104
                 +++l++a ++++eRk+lA++q R+GP ++G++ G+lq++ D+lKl+ Ke iip+kadk +f++apv+ +++a + +a+iP+++  v+ad++vgll ++a
  EPA04702.1  91 FAALIAAGTIFIERKMLAKLQLRVGPFYCGKVeGILQLMGDGLKLISKEIIIPAKADKPIFWAAPVIFVATAAAFVALIPVAPgwVVADVDVGLLAVFA 189
                 56788889**********************766*************************************************889************** PP

                 HHH CS
      NADHdh 105 lss 107
                 ++ 
  EPA04702.1 190 IIG 192
                 986 PP

>> NDUF_B12  NADH-ubiquinone oxidoreductase B12 subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.3   1.3e-05      0.12      16      47 ..      75     106 ..      67     111 .. 0.82
   2 ?   -1.7   0.9      0.36   3.2e+03      33      42 ..     154     163 ..     151     171 .. 0.55
   3 ?   -2.6   1.6      0.65   5.8e+03      26      30 ..     172     175 ..     159     193 .. 0.49

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.3e-05
    NDUF_B12  16 fskakrfkraffpGfglavaafaaavgyEhfl 47 
                 f +   f+ a fpGfg a+ ++a ++ +E  +
  EPA04702.1  75 FMTTDLFRIAAFPGFGFAALIAAGTIFIERKM 106
                 666667777888****************9765 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.36
    NDUF_B12  33 avaafaaavg 42 
                 a ++f+a+ +
  EPA04702.1 154 APVIFVATAA 163
                 5555555543 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 0.65
    NDUF_B12  26 ffpGf 30 
                   pG+
  EPA04702.1 172 A-PGW 175
                 2.566 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1422.70
//
Query:       EPA04703.1  [L=124]
Description: shikimate 5-dehydrogenase domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-28   98.1   0.0    3.7e-28   97.6   0.0    1.2  1  Shikimate_dh_N  Shikimate dehydrogenase substrate binding dom


Domain annotation for each model (and alignments):
>> Shikimate_dh_N  Shikimate dehydrogenase substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.6   0.0     2e-32   3.7e-28       1      83 []       7      89 ..       7      89 .. 0.99

  Alignments for each domain:
  == domain 1  score: 97.6 bits;  conditional E-value: 2e-32
                    EEESS-TT-SHHHHHHHHHHHCTSSEEEEEEE-SCCTHHHHHHHHHHTTESEEEE-TTSCCHHHGGSSEE-HHHHHHT--SEE CS
  Shikimate_dh_N  1 viGnpikhSlSPaihnaafkalglngsyeafeveedelekaveelralglaGlnvTiPfKeaviplldelseeAkaigAvNti 83
                    viG+pi+hSlSP+ih+aaf++l+l++sy+a ++++ ele+ ve+l++ +++G+nvTiP+K ++++++d+l+++   igAvNt+
      EPA04703.1  7 VIGDPIDHSLSPNIHSAAFRELNLDCSYIAYRIPKGELEEGVESLKKIKIDGFNVTIPHKIEMMKYIDKLDDSCSIIGAVNTV 89
                    89********************************************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 946.91
//
Query:       EPA04704.1  [L=45]
Description: hypothetical protein BG20_I2588, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-10   41.7   0.0    1.7e-10   41.6   0.0    1.0  1  DHquinase_I  Type I 3-dehydroquinase


Domain annotation for each model (and alignments):
>> DHquinase_I  Type I 3-dehydroquinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   0.0   9.2e-15   1.7e-10     189     228 ..       2      39 ..       1      40 [. 0.95

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 9.2e-15
                  TTGHHHCHHHHHTB-EEEEESSS-..SSTT-EEHHHHHHH CS
  DHquinase_I 189 lGkiSRilgevfGspvtfasleeakasapGqltarelrei 228
                   G+iSR+l++++Gsp+t+ sl+++   apGq++++e+++i
   EPA04704.1   2 SGRISRVLCLYLGSPYTYVSLGKP--VAPGQFSLDEMKKI 39 
                  7*******************9999..************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       202  (0.0112667); expected 358.6 (0.02)
Passed bias filter:                      195  (0.0108762); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 333.25
//
Query:       EPA04705.1  [L=42]
Description: hypothetical protein BG20_I2587 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.26s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 324.78
//
Query:       EPA04706.1  [L=171]
Description: Met-10+ like-protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-47  160.7   0.1    3.9e-47  160.6   0.1    1.0  1  Met_10           Met-10+ like-protein
    4.9e-05   22.9   0.2      9e-05   22.0   0.1    1.4  2  PrmA             Ribosomal protein L11 methyltransferase (Prm
     0.0019   17.8   0.0     0.0024   17.4   0.0    1.2  1  MTS              Methyltransferase small domain
  ------ inclusion threshold ------
      0.025   14.6   0.1       0.14   12.2   0.0    2.1  3  ADH_zinc_N       Zinc-binding dehydrogenase
      0.037   13.4   0.0      0.061   12.6   0.0    1.3  1  DNA_methylase    C-5 cytosine-specific DNA methylase
      0.044   13.4   0.1      0.081   12.5   0.1    1.4  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
      0.044   13.5   0.0      0.061   13.1   0.0    1.2  1  Methyltransf_16  Lysine methyltransferase
       0.14   12.9   0.0       0.25   12.1   0.0    1.4  1  Methyltransf_25  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.6   0.1   1.8e-50   3.9e-47       2     150 ..      21     169 ..      20     171 .] 0.97

  Alignments for each domain:
  == domain 1  score: 160.6 bits;  conditional E-value: 1.8e-50
                 EEEEETTEEEEEB-TTSSHHHHHHHHHHHHHS.S-SCEEEE-S-SBTTTTB--EEEEEES-.SEEEEEETTEEEEEETTTS---GGGHHHHHHHHTT-- CS
      Met_10   2 kfeiiGdvvilnlreelkeykkvigevildkt.kvktvlrkvsevegefRtfelevlaGsdstetihkEngcrfklDvskvyfsskleaErerlaklve 99 
                 +f++iGd++i++++++l   k++ige++l+     k+v+ + s veg fRt++le++aG+d+tet+ kE gc+f +Dv + +fs++l++Erer+ +lv+
  EPA04706.1  21 SFDQIGDIIIVRIPDSLLSKKELIGETLLNEVkIAKSVFYQSSPVEGDFRTRNLEIIAGEDKTETEYKEFGCKFTVDVENAFFSPRLSTERERISNLVQ 119
                 79***************************9985679*************************************************************** PP

                 TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-T CS
      Met_10 100 egevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkve 150
                 +ge+Vv++fAG+G f+i iak  k+ +v++id+nP + k+ ++ni  Nk++
  EPA04706.1 120 DGETVVNMFAGVGMFSIMIAK-KKKCTVYSIDINPIAAKLCEKNILSNKIS 169
                 ********************9.78888**********************97 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.2   2.6e+03      31      55 ..      33      57 ..       8      97 .. 0.50
   2 !   22.0   0.1     4e-08     9e-05     155     210 ..     114     169 ..     111     171 .] 0.95

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.2
        PrmA 31 iedsklleeedif.epaleeeelkee 55
                i ds  l++++++ e+ l+e+++ ++
  EPA04706.1 33 IPDSL-LSKKELIgETLLNEVKIAKS 57
                44444.33333333555555544333 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 4e-08
        PrmA 155 leklvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkve 210
                 + +lv+ ge+v+ + +G G+ +i  ak    +v+ +Di+++A k  ++N+  Nk++
  EPA04706.1 114 ISNLVQDGETVVNMFAGVGMFSIMIAKKKKCTVYSIDINPIAAKLCEKNILSNKIS 169
                 6789*************************************************986 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.1e-06    0.0024      26      81 ..     116     169 ..      96     171 .] 0.88

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.1e-06
                 HCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC CS
         MTS  26 tlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle 81 
                 +l +   ++v+ + +G+G+ ++++ak+++  +v  +d++  A +++++n+ +nk++
  EPA04706.1 116 NLVQ-DGETVVNMFAGVGMFSIMIAKKKK-CTVYSIDINPIAAKLCEKNILSNKIS 169
                 5555.56679***************9765.59********************9986 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.8   6.2e+03     103     116 ..      48      61 ..      33      79 .. 0.69
   2 ?   -0.6   0.0      0.55   1.2e+03      28      43 ..      85     100 ..      72     124 .. 0.73
   3 ?   12.2   0.0     6e-05      0.14       1      32 [.     130     161 ..     130     163 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.8
                 HHTT-EEEEE-SSC CS
  ADH_zinc_N 103 llkeksilGsllgs 116
                 ll+e++i  s++++
  EPA04706.1  48 LLNEVKIAKSVFYQ 61 
                 56777777777776 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.55
                 HHHHHTTESEEEETTT CS
  ADH_zinc_N  28 elakklGadevinyke 43 
                    k++G++++++ ++
  EPA04706.1  85 TEYKEFGCKFTVDVEN 100
                 5679999999999854 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 6e-05
                 HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH CS
  ADH_zinc_N   1 gvGlaavqlAkalGaeviavdsseeklelakk 32 
                 gvG++ +++Ak  +++v+ +d+++  ++l++k
  EPA04706.1 130 GVGMFSIMIAKKKKCTVYSIDINPIAAKLCEK 161
                 9***********************99999987 PP

>> DNA_methylase  C-5 cytosine-specific DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.7e-05     0.061       3      44 ..     124     165 ..     123     171 .] 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.7e-05
                    EEEES-TT-HHHHHHHHTT-EEEEEEE--TTTHHHHHHH-.- CS
  DNA_methylase   3 fidLfaGiGGfrlgleaagfecvaaseidkkaaktYeanfkk 44 
                    ++ +faG+G f++  ++++  +v++++i++ aak+ e+n+ +
     EPA04706.1 124 VVNMFAGVGMFSIMIAKKKKCTVYSIDINPIAAKLCEKNILS 165
                    799***********************************9873 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   3.6e-05     0.081       3      42 ..     123     163 ..     121     170 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.6e-05
  Methyltransf_15   3 vilDlfsGaGGnviqfalv.fekviaieinleklacaqhNa 42 
                      +++ +f+G G  +i +a++  ++v++i+in+   +++++N 
       EPA04706.1 123 TVVNMFAGVGMFSIMIAKKkKCTVYSIDINPIAAKLCEKNI 163
                      7899************9986789****************96 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.7e-05     0.061      46      93 ..     120     167 ..      98     171 .] 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.7e-05
  Methyltransf_16  46 sklsvlELGsGtGlvGlavaellpeakviltDlee.llellkknielnk 93 
                       + +v+ + +G G++ +++a++ +++ v+  D++  + +l +kni  nk
       EPA04706.1 120 DGETVVNMFAGVGMFSIMIAKK-KKCTVYSIDINPiAAKLCEKNILSNK 167
                      56799*****************.9*********9978999*****9876 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00011      0.25       1      43 [.     124     165 ..     124     170 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00011
                      EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHH CS
  Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraee 43 
                      v+ + +G G +++++ak+ +k++v+ +Di++ + + +++++ +
       EPA04706.1 124 VVNMFAGVGMFSIMIAKK-KKCTVYSIDINPIAAKLCEKNILS 165
                      566779************.69****************999855 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1187.13
//
Query:       EPA04707.1  [L=320]
Description: ABC transporter, ATP-binding protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-19   69.8   0.5    7.7e-19   68.6   0.5    1.6  1  ABC_tran  ABC transporter
    0.00056   19.8   0.5       0.25   11.1   0.0    2.8  3  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
     0.0018   17.7   1.7     0.0041   16.6   1.7    1.6  1  SMC_N     RecF/RecN/SMC N terminal domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.6   0.5   1.3e-22   7.7e-19       8     137 .]      91     212 ..      88     212 .. 0.79

  Alignments for each domain:
  == domain 1  score: 68.6 bits;  conditional E-value: 1.3e-22
                 EETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH...........HHHTCHHHHHHHSTTG CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxxxxx RF
    ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren...........esdeeiekalsklglk 95 
                 +++ge+++i+G n  GK+tL+k++ag +kp+ Gei   +           + +i++ pq  q + + +v              e ++e e++l+ l++k
  EPA04707.1  91 VRKGEVLGIMGANALGKTTLMKMIAGVEKPDVGEI---D----------KKIKIAYKPQYLQNDIDAEV--IalldkangatiEGSQEEEQILEPLKIK 174
                 789********************************...2..........33333344433222222211..122333445556899999********** PP

                 GTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  96 elkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                 +l ++ v    ++LSgG+ q++++a +ll+k +l+ lDEp+a
  EPA04707.1 175 KLYNKSV----KNLSGGELQKISVASCLLQKVDLYALDEPSA 212
                 *******....*****************************75 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1      0.22   1.3e+03      47     101 ..      33      83 ..      19      95 .. 0.69
   2 !   11.1   0.0   4.2e-05      0.25       3      30 ..      98     119 ..      96     182 .. 0.71
   3 !    6.2   0.0    0.0013         8     234     284 ..     181     235 ..     141     248 .. 0.66

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.22
      AAA_21  47 slldlydpeipfefeieeflsqgvryryglrlersqveeklssvetllesgllld 101
                  +ld+y p++ ++f++  ++s +v  +   ++ +      + s+++l++++  + 
  EPA04707.1  33 VFLDGYLPTENVRFRDK-KFSFDVSSSSTDEFQEGSE---IMSYPKLEKKYSSFS 83 
                 56788888888888888.7777776666666666666...677777666666555 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 4.2e-05
      AAA_21   3 vliGpNgsGKSnLLdaldllarldrdve 30 
                 ++ G+N+ GK++L++ + ++       +
  EPA04707.1  98 GIMGANALGKTTLMKMIAGV------EK 119
                 688**************766......22 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.0013
      AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHP.......kllrrllellke 284
                 + +lS G ++ + +++ ll+     +l+++DEp ++L+        k+l ++++ + +
  EPA04707.1 181 VKNLSGGELQKISVASCLLQKV---DLYALDEPSAFLDVedritiaKFLQKFVRSFGK 235
                 4567999999955555555444...9************95554444444444444433 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   1.7   6.9e-07    0.0041      55     204 ..     104     249 ..      50     263 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6.9e-07
                 TTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT.................. CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................. RF
       SMC_N  55 klrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrvkrkgeseykingkevtkkevsellesagiske.................. 135
                 +l +                                                                            +                  
  EPA04707.1 104 ALGK----------------------------------------------------------------------------Ttlmkmiagvekpdvgeid 126
                 3333............................................................................3333444444444444444 PP

                 ........................................................CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHH CS
                 ........................................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       SMC_N 136 ........................................................lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkk 178
                                                                         +LSgGe + +++a        ++  ly lDe  a LD + +  
  EPA04707.1 127 kkikiaykpqylqndidaevialldkangatiegsqeeeqileplkikklynksvkNLSGGELQKISVASC----LLQKVDLYALDEPSAFLDVEDRIT 221
                 444444444444444444444444444444444444444444444444445556669*****988777655....467778****************** PP

                 HHHHHHHHCTT..SEEEEE-SSHHHCCC CS
                 xxxxxxxxxxx..xxxxxxxxxxxxxxx RF
       SMC_N 179 vaellkekskn..aQfivislreemlek 204
                 +a++l++   +     ivi ++ +++  
  EPA04707.1 222 IAKFLQKFVRSfgKTAIVIDHDIQLMDL 249
                 *****98665533567787777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 1994.81
//
Query:       EPA04708.1  [L=104]
Description: hypothetical protein BG20_I2331, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 744.26
//
Query:       EPA04709.1  [L=164]
Description: hypothetical protein BG20_I2333 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-37  127.7   0.0    2.9e-37  127.2   0.0    1.1  1  Ribo_biogen_C  Ribosome biogenesis protein, C-terminal
    8.4e-07   28.7   0.1    1.3e-06   28.1   0.1    1.3  1  RLI            Possible Fer4-like domain in RNase L inhibitor


Domain annotation for each model (and alignments):
>> Ribo_biogen_C  Ribosome biogenesis protein, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.2   0.0   3.2e-41   2.9e-37       1     125 [.      38     159 ..      38     160 .. 0.95

  Alignments for each domain:
  == domain 1  score: 127.2 bits;  conditional E-value: 3.2e-41
                    EEE-TT-SSB--GGGHHHHHHT-EEEE---TTT--GGGTTT-E....EB--S-B--STTTTT-BS---HHHHHHHHHHHTT-HHHHHHHHTSSTTH CS
  Ribo_biogen_C   1 ivlspkakkvlspaDreiveksgiavvdcsWarleevkfkklkakeerlLPyLvAaNpvnYgkplkLscvEAlaaalyilglkeeaeellskfkwg 96 
                    +vl+p+++k+l p+D+++++  +i+ +dcsW+ ++++  kk+    +r+LP L+A+NpvnY+k  kL+++E+l+a+l+ilg++++a ++l+kfkwg
     EPA04709.1  38 LVLDPFSEKTLLPSDKSLIN--SIIGIDCSWTLADQAFSKKF-NGIKRKLPPLLAGNPVNYSKLNKLTTAESLSASLFILGFRDDALAILDKFKWG 130
                    69*************99976..6***********99998888.679************************************************** PP

                    HHHHHHCHHHHHHH.TT--HHHHHHHHHH CS
  Ribo_biogen_C  97 eeFlelnkelleeYakckdseevvevqke 125
                    ++F+eln++ll+eY+k ++++++  + ke
     EPA04709.1 131 HTFYELNQNLLDEYSKLESEDQIDIILKE 159
                    *********************99877766 PP

>> RLI  Possible Fer4-like domain in RNase L inhibitor, RLI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.1   1.4e-10   1.3e-06       9      31 ..       9      31 ..       1      36 [. 0.84

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 1.4e-10
                --------TTHHHHHTTSEEEES CS
         RLI  9 dqCdPKKCtgkkcarfcpvrlvr 31
                 q+dPKKCt+ k+++f+++++++
  EPA04709.1  9 YQDDPKKCTAAKMVKFGIAKNIK 31
                59*****************9855 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 1007.15
//
Query:       EPA04710.1  [L=324]
Description: hypothetical protein BG20_I2332, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       765  (0.0426683); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2072.41
//
Query:       EPA04711.1  [L=100]
Description: hypothetical protein BG20_I0904, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.042   13.7   0.3      0.056   13.3   0.3    1.1  1  Pam17           Mitochondrial import protein Pam17
      0.096   13.3   0.3       0.12   13.0   0.3    1.1  1  Nitr_red_assoc  Conserved nitrate reductase-associated protei
       0.16   12.1   6.7      0.055   13.6   2.9    1.9  2  DUF3408         Protein of unknown function (DUF3408)


Domain annotation for each model (and alignments):
>> Pam17  Mitochondrial import protein Pam17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.3   9.3e-06     0.056     101     137 ..      27      62 ..      22      66 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.3e-06
       Pam17 101 nrkklkqleekekeFlerikknRvdpssqsvsnpvpD 137
                 ++++++qlee e+++l+ri+++R+   +qs+++ v D
  EPA04711.1  27 EKSRKEQLEEYERDYLKRIEQQRI-EDEQSYQEAVED 62 
                 578899******************.578999999988 PP

>> Nitr_red_assoc  Conserved nitrate reductase-associated protein (Nitr_red_assoc)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.3     2e-05      0.12      36      84 ..      32      80 ..      29      93 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2e-05
  Nitr_red_assoc 36 qqlsqeerqaLvelpceteeeikayreaLqelveekageeakeleieee 84
                    +ql++ er+ L ++  ++ e++++y+ea+++ v+++++++ + l+   e
      EPA04711.1 32 EQLEEYERDYLKRIEQQRIEDEQSYQEAVEDAVKSRTNATHSALPKGFE 80
                    58999********************************999888876544 PP

>> DUF3408  Protein of unknown function (DUF3408)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   2.9   9.2e-06     0.055      48      79 ..      15      46 ..       2      56 .. 0.75
   2 ?    0.6   0.3     0.097   5.8e+02       8      11 ..      57      60 ..      44      96 .. 0.42

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.2e-06
     DUF3408 48 ekekkekkkrisekkrktsledYeetFLkrkk 79
                e+++  +++  sek+rk++le+Ye+ +Lkr +
  EPA04711.1 15 EQQQVSSNSGNSEKSRKEQLEEYERDYLKRIE 46
                34444455567899**************9865 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.097
     DUF3408  8 keli 11
                +e +
  EPA04711.1 57 QEAV 60
                2222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2151  (0.119973); expected 358.6 (0.02)
Passed bias filter:                      955  (0.0532657); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 616.35
//
Query:       EPA04712.1  [L=340]
Description: phosphoribosylformylglycinamidine cyclo-ligase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-25   89.0   0.0    7.1e-25   88.0   0.0    1.5  1  AIRS_C    AIR synthase related protein, C-terminal domain
    4.2e-16   59.4   1.3    7.4e-16   58.6   1.3    1.5  1  AIRS      AIR synthase related protein, N-terminal domain


Domain annotation for each model (and alignments):
>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.0   0.0   7.9e-29   7.1e-25       1     152 [.     175     333 ..     175     336 .. 0.87

  Alignments for each domain:
  == domain 1  score: 88.0 bits;  conditional E-value: 7.9e-29
                 STTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTT....TSEHHHHHHHHHHHHHHHHHHHH.HTTECEEEE--TTHHHHHHHHHHHTTTEEEEEECG.. CS
      AIRS_C   1 kpGdvliltgslGlggagtslkrkileeegldds....avqlgdvlleptliyvkralaal.kglvkaahDvTgGGLlgalaemapasgvgaeidld.. 92 
                 k Gd +i+ +s+G++++g+sl+rk l ++   ++     + +g++ll+pt iyvk+ l  + k ++++++++TgG     l ++    ++g++id    
  EPA04712.1 175 KSGDIIIGAKSSGIHSNGYSLARKALLSKYSVKDkvkkVGRIGNALLTPTEIYVKPVLEINqKCKINGFAHITGG-AFTKLLRL---KNIGFNIDNLpk 269
                 57*********************998776544447995556*********************************5.55555555...6699****9996 PP

                 THHHHHHHH....HHHHHHHCSTTTEEEEEEEHGGH.HHHHHHHHHTTCCCEEEEEEEEESSSEE CS
      AIRS_C  93 kvpifdele....splemllsensGrllvavppeea.davlaileeeglpeaavIGevtakeels 152
                  +pi++ ++    +++em++++n+G+++++++p+++ d++++i++++ + e ++IG+++ k+++ 
  EPA04712.1 270 IPPIMELIAeqgvKQEEMYKTFNMGVGFCVIAPKDQgDKIKSIFKKHKI-ESQEIGQIISKKGVF 333
                 555555555888*************************************.8*********98765 PP

>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.6   1.3   8.3e-20   7.4e-16       5      94 .]      57     163 ..      20     163 .. 0.88

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 8.3e-20
                 EEEEEEEEE.EECC....TCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC.....HHHHHHHHHHHHHHHTT-EEEEEEEEEESS........EEE CS
        AIRS   5 vvvttdshnrpvlv....epvhfiGakavavnlsDlaamGArPlalllslalp.....wleevvrglaeaaeelgvplvgGdtsfsne........pti 86 
                 ++ +td+++++v++    +++++iG  +va+n++D+++ GA+P+ +++++a +     +++++v+gl ++a++  +p+vgG+t+ +++        + +
  EPA04712.1  57 LATHTDGVGTKVVIanlmKKYDTIGIDCVAMNVNDIICIGATPVSFVDYIAANkndqvIFKKIVEGLVKGAKKSAMPIVGGETAIMPDvitgkgfsFDL 155
                 478999999*9999555566777*************************************************************998878888888778 PP

                 EEEEEEEE CS
        AIRS  87 svtavGlv 94 
                 + ++vGlv
  EPA04712.1 156 AGMVVGLV 163
                 88888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2329.46
//
Query:       EPA04713.1  [L=49]
Description: hypothetical protein BG20_I0915 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       786  (0.0438396); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 333.45
//
Query:       EPA04714.1  [L=186]
Description: transcription factor [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.9e-55  183.2   0.0    2.2e-27   94.8   0.0    2.0  2  TBP            Transcription factor TFIID (or TATA-binding pr
    6.3e-08   32.6   0.0    0.00046   20.2   0.0    2.3  2  DUF3378        Domain of unknown function (DUF3378)
  ------ inclusion threshold ------
      0.098   12.5   0.2       0.33   10.8   0.1    1.8  2  RTT107_BRCT_5  Regulator of Ty1 transposition protein 107 BRC


Domain annotation for each model (and alignments):
>> TBP  Transcription factor TFIID (or TATA-binding protein, TBP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.8   0.0   3.6e-31   2.2e-27       3      84 ..       9      88 ..       7      89 .. 0.96
   2 !   86.6   0.0   1.4e-28   8.2e-25       2      83 ..      99     178 ..      98     179 .. 0.96

  Alignments for each domain:
  == domain 1  score: 94.8 bits;  conditional E-value: 3.6e-31
                EEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHHHHHHHH CS
         TBP  3 kiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakkiapilkk 84
                 ++Nvvasa++++++dL+++ ++    ++eY p++fpglv+rl++pk++ liF+sGk+v+tG ksee +r+a+k+++++l+k
  EPA04714.1  9 SVENVVASASVDQKMDLNEITRTF--PDVEYHPDQFPGLVFRLKSPKTATLIFTSGKMVCTGSKSEEMARKAVKTVVQKLRK 88
                79******************7665..******************************************************97 PP

  == domain 2  score: 86.6 bits;  conditional E-value: 1.4e-28
                 EEEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHHHHHHH CS
         TBP   2 fkiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakkiapilk 83 
                 ++iqN+vas+nlg +++Le+ a+++    + Yepe+fpgl+ r+ +pk+++l+FssGk+v+tGak+e ++++ ++++  +l+
  EPA04714.1  99 VEIQNIVASINLGGKIHLEQAARTL--PRSMYEPEQFPGLIHRMLDPKTVILLFSSGKLVCTGAKKEPDVYRSVNNLHALLE 178
                 79*******************9887..************************************************9998886 PP

>> DUF3378  Domain of unknown function (DUF3378)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   7.7e-08   0.00046      11      62 ..      25      77 ..      17      88 .. 0.83
   2 !   10.2   0.0    0.0001      0.61      24      57 ..     130     163 ..     122     171 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 7.7e-08
     DUF3378 11 ikkmkeyyksk.lrskkppyavfaakkndttItaYtSgKVlFQGknaeaeAsk 62
                +++++ ++ +      + p+ vf+ k+++t   ++tSgK +  G++ e+ A k
  EPA04714.1 25 LNEITRTFPDVeYHPDQFPGLVFRLKSPKTATLIFTSGKMVCTGSKSEEMARK 77
                556666665543567789*******************************9986 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0001
     DUF3378  24 skkppyavfaakkndttItaYtSgKVlFQGknae 57 
                  ++ p+ + +  +++t+I ++ SgK++  G++ e
  EPA04714.1 130 PEQFPGLIHRMLDPKTVILLFSSGKLVCTGAKKE 163
                 568899999999***************9998876 PP

>> RTT107_BRCT_5  Regulator of Ty1 transposition protein 107 BRCT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   5.6e-05      0.33      18      59 ..      62     107 ..      49     110 .. 0.82
   2 ?   -1.6   0.0      0.42   2.5e+03      19      30 ..     154     165 ..     151     182 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5.6e-05
                    EEEEESSS.TT.....SSHHHHHHHHHTTEEE-SGCCT.-SEEE-S CS
  RTT107_BRCT_5  18 iravlTgceeevn...kedsdkkkLrklGikivqeakk.cntliAp 59 
                     ++v+Tg ++e       ++  +kLrk Gik+ ++a+  ++ ++A+
     EPA04714.1  62 GKMVCTGSKSEEMarkAVKTVVQKLRKGGIKVKKDATVeIQNIVAS 107
                    589*****999667777788899***********887668888885 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.42
                    EEEESSS.TT.. CS
  RTT107_BRCT_5  19 ravlTgceeevn 30 
                    ++v+Tg ++e +
     EPA04714.1 154 KLVCTGAKKEPD 165
                    689999998754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       786  (0.0438396); expected 358.6 (0.02)
Passed bias filter:                      653  (0.0364214); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1316.35
//
Query:       EPA04715.1  [L=411]
Description: transporter, CPA2 family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.6e-61  206.0  50.9      1e-60  205.6  50.9    1.0  1  Na_H_Exchanger  Sodium/hydrogen exchanger family


Domain annotation for each model (and alignments):
>> Na_H_Exchanger  Sodium/hydrogen exchanger family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.6  50.9   5.7e-65     1e-60       6     376 ..      16     394 ..      11     398 .. 0.88

  Alignments for each domain:
  == domain 1  score: 205.6 bits;  conditional E-value: 5.7e-65
                     HHHHHHHH...HHHHTTSXHHHHHHHHHHHHTTTTTS..............HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCTHHHHHHHHHHHHH CS
  Na_H_Exchanger   6 llallvgl...larrlklpeivgliiaGlllGpsglg..lieps.......eedlevlselglilllFlaGleldlrelrknlksilllallgvl 88 
                     +l++ ++l   l+ rlklp ++g++iaG+++Gp+ lg  +i  +       +  + vl e g i++lF aGle+ ++e++k +k+++ +a+lgv+
      EPA04715.1  16 ILLFAAKLmaeLFLRLKLPIVLGELIAGIVIGPFALGayIIGTDglpllhiNNEIRVLGEMGAIVILFMAGLEMTPKEFLKGGKASFTVAILGVV 110
                     334444445568*************************7733333677777779****************************************** PP

                     HHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC.CCCTSTCCCCCCHHHHHHHHHHHCCCCCHHHHHHTX.XXXXTSSSTSXHHHH CS
  Na_H_Exchanger  89 itvvliGlllylllilgiplleallfgailsatdpvvvlailkeegrvperlgtlllgesvlnDavavvllavllalak.eeaggetslllllli 182
                     i++++ Gl++     +g++ l+++l++++l+at++++ +++l+e g++++  ++l++g++v++D++a+ +l+v+ ++a+  +  ++++++ + ++
      EPA04715.1 111 IPFFA-GLVAFQ--MFGFDALQSMLIATALTATSIAISIQVLSEFGKLKTPEARLIIGAAVVDDILAIAVLSVVTSIAGgDGGVANIDIMDVTIT 202
                     *****.998876..689*************************************************************99666677777777777 PP

                     HHHHHHHH.HHHHHHHHHHHHHHHHHSCTHHHHHHHHHHHHHHHHHHHHHTSXXXHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH CS
  Na_H_Exchanger 183 flvvavgg.lllglvigwllrlitrftdddrelevllvlllallaallaellgvsgilgaflaGlvlseyefsnklseklesfreglfnplfFvl 276
                     +l v++++ ++l +++ +++r+it ++++ + +   ++ +  ++aa+la ++g+s i+gaf++G++ls++++ +k++  +++++  +f+plfF++
      EPA04715.1 203 ILQVLGFFaIMLLAAVVVMPRIITPRLWKAKGSVEGIATASFFGAAALAGSIGLSPIVGAFAVGMALSTTKVFEKVEGYVRQIG-LIFAPLFFAI 296
                     7766665505555666777788888889********************************************************.********** PP

                     HHHHSXHHHHHXXHHHHHHHHHHHHHHHTHHHHHHHHHTTTXSSXHHHHHHCCCCSS.BHHHHHHHHHHHHHHXHHHHTTSSTTTCSTSXHHHHH CS
  Na_H_Exchanger 277 vGlsldlkvlnnhlsvlilvllilvaillgrilavflllrllglslrealiigfgglqrgavalalaalgpalgllarelyallivvvlftvlvq 371
                     +G+++dl ++n  l+ l+l  +++++ +++++ +  l + ++ +s  + + +g+g+++rg+v l++a +g ++g+l++++y++++++v  t+++ 
      EPA04715.1 297 IGAQVDLRAVN--LEILALSGVVIIIAIVTKLGGCGLPAMYFLKSKAQGMRVGIGMISRGEVGLIVAGVGISTGVLTSNVYSTIVIMVAATTIIT 389
                     **********7..666666655555555899999877777777999***********************************************99 PP

                     HHHHH CS
  Na_H_Exchanger 372 Glslk 376
                     +++lk
      EPA04715.1 390 PIWLK 394
                     99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       950  (0.0529868); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2564.32
//
Query:       EPA04716.1  [L=108]
Description: putative methionyl-tRNA synthetase, beta subunit [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.9e-22   78.6   0.0    3.3e-22   78.4   0.0    1.0  1  tRNA_bind  Putative tRNA binding domain


Domain annotation for each model (and alignments):
>> tRNA_bind  Putative tRNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.4   0.0   1.8e-26   3.3e-22       1      95 [.      14     105 ..      14     106 .. 0.97

  Alignments for each domain:
  == domain 1  score: 78.4 bits;  conditional E-value: 1.8e-26
                 EEEEEEEEEEEETTSSTEEEEEEEESSSSEEEEEESCTTTSTHHHHTTEEEEEETTSESEEETTEEESSEE-EEECCESSCEEEEEESST--TTC CS
   tRNA_bind   1 lrvGkvleaeehpnadkLlvlkvdvGeeeprqivsgaknvyepeelvakkvvvvanlkpkklrGveSeGMilsaeeldekevgilelpadveaGe 95 
                 +rv+k+++ e++p++ ++++  +d+G+e+ r+++ g +++y+pe++v+k v+v+anl+pk + GveS++M+l+a+   +++   l++++d+++G+
  EPA04716.1  14 IRVAKIVSTEPIPGKTRIIKGVIDLGNEQ-RNVIIGGAQYYNPEDIVGKTVIVLANLEPKTMAGVESNAMLLAAD--VDDKPFWLTVNEDIPLGS 105
                 79***************************.*********************************************..7999***********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       249  (0.0138881); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 758.75
//
Query:       EPA04717.1  [L=187]
Description: DNA-3-methyladenine glycosylase I [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-80  268.9   0.3    2.1e-80  268.6   0.3    1.0  1  Adenine_glyco  Methyladenine glycosylase
  ------ inclusion threshold ------
       0.11   11.5   0.0       0.15   11.1   0.0    1.1  1  DUF3383        Protein of unknown function (DUF3383)


Domain annotation for each model (and alignments):
>> Adenine_glyco  Methyladenine glycosylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  268.6   0.3   2.4e-84   2.1e-80       4     176 ..       9     181 ..       6     182 .. 0.98

  Alignments for each domain:
  == domain 1  score: 268.6 bits;  conditional E-value: 2.4e-84
  Adenine_glyco   4 kdplyvaYhDeeWGvpvtddkklFelLvLegfqaglswetilkkreafreafdgFdlekvakydeekveelladegiirnrlKieavisnAravla 99 
                    kd+l ++YhD+eWG+p++dd+klFe+L+Leg+qagl+w+tilk+re++r+af++Fd++kv+ky+ +++e+ll++++iirn+lKi+++i+nA+ +++
     EPA04717.1   9 KDDLNIEYHDNEWGKPQHDDRKLFEFLILEGAQAGLTWTTILKRREGYRKAFSDFDPDKVSKYTAQHIENLLNNSEIIRNKLKINSAINNAKLFIK 104
                    58899******************************************************************************************* PP

  Adenine_glyco 100 lqeefgsfseylwsfvdgkpiveelksaeevpattelsealskdLkkrGfkfvGptivysflqavGlvndhleeCfr 176
                    +q+efgsf++y+w fv++++i++++k+ +++pa+t+ s+++s dLkk Gf+fvGpti+y+f+qavG+vndh+++Cf 
     EPA04717.1 105 IQKEFGSFDKYIWGFVNHTTITNNFKRLSDIPASTDISKKMSDDLKKYGFNFVGPTICYAFMQAVGMVNDHTSDCFL 181
                    ***************************************************************************96 PP

>> DUF3383  Protein of unknown function (DUF3383)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   1.6e-05      0.15     303     361 ..     121     179 ..     119     184 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 1.6e-05
     DUF3383 303 nnttitlkFkqepgitaev.ltstqadaldaknyNyYgnynnntailqeGvlsggkfiDe 361
                 n+ttit +Fk+ + i+a++ +++++ d l++ + N+ g +   +a++q   +++++  D 
  EPA04717.1 121 NHTTITNNFKRLSDIPASTdISKKMSDDLKKYGFNFVGPT-ICYAFMQAVGMVNDHTSDC 179
                 89*************99754999*****************.9999999988888877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1252.56
//
Query:       EPA04718.1  [L=49]
Description: hypothetical protein BG20_I0919 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.19   11.2   0.5        0.2   11.2   0.5    1.0  1  DUF1129   Protein of unknown function (DUF1129)


Domain annotation for each model (and alignments):
>> DUF1129  Protein of unknown function (DUF1129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.5   1.1e-05       0.2      94     129 ..       2      40 ..       1      47 [. 0.75

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 1.1e-05
     DUF1129  94 llfgilalfskkkqtas...iGlitlllvalvgGlamvl 129
                 +++g + l+   + +++    G+++ +  a+vgG+ +++
  EPA04718.1   2 IIIGAMLLILAPNINQDhpeLGIVSFVGGAIVGGIGFYF 40 
                 566777766666666666778999999999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 329.13
//
Query:       EPA04719.1  [L=372]
Description: glycosyltransferase, group 2 family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.4e-27   95.0   0.0    6.1e-27   94.5   0.0    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
    7.9e-21   75.0   0.0    1.1e-20   74.5   0.0    1.1  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    1.6e-09   37.5   0.1    3.5e-09   36.4   0.0    1.5  2  Glyco_transf_21  Glycosyl transferase family 21
      5e-07   29.5   0.1    7.6e-07   28.9   0.1    1.2  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
    0.00037   21.0   0.0    0.00066   20.2   0.0    1.4  1  Glyco_tranf_2_4  Glycosyl transferase family 2


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.5   0.0   1.7e-30   6.1e-27       1     169 [.      25     197 ..      25     198 .. 0.91

  Alignments for each domain:
  == domain 1  score: 94.5 bits;  conditional E-value: 1.7e-30
                      EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCH...C-TTEEEEEESSS-.HHHHHHHHHHHH--SSEEEEEESSE CS
  Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelak...edprvrvirreenv.GkagalnaglraatgdyilflDaDd 90 
                      s++ p+ Nee+ ++++l+sl++q +y+++eiiv+DD+S D+t +i+ e+ak   +  +v    ++ ++ Gk  a ++g+++atg+++lf DaD+
       EPA04719.1  25 SIILPARNEEEFIEKCLDSLIDQ-DYSNYEIIVIDDSSDDSTNKIISEYAKkhsKIIPVNARSKPDGWmGKNWACMEGFKMATGELLLFTDADT 117
                      8**********************.***************************87777788888899999************************** PP

                      EE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SS..EEEECCHCCCCHCCCCCCSTTCSTCCCEEEEHHHHHC CS
  Glycos_transf_2  91 epdpdwleklvealekdgadvvlgqrprifgetdeiernkrv..generlyfkerkrslkgnlsfeigsaallrrealeel 169
                       ++++ ++  v  l    +  +l ++p+ ++++++   ++ +   +    +  +r +    +++++ gs+++++re +e +
       EPA04719.1 118 KHSKNVISLAVSNLLS-SKLDALSAIPKMRVMDFWTGITLPMisVFLHTRFSAIRVNDPAKKTAYFFGSFFIIKRETYEAV 197
                      ****************.7778999999999999999998888866777777777777777899999999999999988765 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.5   0.0   3.1e-24   1.1e-20       1     206 [.      22     229 ..      21     250 .. 0.90

  Alignments for each domain:
  == domain 1  score: 74.5 bits;  conditional E-value: 3.1e-24
  Glyco_tranf_2_3   1 prdlavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnealravksdlvllv 94 
                      p  ++++ p+ nee+ ++++l+sl+ q+y+++e++v++d sd++t + + e a++++++ + v  +++  g  gk +a  e++++++++l+l+ 
       EPA04719.1  22 PK-VSIILPARNEEEFIEKCLDSLIDQDYSNYEIIVIDDSSDDSTNKIISEYAKKHSKI-IPVNARSKPDGWMGKNWACMEGFKMATGELLLFT 113
                      45.9*****************************************************97.8877778877************************ PP

  Glyco_tranf_2_3  95 DdDtvvePdtlkrllqffltpkvgavgtpvfllnrstl...vsalgalefaerhlrflaarralgvltlnGsgslirrevlkelegldp.lfll 184
                      D+Dt  +++++  ++  +l++k +a+ +   ++  + +   + +   +++  r+  +++ + a++++++ Gs++ i re +++ + + + +  +
       EPA04719.1 114 DADTKHSKNVISLAVSNLLSSKLDALSAIPKMRVMDFWtgiTLPMISVFLHTRFSAIRVNDPAKKTAYFFGSFFIIKRETYEAVGMHEGvKHEI 207
                      ***************9999********87777655544332444455688899999999999999*******************988889**** PP

  Glyco_tranf_2_3 185 tdDyelglrlrragfrtayvpg 206
                       +D  lg  +++ag+++++v g
       EPA04719.1 208 IEDGALGKKVKEAGHKMKIVRG 229
                      *****************98865 PP

>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.3   4.6e+03      18      39 ..      39      60 ..      20      61 .. 0.63
   2 !   36.4   0.0   9.7e-13   3.5e-09      12     147 ..      88     228 ..      78     250 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.3
  Glyco_transf_21 18 KvnnllqaleaakydllvisDs 39
                     K    l   ++ +y+++vi Ds
       EPA04719.1 39 KCLDSLIDQDYSNYEIIVIDDS 60
                     5544445556688999999987 PP

  == domain 2  score: 36.4 bits;  conditional E-value: 9.7e-13
  Glyco_transf_21  12 pvgvnpKvnnllqaleaakydllvisDsdvrvkpdyLeellaaledpkvglVtslpvgsdak...glaaaleaafl.ntlagvlqa.klsglgf 100
                      p g   K+++++ +++ a  +ll++ D+d+  +++ +   + +l ++k   ++++p     +   g++  + ++fl + ++++     ++++  
       EPA04719.1  88 PDGWMGKNWACMEGFKMATGELLLFTDADTKHSKNVISLAVSNLLSSKLDALSAIPKMRVMDfwtGITLPMISVFLhTRFSAIRVNdPAKKTAY 181
                      5555679***********************************************997444332234444455666544444444446889**** PP

  Glyco_transf_21 101 avGksmalrreaLeaiGGfealadeLAeDyalgkllraaGlkvvlsp 147
                       +G++ +++re+ ea+G  e +++e+ eD algk +++aG k+ +++
       EPA04719.1 182 FFGSFFIIKRETYEAVGMHEGVKHEIIEDGALGKKVKEAGHKMKIVR 228
                      ******************************************99886 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.1   2.1e-10   7.6e-07       1     179 [.      25     198 ..      24     211 .. 0.74

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 2.1e-10
  Glyco_tranf_2_2   1 svviplraseerhyieerv..lqkakyydeeielivvddgSsekfleevssiidlnllv...ylkdeddkayslaaarNrGaskaesdlvlFlD 89 
                      s+++p r++ee  +ie  +  l  + y   + e+iv+dd S + + + +s   +++ ++     + ++d   ++  a   G++ a ++l+lF D
       EPA04719.1  25 SIILPARNEEE--FIEKCLdsLIDQDY--SNYEIIVIDDSSDDSTNKIISEYAKKHSKIipvNARSKPDGWMGKNWACMEGFKMATGELLLFTD 114
                      45666666554..69999964444555..89********************9988888744344556777899999999*************** PP

  Glyco_tranf_2_2  90 aDcfissDkfekilklitikklrenidaavvlpvvdlnkedsevlkdvedltassrvledllaakstlvkffapssssilinrraflevG 179
                      aD   s +    +++l+ +  l+   da+ ++p +   +  + +   +  ++ ++r+   ++ + ++  k     +s ++i+r+++  vG
       EPA04719.1 115 ADTKHSKN----VISLAVSNLLSSKLDALSAIPKMRVMDFWTGITLPMISVFLHTRFS--AIRVNDPAKKTAYFFGSFFIIKRETYEAVG 198
                      **999875....5666777888888898888888877777776666666666666666..555555555555555666666666665555 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   1.8e-07   0.00066       1      49 [.      31      83 ..      31     117 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.8e-07
  Glyco_tranf_2_4  1 rneadiLpeflahhlalgfdr..ilvydndstDgtrailkelpe..vkllhvd 49
                     rne+++++++l+ + + ++++  i+v+d+ s+D t +i++e+++   k+++v 
       EPA04719.1 31 RNEEEFIEKCLDSLIDQDYSNyeIIVIDDSSDDSTNKIISEYAKkhSKIIPVN 83
                     8*****************97445****************99754224455544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       852  (0.0475208); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2400.58
//
Query:       EPA04720.1  [L=373]
Description: hypothetical protein BG20_I0934 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     1e-131  439.2   7.1   1.2e-131  439.0   7.1    1.0  1  DUF1512         Protein of unknown function (DUF1512)
  ------ inclusion threshold ------
       0.38   11.2   3.8        1.5    9.3   0.1    2.8  3  Linker_histone  linker histone H1 and H5 family


Domain annotation for each model (and alignments):
>> DUF1512  Protein of unknown function (DUF1512)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  439.0   7.1  1.3e-135  1.2e-131       2     355 ..      21     371 ..      20     372 .. 0.98

  Alignments for each domain:
  == domain 1  score: 439.0 bits;  conditional E-value: 1.3e-135
     DUF1512   2 isliifllllill.llglnqklqlavllrdiekklakleklaeeakkkvvellkklg..kedpkklverlleffviePvdlePtgivkrlehllrtsed 97 
                 i+++i++l ++++ l+g  q++qlav++ +i+k ++kl+++++++++++++++kk+   k+dp+k ++r+l++f+i+Pvd++P+giv++++h++r +ed
  EPA04720.1  21 IMMLIWILPIFIFvLYG--QRIQLAVTSGEIKKGIKKLDEYKTQSRTELIDYIKKNMnpKDDPTKKIDRFLDYFTIMPVDMDPNGIVSKVRHIVRARED 117
                 89***********5665..***********************************9999999************************************** PP

     DUF1512  98 klkklvekllpeadeversnvetaleiasalnliykvvrHylllakktknlvlllqlqmllplllklaeayekalkaflkgkPvGDgaGplvaakllek 196
                   +++v++l p+++++e s+++t+leia++l++iykv++H++l+akk++n+ l+l lqm++p+ll++aea++ka+ af++++P+GDg+Gp+v++k++ +
  EPA04720.1 118 YSREHVRSLSPQTSDIELSKIQTLLEIATSLQMIYKVINHMYLTAKKQNNYPLILPLQMIMPFLLEEAEAMQKAIPAFKTCQPIGDGIGPMVVGKMMLD 216
                 *************************************************************************************************98 PP

     DUF1512 197 kekksleaakdtviaevelegrkvivvkaeGpgstvGrlgeavekiveklkekvdliitvDAalkLEGEetgsvaeGvGvaiGdpGvekikiErvatky 295
                 ++k+  ++a +tv+  +++ +rk++++kaeGp stvGr+g+avekiv+k   ++d+ii+vDA lk+EGEe+++ a+G+G+aiG++G+e+++iE++atk+
  EPA04720.1 217 TKKE--SIAFQTVLGMTDYSERKLLLLKAEGPASTVGRPGDAVEKIVSKD--RPDMIIMVDASLKMEGEESATTAQGFGAAIGGIGTERFQIEDIATKN 311
                 8887..9******************************************9..*********************************************** PP

     DUF1512 296 gipldaviikmsleeAitaMtkeiaeavdkavervkeiikektkegetvivvGvGNtvGv 355
                 +ip+ a+++k+s++eAit Mtkeia+ ++++ +++ e+i+++tk+g+t++++GvGNt+Gv
  EPA04720.1 312 NIPIFAIVVKQSVKEAITLMTKEIADKAENVRSQIYEMIDDNTKPGQTILLIGVGNTMGV 371
                 ***********************************************************9 PP

>> Linker_histone  linker histone H1 and H5 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1   0.00016       1.5       8      39 ..      49      81 ..      45      91 .. 0.83
   2 ?    2.1   0.1     0.029   2.6e+02      21      41 ..     146     164 ..     138     171 .. 0.78
   3 ?   -2.5   0.1      0.76   6.9e+03       8      16 ..     324     332 ..     320     356 .. 0.48

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00016
  Linker_histone  8 ikeAIkalkerkGsSrqaIkkyikakykvv.dv 39
                    ik+ Ik+l+e k  Sr+ +  yik++ + + d+
      EPA04720.1 49 IKKGIKKLDEYKTQSRTELIDYIKKNMNPKdDP 81
                    899***********************9866543 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.029
  Linker_histone  21 sSrqaIkkyikakykvvdvsk 41 
                     +S+q+I k i + y +   +k
      EPA04720.1 146 TSLQMIYKVINHMYLTA--KK 164
                     69*********999753..33 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 0.76
  Linker_histone   8 ikeAIkalk 16 
                     +keAI+ ++
      EPA04720.1 324 VKEAITLMT 332
                     555555333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       905  (0.0504769); expected 358.6 (0.02)
Passed bias filter:                      604  (0.0336884); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.49
# Mc/sec: 2268.00
//
Query:       EPA04721.1  [L=374]
Description: trypsin [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-33  116.2   0.3      4e-33  115.4   0.3    1.4  1  Trypsin_2      Trypsin-like peptidase domain
    1.1e-14   54.8   0.5    5.8e-14   52.4   0.1    2.2  2  Trypsin        Trypsin
    1.5e-13   50.8   4.0    2.9e-13   50.0   0.6    2.7  2  PDZ_2          PDZ domain
    2.6e-06   27.2   2.0      0.015   15.1   0.3    3.3  3  PDZ_6          PDZ domain
     0.0034   17.1   0.1     0.0061   16.3   0.1    1.4  1  Peptidase_S29  Hepatitis C virus NS3 protease
  ------ inclusion threshold ------
       0.01   15.7   2.8      0.027   14.3   0.5    2.4  2  Peptidase_S7   Peptidase S7, Flavivirus NS3 serine protease
       0.01   16.2   2.4        2.6    8.4   0.5    3.3  3  PDZ            PDZ domain
      0.014   14.1   1.1       0.02   13.6   0.3    1.5  2  Peptidase_S46  Peptidase S46
      0.035   13.3   2.5        2.7    7.1   0.4    2.3  2  Peptidase_S32  Equine arteritis virus serine endopeptidase S3


Domain annotation for each model (and alignments):
>> Trypsin_2  Trypsin-like peptidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.4   0.3     2e-36     4e-33       1     150 []      83     221 ..      83     221 .. 0.98

  Alignments for each domain:
  == domain 1  score: 115.4 bits;  conditional E-value: 2e-36
   Trypsin_2   1 GsGflvgsdglilTnaHvvdsadgaavkaikkkveeagadgrevpakvvaadpelDlAllkvssderaglpplplgpsealkggepvyvvGyplggeks 99 
                 GsGf++++ g i+TnaHvv++a++ +v         ++ dgr + a ++++d+ +D+A++kv + + + l+pl lg+s++lk+ge+++++G+p g  + 
  EPA04721.1  83 GSGFVFDKKGDIITNAHVVKNAKNIVV---------TFLDGRSYNADLIGSDEFTDIAVIKV-NADLTRLHPLSLGDSSSLKVGESIAAIGNPFGLSG- 170
                 9********99****************.........****************666*******.**********************************9. PP

   Trypsin_2 100 gsvssGivsgvve.sesaasgegesflqtdaatspGsSGGplfdsdGrvvGl 150
                  s++sGivs++ +  +s ++++ ++++qtdaa++pG+SGGpl++ +G++vG+
  EPA04721.1 171 -SMTSGIVSQLGRlLPSGSGYSIPDVIQTDAAINPGNSGGPLLNMRGEIVGI 221
                 .9*************************************************8 PP

>> Trypsin  Trypsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   0.1   2.9e-17   5.8e-14      23     219 ..      75     246 ..      58     248 .. 0.75
   2 ?   -1.3   0.0      0.76   1.5e+03      61      96 ..     324     356 ..     306     370 .. 0.73

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 2.9e-17
                 C....EEEEEEEEEETT.EEEEEGGGTTTGGGEEEEESESBTTSCTTTEEEEEEEEEEEETTEBTTTTTTTEEEEEESSSSTSBSSBHCCBBCSTTHTT CS
     Trypsin  23 g....khlCgGslisen.wvlTAaHCvsnasdvkvvlgehnlkksegkeqklkvekvivhpnynpstldnDiallklkepvklgdtvrpiclpaasssl 116
                 +    + l +G++ +++  ++T+aH+v+na+++ v + +   ++++     +++         ++ t   Dia++k++++     + +p++l + sssl
  EPA04721.1  75 QsngtSGLGSGFVFDKKgDIITNAHVVKNAKNIVVTFLD--GRSYN-----ADLIG------SDEFT---DIAVIKVNAD---LTRLHPLSLGD-SSSL 153
                 2445555778999999989**********7777663322..22222.....23333......34555...**********...899********.7768 PP

                 STTTEEEEEESSBSSTSSBSSBEEEEEEEEEEHHHHHHHTTTTSTTTEEEEESTTSSSBCTTTTTTSEEEETTTEEEEEEEEESSSSCTTS.EEEEEEG CS
     Trypsin 117 pvgttclvsGwgrtkekgksdtlqevevpvvsretcksaykgkvtenmlcagakeggkdacqGDSGGPlvcsdgelvGivswgkgcakgnr.pgvytkv 214
                 +vg   +++++g+++  +   +++++ v+ + r   +   +g+  ++ ++++a     ++++G+SGGPl+++ ge+vGi+++ ++++ + +  g++++ 
  EPA04721.1 154 KVG--ESIAAIGNPFGLS--GSMTSGIVSQLGRLLPS--GSGYSIPDVIQTDA-----AINPGNSGGPLLNMRGEIVGINTAIQSTTGEFTgVGFAVPS 241
                 888..8899999986666..78888888888885444..4577789*******.....************************96666665568888888 PP

                 GGGHH CS
     Trypsin 215 ssyld 219
                 +++++
  EPA04721.1 242 QTIAK 246
                 87776 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.76
                 SCTTTEEEEEEEEEEEETTEBTTTTTTTEEEEEESS CS
     Trypsin  61 ksegkeqklkvekvivhpnynpstldnDiallklke 96 
                 + +g +q++k+++++vh +  +s    D ++l++ +
  EPA04721.1 324 SVDG-KQVRKIDDILVHLQRAKSV--GDEMVLEILR 356
                 4445.79******99998887776..6777777655 PP

>> PDZ_2  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.2      0.21   4.3e+02      13      36 ..      33      56 ..       5     106 .. 0.64
   2 !   50.0   0.6   1.4e-16   2.9e-13       1      82 []     260     367 ..     260     367 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.21
                ..-EEEEEE-TTSGGGGT.--TT- CS
       PDZ_2 13 tggvlvvsVkeggPaakaglkagD 36
                t+  ++ sV++  Pa   +l   D
  EPA04721.1 33 TSDKSIPSVTQTAPAYSTNLSLID 56
                667778888888888888877733 PP

  == domain 2  score: 50.0 bits;  conditional E-value: 1.4e-16
                 ....XX------............-EEEEEE-TTSGGGGT.--T...............T-EEEEETTB--SSHHHHHHHHH.TS-TT-EEEEEEEETT CS
       PDZ_2   1 pylGvsvsdeed..........tggvlvvsVkeggPaakaglka...............gDvilkvdgkkvksledlislll.kkkpGdtVkltvlRdg 73 
                 p++G++ +d e+          + g l+vsV +++Paakagl+                gD+il+vdgk+v + +d+   l+ +k+ Gd+  l++lRdg
  EPA04721.1 260 PWIGITGRDIEPdlakvlklndAVGFLIVSVIDDSPAAKAGLHGsnetvqvdglnyqigGDIILSVDGKQVRKIDDILVHLQrAKSVGDEMVLEILRDG 358
                 567888888888888888888899*******************99*******************************9999998**************** PP

                 EEEEEEEE- CS
       PDZ_2  74 kkktvevkl 82 
                 ++ +++++l
  EPA04721.1 359 RTTNITITL 367
                 *****9997 PP

>> PDZ_6  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.2   2.4e+03      38      56 .]      54      72 ..      48      72 .. 0.87
   2 !    9.6   0.0   0.00041      0.81       2      16 ..     287     301 ..     286     302 .. 0.92
   3 !   15.1   0.3   7.4e-06     0.015      19      56 .]     319     356 ..     318     356 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.2
       PDZ_6 38 vaallrgsagesvvlvvrr 56
                ++++ + s++  v++ v+r
  EPA04721.1 54 LIDIFEKSEPGVVRVNVQR 72
                6788999999*******98 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00041
       PDZ_6   2 VtaVdpgsPAdrAGl 16 
                 + +V+ +sPA++AGl
  EPA04721.1 287 IVSVIDDSPAAKAGL 301
                 789***********8 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 7.4e-06
       PDZ_6  19 GDiilsvNGqpveglsladvaallr..gsagesvvlvvrr 56 
                 GDiilsv+G+ v  ++++d+   l+   s+g ++vl++ r
  EPA04721.1 319 GDIILSVDGKQV--RKIDDILVHLQraKSVGDEMVLEILR 356
                 9***********..****9765555477778888877765 PP

>> Peptidase_S29  Hepatitis C virus NS3 protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   3.1e-06    0.0061     105     146 ..     202     244 ..     176     247 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.1e-06
  Peptidase_S29 105 elkGssGsPilCdsGhvvGllvaavcsggvvkavrfv.Pvetl 146
                       G sG+P+l  +G +vG+ +a+  + g+ + v f  P +t+
     EPA04721.1 202 INPGNSGGPLLNMRGEIVGINTAIQSTTGEFTGVGFAvPSQTI 244
                    5569*******************************98898876 PP

>> Peptidase_S7  Peptidase S7, Flavivirus NS3 serine protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.17   3.4e+02      50     109 ..      34      94 ..      18     131 .. 0.70
   2 ?   14.3   0.5   1.3e-05     0.027      87     128 ..     196     237 ..     141     239 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.17
                   EXEEEEETTTTEEEESSSXXXXXXXXTXXEEEEE.EEEEEXXXXXTT-TT...SEEE-TTSXE CS
  Peptidase_S7  50 tkpswaSvkedlvkyggslklqgkylgeeyqlyGyglgitdlnlssGsSG...Slvlnqnkqi 109
                   + +s  Sv +   +y++ l+l   ++  e  +    + ++ ++ s+G+SG     v+ +++ i
    EPA04721.1  34 SDKSIPSVTQTAPAYSTNLSLIDIFEKSEPGVVR--VNVQRTDQSNGTSGlgsGFVFDKKGDI 94 
                   4455566666666777777666666666665554..778899999999973323556666655 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 1.3e-05
                   EEEXXXXXTT-TTSEEE-TTSXEEEECEEEEEXTTSXEEEEE CS
  Peptidase_S7  87 gitdlnlssGsSGSlvlnqnkqivgiYfatvevdkkeaevgl 128
                   + td   ++G SG ++ln +++ivgi  a  +++ +   vg+
    EPA04721.1 196 IQTDAAINPGNSGGPLLNMRGEIVGINTAIQSTTGEFTGVGF 237
                   55677789******************9999888855555665 PP

>> PDZ  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.2   2.4e+03      37      55 ..     146     164 ..     136     167 .. 0.78
   2 ?    5.5   0.0     0.011        22      10      55 ..     260     312 ..     251     316 .. 0.72
   3 ?    8.4   0.5    0.0013       2.6      47      81 ..     319     354 ..     317     355 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.2
                 SHHHHHTSSTTEEEEEETT CS
         PDZ  37 gaaeadglkvGDkIlsvNg 55 
                 +  + + lkvG  I ++++
  EPA04721.1 146 SLGDSSSLKVGESIAAIGN 164
                 5566666********9987 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.011
                 SESSEEEEEETTSS.......SSSSEEEEEECTTSHHHHHTSSTTEEEEEETT CS
         PDZ  10 gglGfslkggsdqr.......gdkgifvsevlpggaaeadglkvGDkIlsvNg 55 
                  ++G++++  + +        ++ g+ + +v  +++a+++gl+   + ++v+g
  EPA04721.1 260 PWIGITGRDIEPDLakvlklnDAVGFLIVSVIDDSPAAKAGLHGSNETVQVDG 312
                 567777776666667777777888999*******7777777997666666665 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0013
                 TEEEEEETTEETTTSHHHHHHHHHHTTTS.EEEEEE CS
         PDZ  47 GDkIlsvNgvdvenvsheeavqaikgskg.kvtLti 81 
                 GD+Ilsv+g+ v+++ +  + ++  +s g ++ L+i
  EPA04721.1 319 GDIILSVDGKQVRKIDDILVHLQRAKSVGdEMVLEI 354
                 9*************9877776666665555666655 PP

>> Peptidase_S46  Peptidase S46
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.71   1.4e+03      47      69 ..      81     103 ..      73     106 .. 0.84
   2 ?   13.6   0.3     1e-05      0.02     627     651 ..     198     222 ..     188     233 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.71
                    TTEE-EE-STT-EEEE-HHHHHH CS
  Peptidase_S46  47 ggCtasfVSpeGLvlTNHHCayg 69 
                    g  ++ +  ++G ++TN H++ +
     EPA04721.1  81 GLGSGFVFDKKGDIITNAHVVKN 103
                    66788888999********9876 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 1e-05
                    ES----TT-TT-EEE-TTS-EEEEE CS
  Peptidase_S46 627 stnDitGGNSGSPvlngkgelvGla 651
                    +++ i  GNSG P+ln +ge+vG++
     EPA04721.1 198 TDAAINPGNSGGPLLNMRGEIVGIN 222
                    6777889****************98 PP

>> Peptidase_S32  Equine arteritis virus serine endopeptidase S32
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.4    0.0014       2.7     111     142 ..      80     109 ..      63     202 .. 0.77
   2 ?    6.0   0.1    0.0029       5.7     206     229 ..     203     226 ..     193     238 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0014
                    SSEEEEEEEECTTEEEEEEEHHHH-TSEEEEE CS
  Peptidase_S32 111 sslGsGgvftidgevvvvtashvlgdnkarvs 142
                    s lGsG vf ++g   ++t +hv+ + k  v 
     EPA04721.1  80 SGLGSGFVFDKKG--DIITNAHVVKNAKNIVV 109
                    5567777776655..689******97665543 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0029
                    -GGGTT-EEEETTE.EEEEEEEEE CS
  Peptidase_S32 206 kcGDsGspvvdedgelvGvhtGsn 229
                    ++G+sG p+++  ge+vG+ t  +
     EPA04721.1 203 NPGNSGGPLLNMRGEIVGINTAIQ 226
                    79*****************99755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.50
# Mc/sec: 2255.67
//
Query:       EPA04722.1  [L=99]
Description: hypothetical protein BG20_I0916 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.068   12.9   0.0      0.086   12.5   0.0    1.2  1  DUF3990   Protein of unknown function (DUF3990)


Domain annotation for each model (and alignments):
>> DUF3990  Protein of unknown function (DUF3990)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   4.8e-06     0.086      15      61 ..      35      80 ..      26      97 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.8e-06
     DUF3990 15 dlsksrkkkDFGkGFYlteskeqAkewakrkskrkgkkevvnvyeld 61
                ++ k++++ DF  G+Y+++++e   ++  + + r ++  +v ++e++
  EPA04722.1 35 KIWKCENSVDFLYGYYVGKIEEGTLHYLLKAT-RASAGGFVDIFEIR 80
                6789**********************999887.45555677777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.33s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 582.46
//
Query:       EPA04723.1  [L=289]
Description: carboxymethylenebutenolidase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-51  174.4   0.0    3.1e-51  174.0   0.0    1.1  1  DLH              Dienelactone hydrolase family
    5.6e-06   25.6   0.0    8.3e-06   25.0   0.0    1.3  1  Chlorophyllase   Chlorophyllase
    9.5e-06   25.2   0.0      0.044   13.3   0.1    2.2  2  Peptidase_S9     Prolyl oligopeptidase family
    3.2e-05   23.9   0.2     0.0019   18.1   0.0    2.4  2  BAAT_C           BAAT / Acyl-CoA thioester hydrolase C termin
    6.5e-05   22.7   0.1    9.1e-05   22.2   0.1    1.3  1  Abhydrolase_1    alpha/beta hydrolase fold
    0.00014   20.9   0.0     0.0002   20.4   0.0    1.2  1  Chlorophyllase2  Chlorophyllase enzyme
    0.00065   19.0   0.0     0.0036   16.6   0.0    1.8  2  Hydrolase_4      Serine aminopeptidase, S33
  ------ inclusion threshold ------
      0.021   13.4   0.0       0.12   10.9   0.0    1.8  2  PAF-AH_p_II      Platelet-activating factor acetylhydrolase, 


Domain annotation for each model (and alignments):
>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.0   0.0   1.4e-54   3.1e-51       3     214 ..      82     285 ..      81     288 .. 0.94

  Alignments for each domain:
  == domain 1  score: 174.0 bits;  conditional E-value: 1.4e-54
         DLH   3 aylatpkna.kkpvvvviqeifGvndnikdiserlaeeGYvalaPdlYarqaldpndeaeaaraldelvskvaeekvlddlkaavaylksvpevstkkv 100
                 +yla+p +   +p+v++i+e++G+n+nikd++++la+ GYv+la dlY +++  +++ +ea++++    +  ++++ +++++ a+ yl  +   s++ +
  EPA04723.1  82 GYLARPVSDeSFPGVIMIHEWWGLNNNIKDMAKKLASHGYVVLAVDLYGGHV--ATTSEEARQLV----TSFDKDNGVQNMDSAISYLDDNY--SPESI 172
                 799***99999*****************************************..56666666666....4555557999999******9887..99*** PP

         DLH 101 gvvGfCmGGalalllaaevpevdaavafYGlspekeleeaakikapilalfgeeDefipadevekleealkaanvdlelkvYpgagHaFandsresyne 199
                 g++G+C+GG  +l+la ++p ++a+v++YG s+  + +    i  p+l++f+e D+ i+ ++v+++e+ l + +++ e+ +Ypg++HaFan+s  +y +
  EPA04723.1 173 GSIGWCFGGGQSLNLALNNPSLNATVIYYG-SLVTDSDSLSVIHWPVLGIFAELDKGITTNTVHDFENSLNQLGIQNEIIIYPGVDHAFANPSGLNYAP 270
                 ******************************.9999999************************************************************* PP

         DLH 200 eaaedawervlelfk 214
                 e  +daw+++le++ 
  EPA04723.1 271 EESQDAWQKTLEFLD 285
                 *************97 PP

>> Chlorophyllase  Chlorophyllase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   3.7e-09   8.3e-06       5      84 ..      58     131 ..      54     173 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 3.7e-09
  Chlorophyllase   5 trdvfekGkyktteitvdsssrsspapPkpliivtPaeaGtypvvlflhGtllsnkfyskllnhiashGfivvaPqlykl 84 
                       ++f+ Gky++++ tv+ s+ +      +  ++ P+ +  +p v+++h +   n++  ++ + +ashG++v+a  ly  
      EPA04723.1  58 NSEIFTMGKYDVQTDTVNYSESN------SGYLARPVSDESFPGVIMIHEWWGLNNNIKDMAKKLASHGYVVLAVDLYGG 131
                     5689**********999655544......55789999****************************************965 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.1     2e-05     0.044       8      88 ..     114     194 ..     107     207 .. 0.82
   2 !   10.2   0.0   0.00017      0.37     142     208 ..     214     287 ..     189     289 .] 0.75

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2e-05
                   HHHHCCT-EEEEE--TTSS..TTHCHHHHTTSGGGGHHHHHHHHHHHHHHHHTTS--GGGEEEEEETHHHHHHHHHHHH-GGG CS
  Peptidase_S9   8 qlladrGyvvvvanirGsg..gyGeafhdagkrklgqnefdDfiaaaealakegyvdserlaitGgSyGGyltgaalnqrpdl 88 
                   + la+ Gyvv+++++ G++    +e+ ++ ++   ++n ++ +  a+ +l ++   ++e ++  G+ +GG  ++ ++ ++p+l
    EPA04723.1 114 KKLASHGYVVLAVDLYGGHvaTTSEEARQLVTSFDKDNGVQNMDSAISYLDDN--YSPESIGSIGWCFGGGQSLNLALNNPSL 194
                   5578**************633689**************************544..579**********986555444446665 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00017
                   ---EEEEEEETT-SSS-THHHHHHHHHHH--S-SEEEEEETTS-S.......STTSSHHHHHHHHHHHHHHHHH CS
  Peptidase_S9 142 aypplLlihGlaDdrvppaealklvaaLqkkgknvlllifpdegH.......gvgkprakveelarllaFlkea 208
                   +  p+L i +++D+ ++ ++   + + L++ g + ++ i+p+ +H         + p+ +++  +++l+Fl+++
    EPA04723.1 214 IHWPVLGIFAELDKGITTNTVHDFENSLNQLGIQNEIIIYPGVDHafanpsgLNYAPEESQDAWQKTLEFLDSN 287
                   566899999************************************44444422223444455666666666655 PP

>> BAAT_C  BAAT / Acyl-CoA thioester hydrolase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   8.6e-07    0.0019       8      66 ..     158     214 ..     153     249 .. 0.82
   2 ?    3.4   0.1     0.029        65     197     211 ..     274     288 ..     264     289 .] 0.85

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 8.6e-07
                 HHHHHHHCSTTB--SSEEEEEETHHHHHHHHHHHHSSSEEEEEEES--SB--SSEEEET CS
      BAAT_C   8 eainyllrhpkvkkdkigllGiSkGgelalllasflkkisavvlingsavvvegklvyk 66 
                  ai+yl ++   + + ig +G ++Gg   l la   ++ +a+v++ gs v  ++ l   
  EPA04723.1 158 SAISYLDDN--YSPESIGSIGWCFGGGQSLNLALNNPSLNATVIYYGSLVTDSDSLSVI 214
                 799999999..5557***********************************998876655 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.029
                 HHHHHHHHHHHHHH- CS
      BAAT_C 197 edsWkkilkFlkkhl 211
                 +d+W+k+l+Fl+  l
  EPA04723.1 274 QDAWQKTLEFLDSNL 288
                 79*********9876 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.1   4.1e-08   9.1e-05      16     106 ..     108     203 ..      92     249 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 4.1e-08
                    GTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.......CHHSHHHHHHHHHHHHHHCTTSSEEEEEETHHHHHHHHHHHHHGGGEEEEEEES CS
  Abhydrolase_1  16 waerglapaLakdgfdvillDlrGvgySspapacin......ddygtasvaddldrildalgddkltlvGhSmGGmialayaaeyperVkalvllg 105
                     ++ ++a+ La +g+ v+++Dl G    +++ + ++      +d g  ++   + ++ d +  +++  +G+++GG ++l++a+ +p+  + ++  g
     EPA04723.1 108 NIK-DMAKKLASHGYVVLAVDLYGGHVATTSEEARQlvtsfdKDNGVQNMDSAISYLDDNYSPESIGSIGWCFGGGQSLNLALNNPSLNATVIYYG 202
                    333.677777777*******************99999*8888778888899999999****************************98766666555 PP

                    E CS
  Abhydrolase_1 106 a 106
                    +
     EPA04723.1 203 S 203
                    5 PP

>> Chlorophyllase2  Chlorophyllase enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   8.9e-08    0.0002       9      63 ..      85     140 ..      80     200 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 8.9e-08
  Chlorophyllase2   9 vaPteageYpvllflhGylllnslYsqlLkhiashgfivvapqlykvaeada.kei 63 
                      + P + +++p ++++h +  ln+  +++ k++ashg++v+a+ ly  + a + +e 
       EPA04723.1  85 ARPVSDESFPGVIMIHEWWGLNNNIKDMAKKLASHGYVVLAVDLYGGHVATTsEEA 140
                      679999*************999999*****************99985444443333 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.6e-06    0.0036      19     116 ..     108     210 ..      95     226 .. 0.82
   2 ?    0.9   0.0       0.1   2.3e+02     189     234 ..     213     260 ..     208     263 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.6e-06
  Hydrolase_4  19 ryaelaeaLaaqGfavyalDhrG...hGrsegkrghvpsfdd..yvdDlaafvekvkeehpelplfllGhSmGGliallyllrypdkvaglilsaPal 111
                    +++a++La +G+ v+a+D  G      se +r  v+sfd+   v+ ++++++ + ++++ + +  +G   GG  +l+++l++p+  a +i  ++++
   EPA04723.1 108 NIKDMAKKLASHGYVVLAVDLYGghvATTSEEARQLVTSFDKdnGVQNMDSAISYLDDNYSPESIGSIGWCFGGGQSLNLALNNPSLNATVIYYGSLV 205
                  67899***************9974333455599999999975338*****************************************555888888877 PP

  Hydrolase_4 112 kikak 116
                      +
   EPA04723.1 206 TDSDS 210
                  66655 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.1
  Hydrolase_4 189 kitlPllllhGeaDkvvdpeasrelyerlgsk..dktlklypglyHel 234
                   i++P+l + +e Dk +  +  +++ ++l++   + ++ +ypg  H  
   EPA04723.1 213 VIHWPVLGIFAELDKGITTNTVHDFENSLNQLgiQNEIIIYPGVDHAF 260
                  6789***********9999999888888887777999*******9976 PP

>> PAF-AH_p_II  Platelet-activating factor acetylhydrolase, isoform II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   5.2e-05      0.12      97     163 ..      90     157 ..      74     172 .. 0.73
   2 ?    1.5   0.0     0.039        87     213     283 ..     155     224 ..     137     261 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.2e-05
                  SS-EEEEEEE--TT--TTTTHHHHHHHHHTT-EEEEE-.--SS-SSEEEE-SSHHHHHHT.......- CS
  PAF-AH_p_II  97 kekyPlivFsHGLgafRtlYsalcielAskGfvvaavE.HrDesAaatyvlkdklaaeeeeevvesre 163
                  +e++P ++  H   +  +    ++ +lAs+G+vv+av+    + A+++   ++ + +  +++ v++++
   EPA04723.1  90 DESFPGVIMIHEWWGLNNNIKDMAKKLASHGYVVLAVDlYGGHVATTSEEARQLVTSFDKDNGVQNMD 157
                  3889999999999999999999***************8334566666666666666666656666665 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.039
                  --SS-GGGGTT-EEEEEEEEEEETHHHHHHHHHHHH-TTS-EEEEES---TTS-GGGGGG--S-EEEEEET CS
  PAF-AH_p_II 213 dsdfdlqqlKdnldtskvaviGHsFGgAtvikslsedteFrcaialDaWmlPveeevyskvrqPllfinse 283
                  + d  ++ l dn   +++  iG  FGg  +++   ++     ++++ + +   +++ +s ++ P+l i +e
   EPA04723.1 155 NMDSAISYLDDNYSPESIGSIGWCFGGGQSLNLALNNPSLNATVIYYGSL-VTDSDSLSVIHWPVLGIFAE 224
                  45556788999999999**************9999999999998887654.46778888888888877654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 1996.22
//
Query:       EPA04724.1  [L=110]
Description: hypothetical protein BG20_I0914 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.041   14.3   0.2      0.057   13.8   0.2    1.3  1  IMPa_helical  Immunomodulating metalloprotease helical domain


Domain annotation for each model (and alignments):
>> IMPa_helical  Immunomodulating metalloprotease helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   3.2e-06     0.057      20      72 ..      59     110 .]      42     110 .] 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.2e-06
                   EEETEE-TTSTTH.HHHHHHHHHHHHHHHHHHHTT--GGGSSS-HHHHHHHHH CS
  IMPa_helical  20 dsnvksCdeeaklkeefkkaaesirsalealdsskidlfaeegyrlekllvLl 72 
                   +s  +sC+  ++ + ++k+a ++i +a +++ ++k ++f++e  +lek l Ll
    EPA04724.1  59 TS-LDSCSVLKENDPNYKNALSEIIQAKKQFAQNKSEMFQKEIQELEKKLSLL 110
                   33.689***9************************************9998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1573  (0.087735); expected 358.6 (0.02)
Passed bias filter:                      740  (0.0412739); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.35s 00:00:00.93 Elapsed: 00:00:00.57
# Mc/sec: 583.30
//
Query:       EPA04725.1  [L=528]
Description: lysine--tRNA ligase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   3.2e-109  365.2   0.0     1e-108  363.5   0.0    1.7  2  tRNA-synt_1f     tRNA synthetases class I (K)
     0.0074   16.0   0.0       0.02   14.6   0.0    1.7  1  PolyA_pol_RNAbd  Probable RNA and SrmB- binding site of polym
  ------ inclusion threshold ------
      0.067   11.9   0.2       0.33    9.6   0.0    2.0  2  tRNA-synt_1g     tRNA synthetases class I (M)


Domain annotation for each model (and alignments):
>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  363.5   0.0  1.7e-112    1e-108       2     346 ..      11     364 ..      10     377 .. 0.95
   2 ?   -1.2   0.1      0.12   7.3e+02     302     340 ..     411     447 ..     400     480 .. 0.66

  Alignments for each domain:
  == domain 1  score: 363.5 bits;  conditional E-value: 1.7e-112
  tRNA-synt_1f   2 aWadklaeklieerkkkka.ekdevvvesGispSGliHiGnlrevltadlvaralrkrgeevrlilisDdmDglRkvpenlpekllekylgkpltsi 97 
                   +W+dkla++li er+k+   + d + vesG+++SG +HiG+l++ ++a+ v  al++ g + +li++sDd+DglRk+pe +p++ le++l kp++ i
    EPA04725.1  11 TWIDKLAHELI-EREKTLGrNLDLIRVESGLGASGVPHIGSLGDAVRAYGVKLALENFGYKSELIAYSDDLDGLRKIPEGFPNS-LEEHLAKPVSLI 105
                   6**********.5556656699**************************************************************.************ PP

  tRNA-synt_1f  98 PdpkgkhesyaehfnaelvesLdelgievefisatelYksglydeaikealenrekikeilekyrgeereetyspylpvcekcgrvdttevvevdae 194
                   Pdp+g+h+sy++h+++ l++ Ld++gi++ef +a+++Yk+gl++++i+++l+n++ki + + +  g+e+ ++++py pvc++c+r+ t+e+ e+ ae
    EPA04725.1 106 PDPFGCHDSYGMHMSSILLDGLDKMGIKYEFRRARDTYKNGLLKDQIHTILQNSSKIGDKISELVGQEKFQKFLPYFPVCSNCNRLYTAEAFEYLAE 202
                   ************************************************************************************************* PP

  tRNA-synt_1f 195 eeeieYkc..........eecGeeeevdiregngKLqWkvdwamrWaalgVdfEpaGkDhaaaGgSvdvsskia.eilggeaPekvvYelillkgge 280
                   e++++Ykc          + c +++e+di++  gKL Wkv++a+rWaa++++fE++GkD+++   Sv+v+++++ eil++++P++v Ye++l+kgg+
    EPA04725.1 203 EKKVRYKChdaeigskmiKGCNHDGEADITKDLGKLAWKVEFAARWAAFDIRFEAYGKDIMD---SVKVNDWVSdEILNFPHPHHVKYEMFLDKGGK 296
                   **************************************************************...******************************** PP

  tRNA-synt_1f 281 kmssSkGnvltledwlevaepevlrflilrrkPkkakkldldleilrlvdeYdklerkyf....aeqeee 346
                   k+s+S Gnv+t + wle+++p+++ +l+++ +++ a +l l+ +i++l++eY++le+++f     +++++
    EPA04725.1 297 KISKSLGNVVTGQRWLEFGSPKSILLLLYK-RITGARELGLE-DIPSLMNEYNELEDIFFgkikVDNQAK 364
                   ******************************.***********.*****************6544333333 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.12
  tRNA-synt_1f 302 evlrflilrrkPkkakkldldleilrlvdeYdklerkyf 340
                   ++l + +++ +P ++++  ++    ++ de+d+ e++ +
    EPA04725.1 411 KLLDYGVIK-NPDQEIEKLIE-MAGKFADEFDQQEKIEI 447
                   556666666.66666665555.55666666666655443 PP

>> PolyA_pol_RNAbd  Probable RNA and SrmB- binding site of polymerase A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   3.4e-06      0.02      26      54 ..     391     419 ..     389     426 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.4e-06
  PolyA_pol_RNAbd  26 RifeEllKlLlsghpeaglelLretgLlk 54 
                      R+ +El K++ ++++e+ +++L ++g++k
       EPA04725.1 391 RLLVELGKMFKEDRSERVMKKLLDYGVIK 419
                      99************************987 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.11   6.5e+02      76     147 ..     125     196 ..     114     235 .. 0.72
   2 ?    9.6   0.0   5.5e-05      0.33     308     344 ..     278     314 ..     256     327 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.11
                   HHHHHTT---SEEEETT.SHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG-EE........-T CS
  tRNA-synt_1g  76 elfkklnisfdkygrtt.seehkelvqeifkklkekgliyekeieqlycpkderflpdryvegtCPkckseea 147
                   + ++k++i+++ + r+  + ++  l  +i + l++  +i  k +e +  +k ++flp   v  +C    ++ea
    EPA04725.1 125 DGLDKMGIKYE-FRRARdTYKNGLLKDQIHTILQNSSKIGDKISELVGQEKFQKFLPYFPVCSNCNRLYTAEA 196
                   56677888886.5555404555566677888888899999999999999999999998888777766555554 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 5.5e-05
                   T----S-EEEE--EEE--------------HHHHHHH CS
  tRNA-synt_1g 308 elklpkkvvaheyltvegkKlSkSrgvvvkakealer 344
                   ++  p++v  + +l   gkK+SkS g+vv+ + +le 
    EPA04725.1 278 NFPHPHHVKYEMFLDKGGKKISKSLGNVVTGQRWLEF 314
                   678899************************9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (528 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       841  (0.0469072); expected 358.6 (0.02)
Passed bias filter:                      664  (0.037035); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.74u 0.34s 00:00:01.08 Elapsed: 00:00:00.53
# Mc/sec: 2989.28
//
Query:       EPA04726.1  [L=418]
Description: 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase, CofH subunit [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.8e-21   75.4   0.2    1.1e-20   74.7   0.2    1.3  1  Radical_SAM    Radical SAM superfamily
  ------ inclusion threshold ------
       0.02   14.3   0.0       0.21   11.0   0.0    2.2  2  AP_endonuc_2   Xylose isomerase-like TIM barrel
       0.15   11.2   0.0       0.25   10.5   0.0    1.3  1  PEP_hydrolase  Phosphoenolpyruvate hydrolase-like
        0.2   11.8   1.1       0.38   10.9   0.1    2.0  3  Fer4_14        4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.7   0.2   2.4e-24   1.1e-20       1     164 [.      72     243 ..      72     246 .. 0.91

  Alignments for each domain:
  == domain 1  score: 74.7 bits;  conditional E-value: 2.4e-24
                  EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHG....... CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....... RF
  Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlaklavpgiritvetngtlpd....... 90 
                  +++t+ C  +C fCa++++  re+ g++l++eei++ +ke+ +  g ++++i+ g  p+++ +++e + + +k++ p+i+i+  +++ +++       
   EPA04726.1  72 INFTNVCIKQCGFCAFSRD-FREEEGYFLPTEEIVRRAKEA-YQLGaTEVCIQAGLPPDMDGNLYENICKDIKKEIPDIHIHGFSPEEVLYgasrsnt 167
                  689***************8.9********************.79999*****************99999999999*********************** PP

                  ..HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHHH CS
                  ..xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM  91 ..eeklerllelg.vdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivglpGendeeleell 164
                    +e+l+rl+e+g  +     +e++d +  ++++  ++ ++++++e+++++++ gi+ ++++++ ++ e+ e++++++
   EPA04726.1 168 tiREYLKRLKEAGvNTLPGTAAEILDQK-LRDKISpGRISVKDWIEVIKTAHSIGIN-TTSTMMFGHIETPEDRVNHI 243
                  *************555666666666776.*******99*******************.78888888889999988776 PP

>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0     0.069   3.1e+02      70     114 ..     102     142 ..      90     154 .. 0.79
   2 ?   11.0   0.0   4.8e-05      0.21      25     106 ..     163     240 ..     148     257 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.069
                   HHHHHHHHHHHHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHH CS
  AP_endonuc_2  70 dalkraielaaaLGapllvlhpGtagagpkgseeeawerlaesln 114
                   +++ r ++ a++LGa  + +++G    +p++ +   +e++ ++++
    EPA04726.1 102 EEIVRRAKEAYQLGATEVCIQAG----LPPDMDGNLYENICKDIK 142
                   567788999************99....666666666666666555 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 4.8e-05
                   C.HHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCS..HHHHHHHHHHHHHHHHHHTBSEEEEEBCCGBCTTTSGHHHHH CS
  AP_endonuc_2  25 l.sdeelrelrkaldelglriaslslftrfgypdederear..reesvdalkraielaaaLGapllvlhpGtagagpkgseeeaw 106
                     s +++re+ k+l+e+g++     + t  + +d+ +r++    + sv+++ + i++a+ +G+ +  ++      g+ +++e+++
    EPA04726.1 163 SrSNTTIREYLKRLKEAGVN---TLPGTAAEILDQKLRDKIspGRISVKDWIEVIKTAHSIGINTTSTMMF----GHIETPEDRV 240
                   24889***************...333333333334466777999999*****************9888854....3333333333 PP

>> PEP_hydrolase  Phosphoenolpyruvate hydrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   5.6e-05      0.25      93     154 ..     166     226 ..     150     237 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 5.6e-05
  PEP_hydrolase  93 frkleeflkelkelGfaGvqNfPtvglidgefrenleetglgyekEvelikkAheldlltta 154
                     ++++e+lk+lke+G++ +       ++d+++r+++    ++ +  +e+ik+Ah+ ++ tt+
     EPA04726.1 166 NTTIREYLKRLKEAGVNTLPGT-AAEILDQKLRDKISPGRISVKDWIEVIKTAHSIGINTTS 226
                    457899*******876555433.35689******************************9985 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   8.4e-05      0.38       5      85 ..      75     152 ..      72     176 .. 0.85
   2 ?   -3.1   0.0       1.8   8.2e+03      80     109 ..     217     244 ..     209     250 .. 0.63
   3 ?   -3.4   0.0       2.3     1e+04      81     105 ..     366     390 ..     356     396 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 8.4e-05
     Fer4_14   5 lsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkell.klvkrlkeeypekkiwl 85 
                 ++ C  +C +C  + ++++e g     e+++++   +++++  + ++ +  G P     + +l+ +++k +k+e+p+++i+ 
  EPA04726.1  75 TNVCIKQCGFCAFSRDFREEEGYFLPTEEIVRRA--KEAYQLGATEVCIQAGLPP--DMDGNLYeNICKDIKKEIPDIHIHG 152
                 588*****************99999999998999..6667777799******998..55666662699*******9999985 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.8
     Fer4_14  80 ekkiwletngtleielektpdlkekleals 109
                  ++i ++t  t++  + +    +++++ ++
  EPA04726.1 217 AHSIGINTTSTMMFGHIE--TPEDRVNHIA 244
                 378888888888855444..4455666555 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 2.3
     Fer4_14  81 kkiwletngtleielektpdlkekl 105
                  +   +t +++ ++++k +d ++ l
  EPA04726.1 366 TPAERNTHYKILKKFDKDNDVEDEL 390
                 5555566777766666656655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       795  (0.0443416); expected 358.6 (0.02)
Passed bias filter:                      646  (0.036031); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2880.35
//
Query:       EPA04727.1  [L=57]
Description: hypothetical protein BG20_I0917 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1148  (0.0640303); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.29s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 391.15
//
Query:       EPA04728.1  [L=159]
Description: antioxidant, AhpC/TSA family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.1e-39  133.3   0.2    4.8e-39  133.1   0.2    1.0  1  AhpC-TSA    AhpC/TSA family
    9.5e-27   93.5   0.1    1.1e-26   93.3   0.1    1.0  1  Redoxin     Redoxin
    4.5e-08   33.2   0.1    8.1e-08   32.4   0.1    1.4  1  AhpC-TSA_2  AhpC/TSA antioxidant enzyme
    9.5e-08   31.8   0.0    1.1e-07   31.6   0.0    1.1  1  DUF899      Bacterial protein of unknown function (DUF899)
     0.0013   18.7   0.1     0.0027   17.6   0.1    1.6  1  SCO1-SenC   SCO1/SenC
  ------ inclusion threshold ------
      0.039   13.5   0.1      0.078   12.6   0.0    1.6  2  GSHPx       Glutathione peroxidase


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.1   0.2   1.6e-42   4.8e-39       2     121 ..      10     135 ..       9     138 .. 0.98

  Alignments for each domain:
  == domain 1  score: 133.1 bits;  conditional E-value: 1.6e-42
                 TSB----EEESTTCEEEECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHHH-H.SSEEEE-TTSHHHHHTT- CS
    AhpC-TSA   2 gdkapdfelknadgetvslsdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfiekeslnfpllsDeegkvakaygv 100
                 gd +p+fe+ + +g++v+ sd+kgk+ v++fypkd++p+Ct e+ +++k y++f+++g+e+igvs+d+++shkkf++k ++++pll+D +++++k++gv
  EPA04728.1  10 GDTVPKFEARDSNGNNVKSSDFKGKKHVIYFYPKDFTPGCTVEADEFSKDYKRFQKEGIEIIGVSPDDVDSHKKFCDKMGIKYPLLADVDKTLSKQFGV 108
                 899************************************************************************************************ PP

                 EETT......TTECSCEEEEE-TTSBE CS
    AhpC-TSA 101 lkee......kglalratfvidkegki 121
                 + ++      +++  r+tf++d++gki
  EPA04728.1 109 WGKKqfmgkeYMGVNRSTFLVDEKGKI 135
                 *999**********************9 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.3   0.1   3.6e-30   1.1e-26       2     140 ..       9     149 ..       8     156 .. 0.90

  Alignments for each domain:
  == domain 1  score: 93.3 bits;  conditional E-value: 3.6e-30
                 TTSBB---ECCEETTCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHHHHHHHHHTT-TSEEEE-TTSHHHHH CS
     Redoxin   2 agdkaPdftlplaatdgnsvslsefkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndafvkefwgkeglkfpvlsDgsaaftka 100
                 +gd++P+f+  +  ++gn+v+ s+fkgkk+v++f+p  f+P C+ e+ ++ k ++++ ++g+++++v+ d+ +  k+f++k g+k+p+l+D ++ ++k+
  EPA04728.1   9 EGDTVPKFEARD--SNGNNVKSSDFKGKKHVIYFYPKDFTPGCTVEADEFSKDYKRFQKEGIEIIGVSPDDVDSHKKFCDKMGIKYPLLADVDKTLSKQ 105
                 69*******877..************************************************************************************* PP

                 TT-TTEEE.GGG....EEE-EEEEEEETTEEEEEEESSSCHT.ST CS
     Redoxin 101 lGlrleedaseg....lrtpryavidedgkvvylevepepet.ee 140
                 +G  + +++ +g       ++++++de+gk+ +++  + p +  +
  EPA04728.1 106 FG-VWGKKQFMGkeymGVNRSTFLVDEKGKIFKVYPKVKPAGhAK 149
                 **.5566655558896677889************99999966443 PP

>> AhpC-TSA_2  AhpC/TSA antioxidant enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.1   2.7e-11   8.1e-08       2      55 ..      56     110 ..      55     142 .. 0.87

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 2.7e-11
  AhpC-TSA_2   2 Lsrdkpeldaagvklvaigigdp.sakkFvkltgfpfelyvDpsaklyqalglkr 55 
                 +s+d ++++++g+++++++ +d+ s kkF++  g++++l++D +++l +++g++ 
  EPA04728.1  56 FSKDYKRFQKEGIEIIGVSPDDVdSHKKFCDKMGIKYPLLADVDKTLSKQFGVWG 110
                 578999*****************77***************************985 PP

>> DUF899  Bacterial protein of unknown function (DUF899)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0   3.8e-11   1.1e-07      86     176 ..      47     140 ..      21     153 .. 0.92

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 3.8e-11
      DUF899  86 pgCslladhvdgalahLeardvtlavvsraplekleaykrrmGwtlpwvssaesdfnrdfnvsleeeqaseelpgl..svflrdd.grvfhtYs 176
                 pgC++ ad++ ++ + ++++++ ++ vs   +++ +++ ++mG + p+ ++++++++++f+v  +++ + +e  g+  s+fl d+ g++f+ Y 
  EPA04728.1  47 PGCTVEADEFSKDYKRFQKEGIEIIGVSPDDVDSHKKFCDKMGIKYPLLADVDKTLSKQFGVWGKKQFMGKEYMGVnrSTFLVDEkGKIFKVYP 140
                 89***************************************************************999999**9997789***999******96 PP

>> SCO1-SenC  SCO1/SenC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1     9e-07    0.0027       2     133 ..      14     134 ..      13     135 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 9e-07
   SCO1-SenC   2 gpFelvdqdgeavteedlegkpslvffgFthCpdvCpttlanmaevldalgeeaekvqplfiTvDPerDtpevlkeyleafdpriigltGskeeiakaa 100
                  +Fe  d++g++v+++d++gk  +++f     +  C+++  + ++ ++++++e+ +    +i v P  D+++  k+++++++ ++  l +  +   +++
  EPA04728.1  14 PKFEARDSNGNNVKSSDFKGKKHVIYFYPKDFTPGCTVEADEFSKDYKRFQKEGIE----IIGVSP--DDVDSHKKFCDKMGIKYPLLADVDK---TLS 103
                 589************************99999999999999999999999999544....355555..6888888888888888877765443...345 PP

   SCO1-SenC 101 kefrvyvekvedeesdytvdHsssvyLvdpdgr 133
                 k+f+v  +k+   ++   +    s++Lvd++g+
  EPA04728.1 104 KQFGVWGKKQFMGKE--YMGVNRSTFLVDEKGK 134
                 568888777776666..5667777788887776 PP

>> GSHPx  Glutathione peroxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.6e-05     0.078       3      63 ..      15      77 ..      13     119 .. 0.77
   2 ?   -1.6   0.0      0.66     2e+03      81     107 ..     130     156 ..     100     157 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.6e-05
                GBEEEBTTSSEEEGGGGTTSEEEEE..EEESSSTTHHHHHHHHHHHHHHGGGTEEEEEEEE-T CS
       GSHPx  3 elsakdidgekvkleklrgkvvliv..nvaskCglteqykeleelqkrykdkglvilgfPCnq 63
                +++a+d +g++vk + ++gk  +i       + g t +  e+ + +kr++++g+ i+g   + 
  EPA04728.1 15 KFEARDSNGNNVKSSDFKGKKHVIYfyPKDFTPGCTVEADEFSKDYKRFQKEGIEIIGVSPDD 77
                699****************8666651155667899**********************975544 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.66
                 HTTT-SSEEB--BBSSSTTB-HHHHHH CS
       GSHPx  81 gkyevtfellekievnGekedplykfl 107
                 ++ +  f++  k++  G+ ++ l +fl
  EPA04728.1 130 DEKGKIFKVYPKVKPAGHAKEVLDDFL 156
                 333455777777777777666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1053.77
//
Query:       EPA04729.1  [L=141]
Description: hypothetical protein BG20_I0910 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.051   13.4   8.0       0.94    9.2   0.7    2.1  2  DUF443    Protein of unknown function (DUF443)
      0.073   12.6   0.5        6.6    6.2   0.0    2.1  2  UMPH-1    Pyrimidine 5'-nucleotidase (UMPH-1)
       0.24   11.8   1.5        1.9    8.9   0.0    2.2  2  Tox-WTIP  Toxin with a conserved tryptophan and TIP tripeptid
        2.7    8.3  13.1       0.14   12.5   3.3    2.2  2  DUF3021   Protein of unknown function (DUF3021)


Domain annotation for each model (and alignments):
>> DUF443  Protein of unknown function (DUF443)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   2.3   0.00037       1.7      68     121 ..      18      70 ..       1      81 [. 0.69
   2 ?    9.2   0.7   0.00021      0.94      55     117 ..      75     137 ..      68     141 .] 0.76

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00037
      DUF443  68 alGsavllgnllrklidvfniqlsklvnliillivlllvlvlriyiskklkkkl 121
                  + ++  l++++++ +   + +l++ + +i+  +v+  ++++ +y+ +k++ k 
  EPA04729.1  18 FI-VSASLSAVVAQSLLGYENHLTTTITIITGYVVYFGIFSVLFYLDNKNRYKQ 70 
                 33.34445555555555556699************************9977554 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00021
      DUF443  55 ivkkakkksigllalGsavllgnllrklidvfniqlsklvnliillivlllvlvlriyiskkl 117
                   kk   + i++ ++G ++ lg    +l + ++i++++ +++++  i+  +  ++ + i  + 
  EPA04729.1  75 LIKKEILSMISSFGVGEIIYLGIRWPSLYYFLEINIEPYIASLVSEIIATACYMIAVTIFLRK 137
                 55555666777888999***********************99998887776666666665443 PP

>> UMPH-1  Pyrimidine 5'-nucleotidase (UMPH-1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.2    0.0034        15      97     143 ..       5      52 ..       2      59 .. 0.79
   2 ?    6.2   0.0    0.0015       6.6      92     125 ..      65      98 ..      54     111 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0034
      UMPH-1  97 elfekleklnvPvlifsaGlgdvlee.vlrqanvvysnvkvvsnfldf 143
                 + + +++++ + ++i sa l+ v+ + +l  +n + + + ++  ++ +
  EPA04729.1   5 QQLLQINRNFIICFIVSASLSAVVAQsLLGYENHLTTTITIITGYVVY 52 
                 556678899999**********99761556669999999999887765 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0015
      UMPH-1  92 rdgveelfekleklnvPvlifsaGlgdvleevlr 125
                 +++++++ ++l k+++  +i s G+g+++   +r
  EPA04729.1  65 KNRYKQMSSSLIKKEILSMISSFGVGEIIYLGIR 98 
                 6899************************987776 PP

>> Tox-WTIP  Toxin with a conserved tryptophan and TIP tripeptide motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.5     0.067     3e+02      38      53 ..      40      55 ..      26      59 .. 0.73
   2 ?    8.9   0.0   0.00043       1.9      32      60 ..      76     103 ..      58     110 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.067
    Tox-WTIP 38 kvvaavGvgYliYRgv 53
                +++++  +gY++Y g+
  EPA04729.1 40 TTTITIITGYVVYFGI 55
                333444456****997 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00043
    Tox-WTIP  32 aakkaakvvaavGvgYliYRgvRmlPSLl 60 
                  +k+ +++  + Gvg +iY g+R  PSL 
  EPA04729.1  76 IKKEILSMISSFGVGEIIYLGIRW-PSLY 103
                 456677888999***********5.8885 PP

>> DUF3021  Protein of unknown function (DUF3021)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   3.3   3.1e-05      0.14      65     128 ..      10      73 ..       4      75 .. 0.59
   2 ?    1.3   2.1     0.091   4.1e+02      41      83 ..      87     130 ..      72     139 .. 0.40

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.1e-05
     DUF3021  65 llkqtlihflvvlllvllla.lllgWfplsvigilivilifiiiyliiwlifylsekkevkkiNe 128
                 + ++++i f+v   l  ++a  llg  + ++++ + +i+ +++ ++i  ++fyl +k++ k++  
  EPA04729.1  10 INRNFIICFIVSASLSAVVAqSLLGYEN-HLTTTITIITGYVVYFGIFSVLFYLDNKNRYKQMSS 73 
                 3444555555555555555545555333.444444445666777778888999999999999976 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.091
     DUF3021  41 vllsaliGvlfalaslifese.rlsllkqtlihflvvlllvlll 83 
                 + +  +i +++ ++sl +  e ++   ++ l+  ++ +++++++
  EPA04729.1  87 FGVGEIIYLGIRWPSLYYFLEiNIEPYIASLVSEIIATACYMIA 130
                 22222233333344444444444444444443333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       865  (0.0482459); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 970.52
//
Query:       EPA04730.1  [L=260]
Description: hypothetical protein BG20_I0918 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-06   27.5  11.8      2e-06   27.5  11.8    3.1  3  MscS_porin      Mechanosensitive ion channel porin domain
     0.0031   15.8  18.8     0.0031   15.8  18.8    3.0  3  EzrA            Septation ring formation regulator, EzrA
  ------ inclusion threshold ------
      0.029   14.5   0.2        0.1   12.7   0.2    2.0  1  GBR2_CC         Gamma-aminobutyric acid type B receptor subun
      0.063   13.8  49.9      0.065   13.8  14.5    3.2  3  APG6_N          Apg6 coiled-coil region
       0.11   11.2  41.1       0.17   10.6  25.7    2.1  2  WEMBL           Weak chloroplast movement under blue light
       0.16   11.5  53.1       0.49    9.8  37.4    2.1  2  HMMR_N          Hyaluronan mediated motility receptor N-termi
       0.17    9.4  37.9       0.19    9.2  37.9    1.0  1  DUF3584         Protein of unknown function (DUF3584)
       0.19   10.7  40.3        0.2   10.6   8.1    3.2  3  IFT57           Intra-flagellar transport protein 57
       0.35   11.3  40.0    1.3e+03   -0.4  40.0    2.6  1  Fez1            Fez1
       0.51    9.8   4.1       0.73    9.2   0.7    2.1  2  Mce4_CUP1       Cholesterol uptake porter CUP1 of Mce4, putat
       0.59   10.3  14.4        1.1    9.4   1.2    3.8  3  TRPM_tetra      Tetramerisation domain of TRPM
        1.2    9.7  41.0       0.53   10.9   5.2    3.9  4  HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interac
        1.7    9.1  39.2       0.21   12.0   2.5    5.4  6  FlaC_arch       Flagella accessory protein C (FlaC)
        2.2    8.3  34.6       0.82    9.7  12.8    3.2  3  Laminin_II      Laminin Domain II
        3.7    7.6   9.0        0.8    9.7   0.1    3.7  4  Prp19           Prp19/Pso4-like
        3.8    7.2  43.2        0.9    9.2   2.6    3.8  4  DUF4201         Domain of unknown function (DUF4201)
        4.1    6.2  47.8       0.32    9.8  14.2    3.0  2  Spc7            Spc7 kinetochore protein
        4.9    7.6  30.6       0.47   10.9   2.1    4.4  3  Streptin-Immun  Lantibiotic streptin immunity protein
        5.1    7.1  29.9         11    6.1   2.3    3.4  3  DUF1664         Protein of unknown function (DUF1664)
        6.3    6.9  47.9       0.55   10.3  11.5    3.4  3  TPR_MLP1_2      TPR/MLP1/MLP2-like protein
        7.9    5.5  32.5        0.1   11.7   3.3    3.1  3  FH2             Formin Homology 2 Domain
        8.9    6.6  18.5       0.18   12.1   1.6    3.4  3  DUF948          Bacterial protein of unknown function (DUF948
        9.9    6.6  50.4       0.88    9.9  13.7    3.1  3  Uso1_p115_C     Uso1 / p115 like vesicle tethering protein, C


Domain annotation for each model (and alignments):
>> MscS_porin  Mechanosensitive ion channel porin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   4.3     0.069        54      64     132 ..       9      77 ..       5      84 .. 0.83
   2 !   27.5  11.8   2.6e-09     2e-06      66     147 ..      98     179 ..      86     185 .. 0.87
   3 ?    5.2   2.2     0.017        14     161     201 ..     218     258 ..     209     260 .] 0.66

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.069
  MscS_porin  64 qkkkeeaskeilaklsleeLeqrllqtssqlqelqeqlaqlnsqlvelqtrperaqqqltearqrlqei 132
                 +++++++s+++ + +  e Le ++++ +++  + q ++ ++ ++l       + a + l + ++++++ 
  EPA04730.1   9 EQSNDTKSEKSEEIILKESLETEVESLQNDFRTKQDEIENITKKLHDVKEEYDIATSNLMSVKKEINQK 77 
                 367778888888888889999999999999999999999999999999999999999999998888875 PP

  == domain 2  score: 27.5 bits;  conditional E-value: 2.6e-09
  MscS_porin  66 kkeeaskeilaklsleeLeqrllqtssqlqelqeqlaqlnsqlvelqtrperaqqqltearqrlqeirnrLnstaaageals 147
                  +e+ +k++ +   le  e+ l + +++l++++++ +++n++++e q+++ ++++q+ +a++ l++i++rL + ++++++++
  EPA04730.1  98 VNEKFNKNKKSIEDLEKVESNLSKKKQDLEKTTKEYNEINDKVIEEQSALHEIRAQQIQAQKDLEAITSRLYNARQEEKNIQ 179
                 4677778888888999*******************************************************77666666554 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.017
  MscS_porin 161 leaqieeleqellsnnnrqeLlklqrdllklriqqleqelq 201
                 l++++++ e+e ++ +++ e  +++++++k ++++l+++l+
  EPA04730.1 218 LKSKLSMAEKEIETVQVLLEKERKEHEQTKNELERLKEKLE 258
                 66666666666666666666666666666666666666654 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8  18.8     4e-06    0.0031      47     150 ..      17     121 ..       8     122 .. 0.90
   2 !    5.9  11.7    0.0039         3     352     421 ..     111     180 ..     110     193 .. 0.91
   3 ?    2.6   5.1      0.04        31     276     316 ..     218     258 ..     201     260 .] 0.68

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4e-06
                 TSSS-S---TTTHHHHHHHHHHHHHHHHHHTHHHHHT-GGGT-..-S-SHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHH CS
        EzrA  47 skvkklnltgeseekfeewkkkwdeiktkklpeieellfeaee..lldkykfkkakkklaeleeeldeveekikkileelkelteseeknreeieklke 143
                 +k +++ l++ +e+++e++++++ + ++ ++++i+++l +++e  ++ + +++++kk++++ ++eld++  ++++i+ +l+++ e+ +kn++ ie+l++
  EPA04730.1  17 EKSEEIILKESLETEVESLQNDFRTKQD-EIENITKKLHDVKEeyDIATSNLMSVKKEINQKKMELDTIYLEYNDIKLKLSDVNEKFNKNKKSIEDLEK 114
                 6789999****************98777.************872246799***********************************************99 PP

                 HHHHHHH CS
        EzrA 144 kYrelrk 150
                    +l+k
  EPA04730.1 115 VESNLSK 121
                 8777766 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0039
                 HHHHHHHHHHHHHHHHS-SS---STTGGGTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
        EzrA 352 elkelekdyeeleekleekkvaYSelqeeleeleekleeieekqeeileslkslrkdEkrAreqldeikk 421
                 +l+++e+++ + +++le+ +  Y e+++++ e ++ l ei  +q + +++l+++ +   +Ar++ ++i++
  EPA04730.1 111 DLEKVESNLSKKKQDLEKTTKEYNEINDKVIEEQSALHEIRAQQIQAQKDLEAITSRLYNARQEEKNIQN 180
                 7899999999999****************************************99999999999999987 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.04
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTSSSSSHHHH CS
        EzrA 276 veeelktieeeidsLyddlekEveAkkeveknlkelkekle 316
                  +++l+  e+ei+++  +lekE + +++ +++l++lkekle
  EPA04730.1 218 LKSKLSMAEKEIETVQVLLEKERKEHEQTKNELERLKEKLE 258
                 45566666777777777777777777777777777777665 PP

>> GBR2_CC  Gamma-aminobutyric acid type B receptor subunit 2 coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   0.00013       0.1      13      37 ..     143     167 ..     139     169 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00013
     GBR2_CC  13 lQaenHslRmkitelDKdLEEVTMQ 37 
                  Q+ +H +R + +   KdLE +T  
  EPA04730.1 143 EQSALHEIRAQQIQAQKDLEAITSR 167
                 69*******************9965 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8  14.5   8.4e-05     0.065      44     127 ..      17     110 ..       4     114 .. 0.86
   2 ?    5.7  16.0     0.025        20      17     101 ..     101     178 ..      98     193 .. 0.70
   3 ?    5.5   7.3      0.03        23      11      58 ..     215     259 ..     208     260 .] 0.61

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.4e-05
      APG6_N  44 k..........qdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelqlelleleeeldsleaqye 127
                 +           ++e+e+l++++++ ++e e+  ++L ++++e +   + l + ++e ++++ e +    eyn+ +l+l++ +e+ ++ + ++e
  EPA04730.1  17 EkseeiilkesLETEVESLQNDFRTKQDEIENITKKLHDVKEEYDIATSNLMSVKKEINQKKMELDTIYLEYNDIKLKLSDVNEKFNKNKKSIE 110
                 13456677777899*********************************************************************99887776665 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.025
      APG6_N  17 qleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerf 101
                 ++++ +k ++++e+ +++l k+       +++le++ +e+ +++++  e ++ L e+ +++ + +++l+a+++ l +  +ee++ 
  EPA04730.1 101 KFNKNKKSIEDLEKVESNLSKK-------KQDLEKTTKEYNEINDKVIEEQSALHEIRAQQIQAQKDLEAITSRLYNARQEEKNI 178
                 5555666666666666666665.......34677777788888888888888888888888888888888888777777777664 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.03
      APG6_N  11 leeldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeelek 58 
                 +  l+++l+ aeke+++ +  l+k +ke+++++   +ele+l+e+le+
  EPA04730.1 215 VGSLKSKLSMAEKEIETVQVLLEKERKEHEQTK---NELERLKEKLEQ 259
                 556667777777777777777766666655543...466666666654 PP

>> WEMBL  Weak chloroplast movement under blue light
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6  25.7   0.00021      0.17     268     434 ..      12     174 ..       3     189 .. 0.82
   2 ?    6.0  25.9    0.0053       4.2     238     395 ..      98     259 ..      95     260 .] 0.80

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00021
       WEMBL 268 ayvesklkeeaeeeeee.......kksetsikealasarkELeevkaniekakdevklLkvaaasLrseLekekaeLaslrqregmasiavssLeaels 359
                 + ++s+ +e       e       +++ +s+++   +++ E+e++ +++  +k+e  + +    s+++e++++k eL+++  + +      s +++  +
  EPA04730.1  12 NDTKSEKSE-------EiilkeslETEVESLQNDFRTKQDEIENITKKLHDVKEEYDIATSNLMSVKKEINQKKMELDTIYLEYNDIKLKLSDVNEKFN 103
                 333333333.......24444444888899999999999999999999999999999999999999999999999999999999999999999999999 PP

       WEMBL 360 rtkselelvqakekearekmvelpkeLqeAaqeaeeAkslAqaareelrkakeeaeqakaavstvesrLeavlkE 434
                 + k+ +e +++ e +  +      + L+++++e +e + ++   +  l++ + +  qa+ +++++ srL  + +E
  EPA04730.1 104 KNKKSIEDLEKVESNLSK----KKQDLEKTTKEYNEINDKVIEEQSALHEIRAQQIQAQKDLEAITSRLYNARQE 174
                 999999999988888544....46789999999999999999999999999999999999999999999998887 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0053
       WEMBL 238 LneellsakdlkskletasallldLkaeLaayvesklkeeaeeeeeekksetsikealasarkELeevkaniekakdevklLkvaaasLrseLekekae 336
                 +ne+   +k   + le+ ++ l + k++L   +++  +e +++  ee++  ++i+++  +a+k+Le + + + +a++e k +++         +kek+ 
  EPA04730.1  98 VNEKFNKNKKSIEDLEKVESNLSKKKQDLEKTTKE-YNEINDKVIEEQSALHEIRAQQIQAQKDLEAITSRLYNARQEEKNIQNNDGETSVFTSKEKEF 195
                 56666666666677778888888888888776653.34444555556778889999999**************************999999999***99 PP

       WEMBL 337 Laslrqre.....gmasiavssLeaelsrtkselelvqakekearekmvelpkeLqeAaqeaee 395
                 +a   ++e     ++as+ v sL+  ls +++e+e+vq+  +++r++ +++ +eL++ ++++e+
  EPA04730.1 196 IAGADKKEmkgviEAASVVVGSLKSKLSMAEKEIETVQVLLEKERKEHEQTKNELERLKEKLEQ 259
                 9988887733333579**********************98888888889999999988887776 PP

>> HMMR_N  Hyaluronan mediated motility receptor N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8  37.4   0.00063      0.49     174     333 ..      15     180 ..       7     182 .. 0.75
   2 ?    7.8   7.7    0.0025         2     271     323 ..     204     259 ..     189     260 .] 0.81

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00063
      HMMR_N 174 eakekevsvkQedmeaklqvtqknLeeskakvaqLkeklvslekek.......ieekseteklleyieelsnvseqlekykldiaqleellkekndeie 265
                 ++ + e +++ e++e +++++q+++++ + ++ ++  kl ++++e        +  k   ++  +   el  +  + +  kl++  ++e ++++++ ie
  EPA04730.1  15 KSEKSEEIILKESLETEVESLQNDFRTKQDEIENITKKLHDVKEEYdiatsnlMSVK---KEINQKKMELDTIYLEYNDIKLKLSDVNEKFNKNKKSIE 110
                 44455667899***************************9888877633322222222...2222233345555555566799999******99998776 PP

      HMMR_N 266 sL...kssLeekeqelskqvkdlnekc.kllekekeelvreeeekeqtlsaEleelkeklklkeqeaqklqq 333
                 +L    s+L++k+q l+k++k+ ne   k++e++    ++e + ++ + ++ le ++ +l   +qe++++q 
  EPA04730.1 111 DLekvESNLSKKKQDLEKTTKEYNEINdKVIEEQSA--LHEIRAQQIQAQKDLEAITSRLYNARQEEKNIQN 180
                 55211789***************9976155666655..****************************998886 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0025
      HMMR_N 271 Leekeqelskqvkdlnekckllekekeel...vreeeekeqtlsaEleelkeklkl 323
                 ++   ++ s  v +l++k+++ eke e +   +++e++ +++ + Ele lkekl++
  EPA04730.1 204 MKGVIEAASVVVGSLKSKLSMAEKEIETVqvlLEKERKEHEQTKNELERLKEKLEQ 259
                 555555667789999********99997655578888889999**********987 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2  37.9   0.00025      0.19     281     533 ..       6     257 ..       2     260 .] 0.74

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00025
     DUF3584 281 kqeevqeakaelkqqlrtledelkeaidelnqelsaakaklaakeselealeeqkkkyedadieklkadldqlpsirseleeleeeldaltekhqdvqe 379
                 k++e+ +  ++ k++   l++ l+++++ l+++  +++++++++ ++l  ++e+++    +++ ++k++     + + el  +  e++ +  k  dv+e
  EPA04730.1   6 KKKEQSNDTKSEKSEEIILKESLETEVESLQNDFRTKQDEIENITKKLHDVKEEYDI-ATSNLMSVKKEI---NQKKMELDTIYLEYNDIKLKLSDVNE 100
                 677777788888888889999**************************9999988865.456666666665...556889999***************** PP

     DUF3584 380 kydrrkqkik..eeleeeleklker.leaireekdrl..kaaieealealesqlrkqleaqkeelneeekelesrlselklr.ldsatateEeleqiee 472
                 k++++k+ i+  e+ e +l+k k++ ++ ++e ++      ++++al+++++q+  q ++  e++  + ++ +++ ++ +    +    t+ e+e i+ 
  EPA04730.1 101 KFNKNKKSIEdlEKVESNLSKKKQDlEKTTKEYNEINdkVIEEQSALHEIRAQQI-QAQKDLEAITSRLYNARQEEKNIQNNdGETSVFTSKEKEFIAG 198
                 *******998334667778888888444444444444213333445566655555.4455555555554444433333222202233456777777777 PP

     DUF3584 473 adealekaqeelekaeaevealqaeeeqlrkkrdeadealqkaerrleqlrqaleeleeql 533
                 ad+  ++++  +e+a+  v +l++++  ++k+ ++ +  l+k+++  eq +++le l+e l
  EPA04730.1 199 ADK--KEMKGVIEAASVVVGSLKSKLSMAEKEIETVQVLLEKERKEHEQTKNELERLKEKL 257
                 777..589999**********************************************9987 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   8.1   0.00026       0.2     264     322 ..      25      82 ..       7      92 .. 0.87
   2 ?    8.9  12.3   0.00085      0.66     249     331 ..      90     171 ..      84     180 .. 0.85
   3 ?    3.3   4.5     0.041        32     281     323 ..     217     259 ..     201     260 .] 0.87

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00026
       IFT57 264 rEkylnsqleellqeyreaqeelsevkekykqlsegvseltrelaeiseelekvkqeme 322
                 +E  l++++e+l +++r++q+e++++++k+++++e+    t +l ++++e+++ k e++
  EPA04730.1  25 KE-SLETEVESLQNDFRTKQDEIENITKKLHDVKEEYDIATSNLMSVKKEINQKKMELD 82 
                 44.589999**********************************************9987 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00085
       IFT57 249 klhedisktlekiesrEkylnsqleellqeyreaqeelsevkekykqlsegvseltrelaeiseelekvkqemeergssmtDg 331
                 +++ ++s + ek ++  k ++  le+  ++++++++ l++++++y++++++v e +  l+ei  +  ++++++e  +s++ ++
  EPA04730.1  90 DIKLKLSDVNEKFNKNKKSIE-DLEKVESNLSKKKQDLEKTTKEYNEINDKVIEEQSALHEIRAQQIQAQKDLEAITSRLYNA 171
                 566678889999999999996.6999999999999999999999999999999999999999999999999998877776555 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.041
       IFT57 281 eaqeelsevkekykqlsegvseltrelaeiseelekvkqemee 323
                 +++ +ls +++++++++  +++ ++e +++++ele++k+++e+
  EPA04730.1 217 SLKSKLSMAEKEIETVQVLLEKERKEHEQTKNELERLKEKLEQ 259
                 6788999999999999999999999999999999999999875 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4  40.0       1.7   1.3e+03      19     174 ..      32     252 ..       7     260 .] 0.59

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.7
        Fez1  19 Lkdsqaevtqklseivalkaqlrelrakleekeeeikeleesleektle...............................levcenelqrkkseaellr 86 
                     q++  +k +ei ++  +l++++++ +   ++++++++++++k++e                               le++e++l++kk++ e + 
  EPA04730.1  32 VESLQNDFRTKQDEIENITKKLHDVKEEYDIATSNLMSVKKEINQKKMEldtiyleyndiklklsdvnekfnknkksiedLEKVESNLSKKKQDLEKTT 130
                 456799999999999999999999999999999999999999999999955555555554444444444455555555554455555555444444444 PP

        Fez1  87 ekvekleeelkelreelselsleeeeaa............lesdeakaqrqe................................aeeleelkreverlr 141
                 ++ +++++++ e +++l+e  +++ +a+            +          +                                +  +e+ +  v  l+
  EPA04730.1 131 KEYNEINDKVIEEQSALHEIRAQQIQAQkdleaitsrlynA----------RqeekniqnndgetsvftskekefiagadkkemKGVIEAASVVVGSLK 219
                 44444444444444444444433333335666655555431..........022333444557777777777777777777777445555555556666 PP

        Fez1 142 aeLkeerqkkeeqassFeqERrtWqeeKekVir 174
                 ++L++ +++ e+ +   e+ER+  ++ K+   r
  EPA04730.1 220 SKLSMAEKEIETVQVLLEKERKEHEQTKNELER 252
                 666666666666666666666666665555444 PP

>> Mce4_CUP1  Cholesterol uptake porter CUP1 of Mce4, putative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.2      0.19   1.5e+02      45     101 ..      37      86 ..      23      91 .. 0.59
   2 ?    9.2   0.7   0.00094      0.73      44     113 ..      95     164 ..      87     174 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.19
   Mce4_CUP1  45 delNprlpqlredireladladvYadaapdlldaLdnavttsrTiveqqaeLdalll 101
                 +++ ++ +++++  ++l d+++ Y+ a ++l+         ++ i++++ eLd+++l
  EPA04730.1  37 NDFRTKQDEIENITKKLHDVKEEYDIATSNLM-------SVKKEINQKKMELDTIYL 86 
                 44445555555555666666666666655555.......556667777777777766 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00094
   Mce4_CUP1  44 LdelNprlpqlredireladladvYadaapdlldaLdnavttsrTiveqqaeLdalllaavglsntgadl 113
                 L+++N++ ++ ++ i++l+++    ++  +dl ++ ++    ++ + e+q++L+++ ++ +++ ++++ +
  EPA04730.1  95 LSDVNEKFNKNKKSIEDLEKVESNLSKKKQDLEKTTKEYNEINDKVIEEQSALHEIRAQQIQAQKDLEAI 164
                 89******************************************************99999998887766 PP

>> TRPM_tetra  Tetramerisation domain of TRPM
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   1.4    0.0077         6       5      36 ..      40      71 ..      36      79 .. 0.87
   2 ?    9.4   1.2    0.0014       1.1      14      36 ..      91     113 ..      88     132 .. 0.80
   3 ?    0.3   0.3      0.98   7.7e+02      19      36 ..     134     151 ..     126     168 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0077
  TRPM_tetra  5 rvttERvEnmsmkveevneKenlikaSLqsld 36
                r+ ++ +En++ k+ +v+e   + +++L s+ 
  EPA04730.1 40 RTKQDEIENITKKLHDVKEEYDIATSNLMSVK 71
                778999*************9999999999986 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0014
  TRPM_tetra  14 msmkveevneKenlikaSLqsld 36 
                 + +k+ +vneK n  k+S+ +l+
  EPA04730.1  91 IKLKLSDVNEKFNKNKKSIEDLE 113
                 6789**************98876 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.98
  TRPM_tetra  19 eevneKenlikaSLqsld 36 
                 +e+n+K+   ++ L ++ 
  EPA04730.1 134 NEINDKVIEEQSALHEIR 151
                 799999998888887764 PP

>> HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interacting protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   7.9     0.019        15      27      95 ..      23      73 ..       5      87 .. 0.54
   2 ?    3.2   1.7      0.17   1.4e+02      46      86 ..      73     113 ..      63     122 .. 0.43
   3 ?    3.3  11.2      0.16   1.2e+02      21      87 ..     115     180 ..     104     184 .. 0.85
   4 ?   10.9   5.2   0.00068      0.53      42      94 ..     203     255 ..     188     259 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.019
  HIP1_clath_bdg 27 rekkeleeelerlkeeaerkleeqkeelekLkreleakraelarlkssLesseqsgeqlssqlaaLqaE 95
                      k+                    ++e+e+L++++ +k++e++++ + L++ +++ +  +s+l++ ++E
      EPA04730.1 23 ILKE------------------SLETEVESLQNDFRTKQDEIENITKKLHDVKEEYDIATSNLMSVKKE 73
                    2233..................34455666666666666666666666666666666666666655555 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.17
  HIP1_clath_bdg  46 kleeqkeelekLkreleakraelarlkssLesseqsgeqls 86 
                     +++++k+el+++  e ++ + +l+ +++  +++++s e+l+
      EPA04730.1  73 EINQKKMELDTIYLEYNDIKLKLSDVNEKFNKNKKSIEDLE 113
                     23344444444444444444444444444444444433333 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.16
  HIP1_clath_bdg  21 aqeeverekkeleeelerlkeeaerkleeqkeelekLkreleakraelarlkssLesseqsgeqlss 87 
                       +++ ++k++le++ ++ +e +++ +eeq+    +++++  + +++l+ + s L +  q+++++++
      EPA04730.1 115 VESNLSKKKQDLEKTTKEYNEINDKVIEEQSAL-HEIRAQQIQAQKDLEAITSRLYNARQEEKNIQN 180
                     56789999**********999999888888765.559999999999**************9998865 PP

  == domain 4  score: 10.9 bits;  conditional E-value: 0.00068
  HIP1_clath_bdg  42 eaerkleeqkeelekLkreleakraelarlkssLesseqsgeqlssqlaaLqa 94 
                     e +  +e  +  + +Lk+ l + ++e+++++  Le++ ++ eq +++l+ L++
      EPA04730.1 203 EMKGVIEAASVVVGSLKSKLSMAEKEIETVQVLLEKERKEHEQTKNELERLKE 255
                     44444667788899***********************************9975 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   2.5   0.00027      0.21       3      36 ..      26      59 ..      25      70 .. 0.90
   2 ?    5.2   1.1     0.035        27       5      37 ..      70     102 ..      66     107 .. 0.90
   3 ?    5.5   4.0      0.03        23       8      37 ..     111     140 ..     107     156 .. 0.78
   4 ?   -0.2   0.1       1.8   1.4e+03       7      28 ..     159     180 ..     156     181 .. 0.85
   5 ?    4.4   0.3     0.062        48       9      27 ..     215     233 ..     203     238 .. 0.62
   6 ?    4.4   5.9     0.066        51       6      37 ..     226     257 ..     215     259 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00027
   FlaC_arch  3 delEnklsklsteletvkkeneelsksveelken 36
                ++lE+++++l+  + t ++e+e++ k+++++ke+
  EPA04730.1 26 ESLETEVESLQNDFRTKQDEIENITKKLHDVKEE 59
                579***************************9986 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.035
   FlaC_arch   5 lEnklsklsteletvkkeneelsksveelkenV 37 
                 + +++++ ++el+t+  e ++++ ++ +++e++
  EPA04730.1  70 VKKEINQKKMELDTIYLEYNDIKLKLSDVNEKF 102
                 6789*************************9987 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.03
   FlaC_arch   8 klsklsteletvkkeneelsksveelkenV 37 
                 +l+k++++l+  k+++e+  k+ +e++++V
  EPA04730.1 111 DLEKVESNLSKKKQDLEKTTKEYNEINDKV 140
                 688889999999999999999999999888 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 1.8
   FlaC_arch   7 nklsklsteletvkkeneelsk 28 
                 ++l+ + ++l ++++e +++++
  EPA04730.1 159 KDLEAITSRLYNARQEEKNIQN 180
                 7899999999999999999876 PP

  == domain 5  score: 4.4 bits;  conditional E-value: 0.062
   FlaC_arch   9 lsklsteletvkkeneels 27 
                 +++l+++l++++ke+e ++
  EPA04730.1 215 VGSLKSKLSMAEKEIETVQ 233
                 3445555555555555554 PP

  == domain 6  score: 4.4 bits;  conditional E-value: 0.066
   FlaC_arch   6 EnklsklsteletvkkeneelsksveelkenV 37 
                 E++++ +++ le  +ke e+ ++++e+lke+ 
  EPA04730.1 226 EKEIETVQVLLEKERKEHEQTKNELERLKEKL 257
                 88999999999999999999999999999975 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   4.6    0.0036       2.8      19      70 ..      25      76 ..       8     100 .. 0.84
   2 ?    9.7  12.8    0.0011      0.82       6      87 ..      96     180 ..      91     202 .. 0.80
   3 ?    1.4   2.4      0.37   2.9e+02       2      41 ..     219     258 ..     214     260 .] 0.63

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0036
                XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTT CS
  Laminin_II 19 laplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapq 70
                ++ l++++e ++++  + ++++e++++k++d ++  + A ++   ++k+++q
  EPA04730.1 25 KESLETEVESLQNDFRTKQDEIENITKKLHDVKEEYDIATSNLMSVKKEINQ 76
                678999999****************************999999999999987 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0011
                 XXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH... CS
  Laminin_II   6 aeaneta...kevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeasss 87 
                 +++ne+    k+  e+l++++ nl++ k++l++  ++ +e+n+kv + + a+ + r +  + +k ++ + ++l + +q e++ ++
  EPA04730.1  96 SDVNEKFnknKKSIEDLEKVESNLSKKKQDLEKTTKEYNEINDKVIEEQSALHEIRAQQIQAQKDLEAITSRLYNARQEEKNIQN 180
                 5555554111555678889999******************************************************999999666 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.37
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
  Laminin_II   2 kelaaeanetakevleqlaplsqnlentkeklseinrsve 41 
                 k++++ a++ ++ v+  l++  ++ e+tk++l+++++++e
  EPA04730.1 219 KSKLSMAEKEIETVQVLLEKERKEHEQTKNELERLKEKLE 258
                 4555666666666666666666666666666666666654 PP

>> Prp19  Prp19/Pso4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1     0.001       0.8       5      39 ..      49      83 ..      45      91 .. 0.89
   2 ?   -2.2   0.0       5.5   4.3e+03      25      36 ..     121     132 ..     110     136 .. 0.67
   3 ?   -1.3   0.3       2.8   2.2e+03      23      37 ..     147     161 ..     124     173 .. 0.62
   4 ?    1.5   0.2      0.37   2.9e+02      19      37 ..     232     250 ..     210     260 .] 0.61

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.001
                HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
       Prp19  5 iPslLstlqnEWDalmletfelrkqleqtrqeLsq 39
                i + L+ +++E+D    ++ +++k+++q + eL +
  EPA04730.1 49 ITKKLHDVKEEYDIATSNLMSVKKEINQKKMELDT 83
                66779999************************965 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.5
                 HHHHHHHHHHHH CS
       Prp19  25 elrkqleqtrqe 36 
                 + +++le+t++e
  EPA04730.1 121 KKKQDLEKTTKE 132
                 456777777776 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 2.8
                 HHHHHHHHHHHHHHH CS
       Prp19  23 tfelrkqleqtrqeL 37 
                 ++e+r q  q++++L
  EPA04730.1 147 LHEIRAQQIQAQKDL 161
                 355555555555554 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.37
                 HHHHHHHHHHHHHHHHHHH CS
       Prp19  19 lmletfelrkqleqtrqeL 37 
                 ++  + + rk+ eqt++eL
  EPA04730.1 232 VQVLLEKERKEHEQTKNEL 250
                 4444445555666666655 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   2.6    0.0012       0.9     122     175 ..      14      67 ..       6      69 .. 0.79
   2 ?    3.5  16.6     0.069        53      55     135 ..      71     161 ..      67     166 .. 0.81
   3 ?    1.6   8.5      0.25   1.9e+02      60     121 ..     121     175 ..     118     186 .. 0.52
   4 ?    8.0   4.8    0.0027       2.1      82     134 ..     218     256 ..     199     260 .] 0.45

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0012
     DUF4201 122 dklrkqneklkqqggllrvPaLlkDYdktkekveekrksvkkLrrkvkilemrl 175
                 +k +k  e + +++ + +v++L +D+  +++++e+  k++   +++++i++++l
  EPA04730.1  14 TKSEKSEEIILKESLETEVESLQNDFRTKQDEIENITKKLHDVKEEYDIATSNL 67 
                 555666666666666679999999999999999999999999999999999876 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.069
     DUF4201  55 nkkIeernkeLkrlkkkttktvhalthlkeklh..........mleselselkkelkekeerlaklrkelykvklerdklrkqneklkqqg 135
                 +k+I+ ++ eL  + + +++   +l+++ ek +           +es+ls++k++l++ +++ +++ +++ + +   + +r+q+ + ++++
  EPA04730.1  71 KKEINQKKMELDTIYLEYNDIKLKLSDVNEKFNknkksiedleKVESNLSKKKQDLEKTTKEYNEINDKVIEEQSALHEIRAQQIQAQKDL 161
                 799****************************997777788777788888888888888888888888888888888777777777666655 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.25
     DUF4201  60 ernkeLkrlkkkttktvhalthlkeklhmleselselkkelkekeerlaklrkelykvkler 121
                  ++++L++  k ++    ++ +++  lh++++++ +++k+l+ ++ rl   r+e        
  EPA04730.1 121 KKKQDLEKTTKEYNEINDKVIEEQSALHEIRAQQIQAQKDLEAITSRLYNARQE-------E 175
                 455555555555555555555555555555555555555555555555555544.......3 PP

  == domain 4  score: 8.0 bits;  conditional E-value: 0.0027
     DUF4201  82 lkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqneklkqq 134
                 lk k              l+  e++++ ++  l+k ++e+++ +++ e+lk++
  EPA04730.1 218 LKSK--------------LSMAEKEIETVQVLLEKERKEHEQTKNELERLKEK 256
                 3333..............33333333333333333333333333333333333 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8  14.2   0.00041      0.32     176     261 ..      25     113 ..       6     118 .. 0.42
   2 ?    3.4  20.7     0.036        28     152     255 ..      68     173 ..      62     197 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00041
        Spc7 176 kaeleeeleklqe....aaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeck 261
                 k++le e+e+lq+    +++e+e+i+k +L+ ++ee + + +++ + kke+++++ +l+++  + +++k + s+++e+ ++ ++ +e  +
  EPA04730.1  25 KESLETEVESLQNdfrtKQDEIENITK-KLHDVKEEYDIATSNLMSVKKEINQKKMELDTIYLEYNDIKLKLSDVNEKFNKNKKSIEDLE 113
                 334444444444444334444444332.34444444444444444444444444444444444444444444444444444443333332 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.036
        Spc7 152 eedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesid..keeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkselee 248
                  + k+++++++ eld+++ e++  k +l++  ek ++ ++++e+++  + +L + +++l++  +e++e ++++ e q+ l e++++  ++++  + + +
  EPA04730.1  68 MSVKKEINQKKMELDTIYLEYNDIKLKLSDVNEKFNKNKKSIEDLEkvESNLSKKKQDLEKTTKEYNEINDKVIEEQSALHEIRAQQIQAQKDLEAITS 166
                 455677788888888888877777777777777777777766665533445666666666666666666666666666666666555555555444444 PP

        Spc7 249 eiaeaer 255
                 ++ +a++
  EPA04730.1 167 RLYNARQ 173
                 4443332 PP

>> Streptin-Immun  Lantibiotic streptin immunity protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   2.1   0.00061      0.47      50      84 ..      20      55 ..       6      62 .. 0.84
   2 ?    0.0  10.9       1.5   1.2e+03      20      81 ..      78     139 ..      59     151 .. 0.64
   3 ?    5.3   1.3     0.033        26      54      89 ..     222     257 ..     214     260 .] 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00061
  Streptin-Immun 50 esvtl.eqiekeieklqnelskkideyeelvrkldk 84
                    e + l e +e+e+e+lqn++ +k de e++ +kl  
      EPA04730.1 20 EEIILkESLETEVESLQNDFRTKQDEIENITKKLHD 55
                    55555278*************************975 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.5
  Streptin-Immun  20 kmaevlvnlksedeetrrlakydfsklnl.tesv.tleqiekeieklqnelskkideyeelvrk 81 
                     km    + l+ +d++ + l+  + +k+n   +s+  le++e++++k +++l+k+ +ey+e+  k
      EPA04730.1  78 KMELDTIYLEYNDIKLK-LSDVN-EKFNKnKKSIeDLEKVESNLSKKKQDLEKTTKEYNEINDK 139
                     45445566666665543.33322.2333312344269*********************998766 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.033
  Streptin-Immun  54 leqiekeieklqnelskkideyeelvrkldkfvkvl 89 
                     l   ekeie++q  l+k+ +e+e++   l++  + l
      EPA04730.1 222 LSMAEKEIETVQVLLEKERKEHEQTKNELERLKEKL 257
                     667899*****************9999999876655 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1  11.8      0.12        94      40     108 ..      43     114 ..      15     129 .. 0.48
   2 ?    4.8   7.8     0.035        27      48     100 ..     110     165 ..      88     181 .. 0.49
   3 ?    6.1   2.3     0.014        11      56      98 ..     214     259 ..     198     260 .] 0.73

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.12
     DUF1664  40 sdavesvskqleqvseslaatkrhLs...sridrvdkkldeqkeiskeikeevtevredlseigedvesvke 108
                 +d +e+++k+l +v+e+   +  +L+   ++i++   +ld      ++ik ++++v+e+ ++ ++ +e +++
  EPA04730.1  43 QDEIENITKKLHDVKEEYDIATSNLMsvkKEINQKKMELDTIYLEYNDIKLKLSDVNEKFNKNKKSIEDLEK 114
                 334444444444444444444333331112333334444444444444444444444444444444444444 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.035
     DUF1664  48 kqleqvseslaatkrhLss...ridrvdkkldeqkeiskeikeevtevredlseig 100
                 ++le+v ++l++ k++L++   + +++++k+ e + + +ei+++  ++++dl++i 
  EPA04730.1 110 EDLEKVESNLSKKKQDLEKttkEYNEINDKVIEEQSALHEIRAQQIQAQKDLEAIT 165
                 23455555555555555331113334444444444444444444444455554444 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.014
     DUF1664  56 slaatkrhLs...sridrvdkkldeqkeiskeikeevtevredlse 98 
                  + + k +Ls   ++i++v+  l++  +  +++k+e+++++e+l++
  EPA04730.1 214 VVGSLKSKLSmaeKEIETVQVLLEKERKEHEQTKNELERLKEKLEQ 259
                 4444455553222789999999999999999999999999999876 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3  11.5   0.00071      0.55       5     102 ..      13     110 ..       6     114 .. 0.87
   2 ?    2.3  12.6       0.2   1.6e+02      16      82 ..     111     177 ..     109     199 .. 0.70
   3 ?    6.3   8.6     0.012       9.5      68     110 ..     217     259 ..     207     260 .] 0.74

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00071
  TPR_MLP1_2   5 sleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesakaeleeseesweeqkeele 102
                   ++e+++    ke++e+++++lq+d ++++++ ++  +k +    +   ++ +l ++++e+n+ k e+ ++  e ++ k +l+   e+ ++ k+++e
  EPA04730.1  13 DTKSEKSEEIILKESLETEVESLQNDFRTKQDEIENITKKLHDVKEEYDIATSNLMSVKKEINQKKMELDTIYLEYNDIKLKLSDVNEKFNKNKKSIE 110
                 45555556666689999999*********99999999999999999999999999***********************99999999999999999987 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.2
  TPR_MLP1_2  16 ekeeaeaklqklqedlekqaeiakeaqqk.Yerelvkhaedvkelqalreelnelkaeiaelkaeaes 82 
                 + e+ e++l+k ++dlek +++++e ++k  e++  +h+  ++++qa + +l+ +++++ ++++e ++
  EPA04730.1 111 DLEKVESNLSKKKQDLEKTTKEYNEINDKvIEEQSALHEIRAQQIQAQK-DLEAITSRLYNARQEEKN 177
                 6678888888888888888888888888745777777777777777644.455555555555555544 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.012
  TPR_MLP1_2  68 elkaeiaelkaeaesakaeleeseesweeqkeelekelselek 110
                 +lk++++ +++e e+++  le+++++ e++k+ele+ +++le+
  EPA04730.1 217 SLKSKLSMAEKEIETVQVLLEKERKEHEQTKNELERLKEKLEQ 259
                 5777777777788888888888888888888887777777765 PP

>> FH2  Formin Homology 2 Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   7.3     0.025        19     271     354 ..      25     108 ..       9     111 .. 0.89
   2 ?   -1.0  16.4      0.95   7.4e+02     232     354 ..      52     175 ..      51     196 .. 0.70
   3 ?   11.7   3.3   0.00013       0.1     265     322 ..     202     259 ..     196     260 .] 0.94

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.025
                 HHCCTS-HHHHHHHHHHHHHHHHHHHHHHHHCCTTSSTT-THHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--TTC CS
         FH2 271 kkaakvnleslekevkklekglkklekelessekkeepsdkflevlkeflkeaeeklkkleeelkeakelvkelveYfgedkke 354
                 k++ + ++esl+++ ++ +++++++ k+l + +++ +     l ++k+ +++ + +l+++  e++++k ++ ++ e f+++kk 
  EPA04730.1  25 KESLETEVESLQNDFRTKQDEIENITKKLHDVKEEYDIATSNLMSVKKEINQKKMELDTIYLEYNDIKLKLSDVNEKFNKNKKS 108
                 6667788999999999999999999999999999999999999999999*****************999999999999988874 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.95
                 GCCCSB-S.TTTSBHHHHHHHHHHTTSGGGGGHHHHTTTHHHCCTS-HHHHHHHHHHHHH...HHHHHHHHHHHCCTTSSTT-THHHHHHHHHHHHHHH CS
         FH2 232 kLsdvKst.dnkttLLHylvkiireklpevldfsseLknvkkaakvnleslekevkklek...glkklekelessekkeepsdkflevlkeflkeaeek 326
                 kL dvK + d  t+ L  + k+i +k  e++  + e +++k     +l ++ ++ +k +k   +l+k+e +l++++++ e+  k +  +++ + e ++ 
  EPA04730.1  52 KLHDVKEEyDIATSNLMSVKKEINQKKMELDTIYLEYNDIKL----KLSDVNEKFNKNKKsieDLEKVESNLSKKKQDLEKTTKEYNEINDKVIEEQSA 146
                 899999999999998889999999988888888888888874....44444444444444000455666666666667777777777777778888888 PP

                 HHHHHHHHHHHHHHHHHHHHHT.T--TTC CS
         FH2 327 lkkleeelkeakelvkelveYf.gedkke 354
                 l ++++++ +a++ +++++  + +++++e
  EPA04730.1 147 LHEIRAQQIQAQKDLEAITSRLyNARQEE 175
                 88888888888888888776553333333 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00013
                 HHTTTHHHCCTS-HHHHHHHHHHHHHHHHHHHHHHHHCCTTSSTT-THHHHHHHHHHH CS
         FH2 265 seLknvkkaakvnleslekevkklekglkklekelessekkeepsdkflevlkeflke 322
                 +e+k v +aa+v + sl+++++  ek+++ ++  le+++k++e+ ++ le lke l++
  EPA04730.1 202 KEMKGVIEAASVVVGSLKSKLSMAEKEIETVQVLLEKERKEHEQTKNELERLKEKLEQ 259
                 79**************************************999999999999998876 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.6   0.00023      0.18      26      88 ..      37      99 ..      31     100 .. 0.90
   2 ?    3.6   3.6       0.1        81      24      66 ..      98     143 ..      93     180 .. 0.65
   3 ?    0.8   0.6      0.79   6.2e+02      20      60 ..     214     254 ..     201     260 .] 0.57

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00023
      DUF948 26 ktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvseln 88
                + ++  ++ ie+++k+++ + +e + ++++   + +++n+k  ++d++  + +d+  ++s++n
  EPA04730.1 37 NDFRTKQDEIENITKKLHDVKEEYDIATSNLMSVKKEINQKKMELDTIYLEYNDIKLKLSDVN 99
                556667889****************************************99999999999988 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.1
      DUF948  24 lkktldeaaatieele...kqvdpilkevedllakvnelledvnek 66 
                 +++ +++++++ie+le   +++ +  +++e+++++ ne+ + v e+
  EPA04730.1  98 VNEKFNKNKKSIEDLEkveSNLSKKKQDLEKTTKEYNEINDKVIEE 143
                 5566777777777777333555555555666666666655555444 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.79
      DUF948  20 vllklkktldeaaatieelekqvdpilkevedllakvnell 60 
                 v+ +lk+ l+ a++ ie+++  +++  ke e++ ++ ++l 
  EPA04730.1 214 VVGSLKSKLSMAEKEIETVQVLLEKERKEHEQTKNELERLK 254
                 44556666666666666666555555555555555544433 PP

>> Uso1_p115_C  Uso1 / p115 like vesicle tethering protein, C terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1  14.9     0.017        13       4     106 ..      12     112 ..       7     115 .. 0.87
   2 ?    9.9  13.7    0.0011      0.88      11      78 ..     113     178 ..     110     195 .. 0.88
   3 ?    1.6   8.1      0.43   3.4e+02      19      85 ..     217     253 ..     189     260 .] 0.44

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.017
  Uso1_p115_C   4 seleseaaslkdeneklkaelqslskalesleqkeakkaaesqakeleaenkklekeleklraelkeekekekekqkEldDLLlllgDleeKvekyka 101
                  ++++se+++   ++e+l++e++sl++  + ++ +   ++++++ +++++e +  +++l  +++e+++ k + +    E++D  l l+D  eK +k k+
   EPA04730.1  12 NDTKSEKSEEIILKESLETEVESLQNDFRTKQDE--IENITKKLHDVKEEYDIATSNLMSVKKEINQKKMELDTIYLEYNDIKLKLSDVNEKFNKNKK 107
                  5678888888899999999999999999999988..999999999999999999999999999999988888766999****999******9999999 PP

  Uso1_p115_C 102 rLkel 106
                   +++l
   EPA04730.1 108 SIEDL 112
                  88776 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0011
  Uso1_p115_C  11 aslkdeneklkaelqslskalesleqkeakkaaesqakeleaenkklekeleklraelkeekekekek 78 
                  +++++  +k k++l++++k++++ + k    + +s  +e++a++++ +k+le++ ++l +++++ek+ 
   EPA04730.1 113 EKVESNLSKKKQDLEKTTKEYNEINDK--VIEEQSALHEIRAQQIQAQKDLEAITSRLYNARQEEKNI 178
                  677888899999999999999999999..8889999*****************************854 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.43
  Uso1_p115_C  19 klkaelqslskalesleqkeakkaaesqakeleaenkklekeleklraelkeekekekekqkEldDL 85 
                  +lk++l+ ++                              ke+e+++  l++e+++ +++++El+ L
   EPA04730.1 217 SLKSKLSMAE------------------------------KEIETVQVLLEKERKEHEQTKNELERL 253
                  3333333333..............................333333333333333333333333322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      4085  (0.227843); expected 358.6 (0.02)
Passed bias filter:                      597  (0.033298); expected 358.6 (0.02)
Passed Vit filter:                       153  (0.00853366); expected 17.9 (0.001)
Passed Fwd filter:                        88  (0.00490825); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 1.35u 0.40s 00:00:01.75 Elapsed: 00:00:00.58
# Mc/sec: 1353.65
//
Query:       EPA04731.1  [L=59]
Description: hypothetical protein BG20_I0936 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0036   17.4   0.8     0.0046   17.0   0.8    1.3  1  Zn-ribbon_8     Zinc ribbon domain
  ------ inclusion threshold ------
      0.041   13.8   0.7      0.062   13.2   0.7    1.2  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
        1.3    9.1   7.1        1.1    9.4   0.5    2.3  2  zf-ACC          Acetyl-coA carboxylase zinc finger domain


Domain annotation for each model (and alignments):
>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.8   7.7e-07    0.0046       7      35 ..      15      47 ..      10      53 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 7.7e-07
  Zn-ribbon_8  7 rCeeCghefevlqsisdap....lta.CPeCgs.e 35
                 +C++Cg  fe+ +++++ +    +t+ C +C++ +
   EPA04731.1 15 KCKQCG--FERKRKFKEGDflfaETTkCDSCNGiT 47
                 6*****..**99999999999998888****9865 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.7     1e-05     0.062      20      53 ..       5      44 ..       3      47 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1e-05
  OrfB_Zn_ribbon 20 eevnpayTSktCseCgsknke......alsgrtfkCpnCg 53
                    e++  ayT  +C +Cg + k+       l  +t kC++C+
      EPA04731.1  5 EKITIAYTLEKCKQCGFERKRkfkegdFLFAETTKCDSCN 44
                    567889**************98888877788889999996 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   1.2     0.021   1.2e+02       3       8 ..      15      20 ..      15      21 .. 0.94
   2 ?    9.4   0.5   0.00018       1.1       2      10 ..      38      46 ..      38      48 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.021
      zf-ACC  3 KCpsCg 8 
                KC +Cg
  EPA04731.1 15 KCKQCG 20
                9****8 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00018
      zf-ACC  2 tKCpsCgem 10
                tKC+sC+ +
  EPA04731.1 38 TKCDSCNGI 46
                8*****987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 384.72
//
Query:       EPA04732.1  [L=115]
Description: hypothetical protein BG20_I0925 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0046   16.7   0.1      0.009   15.8   0.0    1.6  1  DUF4364   Domain of unknown function (DUF4364)
  ------ inclusion threshold ------
      0.028   14.4   0.1      0.056   13.4   0.1    1.7  1  HTH_45    Winged helix-turn-helix


Domain annotation for each model (and alignments):
>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0     1e-06     0.009      36      74 ..      73     111 ..      42     113 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1e-06
     DUF4364  36 lqqalseLvesglieeeekenktlykiTekGketlelfe 74 
                 + ++l+  v+ ++i++e    + +y+iT+kG+ +l+lf 
  EPA04732.1  73 FLNYLHLCVDYNFIQKEAVGANVIYSITDKGRVMLNLFI 111
                 44566667999*************************996 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   6.3e-06     0.056      35      68 ..      72     109 ..      35     113 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.3e-06
      HTH_45  35 llnkYLdmLvekgli....kkskekYvlTekGlellek 68 
                  + +YL+  v+ ++i       +  Y++T+kG+ +l+ 
  EPA04732.1  72 SFLNYLHLCVDYNFIqkeaVGANVIYSITDKGRVMLNL 109
                 5789***********5443346789********99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 800.05
//
Query:       EPA04733.1  [L=385]
Description: 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase, CofG subunit [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.3e-12   45.8   0.1      2e-11   44.5   0.0    1.7  2  Radical_SAM    Radical SAM superfamily
  ------ inclusion threshold ------
      0.013   15.6   0.0      0.031   14.4   0.0    1.6  1  BATS           Biotin and Thiamin Synthesis associated domain
      0.055   13.7   0.4         21    5.5   0.0    3.9  5  SpoU_sub_bind  RNA 2'-O ribose methyltransferase substrate bi
       0.45   10.4   0.1       0.45   10.4   0.1    3.5  5  CdvA           CdvA-like coiled-coil domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       2.7   1.2e+04     123     143 ..      28      47 ..      17      53 .. 0.65
   2 !   44.5   0.0   4.6e-15     2e-11       2     164 ..      60     235 ..      59     238 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.7
                  CTSHHHHHHHHHHHHHHTTSE CS
                  xxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM 123 rghtfeevlealeklreagik 143
                    ++++e+  a ++lr++ +k
   EPA04733.1  28 SENNPKELFSAAQMLRKK-FK 47 
                  667788888888888888.44 PP

  == domain 2  score: 44.5 bits;  conditional E-value: 4.6e-15
                  EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGS.............TTHHHHHHHHHHTCCCTEEEEEEEC CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggeplly.............pdfvellerlaklavpgiritvetn 85 
                  ++++ C   Cs+C+ +     e++   +s++ei++++  +k + + v+ ++++g  p  +             +  +e+l ++++l   +  ++  tn
   EPA04733.1  60 NIVNLCKDTCSYCTYKAE-PGEEKISLMSKQEIKQLLSLAK-KYRcVEALFVTGEAPEQRyqeardwlksngfKSTAEYLVHASEL-AIEAGLFPHTN 154
                  67889***********95.*********************6.55559999999999999955555555555555555555555555.59999999999 PP

                  SSCHGHHHHHHHHHTT-SEEEEEEBSSSHH.......HHHHHHTCTSHH......HHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHHH CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM  86 gtlpdeeklerllelgvdrvslgleaadde.......kvlklmnrghtf......eevlealeklreagikrvvdrivglpGendeeleell 164
                  ++ +++e l++l + +   + + le ++d+        +         +      +++le+le+  ++gi+  +++i+++ Ge+  e+ + +
   EPA04733.1 155 AGNLEKEDLKELQKTN-VSMGIMLENVSDRltkkgmpHY---------LasskrpKARLEVLENTGKLGIP-MTTGILIGIGETPIEIIDSI 235
                  99999*********99.*************444433222.........2355555****************.************99988765 PP

>> BATS  Biotin and Thiamin Synthesis associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0     7e-06     0.031       7      50 ..     269     311 ..     252     317 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7e-06
                 --TCCCCHHHHHHHHHHSTTSECCCTCHH-HHHHHHHHHCCT-- CS
        BATS   7 pikdtpllkiiaalRlllPkagillsgResaefrdqlllklGan 50 
                 p ++  +++i+a++R+++Pk +i +    s++  + +l +lG+n
  EPA04733.1 269 PTDENYFKRIVALTRIIMPKMNIQIPPNLSPKSYQSFL-TLGIN 311
                 2344556***************9998888777777777.78887 PP

>> SpoU_sub_bind  RNA 2'-O ribose methyltransferase substrate binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.18   7.8e+02      14      45 ..      17      45 ..       9      51 .. 0.79
   2 ?   -1.4   0.0      0.64   2.9e+03      45      59 ..      82      96 ..      79     100 .. 0.71
   3 ?    5.5   0.0    0.0048        21      12      45 ..      97     131 ..      91     134 .. 0.86
   4 ?    2.7   0.0     0.034   1.5e+02      28      60 ..     155     188 ..     129     191 .. 0.72
   5 ?   -3.3   0.0       2.5   1.1e+04      53      75 ..     332     354 ..     329     355 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.18
  SpoU_sub_bind 14 sgrriekllvtegradkrleellklakkrgik 45
                   s+ +i +++ +++ ++++  el+++a++++ k
     EPA04733.1 17 SRDEIIQIYKNSE-NNPK--ELFSAAQMLRKK 45
                   5556888888888.9999..9***99988655 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.64
  SpoU_sub_bind 45 kvelvdkekLdklsg 59
                   k+ l++k+++++l +
     EPA04733.1 82 KISLMSKQEIKQLLS 96
                   677788888888764 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.0048
  SpoU_sub_bind  12 Lksgrr.iekllvtegradkrleellklakkrgik 45 
                    L+++ r +e+l+vt ++ ++r++e  +++k++g k
     EPA04733.1  97 LAKKYRcVEALFVTGEAPEQRYQEARDWLKSNGFK 131
                    5566666999999999***************9987 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.034
  SpoU_sub_bind  28 adkrleellklakkrgikvelvdkekLdklsg.t 60 
                    a++  +e lk+++k ++++ ++ +++ d+l++ +
     EPA04733.1 155 AGNLEKEDLKELQKTNVSMGIMLENVSDRLTKkG 188
                    44444689999******************99944 PP

  == domain 5  score: -3.3 bits;  conditional E-value: 2.5
  SpoU_sub_bind  53 kLdklsgtanHQGvvaevkpley 75 
                    +++k+ ++ n  G+ ++++ ++y
     EPA04733.1 332 EIKKIEKNSNDAGFELKCRFPTY 354
                    67889999999999999988877 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.6     0.067     3e+02       5      47 ..       6      48 ..       3      55 .. 0.90
   2 ?   10.4   0.1    0.0001      0.45      54      90 ..      92     128 ..      81     136 .. 0.89
   3 ?   -3.4   0.1       1.9   8.4e+03      99     105 ..     161     167 ..     157     186 .. 0.53
   4 ?   -3.3   0.1       1.7   7.8e+03      31      45 ..     238     252 ..     237     255 .. 0.69
   5 ?   -0.4   0.0      0.22   9.7e+02      23      42 ..     361     380 ..     355     383 .. 0.63

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.067
        CdvA  5 ALeeLvsegdipkstyeeikekleealkklkekakelkeklkk 47
                 L+++++++ i++++  +i ++ e+  k+l   a+ l++k kk
  EPA04733.1  6 SLNNVLEDKIISRDEIIQIYKNSENNPKELFSAAQMLRKKFKK 48
                7999999*********************999999999999887 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0001
        CdvA  54 dqikslekalanlkisyasGEidEeaYksaieairel 90 
                 +q+ sl+k +  ++  +++GE +E+ Y++a++ ++++
  EPA04733.1  92 KQLLSLAKKYRCVEALFVTGEAPEQRYQEARDWLKSN 128
                 68999999***********************998875 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 1.9
        CdvA  99 eeikkll 105
                 e++k+l+
  EPA04733.1 161 EDLKELQ 167
                 4444433 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 1.7
        CdvA  31 lkklkekakelkekl 45 
                 +kkl+ek  +++e +
  EPA04733.1 238 IKKLQEKYGNIQEVI 252
                 677777777777765 PP

  == domain 5  score: -0.4 bits;  conditional E-value: 0.22
        CdvA  23 ikekleealkklkekakelk 42 
                 i ++l+ ++k +++++  +k
  EPA04733.1 361 ISKELRGKMKSIEDEEGLVK 380
                 55666666666666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       892  (0.0497518); expected 358.6 (0.02)
Passed bias filter:                      606  (0.0338); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 2685.99
//
Query:       EPA04734.1  [L=528]
Description: histone acetyltransferase, ELP3 family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-26   91.6   0.2    6.3e-26   90.2   0.2    1.8  1  Radical_SAM_C    Radical_SAM C-terminal domain
    1.9e-20   73.9   0.1    7.1e-20   72.0   0.0    1.9  2  Radical_SAM      Radical SAM superfamily
    6.4e-06   26.1   0.0    2.1e-05   24.5   0.1    1.8  2  Acetyltransf_10  Acetyltransferase (GNAT) domain
    5.7e-05   23.3   0.0    0.00013   22.2   0.0    1.6  1  Acetyltransf_1   Acetyltransferase (GNAT) family
  ------ inclusion threshold ------
        1.2    9.2   3.7        1.4    9.0   1.7    2.2  2  SapB_1           Saposin-like type B, region 1


Domain annotation for each model (and alignments):
>> Radical_SAM_C  Radical_SAM C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.2   0.2   1.7e-29   6.3e-26       1      80 [.     296     375 ..     296     377 .. 0.98

  Alignments for each domain:
  == domain 1  score: 90.2 bits;  conditional E-value: 1.7e-29
  Radical_SAM_C   1 pdgvKlypllvikgTeLaelyksgeykplsleeyvdlvadilellppdirvhRltgdipkelliagpwhknlreliekrl 80 
                    pd++K+yp lvi++T+L+++yk++ey+p+s e+++++++++++ +p+++r++R++++i+++++iagp+++nlr++++++l
     EPA04734.1 296 PDMLKIYPSLVIENTPLYDEYKRKEYTPYSDEDMIRVLTEVKKNIPKWVRIMRVQREISSNEIIAGPKSGNLRQMVHQNL 375
                    8****************************************************************************987 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.6   5.8e+03     113     135 ..      31      51 ..      11      59 .. 0.54
   2 !   72.0   0.0     2e-23   7.1e-20       6     158 ..      90     279 ..      86     289 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.6
                  SHHHHHHHHTCTSHHHHHHHHHH CS
                  xxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM 113 ddekvlklmnrghtfeevleale 135
                   + +++k++  ++ +e++ ++ e
   EPA04734.1  31 KE-EIKKIC-AKYALERIPRNHE 51 
                  12.244444.4455555544444 PP

  == domain 2  score: 72.0 bits;  conditional E-value: 2e-23
                  EESS-.-TTTSCCTT.................HHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTC.......... CS
                  xxxxx.xxxxxxxxx.................xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx.......... RF
  Radical_SAM   6 gCnlr.CsfCarpet.................vrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlakla.......... 74 
                  +C+++ C++C+ +                    ++  +++   + +i+++v  ++ ++   + vi+gg   ++ +d++e   + +  a          
   EPA04734.1  90 ACPHGrCTYCPGGIEynspnsytgkepstlnaIENAFDPKLQITTKIEKLVAFGH-DPSkMEIVIVGGTFLFMPKDYQENFIKSCYDAlngvdsknle 186
                  465555*******99***************************************5.66648888888888888888888888888888********** PP

                  .......CCTEEEEEEECSSCHG...HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHH CS
                  .......xxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM  75 .......vpgiritvetngtlpd...eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGende 158
                         +++ir++  t +t+pd    ++++ +l++g++r+++g++++ ++ v k++nrgh++ +v+e++++ ++ag k v ++++glp  + e
   EPA04734.1 187 eaksnneHAKIRNVGFTIETKPDyckQKHVDMMLDYGITRIEIGVQSLQER-VYKIVNRGHDYNDVVESFQISKDAGYKIVAHMMPGLPTMTPE 279
                  *******9999999999999999999*************************.**************************************9986 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.9   6.7e+03      32      51 ..     417     437 ..     398     442 .. 0.64
   2 !   24.5   0.1   5.7e-09   2.1e-05      61     111 ..     471     521 ..     470     526 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.9
  Acetyltransf_10  32 lllvaeeg.gkivGvielrdg 51 
                      ++l +e+  ++i G+++lr+ 
       EPA04734.1 417 VFLSYEDTnDSIYGFLRLRKP 437
                      333333333788899999765 PP

  == domain 2  score: 24.5 bits;  conditional E-value: 5.7e-09
  Acetyltransf_10  61 peyrgqGigkaLleaveeeaekdgikleltvnaspyavpfYeklGFkavge 111
                      +e ++ G gk+L++++e+  +++  +++l v ++   +++Y+klG+   g+
       EPA04734.1 471 KEIQHSGFGKNLMKEAEKISKEEFDSKKLLVISAVGTREYYQKLGYSLYGP 521
                      799****************98888888*******************87765 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   3.6e-08   0.00013      32     117 .]     414     516 ..     388     516 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 3.6e-08
                     TCEEEE.EEET.TEEEEEEEEEEEET......TSTTEEEEEEEEE...........SGGGTTSSHHHHHHHHHHHHHHHT.TESEE.EEEEETTE CS
  Acetyltransf_1  32 aegllv.aeed.geliGfisllkipd......ekggvayieslaV...........speyrgkGlGsaLlealeeraree.gikki.vlaveedn 105
                      ++ ++ +e+  + + Gf++l+k           ++ +++++l+V            +e +++G G+ L++++e++ +ee   kk+ v+    + 
      EPA04734.1 414 GNEVFLsYEDTnDSIYGFLRLRKPSIlahrkeIGRDSCIVRELHVygkslkigekgEKEIQHSGFGKNLMKEAEKISKEEfDSKKLlVI----SA 504
                     3344442333335599999888888886666634456667777779999999999999**********************999997455....77 PP

                     HHHHHHHHHTTE CS
  Acetyltransf_1 106 daairlYeklGF 117
                     ++++++Y+klG+
      EPA04734.1 505 VGTREYYQKLGY 516
                     89*********8 PP

>> SapB_1  Saposin-like type B, region 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   1.7    0.0004       1.4      14      36 ..      17      40 ..      14      41 .. 0.88
   2 ?   -2.5   0.0       1.6   5.6e+03      18      31 ..     114     127 ..     114     127 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0004
                HHHH-.SS--HHHHHHHHHHHHHH CS
      SapB_1 14 eklLk.dNkTeeeIieaLekvCsk 36
                ++lL+ +  T+++++e ++k+C+k
  EPA04734.1 17 QNLLTiNEPTKKQVKEEIKKICAK 40
                79999555**************87 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.6
                 -SS--HHHHHHHHH CS
      SapB_1  18 kdNkTeeeIieaLe 31 
                 k+++T + I++a++
  EPA04734.1 114 KEPSTLNAIENAFD 127
                 6899*9****9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (528 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       986  (0.0549947); expected 358.6 (0.02)
Passed bias filter:                      702  (0.0391544); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.71u 0.30s 00:00:01.01 Elapsed: 00:00:00.50
# Mc/sec: 3186.82
//
Query:       EPA04735.1  [L=234]
Description: MIP family channel protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.1e-54  183.1  18.8    7.2e-54  182.9  18.8    1.0  1  MIP        Major intrinsic protein
     0.0012   18.8   1.5     0.0042   17.1   1.5    2.0  1  Ldr_toxin  Toxin Ldr, type I toxin-antitoxin system


Domain annotation for each model (and alignments):
>> MIP  Major intrinsic protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.9  18.8   8.1e-58   7.2e-54       8     226 ..       4     221 ..       1     222 [. 0.87

  Alignments for each domain:
  == domain 1  score: 182.9 bits;  conditional E-value: 8.1e-58
                 HHHHHHHHHHHHHHHHHHHHHHHCCCSSCSSSSTTSSHHHHHHHHHHHHHHHHHHHHHHHCHT-S-SHHHHHHHHHTTSSSHHHHHHHHHHHHHHHHHH CS
         MIP   8 lravlAEflatlllvfigvgsalnvkkkvsslaslvsvtleavalafglalavlvylaagiSGaHlNPavTlallvarkisllrailYivaQllGaiva 106
                  ra+lAE++at+ lvf+g  s++ ++ ++  ++ l++ +++ ++la+g a+a  vy+++++SGaH+NPavT+ +++++ki ++ ++ Yi++Ql+Gai+a
  EPA04735.1   4 PRAYLAEAIATYGLVFFGPLSVI-LAISSFGET-LTTQSVLFISLAHGGAIALMVYAFGHVSGAHINPAVTIPMMITKKIGIVDGVGYIISQLIGAIAA 100
                 589****************9776.444433333.3345899********************************************************** PP

                 HHHHHHHCHHH.....HHHTTTTSSSSSTTSSHHHHHHHHHHHHHHHHHHHHHHCSTTSSSSTCHGHHHHHHHHHHHHHHHHHHHHST-SSHHHHHHHH CS
         MIP 107 aallklltkgl.....esraglfanslkpglsagqalvvEiiltfvLvlvvfaltddkrkvslgelaplaigllvaliilvgipltGaamNpArslgpa 200
                 aa+lk++  +l       ++g  +  +++++   +++++E iltf+Lvlv+f ++ +k++     l +l+ig +v+li+lv++pltGa++NpAr +gpa
  EPA04735.1 101 AATLKVILPELgakvnFGTQGGPSDLINNSI--SSGFAIEAILTFFLVLVIFMTAVHKKASP--GLHGLSIGGMVFLIHLVAVPLTGASVNPARTFGPA 195
                 *********9954433222233333344444..489******************99999888..569******************************** PP

                 HHHTHSTTTTHHHHHHHHHHHHHHHH CS
         MIP 201 vvlnkfedhwvylvGPliGailgalv 226
                 +++  +e+hw+y+ +P++G+i++al+
  EPA04735.1 196 LISGFWEFHWMYWAAPILGGIIAALI 221
                 ************************97 PP

>> Ldr_toxin  Toxin Ldr, type I toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   1.5   4.7e-07    0.0042      11      30 ..     205     224 ..     199     229 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.7e-07
                 HHHHHHHHHHHHHHHHHHHH CS
   Ldr_toxin  11 WHDLAAPvlAGIlaaaIVnW 30 
                 W   AAP+l GI+aa I n+
  EPA04735.1 205 WMYWAAPILGGIIAALIMNY 224
                 5566*************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.31s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1518.64
//
Query:       EPA04736.1  [L=289]
Description: methionine aminopeptidase, type II, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.9e-33  113.9   1.2    1.5e-32  113.0   1.2    1.5  1  Peptidase_M24  Metallopeptidase family M24
      0.006   16.7   0.3       0.61   10.3   0.1    2.3  2  HSR            HSR domain
  ------ inclusion threshold ------
      0.012   15.2   0.1      0.017   14.7   0.1    1.2  1  ApbE           ApbE family
       0.55   10.9   5.2         19    5.9   0.1    3.2  3  ATP-cone       ATP cone domain


Domain annotation for each model (and alignments):
>> Peptidase_M24  Metallopeptidase family M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.0   1.2   3.4e-36   1.5e-32       8     196 ..       2     186 ..       1     279 [. 0.80

  Alignments for each domain:
  == domain 1  score: 113.0 bits;  conditional E-value: 3.4e-36
                    HHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTTBCS.SSB..--TTEEEEEEEEEEETTEEEEEEEEEECSS CS
  Peptidase_M24   8 riasaaleavleaikpgvterelaaeieattlkrhgarglafppivasgenaavlhytpn.drv..lkegdlvlidagaeydgyasDitrTvlvGk 100
                    +ia++++e v e+   g t +e+++e+e   ++++g  ++afp  v +++n+ ++hyt+  +++  +ke dlv+id+ga+++gy++D+++Tv+   
     EPA04736.1   2 KIAAEVREMVREKNWVGKTVYEICEEVESQ-IIKRG-AKCAFP--VNASINEIAAHYTAEpNDPivIKESDLVKIDLGAQINGYIADTAVTVCQ-- 91 
                    788889998876555799**********88.55555.5789**..8899999999**6633565568*************************99.. PP

                    GSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHTTBCCGBSSCSEEEESS.SSSEE..EEEESSSTTCSSB--TTBEEEEEEEEEEE CS
  Peptidase_M24 101 ftpeqrelyeavleaqeaaikavkpGvtlseidaaarevlesaglakffphglGHgvGl.evhde..gpsvsresndgrkleeGmvftiEpgiyfa 193
                     ++e++ l+++++ea+ +a++++k Gv++s+i+++++++++++g+ k++ ++ GH++ +  +h +   p+++  s  g +l+e+  +++Ep + ++
     EPA04736.1  92 -DAEYEGLIRTAEEALGNAMSMIKVGVKASDIGRTIEKTIKQNGY-KPIANLSGHSLEQyTIHAGrsIPNIW--SIGGFTLAENTAYACEPFVTTE 183
                    .899999**************************************.************98***775567788..44799************66644 PP

                    TTT CS
  Peptidase_M24 194 pge 196
                    +g 
     EPA04736.1 184 KGG 186
                    432 PP

>> HSR  HSR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.011        48      42      68 ..       5      31 ..       2      43 .. 0.86
   2 !   10.3   0.1   0.00014      0.61      63      94 ..     234     265 ..     212     268 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.011
         HSR 42 kesleacrnlvpvqkvvYnvLseLekt 68
                 e+ e+ r++  v k vY++ +e+e +
  EPA04736.1  5 AEVREMVREKNWVGKTVYEICEEVESQ 31
                578999******************987 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00014
         HSR  63 seLektfslsllealfsevnlkeYpdLkeilk 94 
                 +e e+++ ++lle l s+  +++Yp L ei +
  EPA04736.1 234 KEWEEKKARELLEHLISKKSVQAYPVLIEINE 265
                 567899999*******************9975 PP

>> ApbE  ApbE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   3.7e-06     0.017      91     169 ..      42     119 ..      17     153 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.7e-06
                 --HHHHHHHHTT.-GGGEEE......EESTT..-----TTTHHHHHHHHHHHHHHH.TT-EEEEEETTEEEEEC-ECT-EEEEEE- CS
        ApbE  91 psaeeidaalalvgykkiel......lakkgpgmkLDlggiaKGyavdrvaellka.giksalvnlGGdiralGpdgkpwrvgied 169
                 p ++ i+++ a+              + k+ + +k+Dlg+   Gy++d ++ ++++     +l+    + +  G+  +  +vg++ 
  EPA04736.1  42 PVNASINEIAAHYT-----AepndpiVIKESDLVKIDLGAQINGYIADTAVTVCQDaE-YEGLIRTAEEAL--GNAMSMIKVGVKA 119
                 44555555554432.....13333445666779*********************9955.456666655533..4333466666665 PP

>> ATP-cone  ATP cone domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1    0.0042        19      17      50 ..       2      38 ..       1      66 [. 0.66
   2 ?    5.8   0.1    0.0045        20      28      73 ..      92     138 ..      82     141 .. 0.81
   3 ?   -0.4   0.2      0.38   1.7e+03      14      14 ..     237     237 ..     190     288 .. 0.57

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0042
                HHHHHHHHHHHH...-HHHHHHHHHHHHHHHHHHHII CS
    ATP-cone 17 kIkraiekAceg...seeeideiaeeveaevrkrlrd 50
                kI++ +   +++   + ++++ei+eeve+++ kr+ +
  EPA04736.1  2 KIAAEVREMVREknwVGKTVYEICEEVESQIIKRGAK 38
                5555555555556666677888888888888777665 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0045
                 H.-HHHHHHHHHHHHHHHHHHHIIT-BHHHHHHHHHHHHHHSS-HHH CS
    ATP-cone  28 g.seeeideiaeeveaevrkrlrdgisteeIqdlvektliehpdyav 73 
                   + e++ + aee   ++++ ++ g++ ++I+  +ekt++++++  +
  EPA04736.1  92 DaEYEGLIRTAEEALGNAMSMIKVGVKASDIGRTIEKTIKQNGYKPI 138
                 445666777778888889999******************99998766 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.38
                 - CS
    ATP-cone  14 d 14 
                 +
  EPA04736.1 237 E 237
                 2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 1792.05
//
Query:       EPA04737.1  [L=65]
Description: hypothetical protein BG20_I0931 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 416.90
//
Query:       EPA04738.1  [L=241]
Description: hypothetical protein TIGR00161 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.5e-44  150.5   0.0    7.4e-44  150.3   0.0    1.0  1  PAC2      PAC2 family


Domain annotation for each model (and alignments):
>> PAC2  PAC2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.3   0.0   4.1e-48   7.4e-44       2     211 ..      24     224 ..      23     226 .. 0.92

  Alignments for each domain:
  == domain 1  score: 150.3 bits;  conditional E-value: 4.1e-48
                 EEESSCGGGHHHHHHHHHHHHTTEEEEEEEEHCCHSBCCCC.SEEEEETTEEE-SEEEEEETTT.SEEEEEEE...E-HSCHHHHHHHHHHHHHHHTTE CS
        PAC2   2 ilGfpgiGnVgqlavdlLiesleaekvgeidsdyllpfvgprpvvlveegrelepprlyakdsgsrdllvlqg...repilqyeefakalldwaeelgv 97 
                 ++Gf+g+G+Vg lav+++ie+l++e++g+ +s+y lp     p++++++g  ++p+r+ya++  +++++ + +      ++ y  +++a+ldw +++g 
  EPA04738.1  24 FAGFVGAGLVGPLAVNHIIEELKMEEIGFMRSKY-LP-----PSTVFRNGMLRHPFRVYANK--KGTICTIICeitLRMEGIYS-IVSAILDWSDKHGS 113
                 78********************************.9*.....*****************995..499*****996666666666.************** PP

                 SEEEEEEEEEESS-ES..TTS-.EEEEEESSHHHHHHHHCT.....-CEEEEHHHHHHHHHHHHTT-EEEEEEEEEECCC--HHHHHHHHHHHHHHHT- CS
        PAC2  98 kevvvLggldageradvphtrpekvtgaatdeelleelees.....eyggivgitglLlsaakergipavgllaevphylpdPkaaaalleflskllgl 191
                 ke+v+L+g++         +++++  + a +e+l++ + ++     ++g+i+gi g +l+++  r+i++++lla +++ lpdP+aaa+l+e+l++++++
  EPA04738.1 114 KEMVILDGIP----S----DEHDGKAYCAAREDLVRTMADKdisaiPQGFITGIPGGILNECIVRKIQGIVLLAKANKTLPDPEAAATLIEALNRFYEM 204
                 **********....4....46678889999*****99953345778***************************************************** PP

                 --HCHHHHHHHHHHHHHHHH CS
        PAC2 192 evdtedLeedaeeleeqlee 211
                 ++dt+dLe++ e++ ++  e
  EPA04738.1 205 QIDTTDLEKEKERINSEFGE 224
                 **************988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); expected 358.6 (0.02)
Passed bias filter:                      624  (0.0348039); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1553.31
//
Query:       EPA04739.1  [L=166]
Description: ferritin-like protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.6e-41  139.2   0.7      1e-40  139.0   0.7    1.0  1  Ferritin        Ferritin-like domain
      7e-05   23.3   0.9     0.0001   22.7   0.9    1.3  1  Rubrerythrin    Rubrerythrin
  ------ inclusion threshold ------
      0.043   14.3   2.0      0.091   13.2   0.5    2.0  2  Lipoprotein_10  Putative mycoplasma lipoprotein, C-terminal r
        0.2   11.5   0.2        1.1    9.2   0.0    2.1  2  Nuc_rec_co-act  Nuclear receptor coactivator


Domain annotation for each model (and alignments):
>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.0   0.7   2.2e-44     1e-40       2     141 ..       9     144 ..       8     145 .. 0.98

  Alignments for each domain:
  == domain 1  score: 139.0 bits;  conditional E-value: 2.2e-44
                 HHHHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHHC-SSSS.CSSHHHHHHHHHHHHHHHHHHH CS
    Ferritin   2 kaLneqladeltaayqylamawyvkgpgleglaeffdeqaeeerehadklaerilalGgtpvltraeleeieapke.fgsveevleaalehekkvtesl 99 
                 kaLn+q+  e +a++ ylama+++++ g+ g a+ff+ q++eer+h+ k+ ++++++Gg      a++++ ++p + f+s+e++++aal+ e+ vt+++
  EPA04739.1   9 KALNDQIVLEANASNSYLAMASWCENAGYCGAANFFYSQSDEERTHMLKFVHYLNDIGG-----SATIPATKSPANsFKSLESIIRAALNNEQLVTKAI 102
                 89*********************************************************.....******999999999******************** PP

                 HHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
    Ferritin 100 relielaeeegDpatadfledfleeqeeheweleallekler 141
                 + ++e+a++e+D+ t+ fl++f++eq+e+e+++e++l+k+e+
  EPA04739.1 103 YSIVEIAQKEKDHSTHTFLDWFVNEQVEEEKKFETILQKFEL 144
                 ***************************************997 PP

>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.9   2.3e-08    0.0001       2     131 ..      10     137 ..       9     143 .. 0.64

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 2.3e-08
                   HHHHHHHHHHHHHHHHHHHHHCHH.TT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS-------TTGGHHHHHHHHHHHHHHHHH CS
  Rubrerythrin   2 iLekAiagEssarrlYkelaekak.egypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeakpkflttaknLeeaiegayaeee 97 
                    L+  i  E  a + Y ++a+  + +gy   a++F   ++eEr H  ++   l+++ ++  +   +   + ++  ++++  a n e+++        
    EPA04739.1  10 ALNDQIVLEANASNSYLAMASWCEnAGYCGAANFFYSQSDEERTHMLKFVHYLNDIGGSATIPATKSPANSFKSLESIIRAALNNEQLVT------- 99 
                   68888999**************************************************99933333333333333333333333333333....... PP

                   CHHHHHHHHHHHTTSHHHH....HHHHHHHHHHHHHHH CS
  Rubrerythrin  98 emyrfyeelaekegneeak....klfkklaeaEkkHee 131
                   +++ +  e+a+ke++ +++    +++ +  e+Ekk e 
    EPA04739.1 100 KAIYSIVEIAQKEKDHSTHtfldWFVNEQVEEEKKFET 137
                   33334444555555444430000444444555555555 PP

>> Lipoprotein_10  Putative mycoplasma lipoprotein, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.24   1.1e+03      43      73 ..      20      50 ..       4      93 .. 0.67
   2 ?   13.2   0.5     2e-05     0.091      12      37 ..     109     134 ..     104     145 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.24
  Lipoprotein_10 43 kktkkqtaaeffaesasYilPlketlkkdkn 73
                    +++++  a+  + e+a+Y  + + + +++++
      EPA04739.1 20 NASNSYLAMASWCENAGYCGAANFFYSQSDE 50
                    4455555666666677776665555533322 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 2e-05
  Lipoprotein_10  12 aNekedeaTkkFvnWllnskeeweek 37 
                     a ++ d+ T+ F++W++n++ e e+k
      EPA04739.1 109 AQKEKDHSTHTFLDWFVNEQVEEEKK 134
                     668889*************9998877 PP

>> Nuc_rec_co-act  Nuclear receptor coactivator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.35   1.6e+03       2      14 ..       4      16 ..       4      21 .. 0.82
   2 ?    9.2   0.0   0.00024       1.1      17      33 ..     144     160 ..     139     161 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.35
  Nuc_rec_co-act  2 grsDEkALLdQLv 14
                    +++  kAL dQ v
      EPA04739.1  4 SQNTKKALNDQIV 16
                    5777899999986 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00024
  Nuc_rec_co-act  17 LkntDeigLeEiDraLG 33 
                     L + D+i+ +EiD+ LG
      EPA04739.1 144 LIGRDKIAIHEIDKILG 160
                     56789***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1089  (0.0607396); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1198.62
//
Query:       EPA04740.1  [L=69]
Description: hypothetical protein BG20_I0907 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00064   20.1   0.8    0.00078   19.9   0.8    1.1  1  NPV_P10        Nucleopolyhedrovirus P10 protein
    0.00078   19.2   4.5        0.2   11.4   0.3    2.0  2  SKA2           Spindle and kinetochore-associated protein 2
      0.005   17.0   7.2     0.0079   16.3   7.2    1.4  1  JIP_LZII       JNK-interacting protein  leucine zipper II
     0.0053   17.0   6.8     0.0065   16.7   6.8    1.2  1  TMF_TATA_bd    TATA element modulatory factor 1 TATA binding
     0.0064   16.5   4.1     0.0076   16.2   4.1    1.0  1  JAKMIP_CC3     JAKMIP CC3 domain
  ------ inclusion threshold ------
      0.013   14.9   6.2      0.014   14.8   6.2    1.0  1  Dynamitin      Dynamitin
      0.015   15.7   9.4      0.062   13.8   9.4    1.8  1  ZapB           Cell division protein ZapB
      0.019   13.9   9.6      0.024   13.5   9.6    1.2  1  Spc7           Spc7 kinetochore protein
      0.019   15.2   1.3      0.041   14.1   0.7    1.7  2  DUF948         Bacterial protein of unknown function (DUF948)
      0.034   14.5   7.3      0.085   13.2   7.3    1.6  1  BLOC1_2        Biogenesis of lysosome-related organelles comp
      0.038   14.5  11.3      0.051   14.1  11.0    1.4  1  FadA           Adhesion protein FadA
      0.045   13.6   8.4       0.61    9.9   1.9    2.0  2  Dynactin_p22   Dynactin subunit p22
      0.055   14.0   4.2       0.12   13.0   3.5    1.7  2  TipAS          TipAS antibiotic-recognition domain
      0.074   13.4   4.9        1.3    9.4   2.0    2.0  2  CLZ            C-terminal leucine zipper domain of cyclic nuc
      0.076   13.3  10.0        1.1    9.6   3.0    2.0  1  ABC_tran_CTD   ABC transporter C-terminal domain
      0.088   13.0   8.0       0.15   12.3   8.0    1.4  1  Seryl_tRNA_N   Seryl-tRNA synthetase N-terminal domain
      0.089   12.7   3.2       0.27   11.1   3.2    1.9  1  MtrG           Tetrahydromethanopterin S-methyltransferase, s
       0.09   13.1   3.0        2.5    8.5   0.5    2.0  2  PaaX_C         PaaX-like protein C-terminal domain
      0.093   11.4   4.5       0.11   11.2   4.5    1.1  1  Dor1           Dor1-like family
      0.096   12.7  12.2       0.38   10.8   4.8    2.2  2  Bap31_Bap29_C  Bap31/Bap29 cytoplasmic coiled-coil domain
        0.1   13.2   8.0        1.1    9.9   1.4    2.1  2  DUF5344        Family of unknown function (DUF5344)
       0.12   13.0   2.6       0.15   12.7   2.6    1.3  1  DUF883         Bacterial protein of unknown function (DUF883)
       0.13   12.2   7.2       0.14   12.1   7.2    1.0  1  DUF4446        Protein of unknown function (DUF4446)
       0.18   11.1   5.3       0.21   10.8   5.3    1.2  1  DUF3450        Protein of unknown function (DUF3450)
        0.2   12.0   7.8       0.22   11.8   7.8    1.2  1  OmpH           Outer membrane protein (OmpH-like)
       0.23   11.6   4.7       0.61   10.2   4.7    1.7  1  DASH_Dad3      DASH complex subunit Dad3
       0.26   11.5  11.6        1.7    8.9   1.7    2.1  2  DUF3958        Protein of unknown function (DUF3958)
       0.38   11.1   7.5        3.5    8.1   0.4    2.1  2  Syntaxin_2     Syntaxin-like protein
       0.38   10.0   5.0       0.43    9.8   5.0    1.0  1  HemX           HemX, putative uroporphyrinogen-III C-methyltr
       0.82    9.5   8.8        3.1    7.6   1.2    2.0  2  DivIC          Septum formation initiator
        1.3    8.7   6.8        1.5    8.6   6.8    1.1  1  EMC3_TMCO1     Integral membrane protein EMC3/TMCO1-like
        1.4    9.3   4.7        1.7    9.0   4.7    1.2  1  Uteroglobin    Uteroglobin family
        1.5    9.0   7.6          3    8.1   2.2    2.1  2  CotJB          CotJB protein
        1.8    7.5   7.6        2.1    7.3   7.6    1.0  1  Atg14          Vacuolar sorting 38 and autophagy-related subu
          2    7.5  10.3        2.2    7.4  10.3    1.0  1  Tho2           Transcription factor/nuclear export subunit pr
        2.1    8.4   9.7        2.7    8.0   9.7    1.2  1  DUF1640        Protein of unknown function (DUF1640)
        2.5    8.1   8.9       0.99    9.4   2.1    2.0  2  DUF1910        Domain of unknown function (DUF1910)
        3.6    6.4   4.1        4.1    6.2   4.1    1.1  1  LMBR1          LMBR1-like membrane protein
        3.7    8.2   6.2        7.7    7.1   6.2    1.6  1  YtxH           YtxH-like protein
        4.9    7.4  10.0        5.7    7.2  10.0    1.1  1  DUF2951        Protein of unknown function (DUF2951)
        5.6    6.1   7.9        6.3    5.9   7.9    1.1  1  TMPIT          TMPIT-like protein


Domain annotation for each model (and alignments):
>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.8   1.8e-06   0.00078      16      63 ..      12      59 ..       6      62 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.8e-06
     NPV_P10 16 vddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqd 63
                ++d  + l ++ ++++en  d +e+n+kLd+++++ +e++++ ++I+d
  EPA04740.1 12 LQDEYKKLMSEYEELAENKADSNEVNKKLDELTEKHEEINKEFSKITD 59
                5566667778889*********************************97 PP

>> SKA2  Spindle and kinetochore-associated protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.3   0.00046       0.2      46      71 ..       8      33 ..       6      36 .. 0.90
   2 !   10.2   0.4    0.0011      0.48      45      75 ..      38      68 ..      32      69 .] 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00046
        SKA2 46 rlkkvkeelqaLkeqceellaekkel 71
                 ++k+++e+++L+++ eel+++k ++
  EPA04740.1  8 HYEKLQDEYKKLMSEYEELAENKADS 33
                679********************987 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0011
        SKA2 45 erlkkvkeelqaLkeqceellaekkelidki 75
                ++l +++e+++++++++ ++   kke   ki
  EPA04740.1 38 KKLDELTEKHEEINKEFSKITDDKKENSHKI 68
                7899*********************988877 PP

>> JIP_LZII  JNK-interacting protein  leucine zipper II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   7.2   1.8e-05    0.0079       4      63 ..      13      68 ..      10      69 .] 0.89

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.8e-05
    JIP_LZII  4 gkevenLikENteLletknaLnvvkddLIarvdeLtsereiLreEleslqkakerlesri 63
                ++e  +L++E++eL e k   n v     +++deLt+ +e +++E++++++ k++   +i
  EPA04740.1 13 QDEYKKLMSEYEELAENKADSNEVN----KKLDELTEKHEEINKEFSKITDDKKENSHKI 68
                68999**************997777....578*******************999877776 PP

>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   6.8   1.5e-05    0.0065      41      84 ..       8      51 ..       3      68 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.5e-05
  TMF_TATA_bd 41 erdeareeivklmkeneelkelkkeleelekeleelqeryetlL 84
                   +++++e  klm+e eel+e+k++++e++k+l+el+e++e++ 
   EPA04740.1  8 HYEKLQDEYKKLMSEYEELAENKADSNEVNKKLDELTEKHEEIN 51
                 557899**********************************9875 PP

>> JAKMIP_CC3  JAKMIP CC3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   4.1   1.7e-05    0.0076      73     131 ..       6      64 ..       2      68 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.7e-05
  JAKMIP_CC3  73 elrfrqLlaeyqalqrayalLreklggeldaerelkareqleselrktkskikdLeeaL 131
                    +++L  ey++l  +y +L e+++ + +  ++l +  + ++e++k  ski+d +++ 
  EPA04740.1   6 KEHYEKLQDEYKKLMSEYEELAENKADSNEVNKKLDELTEKHEEINKEFSKITDDKKEN 64 
                 4579*********************999999999999999999*********9977665 PP

>> Dynamitin  Dynamitin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   6.2   3.2e-05     0.014      94     146 ..       6      59 ..       2      69 .] 0.85

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.2e-05
   Dynamitin  94 eqklqRLqrEveeleeEvekakeaakeseeeeldpvelaeqleslqkqLeel.e 146
                  + +++Lq E ++l +E+e+ +e++++s+e +++  el+e+ e+++k+ +++ +
  EPA04740.1   6 KEHYEKLQDEYKKLMSEYEELAENKADSNEVNKKLDELTEKHEEINKEFSKItD 59 
                 5679************************************************31 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   9.4   0.00014     0.062      18      57 ..       7      46 ..       6      69 .] 0.79

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00014
        ZapB 18 dtitlLqmeieeLkeeneelkeenreleeeneqlkeerea 57
                + +++Lq e+++L+ e eel+e+++  +e n++l e  e+
  EPA04740.1  7 EHYEKLQDEYKKLMSEYEELAENKADSNEVNKKLDELTEK 46
                56899***************99999988888887744333 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   9.6   5.5e-05     0.024     196     250 ..      14      68 ..       2      69 .] 0.56

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.5e-05
        Spc7 196 idkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeei 250
                  + ++L +  eelae+ka+ +e +k+l+el+e+ ee++++++++++ k+e   +i
  EPA04740.1  14 DEYKKLMSEYEELAENKADSNEVNKKLDELTEKHEEINKEFSKITDDKKENSHKI 68 
                 2344555556666666666666666666666666666666666666666655554 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.7   9.4e-05     0.041      33      87 ..       7      57 ..       4      59 .. 0.75
   2 ?    9.3   0.4    0.0029       1.3      23      57 ..      35      69 .]      33      69 .] 0.76

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 9.4e-05
      DUF948 33 atieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvsel 87
                ++ e+l+++ ++++ e e+l ++  +  ++vn+k   +d+lte+ +++ + +s++
  EPA04740.1  7 EHYEKLQDEYKKLMSEYEELAENKAD-SNEVNKK---LDELTEKHEEINKEFSKI 57
                67789999***********9999888.6666666...566667777776666666 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0029
      DUF948 23 klkktldeaaatieelekqvdpilkevedllakvn 57
                +++k lde+++  ee++k+  +i+++ ++  +k+n
  EPA04740.1 35 EVNKKLDELTEKHEEINKEFSKITDDKKENSHKIN 69
                56788888888888888888888888777777765 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   7.3   0.00019     0.085      31      79 ..       4      52 ..       1      65 [. 0.59

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00019
     BLOC1_2 31 aasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLee 79
                ++ e+y+kl+d+ ++l ++ e+l e ++  ++  +++d++ ++ +e+ +
  EPA04740.1  4 SQKEHYEKLQDEYKKLMSEYEELAENKADSNEVNKKLDELTEKHEEINK 52
                4556666666666666666666666666666666666666655554443 PP

>> FadA  Adhesion protein FadA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1  11.0   0.00012     0.051       2      61 ..       9      67 ..       8      69 .] 0.92

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 0.00012
        FadA  2 lnaLeaelqkLekkeeqrykkekakaeaaaaklakkkelkakieeklakleadsevrfyk 61
                +++L++e++kL++ e +++++ ka +++  +kl++ +e  ++i+++ +k++ d++   +k
  EPA04740.1  9 YEKLQDEYKKLMS-EYEELAENKADSNEVNKKLDELTEKHEEINKEFSKITDDKKENSHK 67
                6789*******96.7788**********************************99998887 PP

>> Dynactin_p22  Dynactin subunit p22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.9    0.0014      0.61     131     154 ..       3      26 ..       1      30 [. 0.90
   2 ?    8.1   0.7    0.0052       2.3     118     143 ..      35      60 ..      28      67 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0014
  Dynactin_p22 131 lkqqeeveelseevkkllekYnkl 154
                    +q+e+ e+l++e kkl+++Y++l
    EPA04740.1   3 YSQKEHYEKLQDEYKKLMSEYEEL 26 
                   689******************997 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0052
  Dynactin_p22 118 elkekLekLsqihlkqqeeveelsee 143
                   e+++kL +L ++h + ++e ++++++
    EPA04740.1  35 EVNKKLDELTEKHEEINKEFSKITDD 60 
                   44555555555555555555555544 PP

>> TipAS  TipAS antibiotic-recognition domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   3.5   0.00027      0.12      25      71 ..       4      48 ..       1      61 [. 0.77
   2 ?    3.9   0.2      0.18        77      29      52 ..      39      62 ..      35      68 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00027
                XXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXX CS
       TipAS 25 lskedweelkaelkelfaklaaalaagkdpdseeaqelaeehralie 71
                 +ke++e+l++e+k+l+ +  ++   + ++ds+e+++  +e+++  e
  EPA04740.1  4 SQKEHYEKLQDEYKKLMSEYEELA--ENKADSNEVNKKLDELTEKHE 48
                5899*******************6..666899999887777766544 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.18
                XXXXXXXXXXXXXXXXXXX..XXX CS
       TipAS 29 dweelkaelkelfaklaaalaagk 52
                +++el+++++e+++++ +  +++k
  EPA04740.1 39 KLDELTEKHEEINKEFSKITDDKK 62
                556677777777777776654333 PP

>> CLZ  C-terminal leucine zipper domain of cyclic nucleotide-gated channels
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1     0.014       6.3      40      57 ..       9      26 ..       5      29 .. 0.85
   2 ?    9.4   2.0     0.003       1.3      18      61 ..      25      68 ..      24      69 .] 0.90

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.014
         CLZ 40 LeaLqtrlarLlaeyess 57
                 e Lq+ +++L++eye+ 
  EPA04740.1  9 YEKLQDEYKKLMSEYEEL 26
                589************986 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.003
         CLZ 18 eaakagaeqkeleekverLessLeaLqtrlarLlaeyessqrkL 61
                e a+ +a+ +e+++k+++L ++ e +++ + ++ ++ ++   k+
  EPA04740.1 25 ELAENKADSNEVNKKLDELTEKHEEINKEFSKITDDKKENSHKI 68
                5688899***************************9999988887 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   3.0    0.0024       1.1      48      69 .]       7      28 ..       2      28 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0024
  ABC_tran_CTD 48 aeleeleaeLeelyerWeeLee 69
                  + +e+l++e ++l++++eeL+e
    EPA04740.1  7 EHYEKLQDEYKKLMSEYEELAE 28
                  5699****************87 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   8.0   0.00035      0.15      55     100 ..      12      57 ..       4      69 .] 0.50

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00035
                   HHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH CS
  Seryl_tRNA_N  55 lskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaelekl 100
                   l+ e +k++ + e+ +e +a+++e++++l++l+++ +e+++e+ k+
    EPA04740.1  12 LQDEYKKLMSEYEELAENKADSNEVNKKLDELTEKHEEINKEFSKI 57 
                   3444444454445555555555555555555555555555555444 PP

>> MtrG  Tetrahydromethanopterin S-methyltransferase, subunit G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   3.2   0.00063      0.27       8      35 ..      29      56 ..       6      61 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00063
        MtrG  8 dpddfnevkkrLdeieekvefvnsEiaq 35
                +++d nev+k+Lde+ ek e +n E ++
  EPA04740.1 29 NKADSNEVNKKLDELTEKHEEINKEFSK 56
                57899*****************999875 PP

>> PaaX_C  PaaX-like protein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.5    0.0056       2.5      11      38 ..       9      36 ..       4      39 .. 0.80
   2 ?    5.9   0.1     0.035        15      10      36 ..      39      65 ..      35      69 .] 0.84

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0056
      PaaX_C 11 ldelaakYeeflaeyrpllkellekeel 38
                 ++l+++Y+++++ey++l +++++++e+
  EPA04740.1  9 YEKLQDEYKKLMSEYEELAENKADSNEV 36
                5789999999999999988888777765 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.035
      PaaX_C 10 dldelaakYeeflaeyrpllkelleke 36
                +ldel++k+ee  +e+++++++++e++
  EPA04740.1 39 KLDELTEKHEEINKEFSKITDDKKENS 65
                589***************887776654 PP

>> Dor1  Dor1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   4.5   0.00025      0.11      38      94 ..       9      65 ..       4      69 .] 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00025
        Dor1 38 yktlidaaealeairqelediraqledLvlklpkLteectrfskkaeeisekrkenk 94
                y  l d  ++l + ++el + +a+ +++ +kl++Lte+ ++++k+ ++i + +ken+
  EPA04740.1  9 YEKLQDEYKKLMSEYEELAENKADSNEVNKKLDELTEKHEEINKEFSKITDDKKENS 65
                666666666777777888888888888899999999999999999999988888875 PP

>> Bap31_Bap29_C  Bap31/Bap29 cytoplasmic coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   4.8   0.00087      0.38      24      42 ..       9      32 ..       6      40 .. 0.76
   2 ?    6.6   1.9     0.018         8      26      49 ..      35      63 ..      32      64 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00087
  Bap31_Bap29_C 24 aeglakEYDrLadehskl.....d 42
                    e l+ EY +L+ e+++l     d
     EPA04740.1  9 YEKLQDEYKKLMSEYEELaenkaD 32
                   699***************765552 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.018
  Bap31_Bap29_C 26 glakEYDrLadehskl.....desedKKd 49
                    ++k  D L+++h+++     + + dKK+
     EPA04740.1 35 EVNKKLDELTEKHEEInkefsKITDDKKE 63
                   578899*********99988777777775 PP

>> DUF5344  Family of unknown function (DUF5344)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   1.9    0.0087       3.8      43      68 ..       7      32 ..       3      35 .. 0.86
   2 ?    9.9   1.4    0.0025       1.1       5      37 ..      30      62 ..      27      68 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0087
     DUF5344 43 ekineleeeleellkaYktlllknve 68
                e +++l++e+++l++ Y++l +++++
  EPA04740.1  7 EHYEKLQDEYKKLMSEYEELAENKAD 32
                568999999********999999875 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0025
     DUF5344  5 klnqaeVeqkLselktaaeelktsipetisgkn 37
                k + +eV +kL+el ++ ee+++++++ +++k+
  EPA04740.1 30 KADSNEVNKKLDELTEKHEEINKEFSKITDDKK 62
                56789*****************99988776654 PP

>> DUF883  Bacterial protein of unknown function (DUF883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   2.6   0.00035      0.15       1      59 [.      10      66 ..      10      69 .] 0.69

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00035
      DUF883  1 eeleaeleslladleellkeaadeageeaeelRerleerlerarerlrdaeeavaerak 59
                e+l++e ++l+++ eel++++ad+  e +++  ++l+e+ e+  +++++ +++ +e+++
  EPA04740.1 10 EKLQDEYKKLMSEYEELAENKADSN-E-VNKKLDELTEKHEEINKEFSKITDDKKENSH 66
                589***************9988743.3.3333356666666666666666666666655 PP

>> DUF4446  Protein of unknown function (DUF4446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   7.2   0.00033      0.14      23      82 ..       8      68 ..       3      69 .] 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00033
     DUF4446 23 klkklkkkykklmkgk.dgksleellkekleeveelkeeseelekeieeleeklkkslqkv 82
                +++kl+++ykklm++  + ++ +   +e  ++++el e++ee++ke+++++++ k++ +k+
  EPA04740.1  8 HYEKLQDEYKKLMSEYeELAENKADSNEVNKKLDELTEKHEEINKEFSKITDDKKENSHKI 68
                6889999999999977466777777888899999999999999999999999998888776 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   5.3   0.00049      0.21      37      82 ..       7      52 ..       2      68 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00049
     DUF3450 37 kkidklddekqellaeyralkeeleslevyneqlerlvasqeqeia 82
                + ++kl+de ++l +ey++l e +++ +  n++l++l ++ e+  +
  EPA04740.1  7 EHYEKLQDEYKKLMSEYEELAENKADSNEVNKKLDELTEKHEEINK 52
                67899******************99999999999999887665333 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   7.8   0.00051      0.22      30      78 ..       7      56 ..       1      69 [] 0.45

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00051
                HHHHHHHHHHHHHHHHHHHHHHHTTTS..-HHHHHHHHHHHHHHHHHHHH CS
        OmpH 30 klqaeleakekelqklqeelqkkakkl.ekeekeqelqkkeqelqqkqqq 78
                +  ++l+++ k+l +++eel ++++++ e ++k  el +k +e+++++++
  EPA04740.1  7 EHYEKLQDEYKKLMSEYEELAENKADSnEVNKKLDELTEKHEEINKEFSK 56
                33344444444444444444433333322444444455555554444333 PP

>> DASH_Dad3  DASH complex subunit Dad3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   4.7    0.0014      0.61      11      47 ..       8      46 ..       6      67 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0014
   DASH_Dad3 11 eYerLaenlktLaselkeLasn..steeildgLReLErk 47
                 Ye+L+++ k+L se +eLa+n   ++e+ ++L eL  k
  EPA04740.1  8 HYEKLQDEYKKLMSEYEELAENkaDSNEVNKKLDELTEK 46
                799999999999999999999955477888888777665 PP

>> DUF3958  Protein of unknown function (DUF3958)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   2.5    0.0044       1.9      81     105 ..       7      31 ..       2      33 .. 0.91
   2 ?    8.9   1.7    0.0038       1.7       4      31 ..      34      61 ..      31      69 .] 0.83

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0044
     DUF3958  81 eeeeeLkrekrqLedqeeelyyekr 105
                 e +e+L+ e+++L+++ eel+++k 
  EPA04740.1   7 EHYEKLQDEYKKLMSEYEELAENKA 31 
                 6799*****************9985 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0038
     DUF3958  4 eelnqelrelaekqeenekelkkqeqlk 31
                +e n++l el+ek ee++ke +k+   k
  EPA04740.1 34 NEVNKKLDELTEKHEEINKEFSKITDDK 61
                8999***************999987655 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.4    0.0079       3.5      67      92 ..       4      29 ..       1      33 [. 0.83
   2 ?    7.4   2.4     0.013       5.6      25      51 ..      30      56 ..      26      69 .] 0.67

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0079
  Syntaxin_2 67 qqklqkekLkkdfkealqeFqkiqrq 92
                +qk   ekL++++k++++e++++ ++
  EPA04740.1  4 SQKEHYEKLQDEYKKLMSEYEELAEN 29
                5677889*************998765 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.013
  Syntaxin_2 25 kkdteelreklhelieeinelikktne 51
                k d+ e+++kl+el+e+  e+ k+ ++
  EPA04740.1 30 KADSNEVNKKLDELTEKHEEINKEFSK 56
                569999999998888877766666544 PP

>> HemX  HemX, putative uroporphyrinogen-III C-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   5.0   0.00099      0.43      33      96 ..       5      68 ..       2      69 .] 0.89

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00099
        HemX 33 ltaevaelqqqlaaleqqlaqveaekeqkqeleerlqqlaeklealekeleqlqkqleelqqql 96
                ++ + ++lq++ ++l +++++++++k++ +e+ ++l++l+ek e+ +ke ++ + + +e+++++
  EPA04740.1  5 QKEHYEKLQDEYKKLMSEYEELAENKADSNEVNKKLDELTEKHEEINKEFSKITDDKKENSHKI 68
                5566799*****************************************9999999999888876 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   1.2    0.0071       3.1      22      51 ..       5      27 ..       3      34 .. 0.49
   2 ?    6.3   2.6     0.018       7.8      22      54 ..      29      61 ..      26      63 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0071
                HHHHHHHHHHHHHHHHHHHHHHHHHHCC-X CS
       DivIC 22 lkqeiaalqaelaklkaeneeLeaevkdLk 51
                +       +++++kl++e ++L +e ++L 
  EPA04740.1  5 Q-------KEHYEKLQDEYKKLMSEYEELA 27
                4.......4455555555555555555543 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.018
                HHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXX CS
       DivIC 22 lkqeiaalqaelaklkaeneeLeaevkdLksde 54
                 k++ ++ +++l++l+++ ee ++e ++ ++d+
  EPA04740.1 29 NKADSNEVNKKLDELTEKHEEINKEFSKITDDK 61
                677888999999999999999999999997765 PP

>> EMC3_TMCO1  Integral membrane protein EMC3/TMCO1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   6.8    0.0033       1.5      40      89 ..       9      59 ..       1      66 [. 0.62

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0033
  EMC3_TMCO1 40 dkkkmekeqkrekelqkrarelqk.ngdklklkklekrqeelmedqsemmm 89
                + k +++++k+++e+++ a++    n  ++kl++l ++ ee++++ s+++ 
  EPA04740.1  9 YEKLQDEYKKLMSEYEELAENKADsNEVNKKLDELTEKHEEINKEFSKITD 59
                344455555555555555554333355589999999999999998887755 PP

>> Uteroglobin  Uteroglobin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   4.7    0.0039       1.7      36      77 ..      10      51 ..       3      66 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0039
                 HS-HHHHHHHHHTT---HHHHHHHHHHHHHHTTS-HHHHHHH CS
  Uteroglobin 36 egseeeYkeeLqkynpdpeaeealaelKqcvdklsnetkenv 77
                 e+ ++eYk+ +++y++ +e ++   e+ +  d+l++++ e  
   EPA04740.1 10 EKLQDEYKKLMSEYEELAENKADSNEVNKKLDELTEKHEEIN 51
                 56789******************************9886544 PP

>> CotJB  CotJB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   2.2    0.0068         3      30      50 ..       5      25 ..       1      29 [. 0.86
   2 ?    4.7   0.3     0.081        35      32      63 ..      34      65 ..      27      69 .] 0.53

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0068
       CotJB 30 alelfnkyskkrkelkkeYee 50
                  e+++k+++++k+l++eYee
  EPA04740.1  5 QKEHYEKLQDEYKKLMSEYEE 25
                5689***************98 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.081
       CotJB 32 elfnkyskkrkelkkeYeekygPLtldgvses 63
                ++ nk  +++ e  +e ++++  +t d++++s
  EPA04740.1 34 NEVNKKLDELTEKHEEINKEFSKITDDKKENS 65
                33333344444444555567777777766665 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   7.6    0.0048       2.1      25      90 ..       3      68 ..       3      69 .] 0.81

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0048
       Atg14 25 yelrerlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdkl 90
                y+ +e + kl+ e + l +++e++ e+k ++++ ++k++ +++k ee+ ++ +++ + ++e ++k+
  EPA04740.1  3 YSQKEHYEKLQDEYKKLMSEYEELAENKADSNEVNKKLDELTEKHEEINKEFSKITDDKKENSHKI 68
                567888999999999999999999999998888888888888888888888888888887777765 PP

>> Tho2  Transcription factor/nuclear export subunit protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4  10.3    0.0049       2.2      23      78 ..       5      66 ..       3      69 .] 0.59

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0049
        Tho2 23 pkeqYekeieklkseieel......akdrsderaaakkkkkekkrlkeliekLeeEkkeqie 78
                 ke+Yek  ++ k+ ++e       + d+++ +++ ++ +++++++++  +k++++kke+++
  EPA04740.1  5 QKEHYEKLQDEYKKLMSEYeelaenKADSNEVNKKLDELTEKHEEINKEFSKITDDKKENSH 66
                56777765555555555543336533333444777777777777777777777777777655 PP

>> DUF1640  Protein of unknown function (DUF1640)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   9.7    0.0062       2.7      66     128 ..       1      68 [.       1      69 [] 0.67

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0062
     DUF1640  66 vqisersefaalrseteklqreleklk......qkLreeidklkadirldlnleKgrireelakleaki 128
                 +  s++++ ++l+ e++kl +e e+l       +++++++d+l+++   ++n+e ++i+++ ++ + ki
  EPA04740.1   1 MDYSQKEHYEKLQDEYKKLMSEYEELAenkadsNEVNKKLDELTEK-HEEINKEFSKITDDKKENSHKI 68 
                 5679**********************72222224555566666555.4466666666666666666655 PP

>> DUF1910  Domain of unknown function (DUF1910)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   2.1    0.0023      0.99      61      90 ..       2      31 ..       1      45 [. 0.88
   2 ?    3.2   1.5      0.19        85      10      36 ..      40      65 ..      30      69 .] 0.51

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0023
     DUF1910 61 kYSlGesieeleadyeelikeleelwedea 90
                 YS+ e+ e+l+++y++l++e+eel e++a
  EPA04740.1  2 DYSQKEHYEKLQDEYKKLMSEYEELAENKA 31
                79**********************987765 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.19
     DUF1910 10 ykesiefdkeriaklkekieelsedee 36
                ++e +e+++e i+k  +ki +++++++
  EPA04740.1 40 LDELTEKHEE-INKEFSKITDDKKENS 65
                3333333333.4444446666665554 PP

>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   4.1    0.0094       4.1     285     333 ..       7      54 ..       3      68 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0094
       LMBR1 285 qkrertekqwkrllekalelediiknksskekefksses..srrgefakqg 333
                 +++e+ ++++k+l+ ++   e++++nk+++++  k++++  ++++e+ k++
  EPA04740.1   7 EHYEKLQDEYKKLMSEY---EELAENKADSNEVNKKLDEltEKHEEINKEF 54 
                 46677777777777777...7777777777666666666665555555543 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   6.2     0.018       7.7      24      69 ..       6      60 ..       3      68 .. 0.57

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.018
        YtxH 24 ketRkdlkekaddlkekakelleeakeka.........kekaedlkekvkekade 69
                ke  ++l++++++l    +el+e+ ++           +ek e++ +++++ +d+
  EPA04740.1  6 KEHYEKLQDEYKKLMSEYEELAENKADSNevnkkldelTEKHEEINKEFSKITDD 60
                5556777777777766666665444444477666444444444444444444444 PP

>> DUF2951  Protein of unknown function (DUF2951)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2  10.0     0.013       5.7      13      69 ..       9      68 ..       2      69 .] 0.82

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.013
     DUF2951 13 lrrleendktmlekldeikdslktqekvyikldk...tleelrkekeideknkkkndkni 69
                  +l+++ k ++++++e+ +++   ++v++kld    + ee++ke  +   +kk+n+++i
  EPA04740.1  9 YEKLQDEYKKLMSEYEELAENKADSNEVNKKLDElteKHEEINKEFSKITDDKKENSHKI 68
                57899999************************9632256789999888888889988776 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   7.9     0.014       6.3       4      61 ..       9      62 ..       3      69 .] 0.34

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.014
       TMPIT  4 weelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk 61
                 e+l++e+k+l ++     ++l+e ++  +++ k++++ +++ +e++++++k++ ++k
  EPA04740.1  9 YEKLQDEYKKLMSEY----EELAENKADSNEVNKKLDELTEKHEEINKEFSKITDDKK 62
                333333333333333....122222222333333333333333333333333333322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3354  (0.187071); expected 358.6 (0.02)
Passed bias filter:                     1011  (0.0563891); expected 358.6 (0.02)
Passed Vit filter:                       191  (0.0106531); expected 17.9 (0.001)
Passed Fwd filter:                        44  (0.00245412); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              41  [number of targets reported over threshold]
# CPU time: 0.62u 0.35s 00:00:00.97 Elapsed: 00:00:00.54
# Mc/sec: 387.48
//
Query:       EPA04741.1  [L=138]
Description: hypothetical protein BG20_I0930 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.6e-10   39.6   0.0      6e-10   39.5   0.0    1.0  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra
    2.4e-05   24.6   0.0      3e-05   24.2   0.0    1.4  1  Polyketide_cyc   Polyketide cyclase / dehydrase and lipid tra
  ------ inclusion threshold ------
      0.066   13.5   0.1      0.077   13.2   0.1    1.2  1  AHSA1            Activator of Hsp90 ATPase homolog 1-like pro


Domain annotation for each model (and alignments):
>> Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   0.0     1e-13     6e-10       1     139 [.       1     133 [.       1     137 [. 0.82

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 1e-13
                      EEEEEEEEEESS-HHHHHHHHTTTTGGGGT-TTEEEEECSESTSSSTTTEEEEECCCSSEEEEEEEEEETTTTEEEEEEE.SSS-TSEEEEEEE CS
  Polyketide_cyc2   1 mvkvtvsvviaappekVwalvsdfenwprWhpevarveleggggpargvegtvrvggrgtvreelvevdpegrllsyrivkpvpvanyvatwtv 94 
                      m++++vsv+i+a+ +kVw++vsd++  p+   + ++v+  +++g+   v ++v+ ++r++  ++ ++++p +  +++++  ++++ +++  +t+
       EPA04741.1   1 MAEIEVSVEINASIDKVWEIVSDLDMEPEFWKGTKEVRNISKNGN--YVTREVTIAFRDQKCMQEIKIEP-KEKIEIKF--TKGIIDGTKIITL 89 
                      7899*************************9999999988888999..999****9999777777788899.99******..6************ PP

                      EECCETEEEEEEEEEEEE--TT--HHHHHHHHHHHHHHHHHHHHH CS
  Polyketide_cyc2  95 tpdgggtrvtwtgefdagplggpfekpaaakavkgdleagLerLk 139
                      t  ++ t +  +++++ ++ +g+f +++++k ++    ++L+++k
       EPA04741.1  90 TSIDEKTILKAKWDIKLTGMMGMF-TGVIKKHIENGTIQALQKIK 133
                      ******998866666655677777.45556666655555555555 PP

>> Polyketide_cyc  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0     5e-09     3e-05       1      49 [.      10      58 ..      10     130 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 5e-09
                    ESS-HHHHHHHHTTTGGCCSCCCCEEEEEE.SSSEE....EEEECSTTSS CS
  Polyketide_cyc  1 vpapadqvyalvadvesypeflphcssvevleeaes.glsadlevgfggl 49
                    ++a++d+v+++v+d +  pef+++ ++v+ ++++++     +++++f  +
      EPA04741.1 10 INASIDKVWEIVSDLDMEPEFWKGTKEVRNISKNGNyV-TREVTIAFRDQ 58
                    79*********************************942.33455544433 PP

>> AHSA1  Activator of Hsp90 ATPase homolog 1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   1.3e-05     0.077       1     121 [.      11     133 ..      11     137 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.3e-05
                 SS-HHHHHHHHH-HHHHHHHEEEEEEEE--STTEEEEEEETTTSEEEEEEEE..EEEEETTTEEEEEEEEETSETEEEEEEEEEEEEETTEEEEEEEE. CS
       AHSA1   1 dapperVfraltdpellkrWftlteaemdlrpGgkfrlrdspdgkefgnege..ylevvpperlvytwrledepeeeestvtieleeegggTrltlth. 96 
                 +a++++V++  +d ++   ++++t+    + + g++ +   +   +f  + +   ++++p e++++++         + t  i+l+  +++T l +++ 
  EPA04741.1  11 NASIDKVWEIVSDLDMEPEFWKGTKEVRNISKNGNYVT--REVTIAFRDQKCmqEIKIEPKEKIEIKFTKG----IIDGTKIITLTSIDEKTILKAKWd 103
                 589****************8888888888888888888..3566677777775556899********6433....6688999**********9999998 PP

                 ......EEEEHCHHHHHHHHHHHHHHHHHHH CS
       AHSA1  97 ......tglprkqkeeegveeGweqsldqLk 121
                        g   +  +++  e+G  q+l+++k
  EPA04741.1 104 ikltgmMGMFTGVIKKH-IENGTIQALQKIK 133
                 77766644444444443.5666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 882.81
//
Query:       EPA04742.1  [L=102]
Description: hypothetical protein BG20_I0913 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.055   13.9   0.1       0.07   13.6   0.1    1.1  1  DUF538    Protein of unknown function, DUF538


Domain annotation for each model (and alignments):
>> DUF538  Protein of unknown function, DUF538
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   3.9e-06      0.07      29     103 ..       4      79 ..       3      86 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.9e-06
      DUF538  29 GklevklksecevevekkksykvrYdsevtgyiekgkikkleGvkvkel.flwlsvseisveesgdkitfsvgvls 103
                 G + ++ +++c ++ +++k+  ++ +s+++ +++k +i k+ G  + +l   w+ + + + +++ +++ + vg+ s
  EPA04742.1   4 GVFAIHSPESCPLNSAASKKVFLNLESKIKSNMKKYQILKVVGFYMSVLeHEWIIILDAKSAHDIEQLCIAVGISS 79 
                 78999*********99888899*************************99788999999999777889999999554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 673.08
//
Query:       EPA04743.1  [L=46]
Description: hypothetical protein BG20_I2128, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.034   13.8   0.0      0.036   13.8   0.0    1.0  1  DUF4197   Protein of unknown function (DUF4197)


Domain annotation for each model (and alignments):
>> DUF4197  Protein of unknown function (DUF4197)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0     2e-06     0.036      90     124 ..       6      40 ..       2      44 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2e-06
     DUF4197  90 smtveDakailkggddaaTqYlkkktssqLaeafk 124
                 +++ +D   ++k   + +T+Ylk+kt+ +L ++fk
  EPA04743.1   6 NLSENDGSVLVKTARKVVTEYLKNKTKLKLEKEFK 40 
                 677799999***********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       997  (0.0556082); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 311.20
//
Query:       EPA04744.1  [L=87]
Description: hypothetical protein BG20_I2124 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-09   36.6   0.1    4.4e-09   36.3   0.1    1.1  1  Methyltransf_31  Methyltransferase domain
    9.2e-08   31.8   0.1      1e-07   31.7   0.1    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    1.7e-06   28.7   0.0    2.4e-06   28.1   0.0    1.2  1  Methyltransf_25  Methyltransferase domain
    3.7e-06   26.6   0.0    4.5e-06   26.3   0.0    1.1  1  MTS              Methyltransferase small domain
    3.4e-05   23.3   0.0    3.9e-05   23.1   0.0    1.0  1  CMAS             Mycolic acid cyclopropane synthetase
    0.00035   21.2   0.1     0.0005   20.8   0.1    1.2  1  Methyltransf_12  Methyltransferase domain
    0.00043   20.2   0.1    0.00053   19.9   0.1    1.1  1  Methyltransf_18  Methyltransferase domain
      0.002   17.7   0.0     0.0022   17.6   0.0    1.1  1  DOT1             Histone methylation protein DOT1
     0.0023   18.5   0.0     0.0037   17.9   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
      0.004   16.9   0.0      0.004   16.9   0.0    1.1  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
     0.0044   16.7   0.1     0.0061   16.3   0.1    1.3  1  UPF0020          Putative RNA methylase family UPF0020
     0.0077   15.6   0.0     0.0088   15.4   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
     0.0086   15.7   0.0     0.0091   15.7   0.0    1.1  1  Cons_hypoth95    Conserved hypothetical protein 95
       0.01   15.3   0.1      0.015   14.8   0.1    1.3  1  Methyltransf_4   Putative methyltransferase
  ------ inclusion threshold ------
      0.013   15.2   0.0      0.014   15.1   0.0    1.1  1  GCD14            tRNA methyltransferase complex GCD14 subunit
      0.014   14.5   0.0      0.015   14.5   0.0    1.1  1  Methyltransf_3   O-methyltransferase
      0.015   15.2   0.0      0.015   15.2   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
      0.016   15.0   0.0      0.017   14.9   0.0    1.1  1  Met_10           Met-10+ like-protein
      0.019   14.9   0.0       0.02   14.9   0.0    1.1  1  Methyltransf_32  Methyltransferase domain
      0.031   13.7   0.0      0.036   13.5   0.0    1.0  1  TehB             Tellurite resistance protein TehB
      0.075   12.6   0.1       0.12   12.0   0.1    1.3  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
      0.083   12.3   0.0      0.089   12.2   0.0    1.1  1  AviRa            RRNA methyltransferase AviRa
       0.14   12.3   0.0       0.16   12.1   0.0    1.1  1  FtsJ             FtsJ-like methyltransferase
       0.16   11.7   0.1       0.18   11.5   0.1    1.1  1  N6_N4_Mtase      DNA methylase


Domain annotation for each model (and alignments):
>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.1   5.9e-12   4.4e-09       7      51 ..      43      86 ..      39      87 .] 0.92

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 5.9e-12
  Methyltransf_31  7 vlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqkl 51
                     v+D+GCG+G +++e+a    + ++v+ iD++e+aiel ++++q+l
       EPA04744.1 43 VYDIGCGSGSISIEAA-IQVETGKVIAIDYDENAIELTKKILQNL 86
                     89**************.77789******************99986 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.1   1.4e-10     1e-07     157     202 ..      35      81 ..      23      86 .. 0.87

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 1.4e-10
        PrmA 157 klvkegeevlDvGtGSGiLai.aaakLgakkvvavDiDevAvkvake 202
                 + + +g+ v D+G+GSG ++i aa ++++ kv+a+D+De A++ +k+
  EPA04744.1  35 ARLCPGHIVYDIGCGSGSISIeAAIQVETGKVIAIDYDENAIELTKK 81 
                 55678999*************78889*****************9986 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   3.2e-09   2.4e-06       1      41 [.      43      83 ..      43      86 .. 0.92

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 3.2e-09
                     EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHH CS
  Methyltransf_25  1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaarera 41
                     v d+GcG+G +++++a +++ +kv+++D++e+++e +++ +
       EPA04744.1 43 VYDIGCGSGSISIEAAIQVETGKVIAIDYDENAIELTKKIL 83
                     78****************989**************999866 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0     6e-09   4.5e-06      33      76 ..      41      84 ..      26      86 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 6e-09
                SEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHH CS
         MTS 33 gkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenle 76
                + v D+GcG G +++++a + ++ +v ++d d +A+e++k+ l+
  EPA04744.1 41 HIVYDIGCGSGSISIEAAIQVETGKVIAIDYDENAIELTKKILQ 84
                5589***********************************99876 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   5.2e-08   3.9e-05      51     107 ..      28      85 ..      13      86 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 5.2e-08
                 HHHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--.EEEEEES-HHHHHHHHHHHHT CS
        CMAS  51 ldlileklelkpGmtlLdiGcGWGslvrraverydv.kvvglTlSkeqaklakkrvde 107
                 + + + k++l pG+ + diGcG Gs+ ++a+ + +  kv+++   ++  +l+kk +++
  EPA04744.1  28 RTIQISKARLCPGHIVYDIGCGSGSISIEAAIQVETgKVIAIDYDENAIELTKKILQN 85 
                 567789*********************9999887644899999999999999998876 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1   6.7e-07    0.0005       2      39 ..      45      82 ..      44      86 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 6.7e-07
  Methyltransf_12  2 eiGcGtGsllralleklpdieytgvDispsaiedakek 39
                     +iGcG+Gs++ + + + ++ +++++D++++aie +k+ 
       EPA04744.1 45 DIGCGSGSISIEAAIQVETGKVIAIDYDENAIELTKKI 82
                     9*******************************666654 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.1   7.1e-07   0.00053      12      58 ..      38      83 ..      28      86 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 7.1e-07
  Methyltransf_18 12 vekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeni 58
                     ++ g++v DiG+  g ++i+++ +  + kvia+D  e+++e  k+ +
       EPA04744.1 38 CP-GHIVYDIGCGSGSISIEAAIQVETGKVIAIDYDENAIELTKKIL 83
                     44.899********************************999888765 PP

>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   2.9e-06    0.0022      35      87 ..      32      84 ..      22      87 .] 0.90

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.9e-06
                HHHTT--TT-EEEEES-TTSHHHHHHHHHH--SEEEEEE--HHHHHHHHHHHH CS
        DOT1 35 ldkvnlkkedvFvDLGSGvGnvvlqaalevgcklsvGvEimdnaselaekqke 87
                ++k  l + ++ +D+G G G + + aa +v++ + + ++  +na el++k  +
  EPA04744.1 32 ISKARLCPGHIVYDIGCGSGSISIEAAIQVETGKVIAIDYDENAIELTKKILQ 84
                789999******************************************98765 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   4.9e-06    0.0037       2      36 ..      45      81 ..      44      86 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 4.9e-06
                     EET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHH CS
  Methyltransf_11  2 dvGcGtGrlaealakrg..arvvgvDlskemlklake 36
                     d+GcG+G+++ + a ++  ++v+++D+++++++l k+
       EPA04744.1 45 DIGCGSGSISIEAAIQVetGKVIAIDYDENAIELTKK 81
                     9*************555578************99886 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   5.4e-06     0.004      69     120 ..      35      85 ..      10      87 .] 0.80

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5.4e-06
                 TT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHH CS
        PCMT  69 lelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkk 120
                  +l +g  v ++G+GsG  + + a +  e+g+v++i++ ++ +e +k+ l++
  EPA04744.1  35 ARLCPGHIVYDIGCGSGSIS-IEAAIQVETGKVIAIDYDENAIELTKKILQN 85 
                 458999***********765.66777778999******99999988887765 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   8.2e-06    0.0061      26      52 ..      37      63 ..      29      86 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 8.2e-06
                --TTS-EEETT-TTSHHHHHHHHHHTT CS
     UPF0020 26 wkpgepllDPmCGsGtilIEaallgan 52
                + pg+  +D  CGsG+i IEaa+++++
  EPA04744.1 37 LCPGHIVYDIGCGSGSISIEAAIQVET 63
                55777778888***********99875 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.2e-05    0.0088      47      93 ..      39      84 ..      22      86 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.2e-05
                     -TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHH CS
  Ubie_methyltran 47 rgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklk 93
                     +g+ v D+ +G+g ++++ + +v+ +gkv+ +D++en ++ ++k l+
       EPA04744.1 39 PGHIVYDIGCGSGSISIEAAIQVE-TGKVIAIDYDENAIELTKKILQ 84
                     577899************998885.79************99998765 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.2e-05    0.0091      40      87 ..      38      86 ..      18      87 .] 0.82

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.2e-05
                   HCC-EEEETT-TTSHHHHHHHHT.T-SEEEEEES-HHHHHHHHHHHCCC CS
  Cons_hypoth95 40 iegarvLDlfaGsGalglEAlSR.gakkavlvekdkeavkilkenleel 87
                     g  v D+ +GsG++++EA+   +  k+++++ d++a+++ k+ l++l
     EPA04744.1 38 CPGHIVYDIGCGSGSISIEAAIQvETGKVIAIDYDENAIELTKKILQNL 86
                   566778899**********86542889************9999887765 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1     2e-05     0.015       3      40 ..      41      78 ..      39      86 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2e-05
                    EEEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHH CS
  Methyltransf_4  3 pvvleiGcGkGeflvalAkknPdknflGiEirvkvvak 40
                     +v +iGcG+G++ ++ A +  + ++++i+  ++ ++ 
      EPA04744.1 41 HIVYDIGCGSGSISIEAAIQVETGKVIAIDYDENAIEL 78
                    5799**************************99988864 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   1.9e-05     0.014      33      80 ..      32      78 ..      13      85 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.9e-05
       GCD14 33 imkLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraek 80
                i k +l pG  v + G Gsgs+s   a  v+ tG++ ++++ e+ +e 
  EPA04744.1 32 ISKARLCPGHIVYDIGCGSGSISIEAAIQVE-TGKVIAIDYDENAIEL 78
                467899*****************98888875.9********9987765 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0     2e-05     0.015      51      93 ..      43      84 ..      16      86 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2e-05
                    EEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHH CS
  Methyltransf_3 51 vleiGvftGyslLatalalPeDGkilaididreayeialkfiq 93
                    v +iG   G   +  a+++ e Gk++aid d++a e+++k++q
      EPA04744.1 43 VYDIGCGSGSISIEAAIQV-ETGKVIAIDYDENAIELTKKILQ 84
                    6678888887777777776.89******************988 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0     2e-05     0.015      25      63 ..      42      82 ..      12      86 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2e-05
  Methyltransf_23 25 rvLdiGcGtGillevlrengf..svtgvDlspeaveiaeka 63
                      v diGcG+G+ + +++ ++   +v+++D +++a+e+ +k+
       EPA04744.1 42 IVYDIGCGSGSISIEAAIQVEtgKVIAIDYDENAIELTKKI 82
                     678********999999998779************997655 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   2.3e-05     0.017      98     142 ..      37      81 ..      19      87 .] 0.79

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.3e-05
                 --TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHH CS
      Met_10  98 veegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylke 142
                   +g +V d+  G G  +i +a   +  +v+aid + +++++ k+
  EPA04744.1  37 LCPGHIVYDIGCGSGSISIEAAIQVETGKVIAIDYDENAIELTKK 81 
                 559************************************998665 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   2.7e-05      0.02      27      74 ..      41      86 ..      21      87 .] 0.85

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.7e-05
  Methyltransf_32 27 ltvvDvGaGkgYLsfvlalkeke.yklkvvgidakeelvekaekraekl 74
                       v D+G+G g  s   a    +    kv++id  e+ +e ++k+ ++l
       EPA04744.1 41 HIVYDIGCGSGSISIEAAI---QvETGKVIAIDYDENAIELTKKILQNL 86
                     5688*************99...4469**************999998776 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   4.8e-05     0.036       7      72 ..      12      83 ..       9      86 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.8e-05
                CHHHHHHT-----HHH..HHHCCC.S-S-E.EEEES-TTSHHHHH..HHHTT-EEEEEES-HHHHHHHHHHH CS
        TehB  7 dyfskkynltathsev..veavki.vkpgk.vldlgcgqgrnsly..lsllgydvtawdknensiafleeik 72
                d f++  n+  t+ ev  ++  k  + pg+ v d+gcg+g  s+   +++   +v a+d +en+i+  ++i 
  EPA04744.1 12 DLFERTENVPITKEEVrtIQISKArLCPGHiVYDIGCGSGSISIEaaIQVETGKVIAIDYDENAIELTKKIL 83
                666666666666666522222222256776367**********97114556789***********9888875 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00015      0.12       3      40 ..      42      81 ..      40      85 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00015
  Methyltransf_15  3 vilDlfsGaGGnviqfalv..fekviaieinleklacaqh 40
                     ++ D+ +G+G  +i+ a +    kviai+++++ ++++++
       EPA04744.1 42 IVYDIGCGSGSISIEAAIQveTGKVIAIDYDENAIELTKK 81
                     6789**********9998855669***********99986 PP

>> AviRa  RRNA methyltransferase AviRa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00012     0.089      48     100 ..      34      84 ..      19      87 .] 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00012
       AviRa  48 kkeegapltlyDpCCGgayLltvlgllhgkkikkvlasDvdeevlelakkNLs 100
                 k++   +  +yD  CG++ +    +   + +  kv+a D de+++el+kk L+
  EPA04744.1  34 KARLCPGHIVYDIGCGSGSISIEAA--IQVETGKVIAIDYDENAIELTKKILQ 84 
                 3444467789********9865444..4567799**************99886 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00021      0.16      17      57 ..      36      74 ..      18      85 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00021
                T-S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS CS
        FtsJ 17 klfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm 57
                + + pg+ v D+g++ G+ s  ++ ++++ gkv+a+D  ++
  EPA04744.1 36 R-LCPGHIVYDIGCGSGSISIEAAIQVET-GKVIAIDYDEN 74
                3.459999************999999986.*******9776 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00024      0.18     187     231 .]      35      81 ..      23      81 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00024
                  HHS-TT-EEEETT-TTTHHHHHHH..HTT-EEEEEESSHHHHHHHHH CS
  N6_N4_Mtase 187 lstkkgdivlDpFaGSGtTavaak..elgrkfiGieieeeyvelaek 231
                  + + +g iv D  +GSG++ ++a+   +  k i i+++e+++el++k
   EPA04744.1  35 ARLCPGHIVYDIGCGSGSISIEAAiqVETGKVIAIDYDENAIELTKK 81 
                  55678*************9876651145678************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 625.45
//
Query:       EPA04745.1  [L=156]
Description: hypothetical protein BG20_I2127 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.3e-26   91.8   0.1    5.1e-26   91.5   0.1    1.0  1  Mut7-C          Mut7-C RNAse domain
    1.9e-05   24.3   0.1    3.1e-05   23.7   0.1    1.4  1  DUF5615         Domain of unknown function (DUF5615)
      0.002   18.3   0.1     0.0047   17.1   0.1    1.7  1  PIN_10          PIN like domain
     0.0073   16.3   0.3     0.0087   16.0   0.3    1.1  1  Cas6            Cas6 Crispr
       0.01   16.1   2.9      0.024   14.9   2.8    1.8  1  RNA_pol_Rpb2_4  RNA polymerase Rpb2, domain 4


Domain annotation for each model (and alignments):
>> Mut7-C  Mut7-C RNAse domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.5   0.1   1.4e-29   5.1e-26       1     114 [.       9     125 ..       9     136 .. 0.91

  Alignments for each domain:
  == domain 1  score: 91.5 bits;  conditional E-value: 1.4e-29
      Mut7-C   1 krfllDamlgklakyLRllGydalyasdvedeellalaakekrillTrdreLlkraklkkg..vlltsrdveeqlreviarlglkl.slkpelsrCvaC 96 
                 ++f +Damlg++ak LRl+Gyd++y sd ede+l+++a++e+ri++++d+eL+k++++ +   + + +++  eq++e+i r +lk  +++ + srC +C
  EPA04745.1   9 PKFFVDAMLGNIAKKLRLMGYDSKYFSDIEDEKLVDIARNENRIIISKDKELIKKTQKLRLrsIHIIKNEEIEQFVEIITRENLKRiQINGNTSRCPQC 107
                 69*****************************************************9998767877777888889999999999976599********** PP

      Mut7-C  97 ngeleevekeevkervpe 114
                 n+  ++++k+++ke++ +
  EPA04745.1 108 NSLTKQIDKNSIKENILK 125
                 ************999755 PP

>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.1   8.6e-09   3.1e-05       2      59 ..      10      61 ..       9      77 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 8.6e-09
     DUF5615  2 klllDenlsprlvellreaghdvlhvrelglegasDeeileyAkeedriivTkDkDFg 59
                k+ +D+ l   ++++lr  g+d+++  +     ++De+ +++A++e+rii++kDk  +
  EPA04745.1 10 KFFVDAMLG-NIAKKLRLMGYDSKYFSD-----IEDEKLVDIARNENRIIISKDKELI 61
                788999998.899*************54.....67*******************9765 PP

>> PIN_10  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   1.3e-06    0.0047       1      67 [.       9      65 ..       9      75 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.3e-06
      PIN_10  1 MkfflDenlppalakaLrelleeeghevvhlrdkfaagtkDeeWiaalaeggwvvltkDrrirkrpa 67
                +kff+D  l+  +ak Lr         ++ +  k++++ +De+++ ++++++ ++++kD+++ k+ +
  EPA04745.1  9 PKFFVDAMLGN-IAKKLR---------LMGYDSKYFSDIEDEKLVDIARNENRIIISKDKELIKKTQ 65
                89*****9999.******.........88999***************************98877654 PP

>> Cas6  Cas6 Crispr
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.3   2.4e-06    0.0087      78     146 ..      41     111 ..      21     137 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.4e-06
        Cas6  78 ktleigghklrlgipkl.rllepastLkarlVvikgaedeeaFleavqr.qLealeikgkkallgkrrtlk 146
                 k ++i+ ++ r++i+k  +l++++++L  r + i ++e+ e+F+e + r +L++++i+g+ + + + ++l+
  EPA04745.1  41 KLVDIARNENRIIISKDkELIKKTQKLRLRSIHIIKNEEIEQFVEIITReNLKRIQINGNTSRCPQCNSLT 111
                 4568999999999986515678999********************987627*********99995444443 PP

>> RNA_pol_Rpb2_4  RNA polymerase Rpb2, domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   2.8   6.6e-06     0.024      11      53 ..      54     103 ..      38     106 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 6.6e-06
                     -S-HCCHHHHHHHHCC.......TTSS-TT-EEEE-TTT--EEEE-SSEE CS
  RNA_pol_Rpb2_4  11 trdpkklvetlRelRR.......kgkiseevsivlnekqkevkiatDgGR 53 
                     +++ k+l+++ ++lR        +++i+++v+i++ e+ k+++i+ +  R
      EPA04745.1  54 ISKDKELIKKTQKLRLrsihiikNEEIEQFVEIITRENLKRIQINGNTSR 103
                     78899**********96666666699******************987766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1450  (0.0808746); expected 358.6 (0.02)
Passed bias filter:                      636  (0.0354733); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1081.27
//
Query:       EPA04746.1  [L=160]
Description: hypothetical protein BG20_I2125 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0003   21.0   3.7    0.00045   20.4   3.7    1.3  1  DUF5379         Family of unknown function (DUF5379)
     0.0039   16.6   4.6     0.0055   16.1   4.6    1.1  1  7TM_GPCR_Srsx   Serpentine type 7TM GPCR chemoreceptor Srsx
     0.0055   16.5   0.4      0.058   13.2   0.0    2.1  2  RSN1_TM         Late exocytosis, associated with Golgi transp
  ------ inclusion threshold ------
       0.05   13.6   0.0      0.087   12.8   0.0    1.6  1  DUF543          Domain of unknown function (DUF543)
      0.056   14.1   3.7      0.081   13.6   3.7    1.3  1  Multi_Drug_Res  Small Multidrug Resistance protein
       0.11   12.5   4.2       0.11   12.5   3.0    1.5  2  Colicin_V       Colicin V production protein
       0.21   12.0   5.1       0.62   10.6   5.1    1.8  1  DUF202          Domain of unknown function (DUF202)
       0.28   10.9   3.8       0.72    9.5   3.8    1.7  1  DUF21           Cyclin M transmembrane N-terminal domain
       0.31   11.6   5.4       0.66   10.6   5.4    1.6  1  Rab5ip          Rab5-interacting protein (Rab5ip)


Domain annotation for each model (and alignments):
>> DUF5379  Family of unknown function (DUF5379)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   3.7   2.2e-07   0.00045      15      88 ..      70     144 ..      60     146 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.2e-07
     DUF5379  15 giifgylanyvytlglgllsglatllflfiglvilghls.akvlgeesltqkqwlgsgvlpfflvaivvwilkyn 88 
                  +i g la +++    g     a+++f++i ++ +  ++ ++ +   s ++k+ +  g+ +++++++ vwil+y 
  EPA04746.1  70 AVIAGTLATFLFEDIEGEERRWASIVFMIIVFIGTIFVAkSMKIQLPSSDRKKIVMQGIGSYIFIYLFVWILTYT 144
                 5678889999998888988999999999998887766653677888999************************97 PP

>> 7TM_GPCR_Srsx  Serpentine type 7TM GPCR chemoreceptor Srsx
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   4.6   2.7e-06    0.0055     158     208 ..      95     147 ..      90     157 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.7e-06
  7TM_GPCR_Srsx 158 vlvllvylvliiilkkkkek..skssskkvlkslsvtvvififtWflstilnt 208
                    v++++v++ +i+++k++k +  s+++ k v++ +   ++i++f W+l+ ++ +
     EPA04746.1  95 VFMIIVFIGTIFVAKSMKIQlpSSDRKKIVMQGIGSYIFIYLFVWILTYTIVH 147
                    788999*******9999988778888999******************988876 PP

>> RSN1_TM  Late exocytosis, associated with Golgi transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   2.9e-05     0.058     102     153 ..      45     108 ..      42     111 .. 0.84
   2 ?    1.2   0.5      0.14   2.7e+02     131     154 ..     119     142 ..     108     148 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.9e-05
     RSN1_TM 102 Pvnatggegedskesk.............sgldklsisnvsegsnrlwahvvvayiftglvlyll 153
                 Pv  +++++e++k+ +              +l ++ ++++ eg++r wa++v+++i+++ ++++ 
  EPA04746.1  45 PVESQDEKSEKDKKLDrlfwlrvgcaviaGTLATFLFEDI-EGEERRWASIVFMIIVFIGTIFVA 108
                 7777777777666666899999999999878999******.999****************99985 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.14
     RSN1_TM 131 gsnrlwahvvvayiftglvlylly 154
                 ++++++++ + +yif+ l++++l+
  EPA04746.1 119 DRKKIVMQGIGSYIFIYLFVWILT 142
                 555566666666666666555554 PP

>> DUF543  Domain of unknown function (DUF543)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   4.4e-05     0.087      11      56 ..      44      96 ..       7     108 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.4e-05
      DUF543 11 apse.sdldekwDaclsnll.vkvglgllvGvvasvllfr.....rRaapval 56
                +p+e +d +   D+ l++l+ ++vg  +++G++a++l+       rR+a++++
  EPA04746.1 44 EPVEsQDEKSEKDKKLDRLFwLRVGCAVIAGTLATFLFEDiegeeRRWASIVF 96
                4444566666778888875438*************9998899999****9987 PP

>> Multi_Drug_Res  Small Multidrug Resistance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   3.7   4.1e-05     0.081       3      77 ..      64     141 ..      62     152 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.1e-05
                     -HHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHHHHH--.-----H.HHHHHHHHH.HHHHHHHHHH CS
  Multi_Drug_Res   3 wvllvlAillevvgailLklsegftkltpsllvivgygisfllLskalks.lpvsvA.YavwsGiGt.vlivlvgill 77 
                     w+ + +A+++   ++ l   +eg+++ + s+++++++ i  ++ +k++k  lp s     v +GiG  ++i+l+ ++l
      EPA04746.1  64 WLRVGCAVIAGTLATFLFEDIEGEERRWASIVFMIIVFIGTIFVAKSMKIqLPSSDRkKIVMQGIGSyIFIYLFVWIL 141
                     8999********************************************965777644145678888525566666655 PP

>> Colicin_V  Colicin V production protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00035      0.69      36      82 ..      71     115 ..      66     123 .. 0.78
   2 ?   12.5   3.0   5.3e-05      0.11      23      78 ..      89     145 ..      84     156 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00035
   Colicin_V  36 vvasllypslaellaelilspalaaiiaflllfllvllivsllgall 82 
                 v+a  l+  l e ++   +++++a+i+ ++++f++++++++ +   l
  EPA04746.1  71 VIAGTLATFLFEDIEG--EERRWASIVFMIIVFIGTIFVAKSMKIQL 115
                 5566666666666666..799******************98877665 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 5.3e-05
   Colicin_V  23 revlsllgwvvafvvasllypslaellaelilspalaaiiaf.lllfllvllivsll 78 
                 r+++s+++++++f+ +++ ++s+  +l +   ++ ++++i+  + ++l+v+++++ +
  EPA04746.1  89 RRWASIVFMIIVFIGTIFVAKSMKIQLPSSDRKKIVMQGIGSyIFIYLFVWILTYTI 145
                 6789*************************8889999998887799*******97655 PP

>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   5.1   0.00031      0.62      11      55 ..      62     107 ..      61     149 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00031
      DUF202  11 LaWlRtslalialglallrffl.tgepsalgkilglilivlgiltl 55 
                 L WlR+++a ia  la + f+  +ge+ ++++i+ +i++ +g++++
  EPA04746.1  62 LFWLRVGCAVIAGTLATFLFEDiEGEERRWASIVFMIIVFIGTIFV 107
                 56****************9988545555555555555555555544 PP

>> DUF21  Cyclin M transmembrane N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   3.8   0.00036      0.72      60     101 ..      66     107 ..      52     156 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00036
       DUF21  60 ntlvnillsalatalfvellaegalavviatvivtllilvfg 101
                    + +++++lat+lf+++ +e++ ++ i++ i++++  +f 
  EPA04746.1  66 RVGCAVIAGTLATFLFEDIEGEERRWASIVFMIIVFIGTIFV 107
                 56699*****************88888888877777766664 PP

>> Rab5ip  Rab5-interacting protein (Rab5ip)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   5.4   0.00033      0.66       3      82 .]      63     143 ..      61     143 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00033
      Rab5ip   3 snlrsltalllGvvaGilgLeslsGflfylllsllvsllfy.alkvkgkskkyfrg.alkelwteglvnglagFvLtWtlfY 82 
                  +lr  +a+++G++a +l +e + G     ++ ++++++f+ ++ v++++k + ++   k+++++g+ + ++ ++ +W+l+Y
  EPA04746.1  63 FWLRVGCAVIAGTLATFL-FEDIEGEERRWASIVFMIIVFIgTIFVAKSMKIQLPSsDRKKIVMQGIGSYIFIYLFVWILTY 143
                 566666777777776655.445544444444444444444444445556666555524679*******************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1828  (0.101958); expected 358.6 (0.02)
Passed bias filter:                      986  (0.0549947); expected 358.6 (0.02)
Passed Vit filter:                       118  (0.00658152); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.59u 0.34s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 994.25
//
Query:       EPA04747.1  [L=67]
Description: hypothetical protein BG20_I2123, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.021   14.4   0.9      0.024   14.2   0.9    1.1  1  TrmK             tRNA (adenine(22)-N(1))-methyltransferase
      0.064   13.2   0.8      0.072   13.0   0.8    1.1  1  Methyltransf_18  Methyltransferase domain


Domain annotation for each model (and alignments):
>> TrmK  tRNA (adenine(22)-N(1))-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.9   2.6e-06     0.024      48      98 ..       2      51 ..       1      54 [. 0.90

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.6e-06
        TrmK 48 ekievrlgdGlavlekedeidviviaGmGgalIaeILeegkekLkkvkrli 98
                ++i+v+lg+  + +++ +++d+i i G Gg +  eI++  ++kLk+  r++
  EPA04747.1  2 KNISVILGNAKEKISELEQADAIFIGGTGGDT-EEIVKLCQNKLKSGGRIV 51
                78****************************87.899999999998876665 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.8     8e-06     0.072      65     114 ..       2      51 ..       1      56 [. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8e-06
  Methyltransf_18  65 dkievrlsdGleklkeee.vdtvviaGmGgelileILeeakeklkkikkli 114
                      ++i+v+l++  ek++e e +d++ i G Gg++  eI++ +++klk+  +++
       EPA04747.1   2 KNISVILGNAKEKISELEqADAIFIGGTGGDT-EEIVKLCQNKLKSGGRIV 51 
                      5799***********8888***********97.578888888888766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.31s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 416.29
//
Query:       EPA04748.1  [L=638]
Description: hypothetical protein BG20_I2126 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.9e-37  127.3   7.5    9.1e-37  126.9   7.5    1.1  1  FbpA       Fibronectin-binding protein A N-terminus (FbpA)
    2.8e-21   76.2   0.0    1.3e-20   74.1   0.0    2.2  2  NFACT-R_1  NFACT protein RNA binding domain
  ------ inclusion threshold ------
      0.021   14.6   3.4      0.064   13.1   3.4    1.8  1  PKcGMP_CC  Coiled-coil N-terminus of cGMP-dependent protein k
        2.1    6.9   6.8        4.5    5.8   1.5    2.2  2  Tweety     Tweety
        4.3    7.8   6.7        2.3    8.7   2.7    2.7  2  FlaC_arch  Flagella accessory protein C (FlaC)


Domain annotation for each model (and alignments):
>> FbpA  Fibronectin-binding protein A N-terminus (FbpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.9   7.5   2.5e-40   9.1e-37       2     430 ..       5     425 ..       4     429 .. 0.85

  Alignments for each domain:
  == domain 1  score: 126.9 bits;  conditional E-value: 2.5e-40
                 HHHHHHHHHHHHHHHTTXEEEEEEEEETTEEEEEEE.ETTEEEEEEEEXXTTTXEEEEXXXXXXXXSSXXHHHHHHHHHHTTXEEEEEEEXTTSSEEEE CS
        FbpA   2 glvlaavvaELqkellggridkiyqpekdelvltlr.anrgrhkLllsahpsyarihltekpkenpkeppnFcmlLRkyLkgarivsieqlgfdRivel 99 
                 g+ l+ +v++++++  +  +++iy ++kd++ ++l+ +++   ++++s     + + lt+ +  +++ep+ +++ LR  L   ++++ieq+  +Ri  +
  EPA04748.1   5 GIELRYLVNQISEATQDYYVSNIYGVTKDSILFKLHhTEKPDIYMMIST----SGVWLTSVKI-EQMEPNRLLKRLRSDLLRLKVKKIEQIASERIAYF 98 
                 5678999*****************************5555555577777....7788876654.79********************************* PP

                 EEEEEXTTSXEEEEEEEEEXXGGGXEEEEEETTTEEEEESSXBXXXSSXSXXBSTTXBXXXSXXXSXBXTTSXXH.HHHHHHHHHS.XXXHHHHHHHBT CS
        FbpA 100 siekrdElgdeeeytLivEimgrhSNiiLvdeenkIidaikhvspkqsrvReilpgekYelPpsqdklnPleaeeleefkellskkekdlvkaLvkafq 198
                 ++e       ++e  ++ E +g+ +Ni+L+++e kI+++ + +  +   +R++  g  Y++Pp  ++l+  +++e ++f+el ++ + +  k+L +++ 
  EPA04748.1  99 TFEGF-----DKEFVIVGEFFGD-GNILLCNNEMKILALQHSIDVR---HRKLGVGLVYTPPPL-NGLDVIDVTE-SDFEEL-KTTDLSAGKWLGRTL- 184
                 *****.....999**********.*******************998...9*********98888.******9999.888888.45679999*******. PP

                 TXXHHHHHHHHTTXSSSH...............HHHHHHHHTXXX....XXEE.....XSSSEESSXXTTXX.SSXXXXSXHHHHHHHHTTTXXX--SH CS
        FbpA 199 GlspllaeelleragldketsakelseedlerlyealqelleeleeekfepqlvlkeekpeefsvvplkslselekesfdslsealdeyYakkaerdrv 297
                 Gl + ++e + e a++d++t  + l++++++++y++ +++++++ ++k ep ++ +e  ++e+ +v+l +l+  + ++++s+ e ld+ +++++ +   
  EPA04748.1 185 GLPKKYVEGIFEIASIDSKTMGNVLTSDQIKKIYDTTKNIVTNVVTGKHEPVIIRNE--KTEIIPVRLGKLD-DNCTPVNSFIEGLDTVFTENLVEIGK 280
                 ***************************************************997665..7888888866655.4569****************988666 PP

                 H.H..HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCGGH..............HHHHCCHH-----------------------.--------------- CS
        FbpA 298 e.q..krsdlekrveneleklekklkklekelekaeka..............enyrligelltaylyaikkgmsevelenyydegeevtIpLdprksps 379
                   q   + + +k++en+++ +ek +++ +++ +   +                +  + +e+l+ +++++  +++ ++l  ++d   + +I+++ +   +
  EPA04748.1 281 SiQtgGSDKKIKELENQIAEQEKAIETVKEKSNHITNVanslfemiskgiisIEDSRANEILSIHNSKL-VKEKGITLI-IID---DEKIKINAQSALQ 374
                 633124567777799999999999999999999888886666666666666644444566666666665.333444444.334...789********** PP

                 --HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-.-HHHHH CS
        FbpA 380 enAqkyfkkykKlkraveaveeqieetkeeleylesveaaleqaesledle 430
                 + A  +f+++k+   a++ +e+   +t+++l +l+++ ++ +++ + ++++
  EPA04748.1 375 SIASILFNEAKRKSGAIKSIEQIKINTQKKLVKLQNKAETEKESVTFAEIR 425
                 *************************************99999776666664 PP

>> NFACT-R_1  NFACT protein RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       4.9   1.7e+04      66      90 ..     125     150 ..     124     151 .. 0.80
   2 !   74.1   0.0   3.6e-24   1.3e-20       2     109 .]     433     541 ..     432     541 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 4.9
   NFACT-R_1  66 eaaqlakanSia.gnklssvdvvyvp 90 
                 e+  la ++Si  + ++  v  vy+p
  EPA04748.1 125 EMKILALQHSIDvRHRKLGVGLVYTP 150
                 67788999999997777799999998 PP

  == domain 2  score: 74.1 bits;  conditional E-value: 3.6e-24
   NFACT-R_1   2 vfwFkssdgylvimGkDkqeneelikkyleesdvwfhvdkessahvylrlsegeleeipeelleeaaqlakanSia.gnklssvdvvyvpasnlsktap 99 
                 ++wF +sdg l i+G+D+ +n  +++k+l ++d  fh d+++s++ +l+  ++e  + p+++l+e+a+ +++ S+a ++ +  v++++v++++++k+ap
  EPA04748.1 433 YRWFFTSDGILAIGGRDAPSNSAVVRKHLGKNDKIFHGDIFGSPFFILK--DTE--NPPPASLNEVAHATVCFSRAwREGMYGVSAFWVNPEQVKKSAP 527
                 68***********************************************..444..79***************************************** PP

   NFACT-R_1 100 ....ldtGsvgfkg 109
                     l++Gs++++g
  EPA04748.1 528 sgqfLPKGSFTIEG 541
                 **********9986 PP

>> PKcGMP_CC  Coiled-coil N-terminus of cGMP-dependent protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   3.4   1.8e-05     0.064       7      28 ..     288     309 ..     287     311 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.8e-05
   PKcGMP_CC   7 DERIRELEkrlaekdeEIqELr 28 
                 D +I+ELE+++ae+++ I+  +
  EPA04748.1 288 DKKIKELENQIAEQEKAIETVK 309
                 88**************998766 PP

>> Tweety  Tweety
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.4    0.0049        17     122     162 ..     286     326 ..     252     347 .. 0.71
   2 ?    5.8   1.5    0.0012       4.5     114     187 ..     360     436 ..     334     444 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.0049
      Tweety 122 kleeeLtkleeifakrtdlletlrlvqeqveevvqqlselp 162
                   ++++++le+++a++++ +et++   +++++v+++l e+ 
  EPA04748.1 286 GSDKKIKELENQIAEQEKAIETVKEKSNHITNVANSLFEMI 326
                 34578999****************99999999999998875 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0012
      Tweety 114 eteesleekleeeLtkleeifakrtd....lletlrlvqeqveevvqqlselpflkkkdvsltelaeqvelvelyRWl 187
                    e+++ + ++ L+++ +i+ ++++     ++++++++ ++++ + +l++ + ++k++v+ +e+  + + +e yRW 
  EPA04748.1 360 IDDEKIKINAQSALQSIASILFNEAKrksgAIKSIEQIKINTQKKLVKLQNKAETEKESVTFAEIR-KKNWYERYRWF 436
                 55678899999999**99998666555667899999999999999999999999999999999986.5689******7 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   2.7   0.00065       2.3       1      37 [.     290     326 ..     290     335 .. 0.86
   2 ?   -1.8   0.1       1.2   4.4e+03      28      43 ..     392     408 ..     373     410 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00065
   FlaC_arch   1 ridelEnklsklsteletvkkeneelsksveelkenV 37 
                 +i+elEn++ + +  +etvk++ +++ +  + l e +
  EPA04748.1 290 KIKELENQIAEQEKAIETVKEKSNHITNVANSLFEMI 326
                 89*********************99998877776665 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.2
   FlaC_arch  28 ksveelkenV.kdllsL 43 
                 ks+e++k n  k+l++L
  EPA04748.1 392 KSIEQIKINTqKKLVKL 408
                 78999988876777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (638 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1547  (0.0862848); expected 358.6 (0.02)
Passed bias filter:                      670  (0.0373696); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.74u 0.29s 00:00:01.03 Elapsed: 00:00:00.47
# Mc/sec: 4073.86
//
Query:       EPA04749.1  [L=40]
Description: hypothetical protein BG20_I2430 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.028   14.8   0.8      0.035   14.5   0.8    1.2  1  zf-met    Zinc-finger of C2H2 type
      0.078   12.9   0.2      0.078   12.9   0.2    1.1  1  zf-like   Cysteine-rich small domain


Domain annotation for each model (and alignments):
>> zf-met  Zinc-finger of C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.8   3.9e-06     0.035       1      21 [.       6      26 ..       6      30 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.9e-06
      zf-met  1 fyCelCnvtfnsesqlksHlq 21
                + C  Cn +f++e+ ++ H +
  EPA04749.1  6 WKCFRCNLSFKDENIADIHKK 26
                8999***************76 PP

>> zf-like  Cysteine-rich small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   8.7e-06     0.078      50      74 ..       6      30 ..       1      37 [. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.7e-06
     zf-like 50 kdCskCllvHkkevadellkklkei 74
                ++C +C+l  k+e++  ++kk+++ 
  EPA04749.1  6 WKCFRCNLSFKDENIADIHKKISNH 30
                9******************999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 282.77
//
Query:       EPA04750.1  [L=37]
Description: hypothetical protein BG20_I2429 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.30u 0.23s 00:00:00.53 Elapsed: 00:00:00.37
# Mc/sec: 301.45
//
Query:       EPA04751.1  [L=193]
Description: hypothetical protein BG20_I2432, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1316.01
//
Query:       EPA04752.1  [L=43]
Description: hypothetical protein BG20_I2433 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.034   14.5   0.8      0.043   14.2   0.8    1.2  1  zf-met    Zinc-finger of C2H2 type


Domain annotation for each model (and alignments):
>> zf-met  Zinc-finger of C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.8   2.4e-06     0.043       1      21 [.       9      29 ..       9      33 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.4e-06
      zf-met  1 fyCelCnvtfnsesqlksHlq 21
                + C  Cn +f++e+ ++ H +
  EPA04752.1  9 WKCFRCNLSFKDENIADIHKK 29
                8999***************76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (43 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.30u 0.27s 00:00:00.57 Elapsed: 00:00:00.40
# Mc/sec: 324.27
//
Query:       EPA04753.1  [L=90]
Description: hypothetical protein BG20_I2194 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 576.56
//
Query:       EPA04754.1  [L=151]
Description: putative fructose-6-phosphate aldolase, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-44  152.3   0.0    2.7e-44  151.6   0.0    1.3  1  TAL_FSA   Transaldolase/Fructose-6-phosphate aldolase


Domain annotation for each model (and alignments):
>> TAL_FSA  Transaldolase/Fructose-6-phosphate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.6   0.0   1.5e-48   2.7e-44      95     239 ..       1     134 [.       1     151 [] 0.92

  Alignments for each domain:
  == domain 1  score: 151.6 bits;  conditional E-value: 1.5e-48
                 HHHHHHHHTT-T..TEEEEEESSHHHHHHHHHHHHTT--EEEEEE-SHHHHHHHHHHT-SEEEEBHHHHHTTT............S-HHHHHHHHHHHH CS
     TAL_FSA  95 ieeArrlialyerenvlIKiPateeGikAikeLkkeGinvnvTliFsleqalaaaeagasviSpFvgRiddllkkleekdklkgkddgvalvkeiynyy 193
                 iee++rl +  +  nv++K+P+t++G+kA+k  + +Gi vnvTl+Fs++qal+aa++ga+++SpF+gR+dd++            +dg+ l+++i +++
  EPA04754.1   1 IEEGKRLREYGK--NVVVKVPMTPDGLKACKSFSLQGIPVNVTLVFSPNQALLAAKSGAKYVSPFIGRLDDIG------------QDGMSLIQDIKTIF 85 
                 79******8888..***********************************************************............7************* PP

                 HHH.T-S-EEEEBS--SHHHHH..HHHT-SEEEE-HHHHHHHT--HHH. CS
     TAL_FSA 194 kkl.gysTkvmaasfrnveeve..elagcdtvTippkllealakhgkts 239
                 k++ +++T+++ as+r++++v+  +++g+d+vT+pp++l+++ +h++t+
  EPA04754.1  86 KNYpEFKTQILVASIRHPMHVIdvAKIGADVVTLPPAVLDKMLQHPLTD 134
                 ***99******************************************93 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1065.29
//
Query:       EPA04755.1  [L=39]
Description: hypothetical protein BG20_I2195 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 252.41
//
Query:       EPA04756.1  [L=141]
Description: universal stress family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-22   80.7   0.0    1.6e-22   80.6   0.0    1.0  1  Usp       Universal stress protein family
  ------ inclusion threshold ------
        0.2   11.4   0.0       0.26   10.9   0.0    1.2  1  SAD_SRA   SAD/SRA domain


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.6   0.0   1.8e-26   1.6e-22       2     141 .]       4     141 .]       3     141 .] 0.97

  Alignments for each domain:
  == domain 1  score: 80.6 bits;  conditional E-value: 1.8e-26
                 -SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTCEEEEEEEESSHHHHHHHHHH CS
         Usp   2 ykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggvkvevvveegdpaeeilevae 100
                 +k+IlV++Dgs++s k l+ A   ak+++a++i ++v+  +   + + + e  ++  +e e   lea++     +++++    ++++ + + +i ++ +
  EPA04756.1   4 IKNILVPLDGSKSSLKGLRLASTIAKSSNAKIIGINVVRYSLGFHFPVSSEIKKKNTKEAESIILEAKK--SVMKDKVIFIGKILKGENIGKTIFDFLK 100
                 69*************************************************999999999999999885..99************************** PP

                 HTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
         Usp 101 eedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                  ++ dliV+Gsrg +  ++++lGSv++y+l+++++p ++V+
  EPA04756.1 101 TKKFDLIVIGSRGPNPGAEVFLGSVANYLLHKSKIPITIVK 141
                 ****************************************8 PP

>> SAD_SRA  SAD/SRA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   2.9e-05      0.26      23      67 ..      45      86 ..      39     105 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 2.9e-05
                TTSS--SS-SEEEE-GGGEEEEEE-S-STT-EEETTEEEEE-SSS CS
     SAD_SRA 23 agvHrplqagIsgskeegAvSivlsggYeddedegdeliYtGsgg 67
                 g+H p+ + I+ +++++A Si+l     ++  ++d++i+ G+  
  EPA04756.1 45 LGFHFPVSSEIKKKNTKEAESIILEA---KKSVMKDKVIFIGKIL 86
                79**********************74...3566788899988754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1115.69
//
Query:       EPA04757.1  [L=338]
Description: putative magnesium and cobalt transport protein CorA [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.4e-68  229.4   1.9    6.3e-68  229.2   1.9    1.0  1  CorA          CorA-like Mg2+ transporter protein
     0.0092   16.1   0.1       0.27   11.4   0.1    2.2  2  DUF1993       Domain of unknown function (DUF1993)
  ------ inclusion threshold ------
      0.029   14.5   1.9       0.15   12.2   0.9    2.6  2  T3SchapCesA   Type III secretion system filament chaperone Ce
       0.12   12.4   1.7        2.1    8.4   0.1    2.7  2  TTRAP         Putative tranposon-transfer assisting protein
       0.16   12.0   0.5       0.69   10.0   0.5    2.0  1  DUF1664       Protein of unknown function (DUF1664)
        0.2   11.2   5.1       0.27   10.7   4.0    1.7  2  DUF3169       Protein of unknown function (DUF3169)
       0.22   11.7   2.2        1.8    8.6   0.4    2.1  2  MnmE_helical  MnmE helical domain


Domain annotation for each model (and alignments):
>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  229.2   1.9   2.4e-71   6.3e-68       2     292 .]      31     332 ..      30     332 .. 0.95

  Alignments for each domain:
  == domain 1  score: 229.2 bits;  conditional E-value: 2.4e-71
        CorA   2 agfvWldlsspteeeleeLaeelgldelaledlldseerprvedyddylllvlpsveldkseeeeeevplsillgdnflitvrreplealdevikrlk. 99 
                 ++f W+dl++p++++ e+++e+++++ l++ed+++++e p++++yd++++++l+++ l  ++  +++++lsi++g++fl+tv++++l++l ++++ +k 
  EPA04757.1  31 KKFLWIDLQNPDRSDVEKVSEQYHFNALNIEDCMTKSELPKLDSYDEHFFVILHFPSLLRQPGISRNSQLSIFIGKDFLVTVHQGDLKPLVDLVSICKn 129
                 689***********************************************************************************************9 PP

        CorA 100 ......deggkpkspgellyrlldeivdrlfellekleeeldeledeledstkkeilrelaqlrrrlvklrralapnrevlkrllakaddkllddedke 192
                       +e+   k pg ll++++d +vd+l+++ +k+ ++ld+lede+  +++k+ +r++a lrr++  +rr+++p+++ + ++ ++     ++++  +
  EPA04757.1 130 dsdqqrKERLLGKLPGNLLHEIIDILVDDLLHISRKVIANLDDLEDEV-FDETKSAARSIALLRREINVMRRIANPLKKFVLEIAKNIKRFSYEEDIVL 227
                 987666666667889*********************************.6777899******************************999999******* PP

        CorA 193 ylrdlldelerllemlealrerleslqdtyssllserlNrvmkvLTvltaiflPlTlitGiyGmNfkglP.......elewsygypfvlllglmallai 284
                 y++d++d++++++e+le  re +e  +dt + l++e++N+v+  LT++ ++ +P T+i+++yGmN++ lP         + +y + f+++++++++ +i
  EPA04757.1 228 YFDDVIDHIDKVIETLEESRETMEIYKDTDFMLSTEKTNKVLAALTIIFTFAIPGTVIGTFYGMNIN-LPggindhsTVFGPY-TSFIIIILASLIPVI 324
                 *******************************************************************.**9887765555566.88899********** PP

        CorA 285 lllfwfkr 292
                 l++++f++
  EPA04757.1 325 LMFIYFRK 332
                 ******97 PP

>> DUF1993  Domain of unknown function (DUF1993)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.041     1e+02      65     121 ..     137     195 ..     113     213 .. 0.62
   2 !   11.4   0.1    0.0001      0.27      71     135 ..     217     281 ..     198     284 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.041
                 CHHCT-GS---.-S..-SSHHHHHHHHHHHHHHHHCS-GGGHCCCCCEEEE.C.CCCCE CS
     DUF1993  65 arlagkeppsl.ede.ektfadlrariaktialLesvdpekldakeekevelklggkel 121
                 +rl gk p +l  +     ++dl    +k+ia L+++++e +d++++ + ++ l  +e+
  EPA04757.1 137 ERLLGKLPGNLlHEIiDILVDDLLHISRKVIANLDDLEDEVFDETKSAARSIALLRREI 195
                 55555555555322224556788888899999999999999999888777776633333 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.0001
                 GS---.-S.-SSHHHHHHHHHHHHHHHHCS-GGGHCCCCCEEEE.C.CCCCEEEEHHHHHHHTHHH CS
     DUF1993  71 eppsl.edeektfadlrariaktialLesvdpekldakeekevelklggkeleftgeeyllefalP 135
                 +  s+ ed    f+d++++i+k+i+ Le+ ++e+++  ++++  l++++++  + + +++ +fa+P
  EPA04757.1 217 KRFSYeEDIVLYFDDVIDHIDKVIETLEE-SRETMEIYKDTDFMLSTEKTNKVLAALTIIFTFAIP 281
                 445553455888*****************.9999*******************************9 PP

>> T3SchapCesA  Type III secretion system filament chaperone CesA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.67   1.7e+03      72      86 ..      15      29 ..       9      33 .. 0.85
   2 ?   12.2   0.9   5.8e-05      0.15      34      90 ..     191     248 ..     148     252 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.67
  T3SchapCesA 72 dsalskieklietlk 86
                  sa s +e+ iet++
   EPA04757.1 15 KSASSTVERKIETIQ 29
                 589999******997 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 5.8e-05
  T3SchapCesA  34 vkesvnilsekaktdpqaaeklnkliegytygeerkly.dsalskieklietlkpars 90 
                  ++ ++n++   a+   +   ++ k i+ ++y e+  ly d  + +i+k+ietl+ +r 
   EPA04757.1 191 LRREINVMRRIANPLKKFVLEIAKNIKRFSYEEDIVLYfDDVIDHIDKVIETLEESRE 248
                  566677777777777777778999***********9987999***********99986 PP

>> TTRAP  Putative tranposon-transfer assisting protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1   0.00083       2.1      24      58 ..     148     181 ..     145     184 .. 0.87
   2 ?    2.3   0.2     0.063   1.6e+02      19      34 ..     238     256 ..     227     273 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00083
                 HHHSTTTS.-HHHHHHHHHHHHHHTT--HHHHHHH CS
       TTRAP  24 lkaalkyleddelreLaestlaKLkaltDaefael 58 
                 l++++  l  d+l+ ++ +++a L+ l+D+ f+e 
  EPA04757.1 148 LHEIIDIL-VDDLLHISRKVIANLDDLEDEVFDET 181
                 66777777.789********************985 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.063
                 HHHHHHHHSTTTS....-H CS
       TTRAP  19 elieelkaalkyl...edd 34 
                 ++ie+l++ ++ +   +d+
  EPA04757.1 238 KVIETLEESRETMeiyKDT 256
                 4555555555555555555 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.5   0.00027      0.69      45     122 ..     165     245 ..     157     254 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00027
     DUF1664  45 svskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseiged...vesvkeavegleskleriee 122
                 +v  +l+++ +++ +  +  ++ i+ + ++++ + +i++ +k+ v e+ +++++++ +   v   ++++ ++++ +e++ee
  EPA04757.1 165 KVIANLDDLEDEVFDETKSAARSIALLRREINVMRRIANPLKKFVLEIAKNIKRFSYEediVLYFDDVIDHIDKVIETLEE 245
                 667778888888888888888888888888888888888888888888888888865511244556777777777777765 PP

>> DUF3169  Protein of unknown function (DUF3169)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.91   2.3e+03      73      93 ..     162     182 ..     158     204 .. 0.83
   2 ?   10.7   4.0    0.0001      0.27       3      74 ..     267     333 ..     264     337 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.91
     DUF3169  73 kakkllkkwdeeddeeseeey 93 
                  ++k+++++d+ +de ++e++
  EPA04757.1 162 ISRKVIANLDDLEDEVFDETK 182
                 579999******999997765 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0001
     DUF3169   3 allkfillmliggliGgiiGfllgafeaekgleelsaalkelllligskilpllliiavlvviis.vvflrka 74 
                 ++l  + +++  ++ G +iG + g+      ++ l +++ ++++++g ++  +++i+a l+++i+ +++ rk+
  EPA04757.1 267 KVLAALTIIFTFAIPGTVIGTFYGMN-----IN-LPGGINDHSTVFGPYTSFIIIILASLIPVILmFIYFRKL 333
                 56677778888889999999999665.....34.789***********8888888899999999967777765 PP

>> MnmE_helical  MnmE helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.4   0.00072       1.8      22      80 ..     139     197 ..     128     207 .. 0.75
   2 ?    2.8   0.1     0.045   1.2e+02     127     186 ..     211     273 ..     198     278 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00072
                   xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  MnmE_helical  22 alrqleGel.skkikelrekllellaeleaaiDFpeedleelseeelaekleelkeelek 80 
                    l +l G+l ++ i+ l ++ll++  ++ a++D  e++  + +++++a++++ l++e++ 
    EPA04757.1 139 LLGKLPGNLlHEIIDILVDDLLHISRKVIANLDDLEDE-VFDETKSAARSIALLRREINV 197
                   456677775156677889******************88.455555678888888888875 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.045
                   xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxx RF
  MnmE_helical 127 aike.leleeieeeplltnaRhkealekalealeeakealeaglpldlv..aedLrealeaLg 186
                   +i++ +++ + ee+ +l     ++++ k++e lee +e++e + + d++  +e+ ++ l aL 
    EPA04757.1 211 EIAKnIKRFSYEEDIVLYFDDVIDHIDKVIETLEESRETMEIYKDTDFMlsTEKTNKVLAALT 273
                   343333322335568888889999999999999999999999987888777777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1203  (0.067098); expected 358.6 (0.02)
Passed bias filter:                      776  (0.0432818); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.49
# Mc/sec: 2074.84
//
Query:       EPA04758.1  [L=131]
Description: hypothetical protein BG20_I2198, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 831.13
//
Query:       EPA04759.1  [L=658]
Description: hypothetical protein BG20_I2200 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.9e-42  141.9  53.2    8.5e-21   74.5  18.8    4.8  4  Big_9            Bacterial Ig domain
    1.3e-28   99.4  50.2    3.9e-15   56.2  14.1    5.0  4  Cadherin_4       Bacterial cadherin-like domain
    1.1e-22   79.8  32.0    1.5e-11   44.1   8.9    4.3  4  Cadherin_5       Cadherin-like domain
  ------ inclusion threshold ------
      0.097   12.9   4.5       0.31   11.3   4.0    2.1  2  Cu-binding_MopE  Putative metal-binding motif
       0.12   12.4   5.2       0.89    9.6   0.0    3.5  3  Cadherin_3       Cadherin-like
        0.2   12.0   1.8        5.1    7.5   0.1    3.3  3  DUF3823          Protein of unknown function (DUF3823) N-term
        7.8    6.9  18.6        2.2    8.7   3.4    3.9  3  Invasin_D3       Invasin, domain 3


Domain annotation for each model (and alignments):
>> Big_9  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.3      0.32   8.1e+02      54      77 ..      90     113 ..      29     130 .. 0.59
   2 !   57.3   4.2   7.9e-19     2e-15      12      88 ..     350     423 ..     345     424 .. 0.86
   3 !   74.5  18.8   3.3e-24   8.5e-21       2      89 ..     430     515 ..     429     516 .. 0.95
   4 !   24.1   8.3   1.7e-08   4.4e-05       2      85 ..     521     634 ..     520     638 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.32
       Big_9  54 panGtvtinadgtltytpnagfsg 77 
                  +   +t  +dg  ++tp + f+g
  EPA04759.1  90 DEVKIATARDDGVNSFTPGTMFTG 113
                 333444444555555555555554 PP

  == domain 2  score: 57.3 bits;  conditional E-value: 7.9e-19
       Big_9  12 ndaPvavddsvtvtedsvla...ndtdpdgdaltvtsltvtlvtapanGtvtinadgtltytpnagfsgtdsftYtvsDg 88 
                 n+aP+a+dds+t++ed++l+    +td+++d+l+     + +v +p+   v++n+dgt++ytp+a+fsgt sf+++++Dg
  EPA04759.1 350 NTAPTAQDDSFTIPEDGSLSasaVATDAENDSLS-----YMIV-GPTPTGVVFNSDGTFSYTPAANFSGTISFQFKANDG 423
                 9*****************5544599999999996.....5565.55555688999************************9 PP

  == domain 3  score: 74.5 bits;  conditional E-value: 3.3e-24
       Big_9   2 atvtvtvtpvndaPvavddsvtvtedsv...landtdpdgdaltvtsltvtlvtapanGtvtinadgtltytpnagfsgtdsftYtvsDgs 89 
                 at+t+tvtpvnd P+a+d + t++ed++   l +  d+dgd++      ++l+t+++nG++++n+dgt+tytpn++f+g dsft+ ++Dg+
  EPA04759.1 430 ATITITVTPVNDIPTANDGTNTTPEDTPvngLVTGNDIDGDSI-----MFVLNTPTSNGSIVVNPDGTYTYTPNTNFNGVDSFTFVANDGT 515
                 8***************************9998899999***98.....57899************************************97 PP

  == domain 4  score: 24.1 bits;  conditional E-value: 1.7e-08
       Big_9   2 atvtvtvtpvndaPvavddsvtvt.........edsvlandtdpdgdaltvtsltvtlvta.................panGtvtinadgt.......l 67 
                 atvt+tvtpvnd+P  ++ ++t           + +++ n +d+dgd+ tvt  ++    +                  a G+v    +gt       +
  EPA04759.1 521 ATVTITVTPVNDPPQCSTPTATPYiwppnhkmvSIGATMNTSDVDGDTVTVTISSIF---QdeptnglgdgdtspdanLALGQVRAERSGTgdgrvyeI 616
                 8*******************7777676665555666699*********986533222...245688888888888888667777777777777778889 PP

       Big_9  68 tytpnagfsgtdsftYtv 85 
                 t t+++g+ gt s t++v
  EPA04759.1 617 TMTASDGHDGTCSGTIQV 634
                 999999999998888776 PP

>> Cadherin_4  Bacterial cadherin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.3      0.14   3.5e+02      42      70 ..      97     129 ..      32     130 .. 0.60
   2 !   34.7   5.1     8e-12     2e-08       9      72 .]     348     404 ..     334     404 .. 0.93
   3 !   56.2  14.1   1.5e-18   3.9e-15       1      72 []     430     495 ..     430     495 .. 0.95
   4 !   21.9   9.0   7.6e-08    0.0002       1      55 [.     521     576 ..     521     629 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.14
  Cadherin_4  42 DvdgddltvtavtvagtyGt....ltlnadGsf 70 
                   d++  ++t  t  + +G     + +n+dG+f
  EPA04759.1  97 ARDDGVNSFTPGTMFTGNGIdgqiVKVNPDGTF 129
                 3344444444444322233134458899***98 PP

  == domain 2  score: 34.7 bits;  conditional E-value: 8e-12
  Cadherin_4   9 gvndaPvavddsatvtedtpltitagnvlandtDvdgddltvtavtvagtyGtltlnadGsftY 72 
                 g n aP+a+dds+t++ed++l+       a +tD+++d+l++ +v   +t   +++n+dG+f+Y
  EPA04759.1 348 GCNTAPTAQDDSFTIPEDGSLSA-----SAVATDAENDSLSYMIVG--PTPTGVVFNSDGTFSY 404
                 569********************.....5789*************9..66677**********9 PP

  == domain 3  score: 56.2 bits;  conditional E-value: 1.5e-18
  Cadherin_4   1 atvtitvtgvndaPvavddsatvtedtpltitagnvlandtDvdgddltvtavtvagtyGtltlnadGsftY 72 
                 at+titvt+vnd P+a+d ++t++edtp+++     l + +D+dgd++ ++  t  +++G++++n+dG++tY
  EPA04759.1 430 ATITITVTPVNDIPTANDGTNTTPEDTPVNG-----LVTGNDIDGDSIMFVLNT-PTSNGSIVVNPDGTYTY 495
                 8******************************.....88888999999***9877.99*************** PP

  == domain 4  score: 21.9 bits;  conditional E-value: 7.6e-08
  Cadherin_4   1 atvtitvtgvndaPvavddsatv....tedtpltitagnvlandtDvdgddltvtavtv 55 
                 atvtitvt+vnd+P  +  +at     +    ++i   + + n +Dvdgd++tvt+ ++
  EPA04759.1 521 ATVTITVTPVNDPPQCSTPTATPyiwpPNHKMVSI---GATMNTSDVDGDTVTVTISSI 576
                 8**************99998874333366777888...8889*********99998874 PP

>> Cadherin_5  Cadherin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       2.7   6.9e+03      57      74 ..      97     114 ..      91     115 .. 0.83
   2 !   43.6   2.3   8.2e-15   2.1e-11       2      98 .]     350     437 ..     339     437 .. 0.77
   3 !   44.1   8.9     6e-15   1.5e-11       1      98 []     439     528 ..     439     528 .. 0.82
   4 !    5.7   2.0    0.0058        15      31      95 ..     559     634 ..     530     637 .. 0.58

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.7
  Cadherin_5  57 dngdGtftftpeanynGe 74 
                 +  dG  +ftp + ++G+
  EPA04759.1  97 ARDDGVNSFTPGTMFTGN 114
                 56799999***9999985 PP

  == domain 2  score: 43.6 bits;  conditional E-value: 8.2e-15
  Cadherin_5   2 ndaPvvssevtlaagseDtaltitaaqLL...anasDvdgdtLsvssltadaenGtvvdngdGtftftpeanynGevtlsYtvsDgeggtttatasltv 97 
                 n           a +++D ++ti ++  L   a a+D+++d+Ls   +  +     vv n+dGtf++tp+an++G+++++++ +Dge  +  at+++tv
  EPA04759.1 350 NT----------APTAQDDSFTIPEDGSLsasAVATDAENDSLSYMIVGPTP--TGVVFNSDGTFSYTPAANFSGTISFQFKANDGEFDSNVATITITV 436
                 34..........445555555555444331116689********99996555..557779***************************999999999999 PP

  Cadherin_5  98 a 98 
                 +
  EPA04759.1 437 T 437
                 6 PP

  == domain 3  score: 44.1 bits;  conditional E-value: 6e-15
  Cadherin_5   1 vndaPvvssevtlaagseDtaltitaaqLLanasDvdgdt.LsvssltadaenGtvvdngdGtftftpeanynGevtlsYtvsDgeggtttatasltva 98 
                 vnd P++++   ++++ eDt++       L    D+dgd+ + v +    ++nG++v n dGt+t+tp++n+nG  ++++  +Dg++++  at+++tv+
  EPA04759.1 439 VNDIPTANDG--TNTTPEDTPVN----G-LVTGNDIDGDSiMFVLNT--PTSNGSIVVNPDGTYTYTPNTNFNGVDSFTFVANDGTTNSNIATVTITVT 528
                 6788877754..56788888763....3.44558*****95666666..5558******************************************9996 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.0058
  Cadherin_5  31 anasDvdgdtLsvssltadaenGtvvdngdGtftftpeanyn.............Gev.tlsYtvsDgeggtttatasl 95 
                  n+sDvdgdt++v+  ++ +++    +ng G+    p+an               G v +++ t sDg+ gt++ t+++
  EPA04759.1 559 MNTSDVDGDTVTVTISSIFQDE---PTNGLGDGDTSPDANLAlgqvraersgtgdGRVyEITMTASDGHDGTCSGTIQV 634
                 599*******777655443311...223333334445555544333333333333655788888888888888777765 PP

>> Cu-binding_MopE  Putative metal-binding motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   4.0   0.00012      0.31      15      30 .]     331     347 ..     329     347 .. 0.96
   2 ?   -2.5   0.0       2.4     6e+03      17      28 ..     621     632 ..     613     632 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00012
  Cu-binding_MopE  15 EvC.DgvDnnCdGvvDe 30 
                      E+C D++Dn+ dG++De
       EPA04759.1 331 EICgDNIDNDRDGQIDE 347
                      9***************8 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.4
  Cu-binding_MopE  17 CDgvDnnCdGvv 28 
                       Dg D  C+G++
       EPA04759.1 621 SDGHDGTCSGTI 632
                      599999999975 PP

>> Cadherin_3  Cadherin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.4   3.6e+03      48      72 ..     376     400 ..     370     423 .. 0.50
   2 ?    2.6   1.3     0.052   1.3e+02       2      70 ..     427     488 ..     426     508 .. 0.57
   3 ?    9.6   0.0   0.00035      0.89       2      65 ..     518     584 ..     517     623 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.4
  Cadherin_3  48 DtppeeltytvvrgpsnGrlelkga 72 
                 D ++++l y +v +   G + + + 
  EPA04759.1 376 DAENDSLSYMIVGPTPTGVVFNSDG 400
                 5555566666666655554433222 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.052
  Cadherin_3   2 sepftleitikpvndeaPvlttntglrvlegsskvittenLsaeDeDtppeeltytvvrgpsnGrlelk 70 
                 s+  t++it++pvnd  P+    t  + +  + ++++    +   +D + +++++ + ++ snG ++++
  EPA04759.1 427 SNVATITITVTPVND-IPTANDGT--NTT-PEDTPVN-GLVTG--NDIDGDSIMFVLNTPTSNGSIVVN 488
                 56789999******9.55444333..222.2223332.23333..333333666666666666666655 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00035
  Cadherin_3   2 sepftleitikpvndeaPvlttntg.lrvlegsskvit.tenLsaeDeDtppeeltyt..vvrgpsnG 65 
                 s+  t++it++pvnd +P+ +t t    ++  ++k+++  ++++++D D ++  +t++  + ++p+nG
  EPA04759.1 518 SNIATVTITVTPVND-PPQCSTPTAtPYIWPPNHKMVSiGATMNTSDVDGDTVTVTISsiFQDEPTNG 584
                 66789**********.9999999965789988888888667777777777766665553244555665 PP

>> DUF3823  Protein of unknown function (DUF3823) N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.21   5.5e+02      37      51 ..     117     132 ..      99     134 .. 0.83
   2 ?    7.5   0.1     0.002       5.1      37      80 ..     390     436 ..     374     442 .. 0.84
   3 ?   -0.4   0.1      0.56   1.4e+03      46      77 ..     490     508 ..     478     524 .. 0.59

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.21
                 --EEEEB-TTSEE.EE CS
     DUF3823  37 epidvyvkqDGtf.nt 51 
                 +++ v+v+ DGtf n 
  EPA04759.1 117 DGQIVKVNPDGTFvNP 132
                 678899*******885 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.002
                 --EEEEB-TTSEEE...EEE-SEEEEEEE-TT-SSB-TT---EEEEE CS
     DUF3823  37 epidvyvkqDGtfn...tllFdGeYklvlkegegpfvkavdtievel 80 
                 +p+ v++++DGtf+   +  F+G+  + +k ++g f ++v ti++++
  EPA04759.1 390 TPTGVVFNSDGTFSytpAANFSGTISFQFKANDGEFDSNVATITITV 436
                 78999*******95333578****************99999999987 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.56
                 TSEEEEEE-SEEEEEEE-TT-SSB-TT---EE CS
     DUF3823  46 DGtfntllFdGeYklvlkegegpfvkavdtie 77 
                 D         G+Y  ++   +++f  +vd+ +
  EPA04759.1 490 D---------GTYTYTP---NTNFN-GVDSFT 508
                 4.........5555555...45555.555555 PP

>> Invasin_D3  Invasin, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.4    0.0034       8.8      49      94 ..     388     435 ..     355     439 .. 0.73
   2 ?    8.7   3.4   0.00085       2.2      33      94 ..     464     526 ..     460     529 .. 0.84
   3 ?   -0.2   1.1       0.5   1.3e+03      23      76 ..     568     628 ..     553     649 .. 0.49

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0034
  Invasin_D3  49 g.tlsavtdngdGtytatLtattagtatitptvnG...vaiaatatvtlt 94 
                 g t ++v  n+dGt ++t  a+ +gt++++++ n    ++  + at+t+t
  EPA04759.1 388 GpTPTGVVFNSDGTFSYTPAANFSGTISFQFKANDgefDS--NVATITIT 435
                 3577788999*********99***********95544444..44445444 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00085
  Invasin_D3  33 gnpvsgltvtfsttsagtlsavtdngdGtytatLtattagtatitptv.nGvaiaatatvtlt 94 
                 gn + g+++ f  +  ++ +++  n dGtyt+t   +  g+ ++t+   +G++ ++ atvt+t
  EPA04759.1 464 GNDIDGDSIMFVLNTPTSNGSIVVNPDGTYTYTPNTNFNGVDSFTFVAnDGTTNSNIATVTIT 526
                 8999*******988555778899************9999999999999455888888888876 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.5
  Invasin_D3  23 tltvtlkDangnp.vsglt.vtfsttsag.tlsavt....dngdG.tytatLtattagtati 76 
                 t+tvt+   +++  + gl     s + a  +l++v+      gdG +y+ t+ta+     t 
  EPA04759.1 568 TVTVTISSIFQDEpTNGLGdGDTSPD-ANlALGQVRaersGTGDGrVYEITMTASDGHDGTC 628
                 45555555444433333221222222.11233333311122233335666666655444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (658 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.68u 0.30s 00:00:00.98 Elapsed: 00:00:00.49
# Mc/sec: 4013.88
//
Query:       EPA04760.1  [L=115]
Description: hypothetical protein BG20_I2199 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 827.21
//
Query:       EPA04761.1  [L=200]
Description: hypothetical protein BG20_I2648, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); expected 358.6 (0.02)
Passed bias filter:                      584  (0.0325729); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1501.84
//
Query:       EPA04762.1  [L=368]
Description: peptidase, M50 family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-12   47.8  14.0    7.8e-09   35.2   0.4    2.8  2  Peptidase_M50  Peptidase family M50
  ------ inclusion threshold ------
      0.019   15.5   0.5      0.054   14.0   0.5    1.7  1  DUF3698        Protein of unknown function (DUF3698)


Domain annotation for each model (and alignments):
>> Peptidase_M50  Peptidase family M50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   7.2   6.9e-07    0.0062       4     108 ..     127     205 ..     124     235 .. 0.82
   2 !   35.2   0.4   8.7e-13   7.8e-09     188     247 ..     255     314 ..     219     318 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6.9e-07
                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX......XXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXX CS
                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Peptidase_M50   4 lllgilvvvHElGHflvAklcgvkveefsigfGpkllsfkkgeteYaiallp......LGGyVkmageepeeelseeeakaflkkspwqrllivlA 93 
                    l l+ ++ +HElGH+++Ak +++k                   ++++i+ lp      +G++++ +g   ++e                 + +++A
     EPA04762.1 127 LSLLGILGIHELGHIIAAKIHKLKTT-----------------WPFFIPGLPvigiptFGAFIQSRGLTINRE---------------ILFDVAIA 190
                    67889999****************94.................455555555555556*********995555...............899***** PP

                    XXXXXXXXXXXXXXX CS
                    xxxxxxxxxxxxxxx RF
  Peptidase_M50  94 Gplanfilailvfvv 108
                    Gp+a++++ai+v + 
     EPA04762.1 191 GPIAGLVIAIIVSIY 205
                    ***********9875 PP

  == domain 2  score: 35.2 bits;  conditional E-value: 8.7e-13
                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Peptidase_M50 188 lssflqllalisvnLgilNLlPipvLDGghllfalleairrkplserkeevanlvglall 247
                    + +++ ++a+i++ +++lNLlP ++LDGgh+++ ll a r++      ++++ l  + l+
     EPA04762.1 255 IMTPVLFAAWIGFLITFLNLLPAWQLDGGHMARTLLGAKRHRYATFGSMAILVLLNYWLM 314
                    568899**********************************88888888887777776666 PP

>> DUF3698  Protein of unknown function (DUF3698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.5     6e-06     0.054      25      95 ..      11     101 ..       3     113 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6e-06
     DUF3698  25 ktpeilfevGdYktenycleqGleel....................kvaikdf.kqklkekLksieeedlfeDkeWsprvlfalvlrkylyq 95 
                    ++lfev  ++ e y le  ++++                    k+ + +  k  + +k  ++++ + + ++ W+pr+lfa+v+   + +
  EPA04762.1  11 SLVNSLFEVSQFNREMYSLEFRIDDIdfkskfenlarkleninyvcKLEQMEDgKYIIIQKFTPKKQ-RKWLNTSWTPRILFAIVIAFVMID 101
                 5678999999999999999999998877777777777666666666444333303333445555444.4455558**********9766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2401.40
//
Query:       EPA04763.1  [L=494]
Description: proton-translocating NADH-quinone oxidoreductase, chain N [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-66  223.0  25.2    4.7e-66  223.0  25.2    2.4  2  Proton_antipo_M  Proton-conducting membrane transporter
  ------ inclusion threshold ------
       0.24   12.0   0.1       0.24   12.0   0.1    2.9  3  DUF5592          Family of unknown function (DUF5592)


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   5.9      0.15   1.4e+03      96     162 ..      65     125 ..       5     128 .. 0.61
   2 !  223.0  25.2   5.3e-70   4.7e-66       1     284 [.     127     414 ..     127     429 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.15
  Proton_antipo_M  96 saqvplhlWlpdayveaPtpvsallAatlvkagvlllirlllllavssneisqlllilaiismllgs 162
                      sa++   + + da  ++  ++ +l+ a+  ++g +  +r      + ++++++ l++l++i+m+l +
       EPA04763.1  65 SALFSEDVLVDDA-FGGFFAIAMLIVAIFTTVGSFNYMRK-----KNYPAVYYSLILLSTIGMVLVA 125
                      5555555545555.56666666666667777777766643.....5678899999999999999976 PP

  == domain 2  score: 223.0 bits;  conditional E-value: 5.3e-70
  Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskal..elglnslelllllllllvgl 92 
                      ++dL++l++++El+++p+y+L+g++kk+p+s+eA+lk+fl ++l+s i+++gi+l y+ltg++++ e+++      +   + +ll   ++++g+
       EPA04763.1 127 STDLVMLFVAWELMSIPTYVLVGFMKKNPSSNEAALKYFLFGALSSAIIVYGISLSYGLTGSTNIGEVIQGYatLDATLLPLALLSVGMFIAGF 220
                      78*****************************************************************9999855445556678888899999** PP

  Proton_antipo_M  93 lvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla.vssneisqlllilaiismllgslvalaqtdiKrllAySsishlGy 185
                       +K+++vp+h+Wlpd y++aP  +++llAa + kag  + ir+++l + v + +++  l ++a+++m +g+++a+ q ++ r+lAySsi+h Gy
       EPA04763.1 221 GFKMGLVPFHQWLPDTYEGAPPTITTLLAAGTKKAGFAATIRIVVLGMvVLNLDWTLALGVIAVMTMTIGNIAAIMQKNLARMLAYSSIAHAGY 314
                      ****************************999**************99989999***************************************** PP

  Proton_antipo_M 186 mlialav..atqygveaaiihllthalfkallFllagsviyerektrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaava 277
                      +li+lav   ++ g+++++ ++l ha++k + F+++ +++  +  ++ i++++gL  +mPi+a  l++ l++laG+Pp+agF+sk++++ +a++
       EPA04763.1 315 ILIGLAVspYSSLGLQGSLYQILNHAVMKGMAFIAVTGIVT-TLAVTHIDKLKGLGRRMPITAFGLVISLFALAGVPPLAGFWSKLMLFGGALD 407
                      *******7778899**********************99855.5599**********************************************99 PP

  Proton_antipo_M 278 vslillv 284
                      +++ + +
       EPA04763.1 408 AGSTIWW 414
                      8865444 PP

>> DUF5592  Family of unknown function (DUF5592)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   2.6e-05      0.24      37      79 ..      72     114 ..      62     119 .. 0.90
   2 ?   -2.1   0.1      0.66     6e+03      17      32 ..     125     140 ..     116     152 .. 0.70
   3 ?   -3.6   0.3       1.9   1.7e+04      27      32 ..     281     286 ..     260     303 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.6e-05
     DUF5592  37 slvhaslvvlfyifviilviflviksktNpklrnykalyLalv 79 
                  lv   +   f+i ++i++if+ + s    +++ny a+y +l+
  EPA04763.1  72 VLVDDAFGGFFAIAMLIVAIFTTVGSFNYMRKKNYPAVYYSLI 114
                 5788899999*****************************9886 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.66
     DUF5592  17 iyLtDlllllvllllt 32 
                  y tDl++l v+  l+
  EPA04763.1 125 AYSTDLVMLFVAWELM 140
                 5778888888876554 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 1.9
     DUF5592  27 vllllt 32 
                 v+ ++t
  EPA04763.1 281 VIAVMT 286
                 222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (494 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       979  (0.0546043); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.71u 0.34s 00:00:01.05 Elapsed: 00:00:00.52
# Mc/sec: 2832.37
//
Query:       EPA04764.1  [L=360]
Description: hypothetical protein BG20_I1733 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.56
# Mc/sec: 1941.19
//
Query:       EPA04765.1  [L=283]
Description: polyprenyl synthetase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-47  162.0   0.1    1.7e-47  161.6   0.1    1.1  1  polyprenyl_synt  Polyprenyl synthetase


Domain annotation for each model (and alignments):
>> polyprenyl_synt  Polyprenyl synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.6   0.1   9.5e-52   1.7e-47       3     200 ..      37     225 ..      35     234 .. 0.95

  Alignments for each domain:
  == domain 1  score: 161.6 bits;  conditional E-value: 9.5e-52
                      HHHHHHHHHHHSSS--HHHHHHHHHHHHHSCGHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEETTEE-HHHCTCHHHHHHHHHHHHHHHHH CS
  polyprenyl_synt   3 lleealeylveagGKrlRpllvllaaealkeeeeelekaavlawivellhaasLvhDDimDdsetRRGqpcahrlvGnklAindgdfllarafe 96 
                      ++ e+l+y +  gGKr+Rp+++ laae +++     ++ +++ ++ve+lh+ s++hDDi+D+ ++RR ++  h ++G ++++++gdf+l++++ 
       EPA04765.1  37 EFIEPLRYSL-EGGKRIRPIILSLAAESVGK---IDDNTLAASCAVEFLHMESIIHDDIIDNETMRRQKEPFHIKYGYNTSVLTGDFVLGLILA 126
                      577899****.*******************3...33789999**************************************************** PP

                      HHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHTTTTTCCC.SHHHHHHHHHHHTHHHCHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHH CS
  polyprenyl_synt  97 llaklfekslellelfsevllqtveGqlldleeekdddlskfsleeyleivkyKTaylfalpvalaallagasdeelealkdiglelGlaFQiq 190
                      + ++l  +++++++ ++++++ + eG++++ + e+++d++   +++yl++++yKTa  f+++++++a++a  s+ee+eal+++g+++G+a+Qi+
       EPA04765.1 127 ISSRL--DNARITKDLATTAMLMSEGEMIESRLESSEDIT---FDDYLKVIEYKTATAFEVAARIGAIIASGSEEEIEALTEYGKNIGIAYQIR 215
                      *****..99**********************888889999...****************************999******************** PP

                      HHHHHHHS-H CS
  polyprenyl_synt 191 DDylDlfgdp 200
                      DD+lD  +++
       EPA04765.1 216 DDLLDWKNED 225
                      *****98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1764.53
//
Query:       EPA04766.1  [L=100]
Description: hypothetical protein BG20_I1740, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0012   18.4   1.4     0.0015   18.2   1.4    1.1  1  NADH5_C   NADH dehydrogenase subunit 5 C-terminus


Domain annotation for each model (and alignments):
>> NADH5_C  NADH dehydrogenase subunit 5 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   1.4   8.2e-08    0.0015      89     180 ..       5      97 ..       2      99 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 8.2e-08
     NADH5_C  89 llkkslkl.nlssfssslwFlpslshrllsklsLklgqklakqlDqgWlEklgpkglaklllklskliqnlqkglikiyLlsflltlllllll 180
                 ++++++ +  ++ ++    +l+ ++   +   +L l+  ++  ++++ +++ + +g++k ++  +k++q +q+g  ++yL++f   ll+++l+
  EPA04766.1   5 FVNSNIFFyAIHKVILNRFYLNAIIYWCFVVAPLWLSRGVFRYFEKTAIDYGMNNGFQKAVSWSAKVVQGTQTGVAQSYLFVFGAGLLFVILI 97 
                 5555555568899999999*****************************************************************999998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       674  (0.0375927); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.34s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 602.84
//
Query:       EPA04767.1  [L=210]
Description: TENA/THI-4 family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-14   53.0   0.3    4.3e-14   52.8   0.3    1.0  1  TENA_THI-4       TENA/THI-4/PQQC family
    8.4e-13   48.5   0.0      1e-12   48.2   0.0    1.1  1  Haem_oxygenas_2  Iron-containing redox enzyme
     0.0075   16.5   0.1      0.028   14.6   0.0    1.8  2  DUF2812          Protein of unknown function (DUF2812)


Domain annotation for each model (and alignments):
>> TENA_THI-4  TENA/THI-4/PQQC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.8   0.3   7.2e-18   4.3e-14      10     208 ..      15     206 ..       4     208 .. 0.81

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 7.2e-18
                 HHHCSHHHHHHHTT-S-HHHHHHHHHHHHHHHHHHHHHHHHHHHC-SSHHHHHHHHHHHHHHHHCHHHHHHHHHHHTT-HHHHHCTTT--HHHHHHHHH CS
  TENA_THI-4  10 eyinHpFvkalakGtlpreqfqayviqdylylknfvrvlaiilskssdlevrrelesrivdhdgeeielhlrlaealGlsreelsktkpspatkayvry 108
                 ++ +HpF++++++G+l+ +++ +y ++++  +k+ + ++  i  k+++     el+++  + ++++i+ + ++  +lG+s+ el ++k +++t+  v  
  EPA04767.1  15 SLLKHPFYQMWSDGKLNLDSLAGYSKEYFQLVKAVPSFMTPIIEKAPNHVIN-ELINNQ-QEESDHIKSWIKFSGELGVSENELINYKGLEKTRKSVMD 111
                 3445********************************************9999.888875.557889******************************998 PP

                 HHHHHCHS-HHHHHHHHHHHHHHHHHHH.HHHCCHHH..S-TSCHHHHHHHHHCSHHHHHHHHHHHHHHHHHHHTSHHHHHHHHHHHHHHHHHHHHHHH CS
  TENA_THI-4 109 lldlarrgslaeavaallpclfvyqeia.erlkeklr..alegpeyyewvkeyaseefraaveeakrllerllakvsdeqleelqeiflkalefetsfl 204
                 l +l ++  +   ++a+++++  +  i+ ++l+++ +    + +e  e++k +++++ r+a ++ k++le +  +      + l +i+ k+  +    l
  EPA04767.1 112 LSELMST--YEGGACAMYAFEKEIPKISqTKLDGLAEfyGISTEEATEYFKLHTEADIRHAASW-KNILEKASSD-----SDNLIQIADKSISAQNLLL 202
                 8888665..5688999999999888887689998888777777778888888888888888888.5555444333.....4667777777777666666 PP

                 HHHH CS
  TENA_THI-4 205 tmal 208
                 ++ +
  EPA04767.1 203 DSCY 206
                 6655 PP

>> Haem_oxygenas_2  Iron-containing redox enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.2   0.0   1.7e-16     1e-12       3     161 ..      38     186 ..      36     199 .. 0.85

  Alignments for each domain:
  == domain 1  score: 48.2 bits;  conditional E-value: 1.7e-16
  Haem_oxygenas_2   3 flrqrapyklvfgdwlalvhsrltdrevkrallenlsEElGdgdlernHvelyrrllkalGldeeplealpel.petlalinlfeavalsrrll 95 
                      + ++++ +++  +  ++ ++ + + ++v ++l+ n+ EE         H + + ++  +lG++e++l + + l ++   +++l e +   +   
       EPA04767.1  38 YSKEYFQLVKAVPSFMTPIIEKAP-NHVINELINNQQEESD-------HIKSWIKFSGELGVSENELINYKGLeKTRKSVMDLSELMSTYE--- 120
                      667899999999************.**************94.......*************************544455555544333322... PP

  Haem_oxygenas_2  96 gallGallalEllvsletlklaeelre.lgldeea.peyfdlHvtiDnaHaamaleaviellateepe 161
                       + ++a++a+E   +++ +  +++l e +g++ e+ +eyf+lH ++D  Haa +  +++e++ +++++
       EPA04767.1 121 -GGACAMYAFEKEIPKISQTKLDGLAEfYGISTEEaTEYFKLHTEADIRHAASWK-NILEKASSDSDN 186
                      .3489999***********************99888******************8.****99988733 PP

>> DUF2812  Protein of unknown function (DUF2812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.35   2.1e+03      75     103 ..      56      84 ..      39      89 .. 0.79
   2 !   14.6   0.0   4.7e-06     0.028      25      82 ..     125     183 ..     118     203 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.35
     DUF2812  75 ifrkeedgkpfelytDeesklekykrlrk 103
                 i++k+ ++  +el ++++++ +++k++ k
  EPA04767.1  56 IIEKAPNHVINELINNQQEESDHIKSWIK 84 
                 66777777888899999999998888755 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 4.7e-06
     DUF2812  25 lgyeFekgepkeyryrvdyike...kskeeseeylelleesGweyvakskewlifrkeedg 82 
                  +y Fek  pk  + ++d   e    s+ee+ ey++l+ e+ +++ a++k+  i++k++++
  EPA04767.1 125 AMYAFEKEIPKISQTKLDGLAEfygISTEEATEYFKLHTEADIRHAASWKN--ILEKASSD 183
                 34****************9999999899*********************96..55555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       777  (0.0433376); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1435.09
//
Query:       EPA04768.1  [L=72]
Description: hypothetical protein BG20_I1731 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.39   10.8   5.2       0.46   10.5   5.2    1.1  1  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
        1.3    7.7   4.0        1.5    7.5   4.0    1.0  1  DUF2207          Predicted membrane protein (DUF2207)


Domain annotation for each model (and alignments):
>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   5.2   5.1e-05      0.46      42      90 ..       9      62 ..       4      70 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 5.1e-05
  Phage_holin_3_6 42 aagvlallalllllvalalala.a....lwlaali.vaavllvlagvlalvglkk 90
                     ++ +++++++++l + l l+l+ +    l l+ l+  +++l v+a++  +++  k
       EPA04768.1  9 ITIFVLCITAFFLYAYL-LMLSeWspivLQLSILMiAGGILGVVAWIGYVMATTK 62
                     33334444444444444.4444445555566666624578888888877777655 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   4.0   0.00016       1.5     384     430 ..       8      59 ..       2      66 .. 0.60

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00016
     DUF2207 384 salglgliilglilillallllvll..........lvfllilllillliaiivlllf 430
                 ++ +++l+i +++     l+++ l+          l++l+i + il+++a+i ++++
  EPA04768.1   8 GITIFVLCITAFF-----LYAYLLMlsewspivlqLSILMIAGGILGVVAWIGYVMA 59 
                 3333333333333.....333333344567888888888888888888888888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       927  (0.0517039); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 551.17
//
Query:       EPA04769.1  [L=103]
Description: hypothetical protein BG20_I1730, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-05   23.4   0.0    5.7e-05   22.9   0.0    1.2  1  Met_10           Met-10+ like-protein
  ------ inclusion threshold ------
      0.074   12.7   0.0      0.081   12.6   0.0    1.2  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F


Domain annotation for each model (and alignments):
>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   6.4e-09   5.7e-05     155     199 .]       2      49 ..       1      49 [. 0.94

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 6.4e-09
                 EEES-GGG---...TT-EEEEEE--TTTGGGGHHHHHHHEEEEEEEEE CS
      Met_10 155 pileDgrevir...eqladrvvmnlpksaieFldkvlaalkdggvihy 199
                 +i++D++++i+   +++ dr +m lp+++ eFl++++++ k gg+ihy
  EPA04769.1   2 SINGDAAKIIQeqlKNKSDRTLMLLPERSDEFLKSAIDTTKSGGIIHY 49 
                 799*******977778899****************************9 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0     9e-06     0.081     104     136 ..      17      49 ..       6      84 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9e-06
                      H--HHHHHHHHHHHHHHHHHHCCCEEEEEEEEE CS
  Methyltr_RsmB-F 104 rrkekdiaqlaklqkellsaaidllkkgGvlvY 136
                      ++++++++ l ++  e l++aid++k+gG++ Y
       EPA04769.1  17 NKSDRTLMLLPERSDEFLKSAIDTTKSGGIIHY 49 
                      6899999***********************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 776.44
//
Query:       EPA04770.1  [L=165]
Description: putative ribosomal-protein-alanine acetyltransferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-20   71.6   0.2    7.7e-20   71.3   0.2    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    1.7e-14   54.0   0.6    1.7e-14   54.0   0.6    1.4  2  Acetyltransf_7   Acetyltransferase (GNAT) domain
    1.3e-12   47.8   0.3    1.9e-12   47.2   0.3    1.3  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    1.2e-09   38.0   0.2    4.9e-09   36.0   0.1    1.8  2  FR47             FR47-like protein
    0.00074   19.2   0.0     0.0025   17.5   0.0    1.9  1  Acetyltransf_8   Acetyltransferase (GNAT) domain
      0.001   19.7   0.0     0.0014   19.3   0.0    1.3  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
     0.0015   18.2   0.0     0.0023   17.6   0.0    1.3  1  GNAT_acetyltran  GNAT acetyltransferase
  ------ inclusion threshold ------
       0.01   15.9   0.0      0.021   14.9   0.0    1.7  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
      0.011   15.9   0.3      0.014   15.5   0.3    1.4  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
      0.015   15.0   0.0       0.02   14.5   0.0    1.2  1  DUF4821          Domain of unknown function (DUF4821)
      0.024   14.7   0.1      0.048   13.8   0.1    1.6  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.3   0.2   4.7e-23   7.7e-20       5     117 .]      25     141 ..      21     141 .. 0.91

  Alignments for each domain:
  == domain 1  score: 71.3 bits;  conditional E-value: 4.7e-23
                     HHHHHHHTHHHHHHHHHHHHHHHHHSTTCEEEEEEETTEEEEEEEEEEEET.......TSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHT CS
  Acetyltransf_1   5 vellvesffppnedaseeefeesfsleaegllvaeedgeliGfisllkipd.......ekggvayieslaVspeyrgkGlGsaLlealeeraree 92 
                     +e+  ++ +++++d ++e        ++e ++vae +g+ +G+i+++  +           +++++ s+aV  e+r+kG+G+aL+e+ +  +r +
      EPA04770.1  25 MEINLKTLPEHYSDYFYESLLAE---IPEAFIVAEIGGKHVGYIMCKTEYGfsnfkklGFVKKGHVVSIAVLQEHRKKGIGKALVEESVNGVRLK 116
                     56666677788888888887777...8999****************************8889****************************99999 PP

                     TESEEEEEEETTEHHHHHHHHHTTE CS
  Acetyltransf_1  93 gikkivlaveedndaairlYeklGF 117
                      +++ +l+v+ +n+ a+rlYeklGF
      EPA04770.1 117 KCDEFYLEVRCSNNEAVRLYEKLGF 141
                     ************************9 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       8.6   1.4e+04      67      72 ..      39      44 ..      24      44 .. 0.60
   2 !   54.0   0.6     1e-17   1.7e-14       3      75 ..      50     142 ..      48     143 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 8.6
                    HHHHHT CS
  Acetyltransf_7 67 kfYekl 72
                     fYe+l
      EPA04770.1 39 YFYESL 44
                    388875 PP

  == domain 2  score: 54.0 bits;  conditional E-value: 1e-17
                     EEEEEEEETTEEEEEEEEEEES.............TCTEE...EEE-GGGTTSSHHHHHHHH......TTSEEEEE.EEEE..THHHHHHHHHHT CS
  Acetyltransf_7   3 gevfVaeddgkivGfialslld.............aeitr...laVdpeyrgkGiGraLlea......aekgiile.qlel..naekaikfYekl 72 
                     + ++Vae +gk+vG+i ++ +              +   +   +aV++e+r+kGiG+aL+e         k++  e +le+  ++++a+++Yekl
      EPA04770.1  50 EAFIVAEIGGKHVGYIMCKTEYgfsnfkklgfvkkG---HvvsIAVLQEHRKKGIGKALVEEsvngvrL-KKCD-EfYLEVrcSNNEAVRLYEKL 139
                     5699************99999999999888775544...1456******************74333220.3343.223333555559******** PP

                     TEE CS
  Acetyltransf_7  73 GFe 75 
                     GF+
      EPA04770.1 140 GFV 142
                     **8 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.2   0.3   1.2e-15   1.9e-12      28     109 ..      47     144 ..      25     164 .. 0.81

  Alignments for each domain:
  == domain 1  score: 47.2 bits;  conditional E-value: 1.2e-15
  Acetyltransf_10  28 egealllvaeeggkivGviel.rdgs.............hisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yavpfYeklG 105
                      e    ++vae ggk+vG+i   ++ +             h+  ++V +e+r++GigkaL+e+  + ++ ++  +  l+v+ s+ +av++YeklG
       EPA04770.1  47 EIPEAFIVAEIGGKHVGYIMCkTEYGfsnfkklgfvkkgHVVSIAVLQEHRKKGIGKALVEESVNGVRLKKCDEfYLEVRCSNnEAVRLYEKLG 140
                      445679*************774444488999***********************************999999999****99999********** PP

  Acetyltransf_10 106 Fkav 109
                      F+  
       EPA04770.1 141 FVIR 144
                      *976 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.35   5.6e+02      67      80 ..      71      84 ..      28      88 .. 0.67
   2 !   36.0   0.1     3e-12   4.9e-09      22      80 ..      85     144 ..      82     152 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.35
                HHHHHHHHHT-EEE CS
        FR47 67 psirlyeklGfeki 80
                   + ++klGf k 
  EPA04770.1 71 YGFSNFKKLGFVKK 84
                55566999999775 PP

  == domain 2  score: 36.0 bits;  conditional E-value: 3e-12
                 SSEEEEEE-GGG-SSSHHHHHHHHHHHHHHH.S-S-EEEEEETT-HHHHHHHHHHT-EEE CS
        FR47  22 gelgalqvlpehrrrGlgsrlvkalakeiae.rgktvllvvvasNtpsirlyeklGfeki 80 
                 g + ++ vl+ehr++G g+ lv++  ++++  + ++  l v+ sN+++ rlyeklGf  +
  EPA04770.1  85 GHVVSIAVLQEHRKKGIGKALVEESVNGVRLkKCDEFYLEVRCSNNEAVRLYEKLGFVIR 144
                 788899***********************98688899999*****************766 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.5e-06    0.0025      30     142 ..      36     146 ..      24     149 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.5e-06
                     HHHHHHHHHC.STTEEEEEEEETTEEEEEEEEEEGGGCGGGGCS---TT-EEEEEEES.SHHHCTTTCHHHHHHHHHHHHHCCTT--EEEE--BT CS
  Acetyltransf_8  30 evrellakldadphsepliglldgepvgyfeiYwakedelaeyydaepgdrGiHllig.eaeargkglttallralvhylfadprtrrvvvEPdv 123
                       +++++ l a+     +++++ g+ vgy+ +    e   +++++      G  + i+  +e+r+kg+++al+++ v+ + ++ +++   +E + 
      EPA04770.1  36 YSDYFYESLLAEIPEAFIVAEIGGKHVGYIMCK--TEYGFSNFKKLGFVKKGHVVSIAvLQEHRKKGIGKALVEESVNGVRLK-KCDEFYLEVRC 127
                     556677777777777777777777777777773..4444566666666666666777755789*****************998.9********** PP

                     T-HHHHHHHHHTT-EEEEE CS
  Acetyltransf_8 124 rNerairllekaGfekeke 142
                     +N +a+rl+ek+Gf+ +++
      EPA04770.1 128 SNNEAVRLYEKLGFVIRQK 146
                     **************98765 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   8.6e-07    0.0014      35     138 .]      46     142 ..      10     142 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 8.6e-07
  Acetyltransf_3  35 eeaeewlerawaeeseeegygwaivlkdtgviGsvglrdleeedeeaelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSi 129
                     +e  e +    a e  ++ +g+++++    + G+ ++ +l    +   +++ + ++++ kG+++  v+  ++ + +  + ++++ ++  +N   +
      EPA04770.1  46 AEIPEAFI--VA-EIGGKHVGYIMCKT---EYGFSNFKKLGFVKKGHVVSIAVLQEHRKKGIGKALVEESVNGV-RLKKCDEFYLEVRCSNNEAV 133
                     33333333..11.22235566777633...358888888887777688999999********************.8889**************** PP

  Acetyltransf_3 130 rvleklGfe 138
                     r++eklGf+
      EPA04770.1 134 RLYEKLGFV 142
                     *******95 PP

>> GNAT_acetyltran  GNAT acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.4e-06    0.0023     177     243 .]      81     150 ..      59     150 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.4e-06
  GNAT_acetyltran 177 vyekgieieidTkedyrrkgLAtivaaalileclkr...glyPsWDaaneaSvaLaekLGYefekeYkvy 243
                       ++kg+ ++i+  +++r+kg  +++ ++ ++    +   + y +  + n+++v+L+ekLG+   ++ ++y
       EPA04770.1  81 FVKKGHVVSIAVLQEHRKKGIGKALVEESVNGVRLKkcdEFYLEVRCSNNEAVRLYEKLGFVIRQKLNAY 150
                      6789******************9999998865432212257888899***************99999887 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.3e-05     0.021      69     124 ..      80     140 ..      12     143 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.3e-05
                     EEEEEEEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--.....SSHHHHHTTT CS
  Acetyltransf_9  69 ktlkaagvtgVavapehrgrgvlskLlaraleemreegqplsllfP.....ssipiYrrfG 124
                       +k + v+++av  ehr++g+ ++L++++++ +r ++    +l        ++++Y+++G
      EPA04770.1  80 GFVKKGHVVSIAVLQEHRKKGIGKALVEESVNGVRLKKCDEFYLEVrcsnnEAVRLYEKLG 140
                     5578899**********************99888776655555554444433356666666 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.3   8.6e-06     0.014      67     151 ..      74     158 ..      13     162 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 8.6e-06
  Acetyltransf_4  67 gqfkkr.akdwkaelsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhkalGFelvgifkkcikkngrwi 151
                     ++fkk    ++   +s+ +  +  +k+g+g++l++  ++  +     +++ e+  +n +++ ++++lGF + ++++ ++ ++   +
      EPA04770.1  74 SNFKKLgFVKKGHVVSIAVL-QEHRKKGIGKALVEESVNGVRLKKCDEFYLEVRCSNNEAVRLYEKLGFVIRQKLNAYYRDGEDAY 158
                     35666653344445666666.579************************************************99999988877666 PP

>> DUF4821  Domain of unknown function (DUF4821)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.2e-05      0.02     182     243 ..      15      71 ..       7      79 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.2e-05
     DUF4821 182 kArvEDhDDlveiferqseelreefGdyflaelieaqdeenkaiVaevegkavGllslstdv 243
                 +A +    Dl++++e + ++l e + dyf   l+++    + +iVae+ gk vG ++ +t+ 
  EPA04770.1  15 RAEP---SDLIPVMEINLKTLPEHYSDYFYESLLAEIP--EAFIVAEIGGKHVGYIMCKTEY 71 
                 4444...589999999**************99999887..8999**********99988875 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   2.9e-05     0.048      12      54 ..      71     114 ..      55     128 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.9e-05
  Acetyltransf_CG  12 vafleYe....vrkegvldfthTeVpeelrGkGiAkkLvkaalddar 54 
                      ++f +++    v+   + ++  + V +e+r kGi+k+Lv++ ++ +r
       EPA04770.1  71 YGFSNFKklgfVK---KGHVVSIAVLQEHRKKGIGKALVEESVNGVR 114
                      5666665222222...33566789*****************999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1046.26
//
Query:       EPA04771.1  [L=201]
Description: orotate phosphoribosyltransferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.5e-15   55.9   0.2    4.7e-15   55.5   0.2    1.2  1  Pribosyltran  Phosphoribosyl transferase domain
    0.00036   20.1   0.1    0.00059   19.4   0.1    1.4  1  PRTase_2      Phosphoribosyl transferase
    0.00055   19.4   0.3    0.00078   18.9   0.3    1.2  1  UPRTase       Uracil phosphoribosyltransferase
     0.0087   15.9   0.4      0.014   15.3   0.2    1.5  2  SmpB          SmpB protein


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.5   0.2   1.1e-18   4.7e-15      15     135 ..      50     162 ..      43     182 .. 0.89

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 1.1e-18
                   EEETTEEEEEE.--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE----TTSEEEEE-SEESSSHHHHHHHHHH CS
  Pribosyltran  15 varlaaeilee.yngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrlledpagkkVliVDDildtGgTllaalelL 110
                   +++l  +i+++    + d +v +++gG+++a++la e   pl yvr++ ++ ++s ++            +++g+kV+++DD+ +tGg++ +a++ L
    EPA04771.1  50 IKHLQNNIIDNtGLDRFDSLVSVPTGGLIIASALAIETVKPLIYVRSKPKDYGTSKSV---------EGQITKGMKVVMIDDVATTGGSVVNAIKSL 137
                   6666677777766678999***************************************.........6899************************** PP

                   HCC-BSEEEEEEEEE-HHHHHHHHH CS
  Pribosyltran 111 kekgpeevriavlvdkpateeevdk 135
                   +e +  +  + v+v++++++ee  k
    EPA04771.1 138 RESDIVIEDAYVIVNRMEGAEETLK 162
                   ****999999999999999988655 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   1.3e-07   0.00059     116     160 ..     109     155 ..      97     184 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.3e-07
    PRTase_2 116 ellaaakelvLvDDEistGktalnliralqek..lprkryvvvslvd 160
                  ++++  ++v++DD ++tG +++n i++l+e+  + ++ yv+v+ ++
  EPA04771.1 109 GQITKGMKVVMIDDVATTGGSVVNAIKSLRESdiVIEDAYVIVNRME 155
                 56778889**********************98655669999987555 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.3   1.7e-07   0.00078     104     168 ..      86     163 ..      68     189 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.7e-07
     UPRTase 104 etlepveyynkLPkki.aert...........vlllDpviaTGgsaaaaiqlLkergvgeekIlvl.svl.aseegvkr 168
                 et +p +y+   Pk+  + ++           v+++D v  TGgs+++ai+ L+e ++  e+  v+ + +  +ee +k+
  EPA04771.1  86 ETVKPLIYVRSKPKDYgT-SKsvegqitkgmkVVMIDDVATTGGSVVNAIKSLRESDIVIEDAYVIvNRMeGAEETLKE 163
                 566777777777777743.3336777777777***********************998776644430222134444444 PP

>> SmpB  SmpB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       1.8   8.3e+03     105     122 ..      12      30 ..       8      31 .. 0.70
   2 !   15.3   0.2   3.1e-06     0.014      28      87 ..     134     196 ..     125     201 .] 0.76

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.8
                 .ESSEEEE.EEEEEEC--S CS
        SmpB 105 kkkglvKv.eialakgkkl 122
                  +kg++K  + +la gkk+
  EPA04771.1  12 YQKGVIKFgDFTLASGKKS 30 
                 4567888746889999985 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 3.1e-06
                 HHHHHH--EESSSEEEEEESS...CEEEEESEE---S--SS--.--TT--EEBB--HHHHHHHH CS
        SmpB  28 vkslragkvnlkdsyvkikng...elfllnvhiseyekgnifn.hdpkrkrkLLlhkkeikkla 87 
                 +kslr+  + ++d+yv +++    e  l+++ ++ y+  ni + +++  ++kL ++ + ++k++
  EPA04771.1 134 IKSLRESDIVIEDAYVIVNRMegaEETLKELGVKMYSLVNIIQiTQALHEQKL-VSDDILEKVR 196
                 9***************99854223789***********888884666666665.4555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       770  (0.0429472); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 1196.73
//
Query:       EPA04772.1  [L=131]
Description: hypothetical protein BG20_I2240, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 957.32
//
Query:       EPA04773.1  [L=569]
Description: hypothetical protein BG20_I2238 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-20   72.5  24.3      9e-16   58.4   2.7    3.9  3  Big_9            Bacterial Ig domain
    2.7e-13   50.3  23.8    4.2e-09   36.9   1.4    4.2  3  Cadherin_4       Bacterial cadherin-like domain
    4.5e-11   42.6  14.4    4.6e-11   42.6   1.8    3.5  3  Cadherin_5       Cadherin-like domain
  ------ inclusion threshold ------
       0.27   11.4   6.2       0.46   10.7   4.6    2.2  2  Cu-binding_MopE  Putative metal-binding motif


Domain annotation for each model (and alignments):
>> Big_9  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.5       0.1   4.7e+02      16      67 ..      74     130 ..      54     133 .. 0.62
   2 !   58.4   2.7     2e-19     9e-16      11      88 ..     351     425 ..     346     426 .. 0.87
   3 !   21.4   7.1   7.2e-08   0.00032       2      85 ..     432     545 ..     431     549 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.1
       Big_9  16 vavdds......vtvtedsvlandtdpdgdaltvtsltvtlvtapanGtvtinadgtl 67 
                 va+d +      ++  +d+v   +t  d+   ++t  t+ + ++ ++  v in+dgt+
  EPA04773.1  74 VAADGThspfsaISGLTDEV-KIATARDDGVNSFTPGTLFTGNGIDGQIVKINPDGTF 130
                 44444444422222223333.3444455555566777777777788888888888887 PP

  == domain 2  score: 58.4 bits;  conditional E-value: 2e-19
       Big_9  11 vndaPvavddsvtvtedsvla...ndtdpdgdaltvtsltvtlvtapanGtvtinadgtltytpnagfsgtdsftYtvsDg 88 
                  n+aP+a+dds+t+ ed++l+    +td+++d+l+     + +v +p+   v++n+dgt++ytp+a+fsgt sf+++++Dg
  EPA04773.1 351 CNTAPTAQDDSFTILEDGSLSasaIATDAENDSLS-----YMIV-GPTPAGVVFNSDGTFSYTPAANFSGTISFQFKANDG 425
                 59*****************5555599******996.....5555.666777999**************************9 PP

  == domain 3  score: 21.4 bits;  conditional E-value: 7.2e-08
       Big_9   2 atvtvtvtpvndaPvavddsvtvt.........edsvlandtdpdgdaltvtsltvtlvta.................panGtvtinadgt.......l 67 
                 at+t+ vtpvndaP  ++ s+t           + +++ n +d+dgd+ tvt  ++    +                  a G+v    +gt       +
  EPA04773.1 432 ATITIIVTPVNDAPQCSTPSATPYiwppnhkmvSIGATMNTSDVDGDTVTVTISSIF---QdeptnglgdgdtspdanLALGQVRAERSGTgdgrvyvI 527
                 8*******************7777676665555666699*********986533222...246689999999999999777777777777788889999 PP

       Big_9  68 tytpnagfsgtdsftYtv 85 
                 t t+++g+ gt s t++v
  EPA04773.1 528 TMTASDGHDGTCSGTVQV 545
                 999999999999999987 PP

>> Cadherin_4  Bacterial cadherin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.5     0.045     2e+02      41      70 ..      97     130 ..      48     131 .. 0.65
   2 !   36.9   1.4   9.4e-13   4.2e-09       9      72 .]     350     406 ..     346     406 .. 0.93
   3 !   19.1   8.4   3.3e-07    0.0015       1      55 [.     432     487 ..     432     546 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.045
  Cadherin_4  41 tDvdgddltvtavtvagtyGt....ltlnadGsf 70 
                 t  d++  ++t  t+ + +G     + +n+dG+f
  EPA04773.1  97 TARDDGVNSFTPGTLFTGNGIdgqiVKINPDGTF 130
                 334555555555554333442333588******9 PP

  == domain 2  score: 36.9 bits;  conditional E-value: 9.4e-13
  Cadherin_4   9 gvndaPvavddsatvtedtpltitagnvlandtDvdgddltvtavtvagtyGtltlnadGsftY 72 
                 g n aP+a+dds+t+ ed++l+       a +tD+++d+l++ +v   +t   +++n+dG+f+Y
  EPA04773.1 350 GCNTAPTAQDDSFTILEDGSLSA-----SAIATDAENDSLSYMIVG--PTPAGVVFNSDGTFSY 406
                 569********************.....4779*************9..88899**********9 PP

  == domain 3  score: 19.1 bits;  conditional E-value: 3.3e-07
  Cadherin_4   1 atvtitvtgvndaPvavddsatv....tedtpltitagnvlandtDvdgddltvtavtv 55 
                 at+ti vt+vndaP  +  sat     +    ++i   + + n +Dvdgd++tvt+ ++
  EPA04773.1 432 ATITIIVTPVNDAPQCSTPSATPyiwpPNHKMVSI---GATMNTSDVDGDTVTVTISSI 487
                 8**************99999874333366777888...8889*********99998874 PP

>> Cadherin_5  Cadherin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1      0.82   3.7e+03      59      74 ..     100     115 ..      86     132 .. 0.64
   2 !   42.6   1.8     1e-14   4.6e-11      13      97 ..     353     438 ..     341     439 .. 0.74
   3 !    6.3   2.2    0.0021       9.3      31      95 ..     470     545 ..     441     548 .. 0.52

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.82
  Cadherin_5  59 gdGtftftpeanynGe 74 
                  dG  +ftp + ++G+
  EPA04773.1 100 DDGVNSFTPGTLFTGN 115
                 4555666665555553 PP

  == domain 2  score: 42.6 bits;  conditional E-value: 1e-14
  Cadherin_5  13 laagseDtaltitaa.qLL..anasDvdgdtLsvssltadaenGtvvdngdGtftftpeanynGevtlsYtvsDgeggtttatasltv 97 
                 +a +++D ++ti ++ +L   a a+D+++d+Ls   +  +   + vv n+dGtf++tp+an++G+++++++ +Dge  +  at+++ v
  EPA04773.1 353 TAPTAQDDSFTILEDgSLSasAIATDAENDSLSYMIVGPTP--AGVVFNSDGTFSYTPAANFSGTISFQFKANDGEFDSNVATITIIV 438
                 3344444444444330444114579999*****99996555..778889**************************9888888888766 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0021
  Cadherin_5  31 anasDvdgdtLsvssltadaenGtvvdngdGtftftpeanyn.............Gev.tlsYtvsDgeggtttatasl 95 
                  n+sDvdgdt++v+  ++ +++    +ng G+    p+an               G v  ++ t sDg+ gt++ t+++
  EPA04773.1 470 MNTSDVDGDTVTVTISSIFQDE---PTNGLGDGDTSPDANLAlgqvraersgtgdGRVyVITMTASDGHDGTCSGTVQV 545
                 599*******777655443311...223333334445555444333333333333555667888888888888777766 PP

>> Cu-binding_MopE  Putative metal-binding motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   4.6    0.0001      0.46      13      30 .]     331     349 ..     328     349 .. 0.90
   2 ?   -1.4   0.0      0.63   2.8e+03      17      28 ..     532     543 ..     528     544 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0001
  Cu-binding_MopE  13 atEvC.DgvDnnCdGvvDe 30 
                        E+C D++Dn+ d+++De
       EPA04773.1 331 TEEICgDNIDNDGDNQIDE 349
                      568***************8 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.63
  Cu-binding_MopE  17 CDgvDnnCdGvv 28 
                       Dg D  C+G+v
       EPA04773.1 532 SDGHDGTCSGTV 543
                      5999999***98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (569 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 3641.45
//
Query:       EPA04774.1  [L=115]
Description: hypothetical protein BG20_I2239 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.55
# Mc/sec: 633.25
//
Query:       EPA04775.1  [L=330]
Description: ribosomal protein L3 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.5e-71  239.5   2.0    1.2e-69  235.1   2.0    2.0  1  Ribosomal_L3  Ribosomal protein L3


Domain annotation for each model (and alignments):
>> Ribosomal_L3  Ribosomal protein L3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  235.1   2.0   6.7e-74   1.2e-69       1     349 [.       1     317 [.       1     329 [. 0.88

  Alignments for each domain:
  == domain 1  score: 235.1 bits;  conditional E-value: 6.7e-74
                   XX.S.SXXXXSSXCCCTTXSBXSXSSXXXSX.XXSBTTTTTXBSEEEEEEEEEEEEEEECHHTTSCCCCCEEEEEEEEEEC--EEEEEEEEEEEETT CS
  Ribosomal_L3   1 mshrkfeaprhgslGflprkRaerergkvksfPkddtskpvkltaflGyKaGmthiVrevdkpgskldkkevveavtvvetppmvivgvvgyvetpr 97 
                   m hrk+ +pr+gs  + pr+Ra++  ++++++P +++++p k+ a  G+KaG  + V  +d+  ++  +k++v+  tv+ tpp+ i+g++gy +  +
    EPA04775.1   1 MGHRKYAQPRRGSAAYYPRGRAKSMEARIRTWPTNNSDEP-KILAHCGFKAGCVQLVTIDDRDKTPNAGKQLVSLGTVLVTPPVSILGIRGYSKDHY 96 
                   99**********************************9966.77799*************************************************** PP

                   EEEEEEEEESSS.SHHHHCCCSTSTTTSSSSSSHCCCCHCSSCCCCCCHHHH...HHHHHHSCSCEEEEEEEECCCSS-SCCSSHHEEEEECHCSCH CS
  Ribosomal_L3  98 Glrslktvwaehlseevkrrlyknwykskkkaftkyskkyeskdvkkliead...leeikkeasvvrviahtvirktkslaqKkahllEiqvngGti 191
                   Gl++  +v+a++  +++ + +                   + k+++  +e     l ++k+    +  i+ +v  + ++l+qKk+ + E  v gG +
    EPA04775.1  97 GLHAEFDVYANEFPKSISKEI-------------------NLKNKEGALENAekiLGRVKE----IFAIV-AVSPRAAGLEQKKPYIFEALVSGGDV 169
                   ***********6666665555...................223333333332011555555....33333.44556678****************** PP

                   HHHHHHHHHCCTCEEECCCCS-TTSEEEEEEEE---EEE-HHHHCT----STTTSSSSSS-S-SS-SSSSS--TTS--SEEESCCEEEEEEEEEEEE CS
  Ribosomal_L3 192 aekldfarealektvavaavFrqgeliDvigvtkGkGfeGvvkRWgvkklprkthrglRkvaaigawdparVsstvaraGqkGyhhRtelnkkiyri 288
                    +++   +e l k ++++++F+ g  iDv+++tkGkG++Gv++R+gvkk++ k  ++ R va++g+  pa V+++v+raGq+G+h+Rte++kki+ i
    EPA04775.1 170 KKQFAHVKELLGKEIKIDQIFETGATIDVAAITKGKGWQGVIQRFGVKKKQHKSRKTVREVASLGPISPASVMYSVPRAGQMGFHQRTEYDKKIMVI 266
                   ************************************************************************************************* PP

                   ETTTSSTTTSSTTT.SS..SS.TTTCTTCB..TSCEEEEES--SSSTTEEEEEEE-SSGGG CS
  Ribosomal_L3 289 gkgedaknastefdltekeitPmGGfvhyGevkndfilvkGsvpGpkkrlvklrkslltqt 349
                   g+        t  +  + +i+P+GG+ h+G vk+dfi++kGsvpG+ +rl+klr  ++ + 
    EPA04775.1 267 GN--------T--ENNQIKINPDGGYKHFGLVKGDFIILKGSVPGTYRRLIKLRSQIRNAP 317
                   **........2..334678***********************************9988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2052.50
//
Query:       EPA04776.1  [L=144]
Description: hypothetical protein BG20_I1625 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-45  154.8   0.1    1.3e-45  154.6   0.1    1.0  1  DUF371    Domain of unknown function (DUF371)


Domain annotation for each model (and alignments):
>> DUF371  Domain of unknown function (DUF371)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.6   0.1   7.4e-50   1.3e-45       1     132 [.      11     143 ..      11     144 .] 0.97

  Alignments for each domain:
  == domain 1  score: 154.6 bits;  conditional E-value: 7.4e-50
                 EEEE--TT-----SSEEEEES-S---TT-TTEEEBS-S--GGGS-HHHHHHHS----EEEEEEE-SS-EEEEEEE--TT-----SSEEEEESSS---TT CS
      DUF371   1 ikarGHenvkaehksTleitkddeltprgdCIigveadkaaadlseelkealkeeeatitvtlevgeledeitgrGspkltlenerdlvvRkSdyvddr 99 
                 i+++GHen++++h++T+eitk+++ltp gdCIigv+a++++a+l+ +lk++l++ ++++t+ ++vg++e +++grG+++l+l++ +d+v+RkSd+v++r
  EPA04776.1  11 IQFSGHENIRSNHQKTIEITKESHLTPSGDCIIGVNATTSCAELPLSLKKKLQNPNSKVTLSIKVGSYEFNVEGRGHENLSLTHLEDIVIRKSDFVCPR 109
                 6889*********************************************************************************************** PP

                 EEEBS-S--GGGS-HHHHHHHHT.T-EEEEEEEE CS
      DUF371 100 TllvkadkaaadldrelveaLkk.gaeltvelev 132
                 Tl+vk+dka++ ++re++  L++ +++  ++++v
  EPA04776.1 110 TLAVKCDKASDLIPREMILLLQNpKTKGIFTIIV 143
                 ***********************88888888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1013.21
//
Query:       EPA04777.1  [L=140]
Description: 50S ribosomal protein L14P [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-31  108.1   1.3    3.2e-31  107.9   1.3    1.0  1  Ribosomal_L14  Ribosomal protein L14p/L23e


Domain annotation for each model (and alignments):
>> Ribosomal_L14  Ribosomal protein L14p/L23e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.9   1.3   1.8e-35   3.2e-31       2     122 .]      20     140 .]      19     140 .] 0.94

  Alignments for each domain:
  == domain 1  score: 107.9 bits;  conditional E-value: 1.8e-35
                    .CSS-EEE--SSSSBSEEEEEEETT-.--....-EE-SSSEEEEEESSS-T...TTSSCEEEEEEEE-SS-EE-TTS-EEEESS-EEEEB-TTS-B CS
  Ribosomal_L14   2 iqlktrlkvaDNsgakevecikvlggkkr....kaasvGdiivvsvkkakpkgkvkkgdvvkavvvrtkkevrrkdGsvirfddnaaVllnkkgep 93 
                    i  ++++ +aDN+gak +e++ v ++++r     aasvGd + v+vkk+     + +++v+ av++r+k  vrr +G+ + f+dnaaVl++ +ge+
     EPA04777.1  20 IPIGAQIVCADNTGAKILEIVMVQRHHTRhaqlAAASVGDFCNVVVKKGPA---ELRKQVYGAVIIRQKYAVRRLNGVRVCFEDNAAVLITPEGEV 112
                    56678999****************99955556699***********99988...99**************************************** PP

                    SS-.B-SBEEHHHHHH.-HHHHHTBSBE. CS
  Ribosomal_L14  94 lGtrifgpvarelrekkflkivslApevl 122
                    +Gt i+gpva+e+ ek ++++++lA++v+
     EPA04777.1 113 KGTDIKGPVAAEASEK-WPRVANLASMVV 140
                    **************99.*********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 894.52
//
Query:       EPA04778.1  [L=76]
Description: hypothetical protein BG20_I1618 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.1e-06   27.4   0.2      4e-06   27.0   0.2    1.2  1  Ribosomal_L22  Ribosomal protein L22p/L17e


Domain annotation for each model (and alignments):
>> Ribosomal_L22  Ribosomal protein L22p/L17e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.2   2.2e-10     4e-06       4      40 ..      22      60 ..      19      67 .. 0.86

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 2.2e-10
                   EEESS-HHHHHHHHHHHTTSBHHHHHHHHHT..-SSTTH CS
  Ribosomal_L22  4 snlrvsfkklrevarlIrgmkveeAlkyLkf..skkkaa 40
                   ++  +s+k++reva +I+g ++e+A +yL+   +k++a 
     EPA04778.1 22 REKDISHKHAREVAVAIKGLSIEKARDYLQAviTKQRAI 60
                   66789**************************97776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 477.56
//
Query:       EPA04779.1  [L=62]
Description: ribosomal protein L29 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-11   44.4   3.2    1.4e-11   44.2   3.2    1.1  1  Ribosomal_L29  Ribosomal L29 protein


Domain annotation for each model (and alignments):
>> Ribosomal_L29  Ribosomal L29 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   3.2   7.8e-16   1.4e-11       1      56 [.       2      58 ..       2      59 .. 0.95

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 7.8e-16
                   HHHHHS-HHHHHHHHHHHHHHHHHHHHHHHHTSSS.-CHHHHHHHHHHHHHHHHHHH CS
  Ribosomal_L29  1 kelrelsdeeLkeklkelkkeLfnLrfqkatgqle.npsrirkvRkdIARikTvlre 56
                   k +rel++++Lk k++e + eL +Lr+  + g+l    ++++ +R+dIAR++T  +e
     EPA04779.1  2 KTIRELNEKDLKSKIQETRSELAKLRVDGSKGTLRkESGKLKPLRHDIARMMTRVNE 58
                   579*******************************7699***************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1023  (0.0570584); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 417.19
//
Query:       EPA04780.1  [L=131]
Description: ribosomal protein S19 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-27   94.9   0.1    2.7e-27   94.4   0.1    1.2  1  Ribosomal_S19  Ribosomal protein S19


Domain annotation for each model (and alignments):
>> Ribosomal_S19  Ribosomal protein S19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.4   0.1   1.5e-31   2.7e-27       1      81 []      33     114 ..      33     114 .. 0.98

  Alignments for each domain:
  == domain 1  score: 94.4 bits;  conditional E-value: 1.5e-31
                    .HHHSS.TTCCCHHHHHHHHHHTS-----EEES-TT-B--GGGTT-EEEEE-SSSEEEEE--CCCTTSBCGGGT-SS----S CS
  Ribosomal_S19   1 rslkkg.pfvqesllkkvrkakaekkkevikthsRdstIlPemvgltvgVynGktfvpveikeemvGhkLgEFspTrkpvkh 81 
                    rsl++g +  +++l+++++ aka k k++ikth+Rd +IlP mvg+tv+++ Gk+f+pv  k em+Gh+LgE+++T+k+v+h
     EPA04780.1  33 RSLTRGiTDDKRKLIEEIKSAKAGKLKNPIKTHLRDLIILPYMVGVTVNIFSGKEFTPVLLKSEMIGHYLGEYVITNKRVSH 114
                    79999999999************9********************************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 944.14
//
Query:       EPA04781.1  [L=88]
Description: hypothetical protein BG20_I1614 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-20   71.7   0.0    3.9e-20   71.6   0.0    1.0  1  UPF0086   Domain of unknown function UPF0086


Domain annotation for each model (and alignments):
>> UPF0086  Domain of unknown function UPF0086
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.6   0.0   2.1e-24   3.9e-20       1      82 [.       5      84 ..       5      86 .. 0.97

  Alignments for each domain:
  == domain 1  score: 71.6 bits;  conditional E-value: 2.1e-24
                HHHCCSXXSS-EEEEEECSSTTTTTEEEEEEEEETTEEEEEECTTEEEEEESTTCEEEEEE.TTEEEEEECCCCSSXHHHHH CS
     UPF0086  1 ekLlkadlhGaeveVvrsknpslvgikGiVvkEtkntlkivtkksrvktvpKegsvFefevkdvlevevdGsqlryrpadRa 82
                ++L++++l+G+++e+++s+np+++g++G++ +Etk+++ + t  ++ k+v K++ v +f++ ++  v ++Gs++  rp dR+
  EPA04781.1  5 DNLTSHELIGLRIEIIESSNPQIIGLNGTITDETKSMFTMST-VNGSKMVTKSNNVWKFSI-NNQDVVLEGSKISKRPHDRI 84
                58****************************************.99****************.6999***************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 665.64
//
Query:       EPA04782.1  [L=146]
Description: hypothetical protein BG20_I1627, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.017   14.7   1.2      0.027   14.1   1.2    1.5  1  Snf7      Snf7
       0.12   12.5   0.0       0.22   11.6   0.0    1.4  1  bPH_4     Bacterial PH domain


Domain annotation for each model (and alignments):
>> Snf7  Snf7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   1.2     3e-06     0.027      40     122 ..       2      79 ..       1     133 [. 0.68

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3e-06
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTCCHHHHHHHHHHHHHHHHHTC CS
        Snf7  40 kdralllLKqkkryekqldqldnqlanleqvslaienlksnkevlnamkqgakamkamnkkvdidkidklmdeiedqmekaee 122
                 ++ a+ +++++++ +k+++++++ + ++eq++l + + +   +v+ ++    + +k  +  ++      +m e + +me  ++
  EPA04782.1   2 NAYAQAYANELVQVRKMKNMVSGAKLSMEQIQLRLNTVSELGDVVVTLSPCMSLIKGLSPSLS-----GIMPEATSSMEDLSQ 79 
                 667999******************************999999999888888877777665555.....666666666655444 PP

>> bPH_4  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   2.4e-05      0.22      27      52 ..      13      42 ..       8      54 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.4e-05
       bPH_4 27 kkirktksplsspalsldrleIkyg....k 52
                 ++rk+k+++s++ ls+++++ + +     
  EPA04782.1 13 VQVRKMKNMVSGAKLSMEQIQLRLNtvseL 42
                589*******************99955554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 895.42
//
Query:       EPA04783.1  [L=251]
Description: ribosomal protein S3 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-20   73.1   0.9    4.6e-20   71.9   0.9    1.7  1  Ribosomal_S3_C  Ribosomal protein S3, C-terminal domain
    3.3e-13   49.3   0.0    8.7e-13   47.9   0.0    1.8  1  KH_2            KH domain
  ------ inclusion threshold ------
       0.03   14.1   0.1       0.44   10.4   0.0    2.4  2  KH_1            KH domain


Domain annotation for each model (and alignments):
>> Ribosomal_S3_C  Ribosomal protein S3, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.9   0.9   7.6e-24   4.6e-20       2      83 .]     100     182 ..      99     182 .. 0.98

  Alignments for each domain:
  == domain 1  score: 71.9 bits;  conditional E-value: 7.6e-24
                     HHHHHTT--HHHHHHHHHHHHHHCC-SEEEEEEEC-SS.TTT--EEEEEEC----..TCHHHH-EEEEEEEEETTEEEEEEEEE CS
  Ribosomal_S3_C   2 aeqlekrvsfRramkkairramkagakGikiqvsGrLggaeiarsekykeGrvpl..htlradidyavaeaktkyGiiGvkVwI 83 
                     a +le++++fRra++ +++++m++ga G++i++sG+L+ ++++  ek+++G +p   h ++  +d+ +a+++t +G iG++++I
      EPA04783.1 100 AAHLERGTAFRRATMWTLKQIMENGAMGVQITISGKLR-GDRSAFEKHTAGILPRagHHAEVIVDEDIAHVETAMGLIGIRIRI 182
                     789***********************************.9*****************************************998 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.9   0.0   1.4e-16   8.7e-13       4      78 .]      19      90 ..      16      90 .. 0.95

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 1.4e-16
                HHHHHHTECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEEEEEEETTTGG CS
        KH_2  4 eslaveikkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdieklegkkVklnivkVkkpel 78
                 +l v ik+ag s+ eI +t+ ++++ +++ +pgivIG++Gs i++++ +l  d++ l++ +++  +v++ kpel
  EPA04783.1 19 DYLRVAIKDAGFSHAEISKTPTGTRVALHVTRPGIVIGRKGSGIRELTDKLATDFG-LKNPQIS--VVEIDKPEL 90
                689999*************************************************8.9999999..99****986 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   7.3e-05      0.44      12      27 ..      52      67 ..      42      72 .. 0.86
   2 ?    0.8   0.0     0.074   4.4e+02      21      36 ..     116     133 ..     116     150 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 7.3e-05
                HHHHTGGGHHHHHHHH CS
        KH_1 12 griIGkgGsnIkeIre 27
                g +IG++Gs I+e+ +
  EPA04783.1 52 GIVIGRKGSGIRELTD 67
                89***********987 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.074
                 HHHHHHHH.H.T-EEEEE CS
        KH_1  21 nIkeIree.t.gakIkvp 36 
                 ++k+I+e    g++I++ 
  EPA04783.1 116 TLKQIMENgAmGVQITIS 133
                 688999844556777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1753  (0.0977746); expected 358.6 (0.02)
Passed bias filter:                      732  (0.0408277); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 1525.01
//
Query:       EPA04784.1  [L=148]
Description: ribosomal protein L24 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-18   66.1   0.4    4.6e-18   65.5   0.4    1.3  1  Ribosomal_L26    Ribosomal proteins L26 eukaryotic, L24P arch
    1.3e-05   24.9   0.7    3.2e-05   23.7   0.7    1.7  1  KOW              KOW motif
  ------ inclusion threshold ------
      0.031   13.6   0.5      0.051   12.9   0.2    1.4  1  Methyltrans_RNA  RNA methyltransferase


Domain annotation for each model (and alignments):
>> Ribosomal_L26  Ribosomal proteins L26 eukaryotic, L24P archaeal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.5   0.4   7.7e-22   4.6e-18       4      82 .]       3     115 ..       1     115 [. 0.95

  Alignments for each domain:
  == domain 1  score: 65.5 bits;  conditional E-value: 7.7e-22
                    xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................xxxxxxxxxxxxxxxxxxxxxxx RF
  Ribosomal_L26   4 rrkqrK.ahfnapshirrklmsapLskeLrekygvrslpir................................gvtrekangttvpvgihpSkvvI 66 
                    + k+r    + a+ h+r+k + +pLs+eLr++yg rs+++                                 gv++ek++g +  + ih S++v+
     EPA04784.1   3 PTKSRNnLIYRATFHTRSKQLGSPLSEELRKRYGKRSIRVIegdtikivrgefkgvdgkiakvstqknsvsieGVKKEKTKGDKFDIYIHTSNLVV 98 
                    66777614699************************************************************************************* PP

                    xxxxx.xxxxxxxxxxx RF
  Ribosomal_L26  67 tklkl.DkdrkkiLerk 82 
                    t l+  Dk r + Le k
     EPA04784.1  99 TGLNTdDKWRIAKLEGK 115
                    *************9976 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.7   5.3e-09   3.2e-05       1      32 []      44      75 ..      44      75 .. 0.95

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 5.3e-09
                TTSEEEESSSTTTTCEEEEEEEETTTTEEEEE CS
         KOW  1 pGdhVkVvsGphkGktGkVvkvdqhkvrVfvd 32
                +Gd+ k+v+G +kG  Gk+ kv  +k+ V ++
  EPA04784.1 44 EGDTIKIVRGEFKGVDGKIAKVSTQKNSVSIE 75
                59************************999987 PP

>> Methyltrans_RNA  RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   8.6e-06     0.051       8      59 ..      33      84 ..      27      95 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.6e-06
                     HHHHHTTTT--TT-EEEEEESSSEEEEEEEEEEESSEEEEEEEEEEE---SS CS
  Methyltrans_RNA  8 ahHlvkVlRlkegdeiklfdgdgkeyeaeieeiskkkvtvkilekeeenkes 59
                      ++ ++  R+ egd+ik++ g+ k ++++i+++s +k +v+i+  ++e+++ 
       EPA04784.1 33 KRYGKRSIRVIEGDTIKIVRGEFKGVDGKIAKVSTQKNSVSIEGVKKEKTKG 84
                     5788999***********************************9877777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       983  (0.0548274); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1073.53
//
Query:       EPA04785.1  [L=107]
Description: ribosomal protein S17P [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.8e-18   65.0   1.3    6.1e-18   64.7   1.3    1.1  1  Ribosomal_S17    Ribosomal protein S17
     0.0013   19.0   0.2     0.0033   17.8   0.0    1.8  2  Ribosomal_S17_N  Ribosomal_S17 N-terminal


Domain annotation for each model (and alignments):
>> Ribosomal_S17  Ribosomal protein S17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.7   1.3   6.8e-22   6.1e-18       1      68 []      36     104 ..      36     104 .. 0.99

  Alignments for each domain:
  == domain 1  score: 64.7 bits;  conditional E-value: 6.8e-22
                    EEEEE--STTEEEEEEEEEEEETTTTEEEEEEEEEEEE-TTTS.--TT-EEEEEEECECSSSEEEEEEE CS
  Ribosomal_S17   1 GvVvsdkmdkTvvVrverlvkhpkykkyvkrrkkylahdenns.vkvGDiVrieecrPlSktkrfvvve 68 
                    G+V+s+k ++T++ + e   +  k+k+y + +  ++ah ++++ v++GD V  +ecrP+Sk++++vvve
     EPA04785.1  36 GKVTSNKAKQTITLQKESPIYYMKFKRYARSKNTIHAHVPECIdVETGDHVLTAECRPISKSVSYVVVE 104
                    99*****************************************************************96 PP

>> Ribosomal_S17_N  Ribosomal_S17 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   3.7e-07    0.0033      35      69 .]       4      34 ..       1      34 [. 0.79
   2 ?   -1.6   0.1      0.41   3.7e+03      25      25 ..      51      51 ..      37      70 .. 0.48

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.7e-07
                     ---TT----GGGGS-----TTSSSSSS----S-EE CS
  Ribosomal_S17_N 35 nvglgfktPkeAiegtYiDkKCPFtGnvsirGriL 69
                     n+gl  k+P    e++  D  CPF G+ s+rG+++
       EPA04785.1  4 NIGLKVKAP----ERECTDTHCPFHGKLSVRGKLF 34
                     566666666....5677899************975 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.41
                     - CS
  Ribosomal_S17_N 25 k 25
                     k
       EPA04785.1 51 K 51
                     1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 689.48
//
Query:       EPA04786.1  [L=270]
Description: ribosomal protein L4/L1 family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.9e-40  136.8   0.1      8e-40  136.6   0.1    1.0  1  Ribosomal_L4  Ribosomal protein L4/L1 family


Domain annotation for each model (and alignments):
>> Ribosomal_L4  Ribosomal protein L4/L1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.6   0.1   4.5e-44     8e-40       1     191 [.      16     257 ..      16     258 .. 0.94

  Alignments for each domain:
  == domain 1  score: 136.6 bits;  conditional E-value: 4.5e-44
                   EEE-HHHHSS---HHHHHHHHHHHHHSS-EE-----.-TTTSS---S-SS-SSSSSS---S-TT............STTSTT---SS---S.EEHHH CS
  Ribosomal_L4   1 veLspkvFaapirrdlihravvaylanrrqgtastk.arsevsgsgrklwkQKGtGrARvgsir............spiargGgvahgpkperdyst 84 
                   veL p +F++p+r++lih+a+++  +++ q++++++ a+++v ++++++ +  G+ +AR+ +++            ++ +rgG++ah+p +e+ + +
    EPA04786.1  16 VEL-PLIFSTPFRPELIHKAFTNLTSHKFQPQGRHPtAGMDVVARSNDPPT--GQHQARIAKMKgggggrqgqaggVASVRGGRQAHPPIVEKVIFK 109
                   688.99*********************************************..******************************************** PP

                   HHHHHHHHHHHHHHHHHHHHTT-EEEES.---.-S............S--HHHHHHHHHHTT-.........................TTSSEEEEE CS
  Ribosomal_L4  85 klnkKvrrlAlrsaLsakakqglllvvd.nleple............esktkelvellkklgl.........................ksksvLivv 143
                   klnkK+ +lAl+sa++a+a+++l++ ++ +++++e            +sk++++ +ll+ l+l                           ksvL+v+
    EPA04786.1 110 KLNKKENKLALCSAIAATASKDLVKSRGhKVDGIEsfpiiisndvenISKASQMSKLLEDLKLmkdverlqsrkprtgqsslrgrskkVGKSVLFVT 206
                   ****************************7555566777889999999*************9998888989988888888888888888889****** PP

                   SSSSCHHHHHHTT-TTEEEEESTT--CHHHHHSSE....EEEEHHHHHHHHH CS
  Ribosomal_L4 144 sekdenlvlaarnlpgvevieveslnvydllkadk....vvitksaveklee 191
                   ++  +++++a+  lpgve   v++l+v+dl+++++    ++++k+a+e++++
    EPA04786.1 207 KD-ASKIIKACGTLPGVEARAVKDLSVLDLAPGSDpirlTIYSKAALEEIAK 257
                   98.99*******************************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1851.43
//
Query:       EPA04787.1  [L=245]
Description: putative proteasome endopeptidase complex, alpha subunit [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.5e-52  176.7   0.3    4.5e-52  176.3   0.3    1.1  1  Proteasome      Proteasome subunit
    3.6e-14   52.1   0.7    1.4e-13   50.2   0.1    2.2  2  Proteasome_A_N  Proteasome subunit A N-terminal signature


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.3   0.3     5e-56   4.5e-52       1     186 [.      31     210 ..      31     214 .. 0.94

  Alignments for each domain:
  == domain 1  score: 176.3 bits;  conditional E-value: 5e-56
                 HHHS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGTCHHHHHHHHHHHHHHHHHHC CS
  Proteasome   1 vkkGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrpipverlvarvaaklqaytqrs 99 
                 v++Gt +vGik+k+gv++a++ +     kl+ ++ ++Kif+iddh+gva+aG ++Dar  v+ ar   q+ ++ y++ + ve++++++a++ q+ tq++
  EPA04787.1  31 VRRGTIAVGIKSKEGVIIAVEEKPR---KLQITDIAQKIFQIDDHVGVAAAGYIPDARSQVDNARFFSQSNKMIYDEAVEVETIAKHLADQCQQFTQYA 126
                 679******************7777...88888889*************************************************************** PP

                 TTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHHSTTBSHHHHHHHHHHHHHHHHHHBTTSCSSEE CS
  Proteasome 100 grrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekeykedltleeavelavkalkealerdklsgknie 186
                 g+rpfgv+l+++gv +++ p++y +dpsG+yi+++ a+aiGsgs+ ++ +lek y+++l+l++a  la  a++ ++e dk + + i+
  EPA04787.1 127 GVRPFGVALILGGVVNNN-PQIYLTDPSGTYISYD-AIAIGSGSDQVTDFLEKTYNKELSLDDASALASAAIYLSSE-DKEGTSHIR 210
                 ***************888.***************6.**************************************999.555555555 PP

>> Proteasome_A_N  Proteasome subunit A N-terminal signature
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.2   0.1   1.6e-17   1.4e-13       1      22 [.       8      29 ..       8      29 .. 0.98
   2 ?   -0.9   0.0      0.15   1.3e+03      13      18 ..      65      70 ..      65      70 .. 0.88

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 1.6e-17
  Proteasome_A_N  1 YDrslttFSPdGRLfQVEYAmk 22
                    YDr++t+FSPdGRL+QVEYA++
      EPA04787.1  8 YDRAITVFSPDGRLYQVEYAIE 29
                    ********************97 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.15
  Proteasome_A_N 13 RLfQVE 18
                    ++fQ++
      EPA04787.1 65 KIFQID 70
                    79**97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       697  (0.0388756); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1717.14
//
Query:       EPA04788.1  [L=113]
Description: hypothetical protein BG20_I1626 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.026   14.4   0.7      0.032   14.2   0.7    1.2  1  WbqC      WbqC-like protein family


Domain annotation for each model (and alignments):
>> WbqC  WbqC-like protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.7   1.8e-06     0.032      50     107 ..      53     109 ..      38     113 .] 0.83

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.8e-06
        WbqC  50 vPvekkasqqklineveidddekwrkkhlksleqaYkkapffeevlpllesvyeaeee 107
                 + v +k+  qk+++ v+++ + +wr k +k++  +Y+k+ +   ++  +++++ ++++
  EPA04788.1  53 LKVGRKSIIQKEVHSVTFE-QAQWRLKNWKMMIANYRKRGYSYPTISRIKKILIQKSK 109
                 5565666666779999998.679****************************9987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 807.00
//
Query:       EPA04789.1  [L=75]
Description: putative 50S ribosomal protein L22P [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.1e-18   64.8   0.0    7.3e-18   64.7   0.0    1.0  1  Ribosomal_L22  Ribosomal protein L22p/L17e
  ------ inclusion threshold ------
      0.071   12.4   0.0      0.073   12.4   0.0    1.0  1  Herpes_UL36    Herpesvirus UL36 tegument protein


Domain annotation for each model (and alignments):
>> Ribosomal_L22  Ribosomal protein L22p/L17e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.7   0.0   8.1e-22   7.3e-18      36     102 ..       6      72 ..       1      73 [. 0.95

  Alignments for each domain:
  == domain 1  score: 64.7 bits;  conditional E-value: 8.1e-22
                    SSTTHHHHHHHHHHHHHHHH..HT-GGGEEEEEEEEEEEEEEEEEEEESTTEEEEEEEEEEEEEEEE CS
  Ribosomal_L22  36 kkkaakfvlklLknaeanaelkgldvdslvIeeiqvnkgpklkrrtyrArGrinpirkspchievvl 102
                    ++k  k+++k+L n e+nae+kg+d d+l I+++ v+kg+ +kr+t+rA+Gr++p ++  +h+e+v 
     EPA04789.1   6 PQKTVKEFIKVLDNLESNAEYKGMDLDRLRIVNATVHKGTIVKRFTPRAMGRASPKNNVLTHVELVA 72 
                    678999**********************************************************986 PP

>> Herpes_UL36  Herpesvirus UL36 tegument protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   8.1e-06     0.073       8      49 ..      12      55 ..       7      72 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.1e-06
  Herpes_UL36  8 diealLeraeskaeFdlveldrlrdlaet..gGydavdlkkrAr 49
                 + + +L++ es+ae+++++ldrlr + +t   G  ++++ +rA 
   EPA04789.1 12 EFIKVLDNLESNAEYKGMDLDRLRIVNATvhKGTIVKRFTPRAM 55
                 56789*******************99888755766669998885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 527.08
//
Query:       EPA04790.1  [L=88]
Description: ribosomal protein L23 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-13   50.6   0.9    3.3e-13   49.8   0.9    1.4  1  Ribosomal_L23   Ribosomal protein L23
  ------ inclusion threshold ------
      0.012   15.3   0.1      0.017   14.8   0.0    1.3  1  DNA_mis_repair  DNA mismatch repair protein, C-terminal domai
        0.1   12.6   0.1       0.11   12.5   0.1    1.1  1  MuF_C           Phage MuF-C-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_L23  Ribosomal protein L23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.8   0.9   5.5e-17   3.3e-13       1      64 [.       8      72 ..       8      84 .. 0.85

  Alignments for each domain:
  == domain 1  score: 49.8 bits;  conditional E-value: 5.5e-17
                   SSEEEE--SHHHHHHHTT.E.EEEEE-SS-THHHHHHHHHHHHT--EEEEEEEEE--EBESSSSS CS
  Ribosomal_L23  1 dvilkPvitEkstklaek.nkyvFeVakdanKleikkaveklFgVkVekVntlnvkgkkkrvgrk 64
                   ++ilkP+itEk+ ++ e+ +k+ F V+++a+K++i +av +l++ k  +Vnt++    kk + ++
     EPA04790.1  8 KIILKPYITEKTFAMVENeSKICFIVDRSASKPDIIQAVDALYNQKAISVNTARTIYGKKAFVQF 72
                   69**************99669*******************************9876666644444 PP

>> DNA_mis_repair  DNA mismatch repair protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   2.8e-06     0.017      20      68 ..       6      54 ..       1      64 [. 0.88

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.8e-06
                    ETTEEEEEEEE-CCG-BTTGGEEEEEETTEEE--HHHHHHHHHHHHCCS CS
  DNA_mis_repair 20 eeqlkieGfiskpelsrskrdkqflfvNgRlvkskelkkaireaYkell 68
                     +++ ++ +i++++++  +++++++f+  R  +++++ +a+++ Y+++ 
      EPA04790.1  6 ASKIILKPYITEKTFAMVENESKICFIVDRSASKPDIIQAVDALYNQKA 54
                    4569999**************************************9765 PP

>> MuF_C  Phage MuF-C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   1.9e-05      0.11      36      87 ..      25      75 ..       4      85 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.9e-05
       MuF_C 36 eenslvvltelkdkdgkpvivalhlngkekgraevneiaSaYgrdn.delkrw 87
                +e ++ ++++     +  +i a++    +++ ++vn  +++Yg++   +++  
  EPA04790.1 25 NESKICFIVDRS-ASKPDIIQAVDAL-YNQKAISVNTARTIYGKKAfVQFETT 75
                555688888877.6666777777776.579*************9955444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 586.82
//
Query:       EPA04791.1  [L=270]
Description: hypothetical protein BG20_I1623 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.1e-52  177.1   0.0    5.8e-52  177.0   0.0    1.0  1  Methyltrn_RNA_3  Putative RNA methyltransferase


Domain annotation for each model (and alignments):
>> Methyltrn_RNA_3  Putative RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.0   0.0   3.2e-56   5.8e-52       2     284 ..       3     262 ..       2     264 .. 0.86

  Alignments for each domain:
  == domain 1  score: 177.0 bits;  conditional E-value: 3.2e-56
  Methyltrn_RNA_3   2 vsiaiPssiisnaqsleqktylagqIARaaaiFnVdeivvfddseseeekkekpseflarlLqYletPpYLrkelFplhkelkyaglLppldap 95 
                      +siaiP+s +s+ + +  kt++++ +ARa++iF++d i+v+++++ +e     + ++l ++L+YletP++Lr++lFp+++elk+ag+L pl++p
       EPA04791.1   3 ISIAIPESALSDESLKLDKTRKISVLARACSIFKIDTIYVYQEGNYKE-----DGNLLVTILKYLETPQFLRRRLFPKMNELKFAGVLLPLRIP 91 
                      89*******************************************998.....789************************************** PP

  Methyltrn_RNA_3  96 hhl.....rsseegeyreGvvvekskekkskkklVniGlkkevklelkqevpegtRVtVklsseesveakvVspsepreeaglywGYsVrlaks 184
                       h+     ++ + g++reGvv++ +   k    +V++G+++ + +    + ++g RVtV+++s        V++  +r+e+ lywGY+V+  ++
       EPA04791.1  92 SHAtpansKKINIGDVREGVVISIKG--KR---FVDVGINEAIPFFG--KTDVGKRVTVQFKS--GYPDFSVKEI-QRNETPLYWGYTVKERSN 175
                      ***99974444489*********965..55...*****999998888..7777********33..4444444444.457999************ PP

  Methyltrn_RNA_3 185 lsavftespfeggydlsigtserge.kveeklaelekkk.efkhllivfGg.vrgleaaleadeelklegekaeelFdlwlntvpnqgsrtirt 275
                      l +++te         +i+ts++g+  ++e+l+++     +   +l+vfG+ ++g+ ++l  +       +++++   + ln++pnq ++t+r+
       EPA04791.1 176 LFSLLTEW-----RGNTIITSRKGRtATKEQLTKY---LsSELPILVVFGSpEKGVHEILGGK------MKNIQN--AKTLNFFPNQATETVRL 253
                      *******7.....5789*******85666666655...336889****************444......333333..3679************* PP

  Methyltrn_RNA_3 276 EEavliaLa 284
                      EEa+l +L+
       EPA04791.1 254 EEALLGTLS 262
                      *******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1803.50
//
Query:       EPA04792.1  [L=214]
Description: ribosomal family S4e, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      9e-18   64.0   0.2    1.5e-17   63.2   0.2    1.4  1  Ribosomal_S4e  Ribosomal family S4e
    1.6e-12   47.3   0.5    2.6e-12   46.6   0.5    1.3  1  RS4NT          RS4NT (NUC023) domain
     0.0015   18.2   0.1     0.0034   17.1   0.1    1.6  1  S4             S4 domain
  ------ inclusion threshold ------
       0.02   14.8   0.1      0.091   12.7   0.0    2.2  2  KOW            KOW motif


Domain annotation for each model (and alignments):
>> Ribosomal_S4e  Ribosomal family S4e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.2   0.2   3.4e-21   1.5e-17       3      75 .]      98     169 ..      96     169 .. 0.98

  Alignments for each domain:
  == domain 1  score: 63.2 bits;  conditional E-value: 3.4e-21
                    EEEEEEE-TTSSEEEEEE-TTCCCEEEEEECEEEEECCCEEEEEETTS-EEEESSTT-STTEEEEEETTTTEE CS
  Ribosomal_S4e   3 enyrllydtkgrfalhkItseeakyKLcKikkkttvkkgipqlvthdGrtirypdpdikvnDtvkidleenkI 75 
                    e yr+++ + + +++ +I+++e++ KL+++++ktt++kg++q+ +hdGr  + + + ++++D+++i+++++kI
     EPA04792.1  98 EIYRMVPMEGKLLKPLQIKESEKSKKLVRVTSKTTISKGRMQIGFHDGRSTISDTK-VNIGDSCLIQIPDQKI 169
                    67*****************************************************9.***************9 PP

>> RS4NT  RS4NT (NUC023) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.6   0.5   5.8e-16   2.6e-12       3      37 .]       6      40 ..       5      40 .. 0.96

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 5.8e-16
                ----EETTTS-TTS---SSSSSEE----SSSS-TT CS
       RS4NT  3 pkkHLKrlaAPkhWpldkkegvfavkPspGPHklr 37
                ++k+LKr+ AP++W + +k+++fa++ +pGPHk++
  EPA04792.1  6 GSKKLKRQLAPQFWGITRKDKRFAITVRPGPHKKE 40
                689******************************96 PP

>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   7.6e-07    0.0034      10      48 .]      53      91 ..      47      91 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 7.6e-07
                TTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-TTCEE CS
          S4 10 lglassrreArqlIehGrVlVNGkvvkdpsyrVkpgDvi 48
                l+++ + reA+  I  G+V+++G v+k+  + ++ +Dv+
  EPA04792.1 53 LKIVTTLREAKASIYTGKVKIDGVVRKSLHHAIGLMDVV 91
                6778899******************************97 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.2   5.3e+03       3       9 ..     123     129 ..     117     129 .. 0.75
   2 ?   12.7   0.0     2e-05     0.091       1      24 [.     177     200 ..     177     210 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.2
                 SEEEESS CS
         KOW   3 dhVkVvs 9  
                 + V+V+s
  EPA04792.1 123 KLVRVTS 129
                 4677776 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 2e-05
                 TTSEEEESSSTTTTCEEEEEEEET CS
         KOW   1 pGdhVkVvsGphkGktGkVvkvdq 24 
                 ++ h  V++G ++G++G+++++++
  EPA04792.1 177 KDSHALVTRGVNAGQVGTIESIEE 200
                 5789*****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1334.03
//
Query:       EPA04793.1  [L=177]
Description: hypothetical protein BG20_I2599 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-05   24.5   0.0    3.4e-05   23.9   0.0    1.3  1  Cupredoxin_1    Cupredoxin-like domain
  ------ inclusion threshold ------
       0.14   12.3   2.6        5.9    7.0   1.3    2.3  2  Arch_flagellin  Archaebacterial flagellin


Domain annotation for each model (and alignments):
>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   3.8e-09   3.4e-05      47      93 ..     101     148 ..      93     158 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 3.8e-09
  Cupredoxin_1  47 lkiknkdktpeefesedlgeekv.lapgktttitiaplkpGeYeftcd 93 
                   l+++n++++p+ ++++ l+ +++ ++pgk++t+ti p k+G Y++++ 
    EPA04793.1 101 LHVQNNGDKPHRLYIDGLDAQTDlIDPGKEFTLTIYPTKKGVYNYYDN 148
                   899****************9976369******************9986 PP

>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   1.3   0.00066       5.9       7      29 ..      24      46 ..      20      50 .. 0.89
   2 ?    4.4   0.0    0.0044        39     115     144 ..     116     145 ..      64     157 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00066
                    HHHHHHHHHHHHHHHHHHHHHHH CS
  Arch_flagellin  7 tlIvfIAmVlVAAvaagvlinta 29
                    t Iv+IA VlV  v   vli+  
      EPA04793.1 24 TKIVIIASVLVGLVSFAVLIGYI 46
                    78*****************9865 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0044
                     ......T-EE-TT-EEEEEEE--TTT---T CS
  Arch_flagellin 115 gsltngdevlekgekvelevnvneddgita 144
                     ++l+++++++++g+ ++l++  +++  ++ 
      EPA04793.1 116 DGLDAQTDLIDPGKEFTLTIYPTKKGVYNY 145
                     456677999999999999999974444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1159.15
//
Query:       EPA04794.1  [L=40]
Description: hypothetical protein BG20_I2600, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      146  (0.00814323); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 254.11
//
Query:       EPA04795.1  [L=427]
Description: transketolase, thiamine diphosphate binding domain protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-50  172.4   0.4    2.7e-49  167.9   0.4    2.1  1  Transketolase_N  Transketolase, thiamine diphosphate binding 
    7.3e-29  100.6   0.2      1e-28  100.1   0.2    1.2  1  Ribul_P_3_epim   Ribulose-phosphate 3 epimerase family
      5e-06   25.9   0.1    4.7e-05   22.7   0.1    2.1  2  DXP_synthase_N   1-deoxy-D-xylulose-5-phosphate synthase
    5.7e-06   25.5   0.0      9e-06   24.8   0.0    1.2  1  E1_dh            Dehydrogenase E1 component
    1.2e-05   25.2   0.0    2.6e-05   24.0   0.0    1.6  1  TPP_enzyme_C     Thiamine pyrophosphate enzyme, C-terminal TP
    3.4e-05   22.8   0.2    0.00046   19.1   0.0    2.1  2  XFP_N            XFP N-terminal domain


Domain annotation for each model (and alignments):
>> Transketolase_N  Transketolase, thiamine diphosphate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.9   0.4   9.1e-53   2.7e-49       6     269 ..      12     281 ..       8     310 .. 0.86

  Alignments for each domain:
  == domain 1  score: 167.9 bits;  conditional E-value: 9.1e-53
                      HHHHHHHHHHHHHHHT-S--HHHHHHHHHHHHHHHHT--B-TTBTT-TTS-EEEESSGGGHHHHHHHHHHTTSS--HHHHTTTTSTT-SS-SS- CS
  Transketolase_N   6 vnaiRvLavDavekaksGhPGaplgladiaevlfkkllkhnPndpkwidRDRfvLsnGhaslllYsllhLtGydlsledlksfrqlgsktpGhP 99 
                      v   R L++ a + a+sGhPG ++++a+i   lf k+lk++P++p+w dRDR vLs Gha+  l+s + + Gy ++ +dl+ +r++gsk  GhP
       EPA04795.1  12 VLRARKLVIKATNTAGSGHPGGSFSMAEILGCLFYKHLKYDPKNPNWEDRDRLVLSKGHAAPGLFSNMAVAGY-FPESDLETLRKFGSKLQGHP 104
                      556799*******************************************************************.66799*************** PP

                      -TTTSTT--S---STTHHHHHHHHHHHHHHHHHHHH-BTTB-S----EEEEEEHHHHHSHHHHHHHHHHHHTT-TTEEEEEEESSEETTEEGGG CS
  Transketolase_N 100 elghtagvevttGPLGqGianavglalaektlaatynkpgfdivdhytyvilgDgclmeGvsseasslagtlkLgkLivlyDdnkisidGetei 193
                      +  + +gve   G LG G++ ++g+ala k   +          +h++y i+gDg   eG   ea+  a++ k+++L ++ D n i  d  te+
       EPA04795.1 105 D-LKCPGVEFCGGSLGTGLSYSIGVALAAKI--D--------QKNHHVYTIIGDGESDEGQVWEAAMTAAKYKVDNLTAFLDRNFIQQDSYTEK 187
                      *.689*********************98764..3........3459****************************************99988876 PP

                      T-.......-S-HH............HHHHHTT-EEEEETTTT-HHHHHHHHHHHHH-TTS-EEEEEE--TTTTSTTTTTSGGGTSS---HHHH CS
  Transketolase_N 194 sf.......tedva............krfeaygWhvievedgedveaikaaieeakaekdkPsliklrtviGygspakagtedvhGapLgedev 268
                       +        +d++            ++++++gW+vie  dg+ +e+i+aai++a+++k  Ps+i  rt+ G g    +++ + hG +   d v
       EPA04795.1 188 IMpldekleGDDISemwkdasrwktgDKWRSFGWNVIE-IDGHRIEQIDAAITKANSTKGIPSIIIARTIKGKGVEHMEDNPQWHGKAPDSDVV 280
                      5422111112333211111112222268999******9.9**********************************************98777766 PP

                      H CS
  Transketolase_N 269 a 269
                       
       EPA04795.1 281 P 281
                      5 PP

>> Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.1   0.2   3.4e-32     1e-28       2     132 ..     293     426 ..     292     427 .] 0.94

  Alignments for each domain:
  == domain 1  score: 100.1 bits;  conditional E-value: 3.4e-32
                     EEEBGGGS-GGGHHHHHHHHHHTT-SEEEEEEEBSSSSS-B-B-HHHHHHHGGGE-S-EEEEEESSSHHHCHHHHHHCT-SEEEEE-S..T-TTH CS
  Ribul_P_3_epim   2 iapSllsadfarlgeevkaveeagadllHvDvmDghfvpNltigplvvealrkltelpldvHLmveevdrivpefaeagasiisvHaE..alehl 94 
                     iapS+++ d+++l++evk+  +  ad++H+DvmDg+fv+  t+    +++lr+lt +p+d HLm++e+ + v e+++ag++ii+vHaE  + +  
      EPA04795.1 293 IAPSIIAGDMNNLENEVKRCVAGRADYIHLDVMDGQFVQTKTFDHRKIKELRPLTVIPFDTHLMINEPVKHVREYVDAGSDIITVHAEvcNESSF 387
                     9***************************************************************************************7666777 PP

                     HHHHHHHHHTTSEEEEEE-TT--GGGGTT.TCCC-SEEE CS
  Ribul_P_3_epim  95 krtiqeikeaGakaglvlnpatplealey.llekldlvl 132
                      ++   +k++ + +gl++np t l  ++y +l++ld ++
      EPA04795.1 388 GEIHDLLKQHQVGVGLAINPDTELPEWSYkFLPSLDQLI 426
                     899999******************888764788888776 PP

>> DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.1   1.6e-08   4.7e-05     110     171 ..     115     177 ..       7     211 .. 0.82
   2 ?    1.0   0.0     0.065   1.9e+02     234     269 ..     216     251 ..     193     255 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.6e-08
  DXP_synthase_N 110 agHsstsisaalGlavardlkgekkkvvaviGDgaltgGmafealnnigelk.kkllvilNdN 171
                      g  +t +s++ G+a a+++++++++v ++iGDg    G  +ea  ++++ k ++l   l  N
      EPA04795.1 115 GGSLGTGLSYSIGVALAAKIDQKNHHVYTIIGDGESDEGQVWEAAMTAAKYKvDNLTAFLDRN 177
                     566789*************************************87666655415666555555 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.065
  DXP_synthase_N 234 feelgfkYlGpidGhdleelikvleevkklkg.pvll 269
                     ++++g + +  idGh +e++  ++++++++kg p ++
      EPA04795.1 216 WRSFGWNVI-EIDGHRIEQIDAAITKANSTKGiPSII 251
                     555666655.69**************99988756555 PP

>> E1_dh  Dehydrogenase E1 component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0     3e-09     9e-06      98     151 ..     115     166 ..      91     173 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 3e-09
                 EE-SSTTTHHHHHHHHHHHHHHHTS---EEEEEEGGGTT-HHHHHHHHHHHHTT CS
       E1_dh  98 ggngivgaqvplvaGialaakiegkkevailliGDgAanqGdvyealnlaalwk 151
                 gg+  +g+  +   G+alaaki++k++ + ++iGDg + +G+v+ea+  aa +k
  EPA04795.1 115 GGS--LGTGLSYSIGVALAAKIDQKNHHVYTIIGDGESDEGQVWEAAMTAAKYK 166
                 444..555555777********************************99888776 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   8.7e-09   2.6e-05      29     151 ..     117     251 ..     109     253 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 8.7e-09
                   -TTTHHHHHHHHHHH....STTSEEEEEEEHHH..HHHTGGGHHHHHHTT-.SEEEEEEE-SBCCCHHHH....HHHHTCCTTTTSBB.BS----HH CS
  TPP_enzyme_C  29 tmGyglpaAiGakla....kpdrevvaivGDGg..flmilqelatavrrnl.pitvvvlnNegygmtggq....qepfggkrksgpagkdlkpvdfa 114
                   ++G gl+++iG++la    +++++v+ i+GDG        ++ +ta+++++ ++t ++  N + +    +     + + ++   ++  kd    +  
    EPA04795.1 117 SLGTGLSYSIGVALAakidQKNHHVYTIIGDGEsdEGQVWEAAMTAAKYKVdNLTAFLDRNFIQQDSYTEkimpLDEKLEGDDISEMWKDASRWKTG 213
                   56666666666666433326679*********84456679999********8888888889888777766667745555555666666689999999 PP

                   HHHHHTTSEEEEESSH.HHHHHHHHHHHH.CSSSEEEE CS
  TPP_enzyme_C 115 klaealGakgarvekadveeleealkeal.ekkgpali 151
                      +++G +++ ++ + +e++++a+ +a  +k+ p++i
    EPA04795.1 214 DKWRSFGWNVIEIDGHRIEQIDAAITKANsTKGIPSII 251
                   9***************************9444445555 PP

>> XFP_N  XFP N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.5e-07   0.00046     124     175 ..     100     155 ..      60     170 .. 0.78
   2 ?    1.5   0.0     0.035     1e+02     253     291 ..     229     266 ..     216     290 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.5e-07
       XFP_N 124 ipshvaaetPGsiheGGelGyalshayG....avldnPdlivacvvGdGeaetGPl 175
                 +  h   + PG    GG lG  ls+++G    a +d+ +  v +++GdGe++ G +
  EPA04795.1 100 LQGHPDLKCPGVEFCGGSLGTGLSYSIGvalaAKIDQKNHHVYTIIGDGESDEGQV 155
                 56788888999999999999777777663222668*****************9976 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.035
       XFP_N 253 eeihdiqkearsneeasrPkwPmiilrtPkGwtgPkyvd 291
                 ++i +i ++   ++++++    +ii+rt kG++  ++ d
  EPA04795.1 229 HRIEQIDAAIT-KANSTKGIPSIIIARTIKGKGVEHMED 266
                 67788876554.444446666799********9877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 2565.16
//
Query:       EPA04796.1  [L=125]
Description: hypothetical protein BG20_I2172 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00084   20.7   0.0     0.0011   20.2   0.0    1.2  1  DUF393    Protein of unknown function, DUF393


Domain annotation for each model (and alignments):
>> DUF393  Protein of unknown function, DUF393
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   6.3e-08    0.0011       1      75 [.      10      81 ..      10      93 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 6.3e-08
      DUF393  1 vlyDgeCplCnravqflerrdrkgrirfadlqsasgkallkelgidaeqldslllvieagrvysgsdAaleiara 75
                ++yD +C lC ++++ +e + r g++ ++   s+ g++ lk+  + ++ l+   + i+++++y g +A + +++a
  EPA04796.1 10 IVYDNQCYLCVKFAKAVEFLTR-GNLTMIGHYSDIGTE-LKKSILGESALEMFWF-IDNNTAYGGRAALIPVIKA 81
                79******************77.789999998999999.6566667677777777.99999****9999988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       967  (0.053935); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 831.91
//
Query:       EPA04797.1  [L=489]
Description: cytosol aminopeptidase family, catalytic domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.3e-119  399.1   0.0   1.7e-119  398.7   0.0    1.1  1  Peptidase_M17    Cytosol aminopeptidase family, catalytic dom
    7.9e-17   61.3   0.2    2.7e-16   59.6   0.0    2.0  2  Peptidase_M17_N  Cytosol aminopeptidase family, N-terminal do


Domain annotation for each model (and alignments):
>> Peptidase_M17  Cytosol aminopeptidase family, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  398.7   0.0  1.9e-123  1.7e-119       2     310 ..     173     482 ..     172     483 .. 0.95

  Alignments for each domain:
  == domain 1  score: 398.7 bits;  conditional E-value: 1.9e-123
                    HHHHHHHS-TTTS-HHHHHHHHHHHHTCCTEEEEEEEECHHHHHTT-HHHHHHHTTSSSS--EEEEEEEE-SSTTSEEEEEEEEEEEEEE-TTSS- CS
  Peptidase_M17   2 lardlvntpaneltpeklaeeaeelakeagkvevevldeeeleekgmgallaVgkgSeeepprlveleykgakekekklalVGKGitfDtGGlslK 97 
                    +++d++n p+n++tp++la+  + l+k++  +++++++++ele+kg+g+++aVg+gS +++p+l+ le++  +++ek+++lVGK++tfDtGG+slK
     EPA04797.1 173 FTKDIANLPPNDCTPTTLANVSKILSKKNR-MKCSIISKKELEKKGFGGIVAVGQGS-KNEPKLIILEHRMGSRNEKPIVLVGKAVTFDTGGISLK 266
                    689*****************8665566665.9*************************.66************************************ PP

                    -HHHHTTGGGGGHHHHHHHHHHHHHHHHT-SSEEEEEEEEEEE--STTSTTTTEEEE-TTS-EEEES-TTGCHHHHHHHHHHHHHGCT--SEEEEE CS
  Peptidase_M17  98 psasmeemkaDmgGAAavlgalkavaelklpvnvvavlplaeNmisgkavkpgdvitamnGktvevlnTDaEGRLvLADalayaeekekpdlivdv 193
                    p+++m+emk D++G+++v+g++kav+elklp+n+v+++p +eNm++g++++pgd+i+ ++Gkt e+lnTDaEGR++L+Dal++ e++++p++i+d+
     EPA04797.1 267 PGEKMDEMKFDKCGGCTVIGIMKAVSELKLPINIVGIIPSVENMPGGESYRPGDIIKLYSGKTAEILNTDAEGRIILSDALSFGEKQYSPKAIIDF 362
                    ************************************************************************************9999******** PP

                    E---THHHHHHTTTSEEEEES-HHHHHHHHHHHHHHS-EEEE----HHHGGGG--SSSSEESS-SSSSTHHHHHHHHHHTTSSECGEEEEE-TTTT CS
  Peptidase_M17 194 ATLTgavvvalGkkaaglfsnddelaeelekageeagervwrlpleeeykkqlkskvaDlknvgkkrragaitAalFLkefvketpWaHlDiagta 289
                    ATLTga+++alG+++ag++snd++l+++++++++++ e++w+lpl+++y +++ks+vaD+knvg +r+ag+itAa+FL++ +k+tpW+H+Diag+a
     EPA04797.1 363 ATLTGACIIALGTNVAGIISNDEKLTQKIKESSKRTTEEIWELPLNNDYMDMIKSDVADMKNVGIGRAAGTITAAAFLRNAIKDTPWVHIDIAGVA 458
                    *****************************************************************9999*************77************ PP

                    ES.BTTB.S......EE--TTHHHH CS
  Peptidase_M17 290 lkekealkke....kgatGvgvrtL 310
                    +++ ++++ +    kgatG+gvr++
     EPA04797.1 459 WTQVATKD-KpynpKGATGFGVRLI 482
                    94433222.235689********87 PP

>> Peptidase_M17_N  Cytosol aminopeptidase family, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.6   0.0     3e-20   2.7e-16      11     126 .]      28     140 ..      19     140 .. 0.84
   2 ?   -2.1   0.1      0.36   3.2e+03      48      65 ..     214     231 ..     208     243 .. 0.81

  Alignments for each domain:
  == domain 1  score: 59.6 bits;  conditional E-value: 3e-20
  Peptidase_M17_N  11 spaaekldealagllsellkegdftGkagevlvlralsgekakrvllVGLGkeeeltaealrkaagaaaralkgakvttiavalplegknsd.e 103
                        + ek+d+++  +l++ +  +d+ G  g+++++++ +++  +r+ll GLGk+e++t +++r + g++a++++++k  +  + +p ++  ++ +
       EPA04797.1  28 VLGLEKVDAKIISSLKQSI--KDMGGMFGKIVFIPSEGKT--SRMLLAGLGKKENFTNDTIRFVSGKIAQKARELKLREFSIIVPPSSIVEPiS 117
                      4444567766655555554..5788899999999999975..*******************************************55666667* PP

  Peptidase_M17_N 104 kaeaaaegallglYrfdrykskk 126
                      ++++++eg+ ++lY+f++ykskk
       EPA04797.1 118 AVSQIVEGCKMSLYKFEKYKSKK 140
                      *********************98 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.36
  Peptidase_M17_N  48 sgekakrvllVGLGkeee 65 
                      +++++  +++VG G+++e
       EPA04797.1 214 EKKGFGGIVAVGQGSKNE 231
                      566688899***999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (489 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 3271.23
//
Query:       EPA04798.1  [L=320]
Description: cytosol aminopeptidase family, catalytic domain protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   3.1e-120  401.1   0.0   3.5e-120  401.0   0.0    1.0  1  Peptidase_M17  Cytosol aminopeptidase family, catalytic domai
  ------ inclusion threshold ------
       0.18   12.3   0.0       0.37   11.3   0.0    1.4  1  DUF2746        Protein of unknown function (DUF2746)


Domain annotation for each model (and alignments):
>> Peptidase_M17  Cytosol aminopeptidase family, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  401.0   0.0  3.9e-124  3.5e-120       2     310 ..       4     313 ..       3     314 .. 0.95

  Alignments for each domain:
  == domain 1  score: 401.0 bits;  conditional E-value: 3.9e-124
                    HHHHHHHS-TTTS-HHHHHHHHHHHHTCCTEEEEEEEECHHHHHTT-HHHHHHHTTSSSS--EEEEEEEE-SSTTSEEEEEEEEEEEEEE-TTSS- CS
  Peptidase_M17   2 lardlvntpaneltpeklaeeaeelakeagkvevevldeeeleekgmgallaVgkgSeeepprlveleykgakekekklalVGKGitfDtGGlslK 97 
                    +++d++n p+n++tp++la+  + l+k++  +++++++++ele+kg+g+++aVg+gS +++p+l+ le++  +++ek+++lVGK++tfDtGG+slK
     EPA04798.1   4 FTKDIANLPPNDCTPTTLANVSKILSKKNR-MKCSIISKKELEKKGFGGIVAVGQGS-KNEPKLIILEHRMGSRNEKPIVLVGKAVTFDTGGISLK 97 
                    689*****************8665566665.9*************************.66************************************ PP

                    -HHHHTTGGGGGHHHHHHHHHHHHHHHHT-SSEEEEEEEEEEE--STTSTTTTEEEE-TTS-EEEES-TTGCHHHHHHHHHHHHHGCT--SEEEEE CS
  Peptidase_M17  98 psasmeemkaDmgGAAavlgalkavaelklpvnvvavlplaeNmisgkavkpgdvitamnGktvevlnTDaEGRLvLADalayaeekekpdlivdv 193
                    p+++m+emk D++G+++v+g++kav+elklp+n+v+++p +eNm++g++++pgd+i+ ++Gkt e+lnTDaEGR++L+Dal++ e++++p++i+d+
     EPA04798.1  98 PGEKMDEMKFDKCGGCTVIGIMKAVSELKLPINIVGIIPSVENMPGGESYRPGDIIKLYSGKTAEILNTDAEGRIILSDALSFGEKQYSPKAIIDF 193
                    ************************************************************************************9999******** PP

                    E---THHHHHHTTTSEEEEES-HHHHHHHHHHHHHHS-EEEE----HHHGGGG--SSSSEESS-SSSSTHHHHHHHHHHTTSSECGEEEEE-TTTT CS
  Peptidase_M17 194 ATLTgavvvalGkkaaglfsnddelaeelekageeagervwrlpleeeykkqlkskvaDlknvgkkrragaitAalFLkefvketpWaHlDiagta 289
                    ATLTga+++alG+++ag++sn+++l+++++++++++ e+vw+lpl+++y +++ks+vaD+knvg +r+ag+itAa+FL++ +k+tpW+H+Diag+a
     EPA04798.1 194 ATLTGACIIALGTNVAGIISNNEKLSQKIKESSKRTTEEVWELPLNNDYMDMIKSDVADMKNVGIGRAAGTITAAAFLRNAIKDTPWVHIDIAGVA 289
                    *****************************************************************9999*************77************ PP

                    ES.BTTB.S......EE--TTHHHH CS
  Peptidase_M17 290 lkekealkke....kgatGvgvrtL 310
                    +++ ++++ +    kgatG+gvr++
     EPA04798.1 290 WTQVATKD-KpynpKGATGFGVRLI 313
                    94433222.235689********87 PP

>> DUF2746  Protein of unknown function (DUF2746)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   4.1e-05      0.37       4      72 ..     185     256 ..     183     265 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.1e-05
     DUF2746   4 fnpdsigdyvtllgvafltfsvp.awftgrarkhssdigeikeqvc.nthdtnlrdd.ldsvkadisdlkei 72 
                 + p +i d+ tl g +++++    a +     k s  i e  ++   +  +  l +d +d +k+d++d+k++
  EPA04798.1 185 YSPKAIIDFATLTGACIIALGTNvAGIISNNEKLSQKIKESSKRTTeEVWELPLNNDyMDMIKSDVADMKNV 256
                 7899***********99998754277888999999999997665541678888876648***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 2316.47
//
Query:       EPA04799.1  [L=337]
Description: putative 3-isopropylmalate dehydrogenase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   7.8e-102  341.0   0.4   8.7e-102  340.8   0.4    1.0  1  Iso_dh    Isocitrate/isopropylmalate dehydrogenase
    0.00068   19.1   0.0     0.0013   18.2   0.0    1.5  1  PdxA      Pyridoxal phosphate biosynthetic protein PdxA
  ------ inclusion threshold ------
      0.036   14.3   0.1      0.078   13.3   0.1    1.5  1  TRL       TRL-like protein family


Domain annotation for each model (and alignments):
>> Iso_dh  Isocitrate/isopropylmalate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  340.8   0.4  1.5e-105  8.7e-102       1     348 []       3     333 ..       3     337 .] 0.94

  Alignments for each domain:
  == domain 1  score: 340.8 bits;  conditional E-value: 1.5e-105
                 EEEEEEESTTHHHHHHHHHHHHHHHHHHHT-EEEEEE---THHHHHHHSSSS-HHHHHHHHHSSEEEEEE---CSSSSSSHHHHHHHHHHHTTEEEEEE CS
      Iso_dh   1 kiallegdgiGpevveaalkvlkaakekaglelefeevdvGgaaidetgeplpeetleaikeadvvllgavgtpkekevrpengLlaLrkeldlfanlr 99 
                 ki+l+ gdgiGpe +++a++vl+++++k +l++e+    +G +a++etg++lp+et++ ik++dv l+++vg            ++ Lr++ldl+an+r
  EPA04799.1   3 KISLITGDGIGPELSDSAISVLNTINDKLDLKFEITTLPAGDKALHETGKALPDETIQTIKNSDVCLKAPVGESA------ADVIVVLRRMLDLYANIR 95 
                 799********************************************************************9888......456889************ PP

                 EEE-BCCTTCCSSBTHHHHCT-EEEEEEE-SSCGGCSSEEEEETTG.GGGEEEEEEEEEHHHHHHHHHHHHHHHHHT.TTSEEEEEESTTTTHHHH.HH CS
      Iso_dh 100 pvkvfeklkvksplkrevveevdlvivReltggiYfgeekekkgsifteevavdtklyseeeieriaraafelAlkr.gkkkvtlvdKanvlksse.lw 196
                 p+k+++     s l++    ++d+vivRe+t+++Y g+e    +       av +  +se++++ria++afe+A++r + kkvt+v+K+nv+++++ l+
  EPA04799.1  96 PAKSYP---HMSALRD----DIDMVIVRENTEDLYTGKEFSLGN------AAVALRIISEDASKRIAKYAFETAKQRnNMKKVTCVHKSNVMRMTDgLF 181
                 *****5...6788996....8****************9988877......59************************98899****************** PP

                 HHHHHHHHCCTTTTSEEEEEEHHHHHHHHHHSGGGGSEEEE-HHHHHHHHHHHHHHTTSGCC-EEEEEETSS-EEEEESS---CCCTTSS-S-THHHHH CS
      Iso_dh 197 rkiveevaeeeypdielehqlvDsaamqlvkspkqfdVivtkNlfGDilSDeaaalvGslGllpSaslgekkvaifEavHGsapdiagkdkaNpiavil 295
                  k + eva+ +ypd+ +e+++vD++am+l+++p++fdVivt+NlfGDilSDe +++vG+lG++p a++g +++a+fE+vHG+a diagk++aNp++ +l
  EPA04799.1 182 AKSCIEVAK-NYPDVLFEQMYVDACAMNLIRQPEKFDVIVTTNLFGDILSDESSQVVGGLGMAPAANIG-DNFALFEPVHGAAFDIAGKNIANPSSFLL 278
                 *********.***********************************************************.78*************************** PP

                 HHHHHHHHTTT-HHHH.......HHHHHHHHHHHHHTSCCHHHCTTSTCCCHHHHHHHHH CS
      Iso_dh 296 SaalmLryslgleeaA.......dkiekAvekvleagivTkDlageaakevstsefgdav 348
                 S+ +mL   lg++++        +k+e+ + + +++g++TkD++g      stsef+ ++
  EPA04799.1 279 SIKMMLDW-LGAKHHDtkcftvaQKLESVIFDLVKSGVKTKDIGGDR----STSEFTREI 333
                 ******98.88777655566666************************....666666544 PP

>> PdxA  Pyridoxal phosphate biosynthetic protein PdxA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   2.2e-07    0.0013     256     281 ..     257     282 ..     245     283 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.2e-07
                 ESS-S-TTCTTTT---THHHHHHHHH CS
        PdxA 256 vDhGtafdiagkgkadekSlleAikl 281
                 + hG afdiagk++a+++S+l +ik+
  EPA04799.1 257 PVHGAAFDIAGKNIANPSSFLLSIKM 282
                 78******************999987 PP

>> TRL  TRL-like protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   1.3e-05     0.078      41      74 ..     153     188 ..     148     189 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.3e-05
         TRL  41 ieaaaknggItkiasvDyetksil..glygkyctiV 74 
                 +e+a+++++++k++ v +++   +  gl++k c+ V
  EPA04799.1 153 FETAKQRNNMKKVTCVHKSNVMRMtdGLFAKSCIEV 188
                 79*****************999999*********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2402.51
//
Query:       EPA04800.1  [L=220]
Description: hypothetical protein BG20_I2273, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1372.66
//
Query:       EPA04801.1  [L=237]
Description: LeuA allosteric (dimerization) domain protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.8e-30  104.2   1.2    6.5e-30  103.7   1.2    1.2  1  LeuA_dimer  LeuA allosteric (dimerisation) domain
      0.006   16.1   0.1      0.015   14.9   0.1    1.4  1  DUF4147     Domain of unknown function (DUF4147)
  ------ inclusion threshold ------
       0.29   11.2   2.0       0.46   10.5   0.1    2.2  2  UPF0154     Uncharacterised protein family (UPF0154)


Domain annotation for each model (and alignments):
>> LeuA_dimer  LeuA allosteric (dimerisation) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.7   1.2   1.1e-33   6.5e-30       1     132 [.      91     225 ..      91     226 .. 0.96

  Alignments for each domain:
  == domain 1  score: 103.7 bits;  conditional E-value: 1.1e-33
                 XXXXXXXXXXXXXXXXXXX..--EEEEEEEEEEETTCEEEEEEEEEE.TTEEEEEEEE-SSHHHHHHHHHHHHHHH..T-EEEEEEEE--TT-TT--EE CS
  LeuA_dimer   1 evtdedlealvkdelleae..erlkleklqvssgedelstatvklevkdgeekeasaeGnGpvdAllnAlrkalgv..dikLldYsvhaitegtdaqae 95 
                 ++td +l ++++d+l+e+e  + ++l  ++vs+g ++++ a vkl++ dg+++  +  G+GpvdA+lnA++k++g+  +i+++dY + +i++g+ a+ e
  EPA04801.1  91 QITDVELLSIASDVLGEKElkRIVQLTGFSVSTGIGTMPYAFVKLNI-DGQDHIGTDYGVGPVDAALNAIQKITGKisEIRIKDYGLASISGGSSALCE 188
                 699**************88857789**********************.*************************************************** PP

                 EEEEEE--GGGEEEEEEEESSHHHHHHHHHHHHHHHH CS
  LeuA_dimer  96 vrVelevddgkkvsgvGvdsdiveASlkAlisalnrl 132
                 v+V++e   g+kvs+ +v +div+ S+kA+i+a+nr+
  EPA04801.1 189 VTVKVEDALGNKVSAKSVGEDIVTTSVKAVIDAINRI 225
                 ******666**************************98 PP

>> DUF4147  Domain of unknown function (DUF4147)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   2.5e-06     0.015      87     127 ..     151     191 ..     141     206 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.5e-06
                 --HHHHHHHHHHHHHHSS--TT-EEEEEE-TTHHHHS--B- CS
     DUF4147  87 PdeesveaarkilelaeklkeddlvlvliSGGgSAllaaPa 127
                 P +++++a +ki   +++++ +d  l+ iSGG+SAl+++ +
  EPA04801.1 151 PVDAALNAIQKITGKISEIRIKDYGLASISGGSSALCEVTV 191
                 66789999****************************99765 PP

>> UPF0154  Uncharacterised protein family (UPF0154)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   7.8e-05      0.46      36      59 ..      60      83 ..      57      84 .. 0.92
   2 ?   -0.9   0.3      0.28   1.7e+03      30      40 ..     222     232 ..     220     234 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 7.8e-05
     UPF0154 36 rammkqmGrkPSekqikqvmrsmk 59
                 am+++ G kP+e q kq+++++k
  EPA04801.1 60 NAMLAEYGVKPTEEQSKQILEKVK 83
                58******************9987 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.28
     UPF0154  30 inekmirammk 40 
                 in  m+++m++
  EPA04801.1 222 INRIMLKKMLQ 232
                 78888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1570.41
//
Query:       EPA04802.1  [L=317]
Description: GatB/GatE catalytic domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-19   69.7   7.0    2.4e-19   69.7   7.0    2.2  2  GatB_Yqey        GatB domain
    3.3e-05   23.4   0.3    8.3e-05   22.1   0.0    1.7  2  GatB_N           GatB/GatE catalytic domain
    0.00029   21.0   0.2     0.0011   19.1   0.0    2.1  2  GAD              GAD domain
  ------ inclusion threshold ------
      0.028   13.0   0.7      0.039   12.5   0.7    1.1  1  Dimeth_Pyl       Dimethylamine methyltransferase (Dimeth_PyL)
       0.21   11.0   0.0       0.35   10.3   0.0    1.3  1  Hist_deacetyl    Histone deacetylase domain
       0.43   10.5   3.2        5.6    6.9   0.1    2.8  3  Glycos_trans_3N  Glycosyl transferase family, helical bundle 


Domain annotation for each model (and alignments):
>> GatB_Yqey  GatB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.2      0.23   6.9e+02      29      67 ..     124     162 ..     120     165 .. 0.78
   2 !   69.7   7.0     8e-23   2.4e-19       2     148 .]     168     309 ..     167     309 .. 0.96

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.23
                 HHHTXXTTCSSTTHHHHHHHHHHHHTTSSGHHHHHHHHH CS
   GatB_Yqey  29 nkegleieelkltpeqlaellkliaegkIskkiakevle 67 
                  k++lei++++++++  + l +l ++ +++ + a+++++
  EPA04802.1 124 TKKELEIAKNNIPKSWDESLNELQKKYNLNLQLAEQIFD 162
                 678888888888888888888888888888888888876 PP

  == domain 2  score: 69.7 bits;  conditional E-value: 8e-23
                 HHHHHHHHSS.HHHHHHHHHTCHHHHHHHHTXXTTCSSTTHHHHHHHHHHHHTTSSGHHHHHHHHHHHHHH.TXXHHHHHHHCTXXXXXXSSXHHHHHH CS
   GatB_Yqey   2 ffeevvkegadaklaanwllnellgelnkegleieelkltpeqlaellkliaegkIskkiakevleellee.gkspeeiieekgLkqisdeeeleklve 99 
                  fe++++++  a++ ++ +l  ++++l+++gl+ +   l+ e++++ +++++eg+I+k++++ ++e ++ + +k++e++i+   ++ +s  ee ek+++
  EPA04802.1 168 IFEKICEKTLTAPIFVASILCSTVTNLERNGLNSNL--LKNEEITKTFRFLEEGRITKESIEIIFENIMSGkSKTIEDAIKNTSIQTLSK-EECEKIID 263
                 7******************************98888..9******************************999****************97.******** PP

                 HHHHTXHHHHHHHTTXXTTSTHHHHHHHHHTTSSXSXHHHHHHHHHHHS CS
   GatB_Yqey 100 eviaenpkavedyksgkekalkflvGqvMkktkGkadpklvnellkekL 148
                 ++ ++n    e ++++ke+a+  l+G  Mk+++Gk+ +++vn +l ek+
  EPA04802.1 264 DITKNN---KEIIQNQKERAVSPLMGIAMKELRGKVSGEMVNSILLEKI 309
                 ******...788899*******************************996 PP

>> GatB_N  GatB/GatE catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   2.8e-08   8.3e-05     214     272 ..      69     128 ..      42     129 .. 0.80
   2 ?   -1.4   0.1       0.4   1.2e+03     109     147 ..     249     290 ..     199     313 .. 0.55

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 2.8e-08
                 HHHHHHHHHHHHHHHH....-EEEEEETTTTEEEEECC----...-EEE-TTS--EE--HHHH CS
                 xxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
      GatB_N 214 iekaieyeierqiell....qeTrkfdedkgetvslRskeeaedYryfpepdlppleiseeli 272
                 i+ aie  i+r  ++      eTr + ++ getv lR+++ a   r++pe+d+pp+ ++++ +
  EPA04802.1  69 IDFAIESIIKRISQAKngvpPETRLAIQT-GETVFLRPRPGA--SRMYPETDIPPIIVTKKEL 128
                 444555555555444466779***99998.**********88..6*************99876 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.4
                 EEEEEEEEE---EEEE....EETTEEEEETTSTT-EEEEEEE- CS
                 xxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxx RF
      GatB_N 109 rierihlEeDaaksvh....eekeeslvdlnRaGvpLiEivte 147
                 +i+++  Ee   k +     ++ke    + +Ra  pL+ i+++
  EPA04802.1 249 SIQTLSKEE-CEKIIDditkNNKEIIQNQKERAVSPLMGIAMK 290
                 444443332.223333443223334445567788888877765 PP

>> GAD  GAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   3.7e-07    0.0011      30      90 ..       8      68 ..       4      73 .. 0.90
   2 ?   -2.6   0.1       2.3   6.8e+03      60      77 ..     252     269 ..     239     276 .. 0.63

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 3.7e-07
                HHHHHHHHTTHSHCEEEEESSGGEETTTCCC.S-HHHHHHHHHHCT--TTEEEEEEEEEHHH CS
         GAD 30 eleefakelgakglawikvegegltgpiakf.lteeevkklleavgaeegDillfvAdkkkt 90
                e+ +++ke g   +++ +++g +++++++ + +  + v+ +++ ++ +e+D++l++A + ++
  EPA04802.1  8 EGIRLGKEIGQLVKFY-GIGGVFHSDELPNYgIEDNDVSIVKKILELNENDAFLIIAAPLEK 68
                5668999999999999.****************************************98665 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.3
                 CS-HHHHHHHHHHCT--T CS
         GAD  60 flteeevkklleavgaee 77 
                  l++ee +k+++ +  ++
  EPA04802.1 252 TLSKEECEKIIDDITKNN 269
                 357777777777666555 PP

>> Dimeth_Pyl  Dimethylamine methyltransferase (Dimeth_PyL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.7   1.3e-05     0.039      14      70 ..     227     282 ..     217     312 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.3e-05
  Dimeth_Pyl  14 yltkekiledieaGiadaadlaevpalsedeiekladilvskeklvsveaGkevvlt 70 
                 ++  e+i+    + i+da+  +++++ls++e ek++d +++++k +  ++ ke +++
  EPA04802.1 227 EIIFENIMSGKSKTIEDAIKNTSIQTLSKEECEKIIDDITKNNKEII-QNQKERAVS 282
                 55567888888999**********************99999998763.444444444 PP

>> Hist_deacetyl  Histone deacetylase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00012      0.35     196     235 ..     139     178 ..     110     187 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00012
                    TT---SGGGTTSEEEEEE-TT-BHHHHHHHHHHCHHHHHC CS
                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Hist_deacetyl 196 ledlgegkgkgfnlnvpleegtgdeeylkvfeeilrpvle 235
                    +++  ++ +k++nln++l e++ d++yl++fe+i+++ l 
     EPA04802.1 139 WDESLNELQKKYNLNLQLAEQIFDSQYLEIFEKICEKTLT 178
                    44555677889***********************998875 PP

>> Glycos_trans_3N  Glycosyl transferase family, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       3.2   9.6e+03      17      27 ..      68      78 ..      67      85 .. 0.75
   2 ?    3.5   0.1     0.021        63       9      31 ..     217     239 ..     208     245 .. 0.83
   3 ?    6.9   0.1    0.0019       5.6      11      29 ..     251     269 ..     243     293 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 3.2
                     HHHHHHHHHHT CS
  Glycos_trans_3N 17 eirfaihgilk 27
                      i fai+ i+k
       EPA04802.1 68 KIDFAIESIIK 78
                     68899998877 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.021
                      TT.---HHHHHHHHHHHHTTSS- CS
  Glycos_trans_3N   9 dgeeLtaeeirfaihgilkgevt 31 
                      + +  t+e i+ +++ i++g+ +
       EPA04802.1 217 EEGRITKESIEIIFENIMSGKSK 239
                      55789***************965 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0019
                      .---HHHHHHHHHHHHTTS CS
  Glycos_trans_3N  11 eeLtaeeirfaihgilkge 29 
                      ++L++ee + +i++i+k++
       EPA04802.1 251 QTLSKEECEKIIDDITKNN 269
                      89**************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1448  (0.080763); expected 358.6 (0.02)
Passed bias filter:                      654  (0.0364772); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1952.46
//
Query:       EPA04803.1  [L=359]
Description: chaperone protein DnaJ [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.4e-38  130.4   0.5    7.7e-38  129.9   0.5    1.2  1  DnaJ_C         DnaJ C terminal domain
    1.3e-26   92.4   1.5    2.2e-26   91.7   1.5    1.4  1  DnaJ           DnaJ domain
    8.2e-13   48.5  19.4    1.5e-12   47.7  19.4    1.5  1  DnaJ_CXXCXGXG  DnaJ central domain
  ------ inclusion threshold ------
        3.1    7.8  20.0        6.2    6.9   5.2    2.9  3  Anti-TRAP      Tryptophan RNA-binding attenuator protein inhi
        5.7    7.1  11.7        0.3   11.2   3.4    2.2  2  VWA_N2         VWA N-terminal


Domain annotation for each model (and alignments):
>> DnaJ_C  DnaJ C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.9   0.5   2.1e-41   7.7e-38       3     148 .]     127     340 ..     125     340 .. 0.96

  Alignments for each domain:
  == domain 1  score: 129.9 bits;  conditional E-value: 2.1e-41
                 EEEEE-HHHHHH-.EEE.EEEE.........................................................................TEEE CS
                 xxxxxxxxxxxxxxxxxxxxxxxxx..................................................................xxxxxxxx RF
      DnaJ_C   3 veleisleelykGktkkikikrnvi..................................................................kkekktle 35 
                 +e  ++le++++Gk+ +i+++++                                                                    kk +k+++
  EPA04803.1 127 YETLVTLEDVLHGKKMEINLQKEILceichgsgckpgtnkntcstcngqgqvrksrsmgfasfvtvepcsvcrgegsiiqtpcseckgngkKKGTKKIS 225
                 67789***************99877****************************************************************9877788*** PP

                 EEE-TT--TT-EEEETT-SSSS...S---EEEEEEE---SS-EEETTEEEEEEEEEHHHHHHTEEEEEE-SS-EEEEEE...--TT-EEEETT-S-EET CS
                 xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxx RF
      DnaJ_C  36 vkipaGikdgqkirlegeGdeeg.gepGDlivtikvkphpvFkrkgndlyveveislaeallGgklevptldgkvklki...tqpgevlrikgkGmpkl 130
                 ++ip G+++g+  ++++eG+e + g +GDliv+i+v+php+Fkr+g d++++ +is+ +a+lG+++ vptldg+ k+k+   +qp++++++kgkG+p++
  EPA04803.1 226 FDIPNGVETGD-YTVPEEGNEMPgGINGDLIVRIRVQPHPKFKRDGMDIFYDQDISMIDAALGREIMVPTLDGTEKIKVesgSQPNTIIKLKGKGVPRM 323
                 **********7.899*****8888*************************************************************************** PP

                 ...TEE--EEEEEEEE-- CS
                 xxxxxxxxxxxxxxxxxx RF
      DnaJ_C 131 kkpgkrGdlyvevkvefP 148
                 + +++rGd++v++ v++P
  EPA04803.1 324 N-SKNRGDQFVRIVVNIP 340
                 7.**************99 PP

>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.7   1.5   6.2e-30   2.2e-26       1      63 []       6      67 ..       6      67 .. 0.98

  Alignments for each domain:
  == domain 1  score: 91.7 bits;  conditional E-value: 6.2e-30
                HHHHHHTSSTTG-HHHHHHHHHHHHHHHSTTTSCCHHHHHHHHHHHHHHHHHHTSHHHHHHHH CS
        DnaJ  1 dyYeiLgvskdasedeIkkaYrklalkyHPDknpkdpeaeekFkeineAyevLsdpekRkqYD 63
                dyYe+Lgvsk +s+deIk++Yrklalk+HPD+n k+ ea e+Fkei+eAy vLsd ekRk+YD
  EPA04803.1  6 DYYEVLGVSKASSSDEIKAQYRKLALKFHPDRN-KSAEAGEHFKEISEAYAVLSDTEKRKIYD 67
                8********************************.8889************************9 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.7  19.4   4.3e-16   1.5e-12       1      67 []     152     216 ..     152     216 .. 0.86

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 4.3e-16
  DnaJ_CXXCXGXG   1 CkkCkGsgakkgk.kktCktCkGsGvvreeqkt.lgpfvqqsqstCpeCeGtGkvikekdkCkkCkGkg 67 
                    C+ C+Gsg+k+g+ k+tC+tC+G+G+vr++++  +++fv  + ++C+ C+G+G++i  +++C++CkG+g
     EPA04803.1 152 CEICHGSGCKPGTnKNTCSTCNGQGQVRKSRSMgFASFV--TVEPCSVCRGEGSII--QTPCSECKGNG 216
                    9*********9776999********98887763355555..789************..779******96 PP

>> Anti-TRAP  Tryptophan RNA-binding attenuator protein inhibitory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   6.8     0.004        14      10      42 ..     149     178 ..     143     191 .. 0.86
   2 ?    5.1   3.3    0.0063        22      11      42 ..     167     204 ..     165     207 .. 0.74
   3 ?    6.9   5.2    0.0017       6.2      11      40 ..     193     216 ..     190     226 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.004
                 EEE-TTTTTTSEETTE......E-TTTTTSSEE CS
   Anti-TRAP  10 EtkCdaCngsGkiepeeprasleCPkCsGkgli 42 
                 E  C+ C+gsG  +++       C  C+G+g +
  EPA04803.1 149 EILCEICHGSGCKPGT---NKNTCSTCNGQGQV 178
                 778*************...5558******9976 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0063
                 EE-TTTTTTSEETTE............E-TTTTTSSEE CS
   Anti-TRAP  11 tkCdaCngsGkiepe......eprasleCPkCsGkgli 42 
                 ++C +Cng G++            +  +C  C G+g i
  EPA04803.1 167 NTCSTCNGQGQVRKSrsmgfaSFVTVEPCSVCRGEGSI 204
                 58*********988755444344445589999999876 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0017
                 EE-TTTTTTSEETTE......E-TTTTTSS CS
   Anti-TRAP  11 tkCdaCngsGkiepeeprasleCPkCsGkg 40 
                 ++C  C g G i  +      +C +C+G+g
  EPA04803.1 193 EPCSVCRGEGSIIQT------PCSECKGNG 216
                 68*************......*******87 PP

>> VWA_N2  VWA N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   3.4   8.4e-05       0.3      10      51 ..     137     183 ..     131     194 .. 0.76
   2 ?    0.9   1.0      0.14   5.1e+02      24      45 ..     194     217 ..     187     234 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 8.4e-05
      VWA_N2  10 asGkkiilnredPehCqiChCdG....vn.ltCeaCqkdgkllvPvv 51 
                  +Gkk+ +n +   +C+iCh  G    +n  tC++C+ +g++     
  EPA04803.1 137 LHGKKMEINLQKEILCEICHGSGckpgTNkNTCSTCNGQGQVRKSRS 183
                 69******************766222255369****99998876555 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.14
      VWA_N2  24 hCqiChCdG..vnltCeaCqkdgk 45 
                  C +C  +G  ++  C+ C+ +gk
  EPA04803.1 194 PCSVCRGEGsiIQTPCSECKGNGK 217
                 699999999333456999987776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.52
# Mc/sec: 2075.57
//
Query:       EPA04804.1  [L=362]
Description: glutamyl-tRNA(Gln) amidotransferase, subunit D, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-53  181.1   0.1    2.2e-53  180.6   0.1    1.2  1  Asparaginase    Asparaginase, N-terminal
    1.2e-28   99.6   0.0    2.4e-28   98.6   0.0    1.5  1  Asparaginase_C  Glutaminase/Asparaginase C-terminal domain


Domain annotation for each model (and alignments):
>> Asparaginase  Asparaginase, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.6   0.1   2.5e-57   2.2e-53       1     184 [.      27     217 ..      27     223 .. 0.96

  Alignments for each domain:
  == domain 1  score: 180.6 bits;  conditional E-value: 2.5e-57
                   EEEEEEEESGGGEEECTTS--CCEES-HHHHHCCTTTCCCCSEEEEEEEEEE-GGG--HHHHHHHHHHHHHHC.CT-SEEEEE--STTHHHHHHHHH CS
  Asparaginase   1 kvlvlatGGTiasekdesggalapalsaeellealpelekiaeleseqlanidSsnmtpadwlklaeaieeal.eeydgfVvlhGTDTlaytAsaLs 96 
                   k+l+l+tGGTias++d+++ga++p l+aeel +++pel+kia++++ +l++  S+n+ p++wlk+ae++++   ++y+g++++hGTDT++yt+s+Ls
    EPA04804.1  27 KILLLSTGGTIASKVDYRTGAVTPVLTAEELNSSVPELAKIANVDAIVLFSEYSENIMPQHWLKIAEKLKNYStSDYSGIIIAHGTDTMHYTSSFLS 123
                   79*********************************************************************99666********************* PP

                   HHEES.SSEEEEE--SS-TTSTT-SHHHHHHHHHHHHHCGGTTSECEEEETTE.......EEETTTEEE-BSSSSS-EEETTT--SEEEETTEEE CS
  Asparaginase  97 lmlknldkpvvltGsqrplselrsDgpeNlldAllvaasseriagvlvvfngk.......llranrvtKvhtssldaFespnlgplaevegskvk 184
                   ++l++++ p+ l+Gsqr++++++sD++ Nl++A+++  +  + +gv++v+++        ++ ++rv+K hts++ aF+++  +p   v +++v 
    EPA04804.1 124 FALAGFPIPIALVGSQRSSDRASSDAALNLIGAIKFLVAC-KTNGVYIVMHQDendetiaCHLGTRVRKNHTSKRGAFQTIGDNPAFIVLNDQVI 217
                   ***********************************99998.99*********99***************************99998888677665 PP

>> Asparaginase_C  Glutaminase/Asparaginase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.6   0.0   2.7e-32   2.4e-28       1     114 []     239     352 ..     239     352 .. 0.99

  Alignments for each domain:
  == domain 1  score: 98.6 bits;  conditional E-value: 2.7e-32
                     -EEEEE--TT--HHHHHHHHHTT--EEEEEEBTTTB--HHHHHHHHHHHTTT-EEEEEESSSBS-----H.....HHHHHTEEE-TT--HHHHHH CS
  Asparaginase_C   1 rVvvlklhpgmdtkvlkallkkgakGvvlegtGvGnlpsallealkeakargivvvatsqcpsgsvsnseyeagkelerlgvisaddmtpeaari 95 
                     +V+++k hpg ++++l+++++  + G+++egtG G++ ++++e +k+a ++gi + +tsqc++g+vs+++ye+g++l +lg+i  ++m pe a +
      EPA04804.1 239 KVALIKYHPGYEPDLLEKIIEMDYNGIIFEGTGLGHIGKTMYENVKRAHEKGIFLGMTSQCIDGRVSMTVYESGRDLLNLGIIPLENMIPEVALV 333
                     7********************************************************************************************** PP

                     HHHHHCTT---HHHHHHHH CS
  Asparaginase_C  96 kLmlllgkgldpaevrklf 114
                     k m++lg+ +  ++v++++
      EPA04804.1 334 KAMWALGNSKVLEDVKQIM 352
                     ****************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2427.26
//
Query:       EPA04805.1  [L=431]
Description: putative chaperone protein DnaK, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   6.1e-184  612.5   8.3     8e-184  612.2   8.3    1.0  1  HSP70          Hsp70 protein
    7.1e-17   61.2   2.4    1.6e-16   60.1   2.4    1.5  1  MreB_Mbl       MreB/Mbl protein
    0.00068   19.4   0.0     0.0011   18.8   0.0    1.4  1  FGGY_C         FGGY family of carbohydrate kinases, C-termina
  ------ inclusion threshold ------
      0.017   14.8   0.0      0.076   12.7   0.0    2.1  1  Raco_middle    RACo middle region
      0.022   14.0   1.0       0.34   10.1   0.3    2.1  2  StbA           StbA protein
       0.13   12.0   0.1       0.31   10.7   0.0    1.6  2  Peptidase_M22  Glycoprotease family
       0.23   12.3   2.2         13    6.7   0.0    2.6  2  DUF4065        Protein of unknown function (DUF4065)


Domain annotation for each model (and alignments):
>> HSP70  Hsp70 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  612.2   8.3  3.1e-187    8e-184     103     527 ..       4     429 ..       2     430 .. 0.99

  Alignments for each domain:
  == domain 1  score: 612.2 bits;  conditional E-value: 3.1e-187
                 ETTEEEEHHHHHHHHHHHHHHHHHHHHTSBEEEEEEEEXTTXXHHHHHHHHHHHHHTTXEEEEEEEHHHHHHHHHHTCCSSSCEEEEEEEEXSSXEEEE CS
       HSP70 103 aagekftpeqisamvLkklketaeaylgkkvtdavitvPaYfndaqRqatkdAgkiAGLnvlRivNepTAaalaYGldkkdkernvlvyDlGggtfdvS 201
                 +++++++p+qisa++L+k+k++aea++g++v++avitvPaYf+d+qRqatkdAg+iAGL+v+Ri+NepTAa+la+Gldk++++ ++lv+D+Gggt dv 
  EPA04805.1   4 IQDKNYKPQQISAFILQKIKKDAEAFIGEPVDKAVITVPAYFDDNQRQATKDAGTIAGLDVVRIINEPTAASLAFGLDKTKQDMKILVFDFGGGTLDVT 102
                 6799*********************************************************************************************** PP

                 EEEEETTEEEEEEEEEETTXSHHHHHHHHHHHHHHHHHHHHSXXGGGSHHHHHHHHHHHHHHHHHTTTSSCSEEEEEEEEEETTT..EEEEEEEEHHHH CS
       HSP70 202 ilelekGvfevkaTagDthlGGedfDealvehlveefkkkegidlskdkkalqrlkeaaekaKkeLSsskqteinleietvdedg..kdlseklsRakf 298
                 i+e++ Gvfev +T+gDt+lGG d+D+++++++++efkkkegidlskd+ a+ r++eaaekaK+eLS+ ++t+inl++++ d +   k+l+ +l+Rak+
  EPA04805.1 103 IMEMGGGVFEVMSTSGDTQLGGTDMDKVVINYILDEFKKKEGIDLSKDSTAMARIREAAEKAKIELSTIMETDINLPFISHDPSSgaKNLELRLTRAKL 201
                 *********************************************************************************986559************ PP

                 HHHHHHHHHHTHHHHHHHHHHCTEEGGGCSEEEEESGGGGSHHHHHHHHHHTTCHHBSSSHTTTHHHHHHHHHHHHHCTCGCSHCCEEEEBESS-EEEE CS
       HSP70 299 eelvedllertlepvekalkdaklkkeeidevvlvGGstRiPkvqelvkelfgkepsktvnpDeavaiGAAvqagvlsgeeevkdllllDvtpLslgie 397
                 +el+++++er++ ++ekal+dak++k++++++v+vGG tRiP v++ v e++gkep+++++p eava+GAA+qag+ +g   ++d++llDvtpL+lgie
  EPA04805.1 202 DELIRPIIERCKPSIEKALEDAKISKSDVSKIVMVGGPTRIPLVKKFVGEVLGKEPESGIDPMEAVAMGAAIQAGIIAG-DVTSDIVLLDVTPLTLGIE 299
                 *******************************************************************************.6789*************** PP

                 ETTTEEEEEESTTCBSSEEEEEEEEESSTTSSSEEEEEEESSSSBGGGSEEEEEEEEECESSCSTTCSEEEEEEEEETTSCEEEEEEETTTCCEEEEEE CS
       HSP70 398 tlggvmtkliernttiptkksqvfstaadnqtaveievlqgerelvkdnkllgsfeldgippaprGvpqieVtfdidanGiltvsakdketgkeeeiti 496
                 tlggv + liernttipt+ks+vf+taadnqtav+i+v+qger +++dn +lgsf+l+++ppaprG pqieV+fdidanGi++v+akd +t+ke++iti
  EPA04805.1 300 TLGGVREPLIERNTTIPTSKSKVFTTAADNQTAVTIHVVQGERPMASDNVSLGSFNLTDLPPAPRGIPQIEVKFDIDANGIINVAAKDLGTKKEAKITI 398
                 *************************************************************************************************** PP

                 ECCSSSBHHHHHHHHHHHHHCHHHHHHHHHH CS
       HSP70 497 easeglseeeiekmvkdaeesaeedkkkkea 527
                 +++++ls+eeiek+ +dae++++edkkkk++
  EPA04805.1 399 TSNSKLSKEEIEKLKQDAEKFSDEDKKKKKK 429
                 ***************************9986 PP

>> MreB_Mbl  MreB/Mbl protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.1   2.4   6.2e-20   1.6e-16      82     317 ..      19     273 ..       4     279 .. 0.74

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 6.2e-20
                 HHHHHT.SS-S...S--EEEEEE-SS--HHHHHHHHHHHHHTT-SEEEEEEHHHHHHHHTT--TTSSS-E.EEEEE-SS-EEEEEEETTEEE.....EE CS
    MreB_Mbl  82 ikkvkk.kksl...skprvvicvPsgiteverrAvkeaakkaGarevllieeplaAAiGaglpveepsgn.mvvdiGggttevavislggiv.....ts 170
                 ++k+kk ++++   + ++ vi+vP   ++ +r+A k+a + aG + v +i+ep aA +  gl+ ++   + +v d Gggt +v+++ +gg v     ts
  EPA04805.1  19 LQKIKKdAEAFigePVDKAVITVPAYFDDNQRQATKDAGTIAGLDVVRIINEPTAASLAFGLDKTKQDMKiLVFDFGGGTLDVTIMEMGGGVfevmsTS 117
                 3344442222212266799*******************************************987766552789**************98552222245 PP

                 EEES-SHHHHHHHHHHHHHHHHSEE--H.............HHHHHHHHHH-BSS--HHHHEEEEEEEETTTTCEE.EEEEEHHHHHHHHHHHHHHHHH CS
    MreB_Mbl 171 ksvrvaGdeldeaiikyirkkynlliGe.............rtaekikieigsavkeeeeekmeikGrdlvtglpk.evevsseevrealkepvsaive 255
                    +++G ++d+ +i+yi  +++   G              + aek kie++++++++ +  +    +d  +g    e++++ +++ e ++  +++   
  EPA04805.1 118 GDTQLGGTDMDKVVINYILDEFKKKEGIdlskdstamarirEAAEKAKIELSTIMETDIN--LPFISHDPSSGAKNlELRLTRAKLDELIRPIIERCKP 214
                 5689**************888876544311111111111113355555555555544443..3345566667754337889999999999999999999 PP

                 HHHHHHHTS-HHHHHHHHHH-EEEESGGGGSBTHHHHHHHHHSS-EEE-SSTTTHHHHHHHH CS
    MreB_Mbl 256 avkevLektppeLaadivdrgivltGGgallkgldkllseetglpvkvaedpltcvakGtgk 317
                 +++++Le+++    +d+ +  iv++GG + +  ++k++ e +g + + + dp+++va G+++
  EPA04805.1 215 SIEKALEDAKIS-KSDVSK--IVMVGGPTRIPLVKKFVGEVLGKEPESGIDPMEAVAMGAAI 273
                 999999998765.567764..9999**********************************976 PP

>> FGGY_C  FGGY family of carbohydrate kinases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   4.2e-07    0.0011     124     196 ..     205     277 ..     123     279 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 4.2e-07
      FGGY_C 124 arAaleavalqlrailealekdsgkpldrlavdGGgskndllmqllAdilg.vpVerpktaeatalGaAilAav 196
                 +r ++e +  ++   le  +  s++++++++++GG ++ +l+ ++ +++lg  p    ++ ea+a+GaAi A++
  EPA04805.1 205 IRPIIERCKPSIEKALEDAKI-SKSDVSKIVMVGGPTRIPLVKKFVGEVLGkEPESGIDPMEAVAMGAAIQAGI 277
                 555555555555555555544.5999*************************777667777************86 PP

>> Raco_middle  RACo middle region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0     3e-05     0.076      52     111 ..     198     257 ..     193     275 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3e-05
  Raco_middle  52 eegleklqkavveeinelieelleeagiekeeiyevvvagNttMlhlllgldpkslakap 111
                  + +l++l + ++e  +  ie++le+a+i+k++++++v++g  t + l+ ++  + l+k+p
   EPA04805.1 198 RAKLDELIRPIIERCKPSIEKALEDAKISKSDVSKIVMVGGPTRIPLVKKFVGEVLGKEP 257
                  567899999*******************************99999999888888888877 PP

>> StbA  StbA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.3   0.00013      0.34     144     208 ..      67     134 ..      47     140 .. 0.73
   2 ?    5.7   0.1    0.0028       7.2     169     284 ..     121     242 ..     115     254 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00013
        StbA 144 vlPeslPagfea.lkeldeleslLiiDlGGttLDvakvr..gklegiskvkgdskiGvslitdavkea 208
                 ++ e   a+    l++ ++  + L+ D+GG tLDv+ ++  g + ++  + gd ++G   + + v ++
  EPA04805.1  67 IINEPTAASLAFgLDKTKQDMKILVFDFGGGTLDVTIMEmgGGVFEVMSTSGDTQLGGTDMDKVVINY 134
                 55555555544314456777789***********9855322778888889999999998888887776 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0028
        StbA 169 DlGGttLDvakvrgklegiskvkgdskiGvslitdavkealetaktrtssfladel....iknrkd..eeyLkrrindedkresvlevinekvkkLker 261
                  lGGt +D   ++  l+++ k  g +    s  +  ++ea e+ak++ s+ +  ++    i++      + L+ r++ ++  e +  +i++ + ++++ 
  EPA04805.1 121 QLGGTDMDKVVINYILDEFKKKEGIDLSKDSTAMARIREAAEKAKIELSTIMETDInlpfISHDPSsgAKNLELRLTRAKLDELIRPIIERCKPSIEKA 219
                 59************************9999*****************9999887763333444332113556666766666666667777777788899 PP

        StbA 262 viravsefsgythvmvvGGGael 284
                 + +a  + s+++++++vGG + +
  EPA04805.1 220 LEDAKISKSDVSKIVMVGGPTRI 242
                 999888899*********98764 PP

>> Peptidase_M22  Glycoprotease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.9   4.9e+03     125     169 ..     119     167 ..     112     181 .. 0.48
   2 ?   10.7   0.0   0.00012      0.31      30      60 ..     209     239 ..     203     242 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.9
                    EEEEEEEESSSEH.HHHHHHHHHHHT..SSCCH....HHHHHHCTCS... CS
  Peptidase_M22 125 ryeilgetlddaa.gealdkvarllglpypggp....kieklakegkkie 169
                    + +++g+ +d+++    ld++++  g++ ++       i ++a+++ kie
     EPA04805.1 119 DTQLGGTDMDKVViNYILDEFKKKEGIDLSKDStamaRIREAAEKA-KIE 167
                    5566666665543144456666666666633221011222222222.244 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00012
                    HHHHHHHHHHHHHHHTSTGGGEEEEEEEEES CS
  Peptidase_M22  30 serllplieealaeaglsledldaIavtkgP 60 
                     er+ p ie+al++a++s++d+++I++  gP
     EPA04805.1 209 IERCKPSIEKALEDAKISKSDVSKIVMVGGP 239
                    5899**********************99998 PP

>> DUF4065  Protein of unknown function (DUF4065)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0051        13      81     105 ..     125     149 ..      72     153 .. 0.88
   2 ?    3.3   1.7     0.057   1.5e+02      48      97 ..     391     421 ..     367     430 .. 0.56

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0051
     DUF4065  81 seeekevidkvikkykdlsaseLse 105
                 ++ +k vi+++++++k++ + +Ls+
  EPA04805.1 125 TDMDKVVINYILDEFKKKEGIDLSK 149
                 67899******************97 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.057
     DUF4065  48 pieekeeeisdeklekkekkeveeleddkeae....lseeekevidkvikkykd 97 
                 ++e k++                        +    ls+ee+e +++  +k++d
  EPA04805.1 391 KKEAKITI-----------------------TsnskLSKEEIEKLKQDAEKFSD 421
                 22222233.......................03334777777777766666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1110  (0.0619109); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.61u 0.35s 00:00:00.96 Elapsed: 00:00:00.48
# Mc/sec: 2683.10
//
Query:       EPA04806.1  [L=55]
Description: hypothetical protein BG20_I1819 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       806  (0.0449551); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.29s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 401.65
//
Query:       EPA04807.1  [L=178]
Description: hypothetical protein BG20_I1820 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-13   49.4   1.7    5.8e-13   49.1   1.7    1.1  1  NT5C      5' nucleotidase, deoxy (Pyrimidine), cytosolic type


Domain annotation for each model (and alignments):
>> NT5C  5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   1.7   3.3e-17   5.8e-13       4     164 ..       3     166 ..       1     176 [. 0.77

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 3.3e-17
        NT5C   4 vlvDlDgvladlygkmlevankrfeatllpeevsswd.leefvkPeqreslyrfltepgl.FadlepipgarevL....eeladegrlvvitaallqfy 96 
                 + +D+Dgvlad+++ +l ++n++  ++ +++++++wd +++f     + + + f++e  + ++d ++ip + + L    ++l++ g++ ++ta+ l   
  EPA04807.1   3 IALDVDGVLADVIESWL-IYNNKIRSNISKDDITNWDfWKKF-----KINRFDFYKELTFcWKDWNSIPPTENDLsiatQNLSNLGQVDIVTARELS-T 94 
                 789*************8.8999************87645555.....22335566666664689999998888774444689999*********999.4 PP

        NT5C  97 davkekveWldehlplipyrnlvlvke...kdlvrgDvlidDapknleklrgrs...ilfdsptnrhied..elRa 164
                 d+      Wl+ h   i y+n v v +   k  +  Dv+idD+p n  k+   +   +l+++p n+hi d  ++R+
  EPA04807.1  95 DSF--VKSWLKLH--DISYQNYVSVIDgtmKANLDYDVFIDDSPLNAMKFLQHKkkvLLYSQPWNQHISDpnIQRI 166
                 443..347*****..9*****99886533488899***********98765444455999********97324555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1210.51
//
Query:       EPA04808.1  [L=222]
Description: PET112 family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-35  122.1   0.0    3.3e-35  121.8   0.0    1.0  1  GatB_N    GatB/GatE catalytic domain


Domain annotation for each model (and alignments):
>> GatB_N  GatB/GatE catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.8   0.0   1.8e-39   3.3e-35       2     172 ..      12     215 ..      11     221 .. 0.91

  Alignments for each domain:
  == domain 1  score: 121.8 bits;  conditional E-value: 1.8e-39
                 EEEEEEEEEB--SB-SSSSSBSSSSCE..........STTSS--TTTTTS...........................TT..--.EEHHHHHHHHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxxxx...........................xxxxxx.xxxxxxxxxxxxxxx RF
      GatB_N   2 viGlEiHaqlktksKlFssasteeege..........epnsevsevdlal...........................PGtlPv.lnkeavelaikaala 62 
                 ++GlEiH+ql+t++KlF+s++  e++e          + +se++e+d a+                           P   P+ l+++a +l++ ++ a
  EPA04808.1  12 KVGLEIHQQLSTNKKLFCSCTPFESDEysikfqrklrAVKSELGEYDPAAlfessksktilyyanlessclveqdeeP---PHeLDSNAKNLVLIISSA 107
                 89******************976544456667777755899999999998************************9998...999*************** PP

                 TTEEE-SEE-EEEEE-TCTTCTTSEEEEESSS.SEEEEEEEE.TEEEEEEEEEEEE---EEEEEETTEEEEETTSTT-EEEEEEE-STB-SHHHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
      GatB_N  63 lnceiaeeskfdRKnyfypdlpkgyQitqkeeplakeGslel.ekkvrierihlEeDaaksvheekeeslvdlnRaGvpLiEivtepdlrspeearavv 160
                 l+++i +e++ +RK+++++++++g+Q+t+    + ++G++++  +k+++++i+lEeDaa+ + ++ +   ++l+R+G+pLiEi+ ep   +++++++++
  EPA04808.1 108 LKSNIFSEIYPMRKTVIDGSNTTGFQRTM---LISQGGHIDVnGEKIGVQSICLEEDAARLLGDKGNIREYSLDRLGIPLIEIALEPVEGDSKKVKKLL 203
                 *****************************...5669*****97789********************9****************************9999 PP

                 HHHHHHHHHHTS CS
                 xxxxxxxxxxxx RF
      GatB_N 161 eklrellralgv 172
                   l++  ++ + 
  EPA04808.1 204 WLLEDYYEVQKR 215
                 888887766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1444.23
//
Query:       EPA04809.1  [L=108]
Description: hypothetical protein BG20_I2665, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 826.90
//
Query:       EPA04810.1  [L=57]
Description: hypothetical protein BG20_I2664, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.4e-06   25.2   1.2     0.0037   17.0   0.1    2.1  2  TPR_1     Tetratricopeptide repeat
    1.1e-05   25.0   0.2    1.5e-05   24.6   0.2    1.1  1  TPR_11    TPR repeat
    7.8e-05   22.5   0.1     0.0019   18.1   0.0    2.1  2  TPR_2     Tetratricopeptide repeat
    0.00021   21.9   0.0    0.00026   21.6   0.0    1.1  1  TPR_14    Tetratricopeptide repeat
    0.00074   20.0   0.0      0.001   19.5   0.0    1.3  1  TPR_19    Tetratricopeptide repeat
    0.00075   19.7   1.9     0.0023   18.2   0.2    2.3  2  TPR_17    Tetratricopeptide repeat
     0.0026   18.3   0.1      0.044   14.4   0.0    2.0  2  TPR_6     Tetratricopeptide repeat
     0.0035   18.0   0.0     0.0041   17.7   0.0    1.1  1  TPR_16    Tetratricopeptide repeat
     0.0053   16.9   0.0     0.0056   16.9   0.0    1.0  1  ANAPC3    Anaphase-promoting complex, cyclosome, subunit 3
     0.0056   16.8   0.4       0.35   11.2   0.0    2.1  2  TPR_8     Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   2.1e-06    0.0037       8      34 .]      16      42 ..      12      42 .. 0.93
   2 !    7.7   0.1    0.0018       3.3       2      13 ..      44      55 ..      43      57 .] 0.85

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.1e-06
                HHHHHHTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1  8 GnayfklgkydeAleyyekALelnPnn 34
                ++ ++++++++ A++ ++k L+ nP+n
  EPA04810.1 16 AMSLMEKNQPKGAIALFNKILKQNPKN 42
                78899********************98 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0018
                HHHHHHHHHHHH CS
       TPR_1  2 kalynlGnayfk 13
                +alyn+G+a+ +
  EPA04810.1 44 EALYNKGLALNQ 55
                89******9976 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.2   8.1e-09   1.5e-05       4      38 ..      19      53 ..      18      56 .. 0.94

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 8.1e-09
      TPR_11  4 yyeqGkyeeAieaYkkAlkldPdnaeayynLGlay 38
                ++e+++ ++Ai+ ++k lk +P+n ea+yn Gla+
  EPA04810.1 19 LMEKNQPKGAIALFNKILKQNPKNIEALYNKGLAL 53
                6899999**************************97 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.1e-06    0.0019       8      34 .]      16      42 ..      16      42 .. 0.96
   2 ?    2.7   0.1     0.095   1.7e+02       2      11 ..      44      53 ..      43      55 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.1e-06
       TPR_2  8 GlayyklgdyeeAleafekAleldPnn 34
                +++++++++++ A+++f+k l+ +P+n
  EPA04810.1 16 AMSLMEKNQPKGAIALFNKILKQNPKN 42
                689**********************97 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.095
       TPR_2  2 ealynlGlay 11
                ealyn Gla+
  EPA04810.1 44 EALYNKGLAL 53
                6777777765 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   1.4e-07   0.00026       9      41 ..      17      49 ..      11      52 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.4e-07
      TPR_14  9 eallalGdpdeAiallrralalaPddaeawlll 41
                  l++  +p++Aial++++l+++P++ ea++  
  EPA04810.1 17 MSLMEKNQPKGAIALFNKILKQNPKNIEALYNK 49
                5688999*********************99765 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   5.7e-07     0.001       1      30 [.      19      50 ..      19      57 .] 0.86

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 5.7e-07
      TPR_19  1 llaegdyaeAlalleqalqedpknaearl..l 30
                l++ +++  A+al+ ++l+++pkn ea++  +
  EPA04810.1 19 LMEKNQPKGAIALFNKILKQNPKNIEALYnkG 50
                78999***********************9444 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.47   8.4e+02      12      17 ..       9      14 ..       6      30 .. 0.57
   2 !   18.2   0.2   1.3e-06    0.0023       1      23 [.      31      53 ..      31      57 .] 0.91

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.47
      TPR_17 12 nadayn 17
                n+d+++
  EPA04810.1  9 NSDLMY 14
                555555 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 1.3e-06
      TPR_17  1 lylkaleldPnnadaynnLAell 23
                l+ k l+++P+n +a++n++ +l
  EPA04810.1 31 LFNKILKQNPKNIEALYNKGLAL 53
                799*****************998 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   2.4e-05     0.044       7      32 ..      16      41 ..      11      42 .. 0.82
   2 ?    2.3   0.0      0.18   3.3e+02       1      10 [.      44      53 ..      44      57 .] 0.85

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.4e-05
                HHHHHHHHHHHHHHHHHHHHHHH-TT CS
       TPR_6  7 alsyrklgdtdkAlealerlikeYPd 32
                a+s+ + +++  A++++++++k+ P+
  EPA04810.1 16 AMSLMEKNQPKGAIALFNKILKQNPK 41
                56666656*****************8 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.18
                HHHHHHHHHH CS
       TPR_6  1 dAlyklalsy 10
                +Aly+ +l++
  EPA04810.1 44 EALYNKGLAL 53
                79*****997 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   2.3e-06    0.0041       4      45 ..      16      54 ..      16      57 .] 0.94

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.3e-06
      TPR_16  4 araalragdyddAaaaleaalkrdpssPdaaeAllllgdaal 45
                a+++++ +++  A+a+++  lk++   P + eAl+++g+a+ 
  EPA04810.1 16 AMSLMEKNQPKGAIALFNKILKQN---PKNIEALYNKGLALN 54
                78999*******************...************985 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   3.1e-06    0.0056      20      67 ..       6      54 ..       3      57 .] 0.88

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.1e-06
                H--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHH CS
      ANAPC3 20 tespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcll 67
                + +++d+++ A +l + +q k A+ l++k  k+n+k+++++y ++ +l 
  EPA04810.1  6 STNNSDLMYDAMSLMEKNQPKGAIALFNKIlKQNPKNIEALYNKGLALN 54
                5688899999********************************8887765 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   0.00019      0.35       8      34 .]      16      42 ..      16      42 .. 0.93
   2 ?    4.2   0.1     0.034        61       2      13 ..      44      55 ..      43      57 .] 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00019
                HHHHHHTT-HHHHHHHHHHHHHHHHH. CS
       TPR_8  8 gsiylklgdyeeAkeyyekaleldpdn 34
                ++ ++++++ + A++ ++k l+ +p+n
  EPA04810.1 16 AMSLMEKNQPKGAIALFNKILKQNPKN 42
                578999*******************97 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.034
                CHHHHHHHHHHH CS
       TPR_8  2 eayynlgsiylk 13
                ea+yn+g+++ +
  EPA04810.1 44 EALYNKGLALNQ 55
                89*****99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.35u 0.28s 00:00:00.63 Elapsed: 00:00:00.43
# Mc/sec: 398.97
//
Query:       EPA04811.1  [L=34]
Description: hypothetical protein BG20_I2454, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (34 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.42
# Mc/sec: 243.34
//
Query:       EPA04812.1  [L=275]
Description: type I secretion target GGXGXDXXX repeat (2 copies), partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-44  149.4 119.3    1.1e-10   41.2  16.2    4.5  6  HemolysinCabind  RTX calcium-binding nonapeptide repeat (4 co
    0.00025   20.7   2.6      0.023   14.5   0.5    3.0  3  Ephrin_rec_like  Putative ephrin-receptor like
     0.0021   18.0   0.1     0.0041   17.1   0.1    1.5  1  NHL              NHL repeat


Domain annotation for each model (and alignments):
>> HemolysinCabind  RTX calcium-binding nonapeptide repeat (4 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   4.9   3.7e-14   2.2e-10       1      34 [.     129     162 ..     129     164 .. 0.98
   2 !   34.5  14.6   2.4e-12   1.4e-08       4      36 .]     159     191 ..     157     191 .. 0.93
   3 !   41.2  16.2   1.9e-14   1.1e-10       1      36 []     165     200 ..     165     200 .. 0.96
   4 !   39.1  14.9     9e-14   5.4e-10       2      36 .]     184     218 ..     183     218 .. 0.97
   5 !   37.4  15.6     3e-13   1.8e-09       2      36 .]     193     227 ..     192     227 .. 0.96
   6 !   23.1  13.2   9.1e-09   5.5e-05       2      36 .]     220     254 ..     219     254 .. 0.94

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 3.7e-14
  HemolysinCabind   1 yGgdGnDtlvGgaGnDtiyGgaGnDtlyGGaGnD 34 
                      +G+ GnD + G++GnD i+G +GnD ++G +GnD
       EPA04812.1 129 DGTPGNDKIKGTNGNDLIFGYEGNDKIDGKKGND 162
                      69*******************************9 PP

  == domain 2  score: 34.5 bits;  conditional E-value: 2.4e-12
  HemolysinCabind   4 dGnDtlvGgaGnDtiyGgaGnDtlyGGaGnDtl 36 
                       GnD ++Gg+GnD i+Gg+G+Dt+ G++G+D +
       EPA04812.1 159 KGNDCIIGGTGNDKIHGGDGDDTIQGNEGDDKI 191
                      6******************************65 PP

  == domain 3  score: 41.2 bits;  conditional E-value: 1.9e-14
  HemolysinCabind   1 yGgdGnDtlvGgaGnDtiyGgaGnDtlyGGaGnDtl 36 
                      +Gg GnD ++Gg+G+Dti G++G+D ++GG+GnD +
       EPA04812.1 165 IGGTGNDKIHGGDGDDTIQGNEGDDKISGGKGNDKI 200
                      6*********************************65 PP

  == domain 4  score: 39.1 bits;  conditional E-value: 9e-14
  HemolysinCabind   2 GgdGnDtlvGgaGnDtiyGgaGnDtlyGGaGnDtl 36 
                      G++G+D + Gg GnD i+Gg+G+D ++GG++nD +
       EPA04812.1 184 GNEGDDKISGGKGNDKIFGGDGDDKINGGKDNDMI 218
                      9********************************86 PP

  == domain 5  score: 37.4 bits;  conditional E-value: 3e-13
  HemolysinCabind   2 GgdGnDtlvGgaGnDtiyGgaGnDtlyGGaGnDtl 36 
                      Gg GnD ++Gg+G+D i+Gg +nD ++GG GnD l
       EPA04812.1 193 GGKGNDKIFGGDGDDKINGGKDNDMISGGLGNDKL 227
                      9********************************65 PP

  == domain 6  score: 23.1 bits;  conditional E-value: 9.1e-09
  HemolysinCabind   2 GgdGnDtlvGgaGnDtiyGgaGnDtlyGGaGnDtl 36 
                      Gg GnD l+Gg+GnD+i+Gg G +  +GG+G +t+
       EPA04812.1 220 GGLGNDKLHGGQGNDSIDGGTGINKCNGGQGINTI 254
                      999****************************9997 PP

>> Ephrin_rec_like  Putative ephrin-receptor like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.5   3.8e-06     0.023       1      44 [.      32      75 ..      32      76 .. 0.94
   2 !   12.3   0.4   1.7e-05       0.1      12      47 ..      60      95 ..      60      96 .. 0.74
   3 !    4.8   0.3    0.0039        23      11      44 ..      76     108 ..      75     110 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.8e-06
  Ephrin_rec_like  1 GtysntgletCipCprgtYqneegqlsClaCPlgtttkkpgats 44
                     G+ys tg ++C+  + g + +++g +  ++C +g+++  +gats
       EPA04812.1 32 GSYSMTGFVPCTFASAGNFVDNVGATFEIPCSPGNYQPGIGATS 75
                     89999********************************9999998 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 1.7e-05
  Ephrin_rec_like 12 ipCprgtYqneegqlsClaCPlgtttkkpgatsesd 47
                     ipC+ g Yq+ +g +sC+    g++   +ga ++++
       EPA04812.1 60 IPCSPGNYQPGIGATSCIISDVGFFVPLSGAIQQTK 95
                     69***************8655555555555555555 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.0039
  Ephrin_rec_like  11 CipCprgtYqneegqlsClaCPlgtttkkpgats 44 
                      Ci    g++ + +g  + ++CP+g  t+ +gats
       EPA04812.1  76 CIISDVGFFVPLSGAIQQTKCPEGS-TSVQGATS 108
                      7777889999999999999***875.55667776 PP

>> NHL  NHL repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   6.8e-07    0.0041       8      28 .]       1      21 [.       1      21 [. 0.95

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6.8e-07
                EEETTTEEEEEECCCTEEEEE CS
         NHL  8 avdsnGdiyVaDsenhrvqvF 28
                avds G+iyV+D en+rvq+F
  EPA04812.1  1 AVDSVGNIYVSDPENNRVQIF 21
                78899***************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       230  (0.0128284); expected 358.6 (0.02)
Passed bias filter:                      144  (0.00803168); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.58
# Mc/sec: 1429.91
//
Query:       EPA04813.1  [L=70]
Description: hypothetical protein BG20_I2455 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-16   59.0   0.9    3.9e-16   58.9   0.9    1.1  1  DUF167    Uncharacterised ACR, YggU family COG1872
      0.001   19.0   1.1     0.0067   16.4   0.3    2.0  2  MinE      Septum formation topological specificity factor Min


Domain annotation for each model (and alignments):
>> DUF167  Uncharacterised ACR, YggU family COG1872
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.9   0.9   4.3e-20   3.9e-16      23      76 ..      15      68 ..       4      69 .. 0.92

  Alignments for each domain:
  == domain 1  score: 58.9 bits;  conditional E-value: 4.3e-20
                -TTTT-------TTIIIIIHHHHHHHHHHHHHS...SEEEE-S-GGGSEEEEEE CS
      DUF167 23 aegrealkvrvaappvdGkANkalikfLakalgvpksdveivsGeksreKvvri 76
                 +++e++ + ++++p +G+ANk++ik L+k ++v+ s+++i sG+ks+eK++++
  EPA04813.1 15 TIKDEQITIGIKSKPIKGEANKEIIKKLSKYFKVSSSKIQIRSGHKSSEKIIQV 68
                467899**********************************************98 PP

>> MinE  Septum formation topological specificity factor MinE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.033   2.9e+02      37      53 ..      11      27 ..       7      34 .. 0.82
   2 !   16.4   0.3   7.5e-07    0.0067      29      59 ..      35      64 ..      31      69 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.033
                HHHH-..-SEEEEEEE- CS
        MinE 37 skYveideekvevklek 53
                +++  i++e++++ +++
  EPA04813.1 11 KDFLTIKDEQITIGIKS 27
                57899*******99984 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 7.5e-07
                HHHHHHHHHHHH-..-SEEEEEEE--.-E..E CS
        MinE 29 keeileviskYveideekvevkleke.kedvs 59
                 +ei++ +skY++++++k++++  ++ +e  +
  EPA04813.1 35 NKEIIKKLSKYFKVSSSKIQIRSGHKsSE--K 64
                58*******************98866343..4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       891  (0.049696); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 493.56
//
Query:       EPA04814.1  [L=67]
Description: acylphosphatase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.2e-16   58.2   0.1    8.8e-16   58.1   0.1    1.0  1  Acylphosphatase  Acylphosphatase


Domain annotation for each model (and alignments):
>> Acylphosphatase  Acylphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.1   0.1   4.9e-20   8.8e-16      22      85 .]       2      65 ..       1      65 [. 0.97

  Alignments for each domain:
  == domain 1  score: 58.1 bits;  conditional E-value: 4.9e-20
  Acylphosphatase 22 AkelglkGyvrNlsdgsVeivaegeeekvekfleelksgppkarvdeveveeleeeeefkdFei 85
                     Ak+ +++G+v+Nl+dg+Ve+v+eg+eekv++++e+ + gp +arv++ve+ +++  +ef++F++
       EPA04814.1  2 AKKNNVSGWVKNLKDGRVEAVLEGDEEKVSRLVEWSHGGPANARVEDVEIRNEKFIGEFSKFDV 65
                     99************************************************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       262  (0.0146132); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.45
# Mc/sec: 449.40
//
Query:       EPA04815.1  [L=244]
Description: ribosomal protein L2, RNA binding domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.9e-35  119.8   2.8    1.3e-34  119.1   2.8    1.3  1  Ribosomal_L2_C  Ribosomal Proteins L2, C-terminal domain
    9.5e-09   35.1   0.0    3.1e-08   33.5   0.0    1.9  2  Ribosomal_L2    Ribosomal Proteins L2, RNA binding domain


Domain annotation for each model (and alignments):
>> Ribosomal_L2_C  Ribosomal Proteins L2, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.1   2.8   1.4e-38   1.3e-34       2     120 ..      92     221 ..      91     227 .. 0.92

  Alignments for each domain:
  == domain 1  score: 119.1 bits;  conditional E-value: 1.4e-38
                     SSS-EBSSSS-TTB-BBSE-SSTTS--SSS-SSSB-EEBB-B.SSEEEEEETTS-EEEEETTSBEBES-BS-TTCTT----STTHHHHT.....T CS
  Ribosomal_L2_C   2 vGnvlplknipeGtivhnielkpgkggklarsaGtyaqvvakegkkvtvklpSgevrkvssecrAtiGvvsngehkekklgkAgrkrwl.....g 91 
                     +Gnv+ ++nip Gtiv+n+e++ g+gg +++saGt a+v+++ ++ vt+klpSg+  +++ ++rA+iG++++g+ +e+ ++ Ag+k  +     +
      EPA04815.1  92 KGNVISVQNIPDGTIVCNVEKHFGDGGAIVKSAGTNATVFSHGEEGVTLKLPSGKFTTLNPKNRAMIGTLAGGGASERFFMSAGNKWRSfrakgK 186
                     7*****************************************99****************************************88877999999 PP

                     BS----SSSS-TTTSSS--SS....SS..--SSSS CS
  Ribosomal_L2_C  92 rrpkvrGvamnpvdHphGGGe....Gk..tksrka 120
                     + p vrGva  ++ HphGGG+    G+  t+sr+a
      EPA04815.1 187 KFPIVRGVAQAAYVHPHGGGRhqhvGQssTVSRNA 221
                     9********************66665533444555 PP

>> Ribosomal_L2  Ribosomal Proteins L2, RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.0   3.5e-12   3.1e-08       1      75 [.      11      82 ..      11      84 .. 0.93
   2 ?   -3.3   0.0         1   9.3e+03      44      64 ..     152     172 ..     151     176 .. 0.66

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 3.5e-12
                  TB-TT.--BSSTT--------EE-B--S---SS--EEEEEEE--TT-SS-EEEEEETTTEEEEEE--SS--SS-EE CS
  Ribosomal_L2  1 Grnns.gritvrhrggGhkkkyrlidfkrnkekvkgkVveieyDpgRsApiAlvkyedgekryiiapeglkvGdtv 75
                  Gr+   +r+t+  + g  k+ky+ ++     e+ +g ++++ +  gR Ap+A v +edg+ +++ a+ g kvG+t+
    EPA04815.1 11 GRGGFqFRSTSTGKVG-SKAKYPRFSLS---EQHEGLIIDLVHERGREAPLAKVRFEDGSVSFMPAVLGTKVGETL 82
                  888888********99.99********4...567788************************************986 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1
                   TT-SS-EEEEEETTTEEEEEE CS
  Ribosomal_L2  44 pgRsApiAlvkyedgekryii 64 
                   p   A i+ ++ +  ++r+++
    EPA04815.1 152 PKNRAMIGTLAGGGASERFFM 172
                   566677888877776666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 1370.45
//
Query:       EPA04816.1  [L=112]
Description: hypothetical protein TIGR00269, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.25   10.9   4.2       0.88    9.2   4.1    2.1  2  RecR      RecR protein


Domain annotation for each model (and alignments):
>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0      0.31   5.6e+03       1      11 [.      45      55 ..      45      61 .. 0.68
   2 ?    9.2   4.1   4.9e-05      0.88      18      35 ..      85     102 ..      80     106 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.31
                HHHHHHHHHHH CS
        RecR  1 eaeeLaeaLqe 11
                e++e+ ++L+ 
  EPA04816.1 45 EIREFLNSLEG 55
                57889999875 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 4.9e-05
                 E-TTT--EESSSS-CCCC CS
        RecR  18 hCsrCgnlteedlCaICs 35 
                  C +Cgn ++  +C++C+
  EPA04816.1  85 ICVKCGNECTGKICSVCN 102
                 6****************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       996  (0.0555525); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 651.21
//
Query:       EPA04817.1  [L=110]
Description: hypothetical protein BG20_I2207 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       679  (0.0378716); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 714.07
//
Query:       EPA04818.1  [L=284]
Description: cell division protein 48 (CDC48), domain 2, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.1e-31  105.9   0.1    3.2e-30  104.1   0.2    1.8  2  CDC48_N          Cell division protein 48 (CDC48), N-terminal
      1e-28  100.4   0.0    1.7e-28   99.7   0.0    1.4  1  AAA              ATPase family associated with various cellul
    4.1e-09   36.1   0.1    8.5e-09   35.1   0.1    1.5  1  CDC48_2          Cell division protein 48 (CDC48), domain 2
      4e-08   33.2   0.0    6.3e-08   32.5   0.0    1.4  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    6.7e-06   26.6   0.1    8.2e-05   23.0   0.0    2.1  2  AAA_16           AAA ATPase domain
    2.7e-05   23.6   0.1    6.8e-05   22.2   0.0    1.7  2  TIP49            TIP49 P-loop domain
    0.00012   22.4   0.0     0.0014   18.9   0.0    2.1  2  AAA_22           AAA domain
    0.00022   21.2   0.2     0.0028   17.7   0.1    2.6  2  AAA_5            AAA domain (dynein-related subfamily)
    0.00023   21.3   0.0    0.00047   20.3   0.0    1.5  1  AAA_2            AAA domain (Cdc48 subfamily)
    0.00059   19.9   0.0     0.0011   19.0   0.0    1.4  1  AAA_14           AAA domain
    0.00077   19.6   0.0     0.0012   19.0   0.0    1.3  1  AAA_33           AAA domain
     0.0013   18.5   0.0      0.002   17.9   0.0    1.3  1  IstB_IS21        IstB-like ATP binding protein
     0.0054   17.0   0.0     0.0092   16.2   0.0    1.4  1  AAA_28           AAA domain
     0.0056   17.0   0.0      0.013   15.9   0.0    1.6  1  RNA_helicase     RNA helicase
     0.0064   16.0   0.0      0.011   15.2   0.0    1.5  1  AAA_7            P-loop containing dynein motor region
     0.0069   16.1   0.0      0.017   14.9   0.0    1.7  1  Sigma54_activat  Sigma-54 interaction domain
     0.0072   15.7   0.1      0.013   14.9   0.1    1.3  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0092   15.3   0.0      0.024   13.9   0.0    1.7  2  Zeta_toxin       Zeta toxin
  ------ inclusion threshold ------
       0.01   15.6   0.0      0.018   14.8   0.0    1.5  1  AAA_24           AAA domain
      0.013   14.8   0.1      0.038   13.3   0.0    1.6  1  ATPase           KaiC
      0.022   15.3   0.0      0.037   14.6   0.0    1.4  1  AAA_18           AAA domain
      0.028   13.6   0.0      0.037   13.2   0.0    1.2  1  DUF815           Protein of unknown function (DUF815)
      0.038   14.0   0.0      0.064   13.3   0.0    1.3  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.057   12.6   0.0      0.091   11.9   0.0    1.2  1  NB-ARC           NB-ARC domain
      0.059   12.5   0.0       0.09   11.8   0.0    1.2  1  Parvo_NS1        Parvovirus non-structural protein NS1
      0.059   12.8   0.0       0.11   12.0   0.0    1.3  1  PhoH             PhoH-like protein
      0.062   12.5   0.0       0.11   11.7   0.0    1.4  2  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.085   12.8   0.1       0.24   11.3   0.0    1.8  1  ATPase_2         ATPase domain predominantly from Archaea
       0.11   13.0   0.0        0.2   12.1   0.0    1.4  1  ABC_tran         ABC transporter
       0.16   11.6   0.0       0.35   10.4   0.0    1.6  1  AAA_25           AAA domain
       0.16   11.8   0.0       0.27   11.1   0.0    1.4  1  AAA_3            ATPase family associated with various cellul
       0.19   11.5   0.0       0.25   11.1   0.0    1.2  1  AAA_11           AAA domain


Domain annotation for each model (and alignments):
>> CDC48_N  Cell division protein 48 (CDC48), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.1   0.2   5.7e-33   3.2e-30       2      84 ..       8      90 ..       7      92 .. 0.98
   2 ?   -1.9   0.0         7   3.9e+03      21      39 ..     200     218 ..     199     245 .. 0.57

  Alignments for each domain:
  == domain 1  score: 104.1 bits;  conditional E-value: 5.7e-33
                EEEECCSS-CSSTTEEEE-HHHHHHHTS-TTSEEEEECCCCEEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEEEEEEE- CS
     CDC48_N  2 LrVaeapqedvgrgivridpedmeelglepgdvveiegkrkTvaivwpaepedegkgiIrmdgvtRknagvsiGdkVtVrkae 84
                L+V ea+ +dvgrg++rid + m+ l+ ++gdv+ei+gkr+Tva+++p++p+degkgiIr+dg+ R+n g+ iGd++tVrk++
  EPA04818.1  8 LKVLEAYTRDVGRGVARIDYDSMDTLNASTGDVIEIKGKRRTVAKCLPLYPSDEGKGIIRIDGLGRNNSGIAIGDTITVRKIK 90
                9*******************************************************************************987 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 7
                 HHHHHHHTS-TTSEEEEEC CS
     CDC48_N  21 pedmeelglepgdvveieg 39 
                 pe +e+lg+e  + v + g
  EPA04818.1 200 PEIFEKLGIEAPKGVLLYG 218
                 7888889888887777755 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.7   0.0   3.1e-31   1.7e-28       1      71 [.     214     283 ..     214     284 .] 0.98

  Alignments for each domain:
  == domain 1  score: 99.7 bits;  conditional E-value: 3.1e-31
                 EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHH CS
         AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidala 71 
                 vllyGppGtGKTllakava+e++++f++isg+e++sk+ gese+++re+fkea+eka psi+f+DEid++a
  EPA04818.1 214 VLLYGPPGTGKTLLAKAVANESQAHFISISGPEIMSKFYGESEARLREIFKEAREKA-PSIIFVDEIDSIA 283
                 79******************************************************9.***********98 PP

>> CDC48_2  Cell division protein 48 (CDC48), domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.1   1.5e-11   8.5e-09       7      60 ..     110     164 ..     104     167 .. 0.91

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 1.5e-11
                 CHHHHCCCTTEEE-TTEEEEECCTCCCEEEEEEEECCCC.SCEEECTSCCEEEST CS
     CDC48_2   7 maylkrqFlgrpvtkGdlvvfefkgqeiklvVvstePkg.pvgitetTeielgtk 60 
                 + yl +++++ p+ kGd v+++++g+ +++ V +++P+  +v +t +T  ++ +k
  EPA04818.1 110 ERYLADALESVPLIKGDNVMVPYFGGRLTFQVIGVTPAAdAVLVTQKTVFHIAEK 164
                 55***********************************98899******9999876 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.0   1.1e-10   6.3e-08      31      96 ..     209     282 ..     185     284 .] 0.79

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 1.1e-10
      RuvB_N  31 ealdhvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrl 96 
                 ea   vllyGpPG Gkt lak +a+e ++++ + sgP +      e ++ l  ++++ +ek   ++f+dei  +
  EPA04818.1 209 EAPKGVLLYGPPGTGKTLLAKAVANESQAHFISISGPEImskfygESEARLREIFKEAREKapSIIFVDEIDSI 282
                 566789*******************************9933222233455666666665543379*****9765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   1.5e-07   8.2e-05      17      58 ..     204     242 ..     181     254 .. 0.78
   2 ?    1.1   0.0       0.8   4.5e+02     122     146 ..     258     281 ..     252     284 .] 0.74

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1.5e-07
      AAA_16  17 ervrsgrpelvllsGesGvGKsslvrellralekdggiflrg 58 
                 e++    p  vll+G++G+GK+ l+++++++ +   ++f++ 
  EPA04818.1 204 EKLGIEAPKGVLLYGPPGTGKTLLAKAVANESQ---AHFISI 242
                 5555566799*******************7554...446554 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.8
      AAA_16 122 llkrllallsrderplvlvlDdlqw 146
                  l+++++ +++ + p ++++D+++ 
  EPA04818.1 258 RLREIFKEARE-KAPSIIFVDEIDS 281
                 46666677777.6679999999985 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       3.6     2e+03     163     187 ..      27      51 ..      19      53 .. 0.76
   2 !   22.2   0.0   1.2e-07   6.8e-05      50     100 ..     211     259 ..     203     274 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.6
                 HHHHHHHT--TT-EEEEETTT--EE CS
       TIP49 163 aeellkekvkegDviviekesGkvk 187
                 ++++++ + ++gDvi i+ ++ +v 
  EPA04818.1  27 YDSMDTLNASTGDVIEIKGKRRTVA 51 
                 5677788888999999987766665 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 1.2e-07
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
       TIP49  50 GravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkktevlt 100
                  ++vLl Gp+gtGkt la a+++e   + +f+++sg e+ s     +e+ +
  EPA04818.1 211 PKGVLLYGPPGTGKTLLAKAVANES--QAHFISISGPEIMSKFYGESEARL 259
                 699********************95..69***********98887777644 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   2.5e-06    0.0014       8      32 ..     214     238 ..     209     265 .. 0.75
   2 ?    1.3   0.0       0.7   3.9e+02      78     103 ..     259     282 ..     249     283 .. 0.63

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.5e-06
      AAA_22   8 lvvtGesGtGKTtllrrlleqldee 32 
                 ++++G++GtGKT+l++ ++++ +++
  EPA04818.1 214 VLLYGPPGTGKTLLAKAVANESQAH 238
                 689*****************98543 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.7
      AAA_22  78 llealeqalraravielliiDEaqhl 103
                 l + + + +r++a  +++ +DE++ +
  EPA04818.1 259 L-REIFKEAREKAP-SIIFVDEIDSI 282
                 3.334444455555.7*******986 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       3.3   1.9e+03      48      79 ..      44      76 ..      39      80 .. 0.75
   2 !   17.7   0.1     5e-06    0.0028       1      37 [.     213     249 ..     213     284 .] 0.67

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 3.3
                ..........--------G-SEEEEESGGG--H CS
       AAA_5 48 k.ngttslvdsplvraaregeilvlDEveraes 79
                k +++t+ +  pl+ + + + i+++D++ r +s
  EPA04818.1 44 KgKRRTVAKCLPLYPSDEGKGIIRIDGLGRNNS 76
                445566777778888888999*****9988776 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 5e-06
                 EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT-- CS
       AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtt 37 
                 +vlL GppGtgK+ la+ +a   ++ +  + +++ ++
  EPA04818.1 213 GVLLYGPPGTGKTLLAKAVANESQAHFISISGPEIMS 249
                 59****************9988877777777776554 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   8.4e-07   0.00047       6      82 ..     214     284 .]     211     284 .] 0.94

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 8.4e-07
                 EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG--- CS
       AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihp 82 
                 +ll gp g+Gkt+laka+a+  ++    ++i +   e++     + + +++   ++  ++a e+   i+++DEid i+p
  EPA04818.1 214 VLLYGPPGTGKTLLAKAVANESQA----HFISISGPEIMS----KFYGESEARLREIFKEAREKApsIIFVDEIDSIAP 284
                 5789****************9996....************....99999999999999999999999********9998 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.9e-06    0.0011       4      75 ..     213     281 ..     210     283 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.9e-06
      AAA_14   4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe.kllelileklkeekktylflDEiqe 75 
                  +++ G+  +GKT l+k +++e+     +++ i+  +   k + ++e +l e+++e  +e+  +++f DEi  
  EPA04818.1 213 GVLLYGPPGTGKTLLAKAVANESQ---AHFISISGPEIMSKFYGESEaRLREIFKEA-REKAPSIIFVDEIDS 281
                 57899***************9988...999999999988866666553555666665.455899*******76 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   2.1e-06    0.0012       2      46 ..     214     260 ..     214     276 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.1e-06
      AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt 46 
                 vll G+pG+GK+ la+ ++++ +  ++ +s ++++++ +g+ + +++
  EPA04818.1 214 VLLYGPPGTGKTLLAKAVANESQahFISISGPEIMSKFYGESEARLR 260
                 7899***************9999999999999999999997665544 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   3.5e-06     0.002      44      74 ..     208     238 ..     198     279 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3.5e-06
   IstB_IS21  44 iekkenivllGpsGvGKshlaialgveavra 74 
                 ie+ ++++l Gp+G+GK+ la a++ e  ++
  EPA04818.1 208 IEAPKGVLLYGPPGTGKTLLAKAVANESQAH 238
                 677789******************9987665 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.6e-05    0.0092       2      49 ..     214     266 ..     213     277 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.6e-05
      AAA_28   2 ivitGgestGKTtlleaLa....argypvv.pEaareileeklakgedalpwv 49 
                 + + G+++tGKT l++a a    a+ +++  pE++ +++ e  a+ +++ +++
  EPA04818.1 214 VLLYGPPGTGKTLLAKAVAnesqAHFISISgPEIMSKFYGESEARLREIFKEA 266
                 6799***************5544447777799999999988888877766554 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.2e-05     0.013       1      33 [.     214     246 ..     214     262 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.2e-05
  RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkds 33 
                   ++lyGp+g+GK++lak +a++ + ++ +++ ++
    EPA04818.1 214 VLLYGPPGTGKTLLAKAVANESQAHFISISGPE 246
                   689****************99998885544444 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0     2e-05     0.011      28      61 ..     206     238 ..     199     282 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2e-05
       AAA_7  28 lllknkkpvllvGptGtGKtviikdllkkldkek 61 
                 l +++ k vll+Gp GtGKt+++k + ++ +  +
  EPA04818.1 206 LGIEAPKGVLLYGPPGTGKTLLAKAVANESQ-AH 238
                 55778899****************9988877.44 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0     3e-05     0.017      21      56 ..     210     242 ..     201     284 .] 0.84

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3e-05
                      SSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEE CS
  Sigma54_activat  21 tdlsvlitGesGtGKellaraiheaskrkekpfvav 56 
                       +  vl+ G  GtGK+lla+a+ ++s+   ++f+++
       EPA04818.1 210 APKGVLLYGPPGTGKTLLAKAVANESQ---AHFISI 242
                      56789*****************99887...456655 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   2.3e-05     0.013      25      42 ..     214     231 ..     206     237 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.3e-05
  Mg_chelatase  25 lllvGppGsGKtmlakrl 42 
                   +ll+GppG+GKt+lak++
    EPA04818.1 214 VLLYGPPGTGKTLLAKAV 231
                   89*************987 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0         6   3.4e+03     130     186 ..      98     155 ..      92     160 .. 0.66
   2 !   13.9   0.0   4.3e-05     0.024      14      51 ..     209     244 ..     200     269 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 6
  Zeta_toxin 130 avkkelSrlgvldRyeeevae.gRlvpkeehdeafeglresvealeeekqldrvkikd 186
                  v + +++  + +Ry++++ e   l++ ++    + g r +++ + ++ ++d v +++
  EPA04818.1  98 VVAPLEAIPPIDERYLADALEsVPLIKGDNVMVPYFGGRLTFQVIGVTPAADAVLVTQ 155
                 5666777777778888774442356666666666677777777777777777777765 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 4.3e-05
  Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrldp 51 
                 e Pk +ll G pG GK+ la+++++e   q  ++ +++
  EPA04818.1 209 EAPKGVLLYGPPGTGKTLLAKAVANES--QAHFISISG 244
                 78************************8..777777765 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   3.2e-05     0.018       4      23 ..     213     234 ..     210     283 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.2e-05
      AAA_24   4 kiliyGpsgiGKTtlakel..g 23 
                  +l+yGp+g+GKT lak    +
  EPA04818.1 213 GVLLYGPPGTGKTLLAKAVanE 234
                 589*************988554 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   6.8e-05     0.038      11      38 ..     202     230 ..     199     239 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.8e-05
      ATPase  11 il.kgGipegrvvlitGepGtGKtifalq 38 
                 i+ k Gi   + vl++G pGtGKt++a+ 
  EPA04818.1 202 IFeKLGIEAPKGVLLYGPPGTGKTLLAKA 230
                 665679999999**************985 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   6.6e-05     0.037       1      22 [.     214     235 ..     214     279 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6.6e-05
      AAA_18   1 IlltGtpGvGKttlakeLskrl 22 
                 +ll G+pG+GKt lak+++++ 
  EPA04818.1 214 VLLYGPPGTGKTLLAKAVANES 235
                 799***************8774 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   6.6e-05     0.037      53      84 ..     211     242 ..     155     280 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.6e-05
      DUF815  53 annvLLwGarGtGKSslvkallneyaeegLrl 84 
                  + vLL+G  GtGK  l ka+ ne +++ + +
  EPA04818.1 211 PKGVLLYGPPGTGKTLLAKAVANESQAHFISI 242
                 4679********************99987554 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   0.00011     0.064      14      49 ..     206     243 ..     185     257 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00011
                 HHHCHTEEEEEEESTTSSHHHHHHHHHHHTT--..--- CS
        TsaE  14 lakalgdvilLeGdLGaGKTtlvrglakalgve..evk 49 
                 l+ ++ + +lL+G+ G+GKT l++++a++ + +  +++
  EPA04818.1 206 LGIEAPKGVLLYGPPGTGKTLLAKAVANESQAHfiSIS 243
                 333334569******************99877655555 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00016     0.091      22      45 ..     213     236 ..     200     242 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00016
                 EEEEEESTTSSHHHHHHHHCCSHC CS
      NB-ARC  22 vvalvGmgGvGKttlakqilnksd 45 
                  v l+G +G GKt lak + n+s+
  EPA04818.1 213 GVLLYGPPGTGKTLLAKAVANESQ 236
                 5889****************9954 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00016      0.09     117     138 ..     214     235 ..     211     239 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00016
   Parvo_NS1 117 vwfyGpantGktnlaeaIakav 138
                 v++yGp+ tGkt la+a a+ +
  EPA04818.1 214 VLLYGPPGTGKTLLAKAVANES 235
                 89****************9865 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00019      0.11      21      41 ..     213     233 ..     203     240 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00019
                 EEEEE--TTSSTTHHHHHHHH CS
        PhoH  21 ivfaiGpaGtGKtylavalav 41 
                  v   Gp GtGKt+la a+a 
  EPA04818.1 213 GVLLYGPPGTGKTLLAKAVAN 233
                 57889***********99985 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       8.2   4.6e+03     288     307 ..      69      88 ..      67      96 .. 0.79
   2 ?   11.7   0.0    0.0002      0.11       4      63 ..     214     266 ..     211     278 .. 0.67

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 8.2
     DUF2075 288 QGleldyvgviiGpdlvyrk 307
                  Gl  +  g+ iG+ +++rk
  EPA04818.1  69 DGLGRNNSGIAIGDTITVRK 88 
                 58889999*******99994 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.0002
     DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvl.vlrealakkeekkkkkea 63 
                 vl  G +GtGKt+++ ++++e        +a+++s ++p+++ + + + + +  ++ +kea
  EPA04818.1 214 VLLYGPPGTGKTLLAKAVANES-------QAHFISISGPEIMsKFYGESEARL-REIFKEA 266
                 6789************999998.......555555555554325555555555.4555555 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00042      0.24      20      46 ..     211     237 ..     200     278 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00042
    ATPase_2  20 neiyfiYGpegsGKtaLlkeiienled 46 
                  + +++YGp g GKt L k ++++++ 
  EPA04818.1 211 PKGVLLYGPPGTGKTLLAKAVANESQA 237
                 556899*************99998854 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00036       0.2       6      37 ..     206     237 ..     205     275 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00036
                 EEEETTSEEEEEESTTSSHHHHHHHHTTSS-- CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran   6 lklkegekvaivGenGaGKStLlkllagllkp 37 
                 l +++ + v + G+ G+GK+ L+k++a++++ 
  EPA04818.1 206 LGIEAPKGVLLYGPPGTGKTLLAKAVANESQA 237
                 5677778899*****************99875 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00063      0.35      36      52 ..     214     230 ..     193     234 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00063
      AAA_25  36 allaGapgtGKttlald 52 
                 +ll+G+pgtGKt la  
  EPA04818.1 214 VLLYGPPGTGKTLLAKA 230
                 79***********9965 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00048      0.27       2      30 ..     214     242 ..     213     279 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00048
       AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                 vll g PG++ktll+ka+a+  +++f  i
  EPA04818.1 214 VLLYGPPGTGKTLLAKAVANESQAHFISI 242
                 7999****************999988665 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00045      0.25      17      41 ..     211     235 ..     193     273 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00045
      AAA_11  17 seitliqGPPGtgKTktivellsql 41 
                 ++ +l+ GPPGtgKT    ++ ++ 
  EPA04818.1 211 PKGVLLYGPPGTGKTLLAKAVANES 235
                 556899*********7777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                       102  (0.00568911); expected 17.9 (0.001)
Passed Fwd filter:                        32  (0.00178482); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              32  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2042.37
//
Query:       EPA04819.1  [L=134]
Description: thrombospondin type 3 repeat protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.8e-10   39.7  33.1    0.00021   20.9   2.1    5.5  7  TSP_3      Thrombospondin type 3 repeat
  ------ inclusion threshold ------
       0.02   14.8   1.5        4.7    7.2   0.1    2.8  2  DUF282     Caenorhabditis protein of unknown function, DUF282
       0.57   10.8   7.8        8.6    7.1   0.0    3.9  5  Excalibur  Excalibur calcium-binding domain
        2.2    8.9   7.4        5.6    7.6   0.4    3.2  3  VCBS       Repeat domain in Vibrio, Colwellia, Bradyrhizobium


Domain annotation for each model (and alignments):
>> TSP_3  Thrombospondin type 3 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.2       1.5   6.8e+03      26      30 ..       1       5 [.       1       7 [. 0.57
   2 !   20.9   2.1   4.8e-08   0.00021      15      33 ..      18      36 ..      16      39 .. 0.92
   3 ?   -0.5   0.1      0.23     1e+03      17      24 ..      43      50 ..      42      51 .. 0.63
   4 !   19.9   0.2   9.5e-08   0.00043      15      33 ..      62      80 ..      61      82 .. 0.91
   5 ?    1.7   0.1     0.046   2.1e+02      24      33 ..      87      96 ..      85      99 .. 0.64
   6 !   16.8   2.8   9.1e-07    0.0041      15      33 ..     104     122 ..     103     124 .. 0.93
   7 ?   -1.8   0.0      0.59   2.6e+03      25      30 ..     128     133 ..     127     134 .] 0.77

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.5
       TSP_3 26 DNCpr 30
                D Cp 
  EPA04819.1  1 DGCPD 5 
                55664 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 4.8e-08
       TSP_3 15 DfDnDgvqddlDNCprnan 33
                D+D+Dg++d  D Cp+ ++
  EPA04819.1 18 DADGDGIPDIKDACPNEPE 36
                9***************997 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.23
       TSP_3 17 DnDgvqdd 24
                D Dg +d+
  EPA04819.1 43 DWDGCPDT 50
                66777665 PP

  == domain 4  score: 19.9 bits;  conditional E-value: 9.5e-08
       TSP_3 15 DfDnDgvqddlDNCprnan 33
                D D+Dg++d+ D Cp  ++
  EPA04819.1 62 DSDKDGIPDKYDSCPSAPE 80
                99*************9987 PP

  == domain 5  score: 1.7 bits;  conditional E-value: 0.046
       TSP_3 24 dlDNCprnan 33
                d D Cp ++ 
  EPA04819.1 87 DTDGCPDTSP 96
                4577777765 PP

  == domain 6  score: 16.8 bits;  conditional E-value: 9.1e-07
       TSP_3  15 DfDnDgvqddlDNCprnan 33 
                 D D Dg+ +d+D Cp +++
  EPA04819.1 104 DDDLDGILNDADKCPLVPE 122
                 9**************9986 PP

  == domain 7  score: -1.8 bits;  conditional E-value: 0.59
       TSP_3  25 lDNCpr 30 
                  D Cp+
  EPA04819.1 128 IDGCPE 133
                 599997 PP

>> DUF282  Caenorhabditis protein of unknown function, DUF282
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1    0.0011       4.7      15      28 ..      21      34 ..      17      37 .. 0.88
   2 ?    5.8   0.2    0.0028        13      17      30 ..      67      80 ..      66      86 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0011
      DUF282 15 GvgiPslsdwCata 28
                G giP+ +d C+ +
  EPA04819.1 21 GDGIPDIKDACPNE 34
                99*********987 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0028
      DUF282 17 giPslsdwCataae 30
                giP+ +d C+ a e
  EPA04819.1 67 GIPDKYDSCPSAPE 80
                9*********9977 PP

>> Excalibur  Excalibur calcium-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0    0.0019       8.6      27      36 ..      16      25 ..       7      25 .. 0.83
   2 ?   -2.3   0.0       1.7   7.6e+03      26      32 ..      40      46 ..      36      47 .. 0.78
   3 ?    5.9   0.1    0.0043        19      29      36 ..      62      69 ..      58      69 .. 0.91
   4 ?   -1.9   0.0       1.2   5.4e+03      23      32 ..      83      90 ..      77      92 .. 0.65
   5 ?   -1.2   0.6      0.75   3.4e+03      29      35 ..     104     110 ..     101     110 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0019
   Excalibur 27 klDrDkDGiA 36
                + D D+DGi+
  EPA04819.1 16 APDADGDGIP 25
                67*******8 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.7
   Excalibur 26 kklDrDk 32
                 +lD D+
  EPA04819.1 40 GYLDWDG 46
                5799997 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.0043
   Excalibur 29 DrDkDGiA 36
                D DkDGi+
  EPA04819.1 62 DSDKDGIP 69
                9******8 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 1.2
   Excalibur 23 kankklDrDk 32
                +  k+ D D+
  EPA04819.1 83 N--KYKDTDG 90
                4..6666664 PP

  == domain 5  score: -1.2 bits;  conditional E-value: 0.75
   Excalibur  29 DrDkDGi 35 
                 D D DGi
  EPA04819.1 104 DDDLDGI 110
                 9999**8 PP

>> VCBS  Repeat domain in Vibrio, Colwellia, Bradyrhizobium and Shewanella
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.4    0.0012       5.6      45      59 ..      13      27 ..       7      27 .. 0.78
   2 ?   -1.8   0.1       1.1   4.9e+03      51      58 ..      42      49 ..      40      52 .. 0.77
   3 ?    3.7   0.3     0.021        93      47      58 ..      59      70 ..      46      72 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0012
        VCBS 45 gvavgDlDgDGdlDl 59
                +  + D DgDG +D+
  EPA04819.1 13 TYKAPDADGDGIPDI 27
                5567899****9998 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.1
        VCBS 51 lDgDGdlD 58
                lD DG +D
  EPA04819.1 42 LDWDGCPD 49
                57888888 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.021
        VCBS 47 avgDlDgDGdlD 58
                +++D D DG +D
  EPA04819.1 59 TLADSDKDGIPD 70
                689*******99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       180  (0.0100396); expected 358.6 (0.02)
Passed bias filter:                      153  (0.00853366); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.37u 0.20s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 1074.49
//
Query:       EPA04820.1  [L=159]
Description: thrombospondin type 3 repeat protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      5e-15   54.9  39.2    0.00012   21.6   0.6    5.9  6  TSP_3        Thrombospondin type 3 repeat
  ------ inclusion threshold ------
      0.025   15.2  11.7        4.2    8.1   0.3    4.4  4  Excalibur    Excalibur calcium-binding domain
      0.082   12.8   4.3         32    4.5   0.0    4.5  5  DUF282       Caenorhabditis protein of unknown function, DUF2


Domain annotation for each model (and alignments):
>> TSP_3  Thrombospondin type 3 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   2.0     3e-07    0.0018      14      30 ..      28      44 ..      27      47 .. 0.93
   2 ?   -1.8   0.0      0.45   2.7e+03      25      30 ..      53      58 ..      51      62 .. 0.82
   3 !   18.0   3.9   2.7e-07    0.0016      15      32 ..      65      82 ..      54      86 .. 0.90
   4 ?    0.6   0.1     0.076   4.6e+02      17      24 ..      90      97 ..      87     102 .. 0.65
   5 !   21.6   0.6   2.1e-08   0.00012      14      34 ..     106     126 ..     103     128 .. 0.92
   6 !   13.8   6.4   5.6e-06     0.034      13      29 ..     143     159 .]     131     159 .] 0.79

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3e-07
       TSP_3 14 kDfDnDgvqddlDNCpr 30
                +D D Dgv++dlD Cp 
  EPA04820.1 28 QDNDHDGVPNDLDQCPH 44
                79**************6 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.45
       TSP_3 25 lDNCpr 30
                +D Cp 
  EPA04820.1 53 VDGCPS 58
                799996 PP

  == domain 3  score: 18.0 bits;  conditional E-value: 2.7e-07
       TSP_3 15 DfDnDgvqddlDNCprna 32
                D+D Dg++dd D+Cp++ 
  EPA04820.1 65 DVDSDGIPDDIDVCPTVR 82
                9**************975 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 0.076
       TSP_3 17 DnDgvqdd 24
                D Dg +d 
  EPA04820.1 90 DDDGCPDI 97
                55555553 PP

  == domain 5  score: 21.6 bits;  conditional E-value: 2.1e-08
       TSP_3  14 kDfDnDgvqddlDNCprnani 34 
                 +D+DnDg+ d  D Cp+ +++
  EPA04820.1 106 ADTDNDGIADFIDSCPTQPET 126
                 6*****************987 PP

  == domain 6  score: 13.8 bits;  conditional E-value: 5.6e-06
       TSP_3  13 dkDfDnDgvqddlDNCp 29 
                   D+D+Dg++d++D Cp
  EPA04820.1 143 TLDTDGDGIPDVVDACP 159
                 57**************9 PP

>> Excalibur  Excalibur calcium-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0      0.01        63      29      36 ..      29      36 ..      20      36 .. 0.89
   2 ?    1.1   0.0       0.1   6.1e+02      29      36 ..      65      72 ..      42      72 .. 0.89
   3 ?    5.9   1.5    0.0034        20      26      36 ..     104     114 ..      83     114 .. 0.81
   4 ?    8.1   0.3    0.0007       4.2      26      36 ..     142     152 ..     127     152 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.01
   Excalibur 29 DrDkDGiA 36
                D D+DG++
  EPA04820.1 29 DNDHDGVP 36
                9*****97 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.1
   Excalibur 29 DrDkDGiA 36
                D D DGi+
  EPA04820.1 65 DVDSDGIP 72
                78999997 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.0034
   Excalibur  26 kklDrDkDGiA 36 
                 +  D D+DGiA
  EPA04820.1 104 ETADTDNDGIA 114
                 677*******9 PP

  == domain 4  score: 8.1 bits;  conditional E-value: 0.0007
   Excalibur  26 kklDrDkDGiA 36 
                 + lD D+DGi+
  EPA04820.1 142 STLDTDGDGIP 152
                 679*******8 PP

>> DUF282  Caenorhabditis protein of unknown function, DUF282
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.031   1.8e+02      17      27 ..      34      44 ..      33      53 .. 0.82
   2 ?    4.5   0.0    0.0054        32      17      29 ..      70      82 ..      67      84 .. 0.87
   3 ?   -2.9   0.0       1.2     7e+03      17      24 ..      93     100 ..      92     105 .. 0.69
   4 ?   -0.2   0.0      0.16   9.6e+02      17      30 ..     112     125 ..     111     126 .. 0.80
   5 ?    3.5   0.1     0.012        69      15      26 ..     148     159 .]     145     159 .] 0.92

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.031
      DUF282 17 giPslsdwCat 27
                g+P+ +d C+ 
  EPA04820.1 34 GVPNDLDQCPH 44
                99*******96 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0054
      DUF282 17 giPslsdwCataa 29
                giP+  d C+t  
  EPA04820.1 70 GIPDDIDVCPTVR 82
                9*********965 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.2
      DUF282  17 giPslsdw 24 
                 g P+ s++
  EPA04820.1  93 GCPDISSY 100
                 67888777 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 0.16
      DUF282  17 giPslsdwCataae 30 
                 gi +  d C+t+ e
  EPA04820.1 112 GIADFIDSCPTQPE 125
                 7788899***9865 PP

  == domain 5  score: 3.5 bits;  conditional E-value: 0.012
      DUF282  15 GvgiPslsdwCa 26 
                 G giP+  d C+
  EPA04820.1 148 GDGIPDVVDACP 159
                 99*********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 993.86
//
Query:       EPA04821.1  [L=48]
Description: hypothetical protein BG20_I2612, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00011   22.6   0.0    0.00012   22.5   0.0    1.1  1  GlutR_dimer  Glutamyl-tRNAGlu reductase, dimerisation domain


Domain annotation for each model (and alignments):
>> GlutR_dimer  Glutamyl-tRNAGlu reductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   6.5e-09   0.00012      58      96 ..       1      40 [.       1      41 [. 0.91

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 6.5e-09
                 -TTHHHHHHHHHHHHHHHHHHSS-TTTT.HHHHHHHHH.. CS
  GlutR_dimer 58 lekltrslvnkllheptarLkeaedeee.ellealrrlFn 96
                 +e+lt+++v  ++ +p++++++a++ ++ +++e++++lF+
   EPA04821.1  1 IEELTKAVVESIVSTPMNNIRKASELGNpDIIEMASKLFD 40
                 79*********************666667**********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 328.72
//
Query:       EPA04822.1  [L=181]
Description: porphobilinogen synthase, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-66  224.4   0.4    2.2e-66  224.2   0.4    1.0  1  ALAD      Delta-aminolevulinic acid dehydratase


Domain annotation for each model (and alignments):
>> ALAD  Delta-aminolevulinic acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  224.2   0.4   1.2e-70   2.2e-66       2     176 ..       6     181 .]       5     181 .] 0.99

  Alignments for each domain:
  == domain 1  score: 224.2 bits;  conditional E-value: 1.2e-70
                 --GGGGGSSHHHHHHC-S----GGGEEEEEEEESS-SS-EE-TTSTT-EEEEGGGHHHHHHHHHHTT--EEEEEEE-SS-BSS-GGGGSTTSHHHHHHH CS
        ALAD   2 krlrrlrksealrelvretrlsasdlilplfvkegeeekeeiksmpgvyrlsvdelvkeveelvklgikavllFgvpeekdeegsealnedglvqrair 100
                 +rlrrlr+se++rel++et+ls +dli+p+fv+e+ +++ +++sm +++rl++d++ +ev ++ +lgi+a++lFg+p++kde+g++a++++g+vq+ai+
  EPA04822.1   6 RRLRRLRTSEKMRELIQETTLSSRDLICPVFVQEDLKTRIKVESMSEIERLPIDDINDEVGTISDLGIPAIMLFGIPAKKDENGTSAFDDNGIVQKAIS 104
                 79************************************************************************************************* PP

                 HHHHH-.TTSEEEEEE-STTTBSS-SSSEEESS.EEHHHHHHHHHHHHHHHHHCT-SEEEE-S--TTHHHHHHHHHH CS
        ALAD 101 aikeev.pelvvitDvclceytshGhcgileekevdndetlellakvavsqaeaGadivapSdmmDgrvaaireaLd 176
                 +i++++ +++v+++Dvclc++ts+Ghcgi++ ++vdnd++le+lak+avsqa+aG+d+v+pS mmDg+va+ir+aLd
  EPA04822.1 105 QIRKNFgDKIVIMADVCLCQFTSTGHCGIIKGNKVDNDTSLETLAKIAVSQAKAGVDTVSPSAMMDGQVATIRKALD 181
                 ******777******************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1209.68
//
Query:       EPA04823.1  [L=195]
Description: hypothetical protein BG20_I2517, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.8e-26   90.7   4.4    9.8e-26   90.7   4.4    1.4  2  NADHdh    NADH dehydrogenase
  ------ inclusion threshold ------
       0.12   12.4   0.3       0.12   12.4   0.3    2.3  3  NDUF_B12  NADH-ubiquinone oxidoreductase B12 subunit family


Domain annotation for each model (and alignments):
>> NADHdh  NADH dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.3      0.41   3.7e+03     243     243 ..      31      31 ..       7      58 .. 0.53
   2 !   90.7   4.4   1.1e-29   9.8e-26       9     107 ..      91     192 ..      83     195 .] 0.94

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.41
                 S CS
      NADHdh 243 w 243
                 +
  EPA04823.1  31 I 31 
                 1 PP

  == domain 2  score: 90.7 bits;  conditional E-value: 1.1e-29
                 HHHHHHHHHHHHHHHHHHHHTTS--S-SSTTT.TTTHHHHHHHHHCCS-----TTS-HHHHHHHHHHHHHHHHCTTTTS-SSS..SSS--TTHHHHHHH CS
      NADHdh   9 vlllvvalltlleRkvlAriqdRlGPnrvGpl.GllqplaDalKlllKediipkkadkllfllapvlalilallafaviPfge..vladlnvglllila 104
                 +++l++a ++++eRk+lA++q R+GP ++G++ G+lq++ D+lKl+ Ke iip+kadk +f++apv+ +++a + +a+iP+++  v+ad++vgll ++a
  EPA04823.1  91 FAALIAAGTIFIERKMLAKLQLRVGPFYCGKVeGILQLMGDGLKLISKEIIIPAKADKPIFWAAPVIFVATAAAFVALIPVAPgwVVADVDVGLLAVFA 189
                 56788889**********************766*************************************************889************** PP

                 HHH CS
      NADHdh 105 lss 107
                 ++ 
  EPA04823.1 190 IIG 192
                 986 PP

>> NDUF_B12  NADH-ubiquinone oxidoreductase B12 subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.3   1.3e-05      0.12      16      47 ..      75     106 ..      67     111 .. 0.82
   2 ?   -1.7   0.9      0.36   3.2e+03      33      42 ..     154     163 ..     151     171 .. 0.55
   3 ?   -2.6   1.6      0.65   5.8e+03      26      30 ..     172     175 ..     159     193 .. 0.49

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.3e-05
    NDUF_B12  16 fskakrfkraffpGfglavaafaaavgyEhfl 47 
                 f +   f+ a fpGfg a+ ++a ++ +E  +
  EPA04823.1  75 FMTTDLFRIAAFPGFGFAALIAAGTIFIERKM 106
                 666667777888****************9765 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.36
    NDUF_B12  33 avaafaaavg 42 
                 a ++f+a+ +
  EPA04823.1 154 APVIFVATAA 163
                 5555555543 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 0.65
    NDUF_B12  26 ffpGf 30 
                   pG+
  EPA04823.1 172 A-PGW 175
                 2.566 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1451.81
//
Query:       EPA04824.1  [L=134]
Description: hypothetical protein BG20_I2516, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-29  102.8   0.0    1.3e-15   57.3   0.0    2.0  2  Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd s
  ------ inclusion threshold ------
      0.039   13.4   0.1      0.063   12.7   0.1    1.3  1  Ribosomal_S5_C  Ribosomal protein S5, C-terminal domain


Domain annotation for each model (and alignments):
>> Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   0.0   1.8e-15   1.6e-11     115     166 ..       1      53 [.       1      62 [. 0.91
   2 !   57.3   0.0   1.4e-19   1.3e-15     203     271 .]      66     134 .]      60     134 .] 0.97

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 1.8e-15
                     S-SSGGGS-------SSBSHHHHHHHHHHHHHHHHHHHHHHHHT--..S-SB- CS
  Complex1_49kDa 115 pYeaYdeldfdvpvgeegDvydRylvrveEmrqSlkIieqaleklpe.gpvla 166
                     pY++Ydeld +  v +egD+y+R  v    m +S++Ii+qal+k+p+ g+v +
      EPA04824.1   1 PYDVYDELDVHTNVMKEGDSYARSKVPWLDMLESCNIIRQALQKMPKsGSVRV 53 
                     9********************************************98677665 PP

  == domain 2  score: 57.3 bits;  conditional E-value: 1.4e-19
                     EEEEEEEETTEEEEEEEEEESSSS-SEEEEE-HHHHTTTTHHHHTTTS-SGGGTHHHHTT---HHHHH- CS
  Complex1_49kDa 203 evyaavEapkGelgvylvsdgsskpyrlkirapsfvnlqaleellkgellaDvvailgsldivlgevDR 271
                      vy++vE+++G lg+y+vsdg+ +pyr+k+   sf nl al++llkge+l  ++ ++ sl++   e+DR
      EPA04824.1  66 TVYKRVESGRGSLGCYIVSDGKPEPYRVKMSVGSFRNLIALPYLLKGEKLGNMPSVYWSLNYWPVEADR 134
                     79****************************************************************998 PP

>> Ribosomal_S5_C  Ribosomal protein S5, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1     7e-06     0.063       3      20 ..      47      64 ..      45      67 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7e-06
                    EETTEEEEEEE--TT--E CS
  Ribosomal_S5_C  3 kfgavkvllkpaprGtGi 20
                    k g+v+v+lkp p+G+G+
      EPA04824.1 47 KSGSVRVKLKPNPKGKGL 64
                    78***************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       243  (0.0135535); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 928.22
//
Query:       EPA04825.1  [L=278]
Description: putative argininosuccinate lyase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    8.7e-24   84.5   0.1    1.6e-22   80.3   0.0    2.3  2  Lyase_1    Lyase
    1.7e-13   51.1   0.0    3.2e-13   50.2   0.0    1.5  1  ASL_C2     Argininosuccinate lyase C-terminal


Domain annotation for each model (and alignments):
>> Lyase_1  Lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.3   0.0   1.8e-26   1.6e-22     225     312 .]       4      87 ..       1      87 [. 0.96
   2 ?    1.9   0.0     0.014   1.2e+02     175     247 ..     150     221 ..     146     229 .. 0.74

  Alignments for each domain:
  == domain 1  score: 80.3 bits;  conditional E-value: 1.8e-26
                 HHCSTEESSSHHHHHHC-HHHHHHHHHHHHHHHHHHHHHHHHHHHTSTTTSSEEEEGCCTSSC-TTSTTTEBTHHHHHHHHHHHHHHH CS
     Lyase_1 225 vtglpvkapnsfeavsdrDavvellgalkllatsLskfaeDlrllssgeaglvelslaesepGSSiMPgKvNPvqlElltgvagrvvG 312
                 ++g   + +ns++a+s+rD+v+e++++l++l+t+Ls+++eD ++ s++e++++el +  ++  SS+MP+K+NP+ lEl++g+ + v+G
  EPA04825.1   4 FDG---IVENSIDATSTRDFVAEYVSMLAILMTNLSRISEDFIIWSTSEFSFIELADEFTS-PSSVMPQKKNPDILELTRGKTAEVIG 87 
                 566...889**************************************************99.8***********************98 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.014
                 HHHHHHHHHHHHHHHHHHHTCEETTTTTTTSSTTTSCCTHHHHHHHHHHHHHCSTEESSSHHHHHHC-HHHHH CS
     Lyase_1 175 yaealerdrerlkellkrllvellgggtavgtglnadpefaelvakelakvtglpvkapnsfeavsdrDavve 247
                 y  al+  ++ +++     ++    +g +v  +++ d+  ++l +ke++k+++ + + pn +  + + + ++ 
  EPA04825.1 150 YLIALDIAEKLVQNGI-PFRTTHKIAGNLVQIAHQYDKSLNKLSVKEISKIALETKVDPNLIMKIIQSTTIIS 221
                 5566666666666666.444444555699999999999999********999966888888877777776665 PP

>> ASL_C2  Argininosuccinate lyase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.2   0.0   3.6e-17   3.2e-13       1      55 [.     150     206 ..     150     225 .. 0.83

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 3.6e-17
                 STTHHHHHHHHHHCTS-HHHHHHHHHHHHHHHHHTT--GGG--HHHHHHH-..TT-- CS
      ASL_C2   1 FstATdlADyLvrkGlpFReAHeivgravrlaeekgkeleeltleelkeis..plle 55 
                 ++ A d+A+ Lv++G+pFR++H+i+g++v+ a + +k+l++l+++e+ +i+  + ++
  EPA04825.1 150 YLIALDIAEKLVQNGIPFRTTHKIAGNLVQIAHQYDKSLNKLSVKEISKIAleTKVD 206
                 6789********************************************886322244 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       816  (0.0455129); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 1773.37
//
Query:       EPA04826.1  [L=200]
Description: hypothetical protein BG20_I0508 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.023   14.9   0.0      0.039   14.1   0.0    1.7  1  CTP_transf_like  Cytidylyltransferase-like
       0.33   11.4   2.3        4.8    7.7   0.1    2.4  2  Ntox35           Bacterial toxin 35


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   4.4e-06     0.039       7      59 ..      11      65 ..       8     188 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.4e-06
                     TT--HHHHHHHHHHHHHSSES...EEEEEESSTHCSST-SCSSTHHHHHHHHHHHT CS
  CTP_transf_like  7 DpiHlGHlrlleqakklleed...livgvpsdeppkkkkkplasaeeRlemlelak 59
                     +p++++H ++++++k+  +      +v+   +++ ++k   ++s e R +m+  + 
       EPA04826.1 11 NPVTNAHVEIINELKNNADIVkimPVVFKSGKNEINSK-SFPFSFEIRKKMITSIF 65
                     9*******************965444444444444433.889**********9983 PP

>> Ntox35  Bacterial toxin 35
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1   0.00053       4.8      19      58 ..      21      60 ..      13      73 .. 0.73
   2 ?    3.2   0.2     0.013   1.2e+02      21      54 ..     152     188 ..     143     193 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00053
      Ntox35 19 lvkknnwkdvkkivvkvmkegkeeaiksakqkvtkikGke 58
                + + +n  d+ ki+  v k+gk+e   + +    +i+ k 
  EPA04826.1 21 INELKNNADIVKIMPVVFKSGKNEINSKSFPFSFEIRKKM 60
                67789999***************98888776644444333 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.013
      Ntox35  21 kknnw.kdvkkivvkvmkeg..keeaiksakqkvtki 54 
                 ++ nw kdv + v ++++e+  + +++   + k+t++
  EPA04826.1 152 EESNWkKDVPESVARIIDENwnVIKKFSEMEDKTTRV 188
                 55675279*********99722556666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:01.56
# Mc/sec: 388.63
//
Query:       EPA04827.1  [L=170]
Description: biotin-requiring enzyme [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.5e-17   60.6   4.6    1.7e-16   59.8   4.6    1.4  1  Biotin_lipoyl    Biotin-requiring enzyme
    2.7e-10   39.9   2.7    1.6e-09   37.4   0.3    2.4  2  Biotin_lipoyl_2  Biotin-lipoyl like
    9.7e-05   23.0   0.5      0.033   14.9   0.1    2.5  2  HlyD_3           HlyD family secretion protein
     0.0011   18.3   1.8      0.061   12.5   0.1    2.7  3  HlyD_D23         Barrel-sandwich domain of CusB or HlyD membr
      0.004   17.1   1.5     0.0078   16.2   1.5    1.5  1  RnfC_N           RnfC Barrel sandwich hybrid domain
  ------ inclusion threshold ------
      0.014   15.3   0.6      0.032   14.1   0.6    1.7  1  GCV_H            Glycine cleavage H-protein
      0.017   14.8   2.0      0.036   13.7   0.7    2.0  2  Big_3_3          Bacterial Ig-like domain (group 3)
      0.022   14.8   0.1      0.074   13.1   0.0    1.9  2  QRPTase_N        Quinolinate phosphoribosyl transferase, N-te
      0.033   14.1   0.6      0.057   13.4   0.1    1.6  2  DUF2118          Uncharacterized protein conserved in archaea
      0.055   13.8   0.0      0.083   13.2   0.0    1.3  1  DUF4164          Domain of unknown function (DUF4164)
      0.076   13.2   2.0       0.76   10.0   0.2    2.6  3  Peptidase_M23    Peptidase family M23
      0.077   12.8   0.3        1.4    8.8   0.0    2.7  2  eIF-1a           Translation initiation factor 1A / IF-1


Domain annotation for each model (and alignments):
>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.8   4.6   1.1e-19   1.7e-16      15      73 .]     110     169 ..     103     169 .. 0.93

  Alignments for each domain:
  == domain 1  score: 59.8 bits;  conditional E-value: 1.1e-19
                    ..ECSESSSTTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEESSTTTEEE-TTCEEEEE CS
  Biotin_lipoyl  15 g.vvevlvkvGdkVkagqvlaeveamKmemeieapkaGvvkeilvkeGdtvevgdllaki 73 
                    g vv++ v++Gd+Vk+g+v++++e+mKm++ i+++k+G +k+i++k G tv  +dl+a+i
     EPA04827.1 110 GkVVSIAVQEGDSVKQGDVVCTLESMKMQVAIKSHKNGSIKSIKIKIGGTVAKNDLVAEI 169
                    34667****************************************************997 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.3   1.1e-12   1.6e-09       4      46 ..     103     145 ..      99     147 .. 0.91
   2 !    5.9   0.4    0.0075        11       3      33 ..     139     169 ..     138     170 .] 0.92

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 1.1e-12
  Biotin_lipoyl_2   4 sIaapvsGrVaqlnVkdGqrVkaGdvLaelDsralqlalaqae 46 
                       ++++++G+V++++V++G+ Vk+Gdv  +l+s + q+a++  +
       EPA04827.1 103 ALKSQIPGKVVSIAVQEGDSVKQGDVVCTLESMKMQVAIKSHK 145
                      6789**********************************98755 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0075
  Biotin_lipoyl_2   3 vsIaapvsGrVaqlnVkdGqrVkaGdvLael 33 
                      v I++  +G ++++ +k G  V + d+ ae+
       EPA04827.1 139 VAIKSHKNGSIKSIKIKIGGTVAKNDLVAEI 169
                      8999999*****************9999998 PP

>> HlyD_3  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   2.2e-05     0.033       2      31 ..     104     133 ..     103     146 .. 0.88
   2 !    6.4   0.0    0.0097        14       2      30 ..     141     169 ..     140     170 .] 0.93

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.2e-05
      HlyD_3   2 lrApvdGvvvelnveegevvqagdelleii 31 
                 l++ + G+vv++ v+eg+ v +gd++ ++ 
  EPA04827.1 104 LKSQIPGKVVSIAVQEGDSVKQGDVVCTLE 133
                 799***********************9986 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0097
      HlyD_3   2 lrApvdGvvvelnveegevvqagdellei 30 
                 +++   G +++++++ g  v+++d ++ei
  EPA04827.1 141 IKSHKNGSIKSIKIKIGGTVAKNDLVAEI 169
                 778889**********************9 PP

>> HlyD_D23  Barrel-sandwich domain of CusB or HlyD membrane-fusion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.39   5.9e+02      77     101 ..      24      51 ..       6      68 .. 0.75
   2 !   12.5   0.1   4.1e-05     0.061     106     141 ..      99     134 ..      83     137 .. 0.71
   3 !    4.9   0.1    0.0088        13     105     139 ..     135     169 ..     132     170 .] 0.79

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.39
                 ....XXXXXXXXXXXXXXXXXXXXXXXX CS
    HlyD_D23  77 e...lleaarerLrllgvseeqiaelek 101
                 e   +++ a+++++ l+++++ i+ +  
  EPA04827.1  24 EyviKINDAEHQIKILKMDSKGIEFVLD 51 
                 2555788899999999999998876655 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 4.1e-05
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
    HlyD_D23 106 qktvtvkapisGvVteknvreGqyvqpgdtlftiad 141
                 ++++ +k++i G V++ +v+eG+ v++gd++ t+ +
  EPA04827.1  99 DTQLALKSQIPGKVVSIAVQEGDSVKQGDVVCTLES 134
                 456667777777777777777777777777766654 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.0088
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
    HlyD_D23 105 vqktvtvkapisGvVteknvreGqyvqpgdtlfti 139
                 ++ +v +k+  +G + + ++  G +v ++d +++i
  EPA04827.1 135 MKMQVAIKSHKNGSIKSIKIKIGGTVAKNDLVAEI 169
                 56678889999999999999999998888877776 PP

>> RnfC_N  RnfC Barrel sandwich hybrid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   1.5   5.2e-06    0.0078      35      82 ..     106     154 ..      94     169 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.2e-06
      RnfC_N  35 sqhiGapakplvkvgdkVlkGqkiaeaeg.fvsapvhasvsGtVkaiek 82 
                 sq  G+  ++ v++gd V++G+++ + e+  +++++ +   G +k+i+ 
  EPA04827.1 106 SQIPGKVVSIAVQEGDSVKQGDVVCTLESmKMQVAIKSHKNGSIKSIKI 154
                 466699999****************99986789*************985 PP

>> GCV_H  Glycine cleavage H-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.6   2.1e-05     0.032      31      74 ..     110     152 ..      99     170 .] 0.87

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.1e-05
                 -SEEEEE---TT-EE-TT-EEEEEEESS-EEEEE-SSSEEEEEE CS
       GCV_H  31 gdvvfvelpevgtkvkkgeslaavEsvKaasevyapvsGevvev 74 
                 g+vv++ ++ +g++vk+g+ + ++Es K+   + +  +G +  +
  EPA04827.1 110 GKVVSIAVQ-EGDSVKQGDVVCTLESMKMQVAIKSHKNGSIKSI 152
                 899999986.59**************************999766 PP

>> Big_3_3  Bacterial Ig-like domain (group 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.22   3.3e+02      65      99 ..      71     104 ..       7     112 .. 0.66
   2 ?   13.7   0.7   2.4e-05     0.036      47      91 ..     112     160 ..      91     168 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.22
     Big_3_3  65 lenlritladaldkskltsial..sGGpasDkVelsw 99 
                 ++n+ it+  ++d   l++i++  sGG+ s   +l+ 
  EPA04827.1  71 IDNVPITINMHTD---LDKIVFkhSGGASSSDTQLAL 104
                 4455555443333...333332226666666666665 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 2.4e-05
     Big_3_3  47 tvsi..segkkisdgavvkglenlritladaldks.kltsials.GGpa 91 
                 +vsi  +eg ++++g vv +le++++++a ++ k  +++si ++ GG++
  EPA04827.1 112 VVSIavQEGDSVKQGDVVCTLESMKMQVAIKSHKNgSIKSIKIKiGGTV 160
                 55555499**********************999999*****99735554 PP

>> QRPTase_N  Quinolinate phosphoribosyl transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0     5e-05     0.074      34      68 ..      99     133 ..      77     140 .. 0.79
   2 ?   -0.9   0.0       1.2   1.8e+03      50      68 ..     152     170 .]     134     170 .] 0.77

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5e-05
                 HHHHHHHHHHTTTEEEESS-TT-EEETTEEEEEEE CS
   QRPTase_N  34 evaeevfellpglevellvkDGervekgdvlleie 68 
                 +   ++ +++pg  v++ v++G++v++gdv++++e
  EPA04827.1  99 DTQLALKSQIPGKVVSIAVQEGDSVKQGDVVCTLE 133
                 555555566689999*****************998 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.2
                 ESS-TT-EEETTEEEEEEE CS
   QRPTase_N  50 llvkDGervekgdvlleie 68 
                 +++k G +v+k+d ++eie
  EPA04827.1 152 IKIKIGGTVAKNDLVAEIE 170
                 5566688888888888875 PP

>> DUF2118  Uncharacterized protein conserved in archaea (DUF2118)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.6   2.4e+03     129     129 ..      46      46 ..      13      92 .. 0.62
   2 ?   13.4   0.1   3.8e-05     0.057      88     134 ..     108     153 ..      98     162 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.6
     DUF2118 129 v 129
                 +
  EPA04827.1  46 I 46 
                 1 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 3.8e-05
     DUF2118  88 vegvkvtlivdvGdrveegdtlaavttrkgevrylrapvegvVvfik 134
                 + g +v++ v++Gd v++gd++  + + k +v  ++++++g +  ik
  EPA04827.1 108 IPGKVVSIAVQEGDSVKQGDVVCTLESMKMQV-AIKSHKNGSIKSIK 153
                 568899*************************9.69*****9886665 PP

>> DUF4164  Domain of unknown function (DUF4164)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   5.6e-05     0.083      34      80 ..      26      75 ..       2      83 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.6e-05
     DUF4164 34 r...deleaeiealgedrsRLaeeLdqaearaarleevnrEvsrrLkaai 80
                    +++e +i+ l+ d + ++  Ldq+  ra++le+ ++E +  ++ + 
  EPA04827.1 26 VikiNDAEHQIKILKMDSKGIEFVLDQKYHRAKYLENSTNEMNLIIDNVP 75
                255599***********************************987666655 PP

>> Peptidase_M23  Peptidase family M23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       3.7   5.5e+03      20      44 ..      12      34 ..       6      46 .. 0.61
   2 ?   10.0   0.2   0.00051      0.76      54      76 ..     114     136 ..     105     149 .. 0.83
   3 ?    2.3   0.1      0.13   1.9e+02      51      72 ..     148     169 ..     138     170 .] 0.86

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 3.7
                   SSEEEEEEEEETTTEEEEEEEECTC CS
  Peptidase_M23 20 adGtVvfagkkegyGnvviidhgdg 44
                    dG+++++    +   v+ i+++++
     EPA04827.1 12 FDGEITQSLG--NNEYVIKINDAEH 34
                   5666666644..3455666666554 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00051
                    EESS-TTEEE-TTCEEEEEBSTS CS
  Peptidase_M23  54 kisvkegqkVkaGqvIGtvgstg 76 
                    +i+v+eg+ Vk+G+v+ t  s +
     EPA04827.1 114 SIAVQEGDSVKQGDVVCTLESMK 136
                    789*************9988765 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.13
                    EESEESS-TTEEE-TTCEEEEE CS
  Peptidase_M23  51 hlskisvkegqkVkaGqvIGtv 72 
                     +++i++k g +V++ + ++++
     EPA04827.1 148 SIKSIKIKIGGTVAKNDLVAEI 169
                    678999***********99986 PP

>> eIF-1a  Translation initiation factor 1A / IF-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00095       1.4       3      27 ..      12      36 ..      10      43 .. 0.86
   2 ?    0.9   0.2      0.27     4e+02      47      47 ..     129     129 ..     106     161 .. 0.54

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00095
                EEEEEEEEETTTEEEEEE.SSSSBE CS
      eIF-1a  3 vigkViealgnnlfrVelpdngkev 27
                + g ++++lgnn + +++ d ++++
  EPA04827.1 12 FDGEITQSLGNNEYVIKINDAEHQI 36
                789**************98766665 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.27
                 E CS
      eIF-1a  47 V 47 
                 V
  EPA04827.1 129 V 129
                 1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1121.40
//
Query:       EPA04828.1  [L=196]
Description: respiratory-chain NADH dehydrogenase, 30 Kd subunit [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-34  119.8   0.0    1.3e-34  119.5   0.0    1.1  1  Complex1_30kDa   Respiratory-chain NADH dehydrogenase, 30 Kd 
  ------ inclusion threshold ------
       0.22   12.0   0.0        1.1    9.8   0.0    1.9  2  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation


Domain annotation for each model (and alignments):
>> Complex1_30kDa  Respiratory-chain NADH dehydrogenase, 30 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.5   0.0   1.4e-38   1.3e-34       2     120 ..      65     195 ..      64     196 .] 0.86

  Alignments for each domain:
  == domain 1  score: 119.5 bits;  conditional E-value: 1.4e-38
                     E--HHHHHHHHHHHHH...TT--EEEEEEEEETT.SSSEEEEEEEE--S-.....-EEEEEE............-S-BEE--TTT-STHHHHHHH CS
  Complex1_30kDa   2 vvepedllevakflkdeeelgfdvlsdltavDek.eerfevvyhllslekn....erirvkvevde........eepevpSvtdlfpgadwyERE 83 
                      v ++d++eva+fl+d  +l+fd++ ++++vD++ ++++evvyhl s+++     + +++ +++++        +++++pS+ ++f +++++ERE
      EPA04828.1  65 NVGKDDIKEVAEFLRD--SLNFDHVESVSGVDYPqDKEIEVVYHLGSYTDSslsrQILVLATRAQReenpipgnDSTKLPSLREIFYSVEFHERE 157
                     6889************..59************9999************655566566777777744445555545999***************** PP

                     HHHHSHHBCTTSSTSS-SSSSTTS.SS-TTSTTS---- CS
  Complex1_30kDa  84 ayDmfGivfeghpdlrrillpedf.eghPLRkdfplsg 120
                     +++mfG+ f+ghpd rr+llped+    PLRkdf ++g
      EPA04828.1 158 IFEMFGVYFQGHPDNRRLLLPEDWaDLPPLRKDFAIKG 195
                     ************************5555******9987 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.15   1.4e+03      56      97 ..      38      83 ..      33     130 .. 0.50
   2 ?    9.8   0.0   0.00012       1.1      17      53 ..     140     176 ..     134     183 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.15
                     HHHHHHHHHHTTSHHHHHHHHHHHH....HTT-HHHHHHHHHHHHH CS
  Alkyl_sulf_dimr 56 eekakrlvelmGgaekvlekakeal....kegdyrwaaellnhlvf 97
                     ++ a ++ve +G + k++    + +     ++d++ +ae+l   + 
       EPA04828.1 38 KDLADKIVEKFGTKTKIAFVKPDRVginvGKDDIKEVAEFLRDSLN 83
                     5667777777776666654333333222244555555555444443 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00012
                      TSGGGSSSSS-HHHHHHHHHHHHH-S--S-GGGTS-- CS
  Alkyl_sulf_dimr  17 nepylreyYGtvehnvraiyqrylGWfdgnPanLnpl 53 
                      + p+lre++ +ve++ r+i++    +f g+P n + l
       EPA04828.1 140 KLPSLREIFYSVEFHEREIFEMFGVYFQGHPDNRRLL 176
                      6799***************************986555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1406.73
//
Query:       EPA04829.1  [L=49]
Description: hypothetical protein BG20_I0513 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       254  (0.014167); expected 358.6 (0.02)
Passed bias filter:                      183  (0.0102069); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 375.69
//
Query:       EPA04830.1  [L=224]
Description: hypothetical protein BG20_I0526 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.047   13.5  10.5       0.42   10.5   1.0    2.8  2  MEF2_binding  MEF2 binding
       0.26   10.0   3.8       0.31    9.8   3.8    1.2  1  Herpes_UL17   Herpesvirus UL17 protein
        8.3    6.5  18.3          7    6.7   0.1    2.3  2  DivIVA        DivIVA protein


Domain annotation for each model (and alignments):
>> MEF2_binding  MEF2 binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   2.7     0.001       6.1       5      29 ..      14      38 ..      13      43 .. 0.92
   2 ?   10.5   1.0     7e-05      0.42      11      19 ..     168     176 ..     161     178 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.001
  MEF2_binding  5 PKGSISEETKQKLKsvILSaQSAAt 29
                  PK S SE TK   Ks+   a  AA 
    EPA04830.1 14 PKVSASETTKDPAKSAAVKAEAAAK 38
                  9*****************9999996 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 7e-05
  MEF2_binding  11 EETKQKLKs 19 
                   EETKQKLK 
    EPA04830.1 168 EETKQKLKK 176
                   9******95 PP

>> Herpes_UL17  Herpesvirus UL17 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   3.8   5.1e-05      0.31     169     238 ..      35     129 ..      12     175 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 5.1e-05
  Herpes_UL17 169 rlpaalpsaakeaaahleac.....apgafdeaaaearlkddfdeilslikraaeavnkraPv.............................aavasg 232
                   + +a+++aa+++a           a+ a+++aaaea+ +++ ++i +++k+aa ++                                   + v+s+
   EPA04830.1  35 AAAKAAAEAARAEA-----EaeaalAKAAAAKAAAEAAAEEEYKAIAAEVKAAATKAP----TftnlrkgeeifrremgepefflakkdrfpRPVLSS 123
                  22333333333333.....344555999999999999999*******99998887654....333333333334333344444444444444666666 PP

  Herpes_UL17 233 llqgal 238
                  + q+ l
   EPA04830.1 124 DEQDEL 129
                  666666 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8  15.2      0.08   4.8e+02      60     126 ..      21      89 ..       2      94 .. 0.61
   2 ?    6.7   0.1    0.0012         7      20      61 ..     160     201 ..     140     205 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.08
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
      DivIVA  60 eleetLkktlvvaqetaeevkanakkeael..iikeAekkaekiveeaeeeakkiaeeieelkrqarlf 126
                 + ++  k + v a+ +a+ + ++a++eae    +++A +++ +  + aeee k ia+e++    +a  f
  EPA04830.1  21 TTKDPAKSAAVKAEAAAKAAAEAARAEAEAeaALAKAAAAKAAAEAAAEEEYKAIAAEVKAAATKAPTF 89 
                 555555666666666666666655554444003334444444444478999999999998877776666 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0012
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCTXXXXXXX CS
      DivIVA  20 edeVdeFLdqvakdyeallkeneelkekvkeleeklkeykel 61 
                 e  V +FL++  +++++l ++ ++ ++ + ++++++++ +++
  EPA04830.1 160 ESGVGKFLEETKQKLKKLKSDPNASEKDIITTQQEIEYLESI 201
                 35699********************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2110  (0.117686); expected 358.6 (0.02)
Passed bias filter:                      772  (0.0430587); expected 358.6 (0.02)
Passed Vit filter:                       122  (0.00680462); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 1393.04
//
Query:       EPA04831.1  [L=248]
Description: glycosyltransferase, group 4 family, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.9e-27   93.9  11.6    9.9e-27   93.9  11.6    1.6  2  Glycos_transf_4  Glycosyl transferase family 4
  ------ inclusion threshold ------
      0.032   13.1   0.9      0.058   12.2   0.9    1.4  1  DUF2254          Predicted membrane protein (DUF2254)
        7.2    6.6   7.1        4.1    7.4   0.0    2.9  4  DUF3043          Protein of unknown function (DUF3043)


Domain annotation for each model (and alignments):
>> Glycos_transf_4  Glycosyl transferase family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.9  11.6   1.7e-30   9.9e-27       9     160 .]       2     150 ..       1     150 [. 0.93
   2 ?   -2.8   0.1      0.94   5.6e+03      70      70 ..     234     234 ..     202     246 .. 0.56

  Alignments for each domain:
  == domain 1  score: 93.9 bits;  conditional E-value: 1.7e-30
  Glycos_transf_4   9 llilllGflDDvlglkarlKlilqilaalililtldlslttlgllltqvlielglilavlltllvivgvtNavNliDGldGlaagvsiiialal 102
                      ++++++G++DD + +  ++K ++ ++aa+++i+++    ++l ++l+ ++++++  l++ ++ll+i ++ N++N iD l+G+a+g ++i++++l
       EPA04831.1   2 FIAFVIGYVDDRKVMGGWFKPLALLFAATPIIFLGT-YHSHLAFPLF-GTVQIP-ALYIGVALLMIPITGNTINSIDVLNGVASGFMTIASFSL 92 
                      6899**************************999887.6677777777.778988.99999********************************** PP

  Glycos_transf_4 103 vvlaavdgrsellllalallgallGfllfNrypAkvFmGDsgslflGlvlavlailgk 160
                       +  ++ +++e+++++l l ++ l+f+ +++ p+k+F GDsg+l+lG++++ +ai+g+
       EPA04831.1  93 SIALFILQNYEIAIISLPLGFVSLAFYKYHKIPSKIFPGDSGALTLGAMYGGIAIIGH 150
                      ***************88888899********************************985 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.94
  Glycos_transf_4  70 t 70 
                       
       EPA04831.1 234 G 234
                      1 PP

>> DUF2254  Predicted membrane protein (DUF2254)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.9   9.7e-06     0.058       5      73 ..      19     101 ..      18     104 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.7e-06
     DUF2254   5 wfipllivllavllalllllldealslsldleelke..............gaeaaralLstiagsmltvagfvfSitvvalql 73 
                 wf pl+++ +a  + +l ++  +   + + + ++++              +  ++ ++L+ +a++++t+a+f++Si +  lq 
  EPA04831.1  19 WFKPLALLFAATPIIFLGTYHSHLAFPLFGTVQIPAlyigvallmipitgNTINSIDVLNGVASGFMTIASFSLSIALFILQN 101
                 5566555555555555555553333333322222225555556666665566677799********************99996 PP

>> DUF3043  Protein of unknown function (DUF3043)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0   0.00068       4.1      69     100 ..       7      37 ..       4      73 .. 0.65
   2 ?   -1.4   0.1      0.34     2e+03      73     105 ..      75     106 ..      70     119 .. 0.60
   3 ?    2.4   0.0     0.024   1.5e+02     106     136 ..     150     180 ..     136     188 .. 0.86
   4 ?   -3.5   0.2       1.6   9.4e+03     114     123 ..     233     242 ..     204     247 .. 0.44

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00068
     DUF3043  69 RDlVDsrrnlgelflplalvvlvl.llvslvkv 100
                   +VD r  +g++f plal++ ++ +++    +
  EPA04831.1   7 IGYVDDRKVMGGWFKPLALLFAATpIIFLG--T 37 
                 569*****************9999543322..2 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.34
     DUF3043  73 Dsrrnlgelflplalvvlvl.llvslvkvpevqa 105
                 D    +++ f+ +a + l + l++   ++ e++ 
  EPA04831.1  75 DVLNGVASGFMTIASFSLSIaLFI--LQNYEIAI 106
                 555667778888888888884444..34444433 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.024
     DUF3043 106 vvsllllvllllvvidgillgrkvkkkvrek 136
                  v++++ v ll +vi+++l+  ++k+ v+++
  EPA04831.1 150 HVEIIAAVALLPAVINSFLFLSSMKRIVEHR 180
                 567889999*****************99987 PP

  == domain 4  score: -3.5 bits;  conditional E-value: 1.6
     DUF3043 114 llllvvidgi 123
                   +l++i +i
  EPA04831.1 233 SGILAIITAI 242
                 2233333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1630.39
//
Query:       EPA04832.1  [L=158]
Description: transferase hexapeptide repeat protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.1e-27   92.9  20.1    1.7e-11   43.4   1.3    4.4  5  Hexapep    Bacterial transferase hexapeptide (six repeats)
    3.6e-19   68.2  12.6    1.7e-11   43.6   2.6    4.5  5  Hexapep_2  Hexapeptide repeat of succinyl-transferase
  ------ inclusion threshold ------
       0.12   12.8   0.2       0.15   12.4   0.2    1.1  1  RuvX       Holliday junction resolvase


Domain annotation for each model (and alignments):
>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.4   1.3   2.8e-15   1.7e-11       2      34 ..      10      42 ..       9      44 .. 0.93
   2 !   23.4   0.2   5.7e-09   3.4e-05       8      34 ..      34      60 ..      34      62 .. 0.95
   3 !   10.9   0.0     5e-05       0.3       3      18 ..      65      80 ..      63      81 .. 0.78
   4 !   32.3   4.0   8.7e-12   5.2e-08       1      36 []      91     126 ..      91     126 .. 0.96
   5 ?   -3.1   0.0       1.3   7.9e+03      20      23 ..     133     136 ..     131     141 .. 0.57

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 2.8e-15
                EEEETTEEE-TTEEEETTEEE-TTEEEETTEEE CS
     Hexapep  2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvi 34
                ++IGsnv+I++f+++g+nV+IGdnvkIg+ v i
  EPA04832.1 10 AKIGSNVKIWHFSYVGDNVEIGDNVKIGSLVHI 42
                79**************************97766 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 5.7e-09
                EEE-TTEEEETTEEE-TTEEEETTEEE CS
     Hexapep  8 vlIgpfaviggnVkIGdnvkIgagvvi 34
                v+Ig+ ++i  nVkIG+n+kI+  ++i
  EPA04832.1 34 VKIGSLVHIDYNVKIGENTKIEGQAYI 60
                79*********************9998 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 5e-05
                EEETTEEE-TTEEEET CS
     Hexapep  3 vIGsnvlIgpfavigg 18
                +IG+nv+Igp av+ +
  EPA04832.1 65 RIGKNVFIGPAAVLTN 80
                6899999999888876 PP

  == domain 4  score: 32.3 bits;  conditional E-value: 8.7e-12
                 TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
     Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36 
                 +++I++n++Ig+ avi ++V IG+n++++ g+v+++
  EPA04832.1  91 GVTIEDNAVIGARAVIKAGVRIGKNSVVAMGAVVTR 126
                 589*******************************85 PP

  == domain 5  score: -3.1 bits;  conditional E-value: 1.3
                 EEE- CS
     Hexapep  20 VkIG 23 
                 V+IG
  EPA04832.1 133 VVIG 136
                 3333 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.2     3e-06     0.018       3      28 ..      11      38 ..       9      43 .. 0.92
   2 ?    2.6   0.0     0.019   1.1e+02       1      10 [.      45      54 ..      45      61 .. 0.72
   3 !   11.0   0.0   4.6e-05      0.27       3      15 ..      65      77 ..      65      79 .. 0.89
   4 !   43.6   2.6   2.9e-15   1.7e-11       2      34 .]      92     126 ..      91     126 .. 0.96
   5 ?   -2.1   0.0      0.56   3.3e+03       7      12 ..     132     137 ..     130     141 .. 0.51

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3e-06
                EE-TT-EE-TT-EES..EEE-TT-EE-T CS
   Hexapep_2  3 iIGdnCliGanagiG..vslGdncvvga 28
                +IG n+ i  ++++G  v++Gdn+++g+
  EPA04832.1 11 KIGSNVKIWHFSYVGdnVEIGDNVKIGS 38
                89************999*********96 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.019
                .EEE-TT-EE CS
   Hexapep_2  1 pviIGdnCli 10
                +v+IG+n+ i
  EPA04832.1 45 NVKIGENTKI 54
                5899999865 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 4.6e-05
                EE-TT-EE-TT-E CS
   Hexapep_2  3 iIGdnCliGanag 15
                +IG+n++iG+ a+
  EPA04832.1 65 RIGKNVFIGPAAV 77
                6********9886 PP

  == domain 4  score: 43.6 bits;  conditional E-value: 2.9e-15
                 EEE-TT-EE-TT-EE..SEEE-TT-EE-TT-EE-S CS
   Hexapep_2   2 viIGdnCliGanagi..GvslGdncvvgaGvvita 34 
                 v+I+dn +iGa+a+i  Gv +G+n+vv++G v+t+
  EPA04832.1  92 VTIEDNAVIGARAVIkaGVRIGKNSVVAMGAVVTR 126
                 99************999****************96 PP

  == domain 5  score: -2.1 bits;  conditional E-value: 0.56
                 T-EE-T CS
   Hexapep_2   7 nCliGa 12 
                  ++iG+
  EPA04832.1 132 SVVIGV 137
                 445555 PP

>> RuvX  Holliday junction resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   2.5e-05      0.15      10      78 ..      87     156 ..      85     158 .] 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.5e-05
                 SSEEEEEEE-S--SS---EEEEE---HHHHHHHHHHHHHHTT--.EEEEE------SSS---SSTTHHHH CS
        RuvX  10 tkriGvAvsdplgilaspletierkskekdleelkelvkeeeve.eiVvGlPlnldgsegesakkvrkfa 78 
                 +k iGv + d+  i a+++     + +++++ ++ ++v++  +e  +V+G+P +++ + +e  kk ++++
  EPA04832.1  87 DKMIGVTIEDNAVIGARAVIKAGVRIGKNSVVAMGAVVTRDVPEdSVVIGVPATIRYTRKEYDKKQKQWI 156
                 589*************99999996667889999999998887653899*******999999988888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1046.20
//
Query:       EPA04833.1  [L=53]
Description: hypothetical protein BG20_I0528 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-06   28.0   0.1    1.9e-06   28.0   0.1    1.1  1  DUF1059   Protein of unknown function (DUF1059)
  ------ inclusion threshold ------
      0.078   13.3   0.0      0.093   13.1   0.0    1.2  1  Fer2_BFD  BFD-like [2Fe-2S] binding domain


Domain annotation for each model (and alignments):
>> DUF1059  Protein of unknown function (DUF1059)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.1   2.2e-10   1.9e-06       1      48 [.       1      47 [.       1      52 [. 0.86

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 2.2e-10
     DUF1059  1 mkefkCgDvgpdCgfeitaeteeEvlrkvaeHakaaHglteippelve 48
                m ++kC D g++C+f  ++e e+ v+++  +H+ ++Hg+    ++l++
  EPA04833.1  1 MAKLKCSDYGFECEFVSEGEIEN-VIEEFGKHTDEVHGIDYSKEALMQ 47
                7789***********99776665.**************9888888876 PP

>> Fer2_BFD  BFD-like [2Fe-2S] binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0     1e-05     0.093       4      25 ..      12      35 ..      12      47 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1e-05
    Fer2_BFD  4 rCegvtegeIrdairr..aglttv 25
                +Ce v+egeI+++i++  ++  +v
  EPA04833.1 12 ECEFVSEGEIENVIEEfgKHTDEV 35
                5*************6654334444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.33u 0.25s 00:00:00.58 Elapsed: 00:00:00.40
# Mc/sec: 398.79
//
Query:       EPA04834.1  [L=89]
Description: hypothetical protein BG20_I0504 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.7e-08   34.3   0.2    7.8e-08   32.8   0.2    1.8  1  Trm112p       Trm112p-like protein
  ------ inclusion threshold ------
      0.062   13.1   0.4       0.12   12.2   0.4    1.6  1  Cys_rich_KTR  Cysteine-rich KTR


Domain annotation for each model (and alignments):
>> Trm112p  Trm112p-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.2   8.6e-12   7.8e-08       3      67 ..       4      49 ..       2      50 .. 0.80

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 8.6e-12
                GGCCC-B-TTTHH.C--HHHHHHHHHTT---S-SS----SCHHTTEECCCCEEEETTTTEEEEEET CS
     Trm112p  3 lllniLaCpackg.pLdwealvevaalglnelpkekpedyellleldieegeLvCpncgraYpIkd 67
                 +++iLaCp++k+ pL++  + e+ +                    ++ eg+L Cp+c r YpI +
  EPA04834.1  4 SMIDILACPIDKNhPLELYEIKEKDN--------------------VVSEGALFCPKCSRFYPIIE 49
                5789************4444444443....................7889**************87 PP

>> Cys_rich_KTR  Cysteine-rich KTR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.4   1.4e-05      0.12      19      35 ..      27      43 ..       8      50 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.4e-05
  Cys_rich_KTR 19 edTvLknfpLfCPKCkq 35
                  +d v  +  LfCPKC +
    EPA04834.1 27 KDNVVSEGALFCPKCSR 43
                  577888899******76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 624.26
//
Query:       EPA04835.1  [L=187]
Description: PBS lyase HEAT-like repeat protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.5e-17   62.5   0.5    7.9e-08   32.6   0.1    2.5  3  HEAT_2          HEAT repeats
    7.8e-11   41.3   0.1     0.0032   17.6   0.0    4.2  4  HEAT            HEAT repeat
    7.1e-06   26.2   2.6       0.42   10.6   0.0    3.2  3  Cnd1            non-SMC mitotic condensation complex subunit 
      2e-05   24.8   1.5       0.52   10.7   0.0    4.0  4  Cohesin_HEAT    HEAT repeat associated with sister chromatid 
    2.3e-05   24.8   0.0      0.094   13.2   0.0    3.3  3  HEAT_EZ         HEAT-like repeat
     0.0003   20.4   0.2        0.1   12.1   0.0    2.2  2  ERAP1_C         ERAP1-like C-terminal domain
     0.0018   18.1   0.9       0.35   10.6   0.1    2.2  2  DNA_pol3_delta  DNA polymerase III, delta subunit
  ------ inclusion threshold ------
      0.028   15.1   0.0         26    5.9   0.1    4.2  5  HEAT_PBS        PBS lyase HEAT-like repeat
      0.029   13.9   0.1      0.094   12.3   0.1    2.0  2  CLASP_N         CLASP N terminal
      0.045   13.5   0.0        7.2    6.3   0.0    2.6  2  DUF4042         Domain of unknown function (DUF4042)
      0.057   13.5   3.1       0.34   11.0   0.2    2.7  3  V-ATPase_H_C    V-ATPase subunit H


Domain annotation for each model (and alignments):
>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   3.9e-05     0.063      17      75 ..      19      76 ..       7      80 .. 0.85
   2 !   32.6   0.1   4.9e-11   7.9e-08       2      87 ..      66     149 ..      64     150 .. 0.94
   3 !   26.1   0.0   5.2e-09   8.5e-06       3      78 ..      98     172 ..      96     176 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.9e-05
      HEAT_2 17 rraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaLkelldddd 75
                +++++++L   +++e+++ +++ l+de+  +R +a  aL+   ++   ++L e ld+ +
  EPA04835.1 19 KIKILESLSFSNDEEIIQKIISKLDDENIQIRGEAFSALVSNENE-ISNLLIENLDSQN 76
                6789999********************************987765.7777777776655 PP

  == domain 2  score: 32.6 bits;  conditional E-value: 4.9e-11
      HEAT_2   2 daLlqalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaLkellddddddvvReaAaeaL 87 
                 ++L++ l ++ ++++r     +L++ ++  ++p +++l +d++++vR+ a  aLg ++  +a ++   +l  d++ +vR +A++a+
  EPA04835.1  66 NLLIENL-DSQNKNIRGYLSLVLANRNDSNSIPEIIKLTNDQSSMVRACALGALGHLKARQAKEVIDNCL-FDPNLEVRKSALQAM 149
                 6799999.9**********************************************************988.78888899999*997 PP

  == domain 3  score: 26.1 bits;  conditional E-value: 5.2e-09
      HEAT_2   3 aLlqalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaLkellddddddv 78 
                   +++  nd +  vr+ a+ aLg ++ ++a + + ++l d++ +vR+ a +a+  +  p + +  ke+l+++d+++
  EPA04835.1  98 EIIKLT-NDQSSMVRACALGALGHLKARQAKEVIDNCLFDPNLEVRKSALQAMIYLEYPISTEKIKEILKEKDSEL 172
                 566755.9***************************************************9*****99999988776 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.015        24       2      25 ..      35      58 ..      34      59 .. 0.85
   2 ?    0.5   0.0      0.63     1e+03       3      17 ..      66      80 ..      64      94 .. 0.84
   3 !   17.6   0.0   1.9e-06    0.0032       2      27 ..      96     121 ..      96     122 .. 0.95
   4 !   12.1   0.0   0.00011      0.18       5      24 ..     130     149 ..     128     152 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.015
                HHHHHHHHT-SSHHHHHHHHHHHH CS
        HEAT  2 lPlllkllsDpspeVReaAakaLg 25
                +  +++ l D++ ++R  A+ aL+
  EPA04835.1 35 IQKIISKLDDENIQIRGEAFSALV 58
                56677889************9996 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.63
                HHHHHHHT-SSHHHH CS
        HEAT  3 PlllkllsDpspeVR 17
                +ll+++l +++ ++R
  EPA04835.1 66 NLLIENLDSQNKNIR 80
                689999999999888 PP

  == domain 3  score: 17.6 bits;  conditional E-value: 1.9e-06
                 HHHHHHHHT-SSHHHHHHHHHHHHHH CS
        HEAT   2 lPlllkllsDpspeVReaAakaLgal 27 
                 +P ++kl +D+s+ VR+ A+ aLg+l
  EPA04835.1  96 IPEIIKLTNDQSSMVRACALGALGHL 121
                 699***99****************87 PP

  == domain 4  score: 12.1 bits;  conditional E-value: 0.00011
                 HHHHHT-SSHHHHHHHHHHH CS
        HEAT   5 llkllsDpspeVReaAakaL 24 
                 + ++l Dp+ eVR++A++a+
  EPA04835.1 130 IDNCLFDPNLEVRKSALQAM 149
                 66889************996 PP

>> Cnd1  non-SMC mitotic condensation complex subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0   0.5     0.007        11      55      97 ..      30      72 ..      19      90 .. 0.74
   2 !    9.4   0.0    0.0006      0.98      57      93 ..      93     129 ..      83     132 .. 0.84
   3 !   10.6   0.0   0.00026      0.42      26      56 ..     130     163 ..     126     181 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.007
        Cnd1 55 kekgflselaklleDenprVvanalaalteiseksenaiynll 97
                 ++++++++ + l+Den +++  a +al    ++ +n+++++l
  EPA04835.1 30 NDEEIIQKIISKLDDENIQIRGEAFSALVSNENEISNLLIENL 72
                5667888888888999999998888888877777445555443 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0006
        Cnd1  57 kgflselaklleDenprVvanalaalteiseksenai 93 
                 ++ + e+ kl +D++++V+a al al  ++ ++ +++
  EPA04835.1  93 SNSIPEIIKLTNDQSSMVRACALGALGHLKARQAKEV 129
                 567899999***************9999999976665 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00026
        Cnd1  26 LrkrLkDedpyVRktaaivvakL...ilndmvke 56 
                 + ++L D++  VRk a+ +++ L   i+ + +ke
  EPA04835.1 130 IDNCLFDPNLEVRKSALQAMIYLeypISTEKIKE 163
                 789********************97776665553 PP

>> Cohesin_HEAT  HEAT repeat associated with sister chromatid cohesion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.031        51      16      35 ..      31      50 ..      12      51 .. 0.86
   2 !    6.5   0.0    0.0066        11      23      39 ..      99     115 ..      89     118 .. 0.82
   3 !   10.7   0.0   0.00032      0.52      20      40 ..     127     147 ..     121     148 .. 0.91
   4 ?   -3.5   0.0       8.5   1.4e+04      16      25 ..     158     167 ..     157     170 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.031
                  SHHHHHHHHHHHHSS-HHHH CS
  Cohesin_HEAT 16 apevldtiarrltDsspsVR 35
                  ++e+++ i+++l D+ +++R
    EPA04835.1 31 DEEIIQKIISKLDDENIQIR 50
                  55788888888******999 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0066
                   HHHHHHSS-HHHHHHHH CS
  Cohesin_HEAT  23 iarrltDsspsVRdAaL 39 
                   i++  +D s++VR+ aL
    EPA04835.1  99 IIKLTNDQSSMVRACAL 115
                   444489*******9876 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00032
                   HHHHHHHHHSS-HHHHHHHHH CS
  Cohesin_HEAT  20 ldtiarrltDsspsVRdAaLe 40 
                   +++i ++l D+   VR++aL+
    EPA04835.1 127 KEVIDNCLFDPNLEVRKSALQ 147
                   68899***************8 PP

  == domain 4  score: -3.5 bits;  conditional E-value: 8.5
                   SHHHHHHHHH CS
  Cohesin_HEAT  16 apevldtiar 25 
                   ++++++++++
    EPA04835.1 158 TEKIKEILKE 167
                   5678888876 PP

>> HEAT_EZ  HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.15   2.5e+02      28      52 ..      33      57 ..      28      58 .. 0.82
   2 !   13.2   0.0   5.8e-05     0.094      30      55 .]      96     121 ..      92     121 .. 0.89
   3 ?    5.2   0.0     0.019        31      35      51 ..     132     148 ..     125     152 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.15
     HEAT_EZ 28 eilpaLlalLnddsdeVRaaAagaL 52
                ei+   ++ L d++  +R+ A  aL
  EPA04835.1 33 EIIQKIISKLDDENIQIRGEAFSAL 57
                67788888888888899*9998887 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 5.8e-05
     HEAT_EZ  30 lpaLlalLnddsdeVRaaAagaLgnl 55 
                 +p+ ++l nd s++VRa A+gaLg l
  EPA04835.1  96 IPEIIKLTNDQSSMVRACALGALGHL 121
                 7889999999999***********76 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.019
     HEAT_EZ  35 alLnddsdeVRaaAaga 51 
                 ++L d++ eVR+ A+ a
  EPA04835.1 132 NCLFDPNLEVRKSALQA 148
                 7899**********988 PP

>> ERAP1_C  ERAP1-like C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   6.2e-05       0.1     180     227 ..       5      47 ..       1      62 [. 0.76
   2 !    7.6   0.1    0.0014       2.4     125     233 ..      47     147 ..      40     176 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.2e-05
                 HHHHHHHHHHHC-SSHHHHHHHHHHHCC-S-HHHHHHHHHHCTTT..S CS
     ERAP1_C 180 aewdallerykdtsapsekeaalralaatpdpellerllnfvlesdev 227
                 + ++++l++    ++ +ek ++l++l++++d+e++++++  + +++++
  EPA04835.1   5 KNIKEMLDL---GTI-DEKIKILESLSFSNDEEIIQKIISKL-DDENI 47 
                 556666666...577.9********************99998.55554 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0014
                 HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHCSTT-S-HHHHHHHHHHHHHHS-HHHHHHHHHHHHC-SSHHHHHHHHHHHCC-S-HHHHHHHHHHCTT CS
     ERAP1_C 125 aqlrslllsaacaagdpevveearklfkawlegddlippdlrwavycalaanggeaewdallerykdtsapsekeaalralaatpdpellerllnfvle 223
                  q r +++sa+++++     +e  +l+ + l++    ++++r+ +  +la + + + + +++++ +d s+   +  al+al++ +  +++e + n +++
  EPA04835.1  47 IQIRGEAFSALVSNE-----NEISNLLIENLDS---QNKNIRGYLSLVLANRNDSNSIPEIIKLTNDQSS-MVRACALGALGHLKARQAKEVIDNCLFD 136
                 566777777776555.....3344444444442...5788888888888766799999****99767676.88**********9998888875555553 PP

                 .T..S-GGGHH CS
     ERAP1_C 224 .sdevrnqdlr 233
                  + evr+  l+
  EPA04835.1 137 pNLEVRKSALQ 147
                 34455554444 PP

>> DNA_pol3_delta  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.1    0.0019       3.2     127     159 ..      30      62 ..       5      74 .. 0.80
   2 !   10.6   0.1   0.00022      0.35      76     157 ..      65     152 ..      59     167 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0019
                     -TTTHHHHHHHHHHHTT-EE-HHHHHHHHHHHT CS
  DNA_pol3_delta 127 keeelkkwiqkraqelglkiekealelLlelve 159
                     + ee++++i +++ +++++i  ea++ L+++ +
      EPA04835.1  30 NDEEIIQKIISKLDDENIQIRGEAFSALVSNEN 62 
                     6799************************98755 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00022
                     -TTHHHHHHHHTTT--SSEEEEEEES.S--HHHHHHHHHTTTEEEEEE---......-TTTHHHHHHHHHHHTT-EE-HHHHHHHHHH CS
  DNA_pol3_delta  76 nekllkeLeeylsnlpedtlLiliapkklderkklvklLkkkatvveaktl......keeelkkwiqkraqelglkiekealelLlel 157
                     +  l+++L ++ +n+  +  L+l  +++ ++  +++kl + ++++v+a  l      k  + k+ i++ + + +l+  k al+ +++l
      EPA04835.1  65 SNLLIENLDSQNKNIRGYLSLVLANRNDSNSIPEIIKLTNDQSSMVRACALgalghlKARQAKEVIDNCLFDPNLEVRKSALQAMIYL 152
                     566889999999************9999999999************************************************988764 PP

>> HEAT_PBS  PBS lyase HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0       0.3   4.9e+02       7      27 .]      24      44 ..      20      44 .. 0.86
   2 ?   -1.2   0.0       3.1     5e+03      19      26 ..      66      73 ..      48      74 .. 0.64
   3 ?   -1.0   0.0       2.5   4.1e+03       8      25 ..      86     103 ..      79     105 .. 0.75
   4 ?    5.9   0.1     0.016        26       7      25 ..     113     134 ..     110     136 .. 0.61
   5 ?    1.0   0.0       0.6   9.8e+02       1      26 [.     141     166 ..     141     167 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.3
                HHHHHCTSGGGHHHHHHHCTC CS
    HEAT_PBS  7 kaLgqlgdeeaipaLleaLqd 27
                ++L   +dee+i+ ++  L+d
  EPA04835.1 24 ESLSFSNDEEIIQKIISKLDD 44
                67888999*******998887 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3.1
                HHHHHHCT CS
    HEAT_PBS 19 paLleaLq 26
                 +L+e+L+
  EPA04835.1 66 NLLIENLD 73
                46777776 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 2.5
                 HHHHCTSGGGHHHHHHHC CS
    HEAT_PBS   8 aLgqlgdeeaipaLleaL 25 
                  L++ +d  +ip ++++ 
  EPA04835.1  86 VLANRNDSNSIPEIIKLT 103
                 688888999999999875 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.016
                 HHHHHCTS...GGGHHHHHHHC CS
    HEAT_PBS   7 kaLgqlgd...eeaipaLleaL 25 
                  aLg+lg+    +a +++ ++L
  EPA04835.1 113 CALGALGHlkaRQAKEVIDNCL 134
                 4555555544488888877777 PP

  == domain 5  score: 1.0 bits;  conditional E-value: 0.6
                 HHHHHHHHHHHCTSGGGHHHHHHHCT CS
    HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLq 26 
                 vR +A+ a+  l  + + + ++e L+
  EPA04835.1 141 VRKSALQAMIYLEYPISTEKIKEILK 166
                 8999****999999888888888776 PP

>> CLASP_N  CLASP N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       0.7   1.1e+03     177     196 ..      34      53 ..      22      80 .. 0.62
   2 ?   12.3   0.1   5.8e-05     0.094     174     226 ..     123     176 ..      52     177 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.7
     CLASP_N 177 iekslkkgleDanptVReta 196
                 i + +++ l D n ++R +a
  EPA04835.1  34 IIQKIISKLDDENIQIRGEA 53 
                 33334444555555555443 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 5.8e-05
     CLASP_N 174 ldliekslkkgleDanptVRetaRstfwef.fkvwPsrAksllssldpkvrkal 226
                  +++++++  +l D+n +VR++a ++++++ + +  ++ k++l++ d+++ ++l
  EPA04835.1 123 ARQAKEVIDNCLFDPNLEVRKSALQAMIYLeYPISTEKIKEILKEKDSELERLL 176
                 48899***********************99666777788889999888887765 PP

>> DUF4042  Domain of unknown function (DUF4042)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.013        21      21      67 ..      78     121 ..      64     126 .. 0.69
   2 ?    6.3   0.0    0.0044       7.2      39      64 ..     124     149 ..     120     157 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.013
     DUF4042  21 slygyWhvllpdevlqerkseatLltillkDpspkvRaaalqvlaal 67 
                  + gy +++l +   ++++s  ++++ l++D s+ vRa+al +l +l
  EPA04835.1  78 NIRGYLSLVLANR--NDSNSIPEIIK-LTNDQSSMVRACALGALGHL 121
                 5556666555555..34444444443.579***********999876 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0044
     DUF4042  39 kseatLltillkDpspkvRaaalqvl 64 
                  ++++++   l+Dp++ vR  alq++
  EPA04835.1 124 RQAKEVIDNCLFDPNLEVRKSALQAM 149
                 56677778889*************97 PP

>> V-ATPase_H_C  V-ATPase subunit H
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0       0.1   1.6e+02      80     109 ..      28      57 ..       5      61 .. 0.75
   2 ?   11.0   0.2   0.00021      0.34      36     109 ..      72     149 ..      57     152 .. 0.72
   3 ?   -3.1   0.1       5.1   8.3e+03      90     101 ..     161     172 ..     158     179 .. 0.47

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.1
  V-ATPase_H_C  80 vleklkaKekimellehedeevkyeALkav 109
                   + ++ ++ +ki++ l++e+ +++ eA  a+
    EPA04835.1  28 FSNDEEIIQKIISKLDDENIQIRGEAFSAL 57 
                   446677778899999999999999998876 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00021
  V-ATPase_H_C  36 leeknfkllkkLiklleeskdk...tvlavalnDigelvkllpegk.kvleklkaKekimellehedeevkyeALkav 109
                   l+++n ++   L  +l + +d+     +  + nD +++v+ +  g   +l+  +aKe+i ++l +++ ev++ AL+a+
    EPA04835.1  72 LDSQNKNIRGYLSLVLANRNDSnsiPEIIKLTNDQSSMVRACALGAlGHLKARQAKEVIDNCLFDPNLEVRKSALQAM 149
                   4455444555555556444443212224446899999999999664278899999*********************97 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 5.1
  V-ATPase_H_C  90 imellehedeev 101
                   i e+l+++d+e+
    EPA04835.1 161 IKEILKEKDSEL 172
                   333444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1036  (0.0577835); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 1298.62
//
Query:       EPA04836.1  [L=107]
Description: hypothetical protein BG20_I0520 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-15   57.5   0.1    1.7e-15   57.0   0.1    1.3  1  FeS_assembly_P  Iron-sulfur cluster assembly protein
  ------ inclusion threshold ------
        0.1   13.1   2.3       0.41   11.1   0.1    2.4  3  HMA             Heavy-metal-associated domain


Domain annotation for each model (and alignments):
>> FeS_assembly_P  Iron-sulfur cluster assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.0   0.1   1.8e-19   1.7e-15       5      74 .]      13      84 ..       9      84 .. 0.93

  Alignments for each domain:
  == domain 1  score: 57.0 bits;  conditional E-value: 1.8e-19
                    HHHHTT-B-TTTSSBCCCCT---EEEE-T-EEEEEE--SSTT-T..THHHHHHHHHHHHC.STT--EEEEEE CS
  FeS_assembly_P  5 laaLrtVtDPelgvdlvslglvreidieggkVsvditltypacs..laeairadaeaalralpgvevveVev 74
                    ++ L++++DPe+++++v+l l+ e+di++++V+vd+ lt+p c+  +   i++d+ + l ++ gv++v+V+v
      EPA04836.1 13 FDELSKIVDPEINTSIVELELIDEVDINNSNVKVDLHLTSPFCPavFGFKICQDIHDNLLKVDGVDDVKVNV 84
                    6779****************************************855568********************97 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       0.6   5.4e+03      37      46 ..       7      16 ..       2      32 .. 0.49
   2 ?    1.4   0.2      0.05   4.5e+02      19      39 ..      27      47 ..      21      53 .. 0.63
   3 ?   11.1   0.1   4.6e-05      0.41      14      36 ..      65      87 ..      62      89 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.6
         HMA 37 tvtVeg.daes 46
                ++ V++ d e 
  EPA04836.1  7 QLRVKLfD-EL 16
                55555532.22 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.05
         HMA 19 vLselpgVesvkvdlatktvt 39
                ++ el+ +++v++++ + +v 
  EPA04836.1 27 SIVELELIDEVDINNSNVKVD 47
                566666677777776654443 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 4.6e-05
         HMA 14 akvekvLselpgVesvkvdlatk 36
                +++ + L++++gV++vkv++ ++
  EPA04836.1 65 QDIHDNLLKVDGVDDVKVNVSNH 87
                68999**************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.34u 0.29s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 773.90
//
Query:       EPA04837.1  [L=364]
Description: ATPase, AAA family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-12   48.2   0.0      4e-12   46.7   0.0    1.8  1  AAA           ATPase family associated with various cellular 
    3.9e-08   33.2   0.0    1.3e-07   31.5   0.0    1.9  2  RuvB_N        Holliday junction DNA helicase RuvB P-loop doma
    1.1e-05   25.4   0.4    5.1e-05   23.3   0.0    2.1  2  Rad17         Rad17 P-loop domain
    0.00078   18.7   0.0     0.0013   18.0   0.0    1.3  1  TIP49         TIP49 P-loop domain
     0.0029   17.6   0.0     0.0083   16.2   0.0    1.9  2  AAA_14        AAA domain
     0.0073   16.3   0.1      0.051   13.6   0.0    2.3  2  AAA_5         AAA domain (dynein-related subfamily)
     0.0093   16.2   0.3       0.34   11.2   0.1    2.8  3  AAA_22        AAA domain
  ------ inclusion threshold ------
       0.01   16.2   0.0      0.022   15.2   0.0    1.6  1  AAA_16        AAA ATPase domain
      0.012   15.2   0.0      0.023   14.2   0.0    1.4  1  AAA_7         P-loop containing dynein motor region
      0.018   15.2   0.0      0.038   14.1   0.0    1.5  1  AAA_2         AAA domain (Cdc48 subfamily)
      0.027   14.6   0.0      0.054   13.6   0.0    1.5  1  AAA_33        AAA domain
      0.028   14.4   0.0       0.07   13.0   0.0    1.7  1  NTPase_1      NTPase
      0.029   14.5   0.5      0.059   13.5   0.1    1.8  2  RFC1          Replication factor RFC1 C terminal domain
      0.031   13.7   0.3       0.12   11.8   0.0    2.0  3  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.054   12.9   0.1        3.2    7.1   0.0    2.9  3  TniB          Bacterial TniB protein
      0.056   14.0   0.1        0.2   12.2   0.0    1.9  2  AAA_18        AAA domain
      0.056   13.1   0.0       0.13   12.0   0.0    1.6  1  AAA_24        AAA domain
      0.096   13.1   0.0       0.19   12.2   0.0    1.5  1  AAA_17        AAA domain
        0.1   11.8   0.0       0.16   11.2   0.0    1.2  1  Zeta_toxin    Zeta toxin
       0.11   12.2   0.0       0.26   11.0   0.0    1.5  1  IstB_IS21     IstB-like ATP binding protein


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   0.0   4.5e-15     4e-12       1      98 [.      38     125 ..      38     153 .. 0.81

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 4.5e-15
                 EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS...TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHT CS
         AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakeka...kpsilfiDEidalaksrsgseseeeervvnqLlteldgv 96 
                 +ll+GppG+GKT++a   ak++g +++ +++s+++      s+++i+e+++ +  +    +   +fiDE+d ++++        +   +++L+  l++ 
  EPA04837.1  38 LLLVGPPGIGKTTIAYITAKQFGYDMVGLNASDVR------SKSRINEILTPVLGNVsllGIPMIFIDEVDGIHGRG-------DYGGAEALIDILKEP 123
                 69*********************************......99********97433357889***********9999.......455566676666666 PP

                 TT CS
         AAA  97 kk 98 
                 + 
  EPA04837.1 124 TV 125
                 55 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.0   1.4e-10   1.3e-07       2      95 ..       7     103 ..       6     136 .. 0.80
   2 ?   -2.4   0.0       3.9   3.5e+03      73      89 ..     263     279 ..     254     301 .. 0.71

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 1.4e-10
      RuvB_N   2 rPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelgvklkitsgPvlekagdlaallt......nleekdvlfideih 94 
                 rP+++++ ig e+ ++++   ie   k ++    +ll+GpPG+Gktt+a i ak++g ++    +  +  ++ +  +lt      +l    ++fide+ 
  EPA04837.1   7 RPQNISDMIGNEESRSSI---IEWFTKWKKGTKPLLLVGPPGIGKTTIAYITAKQFGYDMVGLNASDVRSKSRINEILTpvlgnvSLLGIPMIFIDEVD 102
                 9***********999876...56666666777789************************9999999998888888888722221123334568999986 PP

      RuvB_N  95 r 95 
                  
  EPA04837.1 103 G 103
                 5 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.9
      RuvB_N  73 gdlaalltnleekdvlf 89 
                 + la llt ++e d+l+
  EPA04837.1 263 QTLAKLLTIISEADMLY 279
                 56888999999999987 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   5.7e-08   5.1e-05       9      74 ..       2      64 ..       1      83 [. 0.84
   2 ?   -0.5   0.2       1.1     1e+03      83     178 ..     181     278 ..     158     283 .. 0.58

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 5.7e-08
       Rad17  9 WfekykPekaeelavhkkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgiklr 74
                W eky+P+   ++    +  + + ew+          + LL+ GP+G gk+t+  + +k++g+++ 
  EPA04837.1  2 WSEKYRPQNISDMIGNEESRSSIIEWFTKWKKGT---KPLLLVGPPGIGKTTIAYITAKQFGYDMV 64
                **************************97654444...479999*******************9975 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.1
       Rad17  83 kepdnqksdfkgltekesrf....lsqie.sfkeleLkdakylklqklGddlrtdkklilvedlPnkfyrdsdalrevirkylrssealplilviteie 176
                 k  +  + d++++++  +++     +q e sf+++++ d  +  ++   + +   +++++  ++  k ++d+  +  +i   l  +    l+ +i+e +
  EPA04837.1 181 KVIERSRGDIRSMINLTQSLvtgfNPQTEkSFENINVEDGINAFFK--ANSIDEARSVLYSMQIDPKLKIDA-FYSSIITSNLDNQTLAKLLTIISEAD 276
                 5555556666777666665444445555435666666666664444..455555556666666666666553.34556666666555557777777776 PP

       Rad17 177 sl 178
                  l
  EPA04837.1 277 ML 278
                 66 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.5e-06    0.0013      24      91 ..      12      74 ..       3      88 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.5e-06
                XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
       TIP49 24 eglvGqkkareaagvivelikekklaGravLlaGpsgtGktalaiaiskelgedvpfvalsgsevysl 91
                + ++G +++r +  +i  + k kk + + +Ll+Gp+g Gkt +a   +k++g d   v l++s+v s 
  EPA04837.1 12 SDMIGNEESRSS--IIEWFTKWKK-GTKPLLLVGPPGIGKTTIAYITAKQFGYD--MVGLNASDVRSK 74
                469999999964..5555566666.88*************************66..588999998775 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   9.2e-06    0.0083       3      76 ..      36     104 ..      34     152 .. 0.79
   2 ?   -2.6   0.0       5.7   5.1e+03      31      47 ..     253     269 ..     234     296 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 9.2e-06
      AAA_14   3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev 76 
                 k+l+++G+  +GKTt+++  +k+      +++ +n  d r k++ ++  +l+ +l +++  +  ++f+DE+  +
  EPA04837.1  36 KPLLLVGPPGIGKTTIAYITAKQFG---YDMVGLNASDVRSKSRINE--ILTPVLGNVSLLGIPMIFIDEVDGI 104
                 789**************99998888...99*******9999765544..6777777654468899*****9876 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 5.7
      AAA_14  31 esilyinldderdkkla 47 
                 +si+  nld+++++kl 
  EPA04837.1 253 SSIITSNLDNQTLAKLL 269
                 56677777776665543 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   5.7e-05     0.051       1      22 [.      37      58 ..      37      75 .. 0.85
   2 ?   -0.6   0.0       1.3   1.2e+03      78     101 ..     261     281 ..     258     322 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.7e-05
                EEEEE--SSSSHHHHHHHGGGG CS
       AAA_5  1 dvlLvGppGtgKselaerlaaa 22
                ++lLvGppG+gK+++a   a+ 
  EPA04837.1 37 PLLLVGPPGIGKTTIAYITAKQ 58
                58*************9776665 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.3
                 -HHHHHHHHHHHHSSEEE..-SSS CS
       AAA_5  78 esevlnsLlslleerrllleegge 101
                 + ++l++Ll++++e  +l    g+
  EPA04837.1 261 DNQTLAKLLTIISEADML---YGK 281
                 578899999999999888...444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.1   0.00038      0.34       4      25 ..      34      55 ..      31      89 .. 0.80
   2 ?    1.4   0.0       0.4   3.6e+02      90     129 ..      89     131 ..      61     139 .. 0.67
   3 ?    0.0   0.0         1   9.4e+02      80     115 ..     254     294 ..     163     317 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00038
      AAA_22  4 tagilvvtGesGtGKTtllrrl 25
                + + l+++G++G+GKTt +   
  EPA04837.1 34 GTKPLLLVGPPGIGKTTIAYIT 55
                567799***********98655 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.4
      AAA_22  90 av..ielliiDEaqhlr.s..eealeeLrsllnlsrkgvqliLvG 129
                 +   i+++ iDE++ +  +      e L ++l+  +  v+++L+ 
  EPA04837.1  89 SLlgIPMIFIDEVDGIHgRgdYGGAEALIDILK--EPTVPIVLAA 131
                 3356799*******9955255666666666677..7777777765 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 1
      AAA_22  80 ealeqalrarav.ielliiDEaqhlr....seealeeLrsl 115
                 + ++ +l+++   + l ii Ea+ l     + ++++ Lr l
  EPA04837.1 254 SIITSNLDNQTLaKLLTIISEADMLYgkimRTQNWRLLRYL 294
                 44555555555566788888888886644435555555444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   2.4e-05     0.022      20      51 ..      32      62 ..      15      93 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.4e-05
      AAA_16 20 rsgrpelvllsGesGvGKsslvrellralekd 51
                ++g+   +ll+G++G+GK++++   ++++  d
  EPA04837.1 32 KKGT-KPLLLVGPPGIGKTTIAYITAKQFGYD 62
                5555.7899***********997766666666 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.5e-05     0.023      27      82 ..      29      81 ..      17      88 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.5e-05
       AAA_7 27 elllknkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdii 82
                ++  k  kp+llvGp G GKt+i+  + k++    y ++ +n s   s +++ +i+
  EPA04837.1 29 TKWKKGTKPLLLVGPPGIGKTTIAYITAKQFG---YDMVGLNASDVRSKSRINEIL 81
                55567889***************998888877...777777777777777777776 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   4.2e-05     0.038       6      84 ..      38     109 ..      35     121 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.2e-05
                 EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTSEEEEETGGG----.- CS
       AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegGivllDEidKihpk.e 84 
                 +ll+gp g+Gkt +a  +a+         ++ ++as++      ++ +++ +    g+v+     ++++DE+d ih + +
  EPA04837.1  38 LLLVGPPGIGKTTIAYITAKQFGY----DMVGLNASDVRS----KSRINEILTPVLGNVSLLGIPMIFIDEVDGIHGRgD 109
                 5899****************9997....9***********....*****9999999999999889***********9543 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   6.1e-05     0.054       3      35 ..      39      73 ..      38      85 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.1e-05
      AAA_33  3 llvGlpGsGKstlaerllkklg..avllssdtlrr 35
                llvG+pG GK+t a   +k+ g  +v l+  ++r+
  EPA04837.1 39 LLVGPPGIGKTTIAYITAKQFGydMVGLNASDVRS 73
                79****************99997777777776665 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   7.9e-05      0.07       3      43 ..      39      76 ..      37      81 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.9e-05
                EEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE----- CS
    NTPase_1  3 fiTGppGvGKtTlvkkvlellkssgvkvgGfyteevreggr 43
                ++ GppG+GKtT+    +++    g+ + G+ +++vr++ r
  EPA04837.1 39 LLVGPPGIGKTTIAYITAKQF---GYDMVGLNASDVRSKSR 76
                688**********99999998...************98865 PP

>> RFC1  Replication factor RFC1 C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       8.8   7.9e+03     134     149 ..     133     148 ..     119     150 .. 0.70
   2 ?   13.5   0.1   6.6e-05     0.059       1      23 [.     272     294 ..     272     325 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 8.8
                 XXXXXXXXXXXXXXXX CS
        RFC1 134 kkkedplkkidtkvKa 149
                 ++++d++k+i++ vK+
  EPA04837.1 133 SDESDKMKSIKKVVKT 148
                 5666777777777776 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 6.6e-05
                 HHHHHHHHHHHTTSS-GGGHHHH CS
        RFC1   1 isdgDlvdkkirseqnWsLlpth 23 
                 is++D+++ ki ++qnW Ll++ 
  EPA04837.1 272 ISEADMLYGKIMRTQNWRLLRYL 294
                 9*******************985 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00013      0.12      20      40 ..      33      53 ..      11      61 .. 0.83
   2 ?   -3.0   0.0       4.4   3.9e+03      98     116 ..      84     102 ..      79     106 .. 0.83
   3 ?   -2.3   0.0       2.7   2.4e+03     177     193 ..     306     323 ..     302     326 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00013
  Mg_chelatase 20 aGgHnlllvGppGsGKtmlak 40
                   G+  lllvGppG GKt +a 
    EPA04837.1 33 KGTKPLLLVGPPGIGKTTIAY 53
                  58889*************995 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.4
  Mg_chelatase  98 kpGeislahnGvLfLDElp 116
                     G++sl    ++f+DE+ 
    EPA04837.1  84 VLGNVSLLGIPMIFIDEVD 102
                   569999999999*****85 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2.7
  Mg_chelatase 177 eierY.lsklsgplldRi 193
                   e+ rY + +ls pll+Ri
    EPA04837.1 306 ERIRYsQYNLSWPLLNRI 323
                   445552458********9 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0    0.0036       3.2      35      52 ..      35      52 ..      21      63 .. 0.80
   2 ?    1.2   0.0      0.24   2.1e+02      98     142 ..      71     116 ..      57     140 .. 0.75
   3 ?    0.3   0.0      0.44   3.9e+02      69      93 ..     233     258 ..     222     297 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0036
        TniB 35 mpnlllvGdsnnGKtmiv 52
                ++ lllvG++ +GKt+i+
  EPA04837.1 35 TKPLLLVGPPGIGKTTIA 52
                4579************96 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.24
        TniB  98 lkararvskleqqvlrllrelkvrvLiiDEihnll.agsarkqref 142
                 ++++ r++++   vl   + l++ ++ iDE++ +  +g +   +++
  EPA04837.1  71 VRSKSRINEILTPVLGNVSLLGIPMIFIDEVDGIHgRGDYGGAEAL 116
                 566677777777888888889999*******988623444444444 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.44
        TniB  69 kvpvlv.vqappkpdekrlyaaiLea 93 
                  + vl+ +q+ pk + +++y++i+++
  EPA04837.1 233 ARSVLYsMQIDPKLKIDAFYSSIITS 258
                 3445443899999999*****99975 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00022       0.2       2      37 ..      39      77 ..      38      84 .. 0.88
   2 ?   -1.8   0.0       4.9   4.4e+03      58      58 ..     295     295 ..     213     356 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00022
      AAA_18  2 lltGtpGvGKttlakeLskrlgf...gvnlrdvakengl 37
                ll G+pG GKtt+a   +k  g+   g n +dv +++++
  EPA04837.1 39 LLVGPPGIGKTTIAYITAKQFGYdmvGLNASDVRSKSRI 77
                689**************9999999999999999877665 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.9
      AAA_18  58 d 58 
                 +
  EPA04837.1 295 N 295
                 1 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00015      0.13       5      22 ..      38      55 ..      35      84 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00015
      AAA_24  5 iliyGpsgiGKTtlakel 22
                +l++Gp+giGKTt+a+  
  EPA04837.1 38 LLLVGPPGIGKTTIAYIT 55
                689**********99865 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00021      0.19       1      28 [.      41      70 ..      41      78 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00021
                EE-TTSSHHHHHHHHHHHHTEEEE..EHHH CS
      AAA_17  1 lGgPGsGKgtqceklvekygfthl..saGd 28
                +G+PG GK+t++   ++++g+ ++  +a+d
  EPA04837.1 41 VGPPGIGKTTIAYITAKQFGYDMVglNASD 70
                7***********999***999985336666 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00018      0.16      19      56 ..      38      73 ..      26      82 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00018
  Zeta_toxin 19 illgGqpGAGKselaellkdelerqgnvvrldpDdlRe 56
                +ll+G pG GK+++a  +++++  + ++v l++ d+R+
  EPA04837.1 38 LLLVGPPGIGKTTIAYITAKQF--GYDMVGLNASDVRS 73
                689******************9..9********99997 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00029      0.26      42      66 ..      30      54 ..      18      65 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00029
   IstB_IS21 42 sfiekkenivllGpsGvGKshlaia 66
                ++ +  + ++l+Gp+G+GK+ +a  
  EPA04837.1 30 KWKKGTKPLLLVGPPGIGKTTIAYI 54
                577778889***********99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 2309.47
//
Query:       EPA04838.1  [L=154]
Description: antioxidant, AhpC/TSA family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.9e-33  114.0   0.0    4.6e-33  113.8   0.0    1.1  1  AhpC-TSA    AhpC/TSA family
    2.9e-21   75.7   0.0    3.4e-21   75.5   0.0    1.0  1  Redoxin     Redoxin
  ------ inclusion threshold ------
      0.083   13.0   0.0       0.25   11.5   0.0    1.6  2  AhpC-TSA_2  AhpC/TSA antioxidant enzyme
       0.12   12.3   0.0       0.16   11.9   0.0    1.2  1  SCO1-SenC   SCO1/SenC


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.8   0.0     1e-36   4.6e-33       1     123 [.       5     133 ..       5     134 .. 0.98

  Alignments for each domain:
  == domain 1  score: 113.8 bits;  conditional E-value: 1e-36
                 TTSB----EEESTTCEEEECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHHH-H.SSEEEE-TTSHHHHHTT CS
    AhpC-TSA   1 vgdkapdfelknadgetvslsdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfiekeslnfpllsDeegkvakayg 99 
                 vgd ap+fel++ d +  +l+++kgk+++l f+ ++++p C++e++++++ ++e+ ++g++v+++s d p++ k+f++k++lnfpll+D ++k++++y+
  EPA04838.1   5 VGDIAPNFELPDIDLKMRTLNEFKGKKIILSFFVAASSPICENEMCNFRDSWKEISNLGAQVVAISNDGPFANKAFAQKHNLNFPLLADYNSKTIRDYD 103
                 79************************************************************************************************* PP

                 -EETT......TTECSCEEEEE-TTSBEEE CS
    AhpC-TSA 100 vlkee......kglalratfvidkegkiry 123
                 vl +       +++a r++f+i ++gki y
  EPA04838.1 104 VLMPHllhikdYNAAKRSVFIIMEDGKIGY 133
                 **999***********************88 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.5   0.0   7.5e-25   3.4e-21       2     145 ..       5     148 ..       4     150 .. 0.88

  Alignments for each domain:
  == domain 1  score: 75.5 bits;  conditional E-value: 7.5e-25
                 TTSBB---ECCEETTCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHH.HHHHHHHTT-TSEEEE-TTSHHHH CS
     Redoxin   2 agdkaPdftlplaatdgnsvslsefkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndaf.vkefwgkeglkfpvlsDgsaaftk 99 
                 +gd aP+f+lp+   d +  +l efkgkk+++ f+ +a +P C +e++ +++  +++++ g +vva++ ++ +f  k+f+ k++l+fp+l+D +++  +
  EPA04838.1   5 VGDIAPNFELPD--IDLKMRTLNEFKGKKIILSFFVAASSPICENEMCNFRDSWKEISNLGAQVVAIS-NDGPFaNKAFAQKHNLNFPLLADYNSKTIR 100
                 7999******99..**********************************999998888*******7764.4444469999999***************** PP

                 HTT-TTEEE.GGG...EEE-EEEEEEETTEEEEEEESSSCHTSTTSHHH CS
     Redoxin 100 alGlrleedaseg...lrtpryavidedgkvvylevepepeteesnaea 145
                 ++++ +           + +++++i edgk+ y+ v ++p + e+n+e+
  EPA04838.1 101 DYDVLMPHLLHIKdynAAKRSVFIIMEDGKIGYKWVSEDPLK-EPNYEE 148
                 ***8876555444998899999*************9999976.998887 PP

>> AhpC-TSA_2  AhpC/TSA antioxidant enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   5.6e-05      0.25       5      47 ..      55      98 ..      51     104 .. 0.88
   2 ?   -1.3   0.0      0.52   2.3e+03      96     111 ..     122     137 ..     110     139 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.6e-05
  AhpC-TSA_2  5 dkpeldaagvklvaigigdp.sakkFvkltgfpfelyvDpsakl 47
                + +e+++ g ++vai+ + p   k+F++  + +f+l++D + k 
  EPA04838.1 55 SWKEISNLGAQVVAISNDGPfANKAFAQKHNLNFPLLADYNSKT 98
                4589999*********999988*****************99886 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.52
  AhpC-TSA_2  96 tflfdkqgelvyehrd 111
                 +f++ ++g++ y++  
  EPA04838.1 122 VFIIMEDGKIGYKWVS 137
                 6888888999999976 PP

>> SCO1-SenC  SCO1/SenC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   3.5e-05      0.16       3      61 ..      11      69 ..       9      88 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.5e-05
   SCO1-SenC  3 pFelvdqdgeavteedlegkpslvffgFthCpdvCpttlanmaevldalgeeaekvqpl 61
                +Fel d d + +t ++++gk +++ f+ +    +C  ++ n ++  +++ + +++v ++
  EPA04838.1 11 NFELPDIDLKMRTLNEFKGKKIILSFFVAASSPICENEMCNFRDSWKEISNLGAQVVAI 69
                79999***************************************999999988777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1101.19
//
Query:       EPA04839.1  [L=254]
Description: putative succinate dehydrogenase iron-sulfur subunit [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.9e-31  106.3   0.0    1.7e-30  105.3   0.0    1.5  1  Fer2_3    2Fe-2S iron-sulfur cluster binding domain
    5.4e-12   46.0   4.6    7.1e-12   45.6   2.2    2.1  2  Fer4_8    4Fe-4S dicluster domain
    1.7e-10   40.8   2.5    1.7e-10   40.8   2.5    2.0  2  Fer4_10   4Fe-4S dicluster domain
    3.2e-09   37.2  13.0    2.1e-07   31.4   3.9    2.7  3  Fer4_7    4Fe-4S dicluster domain
    3.7e-09   37.0  12.4    2.1e-07   31.4   3.3    2.5  3  Fer4_17   4Fe-4S dicluster domain
    3.4e-08   33.5  12.1    2.9e-07   30.5   3.0    2.5  3  Fer4_9    4Fe-4S dicluster domain
    5.4e-07   30.5   2.5    5.4e-07   30.5   2.5    2.1  2  Fer4_16   4Fe-4S double cluster binding domain
      1e-05   25.7   4.5      0.029   14.6   0.2    2.7  3  Fer4_18   4Fe-4S dicluster domain
    3.8e-05   23.3   1.1    3.8e-05   23.3   1.1    3.0  3  Fer4      4Fe-4S binding domain
    0.00022   21.1   0.1    0.00022   21.1   0.1    1.8  2  Fer2      2Fe-2S iron-sulfur cluster binding domain
     0.0021   18.1   1.8     0.0021   18.1   1.8    2.9  3  Fer4_6    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.024   14.7   2.0      0.024   14.7   2.0    3.4  3  Fer4_2    4Fe-4S binding domain
      0.087   13.4   1.3      0.087   13.4   1.3    3.1  3  Fer4_4    4Fe-4S binding domain
       0.13   12.4  13.1      0.081   13.1   7.7    2.8  2  Fer4_21   4Fe-4S dicluster domain
       0.87   10.7  21.4       0.38   11.8   4.6    3.2  3  Fer4_3    4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Fer2_3  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.3   0.0   1.4e-33   1.7e-30       1     108 [.      22     126 ..      22     127 .. 0.95

  Alignments for each domain:
  == domain 1  score: 105.3 bits;  conditional E-value: 1.4e-33
      Fer2_3   1 tlkvkRfdprrdrgkqkvqeyeveaeeedtvldaLlkikeevdptlafrasCregiCGscavainGkptlaCtatikdlakqkseieleplpkfpvirD 99 
                 tl++ Rf+p++d+ ++k+ e+++ +e+ +tvl+a+l +k++ d+++a r+sCr++ CGsc++ inGkp+laC ++i++l+++   +++ep+++fp+irD
  EPA04839.1  22 TLRIARFNPEHDD-AKKFMEFTISYERWTTVLEAILDVKQHFDHSVAVRYSCRQATCGSCGMIINGKPRLACFTKISELNSNI--VTVEPMNNFPIIRD 117
                 699******7766.99999************************************************************9875..9************* PP

      Fer2_3 100 LvvDideml 108
                 L v  ++++
  EPA04839.1 118 LAVKFERLF 126
                 ***988765 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0         1   1.2e+03      49      57 ..      70      80 ..      25      83 .. 0.68
   2 !   45.6   2.2   5.9e-15   7.1e-12       2      65 .]     163     236 ..     162     236 .. 0.66

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 1
      Fer4_8 49 wsC..ttcgaC 57
                +sC   tcg+C
  EPA04839.1 70 YSCrqATCGSC 80
                55544566666 PP

  == domain 2  score: 45.6 bits;  conditional E-value: 5.9e-15
      Fer4_8   2 lekCieCgaCqsaCpvlrr...........tk.khlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvgi 65 
                 +++Ci+Cg+C+saCp++ +           ++ +   d+r++ +  +q+ +  ++ +++w+C+  g+C++vCp+g+
  EPA04839.1 163 FSNCIKCGLCNSACPTMATdssfvgpqalaQAyRYVADSRDKGK--DQRLKIIDDSHGIWRCHFAGSCSQVCPKGV 236
                 79************966663333333332222244444444433..35555555699****************986 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.4       1.8   2.2e+03       8      51 ..      76      80 ..      64      83 .. 0.59
   2 !   40.8   2.5   1.5e-13   1.7e-10       3      56 .]     160     233 ..     158     233 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.8
     Fer4_10  8 tCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaC 51
                t                                       cg+C
  EPA04839.1 76 T---------------------------------------CGSC 80
                3.......................................4444 PP

  == domain 2  score: 40.8 bits;  conditional E-value: 1.5e-13
     Fer4_10   3 vidddtCirCgkCvkaCPadl....................tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                 +i+ + Ci+Cg C++aCP+ +                    +++++k+++ ++  +++++++C++ g+C ++CP
  EPA04839.1 160 YIQFSNCIKCGLCNSACPTMAtdssfvgpqalaqayryvadSRDKGKDQRLKIIDDSHGIWRCHFAGSCSQVCP 233
                 578899*************88****************************************************9 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.72   8.6e+02      29      42 ..      68      81 ..      27      95 .. 0.72
   2 !   18.3   1.7   2.2e-06    0.0026      30      51 ..     158     179 ..     128     180 .. 0.77
   3 !   31.4   3.9   1.8e-10   2.1e-07       2      52 .]     166     236 ..     165     236 .. 0.61

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.72
      Fer4_7 29 ekveidpekClgCg 42
                 ++  ++ +C +Cg
  EPA04839.1 68 VRYSCRQATCGSCG 81
                44455555566665 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 2.2e-06
      Fer4_7  30 kveidpekClgCgaCvavCPtg 51 
                 + +i+ ++C+ Cg C ++CPt 
  EPA04839.1 158 EQYIQFSNCIKCGLCNSACPTM 179
                 4478899999999999999985 PP

  == domain 3  score: 31.4 bits;  conditional E-value: 1.8e-10
      Fer4_7   2 CigCgaCvaaCpvkaieldeeenek..............gt.ekv......eidpekClgCgaCvavCPtga 52 
                 Ci+Cg C +aCp+ a +   +  ++              g+ +         +  ++C + g+C +vCP+g+
  EPA04839.1 166 CIKCGLCNSACPTMATDSSFVGPQAlaqayryvadsrdkGKdQ-RlkiiddSHGIWRCHFAGSCSQVCPKGV 236
                 ***********98888866432222222222222222223322.1454554556789************996 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1       2.5     3e+03      48      53 ..      76      81 ..      65     113 .. 0.77
   2 !   18.1   1.7   2.5e-06     0.003      32      58 ..     152     178 ..     128     182 .. 0.79
   3 !   31.4   3.3   1.7e-10   2.1e-07       1      61 []     165     237 ..     165     237 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2.5
     Fer4_17 48 eCgeCe 53
                +Cg C 
  EPA04839.1 76 TCGSCG 81
                344443 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 2.5e-06
     Fer4_17  32 glleeaekeekaslCieCgeCerkCPq 58 
                 ++ ee e+  ++s+Ci+Cg+C+++CP 
  EPA04839.1 152 QSPEELEQYIQFSNCIKCGLCNSACPT 178
                 56778888899***************6 PP

  == domain 3  score: 31.4 bits;  conditional E-value: 1.7e-10
     Fer4_17   1 rCiqCgyClpeCpsyeaydn..epkkllraakl..........glleeaekeekaslCieCgeCerkCPqgld 61 
                 +Ci+Cg C  +Cp+++  ++   p+ l++a+++          ++l+ + +++ + +C+  g C+++CP+g+d
  EPA04839.1 165 NCIKCGLCNSACPTMATDSSfvGPQALAQAYRYvadsrdkgkdQRLKIIDDSHGIWRCHFAGSCSQVCPKGVD 237
                 6**************99777455888888887777766655433444455569*****************997 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1       0.4   4.8e+02      36      42 ..      72      80 ..      39      94 .. 0.72
   2 !   15.5   1.9   1.3e-05     0.015      33      49 ..     159     179 ..     140     181 .. 0.71
   3 !   30.5   3.0   2.5e-10   2.9e-07       1      49 [.     165     235 ..     165     236 .. 0.96

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.4
      Fer4_9 36 C..igCgaC 42
                C   +Cg+C
  EPA04839.1 72 CrqATCGSC 80
                332345555 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.3e-05
      Fer4_9  33 e....eaCigCgaCveaCpkg 49 
                 +    ++Ci+Cg C  aCp+ 
  EPA04839.1 159 QyiqfSNCIKCGLCNSACPTM 179
                 144446899999999999985 PP

  == domain 3  score: 30.5 bits;  conditional E-value: 2.5e-10
      Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase......................eaCigCgaCveaCpkg 49 
                 +C++Cg C +aCp++++  + ++  a  +a+++                      ++C++ g+C ++Cpkg
  EPA04839.1 165 NCIKCGLCNSACPTMATDSSFVGPQALAQAYRYvadsrdkgkdqrlkiiddshgiWRCHFAGSCSQVCPKG 235
                 6******************999999999999999***********************************98 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       3.4   4.1e+03      56      60 ..      76      80 ..      55      83 .. 0.69
   2 !   30.5   2.5   4.5e-10   5.4e-07       1      66 [.     165     234 ..     165     235 .. 0.66

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 3.4
     Fer4_16 56 gCdiC 60
                 C+ C
  EPA04839.1 76 TCGSC 80
                44444 PP

  == domain 2  score: 30.5 bits;  conditional E-value: 4.5e-10
     Fer4_16   1 rCgtCgkCaevCPtnaikekkekeiearecisy.....ntaekkdlaede.ekckkqeaitgCdiCqdvCPa 66 
                 +C++Cg C ++CPt a ++   ++  +   ++y     + ++ kd + ++    +  +++++ + C +vCP 
  EPA04839.1 165 NCIKCGLCNSACPTMATDSS--FVGPQALAQAYryvadSRDKGKDQRLKIiDDSHGIWRCHFAGSCSQVCPK 234
                 6***************9988..33333333333334444444444444441444567**************6 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       3.3   3.9e+03      82      91 ..      74      83 ..      45      91 .. 0.66
   2 !   14.6   0.2   2.4e-05     0.029      32      74 ..     137     179 ..     121     183 .. 0.81
   3 !   12.4   0.1   0.00011      0.14      54      83 ..     215     244 ..     181     246 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 3.3
     Fer4_18 82 qleciscllc 91
                q  c sc+  
  EPA04839.1 74 QATCGSCGMI 83
                4444444443 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 2.4e-05
     Fer4_18  32 krGekiagrkkekkalkekeerkekgagdcidcescvkvcPtg 74 
                  r ++ +++++++  ++ +e+++  + ++ci+c+ c + cPt 
  EPA04839.1 137 IRDDTEIETSAKEFLQSPEELEQYIQFSNCIKCGLCNSACPTM 179
                 56677777788888888899999999***************95 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 0.00011
     Fer4_18  54 kekgagdcidcescvkvcPtgidirkGlql 83 
                  ++g   c   +sc +vcP g+d   G+ql
  EPA04839.1 215 DSHGIWRCHFAGSCSQVCPKGVDPAMGIQL 244
                 355667899999*************99997 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   1.1         3   3.5e+03      11      14 ..      77      80 ..      76      82 .. 0.67
   2 !   23.3   1.1   3.2e-08   3.8e-05       3      22 ..     161     180 ..     160     181 .. 0.90
   3 !    6.9   0.8    0.0049       5.8      12      21 ..     226     235 ..     221     236 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3
                -THH CS
        Fer4 11 CGaC 14
                CG C
  EPA04839.1 77 CGSC 80
                7777 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 3.2e-08
                 EETTTSSS-THHHHHSTTTE CS
        Fer4   3 ideekCigCGaCvevCPvgA 22 
                 i  + Ci+CG+C ++CP+ A
  EPA04839.1 161 IQFSNCIKCGLCNSACPTMA 180
                 67899************977 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0049
                 THHHHHSTTT CS
        Fer4  12 GaCvevCPvg 21 
                 G C +vCP g
  EPA04839.1 226 GSCSQVCPKG 235
                 99******88 PP

>> Fer2  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.1   1.8e-07   0.00022      18      77 ..      54      96 ..      42      97 .. 0.84
   2 ?   -3.4   0.5         8   9.6e+03      40      44 ..     169     173 ..     162     193 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.8e-07
                BHHHHHHH.TTTTTSTTSSSSSSSSTTEEEEEESCECTTSSSSTHHHHHTTEEEEGGGSEE CS
        Fer2 18 tlldaaee.nggidipysCggggCgtClvevlegevqsdetelegeeldegklrlaCqtiv 77
                 +ld+ ++ ++ ++++ysC++++Cg+C   ++            g++      rlaC t++
  EPA04839.1 54 AILDVKQHfDHSVAVRYSCRQATCGSCGMIIN------------GKP------RLACFTKI 96
                48999999999*****************9888............676......78998875 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 8
                 SSTTE CS
        Fer2  40 CgtCl 44 
                 Cg C 
  EPA04839.1 169 CGLCN 173
                 88884 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   1.1       5.6   6.6e+03       8      15 ..      76      80 ..      69      82 .. 0.58
   2 !   18.1   1.8   1.7e-06    0.0021       7      23 ..     164     180 ..     161     181 .. 0.93
   3 ?    1.6   0.1      0.28   3.4e+02      14      22 ..     227     235 ..     225     237 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 5.6
      Fer4_6  8 kCigCgdC 15
                    Cg C
  EPA04839.1 76 T---CGSC 80
                3...5544 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 1.7e-06
      Fer4_6   7 dkCigCgdCvrvCPega 23 
                 ++Ci Cg C ++CP+ a
  EPA04839.1 164 SNCIKCGLCNSACPTMA 180
                 68************987 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.28
      Fer4_6  14 dCvrvCPeg 22 
                  C  vCP g
  EPA04839.1 227 SCSQVCPKG 235
                 6999***87 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.5      0.33     4e+02       9      16 ..      71      80 ..      64      83 .. 0.70
   2 ?   14.7   2.0     2e-05     0.024       9      22 .]     165     178 ..     159     178 .. 0.89
   3 ?    4.9   1.5     0.026        32      13      21 ..     222     233 ..     221     234 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.33
      Fer4_2  9 rCig..CgaC 16
                +C +  Cg+C
  EPA04839.1 71 SCRQatCGSC 80
                5665567777 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 2e-05
      Fer4_2   9 rCigCgaCvsaCPa 22 
                 +Ci Cg C saCP+
  EPA04839.1 165 NCIKCGLCNSACPT 178
                 7************7 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.026
      Fer4_2  13 C...gaCvsaCP 21 
                 C   g+C ++CP
  EPA04839.1 222 ChfaGSCSQVCP 233
                 65557******9 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   1.8       2.6   3.1e+03       6      10 ..      76      80 ..      70      81 .. 0.72
   2 ?   13.4   1.3   7.3e-05     0.087       2      16 ..     164     178 ..     163     190 .. 0.91
   3 ?   -0.4   0.9       1.9   2.2e+03       8      16 ..     226     234 ..     221     237 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 2.6
      Fer4_4  6 gCgsC 10
                 CgsC
  EPA04839.1 76 TCGSC 80
                79999 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 7.3e-05
      Fer4_4   2 erCigCgsCvaaCPq 16 
                 ++Ci Cg C +aCP+
  EPA04839.1 164 SNCIKCGLCNSACPT 178
                 58************5 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.9
      Fer4_4   8 gsCvaaCPq 16 
                 gsC  +CP 
  EPA04839.1 226 GSCSQVCPK 234
                 589999996 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.2       2.3   2.8e+03      39      45 ..      75      81 ..      53      94 .. 0.69
   2 ?   13.1   7.7   6.7e-05     0.081       3      52 ..     161     233 ..     159     238 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2.3
     Fer4_21 39 deCvGCn 45
                 +C  C 
  EPA04839.1 75 ATCGSCG 81
                3344443 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 6.7e-05
     Fer4_21   3 idedkCigCgkCliaCedtshqai..................eidaktvlkvved.....eCvGCnlCssvCP 52 
                 i+ ++Ci+Cg+C  aC++ +++                    ++ ++++lk+++d     +C     Cs+vCP
  EPA04839.1 161 IQFSNCIKCGLCNSACPTMATDSSfvgpqalaqayryvadsrDKGKDQRLKIIDDshgiwRCHFAGSCSQVCP 233
                 67789************99998765566666666666555443334455566655333335777777888888 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   1.3       6.4   7.6e+03       4       7 ..      77      80 ..      72      95 .. 0.59
   2 ?   11.8   4.6   0.00032      0.38       1      13 [.     166     178 ..     166     180 .. 0.93
   3 ?   10.4   1.2   0.00087         1       5      14 ..     226     235 ..     220     236 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 6.4
      Fer4_3  4 CgaC 7 
                Cg C
  EPA04839.1 77 CGSC 80
                5544 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00032
      Fer4_3   1 CtgCgaCvevCPv 13 
                 C+ Cg+C  +CP+
  EPA04839.1 166 CIKCGLCNSACPT 178
                 ************7 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00087
      Fer4_3   5 gaCvevCPvg 14 
                 g C +vCP+g
  EPA04839.1 226 GSCSQVCPKG 235
                 58******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       784  (0.043728); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 1910.95
//
Query:       EPA04840.1  [L=105]
Description: hypothetical protein BG20_I0533 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       804  (0.0448435); expected 358.6 (0.02)
Passed bias filter:                      185  (0.0103185); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 647.94
//
Query:       EPA04841.1  [L=269]
Description: inositol monophosphatase family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    7.3e-28   97.8   0.0    8.8e-28   97.6   0.0    1.0  1  Inositol_P  Inositol monophosphatase family
    0.00035   20.1   0.1     0.0006   19.4   0.1    1.3  1  FBPase      Fructose-1-6-bisphosphatase, N-terminal domain


Domain annotation for each model (and alignments):
>> Inositol_P  Inositol monophosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.6   0.0   9.8e-32   8.8e-28       4     265 ..       2     262 ..       1     268 [. 0.83

  Alignments for each domain:
  == domain 1  score: 97.6 bits;  conditional E-value: 9.8e-32
                 HHHHHHHHHHHHHHHHHHHHTTTSEEEESTTTCCHHHHHHHHHHHHHHHHHHHHHHHHSTTSEEEHHCHHHHCCCT.SSSSSEEEEEEEEETHHHHHHT CS
  Inositol_P   4 evtkaavelaakagevlreefsenelvieekskegeedlvtaadeaveelilealaekfpshkilgeetlakgekseltedgltwivDPiDGTknFvrg 102
                 ev+++  e+ ++++e +++ +++++++ + +      d+  ++d  +e+++l+ l+e   +  +lgee ++ +   +++++  ++i D iDG +n vrg
  EPA04841.1   2 EVIEILQEASRRIYENVKDLAGTDNAAGDFGR-GAGGDISRNIDIIAEKTVLDYLKEINFDCIVLGEECGRVEL--SKQSK-GFIIMDAIDGSANAVRG 96 
                 67888889999999999999997788887777.57899****************9999989999**99999888..45555.8**************** PP

                 -SG-EEEEEEEETTE...EEEEEEEETTTTEEECEETTTEEEETCEEEEECTTSEGGGTEEEEEESSSSSSHHHHCHHHHHHHCCCCCH.EEEBESSHH CS
  Inositol_P 103 ipqvaVsigllvegk...pvlGviaqPllgqlysaakgkGaflngeklplsrappiseallvtlfavssrkdtseasllekvesavsae.gvrsvgssa 197
                  p ++ s+++++e++   ++ Gvi +  +g +y+a+k +Gafln  ++++++++pi + + ++ +++ +++ +++      ++++  ++  +r +g+ a
  EPA04841.1  97 VPFFCSSLAFAKEDRlssITDGVITDLSNGDMYWASKDRGAFLNKSRIKVHDKEPIYKIIGIN-TSGATHELMNR------LHPIFEQHnHIRHFGANA 188
                 ************876222577*********************************999988766.44444444444......55555555456999**** PP

                 HHHHHHHHTSTSEEEEEC..EBHHHHHHHHHHHHHTTEEEEESSSC....SSST.TSSEEEEESCHHHHHHHHH CS
  Inositol_P 198 lklaavaeGkadaylefg.rekkWDhAAGeaileeaGGvvtdakge....grll.largiiaanqkelaellaa 265
                 l++a+ a+G +d++++ + ++   D+AAG +i++eaGG+++da+ +     + +    + iaa+++++ + +++
  EPA04841.1 189 LEMALFARGLLDIFIDLRdKIRVQDIAAGYVIVKEAGGILLDANLNlldaDLSYkTRISFIAASNQKILDDVVS 262
                 *****************999**************************9987555524457777775665555555 PP

>> FBPase  Fructose-1-6-bisphosphatase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   6.6e-08    0.0006      24     116 ..       3      92 ..       1      98 [. 0.80

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 6.6e-08
      FBPase  24 llsalklalkiisskvrk.aelvnllGlagaeNvtGdeqkklDvladeiliealkaseevkvlvSEEeeelivlerekegkyvvafDPlDGSSn 116
                 +++ l++a + i ++v+  a+  n  G  g +   Gd  +++D++a++++ + lk+ +  +++  EE   ++    +k++k  +++D +DGS+n
  EPA04841.1   3 VIEILQEASRRIYENVKDlAGTDNAAGDFG-RGAGGDISRNIDIIAEKTVLDYLKEINFDCIVLGEECGRVEL---SKQSKGFIIMDAIDGSAN 92 
                 567788888888888876355555555554.6789*********************98888888888776654...58888899********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1970.43
//
Query:       EPA04842.1  [L=160]
Description: hypothetical protein BG20_I0522 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.3e-06   25.8   0.6    7.5e-06   25.5   0.6    1.1  1  Lyase_1     Lyase
  ------ inclusion threshold ------
       0.12   12.2   0.0       0.24   11.2   0.0    1.5  1  SMP_C2CD2L  Synaptotagmin-like, mitochondrial and lipid-bindi


Domain annotation for each model (and alignments):
>> Lyase_1  Lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.6   8.4e-10   7.5e-06      28     149 ..      17     126 ..       3     139 .. 0.72

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 8.4e-10
                 HHCHHHHHHHHHHHTTSSTHHHHHHHHHHHHHHHCHCHHCGGHHHBSSSSSHHHHHHHHHHHHHHHHTTHSSGIIIIITTT--HHHHHHHHHHHHHHHH CS
     Lyase_1  28 dikalaalkkaaakanvdlkeeaaaiikaldevleegklddqfvlkviqegsgtavnmnlnevigellgekvepndkvhtgqSsnDqvpTalrlalkka 126
                 di +++a +  + +  ++ k+ +++i+ al+ + +    + +f   +  e+++  ++  + +  g      +   +k ht++S+nDqv++++r+ +++ 
  EPA04842.1  17 DIIGSQAHTLMLYENQIISKNDVKKILIALESLKN----E-KFDNSSGAEDIHELIESLVIKKAG------ITSGGKMHTARSRNDQVALDIRMKIRDD 104
                 55566666666666666666666667666666655....3.666678888888888885555555......899************************* PP

                 HHHTHHHHHHHHHHHHHHHHHHT CS
     Lyase_1 127 lsekLlpaleqLidalkekakef 149
                 + + + + l + i+al+  ak+ 
  EPA04842.1 105 I-NIICNCLLDTIEALVSLAKKS 126
                 *.668777777777777777654 PP

>> SMP_C2CD2L  Synaptotagmin-like, mitochondrial and lipid-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   2.7e-05      0.24      49      89 ..     104     144 ..      92     149 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.7e-05
  SMP_C2CD2L  49 ekvvscnvvgeklqFlvsvtqaspaaaspqtYqvklsplel 89 
                 + ++ cn+  ++++ lvs +++s+++ +   Y+ + s  +l
  EPA04842.1 104 DINIICNCLLDTIEALVSLAKKSSKNCNATLYSFTTSSSRL 144
                 56899****************************99987766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       841  (0.0469072); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1055.98
//
Query:       EPA04843.1  [L=309]
Description: branched-chain-amino-acid transaminase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.2e-45  153.8   0.0    7.4e-45  153.5   0.0    1.1  1  Aminotran_4  Amino-transferase class IV
  ------ inclusion threshold ------
      0.026   14.2   0.1      0.051   13.3   0.1    1.4  1  DUF22        Domain of unknown function DUF22


Domain annotation for each model (and alignments):
>> Aminotran_4  Amino-transferase class IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.5   0.0   8.2e-49   7.4e-45       2     222 ..      40     268 ..      39     269 .. 0.94

  Alignments for each domain:
  == domain 1  score: 153.5 bits;  conditional E-value: 8.2e-49
  Aminotran_4   2 lfEtmrvy.ngei...ffldeHleRLrksaellglelpfdeeelrkileelleannsen.grlrllvsrgggglg...aatsepsvavyvsalppgpe 91 
                  +fE++r+y ng+    f+ldeH++R+r+s +  +++l+f+ e +++++    ++n+ ++ +++r++++ g+ g++   ++++  +va+++ ++    +
   EPA04843.1  40 VFEGVRAYwNGKNlfiFRLDEHIKRFRRSGQFYNISLNFSDEIINNAIIGICKKNKIKKsCYIRPFYFIGDYGINlhlTEKAPTNVAIFIFPFGDLFN 137
                  9*****999666556599*****************************************9***********9988*8888888888888888888877 PP

  Aminotran_4  92 sekelplvtssdvrrdapsplpgaKtln.yldnvlarreakergadevllvdedgnvtEgstsNvfivkggelitPplssgiLpGitrrallelakal 188
                       ++++ s+++ + +s+ p+aK    yl+++ a +eak++g+de++l+d +gnv+E+   N+fiv+ ++litPplss+ L+Gitr+a++++a +l
   EPA04843.1 138 KNGI-TAGVVSWRKFSDMSTPPQAKMGGnYLNSIIATQEAKRNGFDEAILLDHSGNVSEAPGENIFIVREDKLITPPLSSSALNGITRDAIIKIACDL 234
                  7777.9999999*************8877*****************************************************************9999 PP

  Aminotran_4 189 gleveereitlkdleeadeafltntlrgvlpvrs 222
                   + v+e+ei   +l   de+flt+t+++++p+ s
   EPA04843.1 235 DIDVIETEIARSELMISDEIFLTGTAAEITPIIS 268
                  *******************************965 PP

>> DUF22  Domain of unknown function DUF22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   5.7e-06     0.051      11      56 ..     242     287 ..     234     307 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.7e-06
       DUF22  11 eivrekvevepfgytrstvakwelliAdedvevkkGevkkikikei 56 
                 ei r++  ++   + + t a++ ++i+ + +++ +G++ +i  k +
  EPA04843.1 242 EIARSELMISDEIFLTGTAAEITPIISMDGKKIANGKPGEITMKLM 287
                 89999999*********************************98865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2341.92
//
Query:       EPA04844.1  [L=114]
Description: hypothetical protein BG20_I0519 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-07   31.5   3.0    1.8e-07   31.2   3.0    1.2  1  Sdh_cyt         Succinate dehydrogenase/Fumarate reductase tr
  ------ inclusion threshold ------
       0.11   12.6   3.9       0.15   12.2   3.9    1.3  1  Fumarate_red_D  Fumarate reductase subunit D
       0.28   11.7   2.2       0.83   10.2   0.2    2.1  2  DUF4179         Domain of unknown function (DUF4179)


Domain annotation for each model (and alignments):
>> Sdh_cyt  Succinate dehydrogenase/Fumarate reductase transmembrane subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   3.0   3.1e-11   1.8e-07      28     120 ..      12      97 ..       3     108 .. 0.72

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 3.1e-11
     Sdh_cyt  28 itGvallvglllllvwlllalslsspesfarvvallas.piklilllllllallyHllnGiRhllwDlglglelesarksalavlalavalvlv 120
                  t++a +  l+ +++ + l+  ++++  ++ v+a ++  p   +l+++l+l+ + H++nG+R++l+ l      +++rk  +av  + v++ ++
  EPA04844.1  12 GTALAAVA-LVAVHILMRLTQGFAESLQYESVIANYKFlPYAGMLEIILILLSI-HGFNGLRVILLEL------KQGRKYEKAVSYGCVVAMIA 97 
                 45555555.666666666677789999*********998888899888888777.***********87......55555554444444444443 PP

>> Fumarate_red_D  Fumarate reductase subunit D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   3.9   2.5e-05      0.15      22     109 ..      14      99 ..       7     109 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.5e-05
  Fumarate_red_D  22 AlvlpvlililglllplGlldsdalsyekvlafaqswigklvllvviilplwhalhrihhglhdlkihvkkaaklifYglAallsvva 109
                     Al + +l+ +  +l+ l    +++l+ye+v+a  +    + +l +++il+  h+++ ++ +l +lk  +k  +k++ Yg+ +++ +++
      EPA04844.1  14 ALAAVALVAV-HILMRLTQGFAESLQYESVIANYKFLPYAGMLEIILILLSIHGFNGLRVILLELKQGRK-YEKAVSYGCVVAMIALI 99 
                     4544455544.5666666655679******************************************9999.9*******987765554 PP

>> DUF4179  Domain of unknown function (DUF4179)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.2   0.00014      0.83       5      40 ..       9      45 ..       3      54 .. 0.69
   2 ?    1.2   0.1     0.087   5.2e+02       8      25 ..      88     105 ..      78     112 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00014
                XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...--SS- CS
     DUF4179  5 rikkvaaaaaalvllllssrllspalAsal.n.pvigs 40
                +++ +a+aa+alv++  + + l+  +A+ l   +vi +
  EPA04844.1  9 IHYGTALAAVALVAV-HILMRLTQGFAESLqYeSVIAN 45
                344455555555555.9999*******99953344444 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.087
                 XXXXXXXXXXXXXXXXXX CS
     DUF4179   8 kvaaaaaalvllllssrl 25 
                 ++  ++a+++l++++sr+
  EPA04844.1  88 SYGCVVAMIALIAYGSRT 105
                 344455555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 852.20
//
Query:       EPA04845.1  [L=495]
Description: putative acetyl-CoA carboxylase, biotin carboxylase subunit [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.3e-69  231.9   0.0    7.9e-69  231.4   0.0    1.3  1  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
    1.8e-45  154.0   0.1    3.3e-45  153.1   0.1    1.5  1  Biotin_carb_N    Biotin carboxylase, N-terminal domain
    1.8e-33  114.8   0.0      4e-33  113.7   0.0    1.6  1  Biotin_carb_C    Biotin carboxylase C-terminal domain
    2.9e-10   40.0   0.1    5.7e-10   39.0   0.1    1.4  1  ATP-grasp        ATP-grasp domain
    6.2e-08   32.4   0.2    1.5e-07   31.2   0.2    1.5  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    1.2e-06   28.3   0.0    6.4e-06   25.9   0.0    2.0  1  RimK             RimK-like ATP-grasp domain
    1.9e-06   28.0   0.0    4.5e-06   26.8   0.0    1.7  1  ATP-grasp_3      ATP-grasp domain
    1.2e-05   24.9   0.1    4.6e-05   23.1   0.1    1.9  2  ATP-grasp_4      ATP-grasp domain
  ------ inclusion threshold ------
      0.026   14.3   0.0      0.083   12.7   0.0    1.8  2  KRTDAP           Keratinocyte differentiation-associated
      0.058   13.1   0.0       0.55   10.0   0.0    2.2  2  ATPgrasp_Ter     ATP-grasp in the biosynthetic pathway with T
       0.11   12.3   0.4        0.4   10.4   0.0    2.1  3  GARS_A           Phosphoribosylglycinamide synthetase, ATP-gr
       0.15   12.0   0.0       0.32   10.9   0.0    1.5  1  LpxI_N           LpxI N-terminal domain


Domain annotation for each model (and alignments):
>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  231.4   0.0   5.3e-72   7.9e-69       1     209 [.     115     322 ..     115     324 .. 0.99

  Alignments for each domain:
  == domain 1  score: 231.4 bits;  conditional E-value: 5.3e-72
                  SHHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHHSTS-EEEEE--SSSEEEEEE CS
  CPSase_L_D2   1 DkesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaafgnkqvlvekslkgpkeiEve 98 
                  Dk + k+a+ k++vp+vp+s++ v+++eeal+ia++i+yPv++k+ fg+GG+G r+++n++el+e +++ ++e+ +a g++ + vek+l++ ++iE++
   EPA04845.1 115 DKMQCKAAMLKAKVPTVPGSPGLVKDVEEALKIANDISYPVLLKSVFGGGGRGIRLVNNDKELREGFETVTSESISAVGKSAIIVEKFLQKTRHIEYQ 212
                  999*********************************************************************************************** PP

                  EEEETTS-EEEEEEEEECCECTCCCCEEEES-SS--HHHHHHHHHHHHHHHHHHT-EEEEEEEEEEETTTTEEEEEEEESS--CCHHHHHHHHS--HH CS
  CPSase_L_D2  99 vlrDakgnvitvcerenslqlrtqkvievAPsqtLtdeerqalreaavkvvrevgvvgagtveflldpkskeyyviEvNtRlsvesalaekaTGldlv 196
                  + rD++gn+++++ere+s+q+r+qk+ie  Ps+++++++r++++e  vk+ ++v++++ gt efl    ++e+y+iE+N+Rl+ve++++e + Gld v
   EPA04845.1 213 MARDKHGNAVHIFERECSIQRRNQKLIEQTPSPVVDQKTRDRIGELVVKASEAVDYTNLGTAEFLRAD-NGEFYFIEINARLQVEHPISELVSGLDFV 309
                  ****************************************************************9886.***************************** PP

                  HHHHHHHTT--GC CS
  CPSase_L_D2 197 keaakialgekLe 209
                  k ++ ia+ge+L+
   EPA04845.1 310 KLQLDIANGEPLP 322
                  ***********97 PP

>> Biotin_carb_N  Biotin carboxylase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.1   0.1   2.2e-48   3.3e-45       1     110 []       1     110 [.       1     110 [. 0.99

  Alignments for each domain:
  == domain 1  score: 153.1 bits;  conditional E-value: 2.2e-48
                    ---EEEE---HHHHHHHHHHHHHTT-EEEEEEEGGGTTSHHHHHSSEEEEEESSTTCCGGG-HHHHHHHHHHTT-SEEE--SSTTTT-HHHHHHHH CS
  Biotin_carb_N   1 kikkvlianrGeiAvriiravrelgietvavyseedanslhvreadeavelgpasasesYlniekivkaakesgadavhpGyGflsEnaefaeave 96 
                    +i+kvlianrGeiA+r+i++++ lgi+tvavys+ed nslhv++a ea+++g+a++++sYln eki++++ +sgada+hpGyGflsEn++fa+++e
     EPA04845.1   1 MIEKVLIANRGEIALRVIKTCKALGIKTVAVYSDEDYNSLHVKQATEAYHIGEAAPAKSYLNQEKILETILSSGADAIHPGYGFLSENSDFASKCE 96 
                    799********************************************************************************************* PP

                    HTT-EESSS-HHHH CS
  Biotin_carb_N  97 eagivfiGPsaeal 110
                    +++i+fiGPsa+++
     EPA04845.1  97 KNKINFIGPSAASM 110
                    **********9987 PP

>> Biotin_carb_C  Biotin carboxylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.7   0.0   2.7e-36     4e-33       1     107 [.     336     442 ..     336     443 .. 0.99

  Alignments for each domain:
  == domain 1  score: 113.7 bits;  conditional E-value: 2.7e-36
                    EEEEESEETTTTTEE--CE-SEEE---STTEEEEE---TT-EE-TTS-SEEEEEEEEESSHHHHHHHHHHHHHT-EEESS-BSHHHHHHHHH-HHH CS
  Biotin_carb_C   1 eaRinaEdpeknflpssGkvtelelpegpgvRvdsgveegsevspyyDsllaKlivhgetreealarlrraLaelrieGvktnieflrailedeef 96 
                    e+RinaEd   +f+ps+G v  +++p+gp+vR+d+ ++ g +vsp+yDsl+aKl+++g+t ee  +r+ +aL+++ i+Gv+t i+++++il+++e+
     EPA04845.1 336 ECRINAEDTFLDFAPSTGPVPDVTIPSGPSVRCDTYLYPGCTVSPFYDSLMAKLCTWGQTFEESRTRMLNALNDFYIQGVETSIPLYKTILNTDEY 431
                    8*********************************************************************************************** PP

                    HHT---TTTCC CS
  Biotin_carb_C  97 akgeldtkfle 107
                    ++g+l+t+fl+
     EPA04845.1 432 KSGSLSTDFLN 442
                    *********97 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   0.1   3.8e-13   5.7e-10      13     159 ..     137     292 ..     125     294 .. 0.91

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 3.8e-13
                 EECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC........GTTCEEEEE----SEEEEEEEEEETTC-.EEE--EEEEEEET CS
   ATP-grasp  13 aveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal........keekvivEefvpfekElsvlvvrsaeGe.tafypvvetvqed 102
                 +v++ ee+ ++a+++ +pv++K ++ g  G+G  +v+++++l++ +e++        ++  +ivE+f + ++ +   ++r+++G+ +++++    +q++
  EPA04845.1 137 LVKDVEEALKIANDISYPVLLK-SVFGGGGRGIRLVNNDKELREGFETVtsesisavGKSAIIVEKFLQKTRHIEYQMARDKHGNaVHIFERECSIQRR 234
                 578999999*************.889999****************99999999*99999*************************978899999999998 PP

                 TEEEEEEECEE-.SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEETTCTEEEEEEESS CS
   ATP-grasp 103 gilrlsvapaev.sekaqkkaeeiakkiveeLggvGvfavElFvledgellvnElapR 159
                 +   +   p++v ++k   ++ e++ k+ e++++  + + E+   ++ge ++ E+  R
  EPA04845.1 235 NQKLIEQTPSPVvDQKTRDRIGELVVKASEAVDYTNLGTAEFLRADNGEFYFIEINAR 292
                 88877777877615668899*****************************999999887 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.2   9.7e-11   1.5e-07      28     174 ..     144     291 ..     136     292 .. 0.83

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 9.7e-11
                      HHHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHTT......-SCEEEEE--.ESEEEEEEEEETSSCEEEEEEEEE-SSSSS-HH CS
  Dala_Dala_lig_C  28 lekveeelgypvfVKpareGSSvGvskveseeelkeaieeafky......dekvlvEeai.egreievavlgneklevsevgeivvkkgfydye 114
                        k+ + ++ypv+ K++  G   G+  v++ +el+e +e+  +        + ++vE+++ ++r ie  +  + + ++ ++ e+    ++ + +
       EPA04845.1 144 ALKIANDISYPVLLKSVFGGGGRGIRLVNNDKELREGFETVTSEsisavgKSAIIVEKFLqKTRHIEYQMARDKHGNAVHIFEREC--SIQRRN 235
                      5689999****************************998876654122222578*******99**********88888887777665..455667 PP

                      HHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEEEEES CS
  Dala_Dala_lig_C 115 akysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDfflteegeivlnEvNt 174
                      +k ++     +    ++++++++i el++ka +a+d + l+   f+  ++ge+++ E+N 
       EPA04845.1 236 QKLIE----QTPSPVVDQKTRDRIGELVVKASEAVDYTNLGTAEFLRADNGEFYFIEINA 291
                      77763....333345789999**************************************6 PP

>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   4.3e-09   6.4e-06       3     171 ..     115     297 ..     113     310 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 4.3e-09
                 -HHHHHHHHHHTT---..--EEEESS-S-HHHHHHTT-.-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHH.GGG--........EEEEE--SS-SEEE CS
        RimK   3 dKlkslklLakakikv..pntalardeedaekliekiklrfPvvvKsvegsqGikvvlakkeqklkqvlea.lkeai........lvqeyieeaenedi 90 
                 dK+++ + ++kak+++      l++d e+a k+ + i  + Pv++Ksv+g  G ++ l ++ ++l++ +e+ + e+i        +v ++++++    i
  EPA04845.1 115 DKMQCKAAMLKAKVPTvpGSPGLVKDVEEALKIANDI--SYPVLLKSVFGGGGRGIRLVNNDKELREGFETvTSESIsavgksaiIVEKFLQKTR--HI 209
                 99****9999999875214568*************99..7**************************999987444555555555599***98765..55 PP

                 EEEEETTEEEEEEEEE--SSS-.---TTTT-EEEE----HHHH....HHHHHHHHHCT-SEEEEE.EEEETTE.EEEEEEESS--SHH CS
        RimK  91 RvlvvddevvaalrrvskeGdF.RsnlhrGgvaeklqlseeek....elAikaakamelvvaGvD.llrakrg.llvlEvnsspglek 171
                    +  d+   a++   +e    R n ++  ++    ++++ +    el +ka++a++   +G    lra++g ++++E+n+  ++e+
  EPA04845.1 210 EYQMARDKHGNAVHIFERECSIqRRNQKLIEQTPSPVVDQKTRdrigELVVKASEAVDYTNLGTAeFLRADNGeFYFIEINARLQVEH 297
                 6666778877888887777765388888888777776766654334489**************9889999886379******999875 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.0     3e-09   4.5e-06       1     159 [.     113     294 ..     113     296 .. 0.80

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 3e-09
                  HTSHHHHHHHHTTT.S-.--............-EESS--SSSEEEEESS-------B--SS--TTE...................EEEE---.SEEEE CS
  ATP-grasp_3   1 asdKlktykkLkeagvk.vP........tkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve............lvqefie.GkplS 76 
                  + dK+++  ++ +a+v+ vP         +   + ++   +++ +K + G+gg ++r+v++++e+ + +e+v+            +v +f++  +++ 
   EPA04845.1 113 CGDKMQCKAAMLKAKVPtVPgspglvkdVEEALKIANDISYPVLLKSVFGGGGRGIRLVNNDKELREGFETVTsesisavgksaiIVEKFLQkTRHIE 210
                  789999999888885552459888875433344556666*****************************999888899999999999999996367888 PP

                  EEEEE.SSSEEEEEEEEEEEET....TEEEEEEES----H.HHHHHHHHHHHHTTSTT--EEEEEEEEESS..SEEEEEEESS-- CS
  ATP-grasp_3  77 vsllsdgekvlvlavnrqliekaekefvyaGnvtpietel.keevvelaeevvekleglaGyvGvDlvlkd.eepyviEvNPRlt 159
                   ++  d++ + v  + r+   +++++       +p+  ++ ++++ el+ ++ e++ +   +   +++ +d +e y+iE+N+Rl+
   EPA04845.1 211 YQMARDKHGNAVHIFERECSIQRRNQKLIEQTPSPVVDQKtRDRIGELVVKASEAV-DYTNLGTAEFLRADnGEFYFIEINARLQ 294
                  88888888888888888877766666666666666666555889999999999999.888788889**999899*********97 PP

>> ATP-grasp_4  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.1   3.1e-08   4.6e-05       1     151 [.     151     292 ..     151     297 .. 0.86
   2 ?   -1.9   0.0       1.5   2.2e+03      35      71 ..     386     422 ..     381     428 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 3.1e-08
  ATP-grasp_4   1 islPvviKPsvgffSlGVykinneeewkaavaaieeeleqakeeykeevveeesflvEeyieGe.EfavdayfdeeGepvilnilkkefaseedvsdr 97 
                  is+Pv +K + g + +G++ +nn++e+++ ++++ +e          ++v ++ ++vE++++ +  +   +  d++G++v  +i+++e + ++  ++ 
   EPA04845.1 151 ISYPVLLKSVFGGGGRGIRLVNNDKELREGFETVTSE--------SISAVGKSAIIVEKFLQKTrHIEYQMARDKHGNAV--HIFERECSIQRRNQKL 238
                  689*******************************987........3445788999******8652556677778888875..89************** PP

  ATP-grasp_4  98 lyvtsakviee.tlealeellkevnallglknfpvHiElrvsedgkiipiEvnpl 151
                  +  t++ v+ + t +++ el+ ++++++  +n  + +E+   ++g+ + iE+n++
   EPA04845.1 239 IEQTPSPVVDQkTRDRIGELVVKASEAVDYTNLGT-AEFLRADNGEFYFIEINAR 292
                  *9999888765167889*************99987.78888889*********95 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.5
  ATP-grasp_4  35 eeeleqakeeykeevveeesflvEeyieGeEfavday 71 
                   ++l ++ ++++e+     ++l   yi+G E ++ +y
   EPA04845.1 386 MAKLCTWGQTFEESRTRMLNALNDFYIQGVETSIPLY 422
                  55666788888888888888999999***99999887 PP

>> KRTDAP  Keratinocyte differentiation-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       7.5   1.1e+04      14      33 ..      48      67 ..      43      72 .. 0.62
   2 ?   12.7   0.0   5.6e-05     0.083      23      55 ..     422     454 ..     402     456 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 7.5
      KRTDAP 14 nyaagsealkeqfLnvdrlr 33
                 y  g  a  + +Ln +++ 
  EPA04845.1 48 AYHIGEAAPAKSYLNQEKIL 67
                56666666667777776654 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 5.6e-05
      KRTDAP  23 keqfLnvdrlrsafkseeflnWhalfealkkkl 55 
                  + +Ln d ++s+  s +fln + +++ lk+ l
  EPA04845.1 422 YKTILNTDEYKSGSLSTDFLNRYKIIDRLKEDL 454
                 4679**************************988 PP

>> ATPgrasp_Ter  ATP-grasp in the biosynthetic pathway with Ter operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00037      0.55      53     120 ..     259     327 ..     218     337 .. 0.72
   2 ?    0.6   0.0       0.3   4.5e+02      26      60 ..     442     476 ..     411     483 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00037
  ATPgrasp_Ter  53 aerlaeefgldglvnvQv.rededgpkLLEiNpRasGGlgysal.aGvnlpylalklllgleteeveepe 120
                   + +  e++  + l    + r d+++ + +EiN+R +    +s l +G+++++l l+ + g e+   ++++
    EPA04845.1 259 VVKASEAVDYTNLGTAEFlRADNGEFYFIEINARLQVEHPISELvSGLDFVKLQLDIANG-EPLPFKQKD 327
                   5555555555555444431777777**************9996527*************9.555554544 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.3
  ATPgrasp_Ter  26 evlaavpRrKekgglqelekdeelielaerlaeef 60 
                   + + ++ R Ke+ + +++ek+++++ +a    e f
    EPA04845.1 442 NRYKIIDRLKEDLKKEKIEKSDAALAAAIIYSEYF 476
                   4577899****99999******9999987666665 PP

>> GARS_A  Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.5   2.2e+03      41      80 ..      16      55 ..       6      66 .. 0.82
   2 ?   10.4   0.0   0.00026       0.4       2      90 ..     115     204 ..     114     219 .. 0.91
   3 ?   -3.2   0.0       3.9   5.8e+03     136     188 ..     245     292 ..     242     293 .. 0.53

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.5
                EEEEESC-GGGT-EEEESSHHHHHHHHHHHCTS-TTCCCC CS
      GARS_A 41 lVvKadglaagKgvivakseeealkavkeilekkkfGeag 80
                 V+K     + K v v ++e+    +vk+  e  + Gea 
  EPA04845.1 16 RVIKTCKALGIKTVAVYSDEDYNSLHVKQATEAYHIGEAA 55
                5888877777899999999999999999999888888875 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00026
                 BHHHHHHHHHHTT--B-..-EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEESSHHHHHHHHHHHCTS-TTCCCCSSEEEEE--- CS
      GARS_A   2 sKsfakdllkkagipta..eyeaftdpeeakeyieeatakalVvKadglaagKgvivakseeealkavkeilekkkfGeagekvviEelle 90 
                 +K   k+ + ka++pt   +   ++d+eea ++ ++ + ++  +K++   +g+g+ ++++ +e  +  + + ++      ++ +++E++l+
  EPA04845.1 115 DKMQCKAAMLKAKVPTVpgSPGLVKDVEEALKIANDISYPV-LLKSVFGGGGRGIRLVNNDKELREGFETVTSESISAVGKSAIIVEKFLQ 204
                 788889999999**9985566789*****************.9****99***********************9999999999*******97 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 3.9
                 TTS-HHHHHHHHHHTHHHHHHHHHCTT---EEEEEEEEEEETTE.EEEEEEESS CS
      GARS_A 136 pvvteellekikeeileptveglkkegipfkGvLyaglmlvedg.pkvlefnvR 188
                 pvv +++ ++i e +++      ++e ++++ +  a+++  ++g  + +e+n+R
  EPA04845.1 245 PVVDQKTRDRIGELVVK------ASEAVDYTNLGTAEFLRADNGeFYFIEINAR 292
                 55555555555554443......2344555555566666666665566666666 PP

>> LpxI_N  LpxI N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00021      0.32       4      71 ..       6      71 ..       4      74 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00021
      LpxI_N  4 liAGsGrlPllvaeaakaagrevvvvalegeadeelekivdevaevsvgqlgklikaLkregvtevvm 71
                liA +G+++l v++ +ka g+++v+v   +  +    k  ++++ +++g+   + ++L +e++ e ++
  EPA04845.1  6 LIANRGEIALRVIKTCKALGIKTVAVYSDEDYNSLHVK--QATEAYHIGEAAPAKSYLNQEKILETIL 71
                9***********************99999877766666..6778999999999999**9999988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (495 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.68u 0.30s 00:00:00.98 Elapsed: 00:00:00.50
# Mc/sec: 2951.27
//
Query:       EPA04846.1  [L=281]
Description: oxidoreductase NAD-binding domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.2e-14   52.6   0.0      1e-13   51.9   0.0    1.4  1  NAD_binding_1    Oxidoreductase NAD-binding domain
    9.5e-08   32.3   0.0    1.6e-07   31.6   0.0    1.4  1  FAD_binding_6    Oxidoreductase FAD-binding domain
  ------ inclusion threshold ------
      0.045   13.9   0.1       0.16   12.1   0.1    1.9  2  NAD_binding_6    Ferric reductase NAD binding domain
      0.048   12.9   0.0      0.063   12.5   0.0    1.1  1  Methyltransf_34  Putative SAM-dependent methyltransferase


Domain annotation for each model (and alignments):
>> NAD_binding_1  Oxidoreductase NAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.9   0.0   2.3e-17     1e-13       2     106 ..     127     251 ..     126     254 .. 0.85

  Alignments for each domain:
  == domain 1  score: 51.9 bits;  conditional E-value: 2.3e-17
                    EEEGGGGHHHHHHHHHHHHHCTTCSEEEEEEEESSGCGSTTHHHHHHHHHHCTT......EEEEEEEESSCTT....TSSSEESSHHHHHHHHHHH CS
  NAD_binding_1   2 iagGtGiaPvrsvlraileeakdktkvvlvyGnrteedllyreeleelakklpg......rlkvvavvsreea....gweggkgrvqdalleells 87 
                    i+gGtG+aP++s+ +++ +   dk+++++++G+ + ++l y+e l el+++ +       ++++ a+ sr+++    +w+g+ grv++ l+    +
     EPA04846.1 127 IGGGTGLAPFVSFAQHLHAT-GDKREIIVLHGASYVDELSYKELLTELENESKArgkdqwNFTYRAAISRPQEwfnrSWAGQVGRVETFLRPRDNG 221
                    89*****************8.99*************************998887777877788888877776433339********9988765554 PP

                    ...........HSSTTEEEEEECSHHHHHH CS
  NAD_binding_1  88 ...........lkkeethvyvCGppgMika 106
                               ++ke+t++yvCG +g i++
     EPA04846.1 222 mspleeligdkITKENTMFYVCGWQGTIDG 251
                    668999999**99**********8876665 PP

>> FAD_binding_6  Oxidoreductase FAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0   3.6e-11   1.6e-07       3      96 ..       8     106 ..       6     108 .. 0.84

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 3.6e-11
                    EEEEEEECCTTEEEEEEEESTTTS-----TT-EEEEEEC..ET.TCCEEEEEE.BSSTTECCEEEEEEE--...TT-HHHHHHHCS-TT-EEEEEE CS
  FAD_binding_6   3 kltekeevsedtrifrfklpsekqklglpvGqhvflrlk..ik.geaviRsYtpissenekGelellvkvy...pgGkmsqaLdelkigdtleikG 92 
                    ++t ++ + ed+ i+r+ +p++  + ++ +Gq++ l l+  ++ g+ v R+Y+++s+++++ ++el+++ +     G+++  L ++k gd +    
     EPA04846.1   8 TITYVQLLKEDLVIIRL-VPKDGPVPDYQAGQFITLGLPnpVEgGKIVRRAYSIASHPENRKYIELVIRWVrkpLPGRLTTQLFNAKEGDEILWLK 102
                    56667777888888888.455777889***********988663677889*********************88778**************998888 PP

                    EE-S CS
  FAD_binding_6  93 PlGk 96 
                    P+G+
     EPA04846.1 103 PTGR 106
                    8886 PP

>> NAD_binding_6  Ferric reductase NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   3.5e-05      0.16       4      28 ..     124     148 ..     121     189 .. 0.81
   2 ?   -0.9   0.0      0.36   1.6e+03     131     146 ..     232     247 ..     175     254 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.5e-05
                    xxxxxxxxxxxxxxxxxxxxxxxxx RF
  NAD_binding_6   4 vllvagGiGitpfisilkdllkksk 28 
                    ++ ++gG+G++pf+s++++l ++ +
     EPA04846.1 124 IICIGGGTGLAPFVSFAQHLHATGD 148
                    678*****************99987 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.36
                    xxxxxxxxxxxxxxxx RF
  NAD_binding_6 131 khknssvgvfvCGppk 146
                    k  ++++ ++vCG ++
     EPA04846.1 232 KITKENTMFYVCGWQG 247
                    4567888999999876 PP

>> Methyltransf_34  Putative SAM-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.4e-05     0.063      86     147 ..     118     179 ..      83     198 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.4e-05
  Methyltransf_34  86 eekklkvlciGGGag.aElvalaallrekeeekessssslsltlvDiadWssvvkkLekaits 147
                      e+++ +++ciGGG g a +v++a  l+ +  +k++       + vD   +++++++Le++ + 
       EPA04846.1 118 EKDNRRIICIGGGTGlAPFVSFAQHLHAT-GDKREIIVLHGASYVDELSYKELLTELENESKA 179
                      446789********878999999999944.444444445557899999999999999987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 2224.40
//
Query:       EPA04847.1  [L=279]
Description: oxidoreductase NAD-binding domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.8e-11   42.6   0.0    1.6e-10   41.6   0.0    1.5  1  NAD_binding_1    Oxidoreductase NAD-binding domain
    2.8e-08   34.0   0.0    4.5e-08   33.4   0.0    1.3  1  FAD_binding_6    Oxidoreductase FAD-binding domain
  ------ inclusion threshold ------
      0.017   14.4   0.0      0.021   14.1   0.0    1.1  1  Methyltransf_34  Putative SAM-dependent methyltransferase
      0.043   13.9   0.2       0.14   12.2   0.0    1.9  2  NAD_binding_6    Ferric reductase NAD binding domain
       0.19   12.0   0.0       0.29   11.4   0.0    1.3  1  FAD_binding_9    Siderophore-interacting FAD-binding domain


Domain annotation for each model (and alignments):
>> NAD_binding_1  Oxidoreductase NAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   0.0   4.3e-14   1.6e-10       2     104 ..     125     247 ..     124     251 .. 0.86

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 4.3e-14
                    EEEGGGGHHHHHHHHHHHHHCTTCSEEEEEEEESSGCGSTTHHHHHHHHHHCTT......EEEEEEEESSCT....TTSSSEESSHHHHHHHHHHH CS
  NAD_binding_1   2 iagGtGiaPvrsvlraileeakdktkvvlvyGnrteedllyreeleelakklpg......rlkvvavvsree....agweggkgrvqdalleells 87 
                    ++gGtG+aP+ ++ +++ +   dk+++++++G+ + ++l y+e l +l+++  +      ++k+ a+ sr++    ++w+g  grv+  +  +  +
     EPA04847.1 125 VGGGTGLAPFIAFAKHLHDT-GDKREIIVLHGASYVDELSYKELLTNLENESIErgkdqwNFKYRAAISRPKeffnRSWAGHVGRVESFFKPNKNG 219
                    79***************998.99*************************987655566778899999966665222279*********999887777 PP

                    ...........HSSTTEEEEEECSHHHH CS
  NAD_binding_1  88 ...........lkkeethvyvCGppgMi 104
                               ++ ++t vy+CG +g i
     EPA04847.1 220 vspleemvgeeITTANTKVYICGYQGTI 247
                    889999*****99**********88766 PP

>> FAD_binding_6  Oxidoreductase FAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.0   1.2e-11   4.5e-08      26      96 ..      29     104 ..       6     106 .. 0.82

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 1.2e-11
                    S-----TT-EEEEEEC..ETTCCEEEEEE.BSSTTECCEEEEEEE--...TT-HHHHHHHCS-TT-EEEEEEEE-S CS
  FAD_binding_6  26 qklglpvGqhvflrlk..ikgeaviRsYtpissenekGelellvkvy...pgGkmsqaLdelkigdtleikGPlGk 96 
                       ++ +Gq++ + l+   +++ v R+Y+++s+++++ ++e++++ +     G+++  L  +++gd + +  P+G+
     EPA04847.1  29 GMPKYTTGQFLTIGLPipSEQKIVRRAYSIASHPENRDYFEFVIRWVrkpLPGRVTTELFYANVGDEVYLGDPTGN 104
                    444899**********5455677889*********************88778*****************9999997 PP

>> Methyltransf_34  Putative SAM-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   5.8e-06     0.021      79     145 ..     111     175 ..      48     201 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.8e-06
  Methyltransf_34  79 ekeeeekeekklkvlciGGGag.aElvalaallrekeeekessssslsltlvDiadWssvvkkLekai 145
                      +    + + ++ +++c+GGG g a ++a+a  l+++  +k++       + vD   +++++++Le++ 
       EPA04847.1 111 KLP--NGQPDNRRIVCVGGGTGlAPFIAFAKHLHDT-GDKREIIVLHGASYVDELSYKELLTNLENES 175
                      333..23346789********9899********954.4444444455578999999999999998754 PP

>> NAD_binding_6  Ferric reductase NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0     4e-05      0.14       4      28 ..     122     146 ..     119     177 .. 0.88
   2 ?   -1.0   0.0      0.47   1.7e+03     132     146 ..     231     245 ..     165     253 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4e-05
                    xxxxxxxxxxxxxxxxxxxxxxxxx RF
  NAD_binding_6   4 vllvagGiGitpfisilkdllkksk 28 
                    ++ v+gG+G++pfi ++k+l  + +
     EPA04847.1 122 IVCVGGGTGLAPFIAFAKHLHDTGD 146
                    899*****************98877 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.47
                    xxxxxxxxxxxxxxx RF
  NAD_binding_6 132 hknssvgvfvCGppk 146
                      ++++ v++CG ++
     EPA04847.1 231 ITTANTKVYICGYQG 245
                    355677788888776 PP

>> FAD_binding_9  Siderophore-interacting FAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0     8e-05      0.29      62     120 ..      44     104 ..       8     105 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8e-05
  FAD_binding_9  62 elpederpvmRtYtvraldaeae..eldidfvlHgdegpaarwAaqAqpGdelaivgPgga 120
                     +p++++ v R Y++++  ++++  e+ i  v    +g +++    A++Gde+ + +P g+
     EPA04847.1  44 PIPSEQKIVRRAYSIASHPENRDyfEFVIRWVRKPLPGRVTTELFYANVGDEVYLGDPTGN 104
                    4799***********9998888899999******************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2120.45
//
Query:       EPA04848.1  [L=515]
Description: carboxyl transferase domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   4.5e-184  612.7   0.0   5.1e-184  612.5   0.0    1.0  1  Carboxyl_trans  Carboxyl transferase domain
    8.4e-07   28.7   0.0    1.6e-06   27.8   0.0    1.5  1  MdcE            Malonate decarboxylase gamma subunit (MdcE)


Domain annotation for each model (and alignments):
>> Carboxyl_trans  Carboxyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  612.5   0.0  5.7e-188  5.1e-184       2     494 .]      28     513 ..      27     513 .. 0.99

  Alignments for each domain:
  == domain 1  score: 612.5 bits;  conditional E-value: 5.7e-188
                     SCTTCEEEEEEEEHTTSGGGEBEHHHHHHHHHHHHHHH.HHT..EEEEEEEESBETTEEHHHHTTEEEEESSTTSGGGCEEECHHHHHHHHHTEE CS
  Carboxyl_trans   2 ehprGkltareridllldpgsFgeledlffhrvtelgr.kkklprdgvvtgsGaviGravevvaqdktvlggslgpakgekllkaqeeaikagep 95 
                     +h++Gkltareridllld+g F+e++ l+ h  +e+ + kkk+ +dgvv g+G+v+Gr+ +v+a d+tvlgg+l+++ ++k++k ++ aik+g+p
      EPA04848.1  28 QHDKGKLTARERIDLLLDSGTFTEIDPLVTHHYYEYDMqKKKFFTDGVVGGYGTVNGRQIFVFAYDFTVLGGTLSQMGAKKITKLMDHAIKTGCP 122
                     9*************************************999****************************************************** PP

                     EEEEEEE-ESSSGHHSSHHHHHHHHHHHHHHHHHHHCS-EEEEESSEEETHHHHHHHHTSEEEEETTEEEEESSTHHHHHHHHSSCC-SSCHHHH CS
  Carboxyl_trans  96 ligindsgGaegriqegveslrgsGkifgenskasgeIpqislvtgrcaGggaYlpalgdrvimveetskifltGpdvikkvlgreevtseelgG 190
                     +igi dsgGa  riqeg+ sl+g+++if+ n++asg+Ipqi+  +g++aGg +Y+pa++d+vimv++ +++f+tGpdv+k+vlg ee++ ++lgG
      EPA04848.1 123 IIGIMDSGGA--RIQEGIMSLDGFADIFYHNQLASGVIPQITASIGPSAGGSVYSPAMTDFVIMVDKVGTMFVTGPDVVKTVLG-EEISFDDLGG 214
                     **********..************************************************************************.********** PP

                     SHHHHTTTTSSSEEESSHHHHHHHHHHHHTTS-SSTTSGGSS----ECSSGSSSH.....HCS-CTTTS---HHHHHHCEECTTC-EEESTTSST CS
  Carboxyl_trans 191 atqhmtksGvahltaeddeealelirkllsylPkkasnnresaPivetadepdrd...lieivPdnakkpyDvreviarlvdegeFlEikegyAk 282
                     a++h  ksGvah++a+++ e+++ i+kl+s+lP   +nn+e++P+++t d+p+r    li+i+Pdn+ +pyD++e+i  +vd+ eF+E++e +A+
      EPA04848.1 215 AMTHGIKSGVAHFVAKNEYECMDYIKKLISFLP---QNNTEEPPKIKTDDDPNRLdhnLINIIPDNPLQPYDMKEIISSVVDNHEFFEVHELFAP 306
                     *********************************...99999************9888888*********************************** PP

                     TEEEEEEEETTEEEEEEEE--SEEETTEE-HHHHHHHHHHHHHHHHTT--EEEEE-BSEE--SHHHHHTTHHHHHHHHHHHHHT--S-EEEEE-T CS
  Carboxyl_trans 283 tvVvGfArlgGipvGvvAnetrveaGqvlfidsavKaarfirlcdaenlPlviladvrGflvGqrqeyggilkhGaklvdalaeakvPkitvilr 377
                     +vVvGf+rl+G+ vG+vAn++ + aG  l+ids+ Kaarfir+cd +n+ +++l+d++G+++G++qe++gi++hG+kl++a+ ea+vP it++++
      EPA04848.1 307 NVVVGFGRLNGKVVGIVANQPLHLAG-ALDIDSSNKAARFIRFCDSFNIAIITLVDTPGYMPGSNQEHNGIIRHGSKLLYAYCEATVPRITLVIG 400
                     **************************.******************************************************************** PP

                     EEEHHHHHTTTGGGSTTTTEEETTT-EEESS-HHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSHHHHHHTT CS
  Carboxyl_trans 378 kayGGayvvmdskingadlvaawptariaVlgpegaveilfrkekaaaemerkdlaaerkkklkeyeeellnpyvaaargfaDavidpsetrakl 472
                     kayGGay++m+sk+++ d+++awptar aVlg+e av+i++rke+  ++    d ++ +k+ + e+ e++ npyvaa+ g +D+vidp+etr  l
      EPA04848.1 401 KAYGGAYIAMGSKNLRTDVNYAWPTARCAVLGAEAAVKIMYRKELSSSK----DAESLKKQLISEFAEKFENPYVAASHGTVDNVIDPAETRPML 491
                     ********************************************99998....88999************************************* PP

                     SSSEEEHGGGHHHHHHHHHHHH CS
  Carboxyl_trans 473 vialelewkkarklparkrrni 494
                     ++ale++++k++k  +rk++ni
      EPA04848.1 492 IKALEMLANKREKQLPRKHGNI 513
                     ********************97 PP

>> MdcE  Malonate decarboxylase gamma subunit (MdcE)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0   1.8e-10   1.6e-06      64     186 ..     353     483 ..     301     511 .. 0.73

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 1.8e-10
                 --EEEEEEEE--B--SHHHHHHTHHHHHHHHHHHHHHHHHHT--EEEEEEEEEEHHHHHHTT...TT-SEEEEEET-EEESS-HHHHHHHHT-....-H CS
        MdcE  64 krpilvlvDvasQrlgrrdEllGihealahlakalarArlaGhpvigllvGkavsGaflahg...lqanrlialpgvqvavmdkasaArvTkr....sv 155
                 + +i+ lvD+++   g  +E  Gi    + l  a+  A +   p i+l++Gka  Ga++a+g   l +++  a p +  av++  +a ++  r    s 
  EPA04848.1 353 NIAIITLVDTPGYMPGSNQEHNGIIRHGSKLLYAYCEATV---PRITLVIGKAYGGAYIAMGsknLRTDVNYAWPTARCAVLGAEAAVKIMYRkelsSS 448
                 569*********************************9986...99***************98666789999******************9866222222 PP

                 HHHHH.HGGCSGGG--SHHH...HHTTT--SEEEE CS
        MdcE 156 eaLea.laksipvfAydvdn...yarlGlleelld 186
                  + e  + + i+ fA   +n    a+ G++ +++d
  EPA04848.1 449 KDAESlKKQLISEFAEKFENpyvAASHGTVDNVID 483
                 22222022335666666666433345666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (515 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.53
# Mc/sec: 2928.91
//
Query:       EPA04849.1  [L=76]
Description: hypothetical protein BG20_I0503 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
        1.1    9.7   9.8        1.4    9.4   9.8    1.1  1  DUF4212     Domain of unknown function (DUF4212)


Domain annotation for each model (and alignments):
>> DUF4212  Domain of unknown function (DUF4212)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   9.8   7.5e-05       1.4      13      72 ..       7      65 ..       2      69 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 7.5e-05
     DUF4212 13 lilLviWfvvsfglgillaeelntirtflgf.plgFwfaaqgsilvfvvlifvYalrmdrl 72
                  ++v+W+++ +g g +l+  +  ++ + g+  + F++a+    +++++l+++++l  ++l
  EPA04849.1  7 GFVFVMWMLIIIG-GGFLVMIIGPLS-ISGYgEFDFFLASIIKAIIAIILVIIWILILSKL 65
                5689*********.667776666664.5555389*******************99988877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1281  (0.0714485); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.33s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 462.59
//
Query:       EPA04850.1  [L=402]
Description: transporter, major facilitator family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.5e-34  119.5  28.0    1.5e-34  119.5  28.0    1.5  1  MFS_1       Major Facilitator Superfamily
    4.6e-32  111.5  30.8    5.9e-20   71.6  11.1    2.0  2  Sugar_tr    Sugar (and other) transporter
    2.4e-10   39.6  17.4    3.7e-10   38.9  17.4    1.3  1  MFS_2       MFS/sugar transport protein
    0.00048   18.8   5.2    0.00095   17.8   0.6    2.3  2  FPN1        Ferroportin1 (FPN1)
     0.0013   17.8   7.9     0.0094   14.9   1.4    2.6  2  MFS_5       Sugar-tranasporters, 12 TM
     0.0039   16.1   4.6     0.0039   16.1   4.6    2.8  3  MFS_1_like  MFS_1 like family


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.5  28.0   5.1e-38   1.5e-34      34     352 ..      21     355 ..       3     356 .. 0.75

  Alignments for each domain:
  == domain 1  score: 119.5 bits;  conditional E-value: 5.1e-38
       MFS_1  34 igllltl.yalgaavaslplGrl....sdrfGrrrvlllglllfalglllll.....fa...sslw.lllvlrvlqGlgagalfpagaaliadwfpkee 118
                 ++ll+t+  ++ ++++ +++G++    +d++Gr++ +++++++f+ + ++++     +    +  + ll+ lr++qG++ag+ + +ga+++ + +pke+
  EPA04850.1  21 FSLLATFaAYIITLIMRPFGGAFfgnfGDKHGRKKAMMITIIGFSGA-TFATgllptWQmvgIMAPiLLIGLRFMQGFFAGGEWGSGAVITMETVPKEK 118
                 455444434445555555555554444********777777777777.33333223321335556667******************************* PP

       MFS_1 119 rgraigllsagfslGailgpllggllasslg........Wravfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvl 209
                 rg   g+l++gf++G++++ ++   ++s ++        Wr +f+   i +l+a+    + ++ +++e + k+++++  +t+++pl++++++   ++ +
  EPA04850.1 119 RGILSGFLQSGFNFGFVIASVVFFGVVSIFSekefieigWRIMFFTGIIPGLVALF---VRFRMNESEVWLKKQIQR--KTEKSPLKKLLSSKDGRKKF 212
                 *******************8888888889999*********************944...555566666666666666..55777777766666666666 PP

       MFS_1 210 willialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlv 308
                  + li + + + ++++   + p++lq    +    +++ll+ ++   ++++++++g+ls+r+grr+++ ++ ++++++a+  ++      +v   + + 
  EPA04850.1 213 IFSLILMTGLMYAYYTSIGFYPTFLQNYVEIE-KSQVSLLMIVGTTTSLFGQIFTGYLSQRIGRRKTIAFFAIAAIALAIPTFYGLYNAQSVYERATYT 310
                 32333333334477779999999*********.8999999************************99999999999888888888888844444444333 PP

       MFS_1 309 liGf.glgfvfpsllalasdlappeeagtasglfntagslggalg 352
                 +i +  + + f+++ a++s+ +p+e + +asgl+   g + g+ +
  EPA04850.1 311 IILIfVATTGFGPIPAFLSERFPTEVRNSASGLIYNGGLIFGSWA 355
                 333314444488*********************987776666655 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.6  11.1     2e-23   5.9e-20      54     207 ..      32     195 ..      17     202 .. 0.86
   2 !   51.6   9.0   2.2e-17   6.5e-14     232     436 ..     191     388 ..     186     398 .. 0.81

  Alignments for each domain:
  == domain 1  score: 71.6 bits;  conditional E-value: 2e-23
                 THHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTT.....SS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHH CS
    Sugar_tr  54 iflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgk.....nsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlai 147
                 i+l+ + +G+ f+g +gd+ GRkk+++i+++ f+ +++ +++ +        +  +li  R+  G+++G++ +   + + E  pk++Rg+l ++ q++ 
  EPA04850.1  32 ITLIMRPFGGAFFGNFGDKHGRKKAMMITIIGFSGATFATGLLPTWqmvgiMAPILLIGLRFMQGFFAGGEWGSGAVITMETVPKEKRGILSGFLQSGF 130
                 6788999********************************999993345554444444444*************************************** PP

                 HHHHHHHHHHHHHH.HTSS-....TTHHHHHHHCCHHHHHHHHHHGGGS---HHHHHHTT-HHHH CS
    Sugar_tr 148 tfGilvaaifglgl.nktsn....adgwrillglqlvpallllilllflPESPrylvekgkeeea 207
                  fG+++a+++ +g+ + +s+    + gwri+++  ++p l+ l++++ + ES  +l ++ +++  
  EPA04850.1 131 NFGFVIASVVFFGVvSIFSEkefiEIGWRIMFFTGIIPGLVALFVRFRMNESEVWLKKQIQRKTE 195
                 **************6666669***********************************665544433 PP

  == domain 2  score: 51.6 bits;  conditional E-value: 2.2e-17
                 HHHHH.....HTTHHHHSH...HHHHHHHHHHHHHHTTHHHHHHHTTTHHHHSS-THHHHHHHHHHHHHHHHHHHHH...HHHHHS-SHHHHHHHHHHH CS
    Sugar_tr 232 eaeqeeekaswkellssktvrqrlligvvlqifqqltGinaimyysptifenlglsksllvtiivgvvnfvatfvai...flvdrfGRRtllllGaagm 327
                 +++  +ek  +k+llssk+ r++++  + l+ +  + ++ +i +y++ + + + ++ks +v+++++v ++++ f  i   +l+ r+GRR++  + +a++
  EPA04850.1 191 QRK--TEKSPLKKLLSSKDGRKKFIFSLILMTGLMYAYYTSIGFYPTFLQNYVEIEKS-QVSLLMIVGTTTSLFGQIftgYLSQRIGRRKTIAF-FAIA 285
                 333..336799***********************************************.5554444444444444443459********99887.5556 PP

                 HHHHHHHH..HHHHTTSS...CHHHHHHHHHHHHHHHTTTTHHHHHHHHHHSHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHT-HHHHHHHHHH CS
    Sugar_tr 328 aicfvilgivalllvakskaasivaivfialfialfalgwgpvpwvlvsElfpqsvRskalaiavavnwlanflisllfpiiteaigggyvflvfagla 426
                 ai+++i +  ++ l +++++++ +  + i++f+a  ++g+gp+p++l sE fp++vR++a+ + ++   ++     l+  +++++ +  ++ ++ ++ +
  EPA04850.1 286 AIALAIPT--FYGLYNAQSVYERATYTIILIFVA--TTGFGPIPAFL-SERFPTEVRNSASGLIYNGGLIFGSWAPLIAVTMLSKGT-EWIPILLGMNV 378
                 66666665..555555557889998888888877..688*****888.*************************************99.99999999999 PP

                 HHHHHHHHHH CS
    Sugar_tr 427 vlfiifvfff 436
                 +++ i+++++
  EPA04850.1 379 IIGSIIILIG 388
                 9999998876 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9  17.4   1.2e-13   3.7e-10      38     332 ..      25     327 ..      18     336 .. 0.79

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 1.2e-13
       MFS_2  38 vllvarlvDaitDpivGtlidktstrwGrrrPwlllsaiilavsiillftppelsqsakfiwllvtyil...lrilytlfeipyvslvpvltkdydeRt 133
                 + ++a ++ +i+ p+ G++  +   + Gr +  +++  i ++ ++++  + p+++ +   i++ +++i+   ++ +++  e  +++ ++  t  ++ R 
  EPA04850.1  25 ATFAAYIITLIMRPFGGAFFGNFGDKHGRKK-AMMITIIGFSGATFATGLLPTWQMV--GIMAPILLIGlrfMQGFFAGGEWGSGAVITMETVPKEKRG 120
                 4589999************************.8999999998888888888888554..3445555555112455555566677777777778889*** PP

       MFS_2 134 sltsvrsflsvlggvlaailafllvlilgglkserkgylifaliialLmllgviivvlgtkervemrkkekteqkeklslleqlkevfrnraflillll 232
                  l+++ +   ++g v+a+++ f +v i+++ +  + g++i+ +++ +  l++ ++ +  + ++v   kk+ ++++ek +l + l +    ++f+  l+l
  EPA04850.1 121 ILSGFLQSGFNFGFVIASVVFFGVVSIFSEKEFIEIGWRIMFFTGIIPGLVALFVRFRMNESEVW-LKKQIQRKTEKSPLKKLLSSKDGRKKFIFSLIL 218
                 ******************************77788899988777766555555555555554444.577777777788887777777777788777777 PP

       MFS_2 233 fllaalalgvlnglllYyltyvlg.ngsaasvfllvvtisallgiplwqplakrlgkkntyllgalltivllvlvlll........qpsnlllflvllv 322
                     + a++   g +  +l+ +++ ++s++s++++v t+ +l g ++  +l +r+g+++t++++a+++i+l + ++          + + +++ l++++
  EPA04850.1 219 MTGLMYAYYTSIGFYPTFLQNYVEiEKSQVSLLMIVGTTTSLFGQIFTGYLSQRIGRRKTIAFFAIAAIALAIPTFYGlynaqsvyERATYTIILIFVA 317
                 76667777788888888****************************************************999887776788888876777777777777 PP

       MFS_2 323 iagfgvgvaa 332
                  +gfg + a+
  EPA04850.1 318 TTGFGPIPAF 327
                 7777755554 PP

>> FPN1  Ferroportin1 (FPN1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.3     0.014        41     324     367 ..     124     167 ..     105     174 .. 0.93
   2 !   17.8   0.6   3.2e-07   0.00095     242     371 ..     196     321 ..     178     327 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.014
        FPN1 324 gllrtGlislvaqlsclllavasvllpgspmskisvvlllagva 367
                 g l++G+ + ++ +s++   v+s++ +++ ++    +++++g++
  EPA04850.1 124 GFLQSGFNFGFVIASVVFFGVVSIFSEKEFIEIGWRIMFFTGII 167
                 8899************************99999999*****997 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 3.2e-07
        FPN1 242 krvaeavktvvagWkeYvrqpvflaslalslLyltVLsFdtlmtaylkse.glsasvisllrgvsavtgilgTfafpllekrigllrtGlislvaqlsc 339
                 k+  +++ ++++g k+++ + +++++l ++  y t ++F +++   l++   +++s++sll++v+ +t + g + +  l +rig  +t +++ +a +++
  EPA04850.1 196 KSPLKKLLSSKDGRKKFIFSLILMTGLMYA--YYTSIGFYPTF---LQNYvEIEKSQVSLLMIVGTTTSLFGQIFTGYLSQRIGRRKTIAFFAIAAIAL 289
                 444445556779999999999999999888..99*****9875...555548**********************************************9 PP

        FPN1 340 lllavasvllpgspmskisvvlllagvalsRl 371
                  +     ++  +s  +++   ++l+ va+  +
  EPA04850.1 290 AIPTFYGLYNAQSVYERATYTIILIFVATTGF 321
                 99999999999999888888888888887655 PP

>> MFS_5  Sugar-tranasporters, 12 TM
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.1    0.0014         4      86     115 ..      41      70 ..      27     103 .. 0.80
   2 !   14.9   1.4   3.1e-06    0.0094      40     119 ..     217     296 ..     200     305 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0014
       MFS_5  86 gtivgsladkfgrkracltyailyilacit 115
                 g++ g + dk+grk+a ++  i + +a  +
  EPA04850.1  41 GAFFGNFGDKHGRKKAMMITIIGFSGATFA 70 
                 789*******************99988754 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 3.1e-06
       MFS_5  40 llvyslavagdwlqgpyvyalyesygldkgdieilfiagfgssllfgtivgsladkfgrkracltyailyilacitkhsg 119
                 +l+  l+ a     g y  +l +   ++k ++  l+i g  +sl+   + g l+++ gr+++   +ai+ i   i   +g
  EPA04850.1 217 ILMTGLMYAYYTSIGFYPTFLQNYVEIEKSQVSLLMIVGTTTSLFGQIFTGYLSQRIGRRKTIAFFAIAAIALAIPTFYG 296
                 555555555555667777778888899**************998777889******************999888766665 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0     0.083   2.5e+02      42      80 ..      32      70 ..      26      81 .. 0.79
   2 ?    0.1   0.7     0.094   2.8e+02     311     360 ..      83     133 ..      55     153 .. 0.76
   3 !   16.1   4.6   1.3e-06    0.0039       4      79 ..     219     291 ..     216     330 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.083
  MFS_1_like 42 ilpltsilsppiwgvlaDrfgkrkkvvilslllsavlfl 80
                i  +++ ++  ++g+  D+ g++k+++i  + +s ++f+
  EPA04850.1 32 ITLIMRPFGGAFFGNFGDKHGRKKAMMITIIGFSGATFA 70
                555666677889*************99988888877776 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.094
  MFS_1_like 311 enawlvlpievLhgisfgllwaaaveyvskiapksleatgqglls.glyfg 360
                   + l++ + +++g+  g  w++++    + +pk+ ++ + g+l+ g+ fg
  EPA04850.1  83 MAPILLIGLRFMQGFFAGGEWGSGAVITMETVPKEKRGILSGFLQsGFNFG 133
                 467778888999999999999999999999999999999999775156666 PP

  == domain 3  score: 16.1 bits;  conditional E-value: 1.3e-06
  MFS_1_like   4 lkilyFfffaalgsllPYltiylkskglkaseigiitlilpltsilsppiwgvlaDrfgkrkkvvilslllsavlf 79 
                 + +l + ++ ++g    +l+ y    +++ s++ +++ +   ts++++ ++g l+ r+g+rk+++ +++ + a++ 
  EPA04850.1 219 MTGLMYAYYTSIGFYPTFLQNY---VEIEKSQVSLLMIVGTTTSLFGQIFTGYLSQRIGRRKTIAFFAIAAIALAI 291
                 5666777888887655566666...6899************************************99988777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       886  (0.0494171); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.74u 0.35s 00:00:01.08 Elapsed: 00:00:00.52
# Mc/sec: 2339.85
//
Query:       EPA04851.1  [L=244]
Description: respiratory-chain NADH dehydrogenase, 49 kD subunit, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-38  132.5   0.0      2e-38  132.1   0.0    1.1  1  Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd s


Domain annotation for each model (and alignments):
>> Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.1   0.0   1.1e-42     2e-38       2     114 ..     132     244 .]     132     244 .] 0.99

  Alignments for each domain:
  == domain 1  score: 132.1 bits;  conditional E-value: 1.1e-42
                     TT-HHHHHHHHHHHHHHHHHHHHHHSSSSS-TTBESSBBSS---TTHHHHHHHHHHHHHHHHHHHHHHHHSSSSHHHHHSSSS-BSHHHHHHHTT CS
  Complex1_49kDa   2 lGaltvflyafreRekildlleevtGaRltasyiriGGvarDlpegllekikeflkelekkldeleklltknrifkkRtkgvgvlskeealelgl 96 
                     lG+ t+f++   +Re ++dl+e++tGaR+t++ + +GGv++Dlp+++ + + + ++++ek+++e+  ++ +n+i+++Rtk+ g+ls+++a++lg+
      EPA04851.1 132 LGHSTMFMWPAGDRELLIDLMEKMTGARVTHAHFVPGGVRNDLPPNFEDVCLRQVNYFEKRIKEYAAIFYDNPILIARTKDTGILSRQDAIRLGT 226
                     69********************************************************************************************* PP

                     -SSSSGGGT-TTTHHHHS CS
  Complex1_49kDa  97 tGpvlRasGvkyDlRkae 114
                     tG vlRasGv+yDlRk+e
      EPA04851.1 227 TGSVLRASGVDYDLRKKE 244
                     ****************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 1424.49
//
Query:       EPA04852.1  [L=170]
Description: NADH-quinone oxidoreductase, B subunit [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.2e-25   87.3   0.1      1e-24   86.9   0.1    1.2  1  Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit


Domain annotation for each model (and alignments):
>> Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.9   0.1   5.6e-29     1e-24       3     129 ..      47     155 ..      46     157 .. 0.84

  Alignments for each domain:
  == domain 1  score: 86.9 bits;  conditional E-value: 5.6e-29
                  HHHHHHT-TTTTHHHHHHTEEEEEETTT-S--HHHHHHTHTTTSEEEEEESBE...EEEHHHHHHHHGGGSSEEEEESHHHHH-TGGGSTT-TEE-HH CS
  Oxidored_q6   3 GcsisllaleedlldllelielryhetlladskeeeieakekeadvlvveGavtrkpkealellkelaekakaviavGtCAafGGipaaannpsvgee 100
                  +cs+++ a++++ +d+     +r+++  +++ +      + +++d++vv+G++trk++++l+l++++++++k+via+G+CA++GG++   ++++ +  
   EPA04852.1  47 CCSVEFGAASSPRYDV-----ERFGI--IEAFG------SLRQCDLIVVQGTITRKMAPRLRLVYDQMPEPKYVIAMGACAITGGLY--FDSYN-V-- 126
                  4999998888889999.....77754..33333......1239********************************************..44233.3.. PP

                  HHHHHC.S-E.EEE-SSS--HHHHHHHHH CS
  Oxidored_q6 101 vgellevvpvdinipGCPphpeailetll 129
                    ++++v+pvd+++pGCPp+pe+++++ +
   EPA04852.1 127 LPGIDGVLPVDVYVPGCPPRPETLIQGCM 155
                  459*********************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       223  (0.0124379); expected 358.6 (0.02)
Passed bias filter:                      208  (0.0116013); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.30u 0.22s 00:00:00.52 Elapsed: 00:00:00.35
# Mc/sec: 1468.32
//
Query:       EPA04853.1  [L=168]
Description: transcriptional regulator, PadR family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-11   42.6   0.1    7.9e-11   41.8   0.1    1.5  1  PadR      Transcriptional regulator PadR-like family
    1.5e-05   24.9   0.5    0.00021   21.2   0.1    2.4  2  HTH_45    Winged helix-turn-helix
    0.00088   19.9   0.2      0.025   15.2   0.0    2.3  2  RTP       Replication terminator protein
  ------ inclusion threshold ------
      0.014   15.5   0.4       0.12   12.5   0.1    2.4  3  Mrr_N     Mrr N-terminal domain


Domain annotation for each model (and alignments):
>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   0.1   1.8e-14   7.9e-11       1      71 [.      22      84 ..      22      88 .. 0.92

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 1.8e-14
                HHHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCH CS
        PadR  1 iLalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrr 71
                iL+ll+ +   G eii++ +e s+g++++s+G +Yp+L rL +egl+e+ ++ +        Y+lT++G +
  EPA04853.1 22 ILELLKTKAYTGKEIIDHAAEQSNGVWKPSPGLIYPLLGRLLDEGLIEEAKDGK--------YQLTKKGIE 84
                8************************************************98875........888888865 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.1   4.8e-08   0.00021      40      75 ..      59      95 ..      54      97 .. 0.89
   2 ?    1.6   0.1      0.06   2.7e+02      29      45 ..     133     149 ..     112     163 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 4.8e-08
      HTH_45 40 LdmLvekglikk.skekYvlTekGlelleklkeleel 75
                L  L+++gli++ +++kY+lT+kG e+  ++++++++
  EPA04853.1 59 LGRLLDEGLIEEaKDGKYQLTKKGIETAADVDKINDI 95
                7789******7669****************9999876 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.06
      HTH_45  29 anLsykllnkYLdmLve 45 
                 an++ + ++kY ++L  
  EPA04853.1 133 ANMTSEETQKYRKFLEA 149
                 88888999999888864 PP

>> RTP  Replication terminator protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   5.5e-06     0.025       7      74 ..      15      81 ..      13     104 .. 0.82
   2 ?    2.8   0.2     0.041   1.8e+02      69     103 ..     120     154 ..      94     164 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.5e-06
                HHHHHHHHHHHHHTT-EBCTCHHHHHHHHHTTTT----HHHHHHHHHHHHHTTSEEEEEEEBTSSSSS CS
         RTP  7 rAFlklylitlvekkklyglklldelkkeFkelgykPnhseiyralhelvedgilkrrkelkekaklq 74
                r F + ++++l+++k   g +++d+  ++  +  +kP++  iy  l  l+++g+++  k  k +   +
  EPA04853.1 15 RGFSRYFILELLKTKAYTGKEIIDHAAEQ-SNGVWKPSPGLIYPLLGRLLDEGLIEEAKDGKYQLTKK 81
                679999*******9999999999997654.6667***********************99988444433 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.041
                 TSSSSSEEEEEEESS..HHHHHHHHHHHHHHHHHH CS
         RTP  69 ekaklqevviYsltdeGkekaklykkqvkidldrc 103
                 + + +  ++  ++++  +e+ + y+k + ++l + 
  EPA04853.1 120 KMSSIGSILDSNFANMTSEETQKYRKFLEAELKKI 154
                 455566677778999999**********9999875 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.19   8.7e+02       8      31 ..      22      44 ..      19      47 .. 0.79
   2 ?   12.5   0.1   2.7e-05      0.12      61      84 ..      62      85 ..      59      88 .. 0.87
   3 ?   -2.1   0.0      0.99   4.4e+03      41      41 ..     143     143 ..     118     165 .. 0.61

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.19
       Mrr_N  8 lLealadgsehrlkeirervaerf 31
                +Le l+ +  +  kei++ +ae+ 
  EPA04853.1 22 ILELLKTKAYTG-KEIIDHAAEQS 44
                678887777776.9**99999986 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 2.7e-05
       Mrr_N 61 LkkagllespkrgvwkiTekGrev 84
                L  +gl+e+ k g++++T+kG e+
  EPA04853.1 62 LLDEGLIEEAKDGKYQLTKKGIET 85
                5568*****************886 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.99
       Mrr_N  41 l 41 
                 +
  EPA04853.1 143 Y 143
                 2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1177  (0.0656478); expected 358.6 (0.02)
Passed bias filter:                      721  (0.0402142); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1214.99
//
Query:       EPA04854.1  [L=144]
Description: hypothetical protein BG20_I0518 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-07   32.0   4.7    2.2e-07   30.9   4.7    1.6  1  Sdh_cyt         Succinate dehydrogenase/Fumarate reductase tr
  ------ inclusion threshold ------
      0.011   15.9   2.3      0.081   13.0   0.0    2.2  2  Fumarate_red_D  Fumarate reductase subunit D
       0.32   11.1   4.1        0.1   12.7   0.8    1.7  2  Fumarate_red_C  Fumarate reductase subunit C


Domain annotation for each model (and alignments):
>> Sdh_cyt  Succinate dehydrogenase/Fumarate reductase transmembrane subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   4.7   3.7e-11   2.2e-07      17      98 ..      21     100 ..      13     142 .. 0.78

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 3.7e-11
     Sdh_cyt  17 plgawlsilhritGvallvglllllvwlllalslsspesfarvvallas.piklilllllllallyHllnGiRhllwDlglgl 98 
                  ++ ++++l+r++G++ll  +++ +++ + +++l ++ +++++ +l +   + +il +++++  ++H++nGiR++l   g+g+
  EPA04854.1  21 GIERVAYLLMRLSGLGLLA-YFIGHIYET-SSILKGEIGWNEFLQLTQTtEGHAIL-AIVIAMCVFHTVNGIRVMLGHGGIGV 100
                 567889*************.666666544.77789999*****8888776788888.777888888*********98535555 PP

>> Fumarate_red_D  Fumarate reductase subunit D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.4e-05     0.081      44      91 ..      54     101 ..      35     108 .. 0.85
   2 ?    2.4   0.7     0.027   1.6e+02      18      39 ..     122     143 ..     120     144 .] 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.4e-05
  Fumarate_red_D  44 dalsyekvlafaqswigklvllvviilplwhalhrihhglhdlkihvk 91 
                      ++ +++ l+++q++ g+++l++vi++ ++h+++ i+ +l + +i v+
      EPA04854.1  54 GEIGWNEFLQLTQTTEGHAILAIVIAMCVFHTVNGIRVMLGHGGIGVG 101
                     457788999****************************99999777665 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.027
  Fumarate_red_D  18 GmvaAlvlpvlililglllplG 39 
                     G+ +A++l+++ ++ gl + +G
      EPA04854.1 122 GIYSAIILAAIAMMYGLTVMFG 143
                     7899************999887 PP

>> Fumarate_red_C  Fumarate reductase subunit C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.8   1.7e-05       0.1      23      83 ..      26      86 ..      22      93 .. 0.91
   2 ?   -1.1   0.1      0.31   1.9e+03      34      46 ..     127     139 ..     117     143 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.7e-05
  Fumarate_red_C 23 fYmlrEatavlvalfalvlllgllaLaqgeaayeafleflqnPlvlllniiaLaaallhav 83
                    +Y+l  ++ + ++++ +  ++   ++ +ge  +++fl++ q +   ++  i++a++++h+v
      EPA04854.1 26 AYLLMRLSGLGLLAYFIGHIYETSSILKGEIGWNEFLQLTQTTEGHAILAIVIAMCVFHTV 86
                    688888899999999999999999999********************************98 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.31
  Fumarate_red_C  34 valfalvlllgll 46 
                     ++l+a+ +++gl+
      EPA04854.1 127 IILAAIAMMYGLT 139
                     4556666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 991.45
//
Query:       EPA04855.1  [L=72]
Description: hypothetical protein BG20_I0507 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       708  (0.0394891); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 558.34
//
Query:       EPA04856.1  [L=147]
Description: NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.5e-18   65.0   0.9    5.5e-18   65.0   0.9    1.5  2  Oxidored_q4  NADH-ubiquinone/plastoquinone oxidoreductase, ch
  ------ inclusion threshold ------
      0.075   13.2   0.0       0.18   12.0   0.0    1.7  1  MPS-4        MinK-related peptide, potassium channel accessor


Domain annotation for each model (and alignments):
>> Oxidored_q4  NADH-ubiquinone/plastoquinone oxidoreductase, chain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1      0.29   2.6e+03      75      81 ..      36      42 ..      10      51 .. 0.59
   2 !   65.0   0.9   6.2e-22   5.5e-18       4      93 ..      49     139 ..      45     142 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.29
                 HHHHHHH CS
  Oxidored_q4 75 iemllFl 81
                 + m+ F 
   EPA04856.1 36 VLMFGFA 42
                 2222222 PP

  == domain 2  score: 65.0 bits;  conditional E-value: 6.2e-22
                  HHHHHCHSS---.--HHHHS-SSSS--SS---.--HHCHHHHHHHHHHHHHHHHHHHHHHHHSST..HHHHHHHHHHHHHHHHHHHHHHHH CS
  Oxidored_q4   4 llllsallgpkk.pnkeklspYEcGfepvgearlrfsvkfylvallFliFDvevvflfpwavslkelglfgliemllFllillvglvYewk 93 
                  +l++s++++p++ +n+ k  p EcG  p ge r++f +++y + l+F++FDv ++fl++w  +l el   +++ ++ Fl+i+++++++++ 
   EPA04856.1  49 ALVISRMISPRRrSNPVKFLPMECGQVPSGEGRTHFMMQYYAYILMFVVFDVMAIFLYAWGSALLELPKSATLPIIGFLAIMFAAMAFALY 139
                  57899999998868888**********************************************9999999*****************9975 PP

>> MPS-4  MinK-related peptide, potassium channel accessory sub-unit protein 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0     2e-05      0.18      19      69 ..      66     114 ..      57     120 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2e-05
       MPS-4  19 kylleeflkrssscnrisystkyfdfllvviisvvslglvylllwievlln 69 
                 k+l  e  +  s   r  +  +y+ ++l+    v+ + +++l  w   ll+
  EPA04856.1  66 KFLPMECGQVPSGEGRTHFMMQYYAYILMF--VVFDVMAIFLYAWGSALLE 114
                 66667777888888999*******998875..578999*******999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.34s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 843.18
//
Query:       EPA04857.1  [L=371]
Description: hypothetical protein BG20_I0531 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2625.02
//
Query:       EPA04858.1  [L=358]
Description: glutamyl-tRNAGlu reductase, N-terminal domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-25   89.5   0.0    2.8e-25   88.8   0.0    1.3  1  GlutR_N        Glutamyl-tRNAGlu reductase, N-terminal domain
    6.9e-19   68.3   0.0    2.9e-18   66.3   0.0    2.0  2  Shikimate_DH   Shikimate / quinate 5-dehydrogenase
  ------ inclusion threshold ------
      0.019   15.4   0.0      0.048   14.1   0.0    1.6  1  NAD_binding_7  Putative NAD(P)-binding
       0.05   14.2   0.0        0.1   13.2   0.0    1.5  1  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
      0.066   12.3   0.0       0.11   11.6   0.0    1.2  1  K_oxygenase    L-lysine 6-monooxygenase (NADPH-requiring)


Domain annotation for each model (and alignments):
>> GlutR_N  Glutamyl-tRNAGlu reductase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.8   0.0   7.7e-29   2.8e-25       3     146 .]      13     175 ..      12     175 .. 0.84

  Alignments for each domain:
  == domain 1  score: 88.8 bits;  conditional E-value: 7.7e-29
     GlutR_N   3 inhktapvelreklafseee.lkellkeleekvkeaviLsTCNRtEiylsaeeee...................easeellellaevsleelkeklyvl 81 
                 +++k++p++++ ++ f++ + + e++k++  +v+e++i++T  R+Ei+++++ e+                   +++ e l++l+++  ++++++l+v+
  EPA04858.1  13 VTFKNVPLHTLARFRFDDLKtACETFKKI-PGVAECIIIQTASRIEIFTVSNLETgdtpdgrrtegkslvlnqiKETWESLSTLEQIDIDHFDQTLEVY 110
                 689*************7655455666666.4899**************766666678999999887776664333333333345555688888****** PP

     GlutR_N  82 egeeavrHlfrVasGLdSlvlGEdqIlgQvkeayelakeagtlgkvLerlfqkaikvakrvrtet 146
                 +g+++   l+r+a+GLdS+v+G ++Il+ +k+++  ak+ +++g++L++lf++ i+++ r+r+ t
  EPA04858.1 111 KGTDVYVNLLRLACGLDSVVVGKEEILNEIKTSLSNAKNINVSGPILNKLFESIIRISTRIRETT 175
                 **************************************************************976 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.66   2.4e+03      75      98 ..      44      67 ..      26      76 .. 0.77
   2 !   66.3   0.0   8.1e-22   2.9e-18      11     136 ..     200     321 ..     188     323 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.66
                  T-SEEEE-SSSSS-SB-HHHHHCC CS
  Shikimate_DH 75 eadvvisataseepilekeeveea 98
                   a+ +i+ tas+  i++ +++e  
    EPA04858.1 44 VAECIIIQTASRIEIFTVSNLETG 67
                  578899999999999999988876 PP

  == domain 2  score: 66.3 bits;  conditional E-value: 8.1e-22
                   TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSSSS-SB-HHHHHCCHHH.S..EE CS
  Shikimate_DH  11 kekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisataseepilekeeveealkkrkkpll 107
                   ++kk+lliG+Ge a +vak L +kg+    v+  t+er   + + l+g+    +++ee+ +  +++d++++at +  ++++ ++++ +++++kk +l
    EPA04858.1 200 AKKKILLIGTGESAARVAKTLNKKGFA-FDVTSKTIERSTGFSKILGGK---PVAFEEVLSGFDKYDIIFVATTADYFLITFDRIKLVMEEKKKGTL 292
                   689***********************9.******************999...*************************************9999**** PP

                   EEE--SS-SB-TTGGGSTTCCCEEHHHHH CS
  Shikimate_DH 108 lvDiavPRdvepevaeledvrlytvDdLk 136
                   ++D++ PR v++ + +l +++l   D + 
    EPA04858.1 293 IMDLSDPRTVDEGITALPGIKLLFRDQIA 321
                   *******************9997666665 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.3e-05     0.048       7      70 ..     201     269 ..     199     275 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.3e-05
  NAD_binding_7   7 gkkvlvvGgGevAarkvrklleagakvtvvapev..keele...elvklaeeelekd...legadlviaatd 70 
                    +kk+l++G Ge Aar +++l ++g    v ++++  +       +++  ++  +e+    ++++d++++at+
     EPA04858.1 201 KKKILLIGTGESAARVAKTLNKKGFAFDVTSKTIerS---TgfsKILGGKPVAFEEVlsgFDKYDIIFVATT 269
                    699******************************6331...22333333344444444111666778888885 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.8e-05       0.1       1      93 [.     203     295 ..     203     299 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.8e-05
                    EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHH...H-SEEEE-S-HHHHHHHHHHC...GHHHHTTSE CS
  F420_oxidored   1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaae...eadvvvlavkpedveevlsel...akdalkgkl 90 
                    ki +iG+G+ ++ +a+ l ++g     +  ++s++ e+ + + + lg k  a   ee+++   + d++++a    ++  + + +   +++++kg+l
     EPA04858.1 203 KILLIGTGESAARVAKTLNKKG---FAFD-VTSKTIERSTGFSKILGGKPVA--FEEVLSgfdKYDIIFVATTADYFLITFDRIklvMEEKKKGTL 292
                    6789******************...7777.44**************966555..4555444449*******9998888777777666777777777 PP

                    EEE CS
  F420_oxidored  91 vis 93 
                    + +
     EPA04858.1 293 IMD 295
                    776 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   3.1e-05      0.11     184     228 ..     194     240 ..     186     246 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.1e-05
  K_oxygenase 184 rkeellakkriaVvGsGqSaaeifedllrrqkk..velklvtrseal 228
                  +k+ l akk+i+ +G G Saa +++ l ++  +  v+ k + rs+++
   EPA04858.1 194 EKAGLDAKKKILLIGTGESAARVAKTLNKKGFAfdVTSKTIERSTGF 240
                  45567899********************9955412555566666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2452.78
//
Query:       EPA04859.1  [L=288]
Description: putative carboxyvinyl-carboxyphosphonate phosphorylmutase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.5e-50  170.7   0.0    4.1e-50  170.5   0.0    1.0  1  PEP_mutase  Phosphoenolpyruvate phosphomutase
    5.9e-15   54.7   0.1    2.2e-14   52.8   0.0    1.7  2  ICL         Isocitrate lyase family


Domain annotation for each model (and alignments):
>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.5   0.0   4.6e-54   4.1e-50       2     227 ..       5     236 ..       4     248 .. 0.90

  Alignments for each domain:
  == domain 1  score: 170.5 bits;  conditional E-value: 4.6e-54
  PEP_mutase   2 ra.LhakgeplvlpnawDalsakiveeagfkalatsSlavaasl.GvpDgeelpleellaavraiaevvslPlivDledGygespeevaetvrrliaaG 98 
                 +  L+a+ +plv+p ++Da++aki+e+ gf+a+  ++++++a+l G+pD   + ++e+l+++r+i+++vs+P+ivD ++Gyg+ + +v++ vr+l++aG
  EPA04859.1   5 KTmLKAN-KPLVIPGVYDAIGAKIAEKVGFEAMFQTGYGTSATLfGMPDYGFIGATETLDNARRICRAVSVPVIVDSDTGYGN-ALSVWKLVRELESAG 101
                 5547777.9*******************************99999**************************************.88************* PP

  PEP_mutase  99 vvgvniEDk....kknd.aerqlldieefaekiaaaraaaeeagfvinARtdalllsagagleeaieRaraYaeAGAdgvfvpglqkdaeiaelvaavd 192
                 ++g+ +ED+    +++  +++++++ ee +ek+ aa +a ++++f+i+ARtda    a +gl+ aieR+   ++ GAd+vf+   ++ +e++ + +a++
  EPA04859.1 102 ASGIFLEDQrwpkRCGHmKGKEVISQEEYTEKLGAAIDARQSKDFIIVARTDAR---ATEGLDAAIERGLQNKKTGADAVFIEAPRSLEEMRIIGKAIN 197
                 *********997544454788888*****************************3...6899************************************** PP

  PEP_mutase 193 vplnvvp.lkgt...lsvaelaelGvarislgnhllraa 227
                 +pl++ + ++g+    s ++l++lG+++i +  ++l a 
  EPA04859.1 198 APLVANMiEGGAtpmNSATTLHKLGFKIILYPLSVLFAN 236
                 **999996643336699************9987665554 PP

>> ICL  Isocitrate lyase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.8   0.0   2.5e-18   2.2e-14     150     244 ..      74     165 ..      62     181 .. 0.88
   2 ?   -0.8   0.0     0.044     4e+02     435     493 ..     217     277 ..     212     281 .. 0.81

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 2.5e-18
                 --EEEE-TT-SSSHHHHHHHHHHHHHTT-SEEEE-SB-TT---------EEE--HHHHHHHHHHHHHHHHH.TT---EEEEE--GGGEEEES-TT- CS
         ICL 150 rpiiadadtGhGGltavvkltklfierGaaGihiedqasgtkkcGhmaGkvlvpiqehinrlvairaqadi.lgsdllvvartdseaatlitstid 244
                  p+i d+dtG+G   +v kl++ +   Ga+Gi +edq    k+cGhm Gk +++ +e+ ++l a+    d     d ++vartd+ a+  + ++i+
  EPA04859.1  74 VPVIVDSDTGYGNALSVWKLVRELESAGASGIFLEDQR-WPKRCGHMKGKEVISQEEYTEKLGAAI---DArQSKDFIIVARTDARATEGLDAAIE 165
                 59***********************************7.579*******************97643...33035799**********998888876 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.044
                 HHHHTTEEEEEETTHHHHHHHHHHHHHHHHHHHHTHHHH..HHHTHHHHHHHT-GGGSHHH CS
         ICL 435 rlaklGyvwqfitlaGlhtnalisdkfakdyakrGmkay..geevqeeeidnGvdvvkhqk 493
                  l klG+   +  l+ l +n++++ ++ k+  k+G  a    + v+ ++ ++ vd  k qk
  EPA04859.1 217 TLHKLGFKIILYPLSVLFANTFATMNILKELKKTGTTAKfkHKVVNFDQFNDLVDLPKFQK 277
                 578999999999999********************98851134466678888899888888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1714.38
//
Query:       EPA04860.1  [L=570]
Description: succinate dehydrogenase flavoprotein subunit [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-98  330.0   0.1    2.9e-98  329.7   0.1    1.1  1  FAD_binding_2   FAD binding domain
      3e-37  127.5   0.6    4.8e-37  126.8   0.6    1.3  1  Succ_DH_flav_C  Fumarate reductase flavoprotein C-term
      3e-07   30.0   0.0    0.00048   19.5   0.0    2.8  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    0.00082   18.6   0.0      0.045   12.8   0.1    2.2  2  GIDA            Glucose inhibited division protein A
     0.0013   18.2   0.0      0.061   12.7   0.1    2.3  2  FAD_oxidored    FAD dependent oxidoreductase
     0.0014   18.0   0.2     0.0051   16.1   0.1    2.0  2  Thi4            Thi4 family
  ------ inclusion threshold ------
      0.034   13.2   0.1      0.062   12.3   0.1    1.4  1  Lycopene_cycl   Lycopene cyclase protein
      0.043   13.4   0.2       0.42   10.1   0.1    2.3  2  DAO             FAD dependent oxidoreductase
      0.079   11.7   1.0        2.7    6.6   0.1    2.5  3  HI0933_like     HI0933-like protein


Domain annotation for each model (and alignments):
>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  329.7   0.1  1.4e-101   2.9e-98       1     416 [.       8     389 ..       8     390 .. 0.97

  Alignments for each domain:
  == domain 1  score: 329.7 bits;  conditional E-value: 1.4e-101
                    SEEEE--SHHHHHHHHHHHH.TTT.-EEEEESSSGGGSGGGG--S-EE-TT..SSGGSTC.CHHHHHHHHHHHHTTT-S-HHHHHHHHHTHHHHHH CS
  FAD_binding_2   1 DviViGsGlAGLaAAleaae.aGl.kvavvekeqefggatawsqGgidavlspeqkkagikdspelhrtdtlkaldeladqplveafveaapeavd 94 
                    D+i++GsGlAGL+AA+eaa+ + + k+ +v+k+q+++++++ ++Gg +avl  e+    ++d++e+h++dt+k++d ladq+++e ++ ++p+++ 
     EPA04860.1   8 DLIICGSGLAGLRAAIEAARkNPKiKIGIVSKVQVMRSHSVSAEGGTAAVL-FED----EGDTIESHIYDTVKGSDFLADQDVAERLCVEMPKEIY 98 
                    89*****************9566689*************************.333....47*********************************** PP

                    HHHHTT----BCCTSSB-EEE-TT-SSTEEEE-.STT-......HHHHHHHHHHHHHHTCT.EEEEESEEEEEEEECTTEEEEEEEEETTTTCEEE CS
  FAD_binding_2  95 eLeelgvpfsrtedgpvdvrelGglsatartlhdaadarretlvtghallarlvesarkag.vdfqerteadeLivedgrvtGavvenpesgrevr 189
                    +L ++g+p+sr++dg++++r +Gg s + r  + a+d+       g+  + +l+++++k++ ++++++++a+++i++++r  G+++ +++sg+   
     EPA04860.1  99 QLDHWGMPWSRRKDGRIGQRNFGGYSFP-RATY-ASDK------VGFFEMQTLYDTCQKHEnIEYLNEWFATSIIHDGKRFLGITAIELSSGTFYS 186
                    ****************************.****.****......99999***************************999***************** PP

                    EEESEEEE-----GG..........GSSSBSSGTT-S-HHHHHHHCTTSSEES..TT-EEEEEEEET....TTTBB--THHHHTT-EEE-TTSSBT CS
  FAD_binding_2 190 irakavvlatgGfgrallkellgaaaeaettnapavtGdglalalragaalnddrmeevqfhPtslvpirdgsgiLitealrgeGgilvdkdGrrF 285
                    i+ ka+++atgG+gr           +  +t a   t dgl++alrag+al+d  me+vqfhPt+++    +sgiLite++rgeGg+l++++G+rF
     EPA04860.1 187 IKGKALIIATGGAGR----------LYSFSTYALSSTPDGLDMALRAGMALKD--MEFVQFHPTGIL----PSGILITEGARGEGGYLLNNKGERF 266
                    ***************..........****************************..************....************************* PP

                    H.......GGGS-HHHHHHHHH.HHHHTTTS......CCBEEEE-TT.SSHHHHHHHSHHHHHHHHHCCT......S-TTTSEEE.......EEEE CS
  FAD_binding_2 286 m.......nelasrdvvsrailekeiaeggs......eanvyldashgldaegleatleaineeaangldkdfgrgidpadrpipgpfyavkvvpa 368
                    m       +ela+rd+vsra++ +e++eg++       +++ ld++h l+ e+++++l +i+e+ +++ +       dpa++          v+p 
     EPA04860.1 267 MkkyagekMELAPRDIVSRAMM-TEMSEGRGfkhetgVDCMKLDLRH-LGDEKIKEKLGGIREISIKFSG------LDPATEVLD-------VRPV 347
                    **********************.*************999********.*******************999......******666.......**** PP

                    EEEES-EEEBETTSBESTTEEESSBTEEE-STCEESSSSTTS--TTHH CS
  FAD_binding_2 369 qhytmgGvetdengrvldadgqpipGLYAaGevaaggvhganrlgGns 416
                    +hy+mgG++td +g +       ++G +AaGe+a+ +vhg nrlg+ns
     EPA04860.1 348 CHYMMGGIHTDIDGAT------ELQGVWAAGEAACNSVHGSNRLGANS 389
                    ****************......************************98 PP

>> Succ_DH_flav_C  Fumarate reductase flavoprotein C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.8   0.6   2.4e-40   4.8e-37       2     128 .]     447     570 .]     446     570 .] 0.98

  Alignments for each domain:
  == domain 1  score: 126.8 bits;  conditional E-value: 2.4e-40
                     HHHHHHHHHHSSSSB-HHHHHHHHHHHHHHHHH.HTTB--S---SSS-HHHHHHHHHHHHHHHHHHHHHHHHH--S-BTTBEBTTS-SEETTT-S CS
  Succ_DH_flav_C   2 keLgkimqkkvgvfRteegLkealkelkelrer.lknvkvtdkskvaNqelvealelanllelAeaiaksAlaRkESrGaHaredfperdDenwl 95 
                     +eL ++m++k+ vfR+e++L e+lk++++l+++ +k  +v+dk k++N+++ +++el++++++Ae+++ +A +RkESrGaH r+d+p+rdD+n+l
      EPA04860.1 447 QELTDTMNDKAYVFRNEKNLVEGLKKIRQLKQQaWK--HVDDKAKEYNTNFSNVMELDSMFRVAEIVLLGAINRKESRGAHSRTDYPKRDDANFL 539
                     89*******************************999..899****************************************************** PP

                     EEEEE...TT-SS-EEEEEE--GGG--S---SS CS
  Succ_DH_flav_C  96 khtlasldaakeeveleyepveletlkpkeRsY 128
                     +htla++d++  e+ ++++pv++++ +p eR+Y
      EPA04860.1 540 HHTLAYYDPK--EPIMKTHPVTITKYQPVERKY 570
                     *****99977..9*******************9 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   2.4e-07   0.00048       2     112 ..       8     201 ..       7     218 .. 0.76
   2 !    7.0   0.0    0.0015       2.9     236     278 ..     334     375 ..     328     391 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 2.4e-07
                  SEEEE--SHHHHHHHHHHHHH..TS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH........................................ CS
                  xxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................................ RF
  Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqa..gakvtlvelegtclnggcllskallgvaedaeias........................................ 57 
                  d+++ G+G AGl+aa+++a++  ++k+ +v+       ++++ s+ + + ++ a ++                                         
   EPA04860.1   8 DLIICGSGLAGLRAAIEAARKnpKIKIGIVS------KVQVMRSHSVSAEGGTAAVLFedegdtieshiydtvkgsdfladqdvaerlcvempkeiyq 99 
                  899*****************72355566663......2222222222222222222222333334467888888888888888888999999999999 PP

                  .................................................HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEEC...TCEEEEEESEE CS
                  .................................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxx RF
  Pyr_redox_2  58 .................................................evvkklnqgielllgeevvkidpgkkkvklekkke...gdeekiaydkl 103
                                                                   ++     ++ie+l++  +++i+++ k++   +  e   g   +i+ ++l
   EPA04860.1 100 ldhwgmpwsrrkdgrigqrnfggysfpratyasdkvgffemqtlydtcqKH-----ENIEYLNEWFATSIIHDGKRFLGITAIElssGTFYSIKGKAL 192
                  99*********************************9999999887655433.....568877776699999999999998777788888899999*** PP

                  EE---EEE- CS
                  xxxxxxxxx RF
  Pyr_redox_2 104 vlAtGsspr 112
                  ++AtG+  r
   EPA04860.1 193 IIATGGAGR 201
                  ****98655 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0015
                  -EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGC CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Pyr_redox_2 236 GvrpstelleeklglelderggivvdeflrtnvpgiyaiGDva 278
                  G+ p te l+    +     ggi +d  ++t+ +g++a+G  a
   EPA04860.1 334 GLDPATEVLD-VRPVCHYMMGGIHTDIDGATELQGVWAAGEAA 375
                  7777777774.333333458********************998 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.1   2.3e-05     0.045       1      64 [.       8      71 ..       8      79 .. 0.81
   2 ?    3.3   0.0     0.018        35     100     169 ..     142     203 ..     127     228 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.3e-05
                CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT--SSSSEEE-TTHHHHHHHHHHHT-SHH CS
        GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithkldtiaelsCnpsiggiakgllvrEidalgglii 64
                d+i+ G G+AG+ AA++aar++ k+++   +  ++++     + gg+a+ l   E d +++ i 
  EPA04860.1  8 DLIICGSGLAGLRAAIEAARKNPKIKIGIVSKVQVMRSHSVSAEGGTAAVLFEDEGDTIESHIY 71
                6899******************999998777777777777777788888777777777777765 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.018
                 HHHHHHHTSTTEEEEES.-EEEEEECT...TEEEEEEETTS-EEEEC..EEEE--TT-BT-EEEETTEEEESSCTT CS
        GIDA 100 evteklenepnleiiee.eveelivee...kkvkgvvtedgetikak..avviatGtflkgkihigekelsaGrlg 169
                 ++ ++ ++++n+e ++e  ++++i +      ++++ +++g+ ++ k  a +iatG               aGrl 
  EPA04860.1 142 TLYDTCQKHENIEYLNEwFATSIIHDGkrfLGITAIELSSGTFYSIKgkALIIATGG--------------AGRLY 203
                 5567889999999776615566766554444456677899987655444*******8..............34444 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.1   3.1e-05     0.061       1      22 [.       8      29 ..       8      37 .. 0.92
   2 ?    2.9   0.0     0.028        55      90     145 ..     141     198 ..     100     204 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.1e-05
  FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraG 22
                  D++++G+g+aG+ AAi Aar+ 
    EPA04860.1  8 DLIICGSGLAGLRAAIEAARKN 29
                  99******************86 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.028
  FAD_oxidored  90 kavleemlaeagvtvllntrlvevekegkr...iesvtveske.g.rktirAkvfiDATgd 145
                   +++++   + ++++ l + ++++++ +gkr   i+++++   + g  + i++k  i ATg 
    EPA04860.1 141 QTLYDTCQKHENIEYLNEWFATSIIHDGKRflgITAIEL---SsGtFYSIKGKALIIATGG 198
                   55666666788*****************99555555555...44669*********99985 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   2.6e-06    0.0051      13      49 ..       2      39 ..       1      70 [. 0.84
   2 ?   -1.6   0.0      0.66   1.3e+03     213     233 ..     366     387 ..     356     388 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.6e-06
                HHHTEEEEEEE--SHHHHHHHHHHHHC.TTS-EEEEES CS
        Thi4 13 lkyaesDvvivGaGssGLtaayylakk.pdlkvailer 49
                ++ +e D++i G+G +GL aa   a+k p++k+ i+ +
  EPA04860.1  2 VESIEFDLIICGSGLAGLRAAIEAARKnPKIKIGIVSK 39
                677899*******************999****999864 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.66
                 TTEEE-TH.HHHHHHT-EB--S CS
        Thi4 213 pnlyvaGm.evaevdganRmGp 233
                 +++++aG  + + v+g nR+G+
  EPA04860.1 366 QGVWAAGEaACNSVHGSNRLGA 387
                 6778888515689*******97 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   3.1e-05     0.062       1      31 [.       8      38 ..       8      50 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.1e-05
  Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlie 31
                   D+++ G+G+Agl+ A + ++++p++k++++ 
     EPA04860.1  8 DLIICGSGLAGLRAAIEAARKNPKIKIGIVS 38
                   9***************************993 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00021      0.42       1      85 [.       8     113 ..       8     116 .. 0.77
   2 ?   -0.1   0.0      0.28   5.6e+02     130     174 ..     428     472 ..     398     498 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00021
                 EEEEECTSHHHHHHHHHHHHTT....EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTH...................HHH.HHHHHHHHHHHHHHHHH CS
         DAO   1 dvviiGGGiiGlstAyeLarrg....VtllekgdiagsgaSgrnsgllhsglrylpeas...................ela.rlslealeelreleeel 75 
                 d++i G+G +Gl +A e+ar++    + ++ k     s++ ++ +g  +  +++                        ++a rl+ e  +e+++l+   
  EPA04860.1   8 DLIICGSGLAGLRAAIEAARKNpkikIGIVSKVQVMRSHSVSAEGGTAAVLFEDEG--DtieshiydtvkgsdfladqDVAeRLCVEMPKEIYQLDHW- 103
                 789***************99855899999999977777888888887777663222..2245667777888899999844459999999999999964. PP

                 SSTTSEEEEE CS
         DAO  76 gididyrrtG 85 
                 g+++  r+ G
  EPA04860.1 104 GMPWSRRKDG 113
                 8888888777 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.28
                 TTSEEEEETTEEEEEHHHHHHHHHHHHHHTT-EEEESECEEE.EEE CS
         DAO 130 gllgalfypdtgqvdpakltaalaraaealGveilegtevtg.lee 174
                 ++  ++f  + g v+p+++ + l +++ +++  ++++ + ++ l++
  EPA04860.1 428 RIYDGIFRGN-GDVNPYEVKQELTDTMNDKAYVFRNEKNLVEgLKK 472
                 6677777777.999**************999999999775553533 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1    0.0014       2.7       2      27 ..       8      33 ..       7      50 .. 0.89
   2 ?    3.0   0.0     0.016        33     149     187 ..     183     227 ..     125     235 .. 0.67
   3 ?   -3.0   0.1       1.1   2.2e+03     292     351 ..     444     502 ..     437     509 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0014
                 SEEEE--SHHHHHHHHHHHHTT--EE CS
  HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVl 27
                 d+i+ G G AGl aAi+aa+++ ++ 
   EPA04860.1  8 DLIICGSGLAGLRAAIEAARKNPKIK 33
                 89****************99887765 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.016
                  TTEEEEESEEEE----S......S-GGGT--SHHHHHHHHTT--E CS
  HI0933_like 149 seeeleadklvlAtGGl......SiPklGstgkgyklaeqfghti 187
                  +  +++ ++l++AtGG+      S   l st++g ++a  +g+ +
   EPA04860.1 183 TFYSIKGKALIIATGGAgrlysfSTYALSSTPDGLDMALRAGMAL 227
                  3347899*********75555446677889999988888888766 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 1.1
                  BHHHHHTTTS-HHHHHHHHHC..TTT-TTBGGG--HHHHHHHHHHHHSEEE--SEE--TT CS
  HI0933_like 292 slknalaellpkrlvevlleealieeedkklaqlskkelkklaealkaltvkvngteglr 351
                  ++k+ l+++++ +   +  e++l+ e  kk++ql+++  k++ ++ k+++ + ++ ++l+
   EPA04860.1 444 EVKQELTDTMNDKAYVFRNEKNLV-EGLKKIRQLKQQAWKHVDDKAKEYNTNFSNVMELD 502
                  577788888888888888887666.66788888888888888888888777777666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (570 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.67u 0.36s 00:00:01.03 Elapsed: 00:00:00.52
# Mc/sec: 3268.56
//
Query:       EPA04861.1  [L=311]
Description: oxidoreductase, NAD-binding domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.2e-26   91.0   0.0    1.6e-25   90.3   0.0    1.4  1  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
    1.5e-06   28.2   0.1    2.9e-06   27.3   0.1    1.5  1  GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta 
  ------ inclusion threshold ------
      0.034   14.8   0.1       0.59   10.8   0.0    2.2  2  NAD_binding_3   Homoserine dehydrogenase, NAD binding domain
      0.035   13.6   0.3      0.082   12.4   0.0    1.7  2  DUF3228         Protein of unknown function (DUF3228)
      0.081   13.4   0.3       0.27   11.7   0.0    2.1  3  Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domai


Domain annotation for each model (and alignments):
>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.3   0.0   4.4e-29   1.6e-25       1     120 []       1     117 [.       1     117 [. 0.95

  Alignments for each domain:
  == domain 1  score: 90.3 bits;  conditional E-value: 4.4e-29
                   EEEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-GGGHHHHHHHHHHTT-EEEEESSS-S CS
  GFO_IDH_MocA   1 lrvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladpeidavivatpngtheelakaaleagkhvllEKPlat 97 
                   ++++ iG+G  g++h r l   ++l  + a++d +aer+++  e++ v+ ys+l++l + +e d ++v+tp++th e+a ++l+a+khv++EKP++ 
    EPA04861.1   1 MKIVQIGTGGWGKNHTRIL---SQLGVLCAVCDVNAERSKEYGEKYSVKHYSNLDDLIKFEEFDGAFVVTPTSTHTEIATKLLQAKKHVFVEKPMTY 94 
                   58999**********9444...45689********************************************************************** PP

                   SHHHHHHHHHHHHHHTS-EEEE- CS
  GFO_IDH_MocA  98 tveeakelvelaekkgklvsvgy 120
                   + e+ ++++e+aek++++++ gy
    EPA04861.1  95 KSEDGQKILEIAEKNKVILTCGY 117
                   ******************99887 PP

>> GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.1   8.1e-10   2.9e-06      36      82 ..     152     198 ..     129     221 .. 0.75

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 8.1e-10
                     H..HCSTSHHHHTCHHHHHHHHHHHTSEEEEEEEEE.SEEESCTCCSCS CS
  GFO_IDH_MocA_C  36 k..kksgGvlgdlgiHdiDllqwLfGqppsvvaalgrmrqnaeaaeded 82 
                     +   k+ G+ +d ++HdiD ++wLf  +p vv+a+     +++  ed+ 
      EPA04861.1 152 PlhIKDVGIIYDTSVHDIDTANWLFDDMPQVVFARS--GRINHEHEDFA 198
                     3444688****************************7..66766666654 PP

>> NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00016      0.59      24     112 ..      25     111 ..       7     115 .. 0.76
   2 ?    1.7   0.1      0.11   3.8e+02      34      75 ..     249     292 ..     233     303 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00016
                    EEEEEESSEEE-TTHHHHHT--CB---HHHHHHHH..S-EEEEE-S--HHHHTTHHHHHHTTEEEE-S--CGGG-HHHHHHHTSSSTTS-- CS
  NAD_binding_3  24 lvavadrdsllskdrkallasealtldlddliahl..dpdvvVEcasseavaelvlkaLkagkdvvtankgaladealyeeLreaaeanga 112
                    l+av+d + +++ +   +  s + +++lddli+++  d   v  +++ +   e+++k L+a+k+v +        ++ +++++e ae+n++
     EPA04861.1  25 LCAVCDVN-AERSKEYGEKYSVKHYSNLDDLIKFEefDGAFV--VTPTSTHTEIATKLLQAKKHVFVEKPMTY-KSEDGQKILEIAEKNKV 111
                    78899888.444455557789999*********994444444..57777889************988655444.59999999999999987 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.11
                    E-TTHHHHHT--CB---HHHHHHHH..S-EEEEE-S--HHHHTT CS
  NAD_binding_3  34 lskdrkallasealtldlddliahl..dpdvvVEcasseavael 75 
                    ++ ++ ++ ++e+l l++++++  +  ++d+vV       v ++
     EPA04861.1 249 EETEIPRNEKQEPLLLEIQSFLGAIegKNDLVVKSQQAVNVTKI 292
                    44457788999999999999999888889999976554445555 PP

>> DUF3228  Protein of unknown function (DUF3228)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.3e-05     0.082      52     101 ..      84     137 ..      55     145 .. 0.86
   2 ?   -2.2   0.0      0.68   2.4e+03      93     129 ..     214     248 ..     189     261 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.3e-05
     DUF3228  52 khlfvenftdakv....evleiteenekllkseYeaRrekelpvLtRwfpakkv 101
                 kh+fve  +  k     ++lei+e+n+ +l+ +Y++R +  + ++ +++++kk 
  EPA04861.1  84 KHVFVEKPMTYKSedgqKILEIAEKNKVILTCGYIERFNPAVDIVKKFVKEKKF 137
                 9***998776554333489******************************99876 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.68
     DUF3228  93 tRwfpakkvkelkkakyldvilYsreqiakenkamke 129
                 + w++ k+v ++ +a   d i+ s + i +e k  k+
  EPA04861.1 214 SNWITPKRV-RTFSAVCTDAIITS-DFISQEVKVEKK 248
                 467777777.66667777777655.444444444433 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   7.6e-05      0.27       5      94 ..       6      87 ..       2     112 .. 0.75
   2 ?   -2.1   0.0       1.4   4.9e+03      50      82 ..     160     194 ..     118     199 .. 0.64
   3 ?   -2.8   0.0       2.3   8.4e+03      48      78 ..     273     288 ..     241     303 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.6e-05
                    ETTTSHHHHHHHHHHHC.TSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGCTT-SEEEE-SCHHHHHHHHHHHHHTTSEEE CS
  Semialdhyde_dh  5 vGatGyvGqellrlLee.hpevelvvllsssrsaGkklaeavkaleegkdlkvedvdeeelkevdivflalpagvskelapklaeagvkvi 94
                    +G tG  G++  r+L++    + ++ + ++++   k++ e+++    +k ++  d d  +++e d +f  +p +++ e+a kl++a+ +v+
      EPA04861.1  6 IG-TGGWGKNHTRILSQlGVLCAVCDVNAERS---KEYGEKYS----VKHYSNLD-DLIKFEEFDGAFVVTPTSTHTEIATKLLQAKKHVF 87
                    56.78888888888888555556666555555...44444444....22222223.58899**********************99998775 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.4
                     TTECEBEEEGGGGGC..TT-SEEEE-SCHHHHHHH CS
  Semialdhyde_dh  50 egkdlkvedvdeeel..kevdivflalpagvskel 82 
                      + d +v+d+d++++  +++  v++a ++ + +e+
      EPA04861.1 160 IIYDTSVHDIDTANWlfDDMPQVVFARSGRINHEH 194
                     44556666655555445777777777777666665 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 2.3
                     GTTTECEBEEEGGGGGCTT-SEEEE-SCHHH CS
  Semialdhyde_dh  48 leegkdlkvedvdeeelkevdivflalpagv 78 
                     +e+++dl+v++               + a  
      EPA04861.1 273 IEGKNDLVVKS---------------QQAVN 288
                     33444444444...............33333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1966.87
//
Query:       EPA04862.1  [L=138]
Description: hypothetical protein BG20_I1938 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.015   15.6   0.2      0.022   15.1   0.2    1.2  1  DUF4352   Domain of unknown function (DUF4352)


Domain annotation for each model (and alignments):
>> DUF4352  Domain of unknown function (DUF4352)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.2   1.2e-06     0.022      28     111 ..      51     128 ..      28     134 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.2e-06
                 S-CEETT-.SEEEEEEEEEEE-SSS-EEEEGGGEEEEETTEEE-BEEESCCCCTTB--EEEE-TT-EEEEEEEEEESTT-CGEE CS
     DUF4352  28 neylqpdaggeflivdvtvkNkgkealtvnssqfkLkdgdgkeydadlsasskaddlflgtlnpGkkvtGklvFdvpkgkkkle 111
                 n+ l+  +g     ++vtvkN+++ a t+   +  ++++    +d+++s+ ++ +     ++++ ++ + +++F +p+ + +l+
  EPA04862.1  51 NTVLN-TSGSNAISATVTVKNIDSVAHTYRICM--IVKAGALISDTSGSGADCSN---TASISASNTGSTTITFAIPRTTNNLS 128
                 44554.478888999**************6554..45567799******999997...59******************999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       754  (0.0420548); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 882.89
//
Query:       EPA04863.1  [L=146]
Description: hypothetical protein BG20_I1937 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.07   13.7   0.0        0.1   13.1   0.0    1.3  1  Sar8_2    Sar8.2 family
       0.21   12.0   0.0       0.31   11.4   0.0    1.3  1  DciA      Dna[CI] antecedent, DciA


Domain annotation for each model (and alignments):
>> Sar8_2  Sar8.2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.2e-05       0.1      13      46 ..      13      46 ..       2      67 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.2e-05
      Sar8_2 13 lailllvissqadaremskaaapitqamnsnnis 46
                +ail++ ++s + a e s aa pi  +m s+  +
  EPA04863.1 13 FAILVIAVTSGIFAEEFSFAAKPILDDMSSEFFT 46
                69***************************98776 PP

>> DciA  Dna[CI] antecedent, DciA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   3.5e-05      0.31      50      85 ..      15      50 ..       5      57 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.5e-05
        DciA 50 tLvvevesgawateLryqkpqllerlneelgeeavr 85
                 Lv++v+sg  a e +++++ +l+ +++e+  + v+
  EPA04863.1 15 ILVIAVTSGIFAEEFSFAAKPILDDMSSEFFTPTVG 50
                59************************9999776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 937.92
//
Query:       EPA04864.1  [L=133]
Description: hypothetical protein BG20_I1934 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.37s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 752.22
//
Query:       EPA04865.1  [L=95]
Description: hypothetical protein BG20_I1939 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.017   14.6   0.5        3.3    7.3   0.0    2.2  2  DNA_gyraseA_C  DNA gyrase C-terminal domain, beta-propeller
      0.094   12.7   2.1       0.15   12.1   2.1    1.3  1  DUF3185        Protein of unknown function (DUF3185)
       0.18   12.3   2.6       0.24   11.9   2.6    1.1  1  DUF4179        Domain of unknown function (DUF4179)


Domain annotation for each model (and alignments):
>> DNA_gyraseA_C  DNA gyrase C-terminal domain, beta-propeller
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0   0.00056       3.3       3      15 ..      15      27 ..      14      31 .. 0.87
   2 ?    5.8   0.2    0.0016       9.7      25      44 ..      44      63 ..      33      66 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00056
                   EEEEETTSEEEEE CS
  DNA_gyraseA_C  3 llliTsnGyvkrf 15
                   ++++T+ Gy+k +
     EPA04865.1 15 VVMFTNEGYGKSL 27
                   79********976 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0016
                   TTSCTEEGSETTTTSSEEEE CS
  DNA_gyraseA_C 25 RgakGvkgiklkegdklvsv 44
                    ++kG++g++l     ++sv
     EPA04865.1 44 STTKGIIGMNLGTSAGITSV 63
                   579*******9655555555 PP

>> DUF3185  Protein of unknown function (DUF3185)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   2.1   2.6e-05      0.15       3      57 ..       3      64 ..       2      65 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.6e-05
     DUF3185  3 iGiiLlvaGivLlvf....GynasdSlgsqvseaft...GsttdktlllligGgvaaivGlv 57
                iGi ++ +Gi+ +v+    Gy  s + + +v + +t    ++t k+++ + +G  a i+ ++
  EPA04865.1  3 IGILFVLVGIFAVVMftneGYGKSLTTSPNVNKIGTlkvNDSTTKGIIGMNLGTSAGITSVT 64
                8**********99977777*****************99999************999998875 PP

>> DUF4179  Domain of unknown function (DUF4179)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   2.6   4.1e-05      0.24      13      87 ..       6      83 ..       2      84 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.1e-05
                XXXXXXXXXXXXXXXXXXXXXX...--SS-HHHHT--SS-.HHHHSEEEEEEEEETTEEEEEEEEEE-SSEEEEEEEE CS
     DUF4179 13 aaalvllllssrllspalAsal.n.pvigslfeklsdskg.eqeyvkpvnksaednGitvtvnevvaDgnklivsysv 87
                  +lv ++++++++++ + + l   p ++++ ++  ++ + +  ++ +++ sa    +t+t n vva + ++ +++++
  EPA04865.1  6 LFVLVGIFAVVMFTNEGYGKSLtTsPNVNKIGTLKVNDSTtKGIIGMNLGTSAGITSVTITFNSVVAKNDNVNIFFMI 83
                56778889999********999967888888887744444366677779*************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       714  (0.0398237); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 674.17
//
Query:       EPA04866.1  [L=230]
Description: DSBA-like thioredoxin domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.1e-34  118.5   0.0    3.8e-34  118.2   0.0    1.1  1  Thioredoxin_4  Thioredoxin
    4.2e-12   46.2   0.0    8.1e-11   42.0   0.0    2.1  1  DSBA           DSBA-like thioredoxin domain
    6.9e-09   36.1   0.0      1e-08   35.6   0.0    1.3  1  Thioredoxin_2  Thioredoxin-like domain
     0.0069   16.1   0.0      0.011   15.4   0.0    1.3  1  Thioredoxin_5  Thioredoxin
  ------ inclusion threshold ------
      0.029   14.7   0.1        8.3    6.8   0.0    2.4  2  Thioredoxin_8  Thioredoxin-like


Domain annotation for each model (and alignments):
>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.2   0.0   1.1e-37   3.8e-34       2     166 .]      53     227 ..      52     227 .. 0.91

  Alignments for each domain:
  == domain 1  score: 118.2 bits;  conditional E-value: 1.1e-37
                    SSSSEEES-TT-SEEEEEEE-TT-HHHHHHHHHHH.HHHHHHHHTTSEEEEEEE-..---STTTHHHHHHHTT--TTHHHHHHHHHHHHTHHHHTT CS
  Thioredoxin_4   2 tetdiviGnpdApvtvieyedlrCphCakfeeeve.klleeyidtGkvkfiirdfpldkekeslkaamaarcageespeaflaikallysqqeewa 96 
                    t++++v+G+++Ap+t+ie+ d++Cp C k++++++  + ++yi+tGkvk+i+ dfp+ +   s++a   + ca e++   ++ ++++ly++q + +
     EPA04866.1  53 TKGSPVLGESSAPITIIEFGDYQCPFCQKWNQNTKpLIDRDYISTGKVKLIYVDFPIVGPD-SINAHAGSYCADEQG--LYWQYHDFLYKNQGHEN 145
                    67899******************************56889******************998.**************9..****************9 PP

                    S-...HHHHH..........HHHHHTS-------HHHHHHHHHHHHHHT--SS-EEEE...TTEE..E-TT--HHHHHHHHT- CS
  Thioredoxin_4  97 es...lkelaae.....aldkdekfeacleeekldalveaeskeakkagiestPtfii...ngek..veepqtyeelkalida 166
                         +++l+ +     ++ +   f++c++++k+ + v+++++ a k+g +stP+fi+   ng+   ++++q+y+ +k+ id+
     EPA04866.1 146 SGwvsMNNLK-NivsgmEGIDVNLFSNCIDSGKYNDRVKENKNIAVKNGAKSTPSFIVigpNGHGvaISGAQPYSVFKQTIDE 227
                    9976633333.2455568999999**********************************9**88874579************95 PP

>> DSBA  DSBA-like thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0   0.0   2.3e-14   8.1e-11       1     192 [.      67     225 ..      67     226 .. 0.88

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 2.3e-14
                 EEEEEEBTTBHHHHHHHHHHHHHHHHC....CTEEEEEEE-SSSCHHHHCT.S.GGGSHHHHHHHHHHHHHHHHHHT....GGSSHHHHHHHHHHHHHH CS
        DSBA   1 tvdeffDvlCPyCylgkerleklaars....pdvkvvlrpfelagakkasgnvgpselpeklkylledlkrlaeaegiplrfpkdklknstraarllla 95 
                 t++ef D++CP+C   +++ + l+ r+     +vk+ + +f++ g                                           +s +a++  + 
  EPA04866.1  67 TIIEFGDYQCPFCQKWNQNTKPLIDRDyistGKVKLIYVDFPIVGP------------------------------------------DSINAHAGSYC 123
                 799**********************999**777*************..........................................*********** PP

                 HHHHHGHHHHHHHHHHHHHTSSS-TSSHHHHHHHHH.HTTS.HHHHHHHHTSHHHHHHHHHHHHHHHHTT-SSSSEEEE...TTC.EEEESSSSHHHHH CS
        DSBA  96 agaeglaekvvrelfealwsegqaitddqellevae.kaGldaeeldealeseavkeavrentaaaqslgvtGvPtvvv...dgk.rmvfGadrldtla 189
                 a ++gl+ ++   l++    e+    + ++l+ +++   G+d++ +   ++s+++++ v+en + a++ g+  +P ++v   +g+ ++++Ga+++  ++
  EPA04866.1 124 ADEQGLYWQYHDFLYKNQGHENSGWVSMNNLKNIVSgMEGIDVNLFSNCIDSGKYNDRVKENKNIAVKNGAKSTPSFIVigpNGHgVAISGAQPYSVFK 222
                 ****97666666666655555555555566888876156****************************************99877789*********999 PP

                 HHH CS
        DSBA 190 dal 192
                 + +
  EPA04866.1 223 QTI 225
                 877 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.0   2.9e-12     1e-08       8     107 ..      67     223 ..      61     225 .. 0.92

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 2.9e-12
  Thioredoxin_2   8 vlvvftdpdCpyCkklkkelkel........ddvtvrvllfp.lkpsfepkavaiwcakekkkafkd............................. 65 
                    +++ f d +Cp+C+k ++++k+l         +v+ ++++fp ++p++  +++  +ca+e+   ++                              
     EPA04866.1  67 TIIEFGDYQCPFCQKWNQNTKPLidrdyistGKVKLIYVDFPiVGPDSINAHAGSYCADEQGLYWQYhdflyknqghensgwvsmnnlknivsgme 162
                    78889************************9999*****************************9999999999************************ PP

  Thioredoxin_2  66 ...................ieenvelarkygvrgtPtivfldgk.eivarlpGyvpaeelea 107
                                       ++en+  a k g ++tP+++++ ++   v  + G+ p   +++
     EPA04866.1 163 gidvnlfsncidsgkyndrVKENKNIAVKNGAKSTPSFIVIGPNgHGV-AISGAQPYSVFKQ 223
                    *************************************99988885444.6699988777766 PP

>> Thioredoxin_5  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   3.1e-06     0.011     114     186 .]     152     223 ..     135     223 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.1e-06
  Thioredoxin_5 114 ellleiaeka.glDveefkeDlesklakkafqcDlklakemgvtevPtlvffneneeeeglkveglksyevyee 186
                    + l++i++ + g+Dv+ f + + s   ++  ++  ++a   g +++P++++     +++g+ ++g ++y+v+++
     EPA04866.1 152 NNLKNIVSGMeGIDVNLFSNCIDSGKYNDRVKENKNIAVKNGAKSTPSFIVIG--PNGHGVAISGAQPYSVFKQ 223
                    556666665549****************************************9..999************9986 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0    0.0023       8.3       3      42 ..      66     106 ..      65     142 .. 0.85
   2 ?    5.4   0.0    0.0063        23      69      93 ..     183     207 ..     164     208 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0023
                    EEEEEE--SSSHHHHHHHHHHHHHHHHHHH.TTSEEEEEEE CS
  Thioredoxin_8   3 vvlLyfgaswcppckaftpklkelyeklkk.kkkveivyvs 42 
                    ++++ fg+++cp c++ +++ k l ++      kv+++yv 
     EPA04866.1  66 ITIIEFGDYQCPFCQKWNQNTKPLIDRDYIsTGKVKLIYVD 106
                    68899***************998754443348999999997 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0063
                    T-HHHHTT-S--TT-SEEEEE-TT- CS
  Thioredoxin_8  69 kkrnklkkkynvkaiPtlvvldkng 93 
                    k+++ ++ k + k+ P+++v+++ng
     EPA04866.1 183 KENKNIAVKNGAKSTPSFIVIGPNG 207
                    45778888889999**********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       822  (0.0458475); expected 358.6 (0.02)
Passed bias filter:                      650  (0.0362541); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 1430.83
//
Query:       EPA04867.1  [L=39]
Description: hypothetical protein BG20_I1933 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.48
# Mc/sec: 246.14
//
Query:       EPA04868.1  [L=274]
Description: signal peptidase I [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-09   37.2   0.4    3.8e-09   36.4   0.4    1.4  1  Peptidase_S24  Peptidase S24-like
  ------ inclusion threshold ------
      0.014   14.7   1.3       0.02   14.1   0.6    1.7  1  Pho88          Phosphate transport (Pho88)
       0.15   12.8   0.2       0.15   12.8   0.2    3.4  3  DUF4282        Domain of unknown function (DUF4282)
       0.15   11.5  11.4       0.81    9.1   0.2    2.3  2  DUF1129        Protein of unknown function (DUF1129)
       0.17   12.3   5.6        5.2    7.6   1.7    2.5  2  DUF202         Domain of unknown function (DUF202)
        2.2    8.6  13.3        4.1    7.7   4.0    2.9  3  TctB           Tripartite tricarboxylate transporter TctB fam


Domain annotation for each model (and alignments):
>> Peptidase_S24  Peptidase S24-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.4   1.3e-12   3.8e-09       4      67 ..      36     100 ..      35     103 .. 0.92

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 1.3e-12
                    SSTTCCTXXTTXEEEEECTS---TTSEEEEEETTCE-EEEEEEEEETTEEEEE.SST.T.STEEEE CS
  Peptidase_S24   4 GdSMeptlldGdlilVdkfsepkrGdivvfrlpgeeeayiKrviglpgdrvllasnn.e.ypplyi 67 
                    G SM  t+++G +i+ ++++++  Gdi++f  ++++   ++r++++++d + ++ +n + ++p  i
     EPA04868.1  36 GQSMHGTIESGTFIIAKPDPQYYIGDIIAFVNEHDR-SVVHRIVEQTDDGFITKGDNnPrNDPKVI 100
                    89*********************************8.*****************988766777665 PP

>> Pho88  Phosphate transport (Pho88)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.6   6.8e-06      0.02       5      65 ..     171     235 ..     167     244 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.8e-06
       Pho88   5 vtnlviilvlmqvskk..idfedpevllyvRilYvvsqliillvylyikskikkkn..Dlttlky 65 
                 v  l+ii + +q++k   i+f+d     ++ +lY++s  i++ v+++i ++ +kk+  D + lk 
  EPA04868.1 171 VLTLMIIGTNIQIAKTinIPFSDYFEPSIANTLYFCSISIVIFVLYLIDHSLDKKKteDSKYLKL 235
                 78899**********955699999999*************************9999888888875 PP

>> DUF4282  Domain of unknown function (DUF4282)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.7       1.1   3.3e+03      18      39 ..       8      29 ..       4      51 .. 0.60
   2 ?   -3.4   9.3       5.6   1.7e+04      11      62 ..      98     166 ..      96     181 .. 0.46
   3 ?   12.8   0.2   5.1e-05      0.15       4      64 ..     191     250 ..     188     252 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.1
     DUF4282 18 ilgivlialvllslivgafaal 39
                i++++li+++++ + v+ + + 
  EPA04868.1  8 IIFLLLIPVLIYLWPVQLYGDT 29
                4556666666665555555544 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 5.6
     DUF4282  11 kllkvlYilgivlialvllslivgafaal.................seslsagggllllllaviafllm 62 
                 k++++  +lg vl ++  ++++   ++++                 +++++ +  + +++++ iaf+++
  EPA04868.1  98 KVIPFDHVLGRVLFVVPYVGFTTLFLQTSvgmsifgililtvfaskKSKQKKLTSFSSVIVFKIAFVAT 166
                 556666666666666655533333333332223333333344444533444444444444444444433 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 5.1e-05
     DUF4282   4 FnrfitpkllkvlYilgivlialvllslivgafaalseslsagggllllllaviafllmil 64 
                 F+ +  p+++ +lY    + i++++l+li  ++++ ++++s   +l++ l+++++ ll+++
  EPA04868.1 191 FSDYFEPSIANTLYFCS-ISIVIFVLYLIDHSLDKKKTEDSKYLKLIFSLAGIMVLLLQLI 250
                 8999999******9765.678899999******************************9987 PP

>> DUF1129  Protein of unknown function (DUF1129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   6.0    0.0047        14     110     171 ..     115     177 ..     112     191 .. 0.66
   2 ?    9.1   0.2   0.00027      0.81     125     175 ..     213     261 ..     193     270 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0047
     DUF1129 110 siGlitlllvalvgGlamvlv.yrlltrekkkkkrpplwkrllilllllvvwlvlftlvallp 171
                 ++G++tl+l + vg  ++ ++  +++  +k+k+k+   + ++++  +++v+ +v ++l+ ++ 
  EPA04868.1 115 YVGFTTLFLQTSVGMSIFGILiLTVFASKKSKQKKLTSFSSVIVFKIAFVATVVNYVLTLMII 177
                 589****99877777777665055555546666666666677777777777777777777743 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00027
     DUF1129 125 lamvlvyrlltrekkkkkrpplwkrllilllllvvwlvlftlvallpaviN 175
                 ++++l+ + l+  kkk++  + +k ++ l++++v++l l+++v+ +p + N
  EPA04868.1 213 FVLYLIDHSLD--KKKTEDSKYLKLIFSLAGIMVLLLQLISIVNTIPFFSN 261
                 23333444443..7999999*************************998766 PP

>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   1.7    0.0018       5.2      13      56 ..     122     167 ..     119     181 .. 0.62
   2 ?    6.0   0.1    0.0056        17      17      62 ..     207     252 ..     202     256 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0018
      DUF202  13 WlRtslalialglallrffl.....tgepsalgkilglilivlgiltll 56 
                 +l ts+++ ++g+++l +f      +   ++l++  ++i + +++++ +
  EPA04868.1 122 FLQTSVGMSIFGILILTVFAskkskQ---KKLTSFSSVIVFKIAFVATV 167
                 689**************999553332...22333333333333333322 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0056
      DUF202  17 slalialglallrffltgepsalgkilglilivlgiltllvglvry 62 
                 s++++++ l l+   l++ ++  +k l li+ ++gi++ll+ l++ 
  EPA04868.1 207 SISIVIFVLYLIDHSLDKKKTEDSKYLKLIFSLAGIMVLLLQLISI 252
                 6677777777776656666666689***************999876 PP

>> TctB  Tripartite tricarboxylate transporter TctB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1       0.5   1.5e+03     110     124 ..       6      20 ..       2      49 .. 0.71
   2 ?    7.7   4.0    0.0014       4.1      35      89 ..     123     179 ..     102     192 .. 0.62
   3 ?    5.9   0.3    0.0048        14      35      91 ..     206     253 ..     183     272 .. 0.52

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.5
        TctB 110 kalilavvlallvyl 124
                 k++i+ +++++l+yl
  EPA04868.1   6 KIIIFLLLIPVLIYL 20 
                 455555555555554 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0014
        TctB  35 l..gvllallgllllv..aadgekeekearedwrkllklvlallaalllyallleplGf 89 
                 l  +v++ ++g+l+l   a++++k++  + ++  +++ + +a++a ++ y+l+l ++G 
  EPA04868.1 123 LqtSVGMSIFGILILTvfASKKSKQK--KLTSFSSVIVFKIAFVATVVNYVLTLMIIGT 179
                 24589999999555554433333333..333344444355554555555**99999996 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.0048
        TctB  35 lgvllallgllllvaadgekeekearedwrkllklvlallaalllyallleplGfil 91 
                 +++ ++++ +l+l+ ++  +++k++ ++  kl+ + la ++     +lll+ +   +
  EPA04868.1 206 CSISIVIF-VLYLI-DHSLDKKKTEDSKYLKLI-FSLAGIM-----VLLLQLISI-V 253
                 24555555.55556.444444455544444444.3333233.....334444332.2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1033  (0.0576162); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 1563.25
//
Query:       EPA04869.1  [L=130]
Description: hypothetical protein BG20_I1930, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-13   50.6   9.3    2.5e-13   50.4   9.3    1.0  1  EamA             EamA-like transporter family
  ------ inclusion threshold ------
      0.034   14.2   0.7        3.2    7.9   0.1    2.4  2  Insulin_TMD      Insulin receptor trans-membrane segment
      0.042   13.5   5.3      0.053   13.2   5.3    1.2  1  Cation_ATPase_C  Cation transporting ATPase, C-terminus
        4.5    7.4   9.7       0.38   10.8   2.9    2.3  2  DUF3671          Protein of unknown function


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.4   9.3   5.6e-17   2.5e-13       2     113 ..      17     130 .]      16     130 .] 0.90

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 5.6e-17
        EamA   2 lgillallaalfwaiyfvlskil....lrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafllffyalkktsasnasl 96 
                 +g++lal++a++ +++ v+ k l    +++vsp+tl+fv +++ g+++  ++  +     k+++k+wl+l l+g+ + vl+ + +f +lk++sa+na++
  EPA04869.1  17 IGYVLALASAVLASLMHVVPKELldngINNVSPITLAFVIYIVNGLFFTSVSKKSTPIS-KITKKNWLFLSLIGI-AEVLGLITYFFGLKDSSAANAAV 113
                 79********************966666777***********99999966666655555.*************95.888999***************** PP

        EamA  97 itslePvftlilsvlll 113
                 ++s e +f++++++++l
  EPA04869.1 114 LNSSEIIFSIFIAMIIL 130
                 **************997 PP

>> Insulin_TMD  Insulin receptor trans-membrane segment
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0    0.0085        38      20      44 ..      48      72 ..      45      73 .. 0.89
   2 ?    7.9   0.1   0.00071       3.2       1      32 [.      98     129 ..      98     130 .] 0.81

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0085
  Insulin_TMD 20 gPviciillllvigavfvvvkKrQt 44
                  P+ +++++ +v g  f  v K+ t
   EPA04869.1 48 SPITLAFVIYIVNGLFFTSVSKKST 72
                 699999***********99999976 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00071
  Insulin_TMD   1 TYFY.vadyldpsnivkIvigPviciillllvi 32 
                  TYF+ ++d + + n +      +i++i+++++i
   EPA04869.1  98 TYFFgLKD-SSAANAAVLNSSEIIFSIFIAMII 129
                  99994555.6666888888999********998 PP

>> Cation_ATPase_C  Cation transporting ATPase, C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   5.3   1.2e-05     0.053      53     172 ..      16     129 ..       8     130 .] 0.71

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.2e-05
  Cation_ATPase_C  53 ri.liqgllqalvtllvffltlllf...gisekenklssnyaqtmaFitlvlsqifnalnlrsrreslfkfsglfsnkllllaillslllqvli 142
                      +i ++ +l +a+++ l++ ++++     gi++        +  t+aF++ ++  +f + ++++      ++s+++++ +l+l++++++ ++ li
       EPA04869.1  16 NIgYVLALASAVLASLMH-VVPKELldnGINN-------VSPITLAFVIYIVNGLFFTSVSKK----STPISKITKKNWLFLSLIGIAEVLGLI 97 
                      666677777777777777.4444231223333.......458999999999999999999888....34457788888**********999999 PP

  Cation_ATPase_C 143 vyvpglnav..fgtaplsleewlialllalvv 172
                      +y+ gl++    + a l+ +e + ++ +a+++
       EPA04869.1  98 TYFFGLKDSsaANAAVLNSSEIIFSIFIAMII 129
                      99988887633566677777888888777776 PP

>> DUF3671  Protein of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.8      0.15   6.9e+02      81      81 ..      40      40 ..       2      66 .. 0.50
   2 ?   10.8   2.9   8.6e-05      0.38      32     102 ..      69     130 .]      59     130 .] 0.72

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.15
     DUF3671 81 l 81
                l
  EPA04869.1 40 L 40
                1 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 8.6e-05
     DUF3671  32 dkkkfkkkvlkkyglllilpvllpliglivpilfeakskkslkkkelevlatsieklytiffiilvviill 102
                 +k++ + k+ kk  l+l l+ +  ++gli   + + k++        ++++ ++ + + i+f+i++ +i+l
  EPA04869.1  69 KKSTPISKITKKNWLFLSLIGIAEVLGLITYFF-GLKDS--------SAANAAVLNSSEIIFSIFIAMIIL 130
                 5666678899*****************999886.44442........344445556666666666666664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       871  (0.0485805); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 905.40
//
Query:       EPA04870.1  [L=144]
Description: hypothetical protein BG20_I1935 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 967.89
//
Query:       EPA04871.1  [L=64]
Description: hypothetical protein BG20_I2592, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.058   13.9   0.1      0.067   13.7   0.1    1.3  1  DUF3293   Protein of unknown function (DUF3293)


Domain annotation for each model (and alignments):
>> DUF3293  Protein of unknown function (DUF3293)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   3.7e-06     0.067       1      32 [.       6      39 ..       6      60 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.7e-06
     DUF3293  1 iTAwNPasenlsaeeNaaaq..eqLleelkklgl 32
                iTA NP s +++ + N + +  ++L+ +l kl+ 
  EPA04871.1  6 ITATNPDSITAKMAGNVESNkvADLEDQLVKLQK 39
                9***************998833478888877755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       944  (0.0526521); expected 358.6 (0.02)
Passed bias filter:                      605  (0.0337442); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 435.54
//
Query:       EPA04872.1  [L=149]
Description: hypothetical protein BG20_I2591, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       771  (0.043003); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 874.03
//
Query:       EPA04873.1  [L=44]
Description: hypothetical protein BG20_I2391 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0037   17.6   0.1     0.0041   17.4   0.1    1.0  1  zf-C2H2_2  C2H2 type zinc-finger (2 copies)
  ------ inclusion threshold ------
      0.019   13.5   0.0      0.019   13.5   0.0    1.0  1  DUF629     Protein of unknown function (DUF629)
      0.022   15.6   0.4      0.029   15.2   0.4    1.2  1  zf-C2H2_4  C2H2-type zinc finger
      0.031   14.6   0.1      0.037   14.3   0.1    1.1  1  zf-Di19    Drought induced 19 protein (Di19), zinc-binding


Domain annotation for each model (and alignments):
>> zf-C2H2_2  C2H2 type zinc-finger (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   9.1e-07    0.0041       2      29 ..       6      33 ..       4      41 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 9.1e-07
   zf-C2H2_2  2 Clfcekkskeveellehmskkhgffipe 29
                C +c +++++  + l+hm++khgf  p+
  EPA04873.1  6 CAVCGEHFSDDIRFLNHMMDKHGFRNPN 33
                9999999999999999******998875 PP

>> DUF629  Protein of unknown function (DUF629)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   4.3e-06     0.019      58      81 ..       5      28 ..       2      41 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.3e-06
      DUF629 58 vCrtCsekfsdaeeckqHlvqeHv 81
                 C  C e+fsd   +++H++++H 
  EPA04873.1  5 NCAVCGEHFSDDIRFLNHMMDKHG 28
                6**********************7 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.4   6.5e-06     0.029       2      24 .]       5      27 ..       4      27 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 6.5e-06
   zf-C2H2_4  2 kCpiCgksFsskkaLlrHlkthH 24
                 C +Cg+ Fs+  ++l+H+   H
  EPA04873.1  5 NCAVCGEHFSDDIRFLNHMMDKH 27
                5******************9888 PP

>> zf-Di19  Drought induced 19 protein (Di19), zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   8.2e-06     0.037       4      29 ..       5      31 ..       2      34 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.2e-06
     zf-Di19  4 tCPyCgke.ltvkeLveHvedeHrves 29
                +C  Cg++  ++ ++++H++d+H + +
  EPA04873.1  5 NCAVCGEHfSDDIRFLNHMMDKHGFRN 31
                699999973567799999999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 305.23
//
Query:       EPA04874.1  [L=48]
Description: hypothetical protein BG20_I2390 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.089   12.7   0.3      0.097   12.5   0.3    1.0  1  EF-hand_8  EF-hand domain pair


Domain annotation for each model (and alignments):
>> EF-hand_8  EF-hand domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.3   5.4e-06     0.097       6      49 ..       2      44 ..       1      47 [. 0.92

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.4e-06
   EF-hand_8  6 treelrril.rilglkkglseeevdilfrefDtdgdGkisfeEFc 49
                 re l + + + l+++  +se++ ++++ ++D+ +d ++++++ +
  EPA04874.1  2 EREQLTELIqKELKYN--ISEDAKTSVIATVDFLKDEILTLKDIL 44
                6899999999999999..***********************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       943  (0.0525964); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 319.57
//
Query:       EPA04875.1  [L=274]
Description: ABC transporter, ATP-binding protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.7e-19   69.6   0.0    5.7e-19   69.0   0.0    1.2  1  ABC_tran     ABC transporter
      2e-11   43.5   3.4      2e-11   43.5   3.4    2.0  2  RLI          Possible Fer4-like domain in RNase L inhibitor, 
    9.5e-09   34.7  13.4    1.4e-08   34.1   5.3    2.8  3  Fer4         4Fe-4S binding domain
    1.6e-07   31.1  16.5    1.1e-06   28.5   4.5    2.4  2  Fer4_6       4Fe-4S binding domain
    2.1e-06   27.5   2.2    2.1e-06   27.5   2.2    2.4  2  Fer4_2       4Fe-4S binding domain
      6e-06   26.3  12.2    4.9e-05   23.4   1.3    2.3  2  Fer4_10      4Fe-4S dicluster domain
      1e-05   25.6  12.7    1.8e-05   24.8  12.7    1.4  1  Fer4_21      4Fe-4S dicluster domain
    8.8e-05   22.0   1.7     0.0012   18.3   1.7    2.2  1  SMC_N        RecF/RecN/SMC N terminal domain
     0.0001   22.8  11.6    0.00033   21.2  11.9    1.7  2  Fer4_7       4Fe-4S dicluster domain
     0.0014   19.5  10.8     0.0043   18.0   1.6    2.6  2  Fer4_16      4Fe-4S double cluster binding domain
     0.0032   17.6   1.9     0.0032   17.6   1.9    1.8  2  Fer4_9       4Fe-4S dicluster domain
     0.0041   17.0   0.0     0.0089   15.9   0.0    1.7  1  RsgA_GTPase  RsgA GTPase
  ------ inclusion threshold ------
      0.012   16.0   2.6      0.012   16.0   2.6    2.3  2  Fer4_4       4Fe-4S binding domain
      0.021   15.7  15.4      0.045   14.7   5.0    2.3  2  Fer4_3       4Fe-4S binding domain
      0.027   13.7   0.1      0.041   13.1   0.1    1.2  1  RE_XcyI      XcyI restriction endonuclease
      0.036   14.0   0.0      0.083   12.8   0.0    1.6  2  Rad17        Rad17 P-loop domain
      0.054   13.9   0.0        0.1   12.9   0.0    1.5  1  AAA_16       AAA ATPase domain
      0.078   13.5   1.2      0.078   13.5   1.2    2.5  2  Fer4_17      4Fe-4S dicluster domain
      0.084   12.6   0.0       0.17   11.7   0.0    1.4  1  AAA_29       P-loop containing region of AAA domain
      0.086   12.6   4.0        1.6    8.5   1.3    2.4  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
      0.092   12.8   1.5       0.22   11.6   1.5    1.9  1  MMR_HSR1     50S ribosome-binding GTPase
       0.16   10.9   0.0       0.34    9.9   0.0    1.5  1  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
       0.88   10.1   8.9       0.28   11.6   1.7    1.8  2  Fer4_8       4Fe-4S dicluster domain
        7.6    7.3  11.6        1.9    9.3   3.7    2.8  1  Fer4_15      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.0   0.0   7.7e-22   5.7e-19       9     136 ..      98     241 ..      96     242 .. 0.75

  Alignments for each domain:
  == domain 1  score: 69.0 bits;  conditional E-value: 7.7e-22
                 ETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEE...........EETTCEGGG..B-HHHCCHCEEEE-SS....--S-TTSBHHHH.......HHHT CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxx..xxxxxxxxxxxxxxxx....xxxxxxxxxxxx.......xxxx RF
    ABC_tran   9 kegekvaivGenGaGKStLlkllagllkpteGei...........lldgkdlke..qeleslrkeigvlpqe....pqlfpeltvren.......esde 83 
                 ++ge+v+++G+nG GKSt++++l+g+lkp+ G+             + g++lk+  ++++  + + ++ pq+    +q f+              ++de
  EPA04875.1  98 RKGEVVGLLGRNGMGKSTVVNILSGNLKPNLGRYdnppewdeilkYYSGTELKShfEKIKNKQIHASIKPQQvhhvAQAFD------GtgkelieKYDE 190
                 58*******************************988888888887455666665554444444444444555211122222......123345664444 PP

                 C..HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                 x..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  84 e..iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                 +    +++++lgl++  ++++    ++LSgG+ qr+a+a++  k+++++++DEp+
  EPA04875.1 191 RgiSRDLIKELGLENSMEQNL----KELSGGELQRLAIAAVASKDSEFYFFDEPS 241
                 45688999*******999999....*****************************7 PP

>> RLI  Possible Fer4-like domain in RNase L inhibitor, RLI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.5   3.4   2.7e-14     2e-11       2      33 ..       4      32 ..       3      34 .. 0.96
   2 ?   -1.8   0.2         4     3e+03      21      27 ..      58      64 ..      55      69 .. 0.83

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 2.7e-14
                -EEEES---------TTHHHHHTTSEEEESS- CS
         RLI  2 rlAivdadqCdPKKCtgkkcarfcpvrlvrtg 33
                r+A+ d+d C+PKKC   +c+++cpv  +++g
  EPA04875.1  4 RVAVLDKDLCQPKKCGL-ECIKYCPV--NKSG 32
                9****************.********..**99 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4
                HHHTTSE CS
         RLI 21 carfcpv 27
                c++ cp 
  EPA04875.1 58 CVKVCPF 64
                99***96 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       4.9   3.7e+03       2       8 ..       7      13 ..       6      14 .. 0.83
   2 ?    5.3   0.3     0.024        18      13      21 ..      21      29 ..      20      29 .. 0.91
   3 !   34.1   5.3   1.9e-11   1.4e-08       2      24 .]      46      68 ..      45      68 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 4.9
                EEETTTS CS
        Fer4  2 videekC 8 
                v d+++C
  EPA04875.1  7 VLDKDLC 13
                7899*** PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.024
                HHHHHSTTT CS
        Fer4 13 aCvevCPvg 21
                +C++ CPv+
  EPA04875.1 21 ECIKYCPVN 29
                6******98 PP

  == domain 3  score: 34.1 bits;  conditional E-value: 1.9e-11
                EEETTTSSS-THHHHHSTTTEEE CS
        Fer4  2 videekCigCGaCvevCPvgAIt 24
                +ide+ C gCG+Cv+vCP++AIt
  EPA04875.1 46 QIDENVCNGCGICVKVCPFEAIT 68
                79********************7 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   4.2    0.0034       2.5       5      22 ..       9      29 ..       5      36 .. 0.84
   2 !   28.5   4.5   1.4e-09   1.1e-06       1      24 []      44      67 ..      44      67 .. 0.95

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0034
      Fer4_6  5 dpdkCi..gCgd.CvrvCPeg 22
                d+d+C    Cg  C++ CP +
  EPA04875.1  9 DKDLCQpkKCGLeCIKYCPVN 29
                99***9888*999******74 PP

  == domain 2  score: 28.5 bits;  conditional E-value: 1.4e-09
      Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                +++id++ C+gCg Cv+vCP+ ai
  EPA04875.1 44 KAQIDENVCNGCGICVKVCPFEAI 67
                689******************998 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   1.4     0.069        51       3      21 ..       6      27 ..       4      28 .. 0.76
   2 !   27.5   2.2   2.8e-09   2.1e-06       2      21 ..      44      63 ..      43      64 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.069
      Fer4_2  3 vvvdtdrC.i.gCg.aCvsaCP 21
                +v d d C    Cg  C++ CP
  EPA04875.1  6 AVLDKDLCqPkKCGlECIKYCP 27
                677888885335*99******* PP

  == domain 2  score: 27.5 bits;  conditional E-value: 2.8e-09
      Fer4_2  2 pvvvdtdrCigCgaCvsaCP 21
                ++++d++ C+gCg+Cv++CP
  EPA04875.1 44 KAQIDENVCNGCGICVKVCP 63
                579***************** PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   3.7    0.0038       2.9       3      22 ..       7      29 ..       5      45 .. 0.73
   2 !   23.4   1.3   6.6e-08   4.9e-05       2      24 ..      45      68 ..      44      93 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0038
     Fer4_10  3 vidddtC..irCg.kCvkaCPad 22
                v+d+d C   +Cg +C k CP++
  EPA04875.1  7 VLDKDLCqpKKCGlECIKYCPVN 29
                789999*6669***********2 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 6.6e-08
     Fer4_10  2 vvidddtCirCgkCvkaCPadl.t 24
                ++id++ C +Cg Cvk+CP+ + t
  EPA04875.1 45 AQIDENVCNGCGICVKVCPFEAiT 68
                789*****************7642 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8  12.7   2.4e-08   1.8e-05       1      58 [.       6      68 ..       6      69 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 2.4e-08
     Fer4_21  1 AridedkCi..gCg.kCliaCe..dtshqaieidakt.vlkvvedeCvGCnlCssvCPvedcie 58
                A++d+d C   +Cg +C++ C+  +++ ++i ++++t ++++ e+ C GC +C++vCP  ++i+
  EPA04875.1  6 AVLDKDLCQpkKCGlECIKYCPvnKSGADCIILNEETkKAQIDENVCNGCGICVKVCPF-EAIT 68
                6778888854479845*****7335789***988776156677999************7.8887 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   1.7   1.7e-06    0.0012      17     188 ..      93     261 ..      80     272 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.7e-06
                 EEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEETTSEEEE..EE CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xx RF
       SMC_N  17 tvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrvkrkgesey..ki 113
                 +  +p + ++  ++G+NG GKs +++ ++  L  +  +     + ++++++  ++ ++k+   +i  +n++ +++i+ ++v    +++ +   e   k 
  EPA04875.1  93 KLPTPRKGEVVGLLGRNGMGKSTVVNILSGNLKPNLGRYDNPPEWDEILKY-YSGTELKSHFEKI--KNKQIHASIKPQQVHHVAQAFDGTGKELieKY 188
                 46666777888999**********999988888777777778888999998.4444444433333..44444466777776655555554443321145 PP

                 TTEEE-HHHHHHHH..HCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCT CS
                 xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       SMC_N 114 ngkevtkkevsell..esagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksk 188
                 +++ +++  ++el   +s++ + ++LSgGe + +a+a +    + k + +y++De  +  D  ++k va+++++  k
  EPA04875.1 189 DERGISRDLIKELGleNSMEQNLKELSGGELQRLAIAAV----ASKDSEFYFFDEPSSYNDVFQRKSVARVIQSLAK 261
                 5555555555555322344556679*****997777755....778899***********************99876 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   1.3     0.043        32      32      51 ..       7      29 ..       3      30 .. 0.76
   2 !   21.2  11.9   4.4e-07   0.00033       4      52 .]      17      66 ..      12      66 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.043
      Fer4_7 32 eidpekCl..gCga.CvavCPtg 51
                ++d + C+   Cg  C++ CP++
  EPA04875.1  7 VLDKDLCQpkKCGLeCIKYCPVN 29
                56778887557998899999986 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 4.4e-07
      Fer4_7  4 gCg.aCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                +Cg  C ++Cpv+    d    +++t+k++id++ C gCg Cv+vCP++a
  EPA04875.1 17 KCGlECIKYCPVNKSGADCIILNEETKKAQIDENVCNGCGICVKVCPFEA 66
                68889******999999988888899*********************986 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0  11.6   0.00041       0.3       4      66 ..      17      64 ..      13      65 .. 0.69
   2 !   18.0   1.6   5.7e-06    0.0043       2      20 ..      52      70 ..      51      93 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00041
     Fer4_16  4 tCgk.CaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCPa 66
                +Cg  C++ CP+n   ++         ci   ++e+k++++de+ c+      gC+iC++vCP+
  EPA04875.1 17 KCGLeCIKYCPVNKSGAD---------CIIL-NEETKKAQIDENVCN------GCGICVKVCPF 64
                566667777777766666.........4433.455666777777666......**********8 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 5.7e-06
     Fer4_16  2 CgtCgkCaevCPtnaikek 20
                C +Cg C++vCP +ai+  
  EPA04875.1 52 CNGCGICVKVCPFEAITIV 70
                999*********9999855 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8  11.9   6.5e-05     0.049       4      51 .]      17      67 ..      12      67 .. 0.72
   2 !   17.6   1.9   4.3e-06    0.0032       2      24 ..      52      74 ..      51      81 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.5e-05
      Fer4_9  4 gCg.aCveaCpagvvvedaaerkarlraase..eaCigCgaCveaCpkgai 51
                +Cg +C++ Cp +    d+     + ++a+   + C gCg Cv++Cp +ai
  EPA04875.1 17 KCGlECIKYCPVNKSGADCIILNEETKKAQIdeNVCNGCGICVKVCPFEAI 67
                587569****8777777765554444443335578************9876 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 4.3e-06
      Fer4_9  2 CtgCgaCveaCpagvvvedaaer 24
                C+gCg Cv++Cp+++++  + + 
  EPA04875.1 52 CNGCGICVKVCPFEAITIVNLAS 74
                9************9998877665 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.2e-05    0.0089      98     126 ..      99     127 ..      85     177 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.2e-05
                  TTSEEEEECSTTSSHHHHHHHHCTT---- CS
  RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpelelk 126
                  k++++ l+G  G+GKSt++n l ++l+ +
   EPA04875.1  99 KGEVVGLLGRNGMGKSTVVNILSGNLKPN 127
                  678999*****************997655 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   2.8     0.069        51       2      17 .]      11      29 ..      10      30 .. 0.77
   2 ?   16.0   2.6   1.6e-05     0.012       2      16 ..      50      64 ..      49      68 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.069
      Fer4_4  2 erCi..gCg.sCvaaCPqg 17
                + C+   Cg  C+ +CP++
  EPA04875.1 11 DLCQpkKCGlECIKYCPVN 29
                66766689956******75 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1.6e-05
      Fer4_4  2 erCigCgsCvaaCPq 16
                + C+gCg Cv +CP+
  EPA04875.1 50 NVCNGCGICVKVCPF 64
                57************7 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   2.7     0.027        20       3      14 ..      17      29 ..      12      31 .. 0.80
   2 ?   14.7   5.0     6e-05     0.045       1      15 []      52      66 ..      52      66 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.027
      Fer4_3  3 gCg.aCvevCPvg 14
                 Cg  C + CPv+
  EPA04875.1 17 KCGlECIKYCPVN 29
                59966******96 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 6e-05
      Fer4_3  1 CtgCgaCvevCPvgA 15
                C+gCg Cv+vCP  A
  EPA04875.1 52 CNGCGICVKVCPFEA 66
                ************765 PP

>> RE_XcyI  XcyI restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   5.5e-05     0.041      81     144 ..     142     205 ..     139     229 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.5e-05
     RE_XcyI  81 elyrgdkglgkfkklekkGkiakasepeiedlvvaliesaeklldslekdsiteellddltllt 144
                 ++y g +   +f+k+ +k   a+ + ++++ +  a+  +++ l++  +   i+++l+++l l  
  EPA04875.1 142 KYYSGTELKSHFEKIKNKQIHASIKPQQVHHVAQAFDGTGKELIEKYDERGISRDLIKELGLEN 205
                 6888888889*******9999999999*********************************9854 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00011     0.083      46      98 ..     101     155 ..      89     174 .. 0.80
   2 ?   -2.6   0.0       5.9   4.4e+03      85     123 ..     217     257 ..     195     270 .. 0.47

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00011
       Rad17  46 riLLisGPsGCgkstvvkvLskelgiklrewlnpvslkepdn..qksdfkgltek 98 
                 +++ + G  G gkstvv++Ls +l ++l  + np +  e       +++k+ +ek
  EPA04875.1 101 EVVGLLGRNGMGKSTVVNILSGNLKPNLGRYDNPPEWDEILKyySGTELKSHFEK 155
                 46778899**************************987775433466777777766 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 5.9
       Rad17  85 pdnqksdfkgltekesrf..lsqiesfkeleLkdakylklq 123
                  + q+  + ++  k+s+f       s++++  +++   ++q
  EPA04875.1 217 GELQRLAIAAVASKDSEFyfFDEPSSYNDVFQRKSVARVIQ 257
                 44444444444444444433344444444444444444444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00014       0.1      24      88 ..      99     168 ..      89     261 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00014
      AAA_16  24 p.elvllsGesGvGKsslvrellralekd......................ggiflrgkcdqlesaipysalaqalareellrqllde 88 
                   e+v l G  G+GKs++v+ l   l+ +                      + +f + k++q                    + ++ +
  EPA04875.1  99 KgEVVGLLGRNGMGKSTVVNILSGNLKPNlgrydnppewdeilkyysgtelKSHFEKIKNKQI------------------HASIKPQ 168
                 338999**************9999999996555555555555555444444333333333333..................2222222 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4  10.0     0.076        57      44      57 ..      50      63 ..      13      65 .. 0.66
   2 ?   13.5   1.2    0.0001     0.078       2      17 ..      52      67 ..      51      83 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.076
     Fer4_17 44 slCieCgeCerkCP 57
                + C++Cg C+++CP
  EPA04875.1 50 NVCNGCGICVKVCP 63
                55666666666666 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.0001
     Fer4_17  2 CiqCgyClpeCpsyea 17
                C++Cg C+++Cp+ ++
  EPA04875.1 52 CNGCGICVKVCPFEAI 67
                9999999999998765 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00023      0.17      18      39 ..      95     117 ..      87     130 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00023
      AAA_29  18 eidlkg.atlltGpsGsGKSTll 39 
                 +  +kg ++ l G++G GKST++
  EPA04875.1  95 PTPRKGeVVGLLGRNGMGKSTVV 117
                 55667778899**********98 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   1.3    0.0021       1.6       2      48 ..     103     140 ..     102     161 .. 0.72
   2 ?    5.3   0.2      0.02        15     169     268 ..     178     242 ..     124     261 .. 0.58

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0021
      AAA_21   2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipsl 48 
                  +l G+Ng GKS++  +l++         +l+++l+++ ++++++  
  EPA04875.1 103 VGLLGRNGMGKSTVVNILSG---------NLKPNLGRYDNPPEWDEI 140
                 689***************64.........455555555555555544 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.02
      AAA_21 169 lnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpE 267
                     ++++ +++e+++ ++l+++l l ++                                 e ++ elS G ++    ++a+++ ++   ++++DEp 
  EPA04875.1 178 DGTGKELIEKYDERGISRDLIKELGLENS--------------------------------MEQNLKELSGGELQR-LAIAAVASKDS--EFYFFDEPS 241
                 34444444444444444444444333333................................334556889999999.55556665555..999***996 PP

      AAA_21 268 n 268
                 +
  EPA04875.1 242 S 242
                 6 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.5    0.0003      0.22       2      23 ..     103     125 ..     102     272 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0003
                 EEEEESTTSSHHHHHHHHHTS.T CS
    MMR_HSR1   2 vaivGrpNvGKStLinaltge.k 23 
                 v+++Gr   GKSt++n l+g+ k
  EPA04875.1 103 VGLLGRNGMGKSTVVNILSGNlK 125
                 89****************98532 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00045      0.34      28      53 ..      99     124 ..      81     130 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00045
                 -SEEEEEEE-TTSSHHHHHHHHHHHH CS
        MeaB  28 raqvvGltGvPGaGkstlvealglel 53 
                 + +vvGl G  G Gkst+v+ l  +l
  EPA04875.1  99 KGEVVGLLGRNGMGKSTVVNILSGNL 124
                 5689****************998777 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   9.6    0.0069       5.2       7      63 ..      17      64 ..      13      66 .. 0.84
   2 ?   11.6   1.7   0.00038      0.28       5      17 ..      52      64 ..      48      88 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0069
      Fer4_8  7 eCg.aCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63
                +Cg  C + Cpv ++ ++ +  +++ +++ + +e v         C++cg C++vCp 
  EPA04875.1 17 KCGlECIKYCPVNKSGADCIILNEETKKA-QIDENV---------CNGCGICVKVCPF 64
                58767999999999999998888888888.777777.........***********96 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00038
      Fer4_8  5 CieCgaCqsaCpv 17
                C++Cg C + Cp+
  EPA04875.1 52 CNGCGICVKVCPF 64
                8888888888883 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   3.7    0.0025       1.9       3      19 ..      47      63 ..      45      69 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0025
     Fer4_15  3 vDrdaCigcglCvaeap 19
                +D++ C gcg Cv+++p
  EPA04875.1 47 IDENVCNGCGICVKVCP 63
                8***************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       743  (0.0414412); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.58u 0.34s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 1728.90
//
Query:       EPA04876.1  [L=60]
Description: hypothetical protein BG20_I2031 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.073   13.4   0.0      0.079   13.3   0.0    1.1  1  DUF5638   Family of unknown function (DUF5638)


Domain annotation for each model (and alignments):
>> DUF5638  Family of unknown function (DUF5638)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   4.4e-06     0.079      51      89 ..      21      59 ..      13      60 .] 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.4e-06
                HHHHHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHTTT-- CS
     DUF5638 51 ktkeeiveeYeelvlllsqvkngeisadeAleaiekkte 89
                k++++  e + +lv  lsq+kn  i +++Al++ie+ ++
  EPA04876.1 21 KAQDSGHEYFLKLVGDLSQIKNHPIMIKNALNKIEQFSD 59
                55555556677999********************99776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 415.16
//
Query:       EPA04877.1  [L=95]
Description: hypothetical protein BG20_I2037 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-07   30.2   0.1    4.1e-07   29.7   0.1    1.4  1  DUF5615   Domain of unknown function (DUF5615)
     0.0072   16.4   0.0     0.0074   16.4   0.0    1.1  1  Mut7-C    Mut7-C RNAse domain


Domain annotation for each model (and alignments):
>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.1   4.5e-11   4.1e-07       1      56 [.       5      62 ..       5      78 .. 0.92

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 4.5e-11
     DUF5615  1 mklllDenlsprlvellreaghdvlhvrelgleg...asDeeileyAkeedriivTkDk 56
                mk+l+De  +  + e+l++ g+++ +v++l  +g    +D  ++++Ake+++i+vT+D 
  EPA04877.1  5 MKILIDEM-DDGWDEKLSKMGYEAYSVKKLRTDGhklRTDYSVISFAKENNMILVTRDT 62
                9*****95.669******************99988899********************6 PP

>> Mut7-C  Mut7-C RNAse domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   8.2e-07    0.0074       2      73 ..       6      87 ..       5      95 .] 0.77

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 8.2e-07
      Mut7-C  2 rfllDamlgklakyLRllGydalyasdv........edeellalaakekrillTrdreLlkraklkkg..vlltsrdveeql 73
                ++l+D m     + L  +Gy+a   ++         +d ++++ a++++ il+Trd+e  +  ++++   +ll+++++ + +
  EPA04877.1  6 KILIDEMDDGWDEKLSKMGYEAYSVKKLrtdghklrTDYSVISFAKENNMILVTRDTESGQACEENNLpyILLDNEEIFKIV 87
                677888888888889999***9966666678888989*********************988888777665566666665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 614.17
//
Query:       EPA04878.1  [L=125]
Description: hypothetical protein BG20_I2035 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1127  (0.0628591); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 808.68
//
Query:       EPA04879.1  [L=193]
Description: hypothetical protein BG20_I2028 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00096   19.5   0.2     0.0017   18.7   0.1    1.5  2  Penicillinase_R  Penicillinase repressor
  ------ inclusion threshold ------
      0.045   14.3   0.1       0.15   12.6   0.0    1.8  2  AAA_assoc_C      C-terminal AAA-associated domain


Domain annotation for each model (and alignments):
>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   1.9e-07    0.0017       3      88 ..      12      95 ..      10     115 .. 0.84
   2 ?   -2.9   0.0      0.98   8.8e+03     104     114 ..     148     158 ..     134     172 .. 0.62

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.9e-07
                     -S-SHHHHHHHHHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE----XXXXXXXXXXXXXXXXXXXXX CS
  Penicillinase_R  3 elEaevmeilwekgeatvkevveeleeekelaysTVktllrrLvkKgllsrekegrafiYsplvseeeavasavkqlldklfegsv 88
                     e+E+ ++e++ +  +   + +++ +  e ++a++T   +   L++K+++  +k+g++  Y p+++  +  ++ v+ ++++ f+ ++
       EPA04879.1 12 ERERIILEYIKKYPDKHHNALISMIVPE-CMAKATFEKTRDSLLEKEIIGVQKKGNMKFYFPTLNYPDKFQQHVERITNTSFH-NI 95
                     5688888888888888888888887766.7999*****************************************999999996.44 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.98
                      XXXXXXXXXXX CS
  Penicillinase_R 104 ddleeLrelle 114
                      d+  e+++++ 
       EPA04879.1 148 DEHLEIQQMIH 158
                      44444444443 PP

>> AAA_assoc_C  C-terminal AAA-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.39   3.5e+03      82     101 ..      94     113 ..      79     122 .. 0.60
   2 ?   12.6   0.0   1.7e-05      0.15      33      77 ..     124     168 ..     118     190 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.39
  AAA_assoc_C  82 peerfldeLeeklseeeaer 101
                  + +  l+ Le++++++++++
   EPA04879.1  94 NIKTHLKKLESSYQHKDVNE 113
                  34455667777777666665 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 1.7e-05
  AAA_assoc_C  33 dielTelGrkfveadikerKeifreqllklvplaaairrvLdere 77 
                  d++lT+ G +f++++ + +K + r++ l++ ++++++ +v+++++
   EPA04879.1 124 DLMLTDNGFTFLDSNKNPQKTLYRDEHLEIQQMIHQLFTVVNNDK 168
                  89***************************9999999988876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1100  (0.0613531); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1235.96
//
Query:       EPA04880.1  [L=37]
Description: hypothetical protein BG20_I2030 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.49
# Mc/sec: 225.52
//
Query:       EPA04881.1  [L=119]
Description: hypothetical protein BG20_I2036 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 788.12
//
Query:       EPA04882.1  [L=75]
Description: hypothetical protein BG20_I2029 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.30s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 509.68
//
Query:       EPA04883.1  [L=173]
Description: hypothetical protein BG20_I2038, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0091   16.4   0.9       0.02   15.3   0.8    1.5  1  MitMem_reg     Maintenance of mitochondrial structure and fun
  ------ inclusion threshold ------
       0.11   11.1   2.7       0.22   10.2   0.8    2.1  2  SepSecS        O-phosphoseryl-tRNA(Sec) selenium transferase,
       0.25   11.2   2.8       0.35   10.7   2.7    1.4  1  Mt_ATP-synt_D  ATP synthase D chain, mitochondrial (ATP5H)


Domain annotation for each model (and alignments):
>> MitMem_reg  Maintenance of mitochondrial structure and function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.8   3.4e-06      0.02       4      91 ..      38     138 ..      35     145 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.4e-06
  MitMem_reg   4 eigvehllkpsiqdas.stlstglnrqyyslki.lqerldlikdYlkkveegelpvn............heilrnlqkllnllPhleteelekefnvet 88 
                 eig     k  i+  + s++s+ +n+q++s++  ++++ ++ik++ + +++++++++             + +  ++kll++ P  +++ + +++++++
  EPA04883.1  38 EIGKKMYSKSHIE-YElSNVSEAVNSQLKSVHNeIESIFEEIKEFTELIQQNKIEYQerlritihfihiVQSTDAVMKLLSHYPTFKKDRMFSQITRKI 135
                 5555666665554.4469*************8769***************9984444444444556655678888899999999999999999999999 PP

  MitMem_reg  89 nDv 91 
                 nD+
  EPA04883.1 136 NDC 138
                 997 PP

>> SepSecS  O-phosphoseryl-tRNA(Sec) selenium transferase, SepSecS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.8   3.7e-05      0.22     277     349 ..      39     110 ..      11     122 .. 0.81
   2 ?    0.7   0.0     0.028   1.7e+02     279     311 ..     123     155 ..     117     166 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 3.7e-05
                 HHHHHHHHHHHHHHHHHHHHCCCEEESSSTT-SSEEEEE.-CCCHCCCCTHHHHHHHHHHHTTECSSE.EE-SS CS
     SepSecS 277 lkeqkesfkllreklkklaeeveekllevpeNpissalt.letldeikkkarldlaseLfsrkvtGargvrasd 349
                 + +++ s+++++  l + +e+v+ +l +v +N+i s++  ++ + e  ++++++  ++L    ++ ++ v+++d
  EPA04883.1  39 IGKKMYSKSHIEYELSNVSEAVNSQLKSV-HNEIESIFEeIKEFTELIQQNKIEYQERLRI-TIHFIHIVQSTD 110
                 7899********************99877.****988853788888888888888887754.566666666665 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.028
                 HHHHHHHHHHHHHHHHHHCCCEEESSSTT-SSE CS
     SepSecS 279 eqkesfkllreklkklaeeveekllevpeNpis 311
                 ++  +f+++ +k+++  e++ + ++++pe + +
  EPA04883.1 123 KKDRMFSQITRKINDCWENIMNGIIHQPEEEFL 155
                 56789****************999999998765 PP

>> Mt_ATP-synt_D  ATP synthase D chain, mitochondrial (ATP5H)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   2.7   5.8e-05      0.35      69     116 ..      41      88 ..      26     125 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 5.8e-05
                    HHHHHH--------TTTTHHHHHHHHHHHHCHHHHHHHHHHHHHHHHH CS
  Mt_ATP-synt_D  69 ekkYealkipypedkyteevdaeekevkkeikefkeeskkrieeleke 116
                    +k Y++ +i y+ ++++e+v+++ k v++ei++  ee k+  e ++++
     EPA04883.1  41 KKMYSKSHIEYELSNVSEAVNSQLKSVHNEIESIFEEIKEFTELIQQN 88 
                    5889*********99999999999999999999999888877776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1665  (0.0928663); expected 358.6 (0.02)
Passed bias filter:                      675  (0.0376485); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 1184.90
//
Query:       EPA04884.1  [L=77]
Description: hypothetical protein BG20_I2034 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.1e-06   25.7   0.3     0.0036   17.4   0.0    2.1  2  Ycf66_N          Ycf66 protein N-terminus
     0.0019   18.0   0.8     0.0021   17.8   0.8    1.0  1  Oxidored_q3      NADH-ubiquinone/plastoquinone oxidoreductase
  ------ inclusion threshold ------
      0.042   14.0   0.7      0.055   13.6   0.7    1.3  1  Cytochrom_B561   Eukaryotic cytochrome b561
      0.046   13.7   0.0      0.046   13.7   0.0    2.1  2  FixQ             Cbb3-type cytochrome oxidase component FixQ


Domain annotation for each model (and alignments):
>> Ycf66_N  Ycf66 protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.2    0.0019       8.5       2      24 ..       9      31 ..       7      33 .. 0.88
   2 !   17.4   0.0   8.1e-07    0.0036       2      30 ..      47      75 ..      46      76 .. 0.96

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0019
     Ycf66_N  2 llgivlalaslaLYflrffkPel 24
                + g +++l++l L+ + ++ Pe+
  EPA04884.1  9 IAGGIMVLSGLFLFYVVQITPEI 31
                67889999*************98 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 8.1e-07
     Ycf66_N  2 llgivlalaslaLYflrffkPelardeDi 30
                llg+ + la++ LY+++  +P++++d D+
  EPA04884.1 47 LLGMGVTLAGILLYLINRNQPQIQQDFDV 75
                89************************997 PP

>> Oxidored_q3  NADH-ubiquinone/plastoquinone oxidoreductase chain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.8   4.7e-07    0.0021      42     101 ..       6      68 ..       4      77 .] 0.66

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4.7e-07
                  HHIIIIIHHHH...HHHHHHHSSTTS----TTCHHHHHHHHHHHHHHHHHHHTT--......- CS
  Oxidored_q3  42 ilvYvGAilvl...flFvimllesaeeeepeslsrslalaalligllllalllllllessssa 101
                  +++ +G+i+vl   flF ++ ++ + e  +++++ + ++++ll++ + la +ll+l + ++++
   EPA04884.1   6 VIIIAGGIMVLsglFLFYVVQITPEIEPFFRTMKHAGTFVGLLGMGVTLAGILLYLINRNQPQ 68 
                  8999******65549998888878788888888888777776665555555555444333332 PP

>> Cytochrom_B561  Eukaryotic cytochrome b561
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.7   1.2e-05     0.055      76     127 ..       4      58 ..       2      71 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.2e-05
                     HHHHHHHHHHHHHHHHHHHTSS---HHHHHHHHHH.HH..HHHHHHHHHHHHHHH CS
  Cytochrom_B561  76 GlvtvilfllqlvlGfvlfllpklskklralllpl.Hv..llGlvifvlaivtal 127
                     G+v +i   + +++G++lf++ +++ +++++++ + H+  ++Gl+ + + ++ +l
      EPA04884.1   4 GVVIIIAGGIMVLSGLFLFYVVQITPEIEPFFRTMkHAgtFVGLLGMGVTLAGIL 58 
                     899999999***********************99999633556665555555544 PP

>> FixQ  Cbb3-type cytochrome oxidase component FixQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   4.3      0.71   3.2e+03      13      27 ..      11      25 ..       5      25 .. 0.83
   2 ?   13.7   0.0     1e-05     0.046       3      31 ..      35      63 ..      34      74 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.71
        FixQ 13 wgllflvllfygvvi 27
                 g+++l +lf+ +v+
  EPA04884.1 11 GGIMVLSGLFLFYVV 25
                588999999999996 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 1e-05
        FixQ  3 yealrgfadswgllflvllfygvviyafr 31
                ++++++ + ++gll + ++++g+++y+ +
  EPA04884.1 35 FRTMKHAGTFVGLLGMGVTLAGILLYLIN 63
                57899999******************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       734  (0.0409393); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 514.06
//
Query:       EPA04885.1  [L=80]
Description: hypothetical protein BG20_I2032 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 571.19
//
Query:       EPA04886.1  [L=63]
Description: hypothetical protein BG20_I2033 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.026   15.1   0.7        4.1    8.0   0.0    2.1  2  RPA_interact_C  Replication protein A interacting C-terminal
       0.12   11.9   2.0       0.18   11.4   2.0    1.4  1  TF_Zn_Ribbon    TFIIB zinc-binding


Domain annotation for each model (and alignments):
>> RPA_interact_C  Replication protein A interacting C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0   0.00046       4.1      60      77 ..       3      20 ..       1      24 [. 0.86
   2 ?    6.2   0.1    0.0018        16      12      27 ..      37      53 ..      26      62 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00046
  RPA_interact_C 60 veekegveaLlaeCeeCd 77
                    +++++g+e Lla+C +C 
      EPA04886.1  3 IQNEFGMEPLLASCPNCT 20
                    78999************7 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0018
  RPA_interact_C 12 etsevifCe.Cglrlet 27
                    +++ev+fC+ C++ +++
      EPA04886.1 37 ANKEVLFCKlCKFVVSV 53
                    45699999999998776 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   2.0     2e-05      0.18       3      29 ..      16      51 ..      14      60 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2e-05
                  ETTTTCEEC........HEETSTTCE.EESSSSBEE CS
  TF_Zn_Ribbon  3 CPnCgstnl........veDpergel.vCtdCGlVl 29
                  CPnC  ++l        ++D ++ e+ +C+ C  V+
    EPA04886.1 16 CPNCTRSSLycgkiptaLRDMANKEVlFCKLCKFVV 51
                  ******9977**********9999998*****6555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.32s 00:00:00.76 Elapsed: 00:00:00.49
# Mc/sec: 385.79
//
Query:       EPA04887.1  [L=82]
Description: hypothetical protein BG20_I1305 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.018   14.9   0.0      0.032   14.1   0.0    1.4  1  SWIB      SWIB/MDM2 domain


Domain annotation for each model (and alignments):
>> SWIB  SWIB/MDM2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.8e-06     0.032      10      38 ..      53      81 ..      49      82 .] 0.88

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.8e-06
        SWIB 10 aellgekelsrpevvkklweYIkennLqd 38
                ++++g k +  +e +kk+w+++k++ L +
  EPA04887.1 53 EQVFGNKPIAPSEMTKKIWAFVKAKSLSN 81
                67899999999**************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1676  (0.0934798); expected 358.6 (0.02)
Passed bias filter:                      711  (0.0396564); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 542.28
//
Query:       EPA04888.1  [L=356]
Description: oxidoreductase, zinc-binding dehydrogenase family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.2e-28   97.2   0.1    1.3e-27   96.3   0.1    1.4  1  ADH_zinc_N     Zinc-binding dehydrogenase
    1.5e-21   76.3   0.0    2.6e-21   75.6   0.0    1.4  1  ADH_N          Alcohol dehydrogenase GroES-like domain
      1e-17   65.5   0.1    1.7e-17   64.7   0.1    1.4  1  ADH_zinc_N_2   Zinc-binding dehydrogenase
  ------ inclusion threshold ------
      0.099   12.8   0.1       0.34   11.1   0.1    1.9  1  ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthas


Domain annotation for each model (and alignments):
>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.3   0.1   2.9e-31   1.3e-27       1     123 [.     184     312 ..     184     319 .. 0.86

  Alignments for each domain:
  == domain 1  score: 96.3 bits;  conditional E-value: 2.9e-31
                 HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEEEET......TTC.HHHHHHHHHTT.TSSEEEEEESSCSHHHHHHHHHCEEEEEEEEECSC. CS
  ADH_zinc_N   1 gvGlaavqlAkalGaeviavdsseeklelakklGadeviny......kea.dlverikeltg.gegvdvvfecvGsgatleaalkllkpgGrlvvvGg. 90 
                 gvG++++q+Ak ++++via++s + kl+++k+lGad+++++      ke  ++ ++i++ tg + gvd+ f+++G ++ ++  l+llk+gG+lv +G+ 
  EPA04888.1 184 GVGSFGIQIAKLYNCTVIATASPD-KLDKCKELGADYAVDHrkddwqKEVyKITKEIAAKTGvTPGVDLTFDHIG-QTHFNKQLTLLKYGGTLVSCGAt 280
                 9******************98765.8***************766666666666777777778888**********.**********************7 PP

                 .TSSEEEEEHHHHHHTT-EEEEE-SSCHHHHHHH CS
  ADH_zinc_N  91 .gkgeeefdlrnlllkeksilGsllgslreefke 123
                  g++  ++dlr++++k +++lGs+ g+ + e+ +
  EPA04888.1 281 tGYD-AQIDLRHIFFKGINVLGSTQGT-KAEMDD 312
                 4444.33*******************9.888876 PP

>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.6   0.0   5.7e-25   2.6e-21       1     108 [.      31     140 ..      31     141 .. 0.97

  Alignments for each domain:
  == domain 1  score: 75.6 bits;  conditional E-value: 5.7e-25
                 TTEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHTT-GGG-TTBEETTTS...S-SSSB CS
       ADH_N   1 pgevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCkegeenlCeeakllgvs...ldGgfa 96 
                 p+ev+ k+kaa+++  D++ ++g   +  +lp + G +++G v++vg++vk++kvGdrVv + + sc  C+ C++g+e  C +++++g++   ++G+++
  EPA04888.1  31 PDEVVFKLKAAALNYNDIWGMRG-VPIAIPLPHVSGSDAAGDVVAVGEDVKNIKVGDRVVSHSNLSCRVCKLCTSGREFDCLNRQVWGFQtgpMWGAYS 128
                 689********************.8************************************************************************** PP

                 SEEEECGGGEEE CS
       ADH_N  97 eyvvvpekklvk 108
                 e v +pe ++ k
  EPA04888.1 129 ELVHLPEVNISK 140
                 ******999876 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.7   0.1   3.9e-21   1.7e-17       1     131 [.     215     351 ..     215     353 .. 0.80

  Alignments for each domain:
  == domain 1  score: 64.7 bits;  conditional E-value: 3.9e-21
                   TT-SEEEETTSTTHH..............HHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE----.S-EEE-CHHHCTTT-EEEE--GGG... CS
  ADH_zinc_N_2   1 lGAdevidyrtedfe..............aatggegvDvvldtvggealleaslkvlpggGrlvsiggpplsaallkpakkrkgrsvkyeflfsmka 83 
                   lGAd ++d+r++d++               +t   gvD+ +d +g++++  + l++l+ gG+lvs g++    +  + + + +   +k   ++  ++
    EPA04888.1 215 LGADYAVDHRKDDWQkevykitkeiaaktGVT--PGVDLTFDHIGQTHF-NKQLTLLKYGGTLVSCGAT----TGYDAQIDLRHIFFKGINVLGSTQ 304
                   8*********************9998653333..67*********9999.8888999888*****9963....333333333344444444443455 PP

                   -.-HHHHHHHHHHHHHHH----EEEEEEGGGHHHHHHHHHSS--SSEE CS
  ADH_zinc_N_2  84 saqadileelaalieeGklrpvvdrvfpleeaaeAhrylesgrarGKi 131
                   +  + ++++ + ++ +Gk++  +d+v+++e+aaeAh ++ +g+ +GKi
    EPA04888.1 305 G-TKAEMDDGLYWMGKGKIKAEIDSVYTFEQAAEAHTKMLQGKFFGKI 351
                   5.4555*****************************************9 PP

>> ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   7.7e-05      0.34      48      82 ..     152     186 ..     133     194 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 7.7e-05
                    -GGGHHHHHHHHHHHTTSS-TT-EEEEEEEETTTE CS
  ACP_syn_III_C  48 tsaasiplaLdeaveegklkpgdlvllvgfGaGlt 82 
                     ++ +i+   + +v + k+ pg++vl++g G G+ 
     EPA04888.1 152 AASMTILTSWHMLVGRAKITPGQTVLIMGGGSGVG 186
                    467788889999******************99974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2290.61
//
Query:       EPA04889.1  [L=308]
Description: hypothetical protein BG20_I1283, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0067   16.1   0.1      0.033   13.8   0.1    2.1  3  Glyco_hydro_35  Glycosyl hydrolases family 35
  ------ inclusion threshold ------
      0.023   14.1   0.1      0.059   12.7   0.0    1.7  2  Glyco_hydro_42  Beta-galactosidase
       0.22   11.4   0.0       0.35   10.8   0.0    1.3  1  Suv3_C_1        Suv3 C-terminal domain 1


Domain annotation for each model (and alignments):
>> Glyco_hydro_35  Glycosyl hydrolases family 35
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.1   5.6e-06     0.033      42     100 ..       6      59 ..       1      67 [. 0.80
   2 ?   -1.6   0.0      0.28   1.7e+03     221     262 ..     103     142 ..      82     152 .. 0.70
   3 ?   -3.2   0.0      0.84     5e+03      78      89 ..     271     282 ..     262     304 .. 0.53

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.6e-06
                     EEE--HHHH-SCTTB---SGGG-CHHHHHHHHHCT-EEEEEEES---TTBGGGG--GGG CS
  Glyco_hydro_35  42 etYveWnlhepkegkydfeGaldlekFlklaqeagLyvilRpGpYicaEwdaGGlpaWl 100
                     ++Y++Wn++ep +g++d++ +  l   ++  ++++L v+l  +  i++E+  G +p W+
      EPA04889.1   6 NVYIFWNVVEPVKGEFDWTQSDVL---MSYNKNNDLKVTLYFS-VINGET-LGPFPNWI 59 
                     68****************976555...5556789999999876.599996.89999997 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.28
                     -TTS--EEEEEESS---BTTS--HHHHHHHCCHHHHHHHCCC CS
  Glyco_hydro_35 221 spekPlvvsefwtgwfdewgekkaarsaeelaeevervlakn 262
                     +++ P v +e  tg++d+ +ek+ + +    a+++++vl+kn
      EPA04889.1 103 EQNIP-VYKELFTGVYDKIKEKHPTVKIG-NAFALHNVLNKN 142
                     44555.56899999999999996655544.467777777777 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 0.84
                     EEEEEEES---T CS
  Glyco_hydro_35  78 yvilRpGpYica 89 
                     yvi R + Y+c+
      EPA04889.1 271 YVIERLSHYVCS 282
                     555566666654 PP

>> Glyco_hydro_42  Beta-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   9.9e-06     0.059      33      76 ..      10      59 ..       4      71 .. 0.82
   2 ?   -2.2   0.0      0.34     2e+03     212     235 ..     110     133 ..      94     183 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.9e-06
                    -HHHH-SBTTB---HHHHHHHHHHHCTT-EEEEE-S......TTS--HHH CS
  Glyco_hydro_42 33 aWaklePeegkydFewLdevldllekagikviLatp......taapPaWl 76
                     W+ +eP +g++d++  d +++  +++++kv L  +       +  P+W+
      EPA04889.1 10 FWNVVEPVKGEFDWTQSDVLMSYNKNNDLKVTLYFSvingetLGPFPNWI 59
                    5******************************9976655555334456665 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.34
                     HHHHHHHHHHHHHHSTT-EEE-EE CS
  Glyco_hydro_42 212 lefvkaeaeilreyspdipvttnf 235
                     +e+++  +++++e +p + + + f
      EPA04889.1 110 KELFTGVYDKIKEKHPTVKIGNAF 133
                     344444455555555555554333 PP

>> Suv3_C_1  Suv3 C-terminal domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   5.9e-05      0.35       5      29 ..     142     168 ..     139     172 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5.9e-05
    Suv3_C_1   5 lIqpi..pLSlrdRytFcmAPvntrdp 29 
                  +++i  +LS+ d   F+++Pv+t ++
  EPA04889.1 142 NLEHIvtDLSIGDFVAFSYSPVDTLNE 168
                 68999999***************9766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2338.06
//
Query:       EPA04890.1  [L=162]
Description: hypothetical protein BG20_I1294 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       797  (0.0444531); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 931.35
//
Query:       EPA04891.1  [L=394]
Description: amidohydrolase family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.5e-42  143.9   0.7    8.8e-42  143.6   0.7    1.0  1  Amidohydro_1  Amidohydrolase family
    1.2e-15   58.0   0.0    1.8e-09   37.6   0.0    2.3  3  Amidohydro_3  Amidohydrolase family


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.6   0.7   9.9e-46   8.8e-42       2     343 ..      50     389 ..      49     390 .. 0.89

  Alignments for each domain:
  == domain 1  score: 143.6 bits;  conditional E-value: 9.9e-46
                   EEE-EEEEEEECETTECSSSGHHHHH.................STTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHHHHHHHHHHTSSSEEEEEE CS
  Amidohydro_1   2 vlPGlIDaHvHleqsllrgatledwl.................vppetaaealesgiktalksGtttvadmgattstgiealleaaeelplglrilg 81 
                   ++PG+++ H+H+ +s ++++tl++                   ++++++a  +++ +k +l+ G+tt+ d+++  ++g+++l++ ++e p+   ilg
    EPA04891.1  50 LIPGFVNCHTHIGDSIGKDVTLNSSAekrihpvsgakskilknTDKRYLANFMKTTCKSMLNKGITTFVDFREGGIEGVHLLKQVVSESPIRSIILG 146
                   89*************9999977777788899999******************************************************999999999 PP

                   ESSEGGSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEE.EEEEECGTCCSHHHHHHHHHHHHHHHTTEEEEEETSSCHHHHHHHHHHTTTEEEETTTT CS
  Amidohydro_1  82 gkvsldrgsaetskasreklkagaaetikgkadgvvk.valapheapafsdeelkealkeakkrdlpvaiHaletkgevedaeaafgetiehgthle 177
                           ++ + +++++k ++ + ++i +  + +++  +l+ ++a ++s    +++l+  ++  +  aiH +et   ++ +++  +   +++t+  
    EPA04891.1 147 R------LEYYQGPNEIKKNIPLPTHKIDELTELLTNcDGLGVSGANENS----SAVLNYYSRTTKIRAIHSSETIQSISTSKKITH---KSETIRA 230
                   9......*******************************************....77788888999999****999999843333333...5555555 PP

                   STCCHHTTTHCCEEEHCTCEEEHHHHHHHHHHHHHHCEEHHHHHHHHSEHHHHHHHHHHHHTSCEEEEEECTTSSCCGGHHHHHHHHHHHHHHCCTT CS
  Amidohydro_1 178 vaeslglldeiklilahgvhltpteaellkerlkeagvahcpfsnsilrsgrealrkaldeGvkvglgtDgaasgnslnlleelrlalklqrgllye 274
                     ++   +      l+h+++ +  ++   k+     g++ cp++n +l++g+++++ + ++G ++glgtD + ++ns+++++e+ ++ k+++g +++
    EPA04891.1 231 LKMK---P----HFLVHMTYASSRDLLAAKKI--ARGIVICPRANASLAEGIPDIELMKKSGCIIGLGTD-NVMINSPDMFREMDYLWKITMGIHKK 317
                   5444...3....44888888887755555555..999999******************************.*********************99995 PP

                   TTHCHCHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECC...CT......CGGGTTTCTSEEEEEEEETTEE CS
  Amidohydro_1 275 deegglslkealrmaTingAkalglddkvGsievGkdADlvvvdl...di......laafvglkkdgnvkkvivkGkl 343
                   +    +++ke+l+maT ng k+l+   ++G ie Gk AD +++d    d+       a++v  ++   ++ v+++Gk+
    EPA04891.1 318 R----VDPKEILKMATVNGGKILNK--DIGIIENGKLADCIFLDKhalDLepmhnpHASIVHRASESAIRAVMIGGKI 389
                   4....9******************9..9*****************87722556667********************98 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.7e-07    0.0015       3      44 ..      43      85 ..      41      97 .. 0.68
   2 ?   -2.1   0.0      0.22     2e+03     152     188 ..      92     132 ..      74     135 .. 0.72
   3 !   37.6   0.0     2e-13   1.8e-09     332     472 ..     259     390 ..     187     391 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.7e-07
  Amidohydro_3  3 iDakGrlvlPGFvDsHtHl.agggvnlrllrlpdarvtslegv 44
                  iD++G+l++PGFv  HtH+ ++ g +++l ++ ++r + + g+
    EPA04891.1 43 IDCEGLLLIPGFVNCHTHIgDSIGKDVTLNSSAEKRIHPVSGA 85
                  9*****************7334445555555555555555555 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.22
  Amidohydro_3 152 plareaeaaavaaalaalasyGitsv....eagggnvssld 188
                    +++ ++a+++++  + +  +Git+     e+g ++v+ l+
    EPA04891.1  92 NTDKRYLANFMKTTCKSMLNKGITTFvdfrEGGIEGVHLLK 132
                   34888888889999999999999998887777777777666 PP

  == domain 3  score: 37.6 bits;  conditional E-value: 2e-13
  Amidohydro_3 332 agvqpvfnfedelldsrlgperargstpvkellnagvkvalgsD.apvgpfdpwprigaavmrktrrggevlrpdeelsleealalyTrgpAkalgl 427
                   + ++            r ++  a+g++ + ++++ g  + lg+D   ++++d + +   ++ +++ ++g     +++++  e+l++ T ++ k+l++
    EPA04891.1 259 IVIC-----------PRANASLAEGIPDIELMKKSGCIIGLGTDnVMINSPDMFRE---MDYLWKITMG---IHKKRVDPKEILKMATVNGGKILNK 338
                   3333...........34445677888******************655566655555...5555666555...789********************** PP

  Amidohydro_3 428 edrkGtLevGadADlvvldadpldvdppelaear.........vrltvvdGrvv 472
                   +   G +e G+ AD + ld+ +ld++p+++ +a          +r+++++G+++
    EPA04891.1 339 DI--GIIENGKLADCIFLDKHALDLEPMHNPHASivhrasesaIRAVMIGGKII 390
                   99..************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2703.11
//
Query:       EPA04892.1  [L=222]
Description: tetratricopeptide repeat protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.5e-24   82.7   7.6      2e-07   30.6   0.1    5.7  6  TPR_1            Tetratricopeptide repeat
    2.3e-17   61.6   1.0    0.00054   19.9   0.0    6.1  6  TPR_2            Tetratricopeptide repeat
      5e-17   62.0   0.6    7.1e-06   26.2   0.1    4.1  4  TPR_12           Tetratricopeptide repeat
    1.4e-14   52.9   9.2    6.2e-05   22.9   0.1    6.0  6  TPR_8            Tetratricopeptide repeat
    5.5e-11   41.7   0.3       0.01   15.8   0.0    4.8  5  TPR_7            Tetratricopeptide repeat
    8.9e-10   38.1   0.1       0.01   15.7   0.0    3.9  4  TPR_10           Tetratricopeptide repeat
    3.2e-08   33.7   0.0        1.9    9.5   0.0    5.5  6  TPR_14           Tetratricopeptide repeat
    6.5e-08   33.0   0.3     0.0076   16.7   0.1    3.2  3  TPR_19           Tetratricopeptide repeat
      1e-07   32.1   7.5    0.00044   20.4   0.7    2.4  2  ANAPC3           Anaphase-promoting complex, cyclosome, subun
      5e-07   29.9   0.2        4.4    8.1   0.0    5.2  5  TPR_6            Tetratricopeptide repeat
    7.2e-07   29.7   0.0     0.0065   17.1   0.0    3.1  2  TPR_16           Tetratricopeptide repeat
      1e-06   28.8   0.0       0.16   12.1   0.0    3.0  3  TPR_9            Tetratricopeptide repeat
      1e-06   28.7   4.5       0.13   12.7   0.2    4.3  4  TPR_17           Tetratricopeptide repeat
    7.8e-06   25.5   2.0     0.0029   17.3   0.5    3.9  4  TPR_11           TPR repeat
      1e-05   25.5   7.4     0.0031   17.5   0.4    3.2  3  SRP_TPR_like     Putative TPR-like repeat
    4.8e-05   23.4   4.8        4.9    7.3   0.1    4.5  5  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
    0.00019   21.4   0.1       0.26   11.4   0.0    3.0  3  Phage_Treg       Lactococcus bacteriophage putative transcrip
    0.00055   19.0   1.5     0.0016   17.4   0.3    2.0  2  NARP1            NMDA receptor-regulated protein 1
     0.0017   18.5   0.1        3.6    7.7   0.0    4.1  4  DUF3856          Domain of Unknown Function (DUF3856)
     0.0024   18.3   0.5        1.7    9.1   0.1    2.6  3  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
     0.0044   17.1   3.5      0.014   15.4   0.5    3.0  3  MIT              MIT (microtubule interacting and transport) 
     0.0065   15.7   0.1       0.11   11.7   0.3    2.3  2  TPR_15           Tetratricopeptide repeat
     0.0073   16.3   2.1      0.065   13.2   0.1    2.5  3  DUF4919          Domain of unknown function (DUF4919)
  ------ inclusion threshold ------
       0.69   10.3   6.2        3.1    8.1   0.1    3.2  3  UvsY             Recombination, repair and ssDNA binding prot


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.2      0.44   3.3e+02      14      34 .]       4      24 ..       2      24 .. 0.84
   2 !   15.7   0.0   1.3e-05    0.0094       3      30 ..      27      54 ..      26      58 .. 0.90
   3 !   13.0   0.2   9.6e-05     0.071       2      33 ..      60      91 ..      59      92 .. 0.93
   4 !   21.4   0.0   2.1e-07   0.00016       3      33 ..      95     125 ..      93     126 .. 0.93
   5 !   30.6   0.1   2.6e-10     2e-07       3      32 ..     129     158 ..     128     160 .. 0.95
   6 ?   -1.1   0.1       2.6     2e+03      10      20 ..     170     180 ..     169     181 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.44
                TT-HHHHHHHHHHHHHHSTTH CS
       TPR_1 14 lgkydeAleyyekALelnPnn 34
                 gkyd+ l y++k L  nPn+
  EPA04892.1  4 SGKYDDMLNYCNKLLNNNPND 24
                688888899****99999996 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1.3e-05
                HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
       TPR_1  3 alynlGnayfklgkydeAleyyekALel 30
                al n ++a+ +lgk++e + +++k+L++
  EPA04892.1 27 ALQNSALALIHLGKFEESITFCDKVLKI 54
                6778899*******************98 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 9.6e-05
                HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
       TPR_1  2 kalynlGnayfklgkydeAleyyekALelnPn 33
                +al+n+ + + +l++yde l +++  L l+ +
  EPA04892.1 60 YALKNKIYSLEQLKRYDEVLICCKIILDLDSK 91
                79**********************99999976 PP

  == domain 4  score: 21.4 bits;  conditional E-value: 2.1e-07
                 HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
       TPR_1   3 alynlGnayfklgkydeAleyyekALelnPn 33 
                 +l+ +G+ + +l +++eAle+y+k L++n +
  EPA04892.1  95 TLNSMGLSLNELDRHQEALEFYDKTLTINDK 125
                 7999************************966 PP

  == domain 5  score: 30.6 bits;  conditional E-value: 2.6e-10
                 HHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
       TPR_1   3 alynlGnayfklgkydeAleyyekALelnP 32 
                 al n++  + +lg+y+e +eyy+kAL+++ 
  EPA04892.1 129 ALMNKAISLNHLGNYKESIEYYDKALTIDS 158
                 899*************************97 PP

  == domain 6  score: -1.1 bits;  conditional E-value: 2.6
                 HHHHTT-HHHH CS
       TPR_1  10 ayfklgkydeA 20 
                 ay klg+ d+A
  EPA04892.1 170 AYEKLGMEDDA 180
                 89999998877 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.14   1.1e+02      12      34 .]       2      24 ..       1      24 [. 0.89
   2 !   14.7   0.0   3.2e-05     0.024       3      31 ..      27      55 ..      26      58 .. 0.90
   3 ?    4.1   0.0      0.08        60      10      33 ..      68      91 ..      67      92 .. 0.86
   4 !   10.7   0.0   0.00064      0.48       6      33 ..      98     125 ..      95     126 .. 0.83
   5 !   19.9   0.0   7.3e-07   0.00054       3      31 ..     129     157 ..     128     160 .. 0.90
   6 ?    1.3   0.1      0.63   4.7e+02       6      25 ..     166     185 ..     162     193 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.14
       TPR_2 12 yklgdyeeAleafekAleldPnn 34
                +++g+y++ l++++k l  +Pn+
  EPA04892.1  2 FESGKYDDMLNYCNKLLNNNPND 24
                6789999999***********97 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 3.2e-05
       TPR_2  3 alynlGlayyklgdyeeAleafekAleld 31
                al n +la+++lg++ee + +++k+l++ 
  EPA04892.1 27 ALQNSALALIHLGKFEESITFCDKVLKIM 55
                678889********************986 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.08
       TPR_2 10 ayyklgdyeeAleafekAleldPn 33
                ++++l++y+e l +++  l ld +
  EPA04892.1 68 SLEQLKRYDEVLICCKIILDLDSK 91
                789*********999999988865 PP

  == domain 4  score: 10.7 bits;  conditional E-value: 0.00064
       TPR_2   6 nlGlayyklgdyeeAleafekAleldPn 33 
                  +Gl++ +l++++eAle+++k l ++ +
  EPA04892.1  98 SMGLSLNELDRHQEALEFYDKTLTINDK 125
                 567777789**************99976 PP

  == domain 5  score: 19.9 bits;  conditional E-value: 7.3e-07
       TPR_2   3 alynlGlayyklgdyeeAleafekAleld 31 
                 al+n + ++ +lg+y+e +e+++kAl +d
  EPA04892.1 129 ALMNKAISLNHLGNYKESIEYYDKALTID 157
                 68888999999***************998 PP

  == domain 6  score: 1.3 bits;  conditional E-value: 0.63
       TPR_2   6 nlGlayyklgdyeeAleafe 25 
                 +  +ay+klg  ++A  a +
  EPA04892.1 166 AKSKAYEKLGMEDDAFLAAQ 185
                 66789*****9999976655 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       2.8   2.1e+03      16      31 ..       4      19 ..       2      20 .. 0.85
   2 !   12.4   0.0    0.0002      0.15       5      34 ..      28      56 ..      24      63 .. 0.87
   3 !   18.3   0.1   2.7e-06     0.002      45      74 ..      93     122 ..      58     125 .. 0.67
   4 !   26.2   0.1   9.5e-09   7.1e-06       4      53 ..     128     176 ..     126     181 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 2.8
      TPR_12 16 lgrydeAlellekale 31
                 g+yd+ l +++k l+
  EPA04892.1  4 SGKYDDMLNYCNKLLN 19
                699*******999885 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.0002
      TPR_12  5 alnnlaavlrrlgrydeAlellekaleiar 34
                ++ n a++l +lg+++e++++++k+l i++
  EPA04892.1 28 LQ-NSALALIHLGKFEESITFCDKVLKIMS 56
                45.899********************9985 PP

  == domain 3  score: 18.3 bits;  conditional E-value: 2.7e-06
      TPR_12  45 attlrnLgrlyralgryeeAlelleealai 74 
                  +tl+ +g  + +l+r++eAle++ ++l i
  EPA04892.1  93 TWTLNSMGLSLNELDRHQEALEFYDKTLTI 122
                 378888888888888888888888888876 PP

  == domain 4  score: 26.2 bits;  conditional E-value: 9.5e-09
      TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgr 53 
                 tal n a  l++lg+y e++e+++kal i ++l  + + + + ++  Lg+
  EPA04892.1 128 TALMNKAISLNHLGNYKESIEYYDKALTIDSSLK-EASIAKSKAYEKLGM 176
                 56779*************************8885.558888888888885 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0      0.06        45      13      34 .]       3      24 ..       2      24 .. 0.91
   2 !   14.1   0.0   5.5e-05     0.041       3      30 ..      27      54 ..      26      58 .. 0.93
   3 ?    0.2   0.1       1.5   1.2e+03      11      25 ..      69      83 ..      67      92 .. 0.69
   4 !   10.0   0.0    0.0011      0.83       5      33 ..      97     125 ..      95     126 .. 0.89
   5 !   22.9   0.1   8.3e-08   6.2e-05       3      32 ..     129     158 ..     127     160 .. 0.92
   6 ?    1.4   0.1      0.67     5e+02       6      20 ..     166     180 ..     162     186 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.06
                HTT-HHHHHHHHHHHHHHHHH. CS
       TPR_8 13 klgdyeeAkeyyekaleldpdn 34
                + g+y+ +  y++k l  +p++
  EPA04892.1  3 ESGKYDDMLNYCNKLLNNNPND 24
                579***************9986 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 5.5e-05
                HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
       TPR_8  3 ayynlgsiylklgdyeeAkeyyekalel 30
                a++n +++++ lg++ee++ ++ k+l++
  EPA04892.1 27 ALQNSALALIHLGKFEESITFCDKVLKI 54
                67899*********************98 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 1.5
                HHHTT-HHHHHHHHH CS
       TPR_8 11 ylklgdyeeAkeyye 25
                +++l++y+e   +++
  EPA04892.1 69 LEQLKRYDEVLICCK 83
                789*****9766666 PP

  == domain 4  score: 10.0 bits;  conditional E-value: 0.0011
                 HHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
       TPR_8   5 ynlgsiylklgdyeeAkeyyekaleldpd 33 
                 + +g+ + +l +++eA e+y k l+++ +
  EPA04892.1  97 NSMGLSLNELDRHQEALEFYDKTLTINDK 125
                 678999****************9999876 PP

  == domain 5  score: 22.9 bits;  conditional E-value: 8.3e-08
                 HHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
       TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldp 32 
                 a++n++  +  lg+y+e++eyy kal++d 
  EPA04892.1 129 ALMNKAISLNHLGNYKESIEYYDKALTIDS 158
                 78999999********************96 PP

  == domain 6  score: 1.4 bits;  conditional E-value: 0.67
                 HHHHHHHHTT-HHHH CS
       TPR_8   6 nlgsiylklgdyeeA 20 
                  ++++y+klg  + A
  EPA04892.1 166 AKSKAYEKLGMEDDA 180
                 67899****988877 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.51   3.8e+02      11      34 ..       3      24 ..       2      26 .. 0.82
   2 !    9.7   0.0    0.0012      0.92       1      30 [.      27      56 ..      27      60 .. 0.86
   3 ?   -2.1   0.0       7.3   5.5e+03      11      29 ..      71      89 ..      67      92 .. 0.72
   4 !    8.4   0.0    0.0033       2.5       1      29 [.      95     121 ..      95     128 .. 0.82
   5 !   15.8   0.0   1.3e-05      0.01       4      33 ..     132     161 ..     129     164 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.51
       TPR_7 11 rlGdyeeAielyeqsLaltkdped 34
                + G+y++ + ++ +   l + p+d
  EPA04892.1  3 ESGKYDDMLNYCNK--LLNNNPND 24
                679*********99..77777776 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0012
       TPR_7  1 aLlnLarlysrlGdyeeAielyeqsLaltk 30
                aL n a +   lG++ee i+++ ++L + +
  EPA04892.1 27 ALQNSALALIHLGKFEESITFCDKVLKIMS 56
                6889999999**************997665 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 7.3
       TPR_7 11 rlGdyeeAielyeqsLalt 29
                +l +y+e + +++  L l+
  EPA04892.1 71 QLKRYDEVLICCKIILDLD 89
                6778999888888766665 PP

  == domain 4  score: 8.4 bits;  conditional E-value: 0.0033
       TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLalt 29 
                 +L+ ++    +l +++eA+e+y +   lt
  EPA04892.1  95 TLNSMGLSLNELDRHQEALEFYDK--TLT 121
                 68999999999*************..554 PP

  == domain 5  score: 15.8 bits;  conditional E-value: 1.3e-05
       TPR_7   4 nLarlysrlGdyeeAielyeqsLaltkdpe 33 
                 n a     lG+y+e ie+y ++L ++++  
  EPA04892.1 132 NKAISLNHLGNYKESIEYYDKALTIDSSLK 161
                 556666679************998888765 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.059        44       5      31 ..      28      54 ..      25      55 .. 0.86
   2 ?   -2.7   0.0         8     6e+03      25      36 ..      75      86 ..      71      89 .. 0.69
   3 !   15.7   0.0   1.4e-05      0.01       4      31 ..      95     122 ..      93     125 .. 0.94
   4 !   13.6   0.0   6.2e-05     0.046       3      31 ..     128     156 ..     127     157 .. 0.94

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.059
      TPR_10  5 lnNLanalrqrgrydeAealleealai 31
                l N a al ++g+++e+  +++++l i
  EPA04892.1 28 LQNSALALIHLGKFEESITFCDKVLKI 54
                6666899999*************9987 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 8
      TPR_10 25 leealairrrll 36
                ++e+l +++ +l
  EPA04892.1 75 YDEVLICCKIIL 86
                677888777665 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 1.4e-05
      TPR_10   4 slnNLanalrqrgrydeAealleealai 31 
                 +ln ++  l ++ r++eA+++++++l i
  EPA04892.1  95 TLNSMGLSLNELDRHQEALEFYDKTLTI 122
                 8************************987 PP

  == domain 4  score: 13.6 bits;  conditional E-value: 6.2e-05
      TPR_10   3 sslnNLanalrqrgrydeAealleealai 31 
                 ++l N a+ l ++g+y+e+ +++++al i
  EPA04892.1 128 TALMNKAISLNHLGNYKESIEYYDKALTI 156
                 6899**********************986 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0     0.011       8.6      12      39 ..       2      29 ..       1      34 [. 0.88
   2 ?    4.7   0.0     0.089        67       8      29 ..      32      53 ..      27      59 .. 0.89
   3 ?   -0.2   0.0       3.4   2.5e+03      10      35 ..      68      93 ..      60     100 .. 0.80
   4 ?    5.1   0.0     0.069        51       8      42 ..     100     134 ..      93     136 .. 0.86
   5 !    9.5   0.0    0.0025       1.9       8      31 ..     134     157 ..     128     170 .. 0.84
   6 ?    0.7   0.1       1.7   1.3e+03       9      32 ..     169     192 ..     162     197 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.011
      TPR_14 12 lalGdpdeAiallrralalaPddaeawl 39
                +++G++d+++++++++l  +P+d +a+ 
  EPA04892.1  2 FESGKYDDMLNYCNKLLNNNPNDMVALQ 29
                679********************99986 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.089
      TPR_14  8 aeallalGdpdeAiallrrala 29
                a al +lG+++e+i+ ++++l+
  EPA04892.1 32 ALALIHLGKFEESITFCDKVLK 53
                7799************999987 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 3.4
      TPR_14 10 allalGdpdeAiallrralalaPdda 35
                 l++l ++de + +++ +l+l+ +d 
  EPA04892.1 68 SLEQLKRYDEVLICCKIILDLDSKDT 93
                58999999999999999998876664 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.069
      TPR_14   8 aeallalGdpdeAiallrralalaPddaeawllla 42 
                 +  l +l++++eA++ +++ l  + +d +a++  a
  EPA04892.1 100 GLSLNELDRHQEALEFYDKTLTINDKDTTALMNKA 134
                 6678899***************9999999988765 PP

  == domain 5  score: 9.5 bits;  conditional E-value: 0.0025
      TPR_14   8 aeallalGdpdeAiallrralala 31 
                 a  l +lG+++e+i+++++al  +
  EPA04892.1 134 AISLNHLGNYKESIEYYDKALTID 157
                 77899***************9765 PP

  == domain 6  score: 0.7 bits;  conditional E-value: 1.7
      TPR_14   9 eallalGdpdeAiallrralalaP 32 
                 +a++ lG  d+A  +++ +l+++ 
  EPA04892.1 169 KAYEKLGMEDDAFLAAQGVLDKDM 192
                 79999***9*99988888887765 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   0.00039      0.29       2      54 ..       2      54 ..       1      66 [. 0.89
   2 !   16.7   0.1     1e-05    0.0076       6      52 ..     108     154 ..     103     167 .. 0.91
   3 !    8.5   0.2    0.0038       2.8       5      44 ..     141     180 ..     139     199 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00039
      TPR_19  2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpee 54
                +++g+y++ l++  ++l  +p++  a+ + A al+ lg ++e +  +d++++ 
  EPA04892.1  2 FESGKYDDMLNYCNKLLNNNPNDMVALQNSALALIHLGKFEESITFCDKVLKI 54
                6899*******************************************999876 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 1e-05
      TPR_19   6 dyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalp 52 
                 +++eAl+++ + l+ + k+  a+++ A+ l  lg+++e ++  d+++
  EPA04892.1 108 RHQEALEFYDKTLTINDKDTTALMNKAISLNHLGNYKESIEYYDKAL 154
                 89************************************999888876 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0038
      TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeA 44 
                 g+y e ++++ +al+ d    ea ++  +a+ +lg  d+A
  EPA04892.1 141 GNYKESIEYYDKALTIDSSLKEASIAKSKAYEKLGMEDDA 180
                 89***********************************999 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.7   5.9e-07   0.00044       3      76 ..       5      79 ..       3      83 .. 0.83
   2 !   15.2   1.0   2.5e-05     0.019       3      75 ..     107     180 ..     105     187 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 5.9e-07
                T-HHHHHHHHHHHH.HHH--HHHHHHH...HHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHH CS
      ANAPC3  3 nnyknAiflaerllaaetespedayll...AlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAi 76
                ++y++ + ++++ll   +++p+d  +l   Al+l ++g++++ +++++k  k+ s+++ ++  +  +l +Lk+y+e +
  EPA04892.1  5 GKYDDMLNYCNKLL---NNNPNDMVALqnsALALIHLGKFEESITFCDKVlKIMSSDIYALKNKIYSLEQLKRYDEVL 79
                789***********...8888888887788********************6665555555555557778*******86 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 2.5e-05
                 T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHH CS
      ANAPC3   3 nnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeA 75 
                  ++++A+ ++++ l+ + ++  +++ +A +l ++g+yk+ +e+++ka  ++s+ +++ + + +++ kL+  ++A
  EPA04892.1 107 DRHQEALEFYDKTLTINDKDTTALMNKAISLNHLGNYKESIEYYDKAlTIDSSLKEASIAKSKAYEKLGMEDDA 180
                 589***********999999999999*********************999888889999999999999877776 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.047        35      11      32 ..       2      23 ..       1      24 [. 0.88
   2 ?    3.5   0.0      0.17   1.3e+02       2      28 ..      27      53 ..      26      54 .. 0.89
   3 ?    4.7   0.0     0.073        54       6      26 ..      99     119 ..      98     123 .. 0.89
   4 !    8.1   0.0    0.0059       4.4       2      27 ..     129     154 ..     128     157 .. 0.92
   5 ?    1.2   0.1      0.94     7e+02       8      28 ..     169     189 ..     167     191 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.047
                HHHHHHHHHHHHHHHHHHH-TT CS
       TPR_6 11 rklgdtdkAlealerlikeYPd 32
                ++ g++d+ l + ++l+++ P+
  EPA04892.1  2 FESGKYDDMLNYCNKLLNNNPN 23
                56569****************9 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.17
                HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
       TPR_6  2 AlyklalsyrklgdtdkAlealerlik 28
                Al + al+++ lg+ +++++  ++++k
  EPA04892.1 27 ALQNSALALIHLGKFEESITFCDKVLK 53
                77789******99*******9999987 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.073
                 HHHHHHHHHHHHHHHHHHHHH CS
       TPR_6   6 lalsyrklgdtdkAlealerl 26 
                 ++ls+ +l+++++Ale +++ 
  EPA04892.1  99 MGLSLNELDRHQEALEFYDKT 119
                 7999***99*********986 PP

  == domain 4  score: 8.1 bits;  conditional E-value: 0.0059
                 HHHHHHHHHHHHHHHHHHHHHHHHHH CS
       TPR_6   2 AlyklalsyrklgdtdkAlealerli 27 
                 Al++ a s+  lg++ +++e++++ +
  EPA04892.1 129 ALMNKAISLNHLGNYKESIEYYDKAL 154
                 89999******99**********987 PP

  == domain 5  score: 1.2 bits;  conditional E-value: 0.94
                 HHHHHHHHHHHHHHHHHHHHH CS
       TPR_6   8 lsyrklgdtdkAlealerlik 28 
                 ++y+klg  d+A  a + +++
  EPA04892.1 169 KAYEKLGMEDDAFLAAQGVLD 189
                 6899999***99888887776 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0036       2.7       8      62 ..       2      53 ..       2      58 .. 0.93
   2 !   17.1   0.0   8.6e-06    0.0065      11      64 ..     107     157 ..      98     160 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0036
      TPR_16  8 lragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalr 62
                +++g+ydd +++ + +l ++   P +  Al ++++a+ ++g ++e + ++++ l+
  EPA04892.1  2 FESGKYDDMLNYCNKLLNNN---PNDMVALQNSALALIHLGKFEESITFCDKVLK 53
                589*****************...99999********************9999875 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 8.6e-06
      TPR_16  11 gdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraa 64 
                  + ++A++ ++ +l  +     +  Al++++ ++ ++g+++e +++y++al+ +
  EPA04892.1 107 DRHQEALEFYDKTLTIN---DKDTTALMNKAISLNHLGNYKESIEYYDKALTID 157
                 57788888898888888...8899**************************9776 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   0.00029      0.21       8      48 ..       4      44 ..       1      46 [. 0.92
   2 ?    3.1   0.1      0.15   1.1e+02       6      48 ..      70     112 ..      67     113 .. 0.82
   3 !   12.1   0.0   0.00022      0.16       9      66 ..     107     164 ..     101     170 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00029
       TPR_9  8 eedweralavverllllaPddpeerrdRGlllaqlGclsaA 48
                + +++ +l +++ ll  +P+d   +   +l+l +lG +++ 
  EPA04892.1  4 SGKYDDMLNYCNKLLNNNPNDMVALQNSALALIHLGKFEES 44
                568999*******************************9976 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.15
       TPR_9   6 ireedweralavverllllaPddpeerrdRGlllaqlGclsaA 48 
                  + +++++ l ++  +l l+++d   +   Gl l +l++ ++A
  EPA04892.1  70 EQLKRYDEVLICCKIILDLDSKDTWTLNSMGLSLNELDRHQEA 112
                 67899****************9988877777777777777776 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 0.00022
       TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapdae 66 
                 +++++al+ ++  l ++ +d   ++  ++ l +lG++++ ++  + +l ++ +  +a 
  EPA04892.1 107 DRHQEALEFYDKTLTINDKDTTALMNKAISLNHLGNYKESIEYYDKALTIDSSLKEAS 164
                 899******************************************9998777655555 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.2   0.00017      0.13       2      32 ..      14      44 ..      13      46 .. 0.92
   2 ?    4.3   0.0     0.081        61       6      34 .]      86     114 ..      81     114 .. 0.91
   3 !    8.9   0.0    0.0029       2.2       1      33 [.     115     147 ..     115     148 .. 0.93
   4 ?    1.5   0.0      0.66   4.9e+02       1      32 [.     149     180 ..     149     181 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00017
      TPR_17  2 ylkaleldPnnadaynnLAelllknGdlmtA 32
                + k l ++Pn+ +a++n A +l ++G++++ 
  EPA04892.1 14 CNKLLNNNPNDMVALQNSALALIHLGKFEES 44
                889***********************99875 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.081
      TPR_17   6 leldPnnadaynnLAelllknGdlmtArq 34 
                 l+ld ++ + +n ++  l ++ ++++A++
  EPA04892.1  86 LDLDSKDTWTLNSMGLSLNELDRHQEALE 114
                 7899**********************985 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0029
      TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtAr 33 
                 +y k l ++ ++  a+ n+A  l ++G++++ +
  EPA04892.1 115 FYDKTLTINDKDTTALMNKAISLNHLGNYKESI 147
                 599**************************9976 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.66
      TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtA 32 
                 +y kal +d +  +a   + ++++k+G  ++A
  EPA04892.1 149 YYDKALTIDSSLKEASIAKSKAYEKLGMEDDA 180
                 69999999999988888888888888877666 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       4.8   3.6e+03       5      12 ..       2       9 ..       2      24 .. 0.76
   2 ?    2.1   0.0      0.21   1.5e+02       3      23 ..      34      54 ..      32      64 .. 0.71
   3 ?    2.7   0.0      0.14     1e+02       2      33 ..     101     132 ..     100     138 .. 0.81
   4 !   17.3   0.5   3.9e-06    0.0029       7      42 .]     140     175 ..     136     175 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 4.8
      TPR_11  5 yeqGkyee 12
                +e Gky++
  EPA04892.1  2 FESGKYDD 9 
                67899985 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.21
      TPR_11  3 ayyeqGkyeeAieaYkkAlkl 23
                a+  +Gk+ee+i+   k lk+
  EPA04892.1 34 ALIHLGKFEESITFCDKVLKI 54
                66779*******865555555 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.14
      TPR_11   2 dayyeqGkyeeAieaYkkAlkldPdnaeayyn 33 
                   + e+ +  eA+e Y k l ++ ++ +a+ n
  EPA04892.1 101 LSLNELDRHQEALEFYDKTLTINDKDTTALMN 132
                 5677888999********99999888777665 PP

  == domain 4  score: 17.3 bits;  conditional E-value: 3.9e-06
      TPR_11   7 qGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                 +G+y+e+ie Y kAl +d++  ea  +  +ay k+G
  EPA04892.1 140 LGNYKESIEYYDKALTIDSSLKEASIAKSKAYEKLG 175
                 7*********************99999999999998 PP

>> SRP_TPR_like  Putative TPR-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.4   4.1e-06    0.0031      16      65 ..      18      79 ..       3     101 .. 0.65
   2 !    9.7   0.8    0.0011      0.81       4      42 ..     115     155 ..      85     176 .. 0.57
   3 !    9.2   1.7    0.0016       1.2       4      47 ..     115     160 ..     105     221 .. 0.64

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.1e-06
  SRP_TPR_like 16 lkkf.........kvvaliklekyeeaLkllkkgsalsedvrf...EkaYvlYklkkykkal 65
                  l++           ++ali+l+k+ee++++++k  ++ ++ ++    k Y l +lk+y + l
    EPA04892.1 18 LNNNpndmvalqnSALALIHLGKFEESITFCDKVLKIMSSDIYalkNKIYSLEQLKRYDEVL 79
                  5544555555555799*****************98766665552235667777777777654 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0011
  SRP_TPR_like   4 eyekilrlegkelkkf..kvvaliklekyeeaLkllkkgsa 42 
                    y+k l +++k  +    k+++l +l+ y+e++++ +k+ +
    EPA04892.1 115 FYDKTLTINDKDTTALmnKAISLNHLGNYKESIEYYDKALT 155
                   23444444443333334455555555555555555555543 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0016
  SRP_TPR_like   4 eyekilrlegkelkkf..kvvaliklekyeeaLkllkkgsalsedv 47 
                    y+k l +++k  +    k+++l +l+ y+e++++ +k+ ++++++
    EPA04892.1 115 FYDKTLTINDKDTTALmnKAISLNHLGNYKESIEYYDKALTIDSSL 160
                   4556666655555554667888888888888888888777444433 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.1    0.0069       5.1      15      37 ..       5      27 ..       2      29 .. 0.87
   2 !    6.8   0.0    0.0092       6.9       8      30 ..      32      54 ..      30      63 .. 0.93
   3 ?   -0.8   0.0       2.2   1.7e+03      14      31 ..      72      89 ..      71      92 .. 0.86
   4 ?   -1.2   0.0       2.9   2.2e+03      15      31 ..     107     123 ..     105     131 .. 0.79
   5 !    7.3   0.1    0.0065       4.9      13      35 ..     139     161 ..     132     172 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0069
                T-HHHHHHHHHHHHHHTTS-HHH CS
  Fis1_TPR_C 15 geYseArryvdalLeiEPenrQa 37
                g+Y++ ++y++ lL+  P+ + a
  EPA04892.1  5 GKYDDMLNYCNKLLNNNPNDMVA 27
                89****************98755 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0092
                HHHHHHHT-HHHHHHHHHHHHHH CS
  Fis1_TPR_C  8 AlGhyklgeYseArryvdalLei 30
                Al+ + lg+++e+  ++d +L+i
  EPA04892.1 32 ALALIHLGKFEESITFCDKVLKI 54
                8999*****************98 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 2.2
                HT-HHHHHHHHHHHHHHT CS
  Fis1_TPR_C 14 lgeYseArryvdalLeiE 31
                l++Y+e + +++ +L ++
  EPA04892.1 72 LKRYDEVLICCKIILDLD 89
                899*********999875 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 2.9
                 T-HHHHHHHHHHHHHHT CS
  Fis1_TPR_C  15 geYseArryvdalLeiE 31 
                  +++eA+++ d  L i 
  EPA04892.1 107 DRHQEALEFYDKTLTIN 123
                 57899***999999876 PP

  == domain 5  score: 7.3 bits;  conditional E-value: 0.0065
                 HHT-HHHHHHHHHHHHHHTTS-H CS
  Fis1_TPR_C  13 klgeYseArryvdalLeiEPenr 35 
                  lg+Y+e+ +y d  L i+ + +
  EPA04892.1 139 HLGNYKESIEYYDKALTIDSSLK 161
                 59**************9986655 PP

>> Phage_Treg  Lactococcus bacteriophage putative transcription regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0         4     3e+03       9      32 ..      37      58 ..      34      68 .. 0.72
   2 ?    6.4   0.0     0.013       9.5      15      32 ..     109     126 ..     106     129 .. 0.92
   3 !   11.4   0.0   0.00034      0.26       3      30 ..     133     158 ..     131     171 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 4
  Phage_Treg  9 hlGevvyqesvefYkkkLsvqskd 32
                hlG+  + es+ f  k L + s d
  EPA04892.1 37 HLGK--FEESITFCDKVLKIMSSD 58
                5555..478888888888888777 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.013
  Phage_Treg  15 yqesvefYkkkLsvqskd 32 
                 +qe+ efY k L ++ kd
  EPA04892.1 109 HQEALEFYDKTLTINDKD 126
                 59************9998 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00034
  Phage_Treg   3 qekvvthlGevvyqesvefYkkkLsvqs 30 
                 +   ++hlG+  y+es+e+Y k L ++s
  EPA04892.1 133 KAISLNHLGN--YKESIEYYDKALTIDS 158
                 555689***8..9***********9985 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.27     2e+02      18     256 ..       5      55 ..       1      78 [. 0.57
   2 !   17.4   0.3   2.1e-06    0.0016     192     257 ..      93     158 ..      86     181 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.27
                 THHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CHHHHHHHHHT..SSS-HHHHHHHHHHTTTS-TT-SHHHHTHHHH CS
       NARP1  18 gkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpenskYyeglekakklskedeeallalydelaekyprsdaprRlpLdf 116
                 gk                                                                                                 
  EPA04892.1   5 GK------------------------------------------------------------------------------------------------- 6  
                 44................................................................................................. PP

                 --HHHHHHHHHHHHHHHHHCT-TTHHHHHGGGGGGSCHHHHHHHHHHHHHTTTTTSSSSTTGG.GSS----SSHHHHHHHHHHHHHHHHT-SHHHHHHH CS
       NARP1 117 leGeeFkelvdkYlrkaLrkgvPslfanlksLYedkeKvkileelvegyvkslktsgklsesdnedsekepesallwvlyflAqhydklgsrekAleyi 215
                                                                                                            ++  l+y 
  EPA04892.1   7 -------------------------------------------------------------------------------------------YDDMLNYC 14 
                 ...........................................................................................45555555 PP

                 HHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCT CS
       NARP1 216 dkaiehtptlvelyltKarilkhaGdlkkAaevmeearklD 256
                 +k ++++p+ +   ++ a  l h G +++ ++  ++  k+ 
  EPA04892.1  15 NKLLNNNPNDMVALQNSALALIHLGKFEESITFCDKVLKIM 55 
                 55555555555555555555555555555555555544443 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 2.1e-06
                 HHHHHHHHHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTT CS
       NARP1 192 lwvlyflAqhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDl 257
                  w+l+ +    ++l + ++Ale+ dk +  +++ +   ++Ka  l h G+ k+ +e  ++a  +D 
  EPA04892.1  93 TWTLNSMGLSLNELDRHQEALEFYDKTLTINDKDTTALMNKAISLNHLGNYKESIEYYDKALTIDS 158
                 49999999999**************************************************99996 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.064        48      56      83 ..      26      53 ..      14      88 .. 0.85
   2 ?    1.7   0.0      0.33   2.5e+02     104     125 ..      97     118 ..      67     126 .. 0.72
   3 !    7.7   0.0    0.0048       3.6      80     126 ..     111     153 ..      80     161 .. 0.75
   4 ?    1.0   0.0      0.53     4e+02     104     122 ..     165     183 ..     158     196 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.064
                HHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
     DUF3856 56 lchaglsealaklgrydealesadkalr 83
                ++    + al++lg+++e+++  dk l+
  EPA04892.1 26 VALQNSALALIHLGKFEESITFCDKVLK 53
                5555567789999999999999998887 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.33
                 HHHHHHHHHTT-HHHHHHHHHH CS
     DUF3856 104 fsravaleelGrkdealkafrm 125
                  s + +l+el r++eal+ + +
  EPA04892.1  97 NSMGLSLNELDRHQEALEFYDK 118
                 4556677777777777777655 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0048
                 HHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
     DUF3856  80 kalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrma 126
                 +al+++++   +++ +     +a++++a +l+ lG+++e+++++ +a
  EPA04892.1 111 EALEFYDKTLTINDKD----TTALMNKAISLNHLGNYKESIEYYDKA 153
                 4555555554454444....368999**************9999987 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.53
                 HHHHHHHHHTT-HHHHHHH CS
     DUF3856 104 fsravaleelGrkdealka 122
                 + +++a+e+lG +d+a+ a
  EPA04892.1 165 IAKSKAYEKLGMEDDAFLA 183
                 6788999999999999755 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0     0.013       9.5      80     124 ..       2      46 ..       1      57 [. 0.92
   2 ?    4.0   0.0     0.086        64      74     121 ..      30      77 ..      24      86 .. 0.86
   3 !    9.1   0.1    0.0023       1.7      68     121 ..     126     179 ..      97     193 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.013
                      HHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHH CS
  Alkyl_sulf_dimr  80 lkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesat 124
                      +++g+y   ++ +n+l+ ++p++  a +  a al +lg+++es t
       EPA04892.1   2 FESGKYDDMLNYCNKLLNNNPNDMVALQNSALALIHLGKFEESIT 46 
                      57889999999*******************************987 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.086
                      HHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-S CS
  Alkyl_sulf_dimr  74 ekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqae 121
                      + a + +  g+++ +++++++++   +++  a + k+ +leql +  e
       EPA04892.1  30 NSALALIHLGKFEESITFCDKVLKIMSSDIYALKNKIYSLEQLKRYDE 77 
                      56666778899999*****************************98766 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0023
                      SHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-S CS
  Alkyl_sulf_dimr  68 gaekvlekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqae 121
                      +  ++++ka +    g+y+ ++e  +++++ d++ +ea  +k +a+e+lg +  
       EPA04892.1 126 DTTALMNKAISLNHLGNYKESIEYYDKALTIDSSLKEASIAKSKAYEKLGMEDD 179
                      567888899999999**********************************98765 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0         9   6.7e+03      27      53 ..      41      66 ..      38      69 .. 0.62
   2 ?    0.6   0.0      0.83   6.2e+02      19      29 ..     108     118 ..      99     122 .. 0.81
   3 !   15.4   0.5   1.9e-05     0.014       6      32 ..     129     155 ..     126     173 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 9
         MIT 27 YkealelLlqalkekneerrellreki 53
                ++e++  + ++lk   +++  +l++ki
  EPA04892.1 41 FEESITFCDKVLKI-MSSDIYALKNKI 66
                56778888888884.224555566555 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.83
         MIT  19 nyeeAlelYke 29 
                   +eAle Y +
  EPA04892.1 108 RHQEALEFYDK 118
                 579******87 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 1.9e-05
         MIT   6 elvkkAveeDnagnyeeAlelYkeale 32 
                 +l +kA+ +   gny+e +e+Y +al 
  EPA04892.1 129 ALMNKAISLNHLGNYKESIEYYDKALT 155
                 6899*********************96 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.23   1.7e+02     232     276 ..       9      53 ..       5      57 .. 0.83
   2 !   11.7   0.3   0.00014      0.11     110     222 ..      59     166 ..      55     183 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.23
      TPR_15 232 kALeylrkqakenrkdplwllaYADaleqagradeAwrlRrqvwr 276
                   L+y +k +++n++d+  l   A al   g+++e+ +   +v++
  EPA04892.1   9 DMLNYCNKLLNNNPNDMVALQNSALALIHLGKFEESITFCDKVLK 53 
                 56999**************99999999999999999877666665 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00014
      TPR_15 110 prlLssalellerakdydriaellksleeeeaaeqsaafllaraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellkawka 208
                  + L++ +++le++k yd++    k +  ++  +++   l  ++ +  + +++++Al+ y + l+ +++++++  +    l+ lg+++e    ++ + +
  EPA04892.1  59 IYALKNKIYSLEQLKRYDEVLICCKIILDLD--SKDTWTLNSMGLSLNELDRHQEALEFYDKTLTINDKDTTALMNKAISLNHLGNYKE---SIEYYDK 152
                 6788999999999999999999999866554..58888899999999999999999999999999999999998888889999998886...7877777 PP

      TPR_15 209 raesdasLwgplaa 222
                 +   d+sL+++  a
  EPA04892.1 153 ALTIDSSLKEASIA 166
                 77888888887665 PP

>> DUF4919  Domain of unknown function (DUF4919)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.1   8.7e-05     0.065      70     122 ..       4      56 ..       1      61 [. 0.92
   2 ?   -0.2   0.0       1.1   8.5e+02      71     117 ..      73     119 ..      56     125 .. 0.72
   3 ?    1.9   0.2      0.24   1.8e+02      74     120 ..     110     156 ..      89     171 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.7e-05
     DUF4919  70 eeelkeiislaeealkknPfdlkqlnllayaykalgkkeeakiyskrlnkllk 122
                   ++++++++ +++l++nP d+ +l++ a a+ +lgk ee+  + +++ k+++
  EPA04892.1   4 SGKYDDMLNYCNKLLNNNPNDMVALQNSALALIHLGKFEESITFCDKVLKIMS 56 
                 6799***********************************99999999988875 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.1
     DUF4919  71 eelkeiislaeealkknPfdlkqlnllayaykalgkkeeakiyskrl 117
                 + ++e++   + +l+ +  d  +ln +  ++++l++++ea +++++ 
  EPA04892.1  73 KRYDEVLICCKIILDLDSKDTWTLNSMGLSLNELDRHQEALEFYDKT 119
                 55677777777777777788888888888888888888887777765 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.24
     DUF4919  74 keiislaeealkknPfdlkqlnllayaykalgkkeeakiyskrlnkl 120
                 +e++++  + l  n  d ++l++ a+++++lg+ +e+ +y+++   +
  EPA04892.1 110 QEALEFYDKTLTINDKDTTALMNKAISLNHLGNYKESIEYYDKALTI 156
                 56777778888888889999999999999999999999998887665 PP

>> UvsY  Recombination, repair and ssDNA binding protein UvsY
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       9.9   7.4e+03      95     108 ..       7      20 ..       6      33 .. 0.78
   2 ?    8.1   0.1    0.0042       3.1      96     120 ..      42      66 ..      35      75 .. 0.73
   3 ?    2.3   2.0      0.27     2e+02      76     112 ..     185     221 ..     109     222 .] 0.78

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 9.9
                 HHHHHHHHHHHHHH CS
        UvsY  95 idqvldFleealka 108
                 +d++l+++++ l++
  EPA04892.1   7 YDDMLNYCNKLLNN 20 
                 57788999888875 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0042
                 HHHHHHHHHHHHHHHHHHHHHHHHH CS
        UvsY  96 dqvldFleealkaikqrgfsiknai 120
                 ++ + F++++lk++++  +++kn i
  EPA04892.1  42 EESITFCDKVLKIMSSDIYALKNKI 66 
                 4567788888888888888888854 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.27
                 HHHHHTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
        UvsY  76 kvvlaaDeevikidakiqyidqvldFleealkaikqr 112
                 + vl+ D + ik+dak + +    +F+++ ++ ik++
  EPA04892.1 185 QGVLDKDMNQIKLDAKKNKCTVFHQFCQNEFEEIKNQ 221
                 4578888889999999999999999999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       757  (0.0422221); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.55
# Mc/sec: 1207.88
//
Query:       EPA04893.1  [L=47]
Description: hypothetical protein BG20_I1296 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.059   13.4   0.3      0.094   12.8   0.2    1.4  1  VEG       Biofilm formation stimulator VEG


Domain annotation for each model (and alignments):
>> VEG  Biofilm formation stimulator VEG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   5.3e-06     0.094      53      70 ..      25      42 ..      16      43 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.3e-06
         VEG 53 nnkervSysYtDiLtetv 70
                 ++e+vSysY+ +L et+
  EPA04893.1 25 IQQEQVSYSYSKVLNETL 42
                46899*********9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       858  (0.0478554); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 318.28
//
Query:       EPA04894.1  [L=72]
Description: 5-amino-6-(5-phosphoribosylamino)uracil reductase domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.3e-18   65.1   0.0    7.9e-18   65.0   0.0    1.0  1  RibD_C    RibD C-terminal domain


Domain annotation for each model (and alignments):
>> RibD_C  RibD C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.0   0.0   4.4e-22   7.9e-18       1      66 [.       6      70 ..       6      72 .] 0.97

  Alignments for each domain:
  == domain 1  score: 65.0 bits;  conditional E-value: 4.4e-22
                -EEEEEEEEETTSBSSCTTSSGCTSS-HHHHHHHHHHHHTSSEEEEEHHHHHHHT--SS--SSCHS CS
      RibD_C  1 pyvilklavSlDGklaaaggeskwitgeearadvhelraeadailvGrgtvladnpsltvrwvkkr 66
                p+vil +a+S+DGk+a ++g+sk ++++ ++ ++h+lr+++dailvG +tv  d+p ltvr+ k++
  EPA04894.1  6 PHVILSAAISIDGKIASRSGDSK-LSSQIDKVRLHKLRSKVDAILVGKNTVQRDDPLLTVRYTKGK 70
                89*********************.**************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 492.69
//
Query:       EPA04895.1  [L=92]
Description: double-stranded DNA-binding domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.7e-23   83.0   2.2    1.8e-23   82.9   2.2    1.0  1  dsDNA_bind  Double-stranded DNA-binding domain


Domain annotation for each model (and alignments):
>> dsDNA_bind  Double-stranded DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.9   2.2     1e-27   1.8e-23      33     106 ..      16      89 ..       4      92 .] 0.92

  Alignments for each domain:
  == domain 1  score: 82.9 bits;  conditional E-value: 1e-27
                 .S--SSHHHHTTS--HHHHHHHHHHTTT-HHHHHHHHHHHHHHHH--SS-----HHHHHHHHHHHS---XXXXX CS
  dsDNA_bind  33 seeeakqaiLsqiLepeAreRLsrirlvkperaeavenrLiqlaqsGqlrskvteeqLkeLLeqvaekkketki 106
                   +++k++iL+qiL+peAr RL++i++vkpe +e ve++Li +a++G+++s+++++qLk++L ++++ k++ ki
  EPA04895.1  16 DISAQKEQILKQILAPEARMRLNNIKMVKPELSELVEQYLIGIASQGKMNSQINDNQLKQILLSIQQPKRDFKI 89 
                 46899*****************************************************************9999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       728  (0.0406046); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 595.05
//
Query:       EPA04896.1  [L=133]
Description: 6,7-dimethyl-8-ribityllumazine synthase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      3e-26   92.0   0.2    3.4e-26   91.7   0.2    1.0  1  DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase
  ------ inclusion threshold ------
      0.075   12.3   0.0        0.1   11.9   0.0    1.3  1  Metallophos_3  Metallophosphoesterase, calcineurin superfamil


Domain annotation for each model (and alignments):
>> DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.7   0.2   3.8e-30   3.4e-26       9     136 ..       3     124 ..       1     129 [. 0.90

  Alignments for each domain:
  == domain 1  score: 91.7 bits;  conditional E-value: 3.8e-30
                    ESTTHHHHHHHHHHHHHHHHHCTTSSCCEEEEEESSCCCHHHHHHHHCTSTT-.SEEEEEEEEE--SSCHHHHHHHHHHHHHHHHHHHCTS-EEEE CS
  DMRL_synthase   9 arfneeitdkllegaldelkeagvaeenidvvtVPGafElplaakklaesskyldavialGvvirGetphfeyvaeavskglmrvsldtgvPvifg 104
                    ++fnee+t+++l  a++++k  + +     +++VPGa+++p++++ l+++ k +d+v++lG++i+G+t+h+e++a++++++l+++s+++++Pv  g
     EPA04896.1   3 SEFNEEVTSRMLLVAQEKAKIMKLK--INYTCKVPGAYDMPIIVNALLQK-KDVDGVVTLGAIIKGQTKHDELIAHSTARALTELSIKYQKPVSLG 95 
                    89*******************9986..77899*****************5.447****************************************** PP

                    EEEES.SHHCCHHCCTSTCCCHHHHHHHHHHHH CS
  DMRL_synthase 105 vltvd.teeqaleraggkagnkGeeaaeaalem 136
                    +  +  +e  a +r+       +e+a+ea++++
     EPA04896.1  96 ITGPGmQERHAYARI----RPVAERAVEAMVKV 124
                    ****98888899999....45666666666665 PP

>> Metallophos_3  Metallophosphoesterase, calcineurin superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.2e-05       0.1      24      62 ..      44      81 ..      21      96 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.2e-05
                   HHHHHHHH--SEEEEES-----HHHHHHHHHHHHTT--- CS
  Metallophos_3 24 lveviedkdpDllvlvGdlvkaeakadeyesaqeerrep 62
                   +  +++ kd+D +v +G ++k+++k de   a+   r  
     EPA04896.1 44 VNALLQKKDVDGVVTLGAIIKGQTKHDELI-AHSTARAL 81
                   34456778********************99.88877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.52
# Mc/sec: 769.80
//
Query:       EPA04897.1  [L=346]
Description: Sua5/YciO/YrdC/YwlC family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-59  200.3   0.0    2.8e-59  199.6   0.0    1.3  1  Sua5_yciO_yrdC  Telomere recombination
    4.9e-29  101.6   0.0    7.5e-29  101.0   0.0    1.3  1  SUA5            Putative GTP-binding controlling metal-bindin
  ------ inclusion threshold ------
        0.1   12.5   0.6       0.22   11.5   0.2    1.7  2  IL2             Interleukin 2
       0.16   11.8   0.0       0.32   10.8   0.0    1.4  1  Oxidored_q6     NADH ubiquinone oxidoreductase, 20 Kd subunit
       0.24   11.0   2.1       0.62    9.7   0.0    2.8  4  EF-hand_1       EF hand


Domain annotation for each model (and alignments):
>> Sua5_yciO_yrdC  Telomere recombination
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.6   0.0   7.8e-63   2.8e-59       2     179 .]      24     199 ..      23     199 .. 0.98

  Alignments for each domain:
  == domain 1  score: 199.6 bits;  conditional E-value: 7.8e-63
                     HHHTTSEEEEE-SSSEEEEEETTSHHHHHHHHHHHTSHCCC--EEEESSCCCCCCCC-TC--HHHHHHHHCT-SSSCEEEEE..E-TS-HHHHTT CS
  Sua5_yciO_yrdC   2 alrkGgivaiptetvYgLacdatneeaverlreiKgrpsdkplavlvasledlkklaeseveeealkllerfwPGpitlllkrskeklpkevapg 96 
                     +lrkGg+va+ptetvYgL++d  n++a+++++++K+rpsd+pl+ ++++ +d+kk+++ ++++ a kl+e+fwPGp+tl+lk+s+  +pk  ++g
      EPA04897.1  24 ILRKGGLVAFPTETVYGLGADGLNPKAIKKIFQAKNRPSDNPLIFHISNKKDVKKYTK-DIPATAEKLIEKFWPGPLTLILKKSSI-IPKIATGG 116
                     79*******************************************************9.***********************7554.******** PP

                     TTEEEEEE-SSHHHHHHHHHCTS-EEEEES-STTS-S-SSHHHHHHHC-TTSECB-SS---SSS---EEEETTSSTSSECEXX CS
  Sua5_yciO_yrdC  97 lktvGvrlPdtplarlLlealgeplvaTSanlsgepsitdaeeveeelgeivdlildggeiavgvdstVvdltegkpkilRrG 179
                     l+t+++r+P++++a+ L++ lg+p+va+Sanl g+ps+t a++v ++l++++d+++dg +  +g++st++dlt ++p+ilR+G
      EPA04897.1 117 LNTIAIRMPSHKIALSLINSLGNPIVAPSANLFGKPSPTLAKHVLSDLDGKIDAVIDGRNSVIGIESTILDLTTKTPTILRPG 199
                     *********************************************************************************98 PP

>> SUA5  Putative GTP-binding controlling metal-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.0   0.0   2.1e-32   7.5e-29       1     134 []     201     341 ..     201     341 .. 0.80

  Alignments for each domain:
  == domain 1  score: 101.0 bits;  conditional E-value: 2.1e-32
                 .-HHHHHHHS-..--............-------------S-SSEEEEE--GGGHHHH......HHHHHTTS-EEEEEEGGGTGGTSEEEEE..E-TT- CS
        SUA5   1 itleeleevld..avek........keekpraPGmkyrHYaPkapvvlveaeeeeeaake.ekleekkksgkkvgvlatseskeaassvlslslgsrsd 88 
                 i+ eel+++l+  + ++        k  k+++PGmky+HY+P+a+++lve++++++++k+ e +++ ++++k +g++  ++ k++   + +  +g  ++
  EPA04897.1 201 ISYEELKNLLKkvK-YHpsllgkksKLLKVKSPGMKYKHYSPNAKIILVEGSTKNTQKKIhELIKKFQQQKKLIGIINNKNIKKTPFVKFKF-IG--TT 295
                 78899999995321.113344433356677**********************9998888878888888888889999966666554444444.45..99 PP

                 HHHHHHHHHHHHHHHHHS--SEEEEE----STTHHHHHHHHHHHTT CS
        SUA5  89 leeaarnLFaaLrelDeegvdlilvegvpeeglglAvmnRLrkAAg 134
                 ++ +a+nL++ +relD+++vd+i++ +++ ++lg A+mnRLrkAA+
  EPA04897.1 296 KNLIASNLYKSFRELDDQKVDVIIMREIDTSNLGFAIMNRLRKAAS 341
                 999*************99**********999**************6 PP

>> IL2  Interleukin 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.3   4.6e+03      70      70 ..     199     199 ..     157     229 .. 0.56
   2 ?   11.5   0.2     6e-05      0.22      19      59 ..     250     292 ..     243     312 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.3
                 H CS
         IL2  70 l 70 
                  
  EPA04897.1 199 G 199
                 2 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 6e-05
                 XXXXXXXXHHHHHHHHHHH..HHHHHHHBTT--HHHHTCEEEE CS
         IL2  19 sstketqqqleqllldlql..llekvknyknlklsrmltfkly 59 
                 +stk+tq+++++l++ +q+   l ++ n+kn k + +++fk+ 
  EPA04897.1 250 GSTKNTQKKIHELIKKFQQqkKLIGIINNKNIKKTPFVKFKFI 292
                 79************99876115778999*************96 PP

>> Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   8.9e-05      0.32      16      75 ..     207     272 ..     197     275 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 8.9e-05
                  HHHHHTEEEEEETTT-S--HHH........HHHTHTTTSEEEEEESBE...EEEHHHHHHHHGGGSSE CS
  Oxidored_q6  16 ldllelielryhetlladskee........eieakekeadvlvveGavtrkpkealellkelaekaka 75 
                   +l  l +++yh++ll ++ +         + ++ + +a++++veG+  +++k+  el+k++ ++ k+
   EPA04897.1 207 KNL--LKKVKYHPSLLGKKSKLlkvkspgmKYKHYSPNAKIILVEGSTKNTQKKIHELIKKFQQQKKL 272
                  444..245899999999888769999999977777789**********88889999999988887665 PP

>> EF-hand_1  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       0.8   2.9e+03      12      18 ..     163     169 ..     162     170 .. 0.79
   2 ?    9.7   0.0   0.00017      0.62      15      28 ..     199     212 ..     199     213 .. 0.94
   3 ?   -3.5   0.0       2.9     1e+04       4      10 ..     305     311 ..     303     313 .. 0.76
   4 ?   -2.1   0.0       1.1   3.9e+03       5      13 ..     319     327 ..     319     330 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.8
                 TSSSEEE CS
   EF-hand_1  12 DgdGkId 18 
                 D dGkId
  EPA04897.1 163 DLDGKID 169
                 569**98 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00017
                 SEEEHHHHHHHHHH CS
   EF-hand_1  15 GkIdfeEfkellkk 28 
                 GkI++eE+k+llkk
  EPA04897.1 199 GKISYEELKNLLKK 212
                 9***********98 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 2.9
                 HHHHHHT CS
   EF-hand_1   4 eiFrefD 10 
                 + Fre+D
  EPA04897.1 305 KSFRELD 311
                 6799998 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 1.1
                 HHHHHTTTS CS
   EF-hand_1   5 iFrefDkDg 13 
                 i+re+D+ +
  EPA04897.1 319 IMREIDTSN 327
                 799***977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       941  (0.0524848); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2154.63
//
Query:       EPA04898.1  [L=117]
Description: hypothetical protein BG20_I1304 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-22   78.9   0.0    4.6e-22   78.8   0.0    1.0  1  RibD_C    RibD C-terminal domain


Domain annotation for each model (and alignments):
>> RibD_C  RibD C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.8   0.0   2.5e-26   4.6e-22     108     200 .]       4     112 ..       1     112 [. 0.91

  Alignments for each domain:
  == domain 1  score: 78.8 bits;  conditional E-value: 2.5e-26
                 CSCHHHHHHCC.....E......SE-HHHHHHHHHHTT--EEEEEETHHHHHHHHHTTT-SEEEEEEESCE--T.TSBCSSSSST-SS....EEEEEEE CS
      RibD_C 108 eadkekveklk.....v......rvdlkelleeLkergirsllveGGatLagsllraglvDelrlyiaPkllGg.agktlfdgegfka....lklklvk 190
                 ++++e+++kl+     +      +v++k+l+  L++r i+++lveGG+t+++++++++++De+ ++i P+++Gg ++ t+++g gf++    ++l+l++
  EPA04898.1   4 KISNENLKKLNkfpveIimsgenLVNIKSLMTSLSKRKIKTILVEGGGTVNWQFIQNKIFDEIFITISPFIIGGtDAITFVQGKGFDKiiksPQLRLNS 102
                 56677777777777551678889**************************************************************************** PP

                 EEEETTEEEE CS
      RibD_C 191 sealgegvvl 200
                 +++l + +vl
  EPA04898.1 103 IKKLENHLVL 112
                 ****998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.52
# Mc/sec: 682.74
//
Query:       EPA04899.1  [L=119]
Description: ribonuclease P protein component 4 family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-14   53.8   1.6    2.5e-14   53.3   1.6    1.2  1  Rpr2            RNAse P Rpr2/Rpp21/SNM1 subunit domain
  ------ inclusion threshold ------
      0.023   14.7   2.4      0.085   12.9   2.4    1.9  1  zf-Sec23_Sec24  Sec23/Sec24 zinc finger
      0.043   14.2   0.1      0.059   13.7   0.1    1.2  1  DUF3268         zinc-finger-containing domain


Domain annotation for each model (and alignments):
>> Rpr2  RNAse P Rpr2/Rpp21/SNM1 subunit domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.3   1.6   4.1e-18   2.5e-14       1      90 []      12      91 ..      12      91 .. 0.93

  Alignments for each domain:
  == domain 1  score: 53.3 bits;  conditional E-value: 4.1e-18
                HHHHHHHHHH.HHHHH-HHHHHHHHHHHHHHHHHCT---SSTCCCTB-TTT--B--CTTTEEEEEE-SSS-E.........EEEEETTTT CS
        Rpr2  1 rlnfLyqaahlqlaeaspalsrylakqlrevskkaqlrlppsvkrtvCkkCgsvlipgvtcsvrvenkskkkkkkkkkadvlvvtClaCg 90
                r+ +L ++a   +a+++p ls+++a+ ++++s k+++r+p ++k  +CkkC+s++ pg ++++r+ ++s k         ++ + C+ Cg
  EPA04899.1 12 RMHILINSAIS-NAKTNPILSQRYASMAQRISTKHKIRMPYELKIVFCKKCKSFISPGTNSRIRLGRTSVK---------SIRISCNLCG 91
                8999*****99.9****************************************************886654.........3569*****7 PP

>> zf-Sec23_Sec24  Sec23/Sec24 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   2.4   1.4e-05     0.085       1      32 [.      55      93 ..      55      95 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.4e-05
  zf-Sec23_Sec24  1 PirCrrCraylNpfcki.......dfggkrwiCnfCnhk 32
                    ++ C++C++++ p ++           + r  Cn+C+h 
      EPA04899.1 55 IVFCKKCKSFISPGTNSrirlgrtSVKSIRISCNLCGHT 93
                    689**********9888778887433345699****995 PP

>> DUF3268  zinc-finger-containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   9.9e-06     0.059      29      81 ..      54     106 ..      31     111 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9.9e-06
     DUF3268  29 llylCpkCdayvgvhkgtkiplGtlAnaelrklrkeahaaFdklwksgalsrk 81 
                  +  C+kC +++    +++i lG+   +++r   + + +++ k+ ++ ++++k
  EPA04899.1  54 KIVFCKKCKSFISPGTNSRIRLGRTSVKSIRISCNLCGHTYRKIIHKSNVTKK 106
                 3346*********************************9999999988888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       739  (0.0412181); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.49
# Mc/sec: 737.33
//
Query:       EPA04900.1  [L=322]
Description: pyridine nucleotide-disulfide oxidoreductase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.2e-34  117.6   0.0    7.1e-34  117.4   0.0    1.0  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    9.2e-08   32.5   0.9     0.0023   18.5   1.2    3.0  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    2.1e-05   23.9   0.0      0.046   12.9   0.0    3.0  3  K_oxygenase    L-lysine 6-monooxygenase (NADPH-requiring)
     0.0039   17.2   0.1       0.62   10.0   0.0    3.1  3  NAD_binding_9  FAD-NAD(P)-binding
     0.0077   15.5   5.1      0.016   14.4   5.1    1.8  1  Actin_micro    Putative actin-like family
  ------ inclusion threshold ------
       0.21   12.5   0.8       0.48   11.4   0.8    1.7  1  zf-C2H2_4      C2H2-type zinc finger


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.4   0.0   2.4e-37   7.1e-34       1     260 [.      36     321 ..      36     322 .] 0.90

  Alignments for each domain:
  == domain 1  score: 117.4 bits;  conditional E-value: 2.4e-37
                  CSEEEE--SHHHHHHHHHHHH....HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHHHHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEECTC CS
                  xxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaq....agakvtlvelegtclnggcllskallgvaedaeiasevvkklnqgielllgeevvkidpgkkkvklekkkegd 94 
                  k+++++GgG++G+++ ++l++    ++  +t+v ++++ ++++++l++++ g+  +++i +  ++++ ++ +++ + +v+++d +++ v+++ k +g+
   EPA04900.1  36 KKILILGGGFGGMHVLKELQKkldaKNTSITIV-SDNNYFLFTPMLPEVASGMLNPRDITTP-IREFCTSAKFYQA-TVFSVDLQQRLVTITRKFDGK 130
                  589******************988779999999.999999999**************97775.6899999999999.********************* PP

                  EEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-T.................SEEEEES-SHHHHHHHHHHHHHT-......... CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................xxxxxxxxxxxxxxxxxxxxxxxx......... RF
  Pyr_redox_2  95 eekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllp.................krivvvGgGyiGvElAaalaklgk......... 166
                  ++ ++yd+lvlA Gs ++  g +  +en +   +t+++a +l+ + l                    ++vvG+G+ GvE+ ++++ +           
   EPA04900.1 131 NHALEYDYLVLAVGSDNNFYGNKPIEENSFPI-KTVEDAIELRNQTLSmmeiaaqtgsielqqkfLTFTVVGAGFAGVEIIGEINHFVRksvkqaypt 227
                  ***************99999777776777665.9***********99999999999999998777777***************988855466667777 PP

                  ......EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEE CS
                  ......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Pyr_redox_2 167 ......evtlveardrllraldkelsaaleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvavGvrpstelleeklglelderggi 258
                        +  l+   +++l++l+ +l++ ++ +l+k+Gv++   ++vk+id+ ++  +v+l+dge i++ ++++  Gv+ ++ +  ++l +e d++g++
   EPA04900.1 228 inenniNMILISSKNEILPELNYKLGESARSYLKKMGVRII--SNVKAIDAGES--HVELSDGEIIPCTTLIWTGGVTTNSMI--KSLICEHDKGGKV 319
                  777766777********************************..89989998887..8***********************977..8*********999 PP

                  E- CS
                  xx RF
  Pyr_redox_2 259 vv 260
                  +v
   EPA04900.1 320 LV 321
                  87 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0   0.00034         1       1      42 [.      37      84 ..      37      91 .. 0.78
   2 !   18.5   1.2   7.6e-07    0.0023       3      67 ..     198     275 ..     196     286 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00034
                EEEEECSSHHHHHHHHHHHH.TT...SEEEEEESSSSSS..TTSSHHH CS
   Pyr_redox  1 kvvvvGgGyiglElAgalae.lg...kkVtvversdkll..rllDeea 42
                k++++GgG+ g+ + ++l++ l     ++t+v  ++ +l  ++l+e a
  EPA04900.1 37 KILILGGGFGGMHVLKELQKkLDaknTSITIVSDNNYFLftPMLPEVA 84
                799**************944344444799*****99999777776655 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 7.6e-07
                 EEECSSHHHHHHHHHH...............HHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEE CS
   Pyr_redox   3 vvvGgGyiglElAgal...............aelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeie 67 
                 +vvG+G+ g+E  g++               +e + +  ++  ++++l+ l+ ++++  + +l+k+g++++ n k+  i+
  EPA04900.1 198 TVVGAGFAGVEIIGEInhfvrksvkqayptiNENNINMILISSKNEILPELNYKLGESARSYLKKMGVRIISNVKA--ID 275
                 79**************7777666666666655555789*********************************88554..44 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   1.5e-05     0.046     177     227 ..      21      73 ..       9      92 .. 0.82
   2 ?    3.6   0.0      0.01        30     315     340 ..     120     145 ..     103     147 .. 0.83
   3 !    3.8   0.0    0.0088        26     186     212 ..     189     215 ..     167     236 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.5e-05
  K_oxygenase 177 HsseylerkeellakkriaVvGsGqSaaeifedllrr..qkkvelklvtrsea 227
                   ++ + ++k ++ +kk+i++ G+G  + +++++l ++  +k++++++v+ ++ 
   EPA04900.1  21 EAHVIFSHKTDSTSKKKILILGGGFGGMHVLKELQKKldAKNTSITIVSDNNY 73 
                  5555667788899************************6555699999987765 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.01
  K_oxygenase 315 eltlrneesgeeetlevdavvlATGY 340
                   +t++ +++g+++ le+d++vlA G 
   EPA04900.1 120 LVTITRKFDGKNHALEYDYLVLAVGS 145
                  467888999**************997 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.0088
  K_oxygenase 186 eellakkriaVvGsGqSaaeifedllr 212
                  e +++  +++VvG+G  + ei+ ++ +
   EPA04900.1 189 ELQQKFLTFTVVGAGFAGVEIIGEINH 215
                  457777899************987754 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0   0.00021      0.62       2      34 ..      40      71 ..      39      85 .. 0.89
   2 ?    1.8   0.0     0.073   2.2e+02     118     154 ..     105     144 ..      97     146 .. 0.69
   3 ?    1.3   0.0       0.1   3.1e+02       2      14 ..     199     211 ..     198     227 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00021
  NAD_binding_9  2 ivGaGprGlavlerLlarakkkspleitlfdps 34
                   i G+G+ G+ vl++L ++  ++++++it++ ++
     EPA04900.1 40 ILGGGFGGMHVLKELQKKL-DAKNTSITIVSDN 71
                   89****************8.99******99665 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.073
  NAD_binding_9 118 evhraevvdleeradgqavll.adg..aslaadaVvLAlG 154
                    ++++a+v +++ +++ ++++   dg  + l++d++vLA+G
     EPA04900.1 105 KFYQATVFSVDLQQRLVTITRkFDGknHALEYDYLVLAVG 144
                    567777777777776665554334422568*********9 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.1
  NAD_binding_9   2 ivGaGprGlavle 14 
                    +vGaG++G+ ++ 
     EPA04900.1 199 VVGAGFAGVEIIG 211
                    8*******98864 PP

>> Actin_micro  Putative actin-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   5.1   5.2e-06     0.016     224     277 ..       3      59 ..       1     283 [. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.2e-06
  Actin_micro 224 kefsCkvCdvkfev.ekiseHllkkHiikehvkehiteyknk..hkdviekigkrlr 277
                  + ++C  Cd kf++ +k+++H++ +H+ +   k+ i ++     +  v++++ k+l 
   EPA04900.1   3 QLYNCVQCDLKFDSkKKFEAHVIFSHKTDSTSKKKILILGGGfgGMHVLKELQKKLD 59 
                  5699**********9*************88888888877655223333333333333 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.8   0.00016      0.48       1      24 []       5      28 ..       5      28 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00016
   zf-C2H2_4  1 fkCpiCgksFsskkaLlrHlkthH 24
                + C +C+  F skk++  H+   H
  EPA04900.1  5 YNCVQCDLKFDSKKKFEAHVIFSH 28
                78*****************98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       879  (0.0490267); expected 358.6 (0.02)
Passed bias filter:                      710  (0.0396006); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.81
# Mc/sec: 1193.70
//
Query:       EPA04901.1  [L=221]
Description: 3,4-dihydroxy-2-butanone-4-phosphate synthase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.5e-60  202.8   0.0      4e-60  202.7   0.0    1.0  1  DHBP_synthase  3,4-dihydroxy-2-butanone 4-phosphate synthase
  ------ inclusion threshold ------
       0.06   11.8   0.0      0.083   11.4   0.0    1.3  1  PAF-AH_p_II    Platelet-activating factor acetylhydrolase, is


Domain annotation for each model (and alignments):
>> DHBP_synthase  3,4-dihydroxy-2-butanone 4-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.7   0.0   4.4e-64     4e-60       2     191 ..       5     216 ..       4     217 .. 0.91

  Alignments for each domain:
  == domain 1  score: 202.7 bits;  conditional E-value: 4.4e-64
                    HHHHHHHTT--EEEESSTTTT-BEEEEEEGGG--HHHHHHHHHHB-S--EEEEEHHHHHHTT--BSSSS-S.................STT---BB CS
  DHBP_synthase   2 eaiealkaGkfvivvDdedrenegdLiiaAekvtpekvafmirhasGlicvalteeradeLeLplmveene.................dkhktaft 80 
                    + ie+lk+G+fv+++D++ rene d+++aAe+vtpe++a m++ha+Gl+c+a++++ a++LeL++m+e                       + +f+
     EPA04901.1   5 SGIESLKRGEFVLLFDSAGRENEIDMVVAAEFVTPEHIARMRQHAGGLLCMAIDNDFANSLELKYMHE--IlaespisnkemimglapYGDHPTFS 98 
                    5699***************************************************************7..23355677778999999945569*** PP

                    --EEESST-SSS-SHHHHHHHHHHHH-..T.....T--GGGEEEEEEEEEEEE-TTGGGTS-SHHHHHHHHHHHTTS-SBEEEEEBB-TT.SCB-B CS
  DHBP_synthase  81 vsvdaaegttTGIsaaDRalTirklad..p.....kakpedfrrPGhvfplrareggvleRrghTEaavdLarlaglkpaavicellndd.gtmar 168
                    +sv++  +t TGI+++DR+lTir++a+  +     k+ +++f++PGhv +l+a++g + +R+ghTE++v L+++agl+p+ +ice+++ +  t+++
     EPA04901.1  99 ISVNHY-QTYTGITDKDRSLTIREMANifKvdnkkKKFASSFKTPGHVPLLIASKGLLAKRQGHTEMSVYLTQIAGLTPVTAICEMMDAEtYTALS 193
                    *****9.9*******************7625555455679***********************************************988678*** PP

                    HHHHHHHHHHHT-EEEEHHHHHH CS
  DHBP_synthase 169 rdeleefakkhglkiitiedlie 191
                     ++++++ak++ +++i +++l+e
     EPA04901.1 194 VEKAKKYAKQNAIPLIDGKELLE 216
                    ********************987 PP

>> PAF-AH_p_II  Platelet-activating factor acetylhydrolase, isoform II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   9.3e-06     0.083      89     151 ..     134     199 ..      94     220 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.3e-06
                  EET--B--SS-EEEEEEE--TT--T...TTTHHHHHHHHHTT-EEEEE---SS-SSEEEE-SSHHH CS
  PAF-AH_p_II  89 kknellktkekyPlivFsHGLgafR...tlYsalcielAskGfvvaavEHrDesAaatyvlkdkla 151
                  k  + +kt++  Pl++ s GL a R   t  s + +++A    v a  E  D    ++  ++++++
   EPA04901.1 134 KFASSFKTPGHVPLLIASKGLLAKRqghTEMSVYLTQIAGLTPVTAICEMMDAETYTALSVEKAKK 199
                  45689*******************944345677888999999999999999987777666555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1605.94
//
Query:       EPA04902.1  [L=185]
Description: hemerythrin HHE cation binding domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      3e-13   50.5   0.5      2e-12   47.9   0.1    2.3  2  Hemerythrin     Hemerythrin HHE cation binding domain
     0.0021   16.1   0.9     0.0032   15.5   0.9    1.2  1  Prominin        Prominin
  ------ inclusion threshold ------
      0.015   15.9   0.2      0.035   14.7   0.2    1.6  1  UPF0113_N       UPF0113 Pre-PUA domain
      0.016   15.2   2.3      0.065   13.2   1.5    2.2  2  DUF1043         Protein of unknown function (DUF1043)
      0.018   14.8   0.2      0.025   14.3   0.2    1.3  1  EDR1            Ethylene-responsive protein kinase Le-CTR1
      0.025   15.1   2.3       0.03   14.8   1.1    1.7  2  IZUMO           Izumo sperm-egg fusion, Ig domain-associated
      0.042   14.0   0.0        0.1   12.8   0.0    1.6  2  Spore_YtfJ      Sporulation protein YtfJ (Spore_YtfJ)
       0.11   11.9   0.9       0.21   11.1   0.9    1.5  1  Methyltransf_4  Putative methyltransferase


Domain annotation for each model (and alignments):
>> Hemerythrin  Hemerythrin HHE cation binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.9   0.1   8.9e-16     2e-12       4     131 .]       4     136 ..       1     136 [. 0.85
   2 ?   -1.6   0.0       1.7   3.8e+03      34      46 ..     162     174 ..     144     181 .. 0.46

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 8.9e-16
                  HHHHHHHHHHHHHHHHHHHHHHH.HHHHCCC...HCCHHHHHHHHHHHHHHHHHHHHHHCHHHHH...CCC.HHHHHHHHHHHHHHHHHHHHHHHHCH CS
  Hemerythrin   4 ealdeeHralrallerlralada.aaevhga...lrklaelldelvdeleaHhaaEEellfPlle..drpggravldvlereHdeirelleelrellk 95 
                  + l+++H+ + + ++++++  +  +++ + +   l  + ++ + + d+   Hh +EE+ lfP+le  + p   ++++ +  +H++ rel +e++  +k
   EPA04902.1   4 ASLRKDHDLIEKVIKAMESTIQLlKDGKQIPesiLLPVIDFSKNFTDV--CHHSKEEKSLFPALEqaGMPTNMGPIAMMLIDHQRSRELGKEMESSAK 99 
                  67999**********9988777753333333699*************9..********************************************7777 PP

                  TCG.GSTCHHHHHHHHHHHHHHHHHHHHHHHTHHHHH CS
  Hemerythrin  96 gle.epsaaafaelleeladllreHiakEesilfpll 131
                  ++   +++  +  +l+ + + + eH+ kE++ lf+++
   EPA04902.1 100 TYLsSGDSTKLVTDLQQYVEHITEHLWKENNRLFMMA 136
                  76614444444448888889999***********996 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.7
                  HCCHHHHHHHHHH CS
  Hemerythrin  34 lrklaelldelvd 46 
                    k +e++++l++
   EPA04902.1 162 TGKTREHYEQLAE 174
                  3344444444443 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.9   1.4e-06    0.0032     301     386 ..      95     180 ..      77     183 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.4e-06
    Prominin 301 ssleiekldtskcldqlpnvdevlealeevletnlssivkeglarlneipekvknqtaevvpdlkkalakgreqikklakkiprea 386
                 +s+ +++l ++ + + + ++++++e+++e l ++ +++  ++ arl+ +++k++++++++ ++  ++  k+re+ ++la+ + r++
  EPA04902.1  95 ESSAKTYLSSGDSTKLVTDLQQYVEHITEHLWKENNRLFMMAEARLQYVSKKINQELNDIEESKLRETGKTREHYEQLAETLTRDV 180
                 44445577777777999**************************************************************9996655 PP

>> UPF0113_N  UPF0113 Pre-PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.2   1.6e-05     0.035       8      66 ..     107     163 ..     101     165 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.6e-05
   UPF0113_N   8 trivfekLtkyigdnvkelldrkdgtycfrlkkkrVyyvseellklaetikpenlisaG 66 
                  +++ + L++y+   ++ l +  ++++ f + + r+ yvs+++ + +  i+ ++l   G
  EPA04902.1 107 STKLVTDLQQYVEHITEHLWK--ENNRLFMMAEARLQYVSKKINQELNDIEESKLRETG 163
                 5788999****6666666666..5579***********************999997766 PP

>> DUF1043  Protein of unknown function (DUF1043)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       0.7   1.6e+03      71      90 ..      53      72 ..      41      75 .. 0.73
   2 ?   13.2   1.5   2.9e-05     0.065      54     106 ..     107     159 ..     102     179 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.7
     DUF1043 71 hlaksseeLlpeleeqelfq 90
                h +k++++L+p+le++ ++ 
  EPA04902.1 53 HHSKEEKSLFPALEQAGMPT 72
                45778889999999887765 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 2.9e-05
     DUF1043  54 saelLetlaedyqkLyqhlaksseeLlpeleeqelfqqkkleekkaeaeeeee 106
                 s +l+++l++  + + +hl k++++L++ +e   ++++kk++++ ++ ee++ 
  EPA04902.1 107 STKLVTDLQQYVEHITEHLWKENNRLFMMAEARLQYVSKKINQELNDIEESKL 159
                 889***********************999999999999***999988887544 PP

>> EDR1  Ethylene-responsive protein kinase Le-CTR1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2   1.1e-05     0.025      25     132 ..      48     151 ..      41     174 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.1e-05
        EDR1  25 FYdvigillteseeqgkipsleelqavepenssvevvlvdrekDseLkeleqtavklvselnstkelvkklAelVadvmggsvskeeelllrweessse 123
                 F dv+     ++ee++ +p le+   ++++   + ++l+d+++  eL + +++++k++ ++ ++++lv+ l + V +   +  +++++l ++ e +++ 
  EPA04902.1  48 FTDVCH---HSKEEKSLFPALEQAG-MPTNMGPIAMMLIDHQRSRELGKEMESSAKTYLSSGDSTKLVTDLQQYVEHITEHLWKENNRLFMMAEARLQY 142
                 555555...3567778888888765.55668899******************************9*************************999999999 PP

        EDR1 124 lkaslnsvv 132
                 +++++n+ +
  EPA04902.1 143 VSKKINQEL 151
                 998888765 PP

>> IZUMO  Izumo sperm-egg fusion, Ig domain-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.4     3e+03      85      99 ..      12      26 ..       3      58 .. 0.57
   2 ?   14.8   1.1   1.4e-05      0.03      27      83 ..     106     162 ..      87     182 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.4
                HHHHHHHHHHHHHHH CS
       IZUMO 85 llkeLlwllqkqkkk 99
                l+++ ++ ++++++ 
  EPA04902.1 12 LIEKVIKAMESTIQL 26
                333333333333322 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 1.4e-05
                 GHHHHHHHHHHHHHTTT---SGGGGGGSEEEHHHHHHHHHHHHHHHHHHHHS---HH CS
       IZUMO  27 hreklleraealledlsekelaenkflgvvdeetlekvasslkkelkrltdsdlkge 83 
                   +kl+  +++ +e++ e   +en+ l +++e++l+ v++++ +el+ +++s+l++ 
  EPA04902.1 106 DSTKLVTDLQQYVEHITEHLWKENNRLFMMAEARLQYVSKKINQELNDIEESKLRET 162
                 4789999**********************************************9875 PP

>> Spore_YtfJ  Sporulation protein YtfJ (Spore_YtfJ)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       2.9   6.5e+03      65      79 ..       8      24 ..       3      25 .. 0.70
   2 ?   12.8   0.0   4.5e-05       0.1       3      58 ..      33      87 ..      32     103 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.9
  Spore_YtfJ 65 k..ssldklidlvpdvv 79
                k  + ++k+i+++ + +
  EPA04902.1  8 KdhDLIEKVIKAMESTI 24
                44688899998877665 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 4.5e-05
  Spore_YtfJ  3 tgdgtviiPvskvsfGfgaGgsefkskkekepfgggsgaGvsitPvAfLvikkgev 58
                +++ ++++Pv+++s  f       k++k+  p    +g+  ++ P+A++ i++++ 
  EPA04902.1 33 IPE-SILLPVIDFSKNFTDVCHHSKEEKSLFPALEQAGMPTNMGPIAMMLIDHQRS 87
                567.9*******************999999999999***************98865 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.9   9.2e-05      0.21      89     148 ..      84     143 ..      82     181 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.2e-05
                     GGGGSTTSHHHHHHHHHHEEEEEEEEEEESHHHHHHHHHHHHHCSTTEEESSCCCSCCTC CS
  Methyltransf_4  89 hhKrRllqpellkelarvLkkgGvlelaTDveeyaeemlkvleeeplferlskeeeleee 148
                     h++ R l +e+ + +++ L  g + +l+TD+++y e++ ++l +e++  ++  e  l+  
      EPA04902.1  84 HQRSRELGKEMESSAKTYLSSGDSTKLVTDLQQYVEHITEHLWKENNRLFMMAEARLQYV 143
                     7888888999999999*************************9887665555544444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1316  (0.0734006); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1307.34
//
Query:       EPA04903.1  [L=222]
Description: Nep1 ribosome biogenesis protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-39  135.1   0.5    2.5e-39  135.0   0.5    1.0  1  EMG1            EMG1/NEP1 methyltransferase
  ------ inclusion threshold ------
       0.14   12.1   0.0       0.19   11.7   0.0    1.2  1  Glyco_transf_4  Glycosyltransferase Family 4


Domain annotation for each model (and alignments):
>> EMG1  EMG1/NEP1 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.0   0.5   2.8e-43   2.5e-39       1     194 []       4     217 ..       4     217 .. 0.92

  Alignments for each domain:
  == domain 1  score: 135.0 bits;  conditional E-value: 2.8e-43
                 EEEEEES--B--GG................SCGGSB--HHHHCGG.TTSTTGGGSS-CHHHHHHHHHHHCSCHHCTT.EEEEEEETTSEEEEE-TT--- CS
        EMG1   1 ivLeeasLelvkvk................kkseqLLnsddhkkilkklkreakeaRpDIvHqcLlalldspLnkagllqvyihttknvlIevnpqtRi 83 
                 +vL+e+sLelv+++                ++se LL+++ h  ++k + +e k++RpD vH+++l +   pL  ++++++y+ht ++++I++ +++ i
  EPA04903.1   4 LVLAESSLELVPEElqdhpsvlsharklgkNPSEILLDNSWHFAAMKGIDDEIKRGRPDLVHFSILEATTIPLYLHNKIKIYVHTIDDKVIYIGENVHI 102
                 59************************************************************************************************* PP

                 -SSHHHHHHHHHHHHCCSEEEETTEE.SCEEEECS-HHHHCCC...SEEEEE-TTSEE-.................EEEE-SSSS....---HH...EE CS
        EMG1  84 PrtfkrFagLmvqLLkklsirategeekLlkviknpitdhlpp..gskiillsesaekklvdleefv....vkpvvfvigamskgsvkidykee...ei 173
                 P++++rF+gL+++L+ ++ i +++ +  L++v k+++++++++   skii++s++++ k+   +e +    +++ ++vig+++kg+ + ++k++    +
  EPA04903.1 103 PKSYHRFEGLIEKLFLEKVILSNTAT--LMEVKKKSFSELINEikPSKIIGFSTKGQLKS---FEKIsseiSDDTCIVIGGFQKGHFSESIKSKinhLF 196
                 *********************99876..**************99899**********554...454446558899**********66555555455599 PP

                 ESSSS---HHHHHHHHHHHCH CS
        EMG1 174 sisnypLsaavvcskiltafE 194
                 s+ + + +a+vv++++l ++E
  EPA04903.1 197 SVGDISYEAHVVIARMLYEYE 217
                 ****************99887 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.1e-05      0.19      38     108 ..      26      91 ..       5     129 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.1e-05
  Glyco_transf_4  38 elvvrvprvplpllkrllrslaflrrlrrllkrekpDvvHahspaalgaallalrrrlgiplVltvHglye 108
                      + + +++ p  +l ++ + +a+++ +   +kr++pD+vH     a    l      l+ ++ ++vH+ ++
      EPA04903.1  26 SHARKLGKNPSEILLDNSWHFAAMKGIDDEIKRGRPDLVHFSILEATTIPLY-----LHNKIKIYVHTIDD 91 
                     556667777777888999999******************9887666544422.....44455566666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1421.89
//
Query:       EPA04904.1  [L=116]
Description: response regulator receiver domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.6e-21   74.2   0.1    9.6e-21   74.1   0.1    1.0  1  Response_reg  Response regulator receiver domain


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.1   0.1   5.4e-25   9.6e-21       1     111 [.       5     114 ..       5     115 .. 0.95

  Alignments for each domain:
  == domain 1  score: 74.1 bits;  conditional E-value: 5.4e-25
                   EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEESSTSHHHHHHHHHCTESEE CS
  Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviiltahseeedavealkagaddf 97 
                   v+++dDd++ ++l++++lee+++++ +   dg+ a++l++e+k+d+il+Di+mp+ +G++++++i+e dp+ + i++++ s+  + ++  k+g+   
    EPA04904.1   5 VIVIDDDRDTVRLFSEFLEENDIKVLGGGYDGNTAIKLYEEKKPDIILMDIMMPNGSGFHAIRKIQEIDPNAKFIVVSGDSNYLTEEKLEKLGI-PL 100
                   89*********************9999******************************************************9888888888887.68 PP

                   EESSG-HHHHHHHH CS
  Response_reg  98 lsKpfdpeeLlkal 111
                   ++Kpf+ ++Ll+++
    EPA04904.1 101 IQKPFNLKNLLSII 114
                   **********9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 728.39
//
Query:       EPA04905.1  [L=194]
Description: riboflavin synthase, alpha subunit [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.2e-45  151.6   4.8    1.1e-23   83.0   0.1    2.0  2  Lum_binding  Lumazine binding domain


Domain annotation for each model (and alignments):
>> Lum_binding  Lumazine binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.1   1.7   6.5e-24   1.2e-19       1      86 [.       3      88 ..       3      89 .. 0.84
   2 !   83.0   0.1   6.2e-28   1.1e-23       2      87 .]     103     186 ..     102     186 .. 0.95

  Alignments for each domain:
  == domain 1  score: 70.1 bits;  conditional E-value: 6.5e-24
                 -S--SEEEEEEEEE.E.CGCTTEETEES.GGGGG..TTT-EEEETTEEEEEEEEEE.SSEEEEEEEHHHHHHSSGGG--TTSEEEEEE CS
  Lum_binding  1 tGiVeevgtvesieke.ekledltielp.elakylvekGdsiavnGvcLTVvteeveeeeftvdvipeTlerttlgelkvgdkVNlEr 86
                 tGiVe+vg++++i+k+ ++ + ++++++   + + ++ G+s+a+nGvcLT +  ++++++  +++i+eT ++t lg+l++gd VN+Er
   EPA04905.1  3 TGIVEGVGKIQKISKNtKNRSAIQMTVNlGKHAKGLKIGQSVALNGVCLTAT--KITKSNCIFEMIEETTKKTDLGNLNPGDIVNIER 88
                 8************5553555555555556455566699*************9..7899999999***********************8 PP

  == domain 2  score: 83.0 bits;  conditional E-value: 6.2e-28
                  S--SEEEEEEEEE.ECGCTTEETEES.GGGGG..TTT-EEEETTEEEEEEEEEE.SSEEEEEEEHHHHHHSSGGG--TTSEEEEEEE CS
  Lum_binding   2 GiVeevgtvesiekeekledltielp.elakylvekGdsiavnGvcLTVvteeveeeeftvdvipeTlerttlgelkvgdkVNlEra 87 
                  G+V++vg +++i k+ k  ++ +e+p +l+ky+v+kG sia++G++LTVv  +v+++  +v +ip+T+e t+++++++gdk+N+E++
   EPA04905.1 103 GHVDGVGIIKKILKRPKEVQVWFEIPkKLSKYVVKKG-SIAIDGISLTVV--DVKKNLASVCLIPHTMELTNFKTKHIGDKINIETD 186
                  9***********777778999999999**********.***********9..9********************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1305.60
//
Query:       EPA04906.1  [L=367]
Description: succinate-semialdehyde dehydrogenase [NAD(P)+] family protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   3.2e-122  408.3   0.4   3.8e-122  408.1   0.4    1.0  1  Aldedh    Aldehyde dehydrogenase family


Domain annotation for each model (and alignments):
>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  408.1   0.4  2.1e-126  3.8e-122     108     462 .]       7     354 ..       2     354 .. 0.97

  Alignments for each domain:
  == domain 1  score: 408.1 bits;  conditional E-value: 2.1e-126
                 SEEEEEECTTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHHTT-EEEEEE-TTSHHHHHHHHHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTE CS
      Aldedh 108 egevlpssegklalvrrePlGvvgaItPWNfPlllaawklapalaaGNtvvlKPaeetplsalllaelfeeaglPkgvlnvvtgsgsevgealvehpev 206
                 ++evl++ + ++++ + ePlGv+g+I+PWNfP   a++ +ap+l+aGN++v+KPa+ t  s + + ++f e g+P+g+++ v+g   e +++l++  +v
  EPA04906.1   7 ADEVLNT-DARKSFLTFEPLGVIGSIMPWNFPYWQALRFAAPCLMAGNVIVMKPASVTMQSGIEIEKAFTESGMPDGIFQTVVG-SVESANHLID-SDV 102
                 4566666.48999***********************************************************************.7789999998.69* PP

                 SEEEEES-HHHHHHHHHHHHCTTSEEEEEE---EEEEE-TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT CS
      Aldedh 207 dkvsftGstevgrkiakaaaknlkrvtlElGGknplivledaDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdplded 305
                 ++v+ftGst+ g k+ ++aa+nlk+++lElGG +p+ivl+da ++kav+++vkg f+n GQ C+a +r++v ++i+++f+e ++++a++lkvgdp   +
  EPA04906.1 103 NAVTFTGSTTAGAKVGQRAAGNLKKCVLELGGSDPFIVLDDAIIEKAVDGAVKGRFINCGQSCVASKRFFVGKNIAKDFIELFIKKASQLKVGDPTSIE 201
                 *************************************************************************************************** PP

                 -SB---SSHHHHHHHHHHHHHHHHTTSEEEE-TTE.SB-SSSTTEE--EEEES-TTTSHHHHS---SSEEEEEEESSHHHHHHHHHSSSEESEEEEE-S CS
      Aldedh 306 tdvGPliseaqlekvekyveeakeegaklllGgereeaglekgyfvePtvlanvtpdmriaqeEiFGPVlsvikfkdeeeaieiaNdteyGLaagvftk 404
                 tdvGPl ++  le++ ++ve+ake+ga++llGg   ++ ++kgyf++Pt+l+nv+++mria+eE+FGPV++++ +++e ea+++aNdte+GL+a+++tk
  EPA04906.1 202 TDVGPLSNKGGLETISGIVEDAKEKGAEILLGG---SKIDSKGYFYQPTILTNVKQNMRIAKEETFGPVAPITVVENESEAVKLANDTEFGLGASIWTK 297
                 *********************************...8899*********************************************************** PP

                 BHHHHHHHHHHS-SSEEEESSSST--TTTSEB--CGGGEES-BSHHHHHHHTEEEEEE CS
      Aldedh 405 dleraervaerleaGnvyiNdsttgaaealpfgGvkqSglGreggkegleeytevktv 462
                 dl++ae++++r+e G v +N+   +++   pfgG+k+Sg+Gre +++g+ e++++k+v
  EPA04906.1 298 DLAKAEKISRRIESGIVSVNNVVLSDPRI-PFGGIKHSGFGRELSRYGILEFVNIKSV 354
                 ***************************99.**************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.34s 00:00:00.94 Elapsed: 00:00:00.54
# Mc/sec: 2050.37
//
Query:       EPA04907.1  [L=76]
Description: hypothetical protein BG20_I1286 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 485.88
//
Query:       EPA04908.1  [L=150]
Description: ribosomal protein S19e [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.8e-48  162.1   0.0    6.5e-48  161.9   0.0    1.0  1  Ribosomal_S19e  Ribosomal protein S19e
  ------ inclusion threshold ------
       0.12   12.2   0.0        3.3    7.6   0.0    2.3  2  RuvB_C          RuvB C-terminal winged helix domain
       0.12   12.5   0.0       0.24   11.6   0.0    1.5  1  DUF2007         Putative prokaryotic signal transducing prote
       0.14   12.2   0.0       0.32   11.1   0.0    1.9  1  ArsC            ArsC family


Domain annotation for each model (and alignments):
>> Ribosomal_S19e  Ribosomal protein S19e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.9   0.0   1.5e-51   6.5e-48       1     136 [.       3     137 ..       3     138 .. 0.98

  Alignments for each domain:
  == domain 1  score: 161.9 bits;  conditional E-value: 1.5e-51
                     TSSSHHHHHHHHHS--S---S-SSS-SSSS-SS-S-SS-SSTTTHHHHHHHHHHHTS--TTSGGGGS----SS-SSS-------THHHHHHHHHT CS
  Ribosomal_S19e   1 tvkdVpaeelikalaeeLkksgklevPewadlvKtgsakelapededWfyvRaAsilRkvylrgpvGverlrkvYGgkkrrgvrpshfvkasgsv 95 
                     +v+dVp + li++la+ Lk++  + +P+w+ +vKtg++ +++p+d+dW+++R+As++Rk+yl+gp+G+++lrk+YGg + +g+   h+++a g++
      EPA04908.1   3 KVYDVPSDVLISRLAAILKNE-DIPAPSWIPFVKTGAHADKPPQDRDWWHTRCASLMRKIYLHGPLGINELRKIYGGGRPSGYGAAHHKDAGGAI 96 
                     59*****************98.8************************************************************************ PP

                     TSSS--SSS---SS-HHHHHTHHHHH--SS--S--XXXXXX CS
  Ribosomal_S19e  96 irkilqqLeklglvkkekkkgrrltkkGqrlldriaeevak 136
                     ir+++q+Leklg+++k +kkgr+++k+G++ ldr+++e+++
      EPA04908.1  97 IRNAVQALEKLGYIEKVEKKGRVVSKQGMQKLDRLSTEILN 137
                     **************9999*******************9976 PP

>> RuvB_C  RuvB C-terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.036   1.6e+02      10      33 ..      53      76 ..      48      80 .. 0.82
   2 ?    7.6   0.0   0.00074       3.3      50      71 ..     106     128 ..      94     129 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.036
                HHHHHHHHT.TT--B-HHHHHHHT CS
      RuvB_C 10 kyLkllkekfkggpvglktlaail 33
                ++ +l+ + +  gp+g++ l +i 
  EPA04908.1 53 RCASLMRKIYLHGPLGINELRKIY 76
                5567888999********998876 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00074
                 HTTSEEE.ETTEEEE-HHHHHHH CS
      RuvB_C  50 keglIer.tsrGRilTkkglkyl 71 
                 k g+Ie+  ++GR ++k+g++ l
  EPA04908.1 106 KLGYIEKvEKKGRVVSKQGMQKL 128
                 78999984679********9976 PP

>> DUF2007  Putative prokaryotic signal transducing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   5.3e-05      0.24       1      27 [.       1      27 [.       1      28 [. 0.96

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.3e-05
     DUF2007  1 mkelyrtndpveaelikslLeeagIea 27
                m ++y   + v+++++ ++L++++I+a
  EPA04908.1  1 MAKVYDVPSDVLISRLAAILKNEDIPA 27
                89***********************96 PP

>> ArsC  ArsC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   7.1e-05      0.32       9      40 ..     114     146 ..       5     146 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 7.1e-05
                 -TTSHHHHHCT.CCCTTSBHHHHHHHHHH-GGG CS
                 xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
        ArsC   9 skrgttyreLn.ldkedlsedellelilenpsL 40 
                  k+g+ +++ + ++ ++ls++ l eli+enp+L
  EPA04908.1 114 EKKGRVVSKQGmQKLDRLSTEILNELITENPQL 146
                 688889999998899****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 870.62
//
Query:       EPA04909.1  [L=250]
Description: GGDN family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-51  173.8   0.0      5e-51  173.4   0.0    1.1  1  GCH_III          GTP cyclohydrolase III
    1.8e-07   31.4   1.6    0.00092   19.5   0.2    2.2  2  mCpol            minimal CRISPR polymerase domain
     0.0003   20.5   0.2    0.00072   19.2   0.1    1.8  2  Guanylate_cyc    Adenylate and Guanylate cyclase catalytic do
     0.0021   18.3   0.0          1    9.6   0.0    2.1  2  GGDEF_2          GGDEF-like domain
  ------ inclusion threshold ------
      0.024   14.4   0.6       0.17   11.7   0.1    2.5  3  NOG1             Nucleolar GTP-binding protein 1 (NOG1)
      0.043   14.1   2.2       0.24   11.7   0.1    2.2  2  DUF3908          Protein of unknown function (DUF3908)
      0.068   13.3   0.0       0.87    9.7   0.0    2.1  2  F420H2_quin_red  F420H(2)-dependent quinone reductase


Domain annotation for each model (and alignments):
>> GCH_III  GTP cyclohydrolase III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.4   0.0   1.9e-54     5e-51       2     236 ..       5     236 ..       2     244 .. 0.93

  Alignments for each domain:
  == domain 1  score: 173.4 bits;  conditional E-value: 1.9e-54
                 EEEEETTHHHHCCSSS---HHHHHHHHHHHHHHHHHHHHTTT-EEE-TTSSEEEEE-TT--HHHHHHHHHHHHHHSSS-EEEEEEEESSHHHHHHHHHH CS
     GCH_III   2 tviqidnYgpWtvepaprreadlqalqarlyadlqkelaardGlvfatRfDnllaitngidleehkRiqesirnrypvtvsmgigaaetPldaleaase 100
                 ++++i +YgpWt +++++re  lq+lqa +y ++q+ ++ ++ lvf  R D +  ++ng+ le+h  iq+++   + v+ s++ g ae P+ a  +a e
  EPA04909.1   5 SILKITGYGPWTLTLGSDREHALQMLQASIYKEIQQLFSEKNCLVFLNRADEFFVVSNGLTLEDHIEIQKNLEKSFDVKFSISLGYAESPFKANLKAYE 103
                 5789******************************************************************************************99999 PP

                 HHHHH--TT-TT----EEES---SS--EEEEEEEETTHHHHTTTTS-HHHHHHHHHHHHHHHHHHHHTTT---EEEETTEEEEE-TT--HHHHHHHHHH CS
     GCH_III 101 aLreagsaqdeeRkevlsvdelvtegyvqiahiDinnitgtltdivsavrtylevnkvkaklakklekegallqfiGGDnilavcneleeedvldiine 199
                   + ++  +++e   ++   +  +e  v+i h+D+ n+t +  +i s+++ +l + ++ ak+ak   k++ l++f+GGDn++ v++e  ++ v + i+ 
  EPA04909.1 104 G-KINEIVLSKEHT-IFGFIDGKSEPKVSIMHFDVENLT-SKRKIKSPYEITLTIFELYAKMAKFFSKKNSLTFFMGGDNFMVVASEEAKNSVSEFIEL 199
                 7.445556666655.466655567889************.999******************************************************** PP

                 HHHHHS--EEEEEEEESSHHHHHHHHHHHHHHHHTTS CS
     GCH_III 200 vkekvdvdlkaGiGiadtaedaaaladeaLeeiRgkl 236
                 +k+++d+ l+ GiG ++ta+daa+la ++L++iR  +
  EPA04909.1 200 IKNEYDITLNCGIGNGKTARDAANLATKSLDTIREIR 236
                 **********************************654 PP

>> mCpol  minimal CRISPR polymerase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.1   0.00014      0.35      21      91 ..      23      90 ..      16     101 .. 0.78
   2 !   19.5   0.2   3.6e-07   0.00092      14      96 ..     137     221 ..     132     229 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00014
       mCpol 21 deeeleklskevkeaikklkkllkdelgasvifaaGDsilaksslee.dllvelsrvyqkitgltvSiGvGk 91
                 e++l++l +++ ++   +++l++++ ++ v  + +D+  + s+  + ++ +e+++ ++k   +++Si++G 
  EPA04909.1 23 REHALQMLQASIYKE---IQQLFSEK-NCLVFLNRADEFFVVSNGLTlEDHIEIQKNLEKSFDVKFSISLGY 90
                556666666666554...55567777.888999******99998666899************9888888884 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 3.6e-07
       mCpol  14 ealllsndeeeleklskevkeaikklkkllkdelgasvifaaGDsilaksslee.dllvelsrvyqkit..gltvSiGvGktlrea 96 
                 e l ++ ++++  ++  ++ e   k++k+++++ +    f +GD+ ++ +s e+ ++++e+ ++ ++    +l + iG Gkt+r+a
  EPA04909.1 137 ENLTSKRKIKSPYEITLTIFELYAKMAKFFSKK-NSLTFFMGGDNFMVVASEEAkNSVSEFIELIKNEYdiTLNCGIGNGKTARDA 221
                 66778888999999999****************.888899******9999988877788877777776657777888888999887 PP

>> Guanylate_cyc  Adenylate and Guanylate cyclase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       0.8     2e+03      36      65 ..      32      61 ..      21      85 .. 0.62
   2 !   19.2   0.1   2.8e-07   0.00072       5      69 ..     125     190 ..     121     242 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.8
  Guanylate_cyc 36 nelyarfdelldekkvykvktiGdaymvvs 65
                   +++y+++++l +ek++       d + vvs
     EPA04909.1 32 ASIYKEIQQLFSEKNCLVFLNRADEFFVVS 61
                   357777777777777665555555555554 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 2.8e-07
  Guanylate_cyc   5 sydevtilFadIvgftalssahspievvklLnelyarfdelldekkvykvktiGdaymvvsglp.e 69 
                    s  +v+i+  d+++ t+  + +sp e+   + elya++ ++ ++k+     + Gd +mvv+  + +
     EPA04909.1 125 SEPKVSIMHFDVENLTSKRKIKSPYEITLTIFELYAKMAKFFSKKNSLTFFMGGDNFMVVASEEaK 190
                    6679******************************************************99876533 PP

>> GGDEF_2  GGDEF-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.0    0.0033       8.4      37      94 ..      30      89 ..       5      98 .. 0.72
   2 !    9.6   0.0    0.0004         1      50      95 ..     170     214 ..     130     227 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0033
     GGDEF_2 37 llraleealral..gpdalva.vrgdrlvlllpaedeedaeallerlarrlgglsvriGiG 94
                l++ + +++++l   +++lv+ +r d++ ++  + + ed  ++++ l++ ++  +++i +G
  EPA04909.1 30 LQASIYKEIQQLfsEKNCLVFlNRADEFFVVSNGLTLEDHIEIQKNLEKSFDV-KFSISLG 89
                33334444444444678999835888999999999988888**********99.7777766 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0004
     GGDEF_2  50 pdalvavrgdrlvlllpaedeedaeallerlarrlgglsvriGiGs 95 
                  +  +++ gd++ ++ + e++ + ++++e ++++++  ++ +GiG+
  EPA04909.1 170 NSLTFFMGGDNFMVVASEEAKNSVSEFIELIKNEYDI-TLNCGIGN 214
                 4555678999**************************9.77777776 PP

>> NOG1  Nucleolar GTP-binding protein 1 (NOG1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   6.7e-05      0.17      34      58 .]      31      55 ..      26      55 .. 0.95
   2 ?   -0.7   0.0      0.48   1.2e+03      27      46 ..      62      81 ..      60      87 .. 0.82
   3 ?   -3.3   0.0       3.1   7.8e+03      36      49 ..     157     170 ..     156     174 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.7e-05
        NOG1 34 QlsLleeikelfankpvivvlnKiD 58
                Q s+++ei++lf++k+ +v ln +D
  EPA04909.1 31 QASIYKEIQQLFSEKNCLVFLNRAD 55
                99********************988 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.48
        NOG1 27 cgysleeQlsLleeikelfa 46
                 g +le+ +++ +++++ f+
  EPA04909.1 62 NGLTLEDHIEIQKNLEKSFD 81
                57899999999999999998 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 3.1
        NOG1  36 sLleeikelfankp 49 
                 +L+ ++ + f++k+
  EPA04909.1 157 ELYAKMAKFFSKKN 170
                 79999999999876 PP

>> DUF3908  Protein of unknown function (DUF3908)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.3     0.082   2.1e+02      48      99 ..      41      92 ..      21     117 .. 0.58
   2 ?   11.7   0.1   9.4e-05      0.24      38      98 ..     155     216 ..     142     238 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.082
     DUF3908 48 vdekklellfilkdnkfvkv..giekekrvvieklkydkiknvilktplgddkd 99
                 + +k  l+f+ + ++f +v  g   e++++i+k +++k  +v +   lg + +
  EPA04909.1 41 LFSEKNCLVFLNRADEFFVVsnGLTLEDHIEIQK-NLEKSFDVKFSISLG-YAE 92
                3444444555555555555523456677777776.666666777766666.443 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 9.4e-05
     DUF3908  38 illiytkylfvdekklellfilkdnkfvkvgiekekrvvieklkydkik.nvilktplgddk 98 
                 i  +y+k    + kk  l f++  ++f++v  e+ k  v e++++ k + ++ l++ +g+ k
  EPA04909.1 155 IFELYAKMAKFFSKKNSLTFFMGGDNFMVVASEEAKNSVSEFIELIKNEyDITLNCGIGNGK 216
                 45689****9*************999*************99998755441456777777554 PP

>> F420H2_quin_red  F420H(2)-dependent quinone reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.14   3.6e+02      40      80 ..      45      85 ..      42     101 .. 0.83
   2 ?    9.7   0.0   0.00034      0.87      39      91 ..     168     219 ..     163     243 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.14
                     EEEEEEEEETTEEEEE-SGGGGSSS-HHHHHHHH--EEEEE CS
  F420H2_quin_red 40 ktplgfvrdgdsylvvaskgGapkhpswylNlkanPrvevq 80
                     k+ l+f +  d+++vv++ +  + h +   Nl++  +v+  
       EPA04909.1 45 KNCLVFLNRADEFFVVSNGLTLEDHIEIQKNLEKSFDVKFS 85
                     7889999**********999889898888888887777655 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00034
                      EEEEEEEEEETTEEEEE-SGGGGSSS-HHHHHHHH--EEEEEETTEEEEEEEE CS
  F420H2_quin_red  39 rktplgfvrdgdsylvvaskgGapkhpswylNlkanPrvevqvgakkldvtAr 91 
                      +k++l+f   gd+++vvas    +  ++++  +k + ++ ++ g  +   tAr
       EPA04909.1 168 KKNSLTFFMGGDNFMVVASEEAKNSVSEFIELIKNEYDITLNCGIGN-GKTAR 219
                      799******************99999999999999999988866433.23444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1511.96
//
Query:       EPA04910.1  [L=247]
Description: HpcH/HpaI aldolase/citrate lyase family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.2e-44  150.7   0.0    3.6e-44  150.5   0.0    1.0  1  HpcH_HpaI       HpcH/HpaI aldolase/citrate lyase family
    8.4e-13   48.2   0.0    4.4e-07   29.4   0.0    2.1  2  C-C_Bond_Lyase  C-C_Bond_Lyase of the TIM-Barrel fold
  ------ inclusion threshold ------
      0.032   13.1   0.1      0.042   12.7   0.1    1.1  1  PK              Pyruvate kinase, barrel domain


Domain annotation for each model (and alignments):
>> HpcH_HpaI  HpcH/HpaI aldolase/citrate lyase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.5   0.0   6.1e-48   3.6e-44       1     221 []       6     223 ..       6     223 .. 0.96

  Alignments for each domain:
  == domain 1  score: 150.5 bits;  conditional E-value: 6.1e-48
                 EEEEEEESTSHHHHHHHCTC--SEEEEESSTSSSHHHHHHHHHHHHHHHHHHHHCTTTSSEEEEE-SSTTHHHHHHHGG.HHHTTSSEEEESS--SHHH CS
   HpcH_HpaI   1 riglflpganaalaekaaiagaDsvliDlEdavalaeKdaARvlvsealkqldalaaaasevvVRvnsldselikqdle.vldlgaqvvlvPkvetaee 98 
                 r+++f+pg+n++ ++ka +  aD v +DlEd+    eK++AR+l++++l  ++  +++as+++VR n+ +s+ i +dl+ v+++g++++++Pkv++ +e
  EPA04910.1   6 RSLIFVPGNNQRFLDKAKVLSADIVCFDLEDSIPESEKENARNLIKNTLS-IR--SEYASSIFVRTNAPSSGKIPDDLNkVVQKGIDGIVIPKVNNVKE 101
                 7899******************************************9875.33..46788*************************************** PP

                 HHHHHHHTSHTTTS---HCCC-EEEEEE-SHHHHHTHHHHH.TSTTEEEEEE-HHHHHHHTT-TTSTTSHHHHHHHHHHHHTTHCEEEEEEE.E-SSHH CS
   HpcH_HpaI  99 alevvsalrepekgirganketrllaqiEsaegvknaeeIa.avegldgvflGaeDlsadlgtkrspegtevldareriltaaraagiaaldtvasdid 196
                 ++++++ l   e   +++ k ++++  iEs egv n  +Ia  ++++ +v++G  Dl  dlg + +++ +   ++r +i   a+aag++a+d ++ d +
  EPA04910.1 102 LKKIEKNLSLLE--KKRKLKPIQIIPSIESTEGVVNTYSIAsFSKRIPAVVFGVFDLLNDLGIEYTKDPEGGKYSRAKIPVDAKAAGVSAIDAIWQDLN 198
                 **********99..55567**********************999******************************************************* PP

                 HHHHHHHTTHCEEEEEEHHHHHHHH CS
   HpcH_HpaI 197 daegflaegalfvalGfdgkllinp 221
                 d +g+ ++ a +++lG++gk++i+p
  EPA04910.1 199 DIKGLERDCAIGKSLGYSGKSIIHP 223
                 ************************8 PP

>> C-C_Bond_Lyase  C-C_Bond_Lyase of the TIM-Barrel fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   7.3e-11   4.4e-07      12     146 ..      10     135 ..       5     169 .. 0.69
   2 !   17.2   0.0   3.7e-07    0.0022     248     293 ..     198     243 ..     162     247 .] 0.73

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 7.3e-11
  C-C_Bond_Lyase  12 YmPatrediaekilkqklegltslvlclEDavseeeveaAeenlkellkelaeaekekekeelpllFvRvRspeqlkellerlgealelltGfvl 106
                     ++P++++++++   k k+ ++  ++++lED++ e+e e+A + +k++l+  +e            +FvR   p+  k   +  +   + ++G+v+
      EPA04910.1  10 FVPGNNQRFLD---KAKVLSADIVCFDLEDSIPESEKENARNLIKNTLSIRSE--------YASSIFVRTNAPSSGKIPDDLNKVVQKGIDGIVI 93 
                     66666666555...4566677778999*************9999998876555........4568*****9998876444444447889****** PP

  C-C_Bond_Lyase 107 Pkfts.esleeylealkkanek.lgkklllmPilEteevlek 146
                     Pk+++ ++l+++ + l+ +++k   k + ++P +E+ e + +
      EPA04910.1  94 PKVNNvKELKKIEKNLSLLEKKrKLKPIQIIPSIESTEGVVN 135
                     ***652445555555555443303467999*****9987633 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 3.7e-07
  C-C_Bond_Lyase 248 kdldglirEvalDkanGlvGKtvIhPsqialvqallvVskeeyedA 293
                     +d+ gl r  a  k+ G  GK++IhP q+++ ++++  +k e + A
      EPA04910.1 198 NDIKGLERDCAIGKSLGYSGKSIIHPDQLPITHKIFYPNKLEIQWA 243
                     5788***************************999887666666655 PP

>> PK  Pyruvate kinase, barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1     7e-06     0.042     179     238 ..      77     141 ..      61     166 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7e-06
                 HHHHHHHHHCT-SEEEETTE-SHHHHHHHHH...HHTCCC..TTSEEEEEE-SCHHHHTHHHHHH CS
          PK 179 kadlrfgvkqgvdliaasfvrkasDvkevre...vleeeg..keikiiakienqegvenldeile 238
                  +dl+  v++g+d i++  v + +++k++ +   +le++   k i+ii  ie+ egv n   i  
  EPA04910.1  77 PDDLNKVVQKGIDGIVIPKVNNVKELKKIEKnlsLLEKKRklKPIQIIPSIESTEGVVNTYSIAS 141
                 5799999***********99999999999863336666665689**************9877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1691.82
//
Query:       EPA04911.1  [L=88]
Description: hypothetical protein BG20_I1307 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.31s 00:00:00.71 Elapsed: 00:00:00.47
# Mc/sec: 568.02
//
Query:       EPA04912.1  [L=160]
Description: RDD family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-19   69.2   1.4    4.9e-19   68.9   1.4    1.1  1  RDD       RDD family
  ------ inclusion threshold ------
      0.049   13.9   0.3      0.065   13.5   0.3    1.2  1  TctB      Tripartite tricarboxylate transporter TctB family


Domain annotation for each model (and alignments):
>> RDD  RDD family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.9   1.4   5.5e-23   4.9e-19       2     139 ..      13     137 ..      12     139 .. 0.92

  Alignments for each domain:
  == domain 1  score: 68.9 bits;  conditional E-value: 5.5e-23
         RDD   2 aslgrRllAfliDlvllliislllallivallnakasaneavagslllllllvlllvllvyqllllskkgqTlGklllglkvvdedgrklglaqaliRa 100
                 a+++ R++A+liD+v++++is +++  i+    ++  ++ +      +  ++   ++++ y+++l++ kgqT+Gk++l lk+++ +g+k++l+ ++i +
  EPA04912.1  13 AKWSERFFAWLIDFVIISVISTIAISSIFG---SIDYDFNEKFFWAEMTQFIPTSVIFFGYWVILEYLKGQTIGKKILNLKITNMHGKKPDLKGVIISS 108
                 89***********************99999...67889999999999999999999*****************************************99 PP

         RDD 101 lllllllvlglslvlllllligflfvlfsrkrqalhDkl 139
                 +          + ++ll + +g+ +++ ++krq++  k+
  EPA04912.1 109 F----------GKAFLLPIDVGLGWIFTNEKRQRIFNKI 137
                 6..........7888888888889999999**9999887 PP

>> TctB  Tripartite tricarboxylate transporter TctB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.3   7.2e-06     0.065      27      97 ..      16     114 ..       4     143 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.2e-06
        TctB  27 gpgffPlll.gvllallgllllv.aadgekeekearedwrkllklvlallaalllyalllepl.........................Gfilata..lf 96 
                 + +ff +l+  v++ +++++ +       + + +++++w +   +++ + ++++ y+++le+l                         G i++++  +f
  EPA04912.1  16 SERFFAWLIdFVIISVISTIAISsIFGSIDYDFNEKFFWAEMT-QFIPTSVIFFGYWVILEYLkgqtigkkilnlkitnmhgkkpdlkGVIISSFgkAF 113
                 4679999988777777764444442233344445555555555.9999999************9999999999**********************9866 PP

        TctB  97 l 97 
                 l
  EPA04912.1 114 L 114
                 6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       759  (0.0423336); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1049.47
//
Query:       EPA04913.1  [L=184]
Description: hypothetical protein BG20_I2224, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
       0.01   16.2   1.8      0.021   15.1   1.8    1.6  1  Calycin_like  Calycin-like beta-barrel domain


Domain annotation for each model (and alignments):
>> Calycin_like  Calycin-like beta-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   1.8   1.2e-06     0.021      10     113 ..      20     130 ..      15     140 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.2e-06
                   EEEETTEE---B-S-EEEEEE-SSS-EEEE.....EE-GG..G------EEEEEEEEE-SSSSSBEEEEEEEEE-TT--E.....EEEEEE.EEE.E CS
  Calycin_like  10 svsvggeespsdadakvtitknedgtvnls.....Lknfs.fgelplGditvdnvkvtkeggsyttfsgsqkltlagggdaee..atvsls.Gti.s 96 
                    v++++e++++d+++++ i+ +++g++        +++f  ++++++Gdi vd++ vt++  +y  f g+ +    +++ +++  + v+ + G + s
    EPA04913.1  20 GVQITSEKNTKDKKETIEISFDNNGSIIADkkcciIEKFMyLTPIKIGDILVDDLIVTSDA-TY-EFDGKSRRVWIAQDVKKQdtLIVDKQtGLVlS 114
                   5888999999999999999999998885431122255566666****************97.77.88887766665555555557555555566666 PP

                   TTEEEEEEEEE..ETT- CS
  Calycin_like  97 gkklnltitikvkdgam 113
                   ++  ++ ++ik+ d+++
    EPA04913.1 115 DSHKETGLNIKW-DKTE 130
                   666666666666.4444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       821  (0.0457917); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1215.91
//
Query:       EPA04914.1  [L=140]
Description: hypothetical protein BG20_I2227 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.13   12.2   0.0       0.15   12.1   0.0    1.1  1  PepSY_TM_like_2  Putative PepSY_TM-like


Domain annotation for each model (and alignments):
>> PepSY_TM_like_2  Putative PepSY_TM-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   8.1e-06      0.15      19      60 ..       7      49 ..       2     102 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.1e-06
  PepSY_TM_like_2 19 vglllFav..tGitLNhaeqieaepsvtekelelpeellallke 60
                     + +llF+v  tG+++N a++i a+++ ++++++ ++++l++  +
       EPA04914.1  7 I-ILLFSVliTGLIINPANTIFAQTTGNSTNTNSTATTLDESMK 49
                     4.78998555*************999888888777766654433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 877.79
//
Query:       EPA04915.1  [L=277]
Description: methyltransferase domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-10   41.8   0.0    2.2e-10   41.1   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    4.3e-05   24.1   0.0    6.8e-05   23.5   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
     0.0003   20.6   0.0     0.0005   19.9   0.0    1.4  1  Methyltransf_31  Methyltransferase domain
     0.0035   18.0   0.0      0.006   17.3   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
     0.0045   16.9   0.0     0.0099   15.7   0.0    1.7  1  Methyltransf_8   Hypothetical methyltransferase


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   0.0   6.1e-14   2.2e-10       1      95 [.      77     168 ..      77     169 .. 0.87

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 6.1e-14
                      EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHHHHHHHHHHEEEEE CS
  Methyltransf_11   1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedpekalkeiaRvLkpgG 92 
                      +dvG+G  + a  + +++   ++++++++  +l  +     +++ ++ f  ++ +klpf+dns+D v++ e+ +h++ +++++ e +R+Lk +G
       EPA04915.1  77 VDVGSGLSAPAIFWRDKYekLDLFCININYDQLSFS-----GPQKNIHFFNSTSTKLPFADNSVDRVLALESSQHFKPLKDFILESKRILKSNG 165
                      599999999999999888778888888888888333.....4444599********************************************** PP

                      EEE CS
  Methyltransf_11  93 llv 95 
                      +l 
       EPA04915.1 166 ILT 168
                      985 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   1.9e-08   6.8e-05       2      97 .]      77     165 ..      76     165 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.9e-08
                      EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHHHHHHHHHHHHHEEE CS
  Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsdedlekalkeiarvLkp 95 
                      +d+G G    ++ + ++++k ++ ++ i+ ++l     +      n++f +   ++lpf+d+s+D v++  + +h++   l++++ e +r+Lk 
       EPA04915.1  77 VDVGSGLSAPAIFWRDKYEKLDLFCININYDQLSFSGPQK-----NIHFFNSTSTKLPFADNSVDRVLALESSQHFK--PLKDFILESKRILKS 163
                      5888888888888888887788888888888888766655.....9***********************88899998..5889**********9 PP

                      EE CS
  Methyltransf_25  96 gG 97 
                      +G
       EPA04915.1 164 NG 165
                      98 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   1.4e-07    0.0005       2     117 ..      71     177 ..      70     215 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.4e-07
  Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnevlnaladpdkile 95 
                      +k+++++D+G+G ++ ++ +    ++k +++ i i+ + ++++         +n++F  +  ++l+  ++d+++D +l+ e  ++++ +++++ 
       EPA04915.1  71 EKAKNLVDVGSGLSAPAIFWR-DKYEKLDLFCININYDQLSFSGPQ------KNIHFFNSTSTKLP--FADNSVDRVLALESSQHFKPLKDFIL 155
                      689999***************.558899999999999999999885......89************..************************** PP

  Methyltransf_31  96 eiervlkpggilliedprllae 117
                      e +r lk++gil ++ p ++++
       EPA04915.1 156 ESKRILKSNGILTLAIPVTMQN 177
                      *************998886655 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.7e-06     0.006       1      99 []      77     167 ..      77     167 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.7e-06
  Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.ssfDlvvasnvlhhlkdirevldnirklL 93 
                      +++G+G ++ +  +++k + +++ ++ i+ +++      ++  ++    n+++++  + +l+   +s+D v+a++  +h+k++++++ + ++ L
       EPA04915.1  77 VDVGSGLSAPAIFWRDKYEKLDLFCININYDQL-----SFSGPQK----NIHFFNSTSTKLPFAdNSVDRVLALESSQHFKPLKDFILESKRIL 161
                      589999999999999999999999999999999.....5555553....44444444443333356**************************** PP

  Methyltransf_12  94 kpgGrl 99 
                      k +G+l
       EPA04915.1 162 KSNGIL 167
                      ****87 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.8e-06    0.0099     114     157 ..     126     170 ..     102     222 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.8e-06
                     TS-S--TT-EEEEEEES.---SS-HHHHHHHHHHHEEEEEEEEEE CS
  Methyltransf_8 114 akvPledesvdvavfcl.slmgtnladflkeanrvlkvGGllkva 157
                     +k+P +d+svd ++    s   + l+df+ e +r+lk  G+l +a
      EPA04915.1 126 TKLPFADNSVDRVLALEsSQHFKPLKDFILESKRILKSNGILTLA 170
                     79*********7765541667899******************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2042.63
//
Query:       EPA04916.1  [L=274]
Description: phosphoribosylaminoimidazolesuccinocarboxamide synthase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.9e-71  239.6   0.2    4.7e-71  239.3   0.2    1.1  1  SAICAR_synt  SAICAR synthetase


Domain annotation for each model (and alignments):
>> SAICAR_synt  SAICAR synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  239.3   0.2   2.6e-75   4.7e-71       2     249 ..       4     235 ..       3     238 .. 0.93

  Alignments for each domain:
  == domain 1  score: 239.3 bits;  conditional E-value: 2.6e-75
                  EEE-SSEEEEE-SSTTEEEEEEESEEEECCCTEEEEETTHHHHHHHHHHHHHHHHHH--BSEEEE.....-SSSEEEEE-EEEESEEEEEEEE--HHH CS
  SAICAR_synt   2 lyeGKvrdvYeledddklllvakDrisAfdvvlkeeipgKGkvltqlsafwfeklekipnhliksldpeqlegrsmlvkklkmlpvEvvvRgyltGsl 99 
                  l++GKv+d+Y++ d+++ll+ ++Dr+sA+dv+ +e+ip+KGkvl+++++fwf+ l+ +pnh++k+      ++++++vkk+kmlp+E+vvRgy  Gsl
   EPA04916.1   4 LTSGKVKDLYDI-DENTLLFKFSDRVSAYDVKFNENIPQKGKVLCKFAEFWFNELT-VPNHFVKR-----QSDTEIIVKKMKMLPIECVVRGYFYGSL 94 
                  579*********.888***************************************6.8*****77.....689************************* PP

                  .......HH....HH..T-..-TT-EEEEEEEEEEE--CCCT.S-EE-HHHHH.HTT..-HHHHHHHHHHHHHHHHHHHHHHHHTTEEEEEEEEEEEE CS
  SAICAR_synt 100 wkeykksgkvcgirlpegl..kegeklpepiftpstKaeegehDeniseeevvealg..teeeaeeieelalavyekaaelaaergiilvDtKlEFGl 193
                  +  +kk+       lp+g   + + kl epif+p+tK+e   hD +i++ +++e+ +  tee+++ +e++++++y+k+++la++ g il+D KlEFG+
   EPA04916.1  95 VGRWKKGDV----MLPNGTntTLAAKLLEPIFDPTTKSE---HDIPINKTKALEM-NlvTEEQYAWLEKTSIDIYKKMSALADKAGFILADLKLEFGI 184
                  999998877....666655116689************98...6**********55.5699************************************** PP

                  ETTTTEEEEES--.STTTEEEEETTT.....GGGB-STHHHHTT-STHHHHHHHHH CS
  SAICAR_synt 194 deedgelvLaDevltpDssRfwdaetyeegkeqeslDKqfvRdwleeveekwkekl 249
                     dg+++L+D +  pD  R+w++++y+ g++qe +DKq++Rdwl+e  ++++++ 
   EPA04916.1 185 L--DGQITLGDSI-GPDEYRLWPKDSYKIGQTQEAYDKQILRDWLTE--QGYQKQF 235
                  9..7*********.********************************9..9998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1749.24
//
Query:       EPA04917.1  [L=144]
Description: hypothetical protein BG20_I1097 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.3e-19   69.5   0.5    2.8e-19   69.2   0.5    1.0  1  DUF2299    Uncharacterized conserved protein (DUF2299)
  ------ inclusion threshold ------
      0.031   14.6   0.1      0.048   14.0   0.1    1.3  1  HAD_SAK_2  HAD domain in Swiss Army Knife RNA repair proteins


Domain annotation for each model (and alignments):
>> DUF2299  Uncharacterized conserved protein (DUF2299)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.2   0.5   3.1e-23   2.8e-19       2     127 ..       5     129 ..       4     133 .. 0.92

  Alignments for each domain:
  == domain 1  score: 69.2 bits;  conditional E-value: 3.1e-23
                 HHHHHHHTT-EEEE---TTEEEEEEEE-STT..-EEEEEEETT-SSEEEEEEEEE--HHHHHHHHHS-HHHHHHHHHHHHHHHTTTT-EEEEE-TTS-- CS
     DUF2299   2 ikeWLkeeGlkveevpdanaefhilveppqpggvvvdvikpkgksdvvvvgmgvkvseehkkalsslkeeerkeflselkrdLlrlcvdfqlipqdeel 100
                 i++WL++eGl ++e+++ +++f+ilv++  + g + ++++pk++++v+v+g +v +++++++++ ++ e+e+++f    +r+++++c ++q+i+   + 
  EPA04917.1   5 IERWLIHEGLSFQEMKNPENTFQILVKHAGKYGIPTEIFEPKSQPGVIVIGAKVILKDNQIARYLGFTEDEKEKF----ERRVAEYCNSIQAINRIVTE 99 
                 99*************************************************************************....99999999999998887766 PP

                 ...-EEEEEEEEEG.GG--HHHHHHHHHHH CS
     DUF2299 101 ..pqsiqvskeiyk.dgltknelldavkrv 127
                   +q++ v  ++ + ++++++ +lda+++ 
  EPA04917.1 100 dgKQKVGVFVVLDDkENINQQTVLDAINKA 129
                 779*********862666********9875 PP

>> HAD_SAK_2  HAD domain in Swiss Army Knife RNA repair proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   5.3e-06     0.048      63     119 ..      59     119 ..      53     135 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.3e-06
   HAD_SAK_2  63 llkaagrpriigvtpdlpeeeseeekk..sRaqeilewlrrh..eeveawvalDDkaelde 119
                 +lk ++  r +g t+d +e+ ++   +  +  q i + + +   ++v+ +v+lDDk++ ++
  EPA04917.1  59 ILKDNQIARYLGFTEDEKEKFERRVAEycNSIQAINRIVTEDgkQKVGVFVVLDDKENINQ 119
                 5666668899999999999877666668999*********99*************554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       911  (0.0508115); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 903.92
//
Query:       EPA04918.1  [L=37]
Description: hypothetical protein BG20_I1095 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 226.85
//
Query:       EPA04919.1  [L=59]
Description: ribosomal protein S14p/S29e [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-08   33.6   2.7    3.3e-08   33.2   2.7    1.2  1  Ribosomal_S14  Ribosomal protein S14p/S29e
  ------ inclusion threshold ------
      0.058   13.3   3.1       0.12   12.2   3.0    1.7  2  zf-FPG_IleRS   Zinc finger found in FPG and IleRS


Domain annotation for each model (and alignments):
>> Ribosomal_S14  Ribosomal protein S14p/S29e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   2.7   3.7e-12   3.3e-08       7      52 ..      13      57 ..       9      58 .. 0.90

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 3.7e-12
                   -SS..CTTT---SSS--SSSEE-GGG-..EHHHHHHHTTT...TT-EE CS
  Ribosomal_S14  7 rnssptrirnrCrvtGrprGvirkfgL..sRicfRelAlkgelpGvkK 52
                   ++   +r+++ C+ +G   +vi+k+ L  +R cfRe A      G++K
     EPA04919.1 13 KKHDFGRGSKWCKRCGDYTAVIQKYDLmiCRRCFREVATS---LGFRK 57
                   455569********************************99...99988 PP

>> zf-FPG_IleRS  Zinc finger found in FPG and IleRS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.5   0.00045         4      18      27 ..      18      27 ..      18      27 .. 0.95
   2 ?   12.2   3.0   1.4e-05      0.12       4      27 ..      24      45 ..      21      47 .. 0.94

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00045
                  TEEEEE-TTT CS
  zf-FPG_IleRS 18 grstyfCprC 27
                  gr++ +C rC
    EPA04919.1 18 GRGSKWCKRC 27
                  799******* PP

  == domain 2  score: 12.2 bits;  conditional E-value: 1.4e-05
                  -TTT--BBEEEECTTEEEEE-TTT CS
  zf-FPG_IleRS  4 CpRCwryiervgqagrstyfCprC 27
                  C RC+ y++ + +  +  ++C rC
    EPA04919.1 24 CKRCGDYTAVIQK--YDLMICRRC 45
                  *************..********* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.50
# Mc/sec: 355.76
//
Query:       EPA04920.1  [L=174]
Description: transcriptional regulator, ArsR family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-08   34.2   0.0    3.6e-08   33.3   0.0    1.4  1  HTH_20          Helix-turn-helix domain
    3.1e-07   30.2   0.4    2.4e-06   27.3   0.4    2.2  1  HTH_5           Bacterial regulatory protein, arsR family
    1.6e-06   27.9   0.3    3.5e-06   26.9   0.3    1.6  1  HTH_12          Ribonuclease R winged-helix domain
    0.00012   22.2   0.3    0.00027   21.0   0.3    1.7  1  FUR             Ferric uptake regulator family
     0.0073   16.3   1.0      0.023   14.7   0.4    1.9  2  HU-DNA_bdg      DNA-binding domain
  ------ inclusion threshold ------
      0.014   15.4   0.1      0.035   14.2   0.0    1.7  2  Replic_Relax    Replication-relaxation
      0.026   14.5   0.3      0.059   13.3   0.3    1.6  1  Type2_restr_D3  Type-2 restriction enzyme D3 domain
      0.028   14.4   0.8       0.35   10.9   0.8    2.3  1  HTH_11          HTH domain


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.0   1.6e-11   3.6e-08       4      58 ..      22      80 ..      20      83 .. 0.91

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 1.6e-11
                HHHHS-HHHHHHHHHHSTCTTB-HHHHHHHH.....TS-HHHHHHHHHHHHHCTTEEEEC CS
      HTH_20  4 aeALahPvRrrilraLaraegltaselaerl.....dlskntlsyHLrvLeeagLvevvr 58
                a+A+ +P R +i   L   ++l+a ++a +l       + +t+++HL++L + gL+e  +
  EPA04920.1 22 ARAIEDPARSKIIEIL-YHRALSADQIANELkktgyKKALTTVRHHLDILKDSGLIEIAK 80
                789*************.**************666444*******************9765 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.4   1.1e-09   2.4e-06       1      46 [.      27      77 ..      27      77 .. 0.89

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 1.1e-09
                SHHHHHHHHHHTTSSEEHHHHHHHHTS-H.....HHHHHHHHHHHHTTSEE CS
       HTH_5  1 dptRlkILklLaegelcvcelaeelglsq.....stvShHLkkLreaGLVe 46
                dp+R+kI+ +L  + l++ ++a+el+++       tv+hHL +L+++GL+e
  EPA04920.1 27 DPARSKIIEILYHRALSADQIANELKKTGykkalTTVRHHLDILKDSGLIE 77
                8************************9864333339**************96 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.3   1.5e-09   3.5e-06      11      49 ..      39      77 ..      31      89 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 1.5e-09
      HTH_12 11 dkpigakeiaeeLkkrgydigeravRyrLrkleergltr 49
                 + ++a +ia+eLkk+gy+    +vR +L +l + gl++
  EPA04920.1 39 HRALSADQIANELKKTGYKKALTTVRHHLDILKDSGLIE 77
                4679********************************997 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.3   1.2e-07   0.00027       9      66 ..      29      84 ..      26     140 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.2e-07
                HHHHHHHHHHHHSSSBEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEETTS CS
         FUR  9 qRekilevlekseehlsaeevykelkeedpeislaTVYrtLklleeaglvkelefedg 66
                 R ki+e+l++    lsa+++ +elk+++ +  l+TV   L++l+++gl++  ++e++
  EPA04920.1 29 ARSKIIEILYHRA--LSADQIANELKKTGYKKALTTVRHHLDILKDSGLIEIAKIEES 84
                799******9876..9**********************************99988854 PP

>> HU-DNA_bdg  DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.4     1e-05     0.023      14     101 ..      27     115 ..      14     136 .. 0.81
   2 ?    3.0   0.1     0.044        98      17      51 ..     108     142 ..     101     166 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1e-05
                 -----EEEEE----EE-HHHHHHHHHHH-TTS-HHHHHHHHHHHHHH...HHHHHTTT-EEE-SSEEEEEEEES-BC..CCC--TTT-EEE CS
  HU-DNA_bdg  14 dkksdyiaqvessgsltledIidemvkegtevrketienilnlykre...vseaileGysVntglgrasltikGvfegkeekFdpkkhsln 101
                 d  +++i ++   ++l+ ++I++e++k g +   +t+ + l+++k+     +  i+e +   t+++++s ++ G +    ++Fd+k  ++ 
  EPA04920.1  27 DPARSKIIEILYHRALSADQIANELKKTGYKKALTTVRHHLDILKDSgliEIAKIEESRGAITKFYSTSTKLLGYVA--PDDFDSKYSKVI 115
                 566789999***********************************997322356789999999*********999999..999999887774 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.044
                 --EEEEE----EE-HHHHHHHHHHH-TTS-HHHHH CS
  HU-DNA_bdg  17 sdyiaqvessgsltledIidemvkegtevrketie 51 
                 +++  +v++s s+++e+I+ ++  + t  +k   e
  EPA04920.1 108 DSKYSKVIDSTSVKIEKILRAITPKTTRTKKIKGE 142
                 56778999999*********999998887775555 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.7   3.9e+03      98     116 ..       9      27 ..       4      30 .. 0.77
   2 ?   14.2   0.0   1.6e-05     0.035       6      46 ..      38      83 ..      35     107 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.7
  Replic_Relax  98 lavnelflalaaaaRetpd 116
                   + vn ++++ +++aR ++d
    EPA04920.1   9 IKVNRILTTSVKHARAIED 27 
                   6788889999999887665 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 1.6e-05
  Replic_Relax  6 ehrvlTtrqiarllfashra....tarrrLarLrelgllsr.lrkr 46
                  +hr l+++qia+ l +++ +    t+r  L +L++ gl++    ++
    EPA04920.1 38 YHRALSADQIANELKKTGYKkaltTVRHHLDILKDSGLIEIaKIEE 83
                  7**************************************9854433 PP

>> Type2_restr_D3  Type-2 restriction enzyme D3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.3   2.6e-05     0.059      15      62 ..      30      75 ..      28      83 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.6e-05
  Type2_restr_D3 15 RtiilkylleskkrrsleeikayLklagleEdveTIkDDiqgliniGl 62
                    R+ i+++l      +s ++i + Lk  g +  ++T++  +  l + Gl
      EPA04920.1 30 RSKIIEILYHR--ALSADQIANELKKTGYKKALTTVRHHLDILKDSGL 75
                    999*****555..5***********************99888888886 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.8   0.00016      0.35       3      51 ..      31      86 ..      29      87 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00016
      HTH_11  3 lqilelLleargpisgeeLAeeLnvSr.....rtvrrdIkaLeelg....vpIesepg 51
                ++i+e+L+ +r  +s++++A eL+ +      +tvr ++++L+++g    ++Ie ++g
  EPA04920.1 31 SKIIEILY-HR-ALSADQIANELKKTGykkalTTVRHHLDILKDSGlieiAKIEESRG 86
                78999993.33.49*********9995555559*************988888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       734  (0.0409393); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1145.39
//
Query:       EPA04921.1  [L=142]
Description: hypothetical protein BG20_I1072 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-06   28.0   0.0    2.3e-06   28.0   0.0    1.1  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra
     0.0022   18.2   0.0     0.0027   17.9   0.0    1.2  1  Polyketide_cyc   Polyketide cyclase / dehydrase and lipid tra


Domain annotation for each model (and alignments):
>> Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   2.5e-10   2.3e-06       4     107 ..       4     110 ..       1     135 [. 0.78

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 2.5e-10
                      EEEEEEESS-HHHHHHHHTTTTGGGG....T-TTEEEEECSESTSSSTTTEEEEECCCSSEEEEEEEEEETTTTEEEEEEE..SSS-TSEEEEE CS
  Polyketide_cyc2   4 vtvsvviaappekVwalvsdfenwpr....Whpevarveleggggpargvegtvrvggrgtvreelvevdpegrllsyriv.kpvpvanyvatw 92 
                      +  ++ i+a+  kV+++ s+fen+++    ++p+v++  ++g + +  +ve+++r +g + +++    v +++ l+++ i  ++ ++++ +  +
       EPA04921.1   4 IVFEKIIKADRKKVFEITSNFENFQKilpqYYPSVRTISVRG-NTS--VVEEHLRIAG-RELVMMAKHVIDDPILHEIFIIgGDSKGTHITYHY 93 
                      556678*******************85555799999999997.888..999*******.56666666664449**9999977889999666666 PP

                      EEEECCET..EEEEEEE CS
  Polyketide_cyc2  93 tvtpdggg..trvtwtg 107
                      +  p g+    +v w+ 
       EPA04921.1  94 EHIPNGTKliVEVNWKL 110
                      66666665655566765 PP

>> Polyketide_cyc  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   3.1e-07    0.0027       1     129 [.      10     136 ..      10     137 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3.1e-07
                     ESS-HHHHHHHHTTTGGCCSCCCCEE.EEEE.SSSEE...E.EEECSTTSSCEEEEEEEEEEETTTEEECTTCCCCCEEEEEEEECTECCEEECE CS
  Polyketide_cyc   1 vpapadqvyalvadvesypeflphcs.svevleeaesglsa.dlevgfggltesftarvtldppeeitfklvegdfkslegkWtieslppnsggt 93 
                     ++a+ ++v+++ +++e++ ++lp +  sv+ ++  ++ +s+ + ++  +g      a+ + d p   +  +++gd k  +++ + e  p    gt
      EPA04921.1  10 IKADRKKVFEITSNFENFQKILPQYYpSVRTISVRGN-TSVvEEHLRIAGRELVMMAKHVIDDPILHEIFIIGGDSKGTHITYHYEHIPN---GT 100
                     678999*****************99856888888886.555578888888888888888777777789*********************7...** PP

                     EEEEEEEEEEE-SSCHHHHHHHHHHHHHHHHHHHHH CS
  Polyketide_cyc  94 rtkvalevdfkfaspllgalvgqvaervldellaal 129
                     ++ v++ +++k+ ++l   + +q + ++  ++++++
      EPA04921.1 101 KLIVEVNWKLKGVMRLSSIIGRQDISKEYSKIVDEF 136
                     *****************9999998888877777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 937.61
//
Query:       EPA04922.1  [L=123]
Description: hypothetical protein BG20_I1075 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       920  (0.0513135); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 847.06
//
Query:       EPA04923.1  [L=161]
Description: hypothetical protein BG20_I1094 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.6e-10   40.2   1.9    4.6e-10   39.9   1.9    1.1  1  DUF4352      Domain of unknown function (DUF4352)
  ------ inclusion threshold ------
      0.014   15.4   0.9      0.052   13.6   0.1    2.1  3  Aegerolysin  Aegerolysin
        4.3    6.7   7.6       0.52    9.7   2.9    1.7  2  DUF5305      Family of unknown function (DUF5305)


Domain annotation for each model (and alignments):
>> DUF4352  Domain of unknown function (DUF4352)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   1.9   7.6e-14   4.6e-10       2     114 ..      35     142 ..      34     152 .. 0.85

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 7.6e-14
                 STCEEECCTTEEEEEEEEEEEEEETTS-CEETT-.SEEEEEEEEEEE-SSS-EEEEGGGEEEEETTEEE-BEEESCCCCTTB--EEEE-TT-EEEEEEE CS
     DUF4352   2 kvgetvkvgdlevtVnsveytksvgkneylqpdaggeflivdvtvkNkgkealtvnssqfkLkdgdgkeydadlsasskaddlflgtlnpGkkvtGklv 100
                 + ge+v+vg +e+tV      + +g+ne++   ++++f+++++t kN++ e++ ++  qf L+d+++++++++ +     +dl+++ l p+k v  +  
  EPA04923.1  35 NSGESVTVGPVEYTVVFD--GTNQGNNETT---PENTFVKIKITAKNISIEKTRISGGQFYLVDDKQQKVQPTYGK-FTPEDLLDEWLEPNKPVVRTTQ 127
                 78*************655..7777755555...5678**********************************99886.666679**************** PP

                 EEESTT-CG.EEEEE CS
     DUF4352 101 Fdvpkgkkk.leLey 114
                 Fdvp ++ k + + +
  EPA04923.1 128 FDVPFDELKqYNVMI 142
                 ****99986566555 PP

>> Aegerolysin  Aegerolysin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       1.3   8.1e+03     110     128 ..      30      49 ..      23      54 .. 0.54
   2 ?   13.6   0.1   8.7e-06     0.052       4      41 ..      68     101 ..      65     105 .. 0.84
   3 ?   -0.7   0.0      0.23   1.4e+03      83     110 ..     124     152 ..     114     155 .. 0.66

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.3
                  EEEEE-.-CSS--EEEEEEE CS
  Aegerolysin 110 etggwn.essgalgtVtvei 128
                  +  + n  +s ++g V++++
   EPA04923.1  30 NFITANsGESVTVGPVEYTV 49 
                  43333334445666666666 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 8.7e-06
                  EEE.EEEE-SSS-EEEEEEEEEESEEEETTEEEEEE-G CS
  Aegerolysin   4 vkieilnelksedlkirnaklesGkfykendkdkeita 41 
                  vki+    +  ++++i++++++ G+fy   dk++++++
   EPA04923.1  68 VKIK----ITAKNISIEKTRISGGQFYLVDDKQQKVQP 101
                  5554....46779*********************9987 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.23
                  EEEEEEE-TTS.SB-EEEEE---TTEEEE CS
  Aegerolysin  83 ctlyWdcPwgs.ksNkfevsesdkkYkve 110
                  +t ++d P  + k+ +++++ s+++  v+
   EPA04923.1 124 RTTQFDVPFDElKQYNVMIRPSKQQSSVD 152
                  56667777766666666666666665555 PP

>> DUF5305  Family of unknown function (DUF5305)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.7      0.21   1.3e+03     118     135 ..       7      24 ..       2      42 .. 0.51
   2 ?    9.7   2.9   8.6e-05      0.52      34     113 ..      25     103 ..      22     108 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.21
     DUF5305 118 lliilgllaliglvvlir 135
                 ++ii ++++ ++++ + +
  EPA04923.1   7 IIIIGAIIISMAAAMFMY 24 
                 233333333333333333 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 8.6e-05
     DUF5305  34 ndrieeieeelglsvgtsel.tvvlevnvegeidgesieesktsrlpiplteqtyeikkdetdeengeitetvtvkespsl 113
                  ++ +++ ++ ++++  +++  v+++v ++g+ +g++ ++ +++ ++i++t + ++i+k+  +  + ++   ++ k++p++
  EPA04923.1  25 TQYQTNFITANSGES--VTVgPVEYTVVFDGTNQGNNETTPENTFVKIKITAKNISIEKTRISGGQFYLVDDKQQKVQPTY 103
                 555666666555333..333148889999999999**************************99999999999999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1230  (0.0686039); expected 358.6 (0.02)
Passed bias filter:                      744  (0.041497); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.34s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 923.51
//
Query:       EPA04924.1  [L=135]
Description: PPOX class putative F420-dependent enzyme [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.1e-16   57.8   0.0    1.3e-15   57.3   0.0    1.2  1  Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
  ------ inclusion threshold ------
      0.053   13.5   0.0      0.084   12.9   0.0    1.3  1  Pyridox_ox_2    Pyridoxamine 5'-phosphate oxidase
       0.09   12.8   0.0        0.2   11.7   0.0    1.6  1  RcnB            Nickel/cobalt transporter regulator


Domain annotation for each model (and alignments):
>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.3   0.0   2.2e-19   1.3e-15       1      84 [.       1      83 [.       1      86 [. 0.95

  Alignments for each domain:
  == domain 1  score: 57.3 bits;  conditional E-value: 2.2e-19
                    HHHHHHHHHHHSSEEEEEEEETTSEEEEEEEEEEEETTTTEEEEEEETTSHHHHHHHHH-EEEEEEEETT.GSEEEEEEEEEEEE CS
  Putative_PNPOx  1 ldeelreflaeskavvlATvdedGrPnvspvllkagdgrdgivfatnadsrklrnleenprvallfldde.lgrgvrieGtaelv 84
                    +d+++++++++ ++v++AT+ +dG+P++spv+  ++ g   i++ t++ + k++n+ ++prva+++++ +      +i+G++e +
      EPA04924.1  1 MDKKAQKLFEQKNIVFIATIMKDGSPQLSPVWANYDSGY--ILVNTAEGRIKHKNVLRDPRVAVSVISHDnPLDMTTIRGRVEEI 83
                    799*******************************88888..*****************************9999999****9976 PP

>> Pyridox_ox_2  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.4e-05     0.084       5     136 ..       5     123 ..       2     126 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.4e-05
                   HHHHHHC-SEEEEEEEE.TTEEEEEEEEEEEETTEEEEEEETTSHCCHCCCT--.ECEEEEEEEEEEE-SEGGEEEEEEEEEEEEEEEE--HHHHHH CS
  Pyridox_ox_2   5 ilalLdegevgrlafvd.dgepvilPvnyvvdgdslyfhgakgsrlaaalrgap.vcvvvtevdglvlarsfnslnyrSVvvrGraeevtdeeekae 99 
                   + +l +++ +  +a+ + dg p + Pv   +d + +++ +a+g  +++     p v+v+v   d+  l+ +         ++rGr+ee+ ++ +  +
    EPA04924.1   5 AQKLFEQKNIVFIATIMkDGSPQLSPVWANYDSGYILVNTAEGRIKHKNVLRDPrVAVSVISHDNP-LDMT---------TIRGRVEEIISDYDYLH 91 
                   667888888889999886888*********************997777666455599999887772.2222.........48888888855555555 PP

                   HCCCHHHHHSTTT.GGCSB---CCCCCTEEEEEEEEEE CS
  Pyridox_ox_2 100 alellvekivpgr.wenlrpptrkelkatsvlrlkiee 136
                   a++l ++ ++ ++ +       +++ ++  +l++k+e+
    EPA04924.1  92 ADKLTLQ-YMGKEhYP-----FKRDDEKRIILKIKPEH 123
                   5555444.43333233.....22333444566666665 PP

>> RcnB  Nickel/cobalt transporter regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   3.4e-05       0.2      32      49 ..      32      49 ..      30      51 .. 0.96

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.4e-05
        RcnB 32 WvriggdyvLvaiatGvI 49
                W +++  y+Lv+ a G+I
  EPA04924.1 32 WANYDSGYILVNTAEGRI 49
                *****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 925.38
//
Query:       EPA04925.1  [L=86]
Description: phosphoribosylformylglycinamidine synthase, PurS protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-18   65.1   0.8    5.3e-18   65.0   0.8    1.0  1  PurS      Phosphoribosylformylglycinamidine (FGAM) synthase


Domain annotation for each model (and alignments):
>> PurS  Phosphoribosylformylglycinamidine (FGAM) synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.0   0.8     3e-22   5.3e-18       2      76 ..       6      82 ..       5      83 .. 0.93

  Alignments for each domain:
  == domain 1  score: 65.0 bits;  conditional E-value: 3e-22
                EEEEEEE-TTS--HHHHHHHHHHHHT.THTTEEEEEEEEEEEEEEE-SSHHHHHHHHHHHHHHT.TS-TTTEEEEEE CS
        PurS  2 akveVtlKkgvlDpqGkavkkalksl.gyeevedvrvgkyieleleaedeeeaeeeveemcekl.LaNpviedyeie 76
                ++v+++ K+g+ Dp+G+++ ++l    +++ v++++++k+++++++++d+++a+ +v+e+c++l ++Np++ ++ i+
  EPA04925.1  6 VHVTIENKPGISDPEGETILNDLVLKgNHSAVSKIKTAKMLKFTIKEKDKKSAKITVQEICDELrIYNPMVSKVIID 82
                89************************45556***************************************9988665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       866  (0.0483016); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 551.43
//
Query:       EPA04926.1  [L=721]
Description: phosphoribosylformylglycinamidine synthase II [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-49  168.4   0.2    5.7e-29  101.3   0.3    2.2  2  AIRS_C          AIR synthase related protein, C-terminal doma
    6.4e-38  129.3   0.0    2.6e-19   69.7   0.2    2.7  2  AIRS            AIR synthase related protein, N-terminal doma
    5.6e-11   42.8   0.1    1.6e-10   41.3   0.1    1.9  1  FGAR-AT_linker  Formylglycinamide ribonucleotide amidotransfe
  ------ inclusion threshold ------
      0.036   14.7   2.1       0.04   14.5   0.2    2.0  2  T_Ag_DNA_bind   Origin of replication binding protein


Domain annotation for each model (and alignments):
>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.3   0.3   1.3e-32   5.7e-29       1     149 [.     186     332 ..     186     337 .. 0.90
   2 !   65.0   0.0   1.9e-21   8.5e-18       2     148 ..     548     687 ..     547     692 .. 0.95

  Alignments for each domain:
  == domain 1  score: 101.3 bits;  conditional E-value: 1.3e-32
                 STTEEEEEEET....SSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHHHHHHHTTTEEEEEECGTHH CS
      AIRS_C   1 kpGdvliltgs....lGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaalkglvkaahDvTgGGLlgalaemapasgvgaeidldkvp 95 
                 k Gd ++l+g+    +G+gg+ +++ +  le+e  ++savq+ d++ e+  i++ +++   ++l++a++D++gGGL++a++e a+a  +g+e+d+dkv 
  EPA04926.1 186 KKGDIVVLLGGstgrDGIGGSQFAS-D-SLESE--NRSAVQIPDPFIEKLIIEAILEARD-QHLINAMKDLGGGGLSCAVSETADALSIGIEMDVDKVH 279
                 67**********9999999999555.4.34444..4679*********777777766666.5************************************* PP

                 HHHHHHHHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEESS CS
      AIRS_C  96 ifdelesplemllsensGrllvavppeeadavlaileeeglpeaavIGevtake 149
                  ++  +sp e+++se+++r+l++   e+ +++  i+++ ++ +++vIG+vt + 
  EPA04926.1 280 TRESDMSPDEIMVSESQERMLIVTTDEKLKKLQTICKKFRI-TCSVIGHVTSDS 332
                 *****************************************.7********875 PP

  == domain 2  score: 65.0 bits;  conditional E-value: 1.9e-21
                 TTEEEEEEET..SSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHHHHHHHTTTEEEEEECGTHHHHH CS
      AIRS_C   2 pGdvliltgs..lGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaalkglvkaahDvTgGGLlgalaemapasgvgaeidldkvpifd 98 
                 p+d+l+ +g   + lgg+ +++  + +   +++     +++ +  +  + v+++l+++ gl kaahD++ GGL++a++e++   +vg +++ldkvp  +
  EPA04926.1 548 PDDLLVIIGDtkDELGGSEYFEYIHKFIGGKCP-----VVNFEESKSNMTVVLELIQK-GLLKAAHDCSKGGLAVAVSEICMTYNVGCKVSLDKVPGPK 640
                 799********************9999999999.....*******************7.**********************************999998 PP

                 HHHHHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEES CS
      AIRS_C  99 elesplemllsensGrllvavppeeadavlaileeeglpeaavIGevtak 148
                    +   +l+se+  r+l++v++++ +++ +il+   + +   IGe   k
  EPA04926.1 641 L--DVDRILFSESHSRYLLVVSKKNIKKIEDILKTSKI-KHNTIGEFGSK 687
                 6..699********************************.7*****98776 PP

>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.7   0.2   5.8e-23   2.6e-19       6      92 ..      74     173 ..      60     175 .. 0.93
   2 !   56.6   0.0   6.9e-19   3.1e-15       6      93 ..     433     535 ..     419     536 .. 0.91

  Alignments for each domain:
  == domain 1  score: 69.7 bits;  conditional E-value: 5.8e-23
                 EEEEEEEE.EECCTCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC..........HHHHHHHHHHHHHHHTT-EEEEEEEEEESS....EEEEEEE CS
        AIRS   6 vvttdshnrpvlvepvhfiGakavavnlsDlaamGArPlalllslalp..........wleevvrglaeaaeelgvplvgGdtsfsne....ptisvta 90 
                 +++++shn+p++vep+ + +a++v+++++D+++ G rP+a+l+ l ++           ++++v+g+a+++++lg+p++gG+++f+++     ++ v+a
  EPA04926.1  74 TAHIESHNHPSAVEPYGG-AATGVGGVIRDILSAGTRPIAILDGLRFGdiekdmqarwLFKNAVTGIADYGNCLGIPTIGGEVEFDQCysnyALVDVAA 171
                 66899*************.**************************************999**************************9999998899999 PP

                 EE CS
        AIRS  91 vG 92 
                 +G
  EPA04926.1 172 IG 173
                 98 PP

  == domain 2  score: 56.6 bits;  conditional E-value: 6.9e-19
                 EEEEEEEE.EECCTCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC.........HHHHHHHHHHHHHHHTT-EEEEEEEEEESS.......EEEEE CS
        AIRS   6 vvttdshnrpvlvepvhfiGakavavnlsDlaamGArPlalllslalp.........wleevvrglaeaaeelgvplvgGdtsfsne.......ptisv 88 
                  +++d+++++++++p+++ +  +  +++++++++GA+P+++l+ l ++         ++ e ++gl + a+ +++p vgG++s +ne       pt+ +
  EPA04926.1 433 SAKIDGNPKHCYINPREG-AIGCFEEACRNVVCTGAKPIGMLDHLQFGnpenpeifwTFLESLKGLTDFAKYFEIPCVGGKVSLYNEtpsgpikPTPLI 530
                 6799**************.**************************************99**************************999******99999 PP

                 EEEEE CS
        AIRS  89 tavGl 93 
                 +++G+
  EPA04926.1 531 GILGI 535
                 99997 PP

>> FGAR-AT_linker  Formylglycinamide ribonucleotide amidotransferase linker domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   0.1   3.7e-14   1.6e-10      10      50 .]       1      38 [.       1      38 [. 0.94

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 3.7e-14
  FGAR-AT_linker 10 laLsdeEidylqeafeklgrnPtdvElemfaqvwSEHCrHK 50
                    ++L+++E d l++    +gr+Pt +El+++a+ wSEHC++K
      EPA04926.1  1 MSLEPQELDDLTSK---IGRKPTSTELQIVAAEWSEHCSYK 38
                    57899999999999...9**********************9 PP

>> T_Ag_DNA_bind  Origin of replication binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.2   8.9e-06      0.04      15      67 ..     290     341 ..     285     345 .. 0.86
   2 ?   -2.3   0.1       1.5   6.9e+03      23      61 ..     654     691 ..     646     696 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 8.9e-06
  T_Ag_DNA_bind  15 ifsnktleafliyttkeKlkeLykkllekfkvkfkllakyeekavlllitakk 67 
                    i++ + +e  li+tt eKlk+L+  + +kf+++ +++ ++++++++ +   kk
     EPA04926.1 290 IMVSESQERMLIVTTDEKLKKLQT-ICKKFRITCSVIGHVTSDSIMHVKKGKK 341
                    5677888999************85.66****************9998866665 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.5
  T_Ag_DNA_bind  23 afliyttkeKlkeLykkllekfkvkfkllakyeekavll 61 
                     +l++ +k+ +k++++ l ++ k+k +++ ++++k++l+
     EPA04926.1 654 RYLLVVSKKNIKKIEDIL-KTSKIKHNTIGEFGSKNILF 691
                    577788888888887766.77788888888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (721 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.65u 0.28s 00:00:00.93 Elapsed: 00:00:00.46
# Mc/sec: 4736.78
//
Query:       EPA04927.1  [L=117]
Description: hypothetical protein BG20_I1089 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00077   19.7   0.0     0.0011   19.2   0.0    1.3  1  DUF5300   Domain of unknown function (DUF5300)


Domain annotation for each model (and alignments):
>> DUF5300  Domain of unknown function (DUF5300)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   6.2e-08    0.0011       4      41 ..      41      78 ..      39     102 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 6.2e-08
                -EEEEEEE-SSS-BS-EEEESSSS-EEEE--B..-TT- CS
     DUF5300  4 astitikntsafelknvkvkfngekevtvgalekgske 41
                +  iti+n    +l n++v+f  ++++++++l++g+k 
  EPA04927.1 41 TGRITIQNIGSQTLTNIHVNFGAGDTLDIKTLKSGQKI 78
                678*****************************887764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 909.98
//
Query:       EPA04928.1  [L=265]
Description: twin arginine-targeting protein translocase TatC [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-50  172.3  15.9    1.4e-50  172.0  15.9    1.1  1  TatC      Sec-independent protein translocase protein (TatC)


Domain annotation for each model (and alignments):
>> TatC  Sec-independent protein translocase protein (TatC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.0  15.9   7.7e-55   1.4e-50       1     207 []       9     241 ..       9     241 .. 0.84

  Alignments for each domain:
  == domain 1  score: 172.0 bits;  conditional E-value: 7.7e-55
                 -HHHHHHHHHHHHHHHHHHHHHHHHHTHHHH.....................HHHCCHHHHC.C............TTS-EE--SSS-HHHHHHHHHHH CS
        TatC   1 ehLeeLrkrlirallavaiafiitfvfaeel.....................iafllepleeae............eevelivlspleafllklkvslv 66 
                 +hLeeLrkr++r++++++i+f++++ +  +l                                +             +v+li ++p +a+++++ v+ +
  EPA04928.1   9 QHLEELRKRVVRIIIVIGIIFAFVISC--HLypidvsgihlyypqidpinnvA----------AqitthmktslipDGVQLIQTEPGQALFAQIYVGAL 95 
                 5***********999999999998533..221222223222222222222212..........13333333333334699******************* PP

                 HHHHHSHHHHHHHHHCCCTTTTS---STTTHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHT....TTTSSTTEEHHHHHHHHHHHHHHHHHHTTHHHHH CS
        TatC  67 aglvlasPvilyqlwafvapgLykherrlvlvfliaslllfllGaafayfvvlplvlkfll....seevepllslseylsfvlllllafgiaFelPlvl 161
                 +++v+ +P+i+ + + f++p+L+++e +++ ++++ +l lf++G++f+yf+v+p++l+fl+    ++++++ l++ ++++fvl+ llafgi+F++P+v+
  EPA04928.1  96 VAVVFGMPIIIKEAVGFIKPALKEREIKVTSRVALPALGLFITGCLFSYFLVIPYMLEFLYmfgdASGLITFLNIMDFITFVLQYLLAFGISFQIPIVM 194
                 *************************************************************88775566889*************************** PP

                 HHHHHTTSS-HHHHHTTHHHHHHHHHHHHHHH-S..SHHHHHHHHHH CS
        TatC 162 vllarlglvsaetlrkkrryaivvilvvaavltP.pdvisqlllavP 207
                 + l++ g+v  +++rk+ ryai++i++++a++tP  + +++ ++avP
  EPA04928.1 195 YALTMSGIVGDDFWRKNVRYAILAIIIFGAIITPdGSGVTMWFIAVP 241
                 **********************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1110  (0.0619109); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1855.30
//
Query:       EPA04929.1  [L=185]
Description: ribosomal protein L6 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.2e-09   36.4   4.8    0.00046   20.8   0.2    2.2  2  Ribosomal_L6  Ribosomal protein L6
  ------ inclusion threshold ------
      0.057   13.7   3.8         13    6.1   0.1    3.5  4  BON           BON domain
       0.11   12.5   0.3       0.47   10.5   0.3    2.1  1  RL10P_insert  Insertion domain in 60S ribosomal protein L10P


Domain annotation for each model (and alignments):
>> Ribosomal_L6  Ribosomal protein L6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.2   7.7e-08   0.00046       1      72 [.      15      83 ..      15      87 .. 0.82
   2 !   17.6   0.8   7.9e-07    0.0047       1      76 []      99     173 ..      99     173 .. 0.96

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 7.7e-08
                  CSTTEEEEEETTTEEEEEESSEEEEEE-CTT.SEEEEEECSTEEEEEECSESCHHHHHHHHHHHHHHHHHHHH CS
  Ribosomal_L6  1 iPvgvrvsikggqlvlvlGpkgeltreipeg.vtvevkvegnkvtvivvsgidkekvAligtvrslinnmikG 72
                  iP+gv+v++k+   + + Gp g    +++   v++evk  ++kv   ++   ++  +  + t+rs+i+n  +G
    EPA04929.1 15 IPKGVTVTLKK-HMLHFQGPLGKTHKNFRNIpVNIEVK--DGKVILKSQGYRKRDYS-ILHTARSIIRNICEG 83
                  8*********5.*****************987888855..77777766555555555.**********98776 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 7.9e-07
                   CSTTEEEEEETTTEEEEEESSEEEEEE-CTTSEEEEEECSTEEEEEECSESCHHHHHHHHHHHHHHHHHHHHHHTC CS
  Ribosomal_L6   1 iPvgvrvsikggqlvlvlGpkgeltreipegvtvevkvegnkvtvivvsgidkekvAligtvrslinnmikGVteg 76 
                   +P+ v+v+ k + ++++ G++  +  +i  +++v  k e+  +t +v+++i ++ + +i++  ++++++ +++ +g
    EPA04929.1  99 FPITVKVQDKTVLIENFQGERSARVSRIIGNTKVVPKGEDVILTGEVWNDITQTAA-NIELRSKVKDKDHRVFLDG 173
                   7999*******************************999999**************9.**************99987 PP

>> BON  BON domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.6   9.6e+03      44      58 ..       5      19 ..       2      23 .. 0.48
   2 ?    6.0   0.0    0.0024        15      16      35 ..      38      57 ..      34      58 .. 0.85
   3 ?    0.3   0.0      0.15     9e+02      21      35 ..      98     112 ..      90     113 .. 0.82
   4 ?    6.1   0.1    0.0022        13      29      48 ..     133     153 ..     121     165 .. 0.69

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.6
                HHHHHHHHHHCCTTE CS
         BON 44 ekekAveiarnvaGV 58
                ++ek +e+++  +GV
  EPA04929.1  5 QIEKFQEVVEIPKGV 19
                555555555433333 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0024
                HCHTTGCCCEEEEETTCEEE CS
         BON 16 dggldaadinVevenGvVtL 35
                ++++++  +n+ev++G+V+L
  EPA04929.1 38 HKNFRNIPVNIEVKDGKVIL 57
                57788999**********99 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.15
                 GCCCEEEEETTCEEE CS
         BON  21 aadinVevenGvVtL 35 
                 ++ i+V+v++  V++
  EPA04929.1  98 HFPITVKVQDKTVLI 112
                 5789******88976 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.0022
                 ET.TC.EEEECEEECHHHHHHH CS
         BON  29 en.Gv.VtLsGtVdseaekekA 48 
                    G+ V+L+G+V + +  ++A
  EPA04929.1 133 VPkGEdVILTGEV-WNDITQTA 153
                 333778*******.44333333 PP

>> RL10P_insert  Insertion domain in 60S ribosomal protein L10P
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.3   7.9e-05      0.47      10      48 ..      20      60 ..       9     140 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 7.9e-05
  RL10P_insert 10 dviipagplela..PgsiepeLrklglptklkkGkivleed 48
                  +v++++  l+ +   g++ + +r++ +++++k+Gk++l+++
    EPA04929.1 20 TVTLKKHMLHFQgpLGKTHKNFRNIPVNIEVKDGKVILKSQ 60
                  344444444443754788899*****************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1311.52
//
Query:       EPA04930.1  [L=37]
Description: hypothetical protein BG20_I1069 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.057   13.4   0.1      0.066   13.2   0.1    1.2  1  Gram_pos_anchor  LPXTG cell wall anchor motif


Domain annotation for each model (and alignments):
>> Gram_pos_anchor  LPXTG cell wall anchor motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   3.7e-06     0.066      23      42 ..       6      26 ..       1      27 [. 0.63

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.7e-06
                     XXXXXXXXXXXX.XXXXXXXX CS
  Gram_pos_anchor 23 aGllallggllL.lvkrRKke 42
                     +  ++++gg+ L l++rR ++
       EPA04930.1  6 LLTAMAAGGISLwLKRRREQQ 26
                     445666777777588888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 267.84
//
Query:       EPA04931.1  [L=477]
Description: putative amidophosphoribosyltransferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.4e-13   49.9   0.0    8.4e-13   48.7   0.0    1.6  2  GATase_6        Glutamine amidotransferase domain
    1.4e-12   47.6   0.0    2.4e-12   46.8   0.0    1.4  1  GATase_7        Glutamine amidotransferase domain
    6.8e-10   38.7   0.0    1.2e-09   37.8   0.0    1.3  1  Pribosyltran    Phosphoribosyl transferase domain
    1.2e-05   24.3   0.0    2.5e-05   23.3   0.0    1.5  1  GATase_4        Glutamine amidotransferases class-II
    0.00012   21.0   0.0       0.14   10.9   0.0    3.0  3  GATase_2        Glutamine amidotransferases class-II
  ------ inclusion threshold ------
       0.07   12.7   0.0       0.14   11.8   0.0    1.4  1  DUF3919         Protein of unknown function (DUF3919)
      0.097   12.6   0.1       0.25   11.3   0.1    1.7  1  Pribosyltran_N  N-terminal domain of ribose phosphate pyropho
       0.11   12.1   0.1       0.37   10.4   0.0    1.8  3  Dip             gp37/Dip protein
       0.14   11.9   0.0       0.51   10.1   0.0    1.9  2  RQC             RQC domain


Domain annotation for each model (and alignments):
>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.7   0.0   4.2e-16   8.4e-13       6     134 .]      64     200 ..      57     200 .. 0.83
   2 ?   -3.2   0.0       4.3   8.6e+03      52      80 ..     414     442 ..     401     447 .. 0.71

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 4.2e-16
    GATase_6   6 laslvedevalaHvRlaivglaeeegaqPfpsedgrlllvhNGeiynykelreelpalkglafrsrsDtevlla.ll......eelG..eevl.erlrG 94 
                 +++ +++ ++++HvR +++g ++ e aqP+  + + l ++hNG+i n++el++ +      + +  sDt v ++ l+       ++G     l ++++G
  EPA04931.1  64 ISEEYSSPAVIGHVRYSTMGRSTLENAQPL--KVKDLCIAHNGTIANVQELSNLVGG-CSFTPQNASDTLVAAQrLVslisenGQMGkaLSILkNEMVG 159
                 444556779*************77777***..*************************.8888899*******996559996555555655556678888 PP

    GATase_6  95 mfafaiwdkrentlilardrlgvkplyyavd..esglafase 134
                  + f +++ + n +  ard  g +p++ +++  +++ ++ase
  EPA04931.1 160 SYCFTFIS-DDNSVYAARDPKGFRPMVLGYKesDDTYIVASE 200
                 88887666.88889899********99999888999999998 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4.3
    GATase_6  52 nykelreelpalkglafrsrsDtevllal 80 
                 + +el e +++  g++f +++D+e l+++
  EPA04931.1 414 TEEELTEMVRKSIGADFLGYNDAENLANA 442
                 45577777777778888888888877765 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   0.0   1.2e-15   2.4e-12       9     122 ..      86     205 ..      76     206 .. 0.84

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 1.2e-15
    GATase_7   9 seagaQPmvssedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllallea.........ewgeealerlnGmfAfaiwdeeekrlllaRDrlG 98 
                 + ++aQP+     ++l+i++nG+i N +el +      ++ ++ sDt v ++ l +         + +  + +++ G+++f  + +++ ++++aRD+ G
  EPA04931.1  86 TLENAQPLKV---KDLCIAHNGTIANVQELSNLVGGCSFTPQNASDTLVAAQRLVSlisengqmgKALSILKNEMVGSYCFTFISDDN-SVYAARDPKG 180
                 55789**994...789******************9999999********7665555688899665555556699********998888.9********* PP

    GATase_7  99 ikPLyygedk.gdallfaSelkall 122
                 ++P+ +g+++ +d++++aSe +a+ 
  EPA04931.1 181 FRPMVLGYKEsDDTYIVASESSAVS 205
                 *********9999*******99975 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.0   6.2e-13   1.2e-09      28     122 ..     279     383 ..     259     389 .. 0.85

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 6.2e-13
                   GGGEEEEEEETTTHHHHHHHHHHSTT-EE.-EEEEEE-TTT--EE..................EE----TTSEEEEE-SEESSSHHHHHHHHHHHCC CS
  Pribosyltran  28 gkpdvvvgiargGvpfakiladeLevpla.yvrkvkyrpdgseeaargssdes..........rlledpagkkVliVDDildtGgTllaalelLkek 113
                   +  d+v++++  + p a  +a+eL++ ++  ++k +y+++g     +     s             e+++gk+V+++DD l  G++ +a++++L+++
    EPA04931.1 279 HDADLVIPVPDSARPAALGYAQELGLTFDeGLLKDRYSKKGPLRSFIEPHQ-SdrieinrwiiPIREIIEGKHVVVIDDSLVRGTSSKAIIQALRRA 374
                   4459*************************8999999998888877654433.3699***************************************** PP

                   -BSEEEEEE CS
  Pribosyltran 114 gpeevriav 122
                   g++++  + 
    EPA04931.1 375 GAKKISMVI 383
                   ***997665 PP

>> GATase_4  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   1.3e-08   2.5e-05      35     144 ..      37     143 ..      17     179 .. 0.70

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 1.3e-08
    GATase_4  35 GwGiafyegkaarvfkdpepsaesplaelvreypiksknvvaHiRkatqGevklenthpFvRelwgrewifAHnGdlkeykpkl....egrfePvGsTD 129
                  wGia  +++  +  +   + a+s+  ++  e    s  v+ H+R  t G+ +len++p    l+ ++  +AHnG++ ++++ +      +f+P    D
  EPA04931.1  37 AWGIAIPNKEPLKR-LGLVSGASSEFKKISEE--YSSPAVIGHVRYSTMGRSTLENAQP----LKVKDLCIAHNGTIANVQELSnlvgGCSFTPQNASD 128
                 56666544333332.34456666666666555..5799********************9....6789**********9988876566556888888888 PP

    GATase_4 130 sElafCelleelasr 144
                 + +a   l++ ++++
  EPA04931.1 129 TLVAAQRLVSLISEN 143
                 877765555555444 PP

>> GATase_2  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0     0.055   1.1e+02       1      33 [.       6      35 ..       6      39 .. 0.79
   2 !   10.9   0.0   6.9e-05      0.14     199     239 ..      66     110 ..      60     136 .. 0.88
   3 !    4.9   0.0    0.0044       8.9     336     396 ..     166     225 ..     151     240 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.055
                -EEEEEE-SSS--BSHHHHHHHHHHHHGGGGS- CS
    GATase_2  1 CGvgfiaelkgkkshkivekalealenleHRGa 33
                CGv  i +l+g    ++v  a++al+ l+HRG 
  EPA04931.1  6 CGVVGIFSLSG---TNVVPMAIDALRALQHRGQ 35
                66666666665...47999*************6 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 6.9e-05
                 TT--BSEEEEEE---SSSS--GGGSSS-SS....EEEEE--TTHH CS
    GATase_2 199 eelesalalvHsRfstntfPsWelaqPlRl....laHnGEintlr 239
                 ee++s  ++ H R+st    + e aqPl++    +aHnG i  ++
  EPA04931.1  66 EEYSSPAVIGHVRYSTMGRSTLENAQPLKVkdlcIAHNGTIANVQ 110
                 78999999********************9655559******8876 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.0044
                 EE-SSEEEEEE-TT--S--EE.EEETT--EEEESSTTSS---GGGEEEEEE--TT-EEEEET CS
    GATase_2 336 ftdGkvvgavLDRnGLRPaRy.lvtkddlvvlasEvGvldleeeevvekgrlqPGrmllvdl 396
                 ++d + v a  D  G RP    +  +dd+ ++asE+  +    +++     ++PG+++ + +
  EPA04931.1 166 ISDDNSVYAARDPKGFRPMVLgYKESDDTYIVASESSAVSAVGAKLQ--RDVKPGELIKLST 225
                 5788999999********9863566789999****998887776664..5689999998765 PP

>> DUF3919  Protein of unknown function (DUF3919)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   6.8e-05      0.14      55     147 ..      63     156 ..      38     180 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.8e-05
     DUF3919  55 nskiensvieitgtiyYLnGekdtfelsnkLklngryysdnsklalinrLknklldalytpsnlssilnkknkvi.ivdsnnkakklnssdkkl 147
                     e s   + g ++Y    ++t+e  + Lk+ + +++ n  +a +  L n + +  +tp+n s+ l  +++++ ++++n+++ k  s  k+ 
  EPA04931.1  63 KISEEYSSPAVIGHVRYSTMGRSTLENAQPLKVKDLCIAHNGTIANVQELSNLVGGCSFTPQNASDTLVAAQRLVsLISENGQMGKALSILKNE 156
                 455566778899*****9999********************************************98888887664788888888776666655 PP

>> Pribosyltran_N  N-terminal domain of ribose phosphate pyrophosphokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00012      0.25      41      88 ..     342     385 ..     323     389 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00012
  Pribosyltran_N  41 ieesvrgkdvfiiqslskpvndnlmelllmidalrrasakritaViPy 88 
                     i+e + gk+v++i +            + +i+alrra ak+i +Vi y
      EPA04931.1 342 IREIIEGKHVVVIDDSLVR----GTSSKAIIQALRRAGAKKISMVITY 385
                     6666777777777665533....3457899****************98 PP

>> Dip  gp37/Dip protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       2.5     5e+03      58     109 ..     120     171 ..     107     174 .. 0.59
   2 ?   10.4   0.0   0.00019      0.37     112     154 ..     327     369 ..     311     374 .. 0.88
   3 ?   -2.9   0.0         2   3.9e+03      58      94 ..     406     442 ..     378     458 .. 0.71

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.5
                 EE--SS---TTHHHHHHHHHHHHHHGGGSHHHHHHHHHHH.HTSTTEEEESSE CS
         Dip  58 tfkpqsspddamvreyvlsriiadnlkyvdnlylaagavi.cgndeyisdgnv 109
                 +f pq++ d ++v    l  +i++n +    l +    ++      +isd n 
  EPA04931.1 120 SFTPQNASD-TLVAAQRLVSLISENGQMGKALSILKNEMVgSYCFTFISDDNS 171
                 577776654.5555666666777777766666554443330333456666655 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00019
                 EEEEESSTT-EEEEEEEEEEET--GGGTHHHHHHHSSEEE--- CS
         Dip 112 ihiadgvggnklilpviefmpgvhvddisdkliksssyqgifk 154
                  h +d +  n+ i+p+ e++ g hv  i d l++ +s + i++
  EPA04931.1 327 PHQSDRIEINRWIIPIREIIEGKHVVVIDDSLVRGTSSKAIIQ 369
                 58899999***************************99999876 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 2
                 EE--SS---TTHHHHHHHHHHHHHHGGGSHHHHHHHH CS
         Dip  58 tfkpqsspddamvreyvlsriiadnlkyvdnlylaag 94 
                 tf    +  +  + e v   i ad l y d   la  
  EPA04931.1 406 TFSDGKNMTEEELTEMVRKSIGADFLGYNDAENLANA 442
                 5555555555566778888888888888887777654 PP

>> RQC  RQC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.7   3.3e+03       5      23 ..     127     145 ..     123     153 .. 0.77
   2 ?   10.1   0.0   0.00026      0.51      48      80 ..     402     434 ..     394     455 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.7
                 EE-HHHHHHHHHHHHHTTS CS
         RQC   5 vDvteeaqkilscvyrtgq 23 
                  D  ++aq ++s++ + gq
  EPA04931.1 127 SDTLVAAQRLVSLISENGQ 145
                 688899*******998765 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00026
                 GGSTTTTTTTTS-HHHHHHHHHHHHHTTSEEEE CS
         RQC  48 dklstfGigkdlskkewrrlirqLiaegyLeed 80 
                 d+l tf+ gk+++++e+++++r+ i  ++L ++
  EPA04931.1 402 DELATFSDGKNMTEEELTEMVRKSIGADFLGYN 434
                 89************************9999444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (477 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 3027.70
//
Query:       EPA04932.1  [L=92]
Description: hypothetical protein BG20_I1084 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.3e-32  109.6   0.6    5.9e-32  109.4   0.6    1.0  1  NTP_transf_9  Domain of unknown function (DUF427)


Domain annotation for each model (and alignments):
>> NTP_transf_9  Domain of unknown function (DUF427)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.4   0.6   3.3e-36   5.9e-32       1      92 [.       1      87 [.       1      88 [. 0.98

  Alignments for each domain:
  == domain 1  score: 109.4 bits;  conditional E-value: 3.3e-36
                  EEEE-SS-EEEEES--EEEEETTS--EEEB-GGGB-GGGEEEEEEEEEETTTEEEEEEEEEETTEEEEEEEEEESS--TT-GGGTT-BEE-T CS
  NTP_transf_9  1 vrvklngtvvaetddavvveetglppryYfppedvklellkpsdtttvCpwKGeasyyslavdgkevkdaaWsYpeptpeaaeikgyvaFya 92
                  +++++n+t++ae+dd+vvve+     ++Yfp +++k e++k++d tt+C wKG a+yys++++gk++kd aW+Y ep+++a++ikg+vaF++
    EPA04932.1  1 MKAIWNDTIIAESDDTVVVEG-----NHYFPFDSIKQEYFKKTDLTTFCGWKGMANYYSVTINGKTNKDCAWYYAEPNDAAKKIKGRVAFWN 87
                  6899*****************.....*****************************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 663.94
//
Query:       EPA04933.1  [L=114]
Description: hypothetical protein BG20_I1068 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-20   73.5   0.0    1.8e-20   73.1   0.0    1.2  1  DUF1246   Protein of unknown function (DUF1246)
  ------ inclusion threshold ------
       0.08   12.8   0.0       0.17   11.8   0.0    1.5  1  DUF4860   Domain of unknown function (DUF4860)


Domain annotation for each model (and alignments):
>> DUF1246  Protein of unknown function (DUF1246)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.1   0.0     2e-24   1.8e-20       1      61 [.      19      80 ..      19      88 .. 0.92

  Alignments for each domain:
  == domain 1  score: 73.1 bits;  conditional E-value: 2e-24
                EEEESSTTHHHHHHHHHHTT--EEEEC-CCCHHHHHTT.TT-SEEEE.S.S..TTSS--HHH CS
     DUF1246  1 iatlaSHsalqilkgAkkegfrtlavcekgreklYekf.kvidevivldkfkdilkeevqek 61
                i++++SHsal++++gAk+e+f+t++ c+kgre++Y++f +++de+ivldkfkd+++ +  ++
  EPA04933.1 19 IGVMGSHSALEVMDGAKDENFQTVVYCQKGREEPYRRFnRIADEIIVLDKFKDMASPKKSKN 80
                89************************************7788*************9886554 PP

>> DUF4860  Domain of unknown function (DUF4860)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.8e-05      0.17      18      54 ..      12      48 ..       6      53 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.8e-05
     DUF4860 18 DeegavsveelegtqaLvlkeeiddeeyetyiYyydg 54
                +e++ v+++ +  + aL++ +  +de+++t++Y+++g
  EPA04933.1 12 NEYSDVRIGVMGSHSALEVMDGAKDENFQTVVYCQKG 48
                5678899999*************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.30s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 780.96
//
Query:       EPA04934.1  [L=261]
Description: hypothetical protein BG20_I1077 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-43  149.7   1.3    1.7e-43  149.4   1.3    1.1  1  SIMPL     Protein of unknown function (DUF541)


Domain annotation for each model (and alignments):
>> SIMPL  Protein of unknown function (DUF541)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.4   1.3   9.5e-48   1.7e-43       1     200 []      46     256 ..      46     256 .. 0.89

  Alignments for each domain:
  == domain 1  score: 149.4 bits;  conditional E-value: 9.5e-48
       SIMPL   1 ItVtGsaevevapDqatltlsvesegkdaaeakaevaekmnavlealkklgikekdiqtsslslkpeysy......engknkitgyeasqsltvkfrdl 93 
                 I+VtG+a  +v+p+++ ++++ve+++k+a++a a+++e mn+v+ a+k+ gi + +i ts+++++p+y+y       ++ +++ gy++s+ +++k+++l
  EPA04934.1  46 ISVTGNAISSVEPNLVNISFGVEVQEKTAKDALASNSELMNKVITAVKQVGITDAEIGTSQFNIYPVYNYyqekdtGKNVQELIGYKVSNIINIKTEKL 144
                 89**********************************************99**999*******************99889999999************** PP

       SIMPL  94 dklgevldaavka.aneingvsfsls.de.delrdeareeAvkdArakAealAkalgvklgkvvsise.sgsnpyappapamaaaaaa.aasaatpfep 187
                 d++++++d av+a +n++++v fsls d  ++l+d+++e+Av +A+ kAe + + l+ k+ +v+ is  + s py++p+ +ma ++ a ++s++tp+ +
  EPA04934.1 145 DSIAQIIDGAVDAgVNRVDSVYFSLSpDVaSKLKDDLLEKAVLNAKSKAELALSPLNYKIIGVKAISLsEFSIPYPMPMYDMAYSEGAaKSSMPTPIFS 243
                 **************************5447999**************************9988666553233334444444444333369999999999 PP

       SIMPL 188 geievtasVtvvf 200
                 ++++v+ sV+vvf
  EPA04934.1 244 SDQDVNTSVNVVF 256
                 999*********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       976  (0.0544369); expected 358.6 (0.02)
Passed bias filter:                      606  (0.0338); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 1481.73
//
Query:       EPA04935.1  [L=46]
Description: hypothetical protein BG20_I1080 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-05   24.2   0.0    1.6e-05   24.2   0.0    1.0  1  GATase_5         CobB/CobQ-like glutamine amidotransferase do
  ------ inclusion threshold ------
       0.12   12.4   0.1        1.3    9.1   0.0    2.0  2  Molybdopterin_N  Molybdopterin oxidoreductase N-terminal doma


Domain annotation for each model (and alignments):
>> GATase_5  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   1.8e-09   1.6e-05     212     254 ..       1      36 [.       1      40 [. 0.80

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1.8e-09
    GATase_5 212 itspdGRvlalmpHpervveavqksiipeeeeeevspwlrlFe 254
                 ++++dG v+++mpHper+ e+  ++ i++      +p   +Fe
  EPA04935.1   1 MCNEDGNVVGMMPHPERAAESAINP-IDN------KPSSLIFE 36 
                 69*******************9999.543......45555555 PP

>> Molybdopterin_N  Molybdopterin oxidoreductase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0   0.00015       1.3      13      32 ..       4      23 ..       3      26 .. 0.90
   2 ?    2.0   0.0     0.024   2.1e+02      26      38 ..      27      40 ..      22      42 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00015
  Molybdopterin_N 13 kdGkivgvrPfegDpdPspl 32
                     +dG +vg+ P+++ ++ s +
       EPA04935.1  4 EDGNVVGMMPHPERAAESAI 23
                     7************9998876 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.024
  Molybdopterin_N 26 DpdPspll.egvpd 38
                     D  Ps+l+ e++ d
       EPA04935.1 27 DNKPSSLIfESLLD 40
                     889****9887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       169  (0.00942607); expected 358.6 (0.02)
Passed bias filter:                      164  (0.00914719); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 332.72
//
Query:       EPA04936.1  [L=101]
Description: hypothetical protein BG20_I1093 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2055  (0.114619); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 663.99
//
Query:       EPA04937.1  [L=190]
Description: phosphoribosylformylglycinamidine synthase I [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.1e-26   90.5   0.0    1.2e-25   90.1   0.0    1.2  1  GATase_5       CobB/CobQ-like glutamine amidotransferase doma
    1.8e-08   34.2   0.0    3.1e-08   33.5   0.0    1.3  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
    2.8e-08   33.8   0.0    3.4e-08   33.5   0.0    1.3  1  GATase         Glutamine amidotransferase class-I
    4.3e-08   33.1   0.0      6e-08   32.7   0.0    1.2  1  DJ-1_PfpI      DJ-1/PfpI family
    0.00093   19.0   0.2      0.002   18.0   0.2    1.6  1  Peptidase_C26  Peptidase C26
  ------ inclusion threshold ------
      0.066   13.0   0.0      0.098   12.5   0.0    1.2  1  SNO            SNO glutamine amidotransferase family


Domain annotation for each model (and alignments):
>> GATase_5  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.1   0.0   4.1e-29   1.2e-25       3     180 ..       2     160 ..       1     176 [. 0.85

  Alignments for each domain:
  == domain 1  score: 90.1 bits;  conditional E-value: 4.1e-29
    GATase_5   3 kvailreeGvngeyemaaafeka.GfeavdvhmsdllegrvslddfqilalpGGfsygDelgsgkgwakslllneklrealekflnredtlaLGiCnGf 100
                 kv +++++G+n++++m + +++   f+a+        +++   +++  ++lpGGfsygD l sg+++a+     + + ++++k+ ++ +  +LG+CnGf
  EPA04937.1   2 KVGVVVFPGSNCDRDMYHVLTDVfKFNAEY-----FWHEKGLPKNIDAVILPGGFSYGDRLRSGAIAAH-----SPIISDVRKMAEK-GIPILGVCNGF 89 
                 899****************98742455544.....4455555677899*****************9994.....5678999999888.9********** PP

    GATase_5 101 qlLvklglvpggeieeaeksptltrNksgrfesrlvsv.vvsekspsvflkgm.eglslpvahGeGrfvfkseevlkelean 180
                 q+Lv+ gl+pg          +l +N+s +f + ++++ v ++k+p     ++ +++ +p+a GeGr  + ++++lk+l++ 
  EPA04937.1  90 QILVEAGLLPG----------ALLKNTSLNFMCSWTNLiVENNKTPFTNKLKLhQKIPIPIANGEGRYYV-DNDTLKKLKNT 160
                 ***********..........9****************88888999998855526999************.88999999876 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.0     1e-11   3.1e-08      33      90 ..      34      94 ..      18     102 .. 0.85

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 1e-11
    GATase_3 33 kdeslgedadlvilpGgkdtiqdl...allresgldeaikeaaeaggpvlgiCGGlqmLGe 90
                +++ l++++d+vilpGg+++ ++l   a+++ s +  +++++ae+g+p+lg+C G+q+L e
  EPA04937.1 34 HEKGLPKNIDAVILPGGFSYGDRLrsgAIAAHSPIISDVRKMAEKGIPILGVCNGFQILVE 94
                57889999**********8876662226788999*************************76 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.0   1.1e-11   3.4e-08      28      87 ..      26      95 ..      13     165 .. 0.75

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 1.1e-11
                ETTSHHHHHHH.THHSTSEEEEEEESSCTT.........TTTHHHHHHHHCTSTS-EEEETHHHHHHHHH CS
      GATase 28 pidasaeeile.llknpdgilvsgGpgspg.........vegkieaikearenkiPiLGICLGmQllaie 87
                +++a+    ++ l kn+d+++++gG+ +               i+ +++++e++iPiLG+C G+Q+l+++
  EPA04937.1 26 KFNAEYFWHEKgLPKNIDAVILPGGFSYGDrlrsgaiaaHSPIISDVRKMAEKGIPILGVCNGFQILVEA 95
                4444333333345799**********88888855553322223333566666***************987 PP

>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.0     2e-11     6e-08      59     115 ..      39     100 ..      12     112 .. 0.85

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 2e-11
                 CCG-SEEEE--BHHHHHHHHTSH.....HHHHHHHHHHHTT-EEEEETTTHHHHHHTTTTTT CS
   DJ-1_PfpI  59 aaeyDalvlpGGragperlrene.....kvvelvkefaekgklvaaICagpqlLaaagvlkg 115
                 +++ Da++lpGG +  +rlr  +      +++ v+++aekg ++  +C g q+L++ag+l+g
  EPA04937.1  39 PKNIDAVILPGGFSYGDRLRSGAiaahsPIISDVRKMAEKGIPILGVCNGFQILVEAGLLPG 100
                 5689*************9987543333378899***************************98 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.2   6.5e-07     0.002      98     122 ..      72      95 ..      36     115 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 6.5e-07
  Peptidase_C26  98 iraalergvPilgiCrGlqllnval 122
                    +r++ e+g+Pilg+C G+q+l v  
     EPA04937.1  72 VRKMAEKGIPILGVCNGFQIL-VEA 95 
                    68999***************9.443 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.3e-05     0.098      32      82 ..      40      93 ..      33     112 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.3e-05
                CC-SEEEE-SS-HHH....HHHHHHHTT-HHHHHHHHHTT.--EEEETHHHHHHC CS
         SNO 32 aevdaliiPGGesta....mskliertglyedllefvknsekvvlGtCaGlills 82
                +++da+i+PGG s       + ++ +  ++ d++++++++  ++lG C G+ +l 
  EPA04937.1 40 KNIDAVILPGGFSYGdrlrSGAIAAHSPIISDVRKMAEKG-IPILGVCNGFQILV 93
                579********99752211456999999999999999888.9********97664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1504.64
//
Query:       EPA04938.1  [L=130]
Description: ribosomal protein S8 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.6e-21   74.6   0.0    7.7e-21   74.4   0.0    1.1  1  Ribosomal_S8  Ribosomal protein S8


Domain annotation for each model (and alignments):
>> Ribosomal_S8  Ribosomal protein S8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.4   0.0   4.3e-25   7.7e-21       2     127 .]       6     130 .]       5     130 .] 0.86

  Alignments for each domain:
  == domain 1  score: 74.4 bits;  conditional E-value: 4.3e-25
                   HHHHHHHHHHHHHHTT-SEEEE.E--HHHHHHHHHHHHCTSEEEEEEE.CCC..CCCEEEEE-BSSS-SBSSSEEEE-SBTTC--EE-CCC---CGG CS
  Ribosomal_S8   2 piadmltrirNaekakkeevev.pasklkeeilkvLkeeGyikdfeve.eek..kkkikielkynkkkksvikklkrvskpgrrvYakvkelpkvln 94 
                    +a+++ ++ N+e+++k+ +++ p+skl  e+lk L++ Gyi +fe   +++  k kik+  k++k  +++i+   +v+++  +   +++ lp + +
    EPA04938.1   6 VLANLFVTLYNNEARRKSDCTIlPTSKLGIEVLKTLQKDGYIGEFEHIdDKRggKFKIKLLAKITK--CGAISPRFKVKNSEYN-DWEQQYLPAYNR 99 
                   689*******************9************************9444443444777777777..*****99999888777.445677887766 PP

                   GTSEEEEEETTEEEEHHHHHHCT--EEEEEEEE CS
  Ribosomal_S8  95 glGiaivsTskGvmtdkeArkkkvGGevlayvw 127
                     G+++v+T++Gvm++++A +k++GG ++ yv+
    EPA04938.1 100 --GMLLVTTNQGVMSHHDAVNKGLGGFLIGYVY 130
                   ..679***************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 997.65
//
Query:       EPA04939.1  [L=114]
Description: hypothetical protein BG20_I1067, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-47  159.8   0.0    5.7e-47  159.7   0.0    1.0  1  DUF1297   Domain of unknown function (DUF1297)


Domain annotation for each model (and alignments):
>> DUF1297  Domain of unknown function (DUF1297)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.7   0.0   3.2e-51   5.7e-47      34     145 ..       1     112 [.       1     114 [] 0.99

  Alignments for each domain:
  == domain 1  score: 159.7 bits;  conditional E-value: 3.2e-51
                 EEEEEEEETTTTEEEEEEEEEEEEEECCCHCCS-HHHHHCCT----EEEEEEEEEEE-GGGHHHHHHHHHHHHHHHHHHSTT---EEEEEEEEE-TTS- CS
     DUF1297  34 fnlnyfysplkeevellgidrRyesnldglvrlpakeqlelevepeyvvvGnipvvlREsllekvfelgekfveaakklvppGiiGpFcLqsvvtkdle 132
                 +n+nyfy+p++++v+++gi+rR+++n+++++ lpak+ql+++v+ ++++vG++p+ +REsllekv+++g+kfv+aakk+++pGiiGpF+Lqsv+tkdle
  EPA04939.1   1 MNFNYFYTPISKQVDFIGIERRLQTNVHDFNALPAKQQLDINVDLQNIEVGHTPASIRESLLEKVIKMGDKFVSAAKKEYAPGIIGPFSLQSVITKDLE 99 
                 69************************************************************************************************* PP

                 EEEEEEESSB-GG CS
     DUF1297 133 lvvfdvsaRivgg 145
                 lvv+dvs R++g+
  EPA04939.1 100 LVVYDVSLRVPGN 112
                 ***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 836.95
//
Query:       EPA04940.1  [L=61]
Description: hypothetical protein BG20_I1099 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 423.57
//
Query:       EPA04941.1  [L=173]
Description: ribosomal L5P C-terminal domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      5e-21   74.7   0.0    7.9e-21   74.1   0.0    1.4  1  Ribosomal_L5_C  ribosomal L5P family C-terminus
    1.1e-11   44.9   0.1    1.8e-11   44.2   0.1    1.4  1  Ribosomal_L5    Ribosomal protein L5


Domain annotation for each model (and alignments):
>> Ribosomal_L5_C  ribosomal L5P family C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.1   0.0   8.8e-25   7.9e-21       1      83 [.      64     145 ..      64     171 .. 0.88

  Alignments for each domain:
  == domain 1  score: 74.1 bits;  conditional E-value: 8.8e-25
  Ribosomal_L5_C   1 piGvkvtLrgekmyefldkllevvlprlrdFkGiskssfdgrGnvsfGikeqiifpeieydkdkgifGmditivttak.....tdeea 83 
                     piGv vt+rg+++ e+l++ll+++ ++++       +sfd+ Gn+sfGike+i++p+++yd++ gi G+ i++++t++      + ++
      EPA04941.1  64 PIGVAVTVRGDDARELLKRLLDAKGNQIN------GRSFDDFGNFSFGIKEHIDIPGVKYDPQVGILGLGISVTLTRPgygirKRSKH 145
                     8****************************......******************************************98885422233 PP

>> Ribosomal_L5  Ribosomal protein L5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.1     2e-15   1.8e-11       1      57 []       7      60 ..       7      60 .. 0.98

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 2e-15
                  SCTTS-EEEEEEEEEE-SSSSSCHHHHHCCHHHHCCCHSS--EECC--TTCTTTCSC CS
  Ribosomal_L5  1 NvMqvPrleKivinmgvGeagedkkllekaakeLaeItGQkPvvtkakksianFkiR 57
                  ++M+++ leK+v+nmg+G++g+    +  a k L  I+G k   + ak + +++++R
    EPA04941.1  7 SPMKKISLEKVVLNMGLGKSGDI---IIVAKKALDHISGKKSCARNAKETQREWGVR 60
                  59*******************99...******************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.31s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1103.99
//
Query:       EPA04942.1  [L=68]
Description: twin arginine-targeting protein translocase, TatA/E family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.6e-11   42.7   1.5    3.3e-11   42.3   1.5    1.2  1  MttA_Hcf106  mttA/Hcf106 family


Domain annotation for each model (and alignments):
>> MttA_Hcf106  mttA/Hcf106 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   1.5   1.8e-15   3.3e-11       2      46 ..      12      57 ..      11      67 .. 0.81

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 1.8e-15
                 -HHHHHHHHHH.HHHHS-TTTHHHHHHHHHHHHHHHHHHHHHHHH- CS
  MttA_Hcf106  2 gapelliIlvV.alllFGpkkLPEvaraLGktLreFkkavkeleee 46
                 g+ e+liIlv  a+ +FG+kk+PE+a+ LGk+  eF k   e e e
   EPA04942.1 12 GINEILIILVLaAVFIFGAKKIPELAKTLGKAKGEFEKGKIEGERE 57
                 899*****9973588*********************8865555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.25s 00:00:00.58 Elapsed: 00:00:00.38
# Mc/sec: 530.79
//
Query:       EPA04943.1  [L=42]
Description: hypothetical protein BG20_I1087 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.50
# Mc/sec: 254.30
//
Query:       EPA04944.1  [L=95]
Description: hypothetical protein BG20_I1101 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 623.04
//
Query:       EPA04945.1  [L=165]
Description: pentapeptide repeat protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-33  114.2   9.8    7.3e-11   41.5   0.1    4.4  4  Pentapeptide    Pentapeptide repeats (8 copies)
    1.6e-15   57.0   0.0    2.1e-08   34.2   0.0    2.5  2  Pentapeptide_4  Pentapeptide repeats (9 copies)
    6.2e-13   48.7   0.7    0.00011   22.3   0.3    4.1  4  Pentapeptide_3  Pentapeptide repeats (9 copies)


Domain annotation for each model (and alignments):
>> Pentapeptide  Pentapeptide repeats (8 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.1     6e-05      0.36       7      35 ..      11      39 ..      11      43 .. 0.65
   2 !   39.5   0.1   5.2e-14   3.1e-10       4      40 .]      43      79 ..      41      79 .. 0.96
   3 !   41.5   0.1   1.2e-14   7.3e-11       1      39 [.      70     108 ..      70     108 .. 0.96
   4 !   37.1   0.6   2.9e-13   1.8e-09       1      32 [.     110     141 ..     110     141 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 6e-05
                  B-CCSCCEECCCESEEECT-B-TT-EECC CS
  Pentapeptide  7 nLsganLsganlsgAnLtgAnlsgAdLsg 35
                  n+s +n++  +l g nL+++ ls  dL++
    EPA04945.1 11 NFSKTNFDYEDLIGRNLSNSILSEVDLKN 39
                  56666666666666666666666666654 PP

  == domain 2  score: 39.5 bits;  conditional E-value: 5.2e-14
                  TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
  Pentapeptide  4 sgAnLsganLsganlsgAnLtgAnlsgAdLsganLsg 40
                   +A+Lsg++Lsg++lsg+ L ++ l+gAdL+g+ Ls+
    EPA04945.1 43 HNADLSGSDLSGSDLSGTILFYVKLRGADLRGTSLSD 79
                  69*********************************97 PP

  == domain 3  score: 41.5 bits;  conditional E-value: 1.2e-14
                   -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEEC CS
  Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLs 39 
                   A+L+g+ Ls a+L +a+l+gA+L+gA+++gAdL  ++L+
    EPA04945.1  70 ADLRGTSLSDAKLWDADLYGADLRGADIRGADLFYTDLR 108
                   89*******************************999997 PP

  == domain 4  score: 37.1 bits;  conditional E-value: 2.9e-13
                   -B-TT-B-CCSCCEECCCESEEECT-B-TT-E CS
  Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAd 32 
                   A+Ls+AnLsgan ++an++g+ Lt+++++gA+
    EPA04945.1 110 ADLSQANLSGANIRHANFEGSILTDVDFTGAN 141
                   89999999999999999999999999999997 PP

>> Pentapeptide_4  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   2.2e-09   1.3e-05       5      76 ..       9      86 ..       5      87 .. 0.72
   2 !   34.2   0.0   3.6e-12   2.1e-08       2      73 ..      71     142 ..      65     145 .. 0.73

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 2.2e-09
  Pentapeptide_4  5 rcsfnncklsnvnFsearlrdcnFtecrl.....snvnFdecnlsdvdfaevdlkrasFsgcnlknvnfsd.klkdid 76
                       f ++++++ ++   +l ++ ++e++l     +n+ ++ ++ls +d++++ l+++ + g +l+++ +sd kl d+d
      EPA04945.1  9 KRNFSKTNFDYEDLIGRNLSNSILSEVDLknrdiHNADLSGSDLSGSDLSGTILFYVKLRGADLRGTSLSDaKLWDAD 86
                    334555555555555555555555555558888899999999999999999999999999999999999776998876 PP

  == domain 2  score: 34.2 bits;  conditional E-value: 3.6e-12
  Pentapeptide_4   2 eftrcsfnncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnfsdklk 73 
                     +++  s+ ++kl +++++ a+lr++++++++l ++ +++++ls+++++++++++a+F+g+ l++v f +  +
      EPA04945.1  71 DLRGTSLSDAKLWDADLYGADLRGADIRGADLFYTDLRSADLSQANLSGANIRHANFEGSILTDVDFTGANY 142
                     566667777777788888888888888888888888888888888888888888888888888888876555 PP

>> Pentapeptide_3  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.026   1.6e+02      22      28 ..      11      17 ..       6      39 .. 0.43
   2 !    9.6   0.0   0.00017         1       2      46 ..      28      69 ..      24      70 .. 0.73
   3 !   12.3   0.0   2.4e-05      0.14       4      44 ..      65     102 ..      62     106 .. 0.86
   4 !   22.3   0.3   1.9e-08   0.00011      11      47 ..     106     140 ..     103     141 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.026
  Pentapeptide_3 22 sFsnadF 28
                    +Fs ++F
      EPA04945.1 11 NFSKTNF 17
                    3333333 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00017
  Pentapeptide_3  2 sganFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdFsg 46
                    s++++s   d+ +   ++a + s++d++++d+sg++    v ++g
      EPA04945.1 28 SNSILSEV-DLKNRDIHNA-DLSGSDLSGSDLSGTILF-YVKLRG 69
                    67777777.7777777888.888888888888888776.666665 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 2.4e-05
  Pentapeptide_3   4 anFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdF 44 
                     + ++ga d+rg+  s+a    +ad+ +ad++ga +  ++d+
      EPA04945.1  65 VKLRGA-DLRGTSLSDA-KLWDADLYGADLRGADIR-GADL 102
                     568889.9*********.7**************998.8887 PP

  == domain 4  score: 22.3 bits;  conditional E-value: 1.9e-08
  Pentapeptide_3  11 dFrgatFsgaasFsnadFgsadFsgarFtgdvdFsga 47 
                     d+r a  s+a + s+a+++ a+F+g++ t dvdF+ga
      EPA04945.1 106 DLRSADLSQA-NLSGANIRHANFEGSILT-DVDFTGA 140
                     6777777788.788888888888888888.8888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1035.26
//
Query:       EPA04946.1  [L=54]
Description: hypothetical protein BG20_I1085 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00084   18.9   0.6    0.00088   18.8   0.6    1.1  1  Baculo_11_kDa  Baculovirus 11 kDa family
     0.0045   17.1   0.6     0.0045   17.1   0.6    1.0  1  DUF4870        Domain of unknown function (DUF4870)
     0.0085   15.5   0.3     0.0085   15.5   0.3    1.0  1  OSTMP1         Osteopetrosis-associated transmembrane protein
  ------ inclusion threshold ------
      0.018   14.0   0.2      0.018   14.0   0.2    1.0  1  TMEM171        Transmembrane protein family 171
      0.035   13.9   0.2      0.039   13.8   0.2    1.0  1  Arteri_Gl      Arterivirus GL envelope glycoprotein
       0.12   12.9   0.6       0.13   12.7   0.6    1.1  1  DUF2367        Uncharacterized conserved protein (DUF2367)


Domain annotation for each model (and alignments):
>> Baculo_11_kDa  Baculovirus 11 kDa family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.6   2.9e-07   0.00088      35      70 ..      13      49 ..       9      54 .] 0.65

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.9e-07
  Baculo_11_kDa 35 dFvLvicglvvfvvivlfilL.lvvilknaeaeeaek 70
                   d + ++c+++vf++ v+f+++ ++ + +++e    +k
     EPA04946.1 13 DVMWILCAVFVFILGVVFFIIsVIKLKQKMEYDLNKK 49
                   56789*********98888661444444444333333 PP

>> DUF4870  Domain of unknown function (DUF4870)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.6   1.5e-06    0.0045      66     102 ..       6      45 ..       1      52 [. 0.78

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.5e-06
     DUF4870  66 llvligf..ll.lllllllllnlvlviiaaikanegeeyr 102
                 l +  gf  ++ l ++++++l +v+ ii +ik ++++ey 
  EPA04946.1   6 LSISYGFdvMWiLCAVFVFILGVVFFIISVIKLKQKMEYD 45 
                 345557774336899*********************9997 PP

>> OSTMP1  Osteopetrosis-associated transmembrane protein 1 precursor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.3   2.9e-06    0.0085     188     224 ..      13      49 ..       7      54 .] 0.82

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.9e-06
      OSTMP1 188 tvpviavssfvlllpviFYlssflhseqkkrklilpk 224
                 +v+ i+ ++fv++l v+F+++s+++ +qk +  +++k
  EPA04946.1  13 DVMWILCAVFVFILGVVFFIISVIKLKQKMEYDLNKK 49 
                 6788999********************9987655443 PP

>> TMEM171  Transmembrane protein family 171
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2   6.1e-06     0.018     158     194 ..      11      48 ..       3      54 .] 0.83

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.1e-06
     TMEM171 158 gfLslqilGplivl.vGLCffvvahvkkrnnlsvsqda 194
                 gf  + il ++ v+ +G+ ff+++ +k +++++ + + 
  EPA04946.1  11 GFDVMWILCAVFVFiLGVVFFIISVIKLKQKMEYDLNK 48 
                 899999***9998736*************999876554 PP

>> Arteri_Gl  Arterivirus GL envelope glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   1.3e-05     0.039      79     113 ..       8      42 ..       3      47 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.3e-05
   Arteri_Gl  79 vryvlssayaalalvAlvlgvysfvvraarlrlcl 113
                  +y + +++ ++a++ ++lgv+ f++++ +l+  +
  EPA04946.1   8 ISYGFDVMWILCAVFVFILGVVFFIISVIKLKQKM 42 
                 5788999********************99998766 PP

>> DUF2367  Uncharacterized conserved protein (DUF2367)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.6   4.5e-05      0.13      67      90 ..       9      32 ..       4      43 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.5e-05
     DUF2367 67 eddftclGilcaifffPlGilcCl 90
                ++ f  + ilca+f+f lG+++ +
  EPA04946.1  9 SYGFDVMWILCAVFVFILGVVFFI 32
                56789999***********99864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1295  (0.0722293); expected 358.6 (0.02)
Passed bias filter:                      677  (0.0377601); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.41u 0.31s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 370.51
//
Query:       EPA04947.1  [L=185]
Description: putative 3-octaprenyl-4-hydroxybenzoate carboxy-lyase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.8e-30  104.7   0.3    4.6e-30  104.5   0.3    1.0  1  Flavoprotein  Flavoprotein


Domain annotation for each model (and alignments):
>> Flavoprotein  Flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.5   0.3   2.6e-34   4.6e-30       1     125 [.       1     163 [.       1     175 [. 0.89

  Alignments for each domain:
  == domain 1  score: 104.5 bits;  conditional E-value: 2.6e-34
                   EEEEEEE-SSCGGGCHHHHHHHHHHTTEEEEEEESCHHHHCCHHGGS................TCSSHHHHHH.CTTESEEEEEEEEHHHHHHHHTT CS
  Flavoprotein   1 kkillgiTGsvaaikalellekLkkegievqvvltkaAkkfiskeklklaa............redpilhiel.rrwadllviaPasantlakianG 84 
                   +k+++giTGs +ai++++lle Lkk g+e+++++++ A+k i+ e  ++++            +++++  ++   +++d++++aP+s++tl++ianG
    EPA04947.1   1 MKLIVGITGSTGAIYGIRLLEVLKKLGVETHLIMSEWAMKCITME-TEFQIgyvkslatttsdEKNMASSVSSgTHKVDGMIVAPCSMKTLSAIANG 96 
                   799****************************************88.555556677776666654445555544566********************* PP

                   --SSHH..............................HHHHHTHCCTTEEEEE.--HHCCTCSTCHHHHHHH CS
  Flavoprotein  85 iadnll..............................tlilratakkpiliaPamnpamyenpqtlknlekl 125
                   + d+l+                              +l+l   ++ +i+i+P + +++y++p+t+++++++
    EPA04947.1  97 YDDTLVaraagvtikesrklilmvretplsaihlenMLKL---SRLGIVILP-PVTEFYTKPKTIDDIVNH 163
                   *********************************9999999...99*******.***************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.30s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1294.54
//
Query:       EPA04948.1  [L=39]
Description: hypothetical protein BG20_I1074 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       241  (0.0134419); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.23s 00:00:00.54 Elapsed: 00:00:00.36
# Mc/sec: 321.86
//
Query:       EPA04949.1  [L=74]
Description: hypothetical protein BG20_I1098 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0031   17.1   0.1     0.0035   16.9   0.1    1.1  1  5TM-5TMR_LYT     5TMR of 5TMR-LYT
  ------ inclusion threshold ------
      0.017   15.1   0.1       0.02   14.9   0.1    1.1  1  RseC_MucC        Positive regulator of sigma(E), RseC/MucC
      0.026   14.0   0.1      0.027   14.0   0.1    1.0  1  DUF1129          Protein of unknown function (DUF1129)
      0.072   11.7   0.1      0.079   11.6   0.1    1.0  1  Cyt_bd_oxida_I   Cytochrome bd terminal oxidase subunit I
       0.17   12.1   0.2       0.22   11.7   0.2    1.2  1  DUF2407_C        DUF2407 C-terminal domain


Domain annotation for each model (and alignments):
>> 5TM-5TMR_LYT  5TMR of 5TMR-LYT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   9.9e-07    0.0035      89     137 ..      15      63 ..       4      69 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 9.9e-07
  5TM-5TMR_LYT  89 tilagllaGlihrklkrrrkkltvlvalligllveilqmllilllakpf 137
                    +++gl++G+i +++ rr +  +  + l +g+++ i+ +++ ++++  +
    EPA04949.1  15 PVFVGLIGGVIAYWVLRRDDPSKAKKCLYLGIILAIIGIIINIMVVTQI 63 
                   5899*******9999999999999************9999999988665 PP

>> RseC_MucC  Positive regulator of sigma(E), RseC/MucC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.1   5.5e-06      0.02      69     112 ..      10      61 ..       5      69 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.5e-06
   RseC_MucC  69 lvYllPllllilgallgsall........gssellaalgallglvlgflivr 112
                   YllP+++ ++g ++++++l         +   l +++a++g+++ +++v+
  EPA04949.1  10 AWYLLPVFVGLIGGVIAYWVLrrddpskaKKCLYLGIILAIIGIIINIMVVT 61 
                 57*******************9999987555556677888888888887775 PP

>> DUF1129  Protein of unknown function (DUF1129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   7.5e-06     0.027     117     174 ..      16      70 ..       2      74 .] 0.73

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.5e-06
     DUF1129 117 llvalvgGlamvlvyrlltrekkkkkrpplwkrllilllllvvwlvlftlvallpavi 174
                 ++v+l+gG++ + v r  ++  +k k+   + ++l+++++++ ++v++ +  l p+ +
  EPA04949.1  16 VFVGLIGGVIAYWVLRRDDP--SKAKKCLYLGIILAIIGIIINIMVVTQIPDLAPN-F 70 
                 57888888888888877766..8888888888888888888888888777766654.4 PP

>> Cyt_bd_oxida_I  Cytochrome bd terminal oxidase subunit I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   2.2e-05     0.079     191     230 ..      19      59 ..       8      65 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.2e-05
  Cyt_bd_oxida_I 191 ffvagvsawyllr.rekefarkslkialvvalvaallqall 230
                      ++ gv a+++lr ++ + a+k+l +++++a++ +++ +++
      EPA04949.1  19 GLIGGVIAYWVLRrDDPSKAKKCLYLGIILAIIGIIINIMV 59 
                     5799*********555559****************999875 PP

>> DUF2407_C  DUF2407 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   6.1e-05      0.22      85     135 ..       4      51 ..       1      61 [. 0.71

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.1e-05
   DUF2407_C  85 eeskanedlliGlliGfflglfalllllkeegllnkrqkmaviaGvlvnlv 135
                  +s+ n   l+ +++G++ g++a  ++l+++    ++ k ++ +G+++ ++
  EPA04949.1   4 GKSRSNAWYLLPVFVGLIGGVIA-YWVLRRDD--PSKAKKCLYLGIILAII 51 
                 567778888999***********.88888773..56666666666666543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       958  (0.053433); expected 358.6 (0.02)
Passed bias filter:                      626  (0.0349155); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 540.27
//
Query:       EPA04950.1  [L=42]
Description: hypothetical protein BG20_I1088 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.054   13.8   0.1      0.054   13.8   0.1    1.0  1  Vps39_1   Vacuolar sorting protein 39 domain 1


Domain annotation for each model (and alignments):
>> Vps39_1  Vacuolar sorting protein 39 domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1     3e-06     0.054      31      67 ..       4      40 ..       1      42 [] 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3e-06
     Vps39_1 31 dveeiLkkekkykeLidlYygkklheeALeLlkelad 67
                  +e L  +k+++e+++ Y ++k+h  AL+  +  ++
  EPA04950.1  4 LFKEGLAARKQVVEIVKNYLMQKMHYFALQAVTSCIQ 40
                5678899**********************98887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.27s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 310.43
//
Query:       EPA04951.1  [L=81]
Description: transcriptional regulator, AsnC family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.7e-09   36.1   0.5    5.2e-09   36.0   0.5    1.1  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
     0.0019   18.5   0.1     0.0021   18.3   0.1    1.0  1  PRANC           PRANC domain
  ------ inclusion threshold ------
      0.044   14.2   1.1       0.05   14.1   1.1    1.1  1  Terminase_2     Terminase small subunit


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.5   8.7e-13   5.2e-09      15      73 ..      17      75 ..       6      77 .. 0.91

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 8.7e-13
                    HHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEE CS
  AsnC_trans_reg 15 efeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivl 73
                    ++  +l +++ V+e+  + G yd+++kv ++  ++ e+ + +k++++++v +t+t+ v+
      EPA04951.1 17 DVMSELLKIDSVKEAKGTFGVYDIFVKVEAKTAKEVEDTITKKIRKIKHVVSTTTLSVI 75
                    6788999************************************************9775 PP

>> PRANC  PRANC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   3.5e-07    0.0021      14      76 ..      15      76 ..       3      80 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.5e-07
       PRANC 14 nninllvrlinkkklkklk.slkiYgklikkiiksakkrykliekaievlnnicskkslWnlLP 76
                + ++++++l++ +++k+ k ++ +Y  ++k   k+ak+ +  i k i++++ ++s  + ++ +P
  EPA04951.1 15 E-MDVMSELLKIDSVKEAKgTFGVYDIFVKVEAKTAKEVEDTITKKIRKIKHVVST-TTLSVIP 76
                3.489999*********************************************988.8888888 PP

>> Terminase_2  Terminase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   1.1   8.3e-06      0.05      59     111 ..      10      69 ..       3      80 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.3e-06
  Terminase_2  59 rtiieadeVlqellkiaraei.......tdevervklkdseevdkeilrevkegkegvkv 111
                  + ++ +++V+ ellki   ++        d++++v+ k+ +ev+++i +++ ++k +v+ 
   EPA04951.1  10 SVMAHEMDVMSELLKIDSVKEakgtfgvYDIFVKVEAKTAKEVEDTITKKIRKIKHVVST 69 
                  5678899*********999996666666666669*********************96654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1407  (0.0784762); expected 358.6 (0.02)
Passed bias filter:                      609  (0.0339673); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 597.54
//
Query:       EPA04952.1  [L=236]
Description: transcriptional regulator, ArsR family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-09   37.5   0.0    4.2e-09   36.1   0.0    1.7  1  HTH_5        Bacterial regulatory protein, arsR family
    2.7e-08   33.2   0.0    5.6e-08   32.2   0.0    1.5  1  HTH_24       Winged helix-turn-helix DNA-binding
    2.7e-07   30.6   0.0    4.6e-07   29.8   0.0    1.3  1  HTH_20       Helix-turn-helix domain
     0.0014   18.5   0.2     0.0036   17.2   0.2    1.6  1  HTH_11       HTH domain
     0.0042   16.9   0.0     0.0072   16.2   0.0    1.4  1  MarR_2       MarR family
     0.0062   16.0   0.1      0.013   15.0   0.1    1.5  1  RepL         Firmicute plasmid replication protein (RepL)
     0.0077   16.7   0.1      0.023   15.1   0.1    1.9  1  HTH_40       Helix-turn-helix domain
  ------ inclusion threshold ------
      0.022   14.6   0.2      0.041   13.8   0.2    1.4  1  TFIIE_alpha  TFIIE alpha subunit
      0.033   14.5   0.1      0.082   13.3   0.1    1.7  1  Rrf2         Transcriptional regulator
      0.039   13.8   0.0       0.07   13.0   0.0    1.5  1  TrmB         Sugar-specific transcriptional regulator TrmB
      0.074   12.6   0.0       0.26   10.9   0.0    1.9  2  HTH_CodY     CodY helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.0   2.6e-12   4.2e-09       5      46 ..      39      80 ..      36      80 .. 0.97

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 2.6e-12
                HHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
       HTH_5  5 lkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                ++ILk+L + +l++ ++a ++++s + v +HLkk+ eaG+V+
  EPA04952.1 39 REILKILFNDSLTANQIAQKTDISLPLVIYHLKKMQEAGVVK 80
                69**************************************95 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.0   3.4e-11   5.6e-08       4      48 .]      37      80 ..      35      80 .. 0.92

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 3.4e-11
      HTH_24  4 tdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                  r+IL++L    +++ +++A+++++S++ v ++lk+++e+G++k
  EPA04952.1 37 SSREILKILFN-DSLTANQIAQKTDISLPLVIYHLKKMQEAGVVK 80
                56888888888.99*****************************97 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0   2.8e-10   4.6e-07       3      58 ..      29      83 ..      26      86 .. 0.93

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 2.8e-10
                HHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
      HTH_20  3 iaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvr 58
                i e+L++ + r+il+ L  ++ lta+++a+  d+s   + yHL++++eag v+ + 
  EPA04952.1 29 IGEILSSDSSREILKIL-FNDSLTANQIAQKTDISLPLVIYHLKKMQEAGVVKITN 83
                56889************.**********************************9776 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.2   2.2e-06    0.0036       3      47 ..      39      82 ..      38      86 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.2e-06
      HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg.vpIe 47
                + il++L++    ++++++A+++++S   v  ++k+++e+g v+I+
  EPA04952.1 39 REILKILFNDS--LTANQIAQKTDISLPLVIYHLKKMQEAGvVKIT 82
                689****7666..****************************77775 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   4.4e-06    0.0072      17      52 ..      47      80 ..      25      92 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.4e-06
                TTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
      MarR_2 17 rpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                ++   lt++++a+++++s + v ++lk++++aG v 
  EPA04952.1 47 NDS--LTANQIAQKTDISLPLVIYHLKKMQEAGVVK 80
                344..9***************************996 PP

>> RepL  Firmicute plasmid replication protein (RepL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   7.7e-06     0.013      77     111 ..      51      85 ..      43     112 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 7.7e-06
        RepL  77 tnRelaeetgislktvsetlkileeanilkkkanG 111
                 t  ++a++t+isl  v+  lk ++ea+++k  + G
  EPA04952.1  51 TANQIAQKTDISLPLVIYHLKKMQEAGVVKITNIG 85 
                 8889************************9987766 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   1.4e-05     0.023       8      55 ..      45      91 ..      37     106 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.4e-05
      HTH_40  8 lleeglsieeIAkerglkesTIegHLaelieegeeidlerlvseeeek 55
                l++++l+  +IA++  ++   ++ HL ++ e+g  ++++++ +  +e+
  EPA04952.1 45 LFNDSLTANQIAQKTDISLPLVIYHLKKMQEAGV-VKITNIGKNTKER 91
                78*******************************8.9999998665544 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   2.5e-05     0.041      13      77 ..      36      99 ..      26     119 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.5e-05
                 HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEEEE CS
  TFIIE_alpha 13 eeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywrin 77
                 ++  ++l++L  +  +t +++a+++ i l+ +   L +++ea++vk+     + k+    ++ ++
   EPA04952.1 36 DSSREILKILF-NDSLTANQIAQKTDISLPLVIYHLKKMQEAGVVKITNIGKNTKERDMKFYTVD 99
                 67788999998.888999*****************************988777666666666554 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1     5e-05     0.082      25      57 ..      49      81 ..      41      87 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5e-05
                -B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
        Rrf2 25 pvsseeiaerqnispsylekilakLrkaglvks 57
                ++++++ia++++is + +   l+k+++ag+vk 
  EPA04952.1 49 SLTANQIAQKTDISLPLVIYHLKKMQEAGVVKI 81
                499****************************96 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   4.3e-05      0.07      16      57 ..      43      84 ..      33     100 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.3e-05
                HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESS CS
        TrmB 16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekg 57
                ++l ++++ta++ia++++++ + v   L+++ ++G+V++   
  EPA04952.1 43 KILFNDSLTANQIAQKTDISLPLVIYHLKKMQEAGVVKITNI 84
                678899*******************************99874 PP

>> HTH_CodY  CodY helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       2.9   4.7e+03      10      16 ..      12      18 ..       8      20 .. 0.78
   2 ?   10.9   0.0   0.00016      0.26       4      40 ..      49      85 ..      47      90 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.9
    HTH_CodY 10 iaDriGi 16
                iaDr+ i
  EPA04952.1 12 IADRVEI 18
                8999977 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00016
    HTH_CodY  4 rLtaskiaDriGitrsvivnaLrkLesaGiiesrsLG 40
                 Lta +ia +  i    ++  L+k+  aG++    +G
  EPA04952.1 49 SLTANQIAQKTDISLPLVIYHLKKMQEAGVVKITNIG 85
                59****************************9876666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       801  (0.0446762); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1686.10
//
Query:       EPA04953.1  [L=168]
Description: hypothetical protein BG20_I1096 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1294.77
//
Query:       EPA04954.1  [L=149]
Description: co-chaperone GrpE, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.7e-36  123.7   3.7    6.4e-36  123.5   3.7    1.0  1  GrpE           GrpE
     0.0068   15.9   0.5     0.0077   15.7   0.5    1.1  1  EST1_DNA_bind  Est1 DNA/RNA binding domain
  ------ inclusion threshold ------
       0.18   11.7   0.2       0.45   10.5   0.2    1.8  2  DUF3437        Domain of unknown function (DUF3437)
        0.4   10.2   4.9        0.6    9.6   4.9    1.3  1  DUF334         Domain of unknown function (DUF334)


Domain annotation for each model (and alignments):
>> GrpE  GrpE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.5   3.7   1.4e-39   6.4e-36      17     166 .]       2     148 ..       1     148 [. 0.95

  Alignments for each domain:
  == domain 1  score: 123.5 bits;  conditional E-value: 1.4e-39
                 CCCCTTCHHHCTTSCCCCCCTTTTTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC..HHH-HHHHHHHHHHHHHHHHHHHHHTT-EE-- CS
        GrpE  17 leeeleelekevkelkekllrllaefenlrkrtekekeeakkfaiekfakdLLpvlDnleralksakeneeekslleGvemtlkqllkiLekhgvekie 115
                 le+ le+ +++v++++ekl++ la+++nl+++t+ ++e+  +++i +f+ d+L++ D++ ra + + ++++++   eG++ +lk+++  L k+ v++i+
  EPA04954.1   2 LENLLEKEKQKVQDYEEKLKHVLADYQNLNRKTQSDIEKGVNTKIDEFMLDFLKIHDDFIRAKQVF-TESKIN--TEGLDSILKNMDALLTKYDVTPID 97 
                 78889999******************************************************9987.444444..7*********************** PP

                 -TTSB--TTTEEEEEEECSSC...TBEEEEEE--EEETTEEEE-EEEEEEE CS
        GrpE 116 pkgepFDpnlheavstveddekeegtvvevvqkGYklkdrvlRpAmVkVsk 166
                 + ge FDpnlhea+s ++d+e +++t+ ++++kGY  + rv+Rp  V +sk
  EPA04954.1  98 ALGEIFDPNLHEAISIITDTELDNNTITKELRKGYISHKRVIRPTLVEISK 148
                 ************************************************997 PP

>> EST1_DNA_bind  Est1 DNA/RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.5   1.7e-06    0.0077      56     126 ..       2      90 ..       1     112 [. 0.85

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.7e-06
                    HHHHHT-TT-HHHHHHHHHHHHHTT............---HHHHHHHHHHTTHHHHHHHHSTTTT........TSSTTGHHHHHHHHHH CS
  EST1_DNA_bind  56 Lellfekirkklekgenkqskeskq............ektpeellkrliilFlrlhgklftgtsf....k..delerevlkklqillse 126
                    Le+l+ek  +k++++e k++   ++            ek  + +++++++ Fl++h  +++ + +    k   e ++++lk +++ll +
     EPA04954.1   2 LENLLEKEKQKVQDYEEKLKHVLADyqnlnrktqsdiEKGVNTKIDEFMLDFLKIHDDFIRAKQVftesKinTEGLDSILKNMDALLTK 90 
                    899**************9877434489*******9999**************************9774414466666668888888866 PP

>> DUF3437  Domain of unknown function (DUF3437)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.2    0.0001      0.45      32      75 ..      29      73 ..       2      82 .. 0.76
   2 ?   -2.7   0.0       1.3   5.9e+03      27      49 ..     108     130 ..     102     138 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0001
     DUF3437 32 eLar.aardpa.pirktvkktlseFkrthqDtWeedkkkFteeqle 75
                +L r  ++d +  +++++ +++ +F + h D+  + k+ Fte++++
  EPA04954.1 29 NLNRkTQSDIEkGVNTKIDEFMLDFLKIH-DDFIRAKQVFTESKIN 73
                355523344443499999999999*****.77889*******9876 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.3
     DUF3437  27 pevleeLaraardpapirktvkk 49 
                  e+++ +++ + d++ i k+ +k
  EPA04954.1 108 HEAISIITDTELDNNTITKELRK 130
                 55666666677777777777666 PP

>> DUF334  Domain of unknown function (DUF334)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   4.9   0.00013       0.6      61     119 ..      23      82 ..       1      92 [. 0.79

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00013
      DUF334  61 eikeqqdlrekelkeikselkkatkdfrdkskkvrndfvdllqkkl.krvdaeelkiilr 119
                  + + q+l  k + +i+  +    ++f    +k+++df++  q     ++++e l+ il+
  EPA04954.1  23 VLADYQNLNRKTQSDIEKGVNTKIDEFMLDFLKIHDDFIRAKQVFTeSKINTEGLDSILK 82 
                 356789**********************************9997541689***9999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1699  (0.0947627); expected 358.6 (0.02)
Passed bias filter:                      840  (0.0468515); expected 358.6 (0.02)
Passed Vit filter:                       103  (0.00574488); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 951.24
//
Query:       EPA04955.1  [L=81]
Description: hypothetical protein BG20_I2620, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-21   75.4   0.1      3e-21   75.3   0.1    1.0  1  HSP70     Hsp70 protein


Domain annotation for each model (and alignments):
>> HSP70  Hsp70 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.3   0.1   1.7e-25     3e-21       1      73 [.       4      81 .]       4      81 .] 0.93

  Alignments for each domain:
  == domain 1  score: 75.3 bits;  conditional E-value: 1.7e-25
                EEEEEEXSSEEEEEEEETTEEEEEXXTTSX....SSEESEEEEXTT.SEEETHHHHHCTTTTGGGEEEXGGGTTTXBT CS
       HSP70  1 viGiDLGttnsvvavmeggkievianeegn....rttPsvvaFtkk.erlvGeaAkrqavtnpkntvfsvKrliGrkf 73
                +iGiDLGt ns+ av+ ggk+++i  +eg+    ++ PsvvaFtk+ e lvGe+A+rqavtnp+ t++++Kr +G ++
  EPA04955.1  4 IIGIDLGTSNSAAAVVMGGKPTIIPAAEGAtvggKAFPSVVAFTKTgELLVGEPARRQAVTNPDSTIAAAKRKMGSDY 81
                79***********************998763333789**************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.50
# Mc/sec: 490.09
//
Query:       EPA04956.1  [L=414]
Description: putative bifunctional cysteine desulfurase/selenocysteine lyase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   5.3e-151  502.8   0.7   6.1e-151  502.6   0.7    1.0  1  Aminotran_5      Aminotransferase class-V
    5.4e-07   29.1   0.2    4.6e-06   26.0   0.1    2.0  2  Aminotran_1_2    Aminotransferase class I and II
     0.0001   21.0   0.0    0.00025   19.7   0.0    1.6  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    0.00015   21.2   0.1    0.00042   19.7   0.1    1.6  1  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
      0.039   12.7   0.0      0.065   11.9   0.0    1.3  1  Pyridoxal_deC    Pyridoxal-dependent decarboxylase conserved 


Domain annotation for each model (and alignments):
>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  502.6   0.7  1.7e-154  6.1e-151       1     371 []      29     401 ..      29     401 .. 0.99

  Alignments for each domain:
  == domain 1  score: 502.6 bits;  conditional E-value: 1.7e-154
                  EEEBTTTS----HHHHHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC.-TTTSEEEEETTS CS
  Aminotran_5   1 iyldsaAttqkpqeVldalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtteainlvalslars.lkpgdeivvteae 97 
                  +yld+a ttqkp++V+da+++yy+++nan+hr+v+ l++eat+ +e++r+kva++i+++++eeiif++Gtteainlva++++r+ +k++d iv+te e
   EPA04956.1  29 VYLDNASTTQKPNQVIDAINDYYRNHNANIHRAVYALAEEATELYEATRDKVANFIHVKNREEIIFVRGTTEAINLVAYAWGRThIKKDDIIVTTEYE 126
                  7************************************************************************************************* PP

                  HGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--.TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESE CS
  Aminotran_5  98 hhanlvpwqelakrtgakvkvipldeegeldldeleklln.ektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavghipidvkklgvDf 194
                  hh+n+vpwq l +++gak+++i +d++gel ld+l+k+l+  k+klv+++ +snv+Gti + ++i++ +k++g+l+lvD+aqav+h+p+++++lg+Df
   EPA04956.1 127 HHSNIVPWQLLTQEKGAKLEYIGMDDNGELILDDLDKYLAtGKVKLVTFSLMSNVLGTITDAKKIISKCKEHGVLTLVDGAQAVPHMPVNLETLGCDF 224
                  ***************************************659******************************************************** PP

                  EEEETTTTTSSTT-EEEEEEHHHHHTS..SS.STTSEEEEETTEEEEHCTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHC CS
  Aminotran_5 195 lafsghKllgPtGiGvlyvrkellekleplllggemveevsleettfaeapskfeaGTpnvagiiglgaaleyleeigleaiekhekelaeyllerlk 292
                  +afsghK+lgPtGiG+l+vrk++le ++p+++gg+m++ev   ett+++ p+kfeaGTpn+a++ig+gaa++yl ++g++++++he el++y+ e+l+
   EPA04956.1 225 FAFSGHKMLGPTGIGILWVRKSILETMNPFHGGGDMIREVHKYETTWNDLPYKFEAGTPNIADVIGFGAAIDYLTKLGMNNVREHEIELTKYAIEKLS 322
                  ************************************************************************************************** PP

                  TSTTEEEES.-B-CTCBSEEEEEETTCSHHHHHHHHHHTTEEEEEE-TTTHHHHHHTT.S-EEEEE--TTS-HHHHHHH CS
  Aminotran_5 293 slpgvrlygpdkaerrasivsfnfkgvhaedvatlLdeegIavrsGhhcaqplmkrlalegtvRaSlyiynteeevdrl 371
                  +++g+++yg+++  +r +++sfnf++vh++dva+++deegIavrsGhhcaq+lm+rl++++t RaS+yiynt eevd+l
   EPA04956.1 323 QVKGLTIYGTKDISKRGGVISFNFADVHPHDVAQIIDEEGIAVRSGHHCAQVLMERLNVAATSRASFYIYNTIEEVDAL 401
                  *****************************************************************************97 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.1   1.3e-09   4.6e-06      13     189 ..      32     207 ..      29     256 .. 0.74
   2 ?    0.9   0.0     0.056     2e+02     288     353 ..     317     386 ..     293     396 .. 0.62

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 1.3e-09
                    STTSS.HHHHHHHHHHHH...HHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHH..HTTT-EEEEEESS CS
  Aminotran_1_2  13 gdsgk.ptlpevakaeke...galaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllk..lnpgdeilvpdpt 102
                    + +++   +  v+ a ++    ++a+  ++ y   + + el ea+ + +   + + +k+  ++++  G++++i++++ ++   + ++d+i+v    
     EPA04956.1  32 DNASTtQKPNQVIDAINDyyrNHNANIHRAVYALAEEATELYEATRDKVA--NFIHVKNREEIIFVRGTTEAINLVAYAWGrtHIKKDDIIVT-TE 124
                    55555567777777777777767777777777655555555555544444..444466666***************99997665566666654.46 PP

                    -THHHHHHHHT......TSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEET CS
  Aminotran_1_2 103 yasyknilrls......ggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDea 189
                    y++++ni+ +       g+++ ++ ++  ++ +l l++l++ l++      k+k++ +   +N  Gt+ + +   k+++ +k++++l++vD a
     EPA04956.1 125 YEHHSNIVPWQlltqekGAKLEYIGMD--DNGELILDDLDKYLATG-----KVKLVTFSLMSNVLGTITDAK---KIISKCKEHGVLTLVDGA 207
                    777777776651122215556666644..***************95.....68**************99876...66777***********76 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.056
                    HHHHHHHS......TEEEECCSCSSEEEEEETHHCHHHHHHHHHHTCTEEEEEGGGGTSTTEEEEECTTS-H CS
  Aminotran_1_2 288 lrdeLael......glkvlasqsgmflltdlsaetakelskkLleevgvyvtpgtsftvpgrlRitvAglte 353
                      ++L +       g k +++ +g++++   + +       ++++e+g++v+ g ++      R++vA++++
     EPA04956.1 317 AIEKLSQVkgltiyGTKDISKRGGVISFNFADVH--PHDVAQIIDEEGIAVRSGHHCAQVLMERLNVAATSR 386
                    5555544455555566667777777777666655..223344666668888887776663334666665554 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   6.9e-08   0.00025     127     201 ..     158     234 ..     106     242 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 6.9e-08
                      HHHHHHHCCT.TEEEEEEESS-TTTT----HHHHHHHHHHTT-EEEEEGTTTHTTTS-GG.GGT-SEEEEETTTTTT CS
  Cys_Met_Meta_PP 127 leelekaike.ntklvylEtptnpllkvvDiekiaklakkagvlvvvDntfaspllqrpl.klgaDivvhSaTKylg 201
                      l++l k +   ++klv +  ++n l  ++D +ki++ +k++gvl++vD + a p +   l +lg+D    S+ K lg
       EPA04956.1 158 LDDLDKYLATgKVKLVTFSLMSNVLGTITDAKKIISKCKEHGVLTLVDGAQAVPHMPVNLeTLGCDFFAFSGHKMLG 234
                      456677766669******************************************6655552699**99999988775 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1   1.2e-07   0.00042      20     235 ..      55     323 ..      42     381 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.2e-07
                      CS----CCCT--HHHHHHHHHHHH.......HTT-SEEEEES-HHHH.HHHHH...HHH--TTEEEEEETT.-HHHHSSTTHHHHCC--EEEEE CS
  Beta_elim_lyase  20 aamlGdesYgedktvnrLedavae.......lfgkeaalfvpqGtaA.nsill...killqrgeevivtep.ahihfdetgaiaelagvklrdl 101
                      +a++  ++Y+ +++  +L +a+++       +   e ++fv   t A n +++   ++++++ + ++ te   h      + + + +g+kl  +
       EPA04956.1  55 NANIHRAVYALAEEATELYEATRDkvanfihVKNREEIIFVRGTTEAiNLVAYawgRTHIKKDDIIVTTEYeHHSNIVPWQLLTQEKGAKLEYI 148
                      567777889999999999999999999999888899999999877774777779999***777766666656445555557788899******* PP

                      -EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHHHTTSSEEEEE CS
  Beta_elim_lyase 102 knkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaakslgeivkemfsyvDsvtms 195
                        +++G++ l++l + ++       k+kl++     n+  G+   +   +++   +k++g+  ++DgA    a+ ++ + +   + ++D + +s
       EPA04956.1 149 GMDDNGELILDDLDKYLAT--G---KVKLVTFSLMSNV-LGT---ITDAKKIISKCKEHGVLTLVDGAQ---AVPHMPVNL--ETLGCDFFAFS 228
                      *******************..3...69*******9997.455...5566788999************95...554445555..5669******* PP

                      SSSTT--SS-.EEEEE-HH...........................................................HHHHHHHHHHHHT--- CS
  Beta_elim_lyase 196 lkKdllanvG.gvlafrddel.......................................................edylaerveqrkylgggl 233
                      + K  l + G g+l +r++ l                                                       ++  ++ +e+ ky  ++l
       EPA04956.1 229 GHKM-LGPTGiGILWVRKSILetmnpfhgggdmirevhkyettwndlpykfeagtpniadvigfgaaidyltklgmNNVREHEIELTKYAIEKL 321
                      ***7.568999***99999667788888887777777777777777777777777777777777777777766665445455666666666666 PP

                      SS CS
  Beta_elim_lyase 234 rq 235
                      +q
       EPA04956.1 322 SQ 323
                      65 PP

>> Pyridoxal_deC  Pyridoxal-dependent decarboxylase conserved domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.8e-05     0.065     165     282 ..     141     246 ..     109     256 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.8e-05
                    HT-EEEEE--BTTTBB-HHHHHHHHHHHHCTT.EEEEEEEEBS-TTT-BB--HHHHHHHHHHCT-EEEEE-TTGGGGGGSGGGGGGGTTGGGESEE CS
  Pyridoxal_deC 165 lgvklrvipldengklrgaalekaieedkekGlipffvvatlGttvlgaFddlkelgdicekydlwlHvDAAyaGsaficpeirhllkgieradSi 260
                     g kl +i +d+ng+l+ ++l k +   k k      v+  l + vlg   d k++   c+++++   vD A a      p++   l+ +   d +
     EPA04956.1 141 KGAKLEYIGMDDNGELILDDLDKYLATGKVK-----LVTFSLMSNVLGTITDAKKIISKCKEHGVLTLVDGAQAV-----PHMPVNLETLG-CDFF 225
                    567899******************9888877.....55667777888889999*******************998.....77666777665.799* PP

                    EEECCCCTS--SS-EEEEESSC CS
  Pyridoxal_deC 261 tvnphKlllvlldcsalivkdk 282
                    ++++hK+l  + +++ l+v+++
     EPA04956.1 226 AFSGHKML-GPTGIGILWVRKS 246
                    ******76.589*******975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       850  (0.0474092); expected 358.6 (0.02)
Passed bias filter:                      627  (0.0349713); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2774.27
//
Query:       EPA04957.1  [L=54]
Description: hypothetical protein BG20_I0894 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.033   14.2   0.1      0.037   14.0   0.1    1.0  1  Phage_Gp15  Bacteriophage Gp15 protein


Domain annotation for each model (and alignments):
>> Phage_Gp15  Bacteriophage Gp15 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1     2e-06     0.037      18      54 ..       6      42 ..       2      53 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2e-06
  Phage_Gp15 18 idldFrtvlrfedmledeelseeeKinlalellldee 54
                i++  +++l+f ++ +++ l+ eeKi +++e++l  e
  EPA04957.1  6 IKFKEKDYLDFHKIANESGLTPEEKIHKIIEYYLIIE 42
                55555789************************99732 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.27s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 401.25
//
Query:       EPA04958.1  [L=119]
Description: tetratricopeptide repeat protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.3e-16   59.6   1.0      4e-07   29.6   0.0    3.2  3  TPR_1       Tetratricopeptide repeat
      5e-15   54.4   1.0      4e-08   32.8   0.1    3.0  3  TPR_8       Tetratricopeptide repeat
    5.9e-15   54.1   0.4    7.2e-07   28.9   0.0    3.2  3  TPR_2       Tetratricopeptide repeat
    6.3e-11   42.6   0.1    1.3e-07   32.0   0.0    2.1  2  TPR_19      Tetratricopeptide repeat
    2.9e-10   39.8   0.3     0.0051   17.1   0.1    3.6  4  TPR_17      Tetratricopeptide repeat
    7.4e-09   35.7   0.0     0.0084   16.9   0.0    2.8  3  TPR_14      Tetratricopeptide repeat
    2.4e-08   33.4   0.0      0.013   15.5   0.0    3.2  3  TPR_7       Tetratricopeptide repeat
    1.5e-07   31.6   0.1    2.6e-07   30.8   0.1    1.4  1  ANAPC3      Anaphase-promoting complex, cyclosome, subunit 3
    1.9e-07   30.6   0.2      0.016   14.9   0.0    3.1  3  TPR_11      TPR repeat
    7.3e-06   26.2   0.0    0.00015   21.9   0.0    2.4  2  TPR_12      Tetratricopeptide repeat
    5.3e-05   23.6   0.1        0.6   10.9   0.0    3.2  3  TPR_6       Tetratricopeptide repeat
    7.6e-05   22.7   1.7      0.029   14.5   0.1    3.2  3  Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
    0.00011   21.5   0.0    0.00017   20.9   0.0    1.3  1  TPR_15      Tetratricopeptide repeat
    0.00019   20.5   0.1    0.00023   20.3   0.1    1.0  1  ChAPs       ChAPs (Chs5p-Arf1p-binding proteins)
     0.0069   15.3   0.4       0.13   11.2   0.0    1.9  2  NARP1       NMDA receptor-regulated protein 1
  ------ inclusion threshold ------
      0.012   16.3   0.0       0.17   12.5   0.0    2.1  2  TPR_16      Tetratricopeptide repeat
      0.018   15.0   0.5      0.072   13.0   0.2    1.7  2  DUF4919     Domain of unknown function (DUF4919)
       0.14   12.4   0.0        7.2    6.8   0.0    2.1  2  TPR_9       Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0      0.12   1.2e+02      14      22 ..      18      26 ..      15      27 .. 0.79
   2 !   29.6   0.0     4e-10     4e-07       3      34 .]      41      72 ..      39      72 .. 0.91
   3 !   24.7   0.1   1.4e-08   1.4e-05       9      34 .]      81     106 ..      75     106 .. 0.97

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.12
                TT-HHHHHH CS
       TPR_1 14 lgkydeAle 22
                 g+y eAle
  EPA04958.1 18 DGDYTEALE 26
                589999998 PP

  == domain 2  score: 29.6 bits;  conditional E-value: 4e-10
                HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1  3 alynlGnayfklgkydeAleyyekALelnPnn 34
                  + +G +yf l++ ++A+ey+ek L lnPn+
  EPA04958.1 41 YMFMMGSIYFILEESKKAIEYFEKSLNLNPND 72
                56779*************************97 PP

  == domain 3  score: 24.7 bits;  conditional E-value: 1.4e-08
                 HHHHHTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1   9 nayfklgkydeAleyyekALelnPnn 34 
                 na+++l++ deA+++++k ++l+P+n
  EPA04958.1  81 NAHLSLQQKDEAIDCCKKIIKLEPKN 106
                 799*********************98 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0       1.1   1.1e+03      13      22 ..      17      26 ..      15      27 .. 0.79
   2 !   32.8   0.1     4e-11     4e-08       1      34 []      39      72 ..      39      72 .. 0.96
   3 !   18.4   0.0   1.7e-06    0.0017       9      34 .]      81     106 ..      73     106 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.1
                HTT-HHHHHH CS
       TPR_8 13 klgdyeeAke 22
                k gdy eA e
  EPA04958.1 17 KDGDYTEALE 26
                5699***987 PP

  == domain 2  score: 32.8 bits;  conditional E-value: 4e-11
                CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
       TPR_8  1 aeayynlgsiylklgdyeeAkeyyekaleldpdn 34
                a++++++gsiy+ l++ ++A+ey+ek l l+p++
  EPA04958.1 39 ADYMFMMGSIYFILEESKKAIEYFEKSLNLNPND 72
                6899****************************96 PP

  == domain 3  score: 18.4 bits;  conditional E-value: 1.7e-06
                 HHHHHTT-HHHHHHHHHHHHHHHHH. CS
       TPR_8   9 siylklgdyeeAkeyyekaleldpdn 34 
                 +++l+l++++eA+ +++k ++l+p+n
  EPA04958.1  81 NAHLSLQQKDEAIDCCKKIIKLEPKN 106
                 6899********************97 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.077        77      13      23 ..      17      27 ..      14      38 .. 0.82
   2 !   28.9   0.0   7.2e-10   7.2e-07       1      34 []      39      72 ..      39      72 .. 0.96
   3 !   18.4   0.1   1.6e-06    0.0016       9      34 .]      81     106 ..      81     106 .. 0.95

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.077
       TPR_2 13 klgdyeeAlea 23
                k gdy eAle+
  EPA04958.1 17 KDGDYTEALEF 27
                679*****996 PP

  == domain 2  score: 28.9 bits;  conditional E-value: 7.2e-10
       TPR_2  1 aealynlGlayyklgdyeeAleafekAleldPnn 34
                a++ +++G +y+ l + ++A+e+fek+l l+Pn+
  EPA04958.1 39 ADYMFMMGSIYFILEESKKAIEYFEKSLNLNPND 72
                6899****************************97 PP

  == domain 3  score: 18.4 bits;  conditional E-value: 1.6e-06
       TPR_2   9 layyklgdyeeAleafekAleldPnn 34 
                 +a++ l++ +eA+++++k ++l+P+n
  EPA04958.1  81 NAHLSLQQKDEAIDCCKKIIKLEPKN 106
                 6899********************97 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0    0.0023       2.3       1      26 [.      15      40 ..      15      50 .. 0.73
   2 !   32.0   0.0   1.3e-10   1.3e-07       8      68 .]      56     116 ..      51     116 .. 0.96

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0023
      TPR_19  1 llaegdyaeAlalleqalqedpknae 26
                l+++gdy+eAl++ +++ ++  ++a+
  EPA04958.1 15 LVKDGDYTEALEFGKSLQEKFSNDAD 40
                56788999999888887777777766 PP

  == domain 2  score: 32.0 bits;  conditional E-value: 1.3e-10
      TPR_19   8 aeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryasLlAkl 68 
                   A++++e+ l  +p++ e + l  +a+l+l q deA+++++++ + +p++ ++++Ll kl
  EPA04958.1  56 KKAIEYFEKSLNLNPNDVETLTLKTNAHLSLQQKDEAIDCCKKIIKLEPKNYEAHGLLEKL 116
                 57*******************************************************9987 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       4.7   4.6e+03      25      33 ..      17      25 ..      13      26 .. 0.72
   2 !   11.2   0.0    0.0004       0.4       7      34 .]      33      60 ..      20      60 .. 0.91
   3 !   17.1   0.1   5.1e-06    0.0051       1      33 [.      61      93 ..      61      94 .. 0.96
   4 !    7.7   0.0    0.0053       5.3       1      18 [.      95     112 ..      95     113 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 4.7
      TPR_17 25 knGdlmtAr 33
                k Gd+ +A+
  EPA04958.1 17 KDGDYTEAL 25
                568888876 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.0004
      TPR_17  7 eldPnnadaynnLAelllknGdlmtArq 34
                e+  n+ad +++++ ++  + ++++A++
  EPA04958.1 33 EKFSNDADYMFMMGSIYFILEESKKAIE 60
                6689*********************986 PP

  == domain 3  score: 17.1 bits;  conditional E-value: 5.1e-06
      TPR_17  1 lylkaleldPnnadaynnLAelllknGdlmtAr 33
                +++k+l l+Pn+++ ++++ +++l++ ++++A+
  EPA04958.1 61 YFEKSLNLNPNDVETLTLKTNAHLSLQQKDEAI 93
                69*****************************97 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.0053
      TPR_17   1 lylkaleldPnnadaynn 18 
                 +++k ++l+P+n +a+ +
  EPA04958.1  95 CCKKIIKLEPKNYEAHGL 112
                 79************9865 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.43   4.3e+02      13      42 ..      17      46 ..      11      48 .. 0.84
   2 !   16.9   0.0   8.4e-06    0.0084       6      40 ..      44      78 ..      39      82 .. 0.91
   3 !   15.6   0.0   2.1e-05     0.021      10      41 ..      82     113 ..      78     115 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.43
      TPR_14 13 alGdpdeAiallrralalaPddaeawllla 42
                  Gd+ eA++  + + +++ +da++ ++++
  EPA04958.1 17 KDGDYTEALEFGKSLQEKFSNDADYMFMMG 46
                57999***9999999999999999999887 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 8.4e-06
      TPR_14  6 alaeallalGdpdeAiallrralalaPddaeawll 40
                +++++++ l++ ++Ai+++++ l l+P+d e+++l
  EPA04958.1 44 MMGSIYFILEESKKAIEYFEKSLNLNPNDVETLTL 78
                799**************************998876 PP

  == domain 3  score: 15.6 bits;  conditional E-value: 2.1e-05
      TPR_14  10 allalGdpdeAiallrralalaPddaeawlll 41 
                 a+l l++ deAi++++++++l P++ ea+ ll
  EPA04958.1  82 AHLSLQQKDEAIDCCKKIIKLEPKNYEAHGLL 113
                 7899************************9876 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.089        88      10      21 ..      16      27 ..      15      27 .. 0.86
   2 !   15.5   0.0   1.3e-05     0.013       4      31 ..      44      69 ..      42      74 .. 0.81
   3 !   10.8   0.0   0.00042      0.42       4      29 ..      78     103 ..      75     109 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.089
       TPR_7 10 srlGdyeeAiel 21
                +++Gdy eA+e+
  EPA04958.1 16 VKDGDYTEALEF 27
                579******996 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.3e-05
       TPR_7  4 nLarlysrlGdyeeAielyeqsLaltkd 31
                 ++++y+ l + ++Aie++e+sL     
  EPA04958.1 44 MMGSIYFILEESKKAIEYFEKSLN--LN 69
                589******************664..44 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00042
       TPR_7   4 nLarlysrlGdyeeAielyeqsLalt 29 
                    +++ +l++ +eAi+++++ + l+
  EPA04958.1  78 LKTNAHLSLQQKDEAIDCCKKIIKLE 103
                 56799***************966665 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.1   2.6e-10   2.6e-07       3      81 ..      19      98 ..      15      99 .. 0.95

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 2.6e-10
                T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
      ANAPC3  3 nnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81
                ++y +A+ ++  l+++ +++++  ++ +  ++ +++ k+A+e+++k+ +ln+++ + + l+  + l L++ +eAi++ +k
  EPA04958.1 19 GDYTEALEFGKSLQEKFSNDADYMFMMGSIYFILEESKKAIEYFEKSlNLNPNDVETLTLKTNAHLSLQQKDEAIDCCKK 98
                68999999******99999********************************************************98765 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.11   1.1e+02       4      15 ..      15      26 ..      13      26 .. 0.84
   2 !   14.9   0.0   1.6e-05     0.016       1      30 [.      46      75 ..      46      78 .. 0.94
   3 !    9.9   0.0   0.00058      0.58       2      31 ..      81     110 ..      80     113 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.11
      TPR_11  4 yyeqGkyeeAie 15
                +++ G+y+eA+e
  EPA04958.1 15 LVKDGDYTEALE 26
                6788******97 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1.6e-05
      TPR_11  1 GdayyeqGkyeeAieaYkkAlkldPdnaea 30
                G +y+ + + ++Aie ++k l+l+P+++e 
  EPA04958.1 46 GSIYFILEESKKAIEYFEKSLNLNPNDVET 75
                89*************************985 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.00058
      TPR_11   2 dayyeqGkyeeAieaYkkAlkldPdnaeay 31 
                 +a  ++++ +eAi + kk +kl P+n ea+
  EPA04958.1  81 NAHLSLQQKDEAIDCCKKIIKLEPKNYEAH 110
                 678899999*******************99 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   1.6e-07   0.00015      26      74 ..      21      68 ..      15      71 .. 0.90
   2 ?    1.9   0.0      0.27   2.7e+02      14      32 ..      84     102 ..      72     114 .. 0.68

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.6e-07
      TPR_12 26 lekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74
                + +ale  ++l+++ + + a +++ +g +y+ l++ ++A+e++e++l++
  EPA04958.1 21 YTEALEFGKSLQEKFS-NDADYMFMMGSIYFILEESKKAIEYFEKSLNL 68
                7788999999999999.89****************************97 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.27
      TPR_12  14 rrlgrydeAlellekalei 32 
                 + l++ deA+++++k + +
  EPA04958.1  84 LSLQQKDEAIDCCKKIIKL 102
                 3344445999999887765 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.66   6.6e+02      13      22 ..      15      27 ..       6      38 .. 0.66
   2 !   10.9   0.0   0.00061       0.6       2      32 ..      41      71 ..      40      72 .. 0.89
   3 !    7.8   0.0    0.0056       5.6       9      32 ..      82     105 ..      81     106 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.66
                H...HHHHHHHHH CS
       TPR_6 13 l...gdtdkAlea 22
                l   gd+++Ale 
  EPA04958.1 15 LvkdGDYTEALEF 27
                1455899999986 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00061
                HHHHHHHHHH.HHHHHHHHHHHHHHHHHH-TT CS
       TPR_6  2 Alyklalsyr.klgdtdkAlealerlikeYPd 32
                 +++++  y+    ++ kA+e++e+ ++  P+
  EPA04958.1 41 YMFMMGSIYFiLE-ESKKAIEYFEKSLNLNPN 71
                599*******666.***********9999998 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0056
                 HHHHHHHHHHHHHHHHHHHHH-TT CS
       TPR_6   9 syrklgdtdkAlealerlikeYPd 32 
                 ++++l+++d+A++  +++ik  P+
  EPA04958.1  82 AHLSLQQKDEAIDCCKKIIKLEPK 105
                 577767**************9997 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.11   1.1e+02      13      27 ..      17      31 ..      11      34 .. 0.83
   2 ?    3.9   0.1     0.055        55      16      43 ..      54      81 ..      40      89 .. 0.85
   3 !   14.5   0.1   2.9e-05     0.029      10      45 ..      82     117 ..      80     118 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.11
                HHT-HHHHHHHHHHH CS
  Fis1_TPR_C 13 klgeYseArryvdal 27
                k g+Y+eA+++ + l
  EPA04958.1 17 KDGDYTEALEFGKSL 31
                679******997765 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.055
                -HHHHHHHHHHHHHHTTS-HHHHHHHHH CS
  Fis1_TPR_C 16 eYseArryvdalLeiEPenrQaqsLkel 43
                e ++A +y +  L++ P+    ++Lk+ 
  EPA04958.1 54 ESKKAIEYFEKSLNLNPNDVETLTLKTN 81
                557999***************9999975 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 2.9e-05
                 HHHHHT-HHHHHHHHHHHHHHTTS-HHHHHHHHHHH CS
  Fis1_TPR_C  10 GhyklgeYseArryvdalLeiEPenrQaqsLkelie 45 
                 +h+ l++ +eA  +++ ++++EP+n  a  L e +e
  EPA04958.1  82 AHLSLQQKDEAIDCCKKIIKLEPKNYEAHGLLEKLE 117
                 6677777799*********************99876 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   1.7e-07   0.00017     194     273 ..      19      98 ..      11     105 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.7e-07
      TPR_15 194 grraeLrellkawkaraesdasLwgplaaAlllLgrpkkALeylrkqakenrkdplwllaYADaleqagradeAwrlRrq 273
                 g ++e+ e  k ++++ ++da+++  +++ +  L+++kkA ey++k ++ n++d+  l     a+   ++ deA    ++
  EPA04958.1  19 GDYTEALEFGKSLQEKFSNDADYMFMMGSIYFILEESKKAIEYFEKSLNLNPNDVETLTLKTNAHLSLQQKDEAIDCCKK 98 
                 55556666667889999*****************************************9999999999999999876555 PP

>> ChAPs  ChAPs (Chs5p-Arf1p-binding proteins)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   2.3e-07   0.00023     181     274 ..      21     113 ..       9     116 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.3e-07
                 HHT-HHHHHHHHHHHHTT-GGGHHHHHHHHHHTT-HHHHHHHHHHHH-SSS-HHHHHHHHHHHHHHSS--HHHHHHHHHHHHH-TT-HHHHHHH CS
       ChAPs 181 ltkrydralellekLkeeepevvillarvllladeEvdavkllneeleeeekdaelLllqaefllskkkeelAlevakravksaPsefktWalL 274
                  t+ ++ + +l ek+  ++ + + ++  ++++ +e  +a++  +++l+ +++d+e L+l+++  ls ++++ A+++ k+ +k+ P +++   lL
  EPA04958.1  21 YTEALEFGKSLQEKFS-NDADYMFMMGSIYFILEESKKAIEYFEKSLNLNPNDVETLTLKTNAHLSLQQKDEAIDCCKKIIKLEPKNYEAHGLL 113
                 4444555555544443.346788999************************************************************99876666 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   0.00013      0.13      15      72 ..      16      73 ..      10      77 .. 0.92
   2 !    7.6   0.4    0.0016       1.6      19      79 ..      54     114 ..      53     118 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00013
                HHHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-C CS
       NARP1 15 eeagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpens 72
                 + g++ eAle  ++ +++  +   ++ +++++++ L++ ++A +++e+ l+ np++ 
  EPA04958.1 16 VKDGDYTEALEFGKSLQEKFSNDADYMFMMGSIYFILEESKKAIEYFEKSLNLNPNDV 73
                67899*************************************************9865 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0016
                 HHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CHHHHHHH CS
       NARP1  19 kleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpenskYyegle 79 
                 + ++A+e +e++ +   + ++ ++ k++  l L++k+eA    +++++  p n++ +  le
  EPA04958.1  54 ESKKAIEYFEKSLNLNPNDVETLTLKTNAHLSLQQKDEAIDCCKKIIKLEPKNYEAHGLLE 114
                 5678999999999999999999999999999999999999999999999999988776655 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00017      0.17       7      66 ..      15      71 ..      11      73 .. 0.90
   2 ?    1.5   0.0       0.5     5e+02       6      40 ..      82     113 ..      80     113 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00017
      TPR_16  7 alragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66
                +++ gdy++A++  + + +++   + +a+ ++  g +++ + + ++A++++++ l   p+
  EPA04958.1 15 LVKDGDYTEALEFGKSLQEKF---SNDADYMFMMGSIYFILEESKKAIEYFEKSLNLNPN 71
                6889*******777*******...9***************************98877666 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.5
      TPR_16   6 aalragdyddAaaaleaalkrdpssPdaaeAllll 40 
                 a+l +++ d+A+   +  +k+    P ++eA+ ll
  EPA04958.1  82 AHLSLQQKDEAIDCCKKIIKLE---PKNYEAHGLL 113
                 6777888899999999999999...9999998765 PP

>> DUF4919  Domain of unknown function (DUF4919)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.43   4.3e+02      65     102 ..      13      50 ..       6      56 .. 0.78
   2 ?   13.0   0.2   7.3e-05     0.072      71     119 ..      53     101 ..      50     104 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.43
     DUF4919  65 kkelseeelkeiislaeealkknPfdlkqlnllayayk 102
                 kk ++  ++ e++++++++ +k+  d   ++++  +y 
  EPA04958.1  13 KKLVKDGDYTEALEFGKSLQEKFSNDADYMFMMGSIYF 50 
                 67788899999999999999999888888888877775 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 7.3e-05
     DUF4919  71 eelkeiislaeealkknPfdlkqlnllayaykalgkkeeakiyskrlnk 119
                 ee k++i++ e++l+ nP d+++l+l  +a+ +l++k+ea    k++ k
  EPA04958.1  53 EESKKAIEYFEKSLNLNPNDVETLTLKTNAHLSLQQKDEAIDCCKKIIK 101
                 6889*********************************999877777655 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0    0.0073       7.2      36      64 ..      46      74 ..      16      81 .. 0.64
   2 ?    3.9   0.0      0.06        60       3      30 ..      81     108 ..      78     113 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0073
       TPR_9 36 GlllaqlGclsaAladLeaylalapdapd 64
                G +++ l+  ++A++ +e  l l+p++ +
  EPA04958.1 46 GSIYFILEESKKAIEYFEKSLNLNPNDVE 74
                55555555555555555555555554443 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.06
       TPR_9   3 aiaireedweralavverllllaPddpe 30 
                 +++++ ++ ++a+ ++  ++ l P+  e
  EPA04958.1  81 NAHLSLQQKDEAIDCCKKIIKLEPKNYE 108
                 5789999*****************8765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       865  (0.0482459); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.52u 0.33s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 707.39
//
Query:       EPA04959.1  [L=223]
Description: hydroxymethylbilane synthase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.1e-34  117.1   0.0    1.1e-33  116.5   0.0    1.2  1  Porphobil_deam   Porphobilinogen deaminase, dipyromethane cof
    2.5e-11   43.8   0.0    4.4e-11   43.0   0.0    1.4  1  Porphobil_deamC  Porphobilinogen deaminase, C-terminal domain


Domain annotation for each model (and alignments):
>> Porphobil_deam  Porphobilinogen deaminase, dipyromethane cofactor binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.5   0.0   1.2e-37   1.1e-33      86     200 ..       2     117 ..       1     120 [. 0.93

  Alignments for each domain:
  == domain 1  score: 116.5 bits;  conditional E-value: 1.2e-37
  Porphobil_deam  86 elaavlkredprDvlvvks..sleelpegavvgTsSlRRkaqlkklrpdlevkdlRGnvdtRlrkldegeydaiiLAaAGLkRlgleerisevls 178
                     +la ++kre ++D+++ ++  +l+++++gav+gTsSlRR++q++++r+d++v+++RGn++tR++k+ ++ +d+i+LA+AG++Rlg++ + +  ls
      EPA04959.1   2 TLASIPKREMVNDIFISSDgtTLDSIKPGAVIGTSSLRRAVQITRKRSDITVRPIRGNIETRIKKVTDKIFDGIVLAQAGISRLGIDVQYTP-LS 95 
                     7899************644789*********************************************999***************7776666.** PP

  Porphobil_deam 179 peellpavgQGalavevrkede 200
                      +++ p++gQGala+  rk++ 
      EPA04959.1  96 IQDFSPSPGQGALAIVSRKDEP 117
                     ******************9976 PP

>> Porphobil_deamC  Porphobilinogen deaminase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.0   0.0   4.9e-15   4.4e-11       2      74 ..     133     202 ..     132     203 .. 0.87

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 4.9e-15
                      HHHHHHHHHHHHTT--TTSSEEEEEEEETTE.EEEEEEEE-TTS..S-EEEEEEEE-GGGHHHHHHHHHHHHH CS
  Porphobil_deamC   2 levlaERallkeLeGGCsvPiGvyaeveaneelkLkglvlsldglksaveeaeakgeleeaeelGkklaeell 74 
                      le+ aER+l    + GC  PiG+ya+ ++n+ ++L     s dg+k     +e+ g++++++ lGk+++eel 
       EPA04959.1 133 LEIEAERSLSDFVDSGCRFPIGAYAKSNGNQ-MTLSVSAFSVDGKK--SLFVEKSGDKNDPFLLGKSVGEELH 202
                      5899**********************77655.9***********99..55566666669************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       279  (0.0155614); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1615.51
//
Query:       EPA04960.1  [L=690]
Description: PKD domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-14   52.9  53.9    2.7e-09   37.6   2.4    7.6  7  Big_9            Bacterial Ig domain
      5e-06   26.4  22.0      0.022   14.7   0.3    5.6  5  Cadherin_5       Cadherin-like domain
    3.8e-05   23.5  25.8        2.1    8.3   0.3    8.6  8  PKD              PKD domain
    0.00045   20.8   5.4    0.00045   20.8   5.4    7.3  7  Cadherin_4       Bacterial cadherin-like domain
     0.0012   19.1   4.3       0.13   12.6   0.1    4.3  5  Ig_2             Immunoglobulin domain
     0.0018   18.1   2.1        1.1    9.1   0.2    4.1  3  DUF824           Salmonella repeat of unknown function (DUF82
  ------ inclusion threshold ------
      0.053   13.0   0.6       0.22   11.0   0.6    2.1  1  Waikav_capsid_1  Waikavirus capsid protein 1
        4.9    7.3  16.1        1.7    8.8   0.2    5.7  6  TIG              IPT/TIG domain


Domain annotation for each model (and alignments):
>> Big_9  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.3      0.15   3.3e+02      57      88 ..      55      86 ..      10      88 .. 0.45
   2 !   37.6   2.4   1.2e-12   2.7e-09       1      90 []      92     185 ..      92     185 .. 0.85
   3 ?    5.6   0.2     0.012        27       6      90 .]     293     379 ..     289     379 .. 0.76
   4 !   13.0   4.7   5.9e-05      0.13       3      88 ..     385     472 ..     383     474 .. 0.82
   5 !    8.9   5.6    0.0011       2.6       3      88 ..     480     565 ..     478     566 .. 0.64
   6 !    7.1   0.3     0.004         9       5      89 ..     574     663 ..     570     664 .. 0.63
   7 !    6.8   1.5     0.005        11       2      20 ..     669     687 ..     668     689 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.15
       Big_9 57 Gtvtinadgtltytpna...gfsgtdsftYtvsDg 88
                 + t+ +    t+ +++   g+    +ft tv+D+
  EPA04960.1 55 SSYTVAEP---TFMAPEvanGQIKVLTFTLTVTDP 86
                33333322...222222333666667888888886 PP

  == domain 2  score: 37.6 bits;  conditional E-value: 1.2e-12
       Big_9   1 tatvtvtvtpvndaPvavd..dsvtvtedsv...landtdpdgdaltvtsltvtlvtapanGtvtinadgtltytpna...gfsgtdsftYtvsDgsg 90 
                 +atv+v v+pvn+aP++++  d+vt+++ +v   ++++ dpdgdalt++   +  +ta+++ +++ ++   ++  pn    +++ + +f+ tv Dg g
  EPA04960.1  92 SATVEVVVNPVNHAPIVSAgrDQVTFKTINVvtlVSSALDPDGDALTYS---W-KQTAGQQIKLSSTTGKYIQILPNGidfSQANPLTFELTVDDGFG 185
                 69**************99977779998888877788**********953...4.678999999999977788899998*77777777********976 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.012
       Big_9   6 vtvtpvndaPvavddsvtvtedsv....landtdpdgdaltvtsltvtlvtapanGtvtinadgtltytpnagfsgtd.sftYtvsDgsg 90 
                 v v p++  P+a++   ++ + +v    + + t p +++l    +++++ ++ +    + +++  + ++p  g + +  +f+ tv+D++g
  EPA04960.1 293 VKVIPADGMPTANAGPDQTVSENVqvklVGTGTHPKDTNLH---YSWKQISGKNVEIYERTSSSVYFFSPKIGGTPEKlTFELTVTDSQG 379
                 7788999999**998855544444468788*****999996...56777777777777777777799999986666666********997 PP

  == domain 4  score: 13.0 bits;  conditional E-value: 5.9e-05
       Big_9   3 tvtvtvtpvndaPvavdds....vtvtedsvlandtdpdgdaltvtsltvtlvtapanGtvtin.adgtltytpna...gfsgtdsftYtvsDg 88 
                  v vtvt +n +P a++      +  t  +v+ +  dp++ +lt+      +  + a+ +vt++ +  ++++ +++   g++    f+ tv+D+
  EPA04960.1 385 DVAVTVTTTNLPPRANAGPdrkvIGGTNVDVTGSGFDPENGPLTY------SWKQIAGDSVTFDaTKPSFSFKAPTlapGETKRLVFQLTVTDD 472
                 699**************766676666788889***********74......3467888888888445578887777777999999*******96 PP

  == domain 5  score: 8.9 bits;  conditional E-value: 0.0011
       Big_9   3 tvtvtvtpvndaPvavdds.vtvtedsvla...ndtdpdgdaltvtsltvtlvtapanGtvtinadgtltytpnagfsgtdsftYtvsDg 88 
                 ++ + v p+n aP +++   +t +e++v+a   +  dpd  +     +t++ +ta++      n+  t +  p +  + + + t t sDg
  EPA04960.1 480 QLILLVVPENSAPRVNAGPdMTADENTVVAlvcTGNDPDEGDV----ITFKWSTASTAVITDANSASTTVTLPHTTKNESITMTCTGSDG 565
                 5567799**********7769999****554455555665554....4555445554444444544444445555677777777777776 PP

  == domain 6  score: 7.1 bits;  conditional E-value: 0.004
       Big_9   5 tvtvtpvndaPvavdds........vtvtedsvlandtdpdgdaltvtsltvtlvtapanGtvtinadgtltytpna...gfsgtdsftYtvsDgs 89 
                  ++v +v   P+++d          + v+ d++ +   dp+g +l+   + +t+v ++++  ++ +++ t+++t ++   g+     f+ +v D++
  EPA04960.1 574 MINVVNVLNLPIVADAGpdqivnekIKVSLDGSKS--NDPEGQKLS---FMWTQV-SGDKVVLSSTSSKTVSFTSPTvlnGEVKVLVFELKVFDDN 663
                 56777766666666644453433335555555555..55******7...667665.55577777788889***99995555555556666666666 PP

  == domain 7  score: 6.8 bits;  conditional E-value: 0.005
       Big_9   2 atvtvtvtpvndaPvavdd 20 
                 +tvtv v pvn aP a+++
  EPA04960.1 669 DTVTVSVDPVNAAPKATAT 687
                 59**************975 PP

>> Cadherin_5  Cadherin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.2   0.3    0.0093        21      34      97 ..      32      99 ..      12     100 .. 0.77
   2 !   14.7   0.3   9.8e-06     0.022       1      95 [.     102     194 ..     101     195 .. 0.76
   3 ?    3.4   0.1     0.033        74      74      98 .]     367     391 ..     336     391 .. 0.86
   4 ?    4.6   1.5     0.014        32       2      92 ..     489     572 ..     488     578 .. 0.73
   5 !   10.3   0.4   0.00023      0.52      33      97 ..     608     675 ..     603     676 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0093
  Cadherin_5 34 sDvd.gdtLsvssltadaenGtvvdngdGtftftpeanynGev...tlsYtvsDgeggtttatasltv 97
                 D d +d L+ + ++ d e  ++ +    + tf   +  nG++   t++ tv+D  g+t +at+++ v
  EPA04960.1 32 IDDDpNDILTYKWVQNDGEPVKLSSYTVAEPTFMAPEVANGQIkvlTFTLTVTDPVGATDSATVEVVV 99
                555556777777776666666666666667788888889999877799***************99987 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 9.8e-06
  Cadherin_5   1 vndaPvvssevtlaagseDtaltitaaqLLanasDvdgdtLsvssltadaenGtvvdngdGtftftpe.anyn..GevtlsYtvsDgeggtttatasl 95 
                 vn+aP+vs+       ++ t  ti+  +L++ a D+dgd+L+ s  +++ ++ ++ +     + + p+  +++   ++t++ tv+Dg ggt++ ++s+
  EPA04960.1 102 VNHAPIVSA-----GRDQVTFKTINVVTLVSSALDPDGDALTYSWKQTAGQQIKLSSTTGKYIQILPNgIDFSqaNPLTFELTVDDGFGGTASDSVSV 194
                 567776663.....34445677899999**************9998777767777765555667888845887556789999*********9998875 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.033
  Cadherin_5  74 evtlsYtvsDgeggtttatasltva 98 
                 ++t++ tv+D +g++++  + +tv+
  EPA04960.1 367 KLTFELTVTDSQGNSAKDDVAVTVT 391
                 579999************9999986 PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.014
  Cadherin_5   2 ndaPvvssevtlaagseDtaltitaaqLLanasDvd.gdtLsvssltadaenGtvvdngdGtftft.peanynGevtlsYtvsDgeggtttat 92 
                 n aP v++    ++++ D++ ++    L+    D+d gd ++ +  ta++  + ++d +  + t+t p++  n ++t++ t sDg+  +++ +
  EPA04960.1 489 NSAPRVNA---GPDMTADENTVVA---LVCTGNDPDeGDVITFKWSTAST--AVITDANSASTTVTlPHTTKNESITMTCTGSDGR-LSSSDS 572
                 66777774...4677888888887...88889999988999998886655..9999877776666647788889999999999997.444444 PP

  == domain 5  score: 10.3 bits;  conditional E-value: 0.00023
  Cadherin_5  33 asDvdgdtLsvssltadaenGtvvdngdGtftftpeanynGev...tlsYtvsDgeggtttatasltv 97 
                   D++g++Ls    +++ ++  + + +  t++ft  +  nGev    ++ +v D++g ++  t++++v
  EPA04960.1 608 SNDPEGQKLSFMWTQVSGDKVVLSSTSSKTVSFTSPTVLNGEVkvlVFELKVFDDNGRSSMDTVTVSV 675
                 5799*******9999999999999******************97667999**********99999988 PP

>> PKD  PKD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0   0.1    0.0047        11       9      36 ..      20      57 ..      13      95 .. 0.73
   2 !    5.4   0.0    0.0075        17      19      34 ..     128     145 ..     110     159 .. 0.73
   3 ?   -1.0   0.0      0.74   1.7e+03      23      37 ..     171     187 ..     166     197 .. 0.69
   4 !    6.0   0.2    0.0048        11       7      31 ..     215     241 ..     209     265 .. 0.76
   5 ?    3.8   0.1     0.024        53       7      43 ..     311     349 ..     303     383 .. 0.65
   6 !    8.3   0.3   0.00092       2.1       8      70 ..     407     477 ..     399     478 .. 0.76
   7 ?    2.3   0.4      0.07   1.6e+02      19      49 ..     513     544 ..     495     552 .. 0.67
   8 ?    3.2   0.1     0.035        78      21      52 ..     611     644 ..     600     665 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0047
                BSSEEEEEEEES....-SS-SEEEEE--SS.......- CS
         PKD  9 vpgatvaftaav...pdganvtysWdfgdg.......s 36
                + + +v++ +     ++ +++ty W  +dg       +
  EPA04960.1 20 SENLPVTLVGEGiddDPNDILTYKWVQNDGepvklssY 57
                6688999999999877799**********944443331 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0075
                 ES...-SS-SEEEEE--S CS
         PKD  19 av..pdganvtysWdfgd 34 
                 +   pdg+ +tysW    
  EPA04960.1 128 SAldPDGDALTYSWKQTA 145
                 3347**********7544 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.74
                 SS-SEEEEE--SS..-- CS
         PKD  23 ganvtysWdfgdg..sv 37 
                 ++++t++ +++dg  ++
  EPA04960.1 171 ANPLTFELTVDDGfgGT 187
                 67889999999975422 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.0048
                 --BSSEEEEEEEES...-SS-SEEEEE CS
         PKD   7 vlvpgatvaftaav..pdganvtysWd 31 
                  ++ g+tv ++a+   + ga+++ysW 
  EPA04960.1 215 TVHEGETVKLSATGktANGAPIAYSWV 241
                 56789*********9999********5 PP

  == domain 5  score: 3.8 bits;  conditional E-value: 0.024
                 --BSSEEEEEEEES...-SS-SEEEEE--SS--EEEEET CS
         PKD   7 vlvpgatvaftaav..pdganvtysWdfgdgsvvqvlse 43 
                  ++ +  v + ++   p ++n++ysW    g +v + + 
  EPA04960.1 311 TVSENVQVKLVGTGthPKDTNLHYSWKQISGKNVEIYER 349
                 566677777777777799********9999855554443 PP

  == domain 6  score: 8.3 bits;  conditional E-value: 0.00092
                 -BSSEEEEEEEES...-SS-SEEEEE--SS.--EEEEETTEEEEEE-S.....SEEEEEEEEEE-SS-EEE CS
         PKD   8 lvpgatvaftaav..pdganvtysWdfgdg.svvqvlseptvthtYls.....pGeYeVtvtasnavgsat 70 
                 +  g++v  t++   p   ++tysW    g sv+++ + p+++ + ++     +   + ++t++++v+ ++
  EPA04960.1 407 VIGGTNVDVTGSGfdPENGPLTYSWKQIAGdSVTFDATKPSFSFKAPTlapgeTKRLVFQLTVTDDVNQSN 477
                 556777777777777999*******977766*******999998877777555556788888888887776 PP

  == domain 7  score: 2.3 bits;  conditional E-value: 0.07
                 ES....-SS-SEEEEE--SS--EEEEETTEEEEE CS
         PKD  19 av...pdganvtysWdfgdgsvvqvlseptvtht 49 
                 +    + g+ +t+ W +    ++ ++   +++ t
  EPA04960.1 513 TGndpDEGDVITFKWSTAS--TAVITDANSASTT 544
                 3344677*********999..4444444444444 PP

  == domain 8  score: 3.2 bits;  conditional E-value: 0.035
                 .-SS-SEEEEE--SS..--EEEEETTEEEEEE-S CS
         PKD  21 pdganvtysWdfgdg..svvqvlseptvthtYls 52 
                 p g+ +++ W+   g   v  ++s++tv+ t ++
  EPA04960.1 611 PEGQKLSFMWTQVSGdkVVLSSTSSKTVSFTSPT 644
                 889********98887566667777788887766 PP

>> Cadherin_4  Bacterial cadherin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.76   1.7e+03      18      56 ..      14      48 ..       8      88 .. 0.66
   2 !   20.8   5.4     2e-07   0.00045       1      58 [.      93     147 ..      93     261 .. 0.86
   3 ?   -1.7   0.1         2   4.6e+03       5      31 ..     293     320 ..     291     345 .. 0.65
   4 !   10.0   1.5   0.00047       1.1       2      58 ..     385     437 ..     384     451 .. 0.77
   5 ?    1.8   5.9      0.17   3.9e+02       7      54 ..     485     529 ..     479     572 .. 0.64
   6 ?   -0.1   0.1      0.66   1.5e+03      23      58 ..     595     626 ..     549     650 .. 0.65
   7 !    6.4   2.4    0.0064        14       2      18 ..     670     686 ..     669     689 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.76
  Cadherin_4 18 ddsatvtedtpltitagnvlandtDvdgdd.ltvtavtva 56
                  s++v e+ p+t       +   D d +d lt++ v+ +
  EPA04960.1 14 TSSVEVSENLPVTL-----VGEGIDDDPNDiLTYKWVQND 48
                45566666666666.....455556664555777777643 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 2e-07
  Cadherin_4   1 atvtitvtgvndaPvavddsatvtedtpltitagnvlandtDvdgddltvtavtvagt 58 
                 atv + v++vn aP++++   +vt  t  ++   ++ + + D+dgd+lt++  ++ag+
  EPA04960.1  93 ATVEVVVNPVNHAPIVSAGRDQVTFKTINVV---TLVSSALDPDGDALTYSWKQTAGQ 147
                 8**************7776666666665555...4699**********9987765554 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 2
  Cadherin_4   5 itvtgvndaPvavdd.satvtedtplti 31 
                 ++v +++  P+a++    tv e+ ++  
  EPA04960.1 293 VKVIPADGMPTANAGpDQTVSENVQVKL 320
                 5678888888888752346666666654 PP

  == domain 4  score: 10.0 bits;  conditional E-value: 0.00047
  Cadherin_4   2 tvtitvtgvndaPvavddsa.tvtedtpltitagnvlandtDvdgddltvtavtvagt 58 
                  v +tvt +n +P a++     v  +t + +     ++   D+++++lt++  ++ag+
  EPA04960.1 385 DVAVTVTTTNLPPRANAGPDrKVIGGTNVDV-----TGSGFDPENGPLTYSWKQIAGD 437
                 589***********99864326666666666.....7999********9987766654 PP

  == domain 5  score: 1.8 bits;  conditional E-value: 0.17
  Cadherin_4   7 vtgvndaPvavdd.satvtedtpltitagnvlandtDvdgdd.ltvtavt 54 
                 v + n aP +++    t++e+t +         + +D+d +d +t++  t
  EPA04960.1 485 VVPENSAPRVNAGpDMTADENTVVAL-----VCTGNDPDEGDvITFKWST 529
                 77899999988762568888888887.....3445555544436554433 PP

  == domain 6  score: -0.1 bits;  conditional E-value: 0.66
  Cadherin_4  23 vtedtpltitagnvlandtDvdgddltvtavtvagt 58 
                 v+e   ++ +     +  +D++g+ l++  ++v+g+
  EPA04960.1 595 VNEKIKVSLD---G-SKSNDPEGQKLSFMWTQVSGD 626
                 4444444431...1.456788888876644444443 PP

  == domain 7  score: 6.4 bits;  conditional E-value: 0.0064
  Cadherin_4   2 tvtitvtgvndaPvavd 18 
                 tvt++v++vn aP a++
  EPA04960.1 670 TVTVSVDPVNAAPKATA 686
                 9*************987 PP

>> Ig_2  Immunoglobulin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0       0.2   4.5e+02      11      79 .]      19      99 ..      11      99 .. 0.62
   2 ?    3.2   0.0     0.051   1.2e+02       7      34 ..     212     241 ..     205     276 .. 0.70
   3 ?   -1.5   0.1       1.5   3.3e+03       9      79 .]     310     390 ..     303     390 .. 0.54
   4 !   12.6   0.1     6e-05      0.13      10      77 ..     501     575 ..     490     578 .. 0.75
   5 ?   -3.3   0.0       5.5   1.2e+04      29      44 ..     616     633 ..     593     647 .. 0.56

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.2
        Ig_2 11 vtegepvtLtCs.apgnpp..pkvqwykgg.evin.sspn.....ffinavsaedsgt..YtCrarntkggevsrpveltv 79
                v+e+ pvtL  + ++ +p+   +++w +++ e+++ ss       f  ++v  ++     +t +++ + g ++s +ve+ v
  EPA04960.1 19 VSENLPVTLVGEgIDDDPNdiLTYKWVQNDgEPVKlSSYTvaeptFMAPEVANGQIKVltFTLTVTDPVGATDSATVEVVV 99
                566666666666455566655569998666588887443334443444777755544333888888888889999999876 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.051
        Ig_2   7 sptvvtegepvtLtCsap..gnpppkvqwy 34 
                 + ++v+ege+v+L+ +++  +  p+ ++w 
  EPA04960.1 212 PLQTVHEGETVKLSATGKtaNGAPIAYSWV 241
                 4499*********99988764556777775 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.5
        Ig_2   9 tvvtegepvtLtCsap..gnpppkvqwy...kggevinsspn....ffinavs.aedsgtYtCrarntkggevsrpveltv 79 
                 ++v+e+  v+L  ++   ++ +  ++w     ++ +i ++++    ff++++     + t+  +++ ++g   +++v++tv
  EPA04960.1 310 QTVSENVQVKLVGTGThpKDTNLHYSWKqisGKNVEIYERTSssvyFFSPKIGgTPEKLTFELTVTDSQGNSAKDDVAVTV 390
                 556666666665554423333345777643333344443333346666677765556666777777777766666666665 PP

  == domain 4  score: 12.6 bits;  conditional E-value: 6e-05
        Ig_2  10 vvtegepvtLtCsap...gnpppkvqwykggevinsspn.....ffinavsaedsgtYtCrarntkggevsrpvel 77 
                 +  e+  v L C+++       ++++w+  ++++ ++ n     ++++  + + s t tC+ + ++ + +s+++ +
  EPA04960.1 501 TADENTVVALVCTGNdpdEGDVITFKWSTASTAVITDANsasttVTLPHTTKNESITMTCTGSDGRLS-SSDSMMI 575
                 56788889******9887445799*******999988776644333488999999********98854.3333434 PP

  == domain 5  score: -3.3 bits;  conditional E-value: 5.5
        Ig_2  29 pkvqwykgg..evinssp 44 
                  ++ w++ +  +v+ ss+
  EPA04960.1 616 LSFMWTQVSgdKVVLSST 633
                 446666433334444333 PP

>> DUF824  Salmonella repeat of unknown function (DUF824)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.4   0.0    0.0072        16      10      34 ..     217     241 ..     215     244 .. 0.87
   2 !    9.1   0.2   0.00051       1.1      13      40 ..     366     394 ..     365     400 .. 0.82
   3 ?   -1.1   0.0      0.79   1.8e+03      12      23 ..     553     564 ..     551     566 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0072
      DUF824  10 KkGEsipltitvkDasGnPvpnapf 34 
                   GE+++l  t k a G P+++  +
  EPA04960.1 217 HEGETVKLSATGKTANGAPIAYSWV 241
                 57*******************9765 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00051
      DUF824  13 EsipltitvkDasGn.PvpnapftltRgd 40 
                 E ++   tv+D++Gn +  ++++t+t ++
  EPA04960.1 366 EKLTFELTVTDSQGNsAKDDVAVTVTTTN 394
                 6788889********88889****99776 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.79
      DUF824  12 GEsipltitvkD 23 
                  Esi++t t  D
  EPA04960.1 553 NESITMTCTGSD 564
                 59*****98666 PP

>> Waikav_capsid_1  Waikavirus capsid protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.6   9.7e-05      0.22     115     186 ..     530     607 ..     506     610 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9.7e-05
  Waikav_capsid_1 115 lpsilleasssslttltvkdp..aiqsaiclsGsehsigrlGilkisvlnvln....adkaatqevavnvwvkfdkvk 186
                        + ++   +s+ tt+t+ ++  +   ++  +Gs++ ++   ++ i v+nvln    ad    q v+  + v +d+ k
       EPA04960.1 530 ASTAVITDANSASTTVTLPHTtkNESITMTCTGSDGRLSSSDSMMINVVNVLNlpivADAGPDQIVNEKIKVSLDGSK 607
                      44444544444445555544400444456678********************93333344445777777777788876 PP

>> TIG  IPT/TIG domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1      0.87   1.9e+03      53      68 ..      59      77 ..      15     118 .. 0.64
   2 ?   -1.7   0.0       1.4   3.2e+03      38      73 ..     244     279 ..     237     292 .. 0.58
   3 ?   -1.2   0.1      0.96   2.1e+03      36      74 ..     338     377 ..     310     394 .. 0.65
   4 ?    4.6   0.0     0.016        35      14      27 ..     408     424 ..     402     483 .. 0.79
   5 ?    0.4   0.4       0.3   6.8e+02      31      73 ..     521     562 ..     509     575 .. 0.65
   6 ?    8.8   0.2   0.00076       1.7      35      70 ..     621     655 ..     612     673 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.87
         TIG 53 l...vcttPpgpsgllnvs 68
                +   ++++P +++g+++v 
  EPA04960.1 59 VaepTFMAPEVANGQIKVL 77
                2244666666664444443 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.4
         TIG  38 ggtpctvtasvssttlvcttPpgp..sgllnvsvlvdg 73 
                  gt + ++ s +  + ++t+P+ +  + ++ +s++v g
  EPA04960.1 244 IGTGVSLN-SYTGASTTFTAPSLSgtN-EMLLSFQVTG 279
                 55555555.666666677777777422.4444444444 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.96
         TIG  36 tiggtpctvtasvssttlvcttPpgp..sgllnvsvlvdga 74 
                 +i g+++++    +s+++ + +P +   +++l++ ++v + 
  EPA04960.1 338 QISGKNVEIY-ERTSSSVYFFSPKIGgtPEKLTFELTVTDS 377
                 4566666666.666666666666655555566666666554 PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.016
         TIG  14 sgGttititGtnF...g 27 
                  gGt++ +tG++F   +
  EPA04960.1 408 IGGTNVDVTGSGFdpeN 424
                 49***********5440 PP

  == domain 5  score: 0.4 bits;  conditional E-value: 0.3
         TIG  31 sdssvtiggtpctvtasvssttlvcttPpgpsgllnvsvlvdg 73 
                 ++++ ++ ++ + v++  +s + ++t+P ++ ++ +++++  g
  EPA04960.1 521 DVITFKWSTASTAVITDANSASTTVTLPHTT-KNESITMTCTG 562
                 5667788888888887777777777777777.55555555444 PP

  == domain 6  score: 8.8 bits;  conditional E-value: 0.00076
         TIG  35 vtiggtpctvtasvssttlvcttPpgpsgllnvsvl 70 
                 +++ g++++++ s ss t+ +t+P + +g+++v v+
  EPA04960.1 621 TQVSGDKVVLS-STSSKTVSFTSPTVLNGEVKVLVF 655
                 6899999*999.********************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (690 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.68u 0.29s 00:00:00.97 Elapsed: 00:00:00.49
# Mc/sec: 4207.18
//
Query:       EPA04961.1  [L=245]
Description: uroporphyrinogen-III C-methyltransferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.4e-50  170.6   0.0      5e-50  170.4   0.0    1.0  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.4   0.0   2.8e-54     5e-50       3     212 ..       2     212 ..       1     213 [. 0.92

  Alignments for each domain:
  == domain 1  score: 170.4 bits;  conditional E-value: 2.8e-54
  TP_methylase   3 ylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealragkdVvllvsGDPlvygtgsel 99 
                   ylVG+GpGd +l+T+rA+++l++advvl+d+ ++++ +   + + ++     g+ + + ++++++ +e +++ ++++k+Vv+l++GDP ++g+g+e+
    EPA04961.1   2 YLVGAGPGDSKLITLRAVELLQKADVVLYDR-LVSKKIISMISKSAQ-KVYVGRAVGDDTTHQNNTNELMVKFAKSKKNVVRLKGGDPIIFGRGGEE 96 
                   9******************************.999999888888753.33334445778889*********************************** PP

  TP_methylase 100 vealrareagieveviPGvsslqaaaarlgiplteggevlsvl.....lpglakeeereleallangdtlvllkaprklaelaelLkea.lyddttp 190
                   +e l++  + i++e++PG++s    a+++giplt+++ ++sv+     +++ +k+e  ++++l++  dt+v+++++++++ ++++L++  l++ t p
    EPA04961.1  97 AEYLKE--NKIKYEIVPGITSGIGSATYAGIPLTHRKYASSVVfvtghEDPEKKNESVKWKRLAKSVDTIVIMMGLSRIDVICKQLIAGgLDKQT-P 190
                   ******..99**************************************6666889**********************************999955.* PP

  TP_methylase 191 vavveragtedervvrgtleel 212
                   vav+++++t+++++  gt++ +
    EPA04961.1 191 VAVIQNGTTPQQKILIGTVSNI 212
                   ******************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1466.22
//
Query:       EPA04962.1  [L=77]
Description: hypothetical protein BG20_I0891 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.039   13.8   4.2      0.043   13.6   4.2    1.1  1  TatC      Sec-independent protein translocase protein (TatC)
       0.38   10.1   2.1       0.44    9.9   2.1    1.0  1  TMEM43    Transmembrane protein 43
          2    8.5   5.5         12    6.0   5.5    1.9  1  CrgA      Cell division protein CrgA
        2.8    8.2   8.6        6.6    7.0   2.6    2.1  2  TMEM238   TMEM238 protein family
        4.3    7.2   7.3         11    5.9   1.7    2.0  2  DUF2721   Protein of unknown function (DUF2721)


Domain annotation for each model (and alignments):
>> TatC  Sec-independent protein translocase protein (TatC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   4.2   1.2e-05     0.043     112     164 ..      20      71 ..       4      75 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.2e-05
                 HHHHHTHHHHHHHHHTTTTSSTTEEHHHHHHHHHHHHHHHHHHTTH.HHHHHHH CS
        TatC 112 afayfvvlplvlkfllseevepllslseylsfvlllllafgiaFel.Plvlvll 164
                 ++++++++p +++fl+  +++p+l+++e+ + + ++l+afgi F +  l++ ll
  EPA04962.1  20 IIGFLMLVPQLVQFLI--KINPELRMQEVKKSFKRFLFAFGIGFFIiGLLMQLL 71 
                 57999***********..7999********************875414555555 PP

>> TMEM43  Transmembrane protein 43
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   2.1   0.00012      0.44     183     244 ..       5      66 ..       2      76 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00012
      TMEM43 183 klltwllRllGfllmflglllll.splsvlvslipll......gelvglglalvalllslslsllvial 244
                  ++t  l l+G++l ++g+l+l+ +++++l+++ p l      +       ++  +l+++ + +++i+l
  EPA04962.1   5 LMYTQSLDLVGLILEIIGFLMLVpQLVQFLIKINPELrmqevkK-------SFKRFLFAFGIGFFIIGL 66 
                 67899999***********9887256677777777765544431.......444455555555555544 PP

>> CrgA  Cell division protein CrgA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   5.5    0.0035        12      43      84 ..      20      69 ..      10      71 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0035
        CrgA 43 llGllwlv...vyYlage.......eipfmaelgawNlliGfgliivGllmt 84
                ++G l lv   v +l +        e++  ++++++ ++ G+g++i+Gllm 
  EPA04962.1 20 IIGFLMLVpqlVQFLIKInpelrmqEVK--KSFKRFLFAFGIGFFIIGLLMQ 69
                5555544422233333323323211333..6778999*************96 PP

>> TMEM238  TMEM238 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.4    0.0074        27      13      32 ..      11      31 ..       3      37 .. 0.67
   2 ?    7.0   2.6    0.0018       6.6       4      29 ..      52      77 .]      50      77 .] 0.90

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0074
     TMEM238 13 fdvvGlvlLlvGifael.lfg 32
                +d+vGl+l ++G ++ + +  
  EPA04962.1 11 LDLVGLILEIIGFLMLVpQLV 31
                677788777777766554444 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0018
     TMEM238  4 kvflalavvfdvvGlvlLlvGifael 29
                ++++a+++ f ++Gl++ l+ i++el
  EPA04962.1 52 RFLFAFGIGFFIIGLLMQLLSILVEL 77
                579***************99998875 PP

>> DUF2721  Protein of unknown function (DUF2721)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.4    0.0046        17      89     120 ..       6      37 ..       1      46 [. 0.85
   2 ?    5.9   1.7    0.0031        11      96     121 ..      49      74 ..      41      77 .] 0.86

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0046
     DUF2721  89 llsldlsllaailfvlalllllvslllflrEi 120
                 +++ +l+l+  il +++ l+l+  l+ fl+ i
  EPA04962.1   6 MYTQSLDLVGLILEIIGFLMLVPQLVQFLIKI 37 
                 4588999*********************9877 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0031
     DUF2721  96 llaailfvlalllllvslllflrEir 121
                 ++  +lf++++ +++++ll+ l+ i+
  EPA04962.1  49 SFKRFLFAFGIGFFIIGLLMQLLSIL 74 
                 567789*************9999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       858  (0.0478554); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 494.32
//
Query:       EPA04963.1  [L=214]
Description: hypothetical protein BG20_I0878 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1635.27
//
Query:       EPA04964.1  [L=188]
Description: hypothetical protein BG20_I0876 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.011   15.7   0.0      0.019   15.0   0.0    1.4  1  HTH_Tnp_Tc5  Tc5 transposase DNA-binding domain


Domain annotation for each model (and alignments):
>> HTH_Tnp_Tc5  Tc5 transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   1.1e-06     0.019      13      36 ..     103     130 ..      99     149 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.1e-06
                  HHHC-CT---SCHHHHHHHHHHH....H CS
  HTH_Tnp_Tc5  13 rqlrergipitgelirekAqela....s 36 
                   +  ++ +pi++e+i+ekA+e++    +
   EPA04964.1 103 IDYEKTRFPINREIIKEKAREVLgdikV 130
                  5567899**************9754441 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1311.96
//
Query:       EPA04965.1  [L=266]
Description: uroporphyrinogen-III synthase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-45  154.5   0.0      3e-45  154.4   0.0    1.0  1  HEM4             Uroporphyrinogen-III synthase HemD
  ------ inclusion threshold ------
      0.027   14.7   0.0      0.077   13.2   0.0    1.6  1  CTP_transf_like  Cytidylyltransferase-like
       0.16   12.6   0.0       0.38   11.4   0.0    1.7  1  PGM_PMM_II       Phosphoglucomutase/phosphomannomutase, alpha


Domain annotation for each model (and alignments):
>> HEM4  Uroporphyrinogen-III synthase HemD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.4   0.0     5e-49     3e-45       3     230 ..      19     255 ..      17     257 .. 0.95

  Alignments for each domain:
  == domain 1  score: 154.4 bits;  conditional E-value: 5e-49
                 HHHHHHHTTEEEEE---EECCECCHHHHHHHHHT.....--SEEEE--HHHHHHHHHHHH...HTT---HHHHHCSEEESSHHHHHHHHHTT---SEE- CS
        HEM4   3 laealearGaeplelPlieiepaedraelraalddleagkydwliftSanavealfealk...reeedvkalaslkvaavGpaTaraLeelglrvdlvp 98 
                 + +++ ++ a p+ lP+ie +  + ++ ++++ld++++ k+d+ +f+S++av+ lf+++k   + e ++ a a++ v+avGp+T+ aLe+ g+r++ +p
  EPA04965.1  19 FIDLVTKNNARPISLPTIELVS-KGEKIVDEFLDSVKDYKPDYSVFMSSKAVTLLFDTAKkvsKFEQLQLAVANTIVMAVGPKTKIALEKEGIRPAYMP 116
                 667788999*************.999***********************************99999999999*************************** PP

                 ..SSSHHHHGGGS-.---E.EEEEE-SS.S--HHHHHHHHHTTEEEEEE-SEEE..EE-HHHHHHHHHHHHTT--SEEEESSHHHHHHHHHH-S-HH.. CS
        HEM4  99 seegtaegLaeelaeslag.krvlllrgeiarddlaegLeergaevdevevYet..vpaeeepeelkealkagevdavvftSpstvrnllellkdeg.. 192
                 +  ++++g+ e++ + +a  k+v+++r+  + + l+e Le+ g++v+e+++Y+    +++ +  e++e++ +++++++vftS+s+vr+++e+++++   
  EPA04965.1 117 N-IFSSVGVGELFTKLHAVgKKVIVPRSGASTPFLKELLEKIGIDVKEIHLYDVcaFRDTTQWNEFRELFSQNKINGIVFTSASSVRAFFEIMSKDYde 214
                 9.************97777699********************************9888888*********************************999** PP

                 ....HHHCTSEEEEESHHHHHHHHHTT---SEEETS--HHHH CS
        HEM4 193 ....delkevkvaaiGptTaealkklglkvdvvaeeptaegl 230
                     ++l+++ v++iGp T+++lkk+++k+  +++ +t+ g 
  EPA04965.1 215 nsllKNLEKLSVVSIGPFTSDELKKFNIKN-TISQVHTVPGA 255
                 ******************************.99999998876 PP

>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.3e-05     0.077      74     130 ..     148     222 ..     133     229 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.3e-05
                      H...HHHHHTTTT.EEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEE..............HTTCEEEEEEEC CS
  CTP_transf_like  74 r...evlkklkpd.klylvigadvledfsewkeleeilgnvklvvvsrp..............ekqanvllkaek 130
                      +   e+l+k+++d k + + +  +++d+ +w+e++e+++ +k+ +++++              ++++n llk+ +
       EPA04965.1 148 PflkELLEKIGIDvKEIHLYDVCAFRDTTQWNEFRELFSQNKINGIVFTsassvraffeimskDYDENSLLKNLE 222
                      355599****************************************99977777777766666666666666555 PP

>> PGM_PMM_II  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   6.3e-05      0.38      24      54 ..     138     168 ..     113     187 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.3e-05
                 EEE-TT-TTHHHHHHHHHHTT-EEEES---- CS
  PGM_PMM_II  24 vidplhGaggeilkellkelgvdvvelnaep 54 
                 vi p  Ga+  +lkell+++g+dv+e++ + 
  EPA04965.1 138 VIVPRSGASTPFLKELLEKIGIDVKEIHLYD 168
                 788999********************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       836  (0.0466284); expected 358.6 (0.02)
Passed bias filter:                      640  (0.0356964); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 1759.27
//
Query:       EPA04966.1  [L=100]
Description: hypothetical protein BG20_I0889 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 693.27
//
Query:       EPA04967.1  [L=257]
Description: daunorubicin resistance ABC transporter membrane protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.7e-34  117.1  18.0    6.7e-34  117.1  18.0    1.9  2  ABC2_membrane    ABC-2 type transporter
    1.1e-14   54.3  28.4    1.3e-14   54.1  28.4    1.1  1  ABC2_membrane_3  ABC-2 family transporter protein
    2.3e-05   23.8  20.5    2.3e-05   23.8  20.5    2.1  2  ABC2_membrane_2  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.1  18.0   1.1e-37   6.7e-34       3     209 ..       4     217 ..       2     218 .. 0.90
   2 ?   -0.9   1.5      0.15   8.8e+02     108     126 ..     227     245 ..     218     250 .. 0.57

  Alignments for each domain:
  == domain 1  score: 117.1 bits;  conditional E-value: 1.1e-37
  ABC2_membrane   3 ikallkreflqrwrdpslgllwrliqplllalvfgtvfgnlg..nsedglnr...........pgllffsvlflafsaltsvapvferergvlere 85 
                    ++++++re++++++++ +g+l rliqp ++++v+g  f++++   ++                pg+++ +++f++  ++ +v ++++r+ g++++ 
     EPA04967.1   4 TYTIFWRELKRYKKSR-SGVLIRLIQPAIWIIVIGNTFSGTQplIQS----VgfegkyiefmaPGVIILTAIFTS--IFGGVNTLWDRRYGFMNKA 92 
                    6799********9999.6669******************86644222....133456788899************..9999999************ PP

  ABC2_membrane  86 lvsplyslsayvlakvlvelpvsllqalifllivyflvgldls...rfflflllllltalaasslgllisalapsfedasqlaslvllpllllsGf 178
                    l+sp+ s+s+++l+k+ +  ++s+lqa +++ i++ + g+       ++ ++++++l+++ +s+++++++a a+s+e++  +++++ +pl++ls++
     EPA04967.1  93 LTSPV-SRSSIALGKMGAISLISALQASLIVGIALAI-GVSFPnpiMILPIMAIVVLFSMGFSGISVIVAATAKSQETFWGVINFLGMPLFMLSPA 186
                    *****.******************************8.7777654444999********************************************* PP

  ABC2_membrane 179 fipidsmpkwlqwiaylnPltyavealrsnl 209
                    ++p++ +p wl  ia+lnP+ty+v ++r  +
     EPA04967.1 187 LFPLELLPDWLATIAKLNPVTYTVLLVREMM 217
                    ************************9999765 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.15
  ABC2_membrane 108 sllqalifllivyflvgld 126
                    ++l + i+ ++v+++vgl 
     EPA04967.1 227 AFLSIGIICVFVLVMVGLA 245
                    3444445555666666654 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.1  28.4   2.2e-18   1.3e-14     157     344 ..      54     246 ..      25     247 .. 0.92

  Alignments for each domain:
  == domain 1  score: 54.1 bits;  conditional E-value: 2.2e-18
  ABC2_membrane_3 157 snvasflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilllafglgipfgnlglll...llfll 247
                       ++  f+++ ++i+ +++t++f  v+ + +++ + +   l+s+vs++++ l+k+ ++ l+++lq+ li+++a+++g++f n + +l     ++l
       EPA04967.1  54 GKYIEFMAPGVIILTAIFTSIFGGVNTLWDRRYGFMNKALTSPVSRSSIALGKMGAISLISALQASLIVGIALAIGVSFPNPIMILpimAIVVL 147
                      568899***999999999**************************************************9997777799999977666669**** PP

  ABC2_membrane_3 248 fglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwifsiiPffapglgllrlitgd..plweillsliilalfavvy 339
                      f++ ++ ++  + +  k++et  ++i ++ ++l++++ +lfple lp++l++i+ ++P ++  l+   ++tg+   +++ +ls++i ++f++v+
       EPA04967.1 148 FSMGFSGISVIVAATAKSQETFWGVINFLGMPLFMLSPALFPLELLPDWLATIAKLNPVTYTVLLVREMMTGVseGGISAFLSIGIICVFVLVM 241
                      **********************************************************************99953444577************9 PP

  ABC2_membrane_3 340 lllal 344
                      + la 
       EPA04967.1 242 VGLAS 246
                      99986 PP

>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1     0.028   1.7e+02       2      33 ..       6      36 ..       5      53 .. 0.81
   2 !   23.8  20.5   3.8e-09   2.3e-05     106     286 ..      89     252 ..      64     252 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.028
  ABC2_membrane_2  2 aiakkEfrdlvrsrrfllltvllplidvalay 33
                     +i+++E+++  +sr+ +l+ ++ p i  ++ +
       EPA04967.1  6 TIFWRELKRYKKSRSGVLIRLIQPAI-WIIVI 36
                     89*****************9999998.55554 PP

  == domain 2  score: 23.8 bits;  conditional E-value: 3.8e-09
  ABC2_membrane_2 106 lkllLskPvsRdeillgKfigglaiglaiavallatvllalaiilalgivlaledllllvvasvlllllvvflalglllSsvarssreaaalal 199
                      +   L++PvsR++i lgK+ + ++i      al a++++++a+  +++ + +++ l +  +a+v+l+ ++ f ++++ ++++a+s+++   +  
       EPA04967.1  89 MNKALTSPVSRSSIALGKMGAISLI-----SALQASLIVGIALAIGVSFPNPIMILPI--MAIVVLFSMG-FSGISVIVAATAKSQETFWGVIN 174
                      5668***************999999.....6666666665555555555555554444..4444445544.79***********6665555555 PP

  ABC2_membrane_2 200 glfvvlailvpivlygvaellagpavpqeindflsllsptsayntllneilagsdlnalgstatnllilllllavllvlgyvlFkrk 286
                      +l  + +++ + +l+++  l+        +  ++  l+p  +  +l++e+ +g ++   +s++ +++i+++  +v+++l+ ++F r+
       EPA04967.1 175 FLG-MPLFMLSPALFPLELLPD-------WLATIAKLNPVTYTVLLVREMMTGVSE-GGISAFLSIGIICVFVLVMVGLASYVFTRE 252
                      554.555888888888555555.......455699999999999999998888853.38999**********************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       884  (0.0493056); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.35s 00:00:00.96 Elapsed: 00:00:00.53
# Mc/sec: 1454.69
//
Query:       EPA04968.1  [L=402]
Description: phosphoglycerate kinase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-98  329.2   0.0    3.6e-98  329.0   0.0    1.0  1  PGK       Phosphoglycerate kinase


Domain annotation for each model (and alignments):
>> PGK  Phosphoglycerate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  329.0   0.0    2e-102   3.6e-98       1     377 [.       6     383 ..       6     384 .. 0.92

  Alignments for each domain:
  == domain 1  score: 329.0 bits;  conditional E-value: 2e-102
                 GGGS--TT-EEEEEE-----EECT.TEES--HHHHHHHHHHHHHHHTT-EEEEEE--S--TTS-GGG-SHHHHHHHHHHHTT-EEEESSTTSHHHHHHH CS
         PGK   1 vkdldlkgkrvlvRvDfNvplkke.gkitddtriraalpTikyllekgakvvllsHlgrpkgekeklslkpvaerLsellgkeVkfvedvvgeeveeai 98 
                 ++d+dlkgk+v++RvD+N+p++ e  +i  ++ri++a++Tik l  ++ak+v++sH+gr+ g+k+ + ++++a+ L++ +gk++k+ved++g +++++i
  EPA04968.1   6 LDDFDLKGKTVFLRVDMNCPIDPEtMEISGTKRIEEAIETIKSL--EDAKLVVASHQGRV-GNKDYTGMDKHAKVLEKFIGKKIKYVEDTIGIAAQNEI 101
                 589******************99889******************..88999********9.7899999******************************* PP

                 HT-TTT-EEEES-GGGSTTTTTT-H...H....HHHHHHHT-SEEEE--GGGTTS--TTTTHHHHCSEEEE-HHHHHHHHHHHHHHHS--SSEEEEEEE CS
         PGK  99 aelkegevllLeNvrfykeEeknde...e....lakklasladvyVnDAFgtahrahaStvgiakvlsaaaGllmekElealskvlenperplvailGG 190
                 ++lk+ge+llL+N+r  +eE+ + +   +    ++++l++l+d++V D+F +ahr+h S+vg+++vl+a+aG+++e+E++ l+++++  + p v++lGG
  EPA04968.1 102 KNLKSGEILLLDNLRLCAEENYEFAppeAantiMVRRLSKLFDLCVLDSFPSAHRSHPSIVGFPHVLPACAGRIVEREVRNLDEIMTVAKAPHVIVLGG 200
                 ********************7542234313456**********************************99****************************** PP

                 S-HHHCHHHHHHHTTT-..SEEEEETCHHHHHHHHTT...-B-TTSS--GGGHHHHHHHHHHHHHHT-EEE--SEEEEESSSSTTS.EEEECCG--TT- CS
         PGK 191 akvsdkikvienLlekv..dkliigGgmantFlkaqg...leigkslveedklelakellekakkkgvkillpvDvvvakeeaekeakvveveaipede 284
                 +kvsd+++ i+ L+++   d+++++G++ n+F++aqg   + +g s  +e  +  a+ l+ ++    + + +pvD+++ k+    ++  ++v+++++++
  EPA04968.1 201 SKVSDRLEAIKLLIQNGraDHVLLTGLIGNVFMRAQGrirYPLGISREDE-VVTKAHALIGEYP---DVFSTPVDIAIDKDG---DRVEMDVRELESGD 292
                 **************98777****************994334455544433.6788888888876...89**********832...23445999****** PP

                 EEEEE-HHHHHHHHHHHCC-SEEEEES-SS-TTSGCCCHHHHHHHHHHHHHCHTSEEEEESHHHHHHHHHTT-GGGSSEEESSSHHHHHHHCT CS
         PGK 285 malDigpktielfaeaikeaktvvwnGpmGvfeiekfakGTkaiakalaeatkgalsivGGgdsaaaveklgladkvshvStGGgAsLelLeg 377
                 +++D+gpkt++++++ i+ a tv++ Gp+G+fe e+f+ GTk +++ +a++   a++iv+Gg+  +a++k+gla++++h+St+GgA++ +L+g
  EPA04968.1 293 KIYDLGPKTVDHYSKLIAGAGTVFISGPAGFFEKENFSYGTKGLLTSVANSM--ATTIVSGGHLTSALKKYGLAEQIDHISTAGGALVLYLTG 383
                 **************************************************85..6************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2512.68
//
Query:       EPA04969.1  [L=499]
Description: hypothetical protein BG20_I0874 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
       0.13   11.0   1.1       0.21   10.3   1.1    1.2  1  Baculo_E66  Baculovirus E66 occlusion-derived virus envelope 


Domain annotation for each model (and alignments):
>> Baculo_E66  Baculovirus E66 occlusion-derived virus envelope protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.1   1.2e-05      0.21      79     143 ..     386     445 ..     383     455 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 1.2e-05
  Baculo_E66  79 eadptnnvqaplwamarriwnrrkrvinytvnsvlfesgvllqslngllrvpstttstqsfrpai 143
                 ++d t n q p w  +   w + + +     +  +f  g+     +g++++pst   t s   +i
  EPA04969.1 386 KSDTTTNQQIPSWIKNNAGWWKAGSI-----DDNSFVQGIQFLIKEGIMKIPSTVQGTPSGSNQI 445
                 689*******************9987.....4457999*****************9999877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (499 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.55
# Mc/sec: 2739.10
//
Query:       EPA04970.1  [L=265]
Description: putative membrane protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.9e-14   53.4  22.0    8.8e-08   31.4  17.5    2.0  2  MFS_1       Major Facilitator Superfamily
     0.0009   17.8   6.4     0.0011   17.4   6.4    1.2  1  MFS_3       Transmembrane secretion effector
     0.0084   15.0   8.8     0.0095   14.8   8.8    1.2  1  MFS_1_like  MFS_1 like family
  ------ inclusion threshold ------
       0.17   12.0   1.7       0.34   11.0   0.0    2.3  3  CrgA        Cell division protein CrgA
        9.3    7.0  14.6        1.8    9.3   4.8    3.2  4  PrgI        PrgI family protein


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4  17.5   2.5e-11   8.8e-08     126     304 ..       2     175 ..       1     184 [. 0.71
   2 !   24.4   0.1   3.5e-09   1.2e-05     103     164 ..     186     247 ..     180     262 .. 0.88

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 2.5e-11
       MFS_1 126 lsagfslGailgpllggllasslg......Wravfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvp.awkallkdpvlwilliall 217
                 +++++ +G +l + l  +l +++g      +  +f+i  ++++ ++v+ +++  e +++++ +s++        ++l+p   +++lk   l+ +l +++
  EPA04970.1   2 IGTFAMAGGVLLASLPQILQENFGystidsFKPLFLIYLLAGIAVVVIYFFFSKEIEVKKSLDSKTFS------TNLSPkSKQIILKLSSLF-ALDSFA 93 
                 7899********************77777766669999999998877644444555555555554444......444442145555655552.555555 PP

       MFS_1 218 lfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavlll 304
                 ++f++ s++ +++++     +g + l +++l+++++++++ai++++a++++dr+g   +++++ +   ++++++a++++++ a+ l+
  EPA04970.1  94 GGFVIQSIVAFWFFT----KFGVD-LTTLSLIFSVAGVLTAISFFFAAKIADRIGLIYTMVFTHIPSNILLILVAIAPTFHMALGLY 175
                 555444446666666....66666.6666666************************9999999999999999999999994444433 PP

  == domain 2  score: 24.4 bits;  conditional E-value: 3.5e-09
       MFS_1 103 fpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivslla 164
                 +p+ +a+i++++ ++er+ a g+ +++ +++  + p + g++++sl+ +a+f+i + + ++ 
  EPA04970.1 186 VPTRQAYIVAVVEENERTAAAGITNTSRNIAQSISPSITGAIIQSLWLSAPFVIGGMLKIVY 247
                 6899**************************************************99988877 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   6.4   3.2e-07    0.0011      25     174 ..      95     239 ..      69     261 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.2e-07
       MFS_3  25 GtliqevaasWlmtdisasplmvAlvqaaatLPifllsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlligiGaalndPa 123
                 G +iq++ a W+ t+     ++  l+   a + + +   +a  +aD    R  l+ ++++  + s +l +l+a+   +  + l+l l     + +  P+
  EPA04970.1  95 GFVIQSIVAFWFFTKFGVDLTTLSLIFSVAGVLTAISFFFAAKIAD----RIGLIYTMVFTHIPSNILLILVAIAP-TFHMALGLYLARMSLSQMDVPT 188
                 6679999999****99999999999976555444444456666776....55688888999999999998888764.4567788888888889999*** PP

       MFS_3 124 WqAsvgelvkrrdvpaAvaLnsvginiaRsvGPAlgGvlvaavGaalafav 174
                  qA +  +v+ ++  aA  ++    nia s+ P ++G ++ ++   + f +
  EPA04970.1 189 RQAYIVAVVEENERTAAAGITNTSRNIAQSISPSITGAIIQSLWLSAPFVI 239
                 ***************************************998877766665 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   8.8   2.7e-06    0.0095     179     312 ..      32     167 ..       3     234 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.7e-06
  MFS_1_like 179 ysallyvlaallvisllvvlilnetekesklkvtkslqvllnilknpeviifllvalilgmswgiienF......lflYLkelgasntllGslvalgvv 271
                 ++  l+++++l  i+++v++ +  +e e k  +   ++  +n+  + + ii+ l  l   ++ ++++ F      +f+++ + g   t+l+ +  +  v
  EPA04970.1  32 FKP-LFLIYLLAGIAVVVIYFFFSKEIEVKKSLDS-KTFSTNLSPKSKQIILKLSSL--FALDSFAGGFviqsivAFWFFTKFGVDLTTLSLIFSVAGV 126
                 333.4455666666666667787777777766663.333444444444444444333..34455555555556678899*****************999 PP

  MFS_1_like 272 aeiplfffaeklleklGhvklliiallayilrfllyaiien 312
                 ++ + fffa k+ +++G++  ++++++   + ++l+ai   
  EPA04970.1 127 LTAISFFFAAKIADRIGLIYTMVFTHIPSNILLILVAIAPT 167
                 9999**************************99*99999744 PP

>> CrgA  Cell division protein CrgA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   9.6e-05      0.34      34      65 ..      32      63 ..      23      72 .. 0.87
   2 ?   -1.9   0.3      0.99   3.6e+03      39      58 ..     119     141 ..     114     173 .. 0.56
   3 ?   -2.6   0.0       1.7     6e+03      69      87 ..     214     232 ..     196     248 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9.6e-05
        CrgA 34 yvpvmlglmllGllwlvvyYlageeipfmael 65
                ++p++l  +l+G++ +v+y++ ++ei++ ++l
  EPA04970.1 32 FKPLFLIYLLAGIAVVVIYFFFSKEIEVKKSL 63
                89**********************99966666 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.99
        CrgA  39 lglmllGllwlvvyYlage...e 58 
                 l + ++G+l  + +++a++   +
  EPA04970.1 119 LIFSVAGVLTAISFFFAAKiadR 141
                 55666666666666666553332 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.7
        CrgA  69 NlliGfgliivGllmttrW 87 
                 N++  ++  i+G ++   W
  EPA04970.1 214 NIAQSISPSITGAIIQSLW 232
                 3333333344444443333 PP

>> PrgI  PrgI family protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1     0.041   1.5e+02      23      42 ..      37      56 ..      33      67 .. 0.72
   2 ?   -0.8   0.0      0.73   2.6e+03      26      42 ..      94     110 ..      83     116 .. 0.68
   3 ?    9.3   4.8   0.00049       1.8      13      75 ..     110     176 ..     107     199 .. 0.76
   4 ?   -1.8   0.1       1.5   5.3e+03      49      65 ..     228     244 ..     215     257 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.041
        PrgI 23 iflvlallvaiglylllraf 42
                ++++la+++++++y+++++ 
  EPA04970.1 37 LIYLLAGIAVVVIYFFFSKE 56
                45566666688888887765 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.73
        PrgI  26 vlallvaiglylllraf 42 
                 +++++ +i++++++ +f
  EPA04970.1  94 GGFVIQSIVAFWFFTKF 110
                 44455577777777666 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.00049
        PrgI  13 iffgLtlRQliflvlallvaiglylllrafleelasvlvillavP....vaalgfykkdglplekyl 75 
                 +   Lt   lif v+++l+ai ++++ + +     ++ ++++ +P    +++++++   ++ l  yl
  EPA04970.1 110 FGVDLTTLSLIFSVAGVLTAISFFFAAKIADRIGLIYTMVFTHIPsnilLILVAIAPTFHMALGLYL 176
                 5567999***********9999999988888999999999999998876444444433344444444 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 1.5
        PrgI  49 vlvillavPvaalgfyk 65 
                 +  + l++P+++ g+ k
  EPA04970.1 228 IQSLWLSAPFVIGGMLK 244
                 44555677887777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1035  (0.0577277); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1633.48
//
Query:       EPA04971.1  [L=90]
Description: hypothetical protein BG20_I0880 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00025   21.1   0.2    0.00034   20.6   0.2    1.3  1  PRC       PRC-barrel domain
     0.0015   18.8   1.4     0.0057   16.9   2.3    1.5  2  DUF2171   Uncharacterized protein conserved in bacteria (DUF2


Domain annotation for each model (and alignments):
>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.2   3.8e-08   0.00034      13      45 ..      26      58 ..      23      85 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.8e-08
                EEEETTSSEEEEEEEEEEETTTTEEEEEEEEET CS
         PRC 13 eVytedGeklGkVkDvvidekegrvralvvsvg 45
                +V+++dG k+Gk++ +v +++++++++++v +g
  EPA04971.1 26 PVVDIDGHKIGKISRLVRHPDTNELESIEVHDG 58
                9*****************************997 PP

>> DUF2171  Uncharacterized protein conserved in bacteria (DUF2171)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.65   5.9e+03      46      59 ..       5      18 ..       2      19 .. 0.75
   2 !   16.9   2.3   6.4e-07    0.0057       1      63 [.      21      85 ..      21      87 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.65
     DUF2171 46 wVasvdddkVhLsk 59
                 +++ +d++  Ls+
  EPA04971.1  5 YIDKFTDETLLLSR 18
                68888888888876 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 6.4e-07
     DUF2171  1 IkehmeVvgsdGehvGtVDhv.eg.drikLtkddseeg.gqhhyiplswVasvdddkVhLsktade 63
                I+ +++Vv+ dG+++G+  ++ +  d+ +L+  + ++g  ++ +i  s +  v  +k++L++t++e
  EPA04971.1 21 IRTDVPVVDIDGHKIGKISRLvRHpDTNELESIEVHDGiIHSKIIHKSEIWGVG-EKIILKLTKEE 85
                899*****************9544799999999999996777***********9.********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.29s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 626.36
//
Query:       EPA04972.1  [L=47]
Description: hypothetical protein BG20_I0872 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.069   13.3  21.1       0.43   10.7  21.1    1.9  1  Metallothio  Metallothionein


Domain annotation for each model (and alignments):
>> Metallothio  Metallothionein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7  21.1   2.4e-05      0.43       2      31 ..      14      45 ..       1      46 [. 0.92

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 2.4e-05
  Metallothio  2 Dp..eCnCaeggsCvCsdsCkctgCkCtsckk 31
                 Dp  +C+C   g C+Cs++Ckc++  C+ + k
   EPA04972.1 14 DPtySCDCDMQGHCICSADCKCKTDVCKEAVK 45
                 66667*******************99998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       676  (0.0377043); expected 358.6 (0.02)
Passed bias filter:                       97  (0.00541023); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 331.96
//
Query:       EPA04973.1  [L=425]
Description: glutamate-1-semialdehyde-2,1-aminomutase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-73  246.9   0.0    3.5e-73  246.6   0.0    1.0  1  Aminotran_3    Aminotransferase class-III
    2.7e-06   26.8   0.0    3.6e-06   26.4   0.0    1.4  1  Aminotran_1_2  Aminotransferase class I and II
  ------ inclusion threshold ------
      0.031   14.4   0.5      0.084   13.0   0.3    1.8  2  RasGAP_C       RasGAP C-terminus


Domain annotation for each model (and alignments):
>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  246.6   0.0   5.8e-77   3.5e-73       9     388 ..      29     404 ..      24     420 .. 0.93

  Alignments for each domain:
  == domain 1  score: 246.6 bits;  conditional E-value: 5.8e-77
                  SCEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT-..SEEEEESSHHHHHHHHHHH CS
  Aminotran_3   9 lllvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapkgldkvflansGseAvetAlKl 106
                   +++++k++G+ ++d+d+k+y+D+  ++ +++lGh+  +++  v++q+++ ++ +   + +++ ++l++ ++  +p  ++kv l+n+G eA++tA++l
   EPA04973.1  29 YPFFAKKSDGSHIWDEDNKKYIDFCNGYGALLLGHRRKEILTSVSKQLKQGTLFC---TPTNSEIELSKLIIGNFPS-IEKVRLVNTGGEATMTAIRL 122
                  45899**********************************************9999...6666778899999999999.9******************* PP

                  HHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE-TTBGGGTB-HHHHHHHHHHHHHHHHCHTCCCEEEEEE-SCETT CS
  Aminotran_3 107 arkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrlkypdeevlkeneeeeaalleelealekkkkdevaAvivEpiqge 204
                  ar        t+k+kii+f+g++HG     l  +gs    ++++  +  +   +  + + v+++n+      +eele+++  k+++va+vi+Epi ++
   EPA04973.1 123 ARG------FTKKKKIIKFEGCYHGAHDSVLVKAGS-GSAHNGISVSDGGLDEVSKN-TLVAPYNN------SEELEKII-SKNKDVAGVIIEPILAN 205
                  ***......***************************.99999*************99.69999999......78999999.78999************ PP

                  TTSEB--CCHHHHHHHHHHHHT-EEEEE-TTTTT..TTTSSSSGGGGCTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTS...B--TTTT-HHH CS
  Aminotran_3 205 gGvvvaspeflaklrelckkhdvllivDEvqtGf..GrTGklfAlehagvspDlmtlaKaltgGlplsavlataevmqalapgs...hgsTfgGnpla 297
                  +G + ++++fl+ +r+++k++++ li+DEv tGf  +  G   A +++g++pD++tlaK l++G+ ++av++++e+m+ l+pg+   ++sT++Gnp+ 
   EPA04973.1 206 MGLILPQKNFLSDVRKITKDNNIPLIFDEVVTGFrvSPGG---AQQYFGIKPDITTLAKTLGSGFVIAAVAGKKEIMNLLSPGGkvyQASTYAGNPVS 300
                  **********************************655556...99999***********************************99*9*********** PP

                  HHHHHHHHHHHHH..TTHHHHHHHHHHHHHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTC............HHHHHHHHHCTEE-EEETTTE CS
  Aminotran_3 298 cavalavleiiee..ekllenaqelgaalkegLeelqkkyevikevRgkGlmiaielkeeaevke............keilkkakekGvlilsaGdnv 381
                   ++a+a++++i++  ++l  + ++ +a l+++  +l+++ +  +++ +   m+ i ++ ++ v++            k++++ ++++G+ i ++  +v
   EPA04973.1 301 VSAAIASIKTINKikNQLYSKLEKYNAFLTSAIDDLASDMKISHQINSTSSMFQI-FFTDKPVTDyissknadskkfKKMFDVLLKNGIFIAPSQFEV 397
                  ***********998899**************************************.77777778889**********99*************999888 PP

                  EEE---T CS
  Aminotran_3 382 irllppl 388
                  + l  + 
   EPA04973.1 398 VFLSDAH 404
                  8776665 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0     6e-10   3.6e-06     131     340 ..     180     397 ..      69     422 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 6e-10
                    -HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HH.HHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSS CS
  Aminotran_1_2 131 dlealeealkeapegnkktkvilvesphNPtGtvatle.eleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGl 225
                    + e+le+ +++    nk + ++++e +  + G +++ +  l ++ +++k +n+ l++De+  gf   + +a++ ++++++++      +l+K +G+
     EPA04973.1 180 NSEELEKIISK----NKDVAGVIIEPILANMGLILPQKnFLSDVRKITKDNNIPLIFDEVVTGFRVSPGGAQQ-YFGIKPDIT-----TLAKTLGS 265
                    44555665555....56789************988765168999999*******************9778877.******988.....99****96 PP

                    GGG-EEEEEEEHHHHHHHHHHHHHHTS.SHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHS....TEEEECCS.CSSEEEEEETH CS
  Aminotran_1_2 226 aGeRvGyilgnaavvsqlrklsrpfls.ssllqaavaaalsdallkqs.eleemrqrlqkrrkelrdeLael....glkvlasq.sgmflltdlsa 314
                     G+ +++++g++++ + l      +   + ++ ++ + a+ ++ ++++   ++  ++l+k   +l++++++l     +++ ++  s mf +  +++
     EPA04973.1 266 -GFVIAAVAGKKEIMNLLSPGGKVYQAsTYAGNPVSVSAAIASIKTINkIKNQLYSKLEKYNAFLTSAIDDLasdmKISHQINStSSMFQIFFTDK 360
                    .999999**********9999999988555678888888888888888444566788888888888888888888999998888899**9999999 PP

                    H.............CHHHHHHHHHHTCTEEEEEGGGGTS CS
  Aminotran_1_2 315 e.............takelskkLleevgvyvtpgtsftv 340
                                  + k+++++Ll++ g+ + p ++f+v
     EPA04973.1 361 PvtdyissknadskKFKKMFDVLLKN-GIFIAP-SQFEV 397
                    89999999997666666666669999.999999.66665 PP

>> RasGAP_C  RasGAP C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0       2.5   1.5e+04      15      34 ..     216     235 ..     213     238 .. 0.79
   2 ?   13.0   0.3   1.4e-05     0.084      57      94 ..     306     346 ..     301     382 .. 0.72

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 2.5
    RasGAP_C  15 LeelgvisrennyqellneI 34 
                 L++  +i+++nn   + +e+
  EPA04973.1 216 LSDVRKITKDNNIPLIFDEV 235
                 77788899999988888776 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 1.4e-05
    RasGAP_C  57 etlktLseknnylesqlesYkayienvleqlkkkkgk....l 94 
                 + +kt+++ +n+l s+le+Y+a +++++++l++   k    +
  EPA04973.1 306 ASIKTINKIKNQLYSKLEKYNAFLTSAIDDLASDM-KishqI 346
                 5689***************************6662.222221 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       932  (0.0519828); expected 358.6 (0.02)
Passed bias filter:                      615  (0.034302); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 3024.15
//
Query:       EPA04974.1  [L=356]
Description: SufB/sufD domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-63  213.0   0.9    4.9e-63  212.7   0.9    1.1  1  UPF0051   Uncharacterized protein family (UPF0051)
  ------ inclusion threshold ------
       0.04   12.3   0.0      0.064   11.6   0.0    1.2  1  DUF2152   Uncharacterized conserved protein (DUF2152)


Domain annotation for each model (and alignments):
>> UPF0051  Uncharacterized protein family (UPF0051)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  212.7   0.9   5.5e-67   4.9e-63       4     218 .]      72     295 ..      69     295 .. 0.96

  Alignments for each domain:
  == domain 1  score: 212.7 bits;  conditional E-value: 5.5e-67
     UPF0051   4 ertlivveegaevtiieey.....agc.....gvveifvgenAklkyvkvqnwsedavnlstkraeegrdaklelttvslggkltrkepsvelkgegae 92 
                  r++i ++e +++ti++e+     +         ++++v+ nA+l+++++q  ++++vn+st+r+++g+dak++++++ +g+ l+r +++  l+g ga+
  EPA04974.1  72 ARNVIFADESSKATIVQELysskaE-KqqaylELLNTNVAPNAQLDVTTLQMMDQSTVNFSTRRTDLGQDAKINWYSGLFGSMLSRYKIEYFLNGTGAS 169
                 699*************888776651.1456669****************************************************************** PP

     UPF0051  93 aelnglylakgkqhldtrtkvdhngpntssrilskgvlkdearavfrgkikvrkgaqktdahqenrnLllsdkaradtiPeleidaddvkasHgAtvGk 191
                 a+ +++++++++q +d++t+v+h+ p t++r++ k++l++++++ f+g+i+++++a+k++++ + r++ll+++a++d+iP lei+++dvka+H A+v +
  EPA04974.1 170 ANDSEVIFGNNEQSFDIQTNVNHESPSTEGRVVEKSILRNKSKSLFKGMIRIKEKATKSNSFLSGRSILLDKDAKSDAIPGLEIFTNDVKATHSASVAQ 268
                 *************************************************************************************************** PP

     UPF0051 192 ideeqlfYLmsRGlseeeArrlivrgf 218
                 ideeq+fYL++R ls+eeA+r iv+gf
  EPA04974.1 269 IDEEQIFYLKTRCLSKEEAERTIVEGF 295
                 **************************9 PP

>> DUF2152  Uncharacterized conserved protein (DUF2152)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   7.1e-06     0.064     145     236 ..      57     147 ..      50     160 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.1e-06
     DUF2152 145 vrrlrClssdrecvlvsedyyAHRtrPnvlvqeiqitnptervvdlelvvprvsdlpraltsslkkveelgellvlsgrvasvsdgkiilvv 236
                 ++++ Cls d+ + ++++ ++A  +     vqe+  + ++++ + lel   +v++  +   ++l+  ++    + +++r +  +d ki  ++
  EPA04974.1  57 IHIVSCLSDDGISTIARNVIFADESSKATIVQELYSSKAEKQQAYLELLNTNVAPNAQLDVTTLQMMDQ-STVNFSTRRTDLGQDAKINWYS 147
                 89*****999999****************************************9998999999999888.8899999999999999987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2376.43
//
Query:       EPA04975.1  [L=115]
Description: hypothetical protein BG20_I0902 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 757.61
//
Query:       EPA04976.1  [L=40]
Description: hypothetical protein BG20_I0870 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       171  (0.00953762); expected 358.6 (0.02)
Passed bias filter:                      156  (0.00870099); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.30u 0.27s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 309.44
//
Query:       EPA04977.1  [L=278]
Description: hypothetical protein BG20_I0871 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.047   13.8   0.8       0.15   12.2   0.3    2.1  2  TRAF6_Z2  TNF receptor-associated factor 6 zinc finger 2
       0.09   12.8   0.0       0.21   11.6   0.0    1.6  1  CARD_2    Caspase recruitment domain


Domain annotation for each model (and alignments):
>> TRAF6_Z2  TNF receptor-associated factor 6 zinc finger 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.3   1.6e-05      0.15      11      22 ..     148     159 ..     147     161 .. 0.90
   2 ?   -2.8   0.0      0.81   7.3e+03      19      26 ..     208     215 ..     207     215 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.6e-05
    TRAF6_Z2  11 raFQKnqlkeHi 22 
                 r F Knq++eHi
  EPA04977.1 148 RKFKKNQINEHI 159
                 67*********9 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.81
    TRAF6_Z2  19 keHilkdC 26 
                 k+ +l dC
  EPA04977.1 208 KNSMLSDC 215
                 667999*9 PP

>> CARD_2  Caspase recruitment domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   2.3e-05      0.21      21      74 ..     139     190 ..     135     202 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.3e-05
                 -HHHHGGG-T.TS-HHHHHHHHHHHHHHHHHHHHHHHHHHHCT..STTHHHHHH CS
      CARD_2  21 kpseilphltecLteedkeeIraeeenkGniaaaeeLldrllrsekegWfkafl 74 
                 +p+++l+ + ++ +++  e I +++++ G  +a   Lldr+l+  ++  f+ f+
  EPA04977.1 139 NPTHMLDVMRKFKKNQINEHISTVTHTVGIERATPFLLDRILK--STIGFSDFV 190
                 699******99999999**************************..666677775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 2057.03
//
Query:       EPA04978.1  [L=57]
Description: hypothetical protein BG20_I0892 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.7e-17   62.3   0.9    4.1e-17   62.1   0.9    1.0  1  DUF1059        Protein of unknown function (DUF1059)
  ------ inclusion threshold ------
      0.021   14.7   0.1      0.023   14.7   0.1    1.1  1  Sina           Seven in absentia protein family
      0.051   13.6   0.4      0.072   13.1   0.4    1.2  1  Tnp_22_trimer  L1 transposable element trimerization domain
      0.053   14.6   0.2      0.063   14.3   0.2    1.1  1  RNase_J_C      Ribonuclease J C-terminal domain


Domain annotation for each model (and alignments):
>> DUF1059  Protein of unknown function (DUF1059)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.1   0.9   9.3e-21   4.1e-17       2      56 .]       3      56 ..       2      56 .. 0.95

  Alignments for each domain:
  == domain 1  score: 62.1 bits;  conditional E-value: 9.3e-21
     DUF1059  2 kefkCgDvgpdCgfeitaeteeEvlrkvaeHakaaHglteippelvekiksaIkd 56
                k+++C+D+g +Cg+++tae+e+ +++kva+H+ka+H++ e++ e ++kiks Ik+
  EPA04978.1  3 KSISCADAGKNCGWSATAEKED-LMNKVATHVKADHKEIELNSENIAKIKSLIKE 56
                89**************888766.******************************96 PP

>> Sina  Seven in absentia protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   5.1e-06     0.023      43      80 ..       3      46 ..       1      56 [. 0.75

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.1e-06
        Sina 43 rpysCpcpgakCkwqGd......ldellkHlrneHkkvetlege 80
                + +sC  +g++C w  +      ++++  H++ +Hk++e ++++
  EPA04978.1  3 KSISCADAGKNCGWSATaekedlMNKVATHVKADHKEIELNSEN 46
                789***********886222222346789*********887765 PP

>> Tnp_22_trimer  L1 transposable element trimerization domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.4   1.6e-05     0.072      13      40 ..      23      50 ..      19      52 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.6e-05
                   HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
  Tnp_22_trimer 13 EDeieeidrevKereKrkkileQslQvi 40
                   ED ++ + + vK   K +  +  ++  i
     EPA04978.1 23 EDLMNKVATHVKADHKEIELNSENIAKI 50
                   9**********************99776 PP

>> RNase_J_C  Ribonuclease J C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2   1.4e-05     0.063       8      50 ..      15      56 ..      13      57 .] 0.92

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.4e-05
   RNase_J_C  8 GfvyvkeseeLieeakkvvretieealeekesdwnelkrkire 50
                G+    e+e+L+++++ +v++  +e++ + + + +++k+ i+e
  EPA04978.1 15 GWSATAEKEDLMNKVATHVKADHKEIELN-SENIAKIKSLIKE 56
                99999*******************98886.8999****99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1084  (0.0604607); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 412.07
//
Query:       EPA04979.1  [L=331]
Description: daunorubicin resistance ABC transporter, ATP-binding protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.5e-31  107.5   0.0    1.8e-30  106.2   0.0    1.6  1  ABC_tran  ABC transporter
    2.2e-11   44.1   2.7    6.1e-07   29.5   0.1    2.4  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    1.1e-07   32.5   0.8    2.7e-07   31.2   0.8    1.7  1  DUF4162   Domain of unknown function (DUF4162)
    8.5e-05   22.4   4.2      0.013   15.3   0.0    2.9  3  AAA_15    AAA ATPase domain
     0.0014   18.4   0.3     0.0033   17.1   0.3    1.6  1  AAA_29    P-loop containing region of AAA domain
     0.0025   18.3   9.4      0.092   13.2   8.0    2.9  2  AAA_23    AAA domain
     0.0037   17.2   0.0      0.008   16.1   0.0    1.5  1  Rad17     Rad17 P-loop domain
     0.0041   16.6   1.1      0.056   12.9   0.6    2.4  1  SMC_N     RecF/RecN/SMC N terminal domain
     0.0088   15.6   0.1      0.015   14.8   0.1    1.4  1  AAA_7     P-loop containing dynein motor region
  ------ inclusion threshold ------
      0.032   13.8   0.3      0.073   12.7   0.0    1.7  2  SRP54     SRP54-type protein, GTPase domain
       0.11   12.2   0.0        0.2   11.4   0.0    1.4  1  AAA_30    AAA domain
        0.2   11.7   1.8        2.2    8.4   1.8    2.3  1  MMR_HSR1  50S ribosome-binding GTPase


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.2   0.0   1.2e-33   1.8e-30       2     136 ..      20     162 ..      19     163 .. 0.98

  Alignments for each domain:
  == domain 1  score: 106.2 bits;  conditional E-value: 1.2e-33
                 EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.............HHHTCHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............xxxxxxxx RF
    ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.............esdeeiek 87 
                 +++s+ ++ ge+ ++vG+nGaGKSt +++l+ llkp  G+ l+ g d+ + + +++r++ig+++qe+++++ lt ren             + +++i++
  EPA04979.1  20 DDISFAVESGEIFGFVGPNGAGKSTTIMILTTLLKPSTGKALVSGFDVMT-QPKQVRQSIGYVQQESTVDEYLTGRENlllqarlnhipknQINKRIDE 117
                 89*********************************************999.8899**********************************9999999*** PP

                 HHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  88 alsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                 +l+ ++l+++++++v     ++SgG+++r+ +a  ll +pk+l+lDEpt
  EPA04979.1 118 VLELIELSDKQNDPV----VTYSGGMRKRLDIAGGLLHHPKVLFLDEPT 162
                 ***************....*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.4   1.5e-05     0.023       2      22 ..      32      52 ..      31      71 .. 0.83
   2 !   29.5   0.1   4.1e-10   6.1e-07     184     298 ..      93     194 ..      77     199 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.5e-05
      AAA_21  2 nvliGpNgsGKSnLLdaldll 22
                 +++GpNg+GKS+ + +l  l
  EPA04979.1 32 FGFVGPNGAGKSTTIMILTTL 52
                689**************9766 PP

  == domain 2  score: 29.5 bits;  conditional E-value: 4.1e-10
      AAA_21 184 llqrlvrslklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell 282
                  ++ l+ + +l++i+   +++++++            + + e +d q+ p+   S G+++ l ++  ll  +   ++l++DEp  gL+ +  r+++e +
  EPA04979.1  93 GRENLLLQARLNHIPKNQINKRIDE-----------VLELIELSDKQNDPVVTYSGGMRKRLDIAGGLLHHP---KVLFLDEPTVGLDIQTRRKIWEYI 177
                 3444444444444444444444444...........5556666889***********************877...9*********************** PP

      AAA_21 283 kelsr.ngaQviltTHS 298
                 k+ ++     ++ltTH 
  EPA04979.1 178 KKIHKeFEMTIFLTTHY 194
                 555554999*******6 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.8   1.8e-10   2.7e-07       3      81 .]     219     306 ..     218     306 .. 0.85

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 1.8e-10
                 HHHHHTTS-SSEEEEE......--.-----..---EEEE-TTS-EEEEE--.-----------.----EEEEEEEE---HHHHHHHHH CS
     DUF4162   3 leeiKrsygknrieve......ad.aeelleepgveeveeeggelelkled.eeaanellkal.tsgveirsFeeeePsLndIFiekv 81 
                 ++  K+++g++ i +        +  ++l++++ ++++++++++l++  ++ +e+ +++++     +v+i s+++++P+L+d+Fi ++
  EPA04979.1 219 PQNMKNAMGNEVISLVfengnsVEfLSQLKQIEFIKKINQDNNKLTIFTSNgTEVIPKIFHISsILQVKIISISLTQPTLDDVFISYT 306
                 67889*********88887644224666667777999999999*99999999***********55********************986 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   8.6e-06     0.013      25      53 ..      31      59 ..      17     129 .. 0.76
   2 !    7.3   0.1    0.0022       3.3     324     364 ..     153     193 ..     150     194 .. 0.96
   3 ?   -0.6   0.3      0.57   8.6e+02     239     256 ..     250     263 ..     210     318 .. 0.54

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 8.6e-06
      AAA_15 25 ltvliGkNnsGKSsilealdlFlnnkekk 53
                +  ++G+N++GKS+ +++l  +l+ ++ k
  EPA04979.1 31 IFGFVGPNGAGKSTTIMILTTLLKPSTGK 59
                5569*******************988444 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0022
      AAA_15 324 nvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                 +++l+++EP + L +q  + +++++k++ ++ ++ +++tTH
  EPA04979.1 153 PKVLFLDEPTVGLDIQTRRKIWEYIKKIHKEFEMTIFLTTH 193
                 5789************************************* PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.57
      AAA_15 239 teklkeiqeklkeidkkl 256
                 +    e+ +k+++ ++kl
  EPA04979.1 250 I----EFIKKINQDNNKL 263
                 1....1112222222222 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.3   2.2e-06    0.0033      18      50 ..      25      57 ..      14      61 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.2e-06
      AAA_29 18 eidlkg.atlltGpsGsGKSTllDAiqalLvpak 50
                 ++  g ++ ++Gp+G+GKST +  +++lL p++
  EPA04979.1 25 AVES-GeIFGFVGPNGAGKSTTIMILTTLLKPST 57
                3443.358899************99999999987 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   8.0   6.1e-05     0.092      15      46 ..      22      56 ..      11     264 .. 0.76
   2 ?    2.3   0.6      0.13     2e+02      70     129 ..     226     282 ..     203     330 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.1e-05
      AAA_23 15 idF...skgltlItGpNGaGKTTildAiklaLyge 46
                i F   s  ++ ++GpNGaGK+T +  ++  L   
  EPA04979.1 22 ISFaveSGEIFGFVGPNGAGKSTTIMILTTLLKPS 56
                888888889****************9999888554 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.13
      AAA_23  70 kvkayveltfenkdgry....trsiererelskkkgkttkkaklellei..deleqfisellgskk 129
                  ++++++l fen +  +     ++ie+ ++ +++++k t         i  ++ ++ i+++++++ 
  EPA04979.1 226 MGNEVISLVFENGNSVEflsqLKQIEFIKKINQDNNKLT---------IftSNGTEVIPKIFHISS 282
                 456778999988888333333222222222222222222.........222444455555444443 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   5.3e-06     0.008      47     139 ..      31     123 ..      11     161 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.3e-06
       Rad17  47 iLLisGPsGCgkstvvkvLskelgiklre.wlnpvslkepdnqksdfkgltekesrflsqiesfkeleLkdakylklqklGddlrtdkklilve 139
                 i    GP G gkst++ +L+  l ++  +  + +  +   + q+ +  g +++es+    +   ++l L +a+ + + k   + r d  l l+e
  EPA04979.1  31 IFGFVGPNGAGKSTTIMILTTLLKPSTGKaLVSGFDVMTQPKQVRQSIGYVQQESTVDEYLTGRENL-LLQARLNHIPKNQINKRIDEVLELIE 123
                 66779*******************998651578999999999************9776666665555.77788889998888888888777775 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.6   3.8e-05     0.056      29     209 ..      34     202 ..      21     214 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.8e-05
                 EEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       SMC_N  29 ivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrvkrkgeseykingkevtkkevsell 127
                  vGpNG+GKs  +  +  +L  ++ k+l s    d++++  ++ +++ ++v+   +  d+   + +e++ ++ r   +   + +in++  +  e+ el 
  EPA04979.1  34 FVGPNGAGKSTTIMILTTLLKPSTGKALVSG--FDVMTQ-PKQVRQSIGYVQQE-STVDEY-LTGRENLLLQAR--LNHIPKNQINKRIDEVLELIELS 125
                 6899999999988777555555555444332..344444.34444455555553.222222.344444444433..34444567888888888888888 PP

                 HCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEE CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       SMC_N 128 esagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadklv 209
                  +++    + SgG ++ + +a  +     +p+   +lDe    LD + ++k+ e++k+ +k++ +  i l+++ +e+ad+l+
  EPA04979.1 126 DKQNDPVVTYSGGMRKRLDIAGGL---LHHPKV-LFLDEPTVGLDIQTRRKIWEYIKKIHKEFEM-TIFLTTHYMEEADQLC 202
                 888888889999999876666432...244554.568*********************9999875.4557777788887764 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1     1e-05     0.015      30      82 ..      26      78 ..      15      90 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1e-05
       AAA_7 30 lknkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdii 82
                ++++  + +vGp G GK+++i+ l++ l++++ + l+  f  +t+++q+++ i
  EPA04979.1 26 VESGEIFGFVGPNGAGKSTTIMILTTLLKPSTGKALVSGFDVMTQPKQVRQSI 78
                566667779****************************************9987 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.9e-05     0.073       6      39 ..      34      67 ..      30      88 .. 0.90
   2 ?   -2.7   0.0       2.5   3.7e+03     174     185 ..     245     256 ..     220     294 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.9e-05
                EEESTTSSHHHHHHHHHHHHHHTTS-EEEEEEST CS
       SRP54  6 lvGlqGaGKTttlaKLaallkkegkkvllvaaDt 39
                +vG++GaGK tt+  L  llk +  k+l+   D+
  EPA04979.1 34 FVGPNGAGKSTTIMILTTLLKPSTGKALVSGFDV 67
                8********************9999999988886 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.5
                 E-SSSTTGEEE- CS
       SRP54 174 gvGekiedleef 185
                 +  ++ie ++++
  EPA04979.1 245 SQLKQIEFIKKI 256
                 333322222222 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00013       0.2      15      78 ..      27      92 ..      20     133 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00013
      AAA_30 15 tsgdrvavltGpAGtGKttalkalreaweaa.ggrviglAptgkaAkvLaeelgi..eastiakllk 78
                +sg  +   +Gp G+GK+t++  l+ +++ + g+ ++      ++ k++++++g   + st++++l+
  EPA04979.1 27 ESG-EIFGFVGPNGAGKSTTIMILTTLLKPStGKALVSGFDVMTQPKQVRQSIGYvqQESTVDEYLT 92
                455.488899**************9999998676666555555666667777775556666666664 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   1.8    0.0015       2.2       3      40 ..      33      76 ..      31     270 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0015
                EEEESTTSSHHHHHHHHHT.....S.TEEESSSTTSSSSEEEEE CS
    MMR_HSR1  3 aivGrpNvGKStLinaltg.....e.kaivsdkpgtTrdinegr 40
                ++vG   +GKSt i  lt      + ka vs +   T+  + ++
  EPA04979.1 33 GFVGPNGAGKSTTIMILTTllkpsTgKALVSGFDVMTQPKQVRQ 76
                89*************99965555425888888888887665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       992  (0.0553294); expected 358.6 (0.02)
Passed bias filter:                      641  (0.0357521); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2173.34
//
Query:       EPA04980.1  [L=81]
Description: hypothetical protein BG20_I0877 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0036   17.4   0.1     0.0041   17.2   0.1    1.1  1  F420H2_quin_red  F420H(2)-dependent quinone reductase


Domain annotation for each model (and alignments):
>> F420H2_quin_red  F420H(2)-dependent quinone reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   2.3e-07    0.0041      65     104 ..      20      59 ..      14      79 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.3e-07
                      -HHHHHHHH--EEEEEETTEEEEEEEEE--HHHHHHHHHH CS
  F420H2_quin_red  65 pswylNlkanPrvevqvgakkldvtAreveddekarlwkl 104
                       +w+ N  +nP+v ++ ++++ ++ A+ ved++ +r  ++
       EPA04980.1  20 GDWFQNAIKNPDVIIEYKNSTYKGKAKVVEDENLERKISQ 59 
                      58******************************99985443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       802  (0.044732); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.30s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 539.46
//
Query:       EPA04981.1  [L=71]
Description: hypothetical protein BG20_I0879 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00038   20.5   0.0    0.00048   20.1   0.0    1.1  1  PRC       PRC-barrel domain


Domain annotation for each model (and alignments):
>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   2.7e-08   0.00048       2      33 ..      11      42 ..      10      45 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.7e-08
                EECCS---TT-EEEETTSSEEEEEEEEEEETT CS
         PRC  2 defrasdliGkeVytedGeklGkVkDvvidek 33
                ++  a +++Gk+V++++G  +GkVk + i+ k
  EPA04981.1 11 NMATADNFVGKKVIDREGISYGKVKHIHINQK 42
                677899*********************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.29s 00:00:00.63 Elapsed: 00:00:00.43
# Mc/sec: 499.15
//
Query:       EPA04982.1  [L=74]
Description: hypothetical protein BG20_I0893 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.059   13.8   0.0      0.081   13.4   0.0    1.2  1  nlz1          NocA-like zinc-finger protein 1
       0.19   11.3   2.2        0.2   11.1   2.2    1.0  1  E1-E2_ATPase  E1-E2 ATPase
        0.3   11.1   0.5        0.3   11.1   0.5    1.8  2  PsbX          Photosystem II reaction centre X protein (PsbX)


Domain annotation for each model (and alignments):
>> nlz1  NocA-like zinc-finger protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.4e-05     0.081      12      40 ..      20      46 ..      14      54 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.4e-05
        nlz1 12 aYAgYPqqFlphGvtLDptK.sssLvgaql 40
                 YA +P+ F+p   +LDpt  + sLv+a l
  EPA04982.1 20 LYAVFPGPFIP---GLDPTFyTISLVAALL 46
                5**********...*****62446998855 PP

>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   2.2   3.4e-05       0.2     119     166 ..       9      56 ..       1      59 [. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.4e-05
                   HHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHHHHS-TTHHHH CS
  E1-E2_ATPase 119 gkvlvpvvlliallvflialllgkslaeallralallvaaiPcaLpla 166
                     vl++v+ll + +vf   ++ g +++++ ++ +a l+++iP  ++l+
    EPA04982.1   9 KLVLIFVGLLWLYAVFPGPFIPGLDPTFYTISLVAALLIMIPVCMALF 56 
                   456889999999999999999999999****************99986 PP

>> PsbX  Photosystem II reaction centre X protein (PsbX)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.3      0.48   2.9e+03      21      27 ..      11      17 ..      10      20 .. 0.52
   2 ?   11.1   0.5     5e-05       0.3      10      31 ..      39      59 ..      37      61 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.48
                HHHHHHH CS
        PsbX 21 ipiaaaL 27
                + i+++L
  EPA04982.1 11 VLIFVGL 17
                4455555 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 5e-05
                HHHHHHH.HHHHHHHHHHHHHH CS
        PsbX 10 lSLvaGalvVvipiaaaLifvS 31
                +SLva+  ++ ip+ +aL+f S
  EPA04982.1 39 ISLVAAL-LIMIPVCMALFFWS 59
                6999999.***********966 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 448.34
//
Query:       EPA04983.1  [L=46]
Description: hypothetical protein BG20_I0873 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 287.63
//
Query:       EPA04984.1  [L=41]
Description: hypothetical protein BG20_I0869 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       209  (0.0116571); expected 358.6 (0.02)
Passed bias filter:                      167  (0.00931452); expected 358.6 (0.02)
Passed Vit filter:                         3  (0.000167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.41
# Mc/sec: 299.48
//
Query:       EPA04985.1  [L=221]
Description: MIP family channel protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      6e-39  134.1  19.9    7.3e-39  133.8  19.9    1.0  1  MIP       Major intrinsic protein


Domain annotation for each model (and alignments):
>> MIP  Major intrinsic protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.8  19.9     4e-43   7.3e-39       6     227 .]       4     213 ..       2     213 .. 0.91

  Alignments for each domain:
  == domain 1  score: 133.8 bits;  conditional E-value: 4e-43
                 HHHHHHHHHHHHHHHHHHHHHHHHHCCCSSCSSSSTTSSHHHHHHHHHHHHHHHHHHHHHHHCHT-S-SHHHHHHHHHTTSSSHHHHHHHHHHHHHHHH CS
         MIP   6 kflravlAEflatlllvfigvgsalnvkkkvsslaslvsvtleavalafglalavlvylaagiSGaHlNPavTlallvarkisllrailYivaQllGai 104
                 ++l+ ++ E ++t++lv++++gs + +++++       ++++  +a+a  +al+++vy +++iS aH+NPavT++ +++++is++++++Y++a ++Ga+
  EPA04985.1   4 SNLQIFIVELIGTFILVVFATGSIV-YDTQTGG-----TLGIAFAAVAPFIALIIGVYSFGKISLAHFNPAVTIGYFITGHISKIQVLYYFAAEIIGAL 96 
                 578889****************888.6665533.....3567778888899************************************************ PP

                 HHHHHHHHHCHHHHHHTTTTSSSSSTTSSHHHHHHHHHHHHHHHHHHHHHHCSTTSSSSTCHGHHHHHHHHHHHHHHHHHHHHST-SSHHHHHHHHHHH CS
         MIP 105 vaaallklltkglesraglfanslkpglsagqalvvEiiltfvLvlvvfaltddkrkvslgelaplaigllvaliilvgipltGaamNpArslgpavvl 203
                 +++++++ ++      a+l+an+++        + +E++  ++L++v+f+++  k  + +g ++++aig +v l i++ + ++Ga+mNpAr+++pa+++
  EPA04985.1  97 LGSLFVQSFIGT---SANLGANAPNYDFPLFLIFSIEVLASALLMAVIFTVVYTK--GLKG-FSGIAIGGIVGLDIFFLAFISGASMNPARAFAPALLS 189
                 *********998...58999999**************************887544..3434.599********************************** PP

                 THSTTTTHHHHHHHHHHHHHHHHH CS
         MIP 204 nkfedhwvylvGPliGailgalvY 227
                  + +d w y+ +P++G ++ a+++
  EPA04985.1 190 GTLDDLWLYWTAPFVGTMIIAFLF 213
                 *******************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1335.62
//
Query:       EPA04986.1  [L=105]
Description: Rieske [2Fe-2S] domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-18   66.0   0.0    2.4e-18   65.8   0.0    1.0  1  Rieske    Rieske [2Fe-2S] domain
    3.7e-13   49.3   0.0    4.2e-13   49.1   0.0    1.0  1  Rieske_2  Rieske-like [2Fe-2S] domain


Domain annotation for each model (and alignments):
>> Rieske  Rieske [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.8   0.0   2.7e-22   2.4e-18       1      88 [.       6      92 ..       6      93 .. 0.96

  Alignments for each domain:
  == domain 1  score: 65.8 bits;  conditional E-value: 2.7e-22
                CEEEEEEGGGC-TTCEEEEEETTEEEEEEE-TTS-EEEEESC-TTTT-BCGGSEEETT.EEE-TTT--EEE.TTSBEEE-TTHHHEEEE CS
      Rieske  1 swvavakesdvpegdpltvkvggeplvvlrdedgevyAlsdvCtHrgaplsegkidekgvleCpcHgwayd.adGkvikgPaprplaty 88
                +w++++k ++v++g+  ++++ ++++++ ++ +g+++A++ +CtH+ a ls+g + +++ ++Cp+H ++++ ++Gk ++ Pa+ pl+ty
  EPA04986.1  6 QWIKACKLDQVKTGQLFGFTHDDKKILLANQ-KGKIFATDLICTHADADLSTGFL-NDEGVRCPLHLSVFNlQNGKPQNLPAEVPLKTY 92
                69****************************6.***********************.6669***************************99 PP

>> Rieske_2  Rieske-like [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   0.0   4.7e-17   4.2e-13       1     104 []       6     104 ..       6     104 .. 0.95

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 4.7e-17
                 SEEEEEECCCS-TTB-EEEEETTEEEEEEE-TTS-EEEEESS-TTTSSSTCCCSEEEECTTCEEEE-TTT--EEETTT-BBSS.-TTSB-BEE-EEEST CS
    Rieske_2   1 ewvpvckledlvketgvaalvdgkqvalfrlekeevyAidnldpaseanvlsrGlvgdkkgelvvasPlykqkfdLktGecle.deevslkvypvrved 98 
                 +w++ ckl+++  ++      d+k+++l+ + k++++A+d +++ +  + ls G+++d+     v +Pl+ ++f+L++G+ ++  +ev+lk+y+v++++
  EPA04986.1   6 QWIKACKLDQVKTGQLFGFTHDDKKILLANQ-KGKIFATDLICTHA-DADLSTGFLNDE----GVRCPLHLSVFNLQNGKPQNlPAEVPLKTYNVKIDQ 98 
                 7**************************9999.*************5.788*******99....79****************995678************ PP

                 SEEEEE CS
    Rieske_2  99 gkvevr 104
                 ++++v+
  EPA04986.1  99 NEIYVE 104
                 ***995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       293  (0.0163422); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 664.52
//
Query:       EPA04987.1  [L=121]
Description: hypothetical protein BG20_I0903, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.037   13.8   0.3       0.24   11.2   0.0    2.3  3  PAP2      PAP2 superfamily
       0.11   12.7   0.8       0.11   12.7   0.8    2.3  2  LHC       Antenna complex alpha/beta subunit


Domain annotation for each model (and alignments):
>> PAP2  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.18   1.6e+03      95     108 ..      15      28 ..       4      31 .. 0.52
   2 ?   -0.6   0.1      0.12   1.1e+03      58      58 ..      62      62 ..      26      87 .. 0.58
   3 ?   11.2   0.0   2.6e-05      0.24       4      33 ..      87     116 ..      84     120 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.18
        PAP2  95 avlvalsRlylgvH 108
                 +++v++  l+l vH
  EPA04987.1  15 LLVVGFVILSLLVH 28 
                 33444444444444 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.12
        PAP2 58 S 58
                S
  EPA04987.1 62 S 62
                2 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 2.6e-05
        PAP2   4 alllalalaalltsvlKdlvgrpRPfflae 33 
                  l++ ++l+++lt+ +K  ++r RP+f  e
  EPA04987.1  87 TLMILIVLSTILTGYIKCGMDRERPDFDYE 116
                 5677788899999999**********9876 PP

>> LHC  Antenna complex alpha/beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.8   1.2e-05      0.11      12      30 ..      11      29 ..       3      31 .. 0.92
   2 ?   -1.0   0.5      0.24   2.1e+03      14      24 ..      67      77 ..      65      77 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.2e-05
                HHHHHHHHHHHHHHHHHHH CS
         LHC 12 rglvallgffavlAlliHf 30
                r +v+l ++f+ l+ll+Hf
  EPA04987.1 11 RSFVLLVVGFVILSLLVHF 29
                789***************9 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.24
                HHHHHHHHHHH CS
         LHC 14 lvallgffavl 24
                +++++g++++l
  EPA04987.1 67 YMLGFGVLMLL 77
                78999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       834  (0.0465168); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 747.85
//
Query:       EPA04988.1  [L=147]
Description: SUF system FeS assembly protein, NifU family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-29  102.1   0.0    2.7e-29  101.9   0.0    1.0  1  NifU_N    NifU-like N terminal domain
  ------ inclusion threshold ------
      0.057   13.7   0.4       0.09   13.0   0.4    1.3  1  TSCPD     TSCPD domain
       0.11   12.4   0.0       0.14   12.0   0.0    1.3  1  SufE      Fe-S metabolism associated domain


Domain annotation for each model (and alignments):
>> NifU_N  NifU-like N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.9   0.0   4.5e-33   2.7e-29       2     127 ..       8     130 ..       7     132 .. 0.95

  Alignments for each domain:
  == domain 1  score: 101.9 bits;  conditional E-value: 4.5e-33
                 SCHHHHHHHHSSSSBSS-TTSSS--EEEEEEETTTTEEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHHHHHTTSBHHHHCCCCHHHHHHHHTC. CS
      NifU_N   2 ysdkvldhyknPrnvGvleeedakvgvgevgapacGDavrLqikvdeetdriedakFktfGCgsaiAssslltelvkgktleealkitnkeiaeelgg. 99 
                 y++ ++d+ +nP n G +e+ d   ++ +  +p cGD + + +k+d+  ++++d+kF++ GC++ +A+ss+lte+ kgk+l+e+++it++++ +elg  
  EPA04988.1   8 YHEMIIDYSRNPINFGEIENPD---VTFHDSNPLCGDSIDIDMKIDH--NKVTDIKFHGRGCAICMACSSVLTEITKGKNLDEVRNITKHDVLSELGLe 101
                 9*********************...488899****************..5********************************************99866 PP

                 .SCSSSCHCSCHHHHHHHHHHHHHHHHCT CS
      NifU_N 100 .lpkeklhcsvlaedalkaavkkYkakkk 127
                  l +++++c+ l+ ++lk a+++Y +k++
  EPA04988.1 102 hLQAVRIKCALLSLKVLKSALYSYLGKHM 130
                 69***********************9986 PP

>> TSCPD  TSCPD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.4   1.5e-05      0.09       6      49 ..      38      87 ..      33      92 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.5e-05
       TSCPD  6 vCsreieievd.dk.liknvkfvg.GCngnlkg...iskLvegmkveevi 49
                 C+ +i+i+++ d+ +++++kf g GC+  +     ++++ +g++ +ev 
  EPA04988.1 38 LCGDSIDIDMKiDHnKVTDIKFHGrGCAICMACssvLTEITKGKNLDEVR 87
                699999999988656*******9879964333300144555888888886 PP

>> SufE  Fe-S metabolism associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.4e-05      0.14      41     102 ..      39     102 ..       8     113 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.4e-05
                 SSSEEEEEEEEETTS...EEEEEEESSHHHHHHHHHHHHHCTTEECCCCTCC-TCHHHHHTTSHH CS
        SufE  41 Cqsqvwlaaeledgk...lkfeadsdarivkGllalllevlsgktpeeilavdledfleelglse 102
                 C   + ++++++++k   +kf++    +i  +  ++l e+ +gk+ +e+ ++  +d+l+elgl++
  EPA04988.1  39 CGDSIDIDMKIDHNKvtdIKFHGRG-CAICMACSSVLTEITKGKNLDEVRNITKHDVLSELGLEH 102
                 5556667777776666667777765.55788899*****************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1040.62
//
Query:       EPA04989.1  [L=107]
Description: hypothetical protein BG20_I0896 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 827.09
//
Query:       EPA04990.1  [L=466]
Description: FeS assembly protein SufB [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-72  243.8   0.1    2.1e-72  243.4   0.1    1.2  1  UPF0051   Uncharacterized protein family (UPF0051)


Domain annotation for each model (and alignments):
>> UPF0051  Uncharacterized protein family (UPF0051)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  243.4   0.1   1.2e-76   2.1e-72       2     218 .]     212     437 ..     211     437 .. 0.97

  Alignments for each domain:
  == domain 1  score: 243.4 bits;  conditional E-value: 1.2e-76
     UPF0051   2 qfertlivveegaevtiieeyagc............gvveifvgenAklkyvkvqnwsedavnlstkraeegrdaklelttvslggkltrkepsvelkg 88 
                 qfertli+++eg+ev++i   +gc            +vve++++++Akl+y+++qnws+d++nl+tkra   + a++e++++++g+klt+k+p ++l g
  EPA04990.1 212 QFERTLIIADEGSEVHYI---EGCtapvysseslhsAVVELVAHKDAKLRYTTIQNWSSDVYNLVTKRAYAYEGATVEWIDGNIGSKLTMKYPGIYLLG 307
                 89****************...667777777777777*********************************9999************************** PP

     UPF0051  89 egaeaelnglylakgkqhldtrtkvdhngpntssrilskgvlkdearavfrgkikvrkgaqktdahqenrnLllsdkaradtiPeleidaddvkasHgA 187
                 e+a +e  ++++a+++qh+dt+ k+ h +pnt+s+i+sk+v++ ++r+++rg + v+kga++ +a +++++Lll+d+++ dt P++ei+++d++++H+A
  EPA04990.1 308 ERAYGETLSIAFAGKGQHQDTGAKMVHLAPNTTSKITSKSVSRLDGRSTYRGLLNVAKGATNVKATVRCDALLLDDTSKTDTYPYMEINQEDATITHEA 406
                 *************************************************************************************************** PP

     UPF0051 188 tvGkideeqlfYLmsRGlseeeArrlivrgf 218
                 tvGki +eq+fYLm+RG++eeeA +liv+gf
  EPA04990.1 407 TVGKIGDEQIFYLMTRGFTEEEALSLIVNGF 437
                 ******************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (466 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 3049.54
//
Query:       EPA04991.1  [L=51]
Description: hypothetical protein BG20_I2414 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       222  (0.0123822); expected 358.6 (0.02)
Passed bias filter:                      136  (0.00758548); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.46
# Mc/sec: 333.41
//
Query:       EPA04992.1  [L=168]
Description: hypothetical protein BG20_I2413 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-07   31.9   0.0    2.1e-06   28.0   0.0    2.5  2  HEAT_2    HEAT repeats
  ------ inclusion threshold ------
      0.011   15.7   0.0      0.023   14.7   0.0    1.6  1  Cnd1      non-SMC mitotic condensation complex subunit 1
      0.042   14.1   0.0         12    6.5   0.0    3.2  3  HEAT      HEAT repeat
      0.051   13.1   0.0       0.14   11.7   0.0    1.7  1  CLASP_N   CLASP N terminal


Domain annotation for each model (and alignments):
>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.36   1.6e+03       9      26 ..      30      47 ..      14      57 .. 0.59
   2 !   28.0   0.0   4.6e-10   2.1e-06       2      80 ..      64     142 ..      63     150 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.36
      HEAT_2  9 endpdpevrraairaLgr 26
                +n  d+  r+ a++  g+
  EPA04992.1 30 KNERDESRRWDAVWLAGE 47
                333344444444444443 PP

  == domain 2  score: 28.0 bits;  conditional E-value: 4.6e-10
      HEAT_2   2 daLlqalendpdpevrraairaLgrignpealpaLvell.ededpavRraaaeaLgaigdpealpaLkellddddddvvR 80 
                 d+++ +lend +  v+++a+ +++  + ++ +p Lv+ +  d+++ v ++a+e+Lg ++  e+ +  k+ l+d++ dv  
  EPA04992.1  64 DLMVWILENDDNGVVKHEACFQIAARNMRKKIPNLVNSAfYDKSALVKHEAIESLGLMRAFEVENEIKKTLNDPNPDV-S 142
                 567889*******************************9989***************9999889999999887666554.4 PP

>> Cnd1  non-SMC mitotic condensation complex subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   5.1e-06     0.023      59      93 ..     126     159 ..      83     167 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.1e-06
        Cnd1  59 flselaklleDenprVvanalaalteiseksenai 93 
                 + +e++k l+D+np V++ a+++l+ + +   n++
  EPA04992.1 126 VENEIKKTLNDPNPDVSETARFVLKRLERTR-NIT 159
                 4458889999999999999999998887765.444 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.5   6.7e+03      10      23 ..      72      85 ..      67      88 .. 0.72
   2 ?    3.9   0.0     0.018        81       3      25 ..      96     119 ..      95     121 .. 0.83
   3 ?    6.5   0.0    0.0027        12       6      21 ..     131     146 ..     128     152 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.5
                T-SSHHHHHHHHHH CS
        HEAT 10 sDpspeVReaAaka 23
                +D++  V   A+  
  EPA04992.1 72 NDDNGVVKHEACFQ 85
                88888888777765 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.018
                 HHHHHHH.T-SSHHHHHHHHHHHH CS
        HEAT   3 Plllkll.sDpspeVReaAakaLg 25 
                 P l++    D+s+ V   A+++Lg
  EPA04992.1  96 PNLVNSAfYDKSALVKHEAIESLG 119
                 777777559**************9 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.0027
                 HHHHT-SSHHHHHHHH CS
        HEAT   6 lkllsDpspeVReaAa 21 
                  k l+Dp+p+V e+A 
  EPA04992.1 131 KKTLNDPNPDVSETAR 146
                 5789*******99985 PP

>> CLASP_N  CLASP N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   3.1e-05      0.14     167     203 ..     114     152 ..      81     161 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.1e-05
     CLASP_N 167 kleaslll..dliekslkkgleDanptVRetaRstfwef 203
                 ++e  +l+   ++e+ +kk l+D+np V etaR ++ ++
  EPA04992.1 114 AIESLGLMraFEVENEIKKTLNDPNPDVSETARFVLKRL 152
                 4444444422257899*****************887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.33s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1058.67
//
Query:       EPA04993.1  [L=190]
Description: hypothetical protein BG20_I2415, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.012   15.4   0.0      0.044   13.7   0.0    1.9  2  TrmB      Sugar-specific transcriptional regulator TrmB


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.16   2.8e+03       4      43 ..      36      44 ..      32      56 .. 0.57
   2 ?   13.7   0.0   2.5e-06     0.044      18      55 ..     115     152 ..     112     170 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.16
                CHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHH CS
        TrmB  4 lGLseyEakvYlaLlklgpatadeiaeelgvprskvYevL 43
                +G+                                 Ye+L
  EPA04993.1 36 FGIGI-------------------------------YESL 44
                55554...............................5555 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 2.5e-06
                 HHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
        TrmB  18 lklgpatadeiaeelgvprskvYevLrsLedkGlVere 55 
                 ++ +++t++ei ++ ++p+++ Y+ +++L++  + +++
  EPA04993.1 115 VTDKSMTIYEILRKCDIPQTSGYRKIKQLIENNFLTIQ 152
                 56789**************************9998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 1098.53
//
Query:       EPA04994.1  [L=220]
Description: hypothetical protein BG20_I2170 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.6e-07   28.8   0.1    0.00022   21.0   0.0    2.2  2  Redoxin        Redoxin
    1.4e-06   28.2   0.1    2.2e-05   24.3   0.0    2.3  2  AhpC-TSA       AhpC/TSA family
     0.0046   17.3   0.1        4.2    7.8   0.0    2.3  2  Thioredoxin_8  Thioredoxin-like
       0.01   16.0   0.0      0.073   13.2   0.0    2.0  1  Thioredoxin_4  Thioredoxin
  ------ inclusion threshold ------
      0.021   15.2   0.3       0.17   12.3   0.1    2.1  2  Thioredoxin_2  Thioredoxin-like domain
      0.091   12.3   0.0       0.19   11.3   0.0    1.6  1  GSHPx          Glutathione peroxidase


Domain annotation for each model (and alignments):
>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   7.2e-08   0.00022       3      83 ..       6      88 ..       4     153 .. 0.76
   2 !    5.9   0.0    0.0032       9.7      98     134 ..     171     206 ..     166     215 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 7.2e-08
                TSBB---ECCEETTCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHH.HHHTHHHHHHCSTTTEEEEEESSSHHHHHHHHH...T CS
     Redoxin  3 gdkaPdftlplaatdgnsvslsefkgkkvvvnfvpgafcPtCsaehp.yleklaellkekgvdvvavvadndafvkefwgk...e 83
                g+kaP+f   +   +g +++ ++ k++ v+v ++    cP C   ++ +   +++++k+ gv v+++ ++ +++ k+ +++   +
  EPA04994.1  6 GQKAPNFAVSE-WVQGAPTNFDQEKDHIVLVEVFQV-NCPGCFMHALpEAISIYNKYKDDGVRVIGLATAFEDYDKNTLDNlkmL 88
                89******766.89*********8888877777777.*****877777888889999************9999966665553332 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0032
                 HHHTT-TTEEE.GGGEEE-EEEEEEETTEEEEEEESS CS
     Redoxin  98 tkalGlrleedaseglrtpryavidedgkvvylevep 134
                 tk++ +++ e+ + + +tp+++++d++g ++ +  ++
  EPA04994.1 171 TKEYSAETFEKFALQ-GTPSMILVDRKGILRNVSFGQ 206
                 677888877777777.************999887665 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   7.4e-09   2.2e-05       1      89 [.       5     125 ..       5     137 .. 0.74
   2 ?    1.5   0.0     0.088   2.6e+02      96     123 ..     180     201 ..     151     202 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 7.4e-09
                 TTSB----EEEST.TCEEEECHHHTTSEEEEEEESTST-CCHH.HHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHHH-H................ CS
    AhpC-TSA   1 vgdkapdfelkna.dgetvslsdykgkpvvlffypkdwcpvCt.telpalaklyeefkergvevigvsvdspeshkkfiekes................ 81 
                 +g+kap+f + ++ +g + ++++ k+++v++ +++  +cp+C  + lp+    y+++k+ gv vig+ +  ++  k++ +  +                
  EPA04994.1   5 IGQKAPNFAVSEWvQGAPTNFDQEKDHIVLVEVFQV-NCPGCFmHALPEAISIYNKYKDDGVRVIGLATAFEDYDKNTLDNLKmlaetgevvgdtkeal 102
                 8**********7736788888888999999999999.*****62568*********************9988877777777776664444555555555 PP

                 ................SSEEEE- CS
    AhpC-TSA  82 ...............lnfpllsD 89 
                                ++fpl+ D
  EPA04994.1 103 smygqlqpgnklsykIPFPLAMD 125
                 55555555555555555555555 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.088
                 HHTT-EETTTTECSCEEEEE-TTSBEEE CS
    AhpC-TSA  96 kaygvlkeekglalratfvidkegkiry 123
                 +++          +++ +++d++g++r 
  EPA04994.1 180 EKFA------LQGTPSMILVDRKGILRN 201
                 3333......348999*********985 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0014       4.2       3      43 ..      32      72 ..      30      95 .. 0.83
   2 !    7.5   0.0    0.0017       5.1      33      93 ..     137     197 ..     116     199 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0014
                   EEEEEE--SSSHHH.HHHHHHHHHHHHHHHHTTSEEEEEEE- CS
  Thioredoxin_8  3 vvlLyfgaswcppc.kaftpklkelyeklkkkkkveivyvsl 43
                   +vl+ ++  +cp c ++ +p+ + +y+k+k +++v+++ +  
     EPA04994.1 32 IVLVEVFQVNCPGCfMHALPEAISIYNKYK-DDGVRVIGLAT 72
                   899999999***9879*************9.79999997655 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0017
                    TTSEEEEEEE-SS-HHHHHHHGGGS-TTSEE.EE-TT-HHHHTT-S--TT-SEEEEE-TT- CS
  Thioredoxin_8  33 kkkveivyvsldkkeeefekylkknkkpwlsvpfddkkrnklkkkynvkaiPtlvvldkng 93 
                    +k ++++y  + +   + e+y+k+  +    +   ++ + +  +k+ +++ P+++++d++g
     EPA04994.1 137 EKVMQFIYGQIPEFDTQPEEYRKQIIQRVKDYMKTKEYSAETFEKFALQGTPSMILVDRKG 197
                    566666665554444444444444433344433344447888999*************987 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   2.5e-05     0.073      11     149 ..      28     195 ..      23     208 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.5e-05
                    TT-SEEEEEEE-TT-HHHHHHHHHHH.HHHHHHHHTTSEEEEEEE-..---S.TTTHHHHHHHTT--T.T..HHHHHHHHHHHHTHHHHTTS-... CS
  Thioredoxin_4  11 pdApvtvieyedlrCphCakfeeeve.klleeyidtGkvkfiirdfpldkek.eslkaamaarcagee.s..peaflaikallysqqeewaes... 98 
                    ++  ++++e   ++Cp C   +      + ++y +++ v++i    +++++  + l+ + ++   ge+ +  +ea +++ +l +      + s   
     EPA04994.1  28 EKDHIVLVEVFQVNCPGCFMHALPEAiSIYNKY-KDDGVRVIGLATAFEDYDkNTLDNLKMLAETGEVvGdtKEALSMYGQL-QPG---NKLSyki 118
                    78899*************9988777779*****.777788887777666665477877777666666642235555555553.333...2222333 PP

                    .......HHHHH............................HHHHHTS-------HHHHHHHHHHH.HHHT--SS-EEEETTE CS
  Thioredoxin_4  99 .......lkelaae.......................aldkdekfeacleeekldalveaeskea.kkagiestPtfiinge 149
                                 +                       +++ +e  ++ +++ k   + +++s+e  +k  +++tP++i+ ++
     EPA04994.1 119 pfplamdK-----LvktdgkisdekvmqfiygqipefDTQPEEYRKQIIQRVKDYMKTKEYSAETfEKFALQGTPSMILVDR 195
                    55444320.....133345555556777777777755555566666666555444444444444449999999999887544 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.23   6.9e+02       5      20 ..      29      45 ..      25      80 .. 0.77
   2 ?   12.3   0.1   5.7e-05      0.17      35      92 ..     142     198 ..     126     210 .. 0.69

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.23
  Thioredoxin_2  5 gkpvlvvft.dpdCpyC 20
                   + ++++v   +++Cp C
     EPA04994.1 29 KDHIVLVEVfQVNCPGC 45
                   444444444599***99 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 5.7e-05
  Thioredoxin_2  35 vrvllfp.lkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPtivfldgkei 92 
                    +++  +p ++ + e++  +i +       +k++e + e  +k+ ++gtP++++ d k i
     EPA04994.1 142 FIYGQIPeFDTQPEEYRKQIIQRVK--DYMKTKEYSAETFEKFALQGTPSMILVDRKGI 198
                    5555555554444444444444443..3577789999*******************933 PP

>> GSHPx  Glutathione peroxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   6.2e-05      0.19       9      60 ..      18      71 ..      11      96 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.2e-05
                TTSSEEEGGGGTTSEEEEEEEESSS..TTHHHHHHHHHHHHHHGGGTEEEEEEE CS
       GSHPx  9 idgekvkleklrgkvvlivnvaskC..glteqykeleelqkrykdkglvilgfP 60
                ++g ++++++ ++++vl++    +C   + +   e  +++++ykd g++++g  
  EPA04994.1 18 VQGAPTNFDQEKDHIVLVEVFQVNCpgCFMHALPEAISIYNKYKDDGVRVIGLA 71
                57899************99777777325666999*****************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1449.90
//
Query:       EPA04995.1  [L=305]
Description: putative lipoprotein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-05   25.1   3.0    3.6e-05   23.9   2.7    1.7  2  Neur_chan_memb  Neurotransmitter-gated ion-channel transmembr


Domain annotation for each model (and alignments):
>> Neur_chan_memb  Neurotransmitter-gated ion-channel transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.14   2.6e+03      99     119 ..      68      88 ..      63     166 .. 0.74
   2 !   23.9   2.7     2e-09   3.6e-05       2      81 ..     192     271 ..     191     300 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.14
                     TTHHHHHHC------------ CS
  Neur_chan_memb  99 fldklprllfmkrpsevkdne 119
                     f+++ p+++fm+ +++v++  
      EPA04995.1  68 FIETKPKIEFMNGKATVEPIT 88 
                     888999999999887776543 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 2e-09
                     HHHHHHHHHHHHHHHHHHHCT.TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-STTHHHHHHHHHHHHHHHHHHHHHHH CS
  Neur_chan_memb   2 iiPcvlisiLsvlvFyLpsda.gekvtLgIsvlLslTvfllliteilPktSlvipLigkYLlftmvfvtlsivetvfVlnv 81 
                     ++P ++i+ +++l F++      +++ Lg s+lL+     l ++++lP++ + +  +   +++ +++    ++ +v+ + +
      EPA04995.1 192 MLPVIIITTIAMLAFWMSPTNfTARIGLGASTLLAAVAAHLNAANQLPPIGYLTLFDK-IMIIAYALFLNNLLSMVIQMRL 271
                     78***************99999*****************************9987766.6666677666666666654444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       821  (0.0457917); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2002.30
//
Query:       EPA04996.1  [L=204]
Description: hypothetical protein BG20_I2167, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.6e-22   77.6  25.6    4.1e-11   42.9   5.6    2.6  2  Cu-binding_MopE  Putative metal-binding motif


Domain annotation for each model (and alignments):
>> Cu-binding_MopE  Putative metal-binding motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   5.6   2.3e-15   4.1e-11       1      28 [.      11      39 ..      11      40 .. 0.97
   2 !   40.2  12.0   1.6e-14   2.8e-10       1      27 [.      55      82 ..      55      83 .. 0.96

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 2.3e-15
  Cu-binding_MopE  1 DCdDsdpaihPgatEvC.DgvDnnCdGvv 28
                     DC+D+d++i+PgatE++ + +D++CdG++
       EPA04996.1 11 DCNDNDASIYPGATEIPgNSIDEDCDGIA 39
                     9**************************85 PP

  == domain 2  score: 40.2 bits;  conditional E-value: 1.6e-14
  Cu-binding_MopE  1 DCdDsdpaihPgatEvC.DgvDnnCdGv 27
                     DC+D+d++i+PgatE++ Dg+D++C+G+
       EPA04996.1 55 DCNDNDASINPGATEIPnDGIDQDCNGS 82
                     9**************999*********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 1223.13
//
Query:       EPA04997.1  [L=172]
Description: nuclease-like protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-07   32.4   0.0    1.4e-07   31.9   0.0    1.3  1  SNase     Staphylococcal nuclease homologue
  ------ inclusion threshold ------
      0.022   14.9   0.0      0.031   14.5   0.0    1.3  1  SesA      N-terminal domain on NACHT_NTPase and P-loop NTPase
      0.086   13.0   0.0       0.23   11.7   0.0    1.7  1  CC        CC domain


Domain annotation for each model (and alignments):
>> SNase  Staphylococcal nuclease homologue
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0   2.4e-11   1.4e-07      10      79 ..      88     153 ..      79     169 .. 0.77

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 2.4e-11
                 STSSBTTTTTSTTHHHHHHHHHHHHHHCSSEEEEE-S..SBSTTSEEEEEEEETTEEHHHHHHHTTSSEE-- CS
       SNase  10 PetakpkktvqpfgkeAkeflkklvlqkkvvvleldk..kkDkygrllayvylnkknineeLvkeGlArvye 79 
                 Pe +      +  gk Ak+f +  +   ++v++++d    k++y+r+l+ +y+n++n+ne+L++ G+ ++ +
  EPA04997.1  88 PELN------ESDGKIAKDFINGICPVGSSVTVNEDDgqTKGSYDRILGVIYCNGENLNEQLLESGYGSMST 153
                 5555......555899******999766555555555599***************************88554 PP

>> SesA  N-terminal domain on NACHT_NTPase and P-loop NTPases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   5.1e-06     0.031      43      87 ..      27      71 ..      11      91 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.1e-06
        SesA 43 edaksqlesskldedtesaikpvlesckekatkleeifekvapap 87
                ++a +q+ s++++e+t + i+p+l +c  +a++++ + + v + +
  EPA04997.1 27 QSAFDQFTSQTQEESTVTIIQPSLPECTGNARCIKGLVTDVIDGD 71
                5677788888888888888*******************9996654 PP

>> CC  CC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   3.8e-05      0.23      15      26 ..     102     113 ..      95     117 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.8e-05
          CC  15 inGvCPtGyvvv 26 
                 inG CP G++v+
  EPA04997.1 102 INGICPVGSSVT 113
                 9**********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1346.95
//
Query:       EPA04998.1  [L=320]
Description: ABC transporter, ATP-binding protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-19   69.7   0.5    8.4e-19   68.4   0.5    1.6  1  ABC_tran  ABC transporter
    0.00062   19.7   0.5       0.27   11.0   0.0    2.8  3  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
     0.0021   17.5   1.6     0.0047   16.4   1.6    1.5  1  SMC_N     RecF/RecN/SMC N terminal domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.4   0.5   1.4e-22   8.4e-19       8     137 .]      91     212 ..      88     212 .. 0.79

  Alignments for each domain:
  == domain 1  score: 68.4 bits;  conditional E-value: 1.4e-22
                 EETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH...........HHHTCHHHHHHHSTTG CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxxxxx RF
    ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren...........esdeeiekalsklglk 95 
                 +++ge+++i+G n  GK+tL+k++ag +kp+ Gei               + +i++ pq  q + + +v              e ++e e++l+ l++k
  EPA04998.1  91 VRKGEVLGIMGANALGKTTLMKMIAGVEKPDVGEI-------------DKKIKIAYKPQYLQNDIDAEV--IalldkanggtiEGSQEEEQILEPLKIK 174
                 789********************************.............233344444444222222211..12233444555699999*********** PP

                 GTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  96 elkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                 +l ++ v    ++LSgG+ q++++a +ll+k +l+ lDEp+a
  EPA04998.1 175 KLYNKSV----KNLSGGELQKISVASCLLQKVDLYALDEPSA 212
                 *******....*****************************75 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1      0.22   1.3e+03      47     101 ..      33      83 ..      19      95 .. 0.69
   2 !   11.0   0.0   4.5e-05      0.27       3      29 ..      98     118 ..      96     179 .. 0.73
   3 !    6.2   0.0    0.0013         8     234     284 ..     181     235 ..     139     248 .. 0.66

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.22
      AAA_21  47 slldlydpeipfefeieeflsqgvryryglrlersqveeklssvetllesgllld 101
                  +ld+y p++ ++f++  ++s +v  +   ++ +      + s+++l++++  + 
  EPA04998.1  33 VFLDGYLPTENVRFRDK-KFSFDVSSSSTDEFQEGSE---IMSYPKLEKKYSSFS 83 
                 56788888888888888.7777776666666666666...677777666666555 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 4.5e-05
      AAA_21   3 vliGpNgsGKSnLLdaldllarldrdv 29 
                 ++ G+N+ GK++L++ + ++       
  EPA04998.1  98 GIMGANALGKTTLMKMIAGV------E 118
                 688**************766......2 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.0013
      AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHP.......kllrrllellke 284
                 + +lS G ++ + +++ ll+     +l+++DEp ++L+        k+l ++++ + +
  EPA04998.1 181 VKNLSGGELQKISVASCLLQKV---DLYALDEPSAFLDVedritiaKFLQKFVRSFGK 235
                 4567999999955555555444...9************95554444444444444433 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   1.6   7.9e-07    0.0047     124     204 ..      97     249 ..      50     262 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 7.9e-07
                 HHHHHCTT-STT..........................................................................CS-HHHHHHHHHH CS
                 xxxxxxxxxxxx..........................................................................xxxxxxxxxxxxx RF
       SMC_N 124 sellesagiske..........................................................................lLSgGektLvala 148
                   ++    + k+                                                                          +LSgGe + +++a
  EPA04998.1  97 LGIMGANALGKTtlmkmiagvekpdvgeidkkikiaykpqylqndidaevialldkanggtiegsqeeeqileplkikklynksvkNLSGGELQKISVA 195
                 444444444333444444444444444444444444444455555555555555555555555555555555555555555556669*****9887776 PP

                 HHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxx RF
       SMC_N 149 LlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivislreemlek 204
                         ++  ly lDe  a LD + +  +a++l++   +     ivi ++ +++  
  EPA04998.1 196 SC----LLQKVDLYALDEPSAFLDVEDRITIAKFLQKFVRSfgKTAIVIDHDIQLMDL 249
                 55....467778***********************98665533567777777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 1970.46
//
Query:       EPA04999.1  [L=171]
Description: Met-10+ like-protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-46  159.3   0.1    1.1e-46  159.1   0.1    1.0  1  Met_10           Met-10+ like-protein
    0.00012   21.6   0.1    0.00021   20.8   0.0    1.4  2  PrmA             Ribosomal protein L11 methyltransferase (Prm
     0.0037   16.8   0.0     0.0048   16.5   0.0    1.2  1  MTS              Methyltransferase small domain
  ------ inclusion threshold ------
      0.037   14.0   0.0       0.26   11.3   0.0    2.1  2  ADH_zinc_N       Zinc-binding dehydrogenase
      0.054   12.8   0.0       0.09   12.1   0.0    1.3  1  DNA_methylase    C-5 cytosine-specific DNA methylase
       0.07   12.7   0.1       0.13   11.8   0.1    1.4  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
       0.13   12.4   0.0       0.21   11.7   0.0    1.3  1  FtsJ             FtsJ-like methyltransferase
       0.18   12.5   0.0       0.35   11.6   0.0    1.4  1  Methyltransf_25  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.1   0.1     5e-50   1.1e-46       2     149 ..      21     168 ..      20     171 .] 0.97

  Alignments for each domain:
  == domain 1  score: 159.1 bits;  conditional E-value: 5e-50
                 EEEEETTEEEEEB-TTSSHHHHHHHHHHHHHS.S-SCEEEE-S-SBTTTTB--EEEEEES-.SEEEEEETTEEEEEETTTS---GGGHHHHHHHHTT-- CS
      Met_10   2 kfeiiGdvvilnlreelkeykkvigevildkt.kvktvlrkvsevegefRtfelevlaGsdstetihkEngcrfklDvskvyfsskleaErerlaklve 99 
                 +f++iGd++i++++++l   k++ige++l+     k+v+ + s veg fRt++lev+aG+d+tet+ kE gc+f +Dv + +fs++l++Erer+ +lv+
  EPA04999.1  21 SFDQIGDIIIVRIPDSLLSKKELIGETLLNEVkIAKSVFYQSSPVEGDFRTRNLEVIAGEDKTETEYKEFGCKFTVDVENAFFSPRLSTERERISNLVQ 119
                 79***************************9985679*************************************************************** PP

                 TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT- CS
      Met_10 100 egevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkv 149
                 +ge+Vv++fAG+G f+i iak  k+ +v++id+nP + k+ ++ni  Nk+
  EPA04999.1 120 DGETVVNMFAGVGMFSIMIAK-KKKCTVYSIDINPIAAKLCERNILSNKI 168
                 ********************9.78888*********************97 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.2   2.8e+03      40      55 ..      41      57 ..       8      96 .. 0.51
   2 !   20.8   0.0   9.5e-08   0.00021     155     209 ..     114     168 ..     111     171 .] 0.95

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.2
        PrmA 40 edif.epaleeeelkee 55
                ++++ e+ l+e+++ ++
  EPA04999.1 41 KELIgETLLNEVKIAKS 57
                33332544444444333 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 9.5e-08
        PrmA 155 leklvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkv 209
                 + +lv+ ge+v+ + +G G+ +i  ak    +v+ +Di+++A k  ++N+  Nk+
  EPA04999.1 114 ISNLVQDGETVVNMFAGVGMFSIMIAKKKKCTVYSIDINPIAAKLCERNILSNKI 168
                 6789*************************************************97 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   2.1e-06    0.0048      26      80 ..     116     168 ..      96     171 .] 0.88

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.1e-06
                 HCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTG CS
         MTS  26 tlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankl 80 
                 +l +   ++v+ + +G+G+ ++++ak+++  +v  +d++  A +++++n+ +nk+
  EPA04999.1 116 NLVQ-DGETVVNMFAGVGMFSIMIAKKKK-CTVYSIDINPIAAKLCERNILSNKI 168
                 5555.56679***************9765.59******************99986 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.38   8.5e+02      27      43 ..      84     100 ..      70     124 .. 0.71
   2 ?   11.3   0.0   0.00011      0.26       1      31 [.     130     160 ..     130     162 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.38
                 HHHHHHTTESEEEETTT CS
  ADH_zinc_N  27 lelakklGadevinyke 43 
                     k++G++++++ ++
  EPA04999.1  84 ETEYKEFGCKFTVDVEN 100
                 35789999999999854 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00011
                 HHHHHHHHHHHHTT-EEEEEESSHHHHHHHH CS
  ADH_zinc_N   1 gvGlaavqlAkalGaeviavdsseeklelak 31 
                 gvG++ +++Ak  +++v+ +d+++  ++l++
  EPA04999.1 130 GVGMFSIMIAKKKKCTVYSIDINPIAAKLCE 160
                 9**********************99888886 PP

>> DNA_methylase  C-5 cytosine-specific DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0     4e-05      0.09       3      43 ..     124     164 ..     123     171 .] 0.90

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4e-05
                    EEEES-TT-HHHHHHHHTT-EEEEEEE--TTTHHHHHHH-. CS
  DNA_methylase   3 fidLfaGiGGfrlgleaagfecvaaseidkkaaktYeanfk 43 
                    ++ +faG+G f++  ++++  +v++++i++ aak+ e+n+ 
     EPA04999.1 124 VVNMFAGVGMFSIMIAKKKKCTVYSIDINPIAAKLCERNIL 164
                    799********************************999987 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   5.8e-05      0.13       3      42 ..     123     163 ..     121     169 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.8e-05
  Methyltransf_15   3 vilDlfsGaGGnviqfalv.fekviaieinleklacaqhNa 42 
                      +++ +f+G G  +i +a++  ++v++i+in+   +++++N 
       EPA04999.1 123 TVVNMFAGVGMFSIMIAKKkKCTVYSIDINPIAAKLCERNI 163
                      7899************9986789****************96 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   9.5e-05      0.21      17      59 ..     116     156 ..     106     168 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.5e-05
                 T-S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSSHH CS
        FtsJ  17 klfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpmap 59 
                 +l++ g+tvv   a+ G +s +++++ + k+ v+++D++p+a 
  EPA04999.1 116 NLVQDGETVVNMFAGVGMFSIMIAKK-K-KCTVYSIDINPIAA 156
                 4667899*******************.4.49*********954 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00015      0.35       1      42 [.     124     164 ..     124     169 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00015
                      EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHH CS
  Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaarerae 42 
                      v+ + +G G +++++ak+ +k++v+ +Di++ + + +++++ 
       EPA04999.1 124 VVNMFAGVGMFSIMIAKK-KKCTVYSIDINPIAAKLCERNIL 164
                      566779************.69***************999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1201.70
//
Query:       EPA05000.1  [L=117]
Description: hypothetical protein BG20_I2338, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       718  (0.0400469); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 791.51
//
Query:       EPA05001.1  [L=474]
Description: type II/IV secretion system protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-49  168.7   0.0    2.2e-49  168.0   0.0    1.3  1  T2SSE         Type II/IV secretion system protein
     0.0052   16.2   0.0      0.011   15.1   0.0    1.5  1  FtsK_SpoIIIE  FtsK/SpoIIIE family
     0.0073   15.6   0.0      0.013   14.8   0.0    1.4  1  Zeta_toxin    Zeta toxin
     0.0074   16.0   0.0      0.016   15.0   0.0    1.5  1  AAA_29        P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.012   16.1   0.1      0.099   13.2   0.0    2.2  2  ABC_tran      ABC transporter
       0.07   12.9   0.0       0.17   11.7   0.0    1.6  1  DEAD          DEAD/DEAH box helicase
       0.16   12.3   0.1       0.41   11.0   0.0    1.6  2  AAA_16        AAA ATPase domain


Domain annotation for each model (and alignments):
>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.0   0.0   8.7e-53   2.2e-49       5     262 ..      93     357 ..      89     366 .. 0.94

  Alignments for each domain:
  == domain 1  score: 168.0 bits;  conditional E-value: 8.7e-53
       T2SSE   5 leallddekvsdihvekper.vkvrervdgielreveelekaalerlisriaalakldiseerplqdarlpekgvrlrvvllPvvag..ealviRkksa 100
                 +e+l++d+ + +i     +  + v  r  +    ++ + ++++l+ +++++a + ++++s   p++da+lp +g r+++ l   + +   +++iR+ +a
  EPA05001.1  93 IEPLMRDHMIEEISCDGTNIpIYVWHREHESIPTNIIFEKESELNNFARKMAYMCGKHVSIADPIIDASLP-GGSRINLTLGHEITKrgSTFTIRRFRA 190
                 6789999999******9999999999999999999************************************.9999999887776666699******** PP

       T2SSE 101 keltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderivtvEDpvEiqleganqvqlnak.......kakvtfadll 192
                   +t+ dl++ ++++ +ia+ + +  ++r ++lv+GgT sGKtt l+al ++i    +++v +ED+ E++l ++n +  +++        ++++  dll
  EPA05001.1 191 DPITVIDLIKFGTMSIDIAAYMWYLAEKRATMLVAGGTASGKTTALNALATFIRPG-QKVVSIEDTQELNLPHENWIPAVSRqsftdkqIGEINQFDLL 288
                 *************************9*****************************9.*********************999999999877899999*** PP

       T2SSE 193 raaLRlrPDrimvGEiRdketleilkAvnTGHlgslsTlHansaagalerLeqlgaeveaaelkssilav 262
                 raaLR+rPD+i+vGE R++e++++ +A+ TGH g  s++Ha+s+  +l+rL    + v+++ +++s+ ++
  EPA05001.1 289 RAALRQRPDIIIVGETRGREAYTLFQAMATGHGG-YSSIHADSVDATLTRLTSSPMDVPKTLISNSLDLI 357
                 ********************************99.*****************99999******9999877 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   4.2e-06     0.011      40      59 ..     220     239 ..     181     243 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.2e-06
                   .SEEEE--TTSSHHHHHHHH CS
  FtsK_SpoIIIE  40 shllvaGatgsGKStalntL 59 
                   + +lvaG+t sGK+taln+L
    EPA05001.1 220 ATMLVAGGTASGKTTALNAL 239
                   47****************98 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0     5e-06     0.013      15      51 ..     218     254 ..     214     302 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5e-06
  Zeta_toxin  15 rPklillgGqpGAGKselaellkdelerqgnvvrldp 51 
                 + + +l++G++++GK++++++l++ ++++++vv ++ 
  EPA05001.1 218 KRATMLVAGGTASGKTTALNALATFIRPGQKVVSIED 254
                 556799********************99999999975 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   6.1e-06     0.016      21      51 ..     217     248 ..     206     251 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 6.1e-06
      AAA_29  21 lkg.atlltGpsGsGKSTllDAiqalLvpakk 51 
                 +k  ++l++G + sGK+T l A+++ + p +k
  EPA05001.1 217 EKRaTMLVAGGTASGKTTALNALATFIRPGQK 248
                 444579*******************9999886 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.39   9.9e+02      30      80 ..      34     100 ..      30     176 .. 0.64
   2 ?   13.2   0.0   3.9e-05     0.099      12      74 ..     220     292 ..     214     394 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.39
                 HHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.....................H CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....................x RF
    ABC_tran  30 llagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.....................e 80 
                 ll+ +l+   Gei     ++k++ +++l+++i+ + ++ +l+  +++ e+                     +
  EPA05001.1  34 LLMTELSVSLGEI-----KSKKDAERRLKNKISAMIKKYRLKISTKNIEKinyfavrdfiylgkieplmrdH 100
                 5555566666666.....566667788888888888888888777765555666555555555555555440 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 3.9e-05
                 SEEEEEESTTSSHHHHHHHHTTSS--SEEEEEET.TCEGGG.........B-HHHCCHCEEEE-SS--S-TTS CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx.........xxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  12 ekvaivGenGaGKStLlkllagllkpteGeilld.gkdlke.........qeleslrkeigvlpqepqlfpel 74 
                  ++ + G + +GK+t l++la   +p +  + ++  ++l+           + ++++k+ig + q + l   l
  EPA05001.1 220 ATMLVAGGTASGKTTALNALATFIRPGQKVVSIEdTQELNLphenwipavSRQSFTDKQIGEINQFDLLRAAL 292
                 567789********************99999998444454488888888888888889999999987766665 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   6.5e-05      0.17       3      65 ..     208     264 ..     206     317 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.5e-05
                 HHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        DEAD   3 iQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtln 65 
                 i a ++ l+ +   +lva+ T+sGKT+a  + +l++++    ++g k++ +e t+eL   + n
  EPA05001.1 208 IAAYMWYLAEKRATMLVAGGTASGKTTA--LNALATFI----RPGQKVVSIEDTQELNLPHEN 264
                 55666667777889*************9..66666674....699999999999999766655 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0         3   7.7e+03      79     127 ..      13      64 ..       8      69 .. 0.59
   2 ?   11.0   0.0   0.00016      0.41      26     116 ..     221     309 ..     214     343 .. 0.67

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3
      AAA_16  79 eellrqlldeaesaeleawrekleeala.avpelagaea..srllellkrll 127
                  ++++ +l+e +++++e  ++ l ++l+ + +e+++++   +rl +++++++
  EPA05001.1  13 YQIIEPILSERDQKAFEIIKKLLMTELSvSLGEIKSKKDaeRRLKNKISAMI 64 
                 5666666666666666666666666666644444444335577777777777 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00016
      AAA_16  26 lvllsGesGvGKsslvrellralekdggif.lrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekleeala..avpelagaea 116
                  +l+ G  ++GK++ +++l++ ++    ++ ++ + + +   +p   ++ a +r ++  +   e ++  ++  r++l+++    +v+e +g ea
  EPA05001.1 221 TMLVAGGTASGKTTALNALATFIRPGQKVVsIEDTQELN---LPHENWIPAVSRQSFTDKQIGEINQ--FDLLRAALRQRPDiiIVGETRGREA 309
                 689*****************8887775444255555555...8888899888776666666666333..3333333332222335555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       852  (0.0475208); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 3194.08
//
Query:       EPA05002.1  [L=338]
Description: putative UTP--hexose-1-phosphate uridylyltransferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-10   40.5   0.0      1e-09   39.1   0.0    1.7  2  GalP_UDP_transf  Galactose-1-phosphate uridyl transferase, N-
    0.00035   19.5   0.0    0.00076   18.4   0.0    1.5  1  DUF4921          Domain of unknown function (DUF4921)
    0.00036   21.2   0.0       0.06   14.1   0.0    2.3  2  HIT              HIT domain
     0.0018   18.0   0.0     0.0032   17.2   0.0    1.4  1  GalP_UDP_tr_C    Galactose-1-phosphate uridyl transferase, C-


Domain annotation for each model (and alignments):
>> GalP_UDP_transf  Galactose-1-phosphate uridyl transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   0.0   2.2e-13     1e-09      91     184 .]      80     173 ..      68     173 .. 0.91
   2 ?   -2.9   0.0       1.7   7.8e+03     120     135 ..     235     250 ..     230     257 .. 0.79

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 2.2e-13
  GalP_UDP_transf  91 yikteaiaknilfkaepayGrceviifsskheltladlspkdikavvaaWqektaelkakeypkcvlifENkGaamgvsnphPHgqiwaeehlp 184
                       i+te++ +++   +ep yG  ++++ s+k + tla++++++  +v+   q++   l  ++++++v if  +G+  g +nphPH  i++ +++p
       EPA05002.1  80 SIETENSYSDRPHYSEPSYGYHYIVVASPKEKDTLATIDTEQWSNVLVVVQDRLRWLYTQKGVTYVSIFADQGETAGSQNPHPHLNILTFSTIP 173
                      566767777788889*********************************************************************9999988876 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.7
  GalP_UDP_transf 120 kheltladlspkdika 135
                      kh+++++++++k+i++
       EPA05002.1 235 KHTTSFSKITQKEIND 250
                      6889999999999875 PP

>> DUF4921  Domain of unknown function (DUF4921)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.7e-07   0.00076     190     393 ..     112     323 ..      99     332 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.7e-07
     DUF4921 190 assgtlsveeheafiaftvdalkdlykrnryvrYvavfqnWLkpaGasfdhlhkqlvaiDergvqaeaeia......rlrenPnlynelavdyaakhnl 282
                  + +t+ +e+ ++++ +  d l+ ly++ + v Yv++f +  + aG+   h h  + +  ++    e+e++      + +    + + +  ++ + +++
  EPA05002.1 112 DTLATIDTEQWSNVLVVVQDRLRWLYTQ-KGVTYVSIFADQGETAGSQNPHPHLNILTFSTIPPIIEEEAEasykilNEKGVCPMCQIVNEEMGGPRQI 209
                 44568889999999999999*****986.6899********************9999887766544444431110002233345666667777777776 PP

     DUF4921 283 viaendhavafagfGhrypt.levysksatkePweqseeevravsdlvhalhaaag...advpcneeWhhrpidvd.vpmpwrilikwrvstlaGfegg 376
                 +    +  +a+      yp  + +  k +t++  + +++e++++s ++ a+  + +   +dv+ n  +h  p   +   + w+i i   +   +G e g
  EPA05002.1 210 IQ--TEGFIAYCPWAPSYPFeFCISPKKHTTSFSKITQKEINDLSLILRATLGGLSktiKDVSYNLVFHLSPEKKNsRQIHWHIEIYPITKPWSGLERG 306
                 65..56788999999999952667777788888899**************986654222799**********887616799****************** PP

     DUF4921 377 tkiylntisPaelrdrv 393
                   i+ln +sP++ ++++
  EPA05002.1 307 YGIFLNDLSPEQAAEKL 323
                 ***********988876 PP

>> HIT  HIT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.012        54      21      94 ..      94     168 ..      88     171 .. 0.90
   2 !   14.1   0.0   1.3e-05      0.06       9      92 ..     209     291 ..     206     292 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.012
                 SS-SSSSEEEEEESS.TGCSGGGCCHHHHHHHHHHHHHHHHHHHTCTTCCCEEEEEEESGGGT-SSSS-EEEEEE CS
         HIT  21 idpkapghlLvipkk.hlselhdlteeelakllsavkkvakalqkkfknkglrvvinngahagqsvahlHiHvip 94 
                 ++p +  h  v+    + ++l  ++ e  +++l++v+   + l ++   + + ++  +g+ ag   +h H+ +++
  EPA05002.1  94 SEPSYGYHYIVVASPkEKDTLATIDTEQWSNVLVVVQDRLRWLYTQKGVTYVSIFADQGETAGSQNPHPHLNILT 168
                 57888899999999878999999*****************999999999999******************98875 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 1.3e-05
                 EEE-SSEEEEE-SS-SSSSEEEEEESSTGCSGGGCCHHHHHHHHHHHHHHHHHHHTCTTCCCEEEEEEESGGGT-SSSS-EEEE CS
         HIT   9 vyeddlvlafldidpkapghlLvipkkhlselhdlteeelakllsavkkvakalqkkfknkglrvvinngahagqsvahlHiHv 92 
                 +++++ ++a     p +p  + + pkkh++ ++++t++e+ +l  + +     l k++k  ++++v    ++  +s +++H+H+
  EPA05002.1 209 IIQTEGFIAYCPWAPSYPFEFCISPKKHTTSFSKITQKEINDLSLILRATLGGLSKTIKDVSYNLVFHLSPEKKNS-RQIHWHI 291
                 77888888999999*********************************************99999999999998888.89****8 PP

>> GalP_UDP_tr_C  Galactose-1-phosphate uridyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   7.2e-07    0.0032      32     155 ..     209     324 ..     183     334 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 7.2e-07
                    EEEE-SSEEEE--TT--STT-EEEEESS--SSGGG--HHHHHHHHHHHHHHHHHHHHHCTS..---EEEEEE---SCCCTTTT-.-EEEEE--BCS CS
  GalP_UDP_tr_C  32 vvelkdsflavvpylakWPfevlllrkaevkslaeladeekedlaailkklarkydnlfet..sfeysmGlhqaplnaeednsw.lHaHfevpllr 124
                    +  +++ f+a  p+   +Pfe  + +k++++s ++++++e +dl  il+  +   ++l +t  +  y + +h   l++e++ns  +H H+e+  + 
     EPA05002.1 209 I-IQTEGFIAYCPWAPSYPFEFCISPKKHTTSFSKITQKEINDLSLILRATL---GGLSKTikDVSYNLVFH---LSPEKKNSRqIHWHIEIYPIT 297
                    4.44566****************************************99765...67777622556666675...555666666699999999998 PP

                    STTEB----THHHHT-EEESS-HHHHHHHHH CS
  GalP_UDP_tr_C 125 satvrkieVGlelLperlrdllaEqaaerlr 155
                    +   + +e G+ +    l dl +Eqaae+l 
     EPA05002.1 298 KPWSG-LERGYGIF---LNDLSPEQAAEKLG 324
                    87665.57788876...66778888888764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 2451.89
//
Query:       EPA05003.1  [L=233]
Description: nucleotidyl transferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-39  136.6   0.0    1.1e-39  136.5   0.0    1.0  1  NTP_transferase  Nucleotidyl transferase
    2.8e-09   37.5   0.0    3.3e-09   37.3   0.0    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
  ------ inclusion threshold ------
       0.07   12.8   0.0       0.15   11.8   0.0    1.5  2  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.5   0.0   1.9e-43   1.1e-39       1     247 [.       2     228 ..       2     229 .. 0.93

  Alignments for each domain:
  == domain 1  score: 136.5 bits;  conditional E-value: 1.9e-43
                      EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEESS--BGGHHHHHTH CS
  NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlialepegkgtAdAvalaa 94 
                      kavILaGG GtRL P t  l+k+++p ++k +++++ +    ++gi++ +v + ++ + ++e+++++g++fgv++++a+ + +  tA+ ++ a+
       EPA05003.1   2 KAVILAGGLGTRLQPYTTFLPKPMLPLGEK-PILEHLIDWTKKNGIKS-VVLCVSYLKKSIEDYFEDGKRFGVNIEYAVANRPLATAGQLKTAE 93 
                      79****************************.*****************.********************************************* PP

                      HHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEECTTSBEEEEECS-SSHSHCSEECCSEEEEETTHHH CS
  NTP_transferase  95 elledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGvieadeegrverfvEKPkeakaselassGiYvfnsevll 188
                      e++++++     + + gD +++ +++ +vk++++k++   vt+ +++ + +  yGvie+ ++g+v+   EKP+ ++    +++G Yv ++e+l+
       EPA05003.1  94 EFIDETF-----VCMYGDSIFDFNLRSMVKQHKQKKS--FVTMSLYEYKTNLPYGVIETTKSGKVIAWNEKPEIKA---NVNMGCYVMEPEILQ 177
                      ***9776.....8999*********************..9*********************************977...6************** PP

                      HHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEEXSSHHHHHHHHHHHHH CS
  NTP_transferase 189 flakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsDvGtldslleaneklae 247
                      ++       +++   + d+l+k++++ k   +++ k+  +  D+G+  s+ +an+++++
       EPA05003.1 178 MI------PNNKPYGMDDLLKKVMAKNKSVNSIVSKK--GFLDIGNKASYRKANQEYLQ 228
                      **......45556667777888888877777766666..89**************9976 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.0   5.6e-13   3.3e-09       1      60 [.       3      72 ..       3     149 .. 0.75

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 5.6e-13
                  EEEEEESS-TTTTT.....THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHHTTC...TS CS
  NTP_transf_3  1 aviLAGGrSsRmgg.....dKallplggkpllervldalraagvdevvvvggd..eevlaalarl...gv 60
                  aviLAGG ++R++      +K++lplg+kp+le+++d  ++ g++ vv+++ +  +++++++++    gv
    EPA05003.1  3 AVILAGGLGTRLQPyttflPKPMLPLGEKPILEHLIDWTKKNGIKSVVLCVSYlkKSIEDYFEDGkrfGV 72
                  79**********9444689********************************9987677777655422233 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.5e-05      0.15       2      53 ..       2      55 ..       1      68 [. 0.84
   2 ?   -2.9   0.0      0.75   4.5e+03       8      52 ..      86     130 ..      83     137 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.5e-05
                EEEEECTTSSCTT-...SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-G CS
        IspD  2 vvvipAAGsGkRmk...aglpKqflelkgqtllehtvdallaskavdkivvvvse 53
                 +vi A G G+R++   + lpK  l l  +++leh +d   + + ++ +v+ vs 
  EPA05003.1  2 KAVILAGGLGTRLQpytTFLPKPMLPLGEKPILEHLIDWTKK-NGIKSVVLCVSY 55
                69***********8443568*****************98877.889999998875 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.75
                 TTSSCTT-SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE- CS
        IspD   8 AGsGkRmkaglpKqflelkgqtllehtvdallaskavdkivvvvs 52 
                 AG+ k +++  +  f+ + g+++    ++++ ++++ +k  v +s
  EPA05003.1  86 AGQLKTAEEFIDETFVCMYGDSIFDFNLRSMVKQHKQKKSFVTMS 130
                 666677777777788888888888888888887777666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1536.32
//
Query:       EPA05004.1  [L=115]
Description: hypothetical protein BG20_I1761 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.6e-07   30.0   0.2    5.2e-07   29.5   0.2    1.2  1  Ribosomal_S24e  Ribosomal protein S24e
  ------ inclusion threshold ------
      0.063   12.9   0.0      0.092   12.3   0.0    1.2  1  GXGXG           GXGXG motif


Domain annotation for each model (and alignments):
>> Ribosomal_S24e  Ribosomal protein S24e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.2   5.8e-11   5.2e-07      11      78 ..      30      97 ..      22      98 .. 0.92

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 5.8e-11
                    S--HHHHHHHHHHHHTS-CTTEEEEEEEE-SSSSEEEEEEEEES-HHHHHHHS-HHHHHHTTSS---S CS
  Ribosomal_S24e 11 tpskteireklakmykvdpdlvvvfgfrthfGggkttGfakiYdsleaakkfEpkhrlaRnglaekkk 78
                    + +k e  + + k +k + ++v+  +++th G+   tG + +Yd+++ akk  +  +++R + a++k+
      EPA05004.1 30 KLKKLEAVDMITKEFKLSGKVVIPMRLKTHVGKPLITGTFYVYDDEKLAKKQINPVIMERLEKAKAKQ 97
                    6789999999******************************************9999999999888775 PP

>> GXGXG  GXGXG motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0     1e-05     0.092     132     185 ..      41      92 ..      33      99 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1e-05
                 TTTT-EEEEEEE-S-B-SSBTTT--EEEEEEE-SSSTHHHHB-TTT-EEEES-S CS
       GXGXG 132 gceYmtGGvvvvLgktgrnfaaGmsgGiayvldedekfekklnkelvelekved 185
                 + e+   G+vv+  +  ++++  +  G+ yv+d ++  +k++n+ ++e  ++e+
  EPA05004.1  41 TKEFKLSGKVVIPMRLKTHVGKPLITGTFYVYDDEKLAKKQINPVIME--RLEK 92 
                 5688889**************************999999999985544..4444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       858  (0.0478554); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 802.76
//
Query:       EPA05005.1  [L=186]
Description: hypothetical protein BG20_I1763 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-16   59.0   0.1    4.2e-16   58.4   0.1    1.3  1  DUF309    Domain of unknown function (DUF309)
     0.0062   15.6   0.0      0.011   14.8   0.0    1.5  1  DUF5355   Family of unknown function (DUF5355)


Domain annotation for each model (and alignments):
>> DUF309  Domain of unknown function (DUF309)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.4   0.1   4.7e-20   4.2e-16       1      51 [.      87     137 ..      87     144 .. 0.90

  Alignments for each domain:
  == domain 1  score: 58.4 bits;  conditional E-value: 4.7e-20
      DUF309   1 leeaielfnegeffeaHEvlEelWkeageperkllqglIqlAvAlyhlrrg 51 
                 l+++i +fn+++f+e HE lE +Wk+    e++l+qg+I lAvA+ h ++ 
  EPA05005.1  87 LKDGIYYFNNERFWESHESLEGVWKQCYGREKELVQGIILLAVAFAHGQKD 137
                 6799********************666656*****************8875 PP

>> DUF5355  Family of unknown function (DUF5355)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.2e-06     0.011     154     189 ..     119     156 ..      91     182 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.2e-06
     DUF5355 154 kYlealagLlLSleqYqkdelGiAiGliefsllsl..k 189
                 + +++ ++L ++  + qkde+G+ +G++  sl++l  +
  EPA05005.1 119 ELVQGIILLAVAFAHGQKDETGVGVGMLSRSLEKLgdS 156
                 5678899999999999*******************542 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1338.98
//
Query:       EPA05006.1  [L=235]
Description: hypothetical protein BG20_I1758 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0087   15.9   0.0      0.015   15.2   0.0    1.4  1  SprT-like  SprT-like family


Domain annotation for each model (and alignments):
>> SprT-like  SprT-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   8.1e-07     0.015      40      77 ..      64     115 ..       9     123 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 8.1e-07
   SprT-like  40 r..............atvrhhasIeLseklldsrsedrllntLaHElcHlal 77 
                 +                ++ ha I++s++l+ +  +  ++ +LaHE+ H + 
  EPA05006.1  64 SyefgilfartlpvfYDEKFHAVIQISAPLIAYGLKGTIHAILAHEFLHFLD 115
                 05555555555666667899*****************************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1470.31
//
Query:       EPA05007.1  [L=182]
Description: hypothetical protein BG20_I1757, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1174.21
//
Query:       EPA05008.1  [L=63]
Description: ribosomal protein S27a [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-19   70.0   6.2    1.7e-19   69.7   6.2    1.1  1  Ribosomal_S27    Ribosomal protein S27a
    0.00028   20.9   0.8    0.00028   20.9   0.8    1.1  1  DUF1451          Zinc-ribbon containing domain
     0.0084   16.2   2.5      0.014   15.6   2.5    1.4  1  Ribosomal_L37e   Ribosomal protein L37e
  ------ inclusion threshold ------
      0.011   15.5   1.3      0.014   15.1   1.3    1.3  1  Ephrin_rec_like  Putative ephrin-receptor like
       0.04   13.9   0.8      0.042   13.9   0.1    1.5  2  zinc_ribbon_11   Probable zinc-ribbon
      0.063   13.6   2.8       0.15   12.5   1.0    1.9  2  GFA              Glutathione-dependent formaldehyde-activatin
       0.33   10.9   5.5        1.7    8.6   3.9    2.2  2  Nudix_N_2        Nudix N-terminal
       0.45   10.0   6.6        3.2    7.3   0.5    2.2  2  zf-ribbon_3      zinc-ribbon domain
        3.4    7.3   4.9        2.9    7.6   0.3    2.2  2  zf_UBZ           Ubiquitin-Binding Zinc Finger


Domain annotation for each model (and alignments):
>> Ribosomal_S27  Ribosomal protein S27a
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.7   6.2   8.6e-23   1.7e-19       1      45 []      17      59 ..      17      59 .. 0.98

  Alignments for each domain:
  == domain 1  score: 69.7 bits;  conditional E-value: 8.6e-23
                   SSSSCCESSSSSEEESS-B-SS-S-TTSBEEECTTEEEESSTTTE CS
  Ribosomal_S27  1 vlkyYkvddsgkverlrkeCpreCGaGvfMAehkdRkyCGkCglT 45
                   v+ky+k+++ +k +r rk+C r CG+GvfM++hkdR++CGkCglT
     EPA05008.1 17 VYKYFKIEG-DKLTRGRKNCSR-CGKGVFMSKHKDRNTCGKCGLT 59
                   89*******.9***********.********************99 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.8   1.4e-07   0.00028     106     144 ..      24      62 ..      10      63 .] 0.93

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.4e-07
     DUF1451 106 sGevvglGtlvCekCgkelalkkteeippCpkCgateFr 144
                  G+  + G+ +C +Cgk + ++k +  ++C kCg teF+
  EPA05008.1  24 EGDKLTRGRKNCSRCGKGVFMSKHKDRNTCGKCGLTEFN 62 
                 699999********************************6 PP

>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   2.5   6.8e-06     0.014      18      38 ..      34      57 ..      25      62 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 6.8e-06
  Ribosomal_L37e 18 lCrrCgkrsy...hvqkktCascG 38
                     C rCgk  +   h  ++tC++cG
      EPA05008.1 34 NCSRCGKGVFmskHKDRNTCGKCG 57
                    6******999555677789****9 PP

>> Ephrin_rec_like  Putative ephrin-receptor like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   1.3   7.1e-06     0.014       5      35 ..      29      60 ..      25      63 .] 0.84

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 7.1e-06
  Ephrin_rec_like  5 ntgletCipCprgtYqn.eegqlsClaCPlgt 35
                       g + C+ C +g + +   ++++C +C+l+ 
       EPA05008.1 29 TRGRKNCSRCGKGVFMSkHKDRNTCGKCGLTE 60
                     568899*********9978999******9765 PP

>> zinc_ribbon_11  Probable zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   2.1e-05     0.042      92     123 ..      14      45 ..       4      51 .. 0.87
   2 ?   -1.4   0.1       1.1   2.1e+03      26      36 ..      48      58 ..      44      60 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.1e-05
  zinc_ribbon_11  92 lpkvrkwycvlcdedyegkklcpackdgvysv 123
                      p+v k++ +  d+   g+k c +c++gv+  
      EPA05008.1  14 SPNVYKYFKIEGDKLTRGRKNCSRCGKGVFMS 45 
                     588999***********************965 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.1
  zinc_ribbon_11 26 rqdvlcvscgc 36
                    ++  +c  cg 
      EPA05008.1 48 KDRNTCGKCGL 58
                    44567777775 PP

>> GFA  Glutathione-dependent formaldehyde-activating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.0   7.3e-05      0.15      29      66 ..       9      49 ..       1      54 [. 0.76
   2 ?    3.9   0.3     0.033        66      45      58 ..      46      59 ..      44      63 .] 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.3e-05
         GFA 29 lleg.elkeykktadsgnkvtr..sfCpeCgsplyseesaa 66
                  +g ++++yk+ + +g+k+tr  + C++Cg  ++++++++
  EPA05008.1  9 GKKGsSPNVYKYFKIEGDKLTRgrKNCSRCGKGVFMSKHKD 49
                45667888899888899999887799*********975554 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.033
         GFA 45 nkvtrsfCpeCgsp 58
                ++++r+ C +Cg +
  EPA05008.1 46 KHKDRNTCGKCGLT 59
                67899******976 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   1.3     0.014        28      19      29 ..      29      39 ..      20      40 .. 0.73
   2 ?    8.6   3.9   0.00086       1.7       3      31 ..      35      59 ..      33      61 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.014
                SS-EEEETTTT CS
   Nudix_N_2 19 nreRlvCpaCg 29
                +r R  C++Cg
  EPA05008.1 29 TRGRKNCSRCG 39
                46688899998 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00086
                -TTT--B-EEE--TT-SS-EEEETTTTEE CS
   Nudix_N_2  3 CsqCGtpvelripdgDnreRlvCpaCgti 31
                Cs CG+ v +      ++ R +C +Cg +
  EPA05008.1 35 CSRCGKGVFMSK----HKDRNTCGKCGLT 59
                9****9987776....899*******975 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.5    0.0016       3.2       3      10 ..      33      40 ..      25      42 .. 0.63
   2 ?    5.2   6.9    0.0074        15       3      24 ..      33      58 ..      31      59 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0016
  zf-ribbon_3  3 vrCPnCGa 10
                 ++C++CG+
   EPA05008.1 33 KNCSRCGK 40
                 35666665 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0074
  zf-ribbon_3  3 vrCPnCGa.p.ls..sddnvCpyCGt 24
                 ++C++CG+ +  s  +d n+C +CG 
   EPA05008.1 33 KNCSRCGKgVfMSkhKDRNTCGKCGL 58
                 68*****9986663369999****95 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.3    0.0014       2.9       4      12 ..      34      42 ..      31      49 .. 0.81
   2 ?    2.0   0.6     0.079   1.6e+02       3       9 ..      51      57 ..      49      59 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0014
      zf_UBZ  4 lCerCgkei 12
                 C+rCgk +
  EPA05008.1 34 NCSRCGKGV 42
                6*****976 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.079
      zf_UBZ  3 ylCerCg 9 
                 +C +Cg
  EPA05008.1 51 NTCGKCG 57
                69****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.41u 0.30s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 416.03
//
Query:       EPA05009.1  [L=118]
Description: hypothetical protein BG20_I1759 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 743.04
//
Query:       EPA05010.1  [L=145]
Description: acetyltransferase, GNAT family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.6e-19   68.8   0.0    5.4e-19   68.6   0.0    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    1.1e-14   54.5   0.0    1.3e-14   54.2   0.0    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    1.5e-12   47.7   0.1    2.4e-12   47.1   0.1    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    3.6e-06   27.1   0.0    4.5e-06   26.8   0.0    1.2  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
     0.0022   18.0   0.0      0.096   12.7   0.0    2.4  2  FR47             FR47-like protein
     0.0032   17.6   0.0      0.004   17.3   0.0    1.2  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
     0.0051   16.9   0.0     0.0079   16.3   0.0    1.3  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
  ------ inclusion threshold ------
       0.17   12.1   2.8       0.53   10.5   0.1    2.4  2  CdiA_C           Contact-dependent growth inhibition CdiA C-t


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.6   0.0   2.4e-22   5.4e-19      16     117 .]      32     133 ..      12     133 .. 0.85

  Alignments for each domain:
  == domain 1  score: 68.6 bits;  conditional E-value: 2.4e-22
                     HHHHHHHHHHHHHHSTTCEEEEEEETTEEEEEEEEEEEET...TSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTEHH CS
  Acetyltransf_1  16 nedaseeefeesfsleaegllvaeedgeliGfisllkipd...ekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlaveednda 107
                      +++ e +fe++ s+++  + va  dg+++G  +ll+ +      g+v++ie+++V+++y+++G+G + +e+l+++a+++g++k  l++    d 
      EPA05010.1  32 SNEKAEKIFEKINSNPDHIIAVAVLDGKIVGSTTLLIETKfihKGGKVGHIEDVVVDKKYQKNGIGEKIIEHLLKIAKDNGCYKTILDC---TDE 123
                     4455556677777777777777*********************99*************************************7767866...455 PP

                     HHHHHHHTTE CS
  Acetyltransf_1 108 airlYeklGF 117
                       ++YeklGF
      EPA05010.1 124 VKPFYEKLGF 133
                     59*******9 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.2   0.0   5.9e-18   1.3e-14      20     109 ..      37     136 ..      21     144 .. 0.86

  Alignments for each domain:
  == domain 1  score: 54.2 bits;  conditional E-value: 5.9e-18
  Acetyltransf_10  20 ealreri.eegealllvaeeggkivGviel.rdgs.........hisllfVdpeyrgqGigkaLleaveeeaekdgikleltvnaspyavpfYe 102
                      e++ e+i +++++++ va  +gkivG  +l  +++         hi+ ++Vd++y+++Gig++++e++++ a+++g   ++ ++ +++ +pfYe
       EPA05010.1  37 EKIFEKInSNPDHIIAVAVLDGKIVGSTTLlIETKfihkggkvgHIEDVVVDKKYQKNGIGEKIIEHLLKIAKDNGCY-KTILDCTDEVKPFYE 129
                      4555566459******************998888889***********************************666555.*************** PP

  Acetyltransf_10 103 klGFkav 109
                      klGFk  
       EPA05010.1 130 KLGFKHN 136
                      ****975 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   0.1   1.1e-15   2.4e-12       2      75 ..      48     134 ..      46     135 .. 0.77

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 1.1e-15
                     TEEEEEEEETTEEEEEEEEEEES.........TCTEEEEE-GGGTTSSHHHHHHHH..TT...SEEEEEEEEE..THHHHHHHHHHTTEE CS
  Acetyltransf_7   2 kgevfVaeddgkivGfialslld.........aeitrlaVdpeyrgkGiGraLlea..ae...kgiileqlel..naekaikfYeklGFe 75 
                     ++ + Va  dgkivG   l ++          ++i+ ++Vd++y+++GiG +++e+  ++   +g+  +   l  ++ +  +fYeklGF+
      EPA05010.1  48 DHIIAVAVLDGKIVGSTTLLIETkfihkggkvGHIEDVVVDKKYQKNGIGEKIIEHllKIakdNGCYKT--ILdcTD-EVKPFYEKLGFK 134
                     5667899999*****9998888899999888777777******************86622457887633..222222.4567*******8 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.0     2e-09   4.5e-06       2     127 ..       6     135 ..       5     136 .. 0.71

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 2e-09
                     EEEE-GGG.HHHHHHHHHHHTT----H..HHHHHHHHHHT..TSEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEEEEE-CCGTTS-HHHH CS
  Acetyltransf_9   2 irelteed.ldevlellkyaFqdeespleeireyfrklle..esrvlgaedngelvgqlallplelnvpGktlkaagvtgVavapehrgrgvlsk 93 
                     ir+l++ed  +++l+ l+   + ++   e++++ f+k+ +  ++ + +a  +g++vg+ +ll  e ++  k  k++ + +V v+ +++++g+ +k
      EPA05010.1   6 IRKLQKEDlRNGFLSSLDSLRKASDISNEKAEKIFEKINSnpDHIIAVAVLDGKIVGSTTLLI-ETKFIHKGGKVGHIEDVVVDKKYQKNGIGEK 99 
                     566666663233333333333333333223445566666622456666666*******99986.55555566799******************** PP

                     HHHHHHHHHHHTT--EEEE--SSH..HHHHTTT-EE CS
  Acetyltransf_9  94 LlaraleemreegqplsllfPssi..piYrrfGyei 127
                     +++++l+ ++++g   ++l  + +  p+Y+++G+++
      EPA05010.1 100 IIEHLLKIAKDNGCYKTILDCTDEvkPFYEKLGFKH 135
                     *************9999999976556*******975 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.061   1.4e+02      63      76 ..      31      44 ..      27      49 .. 0.89
   2 !   12.7   0.0   4.3e-05     0.096      21      83 ..      79     139 ..      68     142 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.061
                TT-HHHHHHHHHHT CS
        FR47 63 asNtpsirlyeklG 76
                +sN+++++++ek++
  EPA05010.1 31 ISNEKAEKIFEKIN 44
                68**********98 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 4.3e-05
                 TSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHH.S-S-EEEEEETT-HHHHHHHHHHT-EEEEEE CS
        FR47  21 ggelgalqvlpehrrrGlgsrlvkalakeiae.rgktvllvvvasNtpsirlyeklGfekieet 83 
                 +g +  + v+++ ++ G g ++++ l k ia+ +g   +++  ++  +   +yeklGf+   + 
  EPA05010.1  79 VGHIEDVVVDKKYQKNGIGEKIIEHLLK-IAKdNGCYKTILDCTD--EVKPFYEKLGFKHNANA 139
                 599999********************97.5553777777665554..4578*******987655 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.8e-06     0.004      31     136 ..      30     135 ..       4     142 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.8e-06
  Acetyltransf_4  31 vssveefekflealdsekeyvflvae.sdrivGyaylg.qfkkrakdwka.elsvylaerdnnkeglgrelidaleqvlkeqni.enllaeiasp 121
                       s e++ek+ e+++s    +  va  +++ivG  +l  + k+  k +k+  ++  +++++ +k+g+g ++i++l +++k ++  +++l +    
      EPA05010.1  30 DISNEKAEKIFEKINSNPDHIIAVAVlDGKIVGSTTLLiETKFIHKGGKVgHIEDVVVDKKYQKNGIGEKIIEHLLKIAKDNGCyKTILDC---- 120
                     45789999******8777777788888*******99976666664444442455555579*******************777740444444.... PP

  Acetyltransf_4 122 nensiqfhkalGFel 136
                      ++ + f+++lGF+ 
      EPA05010.1 121 TDEVKPFYEKLGFKH 135
                     346788999999985 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   3.5e-06    0.0079      19      64 ..      74     120 ..      54     129 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.5e-06
  Acetyltransf_CG  19 vrkegvldfthTeVpeelrGkGiAkkLvkaalddareegl.kvvptC 64 
                       ++++v +++ ++V+++++  Gi++k++++ l+ a+++g  k ++ C
       EPA05010.1  74 HKGGKVGHIEDVVVDKKYQKNGIGEKIIEHLLKIAKDNGCyKTILDC 120
                      4667788999****************************964777666 PP

>> CdiA_C  Contact-dependent growth inhibition CdiA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.3      0.16   3.5e+02      47      75 ..      29      56 ..      22      79 .. 0.69
   2 ?   10.5   0.1   0.00024      0.53       7      46 ..      82     122 ..      81     136 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.16
      CdiA_C 47 sdlsieeikegieralkwpkkglkeliii 75
                sd+s e+ ++++e++  +p +++  + ++
  EPA05010.1 29 SDISNEKAEKIFEKINSNP-DHIIAVAVL 56
                6677777777777754443.455555555 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00024
      CdiA_C   7 inGevfDvKsptsgngkniisnilkkakk.Qaknivlnlrd 46 
                 i+ +v+D K  ++g g++ii+++lk ak+  +   +l+++d
  EPA05010.1  82 IEDVVVDKKYQKNGIGEKIIEHLLKIAKDnGCYKTILDCTD 122
                 8999*****99999999************999999***996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       739  (0.0412181); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1146.77
//
Query:       EPA05011.1  [L=444]
Description: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.9e-44  150.5   0.0    7.8e-44  149.5   0.0    1.5  2  PhosphMutase   2,3-bisphosphoglycerate-independent phosphogly
    2.3e-30  105.8   0.9    3.2e-30  105.3   0.9    1.0  1  Metalloenzyme  Metalloenzyme superfamily
    0.00077   19.1   0.0      0.023   14.3   0.0    2.1  2  Phosphodiest   Type I phosphodiesterase / nucleotide pyrophos


Domain annotation for each model (and alignments):
>> PhosphMutase  2,3-bisphosphoglycerate-independent phosphoglycerate mutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0         2   1.2e+04      36      45 ..      40      49 ..      36      50 .. 0.82
   2 !  149.5   0.0   1.3e-47   7.8e-44       1     170 []      58     249 ..      58     249 .. 0.96

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 2
                  ---HHHHHHH CS
  PhosphMutase 36 ytGRGplEAl 45
                   +G+ plEA+
    EPA05011.1 40 LNGKTPLEAA 49
                  5799*****8 PP

  == domain 2  score: 149.5 bits;  conditional E-value: 1.3e-47
                   HHTSEEEEEE-----------TCHHHHTT--.HHCH---HHHHHHHHTT----TT-EEEEEEEEEEC..TTCEEETTGGG-..-TTHHHHHHHT-EE CS
  PhosphMutase   1 AkkGetGlldtvpegiapgSdvAnlsilGyd.pkkyytGRGplEAlgiGlelkpgdvafRcnlvtvdeedgiiidrragri.steeakeLikalnee 95 
                   Ak+G++G + +v +giap+Sd+A++++lGy+  ++ y GRG++EA+g+G+++k+gd+a+R+n++t++ ++giiidrragr+ ++e+a+ ++k+++++
    EPA05011.1  58 AKNGVIGEVISVGKGIAPESDIAVFNMLGYKfHHDDYAGRGVIEAIGVGIDFKDGDLALRGNYATLN-DEGIIIDRRAGRHiEREDADGIAKEIEDQ 153
                   89*****************************66789******************************8.599*******9988*************** PP

                   E....TTEEEEEEE-STTEEEEEE......--S-B--S--..SSTTS...........------BS..SGGGHHHHHHHHHHHHHHHHHHHHSHHH CS
  PhosphMutase  96 l..e.egvevkfypgveyrhllvl......lsdkitdtdpphdkegk...........eikellpl.kseeaketaellnelieksqeiLedhpvN 170
                   +  + ++++v + p++++r+ + +      ls++it+tdp++ +++            +i+++lpl ++e+ak+ta+l+ne++e+s++i+++   N
    EPA05011.1 154 IkfSfPNTSVVVSPTIGHRVTVRIrtegekLSSQITNTDPAYARVDGmgiakavgdflRIEKCLPLdETENAKKTAKLVNEFTEQSTKIMKESSTN 249
                   **97799***********************************999999******************999999*******************98877 PP

>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.3   0.9   5.4e-34   3.2e-30       4     241 ..      25     432 ..      23     439 .. 0.95

  Alignments for each domain:
  == domain 1  score: 105.3 bits;  conditional E-value: 5.4e-34
                    EEEEETTBB----GGGTT...HHHS--HHHHHHHHH.......SEEEEEESSSTT----HHHHHHHH............................. CS
                    xxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................. RF
  Metalloenzyme   4 vlvvlDGlGeapadelna...ihvAktPtldkLkkeaPerwlikahgtavglpeddmgnsevgHlel............................. 67 
                    + v+lDG+G+ p  +ln+   ++ A+tPtldkL+k+       +  g+   + +++ + s+++ +++                             
     EPA05011.1  25 IYVLLDGVGDLPHPDLNGktpLEAANTPTLDKLAKN-------GVIGEVISVGKGIAPESDIAVFNMlgykfhhddyagrgvieaigvgidfkdgd 113
                    5689********************************.......899********************99**************************** PP

                    ................................................................................................ CS
                    ................................................................................................ RF
  Metalloenzyme  68 ................................................................................................ 67 
                                                                                                                    
     EPA05011.1 114 lalrgnyatlndegiiidrragrhieredadgiakeiedqikfsfpntsvvvsptighrvtvrirtegeklssqitntdpayarvdgmgiakavgd 209
                    ************************************************************************************************ PP

                    .........................................HHHHTT-----EEEEEE.EE-S---SSHHHHHT--EEEE--SHH........... CS
                    .........................................xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx........... RF
  Metalloenzyme  68 .........................................lrisetvkfahvtffwn.ggrsgyfnpleereeipsdtvitfdl........... 110
                                                             +ri+  +k    +++++ g+++++++p++e +e++  +++ + +           
     EPA05011.1 210 flriekclpldetenakktaklvnefteqstkimkesstnkKRINAKKKSLSCILLRDaGNKYPDVKPINEMYEMNFSCIVDMPVelgisevlkmk 305
                    *****************************************88988888888888776277899*****************999999********* PP

                    ....STT--HHHHHHHHHHHH.CC.-SEEEEEE-HHHHHHHTT-HHHHHHHHHHHHH.HHHHHHTTS-TTTEEEEEE-SSB--TTTSS........ CS
                    ....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Metalloenzyme 111 ....qpemkavevaekaldailsgkfdlvvvniknaDmvGHtgdleatiaaieaaDe.avkeildaieqvdgilvvtADHgnaedmvkrdkqplTs 201
                           ++++e+a+ a++a++    + ++v+ik +D+ GH+gd+ ++++ ie++D+   k +l++i+ ++  +v+ ADH+++   ++        
     EPA05011.1 306 gfaaGGLTDYEEKAKVAAKAMET--ENAIYVHIKGPDEFGHDGDAIGKMKNIEEIDNrFFKTLLENIDFNKVAIVISADHSTPCINKG-------- 391
                    ***9999**************55..59*****************************9568***************************9........ PP

                    -----EEEEEESTT----S--S.SHHHHTT-TTEEEEGGGH CS
                    xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
  Metalloenzyme 202 HtlepVPilivgkglapdkvke.gakfrekggLanvaatll 241
                    H+ +pVP+l+ gk +++d +++ +++ ++kg+++ +++  +
     EPA05011.1 392 HSDDPVPLLVSGKFIKNDGTTRmTENQAKKGSIGLIQGADV 432
                    ****************9999998888888999999987765 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.011        68       4      40 ..      27      69 ..      24      71 .. 0.76
   2 !   14.3   0.0   3.8e-06     0.023     157     238 ..     313     389 ..     228     427 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.011
                  EEETT-B....TTHHHHHG.S..TSHHHHHHHHHSEEESEEE-S CS
  Phosphodiest  4 islDGlr....adlldrla.e..llpnlaaLakegvsapnlrpv 40
                  ++lDG+     +dl  +   e   +p l++Lak+gv ++ +++v
    EPA05011.1 27 VLLDGVGdlphPDLNGKTPlEaaNTPTLDKLAKNGVIGE-VISV 69
                  667777666667776666666679************999.8775 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 3.8e-06
                   HHCHTHSHHHHHCTSSESEEEEEECCCHHHHHHH-TTSHHHHHHHHHHHHHHHHHHHHHHHTTGTTTEEEEEEES---EEEH CS
  Phosphodiest 157 ldaafakvvlekelekpdlllvyleetDtvgHkfGpdspevedalrrvDkaigdLlealderglsaetniilvSDHGmadvs 238
                    d ++++ v++k++e+ + ++v++ ++D +gH    d     ++++++D   +++++ l e+  +++++i++++DH    ++
    EPA05011.1 313 TDYEEKAKVAAKAMETENAIYVHIKGPDEFGHDG--DAIGKMKNIEEID---NRFFKTLLENIDFNKVAIVISADHSTPCIN 389
                   45566666777777999***************65..4444455555555...56666666666677**********988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       859  (0.0479112); expected 358.6 (0.02)
Passed bias filter:                      577  (0.0321825); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 3040.37
//
Query:       EPA05012.1  [L=146]
Description: hypothetical protein BG20_I1766 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-05   23.2   8.7    3.9e-05   22.7   8.7    1.1  1  MFS_1     Major Facilitator Superfamily
  ------ inclusion threshold ------
        0.2   12.2   3.4         13    6.3   4.2    2.9  2  DUF202    Domain of unknown function (DUF202)
        9.3    4.9   9.5        2.7    6.7   4.3    2.0  2  DUF2207   Predicted membrane protein (DUF2207)


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   8.7   6.5e-09   3.9e-05     198     317 ..       5     127 ..       2     144 .. 0.66

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 6.5e-09
       MFS_1 198 pawkallkdpvlwillialllfffgfsglltllplylqevlgls...glllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglal 293
                 + w+a+ +      l++++++ ++ ++++++ +p+  +  +  +   +   ++ +++++ + + ila l+  ls+r+g++++  +++++++++++g+a+
  EPA05012.1   5 K-WSAIASVG----LFAMFVGEMISIYYFMMDTPS--NLEFAVAfepA-PKILQFISIGVAPASILAALSFILSRRYGSKPIGSMIIAGGIILLIGMAY 95 
                 4.99999999....99*******************..66666664451.44444455555555555666777778888888888888888888888888 PP

       MFS_1 294 lavt..ssavllll......vlvliGfglgfv 317
                 + +   + ++ +++      +l+++G+   ++
  EPA05012.1  96 CYTLldKLTPTYIVdtviitPLLFMGVSIPVM 127
                 88886644445555644444555555533322 PP

>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   4.2    0.0021        13      25      63 ..      63      98 ..       7     103 .. 0.77
   2 ?    1.8   0.0     0.056   3.4e+02      13      30 ..     119     136 ..     114     144 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0021
      DUF202 25 lallrffltgepsalgkilglilivlgiltllvglvryl 63
                +al  f    ++  ++k++g ++i+ gi++l+  +++y 
  EPA05012.1 63 AALS-F--ILSRRYGSKPIGSMIIAGGIILLIGMAYCYT 98
                2222.2..223333469******************9996 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.056
      DUF202  13 WlRtslalialglallrf 30 
                 ++ +s+  +++g+ l+r+
  EPA05012.1 119 FMGVSIPVMVFGVILFRI 136
                 555677788888888886 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   4.3   0.00044       2.7     381     441 ..      47     107 ..       3     111 .. 0.86
   2 ?    1.5   0.3     0.016        97     216     244 ..     117     145 ..     107     146 .] 0.51

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.00044
     DUF2207 381 kklsalglgliilglilillallllvlllvfllilllillliaiivlllfsrllgrrteeG 441
                 k+l+++++g++ ++++++l ++l+  +++ +++ ++++ ++i++i ++++++ll+++t+ +
  EPA05012.1  47 KILQFISIGVAPASILAALSFILSRRYGSKPIGSMIIAGGIILLIGMAYCYTLLDKLTPTY 107
                 4577788888888888888888888888999999999999******************986 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.016
     DUF2207 216 lilllllllllliklllwkkygrepkvke 244
                 l+ +++++ ++++ ++l++ ++++pk+++
  EPA05012.1 117 LLFMGVSIPVMVFGVILFRINKKRPKKEY 145
                 22333444445555555555667777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       674  (0.0375927); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 933.10
//
Query:       EPA05013.1  [L=39]
Description: hypothetical protein BG20_I1563 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.016   15.1   0.1      0.016   15.1   0.1    1.0  1  GNVR        G-rich domain on putative tyrosine kinase
      0.048   13.8   0.1      0.049   13.8   0.1    1.1  1  CbtB        Probable cobalt transporter subunit (CbtB)
       0.86    9.0   3.4        1.1    8.6   3.4    1.2  1  UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit T


Domain annotation for each model (and alignments):
>> GNVR  G-rich domain on putative tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.1   2.7e-06     0.016      48      78 ..       5      35 ..       1      38 [. 0.86

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.7e-06
        GNVR 48 vvpekpvkPkkalivvlalllGlllgvalvl 78
                   ++p++ kk+++++ a+++G +++ ++ +
  EPA05013.1  5 KQYKEPMSGKKLFVIIGAVMIGTVVAGLVLF 35
                55678********************988876 PP

>> CbtB  Probable cobalt transporter subunit (CbtB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   8.1e-06     0.049       6      30 ..      12      36 ..       7      38 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.1e-06
        CbtB  6 saqrllqlvaAllLGlllvylvgfs 30
                s + l+++++A+++G+++++lv f 
  EPA05013.1 12 SGKKLFVIIGAVMIGTVVAGLVLFT 36
                678899****************996 PP

>> UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   3.4   0.00019       1.1      14      31 ..      17      34 ..      16      36 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00019
  UCR_Fe-S_N 14 FLyiATgavgaVGaaaaa 31
                F +i+++++g+V+a++++
  EPA05013.1 17 FVIIGAVMIGTVVAGLVL 34
                899************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       827  (0.0461264); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 254.28
//
Query:       EPA05014.1  [L=145]
Description: hypothetical protein BG20_I1562 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.2e-07   29.8   0.0      6e-07   29.5   0.0    1.1  1  Pyridox_ox_2    Pyridoxamine 5'-phosphate oxidase
    4.9e-06   26.6   0.0    7.5e-06   26.1   0.0    1.3  1  Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
  ------ inclusion threshold ------
       0.11   12.1   0.0       0.29   10.7   0.0    1.6  2  Pyrid_ox_like   Pyridoxamine 5'-phosphate oxidase like


Domain annotation for each model (and alignments):
>> Pyridox_ox_2  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.0     1e-10     6e-07       1     133 [.       6     129 ..       6     136 .. 0.76

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 1e-10
                   -HHHHHHHHHC-SE.EEEEEEE.TTEEEEEEEEEEEETTEEEEEEETTSHCCHCCCT--.ECEEEEEEEEEEE-SEGGEEEEEEEEEEEEEEEE--H CS
  Pyridox_ox_2   1 dreeilalLdegev.grlafvd.dgepvilPvnyvvdgdslyfhgakgsrlaaalrgap.vcvvvtevdglvlarsfnslnyrSVvvrGraeevtde 94 
                   d++ i+ +L+++++  rla+ +  g+pv++ + y ++++++y  ++k+++++ +l+++p v ++++  d+           y+ +  +G+a+ v  e
    EPA05014.1   6 DSQKIETILNDTKIpIRLACITsAGYPVVISLWYIMENGKIYCATQKKAKIVSYLKNNPtVGFEIAA-DN----PP-----YKGIRGYGQAKIV--E 90 
                   6788899999555439******7888******************************88888888886.66....44.....*************..5 PP

                   HHHHHHCCCHHHHHSTTTGGCSB.---CCCCCTEEEEEEE CS
  Pyridox_ox_2  95 eekaealellvekivpgrwenlr.pptrkelkatsvlrlk 133
                      + +l+ l++k++ ++  +l    +r +  ++  ++++
    EPA05014.1  91 SIGENILNILIDKYLGKKISTLSeFLKRNS-DTEVAIEIT 129
                   555567888999998888554442222222.223444555 PP

>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   1.3e-09   7.5e-06      15      85 ..      21      90 ..       5      91 .. 0.91

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 1.3e-09
                    EEEEEEETTSEEEEEEEEEEEETTTTEEEEEEETTSHHHHHHHHH-EEEEEEEETT.GSEEEEEEEEEEEES CS
  Putative_PNPOx 15 vvlATvdedGrPnvspvllkagdgrdgivfatnadsrklrnleenprvallfldde.lgrgvrieGtaelvs 85
                     +lA+++  G+P v  ++++  +g+  i+ at+++++ +  l++np v++ ++ d+  ++g+r +G+a++v+
      EPA05014.1 21 IRLACITSAGYPVVISLWYIMENGK--IYCATQKKAKIVSYLKNNPTVGFEIAADNpPYKGIRGYGQAKIVE 90
                    689**********************..*****************************9************997 PP

>> Pyrid_ox_like  Pyridoxamine 5'-phosphate oxidase like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.41   2.5e+03      48      63 ..       4      19 ..       2      34 .. 0.77
   2 ?   10.7   0.0   4.8e-05      0.29      38      86 ..      41      90 ..      36     107 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.41
  Pyrid_ox_like 48 kkdsdkvkeirkdsqv 63
                   k+ds+k++ i +d ++
     EPA05014.1  4 KTDSQKIETILNDTKI 19
                   6788888888888766 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 4.8e-05
  Pyrid_ox_like 38 eedgdlwfltkkdsdkvkeirkdsqvnlafsdeskkkyvsvs..Gtaevve 86
                    e+g++++ t+k+++ v+ ++++++v + ++  ++  y  ++  G+a++ve
     EPA05014.1 41 MENGKIYCATQKKAKIVSYLKNNPTVGFEIAA-DNPPYKGIRgyGQAKIVE 90
                   589************************99876.666676665115666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 969.79
//
Query:       EPA05015.1  [L=181]
Description: hypothetical protein BG20_I1571 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-35  121.0   2.5    5.1e-35  120.3   2.5    1.3  1  DUF1722   Protein of unknown function (DUF1722)


Domain annotation for each model (and alignments):
>> DUF1722  Protein of unknown function (DUF1722)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.3   2.5   2.9e-39   5.1e-35       1     116 [.      48     163 ..      48     164 .. 0.99

  Alignments for each domain:
  == domain 1  score: 120.3 bits;  conditional E-value: 2.9e-39
     DUF1722   1 KyllmahsqkeyrelgrlvanakkepleelaeeYeellmealskpatrkkhinvlqhilgyfkkklsaeekqelleliekYregkvplsvpltlLkhya 99 
                 Ky+lmah+q+e++ lg ++a++kk p++e+++eYe++l+ a+sk +t k+h+nv++hi+gyf k+l+++ekq + + +e+Yr gk++l ++l  ++ + 
  EPA05015.1  48 KYMLMAHDQNELKILGDIIASNKKIPFSEIIDEYENHLKLAMSKSPTTKTHTNVIMHIFGYFLKHLNRNEKQIFFDRLEQYRVGKTTLGKILFEINDVS 146
                 9************************************************************************************************** PP

     DUF1722 100 rkydneylleqtylnpy 116
                  ++dn+yl++qty+  y
  EPA05015.1 147 YRFDNTYLASQTYFLLY 163
                 **************766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       849  (0.0473534); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1157.28
//
Query:       EPA05016.1  [L=126]
Description: hypothetical protein BG20_I1570 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-25   90.1   0.0    1.7e-25   90.0   0.0    1.0  1  DNA_photolyase   DNA photolyase
  ------ inclusion threshold ------
      0.046   13.9   0.3      0.064   13.4   0.3    1.4  1  Cdc13_OB4_dimer  Cdc13 OB4 dimerization domain
      0.066   13.7   0.1         17    6.0   0.0    2.4  2  SPASM            Iron-sulfur cluster-binding domain


Domain annotation for each model (and alignments):
>> DNA_photolyase  DNA photolyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.0   0.0   2.8e-29   1.7e-25       2     118 ..       8     124 ..       7     126 .] 0.94

  Alignments for each domain:
  == domain 1  score: 90.0 bits;  conditional E-value: 2.8e-29
                     EEEESS---STT-HHHHHHHCTTSEEEEEEEE-HH..HHTCGS-CHHHHHHHHHHHHHHHHHHHHTT--EEEEESSHHHHHHHHHHHCTECEEEE CS
  DNA_photolyase   2 lvWfrrDlRlhDNpALaaAaasgepvipvfvldpe..kahklrvgaarvdfllesLadLdeeLrelgirLvvrrgdpadvlpelakelgasavva 94 
                     l+ frrDlRl+DN+ L +A++++++vip+f+ld +  +  +l+++  r++fl esL+dL+e+L ++  +L ++rg++++++++++ e++++ v++
      EPA05016.1   8 LFIFRRDLRLEDNTGLIYALKNSNEVIPCFILDIDilG--NLKKSRLRIKFLNESLKDLNEQLIKRKTNLRIFRGRSEEIIEKIILENKIDGVFL 100
                     677********************************543..44669************************************************** PP

                     E---SHHHHHHHHHHHHHHHHCTS CS
  DNA_photolyase  95 nreyepdererdeavkealrkagi 118
                     n +y+ +++  ++++k+++++++ 
      EPA05016.1 101 NGDYTKFAQLKENKIKKICNQKKY 124
                     *******************98876 PP

>> Cdc13_OB4_dimer  Cdc13 OB4 dimerization domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.3   1.1e-05     0.064      37      89 ..      27      81 ..       8      96 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.1e-05
                     ---T--B-GGG-EEEEEESHHHHHHHHS..SS---GGGCGGGBTSEEEEEEEE.. CS
  Cdc13_OB4_dimer 37 lilkkkvdpkeiLkveilGkenvnyFlg..deealedilraLvlktlkfrllrgk 89
                     l+ +++v p  iL ++ilG+ + +       +e l+d  ++L+++++++r++rg+
       EPA05016.1 27 LKNSNEVIPCFILDIDILGNLKKSRLRIkfLNESLKDLNEQLIKRKTNLRIFRGR 81
                     66789999***********7554443322247999*****************985 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0    0.0029        17      15      41 ..      32      53 ..      22      88 .. 0.76
   2 ?    5.8   0.0    0.0032        19      30      50 ..     105     125 ..      94     126 .] 0.86

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0029
       SPASM 15 dVvpCcvdkktyvee.lklGnireesle 41
                +V+pC++       +  +lGn+++  l+
  EPA05016.1 32 EVIPCFIL------DiDILGNLKKSRLR 53
                8****666......33689999887765 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0032
       SPASM  30 lklGnireesleeIwnseeyq 50 
                  k+  ++e+++++I+n+++y+
  EPA05016.1 105 TKFAQLKENKIKKICNQKKYR 125
                 688999************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       955  (0.0532657); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.53
# Mc/sec: 720.30
//
Query:       EPA05017.1  [L=318]
Description: FAD binding domain of DNA photolyase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.2e-79  264.4   3.0    7.3e-79  264.0   3.0    1.2  1  FAD_binding_7  FAD binding domain of DNA photolyase
     0.0056   16.4   0.0       0.01   15.6   0.0    1.4  1  OprF           OprF membrane domain


Domain annotation for each model (and alignments):
>> FAD_binding_7  FAD binding domain of DNA photolyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  264.0   3.0   8.1e-83   7.3e-79       2     196 ..     126     310 ..     125     316 .. 0.95

  Alignments for each domain:
  == domain 1  score: 264.0 bits;  conditional E-value: 8.1e-83
                    HHHHHHHHHHHHHHHCSTTTTTSSTTGCCTT------HH.HHHHHHTT-SS-HHHHHHHHHHHHHS---HHHHHHHHHHHCTTT-B-HHHHHHHHH CS
  FAD_binding_7   2 lreLlwrefyyallaaepelaeralkekfdripweeseeekleaWkeGrTGfPlvDAamrqLretGwmhnrlRmivasFltkdLlidWregeevFe 97 
                    +++L+wref++++l+++p+ +++++k+kf++ipw+++++ +++ W++G+TGfP+vDA+mrqL++tG+mhnr+RmivasFltkd++idW+ ge++F+
     EPA05017.1 126 INQLYWREFFTYVLHHFPNSKSETFKKKFRKIPWSTNKQ-EYHTWCKGETGFPIVDAGMRQLNKTGFMHNRVRMIVASFLTKDMHIDWKLGERYFA 220
                    589*******************************88866.6******************************************************* PP

                    HH-TT--CCHHHHHHHHHCT-STTS-STT----CCCCHHHCSTT-HHHHHH-GGGTTS-HHHHT-GGGSGCHHHHHHT--TTTSS---SS-HHHHH CS
  FAD_binding_7  98 ellvDadlasnagnwqwlagtgadaapafrifnpvkqgkkfDpegeyirrwvpeLkklpakyihepwkapaeeqkkagvvlgkdYpkpivdhkear 193
                    e+lvD+d+a+nagnwqw+a+tg+da ++frifnp+ q++kfD++++yi++wvpeL++l+ k+ih+ wk             g +Ypkpi++hk ++
     EPA05017.1 221 EKLVDYDPAVNAGNWQWAASTGCDAVQYFRIFNPWIQQEKFDSNCNYIKKWVPELETLQPKHIHNLWKK---------YPEGLTYPKPILNHKIES 307
                    *******************************************************************53.........456899*********998 PP

                    HHH CS
  FAD_binding_7 194 kra 196
                    +++
     EPA05017.1 308 NKT 310
                    876 PP

>> OprF  OprF membrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.1e-06      0.01      74     176 ..     140     243 ..     105     247 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.1e-06
                 EE-------------EEEE.EEEEEEEE-S-SSSEEEEEEEEEEEEEEEEEE-SS-EEEEEEEEEEEEEEEEEESSSSEEEEEEEEEEEE------EEE CS
        OprF  74 vndvrstdetgskkvkGdk.tsldalyhfgtaGdalrpyveaGlahqsitnvadgssGrdqstlanvGaGvkyyftenlyaragveadykldkgdteya 171
                  +   s+ et +kk +    ++ +  yh    G++  p v+aG+ + + t   ++      +++++    + + + e ++a   v+ d +++ g++++a
  EPA05017.1 140 HHFPNSKSETFKKKFRKIPwSTNKQEYHTWCKGETGFPIVDAGMRQLNKTGFMHNRVRMIVASFLTKDMHIDWKLGERYFAEKLVDYDPAVNAGNWQWA 238
                 55556677777777766541445678************************99888887788899999******************************** PP

                 EEEEE CS
        OprF 172 alvGl 176
                 a+ G 
  EPA05017.1 239 ASTGC 243
                 *9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       861  (0.0480228); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 1843.37
//
Query:       EPA05018.1  [L=120]
Description: hypothetical protein BG20_I1564 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 798.67
//
Query:       EPA05019.1  [L=207]
Description: HD domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.8e-17   61.6   0.1    1.1e-16   61.1   0.1    1.3  1  HD        HD domain
  ------ inclusion threshold ------
      0.051   13.8   0.2       0.13   12.5   0.0    1.7  2  VP9       VP9 protein
      0.063   12.6   0.6       0.12   11.7   0.5    1.6  1  DUF4917   Domain of unknown function (DUF4917)
       0.12   12.2   0.1       0.31   10.8   0.1    1.7  1  ClpS      ATP-dependent Clp protease adaptor protein ClpS


Domain annotation for each model (and alignments):
>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.1   0.1   2.6e-20   1.1e-16       2     121 ..      23     125 ..      22     126 .. 0.87

  Alignments for each domain:
  == domain 1  score: 61.1 bits;  conditional E-value: 2.6e-20
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHTTCCHHHHHHH CS
          HD   2 leHsleVaklarrlaedlgeeedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgld...ledvaklirehheswegkkr 97 
                 +eH ++V k a+r++++++   ++ l+l a LlHDi+ +p +d+ +         +  ++ +ae+ ++++k +++    +++++++ir h++s + +  
  EPA05019.1  23 FEHVMRVFKNAQRICKKEK--VNEKLVLSAVLLHDIVSYPKSDKRS---------KLSSVKSAEKSKKILKKFDYTkqeIQIISDAIRDHSFSQNKT-- 108
                 79*****************..*********************9333.........455666777777776666555778***************966.. PP

                 HHHHHCCTSCHHHHHHHHHHHHHH CS
          HD  98 prglaerqlslearivklaDrlaa 121
                        ++++e +i+++aDrl+a
  EPA05019.1 109 -------PKTIEGKILQDADRLDA 125
                 .......***************98 PP

>> VP9  VP9 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.8e-05      0.13       3      34 ..       9      40 ..       7      52 .. 0.81
   2 ?   -3.6   0.0       2.9   1.3e+04      14      25 ..      74      85 ..      68      89 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.8e-05
         VP9  3 vkssflliGektekYEevlltfeavesvrkSe 34
                 +  +l++ +    +E+v+ +f+  +++ k e
  EPA05019.1  9 NEVCILMSNDTAHDFEHVMRVFKNAQRICKKE 40
                55568899999*****************9877 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2.9
         VP9 14 tekYEevlltfe 25
                 ek  ++l+ f+
  EPA05019.1 74 AEKSKKILKKFD 85
                566667777776 PP

>> DUF4917  Domain of unknown function (DUF4917)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.5   2.7e-05      0.12      29     109 ..       6      84 ..       2      90 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.7e-05
     DUF4917  29 llkddvqelfqsldtsDfelvlkvlwqaskvnkslqipddrleqaynklreaLiqtvrnvhpeydevsdhleeiykflkkf 109
                  lk++v  l+ +  ++Dfe+v++v ++a+++ k+ +++++ l   ++ l++ +     +   + + v+ + e+ +k lkkf
  EPA05019.1   6 SLKNEVCILMSNDTAHDFEHVMRVFKNAQRICKKEKVNEK-LVLSAVLLHDIVSYPKSDKRSKLSSVK-SAEKSKKILKKF 84 
                 5777888888888889****************99887654.445555566655555555555555543.334455555555 PP

>> ClpS  ATP-dependent Clp protease adaptor protein ClpS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1     7e-05      0.31       7      30 ..      12      35 ..       8      48 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 7e-05
                EEEEES-S-S-HHHHHHHHHHHSS CS
        ClpS  7 kvvLlNDdvttmefVvevLqkvfg 30
                ++++ ND  + +e+V++v++++ +
  EPA05019.1 12 CILMSNDTAHDFEHVMRVFKNAQR 35
                7899***************87655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1494  (0.0833287); expected 358.6 (0.02)
Passed bias filter:                      581  (0.0324056); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1335.08
//
Query:       EPA05020.1  [L=447]
Description: monoamine oxidase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.4e-26   91.1   0.0    1.1e-25   90.8   0.0    1.1  1  Amino_oxidase   Flavin containing amine oxidoreductase
    5.5e-11   42.5   0.0    9.8e-11   41.7   0.0    1.4  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    1.7e-05   24.6   0.1      0.017   14.8   0.2    2.1  2  DAO             FAD dependent oxidoreductase
    7.5e-05   22.1   0.5      0.011   14.9   0.0    2.4  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
     0.0002   21.9   1.3      0.041   14.4   0.0    2.9  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    0.00021   20.5   0.4      0.018   14.1   0.7    2.1  2  FAD_binding_2   FAD binding domain
     0.0012   17.5   1.2      0.054   12.0   0.1    2.1  2  GDI             GDP dissociation inhibitor
     0.0019   17.7   0.0      0.055   12.8   0.0    2.2  2  FAD_oxidored    FAD dependent oxidoreductase
     0.0021   17.4   0.7       0.11   11.7   0.1    2.6  3  Thi4            Thi4 family
     0.0027   17.0   0.1     0.0042   16.4   0.1    1.2  1  FAD_binding_3   FAD binding domain
     0.0052   15.5   0.2        1.1    7.9   0.2    2.2  2  HI0933_like     HI0933-like protein
  ------ inclusion threshold ------
      0.024   14.2   1.1       0.05   13.2   0.2    2.0  2  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
      0.029   13.2   0.0        1.6    7.4   0.0    2.1  2  MCRA            MCRA family
      0.066   12.3   1.1        2.8    6.9   0.1    2.2  2  GIDA            Glucose inhibited division protein A


Domain annotation for each model (and alignments):
>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.8   0.0   8.9e-29   1.1e-25       1     444 [.      12     431 ..      12     434 .. 0.79

  Alignments for each domain:
  == domain 1  score: 90.8 bits;  conditional E-value: 8.9e-29
                    HHHHHHHHHHHHTTEEEEEEESSSSSBTTS-EEEETTEEEESS--EEET.TTHHHHHHHHHTTCCCCEEEESCCGCEEEEETTEECCTTEECHHHH CS
  Amino_oxidase   1 laGLaaArqLlsaGfdVtvlEardrvGGRirtvrsdGylielGamwftg.agnpllellkelgledslslpdpgapkrvlskggrefpgdlspvpa 95 
                    + GL++ + L++ G+ V ++E ++ +GGR  + ++ ++++++G+++++  + ++++++lk +g+e++l l   + +  + s      ++ +++ p+
     EPA05020.1  12 IGGLTTGTLLANEGYAVKIVEKNSKLGGRTVSMKFRNHILDNGFHIMPFyKKSAIFTVLKLVGIENRLNLTTVD-KISFFS------DTGFHKYPK 100
                    68****************************************************************99976666.444444......8889999** PP

                    HHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHTSTTTTCBHHHHTCC CS
  Amino_oxidase  96 ewealleqgalsaellsleeklrlgleallqktldeldldskslaesleelgrrepgdvevwdrliepelfaklefasglfagdpselsaklalpl 191
                    ++ +ll+      +l+ ++++++l   +l+      ++ +s +  es+  l+       + ++  ++p        ++++f++ +   +a ++  +
     EPA05020.1 101 GMGDLLR-----LSLIPFKSRISLLKILLP------MAFASMQKTESRDNLSL------TEVTKNLDP-------KSNAFFEAVC--MLAFADSSE 170
                    *******.....567778888888888888......33333333333222222......334444444.......5666666633..666666666 PP

                    CCHHHHHTSCCCEE..............TTHTHHHHHHHHH..TTTTEEEETSEEEEEEEEETTC.EEEEETTSTEEEESEEEE-S-HHHHHSSEE CS
  Amino_oxidase 192 lwelegfggslllp..............rgGlsqlpealae..elrgldirlntrVkeikregdg.vtvtledgevveaDaVvvTvplgvlkailf 270
                    +  l +f++ ++++              +gG++++ + la+  ++++++i lnt Vk+i  e++   ++ + d + ++   Vvv  p + + ++lf
     EPA05020.1 171 HISLGEFARTIIRAnpfkggtsefaypvDGGYDSISKVLANfiQEKNGEINLNTSVKRIVIENSVvTGIVTFDDKLIKTNCVVVSYPAYLALNELF 266
                    6666666666666666666777778999*********************************7777466777788989******************* PP

                    ESCC.SHHHHHHHHHS.EEEEEEEEEEEESSGGSGCSTSECE..CECCCEEETTTEEEEECCECCCSTTTEEEEEEEEECHHHHHHHTTS-HHHHH CS
  Amino_oxidase 271 sPpl.pdekaeairnl.gfgsvnkvilefdrkfwednalgqg..vlvseltttlgeafissdfpsrappgkglvllvyvggdaaneleslsdeelv 362
                    +     d+  + i++l + +sv+ v+++   k  ++     +   +v++++ t g  fis+  ps +p g +l    ++ g+    l+  +++ ++
     EPA05020.1 267 EKNIiDDKFIKKIDRLnKKTSVVEVHFALNSKL-DS----RQvvFPVGDNYVTKGIFFISNIAPSVSPLGEHL----MITGTPVSSLVAEDPQKIK 353
                    **999***************************9.22....23457**************************99....3334444444333666666 PP

                    HHHHHHHHHHHTGTSSTCSEEEEEECCTETTT.SSSEEE.B.TTHHHHHHHHHHCHHCSTTEEE.SGGGCTTTTTS.HHHHHHHH CS
  Amino_oxidase 363 qavlrdLrklfgeevpepkatlvtrWhtdpla.rgsysyvs.vgpghedydplakpegdprlffAGehtsreypgt.vegAilSG 444
                    q v ++ +++   ++ +p+ t    W   p+a + + s+v+ +g  ++   p++ p g+++lff G++t    +g  ++ A +S 
     EPA05020.1 354 QIVDDMKKEI---SIIYPNFTSSLIWE-RPMAwNLVESVVKePGMVWKSKMPHQIP-GIKGLFFVGDSTV--SYGIgTDSAAHSS 431
                    6666666666...379**********9.9999766666655134477777777777.***********99..6677788887775 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.7   0.0   7.7e-14   9.8e-11       1      53 [.       7      59 ..       7      71 .. 0.92

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 7.7e-14
                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECETTCEECTS---EE CS
  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyevpgvrvdygahifh 53
                   I+G+G++Gl++  lLa++g+ v ++ek+++lGGr  s ++ ++++d g hi+ 
     EPA05020.1  7 IIGTGIGGLTTGTLLANEGYAVKIVEKNSKLGGRTVSMKFRNHILDNGFHIMP 59
                   9*************************************************975 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.2   1.3e-05     0.017       2      35 ..       5      39 ..       4      47 .. 0.92
   2 !    7.7   0.0    0.0018       2.3     152     299 ..     209     370 ..     190     394 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.3e-05
                EEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSS CS
         DAO  2 vviiGGGiiGlstAyeLarrg..Vtllekgdiagsg 35
                ++iiG Gi Gl+t   La +g  V ++ek++ +g g
  EPA05020.1  5 ICIIGTGIGGLTTGTLLANEGyaVKIVEKNSKLG-G 39
                89****************99**********9999.4 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0018
                 HHHHHHHTT-EEEESECEEEEEEEETCEEEEE..EECTEEEEEEEEEEE--GGGHHHH.HTT.CTT.........TSEEEE......EEEEEEEEEECC CS
         DAO 152 laraaealGveilegtevtgleeedgkvwgve..rttpgendaadavVnaaGawsdll.gll.kel.........dlpisp......vrgqvlvlkpls 231
                 la+ ++++ +ei ++t v+++  e+  v+g+   +       + ++vV++  a+   l +l+ k++         d           v   +++l   +
  EPA05020.1 209 LANFIQEKNGEINLNTSVKRIVIENSVVTGIVtfD---DKLIKTNCVVVSYPAYLA-LnELFeKNIiddkfikkiD----RlnkktsVVEVHFAL---N 296
                 7888999*************977788889993322...22234599********75.2344464445544443331....233222255555555...4 PP

                 THSTGSGCSEEEEEEEETTTTEEEEEE.......TTSEEEEEESSE.EETTCSSTSCSHHHHHHHHHHHHHHSGGG CS
         DAO 232 eklvspaailpvpetdddgrgvyvtpr.......kdgrvlvGgtad.eesgdddpevdeedidellealrklfPql 299
                  kl+s++ ++pv   +   +g++++         ++ ++++ gt++    ++d p+   + +d++ ++++ ++P++
  EPA05020.1 297 SKLDSRQVVFPVG-DNYVTKGIFFISNiapsvspLGEHLMITGTPVsSLVAED-PQKIKQIVDDMKKEISIIYPNF 370
                 4556778999999.677778888888667778877677888888753333333.4666677777777777777775 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0     9e-06     0.011       2      41 ..       4      42 ..       3      87 .. 0.80
   2 ?    4.9   0.1      0.01        13     184     234 ..     204     255 ..     197     256 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 9e-06
                 SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcl 41
                  +++iG G++Gl++ + la+ g+ v +ve ++  l+g+ +
   EPA05020.1  4 PICIIGTGIGGLTTGTLLANEGYAVKIVE-KNSKLGGRTV 42
                 589*************************4.4444444443 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.01
                  HHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEE.EEETTSCEEEESEEEE- CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx RF
  Pyr_redox_2 184 elsaaleealekeGvevklgtsvkeidgngekle.vvledgeeidadlvvva 234
                  ++s+ l++ +++++ e+ l+tsvk+i  +++ ++  v+ d + i++ +vvv+
   EPA05020.1 204 SISKVLANFIQEKNGEINLNTSVKRIVIENSVVTgIVTFDDKLIKTNCVVVS 255
                  688889999999999***********99999888999999999*******97 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   3.2e-05     0.041       2      60 ..       5      60 ..       4      71 .. 0.92
   2 ?    5.2   0.1     0.025        32      41      78 ..     204     241 ..     201     244 .. 0.85
   3 ?   -2.7   0.0         7     9e+03      19      33 ..     280     294 ..     274     303 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.2e-05
                EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECS CS
   Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievlln 60
                + ++G G  gl  ++ la+ g  V++ve ++kl    ++++s  +++++ +ng +++  
  EPA05020.1  5 ICIIGTGIGGLTTGTLLANEGYAVKIVEKNSKLG---GRTVSMKFRNHILDNGFHIMPF 60
                679*******************************...999***9999999999998865 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.025
                 HHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEEE CS
   Pyr_redox  41 easkilqeklekngievllntkveeiegsedgvesvkl 78 
                  +sk+l++ +++++ e+ lnt+v++i+ +++ v+++++
  EPA05020.1 204 SISKVLANFIQEKNGEINLNTSVKRIVIENSVVTGIVT 241
                 5899999********************66655888765 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 7
                 HHTTSEEEEEESSSS CS
   Pyr_redox  19 aelgkkVtvversdk 33 
                  +l+kk++vve +  
  EPA05020.1 280 DRLNKKTSVVEVHFA 294
                 467777777776544 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.7   1.4e-05     0.018       4      39 ..       7      42 ..       5      44 .. 0.94
   2 ?    4.0   0.0     0.017        22     141     182 ..     203     244 ..     145     261 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.4e-05
                   EE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGG CS
  FAD_binding_2  4 ViGsGlAGLaAAleaaeaGlkvavvekeqefggata 39
                   +iG+G++GL+ ++ +a++G  v +vek ++ gg t+
     EPA05020.1  7 IIGTGIGGLTTGTLLANEGYAVKIVEKNSKLGGRTV 42
                   9*******************************9876 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.017
                    HHHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEET CS
  FAD_binding_2 141 hallarlvesarkagvdfqerteadeLivedgrvtGavvenp 182
                      + ++l++ +++ + ++  +t+++++++e+  vtG+v  ++
     EPA05020.1 203 DSISKVLANFIQEKNGEINLNTSVKRIVIENSVVTGIVTFDD 244
                    5677788888888889*********************97654 PP

>> GDI  GDP dissociation inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.3   0.1    0.0091        12       7      49 ..       5      47 ..       3      56 .. 0.91
   2 !   12.0   0.1   4.3e-05     0.054     219     354 ..     190     338 ..     170     364 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0091
                EEEE--SHHHHHHHHHHHHTT--EEEE-SSSSSCGGG-EE-HH CS
         GDI  7 vivlGtGlkecilsGllsvdgkkvlhldrndyyGgesasltle 49
                + ++GtG+       ll+ +g  v  +++n+  Gg + s+++ 
  EPA05020.1  5 ICIIGTGIGGLTTGTLLANEGYAVKIVEKNSKLGGRTVSMKFR 47
                5699***********************************9865 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 4.3e-05
                 SS-SEEEETT.-TTHHHHHHHHHHHHTT-EEETS--ECEEEE-TTS-EEEEEE.TTEEEEECEE.EE-GGG-C............CCEEEEEEEEEEEE CS
         GDI 219 gkspylyply.GlGelpqgfarlsaiyGGtymlnkpvdevvldedgkvvGvks.eeevakakkv.icdpsylp............ekvrkvgkviraic 302
                 g s + yp+  G   + + +a +     G   ln++v+ +v+ e+++v+G+ + +++++k++ v ++ p+yl             + ++k+ ++ +  +
  EPA05020.1 190 GTSEFAYPVDgGYDSISKVLANFIQEKNGEINLNTSVKRIVI-ENSVVTGIVTfDDKLIKTNCVvVSYPAYLAlnelfekniiddKFIKKIDRLNKKTS 287
                 57999999972578899*************************.999****988799999998751678***9888888666666333788888888888 PP

                 EESS--TTSTT-SSEEEEE-GGGCTSSS-EEEEEEEGGGTSS-TT-EEEEEE CS
         GDI 303 ilshpipntddadsvqiiipqkqlgrksdiyvalvssahnvaakgkylaivs 354
                 +++   +  ++ ds q++ p       + i+  +   a  v++ g++l i  
  EPA05020.1 288 VVEVHFALNSKLDSRQVVFPVGDNYVTKGIFF-ISNIAPSVSPLGEHLMITG 338
                 88888888888899999988755444444432.2233455666666666655 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   4.3e-05     0.055       2      40 ..       5      43 ..       4      56 .. 0.93
   2 ?    2.5   0.0     0.059        76      90     129 ..     206     245 ..     173     253 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.3e-05
  FAD_oxidored  2 vvVvGGgpaGvaAAiaAaraGakvlLveergvlGGllts 40
                  ++++G g++G++     a++G  v +ve++  lGG + s
    EPA05020.1  5 ICIIGTGIGGLTTGTLLANEGYAVKIVEKNSKLGGRTVS 43
                  89*********************************9876 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.059
  FAD_oxidored  90 kavleemlaeagvtvllntrlvevekegkriesvtveske 129
                    +vl ++++e++ ++ lnt +++++ e+  ++++++ +++
    EPA05020.1 206 SKVLANFIQEKNGEINLNTSVKRIVIENSVVTGIVTFDDK 245
                   689999*********************988***9998754 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.1   8.8e-05      0.11      19      57 ..       4      41 ..       1      54 [. 0.88
   2 ?    3.2   0.0     0.035        45      97     137 ..     202     241 ..     187     272 .. 0.86
   3 ?   -2.4   0.0       1.8   2.3e+03      92     136 ..     312     356 ..     306     362 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8.8e-05
                EEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTT CS
        Thi4 19 DvvivGaGssGLtaayylakkpdlkvailersvspGGGa 57
                 + i+G+G  GLt++  la++ +  v i+e++  +GG +
  EPA05020.1  4 PICIIGTGIGGLTTGTLLANE-GYAVKIVEKNSKLGGRT 41
                689******************.**********9999965 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.035
                 HHHHHHHHHHHHTSTTEEEEESEEEEEEEEETBTEEEEEEE CS
        Thi4  97 alftstllskvlqlanvkllnavaveDlivregegvaGvvi 137
                    +s++l++ +q  n  +   ++v  +++ + + v+G+v+
  EPA05020.1 202 YDSISKVLANFIQEKNGEINLNTSVKRIVIEN-SVVTGIVT 241
                 56789**************99********999.999**998 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.8
                 EESEHHHHHHHHHHHHHTSTTEEEEESEEEEEEEEETBTEEEEEE CS
        Thi4  92 vvkdaalftstllskvlqlanvkllnavaveDlivregegvaGvv 136
                 +v + + f+s+++  v  l +  +++++ v  l+  + ++++ +v
  EPA05020.1 312 YVTKGIFFISNIAPSVSPLGEHLMITGTPVSSLVAEDPQKIKQIV 356
                 577888999999999999999999999999999999888888777 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   3.3e-06    0.0042       4      35 ..       5      36 ..       3      53 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.3e-06
                   EEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
  FAD_binding_3  4 VlIVGaGpaGlmlallLseaGvrvvlvekrst 35
                   ++I+G+G  Gl++++lL++ G  v +vek s+
     EPA05020.1  5 ICIIGTGIGGLTTGTLLANEGYAVKIVEKNSK 36
                   79***************************986 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.2   0.00083       1.1       3      36 ..       5      38 ..       3      44 .. 0.92
   2 !    5.3   0.0    0.0051       6.5     101     161 ..     195     255 ..     183     258 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00083
                 EEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
  HI0933_like  3 viviGgGaAGlmaAisaakrgkrVlllekakklg 36
                 + +iG G  Gl +   +a++g  V ++ek++klg
   EPA05020.1  5 ICIIGTGIGGLTTGTLLANEGYAVKIVEKNSKLG 38
                 78******************************98 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0051
                  EEETT.-CHHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE- CS
  HI0933_like 101 lFpvsdkaedivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlA 161
                   +pv+    +i ++l + ++e++ +++l+t+vk++  e++ +  + t +++ ++++ +v++
   EPA05020.1 195 AYPVDGGYDSISKVLANFIQEKNGEINLNTSVKRIVIENSVVTGIVTFDDKLIKTNCVVVS 255
                  5888888899*************************99999999998878899999988886 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   3.9e-05      0.05       3      33 ..       5      35 ..       3      40 .. 0.93
   2 ?   -1.7   0.1       1.4   1.8e+03      61     109 ..     314     361 ..     270     365 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.9e-05
                    EEEE--STTHHHHHHHHHHCTSEEEEE-S-H CS
  UDPG_MGDP_dh_N  3 isviGlGYvGlvtaavlaeighevigvDide 33
                    i++iG+G  Gl+t+++la+ g  v +v +++
      EPA05020.1  5 ICIIGTGIGGLTTGTLLANEGYAVKIVEKNS 35
                    9************************999987 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.4
                     TTTEEEES-HHHHHHC-SEEEE-----B-TTTTCB-THHHHHHHHHHHH CS
  UDPG_MGDP_dh_N  61 sgrlsfttdvekaveeadvifiaVgTPskkkgkaaDlkyvesaarsiae 109
                     ++ ++f +++  +v+    +++  gTP+++   a D + ++++++++++
      EPA05020.1 314 TKGIFFISNIAPSVSPLGEHLMITGTPVSS-LVAEDPQKIKQIVDDMKK 361
                     445555566666666666666667777777.333377777777776666 PP

>> MCRA  MCRA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.016        20       5      50 ..       6      47 ..       3     101 .. 0.77
   2 ?    7.4   0.0    0.0012       1.6     204     251 ..     201     243 ..     120     256 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.016
                EEE--SHHHHHHHHHHHHTT---GGGEEEE-SS------------- CS
        MCRA  5 ylvGsGiasLaaAvyLirdakvpgenihileelkvaggsldgagdp 50
                 ++G+Gi++L++ + L ++    g  ++i+e+++++gg + +++  
  EPA05020.1  6 CIIGTGIGGLTTGTLLANE----GYAVKIVEKNSKLGGRTVSMKFR 47
                69**************886....57899****99999988776544 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0012
                 HHHHCCHHHHHHHHHTT-EEE-SEEEEEEEEEEE.TTEEEEEEEEEEE CS
        MCRA 204 qyeslilPlvkyLkeqgVdfqfntkVtdiefeeeeedkktvteielek 251
                  y+s+ + l+++++e++ ++++nt+V+ i +e++     +vt+i + +
  EPA05020.1 201 GYDSISKVLANFIQEKNGEINLNTSVKRIVIENS-----VVTGIVTFD 243
                 5******************************944.....777776654 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1     0.016        21       2      32 ..       5      35 ..       4      48 .. 0.85
   2 ?    6.9   0.1    0.0022       2.8     114     151 ..     222     259 ..     202     282 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.016
                EEEE-SSHHHHHHHHHHHHTT--EEEEES-G CS
        GIDA  2 viViGgGhAGceAAlaaarlGakvlLithkl 32
                + +iG G  G+     +a+ G+ v+++ ++ 
  EPA05020.1  5 ICIIGTGIGGLTTGTLLANEGYAVKIVEKNS 35
                78***********************995554 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0022
                 EES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT- CS
        GIDA 114 ieeeveeliveekkvkgvvtedgetikakavviatGtf 151
                 ++ +v+++++e++ v+g+vt d++ ik+++vv++  ++
  EPA05020.1 222 LNTSVKRIVIENSVVTGIVTFDDKLIKTNCVVVSYPAY 259
                 36789***************************986555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.67u 0.35s 00:00:01.02 Elapsed: 00:00:00.53
# Mc/sec: 2516.95
//
Query:       EPA05021.1  [L=61]
Description: hypothetical protein BG20_I1572, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 397.87
//
Query:       EPA05022.1  [L=151]
Description: hypothetical protein BG20_I1565 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 906.33
//
Query:       EPA05023.1  [L=50]
Description: hypothetical protein BG20_I1558 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.019   14.9   2.5        1.7    8.6   0.1    2.2  2  zf-FCS    MYM-type Zinc finger with FCS sequence motif


Domain annotation for each model (and alignments):
>> zf-FCS  MYM-type Zinc finger with FCS sequence motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.1   9.5e-05       1.7       3      13 ..      17      27 ..      16      29 .. 0.82
   2 ?    6.5   0.4   0.00043       7.8       3      15 ..      31      43 ..      30      46 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 9.5e-05
      zf-FCS  3 kkrCwfCkkyi 13
                +krC+fC+ ++
  EPA05023.1 17 QKRCTFCGIFL 27
                69*****9765 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.00043
      zf-FCS  3 kkrCwfCkkyikg 15
                ++rC +Ck  + +
  EPA05023.1 31 DTRCICCKAVLRT 43
                78******98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 300.33
//
Query:       EPA05024.1  [L=124]
Description: hypothetical protein BG20_I1560 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-05   24.0   0.3      4e-05   23.0   0.3    1.4  1  TF_Zn_Ribbon    TFIIB zinc-binding
  ------ inclusion threshold ------
      0.012   15.5   1.8       0.19   11.7   0.3    2.5  2  DUF1610         Domain of unknown function (DUF1610)
       0.35   10.6   3.2       0.48   10.2   0.8    2.0  2  Ribosomal_S27e  Ribosomal protein S27


Domain annotation for each model (and alignments):
>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.3   6.7e-09     4e-05       6      35 ..      11      40 ..      10      46 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 6.7e-09
                  TTCEECHEETSTTCEEESSSSBEEEECCCC CS
  TF_Zn_Ribbon  6 CgstnlveDpergelvCtdCGlVlednsid 35
                  C+ +n+++D+ +ge+ C++CG+Vl + s +
    EPA05024.1 11 CKRSNVITDEITGEIACSSCGVVLAEKSWE 40
                  9999********************998755 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   3.1e-05      0.19       1      10 [.      27      36 ..      27      38 .. 0.92
   2 ?    2.6   0.1     0.023   1.4e+02       4      11 ..     100     107 ..      99     108 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.1e-05
     DUF1610  1 CtSCGaelap 10
                C+SCG++la+
  EPA05024.1 27 CSSCGVVLAE 36
                ********97 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.023
     DUF1610   4 CGaelapr 11 
                 CG+e++++
  EPA05024.1 100 CGIEIVDP 107
                 *****985 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.8     8e-05      0.48      12      38 ..      10      36 ..       6      38 .. 0.92
   2 ?    0.1   0.1      0.11   6.7e+02      23      40 ..      88     108 ..      82     111 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 8e-05
                    TTS-EEEEESS-SS-EEESSSTCEEEE CS
  Ribosomal_S27e 12 dCenetvvFshaatvvkCisCgkvLve 38
                     C++  v+ +     + C sCg vL+e
      EPA05024.1 10 SCKRSNVITDEITGEIACSSCGVVLAE 36
                    799**********************97 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.11
                     -SS-EEESS...STCEEEEEC CS
  Ribosomal_S27e  23 aatvvkCis...CgkvLvePt 40 
                     ++++v C +   Cg  +v+P+
      EPA05024.1  88 SSKIVFCFIvyvCGIEIVDPR 108
                     567888864444999888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 802.81
//
Query:       EPA05025.1  [L=177]
Description: transcription factor TFIIB repeat protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-23   81.2   2.9    6.9e-12   45.2   0.0    2.1  2  TFIIB     Transcription factor TFIIB repeat
    0.00027   21.2   0.7       0.42   11.0   0.0    2.8  3  Rrf2      Transcriptional regulator
  ------ inclusion threshold ------
      0.024   14.7   0.0       0.07   13.2   0.0    1.7  2  Cyclin_C  Cyclin, C-terminal domain


Domain annotation for each model (and alignments):
>> TFIIB  Transcription factor TFIIB repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   0.0   1.2e-15   6.9e-12       6      70 ..       3      67 ..       1      68 [. 0.96
   2 !   35.7   1.5   1.1e-12   6.6e-09       1      71 []      92     162 ..      92     162 .. 0.98

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 1.2e-15
                HHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHH CS
       TFIIB  6 daleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekt 70
                ++l+Lpe V ++  +++++ +++k+l Grs   i+ A  yi cr+ ++ rt  +i++  +V++k 
  EPA05025.1  3 AKLGLPESVVEQTAYWFRKISAKKILGGRSTVVILCATTYIVCRLTNTPRTIHDIADAGNVKTKH 67
                79***********************************************************9986 PP

  == domain 2  score: 35.7 bits;  conditional E-value: 1.1e-12
                 HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
       TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                 ++r+a+a   +ek ++ A++++  a +++++  + p ++aAA++ +A++k+++k +q  is+v+ +s +ti
  EPA05025.1  92 VTRLAKATSVSEKTQRLAFKILSIAEKKGITTSKNPMSMAAAVVHLASLKNKEKVSQLKISEVSGISAVTI 162
                 6899****************************************************************998 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0     7e-05      0.42       9      51 ..      35      77 ..      30      81 .. 0.89
   2 ?   -0.9   0.0      0.37   2.2e+03      22      37 ..     106     121 ..      91     126 .. 0.46
   3 !    7.3   0.2   0.00098       5.9      12      44 ..     132     164 ..     122     171 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 7e-05
                HHHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHH CS
        Rrf2  9 yalhallyLakeeeeepvsseeiaerqnispsylekilakLrk 51
                + l a +y+  + +++p ++++ia+  n++ ++l++i + L k
  EPA05025.1 35 VILCATTYIVCRLTNTPRTIHDIADAGNVKTKHLQRIYRFLVK 77
                56788999999999999*********************99987 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.37
                 TCC-B-HHHHHHHHTS CS
        Rrf2  22 eeepvsseeiaerqni 37 
                 ++  +++ +iae+ +i
  EPA05025.1 106 QRLAFKILSIAEKKGI 121
                 2222344444444444 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.00098
                 HHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHH CS
        Rrf2  12 hallyLakeeeeepvsseeiaerqnispsylek 44 
                  a+++La+ +++e+vs  +i+e  +is++ ++ 
  EPA05025.1 132 AAVVHLASLKNKEKVSQLKISEVSGISAVTIRD 164
                 68999***999999**************99885 PP

>> Cyclin_C  Cyclin, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.38   2.3e+03      72     102 ..      40      72 ..      22      79 .. 0.55
   2 ?   13.2   0.0   1.2e-05      0.07       5      89 ..      90     172 ..      86     176 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.38
                 C---HHHHHHHHHHHHHHH..HHHHGSS--HHC CS
    Cyclin_C  72 tgyskedlkpcvelilell..ssapssklqavr 102
                 t y +++l +  + i++ +   + ++++lq ++
  EPA05025.1  40 TTYIVCRLTNTPRTIHDIAdaGNVKTKHLQRIY 72 
                 445555555555555665532233333333333 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 1.2e-05
                 HHHHHHHCCSSHT.-HCCHHCHHCHHHHHHCSCCHCCS-HHHHHHHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHHHHHHH CS
    Cyclin_C   5 sFlrrflkaadasedselrtlakylleltlldydflsyppSliAaaalllarstlnspewtetlehytgyskedlkpcvelilel 89 
                  F+ r+ ka +   + +++ la  +l ++     + s  p  +Aaa++ la+   +++  + ++ +++g+s   +++  + i ++
  EPA05025.1  90 EFVTRLAKATSV--SEKTQRLAFKILSIAEKKGITTSKNPMSMAAAVVHLASLKNKEKVSQLKISEVSGISAVTIRDRSKEITKC 172
                 6999999*9665..5478889999998888655555555555566666666655599999*****************99999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1273.92
//
Query:       EPA05026.1  [L=459]
Description: NAD dependent epimerase/dehydratase family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-16   60.4   0.0    3.3e-16   59.7   0.0    1.3  1  NAD_binding_10   NAD(P)H-binding
      3e-12   46.5   0.0    3.9e-11   42.9   0.0    2.1  2  Epimerase        NAD dependent epimerase/dehydratase family
    8.8e-11   41.8   0.0    1.3e-10   41.2   0.0    1.3  1  NmrA             NmrA-like family
    6.3e-09   35.2   0.0    1.5e-08   34.0   0.0    1.6  2  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    0.00012   21.7   0.0    0.00019   21.0   0.0    1.3  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
     0.0022   17.1   0.0     0.0036   16.5   0.0    1.3  1  RmlD_sub_bind    RmlD substrate binding domain
  ------ inclusion threshold ------
      0.018   14.2   0.1      0.056   12.6   0.0    1.9  2  NAD_binding_4    Male sterility protein
      0.045   12.9   0.8       0.33   10.0   0.8    2.1  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
      0.077   12.4   0.0       0.14   11.6   0.0    1.4  1  adh_short        short chain dehydrogenase


Domain annotation for each model (and alignments):
>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.7   0.0   1.6e-19   3.3e-16       1      99 [.      22     125 ..      22     173 .. 0.81

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 1.6e-19
                     TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES-....--TCC........HHHH...HHH CS
  NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsal....ggggk........deeg...akn 80 
                     GAtG +G++l+++l ++ g++v+ + R  +kl+++   ++++ v++dv dve+l+ea++g+++V+  l    g   k        +      a+n
      EPA05026.1  22 GATGFIGSRLISKLSSS-GFTVKGMSR--KKLEDI---PNVKYVQADVFDVEQLEEAMSGTEVVYYLLhsmeGD--KghwrefasR--EriqAQN 106
                     9****************.5******88..567766...69**************************99665422..1345456543..1458*** PP

                     HHHHHHHCT--EEEEEEET CS
  NAD_binding_10  81 ivdaakeagvkRfvlvsai 99 
                      ++aa +a+vkR+++++++
      EPA05026.1 107 FLKAATKANVKRIIYLGGL 125
                     **************99886 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   0.0   1.9e-14   3.9e-11       1     114 [.      18     123 ..      18     126 .. 0.92
   2 ?    1.3   0.0     0.099     2e+02     213     241 .]     195     221 ..     183     221 .. 0.90

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 1.9e-14
                 EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHHHSHHHHHHHHTHHHHHHH CS
   Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggvaassedpadfieknlqgtlnll 99 
                 ilVtGatGfiGs l+ +l + g +v g++r+    + + +++++ v++d+ d ++le++++  + ++v+ l    + +    +  +f+ +  + ++n l
  EPA05026.1  18 ILVTGATGFIGSRLISKLSSSGFTVKGMSRK----KLEDIPNVKYVQADVFDVEQLEEAMS--GTEVVYYL--LHSMEGDKGHWREFASRERIQAQNFL 108
                 8******************************....77888888******************..99******..66666666677789999999****** PP

                 HHHHHHTCTEEEEEE CS
   Epimerase 100 eaarkagvkrllfls 114
                 +aa ka+vkr+++l+
  EPA05026.1 109 KAATKANVKRIIYLG 123
                 *************98 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.099
                 EEHHHHHHHHHHHHHHHTT-STTEEEEES CS
   Epimerase 213 lyveDvaeaillvlehvdagdkgeiyniG 241
                 + v+Dv+e ++  ++h+++  +g+iy iG
  EPA05026.1 195 IAVDDVIEYLVGCMTHPQT--SGKIYEIG 221
                 569*************888..578**998 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   0.0   6.6e-14   1.3e-10       1     228 [.      18     242 ..      18     304 .. 0.84

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 6.6e-14
                 EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHST.TEEEES-TT-HHHHHHHHTT-SEEEE---GG...........S-HHHHHHHHHH CS
        NmrA   1 IlviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaG.velvkgdlddkeslvealkgvdvvfsvtgfy...........skeiedgkklvd 87 
                 Ilv+GaTG +G+ +++ l ++g++v+ + R       k+l++ + v+ v++d+ d e l+ea++g +vv+  + ++           s e  + ++  +
  EPA05026.1  18 ILVTGATGFIGSRLISKLSSSGFTVKGMSR-------KKLEDIPnVKYVQADVFDVEQLEEAMSGTEVVYYLLHSMegdkghwrefaSRERIQAQNFLK 109
                 9************************98888.......567777725678***********************9998999*******855655667899* PP

                 HHHHHS-SEEEEEE---GG.GT.SSS---TTTHHHHHHHHHHHHCTS-EEEEEE-EEGGG-BSSS-SS-BEEE-TTS.-EEEEESS-TTS-EE.-HHHH CS
        NmrA  88 AakeaGvkhfiySslgddndrsnaeepavphfdsKaeieeyvralgipytfvyagffmenflsllaqlkvgdtappedkvtllgpgnpkavll.daeeD 185
                 Aa +a vk++iy +   ++          ph +s   + e + +  ip t ++a +  +   +++a l+   ++       + +p+ +k     +a++D
  EPA05026.1 110 AATKANVKRIIYLGGLVNDSLE-----LSPHMQSRKDVGEILASGNIPVTQLRASLIIGSQGGSYAMLRYLVERLRI----MVTPSWVKSLAQpIAVDD 199
                 ************7655555333.....6899***************************9999999995555555443....44555554444445**** PP

                 HHHHHHHHHHHHHHH.TTEEEEE-SEEE-HHHHHHHHHHHHTS- CS
        NmrA 186 iGafvikilkdprkl.kgkriklagntlsgneivelfekkigkt 228
                 + ++ +  + +p++  k+  i  + ++++++e++++++  ++k+
  EPA05026.1 200 VIEYLVGCMTHPQTSgKIYEIGGP-DIMTYEELMRVYSAYLNKN 242
                 *************99666666555.89***********999987 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.0   7.4e-12   1.5e-08       1     114 [.      19     122 ..      19     126 .. 0.75
   2 ?   -3.4   0.0       1.9   3.7e+03     240     257 ..     342     358 ..     336     362 .. 0.83

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 7.4e-12
   3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihl.aslvdvagkltedeimkvnvkGTrn 98 
                 +vtG++GF+G++l+++L + +   +v+ +    s ++le+   + + k++++Dv d ++leea+ g +vv +l +s+   +g   ++   +  +   +n
  EPA05026.1  19 LVTGATGFIGSRLISKLSSSGF--TVKGM----SRKKLED---IPNVKYVQADVFDVEQLEEAMSGTEVVYYLlHSMEGDKG-HWREFASRERI-QAQN 106
                 69****************9993..55543....3444444...4444589*********************98133333333.33333444445.489* PP

   3Beta_HSD  99 vleacvkagvrvlvYt 114
                  l+a++ka+v++++Y 
  EPA05026.1 107 FLKAATKANVKRIIYL 122
                 ***************6 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.9
   3Beta_HSD 240 svagqayfisddsPvesy 257
                 s+ g +y+  dd P   y
  EPA05026.1 342 SIIGTTYYWLDDRPDV-Y 358
                 68899*******9976.4 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   9.4e-08   0.00019       1      60 [.      19      62 ..      19      82 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 9.4e-08
                   EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE-- CS
  GDP_Man_Dehyd  1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgD 60
                   L+TG +GfiGs l+ +L + g++v g+ r++ + ++ +++                +++D
     EPA05026.1 19 LVTGATGFIGSRLISKLSSSGFTVKGMSRKK-LEDIPNVK---------------YVQAD 62
                   9*************************86644.33333333...............34444 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.8e-06    0.0036       3      49 ..      18      75 ..      16      84 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.8e-06
                   EEEESTTSHHHHHHHHHCTTTSEEEEEE-TT...........T--TTSHHHHHHHHHH CS
  RmlD_sub_bind  3 ilvtGanGqlGseLakqlaeeglevlaltre...........eldltdaeavaellke 49
                   ilvtGa+G +Gs L+ +l+++g+ v +++r+           ++d+ d e+++e+++ 
     EPA05026.1 18 ILVTGATGFIGSRLISKLSSSGFTVKGMSRKkledipnvkyvQADVFDVEQLEEAMSG 75
                   9***************************999888888888888888888888888765 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.8e-05     0.056       1      16 [.      20      35 ..      20      61 .. 0.90
   2 ?   -2.1   0.0      0.89   1.8e+03     193     229 ..     148     183 ..     142     202 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.8e-05
                   EE-TTSHHHHHHHHHH CS
  NAD_binding_4  1 lTGaTGFLGkvLlekL 16
                   +TGaTGF+G++L+ kL
     EPA05026.1 20 VTGATGFIGSRLISKL 35
                   7**************9 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.89
                    HH---EEEEEE-EEE--SSST---TTSHHHHHHHHHH CS
  NAD_binding_4 193 rsglpvvivRpsiitgesktGwingsdlgirgllgli 229
                    ++++pv+ +R s i+g s+ G+    +++++ l +++
     EPA05026.1 148 SGNIPVTQLRASLIIG-SQGGSYAMLRYLVERLRIMV 183
                    4689999999999999.66666666665555555554 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.8   0.00017      0.33       1     124 [.      18     120 ..      18     124 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00017
                      EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-SEEEE------HHHHH CS
  Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvdvvfhaAAlKhVPlve 94 
                      +lvtGa+G iGs+l++++ ++      +   + +kl +i + +        +      v +dv d e+le+a++  + +vv+    l  +    
       EPA05026.1  18 ILVTGATGFIGSRLISKLSSSGF---TVKGMSRKKLEDIPNVK--------Y------VQADVFDVEQLEEAMS--GTEVVYYL--LHSMEGDK 90 
                      89************999866542...33333333444433322........1......2366777777777777..66666654..33333344 PP

                      HSHHHHHHHHHHHHHHHHHHHHHTT-SEEE CS
  Polysacc_synt_2  95 enpleaiktNvlgtenvieaaieagvkkvv 124
                       ++ e  +   + ++n ++aa++a+vk+++
       EPA05026.1  91 GHWREFASRERIQAQNFLKAATKANVKRII 120
                      455555555555666666666666666666 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   6.9e-05      0.14       3      87 ..      18      92 ..      16     148 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.9e-05
                EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEEE---S CS
   adh_short  3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldvLvnNAGi 87
                +lvtGa++ IG  +  +l ++G++v  ++r+  kl    + + +    + ++q+Dv d e++e++++  +  +  l+ +    G 
  EPA05026.1 18 ILVTGATGFIGSRLISKLSSSGFTVKGMSRK--KL----EDIPN----VKYVQADVFDVEQLEEAMSGTEVVYYLLHSMEGDKGH 92
                89***********************887776..44....66776....89*************9999887777666666555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 3129.73
//
Query:       EPA05027.1  [L=45]
Description: hypothetical protein BG20_I1561 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.47   10.6   6.7       0.87    9.8   6.7    1.5  1  zf-Dof    Dof domain, zinc finger


Domain annotation for each model (and alignments):
>> zf-Dof  Dof domain, zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   6.7   4.8e-05      0.87       4      38 ..       4      40 ..       1      43 [. 0.76

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 4.8e-05
      zf-Dof  4 lkCprCestntkFc..YyNNyslsqPRyfCkaCrryW 38
                  Cp C+s+n         N++ s+ +  C +C++ W
  EPA05027.1  4 EGCPTCSSKNFGVLeiIKENNDSSKWKMQCYNCKKFW 40
                57********76531134566678899********** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       835  (0.0465726); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 296.06
//
Query:       EPA05028.1  [L=264]
Description: B12 binding domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-13   50.7   0.0    2.7e-13   50.0   0.0    1.3  1  B12-binding    B12 binding domain
    2.6e-09   37.4   0.0    4.7e-09   36.5   0.0    1.4  1  B12-binding_2  B12 binding domain
  ------ inclusion threshold ------
      0.065   13.0   0.1       0.93    9.3   0.0    2.1  2  IPPT           IPP transferase


Domain annotation for each model (and alignments):
>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.0   0.0   4.5e-17   2.7e-13       3      92 ..     149     237 ..     147     250 .. 0.91

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 4.5e-17
  B12-binding   3 vllatvggdlhplGlavlaaalrdagfeVqllganvenedivaairaekpdvvglSalltsqleavkelvellkrirprvkvvvGGahps 92 
                  +l+ +  g+ h lG +vl  +l+ +gf+V+++   +++e i++ i+ +kpd+v++S++l  +++a ++lv+ +k+   +v+++vGG +++
   EPA05028.1 149 ILVCVPLGEEHHLGCDVLETYLSIKGFKVYNIATSIPTESILSFIEYNKPDIVLISITLEDNISAGQRLVKKIKEQ-YDVPILVGGYAFQ 237
                  566677799***************************************************************9888.56*******8854 PP

>> B12-binding_2  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.0   7.9e-13   4.7e-09       3      73 ..      66     135 ..      65     137 .. 0.94

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 7.9e-13
  B12-binding_2   3 erlhwaivhgdkegieelidealaqgsa...avdvlndvllpamkeVGdlfgagelflpqvllsaevmkkavah 73 
                    + l++++ +gd ++ +++++e +    +   + d+++++l p+m+++G+ +++++++++ ++ +++v ++ v++
     EPA05028.1  66 QMLYKKLTEGDIQSSVKIYQEYI----KifnPGDFFDKILRPVMYKIGEDWASNTISIATEHVASNVAQTLVKI 135
                    67999******************....5567**************************************99987 PP

>> IPPT  IPP transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.035   2.1e+02      84     116 ..      53      83 ..      27      91 .. 0.70
   2 ?    9.3   0.0   0.00016      0.93       4      64 ..     176     234 ..     174     256 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.035
                 HHHHHHHHHHHHSHHHHHHHHHHHC-HHHHTTS CS
        IPPT  84 elraeleeeaeeeglealheelkevdpeaaaki 116
                 +++++ e   ++++++ l+++l+e d ++  ki
  EPA05028.1  53 DIEKREE--STKKSKQMLYKKLTEGDIQSSVKI 83 
                 2332222..23445778*******999887766 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00016
                 TT-HTTTT---HHHHTTS-EESSS-B-TTS---HHHHHHHHHHHHHHHHHTT-EEEEEES- CS
        IPPT   4 rgmdIgTakptaeeragvphhlidildpdeeysvadFqkdalkaieeilargkipilvGGT 64 
                 +  +I T  pt++ ++ +++   di+ +  ++++ d  ++ ++++++i ++ ++pilvGG 
  EPA05028.1 176 KVYNIATSIPTESILSFIEYNKPDIVLI--SITLEDNISAGQRLVKKIKEQYDVPILVGGY 234
                 6679999999999999999999999999..99999999**********************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1188  (0.0662614); expected 358.6 (0.02)
Passed bias filter:                      721  (0.0402142); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 1690.98
//
Query:       EPA05029.1  [L=349]
Description: hypothetical protein BG20_I2499, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.5e-06   26.2   1.0    1.2e-05   25.1   0.7    1.9  1  DUF2334          Uncharacterized protein conserved in bacteri
     0.0012   18.7   0.0     0.0023   17.8   0.0    1.5  1  Polysacc_deac_1  Polysaccharide deacetylase


Domain annotation for each model (and alignments):
>> DUF2334  Uncharacterized protein conserved in bacteria (DUF2334)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.7   1.4e-09   1.2e-05      94     165 ..     122     207 ..      95     278 .. 0.70

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.4e-09
     DUF2334  94 f.......lseseakeriekGi.eilkklgikpkgFeaPhyaaseetykalkky.fsiiyerykeyk..gq...kegltyipenlg 165
                          s++e+ + ++++i eil+++g++p++F++P+ +++e+t+++l ++ f+ ++ +  +++  +    +e l+  pe++ 
  EPA05029.1 122 IgstpftnYSKQEQDKLLKQSIvEILNNAGVRPHIFVPPQNQYNEDTKQVLIENkFTHVSGSVSQEEvlEFplkDETLYKFPETAT 207
                 0334445588999999999998799**************************9888*****88555443411444444444444333 PP

>> Polysacc_deac_1  Polysaccharide deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.6e-07    0.0023      26     122 ..      78     178 ..      51     180 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.6e-07
                      HHHHHCT--EEEEE-HHHHCH-...HHHHHHHHHTT.EEEEE--SS--EGGGSHHHHHHHHHHHHHHHHHHHHS----EEE-GGGEE-HHHHHH CS
  Polysacc_deac_1  26 pvLkkykvkatffvigglvedy...pdevremaasG.veignHtinhsnlkrlseeevrreierakdalrkalgreprlfryPygsasatvlev 115
                      +++ +++++ t+ +i    ++      +v+    +  +ei++ +i  + +++ s++e+++ ++++   + +  g +p+ f +P  ++++++ +v
       EPA05029.1  78 NTFIEKNIPLTVGIIADSFGNDqkiTAIVKDASSKNkIEIASEGIGSTPFTNYSKQEQDKLLKQSIVEILNNAGVRPHIFVPPQNQYNEDTKQV 171
                      5555667777777777653333344788999999999********************************************************* PP

                      HHHTT.E CS
  Polysacc_deac_1 116 arelgfa 122
                      + e  f+
       EPA05029.1 172 LIENKFT 178
                      9988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 2213.80
//
Query:       EPA05030.1  [L=107]
Description: ribosomal protein L7Ae [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.3e-12   45.6   0.5    5.3e-12   45.3   0.5    1.1  1  Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 famil
  ------ inclusion threshold ------
      0.033   14.3   1.5      0.033   14.3   1.5    1.4  2  DUF1694         Protein of unknown function (DUF1694)


Domain annotation for each model (and alignments):
>> Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   0.5   5.9e-16   5.3e-12       3      93 ..       5      93 ..       3      95 .. 0.90

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 5.9e-16
                    HHHHHHHHHHHTEEEESHHHHHHHHHTTTESEEEEETTSSSGGHHHHHHHHHHHTTEEE..EEESCHHHHHHHTTSSSECSEEEEEESTTTHH CS
  Ribosomal_L7Ae  3 ieevlkkakkagklvlGlkevtkalergeaklvilAedvepeekkkllealckekevpy..vkvkskkeLGelvgkkrpvsalaikdegdskd 93
                    +e+ lk ++k +++++G+k+v+ ++++   kl++l+++ ++e+  k +e  +k+ ++p+  ++++s  +LG+l+g++++ s++++++ +d+++
      EPA05030.1  5 LEKMLKDSVKEDQVTMGTKQVLNSMKN--SKLIVLSKSLKKETLAK-IEEDAKKEKIPLvnFQGTS-VALGRLCGLQFRISTISFTSLTDANI 93
                    57899********************86..68***************.************4445667.9***********99999998888765 PP

>> DUF1694  Protein of unknown function (DUF1694)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   1.5   3.7e-06     0.033      35      89 ..       5      60 ..       3      69 .. 0.88
   2 ?   -3.1   0.0      0.87   7.8e+03      51      58 ..      92      99 ..      82     105 .. 0.52

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.7e-06
                EEEEEHHHHTSSS--HHHHHHHHC-SSEEE.EEETTS-HHHHHHHHHHHHHTT--E CS
     DUF1694 35 ilaltkeqveekkvykeleealkkkkalkl.lingkldedilskyiklakkenikf 89
                + ++ k+ v+e++v+   +++l++ k++kl +++++l+++ l k+ + akke+i+ 
  EPA05030.1  5 LEKMLKDSVKEDQVTMGTKQVLNSMKNSKLiVLSKSLKKETLAKIEEDAKKEKIPL 60
                668999******************8886651689******************9985 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.87
                HHHHHHHC CS
     DUF1694 51 eleealkk 58
                +++++lk+
  EPA05030.1 92 NIKSLLKD 99
                34444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       981  (0.0547158); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.55
# Mc/sec: 586.88
//
Query:       EPA05031.1  [L=199]
Description: ribosomal protein S7p/S5e [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.5e-36  123.7   1.1    6.5e-36  123.2   1.1    1.2  1  Ribosomal_S7  Ribosomal protein S7p/S5e


Domain annotation for each model (and alignments):
>> Ribosomal_S7  Ribosomal protein S7p/S5e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.2   1.1   3.6e-40   6.5e-36      15     149 .]      48     199 .]      39     199 .] 0.95

  Alignments for each domain:
  == domain 1  score: 123.2 bits;  conditional E-value: 3.6e-40
                   -SSTTSBHHHHHHHHHSB............TTBHHHHHHHHHHHHHHHHHHHSS-HHHHHHHHHHHCS-SEEEEEEBSSSSBEEEEEEE-HHHHHHH CS
  Ribosomal_S7  15 dpkynselveklinklmk............dGkkslAekivygaldiieektkkdplevleeAlenvkPrvevksrrvGGatyqvpvevrpkRrqal 99 
                    +k++ ++ve+link+m+            +Gkk++  ++v+ a++ii+ kt+++p+e+l++A+en++P+++++++ +GG+ y+v+v+v+p Rr+++
    EPA05031.1  48 FNKAEVNIVERLINKVMHfgkkyakntgrmTGKKTKVLNTVKLAFEIIALKTGQNPVEILVRAIENSAPNEDTTRIVYGGTVYHVSVDVAPIRRVDM 144
                   456899******************************************************************************************* PP

                   HHHHHHHHH...STSSSS-HHHHHHHHHHHHHTT-..SHHHHHHHHHHHHHHHTG CS
  Ribosomal_S7 100 Alrwiieaa...rkrkeksmaekLaeElidAaege..gaavkkreethrmAeanr 149
                   Al++i++     ++ + k+++e++ae+li Aa ++  + +vkk++e++r+A+a+r
    EPA05031.1 145 ALKFIADSIrdsTFSNPKPIEEHMAEQLILAAANDpnAPSVKKKHELERIAQASR 199
                   *******9977778899*****************988889*************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1297.25
//
Query:       EPA05032.1  [L=145]
Description: ribosomal protein S23 (S12) [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-46  156.0   0.3    3.1e-46  155.7   0.3    1.1  1  Ribosom_S12_S23  Ribosomal protein S12/S23


Domain annotation for each model (and alignments):
>> Ribosom_S12_S23  Ribosomal protein S12/S23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.7   0.3   1.7e-50   3.1e-46       1     114 []      30     144 ..      30     144 .. 0.98

  Alignments for each domain:
  == domain 1  score: 155.7 bits;  conditional E-value: 1.7e-50
                      --------S-TSSTTSSEEEEEEEEEEEE---TT--S-EEEEEEEET.TSEEEEEEE-SSS..----TT-EEEEEE--......BTTSTTEEEE CS
  Ribosom_S12_S23   1 rkelrkktksdalegapqkrGvvlekvtveakkPnsAlRkvvrvrLikngkevtafipgegalnfldEhdevlvrGirrk.gkavkDlpGvryk 93 
                      r++l+   k+d+l gapq rG+vlekv++ ak+PnsA+Rk+vrv+Likngk+vtaf+p +ga+nf+dEhdev ++G++ + g a++D+pGvr+k
       EPA05032.1  30 RRKLGIDVKADPLGGAPQGRGIVLEKVGIAAKQPNSAVRKCVRVQLIKNGKTVTAFLPRDGAMNFIDEHDEVHIQGMGATqGGAMGDIPGVRFK 123
                      6889999**********************************************************************9878************* PP

                      BETS---TSSSTTTTT----T CS
  Ribosom_S12_S23  94 vvkvagvslkalskykkekpk 114
                      v kv+g sl +l+ +kkekp+
       EPA05032.1 124 VFKVNGTSLSQLVTGKKEKPR 144
                      *******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 932.98
//
Query:       EPA05033.1  [L=379]
Description: tetratricopeptide repeat protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      2e-20   71.7   0.7    9.3e-08   31.6   0.2    3.3  3  TPR_1       Tetratricopeptide repeat
    1.5e-17   62.2   0.0    1.3e-05   24.9   0.0    3.3  3  TPR_2       Tetratricopeptide repeat
      1e-13   50.6   2.6     0.0011   19.2   0.1    3.4  3  TPR_17      Tetratricopeptide repeat
      1e-11   44.3   2.0    1.7e-05   24.4   0.6    3.3  3  TPR_11      TPR repeat
    1.2e-11   43.8   2.0    7.8e-05   22.6   0.0    3.0  2  TPR_8       Tetratricopeptide repeat
    1.7e-09   37.0   0.0    0.00097   19.0   0.0    3.3  3  TPR_7       Tetratricopeptide repeat
    1.4e-07   31.7   0.0       0.04   14.2   0.0    3.1  2  TPR_12      Tetratricopeptide repeat
    4.5e-07   30.2   0.0       0.24   12.3   0.0    3.2  3  TPR_14      Tetratricopeptide repeat
    1.1e-06   29.1   0.0      0.027   15.1   0.0    2.2  2  TPR_16      Tetratricopeptide repeat
    1.1e-05   25.9   0.0      0.011   16.2   0.1    2.5  2  TPR_19      Tetratricopeptide repeat
      2e-05   24.5   0.1        1.2    9.3   0.0    3.3  3  Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
    2.3e-05   24.1   0.2     0.0066   16.3   0.1    2.3  2  TPR_10      Tetratricopeptide repeat
     0.0014   17.6   0.0      0.082   11.8   0.0    2.1  2  NARP1       NMDA receptor-regulated protein 1
     0.0092   16.6   0.2       0.55   11.0   0.0    2.7  3  TPR_6       Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.019   15.1   0.0       0.99    9.6   0.0    2.1  2  TPR_9       Tetratricopeptide repeat
      0.046   13.8   0.0        2.5    8.2   0.0    2.7  2  DUF3856     Domain of Unknown Function (DUF3856)


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   0.00011      0.13      10      34 .]     212     236 ..     209     236 .. 0.95
   2 !   24.8   0.0   1.2e-08   1.3e-05       5      34 .]     241     270 ..     237     270 .. 0.94
   3 !   31.6   0.2   8.3e-11   9.3e-08       3      34 .]     273     304 ..     271     304 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
                 HHHHTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1  10 ayfklgkydeAleyyekALelnPnn 34 
                 a+++l k+d+ le+++  L+ +Pnn
  EPA05033.1 212 ALYRLCKFDQSLEFFDNSLSKDPNN 236
                 6899********************8 PP

  == domain 2  score: 24.8 bits;  conditional E-value: 1.2e-08
                 HHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1   5 ynlGnayfklgkydeAleyyekALelnPnn 34 
                  n+G a++klg+++  + yy+ AL+++Pn+
  EPA05033.1 241 TNKGSALRKLGNLQGSISYYDLALKIDPNF 270
                 7***************************97 PP

  == domain 3  score: 31.6 bits;  conditional E-value: 8.3e-11
                 HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                 a +n++na+ ++gky e +  yekA+e nPn+
  EPA05033.1 273 AINNKANALASMGKYSESISLYEKAIEKNPNY 304
                 679***************************97 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   6.7e-05     0.075      10      34 .]     212     236 ..     209     236 .. 0.96
   2 !   20.5   0.0   3.1e-07   0.00035       5      33 ..     241     269 ..     237     270 .. 0.92
   3 !   24.9   0.0   1.2e-08   1.3e-05       3      34 .]     273     304 ..     271     304 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.7e-05
       TPR_2  10 ayyklgdyeeAleafekAleldPnn 34 
                 a+y+l ++++ le+f+ +l+ dPnn
  EPA05033.1 212 ALYRLCKFDQSLEFFDNSLSKDPNN 236
                 79**********************8 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 3.1e-07
       TPR_2   5 ynlGlayyklgdyeeAleafekAleldPn 33 
                  n G a++klg+++  + +++ Al++dPn
  EPA05033.1 241 TNKGSALRKLGNLQGSISYYDLALKIDPN 269
                 589*************************9 PP

  == domain 3  score: 24.9 bits;  conditional E-value: 1.2e-08
       TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                 a +n ++a++ +g+y e + ++ekA+e +Pn+
  EPA05033.1 273 AINNKANALASMGKYSESISLYEKAIEKNPNY 304
                 56899*************************96 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   1.5e-06    0.0016       2      31 ..     226     255 ..     225     258 .. 0.92
   2 !   19.2   0.1     1e-06    0.0011       2      31 ..     260     289 ..     259     292 .. 0.90
   3 !   11.3   0.3   0.00033      0.37       1      19 [.     293     311 ..     293     318 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.5e-06
      TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmt 31 
                 + ++l +dPnn++  +n++ +l+k+G+l+ 
  EPA05033.1 226 FDNSLSKDPNNVEIITNKGSALRKLGNLQG 255
                 789************************985 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 1e-06
      TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmt 31 
                 y  al++dPn ++a nn+A++l++ G++ +
  EPA05033.1 260 YDLALKIDPNFVPAINNKANALASMGKYSE 289
                 7889**********************9966 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.00033
      TPR_17   1 lylkaleldPnnadaynnL 19 
                 ly+ka+e++Pn+  a nnL
  EPA05033.1 293 LYEKAIEKNPNYESAKNNL 311
                 7**********97666666 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0016       1.8       4      42 .]     213     251 ..     210     251 .. 0.87
   2 !   19.3   0.0   5.7e-07   0.00064       1      42 []     244     285 ..     244     285 .. 0.97
   3 !   24.4   0.6   1.5e-08   1.7e-05       2      34 ..     279     311 ..     278     317 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0016
      TPR_11   4 yyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                 +y + k+++++e + + l  dP+n+e+  n G a+ k+G
  EPA05033.1 213 LYRLCKFDQSLEFFDNSLSKDPNNVEIITNKGSALRKLG 251
                 555558999999999*******************99987 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 5.7e-07
      TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                 G a++++G++ ++i  Y  Alk+dP+++ a +n ++a++ +G
  EPA05033.1 244 GSALRKLGNLQGSISYYDLALKIDPNFVPAINNKANALASMG 285
                 899**********************************99988 PP

  == domain 3  score: 24.4 bits;  conditional E-value: 1.5e-08
      TPR_11   2 dayyeqGkyeeAieaYkkAlkldPdnaeayynL 34 
                 +a+ + Gky e+i  Y+kA++ +P++ +a +nL
  EPA05033.1 279 NALASMGKYSESISLYEKAIEKNPNYESAKNNL 311
                 99**************************99998 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0     7e-08   7.8e-05       2      33 ..     238     269 ..     237     270 .. 0.93
   2 !   19.4   0.6   7.2e-07    0.0008       2      33 ..     272     303 ..     271     304 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 7e-08
                 CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
       TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                 e+  n+gs+++klg+++ +++yy  al++dp+
  EPA05033.1 238 EIITNKGSALRKLGNLQGSISYYDLALKIDPN 269
                 56789**************************8 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 7.2e-07
                 CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
       TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                 +a +n+++++ ++g+y e+++ yeka+e +p+
  EPA05033.1 272 PAINNKANALASMGKYSESISLYEKAIEKNPN 303
                 6889***********************98887 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.056        63      11      35 ..     215     237 ..     209     238 .. 0.88
   2 !   10.1   0.0    0.0006      0.67       4      31 ..     242     267 ..     239     271 .. 0.83
   3 !   19.0   0.0   8.6e-07   0.00097       1      32 [.     273     302 ..     273     304 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.056
       TPR_7  11 rlGdyeeAielyeqsLaltkdpeda 35 
                 rl ++++ +e++     l kdp+++
  EPA05033.1 215 RLCKFDQSLEFFDN--SLSKDPNNV 237
                 799***********..999999986 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0006
       TPR_7   4 nLarlysrlGdyeeAielyeqsLaltkd 31 
                 n +++ ++lG+ +  i++y    al  d
  EPA05033.1 242 NKGSALRKLGNLQGSISYYDL--ALKID 267
                 889******************..55444 PP

  == domain 3  score: 19.0 bits;  conditional E-value: 8.6e-07
       TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdp 32 
                 a++n a++  ++G+y+e i+lye+  a++k p
  EPA05033.1 273 AINNKANALASMGKYSESISLYEK--AIEKNP 302
                 689*********************..999887 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   0.00013      0.15      42      74 ..     234     266 ..     202     269 .. 0.60
   2 !   14.2   0.0   3.6e-05      0.04       6      31 ..     274     299 ..     270     313 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
      TPR_12  42 pltattlrnLgrlyralgryeeAlelleealai 74 
                 p+ +++  n g ++r+lg+++  ++++  al+i
  EPA05033.1 234 PNNVEIITNKGSALRKLGNLQGSISYYDLALKI 266
                 445666666666666666666666666666665 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 3.6e-05
      TPR_12   6 lnnlaavlrrlgrydeAlellekale 31 
                  nn a++l+ +g+y e+++l+eka+e
  EPA05033.1 274 INNKANALASMGKYSESISLYEKAIE 299
                 569*********************87 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.022        25      10      38 ..     212     240 ..     208     245 .. 0.87
   2 !    8.5   0.0    0.0037       4.1       8      35 ..     244     271 ..     242     277 .. 0.91
   3 !   12.3   0.0   0.00022      0.24       8      37 ..     278     307 ..     273     314 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.022
      TPR_14  10 allalGdpdeAiallrralalaPddaeaw 38 
                 al++l ++d++++ ++  l+++P++ e+ 
  EPA05033.1 212 ALYRLCKFDQSLEFFDNSLSKDPNNVEII 240
                 6888899******************9975 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0037
      TPR_14   8 aeallalGdpdeAiallrralalaPdda 35 
                 ++al+ lG+++++i +++ al+ +P++ 
  EPA05033.1 244 GSALRKLGNLQGSISYYDLALKIDPNFV 271
                 689**********************975 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.00022
      TPR_14   8 aeallalGdpdeAiallrralalaPddaea 37 
                 a al+  G++ e+i l+++a++++P+ + a
  EPA05033.1 278 ANALASMGKYSESISLYEKAIEKNPNYESA 307
                 7899*********************99877 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.4e-05     0.027       4      66 ..     210     269 ..     208     269 .. 0.95
   2 !   12.0   0.0   0.00023      0.26       2      44 ..     276     315 ..     275     317 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.4e-05
      TPR_16   4 araalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                 + a++r+ ++d+ ++ ++  l +d   P ++e   ++g a+ ++g+l++ + +y+ al+ +p+
  EPA05033.1 210 GPALYRLCKFDQSLEFFDNSLSKD---PNNVEIITNKGSALRKLGNLQGSISYYDLALKIDPN 269
                 77899999****************...********************************9996 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00023
      TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaa 44 
                 ++a+a++  g+y + + ++e a++++   P    A ++l++++
  EPA05033.1 276 NKANALASMGKYSESISLYEKAIEKN---PNYESAKNNLNLVL 315
                 589***********************...99888888888776 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   0.00026      0.29       7      57 ..     219     269 ..     209     274 .. 0.90
   2 !   16.2   0.1     1e-05     0.011       3      58 ..     249     304 ..     247     311 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00026
      TPR_19   7 yaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                 +++ l+++ + l++dp+n e+  +   al +lg+l+  +   d +++ dp+
  EPA05033.1 219 FDQSLEFFDNSLSKDPNNVEIITNKGSALRKLGNLQGSISYYDLALKIDPN 269
                 78899******************************9888888888888877 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1e-05
      TPR_19   3 aegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd 58 
                 + g+++  ++++  al+ dp+   a  + A+al ++g + e + l +++ e++p+ 
  EPA05033.1 249 KLGNLQGSISYYDLALKIDPNFVPAINNKANALASMGKYSESISLYEKAIEKNPNY 304
                 56899999999*******************************************94 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0    0.0011       1.2      10      34 ..     212     236 ..     210     240 .. 0.94
   2 ?    5.7   0.0     0.014        16      12      34 ..     248     270 ..     244     275 .. 0.90
   3 ?    5.6   0.1     0.015        16      10      39 ..     280     309 ..     276     319 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0011
                 HHHHHT-HHHHHHHHHHHHHHTTS- CS
  Fis1_TPR_C  10 GhyklgeYseArryvdalLeiEPen 34 
                 + y+l ++++++++ d  L+++P+n
  EPA05033.1 212 ALYRLCKFDQSLEFFDNSLSKDPNN 236
                 68**********************9 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.014
                 HHHT-HHHHHHHHHHHHHHTTS- CS
  Fis1_TPR_C  12 yklgeYseArryvdalLeiEPen 34 
                  klg+ + +  y d  L+i+P++
  EPA05033.1 248 RKLGNLQGSISYYDLALKIDPNF 270
                 59*******************97 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.015
                 HHHHHT-HHHHHHHHHHHHHHTTS-HHHHH CS
  Fis1_TPR_C  10 GhyklgeYseArryvdalLeiEPenrQaqs 39 
                 + + +g+Yse+  + +  +e+ P+ + a++
  EPA05033.1 280 ALASMGKYSESISLYEKAIEKNPNYESAKN 309
                 66779*******************999975 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.014        16       5      31 ..     240     266 ..     238     266 .. 0.90
   2 !   16.3   0.1   5.9e-06    0.0066       4      30 ..     273     299 ..     273     301 .. 0.94

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.014
      TPR_10   5 lnNLanalrqrgrydeAealleealai 31 
                  +N + alr++g+++++  +++ al i
  EPA05033.1 240 ITNKGSALRKLGNLQGSISYYDLALKI 266
                 57889****************999975 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 5.9e-06
      TPR_10   4 slnNLanalrqrgrydeAealleeala 30 
                 + nN anal ++g+y e+  l+e+a++
  EPA05033.1 273 AINNKANALASMGKYSESISLYEKAIE 299
                 57***********************97 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   7.3e-05     0.082     207     256 ..     218     267 ..     212     270 .. 0.92
   2 ?    3.5   0.2     0.024        27      42      82 ..     275     315 ..     269     344 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.3e-05
                 -SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCT CS
       NARP1 207 srekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklD 256
                 + +++le+ d+ ++++p+ ve+ ++K+  l++ G+l++ ++  + a k+D
  EPA05033.1 218 KFDQSLEFFDNSLSKDPNNVEIITNKGSALRKLGNLQGSISYYDLALKID 267
                 66899************************************999999988 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.024
                 HHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CHHHHHHHHHT CS
       NARP1  42 etkaelllkLgrkeeAeatyeaLlernpenskYyeglekak 82 
                 ++ka+ l  +g+++e+ ++ye+ +e+np+ ++  ++l+ ++
  EPA05033.1 275 NNKANALASMGKYSESISLYEKAIEKNPNYESAKNNLNLVL 315
                 689999**********************9998888777666 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       9.9   1.1e+04      16      32 ..     219     235 ..     218     236 .. 0.84
   2 ?    2.6   0.0      0.24   2.7e+02       7      32 ..     244     269 ..     242     269 .. 0.89
   3 !   11.0   0.0   0.00049      0.55       7      32 ..     278     303 ..     276     304 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 9.9
                 HHHHHHHHHHHHHH-TT CS
       TPR_6  16 tdkAlealerlikeYPd 32 
                  d++le +++ +++ P+
  EPA05033.1 219 FDQSLEFFDNSLSKDPN 235
                 68999999999999998 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.24
                 HHHHHHHHHHHHHHHHHHHHHHH-TT CS
       TPR_6   7 alsyrklgdtdkAlealerlikeYPd 32 
                 + ++rklg+ + ++ +++  +k  P+
  EPA05033.1 244 GSALRKLGNLQGSISYYDLALKIDPN 269
                 77899999**********99999887 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00049
                 HHHHHHHHHHHHHHHHHHHHHHH-TT CS
       TPR_6   7 alsyrklgdtdkAlealerlikeYPd 32 
                 a ++ ++g++++++ ++e+ i++ P+
  EPA05033.1 278 ANALASMGKYSESISLYEKAIEKNPN 303
                 66788899*****************8 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0    0.0029       3.2      11      60 ..     219     268 ..     213     269 .. 0.91
   2 ?    9.6   0.0   0.00088      0.99      16      63 ..     258     305 ..     256     310 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0029
       TPR_9  11 weralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalap 60 
                 +++ l+  +  l  +P+ +e +   G +l +lG+l++ +   + +l ++p
  EPA05033.1 219 FDQSLEFFDNSLSKDPNNVEIITNKGSALRKLGNLQGSISYYDLALKIDP 268
                 66678888999999***************************999999988 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00088
       TPR_9  16 avverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdap 63 
                  ++++ l ++P+ +  +   + +la +G +s+ +   e +++++p+ +
  EPA05033.1 258 SYYDLALKIDPNFVPAINNKANALASMGKYSESISLYEKAIEKNPNYE 305
                 689****************************************99654 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.14   1.6e+02     100     125 ..     237     262 ..     197     267 .. 0.61
   2 ?    8.2   0.0    0.0023       2.5      99     128 ..     270     299 ..     267     306 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.14
                 HHHHHHHHHHHHHTT-HHHHHHHHHH CS
     DUF3856 100 iaavfsravaleelGrkdealkafrm 125
                 + ++ +++ al +lG+ + ++ ++  
  EPA05033.1 237 VEIITNKGSALRKLGNLQGSISYYDL 262
                 45677777777777777777776665 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0023
                 HHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
     DUF3856  99 WiaavfsravaleelGrkdealkafrmage 128
                 ++ a+ ++a al+++G+++e++  +++a e
  EPA05033.1 270 FVPAINNKANALASMGKYSESISLYEKAIE 299
                 577999********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 2310.70
//
Query:       EPA05034.1  [L=154]
Description: KH domain protein, NusA family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-18   66.3   2.7    2.5e-12   46.4   0.2    2.1  2  KH_2      KH domain
    8.7e-11   41.6   0.5    0.00017   21.4   0.1    2.2  2  KH_4      KH domain
    5.5e-08   32.8   3.1    2.1e-07   30.9   0.3    2.1  2  KH_5      NusA-like KH domain
     0.0005   19.8   0.5      0.043   13.6   0.1    2.3  2  KH_1      KH domain


Domain annotation for each model (and alignments):
>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4   0.2   5.6e-16   2.5e-12       4      62 ..      15      73 ..      12      99 .. 0.86
   2 !   21.0   0.3   4.9e-08   0.00022      16      58 ..      92     137 ..      79     146 .. 0.76

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 5.6e-16
                HHHHHHTECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHH CS
        KH_2  4 eslaveikkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdiekle 62
                 sl++++++a++++++ +++++rvi+v+ ++++g++IGkgG  ik+++  ++k +e +e
  EPA05034.1 15 MSLFQNVTGATARDCVDDEKHDRVIFVVNTGKMGLAIGKGGIHIKSLQNIVKKTVELVE 73
                689************887788**********************************9887 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 4.9e-08
                 EEEEEEC...CSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHH CS
        KH_2  16 skveIer...tanrviiviresqpgivIGkgGsnikkigkelrkdi 58 
                 s+v+++      +++i+++   ++giv+G++G+n +k +  +++ +
  EPA05034.1  92 SEVKLNTradGSKQAIVMVDPRKKGIVVGREGRNAEKARLLAKRYF 137
                 555554443234899************************9998766 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.1   3.8e-08   0.00017      21      61 ..      28      68 ..      15      72 .. 0.89
   2 !   18.5   0.0   3.1e-07    0.0014       7      60 ..      81     135 ..      79     141 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 3.8e-08
        KH_4 21 teeeeeeeveielnvegedlGrvIGkrGrtldAlqylvsaa 61
                ++ ++e+++++   v++ ++G+ IGk G  +++lq +v+  
  EPA05034.1 28 DCVDDEKHDRVIFVVNTGKMGLAIGKGGIHIKSLQNIVKKT 68
                56678999*****************************9865 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 3.1e-07
        KH_4   7 ilkalvddpeevevtee.eeeeeveielnvegedlGrvIGkrGrtldAlqylvsa 60 
                 +l +l++++   ev+++ + + +++  + v++ ++G+v+G++Gr++   + l+++
  EPA05034.1  81 FLMNLLNSKLVSEVKLNtRADGSKQAIVMVDPRKKGIVVGREGRNAEKARLLAKR 135
                 56666666666778888778999**********************9866666665 PP

>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.3   4.6e-11   2.1e-07       3      68 ..      36      95 ..      34      96 .. 0.95
   2 ?    2.5   0.2     0.035   1.6e+02       5      31 ..     106     127 ..     103     130 .. 0.84

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 4.6e-11
        KH_5  3 ertkvaVkshnpnvdpvGaivgkkGsrikavsseLkgekidvvewseDlaefianalsPaevlsVk 68
                +r++++V  ++     +G ++gk+G  ik++ +   ++ +++ve++eD+a+f  n+l+   v++Vk
  EPA05034.1 36 DRVIFVVNTGK-----MGLAIGKGGIHIKSLQNIV-KKTVELVEFDEDPAKFLMNLLNSKLVSEVK 95
                799********.....***************9999.**********************99999997 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.035
        KH_5   5 tkvaVkshnpnvdpvGaivgkkGsrik 31 
                 ++v+V  ++      G +vg++G++ +
  EPA05034.1 106 AIVMVDPRK-----KGIVVGREGRNAE 127
                 678888888.....9*********986 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.1   9.6e-06     0.043       4      28 ..      40      64 ..      37      89 .. 0.83
   2 !    4.4   0.1    0.0073        33       4      21 ..     108     125 ..     105     129 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.6e-06
                EEEGGGHHHHHHTGGGHHHHHHHHH CS
        KH_1  4 ilvPsslvgriIGkgGsnIkeIree 28
                + v++ ++g+ IGkgG +Ik++++ 
  EPA05034.1 40 FVVNTGKMGLAIGKGGIHIKSLQNI 64
                589999****************984 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0073
                 EEEGGGHHHHHHTGGGHH CS
        KH_1   4 ilvPsslvgriIGkgGsn 21 
                 + v+ ++ g ++G+ G+n
  EPA05034.1 108 VMVDPRKKGIVVGREGRN 125
                 689999**********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.32s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1021.78
//
Query:       EPA05035.1  [L=106]
Description: hypothetical protein BG20_I2095 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 782.01
//
Query:       EPA05036.1  [L=896]
Description: alanine--tRNA ligase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.6e-83  280.0   0.0    3.6e-83  280.0   0.0    2.1  2  tRNA-synt_2c  tRNA synthetases class II (A)
    5.6e-15   55.2   0.9    1.7e-14   53.6   0.9    1.9  1  tRNA_SAD      Threonyl and Alanyl tRNA synthetase second addi
    2.1e-07   31.4  17.0      3e-07   30.9  14.0    2.6  2  DHHA1         DHHA1 domain
     0.0097   15.7   1.0      0.019   14.7   1.0    1.4  1  Slu7          Pre-mRNA splicing Prp18-interacting factor
  ------ inclusion threshold ------
       0.54   10.6   5.8        1.7    9.0   5.3    2.1  2  PVL_ORF50     PVL ORF-50-like family
        4.6    7.7   9.1        2.1    8.7   6.3    1.9  2  ATP-synt_E    ATP synthase E chain


Domain annotation for each model (and alignments):
>> tRNA-synt_2c  tRNA synthetases class II (A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  280.0   0.0   1.2e-86   3.6e-83       8     551 ..      81     579 ..      79     580 .. 0.91
   2 ?   -3.6   3.0      0.93   2.8e+03     413     474 ..     737     802 ..     727     814 .. 0.44

  Alignments for each domain:
  == domain 1  score: 280.0 bits;  conditional E-value: 1.2e-86
                   HHHHCTT-EEE----SS-SSSTTCSS--SGGGGGHHHHTTSS.CGGSSSEEEEEEEEE-EETTEEGGGGTTTSSS--SEEEEEEEEESS...SS-HH CS
  tRNA-synt_2c   8 dfFekkgHtvvksssvvpendptllfvnAgmaqfkpiflgke.akpklkravnsQkciRagGkhnDlenVGktarHhTfFeMlGnfsfg...dYfke 100
                   +fF k+gHt v +++vv +++++l+f++A++++f+ i+ +k+  + ++++++  Q c+R++    DlenVG t+rH+  F M+G++s+     Y+k+
    EPA05036.1  81 SFFVKNGHTSVSRYPVVCRWRDDLYFTIASIVDFQRIMGSKVvFEFPANPLIVPQTCLRFK----DLENVGVTGRHFSSFCMIGQHSIPnsqGYWKD 173
                   6*************************************999966789**************....***********************87889**** PP

                   HHHHHHHHHHHTTTT--GGGEEEEEETTEH..HHHHHHHHTTTTEGGGEEEE-HHHHEEESSSSEEEEEEEEEEEECETTSHHCHCCCCTTCTCCHE CS
  tRNA-synt_2c 101 eaiefawelltkelgldkerlyvtvfeedd..eaveiweklvgvpeerilrfgekdnfwemgdtgpcgpcseiyydrgeeigkrkaaseveadddrv 195
                   e + + + llt+++g++ke++++ +  +++    ++  e +v++ e    +f    +f+    +    + ++i+++ g e++++  +++++a+d ++
    EPA05036.1 174 ECVDLDFRLLTEQFGIKKEEVVFVEDVWAGggSFGSSLEYFVRGLELGNAVF---TEFQGDLGNHTTLDQKIIDMGAGLERFAWITKGTPTAYDCCF 267
                   ****************************999899999999999999999999...8898555558999***************************** PP

                   EEEEEEEEEEEEESTTSHEEEEEEEEEEEEEEHHHHHHHHTTHSSGGGSCCTHHHHHHHHHHHT--TCSTCCHHHHHHHHHHHHHHHHHHHHTT--S CS
  tRNA-synt_2c 196 leiwnlvfmqfnreedgtlkpLpkksidtGmglerlvavLqevrsnydtdlfvpvieaieeisgatyedkdetdealrviaDHvralafaladGvvp 292
                     i n +f++++ ++    +++ +k   +     ++ ++L +vr++  +  +++  +  + i++          e ++ iaDH+r+l fa++dG++p
    EPA05036.1 268 GPITNHLFEKIGIDS---DSEMLRKYFTAIAKNLEIHEDLIDVRKHAVNATGLSQDQINRIITP---------LEGMYLIADHLRTLIFAITDGALP 352
                   ************994...445566777788888999**********999999999999999999.........789********************* PP

                   SSSHHHHHHHHHHHHHHHHHHHTT-SSTHHHHHHHHHHHHHTTTGCCHHCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCC.CSEEXHHHHH CS
  tRNA-synt_2c 293 snegrgYvlRrllRravrhakkLglkekflaklvavvvevlgdvypelkekeekveeiieeEeerFakTlerGlklleelikklkk.kkelsgedaf 388
                   sn+g gY lR++lRr    +++++lk + +++lv+++++ l d+ypel+ek++ v+ i++ E er+ +   r      +++++lk+ +++   ++++
    EPA05036.1 353 SNVGGGYNLRMMLRRINGTMDRMNLKLD-IDELVDMHIDYLRDTYPELDEKRDDVKTILKLESERYVESKVRM----GKMASRLKDkGRAPTVDELI 444
                   ****************************.*************************************9874443....33444444436777889*** PP

                   HHHHCHXXXHHHHHHHHHCTTXEEXHHHHHHHHHHHHHHHCCHHSXSSXXXXXXXXTTSHCHHCCTSTTTXXXXXXTSXXXXXXSEEEEEEEEEETT CS
  tRNA-synt_2c 389 kLydtyGfPvdltkeiaeekglkvdiegfekameeqrerskkekkekklikkdvealkelkkteeflgyeeleaeakvlallkdkefveeveegeev 485
                   +Ly++ G++++  kei    ++  +i+  ++a+    ++s k+k+ +         l+++++t+  l+y++           +  ef ++v ++ + 
    EPA05036.1 445 TLYESDGITPEYLKEI----NVISEIPSSFYAKLSDLHQSDKKKALE------SLPLENIPETDM-LFYKD-----------DPMEFDAKVLKVFDS 519
                   ********99887776....777889999999999999885544444......477888888777.99999...........6789*********** PP

                   EEEESEEXXXXSSSSCSXXXEEEEESSEEEEESEEEEETTEEEEEXSS.XSXXXTTSEEEEEEXHH CS
  tRNA-synt_2c 486 gvvLdrTpfYaesGGqigDeGliekegaefrvkdvqkakgvvlhkgkleegklkvgdkvkaevdee 551
                    vvLd+T+fYa +GGq+ D+G+i + +    v dv+k +gv++hk + +    ++gd+v+++vd +
    EPA05036.1 520 SVVLDKTSFYARGGGQEPDHGVIAGAK----VIDVNKDGGVIVHKLEGQ--VPNEGDTVSCKVDAT 579
                   ***********************9865....9************99985..99***********86 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 0.93
                   XHHHHHHHHHHHHHHHCCHHSXSS..XXXXXX.XXTTSHCHHCCTSTTTXXXXX.XTSXXXXXXSE CS
  tRNA-synt_2c 413 diegfekameeqrerskkekkekk..likkdv.ealkelkkteeflgyeeleae.akvlallkdke 474
                   +ie+ ++++ee++++ k +++e++   +k+++ + l+++++++ +   +e+e++  k+   +++++
    EPA05036.1 737 EIEQAQRLQEEKQKELKDKQREEEklRAKEKIpSLLEQVSAQKSSAIIDEIEINvDKIKSCFTNSK 802
                   333334444444443333333333233333331334444444555555555544134555555555 PP

>> tRNA_SAD  Threonyl and Alanyl tRNA synthetase second additional domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.6   0.9   5.6e-18   1.7e-14       1      44 []     679     722 ..     679     722 .. 0.98

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 5.6e-18
                 EEEEEETT.EEEEESS---SBGGGC-SEEEECCECCCTCEEEEE CS
    tRNA_SAD   1 vrvvsiGdisvelCgGtHvpnTgeIgafkilseesiakglrRIy 44 
                 vr+vsi+d++ve+CgGtHv++T++++++ki++ ++i++g+ R++
  EPA05036.1 679 VRIVSIEDFDVEACGGTHVKKTRDVELIKITKTKRIQDGVVRLE 722
                 9*****************************************86 PP

>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       4.1   1.2e+04      23      62 ..     629     647 ..     621     664 .. 0.49
   2 !   30.9  14.0     1e-10     3e-07      50     138 .]     788     894 ..     734     894 .. 0.62

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 4.1
                 HHHHHHHHHHTCEEECTCEEEEEECHCCHHHHHHHHHHHH CS
       DHHA1  23 aklkaeellekaeevkgvkvlvaevgeewdagalgiaadk 62 
                 ++++ ++++ ka e+                      a +
  EPA05036.1 629 TDQQVADIERKANEIV---------------------AKD 647
                 4444444444444443.....................222 PP

  == domain 2  score: 30.9 bits;  conditional E-value: 1e-10
                 CHHHHHHHHHHHHHHT...........HG..BT.TCEEEEEEEECTEEEEEEEESSH...SS-HHHHHHHHHHHTTCCEEEE.TCEEEEEEEHCHHHHH CS
       DHHA1  50 ewdagalgiaadklks...........kl..kk.pvivfvakeegdkvkvsarskkd...gvdagelakeaaaklgggGGGH.dlAaGagipaekleea 130
                 e++ + +++  ++ k+           +l  ++  ++ + + e g++v+v+a + ++   g +ag++ak +a++lgg GGG  ++A+G+g++ +k++ea
  EPA05036.1 788 EINVDKIKSCFTNSKQydeffhmnfgkRLvkDNpNSVYVGIFESGPTVRVIAYAGDEaskGKNAGNIAKSVAEILGGAGGGDaKFAQGGGKDTSKINEA 886
                 3333333333333333443333322222242564555555555555********988****************************************** PP

                 HHHHHHHH CS
       DHHA1 131 lealeeai 138
                 +++++++i
  EPA05036.1 887 IAKAKSMI 894
                 ***99876 PP

>> Slu7  Pre-mRNA splicing Prp18-interacting factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   1.0   6.4e-06     0.019     162     228 ..     703     774 ..     674     810 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 6.4e-06
        Slu7 162 lqlfAweaeekGe....dvhlqAnPtkaellakefkekkeklkeekkksilekYggeehlkakpkel.llaq 228
                  +l+   ++++ +    ++++ + Pt+ e++++++ e++++l+eek+k++ +k  +ee+l+ak+k   ll+q
  EPA05036.1 703 VELIKITKTKRIQdgvvRLEFVSGPTAREYVKQQEIEQAQRLQEEKQKELKDKQREEEKLRAKEKIPsLLEQ 774
                 5555555555544444588999************************************99998885422233 PP

>> PVL_ORF50  PVL ORF-50-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       2.2   6.7e+03       3      30 ..     430     458 ..     429     460 .. 0.79
   2 ?    9.0   5.3   0.00057       1.7      30      95 ..     711     779 ..     696     783 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.2
   PVL_ORF50   3 ririkpkkltkre.veliekygitpelva 30 
                 r+++k++  t  e + l e+ gitpe ++
  EPA05036.1 430 RLKDKGRAPTVDElITLYESDGITPEYLK 458
                 6788888888877357899******9875 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00057
   PVL_ORF50  30 akrvkdkleldealdarkdsrlkeekekvkskileeekkerklerqrkkeael..rrkkPhlfd..vPqk 95 
                 +kr++d++   e ++++      +++e+ ++++l+eek+++  ++qr++e +l  + k P l +    qk
  EPA05036.1 711 TKRIQDGVVRLEFVSGPTAREYVKQQEIEQAQRLQEEKQKELKDKQREEE-KLraKEKIPSLLEqvSAQK 779
                 699*******************************9999877666776655.4412455687777533455 PP

>> ATP-synt_E  ATP synthase E chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       4.5   1.3e+04      27      49 ..     623     647 ..     622     652 .. 0.50
   2 ?    8.7   6.3   0.00071       2.1      26      80 ..     727     779 ..     723     796 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 4.5
  ATP-synt_E  27 krqrslk..seekkeekereleaqe 49 
                 ++++sl+  + ++ e k++e+ a+ 
  EPA05036.1 623 THHSSLTdqQVADIERKANEIVAKD 647
                 5777776112234455555555555 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00071
  ATP-synt_E  26 akrqrslkseekkeekereleaqekliekakaayakkkqakseakslaegssaki 80 
                  + +++ k +++ e+++r +e+++k++++++++++k +++++ + sl e++sa+ 
  EPA05036.1 727 PTAREYVK-QQEIEQAQRLQEEKQKELKDKQREEEKLRAKEK-IPSLLEQVSAQK 779
                 55667777.889999*******************99988887.999998888763 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (896 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1519  (0.0847231); expected 358.6 (0.02)
Passed bias filter:                      640  (0.0356964); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.89u 0.28s 00:00:01.17 Elapsed: 00:00:00.49
# Mc/sec: 5537.69
//
Query:       EPA05037.1  [L=102]
Description: hypothetical protein BG20_I1707 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 637.87
//
Query:       EPA05038.1  [L=425]
Description: urea ABC transporter, urea binding protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   2.7e-154  513.5   0.0   3.3e-154  513.3   0.0    1.0  1  Peripla_BP_5  Periplasmic binding protein domain
    2.8e-70  237.7   0.0    3.2e-70  237.5   0.0    1.0  1  Peripla_BP_6  Periplasmic binding protein
    1.4e-08   34.3   0.0    2.9e-08   33.2   0.0    1.4  1  ANF_receptor  Receptor family ligand binding region


Domain annotation for each model (and alignments):
>> Peripla_BP_5  Periplasmic binding protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  513.3   0.0  5.5e-158  3.3e-154       1     362 [.      34     394 ..      34     396 .. 1.00

  Alignments for each domain:
  == domain 1  score: 513.3 bits;  conditional E-value: 5.5e-158
  Peripla_BP_5   1 ikvGvLhSlsGtmaisekslkdaallaieeinaagGvlgrkieavvvdpasdwelfaekaeklieedkvevvfGcwtSasRkavlpvveelnalLfY 97 
                   ikvG+LhSl+Gtmaise+++ da+l+aieein +gG+lgr++ ++++d++sdw+ fa +a++li edkv+vvfG+wtSasRk+++pv+ee ++lLfY
    EPA05038.1  34 IKVGILHSLTGTMAISETAVADATLMAIEEINDRGGILGREVVPILKDGKSDWSIFALEAKNLIVEDKVSVVFGGWTSASRKTMKPVFEEYDHLLFY 130
                   8************************************************************************************************ PP

  Peripla_BP_5  98 pvqYEGeEssknviYtGaapnqqaipavdyllselgakrvflvGsdyvypretnrilkallkakggevvgeeYlplgssdvqkivakikkakpdvvl 194
                   p+qYEG E s n+iYtGa+pnqq++pa+d+++++lg  r+flvGsdyv+pr++n+i+k  +++ gg vvgeeY  lg+++++ +v+ki + kpdv+l
    EPA05038.1 131 PIQYEGLEKSPNIIYTGASPNQQVLPAIDWAYENLG-PRFFLVGSDYVFPRSVNEIIKGKVHELGGVVVGEEYKLLGEENFKDVVDKIVESKPDVIL 226
                   ************************************.************************************************************ PP

  Peripla_BP_5 195 stinGdsnvafykelkeagikaekipvvslsvaeeelaaidaealvGhlaawnYfqsvdtpenkafvakfkarvgedrvtndpmeaayiqvklwaqA 291
                   +tinGdsn +f++el+++gi+++ ip +s+s+ae+e++ i+ae+++G++aawnYfqs+d++ n++fv++fk+++gedrv++dpme+ y++v+l+a+A
    EPA05038.1 227 NTINGDSNCSFFNELRQRGITPKVIPTISFSIAEDEIKIIGAEKMAGDYAAWNYFQSLDNKYNNDFVKNFKKKYGEDRVVDDPMESGYVGVYLYAKA 323
                   ************************************************************************************************* PP

  Peripla_BP_5 292 vekagstdvekvreallgqelkapeGevkidpenhhlsktvrigkikadGqfeivwetkkpvkpdpyskyl 362
                   v+ ag++d++ vre+l g +++apeG+v idp+n+hl+k+vrig+i  dGqf+iv ++++++kp+p+++y+
    EPA05038.1 324 VAMAGTDDISIVREKLKGLTFHAPEGAVGIDPQNQHLTKVVRIGQILPDGQFKIVSSSENQIKPNPFPDYK 394
                   *******************************************************************9987 PP

>> Peripla_BP_6  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  237.5   0.0   5.4e-74   3.2e-70       1     341 [.      33     373 ..      33     374 .. 0.99

  Alignments for each domain:
  == domain 1  score: 237.5 bits;  conditional E-value: 5.4e-74
                   EEEEEEEE-SSSTTHHHHHHHHHHHHHHHHHHHHTTEETTEEEEEEEEE-TTSHHHHHHHHHHHHHCT--SEEEE-BSHHHHHHHHHHHHHHT-EEE CS
  Peripla_BP_6   1 pikiGlltplsGpyassgksllagaqaafeeiNaaGGinGrkielverDdaydpdraaeaarrlvdqdgvdalvgplssavaaavaevlakdgvpvi 97 
                   pik+G l +l+G +a+s +++++++ +a+eeiN++GGi+Gr++  +  D ++d +  a  a+ l+ +d+v +++g+++sa ++ + +v+++ + +++
    EPA05038.1  33 PIKVGILHSLTGTMAISETAVADATLMAIEEINDRGGILGREVVPILKDGKSDWSIFALEAKNLIVEDKVSVVFGGWTSASRKTMKPVFEEYDHLLF 129
                   79*********************************************************************************************** PP

                   ESS-HHCCTTSTTEEESS--HHHHHHHHHHHHHHHTTSCEEEEEEESSHHHHHHHHHHHHHHHCCTEEEEEEEEE-TTHHHHHHHHHHHHTTT-SEE CS
  Peripla_BP_6  98 gpagltgekcspyvfslgpsysaqasalveylakelggkkvalvyadyafgregiaalkaaakaaGgevvgeepvplgttdfsaqvlqikaagadav 194
                   +p +++g + sp+++++g+s+++q+  +++++ ++lg  +++lv++dy f+r++++ +k  + ++Gg vvgee+  lg+++f+ +v++i ++++d++
    EPA05038.1 130 YPIQYEGLEKSPNIIYTGASPNQQVLPAIDWAYENLG-PRFFLVGSDYVFPRSVNEIIKGKVHELGGVVVGEEYKLLGEENFKDVVDKIVESKPDVI 225
                   *******************************999988.9*********************************9999********************* PP

                   EEESSHHHHHHHHHHHHHTT-SSSCEEEECCC-CHHHHHHHHHHHHTTEEEEESCSTCCCSHHHHHHHHHHHHHHTTGGC--HHHHHHHHHHHHHHH CS
  Peripla_BP_6 195 llagtgadlaallkaaaeaGldakrillvswsgseedlkalggeaaegvlavtpyfpdldnpavrafvaayeaayggapppsqfaaggyiaadllle 291
                   l +  g++++++++++++ G+++k i+ +s+s++e ++k +g+e+++g +a+ +yf +ldn+ +++fv++++++yg++++ +    +gy+++ l+++
    EPA05038.1 226 LNTINGDSNCSFFNELRQRGITPKVIPTISFSIAEDEIKIIGAEKMAGDYAAWNYFQSLDNKYNNDFVKNFKKKYGEDRVVDDPMESGYVGVYLYAK 322
                   ************************************************************************************************* PP

                   HHHCCTHCCHHHHHHHHHHS-BECCCTCCBEECTTSBEE--EEEEEE-.TS CS
  Peripla_BP_6 292 alkaagsltreavraaleslgfdgllgplkftaedhqasrpvyvvqvd.gg 341
                   a+  ag+ +   vr++l++l+f ++ g +++++++ ++++ v++ q+  +g
    EPA05038.1 323 AVAMAGTDDISIVREKLKGLTFHAPEGAVGIDPQNQHLTKVVRIGQILpDG 373
                   **********************************************87676 PP

>> ANF_receptor  Receptor family ligand binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.0   4.8e-12   2.9e-08       2     302 ..      53     336 ..      52     369 .. 0.76

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 4.8e-12
                   HHHHHHHHHHHHHT-TTSSTTEEEEEEEEE-TT-HHHHHHHHHHHCCC.CEEEEEE-SSHHHHHHHHHHHCCTT-EEEESS---GGGG-TTTTTTEE CS
  ANF_receptor   2 vleAmklAveeinsdpnllpgiklgyeiidtccdfslaleaaldflkg.kvvaviGpssssvsdavaslanlfkiPvisygstspelsdknryptfl 97 
                   v+ A  +A+eein+++++l++ ++  + +d ++d s     a +++   kv +v+G  +s++ ++++ + ++++  ++     +   + ++++p ++
    EPA05038.1  53 VADATLMAIEEINDRGGILGR-EVVPILKDGKSDWSIFALEAKNLIVEdKVSVVFGGWTSASRKTMKPVFEEYDHLLF----YPIQYEGLEKSPNII 144
                   56899**********999975.************9997777777776648****************************....344477888899997 PP

                   ESS--CHHHHHHHHH.HHHHTT--EEEEEEESSHHHHHHHHHHHHHHHHTT.-EEEEEEEEST..CHHHCHHHHHHHHHHTTT--EEEEEE-HHHHH CS
  ANF_receptor  98 rtvpsdtsqaqAivd.ilkhfgWkkvaliysdddygesglqaleeeleerg.icvalkekipe..ssnddevvrkllkeikskarvivlfcssedar 190
                    t  s ++q+   +d   +++g  ++ l+ sd    +s+ + ++ + +e g + v  + k     ++n+++vv+k+    +sk++vi+   ++++  
    EPA05038.1 145 YTGASPNQQVLPAIDwAYENLG-PRFFLVGSDYVFPRSVNEIIKGKVHELGgVVVGEEYK--LlgEENFKDVVDKIV---ESKPDVILNTINGDSNC 235
                   7777777777655550556666.8899999999888888888888******444444444..35699*********8...99*************** PP

                   HHHHHHHHTTS-STTEEEEETCHCCCECTTS-CC.....HHHHHTT-EEEEE.--B-HHHHHHHHHST--CCCSSSTCCGSTTCCHHHHH....HHH CS
  ANF_receptor 191 ellkaarrlgltgeeyvwiasdawtsslvldkpe...ltgleaaegvlgfrl.kdpnspkfsefldkreklsdekqnyenegkeqisyqaa.lmYda 282
                   +++++ r+ g+t +  v       t s++++++e      +++a+      + ++ +++   +f+         k++++++g+ +++   + + Y +
    EPA05038.1 236 SFFNELRQRGITPK--VIP-----TISFSIAEDEikiIGAEKMAGDYAAWNYfQSLDNKYNNDFV---------KNFKKKYGEDRVVDDPMeSGYVG 316
                   *************5..333.....44555555544453356676666665553345666677888.........88888888888555544268*** PP

                   HHHHHHHHHHHHCHHSSSHC CS
  ANF_receptor 283 VyllaeAlnkllrkkkpgra 302
                   Vyl+a+A+  +++++++  +
    EPA05038.1 317 VYLYAKAVAMAGTDDISIVR 336
                   *********99988844433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.50
# Mc/sec: 2554.00
//
Query:       EPA05039.1  [L=45]
Description: hypothetical protein BG20_I1706 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       674  (0.0375927); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 324.32
//
Query:       EPA05040.1  [L=730]
Description: PAS domain S-box [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      4e-17   62.7   2.3    4.7e-17   62.5   0.8    2.0  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    2.8e-15   56.4   0.3    1.7e-14   53.9   0.0    2.5  2  PAS_9        PAS domain
    3.5e-12   46.4   0.2    1.2e-11   44.7   0.1    2.0  2  PAS_3        PAS fold
    2.2e-10   40.5   0.0    4.8e-10   39.4   0.0    1.5  1  PAS          PAS fold
    1.3e-09   38.2   2.3    1.3e-09   38.2   2.3    2.3  3  dCache_1     Cache domain
      1e-08   35.0   1.1    2.6e-08   33.7   0.2    2.2  2  HATPase_c_5  GHKL domain
    1.2e-08   34.9   2.0    1.5e-08   34.5   0.4    2.1  2  HisKA        His Kinase A (phospho-acceptor) domain
    2.5e-07   30.9   0.0    5.3e-07   29.9   0.0    1.6  1  HAMP         HAMP domain
    4.2e-05   23.7   0.0    8.9e-05   22.7   0.0    1.6  1  PAS_4        PAS fold
      0.003   17.6   0.0      0.013   15.5   0.0    2.0  2  PAS_8        PAS domain
  ------ inclusion threshold ------
      0.011   15.6   0.4      0.095   12.5   0.1    2.6  2  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like
       0.05   13.6   0.0       0.12   12.3   0.0    1.6  1  HATPase_c_2  Histidine kinase-like ATPase domain


Domain annotation for each model (and alignments):
>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.5   0.8   3.2e-20   4.7e-17       2     110 ..     622     723 ..     621     725 .. 0.87

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 3.2e-20
                 HHHHHHHHHHHHHHHHHHH.HSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHHHHHHHHHTTTEEEEEEETT CS
   HATPase_c   2 dekrLrqiisnlvdNavkf.atkageieveikaseddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsivkklvelmgGeiwvesepg 99 
                 d+ +++ +++nl+ Na++  +  +g+i++++  ++ ++ i+v D+G Gi  + ++k+fe++++     ++++gtGlGl  vk++ve+++G+++v+++p 
  EPA05040.1 622 DKHKMEVVLINLIYNAIQVlEEGGGTIDIKLLNTKSEIIIEVIDSGSGIKLDPIDKVFEPLVT-----TKQKGTGLGLVSVKSIVEMHNGSVTVKNNP- 714
                 66677889**********933355566666665668***************************.....999***********************9999. PP

                 TEEEEEEEEES CS
   HATPase_c 100 rGttftftlpl 110
                   ttft+++p+
  EPA05040.1 715 --TTFTIKIPK 723
                 ..*****9985 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.9   0.0   1.2e-17   1.7e-14       4     104 .]     405     505 ..     401     505 .. 0.87
   2 ?   -2.1   0.0         3   4.5e+03      34      65 ..     547     575 ..     540     596 .. 0.69

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 1.2e-17
       PAS_9   4 ilidnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetfwvlltaspvkdddgelvgiivilr 100
                 + i +++g+i+++N+ ++r+  ys+ee++gk+++ l     ++e  + l++ l++g    +++ev +  k+g+ fw++ t++p+kd++g++  +++i  
  EPA05040.1 405 VSILDNSGHITFVNDEFCRVSKYSKEELIGKHQKILRadMYPQEFYDQLWDDLRRGA--IWRGEVCNKAKDGSLFWNKTTIVPFKDKNGKIYEFVAIRY 501
                 347789999***********************9999965566666666666666666..*************************************999 PP

       PAS_9 101 Dite 104
                 +it+
  EPA05040.1 502 NITD 505
                 9985 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3
       PAS_9  34 ksitdlfvtdpeanerlraaleqgrkkereve 65 
                  +++ l+  +++  +r+++a+++++  + e+ 
  EPA05040.1 547 LKLKKLL--NENQTKRIDNAIKRITH-QTEEV 575
                 5567777..88888899999999883.33322 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       4.4   6.5e+03      26      52 ..     119     145 ..     113     150 .. 0.78
   2 !   44.7   0.1   8.2e-15   1.2e-11       2      88 ..     415     499 ..     414     500 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 4.4
       PAS_3  26 wldlvhpeDrervrealqealkkgepy 52 
                 + d   p++  + ++++q+a+k+ +++
  EPA05040.1 119 YTDTFPPDEKFKDKKHFQDAVKGETSM 145
                 667778999999999999999887765 PP

  == domain 2  score: 44.7 bits;  conditional E-value: 8.2e-15
       PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeD.rervrealqealkkgepyegeyRirrkdGeyrwveararvirdengkpvrvigv 88 
                 ++v+++++++  ys+eel+gk   + +++  ++  ++++++l++ l++g+ + ge+  + kdG+ +w ++++++++d+ngk+++++++
  EPA05040.1 415 TFVNDEFCRVSKYSKEELIGK---HQKILRADMyPQEFYDQLWDDLRRGAIWRGEVCNKAKDGSLFWNKTTIVPFKDKNGKIYEFVAI 499
                 79*******************...9999999998999***********************************************9986 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   0.0   3.2e-13   4.8e-10      13     107 ..     404     497 ..     393     500 .. 0.90

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 3.2e-13
                 EEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEECTTSSEEEEEEEEEEEEETTEEEEEEE CS
         PAS  13 pifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfklrdgrpihlevraspvrdaggeilgfl 107
                  + ++D +g i++vN+++++   +s ee++gk+  +l+   +++e++++l+  l+ g  +r+ e++ k +dg+ ++  ++ +p+ d+ g+i +f+
  EPA05040.1 404 IVSILDNSGHITFVNDEFCRVSKYSKEELIGKHQKILRADMYPQEFYDQLWDDLRRGAIWRG-EVCNKAKDGSLFWNKTTIVPFKDKNGKIYEFV 497
                 57889*********************************999999*****************9.7777777*******************996655 PP

>> dCache_1  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   2.3   8.8e-13   1.3e-09       8     247 ..      31     293 ..      30     295 .. 0.76
   2 ?   -1.5   0.0       1.1   1.7e+03      68      91 ..     399     419 ..     357     465 .. 0.54
   3 ?   -2.4   0.1       2.2   3.3e+03      19      30 ..     558     569 ..     516     603 .. 0.55

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 8.8e-13
    dCache_1   8 eeqllglaeqlanniedvldslenlaetlasnpslqdlleepnra........neasreslqallksilksnpdisgvylvd.adGqviassdpssppn 97 
                 ++ql +++e+ ++++  ++d+++n+a  +a +  + ++ ++   a          ++r +l++ l s  ++ +d++++ + + + G+ i+ +d+ +p  
  EPA05040.1  31 KDQLVTISESNSDDLVKWIDERKNNAIVIAKDDVVISSTKK--LAdpktsineRFQNRFELESKLGSSIEHFSDFENFIISNaKTGEPIFYTDTFPPDE 127
                 57888999************************888776653..22567788888888888888888899999999999999745999999777777644 PP

    dCache_1  98 legtddpadrdwykealaggggkpvisdpy..vdqt..........ggkpvitiavpiyddsgkfiGvlaadldldnlqdlls.niklgetgyvfivds 183
                      ++ d+  +++a++g+   +  s+++  +             +++p++ i++pi  +   ++G+l+a +++     l++ +++  +t   ++v+s
  EPA05040.1 128 -----KFKDKKHFQDAVKGE---TSMSEVHlsT--KairnqhgfyeYSVPTLFISTPIKGE-AGIEGILTARVNFFAKPALIDhDYN-FHTLDSYLVNS 214
                 .....79***********99...5588888540..3344445666569***********96.4589******996555557775555.56789****** PP

    dCache_1 184 dGniiahpdkdl............lgknlrdelkaq..........ealekalakiesgvssvklng..eeylva.yapiptglgWylv 247
                 +G +++ p+               l          +          + ++k ++++e + +  ++n+   ++ +   +p+  +++W+ +
  EPA05040.1 215 QGYFLSEPKYNInavsygllddpmLK---------LhvknpdsnqlTEIFKLVNNKEIKYNLNGYNNygGHFVIGaISPVG-DTDWSYI 293
                 ********953344455555555533.........1444444444889999999999999999999885555566799997.7***987 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.1
    dCache_1  68 lksnpdisgvylvdadGqviassd 91 
                  +  +    v+++d++G + +++d
  EPA05040.1 399 IDESA---IVSILDNSGHITFVND 419
                 22111...2344455555544433 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 2.2
    dCache_1  19 anniedvldsle 30 
                 ++ i++ +++++
  EPA05040.1 558 TKRIDNAIKRIT 569
                 222222222222 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       7.2   1.1e+04      41      62 ..     238     259 ..     235     264 .. 0.70
   2 !   33.7   0.2   1.7e-11   2.6e-08       5      98 ..     625     721 ..     622     722 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 7.2
  HATPase_c_5  41 sliisieNsyegekkklessks 62 
                  +l ++++N+ +++  ++++  +
   EPA05040.1 238 MLKLHVKNPDSNQLTEIFKLVN 259
                  6778999999998877665444 PP

  == domain 2  score: 33.7 bits;  conditional E-value: 1.7e-11
  HATPase_c_5   5 dlcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyegek....kkle..sskskkeehGiGlksireivkkykgnlsieaedglFtl 96 
                   + v+l nl+ NAi+  ++       I++++ ++k+ +ii++  s +g k    +k++    ++k++  G+Gl s+++iv+ ++g+++++++ ++Ft 
   EPA05040.1 625 KMEVVLINLIYNAIQVLEEGG---GTIDIKLLNTKSEIIIEVIDSGSGIKldpiDKVFepLVTTKQKGTGLGLVSVKSIVEMHNGSVTVKNNPTTFTI 719
                  67799**********999977...69*******************99955555544332555778899*****************************9 PP

  HATPase_c_5  97 sv 98 
                  ++
   EPA05040.1 720 KI 721
                  87 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1       7.8   1.2e+04      36      48 ..     390     402 ..     377     406 .. 0.78
   2 !   34.5   0.4     1e-11   1.5e-08       3      61 ..     523     578 ..     521     582 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 7.8
                 SCHHHHHHHHHHH CS
       HisKA  36 elkeyletiesea 48 
                  l+++l+++++e+
  EPA05040.1 390 ALQQNLRRAIDES 402
                 4788999988876 PP

  == domain 2  score: 34.5 bits;  conditional E-value: 1e-11
                 HHHHHHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHH CS
       HisKA   3 grflagvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedlLdl 61 
                 g++ a ++H++r+PLs+i+  +++Lk +       + + ++i + ++r++h+ e++Ld+
  EPA05040.1 523 GELSARISHDIRNPLSVISNEIQMLKLK---KLLNENQTKRIDNAIKRITHQTEEVLDY 578
                 7999*********************773...345555789*****************98 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.0   3.5e-10   5.3e-07       9      52 ..     337     380 ..     329     381 .. 0.93

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 3.5e-10
                 HHHHHHHHHHHHTTTBTSSTCCTTSSSHHHHHHHHHHHHHHHHH CS
        HAMP   9 PLrrLaraarriaaGdldtrlpvsgrDEiGeLarafNaMldrLr 52 
                 P+++L +aa +i +G++++   ++++DEiGeL  +f+ M+++++
  EPA05040.1 337 PINKLNDAAHEIIKGNFNVKTKINSKDEIGELSNSFEYMVEHIK 380
                 9***************************************9985 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0     6e-08   8.9e-05       7     109 ..     404     507 ..     395     508 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 6e-08
       PAS_4   7 alavldpdgrvlyaNaaaaelfgappeellGktla....ellpeedaarleralrrvlegeepiefleelll.pgeerhyelrllPlrdesGevigvlv 100
                 ++ +ld  g+++++N +++++ +++ eel+Gk+      +++p+e  ++l ++lrr    ++ ++ + + +  +g+  +  ++++P++d +G++  +++
  EPA05040.1 404 IVSILDNSGHITFVNDEFCRVSKYSKEELIGKHQKilraDMYPQEFYDQLWDDLRR----GAIWRGEVCNKAkDGSLFWNKTTIVPFKDKNGKIYEFVA 498
                 56788******************************888888887655555555554....455555555555699999999*****************9 PP

       PAS_4 101 isrDiTerr 109
                 i + iT+++
  EPA05040.1 499 IRYNITDQK 507
                 999999987 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       3.3     5e+03      25      57 ..      78     105 ..      56     113 .. 0.75
   2 !   15.5   0.0   8.8e-06     0.013      13      63 ..     406     454 ..     393     459 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.3
       PAS_8  25 dvNqaalellGysadlkgellgqllpvlrplle 57 
                  +N++++  +      ++++lg  ++++ + + 
  EPA05040.1  78 SINERFQNRFE-----LESKLGSSIEHFSDFEN 105
                 58999999995.....66777777777777665 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 8.8e-06
       PAS_8  13 giavvd.lgdrivdvNqaalellGys.adlkgellgqllpvlrplledaeqll 63 
                 +i  +d  g  i++vN+ +++   ys ++l+g+   ++l+  +++ e+++ql 
  EPA05040.1 406 SI--LDnSGH-ITFVNDEFCRVSKYSkEELIGKHQ-KILRADMYPQEFYDQLW 454
                 33..453666.*************99777777665.88888888888888876 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.71   1.1e+03       5      30 ..     589     616 ..     586     620 .. 0.81
   2 ?   12.5   0.1   6.4e-05     0.095       2      63 ..     625     688 ..     624     712 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.71
  HATPase_c_3   5 kAlaelvdNsldAda..envkievnknr 30 
                  + l+elv+ sld  +   nvki++++n+
   EPA05040.1 589 FNLTELVKESLDTMMipSNVKITISENE 616
                  5699********9874468999998875 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 6.4e-05
  HATPase_c_3   2 slekAlaelvdNsldAdaen...vkievnknrgktgeivieDdGkGmseeelknalrlatsskea 63 
                  ++e++l+ l+ N+++   e    ++i++ + + ++  i + D G+G++ + +++++++  ++k++
   EPA05040.1 625 KMEVVLINLIYNAIQVLEEGggtIDIKLLNTK-SEIIIEVIDSGSGIKLDPIDKVFEPLVTTKQK 688
                  57999**********66554555****99986.6889999****************987777764 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   8.2e-05      0.12      33     110 ..     627     702 ..     610     720 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.2e-05
  HATPase_c_2  33 rlaveEactNavehayleapegpvevrlesdeealtvevaDsGpgfdpetlpdpteeepkeslkegGrGlalikglvD 110
                  ++++  +++Na+++  ++   g++ ++l  ++ ++ +ev DsG g ++ ++++  e+  ++++k  G+Gl  +k++v+
   EPA05040.1 627 EVVLINLIYNAIQVLEEG--GGTIDIKLLNTKSEIIIEVIDSGSGIKLDPIDKVFEPLVTTKQKGTGLGLVSVKSIVE 702
                  555556788999887765..689**********************999999999888889999999999998888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (730 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1048  (0.0584528); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.72u 0.32s 00:00:01.04 Elapsed: 00:00:00.49
# Mc/sec: 4458.53
//
Query:       EPA05041.1  [L=111]
Description: leucyl-tRNA synthetase family protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.6e-14   51.7   0.0    5.6e-14   51.7   0.0    1.3  2  tRNA-synt_1g  tRNA synthetases class I (M)
    4.9e-08   31.7   0.1    5.4e-08   31.5   0.1    1.0  1  tRNA-synt_1   tRNA synthetases class I (I, L, M and V)
    0.00056   19.4   0.0    0.00062   19.2   0.0    1.2  1  tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
     0.0096   14.9   0.0     0.0096   14.9   0.0    1.1  1  tRNA-synt_1d  tRNA synthetases class I (R)


Domain annotation for each model (and alignments):
>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -5.7   2.0       3.5   1.6e+04     269     280 ..       9      20 ..       5      23 .. 0.67
   2 !   51.7   0.0   1.2e-17   5.6e-14       2      72 ..      33     103 ..      32     106 .. 0.96

  Alignments for each domain:
  == domain 1  score: -5.7 bits;  conditional E-value: 3.5
                   SGGGG.G--S.. CS
  tRNA-synt_1g 269 eekwkeyWakdk 280
                   e+kw++ W++ k
    EPA05041.1   9 ESKWRKRWNDSK 20 
                   578999995544 PP

  == domain 2  score: 51.7 bits;  conditional E-value: 1.2e-17
                   EEEE--B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTTS-HHHHHHHHHH CS
  tRNA-synt_1g   2 lvttalpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAekegvtpeelvekvhe 72 
                   ++t+a pY+n+++H+Gh +++  aD++aR+ r++g++vlf  +    Gtpi   A++ + + +e++e+ ++
    EPA05041.1  33 FITVAYPYPNSPQHIGHGRTYTLADVHARFYRMKGYNVLFPMAFHYTGTPILGMAKRVEANDKEIIENLKN 103
                   79**************************************************************9998876 PP

>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.1   1.2e-11   5.4e-08       2      77 ..      12      84 ..      11     104 .. 0.82

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 1.2e-11
  tRNA-synt_1  2 lyekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaie 77
                 + ++W++++ f++    ++++k+fi ++  Py +   HiGh  + tl d+  r++rmkG++vl+ + +   G +i 
   EPA05041.1 12 WRKRWNDSKDFETD--PSDKEKKFI-TVAYPYPNSPQHIGHGRTYTLADVHARFYRMKGYNVLFPMAFHYTGTPIL 84
                 7799********99..555556665.5567899999*****************************99999999984 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.4e-07   0.00062      23      67 ..      45      89 ..      26     106 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.4e-07
                  -BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB--SHHHHHHHHH CS
  tRNA-synt_1e 23 shlGhaRslvafDilrrilqalgYdvqfvqnvtDidDkiikrare 67
                   h+Gh+R++   D+ +r+ +++gY+v f   +      i+  a++
    EPA05041.1 45 QHIGHGRTYTLADVHARFYRMKGYNVLFPMAFHYTGTPILGMAKR 89
                  7*************************9977766666666655555 PP

>> tRNA-synt_1d  tRNA synthetases class I (R)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   2.1e-06    0.0096      13      61 ..      25      71 ..      17     104 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.1e-06
                  .---SST-EEEEE----BTTS--BHHHHHHHHHHHHHHHHHHHCT-EEE CS
  tRNA-synt_1d 13 qkksrekkkvvvdfssPniakemhvGhLrstiiGdavsrlleflGydvi 61
                  ++  +ekk + v +  Pn   + h+Gh r+  + d+ +r + + Gy+v+
    EPA05041.1 25 DPSDKEKKFITVAYPYPN--SPQHIGHGRTYTLADVHARFYRMKGYNVL 71
                  5667899999*******9..588************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 908.27
//
Query:       EPA05042.1  [L=130]
Description: hypothetical protein BG20_I1708 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.018   14.2   0.4       0.02   14.1   0.4    1.1  1  Rac1      Rac1-binding domain


Domain annotation for each model (and alignments):
>> Rac1  Rac1-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.4   1.1e-06      0.02      89     172 ..       5      97 ..       1     112 [. 0.76

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.1e-06
        Rac1  89 elsikfrdsivlk..svesflarieksleapssfadirsl.......ereqkaletllevlltstekktPvraevysllnrlaevkkalssrv 172
                 ++s  ++d+++ +   + + l  + + +    + +di+sl       +++ + +e ++++ ++   k+ P + +   l n+l e+k+++s++ 
  EPA05042.1   5 DVSYIHKDTLKKNllVTSNDLDSLYHIISPNLENSDINSLleqrlnaNQDANIVEQMFKIQIAIFCKNGPSSVDNEELRNELVEIKQSISEQF 97 
                 67777777776542245556777777777777778888873322222346678*************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1402  (0.0781973); expected 358.6 (0.02)
Passed bias filter:                      602  (0.0335769); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1022.29
//
Query:       EPA05043.1  [L=269]
Description: putative Lysine biosynthesis enzyme LysX [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      6e-31  107.5   0.0    8.1e-31  107.1   0.0    1.2  1  RimK             RimK-like ATP-grasp domain
    2.2e-11   43.4   0.0    2.9e-11   43.1   0.0    1.2  1  GSH-S_ATP        Prokaryotic glutathione synthetase, ATP-gras
      3e-09   36.5   0.0    3.1e-05   23.4   0.0    2.7  3  ATPgrasp_ST      Sugar-transfer associated ATP-grasp
    4.8e-08   33.2   0.1    2.9e-07   30.7   0.1    2.0  1  ATP-grasp_3      ATP-grasp domain
      2e-07   30.5   0.0      0.017   14.4   0.0    2.1  2  ATPgrasp_YheCD   YheC/D like ATP-grasp
    7.5e-07   28.9   0.0      1e-05   25.2   0.0    2.3  2  ATP-grasp        ATP-grasp domain
    0.00019   21.3   0.0    0.00031   20.6   0.0    1.3  1  GARS_A           Phosphoribosylglycinamide synthetase, ATP-gr
    0.00035   20.2   0.0     0.0017   17.9   0.0    2.0  3  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
      0.001   18.6   0.0       0.16   11.5   0.0    2.4  2  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
  ------ inclusion threshold ------
      0.028   14.0   0.0      0.053   13.1   0.0    1.5  1  ATP-grasp_4      ATP-grasp domain
      0.079   12.4   0.0       0.15   11.5   0.0    1.4  1  ATP-grasp_5      ATP-grasp domain
      0.084   12.4   0.0       0.22   11.0   0.0    1.7  1  ATP-grasp_2      ATP-grasp domain


Domain annotation for each model (and alignments):
>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.1   0.0   5.4e-34   8.1e-31       3     187 ..      74     262 ..      72     263 .. 0.90

  Alignments for each domain:
  == domain 1  score: 107.1 bits;  conditional E-value: 5.4e-34
                 -HHHHHHHHHHTT-----EEEESS-S-HHHHHHTT-.-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHH......GGG--.EEEEE--SS-SEEEEEEE CS
        RimK   3 dKlkslklLakakikvpntalardeedaekliekiklrfPvvvKsvegsqGikvvlakkeqklkqvlea......lkeai.lvqeyieeaenediRvlv 94 
                 +K+    +L k+++++p+t ++   e a++ +ek+  + P+v+K v gs G +v+  k+++ +  ++e        + +i  +qe i+    +diRv+ 
  EPA05043.1  74 NKMFMTLMLKKHNVPTPKTYFSFTSESASENLEKV--GYPLVIKPVIGSWGRGVMQLKDKDTADALFEIrditdsPHDRIfYLQEVINR-PPRDIRVIT 169
                 6777778999*************************..69**********************9999888766544434455467888865.579****** PP

                 ETTEEEEEEEEE--SSS----TTTT-EEEE----HHHHHHHHHHHHHCT-SEEEEEEE.EETTEEEEEEEESS--SHHHHHHHT--HHHHHHHH CS
        RimK  95 vddevvaalrrvskeGdFRsnlhrGgvaeklqlseeekelAikaakamelvvaGvDll.rakrgllvlEvnsspglekiektlgidiakkliea 187
                 +dde +aa+ r+   G F++n+ +G+  e  ++++e +e+  ka+kam+  ++G+D++ ++krgl+v Evn  ++ ++++k ++ +i k+++e+
  EPA05043.1 170 IDDEPIAAMYRK-SSGGFKTNIALGADPELCEITKEIEEISTKASKAMGGGILGIDIMeDEKRGLVVHEVNNTVEFKGLSKVSRRNIPKEMVEY 262
                 ************.6789***************************************8835789****************************986 PP

>> GSH-S_ATP  Prokaryotic glutathione synthetase, ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   0.0   1.9e-14   2.9e-11       7     155 ..      84     229 ..      74     253 .. 0.83

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 1.9e-14
                 GGCCCS--EEEES-HHHHHHHHHHHSS.EEEEESS--TTTT-EEE-TT-T..THHHHHHHHTTTTTS-EEEEE--GGGGG-EEEEEEETTEE-SEEEEE CS
   GSH-S_ATP   7 sfpelipktlvskdkeeirafleeqgd.vilKPldgkgGegvfrvkksdp..nlksilellteegkepviaqrylpeikeGDkRillvdGepigyalaR 102
                 + +  +pkt  s  +e+ ++ le+ g  +++KP+ g+ G+gv+++k++d+   l  i +++ + + + + +q+ ++   + D R++ +d epi  a+ R
  EPA05043.1  84 KHNVPTPKTYFSFTSESASENLEKVGYpLVIKPVIGSWGRGVMQLKDKDTadALFEIRDITDSPHDRIFYLQEVINRPPR-DIRVITIDDEPIA-AMYR 180
                 4455679999999999999999999887*****************99865225778888888889999999999999877.*************.**99 PP

                 E--SS-S---GGGTSCEEEEE--HHHHHHHHHHHHHHHHTT--EEEEEEETTE CS
   GSH-S_ATP 103 vpaegevRsnlaaggraeatelterdreiaeelapkLkekGllfvGlDvigdk 155
                  + +g +++n+a g+  e  e+t++ +ei+++ ++++   G  + G+D+++d+
  EPA05043.1 181 KS-SGGFKTNIALGADPELCEITKEIEEISTKASKAM---GGGILGIDIMEDE 229
                 75.678************************9988665...66678****9885 PP

>> ATPgrasp_ST  Sugar-transfer associated ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0     2e-08   3.1e-05      10      86 ..      63     135 ..      60     144 .. 0.88
   2 ?   -1.2   0.0      0.64   9.6e+02     143     167 ..     164     184 ..     162     194 .. 0.65
   3 !    9.8   0.0   0.00029      0.43     227     267 ..     204     243 ..     199     255 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 2e-08
  ATPgrasp_ST  10 yNpraefplvddKlkfkelalraglkvpkllgvikeqaeiseleafvkeleegvviKpakgsgGkGilviteredqd 86 
                  +N+ + + +  +K+ ++ +++++ +++pk++ ++  ++ +++le++       +viKp+ gs+G+G++ +++++++d
   EPA05043.1  63 LNKFQVASMCGNKMFMTLMLKKHNVPTPKTYFSFTSESASENLEKVGYP----LVIKPVIGSWGRGVMQLKDKDTAD 135
                  67778888999********************************998554....59**************98877655 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.64
  ATPgrasp_ST 143 tiRvitflkdkkvevmlamlRlgtk 167
                  +iRvit+   +  ++  am R + +
   EPA05043.1 164 DIRVITI---DDEPIA-AMYRKSSG 184
                  9*****9...555555.66665555 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00029
  ATPgrasp_ST 227 evlelaakaaeklpglgylGwDivldeekgplllElNarpg 267
                  e+ e+  ka++  +g g+lG+Di  de++g+++ E+N+++ 
   EPA05043.1 204 EIEEISTKASK-AMGGGILGIDIMEDEKRGLVVHEVNNTVE 243
                  56677888888.8999*********************9865 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.1   1.9e-10   2.9e-07       1     155 [.      72     239 ..      72     243 .. 0.79

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 1.9e-10
                  HTSHHHHHHHHTTT.S---...........-EESS--SSSEEEEESS-------B--SS--TTE.................EEEE---SEEEEEEEEE CS
  ATP-grasp_3   1 asdKlktykkLkeagvkvP.......tkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve..........lvqefieGkplSvslls 81 
                  + +K++++  Lk+++v++P       ++  +e+le++ ++lv+Kp+ G+ g +v+  ++k++a+a +e              +qe i+  p  + ++ 
   EPA05043.1  72 CGNKMFMTLMLKKHNVPTPktyfsftSESASENLEKVGYPLVIKPVIGSWGRGVMQLKDKDTADALFEIRDitdsphdrifYLQEVINRPPRDIRVIT 169
                  78*****************999999888888999999*************************999998777778888887778888888888888888 PP

                  .SSSEEEEEEEEEEEET....TEEEEEEES----HHHHHHHHHHHHHTTSTT--EEEEEEEEESS..SEEEEEEE CS
  ATP-grasp_3  82 dgekvlvlavnrqliekaekefvyaGnvtpietelkeevvelaeevvekleglaGyvGvDlvlkd.eepyviEvN 155
                     +    a+ r+  + + k ++  G   p   e ++e++e+  ++ +++    G++G+D++  +  +++v EvN
   EPA05043.1 170 IDDEPIA-AMYRKSSG-GFKTNIALGA-DPELCEITKEIEEISTKASKAM--GGGILGIDIMEDEkRGLVVHEVN 239
                  4433333.33333332.2343555555.4555588899999999999999..57999999998886788888999 PP

>> ATPgrasp_YheCD  YheC/D like ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   1.1e-05     0.017       9      75 ..      72     137 ..      65     160 .. 0.75
   2 !   14.2   0.0   1.3e-05     0.019     182     254 ..     201     268 ..     177     269 .] 0.80

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.1e-05
  ATPgrasp_YheCD   9 ffnKwevyelLskdpelrpyLPetellesledleemlekyks.vylKpanGskGkgilriek.eekell 75 
                     + nK+ ++ +L+k++      P+t    + e+  e lek +  +++Kp+ Gs G+g+++++  ++++ l
      EPA05043.1  72 CGNKMFMTLMLKKHN---VPTPKTYFSFTSESASENLEKVGYpLVIKPVIGSWGRGVMQLKDkDTADAL 137
                     567777777777766...34588888889999999999999879****************983333444 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 1.3e-05
  ATPgrasp_YheCD 182 ileeleelalelaealeesfgrlgElGlDlgidkegkvWllEvNskpgrsifkeagdkeaarksvkrpleYak 254
                     i++e+ee+++++++a+       g lG+D++ d++  + + EvN     +  ++++ +++ +++v+  ++Y +
      EPA05043.1 201 ITKEIEEISTKASKAMG-----GGILGIDIMEDEKRGLVVHEVNNTVEFKGLSKVSRRNIPKEMVEYAFRYVR 268
                     44444444444444444.....589*********************************************986 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.5   3.7e+03      44      74 ..      10      45 ..       9      49 .. 0.67
   2 !   25.2   0.0   6.9e-09     1e-05       1     156 [.      82     238 ..      82     243 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.5
                TEEEECTCCGHHCHHHHC.....GTTCEEEEE---- CS
   ATP-grasp 44 Gqsvvrseedleqaleal.....keekvivEefvpf 74
                G+ vv +++++ q+ +       + + v++E  v++
  EPA05043.1 10 GHHVVMQDAKITQVNTDSkkedfDFGDVVLERCVSY 45
                677788888888877666455555566777777765 PP

  == domain 2  score: 25.2 bits;  conditional E-value: 6.9e-09
                 HHTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC......GTTCEEEEE----.SEEEEEEEEEETTC-EEE CS
   ATP-grasp   1 leklglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal......keekvivEefvpf.ekElsvlvvrsaeGetaf 92 
                 l+k+++p+p+ ++  ++e+++e +e++g+p+v+K ++ g+ G+G + ++++++++ ++e        +++ +++ e+++   + + v+++ ++    a+
  EPA05043.1  82 LKKHNVPTPKTYFSFTSESASENLEKVGYPLVIK-PVIGSWGRGVMQLKDKDTADALFEIRditdspHDRIFYLQEVINRpPRDIRVITIDDEPI-AAM 178
                 5899*****9999999999***************.*****************9999999887777777777888888875247777777766654.444 PP

                 --EEEEEEETTEEEEEEECEE-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEETTCTEEEEEE CS
   ATP-grasp  93 ypvvetvqedgilrlsvapaevsekaqkkaeeiakkiveeLggvGvfavElFvledgellvnEl 156
                 y       + +i  l   p     ++ k++eei  k+ +++gg G++++ + + e+  l+v E+
  EPA05043.1 179 YRKSSGGFKTNI-ALGADPEL--CEITKEIEEISTKASKAMGG-GILGIDIMEDEKRGLVVHEV 238
                 444444444433.23334443..34777777777777777765.77777777775555777776 PP

>> GARS_A  Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   2.1e-07   0.00031       1      64 [.      73     135 ..      73     148 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.1e-07
                 HBHHHHHHHHHHTT--B-.-EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEESSHHHHH CS
      GARS_A   1 asKsfakdllkkagipta.eyeaftdpeeakeyieeatakalVvKadglaagKgvivakseeeal 64 
                 ++K f+  +lkk+++pt+ +y +ft+ e+a+e +e+++ +  V+K++  + g+gv+  k+++ a 
  EPA05043.1  73 GNKMFMTLMLKKHNVPTPkTYFSFTS-ESASENLEKVGYPL-VIKPVIGSWGRGVMQLKDKDTAD 135
                 58****************77888886.789999********.*************9997776553 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.73   1.1e+03      53      93 ..      10      47 ..       7      51 .. 0.83
   2 !   17.9   0.0   1.1e-06    0.0017       7      68 ..      80     139 ..      74     176 .. 0.78
   3 ?   -3.6   0.0       4.2   6.2e+03      44      59 ..     211     228 ..     203     238 .. 0.64

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.73
                 TEEEESSHHHHHHHHHHHHHHHHHHHSTS-EEEEE--SSSE CS
  CPSase_L_D2 53 Gmrvarneeelaelvkkalaeakaafgnkqvlvekslkgpk 93
                 G +v+ ++++++++ + + +e    f    v +e+ ++ ++
   EPA05043.1 10 GHHVVMQDAKITQVNTDSKKED---FDFGDVVLERCVSYFR 47
                 8889999999999999999988...8888899999988777 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 1.1e-06
                  HHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHH CS
  CPSase_L_D2   7 ealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvk 68 
                   +lkk nvp+ +       t e a +  +++gyP +ik+ +g  G+G    +++++  +l++
   EPA05043.1  80 LMLKKHNVPTPKTYFS--FTSESASENLEKVGYPLVIKPVIGSWGRGVMQLKDKDTADALFE 139
                  5678899999998888..899999***********************999999988777765 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 4.2
                  EETTCCTT..TTEEEESS CS
  CPSase_L_D2  44 kaafglGG..kGmrvarn 59 
                  ka+ ++GG  +G  ++++
   EPA05043.1 211 KASKAMGGgiLGIDIMED 228
                  555555552245555555 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.012        19      17      46 ..      90     119 ..      78     142 .. 0.73
   2 !   11.5   0.0   0.00011      0.16     133     181 ..     200     247 ..     175     262 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.012
                      TTHHCH-H-HHHHHHHHHC-SSEEEEESSS CS
  Dala_Dala_lig_C  17 keeakeekkellekveeelgypvfVKpare 46 
                      ++++ + ++e+ ++  e++gyp+++Kp+  
       EPA05043.1  90 PKTYFSFTSESASENLEKVGYPLVIKPVIG 119
                      4555555667778888***********854 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00011
                      HHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEEEEESS---STT CS
  Dala_Dala_lig_C 133 eveekiqelalkaykaldlrGlaRvDfflteegeivlnEvNtlPGfTei 181
                      e++++i+e++ ka ka+++ G+  +D++ +e+  +v+ EvN    f  +
       EPA05043.1 200 EITKEIEEISTKASKAMGG-GILGIDIMEDEKRGLVVHEVNNTVEFKGL 247
                      7899************987.8999****************976555544 PP

>> ATP-grasp_4  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   3.6e-05     0.053       2      37 ..     109     143 ..     108     160 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.6e-05
  ATP-grasp_4   2 slPvviKPsvgffSlGVykinneeewkaavaaieee 37 
                   +P+viKP++g+  +GV+++++++   +a+ +i++ 
   EPA05043.1 109 GYPLVIKPVIGSWGRGVMQLKDKD-TADALFEIRDI 143
                  79*****************99865.55566666655 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0    0.0001      0.15      19      54 ..      82     117 ..      76     131 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0001
  ATP-grasp_5  19 leaygipvvetrlassaeeaveaaeeigypvvlKiv 54 
                  l+  ++p+++t +  ++e+a e  e++gyp v+K v
   EPA05043.1  82 LKKHNVPTPKTYFSFTSESASENLEKVGYPLVIKPV 117
                  78899*****************************76 PP

>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00015      0.22      10      54 ..      81     124 ..      78     139 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00015
                  HHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE--SSSTCC CS
  ATP-grasp_2  10 ilakygvkvpegevaesaeeaeeaakklgekelvvKaQvlaGGRG 54 
                  +l+k++v++p++   ++ e+a+e ++k+g    v+K  +   GRG
   EPA05043.1  81 MLKKHNVPTPKTYFSFTSESASENLEKVGYPL-VIKPVIGSWGRG 124
                  699*************************9987.****99999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1675.26
//
Query:       EPA05044.1  [L=324]
Description: homocysteine S-methyltransferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-62  212.2   0.0    1.3e-62  212.0   0.0    1.0  1  S-methyl_trans  Homocysteine S-methyltransferase


Domain annotation for each model (and alignments):
>> S-methyl_trans  Homocysteine S-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  212.0   0.0   7.4e-67   1.3e-62       1     267 [.      20     314 ..      20     315 .. 0.86

  Alignments for each domain:
  == domain 1  score: 212.0 bits;  conditional E-value: 7.4e-67
                     EEB---SHHHHHHT.......----STTHHCCHHH-HHHHHHHHHHHHHHT-SEEE-TTTT--GG.....T--HHHHH.HHHHHHHHHHHHHHHH CS
  S-methyl_trans   1 lilDGgmgteLerr.......adlseelwsaelltrpelikeihrdyleaGadiieTnTyqaskik....gleeeeeveelnraavelareaade 84 
                     l++DG+mgte++++       ++ ++ +    +lt+pe ik+ihr+yl+aG+d+ieTn+++++kik    g+   +++ e+n++ ++la e+++e
      EPA05044.1  20 LLFDGAMGTEIQKYdpkpedfPNNQDGFNDGLVLTHPEWIKQIHRNYLDAGSDCIETNSFGSNKIKldeyGFG--DQTIEFNKKIASLAVEVCSE 112
                     689**********9877755444444466777779****************************9988866676..7777**************** PP

                     H.....HEEEEE--HHHHCTS-.--...--HHHHHHHHHHHHHHHHHCT-SEEEEEEE--HHHHHHHHHHHT.....T...--EEEEE-ECCT.. CS
  S-methyl_trans  85 aaa.plfvagsvGpygatlsdg.yd.l.lsfeelveahreqiralleagvDlllietipdlleakaavellaa....e...lpvwisftikdes. 167
                     +++ p++v+gs+Gp g + s   +d      +e+++a++ q+++l+ +gvD lliet +d+le+k ++e+  +    +   +p+++  t+ d+  
      EPA05044.1 113 YNDkPRYVIGSMGPSGYLPSSNdPDlGqKPLDEIRDAFELQAEGLILGGVDALLIETSQDILEVKLVIEACHKamkkTgkkIPIIANTTL-DQYg 206
                     *889**********999988865765259**************99**********************996655454426679********.5544 PP

                     TETTS-BHHH.HHHHHCT-TE.EEEEEES--.GGGHHHHHHHHHTT--S-.EEEE--.....-.S-....----------....-HHHTT..EEE CS
  S-methyl_trans 168 tlrsGetleeavaalaaatqp.lavgvNCak.peelepllkelksetalpavivypn.....sage....vydltpeewaesaeewleag..ani 249
                     ++  G+++++a+++++++    + +g+NC++ p e++p ++ l+++++++ + v pn     +  +    vy++tpe++ e + ++l++   ++i
      EPA05044.1 207 KMLLGTNIQAAYTTVSDM--GiDVFGLNCSTgPVEMTPSVRWLDEQNEHN-ILVVPNagmpeN--QggraVYKMTPEKMGEVLGDFLKQYkkVRI 296
                     5559*************9..5599*******************6555544.99****766541..14578***************9977768*** PP

                     E---TT--HHHHHHHHH. CS
  S-methyl_trans 250 iGGCCgttpehIraiaea 267
                     iGGCCgt+p+hI+a++++
      EPA05044.1 297 IGGCCGTNPQHIAALRKV 314
                     ***************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1990.87
//
Query:       EPA05045.1  [L=253]
Description: 3-hydroxybutyryl-CoA dehydratase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-69  232.6   1.0    4.8e-69  232.5   1.0    1.0  1  ECH_1     Enoyl-CoA hydratase/isomerase
    2.5e-38  132.4   0.9      8e-35  120.9   0.1    2.0  2  ECH_2     Enoyl-CoA hydratase/isomerase
  ------ inclusion threshold ------
      0.074   13.3   0.1       0.14   12.5   0.1    1.5  1  DUF4362   Domain of unknown function (DUF4362)


Domain annotation for each model (and alignments):
>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  232.5   1.0     8e-73   4.8e-69       3     245 ..       9     252 ..       7     253 .] 0.99

  Alignments for each domain:
  == domain 1  score: 232.5 bits;  conditional E-value: 8e-73
                 ETTEEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEE.BTSEEEEEB-HHHHHHHHCHHHHHHHCCHHHHHHHHHHSSSEEEEEE-SEEE CS
       ECH_1   3 eagvaviklnrPeavNalsaelltEliqalekleddksvravvLtG.gdkaFaaGadlkemaeeekakqallkeevlelwtklytvpkpviaavnGaai 100
                 ++g++ +k+nrP+++Na++  + +Eli+ +e+l++d +v++++LtG g+kaF+aGad++ m + ++ +   + ++ +   + +  v  p+iaavnG+a+
  EPA05045.1   9 SDGICTVKINRPDKLNAMNIDVAKELIKTFETLDKDDNVKVIILTGeGEKAFSAGADIEYMSKISPDESVAYAKTGQLVTSTVELVRQPTIAAVNGFAL 107
                 789************************************************************************************************ PP

                 THHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHHHHHT-EEEHHHHHHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHH CS
       ECH_1 101 gGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeeilllgkkisaqealkvGlvdkvvpeeqlleealelaeklaekspaalr 199
                 gGG+ela+ cDi+iaad+a+ g++e+ +G+ pg ggtq+l+r+vG +kA+e++++gk i+a+ea+++Glv++vvp + l+eeal++a+++a +s   ++
  EPA05045.1 108 GGGCELAMSCDIRIAADTAKLGQPEVTIGIPPGWGGTQRLMRIVGIAKAKELVYTGKMIKADEAKEIGLVNQVVPLASLQEEALKMAKQIAANSTMGVQ 206
                 *************************************************************************************************** PP

                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSHHHHHHHHHHHTCSH CS
       ECH_1 200 qlkealnakledalaeqleaeaklfestfskddikeGlqaflEkrk 245
                 + k a+n+  +  l ++l++e     + f + d++e ++af+ k k
  EPA05045.1 207 MSKVAINKGRNADLDTGLAVELLAWRNCFTHSDREERMTAFVNKSK 252
                 *******************************************987 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.9   0.1   1.3e-38     8e-35       3     178 ..      14     187 ..      12     191 .. 0.95
   2 !   11.7   0.1   2.3e-05      0.14     247     309 ..     188     248 ..     184     253 .] 0.89

  Alignments for each domain:
  == domain 1  score: 120.9 bits;  conditional E-value: 1.3e-38
                 EEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THHHHHHHHHHHHHHHHHC-SS-EEEEE-BEEETH CS
       ECH_2   3 vitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkeeeeffreeYklnyliatypkpvvalmdGivmGg 101
                 ++++nrp++lNa++ +++++l +++++ +kdd+vk+++l+g+gekaf+AG D++ + +   +++ +   + ++   + ++++ +++p++a ++G+++Gg
  EPA05045.1  14 TVKINRPDKLNAMNIDVAKELIKTFETLDKDDNVKVIILTGEGEKAFSAGADIEYMSKISPDESVA---YAKTGQLVTSTVELVRQPTIAAVNGFALGG 109
                 789*****************************************************9999997755...999999999********************* PP

                 HHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHCSST.THHHHHHHH---B-HHHHHHTTS--EE--GGGHH CS
       ECH_2 102 GvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsrlpg.elGlylalTGarlkgadalaaglathyvpsekle 178
                 G+ l++++ +r++ +++++  PE++IG+ P  Gg+  L r+ g + ++ l  TG+ +k+ +a ++gl +++vp ++l+
  EPA05045.1 110 GCELAMSCDIRIAADTAKLGQPEVTIGIPPGWGGTQRLMRIVGiAKAKELVYTGKMIKADEAKEIGLVNQVVPLASLQ 187
                 ****************************************988799***************************99887 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 2.3e-05
                 HHHHHHHHHHHHS-HHHHHHHHHHHHHHTTT--HHHHHHHHHHHHHHHHHHSSHHHHHHHHTT CS
       ECH_2 247 ewakktletlkkrsPtslkvtleqlrrgrklsslaevlrmElrlalrllaekDfveGvrallv 309
                 e a k++++++++s + ++++  ++++gr++ +l++ l+ El + +++++++D  e  +a  v
  EPA05045.1 188 EEALKMAKQIAANSTMGVQMSKVAINKGRNA-DLDTGLAVELLAWRNCFTHSDREERMTAF-V 248
                 6688999************************.5********************99998875.4 PP

>> DUF4362  Domain of unknown function (DUF4362)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   2.3e-05      0.14      10      46 ..      24      61 ..      18      85 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.3e-05
     DUF4362 10 eisNvdklekFienveq.kkkdkirivsyTeeGdpile 46
                + +N+d  ++ i+ +e   k+d+++++ +T eG+  ++
  EPA05045.1 24 NAMNIDVAKELIKTFETlDKDDNVKVIILTGEGEKAFS 61
                678************9736779***********98775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 1691.05
//
Query:       EPA05046.1  [L=40]
Description: hypothetical protein BG20_I0417 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       230  (0.0128284); expected 358.6 (0.02)
Passed bias filter:                      154  (0.00858944); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.31s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 254.82
//
Query:       EPA05047.1  [L=204]
Description: cytidyltransferase-like domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-12   47.9   0.0    2.5e-12   47.2   0.0    1.4  1  CTP_transf_like  Cytidylyltransferase-like
  ------ inclusion threshold ------
      0.081   12.5   0.5       0.15   11.6   0.1    1.6  2  Period_C         Period protein 2/3C-terminal region
      0.085   12.7   0.3       0.56   10.1   0.1    2.1  2  FAD_syn          FAD synthetase


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.2   0.0   4.1e-16   2.5e-12       1      96 [.      68     161 ..      68     196 .. 0.83

  Alignments for each domain:
  == domain 1  score: 47.2 bits;  conditional E-value: 4.1e-16
                      EEEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-..SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHHHHHHHTTTTEEEEEEEHH CS
  CTP_transf_like   1 lagGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkk..kplasaeeRlemlelakevdevisvdpweltrevlkklkpdklylvigad 92 
                      lagG+FD+iH GH+  l+ ak+l++  liv v++d+++ k k  +pl s e+R e +  +  vd  +   ++++ + +++  kp+  ++++g d
       EPA05047.1  68 LAGGVFDIIHPGHIYTLNAAKSLGDV-LIVVVATDNTALKMKkrQPLHSKEQRQELVDSLVMVDLCLIGQEDDIFK-TVNLVKPQ--IIALGYD 157
                      79***********************9.*********99988559*******************************7.999999**..*****99 PP

                      HHHH CS
  CTP_transf_like  93 vled 96 
                      ++ +
       EPA05047.1 158 QVHQ 161
                      9877 PP

>> Period_C  Period protein 2/3C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       0.5     3e+03     122     135 ..      46      59 ..      40      62 .. 0.81
   2 ?   11.6   0.1   2.5e-05      0.15     124     157 ..      97     129 ..      91     145 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.5
    Period_C 122 eeVLkeDrekLkal 135
                 +++ keDr +L +l
  EPA05047.1  46 NKLVKEDRSALTEL 59 
                 67899999999876 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 2.5e-05
    Period_C 124 VLkeDrekLkalqksQPlftedqkreLaevhpwl 157
                 V   D  +Lk ++k QPl +++q++eL +    +
  EPA05047.1  97 VVATDNTALK-MKKRQPLHSKEQRQELVDSLVMV 129
                 6677888886.899*************9876655 PP

>> FAD_syn  FAD synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0     0.084     5e+02      76     105 ..      22      51 ..      17      63 .. 0.83
   2 ?   10.1   0.1   9.4e-05      0.56       7      74 ..      65     125 ..      59     145 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.084
     FAD_syn  76 gvdavlvvdFtkefaelsaeeFiekllvek 105
                  +d +    Ft+++  l+ +e i++ lv++
  EPA05047.1  22 HIDNLTKKGFTQKLIDLEIDELIKNKLVKE 51 
                 578888889999999999999999999865 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 9.4e-05
     FAD_syn   7 gavvtlGnFDGvHlGHqallkkaveaakekglpsvvvtFephPrevlakekaparLttleeklellee 74 
                 + v++ G FD +H GH   l+ a+++    ++ +vvv  ++   ++ +    +  L + e++ el+ +
  EPA05047.1  65 RVVLAGGVFDIIHPGHIYTLNAAKSLG---DVLIVVVATDNTALKMKK----RQPLHSKEQRQELVDS 125
                 568899************999999987...566666666665444444....3336666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1348.59
//
Query:       EPA05048.1  [L=387]
Description: argininosuccinate synthase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   6.7e-153  509.6   0.4   7.7e-153  509.4   0.4    1.0  1  Arginosuc_synth  Arginosuccinate synthase


Domain annotation for each model (and alignments):
>> Arginosuc_synth  Arginosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  509.4   0.4  4.3e-157  7.7e-153       8     386 ..       1     375 [.       1     377 [. 0.98

  Alignments for each domain:
  == domain 1  score: 509.4 bits;  conditional E-value: 4.3e-157
  Arginosuc_synth   8 lDtsviikllkeklgeeviavavdvGqeeedldevkekalklgavksvvvDakeefvedyifpaikanalYedrYllgtalaRPliakklveva 101
                      +Dtsv++k+l+e+++++vi+v+vdvGq+ +d  ++++ka+klg +k++ +Da++efve++ifp+ikanalY+++Y l+talaRPlia+k++e+a
       EPA05048.1   1 MDTSVVVKYLQEEYDMDVITVTVDVGQG-DDQRKIEAKAKKLGVKKHYNIDARKEFVEKFIFPSIKANALYQKKYCLATALARPLIAEKVLEIA 93 
                      6***************************.999************************************************************** PP

  Arginosuc_synth 102 kkegaeavahGctGkGnDqvRfevsirslaPdlkviaPvReleltReeeieyakekgipvevtkkkpysiDenllgrsieagiLedpknapped 195
                      kke  + +ahGc GkGnDqvRf++++rs + dl +iaP+R+ +l R +e+++ak++gi++++  +k +siD+nl+gr+ie+g+Ledp  +pp+d
       EPA05048.1  94 KKEKVTSLAHGCSGKGNDQVRFDITLRSGS-DLPIIAPIRDKNLDRVTELAFAKKHGIEIDSV-AKRFSIDQNLWGRAIEGGVLEDPYSEPPDD 185
                      ***************************998.*****************************987.667*************************** PP

  Arginosuc_synth 196 iyeltkdpakapdepeeveiefekGvPvaldgeelsvlelieklneiagkhGvGRiDivedRlvglksReiYeapaalvLikahkdlekltler 289
                      ++ ++k  ++ pd+p ++ei+fekG+Pva+dg+ l++++lie++n+ ag+ GvG +D++edR+vg+ksRe+Ye+p+al Li+ah+dlek++ ++
       EPA05048.1 186 AFIWVKT-KNLPDKPTYIEIKFEKGIPVAVDGKILEPIKLIEYVNKKAGDAGVGIVDHIEDRVVGIKSREVYETPGALCLIEAHSDLEKMVHTK 278
                      ****986.56789********************************************************************************* PP

  Arginosuc_synth 290 evakfkkiveekyaelvYkGlwfsPlkealdafiektqervtGtvrvklfkGsvvvlgReseeslYdeelasydeedefdqkeaeGfikihglq 383
                      +++kfk+i+++++a l Y+Glw++Plk++ld+fie +q+ vtGtv++klfkGs++v+gR+s++slY++++a+y +e++fdqk a+Gf++++g+q
       EPA05048.1 279 HENKFKSIIDDEWAYLAYSGLWQDPLKQDLDSFIETSQKPVTGTVKIKLFKGSMRVVGRKSDYSLYSHKIATYGSESTFDQKMAKGFVELWGIQ 372
                      *********************************************************************************************9 PP

  Arginosuc_synth 384 akl 386
                      +  
       EPA05048.1 373 STE 375
                      875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.52
# Mc/sec: 2227.54
//
Query:       EPA05049.1  [L=394]
Description: HMGL-like protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.2e-66  223.6   0.0    4.2e-66  223.2   0.0    1.1  1  HMGL-like    HMGL-like
  ------ inclusion threshold ------
      0.045   14.1   0.4       0.17   12.2   0.1    2.2  3  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  223.2   0.0   4.7e-70   4.2e-66       1     248 [.      26     267 ..      26     285 .. 0.94

  Alignments for each domain:
  == domain 1  score: 223.2 bits;  conditional E-value: 4.7e-70
                 B-EEEE-TTTHHHHTSSS---HHHHHHHHHHHHHHT-SEE--TSGGGT.THHHHHHHS---TT-B..--EE-SSHHHHHHHHH....TT-SEEEEEEES CS
   HMGL-like   1 kvkivdttLRDGeqalkaalsveeklaiakaLdeagvdeiEvgfpaaseddfevvraiakavkkarilalvrarekdikaavealkgagakrvhvfiat 99 
                 k+k++d+tLR+Geq ++++++ ++ ++ia +Ld +gvd+iE++ p+ s d+ e++++i+k++ ka+i+++ ra ++di+   +      ak    ++ +
  EPA05049.1  26 KIKVLDSTLREGEQHPGVSFTNKQRIQIAWMLDYFGVDQIEIS-PVVSSDHKEATKTIIKQGLKADIVSHGRALKEDIDISLS----VDAKWCAAYLGI 119
                 5899*************************************96.77777**********************************....999********* PP

                 -HHHHHHHHSSTHHHHHHHHHHHHHHHHHTT-ETTT-BTTTBS--HHHHHHHHHHHHHHT-SEEEEEETTS---HHHHHHHHHHHHHHS-.GGGEEEEE CS
   HMGL-like 100 selhlkaklkkdreevakkaeeavkaarslgkdvelsledasrtdleflaevveaaeeaGatriniaDtvGvltPneaaelisalkervkdkvilsvHc 198
                 s++hlk kl+++ree++++a+e v++a+s+g ++++ +ed sr+++ fl++v++a+eeaG++ri+++DtvG++ P  +++ +++++++++  v+l  H 
  EPA05049.1 120 SDIHLKDKLRITREEALDRAVETVEYAKSHGLKIRFTVEDGSRAEPGFLLKVCKAIEEAGVDRISLPDTVGIMRPIGMYNFVKTVRDEID--VPLDAHV 216
                 ******************************************************************************************..******* PP

                 B-TTS-HHHHHHHHHHTT--EEEEBTTS--SSBBB-BHHHHHHHHHHTT.- CS
   HMGL-like 199 HndlGlAvantlaAveaGadrvdgtvnGlGeraGnaaleelvaalealg.v 248
                 Hnd+G Avan+  A  aG+d++ +t+ G+Ger+G ++l e+++al  l   
  EPA05049.1 217 HNDIGFAVANAFSACDAGVDQIHTTIDGIGERTGIPPLAEVAVALTYLYkS 267
                 ********************************************9877642 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   1.9e-05      0.17      60     144 ..      72     153 ..       3     160 .. 0.75
   2 ?   -2.7   0.0      0.74   6.6e+03      92     107 ..     170     185 ..     165     186 .. 0.75
   3 ?   -3.8   0.0       1.7   1.5e+04     100     115 ..     233     248 ..     232     263 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.9e-05
                  STTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT..-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM  60 ypdfvellerlaklavpgiritvetngtlpdeeklerllelg..vdrvslgleaaddekvlklmnrghtfeevlealeklreagikr 144
                   +d  e+++ ++k    g++  +++ g  + +e ++  l     +   +lg+  ++ ++ l+++ r + +++ +e++e+++++g+k 
   EPA05049.1  72 SSDHKEATKTIIKQ---GLKADIVSHGRAL-KEDIDISLSVDakWCAAYLGISDIHLKDKLRIT-REEALDRAVETVEYAKSHGLKI 153
                  34555666666665...9999999999999.6666666665555********************.*******************994 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.74
                  HHHHHHHHTT-SEEEE CS
                  xxxxxxxxxxxxxxxx RF
  Radical_SAM  92 eklerllelgvdrvsl 107
                  ++ +++ e+gvdr+sl
   EPA05049.1 170 KVCKAIEEAGVDRISL 185
                  6778899999999987 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 1.7
                  TT-SEEEEEEBSSSHH CS
                  xxxxxxxxxxxxxxxx RF
  Radical_SAM 100 lgvdrvslgleaadde 115
                  +gvd+++ +++ + ++
   EPA05049.1 233 AGVDQIHTTIDGIGER 248
                  5677777777665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.64
# Mc/sec: 1844.09
//
Query:       EPA05050.1  [L=345]
Description: diphthine synthase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.4e-20   71.5   0.0    3.4e-19   69.6   0.0    1.8  2  TP_methylase    Tetrapyrrole (Corrin/Porphyrin) Methylases
    3.1e-13   49.6   0.2    9.9e-13   48.0   0.1    2.0  2  DUF357          Protein of unknown function (DUF357)
  ------ inclusion threshold ------
      0.077   12.8   0.0       0.25   11.1   0.0    1.8  2  Ala_racemase_C  Alanine racemase, C-terminal domain


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.6   0.0   5.8e-23   3.4e-19       1     212 [.       1     220 [.       1     221 [. 0.76
   2 ?   -0.8   0.0       0.2   1.2e+03      42      88 ..     280     326 ..     241     327 .. 0.50

  Alignments for each domain:
  == domain 1  score: 69.6 bits;  conditional E-value: 5.8e-23
  TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleea....yeeiaealaealragkdVvllvsGDPlvy 93 
                   +l++VG+G+ + + + v+Al++l +ad+v+ ++   ++ + +++     l  +++++  +l e+     e+ +e+  ++++++ +Vvll+ GDP+++
    EPA05050.1   1 MLWFVGLGISGSKSIPVEALEVLSKADIVYFEQ--FTSPIGKADV----LKIKKMTNG-ELKEGkrwlVEDGNEI-LKHAKTK-KVVLLSYGDPYIA 88 
                   699**************************8777..7777765442....233333332.3333314533333333.4444444.4************ PP

  TP_methylase  94 gtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl..lpglakeeereleallangdtlvll.........kaprk.laelae 178
                   +t++el +++ +  + i+++ i + ssl++++   g++ ++ g + +++   ++l ++ +  ++++++ ++t++ll         ++p++ l  l+e
    EPA05050.1  89 TTHIELRTRAIQ--EKIKTHSIHASSSLTSMIGECGLHFYKIGRIATIMseMKSLTTPYYVIYKNIIEGNHTVLLLeynqdkkffMDPKDaLTGLIE 183
                   ******977777..78***********************************888888899****************655444444444423444443 PP

  TP_methylase 179 lLkea...lyddttpvavveragtedervvrgtleel 212
                     k +   + d  t ++v++r+g +d+ ++ g+++ l
    EPA05050.1 184 TEKGQkrnVIDLSTYAIVASRIGFKDQSITSGKISSL 220
                   33322345777888****************9999876 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.2
  TP_methylase  42 dllaeeleleapmgkekepleeayeeiaealaealragkdVvllvsG 88 
                   ++l+e  + + ++++ k  l+ a   i++a + + + + +V++l++G
    EPA05050.1 280 EALEEIIPYYKDQKEFKVILDNAELYIQDAEKFLEDGQDEVAILSIG 326
                   33322222333333333333333333333333333333336666655 PP

>> DUF357  Protein of unknown function (DUF357)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       2.3   1.4e+04      36      54 ..     163     181 ..     160     182 .. 0.77
   2 !   48.0   0.1   1.7e-16   9.9e-13       1      71 [.     273     339 ..     273     341 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 2.3
                 HHHHHHHHHHHTT-HHHHH CS
      DUF357  36 sYleDakyflekgdlvnAl 54 
                  Y +D k f++ +d  + l
  EPA05050.1 163 EYNQDKKFFMDPKDALTGL 181
                 5888889999988877765 PP

  == domain 2  score: 48.0 bits;  conditional E-value: 1.7e-16
                 HHHHHHHHHHHHHH.....TS---HHH...HHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS CS
      DUF357   1 rYirlleealekvkiapdeesplgeaa...eevlemaesYleDakyflekgdlvnAlasfsYaeGwLDagarlg 71 
                 +Y+++++eale++        p+++++   + +l++ae Y++Da+ fle g  + A+ s+ Ya G++Da++ ++
  EPA05050.1 273 KYVPMVREALEEII-------PYYKDQkefKVILDNAELYIQDAEKFLEDGQDEVAILSIGYADGLVDALRLAK 339
                 7*************.......555555334689*************************************9875 PP

>> Ala_racemase_C  Alanine racemase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0      0.92   5.5e+03      16      32 ..      76      92 ..      67      99 .. 0.65
   2 ?   11.1   0.0   4.2e-05      0.25      28      49 ..     314     335 ..     308     342 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.92
                    TTSEESGGGSEE-SSSE CS
  Ala_racemase_C 16 agegvgYgatyvaerdt 32
                    +    +Yg  y+a+ + 
      EPA05050.1 76 KVVLLSYGDPYIATTHI 92
                    44456888888887665 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 4.2e-05
                     -SSSEEEEEES--GGGTCGGGG CS
  Ala_racemase_C  28 aerdtriavvpiGYaDGlpral 49 
                      + + ++a+++iGYaDGl  al
      EPA05050.1 314 EDGQDEVAILSIGYADGLVDAL 335
                     566789***********98766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       710  (0.0396006); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2231.01
//
Query:       EPA05051.1  [L=328]
Description: ABC transporter, substrate-binding protein, aliphatic sulfonates family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-24   86.7   0.0    2.6e-24   86.3   0.0    1.1  1  NMT1_2          NMT1-like family
    1.9e-18   67.2   0.0    3.2e-18   66.5   0.0    1.3  1  NMT1            NMT1/THI5 like
    2.4e-08   33.9   0.0    3.6e-08   33.3   0.0    1.2  1  Phosphonate-bd  ABC transporter, phosphonate, periplasmic sub
      6e-05   22.6   0.0     0.0045   16.4   0.0    2.2  2  SBP_bac_3       Bacterial extracellular solute-binding protei
    6.8e-05   22.6   0.0    9.5e-05   22.1   0.0    1.2  1  OpuAC           Substrate binding domain of ABC-type glycine 
     0.0078   15.7   0.0      0.011   15.2   0.0    1.2  1  NMT1_3          NMT1-like family
  ------ inclusion threshold ------
      0.031   14.5   0.0      0.044   14.0   0.0    1.2  1  ERCC4           ERCC4 domain


Domain annotation for each model (and alignments):
>> NMT1_2  NMT1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.3   0.0     1e-27   2.6e-24       5     246 ..      17     251 ..      13     258 .. 0.90

  Alignments for each domain:
  == domain 1  score: 86.3 bits;  conditional E-value: 1e-27
      NMT1_2   5 keqlklGfialtdaaplvvakekglfake.Glt..velekqaswaelrdkllagelDaahv.ltpapllidlGiggakadmkvlaslnlnGqaitlsnk 99 
                 +++++++++++++++  ++  e+g+fa+e G t  ++++ + s++++ + + ag++D+a+v   pa+ ++ +       ++k+l   ++ G + +++ +
  EPA05051.1  17 ENKIRVAYFPNITHVVPIIGLERGTFANEiGNTitIQPILFDSGPQVIESIFAGSVDIAYVgPGPAINGFLKSE---HHNVKILSGAASGGVSFIVHPD 112
                 6799******9999999999999999999866522699*******************************99998...9******************987 PP

      NMT1_2 100 lkdkkvsdakalkdlvakkkaskplkiavtfpgsthdlllrywLaaaGldp...eadvklvvvpppqmvanlkagtidgfcvgePwnaqavaegiGvta 195
                       s+ ++++d ++k       +ia+++ g+ +d+ lr++L a+Gl+p      v ++ vp++++   +++g+id+++v eP    +v++  G  +
  EPA05051.1 113 ------SKINSAEDFIGK-------RIAAPQIGNSQDISLRTYLSANGLKPaekGGSVIVLNVPNSDIYTLFAKGDIDAAWVAEPTATLLVQKLNGTRL 198
                 ......899999999655.......5667777789****************998889****************************************** PP

      NMT1_2 196 ltsqelwkdhPekv..lgvredfveknpntaralvkalleAtkwldakkenra 246
                 +++ + w+d+      l v+ed+v+++p++ r+ ++a+ +  +w++ ++e  +
  EPA05051.1 199 FDEIDMWPDQKFASvlLIVNEDYVNQHPEVIRKWLEAHQQTIDWINSNPEETR 251
                 *********8444457******************************9665554 PP

>> NMT1  NMT1/THI5 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.5   0.0   1.2e-21   3.2e-18      73     215 ..     103     249 ..      55     250 .. 0.85

  Alignments for each domain:
  == domain 1  score: 66.5 bits;  conditional E-value: 1.2e-21
                 --EEEEEECCC--SSGGGGTTSEEEE-S.-TTHHHHHHHHHHHTT--GGG....-EEEE-.TT-HHHHHHCTSSSEEECEETTTHHHHHHHTT--EEEE CS
        NMT1  73 plsglivlkdsgikspkDLkGkrigyvg.spfekallkallakdggdpsd....vtlvnvggtslakalltgkvDaaiggyenwegvelesegkelrif 166
                    ++iv+ ds+i+s +D+ Gkri+ ++ ++ +++ l++ l+++g++p++    v ++nv +++ ++ +++g +Daa+ + e   ++ +++    + ++
  EPA05051.1 103 GGVSFIVHPDSKINSAEDFIGKRIAAPQiGNSQDISLRTYLSANGLKPAEkggsVIVLNVPNSDIYTLFAKGDIDAAW-VAEPTATLLVQKLNGTRLFD 200
                 55789**********************977789*************886444449***********************.66665555555665566677 PP

                 -GGGTT-----SEEEEEEHHHHHH-HHHHHHHHHHHHHHHHHHHHSHHH CS
        NMT1 167 aladlgvpdyyslvlitnekllkenpelvkkFlrAlkkGyeyalahPee 215
                 +++ +   ++ s +li+ne++++++pe ++k l+A ++ ++++  +Pee
  EPA05051.1 201 EIDMWPDQKFASVLLIVNEDYVNQHPEVIRKWLEAHQQTIDWINSNPEE 249
                 77777777****************************************8 PP

>> Phosphonate-bd  ABC transporter, phosphonate, periplasmic substrate-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.0   1.4e-11   3.6e-08      33     173 ..      54     203 ..      42     240 .. 0.76

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 1.4e-11
                     EE--SSHHHHHHHHHTTS-SEEE--HHHHHHHHHHS-EEEEEEEEETT--SEEEEEEEEETTSS--SHHHHGG-EEEE--TT-TTTTHHHHHHTC CS
  Phosphonate-bd  33 lvvatdyaavvealragqvDiaflgplayvqardqagveplatrvrsdGsasyrsviivradsdiqsledLkgktiafvspsStsGylvpaalLv 127
                        +++  +v+e++ ag+vDia++gp ++++   +++   + + +   G+as    +iv++ds+i+s ed+ gk+ia ++    s  +  +++L 
      EPA05051.1  54 PILFDSGPQVIESIFAGSVDIAYVGPGPAINGFLKSEHHNVKILS---GAASGGVSFIVHPDSKINSAEDFIGKRIAAPQIG-NSQDISLRTYL- 143
                     4456777899*********************98887765555554...68999999**********************9977.5668999999*. PP

                     CCCT--HHHHSSEE.EE-.-HHHHHHHHHTTSSSEEEEEHHHHHHHH............H CS
  Phosphonate-bd 128 keagldpeddfsev.fsg.shdaavlavlsgdadaaavsadaledlv............a 173
                     + +gl+p +  ++v   +   +  +   ++gd+daa v + +++ lv            +
      EPA05051.1 144 SANGLKPAEKGGSViVLNvPNSDIYTLFAKGDIDAAWVAEPTATLLVqklngtrlfdeiD 203
                     8*******999999766657888888999********99988888883333333333333 PP

>> SBP_bac_3  Bacterial extracellular solute-binding proteins, family 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.5   0.0    0.0081        21     113     177 ..      35      97 ..       4     109 .. 0.70
   2 !   16.4   0.0   1.8e-06    0.0045      85     176 ..     103     199 ..      93     214 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0081
                 EEEETTSHHHHHHHHHHHCTSEEEEESSHHHHHHHHHTTSSS.EEEEEHHHHHHHHHHCCGCCEEE CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
   SBP_bac_3 113 vgvqagstaeellkeelkkgaeivefdtleealqaLkngrvd.avvadspvlaylvkknpdkkvvl 177
                 +g  +g+ a e+ +     +++ + fd+ +++++ + +g+vd a+v+  p++++++k +  + ++l
  EPA05051.1  35 IGLERGTFANEIGNT-I--TIQPILFDSGPQVIESIFAGSVDiAYVGPGPAINGFLKSEHHNVKIL 97 
                 777777777744443.1..677779*****************778999999999998887766665 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 1.8e-06
                 EEEEEEEEETTSHGTCCHSSCGCGTTSEEEEETTSHHHHH.HHHHHHC..........TSEEEEESSHHHHHHHHHTTSSSEEEEEHHHHHHHHHHCCG CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
   SBP_bac_3  85 agqvllvrkkdaskissiksladLkgkkvgvqagstaeel.lkeelkk..........gaeivefdtleealqaLkngrvdavvadspvlaylvkknpd 172
                  g++++v+ +     s+i+s +d+ gk++++ +  +++++ l +++ +          g  iv    +++ +++ ++g +da+ + +p++  lv+k ++
  EPA05051.1 103 GGVSFIVHPD-----SKINSAEDFIGKRIAAPQIGNSQDIsL-RTYLSanglkpaekgGSVIVLNVPNSDIYTLFAKGDIDAAWVAEPTATLLVQKLNG 195
                 5788899844.....4688888*********99999999954.4344446777788865555667788999999*********************9988 PP

                 CCEE CS
                 xxxx RF
   SBP_bac_3 173 kkvv 176
                   ++
  EPA05051.1 196 TRLF 199
                 7766 PP

>> OpuAC  Substrate binding domain of ABC-type glycine betaine transport system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   3.7e-08   9.5e-05     131     237 ..     133     244 ..      56     251 .. 0.71

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 3.7e-08
                 HCCHHHH.HHHHHHT-TTCEEEGSCEEEEHH...HHHHHHHTTCSSEEEEETTSTHH..HHTTEEE-B-TTSTS-SS..EEEEEEEEHHHHHHSCT.HH CS
       OpuAC 131 gcekvte.gllkaYgldkvelvegseaamda...elyaaykrgepvvvyawtPdwai..kkydlvvLedpkglfppa..ynvvpvvrkefaekaPe.va 220
                 ++++++  + l a+gl+  e+  gs+  +     ++y+ +++g+++++++ +P++++  +k++ ++L d  +++p +  ++v ++v++++  ++Pe + 
  EPA05051.1 133 NSQDISLrTYLSANGLKPAEK-GGSVIVLNVpnsDIYTLFAKGDIDAAWVAEPTATLlvQKLNGTRLFDEIDMWPDQkfASVLLIVNEDYVNQHPEvIR 230
                 333333338888899964444.477777777889*******************99762277789*************99*****************999 PP

                 HHHHHHC--HHHHHHHH CS
       OpuAC 221 afLeklsldtetlneln 237
                 ++Le+   +++t+   n
  EPA05051.1 231 KWLEA---HQQTIDWIN 244
                 99999...444444444 PP

>> NMT1_3  NMT1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   4.1e-06     0.011      77     179 ..      89     194 ..      67     229 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.1e-06
      NMT1_3  77 kplknlraitmlyaevfqlvvskdsgigsiadlkgkrvsvGpegsGtegsarailealglsekd..lk.lleelgygesadalkdgqldgaalvaGvPv 172
                  ++ n+++++      ++++v  ds+i+s +d+ gkr++  + g++++ s r+ l+a gl+ ++   + ++ ++  ++ ++++++g +d+a ++   ++
  EPA05051.1  89 SEHHNVKILSGAASGGVSFIVHPDSKINSAEDFIGKRIAAPQIGNSQDISLRTYLSANGLKPAEkgGSvIVLNVPNSDIYTLFAKGDIDAAWVAEPTAT 187
                 47788888999999999*******************************************96552322234568889999*********9988876666 PP

      NMT1_3 173 savtqla 179
                   v++l 
  EPA05051.1 188 LLVQKLN 194
                 6666665 PP

>> ERCC4  ERCC4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.7e-05     0.044      60     153 ..     182     299 ..     157     302 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.7e-05
                 EEEEHHHHHHHHCCSHHHHHHHHHHH.H-SEEEEEE.ES...-GGGTT....................................THHH.HHHHHHHHHH CS
       ERCC4  60 erksaddlvasikdgrleeqvsrlkrngykkpillv.eg...ldqykrknknsrnkqykakvrq....................inrktiesaLvqlql 134
                    +a  lv++++ +rl+++++ +    +  ++l+v e+    +  + +++    +q+++++++                    ++++ i ++L+ lq+
  EPA05051.1 182 AEPTATLLVQKLNGTRLFDEIDMWPDQKFASVLLIVnEDyvnQHPEVIRKWLEAHQQTIDWINSnpeetriifnqflkrelgksLSDNLIDESLSKLQI 280
                 56678889****99**********8889********99999999999999999999999999999999999999999999998866667********** PP

                 HHS-EEEEESSHHHHHHHH CS
       ERCC4 135 dfgvsilttesanetaewl 153
                 +++  +  +e+++  a+ l
  EPA05051.1 281 TSDPIVSSIETFAKRADSL 299
                 *998888888887777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.53
# Mc/sec: 1868.55
//
Query:       EPA05052.1  [L=381]
Description: toprim domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-07   32.2   0.4    2.5e-07   31.0   0.4    1.6  1  Toprim_4  Toprim domain
    2.8e-05   24.4   0.0    6.2e-05   23.3   0.0    1.6  1  Toprim_2  Toprim-like
  ------ inclusion threshold ------
      0.048   13.9   0.3       0.14   12.4   0.3    1.9  1  Toprim    Toprim domain


Domain annotation for each model (and alignments):
>> Toprim_4  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.4   4.3e-11   2.5e-07       3      74 ..     173     232 ..     172     253 .. 0.81

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 4.3e-11
    Toprim_4   3 iiiVEgyaDvlalekagiknvvavlggalspldgirpeklktenlveaekkvkevilaldgDaeGeataerl 74 
                 ii+VEg+aDv++l +ag+ n++a+ g  +   + i+ e   +          + ++ + dgD +G    ++l
  EPA05052.1 173 IILVEGRADVINLLRAGYDNAIAIEGAKI--DESIK-ELCAS---------KNTIVAFIDGDRAGGFILKEL 232
                 89***************************..67777.45555.........38999999*****97665555 PP

>> Toprim_2  Toprim-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0     1e-08   6.2e-05       1      69 [.     174     237 ..     174     257 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 1e-08
    Toprim_2   1 vvfEgaiDalSlaqlgikektnvvalgGtalteaalkllerypekkvvlalDnDkaGrkaakrlaellr 69 
                 +++Eg  D++ l+++g +   n++a+ G    ++ +k+l +  ++++v   D D+aG    k+l+++++
  EPA05052.1 174 ILVEGRADVINLLRAGYD---NAIAIEGA-KIDESIKELCAS-KNTIVAFIDGDRAGGFILKELKSVVN 237
                 69***************8...********.667777777777.4778889********99999998775 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.3   2.4e-05      0.14       2      89 ..     173     239 ..     172     253 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.4e-05
                 EEEESSHHHHHHHHHTHTSTEEEEEEESSSSEEEHSTTEEEEEECTTTHHHHHHHHHHHHHHSEEEEECSSSHHHHHHHHHHHHHHT.H CS
      Toprim   2 lvivEgpsdaktiakalgsgfqavtaslGhildletefkpvyeeiedkkkvlkalkelakradeiilatDpDreGeaiawellevlk.e 89 
                 +++vEg +d++++ +a   g+ +++a  G  +d                     +kel    + i+  +D+Dr+G  i +el +v+  +
  EPA05052.1 173 IILVEGRADVINLLRA---GYDNAIAIEGAKIDES-------------------IKELCASKNTIVAFIDGDRAGGFILKELKSVVNiD 239
                 799*************...9*********999887...................69999999****************99999888752 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2350.22
//
Query:       EPA05053.1  [L=55]
Description: putative lysine biosynthesis protein LysW [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-06   28.3   3.7     0.0013   18.6   1.3    2.1  2  zinc_ribbon_4   zinc-ribbon domain
    5.2e-05   23.1   7.1     0.0021   18.0   4.0    2.0  2  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
    0.00011   22.3   0.8     0.0029   17.7   0.1    2.2  2  zf-RING_7       C4-type zinc ribbon domain
    0.00035   20.1   2.7       0.32   10.6   0.1    2.3  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
    0.00071   19.5   2.9     0.0011   18.8   2.9    1.4  1  Prok-RING_1     Prokaryotic RING finger family 1
    0.00089   19.3   2.1     0.0013   18.8   2.1    1.2  1  Zn-ribbon_8     Zinc ribbon domain
     0.0013   18.2   1.0     0.0016   17.9   1.0    1.2  1  TF_Zn_Ribbon    TFIIB zinc-binding
     0.0016   18.2   0.4      0.073   12.8   0.0    2.1  2  zinc_ribbon_5   zinc-ribbon domain
     0.0019   18.4   0.9     0.0027   17.9   0.9    1.2  1  zinc_ribbon_9   zinc-ribbon
     0.0021   17.8   0.9       0.19   11.5   0.0    2.1  2  zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
     0.0022   18.0   0.5     0.0025   17.8   0.5    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
     0.0046   16.7   2.2      0.034   13.9   2.2    1.9  1  zf-HYPF         HypF finger
     0.0052   16.2   0.6      0.092   12.2   0.1    2.2  2  zf-ribbon_3     zinc-ribbon domain
  ------ inclusion threshold ------
      0.016   14.9   2.9      0.049   13.3   2.9    1.8  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
      0.017   15.1   0.7      0.024   14.6   0.7    1.3  1  DZR             Double zinc ribbon
      0.019   14.7   1.4       0.97    9.2   0.1    2.3  2  zinc_ribbon_2   zinc-ribbon domain
       0.02   14.9   3.0      0.045   13.7   0.4    2.0  2  BssC_TutF       BssC/TutF protein
      0.041   13.9   0.3       0.23   11.4   0.0    2.0  2  ADK_lid         Adenylate kinase, active site lid
      0.053   13.5   1.0       0.12   12.4   1.0    1.6  1  zinc-ribbons_6  zinc-ribbons
      0.072   13.2   5.3        1.5    8.9   0.2    2.2  2  UPF0547         Uncharacterised protein family UPF0547
      0.078   12.7   3.2       0.59    9.9   3.2    2.0  1  A2L_zn_ribbon   A2L zinc ribbon domain
      0.099   12.7   1.1       0.12   12.5   1.1    1.1  1  DUF1451         Zinc-ribbon containing domain
       0.11   12.5   1.7          1    9.4   0.2    2.0  2  CpXC            CpXC protein
       0.12   12.2   2.2       0.82    9.6   2.2    2.0  1  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
       0.18   11.9   2.2         12    6.1   0.1    2.1  2  XPA_N           XPA protein N-terminal
       0.23   12.0   0.5        3.9    8.1   0.0    2.1  2  zf-C2H2         Zinc finger, C2H2 type
       0.27   11.3   5.3        6.1    7.0   0.4    2.2  2  zf-ACC          Acetyl-coA carboxylase zinc finger domain
       0.38   10.6   3.5        1.1    9.0   0.1    2.1  2  PADR1           PADR1 (NUC008) domain
       0.73   10.4   2.7        1.6    9.3   0.0    2.1  2  zf-H2C2_2       Zinc-finger double domain
       0.85    9.7   0.2       0.85    9.7   0.2    2.1  2  zf-C2H2_6       C2H2-type zinc finger
        1.2    9.1   6.7        4.8    7.2   6.8    1.8  1  zf-dskA_traR    Prokaryotic dksA/traR C4-type zinc finger


Domain annotation for each model (and alignments):
>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   1.3   2.3e-06    0.0013       5      35 ..       4      32 ..       2      33 .. 0.91
   2 !   15.1   0.0   2.8e-05     0.016       2      15 ..      22      35 ..      22      38 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.3e-06
  zinc_ribbon_4  5 CpsCkakyeiddeklpakgvkvrCskCghvF 35
                   C++C a+ +i+ + + ++   v+C+ Cg++F
     EPA05053.1  4 CEECDAEISIPKDAMEGE--IVTCPECGASF 32
                   *************88877..89*******99 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 2.8e-05
  zinc_ribbon_4  2 kitCpsCkakyeid 15
                   ++tCp+C+a +e++
     EPA05053.1 22 IVTCPECGASFELA 35
                   69*********997 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   4.0   3.6e-06    0.0021       2      26 ..       1      29 [.       1      33 [. 0.94
   2 !   11.2   0.1   0.00048      0.27       5      17 ..      25      37 ..      17      47 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3.6e-06
  PhnA_Zn_Ribbon  2 lpkCplCaSeytY....edgallvCpeCa 26
                    ++kC++C +e +      +g++  CpeC+
      EPA05053.1  1 MSKCEECDAEISIpkdaMEGEIVTCPECG 29
                    79**************************8 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00048
  PhnA_Zn_Ribbon  5 CplCaSeytYedg 17
                    Cp+C+++++++ g
      EPA05053.1 25 CPECGASFELAKG 37
                    9999999999765 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1      0.14        80      24      30 ..       2       8 ..       1       9 [. 0.80
   2 !   17.7   0.1     5e-06    0.0029      20      31 ..      19      30 ..      10      30 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.14
                EE-TTT- CS
   zf-RING_7 24 vtCpeCG 30
                 +C+eC 
  EPA05053.1  2 SKCEECD 8 
                58****6 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 5e-06
                STB-EE-TTT-- CS
   zf-RING_7 20 gdevvtCpeCGR 31
                 +e+vtCpeCG+
  EPA05053.1 19 EGEIVTCPECGA 30
                389********6 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.5     0.001      0.58       4      16 ..       3      16 ..       1      19 [. 0.82
   2 !   10.6   0.1   0.00055      0.32       3      14 ..      23      34 ..      21      36 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.001
      zf_UBZ  4 lCerCgkeipes.e 16
                 Ce+C++ei+++ +
  EPA05053.1  3 KCEECDAEISIPkD 16
                6********99855 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00055
      zf_UBZ  3 ylCerCgkeipe 14
                ++C++Cg++++ 
  EPA05053.1 23 VTCPECGASFEL 34
                69******9975 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   2.9     2e-06    0.0011       5      30 ..       2      32 ..       1      35 [. 0.79

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2e-06
  Prok-RING_1  5 kkCpvCgkelkee.....dDiVvCpeCgtpy 30
                 +kC+ C+ e++         iV+CpeCg+++
   EPA05053.1  2 SKCEECDAEISIPkdameGEIVTCPECGASF 32
                 58******997542344478*********96 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   2.1   2.2e-06    0.0013       7      35 ..       3      31 ..       3      36 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.2e-06
  Zn-ribbon_8  7 rCeeCghefevlqsisdapltaCPeCgse 35
                 +CeeC+ e  +   +++ + ++CPeCg+ 
   EPA05053.1  3 KCEECDAEISIPKDAMEGEIVTCPECGAS 31
                 7*********888888888888*****84 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   1.0   2.7e-06    0.0016       2      27 ..       3      30 ..       2      41 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.7e-06
                  EETTTTCEE.CHEETSTTCE.EESSSSB CS
  TF_Zn_Ribbon  2 kCPnCgstn.lveDpergel.vCtdCGl 27
                  kC +C  +  +  D+++ge+ +C++CG+
    EPA05053.1  3 KCEECDAEIsIPKDAMEGEIvTCPECGA 30
                  899***98889****************7 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1     0.073        42       4      10 ..       3       9 ..       1      18 [. 0.83
   2 !   12.8   0.0   0.00013     0.073       2      16 ..      22      36 ..      22      47 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.073
  zinc_ribbon_5  4 rCpdCdt 10
                   +C++Cd 
     EPA05053.1  3 KCEECDA 9 
                   7****97 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00013
  zinc_ribbon_5  2 iirCpdCdtkFklvd 16
                   i+ Cp+C+  F l+ 
     EPA05053.1 22 IVTCPECGASFELAK 36
                   789*********986 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.9   4.7e-06    0.0027       7      31 ..       6      32 ..       4      32 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 4.7e-06
  zinc_ribbon_9  7 qCdrfVsvspd..edsdvlCPhCgggF 31
                   +Cd ++s+  d  e ++v+CP+Cg  F
     EPA05053.1  6 ECDAEISIPKDamEGEIVTCPECGASF 32
                   8*******7666344447******988 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.2     0.029        17       3      11 ..       3      11 ..       1      15 [. 0.84
   2 !   11.5   0.0   0.00033      0.19       2      19 ..      23      40 ..      22      43 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.029
                    E-SSS--EE CS
  zf-C4_Topoisom  3 kCPkCggdL 11
                    kC++C +++
      EPA05053.1  3 KCEECDAEI 11
                    9****9987 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00033
                    EE-SSS--EEEEEE-SSS CS
  zf-C4_Topoisom  2 ekCPkCggdLvlkrgkkG 19
                    ++CP+Cg+   l +g +G
      EPA05053.1 23 VTCPECGASFELAKGSNG 40
                    79*****98877777776 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.5   4.3e-06    0.0025      72     103 ..       3      38 ..       1      47 [. 0.74

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4.3e-06
                 EETTTS-EEECHHHHH.....S-TTTSSS-EEEEESS CS
        HypA  72 rCreCgkefeleekal.....rCpkCgsadveivsGe 103
                 +C+eC++e+++ ++a+     +Cp+Cg+ ++e+ +G+
  EPA05053.1   3 KCEECDAEISIPKDAMegeivTCPECGA-SFELAKGS 38 
                 8*********77653345667******9.57777775 PP

>> zf-HYPF  HypF finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   2.2   5.8e-05     0.034       2      33 ..       4      34 ..       3      35 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.8e-05
                -HHHHHHHC-TTSTTTT-TT---TTTS--EEE CS
     zf-HYPF  2 CedClrEykdpldRRfhaqfisCtnCGPrlsl 33
                Ce+C +E+  p+d     + ++C++CG  + l
  EPA05053.1  4 CEECDAEISIPKDA-MEGEIVTCPECGASFEL 34
                ************85.789*********99876 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1      0.14        84       4      14 ..       3      15 ..       1      18 [. 0.66
   2 !   12.2   0.1   0.00016     0.092       3      12 ..      23      34 ..      21      39 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.14
  zf-ribbon_3  4 rCPnCGa.p.lss 14
                 +C +C+a + + +
   EPA05053.1  3 KCEECDAeIsIPK 15
                 6888888775555 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00016
  zf-ribbon_3  3 vrCPnCGa.p.l 12
                 v+CP+CGa   l
   EPA05053.1 23 VTCPECGAsFeL 34
                 78*****96655 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   2.9   8.5e-05     0.049       2      25 ..       3      30 ..       3      36 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.5e-05
                    B-SSS--B----S....SS----SSS-- CS
  DNA_RNApol_7kD  2 iCgeCgaevslkk....gdpiRCkeCGh 25
                    +C eC+ae s+ k    g+++ C eCG 
      EPA05053.1  3 KCEECDAEISIPKdameGEIVTCPECGA 30
                    69*********864444899*******5 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.7   4.2e-05     0.024      15      38 ..       4      32 ..       1      39 [. 0.79

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.2e-05
         DZR 15 CseCgtklkavaa.....edrCpsCgekv 38
                C+eC ++++ +++       +Cp+Cg++ 
  EPA05053.1  4 CEECDAEISIPKDamegeIVTCPECGASF 32
                99999998755558889889999999875 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1     0.044        25       1      10 [.       3      12 ..       3      17 .. 0.86
   2 ?    9.2   0.1    0.0017      0.97      16      21 ..      25      30 ..      21      32 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.044
  zinc_ribbon_2  1 fCpnCGaelq 10
                   +C +C ae++
     EPA05053.1  3 KCEECDAEIS 12
                   7****99996 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0017
  zinc_ribbon_2 16 CpyCGt 21
                   Cp+CG+
     EPA05053.1 25 CPECGA 30
                   677766 PP

>> BssC_TutF  BssC/TutF protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.4   7.9e-05     0.045       1      19 [.       1      19 [.       1      22 [. 0.92
   2 ?    2.0   0.1      0.38   2.2e+02       3      15 ..      24      36 ..      22      45 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.9e-05
   BssC_TutF  1 mstCeeCkfffavPedadD 19
                ms+CeeC   +++P+da++
  EPA05053.1  1 MSKCEECDAEISIPKDAME 19
                9***************986 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.38
   BssC_TutF  3 tCeeCkfffavPe 15
                tC eC   f++ +
  EPA05053.1 24 TCPECGASFELAK 36
                8999987777655 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.2       0.9   5.2e+02      23      30 ..       3      10 ..       2      16 .. 0.76
   2 ?   11.4   0.0   0.00041      0.23       3      15 ..      24      41 ..      23      50 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.9
                B-TTT--. CS
     ADK_lid 23 lCDkCGep 30
                +C +C  +
  EPA05053.1  3 KCEECDAE 10
                78888765 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00041
                E-TTT--EEETT.....T CS
     ADK_lid  3 vCpkCGrsYhvv.....f 15
                +Cp CG+s+ ++     f
  EPA05053.1 24 TCPECGASFELAkgsngF 41
                8********765444443 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.0   0.00021      0.12       2      28 ..       3      34 ..       2      41 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00021
                    --SSS-S--E.E-S....SEEE-TTT--EEEE CS
  zinc-ribbons_6  2 kCpeCqqele.krg....eqyhCeaCqedlkk 28
                    kC+eC++e++  ++    e ++C +C ++++ 
      EPA05053.1  3 KCEECDAEISiPKDamegEIVTCPECGASFEL 34
                    57777777774333566677777777776654 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.9     0.016       9.3       2      12 ..       3      13 ..       3      14 .. 0.90
   2 ?    8.9   0.2    0.0027       1.5      17      22 ..      25      30 ..      22      33 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.016
     UPF0547  2 vCPeCeakvPv 12
                +C eC+a++++
  EPA05053.1  3 KCEECDAEISI 13
                799******96 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0027
     UPF0547 17 CphCGy 22
                Cp+CG 
  EPA05053.1 25 CPECGA 30
                666664 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   3.2     0.001      0.59      21      32 ..      22      33 ..       1      34 [. 0.71

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.001
  A2L_zn_ribbon 21 ylvCieCgasfp 32
                   +  C+eCgasf+
     EPA05053.1 22 IVTCPECGASFE 33
                   457*******97 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.1    0.0002      0.12     116     140 ..       3      30 ..       1      33 [. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.0002
     DUF1451 116 vCekCgkelalkk...teeippCpkCga 140
                  Ce+C++e+++ k    +ei +Cp+Cga
  EPA05053.1   3 KCEECDAEISIPKdamEGEIVTCPECGA 30 
                 6**********77333689*******97 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1      0.17        96      39      50 ..       3      14 ..       1      22 [. 0.76
   2 ?    9.4   0.2    0.0017         1      38      49 ..      23      34 ..      17      38 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.17
        CpXC 39 tCpkCgatakle 50
                +C++C+a+++++
  EPA05053.1  3 KCEECDAEISIP 14
                688888887765 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0017
        CpXC 38 atCpkCgatakl 49
                +tCp+Cga+++l
  EPA05053.1 23 VTCPECGASFEL 34
                466666666655 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   2.2    0.0014      0.82      12      32 ..      13      33 ..       1      36 [. 0.82

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0014
                    EEEECSCCCEEEESSSS-EEE CS
  RNA_POL_M_15KD 12 lpkedkegknfeCrqCgYeep 32
                    +pk++ eg ++ C  Cg+ ++
      EPA05053.1 13 IPKDAMEGEIVTCPECGASFE 33
                    89999***99********998 PP

>> XPA_N  XPA protein N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.4      0.02        12       3      10 ..       3      10 ..       1      13 [. 0.82
   2 ?    6.1   0.1      0.02        12       3      13 ..      24      34 ..      23      44 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.02
       XPA_N  3 kCdeCgke 10
                kC+eC+ e
  EPA05053.1  3 KCEECDAE 10
                8****976 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.02
       XPA_N  3 kCdeCgkefld 13
                +C eCg  f+ 
  EPA05053.1 24 TCPECGASFEL 34
                7******9985 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1      0.44   2.5e+02       2       7 ..       3       8 ..       2      14 .. 0.87
   2 ?    8.1   0.0    0.0067       3.9       2      10 ..      24      32 ..      23      35 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.44
               EETTTT CS
     zf-C2H2 2 kCpdCg 7
               kC++C+
  EPA05053.1 3 KCEECD 8
               8****8 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0067
                EETTTTEEE CS
     zf-C2H2  2 kCpdCgksF 10
                +Cp+Cg sF
  EPA05053.1 24 TCPECGASF 32
                7******99 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.5     0.013       7.2       2      10 ..       2      10 ..       2      12 .. 0.83
   2 ?    7.0   0.4     0.011       6.1       3       9 ..      24      30 ..      23      31 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.013
      zf-ACC  2 tKCpsCgem 10
                +KC++C + 
  EPA05053.1  2 SKCEECDAE 10
                6*****985 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.011
      zf-ACC  3 KCpsCge 9 
                 Cp+Cg+
  EPA05053.1 24 TCPECGA 30
                6999998 PP

>> PADR1  PADR1 (NUC008) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.5      0.14        83      13      22 ..       1       9 [.       1      18 [. 0.77
   2 ?    9.0   0.1     0.002       1.1      11      28 ..      20      36 ..      15      44 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.14
       PADR1 13 lekCpeCkeg 22
                + kC+eC   
  EPA05053.1  1 MSKCEECD-A 9 
                57999998.4 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.002
       PADR1 11 GalekCpeCkegqlvfds 28
                G +  CpeC+  ++++ +
  EPA05053.1 20 GEIVTCPECG-ASFELAK 36
                9999******.6665554 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.8       1.1   6.3e+02      16      21 ..       3       8 ..       3      10 .. 0.86
   2 ?    9.3   0.0    0.0027       1.6      14      24 ..      22      32 ..      14      33 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 1.1
   zf-H2C2_2 16 eCplCd 21
                +C++Cd
  EPA05053.1  3 KCEECD 8 
                7****8 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0027
   zf-H2C2_2 14 pyeCplCdkaF 24
                +++Cp+C+ +F
  EPA05053.1 22 IVTCPECGASF 32
                489*****999 PP

>> zf-C2H2_6  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   1.1      0.64   3.7e+02       3       9 ..       3       9 ..       3      10 .. 0.85
   2 ?    9.7   0.2    0.0015      0.85       4      12 ..      25      33 ..      24      33 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.64
   zf-C2H2_6 3 eCsvCsk 9
               +C +C++
  EPA05053.1 3 KCEECDA 9
               7****98 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0015
   zf-C2H2_6  4 CsvCsksFp 12
                C++C++sF+
  EPA05053.1 25 CPECGASFE 33
                ********6 PP

>> zf-dskA_traR  Prokaryotic dksA/traR C4-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   6.8    0.0084       4.8       5      35 ..       3      33 ..       2      34 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0084
  zf-dskA_traR  5 sCeeCGEpIpeaRlralPgarlCveCqekae 35
                  +CeeC  +I  ++    +  + C eC   +e
    EPA05053.1  3 KCEECDAEISIPKDAMEGEIVTCPECGASFE 33
                  4************99999********98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                        31  (0.00172904); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              31  [number of targets reported over threshold]
# CPU time: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 433.29
//
Query:       EPA05054.1  [L=120]
Description: transcriptional regulator, ArsR family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-10   39.0   0.5    9.8e-10   38.2   0.5    1.4  1  HTH_5     Bacterial regulatory protein, arsR family
     0.0038   17.3   0.1     0.0058   16.7   0.1    1.3  1  HTH_20    Helix-turn-helix domain
  ------ inclusion threshold ------
      0.029   14.3   0.1      0.049   13.5   0.1    1.3  1  TrmB      Sugar-specific transcriptional regulator TrmB
      0.058   13.4   0.2       0.12   12.4   0.2    1.5  1  HTH_11    HTH domain
      0.059   12.9   0.0       0.11   12.1   0.0    1.5  1  HTH_24    Winged helix-turn-helix DNA-binding
       0.14   12.2   0.0       0.23   11.5   0.0    1.3  1  HTH_29    Winged helix-turn helix


Domain annotation for each model (and alignments):
>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   0.5   3.3e-13   9.8e-10       3      45 ..      36      78 ..      35      80 .. 0.97

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 3.3e-13
                HHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
       HTH_5  3 tRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLV 45
                tRl+I++lL e+++  ++la el+l   +v hH k+L++ ++V
  EPA05054.1 36 TRLRIIMLLLERSYNTHQLAQELELDYKAVQHHMKVLEKNNMV 78
                8***************************************998 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   1.9e-06    0.0058      11      60 ..      36      84 ..      36      85 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.9e-06
                HHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
      HTH_20 11 vRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvreg 60
                +R+ri  +L  ++     +la++l+l+ + + +H++vLe+   v   +e+
  EPA05054.1 36 TRLRIIMLL-LERSYNTHQLAQELELDYKAVQHHMKVLEKNNMVLKIGER 84
                789999999.99999999*********************99988777665 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   1.6e-05     0.049      17      59 ..      43      85 ..      41      93 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.6e-05
                HHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTT CS
        TrmB 17 LlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrp 59
                Ll + + ++ ++a+el++++  v+  ++ Le+  +V ++ +r+
  EPA05054.1 43 LLLERSYNTHQLAQELELDYKAVQHHMKVLEKNNMVLKIGERY 85
                78899999****************************9998774 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   3.9e-05      0.12       3      43 ..      38      76 ..      36      84 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.9e-05
      HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg 43
                l i+ lLle     +  +LA+eL++  ++v+ ++k Le+  
  EPA05054.1 38 LRIIMLLLERS--YNTHQLAQELELDYKAVQHHMKVLEKNN 76
                56777775555..4899********************9976 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.6e-05      0.11      20      47 ..      51      78 ..      36      78 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.6e-05
      HTH_24 20 qreLAerlglSpstvnrrlkrLeeeGlI 47
                  +LA++l l   +v  ++k Le++  +
  EPA05054.1 51 THQLAQELELDYKAVQHHMKVLEKNNMV 78
                569*********************9765 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   7.7e-05      0.23       1      32 [.      37      68 ..      37      74 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.7e-05
      HTH_29  1 RaqallllaeGvstvsqiAkllglsrrtvyrw 32
                R+++++ll e  +++ q+A+ l l+++ v+++
  EPA05054.1 37 RLRIIMLLLERSYNTHQLAQELELDYKAVQHH 68
                899*******999****************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       772  (0.0430587); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 879.56
//
Query:       EPA05055.1  [L=246]
Description: ABC transporter, permease protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-21   76.6  17.1      2e-21   76.6  17.1    1.5  1  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
        0.2   11.7   0.2        0.5   10.4   0.2    1.7  1  DUF3043       Protein of unknown function (DUF3043)


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.6  17.1   2.2e-25     2e-21       1     171 [.      69     227 ..      65     240 .. 0.90

  Alignments for each domain:
  == domain 1  score: 76.6 bits;  conditional E-value: 2.2e-25
  BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrslpkdlveaaralGasrwqi 97 
                   g+llGil+a  r  ++++ +  l+  l+s+Ps+++++l +       ++g +  ++i+++++++++ v++ +++++++++  ++eaar +Ga+  q+
    EPA05055.1  69 GMLLGILMA--RVETVNQTIGSLVLGLQSIPSVAWVPLAI------LWFGLTDGGIIFVTAIGSMFAVTIATYSGVKNINPHYIEAARNMGAKGTQL 157
                   678999999..*****************************......9************************************************** PP

  BPD_transp_1  98 frkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseisnggvlalviavlllnlv 171
                     +v++P+a+p++i+g+   +++++ g + +e+l+s  Glg ll    + +d+s+      +++++++++ +++
    EPA05055.1 158 ATYVLIPAAFPYLISGFKQGWAFAWRGVIGAELLFSFLGLGFLLNVGRQLNDISQVF----AIMLVIMMVGIAI 227
                   ******************************************************444....4444444444433 PP

>> DUF3043  Protein of unknown function (DUF3043)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.2   5.5e-05       0.5      93     138 ..     199     244 ..     183     246 .] 0.73

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 5.5e-05
     DUF3043  93 llv.slvkvpevqavvsllllvllllvvidgillgrkvkkkvrekFp 138
                 +l+    + + +++v++++l+++++ ++idg+++  k+++kv  +++
  EPA05055.1 199 FLLnVGRQLNDISQVFAIMLVIMMVGIAIDGVIF-KKLENKVMSRWG 244
                 2222467899999******************987.577778877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       836  (0.0466284); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1504.87
//
Query:       EPA05056.1  [L=240]
Description: B12 binding domain protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-19   69.7   0.0    3.4e-19   69.0   0.0    1.3  1  B12-binding    B12 binding domain
    3.3e-19   69.1   0.0    5.6e-19   68.3   0.0    1.4  1  B12-binding_2  B12 binding domain
     0.0018   17.8   0.1     0.0065   15.9   0.0    1.8  2  adh_short      short chain dehydrogenase


Domain annotation for each model (and alignments):
>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.0   0.0   5.7e-23   3.4e-19       2      92 ..     120     210 ..     119     229 .. 0.95

  Alignments for each domain:
  == domain 1  score: 69.0 bits;  conditional E-value: 5.7e-23
  B12-binding   2 kvllatvggdlhplGlavlaaalrdagfeVqllganvenedivaairaekpdvvglSalltsqleavkelvellkrirprvkvvvGGahps 92 
                  k +l+tv+gd+h++G+++++ +++++g+ V++lg +v+ ++++++i + kpd++glSall s+  +++  ve +++++ ++++++GGa+ +
   EPA05056.1 120 KLVLGTVYGDVHDIGKNLVKTIFQNNGYTVYDLGKQVPLQKFLDKIDEVKPDAIGLSALLVSTSKQMQYFVEHARKNNMGIPILCGGAAIN 210
                  7899***********************************************************************************9865 PP

>> B12-binding_2  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.3   0.0   9.4e-23   5.6e-19       8      75 .]      16     107 ..      11     107 .. 0.91

  Alignments for each domain:
  == domain 1  score: 68.3 bits;  conditional E-value: 9.4e-23
  B12-binding_2   8 aivhgdkegieelideala.......................qgsa...avdvlndvllpamkeVGdlfgagelflpqvllsaevmkkavahLe 75 
                     i+++ k+gie ++  a+a                              a ++ln+ llpamkeVGd+fg+gel+lp+vl+sae+mk+av  Le
     EPA05056.1  16 RILNRLKDGIENDVVSAIAekigkneiiknnngalsldvpqtI--ThdgAIRTLNEDLLPAMKEVGDKFGSGELILPFVLKSAECMKAAVGELE 107
                    5899**************99**********9999999988551..3456*****************************************9986 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.16   9.7e+02      66      88 ..      28      51 ..      23      76 .. 0.75
   2 !   15.9   0.0   1.1e-06    0.0065       5      90 ..     126     211 ..     122     226 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.16
                HHHHHHHHHHSSESEEEE---S.S CS
   adh_short 66 alvekavkklgkldvLvnNAGi.t 88
                ++v+++++k+gk +++ nN G  +
  EPA05056.1 28 DVVSAIAEKIGKNEIIKNNNGAlS 51
                689999999999999999999842 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.1e-06
                 EESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE.-TTTSHHHHHHHHHHHHHHHSSESEEEE---SS-- CS
   adh_short   5 vtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiq.vDvtdreevealvekavkklgkldvLvnNAGitgs 90 
                 v G    IG++++k++ +++  +v    ++ +l++ ++++ e + +a+ ++ + v+++++++ +ve+a+k+  ++ +L  +A+i+ s
  EPA05056.1 126 VYGDVHDIGKNLVKTIFQNNGYTVYDLGKQVPLQKFLDKIDEVKPDAIGLSaLLVSTSKQMQYFVEHARKNNMGIPILCGGAAIN-S 211
                 5677788********99987766664455589***********77777765156779**************************94.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1768.01
//
Query:       EPA05057.1  [L=139]
Description: transcriptional regulator, AsnC family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-13   50.7   0.0    2.2e-13   49.8   0.0    1.5  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
      1e-12   47.4   0.2    1.7e-12   46.7   0.2    1.4  1  HTH_24          Winged helix-turn-helix DNA-binding
    3.4e-11   42.9   0.2    5.3e-11   42.3   0.2    1.3  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
     0.0015   18.4   0.4     0.0042   17.0   0.1    1.9  2  HTH_11          HTH domain
     0.0024   17.9   1.6     0.0056   16.7   1.0    1.8  1  NapD            NapD protein
     0.0027   17.5   0.0     0.0048   16.8   0.0    1.3  1  MarR_2          MarR family
     0.0036   17.1   0.0      0.013   15.4   0.0    1.9  2  HTH_5           Bacterial regulatory protein, arsR family
     0.0049   17.4   1.1        2.7    8.6   0.2    2.4  2  ACT_4           ACT domain
     0.0092   16.2   0.3       0.17   12.1   0.0    2.5  3  DUF2774         Protein of unknown function (DUF2774)
     0.0092   15.6   2.8      0.035   13.7   0.2    2.1  2  DDRGK           DDRGK domain
  ------ inclusion threshold ------
      0.011   15.6   0.3      0.027   14.4   0.1    1.7  2  MarR            MarR family
      0.012   15.1   0.0      0.032   13.7   0.0    1.7  1  Sigma70_r4      Sigma-70, region 4
      0.026   14.4   0.1      0.033   14.1   0.1    1.2  1  SCO1-SenC       SCO1/SenC
      0.028   14.3   1.2       0.45   10.4   0.1    2.2  2  TrmB            Sugar-specific transcriptional regulator TrmB
      0.044   13.5   0.3      0.047   13.4   0.3    1.3  1  Stk19           Serine-threonine protein kinase 19
      0.045   13.5   0.0      0.077   12.8   0.0    1.3  1  HTH_IclR        IclR helix-turn-helix domain
      0.048   13.4   0.4       0.19   11.5   0.1    2.0  3  HTH_DeoR        DeoR-like helix-turn-helix domain
       0.05   14.2   0.1        0.1   13.2   0.1    1.5  1  Mga             Mga helix-turn-helix domain
      0.054   13.6   0.1       0.26   11.4   0.0    1.9  2  HTH_9           RNA polymerase III subunit RPC82 helix-turn-h
      0.068   13.8   0.1        0.1   13.2   0.1    1.3  1  RTP             Replication terminator protein


Domain annotation for each model (and alignments):
>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.8   0.0   2.5e-16   2.2e-13       2      41 ..       4      43 ..       4      44 .. 0.98

  Alignments for each domain:
  == domain 1  score: 49.8 bits;  conditional E-value: 2.5e-16
  HTH_AsnC-type  2 DeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrL 41
                   D+iD kI++ L ed+R s+ ++++++ lSes+v+rRv+ L
     EPA05057.1  4 DKIDEKIINFLKEDSRESFVDIGKKLKLSESAVRRRVKNL 43
                   9************************************988 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   0.2   1.9e-15   1.7e-12       2      48 .]       4      50 ..       3      50 .. 0.98

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 1.9e-15
      HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                d++d kI++ L++++r s  ++ ++l lS s+v+rr+k+L+++G Ik
  EPA05057.1  4 DKIDEKIINFLKEDSRESFVDIGKKLKLSESAVRRRVKNLVDSGTIK 50
                99******************************************997 PP

>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.2     6e-14   5.3e-11       1      74 [.      66     136 ..      66     137 .. 0.95

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 6e-14
                     EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEE CS
  AsnC_trans_reg   1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivle 74 
                     vl+s+++    ++ ++ e+l +l+ V+ +y +tG yd+  ++ + ++ ++++ ++  l+++pgv +++t i+l+
      EPA05057.1  66 VLISVDSAT--DTAKVSEKLVKLEGVKTVYEITGQYDITTIISATNISEINNSIDA-LRKIPGVIDSNTVIILR 136
                     789999666..9******************************************99.***************97 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   4.7e-06    0.0042       3      43 ..       8      47 ..       7      56 .. 0.84
   2 ?   -2.3   0.0       5.1   4.6e+03      32      40 ..     113     121 ..     101     125 .. 0.64

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.7e-06
      HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg 43
                ++i+ +L ++++  s  ++ ++L++S+++vrr++k L ++g
  EPA05057.1  8 EKIINFL-KEDSRESFVDIGKKLKLSESAVRRRVKNLVDSG 47
                5899999.677778999********************8888 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 5.1
      HTH_11  32 vrrdIkaLe 40 
                 + + I+aL+
  EPA05057.1 113 INNSIDALR 121
                 455555555 PP

>> NapD  NapD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   1.0   6.3e-06    0.0056      13      69 ..      74     131 ..      60     134 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6.3e-06
        NapD  13 erlaavkaalaalpgvE.vhasdeegklVvviEaesedeladtieaiealpgVlsasl 69 
                  ++a+v+++l +l+gv  v+  +++  +  +i a++  e+ ++i+a++++pgV++ + 
  EPA05057.1  74 TDTAKVSEKLVKLEGVKtVYEITGQYDITTIISATNISEINNSIDALRKIPGVIDSNT 131
                 57899***********63666777799***************************8765 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   5.3e-06    0.0048      23      53 ..      21      51 ..      10      57 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.3e-06
                EHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
      MarR_2 23 tvgelarrlglsksavsrilkrLvaaGLver 53
                +  ++ ++l+ls sav r++k Lv+ G + r
  EPA05057.1 21 SFVDIGKKLKLSESAVRRRVKNLVDSGTIKR 51
                788************************9977 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.4e-05     0.013       6      44 ..       9      48 ..       8      51 .. 0.91
   2 ?   -2.2   0.0       4.3   3.9e+03      13      22 ..      87      96 ..      81     103 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.4e-05
                HHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTS CS
       HTH_5  6 kILklLae.gelcvcelaeelglsqstvShHLkkLreaGL 44
                kI+++L e +  ++ ++ ++l+ls+s+v++  k L ++G 
  EPA05057.1  9 KIINFLKEdSRESFVDIGKKLKLSESAVRRRVKNLVDSGT 48
                79******555************************99995 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4.3
                TSSEEHHHHH CS
       HTH_5 13 egelcvcela 22
                eg ++v e++
  EPA05057.1 87 EGVKTVYEIT 96
                5788999986 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.2     0.003       2.7      35      79 ..      50      93 ..      39      93 .. 0.85
   2 !    7.2   0.0    0.0087       7.8      50      77 ..     101     128 ..      95     129 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.003
       ACT_4 35 vsvnaktrkkdglaeikitveVkdvehLsrviakLraipgVisVe 79
                +  +++  + +++++  + ++V ++ + ++v +kL +++gV++V+
  EPA05057.1 50 KRFTVEIGE-ENTTSAIVLISVDSATDTAKVSEKLVKLEGVKTVY 93
                555555554.7899999*************************995 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0087
       ACT_4  50 ikitveVkdvehLsrviakLraipgVis 77 
                 i+  ++  +++++++ i++Lr+ipgVi+
  EPA05057.1 101 ITTIISATNISEINNSIDALRKIPGVID 128
                 555566679999999***********86 PP

>> DUF2774  Protein of unknown function (DUF2774)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   0.00019      0.17       6      30 ..      11      36 ..       7      46 .. 0.81
   2 ?    1.2   0.0      0.48   4.3e+02      30      51 ..      63      84 ..      51      85 .. 0.81
   3 ?   -1.9   0.0       4.3   3.9e+03      25      36 ..     105     116 ..      90     122 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00019
     DUF2774  6 vhfl.hesgknFveIAkkldirakdv 30
                + fl ++s ++Fv+I+kkl ++   v
  EPA05057.1 11 INFLkEDSRESFVDIGKKLKLSESAV 36
                5588899************9987666 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.48
     DUF2774 30 vaklwveveearekfktrEkVV 51
                 a +  +v+ a   +k  Ek V
  EPA05057.1 63 SAIVLISVDSATDTAKVSEKLV 84
                56788899***99999999988 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 4.3
     DUF2774  25 irakdvaklwve 36 
                 i+a+++ ++  +
  EPA05057.1 105 ISATNISEINNS 116
                 345565555555 PP

>> DDRGK  DDRGK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.2   3.9e-05     0.035      97     144 ..       3      50 ..       1      57 [. 0.94
   2 ?    2.6   0.2       0.1        90     107     149 ..      83     129 ..      60     134 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.9e-05
                 XXXHHHHHHHHHHH-SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS- CS
       DDRGK  97 eeklleefinyikekKvvlleelavkfklktqevierikeLeeqgslt 144
                 ++k+ e++in++ke       ++  k+kl+ + v+ r+k+L ++g+++
  EPA05057.1   3 KDKIDEKIINFLKEDSRESFVDIGKKLKLSESAVRRRVKNLVDSGTIK 50 
                 567889***************************************985 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.1
                 HHHH-SEE-HHHHHHHH-S-HHHHHHHHHH....HHHHSSS-EEE-T CS
       DDRGK 107 yikekKvvlleelavkfklktqevierike....LeeqgsltGvlDd 149
                  +k++ v ++ e++ + +++t   + +i e    +++  ++ Gv+D 
  EPA05057.1  83 LVKLEGVKTVYEITGQYDITTIISATNISEinnsIDALRKIPGVIDS 129
                 56777788888999999998866666665511114566889999985 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   3.1e-05     0.027      21      50 ..      23      52 ..      14      54 .. 0.91
   2 ?   -3.3   0.0       9.9   8.9e+03      30      42 ..      75      87 ..      72      88 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.1e-05
                HHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
        MarR 21 seLakklgvskstvtrvldrLekkGlieRs 50
                 +++kkl++s s+v r ++ L++ G i+R 
  EPA05057.1 23 VDIGKKLKLSESAVRRRVKNLVDSGTIKRF 52
                49*************************995 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 9.9
                -HHHHHHHHHHHH CS
        MarR 30 skstvtrvldrLe 42
                +++ v++ l +Le
  EPA05057.1 75 DTAKVSEKLVKLE 87
                5556666666666 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   3.6e-05     0.032      22      43 ..      21      42 ..      13      46 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.6e-05
                -HHHHHHHHTS-HHHHHHHHHH CS
  Sigma70_r4 22 TleEIgerlgiSrerVrqiekr 43
                ++ +Ig++l +S+++Vr++ k+
  EPA05057.1 21 SFVDIGKKLKLSESAVRRRVKN 42
                7889***************986 PP

>> SCO1-SenC  SCO1/SenC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   3.7e-05     0.033      44      93 ..      49      99 ..      44     134 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.7e-05
   SCO1-SenC 44 maevldalgeeaekvqplfiTvDPerDtpevlkeyleafdpriig.ltGsk 93
                +++ + ++gee+    ++ i+vD ++Dt +v ++ ++  + +++  +tG+ 
  EPA05057.1 49 IKRFTVEIGEENTTSAIVLISVDSATDTAKVSEKLVKLEGVKTVYeITGQY 99
                56777789999999**********************999988887788854 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1    0.0005      0.45      26      55 ..      23      52 ..      13      63 .. 0.88
   2 ?    3.0   0.1       0.1        93      28      59 ..      68      99 ..      54     111 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0005
                CHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
        TrmB 26 deiaeelgvprskvYevLrsLedkGlVere 55
                 +i ++l++++s v + +++L+d G ++r 
  EPA05057.1 23 VDIGKKLKLSESAVRRRVKNLVDSGTIKRF 52
                6999**********************9985 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.1
                HCCCTTSSCHCHHHHHHHHHHCTSEEEESSTT CS
        TrmB 28 iaeelgvprskvYevLrsLedkGlVerekgrp 59
                i+ ++  + +kv e L +Le    V+ + g++
  EPA05057.1 68 ISVDSATDTAKVSEKLVKLEGVKTVYEITGQY 99
                55666677788888888888887777777774 PP

>> Stk19  Serine-threonine protein kinase 19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.3   5.3e-05     0.047      44      96 ..      31      82 ..       7     131 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.3e-05
       Stk19 44 qsptkvereleelirkgklrklvingrgkdisklgevlvltedyeklikesse 96
                 s+ +v r++++l+++g++++++++  ++++     vl+ ++   ++ k s++
  EPA05057.1 31 LSESAVRRRVKNLVDSGTIKRFTVEIGEENT-TSAIVLISVDSATDTAKVSEK 82
                47889********************999773.334566666666655544444 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   8.6e-05     0.077       8      49 ..      10      50 ..       9      51 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.6e-05
                HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
    HTH_IclR  8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                i+++l e  +e ++ ++ +++ l+ S+v+R ++ Lv  G ++
  EPA05057.1 10 IINFLKEDSRE-SFVDIGKKLKLSESAVRRRVKNLVDSGTIK 50
                88999999999.9***********************999776 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00021      0.19       3      46 ..       8      51 ..       7      53 .. 0.94
   2 ?   -2.2   0.0       3.9   3.5e+03      16      28 ..      69      81 ..      68      97 .. 0.76
   3 ?   -1.2   0.0       1.9   1.7e+03       7      27 ..      82     102 ..      77     104 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00021
    HTH_DeoR  3 eqilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltR 46
                e+i+  lk++   s  ++   l+ Se  +RR  ++L+ +g+++R
  EPA05057.1  8 EKIINFLKEDSRESFVDIGKKLKLSESAVRRRVKNLVDSGTIKR 51
                7999999999999999**************************99 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.9
    HTH_DeoR 16 sveelvellgvSe 28
                sv+ +++  +vSe
  EPA05057.1 69 SVDSATDTAKVSE 81
                6777777777776 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.9
    HTH_DeoR   7 ellkqqgklsveelvellgvS 27 
                 +l+k +g  +v e++ +++++
  EPA05057.1  82 KLVKLEGVKTVYEITGQYDIT 102
                 567778888899999999887 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   0.00011       0.1      14      66 ..       3      59 ..       1      66 [. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00011
                HHSHHHHHHHHHHHHSEEEHHHHHHHCT--HHHHHHHHHHHHH..HCHCCT-EE..E CS
         Mga 14 keslkyqllkflfeeeevsieelaqelyiSestlkrkikelnk..lLkefdlel..t 66
                k+ ++ +++ fl e+ + s+ ++ ++l +Ses + r +k+l     +k f  e+  +
  EPA05057.1  3 KDKIDEKIINFLKEDSRESFVDIGKKLKLSESAVRRRVKNLVDsgTIKRFTVEIgeE 59
                5667778999999***************************97533688888888533 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00029      0.26      14      47 ..       6      39 ..       4      47 .. 0.89
   2 ?   -0.7   0.0       1.8   1.6e+03      16      36 ..      77      98 ..      76     111 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00029
                HHHHHHHHHHHHSSBEHHHHHHHHSSTHHHHHHH CS
       HTH_9 14 vvakVvetLlrkgrltlrelvkktkLsldqVkks 47
                + +k++ +L + +r +  ++ kk+kLs + V++ 
  EPA05057.1  6 IDEKIINFLKEDSRESFVDIGKKLKLSESAVRRR 39
                5689***************************975 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.8
                HHHHHHHHH.HSSBEHHHHHHH CS
       HTH_9 16 akVvetLlr.kgrltlrelvkk 36
                akV e L++ +g +t+ e++ +
  EPA05057.1 77 AKVSEKLVKlEGVKTVYEITGQ 98
                5677777764578888887655 PP

>> RTP  Replication terminator protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   0.00011       0.1      29      99 ..      15      87 ..       5      97 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00011
                HHHHHHHHTTTT..----HHHHHHHHHHHHHTTSEEEEE.EEBTSSSSSEEEEEEESS..HHHHHHHHHHHHHH CS
         RTP 29 ldelkkeFkelg..ykPnhseiyralhelvedgilkrrk.elkekaklqevviYsltdeGkekaklykkqvkid 99
                 ++ +++F ++g   k ++s + r +++lv+ g +kr   e+ e++ +  +v+ s++   ++ ak+  k+vk +
  EPA05057.1 15 KEDSRESFVDIGkkLKLSESAVRRRVKNLVDSGTIKRFTvEIGEENTTSAIVLISVDS-ATDTAKVSEKLVKLE 87
                467788999999777888999****************762566888899999999977.89*********9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       816  (0.0455129); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 947.45
//
Query:       EPA05058.1  [L=424]
Description: putative glutamate dehydrogenase (NAD(P)(+)) [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-67  227.5   1.9    2.7e-67  227.0   1.9    1.2  1  ELFV_dehydrog    Glutamate/Leucine/Phenylalanine/Valine dehyd
    9.6e-49  164.6   0.0    1.6e-48  163.8   0.0    1.4  1  ELFV_dehydrog_N  Glu/Leu/Phe/Val dehydrogenase, dimerisation 


Domain annotation for each model (and alignments):
>> ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  227.0   1.9     3e-71   2.7e-67       1     243 []     189     421 ..     189     421 .. 0.98

  Alignments for each domain:
  == domain 1  score: 227.0 bits;  conditional E-value: 3e-71
                    T--TTTTTHHHHHHHHHHHHHHHHTTTS-STTEEEEEE--SHHHHHHHHHHHHCT-EEEEEEESSEEEEETTEE-HHHHHHHHHCSSSSTTHSHHS CS
  ELFV_dehydrog   1 GGsldrpeaTglGvvyyveemlkklkldslegkrvaisGsGnvgsyaallltelgakvvavsDssGviydpeGldieellelkeerksvkeykkss 96 
                    GGsl+r+ aTglGv+y+v+e++k +kl+ l+g++v+ +G+Gn   +a + l+++g kv+avsDs+G i  p+G ++ +lle+k++++sv  ++   
     EPA05058.1 189 GGSLARNVATGLGVAYCVREAAKAIKLN-LKGAKVVLQGFGNASTFAGEYLEKMGSKVIAVSDSKGSISIPNGAKVSKLLEFKTKTGSVVGFPG-- 281
                    9***********************9999.****************************************************************3.. PP

                    TSTSEEESHHSHHHHSS-SEEEE-SSTTSB-HHHHTHTHHTT-SEEE-SSSS-B-HHHHHHHHHTT-EEE-HHHHTTHHHHHHHHHHHHHHCT--- CS
  ELFV_dehydrog  97 ekkaeyieneeellelkvdilvPcAtqneideenakalikngvklvvEgANlpttqeAkeileeagvlvvpdkaaNaGGVtvSslEmlqnlarlsw 192
                        ++i+ e ell++k+dilvP A++n+i+++ a+ ++k  +k+++E+AN+pt +eA+ i+ ++++lv+pd++aN+GGV +S+lE++qn+++++w
     EPA05058.1 282 ---SKKISTE-ELLTTKCDILVPGALENQINAKIAQ-NLK--CKIIAEAANGPTLPEADPIIFKKKILVIPDILANSGGVCISYLEWVQNNMGYYW 370
                    ...4789996.*************************.999..****************************************************** PP

                    -HHHHHHHHHHHHHHHHHHHHHHHHHCT-THHHHHHHHHHHHHHHHHHHCT CS
  ELFV_dehydrog 193 teeevdeklkkimkeifkavveeaeeykqelvkganiagfekvaeamkaqG 243
                    t +ev +k++ + ++ fk+ +++a+++k +++ + +++++ +v+ea +++G
     EPA05058.1 371 TFDEVANKMEGNITKGFKDAYAMANKHKIDMRRATMALAVSRVVEAFNQKG 421
                    **********************************************99988 PP

>> ELFV_dehydrog_N  Glu/Leu/Phe/Val dehydrogenase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.8   0.0   1.8e-52   1.6e-48       1     129 [.      35     169 ..      35     170 .. 0.94

  Alignments for each domain:
  == domain 1  score: 163.8 bits;  conditional E-value: 1.8e-52
                      -SEEEEEEEEEE-TTSBEEEEEEEEEEEE-TTSSEEEEEEE.ETT--HH....HHHHHHHHHHHHHHHTTSS-EEEEEEEES-GG..GS-HHHH CS
  ELFV_dehydrog_N   1 pervlqvtvpvkrdnGelevikgyraqhssalgPakGGiRf.hpsvnld....evkaLaalmtyKnalvdlpfGGakggvkidpk..klseeel 87 
                      p++vl+v++pvk+dnG++++++g+r+qh++ +gP+kGGiR+ +p+   +    ev+aL+++mt+K+a+vd+p+GG+kgg+ ++pk  kls++el
       EPA05058.1  35 PNKVLRVKIPVKMDNGQIRIFTGFRSQHNNDRGPYKGGIRYfNPEGGVEymerEVMALSSWMTWKCAIVDIPLGGGKGGIFVNPKtdKLSDAEL 128
                      899*************************************9445544446677*******************************97789***** PP

                      HHHHHHHHHHHG.GG-BTTTEEEEBBTTB-HHHHHHHHHHHH CS
  ELFV_dehydrog_N  88 eritrrfvrelakkfiGpgiDvpApDvgtgaremawladeyk 129
                      er+tr f+ +++ ++iGpg+D+pApDv+t+ rem  ++d+y+
       EPA05058.1 129 ERLTRGFAFKIS-EIIGPGKDIPAPDVYTTGREMTQIMDTYN 169
                      ************.****************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (424 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 3006.75
//
Query:       EPA05059.1  [L=241]
Description: putative multicatalytic endopeptidase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.2e-48  162.8   2.1    7.9e-48  162.5   2.1    1.1  1  Proteasome      Proteasome subunit
    1.6e-12   46.8   1.7    1.3e-10   40.8   0.2    2.7  2  Proteasome_A_N  Proteasome subunit A N-terminal signature


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.5   2.1   8.8e-52   7.9e-48       1     180 [.      30     203 ..      30     213 .. 0.93

  Alignments for each domain:
  == domain 1  score: 162.5 bits;  conditional E-value: 8.8e-52
                 HHHS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGTCHHHHHHHHHHHHHHHHHHC CS
  Proteasome   1 vkkGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrpipverlvarvaaklqaytqrs 99 
                 vk+Gt ++Gi++k+gv++a++ +      l++++  +Kif++d higva+aG ++Dar+ v+ ar   q  +++y++ + v ++++++a++ ++ tq+s
  EPA05059.1  30 VKRGTLAIGIRSKEGVIMAVEEKPR---ALQTSNVTQKIFQVDYHIGVAAAGYIPDARVQVDNARFFSQGNKMTYDEAVEVATVAKHLADQSHQFTQYS 125
                 799******************7777...67677778*************************************************************** PP

                 TTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHHSTTBSHHHHHHHHHHHHHHHHHHBTT CS
  Proteasome 100 grrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekeykedltleeavelavkalkealerdkl 180
                 g+rp gv+l+iagvd++g  ++y +dpsG+y+++  a+aiG gs+ + ++lek+y+++++l +a  la+ a++  +e +k 
  EPA05059.1 126 GVRPNGVALIIAGVDQKG-ESIYVTDPSGTYVQYA-AIAIGAGSDDVNAFLEKHYNSEMSLSDAASLAIAAINLKVE-QKE 203
                 ***************999.7**************5.************************************98777.334 PP

>> Proteasome_A_N  Proteasome subunit A N-terminal signature
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   0.2   1.4e-14   1.3e-10       1      22 [.       7      28 ..       7      28 .. 0.98
   2 !    4.6   0.1     0.003        26      13      19 ..      64      70 ..      64      70 .. 0.94

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 1.4e-14
  Proteasome_A_N  1 YDrslttFSPdGRLfQVEYAmk 22
                    YD + t++SPdGR++QVEYA++
      EPA05059.1  7 YDMTPTMYSPDGRIYQVEYAIE 28
                    9*******************97 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.003
  Proteasome_A_N 13 RLfQVEY 19
                    ++fQV+Y
      EPA05059.1 64 KIFQVDY 70
                    79***** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       705  (0.0393218); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1634.46
//
Query:       EPA05060.1  [L=227]
Description: riboflavin kinase family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.7e-41  140.0   0.1    5.5e-41  139.5   0.1    1.3  1  CTP-dep_RFKase  Domain of unknown function DUF120
  ------ inclusion threshold ------
      0.029   15.0   1.7        1.6    9.4   0.1    2.4  2  Phage_rep_O     Bacteriophage replication protein O
       0.11   12.4   0.0       0.52   10.2   0.0    2.0  2  HicB            HicB family


Domain annotation for each model (and alignments):
>> CTP-dep_RFKase  Domain of unknown function DUF120
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.5   0.1   9.3e-45   5.5e-41       2     121 .]     102     223 ..     101     223 .. 0.98

  Alignments for each domain:
  == domain 1  score: 139.5 bits;  conditional E-value: 9.3e-45
                     E--SSHHHHHHCSHHHHHHHHHHHSS---SS-EEEEESCC.GHHHHCHHHHS--EEE--EEETTEEE--EEEEEEEEC.CEEEEEEEESS-SS.T CS
  CTP-dep_RFKase   2 vsGlgeGkyyvslegykeqfeeklgfepypGTLNvkldee.slelrkaleklkgieiegfedeertfgavkvypakie.kikaavvvperthyee 94 
                     vsG+geG+yy+sl+gy++qf++k+g+ p+pGTLNv+ld++ ++e+ k++e+l+gi+ie f+d++rt+g+vk+++aki+ +i++++++ erth+++
      EPA05060.1 102 VSGMGEGAYYMSLKGYTKQFKSKIGYIPFPGTLNVRLDKKiHQEAIKQFENLNGITIESFSDGKRTYGWVKCFHAKINqSINCELIILERTHHDN 196
                     89**************************************99***********************************9788************** PP

                     TEEEEE-SS-HHHHTT--TT-EEEEEE CS
  CTP-dep_RFKase  95 dvlEiiapekLReklelkdgdevevev 121
                     +++E+i+++ ++++ +lk+g++v++++
      EPA05060.1 197 SIIELISDVCIKKSGKLKNGSQVTITI 223
                     *************************97 PP

>> Phage_rep_O  Bacteriophage replication protein O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.2    0.0075        45      36      88 ..       9      67 ..       3      74 .. 0.77
   2 ?    9.4   0.1   0.00027       1.6      38      84 ..     165     213 ..     137     224 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0075
  Phage_rep_O 36 virktY....gfkkksdwisnsqlveltgisrtkvskalkeLirekvi..ikegrkvgv 88
                 ++ +tY    g k +   i++  l + ++ s+++ sk l eL + + i  i++gr+++v
   EPA05060.1  9 ILTLTYllskGAKHNFITITTDSLGKNIKKSQQAASKHLLELENNQFIerIITGRNISV 67
                 445555555588888899999***********************998833345566665 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00027
  Phage_rep_O  38 rktYgfkkk.sdwisnsqlveltgisrtkvskalkeLirekviikeg.r 84 
                  ++tYg+ k   ++i++s  +el+ ++rt+  + + eLi+   i+k g  
   EPA05060.1 165 KRTYGWVKCfHAKINQSINCELIILERTHHDNSIIELISDVCIKKSGkL 213
                  58****9972568***************************999999952 PP

>> HicB  HicB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.29   1.7e+03      44      51 .]      53      60 ..      42      60 .. 0.87
   2 ?   10.2   0.0   8.7e-05      0.52      13      32 ..     127     146 ..     122     149 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.29
        HicB 44 NqfveqaL 51
                Nqf+e+++
  EPA05060.1 53 NQFIERII 60
                9***9875 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 8.7e-05
        HicB  13 ekpysGkFnlRvspeLHarl 32 
                 ++p+ G++n+R+++++H+++
  EPA05060.1 127 YIPFPGTLNVRLDKKIHQEA 146
                 57899************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1595.22
//
Query:       EPA05061.1  [L=391]
Description: aminotransferase, acetylornithine/succinylornithine family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   5.3e-116  387.6   0.0   6.7e-116  387.3   0.0    1.0  1  Aminotran_3    Aminotransferase class-III
     0.0011   18.2   0.0     0.0023   17.1   0.0    1.5  1  Aminotran_1_2  Aminotransferase class I and II
  ------ inclusion threshold ------
      0.062   13.0   0.0      0.098   12.3   0.0    1.2  1  DUF2931        Protein of unknown function (DUF2931)


Domain annotation for each model (and alignments):
>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  387.3   0.0  1.1e-119  6.7e-116       8     406 .]      13     382 ..       8     382 .. 0.98

  Alignments for each domain:
  == domain 1  score: 387.3 bits;  conditional E-value: 1.1e-119
                  -SCEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT-..SEEEEESSHHHHHHHHHH CS
  Aminotran_3   8 nlllvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapkgldkvflansGseAvetAlK 105
                   +++ i+k+ G+ ++d dgk+y+D ++++ v+++Gh++ +vvka+k+q++k+  v    l n+  +++ + l+ lapkgl +v l nsG+eA+e+A+K
   EPA05061.1  13 RFPVTIEKGVGAHVWDIDGKEYIDCMGGYGVAIVGHQNKRVVKAIKDQVDKIITVH-SSLYNKTREEFLKTLIGLAPKGLTQVHLNNSGAEAIEAAIK 109
                  56799***********************************************7776.99*************************************** PP

                  HHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE-TTBGGGTB-HHHHHHHHHHHHHHHHCHTCCCEEEEEE-SCET CS
  Aminotran_3 106 larkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrlkypdeevlkeneeeeaalleelealekkkkdevaAvivEpiqg 203
                  +ark       t k+ ++a+kg++HG+ lgals+t + +kyk+ f+p++ +v+++ + d                 +e+l+ ++++++a vi+Epiqg
   EPA05061.1 110 FARK------FTGKKGMVAMKGSYHGKSLGALSLTFN-PKYKKAFEPLVEKVSFASFGD-----------------IESLRSTIDEDTAFVILEPIQG 183
                  ****......***************************.********************9.................9********************* PP

                  TTTSEB--CCHHHHHHHHHHHHT-EEEEE-TTTTTTTTSSSSGGGGCTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTSB--TTTT-HHHHHHH CS
  Aminotran_3 204 egGvvvaspeflaklrelckkhdvllivDEvqtGfGrTGklfAlehagvspDlmtlaKaltgGlplsavlataevmqalapgshgsTfgGnplacava 301
                  e G++va+++fl+++r+lc+++++lli+DE+q G+GrTG l+A+eh++++pD+++laK+++gG p+ a+l++ ++   +++g+h+sTfgGnpl ca+ 
   EPA05061.1 184 ESGINVAPDGFLQEVRKLCDEKGILLIFDEIQAGLGRTGRLWACEHWNTAPDILCLAKGIAGGVPMGATLVRPDILASMSKGEHSSTFGGNPLSCAAG 281
                  ************************************************************************************************** PP

                  HHHHHHHHHTTHHHHHHHHHHHHHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTCHHHHHHHHHCTEE-EEETTTEEEE---TT--HHHHHHHH CS
  Aminotran_3 302 lavleiieeekllenaqelgaalkegLeelqkkyevikevRgkGlmiaielkeeaevkekeilkkakekGvlilsaGdnvirllppliitdeeidell 399
                  +a+l+++ ++ l+en q++g+ ++egLe+l++k+  i+e+RgkGlmi++elk e++    +il ++ ++ vl+l +G+n++r+lppl+it+e++ ++l
   EPA05061.1 282 IATLQALTQDGLIENSQKMGEFFREGLEKLKEKHPIIREIRGKGLMIGVELKFEVK----DILMNLMKERVLMLYSGRNILRILPPLVITKEDVTKVL 375
                  ******************************************************99....9************************************* PP

                  HHHHHHH CS
  Aminotran_3 400 eilkkal 406
                  e+l k+l
   EPA05061.1 376 ETLDKVL 382
                  ***9986 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   3.9e-07    0.0023     129     261 ..     159     281 ..      47     321 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.9e-07
                    EE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--.B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTT CS
  Aminotran_1_2 129 hldlealeealkeapegnkktkvilvesphNPtGt.vatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKaf 223
                      d+e+l   ++e       t ++++e ++  +G  va+   l+++ +l++++++ll++De+ ag+  +  + +a +   +++p+ +++   + a 
     EPA05061.1 159 FGDIESLRSTIDE------DTAFVILEPIQGESGInVAPDGFLQEVRKLCDEKGILLIFDEIQAGLGRTG-RLWA-CEHWNTAPD-ILCLAKGIAG 245
                    4699999999999......789************8356667899*********************99984.5566.777777777.7776666667 PP

                    SSGGG-EEEEEEEHHHHHHHHHHHHHHTS......SHHHHHHHH CS
  Aminotran_1_2 224 GlaGeRvGyilgnaavvsqlrklsrpfls......ssllqaava 261
                    G++    G++l+ ++++  + k   + ++      +     a+ 
     EPA05061.1 246 GVPM---GATLVRPDILASMSKGEHSSTFggnplsC-----AAG 281
                    8887...99999999999999988888887544322.....222 PP

>> DUF2931  Protein of unknown function (DUF2931)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.6e-05     0.098     120     170 ..      67     119 ..      56     149 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.6e-05
     DUF2931 120 kekikkrsgdkdyrdniilGLaPgGkvkvwLtgag...vgndielakgiaeeif 170
                  ++  +++  ++++ + ++GLaP G  +v L+++g    +  i++a++ + +  
  EPA05061.1  67 VHSSLYNK-TREEFLKTLIGLAPKGLTQVHLNNSGaeaIEAAIKFARKFTGKKG 119
                 55555443.345777889***************776666666776666444332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.53
# Mc/sec: 2209.72
//
Query:       EPA05062.1  [L=227]
Description: class I glutamine amidotransferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.7e-23   81.1   0.0    1.3e-22   80.6   0.0    1.1  1  GATase         Glutamine amidotransferase class-I
    1.6e-06   28.1   0.2    1.9e-05   24.5   0.0    2.4  2  Peptidase_C26  Peptidase C26
    5.4e-06   25.5   0.0      1e-05   24.7   0.0    1.4  2  HTS            Homoserine O-succinyltransferase
  ------ inclusion threshold ------
      0.019   14.6   0.4      0.027   14.1   0.0    1.5  2  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
       0.12   11.9   0.2       0.18   11.4   0.2    1.2  1  INTS5_N        Integrator complex subunit 5 N-terminus
       0.16   11.7   0.0       0.28   11.0   0.0    1.4  1  DJ-1_PfpI      DJ-1/PfpI family


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.6   0.0   4.2e-26   1.3e-22      26     174 ..      29     173 ..      20     178 .. 0.87

  Alignments for each domain:
  == domain 1  score: 80.6 bits;  conditional E-value: 4.2e-26
                 EEETTSHHHHHHHTHHSTSEEEEEEESSCTT.....TTTHHHHHHHHCTSTS-EEEETHHHHHHHHHTTTEEEEEECEEEEEEEEEEEETTT.CGGTTT CS
      GATase  26 vvpidasaeeilellknpdgilvsgGpgspg.....vegkieaikearenkiPiLGICLGmQllaiefgrkvvkekekehhggtmrlgddet.allygl 118
                 +  ++a++e+i   +k++  i++ g p s +      +++ ++ik+  e +iP+LGICLG Ql+a+ fg+kv++   k++ g  + l  d++ +l++g 
  EPA05062.1  29 ITSVHAKHENI--PEKKYSLIVILGAPESANddfpyLQEEQKLIKKTVEDNIPLLGICLGSQLIAKTFGAKVYPGP-KKEIGFYHDLVTDNNsKLFSGF 124
                 44455555555..589**************99***9****************************************.7788888887777767****** PP

                 TSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEEEEEEETTTEEEESSBTTST CS
      GATase 119 knevierhrHryevnpkelepaglevtakseddeelmeiiekknpfvgvQFHPEst 174
                  n++++ h+H+++++    +p++ + +a+se+  ++ +++  +  +vg+QFH E+ 
  EPA05062.1 125 TNPFTVFHWHGDTFD----LPEKATRLAHSENY-QNQAFQIGS--AVGLQFHMEVN 173
                 ***************....79999999999887.788877777..5******9986 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.11   3.2e+02     148     176 ..       7      35 ..       2      49 .. 0.85
   2 !   24.5   0.0   6.3e-09   1.9e-05      94     132 ..      66     104 ..      63     171 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.11
  Peptidase_C26 148 shavkvekgsllaellgseeievnslHhq 176
                     h+ ++e ++ l ell+++ ++++s+H  
     EPA05062.1   7 VHNTRIEGSGYLGELLNNDGFDITSVHAK 35 
                    699999***********999*******75 PP

  == domain 2  score: 24.5 bits;  conditional E-value: 6.3e-09
  Peptidase_C26  94 elaLiraalergvPilgiCrGlqllnvalGGtlyqdiee 132
                    e +Li++++e ++P+lgiC+G ql++ ++G ++y   ++
     EPA05062.1  66 EQKLIKKTVEDNIPLLGICLGSQLIAKTFGAKVYPGPKK 104
                    5689**************************999987665 PP

>> HTS  Homoserine O-succinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   3.4e-09     1e-05      85     190 ..      30     132 ..      23     158 .. 0.92
   2 ?   -3.2   0.0       1.1   3.2e+03      76      92 ..     206     222 ..     193     223 .. 0.68

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 3.4e-09
                 HHH-B-GGGTTT--EEEEEE---S-TTS-GGGSTTHHHHHHHHHHHHHHEEEEEEETHHHHHHHHHHH----EEEEEEEEEEEEEEES.S--GGGTT-- CS
         HTS  85 ekfYktfeeikdekfDgliiTGApveqlefeevkYWeelteildwakenvtstlfiCwaaqaalyylygvekkklpeKlfGvfehkvlkekspllrgfd 183
                 ++   + e+i ++k+  ++i GAp ++   ++  Y +e +++++ + e+    l iC+++q  ++   g + +  p+K +G ++  v++++s+l++gf 
  EPA05062.1  30 TSVHAKHENIPEKKYSLIVILGAPESA--NDDFPYLQEEQKLIKKTVEDNIPLLGICLGSQL-IAKTFGAKVYPGPKKEIGFYHDLVTDNNSKLFSGFT 125
                 56678899****************765..57******************************8.88899******************************* PP

                 SEEEEEE CS
         HTS 184 deflvph 190
                 + f+v h
  EPA05062.1 126 NPFTVFH 132
                 **99876 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.1
                 --SS-HHHHHHH-B-GG CS
         HTS  76 skntskehlekfYktfe 92 
                 +    k+ +++fY++f+
  EPA05062.1 206 NISIVKNNMNNFYNNFK 222
                 44556788999999986 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   9.1e-06     0.027      26      92 ..      28      94 ..       4     105 .. 0.78
   2 ?   -3.9   0.3       2.9   8.7e+03       6      16 ..     210     221 ..     207     222 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 9.1e-06
    GATase_3 26 rvrfvplkdeslg.edadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmLGeei 92
                ++  v+ k+e+++ +++ l+++ G  ++ ++  +   ++ ++ ik+ +e+++p+lgiC G q+  +++
  EPA05062.1 28 DITSVHAKHENIPeKKYSLIVILGA-PESANDDFPYLQEEQKLIKKTVEDNIPLLGICLGSQLIAKTF 94
                4555666788887656787777775.45555566666678999********************99886 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 2.9
    GATase_3   6 rlpaisnyt.dl 16 
                   + ++n++ ++
  EPA05062.1 210 VKNNMNNFYnNF 221
                 556788888576 PP

>> INTS5_N  Integrator complex subunit 5 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   5.9e-05      0.18      44      95 ..     166     221 ..     162     226 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.9e-05
     INTS5_N  44 leylaqlfeeaveryleevete....pilkesqinaeldeaieeiqtvleelveen 95 
                 l++  ++ ee+++ +l++ e++    p  + ++i++++de i+ +++ ++++ ++ 
  EPA05062.1 166 LQFHMEVNEEMINLWLDKTEEKlhqiPYIDPKKIRSDIDENISIVKNNMNNFYNNF 221
                 67888999**********99999999999**********************98765 PP

>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   9.5e-05      0.28      50     110 ..      32      93 ..       4      98 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9.5e-05
                 -SEEGGGCTCCG-SEEEE--BHHHH.HHHHTSHHHHHHHHHHHHTT-EEEEETTTHHHHHHT CS
   DJ-1_PfpI  50 vdaslddvkaaeyDalvlpGGragp.erlrenekvvelvkefaekgklvaaICagpqlLaaa 110
                 v a+ +++  ++y ++v+ G  +++ +++   ++ ++l+k+ +e++ ++  IC g ql a++
  EPA05062.1  32 VHAKHENIPEKKYSLIVILGAPESAnDDFPYLQEEQKLIKKTVEDNIPLLGICLGSQLIAKT 93 
                 666778888999*******986654145666667899********************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1454.03
//
Query:       EPA05063.1  [L=277]
Description: pterin binding enzyme [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.4e-31  109.3   0.0    2.8e-31  109.0   0.0    1.0  1  Pterin_bind  Pterin binding enzyme
      3e-05   22.9   0.0    3.7e-05   22.6   0.0    1.1  1  CdhD         CO dehydrogenase/acetyl-CoA synthase delta subun


Domain annotation for each model (and alignments):
>> Pterin_bind  Pterin binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.0   0.0   3.2e-35   2.8e-31       1     244 []      24     257 ..      24     257 .. 0.91

  Alignments for each domain:
  == domain 1  score: 109.0 bits;  conditional E-value: 3.2e-35
                  EEEEETTTTTCHCCHHC.THHHHHHHHHHHHHHTT-SEEEEESS-TSTT--CCHHHHHHHHHHHHHHHHHHHCTSEEEEE-S-HHHHHHHHHT..TSE CS
  Pterin_bind   1 mgilNvtpdsfsdggkf.edldkalaqarkmveeGAdilDiggestrPgaervdeeeelervvpvlealrdeadvpisiDttkaevaeaAlka..gad 95 
                  ++++N  ++++ +++    d d  ++ ar +ve+GA+ lD++++ t       +  +e + ++ ++++l+ e+d p+ iD+t+++v++a +++  g+ 
   EPA05063.1  24 GERINTQGSRKAKQLVLnDDFDGLVDLARTQVEDGAHCLDVCVATT-------ERSDERQFMIHLVKKLSLEIDAPLVIDSTDPDVIKATVEQipGRP 114
                  699************9999***************************.......66778888899999999999************************* PP

                  EEEETTTTS...SSTTHHHHHHHHT-EEEEESECSSTTTHCCCC.CCCSSHHHHHHHHHHHHHHHHHHTT--GGGEEEETTTTS..STTHHHHHHHHH CS
  Pterin_bind  96 ivNdvsgee...rdpkmlelvaeagaavvvmhmrgtpktmqeee.gqyedvveeveaflearveaaeeaGvaperillDpgigf..gkteehnlellr 187
                  i+N++++e    r++k+++++a++g++ +++ +          + g++++  e+ve++     e  +++G++ e+ ++D+++++  +++ e   +  +
   EPA05063.1 115 IINSINLEGdgsRFEKLAPIMAKYGLPAIALCIG---------PkGMAKTPQEKVETAELL-YETGKKYGLQIEQFIFDVLTFTlaTGEDEFLDAGKN 202
                  *******99899**********************.........558999999***999885.567788****************75555555556899 PP

                  THHHHHHTTS....SEBEEEGTTGHHHHHHHCTTCHGHHHHHHHHHHHHHHHTT-SEEEES CS
  Pterin_bind 188 rldelreale....vpvllGvSrksflgrllelgkaeeRdagtaaflalaaaaGadivrVh 244
                  +l+ +r  +e      ++lG+S++sf + +       +R++++++fl++a++ G+d ++V+
   EPA05063.1 203 TLEGIRLVKEkfpnSFTTLGLSNISFGLVPY------ARKVLNSVFLYHAVKSGLDTAIVN 257
                  999999888898787899**********865......9*********************97 PP

>> CdhD  CO dehydrogenase/acetyl-CoA synthase delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   4.1e-09   3.7e-05      51     153 ..      43     148 ..      19     203 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 4.1e-09
                 HHTT-EEE....ETTE.EEE--E.EEEE--SSST.HHHHHHHHHHHCC--SEEEEE-SSHHHHHHHHTTTCCC--EEEEE-TT.T...HHHHHHHHHHT CS
        CdhD  51 rieevvddwakkrvge.kltlda.iairlistdPakkfakavekvakavkvplvlggsdpevlkaalevvederpllyaAtkd.d...ykeiaelaley 143
                  ++ +vd  a+ +v+     ld+ +a   +s++  + + + v+k++ +++ plv+ + dp+v+ka++e +   rp++ + +++ d   ++++a +  +y
  EPA05063.1  43 DFDGLVD-LARTQVEDgAHCLDVcVATTERSDE-RQFMIHLVKKLSLEIDAPLVIDSTDPDVIKATVEQIP-GRPIINSINLEgDgsrFEKLAPIMAKY 138
                 5666666.5777777623456651444455555.3666799*****************************9.69*****99987633366666667788 PP

                 T--EEEE-.S CS
        CdhD 144 kvpvvllsin 153
                 + p ++l i 
  EPA05063.1 139 GLPAIALCIG 148
                 8887776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1649.41
//
Query:       EPA05064.1  [L=262]
Description: DNA (cytosine-5-)-methyltransferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.6e-36  124.7   4.9    5.6e-36  124.4   4.9    1.1  1  N6_N4_Mtase      DNA methylase
    0.00012   21.8   0.0      0.049   13.3   0.0    2.4  3  UPF0020          Putative RNA methylase family UPF0020
      0.003   17.4   0.1     0.0058   16.4   0.1    1.7  2  N6-adenineMlase  Probable N6-adenine methyltransferase
  ------ inclusion threshold ------
       0.11   12.0   0.0       0.55    9.8   0.1    2.0  2  MTS              Methyltransferase small domain


Domain annotation for each model (and alignments):
>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.4   4.9   1.3e-39   5.6e-36       1     231 []      30     249 ..      30     249 .. 0.82

  Alignments for each domain:
  == domain 1  score: 124.4 bits;  conditional E-value: 1.3e-39
                  EEEEEE--SSSSSCS...............GCCGCCHHHHHHHHHHHHHHHHHHHEEEEEEEEEEE-CCCHHTHHHHHHHHHTT-EEEEEEEEEEESS CS
  N6_N4_Mtase   1 vdlivtdpPYntgkdy..........endeqyeeedsyeeyleflekvlkevrrvLkddgsifiniddseikkelkaladeifggffllnvivwkkpn 88 
                  +dli+tdpP+ ++ +           + ++ y+e +   +y +f + ++ke+ r+Lkd+gs++++ + ++ k+  ++ a+++ g f+  n+i+wk++ 
   EPA05064.1  30 IDLIITDPPFAINFKAtkanynrissRVMQGYNEIK-AVDYYDFSYHWMKEAFRILKDSGSMYVFSGWNNLKD--ILRALDDVG-FITVNHIIWKYQF 123
                  89*************666666666644444444444.678889***************************996..555666668.**********997 PP

                  STTTSTCCS-B--EEEEEEEESSTT-..---GGGSSBSS-HHHHHHHHHHCHHHCC-B--BSEEE-SCCCTTSTTS-CHH----SS---HHHHHHHHH CS
  N6_N4_Mtase  89 smpesnkdrltsthEyilvfsknkkyllkfnldaikvpyeekdklekrgaytskkkgkkiediWdlseiqsnekkskgdtkkkHpaqkPvallerlIk 186
                  ++   +k ++ts +  ++v++ +k++ + f   +++++ +  ++++  +        k+ ed+W++++ + +  +++       p++ P++l+e+l+ 
   EPA05064.1 124 GVVTKKK-FVTSHYHCLYVCKDDKQR-KFFPFSRFEKNSKSDKGRSLHY--------KDKEDVWEIKREYWTGDEKT-------PTKLPAELIEKLLH 204
                  7777664.888888888888888888.7777777777777777777766........999****4444433333333.......************** PP

                  HHS-TT-EEEETT-TTTHHHHHHHHTT-EEEEEESSHHHHHHHHH CS
  N6_N4_Mtase 187 lstkkgdivlDpFaGSGtTavaakelgrkfiGieieeeyvelaek 231
                   s++k divlDpF+GSG  av+ k ++r+ +G+ei +ey++ a+k
   EPA05064.1 205 YSSEKKDIVLDPFLGSGQVAVVSKYMNRRHLGFEIVPEYYKFAKK 249
                  ****************************************98875 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   1.1e-05     0.049      97     142 ..       6      51 ..       3      66 .. 0.81
   2 ?   -3.8   0.0       1.9   8.6e+03     150     177 ..      78     104 ..      71     108 .. 0.67
   3 !    6.1   0.0    0.0018       7.9       8      45 ..     190     226 ..     184     256 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.1e-05
                 HHTT-GGGEEEEE--GGG--STTS---EEEE----------HHHH.H CS
     UPF0020  97 ekagvgdliefsqadaakLrlkegevdvivtnpPYGerlgskkal.e 142
                 +k +++++ ++++ +  kL  +++++d+i+t+pP+ +  +++ka+ +
  EPA05064.1   6 KKIEINKIYNMNCIEGMKLI-PKNKIDLIITDPPFAINFKATKANyN 51 
                 66778888888998989998.8889*************999999845 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 1.9
                 HHHHHH-TT..-EEEEEESSHHHHHCC- CS
     UPF0020 150 relkrvlrgggrlvlltsenkalekale 177
                 +e+ r+l+  + +++++s+ ++l+++l+
  EPA05064.1  78 KEAFRILKD-SGSMYVFSGWNNLKDILR 104
                 455555555.777888888777777665 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0018
                 ---SS-HHHHHHHHHHTT--TTS-EEETT-TTSHHHHH CS
     UPF0020   8 gpapLketLAaalvrlagwkpgepllDPmCGsGtilIE 45 
                  p++L ++L   l+  +  k+ +  lDP+ GsG +++ 
  EPA05064.1 190 TPTKLPAELIEKLLHYSSEKK-DIVLDPFLGSGQVAVV 226
                 567777777777787777655.6789*******99985 PP

>> N6-adenineMlase  Probable N6-adenine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   1.3e-06    0.0058      72     106 ..      13      47 ..       2     137 .. 0.75
   2 ?   -2.8   0.0       1.1   4.9e+03      85      96 ..     202     216 ..     173     232 .. 0.58

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.3e-06
  N6-adenineMlase  72 fYdlnnpeelpeelkgkfdviviDPPFlseeclkk 106
                       Y++n  e ++   k+k+d+i++DPPF  +  ++k
       EPA05064.1  13 IYNMNCIEGMKLIPKNKIDLIITDPPFAINFKATK 47 
                      79999999866666*************44433333 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.1
  N6-adenineMlase  85 l...kgkfdviviDP 96 
                      l   +++ + iv+DP
       EPA05064.1 202 LlhySSEKKDIVLDP 216
                      133344444455554 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00012      0.55      83     117 ..      12      49 ..       3      60 .. 0.68
   2 ?   -1.1   0.0      0.27   1.2e+03     121     138 ..      76      93 ..      65     118 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00012
                 EEEE-STTTTST...TS-EEEEEE---STTTCHCHHHH CS
         MTS  83 evvasdvleeve...ekkfdlivsNPPfhagkatelav 117
                 ++++ +++e ++   ++k+dli++ PPf  + ++++a 
  EPA05064.1  12 KIYNMNCIEGMKlipKNKIDLIITDPPFAINFKATKAN 49 
                 45555555554433399***********9887766655 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.27
                 HHHHHHHHEEEEEEEEEE CS
         MTS 121 liaeAkeaLkegGeLliV 138
                  ++eA ++Lk++G++++ 
  EPA05064.1  76 WMKEAFRILKDSGSMYVF 93 
                 578999999999999874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       808  (0.0450667); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1626.35
//
Query:       EPA05065.1  [L=229]
Description: methyltransferase domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-17   63.3   0.0    2.5e-17   63.0   0.0    1.0  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    6.5e-12   45.9   0.0    9.2e-12   45.5   0.0    1.2  1  Methyltransf_11  Methyltransferase domain
    1.3e-11   45.0   0.0    1.9e-11   44.5   0.0    1.2  1  Methyltransf_25  Methyltransferase domain
    3.8e-07   30.1   0.0    4.5e-07   29.8   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    5.4e-07   29.5   0.0    9.8e-07   28.7   0.0    1.4  1  Methyltransf_31  Methyltransferase domain
    2.6e-05   24.9   0.0    4.5e-05   24.1   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
  ------ inclusion threshold ------
       0.08   12.8   0.0       0.13   12.1   0.0    1.3  1  Methyltransf_8   Hypothetical methyltransferase


Domain annotation for each model (and alignments):
>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.0   0.0   9.7e-21   2.5e-17       9     227 ..      10     224 ..       4     229 .] 0.88

  Alignments for each domain:
  == domain 1  score: 63.0 bits;  conditional E-value: 9.7e-21
                      XXXXXX-HHHHHHHHHHHHHTTTHHHHHHHHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEE CS
  Ubie_methyltran   9 vkevfesvaskyDlmndvlslgihrlWkkfveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinief 102
                      v ev  ++   yD++n+ +slg     ++  +    v +g+k+lD  +G g+++ + ++  + k  +++ D    mLk +  + +++     ++
       EPA05065.1  10 VIEVLREIIPVYDKVNSYISLGKDVEHRNRGIA-GRVFPGNKILDAGSGFGNMSKTALKLCDGKISITLYDPLVPMLKNTGTHFEKT----PDL 98 
                      789999****************99998885443.34679***************************************999888765....489 PP

                      EE--TTT-TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEEEEE----SHHHHHHHHHHHH.HHHHHHHHHHS-HH.HHHHHHHHH CS
  Ubie_methyltran 103 lqanaeeLpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvvlefskvelpllsqayelyskevlPvlGkllakdld.syryLvesi 195
                      +++  e++pf+++ fD v  ++ lr+  +   a+ e++rvlk  Gr+v++++ k+   ++++  + y   +lP l  +    l  ++  L  + 
       EPA05065.1  99 INGVFEHIPFKNEEFDAVLCGYSLRDAINLRIAISEIHRVLKDKGRFVIVDLGKPDEAVIRFGVSFYLRFILPILALIAGGRLGlKFGTLYGTY 192
                      99***********************************************************************99755554443267779**** PP

                      HHS--HHHHHHHHHHTTEEEEEEEE.EGGGTEE CS
  Ubie_methyltran 196 rafPdqetlkeliedaGfksveyes.ltgGvva 227
                      +++P++++l++l+ +  f++ve+e+ l gG++ 
       EPA05065.1 193 KRWPQNKKLEKLLLE-KFSKVEFEKdLMGGAIM 224
                      ***********9987.49999998735556554 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   0.0   3.6e-15   9.2e-12       1      96 []      52     147 ..      52     147 .. 0.93

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 3.6e-15
                      EEET-TTSHHHHHHHHTT...SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHHHHHHHHHHEEEE CS
  Methyltransf_11   1 LdvGcGtGrlaealakrg...arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedpekalkeiaRvLkpg 91 
                      Ld+G+G G +++   k +    +++  D+   mlk   ++ ++ +   +++ + +e++pf+++ fD+v++  +l    +++ a++ei+RvLk  
       EPA05065.1  52 LDAGSGFGNMSKTALKLCdgkISITLYDPLVPMLKNTGTHFEKTP---DLINGVFEHIPFKNEEFDAVLCGYSLRDAINLRIAISEIHRVLKDK 142
                      8**************998889999999999999988888777776...89******************************************** PP

                      EEEEE CS
  Methyltransf_11  92 Gllvi 96 
                      G++vi
       EPA05065.1 143 GRFVI 147
                      **996 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.5   0.0   7.6e-15   1.9e-11       1      97 []      51     143 ..      51     143 .. 0.92

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 7.6e-15
                      EEEET-TTSHHHHHHHCTS.TSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHHHHHHHHHHHHHE CS
  Methyltransf_25   1 vLdlGcGtGrltlalakrl.gkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsdedlekalkeiarvL 93 
                      +Ld+G G G++++ ++k + gk ++t  D+   ml+++ +++e+     ++++g +e++pf++++fD+v++ ++  + +  +l+ a++ei+rvL
       EPA05065.1  51 ILDAGSGFGNMSKTALKLCdGKISITLYDPLVPMLKNTGTHFEK---TPDLINGVFEHIPFKNEEFDAVLCGYS--LRDAINLRIAISEIHRVL 139
                      8******************88*********************65...579*********************644..55667899********** PP

                      EEEE CS
  Methyltransf_25  94 kpgG 97 
                      k++G
       EPA05065.1 140 KDKG 143
                      *998 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0   1.8e-10   4.5e-07      19     125 ..      44     155 ..      32     208 .. 0.84

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 1.8e-10
  Methyltransf_23  19 klraggrvLdiGcGtGillevl.ren.gf.svtgvDlspeaveiae.......kakkaqkdqfdeqeaaepqgkfdlIvlrevlehvpdppell 102
                      + ++g+++Ld G G G++++ + + + g+ s+t++D+     ++++       k++  ++  f  + ++++++ fd + + ++l    ++  ++
       EPA05065.1  44 RVFPGNKILDAGSGFGNMSKTAlKLCdGKiSITLYDPLV---PMLKntgthfeKTPDLINGVF--EHIPFKNEEFDAVLCGYSLRDAINLRIAI 132
                      557899************999866667778*******64...454445577777777777777..79999************************ PP

  Methyltransf_23 103 rqiatllkpgGylllseplaslk 125
                      + i++ lk+ G++++ + +++++
       EPA05065.1 133 SEIHRVLKDKGRFVIVDLGKPDE 155
                      *****************999875 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0   3.8e-10   9.8e-07       4     112 ..      48     150 ..      46     161 .. 0.87

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 3.8e-10
  Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgp.kaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnevlnaladpdkilee 96 
                      g+++lD+G+G G+ ++ +  +l++ k+ +++ D    +++   ++ +k       +  g +e+++  ++ e fD +l+   l +  ++  ++ e
       EPA05065.1  48 GNKILDAGSGFGNMSKTAL-KLCDgKISITLYDPLVPMLKNTGTHFEKT----PDLINGVFEHIP--FKNEEFDAVLCGYSLRDAINLRIAISE 134
                      689****************.77776999****************98854....335556666666..66677********************** PP

  Methyltransf_31  97 iervlkpggilliedp 112
                      i+rvlk++g+++i d 
       EPA05065.1 135 IHRVLKDKGRFVIVDL 150
                      ************9886 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   1.7e-08   4.5e-05       1      99 []      52     145 ..      52     145 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.7e-08
  Methyltransf_12   1 LeiGcGtGsllrallekl.pdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlkdirevldnirklL 93 
                      L+ G+G G++++  l+     i++t +D+   +++++ +++ k  ++ n ++e      +       fD+v++   l    ++r ++++i+++L
       EPA05065.1  52 LDAGSGFGNMSKTALKLCdGKISITLYDPLVPMLKNTGTHFEKTPDLINGVFEHIPFKNE------EFDAVLCGYSLRDAINLRIAISEIHRVL 139
                      89***************999**************99999999999877666666666543......9*************************** PP

  Methyltransf_12  94 kpgGrl 99 
                      k+ Gr+
       EPA05065.1 140 KDKGRF 145
                      ***986 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0     5e-05      0.13     113     158 ..     103     149 ..      93     160 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5e-05
                     TTS-S--TT-EEEEEEES---.SS-HHHHHHHHHHHEEEEEEEEEEE CS
  Methyltransf_8 113 lakvPledesvdvavfclslm.gtnladflkeanrvlkvGGllkvae 158
                     + ++P ++e  d +++  sl  + nl+  + e++rvlk  G + + +
      EPA05065.1 103 FEHIPFKNEEFDAVLCGYSLRdAINLRIAISEIHRVLKDKGRFVIVD 149
                     5789****************8357*****************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1686.35
//
Query:       EPA05066.1  [L=104]
Description: nitrogen regulatory protein P-II [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-18   67.6   1.4    3.9e-18   65.9   1.4    1.7  1  P-II      Nitrogen regulatory protein P-II
  ------ inclusion threshold ------
      0.074   12.8   0.0       0.18   11.6   0.0    1.7  1  DUF2179   Uncharacterized protein conserved in bacteria (DUF2
       0.13   12.4   0.0       0.19   11.9   0.0    1.3  1  CaM-KIIN  Calcium/calmodulin-dependent protein kinase II inhi


Domain annotation for each model (and alignments):
>> P-II  Nitrogen regulatory protein P-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.9   1.4   6.6e-22   3.9e-18       1     101 [.       4      96 ..       4      97 .. 0.92

  Alignments for each domain:
  == domain 1  score: 65.9 bits;  conditional E-value: 6.6e-22
                 EEEEEEGGGHHHHHHHHHHTTGGCEEEEEEEEEESTCCEEEECTTEEEEEEEEEEEEEEEEEEGGGHHHHHHHHHHHH-SSSTTSEEEEEEEESEEEET CS
        P-II   1 ieaiirpekleevkeaLekagvkgltvtevkGrGkqkghtelyrgaeyevellpkvkleivvsdedvekvveaiikaaktgeiGDGkiFvlpveeviri 99 
                 ie+i+rpe  +++ +a++k+gv g+t+ +v+G+G+               ++ +k ++  vv+d ++++v+++i k+a tg+ GDGk+Fv+ ve+++ i
  EPA05066.1   4 IEVIVRPELKDKTVSAIKKVGVGGITLFHVQGQGSAD---P-----PLVGQYFSKEMIICVVEDPKLDEVLNTIAKVACTGTKGDGKVFVTSVEDALDI 94 
                 899*****************************99888...3.....3444567799****************************************999 PP

                 TT CS
        P-II 100 rt 101
                  t
  EPA05066.1  95 CT 96 
                 77 PP

>> DUF2179  Uncharacterized protein conserved in bacteria (DUF2179)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0     3e-05      0.18       2      39 ..      27      72 ..      26      73 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3e-05
     DUF2179  2 GvTilkgeGgYsge........ekkvlytvvsrkelsklkeiikei 39
                G+T+++++G  s +         k+++++vv   +l ++ ++i ++
  EPA05066.1 27 GITLFHVQGQGSADpplvgqyfSKEMIICVVEDPKLDEVLNTIAKV 72
                8999999999777799999999*******************99875 PP

>> CaM-KIIN  Calcium/calmodulin-dependent protein kinase II inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   3.2e-05      0.19      39      78 ..      35      76 ..      22      77 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.2e-05
    CaM-KIIN 39 asqakrpPklgqigrakrv..vieddriddvLkgmtdksspG 78
                ++ +  pP +gq   ++ +  v+ed + d+vL  +++ + +G
  EPA05066.1 35 GQGSADPPLVGQYFSKEMIicVVEDPKLDEVLNTIAKVACTG 76
                44456789999998887654489*********9998777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 720.38
//
Query:       EPA05067.1  [L=116]
Description: iron-sulfur cluster assembly accessory protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.5e-22   77.6   0.0    8.4e-22   77.5   0.0    1.0  1  Fe-S_biosyn  Iron-sulphur cluster biosynthesis


Domain annotation for each model (and alignments):
>> Fe-S_biosyn  Iron-sulphur cluster biosynthesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.5   0.0   4.7e-26   8.4e-22       3     110 ..      10     110 ..       8     111 .. 0.97

  Alignments for each domain:
  == domain 1  score: 77.5 bits;  conditional E-value: 4.7e-26
                  EEE-HHHHHHHHHHHHCTTEC...EEEEEECCTSCCGGS.TT.EEEEEEEEESSTSTTTEEEEEETTEEEEEEGGGHHHS.TTEEEEEEEETTEEEEE CS
  Fe-S_biosyn   3 itlteaAaeklkkllaedkke...lrLdvddgggpyskggCsiggkyslvlvdeedeeydevlesnggkvyvksyslvfldeglvldfvedlgtlgLk 97 
                  it++++Aaek+k++++e+  +   lr++v+ gg       Cs g +y + + +++ ee+d v+e  g+k++v+sys   l +g ++d+ e+l+++g+k
   EPA05067.1  10 ITVSPKAAEKIKEFMKEEADNpqyLRVYVQGGG-------CS-GLSYGMGFEKAP-EEDDLVMEETGIKLLVDSYSVDHL-KGANVDYIESLMGSGFK 97 
                  9****************887789**********.......**.************.************************.9**************** PP

                  EETCCEEEEEEEE CS
  Fe-S_biosyn  98 sdngilddnvglg 110
                   +n++++ ++++g
   EPA05067.1  98 INNPNVTKSCSCG 110
                  ************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      595  (0.0331865); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 761.31
//
Query:       EPA05068.1  [L=282]
Description: Lysine biosynthesis enzyme LysX [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-30  105.9   0.0    2.4e-30  105.5   0.0    1.1  1  RimK            RimK-like ATP-grasp domain
    1.4e-08   34.3   0.0    1.9e-08   33.9   0.0    1.2  1  GSH-S_ATP       Prokaryotic glutathione synthetase, ATP-grasp
    2.9e-07   30.7   0.0    4.7e-07   30.0   0.0    1.3  1  ATP-grasp_3     ATP-grasp domain
    0.00028   20.2   0.1       0.27   10.4   0.0    2.5  2  ATPgrasp_ST     Sugar-transfer associated ATP-grasp
     0.0068   15.9   0.0      0.013   15.0   0.0    1.5  1  CPSase_L_D2     Carbamoyl-phosphate synthase L chain, ATP bin
  ------ inclusion threshold ------
      0.053   13.0   0.0      0.091   12.2   0.0    1.3  1  ATP-grasp_5     ATP-grasp domain
      0.059   12.9   0.0       0.11   12.0   0.0    1.6  1  ATP-grasp       ATP-grasp domain
      0.065   12.5   0.0        7.8    5.7   0.0    2.3  2  ATPgrasp_YheCD  YheC/D like ATP-grasp


Domain annotation for each model (and alignments):
>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.5   0.0   1.1e-33   2.4e-30       1     187 [.      86     276 ..      86     277 .. 0.92

  Alignments for each domain:
  == domain 1  score: 105.5 bits;  conditional E-value: 1.1e-33
                 HH-HHHHHHHHHHTT-----EEEESS-S-HHHHHHTT-.-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHH..GGG--EEEEE--SS-S...EEEEEEE CS
        RimK   1 ardKlkslklLakakikvpntalardeedaekliekiklrfPvvvKsvegsqGikvvlakkeqklkqvlea..lkeailvqeyieeaen...ediRvlv 94 
                 a +Kl ++ lL k ++++p +a+a +++ a + +e    + P v+K   gs G  +   +++++++ ++++      i + +y+ee  +   +diR ++
  EPA05068.1  86 AGNKLFTHMLLKKFGVPTPYAAVAFSKDAAIEHLETH--GYPKVIKPTVGSWGRLISKLNDKDSAEGIIDSreSMYPIYQVHYLEEFVSrppRDIRAIM 182
                 569999*********************9998888888..6******************************95444456777999998887889****** PP

                 ETTEEEEEEEEE--SSS----TTTT-EEEE----HHHHHHHHHHHHHCT-SEEEEEEEEE.TTEEEEEEEESS--SHHHHHHHT--HHHHHHHH CS
        RimK  95 vddevvaalrrvskeGdFRsnlhrGgvaeklqlseeekelAikaakamelvvaGvDllra.krgllvlEvnsspglekiektlgidiakkliea 187
                 v+d++vaa+ r+s +G++++n+ +Gg ae+ ++++e +e+ ika ka++ +++GvDl+++ +rgl+v Evn   + ++  +  g+di   +i++
  EPA05068.1 183 VGDKIVAAIYRTSGDGNWKTNMALGGTAEPCKVTPEMEEMCIKAKKAVQGDIVGVDLMESnDRGLVVHEVNNTTEYKNTVRVCGVDIPSLMIDY 276
                 ********************************************************99872689999********************9999986 PP

>> GSH-S_ATP  Prokaryotic glutathione synthetase, ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.0   8.6e-12   1.9e-08       5     153 ..      96     241 ..      88     256 .. 0.78

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 8.6e-12
                 GGGGCCCS--EEEES-HHHHHHHHHHHSS.EEEEESS--TTTT-EEE-TT-TTHHHHHHHHTTTTTS-EEEEE--GGGGG...-EEEEEEETTEE-SEE CS
   GSH-S_ATP   5 alsfpelipktlvskdkeeirafleeqgd.vilKPldgkgGegvfrvkksdpnlksilellteegkepviaqrylpeike...GDkRillvdGepigya 99 
                  ++f   +p + v+ +k++  + le++g   ++KP  g+ G+ + +++++d+  + i++   ++   p+   +yl+e  +    D R ++v  + +  a
  EPA05068.1  96 LKKFGVPTPYAAVAFSKDAAIEHLETHGYpKVIKPTVGSWGRLISKLNDKDS-AEGIIDSRESMY--PIYQVHYLEEFVSrppRDIRAIMVGDKIVA-A 190
                 4566677888899988888778888888769**************9998765.577777654443..3444467777655222599***99888777.* PP

                 EEEE--SS-S---GGGTSCEEEEE--HHHHHHHHHHHHHHHHTT--EEEEEEET CS
   GSH-S_ATP 100 laRvpaegevRsnlaaggraeatelterdreiaeelapkLkekGllfvGlDvig 153
                 + R + +g+ ++n+a gg+ae  ++t + +e++ + +++++ +   +vG+D+++
  EPA05068.1 191 IYRTSGDGNWKTNMALGGTAEPCKVTPEMEEMCIKAKKAVQGD---IVGVDLME 241
                 *********************************9988887765...68888775 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.0   2.1e-10   4.7e-07       1     155 [.      86     253 ..      86     256 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 2.1e-10
                  HTSHHHHHHHHTTT.S---...........-EESS--SSSEEEEESS-------B--SS--TTE................EEEE---SEEEEEEEEE. CS
  ATP-grasp_3   1 asdKlktykkLkeagvkvP.......tkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve.........lvqefieGkplSvsllsd 82 
                  a +Kl+t   Lk+ gv++P       + +  e+le   ++ v+Kp  G+ g  +++ ++k++ae +i++ e          + ef++  p  + +++ 
   EPA05068.1  86 AGNKLFTHMLLKKFGVPTPyaavafsKDAAIEHLETHGYPKVIKPTVGSWGRLISKLNDKDSAEGIIDSREsmypiyqvhYLEEFVSRPPRDIRAIMV 183
                  579*******************999989999999999*******************************9999***88888789**************7 PP

                  SSSEEEEEEEEEEEET....TEEEEEEES----HHHHHHHHHHHHHTTSTT--EEEEEEEE.ESS.SEEEEEEE CS
  ATP-grasp_3  83 gekvlvlavnrqliekaekefvyaGnvtpietelkeevvelaeevvekleglaGyvGvDlv.lkdeepyviEvN 155
                  g +  v a+ r   + ++k ++  G++++   + + e++e++ ++ ++++g   +vGvDl+  +d +++v EvN
   EPA05068.1 184 G-DKIVAAIYRTSGDGNWKTNMALGGTAEPC-KVTPEMEEMCIKAKKAVQG--DIVGVDLMeSNDRGLVVHEVN 253
                  7.66677888888888888877777665543.5778888888888888853..589*****5556999999**9 PP

>> ATPgrasp_ST  Sugar-transfer associated ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   0.00012      0.27      20      85 ..      87     148 ..      76     167 .. 0.85
   2 !    7.3   0.1    0.0011       2.5     227     268 ..     218     258 ..     202     264 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00012
  ATPgrasp_ST  20 ddKlkfkelalraglkvpkllgvikeqaeiseleafvkeleegvviKpakgsgGkGilviteredq 85 
                   +Kl +  l+++ g+++p   + +++ a i++le   +++++  viKp+ gs+G+ i+++++++ +
   EPA05068.1  87 GNKLFTHMLLKKFGVPTPYAAVAFSKDAAIEHLET--HGYPK--VIKPTVGSWGRLISKLNDKDSA 148
                  69999**************9999999999999986..67866..***************9886544 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0011
  ATPgrasp_ST 227 evlelaakaaeklpglgylGwDivldeekgplllElNarpgl 268
                  e+ e++ ka +  ++  ++G+D+   +++g+++ E+N++  +
   EPA05068.1 218 EMEEMCIKAKK-AVQGDIVGVDLMESNDRGLVVHEVNNTTEY 258
                  67799999999.9999*********************98765 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   5.7e-06     0.013       7     108 ..      94     191 ..      88     205 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5.7e-06
                  HHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHHSTS-EEEEE--SS.SEEEEEEEEEET CS
  CPSase_L_D2   7 ealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaafgnkqvlvekslkg.pkeiEvevlrDa 103
                   +lkk++vp+  ++ a   + + a++  +++gyP +ik+++g  G+     ++++  + ++ +  ++ +     +  ++e+++++ p++i + ++ D+
   EPA05068.1  94 MLLKKFGVPTPYAAVA--FSKDAAIEHLETHGYPKVIKPTVGSWGRLISKLNDKDSAEGIIDSRESMYP---IYQVHYLEEFVSRpPRDIRAIMVGDK 186
                  5789999999988777..899********************9999988888888888888776555553...33445899999883589999888888 PP

                  TS-EE CS
  CPSase_L_D2 104 kgnvi 108
                     +i
   EPA05068.1 187 IVAAI 191
                  76666 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0     4e-05     0.091      16      53 ..      93     130 ..      88     152 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4e-05
  ATP-grasp_5  16 kelleaygipvvetrlassaeeaveaaeeigypvvlKi 53 
                  + ll+ +g+p++   +a s+++a+e  e+ gyp v+K 
   EPA05068.1  93 HMLLKKFGVPTPYAAVAFSKDAAIEHLETHGYPKVIKP 130
                  5699********************************96 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   5.1e-05      0.11       2      73 ..      97     172 ..      96     256 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.1e-05
                 HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC.....GTTCEEEEE--- CS
   ATP-grasp   2 eklglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal.....keekvivEefvp 73 
                 +k g+p+p  +++ sk+++ e +e+ g+p v+K +++g+ G+  s +++++++e +++         +  ++Eefv+
  EPA05068.1  97 KKFGVPTPYAAVAFSKDAAIEHLETHGYPKVIK-PTVGSWGRLISKLNDKDSAEGIIDSResmypIYQVHYLEEFVS 172
                 7899****999999*******************.********99999999999999887755555455566777775 PP

>> ATPgrasp_YheCD  YheC/D like ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0    0.0035       7.8      11      76 ..      88     151 ..      77     182 .. 0.65
   2 ?    4.8   0.0    0.0062        14     139     167 ..     186     214 ..     163     235 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0035
  ATPgrasp_YheCD  11 nKwevyelLskdpelrpyLPetellesledleemlekyks.vylKpanGskGkgilriekeekelll 76 
                     nK  ++ lL+k    +py  + + + s+++  e le+++   ++Kp+ Gs G+ i +++ ++++  +
      EPA05068.1  88 NKLFTHMLLKKFGVPTPY--AAVAF-SKDAAIEHLETHGYpKVIKPTVGSWGRLISKLNDKDSAEGI 151
                     566666666665555544..34445.666666677777765799**************994444333 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0062
  ATPgrasp_YheCD 139 evtgiaaRiagkgsittnlsrGGtalple 167
                     ++++++ R++g+g+  tn++ GGta p +
      EPA05068.1 186 KIVAAIYRTSGDGNWKTNMALGGTAEPCK 214
                     478999*******************8865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 1947.74
//
Query:       EPA05069.1  [L=336]
Description: transporter, major facilitator family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.5e-25   89.9  37.6    9.3e-23   80.7  22.2    2.0  2  MFS_1       Major Facilitator Superfamily
    2.3e-06   26.7  23.7    7.1e-06   25.1  22.2    2.2  1  MFS_1_like  MFS_1 like family
    5.2e-06   25.6   8.9    5.2e-06   25.6   8.9    3.0  3  Sugar_tr    Sugar (and other) transporter
  ------ inclusion threshold ------
      0.047   14.1   0.0        0.1   13.0   0.0    1.6  1  DUF4094     Domain of unknown function (DUF4094)


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.7  22.2   2.1e-26   9.3e-23      30     330 ..       8     281 ..       1     286 [. 0.81
   2 !   17.6   6.1   3.3e-07    0.0015     119     165 ..     282     328 ..     277     334 .. 0.92

  Alignments for each domain:
  == domain 1  score: 80.7 bits;  conditional E-value: 2.1e-26
       MFS_1  30 spseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalglllll.fasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigll 126
                 s  eigl+++ ++++++++ + +Gr sd+ G r  ++ +g+++ a++ + l  fa+ + ll+++r+ +G+++g+++pa++a++ +   +++r+  +   
  EPA05069.1   8 SIFEIGLIVASFSFAQILSEIYFGRHSDKKGTRLkFIRIGFIGCAIA-FGLHyFANDISLLFLVRIAAGVASGVMIPAMIAYTYEANIEKKRAATV--- 102
                 7789***************************9999************.44445856666*************************999887777666... PP

       MFS_1 127 sagfslGailgpllggllasslgWravfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsg 225
                  ++ +lG + g +++g+         vf++ a+ ++++++     ++ + p++  ++++e           +  k++ +++ +  l+ +lll ++g ++
  EPA05069.1 103 ISFQALGWLAGIAAAGFAN---DLKIVFLLSAASFFIGLL-----FTIKLPNPLQDKEIEP---------GT-TKKVISKNKF--LFSSLLLRHIGATA 181
                 677779999999999***9...889*************44.....4444444444444444.........12.4555566667..999*********** PP

       MFS_1 226 lltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGfglgfvfpsllal 324
                 + t +pl+l+e lg   l+++++++ +  ++++i + l +  + +l++ +   +++++++++++glal+      ++++ +++l+G+++g+ f++ +  
  EPA05069.1 182 VWTIFPLMLMEKLGAE-LYQVSIVYVANTVMAFITMNLMASKI-KLSNPTKFKIGIGSTSFVFVGLALITDW---WMSMPFMALVGVTWGLLFIAGNFH 275
                 ****************.99999999988888877766666666.3566566666666666666666666666...77777999***********99988 PP

       MFS_1 325 asdlap 330
                 ++++ p
  EPA05069.1 276 LMENNP 281
                 888765 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 3.3e-07
       MFS_1 119 rgraigllsagfslGailgpllggllasslgWravfyilaivsllaf 165
                 r+  +g++s+++s+++++gp+++g +a ++ ++av+y++ ++ ++af
  EPA05069.1 282 RSTSTGIFSSTISISTVVGPVIAGSIAFLFDYHAVMYFAVVIIIVAF 328
                 77889****************************************96 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1  22.2   1.6e-09   7.1e-06      35     373 ..      11     307 ..       5     321 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.6e-09
  MFS_1_like  35 eigiitlilpltsilsppiwgvlaDrfgkrkkvvilslllsavlflsllfippskerqeesklevsvaqdvdaektfwilfllvvlasfflaailvlld 133
                 eig+i++   + +ils+  +g  +D+ g r k ++++ +  a++f   +                       + +++ +lfl+++ a + +  +++ + 
  EPA05069.1  11 EIGLIVASFSFAQILSEIYFGRHSDKKGTRLKFIRIGFIGCAIAFGLHY-----------------------FANDISLLFLVRIAAGVASGVMIPAMI 86 
                 8********************************************9444.......................789999***********9999999999 PP

  MFS_1_like 134 aatlkelgedrkdyGrqrlfGsvGyaifafitGilidhysvnllpysallyvlaallvisllvvlilnetekesklkvtkslqvllnilknpeviifll 232
                 a t+++  e +k+ + ++ f ++G+    ++ G++ d   v l  +sa+ +++ +l++i l  +l  +e e              ++++++ +  +++ 
  EPA05069.1  87 AYTYEANIE-KKRAATVISFQALGWLAGIAAAGFANDLKIVFL--LSAASFFIGLLFTIKLPNPLQDKEIEP----------GTTKKVISKNK--FLFS 170
                 999987533.344589*****************9977766633..234444445555555555443333333..........34455666655..4566 PP

  MFS_1_like 233 valilgmswgiienFlflYL.kelgasntllGslvalgvvae.iplfffaeklleklGhvklliiallayilrfllyaiienawlvlpievLhgisfgl 329
                  +l+ ++   ++++ + l L ++lga  + ++++ +  +v+  i++ ++a+k+  kl+  +   i++ ++ + f+++a+i+++w+ +p+ +L g++ gl
  EPA05069.1 171 SLLLRHIGATAVWTIFPLMLmEKLGAELYQVSIVYVANTVMAfITMNLMASKI--KLSNPTKFKIGIGSTSFVFVGLALITDWWMSMPFMALVGVTWGL 267
                 677777777777777777777***********987666666515566666666..56666667899999****************************** PP

  MFS_1_like 330 lwaaaveyvskiapksleatgqgllsglyfglGralGsliGGll 373
                 l+ a+ ++  +  p+s+ +   g++s++ +++ + +G +i+G +
  EPA05069.1 268 LFIAGNFHLMENNPRSTST---GIFSST-ISISTVVGPVIAGSI 307
                 ********99999988665...777776.677777777777743 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   8.9   1.2e-09   5.2e-06      47     156 ..      11     119 ..       3     142 .. 0.85
   2 ?   -2.7   5.1      0.44     2e+03     274     353 ..     184     263 ..     173     276 .. 0.50
   3 !    7.0   4.9   0.00052       2.3      32      89 ..     274     327 ..     258     335 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.2e-09
                 HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHH.HHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCH.HHHHHHH CS
    Sugar_tr  47 lsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigav.lqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklR.galvsly 143
                  +gliv++f++ +i++ +++g  +d+ G +  ++ ++++ ++ a+ l ++a+    + +l++ R+ +G++ G+    +  y+ E   +k+R  +++s++
  EPA05069.1  11 EIGLIVASFSFAQILSEIYFGRHSDKKGTRLKFIRIGFIGCAIAFgLHYFAN---DISLLFLVRIAAGVASGVMIPAMIAYTYEANIEKKRaATVISFQ 106
                 689***************************9999877775555550566666...9******************************9999955666777 PP

                 HHHHHHHHHHHHH CS
    Sugar_tr 144 qlaitfGilvaai 156
                  l++ +Gi  a +
  EPA05069.1 107 ALGWLAGIAAAGF 119
                 7899999876654 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.44
                 HHHTTTHHHHSS-THHHHHHHHHHHHHHHHHHHHH..HHHH.HS-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS...CHHHH CS
    Sugar_tr 274 myysptifenlglsksllvtiivgvvnfvatfvai..flvd.rfGRRtllllGaagmaicfvilgivalllvakskaasivai 353
                 ++++ +++e+lg +   +v  iv+v n+v+ f+ +  + ++ +++  t + +G+   +++fv l+ +++++ +    ++ v +
  EPA05069.1 184 TIFPLMLMEKLGAELY-QV-SIVYVANTVMAFITMnlMASKiKLSNPTKFKIGIGSTSFVFVGLALITDWWMSMP-FMALVGV 263
                 4455555666665544.33.3344444444444431122223445555555555555555555555555555553.4444444 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.00052
                 STT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHH CS
    Sugar_tr  32 fglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvig 89 
                 f+l +++      s+ +g++ s  ++  ++G ++ag ++  f++  ++ +a+v+ +++
  EPA05069.1 274 FHLMENNPR----STSTGIFSSTISISTVVGPVIAGSIAFLFDYHAVMYFAVVIIIVA 327
                 555555543....3469*********************************99999987 PP

>> DUF4094  Domain of unknown function (DUF4094)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.3e-05       0.1       3      26 ..     124     147 ..     122     170 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.3e-05
     DUF4094   3 kwvllLcvasflagllftnRlwtv 26 
                 k v+lL++asf++gllft +l + 
  EPA05069.1 124 KIVFLLSAASFFIGLLFTIKLPNP 147
                 7799**************998533 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       978  (0.0545485); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 2200.70
//
Query:       EPA05070.1  [L=41]
Description: hypothetical protein BG20_I0386 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      181  (0.0100954); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.43
# Mc/sec: 284.82
//
Query:       EPA05071.1  [L=379]
Description: transporter, major facilitator family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.7e-42  144.2  70.6    4.9e-31  107.9  36.7    2.0  2  MFS_1          Major Facilitator Superfamily
    1.1e-12   47.9  16.8    1.4e-12   47.7  16.8    1.0  1  MFS_4          Uncharacterised MFS-type transporter YbfB
     0.0018   16.7  13.6     0.0074   14.7  13.6    1.9  1  MFS_3          Transmembrane secretion effector
     0.0039   16.3  14.6     0.0044   16.1   8.0    2.2  2  PUCC           PUCC protein
     0.0052   16.8   3.0     0.0067   16.5   0.3    2.6  2  MASE2          MASE2 domain
  ------ inclusion threshold ------
      0.016   15.1   0.1      0.016   15.1   0.1    2.7  3  Phage_holin_8  Putative phage holin
       0.07   11.4  17.2       0.06   11.6   2.5    3.7  4  OATP           Organic Anion Transporter Polypeptide (OATP) f
        0.1   12.1   0.3       0.21   11.0   0.3    1.4  1  DUF5553        Family of unknown function (DUF5553)


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.9  36.7   2.2e-34   4.9e-31       3     322 ..      10     309 ..       8     312 .. 0.88
   2 !   50.0  25.8   9.3e-17   2.1e-13       2     171 ..     207     373 ..     206     378 .. 0.88

  Alignments for each domain:
  == domain 1  score: 107.9 bits;  conditional E-value: 2.2e-34
       MFS_1   3 laaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslwlllvlrvlqGlgaga 101
                 +++++++ ++++ gp+lp++ ++  g++ s +g++  + ++ +++  +++G l d+f    +l +g ++ +++++ll++a+s++ ++ +r+++G++ ++
  EPA05071.1  10 ITGLIIGVSYGLHGPILPIFAKNIIGATYSDLGFIGLANFIPYMFIPVFVGILLDKFNNGYLLAIGTAINSASIYLLSIAQSVPEIMGFRIMTGIAHAF 108
                 6789999******************************************************************77777768888*************** PP

       MFS_1 102 lfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg..Wravfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvp 198
                 ++p ++a+i+  ++++ r r i++++++f +G+++gpllg ++++ l   +r +f i a++++ ++++    l+ ++++  + ++        ++++++
  EPA05071.1 109 FWPPCQAIISNQSNEQTRVRNISWFTMFFVMGFMVGPLLGTVFLEGLDitYRILFQITAFILASSIIC---ALLISRRSITNHNE--------RFSFSS 196
                 ********************************************999999***************995...44444444444443........344667 PP

       MFS_1 199 awkallkdpvlwillialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavt 297
                  +k+++k p +  +++ +++++  f ++l+  p +   + g+s  + ++ll+  +++  +i+  lag++s+r     +    +++++++++gl++ a++
  EPA05071.1 197 -IKEMKKFPEV--IILLIFCTS-SFGIILSIYPAF-LNDNGMS-DVDILLLYFTFGISRVISLALAGKFSRR-----TSQTLIAATIAISFGLIISATS 284
                 .8888888888..777777776.99999******9.9999999.366666677777777777999*****99.....6679999*************** PP

       MFS_1 298 ssavllllvlvliGfglgfvfpsll 322
                 +s ++++++l+ +Gfg++++fp+ l
  EPA05071.1 285 DSFIMFAIALISMGFGFSIFFPLTL 309
                 *********************9866 PP

  == domain 2  score: 50.0 bits;  conditional E-value: 9.3e-17
       MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslw.lllvlrvlqGlga 99 
                 ++++++ + +++i+++++p a  +d g+s   i ll+ ++++  +++  ++G +s r     +l+++ ++ ++g l+++ +s ++ +++++ + +G+g 
  EPA05071.1 207 IILLIFCTSSFGIILSIYP-AFLNDNGMSDVDILLLYFTFGISRVISLALAGKFSRRT--SQTLIAATIAISFG-LIISATSDSFiMFAIALISMGFGF 301
                 5677777788888999999.777999*********99999999999999999998884..55888888888888.66663488899************* PP

       MFS_1 100 galfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlflll 171
                 +++fp+ + +i   ++k   g+ ig + + f++G ++gp +gg +a+s+g +++++++  ++++  +l++ +
  EPA05071.1 302 SIFFPLTLEIILSRTSKGISGKIIGAYETVFGIGWVIGPTIGGPIAQSFGHQSPYMVFFMIGIVITLLAIKY 373
                 ****************************************************************99986655 PP

>> MFS_4  Uncharacterised MFS-type transporter YbfB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.7  16.8   6.1e-16   1.4e-12       6     350 ..      16     359 ..      12     372 .. 0.86

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 6.1e-16
       MFS_4   6 GiGRFsytpiLPallaeg.qlslsqagllaaaNylGYLvGallaafalsagaeRlrllagllatvllllamaltesfaaflliRflaGvasAvvlvfgs 103
                 G+   ++ piLP   ++  + ++s++g+++ aN++ Y+   ++  + l + ++   l +g+    +++   ++++s+  ++  R+++G+a A+      
  EPA05071.1  16 GVSYGLHGPILPIFAKNIiGATYSDLGFIGLANFIPYMFIPVFVGILLDKFNNGYLLAIGTAINSASIYLLSIAQSVPEIMGFRIMTGIAHAFFWPPCQ 114
                 66666899*****99985389*****************9999998888888888889****************************************** PP

       MFS_4 104 slvlahaaaarrervgallfaGvGlGiavsgllvllllqlglsasslWlalavlsavllllvalllp.raalreasaaaeaakaeqkslpllalllaYg 201
                 +++ ++++++ r r ++++     +G +v+ ll ++ l+       + + ++++ ++  ++ all+  r+ +++ +  ++++ +e k++p +++ll + 
  EPA05071.1 115 AIISNQSNEQTRVRNISWFTMFFVMGFMVGPLLGTVFLEGLDITYRILFQITAFILASSIICALLISrRSITNHNERFSFSSIKEMKKFPEVIILLIFC 213
                 *****************9999999*******9988887766555556566666666666666666663666777777888888999************* PP

       MFS_4 202 laGfGYiitatFlvaiardgaggalleallWllvGlaaivgvlvwlrvakrsglrralaaallieavgvllsllspsplglivssvllGltflaitalv 300
                    fG i+     +a+ +d++ + +   ll++ +G++ ++++ +  + ++r  +++ l aa +  + g+++s  s+s ++ +++ + +G  f    +l+
  EPA05071.1 214 TSSFGIILSI--YPAFLNDNGMSDVDILLLYFTFGISRVISLALAGKFSRR--TSQTLIAATIAISFGLIISATSDSFIMFAIALISMGFGFSIFFPLT 308
                 *****77654..49999999**********************999999888..56666666666689******************************** PP

       MFS_4 301 lqlarelappat.rrllglmTasfgigQilGpllasllaeatgslalallv 350
                 l+++     +    +++g+  ++fgig ++Gp + + +a+  g  ++ ++ 
  EPA05071.1 309 LEIILSRTSKGIsGKIIGAYETVFGIGWVIGPTIGGPIAQSFGHQSPYMVF 359
                 ***999988887689************************999987766554 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7  13.6   3.3e-06    0.0074      49     373 ..      43     353 ..      33     378 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.3e-06
       MFS_3  49 lvqaaatLPifllsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlligiGaalndPaWqAsvgelvkrrdvpaAvaLnsvg 147
                 ++  a  +P +++ +++G+l D+f+   +lla+ + + ++s+ l ++a    +s+  ++++ +++gi  a+  P  qA+++++ + +     +   ++ 
  EPA05071.1  43 FIGLANFIPYMFIPVFVGILLDKFNN-GYLLAIGTAINSASIYLLSIA----QSVPEIMGFRIMTGIAHAFFWPPCQAIISNQSNEQTRVRNISWFTMF 136
                 56678889****************97.578888888999999998887....58999****************************9999999******* PP

       MFS_3 148 iniaRsvGPAlgGvlvaavGaalafavnalsyl...alivallrwkrevrksslprEkl.lealraglRftaasreikavlvRaalFglsasavlaLLP 242
                 + +   vGP lg v +  +  ++   ++  +++    +i+all ++r+++++   +E++ ++++++  +f    + i   +  +  Fg+    +l++ P
  EPA05071.1 137 FVMGFMVGPLLGTVFLEGLDITYRILFQITAFIlasSIICALLISRRSITNH---NERFsFSSIKEMKKFP---EVIILLIFCTSSFGI----ILSIYP 225
                 ***************9987766555555555541124788888888887765...5666245666655554...345455555555554....799999 PP

       MFS_3 243 lvardqldgdalvyGillgalGvGAilgalllsrLRerlsserlvllaavalAlvllslalasslwvavlvlllgGaaWitalstlnvavqlavPrWvv 341
                     d+  +d  +  +l  ++G+  +++ +l  +  +r s+ +l   a++a+ + l++ a ++s  + +++l+  G ++ + +      +   + + + 
  EPA05071.1 226 AFLNDNGMSDVDIL-LLYFTFGISRVISLALAGKFSRRTSQ-TL-IAATIAISFGLIISATSDSFIMFAIALISMGFGFSIFFPLTLEIILSRTSKGIS 321
                 99999988886654.67789999999998888888777654.44.46788889999999999**************9998888777777778889999* PP

       MFS_3 342 gRalavYltvlaGglaaGsllWGavaealsvt 373
                 g+ +  Y tv+  g   G  + G +a++ + +
  EPA05071.1 322 GKIIGAYETVFGIGWVIGPTIGGPIAQSFGHQ 353
                 **********9999999999999999988765 PP

>> PUCC  PUCC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.3   0.5    0.0072        16      96     170 ..     100     175 ..      48     220 .. 0.69
   2 !   16.1   8.0     2e-06    0.0044     264     392 ..     252     373 ..     241     379 .] 0.78

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0072
        PUCC  96 llvGlgvslsqTallALladlaeeeerpkvvgllyvmlligivvsaivvgallkdytea.rLirvvqgvalitlvl 170
                 ++ G++      +  A++++ ++e++r + ++   + +++g +v+ +   ++l+ ++ + r++  +++  l++ ++
  EPA05071.1 100 IMTGIAHAFFWPPCQAIISNQSNEQTRVRNISWFTMFFVMGFMVGPLLGTVFLEGLDITyRILFQITAFILASSII 175
                 5778888888888888888888888888888877777888888888888888887665412222233333333333 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 2e-06
        PUCC 264 glvlsrglkkarlaslgvllgllsflllilaallenvallvagvlllGlasGlfavaaltlmldlaaeeraglalGaWGaaQaiaaglavllggalrdl 362
                 +l+l+ +++    ++l ++ +++sf l+ ++a+ ++  +++ +++ +G++  +f   +l ++l+ + ++ +g  +Ga+  +  i   ++  +gg +++ 
  EPA05071.1 252 SLALAGKFSRRTSQTLIAATIAISFGLI-ISATSDSFIMFAIALISMGFGFSIFFPLTLEIILSRTSKGISGKIIGAYETVFGIGWVIGPTIGGPIAQ- 348
                 4555555555556667777777777765.56678999****************************************998877777777777776543. PP

        PUCC 363 lkalaandaalayglVfaleavlliisilv 392
                    +    +  +y + f++ +v+ +++i  
  EPA05071.1 349 --SFG---HQSPYMVFFMIGIVITLLAIKY 373
                 ..333...4679***********9999865 PP

>> MASE2  MASE2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.3     3e-06    0.0067       8      75 ..      74     144 ..      70     151 .. 0.83
   2 ?   -2.3   0.1       2.2     5e+03      15      36 ..     272     291 ..     261     311 .. 0.57

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3e-06
       MASE2   8 lGlllgaliiaaglleqhfs...lalllllvlnallwPhlayllarrsrdplrteqrlLliDallgGlwia 75 
                 +G+++ +++i    + q ++   ++ ++  +++a++wP    +++++s++ +r+++  ++   +++G++++
  EPA05071.1  74 IGTAINSASIYLLSIAQSVPeimGFRIMTGIAHAFFWPPCQAIISNQSNEQTRVRNISWFTMFFVMGFMVG 144
                 667777777777666676664445779999*******************************9999999987 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.2
       MASE2  15 liiaaglleqhfslalllllvl 36 
                 ++i+ gl+    s    +++++
  EPA05071.1 272 IAISFGLIISATS--DSFIMFA 291
                 4444444444444..2222222 PP

>> Phage_holin_8  Putative phage holin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.1   7.3e-06     0.016      46     107 ..     121     182 ..      73     195 .. 0.86
   2 ?   -1.4   0.2      0.99   2.2e+03      92     111 ..     266     285 ..     241     297 .. 0.71
   3 ?   -0.9   0.1       0.7   1.6e+03      58      85 ..     332     357 ..     329     373 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 7.3e-06
  Phage_holin_8  46 akdltlltrlayflvSfiaGvlaaglaaaklatllpatdrvldalgAlvasalavkvlllli 107
                    ++++t+++ +++f + f++G++ ++l+++ + + l  t r l ++ A+++++ ++  ll+  
     EPA05071.1 121 SNEQTRVRNISWFTMFFVMGFMVGPLLGTVFLEGLDITYRILFQITAFILASSIICALLISR 182
                    6799********************************************99998887776554 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.99
  Phage_holin_8  92 Alvasalavkvllllieqaa 111
                     l+a+++a+  +l+++  ++
     EPA05071.1 266 TLIAATIAISFGLIISATSD 285
                    46677777777766666555 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.7
  Phage_holin_8  58 flvSfiaGvlaaglaaaklatllpatdr 85 
                    f + +++G + +g++a+ + +++p+   
     EPA05071.1 332 FGIGWVIGPTIGGPIAQSFGHQSPY--M 357
                    5567999999999999999999888..3 PP

>> OATP  Organic Anion Transporter Polypeptide (OATP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.8     0.025        56      36      85 ..      39      88 ..       5      96 .. 0.89
   2 ?    6.8   0.1   0.00078       1.8     139     193 ..      99     153 ..      89     161 .. 0.93
   3 ?   -0.7   0.1      0.15   3.3e+02     462     496 ..     158     192 ..     155     198 .. 0.86
   4 ?   11.6   2.5   2.7e-05      0.06     129     193 ..     284     348 ..     204     354 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.025
                xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        OATP 36 stsgliassneignillilfvsYfggrghrPrwigigallmalgslllal 85
                s  g+i  +n i ++++ +fv+ + ++ +   +++ig+ + + + +ll++
  EPA05071.1 39 SDLGFIGLANFIPYMFIPVFVGILLDKFNNGYLLAIGTAINSASIYLLSI 88
                67899999999******************************999999876 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.00078
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        OATP 139 qlllGiGatpiytlGisYidDnvkkknsplylgilyalrilGpalGfllGslllk 193
                  ++ Gi+++ +++ +++ i + +++++    +++++++ ++G ++G llG+++l+
  EPA05071.1  99 RIMTGIAHAFFWPPCQAIISNQSNEQTRVRNISWFTMFFVMGFMVGPLLGTVFLE 153
                 5789************************************************996 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.15
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        OATP 462 lflillflvsflgalgrvpallvilRcVkkedksf 496
                 ++ il+ +++f++a++ + all+  R++ +++  f
  EPA05071.1 158 TYRILFQITAFILASSIICALLISRRSITNHNERF 192
                 57799999****************9*998877665 PP

  == domain 4  score: 11.6 bits;  conditional E-value: 2.7e-05
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        OATP 129 sklvllfflaqlllGiGatpiytlGisYidDnvkkknsplylgilyalrilGpalGfllGslllk 193
                 s  +++f +a + +G+G + +++l +  i   ++k  s   +g++ ++  +G+++G ++G+ +++
  EPA05071.1 284 SDSFIMFAIALISMGFGFSIFFPLTLEIILSRTSKGISGKIIGAYETVFGIGWVIGPTIGGPIAQ 348
                 223559**************************************************999998776 PP

>> DUF5553  Family of unknown function (DUF5553)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.3   9.2e-05      0.21     118     188 ..     257     327 ..     249     332 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9.2e-05
     DUF5553 118 svvssktqqptvishssisitfshyppatldsflvle..piklfpvsslrsplclncgscresirisgelign 188
                    s +t q t+i  ++i+i+f     at dsf+++    i +    s+  pl l+    r s  isg++ig 
  EPA05071.1 257 GKFSRRTSQ-TLI-AATIAISFGLIISATSDSFIMFAiaLISMGFGFSIFFPLTLEIILSRTSKGISGKIIGA 327
                 555666666.444.46899**************976411344444569999********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       850  (0.0474092); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.49
# Mc/sec: 2332.74
//
Query:       EPA05072.1  [L=108]
Description: hypothetical protein BG20_I0385 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      4e-07   29.2   0.1      5e-07   29.0   0.1    1.2  1  MttA_Hcf106   mttA/Hcf106 family
    0.00048   19.4   0.4    0.00055   19.2   0.4    1.0  1  DLP_helical   Dynamin-like helical domain
     0.0006   19.7   0.1    0.00068   19.6   0.1    1.1  1  Phage_Mu_Gam  Bacteriophage Mu Gam like protein
  ------ inclusion threshold ------
      0.035   14.2   0.1      0.044   13.9   0.1    1.2  1  COG2          COG (conserved oligomeric Golgi) complex compon
      0.072   13.4   0.1        0.2   12.0   0.1    1.6  2  DUF3852       Protein of unknown function (DUF3852)


Domain annotation for each model (and alignments):
>> MttA_Hcf106  mttA/Hcf106 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.1   1.4e-10     5e-07       5      46 ..       7      49 ..       4      89 .. 0.84

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 1.4e-10
                 HHHHHHHHHH.HHS-TTTHHHHHHHHHHHHHHHHHHHHHHHH- CS
  MttA_Hcf106  5 elliIlvVal.llFGpkkLPEvaraLGktLreFkkavkeleee 46
                 e++iI +Val l+ G ++LP +ar LGk   eF  a  e +++
   EPA05072.1  7 EWIIIIFVALvLILGTNQLPSAARKLGKIAYEFNRARTEVQSQ 49
                 89999999873689*********************99999986 PP

>> DLP_helical  Dynamin-like helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.4   1.5e-07   0.00055      73     155 ..      22     104 ..      18     108 .] 0.96

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.5e-07
  DLP_helical  73 erqlpeaeerleelekevekleesakriekelaelkkeieearielreelkayfsdLilqvkglsletieeFlereiGdegiv 155
                  ++qlp a ++l ++  e ++++++++ + k+++e+  +i+   ++ r++l+   +    +v+g s +++++++ +++G++ ++
   EPA05072.1  22 TNQLPSAARKLGKIAYEFNRARTEVQSQMKNISETTPNISAPVENERQKLETMVKTFGINVEGKSDDDLRKIIAKRMGQNTDN 104
                  589***************************************************************************99776 PP

>> Phage_Mu_Gam  Bacteriophage Mu Gam like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   1.9e-07   0.00068       3      58 ..      24      79 ..      22      95 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.9e-07
                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHH CS
  Phage_Mu_Gam  3 eanwalrkiaelkreleeieaeaneeiaaikekleaeleplkkeieylesllkqYa 58
                  ++ +a rk++++  e +++ +e+++++++i e   +  +p+++e+++le ++k++ 
    EPA05072.1 24 QLPSAARKLGKIAYEFNRARTEVQSQMKNISETTPNISAPVENERQKLETMVKTFG 79
                  677899************************************************96 PP

>> COG2  COG (conserved oligomeric Golgi) complex component, COG2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   1.2e-05     0.044      63     110 ..      24      72 ..      19      98 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.2e-05
        COG2  63 hLvglqeeleevesplaaarkkvesvreklsereeeveskleea.kele 110
                 +L +  ++l ++  ++++ar++v+s ++++se+  ++++ +e+  ++le
  EPA05072.1  24 QLPSAARKLGKIAYEFNRARTEVQSQMKNISETTPNISAPVENErQKLE 72 
                 78888999*******************************9986504454 PP

>> DUF3852  Protein of unknown function (DUF3852)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   5.6e-05       0.2       6      50 ..       9      55 ..       5      64 .. 0.73
   2 ?   -0.3   0.0      0.38   1.4e+03      27      48 ..      57      78 ..      53      82 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.6e-05
     DUF3852  6 liillvvlilaa.llavtalAa.sgdvagaiestwkeaksqiktvvn 50
                +ii++v+l+l++ +   ++ A   g++a   + + +e++sq+k++ +
  EPA05072.1  9 IIIIFVALVLILgTNQLPSAARkLGKIAYEFNRARTEVQSQMKNISE 55
                555555555544045555555578*******************9976 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.38
     DUF3852 27 sgdvagaiestwkeaksqiktv 48
                + ++++++e+  ++ ++ +kt 
  EPA05072.1 57 TPNISAPVENERQKLETMVKTF 78
                5699999999999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1063  (0.0592894); expected 358.6 (0.02)
Passed bias filter:                      678  (0.0378158); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 675.33
//
Query:       EPA05073.1  [L=375]
Description: N-acetyl-ornithine/N-acetyl-lysine deacetylase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-28   99.4   0.5    3.9e-28   98.6   0.5    1.4  1  Peptidase_M20  Peptidase family M20/M25/M40
    2.1e-11   43.7   0.0    4.4e-11   42.6   0.0    1.6  1  M20_dimer      Peptidase dimerisation domain
    8.1e-05   21.8   0.9       0.17   10.9   0.1    2.6  3  Peptidase_M42  M42 glutamyl aminopeptidase
      0.002   17.8   0.0     0.0032   17.2   0.0    1.3  1  Peptidase_M28  Peptidase family M28


Domain annotation for each model (and alignments):
>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.6   0.5   8.6e-32   3.9e-28       1     206 [.      68     364 ..      68     365 .. 0.88

  Alignments for each domain:
  == domain 1  score: 98.6 bits;  conditional E-value: 8.6e-32
                    EEEEES-BSSTTCGGGSSSTTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTTHHHHHHHHHHTTTCESEEEE CS
                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Peptidase_M20   1 llgsHlDvVpeeetdgwttpfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggrgGakallegleerekvdavfe 96 
                    ll +H+DvVp     g     + ++e + lyGrGa+d k+ ++a+l a+++++ +    +gt+ ++ ++dEEg+  G k+l+++     +vd+   
     EPA05073.1  68 LLCGHMDVVP-----G---KVKVRKEGDSLYGRGASDAKAPLMAMLFAAASVQNN----NGTVIFVGTVDEEGNATGVKNLVKN---PMDVDY--- 145
                    5779******.....4...467788878***********************8888....89***********988********3...446666... PP

                    EEEESSSBTCHSTETEEEE............................................................................. CS
                    xxxxxxxxxxxxxxxxxxx............................................................................. RF
  Peptidase_M20  97 lhieepgileagklaigvv............................................................................. 115
                    ++ +ep++ +    ++++                                                                              
     EPA05073.1 146 AVFGEPSGIK----QVTIAykgrlainlkvsvddsahasapwlsknaieetmifskelkegleseqdkkskgmlltatlteinggtshnvtpkecv 237
                    4478888888....334446678999999******************************************************************* PP

                    .................................EEEEEEEEEESHEEEC.CHHHHHHHHHHHHHHHTSC.EEEEEESSSBHTHHHH...TTTEEEE CS
                    .................................xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx...xxxxxxx RF
  Peptidase_M20 116 .................................kvevelleggapvtln.dsplvkalaeaaeelfgek.velivsgpggtdarff...agiptvm 173
                                                     ++ ++ + + +p++++ +s++v+a+   + ++   + ++li +  g+ d++ +   ++ip v 
     EPA05073.1 238 stfdiripvdtncklveqkisvlvneiaqkrkvEAYYSIIDETEPFEAPhNSAIVRAFTLGIMDVEH-TrPTLIRKT-GTGDMNVIgnqWKIPVV- 330
                    ****************************9887644444449999****999*************943.336666555.*********99999755. PP

                    EEESSG.GCTTSTTTEEEHHHHHHHHHHHHHHHH CS
                    xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Peptidase_M20 174 ifgpgs.glaHspnEyvdledlekgikvlarlle 206
                     +gpg+   aH+ +E+v+++++ +gi++l+r++ 
     EPA05073.1 331 TYGPGDpHEAHTIDERVSIDEYLRGIEILKRMIH 364
                    7****88************************986 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.6   0.0   9.9e-15   4.4e-11       4     107 ..     162     267 ..     159     269 .. 0.87

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 9.9e-15
                 -EEEEEEEE.EE-B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC......TCCTCCCCCEECCE-CCCCEESSEEEEEEEEEHHHHHHHHHHHHHHHHH CS
   M20_dimer   4 kGlaggkit.vkgkagHsgapgagaNAieklarllaeledeegdia.eerslprttlnvtgiegGsaknvipdeaeakidiRllpgedpeevleeieei 100
                 kG +  +++   + ++H++ap    NAie+ + +  el++  ++++ ++      t ++t+i+gG++ nv+p e+  ++diR++   + + v+++i  +
  EPA05073.1 162 KGRLAINLKvSVDDSAHASAPWLSKNAIEETMIFSKELKEGLESEQdKKSKGMLLTATLTEINGGTSHNVTPKECVSTFDIRIPVDTNCKLVEQKISVL 260
                 566666666566789*************************999999666666779*****************************999999999999999 PP

                 HTSCCST CS
   M20_dimer 101 lekeape 107
                 +++ a +
  EPA05073.1 261 VNEIAQK 267
                 9888766 PP

>> Peptidase_M42  M42 glutamyl aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0   0.00013      0.59       1      25 [.      54      76 ..      54      89 .. 0.86
   2 !   10.9   0.1   3.7e-05      0.17     132     228 ..      94     187 ..      80     193 .. 0.79
   3 ?   -3.1   0.0      0.68     3e+03     220     246 ..     252     278 ..     245     297 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00013
                   S-EEEEEESSTTSSEEEEEEE--B- CS
  Peptidase_M42  1 GnliakkkgkekepkvmiaAHmDei 25
                   Gn+iakk     +pk+++++HmD +
     EPA05073.1 54 GNIIAKKGT--GSPKILLCGHMDVV 76
                   99***8888..9***********87 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 3.7e-05
                    THHHHHHHHHHHHHHHHHCTSS-SSEEEEEEESTCTTTSHHHHHHHHHH--SEEEEEEEEEE-CSTTSTTTTSSTTS-CEEEEEETTCCSHHHHHH CS
  Peptidase_M42 132 alDdragvavllellkelkeeeleatvylvatvqEEvGlrGaktsaekikpdiaiavDvtaagdtpgskekeaklgkGpvirvkDasgiyhpklrk 227
                    a D +a ++++l ++ ++++++   tv++v+tv EE +  G k+++++  +d+  av   ++g ++ +  ++ +l     ++v D+ +   p l+k
     EPA05073.1  94 ASDAKAPLMAMLFAAASVQNNN--GTVIFVGTVDEEGNATGVKNLVKN-PMDVDYAVFGEPSGIKQVTIAYKGRLAINLKVSVDDSAHASAPWLSK 186
                    5688999999999999999998..*******************99998.77777777777777777777777667777777777777777777766 PP

                    H CS
  Peptidase_M42 228 k 228
                    +
     EPA05073.1 187 N 187
                    5 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 0.68
                    CSHHHHHHHHHHHHHHTT--EEEEEES CS
  Peptidase_M42 220 iyhpklrkkllelAkknnipyqlevls 246
                    ++++k++  + e+A+k +++ +++++ 
     EPA05073.1 252 LVEQKISVLVNEIAQKRKVEAYYSIID 278
                    567788888899999999998887665 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0     7e-07    0.0032       1      86 [.      55     140 ..      55     193 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 7e-07
                    EEEEEESTTCESEEEEEEEE--B-TTT.....TCC..T---TTTTHHHHHHHHHHHHHCHHGGCCSSEEEEEEEESSCSGSSHHHHHHHHHHC CS
  Peptidase_M28   1 NviatlegkatdevlllgAHyDsvgvg.....rgp..ifvGAdDnAsgvaalLelarvlaasgsrpkrgvrflffdaEEagllGSkafakakp 86 
                    N+ia+   +  +  +ll++H+D v+ +     +g+     GA D  ++ +a+L  a  +++    ++ +v+f+ +  EE    G k+++ ++p
     EPA05073.1  55 NIIAKKGTG--SPKILLCGHMDVVPGKvkvrkEGDslYGRGASDAKAPLMAMLFAAASVQN----NNGTVIFVGTVDEEGNATGVKNLV-KNP 140
                    667766444..4689**********999998755577778*************99999886....679********************9.666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2464.80
//
Query:       EPA05074.1  [L=125]
Description: hypothetical protein BG20_I0392 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00028   21.0   0.1     0.0026   18.0   0.1    2.1  1  Toprim    Toprim domain
    0.00064   20.1   0.0     0.0064   16.9   0.0    2.1  1  Toprim_4  Toprim domain
     0.0046   17.4   0.0     0.0081   16.6   0.0    1.5  1  Toprim_2  Toprim-like


Domain annotation for each model (and alignments):
>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   4.3e-07    0.0026       5      88 ..      28      90 ..      24     115 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4.3e-07
                ESSHHHHHHHHHTHTSTEEEEEEESSSSEEEHSTTEEEEEECTTTHHHHHHHHHHHHHHSEEEEECSSSHHHHHHHHHHHHHHT CS
      Toprim  5 vEgpsdaktiakalgsgfqavtaslGhildletefkpvyeeiedkkkvlkalkelakradeiilatDpDreGeaiawellevlk 88
                vEg++da +++++  sg+++ ++  G i++ ++                       +r+++ii+++D Dr G+ ++ + +++l+
  EPA05074.1 28 VEGKRDASALKRLGFSGEVIEFHRFGGIVNFAD---------------------YVSRYEKIIILFDRDRKGRYLTGKTIQLLQ 90
                566666666666533455555555555555555.....................5689********************998887 PP

>> Toprim_4  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.1e-06    0.0064       2      85 ..      24      97 ..      23     100 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.1e-06
    Toprim_4  2 eiiiVEgyaDvlalekagiknvvav...lggalspldgirpeklktenlveaekkvkevilaldgDaeGeataerlaelll.eegvkv 85
                 i+ VEg  D+ al + g+ + v      gg ++ +d ++    ++          +++i+++d D  G   + + ++ll+ +++++ 
  EPA05074.1 24 SIVAVEGKRDASALKRLGFSGEVIEfhrFGGIVNFADYVS----RY----------EKIIILFDRDRKGRYLTGKTIQLLQrRTKIDL 97
                6899*************99987643233566665555555....33..........67********************8876777665 PP

>> Toprim_2  Toprim-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.3e-06    0.0081      34      74 ..      57     100 ..      15     111 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.3e-06
    Toprim_2  34 aalkllerypekkvvlalDnDkaGrkaakrlaellreag.....vr 74 
                 + +++++ry  +k+++ +D D++Gr  + + ++ll+ ++     ++
  EPA05074.1  57 NFADYVSRY--EKIIILFDRDRKGRYLTGKTIQLLQRRTkidlsFK 100
                 667899999..99**********************87665444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 858.91
//
Query:       EPA05075.1  [L=349]
Description: N-acetyl-gamma-glutamyl-phosphate reductase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-35  121.9   0.0    3.3e-35  121.2   0.0    1.4  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
    4.8e-19   69.2   0.0      8e-19   68.4   0.0    1.4  1  Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation dom
    9.6e-05   22.6   0.0    0.00016   21.9   0.0    1.4  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
    0.00049   20.9   0.0    0.00096   20.0   0.0    1.5  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
     0.0006   19.9   0.0     0.0012   18.9   0.0    1.5  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
  ------ inclusion threshold ------
        0.1   13.2   0.0        0.2   12.3   0.0    1.5  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent


Domain annotation for each model (and alignments):
>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.2   0.0   1.1e-38   3.3e-35       1     121 []       3     142 ..       3     142 .. 0.98

  Alignments for each domain:
  == domain 1  score: 121.2 bits;  conditional E-value: 1.1e-38
                     EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGC.TT-SEEEE-SCHHHHHHHHHHHHHTTSEEE CS
  Semialdhyde_dh   1 kvaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavkaleegkdlkvedvdeeel.kevdivflalpagvskelapklaeagvkvi 94 
                     kv++vGa+GyvG e lrlL +hp+ve++ ++s+++  G+ l++  ++l++ +dl++++ d +++ +++d+vf+a+p+g++ e++++l+++g+kvi
      EPA05075.1   3 KVGVVGASGYVGGETLRLLVNHPDVEIAMVTSRQH-VGEYLHRIQPSLKGFTDLTFSELDYDKMtDKCDLVFTAVPHGTATEIVKALYDRGLKVI 96 
                     7********************************99.**********************9999999****************************** PP

                     ESSSTTTTST...................TSEBE-HHHHGGGGGGH CS
  Semialdhyde_dh  95 DlssdfRlkd...................davyvlpevnreaikka 121
                     Dls+d+Rl++                   + v+++pe++reaikka
      EPA05075.1  97 DLSADYRLHNaadydkwygwehphpdylpKSVFGVPELHREAIKKA 142
                     *******************************************986 PP

>> Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.4   0.0   2.7e-22     8e-19       1     184 []     159     319 ..     159     319 .. 0.88

  Alignments for each domain:
  == domain 1  score: 68.4 bits;  conditional E-value: 2.7e-22
                      HHHHHHC.TT.EEEEEEEEEEEGGGCHHHHHHHHHHHHHHHHHSTTS.CTTTSSHHTTSEESTCSTBTTTTCHCBHHHHHHHHHHHHHCTESCS CS
  Semialdhyde_dhC   1 LkPLlda.lgelervivatyqavSGaGkkgvreLlkqvaelqrsdeakpgvfgvpiagNlipyidkeedkgepetreelkavaetkkileftek 93 
                      L+PL+ + l++++++iv+++ + SGaG                      g+ ++  ag + py+   +++++ e+++el+++a +k ++++++ 
       EPA05075.1 159 LAPLIRNdLIDIDHIIVDSKIGSSGAGSG-------------------SGTAHAMRAGVIRPYKPA-KHRHTGEIEQELSEIAGKKIHVSMSP- 231
                      89***999********************5...................99999999**********.*************************9. PP

                      EEEEEEEESBSSEEEEEEEEEES..SSHHHHHHHHHHHHCSTTEEEEESS....HCHHSSHHHHTTCSSSEEEEEEEEETTCTTEEEEEEEEET CS
  Semialdhyde_dhC  94 vsatcvrVPvlrGhseavtiklk..lkdveveeveellaaapevkvvvne....eedrPtpaavaggtnsvsVGRirkdemgdeglklvvvgDN 181
                           + V v+rG++ + ++ +k  l++ e+ +++ + + + e +++         ++P p+ v+g +n++++G ++ de++++ l +++++DN
       EPA05075.1 232 -----HAVDVVRGILCTNHTFMKkdLDEKEIWKIYRETYGQ-ERFIRLIRdkkgLYKFPDPKFVVG-SNFCDIG-FDIDEENHR-LIAISASDN 316
                      .....79***************9555555555555555555.7777655545566789*******9.9******.*****9998.********* PP

                      TTT CS
  Semialdhyde_dhC 182 llk 184
                      l+k
       EPA05075.1 317 LMK 319
                      *97 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   5.5e-08   0.00016       1     102 [.       4     105 ..       4     142 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 5.5e-08
                      EEEE--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH..TTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-SSGGGHHHHHHHHHH CS
  Sacchrp_dh_NADP   1 vliiGa.GsvGqavaellarhfdvdaeitvadrskeklealaaka..lgvrfeaialdaenyeavLaallkegdlvvnlsppissldvlkaCie 91 
                      v ++Ga G+vG  +++ll++h dv  ei+ ++  ++  e l   +  + + f+  ++   +y++    +  + dlv  ++p   + +++ka ++
       EPA05075.1   4 VGVVGAsGYVGGETLRLLVNHPDV--EIAMVTSRQHVGEYLH-RIqpSLKGFTDLTFSELDYDK----MTDKCDLVFTAVPHGTATEIVKALYD 90 
                      679*********************..8888777777765554.443455566666666666666....77889********************* PP

                      HT-EEEESS-....B CS
  Sacchrp_dh_NADP  92 tgvhyvdtsi....s 102
                      +g  ++d s      
       EPA05075.1  91 RGLKVIDLSAdyrlH 105
                      *******88833332 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   3.2e-07   0.00096       1      90 [.       2      96 ..       2      97 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 3.2e-07
                  EEEEEETT.SHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESS.......HHHHHTCTTESEEEE-S-GGGHHHHHHHHHHTT-EEE CS
  GFO_IDH_MocA  1 lrvaiiGa.Gkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysd.......leelladpeidavivatpngtheelakaaleagkhvl 90
                  ++v+++Ga G++g + lr l ++ ++ e++ + +++       + +  ++ ++d       ++++ +  ++d+v+ a+p gt  e++ka+  +g +v+
    EPA05075.1  2 MKVGVVGAsGYVGGETLRLLVNH-PDVEIAMVTSRQHVGEYLHRIQPSLKGFTDltfseldYDKMTD--KCDLVFTAVPHGTATEIVKALYDRGLKVI 96
                  69******999999999777777.9999999999888776666889999988888844444555555..9************************9997 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   4.2e-07    0.0012       1      94 [.       2      95 ..       2      97 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 4.2e-07
                EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHH...HHSSSS--S-BEB.SSHHHHHHH-SEEEE-S-HHHHHHHHHHHHHTT-EE CS
      DapB_N  1 ikvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdag...ellglgklgvavt.ddleevlekadvliDFTtpeavlenlklalekgvkl 94
                +kv+vvGasG +G e ++++ +++d+e++ + +r++   +g+ +      l+   ++++++  d++++++k+d +     +  + e +k+++++g k+
  EPA05075.1  2 MKVGVVGASGYVGGETLRLLVNHPDVEIAMVTSRQH---VGEYLHriqPSLKG-FTDLTFSeLDYDKMTDKCDLVFTAVPHGTATEIVKALYDRGLKV 95
                89********************************98...33332211022222.23333333677777777887766655566667777777777665 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   6.6e-05       0.2       1      95 [.       3      99 ..       3     101 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.6e-05
                   EEEEE.TTSHHHHHHHHHHHHTTS-GGCEEEEEESSC..CCHHHHHHHHC....-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHHCGHHHHTTSEE CS
  F420_oxidored  1 kigii.GaGnmgealasgllaagaqpheivvansrnp..ekaeelaeelg....vkvtavdneeaaeeadvvvlavkpedveevlselakdalkgklv 91
                   k+g++ ++G +g   ++ l+++   + ei +++sr+   e +  ++ +l+     + ++ d+ ++ +++d v+ av+   ++e++++l    ++g  v
     EPA05075.1  3 KVGVVgASGYVGGETLRLLVNHP--DVEIAMVTSRQHvgEYLHRIQPSLKgftdLTFSELDYDKMTDKCDLVFTAVPHGTATEIVKAL---YDRGLKV 95
                   57777456777777777777774..455554544443223333444444478788889999***************************...6777777 PP

                   EEES CS
  F420_oxidored 92 isvl 95
                   i+ +
     EPA05075.1 96 IDLS 99
                   7776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2550.37
//
Query:       EPA05076.1  [L=702]
Description: CoA binding domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.6e-67  226.1   0.7    5.5e-67  225.5   0.7    1.3  1  ATP-grasp_5    ATP-grasp domain
      1e-48  164.6   0.2    2.5e-48  163.4   0.2    1.7  1  Succ_CoA_lig   Succinyl-CoA ligase like flavodoxin domain
    6.8e-24   84.6   0.1    2.3e-23   82.9   0.0    2.0  2  CoA_binding_2  CoA binding domain
    5.4e-08   32.6   0.8    1.1e-07   31.6   0.8    1.5  1  ATP-grasp_2    ATP-grasp domain
    1.1e-07   32.4   1.7    5.3e-07   30.2   0.2    3.0  3  CoA_binding    CoA binding domain
  ------ inclusion threshold ------
      0.015   14.9   0.0      0.034   13.7   0.0    1.6  1  ATP-grasp      ATP-grasp domain


Domain annotation for each model (and alignments):
>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  225.5   0.7   1.9e-70   5.5e-67       4     222 .]      10     227 ..       7     227 .. 0.97

  Alignments for each domain:
  == domain 1  score: 225.5 bits;  conditional E-value: 1.9e-70
  ATP-grasp_5   4 aegrtlLteaeakelleaygipvvetrlassaeeaveaaeeigypvvlKivspdilhKtdvgGvrlnlkdaeevraaaeeilervkekspeariegvl 101
                  + + ++ te+ +k +l+ yg++v+++ l++saeea++ a++ig+p v+K+vsp+ilhKtdvgGv+++l++ ++v+++++++  r+++ +++ +++g+l
   EPA05076.1  10 QTDHKVITEELSKTILKTYGVKVPPFALVTSAEEAAKQAKKIGFPLVMKVVSPQILHKTDVGGVKVGLDNVNDVKKTFKDMYGRLSK-KKGVEVKGIL 106
                  6778999******************************************************************************77.7899****** PP

  ATP-grasp_5 102 VqemakrggrElivgvteDpvFGpvilfGlGGtavevlkdvavalpplnstlareliertkaskllkgvrgekkadlaaleellvrlsqLvvd.lpeI 198
                  +++m++ +g+Elivg+++Dp+FGpvi++GlGG+ +ev+kdva+++ p+++++a+++++++k s llkg+rg++++d++ ++++lv++ +L v+ + +I
   EPA05076.1 107 LEKMVP-KGVELIVGIQNDPQFGPVIMVGLGGIMTEVMKDVAFRMLPISTSDAKSMLNELKGSALLKGFRGSDPIDTNMVAQMLVQIGKLGVEnADYI 203
                  ******.9**********************************************************************************7763788* PP

  ATP-grasp_5 199 reldinPllveeegvvalDarirl 222
                  +++d nP++v+++  +++Da+i l
   EPA05076.1 204 NSIDFNPVVVYPKSHFVVDAKIIL 227
                  *********************975 PP

>> Succ_CoA_lig  Succinyl-CoA ligase like flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.4   0.2   8.3e-52   2.5e-48       2     138 .]     400     536 ..     399     536 .. 0.97

  Alignments for each domain:
  == domain 1  score: 163.4 bits;  conditional E-value: 8.3e-52
  Succ_CoA_lig   2 GkialisqSGalalalldwaasrglgfskvvslGneadvdvadlleylaedpetkvillylEsirdgrkflsaarraark..kpvvvlksGrseaga 96 
                   G++a++sqSG++++++l++a    +g+sk++s+Gn++dvd+ad++ y a+dp+tkvi+ly+E+++dgrkf+++a+r+ ++  kp+v++ksGr++aga
    EPA05076.1 400 GNVAFFSQSGTMGISMLESADV--FGLSKMISFGNRSDVDEADMIWYAANDPQTKVIGLYVEGFGDGRKFINTAKRVMKEqkKPIVIWKSGRTAAGA 494
                   99******************98..6****************************************************97667*************** PP

  Succ_CoA_lig  97 raaashtgalagsdavvdaafrqaGvlrvdsleelfdaaell 138
                   ++aashtg+l gs+a++  af+qaG++ vds +el+ ++++l
    EPA05076.1 495 KQAASHTGSLGGSNAIIMGAFKQAGIISVDSYQELVGVLKAL 536
                   *************************************99986 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       3.3     1e+04      80     107 ..      30      57 ..      16      60 .. 0.66
   2 !   82.9   0.0   7.7e-27   2.3e-23       2     113 ..     254     377 ..     253     380 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.3
                    -SEEEE-TT---HHHHHHHHHTT-EEE. CS
  CoA_binding_2  80 akavwlqpgsedeeaaelaeeagirvvg 107
                    +k+  + + +  eeaa++a++ g ++v+
     EPA05076.1  30 VKVPPFALVTSAEEAAKQAKKIGFPLVM 57 
                    5555555556778888888887777665 PP

  == domain 2  score: 82.9 bits;  conditional E-value: 7.7e-27
                    -EEEET--S-TTSHHHHHHHHHHH...HT--EEEESSS-SEETTEES----T....T--EEEE-S-HHHHGGGHHHHHHH--SEEEE-TT...... CS
  CoA_binding_2   2 tiaVvGasdnpgkfgykvlrylle...hglpvvpVnpkeeeilgekvyaslaedpepvdlvdvftppeatpeivkealalgakavwlqpg...... 88 
                    ++a+vGas++pgk g+ vl  l +   +g +v+p+npk+e+ilg k+y++l++  e+vdlv+v++  +++ +i++ ++++g+  v++ +g      
     EPA05076.1 254 SVALVGASSTPGKIGNSVLIALGKqdyKG-KVFPINPKQESILGIKCYPTLDAINEKVDLVVVCIDLAECGPIMETCAKKGIHNVVIVSGggkelg 348
                    79********************9978777.9*********************856***************************************** PP

                    ....---HHHHHHHHHTT-EEE.ES-HHH CS
  CoA_binding_2  89 ....sedeeaaelaeeagirvvgdrCilv 113
                        + ++++ el  +++irvvg++Ci++
     EPA05076.1 349 gdraTMEAKVKELSLKHKIRVVGPNCIGM 377
                    9999999999999999***********97 PP

>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.8   3.7e-11   1.1e-07       4     122 ..      18     131 ..      15     150 .. 0.83

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 3.7e-11
                  HHHHHHHHHCTT----SEEEESSHHHHHHHHHHHTSSSE..EEEE--SSSTCCCTTCEEE.ESSHHHHHHHHHCCTTSEEE-TTS-TT-EEE--EEEE CS
  ATP-grasp_2   4 Eyqakeilakygvkvpegevaesaeeaeeaakklgekel..vvKaQvlaGGRGKagGvkl.vkskeeakeaakellgkelvtkqtgkeGkkvekvlve 98 
                  E  +k il+ ygvkvp +++++saeea+++akk+g   +  vv  Q+l   +   gGvk+  ++++++k++ k++ g   +     k+G +v+ +l+e
   EPA05076.1  18 EELSKTILKTYGVKVPPFALVTSAEEAAKQAKKIGFPLVmkVVSPQILH--KTDVGGVKVgLDNVNDVKKTFKDMYGRLSK-----KKGVEVKGILLE 108
                  6679*******************************87532278889996..5677****9457899**********97555.....99********** PP

                  E---ECEEEEEEEEEETTTTEEEE CS
  ATP-grasp_2  99 ealdikkElYlsivlDraskkvvv 122
                  ++++   El ++i  D +   +v+
   EPA05076.1 109 KMVPKGVELIVGIQNDPQFG-PVI 131
                  ***99999999998776543.444 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.6   4.8e+03       5      26 ..     129     151 ..     127     158 .. 0.77
   2 !   30.2   0.2   1.8e-10   5.3e-07       4      94 ..     253     341 ..     250     343 .. 0.96
   3 ?   -3.8   0.0         6   1.8e+04      78      92 ..     470     484 ..     468     487 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.6
                  EEEEETTTSHHHHHH.HHHHHHH CS
  CoA_binding   5 kviviGagglgiagl.yhfkekl 26 
                   vi +G gg  ++++  + +++l
   EPA05076.1 129 PVIMVGLGGIMTEVMkDVAFRML 151
                  5999******9999966666666 PP

  == domain 2  score: 30.2 bits;  conditional E-value: 1.8e-10
                  EEEEEETTTSHHHHHH.HHHHHHHHECEE.EEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHHHHHHHHHTT-SEEEEES CS
  CoA_binding   4 tkviviGagglgiagl.yhfkeklkygik.avfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesaqeavdelveagikgiviit 94 
                   +v+++Ga+ + ++++ ++ +   k   k +vf++np+   + +lg+++y+++d + ek  vd  v+++  +++  +++ ++++gi  +vi++
   EPA05076.1 253 ESVALVGASSTPGKIGnSVLIALGKQDYKgKVFPINPK--QESILGIKCYPTLDAINEK--VDLVVVCIDLAECGPIMETCAKKGIHNVVIVS 341
                  68************************************..9******************..*****************************987 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 6
                  HHHHHHHTT-SEEEE CS
  CoA_binding  78 avdelveagikgivi 92 
                  +++++++++ k+ivi
   EPA05076.1 470 TAKRVMKEQKKPIVI 484
                  6788999999*9998 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.1e-05     0.034       2      35 ..      26      59 ..      25     119 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.1e-05
                HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEE CS
   ATP-grasp  2 eklglpvprflaveskeeleeaaeelglpvvvKa 35
                ++ g++vp+f++v+s+ee+ + a+++g+p+v+K 
  EPA05076.1 26 KTYGVKVPPFALVTSAEEAAKQAKKIGFPLVMKV 59
                6789****************************94 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (702 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.50
# Mc/sec: 4236.32
//
Query:       EPA05077.1  [L=267]
Description: acetylglutamate kinase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.6e-38  132.7   3.3    1.8e-38  132.5   3.3    1.0  1  AA_kinase  Amino acid kinase family
  ------ inclusion threshold ------
      0.094   13.0   2.0       0.28   11.5   0.7    2.2  2  DUF5603    Domain of unknown function (DUF5603)
       0.11   12.5   0.1       0.18   11.8   0.1    1.4  1  DUF4947    Domain of unknown function (DUF4947)


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.5   3.3   3.1e-42   1.8e-38       5     241 .]       4     245 ..       1     245 [. 0.94

  Alignments for each domain:
  == domain 1  score: 132.5 bits;  conditional E-value: 3.1e-42
                 EEE-TTCCCCTCCHHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC........E..HHHHHHHHHHHHHHHHHHHHHHHHHTTHG CS
   AA_kinase   5 vKlGGssltdkeeaslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaa....glrstleeagevatrdalaslgerlvaallaaglp 99 
                 +K+GGs++++       + +++i++   + + l++VhGgg+ + +  ++  g ++++ ++    + r+t++e++e+ t++  + +++++v++l+++g++
  EPA05077.1   4 IKIGGSVVDNLHP----STLADIKKV-AETEGLIIVHGGGKEVTKVCEQ-LGKEPKFVTSpsgiKSRYTDKETAEIFTMVISGRINKSIVQMLQKNGIN 96 
                 9********9988....999999999.88899*****************.99999999999999*********************************** PP

                 EEEE-GGGTCEECCCE..................HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEETTTEEEEE-HHHHHHHHHHHCTSSEEEEEESS CS
   AA_kinase 100 avglsaaaldateagr................degsdgnvesvdaeaieelleagvvpvltgfigldeegelgrgssDtiaallAealgAdkliiltdV 182
                 a+gl++ +  +++a+r                d g++g++++v+++ i+ ll++g  pv+++++ ++ee +++++++D++aa++A  +g+dk++++t+V
  EPA05077.1  97 AIGLTGVDAKIIQAERkktlliinekgrkqaiDGGYTGKITKVNSDLIKLLLKQGLTPVISPIA-ISEESDFLNVDGDRAAAYVAGSVGCDKVLFITNV 194
                 **************************************************************76.******99************************** PP

                 SSCESSTTTTCCTTCECCEEEHHHCHHCSSS.TTTHHHHCHHHHHHHHHCTT-EEEEEE CS
   AA_kinase 183 dGVydadpkkvpdarllpeisvdeaeesaselatgGmkvkhpaalaaarrggipvvItn 241
                 dG++ +d       +l+++++  ea+e     +  Gm+ k++a  +a+  g+ ++ I+n
  EPA05077.1 195 DGLLMDD-------KLVTKLTLAEAKE-IRPKIGPGMEKKILASTEALDMGVKEALIAN 245
                 ****998.......5556666666665.5559999*****************9999987 PP

>> DUF5603  Domain of unknown function (DUF5603)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.032   1.9e+02       9      53 ..      40      85 ..      33      86 .. 0.83
   2 ?   11.5   0.7   4.6e-05      0.28       5      62 ..      77     134 ..      73     155 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.032
                -HHHHHHHHHHTT---EE-TTHHHH...HHCTSS.SEEEES..SSE CS
     DUF5603  9 dlnklleelkkeglrveedkekeeklkdeelgki.afvlvgkneks 53
                ++ k+ e+l ke   v    + + +  d+e  +i ++v+ g+ +ks
  EPA05077.1 40 EVTKVCEQLGKEPKFVTSPSGIKSRYTDKETAEIfTMVISGRINKS 85
                5789999*****9999999999999999999997256666777765 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 4.6e-05
                 EEES-HHH.HHHHHHHTT---EE-TTHHHH...HHCTSSSEEEES..SSEEEE--SHHH CS
     DUF5603   5 aikgdlnk.lleelkkeglrveedkekeeklkdeelgkiafvlvgkneksykiygslee 62 
                  i g +nk +++ l+k+g++ +   + + k+ ++e+ k  + ++ ++ +  +i g+   
  EPA05077.1  77 VISGRINKsIVQMLQKNGINAIGLTGVDAKIIQAERKKTLL-IINEKGRKQAIDGGYTG 134
                 57899998578999**********************88765.55556667788888653 PP

>> DUF4947  Domain of unknown function (DUF4947)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1     3e-05      0.18      68     109 ..      42      83 ..      33     124 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3e-05
     DUF4947  68 ekvkeiLGePekvvtdsseiqesleekelenikalfekGklt 109
                  kv e LG+  k vt +s i++++ +ke   i  ++ +G++ 
  EPA05077.1  42 TKVCEQLGKEPKFVTSPSGIKSRYTDKETAEIFTMVISGRIN 83 
                 689999**************************9999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.52
# Mc/sec: 1531.63
//
Query:       EPA05078.1  [L=55]
Description: putative lysine biosynthesis protein LysW [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0002   21.2   0.6       0.14   12.1   0.1    2.1  2  zinc_ribbon_4    zinc-ribbon domain
     0.0017   18.0   0.6       0.11   12.3   0.1    2.2  2  zinc_ribbon_5    zinc-ribbon domain
      0.003   17.4   0.2     0.0046   16.8   0.2    1.3  1  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
     0.0034   16.9   0.7     0.0052   16.3   0.5    1.4  2  TF_Zn_Ribbon     TFIIB zinc-binding
  ------ inclusion threshold ------
      0.038   13.6   1.6        2.8    7.6   0.1    2.3  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
      0.047   13.7   0.5      0.073   13.1   0.5    1.3  1  zinc-ribbons_6   zinc-ribbons
      0.066   12.9   4.0          1    9.1   0.4    2.5  2  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
      0.068   13.2   0.6      0.076   13.0   0.6    1.1  1  HypA             Hydrogenase/urease nickel incorporation, met
      0.079   13.1   2.7        0.8    9.9   0.1    2.0  2  Zn-ribbon_8      Zinc ribbon domain
       0.12   12.2   1.4       0.51   10.1   0.0    2.0  2  zf-HYPF          HypF finger
       0.13   12.7   1.4       0.47   10.9   1.4    1.9  1  Lar_restr_allev  Restriction alleviation protein Lar
       0.18   12.0   2.4        1.9    8.7   0.1    2.1  2  SR1P             SR1 protein


Domain annotation for each model (and alignments):
>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.1    0.0017       2.5       4      17 ..       2      15 ..       1      20 [. 0.88
   2 !   12.1   0.1   9.6e-05      0.14       2      16 ..      21      35 ..      21      41 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0017
  zinc_ribbon_4  4 tCpsCkakyeidde 17
                    C++C a+ +i+d+
     EPA05078.1  2 KCQECDATLNIPDD 15
                   5***********97 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 9.6e-05
  zinc_ribbon_4  2 kitCpsCkakyeidd 16
                   +i+C  C+a +ei+ 
     EPA05078.1 21 IISCSDCGADFEIAK 35
                   69***********86 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1     0.019        29       4      17 ..       2      15 ..       1      19 [. 0.82
   2 !   12.3   0.1   7.1e-05      0.11       2      16 ..      21      35 ..      21      44 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.019
  zinc_ribbon_5  4 rCpdCdtkFklvds 17
                   +C +Cd +  + d+
     EPA05078.1  2 KCQECDATLNIPDD 15
                   7*****99877766 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 7.1e-05
  zinc_ribbon_5  2 iirCpdCdtkFklvd 16
                   ii+C dC+  F ++ 
     EPA05078.1 21 IISCSDCGADFEIAK 35
                   8**********9875 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.2   3.1e-06    0.0046       4      33 ..       3      33 ..       3      36 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.1e-06
                    ESTTTSBEEEEECSCCCE.EEESSSS-EEES CS
  RNA_POL_M_15KD  4 CpkCgNlLlpkedkegkn.feCrqCgYeepa 33
                    C++C   L +++d ++     C+ Cg+ +++
      EPA05078.1  3 CQECDATLNIPDDASVGEiISCSDCGADFEI 33
                    ********98888888778**********98 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.5   3.5e-06    0.0052       1      27 [.       1      29 [.       1      34 [. 0.95
   2 ?   -2.7   0.0         3   4.6e+03      33      40 ..      39      46 ..      36      48 .. 0.62

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.5e-06
                  EEETTTTCEE.CHEETSTTCE.EESSSSB CS
  TF_Zn_Ribbon  1 ykCPnCgstn.lveDpergel.vCtdCGl 27
                  +kC +C  t  +  D++ ge+  C+dCG+
    EPA05078.1  1 MKCQECDATLnIPDDASVGEIiSCSDCGA 29
                  89*******99*****************6 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3
                  CCCCCCHH CS
  TF_Zn_Ribbon 33 sidegpew 40
                  si+e +++
    EPA05078.1 39 SIVELKQA 46
                  66776665 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1    0.0083        12       4      15 ..       2      13 ..       1      17 [. 0.81
   2 ?    7.6   0.1    0.0019       2.8       3      16 ..      22      35 ..      20      37 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0083
      zf_UBZ  4 lCerCgkeipes 15
                 C++C++++ ++
  EPA05078.1  2 KCQECDATLNIP 13
                6*****998766 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0019
      zf_UBZ  3 ylCerCgkeipese 16
                + C++Cg+ +++++
  EPA05078.1 22 ISCSDCGADFEIAK 35
                57******998876 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.5   4.9e-05     0.073       2      28 ..       2      33 ..       1      41 [. 0.60

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.9e-05
                    --SSS-S--E.E-S....SEEE-TTT--EEEE CS
  zinc-ribbons_6  2 kCpeCqqele.krg....eqyhCeaCqedlkk 28
                    kC+eC++ l+  ++    e ++C+ C +d++ 
      EPA05078.1  2 KCQECDATLNiPDDasvgEIISCSDCGADFEI 33
                    57777777664333566666677777766654 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   3.8    0.0011       1.6       2      24 ..       2      28 ..       1      30 [. 0.78
   2 ?    9.1   0.4   0.00069         1       3      15 ..      24      36 ..      22      49 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0011
                    B-SSS--B---....-SSS----SSS- CS
  DNA_RNApol_7kD  2 iCgeCgaevsl....kkgdpiRCkeCG 24
                    +C eC+a   +    + g++i C +CG
      EPA05078.1  2 KCQECDATLNIpddaSVGEIISCSDCG 28
                    69999999998333345899******9 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00069
                    -SSS--B----SS CS
  DNA_RNApol_7kD  3 CgeCgaevslkkg 15
                    C +Cga++++ k+
      EPA05078.1 24 CSDCGADFEIAKK 36
                    *********9776 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.6   5.1e-05     0.076      71     108 ..       1      44 [.       1      48 [. 0.66

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.1e-05
                 EEETTTS-EEECHHH.HH....S-TTTSSS.-EEEEESSSEEEE CS
        HypA  71 vrCreCgkefeleek.al....rCpkCgsa.dveivsGeellvk 108
                 ++C+eC+++ ++ ++ ++    +C +Cg+  ++  ++G+ +++k
  EPA05078.1   1 MKCQECDATLNIPDDaSVgeiiSCSDCGADfEIAKKNGSIVELK 44 
                 58********976642225667*****99534444455555555 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   3.3   0.00093       1.4       7      36 ..       2      31 ..       1      32 [. 0.79
   2 ?    9.9   0.1   0.00053       0.8       8      19 ..      24      35 ..      22      46 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00093
  Zn-ribbon_8  7 rCeeCghefevlqsisdapltaCPeCgsev 36
                 +C+eC+ + ++   +s  + + C +Cg++ 
   EPA05078.1  2 KCQECDATLNIPDDASVGEIISCSDCGADF 31
                 8*****9999777777666677****9865 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00053
  Zn-ribbon_8  8 CeeCghefevlq 19
                 C +Cg +fe+  
   EPA05078.1 24 CSDCGADFEIAK 35
                 *********755 PP

>> zf-HYPF  HypF finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.4      0.21   3.2e+02       2      10 ..       3      11 ..       2      16 .. 0.70
   2 ?   10.1   0.0   0.00034      0.51      21      33 ..      21      33 ..      19      34 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.21
                -HHHHHHHC CS
     zf-HYPF  2 CedClrEyk 10
                C++C + ++
  EPA05078.1  3 CQECDATLN 11
                889976555 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00034
                T---TTTS--EEE CS
     zf-HYPF 21 fisCtnCGPrlsl 33
                 isC +CG  + +
  EPA05078.1 21 IISCSDCGADFEI 33
                69******98876 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   1.4   0.00032      0.47      19      45 ..      16      35 ..       1      52 [. 0.65

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00032
  Lar_restr_allev 19 qrvvaeigqcvyCadCgastpwfkiae 45
                      +    +g+ ++C dCga   +f+ia+
       EPA05078.1 16 AS----VGEIISCSDCGA---DFEIAK 35
                     33....3449********...555544 PP

>> SR1P  SR1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.1    0.0013       1.9       6      20 ..       3      17 ..       2      21 .. 0.79
   2 ?    3.5   0.3     0.051        76       3      11 ..      21      29 ..      18      33 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0013
        SR1P  6 CqtCnatIdhfedek 20
                Cq+C+at +  +d +
  EPA05078.1  3 CQECDATLNIPDDAS 17
                *******98766655 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.051
        SR1P  3 tIvCqtCna 11
                +I C++C+a
  EPA05078.1 21 IISCSDCGA 29
                577****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 344.13
//
Query:       EPA05079.1  [L=253]
Description: ABC transporter, ATP-binding protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.1e-31  108.7   0.0    5.2e-31  108.0   0.0    1.3  1  ABC_tran      ABC transporter
    1.3e-08   35.1   0.0     0.0043   16.9   0.0    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    0.00089   19.2   0.1     0.0019   18.1   0.0    1.6  2  RsgA_GTPase   RsgA GTPase
     0.0014   19.1   0.3      0.014   15.8   0.3    2.2  1  AAA           ATPase family associated with various cellular 
     0.0045   16.7   0.0        0.1   12.3   0.0    2.2  2  AAA_15        AAA ATPase domain
     0.0056   16.6   0.0       0.01   15.8   0.0    1.4  1  Rad17         Rad17 P-loop domain
     0.0061   16.3   0.0      0.012   15.4   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.012   15.0   0.2        1.8    7.9   0.0    2.2  2  SMC_N         RecF/RecN/SMC N terminal domain
       0.02   15.3   0.0      0.032   14.6   0.0    1.4  1  AAA_16        AAA ATPase domain
       0.02   15.2   0.1      0.055   13.7   0.0    1.7  2  AAA_22        AAA domain
      0.021   14.9   0.0      0.039   14.0   0.0    1.7  1  MMR_HSR1      50S ribosome-binding GTPase
      0.025   14.6   0.0      0.066   13.2   0.0    1.7  1  AAA_5         AAA domain (dynein-related subfamily)
      0.028   14.1   0.0        0.4   10.4   0.0    2.1  2  AAA_30        AAA domain
      0.029   14.9   0.0      0.056   13.9   0.0    1.5  1  AAA_23        AAA domain
      0.031   14.0   0.1       0.17   11.6   0.0    2.0  2  IstB_IS21     IstB-like ATP binding protein
      0.038   13.5   0.0      0.079   12.5   0.0    1.5  1  AAA_25        AAA domain
       0.05   14.0   0.0       0.19   12.1   0.0    2.0  2  RNA_helicase  RNA helicase
      0.052   13.7   0.0       0.11   12.7   0.0    1.5  1  AAA_33        AAA domain
      0.061   13.2   0.0       0.12   12.3   0.0    1.5  1  NACHT         NACHT domain
       0.15   12.6   0.0       0.25   11.9   0.0    1.4  1  AAA_18        AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.0   0.0   5.8e-34   5.2e-31       3     137 .]      25     163 ..      23     163 .. 0.86

  Alignments for each domain:
  == domain 1  score: 108.0 bits;  conditional E-value: 5.8e-34
                 EEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH..........HHHTCHHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxxx RF
    ABC_tran   3 nvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren..........esdeeiekalsk 91 
                  v+l+++ ge v +vG++G+GKSt+l+++agl++p+eGeil+dgk++++     +  e  +++qe  lfp l+v++n           ++e+++   + 
  EPA05079.1  25 GVNLEIEDGEFVCLVGPSGCGKSTFLRIVAGLETPEEGEILFDGKPVTT-----TGPERIIVFQEGALFPWLKVQDNvefglkmagiPKEERVQISKRY 118
                 79*********************************************99.....777778999***********************9444444444444 PP

                 STTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  92 lglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                 l++ +  ++ ++s +++LS G+kqrva+aral+ +p++ll+DEp+a
  EPA05079.1 119 LDMMQ-LTKFADSYTYQLSTGMKQRVAIARALVMDPDVLLMDEPFA 163
                 44444.444555666*****************************85 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   4.8e-06    0.0043       1      53 [.      35      75 ..      35     102 .. 0.72
   2 !   16.4   0.0   6.7e-06     0.006     235     298 ..     133     194 ..      89     197 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.8e-06
      AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlyd 53
                + +l+Gp g+GKS++L++  +l            e +  g+i  + +  +++ 
  EPA05079.1 35 FVCLVGPSGCGKSTFLRIVAGL------------ETPEEGEILFDGKPVTTTG 75
                679****************999............4444444444444444444 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 6.7e-06
      AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkllrrll...ellkelsrngaQviltTHS 298
                 ++lS G+k+  a++ al  ++   ++ll DEp + L+ +    ll   +l+ e+++    ++++TH+
  EPA05079.1 133 YQLSTGMKQRVAIARALVMDP---DVLLMDEPFAALDAQTRDLLLvemQLIWEKTK--KTILFVTHN 194
                 799*******9**99***999...9*************999999988888855555..6*******8 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   2.2e-06    0.0019      84     149 ..      17      82 ..       2      88 .. 0.69
   2 ?   -2.7   0.1       5.4   4.8e+03      34      63 ..     183     212 ..     172     233 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.2e-06
                  TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S--------------SEEEEEE CS
  RsgA_GTPase  84 aktkegleelkellkd.ktsvlvGqSGvGKStLinallpelelktgevseklgrGkhTTtavellel 149
                  +++ ++l  ++ +++d ++++lvG+SG GKSt++  +++ ++ + ge+   +g+   TT   +++ +
   EPA05079.1  17 SHRLKALGGVNLEIEDgEFVCLVGPSGCGKSTFLRIVAGLETPEEGEILF-DGKPVTTTGPERIIVF 82 
                  4555556666667777799****************999987777777755.3444445555555555 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.4
                  HHHHHHHHHHHTT-EEEEEEE-GGG--HHH CS
  RsgA_GTPase  34 lldrfLvlaeekgiepvivlnKiDlleeee 63 
                    ++ ++++ ++ +e +++ +Ki + +++ 
   EPA05079.1 183 KTKKTILFVTHNVAEATVLGTKIAIFSNRP 212
                  556667777777777777777777666655 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.3   1.6e-05     0.014       1      66 [.      36     160 ..      36     217 .. 0.55

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.6e-05
                 EEEESSTTSSHHHHHHHHHHH.........HTHE...........................................EEEEETTTCSSS.......... CS
         AAA   1 vllyGppGtGKTllakavake.........lgve...........................................fleisgsellsk.......... 37 
                 v+l+Gp G+GK+++ + va           +  +                                                                 
  EPA05079.1  36 VCLVGPSGCGKSTFLRIVAGLetpeegeilF--DgkpvtttgperiivfqegalfpwlkvqdnvefglkmagipkeeR----------Vqiskryldmm 122
                 79*****************874333333331..022222333333333333333333333333333333333333330..........03333333333 PP

                 ..........STTHHHHHHHHHHHHHHHTSTSEEEEEET CS
         AAA  38 ..........yvgesekkirelfkeakekakpsilfiDE 66 
                           y+  + +k r  +++a  + +p +l++DE
  EPA05079.1 123 qltkfadsytYQLSTGMKQRVAIARALVM-DPDVLLMDE 160
                 33334444334444444444444444444.377777777 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   0.00011       0.1      18      42 ..      27      52 ..      20      61 .. 0.82
   2 ?    2.3   0.0      0.12   1.1e+02     291     365 ..     129     194 ..      91     196 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
      AAA_15 18 eidlsee.ltvliGkNnsGKSsilea 42
                 +++++  + +l+G+ ++GKS++l++
  EPA05079.1 27 NLEIEDGeFVCLVGPSGCGKSTFLRI 52
                45555556***************986 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.12
      AAA_15 291 elplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                 +++ ++ ++G+++ + ++  ++  ++        ++ll++EP a L  q    l   ++ + +++k+ +++ TH+
  EPA05079.1 129 DSYTYQLSTGMKQRVAIA--RALVMDP-------DVLLMDEPFAALDAQTRDLLLVEMQLIWEKTKKTILFVTHN 194
                 566677777777776654..4444444.......89******************************999999997 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.1e-05      0.01      39      67 ..      27      55 ..      14      65 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.1e-05
       Rad17 39 vLesrkkriLLisGPsGCgkstvvkvLsk 67
                 Le +  + + + GPsGCgkst +++++ 
  EPA05079.1 27 NLEIEDGEFVCLVGPSGCGKSTFLRIVAG 55
                5666777788899************9875 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.3e-05     0.012      15      39 ..      26      50 ..      21      65 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.3e-05
      AAA_29 15 htieidlkgatlltGpsGsGKSTll 39
                  +ei+  +++ l+GpsG GKST+l
  EPA05079.1 26 VNLEIEDGEFVCLVGPSGCGKSTFL 50
                56778755599************98 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0     0.002       1.8      24      41 ..      33      50 ..      18      54 .. 0.80
   2 ?    5.2   0.1     0.014        12     136     195 ..     134     192 ..      92     215 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.002
                SSEEEEEESTTSSHHHHH CS
                xxxxxxxxxxxxxxxxxx RF
       SMC_N 24 ksftaivGpNGSGKsnll 41
                 +f ++vGp G+GKs +l
  EPA05079.1 33 GEFVCLVGPSGCGKSTFL 50
                4699***********986 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.014
                 CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHH...HHHHHHHCTTSEEEEE CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxx RF
       SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkv...aellkeksknaQfivi 195
                 +LS G k+ va+a  +    ++p  + l+De  aaLD++ +  +    +l+ ek+k++ ++v+
  EPA05079.1 134 QLSTGMKQRVAIARAL---VMDPD-VLLMDEPFAALDAQTRDLLlveMQLIWEKTKKTILFVT 192
                 7888888777776543...23454.568************99883333667788877655554 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   3.6e-05     0.032      23      45 ..      32      54 ..      18     106 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.6e-05
      AAA_16 23 rpelvllsGesGvGKsslvrell 45
                ++e v l+G+sG+GKs+ +r ++
  EPA05079.1 32 DGEFVCLVGPSGCGKSTFLRIVA 54
                45899*************99776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   6.1e-05     0.055       4      26 ..      32      54 ..      29      82 .. 0.86
   2 ?   -1.9   0.0       4.1   3.7e+03      92      99 ..     153     160 ..     113     197 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.1e-05
      AAA_22  4 tagilvvtGesGtGKTtllrrll 26
                +  +++++G+sG+GK+t lr ++
  EPA05079.1 32 DGEFVCLVGPSGCGKSTFLRIVA 54
                56799************999765 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.1
      AAA_22  92 ielliiDE 99 
                 + +l+ DE
  EPA05079.1 153 PDVLLMDE 160
                 34444444 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   4.3e-05     0.039       2      42 ..      36      82 ..      35     193 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.3e-05
                EEEEESTTSSHHHHHHHHHT.....S.TEEESSSTTSSSSEEEEEEE CS
    MMR_HSR1  2 vaivGrpNvGKStLinaltg.....e.kaivsdkpgtTrdinegrvk 42
                v++vG +  GKSt+++   g     e +     kp tT+ ++++ v 
  EPA05079.1 36 VCLVGPSGCGKSTFLRIVAGletpeEgEILFDGKPVTTTGPERIIVF 82
                89****************98766643467779999999999888765 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   7.4e-05     0.066       2      20 ..      36      54 ..      35      64 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.4e-05
                EEEE--SSSSHHHHHHHGG CS
       AAA_5  2 vlLvGppGtgKselaerla 20
                v+LvGp+G+gKs++ + +a
  EPA05079.1 36 VCLVGPSGCGKSTFLRIVA 54
                8************998876 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00044       0.4      19      45 ..      34      60 ..      27      77 .. 0.82
   2 ?    1.3   0.0      0.27   2.4e+02      37      68 ..     176     207 ..     172     235 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00044
      AAA_30 19 rvavltGpAGtGKttalkalreaweaa 45
                 +++l+Gp G GK+t l+ ++ + + +
  EPA05079.1 34 EFVCLVGPSGCGKSTFLRIVAGLETPE 60
                4899**************998876665 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.27
      AAA_30  37 alreaweaaggrviglAptgkaAkvLaeelgi 68 
                 +++ +we+ +++++ ++++ + A vL++++ i
  EPA05079.1 176 EMQLIWEKTKKTILFVTHNVAEATVLGTKIAI 207
                 56779**********************99987 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   6.3e-05     0.056      11      37 ..      24      51 ..       3      55 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.3e-05
      AAA_23 11 rdqeidF.skgltlItGpNGaGKTTild 37
                ++++++  +  +++++Gp G+GK+T+l+
  EPA05079.1 24 GGVNLEIeDGEFVCLVGPSGCGKSTFLR 51
                5666666444689*************97 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00019      0.17      31      66 ..      16      53 ..       3      66 .. 0.73
   2 ?   -0.0   0.1      0.71   6.3e+02     103     149 ..     147     195 ..     116     200 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00019
   IstB_IS21 31 dkrkvkeLatlsf.iekkenivllGpsGvGKs.hlaia 66
                d +++k+L + +  ie+ e ++l+GpsG GKs +l i 
  EPA05079.1 16 DSHRLKALGGVNLeIEDGEFVCLVGPSGCGKStFLRIV 53
                555666665555448999*************7245555 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.71
   IstB_IS21 103 lkrllkvdllilDdlgllpldqaeaellf...eviekryerrsiiitsnl 149
                  + ++ +d+l++D+  +  ld + + ll+   ++i ++ +++ + +t n+
  EPA05079.1 147 RALVMDPDVLLMDEP-FAALDAQTRDLLLvemQLIWEKTKKTILFVTHNV 195
                 334556788888884.6778888887775333667777777767777665 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   8.8e-05     0.079      31      51 ..      31      51 ..      23      90 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.8e-05
      AAA_25 31 pagelallaGapgtGKttlal 51
                  ge++ l+G++g+GK+t++ 
  EPA05079.1 31 EDGEFVCLVGPSGCGKSTFLR 51
                6799**************985 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00021      0.19       1      17 [.      36      52 ..      36      72 .. 0.84
   2 ?   -1.7   0.0       4.3   3.9e+03      69      70 ..     120     121 ..      91     139 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00021
  RNA_helicase  1 iwlyGpsgeGKStlake 17
                  ++l+Gpsg+GKSt+ + 
    EPA05079.1 36 VCLVGPSGCGKSTFLRI 52
                  689***********987 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 4.3
  RNA_helicase  69 dl 70 
                   d+
    EPA05079.1 120 DM 121
                   33 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00012      0.11       2      20 ..      36      54 ..      35      65 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00012
      AAA_33  2 vllvGlpGsGKstlaerll 20
                v lvG++G+GKst+++ ++
  EPA05079.1 36 VCLVGPSGCGKSTFLRIVA 54
                679***********98665 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00013      0.12       3      21 ..      36      54 ..      34      61 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                EEEEC-TTTCHHHHHHHHH CS
       NACHT  3 vilqGeaGsGKTtLlqkla 21
                v+l G++G+GK+t+l+ +a
  EPA05079.1 36 VCLVGPSGCGKSTFLRIVA 54
                89*************8655 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00028      0.25       1      21 [.      36      56 ..      36      97 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00028
      AAA_18  1 IlltGtpGvGKttlakeLskr 21
                ++l G++G+GK+t+ + ++ +
  EPA05079.1 36 VCLVGPSGCGKSTFLRIVAGL 56
                79************9988655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.53
# Mc/sec: 1441.34
//
Query:       EPA05080.1  [L=54]
Description: hypothetical protein BG20_I2639 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0015   18.1   2.6     0.0035   17.0   2.6    1.6  1  zf-RRN7   Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn


Domain annotation for each model (and alignments):
>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   2.6   1.9e-07    0.0035      10      29 ..       5      26 ..       5      26 .. 0.95

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.9e-07
     zf-RRN7 10 Cgcrsftl.ddGfyy.CrrCht 29
                Cgc +++  ddGf++ C+ C++
  EPA05080.1  5 CGCETWQKnDDGFRVaCVKCGH 26
                ***************9999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 343.79
//
Query:       EPA05081.1  [L=91]
Description: iron dependent repressor, metal binding and dimerization domain protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-18   66.8   0.2    1.6e-18   66.6   0.2    1.1  1  Fe_dep_repr_C  Iron dependent repressor, metal binding and di


Domain annotation for each model (and alignments):
>> Fe_dep_repr_C  Iron dependent repressor, metal binding and dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.6   0.2   8.7e-23   1.6e-18       1      69 [.      17      83 ..      17      84 .. 0.97

  Alignments for each domain:
  == domain 1  score: 66.6 bits;  conditional E-value: 8.7e-23
                   -HHHHHHHHHHHHHHHHHHHHHHHHCT--CCCHHHHCCCCGGGS-HHHHHHHHHHCT-.SB-TTS-B-- CS
  Fe_dep_repr_C  1 TekGrelAkrlvrrhrllerfLvdvlgvdweeaheeAerlEhalseelierldellgfpeecPhgdpip 69
                   T++G++++ +++r+ rlle+++   l+v  +e  e ++ +Eh++++++ ++l+++l++p++cPh ++ip
     EPA05081.1 17 TQDGERIGSSMMRNSRLLEVLMDSALKVAIDE--EMVCGIEHHMNKQFTDALCTMLKHPRKCPHDHEIP 83
                   99*************************98888..**********************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 563.22
//
Query:       EPA05082.1  [L=41]
Description: hypothetical protein BG20_I2638, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      7e-08   32.6   0.0    7.3e-08   32.6   0.0    1.0  1  UPF0047   Uncharacterised protein family UPF0047


Domain annotation for each model (and alignments):
>> UPF0047  Uncharacterised protein family UPF0047
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.0   4.1e-12   7.3e-08      78     115 .]       1      38 [.       1      38 [. 0.94

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 4.1e-12
                 -SEEEEEEETTEE---TTEEEEEEESS-SSEEEEEEEE CS
     UPF0047  78 gssltipvedgklalGtwqsiylveldgpreRkvvvqv 115
                 g+++++ +++gkl++G w++i++ e+dg+r ++v+v++
  EPA05082.1   1 GREVVVAITNGKLDFGPWEQILYGEFDGKRPKRVLVKI 38 
                 57899*****************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       128  (0.00713927); expected 358.6 (0.02)
Passed bias filter:                      120  (0.00669307); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.48
# Mc/sec: 254.92
//
Query:       EPA05083.1  [L=372]
Description: menaquinone biosynthesis protein, SCO4550 family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.6e-15   55.5   0.0    1.2e-14   55.0   0.0    1.2  1  Radical_SAM  Radical SAM superfamily
  ------ inclusion threshold ------
       0.17   11.9   0.0       0.58   10.2   0.0    1.8  2  DUF905       Bacterial protein of unknown function (DUF905)


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.0   0.0   1.3e-18   1.2e-14       3     164 ..      69     239 ..      67     242 .. 0.94

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 1.3e-18
                  EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT..SEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHG........ CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........ RF
  Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg..vkevilgggepllypdfvellerlaklavpgiritvetngtlpd........ 90 
                   t+ C  +C+fCa++++    + +++ls+++i+  vk + +e+     ++i+gg +p+l  +++e ++++++ + p++ ++  +    ++        
   EPA05083.1  69 YTNVCITDCKFCAFYRS-PGSDESYTLSLDQIETRVKTA-WEMFkiRQVLIQGGHNPNLKIEYYENAFKMIRQKFPNVGVHGLSTSEIDMiariekcs 164
                  6899************7.*********************.998886778889999*******************9999999999999977999***** PP

                  .HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHHH CS
                  .xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM  91 .eeklerllelg.vdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivglpGendeeleell 164
                   +e+l rl+e g       g+e++ d  v++ +  ++ +  ++++ ++ ++ +g++  + +++ ++ en  ++++++
   EPA05083.1 165 tKEVLSRLKESGlQSIPGAGAEILVDS-VKDVISpKKISSADWIRIMDEAHTLGLP-ASATMMYGHVENNNDIVDHF 239
                  ************99999*********9.****************************.9*************999875 PP

>> DUF905  Bacterial protein of unknown function (DUF905)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.39   3.5e+03      16      27 ..      65      76 ..      44      79 .. 0.61
   2 ?   10.2   0.0   6.5e-05      0.58      17      56 ..     223     265 ..     209     276 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.39
                HHHH-TTEEEES CS
      DUF905 16 vaaqyqnvaieD 27
                +  +y+nv i D
  EPA05083.1 65 IILNYTNVCITD 76
                566899999887 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 6.5e-05
                 HHH-TTEEEES-SSS--EEEEE...-SS--EEEEEESSSTTHH CS
      DUF905  17 aaqyqnvaieDDqGthlrLvvr...daeGemvWraWnfepdae 56 
                 +  y  v  ++D   h+  +v+   +++G m +  Wnfep+ +
  EPA05083.1 223 TMMYGHVENNNDIVDHFFKIVKlqeKTKGFMAFIPWNFEPNNT 265
                 5567777788888889988887333458************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 2259.52
//
Query:       EPA05084.1  [L=125]
Description: hypothetical protein BG20_I2157 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.05   12.2   0.2      0.056   12.1   0.2    1.1  1  DUF2748   Protein of unknown function (DUF2748)


Domain annotation for each model (and alignments):
>> DUF2748  Protein of unknown function (DUF2748)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   3.1e-06     0.056     371     408 ..      44      84 ..      35     109 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.1e-06
     DUF2748 371 qvvkwGa...dltkeimkdlykiyynevipalieayknltG 408
                 qv + G+   ++t +  +d yk+y +evipa+   y+ lt 
  EPA05084.1  44 QVNQKGKepsKITLKFCPDHYKVYTQEVIPAMPLKYRILTK 84 
                 4444454000566666789*****************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 865.98
//
Query:       EPA05085.1  [L=44]
Description: hypothetical protein BG20_I2158 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       125  (0.00697194); expected 358.6 (0.02)
Passed bias filter:                      112  (0.00624686); expected 358.6 (0.02)
Passed Vit filter:                         2  (0.000111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 301.11
//
Query:       EPA05086.1  [L=480]
Description: menaquinone biosynthesis decarboxylase, SCO4490 family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.9e-152  507.9   0.0   2.2e-152  507.7   0.0    1.0  1  UbiD      3-octaprenyl-4-hydroxybenzoate carboxy-lyase


Domain annotation for each model (and alignments):
>> UbiD  3-octaprenyl-4-hydroxybenzoate carboxy-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  507.7   0.0  1.2e-156  2.2e-152       2     406 .]      11     423 ..      10     423 .. 0.97

  Alignments for each domain:
  == domain 1  score: 507.7 bits;  conditional E-value: 1.2e-156
                 HHCCCTTSEEEEESEB-TBTHHHHHHHHHHHHT--EEEEEEBTTB.TT-EEEE-TTS-HCHHHHHHTS-GHHHHHHHHHHHHHS..-............ CS
        UbiD   2 ealekagelvrikeevdpelEiaeiarrvleeggpallFenvkgkgskfpvltnlfgtrervalalglssleeileklaellepkpp............ 88 
                 ++lek+gel+r+k+evd +lEiaei+rr++ ++gpa+lFenvk++  ++pvl+n+fg+ +r++++l+++++ ei++++ +++++ +p            
  EPA05086.1  11 SELEKNGELKRVKTEVDANLEIAEILRRTMYSNGPAILFENVKNY--SMPVLGNAFGSMKRLEIGLEMTDFTEIGQRIVDMTKMDMPsgflnkikklpe 107
                 68***************************99***********855..7***********************************999899********** PP

                 ......---EE--GCG-GGGSEEECCCCC--HHHS---BSSTTSSS-EEECEEEEEE-TTTT-EEEEEEEEEEEETTEEEE--TTTHCHHHHHHHHHHC CS
        UbiD  89 ......ippkvvesekapcqeevvlegddvdLskLPvltlwpgDgGpyitlglvitrdpetgkrnlgiyRmqvldknklglhwqihkggaehlrkakkk 181
                        +pk  +  ++p+  e+  + + ++ ++LP++++wp+D+G++itlglv+t++petg++nlg+yRmq+ld +++++hwq+hk+ga+h +  k++
  EPA05086.1 108 lskmaeSFPKLES--SGPVT-EI--TSSSASFDDLPIIKSWPDDAGRFITLGLVATKHPETGVKNLGVYRMQILDSTHAMMHWQKHKRGAHHGDISKER 201
                 ****999999885..59***.55..4789***********************************************************99988888888 PP

                 CT--EEEEEEES--HHHHHHCTS--TTT-TCHHHHHHHHTS--EEEE-SSSSSEEETT-SEEEEEEEECCEEEECTTTC-TTSCEEC--CCEEEEEEEE CS
        UbiD 182 ggeplpvavaiGvdPaltlaAvaplPeglsElefaGalrgepvelvkcetvdlevpadAEivleGeidpgetapEGPfgdhtGyysevrdefpvfkVta 280
                 g e++++a++iG++Pa++++++ap+Pegl++++faG+ r++ ++ vkc+t+dlevpa+AEivleG++dp++ ++EGPfgdhtGyy ++ +++p+f++t 
  EPA05086.1 202 G-EKIQAAIIIGCEPATVFSSIAPVPEGLDKYLFAGITRKKGIKTVKCKTIDLEVPANAEIVLEGYVDPHDIRDEGPFGDHTGYY-TPVEPYPTFTLTG 298
                 8.9**********************************************************************************.55577******** PP

                 EEE-TT-EEEE-SSSCCSHHHHCHHHHHHHHHHHHHHCCSTTEEEEEE-GGGTTTCEEEEECHHHTCCHHHHHHHHHHCCTTGGC-SEEEEEEETTS-T CS
        UbiD 281 ithRkdpiypttvvgkppeedallgkalealflpllkkqvpevkdvhlpeeggfhllavvsikkrypghakkvmealwalkqqlsltKlvivvDedvdv 379
                 i++Rk+piy ttvvgkp  eda++gk++e++flpl+++  pev+d+ +p++g f+ +a++sikkrypg+akkvm++lw+++q l ltK+++vvDed++v
  EPA05086.1 299 IMRRKNPIYVTTVVGKPILEDAYIGKVIEQSFLPLIRMFHPEVVDFSMPAAGWFQGFAIISIKKRYPGQAKKVMMGLWGMGQ-LALTKMFVVVDEDINV 396
                 **************************************99****************************************88.**************** PP

                 TSHHHHHHHHHHC--CCCCEEEECCCE CS
        UbiD 380 rdlkevlwaiatrvdpdrDlviiegtr 406
                 +++++v+wai+tr+d++rD++ii++t+
  EPA05086.1 397 HSIDDVIWAITTRADAARDTIIINNTP 423
                 ************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (480 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 2718.75
//
Query:       EPA05087.1  [L=328]
Description: aminotransferase, class III, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      3e-56  190.8   0.0    3.7e-56  190.5   0.0    1.0  1  Aminotran_3  Aminotransferase class-III


Domain annotation for each model (and alignments):
>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.5   0.0   2.1e-60   3.7e-56       9     311 ..      40     327 ..      35     328 .] 0.92

  Alignments for each domain:
  == domain 1  score: 190.5 bits;  conditional E-value: 2.1e-60
                  SCEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT-..SEEEEESSHHHHHHHHHHH CS
  Aminotran_3   9 lllvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapkgldkvflansGseAvetAlKl 106
                   ++v++ ++G  l+dvd+++y D   + ++++lGha  +v + +k+q++k+++     + ne+++kl+e ++k++p   +k+ +++sG+eA++ A++l
   EPA05087.1  40 YPFVVKSSAGKNLVDVDNNKYTDYWMGHWSLILGHAPKQVKESIKKQIDKSWMYG---TVNEQTIKLSELITKAVPV-AEKIRYVTSGTEATMYAVRL 133
                  4589999********************************************7766...99*****************.9******************* PP

                  HHHHHHHTSHCTT-EEEEETTT---SSHHHH.HHSS--TTTTTTCTTB-TSEEEE-TTBGGGTB-HHHHHHHHHHHHHHHHCHTCCCEEEEEE-SCET CS
  Aminotran_3 107 arkyarekkatektkiiafkgafHGrtlgal.svtgskkkyktlfgpflpevvrlkypdeevlkeneeeeaalleelealekkkkdevaAvivEpiqg 203
                  ar+       t k+ i +++g++HG t   l sv ++ ++ ++    +  ++++++y+d             l++ le l  k ++++a++i+Ep+ g
   EPA05087.1 134 ARS------VTGKNIIAKIDGGWHGYTSDLLkSVNWPFTESESSGVVNEEKIISIPYND-------------LEKSLEILN-KVSNDLAGIIIEPVLG 211
                  ***......9*****************99996777775555555555588999999998.............233455544.6789************ PP

                  TTTSEB--CCHHHHHHHHHHHHT-EEEEE-TTTTT.TTTSSSSGGGGCTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTS.........B--TT CS
  Aminotran_3 204 egGvvvaspeflaklrelckkhdvllivDEvqtGf.GrTGklfAlehagvspDlmtlaKaltgGlplsavlataevmqalapgs.........hgsTf 291
                   gG ++a++e+l++++e+ckk++ l+i DE+ tGf  r G l+ ++   + pD++tl+K ++gG+p+ ++++++e+m+  ++++          g+Tf
   EPA05087.1 212 GGGCIPAKAEYLKGIQEFCKKNNSLFILDEIVTGFrFRYGCLYPTM--KIDPDIVTLGKIVGGGMPIGVMCGKKEIMEHSNTKGkkktersyiGGGTF 307
                  ***********************************88*****9988..9*******************************99999*******99**** PP

                  TT-HHHHHHHHHHHHHHHHT CS
  Aminotran_3 292 gGnplacavalavleiieee 311
                  ++np+ +    a+l+ ++++
   EPA05087.1 308 SANPMSMTSGFATLTELKKS 327
                  **************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2242.32
//
Query:       EPA05088.1  [L=44]
Description: hypothetical protein BG20_I1868 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 292.77
//
Query:       EPA05089.1  [L=127]
Description: hypothetical protein BG20_I1870 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-24   86.6   0.1    2.5e-24   86.4   0.1    1.1  1  VIT1      VIT family


Domain annotation for each model (and alignments):
>> VIT1  VIT family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.4   0.1   1.4e-28   2.5e-24       1     106 [.      21     124 ..      21     126 .. 0.97

  Alignments for each domain:
  == domain 1  score: 86.4 bits;  conditional E-value: 1.4e-28
        VIT1   1 lrdavlGanDGLvspfalvaGlsaaslgssktvllaGlaellAGaiSMgiGeYlsvkserdlekaerkreeeeleedpeegeaeelaeilearglseel 99 
                 +rd+v+G+ DG+ + +++ aG+++a + s+++++la+l +++ Ga +M++ +Yl+vk+ r+l+++e +re++e+e+ p e+e++e+++i++a+g+s ++
  EPA05089.1  21 MRDFVFGFGDGINTSLGIAAGVGGADV-SANIIILAALVGMFTGAKAMAVQNYLAVKTHRQLLTSEIEREKWEIENRP-EDERQEIEDIYKAKGFSGKD 117
                 69***********************98.**************************************************.8999**************** PP

        VIT1 100 aqevaae 106
                  ++v+++
  EPA05089.1 118 LEMVVNK 124
                 *999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       851  (0.047465); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 818.30
//
Query:       EPA05090.1  [L=267]
Description: hypothetical protein BG20_I1867 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0001   22.7   0.1       0.28   11.7   0.0    2.3  2  MG2       MG2 domain
     0.0014   18.5   0.9      0.045   13.6   0.1    2.5  2  FlgD_ig   FlgD Ig-like domain
  ------ inclusion threshold ------
      0.018   14.8   0.2      0.043   13.6   0.2    1.6  1  PsbH      Photosystem II 10 kDa phosphoprotein


Domain annotation for each model (and alignments):
>> MG2  MG2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   4.6e-05      0.28      29      95 ..      46     113 ..      35     114 .. 0.77
   2 !    8.9   0.1   0.00035       2.1      34      95 ..     165     226 ..     148     228 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.6e-05
                 SB---.EEEEEEEE-TTSSEEEEEEEEE-CTTEEEEEE.E--TT--SEEEEEEEEECSTTT-EEEEEEE CS
         MG2  29 qglak.lplkltirdpdgkevkelplatdetggaesef.alpeaaklGeysvelsadsaeeslssgsfr 95 
                 +g+ + +p+klt+++pdg +v++ +l   ++g+++  + ++  + + G y+v +  +++  s+++ +f 
  EPA05090.1  46 TGVMSyKPVKLTVTSPDGVVVYSPSLPIAQDGTFKWIVkPTLPNFQNGVYTVIA-SNDDVASIAKIQFT 113
                 4555559*******************999999988776357789999*****99.55555566666665 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00035
                 EEEEEEEE-TTSSEEEEEEEEE-CTTEEEEEEE-..-TT--SEEEEEEEEECSTTT-EEEEEEE CS
         MG2  34 lplkltirdpdgkevkelplatdetggaesefal..peaaklGeysvelsadsaeeslssgsfr 95 
                 + +++ti++p+g+ ++  +l+   +g +++e+++  p   + G y++++  ++  +s +++s++
  EPA05090.1 165 TDITFTITSPNGNLISVAQLTPGPNGEFSTEIKTggPLWKENGFYTITA--NQGLSSEHKQSIK 226
                 569**************************99998445567899999999..5555666666555 PP

>> FlgD_ig  FlgD Ig-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1     0.017        99      25      72 ..      54      98 ..      43     104 .. 0.75
   2 !   13.6   0.1   7.6e-06     0.045       9      74 ..     149     214 ..     142     219 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.017
                EEEEEE-SS--EEEEEEEEESSSEEEEEEE-SB-TTS-B--SEEEEEE CS
     FlgD_ig 25 vtvtikDasGevVrtidlgaqsaGvvsftWdGtdndGnkladGaYtvk 72
                v++t++   G vV++ +l   + G++++    t  +    ++G Ytv 
  EPA05090.1 54 VKLTVTSPDGVVVYSPSLPIAQDGTFKWIVKPTLPN---FQNGVYTVI 98
                8999***********999888887766655544444...667777765 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 7.6e-06
                 S--EEEEEE...ESSSEEEEEEEE-SS--EEEEEEEEESSSEEEEEEE-SB-TTS-B-..-SEEEEEEEE CS
     FlgD_ig   9 dgeaplgve..lpeaadevtvtikDasGevVrtidlgaqsaGvvsftWdGtdndGnkl..adGaYtvkvt 74 
                 +g+++l v+   +++++  t+ti+  +G+++   +l++ + G++s +       G +l  ++G Yt++++
  EPA05090.1 149 TGSNKLLVTgtTTSSVTDITFTITSPNGNLISVAQLTPGPNGEFSTEIK----TGGPLwkENGFYTITAN 214
                 455555566569999999***************************9998....33333226788888775 PP

>> PsbH  Photosystem II 10 kDa phosphoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   7.1e-06     0.043      13      39 ..     229     255 ..     224     257 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.1e-06
        PsbH  13 seyGkvaPGWGttpvmavfilLflvfL 39 
                  e G v+P+ Gt  vm  +++L+ +++
  EPA05090.1 229 IENGVVVPEFGTIAVMILAVALVSIII 255
                 589*******************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       770  (0.0429472); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 1545.68
//
Query:       EPA05091.1  [L=281]
Description: sugar-specific transcriptional regulator TrmB [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.7e-15   55.6   0.0    2.1e-14   53.1   0.0    2.1  2  TrmB            Sugar-specific transcriptional regulator TrmB
    0.00032   20.6   0.0     0.0012   18.8   0.0    1.9  2  MarR            MarR family
    0.00047   20.0   0.0     0.0008   19.3   0.0    1.4  1  MarR_2          MarR family
     0.0015   18.4   0.1     0.0044   16.9   0.0    1.9  2  HTH_11          HTH domain
     0.0017   18.5   0.0     0.0082   16.3   0.0    2.1  2  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
     0.0039   16.7   0.0     0.0077   15.8   0.0    1.6  1  HTH_24          Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.019   14.7   0.0      0.037   13.8   0.0    1.4  1  FtsK_gamma      Ftsk gamma domain
      0.066   13.0   0.0       0.11   12.3   0.0    1.3  1  HTH_IclR        IclR helix-turn-helix domain
       0.13   12.1   1.3       0.26   11.1   1.3    1.5  1  Pedibin         Pedibin/Hym-346 family


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.1   0.0   1.1e-17   2.1e-14       3      68 .]      32      97 ..      30      97 .. 0.97
   2 ?   -0.8   0.0      0.71   1.4e+03      38      48 ..     148     158 ..     145     182 .. 0.84

  Alignments for each domain:
  == domain 1  score: 53.1 bits;  conditional E-value: 1.1e-17
                HCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE--HH CS
        TrmB  3 klGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravdpe 68
                +lG+++ E k+Y aLl+ gp ta+ +a++l+++r+k+Y+++++L+  G++  + ++pk+  ++dpe
  EPA05091.1 32 ALGMNDVEGKAYMALLRTGPITASSLAKDLNIDRAKAYRMVEKLSADGFISMSFSSPKKCIPIDPE 97
                79*************************************************************997 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.71
                 CHHHHHHHHHH CS
        TrmB  38 kvYevLrsLed 48 
                 k+Y+++++L++
  EPA05091.1 148 KIYSAIENLLE 158
                 89999999986 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   5.9e-07    0.0012      12      48 ..      46      82 ..      38      86 .. 0.93
   2 ?   -2.0   0.0       1.7   3.4e+03      33      45 ..     180     192 ..     175     192 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 5.9e-07
                HHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
        MarR 12 lyeqgplsvseLakklgvskstvtrvldrLekkGlie 48
                l + gp++ s Lak l+++++ + r++ +L  +G+i+
  EPA05091.1 46 LLRTGPITASSLAKDLNIDRAKAYRMVEKLSADGFIS 82
                5578********************************7 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.7
                 HHHHHHHHHHHTT CS
        MarR  33 tvtrvldrLekkG 45 
                 ++ + +++Le++G
  EPA05091.1 180 AIPEKITKLEERG 192
                 5556799999998 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0     4e-07    0.0008      12      54 ..      44      84 ..      33      90 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 4e-07
                HHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
      MarR_2 12 aaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                +aL r ++  +t++ la+ l+++++ + r++++L+a G++  +
  EPA05091.1 44 MALLRTGP--ITASSLAKDLNIDRAKAYRMVEKLSADGFISMS 84
                56777777..*****************************9755 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   2.2e-06    0.0044      12      44 ..      48      80 ..      41      95 .. 0.87
   2 ?   -3.8   0.1       6.5   1.3e+04      35      44 ..     184     195 ..     180     202 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.2e-06
      HTH_11 12 argpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                 +gpi+++ LA+ Ln+ r+  +r +++L++ g+
  EPA05091.1 48 RTGPITASSLAKDLNIDRAKAYRMVEKLSADGF 80
                5678**************************995 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 6.5
      HTH_11  35 dIkaLeelg..v 44 
                  I +Lee g  v
  EPA05091.1 184 KITKLEERGgkV 195
                 577888888552 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   4.1e-06    0.0082      14      53 ..      43      82 ..      41      86 .. 0.88
   2 ?   -3.0   0.0       4.5   8.9e+03      19      33 ..     249     263 ..     244     264 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.1e-06
                    HHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
  Fe_dep_repress 14 YtlseekkvvktkdlaerLnvspssVsemlkkLekdGyve 53
                    Y++    ++++ + la+ Ln+  + +  m++kL+ dG++ 
      EPA05091.1 43 YMALLRTGPITASSLAKDLNIDRAKAYRMVEKLSADGFIS 82
                    555556789999*************************975 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.5
                     HHSSB-HHHHHHHHT CS
  Fe_dep_repress  19 ekkvvktkdlaerLn 33 
                     +k+++  ++ +e +n
      EPA05091.1 249 SKDYALSTNASEMIN 263
                     667777777666665 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   3.9e-06    0.0077      11      47 ..      45      81 ..      35      82 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.9e-06
      HTH_24 11 lLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                +L + + i+ + LA+ l++ ++   r +++L  +G+I
  EPA05091.1 45 ALLRTGPITASSLAKDLNIDRAKAYRMVEKLSADGFI 81
                688999*****************************99 PP

>> FtsK_gamma  Ftsk gamma domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.9e-05     0.037      12      52 ..      44      84 ..      37      94 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.9e-05
  FtsK_gamma 12 elvveegkaStSllQRrlriGYnRAarlidqLeeeGiVgpa 52
                   +++g + +S+l + l+i  ++A r++++L ++G+++ +
  EPA05091.1 44 MALLRTGPITASSLAKDLNIDRAKAYRMVEKLSADGFISMS 84
                5678899999****************************976 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   5.7e-05      0.11      16      48 ..      49      81 ..      45      83 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.7e-05
                BSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
    HTH_IclR 16 pqeltlselArrtglpkStvhRlLqtLvelGyv 48
                +++ t s lA+ + + +++++R++  L   G++
  EPA05091.1 49 TGPITASSLAKDLNIDRAKAYRMVEKLSADGFI 81
                677899**********************99997 PP

>> Pedibin  Pedibin/Hym-346 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.3   0.00013      0.26      23      34 ..     104     115 ..     102     116 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00013
     Pedibin  23 LEqKekeLknve 34 
                 LE KekeLkn+ 
  EPA05091.1 104 LERKEKELKNFR 115
                 9*********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2001.18
//
Query:       EPA05092.1  [L=78]
Description: hypothetical protein BG20_I1872, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.023   14.3   0.2      0.024   14.2   0.2    1.1  1  RimK      RimK-like ATP-grasp domain


Domain annotation for each model (and alignments):
>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.2   1.3e-06     0.024      33      71 ..      26      65 ..       8      77 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.3e-06
                HHHTT-.-SSEEEEE-TTTT--EEEEE-SHHHHHHH.HHH CS
        RimK 33 liekiklrfPvvvKsvegsqGikvvlakkeqklkqv.lea 71
                l e+++l++P+vvK v+ sq   v+  k+e ++kq  +++
  EPA05092.1 26 LCEMLGLSSPLVVKDVMLSQTEIVIAVKDEFEAKQKfINS 65
                568999************************9999851344 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       927  (0.0517039); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 543.72
//
Query:       EPA05093.1  [L=63]
Description: hypothetical protein BG20_I1869 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-05   23.6   3.3    4.4e-05   23.5   3.3    1.0  1  VIT1      VIT family


Domain annotation for each model (and alignments):
>> VIT1  VIT family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   3.3   2.4e-09   4.4e-05     164     214 ..       2      52 ..       1      53 [. 0.97

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 2.4e-09
        VIT1 164 lalvvsiavtllalllfGavkalltgssklvsalrmlliGalAaaaaylig 214
                 +al+v+i++++ + + +G++k+++ +++k+v++l+m+ +G + a++ y+ig
  EPA05093.1   2 DALFVAIGISISTSFTVGVIKSKMANTNKIVGGLEMAGLGTGVALIGYGIG 52 
                 5899**********************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.33s 00:00:00.77 Elapsed: 00:00:00.50
# Mc/sec: 378.59
//
Query:       EPA05094.1  [L=445]
Description: transporter, major facilitator family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.1e-27   96.0  65.9    4.1e-21   75.3  33.2    2.1  2  MFS_1       Major Facilitator Superfamily
      2e-06   26.9  31.4    3.8e-06   26.0  31.4    1.4  1  MFS_1_like  MFS_1 like family
     0.0022   16.6   5.2     0.0022   16.6   5.2    3.8  3  MFS_2       MFS/sugar transport protein
  ------ inclusion threshold ------
      0.021   13.3   7.4       0.22    9.8   1.8    2.1  2  MFS_3       Transmembrane secretion effector


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.3  33.2   9.1e-25   4.1e-21      16     352 ..      44     401 ..      28     402 .. 0.75
   2 !   34.6  24.7   2.2e-12   9.7e-09       1     173 [.     259     437 ..     259     444 .. 0.88

  Alignments for each domain:
  == domain 1  score: 75.3 bits;  conditional E-value: 9.1e-25
       MFS_1  16 gpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalglllllfasslw.lllvlrvlqGlgagalfpagaaliad 112
                  +++p ++   lg +++ +g++++l + ++a++++++G ++d++  +r +l++++ +  ++++ l+f +    l+++   ++G++  + +p+ ++l+ +
  EPA05094.1  44 HIVIP-LYVLFLGGNVANVGIVIGLHYGLSAIGAVFWGKVIDKYHLKRaILVTCFSAITICSIGLFF-TKDLsLVVLISSISGFFIIGKNPVTQVLVME 140
                 34444.344458899999**************************99999************666668.555559************************* PP

       MFS_1 113 wfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpeepperkrkspkeee...................kgtg 192
                  +p ++ ++ +  +s+ + +G++ + l+g++    +  r  f+++ai s +a +l   + + +++  +r + +                      k + 
  EPA05094.1 141 SVPNNQWSQLFTRISIITTFGSLGAFLVGSVWDRFFDLRPYFLFCAITSGIATIL--SFGVGSKSIIERHTIVHSIhgirhifnhnrlnfqfiftKVPH 237
                 ******************************************************7..555444444444444444355666777777777777776666 PP

       MFS_1 193 paplvpawkallkdpvlw..illialllfffgfsg....lltllplylqevlgls.glllaglllallalvgailallagrlsdrlgrrrrlllallll 284
                 p+ ++p +  ++ ++  +   + + +l++f++++g    +++++p+   + + ++ +  ++ l++ +  +  + +++++ rl+ r++ +r++ +++l  
  EPA05094.1 238 PHDFKP-IITVFQRK--MshDIGVLFLTNFLFYFGsnifFTAFIPF--LKKFEFTnS--EVFLVYLIQTITLLTIFFFVPRLIARISEERATQISYLPR 329
                 666666.33333333..12313333333333333333358888888..899999952..444445555555555577********99999999998877 PP

       MFS_1 285 llaalglallavt...ssavllllvlvliGf.glgfvfpsllalasdlappeeagtasglfntagslggalg 352
                 +l+ +  a + ++   + ++l+++++ ++ + +++++++s   ++ + +p+   gt++g+++++ ++g++ g
  EPA05094.1 330 ILGIITAATFIPItigDYSLLMAIISSCMMVsAFSIFSVSNSIILFKTIPKGFEGTYLGVNSFMVGVGIFSG 401
                 77777777777773324444444455557788999999999999************************9977 PP

  == domain 2  score: 34.6 bits;  conditional E-value: 2.2e-12
       MFS_1   1 lllaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalg.lllllfa......sslwlllvlr 92 
                 l+l+ fl +++++i+++a+ +   + + ++ se+ l++ + +++ +   +++ rl+ r++  r   +++l  +lg +++++f+       sl + +++ 
  EPA05094.1 259 LFLTNFLFYFGSNIFFTAFIP-FLKKFEFTNSEVFLVYLIQTITLLTIFFFVPRLIARISEERATQISYLPRILGiITAATFIpitigdYSLLMAIISS 356
                 799****************95.5599*************************************************555555844565544555666666 PP

       MFS_1  93 vlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllp 173
                 +++  + +++  +  +++ +  pk   g ++g+ s ++++G+  g+l +g+++++l+++++f i+  + + ++v+f ++l 
  EPA05094.1 357 CMMVSAFSIFSVSNSIILFKTIPKGFEGTYLGVNSFMVGVGIFSGALTAGYISEWLSYSVSFAIAICIIFSSLVMFRFYLK 437
                 66666669****************************************************************999888774 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0  31.4   8.4e-10   3.8e-06      24     383 ..      49     418 ..      28     420 .. 0.78

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 8.4e-10
  MFS_1_like  24 iylkskglkaseigiitlilpltsilsppiwgvlaDrfgkrkkvvilslllsavlflsllfippskerqeesklevsvaqdvdaektfwilfllvvlas 122
                 +y    g +++++gi+  +   +s +++ +wg + D++  + ++++ +  + +++ ++l+                       ++k++ +++l+ ++  
  EPA05094.1  49 LYVLFLGGNVANVGIVIGLHYGLSAIGAVFWGKVIDKYHLKRAILVTCFSAITICSIGLF-----------------------FTKDLSLVVLISSISG 124
                 55556677899*************************************************.......................7899999********* PP

  MFS_1_like 123 fflaailvlldaatlkel..gedrkdyGrq...rlfGsvGyaifafitGilidhysvnllpysallyvlaallvisllvvlilnetekesklkvtksl. 215
                 ff+ + ++++ +++++ +  ++ ++ + r+     fGs+G  ++  +   ++d            ++++a+   i+++++  +  ++  +   +++s  
  EPA05094.1 125 FFIIGKNPVTQVLVMESVpnNQWSQLFTRIsiiTTFGSLGAFLVGSVWDRFFDLRPY--------FLFCAITSGIATILSFGVGSKSIIERHTIVHSIh 215
                 ******************755556779997222469999976666666666666655........2222222222222222222222222222222223 PP

  MFS_1_like 216 .............................qvllnilknpeviifllvalilgmswgiienFlflYLkelgasntllGslvalgvvaeiplfffaeklle 285
                                                +++  + + + +++l+ ++  + ++i+ + +  +Lk+ +++n+ +  +  ++++  +++fff  +l+ 
  EPA05094.1 216 girhifnhnrlnfqfiftkvphphdfkpiITVFQRKMSHDIGVLFLTNFLFYFGSNIFFTAFIPFLKKFEFTNSEVFLVYLIQTITLLTIFFFVPRLIA 314
                 555667999**************9996653344444566788899999999999*****9999************************************ PP

  MFS_1_like 286 klGhvklliiallayilrfllyaii.......enawlvlpievLhgisfgllwaaaveyvskiapksleatgqgllsglyfglGralGsliGGllwdlk 377
                 +++ ++   i+ l  il  +  a++        ++ ++++   +   +f ++ ++      k +pk+ e+t+ g+ s +++g+G ++G+l++G++ ++ 
  EPA05094.1 315 RISEERATQISYLPRILGIITAATFipitigdYSLLMAIISSCMMVSAFSIFSVSNSIILFKTIPKGFEGTYLGVNS-FMVGVGIFSGALTAGYISEWL 412
                 ****99999999988888888877777766554555555555666556666655566667899***********866.669*************99988 PP

  MFS_1_like 378 saiflF 383
                 s  + F
  EPA05094.1 413 SYSVSF 418
                 877777 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   5.2   4.9e-07    0.0022     229     349 ..      29     148 ..      20     171 .. 0.86
   2 ?   -0.1   0.2     0.058   2.6e+02      57      86 ..     172     197 ..     162     211 .. 0.77
   3 ?   -2.9  21.7       0.4   1.8e+03     228     342 ..     258     372 ..     243     438 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.9e-07
       MFS_2 229 llllfllaalalgvlnglllYyltyvlgngsaasvfllvvtisallgiplwqplakrlgkkntyllgalltivllvlvlllqpsnlllflvllviagfg 327
                 ++l++l  + +   l+    +y+ +  gn +++ ++ ++++ ++++g+++w ++  ++  k+++l+   ++i +  + l++ +++l l++++  i+gf+
  EPA05094.1  29 WMLFVLPSSITAEGLHIVIPLYVLFLGGNVANVGIVIGLHYGLSAIGAVFWGKVIDKYHLKRAILVTCFSAITICSIGLFF-TKDLSLVVLISSISGFF 126
                 4445555555555566666777777778*******************************9999999999999999999999.9**************** PP

       MFS_2 328 vgvaallpwsmladvvDygelk 349
                 +++ + +   +++++v  +++ 
  EPA05094.1 127 IIGKNPVTQVLVMESVPNNQWS 148
                 **************99999986 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.058
       MFS_2  57 idktstrwGrrrPwlllsaiilavsiillf 86 
                  d+        rP+ l++ai+ ++++il f
  EPA05094.1 172 WDRFFD----LRPYFLFCAITSGIATILSF 197
                 444444....78999999999999999877 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 0.4
       MFS_2 228 illllfllaalalgvlnglllYyltyvlgngsaasvfllvvtisallgiplwqplakrlgkkntyllgalltivllvlvlllqpsnlllflvllviagf 326
                 +l+l+ +l++++ ++ +++++ +l+++  ++s++ +++l+ ti  l  ++++++l +r++  +++ +++l  i++ + +  + p  +  + +l++i++ 
  EPA05094.1 258 VLFLTNFLFYFGSNIFFTAFIPFLKKFEFTNSEVFLVYLIQTITLLTIFFFVPRLIARISEERATQISYLPRILGIITAATFIPITIGDYSLLMAIISS 356
                 788889999999***************9999999999999999999999**************************999988855666666666666666 PP

       MFS_2 327 gvgvaallpwsmladv 342
                 ++ v+a+ + s    +
  EPA05094.1 357 CMMVSAFSIFSVSNSI 372
                 6555555444444333 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.3   0.00049       2.2     348     391 ..      64     107 ..      53     120 .. 0.84
   2 ?    9.8   1.8     5e-05      0.22     215     397 ..     251     438 ..     246     444 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.00049
       MFS_3 348 YltvlaGglaaGsllWGavaealsvtlaLlaaaaalllaaaill 391
                  + + +G  a G++ WG+v +++ ++ a+l+++ + +    i+l
  EPA05094.1  64 VIGLHYGLSAIGAVFWGKVIDKYHLKRAILVTCFSAITICSIGL 107
                 5667889999********************99987766666655 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 5e-05
       MFS_3 215 aasreikavlvRaalFglsa.savlaLLPlvardqldgdalvyGillgalGvGAilgalllsrLRerlsserlvllaavalAlvllslalasslwv..a 310
                 ++s++i + ++  +lF++ + +   a +P++ + +     ++  +l+ ++ +  i+   +++rL +r+s+er ++++ +   l ++++a   ++ +   
  EPA05094.1 251 KMSHDIGVLFLTNFLFYFGSnIFFTAFIPFLKKFEFTNSEVFLVYLIQTITLLTIF--FFVPRLIARISEERATQISYLPRILGIITAATFIPITIgdY 347
                 799************99977245679**********************99987776..799***************99988777776665554443113 PP

       MFS_3 311 vlvl.llgGaaWitalstlnvavqla....vPrWvvgRalavYltvlaGglaaGsllWGavaealsvtlaLlaaaaalllaaaillllklpe 397
                  l + +++    + a+s + v+  ++    +P+   g  l v   ++  g+  G+l  G ++e ls +++  +a +  + + ++++++ l++
  EPA05094.1 348 SLLMaIISSCMMVSAFSIFSVSNSIIlfktIPKGFEGTYLGVNSFMVGVGIFSGALTAGYISEWLSYSVSFAIAICI-IFSSLVMFRFYLKH 438
                 333314456667899*****999886333369999*****************************9999999887665.55667777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (445 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       751  (0.0418874); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.50
# Mc/sec: 2687.01
//
Query:       EPA05095.1  [L=311]
Description: putative membrane protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.4e-11   44.1  12.1    7.9e-07   29.0   0.2    3.1  3  TM_helix    Conserved TM helix
    5.4e-07   29.4   8.0    5.4e-07   29.4   8.0    3.2  3  MS_channel  Mechanosensitive ion channel


Domain annotation for each model (and alignments):
>> TM_helix  Conserved TM helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.7   8.6e-09   7.7e-05       9      42 ..      52      85 ..      45      93 .. 0.86
   2 !   29.0   0.2   8.8e-11   7.9e-07       3      39 ..     140     176 ..     138     183 .. 0.92
   3 ?   -3.9   0.8       1.6   1.4e+04      22      34 ..     220     232 ..     219     237 .. 0.65

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 8.6e-09
                HHHTTHSHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
    TM_helix  9 ellsflPnLvgAilILlvGwiiAkfvsrlvtkll 42
                +++   P++++ +++L++G+i +k+v +++tk  
  EPA05095.1 52 SVADSAPKIIASVILLIIGLIAGKVVGKVTTKAV 85
                567779************************8865 PP

  == domain 2  score: 29.0 bits;  conditional E-value: 8.8e-11
                 XXSXXHHHHTTHSHHHHHHHHHHHHHHHHHHHHHHHH CS
    TM_helix   3 lnnllnellsflPnLvgAilILlvGwiiAkfvsrlvt 39 
                 l++ l++l   +PnL++++lI ++G i+ +fvs+ + 
  EPA05095.1 140 LSTALTSLWLWVPNLLAFVLIVVIGSIVVNFVSKWIE 176
                 68999*****************************985 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 1.6
                 HHHHHHHHHHHHH CS
    TM_helix  22 lILlvGwiiAkfv 34 
                 l+ +  w+iA  +
  EPA05095.1 220 LVSAFSWSIAVAI 232
                 5666678887655 PP

>> MS_channel  Mechanosensitive ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   1.1      0.23     2e+03       2      31 ..      59      88 ..      58      88 .. 0.82
   2 ?   -1.1   0.9      0.13   1.2e+03      18      43 ..     148     173 ..     124     180 .. 0.71
   3 !   29.4   8.0     6e-11   5.4e-07      18     106 ..     220     307 ..     192     308 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.23
                .HHHHHHHHHHHHHHHHTTT--SCCHHHHH CS
  MS_channel  2 kilkiliivvgilivlsllgvnvsallavl 31
                ki++ +i++++ li+ +++g  +++ +++l
  EPA05095.1 59 KIIASVILLIIGLIAGKVVGKVTTKAVTSL 88
                688889999999999999998888888775 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.13
                 HTTT--SCCHHHHHHHHHHHHHHHHC CS
  MS_channel  18 sllgvnvsallavlGalglalglalk 43 
                 +l+  n+ a++ ++ ++++++ +++k
  EPA05095.1 148 WLWVPNLLAFVLIVVIGSIVVNFVSK 173
                 44444466777777777777777776 PP

  == domain 3  score: 29.4 bits;  conditional E-value: 6e-11
                 HTTT--SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-.SS-TT-EEESSSEEEEEEEE-SSEEEEEETTSEEEEEEHHHHHTS-E CS
  MS_channel  18 sllgvnvsallavlGalglalglalkdlisnlvaGiillfek.pfkiGDlveigdieGtVediglrttkirtfdgrivtiPnsslvtsni 106
                  +  +++s+ +a+ + ++++lg+alkdli   + G     ++  +k+G  v+igdi+GtV+   l+ + +++  ++ ++iP++ +++++i
  EPA05095.1 220 LVSAFSWSIAVAIGASIAIGLGFALKDLIPASIMGASN--QRsILKVGQKVKIGDITGTVTASHLLHVIVTNDRNESIVIPTKLMMNQTI 307
                 4456789999******************9866666544..33489**************************************9999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1405  (0.0783647); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 2134.99
//
Query:       EPA05096.1  [L=52]
Description: hypothetical protein BG20_I2367, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.074   13.0   0.8       0.13   12.2   0.1    1.7  2  HalOD2     Halobacterial output domain 2
       0.11   12.5   3.1       0.75    9.8   0.1    2.1  2  DUF4428    Domain of unknown function (DUF4428)
       0.14   12.4   0.0       0.16   12.2   0.0    1.1  1  Gemini_V2  Geminivirus V2 protein


Domain annotation for each model (and alignments):
>> HalOD2  Halobacterial output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1      0.31   1.8e+03      34      37 ..      18      21 ..      15      25 .. 0.69
   2 ?   12.2   0.1   2.1e-05      0.13      29      39 ..      34      44 ..      27      50 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.31
      HalOD2 34 CtrC 37
                Ct C
  EPA05096.1 18 CTSC 21
                5555 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 2.1e-05
      HalOD2 29 ayvWkCtrCGe 39
                ay W+C +CG+
  EPA05096.1 34 AYLWQCFKCGK 44
                8*********7 PP

>> DUF4428  Domain of unknown function (DUF4428)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00013      0.75       7      27 ..       4      22 ..       3      31 .. 0.91
   2 ?    3.9   0.7    0.0083        50      16      30 ..      30      46 ..      22      52 .] 0.67

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00013
     DUF4428  7 kKigllkrlkleDgyvCkdCl 27
                kKi+l+   ++ +g++C++Cl
  EPA05096.1  4 KKIPLID--DTPEGFLCTSCL 22
                8999998..899********8 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.0083
     DUF4428 16 kleDgyv..CkdClkKl 30
                k+++ y+  C +C kK+
  EPA05096.1 30 KINNAYLwqCFKCGKKY 46
                555665444999*9998 PP

>> Gemini_V2  Geminivirus V2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.7e-05      0.16       4      36 ..       7      39 ..       6      48 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.7e-05
   Gemini_V2  4 PLlnefPetvhGfrcmLAvkylqevektyspdt 36
                PL+++ Pe++    c+L ++y +++++ y  ++
  EPA05096.1  7 PLIDDTPEGFLCTSCLLPMQYQKKINNAYLWQC 39
                9**************************997766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 363.17
//
Query:       EPA05097.1  [L=361]
Description: phosphomethylpyrimidine kinase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.3e-73  245.7   0.9    4.3e-73  245.7   0.9    1.4  2  Phos_pyr_kin  Phosphomethylpyrimidine kinase
      2e-29  102.4   0.0    3.9e-29  101.4   0.0    1.5  1  ThiP_synth    Thiamine-phosphate synthase
    2.9e-10   39.9   0.0    4.6e-10   39.3   0.0    1.2  1  PfkB          pfkB family carbohydrate kinase
    0.00067   19.2   0.1     0.0013   18.3   0.1    1.5  1  Carb_kinase   Carbohydrate kinase
  ------ inclusion threshold ------
      0.027   13.9   0.4       0.11   11.9   0.4    1.9  1  HK            Hydroxyethylthiazole kinase family


Domain annotation for each model (and alignments):
>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  245.7   0.9   1.2e-76   4.3e-73       1     242 [.      10     247 ..      10     251 .. 0.98
   2 ?   -3.2   0.0       1.2   4.3e+03     126     143 ..     278     298 ..     256     333 .. 0.54

  Alignments for each domain:
  == domain 1  score: 245.7 bits;  conditional E-value: 1.2e-76
                   ETTSSSHHHHHHHHHHHTTEEEEEEEEEEEEEETTCEEEEEE--HHHHHHHHHHHHHTS--SEEEE-S--SHHHHHHHHHHHHHTTSSEEEE---SS CS
  Phos_pyr_kin   1 DssGGAGiqADlktfsalgvygmsvitaltaqntkgvkevhplpaelveaqleavledvkvdavKiGmlasaeiievvaeklkkykvpvVlDPVmva 97 
                   D+s+GAGiq D+ktf +l++yg++vita+t qnt +   v+p++++++++ql+++++d+k+d +KiGm++++eii+++ ++lk++k+p+V+DPV+ +
    EPA05097.1  10 DPSSGAGIQSDVKTFDSLNAYGLTVITAITGQNTSNFGMVEPVSQKILKNQLDSIMTDFKIDGIKIGMVYNSEIIKTISKELKNKKIPIVIDPVIKS 106
                   9************************************************************************************************ PP

                   CTSSSBSSHHHHHHHHHHTGGG-SEEE-BHHHHHHHHT---SSHHHHHHHHHHHHHTT-SEEEEEEGGS-SSSEEEEEEEETSSEEEEEEEE----S CS
  Phos_pyr_kin  98 ksgselleeeavealkeeLlplatvitPNlpEaeaLlgekikteedmkeaakkllklgakaVlikGghlegeeavvtdvlydgeeveeleaerietk 194
                   ++g +l+++ a+  +k+ L+platvitPN +Eae L++ kik+++++++aa k++++g+++V+i+G +    + ++ d+++++++++++++++i+ k
    EPA05097.1 107 TTGGQLIDKAAIVDFKKFLIPLATVITPNKFEAEFLSEIKIKSKKSLHKAALKIQAMGVENVIITGLES---NGQISDYILEQKNEYTISSKKIS-K 199
                   ******************************************************************995...55678******************.* PP

                   --BTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHHHHHHHCG-BSTSSS CS
  Phos_pyr_kin 195 nthGtGCtlssaiaaelakgesleeAvkkAkeyvteaikealelgkga 242
                   ++hG+GC +s+++  +l +g +l++Avk +ke+++++ik+a ++g+g+
    EPA05097.1 200 TNHGSGCNYSASLLFSLVNGAPLKDAVKFSKEFTYNSIKNAKNIGHGI 247
                   *********************************************997 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.2
                   BHHHHH...HHHT---SSHHH CS
  Phos_pyr_kin 126 NlpEae...aLlgekikteed 143
                   N+pE++   ++++++ k+ ++
    EPA05097.1 278 NIPECQtnfVFSKKNPKSIKE 298
                   333333222233333333333 PP

>> ThiP_synth  Thiamine-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.4   0.0   1.1e-32   3.9e-29       1     100 [.     261     360 ..     261     361 .] 0.98

  Alignments for each domain:
  == domain 1  score: 101.4 bits;  conditional E-value: 1.1e-32
                 HHHHHHHHHHCC--.GCC--TT-B-EEEE-ST--SGGGEEEETT-EEE-TSSEEE-S-EEETS-CHHHHHHHHHHCC-TT--EEEEEE--HHHHHHHCC CS
  ThiP_synth   1 eleralelleeeeefakliPevgsNiayalpdAksieDvaavpGRIvrvkgrvkvvgepefgasshvarvllaamkfdpevraainirydekilealee 99 
                 el++a++++ ++++++k iPe+++N++++++++ksi+++++++GRIv+++++v+v+g+ ++g+s+hvar+l+ ++k++p++ +ain+ry+e+i+++l++
  EPA05097.1 261 ELTNAINKFLQIKNIHKNIPECQTNFVFSKKNPKSIKEILGISGRIVKTGNTVTVAGDLAYGGSKHVARALIIMNKKFPDMCSAINLRYSEEIISKLRK 359
                 6899*********************************************************************************************98 PP

                 T CS
  ThiP_synth 100 l 100
                 +
  EPA05097.1 360 K 360
                 6 PP

>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   0.0   1.3e-13   4.6e-10     151     282 ..      87     229 ..      73     240 .. 0.79

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 1.3e-13
                 HHHHHHHTTEEEEEECESSSHH..........HHHHHHHHH.CTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSEEEEEEGGGEEEEEE.. CS
        PfkB 151 laeaaknggtfdpnlldplgaq..........fkeallell.aladllkpneeElealtgekledieealaalhklkakgaktvvvtlGkeGalvve.. 236
                 +++  kn++  +p++ dp +++          +  +++++l +la++++pn  E+e+l++ k+++ +++ +a+ k++a g+++v++t  +   ++++  
  EPA05097.1  87 ISKELKNKK--IPIVIDPVIKSttggqlidkaAIVDFKKFLiPLATVITPNKFEAEFLSEIKIKSKKSLHKAALKIQAMGVENVIITGLESNGQISDyi 183
                 555556666..4444444444444444988898899999999********************************************9766666666666 PP

                 ..TTEEEEEEE.SSSS-SBGT.THHHHHHHHHHHHHHTTHHHHHHHHHH CS
        PfkB 237 ..kdgelkvpavpkvkvvDtt.GAGDsfvggflaallegksleealrfa 282
                   +++e+ ++   ++k+  t+ G G  + +++l +l++g++l++a++f 
  EPA05097.1 184 leQKNEYTIS---SKKISKTNhGSGCNYSASLLFSLVNGAPLKDAVKFS 229
                 4244444444...467777767*************************96 PP

>> Carb_kinase  Carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   3.5e-07    0.0013       4     154 ..       6     164 ..       3     227 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.5e-07
                  EE-BTTCHHHHHHHHHHHHCTT..-SEEEEEESSTTTCCCCTTTTTCEECCTTHTTTS...--SSS-SEEEE-TT-SSSHCHHHHCHHHCCCCS-EEE CS
  Carb_kinase   4 igGsedytGAallaalaalrlg..aglvsvateseaiavlksylpevivhplledeqakileklerldavviGpGLgrdekikklleevlekdeplvi 99 
                  igGs+  +GA++ +   +  +    gl+ + +   + +++   ++  + +++l+++  +i+ +  ++d + iG+   + e ik + +e  +k+ p+vi
   EPA05097.1   6 IGGSDPSSGAGIQSDVKTFDSLnaYGLTVITAITGQNTSNFGMVEP-VSQKILKNQLDSIMTDF-KIDGIKIGMV-YNSEIIKTISKELKNKKIPIVI 100
                  9*************99999876547777666655555555555555.55555534444677776.9********5.56677899************** PP

                  E.......GGGGGSGGGG.....TTTTSSEEEE--HHHHHHHCTTTCHHCCSHHHHHHHHHHHH CS
  Carb_kinase 100 D.......AdgLnllaqkne..lserkaeviLTPhkkEfkrLlkaivkkeddrlelarelaqkl 154
                  D       ++ L  +a   +  ++    ++++TP+k E + L++  +k++++  ++a +++++ 
   EPA05097.1 101 DpviksttGGQLIDKAAIVDfkKFLIPLATVITPNKFEAEFLSEIKIKSKKSLHKAALKIQAMG 164
                  *5555543344444444334666777789***************99966666555555554442 PP

>> HK  Hydroxyethylthiazole kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.4   2.9e-05      0.11      55     208 ..      73     225 ..      70     260 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.9e-05
                 EE-TT--HHHHHHHHHHHHHHHHTT--EEEE-TTBTTBHHHHHHHHHHHHHS--.....SEEEEEHHHHHHHHTSSCCSCSSSSSS-SHHHHHHHHHHH CS
          HK  55 lNiGtleekaiealkaAvksakevnrPvvlDPVgvgAtelRrelalellkevkl.....avikGNasEilslaglelkvkGvDskeaataavaavqkvA 148
                 + iG + +   e++k+  k+ k++++P+v+DPV  + t         ++   k+      vi  N+ E   l++++ k+k   s        aa ++ A
  EPA05097.1  73 IKIGMVYN--SEIIKTISKELKNKKIPIVIDPVIKSTTGGQLIDKAAIVDFKKFliplaTVITPNKFEAEFLSEIKIKSKK--SL-----HKAALKIQA 162
                 67899988..88999999***************999998777666666655554223335788888887777777765541..22.....223444444 PP

                 HHHTSEEEE....ESSS.EEEEESSEEEEEE-S-GGGGGSTTHHHHHHHHHHHHHTTBSSHHHHH CS
          HK 149 qklrvvvvv....tGev.DvvsdgkkvyklknGtellgkitasGCllgsvvaaflavkkdkllaa 208
                 + ++ v++      G++ D++ + k++y++++ +++     +sGC +++ +  f  v+ ++l++a
  EPA05097.1 163 MGVENVIITglesNGQIsDYILEQKNEYTISS-KKISKTNHGSGCNYSASLL-FSLVNGAPLKDA 225
                 44444443311114554489999999999976.6677777899999888653.333445555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       901  (0.0502538); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2307.66
//
Query:       EPA05098.1  [L=301]
Description: hypothetical protein BG20_I2496, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0043   17.1   3.7     0.0099   15.9   3.7    1.6  1  Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C
  ------ inclusion threshold ------
      0.012   15.6   0.3        7.5    6.6   0.0    2.5  2  Y_Y_Y         Y_Y_Y domain
      0.039   14.0   0.3        0.1   12.7   0.3    1.7  1  DUF1664       Protein of unknown function (DUF1664)
      0.052   14.4   0.0       0.16   12.8   0.0    1.8  2  Filamin       Filamin/ABP280 repeat
      0.071   13.4   0.2       0.15   12.4   0.2    1.5  1  BLOC1_2       Biogenesis of lysosome-related organelles compl
      0.093   12.8   0.3       0.15   12.1   0.3    1.2  1  TPR_MLP1_2    TPR/MLP1/MLP2-like protein
       0.35   11.3   4.4       0.52   10.7   2.2    2.5  2  FlaC_arch     Flagella accessory protein C (FlaC)
       0.46    9.4   3.3       0.18   10.7   0.8    1.5  2  Ran-binding   RanGTP-binding protein


Domain annotation for each model (and alignments):
>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   3.7   4.4e-06    0.0099      43     107 ..     208     271 ..     197     288 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.4e-06
  Baculo_PEP_C  43 ietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnlnsiltnLlssvtNinst 107
                   + + ++ +s+++ + l+++ ++ +t l++L++ +  + +tl+++  n+++ +t+  +svtNi+++
    EPA05098.1 208 LSQDIGGISNQIIK-LNSVLEETSTELNTLKSEISGFGNTLESASSNIDKSVTSVSNSVTNIEEA 271
                   33444444444444.33333444555555666666666999999999999999999999999875 PP

>> Y_Y_Y  Y_Y_Y domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0034       7.5      34      54 ..      68      88 ..      67      96 .. 0.78
   2 ?    6.4   0.1    0.0038       8.5      30      45 ..     175     190 ..     159     199 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0034
                ES--SEEEEEEEEEEETTS-B CS
       Y_Y_Y 34 tnlppGdYtlkVkakdndgqw 54
                +nlp G+Yt+++  +  +g +
  EPA05098.1 68 SNLPFGTYTIEIISTQQNGLS 88
                69*********9877766655 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0038
                 EEEEES--SEEEEEEE CS
       Y_Y_Y  30 easytnlppGdYtlkV 45 
                  a y ++++G+Y+++V
  EPA05098.1 175 YADYVPKEEGTYVFHV 190
                 789************9 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.3   4.5e-05       0.1      39     109 ..     208     278 ..     202     293 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.5e-05
     DUF1664  39 lsdavesvskqleqvseslaatkrhL...ssridrvdkkldeqkeiskeikeevtevredlseigedvesvkea 109
                 ls+ +  +s+q+ ++ + l++t  +L   +s+i   +++l+    +s++i++ vt+v++ +++i+e +++++++
  EPA05098.1 208 LSQDIGGISNQIIKLNSVLEETSTELntlKSEISGFGNTLE---SASSNIDKSVTSVSNSVTNIEEASSQLNSL 278
                 45555556666666666666665554111445555555554...456677777777777777777777777665 PP

>> Filamin  Filamin/ABP280 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0         4   8.9e+03      65      75 ..      47      57 ..      16      62 .. 0.70
   2 ?   12.8   0.0   6.9e-05      0.16      60      91 ..     148     191 ..      68     200 .. 0.59

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 4
                EEEE-SSSEEE CS
     Filamin 65 evvdnedgtyt 75
                +++ nedgt++
  EPA05098.1 47 QFETNEDGTFE 57
                47888999875 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 6.9e-05
                 .............EEEEEEEE-SSSEEEEEE--SSSCEEEEEEE CS
     Filamin  60 s............svkievvdnedgtytvsYtpeepgtyrvsvk 91 
                 +             +  +++  ++g y + Y p+e+gty  +v 
  EPA05098.1 148 QtthvhlpsgkveTLANNFSTLHQGLYYADYVPKEEGTYVFHVV 191
                 033333333433345568*********************99974 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   6.6e-05      0.15      33      93 ..     216     277 ..     204     279 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.6e-05
     BLOC1_2  33 sekykklkdvaaslekkleklnekyeelqpylqqi.dqiekqvteLeeavseLDeyskeLEa 93 
                 s+++ kl++v+++++++l+ l+++   + + l++   +i+k+vt+  + v  ++e s++L +
  EPA05098.1 216 SNQIIKLNSVLEETSTELNTLKSEISGFGNTLESAsSNIDKSVTSVSNSVTNIEEASSQLNS 277
                 56778999999999999999999999999998876268*********************976 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.3   6.7e-05      0.15      59     109 ..     226     276 ..     220     278 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.7e-05
  TPR_MLP1_2  59 lqalreelnelkaeiaelkaeaesakaeleeseesweeqkeelekelsele 109
                 l+++ +eln+lk+ei+ + + +esa++++++s  s ++  +++e+  s+l+
  EPA05098.1 226 LEETSTELNTLKSEISGFGNTLESASSNIDKSVTSVSNSVTNIEEASSQLN 276
                 788999*******************************99999999998886 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       4.1   9.3e+03      16      30 ..      77      91 ..      74      93 .. 0.64
   2 ?   10.7   2.2   0.00023      0.52       4      48 ..     221     266 ..     218     278 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4.1
   FlaC_arch 16 letvkkeneelsksv 30
                +e + ++++ lsk++
  EPA05098.1 77 IEIISTQQNGLSKKI 91
                555666777777776 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00023
   FlaC_arch   4 elEnklsklsteletvkkeneelsksveelkenV.kdllsLYEvVs 48 
                 +l + l+++stel+t+k+e++   +++e    n+ k + s+   V+
  EPA05098.1 221 KLNSVLEETSTELNTLKSEISGFGNTLESASSNIdKSVTSVSNSVT 266
                 6778899*********************999999666666655555 PP

>> Ran-binding  RanGTP-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1      0.81   1.8e+03      49      72 ..      80     104 ..      75     113 .. 0.77
   2 ?   10.7   0.8   8.3e-05      0.18      70     142 ..     215     288 ..     203     298 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.81
  Ran-binding  49 leklqkkLeskiki.ispaidLiel 72 
                  ++++q+ L++ki++  +++ dLi +
   EPA05098.1  80 ISTQQNGLSKKIDVkFTSSTDLISV 104
                  6778899999999955788899876 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 8.3e-05
  Ran-binding  70 ieliaarGntsLesaveLtksLkkeieelgerleeaaekeekskk.keeekeelkkviedikeLLkrieeaiPl 142
                  i     + n++Le++ +  ++Lk+ei+ +g++le+a+++ +ks +  +++ +++++  +++++L   i  +i +
   EPA05098.1 215 ISNQIIKLNSVLEETSTELNTLKSEISGFGNTLESASSNIDKSVTsVSNSVTNIEEASSQLNSLFFPIVASIGI 288
                  555666779***************************99998765545666677777777787777776666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       840  (0.0468515); expected 358.6 (0.02)
Passed bias filter:                      688  (0.0383736); expected 358.6 (0.02)
Passed Vit filter:                       127  (0.0070835); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.39
# Mc/sec: 2303.54
//
Query:       EPA05099.1  [L=263]
Description: hypothetical protein BG20_I1916 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.4e-06   26.6   0.0      1e-05   25.7   0.0    1.5  1  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
     0.0027   17.7   0.0     0.0089   16.0   0.0    1.9  1  CarbopepD_reg_2  CarboxypepD_reg-like domain
  ------ inclusion threshold ------
      0.064   13.3   0.1       0.16   12.0   0.1    1.6  1  Big_1            Bacterial Ig-like domain (group 1)


Domain annotation for each model (and alignments):
>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   1.7e-09     1e-05       2      47 ..      17      60 ..      16      86 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.7e-09
  CarboxypepD_reg  2 isGrVtdasgapiagatVtvtnadtgtvastttdadGafrlrglpp 47
                     i+G+V d+s +p++ a+V ++    +++ +tt+  dG+f ++  +p
       EPA05099.1 17 ITGKVLDQSHKPVSDAKVQIQ--YPTETVETTSKGDGSFDISPTKP 60
                     9********************..79999************987666 PP

>> CarbopepD_reg_2  CarboxypepD_reg-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.5e-06    0.0089       1      40 [.      17      57 ..      17      67 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.5e-06
  CarbopepD_reg_2  1 isGtVvdketkeplpgatVyvkg..tkkgtvTdenGnFelkn 40
                     i+G+V+d++  +p+  a+V+++    ++ t++  +G+F ++ 
       EPA05099.1 17 ITGKVLDQSH-KPVSDAKVQIQYptETVETTSKGDGSFDISP 57
                     89*****875.8****999886521679999999****9963 PP

>> Big_1  Bacterial Ig-like domain (group 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   2.6e-05      0.16       8      39 ..      16      47 ..      12      59 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.6e-05
       Big_1  8 tltatvkDangnpvagatVtfsvsggalsass 39
                ++t  v D++++pv++a+V ++ + +++ ++s
  EPA05099.1 16 KITGKVLDQSHKPVSDAKVQIQYPTETVETTS 47
                58899*****************9997775332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1551  (0.0865079); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1646.07
//
Query:       EPA05100.1  [L=499]
Description: hypothetical protein BG20_I1919 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.1e-32  110.8   0.0    3.6e-31  108.7   0.0    1.8  1  GSDH      Glucose / Sorbosone dehydrogenase


Domain annotation for each model (and alignments):
>> GSDH  Glucose / Sorbosone dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.7   0.0     2e-35   3.6e-31       3     332 .]      39     362 ..      37     362 .. 0.86

  Alignments for each domain:
  == domain 1  score: 108.7 bits;  conditional E-value: 2e-35
                 -EEEEEE-TTS-EEEEET.TTEEEEEE.TTEE.EEEEE-.----STT-SEEEEEE-TTTTTS-EEEEEEEE-...TTSSEEEEEEEEE-SS..-EEEEE CS
        GSDH   3 hPwslaflpdgrlLvter.sGrlrlvkadgklkepiagvpevvakgqgGlldvalhpdfaenrlvYltyaeaeeekggagtavararlsedeaaledle 100
                 +P +++f+ d +++v er sG +rl+k +g l++++   ++v++ g+ G+l+++ +     + +vY+t a+  +++++ ++++ ++  +++  +l    
  EPA05100.1  39 SPTAMTFVGD-DIFVLERsSGVIRLIK-NGILQQELILDEAVANDGERGMLGITSDGF---KVYVYFTAADV-DAGKAIENRIYKYDWNGE--KLV-NP 128
                 799*****99.8889898799999999.9***99999999*************99984...45667776644.445566889999999887..888.57 PP

                 EEEEEE---TT-------EEE-TTS-EEEE---TT-....GGGGG-TT-SSSEEEEE-TTSSB-TT-TTTT-TTS-TTEEEE--SCE---EE-TTT--E CS
        GSDH 101 vifrqepkvesgahfGsrlafgpdgtLfvtvGdrsk....reeaqdlsselGkilrlnkdGsvpadnpfvgkagakpeiwsyGhRnpqGlaldpdtgeL 195
                 v++++ p+ +++ h+G+ ++    g+++  +Gd+++    +++  + +++   ilr+ + Gs                 +++G Rn  G+++dp tg+L
  EPA05100.1 129 VLLKTLPS-DNHFHNGGAMTSF-GGQIYAVIGDNGNygrlQNRDTEWKNDTSVILRIDPSGSY----------------YAMGIRNSFGITVDPITGNL 209
                 99999999.7789999999866.59***********77666666777899999********96................9******************* PP

                 EEEEE--SSSEEEEEE-TT-B--TTT-S......S-.....-S-TT..S---SEEETT---EEEEEEE........TTEEEEEETTTTEEEEEEEEEE. CS
        GSDH 196 wesEhGprggDelnlieaGknYGWplvsygeeYsgkkigesetreg..lekpvlvwtpsiapsglafytgdafpewkgdllvggLksqsllrleldeg. 291
                 w +E G    De+n i +  n GW ++  g + +++ i +  +  +  + +p +vw++ + p g++f t+++f+   ++++vg  ++ +l+r++l+e+ 
  EPA05100.1 210 WDTENGDDSLDEINFIPENFNSGWIEIM-GITKNQTLIDSLPKYGDfvYSNPEFVWEKPVCPTGITFSTSEKFT-QTDSVFVGDCNNGNLYRFNLNEDr 306
                 ************************9998.9999999999998888855689**********************6.5889****************9889 PP

                 .................EEEEEEEEEE.ESS-.-EEEEEE-TTS-EEEEE-TTTTT... CS
        GSDH 292 .................ekvveeerll.eelgeriRdVeqgpdGalyvltdeedgkllr 332
                                  +  +++e l+ + +g  i dVe+gpdG ly+++  ++gk++r
  EPA05100.1 307 tgfvfssfdlqdntlniG-ESNKEILFgTGFG-AITDVEEGPDGFLYIVSL-SNGKIYR 362
                 9********998776422.3444444456667.9**************988.7898886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (499 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.48
# Mc/sec: 3120.32
//
Query:       EPA05101.1  [L=37]
Description: hypothetical protein BG20_I1920 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 258.98
//
Query:       EPA05102.1  [L=53]
Description: hypothetical protein BG20_I1917 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.022   15.0   4.1      0.033   14.4   4.1    1.4  1  HALZ          Homeobox associated leucine zipper
      0.036   14.2   2.4      0.045   13.9   2.4    1.2  1  Herpes_BLRF2  Herpesvirus BLRF2 protein
      0.051   13.2   4.0      0.058   13.0   4.0    1.0  1  NRBF2         Nuclear receptor-binding factor 2, autophagy re
      0.077   12.8   2.1      0.084   12.7   1.9    1.3  1  DivIC         Septum formation initiator
       0.08   13.0   3.9      0.098   12.7   3.9    1.2  1  DUF5595       Domain of unknown function (DUF5595)
       0.12   12.8   7.6       0.06   13.8   5.2    1.7  2  ZapB          Cell division protein ZapB
       0.46   11.1   3.5       0.46   11.2   3.5    1.1  1  YabA          Initiation control protein YabA


Domain annotation for each model (and alignments):
>> HALZ  Homeobox associated leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   4.1   1.3e-05     0.033      15      41 ..      24      50 ..      19      52 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.3e-05
        HALZ 15 daLksdydsLkkenekLkaelqeLkek 41
                + L+ +   L+ en +Lk+el++Lkek
  EPA05102.1 24 EHLTIELRELQLENTALKTELAKLKEK 50
                678888889*****************9 PP

>> Herpes_BLRF2  Herpesvirus BLRF2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   2.4   1.8e-05     0.045       3      27 ..      22      46 ..      20      52 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.8e-05
  Herpes_BLRF2  3 tvEdlaaelakLkvENkaLkkklks 27
                   vE l+ el  L++EN aLk +l++
    EPA05102.1 22 VVEHLTIELRELQLENTALKTELAK 46
                  59*******************9976 PP

>> NRBF2  Nuclear receptor-binding factor 2, autophagy regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   4.0   2.3e-05     0.058      82     122 ..      10      50 ..       3      52 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.3e-05
       NRBF2  82 eeqatkiadLkrlvelLlaenerLrkenkqLkaekaRLqke 122
                 ee +  ++ L + ve+L+ e   L+ en  Lk+e a+L+++
  EPA05102.1  10 EETRIMLNGLDKVVEHLTIELRELQLENTALKTELAKLKEK 50 
                 556666788*****************************976 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.9   3.3e-05     0.084      22      54 ..      19      50 ..      10      53 .] 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.3e-05
                HHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXX CS
       DivIC 22 lkqeiaalqaelaklkaeneeLeaevkdLksde 54
                l++ ++ l+ el +l+ en +L+ e+++Lk ++
  EPA05102.1 19 LDKVVEHLTIELRELQLENTALKTELAKLK-EK 50
                667788889999999999999999999995.44 PP

>> DUF5595  Domain of unknown function (DUF5595)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   3.9   3.8e-05     0.098      31      71 ..       8      48 ..       1      51 [. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.8e-05
     DUF5595 31 FeeedaeleskLkelynvdeaqlesleeeekrLeeEierle 71
                 +ee   + + L+++++    +l++l+ e++ L++E+++l+
  EPA05102.1  8 LDEETRIMLNGLDKVVEHLTIELRELQLENTALKTELAKLK 48
                455556677888999999999*****************986 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.35   8.9e+02      31      60 ..       2      17 ..       1      24 [. 0.43
   2 ?   13.8   5.2   2.3e-05      0.06      12      49 ..      22      52 ..      11      53 .] 0.56

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.35
        ZapB 31 keeneelkeenreleeeneqlkeereawqe 60
                +e+ + l e              e   + +
  EPA05102.1  2 QEKESDLDE--------------ETRIMLN 17
                344444444..............4444444 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 2.3e-05
        ZapB 12 kiqkaidtitlLqmeieeLkeeneelkeenreleeene 49
                 ++       +L  e++eL+ en +lk e ++l+e+n+
  EPA05102.1 22 VVE-------HLTIELRELQLENTALKTELAKLKEKNK 52
                444.......5555555555555555555555555554 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   3.5   0.00018      0.46      21      59 ..      13      51 ..       1      53 [] 0.67

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00018
                HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXX CS
        YabA 21 leeleelkeelaelleenaeLeleneklrerleeeekke 59
                   l+ l + +++l+ e +eL+len+ l+++l++ ++k+
  EPA05102.1 13 RIMLNGLDKVVEHLTIELRELQLENTALKTELAKLKEKN 51
                345667777788888888888888888888885554443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       875  (0.0488036); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 366.87
//
Query:       EPA05103.1  [L=283]
Description: fibronectin type III domain protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-32  110.1  18.8    8.6e-13   48.5   3.0    3.2  3  fn3              Fibronectin type III domain
  ------ inclusion threshold ------
      0.028   14.8   4.9       0.13   12.7   1.3    2.5  2  PilX             Type IV pilus assembly protein PilX C-term
      0.037   13.2   7.4      0.031   13.4   2.2    2.2  2  SPESP1           Sperm equatorial segment protein 1
      0.045   14.2   3.8       0.66   10.4   0.8    2.6  2  Fimbrillin_C     Major fimbrial subunit protein type IV, Fimb
        0.1   12.6   0.4        6.3    6.9   0.0    2.8  3  Collagen_bind_2  Putative collagen-binding domain of a collag
       0.12   12.0  17.4      0.064   12.9  13.7    1.9  2  DUF4249          Domain of unknown function (DUF4249)


Domain annotation for each model (and alignments):
>> fn3  Fibronectin type III domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.5   3.0   2.9e-16   8.6e-13       1      83 [.      31     111 ..      31     113 .. 0.88
   2 !   37.6   3.6   7.2e-13   2.2e-09       2      81 ..     131     212 ..     130     216 .. 0.84
   3 !   32.7   0.1   2.4e-11   7.2e-08       2      41 ..     234     274 ..     233     282 .. 0.92

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 2.9e-16
                 TCECEEEEEEESSSEEEEEEE-CS.SSSSTEEEEEEEEEETTSTSTEEEEEECSTSSEEEEESSSTTEEEEEEEEEEETSEEEE CS
         fn3   1 saPsnlsvsevtstsltvsWeppk.dgggpitgYeveyrekgseeewneftvprtttsvtltgLkpgteYevrVqavngggegp 83 
                 s+P+++++++++st++++ W+ p+ dg +pitgY+ve+++ ++  +++  +   tt  +  tgL+ gt Y+ +V a+n +g++ 
  EPA05103.1  31 SSPTDITATAISSTQINIFWNTPSnDGASPITGYKVEVKSGTGS-YSVLGNTVDTT--YSHTGLTTGTSYTYKVSAINSVGTSV 111
                 68************************************998555.35656666666..**********************9876 PP

  == domain 2  score: 37.6 bits;  conditional E-value: 7.2e-13
                 CECEEEEEEESSSEEEEEEE-CS.SSSSTEEEEEEEEEETTSTSTEEEEEECSTSSEEEEESSSTTEEEEEEEEEEETSE.E CS
         fn3   2 aPsnlsvsevtstsltvsWeppk.dgggpitgYeveyrekgseeewneftvprtttsvtltgLkpgteYevrVqavnggg.e 81 
                 +P+nl+  + ++ ++t+ W++p+ +gg pitgY++eyr  +++  +   +  +t+t++  ++L  ++ Y+ r++++++ g  
  EPA05103.1 131 KPTNLTGYAASPIKATLFWNAPTnNGGYPITGYKIEYRVNSGTYTELISNTASTSTTYSHNNLVTNSVYTYRIYTITTFGtS 212
                 7************************************8776665344444444445********************998733 PP

  == domain 3  score: 32.7 bits;  conditional E-value: 2.4e-11
                 CECEEEEEEESSSEEEEEEE-CS.SSSSTEEEEEEEEEETT CS
         fn3   2 aPsnlsvsevtstsltvsWeppk.dgggpitgYeveyrekg 41 
                 aP+nl+ s+v++t++++ W++p  +gg+pitgY++ey++ +
  EPA05103.1 234 APTNLTSSAVSPTQVNLFWSAPAnNGGSPITGYKIEYKSGS 274
                 8************************************8764 PP

>> PilX  Type IV pilus assembly protein PilX C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.2     0.047   1.4e+02      17      71 ..      44     106 ..      26     122 .. 0.62
   2 ?   12.7   1.3   4.3e-05      0.13      17      83 ..     141     222 ..     115     223 .. 0.68

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.047
        PilX  17 s.....WttataataatglaavakqP.rYiIE.........ylgdnaagssenltsatsaayvYRITAr.g 71 
                 +     W+t        +++++a+    Y +E          lg + + + ++++  t ++y Y++ A+ +
  EPA05103.1  44 TqinifWNT--------PSNDGASPItGYKVEvksgtgsysVLGNTVDTTYSHTGLTTGTSYTYKVSAInS 106
                 144455766........444444433456666666666665666666666666777888888888888753 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 4.3e-05
        PilX  17 s.......WttataataatglaavakqPrYiIE.....ylgdnaagssen......ltsatsaayvYRITArgfGasantvvvLQ 83 
                 s       W+   + ++++++ +++   +Y ++     +l +n+a++s++       t++  + ++Y IT  g++ ++++ vv+Q
  EPA05103.1 141 SpikatlfWNA-PTNNGGYPITGYK--IEYRVNsgtytELISNTASTSTTyshnnlVTNSVYTYRIYTITTFGTSSTPSSEVVVQ 222
                 04445555766.2333333333333..355555888887777777777778998989999999999999999***********99 PP

>> SPESP1  Sperm equatorial segment protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.2     0.025        75      52     109 ..      98     155 ..      83     157 .. 0.86
   2 ?   13.4   2.2   1.1e-05     0.031      41     109 ..     189     258 ..     179     260 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.025
      SPESP1  52 vsklkellthgdastendvlinpvseettafptsgftleiekkkrtestafWsikPnn 109
                 + k+ ++ + g++++ ++v  +p+s  t + p +   l      + ++t fW    nn
  EPA05103.1  98 TYKVSAINSVGTSVASTEVSATPTSSSTGSLPGKPTNLTGYAASPIKATLFWNAPTNN 155
                 45677788889999999***********9***99999999999999******987776 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 1.1e-05
      SPESP1  41 spnnvdsiepkvsklkellthgdast.endvlinpvseettafptsgftleiekkkrtestafWsikPnn 109
                 s nn+ +    + ++ +++t g++st  ++v+++p s  tt+ p +   l ++   +t++  fWs   nn
  EPA05103.1 189 SHNNLVTNSVYTYRIYTITTFGTSSTpSSEVVVQPKSSSTTTVPGAPTNLTSSAVSPTQVNLFWSAPANN 258
                 6667777777788889999***9999789************************************98887 PP

>> Fimbrillin_C  Major fimbrial subunit protein type IV, Fimbrillin, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1     0.023        68      31      62 ..      90     121 ..      52     133 .. 0.74
   2 ?   10.4   0.8   0.00022      0.66       6      58 ..     170     218 ..     163     239 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.023
  Fimbrillin_C  31 gvvRNniYklnvtsiseiGdpedepevtgdpd 62 
                   g    + Y+ +v++i+++G+++ + ev+ +p 
    EPA05103.1  90 GLTTGTSYTYKVSAINSVGTSVASTEVSATPT 121
                   5555578************9988766554443 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00022
  Fimbrillin_C   6 GvayYtvlikhfddeetpqkklgrygvvRNniYklnvtsiseiGdpedepevt 58 
                       Yt li ++  + t   ++   + v N++Y+ ++  i+++G+++  p  +
    EPA05103.1 170 NSGTYTELISNTASTST---TYSHNNLVTNSVYTYRIYTITTFGTSST-PSSE 218
                   55567777775555544...5899999*****************9888.4443 PP

>> Collagen_bind_2  Putative collagen-binding domain of a collagenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0    0.0021       6.3      35      67 ..      32      64 ..      28      79 .. 0.83
   2 ?   -2.4   0.0       1.6   4.8e+03      45      64 ..     141     160 ..     129     189 .. 0.64
   3 ?    2.5   0.0     0.047   1.4e+02      34      65 ..     233     264 ..     229     279 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0021
  Collagen_bind_2 35 rpitvdlsklsgkkvkasWfdPrtGeltkigev 67
                      p++++ + +s++++++ W  P++  +++i  +
       EPA05103.1 32 SPTDITATAISSTQINIFWNTPSNDGASPITGY 64
                     68899******************9999988744 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.6
  Collagen_bind_2  45 sgkkvkasWfdPrtGeltki 64 
                      s  k+++ W  P ++   +i
       EPA05103.1 141 SPIKATLFWNAPTNNGGYPI 160
                      55566677777776554444 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.047
  Collagen_bind_2  34 grpitvdlsklsgkkvkasWfdPrtGeltkig 65 
                      g p++++ s +s ++v++ W  P ++  ++i 
       EPA05103.1 233 GAPTNLTSSAVSPTQVNLFWSAPANNGGSPIT 264
                      88999999***************998777765 PP

>> DUF4249  Domain of unknown function (DUF4249)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9  13.7   2.1e-05     0.064      39     206 ..      42     207 ..      35     225 .. 0.71
   2 ?    0.2   0.1      0.15   4.6e+02     110     130 ..     223     242 ..     220     278 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.1e-05
     DUF4249  39 dtteirlsrsvpvsesdsieevkavtdAtVtlyvnegqeyelsetkagyyssfrlkpgdtyrLeittpdgkeyvsaettvpsppp..eidtvsaeeste 135
                 ++t+i +++++p  ++d++++   +t+ +V++  ++g+  +l +t +++ys + l +g +y+ ++++ +   ++ a+t+v ++p+  ++ ++ ++  + 
  EPA05103.1  42 SSTQINIFWNTP--SNDGASP---ITGYKVEVKSGTGSYSVLGNTVDTTYSHTGLTTGTSYTYKVSAINSVGTSVASTEVSATPTssSTGSLPGKPTNL 135
                 567888888888..4455555...78*********77666888888889999*****************************999876666666665554 PP

     DUF4249 136 dne..egyeitvdlkDppneenY........Yrwssielcyetefskvlnlast.psrsddsdsefldtelsgdklskykpi 206
                 + +    ++ t+ ++ p+n+  Y        Yr+     +  t+++ +   ++t ++++  s+++++ +++++ ++  y+ +
  EPA05103.1 136 TGYaaSPIKATLFWNAPTNNGGYpitgykieYRV-----NSGTYTELI---SNTaSTSTTYSHNNLVTNSVYTYRI--YTIT 207
                 4449989999999999*******99994444444.....212222222...2444445555666666666665555..2332 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.15
     DUF4249 110 eyvsaettvpspppeidtvsa 130
                 +++s++ttvp +p+++ t sa
  EPA05103.1 223 PKSSSTTTVPGAPTNL-TSSA 242
                 5689999999988733.2222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1858.99
//
Query:       EPA05104.1  [L=142]
Description: hypothetical protein BG20_I1918 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0095   16.4   0.0      0.012   16.0   0.0    1.2  1  MG2       MG2 domain


Domain annotation for each model (and alignments):
>> MG2  MG2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0     7e-07     0.012      13      95 ..      58     138 ..      47     139 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 7e-07
                 TT-EEEEEEEEESTTCSB---.EEEEEEEE-TTSSEEEEEEEEE-CTTEEEEEEE--TT--SEEEEEEEEECSTTT-EEEEEEE CS
         MG2  13 PgetVslkallrdetlqglak.lplkltirdpdgkevkelplatdetggaesefalpeaaklGeysvelsadsaeeslssgsfr 95 
                 P+ + ++++++     +  ++ +++ ++i +pd+ + +  +  ++++g + + f+++++++ G y+v l  + ++ +l+++sf+
  EPA05104.1  58 PHSKYNYEHIIISGYVEDYTRgDEILVVIIHPDQSQNEIHT-HATKKGEIYTLFDISNDSQIGVYNVIL--KYRDAELATTSFE 138
                 77777888888887777777779999********9999888.66677778889****************..6677777888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.31s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 932.54
//
Query:       EPA05105.1  [L=366]
Description: hypothetical protein BG20_I2480, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-12   47.7   0.1      2e-05   25.0   0.0    4.3  5  MG2             MG2 domain
  ------ inclusion threshold ------
      0.032   14.7   0.8       0.59   10.6   0.1    3.1  2  Arrestin_C      Arrestin (or S-antigen), C-terminal domain
       0.11   11.1   0.0        1.5    7.4   0.0    2.1  2  Glyco_hydro_66  Glycosyl hydrolase family 66
       0.15   12.1   0.0       0.36   10.8   0.0    1.6  1  GvpO            Gas vesicle synthesis protein GvpO
       0.72   10.1   4.0         15    5.9   0.3    3.3  3  He_PIG          Putative Ig domain


Domain annotation for each model (and alignments):
>> MG2  MG2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.22   7.8e+02      32      70 ..      17      53 ..       8      58 .. 0.75
   2 ?   -2.8   0.0       2.6   9.4e+03      72      87 ..      70      85 ..      63      90 .. 0.71
   3 !   25.0   0.0   5.4e-09     2e-05       3      96 .]     106     201 ..     104     201 .. 0.80
   4 !    5.0   0.0    0.0091        33       3      20 ..     216     233 ..     214     238 .. 0.88
   5 !   10.7   0.0   0.00015      0.55      54      91 ..     275     310 ..     269     315 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.22
                --EEEEEEEE-TTSSEEEEEEEEE-CTTEEEEEEE--TT CS
         MG2 32 aklplkltirdpdgkevkelplatdetggaesefalpea 70
                 + +++++++ pdg ++++    ++++  ++ ++++p +
  EPA05105.1 17 GGSSVQISLTIPDGSVINSGATINNQR--FSWSWTTPIT 53
                4578999**********9999666666..6666666644 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.6
                -SEEEEEEEEECSTTT CS
         MG2 72 klGeysvelsadsaee 87
                  G y++ + + sa++
  EPA05105.1 70 NYGIYKIHVTTASANK 85
                5788999986666555 PP

  == domain 3  score: 25.0 bits;  conditional E-value: 5.4e-09
                 EEEES-SEE-TT-EEEEEEEEES..TTCSB---EEEEEEEE-TT..SSEEEEEEEEE-CTTEEEEEEE--TT-.-SEEEEEEEEECSTTT-EEEEEEEE CS
         MG2   3 fvytDRglYrPgetVslkallrd..etlqglaklplkltirdpd..gkevkelplatdetggaesefalpeaa.klGeysvelsadsaeeslssgsfrV 96 
                  v t++ lY++ge++++ + +    + +qgl  +++++ + d +   k+++e ++  ++ g+++s f+lp +    Gey++++     ++++++++f+V
  EPA05105.1 106 IVSTEKSLYKAGEKLKVVGNIIAkeQLSQGLIPQRVTVHVLDGKfpYKQIFESTVYPESGGTFQSLFELPVTVfTEGEYKIKA---IYSGKTAEATFSV 201
                 6789**********99876664433888888888888888887644689999999999999*********998356*******...6677777777766 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.0091
                 EEEES-SEE-TT-EEEEE CS
         MG2   3 fvytDRglYrPgetVslk 20 
                  + tD+  Y Pg+tV+++
  EPA05105.1 216 LLATDKSEYYPGDTVNIS 233
                 688************987 PP

  == domain 5  score: 10.7 bits;  conditional E-value: 0.00015
                 EE-CTTEEEEEEE--TT.--SEEEEEEEEECSTTT-EEE CS
         MG2  54 atdetggaesefalpea.aklGeysvelsadsaeeslss 91 
                 + +++g+++++f++p++ ++lG+y+v++   +a+ ++ s
  EPA05105.1 275 RPSSSGSFSHQFQIPNTqSSLGSYEVTV---DAGFATKS 310
                 66889*********9762689*******...55555555 PP

>> Arrestin_C  Arrestin (or S-antigen), C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.15   5.5e+02       9      30 ..     107     128 ..     103     146 .. 0.79
   2 ?   10.6   0.1   0.00017      0.59       2      48 ..     210     254 ..     209     345 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.15
                 EEES-SEEETT--EEEEEEEEE CS
  Arrestin_C   9 aslpkkgyvpGetipvtvkidn 30 
                 +s++k+ y  Ge+++v  +i  
  EPA05105.1 107 VSTEKSLYKAGEKLKVVGNIIA 128
                 899************9999874 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00017
                 ---EEEEEEES-SEEETT--EEEEEEEEE-SSSEEEEEEEEEEEEEE CS
  Arrestin_C   2 dgkvsleaslpkkgyvpGetipvtvkidndskkkvkkikvslvqhvd 48 
                 d k+sl + ++k+ y+pG+t++++ k  +++   ++k  vs++q+vd
  EPA05105.1 210 DAKLSLLLATDKSEYYPGDTVNISGK--PNKLIYIEKFDVSVIQKVD 254
                 7799999************9877665..7788889*********998 PP

>> Glyco_hydro_66  Glycosyl hydrolase family 66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.024        86       1      85 [.     109     201 ..     109     212 .. 0.64
   2 ?    7.4   0.0   0.00042       1.5       1      73 [.     219     303 ..     219     319 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.024
                     ES-SSB-TTS-EEEE-.EEE--SSS-EE..EEEEEEEETTEEEEEE.....E-TT-EEE--TTSEEE-TTSS-..EEEEEEEEE-TT--EEEEE CS
                     xxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxx RF
  Glyco_hydro_66   1 tDkarYkpGeevkltievknkteseisg..svevrvyhlekvvkas.....rleeealstesfewtaPsedfk..GYlvevyakdaagealesg 85 
                     t+k+ Yk+Ge+ k+  +  +k++  ++g  + +v+v  l+ +   +     ++ +e+ +t +  +++P + f+   Y ++++ + +  ea+ s 
      EPA05105.1 109 TEKSLYKAGEKLKVVGNIIAKEQ-LSQGliPQRVTVHVLDGKFPYKqifesTVYPESGGTFQSLFELPVTVFTegEYKIKAIYSGKTAEATFSV 201
                     78********9998765444444.2333355666666666555444446668888888999999999999998766888765555555555444 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00042
                     ES-SSB-TTS-EEEE-.EEE--SSS-EE.EEEEEE.EETTEEEEEE............E-TT-EEE--TTSEEE-TTSS-..EEEEEEE CS
                     xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx.xxxxxxxxxx............xxxxxxxxxxxxxxxxxxxxxx..xxxxxxx RF
  Glyco_hydro_66   1 tDkarYkpGeevkltievknkteseisg.svevrv.yhlekvvkas............rleeealstesfewtaPsedfk..GYlvevy 73 
                     tDk+ Y pG++v+++  + n   + i   +++v+v ++++  v +             +++++++++ s ++++P+++ +  +Y v v 
      EPA05105.1 219 TDKSEYYPGDTVNISG-KPN---KLIYIeKFDVSViQKVDGSVTCGtffcgkhlgpvtSIRPSSSGSFSHQFQIPNTQSSlgSYEVTVD 303
                     8*************99.222...223333666665145666675557888888888888889999999999999988776667877765 PP

>> GvpO  Gas vesicle synthesis protein GvpO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0    0.0001      0.36      58      75 ..     287     304 ..     284     310 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0001
        GvpO  58 rvPdttdilasYevelde 75 
                 ++P+t++ l+sYev++d+
  EPA05105.1 287 QIPNTQSSLGSYEVTVDA 304
                 79**************97 PP

>> He_PIG  Putative Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1      0.02        70      14      47 ..      35      83 ..      22      85 .. 0.63
   2 ?   -1.6   0.0      0.89   3.2e+03      22      31 ..     229     238 ..     228     239 .. 0.86
   3 ?    5.9   0.3    0.0042        15      21      44 ..     278     304 ..     276     308 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.02
      He_PIG 14 sGLtLdsstGtitGt................pdqtvapGsytftVtatdg 47
                sG t+++   + ++t                +++t + G y ++Vt  ++
  EPA05105.1 35 SGATINNQRFSWSWTtpitekplaikqddrsVTKT-NYGIYKIHVTTASA 83
                66677776666677754444444444444445666.66********8766 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.89
      He_PIG  22 tGtitGtpdq 31 
                 t  i+G p++
  EPA05105.1 229 TVNISGKPNK 238
                 788*****96 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.0042
      He_PIG  21 stGtitGt...pdqtvapGsytftVta 44 
                 s+G+++ +   p++ +  Gsy +tV+a
  EPA05105.1 278 SSGSFSHQfqiPNTQSSLGSYEVTVDA 304
                 677777778889999999*******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2626.08
//
Query:       EPA05106.1  [L=136]
Description: hypothetical protein BG20_I2408 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 881.27
//
Query:       EPA05107.1  [L=105]
Description: hypothetical protein BG20_I2409, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-21   76.5   0.1    2.3e-21   76.1   0.1    1.1  1  UPF0047   Uncharacterised protein family UPF0047


Domain annotation for each model (and alignments):
>> UPF0047  Uncharacterised protein family UPF0047
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.1   0.1   1.3e-25   2.3e-21       1      75 [.      28     104 ..      28     105 .] 0.97

  Alignments for each domain:
  == domain 1  score: 76.1 bits;  conditional E-value: 1.3e-25
                 E-HHHHHHHHHHHT.SEEEEEEEESSSSEEEEEEESSSHHHHHHHHHHHHHHSTTT...T-GGGTTS..THHHHHHHH CS
     UPF0047   1 diteeveeavkesgvkeGlvlvfsrhttasltinEnadpdvqeDleealeklvpee...eYrhnaegpdnadaHlkss 75 
                 +it++++++v +s+++eGl+lv ++h +as++in++ ++++++D+e++le l+p+e   +Y+hn+ g+dnadaHlk+ 
  EPA05107.1  28 NITPDIRKLVLKSKIQEGLCLVNAMHISASVFINDD-ESGLHQDFEKWLESLAPHEpinQYKHNNTGEDNADAHLKRQ 104
                 69**********************************.******************9999****************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 718.25
//
Query:       EPA05108.1  [L=163]
Description: eRF1 domain 1, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-20   72.2   0.3    4.8e-20   71.9   0.3    1.1  1  eRF1_1    eRF1 domain 1


Domain annotation for each model (and alignments):
>> eRF1_1  eRF1 domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.9   0.3   2.7e-24   4.8e-20      13     121 ..       8     118 ..       2     125 .. 0.88

  Alignments for each domain:
  == domain 1  score: 71.9 bits;  conditional E-value: 2.7e-24
                 CCEEEEEE-SCHHHHHHHHHCHTTHEEEEEEEECHHH.......-.-CEEEEEEEEEEEEEEECTTSSEEEEEEEEEEG.GGG--TTSEEEEEE-TTSE CS
      eRF1_1  13 sgsvtLipeddedlwhlynliapgdsvrastvrkvqresstgsre.servklkLtikvekvdfdkdagvlrisGkviee.nehvklgafhtldlelkrp 109
                  +s++++ped++dl +l  +i++gd++   t+r ++ e+     +  er+++++ ++vek+ +d   ++lri G++ e+ ne v+ g++h++ l++++ 
  EPA05108.1   8 DNSISVMPEDSDDLLTLRRVIREGDRIVGDTTRVIKLEKDYARPDkGERIRVRIALNVEKISLDDVLDRLRIGGTILESsNESVPHGSHHSFILKINDG 106
                 579********************************997555444448*****************************8752677**************** PP

                 EEEEECEESHHH CS
      eRF1_1 110 ftiikeewdsfa 121
                 +ti+k++w  + 
  EPA05108.1 107 ITITKKKWLPIE 118
                 ********7765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1049.97
//
Query:       EPA05109.1  [L=152]
Description: hypothetical protein BG20_I1131 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1075.12
//
Query:       EPA05110.1  [L=332]
Description: putative rRNA pseudouridine synthase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-25   89.8   0.2    3.2e-15   56.8   0.0    3.3  2  TruB_N    TruB family pseudouridylate synthase (N terminal do
    1.1e-19   70.3   0.0    5.6e-19   68.0   0.0    2.2  2  TruB_C_2  tRNA pseudouridylate synthase B C-terminal domain
    1.2e-19   70.0   0.1    2.1e-19   69.3   0.1    1.4  1  PUA       PUA domain
    4.4e-12   45.9   0.0    1.3e-11   44.3   0.0    1.8  2  DKCLD     DKCLD (NUC011) domain
  ------ inclusion threshold ------
       0.13   12.5   0.0          1    9.7   0.0    2.4  2  UPF0113   UPF0113 PUA domain


Domain annotation for each model (and alignments):
>> TruB_N  TruB family pseudouridylate synthase (N terminal domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.8   0.0   8.9e-19   3.2e-15       1      52 [.      57     108 ..      57     113 .. 0.95
   2 !   26.9   0.0   1.5e-09   5.3e-06      73     149 .]     111     170 ..     107     170 .. 0.96

  Alignments for each domain:
  == domain 1  score: 56.8 bits;  conditional E-value: 8.9e-19
                 HHHTT-S-EEESS---TT-EEEEEEEEGGGGGGHHHCTTS-EEEEEEEEETE CS
      TruB_N   1 krllkakkvGhtGtLDplatGvLvvavgeaTklleylleadKeYeatirlga 52 
                 kr+lk+ k+Gh+GtLDp+++GvL++++geaTk+l +ll  +KeY+a  r++ 
  EPA05110.1  57 KRILKIPKIGHSGTLDPQVSGVLPLGLGEATKALGVLLYGPKEYHALGRFHS 108
                 89********************************************999975 PP

  == domain 2  score: 26.9 bits;  conditional E-value: 1.5e-09
                 -HHHHHHHHHHC-EEE---------------------------------EEEEEEEEEEEEEEEEEEEEEESTTTTH CS
      TruB_N  73 teekleevlkkftGeieqvppmySAvkvnGkrlyelaregeeverkkrkvtiyelelleveepevelevecskGtYi 149
                 ++ekleevl+ f+Gei q pp+ SAv                  r++r+ tiyele+le +e+ +  +v c++GtYi
  EPA05110.1 111 SKEKLEEVLDLFRGEIFQKPPQRSAVL-----------------RQTRTRTIYELEVLEQKERLLLARVLCEAGTYI 170
                 789***********************9.................99******************************8 PP

>> TruB_C_2  tRNA pseudouridylate synthase B C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       0.8   2.9e+03      35      49 ..       2      18 ..       1      37 [. 0.46
   2 !   68.0   0.0   1.6e-22   5.6e-19       1      63 [.     171     237 ..     171     238 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.8
                -HHHHHHHHHHHHT..- CS
    TruB_C_2 35 tledLedavllyke..d 49
                tl++L++++ + ++  d
  EPA05110.1  2 TLKQLQNLIVIDQDitD 18
                66666665543333432 PP

  == domain 2  score: 68.0 bits;  conditional E-value: 1.6e-22
                 HHHHHHHHHHTTS-EEEEEEEEEEETTE.GG-..B-HHHHHHHHHHHHT..--H.HHHHEEEGGGGG CS
    TruB_C_2   1 RtLcdDiGeaLgcgAhveeLRRtrvgpf.deedmvtledLedavllyke..dee.LdrlllPlesal 63 
                 R+L  D+Ge Lg gA ++eLRRtrv +f + + +vtl++L++a++l+ke  de+ L ++++P+e al
  EPA05110.1 171 RKLFYDMGEILGPGATMIELRRTRVDQFyESDGLVTLHELANAYALWKEknDETkLLSMIKPIEYAL 237
                 9**************************9888889***************965559**********98 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.3   0.1   5.8e-23   2.1e-19       2      73 ..     242     313 ..     241     314 .. 0.96

  Alignments for each domain:
  == domain 1  score: 69.3 bits;  conditional E-value: 5.8e-23
                 EEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEEEE CS
         PUA   2 rvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveierv 73 
                  vv+ d+Av+al++ga+L +pG++++  d+++gd+Vai++++ge+va++ +++s ee++++++g + e+ r+
  EPA05110.1 242 SVVIRDSAVDALCHGAQLAIPGILQISPDLKKGDIVAIYTQKGEAVALAESMMSEEEIRDATKGYAFETNRI 313
                 79**************************************************************99888876 PP

>> DKCLD  DKCLD (NUC011) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   0.0   3.7e-15   1.3e-11       7      58 .]       2      53 ..       1      53 [. 0.97
   2 ?   -2.1   0.0       1.2   4.2e+03       8      37 ..     210     239 ..     208     256 .. 0.67

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 3.7e-15
                ...XXX-EEESS-----TTSS--GGG--HHHHHHTEEEEEEE-SSS-HHHHH CS
       DKCLD  7 lLknydkllvrtehytplpaGssPlkRpieeyikyGvinLDKPsnPsSHEVV 58
                 Lk+ ++l+v  +  t+  +G+   kR++e++++yG+i LDKP +P+SHE V
  EPA05110.1  2 TLKQLQNLIVIDQDITDDAYGTYYDKRTLEQLLDYGLIILDKPPGPTSHETV 53
                699***********************************************87 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.2
                 ..XXX-EEESS-----TTSS--GGG--HHH CS
       DKCLD   8 LknydkllvrtehytplpaGssPlkRpiee 37 
                 L n   l+  ++ +t+l +  +P++  ++e
  EPA05110.1 210 LANAYALWKEKNDETKLLSMIKPIEYALSE 239
                 666777777777777776666666655554 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.46   1.7e+03      60      76 .]     156     172 ..     143     172 .. 0.77
   2 ?    9.7   0.0   0.00029         1       2      55 ..     243     296 ..     242     311 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.46
     UPF0113  60 gkivvknlaDiGeYlRr 76 
                 + ++++ l+  G+Y+R+
  EPA05110.1 156 RLLLARVLCEAGTYIRK 172
                 55667789999****96 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00029
     UPF0113   2 vvvkekaeklFLYGrdvlkesilkitesvkenqvvvVlnengeplGiGkirkdt 55 
                 vv++ +a   +  G ++   +il+i++++k+++ v+++ ++ge+++++ +  + 
  EPA05110.1 243 VVIRDSAVDALCHGAQLAIPGILQISPDLKKGDIVAIYTQKGEAVALAESMMSE 296
                 677777888888888888899**************************9997766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2185.94
//
Query:       EPA05111.1  [L=182]
Description: hypothetical protein BG20_I1134 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.05   13.6   0.0      0.096   12.6   0.0    1.4  1  TIR-like  Predicted nucleotide-binding protein containing TIR
       0.08   12.8   0.2       0.12   12.2   0.2    1.2  1  DUF473    Protein of unknown function (DUF473)


Domain annotation for each model (and alignments):
>> TIR-like  Predicted nucleotide-binding protein containing TIR-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.1e-05     0.096       8      48 ..     109     150 ..     105     162 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.1e-05
    TIR-like   8 edeeaaeevkelLeklglepiileeqvnkg.ktiiekleeal 48 
                 + + +  ev+e+L+k+++e  i++++++k  ++i+++ + +l
  EPA05111.1 109 QRTPVVYEVEEILKKYQVEYKIWHDKIKKNvHMIFDNYKVKL 150
                 6678899*********************99999999877665 PP

>> DUF473  Protein of unknown function (DUF473)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   1.4e-05      0.12      50      99 ..      80     129 ..      78     141 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.4e-05
      DUF473  50 vsleDltkGteGiiaevlsveistkrvvessesfieErEttvarvqlkll 99 
                 v++ Dl+kG  Gi aev   +   +++v++   ++ E E +  + q++++
  EPA05111.1  80 VRMVDLKKGLIGIHAEVEVSRDYLQHLVSQRTPVVYEVEEILKKYQVEYK 129
                 7789**************999999999999999999********999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       758  (0.0422779); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1400.47
//
Query:       EPA05112.1  [L=248]
Description: ribosomal protein S5 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.3e-22   77.9   0.8    7.9e-22   77.0   0.8    1.5  1  Ribosomal_S5    Ribosomal protein S5, N-terminal domain
    3.6e-16   58.4   0.3    8.4e-16   57.2   0.1    1.7  2  Ribosomal_S5_C  Ribosomal protein S5, C-terminal domain
  ------ inclusion threshold ------
        1.4    9.0  11.6        2.1    8.4  11.6    1.3  1  RhlB            ATP-dependent RNA helicase RhlB


Domain annotation for each model (and alignments):
>> Ribosomal_S5  Ribosomal protein S5, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.0   0.8   1.3e-25   7.9e-22       1      64 [.      97     160 ..      97     161 .. 0.98

  Alignments for each domain:
  == domain 1  score: 77.0 bits;  conditional E-value: 1.3e-25
                   XEEEEEEEEEEEEEETTEEEEEEEEEEEEEETTTEEEEEEEEESSHHHHHHHHHHHHHHTEEE- CS
  Ribosomal_S5   1 lkekvlkikrvqkvtkgGrrtsfsalvvvGdgnGlvGlGvgkakevatAirkAiekAkknlvpv 64 
                   lk++v+++  +qk+t+ G+ t+f+a+v++G++nG++G+G gk+k+++ Ai+kA+++A +n+ p+
    EPA05112.1  97 LKSEVVDVGIIQKMTSNGQSTRFKAIVATGNQNGYLGIGQGKSKQMRIAIEKATNQALLNVSPI 160
                   799*********************************************************9998 PP

>> Ribosomal_S5_C  Ribosomal protein S5, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.71   4.3e+03      52      62 ..     147     157 ..     138     160 .. 0.77
   2 !   57.2   0.1   1.4e-19   8.4e-16       2      62 ..     183     244 ..     182     247 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.71
                     HHHHHHHHHHT CS
  Ribosomal_S5_C  52 vkAtfeALkkl 62 
                      kAt +AL + 
      EPA05112.1 147 EKATNQALLNV 157
                     58999999875 PP

  == domain 2  score: 57.2 bits;  conditional E-value: 1.4e-19
                     EEETTEEEEEEE--TT--EES-HHHHHHHHHHT--SEE---BS.-SSHHHHHHHHHHHHHHT CS
  Ribosomal_S5_C   2 gkfgavkvllkpaprGtGiiaggavravlelaGikDvlakslg.srnpinvvkAtfeALkkl 62 
                     gk g+v++ ++paprG G++agg ++ +lelaG kD ++ ++g + +   + kA++++Lk++
      EPA05112.1 183 GKGGSVTIEIIPAPRGLGLVAGGKIKRLLELAGLKDAWTTAKGaTPTMNSTSKAILDCLKQT 244
                     899****************************************888888899********98 PP

>> RhlB  ATP-dependent RNA helicase RhlB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4  11.6   0.00036       2.1      57      99 ..      15      54 ..       3      76 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00036
        RhlB 57 gggksgpggasrsgsgggrresagadgkprpprrkprverevd 99
                 gg+ g gg  r g+gg r+  +   gkp    r+pr e+e +
  EPA05112.1 15 PGGRGGSGG--RGGPGG-RGPPTYGGGKPGGQTRRPRREQEEE 54
                367777777..888888.99999999***********998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1595.82
//
Query:       EPA05113.1  [L=436]
Description: FAD dependent oxidoreductase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-41  143.7   0.0    1.4e-41  143.3   0.0    1.1  1  DAO            FAD dependent oxidoreductase
    2.2e-16   59.5   0.0    1.1e-09   37.4   0.0    2.1  2  Mqo            Malate:quinone oxidoreductase (Mqo)
     0.0016   18.7   0.0     0.0039   17.4   0.0    1.7  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
     0.0024   18.4   3.3        1.4    9.5   0.0    3.6  4  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
     0.0026   17.0   0.7        1.4    8.1   0.1    2.3  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
       0.13   12.9   4.3       0.33   11.5   0.2    3.2  3  PepSY_like     Putative beta-lactamase-inhibitor-like, PepSY-


Domain annotation for each model (and alignments):
>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.3   0.0   4.5e-45   1.4e-41       1     344 [.       6     398 ..       6     405 .. 0.79

  Alignments for each domain:
  == domain 1  score: 143.3 bits;  conditional E-value: 4.5e-45
                 EEEEECTSHHHHHHHHHHH.HTT...EEEEESSSSTTSSGGGSSEEEEESSSSTHHS.THHHHHHHHHHHHHHHHHHHHHSSTTSEEEEEEEEEESSHH CS
         DAO   1 dvviiGGGiiGlstAyeLa.rrg...VtllekgdiagsgaSgrnsgllhsglrylpe.aselarlslealeelreleeelgididyrrtGllslaadee 94 
                 dvviiGGGi G+s+ y+L+       ++++e+++ ++ ++Sgrn+g +h+ + y pe +  +a+ +++++e+++e+++  +  i++++ G++ +a d++
  EPA05113.1   6 DVVIIGGGILGSSISYFLSfLNTtkkILVIEQAHSVAFHTSGRNTGKVHAPYLYNPEkKKMFAKAAFHGYEMWEEYSRLKN--IPFKKDGVIEVALDQK 102
                 9*****************64432457**************************656652546669*************9987..89**********9998 PP

                 HHHHHHHHHHHHHHTTT...TEEEEEHHHHHHHSTTSTTTSEEEEETTEEEEEHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEE CS
         DAO  95 elealdkllallleagl...daelldaeevrelepalpgllgalfypdtgqvdpakltaalaraaealGveilegtevtgleeedgkvwgverttpgen 190
                     l+k l+ ++++gl   d +l+d+ee++++ep + ++  al+++ +g  d+  lt  ++++ +++G ++++ t+vt+++++++k w++  t +ge 
  EPA05113.1 103 GTLVLEKYLKWGKQNGLqenDIKLMDKEELKKIEPEI-KCESALYVYKDGSTDYSLLTGEVMNDSKNNGTNFVFDTKVTNIKKTSNK-WKI--TLDGEH 197
                 888898888888889997545589***********55.789****9999********************************887777.***..444443 PP

                 .EEEEEEEE--GGGHH.HHHTTCTT.TSEEEEEEEEEEEEEECCTHSTGSGCSEEEEE.EEETTTTEEEEEETTSEEEEEESSE............... CS
         DAO 191 .daadavVnaaGawsd.llgllkel.dlpispvrgqvlvlkplseklvspaailpvpe.tdddgrgvyvtprkdgrvlvGgtad............... 270
                    a+ ++n+aG  +  ++ ++++  +   + +rg+++   p++ + + +  ++ vpe +d ++ +++ + r dg+  +G++a+               
  EPA05113.1 198 eIFANFIINTAGGEAIdIAHKAGIAeKFTDVHFRGEYWKA-PKEYNNLTKTSVYSVPEyPDYPFLDPHWIIRVDGNCEIGPNAVpvfspygynktenik 295
                 234588********984443332222335599********.65555556669********************************999999998888888 PP

                 ..................EETTCSSTSCSHHHHHH....HHHHHHHHSGGG..CGEEE.EEEEEEE...ETTSSEEEEEEE..TEEEEEEEEECTTTHH CS
         DAO 271 ..................eesgdddpevdeedide....llealrklfPql..gdvlr.kwaGlrp...lpdglpligetp..gvkglylatGhsghGl 339
                                    ++++++++++e +       +++++++++P++   ++++   aG+r    +  g ++ +     g +  ++  +++++G 
  EPA05113.1 296 efipktlemimsgarkaiFDKQFQELAINEIQSSMskssMINRVKRFLPKIdaTKITEkGTAGIRSsviNQEGKFVPDV-IleGDSMSFHILNYNSPGA 393
                 888888888888887776555555533333322224447***********644557754888****6432455333222.1334568899999999999 PP

                 HHHHH CS
         DAO 340 tlapa 344
                 t a+ 
  EPA05113.1 394 TGALP 398
                 98765 PP

>> Mqo  Malate:quinone oxidoreductase (Mqo)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   6.6e-08    0.0002       3      56 ..       5      56 ..       3      68 .. 0.89
   2 !   37.4   0.0   3.6e-13   1.1e-09     176     440 ..     152     403 ..     131     427 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 6.6e-08
         Mqo  3 vdvvliGaGimsatlgvllkelepelsievlerldkvaeessnawnnaGtGHsa 56
                 dvv+iG+Gi+ ++++ +l+ l+ + +i v+e+ ++va   s    n+G  H+ 
  EPA05113.1  5 FDVVIIGGGILGSSISYFLSFLNTTKKILVIEQAHSVAFHTSG--RNTGKVHAP 56
                7*************************************99886..577777765 PP

  == domain 2  score: 37.4 bits;  conditional E-value: 3.6e-13
         Mqo 176 dvnfgaltrqllkalekkkgvelklkhevkdlkreedgkWkvkvkdlktgekkkvkakfvfiGaGGgalklLqksgipeakgyggfPvsGqflvcknpe 274
                   ++  lt ++++   k++g+++ ++++v+++k++++ kWk+++       ++++ a+f+   aGG+a+++ +k+gi e  +++     G++ ++ + e
  EPA05113.1 152 STDYSLLTGEVMNDS-KNNGTNFVFDTKVTNIKKTSN-KWKITLD-----GEHEIFANFIINTAGGEAIDIAHKAGIAE--KFTDVHFRGEYWKAPK-E 240
                 46999*******999.559**************9988.8***998.....567899*********************87..58888889***99875.6 PP

         Mqo 275 vveqheakvYgkaavgaPPmsvpHlDtRvidgkksllfGPfa..gfstkflkegslldllksvklsnllpllavglknldLvkYlieqvl..kskedrl 369
                   +  ++ vY+  +    P   pH   Rv dg+ ++  GP a   fs+    + +++  +   +l+ +++  + ++ + ++ +  i+++   +sk++ +
  EPA05113.1 241 YNNLTKTSVYSVPEYPDYPFLDPHWIIRV-DGNCEI--GPNAvpVFSPYGYNKTENIKEFIPKTLEMIMSGARKAIFDKQFQELAINEIQssMSKSSMI 336
                 77888999****************99995.666554..666532466654444444443444455667777777777777888888876511678889* PP

         Mqo 370 ealreflpeakkedW.elvvaGqRvqvikkdeekggvlefGtevvasadg.slaalLGasPGAstavsimlev 440
                 +++++flp+ +++   e  +aG R  vi+++       +f  +v+ + d  s+  l   sPGA  a +    v
  EPA05113.1 337 NRVKRFLPKIDATKItEKGTAGIRSSVINQEG------KFVPDVILEGDSmSFHILNYNSPGATGALPFSAYV 403
                 *********99887625679********9943......46777777766526666667899998887665555 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.3e-06    0.0039       1      41 [.       9      51 ..       9      61 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.3e-06
                   EE--SHHHHHHHHHHH..CCTEEEEEE-SSSSSSGGG-EECET CS
  NAD_binding_8  1 IvGaGlsGlvaAylLa..kagfdvlllekrdrlGGraasyevp 41
                   I+G+G+ G+++ y+L+  +  +++l++e+++++  + + ++ +
     EPA05113.1  9 IIGGGILGSSISYFLSflNTTKKILVIEQAHSVAFHTSGRNTG 51
                   9***************444589*********999887776655 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0   0.00049       1.4       2      34 ..       7      41 ..       6      57 .. 0.83
   2 ?    0.5   0.0      0.31   9.2e+02      48      68 ..     117     137 ..     104     144 .. 0.87
   3 !    6.4   0.1    0.0045        13      46      78 ..     162     193 ..     157     196 .. 0.83
   4 ?   -3.2   0.0       4.4   1.3e+04      23      41 ..     331     349 ..     322     352 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00049
                EEEECSSHHHHHHHHHHHHTT..SEEEEEESSSSS CS
   Pyr_redox  2 vvvvGgGyiglElAgalaelg..kkVtvversdkl 34
                vv++GgG +g     +l+ l+  kk+ v+e +  +
  EPA05113.1  7 VVIIGGGILGSSISYFLSFLNttKKILVIEQAHSV 41
                8****************665544999999988766 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.31
                 HHHHHTTEEEECSEEEEEEEE CS
   Pyr_redox  48 eklekngievllntkveeieg 68 
                 + l++n i+++ ++++++ie 
  EPA05113.1 117 NGLQENDIKLMDKEELKKIEP 137
                 56899*************996 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0045
                 HHHHHHHTTEEEECSEEEEEEEEETTSEEEEEE CS
   Pyr_redox  46 lqeklekngievllntkveeiegsedgvesvkl 78 
                 +++  ++ng +++++tkv++i++++++++ ++l
  EPA05113.1 162 VMNDSKNNGTNFVFDTKVTNIKKTSNKWK-ITL 193
                 66677899***************999855.665 PP

  == domain 4  score: -3.2 bits;  conditional E-value: 4.4
                 SEEEEEESSSSSSTTSSHH CS
   Pyr_redox  23 kkVtvversdkllrllDee 41 
                 +k +++ r +++l+++D++
  EPA05113.1 331 SKSSMINRVKRFLPKIDAT 349
                 5678899999999988875 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.1   0.00084       2.5       2      31 ..       6      39 ..       5     142 .. 0.65
   2 !    8.1   0.1   0.00047       1.4     188     241 ..     161     214 ..     156     226 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00084
                 SEEEE--SHHHHHHHHHHHH..HTS-EEEEE..T CS
                 xxxxxxxxxxxxxxxxxxxx..xxxxxxxxx..x RF
  Pyr_redox_2  2 dvvviGgGpAGlaaaltlaq..agakvtlve..l 31
                 dvv+iGgG+ G + + +l+      k++++e   
   EPA05113.1  6 DVVIIGGGILGSSISYFLSFlnTTKKILVIEqaH 39
                 6777777777777777777653466666665431 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00047
                  HHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EEES- CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Pyr_redox_2 188 aleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvavGvrpst 241
                  ++++  +++G ++++ t+v++i++ ++k + +l+ ++ei a  ++  +G ++ +
   EPA05113.1 161 EVMNDSKNNGTNFVFDTKVTNIKKTSNKWKITLDGEHEIFANFIINTAGGEAID 214
                  56778899*******************99999999999***9999999988765 PP

>> PepSY_like  Putative beta-lactamase-inhibitor-like, PepSY-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.49   1.5e+03      45      79 ..     115     151 ..      69     154 .. 0.61
   2 ?   11.5   0.2   0.00011      0.33      32      74 ..     154     200 ..     148     206 .. 0.88
   3 ?    0.4   0.1      0.33   9.8e+02      12      60 ..     311     355 ..     302     367 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.49
                 HHH.TTTEEEEEEEECS.SEEEEEETTSEEEEEETTS CS
  PepSY_like  45 kns.ypdekvtkierkk.keyeieleneielyfdedG 79 
                 k++  ++++++  ++++ k++e e++ e  ly  +dG
  EPA05113.1 115 KQNgLQENDIKLMDKEElKKIEPEIKCESALYVYKDG 151
                 3444455666666666666666666666666666666 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00011
                 SGGGS-HHHHHHHHHHTTT....EEEEEEEECSSEEEEEETTSEEEE CS
  PepSY_like  32 plsilpkavlkaiknsypd....ekvtkierkkkeyeieleneiely 74 
                 ++s l  +v++  kn+ ++    +kvt+i++++++++i+l+ e e++
  EPA05113.1 154 DYSLLTGEVMNDSKNNGTNfvfdTKVTNIKKTSNKWKITLDGEHEIF 200
                 5788999*********777799*******************998886 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.33
                 EEEE-TTS-EEEEE-TTSEESGGGS-HHHHHHHHHHTTTEEEEEEEECS CS
  PepSY_like  12 eveFdkkGeWkeiegkkteiplsilpkavlkaiknsypdekvtkierkk 60 
                 ++ Fdk+  ++e+    +ei+ s  ++++++ +k   p+ + tki++k 
  EPA05113.1 311 KAIFDKQ--FQELA--INEIQSSMSKSSMINRVKRFLPKIDATKITEKG 355
                 5666665..55555..568888888888899999888888888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.66u 0.35s 00:00:01.01 Elapsed: 00:00:00.55
# Mc/sec: 2375.08
//
Query:       EPA05114.1  [L=164]
Description: hypothetical protein BG20_I1119 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1305  (0.0727871); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1115.73
//
Query:       EPA05115.1  [L=155]
Description: ribosomal protein L30p/L7e [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-12   46.1   0.0    5.4e-12   45.4   0.0    1.4  1  Ribosomal_L30  Ribosomal protein L30p/L7e
  ------ inclusion threshold ------
       0.13   11.9   0.6       0.74    9.5   0.0    2.3  3  FeS            Putative Fe-S cluster


Domain annotation for each model (and alignments):
>> Ribosomal_L30  Ribosomal protein L30p/L7e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   0.0     6e-16   5.4e-12       1      51 []       5      55 ..       5      55 .. 0.98

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 6e-16
                   EEEEE-S-STTS-HHHHHHHHHTT-SSTTEEEE--SSHHHHHHHHHCCCGE CS
  Ribosomal_L30  1 lfVtrirsiigvppkvrktLqlLgLrkingtvvklntpsirGmLkkVkhlV 51
                   ++V+ri++ +++p +   t+ lL L k  + v+++ + ++ GmL+kVkh+V
     EPA05115.1  5 YLVVRIKGKADCPYWATTTMTLLKLDKKYRAVILPAKDNTLGMLNKVKHYV 55
                   58************************************************9 PP

>> FeS  Putative Fe-S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.36   3.2e+03      28      32 ..      13      17 ..       4      18 .. 0.67
   2 ?   -0.3   0.0       0.1     9e+02      17      29 ..      64      76 ..      62      77 .. 0.84
   3 ?    9.5   0.0   8.3e-05      0.74      11      29 ..      91     109 ..      90     110 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.36
         FeS 28 ledCp 32
                  dCp
  EPA05115.1 13 KADCP 17
                45787 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.1
         FeS 17 fAealvegeaqle 29
                +A+ lv ++a+ e
  EPA05115.1 64 LAKELVDKKARKE 76
                799*****99865 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 8.3e-05
         FeS  11 ypgCmafAealvegeaqle 29 
                 y + +a+A+al+eg+a+l+
  EPA05115.1  91 YDSTDALATALAEGKATLS 109
                 555589**********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 983.62
//
Query:       EPA05116.1  [L=85]
Description: hypothetical protein BG20_I1125 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 547.92
//
Query:       EPA05117.1  [L=154]
Description: hypothetical protein BG20_I1121 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-06   28.0   6.7    2.3e-06   27.2   6.7    1.4  1  SHOCT     Short C-terminal domain
  ------ inclusion threshold ------
      0.023   14.7   0.0      0.047   13.7   0.0    1.5  1  GvpG      Gas vesicle protein G
        1.2    9.4  10.9        1.4    9.1  10.9    1.3  1  TSP_NTD   Tail specific protease N-terminal domain


Domain annotation for each model (and alignments):
>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   6.7   3.8e-10   2.3e-06       3      28 .]     126     151 ..     126     151 .. 0.98

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 3.8e-10
       SHOCT   3 LekLkeLyarGeIteEEFeakKakLL 28 
                 LekL++L++ G+IteEEF +kK+k+L
  EPA05117.1 126 LEKLAKLKELGIITEEEFTKKKKKIL 151
                 8************************8 PP

>> GvpG  Gas vesicle protein G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   7.8e-06     0.047      32      65 ..     124     154 .]      96     154 .] 0.64

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.8e-06
        GvpG  32 nlrkeLaaLqqeLdaGeIdeeeFdrrEeelLdrL 65 
                 ++  +La+L+   + G I+eeeF ++  ++Ldr+
  EPA05117.1 124 EVLEKLAKLK---ELGIITEEEFTKKKKKILDRI 154
                 4555555555...89*****************97 PP

>> TSP_NTD  Tail specific protease N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1  10.9   0.00023       1.4      46     134 ..       4      89 ..       1     153 [. 0.77

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00023
     TSP_NTD  46 fekyreklddalkngdlsfaeeiynlyqkrieerkeyikellkkpfdfskdetleldrekapwakneaelkelwrkrlkneilaelklk 134
                 +e+++ek ++++k+++ + +++++++y++++e+ k++ ke l+k  ++++  ++++ ++k +w + +++  +  +k + + i+  +k++
  EPA05117.1   4 IENNNEKSEKNIKKNKAEHFQDLTKTYENKVERGKQLGKESLEKINEMTT-SSVDFIKSKPQWKSLKNNSLKIKEKSVDSAIM--IKKN 89 
                 57789999***********************************9777777.899**********9999999999999999988..3333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2114  (0.11791); expected 358.6 (0.02)
Passed bias filter:                      599  (0.0334096); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1010.95
//
Query:       EPA05118.1  [L=137]
Description: hypothetical protein BG20_I1117 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   12.3   0.0       0.43   10.5   0.0    2.0  1  FlgD_ig   FlgD Ig-like domain


Domain annotation for each model (and alignments):
>> FlgD_ig  FlgD Ig-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   2.4e-05      0.43      35      72 ..      83     116 ..      76     123 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 2.4e-05
                 -EEEEEEEEESSSEEEEEEE-SB-TTS-B--SEEEEEE CS
     FlgD_ig  35 evVrtidlgaqsaGvvsftWdGtdndGnkladGaYtvk 72 
                 +vV t++ ++q      f Wd ++nd  ++ +G Y+++
  EPA05118.1  83 QVVTTLNPKEQIV----FVWDQMKNDNVPVLEGLYKIS 116
                 5666666655555....*******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1003.81
//
Query:       EPA05119.1  [L=46]
Description: hypothetical protein BG20_I1128 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      0.002   17.4   7.5     0.0032   16.8   7.5    1.4  1  zf-ribbon_3    zinc-ribbon domain
  ------ inclusion threshold ------
      0.026   14.2   8.8      0.052   13.3   8.8    1.6  1  zinc_ribbon_2  zinc-ribbon domain


Domain annotation for each model (and alignments):
>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   7.5   3.6e-07    0.0032       3      24 ..      10      31 ..       8      32 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.6e-07
  zf-ribbon_3  3 vrCPnCGaplssddnvCpyCGt 24
                   C +CG+ +++ + vCpyCG+
   EPA05119.1 10 AICVECGNSIEKCVCVCPYCGE 31
                 67******88***********7 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   8.8   5.8e-06     0.052       2      21 ..      12      31 ..      11      32 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.8e-06
  zinc_ribbon_2  2 CpnCGaelqdnakFCpyCGt 21
                   C +CG+ +++ +  CpyCG+
     EPA05119.1 12 CVECGNSIEKCVCVCPYCGE 31
                   *******************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       887  (0.0494729); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.31s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 295.34
//
Query:       EPA05120.1  [L=195]
Description: hypothetical protein BG20_I1113 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-32  112.5   0.0    2.7e-32  112.1   0.0    1.2  1  AAA_17           AAA domain
    1.1e-06   29.2   0.0    1.8e-06   28.5   0.0    1.4  1  AAA_18           AAA domain
    7.2e-05   22.4   0.3     0.0001   21.9   0.3    1.3  1  KTI12            Chromatin associated protein KTI12
    7.8e-05   22.9   0.1    0.00014   22.1   0.1    1.4  1  Roc              Ras of Complex, Roc, domain of DAPkinase
      8e-05   22.6   2.4     0.0012   18.8   0.4    2.2  2  NTPase_1         NTPase
    0.00015   22.1   0.0    0.00022   21.5   0.0    1.2  1  AAA_28           AAA domain
    0.00024   20.9   0.0    0.00037   20.3   0.0    1.3  1  AAA_30           AAA domain
    0.00036   20.5   0.0    0.00049   20.1   0.0    1.3  1  NACHT            NACHT domain
    0.00039   20.1   0.3    0.00077   19.1   0.2    1.6  1  SRP54            SRP54-type protein, GTPase domain
    0.00041   20.8   0.1     0.0008   19.8   0.1    1.5  1  AAA              ATPase family associated with various cellul
    0.00059   20.4   1.2    0.00071   20.1   1.2    1.5  1  ABC_tran         ABC transporter
    0.00065   20.0   0.0    0.00089   19.5   0.0    1.6  1  AAA_22           AAA domain
    0.00073   19.5   0.1     0.0013   18.7   0.1    1.4  1  ATPase_2         ATPase domain predominantly from Archaea
    0.00074   19.9   0.2      0.001   19.4   0.2    1.6  1  AAA_19           AAA domain
    0.00077   19.1   0.1     0.0014   18.2   0.1    1.5  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
     0.0015   18.6   0.5     0.0022   18.1   0.5    1.7  1  MMR_HSR1         50S ribosome-binding GTPase
     0.0019   18.4   0.0     0.0029   17.8   0.0    1.5  1  AAA_33           AAA domain
     0.0024   18.3   0.0     0.0029   18.0   0.0    1.3  1  AAA_16           AAA ATPase domain
     0.0027   17.4   0.0     0.0047   16.7   0.0    1.4  1  AAA_24           AAA domain
     0.0032   17.3   0.2     0.0061   16.5   0.2    1.5  1  MobB             Molybdopterin guanine dinucleotide synthesis
     0.0075   15.7   0.0      0.012   15.0   0.0    1.2  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0076   16.1   0.3      0.017   14.9   0.1    1.7  2  ATP_bind_1       Conserved hypothetical ATP binding protein
  ------ inclusion threshold ------
      0.011   15.7   0.5      0.026   14.4   0.2    1.7  2  RsgA_GTPase      RsgA GTPase
      0.011   15.5   0.2       0.19   11.5   0.0    2.6  3  CLP1_P           mRNA cleavage and polyadenylation factor CLP
      0.012   15.6   0.1      0.026   14.5   0.1    1.5  1  AAA_5            AAA domain (dynein-related subfamily)
      0.014   15.0   0.1       0.02   14.4   0.1    1.3  1  AAA_7            P-loop containing dynein motor region
      0.015   14.3   0.2      0.026   13.5   0.2    1.3  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
      0.018   14.8   0.0      0.028   14.1   0.0    1.4  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.022   14.3   0.5      0.044   13.4   0.3    1.6  1  Ras              Ras family
      0.023   14.1   0.0      0.041   13.2   0.0    1.4  1  DnaB_C           DnaB-like helicase C terminal domain
      0.027   14.5   0.6      0.059   13.4   0.1    1.8  2  AAA_14           AAA domain
      0.038   13.2   0.0      0.063   12.5   0.0    1.4  1  NB-ARC           NB-ARC domain
      0.048   13.3   0.3       0.15   11.8   0.3    2.1  1  Thymidylate_kin  Thymidylate kinase


Domain annotation for each model (and alignments):
>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.1   0.0   4.9e-35   2.7e-32       1     136 []      13     151 ..      13     151 .. 0.94

  Alignments for each domain:
  == domain 1  score: 112.1 bits;  conditional E-value: 4.9e-35
                 EE-TTSSHHHHHHHHHHHH.....TEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEEEEE-SEEEETTEEEESSHH CS
      AAA_17   1 lGgPGsGKgtqceklveky.....gfthlsaGdllreeakrgglakardemrklpleekkelqkeaaekiaeeakkkgvlvdghprikeqagfldglpk 94 
                 +G+PG+GK+ +++++ve +      +++ s+G++++e ak++g  ++rde+rklp +e+k lqk+aaek+a+   ++ v++d+h  i+ ++g+++glp+
  EPA05120.1  13 VGIPGVGKTSLLKRIVEILkeqnkTVSVNSFGSVMFEIAKSKGI-NDRDELRKLPVSEQKNLQKIAAEKLANL-TDDVVIIDTHVFINSPEGYYPGLPE 109
                 7***************8665555578899***********9997.8*************************86.7889********************* PP

                 HHHHHH..SEEEEEE--HHHHHHHHHHHTTST-TS-SHHHHH CS
      AAA_17  95 evleelkpdaiilleadpeeilerrlkdrtrgrdddneesik 136
                 +vl+ lkp+ ++ ++a+peei++rr+kd+tr+rd  +++ ik
  EPA05120.1 110 HVLAILKPSNFVSVSAKPEEIYNRRMKDDTRNRDNVSIDNIK 151
                 **************************************9997 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0   3.3e-09   1.8e-06       1     119 [.      10     143 ..      10     156 .. 0.68

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 3.3e-09
      AAA_18   1 IlltGtpGvGKttlakeLskrl.gf.........gvnlrdvakenglllevdpealdeskrlde.dkldklldaleenssaleegknlvidghlaeles 88 
                 +++ G+pGvGKt+l k++ + l +          g +  ++ak +g+ + ++     +  + ++ + ++ + ++l +        ++++id h+  + +
  EPA05120.1  10 VVVVGIPGVGKTSLLKRIVEILkEQnktvsvnsfGSVMFEIAKSKGINDRDELR---KLPVSEQkNLQKIAAEKLANL-----TDDVVIIDTHVFINSP 100
                 789***************777633356678777555555555555544444444...222222202222333344443.....35899******99999 PP

      AAA_18  89 eaakdikk............vvLtaspeelleRlekRgyeeak 119
                 e +  +              v + a+pee + R  k+++++++
  EPA05120.1 101 EGYYPGLPehvlailkpsnfVSVSAKPEEIYNRRMKDDTRNRD 143
                 999877769999***************9999998888877654 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.3   1.9e-07    0.0001       4      84 ..      10      99 ..       9     154 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.9e-07
                EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH...TTSS.S--GGGHHHH....HHHHHHHHHHHHTT...SEEEE-S---SHH CS
       KTI12  4 vvltGlPssGKstrakeLakaleeekrsvvviddeslg..iekds.ykdsakekal....RsslrsavkrdLsk..ekvVIvDslnyikg 84
                vv+ G+P +GK+++ k++ + l+e++++v v +  s+   i+k++  +d  + ++l    +++l++ ++++L +  ++vVI+D   +i++
  EPA05120.1 10 VVVVGIPGVGKTSLLKRIVEILKEQNKTVSVNSFGSVMfeIAKSKgINDRDELRKLpvseQKNLQKIAAEKLANltDDVVIIDTHVFINS 99
                89*******************************999995544444455555555542222234444455566533378999999888875 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.1   2.5e-07   0.00014       1      45 [.       9      51 ..       9      67 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 2.5e-07
                EEEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSG CS
         Roc  1 KvvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkik 45
                Kvv+vG  gvGKtsllkr+v  ++ +++++t++v+ + + + +i 
  EPA05120.1  9 KVVVVGIPGVGKTSLLKRIV--EILKEQNKTVSVNSFGSVMFEIA 51
                9*******************..56677788888887765554444 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.4   2.2e-06    0.0012       1      30 [.       9      38 ..       9      43 .. 0.93
   2 ?    3.7   0.1     0.098        53      78     155 ..      70     150 ..      49     157 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.2e-06
                EEEEE--TTSSHHHHHHHHHHHH...GGGE CS
    NTPase_1  1 kvfiTGppGvGKtTlvkkvlellkssgvkv 30
                kv++ G pGvGKt l+k+++e lk+++ +v
  EPA05120.1  9 KVVVVGIPGVGKTSLLKRIVEILKEQNKTV 38
                58999*********************9887 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.098
                 HHHHHHHHHHHHHHHHHHH-EEEE--...-STTGGG-HHHHHHHHHHHT.TTSEEEEE--SS-.-SHHHHHHHT-TT-EEEE- CS
    NTPase_1  78 vesfeelalealrkalseadviviDE...iGkmElkskkfkeaveevLk.sekpvlavihrrk.dlalveeirerkdvkvfev 155
                  ++++++a+e+l +   + dv++iD    i + E   + + e v  +Lk s+ + +   +++  + ++ ++ r+r +v++ ++
  EPA05120.1  70 QKNLQKIAAEKLAN--LTDDVVIIDThvfINSPEGYYPGLPEHVLAILKpSNFVSVSAKPEEIyNRRMKDDTRNRDNVSIDNI 150
                 35589999999987..5899*****6555777777788888888888885555555555555566666667777766666555 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   4.1e-07   0.00022       1      83 [.       9      96 ..       9      99 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 4.1e-07
      AAA_28  1 kivitGgestGKTtlleaLa....ar.gypvvpEaareileeklakgedalpwvedllafaervleeqleeeaaa.aankvlfcDrgll 83
                k+v++G ++ GKT+ll+++     ++ +++ v  ++  ++e    kg ++ ++  ++l + e+   +++++e+ a  +++v+++D+ ++
  EPA05120.1  9 KVVVVGIPGVGKTSLLKRIVeilkEQnKTVSVNSFGSVMFEIAKSKGINDRDEL-RKLPVSEQKNLQKIAAEKLAnLTDDVVIIDTHVF 96
                79**************88774444445777778888888877778888777775.55566555444577777777579********987 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   6.9e-07   0.00037      16      54 ..       7      43 ..       2      97 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 6.9e-07
      AAA_30 16 sgdrvavltGpAGtGKttalkalreaweaaggrviglAp 54
                s+   +v++G +G GKt +lk ++e++++++++v + + 
  EPA05120.1  7 SR--KVVVVGIPGVGKTSLLKRIVEILKEQNKTVSVNSF 43
                34..4899**********************988876554 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0     9e-07   0.00049       1      66 [.       8      74 ..       8      93 .. 0.66

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 9e-07
                SCEEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC.-SEEEEEETTTTTTS-...-HCHHHCCCCTS-- CS
       NACHT  1 rlvilqGeaGsGKTtLlqklalawaegklpqga.fklvFflslrelsrsgnarsladllfsqlpepa 66
                r v++ G +G+GKT Ll+++++ ++e++         + +++ ++ + +++   l++l +s+++ ++
  EPA05120.1  8 RKVVVVGIPGVGKTSLLKRIVEILKEQNKTVSVnSFGSVMFEIAKSKGINDRDELRKLPVSEQKNLQ 74
                5699********************9987544322222344555555555555555555555555555 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.2   1.4e-06   0.00077       3      91 ..       9      93 ..       7     124 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.4e-06
                EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES..TSSTTHHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHHHHHHTTSSEEEEEE CS
       SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllvaaD..tfRaaAveQLktlaeklgvpvikkkeeadpaavakeavekakeekidvvlvDT 91
                 +++vG+ G+GKT+ l ++ ++lk+++k+v + +    +f +a  + ++   e  + pv +   +++  ++a+e++ +  +   dvv++DT
  EPA05120.1  9 KVVVVGIPGVGKTSLLKRIVEILKEQNKTVSVNSFGsvMFEIAKSKGINDRDELRKLPVSE---QKNLQKIAAEKLANLTD---DVVIIDT 93
                5899************************999987652268888888888888888877654...44556777777777766...9999999 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.1   1.5e-06    0.0008       1      65 [.      10      92 ..      10      96 .. 0.60

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.5e-06
                EEEESSTTSSHHHHHHHHHHHHTHE............EEEEETTTCSSS......STTHHHHHHHHHHHHHHHTS..TSEEEEEE CS
         AAA  1 vllyGppGtGKTllakavakelgve............fleisgsellsk......yvgesekkirelfkeakeka..kpsilfiD 65
                v+++G pG+GKT+l k +++ l+ +            ++ei  s+ +++      +    +k+++++ +e  + a  +  +++iD
  EPA05120.1 10 VVVVGIPGVGKTSLLKRIVEILKEQnktvsvnsfgsvMFEIAKSKGINDrdelrkLPVSEQKNLQKIAAE--KLAnlTDDVVIID 92
                5799*****************9755222223333333455555544444677666555555555555533..2333445777777 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   1.2   1.3e-06   0.00071       8      49 ..       4      45 ..       1     189 [. 0.72

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.3e-06
                EETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEG CS
                xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  8 lkegekvaivGenGaGKStLlkllagllkpteGeilldgkdl 49
                l e++kv++vG  G GK++Llk + + lk ++ ++ +++  +
  EPA05120.1  4 LVESRKVVVVGIPGVGKTSLLKRIVEILKEQNKTVSVNSFGS 45
                67899*****************************96653322 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   1.6e-06   0.00089       8      43 ..      10      46 ..       6     164 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.6e-06
      AAA_22  8 lvvtGesGtGKTtllrrlleqldeeakaee.erpevv 43
                +vv+G +G+GKT ll+r++e l+e++k    ++ + v
  EPA05120.1 10 VVVVGIPGVGKTSLLKRIVEILKEQNKTVSvNSFGSV 46
                69********************876555446333333 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   2.4e-06    0.0013      23      91 ..      10      78 ..       3     100 .. 0.64

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.4e-06
    ATPase_2 23 yfiYGpegsGKtaLlkeiienledkdkyviyyialree.siskldefieeeeekkklekalgiavpkael 91
                +++ G  g+GKt+Llk+i+e l++++k v  ++++ ++ ++  +++ i++ +e +kl    +++++k ++
  EPA05120.1 10 VVVVGIPGVGKTSLLKRIVEILKEQNKTVS-VNSFGSVmFEIAKSKGINDRDELRKLPVSEQKNLQKIAA 78
                6888*******************9998554.444444304444444444444444444444444444444 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.2   1.9e-06     0.001       8      40 ..       5      37 ..       2     166 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.9e-06
      AAA_19  8 lkekvllvtaGpGtGKTrvlkhivallvelggv 40
                ++++ ++v++ pG GKT +lk iv++l+e+++ 
  EPA05120.1  5 VESRKVVVVGIPGVGKTSLLKRIVEILKEQNKT 37
                578899*********************987643 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   2.6e-06    0.0014       3      39 ..      10      46 ..       8      65 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.6e-06
                EEEEESTTCCHHHHHHHHHCT--SS-EEEEESS-SSC CS
        cobW  3 tvltGflGsGKTtLlnhllenraglklavivNefgev 39
                +v++G +G GKT+Ll++++e  ++++  v vN fg+v
  EPA05120.1 10 VVVVGIPGVGKTSLLKRIVEILKEQNKTVSVNSFGSV 46
                699****************999999999999999976 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.5     4e-06    0.0022       1      25 [.       9      37 ..       9     177 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 4e-06
                EEEEEESTTSSHHHHHHHHHT....STEE CS
    MMR_HSR1  1 evaivGrpNvGKStLinaltg....ekai 25
                +v++vG p vGK++L++++++    ++  
  EPA05120.1  9 KVVVVGIPGVGKTSLLKRIVEilkeQNKT 37
                699****************9733321222 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   5.3e-06    0.0029       2      75 ..      10      90 ..      10     166 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 5.3e-06
      AAA_33  2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfg.......tdqqsktdytrvldr...lyqilnelarkalsagrn.vil 75
                v++vG pG+GK+ l++r+++ l+    ++s +++ + +f+       +d+       ++++      + l+++a+++l+   + v++
  EPA05120.1 10 VVVVGIPGVGKTSLLKRIVEILKeqNKTVSVNSFGSVMFEiakskgiNDR------DELRKLpvsEQKNLQKIAAEKLANLTDdVVI 90
                789***************99888888888888877766666433223333......3322222225556666666666544333444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   5.4e-06    0.0029      26      52 ..       9      35 ..       5     126 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 5.4e-06
      AAA_16 26 lvllsGesGvGKsslvrellralekdg 52
                 v+++G +GvGK+sl++++ + l++++
  EPA05120.1  9 KVVVVGIPGVGKTSLLKRIVEILKEQN 35
                589*****************9888882 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   8.6e-06    0.0047       2      73 ..       7      93 ..       6     100 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 8.6e-06
      AAA_24  2 klkiliyGpsgiGKTtlakel......gpkplfidtekGlksldadkfpdie..........swedfldevvelaaeladyktlviDt 73
                ++k++++G +g+GKT+l+k++      ++k++ ++ ++++   + +k + i+          s ++ l+++++ + ++ + ++++iDt
  EPA05120.1  7 SRKVVVVGIPGVGKTSLLKRIveilkeQNKTVSVNSFGSV-MFEIAKSKGINdrdelrklpvSEQKNLQKIAAEKLANLTDDVVIIDT 93
                579******************8888877777777666654.44444444444334444444444555555544455555556666666 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.2   1.1e-05    0.0061       2      32 ..      10      40 ..       9      55 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.1e-05
        MobB  2 lgivgksgsGKTtLleklipelkarglrvgt 32
                + +vg  g GKT+Ll++++++lk+++ +v++
  EPA05120.1 10 VVVVGIPGVGKTSLLKRIVEILKEQNKTVSV 40
                5689*********************999986 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.2e-05     0.012      24      73 ..       9      56 ..       5      68 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.2e-05
  Mg_chelatase 24 nlllvGppGsGKtmlakrlpsllpplseeealevakiasvagkkeeekll 73
                  ++++vG pG GKt l kr+ ++l + +  +++ v++  sv+ + +++k +
    EPA05120.1  9 KVVVVGIPGVGKTSLLKRIVEILKEQN--KTVSVNSFGSVMFEIAKSKGI 56
                  6899*******************8765..456677777777655555544 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   3.2e-05     0.017       1      29 [.      12      40 ..      12      42 .. 0.91
   2 ?   -2.9   0.0       8.4   4.6e+03      79      98 ..      73      93 ..      68      94 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.2e-05
  ATP_bind_1  1 vvGpaGsGKttfvgalseilelrgrsvav 29
                vvG +G+GKt++ ++++eil++++++v v
  EPA05120.1 12 VVGIPGVGKTSLLKRIVEILKEQNKTVSV 40
                89*********************887764 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 8.4
  ATP_bind_1 79 ldwl.deelekeeddyllfDt 98
                l+++ +e+l +  dd +++Dt
  EPA05120.1 73 LQKIaAEKLANLTDDVVIIDT 93
                555546677666889999997 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.2   4.8e-05     0.026      98     132 ..       6      40 ..       2      45 .. 0.82
   2 ?   -2.0   0.0       5.4     3e+03     144     158 ..      79      93 ..      53      96 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.8e-05
                  TTSEEEEECSTTSSHHHHHHHHCTT-----S---- CS
  RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpelelktgevse 132
                  +++ +v+vG  GvGK++L++++++ l+ + + vs 
   EPA05120.1   6 ESRKVVVVGIPGVGKTSLLKRIVEILKEQNKTVSV 40 
                  56889*****************9977777666664 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 5.4
                  EEEEEETTTEEEESS CS
  RsgA_GTPase 144 vellelaegglliDt 158
                   +l +l ++ ++iDt
   EPA05120.1  79 EKLANLTDDVVIIDT 93 
                  345555555555555 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       1.4   7.7e+02       4      25 ..      17      38 ..      14      42 .. 0.79
   2 ?   11.5   0.0   0.00036      0.19      86     161 ..      72     151 ..      59     159 .. 0.76
   3 ?    0.7   0.0       0.7   3.8e+02      29      55 ..     153     179 ..     150     189 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.4
      CLP1_P  4 dsGKSTlarlLlNyalrkgrkp 25
                 +GK++l + +++ + ++++++
  EPA05120.1 17 GVGKTSLLKRIVEILKEQNKTV 38
                6899999999999887777665 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00036
      CLP1_P  86 elareveekleenkkakasgliIntpGwvkgl.ga..ellleliealepdvvvvldq..eellnelkrdlp..lskvkvvklp 161
                  l + + ekl++    +++++iI+t+ ++++  g+   l ++++++l+p++ v ++   ee +n   +d +   ++v++ +++
  EPA05120.1  72 NLQKIAAEKLAN---LTDDVVIIDTHVFINSPeGYypGLPEHVLAILKPSNFVSVSAkpEEIYNRRMKDDTrnRDNVSIDNIK 151
                 555556655555...599***********97548655677*********8888888779999999888888566666665555 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.7
      CLP1_P  29 DlDvGqseispPgtislalverpidve 55 
                 +lDv  ++is  ++is ++v++ ++ e
  EPA05120.1 153 ELDVQSGMISACAVISGSPVKHVLNRE 179
                 79**************99999877664 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   4.9e-05     0.026       2      30 ..      10      38 ..       9      47 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.9e-05
                EEEE--SSSSHHHHHHHGGGGBS--EEEE CS
       AAA_5  2 vlLvGppGtgKselaerlaaalnreveyv 30
                v++vG pG+gK++l +r+ + l+ +  +v
  EPA05120.1 10 VVVVGIPGVGKTSLLKRIVEILKEQNKTV 38
                899*******************5444444 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   3.8e-05      0.02      30      68 ..       4      42 ..       1      58 [. 0.82

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.8e-05
       AAA_7 30 lknkkpvllvGptGtGKtviikdllkkldkekylsltin 68
                l ++++v++vG  G+GKt+++k++++ l++++ ++ + +
  EPA05120.1  4 LVESRKVVVVGIPGVGKTSLLKRIVEILKEQNKTVSVNS 42
                567889*********************996665555544 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   4.7e-05     0.026      29      62 ..       7      40 ..       4      45 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.7e-05
                SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEE CS
        MeaB 29 aqvvGltGvPGaGkstlvealglelrrrGkrvav 62
                +++v + G+PG+Gk  l++++++ l+++ k v+v
  EPA05120.1  7 SRKVVVVGIPGVGKTSLLKRIVEILKEQNKTVSV 40
                5678899*********************999988 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   5.2e-05     0.028       2      39 ..      11      45 ..      10      93 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.2e-05
  Viral_helicase1  2 vvhGvpGcGKStlirkllrtsliltvnrptaelltegk 39
                     vv G+pG GK++l++++++    l++ ++t+ + + g+
       EPA05120.1 11 VVVGIPGVGKTSLLKRIVEI---LKEQNKTVSVNSFGS 45
                     899************99965...666666666655555 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.3   8.1e-05     0.044       1      35 [.       9      41 ..       9      57 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.1e-05
                EEEEEESTTSSHHHHHHHHHHSSCSSSCTTTSSEE CS
         Ras  1 KlvlvGdsavGKtslllrfvkdkFkeeyesTigvd 35
                K+v+vG  +vGKtsll r v+    +e+++T+ v+
  EPA05120.1  9 KVVVVGIPGVGKTSLLKRIVEI--LKEQNKTVSVN 41
                9****************98863..45555666555 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   7.5e-05     0.041      19     108 ..       7      93 ..       3     101 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.5e-05
                 TXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHHHHHHHHTXXHHHHHHTTSX.HHHHHHHHH.HHHHHHHSEEEEEE CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx.xxxxxxxxxxxxxx RF
      DnaB_C  19 gdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvqRllsseaeidskklrtgklk.eedweklte.aieelseaklfidd 108
                 +  +++ + p++Gkt+l   i+e    +++++v v s+     +++     s++  d ++lr+  ++ +++++k+++ ++++l++  ++id 
  EPA05120.1   7 SRKVVVVGIPGVGKTSLLKRIVEILK-EQNKTVSVNSFGSVMFEIA----KSKGINDRDELRKLPVSeQKNLQKIAAeKLANLTDDVVIIDT 93 
                 5568999***************9655.6788899988876555544....344444556666666554556666655246666666666655 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   0.00011     0.059       4      47 ..       9      57 ..       6      97 .. 0.58
   2 ?   -2.1   0.0         7   3.8e+03      51      74 ..     129     151 ..     109     159 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00011
      AAA_14  4 ilvitGaRrvGKTtllkqlikell.....vkkesilyinldderdkkla 47
                 +v++G+  vGKT llk++++ l      v+ +s+  + ++  + k ++
  EPA05120.1  9 KVVVVGIPGVGKTSLLKRIVEILKeqnktVSVNSFGSVMFEIAKSKGIN 57
                5899***************966663334433444444444444443333 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 7
      AAA_14  51 kllelileklkeekktylflDEiq 74 
                 ++++  ++  ++ ++  + +D i+
  EPA05120.1 129 EIYNRRMKDDTR-NRDNVSIDNIK 151
                 333333333222.44446666665 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00012     0.063      22      48 ..       9      35 ..       3      94 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                EEEEEESTTSSHHHHHHHHCCSHCCCC CS
      NB-ARC 22 vvalvGmgGvGKttlakqilnksdeve 48
                 v +vG +GvGKt l+k i++ ++e +
  EPA05120.1  9 KVVVVGIPGVGKTSLLKRIVEILKEQN 35
                4889*************9998665544 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.3   0.00027      0.15       3      47 ..      14      52 ..      12     189 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00027
                     ESTTSSHHHHHHHHHHHHHHTTE.EEEESSSTTSHHHHHHHHHHH CS
  Thymidylate_kin  3 GlDGaGKttqaellkerlkeegikvvltrepggteiGekirelll 47
                     G+ G+GKt+ ++ ++e lke+ +        + +++G+++ e+ +
       EPA05120.1 14 GIPGVGKTSLLKRIVEILKEQNKT------VSVNSFGSVMFEIAK 52
                     999******************975......334455555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       912  (0.0508673); expected 358.6 (0.02)
Passed bias filter:                      664  (0.037035); expected 358.6 (0.02)
Passed Vit filter:                       109  (0.00607954); expected 17.9 (0.001)
Passed Fwd filter:                        33  (0.00184059); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              33  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 1353.78
//
Query:       EPA05121.1  [L=107]
Description: hypothetical protein BG20_I1133 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 709.87
//
Query:       EPA05122.1  [L=636]
Description: 2-oxoacid:acceptor oxidoreductase, alpha subunit [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      7e-56  189.6   0.0      1e-55  189.0   0.0    1.2  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
    1.8e-26   93.3   0.0    3.7e-26   92.3   0.0    1.5  1  POR              Pyruvate ferredoxin/flavodoxin oxidoreductas
    7.9e-12   45.4   0.0    1.6e-11   44.4   0.0    1.5  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
    6.6e-06   26.0   0.0    1.4e-05   25.0   0.0    1.5  1  Transketolase_C  Transketolase, C-terminal domain


Domain annotation for each model (and alignments):
>> POR_N  Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.0   0.0   2.2e-59     1e-55       2     230 ..     253     495 ..     252     496 .. 0.89

  Alignments for each domain:
  == domain 1  score: 189.0 bits;  conditional E-value: 2.2e-59
                 HHHHCTEEEEEE--BTTTCC..HHHHHCHCCCCCTT..EE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCCHHHHHHTT--EEEEEEEE CS
       POR_N   2 aaiaagvdviaaYPITPsse..iaeelaellakgev..gdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmienlglaageelPvvivvvaR 96 
                 ++i  g++++++YPITP+s+  ++ e +ell+  +   g + v+q e+Ei+a++++iGA+++G+r+ T TSg+G++Lm e+lg+a+ +e+P+vi++++R
  EPA05122.1 253 GKIVSGCRFQSYYPITPASDesVYLESNELLEVQNDrpGSTIVIQCEDEISAMGMMIGASLTGTRSSTSTSGPGFALMTEALGWAGINEVPIVITLYQR 351
                 567789**************988888888875444456899********************************************************** PP

                 E-STTBEEEEE--TTCHHHH.....S---EEEE-SSHHHHHHHHHHHHHHHHHCTSEEEEEEEHHHH.HEEEEEEC-SGG....GS-----SBXXXXXX CS
       POR_N  97 alpstglsirtdqsDlmaar.....dtglivlasenvqeafdlalvAfnlAekvrvPvivlfDgfllshevekvelpdee...delklikekleeyerk 187
                 ++pstgl++r  q Dl++a      d++ +v as++++e f ++ + fn+A  ++vPvi+++D+fl s  v   ++ +++   d   l ++ + ey+r+
  EPA05122.1 352 SGPSTGLPTRHGQDDLLFAVngghgDFPKLVYASGDIEESFYDTGRCFNYADVYQVPVIHMMDKFLSSSVVTCKKFDPQKitiDRGLLLDKIEGEYKRF 450
                 *******************************************************************77665555555553133334667777778887 PP

                 XX...SXXXBXXTXXTSSXXEEESBXBXTTSXBXXXXHHHHHHHHH CS
       POR_N 188 ey...aldpekpiargtaanpdtglehrekgneaedaaekvveeve 230
                 +    +++p++ +  +   +++tg+e +e g+++ed  + ++++++
  EPA05122.1 451 AFtenGISPRSRLGLDNGVFWNTGDESDEFGHITED-PQIRIKMMD 495
                 77888*******************************.888888775 PP

>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.3   0.0   8.3e-30   3.7e-26       2     177 .]      15     219 ..      12     219 .. 0.88

  Alignments for each domain:
  == domain 1  score: 92.3 bits;  conditional E-value: 8.3e-30
                 TSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGGGEEEEEEEEEECTCGTT-CCHHHCTS CS
         POR   2 GqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetlsehldglkpggiiiynseelkpdelkkakee 100
                 G Gv + +++++k++a+ Gy+++++re+ s+i+G hsy++vr+sde+i  +  v++++l+  +daet+++h+d++  gg iiy+++  k ++ +     
  EPA05122.1  15 GSGVDSGANVFSKVCANMGYQIFGKREFYSNIKGDHSYFTVRVSDEEI--HSNVNAVNLIASFDAETIFRHYDEVVSGGGIIYDADLAKISVDEV-HTL 110
                 99*******************************************954..44447******************************7655444443.333 PP

                 -HHHHHHH.......................T-EEEEE-HHHHHH.........HCCC.CCHHHHHHHHHHHHHHTS-HHHHHHHHHCCS-CH.HHHHH CS
         POR 101 erelkerl.......................gvrvygvdatkiak.........eiggneraaNtvmlGalaallglplealeeaikkrfpkkkeviek 167
                 +   kerl                       gv +y++++++i+          +++g  r+ N++++  +++l+++pl+ l + +   f+kk  + e+
  EPA05122.1 111 DIYFKERLlkelesknkpqtitgvlelaqekGVILYPISFRDILStlsektnnpKLKGMVRLFNVIAVSLSLGLIKMPLDPLFDSLDSIFAKKPLISEL 209
                 444555557799*********************************77655555544444**************************************** PP

                 HHHHHHHHHH CS
         POR 168 Nlkafragye 177
                 N+ka+  +y+
  EPA05122.1 210 NKKAATFAYD 219
                 ******9996 PP

>> PFOR_II  Pyruvate:ferredoxin oxidoreductase core domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.4   0.0   3.5e-15   1.6e-11       2      75 ..     521     590 ..     520     614 .. 0.81

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 3.5e-15
                 SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHH CS
     PFOR_II   2 evvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevk 75 
                 ++ iv  Gs  g + +a  +l++egi++G+++++++ PFP+e++k+l+k++k +++++ n+s    Gql++   
  EPA05122.1 521 DYTIVSWGSPKGPILDALAMLKKEGIHIGFIQMKLIHPFPAEHVKSLIKDAKTIIDIEANHS----GQLGKIFM 590
                 799**********************************************************6....55544333 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   3.1e-09   1.4e-05      11      95 ..     521     600 ..     515     624 .. 0.79

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 3.1e-09
                      SEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSHHHHHHHHHHHCCCTTCSSE CS
  Transketolase_C  11 dvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavkrgGigsevaaalaeeafdgldap 95 
                      d t+v++Gs     l+A ++L+kegi +  + +  + p+  e +++++k  + ++ +e  + +g +g+ +++ + +    ++d +
       EPA05122.1 521 DYTIVSWGSPKGPILDALAMLKKEGIHIGFIQMKLIHPFPAEHVKSLIKDAKTIIDIEA-NHSGQLGKIFMQNVLR----DIDHY 600
                      679*****************************************977777766666655.4546666666555555....44444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (636 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.47
# Mc/sec: 4094.56
//
Query:       EPA05123.1  [L=186]
Description: transcription factor [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-53  177.7   0.0    1.8e-26   91.9   0.0    2.0  2  TBP       Transcription factor TFIID (or TATA-binding protein
    1.1e-07   31.8   0.0     0.0025   17.9   0.0    2.3  2  DUF3378   Domain of unknown function (DUF3378)
     0.0053   16.4   0.3      0.009   15.6   0.3    1.4  1  FlgH      Flagellar L-ring protein


Domain annotation for each model (and alignments):
>> TBP  Transcription factor TFIID (or TATA-binding protein, TBP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.9   0.0   3.1e-30   1.8e-26       2      84 ..       8      88 ..       7      89 .. 0.96
   2 !   84.0   0.0   8.7e-28   5.2e-24       2      83 ..      99     178 ..      98     179 .. 0.96

  Alignments for each domain:
  == domain 1  score: 91.9 bits;  conditional E-value: 3.1e-30
                EEEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHHHHHHHH CS
         TBP  2 fkiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakkiapilkk 84
                + i+Nvvasa+++++ldL  + +k    ++eY pe+fpg v+rl++pk++ l+FssGk+v+tGaks+e +++a++k++ +lkk
  EPA05123.1  8 ISIVNVVASATIDQKLDLVDITKKF--PDVEYHPEQFPGAVFRLKNPKTATLLFSSGKMVCTGAKSQELAETAVAKVVSMLKK 88
                579******************7665..******************************************************97 PP

  == domain 2  score: 84.0 bits;  conditional E-value: 8.7e-28
                 EEEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHHHHHHH CS
         TBP   2 fkiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakkiapilk 83 
                 ++iqN+v s+nlg +++Le+ a+++    + Yepe+fpgl+ r+ +pk+++liFssGk+v++Gak e+++++ +++i  +l+
  EPA05123.1  99 VTIQNIVSSINLGGRVNLEQAARTL--PRSMYEPEQFPGLIHRMLDPKTVILIFSSGKLVCVGAKLEKDVHRSVNQIHSLLE 178
                 79*******************9887..**************************************************99987 PP

>> DUF3378  Domain of unknown function (DUF3378)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   4.2e-07    0.0025      23      61 ..      38      76 ..      21      90 .. 0.89
   2 !   11.9   0.0   3.1e-05      0.18      24      61 ..     130     167 ..     123     181 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 4.2e-07
     DUF3378 23 rskkppyavfaakkndttItaYtSgKVlFQGknaeaeAs 61
                  ++ p+avf+ k+++t   ++ SgK +  G++ ++ A+
  EPA05123.1 38 HPEQFPGAVFRLKNPKTATLLFSSGKMVCTGAKSQELAE 76
                56789******************************9997 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 3.1e-05
     DUF3378  24 skkppyavfaakkndttItaYtSgKVlFQGknaeaeAs 61 
                  ++ p+ + +  +++t+I ++ SgK++  G++ e++  
  EPA05123.1 130 PEQFPGLIHRMLDPKTVILIFSSGKLVCVGAKLEKDVH 167
                 568899999999****************9999998765 PP

>> FlgH  Flagellar L-ring protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.3   1.5e-06     0.009      76     124 ..      69     117 ..      49     122 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.5e-06
        FlgH  76 srsnsltgtitvtVvevlpnGnLvieGekevrvnqekevirlsGiVrpe 124
                 ++s++l  t  ++Vv +l+ G++ i+ e ev++++    i+l G V+ e
  EPA05123.1  69 AKSQELAETAVAKVVSMLKKGKIKIKNEAEVTIQNIVSSINLGGRVNLE 117
                 678999999*************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.62
# Mc/sec: 907.62
//
Query:       EPA05124.1  [L=476]
Description: preprotein translocase, SecY subunit [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-61  207.5  17.1    3.5e-61  207.1  17.1    1.1  1  SecY             SecY translocase
    1.7e-11   43.8   0.7    6.2e-11   41.9   0.7    2.1  1  Plug_translocon  Plug domain of Sec61p


Domain annotation for each model (and alignments):
>> SecY  SecY translocase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.1  17.1   3.9e-65   3.5e-61       1     306 []      79     454 ..      79     454 .. 0.84

  Alignments for each domain:
  == domain 1  score: 207.1 bits;  conditional E-value: 3.9e-65
                 BTTSSTCHHHHHHHHHHHHH.HHHSSSSSSTS.-S.SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC.......HH.HHHHHHHHHHHHHHHHHHHHH CS
        SecY   1 sifaLGImPyitasIilqLl.tvvipkleelk.ke.geegrkkinqitryltvvlalvqalgialslg.......lalllivlqltagtvllmwLgEqi 89 
                 ++++LGI+P++ta++++qLl ++     e+lk +  ++e+r  ++++t+++t v+++ +++++a+++        ++l +++ ql+ +++++m+++E++
  EPA05124.1  79 TLVELGIGPIVTAGLLMQLLrGS-----EILKfDFkKPEERGVFQTATKLVTYVVIIAESIVYATAVYghnvaepWHLYVMIGQLMGASIIIMFMDELV 172
                 899*****************999.....8888776699************************985544699****999********************* PP

                 HH.HSSTTHHHHHHHHHHHHHHC.CHSS..............-HHHH.........SS.......THHHHHHHHHHHHHHHHHCHHHHBEEEECBBBST CS
        SecY  90 te.kGiGnGisllifagivarlp.kals..............gliel.........ale.....gilallllllvtllvillvvyveeaerripvqyak 158
                 ++ +G+G+Gisl+i+ag+++++  + +s                  +         a +     + l+ ++ +l+t  v+l++v+ + ++++ip+ ++k
  EPA05124.1 173 QKgWGLGSGISLFIMAGVAQQILwSLFSplpagdggtigivpY---IaesvasgdlA-NvffraNQLPSIFGFLLTAGVLLILVFTQGMKIEIPIVSTK 267
                 ***********************77777777777665544440...14444334431.044557779*******************************6 PP

                 T....S.S-EEEEETTCCCSCHHHHHHHHHHHHHCCCCS...........................................TCCCS..THHHHHHHHH CS
        SecY 159 rgrkggqssylPlklnyagviPiIfassllalpstiaqfl..........................................lalls..psvlyvvlyv 213
                     +g s  +P+kl+y ++iP+I+as+l a   +i q++                                          +a+l+    + y++++v
  EPA05124.1 268 Y---RGFSAVYPIKLIYVSNIPVILASALTANAVFIGQMFwanfnprnnnafmnilgqfdptspstpiggliyyitpprgiaIAALDpgRAIGYILFMV 363
                 5...499************************76666666666666777766666666666777776666666666666554433333533344777777 PP

                 HHHHHHHHHHHTCT.THHHHHHHCCHHTBSSSCTTT.TCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS.TT.TTHHHHHHHHHHHHHHH CS
        SecY 214 lliifFayfyteit.fnpkevaenlkksggfipgir.pgketakyLekvlsritliGalflaliavlpdllgasligafggtslLivVgvaletv 306
                  ++++F  +++e+  ++pk+ a+nl + + ++pg+r +  +++  L+k+++ +t+iG+++l+l+a ++d+lg   +g  +g ++L++V + ++++
  EPA05124.1 364 GIVVVFGRLWVELGgLSPKSAAQNLLDADVQVPGFRrSNAPVEALLNKYIPSVTIIGSIILGLLAGISDVLGV--FG--SGIGILLMVDILINYY 454
                 77888*******************************99***********************************..87..************9986 PP

>> Plug_translocon  Plug domain of Sec61p
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   0.7   6.9e-15   6.2e-11       1      35 []      45      78 ..      45      78 .. 0.97

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 6.9e-15
                     HHHHHHCCSB-TT--SSS-TCCHTTTCCCCTSSTT CS
  Plug_translocon  1 llYlvlsqiPLyGissssssDpfywlRaifAsnrG 35
                     l+Y+v++q+PL+G + +  +D++++ R+ifAs++G
       EPA05124.1 45 LIYMVMGQTPLFGAT-APEFDFLQFARVIFASAQG 78
                     7*************9.99****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (476 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 2875.85
//
Query:       EPA05125.1  [L=320]
Description: 2-oxoglutarate ferredoxin oxidoreductase subunit beta [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.8e-29  100.6   0.2    1.1e-28   99.9   0.2    1.3  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
    4.8e-15   55.5   0.6    1.2e-13   51.0   0.6    2.4  1  PFO_beta_C    Pyruvate ferredoxin oxidoreductase beta subunit


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.9   0.2   1.2e-32   1.1e-28       2     153 .]      49     196 ..      48     196 .. 0.95

  Alignments for each domain:
  == domain 1  score: 99.9 bits;  conditional E-value: 1.2e-32
                   SSHHHHHHHHHHTTSSSSEEEC.ETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEEEEEEE-SBCCCHHHH...HH CS
  TPP_enzyme_C   2 iGcltlwaarllkvkrprsylt.sgglgtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpitvvvlnNegygmtggq...qe 93 
                   iGc+             +++++  g+++ +G+ l +A G kla+pd +vva+ GDG+ l i   +++ a rrn+++t+++++N++yg+t+gq   + 
    EPA05125.1  49 IGCSGK----------TSHFINtYGVHTLHGRVLTFAQGGKLANPDMTVVAVGGDGDGLGIgAGHFVAAGRRNIDMTYIIFDNGVYGLTKGQaspTL 135
                   677776..........889999899************************************99*****************************99888 PP

                   HHTCCTTTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSSEEEEEE CS
  TPP_enzyme_C  94 pfggkrksgpagkdlkpvdfaklaealGak.garvekadveeleealkealekkgpaliev 153
                   + g+k+ks p++++ ++v++  la a G + +ar  ++dv +l++ + +a+++kg ++++v
    EPA05125.1 136 KLGEKTKSLPSPNTNYNVNPIGLAVASGFTfVARGYSYDVRHLKDLIIKAVRHKGLSFLDV 196
                   899***************************999999***********************97 PP

>> PFO_beta_C  Pyruvate ferredoxin oxidoreductase beta subunit C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0   0.6   1.3e-17   1.2e-13       1      60 [.     200     283 ..     200     287 .. 0.84

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 1.3e-17
                 XTTTXSSSXSXXX............XX-EEEGGGST---EE...........HHHHHHHHT-----EEEEEEEE.TTS--HHHH CS
  PFO_beta_C   1 CvtFNkvnTfdwY............kervykleedgyDpsd...........lekAlekalewgdkiplGifYk.eekptyeer 60 
                 C+t+N++nT dwY              r+ykle++++Dp++           l++Al k+lewg++ip+GifY+ e  + y  r
  EPA05125.1 200 CPTYNDINTRDWYagvdlaqesierHSRIYKLEDTKFDPTVhyedeaevnekLSQALIKSLEWGNSIPIGIFYQnEIISEYSTR 283
                 *************444444444433369******99**************************************6666667666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1924.81
//
Query:       EPA05126.1  [L=141]
Description: ribosomal protein L15 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-15   57.0   0.1    4.5e-15   56.5   0.1    1.3  1  Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27
  ------ inclusion threshold ------
      0.068   12.6   0.0       0.12   11.8   0.0    1.4  1  Ribosomal_L18   Ribosomal protein 60S L18 and 50S L18e


Domain annotation for each model (and alignments):
>> Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.5   0.1     5e-19   4.5e-15       6     127 ..      18     137 ..      13     138 .. 0.69

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 5e-19
                     SSTTTTTTTTT-S--......S--.........---GGG..---..................EEEEHHHHHHTTTTGTTS------EEEGGGTTT CS
  Ribosomal_L27A   6 GrGhkGqkkrsgvkkkpgfeGGqmplyrrlpkrGfknskfkkey..................kvvnlkdLdelideerleladeaeeidleelae 82 
                     G G+ Gq+  sg k   g+  G +       k +f+     ke+                  k  +++dLd+l++++  e++ ++++idl +   
      EPA05126.1  18 GWGQVGQHRASGHKGGLGI-AGLH-------KYHFSTLL--KEMpdhfghdsthpphpiitrKWASVRDLDDLFAKLGKEEG-GKKVIDLITA-- 99 
                     6666666665543333333.2222.......23333222..111222233333333444555999***********999865.89********.. PP

                     TSSS....SE.EEE--S---.--EEEESEE-HHHHHHHHHTT-EEE CS
  Ribosomal_L27A  83 aglikkkdgv.KvlgkgeltkklkvkaskfSkkAkekIeaaGGkve 127
                             g+ K+lg g+++k+ +vk+ +f+++A+ekI++aGG+v 
      EPA05126.1 100 --------GYdKLLGGGKVSKPYTVKVPRFTATAEEKIKSAGGEVL 137
                     ........************************************95 PP

>> Ribosomal_L18  Ribosomal protein 60S L18 and 50S L18e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.3e-05      0.12      99     121 ..     116     138 ..     102     140 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.3e-05
  Ribosomal_L18  99 vaALrftetararilkaGGeilt 121
                    v   rft+ta ++i  aGGe+l+
     EPA05126.1 116 VKVPRFTATAEEKIKSAGGEVLA 138
                    55669****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.30s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 921.09
//
Query:       EPA05127.1  [L=303]
Description: ornithine carbamoyltransferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-51  174.9   0.0    1.7e-51  174.4   0.0    1.2  1  OTCace    Aspartate/ornithine carbamoyltransferase, Asp/Orn b
    1.6e-49  167.7   0.0    2.2e-49  167.3   0.0    1.2  1  OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl


Domain annotation for each model (and alignments):
>> OTCace  Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.4   0.0   1.9e-55   1.7e-51       1     156 [.     151     299 ..     151     300 .. 0.95

  Alignments for each domain:
  == domain 1  score: 174.4 bits;  conditional E-value: 1.9e-55
                 CC.EEEEESSTTSHHHHHHHHHHHHCT-EEEEES-TTSSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEEEE--SSETTCCGGHHHHHHHHCC. CS
      OTCace   1 kglkiafvGdkknnvanslikllarlgmdvvlvaPkglepdkevleeakknakksggsititedleeavkgaDvvytdvwvsmgeekereerlkklkd. 98 
                 kglkia++Gd+ nnv+ns+i++++  g+++++++P+g+epd +v++e kk     + si++t+d+  a+k+aDvv+td+++s++   +  +r+kk+ + 
  EPA05127.1 151 KGLKIAWIGDG-NNVCNSMIYGCSLSGVSISIATPNGFEPDAKVVAESKK-----STSIELTSDPLIAIKNADVVITDTFTSIHT--NDPKRIKKFLPk 241
                 79*********.*********************************77666.....68************************9998..667899999988 PP

                 CSB-HHHHHHS-TT-EEEE-S---BTTTB-HHHHTSTTBHHHHHHHHHHHHHHHHHHH CS
      OTCace  99 yqvteellklakkdaivlHcLPakrgeEvtdeVfdsprsvvfeqaeNrlhtikAllvl 156
                 +qv+e+l+++akk+ai++HcLPakr+ Evt++V+d+p+svv+++aeNrlht+kAll +
  EPA05127.1 242 FQVNEKLMNHAKKNAIFMHCLPAKRDHEVTSSVIDGPQSVVWDEAENRLHTQKALLSS 299
                 *******************************************************975 PP

>> OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.3   0.0   2.5e-53   2.2e-49       1     148 []       6     145 ..       6     145 .. 0.97

  Alignments for each domain:
  == domain 1  score: 167.3 bits;  conditional E-value: 2.5e-53
                 S-BSSGGGS-HHHHHHHHHHHHHHHHHHHTTT-STTTTT-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEESTTTSCTTTGGSTTSSCHHHHHHHHHH CS
    OTCace_N   1 rhllsledlskeeieelldlaaelkekvkkekkekllkgktlallFeepStRTrvSfevAakrlGgkvlslseaediqlssvskgrkEsleDtarvlsr 99 
                 ++ll+l++l+++e++ l+d + +lk++ k + +++llk+ktl+++F++pStRTrvSfevA+++lGg++++ls ++++qls     r+Es+eDta++lsr
  EPA05127.1   6 KDLLTLAELTPKEFTGLIDYSIKLKKELK-SGNKPLLKNKTLTMIFQKPSTRTRVSFEVAMYQLGGHAVNLS-SNEMQLS-----RGESIEDTAKTLSR 97 
                 799**********************9976.789999************************************.8899999.....77************ PP

                 HTSEEEEEESSHHHHHHHHHHHSSEEEEEEETSSB-HHHHHHHHHHHHH CS
    OTCace_N 100 yvdaiviRhpgaeeleelakyasvpviNagdgdgeHPtQaLaDlltire 148
                 y+++i++R+++++ le+l + +s+pviN++ +d  HP+Q+LaD++ti+e
  EPA05127.1  98 YTNCIMARVYDHSLLEKLSQSSSIPVINGL-SDSFHPCQILADFMTIKE 145
                 ******************************.****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2059.98
//
Query:       EPA05128.1  [L=310]
Description: putative transcription initiation factor IIB [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-32  110.3   5.1    4.2e-16   58.7   0.2    2.2  2  TFIIB            Transcription factor TFIIB repeat
    1.2e-10   40.8   1.2    1.9e-10   40.0   1.2    1.4  1  TF_Zn_Ribbon     TFIIB zinc-binding
     0.0003   20.7   2.2       0.16   12.0   0.0    3.3  3  HTH_11           HTH domain
     0.0044   17.1   0.0        3.6    7.7   0.0    2.4  2  Cyclin_C         Cyclin, C-terminal domain
     0.0053   16.6   0.1       0.28   11.1   0.1    2.5  2  HTH_AsnC-type    AsnC-type helix-turn-helix domain
  ------ inclusion threshold ------
       0.01   15.8   0.2        4.5    7.4   0.0    3.3  3  Phage_terminase  Phage terminase small subunit
      0.011   15.6   0.2        3.9    7.4   0.0    2.9  3  HTH_23           Homeodomain-like domain
      0.011   15.3   2.6       0.99    9.1   0.1    2.9  3  Sigma70_r4_2     Sigma-70, region 4
      0.013   15.1   0.1       0.54    9.8   0.0    3.0  3  Sigma70_r4       Sigma-70, region 4
      0.018   14.8   0.2       0.27   11.0   0.1    2.1  2  Cyclin_N         Cyclin, N-terminal domain
      0.022   14.7   0.3      0.049   13.6   0.3    1.5  1  DZR              Double zinc ribbon
      0.027   14.3   0.4        5.1    6.9   0.0    2.3  2  DUF294_C         Putative nucleotidyltransferase substrate bi
      0.033   14.2   0.1       0.12   12.5   0.0    1.8  2  RB_B             Retinoblastoma-associated protein B domain
      0.057   13.4   0.1        0.4   10.7   0.0    2.4  2  MarR             MarR family
      0.067   13.4   0.2       0.17   12.1   0.1    1.7  1  TPR_5            Tetratrico peptide repeat
       0.08   12.5   0.1         18    5.0   0.0    2.8  2  HTH_24           Winged helix-turn-helix DNA-binding
       0.15   12.1   0.7       0.36   10.9   0.1    1.9  1  HypA             Hydrogenase/urease nickel incorporation, met
       0.15   11.8   0.3       0.15   11.8   0.3    2.3  2  zinc_ribbon_2    zinc-ribbon domain
        0.2   11.4   2.2       0.39   10.5   2.2    1.4  1  A2L_zn_ribbon    A2L zinc ribbon domain


Domain annotation for each model (and alignments):
>> TFIIB  Transcription factor TFIIB repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.7   0.2   4.5e-19   4.2e-16       2      71 .]     132     201 ..     131     201 .. 0.96
   2 !   53.6   1.0   1.8e-17   1.7e-14       1      71 []     225     295 ..     225     295 .. 0.99

  Alignments for each domain:
  == domain 1  score: 58.7 bits;  conditional E-value: 4.5e-19
                 HHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
       TFIIB   2 krfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                 +r+ d+l  ++ V ++A +++++al+++++ Grs  +++A++ly Acr  e+ rt+k++s+  ++++k i
  EPA05128.1 132 TRLKDKLAVSDAVVEKAAYIYRKALDKGLVRGRSISALIASALYAACRDTETPRTLKDVSDAGNIKKKDI 201
                 68889************************************************************99976 PP

  == domain 2  score: 53.6 bits;  conditional E-value: 1.8e-17
                 HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
       TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                 i r+a++l+++ek ++ A++++k+a e +  +G+ p g+aAA+ly+ c  + ++ tq++i++ + V+e+ti
  EPA05128.1 225 IARIASKLGISEKTKRYAVKVLKTAQEHEESAGKDPMGLAAAALYLSCVSNSENMTQRDIAEAASVTEVTI 295
                 789******************************************************************98 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   1.2   2.1e-13   1.9e-10       3      43 .]      16      56 ..      14      56 .. 0.97

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 2.1e-13
                  ETTTTCEECHEETSTTCEEESSSSBEEEECCCCCCCHHHHH CS
  TF_Zn_Ribbon  3 CPnCgstnlveDpergelvCtdCGlVlednsidegpewref 43
                  C+ Cg + +++D+++ge +C++CG V+ +   d+gpewr f
    EPA05128.1 16 CKRCGKKGMLTDNDTGERFCGKCGFVISETLQDSGPEWRSF 56
                  *****999*******************************87 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1      0.17   1.6e+02      19      34 ..     132     147 ..     124     149 .. 0.87
   2 ?    4.1   0.1     0.049        46      19      41 ..     226     248 ..     225     252 .. 0.85
   3 !   12.0   0.0   0.00017      0.16      11      41 ..     274     304 ..     268     307 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.17
      HTH_11  19 eeLAeeLnvSrrtvrr 34 
                  +L+++L vS ++v +
  EPA05128.1 132 TRLKDKLAVSDAVVEK 147
                 579********99966 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.049
      HTH_11  19 eeLAeeLnvSrrtvrrdIkaLee 41 
                 +++A +L++S++t r  +k L++
  EPA05128.1 226 ARIASKLGISEKTKRYAVKVLKT 248
                 689**********8888888876 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 0.00017
      HTH_11  11 eargpisgeeLAeeLnvSrrtvrrdIkaLee 41 
                 ++ ++++  ++Ae  +v++ t+r++ k L++
  EPA05128.1 274 SNSENMTQRDIAEAASVTEVTIRNRYKGLRM 304
                 56778*******************9998886 PP

>> Cyclin_C  Cyclin, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0039       3.6      48      89 ..     170     211 ..     161     217 .. 0.76
   2 !    7.0   0.0    0.0062       5.9       3      65 ..     221     280 ..     219     303 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0039
                 HHHHHHHCCHHHHS--S-HHHHHHC--...-HHHHHHHHHHHHHH CS
    Cyclin_C  48 Aaaalllarstlnspewtetlehytgy...skedlkpcvelilel 89 
                  a+al++a++     e  +tl+ ++ +   +k+d+  c++ +++ 
  EPA05128.1 170 IASALYAACRDT---ETPRTLKDVSDAgniKKKDIARCYRILHQE 211
                 467777777774...566777777766666***********9986 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0062
                 HHHHHHHH.HCCSSHT.-HCCHHCHHCHHHHHHCSCCHCCS-HHHHHHHHHHHCCHHHHS--S- CS
    Cyclin_C   3 plsFlrrf.lkaadasedselrtlakylleltlldydflsyppSliAaaalllarstlnspewt 65 
                 p++++ r+ +k + +  + +++  a  +l ++  + ++++ +p  +Aaaal+l++   ns++ t
  EPA05128.1 221 PIQCIARIaSKLGIS--E-KTKRYAVKVLKTAQEHEESAGKDPMGLAAAALYLSCVS-NSENMT 280
                 788888887777334..5.67778888888888888899999************998.444443 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0       0.1        98      21      33 ..     226     238 ..     220     246 .. 0.87
   2 !   11.1   0.1   0.00029      0.28      18      42 .]     279     303 ..     270     303 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.1
  HTH_AsnC-type  21 aeLAervGlSest 33 
                    a++A ++G+Se t
     EPA05128.1 226 ARIASKLGISEKT 238
                    79********987 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00029
  HTH_AsnC-type  18 isyaeLAervGlSestvlrRvrrLe 42 
                    ++ +++Ae+  ++e t+++R++ L+
     EPA05128.1 279 MTQRDIAEAASVTEVTIRNRYKGLR 303
                    789******************9875 PP

>> Phage_terminase  Phage terminase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.24   2.3e+02      20      32 ..     193     205 ..     188     212 .. 0.83
   2 ?    2.3   0.0      0.18   1.7e+02      27      39 ..     227     239 ..     221     247 .. 0.85
   3 ?    7.4   0.0    0.0048       4.5      19      41 ..     275     297 ..     258     301 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.24
  Phage_terminase  20 ggtlklkdIAkvL 32 
                      +g++k kdIA   
       EPA05128.1 193 AGNIKKKDIARCY 205
                      79********865 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.18
  Phage_terminase  27 dIAkvLdvsestv 39 
                       IA  L++se+t 
       EPA05128.1 227 RIASKLGISEKTK 239
                      69*********95 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0048
  Phage_terminase  19 sggtlklkdIAkvLdvsestvrk 41 
                      ++ ++  +dIA+   v e t+r+
       EPA05128.1 275 NSENMTQRDIAEAASVTEVTIRN 297
                      588999***************98 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       6.6   6.2e+03      19      29 ..     197     207 ..     188     210 .. 0.75
   2 ?    5.0   0.0     0.022        21      19      33 ..     224     238 ..     212     244 .. 0.90
   3 ?    7.4   0.0    0.0041       3.9      11      37 ..     268     298 ..     263     303 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 6.6
      HTH_23  19 svreIAreLgv 29 
                  +++IAr + +
  EPA05128.1 197 KKKDIARCYRI 207
                 67888887765 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.022
      HTH_23  19 svreIAreLgvsrrT 33 
                 ++++IA +Lg+s+ T
  EPA05128.1 224 CIARIASKLGISEKT 238
                 689*********988 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0041
      HTH_23  11 llllae....GlsvreIAreLgvsrrTvyrw 37 
                 l+l  +     +++r+IA++  v++ T+++ 
  EPA05128.1 268 LYLSCVsnseNMTQRDIAEAASVTEVTIRNR 298
                 444443455699****************954 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       3.1   2.9e+03       3      12 ..     123     132 ..     121     134 .. 0.79
   2 ?    5.1   0.1     0.018        17      30      42 ..     226     238 ..     225     244 .. 0.84
   3 ?    9.1   0.1     0.001      0.99      25      47 ..     277     299 ..     276     301 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 3.1
                   HHHHHHTTS- CS
  Sigma70_r4_2   3 alrealaeLp 12 
                    lr+al+eL+
    EPA05128.1 123 NLRQALSELT 132
                   6899999997 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.018
                   HHHHHHHT--HHH CS
  Sigma70_r4_2  30 kEIAellgisegt 42 
                   + IA++lgise+t
    EPA05128.1 226 ARIASKLGISEKT 238
                   67*********99 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.001
                   S---HHHHHHHHT--HHHHHHHH CS
  Sigma70_r4_2  25 eglsykEIAellgisegtVksrl 47 
                   e++++++IAe   ++e+t+++r+
    EPA05128.1 277 ENMTQRDIAEAASVTEVTIRNRY 299
                   689******************98 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       2.3   2.2e+03      18      30 ..     182     194 ..     176     200 .. 0.77
   2 ?    1.0   0.0      0.33   3.1e+02      24      36 ..     226     238 ..     225     240 .. 0.85
   3 ?    9.8   0.0   0.00057      0.54      19      42 ..     277     300 ..     267     303 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2.3
                 TTT--HHHHHHHH CS
  Sigma70_r4  18 geglTleEIgerl 30 
                 + ++Tl+++++  
  EPA05128.1 182 ETPRTLKDVSDAG 194
                 6899***999865 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.33
                 HHHHHHHTS-HHH CS
  Sigma70_r4  24 eEIgerlgiSrer 36 
                 + I+ +lgiS+ +
  EPA05128.1 226 ARIASKLGISEKT 238
                 579*******965 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00057
                 TT--HHHHHHHHTS-HHHHHHHHH CS
  Sigma70_r4  19 eglTleEIgerlgiSrerVrqiek 42 
                 e++T+ +I+e   +++ ++r + k
  EPA05128.1 277 ENMTQRDIAEAASVTEVTIRNRYK 300
                 89******************9976 PP

>> Cyclin_N  Cyclin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00028      0.27      29     123 ..     123     213 ..      97     217 .. 0.81
   2 ?    1.9   0.0      0.19   1.8e+02      36      87 ..     223     274 ..     220     303 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00028
                 HHHHHHHHHHHHHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHHHSSS---HHHHHHHTTTSS-HHHHHHHHHHHHHHTT CS
    Cyclin_N  29 emRailidwlvevaekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAaKveeisppkledlvyitdeafteeeilemErliLetLn 123
                 + R+ +++ l+++  k+ ++  ++  a+ ++ + l k  v+ + +  + a++L+ A++  e+ p +l+d+  +  + +++++i +  r + ++L+
  EPA05128.1 123 NLRQ-ALSELTRLKDKLAVSDAVVEKAAYIYRKALDKGLVRGRSISALIASALYAACRDTET-PRTLKDVSDA--GNIKKKDIARCYRILHQELE 213
                 4555.5566999***********************************************999.9999998776..56888888887777766666 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.19
                 HHHHHHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHH CS
    Cyclin_N  36 dwlvevaekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAaKv 87 
                 + + ++a+k+ ++++t   av++l    ++++   ++   ++a++L+l++  
  EPA05128.1 223 QCIARIASKLGISEKTKRYAVKVLKTAQEHEESAGKDPMGLAAAALYLSCVS 274
                 567788889999999999999999999998888888999999******9854 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.3   5.2e-05     0.049       1      23 [.      16      43 ..      15      60 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.2e-05
         DZR  1 CpqCgee.....lppdarfCseCgtklk 23
                C++Cg++     ++ + rfC++Cg  ++
  EPA05128.1 16 CKRCGKKgmltdNDTGERFCGKCGFVIS 43
                999**9999999***********97665 PP

>> DUF294_C  Putative nucleotidyltransferase substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1     0.017        16      62     100 ..     101     139 ..      97     158 .. 0.81
   2 ?    6.9   0.0    0.0054       5.1      54      96 ..     173     215 ..     167     219 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.017
    DUF294_C  62 tnTleRlkalaeagvlsaelaedlleayefllrlrlrhq 100
                  +T+eRl+    ++++ a+  ++l +a++ l+rl+ +  
  EPA05128.1 101 KSTIERLRTWDSRSKVHASSDRNLRQALSELTRLKDKLA 139
                 69***************************9998875544 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0054
    DUF294_C  54 ALeagieatnTleRlkalaeagvlsaelaedlleayefllrlr 96 
                 AL a ++ t T   lk+ ++ag +++++++++ + ++  l+l+
  EPA05128.1 173 ALYAACRDTETPRTLKDVSDAGNIKKKDIARCYRILHQELELK 215
                 89999**************************999998877776 PP

>> RB_B  Retinoblastoma-associated protein B domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00012      0.12      11      92 ..     125     204 ..     120     227 .. 0.82
   2 ?   -1.6   0.0       2.7   2.5e+03      20      45 ..     228     253 ..     222     307 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
        RB_B  11 klaavrlrdLcerLklsselrekiwtlfehvlveetellkdRhlDqillcavYvvakvtkeelsFkeiikaYrkqpqasskv 92 
                 + a + l +L ++L +s+ + ek+  + +++l  ++ l++ R +  ++ +a+Y+ ++ t++ +++k++ +a + +++  ++ 
  EPA05128.1 125 RQALSELTRLKDKLAVSDAVVEKAAYIYRKAL--DKGLVRGRSISALIASALYAACRDTETPRTLKDVSDAGNIKKKDIARC 204
                 56788999999*******99999988888887..568**********************88888888877655555544444 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.7
        RB_B  20 LcerLklsselrekiwtlfehvlvee 45 
                 + ++L +s+++++ + ++++++  +e
  EPA05128.1 228 IASKLGISEKTKRYAVKVLKTAQEHE 253
                 55666666666655555554443333 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       2.5   2.3e+03       8      25 ..     186     203 ..     185     207 .. 0.86
   2 ?   10.7   0.0   0.00042       0.4       7      34 ..     268     295 ..     264     303 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2.5
                 HHHHHHHSTTEEHHHHHH CS
        MarR   8 iLrilyeqgplsvseLak 25 
                 +L  +++ g+++ +++a+
  EPA05128.1 186 TLKDVSDAGNIKKKDIAR 203
                 68889999*******996 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00042
                 HHHHHHHHSTTEEHHHHHHHHTS-HHHH CS
        MarR   7 viLrilyeqgplsvseLakklgvskstv 34 
                 + L ++++++++++ ++a++ +v+  t+
  EPA05128.1 268 LYLSCVSNSENMTQRDIAEAASVTEVTI 295
                 579******************9987665 PP

>> TPR_5  Tetratrico peptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00018      0.17      18      78 ..     146     204 ..     132     212 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00018
       TPR_5  18 dkavplYrraLaeGLagarrrratiqLassLRnlGeaeealaLLraeleapsdelddalaa 78 
                 +ka+ +Yr+aL++GL   r r +   +as+L    +  e+ + L++  +a++ + +d  ++
  EPA05128.1 146 EKAAYIYRKALDKGLV--RGRSISALIASALYAACRDTETPRTLKDVSDAGNIKKKDIARC 204
                 7999***********5..6677777779999999888888888888777776666665555 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.019        18      19      41 ..     224     246 ..     218     249 .. 0.83
   2 ?    4.4   0.0      0.03        28      11      30 ..     272     291 ..     270     301 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.019
      HTH_24  19 sqreLAerlglSpstvnrrlkrL 41 
                 +++ +A +lg+S  t ++ +k L
  EPA05128.1 224 CIARIASKLGISEKTKRYAVKVL 246
                 6789**********999999887 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.03
      HTH_24  11 lLqknprisqreLAerlglS 30 
                 ++    +++qr++Ae+  ++
  EPA05128.1 272 CVSNSENMTQRDIAEAASVT 291
                 55666789*******87665 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00038      0.36      62      94 ..       5      40 ..       3      52 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00038
                EEEEEE--EEEETTTS-EEECHH.H..HHS-TTTSS CS
        HypA 62 LeieevpvkvrCreCgkefelee.k..alrCpkCgs 94
                L +++v+ ++ C++Cgk++ l++ +  +  C+kCg 
  EPA05128.1  5 LVLQSVDTNTGCKRCGKKGMLTDnDtgERFCGKCGF 40
                67889999************7664357668****95 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   2.8      0.51   4.8e+02       2       8 ..      16      22 ..      16      23 .. 0.90
   2 ?   11.8   0.3   0.00016      0.15       8      21 ..      27      40 ..      26      42 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.51
  zinc_ribbon_2  2 CpnCGae 8 
                   C++CG++
     EPA05128.1 16 CKRCGKK 22
                   9999997 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00016
  zinc_ribbon_2  8 elqdnakFCpyCGt 21
                    ++ +++FC +CG+
     EPA05128.1 27 DNDTGERFCGKCGF 40
                   5899*********7 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   2.2   0.00041      0.39       6      30 ..      16      41 ..      12      42 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00041
  A2L_zn_ribbon  6 CsvCggngiln.seqgylvCieCgas 30
                   C+ Cg+ g l   + g+++C +Cg++
     EPA05128.1 16 CKRCGKKGMLTdNDTGERFCGKCGFV 41
                   **********877889********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       835  (0.0465726); expected 358.6 (0.02)
Passed bias filter:                      615  (0.034302); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 1972.70
//
Query:       EPA05129.1  [L=124]
Description: hypothetical protein BG20_I1126 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      3e-07   30.4   0.1    3.5e-07   30.2   0.1    1.1  1  HemS       Haemin-degrading HemS.ChuX domain
    6.7e-07   29.2   0.0    8.6e-07   28.8   0.0    1.1  1  ChuX_HutX  Haem utilisation ChuX/HutX


Domain annotation for each model (and alignments):
>> HemS  Haemin-degrading HemS.ChuX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.1   3.9e-11   3.5e-07      25     115 ..       4      96 ..       2     116 .. 0.93

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 3.9e-11
        HemS  25 alLealeelgevmalvrNegavqektGpvenlkesghwglvlded..idLrlfldqwaeafavkkptedgvvtSlqfFdaeGeaihkvfgerk 115
                 +lL+++ + + v ++ +N+ av e+     +++++++w+ + d+d   +++++ + + +a  v++++ d +  S+ f+d++ e ++  f ++ 
  EPA05129.1   4 DLLSDIVKIDDVLLIIKNNVAVSETRSNSLSIRQKEKWITIGDNDgpSHMHINSELITHAEFVEEQKPDLISFSIRFYDQNQERVIGAFFTKM 96 
                 5899999999**********************************9899**********************************99999887765 PP

>> ChuX_HutX  Haem utilisation ChuX/HutX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0   9.6e-11   8.6e-07      30     118 ..       4      92 ..       2     102 .. 0.87

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 9.6e-11
                 HHHHHHTTS-EEEEEEEESSEEEEEEEE.....--E..EEEE..EESCTSEEEEEEGGGEEEEEEEEEEE.TTEEEEEEEEETTSSEEEEEE CS
   ChuX_HutX  30 allealeelgevmalvrnegavhEkkGkyenv.lpe..yynlagvlgeseldlhLfldhwahifaveeptkrgesrslqffdadGeavhkvy 118
                 +ll ++ ++++v ++++n+ av E   +  ++   +  ++++    ++++ ++h+  + + h+ +vee+  +  s s+ f+d++ e v+  +
  EPA05129.1   4 DLLSDIVKIDDVLLIIKNNVAVSETRSNSLSIrQ-KekWITI--GDNDGPSHMHINSELITHAEFVEEQKPDLISFSIRFYDQNQERVIGAF 92 
                 68999***********************666641.256****..578899*******************975599*********99998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 712.59
//
Query:       EPA05130.1  [L=78]
Description: hypothetical protein BG20_I1135, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      3e-07   30.0   0.0    3.7e-07   29.8   0.0    1.1  1  F420_ligase  F420-0:Gamma-glutamyl ligase


Domain annotation for each model (and alignments):
>> F420_ligase  F420-0:Gamma-glutamyl ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0     2e-11   3.7e-07     203     244 .]       3      44 ..       1      44 [. 0.96

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 2e-11
                  -B-TTS-B-S--EEEHHHHHHHHHHHHC-SSSS---EEEEES CS
  F420_ligase 203 kkdldgkelgttpravtdelgsladLvsGsadegtPvvlvrg 244
                  +kdldg++l++t +av+d+l+++a+  +G+a e+ P++++r+
   EPA05130.1   3 EKDLDGNPLKVTFQAVVDNLATIANHKMGEAAESKPFAIIRD 44 
                  79**************************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.30s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 549.35
//
Query:       EPA05131.1  [L=160]
Description: ribosomal L18p/L5e family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-14   54.0   2.8    1.9e-11   44.2   1.0    2.7  2  Ribosomal_L5e   Ribosomal large subunit proteins 60S L5, and 
  ------ inclusion threshold ------
      0.012   16.0   0.2      0.016   15.5   0.2    1.2  1  Ribosomal_L18p  Ribosomal L18 of archaea, bacteria, mitoch. a


Domain annotation for each model (and alignments):
>> Ribosomal_L5e  Ribosomal large subunit proteins 60S L5, and 50S L18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   1.0   2.1e-15   1.9e-11       7     101 ..       7      94 ..       2     107 .. 0.87
   2 !    9.3   0.0   0.00011         1     131     162 ..      97     126 ..      91     127 .. 0.77

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 2.1e-15
  Ribosomal_L5e   7 frrrregktdYyarkrliiqdknkyntpkyRlvVrvtnkdiicqiayakiegdkvlaaayskelpkygvkvgltnyaaaYatglllarrllkklg 101
                    +rr re kt+Y++r  l+          +  + V +tn+++ +qi +  ++gdkv+a+a+s+ l k g k + ++  aaY+tg+l +++++ +  
     EPA05131.1   7 LRRLREEKTNYRKRGTLLSGR-------RDFITVNITNENTQVQILKPGMTGDKVIASAHSTYLIKKGWKGSRKSVPAAYLTGYLAGKKAIGNGA 94 
                    799**************9754.......44688******************************************************99886654 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00011
  Ribosomal_L5e 131 aiLdvGLartttgakvfgalkgavdgglsiph 162
                    a+L  G +r t  +++ +alkg+vd+gl +p 
     EPA05131.1  97 AVLYTGTRRYT--QRMAAALKGVVDAGLIVPA 126
                    56666666655..6899***********9995 PP

>> Ribosomal_L18p  Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.2   1.8e-06     0.016      13     114 ..      18     122 ..       6     124 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.8e-06
                     HHTTT--TTSSS-EEEEEE-SS-EEEEEE-T..TT--EEEEECS-SCCCT..S-SSSCHHHHHHHHHHHHHHHCHHCHTC-EE--TTSSS-CHHH CS
  Ribosomal_L18p  13 RirkklsgtaerprlvvfrsnrhiyaQvidd..vkgktlasastlekelk..lkstknkeaakkvgeliAerakekgiekvvfDrggykYhGrva 103
                     R r +l     r  ++v  +n++  +Q++    + +k++asa +     k  + s+k+  aa   g l  ++a  +g +++v  +g  +Y  r+a
      EPA05131.1  18 RKRGTLLSG-RRDFITVNITNENTQVQILKPgmTGDKVIASAHSTYLIKKgwKGSRKSVPAAYLTGYLAGKKAIGNGAKDAVLYTGTRRYTQRMA 111
                     445555433.378899*************86337899***998765544444578888889999999999************************* PP

                     HHHHHHHCTSS CS
  Ribosomal_L18p 104 alAdaaReaGl 114
                     a  +++ +aGl
      EPA05131.1 112 AALKGVVDAGL 122
                     98888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1038.07
//
Query:       EPA05132.1  [L=144]
Description: hypothetical protein BG20_I1132 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.49
# Mc/sec: 879.93
//
Query:       EPA05133.1  [L=323]
Description: putative glyoxylate reductase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-60  203.7   0.1      2e-60  203.2   0.1    1.2  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
    3.6e-32  110.8   0.0    4.1e-32  110.6   0.0    1.0  1  2-Hacid_dh     D-isomer specific 2-hydroxyacid dehydrogenase,
    7.5e-07   28.9   0.6    1.4e-06   28.0   0.2    1.6  2  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind
    1.2e-06   28.7   0.3    2.7e-06   27.6   0.2    1.5  2  NAD_binding_2  NAD binding domain of 6-phosphogluconate dehyd
    0.00085   19.9   0.1     0.0035   17.9   0.1    2.1  2  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
      0.057   13.5   0.3        0.1   12.7   0.3    1.4  1  AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD bindi


Domain annotation for each model (and alignments):
>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  203.2   0.1   6.7e-64     2e-60       2     178 .]     111     290 ..     110     290 .. 0.97

  Alignments for each domain:
  == domain 1  score: 203.2 bits;  conditional E-value: 6.7e-64
                   HHHHHHHTTHHHHHHHHHTTCC...HTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEE CS
  2-Hacid_dh_C   2 alllallrrlaeadeevregew...ksekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelvsleellaesDiv 95 
                   +ll+++lrr++e+d+ +r g+w       ++ g +l+gkt+Gi+GlGrIG ++akr+kaf+mk+i+++r+  ++++e++lg+++v++e+l++ sDi+
    EPA05133.1 111 SLLIDILRRVSEGDRIIRCGRWqeiFGAYDYVGVDLQGKTLGILGLGRIGGTLAKRAKAFDMKIIYHNRKAVSKSKEKTLGAKYVTFEKLIKYSDII 207
                   7999******************6665666999****************************************999********************** PP

                   EE-S--STTTTTSBSHHHHHCSTTTEEEEESS-GGGB-HHHHHHHHHTTSCCEEEES--SSSSSGTCHHHHHSTTEEE-SS-T CS
  2-Hacid_dh_C  96 slhlpltpetrhlinaeelakmkkgailiNtaRGglvdeeaLleaLksgkiagaalDvfeeeplpedspllelpnviltPHia 178
                   s+h+p t  t++l++ + ++kmkk+a+liNtaRG++++e++L+ aL+++ iagaalDvfe+ep+ +++pl++ +nv+l PHi+
    EPA05133.1 208 SIHVPHTTLTNQLFDMKIFKKMKKTAVLINTARGKIINEKDLIVALDKKIIAGAALDVFESEPIGKNHPLTKIQNVVLAPHIG 290
                   *********************************************************************************98 PP

>> 2-Hacid_dh  D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.6   0.0   1.4e-35   4.1e-32       1     133 [.       6     321 ..       6     322 .. 0.98

  Alignments for each domain:
  == domain 1  score: 110.6 bits;  conditional E-value: 1.4e-35
                 EEEEST.CHHHHHHHHHTTEEEEEES...CSSHHHCHHHHTTESEEEE-TTS-BSHHHHHHHTT--EEEESSSSCTTB-HHHHHHTT-EEEE-TTTTHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  2-Hacid_dh   1 vlileplreeelellkeegvevevkd...ellteellekakdadalivrsntkvtaevlealpkLkviaragvGvDnvDldaakerGilVtnvpgyste 96 
                 v+++++l++ +l+ lk+ ++++ev++   ++++ +l  k++d+d+li++  +k+++e+++a+++Lkvi++++vG+D++D ++ake+ i V ++p++ t+
  EPA05133.1   6 VFLTRTLHDFALNELKK-RYQIEVHSgkiPIPKTKLRFKIQDIDGLICFPYDKIDKEIIDAAKNLKVISTYSVGFDHIDTQYAKEKKIRVGHTPEVLTD 103
                 56788889999999999.77*******9999999***************************************************************** PP

                 HHHHHH............................................................................................. CS
                 xxxxxx............................................................................................. RF
  2-Hacid_dh  97 svAElt............................................................................................. 102
                 ++A+l+                                                                                             
  EPA05133.1 104 ATADLAfsllidilrrvsegdriircgrwqeifgaydyvgvdlqgktlgilglgriggtlakrakafdmkiiyhnrkavskskektlgakyvtfeklik 202
                 *************************************************************************************************** PP

                 ........................................................................................T-BHHHHHHHH CS
                 ........................................................................................xxxxxxxxxxx RF
  2-Hacid_dh 103 ........................................................................................aaTeeaqenia 113
                                                                                                         ++T+e++e++a
  EPA05133.1 203 ysdiisihvphttltnqlfdmkifkkmkktavlintargkiinekdlivaldkkiiagaaldvfesepigknhpltkiqnvvlaphigSSTKETREKMA 301
                 *************************************************************************************************** PP

                 HHHHHHHHHHHTTCCGTTBC CS
                 xxxxxxxxxxxxxxxxxxxx RF
  2-Hacid_dh 114 eeaaenlvaflkgespanav 133
                 +++++nl   ++g++p + v
  EPA05133.1 302 MITVKNLNLGINGKTPVYSV 321
                 *************9997765 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.1   3.3e+03      40      59 ..      83     102 ..      60     118 .. 0.59
   2 !   28.0   0.2   4.8e-10   1.4e-06       2      96 ..     146     241 ..     145     259 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.1
                 HHHHHHHTT-EEEEHHHHHH CS
        IlvN  40 svkkAkeegfevltvaeavk 59 
                  ++ Ake+ ++v ++ e+ +
  EPA05133.1  83 DTQYAKEKKIRVGHTPEVLT 102
                 34556666666666666654 PP

  == domain 2  score: 28.0 bits;  conditional E-value: 4.8e-10
                 HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HH.HHHHHHHHHTGGG--TT-EEE.ESSS CS
        IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDe.lqkevyeeeiepnlkegkala.fahG 96 
                 l+gk++ ++G G  G + a+  +   +++++ +r+   s +k k  g + +t ++++k +d++ i +P + l +++++ +i +++k+ ++l   a G
  EPA05133.1 146 LQGKTLGILGLGRIGGTLAKRAKAFDMKIIYHNRKAV-SKSKEKTLGAKYVTFEKLIKYSDIISIHVPHTtLTNQLFDMKIFKKMKKTAVLInTARG 241
                 89*****************************999887.88999999**********************8625789************9987514555 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       4.4   1.3e+04      74      90 ..     114     130 ..     103     131 .. 0.73
   2 !   27.6   0.2     9e-10   2.7e-06       2     107 ..     151     256 ..     150     264 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 4.4
                    HSHCCC--TT-EEEE-S CS
  NAD_binding_2  74 egllealkkgdilidgs 90 
                     ++l+++++gd +i ++
     EPA05133.1 114 IDILRRVSEGDRIIRCG 130
                    44788899999999887 PP

  == domain 2  score: 27.6 bits;  conditional E-value: 9e-10
                    EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS.HCCC--TT-EEEE-S---HHH CS
  NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdevieg.llealkkgdilidgstssped 96 
                    +g++GlG +G  +a++ ++ ++k++ +nr++ +  +  + ga  + + e+l++  d++ + v++++ ++++ +  +++++kk ++li+++  ++ +
     EPA05133.1 151 LGILGLGRIGGTLAKRAKAFDMKIIYHNRKAVSKSKEKTLGA-KYVTFEKLIKYSDIISIHVPHTTLTNQLFDMkIFKKMKKTAVLINTARGKIIN 245
                    79**************************98544444444445.5667899***********************99************999888888 PP

                    HHHHHHHHHHT CS
  NAD_binding_2  97 trelakelkek 107
                     ++l  +l +k
     EPA05133.1 246 EKDLIVALDKK 256
                    77777777666 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.6   4.7e+03      72      95 ..      95     117 ..      88     119 .. 0.82
   2 !   17.9   0.1   1.2e-06    0.0035       2      94 ..     151     238 ..     150     241 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.6
                    HHHHHHHHHCGHHHHTTSEEEEES CS
  F420_oxidored  72 edveevlselakdalkgklvisvl 95 
                     +++evl+++  ++l+ +l+i++l
     EPA05133.1  95 GHTPEVLTDA-TADLAFSLLIDIL 117
                    5788999999.8889999999986 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 1.2e-06
                    EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHH.HHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHHC..GHHHHTTSEEEEE CS
  F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekae.elaeelgvkvtavdneeaaeeadvvvlavkpedveevlsel..akdalkgklvisv 94 
                    +gi+G G++g +la+++ a +    +i+     n + +  + +++l  +++ v+ e++++ +d++ + v+ + +++ l ++  +k+ +k  ++i +
     EPA05133.1 151 LGILGLGRIGGTLAKRAKAFD---MKII-Y--HNRKAVSkSKEKTL--GAKYVTFEKLIKYSDIISIHVPHTTLTNQLFDMkiFKKMKKTAVLINT 238
                    89**************99999...8888.4..23333330333455..566666*************99999988877766556666677777665 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.3   3.4e-05       0.1      21     110 ..     146     239 ..     137     263 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.4e-05
                    -TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCTT-EE--HHHCTTT-SEE...E.E-SSSSSSB-HHHHCCS-TTEEEEE-S CS
  AdoHcyase_NAD  21 laGkvavvaGyGdvGkGcaaslkglGarvivtevdPicalqaameGfevvtleevvkkadiv...v.tttGnkdiitlehlkkmkddaivcniG 110
                    l Gk+  + G G +G   a+  k++  ++i  +   ++  +    G + vt+e+++k +di+   v  tt ++++  ++ +kkmk++a++ n  
     EPA05133.1 146 LQGKTLGILGLGRIGGTLAKRAKAFDMKIIYHNRKAVSKSKEKTLGAKYVTFEKLIKYSDIIsihVpHTTLTNQLFDMKIFKKMKKTAVLINTA 239
                    78**********************************************************9732233477888999**************9974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 1838.38
//
Query:       EPA05134.1  [L=212]
Description: integral membrane protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    7.6e-16   58.3  14.5    4.1e-15   55.9  14.5    1.8  1  EMC3_TMCO1  Integral membrane protein EMC3/TMCO1-like
  ------ inclusion threshold ------
       0.62    9.6   9.1        0.3   10.7   3.6    2.6  3  DUF2208     Predicted membrane protein (DUF2208)
        6.2    7.2   9.4          7    7.0   7.1    2.1  3  DUF4199     Protein of unknown function (DUF4199)


Domain annotation for each model (and alignments):
>> EMC3_TMCO1  Integral membrane protein EMC3/TMCO1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.9  14.5   6.9e-19   4.1e-15      16     165 ..      47     204 ..      36     209 .. 0.78

  Alignments for each domain:
  == domain 1  score: 55.9 bits;  conditional E-value: 6.9e-19
  EMC3_TMCO1  16 ivivillvgiltgllsellqkllidkkkmekeqkrekelqkrarelqkngdklklkklekrqeelmedqsemmmdqmkpmivtmipqiliffwlnsffs 114
                 +   +  +gil  l+   ++k+++d++k+ ++ k  +  qk+   +++++d+ k  +l+k++ ++++ ++emm++ m+pm++t++p ilif+++  ++ 
  EPA05134.1  47 F--AVTGFGILLNLFNAAVRKKMVDRTKLARIMKETRSWQKERMSAMRSKDQAKINELNKKSSYMNKMSMEMMQMNMRPMMITFVPLILIFYLVLPVLF 143
                 4..5567899**********************************************************************************9998777 PP

  EMC3_TMCO1 115 gfvvaklpfpltgrfksllqrgl.......esldv...rfvssiswYflcsfglsqiirkl 165
                  ++va  p+ l +    + +           + ++   +  +   wYfl+s+++s+ii k+
  EPA05134.1 144 SHIVALSPVSLDIIPGNFFHLTCtaeqaadPNDVCpaeNALYLWAWYFLSSIAFSGIIMKV 204
                 666666665554444444443344442333333331112345668*************997 PP

>> DUF2208  Predicted membrane protein (DUF2208)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.13   7.8e+02     139     177 ..      20      57 ..       6      71 .. 0.69
   2 ?   10.7   3.6   5.1e-05       0.3      66     118 ..      96     149 ..      67     163 .. 0.71
   3 ?    0.7   0.1     0.057   3.4e+02      19      43 ..     184     209 ..     180     212 .] 0.73

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.13
     DUF2208 139 alflismflrllarrvlkklvmlimatsykvtekGivlk 177
                 ++f++  + +  a+ +  + v  ++ t ++vt  Gi+l+
  EPA05134.1  20 GIFGFLGGGT-HAMGSEDPIVKGVVLTAFAVTGFGILLN 57 
                 5555555553.4556666777777888999999999987 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 5.1e-05
     DUF2208  66 EknalkliekDeelqkelkeqlkasmitllllliviil.ffllyryiiplassl 118
                   + ++l +k   ++k  +e+++++m +++++++ +il f+l+ +++++ +++l
  EPA05134.1  96 QAKINELNKKSSYMNKMSMEMMQMNMRPMMITFVPLILiFYLVLPVLFSHIVAL 149
                 5577888888888999999************88866551455666666555554 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.057
     DUF2208  19 fl.pqylflviilYiivimvimsvlt 43 
                 ++ ++++fl  i++  +im ++ + +
  EPA05134.1 184 LYlWAWYFLSSIAFSGIIMKVTKTSM 209
                 55588888888888888888876655 PP

>> DUF4199  Protein of unknown function (DUF4199)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1      0.16   9.8e+02     140     167 ..      37      65 ..      28      66 .. 0.74
   2 ?    7.0   7.1    0.0012         7     108     165 ..      77     146 ..      38     149 .. 0.38
   3 ?   -2.5   0.0      0.99   5.9e+03     155     163 ..     190     198 ..     175     206 .. 0.51

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.16
     DUF4199 140 piiv.alqsflgnliiGlilsliiAlilk 167
                 pi   ++ +++  + +G++l l+ A++ k
  EPA05134.1  37 PIVKgVVLTAFAVTGFGILLNLFNAAVRK 65 
                 55445788888888999999999998866 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0012
     DUF4199 108 lekleeakeesae.eenaemseeeike...........alesls....piivalqsflgnliiGlilsliiAli 165
                 ++++ ++++e ++ + +  +++++i+e            +e+++    p+  +++++  +li++l+l ++++ i
  EPA05134.1  77 MKETRSWQKERMSaMRS--KDQAKINElnkkssymnkmSMEMMQmnmrPM--MITFVPLILIFYLVLPVLFSHI 146
                 33333333333332222..3333332222233322222222333444443..5555555555555444443333 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 0.99
     DUF4199 155 GlilsliiA 163
                 +++ s+ ++
  EPA05134.1 190 YFLSSIAFS 198
                 222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1929  (0.107591); expected 358.6 (0.02)
Passed bias filter:                      903  (0.0503653); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.51
# Mc/sec: 1249.60
//
Query:       EPA05135.1  [L=186]
Description: putative cytidylate kinase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-12   46.9   0.0    5.1e-12   46.5   0.0    1.2  1  AAA_18           AAA domain
    1.4e-11   44.9   0.3    3.2e-10   40.4   0.3    2.1  1  Cytidylate_kin2  Cytidylate kinase-like family
    2.1e-09   37.9   0.0    3.8e-09   37.1   0.0    1.4  1  AAA_17           AAA domain
    1.2e-07   31.7   0.2    8.2e-05   22.4   0.0    2.1  2  Cytidylate_kin   Cytidylate kinase
      2e-05   24.7   0.3    6.5e-05   23.1   0.0    1.9  2  ADK              Adenylate kinase
      3e-05   24.2   0.3    0.00076   19.6   0.3    2.2  1  SKI              Shikimate kinase
    6.5e-05   23.4   0.0    0.00011   22.7   0.0    1.5  1  AAA              ATPase family associated with various cellul
    0.00031   20.7   0.0     0.0005   20.0   0.0    1.4  1  Rad17            Rad17 P-loop domain
    0.00052   20.3   0.0    0.00094   19.5   0.0    1.5  1  AAA_28           AAA domain
    0.00067   19.8   0.1     0.0011   19.2   0.1    1.6  1  AAA_33           AAA domain
     0.0019   18.5   0.1     0.0045   17.3   0.0    1.6  2  Hydin_ADK        Hydin Adenylate kinase-like domain
     0.0032   17.0   0.1      0.011   15.2   0.1    1.8  1  KTI12            Chromatin associated protein KTI12
     0.0033   17.3   0.5      0.092   12.6   0.1    2.2  2  dNK              Deoxynucleoside kinase
     0.0038   16.7   0.3     0.0061   16.0   0.0    1.4  2  DUF3616          Protein of unknown function (DUF3616)
      0.005   17.2   0.0       0.01   16.2   0.0    1.6  1  RNA_helicase     RNA helicase
     0.0075   16.3   0.2      0.055   13.5   0.1    2.4  1  AAA_14           AAA domain
     0.0078   15.9   0.0      0.016   14.9   0.0    1.6  1  AAA_24           AAA domain
     0.0091   15.6   0.7      0.011   15.3   0.7    1.1  1  DUF4960          Domain of unknown function (DUF4960)
  ------ inclusion threshold ------
      0.016   15.3   0.6       0.02   15.0   0.6    1.2  1  RTX_C            RTX C-terminal domain
      0.016   14.9   0.1      0.024   14.4   0.1    1.3  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      0.019   15.4   0.0      0.019   15.4   0.0    1.2  1  AAA_16           AAA ATPase domain
       0.03   14.6   0.0      0.065   13.5   0.0    1.5  1  AAA_22           AAA domain
       0.08   12.8   0.0       0.14   12.1   0.0    1.5  1  NTPase_1         NTPase
      0.092   13.1   1.1       0.32   11.3   0.0    2.4  2  Nif11            Nif11 domain
       0.12   12.1   1.3        2.7    7.6   0.0    2.4  2  Guanylate_kin    Guanylate kinase


Domain annotation for each model (and alignments):
>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   0.0   7.1e-15   5.1e-12       1     119 [.       5     128 ..       5     145 .. 0.84

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 7.1e-15
      AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpe.......aldeskrldedkldklldaleenssaleegknlvidghlaele 87 
                 I+++G+p+vGKtt+ak L+k+ ++     g++l+++ake g   + d+        ++ ++++   ++++k+ d+l + ++   +g+  vi +    ++
  EPA05135.1   5 IVISGPPAVGKTTVAKGLAKEFNLtylsgGDILKELAKEQGFDVTGDDWwdtesgmKFLNQRETHSEFDKKVDDKLIQLYN---KGGM-VITSYTLPWL 99 
                 99*******************98899***************9988887777889999999999999999999999999865...6666.6666666666 PP

      AAA_18  88 seaakdikkvvLtaspeelleRlekRgyeeak 119
                  ++ ++   ++L  s +   +R+++R++++  
  EPA05135.1 100 VDNGIK---IWLSGSHDSSSKRMQTRDNMTSQ 128
                 655554...*****************987655 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   0.3   4.5e-13   3.2e-10       2     178 ..       5     167 ..       4     168 .. 0.82

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 4.5e-13
  Cytidylate_kin2   2 ITIsreyGsgGetigeaLAekLglpfydr.eiieevakelglseeeveevdersrlssflskllaarvagdtldeklddelfeaqervirelaa 94 
                      I Is+  + g++t+++ LA++++l +++  +i++e+ake g++       d +s   +fl++    r +  ++d+k dd+       +i+ l +
       EPA05135.1   5 IVISGPPAVGKTTVAKGLAKEFNLTYLSGgDILKELAKEQGFDVTGDDWWDTESG-MKFLNQ----RETHSEFDKKVDDK-------LIQ-LYN 85 
                      7799999*********************99*************999988888777.455543....33333334444444.......444.444 PP

  Cytidylate_kin2  95 eesvVivGRgadliLkdrpnvlrvfltapledrvkrvaereglseeearekiketDkrrakyykkytgqdw.gdaenYdlvlnts 178
                      + ++Vi        L   +n ++++l+++ ++  kr+++r +++ +ea++  k + +++++ ykk+++ d  +d++ +d +++t+
       EPA05135.1  86 KGGMVITSYTLPW-L--VDNGIKIWLSGSHDSSSKRMQTRDNMTSQEAYQITKIRYDKNRALYKKLYNFDFgSDTSVFDKIIDTD 167
                      4388887655443.3..3468**************************************************889999*****997 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   0.0   5.4e-12   3.8e-09       2      78 ..       9      93 ..       8     105 .. 0.76

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 5.4e-12
                E-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTT.......SHSSHHHHC.TSHHHHHHHHHHHHHHHHHHHHHSSEEEEEE CS
      AAA_17  2 GgPGsGKgtqceklvekygfthlsaGdllreeakrgg.......lakardemr.klpleekkelqkeaaekiaeeakkkgvlvdg 78
                G+P +GK+t+++ l++++++t+ls Gd+l e ak++g         ++++ m+  ++ e   e++k++ +k+ +  +k+g++++ 
  EPA05135.1  9 GPPAVGKTTVAKGLAKEFNLTYLSGGDILKELAKEQGfdvtgddWWDTESGMKfLNQRETHSEFDKKVDDKLIQLYNKGGMVITS 93
                9***********************************9444433312233444423455556688888888888877777777765 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   1.1e-07   8.2e-05       1      37 [.       5      41 ..       5      65 .. 0.92
   2 !    7.7   0.0    0.0036       2.6      99     209 ..      73     182 ..      56     184 .. 0.71

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.1e-07
                    EEEE-STTSSHHHHHHHHHHHHT-EEEEHHHHHHHHH CS
  Cytidylate_kin  1 iaiDGPagsGKssvaralaeklglkyldtgalYRala 37
                    i i GP + GK +va+ la++++l+yl+ g + + la
      EPA05135.1  5 IVISGPPAVGKTTVAKGLAKEFNLTYLSGGDILKELA 41
                    7799**************************9987765 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0036
                     HHHHHHHHHTT-BSSBEEEEESSIIIIISTT-SEEEEEE--HHHHHHHHHHHHHHTT----HHHHHHHHHHHHHHHHCTSSS-S---TT-E.... CS
  Cytidylate_kin  99 RailvkklrelvkkarvvveGRDigtvvfpdaelKifldAsveeRakRRlkqlkakgtsvsleellaeikeRDklDkerevgpLklaedal.... 189
                      +++ +kl +l +k+++v+     +   ++d  +Ki+l  s +   kR ++ +++  ++++++  + +i+   ++   ++++++   +d      
      EPA05135.1  73 DKKVDDKLIQLYNKGGMVITSY--TLPWLVDNGIKIWLSGSHDSSSKR-MQTRDNMTSQEAYQ--ITKIRYDKNRALYKKLYNFDFGSDTSvfdk 162
                     5666677777777777777643..445678999*******99987665.55544443334443..567777777777899999999999752344 PP

                     EEETTTS-HHHHHHHHHHHH CS
  Cytidylate_kin 190 iidtskltieevvekileli 209
                     iidt++l +++v++ + e++
      EPA05135.1 163 IIDTDNLNATQVINIAKETV 182
                     799**********9877665 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   9.1e-08   6.5e-05       1      37 [.       7      43 ..       7      49 .. 0.92
   2 ?   -2.2   0.0       5.7   4.1e+03      90     110 ..     158     178 ..     154     182 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 9.1e-08
                EEESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHHC CS
                xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
         ADK  1 llGaPgaGKGtqaeklvkkyglahlstGdllRaevks 37
                + G+P+ GK t+a+ l+k+++l+ ls Gd+l++  k+
  EPA05135.1  7 ISGPPAVGKTTVAKGLAKEFNLTYLSGGDILKELAKE 43
                57*****************************987765 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.7
                 HHHHHHHHHHTSEESEEEEEE CS
                 xxxxxxxxxxxxxxxxxxxxx RF
         ADK  90 ealeelleeekvkldlvleld 110
                 + +++++++++ + + v+++ 
  EPA05135.1 158 SVFDKIIDTDNLNATQVINIA 178
                 567888888888888888875 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.3   1.1e-06   0.00076       2     142 ..      12     156 ..      11     178 .. 0.61

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.1e-06
                 TSSHHHHHHHHHHHHTSEEEEHHHHH.....HHHHTS-HHHHHHHHHHHHHHHHHHHH..HHHHCCCS.SEEEEE-TTGGGSHHHHHHHHHHSEEEEEE CS
         SKI   2 GaGKstvGkllAkklglefiDlDeli.....ekrtgksiaeifeeegeegFrelEsev..lkelleee.glViatGGGavlseenrellkekgiviyLd 92 
                 ++GK+tv+k lAk+ +l+++   +++     e+ +  +  +  + e   +F ++ +    +++ ++ +       GG++++s    +l+  +gi i+L 
  EPA05135.1  12 AVGKTTVAKGLAKEFNLTYLSGGDILkelakEQGFDVTGDDWWDTESGMKFLNQRETHseFDKKVDDKlIQLYNKGGMVITSYTLPWLVD-NGIKIWLS 109
                 68*****************98776662223333333555666776666666544322212444444432333344555555555555555.******** PP

                 --HHHHHHHHHHTTSSGGGCSCHHHHHHHHHHH.HHHHHHCCSSCEEEECT CS
         SKI  93 vsleellerlkadkeRPllqekskeeelleela.ereplyeeaadvvvdes 142
                  s ++  +r++ +++  + +++    + ++  + + ++ly+++ +  + ++
  EPA05135.1 110 GSHDSSSKRMQTRDN--MTSQEAY--QITKIRYdKNRALYKKLYNFDFGSD 156
                 **************9..3333333..4444444466777777644444433 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   1.5e-07   0.00011       2      41 ..       6      43 ..       5      85 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.5e-07
                EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTH CS
         AAA  2 llyGppGtGKTllakavakelgvefleisgsellskyvge 41
                +++Gpp +GKT++ak +ake  +++  +sg ++l+++ +e
  EPA05135.1  6 VISGPPAVGKTTVAKGLAKE--FNLTYLSGGDILKELAKE 43
                789*****************..566777888888664444 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   6.9e-07    0.0005      48     115 ..       5      75 ..       2     133 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 6.9e-07
       Rad17  48 LLisGPsGCgkstvvkvLskelgiklrewlnpvslkepdn.qksdfkg....ltekesrflsqiesfkeleLk 115
                 ++isGP+  gk+tv k L+ke+   +     +  lke    q  d+ g    +te   +fl q e+++e+  k
  EPA05135.1   5 IVISGPPAVGKTTVAKGLAKEFNLTYLSG--GDILKELAKeQGFDVTGddwwDTESGMKFLNQRETHSEFDKK 75 
                 689******************99888754..33334433224444444111167778899**********654 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   1.3e-06   0.00094       2      59 ..       5      66 ..       4      92 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.3e-06
      AAA_28  2 ivitGgestGKTtlleaLaar.gypvv..pEaareileeklakgedalpwv.edllafaerv 59
                ivi+G++  GKTt+++ La++ + +++   ++  e+ +e++++ +++  w  e  ++f  ++
  EPA05135.1  5 IVISGPPAVGKTTVAKGLAKEfNLTYLsgGDILKELAKEQGFDVTGDDWWDtESGMKFLNQR 66
                9******************9876665556888888888888766665555555556665554 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   1.5e-06    0.0011       2      41 ..       5      44 ..       5     143 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.5e-06
      AAA_33  2 vllvGlpGsGKstlaerllkklgavllssdtlrrrlfgtd 41
                +++ G+p++GK+t+a++l+k+   + ls  ++++ l++++
  EPA05135.1  5 IVISGPPAVGKTTVAKGLAKEFNLTYLSGGDILKELAKEQ 44
                5788*****************9999999988888887754 PP

>> Hydin_ADK  Hydin Adenylate kinase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   6.2e-06    0.0045       2      34 ..       5      37 ..       4      46 .. 0.89
   2 ?   -1.7   0.0       4.2     3e+03     131     131 ..     116     116 ..      57     145 .. 0.58

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 6.2e-06
   Hydin_ADK  2 iivhGaPlsGKtatavtLakkYeaAlltiDsvv 34
                i++ G+P  GKt+ a  Lak+++  +l+  +++
  EPA05135.1  5 IVISGPPAVGKTTVAKGLAKEFNLTYLSGGDIL 37
                9************************99866665 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 4.2
   Hydin_ADK 131 e 131
                 +
  EPA05135.1 116 S 116
                 1 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   1.5e-05     0.011       4      27 ..       5      28 ..       4      81 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.5e-05
                EEEE--TTSSHHHHHHHHHHHHHH CS
       KTI12  4 vvltGlPssGKstrakeLakalee 27
                +v++G P++GK+t+ak Lak+++ 
  EPA05135.1  5 IVISGPPAVGKTTVAKGLAKEFNL 28
                89******************9976 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.1   0.00013     0.092       1      25 [.       5      29 ..       5      45 .. 0.91
   2 ?    3.4   0.1     0.085        61     125     152 ..     104     134 ..      67     182 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00013
                EEEEESTTSSHHHHHHHHHCCSTCE CS
         dNK  1 ivveGnIgaGKstlvklLskklgvk 25
                iv++G+ ++GK+t++k L+k+++  
  EPA05135.1  5 IVISGPPAVGKTTVAKGLAKEFNLT 29
                89******************99865 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.085
                 EEEEEE--HHHHHHHHHHCTTCCCT...TS- CS
         dNK 125 lliYLkasletclerikkRgreeek...kie 152
                 + i+L  s ++  +r++ R++   +   +i 
  EPA05135.1 104 IKIWLSGSHDSSSKRMQTRDNMTSQeayQIT 134
                 569999*************998766556443 PP

>> DUF3616  Protein of unknown function (DUF3616)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       5.7   4.1e+03     161     170 ..      41      50 ..      34      50 .. 0.84
   2 !   16.0   0.0   8.6e-06    0.0061      67     134 ..     106     174 ..      99     185 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 5.7
     DUF3616 161 sKdnGlDiEG 170
                 +K+ G+D+ G
  EPA05135.1  41 AKEQGFDVTG 50 
                 79*****987 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 8.6e-06
     DUF3616  67 LWlvGShslkRkkpk.eekseeknlerLakvkedanryllariplvkekdaksllkpeaeeekltaakl 134
                 +Wl GSh +  k+++ +++ +++++ +++k++ d+nr l  ++   +  + +s+ ++  ++++l+a+++
  EPA05135.1 106 IWLSGSHDSSSKRMQtRDNMTSQEAYQITKIRYDKNRALYKKLYNFDFGSDTSVFDKIIDTDNLNATQV 174
                 8******7777777756777889999*************999988887777777777777777777665 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.5e-05      0.01       1      47 [.       5      57 ..       5      94 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.5e-05
  RNA_helicase  1 iwlyGpsgeGKStlakeLakallkkl........klkkkdsvysrnpeddfwdgY 47
                  i+++Gp+ +GK+t+ak Lak++  ++        +l k++ +    + dd+wd  
    EPA05135.1  5 IVISGPPAVGKTTVAKGLAKEFNLTYlsggdilkELAKEQGF--DVTGDDWWDTE 57
                  789*******************96666777776444443333..56888888865 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.1   7.6e-05     0.055       3      37 ..       3      32 ..       1     154 [. 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.6e-05
      AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyin 37
                k +vi+G+  vGKTt++k l+ke         y++
  EPA05135.1  3 KSIVISGPPAVGKTTVAKGLAKEFN-----LTYLS 32
                679*****************98866.....44443 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   2.3e-05     0.016       2      39 ..       2      64 ..       1      85 [. 0.69

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.3e-05
      AAA_24  2 klkiliyGpsgiGKTtlakel..gpkplfi..........................dtekGlksld 39
                 ++i+i Gp+ +GKTt+ak l  +  +  +                          dte G+k l+
  EPA05135.1  2 TKSIVISGPPAVGKTTVAKGLakE--FN-LtylsggdilkelakeqgfdvtgddwwDTESGMKFLN 64
                579****************99432..22.2244666666666666666666666666666665555 PP

>> DUF4960  Domain of unknown function (DUF4960)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.7   1.5e-05     0.011      52     160 ..      53     162 ..      27     182 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.5e-05
     DUF4960  52 wfhlhvdntidnekkleaeakaaveaklkeyyekGgnllLsrlavkyvvklgia..ldgkepnnvwGesedseevtdepWsll.ikgkedHplfkgltt 147
                 w+ ++   ++ n+ + ++e ++ v+ kl ++y+kGg  +++++ + + v+ gi   l+g +   +   +   +++++e+++++ i+++++ +l+k l  
  EPA05135.1  53 WWDTESGMKFLNQRETHSEFDKKVDDKLIQLYNKGGM-VITSYTLPWLVDNGIKiwLSGSHDSSSKRMQTRDNMTSQEAYQITkIRYDKNRALYKKLYN 150
                 99999999999************************96.679999*****98876214555555544334444444577777644999********9987 PP

     DUF4960 148 kkgeksaiylldk 160
                  +  ++++ ++dk
  EPA05135.1 151 FDFGSDTS-VFDK 162
                 66544433.3444 PP

>> RTX_C  RTX C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.6   2.8e-05      0.02      21     118 ..      40     135 ..      26     168 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.8e-05
       RTX_C  21 ikkrnkeavtikdWFkeddyakkvleykaekdrvdkslnnkiEeiigkdGeritsqqvdeLiakgngk...isaeelskvinnknkleeklsssesynl 116
                 + k+++  vt  dW+   +   k l+ + ++ + dk  ++k+ ++ +k+G  its  +  L+++g       s++  sk ++      + + s e+y++
  EPA05135.1  40 LAKEQGFDVTGDDWWDT-ESGMKFLNQRETHSEFDKKVDDKLIQLYNKGGMVITSYTLPWLVDNGIKIwlsGSHDSSSKRMQT----RDNMTSQEAYQI 133
                 67788899*******99.899999***************************************99874322244444444444....667777777776 PP

       RTX_C 117 lk 118
                  k
  EPA05135.1 134 TK 135
                 65 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   3.3e-05     0.024      36      60 ..       5      29 ..       1      42 [. 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.3e-05
      RuvB_N 36 vllyGpPGlGkttlakiiakelgvk 60
                ++++GpP +Gktt+ak +ake++ +
  EPA05135.1  5 IVISGPPAVGKTTVAKGLAKEFNLT 29
                899*****************99764 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.0   2.6e-05     0.019      25      51 ..       3      29 ..       1     130 [. 0.85

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.6e-05
      AAA_16 25 elvllsGesGvGKsslvrellralekd 51
                 ++++sG+++vGK+++++ l+++++ +
  EPA05135.1  3 KSIVISGPPAVGKTTVAKGLAKEFNLT 29
                6899*************9999987655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   9.1e-05     0.065       6      30 ..       3      27 ..       2      47 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.1e-05
      AAA_22  6 gilvvtGesGtGKTtllrrlleqld 30
                +++v+ G++ +GKTt+++ l+++++
  EPA05135.1  3 KSIVISGPPAVGKTTVAKGLAKEFN 27
                689***************9999875 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00019      0.14       2      23 ..       5      26 ..       4      76 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00019
                EEEE--TTSSHHHHHHHHHHHH CS
    NTPase_1  2 vfiTGppGvGKtTlvkkvlell 23
                ++i+Gpp vGKtT+ k ++++ 
  EPA05135.1  5 IVISGPPAVGKTTVAKGLAKEF 26
                89*************9998887 PP

>> Nif11  Nif11 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00045      0.32      34      48 .]      39      53 ..      23      53 .. 0.92
   2 ?   -1.0   0.0       3.2   2.3e+03       8      24 ..      61      77 ..      57      79 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00045
       Nif11 34 alAkeaGyefteeel 48
                +lAke+G+++t +++
  EPA05135.1 39 ELAKEQGFDVTGDDW 53
                8************97 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.2
       Nif11  8 aFlekvkqDpalreqlk 24
                +Fl++ ++  ++ ++++
  EPA05135.1 61 KFLNQRETHSEFDKKVD 77
                69999999999999886 PP

>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0038       2.7       2      27 ..       2      27 ..       1      54 [. 0.87
   2 ?    3.1   0.3     0.095        68     124     172 ..     115     164 ..     111     180 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0038
                   SSEEEEESTTTSSHHHHHHHHHHHST CS
  Guanylate_kin  2 rrpvvlvgpsgaGksslkkaLlselp 27
                   ++ +v++gp  +Gk ++ k L +e++
     EPA05135.1  2 TKSIVISGPPAVGKTTVAKGLAKEFN 27
                   689****************9988875 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.095
                    SHHHHHHHHTTSSSSHHHHHHHHHHHHHHHHGGG.CSSEEEEESSHHHHH CS
  Guanylate_kin 124 slkelqrrlksrgkeqeeklakrlaaaekelqey.efdvvivnddleeal 172
                    s k +q+r +  ++e+ + ++ r ++ ++ +++  +fd+  + + +++++
     EPA05135.1 115 SSKRMQTRDNMTSQEAYQITKIRYDKNRALYKKLyNFDFGSDTSVFDKII 164
                    66777777666666666666667777777777776655544444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       854  (0.0476323); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1262.76
//
Query:       EPA05136.1  [L=123]
Description: hypothetical protein BG20_I1106, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
        1.8    9.2  10.6       0.21   12.2   2.1    2.1  2  Ribosomal_60s  60s Acidic ribosomal protein
        3.8    8.7   6.8        4.3    8.6   1.8    2.3  2  Aft1_HRR       Aft1 HRR domain


Domain annotation for each model (and alignments):
>> Ribosomal_60s  60s Acidic ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   1.5     0.033     3e+02      56      84 ..      10      37 ..       2      39 .. 0.48
   2 ?   12.2   2.1   2.3e-05      0.21      23      88 .]      55     121 ..      47     121 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.033
                   XXXXXXXXXXXXXXXXXXXX.XX--SS-- CS
  Ribosomal_60s 56 aaaaaaaaaaaeekkkeeeeeEeedddmG 84
                     +++ +++++ e k e+++ +++d  +G
     EPA05136.1 10 EPKPEPKPEPKPEPKPEPKP-DSSDPFEG 37
                   33333333444444444443.67776666 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 2.3e-05
                    XXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XX--S.S--.STTT CS
  Ribosomal_60s  23 vkllvkale.gkdieellangaaklaaaaaaaaaaaaaaaaaaaaeekkkeeeeeEeedd.dmG.fgLF 88 
                    ++++++a+  g +i+e +++g+ k  ++ + +    + ++ ++++++ k ++ +eEe+     G fg F
     EPA05136.1  55 PETDAEAIRlGAKIHEWIKQGRPK--PGESKPEKKIESEQNEEKQKDDKHKQDKEEEKPKkKRGvFGFF 121
                    567777877799**********99..8888888777777777777777777666433333677878777 PP

>> Aft1_HRR  Aft1 HRR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   1.8   0.00048       4.3      25      54 ..       7      37 ..       1      50 [. 0.64
   2 ?    3.2   0.2     0.024   2.1e+02      29      53 ..      82     103 ..      57     119 .. 0.56

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00048
    Aft1_HRR 25 navtsqPqeapngadavkaeakpa.sdpFdp 54
                +++ ++P+ +p+ ++++k+e+kp  sdpF+ 
  EPA05136.1  7 PKPEPKPEPKPEPKPEPKPEPKPDsSDPFEG 37
                34455555555555556777777689***85 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.024
    Aft1_HRR  29 sqPqeapngadavkaeakpasdpFd 53 
                 s+P+++ + ++    e+k++ d+ +
  EPA05136.1  82 SKPEKKIESEQ---NEEKQKDDKHK 103
                 44433333333...33333333322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1990  (0.110993); expected 358.6 (0.02)
Passed bias filter:                      856  (0.0477439); expected 358.6 (0.02)
Passed Vit filter:                       130  (0.00725082); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 790.95
//
Query:       EPA05137.1  [L=58]
Description: hypothetical protein BG20_I1120 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.094   12.1   0.3      0.094   12.1   0.3    2.4  2  SKG6      Transmembrane alpha-helix domain


Domain annotation for each model (and alignments):
>> SKG6  Transmembrane alpha-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   6.5      0.27   4.9e+03      20      31 ..      11      22 ..       5      26 .. 0.53
   2 ?   12.1   0.3   5.2e-06     0.094      12      37 ..      35      58 .]      31      58 .] 0.67

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.27
        SKG6 20 VaViiivLlail 31
                V+Vi i++++i 
  EPA05137.1 11 VIVIDILIGIII 22
                344444444443 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 5.2e-06
        SKG6 12 IavaVaVPVaViiivLlailifvrRR 37
                I+++ +V+ ++ii+ Ll++ + vrR+
  EPA05137.1 35 IGIGMVVG-GIIIAGLLGY-FKVRRK 58
                67777766.5666666655.559997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       955  (0.0532657); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.51
# Mc/sec: 342.98
//
Query:       EPA05138.1  [L=298]
Description: hypothetical protein BG20_I2468, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.02   15.1   0.1      0.052   13.7   0.0    1.8  2  Tubulin   Tubulin/FtsZ family, GTPase domain
       0.28   11.4   1.3         14    5.9   0.0    3.0  3  DUF3782   Protein of unknown function (DUF3782)


Domain annotation for each model (and alignments):
>> Tubulin  Tubulin/FtsZ family, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   5.8e-06     0.052     135     195 ..       3      67 ..       1      69 [. 0.82
   2 ?   -2.9   0.0       0.7   6.3e+03      51      64 ..     177     190 ..     151     205 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.8e-06
                 HHHHHHHHHTS.TTSEEEEEEEE--.GG.G-HHHHH..HHHHHHHHHHHT-SEEEEEEHHHHHCC CS
     Tubulin 135 pvilevlkeey.pkalvvtvvvlPs.efsevvvepy..nailalkelieesdavividNdaLlki 195
                 +  +e++k++  ++a++ t+  lP  + + v++e    n +  l+  i++sd+ i+i+N+aL ++
  EPA05138.1   3 SAFIEYIKNDTkEHATIATFGLLPEfGWDPVIFEAAaiNIVMNLEYQIKYSDCSILISNKALRQL 67 
                 56678888888778999999****99887777765433889999999***************987 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.7
                 ..EEESBHHHHHTS CS
     Tubulin  51 svaidtdpqvlnei 64 
                 ++++d d++++++ 
  EPA05138.1 177 ALLFDIDESDIRNN 190
                 23455555555444 PP

>> DUF3782  Protein of unknown function (DUF3782)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.46   4.1e+03      11      32 ..      62      83 ..      57      86 .. 0.70
   2 ?    2.8   0.1     0.015   1.3e+02      47      66 ..     212     231 ..     210     233 .. 0.87
   3 ?    5.9   0.0    0.0016        14      37      56 ..     278     296 ..     276     297 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.46
     DUF3782 11 eetkedleelekeieklertig 32
                ++++++++++ek+++k+ ++i+
  EPA05138.1 62 KALRQLAHQHEKKLQKIPSIID 83
                5566777777777777777776 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.015
     DUF3782  47 ReglkeiLeealgvkVekwl 66 
                 Re++k+i++++++++ ++++
  EPA05138.1 212 REAIKRIIKDKFNIEESRMI 231
                 99***********9877776 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.0016
     DUF3782  37 RWGlvsEeafReglkeiLee 56 
                 RWGl +Ee f++gl +++++
  EPA05138.1 278 RWGLSTEE-FKQGLMDVVHQ 296
                 ******98.9****999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.33s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 1768.82
//
Query:       EPA05139.1  [L=102]
Description: hypothetical protein BG20_I2467, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.045   13.5   1.0        6.2    6.7   0.2    2.2  2  DASH_Dam1   DASH complex subunit Dam1
      0.053   13.8   0.8       0.25   11.6   0.1    1.9  2  DUF5082     Domain of unknown function (DUF5082)
      0.065   13.3   0.1       0.14   12.3   0.1    1.5  1  TRPM_tetra  Tetramerisation domain of TRPM


Domain annotation for each model (and alignments):
>> DASH_Dam1  DASH complex subunit Dam1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.2     0.001       6.2       4      33 ..       3      32 ..       1      35 [. 0.91
   2 ?    5.7   0.0    0.0021        13       3      38 ..      58      94 ..      56      95 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.001
   DASH_Dam1  4 afaeLaDsletLdknledLqqihesLsdfN 33
                 f++L+    ++++n ++L +i++sLs++N
  EPA05139.1  3 DFESLENLAIQIKENRSKLYEIEDSLSGVN 32
                58999999999****************998 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0021
   DASH_Dam1  3 pafaeLaDsletLdknledLqq.ihesLsdfNeSFas 38
                +++aeL+++ e+L++  + L++ i +++++f   F+s
  EPA05139.1 58 DKLAELEKAKEQLERTKTGLKStIAKDIATFISDFSS 94
                5677777777777777777764256667666666665 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1     0.094   5.6e+02     100     112 ..      17      29 ..       3      46 .. 0.50
   2 ?   11.6   0.1   4.1e-05      0.25      22      48 ..      56      82 ..      53      95 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.094
     DUF5082 100 Lenqiseaqgvld 112
                  +++++e + +l+
  EPA05139.1  17 NRSKLYEIEDSLS 29 
                 2223333333333 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 4.1e-05
     DUF5082 22 leekIerLkeaktklsdekeslkqkkk 48
                +++k+++L++ak++l+ +k  lk+++ 
  EPA05139.1 56 YDDKLAELEKAKEQLERTKTGLKSTIA 82
                799*******************98764 PP

>> TRPM_tetra  Tetramerisation domain of TRPM
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   2.3e-05      0.14       9      41 ..       5      37 ..       3      41 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.3e-05
  TRPM_tetra  9 ERvEnmsmkveevneKenlikaSLqsldfrLgk 41
                E  En+ ++++e   K   i++SL+ + ++L+ 
  EPA05139.1  5 ESLENLAIQIKENRSKLYEIEDSLSGVNVQLHE 37
                778****************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1088  (0.0606838); expected 358.6 (0.02)
Passed bias filter:                      706  (0.0393775); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 662.81
//
Query:       EPA05140.1  [L=141]
Description: hypothetical protein BG20_I2635, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       745  (0.0415528); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1009.73
//
Query:       EPA05141.1  [L=75]
Description: hypothetical protein BG20_I2634, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 534.97
//
Query:       EPA05142.1  [L=114]
Description: hypothetical protein BG20_I2537, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-41  141.3   0.0    4.1e-41  141.2   0.0    1.0  1  ILVD_EDD  Dehydratase family


Domain annotation for each model (and alignments):
>> ILVD_EDD  Dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.2   0.0   2.3e-45   4.1e-41     410     517 .]       1     108 [.       1     108 [. 0.96

  Alignments for each domain:
  == domain 1  score: 141.2 bits;  conditional E-value: 2.3e-45
    ILVD_EDD 410 EmlkptsallgkglgkkvalitDGRfSGaskglvighvsPEAaegGpialvedGDiieidiekrtlelevseeelaaRraawkpekkvktrgllakyak 508
                 Eml++t+al+g+glgkkva++tDGRfSG+++g+++ghv+PEA++gGpialv+++D i+id e++ ++l+vs+eel++Rr+ w+p k  +t+g+lakya+
  EPA05142.1   1 EMLSTTAALVGQGLGKKVAMVTDGRFSGGTRGFMVGHVAPEAYVGGPIALVKNDDEITIDTETNIIDLHVSAEELEKRRKLWSPPKPNYTTGALAKYAT 99 
                 9***********************************************************************************333345********* PP

    ILVD_EDD 509 lvssaseGA 517
                 lv sa++GA
  EPA05142.1 100 LVGSAAQGA 108
                 ********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.42
# Mc/sec: 815.57
//
Query:       EPA05143.1  [L=100]
Description: hypothetical protein BG20_I2535, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 647.92
//
Query:       EPA05144.1  [L=59]
Description: hypothetical protein BG20_I2536 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1228  (0.0684924); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 386.56
//
Query:       EPA05145.1  [L=163]
Description: eRF1 domain 1, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-20   72.6   0.3    3.8e-20   72.2   0.3    1.1  1  eRF1_1    eRF1 domain 1


Domain annotation for each model (and alignments):
>> eRF1_1  eRF1 domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.2   0.3   2.1e-24   3.8e-20      14     121 ..       9     118 ..       4     125 .. 0.89

  Alignments for each domain:
  == domain 1  score: 72.2 bits;  conditional E-value: 2.1e-24
                 CEEEEEE-SCHHHHHHHHHCHTTHEEEEEEEECHHH.......-.-CEEEEEEEEEEEEEEECTTSSEEEEEEEEEEG.GGG--TTSEEEEEE-TTSEE CS
      eRF1_1  14 gsvtLipeddedlwhlynliapgdsvrastvrkvqresstgsre.servklkLtikvekvdfdkdagvlrisGkviee.nehvklgafhtldlelkrpf 110
                 +s++++ped++dl +l  +i++gd++   t+r ++ e+     +  er+++++ ++vek+ +d   ++lri G++ e+ ne v+ g++h++ l++++ +
  EPA05145.1   9 NSISVMPEDSDDLLTLRRIIREGDRIVGDTTRVIKLEKDYARPDkGERIRVRIALNVEKISLDDVLDRLRIGGTILESsNESVPHGSHHSFILKINDGI 107
                 68********************************997555444448*****************************8752677***************** PP

                 EEEECEESHHH CS
      eRF1_1 111 tiikeewdsfa 121
                 ti+k++w  + 
  EPA05145.1 108 TITKKKWLPIE 118
                 *******7765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 1030.39
//
Query:       EPA05146.1  [L=102]
Description: hypothetical protein BG20_I2406, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-21   76.9   0.1    1.6e-21   76.6   0.1    1.1  1  UPF0047   Uncharacterised protein family UPF0047


Domain annotation for each model (and alignments):
>> UPF0047  Uncharacterised protein family UPF0047
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.6   0.1   8.9e-26   1.6e-21       1      75 [.      25     101 ..      25     102 .] 0.97

  Alignments for each domain:
  == domain 1  score: 76.6 bits;  conditional E-value: 8.9e-26
                 E-HHHHHHHHHHHT.SEEEEEEEESSSSEEEEEEESSSHHHHHHHHHHHHHHSTTT...T-GGGTTS..THHHHHHHH CS
     UPF0047   1 diteeveeavkesgvkeGlvlvfsrhttasltinEnadpdvqeDleealeklvpee...eYrhnaegpdnadaHlkss 75 
                 +it+e++++v +s+v+eGl+lv ++h +as++in++ ++++++D+e++le l+p+e   +Y+hn+ g+dnadaHlk+ 
  EPA05146.1  25 NITPEIRKLVLKSKVQEGLCLVNAMHISASVFINDD-ENGLHQDFEKWLESLAPHEpinQYQHNNTGEDNADAHLKRQ 101
                 69**********************************.******************9999****************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.34s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 599.69
//
Query:       EPA05147.1  [L=136]
Description: hypothetical protein BG20_I2405 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 884.54
//
Query:       EPA05148.1  [L=348]
Description: peptidase, M50 family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-19   69.5   0.6    2.6e-17   62.9   0.6    2.3  1  Peptidase_M50  Peptidase family M50
    3.6e-09   36.8   0.0    6.3e-09   36.0   0.0    1.4  1  PDZ_2          PDZ domain
      1e-07   31.7   0.0    1.7e-07   31.0   0.0    1.3  1  PDZ_6          PDZ domain
     0.0029   17.9   0.1     0.0056   17.0   0.1    1.4  1  PDZ            PDZ domain


Domain annotation for each model (and alignments):
>> Peptidase_M50  Peptidase family M50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.9   0.6   5.9e-21   2.6e-17       1     232 [.      68     313 ..      68     331 .. 0.81

  Alignments for each domain:
  == domain 1  score: 62.9 bits;  conditional E-value: 5.9e-21
                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXX CS
                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Peptidase_M50   1 afilllgilvvvHElGHflvAklcgvkveefsigfGpkllsfkkgeteYaiallpLGGyVkmageepeeelseeeakaflkkspwqrllivlAGpl 96 
                    +f+l + i++v+HE +H++vA l+++k++                   +ai +  + G+V+ ++ee            f+k++ +++l+++ AG  
     EPA05148.1  68 YFLLSIPIVLVIHEGAHGIVATLEKIKIKT----------------GGFAIFIAMFAGFVEPDEEE------------FNKAKKISKLRVIGAGAT 135
                    69999***********************76................44678888888*********............****************** PP

                    XXXXXXXXXXXX................................-EEECE.....CTTTSCEE-SEEEC-XXXXXXXXXXXXXXXXXXXXX.XXXX CS
                    xxxxxxxxxxxx................................xxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
  Peptidase_M50  97 anfilailvfvv................................pkkske.....seeekrgviGvspkpvkkegllealkegvektlkvv.vltv 154
                     n+i+a+++ ++                                p++ +e      +   +++ G++  ++ + + ++ + + + ++  +   +t+
     EPA05148.1 136 SNVIFAFALGLIlltnpffamivpepllsvfydlpdgvtvlsiiPDSGAEkagllANDIITSINGIQILSPLDFQKTDLIPGDIAQVSILRdGQTL 231
                    *******9999999*************999999999999999994444444566666666777788888888888888888888887655426888 PP

                    XXXXXXXXX.XXXXXXXXXXXXXXXXX.......XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                    xxxxxxxxx.xxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Peptidase_M50 155 kalgklitg.klslktlggpisiaqla.......seaaeaglssflqllalisvnLgilNLlPipvLDGghllfalleairrkpls 232
                    +  +++i   + + k l g i   ++a        e  + g+s+fl +l +is+ +gi+N+lP+p+LDGg+++  ++++      s
     EPA05148.1 232 QFPVEIIPSpDDPQKGLIGIIRDNSFAykpvlnfIEWKDPGVSMFLLWLWMISFFIGIINMLPLPILDGGKFIHTIIDKKI----S 313
                    8889999995555558888888888885555555445556666******************************99987543....4 PP

>> PDZ_2  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.0   1.4e-12   6.3e-09      12      81 ..     171     236 ..     162     237 .. 0.89

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 1.4e-12
                 -..-EEEEEE-TTSGGGGT.--TT-EEEEETTB--SSHHHHHHHHHTS-TT-EEEEEEEETTEEEEEEEE CS
       PDZ_2  12 dtggvlvvsVkeggPaakaglkagDvilkvdgkkvksledlislllkkkpGdtVkltvlRdgkkktvevk 81 
                 d  gv+v s+ +++ a+kagl a+D+i++++g ++ s  d+  +     pGd  ++++lRdg+++++ v+
  EPA05148.1 171 D--GVTVLSIIPDSGAEKAGLLANDIITSINGIQILSPLDF--QKTDLIPGDIAQVSILRDGQTLQFPVE 236
                 4..9*******************************555555..557999*****************9997 PP

>> PDZ_6  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.0   3.8e-11   1.7e-07       2      39 ..     175     210 ..     174     212 .. 0.93

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 3.8e-11
       PDZ_6   2 VtaVdpgsPAdrAGlrvGDiilsvNGqpveglsladva 39 
                 V +++p+s A++AGl ++Dii+s+NG+ +  ls+ d++
  EPA05148.1 175 VLSIIPDSGAEKAGLLANDIITSINGIQI--LSPLDFQ 210
                 7899*************************..9999987 PP

>> PDZ  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   1.3e-06    0.0056      27      57 ..     172     202 ..     167     214 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.3e-06
                 SEEEEEECTTSHHHHHTSSTTEEEEEETTEE CS
         PDZ  27 gifvsevlpggaaeadglkvGDkIlsvNgvd 57 
                 g+ v ++ p++ ae++gl ++D+I+s+Ng  
  EPA05148.1 172 GVTVLSIIPDSGAEKAGLLANDIITSINGIQ 202
                 89999*****7788888************65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.34s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 2027.32
//
Query:       EPA05149.1  [L=192]
Description: PP-loop family protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.3e-17   62.4   0.0    6.6e-17   61.8   0.0    1.2  1  ATP_bind_3     PP-loop family
    1.2e-05   24.3   0.0    1.6e-05   23.9   0.0    1.1  1  tRNA_Me_trans  tRNA methyl transferase
     0.0065   16.0   0.2      0.015   14.8   0.2    1.8  1  QueC           Queuosine biosynthesis protein QueC
  ------ inclusion threshold ------
      0.064   13.3   0.0      0.076   13.1   0.0    1.3  1  PAPS_reduct    Phosphoadenosine phosphosulfate reductase fami


Domain annotation for each model (and alignments):
>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.8   0.0   1.5e-20   6.6e-17       2     121 ..      50     181 ..      49     189 .. 0.92

  Alignments for each domain:
  == domain 1  score: 61.8 bits;  conditional E-value: 1.5e-20
                 EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--H............HHCTTSTCCCHHHHHHHHHH CS
  ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklnikleiekvdv............akkkgknleeaARelRYevl 88 
                 v+vAvSgG DS+aLl++++++k++ ++++ ai++d g+    +e  e+v+e+c+kln+++++ + +               +++++      +lR +++
  EPA05149.1  50 VAVAVSGGKDSLALLNVINQMKSTHNFRIKAITIDEGIPGYRNEALEIVQEFCAKLNVEHKVFSYKElfdltldealdlRGNEKTSSCSICGTLRRRAI 148
                 689***********************************************************999999999999998884445677778999******* PP

                 HHCHHCCT.CEEE---BHHHHHHHHHHHHCCT- CS
  ATP_bind_3  89 kealkkegievlllAhhadDqaEtfllrlargs 121
                 ++a++  g++v++++h+ dD + tf++++  g 
  EPA05149.1 149 DHAANYIGADVIATGHNLDDTLQTFVINMLSGD 181
                 **************************9988775 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   3.5e-09   1.6e-05       3     125 ..      50     165 ..      48     182 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 3.5e-09
  tRNA_Me_trans   3 vvvalSgGVDSsvaaallkeqgyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfekeykekvfeefleeyeeGrTPnPdvlC 98 
                    v+va+SgG DS +a++ + +q +++  + +k ++ ++        +e l+ +++ + kl+++++v+++++ +    ++e l+   + +T   +  C
     EPA05149.1  50 VAVAVSGGKDS-LALLNVINQMKSTHNFRIKAITIDEGI--PGYRNEALEIVQEFCAKLNVEHKVFSYKELFDL-TLDEALDLRGNEKTS-SCSIC 140
                    99********7.78999999**********999983333..4688899*********************99975.578899988888885.69999 PP

  tRNA_Me_trans  99 NkeiKfgallekakeelgadalatGHY 125
                     +    +  +++a +  gad +atGH 
     EPA05149.1 141 GTLR-RR-AIDHAANYIGADVIATGHN 165
                    8754.44.46777777**********5 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.2   3.3e-06     0.015       4      68 ..      52     121 ..      49     168 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.3e-06
                 EE--SSHHHHHHHHHHHHH-....SEEEEEEEESS-T..TSHHHHHHHHHHHHT--.-EEEEE-GGGGGGS CS
        QueC   4 vllSGGlDSttvlalakkeg....kevealtfdYgqr..hkkeleaakkiakelgveehkildldllkelg 68 
                 v +SGG DS ++l + ++       +++a+t+d g    +++ le++++++++l+v ehk+++ + l +l+
  EPA05149.1  52 VAVSGGKDSLALLNVINQMKsthnFRIKAITIDEGIPgyRNEALEIVQEFCAKLNV-EHKVFSYKELFDLT 121
                 679******99887665433222379********9877567779************.***99988766655 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.7e-05     0.076       3      61 ..      51     115 ..      49     183 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.7e-05
                  EEE--SSCTCHHHHHHHHHHCTTH....EEEEEE-ST..B-HHHHHHHHHHHHHTT-EEEEEE-S CS
  PAPS_reduct   3 vvsvsgGkdslVllhLalkafkpv....pvvfvdtgh..efpetiefvdeleeryglrlkvyepe 61 
                  +v+vsgGkdsl+ll  + +++       + + +d g     +e +e v+e+  +++++ kv++ +
   EPA05149.1  51 AVAVSGGKDSLALLNVINQMKSTHnfriKAITIDEGIpgYRNEALEIVQEFCAKLNVEHKVFSYK 115
                  799*************9988877444568999999872246788888888888888887777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       886  (0.0494171); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1365.10
//
Query:       EPA05150.1  [L=78]
Description: hypothetical protein BG20_I2656, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 524.78
//
Query:       EPA05151.1  [L=101]
Description: hypothetical protein BG20_I2658, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-13   49.4   0.8    7.6e-13   48.9   0.8    1.2  1  HHH_5            Helix-hairpin-helix domain
    1.2e-07   31.4   0.0    3.8e-07   29.8   0.0    1.7  2  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
    1.9e-06   27.9   0.1    7.1e-06   26.0   0.0    1.9  2  HHH_2            Helix-hairpin-helix motif
     0.0014   18.8   0.0     0.0028   17.9   0.0    1.3  1  DUF4332          Domain of unknown function (DUF4332)
     0.0015   18.8   0.2      0.096   13.1   0.3    2.3  2  HHH_8            Helix-hairpin-helix domain
     0.0028   17.4   1.3     0.0062   16.3   0.1    2.1  3  RNA_pol_A_CTD    Bacterial RNA polymerase, alpha chain C term
     0.0034   17.2   0.1      0.077   12.9   0.0    3.0  3  HHH              Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.038   14.2   0.1       0.24   11.6   0.0    2.0  2  Cdd1             Pathogenicity locus
       0.12   12.5   0.1       0.34   11.0   0.1    2.0  1  TfoX_C           TfoX C-terminal domain


Domain annotation for each model (and alignments):
>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9   0.8   3.8e-16   7.6e-13       3      57 .]      45      99 ..      42      99 .. 0.97

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 3.8e-16
                HHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHHHH CS
       HHH_5  3 eLlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriilelkd 57
                +L +v+GiG+ +A+ l+++Gi++++dla+  v++La+i  iG   A++i+ el++
  EPA05151.1 45 DLVKVKGIGRIRARMLYKHGIKTLDDLANIPVNKLAEIDKIGSTIADNIKSELRK 99
                899**************************************************97 PP

>> DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.1   2.2e+03      30      43 ..      26      39 ..      16      40 .. 0.62
   2 !   29.8   0.0   1.9e-10   3.8e-07       3      42 ..      46      86 ..      45      93 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.1
  DNA_pol_lambd_f 30 akrakLtreqqiGl 43
                      + ++L r   +G+
       EPA05151.1 26 DELDNLRRRITYGI 39
                     33466777777666 PP

  == domain 2  score: 29.8 bits;  conditional E-value: 1.9e-10
  DNA_pol_lambd_f  3 FtkvyGVGpktAkkwyakGirtledlra.krakLtreqqiG 42
                     + kv G+G+ +A+++y+ Gi+tl+dl +   +kL +  +iG
       EPA05151.1 46 LVKVKGIGRIRARMLYKHGIKTLDDLANiPVNKLAEIDKIG 86
                     6799************************7668888888887 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.033        65      34      50 ..      43      59 ..      38      63 .. 0.81
   2 !   26.0   0.0   3.6e-09   7.1e-06       9      53 ..      50      95 ..      46     100 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.033
       HHH_2 34 leeLlevddiGeeiAqs 50
                l +L++v++iG + A+ 
  EPA05151.1 43 LLDLVKVKGIGRIRARM 59
                56899******998875 PP

  == domain 2  score: 26.0 bits;  conditional E-value: 3.6e-09
       HHH_2  9 rhVGektAklLakr.FksldaLkkasleeLlevddiGeeiAqsive 53
                + +G   A+ L k+  k+ld L++  +++L+e+d iG +iA++i++
  EPA05151.1 50 KGIGRIRARMLYKHgIKTLDDLANIPVNKLAEIDKIGSTIADNIKS 95
                6799999*****99678**************************986 PP

>> DUF4332  Domain of unknown function (DUF4332)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.4e-06    0.0028      52      89 ..      43      80 ..      39      88 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.4e-06
     DUF4332 52 lAdLarikgigeeyaeLLeaaGvdsvaeLaqrnpanLh 89
                l dL+++kgig+  a +L + G+++  +La+ ++++L 
  EPA05151.1 43 LLDLVKVKGIGRIRARMLYKHGIKTLDDLANIPVNKLA 80
                569****************************9999996 PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.0     0.005       9.9      34      57 ..      27      54 ..      25      60 .. 0.84
   2 !   13.1   0.3   4.8e-05     0.096       9      64 ..      41      94 ..      41      98 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.005
                CCCC-SS-HHHH.TT...HCTTSTT--H CS
       HHH_8 34 aiealpeeitsl.ee...eltklpgiGk 57
                 +++l ++it + +e   +l k++giG 
  EPA05151.1 27 ELDNLRRRITYGiREellDLVKVKGIGR 54
                68999******995559999*******5 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 4.8e-05
                HHHHHHHHHCT--CCCHHH.HHHHHCCCCC-SS.-HHHHTTHCTTSTT--HHHHHHHH CS
       HHH_8  9 eeladllelkgedpfrvra.YrrAaraiealpe.eitsleeeltklpgiGkkiaakie 64
                eel dl ++kg    r+r  Y+  ++++++l   +++     l +++ iG  ia+ i+
  EPA05151.1 41 EELLDLVKVKGIGRIRARMlYKHGIKTLDDLANiPVNK----LAEIDKIGSTIADNIK 94
                57788888888556666657************999999....999**********995 PP

>> RNA_pol_A_CTD  Bacterial RNA polymerase, alpha chain C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.9   3.8e+03      11      17 ..      15      21 ..      11      31 .. 0.57
   2 ?   -1.0   0.0      0.77   1.5e+03      46      55 ..      45      54 ..      39      55 .. 0.81
   3 !   16.3   0.1   3.1e-06    0.0062      28      66 ..      60      98 ..      56      99 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.9
                   X--BHHH CS
  RNA_pol_A_CTD 11 lsisIee 17
                   +s+++e 
     EPA05151.1 15 ISKHVER 21
                   3444444 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.77
                   HHTTSSS-SS CS
  RNA_pol_A_CTD 46 eLlkikNlGk 55
                   +L k+k +G+
     EPA05151.1 45 DLVKVKGIGR 54
                   8999999997 PP

  == domain 3  score: 16.3 bits;  conditional E-value: 3.1e-06
                   HHHTT--BHHHHHHS-HHHHTTSSS-SSHHHHHHHHHHH CS
  RNA_pol_A_CTD 28 LkragiktvgeLvklseeeLlkikNlGkKSleEIkekLe 66
                   L + gikt+++L+++  ++L +i  +G    + Ik+ L 
     EPA05151.1 60 LYKHGIKTLDDLANIPVNKLAEIDKIGSTIADNIKSELR 98
                   7789*******************************9996 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   3.9e-05     0.077      12      28 ..      45      61 ..      40      63 .. 0.90
   2 ?    0.3   0.0      0.39   7.8e+02       9      17 ..      67      75 ..      66      75 .. 0.89
   3 ?   -1.3   0.0       1.2   2.4e+03      19      29 ..      85      95 ..      78      96 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.9e-05
                HHHTSTT-SHHHHHHHH CS
         HHH 12 eLlalPGVGpktAeaIl 28
                +L++++G+G+ +A+  +
  EPA05151.1 45 DLVKVKGIGRIRARMLY 61
                79***********9765 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.39
                SHHHHHTST CS
         HHH  9 sreeLlalP 17
                ++++L+ +P
  EPA05151.1 67 TLDDLANIP 75
                89****998 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.2
                -SHHHHHHHHH CS
         HHH 19 VGpktAeaIls 29
                +G   A+ I s
  EPA05151.1 85 IGSTIADNIKS 95
                88889998875 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00012      0.24       2      36 ..      40      74 ..      39      84 .. 0.88
   2 ?    0.9   0.0      0.27   5.3e+02       6      22 ..      77      93 ..      74      97 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00012
        Cdd1  2 rkalkelqdiPniGkalaedlvelGirsveelkge 36
                r++l +l ++ +iG+  a++l++ Gi+++++l++ 
  EPA05151.1 40 REELLDLVKVKGIGRIRARMLYKHGIKTLDDLANI 74
                57889999************************975 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.27
        Cdd1  6 kelqdiPniGkalaedl 22
                ++l +i  iG  +a+++
  EPA05151.1 77 NKLAEIDKIGSTIADNI 93
                68999********9876 PP

>> TfoX_C  TfoX C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00017      0.34       8      33 ..      49      74 ..      21      89 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00017
      TfoX_C  8 LpNlglklerlLkkaGIktveeLrel 33
                ++ +g   +r+L k GIkt+++L+++
  EPA05151.1 49 VKGIGRIRARMLYKHGIKTLDDLANI 74
                677888899**************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 732.29
//
Query:       EPA05152.1  [L=198]
Description: hypothetical protein BG20_I2312, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.4e-07   29.7   8.8    5.4e-07   29.7   8.8    1.9  2  DsbD             Cytochrome C biogenesis protein transmembran
  ------ inclusion threshold ------
       0.51   10.5  18.7        1.1    9.4   6.5    2.5  2  EamA             EamA-like transporter family
          1    8.9   7.1        1.4    8.4   7.1    1.2  1  UNC-50           UNC-50 family
        1.1    9.3   5.7        3.3    7.7   2.3    2.3  2  Ninjurin         Ninjurin
        3.2    7.8  16.8       0.17   12.0   4.4    2.4  2  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe


Domain annotation for each model (and alignments):
>> DsbD  Cytochrome C biogenesis protein transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   3.2     0.025        90      85     148 ..      10      75 ..       2      85 .. 0.53
   2 !   29.7   8.8   1.5e-10   5.4e-07       2     153 ..      52     194 ..      51     198 .] 0.82

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.025
        DsbD  85 ivillGlhflgvfkievleklklllkikkkaelsvlgalllGlt..FalgwsPCigPvlasvlala 148
                  v+l+ + ++ ++ + v+  l     ++++ ++++l  l++  +   +++  PC+ P+++ ++ l+
  EPA05152.1  10 TVVLVSFALISLIFVGVIFSLTNEFAVENQGSATYLSWLIIAYVagLSMIVLPCTLPLVFIIVPLS 75 
                 455555555555555555555555555555555555443333331124556677777666666555 PP

  == domain 2  score: 29.7 bits;  conditional E-value: 1.5e-10
        DsbD   2 flaGllsflsPCilpliPaylsyisgvsvedvktekkkvkvllkallFvlGlslvfvslglsaaflgqllk..dvkevirrvaglivillGlhflgvfk 98 
                 + aGl   + PC lpl+ + +     +s++   +     k l  allF  Gl+l++++ g +++ lg+ +   ++++++  vag+ + ++Gl++l +++
  EPA05152.1  52 YVAGLSMIVLPCTLPLVFIIVP----LSMGKGYK-----KGLSMALLFGAGLTLMIAAYGTGISILGETASldQISTIMFLVAGVAAFFFGLSQLKLVS 141
                 789999999******9876554....34443332.....46899*********************99876554899999999**************998 PP

        DsbD  99 ievleklklllkikkkaelsvlgalllGltFalgwsPCigPvlasvlalaaskes 153
                 +++       ++i++++   + +++ +Gl+ +     C  P++  +l++ a  +s
  EPA05152.1 142 FKMPSYSGTPKFIQNRED--YSKSFFMGLLLGNAGVGCPNPLFYWLLIYIAGAGS 194
                 777777777766655555..599***********************999887765 PP

>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   4.2    0.0022       7.8      30      80 ..      13      63 ..       2      72 .. 0.84
   2 ?    9.4   6.5   0.00032       1.1       3      86 ..      87     186 ..      85     192 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0022
        EamA 30 pltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafl 80
                 ++++ +++++ g++++++  +  +++ + ++ +wl++++++ l++++ ++
  EPA05152.1 13 LVSFALISLIFVGVIFSLTNEFAVENQGSATYLSWLIIAYVAGLSMIVLPC 63
                568899999999999999988888888899999***********9998765 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00032
        EamA   3 gillallaalfwaiyfvlskillrkvspltltfvrfliagilllii.................allkegklaklslkd....wllllllgllgtvlafl 80 
                 ++l+    +l+ a+y++ + il ++ s  ++++++fl+ag++ +++                 ++ + +++     +d    ++  lllg  g+ + + 
  EPA05152.1  87 ALLFGAGLTLMIAAYGTGISILGETASLDQISTIMFLVAGVAAFFFglsqlklvsfkmpsysgTPKFIQNR-----EDysksFFMGLLLGNAGVGCPNP 180
                 578888999*************************************6666666655555433322222222.....11222133446666666666666 PP

        EamA  81 lffyal 86 
                 lf+++l
  EPA05152.1 181 LFYWLL 186
                 666665 PP

>> UNC-50  UNC-50 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   7.1    0.0004       1.4      83     200 ..      10     132 ..       2     148 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0004
      UNC-50  83 vmvlvdfllvglliatvlwllvnrlllksekseqdvewaYcFDvhlnaflpilvllyvlqllllplilkkk.....fvslllgntlylvaigyYfyitf 176
                  +vlv f l++l++  v++ l+n++ ++++ s  +++w     v+  +++++ ++l +  ++++pl + k       ++ll+g  l l+ ++y + i+ 
  EPA05152.1  10 TVVLVSFALISLIFVGVIFSLTNEFAVENQGSATYLSWLIIAYVAGLSMIVLPCTLPL-VFIIVPLSMGKGykkglSMALLFGAGLTLMIAAYGTGISI 107
                 6899***********************9999*******99888998888877776655.4677777655544567889999999999999999999999 PP

      UNC-50 177 lGY.nalpflkktevlllpllllav 200
                 lG  ++l+ +++  +l++ ++++++
  EPA05152.1 108 LGEtASLDQISTIMFLVAGVAAFFF 132
                 9951457777766666666655554 PP

>> Ninjurin  Ninjurin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   2.3   0.00092       3.3      43      95 ..      10      61 ..       3      72 .. 0.83
   2 ?    2.7   0.1     0.032   1.2e+02      49      90 ..      84     125 ..      83     140 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00092
    Ninjurin 43 llvLislSllLqvvvgilliliasklnlekekkerrlnklnnaatilvfvitv 95
                 +vL+s+ l+  ++vg+++ l  ++  +e++++++ l  l  a+++   +i++
  EPA05152.1 10 TVVLVSFALISLIFVGVIFSL-TNEFAVENQGSATYLSWLIIAYVAGLSMIVL 61
                689****************99.679*****99999887777777776666654 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.032
    Ninjurin  49 lSllLqvvvgilliliasklnlekekkerrlnklnnaatilv 90 
                 lS++L + +g++l++ a  + +   +++ +l+ + +++ +++
  EPA05152.1  84 LSMALLFGAGLTLMIAAYGTGISILGETASLDQISTIMFLVA 125
                 899999999999999888899999999888888877765544 PP

>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   4.5     0.095   3.4e+02      44      83 ..      11      57 ..       4      73 .. 0.47
   2 ?   12.0   4.4   4.7e-05      0.17      31      98 ..      81     145 ..      74     148 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.095
  Phage_holin_3_6 44 gvlallalllllvala.......lalaa.lwlaalivaavllvlagvl 83
                     +vl+ +al++l++  +       +a+   +  a+ +  ++ + +ag+ 
       EPA05152.1 11 VVLVSFALISLIFVGVifsltneFAV-EnQGSATYLSWLIIAYVAGLS 57
                     34445555555544432222333333.133333333333333333333 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 4.7e-05
  Phage_holin_3_6  31 kragsgagllgaagvlallalllllval..alalaalwlaalivaavllvlagvlalvglkklkkakp.lp 98 
                      k+ +s+a+l+ga++ l++ a ++ +  l   + l        i ++++lv+++++ + gl++lk ++  +p
       EPA05152.1  81 KKGLSMALLFGAGLTLMIAAYGTGISILgeTASL------DQISTIMFLVAGVAAFFFGLSQLKLVSFkMP 145
                      6778888888888888888888888888554566......788999999999************9887566 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       878  (0.0489709); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1492.98
//
Query:       EPA05153.1  [L=212]
Description: hypothetical protein BG20_I2313, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00056   20.0   1.4      0.046   13.9   0.0    3.2  4  HTH_17    Helix-turn-helix domain
    0.00068   19.5   0.0     0.0016   18.4   0.0    1.6  1  HTH_11    HTH domain
     0.0012   19.0   0.5      0.058   13.7   0.0    2.7  3  zf-Di19   Drought induced 19 protein (Di19), zinc-binding
  ------ inclusion threshold ------
      0.022   14.7   0.3      0.056   13.4   0.3    1.7  1  HTH_36    Helix-turn-helix domain
      0.053   13.3   0.6       0.18   11.6   0.3    2.0  2  DUF3449   Domain of unknown function (DUF3449)
      0.068   13.3   2.2        4.2    7.5   0.1    2.7  3  FUR       Ferric uptake regulator family
       0.09   12.4   1.6       0.13   11.8   0.0    2.1  2  Sgf11     Sgf11 (transcriptional regulation protein)
       0.13   12.3   0.2       0.29   11.2   0.2    1.6  1  HTH_22    HTH domain
        2.4    8.3   4.7        4.8    7.3   1.1    3.0  3  zf-BED    BED zinc finger


Domain annotation for each model (and alignments):
>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   2.3e-05     0.046      11      42 ..       3      37 ..       1      46 [. 0.81
   2 ?   -1.5   0.0       1.5   2.9e+03      29      44 ..      71      83 ..      57      85 .. 0.71
   3 ?   -3.5   0.1       6.4   1.3e+04      24      35 ..     116     127 ..     111     127 .. 0.73
   4 ?    3.6   0.0     0.037        74      24      45 ..     162     183 ..     139     185 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.3e-05
      HTH_17 11 Lgvsrstvyrli....rrgelpaakiGrrwriprsd 42
                Lg+s++tvy++i    ++g ++ +k  ++   p+sd
  EPA05153.1  3 LGLSKKTVYNYItklsKTGNIIRLKS-GHFFLPKSD 37
                9***********88888999999998.448888777 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.5
      HTH_17 29 aakiGrrwriprsdle 44
                + k    w+++  +le
  EPA05153.1 71 PIKT---WKYRLRSLE 83
                6666...999999888 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 6.4
      HTH_17  24 rgelpaakiGrr 35 
                 +ge +  kiGr+
  EPA05153.1 116 NGEVIRSKIGRH 127
                 577767789886 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.037
      HTH_17  24 rgelpaakiGrrwriprsdlee 45 
                 + + p++++   +r++ +++e+
  EPA05153.1 162 SQKVPHHGKYADIRFTPKEFEK 183
                 557789988899********97 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   7.9e-07    0.0016      24      51 ..       2      29 ..       1      31 [. 0.90

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 7.9e-07
      HTH_11 24 eLnvSrrtvrrdIkaLeelgvpIesepg 51
                 L++S++tv+++I +L+++g  I  ++g
  EPA05153.1  2 TLGLSKKTVYNYITKLSKTGNIIRLKSG 29
                69******************99988776 PP

>> zf-Di19  Drought induced 19 protein (Di19), zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.086   1.7e+02      28      49 ..      80     114 ..      74     118 .. 0.76
   2 ?   -2.6   0.1       3.6   7.1e+03      20      35 ..     132     147 ..     130     148 .. 0.76
   3 !   13.7   0.0   2.9e-05     0.058       3      28 ..     186     211 ..     185     212 .] 0.93

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.086
     zf-Di19  28 eskevvCPvCa.............ekvtkdlvaHl 49 
                  s e+vC  C+             ek+ + +++H+
  EPA05153.1  80 RSLETVCNTCEvtpydliisnkktEKIMRSFAKHF 114
                 57789*****8777777777766666777888887 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.6
     zf-Di19  20 HvedeHrveskevvCP 35 
                 H ++ H+v++    C+
  EPA05153.1 132 HTTVYHKVQAVRDFCS 147
                 8888898888777775 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 2.9e-05
     zf-Di19   3 ftCPyCgkeltvkeLveHvedeHrve 28 
                 +tC yCg+++ v++L +H+  +H +e
  EPA05153.1 186 VTCTYCGRMILVTRLEAHIRLNHLEE 211
                 79*********************887 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.3   2.8e-05     0.056      34      53 ..       2      21 ..       1      23 [. 0.91

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.8e-05
      HTH_36 34 rlglsknTvsraikeLeqlG 53
                 lglsk+Tv+++i +L ++G
  EPA05153.1  2 TLGLSKKTVYNYITKLSKTG 21
                58***************999 PP

>> DUF3449  Domain of unknown function (DUF3449)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.81   1.6e+03     120     141 ..       1      22 [.       1      28 [. 0.83
   2 ?   11.6   0.3   9.2e-05      0.18      66     112 ..      62     116 ..      35     155 .. 0.66

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.81
                 XXXXXXXXXXXXXXXXXXXXXX CS
     DUF3449 120 kcLgientklfkeitkiedale 141
                 k+Lg+++++ ++ itk+++  +
  EPA05153.1   1 KTLGLSKKTVYNYITKLSKTGN 22 
                 689999999******9987655 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 9.2e-05
                 XXXXXXXXXXXXXXXXXXXXXXXX.XXXXXX......XX.XXXXXXXXXXXXXXX CS
     DUF3449  66 nlplgwdgkPipyWLykLhgLgke.ykCeiC......gn.avYkGrkaFekHFse 112
                 +l    +g+Pi  W y+L+ L++   +Ce+       +n ++ k  ++F kHF++
  EPA05153.1  62 DLLTRKQGMPIKTWKYRLRSLETVcNTCEVTpydliiSNkKTEKIMRSFAKHFQN 116
                 5566689**************8751568754111111331233455778888886 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.1    0.0021       4.2      40      74 ..       5      46 ..       1      85 [. 0.70
   2 ?    5.1   0.0     0.012        24      13      62 ..     103     152 ..      99     175 .. 0.78
   3 ?   -2.3   0.0       2.3   4.7e+03      81      91 ..     186     196 ..     172     203 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0021
                --HHHHHHHHHHHHHTTSEEEEEE.......TTSEEEEEESS CS
         FUR 40 islaTVYrtLklleeaglvkelef.......edgesryelak 74
                +s  TVY+ ++ l++ g + +l+        +d+++ ye++k
  EPA05153.1  5 LSKKTVYNYITKLSKTGNIIRLKSghfflpkSDTREFYEFNK 46
                7899*************9999874222222235556666664 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.012
                 HHHHHHHHSSSBEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEE CS
         FUR  13 ilevlekseehlsaeevykelkeedpeislaTVYrtLklleeaglvkele 62 
                   +++++  +h++  ev ++   ++++   +TVY  ++  ++     +++
  EPA05153.1 103 TEKIMRSFAKHFQNGEVIRSKIGRHDQGMHTTVYHKVQAVRDFCSFYDIT 152
                 5578999999********999999999999*****999988766555555 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2.3
                 EEETTT--EEE CS
         FUR  81 licekCgkvie 91 
                 + c+ Cg+ i 
  EPA05153.1 186 VTCTYCGRMIL 196
                 78999999875 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.4       1.5   2.9e+03       5      10 ..      84      89 ..      81      90 .. 0.79
   2 ?   11.8   0.0   6.5e-05      0.13       4      23 ..     185     204 ..     182     205 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.5
                EE-TTT CS
       Sgf11  5 vtCpnC 10
                ++C+ C
  EPA05153.1 84 TVCNTC 89
                68**99 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 6.5e-05
                 EEE-TTTSSEEEGGGHHHHH CS
       Sgf11   4 yvtCpnCgRqiaasRFApHL 23 
                  vtC +CgR+i  +R  +H+
  EPA05153.1 185 AVTCTYCGRMILVTRLEAHI 204
                 69***********9988875 PP

>> HTH_22  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   0.00015      0.29      50      62 ..       2      14 ..       1      15 [. 0.91

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00015
      HTH_22 50 kLgiSraTvYryL 62
                 Lg S+ TvY+y+
  EPA05153.1  2 TLGLSKKTVYNYI 14
                79**********8 PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       2.3   4.6e+03       3      14 ..      10      21 ..       9      25 .. 0.71
   2 ?    0.2   0.1      0.38   7.7e+02      15      23 ..      82      90 ..      72      92 .. 0.73
   3 ?    7.3   1.1    0.0024       4.8       8      43 ..     177     208 ..     176     209 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.3
                TTSSS----GGS CS
      zf-BED  3 vWkyftpvslke 14
                v++y t++s++ 
  EPA05153.1 10 VYNYITKLSKTG 21
                899999999444 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.38
                S--EETTTT CS
      zf-BED 15 qkavCryCg 23
                  +vC+ C+
  EPA05153.1 82 LETVCNTCE 90
                468999997 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0024
                 ----GGSS--EETTTTEE----SSTHHHHHHHHHS- CS
      zf-BED   8 tpvslkeqkavCryCgkilsrgggttnLkrHLrrkH 43 
                 tp + ++  ++C yCg+ +     +t+L +H+r +H
  EPA05153.1 177 TPKEFEKLAVTCTYCGRMIL----VTRLEAHIRLNH 208
                 555566889*******9884....467877777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       926  (0.0516482); expected 358.6 (0.02)
Passed bias filter:                      714  (0.0398237); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1388.89
//
Query:       EPA05154.1  [L=223]
Description: putative dihydropteroate synthase, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-37  129.2   0.1    4.5e-37  128.0   0.1    1.5  1  Pterin_bind     Pterin binding enzyme
  ------ inclusion threshold ------
      0.076   12.4   0.1       0.12   11.7   0.1    1.5  1  Spermine_synth  Spermine/spermidine synthase domain


Domain annotation for each model (and alignments):
>> Pterin_bind  Pterin binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.0   0.1     5e-41   4.5e-37      50     244 .]       4     201 ..       2     201 .. 0.86

  Alignments for each domain:
  == domain 1  score: 128.0 bits;  conditional E-value: 5e-41
                  -CCHHHHHHHHHHHHHHHHHHHCTSEEEEE-S-HHHHHHHHHTTSEEEEETTTTSSSTTHHHHHHHHT-EEEEESECSSTTTHCCCCCCCSSHHHHHH CS
  Pterin_bind  50 ervdeeeelervvpvlealrdeadvpisiDttkaevaeaAlkagadivNdvsgeerdpkmlelvaeagaavvvmhmrgtpktmqeeegqyedvveeve 147
                  + v+e++el+rv+  ++ +++ +++pis+Dt +a+va+  l+ g++i+Nd+sg++ dpkm+ +v++++  +v+ +++         + +    ++  +
   EPA05154.1   4 TSVSEKTELQRVLDAIKVIQNISNLPISVDTCRANVAKHVLEYGVEIINDISGLKYDPKMIDVVRKYRPSLVLCAFD--------SK-RVIGDIQSTK 92 
                  579******************99******************************************************........22.3334456677 PP

                  HHHHHHHHHHHHTT--GGGEEEETTTTS..........STTH....HHHHHHHHTHHHHHHTTSSEBEEEGTTGHHHHHHHCTTCHGHHHHHHHHHHH CS
  Pterin_bind 148 aflearveaaeeaGvaperillDpgigf..........gkte....ehnlellrrldelrealevpvllGvSrksflgrllelgkaeeRdagtaafla 231
                    l+ +++ a+  G+ +++i+lDp igf          +k +    + +l+++++l+ +  +++ p+l++vS+ksf+g++l  +++++R  g++a+ a
   EPA05154.1  93 DLLKDSLKLAKTTGISSDKIVLDPAIGFfrksgkgsffTKIKsdwfKRDLSVIQNLKSI--KMNHPILISVSNKSFIGKILGKENVSDRLFGSIAAEA 188
                  88999999******************999777655555444422223466677777777..566****************966679************ PP

                  HHHHTT-SEEEES CS
  Pterin_bind 232 laaaaGadivrVh 244
                   ++ +Gad++r+h
   EPA05154.1 189 VSVLNGADVIRTH 201
                  ************9 PP

>> Spermine_synth  Spermine/spermidine synthase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   1.4e-05      0.12      48     113 ..      57     123 ..      31     168 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.4e-05
                     EES-HHHHHHHHHHSHHHHTTCGGCTTEEEEESTCHHHHCTCSS-EEEEEEECCSTTCSSCG..CSSH CS
  Spermine_synth  48 vdiDqkvidfskkflpslaisafndarvklvlgdgfkflkayekkfdvvivdsldpvgpaen..lFsk 113
                        D k+id+ +k+ psl   af+ +rv   ++    +lk+ +k ++  +  s+d +    +  +F k
      EPA05154.1  57 LKYDPKMIDVVRKYRPSLVLCAFDSKRVIGDIQSTKDLLKDSLK-LAKTTGISSDKIVLDPAigFFRK 123
                     5679*************************9***********999.55555555554444444344444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.35s 00:00:00.95 Elapsed: 00:00:00.56
# Mc/sec: 1197.33
//
Query:       EPA05155.1  [L=223]
Description: putative dihydropteroate synthase, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.5e-39  133.7   0.1    1.8e-38  132.6   0.1    1.5  1  Pterin_bind     Pterin binding enzyme
  ------ inclusion threshold ------
      0.065   12.6   0.1        0.1   12.0   0.1    1.3  1  Spermine_synth  Spermine/spermidine synthase domain


Domain annotation for each model (and alignments):
>> Pterin_bind  Pterin binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.6   0.1     2e-42   1.8e-38      51     244 .]       5     201 ..       3     201 .. 0.85

  Alignments for each domain:
  == domain 1  score: 132.6 bits;  conditional E-value: 2e-42
                  CCHHHHHHHHHHHHHHHHHHHCTSEEEEE-S-HHHHHHHHHTTSEEEEETTTTSSSTTHHHHHHHHT-EEEEESECSSTTTHCCCCCCCSSHHHHHHH CS
  Pterin_bind  51 rvdeeeelervvpvlealrdeadvpisiDttkaevaeaAlkagadivNdvsgeerdpkmlelvaeagaavvvmhmrgtpktmqeeegqyedvveevea 148
                   v+e++el+r++  ++ +++ +++pis+Dt +a+va+ Al+ g +i+Nd+sg++ dpkm+ +v++++  +v+ +++         + +    ++  + 
   EPA05155.1   5 SVSEKTELQRILDAIKVIQNISNLPISVDTCRANVAKHALEYGTEIINDISGLKYDPKMIDVVRKYRPSLVLCAFD--------SK-RVIGDIQSTKD 93 
                  699*****************99******************************************************........22.33344566778 PP

                  HHHHHHHHHHHTT--GGGEEEETTTTS..........STTH....HHHHHHHHTHHHHHHTTSSEBEEEGTTGHHHHHHHCTTCHGHHHHHHHHHHHH CS
  Pterin_bind 149 flearveaaeeaGvaperillDpgigf..........gkte....ehnlellrrldelrealevpvllGvSrksflgrllelgkaeeRdagtaaflal 232
                   l+ +++ a+ aG+ +++i+lDp igf          +k +    + +l+++++l+ +  +++ p+l++vS+ksf+g++l  +++++R  g++a+ ++
   EPA05155.1  94 LLKDSLKLANTAGISSDKIVLDPAIGFfrksgkgsffTKIKsdwlKRDLSVIQNLKSI--KMNHPLLISVSNKSFIGKILGKENVSDRLFGSLAAEVI 189
                  8999999******************999877655544343311113455566666666..555****************966679************* PP

                  HHHTT-SEEEES CS
  Pterin_bind 233 aaaaGadivrVh 244
                  ++ +Gadi+r+h
   EPA05155.1 190 SVLNGADIIRTH 201
                  ***********9 PP

>> Spermine_synth  Spermine/spermidine synthase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   1.1e-05       0.1      50     147 ..      59     162 ..      37     166 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.1e-05
                     S-HHHHHHHHHHSHHHHTTCGGCTTEEEEESTCHHHHCTCSS..-EEEEEEECC..S.TTCSSCGCSSHHHHHHHH.HTEEEEEEEEEEE.EETT CS
  Spermine_synth  50 iDqkvidfskkflpslaisafndarvklvlgdgfkflkayek..kfdvvivdsl..d.pvgpaenlFskeffdllk.kvlkedGviilqa.ekpe 137
                      D k+id+ +k+ psl   af+ +rv   ++    +lk+ +k  + + +  d +  d  +g   +  + +ff  +k + lk d  +i q+ +++ 
      EPA05155.1  59 YDPKMIDVVRKYRPSLVLCAFDSKRVIGDIQSTKDLLKDSLKlaNTAGISSDKIvlDpAIGFFRKSGKGSFFTKIKsDWLKRDLSVI-QNlKSIK 152
                     69**************************************99776666666654113223444444444555555424555554444.4447777 PP

                     TCHHHHHHHH CS
  Spermine_synth 138 lekelvinvd 147
                     +++ l+i+v 
      EPA05155.1 153 MNHPLLISVS 162
                     7777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1414.41
//
Query:       EPA05156.1  [L=554]
Description: radical SAM domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.3e-15   56.9   0.2    3.3e-15   56.9   0.2    2.5  3  Radical_SAM  Radical SAM superfamily
    1.1e-06   29.0   0.0    3.2e-06   27.4   0.0    1.8  1  Fer4_12      4Fe-4S single cluster domain
    1.7e-06   28.1   0.0    1.7e-06   28.1   0.0    2.0  2  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   1.1      0.52   3.1e+03       7      18 ..      93     104 ..      92     109 .. 0.87
   2 !   56.9   0.2   5.6e-19   3.3e-15       1     165 [.     112     272 ..     112     274 .. 0.84
   3 ?   -2.4   0.0      0.91   5.5e+03      60      75 ..     459     478 ..     441     513 .. 0.56

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.52
                  ESS--TTTSCCT CS
                  xxxxxxxxxxxx RF
  Radical_SAM   7 CnlrCsfCarpe 18 
                  C+++C  C+++ 
   EPA05156.1  93 CPNNCGLCSNHL 104
                  *********985 PP

  == domain 2  score: 56.9 bits;  conditional E-value: 5.6e-19
                  EEEESEESS--TTTSCCTT....HHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHG..H CS
                  xxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..x RF
  Radical_SAM   1 vvvtrgCnlrCsfCarpet....vrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlaklavpgiritvetngtlpd..e 91 
                  ++vt+ C l C++C ++ +    ++  + + + +v+  ++ +k+   ++  ++ + ++ggep+l+ d+++ ++ ++++     ++ + tng+++   +
   EPA05156.1 112 MIVTNRCDLTCWYCFFYVKkgleGAYMYEPDHTQVRGMMKTLKAE--RPIpGNSIQITGGEPMLREDIADVIKIMKEE--GVDHVQMNTNGIRHAmdP 205
                  579***************986655555555555555555555555..4445*****************9999999999..9***************** PP

                  HHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHHHH CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM  92 eklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGendeeleelle 165
                  e +++ + +g++ ++l+ + ++ +     +n+++ +e +  al+ +r+ g   vv++ ++++  nd+el  +++
   EPA05156.1 206 EAAREVRLAGCNNLYLSFDGVTAR-----TNPKNHWE-IPYALDSCRKTGTT-VVFVPTVIKSINDHELGGIIR 272
                  ***********************9.....86755555.5599*******999.9*************9977665 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 0.91
                  STTHHHHHHHHHHTC....C CS
                  xxxxxxxxxxxxxxx....x RF
  Radical_SAM  60 ypdfvellerlakla....v 75 
                  ++++ e+lerl +++     
   EPA05156.1 459 QDKYNEDLERLQRCDihylT 478
                  44555555555555322331 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   5.4e-10   3.2e-06       3      95 ..     106     200 ..     104     222 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 5.4e-10
     Fer4_12   3 GeGvrlslfvsgCnlsCkgCfnketwsfksgkeft..kelleeiiedlkkesi...egltllGGEPllpenaeallelvkevkeekpekdiwlytgyt 95 
                 + G+  ++ +++C+l C +Cf    +  ++   ++  ++  + +++ lk e+    + + ++GGEP+l   +e++++++k +kee+++ + + ++g  
  EPA05156.1 106 HSGLANMIVTNRCDLTCWYCFFYVKKGLEGAYMYEpdHTQVRGMMKTLKAERPipgNSIQITGGEPML---REDIADVIKIMKEEGVDHVQMNTNGIR 200
                 6788889999***********8777777777777443777777888887655567899**********...999999999999999988888888865 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.9   2.6         3   1.8e+04       7      18 ..      92     103 ..      87     107 .. 0.81
   2 !   28.1   0.0   2.9e-10   1.7e-06       4      92 ..     114     201 ..     112     221 .. 0.78

  Alignments for each domain:
  == domain 1  score: -4.9 bits;  conditional E-value: 3
     Fer4_14   7 gCnlsCkgCdnk 18 
                 +C+ +C  C n+
  EPA05156.1  92 SCPNNCGLCSNH 103
                 79999*9**886 PP

  == domain 2  score: 28.1 bits;  conditional E-value: 2.9e-10
     Fer4_14   4 rlsgCnlsCkgCd......nketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekkiwletngtle 92 
                  +++C l C  C+       + +++ e  + q++ ++ + l  + ++ i  + + +tGGeP++    +++ +++k +kee+   +++++tng  +
  EPA05156.1 114 VTNRCDLTCWYCFfyvkkgLEGAYMYEPDHTQVRGMM-KTL--KAERPIPGNSIQITGGEPMLR---EDIADVIKIMKEEG-VDHVQMNTNGIRH 201
                 589**********776655455566677777777777.444..5666788899*********55...9999*********9.5679*****9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (554 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 3351.40
//
Query:       EPA05157.1  [L=406]
Description: asparagine synthase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-28   99.6   0.0    3.8e-28   99.2   0.0    1.1  1  Asn_synthase   Asparagine synthase
      6e-07   28.8   0.0    9.5e-07   28.2   0.0    1.3  1  NAD_synthase   NAD synthase
    0.00048   19.7   0.0     0.0008   19.0   0.0    1.3  1  QueC           Queuosine biosynthesis protein QueC
    0.00098   18.0   0.0     0.0015   17.4   0.0    1.3  1  tRNA_Me_trans  tRNA methyl transferase
     0.0031   17.3   0.2     0.0073   16.1   0.0    1.7  2  ATP_bind_3     PP-loop family


Domain annotation for each model (and alignments):
>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.2   0.0     1e-31   3.8e-28      20     355 .]      68     391 ..      63     391 .. 0.83

  Alignments for each domain:
  == domain 1  score: 99.2 bits;  conditional E-value: 1e-31
  Asn_synthase  20 vGalLSGGlDSSliaalaarqsk.splktFsigfeekgsdeakyakevaehlgtehtelvlteeelldalpdviyhleepfadrsaiplyllsrlak 115
                   +++ LSGG+DSS++  ++++  + s++k+ +++f +++ de++ ak +a+ + +e+  l +++   l+ lp++i +   pf+d   i +y+++++a 
    EPA05157.1  68 ISISLSGGIDSSVVLLFLKHVFTnSKIKAITVKF-SDSVDETSRAKDIANNFDVEQEILFIEN--YLEKLPQAINVSKLPFWD---IHWYYVAEKA- 157
                   7789***************98776**********.899*****************75555544..7899******9999*997...55********. PP

  Asn_synthase 116 rkgvkvvLsGeGaDElfgGYpyfykaalsrsrefeklp.larslrasllarklrklaellelaeardleelaelyrlkasdsaeaelegedelhrel 211
                   +k +  + sG+G+DEl gGY ++y++ ls  r ++     a++  +   ++++ ++  +++   +++ ++++++y  +         ++  +l++ +
    EPA05157.1 158 KKYSNYLASGDGGDELLGGYVFRYSKFLSLIRPNSTPMeKAQAYIQCHERDHVPDQESIFG---SKSDFSWSDIYNILLPY----FDNSLAPLEQVF 247
                   565******************9999887765555333332222222223444444444444...66666677777766666....578999****** PP

  Asn_synthase 212 yldlktllpgdllrk.DrasmahglEaRvPflDhrlvevalrlppelklrg..gieKyiLRealegylPeeileRpKegfsapvgewklkgelrela 305
                   + d++  l ++      ++  ++g+    P+l ++ +     +++e+k+++  +i+K  LR++le+    ++++ +K gfs+ + +  + +  +e +
    EPA05157.1 248 LADYNGKLLYNFSILnTKIINSFGIKPIIPLLSNEMISHSIHMNAEEKYDKsqNIGKLPLRKILEKNDMLKFFDDQKLGFSVNTINL-WNNYGHEIC 343
                   *****999999888879********************************9999*************88889***********88887.578****** PP

  Asn_synthase 306 eellsdsrlakeglldreaveelleeheagkrnesrqlwslllsleawle 355
                   ++ lsdsrl k g+ld+  + +++++++     + ++   ll s+e w++
    EPA05157.1 344 KHYLSDSRLVKDGWLDKNWILKHIDRKDL-DVRYVNKFLGLL-SFEIWYR 391
                   ************************88887.555666666666.9999975 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   2.6e-10   9.5e-07       3      93 ..      50     139 ..      48     184 .. 0.91

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 2.6e-10
                   HHHHHHHHHHHHHCTTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE---HHHHHHHHHHHH CS
  NAD_synthase   3 eelvdflkeyvkkagakgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievktidikpivrafeqelk 93 
                   +++++++ + v +++ +++ + lSGG+DSs+v  + ++++ + +++a+ + +   s +++  a+ +a+n+++e + + i+++++ + q+++
    EPA05157.1  50 NSIKKSILNSVGNSEPEKISISLSGGIDSSVVLLFLKHVFTNSKIKAITV-KFSDSVDETSRAKDIANNFDVEQEILFIENYLEKLPQAIN 139
                   567889999999**************************************.77777888999*******************9998888765 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   2.2e-07    0.0008       5      62 ..      71     128 ..      67     142 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.2e-07
                 E--SSHHHHHHHHHHHHH-..SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-G CS
        QueC   5 llSGGlDSttvlalakkeg..kevealtfdYgqrhkkeleaakkiakelgveehkildld 62 
                  lSGG+DS++vl+  k+ +   +++a+t+++      e++ ak+ia++++v e++il ++
  EPA05157.1  71 SLSGGIDSSVVLLFLKHVFtnSKIKAITVKFSDSV-DETSRAKDIANNFDV-EQEILFIE 128
                 69**************9985578********9865.68899**********.66666554 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   4.1e-07    0.0015       2      46 ..      67     113 ..      66     155 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.1e-07
  tRNA_Me_trans   2 kvvvalSgGVDSsvaaallkeqg..yevigvflklweeedeegkecc 46 
                    k+ + lSgG+DSsv+++ lk+ +   +++++++k++++ de+++++ 
     EPA05157.1  67 KISISLSGGIDSSVVLLFLKHVFtnSKIKAITVKFSDSVDETSRAKD 113
                    8999*****************98334578999999999888773332 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0     2e-06    0.0073       2      50 ..      68     115 ..      67     140 .. 0.69
   2 ?   -2.5   0.0         1   3.7e+03     147     174 ..     311     338 ..     284     341 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2e-06
                 EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSS.TCHHHHHHHH CS
  ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglr.eeskeeaelv 50 
                 + + +SgG+DS + ll+l++  ++  +k+ ai+v ++ + +e+ + +++ 
  EPA05157.1  68 ISISLSGGIDSSVVLLFLKHVFTN--SKIKAITVKFSDSvDETSRAKDIA 115
                 6799*****************886..567777777765533333333333 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1
                 --HHHHHHHHHHTT---B--CGGGCTTS CS
  ATP_bind_3 147 vskeeleeylkekkikwveDesNadeky 174
                 ++k+++ ++ +++k+ +     N  ++y
  EPA05157.1 311 LEKNDMLKFFDDQKLGFSVNTINLWNNY 338
                 4688999999999988888777766666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2714.15
//
Query:       EPA05158.1  [L=458]
Description: nucleotide sugar dehydrogenase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.1e-38  130.3   0.0    1.5e-37  129.0   0.0    1.6  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
    1.9e-22   79.2   0.1    4.5e-22   78.1   0.1    1.7  1  UDPG_MGDP_dh    UDP-glucose/GDP-mannose dehydrogenase family,
      6e-22   78.0   0.0    2.1e-21   76.3   0.0    1.9  2  UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family,
      9e-06   25.2   0.0       0.83    9.0   0.0    3.4  3  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
    1.3e-05   25.4   0.0    9.6e-05   22.6   0.0    2.5  2  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
    4.1e-05   23.6   0.7        1.2    9.3   0.0    3.6  4  DpaA_N          Dipicolinate synthase subunit A N-terminal do
     0.0094   15.9   0.0       0.26   11.2   0.0    2.6  2  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
  ------ inclusion threshold ------
      0.044   13.7   0.0        0.1   12.5   0.0    1.7  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
      0.069   13.4   0.2       0.16   12.2   0.2    1.6  1  NAD_binding_11  NAD-binding of NADP-dependent 3-hydroxyisobut
      0.085   12.2   0.1       0.17   11.2   0.1    1.5  1  ThiF            ThiF family
       0.11   12.2   0.0       0.23   11.1   0.0    1.5  1  PA28_beta       Proteasome activator pa28 beta subunit
       0.16   12.6   1.1         28    5.4   0.0    3.2  3  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent


Domain annotation for each model (and alignments):
>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.0   0.0   9.8e-41   1.5e-37       2     186 ..      22     207 ..      21     208 .. 0.94

  Alignments for each domain:
  == domain 1  score: 129.0 bits;  conditional E-value: 9.8e-41
                     EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS-.-TTHHHHHHHHCHTTTEEEES-HHHHHHC-SEEEE-----B-TTTTCB CS
  UDPG_MGDP_dh_N   2 kisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiy.epgLeelvkkavesgrlsfttdvekaveeadvifiaVgTPskkkgkaa 95 
                     ki+viG G +Gl+ta+ +a+ g   ig+Di++e v+++n+g++p+  epg  ++ +k+++++++s+tt+++ av +++vi+++ +TP++k ++ +
      EPA05158.1  22 KICVIGIGRIGLPTALSFANSGLSTIGLDINSELVNMVNQGEFPLKdEPGYPTIFEKVLKEKKFSATTKIQDAVPQSNVIVLSLPTPMDK-QNVP 115
                     8*******************************************9659******************************************.8999 PP

                     -THHHHHHHHHHHHHHHCEEEEEE-S---TTHHHHCHHHHHHHHCSS-..TTCEEEEE------TTSHHHHHHS-S-EEEEESSCHHHHHHHH CS
  UDPG_MGDP_dh_N  96 DlkyvesaarsiaealkkgkvvvvkSTvpvgtaeelvkkileeaskkk..gvdfdvvsnPEflregsavkdllnpdrvviGveekkaeaalee 186
                     + +++ s+ r++ e+l++g++v+v+ST+ +g  e+ +k+i+e ++ k   g++f++ ++PE  ++g++++d+ + +r v+  +++ ++ ++++
      EPA05158.1 116 NYDALRSVGRQLHEFLSSGSIVIVESTIEPGFIENELKSIIEGNDLKLvaGKNFSIGVCPETANPGQILNDFERLPRLVGAIDQRTHN-IIKK 207
                     ******************************************98887689***************************98666555444.6655 PP

>> UDPG_MGDP_dh  UDP-glucose/GDP-mannose dehydrogenase family, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.1   0.1     3e-25   4.5e-22       1      93 [.     224     315 ..     224     316 .. 0.97

  Alignments for each domain:
  == domain 1  score: 78.1 bits;  conditional E-value: 3e-25
  UDPG_MGDP_dh   1 etAEliKlaaNaflatkIsfiNelanlcealgidveeVieavgldprigpkflkpglGvGGsclpkDvkaLvalaeelgle.aelleavrevNe 93 
                   +tA ++Kl+ N+f++++I+fiNela ++e+ gid+  V+ea++++ +  +++++pg+GvGG clp+  +++++ a++ g++ ++++e+ r++Ne
    EPA05158.1 224 KTANAVKLTTNVFRDLNIAFINELALIFEKSGIDIMTVLEAAKTKYN--FQVHYPGAGVGGPCLPVNSYQMINFAKTFGFDnFSIVETGRKINE 315
                   589*******************************************9..79*****************************999**********8 PP

>> UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       4.8   7.2e+03      51      73 ..      82     104 ..      69     113 .. 0.75
   2 !   76.3   0.0   1.4e-24   2.1e-21       1     104 [.     342     439 ..     342     440 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 4.8
                     BTCCEEES-CHHHHTT-SEEEE- CS
  UDPG_MGDP_dh_C  51 ekgvevvdsleealkgadaivil 73 
                     ek+ + ++++++a+ ++++iv+ 
      EPA05158.1  82 EKKFSATTKIQDAVPQSNVIVLS 104
                     56777788889999999999875 PP

  == domain 2  score: 76.3 bits;  conditional E-value: 1.4e-24
                     EEE-SSSSTT-S--TT-HHHHHHHHHHHCTSEEEEE-SSTHHCCCCHHGGBTCCEEES-CHHHHTT-SEEEE-S--GGGGGS-HHHHHHCCSS-E CS
  UDPG_MGDP_dh_C   1 ailGlafKkdtdDlReSpaldiieeLleegaevkiyDPkvkeeaveaeleekgvevvdsleealkgadaiviltehdefkeldlaklkelmkpav 95 
                     +ilG+++K+d++D+  +pa  ii +L++ g +vkiyDP++k++         g++  ++l e+lk++da++++t+h+ef +l+   lk+ mk +v
      EPA05158.1 342 LILGVTYKPDVKDVQLTPAEPIISKLQQLGSKVKIYDPYFKNSNL------FGINCESNLLETLKQSDAMIVVTAHKEFHDLEPVFLKSAMKSPV 430
                     69***************************************9886......4799**************************************** PP

                     EEESSS-CC CS
  UDPG_MGDP_dh_C  96 vfDgrnvld 104
                     v+D r +++
      EPA05158.1 431 VIDSRCIIN 439
                     *****9986 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0   0.00056      0.83      35      69 ..      19      53 ..       5      67 .. 0.84
   2 ?    4.5   0.0     0.014        20      78     117 ..      83     123 ..      72     128 .. 0.79
   3 !    7.4   0.0    0.0017       2.6      51     100 ..     363     410 ..     360     418 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00056
                  TTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSH CS
  2-Hacid_dh_C 35 sgktvGiiGlGrIGqavakrlkafgmkviaydrsk 69
                     ++++iG+GrIG  +a  ++  g+  i+ d + 
    EPA05158.1 19 GSLKICVIGIGRIGLPTALSFANSGLSTIGLDINS 53
                  56789************************999875 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.014
                   HTC.EECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCS CS
  2-Hacid_dh_C  78 lgv.elvsleellaesDivslhlpltpetrhlinaeelakm 117
                   +++   +++++++ +s +++l lp   + +++ n ++l+++
    EPA05158.1  83 KKFsATTKIQDAVPQSNVIVLSLPTPMDKQNVPNYDALRSV 123
                   333246799****************9999999999999876 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0017
                   HHHHHHHTT-EEEEESSSHHHHHCHHHHTCEEC.SHHHHHHH-SEEEE-S- CS
  2-Hacid_dh_C  51 vakrlkafgmkviaydrskkkeeeeeelgvelv.sleellaesDivslhlp 100
                   ++ +l+++g kv +yd++ k+++     g++++ +l e l++sD  ++++ 
    EPA05158.1 363 IISKLQQLGSKVKIYDPYFKNSN---LFGINCEsNLLETLKQSDAMIVVTA 410
                   67899*************99655...666766659999******9887665 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   6.4e-08   9.6e-05       1      94 [.      22     145 ..      22     163 .. 0.88
   2 ?   -2.1   0.0       2.5   3.8e+03     130     137 ..     405     412 ..     361     434 .. 0.54

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 6.4e-08
                    EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT.....................EEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS CS
  NAD_binding_2   1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg.....................akaaesieelvasldvvitmvkagkavdevieg 75 
                    ki +iG+G +G + al ++++g ++++ + ++e v+ + + +                     ++a+++i+++v + +v+++ ++   + ++v + 
     EPA05158.1  22 KICVIGIGRIGLPTALSFANSGLSTIGLDINSELVNMVNQGEfplkdepgyptifekvlkekkFSATTKIQDAVPQSNVIVLSLPTPMDKQNVPNY 117
                    699***************************977776666555*********************9******************98887777666555 PP

                    .........HCCC--TT-EEEE-S---H CS
  NAD_binding_2  76 .........llealkkgdilidgstssp 94 
                             l e l++g+i+i  st++p
     EPA05158.1 118 dalrsvgrqLHEFLSSGSIVIVESTIEP 145
                    556666666****************997 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.5
                    EEEEE-HH CS
  NAD_binding_2 130 imvGGsee 137
                    ++v +  +
     EPA05158.1 405 MIVVTAHK 412
                    22223333 PP

>> DpaA_N  Dipicolinate synthase subunit A N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0   0.00078       1.2      31     113 ..      77     164 ..      69     165 .. 0.81
   2 ?    1.5   0.0      0.21   3.1e+02       8      44 ..     198     234 ..     198     271 .. 0.77
   3 ?   -2.6   0.0       3.8   5.7e+03      48      61 ..     335     348 ..     307     357 .. 0.60
   4 !    8.5   0.0    0.0014       2.1      14      57 ..     363     407 ..     362     424 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00078
                 TSSS-BTTEEEE-GGGS-GGG-SEEE--TT-BETTTEE-BSS-SS-EE-.HHHHHTS-TT-EEEE......SS--HHHHHHHHHCT-EEE CS
      DpaA_N  31 eleekiegvekaesleealedadviilPvpgtkdggeintpfseeklsl.eelleklkkgqllfg......Giippelkelaeekgielv 113
                 e+  k +++  ++++++a+ +++vi+l +p   d++++     +   s+ ++l e l++g+++++      G+i++elk+++e ++++lv
  EPA05158.1  77 EKVLKEKKFSATTKIQDAVPQSNVIVLSLPTPMDKQNVPN--YDALRSVgRQLHEFLSSGSIVIVestiepGFIENELKSIIEGNDLKLV 164
                 566788899999*******************9**999999..333444558888889998887766666669999999999999988876 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.21
                 -HHHHHHHHHHHHTT-EEEEES-TSSS-BTTEEEE-G CS
      DpaA_N   8 DaRqlylarkLaekgakvslygleleekiegvekaes 44 
                 D+R   +++k+ ++ ++v l+ ++  ++ + v+ +++
  EPA05158.1 198 DQRTHNIIKKIYKHVFTVDLISMPDCKTANAVKLTTN 234
                 99*******************9966666666655554 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 3.8
                 -GGG-SEEE--TT- CS
      DpaA_N  48 aledadviilPvpg 61 
                 +++++ ++il v++
  EPA05158.1 335 DIKNSTILILGVTY 348
                 34555555555554 PP

  == domain 4  score: 8.5 bits;  conditional E-value: 0.0014
                 HHHHHHHTT-EEEEES-.TSSS-BTTEEEE-GGGS-GGG-SEEE- CS
      DpaA_N  14 larkLaekgakvslygl.eleekiegvekaesleealedadviil 57 
                 ++ kL++ g kv++y    ++++  g++++++l e+l+++d++i+
  EPA05158.1 363 IISKLQQLGSKVKIYDPyFKNSNLFGINCESNLLETLKQSDAMIV 407
                 5889***********5543667777*****************996 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   0.00018      0.26       1      84 [.      22     112 ..      22     174 .. 0.78
   2 ?    1.8   0.0      0.14   2.1e+02      57      84 ..     389     416 ..     378     432 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00018
                     -EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHHS.......SBTTTBTT----TTEEEES-HHHHHTT--EEEE---HHHHHH CS
  NAD_Gly3P_dh_N   1 kiavlGaGswGtalAkvlaenghevrlwvreeelieeineeh.......envkyLpgiklpenlvattdlaealkgadiivlvvPsqalre 84 
                     ki+v+G G  G   A ++a+ g ++     ++el++ +n+ +          + ++++  +++  att +++a+ ++++ivl +P+ + ++
      EPA05158.1  22 KICVIGIGRIGLPTALSFANSGLSTIGLDINSELVNMVNQGEfplkdepGYPTIFEKVLKEKKFSATTKIQDAVPQSNVIVLSLPTPMDKQ 112
                     79********************9999999999999999886511110002344566667788999*******************9966554 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.14
                     EEEES-HHHHHTT--EEEE---HHHHHH CS
  NAD_Gly3P_dh_N  57 lvattdlaealkgadiivlvvPsqalre 84 
                     +  +++l e+lk++d +++v  ++ +++
      EPA05158.1 389 INCESNLLETLKQSDAMIVVTAHKEFHD 416
                     667899***************9998765 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   6.9e-05       0.1       1      38 [.      22      59 ..      22     102 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.9e-05
                EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHH CS
     3HCDH_N  1 kvaviGaGtmGagiaavfasagleVvlvdiseealeka 38
                k+ viG G +G   a  fa++gl++  +di++e ++ +
  EPA05158.1 22 KICVIGIGRIGLPTALSFANSGLSTIGLDINSELVNMV 59
                689****************************9988765 PP

>> NAD_binding_11  NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   0.00011      0.16       3      43 ..     226     266 ..     225     269 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
  NAD_binding_11   3 GqavKlvnnlllainlaaasEalvlaekaGldpekvlevin 43 
                     ++avKl  n+   +n+a + E  ++ ek G+d+ +vle+ +
      EPA05158.1 226 ANAVKLTTNVFRDLNIAFINELALIFEKSGIDIMTVLEAAK 266
                     689**********************************9876 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00011      0.17      11      47 ..      11      49 ..       2     123 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                HHHHHHHT..SEEEEE--SHHHHHHHHHHHHHTTTEEEE CS
                xxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        ThiF 11 dgqekLrd..skvllvGaGglGsellknLalsGvgkltl 47
                ++ + +++   k++++G+G +G + +  +a sG++ + l
  EPA05158.1 11 EFNNSIQSgsLKICVIGIGRIGLPTALSFANSGLSTIGL 49
                56666666669************************8876 PP

>> PA28_beta  Proteasome activator pa28 beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00015      0.23      22     107 ..     363     446 ..     354     451 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00015
   PA28_beta  22 lieklnkvklwiqlliPkiedGnnfGVsvQeevleelsrveeeaanlldqiskyfleraklvskllkyphvedyrealeelDekql 107
                 +i kl+++   +++  P  ++ n fG++   ++le+l+  +++a  + ++ ++ +      ++ ++k p v d r +++++D k++
  EPA05158.1 363 IISKLQQLGSKVKIYDPYFKNSNLFGINCESNLLETLK--QSDAMIVVTAHKEFHDLEPVFLKSAMKSPVVIDSRCIINQFDAKNA 446
                 6677788888888889999*****************99..6677789999999999999***********************9986 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1     0.064        95       1      22 [.      22      43 ..      22      58 .. 0.90
   2 ?    5.4   0.0     0.019        28      41      73 ..      78     109 ..      72     123 .. 0.84
   3 ?   -0.4   0.0       1.2   1.8e+03      46      93 ..     387     433 ..     360     434 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.064
                   EEEEETTSHHHHHHHHHHHHTT CS
  F420_oxidored  1 kigiiGaGnmgealasgllaag 22
                   ki++iG G++g   a+ ++++g
     EPA05158.1 22 KICVIGIGRIGLPTALSFANSG 43
                   79*********99999999999 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.019
                    HHHHHHC-EEECECHHHHHHH-SEEEE-S-HHH CS
  F420_oxidored  41 elaeelgvkvtavdneeaaeeadvvvlavkped 73 
                    +  +e + ++t+ + ++a+ +++v+vl++++ +
     EPA05158.1  78 KVLKEKKFSATT-KIQDAVPQSNVIVLSLPTPM 109
                    666777788999.99**************9876 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.2
                    HC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHHCGHHHHTTSEEEE CS
  F420_oxidored  46 lgvkvtavdneeaaeeadvvvlavkpedveevlselakdalkgklvis 93 
                    +g+++++ +  e+++++d  ++    + ++++     k+a k  +vi+
     EPA05158.1 387 FGINCES-NLLETLKQSDAMIVVTAHKEFHDLEPVFLKSAMKSPVVID 433
                    5666666.7888888888777777777777766666677777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (458 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.65u 0.33s 00:00:00.98 Elapsed: 00:00:00.52
# Mc/sec: 2630.62
//
Query:       EPA05159.1  [L=268]
Description: sugar-specific transcriptional regulator TrmB [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.4e-21   74.5   0.0    1.4e-20   72.9   0.0    1.9  2  TrmB             Sugar-specific transcriptional regulator Trm
    1.2e-07   31.1   0.0    1.5e-07   30.9   0.0    1.1  1  Regulator_TrmB   Archaeal transcriptional regulator TrmB
    3.8e-05   23.4   0.0     0.0002   21.1   0.0    2.1  2  HTH_IclR         IclR helix-turn-helix domain
     0.0012   18.7   0.0     0.0042   17.0   0.0    1.9  2  MarR             MarR family
     0.0063   16.0   0.0      0.016   14.7   0.0    1.7  1  HTH_24           Winged helix-turn-helix DNA-binding
     0.0076   16.6   0.1      0.042   14.2   0.0    2.0  2  Penicillinase_R  Penicillinase repressor
     0.0089   16.5   0.0      0.022   15.2   0.0    1.6  1  HTH_27           Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.053   13.9   0.0       0.17   12.2   0.0    1.8  1  Rrf2             Transcriptional regulator
        0.1   12.5   0.0       0.21   11.5   0.0    1.6  1  PLDc_2           PLD-like domain
       0.13   12.3   0.0       0.31   11.0   0.0    1.7  1  PadR             Transcriptional regulator PadR-like family
       0.18   11.7   0.0       0.31   11.0   0.0    1.4  1  MarR_2           MarR family


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.9   0.0   8.6e-24   1.4e-20       1      67 [.      24      90 ..      24      91 .. 0.98
   2 ?   -2.4   0.0       2.9   4.7e+03      43      51 ..     174     182 ..     174     205 .. 0.77

  Alignments for each domain:
  == domain 1  score: 72.9 bits;  conditional E-value: 8.6e-24
                HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE--H CS
        TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravdp 67
                L+k+GL++yE+++++ Ll++g++ta ++++++gvp+sk+YevL  Le+kG++   ++rp++Y a +p
  EPA05159.1 24 LEKIGLTSYEIRTFTSLLQSGELTAADLSQKSGVPYSKIYEVLGTLEEKGWIGSDDSRPTKYFAKSP 90
                789*************************************************************998 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.9
                 HHHHHHCTS CS
        TrmB  43 LrsLedkGl 51 
                 LrsL dkG+
  EPA05159.1 174 LRSLHDKGV 182
                 678888885 PP

>> Regulator_TrmB  Archaeal transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.0   9.1e-11   1.5e-07       2     130 ..     131     263 ..     130     268 .] 0.84

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 9.1e-11
                     EEEESSHHHHHHHHHHHHHH-SSEEEEEE-...GGGHHHHHHHHHHHHHTT-EEEEEESS----GGGSSSSEEEEEE-S---S.EEEEETTTEEE CS
  Regulator_TrmB   2 vwvvksretvierieelIesAenelivslp...selLeelreeliaaaergvtVllliypdedleeldleevatevrvrrsgapllvivDrkrgv 93 
                     +wv  +  ++ ++i e++es +ne++++lp   +el+++  ++l++ +++gv++ +l +++ d+e  +  + ++ v++ ++     +i+D +++v
      EPA05159.1 131 IWVLSGAINIASKILEMVESCRNEVMIALPeagQELVRQALPKLRSLHDKGVKITILTSDKMDKESIKAISRVATVKIKKGLFGGGIISDNRYVV 225
                     89999**********************99855579*************************99****9***99999*9999988777999*99999 PP

                     EE.-SSS-.EEEE--HHHHHHHHHHHHHH........HH CS
  Regulator_TrmB  94 va.prevl.rdkeeeyaiifkekelihvlshyFlttlWk 130
                     +    e++ +  ++  ai+ + + l+ +   +++++l k
      EPA05159.1 226 ILlGPEMKeMNTSDIVAIWADHTGLAGFA-RSYFEYLLK 263
                     86245566888888899998888887766.444444455 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   1.2e-07    0.0002      16      51 ..      43      78 ..      41      79 .. 0.92
   2 ?   -1.1   0.0         1   1.7e+03       4      20 ..     140     156 ..     137     168 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.2e-07
                BSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
    HTH_IclR 16 pqeltlselArrtglpkStvhRlLqtLvelGyveqd 51
                 +elt ++l++++g+p S+ +  L tL+e G++  d
  EPA05159.1 43 SGELTAADLSQKSGVPYSKIYEVLGTLEEKGWIGSD 78
                589*****************************8665 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1
                 HHHHHHCT-CTTBSS-B CS
    HTH_IclR   4 RalaiLdalaeapqelt 20 
                  a  iL+++++++ e+ 
  EPA05159.1 140 IASKILEMVESCRNEVM 156
                 57789999999998864 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       2.7   4.3e+03      29      46 ..      11      29 ..       9      29 .. 0.67
   2 !   17.0   0.0   2.6e-06    0.0042       1      47 [.      29      75 ..      29      80 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.7
                S-HHHHHHHHHH.HHHTTS CS
        MarR 29 vskstvtrvldr.LekkGl 46
                v++++++  +++ Lek Gl
  EPA05159.1 11 VDRMNISDKTRKsLEKIGL 29
                6778888776544887775 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 2.6e-06
                --HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
        MarR  1 ltltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGli 47
                lt  ++++ ++l ++g+l+ ++L  k+gv  s + +vl +Le+kG+i
  EPA05159.1 29 LTSYEIRTFTSLLQSGELTAADLSQKSGVPYSKIYEVLGTLEEKGWI 75
                6778899999************************************9 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0     1e-05     0.016      12      47 ..      40      75 ..      32      75 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1e-05
      HTH_24 12 LqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                L + + ++ ++L++++g++ s + + l  Lee+G+I
  EPA05159.1 40 LLQSGELTAADLSQKSGVPYSKIYEVLGTLEEKGWI 75
                566799*****************************9 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   2.6e-05     0.042      21      81 ..      44     107 ..      34     122 .. 0.72
   2 ?   -0.5   0.0      0.97   1.6e+03       9      39 ..     156     183 ..     151     203 .. 0.50

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.6e-05
                      HHHHHT.--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE--...--XXXXXXXXXXXXXX CS
  Penicillinase_R  21 kevvee.leeekelaysTVktllrrLvkKgllsrekegrafiYspl...vseeeavasavkqlld 81 
                      +e+ ++ l++++ + ys +  +l+ L++Kg++ ++   r + Y +    +  e  ++++ +++l+
       EPA05159.1  44 GELTAAdLSQKSGVPYSKIYEVLGTLEEKGWIGSDD-SRPTKYFAKspsTGLETTKQKMQNEFLQ 107
                      5555555999999********************987.5666665540004555555555555555 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.97
                      HHHHHHHS-EEHHHHHHT--GGG---HHHHH CS
  Penicillinase_R   9 meilwekgeatvkevveeleeekelaysTVk 39 
                      m +l e+g+  v++    l++ ++l+++ Vk
       EPA05159.1 156 MIALPEAGQELVRQA---LPKLRSLHDKGVK 183
                      555555554444333...3333333333333 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.4e-05     0.022      16      60 ..      43      83 ..      32      89 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.4e-05
      HTH_27 16 rrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrek 60
                 ++ ++adl+++  v +s i ++l  L+ekG++   g+  d r++
  EPA05159.1 43 SGELTAADLSQKSGVPYSKIYEVLGTLEEKGWI---GS-DDSRPT 83
                688999***************************...55.466654 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00011      0.17      16      57 ..      39      77 ..      29      80 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
                HHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
        Rrf2 16 yLakeeeeepvsseeiaerqnispsylekilakLrkaglvks 57
                 L +  e   +++++++++ +++ s +  +l +L+++g++ s
  EPA05159.1 39 SLLQSGE---LTAADLSQKSGVPYSKIYEVLGTLEEKGWIGS 77
                4443333...9*****************************88 PP

>> PLDc_2  PLD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00013      0.21       3      52 ..     146     197 ..     144     233 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
      PLDc_2   3 qliksAkksidiatyyf..vsdreildallkaakrgvkvrilldskkddaga 52 
                 ++ +s++ ++ ia +    +  r+ l +l+ ++++gvk+ il+++k d+ ++
  EPA05159.1 146 EMVESCRNEVMIALPEAgqELVRQALPKLRSLHDKGVKITILTSDKMDKESI 197
                 6667778888888887755555555888999*************95443333 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00019      0.31      29      63 ..      57      86 ..      46      96 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00019
                TTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEE CS
        PadR 29 lseGslYpaLkrLekeglveseweesgegpprkyY 63
                + ++++Y +L +Le++g++ s  +     +p+ky+
  EPA05159.1 57 VPYSKIYEVLGTLEEKGWIGSDDS-----RPTKYF 86
                56789**************99855.....577776 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00019      0.31       2      51 ..      28      75 ..      27      93 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00019
                T--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSE CS
      MarR_2  2 gltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLv 51
                glt  + r    L  +++  lt+++l ++ g++ s +  +l  L+++G++
  EPA05159.1 28 GLTSYEIRTFTSLLQSGE--LTAADLSQKSGVPYSKIYEVLGTLEEKGWI 75
                666667777778889999..*****************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       817  (0.0455686); expected 358.6 (0.02)
Passed bias filter:                      657  (0.0366445); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 1776.25
//
Query:       EPA05160.1  [L=61]
Description: iron dependent repressor, N-terminal DNA binding domain protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-11   44.1   0.1    2.3e-11   43.7   0.1    1.1  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
     0.0054   16.6   0.0     0.0066   16.3   0.0    1.1  1  MarR            MarR family
  ------ inclusion threshold ------
      0.025   14.6   0.0      0.028   14.5   0.0    1.1  1  NLPC_P60        NlpC/P60 family
      0.031   14.2   0.0      0.038   14.0   0.0    1.2  1  HTH_37          Helix-turn-helix domain
      0.048   14.2   0.0      0.063   13.8   0.0    1.2  1  HTH_27          Winged helix DNA-binding domain
      0.051   13.5   0.0      0.063   13.2   0.0    1.2  1  MarR_2          MarR family


Domain annotation for each model (and alignments):
>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.7   0.1   7.9e-15   2.3e-11       4      45 ..      20      61 .]      19      61 .] 0.96

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 7.9e-15
                    HHHHHHHHHHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHH CS
  Fe_dep_repress  4 estEdYLetIYtlseekkvvktkdlaerLnvspssVsemlkk 45
                    e  E+YL++I+ ++e ++ vk + +a+ Lnv+ +sV +mlkk
      EPA05160.1 20 EHVEMYLKAIWHIKERGEDVKISTIAKMLNVRQPSVVQMLKK 61
                    678*************************************98 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   2.2e-06    0.0066       8      40 ..      28      61 .]      25      61 .] 0.90

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.2e-06
                HHHHHHHSTT.EEHHHHHHHHTS-HHHHHHHHHH CS
        MarR  8 iLrilyeqgp.lsvseLakklgvskstvtrvldr 40
                +++ ++e+g+  ++s +ak+l+v +++v  +l++
  EPA05160.1 28 AIWHIKERGEdVKISTIAKMLNVRQPSVVQMLKK 61
                67789999988*********************97 PP

>> NLPC_P60  NlpC/P60 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   9.3e-06     0.028      58      93 ..      12      46 ..       9      58 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 9.3e-06
                EEESGTGGESEEEEEEETTEEEEEETTEEEEEETTS CS
    NLPC_P60 58 vffktkkgisHvgiYlgngkmlhassekvsvsslse 93
                +f++t  +++Hv +Yl+  +++++ +e v++s++ +
  EPA05160.1 12 LFVGT-AEAEHVEMYLKAIWHIKERGEDVKISTIAK 46
                67777.999*********************998865 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.3e-05     0.038       7      53 ..      16      60 ..      14      61 .] 0.76

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.3e-05
                --HHHHHHHHHHHHHHHHHHHHHCT--HHHHHHHHT--HHHHHHHHT CS
      HTH_37  7 eedaeelkaKaqlalaiaeliekrelsqseaaqllgiaqPkvsrllr 53
                 ++ae ++   + ++ i+e  e+   + s +a++l++ qP+v+++l+
  EPA05160.1 16 TAEAEHVEMYLKAIWHIKERGED--VKISTIAKMLNVRQPSVVQMLK 60
                66777777777777888876555..55567***************97 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.1e-05     0.063       9      41 ..      29      61 .]      25      61 .] 0.94

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.1e-05
      HTH_27  9 Lhlirhrrrrkkladlcgrlnvedshisyslkk 41
                +++i++r++ +k++ ++++lnv + +++ +lkk
  EPA05160.1 29 IWHIKERGEDVKISTIAKMLNVRQPSVVQMLKK 61
                79***99999999***************99997 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.1e-05     0.063      13      44 ..      31      61 .]      24      61 .] 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.1e-05
                HHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHH CS
      MarR_2 13 aLgrrpgrdltvgelarrlglsksavsrilkr 44
                ++  r++ d+ ++ +a+ l++ +++v ++lk+
  EPA05160.1 31 HIKERGE-DVKISTIAKMLNVRQPSVVQMLKK 61
                5666664.89********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 454.49
//
Query:       EPA05161.1  [L=39]
Description: hypothetical protein BG20_I1667 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 257.25
//
Query:       EPA05162.1  [L=271]
Description: methyltransferase, FkbM family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.1e-21   75.4   0.7    7.1e-21   75.0   0.7    1.2  1  Methyltransf_21  Methyltransferase FkbM domain
    8.9e-10   38.6   0.5    1.9e-09   37.5   0.3    1.5  1  Met_10           Met-10+ like-protein
      6e-07   29.0   3.6    8.1e-07   28.6   3.6    1.2  1  V_cholerae_RfbT  Vibrio cholerae RfbT protein
    2.1e-05   24.4   0.0    3.2e-05   23.8   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    6.2e-05   22.8   0.2    9.1e-05   22.3   0.2    1.3  1  Methyltransf_31  Methyltransferase domain
    0.00046   20.1   0.6       0.13   12.2   0.1    2.4  2  Methyltransf_18  Methyltransferase domain
     0.0051   16.4   0.0     0.0083   15.7   0.0    1.4  1  MTS              Methyltransferase small domain
     0.0057   16.8   0.0     0.0077   16.4   0.0    1.3  1  FtsJ             FtsJ-like methyltransferase
     0.0068   17.1   0.0       0.02   15.6   0.0    1.9  2  Methyltransf_25  Methyltransferase domain
     0.0098   15.3   0.3      0.015   14.7   0.3    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
  ------ inclusion threshold ------
      0.057   13.0   0.0       0.12   12.0   0.0    1.4  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F


Domain annotation for each model (and alignments):
>> Methyltransf_21  Methyltransferase FkbM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.0   0.7   4.3e-24   7.1e-21       1     171 [.      72     234 ..      72     236 .. 0.76

  Alignments for each domain:
  == domain 1  score: 75.0 bits;  conditional E-value: 4.3e-24
  Methyltransf_21   1 dvGanigvwdsfanltarlcggggevlaiEPvpnslpkfeklranlltlavgndvglyelivegksg.gkyfpfavgdtngfstssvlggedar 93 
                      d Ganig   +++  +a+l g +g+v+a+EP+p+   +fe l+ n   + ++n ++ + ++ +++s+ +++ + + ++  g ++ + l+++ ++
       EPA05162.1  72 DLGANIG---YYTLIAAKLVGDKGKVFAFEPEPK---NFEILKKN---VELNNYQNVILEQ-KAVSDvNEKINLYLSEGIGTHSIK-LKQNIKQ 154
                      88*****...444455689***************...********...****997776644.455554666666666655555555.4479*** PP

  Methyltransf_21  94 yievpvvtldsfleei.kksridllkiDvEGaElevLeGaqkglkrcqpnlivvEvhkfk.efetelfdeirqflrecgy 171
                      +i+v+ ++ld+ + +     +i+++kiDvEGaE+ +L+G +  lk+ +   i+ E+ k    + + ++++++++l + g+
       EPA05162.1 155 TIQVESIRLDDYFSNLnLTDKINFIKIDVEGAEFRALNGMNMILKQSKHLKIFTEFMKNFiVESGTEPKDMLELLINNGF 234
                      **********66555559999******************88888775555555675553334444889999998888887 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.5   0.3   1.2e-12   1.9e-09      94     154 ..      60     121 ..      54     139 .. 0.84

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 1.2e-12
                 HHTT--TT-EEEETT-TTTCCHHHCCHH.TTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEE CS
      Met_10  94 laklveegevVvdvfAGiGpfaipiaky.skakrvlaidlnPesvkylkeniklNkvekvvk 154
                 + + ++ g++Vvd+ A iG++++ +ak+ +++ +v+a + +P+ ++ lk+n++lN+ ++v+ 
  EPA05162.1  60 IKNCIKTGDIVVDLGANIGYYTLIAAKLvGDKGKVFAFEPEPKNFEILKKNVELNNYQNVIL 121
                 55679*****************999986367889************************9994 PP

>> V_cholerae_RfbT  Vibrio cholerae RfbT protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   3.6     5e-10   8.1e-07      72     232 ..      59     214 ..      43     239 .. 0.76

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 5e-10
  V_cholerae_RfbT  72 wivnhckhdttyidiganvgtfcgiaarhit.qgkiiaiepltemensirmnvqlnnplvefhhfgcaigenegenifevyefdnrvsslyfkk 164
                       i n  k     +d+gan+g +  iaa+ +  +gk+ a ep  +  + ++ nv+lnn    +    +    ne  n++    +     s+ +k+
       EPA05162.1  59 IIKNCIKTGDIVVDLGANIGYYTLIAAKLVGdKGKVFAFEPEPKNFEILKKNVELNNYQNVILEQKAVSDVNEKINLYLSEGIG--THSIKLKQ 150
                      355666888899****************99637**********9999**********988777777777788888887655544..46777888 PP

  V_cholerae_RfbT 165 ntdiadkvknsqvlvrklssldisptnsvvikidaegaeieilnqiyeftekhngieyyicfefamgh 232
                      n   + +v+ s  l   +s+l+++      ikid egae   ln +  + ++ + ++  i  ef   +
       EPA05162.1 151 NIKQTIQVE-SIRLDDYFSNLNLTDK-INFIKIDVEGAEFRALNGMNMILKQSKHLK--IFTEFMKNF 214
                      877766664.5567788999999765.4579*************9887766555444..334555555 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0     2e-08   3.2e-05      66     129 ..      57     122 ..      14     128 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 2e-08
                 HHHTT..--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEE CS
        PCMT  66 lelle..lkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivv 129
                 +e ++  +k g+ v+++G+  Gy t + a+lvg+kg+v + e  ++  e  k+n++ ++++nvi+ 
  EPA05162.1  57 TEIIKncIKTGDIVVDLGANIGYYTLIAAKLVGDKGKVFAFEPEPKNFEILKKNVELNNYQNVILE 122
                 5667777999*****************************************************975 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.2   5.6e-08   9.1e-05       3      91 ..      66     150 ..      64     187 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 5.6e-08
  Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnevl.naladpd 91 
                       g  v+DlG++ G++t+ +a+++g+k++v+ ++ +++  e  ++n + ++++nv +eq  + + +     ek++l ls ++  + ++ ++
       EPA05162.1  66 TGDIVVDLGANIGYYTLIAAKLVGDKGKVFAFEPEPKNFEILKKNVELNNYQNVILEQKAVSDVN-----EKINLYLSEGIGtHSIKLKQ 150
                      56679*****************************************************9999977.....56777777655544444444 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.1   7.8e-05      0.13       8      96 ..      60     146 ..      54     161 .. 0.78
   2 !    6.3   0.1    0.0052       8.6      96     136 ..     194     237 ..     146     244 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.8e-05
  Methyltransf_18   8 iaslvekgsrvaDiGtDHgylpiylvk.egkakkviasDinegplekakeniekagledkievrlsdGleklkeeevdtvviaGmGgeli 96 
                      i +++++g++v+D G+  gy ++ ++k  g   kv a + +++ +e  k+n+e +++++ i    ++ ++ ++ e+++  +  G+G++ i
       EPA05162.1  60 IKNCIKTGDIVVDLGANIGYYTLIAAKlVGDKGKVFAFEPEPKNFEILKKNVELNNYQNVI--LEQKAVSDVN-EKINLYLSEGIGTHSI 146
                      78899**************98877765258889********************99997643..3344555554.3366777777776655 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0052
  Methyltransf_18  96 ileILeea...keklkkikklilqpnseaeelRkylvengfkie 136
                      +  IL+++   k  ++ +k++i+++ +e +++ + l++ngf+i 
       EPA05162.1 194 MNMILKQSkhlKIFTEFMKNFIVESGTEPKDMLELLINNGFNIS 237
                      55678777332333446778*********************996 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   5.1e-06    0.0083      28     100 ..      65     135 ..      48     158 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5.1e-06
                 HCCTCSEEEEET-TTSHHHHHHHHHTTC.E.EEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEE CS
         MTS  28 pkelsgkvlDlGcGaGvlgaalakespeae.vtlvdvdarAlesakenleanklevevvasdvleeveekkfdl 100
                 ++   + v+DlG+ +G+ ++ +ak   +   v +++ + +  e+ k+n+e n+ +  ++++ ++++v+ +k++l
  EPA05162.1  65 KT--GDIVVDLGANIGYYTLIAAKLVGDKGkVFAFEPEPKNFEILKKNVELNNYQNVILEQKAVSDVN-EKINL 135
                 33..5569***************99877655*********************************9999.77766 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   4.7e-06    0.0077      18     111 ..      63     158 ..      52     212 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4.7e-06
                 -S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSSHHHTTEEEECS-CCCSSHHHHHCHCHHH......SSEEEEEE--S..-SS-CHHHHHHH CS
        FtsJ  18 lfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpmaplpgvttiqgditdpetiekikealse......rkvdlvvsDga..pdvsgvhdldey 108
                  +k g+ vvDlga  G ++ ++++ +g kgkv+a+   p     + ++++ ++   + ++ i+e+  +      +k++l +s g    +++++++++++
  EPA05162.1  63 CIKTGDIVVDLGANIGYYTLIAAKLVGDKGKVFAFEPEPK----NFEILKKNVELNNYQNVILEQ--KavsdvnEKINLYLSEGIgtHSIKLKQNIKQT 155
                 4678899*****************************9985....555555555444444444321..11122445788888887633466666666666 PP

                 HHC CS
        FtsJ 109 lqs 111
                 +q+
  EPA05162.1 156 IQV 158
                 665 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.2e-05      0.02       1      59 [.      70     130 ..      70     158 .. 0.87
   2 ?   -1.7   0.0         3   4.8e+03      40      40 ..     166     166 ..     135     209 .. 0.58

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.2e-05
                      EEEET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBS CS
  Methyltransf_25   1 vLdlGcGtGrltlalakrlg.kakvtgvDiseemleaareraeeegl.nvefvqgdaedlp 59 
                      v+dlG+  G +tl +ak +g k+kv ++++ ++  e+ ++++e +++ nv ++q+ ++d++
       EPA05162.1  70 VVDLGANIGYYTLIAAKLVGdKGKVFAFEPEPKNFEILKKNVELNNYqNVILEQKAVSDVN 130
                      89*****************779********************9988889998888887765 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3
                      H CS
  Methyltransf_25  40 r 40 
                       
       EPA05162.1 166 Y 166
                      1 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.3   9.1e-06     0.015     153     249 ..      58     155 ..      54     162 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 9.1e-06
        PrmA 153 ealeklvkegeevlDvGtGSGiLaiaaakL.gak.kvvavDiDevAvkvakeNaelNkveaklevalseellk..eekadvivaNILaevlielaedik 247
                 e++ + +k+g+ v+D+G+  G  ++ aakL g k kv+a   ++   ++ k+N+elN+ ++ +   l++++++  +ek+++ ++  + +  i+l ++ik
  EPA05162.1  58 EIIKNCIKTGDIVVDLGANIGYYTLIAAKLvGDKgKVFAFEPEPKNFEILKKNVELNNYQNVI---LEQKAVSdvNEKINLYLSEGIGTHSIKLKQNIK 153
                 5678999**************998666665354448************************966...333333223456776666666666666666665 PP

        PrmA 248 kl 249
                 ++
  EPA05162.1 154 QT 155
                 55 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   7.2e-05      0.12       8      73 ..      66     131 ..      62     139 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.2e-05
                      TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHH CS
  Methyltr_RsmB-F   8 eeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidk 73 
                       ++ ++Dl a  G  T   a+l+ +kg+v+A + + +  + +++n++  + +n+i+ +  ++ +++
       EPA05162.1  66 TGDIVVDLGANIGYYTLIAAKLVGDKGKVFAFEPEPKNFEILKKNVELNNYQNVILEQKAVSDVNE 131
                      67899******************************************9999999998877777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1937.08
//
Query:       EPA05163.1  [L=46]
Description: hypothetical protein BG20_I1666 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.32s 00:00:00.78 Elapsed: 00:00:00.50
# Mc/sec: 279.02
//
Query:       EPA05164.1  [L=194]
Description: NAD-binding protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.7e-44  150.4   0.0    6.2e-44  150.3   0.0    1.0  1  Epimerase        NAD dependent epimerase/dehydratase family
    7.5e-38  130.8   0.1    8.2e-38  130.6   0.1    1.0  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    2.6e-26   92.3   0.2    3.4e-26   91.9   0.2    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    5.2e-22   78.3   0.0    6.1e-22   78.0   0.0    1.0  1  RmlD_sub_bind    RmlD substrate binding domain
    1.2e-16   60.8   0.1    8.7e-16   57.9   0.1    2.0  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
      2e-15   56.7   0.2    2.8e-10   39.8   0.0    2.3  2  NAD_binding_4    Male sterility protein
    2.3e-08   34.1   0.0    2.8e-08   33.8   0.0    1.1  1  NAD_binding_10   NAD(P)H-binding
    5.6e-08   32.9   0.1    1.6e-07   31.4   0.1    1.6  1  KR               KR domain
    2.3e-06   27.3   0.1    3.1e-06   26.9   0.1    1.2  1  NmrA             NmrA-like family
    0.00021   20.8   0.1    0.00052   19.5   0.1    1.5  1  adh_short        short chain dehydrogenase
    0.00039   20.5   0.0    0.00082   19.5   0.0    1.6  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    0.00083   19.6   0.0     0.0015   18.8   0.0    1.4  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
  ------ inclusion threshold ------
      0.025   14.8   0.0      0.045   14.0   0.0    1.4  1  TrkA_N           TrkA-N domain
      0.031   14.1   0.3      0.039   13.8   0.3    1.1  1  AbiGi            Putative abortive phage resistance protein A


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.3   0.0   4.9e-47   6.2e-44       2     196 ..       4     191 ..       3     194 .] 0.96

  Alignments for each domain:
  == domain 1  score: 150.3 bits;  conditional E-value: 4.9e-47
                 EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC..EEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHHHSHHHHHHHHTHHHHHH CS
   Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl..elveldltdrsalerlfkeeqpdavihlAavggvaassedpadfieknlqgtlnl 98 
                 +VtG++GfiGs++vk+ll+++++ i++d+l ++++ +r+  l  e++++d++d ++l++++k  + d v+h Aa  +v++s+++++++i+ n++gt n+
  EPA05164.1   4 VVTGGAGFIGSNIVKQLLKQNHTPIVIDNL-YRGKIERISSLdvEFHKADIRDLDQLQNILK--NSDGVFHEAALTDVQESFTKQQEYIDVNVKGTENV 99 
                 7*****************************.9999999988899******************..99********************************* PP

                 HHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTT CS
   Epimerase  99 leaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklveayaaqyglnaiilrlfnlyGprngegevsrvipalirkileg 196
                 ++ a++ ++ +++++sSs+vYG+++++p +e++   + +p +pY+ +Kl  e l+e+y +++ +++i lr+fn+yG++ ++g+ ++vi++++++++e+
  EPA05164.1 100 FKIAKEFDL-KVVYASSSSVYGNPKKIPITENS---ERNPINPYGKTKLDDEFLAEKYSKDN-VSIIGLRYFNVYGEG-QTGSYAGVITKFLNRLKEK 191
                 *********.******************99999...77899*****************9999.9**************.9999***********9986 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.6   0.1   6.4e-41   8.2e-38       2     207 ..       5     191 ..       4     194 .] 0.90

  Alignments for each domain:
  == domain 1  score: 130.6 bits;  conditional E-value: 6.4e-41
                    EETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHTTSHHH CS
  GDP_Man_Dehyd   2 iTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevynLAAqshVdvsfekPey 97 
                    +TG+aGfiGs+++++Ll+++++ ++i+++ +  +++ri++l          ++++hk+D++D ++l+++l++   d v++ AA   V++sf+k ++
     EPA05164.1   5 VTGGAGFIGSNIVKQLLKQNHTPIVIDNL-YRGKIERISSL----------DVEFHKADIRDLDQLQNILKNS--DGVFHEAALTDVQESFTKQQE 87 
                    9*********************9998754.34455555554..........478******************9..9******************** PP

                    HHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSC CS
  GDP_Man_Dehyd  98 taevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYaaaKlyadwivvnyreayglfavngilfnhesprrgetfv 193
                    +++vnv Gt ++++++++  l    +++ aS+s vYG+++++p+tE+   +P +PY+ +Kl  ++++++y +  ++ ++  ++fn ++  ++ ++ 
     EPA05164.1  88 YIDVNVKGTENVFKIAKEFDL----KVVYASSSSVYGNPKKIPITENSERNPINPYGKTKLDDEFLAEKYSK-DNVSIIGLRYFNVYGEGQTGSY- 177
                    *****************9976....89*******************************************97.799999***********98874. PP

                    CCHHHHHHHHHHTT CS
  GDP_Man_Dehyd 194 trkitravarialg 207
                       it+++ r +++
     EPA05164.1 178 AGVITKFLNRLKEK 191
                    58899988888776 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.9   0.2   2.6e-29   3.4e-26       1     190 [.       4     177 ..       4     192 .. 0.84

  Alignments for each domain:
  == domain 1  score: 91.9 bits;  conditional E-value: 2.6e-29
   3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslvdvag.kltedeimkvnvkGTrn 98 
                 vvtGgaGF+G+++vk+L++ ++  +  v+D   + ++ e++s+++v+ ++++D++d d+l++ l+++d v+h a+l+dv+   ++++e+ +vnvkGT+n
  EPA05164.1   4 VVTGGAGFIGSNIVKQLLKQNH--TPIVIDNLYRGKI-ERISSLDVE-FHKADIRDLDQLQNILKNSDGVFHEAALTDVQEsFTKQQEYIDVNVKGTEN 98 
                 8*******************96..5568999999888.99******9.*******************************994567789*********** PP

   3Beta_HSD  99 vleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKalaEklvlkaNgrtlknggrlyTcaLRpagiyGegdkllv 190
                 v + +++ +++ +vY Ss +v g+  ++ +i+     ++ e ++ ++y ++K   E l  k       +  ++  + LR   +yGeg++   
  EPA05164.1  99 VFKIAKEFDLK-VVYASSSSVYGN-PKKIPIT-----ENSERNPINPYGKTKLDDEFLAEKYSK----D--NVSIIGLRYFNVYGEGQTGSY 177
                 *********97.69******9998.5566666.....445566778899999888877655544....2..356789999999999987654 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.0   0.0   4.8e-25   6.1e-22       1     157 [.       1     174 [.       1     193 [. 0.88

  Alignments for each domain:
  == domain 1  score: 78.0 bits;  conditional E-value: 4.8e-25
                    EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT................T--TTSHHHHHHHHHHH--SEEEE------HHHHHHSHHHHHHHHTH CS
  RmlD_sub_bind   1 mkilvtGanGqlGseLakqlaeeglevlaltre................eldltdaeavaellkeakpdvvvnaAAytavDkaEseeeaayavnae 80 
                    mk +vtG+ G +Gs+++kql ++++  + +++                 ++d++d ++++++lk+   d v + AA t+v +  +++++   vn++
     EPA05164.1   1 MKFVVTGGAGFIGSNIVKQLLKQNHTPIVIDNLyrgkierissldvefhKADIRDLDQLQNILKN--SDGVFHEAALTDVQESFTKQQEYIDVNVK 94 
                    899********************9998888776899****************************9..778************************** PP

                    HHHHHHHHHHHCT-EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHHH-S.SEEE..EEE-SEESSSSS CS
  RmlD_sub_bind  81 avealAeaaaavgalLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavlaagk.kali..vRtswvygekgk 157
                    ++e++ + a++ + ++++ S+  V+   kk p +e++e +P+n YG+tKl+ E   ++++k ++ i  +R   vyge + 
     EPA05164.1  95 GTENVFKIAKEFDLKVVYASSSSVYGNPKKIPITENSERNPINPYGKTKLDDEFLAEKYSKdNVSIigLRYFNVYGEGQT 174
                    ******************************************************9999544245552369999**99443 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.9   0.1   6.8e-19   8.7e-16       2     188 ..       4     190 ..       3     193 .. 0.80

  Alignments for each domain:
  == domain 1  score: 57.9 bits;  conditional E-value: 6.8e-19
                      EEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-SEEEE------HHHHHH CS
  Polysacc_synt_2   2 lvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvdvvfhaAAlKhVPlvee 95 
                      +vtG++G iGs++v+q+lk++ + i++ +    k+ +i++          ++++     +d+rd ++l+++l+  + d vfh AAl  V    +
       EPA05164.1   4 VVTGGAGFIGSNIVKQLLKQNHTPIVIDNLYRGKIERISSLD--------VEFH----KADIRDLDQLQNILK--NSDGVFHEAALTDVQESFT 83 
                      79************************9888888888887643........3334....58*************..******************* PP

                      SHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEG.....GGS........S--SHHHHHHHHHHHHHHHGGG--SSS--EEEEEEE-EETT..G CS
  Polysacc_synt_2  96 npleaiktNvlgtenvieaaieagvkkvvliStD.....KAv........nPtnvmGatKrlaekllqalakeseekktkfvvvRfGNVlg..S 174
                      +  e i+ Nv gtenv ++a+e + k v + S+      K +        nP+n +G tK+  e l+ +++k +      ++  R+ NV g   
       EPA05164.1  84 KQQEYIDVNVKGTENVFKIAKEFDLKVVYASSSSvygnpKKIpitenserNPINPYGKTKLDDEFLAEKYSKDN----VSIIGLRYFNVYGegQ 173
                      ***********************9987766554322222322233333339*************9999998888....899999****985323 PP

                      TTS...SHHHHHHHHHT CS
  Polysacc_synt_2 175 rGS...viplFkkqike 188
                       GS   vi++F +++ke
       EPA05164.1 174 TGSyagVITKFLNRLKE 190
                      45444488888888776 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   7.6e-06    0.0097       1      22 [.       5      26 ..       5      55 .. 0.84
   2 !   39.8   0.0   2.2e-13   2.8e-10      79     216 ..      57     178 ..      37     188 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 7.6e-06
                   EE-TTSHHHHHHHHHHHHHS-. CS
  NAD_binding_4  1 lTGaTGFLGkvLlekLLrttpe 22
                   +TG+ GF+G+ ++++LL+++  
     EPA05164.1  5 VTGGAGFIGSNIVKQLLKQNHT 26
                   7****************99875 PP

  == domain 2  score: 39.8 bits;  conditional E-value: 2.2e-13
                    HHHHHHHHH--EEEE--SS-S.ST...TSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H......HHH--EEEETTT CS
  NAD_binding_4  79 edlqelaeevdviihsaAtvnfde...pykellrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegekeekldederaklkg 171
                    ++lq++ ++ d ++h aA ++++e   + +e ++vNv+Gt++v+++ak+   +  +++ S++ v+g+ + ++                 +++++++
     EPA05164.1  57 DQLQNILKNSDGVFHEAALTDVQEsftKQQEYIDVNVKGTENVFKIAKEFDLK--VVYASSSSVYGNPK-KI---------------PITENSERN 134
                    5689999*****************44344569******************888..88888888888877.33...............578899999 PP

                    CCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE--SSST--- CS
  NAD_binding_4 172 lpntYeqsKalaEklvrearrrsglpvvivRpsiitgesktGwin 216
                      n Y ++K   E l +++++  ++ ++ +R  +++ge +tG+  
     EPA05164.1 135 PINPYGKTKLDDEFLAEKYSKD-NVSIIGLRYFNVYGEGQTGSYA 178
                    9*******************77.999999********99999875 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.0   2.2e-11   2.8e-08       1     130 [.       7     153 ..       7     169 .. 0.69

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 2.2e-11
                     TTTSHHHHHHHHHHHHC-T-EEEEEETT..HHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC......HHHH.........H CS
  NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRn..peklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggk......deeg.........a 78 
                     G+ G +G+ +vk+ll+++ h+  +++ n    k+++++ +  +e  ++d+ d ++l++ lk+ d V+  ++ ++       +  +         +
      EPA05164.1   7 GGAGFIGSNIVKQLLKQN-HT-PIVIDNlyRGKIERIS-SLDVEFHKADIRDLDQLQNILKNSDGVFHEAALTDVqesftkQ--QeyidvnvkgT 96 
                     99***************5.76.5778885567777775.689*************************999555553344321..1456666677* PP

                     HHHHHHHHHCT--EEEEEEETTTTSGCGCHHHHHHH...HCCHHH....HHHHHHHHHH CS
  NAD_binding_10  79 knivdaakeagvkRfvlvsaigvgdevpgefgewnk...ellkay....laakraaeel 130
                     +n+ + ake + k +   s+  v+   p++ + + +   + +++y    l++   ae++
      EPA05164.1  97 ENVFKIAKEFDLKVVYA-SSSSVYG-NPKKIPITENserNPINPYgktkLDDEFLAEKY 153
                     ************65555.5555553.244433322211144544422224555555554 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.1   1.3e-10   1.6e-07       3     146 ..       3     124 ..       2     129 .. 0.85

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 1.3e-10
                 EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS---EEEE---------TTT-- CS
          KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppikGvihaAgvlrdklleemt 101
                 +++tGG+G +G  ++++l+++  + +v+           + +i+++++   +ve+ +aD+ d d+++++l++ +       Gv+h A +++ +      
  EPA05164.1   3 FVVTGGAGFIGSNIVKQLLKQNHTPIVIDNLY-------RGKIERISS--LDVEFHKADIRDLDQLQNILKNSD-------GVFHEAALTDVQESF--- 82 
                 68*************************96555.......446777766..568899***************998.......******999876544... PP

                 HHHHHHHHTTTTHHHHHHHHHTTTS--SEEEEEEEHHHHH--TT- CS
          KR 102 aedleqvlapKvkGawnLhelledesldffvlfSSiagllgsagq 146
                   + ++ +   vkG++n+ ++ +  + d+ v+++S ++++g++++
  EPA05164.1  83 -TKQQEYIDVNVKGTENVFKIAK--EFDLKVVYASSSSVYGNPKK 124
                 .4446678899**********98..69999************986 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.1   2.4e-09   3.1e-06       2      87 ..       4      90 ..       3     100 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 2.4e-09
                EESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEEEE---GG..S-HHHHHHHHHH CS
        NmrA  2 lviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdlddkeslvealkgvdvvfsvtgfy..skeiedgkklvd 87
                +v+G++G +G+ +v+ llk++h + +++ ++ + +++ +++  ve+ k+d+ d + l+++lk++d+vf   +++  ++   ++++ +d
  EPA05164.1  4 VVTGGAGFIGSNIVKQLLKQNH-TPIVIDNLYRGKIERISSLDVEFHKADIRDLDQLQNILKNSDGVFHEAALTdvQESFTKQQEYID 90
                69****************9986.7999*****************************************98887766666666666665 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.1   4.1e-07   0.00052       4     116 ..       4     100 ..       2     107 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 4.1e-07
                 EEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEEE---SS--SSGGGCSHHHHH CS
   adh_short   4 lvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldvLvnNAGitgsgpfselseeewe 102
                 +vtG+++ IG +i+k+l+k++ + +v+d+  +   e +++l      + + ++D++d +++++++++        d + + A++t +    + s ++ +
  EPA05164.1   4 VVTGGAGFIGSNIVKQLLKQNHTPIVIDNLYRGKIERISSLD-----VEFHKADIRDLDQLQNILKNS-------DGVFHEAALTDV----QESFTKQQ 86 
                 8*************************9999887766666665.....89**************99988.......888888888422....23455567 PP

                 HHHHHHTHHHHHHH CS
   adh_short 103 rvievNltgvfllt 116
                 ++i+vN++g+ ++ 
  EPA05164.1  87 EYIDVNVKGTENVF 100
                 78888888876655 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   6.4e-07   0.00082      19      81 ..       8      71 ..       1      93 [. 0.84

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 6.4e-07
                  S-SHHHHHHHHHHHCCT-CEEEEEE..S.SHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE CS
  Shikimate_DH 19 GaGemaelvakhLlakgvkkvvvaN..R.tlerakelaeelkgeeiealkleelkellaeadvvis 81
                  GaG +++ ++k+Ll+++ + +v+ N  R  +er ++l  e+++  + +++l++l+++l+++d v+ 
    EPA05164.1  8 GAGFIGSNIVKQLLKQNHTPIVIDNlyRgKIERISSLDVEFHK--ADIRDLDQLQNILKNSDGVFH 71
                  9**********************99553357788888888854..59***************9995 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.2e-06    0.0015       5      73 ..       8      69 ..       3      80 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.2e-06
                     --SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEE CS
  Sacchrp_dh_NADP  5 GaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlv 73
                     GaG++G+ +++ l+++++    i++   ++ k e++    ++ ++e+++ d+ + ++ L+ +lk  d v
       EPA05164.1  8 GAGFIGSNIVKQLLKQNHT--PIVIDNLYRGKIERI----SSLDVEFHKADIRDLDQ-LQNILKNSDGV 69
                     77***************99..677777778787777....799**************.******99755 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   3.5e-05     0.045       5      58 ..       8      62 ..       3      70 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.5e-05
                S-SHHHHHHHHHHHH.TTEEEEEEESSH.HHHHHHHHTTSEEEES-TTSHHHHHHT CS
      TrkA_N  5 GlGrvGrslaeeLse.ggkdvvvidkde.erveelreeglevvvgdatdeevLeea 58
                G+G +G++++++L + ++   +vid+    ++e+++   +e+ ++d  d + L+++
  EPA05164.1  8 GAGFIGSNIVKQLLKqNH-TPIVIDNLYrGKIERISSLDVEFHKADIRDLDQLQNI 62
                89*************555.68999987636799999999********999999875 PP

>> AbiGi  Putative abortive phage resistance protein AbiGi, antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.3     3e-05     0.039      68     175 ..      46     161 ..      33     164 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3e-05
       AbiGi  68 VlYtledtkllkalleslkdledvlefkesehsklesslelfliyiktfdksenksfylerEWRl..v.pnllsilge....kvteeevtkkkfedken 159
                 V +++ d + l++l + lk+ + v  f e+ +  +++s+ + ++yi  + k+++ +f+  +E  l  v  +  s+ g+     +te+ +  + ++ + +
  EPA05164.1  46 VEFHKADIRDLDQLQNILKNSDGV--FHEAALTDVQESFTKQQEYIDVNVKGTENVFKIAKEFDLkvVyASSSSVYGNpkkiPITEN-SERNPINPYGK 141
                 678899999999999999999988..********************************99998652131344556666886545554.44566777778 PP

       AbiGi 160 tkle.af...kFkpedikyi 175
                 tkl+  f   k++++++ +i
  EPA05164.1 142 TKLDdEFlaeKYSKDNVSII 161
                 88852568889999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       779  (0.0434492); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 1223.53
//
Query:       EPA05165.1  [L=234]
Description: hypothetical protein BG20_I1665 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-09   38.1   0.1    4.2e-08   33.4   0.1    2.1  1  Glyco_transf_4   Glycosyltransferase Family 4
    1.1e-06   28.8   0.4    0.00012   22.1   0.5    2.4  2  Glyco_trans_4_2  Glycosyl transferase 4-like
    0.00011   22.6   0.0    0.00025   21.5   0.0    1.5  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
     0.0007   20.1   0.5      0.007   16.9   0.1    2.2  2  PIGA             PIGA (GPI anchor biosynthesis)
  ------ inclusion threshold ------
       0.01   15.8   0.0      0.015   15.2   0.0    1.2  1  Helicase_IV_N    DNA helicase IV / RNA helicase N terminal
      0.026   14.0   0.2        5.9    6.4   0.0    2.5  3  Glycos_transf_1  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.1   1.4e-11   4.2e-08       5     168 ..      15     153 ..      11     155 .. 0.74

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 1.4e-11
  Glyco_transf_4   5 erhvleLaraLarrGheVtvvtpgddgpleeevelvvrvprvplpllkrllrslaflrrlrrllkrekpDvvHahspaalgaallalrrrlgipl 99 
                     + h++++a+ L++ G++V +                  vp vp+ +lk++ +    +  ++++l+rek+DvvHa++ ++++++ +     + ++ 
      EPA05165.1  15 GGHAFRVAEKLRESGFDVKLMH----------------VPHVPIKNLKNPSFV--IFGMIKAILDREKYDVVHAWNVPSAFVMKF--V--KAKKK 87 
                     5555555555555555555553................333444444445444..45568999*************999977733..3..46789 PP

  Glyco_transf_4 100 VltvHglyekrllkarlkplsrllralerrllrradrviavSeatadelrerygvppekitVipnGvDl 168
                     Vl+vHg y       ++   s ++ + e ++l+ a+ +++ S+++++ ++e++g++    + +p + D+
      EPA05165.1  88 VLSVHGIYSEQVDALHSTATSSMVSNAESKVLKFANVLTTDSKSVQKTYKEKLGLDF---VYLPAPLDT 153
                     ********97777888889999********************************984...666666665 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.011        32      11      31 ..      16      36 ..       2      50 .. 0.76
   2 !   22.1   0.5     4e-08   0.00012      60     121 ..      49     103 ..      36     129 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.011
  Glyco_trans_4_2 11 vhtlrlakeLakrgyeVhvit 31
                     +h  r+a++L++ g++V+++ 
       EPA05165.1 16 GHAFRVAEKLRESGFDVKLMH 36
                     599**************9875 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 4e-08
  Glyco_trans_4_2  60 ylkaf.klkklikkikPDvvhahyakpygllgslaarlsgvipvvlsvwGldvlkfpkksklk 121
                       + +f  +k++++++k+Dvvha ++++ ++  +++    + ++ vlsv+  ++++++ ++ l+
       EPA05165.1  49 SFVIFgMIKAILDREKYDVVHAWNVPSAFV-MKFV----KAKKKVLSVH--GIYSEQVDA-LH 103
                      45567578****************999765.4454....567789****..667776665.33 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   8.5e-08   0.00025      32     149 ..      22     142 ..       6     149 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 8.5e-08
  Glyco_trans_4_4  32 apeleedgvrvhrlpvprrp.spladlaa.lral.rrllrqrrerpdvvhahsptaglaarlarrrrgiplvvtlhglllrrg.sgavrrlyra 121
                      a+ l+e g  v  + vp+ p + l+++++ ++++ +++l  +re++dvvha + ++++++++ ++++++  v+ +++  ++   s+a  +++  
       EPA05165.1  22 AEKLRESGFDVKLMHVPHVPiKNLKNPSFvIFGMiKAIL--DREKYDVVHAWNVPSAFVMKFVKAKKKVLSVHGIYSEQVDALhSTATSSMVSN 113
                      555777787777778888876677888862466536666..***********************8889999999998776666699999999** PP

  Glyco_trans_4_4 122 lerrllrradavlvvseaeaeelra.lgv 149
                      +e+ +l+ a ++++ s ++ +++ + lg+
       EPA05165.1 114 AESKVLKFANVLTTDSKSVQKTYKEkLGL 142
                      ****************9999998886665 PP

>> PIGA  PIGA (GPI anchor biosynthesis)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   2.3e-06     0.007      15      70 ..      31      84 ..      17      97 .. 0.75
   2 ?    1.9   0.1      0.11   3.3e+02      46      65 ..      94     113 ..      87     129 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.3e-06
        PIGA 15 glkvYyvPllvlyrevtlptvlstlpllrnillrekidivhghqalstlaheailh 70
                 +k  +vP +++ +    p+ ++++ ++++il rek d+vh+ +  s++  +++  
  EPA05165.1 31 DVKLMHVPHVPIKN-LKNPS-FVIFGMIKAILDREKYDVVHAWNVPSAFVMKFVKA 84
                67899999988765.45555.6689*******************999998887754 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.11
        PIGA  46 llrekidivhghqalstlah 65 
                 ++ e++d +h+ ++ s++++
  EPA05165.1  94 IYSEQVDALHSTATSSMVSN 113
                 678********988777764 PP

>> Helicase_IV_N  DNA helicase IV / RNA helicase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   5.1e-06     0.015      58     118 ..      80     145 ..      78     171 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.1e-06
  Helicase_IV_N  58 efelkeqkvvrlhGlpweetqqfaqtllssyqqWskeqvqaladvlqkkeeeieefvqqq.....k 118
                    +f+ +++kv ++hG+  e++++++ t++ss+ + ++++v + a+vl++  ++++++ +++      
     EPA05165.1  80 KFVKAKKKVLSVHGIYSEQVDALHSTATSSMVSNAESKVLKFANVLTTDSKSVQKTYKEKlgldfV 145
                    799999********************************************9999988776555552 PP

>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.1   3.2e+03      45      55 ..      45      61 ..      25     106 .. 0.58
   2 ?    5.7   0.1    0.0032       9.7       3      39 ..     154     190 ..     152     196 .. 0.82
   3 ?    6.4   0.0     0.002       5.9      72     112 ..     192     232 ..     186     233 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.1
                     CSCEEEEEES....... CS
  Glycos_transf_1 45 npnvklviaG......n 55
                      +n  +vi G      +
       EPA05165.1 45 LKNPSFVIFGmikailD 61
                     55555555554322221 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0032
                      HHHHHHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHC CS
  Glycos_transf_1   3 ekkrkklgknekkkiilsvgrlekeKgvdllikafal 39 
                      +k  +   +n+ ++ i +vgr + eKg d l k  ++
       EPA05165.1 154 KKFDQIPDINKIENQIAYVGRDSFEKGTDILRKIEPQ 190
                      677788899999****************998776555 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.002
                      TCGGGEEECCHSSSHHHHHHCESEEEEEESSBSS-HHHHHH CS
  Glycos_transf_1  72 sdnviflgevsredleellknadifvlpsisEgfGivllEA 112
                      + ++i+   +s+ d ++ lk+++ +v+ps++E+++ ++ EA
       EPA05165.1 192 KGKIIYCTDMSWIDAMKNLKASSTLVVPSRMESLPQSIKEA 232
                      667777777777777788899**************999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.60u 0.36s 00:00:00.96 Elapsed: 00:00:00.54
# Mc/sec: 1304.32
//
Query:       EPA05166.1  [L=250]
Description: methionine adenosyltransferase, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.7e-70  233.2   0.1    7.8e-69  230.0   0.0    1.9  2  S-AdoMet_synt_C  S-adenosylmethionine synthetase, C-terminal 
    5.3e-34  117.1   0.4    9.4e-34  116.2   0.4    1.4  1  S-AdoMet_synt_M  S-adenosylmethionine synthetase, central dom
  ------ inclusion threshold ------
      0.064   12.9   0.3      0.098   12.3   0.3    1.2  1  Mt_ATP-synt_B    Mitochondrial ATP synthase B chain precursor


Domain annotation for each model (and alignments):
>> S-AdoMet_synt_C  S-adenosylmethionine synthetase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1     0.054   3.2e+02      69     101 ..      39      73 ..      19      88 .. 0.65
   2 !  230.0   0.0   1.3e-72   7.8e-69       1     138 []      98     237 ..      98     237 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.054
                      E-TT-SS-S...EEEEEE-S-BSS-HHHHHH.HHHHH CS
  S-AdoMet_synt_C  69 Yaigvaepv...sisvetfgtekvseeeiae.ivkev 101
                      Y    ++p+   +i ++t++  ++s+e+ia+ i+++v
       EPA05166.1  39 YE--NNKPTkieTIVISTQHAPEISQEQIAKeIIEKV 73 
                      43..444441124667777777788888876144555 PP

  == domain 2  score: 230.0 bits;  conditional E-value: 1.3e-72
                      S-TTTTS-EETTS-TTTTTTTTSS---S---TTB-TTSHHHHHHHHHHHHHHHHHHTTSBSEEEEEEEE-TT-SS-SEEEEEE-S-BSS-HHHH CS
  S-AdoMet_synt_C   1 iGgpkgdaGltgrkiivdtYgglaahgggafsgKdptkvDrsaayaaryvaknlvaaglakkvevqlsYaigvaepvsisvetfgtekvseeei 94 
                      iGgp+gd+Gltgrkiivd+Ygg+++hgggafsgKdp+kvDrsa+y++ry+akn+vaagla+++evq++Yaigvaepvs++v+tfg++k++e+ei
       EPA05166.1  98 IGGPHGDTGLTGRKIIVDSYGGFGRHGGGAFSGKDPSKVDRSACYMCRYIAKNIVAAGLAERCEVQVAYAIGVAEPVSLYVNTFGSSKIPEREI 191
                      8********************************************************************************************* PP

                      HHHHHHH----HHHHHHHHTTTSS--TGGGSS-SSS--..T-TTS. CS
  S-AdoMet_synt_C  95 aeivkevfdlrpaaiieeldLkkpiykktaayghfgre..elpwek 138
                      +e+v+++f+++p++ii++ldLk+piy+kt+a+ghfgr+  e++wek
       EPA05166.1 192 EELVRKNFNMKPSGIISQLDLKRPIYRKTSANGHFGRNepEFTWEK 237
                      *************************************98899**97 PP

>> S-AdoMet_synt_M  S-adenosylmethionine synthetase, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.2   0.4   1.6e-37   9.4e-34      22     120 .]       1      96 [.       1      96 [. 0.96

  Alignments for each domain:
  == domain 1  score: 116.2 bits;  conditional E-value: 1.6e-37
  S-AdoMet_synt_M  22 mPlpillahklaerlaelrkegeleylrpDaKsqvtveYeeelkpvrvdtvvistqhdeevsqeklredlkekvikkvlkeelldekktkllin 115
                      mP+pillahkl+++lae+rk++ l+++rpD+Ksqv+v+Y e++kp++++t+vistqh++e+sqe+++++++ekvik+vl  +l ++ ++k++in
       EPA05166.1   1 MPMPILLAHKLTQKLAEVRKNKVLPWVRPDGKSQVSVRY-ENNKPTKIETIVISTQHAPEISQEQIAKEIIEKVIKPVL-GNLWND-QIKIHIN 91 
                      9**************************************.599************************************.666666.6****** PP

  S-AdoMet_synt_M 116 ptGkF 120
                      ptGkF
       EPA05166.1  92 PTGKF 96 
                      ****9 PP

>> Mt_ATP-synt_B  Mitochondrial ATP synthase B chain precursor (ATP-synt_B)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.3   1.6e-05     0.098      81     145 ..      12      77 ..       7      87 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.6e-05
                    HHHHHHHHHHHHH.CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHC CS
  Mt_ATP-synt_B  81 tkslfevskeqva.leaeaferelqaklareikkkldtlvnaessrrqrlQdelvkgvissVlkel 145
                    t++l ev k++v   + +  ++++ ++  ++  +k++t+v  ++   +  Q++++k +i++V+k +
     EPA05166.1  12 TQKLAEVRKNKVLpWVRPDGKSQVSVRYENNKPTKIETIVISTQHAPEISQEQIAKEIIEKVIKPV 77 
                    6666666666664134555666777788888899****************************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1793.30
//
Query:       EPA05167.1  [L=288]
Description: NAD-binding protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      8e-14   51.7   0.0    7.6e-13   48.5   0.0    2.0  1  Epimerase       NAD dependent epimerase/dehydratase family
    1.6e-11   44.4   0.0    2.3e-11   43.9   0.0    1.2  1  NAD_binding_10  NAD(P)H-binding
    5.2e-10   38.8   1.4    6.1e-07   28.7   0.3    2.4  2  3Beta_HSD       3-beta hydroxysteroid dehydrogenase/isomerase
    3.7e-06   26.3   0.0       0.07   12.2   0.0    2.3  2  RmlD_sub_bind   RmlD substrate binding domain
    6.6e-05   22.2   0.2      0.047   12.9   0.1    2.8  3  NAD_binding_4   Male sterility protein
  ------ inclusion threshold ------
      0.014   15.5   0.2      0.029   14.4   0.2    1.5  1  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
       0.06   13.3   0.0       0.08   12.9   0.0    1.3  1  PAC2            PAC2 family
       0.11   12.6   1.0       0.93    9.6   0.0    2.9  3  Phage_spike_2   Phage spike trimer


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.5   0.0   3.4e-16   7.6e-13       1     226 [.       7     194 ..       7     203 .. 0.83

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 3.4e-16
                 EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHHHSHHHHHHHHTHHHHHHH CS
   Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggvaassedpadfieknlqgtlnll 99 
                 ++VtGa+Gfi ++l k+l +k++++i ++r+ + ++++++      ++  ++ ++++ + k ++ d+ i+l ++g   + +    d+  +n + t +++
  EPA05167.1   7 VVVTGASGFIAKNLRKYLSNKNIKLISVSRR-NFKKFKNET-----KIITKNYDETNIIPKLKNSDVLINLVGIGKQTVDN----DYNLINYEFTKKII 95 
                 68*****************************.444555444.....666666677777777779*******6666655544....445679******** PP

                 HHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSS CS
   Epimerase 100 eaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklveayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkq 198
                 + + k+++ ++++ls     G +++         +pl     Y ++K+ +ek++ +     +ln++i+r++ ++G++      +++  +l ++i+ g+ 
  EPA05167.1  96 NLCIKSKIPKIVYLSG---LGVSKS---------SPL----GYFISKYKSEKQIINS----NLNYVIFRPSYIIGKN------DHLTKYLKKQIKVGQ- 167
                 ***************9...553333.........355....9*************87....5777************......999999999999997. PP

                 SEEEETTST-EEEEEEHHHHHHHHHHHH CS
   Epimerase 199 evtllgdgtalRdflyveDvaeaillvl 226
                  + + g+g+   + +y++Dv ++il v+
  EPA05167.1 168 -INIPGSGNYSIQPIYIDDVSQIILDVI 194
                 .********************9998766 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   0.0     1e-14   2.3e-11       1     154 [.      11     158 ..      11     196 .. 0.74

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 1e-14
                     TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC..HHHH.......HHHHHHHHH CS
  NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggk..deeg.......aknivdaak 86 
                     GA+G +++ l k l ++ ++++  + R+   +++++   + + +     d+  +   lk+ d+ +  +g g++  d++        +k+i++ + 
      EPA05167.1  11 GASGFIAKNLRKYLSNK-NIKLISVSRR--NFKKFK---NETKIITKNYDETNIIPKLKNSDVLINLVGIGKQtvDNDYnlinyefTKKIINLCI 99 
                     9***************9.5887777654..444453...34455556668999*************99999887744446688888********* PP

                     HCT--EEEEEEETTTTSGCGCHHHHHHHHCCHHHHHHHHHHHHHHHHSSSEEEEEEE-CEE-ST..--SE CS
  NAD_binding_10  87 eagvkRfvlvsaigvgdevpgefgewnkellkaylaakraaeellrasgldwTivrpggLtdep..ttky 154
                     ++++ ++v++s++gv +++              y++ k+++e+ + +s+l+++i rp+++  ++   tky
      EPA05167.1 100 KSKIPKIVYLSGLGVSKSS-----------PLGYFISKYKSEKQIINSNLNYVIFRPSYIIGKNdhLTKY 158
                     ****************632...........23799************************85443113333 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.3   2.7e-10   6.1e-07       1     119 [.       8     114 ..       8     122 .. 0.82
   2 !    8.6   0.0   0.00036       0.8     156     225 ..     132     190 ..     121     196 .. 0.76

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 2.7e-10
   3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslvdvagkltedeimkvnvkGTrnv 99 
                 vvtG++GF+ ++l k L + +   +++ + +  +     +++k+++++ i +   d+ ++   l+++dv+i l ++    +++ ++ +  +n++ T+++
  EPA05167.1   8 VVTGASGFIAKNLRKYLSN-K---NIKLISVSRR-----NFKKFKNETKIITKNYDETNIIPKLKNSDVLINLVGIG---KQTVDNDYNLINYEFTKKI 94 
                 8********9999766644.4...4777766544.....456777777788888999999999*********96665...4555777999********* PP

   3Beta_HSD 100 leacvkagvrvlvYtSsaev 119
                 ++ c+k+ ++++vY S ++v
  EPA05167.1  95 INLCIKSKIPKIVYLSGLGV 114
                 ****************9887 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00036
   3Beta_HSD 156 lvlkaNgrtlknggrlyTcaLRpagiyGegdkllvpllkqlaklglalfkigdeevlsdrvYvgNvawah 225
                  ++++         +l+ +  Rp++i G  d+l ++ lk+ +k g ++   g+ +   +++Y + v++++
  EPA05167.1 132 QIINS---------NLNYVIFRPSYIIGKNDHL-TKYLKKQIKVG-QINIPGSGNYSIQPIYIDDVSQII 190
                 44433.........567799********98765.56778888999.677788999999*******99764 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   3.1e-05      0.07       2      36 ..       6      40 ..       5     111 .. 0.81
   2 !   12.0   0.0   3.5e-05     0.079     120     238 ..     118     231 ..     113     253 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.1e-05
                   EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TTT-- CS
  RmlD_sub_bind  2 kilvtGanGqlGseLakqlaeeglevlaltreeld 36
                   +++vtGa+G ++++L+k l+++++++++++r+++ 
     EPA05167.1  6 QVVVTGASGFIAKNLRKYLSNKNIKLISVSRRNFK 40
                   689**************************988543 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 3.5e-05
                    --SSHHHHHHHHHHHHHHHH-SSEEEEEE-SEESSSSS-HHHHHHHHHHH-SEEEEE..SS-EE--EEHHHHHHHHHHHHHHCHH.GGG-EEEE-- CS
  RmlD_sub_bind 120 sPlnvYGrtKlaGEqavlaagkkalivRtswvygekgknfvktmlrlakereelkvv..aDqlgsPTsardlAevllqllekaaeekelagvyHla 213
                    sPl+ Y  +K++ E+ + +++ +++i+R s++ g+  ++ +++ l+++ +  ++++        +P + +d+++++l+++ + ++    + ++ l+
     EPA05167.1 118 SPLG-YFISKYKSEKQIINSNLNYVIFRPSYIIGK--NDHLTKYLKKQIKVGQINIPgsGNYSIQPIYIDDVSQIILDVIIRNKS----NMILDLV 206
                    5666.4579**********************9998..7889999999999999999621466789**************999987....8999999 PP

                    -BS-EEHHHHHHHHHHHHCHTTSEE CS
  RmlD_sub_bind 214 negetswlefArailkeagadseev 238
                    ++++++  ++ ++  ++++++ +++
     EPA05167.1 207 GSESITFKNYVKEFSSQTNTKIKKI 231
                    9999999999999888888855444 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.8   0.0    0.0031       6.8       1      38 [.       9      45 ..       9      66 .. 0.60
   2 ?    0.0   0.0      0.17   3.8e+02     110     136 ..      86     111 ..      76     119 .. 0.81
   3 !   12.9   0.1   2.1e-05     0.047     170     209 ..     116     156 ..      88     186 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0031
                   EE-TTSHHHHHHHHHHHHHS-.T.EEEEEE-SSSHHHHH CS
  NAD_binding_4  1 lTGaTGFLGkvLlekLLrttpev.kiyllvRaksgesae 38
                   +TGa+GF++k L +  L+++ ++  i +  R+ ++ + e
     EPA05167.1  9 VTGASGFIAKNLRKY-LSNK-NIkLISVSRRNFKKFKNE 45
                   7*********98555.5444.352455555544443433 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.17
                    HHHHHHHHHHHHHTSSS--.-EEEEEE CS
  NAD_binding_4 110 vNveGtrevlelakklkklkvllhvST 136
                    +N e t+++++l+ k k    +++ S 
     EPA05167.1  86 INYEFTKKIINLCIKSKIP-KIVYLSG 111
                    7888999******999999.8888875 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 2.1e-05
                    TTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE-.....- CS
  NAD_binding_4 170 kglpntYeqsKalaEklvrearrrsglpvvivRpsiitg.....e 209
                    k+ p +Y  sK+ +Ek + + +    l+ vi+Rps+i+g      
     EPA05167.1 116 KSSPLGYFISKYKSEKQIINSN----LNYVIFRPSYIIGkndhlT 156
                    677899*********9887765....899*********9665440 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.2   1.3e-05     0.029      11      81 ..       3      70 ..       1      85 [. 0.82

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.3e-05
                  TT-EEEEES-.SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE CS
  Shikimate_DH 11 kekkvlliGa.GemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvis 81
                  k+ +v++ Ga G +a+ + k+L++k++k + v  R++++ k+  + + ++   + + + +   l+++dv+i 
    EPA05167.1  3 KNTQVVVTGAsGFIAKNLRKYLSNKNIKLISVSRRNFKKFKNETKIITKN---YDETNIIP-KLKNSDVLIN 70
                  7889*****9899**************************99988877655...55554444.7888888885 PP

>> PAC2  PAC2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   3.6e-05      0.08      80     126 ..      86     126 ..      46     209 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.6e-05
                 HHHHHHHHHHHHHHHTTESEEEEEEEEEESS-ES..TTS-.EEEEEE CS
        PAC2  80 qyeefakalldwaeelgvkevvvLggldageradvphtrpekvtgaa 126
                  ++ef+k++++++ ++++ ++v+L+gl+  ++       p++++   
  EPA05167.1  86 INYEFTKKIINLCIKSKIPKIVYLSGLGVSKS------SPLGYFISK 126
                 3446************************5544......455443322 PP

>> Phage_spike_2  Phage spike trimer
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1       0.4   8.9e+02      38      49 ..      49      60 ..      43      92 .. 0.79
   2 ?   -2.6   0.0       2.6   5.7e+03       6      16 ..     134     144 ..     133     154 .. 0.76
   3 ?    9.6   0.0   0.00042      0.93      42      71 ..     250     280 ..     208     282 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.4
                   ESEEE-TTSEE- CS
  Phage_spike_2 38 eklvWdksniiG 49
                      ++d++nii 
     EPA05167.1 49 ITKNYDETNIIP 60
                   556899999995 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.6
                    E-S-BS-EEEE CS
  Phage_spike_2   6 lnanlnGiiFs 16 
                    +n+nln +iF 
     EPA05167.1 134 INSNLNYVIFR 144
                    68888888885 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00042
                    E-TTSE.E-STTTT--BT-EEEE--SSEEES CS
  Phage_spike_2  42 Wdksni.iGdkhavtRaalnLfelrvssvtn 71 
                     d+ ni iGd +   ++ +nLf++r++s+++
     EPA05167.1 250 VDDLNIlIGDFKGDHKKLQNLFKIRFTSIQK 280
                    56667659999*****************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       950  (0.0529868); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 1888.46
//
Query:       EPA05168.1  [L=231]
Description: CbiD protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-77  258.5   1.2    5.9e-77  258.4   1.2    1.0  1  CbiD      CbiD
  ------ inclusion threshold ------
      0.017   15.2   0.7      0.047   13.7   0.3    1.9  2  DUF3042   Protein of unknown function (DUF3042)


Domain annotation for each model (and alignments):
>> CbiD  CbiD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  258.4   1.2   6.5e-81   5.9e-77       1     210 [.      12     230 ..      12     231 .] 0.98

  Alignments for each domain:
  == domain 1  score: 258.4 bits;  conditional E-value: 6.5e-81
        CbiD   1 lrsGyTtGscAaAAakaAllallkgekleeveielpkgekleipiekvalleee..aavikdaGddpDvTngaeivaeve.....eeieiegGeGvGrv 92 
                 lr+G+TtG+ A+AAakaAll +++++k+e+++++lpkg+ ++ipi+ ++ +e++  ++vikd+GddpDvT+gaei++++      +eiei+gGeGvG+v
  EPA05168.1  12 LRTGFTTGTSATAAAKAALLSIITQTKIENIDVKLPKGSFIKIPIHFCQFDENKarCSVIKDGGDDPDVTHGAEIIVDLLftdriNEIEIDGGEGVGIV 110
                 69************************************************888799***********************99****88************ PP

        CbiD  93 tkpgLevevgeaAInpvprkmieenveevleea..kegvevtisvpeGeelAkkTlNprlGivgGiSiLGTtGivepmSeeallesireelkvaaaegl 189
                 tkpgL +e ++aAInpvp+kmi+en++e+++++  k+g++v isvp+G+el  kT Npr+Gi++GiSiLGT+Giv p+S++++ +sir++l+va a g+
  EPA05168.1 111 TKPGLGLELNKAAINPVPKKMINENLKEIIDKHhlKKGIKVIISVPKGKELGPKTDNPRIGILNGISILGTSGIVIPFSTASYAASIRQNLDVAIAMGN 209
                 *******************************999999************************************************************** PP

        CbiD 190 kelvlvtGnkgeklakkklgl 210
                 +++vl+tG ++e++akk ++l
  EPA05168.1 210 NTVVLTTGGRSEDFAKKIIDL 230
                 ****************97765 PP

>> DUF3042  Protein of unknown function (DUF3042)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.3   5.2e-06     0.047       2      37 ..      10      45 ..       9      49 .. 0.91
   2 ?   -2.4   0.0      0.56     5e+03      27      40 ..     120     131 ..     114     137 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.2e-06
     DUF3042  2 kkFlkGflvGvlatiaavagavfvfKkkviePiEek 37
                +k  +Gf +G+ at+aa a+ + ++ ++ ie i+ k
  EPA05168.1 10 EKLRTGFTTGTSATAAAKAALLSIITQTKIENIDVK 45
                57789*************************999865 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.56
     DUF3042  27 KkkviePiEekeak 40 
                  k  i+P+ +k  +
  EPA05168.1 120 NKAAINPVPKK--M 131
                 57888888776..3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1670.91
//
Query:       EPA05169.1  [L=56]
Description: hypothetical protein BG20_I2545, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-09   37.8   0.0    1.5e-09   37.7   0.0    1.0  1  TAL_FSA   Transaldolase/Fructose-6-phosphate aldolase


Domain annotation for each model (and alignments):
>> TAL_FSA  Transaldolase/Fructose-6-phosphate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.0   8.2e-14   1.5e-09       1      49 [.       3      51 ..       3      55 .. 0.91

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 8.2e-14
                EEEE---HHHHHHHHHTT---EEE--HHHHHH..TTS.-HHHHHHHHHH CS
     TAL_FSA  1 lvlDtadrelikklleekgiqgvTtNPsliekaikykalydeaieeikk 49
                ++lDta++e+i+k+ + + ++g+TtNPsl++k+  + +++ e+i++i k
  EPA05169.1  3 IFLDTANLEAIRKFNDMGLLDGITTNPSLLSKEGGNPKDVMEEIAKIIK 51
                79******************************88888888888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 400.85
//
Query:       EPA05170.1  [L=246]
Description: transketolase, C-terminal domain protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.5e-31  107.0   0.0    7.4e-31  106.6   0.0    1.2  1  Transketolase_C  Transketolase, C-terminal domain
    1.2e-13   51.1   0.0    1.8e-13   50.6   0.0    1.2  1  Transket_pyr     Transketolase, pyrimidine binding domain
     0.0023   18.2   0.0     0.0042   17.4   0.0    1.4  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma


Domain annotation for each model (and alignments):
>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.6   0.0   1.2e-34   7.4e-31       1     111 [.     111     218 ..     111     234 .. 0.93

  Alignments for each domain:
  == domain 1  score: 106.6 bits;  conditional E-value: 1.2e-34
                      TEEEEEETTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSHHHHHHHHHHHCCCTTCSS CS
  Transketolase_C   1 gkaeilregkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavkrgGigsevaaalaeeafdglda 94 
                      gk+ +lr+g+d t+ a G +v++aleAa+ L++egis++V+d++++kp+D e++++++++tg +v+ ee++++gG+gs+va+ ++e    + ++
       EPA05170.1 111 GKGITLRDGSDCTIAACGITVRMALEAADSLNQEGISCRVLDMFSIKPIDAELLEKAARETGGIVTCEEHNIMGGMGSAVAESVSE----RYPV 200
                      78899*********************************************************************************....99** PP

                      EEEEEEE-SS.SSSSGHH CS
  Transketolase_C  95 pvkrvggpdv.iepgsae 111
                      p+kr+g+ d+ +e++   
       EPA05170.1 201 PIKRIGAQDMfGESARDN 218
                      **********99999844 PP

>> Transket_pyr  Transketolase, pyrimidine binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.6   0.0     3e-17   1.8e-13      88     176 ..      10      99 ..       1     100 [. 0.89

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 3e-17
                   G..HHGGHHHHHCHHHHHT--EE.EEESBSGGGSTTGTTTSBSSHHHHHHTSTTEEEE--SSHHHHHHHHHHHHHSSS.SEEEEEE-SSEEC CS
  Transket_pyr  88 A..qiyadqairsgeakgklkvg.vvtrlpigvgedGpehqsaeleaflrlipglkvvrPsdpaetkhllrrairredrkPvvlrlpksllr 176
                   A  qi++  a  s   k++l+v+ vv + +++vg dG +hq +e++a++r+ip+++v+ P+d   + +l r  ++  + +P ++r+ +s+++
    EPA05170.1  10 AvdQIRNGIAYPSSGNKKGLNVKlVVSHGGLSVGPDGGSHQQIEDIAIMRAIPNFRVFIPADTFAVSKLTRLMAN--EYGPFYMRMARSNTP 99 
                   36688888888888899**********************************************************..569*********986 PP

>> PFOR_II  Pyruvate:ferredoxin oxidoreductase core domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0     7e-07    0.0042       2      81 ..     121     197 ..     120     214 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 7e-07
                 SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHHTGGG CS
     PFOR_II   2 evvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaalkks 81 
                 +  i a G++++ a +a+d+l +egi+  +l + ++ P  +e l+++++++  +v+ +  + +g    +++ v+++++++
  EPA05170.1 121 DCTIAACGITVRMALEAADSLNQEGISCRVLDMFSIKPIDAELLEKAARETGGIVTCEEHNIMGG---MGSAVAESVSER 197
                 678999***************************************************99985555...555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1555.08
//
Query:       EPA05171.1  [L=109]
Description: phosphoribosyl-AMP cyclohydrolase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-33  112.9   0.1    5.4e-33  112.6   0.1    1.1  1  PRA-CH    Phosphoribosyl-AMP cyclohydrolase


Domain annotation for each model (and alignments):
>> PRA-CH  Phosphoribosyl-AMP cyclohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.6   0.1     3e-37   5.4e-33       2      74 .]      32     104 ..      31     104 .. 0.99

  Alignments for each domain:
  == domain 1  score: 112.6 bits;  conditional E-value: 3e-37
                 EEEE-HHHHHHHHHHSB-EEEETTTTEEEETTTTTS--EEEEEEEE-TTSSEEEEEEEESS-SSTTSBSSS-- CS
      PRA-CH   2 laymnkealektletgkavyySrsrkklWkKGetSgnvqkvkeirlDcDqDalllkveqkgaaCHtgkesCFy 74 
                 lay+nke+le t +tg+ +++Srsr+klW+KGe+Sgn+qkvkei +DcD+Da+++ v+++g+aCHtg++ CF+
  EPA05171.1  32 LAYTNKESLELTKKTGNSWFWSRSRNKLWMKGEESGNTQKVKEILVDCDSDAIIYLVDPSGPACHTGEKVCFH 104
                 79**********************************************************************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 735.42
//
Query:       EPA05172.1  [L=214]
Description: putative imidazoleglycerol phosphate synthase, cyclase subunit, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.6e-59  200.5   0.7    3.2e-59  200.2   0.7    1.0  1  His_biosynth  Histidine biosynthesis protein
    5.6e-09   35.5   0.3     0.0006   19.0   0.1    2.1  2  Dus           Dihydrouridine synthase (Dus)
    2.3e-05   23.9   0.3      0.097   12.0   0.0    2.1  2  NMO           Nitronate monooxygenase
    6.6e-05   22.3   0.1      0.013   14.9   0.0    2.2  2  TMP-TENI      Thiamine monophosphate synthase
    0.00015   21.1   0.1      0.012   14.8   0.0    2.1  2  DHO_dh        Dihydroorotate dehydrogenase
    0.00016   21.1   0.4        0.1   11.9   0.1    2.2  2  ThiG          Thiazole biosynthesis protein ThiG
     0.0043   16.5   0.1       0.53    9.7   0.1    2.3  2  G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
  ------ inclusion threshold ------
      0.026   13.4   0.3      0.045   12.6   0.1    1.5  2  Trp_syntA     Tryptophan synthase alpha chain
      0.058   12.8   0.8       0.17   11.3   0.1    2.0  2  PcrB          PcrB family


Domain annotation for each model (and alignments):
>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.2   0.7   1.6e-62   3.2e-59      57     226 ..       1     189 [.       1     191 [. 0.95

  Alignments for each domain:
  == domain 1  score: 200.2 bits;  conditional E-value: 1.6e-62
                   THHHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEE.....C.............EE CS
  His_biosynth  57 greanldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarr.....g.............yk 135
                   +r++ ++lv+++a+ ++ip++vGGG++sled++++l +gadkv i+t a+knp +i+el+e fg+q++vvaiDa+r     +             ++
    EPA05172.1   1 QRKTLKELVRKVASVIDIPFTVGGGVKSLEDARNILLNGADKVGINTGAIKNPIVITELMELFGRQCVVVAIDAKRnydiqNdknlfsengkkfwFE 97 
                   588999**********************************************************************66665166677778899*9** PP

                   EEETTTTEEEEEEHHHHHHHHHHTT-SEEEEEETTTTTTSS---HHHHHHHHHHHSSEEEEESS--SHHHHHHHHHTTC.SEEEESHHHHTT CS
  His_biosynth 136 vaikgwreetgldavelakkleelgageilltdidrdGtlsGpdleltkelaeavkipviasGGvgsledlkelksegv.davivgsalyeg 226
                   v+i g+++ tg+d++e+akk++elgageillt+id+dGt++G+d+ lt+e+ ++v+ipviasGG+g+++d+ ++++e   dav+++s+++++
    EPA05172.1  98 VFIFGGKQGTGIDVIEWAKKADELGAGEILLTSIDKDGTKDGYDILLTREIVNSVSIPVIASGGCGKPDDMVDVFKESNaDAVLAASIFHYQ 189
                   ***************************************************************************66666**********86 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1     3e-07    0.0006     175     228 ..       9      62 ..       3      90 .. 0.86
   2 !   15.1   0.0   4.7e-06    0.0093     176     213 ..     146     183 ..     109     206 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 3e-07
                 HHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTHHHH.HHH CS
         Dus 175 IkevkqavsipviaNGdIkdaedaqaileetGadgvmigrgalgnPwlfae.sta 228
                 +++v   + ip+ + G++k++eda++il + Gad v i  ga +nP ++ e ++ 
  EPA05172.1   9 VRKVASVIDIPFTVGGGVKSLEDARNILLN-GADKVGINTGAIKNPIVITElMEL 62 
                 677888888*******************99.*****************9876554 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 4.7e-06
                 HHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEES CS
         Dus 176 kevkqavsipviaNGdIkdaedaqaileetGadgvmig 213
                 +e+ ++vsipvia G++ +++d+ ++ +e+ ad+v+++
  EPA05172.1 146 REIVNSVSIPVIASGGCGKPDDMVDVFKESNADAVLAA 183
                 689999*****************************986 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0   0.00017      0.35     180     223 ..       4      47 ..       1      51 [. 0.91
   2 !   12.0   0.0   4.9e-05     0.097     181     212 ..     141     172 ..     107     189 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00017
         NMO 180 glfaLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigt 223
                  l +Lv +v++++diP    GG+   ++   +L  GA  v i t
  EPA05172.1   4 TLKELVRKVASVIDIPFTVGGGVKSLEDARNILLNGADKVGINT 47 
                 56789*********************************999887 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 4.9e-05
         NMO 181 lfaLvpqvldavdiPviAaGGiidrrgvaaaL 212
                  + L  ++++ v+iPviA GG  +  ++  ++
  EPA05172.1 141 DILLTREIVNSVSIPVIASGGCGKPDDMVDVF 172
                 4689999**************99887766555 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.3   0.0    0.0055        11     140     175 ..       7      43 ..       3      48 .. 0.81
   2 !   14.9   0.0   6.3e-06     0.013     114     175 ..     115     180 ..     109     186 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0055
    TMP-TENI 140 eglkelaealeiPvvaiGGit.lenvaevleagadgv 175
                 e+++++a+ + iP+ + GG++ le++ ++l  gad v
  EPA05172.1   7 ELVRKVASVIDIPFTVGGGVKsLEDARNILLNGADKV 43 
                 45677888888********973699999999999987 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 6.3e-06
    TMP-TENI 114 algadYigvGpifpTdtKkdaeplglegl..kelaealeiPvvaiGGi.tlenvaevl.eagadgv 175
                 a++ad +g+G i  T+  kd +  g + l  +e++++++iPv+a GG  +++++ +v+ e++ad v
  EPA05172.1 115 AKKADELGAGEILLTSIDKDGTKDGYDILltREIVNSVSIPVIASGGCgKPDDMVDVFkESNADAV 180
                 568999**********999986666665555****************9346677777645666655 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   6.3e-06     0.012     232     284 ..       7      57 ..       2      62 .. 0.86
   2 !    4.4   0.0    0.0093        19     235     263 ..     146     172 ..     140     202 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 6.3e-06
                 HHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHH CS
      DHO_dh 232 kvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegpkia 284
                 +++r+++++++  ip    GG++s eDa + +  GA  v + t+ +++  +i 
  EPA05172.1   7 ELVRKVASVID--IPFTVGGGVKSLEDARNILLNGADKVGINTGAIKNPIVIT 57 
                 57888999888..99999***************************87765554 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0093
                 HHHHHHTTT.S-EEEESS--SHHHHHHHH CS
      DHO_dh 235 relykrlkkeipiIgvGGiesgeDaleki 263
                 re+ + ++  ip+I++GG    +D ++ +
  EPA05172.1 146 REIVNSVS--IPVIASGGCGKPDDMVDVF 172
                 77788888..********99999988765 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0     0.001         2     165     215 ..       7      55 ..       2      82 .. 0.83
   2 !   11.9   0.1   5.2e-05       0.1     166     205 ..     144     184 ..     108     193 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.001
                 HHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSHHH CS
        ThiG 165 ealkiiieeakvPvivDAGigspsdaaqamelGadavllntavaeakdpva 215
                 e ++ + + +++P  v  G+ s +da + +  Gad v +nt     k+p+ 
  EPA05172.1   7 ELVRKVASVIDIPFTVGGGVKSLEDARNILLNGADKVGINTGA--IKNPIV 55 
                 5677788889******************************953..345555 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 5.2e-05
                 HHHHHHHH-SS-BEEES---SHHHHHHHH.HTT-SEEEESH CS
        ThiG 166 alkiiieeakvPvivDAGigspsdaaqam.elGadavllnt 205
                   + i++++++Pvi   G g+p d + ++ e  adavl ++
  EPA05172.1 144 LTREIVNSVSIPVIASGGCGKPDDMVDVFkESNADAVLAAS 184
                 4577999*******************99757899***9876 PP

>> G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.1   0.00026      0.53     128     166 ..       6      44 ..       3      50 .. 0.90
   2 ?    4.5   0.0      0.01        20     131     165 ..     145     180 ..     140     184 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00026
                   HHHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEE CS
  G3P_antiterm 128 pkvikeikkelkipiiaGGLietkedveealkaGaiavs 166
                   +++++++ + ++ip+  GG +++ ed +++l +Ga+ v 
    EPA05172.1   6 KELVRKVASVIDIPFTVGGGVKSLEDARNILLNGADKVG 44 
                   67899******************************9885 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.01
                   HCTSTTS...EEEEESS--SHHHHHHHCT.T.SSEE CS
  G3P_antiterm 131 ikeikkelkipiiaGGLietkedveealk.aGaiav 165
                   ++ei ++++ip+ia+G   + +d+ +++k + a+av
    EPA05172.1 145 TREIVNSVSIPVIASGGCGKPDDMVDVFKeSNADAV 180
                   6789999*******9988888887776651456666 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   2.2e-05     0.045     184     223 ..       3      43 ..       1      59 [. 0.90
   2 ?   -2.9   0.0       1.2   2.4e+03     206     234 ..     161     191 ..     145     210 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.2e-05
                 TTHHHHHHHHHHCTSS-EEEESSS-SHHHHHHHH.TT-SEE CS
   Trp_syntA 184 aevdelverlkkltavPvavGFGistkeqvkqva.kvadGv 223
                 ++++elv+++ ++ + P  vG G+++ e+++++  ++ad v
  EPA05172.1   3 KTLKELVRKVASVIDIPFTVGGGVKSLEDARNILlNGADKV 43 
                 6799*****************************99999977 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.2
                 SS-SHHHHHHHH..TT-SEEEE-HHHHHHHH CS
   Trp_syntA 206 Gistkeqvkqva..kvadGvivGSalvkkie 234
                 G  +++++  v   + ad+v+  S    +i+
  EPA05172.1 161 GCGKPDDMVDVFkeSNADAVLAASIFHYQIH 191
                 5555555444443445555555555444444 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   8.7e-05      0.17     171     205 ..       9      43 ..       2      61 .. 0.75
   2 ?   -2.0   0.0      0.97   1.9e+03      19      36 ..     165     182 ..     161     198 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.7e-05
                 HHHHHHHHSSSEEEEESS--SHHHHHHHHCC.SSEE CS
        PcrB 171 vialkkklekarlivGGGirsaEkAkevvea.ADvi 205
                 v ++   + ++ + vGGG++s E+A++++   AD +
  EPA05172.1   9 VRKVA-SVIDIPFTVGGGVKSLEDARNILLNgADKV 43 
                 33443.44467889***************999*986 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.97
                 CHHHHHHHHCTT-SEEEE CS
        PcrB  19 pdEiveiviesgtDavmi 36 
                 pd++v++  es +Dav+ 
  EPA05172.1 165 PDDMVDVFKESNADAVLA 182
                 788899999999999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1522.72
//
Query:       EPA05173.1  [L=79]
Description: hypothetical protein BG20_I1607 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 489.03
//
Query:       EPA05174.1  [L=1174]
Description: hypothetical protein BG20_I1601, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.75u 0.30s 00:00:01.05 Elapsed: 00:00:00.46
# Mc/sec: 7727.28
//
Query:       EPA05175.1  [L=273]
Description: putative threonine synthase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.5e-49  167.4   0.6    5.1e-49  167.3   0.6    1.0  1  PALP           Pyridoxal-phosphate dependent enzyme
  ------ inclusion threshold ------
      0.028   14.6   0.0      0.087   13.0   0.0    1.9  1  ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthas
      0.076   13.0   0.0       0.29   11.0   0.0    1.8  2  Peptidase_C14  Caspase domain


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.3   0.6   8.6e-53   5.1e-49      67     294 .]       2     242 ..       1     242 [. 0.96

  Alignments for each domain:
  == domain 1  score: 167.3 bits;  conditional E-value: 8.6e-53
                 HHHHHHHHHHHT-EEEEEEETTS-HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHHTT.TTEEEEEEE CS
        PALP  67 gralAaaaallGlkvtivvpadaspekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEileqlg.gkpdavvvp 164
                 + a+Aa aa++G++++++ p++   +k+a+  ++Ga+ + v+g+yd+a ++aa++  + +g+ +v+    ++ +eg +t+++E++eql+ ++pd ++vp
  EPA05175.1   2 ASATAAHAAKAGFPCHVFAPSNIEMAKIAQALSYGANYIAVDGTYDDANRIAAQIGDS-KGIGIVNINMRSHYVEGSKTLAYEVAEQLDwQVPDQLIVP 99 
                 88********************************************************.**************************************** PP

                 -SSSHHHHHHHHHHHH........HSTT-EEEEEEECTTCGGTTCCS..S.SS..B...SSS.CCSTCS..CGTTCCHHHHSEEEEEEEEEEHHHHHHH CS
        PALP 165 vGgGgliaGiaaglke........rrpdvrvigvepegsdalarslragrrvtvpvs..dtiadglavg..spselafelldrlvdeivtvsdeealea 251
                 vG+G+++ +i++g+ e        + ++ ++i+++p g++++ +++++++ + +pv+  dtia++la+g   +++++++ l+++++ + + ++ e+l+a
  EPA05175.1 100 VGSGAMLNAICKGFEElqqvsllsNVSNMHMIAAQPHGCAPIVDAFKKKSKEVIPVEnpDTIAKSLAIGdpGDGRYVLKRLQQYNGFAEECNNREILDA 198
                 ****************888887655555******************8777777777778**********9999************************** PP

                 HHHHHHHHSB-B-HHHHHHHHHH.HHHHHHCCTTCEEEEEEE-B CS
        PALP 252 mrllarregivvepssaaalaal.klreagelkegdrvvviltg 294
                 + lla++egi++ep++++++a+l k++e+g+++++d+vv+ +tg
  EPA05175.1 199 ILLLAKTEGIFTEPAGGVSVAVLqKMVEQGKIDKNDSVVCYVTG 242
                 *****************************************998 PP

>> ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.5e-05     0.087      54      89 ..     218     253 ..     213     254 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.5e-05
                    HHHHHHHHHTTSS-TT-EEEEEEEETTTEEEEEEEE CS
  ACP_syn_III_C  54 plaLdeaveegklkpgdlvllvgfGaGltwgaallr 89 
                    +  L+++ve+gk++++d v+   +G Gl  + a+++
     EPA05175.1 218 VAVLQKMVEQGKIDKNDSVVCYVTGNGLKATEAIME 253
                    5689************************99888776 PP

>> Peptidase_C14  Caspase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.26   1.5e+03     191     216 ..     102     126 ..      97     140 .. 0.74
   2 ?   11.0   0.0   4.9e-05      0.29      29      92 ..     178     256 ..     172     272 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.26
                    EEHHHHHHHHHHHHHTTTSBHHHHHH CS
  Peptidase_C14 191 gsaftqalqkvleekggkislkelln 216
                    + a+ +a++k +ee ++  sl++ ++
     EPA05175.1 102 SGAMLNAICKGFEELQQ-VSLLSNVS 126
                    45999*******99888.55554444 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 4.9e-05
                    HHHHHHHTTEEEEEEEGGEES..................-CHHHHHHHHHHHHCHSGGTTESEEEEEEESEEET.......EEEC CS
  Peptidase_C14  29 aklLvkrlgFevenililtdd..................ptgknirkalkwlvksadhspgDslvvhysGHGtrvpae...civp 92 
                    ++ L ++ gF++e+     +                   p g      l+++v++ +  ++Ds+v++  G G +   e    i+p
     EPA05175.1 178 KR-LQQYNGFAEEC----NNReildailllaktegiftePAGGVSVAVLQKMVEQGKIDKNDSVVCYVTGNGLKA-TEaimEILP 256
                    44.44888999999....22235556666777799999999999999*************************942.222464444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1742.88
//
Query:       EPA05176.1  [L=446]
Description: bacteriocin biosynthesis cyclodehydratase, SagC family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-64  216.9   0.4    3.7e-64  216.4   0.4    1.1  1  ThiF             ThiF family
    2.2e-08   34.6   0.0    7.3e-08   32.9   0.0    1.9  1  ThiS             ThiS family
    0.00034   20.9   2.6     0.0016   18.7   2.2    2.2  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
  ------ inclusion threshold ------
      0.019   15.0   0.1      0.048   13.7   0.1    1.7  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
      0.053   12.9   0.0      0.092   12.1   0.0    1.3  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas


Domain annotation for each model (and alignments):
>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  216.4   0.4     1e-67   3.7e-64       1     238 [.     104     334 ..     104     344 .. 0.95

  Alignments for each domain:
  == domain 1  score: 216.4 bits;  conditional E-value: 1e-67
                 THHHHHH..HHHHHHHHHHTSEEEEE--SHHHHHHHHHHHHHTTTEEEEEESSB--GGGGGTBTTS-GGGTTSBHHHHHHHHHHHT-TTSEEEEEES-C CS
                 xxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        ThiF   1 ysrqlal..lgedgqekLrdskvllvGaGglGsellknLalsGvgkltlvDnDkielsNlnRqflfreediGkpKaevaaealqeinpdveveavteri 97 
                 ysrq++l  +g  gq kL++sk+++vG+GglG+++ + La++Gvg l++vD D+ielsNl+Rq +f e+d+G+ K+evaa++lq++npd+++ea+  ++
  EPA05176.1 104 YSRQVMLeeIGYGGQLKLKNSKICVVGVGGLGNPITTRLAAMGVGTLRIVDRDVIELSNLHRQTMFDEDDVGQVKVEVAAKKLQKLNPDCKIEALAVSV 202
                 789988899999*************************************************************************************** PP

                 CGCCS-HHHHTT-SEEEEESSSHHHHHHHHHHHHHHT-EEEEEEEETTEEEEEEEEECCS-ECTSS-TGGS.EECCCCEEHHHHHHCTE-B-HHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        ThiF  98 tdetvleellesvDlVvdalDniearrlvnracvkkgiplieagtlgfegqvvviipgktgcyeCldpsstedptekkvplctsiagnipaiatttavv 196
                 +d t + e++ ++D++vdalD++ ar+++n+acvk gip+++++++g++gq+++iipg+++cy+C++p      +e++ p+c s  g   +  +++++v
  EPA05176.1 203 NDYT-ALEVVDGCDVIVDALDSVNARYALNKACVKFGIPFVTGAAVGVSGQIFTIIPGTSACYHCMFP----SLDEDTMPTC-SLEG---VHPSILSIV 292
                 **55.45************************************************************9....8889999***.9999...88888**** PP

                 HHHHHHHHHHHHTTBCGGGCCEEEECCTTTTEEEEECCEEEE CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        ThiF 197 aglaalellkllsgkeklenslltqvdllesrfenvelerak 238
                 +g+ ++e++k++ gk+++   +   vd+++  f++++  + +
  EPA05176.1 293 GGIEVAEAVKVITGKKPSLSDKILHVDIENLDFTTTRTFKVE 334
                 ************999999999999*********999887655 PP

>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.0     2e-11   7.3e-08      25      77 .]      29      92 ..      14      92 .. 0.78

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 2e-11
                HHHHHHHHHHTCHHG..........TTTTEEEEETTEEEGC.CTTTSB--TTCEEEEEESTTC- CS
        ThiS 25 aelleaLgerypela..........lerrvavavNgeivpr.lwldtelkdgDevailppVaGG 77
                ++++ +++e  +  +           +  +++++Ng++ ++ ++ +t lkdgDev ilp+VaGG
  EPA05176.1 29 QDAFTKISEVMGDDFkrrvlegdgtPRSLINIYINGKNSKFsNGMETLLKDGDEVYILPAVAGG 92
                55555554444444455666677777799************99********************9 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   2.2   4.5e-07    0.0016       1     100 [.     126     245 ..     126     263 .. 0.90
   2 ?   -2.3   0.0       1.3   4.8e+03      69      95 ..     259     285 ..     249     286 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 4.5e-07
                      EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH.......................TTTCEEEEE--TTTHHHHHHHHHTTSS CS
  Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka.......................lgvrfeaialdaenyeavLaallkegd 71 
                      + ++G G+ G +++  la+ +    ++ ++dr+  +l +l  ++                          ++ea a+ +++y+a L+  + + d
       EPA05176.1 126 ICVVGVGGLGNPITTRLAAMGVG--TLRIVDRDVIELSNLHRQTmfdeddvgqvkvevaakklqklnPDCKIEALAVSVNDYTA-LEV-VDGCD 215
                      6799***************9976..9**************9999*********************99999999999999****9.765.8999* PP

                      EEEE-SSGG.GHHHHHHHHHHHT-EEEESS CS
  Sacchrp_dh_NADP  72 lvvnlsppi.ssldvlkaCietgvhyvdts 100
                      ++v+++ ++    ++ kaC++ g+ +v+ +
       EPA05176.1 216 VIVDALDSVnARYALNKACVKFGIPFVTGA 245
                      *********7777*************9944 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.3
                      TSSEEEE-SSGGGHHHHHHHHHHHT-E CS
  Sacchrp_dh_NADP  69 egdlvvnlsppissldvlkaCietgvh 95 
                      ++ ++ +++ p +++d + +C   gvh
       EPA05176.1 259 GTSACYHCMFPSLDEDTMPTCSLEGVH 285
                      567788999************999998 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   1.3e-05     0.048       9      56 ..     120     167 ..     115     190 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.3e-05
                   ..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHH CS
  Shikimate_DH   9 slkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeel 56 
                   +lk++k++++G G +++ +++ L+a gv  + ++ R++   ++l ++ 
    EPA05176.1 120 KLKNSKICVVGVGGLGNPITTRLAAMGVGTLRIVDRDVIELSNLHRQT 167
                   6899*********************************99888887765 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.6e-05     0.092      31      66 ..     118     154 ..      97     177 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.6e-05
                   BS-GTTSEEEEES-SHHHHHHHHHHHHTT-.EEEEES CS
  2-Hacid_dh_C  31 gkelsgktvGiiGlGrIGqavakrlkafgm.kviayd 66 
                   + +l++++++++G+G +G+ +  rl+a+g+  + ++d
    EPA05176.1 118 QLKLKNSKICVVGVGGLGNPITTRLAAMGVgTLRIVD 154
                   4589*************************94444555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 2880.14
//
Query:       EPA05177.1  [L=85]
Description: hypothetical protein BG20_I1605 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.014   15.7   1.9      0.019   15.2   1.9    1.2  1  C1_2        C1 domain
       0.27   11.0   0.4       0.27   11.0   0.4    1.5  2  zf-C2H2_11  zinc-finger C2H2-type


Domain annotation for each model (and alignments):
>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   1.9   2.2e-06     0.019      17      38 ..       4      26 ..       1      34 [. 0.83

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.2e-06
        C1_2 17 esfnCsaCgrk.idgffYsCseC 38
                 s +C+ C+++ ++ f+Y+C+eC
  EPA05177.1  4 TSLQCRECKKEyGTAFKYICDEC 26
                5679*******888888****** PP

>> zf-C2H2_11  zinc-finger C2H2-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.4     3e-05      0.27       3      14 ..       4      15 ..       3      18 .. 0.86
   2 ?   -3.8   0.6       1.3   1.2e+04       7      10 ..      23      26 ..      23      27 .. 0.48

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3e-05
  zf-C2H2_11  3 stcqCleCGlcf 14
                +++qC+eC+  +
  EPA05177.1  4 TSLQCRECKKEY 15
                79*******877 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 1.3
  zf-C2H2_11  7 CleC 10
                C eC
  EPA05177.1 23 CDEC 26
                5555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 639.75
//
Query:       EPA05178.1  [L=48]
Description: hypothetical protein BG20_I1606 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       883  (0.0492498); expected 358.6 (0.02)
Passed bias filter:                      580  (0.0323498); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.34s 00:00:00.79 Elapsed: 00:00:00.51
# Mc/sec: 285.58
//
Query:       EPA05179.1  [L=336]
Description: putative bifunctional phosphoglucose/phosphomannose isomerase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-32  113.0   0.1    1.8e-32  112.5   0.1    1.3  1  bact-PGI_C  Bacterial phospho-glucose isomerase C-terminal SI
    0.00026   20.9   0.1    0.00051   19.9   0.1    1.5  1  SIS         SIS domain


Domain annotation for each model (and alignments):
>> bact-PGI_C  Bacterial phospho-glucose isomerase C-terminal SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.5   0.1     2e-36   1.8e-32       3     151 ..     193     335 ..     191     336 .] 0.97

  Alignments for each domain:
  == domain 1  score: 112.5 bits;  conditional E-value: 2e-36
                 -HHHHHHHHHTTSEEEEE-..TT-THHHHHHHHHHHHTT----B---.SSHHHHHHHTTSS-GGGGTTEEEEEESSHH........HHHHHHHHTTTSS CS
  bact-PGI_C   3 npakqlAlelagklpviygssellevaArRfknqlnenAKipafagvlpeanhneivgleaeeelkkrlrlvllrdeeehprvkkraeivkelaeergv 101
                 n + +lA +++g +p+iy   + l++aA+Rfk+ l+enAK++++ + + ea+hn iv++    e+ + ++ +l+r +++  ++k+r  i+k++++++++
  EPA05179.1 193 NHSLELAAWISG-IPLIYY-PHGLQSAAIRFKSSLQENAKSHVIIEDVIEASHNGIVAW----EKISIVQPILIRGQDDYIKTKERWIIIKKYLTKKNI 285
                 778899*****9.******.***************************************....899*********88889******************* PP

                 EEEEE---SSSHHHHHHHHHHHHHHHHHHHHHHCT---S-TTTTHHHHH. CS
  bact-PGI_C 102 rvtevkaegesplerlaslillgDfvSvylAllrgvDPtpvpaIdelKee 151
                 ++ e+++  ++ l +l+ li+l+D++S+y A+l ++DP+pv aId+ K+ 
  EPA05179.1 286 DFKEIESVSGNILTKLVTLIYLLDYASIYKAVLDKIDPSPVLAIDYVKKN 335
                 ************************************************86 PP

>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.1   5.7e-08   0.00051       4     104 ..      41     137 ..      38     159 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 5.7e-08
                 TSSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHHTTSEEEEEES.STTSHHHHHSSEE CS
         SIS   4 kakriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelakergakiiaITd.skgsplareadla 101
                 + ++i++ G G s+a+++ l+  l + ++ +v  ++ + l      +id+++lvi+ s sg + ++  ++e a+++   i+++ +  k+   +++++++
  EPA05179.1  41 EINHIVFAGVGGSGAVGDLLSSIL-SKSNLHVTLVKGYLLPK----TIDKNTLVIVTSVSGDSIETMTVLESASKQTCSILVFSSgGKMEKFCKQNKIN 134
                 668*********************.88999999999999444....6**************************99999998775314455555555555 PP

                 EEE CS
         SIS 102 lyi 104
                 ++ 
  EPA05179.1 135 FRK 137
                 555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       838  (0.0467399); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 2464.37
//
Query:       EPA05180.1  [L=62]
Description: hypothetical protein BG20_I2186 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.1   11.9   0.0       0.11   11.7   0.0    1.0  1  UbiA      UbiA prenyltransferase family


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   6.3e-06      0.11     128     176 ..       6      56 ..       1      58 [. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.3e-06
        UbiA 128 lppllgwaa.vtgsl.sllalllalavflltwaialandlrdregDrkagi 176
                 + ++++++  +tg++   +++ll+ a ++ + ai+++ +++dr+  +k ++
  EPA05180.1   6 VSIPIAFVSpTTGEIrEHPFILLFYASIAGISAIIIFSSYKDRKQRQKDNV 56 
                 44556666678999998899***********************99877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       786  (0.0438396); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.51
# Mc/sec: 362.71
//
Query:       EPA05181.1  [L=51]
Description: hypothetical protein BG20_I2187 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.31s 00:00:00.74 Elapsed: 00:00:00.49
# Mc/sec: 314.42
//
Query:       EPA05182.1  [L=406]
Description: hypothetical protein BG20_I2182, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.5e-63  212.9   6.1    7.5e-63  212.9   6.1    1.3  1  AIPR      AIPR protein
  ------ inclusion threshold ------
       0.05   13.9   0.6       0.21   11.9   0.1    2.3  2  RGS       Regulator of G protein signaling domain


Domain annotation for each model (and alignments):
>> AIPR  AIPR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  212.9   6.1   8.4e-67   7.5e-63       1     272 [.      50     319 ..      50     354 .. 0.90

  Alignments for each domain:
  == domain 1  score: 212.9 bits;  conditional E-value: 8.4e-67
        AIPR   1 lekNvReflgttgkvNkgIreTlreepekFflyNNGItitaekiklekkesgseviielenlqIVNGgQTtasIykalkkkldlskvyVqvklikvaed 99 
                 +e+N+R++++ +++vNkg+reTl+++p kFf+yNNGIti++++++       ++ +iel+ +qIVNG+QT +sI+++ k+ ++  + +++v++ik   d
  EPA05182.1  50 FESNIRQWMQFKTTVNKGLRETLQSNPGKFFFYNNGITIVVSDFEEL-----GDNMIELHAPQIVNGAQTSNSILDHSKRTKN-MDGSMTVTIIKA--D 140
                 8********************************************75.....45689**********************9987.99**********..9 PP

        AIPR 100 eedlikeIsraaNsQnkVsdkdlasndefhkrlekllreeqtkvfYerargefdnek.............afk...pkskkitktdlakvlnalflqkP 182
                 +e+++++I++++NsQn+V+ kdl+s+ +fhk +++ l+  ++++fYe+++g+fd+++             ++    +++k+i ++d++++l+a ++q+P
  EPA05182.1 141 DEQEQNNITKYRNSQNSVRGKDLVSLMDFHKSIKSQLK--NCGYFYEIQAGSFDTKSkskqleyegdliyNEYlpdNHKKVIVAKDAIQALVAGIEQRP 237
                 99************************************..*****************999999999888744477788999****************** PP

        AIPR 183 hqaskgkaklekkyekeeekgskyekifkeklt..ykkliasvilfkklekkikke..lkegykanivyyilaalrkllkkkldllkiweeqki 272
                 ++a+++ a+       + ++gsky++if+++l+  y+ l++ +++ ++++k +k    +  ++k+++++  ++++ ++l+kk     i+e+++ 
  EPA05182.1 238 TEAYSSPAQ-------FLPRGSKYDDIFNDNLKddYRILLYPYLVKEYAKKTLKYGkqGGHKTKRYATLFYVGVYFRILHKK-----ILETKGD 319
                 *********.......899*********9999999******************9994444555699999***********97.....5555543 PP

>> RGS  Regulator of G protein signaling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   2.3e-05      0.21      17      87 ..     168     239 ..     160     260 .. 0.82
   2 ?   -2.4   0.0      0.64   5.7e+03      43      62 ..     337     356 ..     319     390 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.3e-05
                 HHHHHTTCT.HHHHHHHHHH..HHHTSSHHHHHHHHHHHHHHHHTSTTSTTSSTS-HHHHHHHHHHHCSSSTTT CS
         RGS  17 eFlesefse.enlsFwlave..efkkakeqeelkkkakeIyneylapsspkelnidkklreelekrlekeqpsr 87 
                 +F +s +s+ +n+ ++ +++   f++++++++l  + + Iyneyl p+  k++ + k+  + l + +e+ +p++
  EPA05182.1 168 DFHKSIKSQlKNCGYFYEIQagSFDTKSKSKQLEYEGDLIYNEYL-PDNHKKVIVAKDAIQALVAGIEQ-RPTE 239
                 5666666667788888777744699999999**************.999999999***99999999999.5554 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.64
                 HHHHHHHHHHHHHHHTSTTS CS
         RGS  43 qeelkkkakeIyneylapss 62 
                 ++ ++k a++++ ++l++  
  EPA05182.1 337 NSRILKIADVVVTKFLEDTV 356
                 55666667777777776544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       888  (0.0495287); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 2448.00
//
Query:       EPA05183.1  [L=86]
Description: hypothetical protein BG20_I2185 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-15   55.8   0.4    3.9e-15   55.6   0.4    1.1  1  HTH_45           Winged helix-turn-helix
    0.00024   20.9   0.2    0.00024   20.9   0.2    1.1  1  DUF4364          Domain of unknown function (DUF4364)
     0.0026   17.7   0.1     0.0034   17.3   0.1    1.2  1  PadR             Transcriptional regulator PadR-like family
     0.0029   17.8   0.3     0.0037   17.4   0.3    1.3  1  HTH_34           Winged helix DNA-binding domain
     0.0041   16.5   0.0     0.0049   16.3   0.0    1.1  1  RNA_pol_Rpc34    RNA polymerase Rpc34 subunit
  ------ inclusion threshold ------
      0.016   13.6   0.1      0.016   13.6   0.1    1.1  1  DUF505           Protein of unknown function (DUF505)
      0.026   14.9   0.1       0.05   13.9   0.1    1.5  2  Rrf2             Transcriptional regulator
      0.062   13.4   0.1      0.084   13.0   0.1    1.5  1  PilN             Fimbrial assembly protein (PilN)
      0.071   13.0   0.0      0.094   12.6   0.0    1.4  1  TrmB             Sugar-specific transcriptional regulator Trm
      0.072   13.2   0.0      0.092   12.9   0.0    1.4  1  Mrr_N            Mrr N-terminal domain
       0.12   12.4   0.1       0.21   11.5   0.1    1.4  2  MarR             MarR family
       0.13   11.5   0.0       0.14   11.5   0.0    1.0  1  Mannosyl_trans2  Mannosyltransferase (PIG-V)


Domain annotation for each model (and alignments):
>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.6   0.4   2.6e-18   3.9e-15       6      76 ..       2      79 ..       1      80 [. 0.87

  Alignments for each domain:
  == domain 1  score: 55.6 bits;  conditional E-value: 2.6e-18
      HTH_45  6 eIiadILeaisegea...kkTkimykanLsykllnkYLdmLvekgli....kkskekYvlTekGlelleklkeleela 76
                +I+ad+L a++++++   k T+++ kanLs ++l+k+L+ L+  gli     ++k+++v+TekG+++le++ ++ ++a
  EPA05183.1  2 QIVADLLTATEQSGQhgiKTTSLLTKANLSHSRLSKFLENLTGSGLInkieFDNKNTFVITEKGRQYLESYAKFSSIA 79
                8*********9655433389**************************977654599******************98875 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.2   1.6e-07   0.00024      27      73 ..      26      72 ..       8      82 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.6e-07
     DUF4364 27 eneytnYfdlqqalseLvesglieeeekenktlykiTekGketlelf 73
                 +  ++   l+++l++L+ sgli++ e +nk+++ iTekG++ le  
  EPA05183.1 26 TKANLSHSRLSKFLENLTGSGLINKIEFDNKNTFVITEKGRQYLESY 72
                56667777899********************************9976 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   2.3e-06    0.0034       2      74 ..       8      70 ..       7      71 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.3e-06
                HHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHHH CS
        PadR  2 LalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrela 74
                L   e++ ++G + ++ l++      +ls+++l + L+ L  +gl+++ + +     +++++ +T++Gr++l+
  EPA05183.1  8 LTATEQSGQHGIKTTSLLTKA-----NLSHSRLSKFLENLTGSGLINKIEFD-----NKNTFVITEKGRQYLE 70
                555567788999988888888.....59********************9998.....7************997 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.3   2.5e-06    0.0037      15      74 ..      19      74 ..       2      77 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.5e-06
      HTH_34 15 adfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkkyvk 74
                ++ ++l ++ +++ ++Ls+ l+ L   g i+ ++ef++k    ++ iT++Gr+  ++y k
  EPA05183.1 19 IKTTSLLTKANLSHSRLSKFLENLTGSGLIN-KIEFDNK---NTFVITEKGRQYLESYAK 74
                55667778889999999***********886.8999999...6788**********9976 PP

>> RNA_pol_Rpc34  RNA polymerase Rpc34 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   3.3e-06    0.0049      93     135 ..       9      51 ..       5      60 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.3e-06
                    HHHHHHXSSXEEHHHHHHTTGXXHHHHHHHHHHHHHTTXXEEE CS
  RNA_pol_Rpc34  93 siIeesGneGIwsrtiksklnLhksvvkkcLksLeskkyiksv 135
                     + e+sG++GI +  + +k nL +s + k L +L + ++i ++
     EPA05183.1   9 TATEQSGQHGIKTTSLLTKANLSHSRLSKFLENLTGSGLINKI 51 
                    56799********************************999865 PP

>> DUF505  Protein of unknown function (DUF505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   1.1e-05     0.016     365     411 ..      34      78 ..       9      81 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.1e-05
      DUF505 365 dlreaLysLesfeLieseveekgkevyvlTeyGekvledqekklrev 411
                  l + L +L + +Li++  e ++k+++v+Te+G++ le  + k++++
  EPA05183.1  34 RLSKFLENLTGSGLINKI-EFDNKNTFVITEKGRQYLESYA-KFSSI 78 
                 578899*********998.789***************9775.46665 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   3.4e-05      0.05      16      57 ..      10      50 ..       1      52 [. 0.77
   2 ?   -2.1   0.0       3.4   5.1e+03      26      36 ..      73      83 ..      58      85 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.4e-05
                HHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
        Rrf2 16 yLakeeeeepvsseeiaerqnispsylekilakLrkaglvks 57
                  +++++++ ++++++ ++ n+s+s l+k l++L+ +gl++ 
  EPA05183.1 10 A-TEQSGQHGIKTTSLLTKANLSHSRLSKFLENLTGSGLINK 50
                2.33444444*****************************985 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.4
                B-HHHHHHHHT CS
        Rrf2 26 vsseeiaerqn 36
                ++ ++iae+++
  EPA05183.1 73 AKFSSIAESFG 83
                55667777765 PP

>> PilN  Fimbrial assembly protein (PilN)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   5.6e-05     0.084      33      59 ..      30      56 ..       7      82 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.6e-05
        PilN 33 vsndeVaefmrnLegspffknidlksa 59
                 s+ ++++f++nL gs+++ +i++ + 
  EPA05183.1 30 LSHSRLSKFLENLTGSGLINKIEFDNK 56
                59******************9998765 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   6.3e-05     0.094      25      59 ..      21      56 ..      15      79 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.3e-05
                HCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES.STT CS
        TrmB 25 adeiaeelgvprskvYevLrsLedkGlVerek.grp 59
                ++ +  ++++++s+  + L++L   Gl+++++  ++
  EPA05183.1 21 TTSLLTKANLSHSRLSKFLENLTGSGLINKIEfDNK 56
                6678889**********************9984444 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   6.2e-05     0.092      50      86 ..      31      70 ..       4      71 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.2e-05
       Mrr_N 50 fknrvgWartyLkkagllespk...rgvwkiTekGrevlk 86
                 ++r++  + +L+  gl+++ +   + ++ iTekGr++l+
  EPA05183.1 31 SHSRLSKFLENLTGSGLINKIEfdnKNTFVITEKGRQYLE 70
                5667777788999999999988887999*********997 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00014      0.21      13      49 ..      12      50 ..       5      54 .. 0.84
   2 ?   -3.1   0.0       5.1   7.6e+03      19      29 ..      74      84 ..      67      85 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00014
                HHSTTEEHH..HHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
        MarR 13 yeqgplsvs..eLakklgvskstvtrvldrLekkGlieR 49
                +++g++ ++   L  k ++s s ++++l  L   Gli++
  EPA05183.1 12 EQSGQHGIKttSLLTKANLSHSRLSKFLENLTGSGLINK 50
                66677666666**************************97 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.1
                EHHHHHHHHTS CS
        MarR 19 svseLakklgv 29
                + s +a+ +g+
  EPA05183.1 74 KFSSIAESFGL 84
                55677777765 PP

>> Mannosyl_trans2  Mannosyltransferase (PIG-V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   9.2e-05      0.14      15      84 ..       5      76 ..       1      84 [. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.2e-05
  Mannosyl_trans2 15 vllLviLfrialipddtsealnppcl..laspslvdslvekllenlvsWDsvyflkiaenGyeyeheyaflp 84
                       lL++  ++ +   +t+ +l +  l     + ++++l+   l n + +D    + i+e+G +y + ya + 
       EPA05183.1  5 ADLLTATEQSGQHGIKTTSLLTKANLshSRLSKFLENLTGSGLINKIEFDNKNTFVITEKGRQYLESYAKFS 76
                     5567777777777777777777766543456899**********************************9665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 633.53
//
Query:       EPA05184.1  [L=167]
Description: hypothetical protein BG20_I2184 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0006   19.4   1.2    0.00077   19.1   1.2    1.2  1  FAM221       Protein FAM221A/B
  ------ inclusion threshold ------
      0.088   12.7   0.0       0.16   11.9   0.0    1.4  1  RNaseH_like  Ribonuclease H-like


Domain annotation for each model (and alignments):
>> FAM221  Protein FAM221A/B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   1.2   8.6e-08   0.00077     101     137 ..      92     127 ..      84     160 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 8.6e-08
      FAM221 101 qklrCrCkhkaeeHseaakkkCkr.kcgskCsgfkssy 137
                 ++  C+C h+ae+H+e    +C   +c+  C++f+s  
  EPA05184.1  92 NDALCECGHSAEDHDEGDGDICLYnECN--CKKFSSFQ 127
                 6678******************986885..****9965 PP

>> RNaseH_like  Ribonuclease H-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.8e-05      0.16      16      54 ..      35      79 ..      28     104 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.8e-05
  RNaseH_like 16 akykliiGtDSqvkreetkfvtaivihr......vgkGaryfyrk 54
                 ++y +iiG+DSq  +++  f  ++          +g+G+ +++r 
   EPA05184.1 35 DEYWIIIGSDSQRPESNLSFFKVLQKSEnyerfkKGHGGEAYLRL 79
                 689*********999999999988754344445577888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1179.80
//
Query:       EPA05185.1  [L=54]
Description: hypothetical protein BG20_I2183 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0066   16.3   2.9      0.014   15.3   2.9    1.6  1  DUF4428      Domain of unknown function (DUF4428)
  ------ inclusion threshold ------
      0.016   14.8   0.3        4.2    7.1   0.1    2.1  2  zf-RRN7      Zinc-finger of RNA-polymerase I-specific TFIIB, 
      0.064   12.7   1.3      0.087   12.2   1.3    1.1  1  Vps36-NZF-N  Vacuolar protein sorting 36 NZF-N zinc-finger do


Domain annotation for each model (and alignments):
>> DUF4428  Domain of unknown function (DUF4428)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   2.9   2.4e-06     0.014       1      29 [.       6      37 ..       6      49 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.4e-06
     DUF4428  1 iCaiCgkKigl....lkrlkleDgyvCkdClkK 29
                +C iC +Ki+l    ++   ++ g +C dC++K
  EPA05185.1  6 KCTICSNKITLrfnpMEEWSIK-GPLCGDCYSK 37
                7**********74444444444.88******99 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0012         7       2      13 ..       2      15 ..       1      23 [. 0.71
   2 ?    7.1   0.1    0.0007       4.2       2      18 ..      26      45 ..      25      46 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0012
     zf-RRN7  2 ekgppCgvCgc..r 13
                + ++ C +C++  +
  EPA05185.1  2 GSKEKCTICSNkiT 15
                67899*****9653 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0007
     zf-RRN7  2 ekgppCgvCgc...rsftld 18
                +kgp Cg C +   ++f++ 
  EPA05185.1 26 IKGPLCGDCYSkkiDEFYPG 45
                69*******99999999984 PP

>> Vps36-NZF-N  Vacuolar protein sorting 36 NZF-N zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.3   1.5e-05     0.087      12      39 ..       7      34 ..       3      35 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.5e-05
  Vps36-NZF-N 12 CpICsfsNevpsnfdp..nastplPpClaC 39
                 C+IC  sN+++  f+p  + s + P C  C
   EPA05185.1  7 CTIC--SNKITLRFNPmeEWSIKGPLCGDC 34
                 ****..5*********9888999*****99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 377.75
//
Query:       EPA05186.1  [L=284]
Description: prephenate dehydrogenase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-24   86.2   0.3    2.1e-24   86.0   0.3    1.1  1  PDH             Prephenate dehydrogenase
    4.8e-06   26.0   0.1    9.2e-06   25.1   0.1    1.5  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
    1.6e-05   25.1   0.2      6e-05   23.3   0.0    1.9  3  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
     0.0001   22.8   0.9     0.0012   19.3   0.0    3.1  3  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
    0.00034   20.6   0.3     0.0011   18.9   0.0    2.0  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
  ------ inclusion threshold ------
       0.01   15.8   0.8          9    6.2   0.0    3.1  3  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
       0.03   13.9   0.8        1.2    8.6   0.1    2.6  3  NmrA            NmrA-like family
      0.037   14.1   0.1       0.17   11.9   0.0    2.2  2  DpaA_N          Dipicolinate synthase subunit A N-terminal do
      0.057   13.5   0.1       0.16   12.1   0.0    1.7  2  DUF1392         Protein of unknown function (DUF1392)
      0.059   13.8   0.0        4.8    7.6   0.0    2.9  2  Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domai
      0.063   12.9   0.1       0.19   11.3   0.0    1.9  2  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
       0.13   11.7   0.0       0.35   10.3   0.0    1.8  2  Epimerase       NAD dependent epimerase/dehydratase family


Domain annotation for each model (and alignments):
>> PDH  Prephenate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.0   0.3   1.4e-27   2.1e-24      13     257 ..      28     256 ..      18     257 .. 0.90

  Alignments for each domain:
  == domain 1  score: 86.0 bits;  conditional E-value: 1.4e-27
                 EEEEE-SSHHHHHHHHHTTSSSEEES-GGGGCCGSEEEE-S-GGGHHHHHHHHHHHS-TT-EEEE--S--CHHHHHHHHHCC..GCEEEEEES---S-S CS
         PDH  13 tvigydideekaeaalelglvdeatddieavkeadivvlavPvevilevlkelaphlkedalitDvgsvKekvvreleellkegksfvgghPmaGteks 111
                  v+gyd +++ + ++  l+    a+  +  + +ad vvl++P + + e+++ +a+ +k++  ++ ++s K kvv  l+++ + + + +  hPm+G+   
  EPA05186.1  28 EVTGYDTENKISGKG-ILQ----ADSLVGGILKADYVVLCTPTRRTPEIIRLIAKEMKRGTYLIEISSEKSKVVTSLSKMPA-KINPICIHPMFGP--- 117
                 688888888877777.333....33336679************************************************998.99***********... PP

                 SGGG--TTTTTT-EEEEEE-TTS-HHHHHHHHHHHHHCT-EEEE--HHHHHHHHHHHTHHHHHHHHHHHHHHHCHHCCCCHHHHCGTCCHHHHH....C CS
         PDH 112 GvdaareelfenavviLtPtektdkealekvkelleevgarvilmspeeHDrvvavvshlphvvaialaatlkekkndekeirklasggfrdvt....R 206
                       +++ +++  i  P + + k+ l  +kel+   ga ++ +++ eHD+ +av+ +l+h++    a+ + +k ++  +  k ++  fr        
  EPA05186.1 118 -----GAKSIKGQNIISVPIK-DAKKELTVAKELFD--GANFVTIDAVEHDKKIAVILGLTHLMNLVFAN-IIAKDEKMSLTEKMSGTTFRVQKilaeS 207
                 .....7899***********9.66799********8..799**********************9999999.77778888899*********87767779 PP

                 GGGS-HHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHH CS
         PDH 207 iaksnPelwadilleNkeavlealdkfikelkklkelienedaeeLvellk 257
                 i+  +Pel + i+ +N e +  + ++  k++ +l +++++ ++ee + ++k
  EPA05186.1 208 IMTESPELIETII-ANPE-IRRVAEELWKDIGRLLTAVQESKTEEVIDYIK 256
                 999*******996.7999.**************************999987 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.1   6.2e-09   9.2e-06      36     127 ..       2      89 ..       1      99 [. 0.86

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 6.2e-09
                   TSEEEEES-S.HHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTC.EECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCSTTTEEEEESS CS
  2-Hacid_dh_C  36 gktvGiiGlG.rIGqavakrlkafgmkviaydrskkkeeeeeelgv.elvsleellaesDivslhlpltpetrhlinaeelakmkkgailiNta 127
                   +k++ iiG+G ++Gq +ak+++a +++v++yd+ +k     + +g+ + +sl   + ++D+v+l++p t  t ++i     ++mk+g +li ++
    EPA05186.1   2 KKKITIIGAGgQMGQWFAKYFAANDFEVTGYDTENKI----SGKGIlQADSLVGGILKADYVVLCTP-TRRTPEIIRLI-AKEMKRGTYLIEIS 89 
                   58999***9548**********************773....344555999**************999.88899988654.488*******9876 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0     4e-08     6e-05       1     102 [.       4     101 ..       4     111 .. 0.90
   2 ?   -2.0   0.0       2.4   3.6e+03      57      67 ..     161     171 ..     123     224 .. 0.54
   3 ?   -1.2   0.0       1.4     2e+03      48      65 ..     228     245 ..     162     270 .. 0.59

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 4e-08
                    EEEEE--.SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHCCC--TT-EEEE-S---HH CS
  NAD_binding_2   1 kigfiGl.GvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdeviegllealkkgdilidgstsspe 95 
                    ki +iG  G+MG+ +a+ +++++++v++y+ +    +++  +g+  a+s+   + ++d v+++ +  + + e+i+ +++++k+g++li+ s+ + +
     EPA05186.1   4 KITIIGAgGQMGQWFAKYFAANDFEVTGYDTE----NKISGKGILQADSLVGGILKADYVVLCTPT-RRTPEIIRLIAKEMKRGTYLIEISSEKSK 94 
                    6889998459********************88....788999999******************997.7899*********************9988 PP

                    HHHHHHH CS
  NAD_binding_2  96 dtrelak 102
                      + l+k
     EPA05186.1  95 VVTSLSK 101
                    7776665 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.4
                    SEEEE-SSSHH CS
  NAD_binding_2  57 dvvitmvkagk 67 
                    +++ +++  ++
     EPA05186.1 161 KKIAVILGLTH 171
                    33333333333 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.4
                    SHHHHHHHCSEEEE-SSS CS
  NAD_binding_2  48 sieelvasldvvitmvka 65 
                     +eel +++   +t v++
     EPA05186.1 228 VAEELWKDIGRLLTAVQE 245
                    223333333455555544 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   8.3e-07    0.0012       1      95 [.       4      89 ..       4      91 .. 0.79
   2 ?   -3.1   0.0       8.1   1.2e+04      66      78 ..     127     139 ..     118     154 .. 0.64
   3 ?   -0.4   0.1       1.2   1.8e+03      54      77 ..     228     251 ..     162     262 .. 0.56

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 8.3e-07
                   EEEEE.TTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHHCGHHHHTTSEEEEES CS
  F420_oxidored  1 kigii.GaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevlselakdalkgklvisvl 95
                   ki ii ++G+mg+ +a+ ++a++    e++ +   +++k+     + g  ++a +    + +ad vvl+ +++ ++e+++ +ak+ ++g+ +i ++
     EPA05186.1  4 KITIIgAGGQMGQWFAKYFAAND---FEVT-G-YDTENKI---SGK-G-ILQADSLVGGILKADYVVLCTPTRRTPEIIRLIAKEMKRGTYLIEIS 89
                   799**5568**************...9999.7.4445444...322.2.2233345566778******************************9986 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 8.1
                    EE-S-HHHHHHHH CS
  F420_oxidored  66 vlavkpedveevl 78 
                    +++v+ +d+++ l
     EPA05186.1 127 IISVPIKDAKKEL 139
                    4566666665544 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.2
                    CHHHHHHH-SEEEE-S-HHHHHHH CS
  F420_oxidored  54 dneeaaeeadvvvlavkpedveev 77 
                     +ee+ ++   ++ av+ +++eev
     EPA05186.1 228 VAEELWKDIGRLLTAVQESKTEEV 251
                    233333333444444444444444 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   7.4e-07    0.0011       1      42 [.       4      46 ..       4      80 .. 0.89
   2 ?   -1.1   0.1         1   1.5e+03      30      49 ..     243     262 ..     214     283 .. 0.54

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 7.4e-07
                EEEEE--.SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHH CS
     3HCDH_N  1 kvaviGa.GtmGagiaavfasagleVvlvdiseealekaleki 42
                k+++iGa G+mG+  a+ fa++++eV+ +d+++++  k+  ++
  EPA05186.1  4 KITIIGAgGQMGQWFAKYFAANDFEVTGYDTENKISGKGILQA 46
                69*****88***********************99988876655 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1
                 S-HHHHHHHHHHHHHHHHCC CS
     3HCDH_N  30 iseealekalekiekslekl 49 
                 ++e++ e++ + i++  ekl
  EPA05186.1 243 VQESKTEEVIDYIKTCQEKL 262
                 33333344444444333333 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1    0.0064       9.5       1      33 [.       4      37 ..       4      46 .. 0.88
   2 ?    6.2   0.0     0.006         9      62     102 ..      48      88 ..      36     103 .. 0.87
   3 ?   -0.1   0.0      0.54     8e+02      35      76 ..     240     281 ..     213     283 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0064
                    -EEEE--S.HHHHHHHHHHHTTT--EEEE-S-HH CS
  NAD_Gly3P_dh_N  1 kiavlGaG.swGtalAkvlaenghevrlwvreee 33
                    ki+++GaG + G  +Ak +a n  ev+ +  e++
      EPA05186.1  4 KITIIGAGgQMGQWFAKYFAANDFEVTGYDTENK 37
                    79****85389***************99988876 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.006
                     -HHHHHTT--EEEE---HHHHHHHHHHHCCC--TT-EEEE- CS
  NAD_Gly3P_dh_N  62 dlaealkgadiivlvvPsqalrevlkklkgllkkkailvsl 102
                      l   + +ad++vl  P+  + e+++ +++ +k+ + l+ +
      EPA05186.1  48 SLVGGILKADYVVLCTPTRRTPEIIRLIAKEMKRGTYLIEI 88 
                     56667789*************************99999876 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.54
                     HHHHHHHSSBT..TTBTT----TTEEEES-HHHHHTT--EEEE- CS
  NAD_Gly3P_dh_N  35 ieeineehenv..kyLpgiklpenlvattdlaealkgadiivlv 76 
                     +++++e+++++  +y++  +++e+l  +t+l+++ k+ + +v v
      EPA05186.1 240 LTAVQESKTEEviDYIK--TCQEKLSSNTNLEDSYKKLTKMVNV 281
                     44444444433113444..5788888888888888877766665 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.1   0.00082       1.2       1      25 [.       5      29 ..       5      34 .. 0.95
   2 ?   -2.7   0.0       2.3   3.5e+03     181     208 ..      76     103 ..      54     106 .. 0.63
   3 ?    3.1   0.1     0.041        61     182     229 ..     232     279 ..     198     281 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00082
                EEESSTTSHHHHHHHHHHHHHT-EE CS
        NmrA  1 IlviGaTGrqGksvvrallkaghkv 25
                I++iGa G++G+ +++++++++++v
  EPA05186.1  5 ITIIGAGGQMGQWFAKYFAANDFEV 29
                89********************998 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.3
                 -HHHHHHHHHHHHHHHHHHHTTEEEEE- CS
        NmrA 181 daeeDiGafvikilkdprklkgkrikla 208
                  +e   G++ i+i ++++k+ ++  k++
  EPA05186.1  76 AKEMKRGTYLIEISSEKSKVVTSLSKMP 103
                 5666667777777777766655555554 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.041
                 HHHHHHHHHHHHHHHHHHHTTEEEEE-SEEE-HHHHHHHHHHHHTS-E CS
        NmrA 182 aeeDiGafvikilkdprklkgkriklagntlsgneivelfekkigktv 229
                   +DiG+   ++ + +++  + +ik  ++ ls n+ +e   kk+ k v
  EPA05186.1 232 LWKDIGRLLTAVQESKTEEVIDYIKTCQEKLSSNTNLEDSYKKLTKMV 279
                 458****999998889999**************998887777777666 PP

>> DpaA_N  Dipicolinate synthase subunit A N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00012      0.17      13      64 ..      17      68 ..       4     101 .. 0.83
   2 ?   -1.1   0.0       1.3   1.9e+03      54      82 ..     164     193 ..     136     231 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00012
                HHHHHHHHTT-EEEEES-TSSS-BTTEEEE-GGGS-GGG-SEEE--TT-BET CS
      DpaA_N 13 ylarkLaekgakvslygleleekiegvekaesleealedadviilPvpgtkd 64
                + a+++a+++++v+ y  e++ + +g+ +a+sl   + +ad+++l +p  + 
  EPA05186.1 17 WFAKYFAANDFEVTGYDTENKISGKGILQADSLVGGILKADYVVLCTPTRRT 68
                6799*****************************************9996554 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.3
                 EEE--TT-BETTTEE-BSS-SS-EE-.HHH CS
      DpaA_N  54 viilPvpgtkdggeintpfseeklsl.eel 82 
                 ++il ++ + +    n   ++ek+sl e++
  EPA05186.1 164 AVILGLTHLMNLVFANIIAKDEKMSLtEKM 193
                 445555444444444445555555554433 PP

>> DUF1392  Protein of unknown function (DUF1392)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       4.7     7e+03      72     125 ..      38      89 ..      30     100 .. 0.50
   2 ?   12.1   0.0   0.00011      0.16      77     132 ..     135     190 ..     121     204 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 4.7
     DUF1392  72 iiatgqlkkltvkkpafkLGdlveldfaekgtkqrlilGialvkkswlYavelv 125
                 i++ g l+  ++     k   +v  + + +++   +i  ia   k   Y++e+ 
  EPA05186.1  38 ISGKGILQADSLVGGILKADYVVLCTPTRRTPE--IIRLIAKEMKRGTYLIEIS 89 
                 555555555555444444433333333333333..4444444444455555554 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00011
     DUF1392  77 qlkkltvkkpafkLGdlveldfaekgtkqrlilGialvkkswlYavelvsPtlset 132
                   k+ltv+k+ f   + v++d++e+++k+ +ilG++ + +  + ++      +s t
  EPA05186.1 135 AKKELTVAKELFDGANFVTIDAVEHDKKIAVILGLTHLMNLVFANIIAKDEKMSLT 190
                 45789******************************999887776666555555555 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0032       4.8       1      98 [.       4      90 ..       4     102 .. 0.58
   2 ?   -0.7   0.0       1.2   1.9e+03      49      83 ..     218     252 ..     164     273 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0032
                    EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGCTT-SEEEE-SCHHHHHHHHHHH...HHTTSEEE CS
  Semialdhyde_dh  1 kvaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavkaleegkdlkvedvdeeelkevdivflalpagvskelapkl...aeagvkvi 94
                    k+ i+Ga G +Gq ++++ + + ++e++   ++++  Gk + +a        d  v       + ++d+v+l++p   + e+ + +   +++g+++i
      EPA05186.1  4 KITIIGAGGQMGQWFAKYFAAN-DFEVTGYDTENKISGKGILQA--------DSLVG-----GILKADYVVLCTPTRRTPEIIRLIakeMKRGTYLI 86
                    5788888888888888888873.344444333333333333333........22222.....24466777777777776666666633345555666 PP

                    ESSS CS
  Semialdhyde_dh 95 Dlss 98
                      ss
      EPA05186.1 87 EISS 90
                    6665 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.2
                     TTTECEBEEEGGGGGCTT-SEEEE-SCHHHHHHHH CS
  Semialdhyde_dh  49 eegkdlkvedvdeeelkevdivflalpagvskela 83 
                     + +++ +++ v ee +k++  +++a+ ++ ++e+ 
      EPA05186.1 218 TIIANPEIRRVAEELWKDIGRLLTAVQESKTEEVI 252
                     44455555556666667777777777776666665 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00013      0.19       4     121 ..       2     118 ..       1     127 [. 0.77
   2 ?   -1.5   0.0       1.1   1.7e+03      88     104 ..     164     180 ..     128     216 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00013
                 TS-EEEES-SHH.HHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHHHHHHHHHTGGG--TT-EEE..ESSSHHH CS
        IlvN   4 gkkiaviGyGsq.GhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDelqkevyeeeiepnlkegkala..fahGfni 99 
                 +kki++iG G q G+  a+ +  + ++v+ g  +++   k   +  ++  ++   + kad v++ +P +   e++ + i++++k+g++l    +   ++
  EPA05186.1   2 KKKITIIGAGGQmGQWFAKYFAANDFEVT-GYDTEN---KISGKGILQADSLVGGILKADYVVLCTPTRRTPEII-RLIAKEMKRGTYLIeiSSEKSKV 95 
                 69*******99979999**********97.444444...233344466777788899******************.89********9875224556677 PP

                 HTTSS---TTSEEEEEEES.S-S CS
        IlvN 100 hfglikppkdvdvvlvAPk.gpG 121
                 + +l k+p++++ + + P  gpG
  EPA05186.1  96 VTSLSKMPAKINPICIHPMfGPG 118
                 77777888888877777753555 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.1
                 T-EEEESSSHHHHTTSS CS
        IlvN  88 gkalafahGfnihfgli 104
                   +l  +h +n++f  i
  EPA05186.1 164 AVILGLTHLMNLVFANI 180
                 33444444444444444 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00023      0.35       1      36 [.       5      40 ..       5      94 .. 0.79
   2 ?   -2.5   0.0       1.9   2.8e+03      54      99 ..     237     282 ..     221     283 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00023
                EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTT CS
   Epimerase  1 ilVtGatGfiGsalvkallekgyevigldrlssasn 36
                i ++Ga G++G+ ++k++++++ ev+g d +++ s 
  EPA05186.1  5 ITIIGAGGQMGQWFAKYFAANDFEVTGYDTENKISG 40
                789**************************9955444 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.9
                 HHHHHHHHHHT-SEEEE--S---HHHHHHSHHHHHHHHTHHHHHHH CS
   Epimerase  54 salerlfkeeqpdavihlAavggvaassedpadfieknlqgtlnll 99 
                  +l  +++e + ++vi     +  + ss+++ +  +k l  ++n++
  EPA05186.1 237 GRLLTAVQESKTEEVIDYIKTCQEKLSSNTNLEDSYKKLTKMVNVI 282
                 4555666666777777775555666666666666666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       919  (0.0512577); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 2078.42
//
Query:       EPA05187.1  [L=440]
Description: thiamine biosynthesis protein ThiC [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   5.5e-172  572.3   0.4   6.3e-172  572.1   0.4    1.0  1  ThiC_Rad_SAM  Radical SAM ThiC family


Domain annotation for each model (and alignments):
>> ThiC_Rad_SAM  Radical SAM ThiC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  572.1   0.4  3.5e-176  6.3e-172       1     414 [.       3     423 ..       3     427 .. 0.98

  Alignments for each domain:
  == domain 1  score: 572.1 bits;  conditional E-value: 3.5e-176
  ThiC_Rad_SAM   1 tqleaarkgiiteemeevaekenvepefvreevaeGrivipanknhkek..pvaiGkglrtkvnaniGtsadasdieeEveKlkvalkagadtvmdL 95 
                   tq+++ar+gi t+em++va++e+v+ + +  ++a+G+i+ip+n+ +++k   v+iGkgl+tkvn+niGts+  +++eeE+eK+kva+k+ adt+mdL
    EPA05187.1   3 TQMSSARRGIATDEMKRVAKDEDVTLDWLIPKIARGSIIIPSNNVRSQKihNVGIGKGLKTKVNVNIGTSTLNVNLEEEIEKAKVAVKYHADTIMDL 99 
                   8*******************************************99444469********************************************* PP

  ThiC_Rad_SAM  96 stggdideirekileespvpvgtvpiYqalee...kekkveelteeellevieeqaedGvdfltiHagvtlellellkkekRltgivSrgGsllaaw 189
                   s ggd+++ir+++l+ +p+++gtvpiY+a++    ++k+  +l+e+++l++ e++a+dGvd+ tiH+g+t+++++++ k kR+ g+vS+gG+++aaw
    EPA05187.1 100 SDGGDVRKIRQSLLTVAPITFGTVPIYEAYNYgveVHKNPLNLSEDDFLNAFENNAKDGVDYTTIHCGITKDIAKRILKVKRYGGVVSKGGTITAAW 196
                   ******************************988889************************************************************* PP

  ThiC_Rad_SAM 190 mlanekenplyeefdelleilkeydvtlSlgdglRpGsiaDatdeaqlaelivlgelvkrareagvqvmveGPGHvpldeieanvklqkklckeaPf 286
                   ml+++kenp+ +++d+l+e++k+yd+t+Slgd+lRpGsi D++de q++e+i++++l+kra+e+++qvmveGPGHvpl+e++anv l k+l  ++P+
    EPA05187.1 197 MLKHDKENPYITHYDYLIELAKKYDITFSLGDALRPGSILDSHDELQVQEMINISQLTKRAHEQDIQVMVEGPGHVPLNEVSANVILAKSLIGDVPY 293
                   ************************************************************************************************* PP

  ThiC_Rad_SAM 287 yvlGplvtDiapgYDhitsaiGaalaaaaGadllCyvtpaEHlglPdeedvkeGviaakiaahaadlakglkkarerdkalskaRkeldwekqfela 383
                   yvlGplvtD+a g+Dhi+saiGaa++a++G+dllCy+tp+EHl+lP++e+vk+G+ia++iaahaadl+k ++ka ++d a+++aR++ldwekq++l+
    EPA05187.1 294 YVLGPLVTDVASGHDHIASAIGAAVSASQGVDLLCYLTPSEHLALPNAEEVKSGLIAYRIAAHAADLVKIRDKAIKWDMAMTEARRTLDWEKQIALS 390
                   ************************************************************************************************* PP

  ThiC_Rad_SAM 384 ldpekareireeklpe..eeeaCsmCgekCavk 414
                   +dpe+a +i++++ ++  ++  C+mCg  C + 
    EPA05187.1 391 IDPEEAARIHSRTGQRlgNNVPCTMCGGACVYV 423
                   ************9998889999********875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 2661.83
//
Query:       EPA05188.1  [L=134]
Description: hydrolase, NUDIX family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.4e-12   46.5   0.0    3.7e-12   46.4   0.0    1.0  1  NUDIX           NUDIX domain
    0.00014   21.8   0.0    0.00019   21.4   0.0    1.2  1  NUDIX_4         NUDIX domain
  ------ inclusion threshold ------
      0.025   14.8   0.1      0.033   14.4   0.1    1.2  1  Protamine_like  Protamine and protamine like


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4   0.0   6.2e-16   3.7e-12       6     128 ..       7     130 ..       2     133 .. 0.83

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 6.2e-16
                 EEEEEEETTSEEEEEEES..SSSTTT.EESSEEECBTTSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE.EEECSGCSSTS CS
       NUDIX   6 vgvvllnekgevLlvrrs..kkpfpg.WelPgGkvepgEtpeeAArREleEEtGleaellellgrlhylapydgpygdeheilyvfl.eevegelepnd 100
                 v  ++ +++ ++L+++rs   k+ +g W+ + G +e++E+p   A  E+ EE+G+++++l+l+ +  +l+     y++ ++ ++ fl e ++ e+++n 
  EPA05188.1   7 VTSFIQDGQ-KLLILKRSnnVKTMKGlWAGISGIIEKDEEPLKRAKIEIHEEIGISENQLKLIKSANTLKINSPQYENHEWDVFPFLfEVKNPEIKLN- 103
                 556777788.5*******987777889*************************************9999999999999644444555568888888888. PP

                 TTTEEEEEEEEHHHHHHHHTHCTHHHHH CS
       NUDIX 101 enevsevrwvpleellkeklaaesrkll 128
                   e se++w++ +el+  k +++ +k+l
  EPA05188.1 104 -WENSEFKWITKDELKNYKTVPSLEKVL 130
                 .88899*********7777777777766 PP

>> NUDIX_4  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   3.2e-08   0.00019       5     108 ..      11     130 ..       7     132 .. 0.64

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 3.2e-08
                 EEECTEEEEEE--TT.SSSTT-EE-SEEE.-TTS-.HHHHHH...HHHHS-EEE......EEEE..EEEE.EEETTEEEEEEEEEEEEE.S..---... CS
     NUDIX_4   5 irddgrvllekRpek.gllggLwefPgge.eegee.leeala...reelgieve......elep..gtvk.HvftHfrltltvylvrveegeeapa... 85 
                 i+d++++l+ kR ++ + ++gLw   +g  e++ee l++ ++   +ee+gi+++      +  +  +++   ++   ++++  +l++v++ e   +   
  EPA05188.1  11 IQDGQKLLILKRSNNvKTMKGLWAGISGIiEKDEEpLKR-AKieiHEEIGISENqlklikS--AntLKINsPQYENHEWDVFPFLFEVKNPEI--Klnw 104
                 555588999999886347788887776555666663433.323567899994442544432..03333333789999*****77687763322..1347 PP

                 ...EEEEEEGGGGGGS---CCCHCCH CS
     NUDIX_4  86 ...elrwvtpeeleeyalptavrkll 108
                    e++w+t++el++y      +k+l
  EPA05188.1 105 ensEFKWITKDELKNYKTVPSLEKVL 130
                 7889**********998766666665 PP

>> Protamine_like  Protamine and protamine like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   5.4e-06     0.033       3      49 ..      23      70 ..      21      79 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.4e-06
  Protamine_like  3 snnvneckslwngiisisakdespkgltemcnh.pirrapqkckpmks 49
                    snnv+  k lw gi  i  kde p   +++  h  i  + ++ k +ks
      EPA05188.1 23 SNNVKTMKGLWAGISGIIEKDEEPLKRAKIEIHeEIGISENQLKLIKS 70
                    8**********************9877776555246666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 1074.01
//
Query:       EPA05189.1  [L=456]
Description: chorismate mutase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-62  210.2   0.0    7.2e-62  209.6   0.0    1.2  1  Aminotran_1_2    Aminotransferase class I and II
    5.7e-11   42.6   1.0    1.8e-10   41.0   1.0    1.9  1  CM_2             Chorismate mutase type II
    2.7e-06   26.6   0.0    4.8e-06   25.8   0.0    1.4  1  Aminotran_5      Aminotransferase class-V
    4.7e-05   22.1   0.0    7.3e-05   21.5   0.0    1.3  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    0.00019   20.9   0.0    0.00028   20.3   0.0    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    0.00039   19.4   0.8     0.0062   15.5   0.1    2.7  3  Alliinase_C      Allinase
  ------ inclusion threshold ------
      0.011   15.6   0.1      0.045   13.6   0.0    1.9  2  LppX_LprAFG      LppX_LprAFG lipoprotein
      0.037   14.1   1.2       0.12   12.5   1.2    1.9  1  SPATA1_C         Spermatogenesis-associated C-terminus


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  209.6   0.0   3.2e-65   7.2e-62       2     357 ..     108     442 ..     107     448 .. 0.92

  Alignments for each domain:
  == domain 1  score: 209.6 bits;  conditional E-value: 3.2e-65
                    EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEE CS
  Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeil 97 
                    ++i + ++e++++    +++ v+ a +e     +++ +yg ++glp++++alak+++++ + ++  e +++v++Ga  +i  +i+ l lnpgdei+
     EPA05189.1 108 KIIHMEVGEPDFA----PPEIVKNALQE--VFDKGFFKYGQTRGLPSFRNALAKYASKKFNANVSEE-NILVSPGARFAIFSAITTL-LNPGDEII 195
                    789999******9....65555555555..88899**********************8888888888.*******************.******** PP

                    EEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTC CS
  Aminotran_1_2  98 vpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagf 193
                    v +p ++ yk+++ +sg++v+++ ++ e +++ ++e++++ ++        tk+i+++ p+NPtG++++++   +++++  k+nl++++De+Y++ 
     EPA05189.1 196 VIEPAWPAYKDCALNSGIKVRTITTTLESKWEPTIEQIQKVINA------NTKMIVLNYPNNPTGKILPEKLQDEIVRISMKNNLYILSDEIYSEY 285
                    *******************************************9......99******************************************** PP

                    BSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
  Aminotran_1_2 194 vfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaavvsqlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrke 287
                    +f++    +  ++  ++++ +i++s+sK+ +++G+R+Gy+++++++++ + kl +  l   s++ q+++++ l+ +       +++  ++ +r k+
     EPA05189.1 286 AFTNW---K-SVLSYNYDKSIITQSFSKSHAMTGFRIGYAIASPEIINKMSKLEALCLTnvSEPIQYVAMKGLESDI------SNNTNTIRTRLKV 371
                    ***53...3.3444445556************************************99999**************55......789999999**** PP

                    HHHHHHHSTEEEECCSCSSEEEEEETHH..CHHHHHHHHHHTCTEEEEEGGGGTS.TTEEEEECTTS-HHHHH CS
  Aminotran_1_2 288 lrdeLaelglkvlasqsgmflltdlsae..takelskkLleevgvyvtpgtsftv.pgrlRitvAglteeele 357
                    l+++ +e+ l++  ++++m+ + ++++e  +  +++ +Lle+ g++v pg+ f+  ++++Ri+  + +e++l 
     EPA05189.1 372 LTEKVKEIKLDFAVPDGAMYIFARVNQEgfSGVQFANELLEK-GLAVAPGEGFGDyRNFIRISA-CQDEKTLM 442
                    ******************************************.***********99*******9.77777765 PP

>> CM_2  Chorismate mutase type II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   1.0   7.9e-14   1.8e-10       1      74 [.       8      85 ..       8      86 .. 0.95

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 7.9e-14
                HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSGSS-HHHHHHHHHHHHH....HHS-HHHHHHHHHHHHHHHHHHH CS
        CM_2  1 RkeIdeiDdeileLLaeRaelakevgeyKkeeglpvydpeReaevlerlee....galdeeaierifreiisasralq 74
                R++Idei  e++++L+ R +++ke+ge+Kk+ g+ + d++Re+ + +++ +      +de+ + ++++ ++++s+++q
  EPA05189.1  8 RNKIDEITIEMIKMLKIRTDISKEIGEIKKNIGKGITDESREDNLRKQVITlckgLNFDESIASKFLNFLLNESIKVQ 85
                99*************************************************8754339******************99 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   2.2e-09   4.8e-06      56     173 ..     161     277 ..     150     336 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 2.2e-09
                  HT-STGGGEEEESSHHH.HHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEE..EBETTSCBEGGGHHHH--TTEEEEEEESBET CS
  Aminotran_5  56 inaeseeeiiftsGtte.ainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvi..pldeegeldldelekllnektklvaithvsn 150
                  +na+ +ee i +s +++ ai  ++ +l   l+pgdei+v e    a      + a   g+kv+ i  +l++++e ++++++k +n +tk++ ++  +n
   EPA05189.1 161 FNANVSEENILVSPGARfAIFSAITTL---LNPGDEIIVIEPAWPAYK----DCALNSGIKVRTIttTLESKWEPTIEQIQKVINANTKMIVLNYPNN 251
                  566666666677766666*********...*********998877777....888889999999955688999************************* PP

                  TTTEB--HH...HHHHHHHHTT-EEE CS
  Aminotran_5 151 vtGtiqpve...eigklakkkgalvl 173
                   tG i p +   ei+++  k++ ++l
   EPA05189.1 252 PTGKILPEKlqdEIVRISMKNNLYIL 277
                  ****9996522255555555555555 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   3.2e-08   7.3e-05      71     173 ..     170     279 ..     144     337 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 3.2e-08
                      EEESSHH.HHHHHHHHTTS-TTEEEEEESTSSHHHHHH.HHHTHHHTTCEEEEEST..TSHHHHHHHCCTTEEEEEEESS-TTTT----...HH CS
  Cys_Met_Meta_PP  71 lavssGm.aAiaaailallkaGdeivvsddlYggtqrl.lkkvlkklgievkfvdt..sdleelekaikentklvylEtptnpllkvvD...ie 157
                      ++vs G   Ai++ai++ll+ Gdei+v + ++   ++  l++ +k   i+++   +    +e+++k+i+ ntk++ l  p np+ k++      
       EPA05189.1 170 ILVSPGArFAIFSAITTLLNPGDEIIVIEPAWPAYKDCaLNSGIKVRTITTTLESKwePTIEQIQKVINANTKMIVLNYPNNPTGKILPeklQD 263
                      5555554269*******************998877665134444444455444443336789**********************9986412123 PP

                      HHHHHHHHTT-EEEEE CS
  Cys_Met_Meta_PP 158 kiaklakkagvlvvvD 173
                      +i+++  k+++ ++ D
       EPA05189.1 264 EIVRISMKNNLYILSD 279
                      5666666666665555 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   1.3e-07   0.00028       8     223 ..     127     359 ..     123     379 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.3e-07
                      HHHHHHHTSS-SSSSHH..HHHHHHHHHHHHT-SEEEEESS.....HHHHHHHHHHH..TTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B CS
  DegT_DnrJ_EryC1   8 eaveevlksgwltsgpe..veeFEkafaaylgvkhaiavss.....GtaAlhlaLra..lgvgpgdeVIvpsltFvatanavlelgakpvfvDv 92 
                      +a++ev + g++  g++    +F +a+a+y  +k+   vs         A   + +a    ++pgde+Iv    + a   ++l++g k+  +  
       EPA05189.1 127 NALQEVFDKGFFKYGQTrgLPSFRNALAKYASKKFNANVSEenilvSPGARFAIFSAitTLLNPGDEIIVIEPAWPAYKDCALNSGIKVRTITT 220
                      566777777766664441145777777777777666555532222222333334444334578**************************99887 PP

                      -.TTTSSB-GGGCGGG--TTEEEEE...EB-GGGB--..-H.HHHHHHHHHCT-EEEEE-TT-TT-EETTEECCCSS...SEEEEE-BTTSSS- CS
  DegT_DnrJ_EryC1  93 d.pdtynidpaaieaaitertkaIl...pVhlyGqva..dm.dalkaiaakhglkvieDaAhAlGatykgkkvGalg...daavfSFyptKnlt 176
                      + +  + ++ ++i+++i+ +tk I+   p +  G++    + d++ +i+ k +l++++D   +  a  + k v ++    ++ + SF  ++ +t
       EPA05189.1 221 TlESKWEPTIEQIQKVINANTKMIVlnyPNNPTGKILpeKLqDEIVRISMKNNLYILSDEIYSEYAFTNWKSVLSYNydkSIITQSFSKSHAMT 314
                      62678*******************944457888998765444799999999***9999998888888777888777665678888999999998 PP

                      SSS-EEEEESTHHHHHHHHHHHBTTCECCTCSSCECCSS---B-B-B CS
  DegT_DnrJ_EryC1 177 tGeGGavvtndeelaekarvlrnhGlkrkaekryvgevelGynyrlt 223
                       +  G  +  ++e+ +k+++l++  l + +e+ ++  +  G ++ ++
       EPA05189.1 315 GFRIGYAI-ASPEIINKMSKLEALCLTNVSEPIQYVAM-KGLESDIS 359
                      88888754.56788888888877777765555555555.56666555 PP

>> Alliinase_C  Allinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0     0.075   1.7e+02     210     242 ..      66      99 ..      59     115 .. 0.73
   2 !   15.5   0.1   2.8e-06    0.0062     120     238 ..     223     352 ..     161     376 .. 0.74
   3 ?   -1.0   0.0      0.28   6.3e+02     314     357 ..     403     446 ..     389     452 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.075
                  -HHHHHHHHHHHHHHHSS--HH.HHHHHHHHHHH CS
  Alliinase_C 210 dkevakklveyieknsiGvske.sqlrvlkilkv 242
                  d+++a+k+++++ ++si v  e  q++    lk 
   EPA05189.1  66 DESIASKFLNFLLNESIKVQSEnKQTHLSIFLKA 99 
                  999*************999655156666666664 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 2.8e-06
                  TEEEEEESTT-.--S..S-EEEEEESS-TTT--.....------...-TT-EEEEEE-TT-STTTS-....--S-B--SEEEEEHHHHHS-GGG-EEE CS
  Alliinase_C 120 lykweGdaaayvkkknpeefielvtsPnnPdgl.....lreavv...kgseakviyDlayYWPhytp....itskadedimLftlskltGhaGsrlGW 205
                  + kwe + ++ +k  n++  + +   PnnP g+     l++++v    +++  ++ D +y    +t+    + ++ d+ i+  ++sk    +G r+G+
   EPA05189.1 223 ESKWEPTIEQIQKVINANTKMIVLNYPNNPTGKilpekLQDEIVrisMKNNLYILSDEIYSEYAFTNwksvLSYNYDKSIITQSFSKSHAMTGFRIGY 320
                  45788888888777777777778889*****973222257788855434455678899997777776222256889********************** PP

                  EEES-HHHHHHHHHHHHHHHSS--HHHHHHHHH CS
  Alliinase_C 206 alvkdkevakklveyieknsiGvskesqlrvlk 238
                  a+    e+ +k+ +        vs   q  ++k
   EPA05189.1 321 AIA-SPEIINKMSKLEALCLTNVSEPIQYVAMK 352
                  *76.56788999887777666677666665555 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.28
                  ..-HHHHHHTTTEEEEEGGGGTS-TTEEEEESSS-HHHHHHHHH CS
  Alliinase_C 314 dedcaevlrekkiltrsGevfeaesryvrlsllkrdddfdvlle 357
                    + a+ l ek++    Ge f++ ++++r+s  + ++     ++
   EPA05189.1 403 GVQFANELLEKGLAVAPGEGFGDYRNFIRISACQDEKTLMEGMN 446
                  4566788999999999***************9888776655555 PP

>> LppX_LprAFG  LppX_LprAFG lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       0.7   1.6e+03      64      97 ..     272     303 ..     256     311 .. 0.81
   2 ?   13.6   0.0     2e-05     0.045      24     106 ..     341     425 ..     327     440 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.7
                  EEEEEETTEEEEEECTTEEEEEEEHGHCHHHHCG CS
  LppX_LprAFG  64 vkfvvvdgklyaklppetwsdlgpaekiydpavl 97 
                   +  ++ +++y +  +++w+++ +    yd +++
   EPA05189.1 272 NNLYILSDEIYSEYAFTNWKSVLSY--NYDKSII 303
                  567788999*****99999999877..6777766 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 2e-05
                  EEEC--TTSTEEEEEEEEETTTT.EEEEEEEEEET.TCEEEEEEEEETTEEEE..EECTTEEEEEEEHGHCHHHHCGG-TTTSHHH CS
  LppX_LprAFG  24 tvngkvdglpvesvegdltnqpagaakgnakvtla.gqavdvkfvvvdgklya..klppetwsdlgpaekiydpavlLdpdkGlan 106
                  +v++ ++ + ++ +e d++n+ +  +   +kv ++  ++++ +f v dg +y+  ++++e +s ++ a+++++ +   +p +G+++
   EPA05189.1 341 NVSEPIQYVAMKGLESDISNNTN-TIRTRLKVLTEkVKEIKLDFAVPDGAMYIfaRVNQEGFSGVQFANELLEKGLAVAPGEGFGD 425
                  688889999************99.8*******88889999***********963377889********************999975 PP

>> SPATA1_C  Spermatogenesis-associated C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.2   5.2e-05      0.12     111     148 ..       2      39 ..       1      41 [. 0.94

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.2e-05
    SPATA1_C 111 heidelkrkledakmklvaElklRkqaaeelkaLrael 148
                 ++i++l++k+++  +++++ lk R  +++e+ ++++++
  EPA05189.1   2 SDINQLRNKIDEITIEMIKMLKIRTDISKEIGEIKKNI 39 
                 58********************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (456 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       790  (0.0440627); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 2826.05
//
Query:       EPA05190.1  [L=176]
Description: putative chorismate synthase, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-64  217.8   0.3    1.7e-64  217.6   0.3    1.0  1  Chorismate_synt  Chorismate synthase


Domain annotation for each model (and alignments):
>> Chorismate_synt  Chorismate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  217.6   0.3   9.3e-69   1.7e-64     168     326 ..       2     166 ..       1     167 [. 0.96

  Alignments for each domain:
  == domain 1  score: 217.6 bits;  conditional E-value: 9.3e-69
                      CHHHHHHHHHHHHHTT--B-EEEEEEEES--TT-SBTTTB-HHHHHHHHHHTSTTEEEEEETTGGGGGGSBHHHHS--EE......EESS-TTT CS
  Chorismate_synt 168 aaeemeeaieeakkegdslGgvvevvvkgvpaGlGepvfdkldakLakalmsipAvkgveiGsGfeaaelkGseanDeiv......lrktnnaG 255
                      +a++m+e i +a+k+gdslGg++e v++++p+GlGep+f +l+++L+ka++sip+vkgve+GsGf+++el Gse+nD ++      ++ktnn+G
       EPA05190.1   2 TAKKMKESILDARKKGDSLGGIIESVTTNIPVGLGEPIFGSLESDLSKAIFSIPSVKGVEFGSGFAGSELFGSENNDLYTikkgkiVTKTNNSG 95 
                      689***************************************************************************9966665544****** PP

                      TEETTEEBSS-EEEEEEE--SS--SSEEEEEBTTS-E-EEEE--S-S-S-THHHHHHHHHHHHHHHHHHHH CS
  Chorismate_synt 256 GieGGisnGepivvrvavKpipsiakeqktvdletkeevelevkgrhDpcvvpravvvveamvalvladal 326
                      Gi+GGisnG+pi++r+a+Kp +sia++q+tvd++tk+e+ levkgrhDpcvvpra +vv+++val+lad++
       EPA05190.1  96 GILGGISNGMPITMRIAFKPASSIAQKQSTVDIKTKKETVLEVKGRHDPCVVPRAPPVVDSLVALTLADHA 166
                      *********************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       279  (0.0155614); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1296.09
//
Query:       EPA05191.1  [L=50]
Description: hypothetical protein BG20_I2265, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.016   13.7   0.1      0.017   13.6   0.1    1.0  1  TMEM214     TMEM214, C-terminal, caspase 4 activator
      0.052   12.6   0.3      0.056   12.4   0.3    1.0  1  Type_ISP_C  Type ISP C-terminal specificity domain


Domain annotation for each model (and alignments):
>> TMEM214  TMEM214, C-terminal, caspase 4 activator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   1.9e-06     0.017     365     402 ..       8      45 ..       4      48 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.9e-06
     TMEM214 365 pkcpedmkkelieslieCLlvddqclsvWrqlYkkhll 402
                 +k  +d +++lies + C++ +++ +++ r  Y+khl 
  EPA05191.1   8 SKWSKDLREKLIESNTLCMNHEKNMNKIFRGFYEKHLK 45 
                 5667899*****************************96 PP

>> Type_ISP_C  Type ISP C-terminal specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.3   6.2e-06     0.056      48      90 ..       2      44 ..       1      46 [. 0.93

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.2e-06
  Type_ISP_C 48 tkdstkikwsralkkdlkknkklefdeekiveilYRPFdkqwl 90
                 kd+++ kws++l+++l ++++l  + ek     +R F +++l
  EPA05191.1  2 SKDKQQSKWSKDLREKLIESNTLCMNHEKNMNKIFRGFYEKHL 44
                589***********************99999999***999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1119  (0.0624129); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 334.92
//
Query:       EPA05192.1  [L=30]
Description: hypothetical protein BG20_I2269, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (30 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      195  (0.0108762); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 226.05
//
Query:       EPA05193.1  [L=78]
Description: hypothetical protein BG20_I2267 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.7e-22   77.6   0.0    5.2e-22   77.4   0.0    1.0  1  TusA      Sulfurtransferase TusA


Domain annotation for each model (and alignments):
>> TusA  Sulfurtransferase TusA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.4   0.0   2.9e-26   5.2e-22       1      70 []       7      76 ..       7      76 .. 0.98

  Alignments for each domain:
  == domain 1  score: 77.4 bits;  conditional E-value: 2.9e-26
                EEEEBTT-STTCCHHHHHHHHCCCGCT-EEEEEESSCHHHHHHHHHHHHHTEEEEEEE-GCC-EEEEEEE CS
        TusA  1 ielDlrGlvCPePllklkkalekleegevlevladdpaatediprfakklghelveveeedgeyrivirk 70
                ++lD++Gl CPeP+ ++k ++ek++ g+vl v addpaa+ di+r++ ++gh+l+  +++++++++ i+k
  EPA05193.1  7 KKLDATGLFCPEPVFRTKIEIEKMQVGQVLTVSADDPAAEDDISRWVTRNGHTLLNLKKDGNTITFQIKK 76
                58****************************************************************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 573.24
//
Query:       EPA05194.1  [L=330]
Description: pyridoxal-phosphate dependent protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-64  217.8   0.0    2.9e-64  217.3   0.0    1.2  1  PALP      Pyridoxal-phosphate dependent enzyme


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  217.3   0.0   1.6e-68   2.9e-64       4     291 ..      12     292 ..       9     295 .. 0.91

  Alignments for each domain:
  == domain 1  score: 217.3 bits;  conditional E-value: 1.6e-68
                 CSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHH.HHTT...TTTSEEEEEBSSHHHHHHHHHHHHHT-EEEEEEETTS-HHHHHHHH CS
        PALP   4 gigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllar.lkeg...tgaktvveassGNhgralAaaaallGlkvtivvpadaspekvallr 98 
                  +g+TPlv+l++ls + +++ f+KlE++np+gS+KdR+a++++++ +++g   +g+  ++e +sGN+g+al  +a+llG+kv+iv+p++as+e ++ +r
  EPA05194.1  12 RVGNTPLVKLDSLS-HNNIQYFAKLEGHNPFGSVKDRAAYWMIKDgEEKGkltKGKSIIIEPTSGNTGIALTGIAKLLGYKVEIVIPEKASNETKDIIR 109
                 589**********9.77888*************************6444499999******************************************** PP

                 HTT-EEEEE........CCHHHHHHHHHHHHHHH.STTCEE--TTTSHHHHHH.HHTHHHHHHHHTTTTEEEEEEE-SSSHHHHHHHHHHHHHSTT-EE CS
        PALP  99 llGaevvev........ggdydeavaaaaelaae.gegaylvsqfdnptvieg.ygtiglEileqlggkpdavvvpvGgGgliaGiaaglkerrpdvrv 187
                  lGa+v e+        g ++d++ a+a  +a++  + +y  +q+ n++++ g y  +g+Ei++q++gk+++++ +vG+Gg+i+Gi+++lke++p+v++
  EPA05194.1 110 NLGAKVFETsddlcpkvGAGTDQSIALATSIASSrPDTYYSPNQYANEANFMGhYVGTGPEIWKQTDGKVTHFFTGVGTGGTITGIGTYLKEKNPNVKI 208
                 *********88888888788************99666777789999***************************************************** PP

                 EEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCS.CGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHHHHHHHHCCTTC CS
        PALP 188 igvepegsdalarslragrrvtvpvsdtiadglavg.spselafelldrlvdeivtvsdeealeamrllarregivvepssaaalaalklreagelkeg 285
                 ig +p++++ + + +                      s+ ++ f   ++ vd+ v+v+++ea++ ++++ +++++++ pssaa++a +   ++ +++++
  EPA05194.1 209 IGCQPQQNHLIQGWR----------------NF--EeSAKPDLFLKRENVVDDWVSVDNDEAFAVVKEVLEKDKLLISPSSAAVYACM---KKYKVDGD 286
                 ******999998888................33..2357778888889****************************************...77777777 PP

                 EEEEEE CS
        PALP 286 drvvvi 291
                 + vv i
  EPA05194.1 287 AYVVGI 292
                 666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2079.59
//
Query:       EPA05195.1  [L=293]
Description: trypsin [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-33  116.6   0.3    2.9e-33  115.9   0.3    1.4  1  Trypsin_2      Trypsin-like peptidase domain
    1.1e-14   54.5   0.2    1.1e-14   54.5   0.2    2.0  3  PDZ_2          PDZ domain
    1.6e-14   54.3   0.3      3e-14   53.3   0.3    1.5  1  Trypsin        Trypsin
    2.6e-05   24.0   1.5      0.023   14.5   0.1    3.2  3  PDZ_6          PDZ domain
     0.0013   19.0   2.6        3.1    8.2   1.6    3.7  2  PDZ            PDZ domain
     0.0091   15.7   0.0      0.028   14.2   0.0    1.9  1  Peptidase_S29  Hepatitis C virus NS3 protease
  ------ inclusion threshold ------
      0.079   11.6   0.8       0.14   10.8   0.8    1.3  1  Peptidase_S46  Peptidase S46


Domain annotation for each model (and alignments):
>> Trypsin_2  Trypsin-like peptidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.9   0.3   1.1e-36   2.9e-33       1     150 []       2     143 ..       2     143 .. 0.98

  Alignments for each domain:
  == domain 1  score: 115.9 bits;  conditional E-value: 1.1e-36
   Trypsin_2   1 GsGflvgsdglilTnaHvvdsadgaavkaikkkveeagadgrevpakvvaadpelDlAllkv.ssderaglpplplgpsealkggepvyvvGyplggek 98 
                 GsGf+++++g+i+Tn+Hvv++ d++ v         a ++g  ++akv+++d   D+A+l++ ++ ++ +l p+ +++s+++k+ge+v+++G+p g  +
  EPA05195.1   2 GSGFVYDNEGHIITNYHVVAGVDNVDV---------ALSNGDIFSAKVIGTDKFNDIAVLQLtDNYSDESLTPVSFADSSQIKVGEQVIAIGNPFGLSN 91 
                 9**************************.........****************555******************************************** PP

   Trypsin_2  99 sgsvssGivsgvve..sesaasgegesflqtdaatspGsSGGplfdsdGrvvGl 150
                   ++++Givs++ +   ++  +++ ++++qtdaa++pG+SGGpl+d +G+++G+
  EPA05195.1  92 --TMTTGIVSQIGRllPNQEIGFSIPNIIQTDAAINPGNSGGPLLDNTGNLIGM 143
                 ..9************999999********************************8 PP

>> PDZ_2  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.9   7.5e+03      37      47 ..      19      29 ..      10      66 .. 0.60
   2 ?   -2.4   0.0       2.5   6.3e+03      27      42 ..      69      84 ..      47      85 .. 0.80
   3 !   54.5   0.2   4.4e-18   1.1e-14       1      82 []     182     286 ..     182     286 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.9
                EEEEETTB--S CS
       PDZ_2 37 vilkvdgkkvk 47
                v+  vd+++v 
  EPA05195.1 19 VVAGVDNVDVA 29
                66666666662 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.5
                GGGT.--TT-EEEEET CS
       PDZ_2 27 aakaglkagDvilkvd 42
                a+ +++k g ++++++
  EPA05195.1 69 ADSSQIKVGEQVIAIG 84
                6677889999998886 PP

  == domain 3  score: 54.5 bits;  conditional E-value: 4.4e-18
                 ....XX------.............-EEEEEE-TTSGGGGT.--T...........T-EEEEETTB--SSHHHHHHHHH.TS-TT-EEEEEEEETTEEE CS
       PDZ_2   1 pylGvsvsdeed...........tggvlvvsVkeggPaakaglka...........gDvilkvdgkkvksledlislll.kkkpGdtVkltvlRdgkkk 76 
                 p+lG+s + +++            +g+++ ++ ++gPa kaglk             D+++++d+++vk  +d+i +++ +k+ Gd+V+l+v+Rdg   
  EPA05195.1 182 PWLGISGTTLTPklaekfnlpknFRGAVINDIVKDGPAGKAGLKGalfsstgeivsADIVTSIDNVPVKRIDDIIAYVSeNKSVGDKVTLQVYRDGSVI 280
                 6788888888888888888888889************************************************************************** PP

                 EEEEE- CS
       PDZ_2  77 tvevkl 82 
                 tv+++l
  EPA05195.1 281 TVNIEL 286
                 ***997 PP

>> Trypsin  Trypsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.3   0.3   1.2e-17     3e-14      28     220 ..       3     169 ..       1     170 [. 0.79

  Alignments for each domain:
  == domain 1  score: 53.3 bits;  conditional E-value: 1.2e-17
                 EEEEEETT.EEEEEGGGTTTGGGEEEEESESBTTSCTTTEEEEEEEEEEEETTEBTTTTTTTEEEEEESSSSTSBSSBHCCBBCSTTHTTSTTTEEEEE CS
     Trypsin  28 gGslisen.wvlTAaHCvsnasdvkvvlgehnlkksegkeqklkvekvivhpnynpstldnDiallklkepvklgdtvrpiclpaassslpvgttclvs 125
                 +G++++++  ++T+ H+v + ++v+v         s+g+   ++ +        + ++  nDia+l+l+ +    ++  p++ ++ ss+++vg   +v+
  EPA05195.1   3 SGFVYDNEgHIITNYHVVAGVDNVDV-------ALSNGD--IFSAKV------IGTDK-FNDIAVLQLTDN-YSDESLTPVSFAD-SSQIKVG--EQVI 81 
                 5888888889*********9666666.......566774..333333......34444.58**********.88899********.6645555..9999 PP

                 ESSBSSTSSBSSBEEEEEEEEEEHHHHHHHTTTTSTTTEEEEESTTSSSBCTTTTTTSEEEETTTEEEEEEEEE.SSSSCTTSEEEEEEGGGGHHH CS
     Trypsin 126 GwgrtkekgksdtlqevevpvvsretcksaykgkvtenmlcagakeggkdacqGDSGGPlvcsdgelvGivswg.kgcakgnrpgvytkvssyldw 220
                 ++g+++  +  +t++++ v+ + r   +++++    +n ++++a     ++++G+SGGPl+ ++g l+G++++   + ++    g++++ ++++++
  EPA05195.1  82 AIGNPFGLS--NTMTTGIVSQIGRLLPNQEIGFS-IPNIIQTDA-----AINPGNSGGPLLDNTGNLIGMNTAIqSNVGEFAGVGFAVPSNTIKKV 169
                 999996666..99999999999998777766665.59*******.....************************95444544448888888888776 PP

>> PDZ_6  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.43   1.1e+03       9      27 ..      67      85 ..      61      85 .. 0.82
   2 !    6.7   0.1    0.0025       6.5       1      17 [.     209     225 ..     209     226 .. 0.90
   3 !   14.5   0.1   9.2e-06     0.023      18      56 .]     237     275 ..     230     275 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.43
       PDZ_6  9 sPAdrAGlrvGDiilsvNG 27
                s Ad   ++vG +++++++
  EPA05195.1 67 SFADSSQIKVGEQVIAIGN 85
                77888889*******9975 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0025
       PDZ_6   1 vVtaVdpgsPAdrAGlr 17 
                 v+  +++++PA +AGl+
  EPA05195.1 209 VINDIVKDGPAGKAGLK 225
                 57899**********96 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 9.2e-06
       PDZ_6  18 vGDiilsvNGqpveglsladvaallr..gsagesvvlvvrr 56 
                   Di++s++++pv  + ++d++a++    s+g +v+l+v r
  EPA05195.1 237 SADIVTSIDNVPV--KRIDDIIAYVSenKSVGDKVTLQVYR 275
                 56***********..**********9666788888888876 PP

>> PDZ  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.014        37      35      55 ..      65      85 ..      61     101 .. 0.80
   2 !    8.2   1.6    0.0012       3.1      26      81 ..     206     273 ..     173     274 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.014
                TTSHHHHHTSSTTEEEEEETT CS
         PDZ 35 pggaaeadglkvGDkIlsvNg 55
                p + a+ + +kvG +++++++
  EPA05195.1 65 PVSFADSSQIKVGEQVIAIGN 85
                556777778**********98 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0012
                 SSEEEEEECTTSHHHHH..........T.SSTTEEEEEETTEETTTSHH.HHHHHHHHTTTSEEEEEE CS
         PDZ  26 kgifvsevlpggaaead..........g.lkvGDkIlsvNgvdvenvsh.eeavqaikgskgkvtLti 81 
                 +g+++++++++g+a ++          g +   D+++s+++v+v+ + +  + v ++k+ ++kvtL++
  EPA05195.1 206 RGAVINDIVKDGPAGKAglkgalfsstGeIVSADIVTSIDNVPVKRIDDiIAYVSENKSVGDKVTLQV 273
                 68888888888555544122222222255557899999999999999551466888888888999987 PP

>> Peptidase_S29  Hepatitis C virus NS3 protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   1.1e-05     0.028     104     147 ..     123     167 ..      94     169 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.1e-05
  Peptidase_S29 104 selkGssGsPilCdsGhvvGllvaavcsggvvkavrfv.Pvetle 147
                    +   G sG+P+l + G  +G+ +a+  + g+   v f  P +t++
     EPA05195.1 123 AINPGNSGGPLLDNTGNLIGMNTAIQSNVGEFAGVGFAvPSNTIK 167
                    55679******************************9988988876 PP

>> Peptidase_S46  Peptidase S46
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.8   5.4e-05      0.14     627     651 ..     120     144 ..      90     154 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5.4e-05
                    ES----TT-TT-EEE-TTS-EEEEE CS
  Peptidase_S46 627 stnDitGGNSGSPvlngkgelvGla 651
                    +++ i  GNSG P+l++ g+l+G++
     EPA05195.1 120 TDAAINPGNSGGPLLDNTGNLIGMN 144
                    7788899****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2004.14
//
Query:       EPA05196.1  [L=225]
Description: CobQ/CobB/MinD/ParA nucleotide binding domain protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.7e-19   68.4   0.0    7.6e-19   68.0   0.0    1.2  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    1.4e-13   51.2   0.5    3.6e-07   30.2   0.0    2.1  2  AAA_26       AAA domain
     0.0063   15.9   0.2      0.015   14.6   0.0    1.6  2  CTP_synth_N  CTP synthase N-terminus
  ------ inclusion threshold ------
      0.047   13.1   0.3       0.26   10.7   0.0    1.9  2  ParA         NUBPL iron-transfer P-loop NTPase
       0.11   12.0   0.0       0.21   11.0   0.0    1.4  1  CBP_BcsQ     Cellulose biosynthesis protein BcsQ
       0.11   12.7   0.0         32    4.8   0.0    2.6  3  Roc          Ras of Complex, Roc, domain of DAPkinase
       0.13   12.0   0.2       0.54   10.0   0.0    1.9  2  IstB_IS21    IstB-like ATP binding protein


Domain annotation for each model (and alignments):
>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.0   0.0     3e-22   7.6e-19       1     119 [.       6     184 ..       6     193 .. 0.92

  Alignments for each domain:
  == domain 1  score: 68.0 bits;  conditional E-value: 3e-22
                 EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH............................................. CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................................. RF
        CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep............................................. 54 
                 i+ia+ ++GvGKT+++++++ al+++g+ V++++++p+    ++l   ++ ++                                              
  EPA05196.1   6 ITIAGATSGVGKTSITCAIIYALQKKGFSVQPFKVGPDYIDPSYLSSISKHEAFnldvwlmgknqllnsfvsnsnsdisiiegvmgyydgfggdsnfas 104
                 79************************************888885444444444488899999999********************************** PP

                 ................CCHCCCHHHHHHCHCHHHH.....EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHC CS
                 ................xxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        CbiA  55 ................dlkrllellealgkkkall...lkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeava 119
                                 d+++ +++++a  ++++++    +i+g++ln+++++++e l +eale +    ++p++gvi ++ +++
  EPA05196.1 105 thhvasitkspvililDASKTSRSIAATAIGFQKFhrnSRIMGIILNKIGSKKHEILCREALEIT----KLPIIGVIYKNLELN 184
                 *********************************99***************************998....8********999884 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.3     3e-07   0.00078       3      36 ..       6      39 ..       4      45 .. 0.93
   2 !   30.2   0.0   1.4e-10   3.6e-07      85     194 ..      69     183 ..      42     187 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 3e-07
      AAA_26  3 ifvtgtdtgvGKTvvslgLvralkrkgvkvgyfK 36
                i ++g + gvGKT+++ ++++al++kg++v+ fK
  EPA05196.1  6 ITIAGATSGVGKTSITCAIIYALQKKGFSVQPFK 39
                88**************************998777 PP

  == domain 2  score: 30.2 bits;  conditional E-value: 1.4e-10
      AAA_26  85 didlekivkelekdadivvVEGagglgvpit..ee.llnadiaknlgapvilVarg..glgtinqllltiealrqknvrvlGvilNkvrnpe...nvet 175
                  + l+++    + ++di ++EG+ g+ ++    ++ +++  +a   ++pvil++ +  ++++i+++++  + +++ n r++G+ilNk+ +++     ++
  EPA05196.1  69 NQLLNSF--VSNSNSDISIIEGVMGYYDGFGgdSNfASTHHVASITKSPVILILDAskTSRSIAATAIGFQKFHR-NSRIMGIILNKIGSKKheiLCRE 164
                 4555666..456789*********99988541133588999************9994344679999999998887.89*********877754456677 PP

      AAA_26 176 lekksgipvlGvvPylpdl 194
                 + + +++p++Gv+  + +l
  EPA05196.1 165 ALEITKLPIIGVIYKNLEL 183
                 7778899****99777666 PP

>> CTP_synth_N  CTP synthase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   5.9e-06     0.015       7      60 ..       9      61 ..       6      64 .. 0.90
   2 ?   -3.1   0.0       1.5   3.8e+03     104     130 ..     184     210 ..     175     221 .. 0.55

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.9e-06
                 E--STTTTHHHHHHHHHHHHHCTT--EEEEEEE-SSSSSSTT--CCCC--EEE- CS
  CTP_synth_N  7 GGvvSglGkGiiaaslgallksrglkvtlikiDPYlnvdagtlsplehGEvfvl 60
                  G +Sg+Gk  i+ ++   l+++g++v+  k+ P   +d++ ls++ + E f l
   EPA05196.1  9 AGATSGVGKTSITCAIIYALQKKGFSVQPFKVGPD-YIDPSYLSSISKHEAFNL 61
                 5889******************************4.479*******99999966 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.5
                  TTTT----CCCHHHHHHHHHHHHHH.H CS
  CTP_synth_N 104 dylGktvqviphvtdeikeriekvakk 130
                  ++  + + +ip   +++k++iek +k+
   EPA05196.1 184 NFESRHLGLIPVGEKNLKSKIEKNSKI 210
                  455555555555555666666665554 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0    0.0001      0.26       6      35 ..       6      35 ..       4      39 .. 0.92
   2 ?    0.3   0.0      0.15   3.8e+02     139     226 ..     116     211 ..      98     224 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0001
        ParA  6 iavlSgKGGVGKStvavnlAlaLakkglkv 35
                i+++ +  GVGK+++++ + +aL+kkg++v
  EPA05196.1  6 ITIAGATSGVGKTSITCAIIYALQKKGFSV 35
                77888899*******************988 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.15
        ParA 139 aviVttpqevaladvkkaiemfk.kvkvkvlGvveNmsgfvcpk..cgekteifgk....gggeklaeelgvpllgeipldp.eireasdegkplv 226
                 ++++    + + +++  ai + k + + +++G++ N  g + ++  c+e  ei +        ++l  +++ + lg ip+ + ++++++++ ++++
  EPA05196.1 116 VILILDASKTSRSIAATAIGFQKfHRNSRIMGIILNKIGSKKHEilCREALEITKLpiigVIYKNLELNFESRHLGLIPVGEkNLKSKIEKNSKII 211
                 555555666666667777777664556788888888755544432255555555441111223444444555667777775414455555555544 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   8.4e-05      0.21       3      33 ..       5      35 ..       3      45 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8.4e-05
    CBP_BcsQ  3 vlalqGvRGGvGttsllaaLawalhelgesv 33
                 +++ G   GvG+ts++ a+ +al++ g sv
  EPA05196.1  5 RITIAGATSGVGKTSITCAIIYALQKKGFSV 35
                68999*********************99887 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.013        35       8      61 ..      13      64 ..       5      71 .. 0.56
   2 ?   -1.0   0.0      0.75   1.9e+03      10      25 ..      66      81 ..      64      89 .. 0.84
   3 ?    4.8   0.0     0.013        32      63     118 ..      96     153 ..      91     155 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.013
                TTSSHHHHHHCHCT-CCC-E...EETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEE CS
         Roc  8 sgvGKtsllkrfvedkfsek...ekstigvdfltkevtkikgvendkkvkkvklniW 61
                sgvGKts+   ++    ++    +   +g d+++ ++  +++++   k + ++l++W
  EPA05196.1 13 SGVGKTSITCAIIYALQKKGfsvQPFKVGPDYIDPSY--LSSIS---KHEAFNLDVW 64
                79*****988776543332211144556666665543..33332...2345666666 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.75
                SSHHHHHHCHCT-CCC CS
         Roc 10 vGKtsllkrfvedkfs 25
                +GK  ll++fv+++ s
  EPA05196.1 66 MGKNQLLNSFVSNSNS 81
                69********998765 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.013
                 E-SGGCTTTT-HHHHCTSCEEEEEEE.GHHHHCHHHHHHHHHHHCSSS-EE.EEEE-T CS
         Roc  63 taGqerfrslhplylreaalailvyd.srssenlkeWlkelkkvagkspvi.lvgnki 118
                 ++G  +f s+h++    ++ +il++d s++s+++      ++k  ++s ++ ++ nki
  EPA05196.1  96 FGGDSNFASTHHVASITKSPVILILDaSKTSRSIAATAIGFQKFHRNSRIMgIILNKI 153
                 799*********9999999999999966678888888888888888887776888997 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00021      0.54      52      79 ..       8      36 ..       4      43 .. 0.83
   2 ?   -0.8   0.0      0.42   1.1e+03      44      79 ..     111     146 ..     101     156 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00021
   IstB_IS21 52 llG.psGvGKshlaialgveavraglsvl 79
                + G  sGvGK+ +++a+ ++  ++g+sv 
  EPA05196.1  8 IAGaTSGVGKTSITCAIIYALQKKGFSVQ 36
                556247********************996 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.42
   IstB_IS21  44 iekkenivllGpsGvGKshlaialgveavraglsvl 79 
                 i+k+  i++l  s + +s  a+a+g +  +++ +++
  EPA05196.1 111 ITKSPVILILDASKTSRSIAATAIGFQKFHRNSRIM 146
                 566667778888888888889999988888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1437.85
//
Query:       EPA05197.1  [L=668]
Description: oligosaccharyl transferase STT3 subunit, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-35  121.3  30.5    8.2e-35  120.7  30.5    1.4  1  STT3      Oligosaccharyl transferase STT3 subunit
    0.00083   17.7   0.3    0.00083   17.7   0.3    2.5  2  Dpy19     Q-cell neuroblast polarisation


Domain annotation for each model (and alignments):
>> STT3  Oligosaccharyl transferase STT3 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.7  30.5   9.2e-39   8.2e-35      30     485 ..       3     493 ..       1     495 [. 0.81

  Alignments for each domain:
  == domain 1  score: 120.7 bits;  conditional E-value: 9.2e-39
                 --SSCHHHHHHHCCCHHHT-C.....CCHHSSEETTSSTTT-EEESTTCCHCCC.CHHHHHHCCHHC..HHHHHHHHCCHHHHHHHHCHHHHHHHHHHS CS
        STT3  30 lsefDpYYnyRltenllnnGfpGdvvikkknwfdhsqyyPpGsrvdygplivlLamlasaiinhsld..vsirevclwlpallgsLlaIpiyflvrelk 126
                 l efDp++nyR+t+++++nG+      +   w d+ ++yP G+ v   ++ v+L  l++a +++++   +++ +  +++p ++gsL  I+i+ lvr+++
  EPA05197.1   3 LNEFDPFFNYRATQYIIDNGI-----NAYFEWNDNLSWYPHGRDVS-QTSQVIL-HLTAATTYWMFGggMQLYDFTVLFPVVFGSLSCIVIFALVRVIA 94 
                 68*******************.....88888999999*****6666.5666667.56666666666668****************************** PP

                 -CCCHHHHHHHCCC-CCCCCTTSTT--STCCCCHHHHHHHHHHHHHHHHCCSTTCHHH..HHHHHHHHHHHTTSCCGGHHHHCCHHHHHHHHHCTTTS- CS
        STT3 127 sdiaGllAAlllaiaPgYlsrtvaGfyDtdmfeivlllfvlffflkaiktksnkisla..viaaliiflivlaWggyailiyallllfilalLiigrfe 223
                 +  aGl++All +++   + r   G++  + + i+l +++l+f+l +i++k+ ki+      a++++ l  +aWgg   ++++ + +f++ l  +    
  EPA05197.1  95 GTSAGLFSALLFSVSLPMILRGTIGWFKSEPLGIFLGILALYFLLSGINSKNHKIAIIklISAGIVLPLSLSAWGGS-QFFIIPIGIFFFTLPFFRTDH 192
                 **************99999*********************************887765115689************8.899999999999998888889 PP

                 CCHHHHHHHHHHHHHHH..CCCCCCCTTCHHHSTTTCHHCCCCHHHHHHHHCCCHHC..CCCCCHHCC.CHHTT.HHHHTT--GGGHHHHHHHHHHHHC CS
        STT3 224 lklkiavtfsviiaflviaiivllflgfqvvavseiigalgifgllqlvafgsvvvlvaelkfyqfis.lfqpgilsevlgligevvtalavlglialw 321
                 +++ +a+ ++++++fl     +l+f  ++    ++++g+ + +++++l+    + +     + ++++  lf    + +++ +i   ++ +++l l+++ 
  EPA05197.1 193 KFIVWAIPLFTVMVFLI----SLNFERLSLGFLFGLGGVSLLVPTIFLISCIFIQRK--SSENKKTRNgLFFLISIMIIGTVILIINANSEFLELPSYR 285
                 99999996666666666....455555554345788888888888887766666655..3344444446544444888888888889999999999987 PP

                 CCCCCTS-----TTHHHHHHHHHS---S--CCHHHCCSSSTTTTCCCHHHCHHCCHHCTCHHHHHHH.........HHHHHHCCC-SCHCCCCCHHHHH CS
        STT3 322 lgilyslldleyaklkikiiilvsvwlpvgllaltkglrfliftvPlgiifvgllleflavfvkiys.........vsqilfsgvvvillmltllpvla 411
                     ++ ++   +  +i+++ +v+++  ++++  +    +l+  + lgi++++++ + + + +++           +  i++s + v+l+++  l+ ++
  EPA05197.1 286 Y---LNAIN-PFLTTSIPLVDSVAEHASTTISQSFYFHSILMIFAGLGIWLIIKNNKTKESSFIKNDmlsftliigLIGIYVSSAFVRLEVFASLSLII 380
                 6...33332.45789************9999877766666677788999*****9999999999988899****9999999999999988887666555 PP

                 HHCC...CHHHHHHHHCCHHHHHHHHHHHHHH.....................................HHHHCT.TTTTHHH.TTHHHCHHHHHHHHH CS
        STT3 412 llaa...vkiskifstykdekeakikvaakav.....................................aptksnglkeslew.kantnrdsvvitwwd 469
                 l+++   + i++i+++ + +k +++++  k+                                       p+  + + e +ew k+nt++d+vv +wwd
  EPA05197.1 381 LSSIglsLLIKEIVKNTEYKKMKNLII--KSSflagiiilliipitfptsgnwvsaakapptilnggssYPVSTDDWLETMEWiKNNTPKDAVVASWWD 477
                 554322245566666555555555554..3334567889999999999999999999999*************************************** PP

                 HHHHHHHHHHHHHHHH CS
        STT3 470 yghilaveadrpVtfd 485
                 yg+ + +  +r +++d
  EPA05197.1 478 YGYWISTLGERATIAD 493
                 ****999999988877 PP

>> Dpy19  Q-cell neuroblast polarisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -7.9  16.1         2   1.8e+04     109     314 ..      70     271 ..      18     290 .. 0.55
   2 !   17.7   0.3   9.3e-08   0.00083     408     525 ..     336     474 ..     316     479 .. 0.72

  Alignments for each domain:
  == domain 1  score: -7.9 bits;  conditional E-value: 2
       Dpy19 109 FYvevVfllqgvtvlvLflystllsesvlgGllavllflfnhsevtrveftppLREnFalPflllqmllltiilkrkikeqkkslsellkiillslstv 207
                 F v + ++ ++++ +v+f +  +++++  +Gl ++llf +    + r        E  +   ++l +l+l+++l+   +++++++  ++k+i   ++  
  EPA05197.1  70 FTVLFPVVFGSLSCIVIFALVRVIAGT-SAGLFSALLFSVSLPMILRGTIGWFKSEPLG---IFLGILALYFLLSGI-NSKNHKI-AIIKLISAGIVLP 162
                 555555555566666666666666655.3555555555555555555444444434333...577788888888874.4445563.5667777777888 PP

       Dpy19 208 lflltWqFsqFvlltqilslfaldllglipteklal.illihllslllafvlqfgnsmlllsl..llsvllslllilvlqrkvkskrlllklillllkl 303
                 l l  W  sqF ++   + +f+l +++ ++++ + + i l+ ++ +l++  ++  +  +l+ l  +  ++ +++li ++  + ks ++    + l++ +
  EPA05197.1 163 LSLSAWGGSQFFIIPIGIFFFTLPFFR-TDHKFIVWaIPLFTVMVFLISLNFERLSLGFLFGLggVSLLVPTIFLISCIFIQRKSSENKKTRNGLFFLI 260
                 8999*******9999999999999999.44443333244444444444444444444445544112223335555555554444444333333333333 PP

       Dpy19 304 llsialtlilk 314
                  ++i++t+il 
  EPA05197.1 261 SIMIIGTVILI 271
                 33333333332 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 9.3e-08
       Dpy19 408 eskkeedrfkerpevvYhllqllvftllallimrLklLwtphlcviaslvlskklfkfllk..................kifisavlavlllsmsvkgv 488
                 ++k +e++f ++  + ++l+  l+ + ++ ++ rL ++++  l +++s++ls  + +++++                   i+  ++++++  s ++  +
  EPA05197.1 336 NNKTKESSFIKNDMLSFTLIIGLIGIYVSSAFVRLEVFASLSLIILSSIGLSLLIKEIVKNteykkmknliikssflagIIILLIIPITFPTSGNWVSA 434
                 5567777888999999999999999**************************877755555555666666555555543333333333333333333333 PP

       Dpy19 489 pnleee..lselrefsnpdt.eeLleWIksntekdavfaG 525
                  +      +   ++  ++d+  e +eWIk+nt+kdav a+
  EPA05197.1 435 AKAPPTilNGGSSYPVSTDDwLETMEWIKNNTPKDAVVAS 474
                 33322211233457778899999**************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (668 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1089  (0.0607396); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.71u 0.32s 00:00:01.03 Elapsed: 00:00:00.47
# Mc/sec: 4260.13
//
Query:       EPA05198.1  [L=265]
Description: S1 RNA binding domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-18   67.3   0.6    1.1e-18   67.3   0.6    1.9  2  EIF_2_alpha  Eukaryotic translation initiation factor 2 alpha
    1.6e-12   47.6   0.2    8.3e-12   45.3   0.1    2.2  2  S1           S1 RNA binding domain
  ------ inclusion threshold ------
      0.023   15.3   0.2      0.079   13.6   0.1    2.1  2  EXOSC1       Exosome component EXOSC1/CSL4


Domain annotation for each model (and alignments):
>> EIF_2_alpha  Eukaryotic translation initiation factor 2 alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.3   0.6   1.9e-22   1.1e-18       5     115 ..     124     226 ..     121     227 .. 0.90
   2 ?   -2.5   0.2      0.88   5.2e+03      47      63 ..     230     246 ..     228     249 .. 0.80

  Alignments for each domain:
  == domain 1  score: 67.3 bits;  conditional E-value: 1.9e-22
                  THHHHTTTTS-HHHHH.HHHHSTTHHHHHTTS-TTTHHHHHHCTHHHHHHT-EEEEEEEEEEE-STTHHHHHHHHHHHHST.S..TTSSSEEEEEEEE CS
  EIF_2_alpha   5 vgwklyekyghaydaF.klaitdeevldkleipeeveeaLveiikkklkpqkvkiradieltcftkdGveaIkeaLkageeasneeeveeeeevkikl 101
                  +   +y k++++ydaF ++  ++ e +++l+ip++++ ++ e+i  k+k + v+ir+ +e+t  ++dGve Ik+aL  +        ++++ +++i++
   EPA05198.1 124 LEDMIYSKFDSVYDAFiEIGRNGIESIKELKIPKKTATVI-EEICSKIKLPSVEIRGIMEITNNKSDGVEIIKKALLDA--------TKKDPTIDITY 212
                  566799***************************9998776.667778******************************33........345699***** PP

                  SSSSEEEEEEEES. CS
  EIF_2_alpha 102 iapPeYvltvetld 115
                   ++P+Y+l+++++d
   EPA05198.1 213 LGAPKYRLSITSED 226
                  **********9987 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.88
                  THHHHHHT-EEEEEEEE CS
  EIF_2_alpha  47 ikkklkpqkvkiradie 63 
                  ++k lkp  v+i+  ie
   EPA05198.1 230 AEKTLKPILVEIQESIE 246
                  67889999999998887 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   0.1   1.4e-15   8.3e-12       2      75 .]       9      83 ..       8      83 .. 0.97
   2 ?   -1.2   0.0      0.43   2.6e+03      19      29 ..     137     148 ..     133     154 .. 0.85

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 1.4e-15
                STTTCEEEEEEEEEETTEEEEEET..TTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTTEEEEEEC CS
          S1  2 pekgevveGeVtsvtkgGafVelg..ngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrrriilsik 75
                pe ge+v +++t+v+++Ga+V l+  ng++gf+++se++    +++ ++ +k G++  + v kv+ dr+ i+ls+k
  EPA05198.1  9 PEQGEIVLATITKVMDHGAYVTLDeyNGIQGFLHISEIAPG-WIRSVSRFVKDGEKKVLLVKKVNQDRGDIDLSLK 83
                789************************************99.9*******************************86 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.43
                 EEEEEET.TTEE CS
          S1  19 GafVelg.ngve 29 
                  af+e+g ng+e
  EPA05198.1 137 DAFIEIGrNGIE 148
                 69*****99987 PP

>> EXOSC1  Exosome component EXOSC1/CSL4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   1.3e-05     0.079       1      74 [.       8      83 ..       8     130 .. 0.76
   2 ?   -1.6   0.0      0.66     4e+03      37      50 ..     181     194 ..     145     238 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.3e-05
                -S-TT-EEEEEEEEEESSEEEEEEEEECTBSBCCCEEECCCTTSS--STS.TTSSCCHCTE.EETTS...STTTT.SEE CS
      EXOSC1  1 lPkegdvVLarvtrlrkkqalveilsvegennvlsdsgvgangegavkei.eagggldsll.svatv...ssdlgetfk 74
                +P++g++VLa +t++  + a+v +      n + + +++++   g ++++ + + ++++++  v++v     d+++++k
  EPA05198.1  8 MPEQGEIVLATITKVMDHGAYVTLDEY---NGIQGFLHISEIAPGWIRSVsRFVKDGEKKVlLVKKVnqdRGDIDLSLK 83
                6********************998777...5567888888888888888876665555544044444444555566665 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.66
                 EECCCTTSS--STS CS
      EXOSC1  37 sgvgangegavkei 50 
                 + + +n++  v+ i
  EPA05198.1 181 MEITNNKSDGVEII 194
                 34444444444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1794  (0.100061); expected 358.6 (0.02)
Passed bias filter:                      633  (0.0353059); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 1741.78
//
Query:       EPA05199.1  [L=176]
Description: cob(I)yrinic acid a,c-diamide adenosyltransferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.8e-60  203.5   0.4    3.1e-60  203.3   0.4    1.0  1  CobA_CobO_BtuR  ATP:corrinoid adenosyltransferase BtuR/CobO/C
     0.0077   16.3   0.4      0.012   15.6   0.1    1.5  2  AAA_14          AAA domain


Domain annotation for each model (and alignments):
>> CobA_CobO_BtuR  ATP:corrinoid adenosyltransferase BtuR/CobO/CobP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  203.3   0.4   3.5e-64   3.1e-60       2     172 .]       3     176 .]       2     176 .] 0.97

  Alignments for each domain:
  == domain 1  score: 203.3 bits;  conditional E-value: 3.5e-64
  CobA_CobO_BtuR   2 kglihvytGdGKGKttAAlGlalRalgaglkvlvvqFlKgekesgElaalkkl..eielerlgkegfv..kmeeeekeedaaaakealekakeal 92 
                      gl +vytG+GKGKttAAlG++lRa+g  +kv+++qF+Kg++++gE  + k+l  e+e++ +g +gfv    +++ k e+++ a ea++  +e++
      EPA05199.1   3 DGLTIVYTGKGKGKTTAALGIVLRATGYAKKVCMIQFIKGSWHYGEMYSSKRLepEFEMVAIG-KGFVgiIDDKSPKVEHERIAVEAIKISTEKI 96 
                     5899*************************************************766*******.9***9877788899***************** PP

  CobA_CobO_BtuR  93 aseeydlvvlDEinyalklglldeeevlellkkkpeklelvlTGrnapeelleaADlvtemkkvkHpydkgikarkGiey 172
                     +s++yd+v+lDEinya++lgl+++e+v++l+k+kp+kl+l+lTG +a+++++e+ADlvtemk++kHp+++gika+kGi++
      EPA05199.1  97 HSGKYDIVILDEINYAINLGLVKIEDVINLIKTKPPKLDLILTGNYAKDKIIELADLVTEMKEIKHPFQRGIKAKKGIDF 176
                     ******************************************************************************98 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.53   4.7e+03      14      23 ..      15      24 ..       8      53 .. 0.71
   2 !   15.6   0.1   1.4e-06     0.012      51     112 ..      87     153 ..      66     164 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.53
      AAA_14 14 GKTtllkqli 23
                GKTt +  ++
  EPA05199.1 15 GKTTAALGIV 24
                8888776554 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 1.4e-06
      AAA_14  51 kllelileklkeekktylflDEiqev.....pewekalkslvdegknldvivtGSnskllskeiats 112
                 + +++  ek+++ k  +++lDEi ++      ++e++++ +  + ++ld+i+tG  +k++  e+a+ 
  EPA05199.1  87 EAIKISTEKIHSGKYDIVILDEINYAinlglVKIEDVINLIKTKPPKLDLILTGNYAKDKIIELADL 153
                 45566666665557778*********7777788999******************9999987776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1125.10
//
Query:       EPA05200.1  [L=77]
Description: hypothetical protein BG20_I2242 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       915  (0.0510346); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.31s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 489.85
//
Query:       EPA05201.1  [L=55]
Description: hypothetical protein BG20_I2245 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.43
# Mc/sec: 388.30
//
Query:       EPA05202.1  [L=40]
Description: hypothetical protein BG20_I2243 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       126  (0.00702772); expected 358.6 (0.02)
Passed bias filter:                       95  (0.00529868); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.44
# Mc/sec: 272.57
//
Query:       EPA05203.1  [L=259]
Description: hypothetical protein BG20_I2244 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.16   12.1   0.2       0.16   12.1   0.2    2.5  2  ETRAMP    Malarial early transcribed membrane protein (ETRAMP


Domain annotation for each model (and alignments):
>> ETRAMP  Malarial early transcribed membrane protein (ETRAMP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   8.8e-06      0.16      16      73 ..      45      99 ..      30     107 .. 0.74
   2 ?   -0.9   0.4     0.098   1.8e+03      61      76 ..     200     215 ..     197     220 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.8e-06
      ETRAMP 16 vnlltpeslcdevnkkkekakkaikkiddkiekkkkkkKliiistiatalallvasal 73
                   ++ +++ ++ +k+ ek++k+i+ i       kk++K  ii +i+ ++   +  ++
  EPA05203.1 45 FGAIIYGVNLYNKEKI-EKNEKDITTIIALCVSSKKSRKFFIITSIVYGVFFSL--VS 99
                3446777788888877.9**********9999999************9996555..44 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.098
      ETRAMP  61 iatalallvasalGlg 76 
                 ++t + + +++a+G+ 
  EPA05203.1 200 AGTFMSIFIGTASGIA 215
                 5688889999999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1100  (0.0613531); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1609.33
//
Query:       EPA05204.1  [L=364]
Description: cation transport protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-15   55.8  30.4    5.7e-09   35.0  10.2    3.2  2  TrkH      Cation transport protein
  ------ inclusion threshold ------
       0.01   15.8   4.6      0.012   15.6   2.6    2.1  2  DUF2723   Protein of unknown function (DUF2723)
          8    6.0   8.8        3.6    7.2   1.9    2.8  2  PIRT      Phosphoinositide-interacting protein family


Domain annotation for each model (and alignments):
>> TrkH  Cation transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4  12.7   3.1e-09   1.9e-05      62     243 ..       9     166 ..       2     182 .. 0.71
   2 !   35.0  10.2   9.5e-13   5.7e-09     304     491 ..     188     360 ..     176     363 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 3.1e-09
        TrkH  62 afldalfeavsgltttglsvivveeslprsgltlraqlqqiGglgvvvlaylsl.ptlgrgsaflylseaqkeelggkelrsl..selikil.vvyyvg 156
                 +f++a f++v g+tttg+s+i + e+lp+s +++r+++q +Gg++++ la + + p  ++           ++++g ++ rsl  +el  ++ +++++ 
  EPA05204.1   9 GFANAFFSSVAGFTTTGISLIHEPENLPQSFTFYRSFTQLVGGMSFIYLAIAAFyPESKI-----------QSMRGFISGRSLhmRELFGTItIIFLIY 96 
                 5899***************************************65555555444444443...........4444444444431133443330444444 PP

        TrkH 157 leilafvllvvliytakaysevvdstgvsplwwaffhsmSafnnlGfsltpnSlasfnknivillvaiifiilGnigFpillrviia 243
                 + i +f+++         +++        ++ + f   +Saf ++Gf  t+  l+ f+     +l+++  +i+G+  F+ ++++  +
  EPA05204.1  97 IVIFSFLFY--------LFGNL-------NIIDDFSLIVSAFATGGFLPTSTILNDFDW--QEKLIVMGAMIFGALPFTFHYSFVRK 166
                 445566666........23333.......7778899999********999999999998..67788888999*********998755 PP

  == domain 2  score: 35.0 bits;  conditional E-value: 9.5e-13
        TrkH 304 slvvksipkgsrvlkalFqsvstrta.GFsvvdlsnlhpaikvllvlmmyigglpgStaggIrrtnvyeefslgkyeieqekepkavskksidgkhler 401
                 +l++ s++  +  l ++F  vs++t+ G++++ + n +  i v+l++ m igg++ St ggI++ +++ +++  k +  ++++ +++s+k+ +++ +  
  EPA05204.1 188 TLLFMSLSNLD-PLSSAFYTVSASTTsGLNSQVMINFSGPIHVILIILMIIGGCGFSTSGGIKIFRLLQLRECKKIF--NKNHRSELSPKR-KKELIST 282
                 55555555333.355677777777777*****************************************998766553..333333467776.4455555 PP

        TrkH 402 qllvdlwslflvlliilileglklsdvqepdfsffdiLfevvSaygtvGLSlGaknaslsaqlttisklvlialmirGrlrglpvlldra 491
                  l++  +   + l+ i++ +   ++d      sf  ++ e +  ++t+GL +      +  +     k++ ++lmi+Gr++++ ++  ++
  EPA05204.1 283 ILIILAFPGTIFLTSIYLTT---IEDT-----SFENAFYEATGIITTAGLTSN----VINFDTDATIKVIVSVLMIIGRMEIIAIIYIFV 360
                 55566665444444445544...5555.....5889**************998....777777777899***************998887 PP

>> DUF2723  Protein of unknown function (DUF2723)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   2.6   1.9e-06     0.012      22      92 ..      92     163 ..      90     195 .. 0.86
   2 ?   -1.9   0.1      0.45   2.7e+03      58      87 ..     216     243 ..     176     247 .. 0.44

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.9e-06
     DUF2723  22 lflllgrlfslla.daekvalrvnllsalssaltilflfltitlllr.skakkiailgaglvgalafafsdtf 92 
                 +fl++  +fs+l+  +++    +  +s ++sa++   +  t t l + ++++k++++ga+++gal f+f  +f
  EPA05204.1  92 IFLIYIVIFSFLFyLFGN-LNIIDDFSLIVSAFATGGFLPTSTILNDfDWQEKLIVMGAMIFGALPFTFHYSF 163
                 588889999999955555.5568889***************999999**********************8776 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.45
     DUF2723  58 lfltitlllr.....skakkiailgaglvgalafa 87 
                          +     s   ++++++ +++g++ f+
  EPA05204.1 216 NS-------QvminfSGPIHVILIILMIIGGCGFS 243
                 22.......13333333444555556666666555 PP

>> PIRT  Phosphoinositide-interacting protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.6     0.021   1.2e+02      67     102 ..     205     240 ..     179     271 .. 0.65
   2 ?    7.2   1.9   0.00059       3.6      38      70 ..     272     323 ..     266     363 .. 0.67

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.021
        PIRT  67 ttlsrnstlknkdkevfklsGpaflslGlmllvcGl 102
                  t+s ++t+  +++ + ++sGp+ + l +++++ G 
  EPA05204.1 205 YTVSASTTSGLNSQVMINFSGPIHVILIILMIIGGC 240
                 35578888888999999*****99888777776443 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00059
        PIRT  38 gprskwdvykkpiivlsvGgavfllGvvittl...................s 70 
                 +p+ k ++    +i+l+  g++fl  + +tt+                    
  EPA05204.1 272 SPKRKKELISTILIILAFPGTIFLTSIYLTTIedtsfenafyeatgiittaG 323
                 5778888889999*******************66555555555555555441 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       809  (0.0451224); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.52
# Mc/sec: 2112.11
//
Query:       EPA05205.1  [L=46]
Description: hypothetical protein BG20_I2593 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 329.70
//
Query:       EPA05206.1  [L=147]
Description: copper binding protein, plastocyanin/azurin family, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.9e-10   40.5   0.1    4.5e-10   39.8   0.1    1.3  1  Copper-bind   Copper binding proteins, plastocyanin/azurin fa
    3.3e-06   27.2   1.1    0.00025   21.1   0.3    2.2  2  Cupredoxin_1  Cupredoxin-like domain
    8.5e-05   22.1   0.1    0.00013   21.5   0.1    1.3  1  SoxE          Sulfocyanin (SoxE) domain


Domain annotation for each model (and alignments):
>> Copper-bind  Copper binding proteins, plastocyanin/azurin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.8   0.1   7.6e-14   4.5e-10       5      99 .]      39     147 .]      36     147 .] 0.73

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 7.6e-14
                  EEETTETSEEESSEEEEETTEEEEEEEE.SSSSBEEEEETTSSTTTGGGTTSCTTC............EEEEBSTTEEEEEEEE..SSEEEEEEET.T CS
  Copper-bind   5 lgvesgdlqFetkeitvkkgekvtfvnl.avmgHNvvldkdgvpagvdkdkvkaed............etkliggGekdsvtfd..eagtYkffCs.P 86 
                  ++v+ ++l+F ++ei++++g + + + +  v  H +v+   + ++ vdk ++ +++            +   + +G++ +  +   ++g+Y   C  P
   EPA05206.1  39 VTVDATELKFVPSEIQINSGMTKFVMINnGVGEHELVVYDVSKKEIVDKAELAEDEetiakniifeidH---TPAGQTAESDVIdlKTGSYIIGCHiP 133
                  6899999*************9988765515566***999844444455555554444454455774334...478888877665466777******** PP

                  .TTTTTSEEEEEEE CS
  Copper-bind  87 .HaaagMkgkvtve 99 
                   H+ agMkg++t++
   EPA05206.1 134 gHYEAGMKGTLTIN 147
                  ***********985 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.3   4.2e-08   0.00025      20      74 ..      36      89 ..      21      99 .. 0.90
   2 !    5.2   0.0    0.0038        22      71     104 .]     109     146 ..      94     146 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 4.2e-08
  Cupredoxin_1 20 ektveitvkdggfePskievkagekvklkiknkdktpeefesedlgeekvlapgk 74
                   + v++ +++ +f Ps+i++++g  +k+ + n++   +e++++d+++++ +++ +
    EPA05206.1 36 VQIVTVDATELKFVPSEIQINSGM-TKFVMINNGVGEHELVVYDVSKKEIVDKAE 89
                  67899999999************9.**********************99998765 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0038
  Cupredoxin_1  71 apgktttitiaplkpGeYeftcdmhm...d.akGkliV 104
                   + g+t++ ++  lk G+Y + c +       +kG+l++
    EPA05206.1 109 PAGQTAESDVIDLKTGSYIIGCHIPGhyeAgMKGTLTI 146
                   57999999999***********9544333569999985 PP

>> SoxE  Sulfocyanin (SoxE) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.1   2.1e-08   0.00013      52     136 ..      63     144 ..      43     147 .] 0.76

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2.1e-08
        SoxE  52 klvneeslphnlvlvq.nntaiPnsleissdGkillivGattsnyavsGissGqsasGlledlsaGtywlacgilGhaesGmWvdl 136
                  ++n+   +h+lv+    + +i +++e+++d   +     ++  ++ +   +Gq+a+  + dl +G y++ c i+Gh e+Gm   l
  EPA05206.1  63 VMINNGVGEHELVVYDvSKKEIVDKAELAEDEETIA----KNIIFEIDHTPAGQTAESDVIDLKTGSYIIGCHIPGHYEAGMKGTL 144
                 455666667777776414567788888888877664....466788888999******99**********************7666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1070.41
//
Query:       EPA05207.1  [L=79]
Description: hypothetical protein BG20_I0193 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.3e-05   25.5   0.0    2.3e-05   24.6   0.0    1.4  1  PP-binding  Phosphopantetheine attachment site


Domain annotation for each model (and alignments):
>> PP-binding  Phosphopantetheine attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   1.3e-09   2.3e-05       2      67 .]       4      70 ..       3      70 .. 0.93

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.3e-09
  PP-binding  2 klrelvaevlgvpleeidpdtdlfdlG.lDSllavellaaleeefgveiplsdlfehptlaelaayl 67
                kl elv+++++vp +ei++d+   +    DS ++  ll+++e ef+++++l++ +  ++++++ ++l
  EPA05207.1  4 KLYELVSQIMHVPISEIKDDSGPQSIEtWDSFNLYLLLNEIENEFKIRFTLDESLSIKNVSDFKKHL 70
                7899*************99999999887************************999******998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 590.54
//
Query:       EPA05208.1  [L=583]
Description: putative flagellar protein FliS [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-06   28.0   0.3     0.0013   18.7   0.1    2.5  2  Acid_PPase      Acid Phosphatase
    3.7e-05   23.5   0.0     0.0001   22.1   0.0    1.8  1  NIF             NLI interacting factor-like phosphatase
  ------ inclusion threshold ------
      0.036   13.2   0.0       0.22   10.6   0.1    2.1  2  Methyltransf_3  O-methyltransferase


Domain annotation for each model (and alignments):
>> Acid_PPase  Acid Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.0    0.0011       6.3       4      15 ..     234     245 ..     232     254 .. 0.89
   2 !   18.7   0.1   2.1e-07    0.0013      51     141 ..     272     355 ..     266     373 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0011
                 SEEEE-STTTSS CS
  Acid_PPase   4 klivFDLDyTLW 15 
                 k iv+DLD TLW
  EPA05208.1 234 KCIVLDLDNTLW 245
                 78********** PP

  == domain 2  score: 18.7 bits;  conditional E-value: 2.1e-07
                 HHHHHHHHHTT--EEEEE--S-HHHHHHHHHHTT-G..........GGESEEEESSS-HHHHHHHHHHHH---GGGEEEEES-HHHHHHHH CS
  Acid_PPase  51 eeileelkskevklavaSrtdepdlarelLklleindakekekklldvfddveiykgsktkhfeklkkktgieyedmlfFDdesrnieves 141
                 ++ l +l+++++ la+ S+ ++pd a+++++              ++ f ++ i   +k++ ++ ++ + +i  ++m+fFDd   n+e  +
  EPA05208.1 272 QKRLLALQQRGIILAINSK-NNPDDAMQVIRNHPYM------ILRENHFASMRINWTDKVTNMKDIASELNIGLDSMVFFDDDPMNRELIH 355
                 5667778888999999888.5688888888876666......455678999***********************************99776 PP

>> NIF  NLI interacting factor-like phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   1.8e-08    0.0001       1     119 [.     234     353 ..     234     369 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.8e-08
         NIF   1 ktLVLDLDetLvhsklekskklkvegekvevsvlkR.....pgldefLkelsklyevvi.fTasseeyaeavidildpekkllshr....lyrescvkk 89 
                 k++VLDLD+tL+   +         ge+    +++        + ef+k+l  l + +i    +s+++ ++ ++++ ++  ++ ++     +r ++ ++
  EPA05208.1 234 KCIVLDLDNTLWGGIV---------GEDGYDGINLGptppgNAFVEFQKRLLALQQRGIiLAINSKNNPDDAMQVIRNHPYMILREnhfaSMRINW-TD 322
                 79**********8886.........44444444444333228999*****9999777665999*************99998766666655666666.56 PP

         NIF  90 kgeyvKdLsl.lgrdlsrvvivDdspdsfel 119
                 k   +Kd+   l+  l+++v++Dd+p++ el
  EPA05208.1 323 KVTNMKDIASeLNIGLDSMVFFDDDPMNREL 353
                 88999**9763788*************9887 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   3.8e-05      0.22     135     167 ..     220     252 ..     204     261 .. 0.86
   2 ?   -1.0   0.0      0.14   8.3e+02     135     156 ..     267     288 ..     263     293 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 3.8e-05
                     GHHHHHHHHHHTEEEEEEEEEE-TTGGGGGG-S CS
  Methyltransf_3 135 syvnyyeklleLvkvGgliaiDntLWeGkvvee 167
                     ++  y +  l L k+  ++ +DntLW G v e+
      EPA05208.1 220 DFLSYIKAFLGLSKKCIVLDLDNTLWGGIVGED 252
                     57889999*********************9887 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.14
                     GHHHHHHHHHHTEEEEEEEEEE CS
  Methyltransf_3 135 syvnyyeklleLvkvGgliaiD 156
                     ++v++ ++ll L ++G ++ai+
      EPA05208.1 267 AFVEFQKRLLALQQRGIILAIN 288
                     68899*************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (583 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       821  (0.0457917); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.71u 0.33s 00:00:01.04 Elapsed: 00:00:00.55
# Mc/sec: 3183.81
//
Query:       EPA05209.1  [L=367]
Description: putative membrane protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00033   20.0  30.7      0.035   13.3  18.1    3.2  2  Polysacc_synt_3  Polysaccharide biosynthesis protein
      0.003   17.0  48.7      0.072   12.5  32.6    3.4  2  Polysacc_synt    Polysaccharide biosynthesis protein
  ------ inclusion threshold ------
          4    7.5  47.7       0.23   11.5   6.8    3.8  4  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai


Domain annotation for each model (and alignments):
>> Polysacc_synt_3  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3  18.1   5.9e-06     0.035      82     228 ..      85     221 ..      13     235 .. 0.70
   2 !    8.4   4.5   0.00019       1.1      54     163 ..     246     356 ..     241     365 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.9e-06
  Polysacc_synt_3  82 vtvlrvlalvlilsglssvqeallrrelkFkklfkitlvssvvgvivaivlAllglgvwALvigtllssllslvllwlaskwrprlkfslkslk 175
                         + v         ++s+ +a +  +  Fk+ +kit++ ++++vi+ai l +l+ +   ++i  ++ s++ +++l++    + ++  ++k lk
       EPA05209.1  85 GASIHVF-----SYVIFSLITAEFLGRKFFKSYMKITIIQKLLMVILAIPLYYLLDSNG-III-GIALSFVPFIALYYKEFKTTKI--NFKILK 169
                      4444444.....44444555555555556**********************99998864.444.4788899998888766665555..888999 PP

  Polysacc_synt_3 176 elfsfglklllsnllnylarnldnlliGkvlssaaLGlYsvakrlaslpvaei 228
                         +f ++  l ++++++a+++d+++i  +++   LG Y+ ++++ ++++ +i
       EPA05209.1 170 GKKEFMINNYLLSFTRMFASSIDKIIIVPIFGFGILGNYALGMQFYMVLL-II 221
                      999*****************************************987765.44 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00019
  Polysacc_synt_3  54 nlvlgllialvlfllaplias.fy.nqpelvtvlrvlalvlilsglssvqeallrrelkFkklfkitlvssvvgvivaivlAllglgvwALvig 145
                      ++++++ ++++ ++l+p+i + ++ + +e+v ++++++l +i  ++++v  +++  +l+ k  + i+   ++v++i+++++   ++ v  ++  
       EPA05209.1 246 TILISVGLTVLGIVLSPVIIKwMFpKFEEAVIIVQIISLGIIPGTINLVYISKFLGNLQNKI-VLISSGIFLVSIILGMIVLGKLYDVHGIAAA 338
                      67888888888777777665446625699*****************************9875.5566677888888888888888888888888 PP

  Polysacc_synt_3 146 tllssllslvllwlaskw 163
                       +l+ +  +++l+++ k+
       EPA05209.1 339 FVLAGAAESIFLLISNKY 356
                      888888888888887776 PP

>> Polysacc_synt  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5  32.6   1.2e-05     0.072      15     265 ..       3     229 ..       1     231 [. 0.83
   2 !    7.9   8.2   0.00029       1.7      79     196 ..     245     362 ..     239     366 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.2e-05
  Polysacc_synt  15 tkllafvtlvylarilgpegfGlvalalaivtllviltdlGlnaalvreiakyrekkelvslillnvllvllvlvllfllllliaaflglpelavl 110
                      ++++++ +y+a ++g e +G  +++l+i+++ + +t lG+ ++l+ + ak ++   l  +i l ++ ++++ +++++++++    lg+++ ++ 
     EPA05209.1   3 PTIIGAIFWFYIASLIGVEKYGEITYYLTIAGIVSGITMLGTQNSLTVYAAKGEK---LLPVISLITFPISVIGAIVVFFTFFN---LGASIHVFS 92 
                    5699************************************************996...88888888888888888777777776...9******99 PP

  Polysacc_synt 111 ylilalmllllvgvasfrrglfqglermkyaavsqvveqlsrvilvliavflfldivaavlgavlaalvggivslavlrkkfrprfvils.lklvr 205
                    y+i++l+ +           ++ ++ +  y  ++ +++ l ++  ++i +++ ld  ++++g++l+ +     ++a+++k+f+ ++ +++ lk  +
     EPA05209.1  93 YVIFSLITA----------EFLGRKFFKSYMKITIIQKLLMVI--LAIPLYYLLDSNGIIIGIALSFV----PFIALYYKEFKTTKINFKiLKGKK 172
                    999999988..........888888888999999999888888..77777777776666666666554....457778888976666666689999 PP

  Polysacc_synt 206 ellsfsapltisslaillytyidsillglllgaeavGiYnaayqllvaisgllapivtaa 265
                    e++  +  l ++++   +   id i++  + g + +G+Y ++ q+++++ ++ + i + +
     EPA05209.1 173 EFMINNYLLSFTRM---FASSIDKIIIVPIFGFGILGNYALGMQFYMVLLIIPNIIYQYV 229
                    99987777666665...66799**************************999999988855 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00029
  Polysacc_synt  79 lnvllvllvlvllfllllliaa..flglpelavlylilalmllllvgvasfrrglfqglermkyaavsqvveqlsrvilvliavflfldivaavlg 172
                    l +l++++++vl ++l+++i    f   +e++++++i++l + + +++  +++ ++  l+ +k +++s+ +  +s++ l +i++   +d+ +++++
     EPA05209.1 245 LTILISVGLTVLGIVLSPVIIKwmFPKFEEAVIIVQIISLGIIPGTINLVYISKFLGNLQ-NKIVLISSGIFLVSII-LGMIVLGKLYDVHGIAAA 338
                    56789999************9997778888888888888888866666677777766666.6888888888666665.777777666768888887 PP

  Polysacc_synt 173 avlaalvggivslavlrkkf.rprf 196
                     vla  + +i +l+++ k++ +p++
     EPA05209.1 339 FVLAGAAESI-FLLISNKYYdKPKK 362
                    7777777755.55566667744544 PP

>> Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   5.9     0.095   5.7e+02      71     138 ..       8      81 ..       2      86 .. 0.48
   2 ?   11.3  14.3   4.5e-05      0.27       8     140 ..      89     221 ..      84     224 .. 0.79
   3 ?   -4.7   4.9         3   1.8e+04      88     101 ..     243     256 ..     199     276 .. 0.45
   4 ?   11.5   6.8   3.8e-05      0.23       2      74 ..     279     351 ..     278     360 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.095
  Polysacc_synt_C  71 vlnlyalrrllgiklellrrllkpllaalvmgivvyl.llllllglllla........al.alllavlvgalvYllll 138
                      ++ ++++  l+g+       ++ + +a++v gi +++  ++l++ +            +l ++ ++v +ga+v ++  
       EPA05209.1   8 AIFWFYIASLIGVEK-YGEITYYLTIAGIVSGITMLGtQNSLTVYAA--KgekllpviSLiTFPISV-IGAIVVFFTF 81 
                      555677777777777.2333334444444444442210233333333..234666555332444444.7777776655 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 4.5e-05
  Polysacc_synt_C   8 siiflslstvlssiLqglgrqkialkalvigalvklilnllliplfgivGaaiatvlallvvavlnlyalrr.llgikl.ellrrll..kplla 97 
                       ++ ++++++ ++ + g +  k ++k+++i  l+ +il ++l +l+  +G++i+++l+++  ++l +   +  ++++k+ +  + ++   +ll+
       EPA05209.1  89 HVFSYVIFSLITAEFLGRKFFKSYMKITIIQKLLMVILAIPLYYLLDSNGIIIGIALSFVPFIALYYKEFKTtKINFKIlKGKKEFMinNYLLS 182
                      55666677999999*********************************************99999987777765566666844555556788899 PP

  Polysacc_synt_C  98 alvmgivvylllllllgllllaalalllavlvgalvYllllll 140
                         m++    + ++++  +++  + +l   ++g+ +Y++ll++
       EPA05209.1 183 FTRMFAS--SIDKIIIVPIFG--FGILGNYALGMQFYMVLLII 221
                      9999988..244444433333..57888888999999999886 PP

  == domain 3  score: -4.7 bits;  conditional E-value: 3
  Polysacc_synt_C  88 lrrllkpllaalvm 101
                       + ++ + +   v+
       EPA05209.1 243 KKLTILISVGLTVL 256
                      22222222222222 PP

  == domain 4  score: 11.5 bits;  conditional E-value: 3.8e-05
  Polysacc_synt_C   2 LailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplfgivGaaiatvlallvvavlnl 74 
                      ++i++l+ii+ +++ v+ s + g  ++ki+l+++ i ++  ++  ++l  l+ + G+a+a vla ++ ++++l
       EPA05209.1 279 VQIISLGIIPGTINLVYISKFLGNLQNKIVLISSGIFLVSIILGMIVLGKLYDVHGIAAAFVLAGAAESIFLL 351
                      79***********************************999999999999**************9887776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       929  (0.0518155); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2251.38
//
Query:       EPA05210.1  [L=329]
Description: hypothetical protein BG20_I0180 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00021   21.6   0.0    0.00041   20.7   0.0    1.5  1  Glyco_trans_1_2  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   2.3e-08   0.00041       9      89 ..     236     320 ..     216     323 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.3e-08
  Glyco_trans_1_2   9 espnlrlfEaaacGafaltdda...egleelftpgkevilfedleelaekirylla..npeerraiaeaarervlaehtydhraeq 89 
                      + p+ r+ E++a+G++   + +    g    +++++++i+  ++++   k++++l+  +  ++ +ia+a+r+ +l+e++ d++ + 
       EPA05210.1 236 YFPTIRYWEVPAAGCLTFMEITeknNGRYLGYKDEETAIF-INEKNYKSKFEEYLEdiDNPKWLEIANAGRQYALSELNNDKATDS 320
                      56999**********9999955753333334667655555.588************888899**************9998877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       710  (0.0396006); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2424.74
//
Query:       EPA05211.1  [L=221]
Description: hypothetical protein BG20_I0220 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0002   21.3   0.1    0.00062   19.7   0.1    1.8  1  HTH_11    HTH domain
  ------ inclusion threshold ------
      0.025   14.4   0.0       0.14   12.0   0.0    2.1  2  HTH_30    PucR C-terminal helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1     7e-08   0.00062      16      42 ..       7      33 ..       4      40 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 7e-08
      HTH_11 16 isgeeLAeeLnvSrrtvrrdIkaLeel 42
                +s+ ++A eL+v r t+ +dIk L++ 
  EPA05211.1  7 FSAIKIASELEVNRNTINQDIKFLRSD 33
                78899*******************985 PP

>> HTH_30  PucR C-terminal helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.6e-05      0.14       7      31 ..       1      25 [.       1      30 [. 0.94
   2 ?   -0.7   0.0      0.15   1.3e+03      35      50 ..     140     155 ..     138     157 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.6e-05
                HHHHTTT-HHHHHHHHTS-HHHHHH CS
      HTH_30  7 aylenggnisatAkaLhvHrnTlry 31
                +y+e g+++ + A +L v rnT+++
  EPA05211.1  1 MYFEKGFSAIKIASELEVNRNTINQ 25
                59********************986 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.15
                 HHHHHHS--TTSHHHH CS
      HTH_30  35 rieellgldlddpddr 50 
                 +++el+++d + +   
  EPA05211.1 140 KARELFKCDYTHAKKI 155
                 899******9987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       936  (0.0522059); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1456.58
//
Query:       EPA05212.1  [L=336]
Description: putative bifunctional phosphoglucose/phosphomannose isomerase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-36  126.1   0.0    2.5e-36  125.0   0.0    1.5  2  bact-PGI_C  Bacterial phospho-glucose isomerase C-terminal SI
    2.1e-09   37.3   0.3    5.3e-09   36.0   0.1    1.8  2  SIS         SIS domain


Domain annotation for each model (and alignments):
>> bact-PGI_C  Bacterial phospho-glucose isomerase C-terminal SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0      0.73   6.6e+03      33      47 ..     104     118 ..      86     120 .. 0.65
   2 !  125.0   0.0   2.7e-40   2.5e-36       2     152 .]     191     335 ..     190     335 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.73
                 HHHHHHHTT----B- CS
  bact-PGI_C  33 fknqlnenAKipafa 47 
                 + + +++ +Ki+af+
  EPA05212.1 104 LDSAFKKKSKIIAFS 118
                 567788899999987 PP

  == domain 2  score: 125.0 bits;  conditional E-value: 2.7e-40
                 G-HHHHHHHHHTTSEEEEE-..TT-THHHHHHHHHHHHTT----B---.SSHHHHHHHTTSS-GGGGTTEEEEEESSHH........HHHHHHHHTTTS CS
  bact-PGI_C   2 knpakqlAlelagklpviygssellevaArRfknqlnenAKipafagvlpeanhneivgleaeeelkkrlrlvllrdeeehprvkkraeivkelaeerg 100
                 +np+  lA+++ g +p+iy     l+++A+Rfkn+l+enAKi+a+a+ + ea hn iv +    e+k++++ +ll+  ++  ++k+r +++++++++++
  EPA05212.1 191 NNPSLDLAEWITG-IPMIYY-PFGLQSVAIRFKNTLQENAKIHAIAEDVVEACHNGIVSW----EKKSNVKPILLQGADDYIKTKERWNVLEKYFKDNK 283
                 799**********.******.999************************************....89**********88889****************** PP

                 SEEEEE---SSSHHHHHHHHHHHHHHHHHHHHHHCT---S-TTTTHHHHH.. CS
  bact-PGI_C 101 vrvtevkaegesplerlaslillgDfvSvylAllrgvDPtpvpaIdelKeel 152
                 +++ +v+++++s l+++++li+l+D++++ylA+l + DP+pv++Id++K+++
  EPA05212.1 284 IDFRKVSSNKGSILSKIINLIYLLDYTTIYLAILSKTDPSPVSSIDYIKQRM 335
                 *************************************************986 PP

>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.1   5.9e-13   5.3e-09       6     122 ..      42     155 ..      38     164 .. 0.75
   2 ?   -1.9   0.0       0.3   2.7e+03      18      44 ..     215     241 ..     213     246 .. 0.77

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 5.9e-13
                 SEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHHTTSEEEEEESSTTSHHHHHSSEEEEE CS
         SIS   6 kriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelakergakiiaITdskgsplareadlalyi 104
                 ++i++ G+G s+ai++ ++  l + ++i+v v++ + l +     +d+++lvi +s sg+t++++a +  a +++ kiia+  s g  l   ++++++ 
  EPA05212.1  42 DHIVFAGMGGSGAIGDTFSSIL-SKTKIHVNVVKGYLLPTT----VDPNTLVITVSVSGNTAETLAILDSAFKKKSKIIAFS-SGGKMLEYCTKNKIEH 134
                 79********************.8889*********95555....***********************************98.3333333333444443 PP

                 EEECHC...SSSHCHHHHHHH CS
         SIS 105 naepet...lvastksltaql 122
                 + +p+     + +t+ l+++l
  EPA05212.1 135 ILVPQChspRASFTSYLYTML 155
                 333333345555555555555 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.3
                 HHHHHHHHHHHHHHTSEEEEEEHHHHH CS
         SIS  18 aiakelalkleeiggivvevedaselk 44 
                 ++a  ++ +l+e ++i++ +ed  e  
  EPA05212.1 215 SVAIRFKNTLQENAKIHAIAEDVVEAC 241
                 677788999999999999988877755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       892  (0.0497518); expected 358.6 (0.02)
Passed bias filter:                      585  (0.0326287); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 2032.05
//
Query:       EPA05213.1  [L=251]
Description: cytidylyltransferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-31  109.9   2.3      2e-31  109.6   2.3    1.0  1  CTP_transf_3  Cytidylyltransferase


Domain annotation for each model (and alignments):
>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.6   2.3   1.1e-35     2e-31       2     219 ..       6     234 ..       5     237 .. 0.88

  Alignments for each domain:
  == domain 1  score: 109.6 bits;  conditional E-value: 1.1e-35
                   EEEEE-SSSSSSTTGGGSEETT.EEHHHHHHHHHHHTTTTSEEEEEES-HHHHHH.HHHTT.SEEEE--TTCSSHHHHHHHHHHHHTTT.TTSEEEE CS
  CTP_transf_3   2 aIipARsgSkRlpgKnlldlgg.kpliayvleaalkskafekvivaTDseeiknv.akefg.asvlvtrsslesdterflevvkaflmseneeiivn 95 
                   +Ii+AR+gS+RlpgK+++++ + +  + yv+ +++ sk+++k++vaT++   ++v + ++  +++ ++r+s e++++r ++  k+f+++     iv+
    EPA05213.1   6 CIIQARMGSTRLPGKVMEKIDStNVVLNYVINQVKFSKKIKKIVVATTDLIEDDViCRNLSsQKIEFFRGSSEDVLDRYYQCAKKFSID----NIVR 98 
                   8*******************8835679********************999888862667779***************************....9*** PP

                   E-TT-TT--HHHHHHHHHHHHHSTTSSEEEEEE...ETTSHHHHTSTTSTEEEETTTSBEEEEESSESSEEHHHHHCTS.......TTTSEEEEEEE CS
  CTP_transf_3  96 lqGdnPllqeevikkaietlkenqedylstlvk...kvgkeeevlnandlkvllddagkalyfeesvipyireeplels.......rrlylshagiy 182
                   +++dnPl+++  i+ +i+++++n+ dy+s++     ++g e ev+++++l+ ++++a k+   +e+v+p+i++  +e+        ++l +++ +i+
    EPA05213.1  99 VTADNPLIDPNIIDLVIDEYENNKCDYVSNTLHrtyPYGTEVEVFSFKSLENAWKNA-KKPSEREHVTPFIYNPQNEFIlinkenqEDLSYLRYTID 194
                   **************************888775422289*******************.9999***************99899999989999999999 PP

                   EEEHHHHHHHHHHSHHHHH.SHHHHHT-TTHH..HHHTT- CS
  CTP_transf_3 183 tfrkeqplkelvidtptse.ilekiekleqlr..vllegk 219
                   + ++ + ++e  +  pt+   ++ i +l+ +r  +++ +k
    EPA05213.1 195 RIEDLKLVREIIKNIPTRPiLIQDIIELYKKRteIFEINK 234
                   9999888888877777777667778888666666777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       867  (0.0483574); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1692.11
//
Query:       EPA05214.1  [L=378]
Description: N-acetyl sugar amidotransferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.012   15.5   0.1      0.034   14.0   0.0    1.7  1  B3        B3 DNA binding domain
       0.21   11.5   0.8        4.7    7.2   0.0    3.0  3  Pox_TAA1  Poxvirus trans-activator protein A1 C-terminal


Domain annotation for each model (and alignments):
>> B3  B3 DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   3.8e-06     0.034      60      88 ..     193     221 ..     184     233 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.8e-06
                 EEEETTHHHHHHHTT--TTSEEEEEE-SC CS
          B3  60 yvltkGWkeFvkangLkegDfvvFeligd 88 
                   l++GWke+ +  g++e+D ++F+++++
  EPA05214.1 193 QTLSSGWKEYLEVEGVEEKDLYLFHYDRK 221
                 5699*********************9864 PP

>> Pox_TAA1  Poxvirus trans-activator protein A1 C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0   0.00053       4.7      39      60 ..      20      41 ..      17      43 .. 0.92
   2 ?   -1.1   0.0       0.2   1.8e+03       6      15 ..     115     124 ..     114     140 .. 0.83
   3 ?    0.8   0.1     0.052   4.6e+02      33      62 ..     315     344 ..     301     345 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00053
    Pox_TAA1 39 keGvYGscffkenkksiqisLr 60
                ++Gv G c+++++k+ i+  Lr
  EPA05214.1 20 ENGVCGACVWEKEKEKIDWDLR 41
                78****************9998 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.2
    Pox_TAA1   6 lvaLREePKi 15 
                 +++LR +PK+
  EPA05214.1 115 VISLRPNPKV 124
                 6899****98 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.052
    Pox_TAA1  33 InelrnkeGvYGscffkenkksiqisLrsl 62 
                 ++ +r+ +G   +++ k+  + i i L+s+
  EPA05214.1 315 LELVRKYDGKCSEVYIKKFCDYIGIDLKSF 344
                 56788999999999**************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2358.11
//
Query:       EPA05215.1  [L=320]
Description: NAD-binding protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-52  177.5   0.0    3.7e-52  177.2   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    2.3e-51  175.2   0.0    3.4e-51  174.6   0.0    1.2  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
      1e-21   77.4   0.1    8.5e-21   74.3   0.1    1.9  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    5.6e-20   71.5   0.1    7.6e-20   71.0   0.1    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    1.4e-17   63.8   0.0    1.8e-17   63.4   0.0    1.1  1  RmlD_sub_bind    RmlD substrate binding domain
    2.4e-08   33.4   0.0    3.6e-06   26.3   0.0    2.6  1  NAD_binding_4    Male sterility protein
    5.8e-06   25.9   0.0    0.00087   18.8   0.0    2.4  2  adh_short        short chain dehydrogenase
    6.4e-06   26.2   0.0    1.8e-05   24.7   0.0    1.7  2  NAD_binding_10   NAD(P)H-binding
    4.4e-05   23.2   0.1      9e-05   22.1   0.0    1.5  2  NmrA             NmrA-like family
    0.00034   20.6   0.0    0.00075   19.5   0.0    1.6  1  KR               KR domain
  ------ inclusion threshold ------
      0.076   12.9   0.0       0.12   12.2   0.0    1.3  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.2   0.0   2.3e-55   3.7e-52       1     241 []       8     242 ..       8     242 .. 0.96

  Alignments for each domain:
  == domain 1  score: 177.2 bits;  conditional E-value: 2.3e-55
                 EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.....EEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHHHSHHHHHHHHTHH CS
   Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl.....elveldltdrsalerlfkeeqpdavihlAavggvaassedpadfieknlqg 94 
                 +l+tG++GfiGs+l+++l +++++ i+ d+ s+++++++ + l     el+ +dl +++++  ++   ++ +v+h+Aa+  v++ +e+p+  +++n++ 
  EPA05215.1   8 VLITGGAGFIGSHLADRLVNNNINTIVYDNFSTGNKKNLVNCLkrtnfELIVGDLNNSKKISSILP--RIKTVFHIAAYPEVRTGFENPEIAFNENIKN 104
                 79*****************************888887776666999********************..9****************************** PP

                 HHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHH CS
   Epimerase  95 tlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklveayaaqyglnaiilrlfnlyGprngegevsrvipalirki 193
                 t+ lle +rk++vk+++f+sSs vYG+ +++p++e+   gpl p spY+ +Kla e l+ ay + yg++ iilr  n++G r    + ++vi  +i+k+
  EPA05215.1 105 TYLLLEQIRKSNVKKIVFASSSVVYGDAKKIPTSEEY--GPLLPISPYGGSKLACEGLISAYCHNYGIQGIILRFANVIGSR----SKHGVIWDFINKL 197
                 *******************************966666..7******************************************....9************ PP

                 HTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT-STTEEEEES CS
   Epimerase 194 legkqevtllgdgtalRdflyveDvaeaillvlehvdagdkgeiyniG 241
                 +++k+++ +lgdgt+   +++++D+++++l +++    +++ +++niG
  EPA05215.1 198 HQNKKKLEILGDGTQTKSYIHISDCVDGFLKAADS---KNPVDVFNIG 242
                 **********************************9...677789***9 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.6   0.0   2.1e-54   3.4e-51       1     330 [.       9     309 ..       9     311 .. 0.87

  Alignments for each domain:
  == domain 1  score: 174.6 bits;  conditional E-value: 2.1e-54
                    EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHTTSHH CS
  GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevynLAAqshVdvsfekPe 96 
                    LiTG+aGfiGs+la++L++++ + ++ + + s+ n +++ +  k      ++n++l+ gDl++s+++ ++l ++  ++v++ AA   V++ fe+Pe
     EPA05215.1   9 LITGGAGFIGSHLADRLVNNNINTIVYD-NFSTGNKKNLVNCLK------RTNFELIVGDLNNSKKISSILPRI--KTVFHIAAYPEVRTGFENPE 95 
                    9*******************99987654.445556666666553......469******************998..79****************** PP

                    HHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TT.S-----SHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TT CS
  GDP_Man_Dehyd  97 ytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEt.tpfyPrsPYaaaKlyadwivvnyreayglfavngilfnhesprrget 191
                      ++ n+  t+ LLe ir+ +++   ++++aS+s vYG+++++p +E+  p+ P sPY+ +Kl+++ ++ +y ++yg++ ++ ++ n  + r  ++
     EPA05215.1  96 IAFNENIKNTYLLLEQIRKSNVK---KIVFASSSVVYGDAKKIPTSEEyGPLLPISPYGGSKLACEGLISAYCHNYGIQGIILRFANVIGSRS-KH 187
                    *******************9985...8999**************865549*****************************************95.44 PP

                    SCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHHHHHHHHCSS-.--EEE-TT-EEECHHCHHCCHHCCCHHHHHH............T CS
  GDP_Man_Dehyd 192 fvtrkitravarialgkqevlylGnldakRdwghvkDyveamwlmlqqdkp.edyviatgethsvrefvelaflelgktiewegkgeeevgrakes 286
                         i +++ + +++k++  +lG++ +++++ h++D v+++ ++  +++p + ++i++++ +sv +++++ + ++  +         +v+ +++ 
     EPA05215.1 188 ---GVIWDFINKLHQNKKKLEILGDGTQTKSYIHISDCVDGFLKAADSKNPvDVFNIGNNDRTSVTDIANIVIDKMNLK---------NVKIITKG 271
                    ...569999***99999999999***********************999883558999999999999999888887754.........23333333 PP

                    TGGCCCEECGG--SS--SB--B-THHHHHHH----SS-HHHHHH CS
  GDP_Man_Dehyd 287 gkvvvevdpkyfrpgevdlllgdaskakeeLgWkpkvsfeelvr 330
                         ++d +   pg+v+++  d++k+k + gW+pk + ++ ++
     EPA05215.1 272 ----GTFDGRG-WPGDVKKMHLDIKKLK-RTGWEPKLNSNSAIK 309
                    ....3566555.5**************9.78*****99888776 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.3   0.1   5.2e-24   8.5e-21       1     251 [.       8     264 ..       8     275 .. 0.84

  Alignments for each domain:
  == domain 1  score: 74.3 bits;  conditional E-value: 5.2e-24
                      EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-SEEEE------HHHHH CS
  Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvdvvfhaAAlKhVPlve 94 
                      vl+tG++G iGs+l ++++++++++i+  + +  +  ++ + l    k  ++++e   ++gd++++++++++l   ++++vfh AA+ +V +  
       EPA05215.1   8 VLITGGAGFIGSHLADRLVNNNINTIVYDNFSTGNKKNLVNCL----K--RTNFE--LIVGDLNNSKKISSILP--RIKTVFHIAAYPEVRTGF 91 
                      89**********************9987777777777776666....2..34344..78***************..****************** PP

                      HSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEE.....G.GGSS.........--SHHHHHHHHHHHHHHHGGG--SSS--EEEEEEE-EETT CS
  Polysacc_synt_2  95 enpleaiktNvlgtenvieaaieagvkkvvliSt.....D.KAvn.........PtnvmGatKrlaekllqalakeseekktkfvvvRfGNVlg 173
                      enp  a++ N+  t  ++e   +++vkk+v+ S+     D K +          P++ +G +K+++e l+ a+ ++      + ++ Rf NV+g
       EPA05215.1  92 ENPEIAFNENIKNTYLLLEQIRKSNVKKIVFASSsvvygDaKKIPtseeygpllPISPYGGSKLACEGLISAYCHNY---GIQGIILRFANVIG 182
                      *******************************99733333233221233333344999***************99998...78999********* PP

                      GTT..SSHHHHHHHHHTT.SSEEE.S-TT-EEEEE-HHHHHHHHHHHHHH--SS-EEEE--.-EEEHHHHHHHH........ CS
  Polysacc_synt_2 174 SrG..SviplFkkqikeg.gpvtv.TdpemtRyfmtieeavqLvlqalalakggeifvldmGepvkivdlakalielsglee 251
                      Sr    vi  F ++++++ +++ +  d + t+ ++ i++ v+  l+a+   +  ++f     + ++++d+a+ +i+ ++l++
       EPA05215.1 183 SRSkhGVIWDFINKLHQNkKKLEIlGDGTQTKSYIHISDCVDGFLKAADSKNPVDVFNIGNNDRTSVTDIANIVIDKMNLKN 264
                      985335888888887776588987368999***************************999999***********98887654 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.0   0.1   4.7e-23   7.6e-20       1     221 [.       9     222 ..       9     233 .. 0.85

  Alignments for each domain:
  == domain 1  score: 71.0 bits;  conditional E-value: 4.7e-23
   3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkk..viegDvtdkdkleealegvdvvihlaslvdvag.kltedeimkvnvkGT 96 
                 ++tGgaGF+G++l  +Lv+ + + +  v+D     ++++ ++ +++++  +i gD+++ +k++  l  ++ v+h+a++ +v+    + +   + n+k T
  EPA05215.1   9 LITGGAGFIGSHLADRLVNNN-I-NTIVYDNFSTGNKKNLVNCLKRTNfeLIVGDLNNSKKISSILPRIKTVFHIAAYPEVRTgFENPEIAFNENIKNT 105
                 69****************998.4.555999777777767777777776779******************************984666777789****** PP

   3Beta_HSD  97 rnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKalaEklvlkaNgrtlknggrlyTcaLRpagiyGegdk..llvpll 193
                   +le  +k++v+++v+ Ss  v g+   +++i  ++E  + + l+ ++y  sK   E l+ +       n   +  + LR a + G ++k  ++  ++
  EPA05215.1 106 YLLLEQIRKSNVKKIVFASSSVVYGD---AKKIPTSEE--YGPLLPISPYGGSKLACEGLISAYCH----NY-GIQGIILRFANVIGSRSKhgVIWDFI 194
                 ********************999999...888885555..5677899**************88766....33.47889*********9998335779** PP

   3Beta_HSD 194 kqlaklglalfkigdeevlsdrvYvgNv 221
                 ++l +++++l  +gd  ++++++     
  EPA05215.1 195 NKLHQNKKKLEILGDGTQTKSYIHISDC 222
                 ****************999999887665 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.4   0.0   1.1e-20   1.8e-17       3     239 ..       8     266 ..       6     309 .. 0.85

  Alignments for each domain:
  == domain 1  score: 63.4 bits;  conditional E-value: 1.1e-20
                    EEEESTTSHHHHHHHHHCTTTSEEEEEE-TT....................T--TTSHHHHHHHHHHH--SEEEE------HHHHHHSHHHHHHHH CS
  RmlD_sub_bind   3 ilvtGanGqlGseLakqlaeeglevlaltre....................eldltdaeavaellkeakpdvvvnaAAytavDkaEseeeaayavn 78 
                    +l+tG+ G +Gs+La++l +++++++  ++                       dl++++++ ++l  +k   v + AAy +v    +++e a++ n
     EPA05215.1   8 VLITGGAGFIGSHLADRLVNNNINTIVYDNFstgnkknlvnclkrtnfeliVGDLNNSKKISSILPRIKT--VFHIAAYPEVRTGFENPEIAFNEN 101
                    8************************99976678999************999899**********998665..************************ PP

                    THHHHHHHHHHHHCT-.EEEEEEEGGGS-S-TTS-.B-TTS----SSHHHHHHHHHHHHHHHH-SSE....EEEEE-SEESS.SSS-HHH.HHHHH CS
  RmlD_sub_bind  79 aeavealAeaaaavga.lLihvStDyVFdGekkrp.YeeddetsPlnvYGrtKlaGEqavlaagkka....livRtswvyge.kgknfvk.tmlrl 166
                     + +  l e+ ++ ++ ++++ S+  V+  +kk p  ee  +  P++ YG +Kla E  + a+++++    +i+R++ v g+ +++  +   + +l
     EPA05215.1 102 IKNTYLLLEQIRKSNVkKIVFASSSVVYGDAKKIPtSEEYGPLLPISPYGGSKLACEGLISAYCHNYgiqgIILRFANVIGSrSKHGVIWdFINKL 197
                    *************998459999**9999888777757778899*******************77654333399*******8834555555155566 PP

                    HHH-SEEEEESS-EE--EEHHHHHHHHHHHHHHCHH.GGG-EEEE---BS-EEHHHHHHHHHHHHCHTTSEEE CS
  RmlD_sub_bind 167 akereelkvvaDqlgsPTsardlAevllqllekaaeekelagvyHlanegetswlefArailkeagadseevk 239
                     +++++l++  D + + ++   +++++   l++a + k+   v+ ++n++ ts  ++A+ ++++++ ++  vk
     EPA05215.1 198 HQNKKKLEILGDGTQTKSYI-HISDCVDGFLKAADS-KNPVDVFNIGNNDRTSVTDIANIVIDKMNLKN--VK 266
                    69999*******77665554.577777777766664.6679***********************99965..43 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   2.2e-09   3.6e-06       1     215 [.      10     190 ..      10     199 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 2.2e-09
                    EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSHHHHHHHHHHHT-SS-HHHHHHHHHTTTEEEEE--TTSGGGG--HHHHHHHHHH--EEEE--S CS
  NAD_binding_4   1 lTGaTGFLGkvLlekLLrttpevkiyllvRaksgesaeeRleeelekkelfsallkelaerikvveGDlseprlGLseedlqelaeevdviihsaA 96 
                    +TG+ GF+G++L  +L++++ + +i+            + + ++  kk+l + l+   + + + ++GDl++++      ++  +  +++ ++h+aA
     EPA05215.1  10 ITGGAGFIGSHLADRLVNNNIN-TIV-----------YDNF-STGNKKNLVNCLK---RTNFELIVGDLNNSK------KISSILPRIKTVFHIAA 83 
                    8****************99876.332...........2334.5556666777776...889999******876......9**************** PP

                    S-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H......HHH--EEEETTTCCCHHHHHHHHHHHHHHH CS
  NAD_binding_4  97 tvnfdepyke...llrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegekeekldederaklkglpntYeqsKalaEklvre 189
                      ++    ++   +++ N++ t  +le  +k + +  +++ S+++v+g+ + ++               + e+         Y  sK + E l+ +
     EPA05215.1  84 YPEVRTGFENpeiAFNENIKNTYLLLEQIRKSNVK-KIVFASSSVVYGDAK-KI--------------PTSEEYGPLLPISPYGGSKLACEGLISA 163
                    88777655553338888888888888888877666.9*************9.44..............44555555556679************** PP

                    HHHHH---EEEEEE-EEE-.-SSST-- CS
  NAD_binding_4 190 arrrsglpvvivRpsiitg.esktGwi 215
                    + ++ g++ +i+R  +++g +sk G+i
     EPA05215.1 164 YCHNYGIQGIILRFANVIGsRSKHGVI 190
                    ***************999967777876 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   5.4e-07   0.00087       1      72 [.       6      76 ..       6      80 .. 0.83
   2 ?    4.6   0.0     0.012        20     146     172 ..     147     173 ..     137     181 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 5.4e-07
                SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHH CS
   adh_short  1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekav 72
                k vl+tG+++ IG  +a++l++++++++v+d+ +   ++ + ++ + ++++  i +D++++++++ ++ +++
  EPA05215.1  6 KSVLITGGAGFIGSHLADRLVNNNINTIVYDNFSTGNKKNLVNCLK-RTNFELIVGDLNNSKKISSILPRIK 76
                679**************************99877766655555554.47899*******9999998877665 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.012
                 BHHHHHHHHHHHHHHHHHHHHHGGGTE CS
   adh_short 146 vaaYsAsKaavagltrslakelaptgi 172
                  ++Y+ sK a +gl+++  + +  +gi
  EPA05215.1 147 ISPYGGSKLACEGLISAYCHNYGIQGI 173
                 689*****************9999887 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   1.1e-08   1.8e-05       1     106 [.      12     133 ..      12     179 .. 0.77
   2 ?   -1.5   0.0       1.2   1.9e+03      65      91 ..     238     266 ..     219     311 .. 0.71

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.1e-08
                     TTTSHHHHHHHHHHHHC-T-EEEEEETT.....HHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC.....HHHH........ CS
  NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRn.....peklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggk.....deeg........ 77 
                     G+ G +G++l+++l++++ ++ t++  n     ++ l +  ++ + e+++gd+++++++ + l  + +V+  ++  +      +           
      EPA05215.1  12 GGAGFIGSHLADRLVNNN-IN-TIVYDNfstgnKKNLVNCLKRTNFELIVGDLNNSKKISSILPRIKTVFHIAAYPEVrtgfeN--Peiafneni 102
                     99***************5.77.455555333336666666689**************************998844444333331..133455555 PP

                     ..HHHHHHHHHHCT--EEEEEEETTTTSGCG CS
  NAD_binding_10  78 ..aknivdaakeagvkRfvlvsaigvgdevp 106
                       +  +++  ++++vk++v+ s+  v+ +++
      EPA05215.1 103 knTYLLLEQIRKSNVKKIVFASSSVVYGDAK 133
                     778888*****************99986544 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.2
                     EES---TCC..HHHHHHHHHHHHHHCT-- CS
  NAD_binding_10  65 vsalggggk..deegaknivdaakeagvk 91 
                     v+++g++++   +++a+ ++d ++ ++vk
      EPA05215.1 238 VFNIGNNDRtsVTDIANIVIDKMNLKNVK 266
                     45555555434555577788888888885 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   5.5e-08     9e-05       1     101 [.       8     124 ..       8     142 .. 0.86
   2 ?   -2.7   0.0       2.2   3.6e+03     161     197 ..     198     233 ..     191     263 .. 0.56

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 5.5e-08
                 EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S.....-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEEEE---GG.............S-HHHH CS
        NmrA   1 IlviGaTGrqGksvvrallkaghkvralvRdt.....kselakslkeaGvelvkgdlddkeslvealkgvdvvfsvtgfy.............skeied 81 
                 +l++G++G +G+++++ l++++ ++  +v d      k++l++ lk    el+ gdl++ + ++++l   ++vf   ++              +++i+ 
  EPA05215.1   8 VLITGGAGFIGSHLADRLVNNNINT--IVYDNfstgnKKNLVNCLKRTNFELIVGDLNNSKKISSILPRIKTVFHIAAYPevrtgfenpeiafNENIKN 104
                 79****************9877665..6667778999*************************************9998657888888888888888888 PP

                 HHHHHHHHHHHS-SEEEEEE CS
        NmrA  82 gkklvdAakeaGvkhfiySs 101
                    l + + +  vk+++++s
  EPA05215.1 105 TYLLLEQIRKSNVKKIVFAS 124
                 88888888888888888876 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.2
                 -TTS.-EEEEESS-TTS-EE-HHHHHHHHHHHHHHHH CS
        NmrA 161 appedkvtllgpgnpkavlldaeeDiGafvikilkdp 197
                 +++++k+++lg+g     ++ +  D     +k+++ +
  EPA05215.1 198 HQNKKKLEILGDGTQTKSYI-HISDCVDGFLKAADSK 233
                 55556777777776555555.5555555555555444 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   4.6e-07   0.00075       3     136 ..       8     125 ..       6     136 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 4.6e-07
                 EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS---EEEE---------TTT-- CS
          KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppikGvihaAgvlrdklleemt 101
                 +litGG+G +G +la+ l+++  +++v+   s   + ++k+l++ l++  ++ e++  D+ ++++++++l +i       k v+h A   + +    + 
  EPA05215.1   8 VLITGGAGFIGSHLADRLVNNNINTIVYDNFS---TGNKKNLVNCLKR--TNFELIVGDLNNSKKISSILPRI-------KTVFHIAAYPEVR----TG 90 
                 79*************************98888...4566679999998..67888999999999998888655.......5677777665533....34 PP

                 HHHHHHHHTTTTHHHHHHHHHTTTS--SEEEEEEE CS
          KR 102 aedleqvlapKvkGawnLhelledesldffvlfSS 136
                  e+ e +++  +k +  L e +++++++ +v+ SS
  EPA05215.1  91 FENPEIAFNENIKNTYLLLEQIRKSNVKKIVFASS 125
                 44444445555555666666666666665555544 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   7.5e-05      0.12       6     114 ..      13     126 ..       8     130 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.5e-05
                 --SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHH.CCTTTTSS-HHHHCCCHHCEEEES-HHHHHC-SEEEE....-S-SSHHHHHHHHHH CS
     3HCDH_N   6 GaGtmGagiaavfasagleVvlvdiseealekalekieksle.klvekgklkeeeveaalarisfttdleeavdadlviE....avvEnlelKrkvfae 99 
                 GaG +G+ +a  ++++++++ ++d  +   +k l ++ k+++ +l+     + ++++++l ri++  +++++ ++   +E    a  En++    ++++
  EPA05215.1  13 GAGFIGSHLADRLVNNNINTIVYDNFSTGNKKNLVNCLKRTNfELIVGDLNNSKKISSILPRIKTVFHIAAYPEVRTGFEnpeiAFNENIKNTYLLLEQ 111
                 9***********************977766666666655444034444444578999************999999999994433345555555567888 PP

                 HHCCS-TTSEEEE-- CS
     3HCDH_N 100 lekiakpdailasnT 114
                 + k   ++ ++as++
  EPA05215.1 112 IRKSNVKKIVFASSS 126
                 888888888888864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.57u 0.34s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 2003.64
//
Query:       EPA05216.1  [L=406]
Description: GMP synthase (glutamine-hydrolyzing), C-terminal domain protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-35  120.4   0.0    5.7e-35  119.3   0.0    1.6  1  GMP_synt_C     GMP synthase C terminal domain
    3.5e-15   56.3   0.0      6e-15   55.5   0.0    1.3  1  GATase         Glutamine amidotransferase class-I
    3.8e-12   45.8   0.1    4.8e-06   25.9   0.0    2.2  2  NAD_synthase   NAD synthase
    2.6e-06   27.1   0.0    0.00029   20.5   0.0    2.3  2  ThiI           Thiamine biosynthesis protein (ThiI)
     0.0001   21.2   0.0     0.0035   16.2   0.0    2.2  2  tRNA_Me_trans  tRNA methyl transferase
     0.0057   16.2   0.0       0.38   10.2   0.0    2.2  2  QueC           Queuosine biosynthesis protein QueC
  ------ inclusion threshold ------
      0.018   14.8   0.0      0.036   13.8   0.0    1.5  1  Peptidase_C26  Peptidase C26
       0.11   12.2   0.1       0.24   11.1   0.0    1.5  2  ATP_bind_3     PP-loop family


Domain annotation for each model (and alignments):
>> GMP_synt_C  GMP synthase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.3   0.0   2.5e-38   5.7e-35       2      91 ..     315     404 ..     314     405 .. 0.98

  Alignments for each domain:
  == domain 1  score: 119.3 bits;  conditional E-value: 2.5e-38
                 CCCTTT-GGGSSEEEEEEEEEEE----------EEEEEEEEE---------B----HHHHHHHHHHHHHHSTT---EEEE---TTTS-S- CS
  GMP_synt_C   2 elkkaglykkiwQafavllpvksvGvmgdkRtyeyvvalRaveseDamtadvaelpyevLekissrivnevkgvnrvvyditskPpatiE 91 
                 el +ag+y k+wQa+a++ + k+vGv gd+R+y+++v++R+v+s Damtad+++lp+e+Lekis+ri+nev++v+ v+y i+skPpatiE
  EPA05216.1 315 ELITAGFYGKVWQAYAAVGDDKAVGVVGDERKYGNIVMIRVVDSIDAMTADWTRLPHELLEKISNRITNEVEDVTWVTYAISSKPPATIE 404
                 77889************************************************************************************9 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.5   0.0   2.7e-18     6e-15     112     189 ..      11      84 ..       2      85 .. 0.90

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 2.7e-18
                 TCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEEEEEEETTTEEEESSBTTSTTSTTHHHHHHHHHHH CS
      GATase 112 tallyglknevierhrHryevnpkelepaglevtakseddeelmeiiekknpfvgvQFHPEststpegpellfnflik 189
                 ++ll+g +++v+++++H++e+++    p g++v++++e+  + ++i  +++ ++g+QFHPE+++t++g+e+l+nf++k
  EPA05216.1  11 ENLLSGIGKSVRAWMSHGDEAEQ---IPPGFKVIGHTESA-KAAAIASEEKSIYGIQFHPEVVHTEQGTEILKNFVLK 84 
                 478999****************9...***********887.68888888888***********************987 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   2.2e-09   4.8e-06       6      82 ..      95     173 ..      92     196 .. 0.76
   2 !   17.7   0.0   6.5e-07    0.0015     148     177 ..     254     283 ..     241     286 .. 0.94

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 2.2e-09
                   HHHHHHHHHHCTT..SEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE---H CS
  NAD_synthase   6 vdflkeyvkkaga..kgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievktidik 82 
                   + f+ + v+k      +v+ G+SGG+DS+++a l  ka+g+ +    +  +    +e++e   ++ +n++++++ +d  
    EPA05216.1  95 EGFIDSAVEKISKieGNVLCGVSGGIDSTVAALLIHKAIGDRQKCVFVNNGLLRLNEEKEIEEMFKNNFNVNFTSVDAV 173
                   56888888887655345777*******************9888766666677777777777788888888888887754 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 6.5e-07
                   BETTTTS-HHHHHHHHHHTT--HHHHCS-- CS
  NAD_synthase 148 lapiaellKtevkeLakelnvPervlkkpP 177
                   l+p+ el+K ev+++ak l+vPe+++ ++P
    EPA05216.1 254 LEPLRELYKDEVRKIAKILGVPEKLYMRHP 283
                   68**************************99 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   1.3e-07   0.00029       3      64 ..     109     171 ..     107     210 .. 0.72
   2 ?    4.3   0.0     0.012        27     136     161 ..     249     274 ..     238     282 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.3e-07
        ThiI   3 qgkvlaLlSgGiDSpVaaylllkR.Gcrvvlvhlknepgtseeaiekveklaellaeyqtsle 64 
                 +g+vl+ +SgGiDS Vaa l+ k  G r ++v+++n +   +e++e  e+  + ++ + ts++
  EPA05216.1 109 EGNVLCGVSGGIDSTVAALLIHKAiGDRQKCVFVNNGLLRLNEEKEIEEMFKNNFNVNFTSVD 171
                 699***************999985599999999988888888888887887777776555443 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.012
        ThiI 136 vnllilrPLigldKeeiiklAkeigt 161
                  +l il+PL  l K+e+ k+Ak +g 
  EPA05216.1 249 LDLQILEPLRELYKDEVRKIAKILGV 274
                 6899******************9986 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.6e-06    0.0035       2      32 ..     111     141 ..     110     178 .. 0.78
   2 ?    2.8   0.0     0.018        41     165     185 ..     254     274 ..     249     279 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.6e-06
  tRNA_Me_trans   2 kvvvalSgGVDSsvaaallkeqgyevigvfl 32 
                    +v++++SgG+DS+vaa+l++++  + +++++
     EPA05216.1 111 NVLCGVSGGIDSTVAALLIHKAIGDRQKCVF 141
                    79*****************998765554443 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.018
  tRNA_Me_trans 165 lfPlgeltKeevrkiAkeagl 185
                    l Pl el K+evrkiAk  g+
     EPA05216.1 254 LEPLRELYKDEVRKIAKILGV 274
                    569*************97665 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0   0.00017      0.38       3      60 ..     113     171 ..     111     185 .. 0.73
   2 ?    3.6   0.0     0.018        39     147     178 ..     238     277 ..     215     280 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00017
                 EEE--SSHHHHHHHHHHHHH.-SEEEEEEEESS-T.TSHHHHHHHHHHHHT--.-EEEEE CS
        QueC   3 vvllSGGlDSttvlalakke.gkevealtfdYgqr.hkkeleaakkiakelgveehkild 60 
                 ++ +SGG+DSt++++l +k+ g++ +++ ++ g    ++e e+ + + ++++v + + +d
  EPA05216.1 113 LCGVSGGIDSTVAALLIHKAiGDRQKCVFVNNGLLrLNEEKEIEEMFKNNFNV-NFTSVD 171
                 6779********98877766258888888888864377777777777777887.555555 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.018
                 H........HTS--EEE-TTTT--HHHHHHHHHHTTHHHH CS
        QueC 147 g........edkkieieaPlidlsKaeivklgkelgvple 178
                 +         + +++i  Pl +l K e+ k++k lgvp +
  EPA05216.1 238 ShhnvgglpDWLDLQILEPLRELYKDEVRKIAKILGVPEK 277
                 33333355577889**********************9865 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.6e-05     0.036     167     216 .]      20      67 ..       4      67 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.6e-05
  Peptidase_C26 167 eievnslHhqaikelaeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                    +++    H    +++ ++++v+ ++e     ai see+   ++g+Q+HPE
     EPA05216.1  20 SVRAWMSHGDEAEQIPPGFKVIGHTESAKAAAIASEEK--SIYGIQFHPE 67 
                    55556679999999**************999**99994..5********9 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00011      0.24       2      50 ..     112     159 ..     111     190 .. 0.63
   2 ?   -3.7   0.0       3.9   8.7e+03     139     157 ..     252     270 ..     248     273 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00011
                 EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSS.TCHHHHHHHH CS
  ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglr.eeskeeaelv 50 
                 vl +vSgG+DS++  ll++k   +   + ++++ +  lr +e ke +e+ 
  EPA05216.1 112 VLCGVSGGIDSTVAALLIHKAIGD--RQKCVFVNNGLLRlNEEKEIEEMF 159
                 789**********99999888554..344455445555633444433333 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 3.9
                 CEE-CCCT--HHHHHHHHH CS
  ATP_bind_3 139 rlvRPlLkvskeeleeylk 157
                 +++ Pl +++k+e+++++k
  EPA05216.1 252 QILEPLRELYKDEVRKIAK 270
                 7889999999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 2825.04
//
Query:       EPA05217.1  [L=243]
Description: cephalosporin hydroxylase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.9e-85  283.4   0.3    1.2e-84  283.1   0.3    1.0  1  CmcI             Cephalosporin hydroxylase
      4e-09   37.4   0.0    5.8e-09   36.9   0.0    1.2  1  Methyltransf_24  Methyltransferase domain
  ------ inclusion threshold ------
      0.018   14.9   0.1      0.025   14.3   0.1    1.3  1  Methyltransf_31  Methyltransferase domain
      0.018   15.3   0.0      0.038   14.2   0.0    1.5  1  Mur_ligase_C     Mur ligase family, glutamate ligase domain
      0.025   13.9   0.1      0.044   13.1   0.1    1.5  1  TylF             Macrocin-O-methyltransferase (TylF)
      0.068   13.5   0.5       0.13   12.5   0.2    1.6  2  DUF1269          Protein of unknown function (DUF1269)
       0.11   12.4   3.5       0.21   11.6   1.2    2.4  2  RST              RCD1-SRO-TAF4 (RST) plant domain


Domain annotation for each model (and alignments):
>> CmcI  Cephalosporin hydroxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  283.1   0.3   4.6e-88   1.2e-84       2     204 ..      39     240 ..      38     242 .. 0.99

  Alignments for each domain:
  == domain 1  score: 283.1 bits;  conditional E-value: 4.6e-88
        CmcI   2 kylykfswlgvpiiklpqDlvayQeliwelkPdliietGiahGGsalfsasllallkskrkvlaididireknrqaieahplasrieliegssvdpeiv 100
                 +y+y+f+wlg+pii++pqD++a+Qe+iw++kPd+iietGia GGs++fsas+l+l+ +k+kv++ididire+n+++i++h l +r+++iegssvd +++
  EPA05217.1  39 EYSYHFKWLGRPIIQYPQDIIALQEIIWDVKPDIIIETGIARGGSLVFSASMLQLI-GKGKVIGIDIDIREHNKKEIKKHHLYKRMKMIEGSSVDEKTI 136
                 699*****************************************************.9***************************************** PP

        CmcI 101 eqvkslakekekvlvilDsdHthehvlaeLeayaplvsaGsYivveDtviedlpesafsdrpwgkgnnPkeAveeflkeepefeidkeieekllitvap 199
                 ++v ++ k+++kvlvilDs+Hthehvl+eLeay++lv++ sY++v+Dtvie+lpe++f+++pw k  nPk Av+ fl ++++f+ dk+i++kllit+ap
  EPA05217.1 137 KKVFQMVKSTDKVLVILDSNHTHEHVLKELEAYSKLVTKDSYLIVFDTVIEELPEKLFTKKPWSKKYNPKSAVRLFLTKNKRFKADKTITDKLLITAAP 235
                 *************************************************************************************************** PP

        CmcI 200 dgfLk 204
                 +g+Lk
  EPA05217.1 236 EGYLK 240
                 ****9 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.0   2.3e-12   5.8e-09       1     103 [.      74     181 ..      74     184 .. 0.85

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 2.3e-12
  Methyltransf_24   1 vEiGvysGvstlwllralrrngagrlvavdhdpgaeeaaalareaglddrvrlikads..eealasla..agsiD..llfiDgghaaeavledl 88 
                      +E G+  G s ++ +++l+  g+g+++ +d d   e++++ +++++l +r+++i++ s  e++++++    +s D  l+++D +h++e+vl++l
       EPA05217.1  74 IETGIARGGSLVFSASMLQLIGKGKVIGIDIDI-REHNKKEIKKHHLYKRMKMIEGSSvdEKTIKKVFqmVKSTDkvLVILDSNHTHEHVLKEL 166
                      699****************************99.678899999***************76334443333424455559999************* PP

  Methyltransf_24  89 eallprlapggvvlf 103
                      ea  +++++++++++
       EPA05217.1 167 EAYSKLVTKDSYLIV 181
                      *********998776 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   9.9e-06     0.025      22     122 ..      88     193 ..      71     229 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 9.9e-06
  Methyltransf_31  22 ae..elgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnevl.......naladpdkileeiervlkpggi 106
                      a+  +l+ k++v+GiDi+ +  +  +e+ +++ ++++++ +g+  + ++ ++ + f ++ s + +       ++  +  k le  +++++++++
       EPA05217.1  88 ASmlQLIGKGKVIGIDIDIREHN-KKEIKKHHLYKRMKMIEGSSVDEKT-IK-KVFQMVKSTDKVlvildsnHTHEHVLKELEAYSKLVTKDSY 178
                      333688889********988744.456789999********99999665.56.678887776555467777666777778888899999***** PP

  Methyltransf_31 107 lliedprllaelpakv 122
                      l++ d    +elp+k+
       EPA05217.1 179 LIVFDTV-IEELPEKL 193
                      ***9999.99998665 PP

>> Mur_ligase_C  Mur ligase family, glutamate ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.5e-05     0.038       5      81 ..     140     217 ..     137     225 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.5e-05
                   SEEEEETTTEEEEEET--SHHHHHHHHHHHHHHSSSSEEEEEE.EESTT.CCSCHCTHHHHHHHHCCHSSEEEEEESS CS
  Mur_ligase_C   5 levvgeadgvtvidDyahnpdslsaalkalreiapdkrlilvf.gpggelgertrtfhdefgrlasaladslvvlgdy 81 
                   +++v+++d+v+vi D +h+ + + + l+a+ +++++   ++vf + ++el e+  t+ ++ ++   + a++l++++++
    EPA05217.1 140 FQMVKSTDKVLVILDSNHTHEHVLKELEAYSKLVTKDSYLIVFdTVIEELPEKLFTKKPWSKKYNPKSAVRLFLTKNK 217
                   7999*****************************997777777724567788888888888888888888888887664 PP

>> TylF  Macrocin-O-methyltransferase (TylF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   1.7e-05     0.044      75     109 ..      62      96 ..       5     148 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.7e-05
        TylF  75 edvleegvpGdliEtGvWRGGaailmrgvLkaegv 109
                 ++++ +  p  +iEtG+ RGG+ ++ +++L+  g 
  EPA05217.1  62 QEIIWDVKPDIIIETGIARGGSLVFSASMLQLIGK 96 
                 5555555566689*****************98765 PP

>> DUF1269  Protein of unknown function (DUF1269)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       3.9     1e+04      31      52 ..      93     114 ..      82     117 .. 0.59
   2 ?   12.5   0.2   5.1e-05      0.13      36      83 ..     127     174 ..     123     187 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.9
     DUF1269  31 lvgalsdvgidddflkelgekl 52 
                 l g+ + +gid d+ ++ ++++
  EPA05217.1  93 LIGKGKVIGIDIDIREHNKKEI 114
                 5566666666666655555544 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 5.1e-05
     DUF1269  36 sdvgidddflkelgeklkpgtsalfllvekatvdkvlealaklggkvl 83 
                 +  ++d++ +k++ + +k     l++l +++t ++vl++l+ +   v 
  EPA05217.1 127 EGSSVDEKTIKKVFQMVKSTDKVLVILDSNHTHEHVLKELEAYSKLVT 174
                 5679************************************99986554 PP

>> RST  RCD1-SRO-TAF4 (RST) plant domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.43   1.1e+03      38      47 ..      25      34 ..      14      35 .. 0.84
   2 ?   11.6   1.2     8e-05      0.21      33      65 ..     107     139 ..      95     141 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.43
         RST 38 kkIsreefvr 47
                kkIsre f++
  EPA05217.1 25 KKISREWFLK 34
                89****9987 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 8e-05
         RST  33 edlkkkkIsreefvrklRsivGDklLksvikkl 65 
                 +++ kk+I++++++++++ i G  +  ++ikk+
  EPA05217.1 107 REHNKKEIKKHHLYKRMKMIEGSSVDEKTIKKV 139
                 5789****************9999888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1110  (0.0619109); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1491.79
//
Query:       EPA05218.1  [L=50]
Description: hypothetical protein BG20_I0211 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.29s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 358.63
//
Query:       EPA05219.1  [L=357]
Description: glycosyltransferase, group 2 family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-26   92.9   0.0    3.1e-26   92.2   0.0    1.4  1  Glycos_transf_2  Glycosyl transferase family 2
    2.9e-19   69.9   0.0    4.3e-19   69.3   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    6.2e-07   29.5   0.0    9.8e-07   28.9   0.0    1.3  1  Glyco_trans_2_3  Glycosyl transferase family group 2
     0.0038   17.7   0.0     0.0076   16.7   0.0    1.5  1  Glyco_tranf_2_4  Glycosyl transferase family 2
  ------ inclusion threshold ------
      0.061   12.8   0.0       0.12   11.8   0.0    1.4  1  Glyco_transf_21  Glycosyl transferase family 21


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.2   0.0   8.6e-30   3.1e-26       1     169 [.      19     189 ..      19     190 .. 0.93

  Alignments for each domain:
  == domain 1  score: 92.2 bits;  conditional E-value: 8.6e-30
                      EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--SSEEEEEESSEEE-T CS
  Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatgdyilflDaDdepdp 94 
                      s++i  yN  ++lle++es+l+   y ++ei+vvD++S+D++++ ++e    +p + +i ++en G+  + n g+r a+g yi++l+ D+ +dp
       EPA05219.1  19 SIIILNYNAGDLLLECVESILNT-RYNNYEILVVDNASKDNSHSRCKEK---FPMINLIENKENLGYCEGNNIGIRIAKGTYIVILNPDTLVDP 108
                      8*********************9.*************************...69**************************************** PP

                      THHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SS......EEEECCHCCCCHCCCCCCSTTCSTCCCEEEEHHHHHC CS
  Glycos_transf_2  95 dwleklvealekdgadvvlgqrprifgetdeiernkrv......generlyfkerkrslkgnlsfeigsaallrrealeel 169
                      dwl  l++ +e  g+++  +++  + +++  ++    +      + + ++++ ++++++   + f +g++   + ++ +++
       EPA05219.1 109 DWLDGLIQGYEMYGEGLYQPKFLTTTDHNVLMSSGNMIqifgfgYSRGKGQIDTKQFEKHEIVGFASGTCLFTHINVMKKI 189
                      ***********************9999999999886669999988888888888888888889999999888777777665 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.3   0.0   1.2e-22   4.3e-19       4     229 ..      18     250 ..      15     251 .. 0.84

  Alignments for each domain:
  == domain 1  score: 69.3 bits;  conditional E-value: 1.2e-22
  Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnealravksdlvllvDdD 97 
                      +++++ ++n+ d l+e++es+l+  y ++e+ vv++ s++   ++++e   ++p +  +++ n++nlg   + ++ n ++r++k++++++++ D
       EPA05219.1  18 VSIIILNYNAGDLLLECVESILNTRYNNYEILVVDNASKDNSHSRCKE---KFPMI--NLIENKENLG---YCEGNNIGIRIAKGTYIVILNPD 103
                      89********************************************99...9*995..9**9999998...56666****************** PP

  Glyco_tranf_2_3  98 tvvePdtlkrllqff..ltp....kvgavg.tpvfll.nrstlvsal..galefaerhlrflaarralgvltlnGsgslirrevlkelegldp. 180
                      t+v+Pd l+ l q +         ++++++ t+ ++l    ++++    g+ + +  ++++ ++ +   v + +G++++    v+k ++ +d  
       EPA05219.1 104 TLVDPDWLDGLIQGYemY-GeglyQPKFLTtTDHNVLmSSGNMIQIFgfGYSR-GKGQIDTKQFEKHEIVGFASGTCLFTHINVMKKIGMFDSf 195
                      **************9642.2466788888855556652455666655443323.44455666666544455557*******************9 PP

  Glyco_tranf_2_3 181 lflltdDyelglrlrragfrtayvpgaavrev......fpsslkayikqrnRwvy 229
                      lf   dD +lg r+   g++++y p+++v++       ++s+ k y  +rnR ++
       EPA05219.1 196 LFAYLDDMDLGWRALLLGIKSHYIPKSIVYHPpegfsfKWSNYKFYLLERNRLYC 250
                      99999**************************988888888************986 PP

>> Glyco_trans_2_3  Glycosyl transferase family group 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   2.7e-10   9.8e-07       1     124 [.      96     226 ..      96     284 .. 0.76

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 2.7e-10
  Glyco_trans_2_3   1 iilllDaDtvlppdclreiaaelaspevaivqgpvlvm...nvanwleelaalf.faedhgkdilvrealgr..vvpsv.Gsgaflrrsalqev 87 
                      +i++l  Dt+++pd l ++++ ++    +++q + l +   nv     +++ +f f  + gk ++ ++++ +   v ++ G + f+++ +++++
       EPA05219.1  96 YIVILNPDTLVDPDWLDGLIQGYEMYGEGLYQPKFLTTtdhNVLMSSGNMIQIFgFGYSRGKGQIDTKQFEKheIVGFAsGTCLFTHINVMKKI 189
                      79*******************9995456****997664335777777777777797777788888888775444888888************** PP

  Glyco_trans_2_3  88 ggwdgdessvsEDfdmglrlqrkGyrvrfvpeslvke 124
                      g +d+  ++  +D+d+g r++ +G + +++p s+v+ 
       EPA05219.1 190 GMFDSFLFAYLDDMDLGWRALLLGIKSHYIPKSIVYH 226
                      ****999**************************5542 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   2.1e-06    0.0076       1      50 [.      25      77 ..      25     110 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.1e-06
  Glyco_tranf_2_4  1 rneadiLpeflahhlalgfdr..ilvydndstDgtrailkel.pevkllhvdk 50
                     +n+ d+L e+++ +l+ ++++  ilv+dn s+D++   +ke  p ++l+++++
       EPA05219.1 25 YNAGDLLLECVESILNTRYNNyeILVVDNASKDNSHSRCKEKfPMINLIENKE 77
                     6999**************97555****************99658888888875 PP

>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.4e-05      0.12      26     151 ..      89     224 ..      84     236 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.4e-05
  Glyco_transf_21  26 leaakydllvisDsdvrvkpdyLeellaaledpkvglVtslpvgsdakg...laaaleaafl...ntlagvlqa.kl...sglgfavGksmalr 109
                      ++ ak  ++vi+  d++v+pd L+ l +  e  + gl +   +++  ++     +++ + f    + + g ++  ++   + +gfa G ++  +
       EPA05219.1  89 IRIAKGTYIVILNPDTLVDPDWLDGLIQGYEMYGEGLYQPKFLTTTDHNvlmSSGNMIQIFGfgySRGKGQIDTkQFekhEIVGFASGTCLFTH 182
                      5668999************************98888877655555555544344455555534544555556556553225779********** PP

  Glyco_transf_21 110 reaLeaiGGfealadeLAeDyalgkllraaGlkvvlspapia 151
                       +++++iG f ++     +D+ lg++    G+k +  p+ i+
       EPA05219.1 183 INVMKKIGMFDSFLFAYLDDMDLGWRALLLGIKSHYIPKSIV 224
                      ********************************9998887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2521.15
//
Query:       EPA05220.1  [L=293]
Description: glycosyltransferase, group 2 family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      8e-24   84.3   0.1    1.1e-23   83.9   0.1    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
      8e-05   22.6   0.0    0.00011   22.1   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
  ------ inclusion threshold ------
      0.013   16.2   0.1       0.04   14.5   0.1    1.9  2  PGM_PMM_II       Phosphoglucomutase/phosphomannomutase, alpha
      0.016   15.2   0.0       0.47   10.5   0.0    2.9  3  TTRAP            Putative tranposon-transfer assisting protei
       0.02   14.8   0.0      0.026   14.5   0.0    1.2  1  CTP_transf_3     Cytidylyltransferase
       0.12   12.9   0.0       0.21   12.1   0.0    1.4  1  Glyco_tranf_2_4  Glycosyl transferase family 2
       0.13   11.9   2.6       0.24   11.0   2.6    1.4  1  TMEM100          Transmembrane protein 100
       0.29    9.9   5.2       0.37    9.5   5.2    1.4  1  DUF2207          Predicted membrane protein (DUF2207)


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.9   0.1     5e-27   1.1e-23       3     168 ..       6     160 ..       4     162 .. 0.93

  Alignments for each domain:
  == domain 1  score: 83.9 bits;  conditional E-value: 5e-27
                      EEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--SS...EEEEEESSEEE- CS
  Glycos_transf_2   3 viptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatgd...yilflDaDdepd 93 
                      +ip+yNeek ++  +++ l+      ++++v DDgS+D+t + + ++     + +vi++e+n Gk++al   +++a+     +++++D D ++ 
       EPA05220.1   6 CIPAYNEEKPIADIIKRSLNY----VDRVVVCDDGSNDSTSKNATDA-----GAIVIKHEKNMGKGAALKSLFDYARNAnadVMVTIDGDGQFL 90 
                      8********************....**********************.....9*******************9998887778************ PP

                      TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTCSTCCCEEEEHHHHH CS
  Glycos_transf_2  94 pdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfeigsaallrrealee 168
                      p+   kl++++ + + d+vlg+r+ +++e   +++       ++++ k+++   +    +  ++++ ++++a+++
       EPA05220.1  91 PEEMNKLIDPIIEKNFDIVLGNRFQTKKEMPSYRKV-----GNMMFDKITQLASDLPFNDTQSGYRSYSKNAIQK 160
                      ***********************************8.....5788888888888888888888888888888877 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0     5e-08   0.00011       7     125 ..       6     114 ..       4     171 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 5e-08
  Glyco_tranf_2_3   7 lVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnealravksdlvllvDdDtvv 100
                       +p++nee+ + +++   l++    ++vvv++d+s ++t ++a       ++    v+  ++n g++++  +l++  r+++ d+ + +D+D   
       EPA05220.1   6 CIPAYNEEKPIADIIKRSLNY---VDRVVVCDDGSNDSTSKNATD----AGA---IVIKHEKNMGKGAALKSLFDYARNANADVMVTIDGDGQF 89 
                      69*****************96...99***************9975....333...46788999*****************************99 PP

  Glyco_tranf_2_3 101 ePdtlkrllqffltpkvgavgtpvf 125
                       P+   +l   +  ++ ++v +++f
       EPA05220.1  90 LPEEMNKLIDPIIEKNFDIVLGNRF 114
                      9999999999888888888887775 PP

>> PGM_PMM_II  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   1.8e-05      0.04      61      93 ..      55      87 ..      25      89 .. 0.85
   2 ?   -2.8   0.0       4.5     1e+04       6      27 ..     178     196 ..     163     217 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.8e-05
                SS----TT-TTTTHHHHGGGGG-SEEEEE-TTS CS
  PGM_PMM_II 61 kapnpeekealkllielvkkegadlglafDgDa 93
                +  n+ + +alk+l++++++ +ad+++ +DgD+
  EPA05220.1 55 HEKNMGKGAALKSLFDYARNANADVMVTIDGDG 87
                777888889***********************8 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.5
                 HGGGTS-HHHHHHHT-EEEEE- CS
  PGM_PMM_II   6 alkekvdseaikksglkvvidp 27 
                 a++++++   i +++++v++++
  EPA05220.1 178 AVQKNLK---IVEENITVIYNT 196
                 3333333...444445555544 PP

>> TTRAP  Putative tranposon-transfer assisting protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.53   1.2e+03      30      46 ..      89     104 ..      71     106 .. 0.78
   2 ?    0.1   0.0      0.36   8.2e+02      38      52 ..     152     166 ..     130     167 .. 0.77
   3 ?   10.5   0.0   0.00021      0.47       5      40 ..     187     220 ..     183     222 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.53
                 TS.-HHHHHHHHHHHHH CS
       TTRAP  30 yleddelreLaestlaK 46 
                 +l  +e+ +L++ +++K
  EPA05220.1  89 FL-PEEMNKLIDPIIEK 104
                 55.689****9999998 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.36
                 HHHHHHHHHHTT--H CS
       TTRAP  38 eLaestlaKLkaltD 52 
                   ++++++K+k +t+
  EPA05220.1 152 SYSKNAIQKIKFMTN 166
                 56789999*999996 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.00021
                 HHHHHHHH--SHHHHHHHHHHHSTTTS.-HHHHHHH CS
       TTRAP   5 ElnLiaiynegtRkelieelkaalkyleddelreLa 40 
                 E n++ iyn+g+++ + +  ++ +++l  + l+eL+
  EPA05220.1 187 EENITVIYNTGGKTSTKDPVSHSVSVL--TSLIELI 220
                 89****************999999999..8888887 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.2e-05     0.026      35     120 ..      24     106 ..      13     157 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.2e-05
                   HHTTTTSEEEEEES-HHHHHHHHHTT.SEEEE--TTCSSHHHHHHHHHHHHTTT.TTSEEEEE-TT-TT--HHHHHHHHHHHHHSTT CS
  CTP_transf_3  35 lkskafekvivaTDseeiknvakefg.asvlvtrsslesdterflevvkaflmseneeiivnlqGdnPllqeevikkaietlkenqe 120
                   l+   +++ +v +D+ + + + k++  a+ +v++ + + ++ + l+ + +++ + n+++ v + Gd  +l+ee + k+i+ + e++ 
    EPA05220.1  24 LN--YVDR-VVVCDDGSNDSTSKNATdAGAIVIKHEKNMGKGAALKSLFDYARNANADVMVTIDGDGQFLPEE-MNKLIDPIIEKNF 106
                   44..5677.677**********************************************************996.4555555555444 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   9.5e-05      0.21       2      81 ..      11      86 ..      10      98 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.5e-05
  Glyco_tranf_2_4  2 neadiLpeflahhlalgfdrilvydndstDgtrailkelpevkllhvdksyederrqvellkalla..ryaeadwvlvvDaD 81
                     ne++ +   ++  l++ +dr++v+d++s D t++      +  +++++k++ +     ++lk l++  r a+ad ++++D D
       EPA05220.1 11 NEEKPIADIIKRSLNY-VDRVVVCDDGSNDSTSKNATDAGA-IVIKHEKNMGK----GAALKSLFDyaRNANADVMVTIDGD 86
                     8888888888888899.9**************998887544.45555555543....3444444432234567777777777 PP

>> TMEM100  Transmembrane protein 100
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   2.6   0.00011      0.24      61     115 ..     233     291 ..     229     293 .] 0.74

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00011
     TMEM100  61 gvvvLvaGvvvtavaytfnshgsvisv....lglvLLsaGlvllassavCWkvrrrrkk 115
                 g + Lv+G+v   +  +    ++v sv    ++l  L  Gl+ll++sav + + r  ++
  EPA05220.1 233 GFILLVIGIVYSFIVISIFNDTRVFSVpstlVALGSLVVGLMLLLMSAVLFSISRMARR 291
                 7899******99888875556666665221244555889***********999887744 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   5.2   0.00017      0.37     348     438 ..     155     292 ..      44     293 .] 0.66

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00017
     DUF2207 348 k...............kakkfkkalkkwksavkk..............kergyfdkkg...............kkklkklsalglgliilglilillal 402
                 k               + + + +a++k  + v++              k                         +++  l++lg+ ++il++i+i++++
  EPA05220.1 155 KnaiqkikfmtngfgvDSEILIDAVQKNLKIVEEnitviyntggktstK--------DpvshsvsvltslielIAIRHPLRYLGIPGFILLVIGIVYSF 245
                 3344455555555555555555555555555555444455322222220........134444444444444457788999999999999999999999 PP

     DUF2207 403 lllvll.............lvfllilllillliaiivlllfsrllgrrt 438
                 +++ ++               + l+++l+lll++++++ ++  ++ rrt
  EPA05220.1 246 IVISIFndtrvfsvpstlvALGSLVVGLMLLLMSAVLFSIS--RMARRT 292
                 999988***********877777777777777776666665..788887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       962  (0.0536561); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 1962.77
//
Query:       EPA05221.1  [L=344]
Description: glycosyltransferase, group 1 family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.7e-27   93.6   0.0    1.6e-26   92.9   0.0    1.3  1  Glycos_transf_1  Glycosyl transferases group 1
    4.2e-21   75.8   0.0      6e-21   75.3   0.0    1.2  1  Glyco_trans_1_4  Glycosyl transferases group 1
    1.3e-11   44.8   0.0    2.8e-10   40.5   0.0    2.2  1  Glyco_transf_4   Glycosyltransferase Family 4
  ------ inclusion threshold ------
      0.043   14.2   0.0      0.083   13.3   0.0    1.5  1  Glyco_trans_1_2  Glycosyl transferases group 1
       0.15   12.3   0.2       0.51   10.6   0.0    2.0  2  NUMOD4           NUMOD4 motif


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.9   0.0   4.5e-30   1.6e-26      13     160 ..     167     313 ..     162     321 .. 0.96

  Alignments for each domain:
  == domain 1  score: 92.9 bits;  conditional E-value: 4.5e-30
                      TT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHHHCESEEEEEESSBSS- CS
  Glycos_transf_1  13 ekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleellknadifvlpsisEgfG 106
                       +++ +l+vg l+++K v++li ++++l k+  p+ +l i+G gee  +l+k++  l+l+ nv+++g++++++l+  + ++di+v  s+ E  +
       EPA05221.1 167 RGEPQLLFVGGLRPYKKVSVLISSMPKLLKK-YPKSHLQIVGIGEEMTSLEKMINDLKLERNVELTGKINNDELKLRYASCDIYVSASTFEVCP 259
                      6899*************************99.************************************************************** PP

                      HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHH CS
  Glycos_transf_1 107 ivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledee 160
                      ++ lEAma+g+p + +++++ +e+++    G ++  ++  +++  ++++ ++++
       EPA05221.1 260 VPTLEAMASGKPLVLYDIEPHREIIEISNAGKIFSFTENSDFVSIVDDVYKNKD 313
                      ********************************9999999999999999999875 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.3   0.0   1.7e-24     6e-21       2     131 ..     170     308 ..     169     311 .. 0.86

  Alignments for each domain:
  == domain 1  score: 75.3 bits;  conditional E-value: 1.7e-24
                      EEEEEES---GG.GTHHHHHHHHHHHH.H.H.EEEEEES---...HHHHHHHT..T-T.TEEEE---..THHHHHHHH-SEEEE--..---SHH CS
  Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkk.d.vrlvivGdgp.rpeeleelaa..gleerveftGfv..edlaellaaadvfvaPs..egfglk 86 
                      p +lfvG l +++k v +l+  +p+l+kk +  +l ivG g+ +  +le++++  +le +ve+tG++  ++l+  +a++d++v  s  e +++ 
       EPA05221.1 170 PQLLFVGGL-RPYKKVSVLISSMPKLLKKyPkSHLQIVGIGEeM-TSLEKMINdlKLERNVELTGKInnDELKLRYASCDIYVSAStfEVCPVP 261
                      889******.677**********9999896469******99855.59*999987999999*******9666***************999***** PP

                      HHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHH CS
  Glyco_trans_1_4  87 llEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrL 131
                      +lEama+g+p V  d++  +e++   ++g +++  + ++++  + ++
       EPA05221.1 262 TLEAMASGKPLVLYDIEPHREIIeiSNAGKIFSFTENSDFVSIVDDV 308
                      ****************877**99876778666666677777666555 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.5   0.0   7.7e-14   2.8e-10       9     169 ..      24     155 ..      18     156 .. 0.69

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 7.7e-14
  Glyco_transf_4   9 leLaraLarrGheVtvvtpgddgpleeevelvvrvprvplpllkrllrslaflrrlrrllkrekpDvvHahspaalgaallalrrrlgiplVltv 103
                      +L+ +L ++G++  + +++ d p++ +                  +  l  l++l   + + ++D++  h++++ ++ l   +   ++p++l++
      EPA05221.1  24 NNLCIELDKMGYRTAIGAFSFDSPPPPN----------------VKQVKLKKLKSLFYGVNNLGYDIIYLHQSFPNYFLLT-KK--PNKPVILYY 99 
                     5555555555555555555555555555................22233333333444455669***********966543.33..7******** PP

  Glyco_transf_4 104 HglyekrllkarlkplsrllralerrllrradrviavSeatadelreryg.vppekitVipnGvDle 169
                     Hg          +  +++ ++ ++    +r  ++i vS+a  +++++  g ++    +Vi+nGvD+e
      EPA05221.1 100 HGAS--------NTIQKINFKIMMMLYKNRISQIISVSKAGVNQMKKMIGdIS---AEVIYNGVDTE 155
                     ****........56666666666666689******************999555...6*********8 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.3e-05     0.083      12      83 ..     259     328 ..     242     337 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.3e-05
  Glyco_trans_1_2  12 nlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarervlaehty 83 
                       + ++Ea+a+G +++  d+e ++e++++ + + +f+  +  +++  ++ + +n ++ +   + + e+  ++h++
       EPA05221.1 259 PVPTLEAMASGKPLVLYDIEPHREIIEISNAGKIFSftENSDFVSIVDDVYKNKDLFK---ISGLEF-AKKHDW 328
                      5689************************9987777777999****9999998888754...455555.455555 PP

>> NUMOD4  NUMOD4 motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       2.2   7.9e+03      12      19 ..      64      71 ..      53      77 .. 0.63
   2 ?   10.6   0.0   0.00014      0.51       4      29 ..     275     300 ..     274     325 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.2
      NUMOD4 12 kYevSnyG 19
                 Y v+n+G
  EPA05221.1 64 FYGVNNLG 71
                35666665 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00014
      NUMOD4   4 kdIpgyegkYevSnyGRvrslkrkvt 29 
                 +dI+ ++++ e+Sn G++ s+++++ 
  EPA05221.1 275 YDIEPHREIIEISNAGKIFSFTENSD 300
                 5888888899************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2251.58
//
Query:       EPA05222.1  [L=54]
Description: hypothetical protein BG20_I0187 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.8e-09   35.5   0.0    6.8e-09   35.5   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    8.1e-08   32.0   0.0    8.6e-08   31.9   0.0    1.0  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    9.5e-05   21.9   0.0    9.5e-05   21.9   0.0    1.0  1  adh_short        short chain dehydrogenase
    0.00015   21.0   0.0    0.00015   21.0   0.0    1.0  1  RmlD_sub_bind    RmlD substrate binding domain
    0.00031   20.7   0.0    0.00035   20.5   0.0    1.0  1  NAD_binding_10   NAD(P)H-binding
    0.00039   20.0   0.0    0.00041   20.0   0.0    1.0  1  NmrA             NmrA-like family
     0.0018   17.5   0.0     0.0018   17.5   0.0    1.0  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
     0.0031   16.5   0.0     0.0031   16.5   0.0    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
     0.0074   15.5   0.0     0.0079   15.4   0.0    1.1  1  NAD_binding_4    Male sterility protein
  ------ inclusion threshold ------
      0.042   14.0   0.0      0.045   13.9   0.0    1.1  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
      0.097   12.8   0.0      0.097   12.8   0.0    1.1  1  Ldh_1_N          lactate/malate dehydrogenase, NAD binding do


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.0   4.2e-12   6.8e-09       1      31 [.       6      36 ..       6      53 .. 0.92

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 4.2e-12
                EEEETTTSHHHHHHHHHHHHCTSEEEEEES- CS
   Epimerase  1 ilVtGatGfiGsalvkallekgyevigldrl 31
                +lVtGa GfiGs+l++ ll+++yevi+++r+
  EPA05222.1  6 VLVTGADGFIGSHLCDILLKNNYEVIAVSRN 36
                79***************************98 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0   5.3e-11   8.6e-08       1      32 [.       7      38 ..       7      46 .. 0.92

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 5.3e-11
                   EEETTTSHHHHHHHHHHHHCT-CCEEEEEEES CS
  GDP_Man_Dehyd  1 LiTGiaGfiGsylaelLlekgyevhgivrrss 32
                   L+TG  GfiGs+l++ Ll+++yev+ + r+ +
     EPA05222.1  7 LVTGADGFIGSHLCDILLKNNYEVIAVSRNFK 38
                   9************************9998765 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   5.8e-08   9.5e-05       2      39 ..       5      42 ..       4      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 5.8e-08
                EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHH CS
   adh_short  2 vvlvtGassGIGraiakelakeGakvvvvdrseeklee 39
                 vlvtGa++ IG  +++ l+k++++v++v+r+ +kl  
  EPA05222.1  5 KVLVTGADGFIGSHLCDILLKNNYEVIAVSRNFKKLLM 42
                59******************************998855 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   9.2e-08   0.00015       1      33 [.       4      36 ..       4      49 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 9.2e-08
                   EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT CS
  RmlD_sub_bind  1 mkilvtGanGqlGseLakqlaeeglevlaltre 33
                   mk+lvtGa+G +Gs+L + l ++++ev+a++r+
     EPA05222.1  4 MKVLVTGADGFIGSHLCDILLKNNYEVIAVSRN 36
                   89****************************987 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   2.1e-07   0.00035       1      32 [.      10      40 ..      10      46 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.1e-07
                    TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHC CS
  NAD_binding_10  1 GAtGkvGrllvkellargghevtalvRnpekl 32
                    GA G +G++l++ ll++ ++ev a+ Rn +kl
      EPA05222.1 10 GADGFIGSHLCDILLKN-NYEVIAVSRNFKKL 40
                    9****************.6*********8876 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   2.5e-07   0.00041       1      35 [.       6      40 ..       6      48 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.5e-07
                EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SH CS
        NmrA  1 IlviGaTGrqGksvvrallkaghkvralvRdtkse 35
                +lv+Ga G +G+++ ++llk++++v a+ R+ k+ 
  EPA05222.1  6 VLVTGADGFIGSHLCDILLKNNYEVIAVSRNFKKL 40
                79*****************************9875 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.1e-06    0.0018       1      35 [.       6      39 ..       6      52 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.1e-06
                     EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHH CS
  Polysacc_synt_2  1 vlvtGagGsiGselvrqilkkkpkkiillerdElk 35
                     vlvtGa G iGs+l++ +lk++ + i + +r+ +k
       EPA05222.1  6 VLVTGADGFIGSHLCDILLKNNYEVIAV-SRNFKK 39
                     8***************999988776655.454444 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.9e-06    0.0031       1      22 [.       7      28 ..       7      48 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.9e-06
   3Beta_HSD  1 vvtGgaGFlGralvkeLvrlee 22
                +vtG+ GF+G++l+  L++ + 
  EPA05222.1  7 LVTGADGFIGSHLCDILLKNNY 28
                69****************9884 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   4.9e-06    0.0079       1      28 [.       8      33 ..       8      42 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 4.9e-06
                   EE-TTSHHHHHHHHHHHHHS-.TEEEEE CS
  NAD_binding_4  1 lTGaTGFLGkvLlekLLrttpevkiyll 28
                   +TGa GF+G++L   LL+++ e  ++++
     EPA05222.1  8 VTGADGFIGSHLCDILLKNNYE--VIAV 33
                   7******************985..5554 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.7e-05     0.045       1      35 [.       4      37 ..       4      46 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.7e-05
                EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETT CS
      DapB_N  1 ikvavvGasGrmGkevvkaveeaedlelvaavdrk 35
                +kv+v+Ga G +G+++++ + + +++e+ a+  + 
  EPA05222.1  4 MKVLVTGADGFIGSHLCDILLK-NNYEVIAVSRNF 37
                89*****************999.888888876654 PP

>> Ldh_1_N  lactate/malate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     6e-05     0.097       1      25 [.       4      28 ..       4      45 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6e-05
                EEEEEETTTSHHHHHHHHHHHHTTS CS
     Ldh_1_N  1 vkvavvGaaGgiGqslalllankkl 25
                +kv v+Ga G+iG++l   l+++++
  EPA05222.1  4 MKVLVTGADGFIGSHLCDILLKNNY 28
                69*************9877766654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 403.64
//
Query:       EPA05223.1  [L=354]
Description: CDP-glucose 4,6-dehydratase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.8e-35  120.8   0.0    2.4e-34  119.3   0.0    1.8  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    2.4e-31  109.0   0.0    3.7e-31  108.4   0.0    1.2  1  Epimerase        NAD dependent epimerase/dehydratase family
      1e-14   54.4   0.0    6.3e-14   51.8   0.0    2.0  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    2.6e-09   36.5   0.0    3.4e-09   36.1   0.0    1.2  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    2.1e-07   30.3   0.0    2.8e-07   29.9   0.0    1.1  1  RmlD_sub_bind    RmlD substrate binding domain
    1.6e-05   24.2   0.0    6.9e-05   22.1   0.0    2.1  2  NAD_binding_4    Male sterility protein
  ------ inclusion threshold ------
        1.1    9.3   5.5        9.9    6.2   0.2    2.9  3  DMP12            DNA-mimic protein


Domain annotation for each model (and alignments):
>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.3   0.0   9.2e-38   2.4e-34       1     330 [.      12     325 ..      12     327 .. 0.79

  Alignments for each domain:
  == domain 1  score: 119.3 bits;  conditional E-value: 9.2e-38
                    EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHTTSHH CS
  GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevynLAAqshVdvsfekPe 96 
                    L+TG +Gf Gs+l  lL + + +v+g+ +    +n  ++ +la     ++e+ ++ + gD++D ++le  ++e++p+ v+++AAq   ++s+++P 
     EPA05223.1  12 LVTGHTGFKGSWLSLLLQRLNADVVGFSKSIP-TN-PSLFELA-----HIENGMTSIIGDICDYDKLEFTIKEHKPEIVIHMAAQAILRESYSNPI 100
                    9*************************854322.23.3343443.....56778999**************************************** PP

                    HHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSS.B-TTS-----SHHHHHHHHHHHHHHHHHHH.........H---EEEEEE-E CS
  GDP_Man_Dehyd  97 ytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevp.qtEttpfyPrsPYaaaKlyadwivvnyrea.........yglfavngilfn 182
                    +t+ +nv+Gt++LLe ir++   + + ++ + t+ +Y   ++ +   Et ++    PY+ +K+ ++ ++ ++r++         +g    + +  n
     EPA05223.1 101 ETYSTNVMGTVNLLESIRKTS--DVKVILNVTTDKCYEPNESLKgHIETDRLGGYDPYSNSKACSELVTASFRDSffnpkehqkHGTSLASCRAGN 194
                    ******************985..456789********8888766367**************************99555444333344444455555 PP

                    EESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHHHHHHHHCSS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH..... CS
  GDP_Man_Dehyd 183 hesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyveamwlmlqqdkpedyviatgethsvrefvelaflelgktiewegkgee 278
                      +         r+i++++  i++++  ++++ n +++R w++v D  +++ ++ ++        ++g ++s +   +   ++  k ++w  ++ +
     EPA05223.1 195 VIGGG--DWGKDRLIPDIIRGILNNE--IIKIRNPNSTRPWQYVLDPLNGYLTLAEKL------WSSGSEFSEG--WNFGPQDDEKPVKWIVEKIT 278
                    54444..346799********99976..88999******************9877654......4556555443..22223333344555544444 PP

                    .......TTGGCCCEECGG--SS--SB--B-THHHHHHH----SS-HHHHHH CS
  GDP_Man_Dehyd 279 evgrakesgkvvvevdpkyfrpgevdlllgdaskakeeLgWkpkvsfeelvr 330
                    e    + s++++  vd  +  p e++ l  ++ska+++L+W pk ++e++++
     EPA05223.1 279 E----QWSKDIRWDVDNGT-NPHEENHLRLNCSKANSRLEWMPKLNVEQGLE 325
                    3....44567888898665.59***************************986 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.4   0.0   1.4e-34   3.7e-31       1     228 [.      11     247 ..      11     256 .. 0.92

  Alignments for each domain:
  == domain 1  score: 108.4 bits;  conditional E-value: 1.4e-34
                 EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTC.HHCHHC....EEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHHHSHHHHHHHHTHH CS
   Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasnt.arledl....elveldltdrsalerlfkeeqpdavihlAavggvaassedpadfieknlqg 94 
                 +lVtG+tGf Gs l   l++ + +v+g+++   ++++  +l+++    + + +d++d ++le  +ke++p++vih+Aa++  ++s ++p +++ +n++g
  EPA05223.1  11 VLVTGHTGFKGSWLSLLLQRLNADVVGFSKSIPTNPSlFELAHIengmTSIIGDICDYDKLEFTIKEHKPEIVIHMAAQAILRESYSNPIETYSTNVMG 109
                 79**************************9996555541445555999**************************************************** PP

                 HHHHHHHHHHH.TCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHHHHHHH.T........-EEEEEEESEEESTTS-TTSTT CS
   Epimerase  95 tlnlleaarka.gvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklveayaaqy.g........lnaiilrlfnlyGprngegevs 183
                 t+nlle +rk+ +vk +l++ ++  Y ++++   +  ++t+ l    pY+ +K+++e ++ ++++++ +        ++  + r  n++G +  +   +
  EPA05223.1 110 TVNLLESIRKTsDVKVILNVTTDKCYEPNES--LKGHIETDRLGGYDPYSNSKACSELVTASFRDSFfNpkehqkhgTSLASCRAGNVIGGG--DWGKD 204
                 *********998***************9999..6677777799********************99885588888888***************..788** PP

                 SHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHH CS
   Epimerase 184 rvipalirkilegkqevtllgdgtalRdflyveDvaeaillvleh 228
                 r+ip +ir il+++  ++ + + ++ R++ yv D  +++l+++e+
  EPA05223.1 205 RLIPDIIRGILNNE--IIKIRNPNSTRPWQYVLDPLNGYLTLAEK 247
                 ***********987..99999****************99999998 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.8   0.0   2.5e-17   6.3e-14       1     199 [.      11     227 ..      11     236 .. 0.67

  Alignments for each domain:
  == domain 1  score: 51.8 bits;  conditional E-value: 2.5e-17
                      EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-SEEEE------HHHHH CS
  Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvdvvfhaAAlKhVPlve 94 
                      vlvtG +G  Gs l   +l++  + ++ ++++  +  ++ +         +++  ++++igd+ d ++le +++e+k+++v+h AA   +    
       EPA05223.1  11 VLVTGHTGFKGSWLSL-LLQRLNADVVGFSKSIPTNPSLFEL-------AHIENGMTSIIGDICDYDKLEFTIKEHKPEIVIHMAAQAILRESY 96 
                      5677777777766543.4444444555555554444333332.......2344456789*********************************** PP

                      HSHHHHHHHHHHHHHHHHHHHHH.TT-SEEEEEEEGGGSS--SH.........HH......HHHHHHHHHHHHGGG--SSS-......-EEEEE CS
  Polysacc_synt_2  95 enpleaiktNvlgtenvieaaie.agvkkvvliStDKAvnPtnv.........mG......atKrlaekllqalakeseekk......tkfvvv 166
                      +np+e+ +tNv+gt n++e   + ++vk ++ + tDK  +P            +G       +K+++e+++ +++++  + k      t ++  
       EPA05223.1  97 SNPIETYSTNVMGTVNLLESIRKtSDVKVILNVTTDKCYEPNESlkghietdrLGgydpysNSKACSELVTASFRDSFFNPKehqkhgTSLASC 190
                      ******************98765278999999*********75311111222222232222689999999888776543322334456999999 PP

                      EE-EETTG....TTSSHHHHHHHHHTTSSEEES-TT- CS
  Polysacc_synt_2 167 RfGNVlgS....rGSviplFkkqikeggpvtvTdpem 199
                      R GNV+g     +  +ip   + i +++ + + +p+ 
       EPA05223.1 191 RAGNVIGGgdwgKDRLIPDIIRGILNNEIIKIRNPNS 227
                      9999998522113345555555555555555555555 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.0   1.3e-12   3.4e-09       1     157 [.      12     167 ..      12     235 .. 0.75

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 1.3e-12
   3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlD..lrespelleelskvnvkkviegDvtdkdkleealegvd..vvihlaslvdvagklte.deimkvnvk 94 
                 +vtG +GF G+ l   L rl+   +v  +   + ++p+l e ++  n  + i gD++d dkle  +++ +  +vih+a+   ++  +++  e ++ nv 
  EPA05223.1  12 LVTGHTGFKGSWLSLLLQRLN--ADVVGFSksIPTNPSLFELAHIENGMTSIIGDICDYDKLEFTIKEHKpeIVIHMAAQAILRESYSNpIETYSTNVM 108
                 69*********9977777776..466666534667777877777777777****************9874449****99999988655415799***** PP

   3Beta_HSD  95 GTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKalaEklv 157
                 GT n+le+ +k++  +++ + + +  ++    +e l+g+ e+ +     d+y++sKa +E + 
  EPA05223.1 109 GTVNLLESIRKTSDVKVILNVTTDKCYE---PNESLKGHIETDRLG-GYDPYSNSKACSELVT 167
                 *********9987666666666666666...455555887776654.5699******999543 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.0   1.1e-10   2.8e-07       2     135 ..      10     166 ..       9     174 .. 0.91

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 1.1e-10
                    EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT....................T--TTSHHHHHHHHHHH--SEEEE------HHHHHHSHHHHHHH CS
  RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltre....................eldltdaeavaellkeakpdvvvnaAAytavDkaEseeeaayav 77 
                    k+lvtG +G  Gs L  +l++ +++v++++++                      d+ d ++++ ++ke+kp++v+++AA     +  s++ + y  
     EPA05223.1  10 KVLVTGHTGFKGSWLSLLLQRLNADVVGFSKSiptnpslfelahiengmtsiIGDICDYDKLEFTIKEHKPEIVIHMAAQAILRESYSNPIETYST 105
                    79***************************999******************9999****************************************** PP

                    HTHHHHHHHHHHHHC.T-E.EEEEEEGGGS-S-TTS-.B-TTS----SSHHHHHHHHHHHH CS
  RmlD_sub_bind  78 naeavealAeaaaav.gal.LihvStDyVFdGekkrp.YeeddetsPlnvYGrtKlaGEqa 135
                    n+ ++ +l e  +++ +++ ++ v tD  ++ +++ +   e+d+ +    Y ++K+  E +
     EPA05223.1 106 NVMGTVNLLESIRKTsDVKvILNVTTDKCYEPNESLKgHIETDRLGGYDPYSNSKACSELV 166
                    ********9998776255515689******9997766699**************9988865 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.36   9.2e+02       1      12 [.      13      24 ..      13      36 .. 0.76
   2 !   22.1   0.0   2.7e-08   6.9e-05      89     190 ..      81     170 ..      57     216 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.36
                   EE-TTSHHHHHH CS
  NAD_binding_4  1 lTGaTGFLGkvL 12
                   +TG TGF G+ L
     EPA05223.1 13 VTGHTGFKGSWL 24
                   7******99877 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 2.7e-08
                    -EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H......HHH--EEEETTTCCCHHHHHHH CS
  NAD_binding_4  89 dviihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegekeekldederaklkglpntYeqsKa 181
                    +++ih+aA+  + e+y++    +++Nv+Gt+++le  +k++  kv+l v T  +++ +e+               l++  +++  g  + Y++sKa
     EPA05223.1  81 EIVIHMAAQAILRESYSNpieTYSTNVMGTVNLLESIRKTSDVKVILNVTTDKCYEPNES---------------LKGHIETDRLGGYDPYSNSKA 161
                    79***************86667899**************************666666663...............456666666666789999**9 PP

                    HHHHHHHHH CS
  NAD_binding_4 182 laEklvrea 190
                    ++E +  + 
     EPA05223.1 162 CSELVTASF 170
                    999887665 PP

>> DMP12  DNA-mimic protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       2.3     6e+03      22      46 ..     200     224 ..     198     234 .. 0.78
   2 ?    6.2   0.2    0.0039       9.9      48      93 ..     247     296 ..     240     308 .. 0.75
   3 ?    4.5   0.7     0.013        34      21      46 ..     328     353 ..     317     354 .] 0.87

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.3
                 HHHHHTTTSTTEEEE-HHHHHHHHH CS
       DMP12  22 dwaykniqsetvveitenqiieyqn 46 
                 dw  + +  + +  i +n+ii+ +n
  EPA05223.1 200 DWGKDRLIPDIIRGILNNEIIKIRN 224
                 6777777778888888899988777 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0039
                 THHHHHHHHHS--TTS--SEE....EEE-HHHHHHHHHHHHTSTTTTSHH CS
       DMP12  48 glwrlvseitdnwlfgpsegd....wlidkesilavkeklqnsdfstepl 93 
                  lw+  se ++ w fgp + +    w+++k +    k+   + d  t+p 
  EPA05223.1 247 KLWSSGSEFSEGWNFGPQDDEkpvkWIVEKITEQWSKDIRWDVDNGTNPH 296
                 69***************986433448888877666666666666666665 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.013
                 HHHHHHTTTSTTEEEE-HHHHHHHHH CS
       DMP12  21 vdwaykniqsetvveitenqiieyqn 46 
                 ++w  +  q++ + eite+qi e+q+
  EPA05223.1 328 IQWYKQYEQNKDMKEITEQQIEEFQK 353
                 78988889999************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 2395.03
//
Query:       EPA05224.1  [L=381]
Description: putative membrane protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.8e-09   35.8  13.2    8.8e-09   35.8  13.2    2.9  3  PMT_2     Dolichyl-phosphate-mannose-protein mannosyltransfer
  ------ inclusion threshold ------
        2.1    8.3   4.1         20    5.2   1.9    2.8  2  Sec20     Sec20


Domain annotation for each model (and alignments):
>> PMT_2  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.15   1.3e+03      23      40 ..      21      38 ..      12      51 .. 0.55
   2 !   35.8  13.2   9.8e-13   8.8e-09       9     158 ..      80     231 ..      77     232 .. 0.80
   3 ?    1.0   3.8      0.05   4.5e+02      30     112 ..     286     371 ..     276     376 .. 0.63

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.15
       PMT_2 23 airlvsalagvltillly 40
                ++ l++++++v  ++ ly
  EPA05224.1 21 SLLLLAIICVVAIVIRLY 38
                333334444444444333 PP

  == domain 2  score: 35.8 bits;  conditional E-value: 9.8e-13
       PMT_2   9 llalftklfgfselairl.....vsalagvltilllyllarrlfgkraallaalllavvplfvalsalftpdaplvllwalalylllraleknklkywl 102
                 +l+lf+++f+++++  ++     vs++++ +t++ +y++ +++f++  +l++al+ a+ p +++ s+l+  + + ++++   ++ ++ +l +nk ky +
  EPA05224.1  80 FLSLFFMIFHSDNFMDYMnlqrgVSVVLSGITVIPVYFICKKFFNNYYSLIGALIFALDPRIIINSTLGISEPLYIFAI---TLGIMFFLNSNK-KYVY 174
                 6899999998755543322333399***********************************9999999665444444444...444555677888.899* PP

       PMT_2 103 lagvlfGlgflsKytaallliaall.yllisarrilkekkpyl.alllalllfspvli 158
                 l+  +f++++ ++++  +  +a+++ y+l   r+  k+ ++++ al+++ll+ sp+++
  EPA05224.1 175 LSFGFFAWATIIRPEGQFWFVAFTIiYFLRF-RKSRKDCMLFIiALAVFLLVLSPFVY 231
                 ******************9999998888888.777777555555**********9986 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.05
       PMT_2  30 lagvltilllyllarrlfgkraallaalllavvplfvalsa...lftpdaplvllwalalylllraleknklkywllagvlfGlgf 112
                 ++++l+ ++l  ++++l  ++  l+ a  + ++p+++ +s    +  ++ ++  + +++l+ +   +ek + k  +l+ +++G++f
  EPA05224.1 286 IFVILVPIGLIPILKQLRYPNYLLVLAPAVLAIPIMYSVSIapdTRYVYPLFPIFCVISLFGISWIVEKFSNKKVILSVIVIGIIF 371
                 68888888888889998776666655555555565555555332222222333444445555555666777888888888888877 PP

>> Sec20  Sec20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.023   2.1e+02      68      82 ..     168     182 ..     166     186 .. 0.83
   2 ?    5.2   1.9    0.0022        20      64      92 .]     206     234 ..     197     234 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.023
       Sec20  68 tdkllvflalglfla 82 
                 ++k  v+l++g+f  
  EPA05224.1 168 SNKKYVYLSFGFFAW 182
                 57899********65 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0022
       Sec20  64 rrdktdkllvflalglflacvvyvvkkRi 92 
                 r++++d +l ++al+ fl++ +  v++Ri
  EPA05224.1 206 RKSRKDCMLFIIALAVFLLVLSPFVYQRI 234
                 78999******************9*9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       920  (0.0513135); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 2243.38
//
Query:       EPA05225.1  [L=412]
Description: C-methyltransferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-65  219.1   0.0    4.7e-65  218.3   0.0    1.4  1  Methyltransf_14  C-methyltransferase C-terminal domain
    2.9e-19   69.1   1.0    5.1e-19   68.3   1.0    1.4  1  Methyltransf_13  Putative zinc binding domain
      4e-14   52.8   0.0    7.4e-14   51.9   0.0    1.4  1  Methyltransf_23  Methyltransferase domain
    1.1e-08   35.7   0.0    3.3e-08   34.2   0.0    1.8  2  Methyltransf_12  Methyltransferase domain
    1.7e-08   34.4   0.1    3.7e-08   33.3   0.1    1.8  1  Methyltransf_31  Methyltransferase domain
    4.8e-07   30.3   0.0    1.3e-06   28.9   0.0    1.8  2  Methyltransf_11  Methyltransferase domain
    8.5e-05   23.2   0.0    0.00027   21.6   0.0    1.9  2  Methyltransf_25  Methyltransferase domain
  ------ inclusion threshold ------
      0.066   12.8   0.0       0.11   12.1   0.0    1.3  1  MetW             Methionine biosynthesis protein MetW


Domain annotation for each model (and alignments):
>> Methyltransf_14  C-methyltransferase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.3   0.0   2.1e-68   4.7e-65       1     160 []     248     407 ..     248     407 .. 1.00

  Alignments for each domain:
  == domain 1  score: 218.3 bits;  conditional E-value: 2.1e-68
  Methyltransf_14   1 pthGGslrvyaakkeeakkevseavaellaeEkaagldeletyaeFaervekvkeellalllelkaegkkvvgYGAaakgntllnycgigpdll 94 
                      pthGGslr+y++++e +  +v+++v+ ll++Ek +gl++++ty++F ++ve+vk++l+++ ++ k++gkk+v YGAaakgntllnycgig++++
       EPA05225.1 248 PTHGGSLRIYVKHSEYEGISVNQTVNILLEKEKLFGLENISTYTDFIKNVERVKKKLYEFFKDSKNSGKKIVCYGAAAKGNTLLNYCGIGNNFI 341
                      79******************************************************************************************** PP

  Methyltransf_14  95 dyvvDrnpaKqgkflPgthiPivspeklkeekpdyvlilaWnlkeeileqlaeirekggkfivpvP 160
                      dyvvD+np+Kqg +lPgthiPi sp++++++kpdy++i++Wnlk+ei+eq+++ir++ggkf++p+P
       EPA05225.1 342 DYVVDQNPYKQGLYLPGTHIPIKSPDEIQNTKPDYLVIIPWNLKDEIIEQMKYIRDWGGKFVIPIP 407
                      *****************************************************************9 PP

>> Methyltransf_13  Putative zinc binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.3   1.0   2.3e-22   5.1e-19       1      62 []       8      69 ..       8      69 .. 0.99

  Alignments for each domain:
  == domain 1  score: 68.3 bits;  conditional E-value: 2.3e-22
  Methyltransf_13  1 CRiCgsellepvldLgeqplansflkpeqldepepfyplrlvvCedCglvQleevvdpeelF 62
                     CR+C+++l++ ++dLg +pl+nsflk+e  +  e++ypl ++vC++C+lvQl e+ +pe++F
       EPA05225.1  8 CRFCNKPLTNIFVDLGITPLSNSFLKKEIIHNSEKKYPLCTYVCSSCFLVQLPEFEKPENIF 69
                     ************************************************************99 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.9   0.0   3.3e-17   7.4e-14      21     162 ..     100     241 ..      82     244 .. 0.87

  Alignments for each domain:
  == domain 1  score: 51.9 bits;  conditional E-value: 3.3e-17
  Methyltransf_23  21 raggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae.....kakkaqkdqfdeqeaaepqgkfdlIvlrevlehvpdppellrqiatll 109
                      ++++ v++i+ ++G+ll+ ++e+   + g+++  + v++++      +++ +++   ++e + +++k dlI+ ++vl hvp++   ++ ++ ll
       EPA05225.1 100 DEKKLVIEIASNDGYLLQFFKEKDIPILGIEPAVN-VAKVAkekgiPTITKFFSADTAEELKSEDKKADLIIGNNVLAHVPNLNDFVKGLKILL 192
                      667889**************************755.5555569999555555555558889999****************************** PP

  Methyltransf_23 110 kpgGylllseplaslkedrllldwlylvpagrhisffsarslkelleeaGlev 162
                      kp G + l+ p    + ++l+++++++ + ++h+s+fs  + k+++   Gl++
       EPA05225.1 193 KPTGIITLEFP----HLLQLIQKNQFDTIYHEHFSYFSLITAKKIFSFHGLTI 241
                      ***********....9****************************999999987 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.0   1.5e-11   3.3e-08       2      99 .]     107     198 ..     106     198 .. 0.95
   2 ?   -3.2   0.0       6.7   1.5e+04      64      72 ..     211     219 ..     203     236 .. 0.54

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 1.5e-11
  Methyltransf_12   2 eiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlkdirevldnirklLkp 95 
                      ei +++G ll+ + ek  di ++g+++  ++ + akek    + ++++  + e+l ++d+    + Dl++ +nvl h+++++++++ ++ lLkp
       EPA05225.1 107 EIASNDGYLLQFFKEK--DIPILGIEPAVNVAKVAKEKGIPTITKFFSADTAEELKSEDK----KADLIIGNNVLAHVPNLNDFVKGLKILLKP 194
                      8999************..*************************99999999999997766....9***************************** PP

  Methyltransf_12  96 gGrl 99 
                       G++
       EPA05225.1 195 TGII 198
                      *975 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 6.7
  Methyltransf_12  64 gssfDlvva 72 
                      +++fD+++ 
       EPA05225.1 211 KNQFDTIYH 219
                      345666543 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.1   1.7e-11   3.7e-08       5     126 ..     103     213 ..      99     329 .. 0.86

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 1.7e-11
  Methyltransf_31   5 lrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDlilsnevlnaladpdkileei 97 
                      + v++++++ G+l+  + e+    + + Gi+   ++ ++A+e   k   +  +F  +d  e l+   ed+k Dli+ n+vl+++++++++ +++
       EPA05225.1 103 KLVIEIASNDGYLLQFFKEKD---IPILGIEPAVNVAKVAKE---KGIPTITKFFSADTAEeLK--SEDKKADLIIGNNVLAHVPNLNDFVKGL 188
                      5689999*****999999775...55***9766666666665...55566889*****999788..68************************** PP

  Methyltransf_31  98 ervlkpggilliedprllaelpakveees 126
                      + +lkp gi+ +e p+    l++ +++++
       EPA05225.1 189 KILLKPTGIITLEFPH----LLQLIQKNQ 213
                      ************9999....444444444 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0     6e-10   1.3e-06       2      94 ..     107     198 ..     106     200 .. 0.89
   2 ?   -4.2   0.0         8   1.8e+04      58      69 ..     210     221 ..     209     224 .. 0.77

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 6e-10
                      EET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEE.CCCTSS-TT-EEEEEEES-CCC-CCHHHHHHHHHHHEEEEEEE CS
  Methyltransf_11   2 dvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvad.aeklpfednsfDlvvssevlhhvedpekalkeiaRvLkpgGll 94 
                      ++++  G+l++ ++++   ++g++++ ++ k+akek+ +     +f  ad ae+l+ ed++ Dl++ ++vl hv+++++++k ++ +Lkp G++
       EPA05225.1 107 EIASNDGYLLQFFKEKDIPILGIEPAVNVAKVAKEKGIPTI--TKFFSADtAEELKSEDKKADLIIGNNVLAHVPNLNDFVKGLKILLKPTGII 198
                      6778889999999988899******************9998..56766661557**************************************97 PP

  == domain 2  score: -4.2 bits;  conditional E-value: 8
                      -TT-EEEEEEES CS
  Methyltransf_11  58 ednsfDlvvsse 69 
                      ++n+fD ++  +
       EPA05225.1 210 QKNQFDTIYHEH 221
                      579999998765 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   1.2e-07   0.00027       1      97 []     105     196 ..     105     196 .. 0.87
   2 ?   -2.8   0.0       4.7   1.1e+04      61      79 ..     210     227 ..     206     235 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.2e-07
                      EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBC.CGBSSSTTTEEEEEEESTGGGSSHHHHHHHHHHHHHH CS
  Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgda.edlpfedgsfDlvvssgalhhlsdedlekalkeiarv 92 
                      v++++   G l++ + ++  +  ++g++++ +  + a+e+     +   +f  +d  e+l+ ed++ Dl++ +++l h++  +l +++k ++ +
       EPA05225.1 105 VIEIASNDGYLLQFFKEK--DIPILGIEPAVNVAKVAKEKGI---PtITKFFSADTaEELKSEDKKADLIIGNNVLAHVP--NLNDFVKGLKIL 191
                      789999999999999998..499****************994...33566766666499*************88899987..899********* PP

                      EEEEE CS
  Methyltransf_25  93 LkpgG 97 
                      Lkp G
       EPA05225.1 192 LKPTG 196
                      ***98 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.7
                      STTTEEEEEEESTGGGSSH CS
  Methyltransf_25  61 edgsfDlvvssgalhhlsd 79 
                      ++++fD ++   +++++s 
       EPA05225.1 210 QKNQFDTIYH-EHFSYFSL 227
                      5689999998.57777764 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   4.7e-05      0.11      14      93 ..     102     183 ..      88     204 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.7e-05
        MetW  14 gsrvldlGcGdGellellkeekqvdgrGleldeegvaecvakGlsviqg....dldkdlenfedksfdyvvlsqtlqatrnpke 93 
                 +  v+++ + dG ll+++ke k++   G+e   +  + + +kG+  i +    d  ++l+  edk+ d+++ +  l  + n + 
  EPA05225.1 102 KKLVIEIASNDGYLLQFFKE-KDIPILGIEPAVNVAKVAKEKGIPTITKffsaDTAEELK-SEDKKADLIIGNNVLAHVPNLND 183
                 566999************77.*********99999999999***8886522115555554.58999999999998888776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       842  (0.046963); expected 358.6 (0.02)
Passed bias filter:                      619  (0.0345251); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 2631.11
//
Query:       EPA05226.1  [L=234]
Description: methyltransferase, FkbM family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.4e-17   62.1   1.8      2e-16   60.5   1.8    1.7  1  Methyltransf_21  Methyltransferase FkbM domain
    3.7e-08   33.0   2.3    4.4e-08   32.7   2.3    1.2  1  V_cholerae_RfbT  Vibrio cholerae RfbT protein
    1.3e-06   28.3   0.1    2.5e-06   27.4   0.1    1.4  1  Met_10           Met-10+ like-protein
  ------ inclusion threshold ------
      0.014   15.6   0.5      0.014   15.6   0.5    2.0  2  Methylase_S      Type I restriction modification DNA specific
       0.15   11.5   0.1       0.21   11.0   0.1    1.2  1  DUF5009          Domain of unknown function (DUF5009)
       0.27   11.3   4.9        1.1    9.3   1.0    2.8  3  SL4P             Uncharacterized Strongylid L4 protein


Domain annotation for each model (and alignments):
>> Methyltransf_21  Methyltransferase FkbM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.5   1.8   6.9e-20     2e-16       1     171 [.      61     216 ..      61     218 .. 0.67

  Alignments for each domain:
  == domain 1  score: 60.5 bits;  conditional E-value: 6.9e-20
  Methyltransf_21   1 dvGanigvwdsfanltarlcggggevlaiEPvpnslpkfeklranlltlavgndvglyelivegksg..gkyfpfavgdtngfstssvlggeda 92 
                      dvGa+ig +   a ++++ c++g+ ++++EP ++   ++e l +n     ++    +++ i++ + +  +++    ++ +   s +s++  + +
       EPA05226.1  61 DVGAHIGLF---ALFASQFCKNGK-IYCFEPIKE---NYEMLSDN---TNLN----EIKNIIPLNLAvsKENEHVRIYLDLDESAHSIF-PQGN 139
                      9******44...444456799999.55*******...88888888...5555....333333333222122222222223333333333.4899 PP

  Methyltransf_21  93 ryievpvvtldsfleeikksridllkiDvEGaElevLeG..aqkglkrcqpnlivvEvhkfkefetelfdeirqflrecgy 171
                      + ++v  +t+  f++e+k++ +dl+kiD+EGaE+e++ +  +++  +   +n i++E h    +  el ++++++l+++ +
       EPA05226.1 140 TFVDVKSTTVKRFFDEYKIENCDLVKIDCEGAEYEIIDSipEEYFSR---INKIIIEYHLID-KKLELYQNLLKKLENMSF 216
                      99***********************************8884555554...566668998753.333677777777777665 PP

>> V_cholerae_RfbT  Vibrio cholerae RfbT protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   2.3   1.5e-11   4.4e-08      80     219 ..      56     189 ..      20     214 .. 0.82

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 1.5e-11
  V_cholerae_RfbT  80 dttyidiganvgtfcgiaarhitqgkiiaiepltemensirmnvqlnnplvefhhfgcaigenegenifevyefdnrvsslyfkkntdiadkvk 173
                      +   +d+ga +g f+  a+++  +gki + ep+ e  + +  n +ln+ + ++  +  a+ + e e +    ++d+   s++ + nt +   vk
       EPA05226.1  56 NDIIVDVGAHIGLFALFASQFCKNGKIYCFEPIKENYEMLSDNTNLNE-IKNIIPLNLAVSK-ENEHVRIYLDLDESAHSIFPQGNTFVD--VK 145
                      55679****************************************987.5667777777753.4455555579**************885..55 PP

  V_cholerae_RfbT 174 nsqvlvrklssldisptnsvvikidaegaeieilnqiye.ftekhng 219
                       +  + r +    i   n  ++kid+egae ei++ i e +  + n 
       EPA05226.1 146 ST-TVKRFFDEYKIE--NCDLVKIDCEGAEYEIIDSIPEeYFSRINK 189
                      44.445777777775..77789**************96525555554 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.1   8.2e-10   2.5e-06      98     158 ..      53     112 ..      47     152 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 8.2e-10
                 --TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES CS
      Met_10  98 veegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpile 158
                 +++++++vdv A iG fa+ +++++k+ +++  +   e +++l +n +lN++++++ p++ 
  EPA05226.1  53 IRDNDIIVDVGAHIGLFALFASQFCKNGKIYCFEPIKENYEMLSDNTNLNEIKNII-PLNL 112
                 679***************************************************99.6654 PP

>> Methylase_S  Type I restriction modification DNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.5   4.7e-06     0.014      39     103 ..      34      95 ..       7     123 .. 0.70
   2 ?   -0.4   0.2      0.38   1.1e+03      94     125 ..     194     224 ..     172     227 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.7e-06
                  HCCTEE-HHHHCCTT---B-..TT-EEEE-SSSTT-EEEESS-BEE-TTEEEEEESTTT--HHHHHH CS
  Methylase_S  39 ilnnkvvkdglgykkkyilp..kgdilissratiGkvayrdkkyylnqsvivlipknkkkineflyl 103
                  i++  ++ ++++ ++   ++   +di++  +a+iG +a++   ++ n ++++++p++  +  +++ l
   EPA05226.1  34 IMQL-GTVWFTNDYNMPGFEirDNDIIVDVGAHIGLFALFASQFCKNGKIYCFEPIK--E--NYEML 95 
                  3444.677777777765555448********************************75..2..34444 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.38
                  TT--HHHHHHHHHHCHHHHHHHCCSSTTT--- CS
  Methylase_S  94 kkkineflylylllklkklkslsvgstqpklt 125
                   ++i    + +++++lkkl++ s+ + + k++
   EPA05226.1 194 YHLI-DKKLELYQNLLKKLENMSFKTKTRKIS 224
                  4555.334445556677777777777776665 PP

>> DUF5009  Domain of unknown function (DUF5009)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   7.1e-05      0.21     135     200 ..      11      79 ..       1      86 [. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 7.1e-05
     DUF5009 135 lsikkklkkkaalvikvvafllaialllllqfkngk...kfslyksdiiilvlanmalfgsliylltqk 200
                 ++ +  l+ + +l ik+ ++   i+ l ++ f+n+    +f++  +dii+ v a + lf+ +   + ++
  EPA05226.1  11 KKDQVILETRNKLKIKIRTHSTDIMQLGTVWFTNDYnmpGFEIRDNDIIVDVGAHIGLFALFASQFCKN 79 
                 334445789999********************9986233699**************9999776666555 PP

>> SL4P  Uncharacterized Strongylid L4 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.048   1.4e+02      52      82 ..      97     128 ..      86     133 .. 0.76
   2 ?   -3.3   0.0       3.2   9.6e+03      39      55 ..     155     171 ..     149     176 .. 0.56
   3 ?    9.3   1.0   0.00037       1.1      12      45 ..     183     219 ..     181     230 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.048
        SL4P  52 edgdrilirnaddLleavk.dnavvklyvrde 82 
                 ++++  +i+n   L  av+ +n++v++y+  +
  EPA05226.1  97 DNTNLNEIKNIIPLNLAVSkENEHVRIYLDLD 128
                 677889999999999666659******98755 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.2
        SL4P  39 elgipldevywvdedgd 55 
                 e++i    +  +d +g 
  EPA05226.1 155 EYKIENCDLVKIDCEGA 171
                 44555555555555555 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.00037
        SL4P  12 yrekvprftItYk..Dkd.dLfekfkkklkelgipld 45 
                 y++++ +++I+Y   Dk+ +L++ + kkl+ ++++ +
  EPA05226.1 183 YFSRINKIIIEYHliDKKlELYQNLLKKLENMSFKTK 219
                 778999******99987549***********999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       900  (0.050198); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.54
# Mc/sec: 1311.49
//
Query:       EPA05227.1  [L=144]
Description: hypothetical protein BG20_I0207 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1014.81
//
Query:       EPA05228.1  [L=347]
Description: methyltransferase domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-14   54.9   0.0    2.1e-14   53.9   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
    1.3e-13   51.4   0.0    2.8e-13   50.4   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
      1e-10   41.6   0.0    1.7e-10   40.9   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    3.5e-09   36.7   0.0    5.4e-09   36.1   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    4.2e-07   30.6   0.0    7.8e-07   29.8   0.0    1.5  1  Methyltransf_12  Methyltransferase domain
     0.0013   18.2   0.0     0.0026   17.2   0.0    1.5  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
     0.0034   16.4   0.0     0.0053   15.7   0.0    1.2  1  Methyltransf_9   Protein of unknown function (DUF1698)
  ------ inclusion threshold ------
      0.012   15.2   0.0      0.025   14.2   0.0    1.4  1  MetW             Methionine biosynthesis protein MetW
      0.057   13.9   0.0       0.11   13.0   0.0    1.5  1  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
       0.22   10.5   0.0       0.35    9.8   0.0    1.2  1  Glucokinase      Glucokinase


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.9   0.0   1.2e-17   2.1e-14       1      95 [.     114     207 ..     114     208 .. 0.90

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 1.2e-17
                      EEET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHHHHHHHHHHEEEEEE CS
  Methyltransf_11   1 LdvGcGtGrlaealakrg.arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedpekalkeiaRvLkpgGl 93 
                      Ld+G+G G  a+ l  +  a v+++D s+ +   a +k+  +  ++ f++ad+++lpf++n fD v+s +vlhh ++ e  +k + + Lk+ G+
       EPA05228.1 114 LDAGTGLGNSANFLSTNKqALVFAIDASESVN-FAYKKYGSAA-NIHFLQADLRQLPFKKNFFDYVYSDQVLHHTKNTETSFKYLTKFLKKAGH 205
                      8**************66679******888876.7766666666.499**********************************************9 PP

                      EE CS
  Methyltransf_11  94 lv 95 
                      + 
       EPA05228.1 206 IS 207
                      86 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.4   0.0   1.5e-16   2.8e-13       1      97 []     113     204 ..     113     204 .. 0.87

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 1.5e-16
                      EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHHHHHHHHHHHHHEE CS
  Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsdedlekalkeiarvLk 94 
                      +Ld+G+G G+ +  l+++ ++a v ++D se+  + a +++ +  +n++f+q+d+++lpf+++ fD+v+s ++lhh++  ++e+ +k + + Lk
       EPA05228.1 113 ILDAGTGLGNSANFLSTN-KQALVFAIDASESV-NFAYKKYGS-AANIHFLQADLRQLPFKKNFFDYVYSDQVLHHTK--NTETSFKYLTKFLK 201
                      8***************99.69********9765.677777744.46************************666***77..56788999999999 PP

                      EEE CS
  Methyltransf_25  95 pgG 97 
                      + G
       EPA05228.1 202 KAG 204
                      877 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   0.0   9.2e-14   1.7e-10       6     113 ..     112     212 ..     109     258 .. 0.85

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 9.2e-14
  Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDlilsnevlnaladpdkileeie 98 
                      ++lD+G+G G+ +  l    +++a v+ iD s e++++A +   k g+  n++F q+d  +l+  ++++ fD++ s++vl+++++ +  ++ ++
       EPA05228.1 112 YILDAGTGLGNSANFLS--TNKQALVFAIDAS-ESVNFAYK---KYGSAaNIHFLQADLRQLP--FKKNFFDYVYSDQVLHHTKNTETSFKYLT 197
                      79***************..789999*****98.589***99...566666*************..***************************** PP

  Methyltransf_31  99 rvlkpggilliedpr 113
                      + lk+ g++ i  ++
       EPA05228.1 198 KFLKKAGHISIYVYN 212
                      ********9987666 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.0     3e-12   5.4e-09      20     146 ..     107     235 ..      84     248 .. 0.79

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 3e-12
  Methyltransf_23  20 lraggrvLdiGcGtGillevlren.gfsvtgvDlspeaveiae...kakkaqkdqfdeqeaaepqgkfdlIvlrevlehvpdppellrqiatll 109
                      l ++  +Ld G+G G+ ++ l++n ++ v ++D+s+  +  ++   +a + ++ q+d  + +++++ fd++++ +vl+h ++ +  ++ + + l
       EPA05228.1 107 LLTKHYILDAGTGLGNSANFLSTNkQALVFAIDASESVNFAYKkygSAANIHFLQADLRQLPFKKNFFDYVYSDQVLHHTKNTETSFKYLTKFL 200
                      457789***************9994557779***976555555999************************************************ PP

  Methyltransf_23 110 kpgGylllseplaslkedrllldwlylvpagrhisff 146
                      k  G++ + +++++++  r + d  y++ + +++s+ 
       EPA05228.1 201 KKAGHISIYVYNKKAP-IREFAD-DYIRSKTTKMSVS 235
                      ***********99854.444443.3445555555555 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0   4.4e-10   7.8e-07       1      99 []     114     206 ..     114     206 .. 0.82

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 4.4e-10
  Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.ssfDlvvasnvlhhlkdirevldnirklL 93 
                      L+ G+G G+ +  l  + +++ + ++D s+s+   a +k  +  n ++ + +l++l       + + fD+v++ +vlhh+k+++ +++ + k L
       EPA05228.1 114 LDAGTGLGNSANFLSTN-KQALVFAIDASESVN-FAYKKYGSAANIHFLQADLRQLPF-----KkNFFDYVYSDQVLHHTKNTETSFKYLTKFL 200
                      899*****999888888.788888*********.666666666665666666665554.....3368*************************** PP

  Methyltransf_12  94 kpgGrl 99 
                      k+ G++
       EPA05228.1 201 KKAGHI 206
                      *99985 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.4e-06    0.0026      48     152 ..     110     209 ..      92     226 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.4e-06
                      TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES-GGG-S-HHHHHHHHHH CS
  Ubie_methyltran  48 gakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtvsfGlrnvtDklkaLkeayr 141
                       + +lD  +G g+ a  ls   +++  v  +D +e++ + + kk    +  ni+flqa+  +Lpf+++ fD+v     l  + ++++++k + +
       EPA05228.1 110 KHYILDAGTGLGNSANFLST--NKQALVFAIDASESV-NFAYKKY--GSAANIHFLQADLRQLPFKKNFFDYVYSDQVLHHTKNTETSFKYLTK 198
                      55677777777776666654..456667778877764.4555544..45669****************************************** PP

                      HEEEEEEEEEE CS
  Ubie_methyltran 142 vlkpGGrlvvl 152
                       lk  G++ + 
       EPA05228.1 199 FLKKAGHISIY 209
                      ******98765 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0     3e-06    0.0053     103     215 ..      96     206 ..      84     212 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3e-06
                     HHHHHGGGS..--TT-EEEEET-TTSHHHHHHHHCT-SEEEEE---HHHHHHHHHHHCCTTTTSSEEEE---GGGS-T.---EEEEEEES-GGG- CS
  Methyltransf_9 103 kWdrvlphls.dlkgrtildvGcgnGyhlwrmvgegaklvvGidPselfliqfeavrkllgedqrahllplgieqlpe.leafdtvfsmGvlyhr 195
                     +W+ + +     l+++ ild G g G     + +++ +lv+ id se   + +   +k  g+  + h l   + qlp   + fd v+s  vl+h 
      EPA05228.1  96 QWKTLDNFNKfLLTKHYILDAGTGLGNSANFLSTNKQALVFAIDASESVNFAY---KK-YGSAANIHFLQADLRQLPFkKNFFDYVYSDQVLHHT 186
                     45544443331278899************99***************9876655...34.57888999999*******857789************ PP

                     S-HHHHHHHHHCTEEEEEEE CS
  Methyltransf_9 196 rsPldhllqlkdqlvkgGel 215
                     +     +  l + l+k G++
      EPA05228.1 187 KNTETSFKYLTKFLKKAGHI 206
                     *9999999999999999976 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.4e-05     0.025      13      97 ..     109     195 ..      99     208 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.4e-05
        MetW  13 pgsrvldlGcGdGellellkeekqvdgrGleldeegvaecvakGlsviqgdldkdlen..fedksfdyvvlsqtlqatrnpkevlde 97 
                  +  +ld G+G G+  ++l  +kq     ++ +e+   +  + G +     l+ dl +  f+ + fdyv   q l  t+n+++ ++ 
  EPA05228.1 109 TKHYILDAGTGLGNSANFLSTNKQALVFAIDASESVNFAYKKYGSAANIHFLQADLRQlpFKKNFFDYVYSDQVLHHTKNTETSFKY 195
                 56779**************************9987655555557655555556666543389999***************9876655 PP

>> Zn_ribbon_recom  Recombinase zinc beta ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   6.1e-05      0.11       2      36 ..       5      44 ..       4      63 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.1e-05
  Zn_ribbon_recom  2 LsGllrCgeCGspmtrrkrkgkr.....hyYrCstyrrkg 36
                     L+  l+C  C++ +t + +k+++      y +C ++++ +
       EPA05228.1  5 LTEYLVCPTCQKFFTIKITKKSKeeiieGYLICANKHKFK 44
                     7889************7666555579*9********9876 PP

>> Glucokinase  Glucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0    0.0002      0.35     128     183 ..     109     166 ..      91     179 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0002
  Glucokinase 128 apiavlGaGTGLGvalli.pekerrvvlasEGGh.vdfapeseeevelleilrkklgr 183
                   ++ +l aGTGLG +  +  ++++  v+a  ++  v+fa ++   ++ +++l+++l +
   EPA05228.1 109 TKHYILDAGTGLGNSANFlSTNKQALVFAIDASEsVNFAYKKYGSAANIHFLQADLRQ 166
                  56789********976550555666699999985489999999888888888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2169.05
//
Query:       EPA05229.1  [L=352]
Description: NeuB family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-81  273.5   0.0    1.7e-81  273.2   0.0    1.1  1  NeuB         NeuB family
  ------ inclusion threshold ------
      0.013   16.1   0.0      0.035   14.7   0.0    1.7  1  SAF          SAF domain
       0.09   12.9   0.0       0.31   11.2   0.0    1.9  2  COMM_domain  COMM domain


Domain annotation for each model (and alignments):
>> NeuB  NeuB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  273.2   0.0   2.9e-85   1.7e-81       1     241 []      39     278 ..      39     278 .. 0.97

  Alignments for each domain:
  == domain 1  score: 273.2 bits;  conditional E-value: 2.9e-85
                 HHHHHHHHT-SEEEEEE--HHHH--GGGGG--......TT-S-HHHHHHHH---HHHHHHHHHHHHHTT-EEEEEE-SHHHHHHHHHHT-S-EEE-GGG CS
        NeuB   1 lieaAaeagadavKfQtfkaeelvskeakkaeyqkkekekeesqlellkklelseeehkelkeyceekgieflstpfdlesvdlleslgveayKiaSge 99 
                 li++Aa+agada+KfQt+++e+ + ++  k++y +k+   e+++ +++++ ++++e+  el + c++++i f+stpf+ ++++ + +  ++++KiaS+e
  EPA05229.1  39 LIKTAAKAGADAIKFQTYRPETTYVSNPGKSNYLSKSG-YEKNIEDIFDEHSMPYEMIPELEKSCNDENILFMSTPFSIQDARSI-DPYTTIHKIASFE 135
                 79******************************999965.7779******************************************.7779********* PP

                 TT-HHHHHHHHTT-S-EEEE-TT--HHHHHHHHHHH.HHHT--EEEEE----SS--GGG--THHHHHHHHH-TSEEEEE--SS.SSHHHHHHHHHT--E CS
        NeuB 100 ltnlpllekiaktgkpvilStGmatleeieeavevlreagaeklvllhCtseYPapledvnLkaietlkeafgvpvGySDHtl.giavaiaAvalGAkv 197
                 +++++l+e +aktgkp+++StG++t eei+  v+++++ g++++vll+Cts+YP+p+e++nL++i+++k+++++p+G+SDH+   +++++ Av lGA+v
  EPA05229.1 136 INHVRLIEFLAKTGKPILVSTGASTYEEIDFCVNLIKKFGNNNIVLLQCTSKYPCPIESLNLSVIPKMKSRYKIPIGFSDHSInPMVAPVLAVGLGATV 234
                 **********************************************************************************967999*********** PP

                 EEEEB-S-TT--STTGGG-B-HHHHHHHHHHHHHHHHHSS--TT CS
        NeuB 198 iEkHftldrnlegpDhkaSlepeelkelveairnvekalgegek 241
                 iEkHftld+n +gpDh+++l+peelk+++++ir++e a+g+g+k
  EPA05229.1 235 IEKHFTLDKNSPGPDHSFALNPEELKSMINSIRQAELAYGTGQK 278
                 ****************************************9986 PP

>> SAF  SAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   5.9e-06     0.035       2      58 ..     293     349 ..     292     350 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.9e-06
                 EEEEESSTB-TT-BE.BTTTEEEECECGGCCTSCCCGGHHHHTTEEESS-B-TT-B-B CS
         SAF   2 nVvvAardikaGevi.teddltlkrpiashkigllpiaygeviGkratrdikaGepvh 58 
                 +++ A+++i++G+++ ++++  + rp+ +   gl ++ ++ v Gk+at+ i++G+ ++
  EPA05229.1 293 RSIQATTNISKGDILhEGKNFDILRPGNR-IRGLEARFLDTVNGKKATKYIEKGDGIT 349
                 567899********************988.99999999****************9887 PP

>> COMM_domain  COMM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       2.5   1.5e+04      45      58 ..     133     146 ..     127     147 .. 0.81
   2 ?   11.2   0.0   5.3e-05      0.31      32      63 ..     239     269 ..     234     271 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 2.5
  COMM_domain  45 tlelskeqLqeLln 58 
                  ++e ++  L e+l 
   EPA05229.1 133 SFEINHVRLIEFLA 146
                  69999999999886 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 5.3e-05
  COMM_domain  32 LklqngsgnsenvtlelskeqLqeLlneLeei 63 
                  ++l+++s  + ++++ l++e+L+ ++n+++++
   EPA05229.1 239 FTLDKNSP-GPDHSFALNPEELKSMINSIRQA 269
                  56666665.444****************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.58
# Mc/sec: 1838.16
//
Query:       EPA05230.1  [L=125]
Description: RmlD substrate binding domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.6e-21   74.7   0.0    7.7e-21   74.4   0.0    1.0  1  RmlD_sub_bind    RmlD substrate binding domain
    2.2e-15   56.8   0.1    2.6e-15   56.6   0.1    1.0  1  Epimerase        NAD dependent epimerase/dehydratase family
    6.8e-09   35.3   2.5    1.7e-07   30.7   0.3    2.0  2  Polysacc_synt_2  Polysaccharide biosynthesis protein
    2.2e-08   33.5   3.0    7.6e-08   31.7   3.0    1.7  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    1.1e-07   31.5   1.1    1.1e-06   28.3   1.1    1.9  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    7.6e-06   25.3   0.5    2.1e-05   23.9   0.1    1.7  2  NAD_binding_4    Male sterility protein
     0.0051   17.2   0.0     0.0057   17.1   0.0    1.2  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
  ------ inclusion threshold ------
      0.012   15.1   0.8      0.018   14.4   0.8    1.3  1  Phage_head_fibr  Head fiber protein
      0.064   13.4   0.1      0.099   12.8   0.1    1.6  1  DapB_N           Dihydrodipicolinate reductase, N-terminus


Domain annotation for each model (and alignments):
>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.4   0.0   3.9e-24   7.7e-21       1      96 [.       1     104 [.       1     108 [. 0.93

  Alignments for each domain:
  == domain 1  score: 74.4 bits;  conditional E-value: 3.9e-24
                    EEEEEESTTSHHHHHHHHHCTT.TSEEEEEE-TT.......T--TTSHHHHHHHHHHH--SEEEE------HHHHHHSHHHHHHHHTHHHHHHHHH CS
  RmlD_sub_bind   1 mkilvtGanGqlGseLakqlae.eglevlaltre.......eldltdaeavaellkeakpdvvvnaAAytavDkaEseeeaayavnaeavealAea 88 
                    mkilv+G++G +G +L+k l++ ++++++ l+++       +ld+t++e   +l+ ++kpd+++++AA t+vDk+E+e+++a+ +n+e+++++ e 
     EPA05230.1   1 MKILVVGGSGVIGFNLIKYLKNtNDVSYTFLNNKisesngyQLDITNKEDTINLICKIKPDIIIHTAALTNVDKCETEKQLANLINVEGTKNIVEG 96 
                    89******************994556666667769************************************************************* PP

                    HHHCT-EE CS
  RmlD_sub_bind  89 aaavgalL 96 
                    a++++a+L
     EPA05230.1  97 AKKIKAKL 104
                    ****9988 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.6   0.1   1.3e-18   2.6e-15       1     113 [.       3     108 ..       3     109 .. 0.94

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 1.3e-18
                 EEEETTTSHHHHHHHHHHHHCT.SEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHHHSHHHHHHHHTHHHHHH CS
   Epimerase   1 ilVtGatGfiGsalvkallekg.yevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggvaassedpadfieknlqgtlnl 98 
                 ilV+G++G iG +l+k+l++ + +  + l+++ s+sn         ++ld+t+++++ +l+ + +pd++ih Aa  +v+   ++++    +n++gt n+
  EPA05230.1   3 ILVVGGSGVIGFNLIKYLKNTNdVSYTFLNNKISESN--------GYQLDITNKEDTINLICKIKPDIIIHTAALTNVDKCETEKQLANLINVEGTKNI 93 
                 8*******************99777999999966665........67****************************************99********** PP

                 HHHHHHHTCTEEEEE CS
   Epimerase  99 leaarkagvkrllfl 113
                 +e a+k ++k +l+l
  EPA05230.1  94 VEGAKKIKAKLFLYL 108
                 *********999986 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.2    0.0023       4.5       1      39 [.       3      43 ..       3      49 .. 0.67
   2 !   30.7   0.3   8.6e-11   1.7e-07      61     125 ..      43     107 ..      27     109 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0023
                     EEEETTTSHHHHHHHHHHHHHB-SEEEEEES..-HHHHHHH CS
  Polysacc_synt_2  1 vlvtGagGsiGselvrqilkkkpkkiiller..dElklyei 39
                     +lv G++G iG +l++ + +++  +   l++  +E + y++
       EPA05230.1  3 ILVVGGSGVIGFNLIKYLKNTNDVSYTFLNNkiSESNGYQL 43
                     89**************9988854433333321256666655 PP

  == domain 2  score: 30.7 bits;  conditional E-value: 8.6e-11
                      --TT-HHHHHHHTT..T-SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEE CS
  Polysacc_synt_2  61 gdvrdkerlekaleelkvdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvl 125
                       d+++ke   +++ ++k+d+++h+AAl +V  +e++   a   Nv gt+n++e a++ + k +++
       EPA05230.1  43 LDITNKEDTINLICKIKPDIIIHTAALTNVDKCETEKQLANLINVEGTKNIVEGAKKIKAKLFLY 107
                      699999999999999******************************************99988765 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   3.0   3.8e-11   7.6e-08       1     114 [.       4     108 ..       4     121 .. 0.80

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 3.8e-11
   3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegv..dvvihlaslvdvag.kltedeimkvnvkGT 96 
                 +v+Gg+G +G +l+k L ++++        +   + l +++s++n     + D+t+k++  + + ++  d++ih+a+l++v + +++++    +nv+GT
  EPA05230.1   4 LVVGGSGVIGFNLIKYLKNTND--------VSY-TFLNNKISESNGY---QLDITNKEDTINLICKIkpDIIIHTAALTNVDKcETEKQLANLINVEGT 90 
                 699************9988884........332.3343445555554...99***998877777665338*************66666667779***** PP

   3Beta_HSD  97 rnvleacvkagvrvlvYt 114
                 +n++e ++k   + ++Y 
  EPA05230.1  91 KNIVEGAKKIKAKLFLYL 108
                 ***********9999995 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   1.1   5.4e-10   1.1e-06       1     118 [.       4     102 ..       4     110 .. 0.80

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 5.4e-10
                    EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHTTSHH CS
  GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevynLAAqshVdvsfekPe 96 
                    L+ G++G iG +l+++L + +   + + ++       +i++             + ++ D+t+++  ++l+ +++pd +++ AA   Vd+  ++ +
     EPA05230.1   4 LVVGGSGVIGFNLIKYLKNTNDVSYTFLNN-------KISE------------SNGYQLDITNKEDTINLICKIKPDIIIHTAALTNVDKCETEKQ 80 
                    788888888888888887775544443332.......2322............123689*******************************999999 PP

                    HHHHHHTHHHHHHHHHHHHCT. CS
  GDP_Man_Dehyd  97 ytaevnvlGtlrLLeairalgl 118
                        +nv Gt +++e +++++ 
     EPA05230.1  81 LANLINVEGTKNIVEGAKKIKA 102
                    99999************99764 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.28   5.6e+02       2      20 ..       6      24 ..       5      40 .. 0.78
   2 !   23.9   0.1     1e-08   2.1e-05      88     133 ..      60     107 ..      42     115 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.28
                   E-TTSHHHHHHHHHHHHHS CS
  NAD_binding_4  2 TGaTGFLGkvLlekLLrtt 20
                    G++G +G  L++ L +t+
     EPA05230.1  6 VGGSGVIGFNLIKYLKNTN 24
                   69********998775554 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 1e-08
                    --EEEE--SS-S.ST..TSSE...EHHHHHHHHHHHHHHHTSSS--.-EEE CS
  NAD_binding_4  88 vdviihsaAtvnfde..pyke...llrvNveGtrevlelakklkklkvllh 133
                     d+iih aA +n+d+  +  e   +  +NveGt++++e akk+k++ ++l+
     EPA05230.1  60 PDIIIHTAALTNVDKceT--EkqlANLINVEGTKNIVEGAKKIKAK-LFLY 107
                    49***********99532..32446779****************99.8887 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   2.9e-06    0.0057       1      54 [.       2      54 ..       2      93 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.9e-06
                    EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTT.TTTSBHHHHSGGGTTTECE CS
  Semialdhyde_dh  1 kvaivGatGyvGqellrlLeehpevelvvllsssr.saGkklaeavkaleegkdl 54
                    k+ +vG++G +G +l+++L++  +v+ ++l  + + s+G +l+  +k  e++ +l
      EPA05230.1  2 KILVVGGSGVIGFNLIKYLKNTNDVSYTFLNNKISeSNGYQLDITNK--EDTINL 54
                    688***********************999987765578888777766..334443 PP

>> Phage_head_fibr  Head fiber protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.8   9.2e-06     0.018      91     153 ..      35      99 ..      21     111 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 9.2e-06
  Phage_head_fibr  91 slavfGyaveeakeGqlvtviiskafdkliladDlgeal..daGkvlleitaadGatnkvidvka 153
                       +   Gy+++ +++  ++++i     d++i ++ l +++  ++ k+l ++   +G++n+v  +k 
       EPA05230.1  35 ISESNGYQLDITNKEDTINLICKIKPDIIIHTAALTNVDkcETEKQLANLINVEGTKNIVEGAKK 99 
                      56678*******************************9874478899*************985553 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1     5e-05     0.099       1      34 [.       1      34 [.       1     100 [. 0.77

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5e-05
                EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEET CS
      DapB_N  1 ikvavvGasGrmGkevvkaveeaedlelvaavdr 34
                +k++vvG sG +G +++k +++++d+  +   ++
  EPA05230.1  1 MKILVVGGSGVIGFNLIKYLKNTNDVSYTFLNNK 34
                89**********************9987655333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       827  (0.0461264); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.55u 0.34s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 741.35
//
Query:       EPA05231.1  [L=352]
Description: glucose-1-phosphate thymidylyltransferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-54  185.2   0.0    1.9e-54  184.9   0.0    1.1  1  NTP_transferase  Nucleotidyl transferase
    1.6e-10   40.3  14.0    2.8e-06   26.8   0.8    3.3  3  Hexapep          Bacterial transferase hexapeptide (six repea
    1.7e-10   41.5   0.0    2.3e-10   41.0   0.0    1.1  1  NTP_transf_3     MobA-like NTP transferase domain
    1.6e-05   24.5   8.6    0.00018   21.2   6.0    2.9  2  Hexapep_2        Hexapeptide repeat of succinyl-transferase
  ------ inclusion threshold ------
      0.098   12.5   0.1       0.26   11.1   0.0    1.8  2  STN              Secretin and TonB N terminus short domain
       0.17   10.8   3.7       0.38    9.6   3.7    1.6  1  Fucokinase       L-fucokinase


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.9   0.0   6.4e-58   1.9e-54       1     246 [.       2     234 ..       2     236 .. 0.97

  Alignments for each domain:
  == domain 1  score: 184.9 bits;  conditional E-value: 6.4e-58
                      EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEESS--BGGHHHHHTH CS
  NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlialepegkgtAdAvalaa 94 
                      k++IL+ G GtRL+PLt+t +k+l+p+++k ++ q++l+ + + gi++i +++    s  v+e++++g+kfgv+++++ +++++g+A+A++l +
       EPA05231.1   2 KGIILHAGHGTRLRPLTHTGPKQLLPIANK-PMSQYCLESIKDTGITDIAIIIGGVGSNKVKEYYEDGKKFGVKITYVEQDSPRGIAHAIRLCK 94 
                      79****************************.*************************************************************** PP

                      HHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEECTTSBEEEEECS-SSHSHCSEECCSEEEEETTHHH CS
  NTP_transferase  95 elledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGvieadeegrverfvEKPkeakaselassGiYvfnsevll 188
                      +++++ek    +lv+ gD +i+  ++++ +++++++a  ++++++ +v++++++G++ +++ g ++++ EKPk ++ ++la++GiY+ ++ +++
       EPA05231.1  95 DFIGNEK----FLVFLGDNIIQRRISDFADEFEKSDA--KAMILLCEVDNPSRFGIADVQN-GIIKKIMEKPKDPP-TNLAVTGIYFLTPIIFD 180
                      *******....799999999999**************..9*****************9998.8*************.***************** PP

                      HHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEEXSSHHHHHHHHHHHH CS
  NTP_transferase 189 flakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsDvGtldslleanekla 246
                      ++ ++l++++r e eitd+l  +l+++k  ++ + +d  yW+D+Gt+++++ an+ ++
       EPA05231.1 181 II-DNLKPSWRNELEITDALDILLQNHKITYN-VITD--YWKDTGTPEDIIHANMTIL 234
                      **.89*************************99.5666..7**************9886 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   3.3   2.4e-07   0.00072      13      36 .]     248     271 ..     242     271 .. 0.92
   2 !   26.8   0.8   9.5e-10   2.8e-06       2      27 ..     273     298 ..     272     301 .. 0.91
   3 ?   -0.8   0.1      0.49   1.5e+03      24      35 ..     321     332 ..     307     333 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.4e-07
                 TEEEETTEEE-TTEEEETTEEEES CS
     Hexapep  13 faviggnVkIGdnvkIgagvvigg 36 
                  ++i gnV IG+n++I ++vvi+g
  EPA05231.1 248 DVKINGNVMIGENTIIKSNVVING 271
                 799*******************86 PP

  == domain 2  score: 26.8 bits;  conditional E-value: 9.5e-10
                 EEEETTEEE-TTEEEETTEEE-TTEE CS
     Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvk 27 
                 t+IG+n++I ++++ig+n+ IGdn+ 
  EPA05231.1 273 TIIGKNCVIESGSKIGPNTSIGDNSN 298
                 89**********************96 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.49
                 TTEEEETTEEEE CS
     Hexapep  24 dnvkIgagvvig 35 
                 +n++I+ ++ ++
  EPA05231.1 321 RNSIIAFNSELT 332
                 799999999875 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   0.0   7.8e-14   2.3e-10       1     120 [.       3     131 ..       3     146 .. 0.80

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 7.8e-14
                   EEEEEESS-TTTT.....TTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH......CHHHHHHTTCTS-EEE-TTS.S-SHHHHHHHHHHHH.S CS
  NTP_transf_3   1 aviLAGGrSsRmg.....gdKallplggkpllervldalraagvdevvvvggd......eevlaalarlgvrvvededp.gkgplaslaaalraaad 85 
                   ++iL +G+++R+      g+K+llp+++kp+ +++l+++++ g+ ++ ++ g       +e +++ +++gv++++ e+   +g++++++   + + +
    EPA05231.1   3 GIILHAGHGTRLRplthtGPKQLLPIANKPMSQYCLESIKDTGITDIAIIIGGvgsnkvKEYYEDGKKFGVKITYVEQDsPRGIAHAIRLCKDFI-G 98 
                   79**********6554447*************************99999976645433335555556778887655444169*******999999.9 PP

                   SSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEE CS
  NTP_transf_3  86 adavlvlacDmPlltpelverllaaaaasgadvvv 120
                   ++ +lv+++D +   +  +  +++++++s+a++++
    EPA05231.1  99 NEKFLVFLGDNII--QRRISDFADEFEKSDAKAMI 131
                   **********976..66788888888888877655 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   6.0     6e-08   0.00018       1      32 [.     254     287 ..     254     289 .. 0.90
   2 ?    2.3   0.0     0.048   1.4e+02       2      10 ..     291     299 ..     290     299 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 6e-08
                 .EEE-TT-EE-TT-EE..SEEE-TT-EE-TT-EE CS
   Hexapep_2   1 pviIGdnCliGanagi..GvslGdncvvgaGvvi 32 
                 +v IG+n++i +n +i  ++++G+ncv+++G+ i
  EPA05231.1 254 NVMIGENTIIKSNVVIngPTIIGKNCVIESGSKI 287
                 588**************66************866 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.048
                 EEE-TT-EE CS
   Hexapep_2   2 viIGdnCli 10 
                 ++IGdn+++
  EPA05231.1 291 TSIGDNSNL 299
                 789999875 PP

>> STN  Secretin and TonB N terminus short domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   8.9e-05      0.26      15      42 ..     186     212 ..     177     216 .. 0.81
   2 ?   -3.3   0.0       2.7   8.2e+03       3      13 ..     325     335 ..     325     337 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 8.9e-05
         STN  15 tvslnignvtideaLdeLLkgtgLqyki 42 
                 ++s + + ++i +aLd+LL+++ ++y +
  EPA05231.1 186 KPSWR-NELEITDALDILLQNHKITYNV 212
                 56666.789****************976 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.7
         STN   3 fiydselvrgn 13 
                 ++++sel+++ 
  EPA05231.1 325 IAFNSELTTNQ 335
                 78998888774 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   3.7   0.00013      0.38     269     340 ..     250     336 ..     216     347 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00013
  Fucokinase 269 kk.......kesavvinSvlessvsvgegsvie.hsslkgnvsigsnsivsglelessee........slelpddtilqtlslklske 340
                 k+       +++++  n v+++   +g+++vie  s++++n+sig ns +  +++++s          ++++++ +i  + +l ++++
  EPA05231.1 250 KIngnvmigENTIIKSNVVINGPTIIGKNCVIEsGSKIGPNTSIGDNSNL-RCDIAESIVmsecnitcDIKIRNSIIAFNSELTTNQN 336
                 33334444444444455566666666677777733666677777777766.5666655435555566666666666666666655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2323.70
//
Query:       EPA05232.1  [L=261]
Description: DegT/DnrJ/EryC1/StrS aminotransferase family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-71  240.9   0.0      3e-71  240.6   0.0    1.0  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family


Domain annotation for each model (and alignments):
>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  240.6   0.0   1.7e-75     3e-71      91     358 ..       2     254 ..       1     256 [. 0.92

  Alignments for each domain:
  == domain 1  score: 240.6 bits;  conditional E-value: 1.7e-75
                      -B-TTTSSB-GGGCGGG--TTEEEEEEB-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT-EETTEECCCSSSEEEEE-BTTSSS-SSS-EEEE CS
  DegT_DnrJ_EryC1  91 DvdpdtynidpaaieaaitertkaIlpVhlyGqvadmdalkaiaakhglkvieDaAhAlGatykgkkvGalgdaavfSFyptKnlttGeGGavv 184
                      Dv+pdt++idp++i++ it++t+ IlpVh++G ++d+d++ ++  k +l +ieDaAhA Ga+yk+kk+G++g+a +fSF+p Knl++  GGa++
       EPA05232.1   2 DVKPDTLCIDPEMIKKSITKKTAMILPVHFAGFPCDLDEIIELRGKFNLEIIEDAAHAAGASYKNKKIGSHGNAVCFSFHPVKNLAMPSGGAIT 95 
                      9********************************************************************************************* PP

                      ESTHHHHHHHH...HHHBTTCECCTCSSCECCSS---B-B-BHHHHHHHHHHHCTHHHHHHHHHHHHHHHHHHHHTCCCCEESCGGTTSSSEEE CS
  DegT_DnrJ_EryC1 185 tndeelaekar...vlrnhGlkrkaekryvgevelGynyrlteiqAAiglaqLerldelvarRreiaelykeeLaelegtaelttpketkkhaw 275
                       nd++     +     r  G+++++  +y  +  +G ny ++e++AAig++qL++ld+++++R+eia +y++eL   +   ++++  +++  ++
       EPA05232.1  96 LNDKNERGFTEdlkSKRWMGISNRKGSKYDVKD-IGWNYYMNEFSAAIGIEQLKKLDKTNSKRKEIACRYSKELHVEQ---KIPF--NRN-CSY 182
                      ***9986555511155678***99999999988.***************************************98644...3455..555.57* PP

                      SCEEEEEHCCHHHCHHHHHHHHHHCCEE-B-SGSCHGGGSCCHHHHHHCCCHC-HHHHHHHHHEEEEEGGTTGSHHHHHHHHH CS
  DegT_DnrJ_EryC1 276 hlyavlveeeaevkrdelvealkeegigtrvhypnplhrqpvyaerkeeasgdlpnaerlaervlsLplypelteedvdrVve 358
                      h + ++v+     +rd++++++++++i+  +hy  p+h++++y+++      +lp +e+++++++sLp++p+lt++d+d++++
       EPA05232.1 183 HIFWITVN-----NRDNFIKKMQQNKIEIGIHY-LPIHKMKFYNSKS-----KLPITEKITKNIVSLPIHPNLTDDDIDKIIK 254
                      ********.....89******************.7********9994.....58***************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       803  (0.0447878); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1611.33
//
Query:       EPA05233.1  [L=158]
Description: toxin-antitoxin system, toxin component, MazF domain protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.7e-06   26.2   0.2    3.2e-05   24.0   0.2    1.8  1  Glyco_transf_4   Glycosyltransferase Family 4
     0.0054   17.2   0.0      0.012   16.1   0.0    1.6  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
  ------ inclusion threshold ------
      0.015   14.2   0.0      0.019   13.8   0.0    1.2  1  Epimerase_2      UDP-N-acetylglucosamine 2-epimerase
      0.098   11.9   0.0       0.19   11.0   0.0    1.4  1  Glyco_trans_1_3  Glycosyl transferase family 1


Domain annotation for each model (and alignments):
>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.2     7e-09   3.2e-05      43     152 ..      35     148 ..      13     157 .. 0.67

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 7e-09
  Glyco_transf_4  43 vprvplpllkrllrslaflrrlrrllkrekpDvvHahspaalgaallalrrrlgiplVltvHglye........krllkarlkplsrllralerr 129
                           +++++    ++ +r++ +l+ ++kpDv+ +     +  al+a++  l+iplV+++ g           + +    ++   +++ ++ r+
      EPA05233.1  35 TDICKGFPSRKVTDCFQTRRKFEQLISEFKPDVILVDRQRHF--ALAAAK--LNIPLVIHLRGNIWkemewakhTLYKSLPKRIVLQIWIYMTRK 125
                     444555677888899999****************88876666..444555..8*******99999877776543111222222333333334555 PP

  Glyco_transf_4 130 llrradrviavSeatadelrery 152
                     +++++  ++ ++e++ + ++++y
      EPA05233.1 126 TFQKSSLIVPICEHLEKIVKQNY 148
                     58999999998988888888855 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   2.7e-06     0.012      60     141 ..      53     141 ..      13     153 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.7e-06
  Glyco_trans_4_4  60 lralrrllrqrrerpdvvhahsptaglaarlarrrrgiplvvtlh..........glllrrg.....sgavrrlyralerrllrradavlvvse 138
                       r +++l+   +++pdv+ +        a++a+ + +iplv++l+           ++         ++ v +++  + r +++   +++ ++e
       EPA05233.1  53 RRKFEQLI--SEFKPDVILVDRQRHF--ALAAA-KLNIPLVIHLRgniwkemewaKHT---LykslpKRIVLQIWIYMTRKTFQKSSLIVPICE 138
                      37889999..9********9997433..34455.789*******94333333222111...122123444555556668888888888888887 PP

  Glyco_trans_4_4 139 aea 141
                      ++ 
       EPA05233.1 139 HLE 141
                      766 PP

>> Epimerase_2  UDP-N-acetylglucosamine 2-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.3e-06     0.019      55      99 ..      52      93 ..      14      95 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.3e-06
                 HHHHHHHHHHHH--SEEEEESSSHHHHHHHHHHHHTT-E.EEEET- CS
  Epimerase_2 55 vligleevleeekpDlvlvlGDtnetlagalaAfklrip.vaHveA 99
                 +  ++e++++e kpD++lv  D+   +a  laA+kl+ip v+H+ +
   EPA05233.1 52 TRRKFEQLISEFKPDVILV--DRQRHFA--LAAAKLNIPlVIHLRG 93
                 5679**************9..9**9998..9*******95678765 PP

>> Glyco_trans_1_3  Glycosyl transferase family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   4.1e-05      0.19      78     132 ..      47     101 ..      36     120 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.1e-05
  Glyco_trans_1_3  78 aklaknvkalvelvedfrpdlvvtDFealtallakrhkLPvisvdnqqvvnrtdy 132
                      ++  ++ +++ +l+ +f+pd+++ D     al+a++ ++P++     ++ +++++
       EPA05233.1  47 TDCFQTRRKFEQLISEFKPDVILVDRQRHFALAAAKLNIPLVIHLRGNIWKEMEW 101
                      5556677889999***************************986655555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 956.95
//
Query:       EPA05234.1  [L=246]
Description: methyltransferase domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.1e-17   62.2   0.0    6.8e-17   61.8   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    1.5e-11   44.8   0.0    2.4e-11   44.1   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
      1e-10   42.2   0.0      2e-10   41.3   0.0    1.5  1  Methyltransf_12  Methyltransferase domain
      7e-09   36.3   0.0    1.4e-08   35.4   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
      1e-06   28.6   0.0    1.5e-06   28.0   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    3.4e-05   23.5   0.0    4.7e-05   23.0   0.0    1.4  1  Methyltransf_PK  AdoMet dependent proline di-methyltransferas
    0.00081   18.8   0.0     0.0012   18.4   0.0    1.4  1  TehB             Tellurite resistance protein TehB
     0.0042   16.7   0.0      0.022   14.4   0.0    1.9  2  MetW             Methionine biosynthesis protein MetW
  ------ inclusion threshold ------
      0.079   12.6   0.0       0.13   11.9   0.0    1.4  1  TPMT             Thiopurine S-methyltransferase (TPMT)


Domain annotation for each model (and alignments):
>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.8   0.0   3.4e-20   6.8e-17      15     161 ..      52     195 ..      40     214 .. 0.77

  Alignments for each domain:
  == domain 1  score: 61.8 bits;  conditional E-value: 3.4e-20
  Methyltransf_23  15 rll..pklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiaekakkaqkdqfdeqeaaepqgkfdlIvlrevlehvpdppellrqia 106
                      +++  +k ++++r L+iGcG G +   ++e+gf+v g+++++++v+++ ++ k+ +  +   e+   +g +d+I  ++v+eh+  p  llr+ +
       EPA05234.1  52 QFAycKKYFKNKRFLEIGCGPGQTIFWFEEEGFDVSGIEPDERNVGLINQKLKSGHCEVGFAEEFSISGNYDIIWISHVFEHLVRPDLLLRKCK 145
                      444446689**************************************9755555555555556666899************************* PP

  Methyltransf_23 107 tllkpgGylllseplaslkedrllldwlylvpagrhisffsarslkelleeaGle 161
                      ++l+p+G l++++p++  ++++ l++  ++ p       f+ +sl +l+ +a+++
       EPA05234.1 146 EHLNPNGILFIEVPNC--ENAEILKSSVFEQPS---TFHFTKKSLMNLAIKANFK 195
                      **************75..555555544444333...2223335555555555555 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   0.0   1.2e-14   2.4e-11       1      96 []      66     156 ..      66     156 .. 0.95

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 1.2e-14
                      EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHHHHHHHHHHEEEEEEE CS
  Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedpekalkeiaRvLkpgGll 94 
                      L++GcG G+   ++++ g +v g++++++ + l ++k +  +    + v+ ae++ +    +D++++s+v++h+ +p+ +l++++  L p+G+l
       EPA05234.1  66 LEIGCGPGQTIFWFEEEGFDVSGIEPDERNVGLINQKLKSGH----CEVGFAEEFSISG-NYDIIWISHVFEHLVRPDLLLRKCKEHLNPNGIL 154
                      89************************************9988....7999999987755.99*******************************9 PP

                      EE CS
  Methyltransf_11  95 vi 96 
                      +i
       EPA05234.1 155 FI 156
                      86 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   0.0   9.8e-14     2e-10       1      99 []      66     154 ..      66     154 .. 0.84

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 9.8e-14
  Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlkdirevldnirklLk 94 
                      LeiGcG G++++ ++e+  + ++ g++++++ +    +kl++ +     +v + ++ +++    + +D++++s+v++hl  ++ +l++++++L+
       EPA05234.1  66 LEIGCGPGQTIFWFEEE--GFDVSGIEPDERNVGLINQKLKSGHC----EVGFAEEFSIS----GNYDIIWISHVFEHLVRPDLLLRKCKEHLN 149
                      8****************..**************777777777663....33333333332....39**************************** PP

  Methyltransf_12  95 pgGrl 99 
                      p+G+l
       EPA05234.1 150 PNGIL 154
                      ***87 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   0.0   6.8e-12   1.4e-08       2      97 .]      66     152 ..      65     152 .. 0.92

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 6.8e-12
                      EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHHHHHHHHHHHHHEEE CS
  Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsdedlekalkeiarvLkp 95 
                      L++GcG+G++++++ +++   +v g++++e+ +  ++++++    + ++++g ae+++   g +D++++s++++hl ++d   +l++++++L+p
       EPA05234.1  66 LEIGCGPGQTIFWFEEEG--FDVSGIEPDERNVGLINQKLK----SGHCEVGFAEEFSIS-GNYDIIWISHVFEHLVRPD--LLLRKCKEHLNP 150
                      9****************5..********************5....568999999***976.69******988***99888..67********** PP

                      EE CS
  Methyltransf_25  96 gG 97 
                      +G
       EPA05234.1 151 NG 152
                      99 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   7.7e-10   1.5e-06       3     121 ..      61     166 ..      60     222 .. 0.81

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 7.7e-10
  Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnevlnaladpdkilee 96 
                      k++r+l++GCG G+ +f +  e g+  +v Gi+ +e+ + l ++   kl++  +e+  ++ ++++      ++D+i    v+ +l  pd  l++
       EPA05234.1  61 KNKRFLEIGCGPGQTIFWFE-EEGF--DVSGIEPDERNVGLINQ---KLKSGHCEVGFAEEFSIS-----GNYDIIWISHVFEHLVRPDLLLRK 143
                      799*********99877666.6554..688***********999...677776777666667766.....88********************** PP

  Methyltransf_31  97 iervlkpggilliedprllaelpak 121
                       ++ l+p+gil ie p+   e++++
       EPA05234.1 144 CKEHLNPNGILFIEVPN--CENAEI 166
                      **************999..333333 PP

>> Methyltransf_PK  AdoMet dependent proline di-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   2.4e-08   4.7e-05     111     161 ..     110     158 ..      28     202 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 2.4e-08
  Methyltransf_PK 111 vglqeftPeegrYdliWiqWcvghLtDedlvaflkrckkalkpnGlivvke 161
                      vg+ e    +g+Yd+iWi  +  hL+  dl+  l++ck+ l+pnG++ +  
       EPA05234.1 110 VGFAEEFSISGNYDIIWISHVFEHLVRPDLL--LRKCKEHLNPNGILFIEV 158
                      455444445799******************6..9************99863 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   5.8e-07    0.0012      27     129 ..      58     153 ..      27     185 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 5.8e-07
                 CCS-S-EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG----S-EEEEEEESSGGGS-GGGHHHHHHHHHHTEE CS
        TehB  27 kivkpgkvldlgcgqgrnslylsllgydvtawdknensiafleeikekenlknistalydineaklderydfilstvvlmfleaeripsiienmqectk 125
                 k  k  + l++gcg g+  ++++  g+dv+ ++ +e  ++ +++       k+ ++++   +e +++ +yd+i  + v+  l +     +++  +e+ +
  EPA05234.1  58 KYFKNKRFLEIGCGPGQTIFWFEEEGFDVSGIEPDERNVGLINQKL-----KSGHCEVGFAEEFSISGNYDIIWISHVFEHLVRPD--LLLRKCKEHLN 149
                 66778899********************************999854.....444556777789999*****998888887775543..35666777777 PP

                 EEEE CS
        TehB 126 vggy 129
                 + g 
  EPA05234.1 150 PNGI 153
                 6665 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   1.1e-05     0.022      14      96 ..      62     142 ..      51     160 .. 0.77
   2 ?    0.2   0.0      0.24   4.8e+02     131     172 ..     165     206 ..     154     220 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.1e-05
        MetW  14 gsrvldlGcGdGellellkeekqvdgrGleldeegvaecvakGlsviqgdldkdlenfedksfdyvvlsqtlqatrnpkevld 96 
                 + r l++GcG G+ + ++ ee + d  G+e de++v    +  l+  + ++    e+  + ++d++ +s  +  + +p+ +l+
  EPA05234.1  62 NKRFLEIGCGPGQTIFWF-EEEGFDVSGIEPDERNVGLINQ-KLKSGHCEVGFAEEFSISGNYDIIWISHVFEHLVRPDLLLR 142
                 4689**************.569*************976544.46666666666666666777777777777777777766665 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.24
        MetW 131 dalPyeWydtpnihlltikdfvelceelnlkvedrvaldekg 172
                 + l  + ++ p     t k +++l+ + n+k+e+   +++ +
  EPA05234.1 165 EILKSSVFEQPSTFHFTKKSLMNLAIKANFKIERCDCFRSPS 206
                 556667788888877888999999999999999887777655 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   6.5e-05      0.13      19      75 ..      43      99 ..      20     136 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.5e-05
                -SS--HHHHHHHHT.T-S--EEEEEET-TT-HHHHHH-BTTEEEEEE-S-HHHHHHH CS
        TPMT 19 qeevnpllkkfldalkakaglrvlvPlCGkaldlvwlAeqgrevvGvelselAvekf 75
                q++  + +++f    k  +++r l  +CG ++ + w+ e+g +v G+e  e  v   
  EPA05234.1 43 QGKKRQWISQFAYCKKYFKNKRFLEIGCGPGQTIFWFEEEGFDVSGIEPDERNVGLI 99
                55566778888888888999999*9***********************888877664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1589.98
//
Query:       EPA05235.1  [L=194]
Description: hypothetical protein BG20_I0208 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-09   38.2   0.0    1.4e-09   38.0   0.0    1.1  1  Formyl_trans_N  Formyl transferase


Domain annotation for each model (and alignments):
>> Formyl_trans_N  Formyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   0.0   7.6e-14   1.4e-09      71     163 ..      72     164 ..      13     178 .. 0.79

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 7.6e-14
                     HHHHHHCTT-SEEEEES--S---HHHHHSSTTSEEEEESSSTTTTBSS-HHHHHHHTTSSEEEEEEEE--SSSSTS-EEEEEEEE--TT--HH CS
  Formyl_trans_N  71 laeelkelkadlivlagymkllpkelvqavrlkilniHpSLLPrfkGaaaiqraleaGdketGvtihfvdeelDtGailaqkkveiiaedtke 163
                     + e  +  + d+i+ +++  l+pk+++++ +     iH   LP++ G+++i++a+ + ++e   + h ++  +D+G++    + +i+ +++ +
      EPA05235.1  72 NHEFDDFPECDFIIEVSWRYLIPKNILKKANIASFGIHRGKLPEYAGSEPIKQAFNHNENEIVLSAHDLNAAIDQGEVFETISHPITYDNSIS 164
                     4444445578********************************************************************999888888877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1279.71
//
Query:       EPA05236.1  [L=136]
Description: hypothetical protein BG20_I0181 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.05   14.4   4.3       0.17   12.7   4.3    1.9  1  KMP11     Kinetoplastid membrane protein 11


Domain annotation for each model (and alignments):
>> KMP11  Kinetoplastid membrane protein 11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   4.3   9.6e-06      0.17      17      69 ..      61     118 ..      48     135 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.6e-06
       KMP11  17 eefakkmeeqn.kkffadkpdeatlspemkehyekf...ekmi..kehtekfnkkmreh 69 
                 eef  k +eqn ++++ad   e+ ls e+ +h ekf   ek+   keh   +n k+ + 
  EPA05236.1  61 EEFISKNKEQNlTHIIADEYSESILS-EVYNHEEKFpylEKIYesKEHGYEYNLKLYKI 118
                 79999*****945689********98.78899999855466643378888888887654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       798  (0.0445089); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 997.12
//
Query:       EPA05237.1  [L=256]
Description: glucose-1-phosphate cytidylyltransferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-20   72.1   0.0    8.7e-20   71.3   0.0    1.4  1  NTP_transferase  Nucleotidyl transferase
    3.8e-09   37.1   0.0      6e-09   36.5   0.0    1.4  1  NTP_transf_3     MobA-like NTP transferase domain
  ------ inclusion threshold ------
      0.033   13.9   0.0      0.054   13.2   0.0    1.3  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.3   0.0   1.5e-23   8.7e-20       1     192 [.       2     201 ..       2     232 .. 0.87

  Alignments for each domain:
  == domain 1  score: 71.3 bits;  conditional E-value: 1.5e-23
                      EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEESS--.......... CS
  NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlialepegk.......... 84 
                      kavILaGG GtR+   t+ ++k+++ ++gk +++ + ++  ++ gi+e  v++  ++  +++e++++    + +v++ +++++           
       EPA05237.1   2 KAVILAGGLGTRISEETHLRPKPMIEIGGK-PILWHIMKSYSAYGINE-FVICCGYKGYMIKEYFANYFLHTSDVTFDMQNNKMevhrkfaepw 93 
                      79****************************.*****************.9****************9876666777777777667788888888 PP

                      ...........BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEECTTSBEEEEECS-S CS
  NTP_transferase  85 ...........gtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGvieadeegrverfvEKPk 167
                                  t + ++ +++++++e     + +  gD + + +++++++++++++     +  ++  +++ ++G   +++ +r+++f+EKP+
       EPA05237.1  94 kvtlvdtgletMTGGRLKRIKNFIDNET----FCFTYGDGVSDVNISKLIEFHKNNKT----VATVTAIQPPGRFGTLDISG-NRITSFKEKPA 178
                      8889988776677888888889998877....8*********************9999....4455677899********98.5********** PP

                      SHSHCSEECCSEEEEETTHHHHHHH CS
  NTP_transferase 168 eakaselassGiYvfnsevllflak 192
                      ++   ++++ G +v +++v++++  
       EPA05237.1 179 GDG--NWVNGGFFVLEPKVFDYIEG 201
                      *88..9***************9943 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.0     1e-12     6e-09       1      49 [.       3      56 ..       3     100 .. 0.86

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 1e-12
                  EEEEEESS-TTTTT.....THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSHC CS
  NTP_transf_3  1 aviLAGGrSsRmgg.....dKallplggkpllervldalraagvdevvvvggde 49
                  aviLAGG ++R  +     +K+++++ggkp+l++++++ +a g++e v+++g++
    EPA05237.1  3 AVILAGGLGTRISEethlrPKPMIEIGGKPILWHIMKSYSAYGINEFVICCGYK 56
                  79**********8545666********************************996 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0     9e-06     0.054       2      48 ..       2      51 ..       1      66 [. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9e-06
                EEEEECTTSSCTT-SS...S-GGGSEETTEEHHHHHHHHHHCTTTEEEEE CS
        IspD  2 vvvipAAGsGkRmkag...lpKqflelkgqtllehtvdallaskavdkiv 48
                 +vi A G G+R+ ++   +pK  +e+ g+++l h +++  a++  + ++
  EPA05237.1  2 KAVILAGGLGTRISEEthlRPKPMIEIGGKPILWHIMKSYSAYGINEFVI 51
                69***********99844469***************99999887665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1673.04
//
Query:       EPA05238.1  [L=209]
Description: hypothetical protein BG20_I0202 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1047  (0.058397); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1516.72
//
Query:       EPA05239.1  [L=173]
Description: transferase hexapeptide repeat protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    8.4e-08   31.6  14.4    0.00011   21.7   4.0    3.8  4  Hexapep    Bacterial transferase hexapeptide (six repeats)
    8.1e-05   22.3  13.3       0.56   10.0   0.2    4.4  3  Hexapep_2  Hexapeptide repeat of succinyl-transferase


Domain annotation for each model (and alignments):
>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0   8.6e-05      0.77      19      34 ..      59      74 ..      57      75 .. 0.90
   2 !    5.9   0.1    0.0013        11      22      34 ..      84      96 ..      82     102 .. 0.62
   3 !   21.7   4.0   1.3e-08   0.00011       1      34 [.     119     152 ..     119     154 .. 0.94
   4 ?   -1.4   0.1      0.26   2.3e+03      13      17 ..     159     163 ..     156     165 .. 0.41

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 8.6e-05
                TEEE-TTEEEETTEEE CS
     Hexapep 19 nVkIGdnvkIgagvvi 34
                +VkIG+n++  ++v i
  EPA05239.1 59 GVKIGKNCHFSSYVLI 74
                8*********999987 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0013
                E-TTEEEETTEEE CS
     Hexapep 22 IGdnvkIgagvvi 34
                I dnv+I +++ i
  EPA05239.1 84 IEDNVTISHNAMI 96
                5555555555555 PP

  == domain 3  score: 21.7 bits;  conditional E-value: 1.3e-08
                 TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEE CS
     Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvi 34 
                 +++I ++++I p+a+i ++V+IG n++I  g+v+
  EPA05239.1 119 NVTIKQGAVISPGAIITAGVTIGQNSIISVGSVV 152
                 6899***************************998 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 0.26
                 TEEEE CS
     Hexapep  13 favig 17 
                 ++v+ 
  EPA05239.1 159 NCVVV 163
                 33333 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.2   6.2e-05      0.56       2      32 ..      60      96 ..      59      98 .. 0.74
   2 !    5.5   0.1    0.0016        14      18      34 .]     120     136 ..     117     136 .. 0.91
   3 !    7.9   5.0   0.00028       2.5       2      26 ..     138     162 ..     137     165 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 6.2e-05
                EEE-TT-EE-TT-EES......EEE-TT-EE-TT-EE CS
   Hexapep_2  2 viIGdnCliGanagiG......vslGdncvvgaGvvi 32
                v+IG+nC + +   i       v+++dn++++ + +i
  EPA05239.1 60 VKIGKNCHFSSYVLIDllyphlVNIEDNVTISHNAMI 96
                89*****664444475555589999999999988887 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0016
                 EEE-TT-EE-TT-EE-S CS
   Hexapep_2  18 vslGdncvvgaGvvita 34 
                 v++  ++v+++G +ita
  EPA05239.1 120 VTIKQGAVISPGAIITA 136
                 88999**********97 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.00028
                 EEE-TT-EE-TT-EESEEE-TT-EE CS
   Hexapep_2   2 viIGdnCliGanagiGvslGdncvv 26 
                 v+IG+n++i + +++  ++ dncvv
  EPA05239.1 138 VTIGQNSIISVGSVVSEDIPDNCVV 162
                 7888888888888888888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1185.96
//
Query:       EPA05240.1  [L=233]
Description: hypothetical protein BG20_I0197 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-23   82.9   0.0      3e-23   82.4   0.0    1.1  1  TylF             Macrocin-O-methyltransferase (TylF)
    3.2e-09   37.8   0.0    4.5e-09   37.3   0.0    1.2  1  Methyltransf_24  Methyltransferase domain


Domain annotation for each model (and alignments):
>> TylF  Macrocin-O-methyltransferase (TylF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.4   0.0   3.3e-27     3e-23      79     240 ..      68     217 ..      60     226 .. 0.82

  Alignments for each domain:
  == domain 1  score: 82.4 bits;  conditional E-value: 3.3e-27
        TylF  79 eegvpGdliEtGvWRGGaailmrgvLkaegvedRkvwvaDsFeglPkpdeeklaedagdklkeleevlavseeevrenFrrygLlddqvrflkGwFkdt 177
                 + ++ Gd+ E+Gv+ GG+a ++    +++   + k++++D+FeglPk   +  ++  g k  + +++ ++  e+vr+  ++y    + v f kG F dt
  EPA05240.1  68 QSKISGDMAEVGVYQGGSAKII---CEVK--GNNKLHLFDTFEGLPKISDK--DTHFGIKYWTDKQFSNTDIESVRKYLKDY----EDVSFYKGKFPDT 155
                 678**************98643...3344..4557999********98443..23333444444444557788888888877....69*********** PP

        TylF 178 LptapieklallRlDgdlyestldaleaLYdkvskGGfviiDDyaaveecreavedfreakgi 240
                    +  +k++ + lD dlyest++ l+  Y+++ kGG ++  Dy++ +++++a ++f + k+i
  EPA05240.1 156 SVPVTDSKFSFVHLDVDLYESTTECLKFFYPRLVKGGIILTHDYHT-NGVHSAFTEFFQGKNI 217
                 **********************************************.9*********998887 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.0     5e-13   4.5e-09       2     106 .]      77     199 ..      76     199 .. 0.81

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 5e-13
  Methyltransf_24   2 EiGvysGvstlwllralrrngagrlvavdhdpg.....................aeeaaalare......aglddr..vrlikadseealasla 66 
                      E+Gvy+G s+ ++++  + n+  +l+ +d+++g                     +       ++      ++l+d+  v + k++++++   + 
       EPA05240.1  77 EVGVYQGGSAKIICEV-KGNN--KLHLFDTFEGlpkisdkdthfgikywtdkqfS-------NTdiesvrKYLKDYedVSFYKGKFPDTSVPVT 160
                      9************965.4444..49*******99999988777777654433221.......3245455567777778**********966666 PP

  Methyltransf_24  67 agsiDllfiDgghaaeavledleallprlapggvvlfdDi 106
                      ++++ ++++D +  +e++ e l+ + prl +gg++l +D+
       EPA05240.1 161 DSKFSFVHLDVD-LYESTTECLKFFYPRLVKGGIILTHDY 199
                      7***********.8*************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1679.05
//
Query:       EPA05241.1  [L=329]
Description: NAD-binding protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-96  322.9   0.3      2e-96  322.6   0.3    1.1  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    1.2e-29  103.4   0.1    1.1e-28  100.4   0.1    2.0  1  Epimerase        NAD dependent epimerase/dehydratase family
    5.4e-22   78.1   0.2    1.2e-20   73.7   0.1    2.1  2  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    6.6e-21   75.0   0.0    7.5e-19   68.3   0.0    2.1  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    6.5e-16   58.3   0.0    7.7e-14   51.5   0.0    2.5  2  RmlD_sub_bind    RmlD substrate binding domain
    2.7e-11   43.7   0.0    4.8e-11   42.9   0.0    1.5  1  NAD_binding_10   NAD(P)H-binding
    5.2e-11   42.2   2.4      9e-08   31.6   2.2    3.0  2  NAD_binding_4    Male sterility protein
    1.7e-07   31.1   0.1    2.7e-07   30.4   0.1    1.5  1  NmrA             NmrA-like family
    1.8e-07   30.8   0.0    3.3e-07   29.9   0.0    1.5  1  adh_short        short chain dehydrogenase
    2.3e-05   24.4   0.0      4e-05   23.6   0.0    1.4  1  KR               KR domain
     0.0048   17.0   0.3      0.025   14.6   0.0    2.3  3  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
  ------ inclusion threshold ------
      0.013   16.0   0.0      0.063   13.9   0.0    2.1  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
      0.045   14.2   0.0       0.63   10.5   0.0    2.5  2  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
       0.13   12.3   0.0       0.33   10.9   0.0    1.8  2  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge


Domain annotation for each model (and alignments):
>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  322.6   0.3   1.5e-99     2e-96       1     291 [.       7     280 ..       7     283 .. 0.97

  Alignments for each domain:
  == domain 1  score: 322.6 bits;  conditional E-value: 1.5e-99
                      EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-SEEEE------HHHHH CS
  Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvdvvfhaAAlKhVPlve 94 
                      +l+tG++Gs+G +l++++lk+++  +++++rdE k+ ++++++    ++k+l++     igdvrdk+rl++a+e  ++dvvfh+AAlKhVP++e
       EPA05241.1   7 ILITGGTGSLGTALTHRLLKENVGVVRIYSRDEWKQTQMQEKI----RDKRLRFL----IGDVRDKDRLSRAME--GIDVVFHTAALKHVPVAE 90 
                      89**************************************998....57789887....***************..****************** PP

                      HSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEGGGSS--SHHHHHHHHHHHHHHHGGG--SSS--EEEEEEE-EETTGTTSSHHHHHHHHHT CS
  Polysacc_synt_2  95 enpleaiktNvlgtenvieaaieagvkkvvliStDKAvnPtnvmGatKrlaekllqalakeseekktkfvvvRfGNVlgSrGSviplFkkqike 188
                      +np+eaiktNv+gt+nvie +++++vk  ++i tDKAv+P n++GatK+l+e +++a++ +++++kt f++vR+GNVlgSrGSv p+F +qi++
       EPA05241.1  91 YNPFEAIKTNVIGTQNVIESCLDNEVKMALAIGTDKAVSPLNTYGATKLLMERMFTAANFYKGAHKTDFLCVRYGNVLGSRGSVAPKFIEQIQK 184
                      ********************************************************************************************** PP

                      TSSEEES-TT-EEEEE-HHHHHHHHHHHHHH--SS-EEEE--.-EEEHHHHHHHH..........SSSS-EEE----TT--SS-EEE-GGGGGG CS
  Polysacc_synt_2 189 ggpvtvTdpemtRyfmtieeavqLvlqalalakggeifvldmGepvkivdlakalielsgleekkeedieikitGlRpGEklyEeLlieeesve 282
                      +g++t+Tdp+mtR+ +t+++a +L++ a++++k+ge+f+ +  +++++ +l +a+ie++g+      +i+++ + +RpGEk++E+L++++e + 
       EPA05241.1 185 DGKITITDPRMTRFNITMKQALDLIFRAIKNGKDGEVFIPKL-KAYTVDELKNAIIEIIGK------KIQVQKIPVRPGEKFHETLINKDEIAY 271
                      ******************************************.****************94......7999*******************9999 PP

                      EEE-SSEEE CS
  Polysacc_synt_2 283 etelekilr 291
                      + e ++ ++
       EPA05241.1 272 TFESKDDYI 280
                      888777665 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.4   0.1   8.3e-32   1.1e-28       1     204 [.       7     192 ..       7     223 .. 0.87

  Alignments for each domain:
  == domain 1  score: 100.4 bits;  conditional E-value: 8.3e-32
                 EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.....EEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHHHSHHHHHHHHTHH CS
   Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl.....elveldltdrsalerlfkeeqpdavihlAavggvaassedpadfieknlqg 94 
                 il+tG+tG +G+al+++ll++++ v+ + ++ + ++t+ +e++     ++  +d++d+++l r+++  ++d+v+h Aa ++v++   +p + i++n++g
  EPA05241.1   7 ILITGGTGSLGTALTHRLLKENVGVVRIYSRDEWKQTQMQEKIrdkrlRFLIGDVRDKDRLSRAME--GIDVVFHTAALKHVPVAEYNPFEAIKTNVIG 103
                 8*********************999999999899999888888999********************..******************************* PP

                 HHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHH...HHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHH CS
   Epimerase  95 tlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklvea...yaaqyglnaiilrlfnlyGprngegevsrvipali 190
                 t+n++e + +++vk  l ++++           +       + p + Y+a+Kl++e++ +a   y+ +++++++++r+ n+ G r       +v p++i
  EPA05241.1 104 TQNVIESCLDNEVKMALAIGTD-----------KA------VSPLNTYGATKLLMERMFTAanfYKGAHKTDFLCVRYGNVLGSR------GSVAPKFI 179
                 *********************2...........22......257799************99333446667***************......******** PP

                 HHHHTTSSSEEEET CS
   Epimerase 191 rkilegkqevtllg 204
                 ++i++   ++t+ +
  EPA05241.1 180 EQIQKDG-KITITD 192
                 ****988.888764 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.7   0.1     9e-24   1.2e-20       1     113 [.       8     121 ..       8     132 .. 0.82
   2 ?    2.9   0.0     0.036        46     142     203 ..     130     189 ..     123     201 .. 0.84

  Alignments for each domain:
  == domain 1  score: 73.7 bits;  conditional E-value: 9e-24
   3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvl..DlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslvdvag.kltedeimkvnvkGT 96 
                 ++tGg+G lG al ++L++++ +  vr++  D  ++++++e+++  + + ++ gDv+dkd+l++a+eg+dvv+h+a+l  v   +++  e  k nv GT
  EPA05241.1   8 LITGGTGSLGTALTHRLLKEN-VGVVRIYsrDEWKQTQMQEKIRDKRLR-FLIGDVRDKDRLSRAMEGIDVVFHTAALKHVPVaEYNPFEAIKTNVIGT 104
                 69*****************99.566666511555566666666666555.****************************99976588888999******* PP

   3Beta_HSD  97 rnvleacvkagvrvlvY 113
                 +nv+e+c++++v++ + 
  EPA05241.1 105 QNVIESCLDNEVKMALA 121
                 ************98665 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.036
   3Beta_HSD 142 hqdaypesKalaEklvlkaNgrtlknggrlyTcaLRpagiyGegdkllvpllkqlaklglal 203
                 + ++y  +K l E++  +aN    k+  +    ++R   + G + ++  ++++q+ k g++ 
  EPA05241.1 130 PLNTYGATKLLMERMFTAANF--YKGAHKTDFLCVRYGNVLGSRGSVAPKFIEQIQKDGKIT 189
                 67899***************9..56666888899***********************99543 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.3   0.0   5.8e-22   7.5e-19       1     274 [.       8     250 ..       8     284 .. 0.79

  Alignments for each domain:
  == domain 1  score: 68.3 bits;  conditional E-value: 5.8e-22
                    EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHTTSHH CS
  GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevynLAAqshVdvsfekPe 96 
                    LiTG++G  G  l+++Ll+++  v+ i  r++  +t+  e++++       ++l++  gD++D+++l r+++ +  d v++ AA +hV+v   +P 
     EPA05241.1   8 LITGGTGSLGTALTHRLLKENVGVVRIYSRDEWKQTQMQEKIRD-------KRLRFLIGDVRDKDRLSRAMEGI--DVVFHTAALKHVPVAEYNPF 94 
                    9*******************************999999998864.......579*****************998..9******************* PP

                    HHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHHHHHHHHHHHHHH...HHHHH---EEEEEE-EEESTTS- CS
  GDP_Man_Dehyd  97 ytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYaaaKlyadwivvn...yreayglfavngilfnhesprrg 189
                    + +++nv+Gt++++e + +     +v++                +  ++ ++P + Y+a+Kl  + + ++   y+ a++   +  ++ n  + r  
     EPA05241.1  95 EAIKTNVIGTQNVIESCLDN----EVKMA-------------LAIGTDKAVSPLNTYGATKLLMERMFTAanfYKGAHKTDFLCVRYGNVLGSRG- 172
                    ****************9654....45552.............23444567888999999999888876652335555666666666666666663. PP

                    TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHHHHHHHHCSS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH. CS
  GDP_Man_Dehyd 190 etfvtrkitravarialgkqevlylGnldakRdwghvkDyveamwlmlqqdkpedyviatgethsvrefvelaflelgktieweg 274
                            ++++ +i+++   ++++ + + +R     k   + + ++++++k  ++ i + + ++v+e+ ++ ++ +gk+i+ ++
     EPA05241.1 173 -----SVAPKFIEQIQKDG--KITITDPRMTRFNITMKQALDLIFRAIKNGKDGEVFIPKLKAYTVDELKNAIIEIIGKKIQVQK 250
                    .....45566677776654..4667788888888888888888888888888888888888899998888888888888887664 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.5   0.0     6e-17   7.7e-14       2     165 ..       6     181 ..       5     197 .. 0.86
   2 ?    1.2   0.0      0.12   1.6e+02       5      51 ..     167     214 ..     166     217 .. 0.82

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 6e-17
                    EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT....................T--TTSHHHHHHHHHHH--SEEEE------HHHHHHSHHHHHHH CS
  RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltre....................eldltdaeavaellkeakpdvvvnaAAytavDkaEseeeaayav 77 
                    kil+tG++G lG++L+++l +e++ v+ + ++                      d++d++++ ++++    dvv ++AA + v  aE ++ +a + 
     EPA05241.1   6 KILITGGTGSLGTALTHRLLKENVGVVRIYSRdewkqtqmqekirdkrlrflIGDVRDKDRLSRAMEG--IDVVFHTAALKHVPVAEYNPFEAIKT 99 
                    89**************************966669***************999999********99998..799*********************** PP

                    HTHHHHHHHHHHHHCT-EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHH.......H-SSEEEEEE-SEESSSSS-HHHHHHH CS
  RmlD_sub_bind  78 naeavealAeaaaavgalLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavla.......agkkalivRtswvygekgknfvktmlr 165
                    n+ +++++ e +   ++++               +  +d ++sPln+YG+tKl++E++  a       ++ ++l vR + v+g++g    k + +
     EPA05241.1 100 NVIGTQNVIESCLDNEVKMAL-------------AIGTDKAVSPLNTYGATKLLMERMFTAanfykgaHKTDFLCVRYGNVLGSRGSVAPKFIEQ 181
                    ****************99853.............34457899***************99986777665567899999999999988765554443 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.12
                    EESTTSHHHHHHHHHCTTTS.EEEEEE-TTT--TTSHHHHHHHHHHH- CS
  RmlD_sub_bind   5 vtGanGqlGseLakqlaeeg.levlaltreeldltdaeavaellkeak 51 
                    v+G++G ++ + ++q++++g + ++ +  +++++t ++a++ +++++k
     EPA05241.1 167 VLGSRGSVAPKFIEQIQKDGkITITDPRMTRFNITMKQALDLIFRAIK 214
                    78***************988234444566799*****99999998876 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   0.0   3.8e-14   4.8e-11       1     101 [.      11     127 ..      11     192 .. 0.73

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 3.8e-14
                     TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHH...CTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC.........HHHH...... CS
  NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaele...aeeglevvegdvtdvedlaealkgadaVvsalggggk.........deeg...... 77 
                     G+tG+ G +l+++ll+++   v+++ R++ k ++++   ++++l+ + gdv d++ l +a++g+d+V+ +++ ++             +      
      EPA05241.1  11 GGTGSLGTALTHRLLKENVGVVRIYSRDEWKQTQMQekiRDKRLRFLIGDVRDKDRLSRAMEGIDVVFHTAALKHVpvaeynpfeA--Iktnvig 103
                     9****************95578999***76666554333679*****************************554444433334330..1555678 PP

                     HHHHHHHHHHCT--EEEEEEETTT CS
  NAD_binding_10  78 aknivdaakeagvkRfvlvsaigv 101
                     ++n+++ +  ++vk  + +++ ++
      EPA05241.1 104 TQNVIESCLDNEVKMALAIGTDKA 127
                     *********999986666555444 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   2.2     7e-11     9e-08       1     127 [.       9     116 ..       9     129 .. 0.82
   2 !    6.2   0.0    0.0039       5.1     166     210 ..     124     171 ..     113     217 .. 0.68

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 7e-11
                    EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSHHHHHHHHHHHT-SS-HHHHHHHHHTTTEEEEE--TTSGGGG--HHHHHHHHHH--EEEE--S CS
  NAD_binding_4   1 lTGaTGFLGkvLlekLLrttpevkiyllvRaksgesaeeRleeelekkelfsallkelaerikvveGDlseprlGLseedlqelaeevdviihsaA 96 
                    +TG+TG LG+ L ++LL+++       +vR  s         +e+++++++++++    +r++++ GD+ +++      +l + +e +dv++h aA
     EPA05241.1   9 ITGGTGSLGTALTHRLLKENVG-----VVRIYSR--------DEWKQTQMQEKIR---DKRLRFLIGDVRDKD------RLSRAMEGIDVVFHTAA 82 
                    8******************976.....5666544........7888999999998...9***********876......899999*********** PP

                    S-S..STTSSE..EHHHHHHHHHHHHHHHTSSS- CS
  NAD_binding_4  97 tvnf.depyke..llrvNveGtrevlelakklkk 127
                      ++ +++y+   ++++Nv Gt++v+e +   + 
     EPA05241.1  83 LKHVpVAEYNPfeAIKTNVIGTQNVIESCLDNEV 116
                    99974345653349*************9985544 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0039
                    EEETTTCCCHHHHHHHHHHHHHHHHH...HHH---EEEEEE-EEE--S CS
  NAD_binding_4 166 raklkglpntYeqsKalaEklvrear...rrsglpvvivRpsiitges 210
                     +k  +  ntY  +K l E++  +a+     ++  ++ vR ++++g+ 
     EPA05241.1 124 TDKAVSPLNTYGATKLLMERMFTAANfykGAHKTDFLCVRYGNVLGSR 171
                    56777889*************998861113455667888888888833 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.1   2.1e-10   2.7e-07       1     175 [.       7     196 ..       7     273 .. 0.71

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 2.1e-10
                 EEESSTTSHHHHHHHHHHHHHT-E.EEEEES-S..-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEEEE---GGS-HHHHHHHHHHHHHHH..S- CS
        NmrA   1 IlviGaTGrqGksvvrallkaghk.vralvRdt..kselakslkeaGvelvkgdlddkeslvealkgvdvvfsvtgfyskeiedgkklvdAakea..Gv 94 
                 Il++G+TG++G ++++ llk++   vr+  Rd+  +++  +++ ++   ++ gd+ dk+ l++a++g dvvf + ++++  +++  +  +A+k    G 
  EPA05241.1   7 ILITGGTGSLGTALTHRLLKENVGvVRIYSRDEwkQTQMQEKIRDKRLRFLIGDVRDKDRLSRAMEGIDVVFHTAALKHVPVAE-YNPFEAIKTNviGT 104
                 89******************8875279******98888999********************************99976666654.45567777642367 PP

                 SEEEEEE---GG.GT.......SSS---TTTHHHHHHHHHHHHC....TS-EEEEEE-EEGGG-BS..SS-SS-BEEE-TTS.-EEEEESS-T CS
        NmrA  95 khfiySslgddndrs......naeepavphfdsKaeieeyvral....gipytfvyagffmenfls..llaqlkvgdtappedkvtllgpgnp 175
                 +++i S l ++++        +a+ p  +  ++K   e++  a+    g   t ++++ + +++ s  ++a++++++ ++++ k+t+  p  +
  EPA05241.1 105 QNVIESCLDNEVKMAlaigtdKAVSPLNTYGATKLLMERMFTAAnfykGAHKTDFLCVRYGNVLGSrgSVAPKFIEQIQKDG-KITITDPRMT 196
                 7777777776666422222214555555566677777777777766666677777777777765432256777777777776.7777777664 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.0   2.6e-10   3.3e-07       1     122 [.       5     114 ..       5     168 .. 0.82

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 2.6e-10
                 SEEEEESTTSHHHHHHHHHHHHTT-EEEE.EESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEEE---SS--SSGGGCSH CS
   adh_short   1 kvvlvtGassGIGraiakelakeGakvvv.vdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldvLvnNAGitgsgpfselse 98 
                 k +l+tG+++ +G a+ ++l+ke++ vv  ++r e k  ++ +++++  +++ ++ +Dv+d++++++++e +       dv+ + A++ + +p++e++ 
  EPA05241.1   5 KKILITGGTGSLGTALTHRLLKENVGVVRiYSRDEWKQTQMQEKIRD--KRLRFLIGDVRDKDRLSRAMEGI-------DVVFHTAAL-KHVPVAEYNP 93 
                 689************************99899999999999999998..58**************9998876.......889998988.5666666655 PP

                 HHHHHHHHHHTHHHHHHHHHHHHH CS
   adh_short  99 eewervievNltgvflltravlpa 122
                     + i++N+ g+ ++++++l++
  EPA05241.1  94 F---EAIKTNVIGTQNVIESCLDN 114
                 3...45778888887777777765 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   3.1e-08     4e-05       4      79 ..       8      78 ..       6     117 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 3.1e-08
                EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHS CS
          KR  4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaee 79
                litGG+G+LG++l++ l+++    + + sR++ ++ +++++i+     + + +++  Dv dkd +++++e i+  +
  EPA05241.1  8 LITGGTGSLGTALTHRLLKENVGVVRIYSRDEWKQTQMQEKIR-----DKRLRFLIGDVRDKDRLSRAMEGIDVVF 78
                9******************************665556555554.....56889999************99987544 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0     2e-05     0.025      10      88 ..       2      86 ..       1     107 [. 0.81
   2 ?   -2.0   0.0       2.6   3.4e+03     126     137 ..     225     236 ..     222     237 .. 0.82
   3 ?   -1.5   0.0       1.9   2.4e+03      72     101 ..     263     292 ..     240     323 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2e-05
                  .TT-EEEEE.S-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-E.....EEEGCGHHHHHHT-SEEEE-SSSSS- CS
  Shikimate_DH 10 lkekkvlli.GaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeie.....alkleelkellaeadvvisataseep 88
                  l++kk+l+  G+G +++ +++ Ll+++v  v +  R+  +  ++ e++++++++     +++ + l+++++ +dvv+   a +++
    EPA05241.1  2 LQGKKILITgGTGSLGTALTHRLLKENVGVVRIYSRDEWKQTQMQEKIRDKRLRfligdVRDKDRLSRAMEGIDVVFHTAALKHV 86
                  678999998458************************************9998762222245778899999999999987666554 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.6
                   TCCCEEHHHHHH CS
  Shikimate_DH 126 dvrlytvDdLke 137
                   + ++ytvD+Lk+
    EPA05241.1 225 KLKAYTVDELKN 236
                   5689******96 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.9
                   HHHT-SEEEE-SSSSS-SB-HHHHHCCHHH CS
  Shikimate_DH  72 llaeadvvisataseepilekeeveealkk 101
                   l+++ ++  +  +  ++i+++  ve +++ 
    EPA05241.1 263 LINKDEIAYTFESKDDYIIRSPGVETLSDV 292
                   344455555666666677777666665543 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   4.9e-05     0.063       4      74 ..       9      86 ..       6      92 .. 0.79
   2 ?   -1.4   0.0       2.8   3.6e+03       8      36 ..     172     195 ..     167     236 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.9e-05
                   EE.TTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC..........-EEECECHHHHHHH-SEEEE-S-HHHH CS
  F420_oxidored  4 ii.GaGnmgealasgllaagaqpheivvansrnpekaeelaeelg..........vkvtavdneeaaeeadvvvlavkpedv 74
                   i  G+G++g al+++ll+++     +v + sr++ k ++++e++           v+ +    + a+e  dvv+ +   ++v
     EPA05241.1  9 ITgGTGSLGTALTHRLLKEN---VGVVRIYSRDEWKQTQMQEKIRdkrlrfligdVRDKD-RLSRAMEGIDVVFHTAALKHV 86
                   4469****************...5555577*************99999988886554444.677888888888877666665 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.8
                    SHHHHHHHHHHHHTTS-GGCEEEEEESSC CS
  F420_oxidored   8 Gnmgealasgllaagaqpheivvansrnp 36 
                    G+++  +++++++ g    +i+++ ++  
     EPA05241.1 172 GSVAPKFIEQIQKDG----KITIT-DPRM 195
                    666667777777777....66644.4333 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00049      0.63       1      72 [.       6      79 ..       6     121 .. 0.75
   2 ?    1.0   0.0      0.42   5.4e+02       4      27 ..     167     190 ..     166     227 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00049
                    EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSG.GGTTTECEBEEE..GGGGGCTT-SEEEE CS
  Semialdhyde_dh  1 kvaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavk.aleegkdlkved..vdeeelkevdivfl 72
                    k+ i G+tG  G++l  +L +  +v +v+++s+++ + ++++e+ + +        v+d    + +++++d+vf 
      EPA05241.1  6 KILITGGTGSLGTALTHRLLK-ENVGVVRIYSRDEWKQTQMQEKIRdKRLRFLIGDVRDkdRLSRAMEGIDVVFH 79
                    57899**********777776.47999*******97777777776642222222223331144455588899885 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.42
                     EETTTSHHHHHHHHHHHCTSSEEE CS
  Semialdhyde_dh   4 ivGatGyvGqellrlLeehpevel 27 
                     ++G +G v  ++++ ++++ ++++
      EPA05241.1 167 VLGSRGSVAPKFIEQIQKDGKITI 190
                     789999999999988888776665 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00026      0.33       6      73 ..      12      77 ..       6     110 .. 0.75
   2 ?   -2.7   0.0       3.9     5e+03      49      70 ..     255     276 ..     225     285 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00026
                    --SHHHHHHHH.HHHTTT--EEEE-S-HHHHHHHHHHSSBTTTBTT----TTEEEES-HHHHHTT--EE CS
  NAD_Gly3P_dh_N  6 GaGswGtalAk.vlaenghevrlwvreeelieeineehenvkyLpgiklpenlvattdlaealkgadii 73
                    G+Gs Gtal   +l+en   vr+++r+e   ++++e+ ++++ L+   l  +++ ++ l +a++g d++
      EPA05241.1 12 GTGSLGTALTHrLLKENVGVVRIYSRDEWKQTQMQEKIRDKR-LR--FLIGDVRDKDRLSRAMEGIDVV 77
                    89*******962677888999*******88888888776665.33..2444555555555555555555 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.9
                     TT----TTEEEES-HHHHHTT- CS
  NAD_Gly3P_dh_N  49 pgiklpenlvattdlaealkga 70 
                     pg k++e+l  ++++a + +  
      EPA05241.1 255 PGEKFHETLINKDEIAYTFESK 276
                     4455555555555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.68u 0.32s 00:00:01.00 Elapsed: 00:00:00.50
# Mc/sec: 1965.41
//
Query:       EPA05242.1  [L=157]
Description: hypothetical protein BG20_I0178 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.072   13.3   0.1       0.11   12.6   0.1    1.2  1  DUF2526   Protein of unknown function (DUF2526)


Domain annotation for each model (and alignments):
>> DUF2526  Protein of unknown function (DUF2526)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   6.3e-06      0.11      22      50 ..     111     142 ..     107     150 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.3e-06
     DUF2526  22 hmnellialsddaqlsreery...qqqqrlrt 50 
                 +m elli ls +++ls ee     ++q +lr 
  EPA05242.1 111 KMSELLIKLSKNERLSEEETNeiiSLQNQLRE 142
                 79***************987511157888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1073  (0.0598472); expected 358.6 (0.02)
Passed bias filter:                      582  (0.0324614); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.33s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 974.69
//
Query:       EPA05243.1  [L=140]
Description: hypothetical protein BG20_I0212 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-10   40.4   0.0    2.2e-10   40.1   0.0    1.0  1  RmlD_sub_bind  RmlD substrate binding domain


Domain annotation for each model (and alignments):
>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   0.0   1.2e-14   2.2e-10     150     269 ..       9     122 ..       7     138 .. 0.90

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 1.2e-14
                    SEESSSSS-HHHHHHHHHHH-SEEEEESS-EE--EEHHHHHHHHHHHHHHCHH.GGG-EEEE---BS-EEHHHHHHHHHHHHCHTTSEEEEE-CCC CS
  RmlD_sub_bind 150 wvygekgknfvktmlrlakereelkvvaDqlgsPTsardlAevllqllekaaeekelagvyHlanegetswlefArailkeagadseevkpistae 245
                    wv   +  n v ++++ +k+   lk +aD l +PT++ d+ + +++l++         g++Hl++ + ++++++A   ++ +  ++e ++pi+++e
     EPA05243.1   9 WVEKWQHTNSVLRVIETLKSGTILKEIADWLNTPTYVPDIVKSTAKLIQINET-----GIFHLTGPDFINRYDLAILTAEIFCLKKEMIQPINSKE 99 
                    66666788999999**********************************98885.....************************************** PP

                    S--SS---SBE-B--HHHHHCCT- CS
  RmlD_sub_bind 246 yptpAkRPanSvLdtekleatfgi 269
                       +AkR  n +L++ek+ +++gi
     EPA05243.1 100 LGLAAKRS-NVKLNNEKTCKKTGI 122
                    *******6.678888887776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 959.70
//
Query:       EPA05244.1  [L=331]
Description: dTDP-glucose 4,6-dehydratase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      9e-74  248.8   0.0    1.1e-73  248.6   0.0    1.1  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
      2e-55  187.9   0.0    2.5e-55  187.6   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    1.1e-20   73.8   0.1    1.4e-20   73.4   0.1    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
      5e-14   52.1   0.0    3.8e-13   49.2   0.0    1.9  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    6.3e-14   51.7   0.0    7.5e-14   51.5   0.0    1.2  1  RmlD_sub_bind    RmlD substrate binding domain
      2e-11   43.6   0.7    3.5e-10   39.5   0.7    2.4  1  NAD_binding_4    Male sterility protein


Domain annotation for each model (and alignments):
>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  248.6   0.0   3.6e-77   1.1e-73       1     331 [.       4     301 ..       4     302 .. 0.89

  Alignments for each domain:
  == domain 1  score: 248.6 bits;  conditional E-value: 3.6e-77
                    EEETTTSHHHHHHHHHHHHC..T-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHTTS CS
  GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlek..gyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevynLAAqshVdvsfek 94 
                    L+TG+ GfiGs+++  +l +  +ye+++i+   +  + ++++ ++k      ++++k++kg++t++  +++l+++v  d v+n+AA+shVd+s+ +
     EPA05244.1   4 LVTGGLGFIGSNFILDILLRfpNYEIINIDAEIEGSSHNNLKDIKK------NRKYKFVKGNITNQLLIDKLISKV--DIVFNFAAESHVDRSILS 91 
                    9***********9977777634666666665555555555555543......5689******************99..89**************** PP

                    HHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-T CS
  GDP_Man_Dehyd  95 PeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYaaaKlyadwivvnyreayglfavngilfnhesprrge 190
                    P+ +++ n++G++++Le +r+++    ++++q+St+Ev+G+ ++   +E+ +++P sPY+ +K++a+ +v +y ++yg+ a+++++ n+ +pr+  
     EPA05244.1  92 PKNFIKSNIVGMFTILESVRKYK----KKLIQISTDEVFGSINKGSASEESHLNPSSPYSSSKASAELLVNSYVKTYGIEAIVTRCTNNFGPRQ-- 181
                    *********************95....59****************************************************************7.. PP

                    TSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHHHHHHHHCSS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............T CS
  GDP_Man_Dehyd 191 tfvtrkitravarialgkqevlylGnldakRdwghvkDyveamwlmlqqdkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakes 286
                       +++i+r++  +++  q+++++G ++a+Rdw +vkD+++a+  + +++k        ge++++   +e+ ++ ++k+i +              
     EPA05244.1 182 -HTEKLIPRIILFAKN-DQKIPIYGSGKAVRDWIYVKDHCNAIIEIYKSGK-------WGESYNISANNEMDNITIVKKILKI------------L 256
                    .467999999986555.679999**************************99.......7******************998754............3 PP

                    TGGCCCEECGG--SS--SB--B-THHHHHHH----SS-HHHHHHH CS
  GDP_Man_Dehyd 287 gkvvvevdpkyfrpgevdlllgdaskakeeLgWkpkvsfeelvre 331
                    gk    +    +rpg++ ++  d sk++++L Wk +++f++ +++
     EPA05244.1 257 GKPSDLFYHTEDRPGHDLRYSLDSSKIRKQLKWKTEFGFDDALEQ 301
                    455556667889****************************99987 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.6   0.0   8.3e-59   2.5e-55       2     240 ..       4     237 ..       3     238 .. 0.95

  Alignments for each domain:
  == domain 1  score: 187.6 bits;  conditional E-value: 8.3e-59
                 EEETTTSHHHHHHHHHHHHCT..SEEEEEES-STTTTCHHCHHC......EEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHHHSHHHHHHHHT CS
   Epimerase   2 lVtGatGfiGsalvkallekg..yevigldrlssasntarledl......elveldltdrsalerlfkeeqpdavihlAavggvaassedpadfieknl 92 
                 lVtG+ GfiGs+++  +l +   ye+i++d + ++s +++l+d+      ++v++++t++  +++l++  ++d+v+++Aa+++v++s+ +p+ fi++n+
  EPA05244.1   4 LVTGGLGFIGSNFILDILLRFpnYEIINIDAEIEGSSHNNLKDIkknrkyKFVKGNITNQLLIDKLIS--KVDIVFNFAAESHVDRSILSPKNFIKSNI 100
                 9***********88776665557*********************************************..9**************************** PP

                 HHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHH CS
   Epimerase  93 qgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklveayaaqyglnaiilrlfnlyGprngegevsrvipalir 191
                 +g+ ++le +rk++  +l+++s++ev+G  ++    + +++++l+p+spY+ +K+ +e lv +y ++yg++ai++r++n++Gpr   ++ +++ip++i 
  EPA05244.1 101 VGMFTILESVRKYKK-KLIQISTDEVFGSINK---GSASEESHLNPSSPYSSSKASAELLVNSYVKTYGIEAIVTRCTNNFGPR---QHTEKLIPRIIL 192
                 *************99.************8777...45555569*****************************************...99********** PP

                 HHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT-STTEEEEE CS
   Epimerase 192 kilegkqevtllgdgtalRdflyveDvaeaillvlehvdagdkgeiyni 240
                  +++ + ++ ++g+g+a+Rd++yv+D+++ai+ + +    g+ ge yni
  EPA05244.1 193 FAKNDQ-KIPIYGSGKAVRDWIYVKDHCNAIIEIYKS---GKWGESYNI 237
                 999998.**************************9999...888999998 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.4   0.1   4.8e-24   1.4e-20       1     226 [.       4     223 ..       4     228 .. 0.86

  Alignments for each domain:
  == domain 1  score: 73.4 bits;  conditional E-value: 4.8e-24
   3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkk...viegDvtdkdkleealegvdvvihlaslvdvag.kltedeimkvnvkG 95 
                 +vtGg GF+G++ +  ++ + +  e+  +D +++ + +++l+ ++ +    +++g +t++  +++ + +vd+v+  a+ + v    l+ +++ k n+ G
  EPA05244.1   4 LVTGGLGFIGSNFILDILLRFPNYEIINIDAEIEGSSHNNLKDIKKNRkykFVKGNITNQLLIDKLISKVDIVFNFAAESHVDRsILSPKNFIKSNIVG 102
                 69**********998877777789******887766666666655544455******************************9875789999******** PP

   3Beta_HSD  96 TrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKalaEklvlkaNgrtlknggrlyTcaLRpagiyGegd..kllvpl 192
                   ++le+ +k   ++l+  S+ ev g       i +g  ++e + +++++y++sKa aE lv +     +k    +  +  R +  +G+++  ++l p+
  EPA05244.1 103 MFTILESVRKYK-KKLIQISTDEVFGS------INKGSASEESHLNPSSPYSSSKASAELLVNSY----VKTY-GIEAIVTRCTNNFGPRQhtEKLIPR 189
                 ******999887.89******999999......999999999*****************999544....4443.366777799******97225799** PP

   3Beta_HSD 193 lkqlaklglalfkigdeevlsdrvYvgNvawahi 226
                 +   ak+ +++  +g+ +++ d++Yv     a+i
  EPA05244.1 190 IILFAKNDQKIPIYGSGKAVRDWIYVKDHCNAII 223
                 **************************98777776 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2   0.0   1.3e-16   3.8e-13       1     249 [.       3     258 ..       3     273 .. 0.78

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 1.3e-16
                      EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-SEEEE------HHHHH CS
  Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvdvvfhaAAlKhVPlve 94 
                      +lvtG+ G iGs+++  il + p+  i+   +E +  + ++ l++ +k++k+k+    v g+++++  ++k+++  kvd+vf+ AA  hV    
       EPA05244.1   3 LLVTGGLGFIGSNFILDILLRFPNYEIINIDAEIEGSSHNN-LKDIKKNRKYKF----VKGNITNQLLIDKLIS--KVDIVFNFAAESHVDRSI 89 
                      59**************9999877665555556666555443.444455555544....58**************..****************** PP

                      HSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEGGG..............SS--SHHHHHHHHHHHHHHHGGG--SSS--EEEEEEE-EETTG CS
  Polysacc_synt_2  95 enpleaiktNvlgtenvieaaieagvkkvvliStDKA..............vnPtnvmGatKrlaekllqalakeseekktkfvvvRfGNVlgS 174
                        p + ik N++g+ +++e   +++ kk++ iStD                 nP + +  +K+ ae+l+ ++ k+      + +v+R  N +g 
       EPA05244.1  90 LSPKNFIKSNIVGMFTILESVRKYK-KKLIQISTDEVfgsinkgsaseeshLNPSSPYSSSKASAELLVNSYVKTY---GIEAIVTRCTNNFGP 179
                      ******************9988887.89*******87222222222222223566667777777777777776666...589999999999998 PP

                      TT...SSHHHHHHHHHTTSSEEES.-TT-EEEEE-HHHHHHHHHHHHHH--SS-EEEE--.-EEEHHHHHHHH...... CS
  Polysacc_synt_2 175 rG...SviplFkkqikeggpvtvT.dpemtRyfmtieeavqLvlqalalakggeifvldmGepvkivdlakalielsgl 249
                      r     +ip      k+++++++    + +R ++ +++ ++ +++  + +k ge +   + + +  + ++k+++++ g+
       EPA05244.1 180 RQhteKLIPRIILFAKNDQKIPIYgSGKAVRDWIYVKDHCNAIIEIYKSGKWGESYNISANNEMDNITIVKKILKILGK 258
                      75222689999999999999999625689999*************9999999999999888888888888888888875 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.5   0.0   2.5e-17   7.5e-14       1     154 [.       1     179 [.       1     267 [. 0.86

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 2.5e-17
                    EEEEEESTTSHHHHH..HHHHCTTTSEEEEEE-TT.....................T--TTSHHHHHHHHHHH--SEEEE------HHHHHHSHHH CS
  RmlD_sub_bind   1 mkilvtGanGqlGse..Lakqlaeeglevlaltre.....................eldltdaeavaellkeakpdvvvnaAAytavDkaEseeea 73 
                    mk+lvtG+ G +Gs+  L  +l+  ++e++ ++ e                     + ++t++  +++l+++   d+v n AA   vD+    +++
     EPA05244.1   1 MKLLVTGGLGFIGSNfiLDILLRFPNYEIINIDAEiegsshnnlkdikknrkykfvKGNITNQLLIDKLISK--VDIVFNFAAESHVDRSILSPKN 94 
                    89************94334566779*******9999*******************99*************98..899******************* PP

                    HHHHHTHHHHHHHHHHHHCT-EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHHH-S....SEEEEEE-SEESS CS
  RmlD_sub_bind  74 ayavnaeavealAeaaaavgalLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavlaagk....kalivRtswvyge 154
                      + n  +  ++ e  ++++ +Li++StD VF   +k   +e+++ +P + Y  +K+  E  v++++k    +a++ R +  +g 
     EPA05244.1  95 FIKSNIVGMFTILESVRKYKKKLIQISTDEVFGSINKGSASEESHLNPSSPYSSSKASAELLVNSYVKtygiEAIVTRCTNNFGP 179
                    *************************************************************999966511225667777666654 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   0.7   1.2e-13   3.5e-10       1     205 [.       5     175 ..       5     231 .. 0.79

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 1.2e-13
                    EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSHHHHHHHHHHHT-SS-HHHHHHHHHTTTEEEEE--TTSGGGG--HHHHHHHHHH--EEEE--S CS
  NAD_binding_4   1 lTGaTGFLGkvLlekLLrttpevkiyllvRaksgesaeeRleeelekkelfsallkelaerikvveGDlseprlGLseedlqelaeevdviihsaA 96 
                    +TG+ GF+G+ ++ ++L + p+++i+            + + e   +++l++       ++ k+v+G+++++ l      +++l+++vd++++ aA
     EPA05244.1   5 VTGGLGFIGSNFILDILLRFPNYEIINI---------DAEI-EGSSHNNLKDIK---KNRKYKFVKGNITNQLL------IDKLISKVDIVFNFAA 81 
                    7999999999999999999998766532.........2223.222233333333...36799********9875......99************** PP

                    S-S.STTS...SEEHHHHHHHHHHHHHHHTSSS--.-EEEEEE.GGGTTS-TTT--SSS-H......HHH--EEEETTTCCCHHHHHHHHHHHHHH CS
  NAD_binding_4  97 tvnfdepy...kellrvNveGtrevlelakklkklkvllhvST.ayvngeregeveekvyeegekeekldederaklkglpntYeqsKalaEklvr 188
                      ++d+++   k++++ N+ G+  +le  +k kk+  l+++ST  ++   ++g                   +++++ + +  Y+ sKa aE lv+
     EPA05244.1  82 ESHVDRSIlspKNFIKSNIVGMFTILESVRKYKKK--LIQISTdEVFGSINKGS-----------------ASEESHLNPSSPYSSSKASAELLVN 158
                    ******65333789****************99888..******76666666654.................56778899999************** PP

                    HHHHHH---EEEEEE-E CS
  NAD_binding_4 189 earrrsglpvvivRpsi 205
                    ++ +  g+ +++ R+++
     EPA05244.1 159 SYVKTYGIEAIVTRCTN 175
                    **************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       739  (0.0412181); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.51
# Mc/sec: 1943.28
//
Query:       EPA05245.1  [L=270]
Description: NAD dependent epimerase/dehydratase family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-39  136.0   0.0      3e-39  135.3   0.0    1.3  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    1.3e-35  123.0   0.0    1.5e-35  122.8   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    1.3e-08   34.3   0.0    1.7e-08   33.9   0.0    1.3  1  RmlD_sub_bind    RmlD substrate binding domain
     0.0021   17.2   0.0      0.014   14.5   0.0    2.1  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
     0.0033   16.6   0.0     0.0048   16.1   0.0    1.2  1  NAD_binding_4    Male sterility protein


Domain annotation for each model (and alignments):
>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.3   0.0   8.4e-43     3e-39      53     330 ..       3     259 ..       1     261 [. 0.91

  Alignments for each domain:
  == domain 1  score: 135.3 bits;  conditional E-value: 8.4e-43
                    CEEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS--- CS
  GDP_Man_Dehyd  53 nlklhkgDltDssslerllaevqpdevynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfy 148
                    +++l k+D+tD s+l +++   +pd +++LA++   ++sfe+P y ++vn+  tl +Le ir+ +l  +++f+  St  v Gk++  p++Et   +
     EPA05245.1   3 KIHLCKVDVTDFSELSKIIIANKPDIIIHLAGETSHKKSFENPMYDVDVNLKSTLCILETIRTSKL--NCKFILGSTFIVVGKPDTLPINETINCN 96 
                    6899***********************************************************998..6*************************** PP

                    --SHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHH.HHHTTS-C-EECTTTT-EEEEEEHHHHHHHHHHHHHCSS-- CS
  GDP_Man_Dehyd 149 PrsPYaaaKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitrava.rialgkqevlylGnldakRdwghvkDyveamwlmlqqdkpe 243
                    P+  Y+ ++l+++++++ y++ y+l +++ ++ n  +pr +   +t++  +++  ++  gk +v+++ n++  Rd  +v D+v+a++++++++kp 
     EPA05245.1  97 PTTVYGTTRLASEHLCKIYQNVYDLDTLSFRITNAFGPREQYLTPTKNALNYLIyQAYCGK-DVTIYNNGQFFRDIIFVTDVVSALQTIMERGKP- 190
                    ****************************************999999998887551566665.9999****************************8. PP

                    -EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB--B-THHHHHHH----SS-HHHHHH CS
  GDP_Man_Dehyd 244 dyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdlllgdaskakeeLgWkpkvsfeelvr 330
                          g+ + + +  +  f e+ + +       ee  +     k++    p+y  + +v + l d+sk+k  LgW  k+s++++++
     EPA05245.1 191 ------GNLYWISSYKKTWFYEIAQWL-------EELTN----CKIKYVDPPSYTSKVDVGNFLVDNSKLK-SLGWDLKISVKDGIK 259
                    ......888888888888888887633.......23322....3455666799*****************9.9***********998 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.8   0.0   4.3e-39   1.5e-35      42     238 ..       3     194 ..       1     197 [. 0.95

  Alignments for each domain:
  == domain 1  score: 122.8 bits;  conditional E-value: 4.3e-39
                 HCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCT.EEEEEEEGGGGTSCSSSSBSTCSTTS----S CS
   Epimerase  42 dlelveldltdrsalerlfkeeqpdavihlAavggvaassedpadfieknlqgtlnlleaarkagvk.rllflsSsevYGkdaeqpkeettltgplkpn 139
                 +++l+++d+td s+l +++  ++pd++ihlA++ + + s+e+p + ++ nl+ tl +le +r+++++ +++  s+  v Gk+++ p +et+   +++p+
  EPA05245.1   3 KIHLCKVDVTDFSELSKIIIANKPDIIIHLAGETSHKKSFENPMYDVDVNLKSTLCILETIRTSKLNcKFILGSTFIVVGKPDTLPINETI---NCNPT 98 
                 4589**********************************************************997777***********************...***** PP

                 SHHHHHHHHHHHHHHHHHHHHT-EEEEEEESEEESTT.S-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT-STTEE CS
   Epimerase 140 spYaaaKlageklveayaaqyglnaiilrlfnlyGpr.ngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvlehvdagdkgei 237
                 + Y+ + la+e+l++ y++ y+l+++++r++n +Gpr ++ +  ++ + +li +++ gk +vt++++g+  Rd ++v Dv+ a+ +++e+   g++g+ 
  EPA05245.1  99 TVYGTTRLASEHLCKIYQNVYDLDTLSFRITNAFGPReQYLTPTKNALNYLIYQAYCGK-DVTIYNNGQFFRDIIFVTDVVSALQTIMER---GKPGNL 193
                 *************************************55555599**************.******************************...777776 PP

                 E CS
   Epimerase 238 y 238
                 y
  EPA05245.1 194 Y 194
                 6 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.0   4.7e-12   1.7e-08      34     138 ..       8     114 ..       2     230 .. 0.86

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 4.7e-12
                    T--TTSHHHHHHHHHHH--SEEEE------HHHHHHSHHHHHHHHTHHHHHHHHH..HHHCT-EEEEEEEGGGS-S-TTS-B-TTS----SSHHHH CS
  RmlD_sub_bind  34 eldltdaeavaellkeakpdvvvnaAAytavDkaEseeeaayavnaeavealAea..aaavgalLihvStDyVFdGekkrpYeeddetsPlnvYGr 127
                    ++d+td +++ +++ ++kpd+++++A  t   k  +++  +  vn +++  + e   +++ + ++i  St  V     + p +e+ + +P +vYG 
     EPA05245.1   8 KVDVTDFSELSKIIIANKPDIIIHLAGETSHKKSFENPMYDVDVNLKSTLCILETirTSKLNCKFILGSTFIVVGKPDTLPINETINCNPTTVYGT 103
                    79**************************************************98623678899**********9999999**************** PP

                    HHHHHHHHHHH CS
  RmlD_sub_bind 128 tKlaGEqavla 138
                    t+la E+  + 
     EPA05245.1 104 TRLASEHLCKI 114
                    ******97654 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   3.9e-06     0.014      61     157 ..       9     120 ..       2     222 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.9e-06
                      --TT-HHHHHHHTT..T-SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-S.EEEEEEE.......GG.......GSS--SHHH CS
  Polysacc_synt_2  61 gdvrdkerlekaleelkvdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvk.kvvliSt.......DK.......AvnPtnvmG 139
                       dv+d ++l+k++ + k+d+++h A         enp+  ++ N  +t  ++e+  +++ + k++l St       D         +nPt v+G
       EPA05245.1   9 VDVTDFSELSKIIIANKPDIIIHLAGETSHKKSFENPMYDVDVNLKSTLCILETIRTSKLNcKFILGSTfivvgkpDTlpinetiNCNPTTVYG 102
                      699**********************98888888889*****************999999875688888744443333232222235799***** PP

                      HHHHHHHHHHHHGGG--S CS
  Polysacc_synt_2 140 atKrlaekllqalakese 157
                      +t++++e l+  +++   
       EPA05245.1 103 TTRLASEHLCKIYQNVYD 120
                      ********9998888764 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.3e-06    0.0048      84     201 ..      22     162 ..      12     190 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.3e-06
                    HHHH--EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEE.GGGTTS-TTT--SSS-H...................... CS
  NAD_binding_4  84 laeevdviihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvST.ayvngeregeveekvyeege................... 156
                    +a++ d+iih a+ ++++++ ++    ++vN+++t  +le  ++ k +  ++  ST  +v + ++  ++e++  ++                    
     EPA05245.1  22 IANKPDIIIHLAGETSHKKSFENpmyDVDVNLKSTLCILETIRTSKLNCKFILGSTfIVVGKPDTLPINETINCNPTtvygttrlasehlckiyqn 117
                    58899*****************95434699***************99999******5555555555555555554446777777777777777665 PP

                    ....HHH--EEEETTTCCCHH.HHHHHHHHHHHHHHHHHH---EEEE CS
  NAD_binding_4 157 .keekldederaklkglpntY.eqsKalaEklvrearrrsglpvviv 201
                      +  + +   ++  g  ++Y + +K +  +l+ +a   +g  v+i+
     EPA05245.1 118 vYDLDTLSFRITNAFGPREQYlTPTKNALNYLIYQAY--CGKDVTIY 162
                    5444455555555666666663446666666666666..66666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 1801.12
//
Query:       EPA05246.1  [L=147]
Description: hypothetical protein BG20_I0200 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-22   80.0   0.4    1.5e-22   79.7   0.4    1.0  1  FdtA      WxcM-like, C-terminal
    3.3e-05   23.5   0.1     0.0003   20.4   0.1    2.1  1  Cupin_2   Cupin domain
    0.00062   19.4   0.0    0.00073   19.2   0.0    1.2  1  Cupin_1   Cupin
  ------ inclusion threshold ------
      0.067   13.4   0.1      0.087   13.0   0.1    1.3  1  ARD       ARD/ARD' family


Domain annotation for each model (and alignments):
>> FdtA  WxcM-like, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.7   0.4   3.4e-26   1.5e-22       7     118 ..      13     130 ..       7     142 .. 0.85

  Alignments for each domain:
  == domain 1  score: 79.7 bits;  conditional E-value: 3.4e-26
                 EEEEEEET..TEEEEEEEBTTT..BSS--SEEEEEES--TTTEEEEEEESS--EEEEEEES-EEEEEE-SS.-EEEEEE-STT.EEEEE-TT-EEEEE- CS
        FdtA   7 elpkikde..rgnLsvieeeke..vpfeikrvyyvydvpegeerGeHahkkleqllialsGsvevllddgk.kkkeilldsps.kglyipkmiWrelin 99 
                 e +++ d+  +g+L+vi+++++  + +++k+vy+++  p ++ +G H+h k+++ +++++G+v ++++d + ++kei   + +   +y+pk+i++++in
  EPA05246.1  13 ETKSVIDShvNGSLTVIWRDWDeiIKNHPKMVYVSSVNPGEI-KGPHLHTKRNSYFVCIHGKVVFVIKDEQgNYKEIESSEENpVLVYVPKNIPSAHIN 110
                 55555554469**********999*********877666555.*********************99988762679999888776999************ PP

                 --TT.-EEEEEESS---GGG CS
        FdtA 100 fsed.avllvlasesydeed 118
                  s d + +l la+  + ++d
  EPA05246.1 111 ISDDvSRVLALADIAWRPND 130
                 ****99************99 PP

>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.1   6.8e-08    0.0003       3      69 ..      47     120 ..      45     122 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 6.8e-08
                 EEEETTEEEEEECSSSEEEEEEEEESEEEEEECTE.....EEEEETTE..EEEE-TT-EEEEEE-SSS-EEEEE CS
     Cupin_2   3 velppGesapshrHpgedeffyVleGegeltvdge.....eveleaGd..svyfpagtpHrfrNtgdeparllv 69 
                  ++ pGe  ++h H+    +f+++ G++++ + +e     e+e ++    +vy+p++ p +++N +d+  r+l 
  EPA05246.1  47 SSVNPGEIKGPHLHTKRNSYFVCIHGKVVFVIKDEqgnykEIESSEENpvLVYVPKNIPSAHINISDDVSRVLA 120
                 5799***999*******9*************776647676444444433389**************99888875 PP

>> Cupin_1  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.6e-07   0.00073      33     116 ..      43     125 ..      15     140 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.6e-07
                 EEEEEEEE.TTEEEEEEEESSS-EEEEEEESEEEEEEEETTSS.EEEEEEEETTEEEEE-TT-EEEEEEESSSSEEEEEEEESS CS
     Cupin_1  33 isaarvdlepgglllPhyhpnateiayvlqGegrvgfvvpgngnrdfhkklreGdvfvvPaglvhfqynsgdepavaivvfdtn 116
                 ++ ++ + +pg +  Ph h++ ++ +++++G++ +++  ++ +++ +++  +   +++vP++++ +++n+ d+   ++++ d++
  EPA05246.1  43 MVYVSSV-NPGEIKGPHLHTKRNSYFVCIHGKVVFVIKDEQGNYKEIESSEENPVLVYVPKNIPSAHINISDDVSRVLALADIA 125
                 4444444.5999*********************9666666666888888888888999************97777776666665 PP

>> ARD  ARD/ARD' family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   1.9e-05     0.087      86     132 ..      56     105 ..       4     108 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.9e-05
         ARD  86 eEhlhedeei.rliveGtgyFdvrskdeawirvlvekGD..LivlPagiy 132
                  +hlh+  +   ++++G+ +F+++++++++ ++   +    L+ +P++i 
  EPA05246.1  56 GPHLHTKRNSyFVCIHGKVVFVIKDEQGNYKEIESSEENpvLVYVPKNIP 105
                 57888876541569****************99987544333999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1037.01
//
Query:       EPA05247.1  [L=177]
Description: dTDP-4-dehydrorhamnose 3,5-epimerase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.2e-63  211.5   0.0    6.9e-63  211.3   0.0    1.0  1  dTDP_sugar_isom  dTDP-4-dehydrorhamnose 3,5-epimerase
     0.0026   17.5   0.0     0.0041   16.9   0.0    1.3  1  FdtA             WxcM-like, C-terminal


Domain annotation for each model (and alignments):
>> dTDP_sugar_isom  dTDP-4-dehydrorhamnose 3,5-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  211.3   0.0   7.6e-67   6.9e-63       1     168 [.       5     175 ..       5     176 .. 0.98

  Alignments for each domain:
  == domain 1  score: 211.3 bits;  conditional E-value: 7.6e-67
                      E-SSTTCEEEEE-EEEETTEEEEEEEEHHHHHHHTS-----EEEEEEE.ETTBEEEEEEESSCS---EEEEEEESEEEEEEEE-BTTSTTTT-E CS
  dTDP_sugar_isom   1 eteiegvlliepkvfgDeRGfflesfneeefaeagleaefvqdnlsvs.kkgvlRGlHfqkepkaqaklvrvvrGevldvaVDlRkgSptfgkw 93 
                      et+++g+++ie ++ +DeRGff+++++++ ++e+gl+ ++vq ++s++ +kg++RG+Hfqk+p++++k+vr++rG+++dv++DlR++Sptf kw
       EPA05247.1   5 ETDLSGAYIIEIEKCEDERGFFARTWDSNVYKENGLNPNLVQSSISFNiEKGTIRGMHFQKPPHEEDKVVRCTRGKIFDVIIDLRNNSPTFTKW 98 
                      689******************************************************************************************* PP

                      EEEEEETTT--EEEE-TTEEEEEEE-SSEEEEEEEESS---GGGEEEE-TT-TTTT---..SS.B--HHHHT-B-HH CS
  dTDP_sugar_isom  94 vgveLsaenkrqlyipegfahGflvlsdeaevlYkvteyyapesergirwnDpelgidw..eelilSekDkaapsla 168
                      +g+eLs++n++++yip+gfahGf+++++++ev+Y+++ey+ pe+ +g+rw+Dp+++i+w     ++S+kD ++  ++
       EPA05247.1  99 QGFELSENNHKMIYIPKGFAHGFQTMEKDSEVFYQMSEYFMPEYASGVRWDDPAFKITWplPISVISKKDLSYSHFK 175
                      ************************************************************96689*****9988876 PP

>> FdtA  WxcM-like, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   4.5e-07    0.0041       5     116 ..      13     140 ..       9     144 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.5e-07
                 EEEEEEEEETTEEEEEEEBTTT.....BSS--SEEEEEES--TTTEEEEEEES...S--EEEEEEES-.EEEEEE-SS-E......EEEEE-STT.EEE CS
        FdtA   5 lielpkikdergnLsvieeeke.....vpfeikrvyyvydvpegeerGeHahk...kleqllialsGs.vevllddgkkk......keilldsps.kgl 87 
                 +ie++k +derg  +  + ++      ++ +  +  +++++++g+ rG H  k   +  +++ + +G+ ++v++d  +++      + + l +++ k++
  EPA05247.1  13 IIEIEKCEDERGFFARTWDSNVykengLNPNLVQSSISFNIEKGTIRGMHFQKpphEEDKVVRCTRGKiFDVIIDLRNNSptftkwQGFELSENNhKMI 111
                 78999999999977777766543334466666677799*************984334567999****95689998777662222224566777766*** PP

                 EE-TT-EEEEE---TT-EEEEEESS---G CS
        FdtA  88 yipkmiWrelinfsedavllvlasesyde 116
                 yipk+  +    +++d+ +    se++ +
  EPA05247.1 112 YIPKGFAHGFQTMEKDSEVFYQMSEYFMP 140
                 ********999999999998888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1089.38
//
Query:       EPA05248.1  [L=185]
Description: hypothetical protein BG20_I0210 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.082   13.2   0.0       0.13   12.5   0.0    1.3  1  Strep_pep  Ribosomally synthesized peptide in Streptomyces sp


Domain annotation for each model (and alignments):
>> Strep_pep  Ribosomally synthesized peptide in Streptomyces species
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   7.5e-06      0.13      22      46 ..      85     109 ..      75     118 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.5e-06
   Strep_pep  22 ayDaalqlNVLadGrpAiaDralLa 46 
                 ++D+al lNVL  G + + D+ lL+
  EPA05248.1  85 TWDSALVLNVLRYGDINVLDEILLK 109
                 79*******************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1332.12
//
Query:       EPA05249.1  [L=273]
Description: polysaccharide deactylase family protein, PEP-CTERM locus family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-33  114.6   0.1    5.2e-33  113.8   0.1    1.4  1  DUF3473          Domain of unknown function (DUF3473)
    5.3e-22   78.0   0.0    8.4e-22   77.4   0.0    1.2  1  Polysacc_deac_1  Polysaccharide deacetylase
    9.7e-06   25.4   0.0    2.2e-05   24.2   0.0    1.6  1  DUF2334          Uncharacterized protein conserved in bacteri


Domain annotation for each model (and alignments):
>> DUF3473  Domain of unknown function (DUF3473)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.8   0.1   8.7e-37   5.2e-33       1     129 [.     139     271 ..     139     272 .. 0.90

  Alignments for each domain:
  == domain 1  score: 113.8 bits;  conditional E-value: 8.7e-37
     DUF3473   1 SSvfPvrhdlyGipdaprk.......pfrikkekgkllElPvstlklggr.nlplaGGgyfRlfPyalikallrrlnregrpavlYfHpwEldpdqprv 91 
                 SS+fPvr+ lyG+p+apr+          +++ek++l E+P++t++++ + n+p+aGG+ +R+fPy++ik++l+++n++++++++Y+Hp +ldp+ pr+
  EPA05249.1 139 SSIFPVRTPLYGVPNAPRFiykpniiNPIVEDEKSNLSEIPLATHRIPIIgNIPIAGGFHLRFFPYSYIKYGLNKINKNNNSFIFYIHPKDLDPKMPRI 237
                 9******************66655442234445566*********999888************************************************ PP

     DUF3473  92 kgaslksrfrhylnlkrteerlrrllsdfeFttveell 129
                 k    +  ++ y+nlk + ++++++l+df+F+t++e l
  EPA05249.1 238 K----EYGWHYYHNLKGALKKFENILEDFKFVTAKEQL 271
                 8....678899**********************99865 PP

>> Polysacc_deac_1  Polysaccharide deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.4   0.0   1.4e-25   8.4e-22      18     114 ..      30     126 ..       8     133 .. 0.92

  Alignments for each domain:
  == domain 1  score: 77.4 bits;  conditional E-value: 1.4e-25
                      CSCHHHHHHHHHHCT--EEEEE-HHHHCH-HHHHHHHHHTTEEEEE--SS--EGGGSHHHHHHHHHHHHHHHHHHHHS----EEE-GGGEE-HH CS
  Polysacc_deac_1  18 rdntteilpvLkkykvkatffvigglvedypdevremaasGveignHtinhsnlkrlseeevrreierakdalrkalgreprlfryPygsasat 111
                       +nt  il++++k++vkatffv+g  +e  p++++e+ ++G+ei++H++ h ++++ ++ee++++++++ d l++++ +++  fr+Py s++++
       EPA05249.1  30 VENTSLILDLFAKHDVKATFFVVGYIAELFPELIKEIDRKGHEIASHSYAHIDIRKSTQEEFEKDLKKSLDTLENITTKKVIGFRAPYFSITKN 123
                      68999*******************99****************************************************************9998 PP

                      HHH CS
  Polysacc_deac_1 112 vle 114
                      +  
       EPA05249.1 124 SFW 126
                      755 PP

>> DUF2334  Uncharacterized protein conserved in bacteria (DUF2334)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   3.7e-09   2.2e-05      57     195 ..      59     244 ..      55     262 .. 0.70

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 3.7e-09
     DUF2334  57 fvevLkylqakGgeialHGYtHqygtvksevsgegfeflseseakeriekGieilkklgi.kpkgFeaPhyaaseetykalkkyfsiiyerykeykgq. 153
                 f e++k++ +kG+eia H Y H +     + + e+f        ++ ++k++++l++    k+ gF aP +++++++  a+k     i+ +y  y+++ 
  EPA05249.1  59 FPELIKEIDRKGHEIASHSYAHIDI---RKSTQEEF--------EKDLKKSLDTLENITTkKVIGFRAPYFSITKNSFWAIK-----ILSKYLRYDSSi 141
                 56789*******************9...55455555........557**********99889***************99999.....333333333122 PP

     DUF2334 154 ......................................................kegltyipenlgyveedeeienaealkvrdglasffyHpyl.... 194
                                                                         +l++ p   +y+++   ++++++   +++ + f++Hp+     
  EPA05249.1 142 fpvrtplygvpnaprfiykpniinpivedeksnlseiplathripiignipiagGFHLRFFP--YSYIKY--GLNKINK---NNNSFIFYIHPKDldpk 233
                 34445566667778888888888889998888888887777777777777775544455555..566655..2333333...56679999999886666 PP

     DUF2334 195 ..........t 195
                           +
  EPA05249.1 234 mprikeygwhY 244
                 66665555541 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1945.31
//
Query:       EPA05250.1  [L=137]
Description: putative methylmalonyl-CoA epimerase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-15   57.6   0.0    1.7e-15   57.2   0.0    1.2  1  Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxyge
      0.007   16.6   0.0       0.01   16.0   0.0    1.4  1  Glyoxalase    Glyoxalase/Bleomycin resistance protein/Dioxyge
  ------ inclusion threshold ------
      0.039   13.4   0.0      0.041   13.3   0.0    1.1  1  PTE           Phosphotriesterase family
       0.14   12.5   0.0       0.58   10.5   0.0    1.9  2  CbiX          CbiX
       0.18   11.9   0.0        0.4   10.8   0.0    1.5  2  Glyoxalase_3  Glyoxalase-like domain


Domain annotation for each model (and alignments):
>> Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.2   0.0   4.7e-19   1.7e-15       1     108 [.       5     113 ..       5     114 .. 0.88

  Alignments for each domain:
  == domain 1  score: 57.2 bits;  conditional E-value: 4.7e-19
                   EEEEEE-S-HHHHHHHHHH.TT-EESS-.-E.EETTTTEEEEEEEETTEEEEEEEESSTT-THHH...TS-EEEEEEEEES-HHHHHHHHCTTTEEE CS
  Glyoxalase_4   1 dQigivVeDleaavarfsallGvgpwqr.yrdepqevdlafallgsgsvqieLieplegpeflae...hgeglhhlaywvddldaavarleeqGfev 93 
                   ++igivV  +     ++++ + ++++++ +  ++q+v+++f++ g+  + +eLiep+ +++++a    +g+g+hhl+++v+++ ++++++ ++G+++
    EPA05250.1   5 HHIGIVVSKISNSFPELTKYIKFEKTTIpIFITSQKVNVCFLKIGE--FNLELIEPVGEDSPVATfanKGGGFHHLCFEVKNIREKLDEFVKNGARI 99 
                   8**********************988553889************99..8**********955555555****************************9 PP

                   EEEEE-GGGTT-EEE CS
  Glyoxalase_4  94 vqkgvragaagrrfa 108
                   + +    g +gr  a
    EPA05250.1 100 IVEP-VIGFEGRLTA 113
                   8865.6777777665 PP

>> Glyoxalase  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   2.8e-06      0.01       2     116 ..       4     114 ..       3     129 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.8e-06
                 EEEEEEEESHHHHHHHHHHHHHTSEEEEEEEEEESTEEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSCTSEEEEEEEEEHCHHHHHHHHHHHTTGE CS
  Glyoxalase   2 idhvallvgdleksldFYtkvLGfklvkktdnteeteglriaffhaggghielvlneapsgaakhvkkieetvhhvafialdvedvgkaldrlkeagvk 100
                 ++h+ ++v+ ++ s +  tk   f+ +      +  ++++  f+ +g+  +el+    ++++ + +    +++ ++++++++v ++ + ld++ ++g +
  EPA05250.1   4 LHHIGIVVSKISNSFPELTKYIKFEKTTIPI-FITSQKVNVCFLKIGEFNLELIEPVGEDSPVATF---ANKGGGFHHLCFEVKNIREKLDEFVKNGAR 98 
                 5666666666666666666655554433222.5666999999************999999999888...45899************************* PP

                 EEEEEECHHCTEEEEE CS
  Glyoxalase 101 vvaepgrhyfgalysf 116
                 +  ep   + g+l  f
  EPA05250.1  99 IIVEPVIGFEGRLTAF 114
                 **99976666666555 PP

>> PTE  Phosphotriesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.1e-05     0.041      14      82 ..       6     127 ..       1     131 [. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.1e-05
                 -SCEE-HHHHCHCCCCC--HHH......................................................HHHHHHHHHHHHHHTTEEEEEE- CS
         PTE  14 hltitldefkqnvpealevedk......................................................evaaiieellelkarGvdalvel 58 
                 h+ i ++++ +  pe  +   k                                                      ev  i+e+l e+   G++ +ve 
  EPA05250.1   6 HIGIVVSKISNSFPELTKY-IKfekttipifitsqkvnvcflkigefnleliepvgedspvatfankgggfhhlcfEVKNIREKLDEFVKNGARIIVEP 103
                 6667777777777665552.223446677777777777777777777777777777777888888888888888889********************** PP

                 --CCCT--HHHHHHHHCCHSSEEE CS
         PTE  59 tttglgRdvqtlkrvaeetgvniv 82 
                      gR   +++  +++t++n+v
  EPA05250.1 104 VIGFEGRLTAFVLLNMKDTKINLV 127
                 99999*****************98 PP

>> CbiX  CbiX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0       0.3   1.1e+03      28      99 ..      41      63 ..      17      71 .. 0.62
   2 ?   10.5   0.0   0.00016      0.58      33      72 ..      78     116 ..      65     136 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.3
                CEECESCCCECCSCCSSHHHHC-SBSEEEEEEESSSSSHHHHTHHHHHCT--SSSS-TTEEEEE---CCCSC CS
        CbiX 28 velgfleleepsleealrelaeqgvkrivvvPlflfaGvhvkeDIpeeleeaeeahpkdveieytepLGthp 99
                v ++fl++                                                 ++ ++e+ ep+G++ 
  EPA05250.1 41 VNVCFLKI-------------------------------------------------GEFNLELIEPVGEDS 63
                33333333.................................................345555556666555 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00016
                 SCCCECCSCCSSHHHHC-SBSEEEEEEESSSSSHHHHTHH CS
        CbiX  33 leleepsleealrelaeqgvkrivvvPlflfaGvhvkeDI 72 
                 l +e  +++e l+e++++g+ ri+v P+  f+G ++  ++
  EPA05250.1  78 LCFEVKNIREKLDEFVKNGA-RIIVEPVIGFEGRLTAFVL 116
                 456789*********99887.7999*********998765 PP

>> Glyoxalase_3  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.74   2.6e+03       1      13 [.       4      16 ..       4      28 .. 0.80
   2 ?   10.8   0.0   0.00011       0.4      49     123 ..      53     121 ..      41     134 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.74
  Glyoxalase_3  1 lDHvvlavpdlee 13
                  l+H++++v+++ +
    EPA05250.1  4 LHHIGIVVSKISN 16
                  89****9998765 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00011
  Glyoxalase_3  49 lElla.vdpeapaperprlfgldrlakgeglhtlalrtddidataarlraaGvdeagrrv.rpdggdlrwrllflad 123
                   lEl++ v ++ p +          ++kg+g+h+l++++++i +  +++ ++G    +++v   +g+  ++ ll ++d
    EPA05250.1  53 LELIEpVGEDSPVA--------TFANKGGGFHHLCFEVKNIREKLDEFVKNGARIIVEPViGFEGRLTAFVLLNMKD 121
                   55555333333332........23469**********************9997655555557777778888877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 877.92
//
Query:       EPA05251.1  [L=119]
Description: putative holo-[acyl-carrier-protein] synthase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.8e-14   52.2   0.5    6.7e-14   52.0   0.5    1.1  1  ACPS      4'-phosphopantetheinyl transferase superfamily
  ------ inclusion threshold ------
      0.017   15.0   4.0      0.086   12.7   0.6    2.1  2  DUF5001   Ig-like domain
      0.064   13.5   1.7       0.33   11.2   0.0    2.0  2  Ta0938    Ta0938


Domain annotation for each model (and alignments):
>> ACPS  4'-phosphopantetheinyl transferase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.0   0.5   1.1e-17   6.7e-14       2     113 ..       8     110 ..       7     111 .. 0.80

  Alignments for each domain:
  == domain 1  score: 52.0 bits;  conditional E-value: 1.1e-17
                 EEEEEEEHHHHH.HHH-----HHHHHS-HHHHHHHTT--HHHHHHHHHHHHHHHHHHHHHTTS-SSSS--GGG-EEEE-TTS-EEEE-S-SSEEEEEEE CS
        ACPS   2 vGiDieklsrlrkrvkrrgakilkrifteeErkllkssdeearaelfarlWaaKEAllKalgpglrklldfksievledstgrptlellseakkkawkl 100
                 +GiDi++++r++k    +++k+ ++if+++E++++ + +++ r  +fa+ +a+KEA  K+l++++    +f +ie ++  +++p ++ +++ ++++  +
  EPA05251.1   8 LGIDIVEVKRFQKIPYDKNKKFYNKIFNKSEINYCLKFKDSYR--HFAGKFAIKEATKKSLSKKI----SFLQIETSH-IKNKPVVK-IKDNADYSFLV 98 
                 8*************999999**********************9..********************....777777766.45566666.44444444333 PP

                 E-....SSEEEEE CS
        ACPS 101 eslkidkdyviav 113
                  sl+++k  ++av
  EPA05251.1  99 -SLSHEKTMAVAV 110
                 .344446666665 PP

>> DUF5001  Ig-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.6   1.4e-05     0.086       4      54 ..      16      67 ..      13      71 .. 0.83
   2 ?    3.8   0.2    0.0088        53       2      36 ..      74     106 ..      69     119 .] 0.72

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.4e-05
                E...EEE...TTEEEEEEEE-SSS-EEEEE-S--TTEE--SEEEE-TTEEEEEE CS
     DUF5001  4 e...psnytetkvleveikNkSdidFeLentseytfynypevitipanstttvv 54
                +   ++ y+++k+ + +i NkS i++ L+ +++y+    + ++ i+  ++++++
  EPA05251.1 16 KrfqKIPYDKNKKFYNKIFNKSEINYCLKFKDSYRH--FAGKFAIKEATKKSLS 67
                4444889999***********************995..6689999888888775 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.0088
                 EEEEEE...TTEEEEEEEE-SSS-EEEEE-S--TT CS
     DUF5001   2 eiepsnytetkvleveikNkSdidFeLentseytf 36 
                 +ie s++  +++  v+ik + d  F   ++ e+t 
  EPA05251.1  74 QIETSHI--KNKPVVKIKDNADYSFLVSLSHEKTM 106
                 4444553..57778999999999999888888775 PP

>> Ta0938  Ta0938
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.3     0.052   3.1e+02      63     100 ..       3      40 ..       2      48 .. 0.77
   2 ?   11.2   0.0   5.5e-05      0.33      51      98 ..      58     105 ..      50     111 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.052
                 S---EE---TTT-S--EEEE-----TT-SS-----HHH CS
      Ta0938  63 ideleingnyykgrnveaksgekelkfyvkfnddaeie 100
                 id+l++  +  + +  +    +k+ kfy k+ +++ei+
  EPA05251.1   3 IDNLNLGIDIVEVKRFQKIPYDKNKKFYNKIFNKSEIN 40 
                 67777777777777777777889999**9999998886 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 5.5e-05
                 THHHHHHHHHHHS---EE---TTT-S--EEEE-----TT-SS-----H CS
      Ta0938  51 lnevkkrtglskideleingnyykgrnveaksgekelkfyvkfnddae 98 
                 ++e+ k+   +ki  l+i+  + k + v+  +++ +++f v ++++ +
  EPA05251.1  58 IKEATKKSLSKKISFLQIETSHIKNKPVVKIKDNADYSFLVSLSHEKT 105
                 789999999*********************************998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       909  (0.0507); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 708.11
//
Query:       EPA05252.1  [L=418]
Description: hypothetical protein BG20_I0203 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00017   20.7   1.8     0.0015   17.6   1.8    2.1  1  Glyphos_transf  CDP-Glycerol:Poly(glycerophosphate) glyceroph
     0.0002   20.4   0.1    0.00043   19.2   0.1    1.6  2  Epimerase_2     UDP-N-acetylglucosamine 2-epimerase


Domain annotation for each model (and alignments):
>> Glyphos_transf  CDP-Glycerol:Poly(glycerophosphate) glycerophosphotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   1.8   1.6e-07    0.0015     126     299 ..     176     353 ..      51     360 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.6e-07
                     HHHHHHHTT-SEEEESSHHHHHHHHHHTT--GGGEEES--GGGHHHHHSTT-H.HHHHHHHTT--SS-EEEEEE----GGG--.......GSS-- CS
  Glyphos_transf 126 qellrevsswdylisaneestsifarafnikkeeiletGyPrnDvlvkaesed.vkrireelgipkdkkvilyaPTwRddevg.......esyrf 212
                     + ++  +  +d + +  +++++ + + +n+++++il++G Pr D  + +e+ + ++ri             l    +  ++         +  + 
      EPA05252.1 176 DIFSMYSLFKDKIAVWGDTQKQYLIKQHNLDEKRILNVGSPRHDIFFMKEKSKqKQRI-------------LLLTIHPISNISgqstvdlYIKFE 257
                     5666677778888888899999999********************9999888823332.............222222222222111223333455 PP

                     --TT-HHHHHHHHTTTEEEEE--SHH.HHTT---...TT-TTTEEE-TT-S-HHHHHHT-SEEEE......SS-THHHHHGGGT--EEEE-TTTT CS
  Glyphos_transf 213 elkldlerlakalgedyvillklHpl.iqekiki...keksdyvvdvsdeedvedlllasDiLiT......DYSSvmFDyavldrPiifyayDle 297
                     +l +++ +++k++  +  +++klHp  i ++++i   ++k d  + v  ++++ dlll  D L+       D S vm + ++l+ P++    D  
      EPA05252.1 258 KLIINFCKIIKKI-PNLQLIVKLHPSqIPHNVQIlnlFKKIDSKIPVFLNKSILDLLLECDTLVNispegyDPSTVMMEALILKIPVMNVILDNS 351
                     6666777766654.689999999997355666668888999998999999999999999999996666666889999999999999988888877 PP

                     TT CS
  Glyphos_transf 298 eY 299
                      Y
      EPA05252.1 352 LY 353
                     77 PP

>> Epimerase_2  UDP-N-acetylglucosamine 2-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0      0.29   2.6e+03     206     263 ..      64     126 ..      57     129 .. 0.61
   2 !   19.2   0.1   4.8e-08   0.00043     134     284 ..     196     346 ..     187     395 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.29
                  HHHHHHHHH--EEEEE--..HHHHHHHHHHHHH-T.....TEEEE----..HHHHHHHHHC-SEE CS
  Epimerase_2 206 alkalakekdvevvvpvhnnprtrkrlleeleele.....nvtlieplg..yldflsllknaklv 263
                  ++++l+++  ++++ ++ +n+   ++++  le+++     +  l+e+ +    ++++ + ++k++
   EPA05252.1  64 LIEKLSEK-YIKIITTIWENDSIFDEIF-SLEGFSywgfiKTPLLESYKnrMNEYVRTIFASKII 126
                  66777776.7888999999999888886.355554344444444444431134555555555555 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 4.8e-08
                  HHHHH.HTT--GGGEEE---HHHHHHHHHHHHHH...T-HHHHHH--SS-EEEEE---HHHHTSHHH......H.HHHHHHHHHHHHHH--EEEEE-- CS
  Epimerase_2 134 renLl.kegeeeerifvvGntviDalllskeeieeklkaseilkelkekkyvlvtlHrrenedeper......l.keilealkalakekdvevvvpvh 223
                  ++ L+ + + +e+ri++vG++  D ++++ e+ +            ++++++l+t+H+ +n + +++      + k i+++ k ++k ++++++v +h
   EPA05252.1 196 KQYLIkQHNLDEKRILNVGSPRHDIFFMK-EKSK------------QKQRILLLTIHPISNISGQSTvdlyikFeKLIINFCKIIKKIPNLQLIVKLH 280
                  5555515678**************99886.3332............56899**********99776522222231334555555555599******** PP

                  ..HHHHHHHHHHHHH-TTEEE.E----HHHHHHHHHC-SEEEE......S-HHHHHHHHHCT--EEES CS
  Epimerase_2 224 nnprtrkrlleeleelenvtl.ieplgyldflsllknaklvlt......dSgGiqeEapslgvpvvnl 284
                    p    +  ++l+ ++++   i+ +  +++l ll +++ ++       d +++  Ea +l++pv n+
   EPA05252.1 281 --PSQIPHNVQILNLFKKIDSkIPVFLNKSILDLLLECDTLVNispegyDPSTVMMEALILKIPVMNV 346
                  ..655444445555555555413334556778888888888753344557788999999999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       866  (0.0483016); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2920.58
//
Query:       EPA05253.1  [L=187]
Description: glycosyltransferase, group 1 family protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-19   70.2   0.0      2e-19   69.8   0.0    1.2  1  Glycos_transf_1  Glycosyl transferases group 1
    3.8e-19   69.5   0.0    4.7e-19   69.1   0.0    1.2  1  Glyco_trans_1_4  Glycosyl transferases group 1
    1.6e-09   38.0   0.0    2.2e-09   37.6   0.0    1.2  1  Glyco_trans_1_2  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.8   0.0   3.3e-23     2e-19      44     171 ..      44     169 ..      32     170 .. 0.91

  Alignments for each domain:
  == domain 1  score: 69.8 bits;  conditional E-value: 3.3e-23
                      HCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCH.SSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTS CS
  Glycos_transf_1  44 lnpnvklviaGngeeekelkklaeelelsdnviflgevs.redleellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdget 136
                      + p+v +  aG+g++++++ +    l+  +n ++lg +  ++++ e+l+  d+++l s  +  +++l EA   ++pv+a+n+gg++e+ k++et
       EPA05253.1  44 SMPDVTFYWAGDGPYREKILAV---LGKYNNFKWLGPLQyPDKVREYLTEIDVYALVSGIDMSPLTLQEAQLMKKPVVATNVGGIPELMKNNET 134
                      3788999999999998877777...555566********9****************************************************** PP

                      EEEE-TT-HHHHHHHHHHHHHSHHHHHHHHHHHHH CS
  Glycos_transf_1 137 Gllvkpnnaealaeairklledeelrerlgenark 171
                      G+lv++++a  ++e++  l++de++r+ +g ++rk
       EPA05253.1 135 GFLVEKGDANGWIEKLSLLINDEQKRKTMGGEGRK 169
                      *****************************999987 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.1   0.0   7.9e-23   4.7e-19      23     134 .]      40     156 ..      18     156 .. 0.84

  Alignments for each domain:
  == domain 1  score: 69.1 bits;  conditional E-value: 7.9e-23
                      HHHHHH.H..HEEEEEES---...HHHHHHHTT-T.TEEEE---...THHHHHHHH-SEEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT- CS
  Glyco_trans_1_4  23 avpllrkk..dvrlvivGdgp.rpeeleelaagleerveftGfv...edlaellaaadvfvaPs..egfglkllEamaaglpvVatdvggiaev 108
                       v   +k+  dv+++ +Gdgp r+ ++ + + g  ++++++G +   ++++e+l + dv+ + s     +l+l Ea  +++pvVat+vggi+e+
       EPA05253.1  40 SV---LKSmpDVTFYWAGDGPyRE-KILAVL-GKYNNFKWLGPLqypDKVREYLTEIDVYALVSgiDMSPLTLQEAQLMKKPVVATNVGGIPEL 128
                      33...3232269*********765.776455.4458********99555***************98889************************* PP

                      -..TTSSEE--TT-HHHHHHHHHHHHH- CS
  Glyco_trans_1_4 109 v..gengllvppgdpealaeailrLled 134
                      +  +e+g+lv++gd++ ++e++  L++d
       EPA05253.1 129 MknNETGFLVEKGDANGWIEKLSLLIND 156
                      *988******************999987 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   0.0   3.6e-13   2.2e-09      14      92 .]     106     186 ..      81     186 .. 0.94

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 3.6e-13
  Glyco_trans_1_2  14 rlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarervlaehtydhraeqlla 92 
                       l Ea  +  +++++   g++el +++++++l+e  d + ++ek+  l++++++r+ ++ ++r++v++++++++ a+++l+
       EPA05253.1 106 TLQEAQLMKKPVVATNVGGIPELMKNNETGFLVEkgDANGWIEKLSLLINDEQKRKTMGGEGRKFVEENFNWNKIAKEFLE 186
                      5668899999*****9**************************************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1318.85
//
Query:       EPA05254.1  [L=169]
Description: hypothetical protein BG20_I1310 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.019   15.1   0.2      0.028   14.6   0.2    1.2  1  RTT107_BRCT_6  Regulator of Ty1 transposition protein 107 BRC


Domain annotation for each model (and alignments):
>> RTT107_BRCT_6  Regulator of Ty1 transposition protein 107 BRCT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.2   1.6e-06     0.028       5     106 ..      12     120 ..       9     126 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.6e-06
  RTT107_BRCT_6   5 rakikkiNlvsdipggtevissiLkahGikevkvlskklkiedlvkn........ekkkkkekkkspeyvliatkasqvkkfkkllkeekenkkvl 92 
                    r +i+++  +  i g ++ i+s+    G++++++ s  l+ +d +kn         ++ + e  +++ ++++a+  s+   ++ ++   k +++ l
     EPA05254.1  12 RRGISQVMGSVVILGVVTSIGSVVLFNGMNQINAFSYDLSFHDKTKNeayrenllFEHVRFEPGTDQMILFLANIGSTESTIESITV-VKIDTQDL 106
                    6677777777789999*******************************6666655544444455555777778888888889988876.689999** PP

  RTT107_BRCT_6  93 vveWdWcvksifnl 106
                    vv+W+  v+s  ++
     EPA05254.1 107 VVDWNANVNSNIQI 120
                    *****999986655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.31s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1099.25
//
Query:       EPA05255.1  [L=219]
Description: hypothetical protein BG20_I1329 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-16   60.5   0.1    2.1e-16   60.1   0.1    1.1  1  Guanylate_cyc  Adenylate and Guanylate cyclase catalytic doma


Domain annotation for each model (and alignments):
>> Guanylate_cyc  Adenylate and Guanylate cyclase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.1   0.1   1.1e-20   2.1e-16       9     157 ..      44     203 ..      38     215 .. 0.83

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 1.1e-20
  Guanylate_cyc   9 vtilFadIvgftalssahspievvklLnelyarfdelldekkvykvktiGda...ymvvsglp.eekaahaaklaelaLdmleal.eevaveskeg 99 
                    + +++ d+vg+t++ss+ +p+   +++    +++  ++++ ++y  k++Gda   y  +s+      ++ + ++  ++L + +a+    ++++ ++
     EPA05255.1  44 MFVVYVDLVGSTKMSSELDPEIFNTIIRVFSQEMAYVIEHFDGYVLKFVGDAvlgYFLASEKVaFVANKTIMCAKTMQLVIKNAInPLLENKNYPK 139
                    56899****************9999999999********************9444444444333456677888889*********666667779** PP

  Guanylate_cyc 100 lkvrvGihtGpvvagviG..akkprydvwGntvnlAsrmestgkagkiqvseetyellk....e 157
                    lk+++ ++ G + +   G  ++  + d++G t nlA++m++ +++++i + +++ye l+    +
     EPA05255.1 140 LKIKITLDFGNCSIIRYGsdRNLSHIDLIGLTLNLAAKMQQKTQPDQITIGDHVYEKLNyknkR 203
                    ************9999995555679*********************************975322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1380.70
//
Query:       EPA05256.1  [L=366]
Description: oxidoreductase, aldo/keto reductase family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      5e-25   88.3   0.2    1.5e-19   70.3   0.2    2.5  2  Aldo_ket_red  Aldo/keto reductase family
  ------ inclusion threshold ------
      0.054   13.6   0.8       0.12   12.5   0.1    1.9  2  Arc_PepC      Archaeal Peptidase A24 C-terminal Domain
       0.29   10.8   3.2       0.22   11.2   0.5    2.2  2  DUF321        Protein of unknown function (DUF321)


Domain annotation for each model (and alignments):
>> Aldo_ket_red  Aldo/keto reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.3   0.2   2.6e-23   1.5e-19       2     197 ..      36     299 ..      35     305 .. 0.77
   2 !   15.5   0.0   1.2e-06    0.0074     242     291 ..     312     362 ..     305     365 .. 0.90

  Alignments for each domain:
  == domain 1  score: 70.3 bits;  conditional E-value: 2.6e-23
                   EEEE-SSS-ST.TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH....-TTTGGG-EEEEEE.......................- CS
  Aldo_ket_red   2 lglGtwqlgskeeiskeealellrraleaGinffDtAevYgkgqseellGealkk....srkkreeviiatKv.......................d 71 
                   +g+Gt  lg+++e+++e + +++++ +  Gin +DtA  Y+  ++e+ +G+a+++     +  r++++i+tK                        +
    EPA05256.1  36 VGVGTY-LGDPNEKTDELVKNAIKTSILSGINVIDTAINYRAQKAERSVGKAISElineGKITRDQIFISTKNgyitndadvkqefweyvkneyaqK 131
                   788888.88889*********************************************888889****************999997776555554440 PP

                   -SSSTTSSSS-HH.................HHHHHHHHHHHHHT-S-EEEEEE-S--TTS-...........HHHHHHHHHHHHHTTSEEEEEEES- CS
  Aldo_ket_red  72 lrdaeiksglske.................niresleeslkrLgtdyvDllllHrpdpslp..........sieevldaleelvkeGkiraiGvSnf 141
                                                  ++ +le+slk+Lg+d+vDl +lH+                ++  v+++ e+ ++ Gkir +G + +
    EPA05256.1 132 ------------GvlkegdvtsgyhcmtvtYLNDQLERSLKNLGLDCVDLMYLHNAVEGQIkdvskekfleNLKSVFEFYEQKRRDGKIRFYGMATW 216
                   ............233345555566666777************************97554445999******************************76 PP

                   -HHHHHHH................HHTTT--EEEEE-B-BTT...........-HHHHTTHHHHHHHTT-EEEEBSTTGGGTT CS
  Aldo_ket_red 142 sveqleka................kkkkkvkivavqveynll...........releeegllelckkkgvpliaysplggGll 197
                   +  ++ +                    + + + ++q  +n++            + ++  lle++ k++v++ +  pl++G l
    EPA05256.1 217 ECFRVPSDnpqylslqdtvdlakkVGGENHGFRFIQLPFNMYydqallaknqtLDGKSVSLLEAAVKLNVGVFTSVPLMQGRL 299
                   63333222244446666676654444555667777777777777777776544444555666666667777777777777765 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.2e-06
                   -HHHHHHHHHTTSTT-SEEEE--SSHHHHHHHHGGGG-.---HHHHHHHHH CS
  Aldo_ket_red 242 slaqlalryalsqpavgivipgasnieqlednldalel.klseeevaelde 291
                   +++  al+++ s+p+v  +++g +++e++ +nl+ +++ ++se+e+ +l +
    EPA05256.1 312 KPSLRALQFIRSSPGVLAPLIGQKSPEHVSENLEIMKIpPMSEDEFLTLVK 362
                   567779**************************************9988765 PP

>> Arc_PepC  Archaeal Peptidase A24 C-terminal Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1     2e-05      0.12      10      70 ..      66     128 ..      59     147 .. 0.80
   2 ?   -2.2   0.1      0.73   4.3e+03      53      68 ..     183     198 ..     172     209 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2e-05
    Arc_PepC  10 kliskvi.kaltkeelsdkkkveeL.kEGdiladiilekeddevtvddksllkrlkealktgd 70 
                 ++i   i +  +k+e s  k ++eL  EG+i +d+i ++ ++ + ++d+++ + + e +k++ 
  EPA05256.1  66 NVIDTAInYRAQKAERSVGKAISELiNEGKITRDQIFISTKNGYITNDADVKQEFWEYVKNEY 128
                 555555524556778888999***968**********999999************99999654 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.73
    Arc_PepC  53 vddksllkrlkealkt 68 
                 v ++++l+ lk +++ 
  EPA05256.1 183 VSKEKFLENLKSVFEF 198
                 5677888888888874 PP

>> DUF321  Protein of unknown function (DUF321)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.22   1.3e+03      15      20 .]     206     211 ..     206     211 .. 0.94
   2 ?   11.2   0.5   3.7e-05      0.22       4      13 ..     242     251 ..     241     251 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.22
      DUF321  15 GKsrvy 20 
                 GK+r+y
  EPA05256.1 206 GKIRFY 211
                 9***99 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 3.7e-05
      DUF321   4 WRENHGFtFL 13 
                 ++ENHGF+F+
  EPA05256.1 242 GGENHGFRFI 251
                 68*******5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2272.26
//
Query:       EPA05257.1  [L=144]
Description: hypothetical protein BG20_I1331 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       722  (0.04027); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1017.62
//
Query:       EPA05258.1  [L=177]
Description: hypothetical protein BG20_I1324 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-11   43.5   0.4    4.4e-11   42.5   0.0    1.8  2  RNA_pol_Rpb6    RNA polymerase Rpb6
  ------ inclusion threshold ------
      0.011   15.8   0.7      0.024   14.7   0.7    1.6  1  Med9            RNA polymerase II transcription mediator comp
      0.013   16.0   1.0      0.023   15.2   1.0    1.4  1  DUF5344         Family of unknown function (DUF5344)
       0.37   10.9   4.6       0.23   11.5   1.1    2.5  3  Unstab_antitox  Putative addiction module component


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb6  RNA polymerase Rpb6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       1.4   6.1e+03      18      28 ..      73      79 ..      70      95 .. 0.53
   2 !   42.5   0.0   9.9e-15   4.4e-11       4      49 .]     106     157 ..     103     157 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.4
                  HHHHHH....H CS
  RNA_pol_Rpb6 18 kRArQieeges 28
                  kR ++i    +
    EPA05258.1 73 KRIKEI----E 79
                  566666....2 PP

  == domain 2  score: 42.5 bits;  conditional E-value: 9.9e-15
                   TSS--HHHHHHHHHHHHHHH....HT.........S.S-SSSSTTCHHHHTT-S-- CS
  RNA_pol_Rpb6   4 skvltrYelvriaakRArQieegesl.........e.tqkpvviAlrEiaegkipi 49 
                   +++ltr+e++ri ++RA+Q+    sl           +   ++iA++E+++  ipi
    EPA05258.1 106 PPTLTRFEKARIMGARALQL----SLgaptfipipKtARISLDIAMEELEQRVIPI 157
                   699*****************....99999999988435699*************97 PP

>> Med9  RNA polymerase II transcription mediator complex subunit 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.7   5.3e-06     0.024      30      70 ..      42      82 ..      21      88 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.3e-06
        Med9 30 elrhkLkkarelirelpgidrsveeqeaeieeleeqlakKr 70
                +l++ L++ r+li++++g++  +e q++ +e+  +++++++
  EPA05258.1 42 GLNKALDTYRKLIEKNEGLEPLTEKQQEALEKRIKEIEARE 82
                69999****************************99999875 PP

>> DUF5344  Family of unknown function (DUF5344)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   1.0   5.2e-06     0.023      23      81 ..      31      91 ..      23      93 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.2e-06
     DUF5344 23 eelktsipetisgknsldvvekineleeeleellkaYktlllknvedte..saVdslkeaD 81
                e ++++++  ++ ++ ld+ +k+ e +e le l+++ +++l+k ++++e  ++V++++e +
  EPA05258.1 31 EVFDVDVEVNTGLNKALDTYRKLIEKNEGLEPLTEKQQEALEKRIKEIEarEVVETIEEHE 91
                556688888888899******************************9865338999999875 PP

>> Unstab_antitox  Putative addiction module component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.1   5.2e-05      0.23      21      46 ..      58      83 ..      51      89 .. 0.85
   2 ?   -2.2   0.0      0.97   4.3e+03       2      11 ..     109     118 ..     108     135 .. 0.81
   3 ?   -1.7   0.1      0.69   3.1e+03      31      37 ..     147     153 ..     140     154 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.2e-05
  Unstab_antitox 21 eadpelpaawkaElerRlaeyeaGkv 46
                    e ++ l++ +++ le+R++e+ea +v
      EPA05258.1 58 EGLEPLTEKQQEALEKRIKEIEAREV 83
                    56777*****************9775 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.97
  Unstab_antitox   2 LppaERleLa 11 
                     L++ E+++++
      EPA05258.1 109 LTRFEKARIM 118
                     7778888887 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.69
  Unstab_antitox  31 kaElerR 37 
                      +Ele+R
      EPA05258.1 147 MEELEQR 153
                     6899999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1120  (0.0624686); expected 358.6 (0.02)
Passed bias filter:                      707  (0.0394333); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1112.51
//
Query:       EPA05259.1  [L=364]
Description: deoxyhypusine synthase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-77  261.2   0.1    1.4e-77  260.9   0.1    1.1  1  DS        Deoxyhypusine synthase


Domain annotation for each model (and alignments):
>> DS  Deoxyhypusine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  260.9   0.1   7.5e-82   1.4e-77       1     286 [.      24     320 ..      24     322 .. 0.91

  Alignments for each domain:
  == domain 1  score: 260.9 bits;  conditional E-value: 7.5e-82
          DS   1 ellesyekigfqatslgeaidilnkmrkdekctiflgltsnlissGlreiiadlvkeklvdvivtTaggieeDlikalgkktylgdfelddeeLrekgi 99 
                 +l++ ++++g+++++lg+a+++++km  +e++ti+l++++++++ G+ +ii++l++++++d+i+tT++++ ++ + a+g  + +g+f++dd +L+e++i
  EPA05259.1  24 DLVDVFASSGYNGRQLGDAAKLYAKM-IKEDATICLTVSGAMTPVGFGGIIKTLIERGFIDWIITTGANVYHEDHFAWGLPVKQGSFDVDDMKLYENEI 121
                 58999*********************.67899******************************************************************* PP

          DS 100 nRignllvpnenyckfedwvre..ildkleeeqkvwspselikelGkein.....deeSilywAykndipvfcpaltDgslGdqlllfhsvkekkklkl 191
                  Ri +++++ ++  ++ed++ +  ++dk+++  k ++++e+++ +Gk  +      e+S++++Ay+ d+pv+++++ D+sl+++l++++   ++k  +l
  EPA05259.1 122 VRIRDVYIKFHETLEAEDHIIQkmFADKFTD--KPFTTAEFCNLMGKISKekskhPEKSFITTAYDYDVPVYISTMKDSSLALNLAVHR-L-QNKVYNL 216
                 **********999888887765334455554..578**********87776666678**************************666655.4.6666*** PP

          DS 192 divkDirelndialkakktgaiilGGGvpKhhilnanlm........rngadyavyittaqefdGslsgatldEavSwgkika.eaksvkvyaDaTivl 281
                 d vk+i e ++i +++kk+g++ lGGGvpK+ ++++  m        + g dy+++it a++ +G+lsgatl+E++Swgk+++ +++ ++vyaDaTi++
  EPA05259.1 217 DFVKEIIEQASILYHSKKSGILELGGGVPKNTAQQTGPMldqilqrnDGGQDYVIQITDARPDTGGLSGATLQEGKSWGKVQDaHHDMITVYADATIAF 315
                 *************************************999****975459*******************************9945599*********** PP

          DS 282 PLlva 286
                 P+l+ 
  EPA05259.1 316 PILAL 320
                 **986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2331.01
//
Query:       EPA05260.1  [L=315]
Description: asparagine synthase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.3e-37  128.6   0.0    5.5e-21   75.6   0.0    2.0  2  Asn_synthase   Asparagine synthase
    1.4e-05   24.4   0.1    2.7e-05   23.4   0.1    1.4  1  NAD_synthase   NAD synthase
    6.3e-05   22.6   1.5    0.00015   21.3   0.1    2.4  2  QueC           Queuosine biosynthesis protein QueC
    0.00014   21.6   0.0    0.00031   20.5   0.0    1.6  1  ATP_bind_3     PP-loop family
     0.0013   18.3   0.0     0.0027   17.3   0.0    1.5  1  ThiI           Thiamine biosynthesis protein (ThiI)
     0.0038   16.1   0.0      0.012   14.5   0.0    1.8  2  tRNA_Me_trans  tRNA methyl transferase
  ------ inclusion threshold ------
       0.19   11.8   2.4       0.73    9.9   0.6    2.3  2  DZR            Double zinc ribbon
        1.3    8.5   3.6       0.48    9.9   0.4    1.9  2  zf-ribbon_3    zinc-ribbon domain
        1.4    8.5   7.3       0.14   11.8   1.6    2.3  2  RecR           RecR protein
        2.1    8.1   5.3         88    3.0   6.1    2.6  2  zinc_ribbon_2  zinc-ribbon domain
        2.2    8.5   5.4          7    6.9   0.1    2.6  2  Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (


Domain annotation for each model (and alignments):
>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.6   0.0   3.4e-24   5.5e-21       3     140 ..       6     142 ..       4     154 .. 0.89
   2 !   51.0   0.0     1e-16   1.6e-13     228     334 ..     165     287 ..     156     299 .. 0.88

  Alignments for each domain:
  == domain 1  score: 75.6 bits;  conditional E-value: 3.4e-24
  Asn_synthase   3 relLedaVkrrlradvpvGalLSGGlDSSliaalaarqsksplktFsigfeekgsdeakyakevaehlgtehtelvlteeelldalpdviyhlee.. 97 
                    + L +  k+ +++    ++ LSGGlDS++ia+l+++  +   +t++i  ++   +++ y ++v+++++++ t  +++  ++l+a++++i++l +  
    EPA05260.1   6 SHKLYQMLKESCESCESNTIALSGGLDSTIIAYLLKERKP---NTVAIIAKDFVASDLTYCQRVSKEFNLPLTINQVNTTDILSAVEETIKILKNfn 99 
                   567777788888888888999****************877...667776666699*****************************************9 PP

  Asn_synthase  98 pfadrsaiplyllsrlakrkgvkvvLsGeGaDElfgGYpyfyk 140
                    + +r +i +y++ + ak+++++ +++G+GaDElf+GY+++ +
    EPA05260.1 100 DIEIRNNIVMYMALKWAKEQNYTGIITGDGADELFAGYNFLIN 142
                   99*************************************5554 PP

  == domain 2  score: 51.0 bits;  conditional E-value: 1e-16
  Asn_synthase 228 rasmahglEaRvPflDhrlvevalrlppelklrg....gieKyiLRealegylPeeileRpKegfsapvgewklkgelrelaeellsds........ 312
                   ++  a g+ +  Pfl  +++e+a ++ ++lk+r     + +K+iLR+a+e+ +P++i++R+K+++++++g+     +l +l +  +sd+        
    EPA05260.1 165 KIGKALGISVESPFLNEKIIEFAKTVSIDLKVRYeqgkKHGKWILRKAFEKNIPSQIIWREKSPMQDGSGTA----GLTNLFNSVISDQiflekkkk 257
                   5667889999**********************9999999********************************9....677777777777777779999 PP

  Asn_synthase 313 ........rlakeglldreaveelleehea 334
                             +ke++ + e+++++++ +e+
    EPA05260.1 258 iedadnviIRTKESMHYYEIFKKMYDVPEK 287
                   999999987788889999999999987776 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.1   1.6e-08   2.7e-05       5     137 ..       9     137 ..       3     141 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.6e-08
                   HHHHHHHHHHHCTTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHH..HTSEEEE---HHHHHHHHHHHHHHH-HH CS
  NAD_synthase   5 lvdflkeyvkkagakgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaen..lgievktidikpivrafeqelkeakedl 99 
                   l ++lke  ++++++   + lSGG+DS+++a+l ++   k n +a++  + v+  +d++  + + ++  l + +++++ ++i++a+e+++k  k ++
    EPA05260.1   9 LYQMLKESCESCESNT--IALSGGLDSTIIAYLLKER--KPNTVAIIAKDFVA--SDLTYCQRVSKEfnLPLTINQVNTTDILSAVEETIKILK-NF 98 
                   5566666666666665..579************9996..58899999855555..5566666666651155677899999********999988.99 PP

                   HHHHHHHHHHHHHHHHHHHHHTEEEB---B.HHHHTTT- CS
  NAD_synthase 100 akgNlkaRiRmailyaianklnllvlgTgn.ksElvvGy 137
                   ++  ++  i m +  ++a+++n+  + Tg+ + El  Gy
    EPA05260.1  99 NDIEIRNNIVMYMALKWAKEQNYTGIITGDgADELFAGY 137
                   9999***************99998666655167899999 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.1   9.4e-08   0.00015       4     123 ..      25     130 ..      22     138 .. 0.78
   2 ?   -2.5   0.0       1.8     3e+03     161     199 ..     252     297 ..     249     299 .. 0.60

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 9.4e-08
                 EE--SSHHHHHHHHHHHHH-.SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-GGGGGGSCGGG-----------...--------TTHHHHH CS
        QueC   4 vllSGGlDSttvlalakkeg.kevealtfdYgqrhkkeleaakkiakelgveehkildldllkelggsaLtdeeievpkeeleeeelpntfVpaRNlif 101
                 + lSGGlDSt++++l k++  + v+++  d+    +++l + ++++ke+++   +   ++ +++    + ++e+i++ k +          +  RN i+
  EPA05260.1  25 IALSGGLDSTIIAYLLKERKpNTVAIIAKDF---VASDLTYCQRVSKEFNL-PLT---INQVNTTDILSAVEETIKILK-N-------FNDIEIRNNIV 108
                 579************9998724555555555...6899*************.555...554555666677888888888.2.......234789***** PP

                 HHHHHHHHHHHT-SEEEE---S CS
        QueC 102 lslaasyaealgaeaiiiGvne 123
                 + +a+ +a++++++ ii+G  +
  EPA05260.1 109 MYMALKWAKEQNYTGIITGDGA 130
                 *****************99655 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.8
                 --HHHHHHHHHHTTHHHHH-B-STTS........-BTTTTSSSHHH CS
        QueC 161 lsKaeivklgkelgvpleetlsCYege.......eegkaCgeCdaC 199
                 l+K++ ++ ++++ + ++e++  Ye         e++++ ++C+ C
  EPA05260.1 252 LEKKKKIEDADNVIIRTKESMHYYEIFkkmydvpEKKEGIRTCPYC 297
                 5666666666666666666666665433455555666777777777 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   1.9e-07   0.00031       3      69 ..      24      87 ..      22     135 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.9e-07
                EEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--H.....H CS
  ATP_bind_3  3 lvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklnikleiekvdv.....a 69
                 +A+SgGlDS+++ +ll++ k +   ++++i  d+      +++ +++++++k++n++l+i++v++     a
  EPA05260.1 24 TIALSGGLDSTIIAYLLKERKPN---TVAIIAKDF-----VASDLTYCQRVSKEFNLPLTINQVNTtdilsA 87
                69*****************9885...444444444.....46788999999999999999999996433330 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.7e-06    0.0027       9     116 ..      26     128 ..      19     132 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.7e-06
        ThiI   9 LlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlkeilekvkekltivllkrkmlriAekvaeee 107
                  lSgG+DS + ayll +R  + v++  k+  +  +      +++ + ++   t    ++ + d  + ++e ++ +k+   i +    ++ +A k a+e+
  EPA05260.1  26 ALSGGLDSTIIAYLLKERKPNTVAIIAKD--F-VASDLTYCQRVSKEFNLPLT--INQVNTTDILSAVEETIKILKNFNDIEIRNNIVMYMALKWAKEQ 119
                 58*****************9999998863..2.33344556666665555554..33455667777777777777888888888889999********* PP

        ThiI 108 gakalvtGe 116
                 +++ ++tG+
  EPA05260.1 120 NYTGIITGD 128
                 ********9 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   7.2e-06     0.012       5      37 ..      25      57 ..      22      97 .. 0.82
   2 ?   -2.4   0.0      0.94   1.5e+03     291     316 ..     181     206 ..     162     214 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7.2e-06
  tRNA_Me_trans  5 valSgGVDSsvaaallkeqgyevigvflklwee 37
                   +alSgG DS++ a+llke+  ++++++ k    
     EPA05260.1 25 IALSGGLDSTIIAYLLKERKPNTVAIIAKDFVA 57
                   79*********************9998776554 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.94
  tRNA_Me_trans 291 aeelkekealelevkvrhkqelvkak 316
                    ++ ++ ++++++++kvr++q +++ k
     EPA05260.1 181 EKIIEFAKTVSIDLKVRYEQGKKHGK 206
                    34555667788888888888777665 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.37     6e+02      28      37 ..      14      23 ..       3      28 .. 0.71
   2 ?    9.9   0.6   0.00045      0.73       1      19 [.     294     311 ..     280     314 .. 0.64

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.37
         DZR 28 edrCpsCgek 37
                ++ C sC++ 
  EPA05260.1 14 KESCESCESN 23
                4678888765 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00045
         DZR   1 CpqCgeelppdarfCseCg 19 
                 Cp C+  + ++++fC  Cg
  EPA05260.1 294 CPYCNFII-EESKFCRMCG 311
                 55555544.3455555555 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.2       3.9   6.4e+03      19      23 ..      17      21 ..      15      23 .. 0.60
   2 ?    9.9   0.4   0.00029      0.48       4      24 ..     293     312 ..     291     313 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 3.9
  zf-ribbon_3 19 CpyCG 23
                 C +C 
   EPA05260.1 17 CESCE 21
                 66664 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00029
  zf-ribbon_3   4 rCPnCGaplssddnvCpyCGt 24 
                  +CP+C+ +  ++ ++C  CG+
   EPA05260.1 293 TCPYCNFI-IEESKFCRMCGA 312
                  8******7.6999*******7 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.4       2.3   3.8e+03      30      36 ..      16      22 ..      14      24 .. 0.61
   2 ?   11.8   1.6   8.5e-05      0.14      13      34 ..     288     310 ..     286     312 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.3
                S-CCCCS CS
        RecR 30 lCaICsd 36
                 C+ C +
  EPA05260.1 16 SCESCES 22
                5666665 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 8.5e-05
                 HHH-EE-TTT--E.ESSSS-CCC CS
        RecR  13 kekvrhCsrCgnl.teedlCaIC 34 
                 ke++r C+ C+ +  e+  C+ C
  EPA05260.1 288 KEGIRTCPYCNFIiEESKFCRMC 310
                 899**********455567**** PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.8      0.08   1.3e+02      14      19 ..     292     297 ..     287     301 .. 0.81
   2 ?    3.0   6.1     0.054        88       2      21 ..     294     312 ..     293     313 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.08
  zinc_ribbon_2  14 kFCpyC 19 
                    + CpyC
     EPA05260.1 292 RTCPYC 297
                    67***9 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.054
  zinc_ribbon_2   2 CpnCGaelqdnakFCpyCGt 21 
                    Cp C   + +++kFC  CG+
     EPA05260.1 294 CPYCNF-IIEESKFCRMCGA 312
                    777777.67899*******7 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1    0.0043         7      11      23 ..      10      24 ..       7      29 .. 0.83
   2 ?    1.7   2.4      0.18   2.9e+02      17      39 ..     293     310 ..     292     311 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0043
  Auto_anti-p27 11 wtMLaetCpvC..gv 23
                   + ML e+C+ C  ++
     EPA05260.1 10 YQMLKESCESCesNT 24
                   78*********6555 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.18
  Auto_anti-p27  17 tCpvCgvPLmrdrkggkvyCvaC 39 
                    tCp C+ ++ +++     +C  C
     EPA05260.1 293 TCPYCNFIIEESK-----FCRMC 310
                    8*****9998853.....77776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       964  (0.0537676); expected 358.6 (0.02)
Passed bias filter:                      613  (0.0341904); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 1867.65
//
Query:       EPA05261.1  [L=100]
Description: hypothetical protein BG20_I1309, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 675.67
//
Query:       EPA05262.1  [L=102]
Description: putative DNA-binding protein Alba [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-09   37.1   0.4    2.9e-09   36.6   0.4    1.3  1  Alba          Alba
  ------ inclusion threshold ------
      0.048   13.6   0.1       0.13   12.2   0.1    1.7  2  Ribosomal_L2  Ribosomal Proteins L2, RNA binding domain


Domain annotation for each model (and alignments):
>> Alba  Alba
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.4   3.3e-13   2.9e-09       2      64 ..      20      79 ..      19      82 .. 0.94

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 3.3e-13
                EEEE-STS-HHHHHHHHHHHHTHTTESEEEEEEETTHHHHHHHHHHHHHHHTCTT.EEEEEEE CS
        Alba  2 eiyVsskspimsyvkralklLsnkkeeeVvlkatGraIskAvsvaeilkrrfgkglyqvnvlt 64
                +i +   +p+m+++  +l +L  ++++ V+l a+G +I +Av va+i+ +++++g  +v +++
  EPA05262.1 20 IINIRY-DPVMQAAIDILPIL--GNKKKVILRAVGESIPNAVAVANIVTEKLLHGNSKVQKIK 79
                678888.9*************..************************************9997 PP

>> Ribosomal_L2  Ribosomal Proteins L2, RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   1.5e-05      0.13      30      66 ..      13      49 ..       3      59 .. 0.81
   2 ?   -1.3   0.0      0.24   2.2e+03      35      52 ..      73      90 ..      64      94 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.5e-05
                  -SS--EEEEEEE--TT-SS-EEEEEETTTEEEEEE-- CS
  Ribosomal_L2 30 kekvkgkVveieyDpgRsApiAlvkyedgekryiiap 66
                  + k + ++++i+yDp ++A i  + ++ ++k+ i+ +
    EPA05262.1 13 QIKSEDTIINIRYDPVMQAAIDILPILGNKKKVILRA 49
                  3447889**************9999999999988865 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.24
                  EEEEEEE--TT-SS-EEE CS
  Ribosomal_L2 35 gkVveieyDpgRsApiAl 52
                   kV++i  D    A i++
    EPA05262.1 73 SKVQKIKLDTEAAAGIGR 90
                  688888888888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 723.25
//
Query:       EPA05263.1  [L=70]
Description: hypothetical protein BG20_I1328 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.51
# Mc/sec: 409.56
//
Query:       EPA05264.1  [L=150]
Description: hypothetical protein BG20_I1314 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1030.99
//
Query:       EPA05265.1  [L=116]
Description: hypothetical protein BG20_I1326 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-09   36.1   0.0    6.7e-09   35.6   0.0    1.3  1  Cyclophil_like   Cyclophilin-like
    4.6e-08   33.0   0.0    7.5e-08   32.3   0.0    1.3  1  Cyclophil_like2  Cyclophilin-like family
  ------ inclusion threshold ------
      0.012   15.3   0.0      0.038   13.7   0.0    1.7  2  DUF3830          Protein of unknown function (DUF3830)


Domain annotation for each model (and alignments):
>> Cyclophil_like  Cyclophilin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.0   1.1e-12   6.7e-09       9     114 ..       6     107 ..       1     111 [. 0.87

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 1.1e-12
                     TEEEEEEEETT...HHHHHHHHC-SEEEEEEECTTEE.EEE-S-----SSSEESSB-TTEEEEECCCTEEEEESS--TT-TTSB--SSSEEEEEE CS
  Cyclophil_like   9 sseveveLddt...etaraikealPiesrvntWgeEi.YfstpvklekeenakevveagdiaywppGkalclffGktPisddeirpaspvnviGr 99 
                     ++++  +L+ +   +t+  i+ +lP+e++++  g+ i Yf+t+v+ + +e ++++ ++gdia+      +c f           +       iG+
      EPA05265.1   6 KTKIRCDLKRHlspRTVGTIMRSLPLEGHAHYLGKNIaYFETSVDSG-SERSTKDFKKGDIAFLSSAGSICFFIEDV-------TSGKLMTPIGK 92 
                     67788888887778999****************99988*********.899999*****************998766.......556667789** PP

                     EEC-GGGGGG--TTE CS
  Cyclophil_like 100 ivedlellkkvkdge 114
                     ++e+++ lk++k+g+
      EPA05265.1  93 MLENTDALKNIKSGD 107
                     *********999987 PP

>> Cyclophil_like2  Cyclophilin-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.0   1.3e-11   7.5e-08      20     106 ..      24     105 ..      18     112 .. 0.81

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 1.3e-11
  Cyclophil_like2  20 alleklPltltmedyngnEkiaylpeklptddapegssikaGdlayyapwgnlvlfykdfeesysygltrlGrieedaeelaealke 106
                      ++++ lPl+     ++    iay++ ++++ ++ ++++ k+Gd+a+ ++ g++++f +d+++   + +t++G++ e ++++ + +k+
       EPA05265.1  24 TIMRSLPLEGHAHYLG--KNIAYFETSVDSGSERSTKDFKKGDIAFLSSAGSICFFIEDVTS--GKLMTPIGKMLE-NTDALKNIKS 105
                      5666667666666666..6799999***********************************66..89*******955.5666455655 PP

>> DUF3830  Protein of unknown function (DUF3830)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   6.3e-06     0.038       6      77 ..       5      70 ..       2      93 .. 0.87
   2 ?   -0.7   0.0      0.18   1.1e+03      68      77 ..     104     113 ..      87     116 .] 0.78

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.3e-06
                TTEEEEEEE-TTTSHHHHHHHHHH--EEEE-EE-SSSSSEEEEEEE--SSS---S-SEESS--TTEEEEEEE CS
     DUF3830  6 rgvsataeLledkAPetcaavwealplssdviHakyagneiyvllpefaatelpaENaTvtPipGdvvlfsf 77
                 +++++++L     P+t+  ++  lpl++   Ha+y g++i     +++    + E  T   ++Gd+ + s 
  EPA05265.1  5 GKTKIRCDLKRHLSPRTVGTIMRSLPLEG---HAHYLGKNIAYFETSVD---SGSERSTKDFKKGDIAFLSS 70
                578899*********************98...99*******98877777...88999999999999888754 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.18
                 -TTEEEEEEE CS
     DUF3830  68 ipGdvvlfsf 77 
                 + Gdv +f+ 
  EPA05265.1 104 KSGDVFYFYE 113
                 4799999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 742.68
//
Query:       EPA05266.1  [L=207]
Description: hypothetical protein BG20_I1311 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1259.00
//
Query:       EPA05267.1  [L=121]
Description: hypothetical protein BG20_I1319 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 891.28
//
Query:       EPA05268.1  [L=106]
Description: hypothetical protein BG20_I1325 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.4e-10   40.0   4.7    4.4e-10   39.7   4.7    1.1  1  Ribosomal_S25  S25 ribosomal protein
     0.0086   15.7   2.8      0.024   14.2   2.8    1.6  1  DDRGK          DDRGK domain
     0.0098   15.8   0.1      0.012   15.5   0.1    1.1  1  DUF977         Bacterial protein of unknown function (DUF977)
  ------ inclusion threshold ------
      0.024   14.5   0.1      0.031   14.1   0.1    1.2  1  TrmB           Sugar-specific transcriptional regulator TrmB
      0.045   13.3   0.0      0.061   12.9   0.0    1.2  1  HTH_24         Winged helix-turn-helix DNA-binding
       0.06   13.2   0.0      0.078   12.9   0.0    1.3  1  MarR_2         MarR family


Domain annotation for each model (and alignments):
>> Ribosomal_S25  S25 ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   4.7   1.5e-13   4.4e-10       5      98 ..      10     101 ..       4     103 .. 0.71

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 1.5e-13
  Ribosomal_S25   5 akkakaaaakaggkakkKKwskgkvk...dklnnavlfdketydkllkevpkyklitpsvvserlkingslArraLreleekgliklvskhraqvi 97 
                    ak++ka+ ak g+    KK  k k +    k++ +v+++++     +k ++++k++t+  ++ +  +++s A ++Lr+ ++kg+ik+v   + ++i
     EPA05268.1  10 AKQDKAQGAKDGKD--SKKSRKDKGEsgpRKAEITVMVNEKE---AIKIIQNAKVVTVHDLARQTGVKVSAANAFLRDSAKKGTIKRVGGYSGHYI 100
                    44555555544443..33333444330014444456666665...555579********************************************* PP

  Ribosomal_S25  98 Y 98 
                    Y
     EPA05268.1 101 Y 101
                    * PP

>> DDRGK  DDRGK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   2.8   8.2e-06     0.024     101     155 ..      47     101 ..      10     105 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 8.2e-06
                 HHHHHHHHHH-SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EEE-TT--EEE CS
       DDRGK 101 leefinyikekKvvlleelavkfklktqevierikeLeeqgsltGvlDdrGkyiy 155
                  +e i+ i+++Kvv++++la + ++k + +   +++  ++g+++ v    G yiy
  EPA05268.1  47 EKEAIKIIQNAKVVTVHDLARQTGVKVSAANAFLRDSAKKGTIKRVGGYSGHYIY 101
                 36789*****************************************999999999 PP

>> DUF977  Bacterial protein of unknown function (DUF977)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   4.1e-06     0.012      16      62 ..      49      95 ..      36     105 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.1e-06
      DUF977 16 riiGlvkkneritisdleritGvgrtsvrkylvdvlerGdlirpGky 62
                  i ++++ + +t+ dl r tGv+  +++ +l+d  ++G + r G y
  EPA05268.1 49 EAIKIIQNAKVVTVHDLARQTGVKVSAANAFLRDSAKKGTIKRVGGY 95
                46888999999******************************999877 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1     1e-05     0.031      19      66 ..      56     105 ..      44     106 .] 0.87

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1e-05
                 HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST..TTEEEE-- CS
        TrmB  19 klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr..pklYravd 66 
                 + +  t+ ++a+++gv  s ++  Lr   +kG ++r+ g    ++Y+av+
  EPA05268.1  56 NAKVVTVHDLARQTGVKVSAANAFLRDSAKKGTIKRVGGYsgHYIYQAVS 105
                 56778********************************97788999*9996 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     2e-05     0.061       9      48 .]      51      90 ..      46      90 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2e-05
      HTH_24  9 LelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                ++++q     +  +LA+++g+ +s+ n+ l+   ++G Ik
  EPA05268.1 51 IKIIQNAKVVTVHDLARQTGVKVSAANAFLRDSAKKGTIK 90
                677788777********************99888888775 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.6e-05     0.078      22      54 ..      60      92 ..      33      97 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.6e-05
                EEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
      MarR_2 22 ltvgelarrlglsksavsrilkrLvaaGLverr 54
                +tv +lar +g++ sa++  l++  ++G + r+
  EPA05268.1 60 VTVHDLARQTGVKVSAANAFLRDSAKKGTIKRV 92
                6***************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       888  (0.0495287); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 782.27
//
Query:       EPA05269.1  [L=296]
Description: prenyltransferase, UbiA family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.8e-26   90.9  13.4    7.8e-26   90.9  13.4    1.3  1  UbiA       UbiA prenyltransferase family
  ------ inclusion threshold ------
      0.038   14.1   1.5       0.15   12.3   0.2    2.4  2  T4SS_CagC  Cag pathogenicity island, type IV secretory system
       0.35   10.4   3.8       0.41   10.2   0.3    2.8  2  Tom6       Mitochondrial import receptor subunit Tom6, fungal
        2.1    7.3   9.6      0.035   13.0   2.0    1.8  2  DUF3488    Domain of unknown function (DUF3488)


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.9  13.4   1.7e-29   7.8e-26       2     233 ..      18     256 ..      17     279 .. 0.78

  Alignments for each domain:
  == domain 1  score: 90.9 bits;  conditional E-value: 1.7e-29
        UbiA   2 lipalvg..lalaaggspdlllllllllgtllaaaaanalNdyfDreiDadme..rtpnRP....lvsGrispkealifaivllilgllll...allln 89 
                 +i++ vg  + +  ++ +++  ++++++g+l+++a++ +lNdy+D++ + d+   rt+       l+ G+++p ++++++i +lilg l++   +l  +
  EPA05269.1  18 VIAVSVGlvIHWHLNSAISTVDAAITFAGVLALHASVDLLNDYWDFKRGIDTVtkRTKMSGgtgvLPEGLLKPSTVYRAGIGFLILGSLIGfyfVLSNG 116
                 56677773344445566666999**********************98766654225554426666***********************99998666666 PP

        UbiA  90 pltallgllalllyvvYtglrlKrrtllgtvvggiafglppllgwaavtgslsllalllalavflltwaialandlrdregDrkagiktlpvvlGrkaa 188
                  ++a+++ +a+l  ++Y+     +++l +++++++ +++++l+  ++++++++l+ +l ++ v++l+  ++++ +++d++ D+  g+ktl++  G+k+a
  EPA05269.1 117 ITIAIILGFAILSIYFYS-TKIVDSGL-AEFFVAVKGTMIVLGTSFIQSNQITLESILGGIVVGVLSSLVLFIASFPDHDADKSKGRKTLVIAVGKKNA 213
                 88888888999999****.59******.*********************************************************************** PP

        UbiA 189 rillalllavlllallllllalllllylllalllaalallraarl 233
                 + l++l+ a+ + +++l    +  +++ ++++++++l++   a +
  EPA05269.1 214 ALLFWLFPAISYSVIILGISIGIFPILSFITFFSIPLMFK--AGF 256
                 *976666666666633333333333333333333333333..333 PP

>> T4SS_CagC  Cag pathogenicity island, type IV secretory system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.27   1.2e+03      27      75 ..      23      66 ..       5      78 .. 0.52
   2 ?   12.3   0.2   3.3e-05      0.15      35      89 ..     161     215 ..     142     231 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.27
   T4SS_CagC 27 eGgevksklvsetktlviilisllvlvGicvalflivkriadaddikek 75
                 G  ++ +l s+  t+   ++    + G+  al   v  + d  d k++
  EPA05269.1 23 VGLVIHWHLNSAISTVDAAIT----FAGV-LALHASVDLLNDYWDFKRG 66
                444444455555555444433....2222.2344555555555555555 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 3.3e-05
   T4SS_CagC  35 lvsetktlviilisllvlvGicvalflivkriad..addikeksevvfavarviall 89 
                 + s+  tl  il +++  vG+  +l+l +  ++d  ad  k ++  v av++  a l
  EPA05269.1 161 IQSNQITLESILGGIV--VGVLSSLVLFIASFPDhdADKSKGRKTLVIAVGKKNAAL 215
                 4555667777777765..78888889999999987688888889999***9875432 PP

>> Tom6  Mitochondrial import receptor subunit Tom6, fungal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.3   9.2e-05      0.41      17      36 ..     145     164 ..     143     168 .. 0.92
   2 ?   -0.6   0.3      0.21   9.5e+02      27      37 ..     281     291 ..     275     294 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 9.2e-05
        Tom6  17 ftvllnvaLFvaGVaFIqSp 36 
                 f v++++++ v+G  FIqS 
  EPA05269.1 145 FFVAVKGTMIVLGTSFIQSN 164
                 88*****************5 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.21
        Tom6  27 vaGVaFIqSpL 37 
                 v GV+F+ S L
  EPA05269.1 281 VTGVLFVLSFL 291
                 57888887755 PP

>> DUF3488  Domain of unknown function (DUF3488)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   1.0      0.43   1.9e+03      52      78 ..      16      44 ..       3      58 .. 0.42
   2 ?   13.0   2.0   7.9e-06     0.035      60     175 ..     109     224 ..      80     230 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.43
     DUF3488 52 lllallav.allllsygtllg.rdagval 78
                + + +++v +++ +++++ ++ +da++++
  EPA05269.1 16 ASVIAVSVgLVIHWHLNSAIStVDAAITF 44
                22222222233333333322223333333 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 7.9e-06
     DUF3488  60 allllsygtllgrdagvalL.vlllalKllElrsrRDalvllllgffllatsflfsqsllfalylllalllllaalvalhasasapslaralrlalkll 157
                 + ++ls g+++    g a+L + +++ K++++    +++v +   +++l tsf+ s+++ +  +l  +++++l +lv++ as + +   +   + ++++
  EPA05269.1 109 FYFVLSNGITIAIILGFAILsIYFYSTKIVDS-GLAEFFVAVKGTMIVLGTSFIQSNQITLESILGGIVVGVLSSLVLFIASFPDHDADKSKGRKTLVI 206
                 44455555555533444433144555555554.4567888888999**********************************99***************** PP

     DUF3488 158 llalPlalvLFllfPRlq 175
                 + +   a++LF+lfP ++
  EPA05269.1 207 AVGKKNAALLFWLFPAIS 224
                 ***************775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       804  (0.0448435); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 1928.85
//
Query:       EPA05270.1  [L=868]
Description: hypothetical protein BG20_I1316 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-05   24.7   3.3    1.7e-05   24.7   3.3    3.7  4  Big_1            Bacterial Ig-like domain (group 1)
    0.00027   21.2  21.2       0.01   16.2   1.5    5.7  5  Invasin_D3       Invasin, domain 3
     0.0094   16.2   2.7      0.019   15.3   0.4    2.7  4  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
  ------ inclusion threshold ------
       0.02   13.4   0.0       0.03   12.8   0.0    1.2  1  Rhabdo_glycop    Rhabdovirus spike glycoprotein
      0.084   13.2   1.9       0.18   12.2   0.2    2.5  2  Big_3            Bacterial Ig-like domain (group 3)
       0.21   11.3   0.6       0.52   10.1   0.6    1.7  1  Spore_YhaL       Sporulation protein YhaL


Domain annotation for each model (and alignments):
>> Big_1  Bacterial Ig-like domain (group 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.3       1.5   4.6e+03      45      52 ..     116     123 ..      95     130 .. 0.60
   2 ?   -0.6   0.1      0.45   1.4e+03      11      20 ..     272     281 ..     266     299 .. 0.87
   3 !   24.7   3.3   5.8e-09   1.7e-05       6      56 ..     739     790 ..     737     793 .. 0.94
   4 ?   -3.7   0.2       4.1   1.2e+04       3      21 ..     808     826 ..     807     826 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.5
       Big_1  45 nGkatvtl 52 
                  G++t+t 
  EPA05270.1 116 TGEVTITA 123
                 33333333 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.45
       Big_1  11 atvkDangnp 20 
                 + v+D++gnp
  EPA05270.1 272 VNVVDSDGNP 281
                 789******9 PP

  == domain 3  score: 24.7 bits;  conditional E-value: 5.8e-09
       Big_1   6 tntltatvkDangnpvagatVtfsvsg.galsassgtTdanGkatvtltstk 56 
                 +++++  + D+n   v+ga+++++++g ++++++ ++T+++G a+v++t t+
  EPA05270.1 739 QVEIKLFIDDENAESVPGASIKITTDGnSQVTPNIVRTNSDGSAVVSVTATN 790
                 6889999********************88888*****************985 PP

  == domain 4  score: -3.7 bits;  conditional E-value: 4.1
       Big_1   3 GvdtntltatvkDangnpv 21 
                 G+dt t+++ + D+  n+v
  EPA05270.1 808 GKDTLTINVDAPDKTLNAV 826
                 8999999999988877765 PP

>> Invasin_D3  Invasin, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1      0.12   3.5e+02      59      84 ..     106     129 ..      53     138 .. 0.58
   2 ?    3.3   0.2     0.034     1e+02       7      44 ..     253     291 ..     248     309 .. 0.74
   3 !    8.5   0.6   0.00081       2.4      53      88 ..     468     505 ..     447     512 .. 0.66
   4 ?    2.0   0.1     0.089   2.7e+02      12      47 ..     629     664 ..     618     724 .. 0.65
   5 !   16.2   1.5   3.4e-06      0.01      21      93 ..     739     816 ..     727     819 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.12
  Invasin_D3  59 dGtytatLtattagtatitptvnGva 84 
                 +   ++tL  + +g++tit+t++ ++
  EPA05270.1 106 ASFNISTL--SGTGEVTITATLGTKT 129
                 33444445..4458999999985543 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.034
  Invasin_D3   7 ftaspasivAdGkststltvtlkDangnp.vsgltvtfs 44 
                 + + p+ i  d k++  + v++ D +gnp v+ + +t++
  EPA05270.1 253 INVFPKLISTDVKKQLDVFVNVVDSDGNPtVTPEDITLN 291
                 66778889999999999************8665555554 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.00081
  Invasin_D3  53 avtdngdGtytatLta.ttagtatitptvnG..vaiaat 88 
                 ++ ++g+   ta++t+ +++g++ i+++++G  +++a t
  EPA05270.1 468 KI-ESGNSFGTAIITSgQKSGSVLISASIQGvgSDSALT 505
                 33.55666678999**9**************54444444 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.089
  Invasin_D3  12 asivAdGkststltvtlkDangnp.vsgltvtfstts 47 
                 ++i A+ ++++   ++l D +gnp +    v+ + ts
  EPA05270.1 629 DKINAN-HKNNIGIIQLVDLQGNPiIPSFDVKSKITS 664
                 456666.77888999*********8777667666552 PP

  == domain 5  score: 16.2 bits;  conditional E-value: 3.4e-06
  Invasin_D3  21 tstltvtlkDangnpvsgltvtfstt..sagtlsavtdngdGtytatLtatt..agtatitptvnG.vaiaatatvtl 93 
                 +  +++ + D+n + v g++++++t+  s++t + v++n+dG   + +tat+    ++++ +t +G +++++t t+++
  EPA05270.1 739 QVEIKLFIDDENAESVPGASIKITTDgnSQVTPNIVRTNSDGSAVVSVTATNgpNISLNLIATAEGySEGKDTLTINV 816
                 556788899999999*********9954444888899*************7734456889999999888888877765 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       5.4   1.6e+04      42      56 ..     110     125 ..     107     139 .. 0.50
   2 ?   -3.4   0.0       4.1   1.2e+04       6      13 ..     274     281 ..     272     294 .. 0.76
   3 ?   -2.0   0.0       1.5   4.4e+03      43      66 ..     331     354 ..     328     364 .. 0.72
   4 !   15.3   0.4   6.2e-06     0.019       6      78 ..     746     824 ..     741     830 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 5.4
  CarboxypepD_reg  42 lrglpp.gtysvtvsa 56 
                      ++ l   g+ ++t++ 
       EPA05270.1 110 ISTLSGtGEVTITATL 125
                      5544444555555533 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 4.1
  CarboxypepD_reg   6 Vtdasgap 13 
                      V+d++g+p
       EPA05270.1 274 VVDSDGNP 281
                      78888877 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.5
  CarboxypepD_reg  43 rglppgtysvtvsapGyatatree 66 
                      ++l   ++ + vsa+Gy  at + 
       EPA05270.1 331 SNLLSNDIVIGVSAEGYGIATDTF 354
                      566677788899*****9888653 PP

  == domain 4  score: 15.3 bits;  conditional E-value: 6.2e-06
  CarboxypepD_reg   6 VtdasgapiagatVtvtnadtgtv..astttdadGafrlrglpp.....gtysvtvsapGyatatreevtltagqt.ttld 78 
                      + d++ + ++ga++ +t++++++v    ++t++dG+  ++ +++      + ++ ++a+Gy +    ++t++++ + +tl+
       EPA05270.1 746 IDDENAESVPGASIKITTDGNSQVtpNIVRTNSDGSAVVS-VTAtngpnISLNLIATAEGYSEGKD-TLTINVDAPdKTLN 824
                      5688999**********877665422559*********97.65557555689999******99996.57777766523444 PP

>> Rhabdo_glycop  Rhabdovirus spike glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     1e-05      0.03     435     479 ..     812     854 ..     762     859 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1e-05
  Rhabdo_glycop 435 lfvetdlsdvskkiesvdlglshWsffvlisaligiflvLlvala 479
                    l  ++d +d  k ++ vdl+l++W  +v+i+a+ +i ++++++l+
     EPA05270.1 812 LTINVDAPD--KTLNAVDLELPEWIVYVVIAAILLIGVLVVLFLK 854
                    445677788..9********************9999888888775 PP

>> Big_3  Bacterial Ig-like domain (group 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.1       5.3   1.6e+04      49      57 ..     115     123 ..     109     130 .. 0.56
   2 ?   12.2   0.2   5.9e-05      0.18      18      50 ..     269     302 ..     265     304 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 5.3
       Big_3  49 Geytvtvty 57 
                 G+ +vt+t 
  EPA05270.1 115 GTGEVTITA 123
                 455555543 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 5.9e-05
       Big_3  18 dlfvsatykdGdaevpfddvevsg.svdstkaGe 50 
                 d+fv ++++dG+  v+++d+++ + s d++++G 
  EPA05270.1 269 DVFVNVVDSDGNPTVTPEDITLNFfSNDQHTVGN 302
                 99**********99**********9999999996 PP

>> Spore_YhaL  Sporulation protein YhaL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.6   0.00017      0.52       2      32 ..     831     863 ..     830     867 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00017
  Spore_YhaL   2 PwW.vYlviagIlfSgymavktakeEre.ldqe 32 
                 P W vY+via+Il+ g ++v  +k+ +  +++e
  EPA05270.1 831 PEWiVYVVIAAILLIGVLVVLFLKKSKTpIEEE 863
                 55538*************999888776424555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (868 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.67u 0.28s 00:00:00.95 Elapsed: 00:00:00.42
# Mc/sec: 6207.85
//
Query:       EPA05271.1  [L=68]
Description: hypothetical protein BG20_I1332 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 430.94
//
Query:       EPA05272.1  [L=366]
Description: hypothetical protein BG20_I1312 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0021   18.3   0.6       0.03   14.6   0.8    2.4  2  NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosi


Domain annotation for each model (and alignments):
>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0     0.035   6.3e+02       4      25 ..      69      90 ..      66      93 .. 0.82
   2 !   14.6   0.8   1.7e-06      0.03       3      63 ..     176     239 ..     174     251 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.035
  NPCBM_assoc  4 Getvtltltvtndgtaaatnvs 25
                 ++++ l+++v ndg+ +++ ++
   EPA05272.1 69 DSSNILKVVVDNDGQNPVEILR 90
                 6788899**********98665 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 1.7e-06
  NPCBM_assoc   3 pGetvtltltvtndgtaaatnv...slslslPe...GWtvvevspasaaslapGetveatvkVtppa 63 
                   G+ vt+ + vtn+g++++++v     +++ P    GW+   +++  + +l pGe+v + ++  ++ 
   EPA05272.1 176 IGQNVTVAMIVTNTGSSTIESVipvTPTVTPPLavlGWS---SATPAIVDLTPGESVMFSWDYMISG 239
                  59**************99998632256777784555***...8888999***********9876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2562.44
//
Query:       EPA05273.1  [L=48]
Description: hypothetical protein BG20_I1321 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-11   44.1   0.1      2e-11   43.8   0.1    1.1  1  YHS              YHS domain
    5.5e-05   23.8   0.5    6.9e-05   23.5   0.5    1.1  1  ATPase-cat_bd    Putative metal-binding domain of cation tran
    0.00069   19.9   0.2    0.00069   19.9   0.2    1.1  1  Ta0938           Ta0938
     0.0056   17.0   1.1     0.0076   16.6   1.1    1.2  1  Arc_trans_TRASH  Archaeal TRASH domain


Domain annotation for each model (and alignments):
>> YHS  YHS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   0.1   4.4e-15     2e-11       3      45 ..       4      45 ..       3      47 .. 0.92

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 4.4e-15
         YHS  3 dPvcgmkvdkekaeekseYkGkeYyFcSegCkdkFedePekYa 45
                dPvcg  +  e+   + eY+Gk+ +Fc+ gC+ +F + P+k +
  EPA05273.1  4 DPVCGIEL-AEELAVTHEYEGKKLFFCCNGCRKIFIRKPKKWK 45
                9*******.777999*************************975 PP

>> ATPase-cat_bd  Putative metal-binding domain of cation transport ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.5   1.5e-08   6.9e-05       5      35 ..       7      37 ..       6      39 .. 0.95

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.5e-08
  ATPase-cat_bd  5 CglpveesaklkaeiegeerefCCkGCqava 35
                   Cg ++ e+ +++ e+eg++  fCC+GC+ ++
     EPA05273.1  7 CGIELAEELAVTHEYEGKKLFFCCNGCRKIF 37
                   ***************************9875 PP

>> Ta0938  Ta0938
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.2   1.5e-07   0.00069      29      55 ..      19      45 ..       5      48 .] 0.80

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.5e-07
                -B-TT--BSSS--SSSS-TTS-THHHH CS
      Ta0938 29 eevdgeklffccdicakefvnllnevk 55
                +e +g+klffcc+ c k f+   ++ k
  EPA05273.1 19 HEYEGKKLFFCCNGCRKIFIRKPKKWK 45
                6889**************997665555 PP

>> Arc_trans_TRASH  Archaeal TRASH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   1.1   1.7e-06    0.0076       4      33 ..       7      37 ..       6      41 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.7e-06
  Arc_trans_TRASH  4 CGkeivge.PivyklknkvYyvCCktCksel 33
                     CG e+ +e  ++ ++  k  ++CC+ C++ +
       EPA05273.1  7 CGIELAEElAVTHEYEGKKLFFCCNGCRKIF 37
                     99999988456778999**********9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.31s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 319.35
//
Query:       EPA05274.1  [L=141]
Description: hypothetical protein BG20_I1330 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-10   41.0   0.0    1.6e-10   40.8   0.0    1.1  1  Prok-JAB  Prokaryotic homologs of the JAB domain


Domain annotation for each model (and alignments):
>> Prok-JAB  Prokaryotic homologs of the JAB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   0.0   8.8e-15   1.6e-10       2     105 ..      25     118 ..      24     132 .. 0.81

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 8.8e-15
    Prok-JAB   2 esvlsalvaharrahpeEtcGlllgkeseseevivvplvnewsnrfeipdpedslarlkfearerglevvgiwHSHpggsarPSetDrrdaaalarvka 100
                 ++vl+ ++   +  hp+E+  +l gk+ ++   ++++ + ++  +f++ ++ +s   ++  +  ++ ++vg++HSHp g + PS tD++++ +     +
  EPA05274.1  25 KDVLDSILSFCQIKHPNEAILILRGKS-KKGN-VLIDGLVIP--PFAF-NAHASSGFPH-YMLPADISYVGTVHSHPIGNPSPSITDLNNFYE----LI 113
                 6799999999****************9.4444.444444322..6889.9999999999.*******************************99....45 PP

    Prok-JAB 101 lliiv 105
                 +li++
  EPA05274.1 114 SLIVG 118
                 55554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 989.77
//
Query:       EPA05275.1  [L=158]
Description: hypothetical protein BG20_I1323 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.3e-05   22.7   0.0    0.00017   21.5   0.0    1.7  1  HTH_3           Helix-turn-helix
  ------ inclusion threshold ------
       0.01   15.6   0.0      0.018   14.8   0.0    1.4  1  HTH_23          Homeodomain-like domain
      0.081   12.9   0.0       0.22   11.5   0.0    1.7  1  HTH_11          HTH domain
       0.17   11.8   0.0       0.57   10.1   0.0    2.0  1  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
       0.17   12.2   0.9       0.34   11.2   0.9    1.9  1  Rpr2            RNAse P Rpr2/Rpp21/SNM1 subunit domain


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   4.8e-08   0.00017       3      38 ..      43      79 ..      40      86 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 4.8e-08
                HHHHHTTHHHHHHHHHHTSSHHHHHHHHTT.SSCSBH CS
       HTH_3  3 elRkqlglsqeeLAeklGvsrstisriEnG.ernPsl 38
                +l + +++   e++++lGv+++++s++++G +  Psl
  EPA05275.1 43 KLAEDHNIREDEISKMLGVTQAAVSNYIRGtRGDPSL 79
                56678899999*******************7777775 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   5.1e-06     0.018       7      40 ..      37      72 ..      34      80 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.1e-06
      HTH_23  7 Rlrillllae..GlsvreIAreLgvsrrTvyrwlkr 40
                R+  ++ lae   ++  eI+++Lgv++  v+++++ 
  EPA05275.1 37 RAILAKKLAEdhNIREDEISKMLGVTQAAVSNYIRG 72
                6666677777799********************996 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   6.2e-05      0.22       5      37 ..      39      71 ..      36      72 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.2e-05
      HTH_11  5 ilelLleargpisgeeLAeeLnvSrrtvrrdIk 37
                il   l+++ +i  +e+++ L+v+ ++v ++I+
  EPA05275.1 39 ILAKKLAEDHNIREDEISKMLGVTQAAVSNYIR 71
                555533566669999****************95 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00016      0.57      16      34 ..      57      75 ..      38      91 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00016
  YdaS_antitoxin 16 ealgvsqqaVsqWlkgkkq 34
                    + lgv+q+aVs+ ++g+++
      EPA05275.1 57 KMLGVTQAAVSNYIRGTRG 75
                    679***********99887 PP

>> Rpr2  RNAse P Rpr2/Rpp21/SNM1 subunit domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.9   9.4e-05      0.34      37      58 ..     132     153 ..      11     157 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 9.4e-05
                 ---SSTCCCTB-TTT--B--CT CS
        Rpr2  37 lrlppsvkrtvCkkCgsvlipg 58 
                  +l+ ++ ++vCk+C+++l++g
  EPA05275.1 132 HNLESNIDEKVCKECENMLLKG 153
                 468999*************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       851  (0.047465); expected 358.6 (0.02)
Passed bias filter:                      666  (0.0371465); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1029.27
//
Query:       EPA05276.1  [L=207]
Description: archaeal flagellin N-terminal-like domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.01   16.7   3.2       0.01   16.7   3.2    1.9  2  Pilin_N   Archaeal Type IV pilin, N-terminal


Domain annotation for each model (and alignments):
>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.7   3.2   5.7e-07      0.01       1      42 [.      14      57 ..      14     106 .. 0.76
   2 ?   -2.0   0.0      0.39     7e+03      28      28 ..     172     172 ..     143     200 .. 0.57

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.7e-07
     Pilin_N  1 eAVSpViGviLmvaitvIlaAviaafvlgl..asneekapqasi 42
                +AV p+i  +L+vai v+  +++ +f  g+  + + + ap+++ 
  EPA05276.1 14 RAVAPIIATLLLVAIAVVGGSIVFVFSQGFfsSAQVSGAPNIES 57
                69***************************975455566777654 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.39
     Pilin_N  28 l 28 
                 l
  EPA05276.1 172 L 172
                 2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       735  (0.040995); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 1148.04
//
Query:       EPA05277.1  [L=74]
Description: hypothetical protein BG20_I1313 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.34s 00:00:00.88 Elapsed: 00:00:00.54
# Mc/sec: 409.65
//
Query:       EPA05278.1  [L=231]
Description: CbiD protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-78  261.9   0.8    5.4e-78  261.8   0.8    1.0  1  CbiD      CbiD
  ------ inclusion threshold ------
      0.031   14.3   0.2        0.1   12.6   0.2    1.9  2  DUF3042   Protein of unknown function (DUF3042)


Domain annotation for each model (and alignments):
>> CbiD  CbiD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  261.8   0.8     6e-82   5.4e-78       1     210 [.      12     230 ..      12     231 .] 0.98

  Alignments for each domain:
  == domain 1  score: 261.8 bits;  conditional E-value: 6e-82
        CbiD   1 lrsGyTtGscAaAAakaAllallkgekleeveielpkgekleipiekvalleee..aavikdaGddpDvTngaeivaeve.....eeieiegGeGvGrv 92 
                 lr+GyTtG+ A+AAakaAll +++++k+e+++++lpkg+ ++ipi+ ++ +e++  ++vikd+GddpDvT+gaei+++++     +eiei+gGeGvG+v
  EPA05278.1  12 LRTGYTTGTSATAAAKAALLSIITQTKIENIDVKLPKGSFIKIPIHFCQFDENKarCSVIKDGGDDPDVTHGAEIIVDLSfsdriNEIEIDGGEGVGIV 110
                 69************************************************888799*****************************88************ PP

        CbiD  93 tkpgLevevgeaAInpvprkmieenveevleea..kegvevtisvpeGeelAkkTlNprlGivgGiSiLGTtGivepmSeeallesireelkvaaaegl 189
                 tkpgL +e +++AInpvp+kmi+en++e+++++  k+g++v isvp+G+el  kT Npr+Gi++GiSiLGT+Giv p+S++++ +sir++l+va a g+
  EPA05278.1 111 TKPGLGLELNKSAINPVPKKMINENLREIMDKHhlKKGIKVVISVPKGRELGPKTDNPRIGILNGISILGTSGIVIPFSTASYAASIRQNLDVAIAMGN 209
                 *******************************999999************************************************************** PP

        CbiD 190 kelvlvtGnkgeklakkklgl 210
                 +++vl+tG ++e++akk ++l
  EPA05278.1 210 NTVVLTTGGRSEDYAKKIIDL 230
                 ****************97765 PP

>> DUF3042  Protein of unknown function (DUF3042)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   1.2e-05       0.1       2      37 ..      10      45 ..       9      49 .. 0.90
   2 ?   -2.5   0.0       0.6   5.4e+03      27      37 ..     120     130 ..     114     137 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.2e-05
     DUF3042  2 kkFlkGflvGvlatiaavagavfvfKkkviePiEek 37
                +k  +G+ +G+ at+aa a+ + ++ ++ ie i+ k
  EPA05278.1 10 EKLRTGYTTGTSATAAAKAALLSIITQTKIENIDVK 45
                57789*************************999865 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.6
     DUF3042  27 KkkviePiEek 37 
                  k  i+P+ +k
  EPA05278.1 120 NKSAINPVPKK 130
                 58889998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.32s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1412.28
//
Query:       EPA05279.1  [L=167]
Description: hypothetical protein BG20_I1884 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0079   16.0   0.0      0.021   14.7   0.0    1.6  1  LapA_dom  Lipopolysaccharide assembly protein A domain


Domain annotation for each model (and alignments):
>> LapA_dom  Lipopolysaccharide assembly protein A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.1e-06     0.021      19      62 ..      14      59 ..       8      60 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.1e-06
    LapA_dom 19 LsllllvafgiGallgwllslwsylrlrrelrrl..kkkikkleke 62
                 +l++ ++ ++G l+g  +++++ + ++r ++rl   k+i++ ek 
  EPA05279.1 14 TALWITFFTIMGTLIGTAFTIYKHFTTQRDNKRLglIKQIEHYEKA 59
                589*******************************999999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1238  (0.0690501); expected 358.6 (0.02)
Passed bias filter:                      698  (0.0389313); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1141.87
//
Query:       EPA05280.1  [L=244]
Description: oxidoreductase, short chain dehydrogenase/reductase family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.3e-55  186.1   0.0    9.2e-55  185.7   0.0    1.0  1  adh_short_C2   Enoyl-(Acyl carrier protein) reductase
    7.2e-52  175.7   0.1    9.1e-52  175.4   0.1    1.1  1  adh_short      short chain dehydrogenase
    5.7e-10   39.4   0.0      3e-09   37.0   0.0    1.9  1  KR             KR domain
    6.7e-08   32.3   0.0      2e-07   30.8   0.0    1.8  2  Epimerase      NAD dependent epimerase/dehydratase family
  ------ inclusion threshold ------
      0.051   13.0   0.3       0.15   11.4   0.3    1.8  1  P3A            Poliovirus 3A protein like
      0.058   12.7   0.0        0.1   11.9   0.0    1.4  1  THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase,
        0.3   11.2   2.8       0.36   10.9   1.1    1.9  2  DUF840         Lagovirus protein of unknown function (DUF840)


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.7   0.0   3.6e-58   9.2e-55       3     234 .]      14     240 ..      12     240 .. 0.92

  Alignments for each domain:
  == domain 1  score: 185.7 bits;  conditional E-value: 3.6e-58
                   TTSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEE.EE--TTSHHHHHHHHHHHHHHHSSEEEEEE-----EGCSS-GGGH.-HHHHHH CS
  adh_short_C2   3 asgIGraiAkalaeeGaevvltdlneeakkrveelaeelgaev.lecDVtdeeqvealveevvekfgklDilvnnagiapklkgpflet.sreefdr 97 
                    +gIG+ ++  ++++ + v+ +  + +         +e +a++ + cD+++++q+++ ++++v+k+gk+D+l+nna+i+ +  +p+ e  s+e +++
    EPA05280.1  14 SRGIGKNMVDYFKDKNWIVITCASSTNW-------LSESKADFsFVCDIRKQNQIKNGIKKIVKKYGKIDVLINNAAISGN--NPLNEQsSDEIWHN 101
                   5899999999999999988887666665.......555678877*************************************..88887549999*** PP

                   HHHHHTHHHHHHHHHHHHHCTSC.CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHHHHHHGGGTEEEEEEEE--BHCTG.GGGSTTHHHHHHHH CS
  adh_short_C2  98 aldvnlyslfllakaalplmkeg.gsivnlssvgaervvpnynaygaaKaalealtrylAvelgpkgiRvNavspgpikTla.asgikgfdelleel 192
                   ++d+nl+++++++k+ lp++k++ g+i+n+ssv + ++vp+++ay++aK+a+++lt+++A   +p+ i+vN+++pg+++T++ +++i++ +  +  +
    EPA05280.1 102 IIDTNLNGVYYMCKYSLPYIKDNvGRIINISSVLGIMGVPDQSAYSVAKHAIIGLTKCFALYAAPRHITVNSICPGWVETEMmQKRIRSLSLNKIDI 198
                   *********************999********************************************************99667788777777889 PP

                   HHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEEEESTTGG CS
  adh_short_C2 193 earaplgrlgtpeevaeaalfLasdeasyitGqtlvvDgGlt 234
                   ++ +pl ++ +p e+ ++a +L s+eas  tGq++v+DgG t
    EPA05280.1 199 QNTIPLSKILKPIEISALAFYLSSPEASNLTGQEIVIDGGQT 240
                   9***************************************75 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.4   0.1   3.6e-55   9.1e-52       1     190 [.       6     187 ..       6     191 .. 0.96

  Alignments for each domain:
  == domain 1  score: 175.4 bits;  conditional E-value: 3.6e-55
                 SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEEE---SS--SSGGGCSHH CS
   adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldvLvnNAGitgsgpfselsee 99 
                 ++vl+tG+s+GIG+++++ +  +++ v+ +++s +    +++e k+     + + +D+++++++++ ++k+vkk+gk+dvL+nNA+i+g++p +e s++
  EPA05280.1   6 QIVLITGGSRGIGKNMVDYFKDKNWIVITCASSTN----WLSESKA----DFSFVCDIRKQNQIKNGIKKIVKKYGKIDVLINNAAISGNNPLNEQSSD 96 
                 58*******************************77....5577776....58899******************************************** PP

                 H.HHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHH CS
   adh_short 100 e.wervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaavagltrslakelaptgirvnavaPGlvdTdmakel 190
                 e w ++i++Nl+gv+ +++  lp+ +k + GrI+n+sSv g ++v+ ++aYs +K+a++glt+++a   ap+ i+vn+++PG v+T+m++++
  EPA05280.1  97 EiWHNIIDTNLNGVYYMCKYSLPY-IKDNVGRIINISSVLGIMGVPDQSAYSVAKHAIIGLTKCFALYAAPRHITVNSICPGWVETEMMQKR 187
                 ************************.88*************************************************************9986 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.0   1.2e-12     3e-09       3     155 ..       8     152 ..       6     166 .. 0.85

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 1.2e-12
                 EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS---EEEE---------TTT-- CS
          KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppikGvihaAgvlrdklleemt 101
                 +litGG  g+G+ +++   +k    +v++  s          ++ l+++ a+ ++  +D+ +++++++ +++i ++ ++i   i+ A ++ +++l+e++
  EPA05280.1   8 VLITGGSRGIGKNMVDYFKDKNW--IVITCAS---------STNWLSESKADFSF-VCDIRKQNQIKNGIKKIVKKYGKIDVLINNAAISGNNPLNEQS 94 
                 799**********9999988755..4554444.........12345566666665.59*************************************9987 PP

                 HHH.HHHHHTTTTHHHHHHHHHTTT...S--SEEEEEEEHHHHH--TT-HHHHHHHHH CS
          KR 102 aed.leqvlapKvkGawnLhelled...esldffvlfSSiagllgsagqanYaaaNaf 155
                 +++ +++++   ++G+  + +++ +   +++  ++ +SS+ g++g + q++Y+ a + 
  EPA05280.1  95 SDEiWHNIIDTNLNGVYYMCKYSLPyikDNVGRIINISSVLGIMGVPDQSAYSVAKHA 152
                 66549****************998878899************************9876 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.0   7.6e-11     2e-07       1     120 [.       8     136 ..       8     172 .. 0.75
   2 ?   -3.5   0.0       2.2   5.6e+03      39      81 ..     187     227 ..     180     233 .. 0.63

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 7.6e-11
                 EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.EEEE--TT-HH....HHHHHHHHH.T-SEEEE--S.---HHHHHHSHHHHHH... CS
   Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl.elveldltdrs....alerlfkee.qpdavihlAa.vggvaassedpadfie... 89 
                 +l+tG++  iG+++v+++++k++ vi+ ++ ++   + ++ ++     +d+++++     +++++k++ ++d+ i+ Aa  g+ + + ++  ++++   
  EPA05280.1   8 VLITGGSRGIGKNMVDYFKDKNWIVITCASSTN---WLSESKAdFSFVCDIRKQNqiknGIKKIVKKYgKIDVLINNAAiSGNNPLNEQSSDEIWHnii 103
                 79********************88888888843...444444446678999999955556789999999**********88888888888877655222 PP

                 .HHTHHHHHHHHHHH...HHTCTEEEEEEEGGGGT CS
   Epimerase  90 .knlqgtlnlleaar...kagvkrllflsSsevYG 120
                  +nl+g++ +++++    k +v r++++sS  v G
  EPA05280.1 104 dTNLNGVYYMCKYSLpyiKDNVGRIINISS--VLG 136
                 27888888888888866566999******9..444 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.2
                 HCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S.---HHHHH CS
   Epimerase  39 rledlelveldltdrsalerlfkeeqpdavihlAa.vggvaass 81 
                 r++ l+l ++d+ +   l +++k   p ++  lA   ++++as+
  EPA05280.1 187 RIRSLSLNKIDIQNTIPLSKILK---PIEISALAFyLSSPEASN 227
                 45555777777777777777766...555666666566666665 PP

>> P3A  Poliovirus 3A protein like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.3     6e-05      0.15      32      52 ..      20      39 ..      17      41 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6e-05
                HHHHHHHHHT--TT-SSS--S CS
         P3A 32 EvrdYCekkgWivnitsevsi 52
                +++dY ++k+Wiv it   s+
  EPA05280.1 20 NMVDYFKDKNWIV-ITCASST 39
                578**********.9987665 PP

>> THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   3.9e-05       0.1      36      81 ..       5      48 ..       1      96 [. 0.74

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.9e-05
                   T-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTSCCHHHHHCCSS CS
  THF_DHG_CYH_C 36 gkkvvvvGrsnivgkplallLleknatVtvchsktkdlaeitread 81
                   ++ v++ G s+ +gk +   ++ kn +V +c s+t+ l+e   +ad
     EPA05280.1  5 NQIVLITGGSRGIGKNMVDYFKDKNWIVITCASSTNWLSES--KAD 48
                   5668899****************************999875..444 PP

>> DUF840  Lagovirus protein of unknown function (DUF840)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   1.1   0.00014      0.36      51     100 ..      25      74 ..       3      87 .. 0.81
   2 ?   -1.2   0.0      0.84   2.1e+03      91     108 ..     184     202 ..     178     207 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00014
      DUF840  51 nevknvivgnsfssnvrlsnmhndasvvnaynvynpasngirkkikslnn 100
                  + kn iv    ss   ls+ + d s v      n   ngi+k +k   +
  EPA05280.1  25 FKDKNWIVITCASSTNWLSESKADFSFVCDIRKQNQIKNGIKKIVKKYGK 74 
                 45699**************************************9997654 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.84
      DUF840  91 irkkiksln.nsvkiyntt 108
                 ++k+i+sl  n + i nt 
  EPA05280.1 184 MQKRIRSLSlNKIDIQNTI 202
                 6899999965889999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       729  (0.0406604); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1476.74
//
Query:       EPA05281.1  [L=283]
Description: NAD-binding protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-11   44.4   0.0      1e-10   41.5   0.0    2.0  1  Epimerase        NAD dependent epimerase/dehydratase family
    4.5e-10   39.7   0.0    6.5e-10   39.2   0.0    1.3  1  NAD_binding_10   NAD(P)H-binding
    1.6e-07   31.1   1.4    5.3e-07   29.4   1.4    1.7  1  NmrA             NmrA-like family
      2e-07   30.3   0.2    0.00014   20.9   0.3    2.3  2  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    2.1e-05   23.8   0.4       0.22   10.7   0.0    2.8  3  NAD_binding_4    Male sterility protein
    0.00032   19.9   0.0      0.017   14.3   0.0    2.2  2  RmlD_sub_bind    RmlD substrate binding domain
  ------ inclusion threshold ------
      0.035   13.5   0.0      0.055   12.9   0.0    1.2  1  AP_endonuc_2     Xylose isomerase-like TIM barrel
      0.041   13.0   0.2       0.62    9.1   0.2    2.2  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
        0.5   10.4   2.4       0.57   10.2   0.2    2.2  3  Shikimate_DH     Shikimate / quinate 5-dehydrogenase


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5   0.0   5.1e-14     1e-10       1     232 [.       7     198 ..       7     208 .. 0.80

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 5.1e-14
                 EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC...EEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHHHSHHHHHHHHTHHHH CS
   Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl...elveldltdrsalerlfkeeqpdavihlAavggvaassedpadfieknlqgtl 96 
                 i +tG +G++ ++l k + +k++ v++++r +  ++ ++++++   ++ +ld++         + +++++ ihl  +++  +++++    ++++++ t 
  EPA05281.1   7 IAITGSNGYVARHLRKFFSSKKIAVLAISRTNF-QKYKLEKKVitpKFSKLDIL--------PELKKCNILIHL--ISTTTQTVNK--NHFDSTVESTK 92 
                 689***************************944.44444443235555555554........44458*******..8888887776..6689******* PP

                 HHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHT CS
   Epimerase  97 nlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklveayaaqyglnaiilrlfnlyGprngegevsrvipalirkile 195
                 +++e ++ +++k+++++s     G+++             +++s Y ++K+++e+ +       g+ ++i+r++ + G     +  s+ +    ++i++
  EPA05281.1  93 KIIELCKICNIKKIIYISG---LGASK-------------NTTSGYFISKYLAEQEIIHS----GICYTIFRPSDILGYD---DYLSKNLK---KQIKS 165
                 ******************9...55333.............4579***********99975....9**************9...33444433...55555 PP

                 TSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT- CS
   Epimerase 196 gkqevtllgdgtalRdflyveDvaeaillvlehvdag 232
                    ++++ g+g+ + + ++v+Dv ++i  +l +   +
  EPA05281.1 166 D--KIIIPGSGKYVFQPIFVDDVSKIIFDALSKK--K 198
                 5..6***********************9999992..2 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   0.0   3.3e-13   6.5e-10       1     146 [.      11     148 ..      11     196 .. 0.82

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 3.3e-13
                     TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC.......HHHH..HHHHHHHHH CS
  NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggk.......deeg..aknivdaak 86 
                     G +G v+r+l k   ++ +++v a+ R+  +  +le+    +v++  + ++ d+   lk +++ +  ++++ +       d+++  +k+i++ +k
      EPA05281.1  11 GSNGYVARHLRKFFSSK-KIAVLAISRTNFQKYKLEK----KVITPKF-SKLDILPELKKCNILIHLISTTTQtvnknhfDSTVesTKKIIELCK 99 
                     89**********99999.5********9877776864....4555555.46789999*****988888665554544555333377********* PP

                     HCT--EEEEEEETTTTSGCGCHHHHHHHHCCHHHHHHHHHHHHHHHHSSSEEEEEEE-CE CS
  NAD_binding_10  87 eagvkRfvlvsaigvgdevpgefgewnkellkaylaakraaeellrasgldwTivrpggL 146
                       ++k+++++s++g+ +           ++ + y++ k+ ae+++ +sg+ +Ti rp+ +
      EPA05281.1 100 ICNIKKIIYISGLGASK-----------NTTSGYFISKYLAEQEIIHSGICYTIFRPSDI 148
                     ***************94...........45689************************865 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   1.4   2.7e-10   5.3e-07       1     224 [.       7     224 ..       7     231 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 2.7e-10
                 EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S.......-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEEEE---GGS-HHHHHHHHHHHHHHH CS
        NmrA   1 IlviGaTGrqGksvvrallkaghkvralvRdt.......kselakslkeaGvelvkgdlddkeslvealkgvdvvfsvtgfyskeiedgkklvdAakea 92 
                 I+++G+ G+ ++++ +++ +++  v a+ R         k+    ++++     +  +l+  ++l +++++      + + ++  +e  kk+++  k  
  EPA05281.1   7 IAITGSNGYVARHLRKFFSSKKIAVLAISRTNfqkykleKKVITPKFSKLD---ILPELKKCNILIHLISTTTQTV-NKNHFDSTVESTKKIIELCKIC 101
                 899999999999999999999999999999988866654444445555543...4678888888888888765443.4444599*************** PP

                 S-SEEEEEE---GG.GT.SSS---TTTHHHHHHHHHHHHCTS-EEEEEE-...EEGGG-BSSS-SS-BEEE-TTS.-EEEEESS-TTS-EE-HHHHHHH CS
        NmrA  93 GvkhfiySslgddndrsnaeepavphfdsKaeieeyvralgipytfvyag...ffmenflsllaqlkvgdtappedkvtllgpgnpkavlldaeeDiGa 188
                  +k++iy s   +++++         f sK+  e+ +  +gi yt++++     +  +++++l++      + + dk++++g g+    + + ++D+ +
  EPA05281.1 102 NIKKIIYISGLGASKNT-----TSGYFISKYLAEQEIIHSGICYTIFRPSdilGYDDYLSKNLKK------QIKSDKIIIPGSGKYVFQP-IFVDDVSK 188
                 *******7777777677.....5778**********************98333466666665555......6666788888888854444.59****** PP

                 HHHHHHHHHHHHTTEEEEE-S.EEE-HHHHHHHHHHH CS
        NmrA 189 fvikilkdprklkgkriklag.ntlsgneivelfekk 224
                 ++  +l++ +k+++k+i+l g +t+++++ v+lf k+
  EPA05281.1 189 IIFDALSK-KKYNNKIISLVGpETITFEKYVTLFLKN 224
                 ****9975.789999999886599*********9886 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.3   7.3e-08   0.00014       2     120 ..       9     115 ..       8     126 .. 0.64
   2 !    7.4   0.0   0.00095       1.9     150     233 ..     126     198 ..     114     212 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 7.3e-08
   3Beta_HSD   2 vtGgaGFlGralvkeLvrleelkevrvlDlrespellee.lskvnvkkviegDvtdkdkleealegvdvvihlaslvdvagkltedeimkvnvkGTrnv 99 
                 +tG+ G++ r+l +++++ ++   + vl +   +  + +  +kv + k+ + D++        l++ +++ihl  ++  +++++++   +  v+ T+++
  EPA05281.1   9 ITGSNGYVARHL-RKFFSSKK---IAVLAISRTNFQKYKlEKKVITPKFSKLDIL------PELKKCNILIHL--ISTTTQTVNKN-HFDSTVESTKKI 94 
                 788888888887.56666664...5555544433332220223333335555554......346677888888..44455544555.66789******* PP

   3Beta_HSD 100 leacvkagvrvlvYtSsaevv 120
                 +e c+ +++++++Y S +++ 
  EPA05281.1  95 IELCKICNIKKIIYISGLGAS 115
                 ****************98765 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00095
   3Beta_HSD 150 KalaEklvlkaNgrtlknggrlyTcaLRpagiyGegdkllvpllkqlaklglalfkigdeevlsdrvYvgNvawahilAaralq 233
                 K laE+ ++++          ++    Rp+ i G +d+ l++ lk+ +k+  +++  g+ + ++++++v+ v++++  A  + +
  EPA05281.1 126 KYLAEQEIIHSG---------ICYTIFRPSDILG-YDDYLSKNLKKQIKSD-KIIIPGSGKYVFQPIFVDDVSKIIFDALSKKK 198
                 555555555442.........344458*******.5677788888888888.788999***************99877766555 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.43   8.6e+02       1      16 [.       9      23 ..       9      48 .. 0.72
   2 !   10.7   0.2   0.00011      0.22      86     136 ..      63     111 ..      53     119 .. 0.81
   3 !   10.7   0.0   0.00011      0.22     169     208 ..     115     150 ..     111     179 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.43
                   EE-TTSHHHHHHHHHH CS
  NAD_binding_4  1 lTGaTGFLGkvLlekL 16
                   +TG+ G+++++L +k 
     EPA05281.1  9 ITGSNGYVARHL-RKF 23
                   89******9997.444 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00011
                    HH--EEEE--SS-S.STTSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEE CS
  NAD_binding_4  86 eevdviihsaAtvnfdepykellrvNveGtrevlelakklkklkvllhvST 136
                    +++++ ih   t++ +   k+ ++  ve+t++++el+k ++ +  ++++S 
     EPA05281.1  63 KKCNILIHLISTTTQT-VNKNHFDSTVESTKKIIELCKICNIK-KIIYISG 111
                    7888999998887744.457788999************99998.9999996 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00011
                    TTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE- CS
  NAD_binding_4 169 lkglpntYeqsKalaEklvrearrrsglpvvivRpsiitg 208
                    +k+ + +Y  sK+laE+ + +     g+  +i+Rps i+g
     EPA05281.1 115 SKNTTSGYFISKYLAEQEIIHS----GICYTIFRPSDILG 150
                    567889**********988654....5899******9988 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   8.3e-06     0.017       2      39 ..       6      43 ..       5     111 .. 0.77
   2 ?    3.7   0.0     0.014        27     124     202 ..     121     199 ..     114     236 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.3e-06
                   EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TTT--TTS CS
  RmlD_sub_bind  2 kilvtGanGqlGseLakqlaeeglevlaltreeldltd 39
                   +i +tG+nG ++++L+k +++++++vla++r++++  +
     EPA05281.1  6 NIAITGSNGYVARHLRKFFSSKKIAVLAISRTNFQKYK 43
                   689**************************999665443 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.014
                    HHHHHHHHHHHHHHHH-SSEEEEEE-SEESSSSS-HHHHHHHHHHH-SEEEE..ESS-EE--EEHHHHHHHHHHHHHHCHH CS
  RmlD_sub_bind 124 vYGrtKlaGEqavlaagkkalivRtswvygekgknfvktmlrlakereelkv..vaDqlgsPTsardlAevllqllekaae 202
                     Y  +K++ Eq + ++g  ++i+R s ++g    +++++ l+++ +++++ +      + +P  ++d++++++++l+k++ 
     EPA05281.1 121 GYFISKYLAEQEIIHSGICYTIFRPSDILGY--DDYLSKNLKKQIKSDKIIIpgSGKYVFQPIFVDDVSKIIFDALSKKKY 199
                    57779***********************998..566666666666666655521234456677777777777777766654 PP

>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.8e-05     0.055      36      92 ..      61     111 ..      52     136 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.8e-05
                   HHHHTTSEEEEEEECCCHSTCTHCHTTCSHHHHHHHHHHHHHHHHHHTBSEEEEEBC CS
  AP_endonuc_2  36 aldelglriaslslftrfgypdederearreesvdalkraielaaaLGapllvlhpG 92 
                    l++ ++ i+++s++t+  +   ++ ++     v+ +k+ iel++ ++++ ++  +G
    EPA05281.1  61 ELKKCNILIHLISTTTQTVN--KNHFDST----VESTKKIIELCKICNIKKIIYISG 111
                   67788888999999999988..5679999....********************9999 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.2   0.00031      0.62     101     150 ..      84     134 ..       7     141 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00031
                      HHHHHHHHHHHHHHHHHTT-SEEEEEEEGGGS.S--SHHHHHHHHHHHHHH CS
  Polysacc_synt_2 101 iktNvlgtenvieaaieagvkkvvliStDKAv.nPtnvmGatKrlaekllq 150
                      ++  v +t+++ie ++ +++kk+++iS   A  n t+ + ++K lae+ ++
       EPA05281.1  84 FDSTVESTKKIIELCKICNIKKIIYISGLGASkNTTSGYFISKYLAEQEII 134
                      4566899********************988872567789999999998765 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.2   0.00028      0.57      20     103 ..      13      92 ..       3     104 .. 0.82
   2 ?   -2.7   0.0       2.8   5.6e+03       5      22 ..     158     175 ..     155     177 .. 0.73
   3 ?   -2.0   0.1       1.7   3.4e+03     124     136 ..     243     255 ..     225     257 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00028
                   -SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSSSS-SB-HHHHHCCHHH.S CS
  Shikimate_DH  20 aGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisataseepilekeeveealkkrk 103
                   +G +a+ + k +++k++  v+ + Rt  +  +l +++ +   ++ kl+ l   l++++++i  +++++  ++k+++ ++++++k
    EPA05281.1  13 NGYVARHLRKFFSSKKIA-VLAISRTNFQKYKLEKKVITP--KFSKLDILP-ELKKCNILIHLISTTTQTVNKNHFDSTVESTK 92 
                   578888888888888888.8888999999999*9999555..677887776.799*********************99997754 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.8
                   HHHS..TT-EEEEES-SH CS
  Shikimate_DH   5 kkleslkekkvlliGaGe 22 
                   +  +++k+ k+++ G G+
    EPA05281.1 158 NLKKQIKSDKIIIPGSGK 175
                   444578889999999987 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.7
                   STTCCCEEHHHHH CS
  Shikimate_DH 124 ledvrlytvDdLk 136
                   ++d+ ly vDdL+
    EPA05281.1 243 HNDNVLYGVDDLN 255
                   4678899999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       778  (0.0433934); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 1885.97
//
Query:       EPA05282.1  [L=250]
Description: methionine adenosyltransferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.4e-70  233.5   0.1    7.8e-69  230.0   0.0    2.0  2  S-AdoMet_synt_C  S-adenosylmethionine synthetase, C-terminal 
    4.7e-34  117.2   0.4    8.3e-34  116.4   0.4    1.4  1  S-AdoMet_synt_M  S-adenosylmethionine synthetase, central dom


Domain annotation for each model (and alignments):
>> S-AdoMet_synt_C  S-adenosylmethionine synthetase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1     0.029   2.6e+02      67     101 ..      35      73 ..      18      88 .. 0.66
   2 !  230.0   0.0   8.7e-73   7.8e-69       1     138 []      98     237 ..      98     237 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.029
                      EEE-TT-SS-S...EEEEEE-S-BSS-HHHHHH.HHHHH CS
  S-AdoMet_synt_C  67 lsYaigvaepv...sisvetfgtekvseeeiae.ivkev 101
                      +s     ++p+   +i ++t++  ++s+e+ia+ i+++v
       EPA05282.1  35 VSVRYENNKPIkieTIVISTQHAPEISQEQIAKeIIEKV 73 
                      444455667772224556666666778888875144555 PP

  == domain 2  score: 230.0 bits;  conditional E-value: 8.7e-73
                      S-TTTTS-EETTS-TTTTTTTTSS---S---TTB-TTSHHHHHHHHHHHHHHHHHHTTSBSEEEEEEEE-TT-SS-SEEEEEE-S-BSS-HHHH CS
  S-AdoMet_synt_C   1 iGgpkgdaGltgrkiivdtYgglaahgggafsgKdptkvDrsaayaaryvaknlvaaglakkvevqlsYaigvaepvsisvetfgtekvseeei 94 
                      iGgp+gd+Gltgrkiivd+Ygg+++hgggafsgKdp+kvDrsa+y++ry+akn+vaagla+++evq++Yaigvaepvs++v+tfg++k++e+ei
       EPA05282.1  98 IGGPHGDTGLTGRKIIVDSYGGFGRHGGGAFSGKDPSKVDRSACYMCRYIAKNIVAAGLAERCEVQVAYAIGVAEPVSLYVNTFGSSKIPEREI 191
                      8********************************************************************************************* PP

                      HHHHHHH----HHHHHHHHTTTSS--TGGGSS-SSS--..T-TTS. CS
  S-AdoMet_synt_C  95 aeivkevfdlrpaaiieeldLkkpiykktaayghfgre..elpwek 138
                      +e+v+++f+++p++ii++ldLk+piy+kt+a+ghfgr+  e++wek
       EPA05282.1 192 EELVRKNFNMKPSGIISQLDLKRPIYRKTSANGHFGRNepEFTWEK 237
                      *************************************98899**97 PP

>> S-AdoMet_synt_M  S-adenosylmethionine synthetase, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.4   0.4   9.3e-38   8.3e-34      22     120 .]       1      96 [.       1      96 [. 0.96

  Alignments for each domain:
  == domain 1  score: 116.4 bits;  conditional E-value: 9.3e-38
  S-AdoMet_synt_M  22 mPlpillahklaerlaelrkegeleylrpDaKsqvtveYeeelkpvrvdtvvistqhdeevsqeklredlkekvikkvlkeelldekktkllin 115
                      mP+pillahkl+++lae+rk++ l+++rpD+Ksqv+v+Y e++kp++++t+vistqh++e+sqe+++++++ekvik+vl  +l ++ ++k++in
       EPA05282.1   1 MPMPILLAHKLTQKLAEVRKNKVLPWVRPDGKSQVSVRY-ENNKPIKIETIVISTQHAPEISQEQIAKEIIEKVIKPVL-GNLWND-QIKIHIN 91 
                      9**************************************.599************************************.666666.6****** PP

  S-AdoMet_synt_M 116 ptGkF 120
                      ptGkF
       EPA05282.1  92 PTGKF 96 
                      ****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1531.55
//
Query:       EPA05283.1  [L=246]
Description: oxidoreductase, short chain dehydrogenase/reductase family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.5e-54  182.6   0.1      1e-52  179.1   0.1    2.0  1  adh_short_C2   Enoyl-(Acyl carrier protein) reductase
    1.9e-44  151.5   3.6    8.3e-40  136.3   0.3    2.1  2  adh_short      short chain dehydrogenase
    0.00034   20.2   0.3     0.0013   18.2   0.3    1.8  1  Epimerase      NAD dependent epimerase/dehydratase family
     0.0084   16.0   0.0      0.016   15.1   0.0    1.4  2  KR             KR domain
  ------ inclusion threshold ------
      0.021   13.9   0.0       0.03   13.4   0.0    1.2  1  RmlD_sub_bind  RmlD substrate binding domain
       0.13   12.9   0.4       0.49   11.1   0.0    2.1  3  NAD_binding_3  Homoserine dehydrogenase, NAD binding domain


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.1   0.1   3.4e-56     1e-52      31     234 .]      26     244 ..      15     244 .. 0.89

  Alignments for each domain:
  == domain 1  score: 179.1 bits;  conditional E-value: 3.4e-56
                   HHHHHHHHHHTTSEE.....EE--TTSHHHHHHHHHHHHHHHSSEEEEEE-----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC.. CS
  adh_short_C2  31 kkrveelaeelgaev.....lecDVtdeeqvealveevvekfgklDilvnnagiapklkgpfletsreefdraldvnlyslfllakaalplmkeg.. 120
                    k+++el e+lga+v      e++ ++ + +++ +++vv++fg++Dil+nnagi++   g+++ets e+++++l +n+++ fll+k ++p+mk++  
    EPA05283.1  26 GKATKELLENLGAKVvgfdlPEINLKNLDLINSHIQNVVSEFGTIDILINNAGITTI--GDIVETSLEDIEDVLTINFKAPFLLMKSVIPIMKKNkg 120
                   67899999999999546666788999*******************************..*******************************9998888 PP

                   CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHHHHHHGGGTEEEEEEEE--BHCTGGGGSTT..........HHHHHHHHHHHSTTSS-B-HHHH CS
  adh_short_C2 121 gsivnlssvgaervvpnynaygaaKaalealtrylAvelgpkgiRvNavspgpikTlaasgikg..........fdelleelearaplgrlgtpeev 207
                   gsivn++s +  ++ ++ ++yga+Kaal +lt+++A ++ +++iR+Nav+pg+++T++ +++ +            + +   + ++plgrl+ p+ev
    EPA05283.1 121 GSIVNTTSDQVFVGKKHCAIYGASKAALAQLTKSAAIDWSEYNIRINAVAPGATDTPMLKNVFKkintlypklfPTDNETFYKTSIPLGRLALPNEV 217
                   **********************************************************87765445556544533346777899************* PP

                   HHHHHHHCSGGGTT--SEEEEESTTGG CS
  adh_short_C2 208 aeaalfLasdeasyitGqtlvvDgGlt 234
                   a +++fLasd+as+++G+++ vDgG+t
    EPA05283.1 218 AWMIAFLASDAASFVNGTIVSVDGGFT 244
                   *************************98 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.2   1.1e-06    0.0032       1      32 [.      14      45 ..      14      54 .. 0.88
   2 !  136.3   0.3   2.8e-43   8.3e-40      59     193 ..      51     185 ..      45     187 .. 0.95

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.1e-06
                SEEEEESTTSHHHHHHHHHHHHTT-EEEEEES CS
   adh_short  1 kvvlvtGassGIGraiakelakeGakvvvvdr 32
                k+++vtG  sGIG+a+ + l + Gakvv +d 
  EPA05283.1 14 KIAIVTGHKSGIGKATKELLENLGAKVVGFDL 45
                79*************************98776 PP

  == domain 2  score: 136.3 bits;  conditional E-value: 2.8e-43
                 TSHHHHHHHHHHHHHHHSSESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHH CS
   adh_short  59 tdreevealvekavkklgkldvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaava 157
                 ++ + ++  ++++v+++g++d+L+nNAGit  g++ e+s e++e+v+ +N++++fll+++v+p m+k+++G+Ivn++S + +v+ ++ a Y+AsKaa+a
  EPA05283.1  51 KNLDLINSHIQNVVSEFGTIDILINNAGITTIGDIVETSLEDIEDVLTINFKAPFLLMKSVIPIMKKNKGGSIVNTTSDQVFVGKKHCAIYGASKAALA 149
                 56666788899**************************************************************************************** PP

                 HHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHHCTH CS
   adh_short 158 gltrslakelaptgirvnavaPGlvdTdmakelrek 193
                 +lt+s+a ++++++ir+navaPG++dT+m k++ +k
  EPA05283.1 150 QLTKSAAIDWSEYNIRINAVAPGATDTPMLKNVFKK 185
                 *******************************99876 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.3   4.4e-07    0.0013       2     119 ..      17     132 ..      16     177 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 4.4e-07
                 EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHH.T-SEEEE--S---HHH....HHHSHHHHHHHHTHH. CS
   Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkee.qpdavihlAavggvaa....ssedpadfieknlqg. 94 
                 +VtG++  iG+a+ + l++ g +v+g+d            +++l +ldl ++  ++++++e+  +d+ i+ A++ ++++    s ed +d++ +n++  
  EPA05283.1  17 IVTGHKSGIGKATKELLENLGAKVVGFDLP----------EINLKNLDLINSH-IQNVVSEFgTIDILINNAGITTIGDivetSLEDIEDVLTINFKAp 104
                 8***************************99..........5577799999866.888899888**********99987611115555566666665441 PP

                 ...HHHHHHHHHHHTCTEEEEEEEGGGG CS
   Epimerase  95 ...tlnlleaarkagvkrllflsSsevY 119
                    +  ++  ++k++   +++  S++v+
  EPA05283.1 105 fllMKSVIPIMKKNKGGSIVNTTSDQVF 132
                 1113334444445544466666665555 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   5.5e-06     0.016      29     159 ..      17     151 ..      10     159 .. 0.85
   2 ?   -0.3   0.0      0.29   8.7e+02      24      79 ..     134     190 ..     120     193 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.5e-06
                 EEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT.. CS
          KR  29 vllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled.. 125
                 ++++ ++   ++ k+l+++l a+ +  ++ ++ + + d +++ ++++ +e+++i   i+ Ag++  + + e++ ed+e vl   +k+   L + + +  
  EPA05283.1  17 IVTGHKSGIGKATKELLENLGAKVVGFDLPEINLKNLDLINSHIQNVVSEFGTIDILINNAGITTIGDIVETSLEDIEDVLTINFKAPFLLMKSVIPim 115
                 55666777788889999****************************************************************999999988887544333 PP

                 ..S--SEEEEEEEHHHHH--TT-HHHHHHHHHHHHH CS
          KR 126 ..esldffvlfSSiagllgsagqanYaaaNaflDal 159
                   ++   +v ++S   ++g+++ a Y a  a l +l
  EPA05283.1 116 kkNKGGSIVNTTSDQVFVGKKHCAIYGASKAALAQL 151
                 337888888899999999999999888888777666 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.29
                 HS-EEEEE-SS...--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHS CS
          KR  24 garhlvllsRsa.aadedskaliaelealgaevevvaaDvsdkdavealleeikaee 79 
                 g++h ++ + s+ a  +  k+    ++++++++++va   +d   +++++++i++  
  EPA05283.1 134 GKKHCAIYGASKaALAQLTKSAAIDWSEYNIRINAVAPGATDTPMLKNVFKKINTLY 190
                 555555555554122222333444577778888888888888888888888887655 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0     1e-05      0.03       4     112 ..      17     139 ..      14     156 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1e-05
                    EEESTTSHHHHHHHHHCTTTSEEEEEE-TTT--TTSHHHHHHHHHHH.....--SEEEE------H.HHHHHS...HHHHHHHHTHHHHHHHHHH. CS
  RmlD_sub_bind   4 lvtGanGqlGseLakqlaeeglevlaltreeldltdaeavaellkea.....kpdvvvnaAAytav.DkaEse...eeaayavnaeavealAeaa. 89 
                    +vtG +  +G++ +++l++ g++v++++ +e++l++ + +++ ++++       d+++n A  t + D +E+     e    +n +a+  l +   
     EPA05283.1  17 IVTGHKSGIGKATKELLENLGAKVVGFDLPEINLKNLDLINSHIQNVvsefgTIDILINNAGITTIgDIVETSledIEDVLTINFKAPFLLMKSVi 112
                    69********************************9998887777554111124568888777666548899764225667899****987776532 PP

                    ....HHCT-EEEEEEEGGGS-S-TTS- CS
  RmlD_sub_bind  90 ....aavgalLihvStDyVFdGekkrp 112
                        ++ g  ++   +D VF G+k+ +
     EPA05283.1 113 pimkKNKGGSIVNTTSDQVFVGKKHCA 139
                    33338899**************98765 PP

>> NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.8   5.3e+03      80     106 ..      11      35 ..       6      46 .. 0.71
   2 ?   11.1   0.0   0.00016      0.49      49      93 ..      58     103 ..      44     110 .. 0.87
   3 ?   -2.4   0.0       2.5   7.4e+03      87      99 ..     141     153 ..     134     157 .. 0.62

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.8
                    HHTTEEEE-S--CGGG-HHHHHHHTSS CS
  NAD_binding_3  80 LkagkdvvtankgaladealyeeLrea 106
                    L++++ +vt  k+ +   + ++eL+e+
     EPA05283.1  11 LNNKIAIVTGHKSGIG--KATKELLEN 35 
                    7888888888887777..555565554 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00016
                    --HHHHHHHH.S-EEEEE-S--HHHHTTHHHHHHTTEEEE-S--CG CS
  NAD_binding_3  49 ldlddliahl.dpdvvVEcasseavaelvlkaLkagkdvvtankga 93 
                    + +++++++   +d+++ +a+ + + ++v+  L+   dv+t n +a
     EPA05283.1  58 SHIQNVVSEFgTIDILINNAGITTIGDIVETSLEDIEDVLTINFKA 103
                    566777776656*******************************988 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 2.5
                    E-S--CGGG-HHH CS
  NAD_binding_3  87 vtankgaladeal 99 
                      a+k+ala +++
     EPA05283.1 141 YGASKAALAQLTK 153
                    4478899885554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.89
# Mc/sec: 838.30
//
Query:       EPA05284.1  [L=274]
Description: glycosyltransferase, group 2 family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-19   69.6   0.4      4e-19   69.1   0.4    1.3  1  Glycos_transf_2  Glycosyl transferase family 2
    4.2e-06   26.8   0.0    5.3e-06   26.5   0.0    1.1  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    4.7e-05   23.0   0.4    4.7e-05   23.0   0.4    1.8  2  Glyco_tranf_2_2  Glycosyltransferase like family 2


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.1   0.4   6.7e-23     4e-19       1     133 [.       5     139 ..       5     165 .. 0.83

  Alignments for each domain:
  == domain 1  score: 69.1 bits;  conditional E-value: 6.7e-23
                      EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--SSEEEEEESSEEE-T CS
  Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatgdyilflDaDdepdp 94 
                      ++++p+   e  +++++ s+l+q  y+++e+i++ D    +  +il++    d+r++++  ++  G ++a+n g++ a+g++i++lDaDde+d 
       EPA05284.1   5 TIIMPANKAETFIERSVQSILNQ-SYKNWELIIIYDDNV-DYFSILKNQGITDERIKFVSTNK-LGISTARNIGIEIASGNIIAILDADDEFDS 95 
                      699***999**************.******988866664.66799999999**********95.5***************************** PP

                      THHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SS.....E CS
  Glycos_transf_2  95 dwleklvealekdgadvvlgqrprifgetdeiernkrv.....g 133
                      ++l+  v   +k+     +  ++  +g++ ++  nk+      +
       EPA05284.1  96 EKLKCCVPLTQKNYLVSCALEIRDVNGNNLKYVGNKEQgilqsS 139
                      ************88877788888888888888888764444431 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   8.9e-10   5.3e-06       4     112 ..       4     105 ..       3     171 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 8.9e-10
  Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnealravksdlvllvDdD 97 
                      ++++ p+ ++e+ +++ + s+l+q+y + e++++ d + +   + ++   +   d+r++ v + + lg+ +++r  n +++++++ +++++D+D
       EPA05284.1   4 VTIIMPANKAETFIERSVQSILNQSYKNWELIIIYDDNVDY-FSILKN--QGITDERIKFVSTNK-LGI-STAR--NIGIEIASGNIIAILDAD 90 
                      68999*****************************9988887.555665..466788***997755.887.5555..8***************** PP

  Glyco_tranf_2_3  98 tvvePdtlkrllqff 112
                      +  + + lk  +++ 
       EPA05284.1  91 DEFDSEKLKCCVPLT 105
                      ****99999988886 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.4   7.8e-09   4.7e-05       3     107 ..       5     106 ..       3     127 .. 0.80
   2 ?   -1.5   0.2      0.24   1.4e+03     181     203 ..     163     183 ..     144     216 .. 0.69

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 7.8e-09
  Glyco_tranf_2_2   3 viplraseerhyieervlqkakyydeeielivvddgSsekfleevss..iidlnllvylkdeddkayslaaarNrGaskaesdlvlFlDaDcfi 94 
                       i + a++ + +ie  v  + ++  ++ eli++ d   +   + +++  i d + +     +  +  + + arN G++ a ++++  lDaD+ +
       EPA05284.1   5 TIIMPANKAETFIERSVQSILNQSYKNWELIIIYDDNVDY-FSILKNqgITDERIKFV--ST--NKLGISTARNIGIEIASGNIIAILDADDEF 93 
                      456667777789*****777776669*******9999988.67888733555555543..33..3589999*********************99 PP

  Glyco_tranf_2_2  95 ssDkfekilklit 107
                       s+k++  + l +
       EPA05284.1  94 DSEKLKCCVPLTQ 106
                      9999988777655 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.24
  Glyco_tranf_2_2 181 yDErfrGhgaEDfdlllRlakai 203
                      yDE++     ED +++l     i
       EPA05284.1 163 YDEKL--SCMEDLEFMLNCFEII 183
                      67777..7777777776554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2025.71
//
Query:       EPA05285.1  [L=91]
Description: hypothetical protein BG20_I0127 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.1   12.9   2.2        1.8    8.9   0.2    2.1  2  PRD       PRD domain


Domain annotation for each model (and alignments):
>> PRD  PRD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1    0.0016        29      49      73 ..      27      51 ..       6      54 .. 0.70
   2 ?    8.9   0.2    0.0001       1.8      43      75 ..      52      83 ..      48      86 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0016
                HHHHTHHHHHHHHHHHHHHHHHHTS CS
         PRD 49 ikekypkefeiakeileeleeeldi 73
                +  +y++  ++a+ei++ l+  + +
  EPA05285.1 27 LTLDYKEDLNLAREIFSRLKIDFSV 51
                4446888999999999999987655 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0001
                HHHHHHHHHHTHHHHHHHHHHHHHHHHHHTST- CS
         PRD 43 nplleeikekypkefeiakeileeleeeldiel 75
                n+ll+ ++++ pk+ ei++ ++e+++ +++ ++
  EPA05285.1 52 NELLDLFEKN-PKLLEITEPLIEKWNTNYNKNI 83
                7888888875.*******************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 672.75
//
Query:       EPA05286.1  [L=332]
Description: NAD dependent epimerase/dehydratase family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-11   43.0   0.0    4.8e-11   42.6   0.0    1.2  1  Epimerase        NAD dependent epimerase/dehydratase family
    6.5e-10   38.5   0.0    9.7e-10   37.9   0.0    1.3  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    4.7e-07   29.2   0.1    0.00091   18.4   0.0    2.1  2  Polysacc_synt_2  Polysaccharide biosynthesis protein
    0.00013   21.2   0.0    0.00071   18.8   0.0    1.9  2  NAD_binding_4    Male sterility protein
  ------ inclusion threshold ------
      0.031   14.9   0.0      0.085   13.4   0.0    1.8  1  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
       0.04   14.4   0.0      0.099   13.1   0.0    1.7  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
      0.058   12.6   0.0       0.13   11.5   0.0    1.7  2  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
      0.097   11.9   0.0       0.15   11.3   0.0    1.3  1  FAD_binding_3    FAD binding domain
       0.12   11.9   0.0       0.19   11.3   0.0    1.2  1  DAO              FAD dependent oxidoreductase
       0.13   12.5   0.0       0.32   11.2   0.0    1.7  1  NAD_binding_8    NAD(P)-binding Rossmann-like domain


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.6   0.0   2.7e-14   4.8e-11       6     215 ..      10     214 ..       6     248 .. 0.80

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 2.7e-14
                 TTSHHHHHHHHHHHHCT.SEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHHHSHHHHHHHHTHHHHHHHHHHH CS
   Epimerase   6 atGfiGsalvkallekg.yevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggvaassedpadfieknlqgtlnlleaar 103
                 ++Gf+G+ l++ l++   ++   + ++ss      + ++    +d+td ++l+++ +   p ++ih  a+  ++  +ed++  ++ n++gt+n++e ++
  EPA05286.1  10 GSGFVGTSLAHFLQNYFsVKTFDIVSQSSLL---TNSKIPHELIDITDFNSLQKIGN---PKVIIHS-AIIQIPKINEDKNLGYNVNVKGTQNICEIVS 101
                 47***********997654444444443333...3333455789**********977...*******.66777777888888899*************9 PP

                 HH.TCTEEEEEEEGGGGTSCSSSS.BSTCSTTS--...--SSHHHHHHHHHHHHHHHHHHHH.T-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTT CS
   Epimerase 104 ka.gvkrllflsSsevYGkdaeqp.keettltgpl...kpnspYaaaKlageklveayaaqy.glnaiilrlfnlyGprngegevsrvipalirkileg 196
                 ++  ++ +l +sS ++YG+++ +   +e++ + p       + Ya++K+  e l++ y ++  +  + +l++ ++ G++            +i+k+ +g
  EPA05286.1 102 QNsSIQGMLLISSWHTYGEQQLKGlLQENIGYRPDmveDRARLYALSKTIQECLIRFYDEKTpNKIFGALKIGTVLGEG---MPKGTAANLFIEKAISG 197
                 987899************99996458999999999999999*********************9999999**********...33555666789999999 PP

                 SSSEEEETTST-EEEEEEH CS
   Epimerase 197 kqevtllgdgtalRdflyv 215
                 + ++t ++  +  R+ ly+
  EPA05286.1 198 E-KLTPFKH-SMNRPMLYA 214
                 9.8888864.444666654 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.0   5.4e-13   9.7e-10       5     158 ..      10     157 ..       6     193 .. 0.76

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 5.4e-13
   3Beta_HSD   5 gaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslvdvag.kltedeimkvnvkGTrnvlea 102
                 g+GF+G +l + L +      v+ +D++ +++l   l+++++      D+td ++l++   + +v+ih  +++++ + +  ++  ++vnvkGT+n+ e 
  EPA05286.1  10 GSGFVGTSLAHFLQNY---FSVKTFDIVSQSSL---LTNSKIP-HELIDITDFNSLQKI-GNPKVIIHS-AIIQIPKiNEDKNLGYNVNVKGTQNICEI 99 
                 89*******8876554...57********9999...5555655.4568********995.6789****9.566666537777888*************8 PP

   3Beta_HSD 103 cvk.agvrvlvYtSsaevvgpnslgeeilngdEeleyesl....hqdaypesKalaEklvl 158
                   + ++++ ++  Ss    g+ +l+  ++   E+  y +         y+ sK + E l+ 
  EPA05286.1 100 VSQnSSIQGMLLISSWHTYGEQQLKGLLQ---ENIGYRPDmvedRARLYALSKTIQECLIR 157
                 765268**************955555444...66555544223356689999999998886 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   5.1e-07   0.00091      55     128 ..      44     114 ..      23     125 .. 0.83
   2 !    8.8   0.0   0.00044      0.78     137     252 ..     144     271 ..     136     286 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 5.1e-07
                      E....E--TT-HHHHHHHTT..T-SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHH.HHHTT-SEEEEEEE CS
  Polysacc_synt_2  55 eivpvigdvrdkerlekaleelkvdvvfhaAAlKhVPlveenpleaiktNvlgtenviea.aieagvkkvvliSt 128
                      +i   + d++d ++l+k+ +   ++v++h+A + ++P ++e    + + Nv gt+n++e+ ++++ ++ ++liS+
       EPA05286.1  44 KIPHELIDITDFNSLQKIGN---PKVIIHSA-IIQIPKINEDKNLGYNVNVKGTQNICEIvSQNSSIQGMLLISS 114
                      3445699*********9998...******87.569***********************97256678999999996 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00044
                      HHHHHHHHHHHHHHHGGG--SSS--EEEEEEE-EETTG...TTSSHHHHHHHHHTTSSEEES-TT-EEEEE..-HHH...H....HHHHHHHHH CS
  Polysacc_synt_2 137 vmGatKrlaekllqalakeseekktkfvvvRfGNVlgS...rGSviplFkkqikeggpvtvTdpemtRyfm..tiee...a....vqLvlqala 218
                      ++ ++K ++e l+  +++++   ++ f + + G Vlg    +G    lF ++  +g+++t   ++m R ++  +i++   a    v+L+++  +
       EPA05286.1 144 LYALSKTIQECLIRFYDEKT--PNKIFGALKIGTVLGEgmpKGTAANLFIEKAISGEKLTPFKHSMNRPMLyaSITDickAtknfVNLIIEQKK 235
                      67899********9999998..7899**********954449**************************77633454411122222678888888 PP

                      H--SS-EEEE--...-EEEHHHHHHHH......... CS
  Polysacc_synt_2 219 lakggeifvldmG..epvkivdlakalielsgleek 252
                      +++++   v+++   +p++i+dla+ + + +++ ++
       EPA05286.1 236 TSNNSIEHVMNIAypHPISILDLAHIISNSVNKYTN 271
                      888876666666422789999999988666554333 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0     4e-07   0.00071      87     201 ..      63     168 ..      50     219 .. 0.78
   2 ?   -0.1   0.0      0.23   4.2e+02      96     153 ..     222     280 ..     215     310 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 4e-07
                    H--EEEE--SS-..S.STTSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEE..GGGTTS-TTT--SSS-H......HHH--EEEETTTCCCHHHH CS
  NAD_binding_4  87 evdviihsaAtv..nfdepykellrvNveGtrevlelakklkklkvllhvST..ayvngeregeveekvyeegekeekldederaklkglpntYeq 178
                    + +viihsa     +++e+ +  ++vNv+Gt++++e+ ++ ++ + +l +S+   y +++ +g ++e             +  ++  ++ ++ Y  
     EPA05286.1  63 NPKVIIHSAIIQipKINEDKNLGYNVNVKGTQNICEIVSQNSSIQGMLLISSwhTYGEQQLKGLLQE-----------NIGYRPDMVEDRARLYAL 147
                    556888887532226778888899****************************877777777777755...........578899999999999*** PP

                    HHHHHHHHHHHHHHHH---EEEE CS
  NAD_binding_4 179 sKalaEklvrearrrsglpvviv 201
                    sK + E l+r +   ++ p  i+
     EPA05286.1 148 SKTIQECLIRFYD--EKTPNKIF 168
                    *********9999..56776665 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.23
                    SS-S.STTSSEEHHHHHHHHHHHHHHHT..SSS--.-EEEEEEGGGTTS-TTT--SSS-H CS
  NAD_binding_4  96 AtvnfdepykellrvNveGtrevlelak..klkklkvllhvSTayvngeregeveekvye 153
                    At nf++ + e +++  +++++v+++a    ++ l  l h+ +  vn++ +g+++ +v  
     EPA05286.1 222 ATKNFVNLIIEQKKTSNNSIEHVMNIAYphPISIL-DLAHIISNSVNKYTNGKIKPEVSI 280
                    77788888888889999999999999984445556.556666666777777677666544 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   4.8e-05     0.085       2      38 ..       6      45 ..       5      72 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.8e-05
                EEEECSSHHHHHHHHHHHH.TTSEEEEEESSSSSS..TTS CS
   Pyr_redox  2 vvvvGgGyiglElAgalae.lgkkVtvversdkll..rll 38
                v+++G+G++g  lA +l++ +  k+  ++ ++ ll  +++
  EPA05286.1  6 VAIIGSGFVGTSLAHFLQNyFSVKTFDIVSQSSLLtnSKI 45
                89***************99566666544444444424444 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   5.5e-05     0.099       2      35 ..       6      38 ..       5      60 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.5e-05
                    EEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTT CS
  Semialdhyde_dh  2 vaivGatGyvGqellrlLeehpevelvvllsssr 35
                    vai+G +G vG+ l+  L++ ++v+   ++s+s+
      EPA05286.1  6 VAIIG-SGFVGTSLAHFLQNYFSVKTFDIVSQSS 38
                    9****.*******************999999886 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   7.3e-05      0.13       1      27 [.       4      31 ..       4     103 .. 0.79
   2 ?   -3.6   0.0       2.9   5.2e+03     163     189 ..     130     155 ..     127     160 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.3e-05
                 CSEEEE--SHHHHHHHHHHHH.HTS-EE CS
                 xxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
  Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaq.agakvt 27
                 +dv++iG+G+ G+++a++l++  ++k+ 
   EPA05286.1  4 YDVAIIGSGFVGTSLAHFLQNyFSVKTF 31
                 69*****************994355544 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2.9
                  HHT-EEEEEESSSSSSTTS-HHHHHHH CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Pyr_redox_2 163 klgkevtlveardrllraldkelsaal 189
                  ++g++  +ve+r rl+ al k ++++l
   EPA05286.1 130 NIGYRPDMVEDRARLY-ALSKTIQECL 155
                  6778888999999999.7777777776 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   8.4e-05      0.15       2      23 ..       4      25 ..       3      49 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.4e-05
                   EEEEEE--SHHHHHHHHHHHHT CS
  FAD_binding_3  2 tdVlIVGaGpaGlmlallLsea 23
                   +dV+I+G+G +G +la++L+++
     EPA05286.1  4 YDVAIIGSGFVGTSLAHFLQNY 25
                   79*****************987 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00011      0.19       1      19 [.       5      23 ..       5      34 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00011
                EEEEECTSHHHHHHHHHHH CS
         DAO  1 dvviiGGGiiGlstAyeLa 19
                dv+iiG+G +G s A++L+
  EPA05286.1  5 DVAIIGSGFVGTSLAHFLQ 23
                9****************95 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00018      0.32       1      27 [.       8      33 ..       8      47 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00018
                   EE--SHHHHHHHHHHHCCTEEEEEE-S CS
  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllek 27
                   I+G+G+ G ++A++L+++ f+v  ++ 
     EPA05286.1  8 IIGSGFVGTSLAHFLQNY-FSVKTFDI 33
                   9***************98.77777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       753  (0.041999); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2233.35
//
Query:       EPA05287.1  [L=194]
Description: putative phosphoheptose isomerase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.3e-28   97.5   0.3    9.1e-28   97.0   0.3    1.2  1  SIS_2     SIS domain
      8e-06   25.7   0.5    0.00033   20.5   0.0    2.5  2  SIS       SIS domain
  ------ inclusion threshold ------
      0.032   13.5   0.5      0.056   12.7   0.5    1.4  1  Vps54_N   Vacuolar-sorting protein 54, of GARP complex
      0.074   13.5   0.4       0.45   11.0   0.2    2.1  2  Tex_YqgF  Tex protein YqgF-like domain


Domain annotation for each model (and alignments):
>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.0   0.3     2e-31   9.1e-28      10     138 .]      21     148 ..      14     148 .. 0.94

  Alignments for each domain:
  == domain 1  score: 97.0 bits;  conditional E-value: 2e-31
                 HHHHHHHSHHHHHHHHHHHHHHHHTT--EEEEESGGGHHHHHHTSSSTT-BTTEEEE--GGGSSSSST..THHHHHTT-TTHHHHHHHHTT-..-TT-E CS
       SIS_2  10 lerivetqaeaiekaaeliadslenggkvlvfGsGhSaalaeelaaragglaeferialpalalhtdaeatkssalerdegyakqilrlvrl..kpgDv 106
                 +++  ++q ++iek +++i ++l+ng+k+++fG+G+Saa+a++++a+++g++++er  lpa+al++++  ++ +al++d  ++++++r+ ++  ++gDv
  EPA05287.1  21 IKNS-NSQIKEIEKSIKVIIECLKNGKKIVIFGNGGSAADAQHIVAEFIGRFKLERKCLPAIALTSNT--SILTALANDYSFDSIFSRQCEGlvEKGDV 116
                 5555.78999******************************************************9987..9******************88778***** PP

                 EEEE-SS--SHHHHHHHHHHHHHT-EEEEEE- CS
       SIS_2 107 LlviSnsGnnavvveaaeaakergmkviAlts 138
                  + iS+sGn+++v + + a k++g+ +i+l++
  EPA05287.1 117 VIGISTSGNSTNVKKGLVASKKIGALTIGLLG 148
                 *****************************986 PP

>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1     0.019        85       3      24 ..      43      64 ..      41      72 .. 0.82
   2 !   20.5   0.0   7.3e-08   0.00033      49     106 ..     109     166 ..      90     182 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.019
                CTSSEEEEEESHHHHHHHHHHH CS
         SIS  3 akakriyvlGaGtsyaiakela 24
                 + k+i+++G G s+a a+ + 
  EPA05287.1 43 KNGKKIVIFGNGGSAADAQHIV 64
                6679**********99888775 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 7.3e-08
                 GG-STTCEEEEEESSSHHHHHHHHHHHHHHTTSEEEEEESSTTSHHHHHSSEEEEEEE CS
         SIS  49 alideddlvilisfsgetkdlvaaaelakergakiiaITdskgsplareadlalyina 106
                 +l++++d+vi is+sg++ ++++ +   k+ ga +i++ +skg ++ + + + +++ +
  EPA05287.1 109 GLVEKGDVVIGISTSGNSTNVKKGLVASKKIGALTIGLLGSKGGTIGKICNISIIVKS 166
                 799*******************************************999965555544 PP

>> Vps54_N  Vacuolar-sorting protein 54, of GARP complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.5   1.2e-05     0.056      46      89 ..       5      48 ..       1      57 [. 0.92

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.2e-05
     Vps54_N 46 vvskklsqlilekreefvkelseveeiekelkesvvickngrra 89
                 +sk + + ile+++ +++  s+++eiek +k  +   kng++ 
  EPA05287.1  5 QISKSIEKSILESSKVIKNSNSQIKEIEKSIKVIIECLKNGKKI 48
                699********************************999999986 PP

>> Tex_YqgF  Tex protein YqgF-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.2    0.0001      0.45      29      84 ..      19      74 ..       5      96 .. 0.70
   2 ?    0.0   0.0      0.24   1.1e+03      23      51 ..     155     183 ..     151     189 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0001
                EEE--STTT--HHHHHHHHHHHHH..HTT--EEEEESSTTHHHHHHHHHHHHHHGGG- CS
    Tex_YqgF 29 aviyphepkkkveeakkklkklvk..kykveliaiGnGtasreteklvaelikeeelk 84
                +vi    ++++++e +k++k +++  k   +++  GnG ++ +++++vae+i + +l+
  EPA05287.1 19 KVIKN--SNSQIKEIEKSIKVIIEclKNGKKIVIFGNGGSAADAQHIVAEFIGRFKLE 74
                34443..3455555555555555422456789999****************9886554 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.24
                 S-EEEEEEE--STTT--HHHHHHHHHHHH CS
    Tex_YqgF  23 gkvletaviyphepkkkveeakkklkklv 51 
                 gk+++ ++i   +++ +++ea++++ +++
  EPA05287.1 155 GKICNISIIVKSSSTPRIQEAHRTIYHII 183
                 89999999999999999999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1208  (0.0673769); expected 358.6 (0.02)
Passed bias filter:                      788  (0.0439511); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 1529.48
//
Query:       EPA05288.1  [L=118]
Description: hypothetical protein BG20_I0158 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00093   18.7   0.0     0.0016   17.9   0.0    1.4  1  Epimerase      NAD dependent epimerase/dehydratase family
  ------ inclusion threshold ------
       0.11   11.9   0.0       0.14   11.5   0.0    1.2  1  GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.8e-07    0.0016     206     241 .]       6      40 ..       2      40 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.8e-07
                 ST-EEEEEEHHHHHHHHHHHHHHHTT-STTEEEEES CS
   Epimerase 206 gtalRdflyveDvaeaillvlehvdagdkgeiyniG 241
                 g  +R +++++Dva+++l+ +e+ ++  k+e yn+G
  EPA05288.1   6 GHFQRNYIHIQDVARVFLHGIENFEEM-KNESYNVG 40 
                 7889*******************9995.679****9 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   1.5e-05      0.14     253     331 ..      24     102 ..       2     103 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1.5e-05
                    EECHHCHHCCHHCCCHHHHHH.............TTGGCCCEECGG--SS--SB--B-THHHHHHH----SS-HHHHHHH CS
  GDP_Man_Dehyd 253 hsvrefvelaflelgktiewegk.geeevgrakesgkvvvevdpkyfrpgevdlllgdaskakeeLgWkpkvsfeelvre 331
                    h +++f e+++++    +   +  + e  +++ke+ ++ v ++ +  ++ + + ++  ++k++   g+kpk+s++ +++e
     EPA05288.1  24 HGIENFEEMKNESYNVGLSDANLsKLELCEKIKEHISDFVFIESNLGKDPDKRDYIVSNEKIE-STGFKPKYSIDFGIKE 102
                    44556666666555554443333033334567888899999999******************9.89*********99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 760.82
//
Query:       EPA05289.1  [L=58]
Description: hypothetical protein BG20_I0126 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1033  (0.0576162); expected 358.6 (0.02)
Passed bias filter:                      577  (0.0321825); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 381.60
//
Query:       EPA05290.1  [L=86]
Description: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-12   47.5   0.0    2.2e-12   47.2   0.0    1.0  1  Hydrolase_3    haloacid dehalogenase-like hydrolase
     0.0019   18.5   0.0     0.0025   18.1   0.0    1.2  1  Hydrolase      haloacid dehalogenase-like hydrolase
     0.0097   16.0   0.0      0.016   15.3   0.0    1.3  1  HAD_2          Haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.046   14.0   4.0       0.89    9.9   0.6    2.1  2  Gamma-thionin  Gamma-thionin family
       0.12   12.6   5.7          2    8.7   0.8    2.2  2  Toxin_3        Scorpion toxin-like domain


Domain annotation for each model (and alignments):
>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.2   0.0   6.2e-16   2.2e-12     188     253 ..       5      70 ..       3      72 .. 0.94

  Alignments for each domain:
  == domain 1  score: 47.2 bits;  conditional E-value: 6.2e-16
                  HHHHHHHHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--GGGTHHHH CS
  Hydrolase_3 188 KgtalkklakelnisleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksnnedGVak 253
                  K    kk++k++n+s+++++ +GD+ NDi++L+ +gl+   +++++ +kk ++yv+++n   GV +
   EPA05290.1   5 KRRYCKKVCKQYNVSPSQIAYIGDDVNDINLLKLVGLAAVPKDGTKIAKKSCNYVCETNGGKGVFR 70 
                  6666799*****************************************************999986 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0     7e-07    0.0025     178     209 ..       8      39 ..       2      40 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 7e-07
                 HHHHHHHHHTSTGGGEEEEESSHHHHHHHHHT CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
   Hydrolase 178 gkvaaireLqgkpeevamVGDgvnDaaalaaA 209
                   ++++++++++p+++a +GD vnD+  l+ +
  EPA05290.1   8 YCKKVCKQYNVSPSQIAYIGDDVNDINLLKLV 39 
                 56789*********************988865 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   4.4e-06     0.016     141     172 ..       9      40 ..       5      44 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.4e-06
       HAD_2 141 iekaleklklkkeeviyvGDsptDieaakkag 172
                  +k++++++++++++ y+GD  +Di   k +g
  EPA05290.1   9 CKKVCKQYNVSPSQIAYIGDDVNDINLLKLVG 40 
                 6899*********************8666555 PP

>> Gamma-thionin  Gamma-thionin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.6   0.00025      0.89      13      28 ..       2      17 ..       1      21 [. 0.87
   2 ?    5.6   0.2    0.0053        19      15      29 ..      51      65 ..      47      67 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00025
                   ---THHHHHHHHHHTT CS
  Gamma-thionin 13 pClsdsnCasvCkneg 28
                    C++ + C++vCk+ +
     EPA05290.1  2 YCVKRRYCKKVCKQYN 17
                   5************976 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0053
                   -THHHHHHHHHHTTS CS
  Gamma-thionin 15 lsdsnCasvCknegf 29
                   +++++C+ vC+++g+
     EPA05290.1 51 IAKKSCNYVCETNGG 65
                   67899******9986 PP

>> Toxin_3  Scorpion toxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.8   0.00056         2      14      29 ..       2      16 ..       1      26 [. 0.88
   2 ?    6.7   0.3    0.0023       8.3      19      33 ..      53      67 ..      46      69 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00056
                B-SSTHHHHHHHHHHT CS
     Toxin_3 14 sCaprnsyCdklCkkn 29
                +C++   yC+k Ck++
  EPA05290.1  2 YCVK-RRYCKKVCKQY 16
                8999.9*******986 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0023
                HHHHHHHHHHTT-SE CS
     Toxin_3 19 nsyCdklCkkngAks 33
                ++ C+  C+ ng+k+
  EPA05290.1 53 KKSCNYVCETNGGKG 67
                577888888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 620.64
//
Query:       EPA05291.1  [L=268]
Description: sugar-specific transcriptional regulator TrmB [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-21   74.6   0.0    1.4e-20   72.9   0.0    1.9  2  TrmB             Sugar-specific transcriptional regulator Trm
      1e-07   31.4   0.0    1.3e-07   31.1   0.0    1.1  1  Regulator_TrmB   Archaeal transcriptional regulator TrmB
    3.8e-05   23.4   0.0     0.0002   21.1   0.0    2.1  2  HTH_IclR         IclR helix-turn-helix domain
     0.0012   18.7   0.0     0.0042   17.0   0.0    1.9  2  MarR             MarR family
     0.0063   16.0   0.0      0.016   14.7   0.0    1.7  1  HTH_24           Winged helix-turn-helix DNA-binding
     0.0067   16.8   0.1      0.042   14.2   0.0    2.1  2  Penicillinase_R  Penicillinase repressor
     0.0082   16.6   0.0      0.022   15.2   0.0    1.7  1  HTH_27           Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.056   13.8   0.0       0.17   12.2   0.0    1.8  1  Rrf2             Transcriptional regulator
      0.089   12.7   0.0       0.19   11.6   0.0    1.6  1  PLDc_2           PLD-like domain
       0.13   12.3   0.0       0.31   11.0   0.0    1.7  1  PadR             Transcriptional regulator PadR-like family
       0.17   11.8   0.0       0.31   11.0   0.0    1.4  1  MarR_2           MarR family


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.9   0.0   8.6e-24   1.4e-20       1      67 [.      24      90 ..      24      91 .. 0.98
   2 ?   -2.2   0.0       2.5   4.1e+03      43      51 ..     174     182 ..     174     208 .. 0.70

  Alignments for each domain:
  == domain 1  score: 72.9 bits;  conditional E-value: 8.6e-24
                HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE--H CS
        TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravdp 67
                L+k+GL++yE+++++ Ll++g++ta ++++++gvp+sk+YevL  Le+kG++   ++rp++Y a +p
  EPA05291.1 24 LEKIGLTSYEIRTFTSLLQSGELTAADLSQKSGVPYSKIYEVLGTLEEKGWIGSDDSRPTKYFAKSP 90
                789*************************************************************998 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.5
                 HHHHHHCTS CS
        TrmB  43 LrsLedkGl 51 
                 LrsL dkG+
  EPA05291.1 174 LRSLHDKGV 182
                 677777774 PP

>> Regulator_TrmB  Archaeal transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.0   7.7e-11   1.3e-07       2     130 ..     131     263 ..     130     268 .] 0.84

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 7.7e-11
                     EEEESSHHHHHHHHHHHHHH-SSEEEEEE-...GGGHHHHHHHHHHHHHTT-EEEEEESS----GGGSSSSEEEEEE-S---S.EEEEETTTEEE CS
  Regulator_TrmB   2 vwvvksretvierieelIesAenelivslp...selLeelreeliaaaergvtVllliypdedleeldleevatevrvrrsgapllvivDrkrgv 93 
                     +wv  +  ++ ++i e++es +ne++++lp   +el+++  ++l++ +++gv++ +l +++ d++  +  + ++ v++ ++     +i+D +++v
      EPA05291.1 131 IWVLSGAINIASKILEMVESCRNEVMIALPeagQELVRQALPKLRSLHDKGVKITILTSDKMDKDSIKAISRVATVKIKKGLFGGGIISDNRYVV 225
                     89999**********************99855579*************************99999999999999999999988777999*99999 PP

                     EE.-SSS-.EEEE--HHHHHHHHHHHHHH........HH CS
  Regulator_TrmB  94 va.prevl.rdkeeeyaiifkekelihvlshyFlttlWk 130
                     +    e++ +  ++  ai+ + + l+ +   +++++l k
      EPA05291.1 226 ILlGPEMKeMNTSDIVAIWADHTGLAGFA-RSYFEYLLK 263
                     86245566888888899998888887766.444444455 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   1.2e-07    0.0002      16      51 ..      43      78 ..      41      79 .. 0.92
   2 ?   -1.1   0.0         1   1.7e+03       4      20 ..     140     156 ..     137     168 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.2e-07
                BSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
    HTH_IclR 16 pqeltlselArrtglpkStvhRlLqtLvelGyveqd 51
                 +elt ++l++++g+p S+ +  L tL+e G++  d
  EPA05291.1 43 SGELTAADLSQKSGVPYSKIYEVLGTLEEKGWIGSD 78
                589*****************************8665 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1
                 HHHHHHCT-CTTBSS-B CS
    HTH_IclR   4 RalaiLdalaeapqelt 20 
                  a  iL+++++++ e+ 
  EPA05291.1 140 IASKILEMVESCRNEVM 156
                 57789999999998864 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       2.7   4.3e+03      29      46 ..      11      29 ..       9      29 .. 0.67
   2 !   17.0   0.0   2.6e-06    0.0042       1      47 [.      29      75 ..      29      80 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.7
                S-HHHHHHHHHH.HHHTTS CS
        MarR 29 vskstvtrvldr.LekkGl 46
                v++++++  +++ Lek Gl
  EPA05291.1 11 VDRMNISDKTRKsLEKIGL 29
                6778888776544887775 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 2.6e-06
                --HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
        MarR  1 ltltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGli 47
                lt  ++++ ++l ++g+l+ ++L  k+gv  s + +vl +Le+kG+i
  EPA05291.1 29 LTSYEIRTFTSLLQSGELTAADLSQKSGVPYSKIYEVLGTLEEKGWI 75
                6778899999************************************9 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0     1e-05     0.016      12      47 ..      40      75 ..      32      75 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1e-05
      HTH_24 12 LqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                L + + ++ ++L++++g++ s + + l  Lee+G+I
  EPA05291.1 40 LLQSGELTAADLSQKSGVPYSKIYEVLGTLEEKGWI 75
                566799*****************************9 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   2.6e-05     0.042      21      81 ..      44     107 ..      34     122 .. 0.72
   2 ?   -0.3   0.0      0.79   1.3e+03      14      96 ..     161     187 ..     151     204 .. 0.46

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.6e-05
                      HHHHHT.--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE--...--XXXXXXXXXXXXXX CS
  Penicillinase_R  21 kevvee.leeekelaysTVktllrrLvkKgllsrekegrafiYspl...vseeeavasavkqlld 81 
                      +e+ ++ l++++ + ys +  +l+ L++Kg++ ++   r + Y +    +  e  ++++ +++l+
       EPA05291.1  44 GELTAAdLSQKSGVPYSKIYEVLGTLEEKGWIGSDD-SRPTKYFAKspsTGLETTKQKMQNEFLQ 107
                      5555555999999********************987.5666665540004555555555555555 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.79
                      HHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE----XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
  Penicillinase_R  14 ekgeatvkevveeleeekelaysTVktllrrLvkKgllsrekegrafiYsplvseeeavasavkqlldklfegsvkelvaafv 96 
                      e+g+  v                                                        +q l kl + + k +   ++
       EPA05291.1 161 EAGQELV--------------------------------------------------------RQALPKLRSLHDKGVKITIL 187
                      4444333........................................................33333333333333333344 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.4e-05     0.022      16      60 ..      43      83 ..      32      89 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.4e-05
      HTH_27 16 rrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrek 60
                 ++ ++adl+++  v +s i ++l  L+ekG++   g+  d r++
  EPA05291.1 43 SGELTAADLSQKSGVPYSKIYEVLGTLEEKGWI---GS-DDSRPT 83
                688999***************************...55.466654 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00011      0.17      16      57 ..      39      77 ..      29      80 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
                HHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
        Rrf2 16 yLakeeeeepvsseeiaerqnispsylekilakLrkaglvks 57
                 L +  e   +++++++++ +++ s +  +l +L+++g++ s
  EPA05291.1 39 SLLQSGE---LTAADLSQKSGVPYSKIYEVLGTLEEKGWIGS 77
                4443333...9*****************************88 PP

>> PLDc_2  PLD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00011      0.19       3      53 ..     146     198 ..     144     226 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
      PLDc_2   3 qliksAkksidiatyyf..vsdreildallkaakrgvkvrilldskkddagav 53 
                 ++ +s++ ++ ia +    +  r+ l +l+ ++++gvk+ il+++k d++++ 
  EPA05291.1 146 EMVESCRNEVMIALPEAgqELVRQALPKLRSLHDKGVKITILTSDKMDKDSIK 198
                 6667778888888887755555555888999*************976655543 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00019      0.31      29      63 ..      57      86 ..      46      96 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00019
                TTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEE CS
        PadR 29 lseGslYpaLkrLekeglveseweesgegpprkyY 63
                + ++++Y +L +Le++g++ s  +     +p+ky+
  EPA05291.1 57 VPYSKIYEVLGTLEEKGWIGSDDS-----RPTKYF 86
                56789**************99855.....577776 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00019      0.31       2      51 ..      28      75 ..      27      93 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00019
                T--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSE CS
      MarR_2  2 gltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLv 51
                glt  + r    L  +++  lt+++l ++ g++ s +  +l  L+++G++
  EPA05291.1 28 GLTSYEIRTFTSLLQSGE--LTAADLSQKSGVPYSKIYEVLGTLEEKGWI 75
                666667777778889999..*****************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       805  (0.0448993); expected 358.6 (0.02)
Passed bias filter:                      646  (0.036031); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 1969.70
//
Query:       EPA05292.1  [L=126]
Description: hypothetical protein BG20_I0115 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.11   12.4   1.7        4.6    7.0   0.1    2.1  2  DUF1494   Protein of unknown function (DUF1494)


Domain annotation for each model (and alignments):
>> DUF1494  Protein of unknown function (DUF1494)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1   0.00026       4.6      26      74 ..       4      50 ..       2      59 .. 0.75
   2 ?    5.3   0.3   0.00087        16      19      43 ..      65      89 ..      48     122 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00026
     DUF1494 26 ywqrrllisskrkerlykiflqeskaykklrelflstialealeedvls 74
                yw+rr ++  +    +y +f    +   ++  ++++ i+ e+  +d +s
  EPA05292.1  4 YWTRRRWVDGRTGHAIYLMFPLTMIN--FIIVTYRFLIEGESELKDLIS 50
                9*****************99766554..455566666666666655555 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.00087
     DUF1494 19 lllgalGywqrrllisskrkerlyk 43
                 +   +G+w+rr  +s  ++ +   
  EPA05292.1 65 PISIIIGFWHRRTQLSVENNIKYLE 89
                334458*********9988766444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       969  (0.0540465); expected 358.6 (0.02)
Passed bias filter:                      579  (0.032294); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 826.68
//
Query:       EPA05293.1  [L=274]
Description: AP endonuclease, family 2 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.4e-15   56.6   0.0    3.2e-15   56.1   0.0    1.1  1  AP_endonuc_2  Xylose isomerase-like TIM barrel
  ------ inclusion threshold ------
      0.019   14.8   0.5      0.033   14.0   0.5    1.4  1  DUF1463       Protein of unknown function (DUF1463)
      0.073   13.4   0.0       0.28   11.5   0.0    2.0  1  TSC22         TSC-22/dip/bun family


Domain annotation for each model (and alignments):
>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.1   0.0   5.4e-19   3.2e-15       1     208 [.      32     224 ..      32     226 .. 0.93

  Alignments for each domain:
  == domain 1  score: 56.1 bits;  conditional E-value: 5.4e-19
                   HHHHHHCT-SEEEEECCTCSHHHHCHHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCSHHHHHHHHHHHHHHHHHHTBSEEEEEBCCGBCT CS
  AP_endonuc_2   1 laaaaeaGfdgvElfgrdlvpvselsdeelrelrkaldelglriaslslftrfgypdederearreesvdalkraielaaaLGapllvlhpGtagag 97 
                   +++a+++G d++E+ +++ +++    +++  e+ +++ +  ++i s+++ ++  + + +e e + ++ +d lk+ +  ++ +G++++ ++     + 
    EPA05293.1  32 FELAHKIGLDSIEWIFDTFDKNPV-MEKKFHEINNLISKFQININSVCADYFMVNKLFNESEFNIRKNLDTLKQLAINCKNIGVKIIEIPLV---DN 124
                   689***********9999888754.489***************************9999777779999**********************99...99 PP

                   TTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTSSSTCHHHHHHHHHHTTTTEEEEEEHHHHHHHTTTHHHHHHHHHGGEEEEEE.EESST CS
  AP_endonuc_2  98 pkgseeeawerlaeslneladyaekegvklalEtlagsgvelgdeelarlldavdspnvgvclDtgHlliaeedvddalraladrikhvHikDakgd 194
                   ++   e   + l+++l+ ++++  + g  +alEt  ++       e+++ll++ +   v  ++Dtg++   +++v+++l+ l+ +ik +H+kD    
    EPA05293.1 125 SSLKSEKHKNELVKNLDSILPEINDLGLIIALETDLPPI------EFLNLLNRFEKNIVFANYDTGNSASLGFNVNEELEILKHKIKNIHLKDRLF- 214
                   999999****************************99998......999*******777***********************************988. PP

                   TTTSSTTEESTTSS CS
  AP_endonuc_2 195 lgagrdrhvpigeG 208
                        +  vp+g G
    EPA05293.1 215 ----NGKTVPFGSG 224
                   ....7777777776 PP

>> DUF1463  Protein of unknown function (DUF1463)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.5   5.6e-06     0.033      45     103 ..      60     118 ..      43     146 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.6e-06
     DUF1463  45 lrdpktvvyvfdlevskgsldyklltklsdeqfyeldvrke.dklkdlvfn.drialkiis 103
                 + + + ++  f++++     dy ++ kl +e  ++  +rk+ d lk+l +n  +i++kii 
  EPA05293.1  60 FHEINNLISKFQININSVCADYFMVNKLFNESEFN--IRKNlDTLKQLAINcKNIGVKIIE 118
                 5666777888*********************9887..7876589*****994469****95 PP

>> TSC22  TSC-22/dip/bun family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   4.6e-05      0.28       9      26 ..     190     207 ..     188     215 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.6e-05
       TSC22   9 mfAVrEeVevLkekIkeL 26 
                  f V+Ee e+Lk kIk+ 
  EPA05293.1 190 GFNVNEELEILKHKIKNI 207
                 589*************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1813.02
//
Query:       EPA05294.1  [L=166]
Description: putative histidinol-phosphatase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-11   44.0   4.9    1.9e-09   37.9   4.9    2.1  1  HAD_2            Haloacid dehalogenase-like hydrolase
    6.7e-11   42.1   0.0    9.9e-11   41.6   0.0    1.3  1  Hydrolase_like   HAD-hyrolase-like
    1.2e-10   41.3   1.0    1.5e-10   41.0   1.0    1.2  1  PNK3P            Polynucleotide kinase 3 phosphatase
    2.2e-05   24.9   0.0    2.7e-05   24.7   0.0    1.1  1  HAD              haloacid dehalogenase-like hydrolase
    0.00016   22.0   0.0    0.00026   21.4   0.0    1.4  1  Hydrolase        haloacid dehalogenase-like hydrolase
    0.00064   19.4   0.2    0.00095   18.8   0.2    1.2  1  Acid_phosphat_B  HAD superfamily, subfamily IIIB (Acid phosph
     0.0097   16.2   0.1     0.0099   16.2   0.1    1.3  1  HAD_SAK_2        HAD domain in Swiss Army Knife RNA repair pr
  ------ inclusion threshold ------
      0.012   15.8   0.0      0.019   15.0   0.0    1.4  1  Hydrolase_6      Haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   4.9   8.3e-13   1.9e-09      61     177 ..      14     146 ..       3     147 .. 0.89

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 8.3e-13
       HAD_2  61 kieellrkyneekkkkevkpydgvkelLeeLkeagyklgivTsk..sreaveekleqlgiesyFdvivtsedvekk................KPdpevi 141
                  i++  ++y++  ++  +++++++ +++ +++e g+ + i+T++   ++++ ++ + ++i++y+  i+ ++ ++ +                KP++ +i
  EPA05294.1  14 VINKKKSDYVKDIHE--FEFLPDIFNAIRKINELGIIIIIITNQsvINRQIISEKKLNQIHDYMLAILAKNSCKISkiyycphhpdencdcrKPKTGMI 110
                 677788888888888..**************************9666888889999999*********999988766666667778888888******* PP

       HAD_2 142 ekaleklklkkeeviyvGDsptDieaakkagikvia 177
                 ++a++ +k++ ++++ +GDs +Di+aa  + ik+i 
  EPA05294.1 111 KQAVKDFKIDLSNALLIGDSDSDIQAANSMKIKSIK 146
                 *********************************985 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   0.0   4.4e-14   9.9e-11       2      51 ..     102     150 ..     101     163 .. 0.91

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 4.4e-14
                     .STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSS CS
  Hydrolase_like   2 lgKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltG 51 
                     ++KP  +m+++a++++++d ++ l+iGD+ ++Di++An +++ks+ ++t 
      EPA05294.1 102 CRKPKTGMIKQAVKDFKIDLSNALLIGDS-DSDIQAANSMKIKSIKIKTN 150
                     89***************************.***************99995 PP

>> PNK3P  Polynucleotide kinase 3 phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   1.0   6.7e-14   1.5e-10       5     129 ..       9     132 ..       5     161 .. 0.78

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 6.7e-14
       PNK3P   5 FDlDstliktksgkefakdaddwkllsesvlekLkklkeegykivifsNqggvvek.ktkkslekfkekieallkeldvpl.lvyaatkk.d...kyRK 97 
                  D D+ + k+ks     kd +++++l + + + ++k +e g +i+i++Nq+ + ++  ++k+l+++ + + a+l++   ++  +y  +++ d     RK
  EPA05294.1   9 LDRDGVINKKKS--DYVKDIHEFEFLPD-IFNAIRKINELGIIIIIITNQSVINRQiISEKKLNQIHDYMLAILAKNSCKIsKIYYCPHHpDencDCRK 104
                 455555555555..5568899***9976.*************************9988899999999999999998866642455555543445679** PP

       PNK3P  98 PetGmweelkkdleekleidkeksfyvGDaag 129
                 P+tGm+++  kd++    id ++ + +GD   
  EPA05294.1 105 PKTGMIKQAVKDFK----IDLSNALLIGDSDS 132
                 *****998888765....68899999999755 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   1.2e-08   2.7e-05      76     187 ..      22     137 ..       2     138 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.2e-08
         HAD  76 fvaevirpklldpgalellaahraaGdrvvvvSgglrplvepll.aelg..adevlatelevdd......rltgelglegkpvrgegkvaalrewlaae 165
                 +v ++++   + p++  ++++  + G+ ++++++   ++ +++  ++l+  +d+ la  l+++       ++  ++  e+ ++r+  k   +++  a +
  EPA05294.1  22 YVKDIHEFE-FLPDIFNAIRKINELGIIIIIITNQSVINRQIISeKKLNqiHDYMLAI-LAKNSckiskiYYCPHHPDENCDCRK-PKTGMIKQ--AVK 115
                 455555555.5699999999999*********************88***998888888.55555666669888884444445555.99999**9..999 PP

         HAD 166 gegidleevvayGDspsDlpll 187
                   +idl++   +GDs sD++++
  EPA05294.1 116 DFKIDLSNALLIGDSDSDIQAA 137
                 99******************98 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   1.2e-07   0.00026     115     208 ..      27     139 ..       5     141 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.2e-07
                 HTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHH.TT.............GGGESEEEEHHCES...............STTTSHHHHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx.............xxxxxxxxxxxxxx...............xxxxxxxxxxxxxx RF
   Hydrolase 115 dplkvkpeaaeavasLkaagievvlltgdnpetaeraanq.lG.............ddyfdaviasdiet...............vakpspegkvaair 184
                 ++ +  p++  a++++++ gi ++++t+++  + + + ++ l+                                          + kp+  + ++a++
  EPA05294.1  27 HEFEFLPDIFNAIRKINELGIIIIIITNQSVINRQIISEKkLNqihdymlailaknS------CK----IskiyycphhpdencdCRKPKTGMIKQAVK 115
                 4556789999*****************999844444444334444256532222221......11....1223566667788899************** PP

                 HHTSTGGGEEEEESSHHHHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxx RF
   Hydrolase 185 eLqgkpeevamVGDgvnDaaalaa 208
                  ++++ ++ + +GD+  D++a+  
  EPA05294.1 116 DFKIDLSNALLIGDSDSDIQAANS 139
                 *********************975 PP

>> Acid_phosphat_B  HAD superfamily, subfamily IIIB (Acid phosphatase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.2   4.3e-07   0.00095     116     222 ..      30     147 ..      15     153 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 4.3e-07
                      CCECCHHHHHHHHHHTTEEEEEEEEEECCCHHH.HHHHHHHCT..........-TTBSCCEEECCSTTC---HHHHHHHHHHHHHHTTEEE... CS
  Acid_phosphat_B 116 kaipgalelikkvverGvkiffvsgRseeqkaa.TvenLkkag..........fssweklilkgkkdkqkksvvsyKeerrqklekkGyni... 195
                      + +p  ++ i+k++e+G+ i+ +++ s  +++   +++L +              + +k++    ++ ++ +  + K+   ++ +k+ ++i   
       EPA05294.1  30 EFLPDIFNAIRKINELGIIIIIITNQSVINRQIiSEKKLNQIHdymlailaknSCKISKIYYCPHHPDENCDCRKPKTGMIKQAVKD-FKIdls 122
                      557888999*******************966651555666666777777665545778999999999999999999**********9.***888 PP

                      .EEEEESSGGGCHCCHHCTCCCCEEEE- CS
  Acid_phosphat_B 196 .vlniGDnlsDlngakeaeargeriikl 222
                        l+iGD++sD+++a++ + +   +ik+
       EPA05294.1 123 nALLIGDSDSDIQAANSMKIK---SIKI 147
                      8888**********5555554...4444 PP

>> HAD_SAK_2  HAD domain in Swiss Army Knife RNA repair proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   4.4e-06    0.0099       1      56 [.       6      59 ..       6     150 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.4e-06
   HAD_SAK_2  1 viFLDiDGVLnpekskkrregeedealdpeaverlkriveatgakiVlsstWrrre 56
                v+FLD DGV+n++ks   ++ +e  ++ p++ +++++ +++ g+ i++ ++     
  EPA05294.1  6 VLFLDRDGVINKKKSDYVKDIHE-FEFLPDIFNAIRK-INELGIIIIIITNQSVIN 59
                79*************99877554.4488889999999.667777666666554444 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   8.7e-06     0.019       2      49 ..       8      65 ..       7      82 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8.7e-06
                 EEESTTTSE..........ETTEE-TTHHHHHHHHHHTT-EEEEEE---SS-HHHHHH CS
  Hydrolase_6  2 lfDidGvLw..........rgdkaipgaaealnalraagkpvvllTNnsskseeeyak 49
                 ++D dGv+           ++ + +p   +a++ +++ g+ ++++TN+s  +++ + +
   EPA05294.1  8 FLDRDGVINkkksdyvkdiHEFEFLPDIFNAIRKINELGIIIIIITNQSVINRQIISE 65
                 7899****98888888888899****************************99887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1131  (0.0630822); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.58u 0.35s 00:00:00.93 Elapsed: 00:00:00.55
# Mc/sec: 902.67
//
Query:       EPA05295.1  [L=198]
Description: hypothetical protein BG20_I0163 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.8e-10   38.4   0.0    1.3e-09   37.8   0.0    1.2  1  AP_endonuc_2  Xylose isomerase-like TIM barrel
  ------ inclusion threshold ------
      0.011   15.0   0.2      0.015   14.5   0.2    1.2  1  DUF692        Protein of unknown function (DUF692)


Domain annotation for each model (and alignments):
>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.0   1.5e-13   1.3e-09      73     203 ..       3     154 ..       2     161 .. 0.89

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 1.5e-13
                   HHHHHHHHHHTBSEEEEEBCC..........GBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE.--TTTTSSSTC...........HHHHHH CS
  AP_endonuc_2  73 kraielaaaLGapllvlhpGt..........agagpkgseeeawerlaeslneladyaekegvklalE.tlagsgvelgd...........eelarl 147
                   ++ai+ + ++  p+ ++h+G           +++ +  +++ a++++++s  +++dya+  g+k+a+E +   +++ +             +e+  +
    EPA05295.1   3 EKAIDVCCEIESPIFTFHAGFtvdpielgkrFPRTGVVERKIAIDTFIDSSYKILDYARSFGIKIAMElNVVQKFNLD-HgknklllfaeyDETMIF 98 
                   589*****************9********998899999999***************************4444444444.3599************** PP

                   HHHHTTTTEEEEEEHHHHHHH....TTTHHHHHHHHHGGEEEEEE.EESSTTTTSSTTEE CS
  AP_endonuc_2 148 ldavdspnvgvclDtgHllia....eedvddalraladrikhvHikDakgdlgagrdrhv 203
                   l+  +   +g+ lD gH+        +d d++ +++++ ++ +Hi+ ++g     +d+h 
    EPA05295.1  99 LKNFKKNEIGILLDLGHTSVTshwlNFDKDEFTEKIKKFVSVIHISNNNG----LQDQHK 154
                   *****999*************************************98888....555555 PP

>> DUF692  Protein of unknown function (DUF692)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.2   1.7e-06     0.015     146     241 ..      91     178 ..      83     196 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.7e-06
      DUF692 146 elsEaeFlaelvertgcglllDvnNvyvnavNhgfdpeayldalplervaeiHlAGheekeelliDtHgapvadevwalleealarlgpvptllEr 241
                 e++E+  + + +++ ++g+llD+    v+++  +fd +++ ++++ + v  iH++      + l D+H++  + ++w++ +  l+r+++ p++lE 
  EPA05295.1  91 EYDETMIFLKNFKKNEIGILLDLGHTSVTSHWLNFDKDEFTEKIK-KFVSVIHISNN----NGLQDQHKQ-LTTDCWQVSK--LKRFKNKPITLET 178
                 677777777778999***************************996.79******988....5799***86.5677999865..7889999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       837  (0.0466841); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.34s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 1127.01
//
Query:       EPA05296.1  [L=197]
Description: NAD-binding protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-23   82.8   0.0    2.9e-23   82.6   0.0    1.0  1  Epimerase        NAD dependent epimerase/dehydratase family
    9.6e-22   77.8   0.0    1.1e-21   77.6   0.0    1.0  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    2.1e-15   56.6   0.0    2.5e-15   56.4   0.0    1.0  1  RmlD_sub_bind    RmlD substrate binding domain
    9.1e-14   51.1   0.0    1.1e-13   50.8   0.0    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    2.5e-13   49.8   0.0    2.2e-12   46.7   0.0    1.9  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    1.9e-05   23.9   0.5     0.0048   16.1   0.5    2.8  1  NAD_binding_4    Male sterility protein
    0.00046   20.1   0.0    0.00051   20.0   0.0    1.2  1  NAD_binding_10   NAD(P)H-binding
    0.00047   19.7   0.0     0.0007   19.1   0.0    1.3  1  adh_short        short chain dehydrogenase
     0.0005   19.7   0.0    0.00067   19.3   0.0    1.2  1  NmrA             NmrA-like family
     0.0019   18.5   0.0     0.0026   18.0   0.0    1.4  1  TrkA_N           TrkA-N domain
     0.0024   18.1   0.0     0.0039   17.5   0.0    1.3  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
  ------ inclusion threshold ------
      0.051   13.5   0.1      0.079   12.9   0.1    1.4  1  KR               KR domain
       0.11   13.1   0.0       0.22   12.1   0.0    1.5  1  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
       0.18   11.0   0.0       0.28   10.4   0.0    1.3  1  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.6   0.0   2.2e-26   2.9e-23       1     176 [.       4     172 ..       4     194 .. 0.85

  Alignments for each domain:
  == domain 1  score: 82.6 bits;  conditional E-value: 2.2e-26
                 EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC....EEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHHHSHHHHHHHHTHHH CS
   Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl....elveldltdrsalerlfkeeqpdavihlAavggvaassedpadfieknlqgt 95 
                 il+tG+ G+iGs l k+ll++gy v++ld+ ++++n+ ++       +++++d++d+  l++ ++  + d +ihlAa  g +  ++++ + + +n+q t
  EPA05296.1   4 ILITGGGGYIGSVLSKYLLNNGYSVTVLDNFRYNQNSLLNCCYdenfSVIRGDVRDEHTLAKSIH--DQDFIIHLAALVGAPICNINKDEALSTNFQST 100
                 8******************************9999987766558999******************..78********6666777777788899****** PP

                 HHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHHHHHHHT-EEEEEEESEEESTT CS
   Epimerase  96 lnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklveayaaqyglnaiilrlfnlyGpr 176
                   ll+  +k +  ++l+  + + YG +++   +  t+++pl+p s Y+ +K+ +ek + +     + n i++rl +++G  
  EPA05296.1 101 KLLLKLRKKEQ--KILYPCTNSGYGIGQK--GKFCTEKTPLQPISFYGQTKVNAEKAILN-----DYNSISFRLATVFGVS 172
                 *9999877663..7*************99..55555555*****************9996.....45899*******9987 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.6   0.0   8.8e-25   1.1e-21       1     168 [.       5     158 ..       5     177 .. 0.87

  Alignments for each domain:
  == domain 1  score: 77.6 bits;  conditional E-value: 8.8e-25
                    EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHTTSHH CS
  GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevynLAAqshVdvsfekPe 96 
                    LiTG+ G+iGs l ++Ll++gy v+++++  ++ n  ++ +       +++en+++++gD++D++ l + +++   d +++LAA    +    + +
     EPA05296.1   5 LITGGGGYIGSVLSKYLLNNGYSVTVLDNFRYNQN--SLLNC------CYDENFSVIRGDVRDEHTLAKSIHDQ--DFIIHLAALVGAPICNINKD 90 
                    9**************************99988866..44443......34679******************998..89*******99998888889 PP

                    HHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSS.B-TTS-----SHHHHHHHHHHHHHHHHH CS
  GDP_Man_Dehyd  97 ytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevp.qtEttpfyPrsPYaaaKlyadwivvnyr 168
                    + + +n+  t  LL++ ++     + +++  +t   YG  q+ + +tE+tp++P s Y+ +K+ a+  + n +
     EPA05296.1  91 EALSTNFQSTKLLLKLRKK-----EQKILYPCTNSGYGIGQKGKfCTEKTPLQPISFYGQTKVNAEKAILNDY 158
                    9**********99999766.....45899**********9987747*****************9998766544 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.4   0.0   1.9e-18   2.5e-15       2     155 ..       3     172 ..       1     188 [. 0.92

  Alignments for each domain:
  == domain 1  score: 56.4 bits;  conditional E-value: 1.9e-18
                    EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT...................T--TTSHHHHHHHHHHH--SEEEE------HHHHHHSHHHHHHHH CS
  RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltre...................eldltdaeavaellkeakpdvvvnaAAytavDkaEseeeaayavn 78 
                    kil+tG++G +Gs L k l ++g++v+ l++                    + d++d++++a+ +++   d+++++AA      +  ++++a   n
     EPA05296.1   3 KILITGGGGYIGSVLSKYLLNNGYSVTVLDNFrynqnsllnccydenfsviRGDVRDEHTLAKSIHD--QDFIIHLAALVGAPICNINKDEALSTN 96 
                    6****************************766789*******************************9..789************************ PP

                    THHHHHHHHHHHHCT-EEEEEEEGGGS-.S-TTS-B-TTS----SSHHHHHHHHHHHHHHHH-SSEEEEEE-SEESSS CS
  RmlD_sub_bind  79 aeavealAeaaaavgalLihvStDyVFd.GekkrpYeeddetsPlnvYGrtKlaGEqavlaagkkalivRtswvygek 155
                     ++++ l ++ ++ + ++++  t   +  G+k +  +e+ + +P+++YG+tK++ E+a+l++  + + +R + v+g +
     EPA05296.1  97 FQSTKLLLKL-RKKEQKILYPCTNSGYGiGQKGKFCTEKTPLQPISFYGQTKVNAEKAILNDY-NSISFRLATVFGVS 172
                    ****999987.66788999****999976889999999**********************765.56779******965 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.8   0.0   8.8e-17   1.1e-13       1     162 [.       5     159 ..       5     177 .. 0.78

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 8.8e-17
   3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkk...viegDvtdkdkleealegvdvvihlaslvdvag.kltedeimkvnvkG 95 
                 ++tGg+G++G+ l k L++ +    v vlD    ++   +l ++  ++   vi gDv+d+++l + +++ d +ihla+lv     ++++de  + n + 
  EPA05296.1   5 LITGGGGYIGSVLSKYLLNNG--YSVTVLDNFRYNQN--SLLNCCYDEnfsVIRGDVRDEHTLAKSIHDQDFIIHLAALVGAPIcNINKDEALSTNFQS 99 
                 69****************999..69*****5443333..233333332344***************************99776559************* PP

   3Beta_HSD  96 TrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKalaEklvlkaNg 162
                 T+ +l+  +k   ++++Y  + +  g  ++g+      E+++++  + + y ++K  aEk++l+  +
  EPA05296.1 100 TKLLLKLRKKE--QKILYPCTNSGYGIGQKGKFC---TEKTPLQ--PISFYGQTKVNAEKAILNDYN 159
                 *****987766..688898887777763344433...5777765..6799************97655 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   0.0   1.7e-15   2.2e-12       1     151 [.       4     156 ..       4     171 .. 0.76

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 1.7e-15
                      EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-SEEEE------HHHHH CS
  Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvdvvfhaAAlKhVPlve 94 
                      +l+tG+gG iGs l + +l++   ++ +l++  +++ ++ + +    ++ ++     ++ gdvrd+++l+k ++  + d+++h AAl   P+++
       EPA05296.1   4 ILITGGGGYIGSVLSKYLLNNG-YSVTVLDNFRYNQNSLLNCCY---DE-NF----SVIRGDVRDEHTLAKSIH--DQDFIIHLAALVGAPICN 86 
                      89**********9998888765.679999*******99998863...33.33....3567*************9..9***************** PP

                      HSHHHHHHHHHHHHHHHHHHHHH............TT-SEEEEEEEGGG.SS--SHHHHHHHHHHHHHHH CS
  Polysacc_synt_2  95 enpleaiktNvlgtenvieaaie............agvkkvvliStDKA.vnPtnvmGatKrlaekllqa 151
                       n  ea++tN  +t+ +++  ++            +g+ +     t K   +P++ +G tK  aek + +
       EPA05296.1  87 INKDEALSTNFQSTKLLLKLRKKeqkilypctnsgYGIGQKGKFCTEKTpLQPISFYGQTKVNAEKAILN 156
                      ***************9998755411111111111134455555667776468888888888888887665 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.5   3.7e-06    0.0048       1     187 [.       6     154 ..       6     178 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.7e-06
                    EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSHHHHHHHHHHHT-SS-HHHHHHHHHTTTEEEEE--TTSGGGG--HHHHHHHHHH--EEEE--S CS
  NAD_binding_4   1 lTGaTGFLGkvLlekLLrttpevkiyllvRaksgesaeeRleeelekkelfsallkelaerikvveGDlseprlGLseedlqelaeevdviihsaA 96 
                    +TG+ G++G+vL + LL++     +++l            +     +++l +  +    e+ +v+ GD+ +++      +l + ++  d iih aA
     EPA05296.1   6 ITGGGGYIGSVLSKYLLNNGY--SVTVLD----------NF--RYNQNSLLNCCY---DENFSVIRGDVRDEH------TLAKSIHDQDFIIHLAA 78 
                    677777777777777777766..344431..........11..123344555554...788899999999765......777777889******** PP

                    S-S....STTSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEE..GGGTTS-TTT--SSS-H......HHH--EEEETTTCCCHHHHHHHHHHHHH CS
  NAD_binding_4  97 tvn...fdepykellrvNveGtrevlelakklkklkvllhvST..ayvngeregeveekvyeegekeekldederaklkglpntYeqsKalaEklv 187
                     v     + + +e+l++N ++t+ +l+l kk +k    l+  T  +y  g++ +                   ++++  +    Y q+K+ aEk +
     EPA05296.1  79 LVGapiCNINKDEALSTNFQSTKLLLKLRKKEQKI---LYPCTnsGYGIGQKGKF-----------------CTEKTPLQPISFYGQTKVNAEKAI 154
                    **82224668999***************9966554...55555325555555532.................233333444444555555555544 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0     4e-07   0.00051       1      68 [.       8      77 ..       8     140 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 4e-07
                    TTTSHHHHHHHHHHHHC-T-EEEEE..ET.THHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES- CS
  NAD_binding_10  1 GAtGkvGrllvkellargghevtal..vR.npeklaeleaeeglevvegdvtdvedlaealkgadaVvsal 68
                    G+ G +G+ l k ll++g ++vt+l   R n+++l +   +e+ +v+ gdv d+ +la+ + ++d ++  +
      EPA05296.1  8 GGGGYIGSVLSKYLLNNG-YSVTVLdnFRyNQNSLLNCCYDENFSVIRGDVRDEHTLAKSIHDQDFIIHLA 77
                    899**************5.***9975533367777767689************************876544 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   5.4e-07    0.0007       1      66 [.       2      65 ..       2      80 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 5.4e-07
                SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHH CS
   adh_short  1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevea 66
                k +l+tG+++ IG  ++k l+++G++v+v+d+   + + +++ + +e  ++ +i++Dv+d++ + +
  EPA05296.1  2 KKILITGGGGYIGSVLSKYLLNNGYSVTVLDNFRYNQNSLLNCCYDE--NFSVIRGDVRDEHTLAK 65
                689****************************9999999999998875..79********9988766 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   5.2e-07   0.00067       1      72 [.       4      77 ..       4      91 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 5.2e-07
                EEESSTTSHHHHHHHHHHHHHT-EEEEE..ES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEEEE-- CS
        NmrA  1 IlviGaTGrqGksvvrallkaghkvral..vRdtkselakslkeaGvelvkgdlddkeslvealkgvdvvfsvt 72
                Il++G+ G++G+ + ++ll++g++v +l   R  ++ l++   ++   ++ gd+ d+  l++ +++ d ++   
  EPA05296.1  4 ILITGGGGYIGSVLSKYLLNNGYSVTVLdnFRYNQNSLLNCCYDENFSVIRGDVRDEHTLAKSIHDQDFIIHLA 77
                89*************************9667888********************************99998765 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.1e-06    0.0026       5      58 ..       9      66 ..       4     115 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.1e-06
                S-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHH....HHTTSEEEES-TTSHHHHHHT CS
      TrkA_N  5 GlGrvGrslaeeLse.ggkdvvvidkdeerveel....reeglevvvgdatdeevLeea 58
                G G +G+ l ++L + g+ +v+v d+ + + ++l     +e++ v+ gd+ de++L++ 
  EPA05296.1  9 GGGYIGSVLSKYLLNnGY-SVTVLDNFRYNQNSLlnccYDENFSVIRGDVRDEHTLAKS 66
                7899***********666.6*****9875544443333888999************974 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0     3e-06    0.0039       1      77 [.       4      77 ..       4      84 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3e-06
                     EEEE--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-S CS
  Sacchrp_dh_NADP  1 vliiGa.GsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnls 77
                     +li G+ G++G+++ ++l++++ +   +tv d  + + + l++    ++f+ i  d+ ++   La+ + ++d++++l+
       EPA05296.1  4 ILITGGgGYIGSVLSKYLLNNG-Y--SVTVLDNFRYNQNSLLNCCYDENFSVIRGDVRDEHT-LAKSIHDQDFIIHLA 77
                     6788888******999999998.5..7**********99999888****************9.*************98 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   6.2e-05     0.079       4      74 ..       5      69 ..       3     101 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.2e-05
                EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHH CS
          KR  4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdaveallee 74
                litGG G +G +l++ l+++g +  vl   +     ++++l++    ++ + +v++ Dv d++ +++ +++
  EPA05296.1  5 LITGGGGYIGSVLSKYLLNNGYSVTVLDNFR----YNQNSLLNC--CYDENFSVIRGDVRDEHTLAKSIHD 69
                9********************8877775555....233334553..3455677788888888887777665 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00017      0.22       6      30 ..       9      33 ..       3      41 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00017
                CSSHHHHHHHHHHHHTTSEEEEEES CS
   Pyr_redox  6 GgGyiglElAgalaelgkkVtvver 30
                GgGyig  l ++l + g +Vtv+++
  EPA05296.1  9 GGGYIGSVLSKYLLNNGYSVTVLDN 33
                89********************976 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00022      0.28     149     173 ..       9      33 ..       2      53 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00022
                  S-SHHHHHHHHHHHHHT-EEEEEES CS
                  xxxxxxxxxxxxxxxxxxxxxxxxx RF
  Pyr_redox_2 149 GgGyiGvElAaalaklgkevtlvea 173
                  GgGyiG++l+ +l + g+ vt+++ 
   EPA05296.1   9 GGGYIGSVLSKYLLNNGYSVTVLDN 33 
                  689******************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1361.34
//
Query:       EPA05297.1  [L=42]
Description: hypothetical protein BG20_I0139 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.34s 00:00:00.75 Elapsed: 00:00:00.49
# Mc/sec: 260.30
//
Query:       EPA05298.1  [L=389]
Description: putative ATP synthase F0, A subunit [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.2e-07   29.4   1.5    7.2e-07   29.4   1.5    4.4  4  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
    0.00072   18.9  25.2      0.017   14.4   3.0    3.2  3  Polysacc_synt_3  Polysaccharide biosynthesis protein
  ------ inclusion threshold ------
       0.28   11.0   1.7        1.1    9.0   0.1    2.6  2  DUF4538          Domain of unknown function (DUF4538)
        1.9    7.8  40.5       0.12   11.7  24.9    3.5  2  Polysacc_synt    Polysaccharide biosynthesis protein


Domain annotation for each model (and alignments):
>> Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   7.3      0.41   1.8e+03      72     136 ..      33     104 ..      12     107 .. 0.49
   2 !    5.7   0.5    0.0033        15      34      85 ..     139     189 ..     133     208 .. 0.77
   3 ?    0.9   2.3     0.098   4.4e+02       2      53 ..     241     292 ..     240     294 .. 0.81
   4 !   29.4   1.5   1.6e-10   7.2e-07       1      73 [.     302     374 ..     302     386 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.41
  Polysacc_synt_C  72 lnlyalrrllgiklellrrll.....kpllaalvmgivvylllllllglllla......al.alllavlvgalvYll 136
                      l +++l  llg     +  l        +l +++ ++++ +ll ++++    +       + +l+ + +vg+  Y++
       EPA05298.1  33 LFWIYLASLLGTEK--YGELGyllaiIGILGGIASFGAANTLLVYVPKG---EkiqaviFFvVLISGTIVGITSYFI 104
                      34455555555555..223321001122333333333333333333333...2555555224666666788888876 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0033
  Polysacc_synt_C  34 alvigalvklilnllliplfgivGaaiatvlallvvavlnlyalrrllgikl 85 
                      ++v+   + ++l+l+l  + gi G++++  l+++   +l++   r   +i++
       EPA05298.1 139 YMVLQRTLMVVLSLVLYKYQGIDGIIFGYSLSFFPFGILMYKSFRE-SKIDF 189
                      6666667889*******999*************9999988665554.44444 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.098
  Polysacc_synt_C   2 LailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplf 53 
                      La+l++ +++++     +s +  l+  k++++ ++i  ++ + l+ + ip+f
       EPA05298.1 241 LAMLVPNVVIQYTLPHDASGIKNLKLKKYTVLTSIIITIITISLSPIIIPQF 292
                      6777777777777777777777788889999999999*******99999998 PP

  == domain 4  score: 29.4 bits;  conditional E-value: 1.6e-10
  Polysacc_synt_C   1 vLailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplfgivGaaiatvlallvvavln 73 
                      v++i++ls++++sls+++ss L g gr+ki+l+a++i++    +  +l+  ++g+ G+ ++ v++ ++ ++++
       EPA05298.1 302 VIQIMSLSFVPQSLSILYSSELLGSGRTKIILIATIISISTLSVGIILFGEKYGLFGITVSFVIGKIAEFLFI 374
                      689*************************************************************998766655 PP

>> Polysacc_synt_3  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.7   1.2    0.0016       7.3       2      64 ..      38     100 ..      37     113 .. 0.86
   2 !   14.4   3.0   3.8e-06     0.017     124     226 ..     146     244 ..     118     265 .. 0.73
   3 !   10.0   6.1     8e-05      0.36      54     156 ..     270     373 ..     266     381 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0016
  Polysacc_synt_3   2 LARLLspedFGvvaialvvislanlfvdmGlssaliqkedlteedlstvftfnlvlgllialv 64 
                      LA LL  e +G ++ +l++i+++  ++++G  + l+      e+   ++f + l++g+++ + 
       EPA05298.1  38 LASLLGTEKYGELGYLLAIIGILGGIASFGAANTLLVYVPKGEKIQAVIFFVVLISGTIVGIT 100
                      899***************************999988888777777889999999999887654 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 3.8e-06
  Polysacc_synt_3 124 vgvivaivlAllglgvwALvigtllssllslvllwlaskwrprlkfslkslkelfsfglklllsnllnylarnldnlliGkvlssaaLGlYsva 217
                      ++v++++vl + + g+  +++g  l     + + +l++k   + k++++ lk  ++f ++  ++++l +++ n+d+l+i  +++s+ LG Y+ +
       EPA05298.1 146 LMVVLSLVL-YKYQGIDGIIFGYSL---SFFPFGILMYKSFRESKIDFSILKGKMGFIINNYVKQILTIVNFNVDKLIIFPFFGSSVLGPYQLG 235
                      555555444.555555555555433...333333444444445668899********************************************* PP

  Polysacc_synt_3 218 krlaslpva 226
                       ++  l + 
       EPA05298.1 236 FQIFVLAML 244
                      *99876654 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 8e-05
  Polysacc_synt_3  54 nlvlgllialvlfllaplias.fy.nqpelvtvlrvlalvlilsglssvqeallrrelkFkklfkitlvssvvgvivaivlAllglgvwALvig 145
                      +++++++i+++++ l+p+i   f+ + +e ++v+++++l+++ ++ls + ++ l  + + k + ++t++s + ++ v+i+l    +g++ + ++
       EPA05298.1 270 TVLTSIIITIITISLSPIIIPqFLpKFDESIQVIQIMSLSFVPQSLSILYSSELLGSGRTKIILIATIIS-ISTLSVGIILFGEKYGLFGITVS 362
                      6899*************98652553669*******************************99999998876.56677888887777777777777 PP

  Polysacc_synt_3 146 tllssllslvl 156
                       ++ ++  +++
       EPA05298.1 363 FVIGKIAEFLF 373
                      77766666555 PP

>> DUF4538  Domain of unknown function (DUF4538)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.2      0.22   9.9e+02       8      24 ..      91     104 ..      79     107 .. 0.62
   2 ?    9.0   0.1   0.00025       1.1       1      26 [.     264     289 ..     264     300 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.22
     DUF4538   8 llvggvvgliglalYPi 24 
                 l+ g   +++g++ Y i
  EPA05298.1  91 LISG---TIVGITSYFI 104
                 2223...4567788866 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00025
     DUF4538   1 lrglkyvllvggvvgliglalYPiii 26 
                 l+ +ky++l + ++++i+++l Piii
  EPA05298.1 264 LKLKKYTVLTSIIITIITISLSPIII 289
                 5889*********************8 PP

>> Polysacc_synt  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7  24.9   2.7e-05      0.12       3     263 ..      15     251 ..      14     255 .. 0.78
   2 ?   -5.3   8.7         4   1.8e+04      84     183 ..     274     369 ..     246     388 .. 0.45

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.7e-05
  Polysacc_synt   3 kgvivlllsqlitkllafvtlvylarilgpegfGlvalalaivtllviltdlGlnaalvreiakyrekkelvslillnvllvllvlvllfllllli 98 
                    k++++  +s+l+++ ++ ++ +yla +lg+e +G + ++lai+++l  ++++G  ++l  ++ k ++       i   +++v+l++ +++ ++ ++
     EPA05298.1  15 KNITSVGISNLTSNAISGLFWIYLASLLGTEKYGELGYLLAIIGILGGIASFGAANTLLVYVPKGEK-------IQAVIFFVVLISGTIVGITSYF 103
                    8999************************************************************996.......4444556666666666444444 PP

  Polysacc_synt  99 aaflglpelavlylilalmllllvgvasfrrglfqglermkyaavsqvveqlsrvilvliavflfldivaavlgavlaalvggivslavlrkkfrp 194
                      f ++++l +++ + +++++        +  l   + + +y    +v++++  v+l+l++  + + i ++++g++l+ +  gi+ +  +r + + 
     EPA05298.1 104 -IFQNESILLYPLGYVIFSVV--------IFDLAGKKCFANYGKY-MVLQRTLMVVLSLVLYKYQG-IDGIIFGYSLSFFPFGILMYKSFR-ESKI 187
                    .36666666555555555555........3356777777777776.45555556668888888888.999999999888877666555555.3446 PP

  Polysacc_synt 195 rfvilslklvrellsfsapltisslaillytyidsillglllgaeavGiYnaayqllvaisgllapivt 263
                    +f+il     +  + f ++  + ++++ +++++d +++  + g++++G Y+++ q+ v++  + ++ ++
     EPA05298.1 188 DFSIL-----KGKMGFIINNYVKQILTIVNFNVDKLIIFPFFGSSVLGPYQLGFQIFVLAMLVPNVVIQ 251
                    77777.....556667788999*********************************99988777666665 PP

  == domain 2  score: -5.3 bits;  conditional E-value: 4
  Polysacc_synt  84 vllvlvllfllllliaa.flglpelav.lylilalmllllvgvasfrrglfqglermkyaavsqvveqlsrvilvliavflfldivaavlgavlaa 177
                    +++++++ + l++ i   fl + + ++ +++i++l+++++   +++ + l+ g  r k +++ ++++   + +l++  ++ +    + ++g++++ 
     EPA05298.1 274 SIIITIITISLSPIIIPqFLPKFDESIqVIQIMSLSFVPQSLSILYSSELL-GSGRTKIILIATIIS---ISTLSVGIILFGE--KYGLFGITVSF 363
                    222222222222222223332222222145555555554444444444443.334444444444433...3323222222222..24455555555 PP

  Polysacc_synt 178 lvggiv 183
                    ++g i+
     EPA05298.1 364 VIGKIA 369
                    555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       817  (0.0455686); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2438.08
//
Query:       EPA05299.1  [L=223]
Description: hypothetical protein BG20_I0130 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.7e-33  114.0   0.0      1e-32  113.6   0.0    1.2  1  adh_short_C2   Enoyl-(Acyl carrier protein) reductase
    6.4e-16   58.4   0.0    8.8e-15   54.7   0.0    2.1  2  adh_short      short chain dehydrogenase
    4.2e-07   29.4   0.0    6.5e-07   28.7   0.0    1.3  1  RmlD_sub_bind  RmlD substrate binding domain
    1.5e-06   27.8   0.0    4.7e-06   26.2   0.0    1.9  1  Epimerase      NAD dependent epimerase/dehydratase family


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.6   0.0   2.3e-36     1e-32      53     234 .]      40     221 ..      11     221 .. 0.83

  Alignments for each domain:
  == domain 1  score: 113.6 bits;  conditional E-value: 2.3e-36
                   HHHHHHHHHHHHHHHSSEEEEEE-----EG.....CSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSCCEEEEEEEGGGTSB........ST CS
  adh_short_C2  53 eeqvealveevvekfgklDilvnnagiapk.....lkgpfletsreefdraldvnlyslfllakaalplmkeggsivnlssvgaerv........vp 136
                   ee v +++++     +k D+lvn+ ++ ++     ++g + +++ e+f++ l++nl++lf++++++++  +++g ivn s + + ++          
    EPA05299.1  40 EEFVIDFFRN-----NKADCLVNCFAFNDHvkkgkKRGTIFDITLESFNEFLEINLTALFSVCRQFAK-NNHNGIIVNFSATTGIVSarpdiydgAH 130
                   4444444443.....688**********99999989999**************************987.4667999999988877652111111134 PP

                   TTTHHHHHHHHHHHHHHHHHHHHGGGTEEEEEEEE--BHCTGGGGSTTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEEEESTTG CS
  adh_short_C2 137 nynaygaaKaalealtrylAvelgpkgiRvNavspgpikTlaasgikgfdelleelearaplgrlgtpeevaeaalfLasdeasyitGqtlvvDgGl 233
                   ++ ay+++Ka++++lt+ lA +l+p +iRvN+++pg  +      +++ ++++e+  + +p++r+++ +e  e++ fL+s  +syitG+t+vvDgG+
    EPA05299.1 131 KHPAYSISKAGVINLTKFLATHLAP-NIRVNCIAPGGAR------FDQDENFIEKYSKLTPMKRMMEKNELNELVEFLCSSGSSYITGATIVVDGGW 220
                   455**********************.**********999......66778899*******************************************9 PP

                   G CS
  adh_short_C2 234 t 234
                   t
    EPA05299.1 221 T 221
                   7 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.05   2.3e+02       3      26 ..       3      25 ..       1      33 [. 0.78
   2 !   54.7   0.0     2e-18   8.8e-15      77     183 ..      51     168 ..      34     179 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.05
                EEEESTTSHHHHHHHHHHHHTT-E CS
   adh_short  3 vlvtGassGIGraiakelakeGak 26
                ++vtG  + +G +i++ l k+  +
  EPA05299.1  3 IIVTGSEGFLGSEISQYLEKN-NE 25
                89*****99*****9987665.44 PP

  == domain 2  score: 54.7 bits;  conditional E-value: 2e-18
                 SESEEEE---S.......S--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTS........B-TTBHHHHHHHHHHHHHH CS
   adh_short  77 kldvLvnNAGi.......tgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkv........pvagvaaYsAsKaavaglt 160
                 k d+Lvn+ +        +++g++ +++ e +++ +e+Nlt++f+++r+++++   +++G Ivn s ++g v        +    +aYs sKa+v+ lt
  EPA05299.1  51 KADCLVNCFAFndhvkkgKKRGTIFDITLESFNEFLEINLTALFSVCRQFAKN---NHNGIIVNFSATTGIVsarpdiydGAHKHPAYSISKAGVINLT 146
                 6699999999999999988999999**************************99...9*************7622222222456789************* PP

                 HHHHHHHGGGTEEEEEEEESSBS CS
   adh_short 161 rslakelaptgirvnavaPGlvd 183
                 + la  lap  irvn++aPG+ +
  EPA05299.1 147 KFLATHLAPN-IRVNCIAPGGAR 168
                 *********5.*********876 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0   1.5e-10   6.5e-07       1      64 [.       1      64 [.       1      83 [. 0.91

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 1.5e-10
                   EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT.T--TTSHHHHHHHHHHH--SEEEE------H CS
  RmlD_sub_bind  1 mkilvtGanGqlGseLakqlaeeglevlaltre.eldltdaeavaellkeakpdvvvnaAAytav 64
                   m+i+vtG++G lGse+ + l++++ ev+ l+ +   dlt++e v ++++++k d++vn+ A+ + 
     EPA05299.1  1 MRIIVTGSEGFLGSEISQYLEKNN-EVIRLDIKlGHDLTNEEFVIDFFRNNKADCLVNCFAFNDH 64
                   89*******************888.99999766599************************99875 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0     1e-09   4.7e-06       1      83 [.       3      71 ..       3     151 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 1e-09
                EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S.---HHHHHHS CS
   Epimerase  1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAa.vggvaassed 83
                i+VtG  Gf+Gs + ++l++++ evi ld +                 dlt+++ + ++f+++++d+ +++ a   +v+   ++
  EPA05299.1  3 IIVTGSEGFLGSEISQYLEKNN-EVIRLDIK--------------LGHDLTNEEFVIDFFRNNKADCLVNCFAfNDHVKKGKKR 71
                89****************9876.99999999..............688***********************7768888875544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1760.74
//
Query:       EPA05300.1  [L=281]
Description: polysaccharide deactylase family protein, PEP-CTERM locus family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.5e-29  101.1   0.0    8.4e-29  100.2   0.0    1.5  1  DUF3473          Domain of unknown function (DUF3473)
    2.1e-14   53.5   0.0    3.7e-13   49.5   0.0    2.1  2  Polysacc_deac_1  Polysaccharide deacetylase
  ------ inclusion threshold ------
      0.052   13.2   0.1       0.11   12.2   0.1    1.6  1  DUF2334          Uncharacterized protein conserved in bacteri


Domain annotation for each model (and alignments):
>> DUF3473  Domain of unknown function (DUF3473)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.2   0.0   1.4e-32   8.4e-29       1     128 [.     147     280 ..     147     281 .] 0.92

  Alignments for each domain:
  == domain 1  score: 100.2 bits;  conditional E-value: 1.4e-32
     DUF3473   1 SSvfPvrhdlyGipdaprkpfrikkekgk......llElPvstlklggrnlplaGGgyfRlfPyalikallrrlnregrpavlYfHpwEldpdqp.rvk 92 
                 SS++P++++lyG++da+ +p++i+++         l+E+P+ ++k++g+++p++GG+++R++P+++i ++++++++ + pa +Y+H wEl p+    + 
  EPA05300.1 147 SSIVPAKTKLYGFNDADVAPYNISSDFLMgdnkssLIEFPLLITKVFGKKIPAGGGFFLRFLPLKIIDSAIKSYQKLHIPATFYIHSWELTPELMpSL- 244
                 9******************9999886333556667*********************************************************986255. PP

     DUF3473  93 gaslksrfrhylnlkrteerlrrllsdfeFttveel 128
                  +s+  +f +y+nl+++  ++++l+++++Ft++e++
  EPA05300.1 245 PLSISDKFITYHNLRNALPKMTKLIKKYQFTSFERY 280
                 699*****************************9987 PP

>> Polysacc_deac_1  Polysaccharide deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.5   0.0   6.2e-17   3.7e-13      22     113 ..      44     132 ..      41     139 .. 0.90
   2 ?    1.8   0.0     0.035   2.1e+02      24      41 ..     216     233 ..     209     273 .. 0.83

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 6.2e-17
                      HHHHHHHHHCT--EEEEE-HHHHCH-HHHHHHHHHTTEEEEE--SS--EGGGSHHHHHHHHHHHHHHHHHHHHS----EEE-GGGEE-HHHH CS
  Polysacc_deac_1  22 teilpvLkkykvkatffvigglvedypdevremaasGveignHtinhsnlkrlseeevrreierakdalrkalgreprlfryPygsasatvl 113
                      +++l+ L+k++  atff++g+l e+ p+++ ++ ++G+ei+ Ht++h++l     +++++ +e+  d + k +  +++ fr+P+ s ++++ 
       EPA05300.1  44 DKMLDWLRKNETFATFFMVGELLEKKPELLDKIIENGHEIAFHTMQHNRL---DDNNFKEKFEKELDLFDKLTSGKSKGFRAPTFSLNKNTS 132
                      689********************************************995...5667777777777999999*************9999984 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.035
                      HHHHHHHCT--EEEEE-H CS
  Polysacc_deac_1  24 ilpvLkkykvkatffvig 41 
                      +++  +k +++atf++ +
       EPA05300.1 216 AIKSYQKLHIPATFYIHS 233
                      56667899*******976 PP

>> DUF2334  Uncharacterized protein conserved in bacteria (DUF2334)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   1.8e-05      0.11      59     146 ..      71     147 ..      66     235 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.8e-05
     DUF2334  59 evLkylqakGgeialHGYtHqygtvksevsgegfeflseseakeriekGieilkklgi.kpkgFeaPhyaaseetykalkky..fsiiyer 146
                 e+L+++ ++G+eia H  +H                   + +ke+ ek +++++kl   k kgF aP ++ +++t  a+ +    +++y++
  EPA05300.1  71 ELLDKIIENGHEIAFHTMQHNRLD--------------DNNFKEKFEKELDLFDKLTSgKSKGFRAPTFSLNKNTSWAIDHLieKKYLYDS 147
                 5799999***********999972..............34459999999999999998799999999999999999999855222334433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1960.34
//
Query:       EPA05301.1  [L=302]
Description: asparagine synthase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.2e-26   92.5   0.0    5.5e-26   92.1   0.0    1.1  1  Asn_synthase  Asparagine synthase


Domain annotation for each model (and alignments):
>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.1   0.0   3.1e-30   5.5e-26      61     355 .]       5     286 ..       3     286 .. 0.80

  Alignments for each domain:
  == domain 1  score: 92.1 bits;  conditional E-value: 3.1e-30
  Asn_synthase  61 kyakevaehlgtehtelvlteeelldalpdviyhleepfadrsaiplyllsrlakrkgvkvvLsGeGaDElfgGYpyfykaalsrsrefeklplars 157
                   k+ k++a+ l+t h+ ++++    +++lp++i+++  pf+d     +y+l+++a ++ +  ++sG+G+DElfgGY+++y+  l   + ++   + r+
    EPA05301.1   5 KMPKKIADNLNTAHHIIEVE--NYFEELPKAISITKLPFWDI---HWYYLAKYA-SSYSNAIISGDGGDELFGGYTFRYNSFLALINSKS---TKRE 92 
                   56799********9766665..589*************9975...5********.888******************88886644433332...2333 PP

  Asn_synthase 158 lrasllarklrklaelle.laeardleelaelyrlkasdsaeaelegedelhrelyldlktllpgdllrk.DrasmahglEaRvPflDhrlvevalr 252
                   +  s l+ + r++    e l+ ++  ++++++y+   +       ++  +l++ ++ d++  l ++ l+   ++   + l    PflD +l+++   
    EPA05301.1  93 KTVSYLNCHNRDWIPEQEqLFGEKLHFNWEKIYTIIDE----YFDNSLNALDQVFLADFNGKLLYNWLQLnPKINSFFNLQSISPFLDPKLINFTSH 185
                   33333333333333222201223333333333333322....45678999*********998888888887************************** PP

  Asn_synthase 253 lppelklrg..gieKyiLRealegylPeeileRpKegfsapvgewklkgelrelaeellsdsrlakeglldreaveelleeheagkrnesrqlwsll 347
                   +p e+k+++  + +K iLR +l+ +  e+++  +K+gfs+ +++  +k+  ++l+e  l d    k +l+++  +++ +++  +    + ++   ll
    EPA05301.1 186 IPNEMKYDPtkKLGKLILRNILKEFNVEKFVIPKKQGFSVDTKSL-WKNYGKKLCETFLVDGEIIKDKLINKNWIDDNIDKELD--IRHVNKFYGLL 279
                   ********9999*************99************988888.899******************************99999..77788888888 PP

  Asn_synthase 348 lsleawle 355
                    +le w++
    EPA05301.1 280 -ALEIWHR 286
                   .9999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 2009.84
//
Query:       EPA05302.1  [L=333]
Description: oxidoreductase, NAD-binding domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      9e-21   74.9   0.0    1.3e-20   74.4   0.0    1.3  1  GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fol
  ------ inclusion threshold ------
       0.18   11.7   0.8        1.1    9.1   0.1    2.3  2  Rad60-SLD     Ubiquitin-2 like Rad60 SUMO-like


Domain annotation for each model (and alignments):
>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.4   0.0   1.5e-24   1.3e-20       1     120 []       5     124 ..       5     124 .. 0.94

  Alignments for each domain:
  == domain 1  score: 74.4 bits;  conditional E-value: 1.5e-24
                   EEEEEETTSHH.HHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-GGGHHHHHHHHHHTT-EEEEESSS- CS
  GFO_IDH_MocA   1 lrvaiiGaGki.gskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladpeidavivatpngtheelakaaleagkhvllEKPla 96 
                   +r++iiG+ +i  s  ++++ es + +e+  + ++ +++a+++a++f+++ y  +ee+l+d ++dav++ +p g+he+  ++a++agkh+l+EK  +
    EPA05302.1   5 IRFGIIGCSRIsDSSTIPAIIES-QYAELEFIGSRTTAKAKRFAKKFDCKKYGTYEEVLKDNQVDAVYISVPIGLHEKWSIRAARAGKHILCEKSST 100
                   699********555667566666.999********************************************************************** PP

                   SSHHHHHHHHHHHHHHTS-EEEE- CS
  GFO_IDH_MocA  97 ttveeakelvelaekkgklvsvgy 120
                    ++e ak++v   +k++++++ g+
    EPA05302.1 101 SSYESAKKMVSESKKNNVRIMEGF 124
                   ******************999875 PP

>> Rad60-SLD  Ubiquitin-2 like Rad60 SUMO-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0     0.077   6.9e+02       2      17 ..     214     229 ..     205     231 .. 0.70
   2 ?    9.1   0.1   0.00013       1.1       5      47 ..     264     304 ..     260     316 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.077
                 EEEEEESSS--EEEEE CS
   Rad60-SLD   2 kiilkgkdgkevkikV 17 
                 +i l  kdgk  +++V
  EPA05302.1 214 NILLIFKDGKVAEMNV 229
                 5667777777777766 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00013
                 EEESSS--EEEEEETTSBHHHHHHHHHHHHT----TT-EEEET CS
   Rad60-SLD   5 lkgkdgkevkikVkptttvskLieayrkkkgipeeqkvrLiFD 47 
                 lk ++ k ++ik+kp+++++ +i+ + k+ + ++  k  + F+
  EPA05302.1 264 LKINTEKIMEIKIKPENHFKLMIDSFSKEIQGQR--KHSFNFE 304
                 777888999*****************99877666..5555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2121.17
//
Query:       EPA05303.1  [L=228]
Description: NeuB family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-51  173.8   0.0    4.9e-51  173.5   0.0    1.1  1  NeuB      NeuB family
  ------ inclusion threshold ------
      0.069   13.8   0.0       0.16   12.6   0.0    1.7  2  SAF       SAF domain


Domain annotation for each model (and alignments):
>> NeuB  NeuB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.5   0.0   5.5e-55   4.9e-51      89     241 .]       2     155 ..       1     155 [. 0.97

  Alignments for each domain:
  == domain 1  score: 173.5 bits;  conditional E-value: 5.5e-55
                 T-S-EEE-GGGTT-HHHHHHHHTT-S-EEEE-TT--HHHHHHHHHHH..HHHT--EEEEE----SS--GGG--THHHHHHHHH-TSEEEEE--SSSSHH CS
        NeuB  89 gveayKiaSgeltnlpllekiaktgkpvilStGmatleeieeavevl.reagaeklvllhCtseYPapledvnLkaietlkeafgvpvGySDHtlgiav 186
                 g++a+Ki++ + tn+ +l ++ak++kp+ilStG++t e +++av++l + + ++kl+ll+ ts+YP+p+edvnL++i+++ +++++pvG+SDHt ++ +
  EPA05303.1   2 GISAFKISASDTTNHLFLTYVAKQQKPIILSTGLSTSEHVDNAVALLtKLKMRNKLILLQTTSDYPTPYEDVNLRVIPEYIKRYDLPVGLSDHTPDYLA 100
                 789********************************************44467899******************************************** PP

                 HHHHHHHT--EEEEEB-S-TT--STTGGG-B-HHHHHHHHHHHHHHHHHSS--TT CS
        NeuB 187 aiaAvalGAkviEkHftldrnlegpDhkaSlepeelkelveairnvekalgegek 241
                 ++ Ava+GA+v+EkHftl+++l+gpD++ Sl+p elk+ ++++r++e +lg+++k
  EPA05303.1 101 SLGAVAMGACVLEKHFTLNKKLSGPDQSSSLDPIELKNWIKNVRSMEIILGSKNK 155
                 ***************************************************9876 PP

>> SAF  SAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0         2   1.8e+04      36      44 ..      82      90 ..      72      92 .. 0.62
   2 ?   12.6   0.0   1.8e-05      0.16       7      63 .]     173     228 .]     170     228 .] 0.95

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2
                CGGHHHHTT CS
         SAF 36 piaygeviG 44
                 ++y+ ++G
  EPA05303.1 82 IKRYDLPVG 90
                334788887 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 1.8e-05
                 SSTB-TT-BEBTTTEEEECECGGCCTSCCCGG..HHHHTTEEESS-B-TT-B-BGGGEE CS
         SAF   7 ardikaGeviteddltlkrpiashkigllpia..ygeviGkratrdikaGepvhahnle 63 
                 +++ k+G++it   l +kr++     g+lp +  +  ++Gk+++++ik  + + ++++e
  EPA05303.1 173 IKPAKKGSTITSNLLNAKRGN---IYGILPLEqnICKILGKKLKKEIKFETQLKWSMIE 228
                 6899****************9...********************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1616.36
//
Query:       EPA05304.1  [L=99]
Description: hypothetical protein BG20_I0160 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-10   41.4   0.0    1.6e-10   41.3   0.0    1.0  1  CTP_transf_3  Cytidylyltransferase


Domain annotation for each model (and alignments):
>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   0.0   9.2e-15   1.6e-10      74     171 ..       1      96 [.       1      99 [] 0.90

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 9.2e-15
                   HHHHHHHHHHHTTT.TTSEEEEE-TT-TT--HHHHHHHHHHHHHSTTSSEEEEEE...ETTSHHHHTSTTSTEEEETTTSBEEE.EESSESSEEHHH CS
  CTP_transf_3  74 terflevvkaflmseneeiivnlqGdnPllqeevikkaietlkenqedylstlvk...kvgkeeevlnandlkvllddagkaly.feesvipyiree 166
                   ++r ++  k+++++     iv++++dnPl+++e i+ a+e++++ + d ++t++k   ++g + ev+++++lk+ + +a   ly  +e+vi+yi+++
    EPA05304.1   1 MDRHYQCAKKYSFD----PIVRVTSDNPLVDPEIIDLAVEKYEKGGFDMVTTCNKrsfPYGISVEVFSFDALKKSWNNA--VLYsEREHVILYIQNK 91 
                   58999999******....9*****************************9999998555799*****************9..66615689******99 PP

                   HHCTS CS
  CTP_transf_3 167 plels 171
                    ++l+
    EPA05304.1  92 KIILK 96 
                   99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 694.85
//
Query:       EPA05305.1  [L=277]
Description: NeuB family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-67  228.1   0.1    1.2e-67  227.9   0.1    1.0  1  NeuB      NeuB family


Domain annotation for each model (and alignments):
>> NeuB  NeuB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  227.9   0.1   6.7e-72   1.2e-67       1     241 []      22     259 ..      22     259 .. 0.96

  Alignments for each domain:
  == domain 1  score: 227.9 bits;  conditional E-value: 6.7e-72
                 HHHHHHHHT-SEEEEEE--HHHH--GGGGG--......TT-S-HHHHHHHH---HHHHHHHHHHHHHTT-EEEEEE-SHHHHHHHHHHT-S-EEE-GGG CS
        NeuB   1 lieaAaeagadavKfQtfkaeelvskeakkaeyqkkekekeesqlellkklelseeehkelkeyceekgieflstpfdlesvdlleslgveayKiaSge 99 
                 li++A +ag+davKfQ+++ e+++ske  ++   +++++++ +q +  k le++ +++k++ +yc++k+i +  + +d++s  l++++++++ K+aS+ 
  EPA05305.1  22 LIDVAISAGCDAVKFQKRTIEKVYSKEILDSP--RDSPWGT-TQRDQKKGLEFTVSDYKKINQYCKSKKIPWYLSCWDVDSQILMRQFKTKYNKVASAM 117
                 79************************976666..5666665.9******************************************************** PP

                 TT-HHHHHHHHTT-S-EEEE-TT--HHHHHHHHHHH.HHHT--EEEEE----SS--GGG--THHHHHHHHH-TSEEEEE--SS.SSHHHHHHHHHT--E CS
        NeuB 100 ltnlpllekiaktgkpvilStGmatleeieeavevlreagaeklvllhCtseYPapledvnLkaietlkeafgvpvGySDHtl.giavaiaAvalGAkv 197
                 l+n +ll+ ia+ +k  ++StGm+t+++i++a++++ ++    + l+h  s+YP+++e++nLk+i+tlk++f++ vGyS+H++  + v+++Av lGA+ 
  EPA05305.1 118 LVNEKLLKIIAEEKKYTFISTGMSTMGQISDAIRIF-KKYDCPFELMHSHSAYPMKIEEANLKVIQTLKKKFKCDVGYSGHESsAYLVCVTAVVLGATS 215
                 ************************************.666779**************************************9967889*********** PP

                 EEEEB-S-TT--STTGGG-B-HHHHHHHHHHHHHHHHHSS--TT CS
        NeuB 198 iEkHftldrnlegpDhkaSlepeelkelveairnvekalgegek 241
                 iE+H+tldr++ g+D++aSlep  l ++v++ir++ k+lg+g+k
  EPA05305.1 216 IERHITLDRSMYGSDQAASLEPIGLMRMVKDIRTLDKILGDGRK 259
                 ****************************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2013.56
//
Query:       EPA05306.1  [L=61]
Description: iron dependent repressor, N-terminal DNA binding domain protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-11   44.2   0.1    2.3e-11   43.7   0.1    1.2  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
     0.0054   16.6   0.0     0.0066   16.3   0.0    1.1  1  MarR            MarR family
  ------ inclusion threshold ------
      0.025   14.6   0.0      0.028   14.5   0.0    1.1  1  NLPC_P60        NlpC/P60 family
      0.031   14.2   0.0      0.038   14.0   0.0    1.2  1  HTH_37          Helix-turn-helix domain
      0.047   14.2   0.0      0.063   13.8   0.0    1.2  1  HTH_27          Winged helix DNA-binding domain
      0.051   13.5   0.0      0.063   13.2   0.0    1.2  1  MarR_2          MarR family


Domain annotation for each model (and alignments):
>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.7   0.1   7.9e-15   2.3e-11       4      45 ..      20      61 .]      19      61 .] 0.96

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 7.9e-15
                    HHHHHHHHHHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHH CS
  Fe_dep_repress  4 estEdYLetIYtlseekkvvktkdlaerLnvspssVsemlkk 45
                    e  E+YL++I+ ++e ++ vk + +a+ Lnv+ +sV +mlkk
      EPA05306.1 20 EHVEMYLKAIWHIKERGEDVKISTIAKMLNVRQPSVVQMLKK 61
                    678*************************************98 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   2.2e-06    0.0066       8      40 ..      28      61 .]      25      61 .] 0.90

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.2e-06
                HHHHHHHSTT.EEHHHHHHHHTS-HHHHHHHHHH CS
        MarR  8 iLrilyeqgp.lsvseLakklgvskstvtrvldr 40
                +++ ++e+g+  ++s +ak+l+v +++v  +l++
  EPA05306.1 28 AIWHIKERGEdVKISTIAKMLNVRQPSVVQMLKK 61
                67789999988*********************97 PP

>> NLPC_P60  NlpC/P60 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   9.3e-06     0.028      58      93 ..      12      46 ..       9      58 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 9.3e-06
                EEESGTGGESEEEEEEETTEEEEEETTEEEEEETTS CS
    NLPC_P60 58 vffktkkgisHvgiYlgngkmlhassekvsvsslse 93
                +f++t  +++Hv +Yl+  +++++ +e v++s++ +
  EPA05306.1 12 LFVGT-AEAEHVEMYLKAIWHIKERGEDVKISTIAK 46
                67777.999*********************998865 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.3e-05     0.038       7      53 ..      16      60 ..      14      61 .] 0.76

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.3e-05
                --HHHHHHHHHHHHHHHHHHHHHCT--HHHHHHHHT--HHHHHHHHT CS
      HTH_37  7 eedaeelkaKaqlalaiaeliekrelsqseaaqllgiaqPkvsrllr 53
                 ++ae ++   + ++ i+e  e+   + s +a++l++ qP+v+++l+
  EPA05306.1 16 TAEAEHVEMYLKAIWHIKERGED--VKISTIAKMLNVRQPSVVQMLK 60
                66777777777777888876555..55567***************97 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.1e-05     0.063       9      41 ..      29      61 .]      25      61 .] 0.94

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.1e-05
      HTH_27  9 Lhlirhrrrrkkladlcgrlnvedshisyslkk 41
                +++i++r++ +k++ ++++lnv + +++ +lkk
  EPA05306.1 29 IWHIKERGEDVKISTIAKMLNVRQPSVVQMLKK 61
                79***99999999***************99997 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.1e-05     0.063      13      44 ..      31      61 .]      24      61 .] 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.1e-05
                HHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHH CS
      MarR_2 13 aLgrrpgrdltvgelarrlglsksavsrilkr 44
                ++  r++ d+ ++ +a+ l++ +++v ++lk+
  EPA05306.1 31 HIKERGE-DVKISTIAKMLNVRQPSVVQMLKK 61
                5666664.89********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 387.42
//
Query:       EPA05307.1  [L=549]
Description: radical SAM domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.8e-15   55.8   0.0    1.3e-13   51.7   0.0    2.3  2  Radical_SAM  Radical SAM superfamily
    1.6e-14   54.0   0.0    3.2e-14   53.0   0.0    1.4  1  B12-binding  B12 binding domain
  ------ inclusion threshold ------
       0.55    9.8   3.7        1.8    8.1   1.5    3.0  4  Plasmo_rep   Plasmodium repeat family


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.061   3.6e+02      39      73 ..      91     122 ..      74     152 .. 0.75
   2 !   51.7   0.0   2.2e-17   1.3e-13       5     165 ..     213     405 ..     209     406 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.061
                  HHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHT CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM  39 kelkaekgvkevilgggepllypdfvellerlakl 73 
                  ++  a k    +i ggg  +++pd+++ l  ++ l
   EPA05307.1  91 RKH-A-K-DSIIIAGGGWITYNPDEIMQLIPEIDL 122
                  333.2.2.78899999*******999988766665 PP

  == domain 2  score: 51.7 bits;  conditional E-value: 2.2e-17
                  SEESS--TTTSCCTT............................HHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHT CS
                  xxxxxxxxxxxxxxx............................xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM   5 rgCnlrCsfCarpet............................vrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlakl 73 
                  rgC+++C+fC+ + +                                 ++r  ++++ ++ v  l+ ek  +++++++  + + +++ + +  +l  +
   EPA05307.1 213 RGCPRGCTFCSHNGMsridmqnilgrgdrkagellvreidkdnDTFQLPARWPTPRYAVDNVSLLY-EKYnIDFLTISDENMTSNAKWTNEFCKLYVE 309
                  8************99****************************99999*****************5.6666**************9998888888888 PP

                  CCCTEEEEEEECSSCHG....HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHHHH CS
                  xxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM  74 avpgiritvetngtlpd....eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGendeeleelle 165
                  +  + ++   t g  p+    +e ++ ++++g+ ++s+g e+a+d++  + + +g+t e++ +++ ++ ++g+ ++ ++++g p e   +l e++ 
   EPA05307.1 310 EGLDKKVKWGTLGDAPSvatkPELIKVMKDAGCSYISFGFESASDKVLSQDIQKGQTQEHLQKTINAIQNSGLQPIATFMIGNPHEDINDLMETVT 405
                  866666666666666666667*************************9999999************************************9999975 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.0   0.0   5.3e-18   3.2e-14      14     120 ..      20     135 ..      15     136 .. 0.94

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 5.3e-18
  B12-binding  14 plGlavlaaalrdagfeVqllganven..........edivaairaekpdvvglSalltsqleavkelvellkrirprvkvvvGGahpsldpeetlea 101
                  pl++ +la ++++++ +V +l++n+            + i+++i +ek d++g+   lts+++ +k+++ ++++  ++ ++++GG   ++ p+e+++ 
   EPA05307.1  20 PLWAGILASIVEKKNGHVGILDLNALRmnygggyvpsKVIEEEISSEKWDLIGIGG-LTSTYSRMKQIIPMIRKHAKDSIIIAGGGWITYNPDEIMQL 116
                  89999********9999****999999999999999999999************99.**************999999999999999**********87 PP

  B12-binding 102 klgiddvvvgegedaleal 120
                   ++id +++gege ++e++
   EPA05307.1 117 IPEIDLACIGEGEITFEEV 135
                  7***************986 PP

>> Plasmo_rep  Plasmodium repeat family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.62   3.7e+03       6      13 ..     107     113 ..     107     115 .. 0.73
   2 ?   -2.4   0.0      0.63   3.8e+03      12      22 ..     250     260 ..     249     260 .. 0.82
   3 ?   -0.9   0.0      0.21   1.2e+03       4      15 ..     489     500 ..     489     502 .. 0.86
   4 ?    8.1   1.5   0.00031       1.8       4      15 ..     532     543 ..     532     546 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.62
  Plasmo_rep   6 vYspkqEi 13 
                 +Y+p+ Ei
  EPA05307.1 107 TYNPD-EI 113
                 59999.76 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.63
  Plasmo_rep  12 EieqNrEIYnL 22 
                 Ei++++++ +L
  EPA05307.1 250 EIDKDNDTFQL 260
                 999**998776 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.21
  Plasmo_rep   4 nEvYspkqEieq 15 
                 +E+Y+ kq +++
  EPA05307.1 489 PELYALKQFMYK 500
                 79*****98886 PP

  == domain 4  score: 8.1 bits;  conditional E-value: 0.00031
  Plasmo_rep   4 nEvYspkqEieq 15 
                 ++++ ++qEi+q
  EPA05307.1 532 CQICKSEQEIYQ 543
                 79*********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (549 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       909  (0.0507); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.50
# Mc/sec: 3283.60
//
Query:       EPA05308.1  [L=276]
Description: glycosyltransferase, group 2 family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.5e-23   80.8   0.0    1.4e-22   80.3   0.0    1.3  1  Glycos_transf_2  Glycosyl transferase family 2
    3.9e-16   59.6   0.0    6.8e-16   58.8   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    0.00036   20.1   1.4     0.0016   17.9   0.1    2.2  3  Glyco_tranf_2_2  Glycosyltransferase like family 2
  ------ inclusion threshold ------
      0.022   14.2   0.0      0.041   13.4   0.0    1.4  1  Glyco_transf_21  Glycosyl transferase family 21
      0.053   14.0   0.1       0.36   11.4   0.0    2.1  2  Glyco_tranf_2_4  Glycosyl transferase family 2
      0.091   12.5   1.8       0.12   12.1   0.2    2.1  2  zf-TRM13_CCCH    CCCH zinc finger in TRM13 protein


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.3   0.0   4.7e-26   1.4e-22       1     116 [.       8     119 ..       8     166 .. 0.91

  Alignments for each domain:
  == domain 1  score: 80.3 bits;  conditional E-value: 4.7e-26
                      EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--SSEEEEEESSEEE-T CS
  Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatgdyilflDaDdepdp 94 
                      s++i  yN  k+ll ++esll+   y+++e+ivvD+ S+D++++ +++    +p+++++++  n G+ g+ n g+++a+g+++++l+ D++++ 
       EPA05308.1   8 SIIILNYNAGKLLLDCIESLLKL-SYENVELIVVDNVSNDDSQNECKKK---YPHIKLVQNQINSGYCGGNNIGIKEANGEFLVILNPDTIVES 97 
                      8**********************.*************************...89**************************************** PP

                      THHHHHHHHHHH.TTCEEEEEE CS
  Glycos_transf_2  95 dwleklvealekdgadvvlgqr 116
                      d + +l++a+  +g+++  +++
       EPA05308.1  98 DLIDELMKAYYIHGDGLYQPKI 119
                      *********9988887766665 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   0.0   2.3e-19   6.8e-16       4     228 ..       7     237 ..       5     238 .. 0.77

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 2.3e-19
  Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnealravksdlvllvDdD 97 
                      +++++ ++n+ + l++++esll+ +y +ve++vv++ s ++  ++++    ++p++  ++v+n+ n    g+  + n +++ ++++++++++ D
       EPA05308.1   7 VSIIILNYNAGKLLLDCIESLLKLSYENVELIVVDNVSNDDSQNECKK---KYPHI--KLVQNQINS---GYCGGNNIGIKEANGEFLVILNPD 92 
                      89*********************************8887777887876...9***7..788887653...688888****************** PP

  Glyco_tranf_2_3  98 tvvePdtlkrllqff.ltpkvgavgtpv.fllnrstlvsalgalefaerhlrflaar...........ralgvltlnGsgslirrevlkelegl 178
                      t+ve d+++ l  ++      + +++p+ ++l  +++++ +g++   ++ + f +ar           +  ++ + +G++++  r+ +  l ++
       EPA05308.1  93 TIVESDLIDELMKAYyI--HGDGLYQPKiLSLENKRVLQSTGNM---IHIFGFGFARnkgtvdnneinKVMKIGYAAGTCLFSSRSTFFKLNLF 181
                      **************943..3356665553555555554445442...22222222222222344334344455555688888888888888888 PP

  Glyco_tranf_2_3 179 dp.lflltdDyelglrlrragfrtayvpgaavrev.....fpsslkayikqrnRwv 228
                      d+ lfl  dD++lg r+ + g+ +++vp+  ++++     ++s+ k ++ +rnR +
       EPA05308.1 182 DEfLFLYHDDLDLGWRALQVGISSYIVPQTKIYHAesyslKWSKKKFFWLERNRRY 237
                      8889*******************************777777788999999999976 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.1   5.5e-07    0.0016      15     104 ..      20     105 ..       8     111 .. 0.79
   2 ?   -3.0   0.0       1.4   4.1e+03      58      77 ..     130     148 ..     118     159 .. 0.68
   3 ?    0.5   0.1      0.11   3.3e+02     247     264 ..     211     228 ..     193     240 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 5.5e-07
  Glyco_tranf_2_2  15 ieerv..lqkakyydeeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrGaskaesdlvlFlDaDcfissDkfekilk 104
                      + + +  l+k +y  e++elivvd+ S ++  +e ++   + +lv   ++     +     N G+++a++++++ l+ D  + sD ++ ++k
       EPA05308.1  20 LLDCIesLLKLSY--ENVELIVVDNVSNDDSQNECKKKYPHIKLVQ--NQ--INSGYCGGNNIGIKEANGEFLVILNPDTIVESDLIDELMK 105
                      5566655777888..9**************9999888777777665..33..445666779************************9999887 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.4
  Glyco_tranf_2_2  58 ylkdeddkayslaaarNrGa 77 
                      +  ++  + ++ + arN+G+
       EPA05308.1 130 STGNM-IHIFGFGFARNKGT 148
                      44444.44789999999997 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.11
  Glyco_tranf_2_2 247 fhlYheepksedylkkkd 264
                       ++Yh e+ s+++ kkk 
       EPA05308.1 211 TKIYHAESYSLKWSKKKF 228
                      589**********99984 PP

>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.4e-05     0.041      25     151 ..      77     213 ..      72     232 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.4e-05
  Glyco_transf_21  25 aleaakydllvisDsdvrvkpdyLeellaaledpkvglVtslpvgsdakglaaaleaafl......ntlagvlqa....klsglgfavGksmal 108
                      ++++a+ ++lvi+  d++v++d ++el++a    + gl +  ++  + k + +   + ++      + + g+++     k+ ++g a G ++  
       EPA05308.1  77 GIKEANGEFLVILNPDTIVESDLIDELMKAYYIHGDGLYQPKILSLENKRVLQSTGNMIHifgfgfARNKGTVDNneinKVMKIGYAAGTCLFS 170
                      7889999************************99899999988889999987766666665333333444666666655556799********** PP

  Glyco_transf_21 109 rreaLeaiGGfealadeLAeDyalgkllraaGlkvvlspapia 151
                      +r+++ ++  f ++     +D+ lg++  + G++ +++p++  
       EPA05308.1 171 SRSTFFKLNLFDEFLFLYHDDLDLGWRALQVGISSYIVPQTKI 213
                      ***************************************9844 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00012      0.36       1      49 [.      14      65 ..      14     104 .. 0.86
   2 ?    0.3   0.0      0.35     1e+03      16      66 ..     179     228 ..     175     246 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
  Glyco_tranf_2_4  1 rneadiLpeflahhlalgfdr..ilvydndstDgtrailkel.pevkllhvd 49
                     +n+ ++L  +++ +l+l +++  ++v+dn s D++ + +k+  p++kl++++
       EPA05308.1 14 YNAGKLLLDCIESLLKLSYENveLIVVDNVSNDDSQNECKKKyPHIKLVQNQ 65
                     58999999*********998555************99997744999998875 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.35
  Glyco_tranf_2_4  16 algfdrilvydndstDgtrailkelpevkllhvdksyederrqvellkall 66 
                      +l fd++l++ +d+ D  ++ l+      +++ +k y+ e +  ++ k+ +
       EPA05308.1 179 NL-FDEFLFLYHDDLDLGWRALQVGISSYIVPQTKIYHAESYSLKWSKKKF 228
                      55.888888888888888888877544445555566666666666665543 PP

>> zf-TRM13_CCCH  CCCH zinc finger in TRM13 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1       2.2   6.6e+03      21      26 ..      67      72 ..      66      72 .. 0.79
   2 ?   12.1   0.2   4.2e-05      0.12       5      17 ..     229     241 ..     229     247 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.2
  zf-TRM13_CCCH 21 gsryCg 26
                   +s yCg
     EPA05308.1 67 NSGYCG 72
                   678997 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 4.2e-05
  zf-TRM13_CCCH   5 ffipnKkRfCkmt 17 
                    f++++ +R+C mt
     EPA05308.1 229 FWLERNRRYCLMT 241
                    9***********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1702.11
//
Query:       EPA05309.1  [L=61]
Description: hypothetical protein BG20_I0109 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0011   18.6   0.4     0.0013   18.4   0.4    1.1  1  Phage_endo_I   Phage endonuclease I
  ------ inclusion threshold ------
      0.028   14.4   0.0      0.031   14.2   0.0    1.0  1  Helicase_IV_N  DNA helicase IV / RNA helicase N terminal


Domain annotation for each model (and alignments):
>> Phage_endo_I  Phage endonuclease I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.4   1.4e-07    0.0013      88     130 ..      11      53 ..       5      60 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.4e-07
                   SEEEEEES-TTSBSSTT-SSBHHHHHHHCT-EEEESS--HHHH CS
  Phage_endo_I  88 ldirlvfsssrtklykgspttyaewceknGikfadkliPvewl 130
                   l i  vfs+   kl+ +s ++ a + e + +k+adkl     +
    EPA05309.1  11 LSIHGVFSEQVKKLHSNSVSSIASFTESKVVKWADKLTTDSKI 53 
                   78999********************************877666 PP

>> Helicase_IV_N  DNA helicase IV / RNA helicase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   3.4e-06     0.031      64     105 ..       8      49 ..       2      60 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.4e-06
  Helicase_IV_N  64 qkvvrlhGlpweetqqfaqtllssyqqWskeqvqaladvlqk 105
                    +kv ++hG+  e++++++ + +ss+ ++ +++v + ad+l++
     EPA05309.1   8 KKVLSIHGVFSEQVKKLHSNSVSSIASFTESKVVKWADKLTT 49 
                    899*******************************99999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       808  (0.0450667); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 406.61
//
Query:       EPA05310.1  [L=389]
Description: glycosyltransferase, group 1 family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-34  118.3   1.1      5e-34  117.3   1.1    1.5  1  Glycos_transf_1  Glycosyl transferases group 1
    2.3e-25   89.6   0.0    4.3e-25   88.7   0.0    1.4  1  Glyco_trans_1_4  Glycosyl transferases group 1
    3.1e-05   24.0   0.0    7.7e-05   22.8   0.0    1.6  1  Glyco_transf_4   Glycosyltransferase Family 4
     0.0065   16.8   0.0      0.022   15.2   0.0    1.9  1  Glyco_trans_1_2  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.3   1.1   1.1e-37     5e-34       3     166 ..     202     365 ..     200     367 .. 0.96

  Alignments for each domain:
  == domain 1  score: 117.3 bits;  conditional E-value: 1.1e-37
                      HHHHHHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHHHCESEE CS
  Glycos_transf_1   3 ekkrkklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleellknadif 96 
                      +k  +k  ++ + +++l+vgrl+k+Kg++ll++ f +l+ +  +n+kl+i+G+g+ ++ +k+ ++++ l++++i++g++++e+   ++++a ++
       EPA05310.1 202 NKVAEKISLDVNFRYLLYVGRLTKNKGLELLLEIFNELNFK-FENIKLIIIGDGPLLEFIKNFIKNHDLEKKIILTGRLNHEKACYYYNIATVL 294
                      56667888888999************************998.**************************************************** PP

                      EEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTT.SEEEE-TT-HHHHHHHHHHHHHSHHHHHHHH CS
  Glycos_transf_1  97 vlpsisEgfGivllEAmaaglpviasnaggpaevvkdge.tGllvkpnnaealaeairklledeelrerlg 166
                      v +  s g++ v++E++a+g+p+i++n+g  +e++ +++ +G+++kp n ++l++ai+ +le+e++ +++ 
       EPA05310.1 295 VNTGLSAGLPNVIIESLASGTPTITTNVGASKEYIDEEKnNGIVIKPSNKDELKNAIITILENEKKFKNWD 365
                      ***************************************9************************9988885 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.7   0.0   9.6e-29   4.3e-25       3     134 .]     216     357 ..     215     357 .. 0.89

  Alignments for each domain:
  == domain 1  score: 88.7 bits;  conditional E-value: 9.6e-29
                      EEEEES---GG.GTHHHHHHHHHHHH.H..HEEEEEES---...HHHHHHHT..T-T.TEEEE---..THHHHHHHH-SEEEE--..---SHHH CS
  Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkk..dvrlvivGdgp.rpeeleelaa..gleerveftGfv..edlaellaaadvfvaPs..egfglkl 87 
                       +l+vGrl++n kg++llle + +l  k  +++l+i+Gdgp  +  +++ ++  +le+++++tG++  e+   +++ a+v+v++    g+++++
       EPA05310.1 216 YLLYVGRLTKN-KGLELLLEIFNELNFKfeNIKLIIIGDGPlLE-FIKNFIKnhDLEKKIILTGRLnhEKACYYYNIATVLVNTGlsAGLPNVI 307
                      589*****878.*************977645**********875.88887766799999*******9666777899999999998978****** PP

                      HHHHHTT-EEEE-TGGGTTT--...TTSSEE--TT-HHHHHHHHHHHHH- CS
  Glyco_trans_1_4  88 lEamaaglpvVatdvggiaevv...gengllvppgdpealaeailrLled 134
                      +E++a+g+p+++t+vg+ +e++   ++ng++++p + ++l +ai+++le+
       EPA05310.1 308 IESLASGTPTITTNVGASKEYIdeeKNNGIVIKPSNKDELKNAIITILEN 357
                      ***************989****9755899******************987 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   1.7e-08   7.7e-05       8     169 ..      35     194 ..      33     195 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.7e-08
  Glyco_transf_4   8 vleLaraLarrGheVtvvtpgddgpleeev.elvvrvprvplpllkrllrslaflrrlrrllkrekpDvvHahspaalgaallalrr......rl 95 
                      +++a+aL  + +e  v+  ++++ + +   ++++ ++r+p  + + l   + ++++l + +k+ ++ +    s +++++ +            +
      EPA05310.1  35 YHRIAKALSSKQFEPIVYYMSQEKIEKKFIhKYGHTIIRIPAKKINFLHEPIIYSPQLIKNIKK-NYEICNFVSGYYVMYKVPDMFDysvfklYK 128
                     5899**************76666655555569*******************************7.9****6666666666555555455554466 PP

  Glyco_transf_4  96 giplVltvHglyekrllkarlkplsrllralerrllrradrviavSeatadelrerygvppekitVipnGvDle 169
                     ++p+V+   g          +k+l ++++ + + +l+++d++++ S ++ + l+e + +++e+i  i n++Dl+
      EPA05310.1 129 KMPIVARWAGGN--------NKWLIPIRKSIKKAALQKCDKILVSSIEEINVLQEVFCIKRENISQIVNPIDLT 194
                     666666655555........89999999999*****************************************96 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   4.9e-06     0.022       4      66 ..     296     361 ..     291     381 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.9e-06
  Glyco_trans_1_2   4 npsrsespnlrlfEaaacGafaltddaegleelftpgk.evilfe..dleelaekiryllanpeer 66 
                      n+  s ++  ++ E +a+G++ +t+   +  e+++++k  +i+++  + +el  +i   l+n+++ 
       EPA05310.1 296 NTGLSAGLPNVIIESLASGTPTITTNVGASKEYIDEEKnNGIVIKpsNKDELKNAIITILENEKKF 361
                      666677888899*************9999999999887455666689***************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       884  (0.0493056); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2550.83
//
Query:       EPA05311.1  [L=183]
Description: hypothetical protein BG20_I0150 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-23   83.7   0.3    1.4e-23   83.5   0.3    1.0  1  TylF             Macrocin-O-methyltransferase (TylF)
      6e-13   49.7   0.0    8.1e-13   49.3   0.0    1.2  1  Methyltransf_24  Methyltransferase domain
     0.0003   20.6   0.0     0.0023   17.6   0.0    2.1  3  CmcI             Cephalosporin hydroxylase
  ------ inclusion threshold ------
      0.061   12.5   0.7       0.54    9.4   0.6    2.0  2  Methyltransf_3   O-methyltransferase


Domain annotation for each model (and alignments):
>> TylF  Macrocin-O-methyltransferase (TylF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.5   0.3   3.1e-27   1.4e-23      80     240 ..       4     167 ..       1     178 [. 0.82

  Alignments for each domain:
  == domain 1  score: 83.5 bits;  conditional E-value: 3.1e-27
        TylF  80 egvpGdliEtGvWRGGaailmrgvLkaegvedRkvwvaDsFeglPkpdeeklaedagdklkeleevlavseeevrenFrrygLlddqvrflkGwFkdtL 178
                 ++++Gd++E G  +GG++il + +L++ +   Rk++ +D F+glP +de   ++++++++ +l++   +s+e v+++F+++++ dd++  + G+F++tL
  EPA05311.1   4 KNLKGDVLELGTHKGGSTILFAKYLQNIND-PRKIYAVDWFKGLPYSDEFGNTDEKKKAKGRLND---TSKEFVESKFKQFNV-DDKIIVVDGLFEETL 97 
                 6899*********************99875.69**************997777777777777777...9************96.778999********* PP

        TylF 179 ptapiek.lallRlDgdlyestldaleaLYdkvskGGfviiDDyaavee.......creavedfreakgi 240
                  +   +k ++ + +D dly+s   ale++ +++ k G v + Dy+ + +       + +a++++ +++++
  EPA05311.1  98 YEKLNDKvFSFVFIDCDLYKSAKFALEYIDNHLEKDGIVFLHDYSNFLNrpkydwgIIKATDEYVREHKV 167
                 87655552789*********************************87632111112245566666666665 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.3   0.0   1.8e-16   8.1e-13       1     106 []      11     141 ..      11     141 .. 0.87

  Alignments for each domain:
  == domain 1  score: 49.3 bits;  conditional E-value: 1.8e-16
  Methyltransf_24   1 vEiGvysGvstlwllralrrnga.grlvavdhdpg........................aeeaaalareaglddrvrlikadseeala.slaag 68 
                      +E+G+++G st+++++ l++ ++  +++avd ++g                        +e ++  +++ ++dd + ++ + +ee+l  +l+++
       EPA05311.1  11 LELGTHKGGSTILFAKYLQNINDpRKIYAVDWFKGlpysdefgntdekkkakgrlndtsKEFVESKFKQFNVDDKIIVVDGLFEETLYeKLNDK 104
                      7*******************77779*************9999999988777777644433334444455999************9876488899 PP

  Methyltransf_24  69 siDllfiDgghaaeavledleallprlapggvvlfdDi 106
                       + ++fiD++  +++++++le + ++l ++g+v+++D+
       EPA05311.1 105 VFSFVFIDCD-LYKSAKFALEYIDNHLEKDGIVFLHDY 141
                      9********9.8*************************8 PP

>> CmcI  Cephalosporin hydroxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   5.2e-07    0.0023      36      68 ..      10      42 ..       3      51 .. 0.92
   2 ?   -3.0   0.0       1.1   4.9e+03     143     148 ..      86      91 ..      67     106 .. 0.58
   3 ?    0.1   0.0      0.12   5.5e+02     156     184 ..     143     170 ..     122     182 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 5.2e-07
        CmcI 36 iietGiahGGsalfsasllallkskrkvlaidi 68
                ++e+G++ GGs +++a+ l++++  rk+ a+d 
  EPA05311.1 10 VLELGTHKGGSTILFAKYLQNINDPRKIYAVDW 42
                68*****************************96 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.1
        CmcI 143 ivveDt 148
                 i+v D+
  EPA05311.1  86 IIVVDG 91 
                 444444 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.12
        CmcI 156 safsdrpwgkgnnPkeAveeflkeepe.fe 184
                 ++ ++++++ g    +A+ e+++e++  f+
  EPA05311.1 143 NFLNRPKYDWG--IIKATDEYVREHKVqFT 170
                 34555667777..77888899888876354 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0     0.036   1.6e+02      50      70 ..       9      29 ..       1      45 [. 0.68
   2 ?    9.4   0.6   0.00012      0.54      86     140 ..      71     122 ..      61     175 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.036
                    EEEEE--TTSHHHHHHHTTS- CS
  Methyltransf_3 50 rvleiGvftGyslLatalalP 70
                     vle+G+++G s +  a  l 
      EPA05311.1  9 DVLELGTHKGGSTILFAKYLQ 29
                    69**********999886553 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00012
                     HHHHHHHHHTT-GGGEEEEES-HHHHHHHHHTSSS---EEEEEE-S-GGGHHHHH CS
  Methyltransf_3  86 eialkfiqkagvaekieliegdalkvLeelvkdkklpefDfifvDaDkssyvnyy 140
                     e   + +++  v++ki +  g   ++L e ++dk    f f+f+D D  +  ++ 
      EPA05311.1  71 EFVESKFKQFNVDDKIIVVDGLFEETLYEKLNDKV---FSFVFIDCDLYKSAKFA 122
                     45555678889****************99999995...*********76665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 1180.76
//
Query:       EPA05312.1  [L=429]
Description: hypothetical protein BG20_I0149 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-07   29.1   0.1    8.4e-07   28.2   0.1    1.5  1  Epimerase_2      UDP-N-acetylglucosamine 2-epimerase
    1.7e-05   24.0   1.8    0.00017   20.7   1.7    2.2  1  Glyphos_transf   CDP-Glycerol:Poly(glycerophosphate) glycerop
  ------ inclusion threshold ------
      0.018   15.3   0.0      0.055   13.7   0.0    1.8  1  tRNA_NucTransf2  tRNA nucleotidyltransferase, second domain
      0.034   14.4   0.0      0.075   13.3   0.0    1.5  1  ChiW_Ig_like     Chitinase W immunoglobulin-like domain
      0.075   12.5   0.1       0.13   11.7   0.1    1.3  1  Capsule_synth    Capsule polysaccharide biosynthesis protein


Domain annotation for each model (and alignments):
>> Epimerase_2  UDP-N-acetylglucosamine 2-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.1   2.3e-10   8.4e-07     137     344 ..     214     420 ..     200     423 .. 0.68

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 2.3e-10
                  HHHTT--GGGEEE---HHHHHHHHHHHHHH...T-HHHHHH.--SS-EEEEE---HHHHTSHHHHHHHHHHHHHHHHHH--EEEEE--..HHHHHHH. CS
  Epimerase_2 137 LlkegeeeerifvvGntviDalllskeeieeklkaseilke.lkekkyvlvtlHrrenedeperlkeilealkalakekdvevvvpvhnnprtrkrl. 232
                   l+ ++++++ +++Gn+ +D+l+  k +  +++    il +     + +  t+       +    + + e+l++l+k  + +vv+ +h  p+  + + 
   EPA05312.1 214 CLDHKVDSNKLVITGNPRYDELFNRKVRTTDNY----ILITlSGIASTAWSTFFSSLLILKY--ENMFKEVLNSLSKY-KKNVVIKLH--PTQDSVId 302
                  5677889999************99988888888....3333345566677777777777744..67777888888886.6669*****..87777666 PP

                  .HHHHHH-.TTEEEE----HHHHHHHHHC-SEEEES-HHHHHHHHHCT--EEESSSS-S-THH.HHTTSEEE-TT-HHHHHHHHHHHCT-..--.... CS
  Epimerase_2 233 .leeleel.envtlieplgyldflsllknaklvltdSgGiqeEapslgvpvvnlReeteRpeg.veagtnvlvgtdkeeIvaaleklledkkelekma 327
                   + +++e+ ++++++++ +    + l++na+lv++ S+ ++ Ea +l++pv       +      e+ ++vl+ ++ +eI +++e++l dk+  ++++
   EPA05312.1 303 vKGIVNEIlPHAQIYKNAN---TYDLISNAELVISPSSSVITEALILDKPVFLFKFLANDSGIpYEKYNAVLATESINEIGSKIEHILFDKNIRRDLE 397
                  5556666666888887765...567899**********9999*********98743333222213455555577777777777777776644444444 PP

                  ..--TT......-SS-HHHHHHH CS
  Epimerase_2 328 naknpY......gdGkaserive 344
                    ++ +       +G++se+i++
   EPA05312.1 398 VGRKRFlehvleYQGNSSEEIIK 420
                  43333322222235666666666 PP

>> Glyphos_transf  CDP-Glycerol:Poly(glycerophosphate) glycerophosphotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   1.7   4.8e-08   0.00017     153     365 ..     217     422 ..     207     424 .. 0.70

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 4.8e-08
                     TT--GGGEEES--GGGHHHHHSTT-HHHHHHHHTT--SS-EEEEEE----GGG--GSS----TT-HHHHHHHHTTTEEEEE--SHHHHTT---TT CS
  Glyphos_transf 153 fnikkeeiletGyPrnDvlvkaesedvkrireelgipkdkkvilyaPTwRddevgesyrfelkldlerlakalgedyvillklHpliqekikike 247
                     ++++ +++++tG Pr+D l++++  +     + + i+    + +   T+  +  +    +  ++  e l    + + ++++klHp  ++ i+ k 
      EPA05312.1 217 HKVDSNKLVITGNPRYDELFNRKVRT---TDNYILITLSGIASTAWSTFFSSLLIL---KYENMFKEVLNSLSKYKKNVVIKLHPTQDSVIDVKG 305
                     578999****************6665...333333444333444466777777774...4444445666666777778999**********8855 PP

                     -TTTEE...E-TT-S-HHHHHHT-SEEEESS-THHHHHGGGT--EEEE-TTTTTTTTTSSBSS-.TTTSSSS-EESSHHHHHHHHTTHHHHHHHT CS
  Glyphos_transf 248 ksdyvv...dvsdeedvedlllasDiLiTDYSSvmFDyavldrPiifyayDleeYsekrgfyld.yekelPGpvveteeelieelksidkedeey 338
                       + ++    + ++++ +dl+  +++ i+  SSv+ + ++ld+P++ + +      ++ g+ ++ y++ l  + +++  + ie +   ++   + 
      EPA05312.1 306 IVNEILphaQIYKNANTYDLISNAELVISPSSSVITEALILDKPVFLFKFLA----NDSGIPYEkYNAVLATESINEIGSKIEHILFDKNIRRDL 396
                     444443222445566899****************************998866....444543333666666665555555555555545555556 PP

                     HHHHHHHHHHHSTT--S-HHHHHHHHH CS
  Glyphos_transf 339 eekrrafrdkfckydDgrsservvrli 365
                     e  r++f + + +y+ g+sse +++l+
      EPA05312.1 397 EVGRKRFLEHVLEYQ-GNSSEEIIKLV 422
                     667888888888887.88888888876 PP

>> tRNA_NucTransf2  tRNA nucleotidyltransferase, second domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.5e-05     0.055      22      62 ..     256     297 ..     248     325 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.5e-05
                      T-SB-HHHHHHHHHHHSS.HHHHHHHHTT--TTEEEE..... CS
  tRNA_NucTransf2  22 vkGfsGYlaEllvleygs.feevleaaakwkpkvvidleeke 62 
                       + +s + + ll+l+y++ f+evl++ +k+k++vvi+l+ ++
       EPA05312.1 256 STAWSTFFSSLLILKYENmFKEVLNSLSKYKKNVVIKLHPTQ 297
                      5668999*********8649****************865544 PP

>> ChiW_Ig_like  Chitinase W immunoglobulin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.1e-05     0.075      22      73 ..     206     259 ..     198     273 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.1e-05
  ChiW_Ig_like  22 vltlskGvakdGvldaev.eltGlPeG.lditaeGdssdntititvsrtaasav 73 
                     +lsk +  d ++d++   +tG P     ++   +++dn i it+s+ a+ a 
    EPA05312.1 206 YGNLSKQICLDHKVDSNKlVITGNPRYdELFNRKVRTTDNYILITLSGIASTAW 259
                   569**************989*****9966678899****************996 PP

>> Capsule_synth  Capsule polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   3.6e-05      0.13     172     260 ..     274     352 ..     270     355 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.6e-05
  Capsule_synth 172 allevLesfaeeapadaeliiKtHPldeglikyrrvikgyltelaalkkrvllvedvnlpsLldqvdgvvvvnStaGleALlhgkpvvt 260
                     ++evL+s  + +    +++iK HP   ++i+     kg ++e   l++++++ ++ n+  L+ + + v+   S +  eAL+  kpv  
     EPA05312.1 274 MFKEVLNSLSKYKK---NVVIKLHPTQDSVIDV----KGIVNEI--LPHAQIY-KNANTYDLISNAELVISPSSSVITEALILDKPVFL 352
                    56777777776655...9**************9....6666664..5666776.56799999************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 3096.81
//
Query:       EPA05313.1  [L=554]
Description: radical SAM domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.3e-15   56.9   0.2    3.3e-15   56.9   0.2    2.5  3  Radical_SAM  Radical SAM superfamily
    1.1e-06   29.0   0.0    3.2e-06   27.4   0.0    1.8  1  Fer4_12      4Fe-4S single cluster domain
    1.7e-06   28.1   0.0    1.7e-06   28.1   0.0    2.0  2  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   1.1      0.52   3.1e+03       7      18 ..      93     104 ..      92     109 .. 0.87
   2 !   56.9   0.2   5.6e-19   3.3e-15       1     165 [.     112     272 ..     112     274 .. 0.84
   3 ?   -2.4   0.0      0.91   5.5e+03      60      75 ..     459     478 ..     441     513 .. 0.56

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.52
                  ESS--TTTSCCT CS
                  xxxxxxxxxxxx RF
  Radical_SAM   7 CnlrCsfCarpe 18 
                  C+++C  C+++ 
   EPA05313.1  93 CPNNCGLCSNHL 104
                  *********985 PP

  == domain 2  score: 56.9 bits;  conditional E-value: 5.6e-19
                  EEEESEESS--TTTSCCTT....HHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHG..H CS
                  xxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..x RF
  Radical_SAM   1 vvvtrgCnlrCsfCarpet....vrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlaklavpgiritvetngtlpd..e 91 
                  ++vt+ C l C++C ++ +    ++  + + + +v+  ++ +k+   ++  ++ + ++ggep+l+ d+++ ++ ++++     ++ + tng+++   +
   EPA05313.1 112 MIVTNRCDLTCWYCFFYVKkgleGAYMYEPDHTQVRGMMKTLKAE--RPIpGNSIQITGGEPMLREDIADVIKIMKEE--GVDHVQMNTNGIRHAmdP 205
                  579***************986655555555555555555555555..4445*****************9999999999..9***************** PP

                  HHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHHHH CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM  92 eklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGendeeleelle 165
                  e +++ + +g++ ++l+ + ++ +     +n+++ +e +  al+ +r+ g   vv++ ++++  nd+el  +++
   EPA05313.1 206 EAAREVRLAGCNNLYLSFDGVTAR-----TNPKNHWE-IPYALDSCRKTGTT-VVFVPTVIKSINDHELGGIIR 272
                  ***********************9.....86755555.5599*******999.9*************9977665 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 0.91
                  STTHHHHHHHHHHTC....C CS
                  xxxxxxxxxxxxxxx....x RF
  Radical_SAM  60 ypdfvellerlakla....v 75 
                  ++++ e+lerl +++     
   EPA05313.1 459 QDKYNEDLERLQRCDihylT 478
                  44555555555555322331 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   5.4e-10   3.2e-06       3      95 ..     106     200 ..     104     222 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 5.4e-10
     Fer4_12   3 GeGvrlslfvsgCnlsCkgCfnketwsfksgkeft..kelleeiiedlkkesi...egltllGGEPllpenaeallelvkevkeekpekdiwlytgyt 95 
                 + G+  ++ +++C+l C +Cf    +  ++   ++  ++  + +++ lk e+    + + ++GGEP+l   +e++++++k +kee+++ + + ++g  
  EPA05313.1 106 HSGLANMIVTNRCDLTCWYCFFYVKKGLEGAYMYEpdHTQVRGMMKTLKAERPipgNSIQITGGEPML---REDIADVIKIMKEEGVDHVQMNTNGIR 200
                 6788889999***********8777777777777443777777888887655567899**********...999999999999999988888888865 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.9   2.6         3   1.8e+04       7      18 ..      92     103 ..      87     107 .. 0.81
   2 !   28.1   0.0   2.9e-10   1.7e-06       4      92 ..     114     201 ..     112     221 .. 0.78

  Alignments for each domain:
  == domain 1  score: -4.9 bits;  conditional E-value: 3
     Fer4_14   7 gCnlsCkgCdnk 18 
                 +C+ +C  C n+
  EPA05313.1  92 SCPNNCGLCSNH 103
                 79999*9**886 PP

  == domain 2  score: 28.1 bits;  conditional E-value: 2.9e-10
     Fer4_14   4 rlsgCnlsCkgCd......nketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekkiwletngtle 92 
                  +++C l C  C+       + +++ e  + q++ ++ + l  + ++ i  + + +tGGeP++    +++ +++k +kee+   +++++tng  +
  EPA05313.1 114 VTNRCDLTCWYCFfyvkkgLEGAYMYEPDHTQVRGMM-KTL--KAERPIPGNSIQITGGEPMLR---EDIADVIKIMKEEG-VDHVQMNTNGIRH 201
                 589**********776655455566677777777777.444..5666788899*********55...9999*********9.5679*****9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (554 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3999.77
//
Query:       EPA05314.1  [L=215]
Description: methyltransferase, FkbM family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-11   45.1   0.3    1.9e-11   44.3   0.3    1.4  1  Methyltransf_21  Methyltransferase FkbM domain
    6.7e-06   26.0   0.0    1.1e-05   25.3   0.0    1.3  1  Met_10           Met-10+ like-protein
    0.00023   21.0   0.0    0.00029   20.6   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
  ------ inclusion threshold ------
      0.011   15.2   0.0      0.016   14.6   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
      0.064   13.1   0.2      0.091   12.6   0.2    1.3  1  Methyltransf_31  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltransf_21  Methyltransferase FkbM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   0.3   5.2e-15   1.9e-11       1     140 [.      88     214 ..      88     215 .] 0.83

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 5.2e-15
  Methyltransf_21   1 dvGanigvwdsfanltarlcggggevlaiEPvpnslpkfeklranlltlavgndvgl.yelivegksggkyfpfavgdtngfstssvlggedar 93 
                      d+Ga ig   + +++  +  g +g v+++EP p+    fe l+ n     +++ ++l +e++        +++    +  +f +     ++   
       EPA05314.1  88 DIGAKIG--IYSLAFC-KFVGDTGNVFSFEPTPE---SFEILQKN---KQINHLKNLtIEEKAVTD----KTNIELLELCKFNGNNRINNNCVN 168
                      99*****..4444444.679**************...99999999...899998877777666555....777777777777777666678999 PP

  Methyltransf_21  94 yievpvvtldsfleeikksridllkiDvEGaElevLeGaqkglkrcq 140
                       i+v++v ld+ + e+ +++i ++kiDvEG E  vL G ++ lk+ q
       EPA05314.1 169 GIQVNCVSLDDYFSEF-QEKIFFIKIDVEGLEPKVLSGMKEILKKIQ 214
                      **********888888.8********************999998865 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0     3e-09   1.1e-05      96     152 ..      78     135 ..      70     153 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 3e-09
                 TT--TT-EEEETT-TTTCCHHHCCHH.TTSSEEEEEES-HHHHHHHHHHHHHTT-TTC CS
      Met_10  96 klveegevVvdvfAGiGpfaipiaky.skakrvlaidlnPesvkylkeniklNkvekv 152
                 + +++g+ V+d+ A iG ++++  k+ ++   v++ +  Pes++ l++n + N++++ 
  EPA05314.1  78 NEISKGDNVIDIGAKIGIYSLAFCKFvGDTGNVFSFEPTPESFEILQKNKQINHLKNL 135
                 56899*****************9997468889**********************9985 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   8.2e-08   0.00029      52     129 ..      59     138 ..      13     144 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 8.2e-08
                 TTEEE--HHHHHHHHHHTT..--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEE CS
        PCMT  52 ynatiSaphmvalalelle..lkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivv 129
                  ++++S+     +  +lle  ++kg++v+++G+  G+ +  + ++vg++g+v s e ++e  e  ++n + ++l+n+++ 
  EPA05314.1  59 EGNYSSENFYKDYYFDLLEneISKGDNVIDIGAKIGIYSLAFCKFVGDTGNVFSFEPTPESFEILQKNKQINHLKNLTIE 138
                 34889999999999****999***************************************99999999999999888775 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   4.5e-06     0.016     154     214 ..      75     138 ..      72     152 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.5e-06
        PrmA 154 aleklvkegeevlDvGtGSGiLaiaaakL..gakkvvavDiDevAvkvakeNaelNkvea.kle 214
                 +le+ + +g++v+D+G+  Gi ++a  k+  ++ +v+     + + ++ ++N ++N++++  +e
  EPA05314.1  75 LLENEISKGDNVIDIGAKIGIYSLAFCKFvgDTGNVFSFEPTPESFEILQKNKQINHLKNlTIE 138
                 7999**********************9984446799**********************995443 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   2.5e-05     0.091       2      68 ..      81     147 ..      80     188 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.5e-05
  Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieelek 68 
                      +kg +v+D+G+  G +++++ + +g+ ++v++++ ++e+ e  ++n q + l+n++ e+  ++++ +
       EPA05314.1  81 SKGDNVIDIGAKIGIYSLAFCKFVGDTGNVFSFEPTPESFEILQKNKQINHLKNLTIEEKAVTDKTN 147
                      7999******************************************************999888654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1346.65
//
Query:       EPA05315.1  [L=257]
Description: GMP synthase (glutamine-hydrolyzing), C-terminal domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-35  120.5   0.1    5.1e-35  119.4   0.1    1.6  1  GMP_synt_C    GMP synthase C terminal domain
    0.00039   19.6   0.0    0.00078   18.6   0.0    1.4  1  NAD_synthase  NAD synthase


Domain annotation for each model (and alignments):
>> GMP_synt_C  GMP synthase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.4   0.1   5.7e-39   5.1e-35       2      91 ..     166     255 ..     165     256 .. 0.97

  Alignments for each domain:
  == domain 1  score: 119.4 bits;  conditional E-value: 5.7e-39
                 CCCTTT-GGGSSEEEEEEEEEEE----------EEEEEEEEE---------B----HHHHHHHHHHHHHHSTT---EEEE---TTTS-S- CS
  GMP_synt_C   2 elkkaglykkiwQafavllpvksvGvmgdkRtyeyvvalRaveseDamtadvaelpyevLekissrivnevkgvnrvvyditskPpatiE 91 
                 el   gly k+wQa+a++ + k+vGv gd+R+y+++v++R+v+s Damtad+++lp+e+Lekis+ri+nev++v+ v+y i+skPpatiE
  EPA05315.1 166 ELIVYGLYGKVWQAYAAVGDDKAVGVVGDERKYGNIVMIRVVDSIDAMTADWTRLPHELLEKISNRITNEVEDVTWVTYAISSKPPATIE 255
                 566689***********************************************************************************9 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   8.7e-08   0.00078     148     177 ..     105     134 ..      92     137 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 8.7e-08
                   BETTTTS-HHHHHHHHHHTT--HHHHCS-- CS
  NAD_synthase 148 lapiaellKtevkeLakelnvPervlkkpP 177
                   l+p+ el+K ev+++ak l+vPe+++ ++P
    EPA05315.1 105 LEPLRELYKDEVRKIAKILGVPEKLYMRHP 134
                   68**************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1918.50
//
Query:       EPA05316.1  [L=393]
Description: radical SAM domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-13   51.4   4.7    3.8e-13   49.8   3.9    2.4  2  SPASM        Iron-sulfur cluster-binding domain
    1.2e-07   32.3   0.0    2.1e-07   31.4   0.0    1.4  1  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.63   5.6e+03       7      15 ..     183     191 ..     179     226 .. 0.66
   2 !   49.8   3.9   4.2e-17   3.8e-13       1      67 [.     294     361 ..     294     363 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.63
       SPASM   7 slfInsdGd 15 
                  l+I++dG+
  EPA05316.1 183 KLVIDVDGT 191
                 577788876 PP

  == domain 2  score: 49.8 bits;  conditional E-value: 4.2e-17
       SPASM   1 CfapsrslfInsdGdVvpCcvdkktyveelklGnireesleeIwnseeyqefr....kskkfplielCrnC 67 
                 C++p++ +++n+ Gd++pCc+      ++  +Gni+ee le+Iwn+e y   r    ++k+   + +C+ C
  EPA05316.1 294 CHWPWSGFVVNWSGDIAPCCIV---DDSDSDFGNIFEEGLEKIWNNEYYVSARsefsNNKEMTKFTICNMC 361
                 9******************999...23359********************977544344444445556666 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.0   2.4e-11   2.1e-07       1     145 [.      84     229 ..      84     251 .. 0.84

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 2.4e-11
                  EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHG.HHHHHHH CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
  Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritvetngtlpd.eeklerl 97 
                  +++t+ Cnl C+ C+++   + ++   +l++e+ + +++++ ++   +  ++  ge +l + + + ++ ++ +   +i + ++tn   ++  e+le l
   EPA05316.1  84 IEPTNICNLHCPLCSTGIN-AETRSKGTLTLEKFKILIDQI-KDVALELYLQNWGESTLVKLLPDMIKYASDN---KIFVNLSTNFSIDYsNEYLENL 176
                  689**************96.99999****************.57768888888******99888888888887...9********999779******* PP

                  HHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET......E CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......x RF
  Radical_SAM  98 lelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikr......v 145
                  l+ g+  + ++++ ++ e + k+   g+ +e vl++++++ +   ++      +
   EPA05316.1 177 LKSGLGKLVIDVDGTTQEIFEKYR-IGGKLETVLKNIRTAVKFKKENnlkfpiI 229
                  ******************666666.99*************99965546555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       948  (0.0528752); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 2417.18
//
Query:       EPA05317.1  [L=294]
Description: methyltransferase domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.7e-19   68.0   0.0    1.3e-18   67.4   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    4.2e-10   39.6   0.0    7.7e-10   38.8   0.0    1.4  1  Methyltransf_31  Methyltransferase domain
    6.9e-10   39.6   0.0    1.5e-09   38.5   0.0    1.6  1  Methyltransf_12  Methyltransferase domain
      7e-09   36.2   0.0    1.4e-08   35.2   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
    8.7e-08   32.0   0.2    1.5e-07   31.2   0.2    1.2  1  MetW             Methionine biosynthesis protein MetW
    3.6e-07   30.8   0.0      1e-06   29.4   0.0    1.8  2  Methyltransf_25  Methyltransferase domain
    7.3e-05   21.8   0.1    0.00011   21.2   0.1    1.2  1  Methyltransf_9   Protein of unknown function (DUF1698)
     0.0029   16.8   0.1     0.0048   16.0   0.1    1.3  1  DREV             DREV methyltransferase
     0.0086   16.2   0.3       0.02   15.0   0.3    1.6  1  Sep15_SelM       Sep15/SelM redox domain
  ------ inclusion threshold ------
      0.023   14.7   0.0       0.04   13.9   0.0    1.3  1  Methyltransf_32  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.4   0.0   7.2e-22   1.3e-18      17     162 ..      86     232 ..      71     235 .. 0.81

  Alignments for each domain:
  == domain 1  score: 67.4 bits;  conditional E-value: 7.2e-22
  Methyltransf_23  17 lpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiaekakkaqkdqfdeqeaaepqg.....kfdlIvlrevlehvpdppellrqi 105
                       +  +++gr+L+iG G+G ll+ l+e  fsvtg++ s     i+ ++k a+++q+   + +++ +       d Iv+++vleh+ dp   l+++
       EPA05317.1  86 KKITPKNGRILEIGSGHGFLLKKLQELKFSVTGIEVSKD-RRII-SKKVAPNVQV--LDMDVNGNipkisNLDSIVMFHVLEHIVDPIIFLKKA 175
                      3447899*****************************964.4444.5666666666..2333333366777************************ PP

  Methyltransf_23 106 atllkpgGylllseplasl...kedrllldwlylvpagrhisffsarslkelleeaGlev 162
                      ++ll+ +G +++++p+ ++    +++ +++w +++    h+++fs   lk+++ ++G ++
       EPA05317.1 176 RKLLSKNGKIIVEVPNINDlqlDQNEYYRNWYWQR---AHLHYFSPNILKNIFLRSGMKN 232
                      ***************99997656777788887777...5*****************9876 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.0   4.3e-13   7.7e-10       3     132 ..      91     208 ..      90     247 .. 0.82

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 4.3e-13
  Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDlilsnevlnaladpdkile 95 
                      k+ r+l++G+G G+l+++l e+ +    v+Gi+ s+      r + +k+   nv++   d++  ++k    ++ D i+ + vl ++ dp  +l+
       EPA05317.1  91 KNGRILEIGSGHGFLLKKLQELKF---SVTGIEVSK-----DRRIISKKVAPNVQVLDMDVNGnIPKI---SNLDSIVMFHVLEHIVDPIIFLK 173
                      6889****************7644...59***9765.....57778888888**************87...78********************* PP

  Methyltransf_31  96 eiervlkpggilliedprllaelpakveeeskay...evv 132
                      ++ ++l+++g +++e p+     +  ++ ++++y   + +
       EPA05317.1 174 KARKLLSKNGKIIVEVPN-----INDLQLDQNEYyrnWYW 208
                      ******************.....55555555554444333 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   0.0   8.2e-13   1.5e-09       1      99 []      96     185 ..      96     185 .. 0.85

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 8.2e-13
  Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlkdirevldnirklLk 94 
                      LeiG+G G ll+ l e     ++tg+++s++     ++k a + +     v+ +   +      s  D +v+++vl+h+ d+  +l+++rklL+
       EPA05317.1  96 LEIGSGHGFLLKKLQEL--KFSVTGIEVSKDRR-IISKKVAPNVQVLDMDVNGNIPKI------SNLDSIVMFHVLEHIVDPIIFLKKARKLLS 180
                      8****************..***********999.666666666655555555555554......599*************************** PP

  Methyltransf_12  95 pgGrl 99 
                      ++G++
       EPA05317.1 181 KNGKI 185
                      ***86 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.0     8e-12   1.4e-08       1      96 []      96     187 ..      96     187 .. 0.88

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 8e-12
                      EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECC.CTSS-T.T-EEEEEEES-CCC-CCHHHHHHHHHHHEEEEE CS
  Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadae.klpfed.nsfDlvvssevlhhvedpekalkeiaRvLkpgG 92 
                      L++G+G G l+++l++   +v+g+++sk  + ++k+ a++    v+++ +d+  ++p  + +  D +v+++vl+h+ dp  +lk+++++L ++G
       EPA05317.1  96 LEIGSGHGFLLKKLQELKFSVTGIEVSKDRRIISKKVAPN----VQVLDMDVNgNIP--KiSNLDSIVMFHVLEHIVDPIIFLKKARKLLSKNG 183
                      89*************999***********99777666665....5679999994455..3369******************************* PP

                      EEEE CS
  Methyltransf_11  93 llvi 96 
                      ++++
       EPA05317.1 184 KIIV 187
                      *986 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.2   8.2e-11   1.5e-07       5     112 ..      83     192 ..      80     198 .. 0.83

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 8.2e-11
        MetW   5 eliaelikpgsrvldlGcGdGellellkeek.qvdgrGleldeegvaecvakGlsviqgdldkdlenfedksfdyvvlsqtlqatrnpkevlde...ll 99 
                 +li+++ +++ r+l++G+G+G ll+ l+e k  v+g  + +d++ + + va  ++v++ d++ ++ +   +++d +v+   l  + +p   l++   ll
  EPA05317.1  83 NLIKKITPKNGRILEIGSGHGFLLKKLQELKfSVTGIEVSKDRRIISKKVAPNVQVLDMDVNGNIPKI--SNLDSIVMFHVLEHIVDPIIFLKKarkLL 179
                 578999999******************995535566666677889***************99999876..569***************99998622256 PP

        MetW 100 rigrraivsfPnf 112
                     ++iv  Pn 
  EPA05317.1 180 SKNGKIIVEVPNI 192
                 6677899999996 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   5.6e-10     1e-06       1      97 []      95     183 ..      95     183 .. 0.86
   2 ?    2.5   0.0      0.13   2.4e+02      34      81 ..     172     220 ..     170     226 .. 0.72

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 5.6e-10
                      EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCG.BSSSTTTEEEEEEESTGGGSSHHHHHHHHHHHHHHE CS
  Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaed.lpfedgsfDlvvssgalhhlsdedlekalkeiarvL 93 
                      +L++G G+G l+++l++   k +vtg+++s++   + ++ a    +nv+++ +d++  +p + +  D +v++++l+h+ d+    +lk+++++L
       EPA05317.1  95 ILEIGSGHGFLLKKLQEL--KFSVTGIEVSKDRRIISKKVA----PNVQVLDMDVNGnIP-KISNLDSIVMFHVLEHIVDP--IIFLKKARKLL 179
                      8**************998..4**********9966666666....8*********76266.5569******877***8855..479******** PP

                      EEEE CS
  Methyltransf_25  94 kpgG 97 
                       ++G
       EPA05317.1 180 SKNG 183
                      9998 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.13
                      HHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEE.EST.GGGSSHHH CS
  Methyltransf_25  34 leaareraeeeglnvefvqgdaedlpfedgsfDlvvs.sga.lhhlsded 81 
                      l++ar+ ++++g ++ +++ +++dl+++++++   +  + a lh++s++ 
       EPA05317.1 172 LKKARKLLSKNG-KIIVEVPNINDLQLDQNEYYRNWYwQRAhLHYFSPNI 220
                      789999998776.9***********9877766554441445688888654 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.1   6.2e-08   0.00011      97     275 ..      71     245 ..      63     256 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 6.2e-08
                     SEEHHHHHHHHGGGS.--..TT-EEEEET-TTSHHHHHHHHCT-SEEEEE---HHHHHHHHHHHCCTTTTSSEEEE---GG.GS-T---EEEEEE CS
  Methyltransf_9  97 eWrsdwkWdrvlphlsdl..kgrtildvGcgnGyhlwrmvgegaklvvGidPselfliqfeavrkllgedqrahllplgie.qlpeleafdtvfs 188
                     e rs     r  + + ++  k+ +il++G g G+ l + + e   +v Gi+ s+   i    + k ++ + ++ ++   ++ ++p+++ +d +  
      EPA05317.1  71 ENRSSVDLTRRINLIKKItpKNGRILEIGSGHGFLL-KKLQELKFSVTGIEVSKDRRI----ISKKVAPNVQVLDM--DVNgNIPKISNLDSIVM 158
                     6666666666444444431155679********865.66778888999***9998755....45555555555554..554389*********** PP

                     ES-GGG-S-HHHHHHHHHCTEEEEEEEEEEEE-BSS.-TT-EE--SS-BTTBSS-.--EEBHHHHHHHHHHTT-EEEEEEEEEE--TTT CS
  Methyltransf_9 189 mGvlyhrrsPldhllqlkdqlvkgGelvletlvieG.denavlvPedryakmrnv.yfiPsaaalkvWlekvgfvdvrivdesvttlee 275
                       vl h   P+  l + ++ l k+G++++e   i+  + ++    ++ y +     yf P  ++lk+ + + g+++++i+ ++  +le+
      EPA05317.1 159 FHVLEHIVDPIIFLKKARKLLSKNGKIIVEVPNINDlQLDQNEYYRNWYWQRAHLhYFSP--NILKNIFLRSGMKNMKIIAVQRYSLEN 245
                     ******************************999875234455556677766555416655..679999999********9999888875 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   2.7e-06    0.0048      94     187 ..      91     188 ..      75     194 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.7e-06
        DREV  94 edkklldlGaGdGeitkrvaptfeevyatelsetmrdrlkkkkynv..lsalelq.e..tdvkldlilclnlldrcfdplklledirsalepngrviva 187
                 ++ ++l++G+G G + k++++    v   e+s+  r   kk   nv  l + +++ +     +ld i+ + +l+   dp+ +l+  r+ l  ng++iv 
  EPA05317.1  91 KNGRILEIGSGHGFLLKKLQELKFSVTGIEVSKDRRIISKKVAPNVqvLDM-DVNgNipKISNLDSIVMFHVLEHIVDPIIFLKKARKLLSKNGKIIVE 188
                 6689******************999*******9877666665555410432.22212113459**********************************96 PP

>> Sep15_SelM  Sep15/SelM redox domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.3   1.1e-05      0.02       3      39 ..       2      39 ..       1      48 [. 0.88

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.1e-05
                EEEETT---STTHHHHHHTTTHH..HHBTTEEEEEESS CS
  Sep15_SelM  3 vlevcgcklnrlpevkaFvkeda.aakfpnlevkyvrg 39
                v+++c ck ++l+ + +Fv++   ++  ++l+ ++++ 
  EPA05317.1  2 VESCCLCKYKNLKVISNFVRDSPiHKIVKCLNCNHIQL 39
                89*****************9987677788999999875 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.2e-05      0.04      24      75 ..      90     137 ..      75     155 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.2e-05
  Methyltransf_32  24 sgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklg 75 
                       ++ +++++G+G g+L   l+     +k++v+gi++++++   ++k+a +++
       EPA05317.1  90 PKNGRILEIGSGHGFLLKKLQE----LKFSVTGIEVSKDRRIISKKVAPNVQ 137
                      445789**************99....7***********99999998888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       725  (0.0404373); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 1703.47
//
Query:       EPA05318.1  [L=132]
Description: hypothetical protein BG20_I0116 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.014   16.0   0.1      0.025   15.2   0.1    1.5  1  WBP-1     WW domain-binding protein 1
      0.041   13.8   2.0      0.055   13.4   2.0    1.2  1  Fig1      Ca2+ regulator and membrane fusion protein Fig1
       0.31   10.4   1.9       0.37   10.1   1.9    1.1  1  DUF3810   Protein of unknown function (DUF3810)


Domain annotation for each model (and alignments):
>> WBP-1  WW domain-binding protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.1   4.1e-06     0.025      20      55 ..      51      87 ..      46     122 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.1e-06
       WBP-1 20 Elwwfwlvwtllil.lsCicalakrraklrleqqerq 55
                Elw+f++v+  l++ +s i+++ +rr++lr+e +   
  EPA05318.1 51 ELWIFVVVFLALYIpVSIIIGFWHRRTQLRVETTLSM 87
                9*********8888899**********9888765444 PP

>> Fig1  Ca2+ regulator and membrane fusion protein Fig1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   2.0   9.2e-06     0.055      85     136 ..      22      70 ..      15      89 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.2e-06
        Fig1  85 aiiLtlllfllllyfplgseipllPfkskavskvalvlsflllllwlvgalw 136
                 ++iLt++ f+l++y      i+++Pf ++ v ++ + ++++l+l + v+++ 
  EPA05318.1  22 IFILTFVNFVLISYRL---LIEKIPFLKEIVPELWIFVVVFLALYIPVSIII 70 
                 689*********9955...89***********************99999875 PP

>> DUF3810  Protein of unknown function (DUF3810)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   1.9   6.2e-05      0.37      19     108 ..      10     118 ..       6     128 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 6.2e-05
     DUF3810  19 lfpFSvgellivllillvilylvlai.klkkrkkkkkrllkvllrvllvllvvyflftllwglnYyreplserlglk..................keey 98 
                 +  F +g  +++++il ++ ++++    l ++  + k+++  l  +++v+l++y+   +  g+ + r++l  ++ l+                  + + 
  EPA05318.1  10 WWEFRMGHSTYLIFILTFVNFVLISYrLLIEKIPFLKEIVPELWIFVVVFLALYIPVSIIIGFWHRRTQLRVETTLSmeqnpfvakmfrtmldvqTGKA 108
                 55666666666666655554444444334445556566666677777778888888899*********9888887664455555555555555544444 PP

     DUF3810  99 seeelaelae 108
                 ++ee+++++e
  EPA05318.1 109 TKEEIEKFRE 118
                 5555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1326  (0.0739584); expected 358.6 (0.02)
Passed bias filter:                      770  (0.0429472); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.35s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 763.61
//
Query:       EPA05319.1  [L=325]
Description: toxin secretion/phage lysis holin [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-12   48.3   0.0    2.5e-12   47.4   0.0    1.5  1  Glyco_trans_1_4  Glycosyl transferases group 1
    0.00029   20.4   0.1     0.0012   18.4   0.0    2.1  2  Glycos_transf_1  Glycosyl transferases group 1
     0.0017   18.7   0.0      0.014   15.8   0.0    2.2  2  Glyco_trans_1_2  Glycosyl transferases group 1
  ------ inclusion threshold ------
      0.031   14.3   0.0      0.054   13.5   0.0    1.4  1  Glyco_transf_4   Glycosyltransferase Family 4
      0.032   14.4   0.3      0.093   12.9   0.3    1.8  1  DUF3654          Protein of unknown function (DUF3654)


Domain annotation for each model (and alignments):
>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.4   0.0   6.8e-16   2.5e-12       7     131 ..     163     287 ..     157     290 .. 0.76

  Alignments for each domain:
  == domain 1  score: 47.4 bits;  conditional E-value: 6.8e-16
                      ES---G...G.GTHHHHHHHHHHHH.HHEEEEEES---..HHHHHHHTT-T.TEEEE---THHHHHHHH-SEEEE--....-..--SHHHHHHH CS
  Glyco_trans_1_4   7 vGrlee...nvkgvdllleavpllrkkdvrlvivGdgprpeeleelaagleerveftGfvedlaellaaadvfvaPs....e..gfglkllEam 91 
                      vG + +   n++g+d++ + v +    ++++v++G+  + + ++++++  +++ ef+G v+d ++ l++++v+ aP     +  g ++k lEa+
       EPA05319.1 163 VGPFLPgtiNYEGLDIISKIVTRFP--KIKFVFIGKT-N-QFFRSQLN--NKNTEFLGVVNDYKNTLRKCSVLFAPYpnyaRylGSKNKFLEAA 250
                      5555333457788888888888887..58******55.4.47887776..378************************9887477********** PP

                      HTT-EEEE-TGGGTTT--TTSSEE--TT-.HHHHHHHHHHH CS
  Glyco_trans_1_4  92 aaglpvVatdvggiaevvgengllvppgd.pealaeailrL 131
                      a+++p+++t++ g+ +   +n ll   gd  e++ + i+ L
       EPA05319.1 251 ACKMPIITTSA-GAVD--FRNDLLSI-GDtIEEISNLIEVL 287
                      ***********.5455..56666653.44366665555555 PP

>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.51   1.8e+03      39      65 ..     109     135 ..      94     157 .. 0.54
   2 !   18.4   0.0   3.4e-07    0.0012      43     126 ..     185     263 ..     172     303 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.51
                      CCCCCHCSCEEEEEES.STTHHHHHHH CS
  Glycos_transf_1  39 llkkqlnpnvklviaGngeeekelkkl 65 
                      +++ +l +n++ +i+ +++ +++++k 
       EPA05319.1 109 RVETKLFKNAVHLICSSEDIQEKVQKI 135
                      333334444444444444444444444 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 3.4e-07
                      CHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHHHCESEEEEEESS..BSS-H..HHHHHHHTT--EEEETTTT CS
  Glycos_transf_1  43 qlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleellknadifvlpsis..EgfGi..vllEAmaaglpviasnagg 126
                      +  p++k+v++G  + ++ ++++     +++n++flg v+  d ++ l++++++++p  +    +G     lEA a+++p+i++ ag 
       EPA05319.1 185 R-FPKIKFVFIG--KTNQFFRSQ----LNNKNTEFLGVVN--DYKNTLRKCSVLFAPYPNyaRYLGSknKFLEAAACKMPIITTSAGA 263
                      3.899*******..444455554....56799********..**************976688666662268*************9886 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.37   1.3e+03      35      61 ..     113     137 ..     107     145 .. 0.70
   2 !   15.8   0.0   3.8e-06     0.014       7      82 ..     238     309 ..     228     318 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.37
  Glyco_trans_1_2  35 elftpgkevilfedleelaekirylla 61 
                      +lf++  ++i+  + e+++ek+++  +
       EPA05319.1 113 KLFKNAVHLIC--SSEDIQEKVQKIQN 137
                      56777777777..67788888887544 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 3.8e-06
  Glyco_trans_1_2   7 rsespnlrlfEaaacGafaltddaegleelftpgkevilfe.dleelaekiryllanpeerraiaeaarervlaeht 82 
                      r+ + + +++Eaaac  +++t++a g  ++    ++++ +  + ee+   i ++l ++  r++i+++ r++++++++
       EPA05319.1 238 RYLGSKNKFLEAAACKMPIITTSA-GAVDFR---NDLLSIGdTIEEISNLI-EVLMDENTRKEIGRKLRNEIEKKYN 309
                      5566789***************55.555553...45666672555555555.577899*************999886 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.5e-05     0.054      74     166 ..      54     145 ..      19     149 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.5e-05
  Glyco_transf_4  74 DvvHahspaalgaallalrrrlgiplVltvHglye............krllkarlkplsrllralerrllrradrviavSeatadelrerygvpp 156
                      +vHah++     +    r+  + ++ + +Hgl++            +++ k+    +s++++++e +l+++a ++i+ Se +++ +++   +++
      EPA05319.1  54 SLVHAHQFS----G----RLLENEKFFVDIHGLEYiqsknlskgfpiTSWKKYGYIAKSIFYKRVETKLFKNAVHLICSSEDIQEKVQK---IQN 137
                     689999932....2....23368899999999999999999999995444444444668899999***********************9...443 PP

  Glyco_transf_4 157 ekitVipnGv 166
                        t i n+v
      EPA05319.1 138 --STLIRNAV 145
                     ..57777776 PP

>> DUF3654  Protein of unknown function (DUF3654)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   2.6e-05     0.093      60     108 ..     278     325 .]     273     325 .] 0.93

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.6e-05
     DUF3654  60 drksfllelyaeglmlkalkakldeeeveepllavvdhelLidahkeyk 108
                 +++s l+e++  + ++k +  kl ++e+e++  a++++++L++ ++ey+
  EPA05319.1 278 EEISNLIEVLMDENTRKEIGRKL-RNEIEKKYNAIIEINKLVKLYNEYG 325
                 67899******************.67**********************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1010  (0.0563333); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2085.25
//
Query:       EPA05320.1  [L=198]
Description: hypothetical protein BG20_I0151 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1522.80
//
Query:       EPA05321.1  [L=98]
Description: hypothetical protein BG20_I0132 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0034   17.5   0.2     0.0095   16.0   0.2    1.8  1  Hydrolase_6  Haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.034   14.4   0.3        1.4    9.1   0.2    2.0  2  Hydrolase    haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.2   1.1e-06    0.0095       1      51 [.      15      76 ..      15      96 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.1e-06
                 EEEESTTTSEETTEE-TTHHHHHHHHHHTT...........-EEEEEE---SS-HHHHHHHH CS
  Hydrolase_6  1 flfDidGvLwrgdkaipgaaealnalraag...........kpvvllTNnsskseeeyakkl 51
                 +l+D+dGvL +g+  +    ++++ ++a+            +p++++T +++   ++  k +
   EPA05321.1 15 VLTDVDGVLTNGGMYYSSKGDVMKKFHARDgmgisllrknkIPTIIITKENTMMVKKWSKNM 76
                 689***********************999889999999999*******99888877776666 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.2   0.00016       1.4       1      18 [.      12      29 ..      12      43 .. 0.85
   2 ?    3.7   0.0    0.0073        66     129     166 ..      50      87 ..      47      93 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00016
                SSEEEEESBTTTBCHHHH CS
                xxxxxxxxxxxxxxxxxx RF
   Hydrolase  1 iktvvfDkdGTLttgeps 18
                ik+v+ D+dG+Lt+g + 
  EPA05321.1 12 IKVVLTDVDGVLTNGGMY 29
                89************9864 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.0073
                 HHHHTTEEEEEEESSEHHHHHHHHHHTTGGGESEEEEH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
   Hydrolase 129 sLkaagievvlltgdnpetaeraanqlGddyfdavias 166
                  L++++i+++++t  n  ++++  +++ ++ fd+v+++
  EPA05321.1  50 LLRKNKIPTIIITKENTMMVKKWSKNMKAELFDGVLCK 87 
                 69999***********9999988888877777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.32s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 630.23
//
Query:       EPA05322.1  [L=350]
Description: GHMP kinase, N-terminal domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.5e-12   45.1   0.4    1.6e-11   44.2   0.4    1.5  1  GHMP_kinases_N  GHMP kinases N terminal domain
    1.7e-05   25.1   1.7    1.8e-05   25.0   0.0    1.8  2  GHMP_kinases_C  GHMP kinases C terminal


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.4   1.8e-15   1.6e-11       5      66 .]     109     173 ..     105     173 .. 0.90

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 1.8e-15
                     EESSHTTSSSCHHHHHHHHHHHHHHHHTTEHH.HH..HHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
  GHMP_kinases_N   5 kseiPvgaGLGSSAAlavalvaAllallglsl.ee..aklaleaerlaqggngsggDvaasvyGg 66 
                      s+  +g+GLGSS+++++++v Al ++  lsl +   a+la ++er     +g+++D++a+++Gg
      EPA05322.1 109 ASDSAPGSGLGSSTSIVTSIVGALKSYMRLSLtSYeiAELAHKIERVNLSIKGGIQDQYACTFGG 173
                     577788**********************999864467********9999999************8 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.6       1.3   1.2e+04      53      61 ..     113     121 ..     112     126 .. 0.83
   2 !   25.0   0.0     2e-09   1.8e-05       4      63 ..     246     305 ..     243     324 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.3
  GHMP_kinases_C  53 lsGaGgGpt 61 
                      +G+G+G++
      EPA05322.1 113 APGSGLGSS 121
                     58*****97 PP

  == domain 2  score: 25.0 bits;  conditional E-value: 2e-09
  GHMP_kinases_C   4 alergdlellgellnlsqrselkavvgilppeleellealselGalgaklsGaGgGptvf 63 
                      l++gd+e +++ l++s+  ++k    i++  +e++ + ++++Ga+++k+ GaGgG+   
      EPA05322.1 246 QLLKGDVEDFANELHESWLTKKKISDIISTKKIEKIYSNARKHGAISGKVLGAGGGGHML 305
                     6789****************9999********************************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2323.49
//
Query:       EPA05323.1  [L=461]
Description: nucleotide sugar dehydrogenase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-40  138.0   0.3    5.4e-40  137.0   0.3    1.5  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
    2.9e-21   75.5   0.0    5.4e-21   74.6   0.0    1.5  1  UDPG_MGDP_dh    UDP-glucose/GDP-mannose dehydrogenase family,
    3.3e-21   75.7   0.0    1.3e-20   73.8   0.0    1.9  2  UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family,
    1.1e-06   28.7   0.1    0.00051   20.0   0.0    2.5  2  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
    6.1e-06   25.7   2.2      0.029   13.7   0.0    3.3  3  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
    0.00014   21.8   0.0    0.00027   20.9   0.0    1.5  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
     0.0025   18.3   0.5        4.1    8.0   0.0    2.9  2  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
     0.0026   17.2   0.0     0.0051   16.2   0.0    1.5  1  ThiF            ThiF family
     0.0057   16.8   0.0      0.092   12.9   0.0    2.5  2  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
  ------ inclusion threshold ------
      0.022   15.0   0.1      0.045   14.0   0.1    1.5  1  NAD_binding_11  NAD-binding of NADP-dependent 3-hydroxyisobut
       0.12   12.0   0.0       0.25   11.0   0.0    1.5  1  ApbA            Ketopantoate reductase PanE/ApbA
       0.15   12.1   0.0       0.39   10.8   0.0    1.6  1  SRR1            SRR1


Domain annotation for each model (and alignments):
>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.0   0.3   3.6e-43   5.4e-40       2     181 ..      26     207 ..      25     212 .. 0.96

  Alignments for each domain:
  == domain 1  score: 137.0 bits;  conditional E-value: 3.6e-43
                     EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS-.-TTHHHHHHHHCHTTTEEEES-HHHHHHC-SEEEE-----B-TTTTCB CS
  UDPG_MGDP_dh_N   2 kisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiy.epgLeelvkkavesgrlsfttdvekaveeadvifiaVgTPskkkgkaa 95 
                     k++v+G G +Gl+ta+++a+ g + igvDi+++ v+k+n++ +p+  epg++e+ ++++++++l +t d+++a+++ +v++++ +TP+ + ++ +
      EPA05323.1  26 KVAVVGIGRIGLPTAILFAKSGLTTIGVDINQNLVEKINHSIFPLDdEPGMKEIFNDVIKNKKLIATVDIKHALSQVNVVILSLPTPMTD-NNIP 119
                     89*******************************************549******************************************.9999 PP

                     -THHHHHHHHHHHHHHHCEEEEEE-S---TTHHHHCHHHHHHHHCSS-..TTCEEEEE------TTSHHHHHHS-S-EEEEESSCHHH CS
  UDPG_MGDP_dh_N  96 DlkyvesaarsiaealkkgkvvvvkSTvpvgtaeelvkkileeaskkk..gvdfdvvsnPEflregsavkdllnpdrvviGveekkae 181
                     D + +es+ ++i ++l  +++v+v+STv +g  e+++ +i+e ++kk   g++f++ ++PE  ++g+++kd+ + +r v+G ++k++e
      EPA05323.1 120 DYSSLESVGKQIHDFLCPNSLVIVESTVEPGFIENILIPIIEGQDKKFeaGKSFSIGVCPETANPGEILKDFKTLPRLVGGINNKSSE 207
                     ******************************************888766889**********************************998 PP

>> UDPG_MGDP_dh  UDP-glucose/GDP-mannose dehydrogenase family, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.6   0.0   3.6e-24   5.4e-21       1      93 [.     228     319 ..     228     320 .. 0.97

  Alignments for each domain:
  == domain 1  score: 74.6 bits;  conditional E-value: 3.6e-24
  UDPG_MGDP_dh   1 etAEliKlaaNaflatkIsfiNelanlcealgidveeVieavgldprigpkflkpglGvGGsclpkDvkaLvalaeelgle.aelleavrevNe 93 
                   +tA ++Kl+ N+f++++I+f+Nela l+e+lgid+  V++a++ + +  +++++pg GvGG clp+  +++++ a +++l+ ++l++  re+Ne
    EPA05323.1 228 KTANAVKLTTNVFRDVNIAFVNELALLFEKLGIDIFTVLDAAKRKYN--FQVHYPGSGVGGPCLPVNSYQIINSALSNSLPiPKLISVSREINE 319
                   589******************************************99..79******************************99**********8 PP

>> UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       2.5   3.7e+03      52      77 ..      87     112 ..      71     129 .. 0.69
   2 !   73.8   0.0   8.4e-24   1.3e-20       2     104 ..     347     443 ..     346     444 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.5
                     TCCEEES-CHHHHTT-SEEEE-S--G CS
  UDPG_MGDP_dh_C  52 kgvevvdsleealkgadaiviltehd 77 
                     k++  + ++++al++++++++  + +
      EPA05323.1  87 KKLIATVDIKHALSQVNVVILSLPTP 112
                     44445557899999999999876655 PP

  == domain 2  score: 73.8 bits;  conditional E-value: 8.4e-24
                     EE-SSSSTT-S--TT-HHHHHHHHHHHCTSEEEEE-SSTHHCCCCHHGGBTCCEEES-CHHHHTT-SEEEE-S--GGGGGS-HHHHHHCCSS-EE CS
  UDPG_MGDP_dh_C   2 ilGlafKkdtdDlReSpaldiieeLleegaevkiyDPkvkeeaveaeleekgvevvdsleealkgadaiviltehdefkeldlaklkelmkpavv 96 
                     ilG+++K++++D+  +pa +ii eL++ ++++ki+DP++ + +v       ++++ +++e+ ++++dai+ilt+h++f +++ + +++lmk+++v
      EPA05323.1 347 ILGVSYKPNVKDIQLAPAEKIISELKSLECNIKIFDPYFISTDVF------SIRTEQKIEDMISNSDAILILTAHQNFFSINPEIFNKLMKKPIV 435
                     9****************************************9985......59999*************************************** PP

                     EESSS-CC CS
  UDPG_MGDP_dh_C  97 fDgrnvld 104
                     +D+r+++d
      EPA05323.1 436 IDTRGIFD 443
                     *****997 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   3.4e-07   0.00051       1      86 [.      26     118 ..      26     131 .. 0.85
   2 !    6.1   0.0    0.0066       9.9      32     108 ..     365     443 ..     350     459 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 3.4e-07
                     -EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHH.......SSBTTTBTT----TTEEEES-HHHHHTT--EEEE---HHHHHHHH CS
  NAD_Gly3P_dh_N   1 kiavlGaGswGtalAkvlaenghevrlwvreeelieeinee.......henvkyLpgiklpenlvattdlaealkgadiivlvvPsqalrevl 86 
                     k+av+G G  G   A+++a+ g ++     +++l+e+in++          ++ ++++  +++l at d+++al+++++++l +P+ ++ + +
      EPA05323.1  26 KVAVVGIGRIGLPTAILFAKSGLTTIGVDINQNLVEKINHSifplddePGMKEIFNDVIKNKKLIATVDIKHALSQVNVVILSLPTPMTDNNI 118
                     79******************************99999997522211114567888999999************************99887766 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0066
                     HHHHHHHHHHSSBTTTBTT----TT...EEEES-HHHHHTT--EEEE---HHHHHHHHHHHCCC--TT-EEEE---SEET CS
  NAD_Gly3P_dh_N  32 eelieeineehenvkyLpgiklpen...lvattdlaealkgadiivlvvPsqalrevlkklkgllkkkailvsliKGiee 108
                     e+ i e+++ ++n k ++ + ++++   ++ ++ +++ ++++d i++   +q + ++  ++ ++l kk  +v+ ++Gi +
      EPA05323.1 365 EKIISELKSLECNIKIFDPYFISTDvfsIRTEQKIEDMISNSDAILILTAHQNFFSINPEIFNKLMKKP-IVIDTRGIFD 443
                     5667777777777777777777775111578899************************99999996655.5556778833 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0     2e-05     0.029      31      74 ..      19      62 ..       7      80 .. 0.83
   2 ?    1.4   0.0      0.12   1.7e+02      66     113 ..      82     123 ..      72     131 .. 0.67
   3 !    8.4   0.1   0.00087       1.3      49     126 ..     365     438 ..     334     441 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2e-05
                  BS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHC CS
  2-Hacid_dh_C 31 gkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeee 74
                  + +l   +v+++G+GrIG  +a ++++ g+  i++d +++  e+
    EPA05323.1 19 QLNLDSIKVAVVGIGRIGLPTAILFAKSGLTTIGVDINQNLVEK 62
                  45778889*****************************9885554 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.12
                   SSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE-S--STTTTTSBSHHH CS
  2-Hacid_dh_C  66 drskkkeeeeeelgvelvsleellaesDivslhlpltpetrhlinaee 113
                   d+ k+      ++ +  v+++ +l++  +v+l lp     +++ + ++
    EPA05323.1  82 DVIKN------KKLIATVDIKHALSQVNVVILSLPTPMTDNNIPDYSS 123
                   44433......23456799***************95555555555555 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.00087
                   HHHHHHHHHTT-EEEEESSSHHHHHCHHHHTC.EECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCSTTTEEEEES CS
  2-Hacid_dh_C  49 qavakrlkafgmkviaydrskkkeeeeeelgv.elvsleellaesDivslhlpltpetrhlinaeelakmkkgailiNt 126
                   ++++  lk++++++ ++d++  +++      + + +++e+++++sD + + +   +++   in e ++k+ k+ i+i t
    EPA05323.1 365 EKIISELKSLECNIKIFDPYFISTD---VFSIrTEQKIEDMISNSDAILILTA--HQNFFSINPEIFNKLMKKPIVIDT 438
                   5788899*************88655...455524569***********99987..788999999999999998888876 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   1.8e-07   0.00027       1      44 [.      26      69 ..      26     109 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.8e-07
                EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHH CS
     3HCDH_N  1 kvaviGaGtmGagiaavfasagleVvlvdiseealekalekiek 44
                kvav+G G +G   a +fa++gl++  vdi+++ +ek +++i  
  EPA05323.1 26 KVAVVGIGRIGLPTAILFAKSGLTTIGVDINQNLVEKINHSIFP 69
                79**********************************99988864 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.1    0.0048       7.1       1      81 [.      26     121 ..      26     133 .. 0.72
   2 !    8.0   0.0    0.0028       4.1      48      94 ..     393     438 ..     369     439 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0048
                    EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC...................-EEECECHHHHHHH-SEEEE-S-HHHHHHH CS
  F420_oxidored   1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg...................vkvtavdneeaaeeadvvvlavkpedveev 77 
                    k++++G G++g   a  ++++g   + i    + n++ +e++  ++                      + +vd + a+++ +vv+l++++ ++++ 
     EPA05323.1  26 KVAVVGIGRIGLPTAILFAKSGL--TTIG--VDINQNLVEKINHSIFplddepgmkeifndviknkKLIATVDIKHALSQVNVVILSLPTPMTDNN 117
                    68888899998888888888883..3333..244444444444443344467778888888888887788889****************9999877 PP

                    HHHC CS
  F420_oxidored  78 lsel 81 
                    + + 
     EPA05323.1 118 IPDY 121
                    6655 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0028
                    -EEECECHHHHHHH-SEEEE-S-HHHHHHHHHHCGHHHHTTSEEEEE CS
  F420_oxidored  48 vkvtavdneeaaeeadvvvlavkpedveevlselakdalkgklvisv 94 
                    +++++ + e++++++d +++    +++ ++  e+++++ k+ +vi++
     EPA05323.1 393 IRTEQ-KIEDMISNSDAILILTAHQNFFSINPEIFNKLMKKPIVIDT 438
                    55666.899************************************97 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   3.4e-06    0.0051      11      57 ..      17      64 ..       7     125 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.4e-06
                HHHHHHHTSEEEEE--SHHHHHHHHHHHHHTTTEEEE.EESSB--GGG CS
                xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
        ThiF 11 dgqekLrdskvllvGaGglGsellknLalsGvgkltl.vDnDkielsN 57
                 +q  L + kv++vG+G +G + + ++a+sG+  + + + +  +e+ N
  EPA05323.1 17 NSQLNLDSIKVAVVGIGRIGLPTAILFAKSGLTTIGVdINQNLVEKIN 64
                56788999**************************99866666666666 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   6.1e-05     0.092       1      94 [.      26     149 ..      26     155 .. 0.78
   2 ?    0.7   0.0      0.34   5.1e+02      43      89 ..     393     438 ..     366     450 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.1e-05
                    EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT.....................EEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS CS
  NAD_binding_2   1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg.....................akaaesieelvasldvvitmvkagkavdevieg 75 
                    k++++G+G +G + a  ++k+g ++++++ +++ ve++ ++                      + a+ +i+ ++++++vvi+ ++     +++ + 
     EPA05323.1  26 KVAVVGIGRIGLPTAILFAKSGLTTIGVDINQNLVEKINHSIfplddepgmkeifndviknkkLIATVDIKHALSQVNVVILSLPTPMTDNNIPDY 121
                    699*****************************9999999887888889999999999999988778888889999999999888764332222221 PP

                    .........HCCC--TT-EEEE-S---H CS
  NAD_binding_2  76 .........llealkkgdilidgstssp 94 
                             + + l +++++i  st++p
     EPA05323.1 122 sslesvgkqIHDFLCPNSLVIVESTVEP 149
                    3333333337888888888888888765 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.34
                    EEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHCCC--TT-EEEE- CS
  NAD_binding_2  43 akaaesieelvasldvvitmvkagkavdeviegllealkkgdilidg 89 
                    +++ ++ie+++++ d+++ +++a ++  ++  +++++l k  i+id+
     EPA05323.1 393 IRTEQKIEDMISNSDAIL-ILTAHQNFFSINPEIFNKLMKKPIVIDT 438
                    566678999999999876.5788899999999999999999999996 PP

>> NAD_binding_11  NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1     3e-05     0.045       3      42 ..     230     269 ..     229     273 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3e-05
  NAD_binding_11   3 GqavKlvnnlllainlaaasEalvlaekaGldpekvlevi 42 
                     ++avKl  n+   +n+a + E  +l ek+G+d+ +vl++ 
      EPA05323.1 230 ANAVKLTTNVFRDVNIAFVNELALLFEKLGIDIFTVLDAA 269
                     689*********************************9986 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00017      0.25       1      88 [.      27     121 ..      27     131 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00017
                 EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETTCEEEEEECEEECCH......SCCCCS-ESEEEE-SSGGGHHHHHHHH CS
        ApbA   1 iailGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseggeeilrppealsae......ekselepidlvivtvKayqteealeei 88 
                 +a++G+G iG   a   ak g + + ++ ++  +e++++  + l++e g + + +++  +++       k+ l+++ +vi+++++  t++++ ++
  EPA05323.1  27 VAVVGIGRIGLPTAILFAKSGLTTIGVDINQnLVEKINHSIFPLDDEPGMKEIFNDVIKNKKliatvdIKHALSQVNVVILSLPTPMTDNNIPDY 121
                 69**********************************************55555555555555577788788999*********999999998876 PP

>> SRR1  SRR1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00026      0.39      17      48 ..     359     389 ..     350     393 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00026
        SRR1  17 yQLAlllelveelkiessrsvyaqDPvftevD 48 
                 +QLA + ++++elk  + + + ++DP f ++D
  EPA05323.1 359 IQLAPAEKIISELKSLECN-IKIFDPYFISTD 389
                 8***************988.********9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (461 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.72u 0.31s 00:00:01.03 Elapsed: 00:00:00.54
# Mc/sec: 2568.09
//
Query:       EPA05324.1  [L=184]
Description: dTDP-4-dehydrorhamnose 3,5-epimerase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-70  235.3   0.0    3.4e-70  235.1   0.0    1.0  1  dTDP_sugar_isom  dTDP-4-dehydrorhamnose 3,5-epimerase


Domain annotation for each model (and alignments):
>> dTDP_sugar_isom  dTDP-4-dehydrorhamnose 3,5-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  235.1   0.0   1.9e-74   3.4e-70       2     168 ..       8     176 ..       7     177 .. 0.99

  Alignments for each domain:
  == domain 1  score: 235.1 bits;  conditional E-value: 1.9e-74
                      -SSTTCEEEEE-EEEETTEEEEEEEEHHHHHHHTS-----EEEEEEEETTBEEEEEEESSCS---EEEEEEESEEEEEEEE-BTTSTTTT-EEE CS
  dTDP_sugar_isom   2 teiegvlliepkvfgDeRGfflesfneeefaeagleaefvqdnlsvskkgvlRGlHfqkepkaqaklvrvvrGevldvaVDlRkgSptfgkwvg 95 
                      +ei++++li+p+ f DeRG+f+e+f++++f+++g+ ++f+q+n s+skk+v+RGlHfqk pkaq+kl++v  Ge++dvaVDlRk+S+t+g+w++
       EPA05324.1   8 LEIPDLVLITPNLFYDERGYFFENFHNSDFKKNGVCENFAQENFSFSKKNVIRGLHFQKLPKAQSKLITVSLGEIFDVAVDLRKNSSTYGQWIS 101
                      68*********************************99********************************************************* PP

                      EEEETTT--EEEE-TTEEEEEEE-SSEEEEEEEESS---GGGEEEE-TT-TTTT---..SS.B--HHHHT-B-HH CS
  dTDP_sugar_isom  96 veLsaenkrqlyipegfahGflvlsdeaevlYkvteyyapesergirwnDpelgidw..eelilSekDkaapsla 168
                        Ls++n+++l+ipegfahGf+vls+ea vlYk+++ y+pe+++gi wnDp+l+i+w  +++ilS+kD+++p l+
       EPA05324.1 102 EILSENNHKSLFIPEGFAHGFCVLSNEAIVLYKTNQEYSPEHDGGILWNDPKLNISWpiSNPILSKKDQNLPLLK 176
                      ***********************************99**********************99***********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1240.37
//
Query:       EPA05325.1  [L=277]
Description: hypothetical protein BG20_I0119 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       892  (0.0497518); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1941.76
//
Query:       EPA05326.1  [L=344]
Description: glucose-1-phosphate thymidylyltransferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.8e-55  185.8   0.0    1.2e-54  185.5   0.0    1.1  1  NTP_transferase  Nucleotidyl transferase
    3.4e-08   34.0   0.0    4.4e-08   33.6   0.0    1.1  1  NTP_transf_3     MobA-like NTP transferase domain
    3.8e-07   29.6  14.2    2.1e-05   24.1   3.7    3.6  2  Hexapep          Bacterial transferase hexapeptide (six repea
    0.00021   20.4   2.5    0.00031   19.8   2.5    1.2  1  Fucokinase       L-fucokinase
     0.0067   16.1   5.1     0.0067   16.1   5.1    3.7  3  Hexapep_2        Hexapeptide repeat of succinyl-transferase
  ------ inclusion threshold ------
      0.055   13.4   0.0        0.1   12.5   0.0    1.4  1  CTP_transf_3     Cytidylyltransferase


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.5   0.0     4e-58   1.2e-54       1     246 [.       2     235 ..       2     237 .. 0.94

  Alignments for each domain:
  == domain 1  score: 185.5 bits;  conditional E-value: 4e-58
                      EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEESS--BGGHHHHHTH CS
  NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlialepegkgtAdAvalaa 94 
                      k++IL+GG GtRL+PLt+t +k+l+ +++k ++ q++l+ l ++gi +i +++ +   + v+e +++g+kfgv++++++++++ g+A+A+ l +
       EPA05326.1   2 KGIILHGGHGTRLRPLTHTGPKQLIKIANK-PMSQYVLEDLRDAGIIDIAIIIGDVYPEKVKEFYGNGKKFGVNLTYIYQNKPHGIAHAISLCK 94 
                      79****************************.*************************************************************** PP

                      HHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEECTTSBEEEEECS-SSHSHCSEECCSEEEEETTHHH CS
  NTP_transferase  95 elledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGvieadeegrverfvEKPkeakaselassGiYvfnsevll 188
                      ++++++k    v++L gD + +  +  +v+k++++++  ++ +++ +ve+++++Gv++++++ ++ +++EKPke++ s++a+ G+Y+ ++++++
       EPA05326.1  95 DFIGENKF---VVYL-GDNILRTGLLSYVQKFESSSK--EAQILLAEVENPSAFGVVKIKDN-KILHIIEKPKEPP-SNFAVIGVYFLTPKIFK 180
                      *******5...5555.5666677**************..9********************95.9************.***************** PP

                      HHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEEXSSHHHHHHHHHHHH CS
  NTP_transferase 189 flakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsDvGtldslleanekla 246
                      ++ k+l++++rge eit++l+ ++++g +      +++  W+D+Gt++++l an+ ++
       EPA05326.1 181 II-KQLKPSWRGELEITEALQLLMDSGFELDHDYVTGW--WKDTGTPNDILHANKLIL 235
                      **.89*********************976655566774..*************98776 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.0   1.5e-11   4.4e-08       1     101 [.       3     113 ..       3     147 .. 0.69

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 1.5e-11
                   EEEEEESS-TTTT.....TTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHHTTC....T..S-EEE-TTSS-SHHHHHHHHHHHH. CS
  NTP_transf_3   1 aviLAGGrSsRmg.....gdKallplggkpllervldalraagvdevvvvggd..eevlaalarl....g..vrvvededpgkgplaslaaalraaa 84 
                   ++iL GG+++R+      g+K+l+++++kp+ ++vl+ lr+ag+ ++ ++ gd  +e  +++ +     g  ++++++ +p  g+++++    + + 
    EPA05326.1   3 GIILHGGHGTRLRplthtGPKQLIKIANKPMSQYVLEDLRDAGIIDIAIIIGDvyPEKVKEFYGNgkkfGvnLTYIYQNKP-HGIAHAISLCKDFI- 97 
                   79**********6554447************************99999999887744334444441122322444444433.35555555554545. PP

                   SSSCEEEEETT-TT--H CS
  NTP_transf_3  85 dadavlvlacDmPlltp 101
                   ++  ++v ++D +l ++
    EPA05326.1  98 GENKFVVYLGDNIL-RT 113
                   78888888888765.44 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   3.7   6.9e-09   2.1e-05       1      30 [.     247     276 ..     247     277 .. 0.94
   2 !   10.4   1.4   0.00014      0.43       2      28 ..     277     307 ..     276     309 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 6.9e-09
                 TEEEETTEEE-TTEEEETTEEE-TTEEEET CS
     Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIga 30 
                 +++IG+n++I++ ++i g+V+I dn++I +
  EPA05326.1 247 GIFIGKNCIIDSESKIIGPVIIDDNCVISS 276
                 579*************************76 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00014
                 EEEETTEEE-T.....TEEEETTEEE-TTEEE CS
     Hexapep   2 tvIGsnvlIgp.....faviggnVkIGdnvkI 28 
                 ++IG  v Ig+     +++i  n +I dn++I
  EPA05326.1 277 SIIGPYVSIGKnsflkNCQI-KNSIIMDNCII 307
                 67888888888888889999.88889999988 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   2.5     1e-07   0.00031     277     324 ..     258     313 ..     222     338 .. 0.63

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1e-07
  Fucokinase 277 inSvlessvsvgegsviehsslkgnvsigsnsivsglelessee........slel 324
                  +S++ + v +++++vi +s +++ vsig+ns++ ++++++s           +++
  EPA05326.1 258 SESKIIGPVIIDDNCVISSSIIGPYVSIGKNSFLKNCQIKNSIImdnciidtPIKI 313
                 35677788888888888888888888888888888888887632333344434444 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.7       3.4     1e+04      18      22 ..      51      55 ..      44      55 .. 0.59
   2 !   16.1   5.1   2.3e-06    0.0067       4      27 ..     250     275 ..     247     279 .. 0.87
   3 !    5.6   0.9    0.0044        13       2      27 ..     283     308 ..     281     309 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 3.4
                EEE-T CS
   Hexapep_2 18 vslGd 22
                +++Gd
  EPA05326.1 51 IIIGD 55
                66665 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 2.3e-06
                 E-TT-EE-TT-EE.S.EEE-TT-EE- CS
   Hexapep_2   4 IGdnCliGanagi.G.vslGdncvvg 27 
                 IG+nC+i + + i G v++ dncv++
  EPA05326.1 250 IGKNCIIDSESKIiGpVIIDDNCVIS 275
                 9***********6655********97 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.0044
                 EEE-TT-EE-TT-EE.SEEE-TT-EE- CS
   Hexapep_2   2 viIGdnCliGanagi.GvslGdncvvg 27 
                 v+IG+n+++ +n+ i   ++ dnc+++
  EPA05326.1 283 VSIGKNSFL-KNCQIkNSIIMDNCIID 308
                 99******9.88888766777888875 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.4e-05       0.1      16      44 ..      23      51 ..      21      60 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.4e-05
                  GGGSEETTEEHHHHHHHHHHHTTTTSEEE CS
  CTP_transf_3 16 Knlldlggkpliayvleaalkskafekvi 44
                  K l+++++kp+ +yvle +++++ ++  i
    EPA05326.1 23 KQLIKIANKPMSQYVLEDLRDAGIIDIAI 51
                  99*********************998744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 1956.47
//
Query:       EPA05327.1  [L=301]
Description: methyltransferase, FkbM family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.1e-23   82.0   0.6    7.7e-23   81.4   0.6    1.3  1  Methyltransf_21  Methyltransferase FkbM domain
     0.0015   18.3   0.8     0.0053   16.5   0.6    1.9  2  Met_10           Met-10+ like-protein
     0.0019   18.0   0.0     0.0031   17.3   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
  ------ inclusion threshold ------
      0.015   15.2   0.0      0.019   14.8   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
      0.018   14.2   0.0      0.044   12.9   0.0    1.6  1  Methyltransf_3   O-methyltransferase


Domain annotation for each model (and alignments):
>> Methyltransf_21  Methyltransferase FkbM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.4   0.6   2.1e-26   7.7e-23       1     172 [.      90     253 ..      90     254 .. 0.83

  Alignments for each domain:
  == domain 1  score: 81.4 bits;  conditional E-value: 2.1e-26
  Methyltransf_21   1 dvGanigvwdsfanltarlcggggevlaiEPvpns......lpkfeklranll..tlavgndvglyelivegksggkyfpfavgdtngfstssv 86 
                      d+G nig   +++ l +++ g +g v+aiEP p++      ++k+++++ + +  ++a+g++++++e+i+  k      +++   +++     +
       EPA05327.1  90 DIGSNIG---YYVLLESKKVGLTGNVWAIEPSPENysvlldNIKLQNNKNI-IafNFAIGDKNEEIEFIISKK-----SNWSKIKEENDK---I 171
                      99*****...777788899***************77777765555555444.2699***********999555.....555444443333...3 PP

  Methyltransf_21  87 lggedaryievpvvtldsfleeikksridllkiDvEGaElevLeGaqkglkrcqpnlivvEvhkfkefetelfdeirqflrecgyr 172
                      l  ++ + i+vp +tld f ee++ ++idll +DvEG+E  ++ G+ + l++++p ++ +Evhk    +++++++i+++++e +y+
       EPA05327.1 172 L--SEDKIIKVPLKTLDLFVEENNLRKIDLLRMDVEGFESRIIFGGLEFLRKFKPIIM-IEVHKMIM-GKNETKKILEKIKEINYE 253
                      3..4789************************************999**********98.*****874.45789**********998 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.6   1.5e-06    0.0053      94     156 ..      78     140 ..      66     253 .. 0.79
   2 ?   -0.5   0.1      0.24   8.6e+02      23      46 ..     228     251 ..     213     269 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.5e-06
                 HHTT--TT-EEEETT-TTTCCHHH.CCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEE CS
      Met_10  94 laklveegevVvdvfAGiGpfaip.iakyskakrvlaidlnPesvkylkeniklNkvekvvkpi 156
                 + +  +eg   +d+   iG++ +   +k +    v+ai+  Pe +  l +nikl + ++++ ++
  EPA05327.1  78 ILNELSEGMNCLDIGSNIGYYVLLeSKKVGLTGNVWAIEPSPENYSVLLDNIKLQNNKNII-AF 140
                 6677889999999********975156778999*********************9988888.44 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.24
                 HHHHHHHHHHSS-SCEEEE-S-SB CS
      Met_10  23 kvigevildktkvktvlrkvseve 46 
                  ++ ++i+ k++ k +l+k +e++
  EPA05327.1 228 IEVHKMIMGKNETKKILEKIKEIN 251
                 567888899999999999988885 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   8.6e-07    0.0031      70     127 ..      80     138 ..      47     150 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 8.6e-07
                 T.--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEE CS
        PCMT  70 e.lkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvi 127
                 + l++g++ L++Gs  Gy   + ++ vg +g+v +ie ++e ++    n+k ++ +n+i
  EPA05327.1  80 NeLSEGMNCLDIGSNIGYYVLLESKKVGLTGNVWAIEPSPENYSVLLDNIKLQNNKNII 138
                 349**************************************999999999999988775 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   5.2e-06     0.019      19      62 ..      81     133 ..      69     234 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.2e-06
  Methyltransf_23  19 klraggrvLdiGcGtG.illevlrengf..svtgvDlspeaveiae......k 62 
                      +l +g+++LdiG + G ++l + ++ g   +v ++++spe+ + +       +
       EPA05327.1  81 ELSEGMNCLDIGSNIGyYVLLESKKVGLtgNVWAIEPSPENYSVLLdniklqN 133
                      467899**********778999999999999********97665434443432 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.2e-05     0.044      42     103 ..      79     140 ..      73     170 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.2e-05
                     HHHHHT--EEEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHHHTT-GGGEEE CS
  Methyltransf_3  42 LvklvnakrvleiGvftGyslLatalalPeDGkilaididreayeialkfiqkagvaekiel 103
                     L +l++  + l+iG   Gy +L  + ++   G++ ai+  +e+y + l+ i+    ++ i +
      EPA05327.1  79 LNELSEGMNCLDIGSNIGYYVLLESKKVGLTGNVWAIEPSPENYSVLLDNIKLQNNKNIIAF 140
                     66889999***************************************999988777776644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       822  (0.0458475); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.62u 0.34s 00:00:00.96 Elapsed: 00:00:00.54
# Mc/sec: 1683.67
//
Query:       EPA05328.1  [L=163]
Description: GMP synthase domain protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-15   57.0   0.0    2.9e-15   56.5   0.0    1.2  1  GATase         Glutamine amidotransferase class-I
    4.4e-06   26.0   0.0    6.2e-06   25.5   0.0    1.2  1  NAD_synthase   NAD synthase
    0.00013   21.6   0.0    0.00019   21.1   0.0    1.3  1  ThiI           Thiamine biosynthesis protein (ThiI)
    0.00086   18.2   0.0     0.0011   17.8   0.0    1.2  1  tRNA_Me_trans  tRNA methyl transferase
     0.0089   15.8   0.0      0.013   15.2   0.0    1.3  1  Peptidase_C26  Peptidase C26
  ------ inclusion threshold ------
      0.052   13.0   0.0      0.096   12.2   0.0    1.4  1  Proteasome     Proteasome subunit
      0.097   12.4   0.0       0.14   11.9   0.0    1.2  1  ATP_bind_3     PP-loop family
       0.12   12.4   0.0       0.19   11.8   0.0    1.4  1  PAPS_reduct    Phosphoadenosine phosphosulfate reductase fami


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.5   0.0   1.3e-18   2.9e-15     110     189 ..       9      84 ..       1      85 [. 0.90

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 1.3e-18
                 TTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEEEEEEETTTEEEESSBTTSTTSTTHHHHHHHHHHH CS
      GATase 110 detallyglknevierhrHryevnpkelepaglevtakseddeelmeiiekknpfvgvQFHPEststpegpellfnflik 189
                 ++++ll+g +++v+++++H++e+++    p g++v++++e+  + ++i   ++ ++g+QFHPE+++t++g+e+l+nf++k
  EPA05328.1   9 NNENLLSGIGKSVRAWMSHGDEAEQ---IPPGFKVIGHTESA-KAAAIASYEKSIYGIQFHPEVVHTEQGTEILKNFVLK 84 
                 4568999*****************9...***********887.68888888888***********************987 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   2.8e-09   6.2e-06       6      47 ..      95     138 ..      92     160 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 2.8e-09
                   HHHHHHHHHHCTT..SEEEEEE-SSHHHHHHHHHHHHHHTCGEE CS
  NAD_synthase   6 vdflkeyvkkaga..kgvvlGlSGGvDSslvaalavkalgkenv 47 
                   + f+ + v+k      +v+ G+SGG+DS+++a l  ka+g+ + 
    EPA05328.1  95 EGFIDSAVEKISKiqGNVLCGVSGGIDSTVAALLIHKAIGDRQK 138
                   56888889887655245667*******************98775 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   8.3e-08   0.00019       3      51 ..     109     158 ..     107     163 .] 0.76

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 8.3e-08
        ThiI   3 qgkvlaLlSgGiDSpVaaylllkR.Gcrvvlvhlknepgtseeaiekvek 51 
                 qg+vl+ +SgGiDS Vaa l+ k  G r ++v+++n +   +e++e  e+
  EPA05328.1 109 QGNVLCGVSGGIDSTVAALLIHKAiGDRQKCVFVNNGLLRLNEEKEIEEM 158
                 9*****************99988648888888887766666655554444 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   5.1e-07    0.0011       2      31 ..     111     140 ..     110     161 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 5.1e-07
  tRNA_Me_trans   2 kvvvalSgGVDSsvaaallkeqgyevigvf 31 
                    +v++++SgG+DS+vaa+l++++  + ++++
     EPA05328.1 111 NVLCGVSGGIDSTVAALLIHKAIGDRQKCV 140
                    79*****************99875555443 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0     6e-06     0.013     163     216 .]      17      67 ..       2      67 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 6e-06
  Peptidase_C26 163 lgseeievnslHhqaikelaeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                    +g ++++    H    +++ ++++v+ ++e     ai s e+   ++g+Q+HPE
     EPA05328.1  17 IG-KSVRAWMSHGDEAEQIPPGFKVIGHTESAKAAAIASYEK--SIYGIQFHPE 67 
                    44.56667778999999****************99**99994..5********9 PP

>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   4.3e-05     0.096      17      54 ..      85     120 ..      78     128 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.3e-05
                 EEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESH CS
  Proteasome  17 vlaadkratagskllskstveKifkiddhigvafaGla 54 
                 v++a +  t++  + ++  veKi+ki+ +++++++G +
  EPA05328.1  85 VCGAKQDWTMEGFI-DSA-VEKISKIQGNVLCGVSGGI 120
                 56777777877777.566.9****************75 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   6.3e-05      0.14       2      45 ..     112     154 ..     111     162 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.3e-05
                 EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSS.TCHHH CS
  ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglr.eeske 45 
                 vl +vSgG+DS++  ll++k   +   + ++++ +  lr +e ke
  EPA05328.1 112 VLCGVSGGIDSTVAALLIHKAIGD--RQKCVFVNNGLLRlNEEKE 154
                 789*********999998888554..3444444444455334444 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   8.4e-05      0.19       4      36 ..     114     147 ..     111     162 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.4e-05
                  EE--SSCTCHHHHHHHHHHCTTH.EEEEEE-STB CS
  PAPS_reduct   4 vsvsgGkdslVllhLalkafkpv.pvvfvdtghe 36 
                    vsgG+ds+V   L+ ka  ++ + vfv+ g  
   EPA05328.1 114 CGVSGGIDSTVAALLIHKAIGDRqKCVFVNNGLL 147
                  569*******************736****99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 962.39
//
Query:       EPA05329.1  [L=176]
Description: transferase hexapeptide repeat protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.5e-11   43.5  11.2    3.1e-06   26.7   2.0    3.7  4  Hexapep    Bacterial transferase hexapeptide (six repeats)
    3.9e-08   32.9   7.6     0.0017   18.0   4.2    3.7  3  Hexapep_2  Hexapeptide repeat of succinyl-transferase


Domain annotation for each model (and alignments):
>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   3.7e-05      0.33      19      34 ..      61      76 ..      60      77 .. 0.89
   2 !   10.7   0.1   3.8e-05      0.34      20      34 ..      84      98 ..      83     102 .. 0.69
   3 !   26.7   2.0   3.4e-10   3.1e-06       1      35 [.     120     154 ..     120     155 .. 0.95
   4 ?   -2.1   0.1      0.43   3.9e+03      14      18 ..     162     166 ..     160     170 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 3.7e-05
                TEEE-TTEEEETTEEE CS
     Hexapep 19 nVkIGdnvkIgagvvi 34
                +VkIG+n+++ ++v i
  EPA05329.1 61 GVKIGKNCHLSPYVLI 76
                89*******9999987 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 3.8e-05
                EEE-TTEEEETTEEE CS
     Hexapep 20 VkIGdnvkIgagvvi 34
                VkI +nv+Ig+++ i
  EPA05329.1 84 VKIDNNVTIGSNTMI 98
                667777777776666 PP

  == domain 3  score: 26.7 bits;  conditional E-value: 3.4e-10
                 TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
     Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                 s++I s++++ p+++i ++V+IG+n+ +gag+v+ 
  EPA05329.1 120 SVHIKSGAVLFPGCIITAGVTIGENALVGAGSVVS 154
                 689******************************95 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 0.43
                 EEEET CS
     Hexapep  14 avigg 18 
                 +v+g+
  EPA05329.1 162 VVVGN 166
                 44554 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0   0.00024       2.2      17      27 ..      61      71 ..      52      77 .. 0.80
   2 !    5.7   0.1    0.0014        12      18      32 ..      84      98 ..      83     100 .. 0.55
   3 !   18.0   4.2   1.9e-07    0.0017      12      33 ..     131     154 ..     121     155 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00024
                SEEE-TT-EE- CS
   Hexapep_2 17 GvslGdncvvg 27
                Gv++G+nc+++
  EPA05329.1 61 GVKIGKNCHLS 71
                78888888876 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0014
                EEE-TT-EE-TT-EE CS
   Hexapep_2 18 vslGdncvvgaGvvi 32
                v++ +n+++g++ +i
  EPA05329.1 84 VKIDNNVTIGSNTMI 98
                445555555555555 PP

  == domain 3  score: 18.0 bits;  conditional E-value: 1.9e-07
                 TT-EE..SEEE-TT-EE-TT-EE- CS
   Hexapep_2  12 anagi..GvslGdncvvgaGvvit 33 
                 + ++i  Gv++G+n+ vgaG+v+ 
  EPA05329.1 131 PGCIItaGVTIGENALVGAGSVVS 154
                 5799889***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       268  (0.0149478); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1183.90
//
Query:       EPA05330.1  [L=42]
Description: hypothetical protein BG20_I0172 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      197  (0.0109878); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.24s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 333.78
//
Query:       EPA05331.1  [L=56]
Description: hypothetical protein BG20_I0159 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      167  (0.00931452); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 396.86
//
Query:       EPA05332.1  [L=190]
Description: hypothetical protein BG20_I0120 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-10   40.2   0.0      3e-10   40.1   0.0    1.1  1  Capsule_synth    Capsule polysaccharide biosynthesis protein
  ------ inclusion threshold ------
      0.084   12.8   2.7        1.7    8.6   0.5    2.9  2  SF3a60_bindingd  Splicing factor SF3a60 binding domain


Domain annotation for each model (and alignments):
>> Capsule_synth  Capsule polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   0.0   3.3e-14     3e-10     176     268 ..       3      92 ..       1     131 [. 0.89

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 3.3e-14
  Capsule_synth 176 vLesfaeeapadaeliiKtHPldeglikyrrvikgyltelaalkkrvllvedvnlpsLldqvdgvvvvnStaGleALlhgkpvvtlGravYdi 268
                    v e  a+  p d  l +K+HP  +gl+++ r  +++ ++ ++l++++l+   +n++ L+ ++  vv ++  +G+eAL  +kpv+ +   +Yd 
     EPA05332.1   3 VVENIARSIPIDFILYVKEHPG-QGLKQW-R-STEFYKKIHELPNVKLIHPSINSQDLISKCSCVVSITGSTGFEALFYKKPVILFADEYYDC 92 
                    56777888899999*******6.688888.4.567777778*************************************************996 PP

>> SF3a60_bindingd  Splicing factor SF3a60 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1      0.01        90       9      17 ..      33      41 ..      33      42 .. 0.83
   2 ?    8.6   0.5   0.00019       1.7       7      16 ..     165     174 ..     159     175 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.01
  SF3a60_bindingd  9 seFYkrLke 17
                     +eFYk++ e
       EPA05332.1 33 TEFYKKIHE 41
                     59***9987 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00019
  SF3a60_bindingd   7 pFseFYkrLk 16 
                      +F++FYk++k
       EPA05332.1 165 EFNNFYKKYK 174
                      8*******99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       824  (0.0459591); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 1174.20
//
Query:       EPA05333.1  [L=46]
Description: hypothetical protein BG20_I0108 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 318.93
//
Query:       EPA05334.1  [L=273]
Description: methyltransferase domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-16   59.3   0.0    6.5e-16   58.6   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
    1.3e-12   48.3   0.0    2.5e-12   47.4   0.0    1.5  1  Methyltransf_12  Methyltransferase domain
    1.7e-08   35.0   0.0    2.5e-08   34.4   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    3.3e-08   33.5   0.0    4.8e-08   32.9   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    4.8e-07   30.4   0.0    9.5e-07   29.4   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    0.00051   19.7   0.0    0.00064   19.4   0.0    1.3  1  MetW             Methionine biosynthesis protein MetW
     0.0022   17.5   0.1     0.0055   16.2   0.0    1.6  2  CheR             CheR methyltransferase, SAM binding domain
  ------ inclusion threshold ------
      0.015   14.6   0.5       0.11   11.8   0.5    2.1  1  CMAS             Mycolic acid cyclopropane synthetase
      0.021   14.4   0.0       0.04   13.5   0.0    1.5  1  MTS              Methyltransferase small domain
      0.028   13.4   0.1       0.12   11.3   0.1    1.9  1  Methyltransf_9   Protein of unknown function (DUF1698)
      0.047   13.8   0.8       0.12   12.5   0.8    1.6  1  Elf1             Transcription elongation factor Elf1 like
      0.053   12.6   0.0       0.21   10.6   0.0    1.7  2  DREV             DREV methyltransferase
      0.079   12.6   1.2       0.16   11.7   1.2    1.5  1  TackOD1          Thaumarchaeal output domain 1
       0.08   12.9   0.0       0.13   12.2   0.0    1.3  1  Methyltransf_32  Methyltransferase domain
        0.2   11.7   0.9       0.38   10.8   0.9    1.4  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
       0.24   11.2   3.0       0.46   10.3   1.7    2.2  2  zinc_ribbon_5    zinc-ribbon domain


Domain annotation for each model (and alignments):
>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.6   0.0   5.8e-19   6.5e-16      14     164 ..      78     227 ..      65     228 .. 0.76

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 5.8e-19
  Methyltransf_23  14 erllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiaekakkaqkdqfdeq.........eaaepqgkfdlIvlrevlehvpdp 98 
                       ++  k++++g + d+GcG G+ll+ + +n ++  g D s+ a+         +k +f e+           +e+ + fd++v+ +v+eh++ p
       EPA05334.1  78 SKFI-KEQKPGTIFDVGCGLGYLLSDI-PNSWEKHGCDESEFAILF-------IKNKFKEIiineldlknPPPENLRNFDIVVCYHVIEHIEQP 162
                      4455.38999*************8888.445555555555443332.......233333331111111112222447***************** PP

  Methyltransf_23  99 pellrqiatllkpgGylllseplaslkedrllldwlylvpagrhisffsarslkelleeaGlevve 164
                         ++++  ++k +G+l++ +p++ +  +r+++ +  l    +h+s+f+  +lk+l+e++++++++
       EPA05334.1 163 DIFFKHLSMMVKKNGVLIVGTPNVGSFVARRFKGNFRLLGI-GHLSLFNNNNLKKLFEKNDFKIIK 227
                      *************************9********9666666.9********************986 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.4   0.0   2.2e-15   2.5e-12       2      99 .]      91     179 ..      90     179 .. 0.90

  Alignments for each domain:
  == domain 1  score: 47.4 bits;  conditional E-value: 2.2e-15
  Methyltransf_12   2 eiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlkdirevldnirklLkp 95 
                      ++GcG G ll+ + ++   +e +g+D s+ ai   k+k+++++ n    ++l++   ++l     fD+vv+ +v++h+++++ +++++  ++k+
       EPA05334.1  91 DVGCGLGYLLSDIPNS---WEKHGCDESEFAILFIKNKFKEIIINE---LDLKNPPPENLR---NFDIVVCYHVIEHIEQPDIFFKHLSMMVKK 175
                      9************999...************************755...555555555443...9***************************** PP

  Methyltransf_12  96 gGrl 99 
                      +G+l
       EPA05334.1 176 NGVL 179
                      **97 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.0   2.2e-11   2.5e-08       2      96 .]      91     181 ..      90     181 .. 0.88

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 2.2e-11
                      EET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-T.T-EEEEEEES-CCC-CCHHHHHHHHHHHEEEEEEE CS
  Methyltransf_11   2 dvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfed.nsfDlvvssevlhhvedpekalkeiaRvLkpgGll 94 
                      dvGcG G+l+ ++  +  +  g+D s+ ++   k+k +e      + + d+++ p e+   fD+vv+++v++h+e+p+ ++k +  ++k++G+l
       EPA05334.1  91 DVGCGLGYLLSDIP-NSWEKHGCDESEFAILFIKNKFKEII----INELDLKNPPPENlRNFDIVVCYHVIEHIEQPDIFFKHLSMMVKKNGVL 179
                      9*************.55699****99999988888877755....6999***96444446*********************************9 PP

                      EE CS
  Methyltransf_11  95 vi 96 
                      ++
       EPA05334.1 180 IV 181
                      86 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.0   4.3e-11   4.8e-08       3     114 ..      85     190 ..      83     245 .. 0.83

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 4.3e-11
  Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDlilsnevlnaladpdkile 95 
                      k  ++ D+GCG G+l+  +        e +G D se+ai + ++     +++++   + d  +  ++  + ++fD++++  v+ ++  pd +++
       EPA05334.1  85 KPGTIFDVGCGLGYLLSDIPN----SWEKHGCDESEFAILFIKN-----KFKEIIINELDLKNpPPE--NLRNFDIVVCYHVIEHIEQPDIFFK 167
                      566899***********9993....45689*********99999.....588899999999996663..4578********************* PP

  Methyltransf_31  96 eiervlkpggilliedpr....l 114
                       ++  +k++g+l++ +p+    +
       EPA05334.1 168 HLSMMVKKNGVLIVGTPNvgsfV 190
                      ****************9944442 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   8.5e-10   9.5e-07       1      97 []      89     177 ..      89     177 .. 0.89

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 8.5e-10
                      EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBS.SSTTTEEEEEEESTGGGSSHHHHHHHHHHHHHHE CS
  Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlp.fedgsfDlvvssgalhhlsdedlekalkeiarvL 93 
                      + d+GcG G l+ ++ +     + +g+D se ++  ++++++    ++ + + d+++ p ++ + fD+vv+ ++++h++++d   ++k+++ ++
       EPA05334.1  89 IFDVGCGLGYLLSDIPNS---WEKHGCDESEFAILFIKNKFK----EIIINELDLKNPPpENLRNFDIVVCYHVIEHIEQPD--IFFKHLSMMV 173
                      78*************988...699*****************4....7999*****997626778*******777****9887..6899999999 PP

                      EEEE CS
  Methyltransf_25  94 kpgG 97 
                      k++G
       EPA05334.1 174 KKNG 177
                      9988 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   5.7e-07   0.00064       6     118 ..      76     192 ..      71     263 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 5.7e-07
        MetW   6 liaelikpg..srvldlGcGdGellellkeekqvdgrGleldeegvaecvakGlsviqgdldkdlenfed.ksfdyvvlsqtlqatrnpkevldellri 101
                 +i ++ik++   +++d+GcG G ll+ + +    + +G + +e ++    +k  ++i ++ld      e+ ++fd+vv    +  + +p+  +++l  +
  EPA05334.1  76 EISKFIKEQkpGTIFDVGCGLGYLLSDIPN--SWEKHGCDESEFAILFIKNKFKEIIINELDLKNPPPENlRNFDIVVCYHVIEHIEQPDIFFKHLSMM 172
                 57777876633589************9977..78899**************9999999999866554443389*****************998887555 PP

        MetW 102 grr...aivsfPnfGhWrvr 118
                  ++    iv  Pn G +  r
  EPA05334.1 173 VKKngvLIVGTPNVGSFVAR 192
                 554233699******88766 PP

>> CheR  CheR methyltransferase, SAM binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       2.5   2.8e+03      26      43 ..      80      97 ..      71      99 .. 0.79
   2 !   16.2   0.0   4.9e-06    0.0055      91     175 ..     101     183 ..      97     195 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.5
                HHHTSSSEEEEEES-TTT CS
        CheR 26 kaknekrvriwsagcssG 43
                 +k++k+ +i+ +gc+ G
  EPA05334.1 80 FIKEQKPGTIFDVGCGLG 97
                4566788999*****988 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 4.9e-06
                 TTS-HHHHHHHEEEEETTCEEE-HHHHTTEEEEE--TTT.-SGGG--EEEEEE-SSGGGC-CHHHHHHHHHHHCCEEEEEEEEE-T CS
        CheR  91 eglseelleryfekseddsykvkkeikelvkFeklnlle.kksvlgklDvifcrnvliYfdeetqekvlerfaeklkpgglLllGh 175
                 +++++++ ++ + +se     +k++ ke++  ++l+l +   + l+++D+++c  v+  +++++     ++++ ++k++g+L++G 
  EPA05334.1 101 SDIPNSWEKHGCDESEFAILFIKNKFKEII-INELDLKNpPPENLRNFDIVVCYHVIEHIEQPDI--FFKHLSMMVKKNGVLIVGT 183
                 667777777777555555555888887766.799*****99999*************99998875..6899**************7 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.5   9.5e-05      0.11      65     166 ..      88     183 ..      43     229 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.5e-05
                 EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG-----SEEEEES-GGGTSGGGHHHHHHHHHHHS-TT-EEE CS
        CMAS  65 tlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedldekvdrvvsvgafehvgkenydtffkklkkllkedGlll 163
                 t+ d+GcG G+l+    + ++    g   S+      k++++e+ ++ + ++k    e+l+ ++d vv   ++eh+   + d ffk+l+ ++k++G+l+
  EPA05334.1  88 TIFDVGCGLGYLLSDIPNSWE--KHGCDESEFAILFIKNKFKEIIIN-ELDLKNPPPENLR-NFDIVVCYHVIEHIE--QPDIFFKHLSMMVKKNGVLI 180
                 678888888888887777654..446666777777777777776533.3445555555554.7************95..5689**************99 PP

                 EEE CS
        CMAS 164 lht 166
                 + t
  EPA05334.1 181 VGT 183
                 865 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.5e-05      0.04      27      77 ..      81     128 ..      77     161 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.5e-05
                 CHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHH CS
         MTS  27 lpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenlea 77 
                 +++++ g++ D+GcG G+l   + + +++   + +d++  A+ + k+ +++
  EPA05334.1  81 IKEQKPGTIFDVGCGLGYLLSDIPNSWEK---HGCDESEFAILFIKNKFKE 128
                 56667899***********9999998888...89********999988775 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00011      0.12     104     219 ..      74     183 ..      63     188 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00011
                     HHHHGGGS.--TT-EEEEET-TTSHHHHHHHHCT-SEEEEE---HHHHHHHH.HHHCCTTTTSSEEEE---GGGS-T---EEEEEEES-GGG-S- CS
  Methyltransf_9 104 WdrvlphlsdlkgrtildvGcgnGyhlwrmvgegaklvvGidPselfliqfe.avrkllgedqrahllplgieqlpeleafdtvfsmGvlyhrrs 197
                     +  +++ + + k  ti dvGcg Gy l  +         G d se  ++  +   +++       ++l l     ++l  fd+v    v+ h + 
      EPA05334.1  74 YGEISKFIKEQKPGTIFDVGCGLGYLLSDIPNS--WEKHGCDESEFAILFIKnKFKEI-----IINELDLKNPPPENLRNFDIVVCYHVIEHIEQ 161
                     5678899999999************98776544..44468888775444333023333.....34444444444445999999999999999999 PP

                     HHHHHHHHHCTEEEEEEEEEEE CS
  Methyltransf_9 198 PldhllqlkdqlvkgGelvlet 219
                     P   +  l   ++k+G l++ t
      EPA05334.1 162 PDIFFKHLSMMVKKNGVLIVGT 183
                     9888889999999999999877 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.8    0.0001      0.12      23      74 ..       4      54 ..       2      55 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.0001
        Elf1 23 dCpfCnheksvevkldkkekiaevsCkvCgesfetkvnalsepvDvYskwiD 74
                +Cp C ++  ++ kl   + + + +C  C+  f+  +++ s + D +++ iD
  EPA05334.1  4 QCPLCRSK-KINFKLVDYKMNQYWECDDCEFLFQNPITEYSYNEDYWTNAID 54
                7*******.9************************999999988888877776 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00019      0.21      91     186 ..      82     181 ..      72     186 .. 0.79
   2 ?   -1.0   0.0      0.68   7.6e+02      64      88 ..     200     224 ..     187     230 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00019
        DREV  91 sdqedkklldlGaGdGeitkrvaptfeevyatelsetmrdrlkkkkynvlsalelqe....tdvkldlilclnlldrcfdplklledirsalepngrvi 185
                  +q++ +++d+G G G +   + +  e+    e    +    +k k  ++ +l+l++       ++d+++c+ +++   +p  +++ +  + + ng  i
  EPA05334.1  82 KEQKPGTIFDVGCGLGYLLSDIPNSWEKHGCDESEFAILFIKNKFKEIIINELDLKNpppeNLRNFDIVVCYHVIEHIEQPDIFFKHLSMMVKKNGVLI 180
                 578999******************99996666655555544445555577788887622213469*************************999999988 PP

        DREV 186 v 186
                 v
  EPA05334.1 181 V 181
                 8 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.68
        DREV  64 llgrGsmfvlseeqfrkllaiekes 88 
                 llg G + ++ ++ ++kl+  ++++
  EPA05334.1 200 LLGIGHLSLFNNNNLKKLFEKNDFK 224
                 7899999999999999999888775 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.2   0.00014      0.16     124     162 ..       3      41 ..       1      44 [. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00014
     TackOD1 124 leCpkCk.tkLrhiGvDYdrplevykCnsCkslfsepevk 162
                  +Cp C+ +k++   vDY ++ + ++C++C+ lf++p ++
  EPA05334.1   3 NQCPLCRsKKINFKLVDY-KMNQYWECDDCEFLFQNPITE 41 
                 58****8356888889**.58999***********99876 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00012      0.13      13      41 ..      77     101 ..      68     118 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00012
  Methyltransf_32  13 vakllkelakesgaltvvDvGaGkgYLsf 41 
                      ++k++ke    +++ t+ DvG+G gYL +
       EPA05334.1  77 ISKFIKE----QKPGTIFDVGCGLGYLLS 101
                      5555555....999************955 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.9   0.00034      0.38      20      44 ..       4      32 ..       2      33 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00034
  Zn_Tnp_IS1595 20 vCPhCgsr....kayriktrglfqCkeCr 44
                    CP C s+    k+  +k  ++++C +C 
     EPA05334.1  4 QCPLCRSKkinfKLVDYKMNQYWECDDCE 32
                   6*******88888888888*********6 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.7   0.00041      0.46       1      32 [.       1      32 [.       1      36 [. 0.80
   2 ?   -2.8   0.0       5.2   5.8e+03      12      24 ..     166     178 ..     160     179 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00041
  zinc_ribbon_5  1 LiirCpdCdtk...FklvdsklKksgkkVrCakCa 32
                   +  +Cp C++k   Fklvd k   ++ +  C  C 
     EPA05334.1  1 MKNQCPLCRSKkinFKLVDYK--MNQYW-ECDDCE 32
                   5669******8888*****99..89988.677776 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 5.2
  zinc_ribbon_5  12 FklvdsklKksgk 24 
                    Fk  +  +Kk+g+
     EPA05334.1 166 FKHLSMMVKKNGV 178
                    7777778999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1874.14
//
Query:       EPA05335.1  [L=334]
Description: dTDP-glucose 4,6-dehydratase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-75  254.7   0.0    1.7e-75  254.5   0.0    1.0  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    2.2e-56  191.0   0.0    2.8e-56  190.7   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    1.3e-18   67.0   0.3    1.6e-18   66.7   0.3    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    6.7e-15   54.9   0.0    8.7e-15   54.6   0.0    1.2  1  RmlD_sub_bind    RmlD substrate binding domain
      3e-13   49.6   0.0    1.6e-12   47.2   0.0    1.8  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    5.5e-11   42.1   0.1      8e-10   38.3   0.0    2.1  2  NAD_binding_4    Male sterility protein
  ------ inclusion threshold ------
      0.048   13.6   0.3      0.048   13.6   0.3    2.1  3  DUF4868          Domain of unknown function (DUF4868)


Domain annotation for each model (and alignments):
>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  254.5   0.0   6.5e-79   1.7e-75       1     332 []       4     303 ..       4     303 .. 0.92

  Alignments for each domain:
  == domain 1  score: 254.5 bits;  conditional E-value: 6.5e-79
                    EEETTTSHHHHHHHH.HHHHC.T-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHTTS CS
  GDP_Man_Dehyd   1 LiTGiaGfiGsylae.lLlek.gyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevynLAAqshVdvsfek 94 
                    L+ G++GfiGs +++ ++l++ +  v++++++s   n ++++ l +d       +++++k D++++  + +l++++  d v+n+AA+shVd+s+++
     EPA05335.1   4 LVCGGSGFIGSTFIRnYFLNNpKSSVTNLDNLSIGSNQENLNDLPTDI------HYQFIKDDIRNEIVIVDLIKNY--DVVINFAAESHVDRSISN 91 
                    8**********9986344544378899999999999999999987654......589******************9..9***************** PP

                    HHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-S.SSSB-TTS-----SHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS- CS
  GDP_Man_Dehyd  95 PeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvq.evpqtEttpfyPrsPYaaaKlyadwivvnyreayglfavngilfnhesprrg 189
                    P+ ++e+n+ Gt+ LLe ir++     + f+++St+EvYG+++ +  ++E+ +++P +PY+a+K++ad++v +y+++yg+ +++++++n+ +p + 
     EPA05335.1  92 PKPFIETNIFGTYCLLEGIRKHD----KLFIHISTDEVYGDAEtKQSFNEKSQINPSNPYSATKASADHLVASYYRTYGIKCITTRCSNNFGPNQ- 182
                    ********************985....58*************845669**********************************************6. PP

                    TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHHHHHHHHCSS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............ CS
  GDP_Man_Dehyd 190 etfvtrkitravarialgkqevlylGnldakRdwghvkDyveamwlmlqqdkpedyviatgethsvrefvelaflelgktiewegkgeeevgrake 285
                      f++++i++++ r+ +++ +v+++G+++++R+w +v+D+v+a++ ++ ++k        ge++++ +  e++++ ++++i   +           
     EPA05335.1 183 --FPEKLIPKTIIRTIKNL-KVPIYGDGEQIRSWIYVNDHVDAIQSLILNGK-------MGEVYNITSYEEISNKTIVEKILNIM----------- 257
                    ..************99987.7899**********************999998.......8******************9987643........... PP

                    TTGGCCCEECGG--SS--SB--B-THHHHHHH----SS-HHHHHHHH CS
  GDP_Man_Dehyd 286 sgkvvvevdpkyfrpgevdlllgdaskakeeLgWkpkvsfeelvrem 332
                     +k +  ++++++rpg+++++ +d sk++++++Wkpk++f+  ++e+
     EPA05335.1 258 -NKPYDMIEYVPDRPGHDKRYSIDSSKIENKINWKPKYDFNHALKET 303
                    .456778999*******************************999886 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.7   0.0   1.1e-59   2.8e-56       1     240 [.       3     238 ..       3     239 .. 0.95

  Alignments for each domain:
  == domain 1  score: 190.7 bits;  conditional E-value: 1.1e-59
                 EEEETTTSHHHHHHHHHHHHCT..SEEEEEES-STTTTCHHCHHC......EEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHHHSHHHHHHHH CS
   Epimerase   1 ilVtGatGfiGsalvkallekg..yevigldrlssasntarledl......elveldltdrsalerlfkeeqpdavihlAavggvaassedpadfiekn 91 
                 ilV G++GfiGs ++++   ++    v++ld+ls +sn+++l+dl      ++++ d++++  + +l+k  + d+vi++Aa+++v++s+++p+ fie+n
  EPA05335.1   3 ILVCGGSGFIGSTFIRNYFLNNpkSSVTNLDNLSIGSNQENLNDLptdihyQFIKDDIRNEIVIVDLIK--NYDVVINFAAESHVDRSISNPKPFIETN 99 
                 89***********9997655554456*******************************************..99************************** PP

                 THHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHH CS
   Epimerase  92 lqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklveayaaqyglnaiilrlfnlyGprngegevsrvipali 190
                 + gt+ lle +rk++   ++++s++evYG+ ++  k++  ++++++p++pY+a+K+ +++lv +y ++yg+++i++r++n++Gp+   ++++++ip+ i
  EPA05335.1 100 IFGTYCLLEGIRKHDK-LFIHISTDEVYGDAET--KQSFNEKSQINPSNPYSATKASADHLVASYYRTYGIKCITTRCSNNFGPN---QFPEKLIPKTI 192
                 ***************9.************9999..56666666******************************************...99********9 PP

                 HHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT-STTEEEEE CS
   Epimerase 191 rkilegkqevtllgdgtalRdflyveDvaeaillvlehvdagdkgeiyni 240
                  +  ++  +v ++gdg++ R ++yv+D+++ai  ++ +   g+ ge+yni
  EPA05335.1 193 IRTIKNL-KVPIYGDGEQIRSWIYVNDHVDAIQSLILN---GKMGEVYNI 238
                 9999999.9*****************************...99999***9 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.7   0.3   6.4e-22   1.6e-18       1     238 [.       4     232 ..       4     263 .. 0.81

  Alignments for each domain:
  == domain 1  score: 66.7 bits;  conditional E-value: 6.4e-22
   3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlD...lrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslvdvag.kltedeimkvnvkG 95 
                 +v Gg+GF+G++ +++ +  +++  v  lD   +  ++e l++l +    ++i+ D++++  + + +++ dvvi  a+ + v     + + + + n+ G
  EPA05335.1   4 LVCGGSGFIGSTFIRNYFLNNPKSSVTNLDnlsIGSNQENLNDLPTDIHYQFIKDDIRNEIVIVDLIKNYDVVINFAAESHVDRsISNPKPFIETNIFG 102
                 699***************************765555555555554444445*******************************8845667889******* PP

   3Beta_HSD  96 TrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKalaEklvlkaNgrtlknggrlyTcaLRpagiyGegd...kllvp 191
                 T  +le  +k++ + +++ S+ ev g+  +++ +    E  + + +++++y+ +Ka a++lv +        g  +  +  R +  +G+ +   kl+ +
  EPA05335.1 103 TYCLLEGIRKHD-KLFIHISTDEVYGDAETKQSFN---E--KSQINPSNPYSATKASADHLVASYYR---TYG--IKCITTRCSNNFGPNQfpeKLIPK 190
                 *********999.99************88888776...5..5667899**************87766...334..556667********8543256666 PP

   3Beta_HSD 192 llkqlaklglalfkigdeevlsdrvYvgNvawahilAaralqdpkkk 238
                 ++ +++k+  ++  +gd e++ +++Yv+     h+ A + l  + k+
  EPA05335.1 191 TIIRTIKNL-KVPIYGDGEQIRSWIYVND----HVDAIQSLILNGKM 232
                 777777765.9***************986....66666666666555 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.6   0.0   3.4e-18   8.7e-15       1     236 [.       1     262 [.       1     308 [. 0.77

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 3.4e-18
                    EEEEEESTTSHHHHHHHHHCTTTS..EEEEEE-TT.....................T--TTSHHHHHHHHHHH--SEEEE------HHHHHHSHHH CS
  RmlD_sub_bind   1 mkilvtGanGqlGseLakqlaeeg..levlaltre.....................eldltdaeavaellkeakpdvvvnaAAytavDkaEseeea 73 
                    mkilv G++G +Gs  +++   ++   +v+ l++                      + d++++  + +l+k+   dvv+n AA   vD+  s+++ 
     EPA05335.1   1 MKILVCGGSGFIGSTFIRNYFLNNpkSSVTNLDNLsigsnqenlndlptdihyqfiKDDIRNEIVIVDLIKN--YDVVINFAAESHVDRSISNPKP 94 
                    89*************999865444004555554447888999999999999999999999999999999998..89******************** PP

                    HHHHHTHHHHHHHHHHHHCT-EEEEEEEGGGS.-S-TTS-B-TTS----SSHHHHHHHHHHHHHHH....H-SSEEEEEE-SEESS...SSS-HHH CS
  RmlD_sub_bind  74 ayavnaeavealAeaaaavgalLihvStDyVF.dGekkrpYeeddetsPlnvYGrtKlaGEqavla....agkkalivRtswvyge...kgknfvk 161
                      + n  ++  l e  ++++ l+ih+StD V+ d+e+k+ ++e+++ +P n Y +tK+   + v++    +g k++  R s  +g     +k   k
     EPA05335.1  95 FIETNIFGTYCLLEGIRKHDKLFIHISTDEVYgDAETKQSFNEKSQINPSNPYSATKASADHLVASyyrtYGIKCITTRCSNNFGPnqfPEKLIPK 190
                    ********************************56667788************************99555556678889999999874433455556 PP

                    HHHHHHHH.-SEEEEESS-EE--EEHHHHHHHHHHHHHHCHH.GGG-EEEE---BS-EEHHHHHHHHHHHHCHTTS CS
  RmlD_sub_bind 162 tmlrlake.reelkvvaDqlgsPTsardlAevllqllekaaeekelagvyHlanegetswlefArailkeagadse 236
                    t++r  k+ + ++     q++s  +++d  +++ +l+ + +      +vy +++ +e+s   + ++il+ +++   
     EPA05335.1 191 TIIRTIKNlKVPIYGDGEQIRSWIYVNDHVDAIQSLILNGKM----GEVYNITSYEEISNKTIVEKILNIMNKPYD 262
                    666665431234444556888888999998888888877775....788999999988888888888887776554 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.2   0.0   6.1e-16   1.6e-12       1     265 [.       3     270 ..       3     283 .. 0.80

  Alignments for each domain:
  == domain 1  score: 47.2 bits;  conditional E-value: 6.1e-16
                      EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-SEEEE------HHHHH CS
  Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvdvvfhaAAlKhVPlve 94 
                      +lv G++G iGs+++r+   ++pk+  + + d l++ + +++l+ +l + +++++   +  d+r++  + ++++  + dvv++ AA  hV    
       EPA05335.1   3 ILVCGGSGFIGSTFIRNYFLNNPKS-SVTNLDNLSIGSNQENLN-DLPT-DIHYQ--FIKDDIRNEIVIVDLIK--NYDVVINFAAESHVDRSI 89 
                      89*******************9987.567888888888888774.4444.35444..66789************..99**************** PP

                      HSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEGGG...............SS--SHHHHHHHHHHHHHHHGGG--SSS--EEEEEEE-EETT CS
  Polysacc_synt_2  95 enpleaiktNvlgtenvieaaieagvkkvvliStDKA...............vnPtnvmGatKrlaekllqalakeseekktkfvvvRfGNVlg 173
                      +np   i+tN++gt  ++e   ++  k ++ iStD                 +nP n + atK+ a+ l+ ++ ++      k +++R  N +g
       EPA05335.1  90 SNPKPFIETNIFGTYCLLEGIRKH-DKLFIHISTDEVygdaetkqsfneksqINPSNPYSATKASADHLVASYYRTY---GIKCITTRCSNNFG 179
                      ***************999976665.599*******6433333333444444589****************9999998...78999999999999 PP

                      GTT...SSHHHHHHHHHTTSSEEE.S-TT-EEEEE-HHHHHHHHHHHHHH--SS-EEEE--.-EEEHHHHHHHH..........SSSS-EEE-- CS
  Polysacc_synt_2 174 SrG...SviplFkkqikeggpvtv.TdpemtRyfmtieeavqLvlqalalakggeifvldmGepvkivdlakalielsgleekkeedieikitG 263
                       +     +ip+   +  ++ +v++  d e +R ++ +++ v+ + + + ++k ge++     e ++ + +++++++++++         i+++ 
       EPA05335.1 180 PNQfpeKLIPKTIIRTIKNLKVPIyGDGEQIRSWIYVNDHVDAIQSLILNGKMGEVYNITSYEEISNKTIVEKILNIMNKPY-----DMIEYVP 268
                      8753336888776666666677774689999************999999******998887799998999999888876432.....2355555 PP

                      -- CS
  Polysacc_synt_2 264 lR 265
                       R
       EPA05335.1 269 DR 270
                      55 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.048   1.2e+02       2      20 ..       6      24 ..       5      32 .. 0.77
   2 !   38.3   0.0   3.1e-13     8e-10      83     208 ..      68     179 ..      62     251 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.048
                   E-TTSHHHHHHHHHHHHHS CS
  NAD_binding_4  2 TGaTGFLGkvLlekLLrtt 20
                    G++GF+G+ ++++   ++
     EPA05335.1  6 CGGSGFIGSTFIRNYFLNN 24
                   6***********9865555 PP

  == domain 2  score: 38.3 bits;  conditional E-value: 3.1e-13
                    HHHHH--EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H......HHH--EEEETTTCCCH CS
  NAD_binding_4  83 elaeevdviihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegekeekldederaklkglpnt 175
                    +l+++ dv+i+ aA  ++d+++++   ++++N+ Gt  +le  +k  kl  ++h+ST  v+g+ e+               +++ +++++ + +n 
     EPA05335.1  68 DLIKNYDVVINFAAESHVDRSISNpkpFIETNIFGTYCLLEGIRKHDKL--FIHISTDEVYGDAET---------------KQSFNEKSQINPSNP 146
                    6899****************999877799************99977655..******888888885...............467788889999*** PP

                    HHHHHHHHHHHHHHHHHHH---EEEEEE-EEE- CS
  NAD_binding_4 176 YeqsKalaEklvrearrrsglpvvivRpsiitg 208
                    Y+ +Ka a++lv ++ r  g++++  R+s+  g
     EPA05335.1 147 YSATKASADHLVASYYRTYGIKCITTRCSNNFG 179
                    ****************************98666 PP

>> DUF4868  Domain of unknown function (DUF4868)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.2         1   2.6e+03     132     159 ..      54      81 ..      18      91 .. 0.55
   2 ?   -2.9   0.0       2.2   5.7e+03      30      55 ..     110     136 ..     101     142 .. 0.75
   3 ?   13.6   0.3   1.9e-05     0.048      87     162 ..     215     287 ..     212     308 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1
     DUF4868 132 gvll..ykqedlieklkkvpklklnikfea 159
                 ++++  + +e +i  l+k+   ++ i+f a
  EPA05335.1  54 QFIKddIRNEIVIVDLIKNY--DVVINFAA 81 
                 33333455555555555544..45555544 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.2
     DUF4868  30 lkkskklillifqdnef.kkvdkdllr 55 
                 ++k  kl++ i++d+ + + ++k++++
  EPA05335.1 110 IRKHDKLFIHISTDEVYgDAETKQSFN 136
                 677788888888888888888888775 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 1.9e-05
     DUF4868  87 ikeeaqkviseieelglienveklkeyveindlkklrklakikkkgvllykqedlieklkkvpklkln..ikfea.ngk 162
                 + +    +i++++  g++ +v  +++y+ei++++++ k++ i++k++      d+ie + + p  + +  i+ ++ ++k
  EPA05335.1 215 YVNDHVDAIQSLILNGKMGEVYNITSYEEISNKTIVEKILNIMNKPY------DMIEYVPDRPGHDKRysIDSSKiENK 287
                 667777889999999999****************************8......66666666665333300333334444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       739  (0.0412181); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.62u 0.34s 00:00:00.96 Elapsed: 00:00:00.52
# Mc/sec: 1932.05
//
Query:       EPA05336.1  [L=181]
Description: acetyltransferase, GNAT family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-13   51.1   0.1    1.9e-13   50.7   0.1    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    3.8e-10   40.6   0.1    4.7e-10   40.3   0.1    1.2  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
    4.3e-08   33.4   2.8    5.7e-08   33.0   2.8    1.1  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    6.3e-07   29.7   0.4    9.3e-07   29.2   0.4    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    7.8e-07   29.1   0.1    1.1e-06   28.6   0.1    1.2  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    1.2e-06   28.4   0.0    2.6e-06   27.3   0.0    1.5  1  FR47             FR47-like protein
    0.00018   21.2   1.0     0.0044   16.6   0.1    2.1  2  GNAT_acetyltran  GNAT acetyltransferase
     0.0062   16.2   0.0     0.0082   15.8   0.0    1.2  1  Acetyltransf_8   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.7   0.1   8.4e-17   1.9e-13      27     117 .]      48     138 ..      25     138 .. 0.86

  Alignments for each domain:
  == domain 1  score: 50.7 bits;  conditional E-value: 8.4e-17
                     HHHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTEHHHHHHHHHTTE CS
  Acetyltransf_1  27 sfsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlaveedndaairlYeklGF 117
                      + ++ +  +++  ++eliG+  l+k    +++++ ++++++  +++gkG G +  ++++e a ++ ++ki+l++  dn+aa ++Y+klGF
      EPA05336.1  48 ELKDNKKIRFFIFLENELIGYSFLSKFIRKSKKHVCTYGIVIGDKWQGKGFGYQICKHMIETAWKKKFEKIWLTTYYDNKAALKVYKKLGF 138
                     2344444778889999******999999999*******************************************************88**9 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.1   2.1e-13   4.7e-10      42     137 ..      42     138 ..      11     139 .. 0.88

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 2.1e-13
  Acetyltransf_3  42 era.waeeseeegygwaivlkdtgviGsvglrdleeedee..aelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvle 133
                     e++ + e +++++  + i+l+++  iG+  l ++ +++++  +  g++++++++gkG++   ++ ++e a+++   e+++ ++  +N+a  +v++
      EPA05336.1  42 EKIiFSELKDNKKIRFFIFLENE-LIGYSFLSKFIRKSKKhvCTYGIVIGDKWQGKGFGYQICKHMIETAWKKK-FEKIWLTTYYDNKAALKVYK 134
                     33356667778899999998888.9*****999999988899*****************************999.******************** PP

  Acetyltransf_3 134 klGf 137
                     klGf
      EPA05336.1 135 KLGF 138
                     ***9 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   2.8   2.6e-11   5.7e-08       5     150 ..      11     154 ..       8     158 .. 0.83

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 2.6e-11
  Acetyltransf_4   5 teeDakeilaiyaeyvvntaitfeyevssveefekfleal.dsekeyvflvaesdrivGyaylgqfkkrakdwkaelsvylaerdnnkeglgrel 98 
                     +++D+k++l  ++++ +n +  f     s++ +ek++ +  +  k++ f ++ + +++Gy  l++f  + k++ +   + +   + + +g g ++
      EPA05336.1  11 EKKDFKNMLLGLSQKTLNDFTYFG--KISKKNVEKIIFSElKDNKKIRFFIFLENELIGYSFLSKFIRKSKKHVCTYGIVIG-DKWQGKGFGYQI 102
                     567888888877765555544455..367888899988876788899999999999********999967777777777775.589********* PP

  Acetyltransf_4  99 idaleqvlkeqnienllaeiaspnensiqfhkalGFelvgifkkcikkngrw 150
                      +++++ + +  +e++   ++++n+++ +++k+lGF ++gif +  k+ g++
      EPA05336.1 103 CKHMIETAWKKKFEKIWLTTYYDNKAALKVYKKLGFIVEGIFINEEKIHGKP 154
                     ******************************************9998888876 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.4   4.2e-10   9.3e-07       5      75 ..      57     139 ..      44     140 .. 0.71

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 4.2e-10
                     EEEEEETTEEEEEEEEEEES......TCTEE...EEE-GGGTTSSHHHHHHHH......TTSEEE.EE.EEEETHHHHHHHHHHTTEE CS
  Acetyltransf_7   5 vfVaeddgkivGfialslld......aeitr...laVdpeyrgkGiGraLlea......aekgii.le.qlelnaekaikfYeklGFe 75 
                     +f +  +++ +G+  ls             +   +++  +++gkG G ++ ++      + k+++ ++ +++ ++++a+k Y+klGF+
      EPA05336.1  57 FF-IFLENELIGYSFLSKFIrkskkhV---CtygIVIGDKWQGKGFGYQICKHmietawK-KKFEkIWlTTYYDNKAALKVYKKLGFI 139
                     66.445688889988888878776533...1357******************85543331.222223433444555999********7 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.1   4.7e-10   1.1e-06      26     110 ..      49     142 ..      23     154 .. 0.72

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 4.7e-10
  Acetyltransf_10  26 ieegealllvaeeggkivGvi....el.rdgshisll..fVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yavpfYeklGFkavg 110
                      +++++++ +  + +++++G+      + ++++h++    ++ ++++g+G g ++ ++++e a k++ ++  lt   ++ +a ++Y+klGF + g
       EPA05336.1  49 LKDNKKIRFFIFLENELIGYSflskFIrKSKKHVCTYgiVIGDKWQGKGFGYQICKHMIETAWKKKFEKiWLTTYYDNkAALKVYKKLGFIVEG 142
                      3344455555556679999986664443444498876559*********************888888888666666665***********9876 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   1.1e-09   2.6e-06      25      79 ..      85     140 ..      75     146 .. 0.92

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 1.1e-09
                 EEEEE-GGG-SSSHHHHHHHHHHHHHHH.S-S-EEEEEETT-HHHHHHHHHHT-EE CS
        FR47  25 galqvlpehrrrGlgsrlvkalakeiae.rgktvllvvvasNtpsirlyeklGfek 79 
                 +++ + ++ +++G+g ++ k +++   + + +++ l +  +N+++ ++y+klGf +
  EPA05336.1  85 YGIVIGDKWQGKGFGYQICKHMIETAWKkKFEKIWLTTYYDNKAALKVYKKLGFIV 140
                 56778899****************999978899*********************75 PP

>> GNAT_acetyltran  GNAT acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1     0.014        32      37      78 ..      26      66 ..      12      89 .. 0.66
   2 !   16.6   0.1     2e-06    0.0044     189     237 ..      90     141 ..      69     145 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.014
  GNAT_acetyltran 37 vlgdfvflaGepneefaeelvleekekkeekrfilvpqseew 78
                     +l df++ +G+ +++  e++++ e + +++ rf ++ ++e +
       EPA05336.1 26 TLNDFTY-FGKISKKNVEKIIFSELKDNKKIRFFIFLENELI 66
                     4569999.9**7767778888666666666666666665544 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 2e-06
  GNAT_acetyltran 189 kedyrrkgLAtivaaalileclkrglyPsWDaa...neaSvaLaekLGYefe 237
                        + ++kg+ + +++++i+++ k++    W +    n+a++++++kLG+  e
       EPA05336.1  90 GDKWQGKGFGYQICKHMIETAWKKKFEKIWLTTyydNKAALKVYKKLGFIVE 141
                      5789**************************998999*************876 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   3.6e-06    0.0082      75     141 ..      78     142 ..      47     145 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.6e-06
                     --TT-EEEEEEESSHHHCTTTCHHHHHHHHHHHHHCCTT--EEEE--BTT-HHHHHHHHHTT-EEEE CS
  Acetyltransf_8  75 aepgdrGiHlligeaeargkglttallralvhylfadprtrrvvvEPdvrNerairllekaGfekek 141
                      +++ +   ++ig++++ gkg++ ++ +++++ ++++ + +++ +   ++N++a+++++k+Gf  e+
      EPA05336.1  78 SKKHVCTYGIVIGDKWQ-GKGFGYQICKHMIETAWKK-KFEKIWLTTYYDNKAALKVYKKLGFIVEG 142
                     56677777889998877.*****************99.9************************8766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       756  (0.0421663); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1129.35
//
Query:       EPA05337.1  [L=301]
Description: NAD-binding protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.6e-54  183.4   0.3    5.5e-54  183.2   0.3    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    3.7e-50  171.2   2.4    1.5e-49  169.2   2.4    1.7  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    7.1e-26   90.8   4.5    9.8e-26   90.4   4.5    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
      1e-18   67.5   5.0    5.2e-18   65.2   5.0    1.8  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    3.2e-18   65.8   0.0    3.7e-18   65.6   0.0    1.0  1  RmlD_sub_bind    RmlD substrate binding domain
    2.9e-12   46.3   0.8    4.2e-07   29.4   0.1    2.7  2  NAD_binding_4    Male sterility protein
    2.7e-08   33.9   0.0    6.8e-08   32.6   0.0    1.6  1  KR               KR domain
      7e-08   32.6   0.0      1e-07   32.0   0.0    1.2  1  NAD_binding_10   NAD(P)H-binding
    1.1e-06   28.2   0.1      2e-06   27.4   0.1    1.5  1  adh_short        short chain dehydrogenase
    0.00025   21.3   0.1    0.00056   20.2   0.1    1.6  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
    0.00093   18.8   0.8     0.0023   17.5   0.2    1.9  2  NmrA             NmrA-like family
     0.0062   16.6   0.3      0.018   15.1   0.3    1.9  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
  ------ inclusion threshold ------
      0.015   15.6   1.5      0.029   14.6   0.5    2.2  2  TrkA_N           TrkA-N domain
      0.042   13.4   0.1      0.074   12.6   0.1    1.4  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
      0.095   12.8   0.9       0.23   11.6   0.9    1.7  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
       0.13   11.1   0.0       0.19   10.5   0.0    1.2  1  UDPGT            UDP-glucoronosyl and UDP-glucosyl transferas
       0.13   12.8   1.1       0.42   11.2   0.1    2.4  2  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.2   0.3   5.2e-57   5.5e-54       2     241 .]       4     234 ..       3     234 .. 0.96

  Alignments for each domain:
  == domain 1  score: 183.2 bits;  conditional E-value: 5.2e-57
                 EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC....EEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHHHSHHHHHHHHTHHHH CS
   Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl....elveldltdrsalerlfkeeqpdavihlAavggvaassedpadfieknlqgtl 96 
                 +VtG++GfiGs +v++l ++g  v+++d+l ++++ ++++d+    e+v++d+++ +++++++   ++d ++h Aa   v++s+++++++ e n++gt 
  EPA05337.1   4 VVTGGAGFIGSRIVRELVNEGNSVTVIDNL-HTGKIQNIQDVyneiEFVKMDIRNYEEMKKIIY--DFDGIFHEAALTIVQESFTNQNEYNEVNVIGTE 99 
                 7*****************************.666667777778*********************..89******************************* PP

                 HHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHT CS
   Epimerase  97 nlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklveayaaqyglnaiilrlfnlyGprngegevsrvipalirkile 195
                 n+++ a+++++ +++f+sSs+vYG++ ++p +e+    p +p +pY+++Kl  e l+e+y + + l++i lr+fn+yG + ++g+ ++vi+++++k++e
  EPA05337.1 100 NIFKIAQEKNI-KVVFASSSSVYGNVVKIPIKESF---PKNPINPYGITKLKDEILAEKYSKMN-LDVIGLRYFNVYGIG-QTGSYAGVITKFLTKLKE 192
                 ***********.***********************...9*********************9888.***************.9999************** PP

                 TSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT-STTEEEEES CS
   Epimerase 196 gkqevtllgdgtalRdflyveDvaeaillvlehvdagdkgeiyniG 241
                 +k  + + g+g++ Rdf++v+D+a+a++  ++    + k + +niG
  EPA05337.1 193 KK-HLQINGNGEQIRDFIFVDDIAKANIVSMKS---KIKEGFFNIG 234
                 **.*****************************9...7777899998 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.2   2.4   1.4e-52   1.5e-49       2     329 ..       5     294 ..       4     297 .. 0.83

  Alignments for each domain:
  == domain 1  score: 169.2 bits;  conditional E-value: 1.4e-52
                    EETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHTTSHHH CS
  GDP_Man_Dehyd   2 iTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevynLAAqshVdvsfekPey 97 
                    +TG+aGfiGs +++ L+++g  v++i+++++  ++++i+ ++        ++++++k+D+++ +++++++ +   d +++ AA   V++sf++  +
     EPA05337.1   5 VTGGAGFIGSRIVRELVNEGNSVTVIDNLHT-GKIQNIQDVY--------NEIEFVKMDIRNYEEMKKIIYDF--DGIFHEAALTIVQESFTNQNE 89 
                    9***********************9987643.3555555555........4689****************875..********************* PP

                    HHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSC CS
  GDP_Man_Dehyd  98 taevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYaaaKlyadwivvnyreayglfavngilfnhesprrgetfv 193
                    + evnv+Gt ++++++++    k++++++aS+s vYG+v ++p++E+ p +P +PY+++Kl  + ++++y +  +l ++  ++fn ++  ++ +  
     EPA05337.1  90 YNEVNVIGTENIFKIAQE----KNIKVVFASSSSVYGNVVKIPIKESFPKNPINPYGITKLKDEILAEKYSK-MNLDVIGLRYFNVYGIGQTGS-Y 179
                    ***************976....679*********************************************87.89***************9888.5 PP

                    CCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHHHHHHHHC.SS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTG CS
  GDP_Man_Dehyd 194 trkitravarialgkqevlylGnldakRdwghvkDyveamwlmlqq.dkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgk 288
                       it+++++ +++k+   + Gn++++Rd+ +v+D+++a    +++  k   ++i+tg  ++++ ++e+ ++  g++i+   ++e           
     EPA05337.1 180 AGVITKFLTKLKEKKHLQ-INGNGEQIRDFIFVDDIAKANIVSMKSkIKEGFFNIGTGIGTTINHLAEILIEISGEDITSVHSEEL---------- 264
                    59*******999887544.46******************666555515666789**********9999877777666654433332.......... PP

                    GCCCEECGG--SS--SB--B-THHHHHHH----SS-HHHHH CS
  GDP_Man_Dehyd 289 vvvevdpkyfrpgevdlllgdaskakeeLgWkpkvsfeelv 329
                               +g+ ++  +d+s  ++  gWk ++ ++e++
     EPA05337.1 265 -----------EGDIKFSQADTSLTEQVFGWKFQTVLNEGL 294
                    ...........355555555666666666666666666655 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.4   4.5   9.3e-29   9.8e-26       1     230 [.       4     223 ..       4     229 .. 0.86

  Alignments for each domain:
  == domain 1  score: 90.4 bits;  conditional E-value: 9.3e-29
   3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslvdvag.kltedeimkvnvkGTrn 98 
                 vvtGgaGF+G+++v+eLv++++   v v+D  +  ++++ +   n +++++ D+++ +++++ + + d ++h a+l+ v+   ++++e+ +vnv GT+n
  EPA05337.1   4 VVTGGAGFIGSRIVRELVNEGN--SVTVIDNLHTGKIQNIQDVYNEIEFVKMDIRNYEEMKKIIYDFDGIFHEAALTIVQEsFTNQNEYNEVNVIGTEN 100
                 8********************6..9******************************************************995667889*********** PP

   3Beta_HSD  99 vleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKalaEklvlkaNgrtlknggrlyTcaLRpagiyGegdkllvpllk... 194
                 + + + +++++ +v+ Ss +v g+ + + +i      +  ++++ ++y  +K   E l  k          +l  + LR   +yG g++   + +    
  EPA05337.1 101 IFKIAQEKNIK-VVFASSSSVYGN-VVKIPIK-----ESFPKNPINPYGITKLKDEILAEKYSK------MNLDVIGLRYFNVYGIGQTGSYAGVItkf 186
                 **********8.69****999988.7777776.....667889999******999976655555......357889*********99986544332111 PP

   3Beta_HSD 195 .qlaklglalfkigdeevlsdrvYvgNvawahilAar 230
                  + +k +++l   g+ e++ d+++v+ +a+a i+ ++
  EPA05337.1 187 lTKLKEKKHLQINGNGEQIRDFIFVDDIAKANIVSMK 223
                 1445667799999********************9877 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.2   5.0   4.9e-21   5.2e-18       2     253 ..       4     258 ..       3     273 .. 0.83

  Alignments for each domain:
  == domain 1  score: 65.2 bits;  conditional E-value: 4.9e-21
                      EEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-SEEEE------HHHHHH CS
  Polysacc_synt_2   2 lvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvdvvfhaAAlKhVPlvee 95 
                      +vtG++G iGs++vr+++++  +  ++ + +  k+++i++ ++      ++++    v  d+r+ e+++k++   + d +fh AAl  V    +
       EPA05337.1   4 VVTGGAGFIGSRIVRELVNEGNSVTVIDNLHTGKIQNIQDVYN------EIEF----VKMDIRNYEEMKKIIY--DFDGIFHEAALTIVQESFT 85 
                      69****************9998877777778888888888762......3433....357************9..99***************** PP

                      SHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEG...GGS..........S--SHHHHHHHHHHHHHHHGGG--SSS--EEEEEEE-EE..TTG CS
  Polysacc_synt_2  96 npleaiktNvlgtenvieaaieagvkkvvliStD...KAv..........nPtnvmGatKrlaekllqalakeseekktkfvvvRfGNV..lgS 174
                      n  e  + Nv+gten+ ++a+e+++k v + S+      v          nP+n +G+tK+  e l+ +++k +      ++  R+ NV  +g 
       EPA05337.1  86 NQNEYNEVNVIGTENIFKIAQEKNIKVVFASSSSvygNVVkipikesfpkNPINPYGITKLKDEILAEKYSKMN----LDVIGLRYFNVygIGQ 175
                      *************************98777776433312222233334448**************999999988....899********44345 PP

                      TTS...SHHHHHHHHHTTSSEEES.-TT-EEEEE-HHHHHHHHHHHHHH--SS-EEEE--.-EEEHHHHHHHH.......... CS
  Polysacc_synt_2 175 rGS...viplFkkqikeggpvtvT.dpemtRyfmtieeavqLvlqalalakggeifvldmGepvkivdlakalielsgleekk 253
                       GS   vi++F  ++ke++ + +  + e +R f+ +++ ++  + +++   +   f    G  ++i +la+ lie+sg + ++
       EPA05337.1 176 TGSyagVITKFLTKLKEKKHLQINgNGEQIRDFIFVDDIAKANIVSMKSKIKEGFFNIGTGIGTTINHLAEILIEISGEDITS 258
                      666555*****************7356899*********9999999999999999**********************987665 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.6   0.0   3.5e-21   3.7e-18       1     239 [.       1     260 [.       1     288 [. 0.87

  Alignments for each domain:
  == domain 1  score: 65.6 bits;  conditional E-value: 3.5e-21
                    EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT..................T--TTSHHHHHHHHHHH--SEEEE------HHHHHHSHHHHHHHH CS
  RmlD_sub_bind   1 mkilvtGanGqlGseLakqlaeeglevlaltre..................eldltdaeavaellkeakpdvvvnaAAytavDkaEseeeaayavn 78 
                    mk +vtG+ G +Gs ++++l +eg +v+ +++                   ++d+++ e++++++ +   d + + AA t v +  +++++ ++vn
     EPA05337.1   1 MKYVVTGGAGFIGSRIVRELVNEGNSVTVIDNLhtgkiqniqdvyneiefvKMDIRNYEEMKKIIYD--FDGIFHEAALTIVQESFTNQNEYNEVN 94 
                    899*********************99999977689*******************************9..677************************ PP

                    THHHHHHHHHHHHCT-EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHH...H-SSEEEEEE-SEESS....SSS-HHHHHHHHH CS
  RmlD_sub_bind  79 aeavealAeaaaavgalLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavla...agkkalivRtswvyge....kgknfvktmlrla 167
                    + ++e++ + a++ ++++++ S+  V+    k p +e+ +++P+n YG tKl+ E   ++    + +++ +R   vyg     +    ++++l ++
     EPA05337.1  95 VIGTENIFKIAQEKNIKVVFASSSSVYGNVVKIPIKESFPKNPINPYGITKLKDEILAEKyskMNLDVIGLRYFNVYGIgqtgSYAGVITKFLTKL 190
                    *******************************************************9999843233466679******8743333456677888888 PP

                    HH-SEEEEE..SS-EE--EEHHHHHHHHHHHHHHCHH.GGG-EEEE---BS-EEHHHHHHHHHHHHCHTTSEEE CS
  RmlD_sub_bind 168 kereelkvv..aDqlgsPTsardlAevllqllekaaeekelagvyHlanegetswlefArailkeagadseevk 239
                    ke+++l++     q++    ++d+A++ +  ++ +++     g++ ++    t+   +A+  ++ +g+d + v+
     EPA05337.1 191 KEKKHLQINgnGEQIRDFIFVDDIAKANIVSMKSKIK----EGFFNIGTGIGTTINHLAEILIEISGEDITSVH 260
                    9999888862257999999999999999988888887....899998888889999999888888777655554 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.1   1.8e-05     0.019       1      36 [.       5      40 ..       5      58 .. 0.81
   2 !   29.4   0.1     4e-10   4.2e-07      79     256 ..      59     217 ..      57     218 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.8e-05
                   EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSHHH CS
  NAD_binding_4  1 lTGaTGFLGkvLlekLLrttpevkiyllvRaksges 36
                   +TG+ GF+G++++++L+++ + v+++  +++ + ++
     EPA05337.1  5 VTGGAGFIGSRIVRELVNEGNSVTVIDNLHTGKIQN 40
                   7******************99888876666665555 PP

  == domain 2  score: 29.4 bits;  conditional E-value: 4e-10
                    HHHHHHHHH--EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H......HHH--EEEETTT CS
  NAD_binding_4  79 edlqelaeevdviihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegekeekldederaklkg 171
                    e++++++   d i+h aA + ++e+  +     +vNv Gt++++++a++ + +  +++ S++ v+g+   ++                 +++  k+
     EPA05337.1  59 EEMKKIIYDFDGIFHEAALTIVQESFTNqneYNEVNVIGTENIFKIAQEKNIK--VVFASSSSVYGNVV-KI---------------PIKESFPKN 136
                    688999999*************997654334999**************66555..88888877777766.33...............355667788 PP

                    CCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE--SSST---TTSHHHHHHHHHHHH-EEES-SB---TT--EEEHHHHHHH CS
  NAD_binding_4 172 lpntYeqsKalaEklvrearrrsglpvvivRpsiitgesktGwingsdlgirgllgliakgvlpeilgdkeavldlvpvDyvana 256
                      n Y  +K   E l +++++  +l v+ +R  +++g  +tG+  g    +++l  l +k++l+ i+g+ e+  d++ vD +a+a
     EPA05337.1 137 PINPYGITKLKDEILAEKYSKM-NLDVIGLRYFNVYGIGQTGSYAGVI--TKFLTKLKEKKHLQ-INGNGEQIRDFIFVDDIAKA 217
                    99******************77.**************99999999987..88888888888888.99999999999999999886 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.0   6.5e-11   6.8e-08       3     144 ..       3     124 ..       2     128 .. 0.83

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 6.5e-11
                 EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS---EEEE---------TTT-- CS
          KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppikGvihaAgvlrdklleemt 101
                 y++tGG+G +G  ++r l+++g++  v+   +       + +i+++++   e+e+v++D+ + +++++++ +++       G++h A ++    + + +
  EPA05337.1   3 YVVTGGAGFIGSRIVRELVNEGNSVTVIDNLH-------TGKIQNIQDVYNEIEFVKMDIRNYEEMKKIIYDFD-------GIFHEAALT----IVQES 83 
                 9*********************9877764444.......56899***************************998.......****88764....34444 PP

                 HHHHHHHHTTTTHHHHHHHHHTTTS--SEEEEEEEHHHHH--T CS
          KR 102 aedleqvlapKvkGawnLhelledesldffvlfSSiagllgsa 144
                   + ++  +  v G++n+ ++ ++++++  v+f+S ++++g+ 
  EPA05337.1  84 FTNQNEYNEVNVIGTENIFKIAQEKNIK--VVFASSSSVYGNV 124
                 4455566667799*********988776..7788888888886 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.0   9.7e-11     1e-07       1     120 [.       7     141 ..       7     170 .. 0.71

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 9.7e-11
                     TTTSHHHHHHHHHHHHC-T-EEEEEETT..HHHCHHHHCT.TTCEEEE--TT-CCHHHHHHTT-SEEEES-.........--TCCHHHH...... CS
  NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRn..peklaeleae.eglevvegdvtdvedlaealkgadaVvsal.........ggggkdeeg...... 77 
                     G+ G +G+++v+el+++g  +vt++  n  + k++++++  +++e v++d+ + e++++ + + d ++  +          +      +      
      EPA05337.1   7 GGAGFIGSRIVRELVNEG-NSVTVI-DNlhTGKIQNIQDVyNEIEFVKMDIRNYEEMKKIIYDFDGIFHEAaltivqesfTN------Qneynev 93 
                     99***************6.687765.54337899999877799*************************99967766644311......1223455 PP

                     ....HHHHHHHHHHCT--EEEEEEETTTTSGCGCHHHHHHH.HCCHHH CS
  NAD_binding_10  78 ....aknivdaakeagvkRfvlvsaigvgdevpgefgewnk.ellkay 120
                         ++ni + a+e+++k +   s+   g+ v+ + +e    + +++y
      EPA05337.1  94 nvigTENIFKIAQEKNIKVVFASSSSVYGNVVKIPIKESFPkNPINPY 141
                     7789*************7777766666666555555443331444555 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.1   1.9e-09     2e-06       4      69 ..       4      66 ..       2     122 .. 0.86

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 1.9e-09
                EEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHH CS
   adh_short  4 lvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealve 69
                +vtG+++ IG  i++el++eG +v+v+d+      + ++ + +   ++ ++++D++++ee+++++ 
  EPA05337.1  4 VVTGGAGFIGSRIVRELVNEGNSVTVIDNLHTGKIQNIQDVYN---EIEFVKMDIRNYEEMKKIIY 66
                8**************************9998877555555555...6***************9875 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.1   5.3e-07   0.00056       5      70 ..       8      68 ..       4      83 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 5.3e-07
                     --SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTS CS
  Sacchrp_dh_NADP  5 GaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkeg 70
                     GaG++G+ ++++l+++++    +tv+d  +++  + +++    ++e++++d+ nye+ +++++ + 
       EPA05337.1  8 GAGFIGSRIVRELVNEGNS---VTVIDNLHTGKIQNIQD-VYNEIEFVKMDIRNYEE-MKKIIYDF 68
                     88***************96...******99987666666.7899*************.99888666 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.2   2.2e-06    0.0023       2      75 ..       4      78 ..       3     133 .. 0.83
   2 ?   -1.1   0.0       1.1   1.2e+03       4      22 ..     173     191 ..     170     233 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.2e-06
                EESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTT..EEEES-TT-HHHHHHHHTT-SEEEE---GG CS
        NmrA  2 lviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGv..elvkgdlddkeslvealkgvdvvfsvtgfy 75
                +v+G++G +G+ +vr l+++g++v + + ++++ +++++++  +  e+vk d+ ++e +++++ + d++f   +++
  EPA05337.1  4 VVTGGAGFIGSRIVRELVNEGNSVTV-IDNLHTGKIQNIQDVYNeiEFVKMDIRNYEEMKKIIYDFDGIFHEAALT 78
                69**********************86.6899999999999965511679*******************99876644 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.1
                 SSTTSHHHHHHHHHHHHHT CS
        NmrA   4 iGaTGrqGksvvrallkag 22 
                 iG TG+ ++ ++++l+k +
  EPA05337.1 173 IGQTGSYAGVITKFLTKLK 191
                 5667777777777666633 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.3   1.7e-05     0.018      17      82 ..       6      74 ..       1     121 [. 0.74

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.7e-05
                  EES-SHHHHHHHHHHHCCT-CEEEEEESS...HHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE- CS
  Shikimate_DH 17 liGaGemaelvakhLlakgvkkvvvaNRt...lerakelaeelkgeeiealkleelkellaeadvvisa 82
                    GaG +++++++ L+++g    v+ N     +++ +++ +e++ +++ ++++ee+k+++ ++d ++  
    EPA05337.1  6 TGGAGFIGSRIVRELVNEGNSVTVIDNLHtgkIQNIQDVYNEIEFVKMDIRNYEEMKKIIYDFDGIFHE 74
                  459*****************9777778661114555666777788899999*************99963 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.5   2.8e-05     0.029       5      58 ..       8      64 ..       3     126 .. 0.83
   2 ?   -2.8   0.0       7.2   7.6e+03       5      26 ..     236     258 ..     229     270 .. 0.51

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.8e-05
                S-SHHHHHHHHHHHHTTEEEEEEESSH.HHHHHHHHTT..SEEEES-TTSHHHHHHT CS
      TrkA_N  5 GlGrvGrslaeeLseggkdvvvidkde.erveelreeg..levvvgdatdeevLeea 58
                G+G +G+++++eL ++g++v+vid+ +  +++++++    +e+v+ d  + e ++++
  EPA05337.1  8 GAGFIGSRIVRELVNEGNSVTVIDNLHtGKIQNIQDVYneIEFVKMDIRNYEEMKKI 64
                89*************6667******88455777776555577888888888877775 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 7.2
                 S-SHHHHHHHHHHHH.TTEEEEE CS
      TrkA_N   5 GlGrvGrslaeeLse.ggkdvvv 26 
                 G G++  +lae L e +g+d++ 
  EPA05337.1 236 GIGTTINHLAEILIEiSGEDITS 258
                 33444444444444444434443 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   7.1e-05     0.074       6      82 ..      12      87 ..       7     122 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.1e-05
                  HHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSE.EEE--TTSHHHHHHHHHHHHHHHSSEEEEEE-----EG CS
  adh_short_C2  6 IGraiAkalaeeGaevvltdlneeakkrveelaeelgae.vlecDVtdeeqvealveevvekfgklDilvnnagiapk 82
                  IG  i+++l +eG +v + d    +  +++++++ +++  ++++D+++ e++++++ +    f +    +    ++++
    EPA05337.1 12 IGSRIVRELVNEGNSVTVIDNLHTG--KIQNIQDVYNEIeFVKMDIRNYEEMKKIIYDFDGIFHEAALTIVQESFTNQ 87
                  9*******************99998..79999988886659************9988755554444444444444443 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.9   0.00021      0.23       1     110 [.       1     111 [.       1     128 [. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00021
                 EEEEEETTTSHHHHHHHHHHHH.STTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEBSSHHHHHHH-SEEEE-S-HHHHHHHHHHHHHTT-EEEE-- CS
      DapB_N   1 ikvavvGasGrmGkevvkavee.aedlelvaavdrkeselegkdagellglgklgvavtddleevlekadvliDFTtpeavlenlklalekgvklViGT 98 
                 +k +v+G +G +G+++v+ + +  +++++   +++ +   + +d+ + +++ k+++  ++++++++ ++d +    + + v e +    e++   ViGT
  EPA05337.1   1 MKYVVTGGAGFIGSRIVRELVNeGNSVTVIDNLHTGK-IQNIQDVYNEIEFVKMDIRNYEEMKKIIYDFDGIFHEAALTIVQESFTNQNEYNEVNVIGT 98 
                 7899************987666156677777777765.66678999999999******************99988888888888888888888889998 PP

                 SS-.-HHHHHHHH CS
      DapB_N  99 TGl.seeelaele 110
                   + + ++ ++++
  EPA05337.1  99 ENIfKIAQEKNIK 111
                 6543445555554 PP

>> UDPGT  UDP-glucoronosyl and UDP-glucosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00018      0.19      17     129 ..      14     120 ..       6     135 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00018
       UDPGT  17 keileelvqrghevvvlrksaslllkpkkesnlkletypvsltkeeleeevlklvkklfeeasektvlkllealkeasdlleklCkevvsnkkllkklq 115
                 + i++elv++g++v+v+ +  +  +++ ++   ++e +++ +++ e+ ++++  ++ +f+ea+ + v++ +++ +e++++       v+  ++++k +q
  EPA05337.1  14 SRIVRELVNEGNSVTVIDNLHTGKIQNIQDVYNEIEFVKMDIRNYEEMKKIIYDFDGIFHEAALTIVQESFTNQNEYNEVN------VIGTENIFKIAQ 106
                 579***********************99999999*********99999999999*****************9999988764......555566666666 PP

       UDPGT 116 eskfdvvladpvlp 129
                 e +  vv+a + + 
  EPA05337.1 107 EKNIKVVFASSSSV 120
                 66666666655444 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1    0.0004      0.42       2      31 ..       4      33 ..       3      43 .. 0.90
   2 ?   -1.9   0.0         5   5.3e+03      54      71 ..      92     109 ..      70     117 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0004
                EEEECSSHHHHHHHHHHHHTTSEEEEEESS CS
   Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvvers 31
                vv  G+G+ig     +l + g++Vtv+++ 
  EPA05337.1  4 VVTGGAGFIGSRIVRELVNEGNSVTVIDNL 33
                57779**********************986 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5
                 TEEEECSEEEEEEEEETT CS
   Pyr_redox  54 gievllntkveeiegsed 71 
                  ++v+  +++ +i ++++
  EPA05337.1  92 EVNVIGTENIFKIAQEKN 109
                 555555555544444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       920  (0.0513135); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.61u 0.35s 00:00:00.96 Elapsed: 00:00:00.50
# Mc/sec: 1794.43
//
Query:       EPA05338.1  [L=118]
Description: putative holo-[acyl-carrier-protein] synthase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-15   55.8   0.4    5.2e-15   55.6   0.4    1.0  1  ACPS      4'-phosphopantetheinyl transferase superfamily
  ------ inclusion threshold ------
       0.13   12.4   0.0        0.4   10.8   0.0    1.7  1  4PPT_N    4'-phosphopantetheinyl transferase N-terminal domai


Domain annotation for each model (and alignments):
>> ACPS  4'-phosphopantetheinyl transferase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.6   0.4   5.8e-19   5.2e-15       1     113 [.       6     111 ..       6     112 .. 0.87

  Alignments for each domain:
  == domain 1  score: 55.6 bits;  conditional E-value: 5.8e-19
                 EEEEEEEEHHHHH.HHH-----HHHHHS-HHHHHHHTT--HHHHHHHHHHHHHHHHHHHHHTTS-SSSS--GGG-EEEE-TTS-EEEE-S-SSEEEEEE CS
        ACPS   1 gvGiDieklsrlrkrvkrrgakilkrifteeErkllkssdeearaelfarlWaaKEAllKalgpglrklldfksievledstgrptlellseakkkawk 99 
                 g+GiDi ++++++k +  + +++ k+if ++E+k++ + +++ +  +fa+ +a+KEA+ Ka+++ +    ++ +ie ++ s+++p ++l ++ k k+  
  EPA05338.1   6 GIGIDITDIEQFKKISYLKKPNFYKKIFLPSEIKYCLKYKNSYE--HFAGKFAIKEAVKKAINKHV----SMLDIETSH-SNSKPIVNLKGKLKNKYKF 97 
                 79***********99888999**********************9..********************....777777777.8889999977777777766 PP

                 EE-....SSEEEEE CS
        ACPS 100 leslkidkdyviav 113
                 l s +++k+ +i++
  EPA05338.1  98 LVSISHEKKIAISI 111
                 66666668888876 PP

>> 4PPT_N  4'-phosphopantetheinyl transferase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   4.5e-05       0.4      16      67 ..      49     112 ..      40     113 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 4.5e-05
      4PPT_N  16 eFlaGRicAraalarl...gleav.pllsgerraPlwp........aglvgSIsHtdglaaAav 67 
                 e++aG ++ ++a ++    + ++    +s+++ +P+           ++ +SIsH++++a++++
  EPA05338.1  49 EHFAGKFAIKEAVKKAinkHVSMLdIETSHSNSKPIVNlkgklknkYKFLVSISHEKKIAISII 112
                 777888888888877733233344233445577787766666655346999*********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       861  (0.0480228); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.34s 00:00:00.88 Elapsed: 00:00:00.54
# Mc/sec: 659.76
//
Query:       EPA05339.1  [L=513]
Description: putative membrane protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-10   41.4  15.9    1.7e-10   41.4  15.9    2.9  3  PMT_2            Dolichyl-phosphate-mannose-protein mannosylt
    0.00045   19.2  22.8    0.00045   19.2  22.8    1.6  1  DUF2079          Predicted membrane protein (DUF2079)
     0.0016   18.1  16.8     0.0058   16.3  16.8    2.0  1  PMT              Dolichyl-phosphate-mannose-protein mannosylt
  ------ inclusion threshold ------
       0.08   13.3   8.1       0.11   12.8   1.1    3.3  2  Phage_holin_5_2  Phage holin family Hol44, in holin superfami


Domain annotation for each model (and alignments):
>> PMT_2  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       2.1   9.5e+03      94     125 ..       8      39 ..       4      55 .. 0.62
   2 !   41.4  15.9   3.7e-14   1.7e-10      24     154 ..      93     219 ..      70     224 .. 0.83
   3 ?   -0.7   7.5      0.33   1.5e+03      23      96 ..     271     342 ..     256     367 .. 0.59

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.1
       PMT_2  94 eknklkywllagvlfGlgflsKytaallliaa 125
                 +k++ +++l + ++f +g+ ++ + + +++++
  EPA05339.1   8 TKDRYRHFLPLIIIFFIGLEFRIYYFPYGLPL 39 
                 56666777666666666666666655555554 PP

  == domain 2  score: 41.4 bits;  conditional E-value: 3.7e-14
       PMT_2  24 irlvsalagvltilllyllarrlfgkraallaalllavvplfvalsalftpdaplvllwalalylllraleknklkywllagvlfGlgflsKytaalll 122
                  r+ s+++++lti+ +y+l +++f+++ +l++a + a+ p ++  s+l+ ++ +++l  +++l ++l++  k+     +++ +l+ l++ ++ + ++l 
  EPA05339.1  93 QRFTSIILSSLTIVPIYFLCKKFFNNKLSLIGASIFAFEPRIILNSLLGITEPLFILISTITLVFFLKYERKE----IVISFILVSLCTIIRSEGIFLF 187
                 4899*******************************************99999999999999999999987777....49******************** PP

       PMT_2 123 iaallyllisarrilkekkpylalllalllfs 154
                 +++++ ++i+ r + k  k+yl++l++++l++
  EPA05339.1 188 FTLTILFFIKFRFHKKYLKTYLVGLIIFCLIL 219
                 *9999888883445555788886666666664 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.33
       PMT_2  23 airlvsalagvltilllyllarrlfgkraallaalllavvplfvalsalftpdaplvllwalalylllralekn 96 
                 +i ++s+++ v   +++   ++++ + +  ++ +l+++ +p+f+a+  +       ++l+ ++++++l a+ek 
  EPA05339.1 271 WIMIPSFIIFVP--YGIIQFFKKRNKDTKFIFVILIINSIPIFYAYIMQAHDTRYIYVLYPIFCLISLFAIEKY 342
                 455555554443..344444455545666667777788888888888866666666777777777777777753 PP

>> DUF2079  Predicted membrane protein (DUF2079)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2  22.8     1e-07   0.00045      68     337 ..      98     368 ..      92     384 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1e-07
     DUF2079  68 alllslgglplyrlarerllsrrlalliallYllspvvinptl.fdFhpevlaiPllllalllalrrrkwllllvlilllllvredlslvvvilglwli 165
                 ++l sl+++p+y l+++ + +++l+l+ a ++ + p +i   l     p+ ++i  + l ++l ++r+++ + ++l+ l+  +r + ++++++l+++++
  EPA05339.1  98 IILSSLTIVPIYFLCKKFF-NNKLSLIGASIFAFEPRIILNSLlGITEPLFILISTITLVFFLKYERKEIVISFILVSLCTIIRSEGIFLFFTLTILFF 195
                 57789**************.****************998776636667788888999999999************************************ PP

     DUF2079 166 lrerkrrkiglillllglawvilvtsvliPlfsstksqvfgverysylgsSlleillnlitqpl.lvlq..ellspegdklky.llllflplgflplls 260
                 ++ r  +k  l + l+gl+++ l   +liP+ +  ++++   + +   ++++++ l++l ++ +  +++  +l+++    +    +++f+p g + +++
  EPA05339.1 196 IKFRFHKK-YLKTYLVGLIIFCL---ILIPVINYRIEVTGTDGIFLRATQGTTQTLSTLNQDEGvKIFEgiKLFISYLSWIMIpSFIIFVPYGIIQFFK 290
                 *9855555.45555555554444...5778887777767677788888899999999888887743433112333332233223688888888888888 PP

     DUF2079 261 .........spawLlvalPllllnllsgyspqlslgyqYsllvipflvlaaifglaklsssvelrrikriwsvalvlvlvltlfln 337
                            +  + ++P++ + +++ ++       +Y++++ p++ l ++f+++k  s++ ++ +  i+  ++   l++++++ 
  EPA05339.1 291 krnkdtkfiFVILIINSIPIFYAYIMQAHD------TRYIYVLYPIFCLISLFAIEKYISKFNQKNL--ILILMIIGILASSIIFY 368
                 999999886666677789999999999887......89999999**************987777744..44444444445666665 PP

>> PMT  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3  16.8   1.3e-06    0.0058      80     233 ..      87     225 ..      69     227 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.3e-06
         PMT  80 vpyvsl.RlfsallgslivplvyltllelgfskltallaallvllenslitlsryilldspLlfftllsmyclvkferkapfsrswwlwllltgvalgl 177
                  +y+ l R+ s++l+sl+ +  y +l ++ f+   +l+ a ++++e++ i +s + ++++ +++  + ++++++k+e     +++  +   +  v+l  
  EPA05339.1  87 LQYMELqRFTSIILSSLTIVPIY-FLCKKFFNNKLSLIGASIFAFEPRIILNSLLGITEPLFILISTITLVFFLKYE-----RKE--IVISFILVSLC- 176
                 45666526777777777665555.55667899999*****************************************7.....333..33333345554. PP

         PMT 178 avsvKwvglftvllvgllliwelwqllgdkslllksivkhllaralaliviPvtly 233
                    + + g+f+++ + +l++++   ++ +k l+++     +   +++li+iPv  y
  EPA05339.1 177 -TIIRSEGIFLFFTLTILFFIKF--RFHKKYLKTY----LVGLIIFCLILIPVINY 225
                 .5555555555555555555553..3333344444....445899*******9765 PP

>> Phage_holin_5_2  Phage holin family Hol44, in holin superfamily V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   1.0     0.046   2.1e+02       2      35 ..     279     311 ..     278     331 .. 0.67
   2 ?   12.8   1.1   2.4e-05      0.11      11      62 ..     339     394 ..     330     398 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.046
  Phage_holin_5_2   2 vvilyiiGeilKktekvkd.kyIPlilgiiGiilg 35 
                      +++ y i  + Kk +   d k+I +il+i +i + 
       EPA05339.1 279 IFVPYGIIQFFKKRN-K-DtKFIFVILIINSIPIF 311
                      556666666777774.4.45********9998766 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 2.4e-05
  Phage_holin_5_2  11 ilKktekvkdkyIPlilgiiGiilgvvivft.a...dfqaedilifgaiiqGilsg 62 
                      i K ++k+++k  +lil+iiGi+ + +i++  +     ++++++ +g i++ i sg
       EPA05339.1 339 IEKYISKFNQKNLILILMIIGILASSIIFYEyKkmdYEKEKEMYEIGKITVQITSG 394
                      568899999****************9999985478555667777777555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (513 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1291  (0.0720062); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.45
# Mc/sec: 3450.11
//
Query:       EPA05340.1  [L=39]
Description: hypothetical protein BG20_I0148 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.26s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 293.84
//
Query:       EPA05341.1  [L=123]
Description: hypothetical protein BG20_I0165 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.1e-19   67.9   0.3    1.1e-18   67.5   0.3    1.1  1  NeuB      NeuB family
  ------ inclusion threshold ------
      0.062   13.4   0.0       0.11   12.6   0.0    1.4  1  DUF4839   Domain of unknown function (DUF4839)


Domain annotation for each model (and alignments):
>> NeuB  NeuB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.5   0.3   1.3e-22   1.1e-18       1      88 [.      34     118 ..      34     122 .. 0.95

  Alignments for each domain:
  == domain 1  score: 67.5 bits;  conditional E-value: 1.3e-22
                 HHHHHHHHT-SEEEEEE--HHHH--GGGGG--......TT-S-HHHHHHHH---HHHHHHHHHHHHHTT-EEEEEE-SHHHHHHHHHH CS
        NeuB   1 lieaAaeagadavKfQtfkaeelvskeakkaeyqkkekekeesqlellkklelseeehkelkeyceekgieflstpfdlesvdllesl 88 
                 +i+ Aa+++ da+KfQ+f ++++  ke+kk +yq+k ++   s++e lkk e s + +k+l++yc++k+i flstp+d+esv++ +++
  EPA05341.1  34 MIDLAAKCKSDAIKFQSFITDNMQLKESKKPRYQNKLPW---SYYEQLKKSESSFDFQKKLINYCKKKKILFLSTPYDEESVNFFSRY 118
                 89**********************************886...679**************************************98765 PP

>> DUF4839  Domain of unknown function (DUF4839)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.3e-05      0.11      20      73 ..      34      88 ..      22      96 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.3e-05
     DUF4839 20 vadFAkkykGrtieFdGsia.alvnhgdkktrydillgagdydeetakGPaFkfe 73
                + d A+k k + i+F+  i+ +++ + +kk+ry+  l    y++ +++  +F f+
  EPA05341.1 34 MIDLAAKCKSDAIKFQSFITdNMQLKESKKPRYQNKLPWSYYEQLKKSESSFDFQ 88
                6799***************944666778*****9888888888777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       843  (0.0470188); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 941.52
//
Query:       EPA05342.1  [L=108]
Description: hypothetical protein BG20_I0134 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-18   66.5   0.0    2.6e-18   66.2   0.0    1.1  1  adh_short        short chain dehydrogenase
    1.4e-15   57.5   0.0    2.3e-15   56.8   0.0    1.3  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
  ------ inclusion threshold ------
      0.095   12.2   0.0        0.1   12.1   0.0    1.0  1  Chorismate_bind  chorismate binding enzyme


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.2   0.0   4.3e-22   2.6e-18     123     193 ..       1      71 [.       1      73 [. 0.96

  Alignments for each domain:
  == domain 1  score: 66.2 bits;  conditional E-value: 4.3e-22
                 HHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHHCTH CS
   adh_short 123 mlkqssGrIvnvsSvagkvpvagvaaYsAsKaavagltrslakelaptgirvnavaPGlvdTdmakelrek 193
                 m+++++GrI+n++S  + +++ +++ Y++sK+a+ gl+rsl  el++++irv ++ PG ++T+m k+ +++
  EPA05342.1   1 MKEKKWGRIINIGSSSSYQGFSEGTIYCSSKHALLGLSRSLFAELKESKIRVFSISPGSIKTKMGKQDKKQ 71 
                 899*************************************************************9987765 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.8   0.0   3.8e-19   2.3e-15     120     185 ..       4      71 ..       1      91 [. 0.86

  Alignments for each domain:
  == domain 1  score: 56.8 bits;  conditional E-value: 3.8e-19
                   C..CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHHHHHHGGGTEEEEEEEE--BHCTGGGGSTTH CS
  adh_short_C2 120 g..gsivnlssvgaervvpnynaygaaKaalealtrylAvelgpkgiRvNavspgpikTlaasgikgf 185
                   +  g+i+n+ s ++ +++++ ++y+ +K+al +l+r+l +el + +iRv ++spg ikT++ ++ k++
    EPA05342.1   4 KkwGRIINIGSSSSYQGFSEGTIYCSSKHALLGLSRSLFAELKESKIRVFSISPGSIKTKMGKQDKKQ 71 
                   335**********************************************************8876643 PP

>> Chorismate_bind  chorismate binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   1.8e-05       0.1      58     119 ..      27      86 ..      10     100 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.8e-05
                      EEEETTEEEEEEESSEEEEEETTSEEEEECEE.EEEEHSSSHHHHHHHHHHHHCCHHHHHHHH CS
  Chorismate_bind  58 lleledsellgaSPElllkveggrrietepia.GTrargktpeedealeeelledeKeraEhl 119
                      +++  ++ llg S  l+ +++++ +i++  i  G++ ++k  ++d++++ +   d+Ke aE  
       EPA05342.1  27 YCSS-KHALLGLSRSLFAELKES-KIRVFSISpGSI-KTKMGKQDKKQNYKTFLDPKEVAEYI 86 
                      3444.3679************76.999999984666.666777899999***********965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 784.31
//
Query:       EPA05343.1  [L=109]
Description: hypothetical protein BG20_I0111 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-18   67.1   0.0    1.5e-18   66.9   0.0    1.1  1  Glycos_transf_1  Glycosyl transferases group 1
    1.3e-12   48.3   0.0    1.6e-12   48.0   0.0    1.1  1  Glyco_trans_1_4  Glycosyl transferases group 1
      2e-06   28.1   0.0    2.5e-06   27.8   0.0    1.1  1  Glyco_trans_1_2  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.9   0.0   2.5e-22   1.5e-18      88     170 ..       2      83 ..       1      85 [. 0.93

  Alignments for each domain:
  == domain 1  score: 66.9 bits;  conditional E-value: 2.5e-22
                      HHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHHHHHHHHH CS
  Glycos_transf_1  88 ellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelrerlgenar 170
                      +llk+++++++ps++E++++++ EA+ +++pv+ +n+gg++e++++ +tG+lv++++  +l+ +i+k+l+++ ++ +++++a+
       EPA05343.1   2 KLLKSSSVLAVPSRMESLPTNIKEAFFLKIPVVGTNVGGIPELIQHTKTGILVPSGDSTKLSSEINKILKNK-ENSEMIQAAY 83 
                      6899*******************************************************************8.5666666665 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.0   0.0   2.7e-16   1.6e-12      68     134 .]       2      72 ..       1      72 [. 0.96

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 2.7e-16
                      HHHHH-SEEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHHH- CS
  Glyco_trans_1_4  68 ellaaadvfvaPs..egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLled 134
                      +ll++++v+ +Ps  e+++  + Ea+ +++pvV t+vggi+e++   ++g+lvp+gd+ +l  +i ++l++
       EPA05343.1   2 KLLKSSSVLAVPSrmESLPTNIKEAFFLKIPVVGTNVGGIPELIqhTKTGILVPSGDSTKLSSEINKILKN 72 
                      5899*********999****************************9779*******************9986 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0   4.2e-10   2.5e-06       4      87 ..      11      96 ..       8     101 .. 0.91

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 4.2e-10
  Glyco_trans_1_2  4 n.psrsespnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarervlaehtydhra 87
                     + psr es+ + + Ea    ++++ +   g++el++  k++il+   d   l   i++ l+n e  +++ +aa+e+v +e ++++ +
       EPA05343.1 11 AvPSRMESLPTNIKEAFFLKIPVVGTNVGGIPELIQHTKTGILVPsgDSTKLSSEINKILKNKEN-SEMIQAAYEFVTNEMSWKKII 96
                     44899999999**********************************9999**********988777.8899*************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 863.31
//
Query:       EPA05344.1  [L=567]
Description: FkbH domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00017   21.4   4.6     0.0031   17.4   3.4    2.8  1  Acid_PPase      Acid Phosphatase
    0.00094   19.3   0.5     0.0061   16.7   0.1    2.5  2  Acetyltransf_4  Acetyltransferase (GNAT) domain
     0.0026   17.5   0.1     0.0082   15.9   0.1    2.0  1  NIF             NLI interacting factor-like phosphatase
  ------ inclusion threshold ------
       0.19   12.1   4.2         15    6.0   0.1    3.4  3  Ribosomal_L22e  Ribosomal L22e protein family


Domain annotation for each model (and alignments):
>> Acid_PPase  Acid Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   3.4   6.9e-07    0.0031       4     150 ..     217     346 ..     215     365 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 6.9e-07
                 SEEEE-STTTSSSS-TTTSS-S-EEE-TTS.-EEETT--EE---TTHHHHHHHHHHTT--EEEEE--S-HHHHHHHHHHTT-G..........GGESEE CS
  Acid_PPase   4 klivFDLDyTLWpfevdtlvsaplkkeskksevvDrrgeelklypdveeileelkskevklavaSrtdepdlarelLklleindakekekklldvfddv 102
                 k iv+DLD TLW   v     + ++   +          + + y + ++il +l+++++ la+ S+ +  d a +++k      ++   +  ++ f ++
  EPA05344.1 217 KCIVLDLDNTLWGGIVGEDGFNGIRLGPEP---------SGNTYFEFQKILLSLNQRGIILAINSKNNYDD-ALKVIK------EHPYMVLREEQFASM 299
                 6899********888777777777766666.........3345788899*****************88765.333333......33455777899**** PP

                 EESSS-HHHHHHHHHHHH---GGGEEEEES-HHHHHHHHTTT-EEEE- CS
  Acid_PPase 103 eiykgsktkhfeklkkktgieyedmlfFDdesrnievesrlgvtfvlv 150
                  i   +k++ ++++ ++ +i  ++++fFDd   n+e  + l++  vl+
  EPA05344.1 300 RINWNDKVSNMKEIINELNIGADSVVFFDDDPVNQEYMK-LNMPEVLT 346
                 **********************************99988.88776665 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.39   1.7e+03      43      66 ..     189     214 ..     154     217 .. 0.78
   2 !   16.7   0.1   1.4e-06    0.0061      93     138 ..     494     545 ..     437     554 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.39
  Acetyltransf_4  43 al.dsekeyvflvae.sdrivGyayl 66 
                     ++ +s++++++l+ +  + i+G + l
      EPA05344.1 189 DMkISLERIPYLANDlMGYIIGHLGL 214
                     4435899999*999999999998776 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 1.4e-06
  Acetyltransf_4  93 glgre....lidaleqvlkeqnienllaeiasp..nensiqfhkalGFelvg 138
                     ++gre    ++ ++++++ke+++e+++a+ +++  n++  +f+++ GF + g
      EPA05344.1 494 IMGREiekgMLGHIINIAKENGVEQITAQFIASkkNKPIEDFLQNNGFHKDG 545
                     333333355********************876645666889*******9876 PP

>> NIF  NLI interacting factor-like phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   1.8e-06    0.0082       1     123 [.     217     340 ..     217     406 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.8e-06
         NIF   1 ktLVLDLDetLvhsklekskklkvegek.....vevsvlkRpgldefLkelskl.yevvifTasseeyaeavidildpekkllshr....lyrescvkk 89 
                 k++VLDLD+tL+   +         ge+       +       + ef+k l +l    +i   +s+++ ++ +++++++  ++ ++     +r ++  +
  EPA05344.1 217 KCIVLDLDNTLWGGIV---------GEDgfngiRLGPEPSGNTYFEFQKILLSLnQRGIILAINSKNNYDDALKVIKEHPYMVLREeqfaSMRINW-ND 305
                 79**********8886.........444111112344455588999***97666155566999*************99986644445555555555.33 PP

         NIF  90 kgeyvKdL.sllgrdlsrvvivDdspdsfelqpen 123
                 k + +K++ + l+   ++vv++Dd+p + e  + n
  EPA05344.1 306 KVSNMKEIiNELNIGADSVVFFDDDPVNQEYMKLN 340
                 55566654255677999*********987765555 PP

>> Ribosomal_L22e  Ribosomal L22e protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1    0.0039        18      24      72 ..     293     341 ..     276     375 .. 0.84
   2 ?   -2.6   0.1       1.5   6.9e+03      15      35 ..     392     412 ..     384     418 .. 0.67
   3 ?    6.0   0.1    0.0033        15       3      42 ..     429     468 ..     427     482 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0039
  Ribosomal_L22e  24 fekfLkerikvngktgnlgdkveieregkskvtvtsevkfskrylkylt 72 
                      e+f + ri+ n+k+ n+++ ++  + g+++v+   + ++++ y+k  +
      EPA05344.1 293 EEQFASMRINWNDKVSNMKEIINELNIGADSVVFFDDDPVNQEYMKLNM 341
                     58999***************99999999999***************765 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.5
  Ribosomal_L22e  15 edkildvaefekfLkerikvn 35 
                     e++i d+++f k L+ +i ++
      EPA05344.1 392 ENSIPDLKSFLKNLELKILIK 412
                     666777777777777666554 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.0033
  Ribosomal_L22e   3 klkftidcskpvedkildvaefekfLkerikvngktgnlg 42 
                     +++f++ +++  e +i++ ++ ek+L   ++v++k g  g
      EPA05344.1 429 TNQFNLTTKRYQESEIIKFSNDEKYLVGCVQVEDKFGDNG 468
                     6899******************************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (567 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 3574.03
//
Query:       EPA05345.1  [L=294]
Description: glycosyltransferase, group 2 family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-17   64.3   0.0    1.5e-17   63.9   0.0    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
  ------ inclusion threshold ------
      0.015   15.8   0.0       0.03   14.8   0.0    1.5  1  Glyco_tranf_2_4  Glycosyl transferase family 2
      0.018   14.9   0.0      0.029   14.3   0.0    1.3  1  Glyco_tranf_2_3  Glycosyltransferase like family 2


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.9   0.0   2.6e-21   1.5e-17       4     169 ..       8     164 ..       5     165 .. 0.88

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 2.6e-21
                      EEESS-TTTHHHHHHHHHHHGGCCEEEEEEE.EES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--SS...EEEEEESSEEE- CS
  Glycos_transf_2   4 iptyNeektlletlesllaqdpypdfeiivv.DDgStDetveileelakedprvrvirreenvGkagalnaglraatgd...yilflDaDdepd 93 
                       p++Neek+++  +  l+++     +e+i+v DDgS+D t++i e+      + +vi++++n G+++a++  + +a      +++++D+D ++ 
       EPA05345.1   8 LPSFNEEKNIASIILQLKKN-----YELILVcDDGSSDLTAAISEKM-----GAIVIKHKKNLGYGAAIRSLFLKAHELecdILVTFDSDGQHR 91 
                      79*********999999997.....7766544***************.....9********************999876777************ PP

                      TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTCSTCCCEEEEHHHHHC CS
  Glycos_transf_2  94 pdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfeigsaallrrealeel 169
                        ++e +v+++ k++ad+v+g+r+  + +    + +k+     +  +   + ++  ++++  ++++++++ +le++
       EPA05345.1  92 VLDIETVVAPILKNDADIVIGSRFLGSIKGEIPSYRKF---GMNTITNLVNANTEKKITDSQSGFRAYNKTVLEKI 164
                      ************************99988888888874...77777777788888888888888999999888876 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0     5e-06      0.03       2      81 ..      12      87 ..      11      89 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5e-06
  Glyco_tranf_2_4  2 neadiLpeflahhlalgfdrilvydndstDgtrailkelpevkllhvdksyederrqvellkallaryaea.dwvlvvDaD 81
                     ne++ + + +  ++++ ++ ilv+d++s+D t+ai +++ ++ +++++k+     ++ +++  +l+ +  + d ++++D+D
       EPA05345.1 12 NEEKNIASIILQLKKN-YELILVCDDGSSDLTAAISEKMGAI-VIKHKKNLG---YGAAIRSLFLKAHELEcDILVTFDSD 87
                     7888888888888888.999***************9998555.556666664...77777777777665444888888888 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   4.8e-06     0.029       4      97 ..       4      87 ..       2     122 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.8e-06
  Glyco_tranf_2_3  4 lavlVptfneedvlgevlesllaqeyprvevvvvv.desdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnealravksdlvllvDdD 97
                     +a+  p+fnee+ + +++ +l +    ++e+++v+ d+s++ t++  e    + +++   v+  ++nlg ++++r+l+   +  ++d+++ +D+D
       EPA05345.1  4 IAIGLPSFNEEKNIASIILQLKK----NYELILVCdDGSSDLTAAISE----KMGAI---VIKHKKNLGYGAAIRSLFLKAHELECDILVTFDSD 87
                     78889999998888888888877....79*999995667777666443....56665...6777899***************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 1704.09
//
Query:       EPA05346.1  [L=67]
Description: hypothetical protein BG20_I0169 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
       0.16   12.4   0.0       0.23   11.9   0.0    1.3  1  PP-binding  Phosphopantetheine attachment site


Domain annotation for each model (and alignments):
>> PP-binding  Phosphopantetheine attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.3e-05      0.23      37      67 .]      28      58 ..      21      58 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.3e-05
  PP-binding 37 llaaleeefgveiplsdlfehptlaelaayl 67
                ll +le ef+v+++ ++ ++ + ++++ ++l
  EPA05346.1 28 LLYELESEFKVKFTIDEAMDVKKISDIKRHL 58
                7779***********************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 460.26
//
Query:       EPA05347.1  [L=296]
Description: putative dTDP-4-dehydrorhamnose reductase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-71  240.5   0.0    2.2e-71  240.3   0.0    1.0  1  RmlD_sub_bind    RmlD substrate binding domain
    7.5e-20   71.4   0.0    1.1e-19   70.8   0.0    1.3  1  Epimerase        NAD dependent epimerase/dehydratase family
      3e-11   43.3   0.1    2.9e-10   40.1   0.1    2.1  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    9.9e-08   31.3   0.0    5.6e-07   28.8   0.0    2.2  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    2.4e-07   30.2   0.2    8.5e-06   25.1   0.1    2.7  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    5.1e-07   29.1   0.1    5.2e-05   22.5   0.0    2.7  2  NAD_binding_4    Male sterility protein


Domain annotation for each model (and alignments):
>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  240.3   0.0   7.3e-75   2.2e-71       1     285 [.       1     290 [.       1     292 [. 0.97

  Alignments for each domain:
  == domain 1  score: 240.3 bits;  conditional E-value: 7.3e-75
                    EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT.........T--TTSHHHHHHHHHHH--SEEEE------HHHHHHSHHHHHHHHTHHHHHHHH CS
  RmlD_sub_bind   1 mkilvtGanGqlGseLakqlaeeglevlaltre.........eldltdaeavaellkeakpdvvvnaAAytavDkaEseeeaayavnaeavealAe 87 
                    mk +vtG+ G++G +L+  l+++g  v+++ ++         +ldl + +++ ++l++ +pdv++++AA t+v k+Ese+++ay +n +a+e++ +
     EPA05347.1   1 MKYVVTGSAGLIGNQLVSDLEQSGQTVYSCYNKhkplhgiptKLDLLNLKEISNVLRKLQPDVIIHLAALTDVEKCESEPNLAYLINTKATEHIVK 96 
                    899***************************65569************************************************************* PP

                    HHHHCT-EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHHH-SSEEEEEE-SEESS..SSS-HHHHHHHHHHH-SEEEEESS-EE CS
  RmlD_sub_bind  88 aaaavgalLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavlaagkkalivRtswvyge..kgknfvktmlrlakereelkvvaDqlg 181
                    +++++g +L ++StDyVFdG+k   Y edd ++Pln YG+tKl+GE+av++   ++ i+Rts  +g+   ++ f   +++  k+++ l++++Dq+ 
     EPA05347.1  97 ETNQIGCFLTYLSTDYVFDGKKG-LYYEDDFPNPLNQYGKTKLEGEKAVEHCISHWSIIRTSTPFGNhlIKQTFPLWIIENIKKNNMLNLIEDQFT 191
                    ********************965.599****************************************6669************************* PP

                    --EEHHHHHHHHHHHHHHCHH.GGG-EEEE---BS-EEHHHHHHHHHHHHCHTTSEEEEE-CCCS--SS---SBE-B--HHHHHCCT----BHHHH CS
  RmlD_sub_bind 182 sPTsardlAevllqllekaaeekelagvyHlanegetswlefArailkeagadseevkpistaeyptpAkRPanSvLdtekleatfgiklrewrea 277
                    +PT++ +l +++++++++ +      g++Hl+++  +s++ fA+ i+++++ d++ +kp++++ +  +AkRP++S+L+ +k++++   k+ + +++
     EPA05347.1 192 TPTYVPNLTKMIIDVTTNNLV-----GYFHLSGSTRISRYSFAKMIADKLNLDKSFLKPVKMDMMQWKAKRPSDSSLNVSKANSILTQKPLPIEQS 282
                    *****************9995.....********************************************************************** PP

                    HHHHHHHH CS
  RmlD_sub_bind 278 lkevlkel 285
                    l e+l ++
     EPA05347.1 283 LDEYLSQF 290
                    ***99886 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.8   0.0   3.8e-23   1.1e-19       2     196 ..       4     180 ..       3     198 .. 0.86

  Alignments for each domain:
  == domain 1  score: 70.8 bits;  conditional E-value: 3.8e-23
                 EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHHHSHHHHHHHHTHHHHHHHH CS
   Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggvaassedpadfieknlqgtlnlle 100
                 +VtG +G+iG++lv  l++ g++v    ++ ++  ++       ++ldl++ +++ +++++ qpd++ihlAa  +v+   ++p+  + +n++ t ++++
  EPA05347.1   4 VVTGSAGLIGNQLVSDLEQSGQTVYSCYNK-HKPLHG-----IPTKLDLLNLKEISNVLRKLQPDVIIHLAALTDVEKCESEPNLAYLINTKATEHIVK 96 
                 7****************************9.222222.....567****************************************************** PP

                 HHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTT CS
   Epimerase 101 aarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklveayaaqyglnaiilrlfnlyGprngegevsrvipalirkileg 196
                 + ++ g+  l +ls++ v+  ++     e+      +p + Y+ +Kl gek ve           i+r ++ +G +      + +   +i++i+++
  EPA05347.1  97 ETNQIGC-FLTYLSTDYVFDGKKGL-YYEDD---FPNPLNQYGKTKLEGEKAVEHCISHW----SIIRTSTPFGNH---LIKQTFPLWIIENIKKN 180
                 *******.9**********988885.33333...359*****************987666....689999999988...55666666666666655 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   0.1   9.6e-14   2.9e-10       2     183 ..       5     163 ..       4     177 .. 0.88

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 9.6e-14
                    EETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHTTSHHH CS
  GDP_Man_Dehyd   2 iTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevynLAAqshVdvsfekPey 97 
                    +TG aG iG+ l+  L + g++v+   ++++         l   p           k Dl + +++ ++l++ qpd +++LAA   V++  ++P  
     EPA05347.1   5 VTGSAGLIGNQLVSDLEQSGQTVYSCYNKHKP--------LHGIP----------TKLDLLNLKEISNVLRKLQPDVIIHLAALTDVEKCESEPNL 82 
                    9**********************987665544........33333..........579************************************** PP

                    HHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHHHHHHHHHHHHHHHHHHH---EEEEEE-EE CS
  GDP_Man_Dehyd  98 taevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYaaaKlyadwivvnyreayglfavngilfnh 183
                     + +n  +t ++++   ++g+     +   St+ v+    +  + E+   +P + Y+ +Kl  +  v+ +   + +  +++ + nh
     EPA05347.1  83 AYLINTKATEHIVKETNQIGC----FLTYLSTDYVFDGK-KGLYYEDDFPNPLNQYGKTKLEGEKAVEHCISHWSIIRTSTPFGNH 163
                    ***************999985....58899******544.5677788888******************999999999998888887 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0   1.9e-10   5.6e-07       1     226 [.       4     204 ..       4     211 .. 0.75

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 1.9e-10
   3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegv..dvvihlaslvdvag.kltedeimkvnvkGT 96 
                 vvtG+aG +G++lv+ L + ++  +v ++  +++p         + +   + D+++ ++++++l++   dv+ihla+l+dv + + + +  + +n k T
  EPA05347.1   4 VVTGSAGLIGNQLVSDLEQSGQ--TVYSCYNKHKPL--------HGI-PTKLDLLNLKEISNVLRKLqpDVIIHLAALTDVEKcESEPNLAYLINTKAT 91 
                 89***************99995..666554444433........344.5789************976448*************88899999******** PP

   3Beta_HSD  97 rnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKalaEklvlkaNgrtlknggrlyTcaLRpagiyGeg...dkllvpl 192
                 + +++   + g  +l Y S+ + v++   ++ +      +  ++++ + y ++K   Ek+v +                +R ++ +G+    +++ +  
  EPA05347.1  92 EHIVKETNQIGC-FLTYLST-DYVFD--GKKGLY----YEDDFPNPLNQYGKTKLEGEKAVEHCIS----H-----WSIIRTSTPFGNHlikQTFPLWI 173
                 *******99996.7899987.78888..444444....4445667888999*******99987766....2.....35678888888753213333444 PP

   3Beta_HSD 193 lkqlaklglalfkigdeevlsdrvYvgNvawahi 226
                 +++++k++  ++++ +++  + ++Yv N+++++i
  EPA05347.1 174 IENIKKNN--MLNLIEDQF-TTPTYVPNLTKMII 204
                 55555555..777776655.77888888888887 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.1   2.8e-09   8.5e-06      58     153 ..      41     148 ..       3     191 .. 0.74

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 2.8e-09
                      ..E--TT-HHHHHHHTT..T-SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEGGGS.............S--SHH CS
  Polysacc_synt_2  58 pvigdvrdkerlekaleelkvdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliStDKAv.............nPtnvm 138
                      p+  d+ + ++++++l++l++dv++h AAl  V  +e++p  a   N  +te++++ + + g   + ++StD                nP n +
       EPA05347.1  41 PTKLDLLNLKEISNVLRKLQPDVIIHLAALTDVEKCESEPNLAYLINTKATEHIVKETNQIGCF-LTYLSTDYVFdgkkglyyeddfpNPLNQY 133
                      44468889999*********************************************98877753.56799985432222223333333678888 PP

                      HHHHHHHHHHHHHGG CS
  Polysacc_synt_2 139 GatKrlaekllqala 153
                      G tK+  ek + ++ 
       EPA05347.1 134 GKTKLEGEKAVEHCI 148
                      888877777776655 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.011        34       1      23 [.       5      27 ..       5      39 .. 0.83
   2 !   22.5   0.0   1.7e-08   5.2e-05      87     205 ..      60     158 ..      43     207 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.011
                   EE-TTSHHHHHHHHHHHHHS-.T CS
  NAD_binding_4  1 lTGaTGFLGkvLlekLLrttpev 23
                   +TG+ G +G+ L+ +L ++ + v
     EPA05347.1  5 VTGSAGLIGNQLVSDLEQSGQTV 27
                   7**************98777754 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 1.7e-08
                    H--EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H......HHH--EEEETTTCCCHHHHH CS
  NAD_binding_4  87 evdviihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegekeekldederaklkglpntYeqs 179
                    + dviih aA +++++  +e   ++ +N+++t+++++  +++     l + ST yv + ++g                    +++  +  n+Y ++
     EPA05347.1  60 QPDVIIHLAALTDVEKCESEpnlAYLINTKATEHIVKETNQIGCF--LTYLSTDYVFDGKKGLY-----------------YEDDFPNPLNQYGKT 136
                    559**********999777767799***************99766..******99999999754.................2456677889***** PP

                    HHHHHHHHHHHHHHH---EEEEEE-E CS
  NAD_binding_4 180 KalaEklvrearrrsglpvvivRpsi 205
                    K ++Ek v++  ++    ++i+R s+
     EPA05347.1 137 KLEGEKAVEHCISH----WSIIRTST 158
                    ********998833....57888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 1762.29
//
Query:       EPA05348.1  [L=186]
Description: cytidylyltransferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-20   74.1   0.1    2.1e-20   73.6   0.1    1.2  1  CTP_transf_3  Cytidylyltransferase
     0.0011   19.0   0.1      0.017   15.3   0.1    2.4  2  DUF2023       Protein of unknown function (DUF2023)
     0.0018   18.7   0.0     0.0021   18.4   0.0    1.1  1  NTP_transf_3  MobA-like NTP transferase domain
     0.0053   16.8   0.1      0.014   15.4   0.1    1.7  1  KH_5          NusA-like KH domain


Domain annotation for each model (and alignments):
>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.6   0.1   4.6e-24   2.1e-20       3     123 ..      12     130 ..      11     174 .. 0.92

  Alignments for each domain:
  == domain 1  score: 73.6 bits;  conditional E-value: 4.6e-24
                   EEEE-SSSSSSTTGGGSEETTEEHHHHHHHHHHHTTTTSEEEEEES-HHHHHHHHHTT..SEEEE--TTCSSHHHHHHHHHHHHTTT.TTSEEEEE- CS
  CTP_transf_3   3 IipARsgSkRlpgKnlldlggkpliayvleaalkskafekvivaTDseeiknvakefg..asvlvtrsslesdterflevvkaflmseneeiivnlq 97 
                    i+AR++SkRlp K l  +gg p ++ ++ +++ +k+f k+iv T+  ++++ + ef    ++  +r+++++ ++r+l++ k f+ +    ii+++q
    EPA05348.1  12 FILARLDSKRLPKKQLSLIGGVPVLKLLINRIKFAKKFRKIIVCTTTRNTDDPLIEFLekEKIEYFRGNEKDILDRLLNAAKFFQTD----IIIDVQ 104
                   59******************************************************999999*************************....****** PP

                   TT-TT--HHHHHHHHHHHHHSTTSSE CS
  CTP_transf_3  98 GdnPllqeevikkaietlkenqedyl 123
                   Gd+  ++++ i+k+i++lke++ d +
    EPA05348.1 105 GDKIYTDPKYIDKVIDKLKESNVDFI 130
                   *********************87633 PP

>> DUF2023  Protein of unknown function (DUF2023)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   3.7e-06     0.017       9      43 ..      44      78 ..      37     104 .. 0.86
   2 ?    1.0   0.0       0.1   4.5e+02      24      48 ..     112     136 ..     107     141 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.7e-06
                HHHCTS-SEEEEEEEGGGHHHHHHHHHHTT--EEE CS
     DUF2023  9 eykkgvRklvlltlkkkeeelvvkrLekkeieylv 43
                 + k  Rk++++t+++++ + +++ Lek++iey+ 
  EPA05348.1 44 KFAKKFRKIIVCTTTRNTDDPLIEFLEKEKIEYFR 78
                699******************************86 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.1
                 GGGHHHHHHHHHHTT--EEEEE-TS CS
     DUF2023  24 kkeeelvvkrLekkeieylvqevse 48 
                  k+ ++v+++L++++++++  + ++
  EPA05348.1 112 PKYIDKVIDKLKESNVDFISGSDNS 136
                 567889999******9998766555 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   4.8e-07    0.0021      15     128 ..      24     149 ..      12     177 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 4.8e-07
                   THHHHCCCCCCHHHHHHHHHCTT..-CEEEEECSH....CHHHHHHTTCTS-EEE-TTSS-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHH CS
  NTP_transf_3  15 dKallplggkpllervldalraa.gvdevvvvggd....eevlaalarlgvrvvededpgkgplaslaaalraaadadavlvlacDmPlltpelver 106
                    K+l  +gg p+l+ ++++++ a ++++++v++      +++ + l++ ++++++    +k +l  l+ a++   ++d ++ + +D ++ +p+ +++
    EPA05348.1  24 KKQLSLIGGVPVLKLLINRIKFAkKFRKIIVCTTTrntdDPLIEFLEKEKIEYFRGN--EKDILDRLLNAAKFF-QTDIIIDVQGDKIYTDPKYIDK 117
                   6777788****************559******86633444677788999*****998..799***********9.9********************* PP

                   HHHCHHHHTSSEEEEESSSEE..........E CS
  NTP_transf_3 107 llaaaaasgadvvvptyeger..........g 128
                   +++++++s+ d +  +++ +           +
    EPA05348.1 118 VIDKLKESNVDFISGSDNSRTfnpsdhfihgI 149
                   ******99998877777766645554444444 PP

>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   3.2e-06     0.014      16      54 ..     101     139 ..      95     142 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.2e-06
        KH_5  16 vdpvGaivgkkGsrikavsseLkgekidvvewseDlaef 54 
                 +d  G  +   +++i +v+++Lk+ ++d +  s++ ++f
  EPA05348.1 101 IDVQGDKIYTDPKYIDKVIDKLKESNVDFISGSDNSRTF 139
                 788888999999***********************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1244.76
//
Query:       EPA05349.1  [L=43]
Description: hypothetical protein BG20_I0164 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.095   12.4   0.0      0.095   12.4   0.0    1.0  1  Fungal_KA1  Fungal kinase associated-1 domain


Domain annotation for each model (and alignments):
>> Fungal_KA1  Fungal kinase associated-1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   5.3e-06     0.095      19      56 ..       2      39 ..       1      42 [. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.3e-06
  Fungal_KA1 19 lktslskkelrqelaklLreWkkyGlkdvksdkesnti 56
                ++ts+s  +  q++ k+L e++k G+++v+  + ++ +
  EPA05349.1  2 IYTSTSCLKNPQNIIKVLDEYEKGGIQNVELGSVHSYF 39
                677788888899******************98887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (43 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.25s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 326.89
//
Query:       EPA05350.1  [L=326]
Description: hypothetical protein BG20_I0125 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.8e-19   69.0   0.1    7.9e-19   68.0   0.1    1.5  1  MAF_flag10  Protein of unknown function DUF115


Domain annotation for each model (and alignments):
>> MAF_flag10  Protein of unknown function DUF115
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.0   0.1   4.4e-23   7.9e-19       1     170 [.      32     229 ..      32     230 .. 0.81

  Alignments for each domain:
  == domain 1  score: 68.0 bits;  conditional E-value: 4.4e-23
  MAF_flag10   1 knllknlkenlkpslkellnkf.kgnkpaiivgaGPSLek..nlellkelrdkaviiaadtalkaLlkegIkPD.....ivvslDpqeasyevfkeaek 91 
                 kn++ nl+++ +   +++ln+    nk+ai++g GPSL+k  +l++l+e + + vii++d+al + lk+g++P      +vv++Dp e + +++++   
  EPA05350.1  32 KNFALNLQKIWTGYSSKILNEVgV-NKTAIVIGRGPSLQKfnHLKKLSESKFNEVIICCDGALITALKAGVTPKkfkkfFVVTIDPREDTRKFYDDEIV 129
                 688899999999556777775634.6*************866899999999**********************8888879999*********9877776 PP

  MAF_flag10  92 kg...diplvfasgvnpellkkykgpki.flvtgstqa...........lelleeekne.........ilfgGgsvantaldlA.vklgfkeIiliGqD 165
                 +    +i  +f++++np ++++ ++  i + + +s +            ++l+                +++Gg+v++ ++++    l++++I+liG++
  EPA05350.1 130 DLygnEIKGIFSTVSNPTTIERAEKAGIkIHWMHSLVDynegeksfnqiSALMT----RaknhtnglpAIQTGGNVGTSSWFVGwKILKCSKIVLIGIN 224
                 66789****************999887754444433335788888666522222....144447789*99*************95569*********** PP

  MAF_flag10 166 laytd 170
                 +++++
  EPA05350.1 225 HGWEE 229
                 *9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 2102.29
//
Query:       EPA05351.1  [L=112]
Description: hypothetical protein BG20_I0113 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-06   28.5   0.0    1.4e-06   28.2   0.0    1.1  1  Asn_synthase   Asparagine synthase
  ------ inclusion threshold ------
       0.01   14.7   0.0      0.013   14.3   0.0    1.2  1  tRNA_Me_trans  tRNA methyl transferase
      0.029   14.1   0.0       0.04   13.7   0.0    1.3  1  ATP_bind_3     PP-loop family


Domain annotation for each model (and alignments):
>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   2.3e-10   1.4e-06      14      65 ..      58     109 ..      50     112 .] 0.90

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 2.3e-10
  Asn_synthase  14 lradvpvGalLSGGlDSSliaalaarqsk.splktFsigfeekgsdeakyake 65 
                   l+    vG+ LS G+DS+l+ al+++  +  ++++Fsi f +++ de+k ak+
    EPA05351.1  58 LEKKSNVGISLSSGVDSTLLLALLKQAIPkLDVNSFSIRF-SDSLDETKNAKK 109
                   566779******************99988789********.8999****9997 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   2.2e-06     0.013       2      43 ..      63     109 ..      62     112 .] 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.2e-06
  tRNA_Me_trans   2 kvvvalSgGVDSsvaaallkeqg..yevigvflklweeedeeg...k 43 
                    +v + lS+GVDS++ +allk++    +v  + ++++++ de++   k
     EPA05351.1  63 NVGISLSSGVDSTLLLALLKQAIpkLDVNSFSIRFSDSLDETKnakK 109
                    68999****************98445789999999999887773323 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   6.7e-06      0.04       2      37 ..      64      99 ..      63     112 .] 0.73

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.7e-06
                EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE- CS
  ATP_bind_3  2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdh 37
                v + +S G+DS++Ll ll++   kl ++ + i +  
  EPA05351.1 64 VGISLSSGVDSTLLLALLKQAIPKLDVNSFSIRFSD 99
                56899***************9888776655555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 724.46
//
Query:       EPA05352.1  [L=244]
Description: cytidylyltransferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-29  103.7   1.1    1.6e-29  103.4   1.1    1.1  1  CTP_transf_3   Cytidylyltransferase
    0.00077   19.9   0.0     0.0012   19.2   0.0    1.3  1  NTP_transf_3   MobA-like NTP transferase domain
  ------ inclusion threshold ------
       0.32   10.9   2.4        1.2    9.0   0.1    2.6  3  PriA_3primeBD  3′ DNA-binding domain (3′BD)


Domain annotation for each model (and alignments):
>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.4   1.1   2.7e-33   1.6e-29       2     194 ..       4     189 ..       3     231 .. 0.82

  Alignments for each domain:
  == domain 1  score: 103.4 bits;  conditional E-value: 2.7e-33
                   EEEEE-SSSSSSTTGGGSEETTEEHHHHHHHHHHHTTTTSEEEEEES-HHHHHHHHHTT..SEEEE--TTCSSHHHHHHHHHHHHTTT.TTSEEEEE CS
  CTP_transf_3   2 aIipARsgSkRlpgKnlldlggkpliayvleaalkskafekvivaTDseeiknvakefg..asvlvtrsslesdterflevvkaflmseneeiivnl 96 
                   +I++AR++S+Rl gK+l+++  +p + yvl+++++sk+++kv+vaT++ ei+++++++   + v v+r+s  ++++r ++  k+++++     iv++
    EPA05352.1   4 CIVQARMNSTRLYGKVLKKIDKNPVLYYVLKQINESKLIKKVVVATSELEIDDAIEKYAkkMNVEVFRGSPTDVLDRHYQCAKKYSFD----PIVRV 96 
                   8**********************************************************999**************************....***** PP

                   -TT-TT--HHHHHHHHHHHHHSTTSSEEEEEEETT...SHHHHTSTTSTEEEETTTSBEEEEESSESSEEHHHHHCTS.....TTTSEEEEEEEEEE CS
  CTP_transf_3  97 qGdnPllqeevikkaietlkenqedylstlvkkvg...keeevlnandlkvllddagkalyfeesvipyireeplels.....rrlylshagiytfr 185
                   ++dnPl +++ i+kaie++k  + d ++t   +++       v + + l +++++     y +e v+pyi ++  +++     + + lsh+      
    EPA05352.1  97 TADNPLNDPQIIDKAIEKMKSGKFDCITTSLLQTFpkgIHVDVISMDILRKAWKNS-SIPYEREYVTPYIFNNSKKFKiynlvNPVNLSHIN----- 187
                   *************************6666665555111346777777777777777.77899999*****9999999944444333333333..... PP

                   HHHHHHHHH CS
  CTP_transf_3 186 keqplkelv 194
                          ++
    EPA05352.1 188 -------FT 189
                   .......44 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0     2e-07    0.0012      11     117 ..       9     121 ..       8     149 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2e-07
                   TTTT....THHHHCCCCCCHHHHHHHHHCTT..-CEEEEECSH....CHHHHHHTTCTS-EEE-TTSS-SHHHHHHHHHHHH.SSSCEEEEETT-TT CS
  NTP_transf_3  11 Rmgg....dKallplggkpllervldalraag.vdevvvvggd....eevlaalarlgvrvvededpgkgplaslaaalraaadadavlvlacDmPl 98 
                   Rm++     K l ++++ p+l +vl+++++++ +++vvv++ +    +++++++++ +v+v++ ++  +  l   +  +++  + d+++ +++D Pl
    EPA05352.1   9 RMNStrlyGKVLKKIDKNPVLYYVLKQINESKlIKKVVVATSEleidDAIEKYAKKMNVEVFRGSP--TDVLDRHYQCAKKY-SFDPIVRVTADNPL 102
                   5654445569999******************85799999999954444566666666888888874..67888888888887.8************* PP

                   --HHHHHHHHHCHHHHTSS CS
  NTP_transf_3  99 ltpelverllaaaaasgad 117
                    +p+++++ ++++++ + d
    EPA05352.1 103 NDPQIIDKAIEKMKSGKFD 121
                   ***********99865555 PP

>> PriA_3primeBD  3′ DNA-binding domain (3′BD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1   0.00021       1.2      24      82 ..       2      61 ..       1      72 [. 0.78
   2 ?   -1.6   0.0      0.43   2.6e+03      49      73 ..      85     108 ..      77     117 .. 0.70
   3 ?    0.6   0.1     0.086   5.1e+02      52      65 ..     210     223 ..     187     229 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00021
  PriA_3primeBD 24 iGsrVlVpfgkrklvGiVvalkeeseveeeklkpiee.vldeepllteellelaewlaey 82
                   iG++V+  +++ +l G V++  ++++v  + lk+i+e  l ++ ++  + le+ + +++y
     EPA05352.1  2 IGCIVQARMNSTRLYGKVLKKIDKNPVLYYVLKQINEsKLIKKVVVATSELEIDDAIEKY 61
                   7**********************************7513445666666666666666665 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.43
  PriA_3primeBD  49 eveeeklkpieevldeepllteell 73 
                    + ++++  pi +v  ++pl +++++
     EPA05352.1  85 A-KKYSFDPIVRVTADNPLNDPQII 108
                    4.56777888888888888887776 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.086
  PriA_3primeBD  52 eeklkpieevldee 65 
                    +  lk+i++++d+e
     EPA05352.1 210 PILLKDILKLIDKE 223
                    33455555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       850  (0.0474092); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1502.49
//
Query:       EPA05353.1  [L=37]
Description: hypothetical protein BG20_I0173 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.28s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 260.99
//
Query:       EPA05354.1  [L=342]
Description: DegT/DnrJ/EryC1/StrS aminotransferase family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-87  293.0   0.0      4e-87  292.9   0.0    1.0  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    7.6e-05   21.8   0.0    0.00014   21.0   0.0    1.3  1  Aminotran_5      Aminotransferase class-V
    0.00081   18.7   0.0     0.0013   17.9   0.0    1.3  1  Aminotran_1_2    Aminotransferase class I and II
  ------ inclusion threshold ------
      0.066   13.0   0.2       0.21   11.4   0.2    1.8  1  DUF1439          Protein of unknown function (DUF1439)


Domain annotation for each model (and alignments):
>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  292.9   0.0   8.8e-91     4e-87      14     359 ..       1     334 [.       1     336 [. 0.94

  Alignments for each domain:
  == domain 1  score: 292.9 bits;  conditional E-value: 8.8e-91
                      HTSS-SSSSHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GGGCGGG CS
  DegT_DnrJ_EryC1  14 lksgwltsgpeveeFEkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdtynidpaaieaa 107
                      ++s+w+++gp +++FE ++++yl+++ ++ v++Gt+A++ aL a + + gd V+vp +tF+at +a   lgak++ +Dvdp+t+ni+p+++e+ 
       EPA05354.1   1 MESDWYSQGPLTKKFEDDLSTYLNSNVSV-VNNGTSAILCALLANNFKSGDRVLVPDFTFFATLSAPKFLGAKVMTADVDPTTFNISPEQVEEI 93 
                      689********************998776.9*************************************************************** PP

                      --TTE.EEEEEB-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT-EETTEECCCSSSEEEEE-BTTSSS-SSS-EEEEESTHHHHHHHHHHHBT CS
  DegT_DnrJ_EryC1 108 itert.kaIlpVhlyGqvadmdalkaiaakhglkvieDaAhAlGatykgkkvGalgdaavfSFyptKnlttGeGGavvtndeelaekarvlrnh 200
                      + ++  k +++V+++G + d+da +++a+k++  +ieDaA+AlG++yk+kkvG++  +++fSF+ +K++tt eGG v +nde++ +++++lr h
       EPA05354.1  94 VKSNDiKFVIVVDIAGLPIDIDAFEDLAKKYKFTLIEDAAQALGSEYKNKKVGSFNHTTTFSFHIAKQITTIEGGCVSSNDENISKRIKQLRDH 187
                      **9988**************************************************************************************** PP

                      TCECCTCSSCECCSS---B-B-BHHHHHHHHHHHCTHHHHHHHHHHHHHHHHHHHHTCCCCEESCGGTTSSSEEESCEEEEEHCCHHHCHHHHH CS
  DegT_DnrJ_EryC1 201 GlkrkaekryvgevelGynyrlteiqAAiglaqLerldelvarRreiaelykeeLaelegtaelttpketkkhawhlyavlveeeaevkrdelv 294
                      G+   ++k+y +++ +G+n+r+t++q++ig++qL++++  + +R++i + yk+++++++ + + +t     kh+ + +  + +++    rd+  
       EPA05354.1 188 GRI--DTKNYIHNI-IGSNFRITDLQSSIGIEQLKKIEIYILQRNAISKKYKDKIKNVGFQ-QNPTYSI--KHSNMMFFTVYPNKT--IRDKNF 273
                      *88..79*******.*******************************************953.3333333..356666777777662..59999* PP

                      HHHHHCCEE-B-SGSCHGGGSCCHHHHHHCCCHC-HHHHHHHHHEEEEEGGTTGSHHHHHHHHHH CS
  DegT_DnrJ_EryC1 295 ealkeegigtrvhypnplhrqpvyaerkeeasgdlpnaerlaervlsLplypelteedvdrVvea 359
                      + l+e+g+++++  p plh+qp+  e +++ +   +n+  +++ +l Lp+  ++t+e++d+V+e+
       EPA05354.1 274 KILHENGVDAKLPWP-PLHSQPANSELNKNIH---ENTRIISDTALMLPIFNGMTDEEADYVIEC 334
                      **************5.***********87765...9**************************986 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   3.1e-08   0.00014      61     182 ..      24     138 ..      12     145 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3.1e-08
                  GGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTS.CBEGGGHHHH--.TTEEEEEEESBETTTTEB- CS
  Aminotran_5  61 eeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeeg.eldldeleklln.ektklvaithvsnvtGtiq 156
                  ++++ ++ ++t+ai +++l+   ++k gd+++v +    a+l     + k+ gakv  + +d++  ++ ++++e+ ++ +++k v++     + G   
   EPA05354.1  24 NSNVSVVNNGTSAILCALLAN--NFKSGDRVLVPDFTFFATL----SAPKFLGAKVMTADVDPTTfNISPEQVEEIVKsNDIKFVIVV---DIAGLPI 112
                  567888999998887776555..59*****************....8888999********98653899*******975888888876...579**** PP

                  -HHHHHHHHHHTT-EEEEE-TTTTTT CS
  Aminotran_5 157 pveeigklakkkgalvlvDaaqavgh 182
                  +++++ +lakk++  ++ Daaqa+g+
   EPA05354.1 113 DIDAFEDLAKKYKFTLIEDAAQALGS 138
                  ***********************997 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0     3e-07    0.0013      45     188 ..      11     132 ..       4     149 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3e-07
                    HHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHT CS
  Aminotran_1_2  45 glpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealk 140
                    + +++e +l  +l+         +   vv +G++a++ al +   +  gd++lvpd t+     + +  g++v++    ++ +f++  e++ee +k
     EPA05354.1  11 LTKKFEDDLSTYLN--------SN-VSVVNNGTSAILCALLANN-FKSGDRVLVPDFTFFATLSAPKFLGAKVMTAD-VDPTTFNISPEQVEEIVK 95 
                    56788888888888........33.3367788888888888777.9*******************************.55*************999 PP

                    THHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEE CS
  Aminotran_1_2 141 eapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDe 188
                    +   +++  k+++v  +    G  ++ +  e+l   akky++ l+ D 
     EPA05354.1  96 S---NDI--KFVIVVDI---AGLPIDIDAFEDL---AKKYKFTLIEDA 132
                    9...455..99998766...4888888888888...888888877776 PP

>> DUF1439  Protein of unknown function (DUF1439)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   4.8e-05      0.21       8      61 ..     182     235 ..     175     257 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.8e-05
     DUF1439   8 kyLakkleiekkvglpgllkadvkledlqvqlgreerdkvalsarakvklsall 61 
                 k+L ++ +i +k  +++++  +++++dlq+++g e+ +k+++ +  + ++s + 
  EPA05354.1 182 KQLRDHGRIDTKNYIHNIIGSNFRITDLQSSIGIEQLKKIEIYILQRNAISKKY 235
                 579999************************************998888887633 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.54
# Mc/sec: 1910.06
//
Query:       EPA05355.1  [L=141]
Description: MaoC-like protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-21   75.2   0.0    3.8e-21   74.9   0.0    1.1  1  MaoC_dehydratas  MaoC like domain
    5.1e-10   39.6   0.0    1.1e-09   38.5   0.0    1.5  1  MaoC_dehydrat_N  N-terminal half of MaoC dehydratase
  ------ inclusion threshold ------
      0.056   13.8   0.0      0.084   13.2   0.0    1.3  1  4HBT             Thioesterase superfamily
      0.063   12.3   0.0      0.094   11.7   0.0    1.2  1  Sipho_Gp37       Siphovirus ReqiPepy6 Gp37-like protein


Domain annotation for each model (and alignments):
>> MaoC_dehydratas  MaoC like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.9   0.0   8.4e-25   3.8e-21      11     117 ..      14     119 ..       7     125 .. 0.90

  Alignments for each domain:
  == domain 1  score: 74.9 bits;  conditional E-value: 8.4e-25
                      EEEEEEEEEHHHHHHHHHHHT---GGGT-HHHHHHTTTSSSB--HHHHHHHHHHHHHHHHSTTEGGGEEEEEEEE-S--BTTCEEEEEEEEEEE CS
  MaoC_dehydratas  11 etekeitvteadialyalvsgDlnpiHvdpefAkkagfggpIahGmltlaivaklveeelgdnvvarvgeikvrFtkpVlpgdtlkvelevvgk 104
                      +t+ +i++ e+ ++ +a ++gD+n +H+d+e+A+k++fg++I hGml +++ ++lv   ++ ++ a + ++++ F++p ++gd ++ e +v +k
       EPA05355.1  14 KTKFTIKIEESIVNEFAKITGDYNSLHMDEEYAAKTKFGKRICHGMLLSSFFSRLVGMYIPGKN-ALYFSQTLNFQAPCFIGDIITIEGKVIEK 106
                      444589999***********************************************99999965.9999************************* PP

                      EEEEEEEEEEEEE CS
  MaoC_dehydratas 105 rdvrktkkvevtk 117
                       + +k+++ ++t 
       EPA05355.1 107 SQSTKIITIKTTA 119
                      **99998877765 PP

>> MaoC_dehydrat_N  N-terminal half of MaoC dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   0.0   2.5e-13   1.1e-09       8     130 ..      15     128 ..       9     130 .. 0.88

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 2.5e-13
  MaoC_dehydrat_N   8 epvkaevereavrefakavgetnpayldeeaaraagyrsliaPptflivlatkapellealgidlsrllhgeqefeyhepiraGDelttesria 101
                      ++ ++++e++ v+efak +g++n +++dee+a+++++++ i   ++l+ +  +       + i++++ l  +q++ +++p   GD +t+e ++ 
       EPA05355.1  15 TKFTIKIEESIVNEFAKITGDYNSLHMDEEYAAKTKFGKRICHGMLLSSFFSRL----VGMYIPGKNALYFSQTLNFQAPCFIGDIITIEGKVI 104
                      567899***************************999999998888877665544....6778****************************9976 PP

  MaoC_dehydrat_N 102 dvydkkgvGalefivvettvtnqrGepva 130
                      + ++     ++++i+ +tt  nq G+ ++
       EPA05355.1 105 EKSQ-----STKIITIKTTAHNQTGKCLV 128
                      5554.....79**************9776 PP

>> 4HBT  Thioesterase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.9e-05     0.084      31      63 ..      78     110 ..      55     127 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.9e-05
                 EEEEEEEEEESS-BBTTCEEEEEEEEEEEESSE CS
        4HBT  31 vvvvelsidflrpvrlgdeltvearvlrlgrts 63 
                 +   + +++f +p  +gd +t+e++v++ + ++
  EPA05355.1  78 ALYFSQTLNFQAPCFIGDIITIEGKVIEKSQST 110
                 55567799******************9865443 PP

>> Sipho_Gp37  Siphovirus ReqiPepy6 Gp37-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.1e-05     0.094     302     342 ..      82     122 ..      75     127 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.1e-05
  Sipho_Gp37 302 ggdlkyekdydlGDiVtveeekvgvtvddrItevtevyeeg 342
                 +++l++++ +++GDi+t+e +  + ++++ I++++++  ++
  EPA05355.1  82 SQTLNFQAPCFIGDIITIEGKVIEKSQSTKIITIKTTAHNQ 122
                 67899999**************************9998744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 953.06
//
Query:       EPA05356.1  [L=323]
Description: ATPase, AAA family, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.6e-60  201.8   0.0    2.1e-43  147.9   0.0    2.2  2  AAA              ATPase family associated with various cellul
    7.9e-13   48.0   0.0    1.8e-12   46.8   0.0    1.6  1  AAA_lid_3        AAA+ lid domain
      5e-08   33.5   0.1    2.8e-05   24.6   0.1    2.6  2  AAA_16           AAA ATPase domain
    2.2e-06   27.9   0.0    5.2e-06   26.7   0.0    1.6  1  AAA_2            AAA domain (Cdc48 subfamily)
    7.3e-05   22.8   0.2     0.0031   17.5   0.1    3.2  2  AAA_5            AAA domain (dynein-related subfamily)
    9.5e-05   22.7   0.1     0.0014   18.9   0.1    2.3  2  AAA_22           AAA domain
    0.00013   21.3   0.0    0.00024   20.4   0.0    1.4  1  TIP49            TIP49 P-loop domain
    0.00027   21.1   0.0    0.00052   20.2   0.0    1.6  1  AAA_33           AAA domain
      0.001   18.8   0.0     0.0034   17.1   0.0    1.9  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
     0.0023   17.7   0.1      0.013   15.2   0.0    2.1  2  Sigma54_activat  Sigma-54 interaction domain
     0.0075   16.0   0.0      0.013   15.2   0.0    1.3  1  IstB_IS21        IstB-like ATP binding protein
     0.0089   16.1   0.0      0.016   15.2   0.0    1.4  1  AAA_14           AAA domain
  ------ inclusion threshold ------
       0.01   15.9   0.3      0.029   14.4   0.1    1.7  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.018   14.9   0.1       0.28   11.1   0.2    2.2  2  NACHT            NACHT domain
      0.043   13.3   0.1      0.086   12.3   0.1    1.4  1  PhoH             PhoH-like protein
      0.046   14.1   0.0       0.09   13.2   0.0    1.6  1  RNA_helicase     RNA helicase
      0.046   13.2   0.0       0.12   11.8   0.0    1.7  1  AAA_7            P-loop containing dynein motor region
      0.047   13.5   0.1        1.3    8.9   0.0    2.2  2  Bac_DnaA         Bacterial dnaA  protein
      0.063   12.7   0.5       0.16   11.3   0.1    1.8  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.092   12.1   0.0       0.41    9.9   0.0    1.9  2  ATPase           KaiC
       0.11   12.8   0.0       0.22   11.7   0.0    1.6  1  AAA_28           AAA domain
       0.11   13.0   0.2       0.39   11.3   0.0    2.1  2  AAA_18           AAA domain
       0.13   11.8   1.0        1.3    8.6   0.9    2.3  1  AAA_25           AAA domain
       0.13   12.7   0.0       0.27   11.8   0.0    1.6  1  ABC_tran         ABC transporter
       0.14   12.0   0.0       0.37   10.6   0.0    1.6  2  CPT              Chloramphenicol phosphotransferase-like prot
       0.15   11.8   0.0       0.26   11.0   0.0    1.4  1  Cytidylate_kin   Cytidylate kinase
       0.17   11.6   0.0       0.37   10.5   0.0    1.6  1  AAA_24           AAA domain
       0.18   11.0   0.1       0.48    9.6   0.1    1.7  2  NB-ARC           NB-ARC domain


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.9   0.0   1.5e-16   9.9e-14      77     131 ..       4      58 ..       1      59 [. 0.92
   2 !  147.9   0.0   3.3e-46   2.1e-43       1     121 [.     202     321 ..     202     323 .] 0.97

  Alignments for each domain:
  == domain 1  score: 51.9 bits;  conditional E-value: 1.5e-16
                 CCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
         AAA  77 seseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                  + e+e+rvv+q+l+ +dg++ + +kvivi+atnrp+ +dpal+r gRfdr+iei+
  EPA05356.1   4 VTGEVERRVVSQMLSLMDGLEAR-GKVIVIAATNRPNAIDPALRRpGRFDREIEIK 58 
                 56789*****************6.77***************************986 PP

  == domain 2  score: 147.9 bits;  conditional E-value: 3.3e-46
                 EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH.TTCCCHHHHHHHHHHHHHHHHTTT CS
         AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr.sgseseeeervvnqLlteldgvkk 98 
                 +ll+Gp GtGKTllakava++++++f+++ g+ellsk+vgese+ ire+f++a++ + p+++f+DEid++a+ r  g+e+ ++ervv+qLlteldg+++
  EPA05356.1 202 ILLHGPSGTGKTLLAKAVATQSEANFVSVRGPELLSKWVGESERGIREIFRRARQAS-PCVVFFDEIDSIAPIRgAGGETAVTERVVSQLLTELDGMEN 299
                 69******************************************************9.****************9999********************* PP

                 SSSTEEEEEEESSGGGSTHHHHS CS
         AAA  99 keskvivigatnrpdkldpallr 121
                   + v+v++atnrpd++dpallr
  EPA05356.1 300 M-HGVVVLAATNRPDMIDPALLR 321
                 7.55*****************97 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   0.0   2.8e-15   1.8e-12       1      42 [.      81     122 ..      81     125 .. 0.96

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 2.8e-15
   AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeitmed 42 
                 dv+++++ + ++Gy+GADl+ lc+eAa+ +lrr ++e++me+
  EPA05356.1  81 DVNVEKISSVSHGYVGADLEYLCKEAAMKCLRRLLPELNMEE 122
                 9************************************99997 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.1   4.4e-08   2.8e-05      16      58 ..     191     230 ..     189     244 .. 0.81
   2 ?    6.3   0.0     0.018        12     123     147 ..     247     270 ..     242     306 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 4.4e-08
      AAA_16  16 lervrsgrpelvllsGesGvGKsslvrellralekdggiflrg 58 
                 ++++    p+ +ll+G+sG+GK+ l+++++++ e++   f++ 
  EPA05356.1 191 YDKLGHKMPRGILLHGPSGTGKTLLAKAVATQSEAN---FVSV 230
                 667777889*********************988887...4444 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.018
      AAA_16 123 lkrllallsrderplvlvlDdlqwa 147
                 ++++++++++ ++p v+++D+++ +
  EPA05356.1 247 IREIFRRARQ-ASPCVVFFDEIDSI 270
                 6788899999.999********965 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   8.2e-09   5.2e-06       6     105 ..     202     296 ..     199     302 .. 0.90

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 8.2e-09
                 EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG----.---------HHHHHHHHH CS
       AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpk.essgadvSregVqrdLLq 101
                 ill gp+g+Gkt+laka+a   ++    +++ +   ell     + + +++ g ++   +a +    +v++DEid i+p  +  g+    e V+  LL 
  EPA05356.1 202 ILLHGPSGTGKTLLAKAVATQSEA----NFVSVRGPELLS----KWVGESERGIREIFRRARQASpcVVFFDEIDSIAPIrGAGGETAVTERVVSQLLT 292
                 7999***************99985....************....99999999******999999999************97777777888999999988 PP

                 HHH- CS
       AAA_2 102 ileg 105
                  l+g
  EPA05356.1 293 ELDG 296
                 7776 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.74   4.8e+02     113     136 ..      25      47 ..       3      48 .. 0.72
   2 !   17.5   0.1   4.8e-06    0.0031       2     124 ..     202     313 ..     201     321 .. 0.68

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.74
                 ....-EEEEEESS--.-TT-TTHHHHT CS
       AAA_5 113 r...frviatanpldrslnelspalrs 136
                 +   + via++n+++     ++palr+
  EPA05356.1  25 ArgkVIVIAATNRPN----AIDPALRR 47 
                 134589999999999....89999986 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 4.8e-06
                 EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..- CS
       AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEveraesevlnsLlslleerrlllee 98 
                 +lL Gp+GtgK+ la+ +a   +++++ v +++      l+ ++    g+ ++   ++ r ar  +++++++DE++ + +   +   +   er ++   
  EPA05356.1 202 ILLHGPSGTGKTLLAKAVATQSEANFVSVRGPE------LLSKWV---GESERGIREIFRRARqaSPCVVFFDEIDSIAPIRGAGGETAVTERVVS-QL 290
                 89*****************99999999999987......667777...455555577777777799999999999988765555555555555555.33 PP

                 SSSEEE---......-EEEEEESS-- CS
       AAA_5  99 ggelvkaknddllerfrviatanpld 124
                 ++el + +n   +  + v+a++n++d
  EPA05356.1 291 LTELDGMEN---MHGVVVLAATNRPD 313
                 444444443...34466666666655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   2.2e-06    0.0014       8      42 ..     202     227 ..     197     253 .. 0.82
   2 ?    1.1   0.0      0.68   4.4e+02      83     106 ..     251     284 ..     240     310 .. 0.56

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.2e-06
      AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpev 42 
                 ++++G+sGtGKT+l++ ++ q          ++ +
  EPA05356.1 202 ILLHGPSGTGKTLLAKAVATQS---------EANF 227
                 89*****************997.........4444 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.68
      AAA_22  83 eqalraravielliiDEaqhlr...s........e 106
                  + +r+++ + ++  DE++ +             e
  EPA05356.1 251 FRRARQAS-PCVVFFDEIDSIApirGaggetavtE 284
                 33333333.589*******9976541344444442 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   3.8e-07   0.00024      47     106 ..     197     254 ..     193     257 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 3.8e-07
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXX CS
       TIP49  47 klaGravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkktev.ltqalrks 106
                 k+  r++Ll GpsgtGkt la a++ +  ++  fv++ g e+ s  v  +e  + + +r++
  EPA05356.1 197 KMP-RGILLHGPSGTGKTLLAKAVATQ--SEANFVSVRGPELLSKWVGESERgIREIFRRA 254
                 454.9*******************986..5789*************999996477888887 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   8.1e-07   0.00052       2      46 ..     202     248 ..     202     310 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 8.1e-07
      AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt 46 
                 +ll+G++G+GK+ la+ ++ +    +v ++ ++l+++ +g+ ++ ++
  EPA05356.1 202 ILLHGPSGTGKTLLAKAVATQSEanFVSVRGPELLSKWVGESERGIR 248
                 689****************9999889999999999988886655554 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   5.4e-06    0.0034      35      70 ..     201     236 ..     165     274 .. 0.77
   2 ?   -3.2   0.0       9.6   6.2e+03      20      38 ..     302     320 ..     291     321 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.4e-06
      RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgPvle 70 
                  +ll+Gp G Gkt lak +a++ ++++ +  gP l 
  EPA05356.1 201 GILLHGPSGTGKTLLAKAVATQSEANFVSVRGPELL 236
                 59******************************9873 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 9.6
      RuvB_N  20 kifieaakkreealdhvll 38 
                  +++ aa +r + +d  ll
  EPA05356.1 302 GVVVLAATNRPDMIDPALL 320
                 5788888888888887766 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0     2e-05     0.013      22      53 ..     199     227 ..     191     239 .. 0.83
   2 ?   -1.0   0.0         2   1.3e+03      90     106 ..     255     271 ..     251     311 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2e-05
                      SS-EEEECSTTSSHHHHHHHHHHHSTTTTS-E CS
  Sigma54_activat  22 dlsvlitGesGtGKellaraiheaskrkekpf 53 
                      +  +l++G sGtGK+lla+a+ ++s+   ++f
       EPA05356.1 199 PRGILLHGPSGTGKTLLAKAVATQSE---ANF 227
                      5679****************998876...444 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2
                      HHTTTSEEEEETGGGS- CS
  Sigma54_activat  90 ekadgGtlfLDeigelp 106
                      ++a+  ++f+Dei ++ 
       EPA05356.1 255 RQASPCVVFFDEIDSIA 271
                      57888899999999875 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0     2e-05     0.013      49      74 ..     201     226 ..     197     245 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2e-05
   IstB_IS21  49 nivllGpsGvGKshlaialgveavra 74 
                 +i+l GpsG+GK+ la a++++  ++
  EPA05356.1 201 GILLHGPSGTGKTLLAKAVATQSEAN 226
                 689****************9987655 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   2.6e-05     0.016       5      77 ..     202     271 ..     199     301 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.6e-05
      AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqevp 77 
                 +++ G+  +GKT l+k ++ ++     +++ +   +   k   ++e+ +++i++++++    ++f+DEi  + 
  EPA05356.1 202 ILLHGPSGTGKTLLAKAVATQSE---ANFVSVRGPELLSKWVGESERGIREIFRRARQASPCVVFFDEIDSIA 271
                 7899**************97777...6777777666666666666544555555444458899******9874 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       2.9   1.9e+03      82     103 ..     166     187 ..     159     199 .. 0.66
   2 ?   14.4   0.1   4.5e-05     0.029      13      49 ..     193     231 ..     185     236 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.9
                 HCTTCCCCSTSCEEEEETGGGG CS
        TsaE  82 elgleeyleeeavvlvEWpekl 103
                 e+g  e +++e   +vEWp k+
  EPA05356.1 166 EVGGLEDVKRELQEAVEWPMKY 187
                 5544444544456799**9885 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 4.5e-05
                 HHHHCHTEEEEEEESTTSSHHHHHHHHHHHTT--..--- CS
        TsaE  13 klakalgdvilLeGdLGaGKTtlvrglakalgve..evk 49 
                 kl++++ + ilL+G+ G+GKT l++++a + + +  +v+
  EPA05356.1 193 KLGHKMPRGILLHGPSGTGKTLLAKAVATQSEANfvSVR 231
                 555555557*******************99887655565 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   0.00044      0.28       3      23 ..     202     222 ..     200     228 .. 0.89
   2 ?    1.2   0.0      0.48   3.1e+02      58     112 ..     236     294 ..     229     316 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00044
                 EEEEC-TTTCHHHHHHHHHHH CS
       NACHT   3 vilqGeaGsGKTtLlqklala 23 
                 ++l+G++G GKT L++ +a++
  EPA05356.1 202 ILLHGPSGTGKTLLAKAVATQ 222
                 89**************99975 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.48
                 HCCCCTS--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH..............HHHH CS
       NACHT  58 lfsqlpepaapvsevwavllelperlLlilDglDelvtdlgq.....kekqpvrtlLsel 112
                 l +   e+++ ++e +  +++++   +  +D +D ++ + g+      +++ v +lL+el
  EPA05356.1 236 LSKWVGESERGIRE-IFRRARQASPCVVFFDEIDSIAPIRGAggetaVTERVVSQLLTEL 294
                 55555566666666.666778888889999999999999999754444444444444444 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00013     0.086      24      42 ..     204     222 ..     195     230 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                 EE--TTSSTTHHHHHHHHH CS
        PhoH  24 aiGpaGtGKtylavalave 42 
                   Gp+GtGKt+la a+a +
  EPA05356.1 204 LHGPSGTGKTLLAKAVATQ 222
                 68*************9987 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00014      0.09       1      26 [.     202     227 ..     202     269 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00014
  RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl 26 
                   i+l+Gpsg+GK++lak +a++ + ++
    EPA05356.1 202 ILLHGPSGTGKTLLAKAVATQSEANF 227
                   689**************888766554 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00019      0.12      34      58 ..     200     224 ..     190     232 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00019
       AAA_7  34 kpvllvGptGtGKtviikdllkkld 58 
                 + +ll Gp+GtGKt+++k + ++ +
  EPA05356.1 200 RGILLHGPSGTGKTLLAKAVATQSE 224
                 679**************99877766 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.21   1.3e+02     118     177 ..      15      71 ..       8      97 .. 0.73
   2 ?    8.9   0.0     0.002       1.3      37      65 ..     202     230 ..     194     238 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.21
                 HHHHHHHHHHTTT-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHHHHH CS
    Bac_DnaA 118 elfhtfnalleegkqvvlssDrsPkeleeledrlrsrfeaGlvvdieppdletrlailkk 177
                 +++ +++ l   gk +v+++   P++++    r   rf++   ++i+ pd++ r +il  
  EPA05356.1  15 QMLSLMDGLEARGKVIVIAATNRPNAIDPAL-RRPGRFDRE--IEIKVPDKKGRKDILAI 71 
                 5667788889999***********9987654.335788775..66777899999888864 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.002
                 EEEE-SSSSSHHHHHHHHHHHHHHHSSSS CS
    Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapel 65 
                 ++++g++G Gkt L ka++ + ++n+ + 
  EPA05356.1 202 ILLHGPSGTGKTLLAKAVATQSEANFVSV 230
                 79*****************9998887665 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       4.7     3e+03      39      54 ..     108     123 ..     104     148 .. 0.79
   2 ?   11.3   0.1   0.00025      0.16      25      43 ..     202     220 ..     196     225 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 4.7
  Mg_chelatase  39 akrlpsllpplseeea 54 
                    k+l  llp+l++ee 
    EPA05356.1 108 MKCLRRLLPELNMEEE 123
                   5789999999998764 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00025
  Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                   +ll Gp+G+GKt+lak+++
    EPA05356.1 202 ILLHGPSGTGKTLLAKAVA 220
                   89**************976 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00064      0.41      15      42 ..     195     222 ..     185     230 .. 0.80
   2 ?   -1.4   0.0       1.9   1.2e+03     125     154 ..     267     297 ..     248     308 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00064
      ATPase  15 GipegrvvlitGepGtGKtifalqFlik 42 
                 G  + r +l+ G +GtGKt++a+  + +
  EPA05356.1 195 GHKMPRGILLHGPSGTGKTLLAKAVATQ 222
                 55566789*************9876655 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.9
      ATPase 125 iDsitgl.ayeekeavaReilrqlvrvlkkl 154
                 iDsi+++     ++av+ + + ql+++l ++
  EPA05356.1 267 IDSIAPIrGAGGETAVTERVVSQLLTELDGM 297
                 8999999777778888888999999988665 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00035      0.22       2      32 ..     202     237 ..     201     266 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00035
      AAA_28   2 ivitGgestGKTtlleaLaar...gypvv..pEaar 32 
                 i + G+++tGKT l++a a +   +++ v  pE   
  EPA05356.1 202 ILLHGPSGTGKTLLAKAVATQseaNFVSVrgPELLS 237
                 7899***************66545554444666554 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       6.3   4.1e+03      15      60 ..     103     143 ..     100     152 .. 0.70
   2 ?   11.3   0.0    0.0006      0.39       1      21 [.     202     222 ..     202     306 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 6.3
      AAA_18  15 akeLskrlgfgvnlrdvakenglllevdpealdeskrldedkldkl 60 
                 +ke + ++     lr +++e ++++e  p+++ ++++++ +  +k+
  EPA05356.1 103 CKEAAMKC-----LRRLLPELNMEEEKLPPETLDKLIVNNEDFQKA 143
                 66666665.....788888999999988886666666666555444 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.0006
      AAA_18   1 IlltGtpGvGKttlakeLskr 21 
                 Ill G++G+GKt lak+++  
  EPA05356.1 202 ILLHGPSGTGKTLLAKAVATQ 222
                 89***************9654 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.9     0.002       1.3      36      56 ..     202     222 ..     196     306 .. 0.49

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.002
      AAA_25  36 allaGapgtGKttlaldlala 56 
                 +ll G++gtGKt la  +a  
  EPA05356.1 202 ILLHGPSGTGKTLLAKAVATQ 222
                 689*********988655432 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00042      0.27      14      37 ..     202     225 ..     193     299 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00042
                 EEEEESTTSSHHHHHHHHTTSS-- CS
                 xxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  14 vaivGenGaGKStLlkllagllkp 37 
                 + + G++G+GK+ L+k++a +++ 
  EPA05356.1 202 ILLHGPSGTGKTLLAKAVATQSEA 225
                 5789**************998764 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       9.8   6.2e+03      92     109 ..     101     118 ..      95     120 .. 0.71
   2 ?   10.6   0.0   0.00058      0.37       4      32 ..     202     230 ..     200     246 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 9.8
                 -TTTHHHHHHHHHHHTTS CS
         CPT  92 ilekewlvdllrrllsgl 109
                 +l ke+++++lrrll +l
  EPA05356.1 101 YLCKEAAMKCLRRLLPEL 118
                 555667899999999765 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00058
                 EEEEE-TTSSHHHHHHHHHHHSSS-EEEE CS
         CPT   4 ilLnGgsssGKsslaralqevldepwlhl 32 
                 ilL+G s +GK+ la+a+ +++++ ++ +
  EPA05356.1 202 ILLHGPSGTGKTLLAKAVATQSEANFVSV 230
                 9**********************999876 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00041      0.26       2      27 ..     203     228 ..     202     231 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00041
                     EEE-STTSSHHHHHHHHHHHHT-EEE CS
  Cytidylate_kin   2 aiDGPagsGKssvaralaeklglkyl 27 
                      + GP+g+GK  +a+a+a++ +++++
      EPA05356.1 203 LLHGPSGTGKTLLAKAVATQSEANFV 228
                     578*****************999887 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00058      0.37       3      22 ..     200     219 ..     198     239 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00058
      AAA_24   3 lkiliyGpsgiGKTtlakel 22 
                 + il+ Gpsg+GKT lak  
  EPA05356.1 200 RGILLHGPSGTGKTLLAKAV 219
                 5699*************976 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       7.7   4.9e+03      51     145 ..      51      80 ..      48      93 .. 0.53
   2 ?    9.6   0.1   0.00075      0.48      23      44 ..     202     223 ..     189     232 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 7.7
                 BTEEEEEEEESXXHHHHHHHXXHHHHHCCCTTSSSS-STTSHHHHHHHHCCCTTEEEEEEEE-SHHHH.....HHHHCHTTSEEEEEESBCCCCC CS
      NB-ARC  51 FdsvawvvvsktdkseeiletilkeLslseddleekeeveslkrklvrlLltkrfllvlDDVweeedwdkigvvlparenrlrvllTTRdeevan 145
                 Fd+ + + v ++   ++il    +++ ls                                                                 +
  EPA05356.1  51 FDREIEIKVPDKKGRKDILAIHSRNMPLS-----------------------------------------------------------------D 80 
                 55555555555555555555444444333.................................................................3 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00075
                 EEEEESTTSSHHHHHHHHCCSH CS
      NB-ARC  23 valvGmgGvGKttlakqilnks 44 
                 + l+G  G GKt lak +  +s
  EPA05356.1 202 ILLHGPSGTGKTLLAKAVATQS 223
                 789*************998873 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); expected 17.9 (0.001)
Passed Fwd filter:                        28  (0.00156172); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              28  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 1952.08
//
Query:       EPA05357.1  [L=55]
Description: hypothetical protein BG20_I1912 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       814  (0.0454013); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 375.52
//
Query:       EPA05358.1  [L=213]
Description: DnaJ, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-33  116.2   1.7    1.9e-33  115.6   1.7    1.2  1  DnaJ_C         DnaJ C terminal domain
    1.8e-13   50.7  19.6    3.6e-13   49.7  19.6    1.5  1  DnaJ_CXXCXGXG  DnaJ central domain
  ------ inclusion threshold ------
       0.39   10.7  20.6        2.3    8.3   6.0    3.2  4  Anti-TRAP      Tryptophan RNA-binding attenuator protein inhi


Domain annotation for each model (and alignments):
>> DnaJ_C  DnaJ C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.6   1.7   3.2e-37   1.9e-33      27     148 .]      59     194 ..      17     194 .. 0.86

  Alignments for each domain:
  == domain 1  score: 115.6 bits;  conditional E-value: 3.2e-37
                 .................TEEEEEE-TT--TT-EEEETT-SSSS...S---EEEEEEE---SS-EEETTEEEEEEEEEHHHHHHTEEEEEE-SS-EEEEE CS
                 x............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
      DnaJ_C  27 i............kkekktlevkipaGikdgqkirlegeGdeeg.gepGDlivtikvkphpvFkrkgndlyveveislaeallGgklevptldgkvklk 112
                 i            kk +k+++++ip G+++g+  ++++eG+e + g +GDliv+i+v+php+Fkr+g d++++ ++s+++a+lG+++ vptldg+ k+k
  EPA05358.1  59 IqtpcseckgngkKKGTKKISFDIPSGVETGD-YTVPEEGNEMPgGINGDLIVRIRVQPHPKFKRDGMDIFYDQDVSMVDAALGREIIVPTLDGTEKIK 156
                 0555555556554777889************7.899*****8888****************************************************** PP

                 E...--TT-EEEETT-S-EET...TEE--EEEEEEEE-- CS
                 x...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
      DnaJ_C 113 i...tqpgevlrikgkGmpklkkpgkrGdlyvevkvefP 148
                 +   +qp++++++kgkG+p+++ +++rGd++v++ v++P
  EPA05358.1 157 VesgSQPNTIIKLKGKGVPRMN-SKNRGDQFVRIVVTIP 194
                 *********************7.**************99 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.7  19.6     6e-17   3.6e-13       1      67 []       6      70 ..       6      70 .. 0.86

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 6e-17
  DnaJ_CXXCXGXG  1 CkkCkGsgakkgk.kktCktCkGsGvvreeqkt.lgpfvqqsqstCpeCeGtGkvikekdkCkkCkGkg 67
                   C+ C+Gsg+k+g+ k+tC+tC+G+G+vr++++  +++fv  + ++C++C+G+G++i  +++C++CkG+g
     EPA05358.1  6 CEICHGSGCKPGTnKNTCSTCNGQGQVRKSRSMgFASFV--TVEPCSACRGEGSII--QTPCSECKGNG 70
                   9*********9776999********98887763355555..789************..779******96 PP

>> Anti-TRAP  Tryptophan RNA-binding attenuator protein inhibitory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   6.6    0.0012       6.9      10      42 ..       3      32 ..       1      45 [. 0.86
   2 ?    6.8   4.1    0.0011       6.7      11      42 ..      21      58 ..      19      60 .. 0.76
   3 ?    8.3   6.0   0.00038       2.3      11      40 ..      47      70 ..      45      80 .. 0.90
   4 ?    8.0   0.8   0.00047       2.8      10      34 ..      60      83 ..      59      87 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0012
                EEE-TTTTTTSEETTE......E-TTTTTSSEE CS
   Anti-TRAP 10 EtkCdaCngsGkiepeeprasleCPkCsGkgli 42
                E  C+ C+gsG  +++       C  C+G+g +
  EPA05358.1  3 EILCEICHGSGCKPGT---NKNTCSTCNGQGQV 32
                778*************...5558******9976 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0011
                EE-TTTTTTSEETTE............E-TTTTTSSEE CS
   Anti-TRAP 11 tkCdaCngsGkiepe......eprasleCPkCsGkgli 42
                ++C +Cng G++            +  +C +C G+g i
  EPA05358.1 21 NTCSTCNGQGQVRKSrsmgfaSFVTVEPCSACRGEGSI 58
                58*********98875555444444569******9976 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.00038
                EE-TTTTTTSEETTE......E-TTTTTSS CS
   Anti-TRAP 11 tkCdaCngsGkiepeeprasleCPkCsGkg 40
                ++C aC g G i  +      +C +C+G+g
  EPA05358.1 47 EPCSACRGEGSIIQT------PCSECKGNG 70
                69*************......*******98 PP

  == domain 4  score: 8.0 bits;  conditional E-value: 0.00047
                EEE-TTTTTTSEETTE......E-T CS
   Anti-TRAP 10 EtkCdaCngsGkiepeeprasleCP 34
                 t+C +C+g Gk +++ ++ s++ P
  EPA05358.1 60 QTPCSECKGNGKKKGT-KKISFDIP 83
                589**********999.66666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1549.16
//
Query:       EPA05359.1  [L=635]
Description: glutamyl-tRNA(Gln) amidotransferase, subunit E [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.2e-61  207.1   0.1    5.8e-61  206.3   0.1    1.4  1  GatB_N     GatB/GatE catalytic domain
    4.9e-18   65.4   9.2    4.9e-18   65.4   9.2    2.0  2  GatB_Yqey  GatB domain
    4.4e-09   36.5   1.3    7.3e-09   35.7   0.1    2.1  2  GAD        GAD domain
  ------ inclusion threshold ------
        0.1   12.8   1.8       0.34   11.1   1.2    2.3  2  RFC1       Replication factor RFC1 C terminal domain
       0.17   12.0  10.2      0.029   14.5   3.3    2.5  2  p25-alpha  p25-alpha


Domain annotation for each model (and alignments):
>> GatB_N  GatB/GatE catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  206.3   0.1   1.6e-64   5.8e-61       2     270 ..      12     445 ..      11     448 .. 0.96

  Alignments for each domain:
  == domain 1  score: 206.3 bits;  conditional E-value: 1.6e-64
                 EEEEEEEEEB--SB-SSSSSBSSSSCE..........STTSS--TTTTTS...........................TT..--.EEHHHHHHHHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxxxx...........................xxxxxx.xxxxxxxxxxxxxxx RF
      GatB_N   2 viGlEiHaqlktksKlFssasteeege..........epnsevsevdlal...........................PGtlPv.lnkeavelaikaala 62 
                 ++GlEiH+ql+t++KlF++++  e++e          + +se++e+d a+                           P   P+ l+ +a +l++ ++ a
  EPA05359.1  12 KVGLEIHQQLSTNKKLFCNCRPFESDEytikfqrrlrAVKSELGEYDPAAlferskfktmmyyanqessclveqdeeP---PHqLDGNAKNLVLIISSA 107
                 89******************977544466777777755899999999999************************9998...999*************** PP

                 TTEEE-SEE-EEEEE-TCTTCTTSEEEEESSS.SE.EEEEEEE.TEEEEEEEEEEEE---EEEEEETTEEEEETTSTT-EEEEEEE-STB-SHHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
      GatB_N  63 lnceiaeeskfdRKnyfypdlpkgyQitqkeepla.keGslel.ekkvrierihlEeDaaksvheekeeslvdlnRaGvpLiEivtepdlrspeearav 159
                 l+++i +e++ +RK+++++++++g+Q+t+    l+ ++G++e+  +k+++++i+lEeDaa+ + ++ +   ++l+R+GvpLiEi+ ep   ++++++++
  EPA05359.1 108 LKSNIFSEIYPMRKTVIDGSNTTGFQRTM----LVsQGGYIEVdGEKIGVQSICLEEDAARLLGDKGDIREYSLDRLGVPLIEIALEPVEGDSKKIKKI 202
                 *****************************....555999***97789**************************************************** PP

                 HHHHHHHHHHHTSB--SGGGTTEEEEEEEEECTSETTSSS.--EEEEEE-SHHHHHHHHHHHHHHHHHHH............................. CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................. RF
      GatB_N 160 veklrellralgvsdgnmeeGslRcDvNvSvreeekgeeegtrvEiKnlnslksiekaieyeierqiell............................. 229
                 + +l++llr+++++++++  Gs+R+DvNvS+r++      g  vE+K++++l+++ek++e+e++rq  l+                             
  EPA05359.1 203 ALSLGRLLRSTKKVTRGI--GSIRQDVNVSIRDG------GGVVEVKGVQQLDQLEKVVEFEAKRQHGLVkiaeklqnssfdkisretdifditndfki 293
                 ******************..************66......789******************************************************** PP

                 ................................................................................................... CS
                 ................................................................................................... RF
      GatB_N 230 ................................................................................................... 229
                                                                                                                    
  EPA05359.1 294 cqskiiqkaikdesiikairirnfagmfgysphegirlgkeigqlvkfygiggvfhsdelpnygieesdvvivkkiletnendafliiaaplekidfai 392
                 *************************************************************************************************** PP

                 ...............-EEEEEETTTTEEEEECC----...-EEE-TTS--EE--HH CS
                 ...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
      GatB_N 230 ...............qeTrkfdedkgetvslRskeeaedYryfpepdlppleisee 270
                                 eTr ++++ get+ lR+++ a   r++pe+d+pp+ ++++
  EPA05359.1 393 esiinrisqakngvpAETRLATQT-GETTFLRPRPGA--SRMYPETDIPPIIVTNK 445
                 *********************999.**********88..6***********99986 PP

>> GatB_Yqey  GatB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.2       2.9     1e+04      65     101 ..     365     399 ..     363     405 .. 0.59
   2 !   65.4   9.2   1.4e-21   4.9e-18       2     148 .]     487     628 ..     486     628 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 2.9
                 HHHHHHHHTXXHHHHHHHCTXXXXXXSSXHHHHHHHH CS
   GatB_Yqey  65 vleelleegkspeeiieekgLkqisdeeeleklveev 101
                 +++++le++++ + +i    L++i    ++e++++ +
  EPA05359.1 365 IVKKILETNENDAFLIIAAPLEKID--FAIESIINRI 399
                 5667776655555555555577773..4777777665 PP

  == domain 2  score: 65.4 bits;  conditional E-value: 1.4e-21
                 HHHHHHHHSS.HHHHHHHHHTCHHHHHHHHTXXTTCSSTTHHHHHHHHHHHHTTSSGHHHHHHHHHHHHHH.TXXHHHHHHHCTXXXXXXSSXHHHHHH CS
   GatB_Yqey   2 ffeevvkegadaklaanwllnellgelnkegleieelkltpeqlaellkliaegkIskkiakevleellee.gkspeeiieekgLkqisdeeeleklve 99 
                  fe+++++++  ++ ++ +l   +++l+++gl+ +   l+ e++ + +++++++kI+k++++ ++e ++ + +k++e++i+   ++ +s  ee ek++e
  EPA05359.1 487 IFEKICEKTSTTPTFVASILCSSITSLERNGLNSQL--LKNEEISKTFEFLEDKKITKESIEIIFENVMSGkSKTIEQAIKNTSIETLSK-EEFEKIIE 582
                 7********9988888888888999*****998888..9******************************999****************98.******** PP

                 HHHHTXHHHHHHHTTXXTTSTHHHHHHHHHTTSSXSXHHHHHHHHHHHS CS
   GatB_Yqey 100 eviaenpkavedyksgkekalkflvGqvMkktkGkadpklvnellkekL 148
                  ++++n    e ++++ke+++  l+G  Mk+++Gk+ +++vn+ l ek+
  EPA05359.1 583 SIVKNN---KEIIQNQKERSVSPLMGIAMKELRGKVSGEMVNNTLLEKI 628
                 ******...778889999***************************9986 PP

>> GAD  GAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.1     2e-12   7.3e-09       1      90 [.     299     387 ..     299     392 .. 0.95
   2 ?   -3.3   0.1       3.2   1.1e+04      61      75 ..     572     586 ..     560     593 .. 0.64

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 2e-12
                 HHHHHHSTEEEEEEEETTG-TTTSHHHHHHHHHHHHHTTHSHCEEEEESSGGEETTTCCC.S-HHHHHHHHHHCT--TTEEEEEEEEEHHH CS
         GAD   1 fsealksggsvkalrvpggaaklsrkeideleefakelgakglawikvegegltgpiakf.lteeevkklleavgaeegDillfvAdkkkt 90 
                 +++a+k+ +++ka+r+++ +a++ +    e+ +++ke g   +++ +++g +++++++ + + e  v  +++ ++++e+D++l++A + ++
  EPA05359.1 299 IQKAIKDESIIKAIRIRN-FAGMFGYSPHEGIRLGKEIGQLVKFY-GIGGVFHSDELPNYgIEESDVVIVKKILETNENDAFLIIAAPLEK 387
                 6899**************.8*************************.****************************************98665 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.2
                 S-HHHHHHHHHHCT- CS
         GAD  61 lteeevkklleavga 75 
                 l++ee++k++e +  
  EPA05359.1 572 LSKEEFEKIIESIVK 586
                 567777777776544 PP

>> RFC1  Replication factor RFC1 C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.2   9.5e-05      0.34      85     153 ..     510     579 ..     461     583 .. 0.68
   2 ?    3.9   0.1     0.015        54      96     130 ..     552     586 ..     546     600 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.5e-05
                 THHHHHH.HHS---------HHHHHHTTT--SHHHHHHHHHH-X....XXXXXXXXXXX..XXXXXXXXXXXX CS
        RFC1  85 lpllkkk.lvkpLkeegkdgveevielmdeysLtkedvdslvelslv.kgekkkedplk..kidtkvKaaftr 153
                 ++ l +  l ++L +  +++++++ e++++ ++tke ++ + e ++  k  k+ e+ +k  +i+t  K +f +
  EPA05359.1 510 ITSLERNgLNSQLLK--NEEISKTFEFLEDKKITKESIEIIFENVMSgKS-KTIEQAIKntSIETLSKEEFEK 579
                 333333335566777..678***********************9887433.3333333333777777777765 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.015
                 --------HHHHHHTTT--SHHHHHHHHHH-X... CS
        RFC1  96 LkeegkdgveevielmdeysLtkedvdslvelslv 130
                  ++ +++ +e++i+  +   L+ke+++++ e  ++
  EPA05359.1 552 VMSGKSKTIEQAIKNTSIETLSKEEFEKIIESIVK 586
                 45544556***********************9766 PP

>> p25-alpha  p25-alpha
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.6      0.13   4.8e+02      17      51 ..     267     303 ..     254     320 .. 0.67
   2 ?   14.5   3.3   8.2e-06     0.029      35      95 ..     535     595 ..     518     615 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.13
   p25-alpha  17 gkemdnknfsKlckDckiid..kkvtstdvDiiFsKv 51 
                 +++++n+ f+K+ ++ +i+d    ++  +  ii + +
  EPA05359.1 267 AEKLQNSSFDKISRETDIFDitNDFKICQSKIIQKAI 303
                 5678899999999999999953344444444444444 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 8.2e-06
   p25-alpha  35 id.kkvtstdvDiiFsKvkaksarkitfeqfkealeelaekkfkkkkkeeeleliekliegk 95 
                 ++ kk+t+++++iiF+ v++ ++++i+ +  ++ +e l +++f+k  +   + + +++i+++
  EPA05359.1 535 LEdKKITKESIEIIFENVMSGKSKTIEQAIKNTSIETLSKEEFEKIIESIVK-NNKEIIQNQ 595
                 555****************************************666555555.444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (635 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1485  (0.0828267); expected 358.6 (0.02)
Passed bias filter:                      598  (0.0333538); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.73u 0.31s 00:00:01.04 Elapsed: 00:00:00.48
# Mc/sec: 3982.38
//
Query:       EPA05360.1  [L=120]
Description: hypothetical protein BG20_I1908, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.9e-10   39.8   0.2    6.6e-10   38.6   0.2    1.6  1  AAA_lid_3  AAA+ lid domain


Domain annotation for each model (and alignments):
>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6   0.2   3.7e-14   6.6e-10       2      45 .]      39      97 ..      38      97 .. 0.87

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 3.7e-14
   AAA_lid_3  2 vdlkeLAerTeGySGADlaalcreAallAlrr..............gike.itmedfee 45
                vd++++Ae+T+G SGAD aa+ + A+ l + +              ++++ +tm++fe+
  EPA05360.1 39 VDIDKIAELTDGLSGADTAAIANTAVSLVIHEfldahpdvkdieksSTDAkVTMKHFEA 97
                9*****************************998888888887776556645******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       956  (0.0533214); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 716.35
//
Query:       EPA05361.1  [L=178]
Description: hypothetical protein BG20_I1913 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-13   50.7   1.7    2.4e-13   50.4   1.7    1.1  1  NT5C      5' nucleotidase, deoxy (Pyrimidine), cytosolic type


Domain annotation for each model (and alignments):
>> NT5C  5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.4   1.7   1.3e-17   2.4e-13       4     165 ..       3     167 ..       1     176 [. 0.74

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 1.3e-17
        NT5C   4 vlvDlDgvladlygkmlevankrfeatllpeevsswd.leefvkPeqreslyrfltepgl.FadlepipgarevL....eeladegrlvvitaallqfy 96 
                 + +D+Dgvlad+++ +l ++n++  ++ +++++++wd +++f     + + + f+ e  + ++d ++ip + + L    ++l++ g++ ++ta+ l   
  EPA05361.1   3 IALDVDGVLADVIESWL-IYNNKIRSNISKNDITNWDfWKKF-----KINRFDFYEELTFcWKDWNSIPPTENNLsvitQNLSNLGQVDIVTARELS-T 94 
                 789*************8.8999************87745556.....223355666666545778888777776622234678889999*****999.4 PP

        NT5C  97 davkekveWldehlplipyrnlvlvke...kdlvrgDvlidDapknleklrgrs...ilfdsptnrhied..elRaa 165
                 d+     +Wl+ h   i y+n v v +   k  +  Dv+idD+p n  k+   +   +l+++p n+hi d  ++R+ 
  EPA05361.1  95 DSF--VKNWLKLH--DISYQNYVSVIDgtmKADLDYDVFIDDSPLNAIKFLQHKkkiLLYSQPWNQHISDpnIQRIS 167
                 443..459*****..9*****998865333778999**********8876544446478899******973345555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.54
# Mc/sec: 994.87
//
Query:       EPA05362.1  [L=429]
Description: glutamyl-tRNA(Gln) amidotransferase, subunit D [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-53  181.3   0.1    2.2e-53  180.7   0.1    1.2  1  Asparaginase    Asparaginase, N-terminal
    1.5e-29  102.5   0.0    2.9e-29  101.6   0.0    1.5  1  Asparaginase_C  Glutaminase/Asparaginase C-terminal domain
    5.8e-17   60.8   3.0    5.8e-17   60.8   3.0    2.2  3  GatD_N          GatD N-terminal domain


Domain annotation for each model (and alignments):
>> Asparaginase  Asparaginase, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.7   0.1   3.7e-57   2.2e-53       1     184 [.      94     284 ..      94     290 .. 0.96

  Alignments for each domain:
  == domain 1  score: 180.7 bits;  conditional E-value: 3.7e-57
                   EEEEEEEESGGGEEECTTS--CCEES-HHHHHCCTTTCCCCSEEEEEEEEEE-GGG--HHHHHHHHHHHHHHC.CT-SEEEEE--STTHHHHHHHHH CS
  Asparaginase   1 kvlvlatGGTiasekdesggalapalsaeellealpelekiaeleseqlanidSsnmtpadwlklaeaieeal.eeydgfVvlhGTDTlaytAsaLs 96 
                   k+l+l+tGGTias++d+++ga++p l+aeel +++pel+kia++++ +l++  S+n+ p++wlk+a+++++   ++y+g++++hGTDT++yt+s+Ls
    EPA05362.1  94 KILLLSTGGTIASKVDYRTGAVTPVLTAEELNSSVPELAKIANVDAVVLFSEYSENIMPEHWLKIADKLKDYStSDYSGIIIAHGTDTMHYTSSFLS 190
                   79**********************************************************************9666********************* PP

                   HHEES.SSEEEEE--SS-TTSTT-SHHHHHHHHHHHHHCGGTTSECEEEETTE.......EEETTTEEE-BSSSSS-EEETTT--SEEEETTEEE CS
  Asparaginase  97 lmlknldkpvvltGsqrplselrsDgpeNlldAllvaasseriagvlvvfngk.......llranrvtKvhtssldaFespnlgplaevegskvk 184
                   ++l++++ p+ l+Gsqr++++++sD++ Nl++A+++  +  + +gv++v+++        ++ ++rv+K hts++ aF+++  +p   v +++v 
    EPA05362.1 191 FALAGFPIPIALVGSQRSSDRASSDAALNLIGAIKFLVAC-KTNGVYIVMHQDendetiaCHLGTRVRKNHTSKRGAFQTIGDNPAFIVLNDQVI 284
                   ***********************************99998.99*********99***************************99998888677665 PP

>> Asparaginase_C  Glutaminase/Asparaginase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.6   0.0   4.9e-33   2.9e-29       1     114 []     306     419 ..     306     419 .. 0.99

  Alignments for each domain:
  == domain 1  score: 101.6 bits;  conditional E-value: 4.9e-33
                     -EEEEE--TT--HHHHHHHHHTT--EEEEEEBTTTB--HHHHHHHHHHHTTT-EEEEEESSSBS-----H.....HHHHHTEEE-TT--HHHHHH CS
  Asparaginase_C   1 rVvvlklhpgmdtkvlkallkkgakGvvlegtGvGnlpsallealkeakargivvvatsqcpsgsvsnseyeagkelerlgvisaddmtpeaari 95 
                     +V+++k hpg d+++l+++++ +++G+++egtG G++ ++++e +k+a ++gi + +tsqc++g+vs+++ye+g++l +lg+i  ++m pe a +
      EPA05362.1 306 KVALVKYHPGYDPSILEKIIEMNYRGIIFEGTGLGHIGKTMYENVKRANEKGIFLGMTSQCIDGRVSMTVYESGRDLLNLGIIPLENMIPEVALV 400
                     7********************************************************************************************** PP

                     HHHHHCTT---HHHHHHHH CS
  Asparaginase_C  96 kLmlllgkgldpaevrklf 114
                     k m++lg+ ++ ++v+ ++
      EPA05362.1 401 KAMWVLGNSKKVEDVKYMM 419
                     ***************9887 PP

>> GatD_N  GatD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.8   3.0   9.7e-21   5.8e-17       1      55 []      20      73 ..      20      73 .. 0.95
   2 ?   -3.1   0.0      0.84     5e+03      14      23 ..     168     177 ..     163     182 .. 0.76
   3 ?   -3.3   0.1      0.96   5.7e+03       6      19 ..     324     337 ..     323     339 .. 0.75

  Alignments for each domain:
  == domain 1  score: 60.8 bits;  conditional E-value: 9.7e-21
                --TT-EEEEE-SS-EEEEEE----TTS-SSEEEEEETTS-EEEEE-TT-.---EE CS
      GatD_N  1 ievGDlikvekkgreyeGilmPrselsdddiivlKLdnGYNiGikieeiekiell 55
                i+vGD +k+   + +y Gi+mPr+e +dd+++vlKL++GYN+G++ie i+kie++
  EPA05362.1 20 INVGDSVKIL-SDLTYLGIIMPRYEHNDDKHLVLKLKSGYNVGLEIETIKKIEKI 73
                679*****95.689***************************************97 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.84
                 -EEEEEE--- CS
      GatD_N  14 reyeGilmPr 23 
                 ++y+Gi++ +
  EPA05362.1 168 SDYSGIIIAH 177
                 7899999876 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 0.96
                 EEEEE-SS-EEEEE CS
      GatD_N   6 likvekkgreyeGi 19 
                 +i+  ++g+ +eG+
  EPA05362.1 324 IIEMNYRGIIFEGT 337
                 57778888888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2897.66
//
Query:       EPA05363.1  [L=84]
Description: hypothetical protein BG20_I2072 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.011   15.6   0.3      0.012   15.4   0.3    1.0  1  KASH_CCD        Coiled-coil region of CCDC155 or KASH
      0.035   14.4   0.9        0.3   11.4   0.4    1.9  2  Retrotrans_gag  Retrotransposon gag protein
      0.046   13.8   1.4       0.07   13.2   1.4    1.3  1  Swi5            Swi5


Domain annotation for each model (and alignments):
>> KASH_CCD  Coiled-coil region of CCDC155 or KASH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.3   2.1e-06     0.012      21      97 ..       2      76 ..       1      81 [. 0.89

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.1e-06
    KASH_CCD 21 aeenskLkkavetaeetnakLteeieeLkkklkstQqalqkaklleeEleelkalvkeleEkrarlkaqnkqleken 97
                 +e  kL+k+v    ++ a+L  ei e+k   k+   + +k    e+ + e k+  ++  E   +++   + ++ke+
  EPA05363.1  2 TDELGKLQKTVKEYSDNLARLGKEIAEIKFNYKIIENTTEK--YWEDKIVEFKKYNEKATEYYIQAHSLMNLIDKEQ 76
                58899******************************998765..5789999999999999999999999999999997 PP

>> Retrotrans_gag  Retrotransposon gag protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.031   1.8e+02      60      78 ..       9      27 ..       1      35 [. 0.76
   2 ?   11.4   0.4   5.1e-05       0.3      35      79 ..      30      74 ..      27      82 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.031
  Retrotrans_gag 60 tesvreYvtrfktladqld 78
                    +++v+eY +++ +l  ++ 
      EPA05363.1  9 QKTVKEYSDNLARLGKEIA 27
                    469******9999987776 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 5.1e-05
  Retrotrans_gag 35 aflktflpserkdqleeelsslrQgtesvreYvtrfktladqlde 79
                    +f+ +  ++ +++  e+++ ++++ +e+ +eY+ + ++l++ +d+
      EPA05363.1 30 KFNYKIIENTTEKYWEDKIVEFKKYNEKATEYYIQAHSLMNLIDK 74
                    577788888999999**************************9995 PP

>> Swi5  Swi5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.4   1.2e-05      0.07       7      48 ..       7      56 ..       1      57 [. 0.70

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.2e-05
                HHHHHHHHHHHHHHHHHHHHHHHH.........HHHHHHHHHHHHHHHHH CS
        Swi5  7 eleeqleelekelaelkeelkekk........dpeetvkrhIklLheYNE 48
                +l+++++e+ ++la l +e  e k        + e+  +++I   ++YNE
  EPA05363.1  7 KLQKTVKEYSDNLARLGKEIAEIKfnykiienTTEKYWEDKIVEFKKYNE 56
                5555555555555555555555555555555899***************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1295  (0.0722293); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 590.28
//
Query:       EPA05364.1  [L=61]
Description: hypothetical protein BG20_I2069 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.3e-14   51.9   0.1    8.5e-14   51.5   0.1    1.3  1  DUF1059   Protein of unknown function (DUF1059)
  ------ inclusion threshold ------
       0.13   12.5   0.0       0.14   12.4   0.0    1.1  1  DUF2653   Protein of unknown function (DUF2653)


Domain annotation for each model (and alignments):
>> DUF1059  Protein of unknown function (DUF1059)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.5   0.1   9.4e-18   8.5e-14       2      50 ..       3      51 ..       2      57 .. 0.95

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 9.4e-18
     DUF1059  2 kefkCgDvgpdCgfeitaeteeEvlrkvaeHakaaHglteippelveki 50
                k+fkC D+g++C+++++a +  +++ k+a+H+ + H++ +++ +l  ki
  EPA05364.1  3 KSFKCSDIGMKCDWTTRAFNMVDLMSKIARHVDEKHNISSLSNDLKLKI 51
                9********************************************9888 PP

>> DUF2653  Protein of unknown function (DUF2653)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.6e-05      0.14      53      87 ..      19      53 ..       9      54 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.6e-05
     DUF2653 53 qvlveanlieairkyleeelnvnpfaaqieLeldd 87
                  ++  +l++ i ++++e++n+ + ++ ++L++d+
  EPA05364.1 19 RAFNMVDLMSKIARHVDEKHNISSLSNDLKLKIDR 53
                56778899*************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 391.08
//
Query:       EPA05365.1  [L=332]
Description: thioredoxin-disulfide reductase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-52  178.4   0.8    2.2e-52  178.2   0.8    1.0  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    8.9e-26   90.8   3.5    1.2e-22   80.6   0.4    2.1  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    1.9e-18   66.8   3.4    3.1e-17   62.9   0.2    2.9  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    7.7e-07   28.5   2.1     0.0095   15.1   0.1    3.4  3  GIDA           Glucose inhibited division protein A
      3e-05   23.3   0.1       0.16   11.1   0.0    3.2  3  K_oxygenase    L-lysine 6-monooxygenase (NADPH-requiring)
    9.5e-05   22.1   2.3      0.033   13.8   0.0    2.9  2  DAO            FAD dependent oxidoreductase
    0.00015   21.2   1.0       0.12   11.6   0.1    2.7  3  FAD_binding_3  FAD binding domain
    0.00046   19.7   0.1     0.0012   18.3   0.0    1.7  2  FAD_oxidored   FAD dependent oxidoreductase
    0.00051   19.4   0.0     0.0058   15.9   0.0    2.2  2  Thi4           Thi4 family
     0.0006   19.0   3.8     0.0096   15.0   0.1    3.4  4  FAD_binding_2  FAD binding domain
     0.0053   16.8   4.2        1.2    9.1   0.0    3.3  3  NAD_binding_9  FAD-NAD(P)-binding
     0.0082   14.9   2.7       0.17   10.6   0.1    3.0  4  HI0933_like    HI0933-like protein
  ------ inclusion threshold ------
      0.012   16.1   0.3      0.049   14.1   0.1    2.0  2  NAD_binding_7  Putative NAD(P)-binding
      0.012   15.9   0.4      0.044   14.0   0.1    2.0  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain
      0.027   14.2   0.0        6.3    6.5   0.0    2.6  2  MAF_flag10     Protein of unknown function DUF115


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.2   0.8   1.8e-55   2.2e-52       1     291 [.      28     312 ..      28     315 .. 0.92

  Alignments for each domain:
  == domain 1  score: 178.2 bits;  conditional E-value: 1.8e-55
                  CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH.........HHHHCHHHHCCCCHCCTCEEEEESCEEEEETE CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias.........evvkklnqgielllgeevvkidpgkkkvklek 89 
                  +d+v+iG+Gp G++a ++ ++ag++++++   g +++g+ + ++++++++++++ +          ++++++    +++ + evv++d+ +k +k+ +
   EPA05365.1  28 FDIVIIGAGPSGYTAGIYSSRAGYDTLIL--SGILPGGQLVNTTEVENYPGFEKGIMgpdlmiemrKQTQRM---GTTIIDDEVVDVDFRHKPFKVLT 120
                  59***********************7777..9*********************99999****8655443333...44555669*************65 PP

                  EECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHH CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Pyr_redox_2  90 kkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllpkrivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsa 187
                        e+++  ++++AtG++pr+lg+ G+++ +gk+v++++++++    +++  ++vvGgG  ++E A +l+k++  v+lv++r+ l       +s+
   EPA05365.1 121 A----SEEYEGRAVIIATGANPRKLGLAGEQTFAGKGVSYCATCDGPFFRNQE--LIVVGGGDSAIEEATFLTKFATTVHLVHRRESLR------ASK 206
                  4....469*******************************************99..*********************************7......9** PP

                  HHHHHHHHT.TEEEEESCEEEEEEETTE....EEE.EEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGCT CS
                  xxxxxxxxx.xxxxxxxxxxxxxxxxxx....xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Pyr_redox_2 188 aleealeke.Gvevklgtsvkeidgnge....kle.vvledgeeidadlvvvavGvrpstelleeklglelderggivvdeflrtnvpgiyaiGDvag 279
                  +++++ ek+ ++++++++ v +i+g+++     l+  ++++++++++  ++va+G +p+t+l+  k ++ ld+ g+i  + +  tn++g++a+GDv  
   EPA05365.1 207 IMQDRAEKNnKIKFHWNSAVIDIKGDQKmqqaVLKnIKTGEEKTLNVGGLFVAIGHEPNTKLF--KNQIDLDNEGYIILKNKTHTNIEGVFAAGDVH- 301
                  ********99******************9987777999************************6..889999**************************. PP

                  ECCSS--HHHHH CS
                  xxxxxxxxxxxx RF
  Pyr_redox_2 280 gkggpelaqaAv 291
                   ++++++a +A 
   EPA05365.1 302 -DRNYRQAITAA 312
                  .89999998886 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.2   0.00014      0.17       1      27 [.      31      56 ..      31      76 .. 0.82
   2 !   80.6   0.4   9.6e-26   1.2e-22     101     305 .]     103     298 ..      90     298 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00014
  Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylil 27
                 +IiGaGP G +a+i   +ag  d lil
   EPA05365.1 31 VIIGAGPSGYTAGIYSSRAGY-DTLIL 56
                 7********************.56776 PP

  == domain 2  score: 80.6 bits;  conditional E-value: 9.6e-26
  Pyr_redox_3 101 feeVesvkkedegfevetsketyeAkkviiAtGefdkPnklnipGeek...lvkhyskvkefhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtr 195
                  + eV +v+  ++ f+v t +e+ye + viiAtG   +P+kl+  Ge+    + + y    +   +++q+++V+Gg++Sa++ A+ l +   +V++v+r
   EPA05365.1 103 DDEVVDVDFRHKPFKVLTASEEYEGRAVIIATGA--NPRKLGLAGEQTfagKGVSYCATCDGPFFRNQELIVVGGGDSAIEEATFLTKFATTVHLVHR 198
                  568999***************************9..***********7633444555555665678******************************** PP

  Pyr_redox_3 196 gseiekeesdpsyslkpdienrleelvkeekikvlfnaevkeik...ekeeeykvktedgkkvevk.ddvvlatGykpdlsflkkslfeldedgrpvl 289
                  +++++++          ++++r e+   ++kik++ n+ v +ik   ++++ +  + ++g++ + +    ++a+G +p+++++k ++++ld++g++ l
   EPA05365.1 199 RESLRAS---------KIMQDRAEK---NNKIKFHWNSAVIDIKgdqKMQQAVLKNIKTGEEKTLNvGGLFVAIGHEPNTKLFK-NQIDLDNEGYIIL 283
                  *966665.........466677665...577999999999999833222333333344444444430556778**********9.9999*9*****99 PP

  Pyr_redox_3 290 teeteetnvpglflaG 305
                  +++t  tn++g+f aG
   EPA05365.1 284 KNKT-HTNIEGVFAAG 298
                  8877.69*******99 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.4     0.085     1e+02       2      24 ..      30      52 ..      29     108 .. 0.79
   2 !   62.9   0.2   2.6e-20   3.1e-17       2      77 ..     170     239 ..     169     246 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.085
                EEEECSSHHHHHHHHHHHHTTSE CS
   Pyr_redox  2 vvvvGgGyiglElAgalaelgkk 24
                +v++G+G +g  ++ + ++ g +
  EPA05365.1 30 IVIIGAGPSGYTAGIYSSRAGYD 52
                89*******99888888877754 PP

  == domain 2  score: 62.9 bits;  conditional E-value: 2.6e-20
                 EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHT.TEEEECSEEEEEEEEETTSEEEEE CS
   Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekn.gievllntkveeiegsedgvesvk 77 
                 ++vvGgG++++E+A++l++++  V++v+r++ l+      aski+q++ ekn +i++++n+ v  i+g+++ +++ +
  EPA05365.1 170 LIVVGGGDSAIEEATFLTKFATTVHLVHRRESLR------ASKIMQDRAEKNnKIKFHWNSAVIDIKGDQK-MQQAV 239
                 79********************************......*********9999****************98.55555 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   7.9e-06    0.0095       1      28 [.      29      56 ..      29      83 .. 0.84
   2 !   10.1   0.1   0.00025       0.3     111     222 ..      99     222 ..      85     253 .. 0.74
   3 ?    0.7   0.0      0.18   2.2e+02     350     388 ..     287     326 ..     281     330 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 7.9e-06
                CEEEE-SSHHHHHHHHHHHHTT--EEEE CS
        GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi 28
                d+++iG+G +G+ A + ++r+G+++l++
  EPA05365.1 29 DIVIIGAGPSGYTAGIYSSRAGYDTLIL 56
                79***********************988 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00025
                 EEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT.............-BT-EEEETTEEEESSCTTC--B-THHHHHHHTT--EEEEEEEE-- CS
        GIDA 111 leiieeeveeliveekkvkgvvtedgetikakavviatGt.............flkgkihigekelsaGrlgeltseglseslkelgfellrlktgtpp 196
                  +ii +ev +++ ++k  k+  ++  e+++ +av+iatG+               kg +++ +   +  r++el   g  +s  e  + l ++ t++  
  EPA05365.1  99 TTIIDDEVVDVDFRHKPFKV--LTASEEYEGRAVIIATGAnprklglageqtfAGKGVSYCATCDGPFFRNQELIVVGGGDSAIEEATFLTKFATTVHL 195
                 58999999999885555554..4456789***********99999999999955678888888888999999999988888888888888999999999 PP

                 EEEGGGS-TTTSEEE---.SS-B-SSS CS
        GIDA 197 ridkesidfskleeqsgd.kegeefsy 222
                 + ++es   sk+++   + +++++f  
  EPA05365.1 196 VHRRESLRASKIMQDRAEkNNKIKFHW 222
                 999999999998888877344444433 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.18
                 SBBSSSBTEEE-CGGGTB-SHHH...HHHHHHHHHHHHHHHH CS
        GIDA 350 LetkkvkgLflAGqinGteGYeE...aaaqGllAGinaarka 388
                  +t+ ++g+f+AG++   + Y     aa+ G++A+i + +++
  EPA05365.1 287 THTN-IEGVFAAGDVHDRN-YRQaitAAGFGCMAAIDVDKYL 326
                 4554.999******99887.7551115669999999888776 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.072        86     191     203 ..      27      39 ..       5      50 .. 0.69
   2 !   11.1   0.0   0.00014      0.16     118     230 ..     105     204 ..      91     210 .. 0.68
   3 !    6.6   0.0     0.003       3.6     285     341 ..     208     263 ..     204     264 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.072
  K_oxygenase 191 kkriaVvGsGqSa 203
                  k +i+++G+G S+
   EPA05365.1  27 KFDIVIIGAGPSG 39 
                  4455555555554 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00014
  K_oxygenase 118 eveevepdeeeeeelltveskdaegeeeelearnlvlgvGtepkiPevlekle.gkervvHsseylerkee.llakkriaVvGsGqSaaeifedllrr 213
                  ev +v+++++     ++v +      +ee+e r++++++G +p    ++ + +   + v    +y  + +    ++++++VvG+G Sa e +  l++ 
   EPA05365.1 105 EVVDVDFRHK----PFKVLT-----ASEEYEGRAVIIATGANPRKLGLAGEQTfAGKGV----SYCATCDGpFFRNQELIVVGGGDSAIEEATFLTKF 189
                  5555555554....366666.....5789999999999998876433333222122233....333333334578999************98888766 PP

  K_oxygenase 214 qkkvelklvtrsealep 230
                  ++  +++lv r+e+l++
   EPA05365.1 190 AT--TVHLVHRRESLRA 204
                  55..9999999999876 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.003
  K_oxygenase 285 yeqkvkgeerlrllpnrevesaeaegkgeveltlrneesgeeetlevdavvlATGYr 341
                   +++ ++++++++  n++v +++ ++k   +  l+n ++gee+tl+v  +++A G +
   EPA05365.1 208 MQDRAEKNNKIKFHWNSAVIDIKGDQK-MQQAVLKNIKTGEEKTLNVGGLFVAIGHE 263
                  56788889999************9996.889999*****************999975 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.5    0.0029       3.4       1      26 [.      29      56 ..      29      73 .. 0.83
   2 !   13.8   0.0   2.8e-05     0.033     147     210 ..      85     144 ..      74     263 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0029
                EEEEECTSHHHHHHHHHHHHTT..EEEE CS
         DAO  1 dvviiGGGiiGlstAyeLarrg..Vtll 26
                d+viiG+G  G ++  + +r+g  +++l
  EPA05365.1 29 DIVIIGAGPSGYTAGIYSSRAGydTLIL 56
                9*****************9999965555 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 2.8e-05
                 HHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHHHHHTT CS
         DAO 147 kltaalaraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsdllgll 210
                  l+  ++++ ++ G +i+   ev++++ +  k  +v   t+ +e  + +av++a+Ga  ++lgl+
  EPA05365.1  85 DLMIEMRKQTQRMGTTIIDD-EVVDVDFR-HKPFKV--LTAsEEY-EGRAVIIATGANPRKLGLA 144
                 58999***************.99999554.356777..5553554.459********98865333 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.1    0.0001      0.12       2      30 ..      28      56 ..      27      59 .. 0.92
   2 ?   -0.4   0.0      0.46   5.5e+02       4      35 ..     170     201 ..     167     205 .. 0.89
   3 !    7.0   0.0    0.0025         3     106     153 ..     203     251 ..     190     254 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0001
                   EEEEEE--SHHHHHHHHHHHHTTHHEEEE CS
  FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlv 30
                    d++I+GaGp+G +++   s+aG +++++
     EPA05365.1 28 FDIVIIGAGPSGYTAGIYSSRAGYDTLIL 56
                   6899********************99997 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.46
                    EEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
  FAD_binding_3   4 VlIVGaGpaGlmlallLseaGvrvvlvekrst 35 
                     ++VG+G + +  a++L++    v+lv +r++
     EPA05365.1 170 LIVVGGGDSAIEEATFLTKFATTVHLVHRRES 201
                    579****************9999999999875 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0025
                    HHHHHHHHHHHHHT.EEETCSEEEECCEECCCCCCCEEEECCTTEEEEE CS
  FAD_binding_3 106 eleriLvehaeerg.lqvrfktevesleqdeegvtaevrdketgeeetv 153
                    +  +i+ ++ae+   ++++++  v  ++ d++  +a++++ +tgee+t+
     EPA05365.1 203 RASKIMQDRAEKNNkIKFHWNSAVIDIKGDQKMQQAVLKNIKTGEEKTL 251
                    5689******************************************998 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   9.8e-07    0.0012       1      39 [.      29      66 ..      29     115 .. 0.88
   2 ?   -1.5   0.0         1   1.2e+03       4      32 ..     172     200 ..     169     252 .. 0.57

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 9.8e-07
  FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGllt 39
                  D+v++G+gp+G++A i + raG  +l+++     GG+l 
    EPA05365.1 29 DIVIIGAGPSGYTAGIYSSRAGYDTLILS-GILPGGQLV 66
                  9************************9985.456666665 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1
  FAD_oxidored   4 VvGGgpaGvaAAiaAaraGakvlLveerg 32 
                   VvGGg + +  A    +   +v Lv++r+
    EPA05365.1 172 VVGGGDSAIEEATFLTKFATTVHLVHRRE 200
                   55555555544444444444444444443 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   4.9e-06    0.0058      17      48 ..      27      57 ..      19      69 .. 0.82
   2 ?    0.5   0.0      0.25     3e+02      17      39 ..     167     189 ..     162     203 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.9e-06
                EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEE CS
        Thi4 17 esDvvivGaGssGLtaayylakkpdlkvaile 48
                + D+vi+GaG+sG ta+ y +++ +  ++il 
  EPA05365.1 27 KFDIVIIGAGPSGYTAGIYSSRA-GYDTLILS 57
                67*****************9999.88888875 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.25
                 EEEEEEE--SHHHHHHHHHHHHC CS
        Thi4  17 esDvvivGaGssGLtaayylakk 39 
                 ++++++vG+G s +  a  l+k 
  EPA05365.1 167 NQELIVVGGGDSAIEEATFLTKF 189
                 5789**********999999886 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1     8e-06    0.0096       1      31 [.      29      59 ..      29      69 .. 0.90
   2 ?   -2.0   0.0       1.2   1.5e+03     189     204 ..     124     139 ..     117     185 .. 0.69
   3 ?    1.1   0.1      0.13   1.6e+02     146     191 ..     207     252 ..     139     272 .. 0.79
   4 ?    1.6   0.0     0.093   1.1e+02     386     402 ..     285     301 ..     272     315 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8e-06
                   SEEEE--SHHHHHHHHHHHHTTT-EEEEESS CS
  FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavveke 31
                   D+++iG+G +G++A++  ++aG ++++++  
     EPA05365.1 29 DIVIIGAGPSGYTAGIYSSRAGYDTLILSGI 59
                   99*************************9976 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.2
                    EEEESEEEE-----GG CS
  FAD_binding_2 189 rirakavvlatgGfgr 204
                    +++ +av++atg+ +r
     EPA05365.1 124 EYEGRAVIIATGANPR 139
                    5677788888888777 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.13
                    HHHHHHHTCT.EEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEE CS
  FAD_binding_2 146 rlvesarkag.vdfqerteadeLivedgrvtGavvenpesgrevrir 191
                     + ++a+k++ ++f+ + ++ ++   d+++  av++n ++g+e +++
     EPA05365.1 207 IMQDRAEKNNkIKFHWNSAVIDI-KGDQKMQQAVLKNIKTGEEKTLN 252
                    45566666666999999999998.55889999999999988888765 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.093
                    TTEEESSBTEEE-STCE CS
  FAD_binding_2 386 dadgqpipGLYAaGeva 402
                    +++ ++i+G +AaG v 
     EPA05365.1 285 NKTHTNIEGVFAAGDVH 301
                    577899********986 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.7      0.11   1.3e+02       1      11 [.      31      41 ..      31      45 .. 0.87
   2 !    9.1   0.0     0.001       1.2     113     155 ..      95     136 ..      86     137 .. 0.84
   3 ?    4.5   0.0     0.026        31     108     155 ..     209     262 ..     201     263 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.11
  NAD_binding_9  1 aivGaGprGla 11
                   +i+GaGp+G +
     EPA05365.1 31 VIIGAGPSGYT 41
                   7********86 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.001
  NAD_binding_9 113 egvtvevhraevvdleeradgqavlladgaslaadaVvLAlGh 155
                    +++  +++ +evvd++ r++ ++v l+  ++++ +aV++A+G 
     EPA05365.1  95 QRMGTTIIDDEVVDVDFRHKPFKV-LTASEEYEGRAVIIATGA 136
                    45678899*************999.6677899*********95 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.026
  NAD_binding_9 108 larlpegvtvevh.raevvdleeradgqavll.....adgaslaadaVvLAlGh 155
                    ++r++++ ++++h ++ v+d++ +++ q+ +l      ++++l +  +++A+Gh
     EPA05365.1 209 QDRAEKNNKIKFHwNSAVIDIKGDQKMQQAVLkniktGEEKTLNVGGLFVAIGH 262
                    567889999**99788999***99988744442553234467899999999999 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.1   0.00014      0.17       1      29 [.      28      56 ..      28      62 .. 0.92
   2 ?    2.9   0.0      0.03        36     128     164 ..     102     136 ..      86     146 .. 0.76
   3 ?   -2.0   0.0      0.93   1.1e+03       2      34 ..     169     201 ..     168     208 .. 0.78
   4 ?   -1.7   0.0      0.76   9.1e+02     120     144 ..     214     238 ..     188     264 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00014
                 -SEEEE--SHHHHHHHHHHHHTT--EEEE CS
  HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlll 29
                 +d+++iG+G++G  a i  +++g ++l+l
   EPA05365.1 28 FDIVIIGAGPSGYTAGIYSSRAGYDTLIL 56
                 589********************999987 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.03
                  -S--EEEEECETTE.EEEEE.TTEEEEESEEEE---- CS
  HI0933_like 128 letevksvekeedgkfrvktkseeeleadklvlAtGG 164
                   + ev +v+ +++  f+v t  +ee+e +++++AtG 
   EPA05365.1 102 IDDEVVDVDFRHKP-FKVLT-ASEEYEGRAVIIATGA 136
                  56678888765555.88888.89************96 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.93
                  SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSS CS
  HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakk 34 
                  ++iv+GgG + +  A  + k    V l+ + ++
   EPA05365.1 169 ELIVVGGGDSAIEEATFLTKFATTVHLVHRRES 201
                  689*****9999888888888888888777665 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 0.76
                  HHHT-EEE-S--EEEEECETTE.EE CS
  HI0933_like 120 keagvklrletevksvekeedgkfr 144
                  k++++k++ +++v +++ +++ +  
   EPA05365.1 214 KNNKIKFHWNSAVIDIKGDQKMQQA 238
                  3456777777777777443332211 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       2.7   3.2e+03       7      21 ..      27      41 ..      24      60 .. 0.81
   2 ?   14.1   0.1   4.1e-05     0.049       5      84 ..     165     245 ..     164     254 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2.7
  NAD_binding_7  7 gkkvlvvGgGevAar 21
                   +  ++++G+G+ +++
     EPA05365.1 27 KFDIVIIGAGPSGYT 41
                   56789*****98875 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 4.1e-05
  NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvklaeeelekd....legadlviaatddrelneriaeaaka 84 
                    +++++ +vvGgG+ A + +  l ++  +v++v  +   e+ +  k+ ++ +ek+    + +   vi +  d+++++++ +++k+
     EPA05365.1 165 FRNQELIVVGGGDSAIEEATFLTKFATTVHLVHRR---ESLRASKIMQDRAEKNnkikFHWNSAVIDIKGDQKMQQAVLKNIKT 245
                    678999****************************9...5445555555555544233355667999999999999999888875 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   3.7e-05     0.044       1      27 [.      32      57 ..      32      80 .. 0.86
   2 ?   -1.2   0.0         2   2.4e+03       1      27 [.     172     198 ..     172     205 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.7e-05
                   EE--SHHHHHHHHHHHCCTEEEEEE-S CS
  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllek 27
                   I+GaG sG +a  + ++ag+d l+l +
     EPA05365.1 32 IIGAGPSGYTAGIYSSRAGYDTLIL-S 57
                   9*********************998.4 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2
                    EE--SHHHHHHHHHHHCCTEEEEEE-S CS
  NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllek 27 
                    +vG+G s+   A +L+k    v+l+ +
     EPA05365.1 172 VVGGGDSAIEEATFLTKFATTVHLVHR 198
                    899999998888888886566666555 PP

>> MAF_flag10  Protein of unknown function DUF115
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.016        19      18      36 ..      20      38 ..       5      38 .. 0.65
   2 ?    6.5   0.0    0.0053       6.3      68     150 ..     101     186 ..      97     194 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.016
  MAF_flag10 18 llnkfkgnkpaiivgaGPS 36
                + +k k + +++i+gaGPS
  EPA05365.1 20 MPDKKKTKFDIVIIGAGPS 38
                3343333589********9 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0053
  MAF_flag10  68 IkPDivvslDpqeasyevfkeaekkgdiplvfasgvnpellkkykgpkiflvtgstqa....lelleeekneilfgGgsvantaldl 150
                 I+ D vv +D  +  ++v+   e+ +   ++ a+g+np++l    ++ + + +g+ ++     +++++++ ++++gG s ++ a +l
  EPA05365.1 101 IIDDEVVDVDFRHKPFKVLTASEEYEGRAVIIATGANPRKLGLAGEQTF-AGKGVSYCatcdGPFFRNQELIVVGGGDSAIEEATFL 186
                 7778999****9999**99999999999*************87766655.6888888778887777555555888888877777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 2303.91
//
Query:       EPA05366.1  [L=274]
Description: hypothetical protein BG20_I2066 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   12.9   0.0        0.2   12.1   0.0    1.5  1  NERD      Nuclease-related domain


Domain annotation for each model (and alignments):
>> NERD  Nuclease-related domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   1.1e-05       0.2      10      60 ..      68     124 ..      63     184 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.1e-05
        NERD  10 akeLkelkedeylvlhdvrlrpgtg.....eiDhlvispkgifviEvKn..wsGwifg 60 
                 ++++++l++ + l  +++r++ + g     eiD++ +s ++ f iE+K+  ++G+ +g
  EPA05366.1  68 ENYIADLLPYYDLQVSGIRVKIK-GkcalhEIDLIGLSSSKQFMIECKHnsYRGTYIG 124
                 55666666677777778777555.335678*******************555565444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1847.05
//
Query:       EPA05367.1  [L=69]
Description: hypothetical protein BG20_I2071 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0095   15.8   0.2     0.0095   15.8   0.2    1.9  2  zf-C2HC_2     zinc-finger of a C2HC-type
  ------ inclusion threshold ------
      0.023   14.5   1.0       0.55   10.1   0.1    2.2  2  zf-C2H2_3     zinc-finger of acetyl-transferase ESCO
      0.032   14.8   0.1      0.034   14.7   0.1    1.1  1  ECM11         Extracellular mutant protein 11
      0.041   13.8   2.8        2.2    8.3   0.3    2.2  2  zf-RING_5     zinc-RING finger domain
      0.054   13.5   1.2        2.3    8.3   0.1    2.2  2  zf-RING_UBOX  RING-type zinc-finger
      0.057   13.3   2.5        4.2    7.3   0.3    2.2  2  zf-C3HC4      Zinc finger, C3HC4 type (RING finger)


Domain annotation for each model (and alignments):
>> zf-C2HC_2  zinc-finger of a C2HC-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.2   3.2e-06    0.0095       4      15 ..       5      16 ..       4      18 .. 0.91
   2 ?   -1.4   0.7      0.81   2.4e+03       5       8 ..      51      54 ..      50      54 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.2e-06
   zf-C2HC_2  4 pCpkCgRsFnpd 15
                +C+kC R+Fn++
  EPA05367.1  5 QCKKCLRKFNEK 16
                9*********86 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.81
   zf-C2HC_2  5 CpkC 8 
                C++C
  EPA05367.1 51 CENC 54
                9999 PP

>> zf-C2H2_3  zinc-finger of acetyl-transferase ESCO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1     0.023        70      14      19 ..       4       9 ..       1      18 [. 0.75
   2 ?   10.1   0.1   0.00019      0.55      14      28 ..      49      63 ..      40      64 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.023
   zf-C2H2_3 14 sqCkeC 19
                 qCk+C
  EPA05367.1  4 AQCKKC 9 
                68**** PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00019
   zf-C2H2_3 14 sqCkeCgMvYnpgsp 28
                s C +C M+Y++ s 
  EPA05367.1 49 SFCENCIMEYSKIST 63
                33*********9775 PP

>> ECM11  Extracellular mutant protein 11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   1.1e-05     0.034      46      84 ..      25      63 ..       2      67 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.1e-05
       ECM11 46 eelknlneke.qheffsslsideWeeaGdwlldqfsellk 84
                + ++++ + +  +eff++l+i eW+++ ++ + ++s++ +
  EPA05367.1 25 Q-YRKKPPYDwTREFFKTLEIGEWDSFCENCIMEYSKIST 63
                2.34444444589*********************999865 PP

>> zf-RING_5  zinc-RING finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.3   0.00073       2.2       1      17 [.       5      20 ..       5      23 .. 0.77
   2 ?    6.0   0.1    0.0039        12      24      33 ..      50      59 ..      49      65 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00073
   zf-RING_5  1 hCnkCfeklskeekfyl 17
                +C+kC +k+ +e+++y+
  EPA05367.1  5 QCKKCLRKF-NEKDIYT 20
                5********.7766665 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0039
   zf-RING_5 24 fCekClkkll 33
                fCe+C+++++
  EPA05367.1 50 FCENCIMEYS 59
                9****99876 PP

>> zf-RING_UBOX  RING-type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1     0.011        34      21      26 ..       6      16 ..       5      32 .. 0.61
   2 ?    8.3   0.1   0.00077       2.3      19      26 ..      49      59 ..      49      69 .] 0.62

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.011
  zf-RING_UBOX 21 CreCl.....w 26
                  C++Cl     +
    EPA05367.1  6 CKKCLrkfneK 16
                  99999544331 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00077
  zf-RING_UBOX 19 tFCreCl...w 26
                  +FC++C+    
    EPA05367.1 49 SFCENCImeyS 59
                  6******5431 PP

>> zf-C3HC4  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1    0.0031       9.3      22      32 ..       6      16 ..       4      30 .. 0.83
   2 ?    7.3   0.3    0.0014       4.2      20      31 ..      49      60 ..      49      65 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0031
                -CHHHHHHHHC CS
    zf-C3HC4 22 CskCirkilks 32
                C+kC+rk +++
  EPA05367.1  6 CKKCLRKFNEK 16
                9*****99884 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0014
                -B-CHHHHHHHH CS
    zf-C3HC4 20 sfCskCirkilk 31
                sfC++Ci ++ k
  EPA05367.1 49 SFCENCIMEYSK 60
                69*****99977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       749  (0.0417759); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 511.14
//
Query:       EPA05368.1  [L=119]
Description: hypothetical protein BG20_I2067 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       710  (0.0396006); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 796.28
//
Query:       EPA05369.1  [L=111]
Description: response regulator receiver domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-13   51.1   0.2    1.5e-13   50.9   0.2    1.1  1  Response_reg  Response regulator receiver domain
  ------ inclusion threshold ------
      0.021   15.0   0.1      0.032   14.4   0.1    1.6  1  DUF2584       Protein of unknown function (DUF2584)
       0.14   12.9   0.0       0.18   12.5   0.0    1.2  1  CNDH2_M       PF16858


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.9   0.2   2.6e-17   1.5e-13       1      94 [.       3      98 ..       3     103 .. 0.85

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 2.6e-17
                  EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCT...TTSEEEEEESSTSHHHHHHHHHCTE CS
  Response_reg  1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireed...pelpviiltahseeedavealkaga 94
                  +l +dD+p + ++++++l+ ++  + ++ +dgk  l ++ ++++dlillD+ mp+ +G+++l  +++e+    +  vi+ + + +e +++   k+g+
    EPA05369.1  3 ILHIDDSPEISKVFSDVLKTKNH-DFESITDGKVGLGMVLKNQYDLILLDMCMPNYNGIDFLLDLKKEKsseIQKTVIVSSLELDEHQTEFLTKLGV 98
                  788****************9999.99***************************************99885433345566566666666666667776 PP

>> DUF2584  Protein of unknown function (DUF2584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   5.4e-06     0.032      38      71 ..      60      93 ..      25     102 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.4e-06
                SSSEEEEESS----EEEEEEEEEEEEETTEEEEE CS
     DUF2584 38 ldvplevrktkeseksgtaiiekLewennkTtvt 71
                +d  l+++k+k+se + t+i+  Le+++++T   
  EPA05369.1 60 IDFLLDLKKEKSSEIQKTVIVSSLELDEHQTEFL 93
                8999***************************865 PP

>> CNDH2_M  PF16858
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     3e-05      0.18      25      66 ..      38      78 ..      34     107 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3e-05
     CNDH2_M 25 latlglyrDFllldtCdahavg.afLlelqgkslsekedsvas 66
                + +l +  D +lld C+++  g +fLl+l++++ s++ +++  
  EPA05369.1 38 GMVLKNQYDLILLDMCMPNYNGiDFLLDLKKEK-SSEIQKT-V 78
                67888899**********987659*********.5555532.2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 767.04
//
Query:       EPA05370.1  [L=217]
Description: hypothetical protein BG20_I2146, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.9e-08   34.3   3.2      3e-08   33.6   3.2    1.4  1  MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalli


Domain annotation for each model (and alignments):
>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   3.2   1.7e-12     3e-08      20     114 ..      16     104 ..       3     133 .. 0.76

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 1.7e-12
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH..............HHHHH CS
   MCPsignal  20 nvvkqmeeieksskeisdiieVideiadQTNlLALNAaiEAARAGeqGrGFaVVAdEVrkLAersaqaakeiealiieiqkeindsvesleetrq 114
                 +vv+++    +  +ei++ ++ i+ i   T +L + A iEA R G+ G+ F VV + + +L +++ +   ++++      +ei++  +++e+   
  EPA05370.1  16 QVVDKTL---SINNEINRALKSIKAINGRTHMLSITAKIEANRTGDIGKKFLVVSNSIDELSAKTDNVLDKMKSET---IQEIETISRIIENKSV 104
                 3333333...33679**************************************************99887776543...3666666666665544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       942  (0.0525406); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1352.71
//
Query:       EPA05371.1  [L=118]
Description: hypothetical protein BG20_I2152, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.031   14.5   0.7       0.13   12.5   0.1    2.0  2  T3SS_needle_F  Type III secretion needle MxiH, YscF, SsaG, Ep


Domain annotation for each model (and alignments):
>> T3SS_needle_F  Type III secretion needle MxiH, YscF, SsaG, EprI, PscF, EscF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   7.2e-06      0.13      41      70 ..      19      48 ..      16      49 .. 0.90
   2 ?    0.2   0.1     0.048   8.7e+02       6      23 ..      69      86 ..      57     101 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.2e-06
                   HHHHCHHHHHCHHHHHHHHHHHHHHHHHTT CS
  T3SS_needle_F 41 fklqqYsvfinaqStavKaikDilqgIiqk 70
                   f+ q+ +vf++a  +++ ++kD +qgI +k
     EPA05371.1 19 FSFQENNVFTDASGNLIESVKDNMQGIGSK 48
                   577999********************9665 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.048
                   HHHHCCTHHHHHHHHHHH CS
  T3SS_needle_F  6 salsqkvskaekelqdal 23
                   ++ s+++++a+++ q+ l
     EPA05371.1 69 NKISDGINNAKESSQSLL 86
                   444555555544444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       922  (0.0514251); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 772.92
//
Query:       EPA05372.1  [L=75]
Description: hypothetical protein BG20_I2150 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1167  (0.0650901); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.31s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 483.83
//
Query:       EPA05373.1  [L=93]
Description: hypothetical protein BG20_I2151 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.013   15.5   2.9      0.016   15.3   2.9    1.1  1  HTH_56         Cch helix turn helix domain
      0.019   15.0   1.2      0.022   14.9   1.2    1.1  1  DUF1325        SGF29 tudor-like domain
       0.12   12.5   1.2       0.48   10.5   0.2    2.1  2  Aurora-A_bind  Aurora-A binding


Domain annotation for each model (and alignments):
>> HTH_56  Cch helix turn helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   2.9   2.6e-06     0.016      41     108 ..      21      89 ..       5      92 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.6e-06
      HTH_56  41 kkekte...vyIlknvfdkileeagFedtkvvlkelkekGllesekdrntkkrtvkkksegkkvrvyvlkl 108
                 k+ k++   + I+k++f++il+++   d+  + +++ ++G  + +k++  + ++++ +++ k +++ +lk+
  EPA05373.1  21 KN-KLKeeeIEIIKSIFKEILDKGERYDVDDIESWFENEGSWQ-NKNSRIRVINLSHYIQDKHEQTARLKI 89 
                 33.33346699************9877***************9.566888888889999999999999987 PP

>> DUF1325  SGF29 tudor-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   1.2   3.6e-06     0.022      10      72 ..      20      84 ..       7      92 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.6e-06
     DUF1325 10 kkkekeeeeewilaeVvk.iegkknrYeveDadpde.ekekkkyklsaksiiplpkskakpeskl 72
                +k++ +eee  i+ +++k i +k +rY+v+D++    ++++ + k s+ ++i l +  +++++++
  EPA05373.1 20 DKNKLKEEEIEIIKSIFKeILDKGERYDVDDIESWFeNEGSWQNKNSRIRVINLSHYIQDKHEQT 84
                333455666667777777799999*********44357777778889999999998877766654 PP

>> Aurora-A_bind  Aurora-A binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0     0.075   4.5e+02      43      64 ..       6      27 ..       3      31 .. 0.83
   2 ?   10.5   0.2     8e-05      0.48      27      47 ..      47      67 ..      33      84 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.075
  Aurora-A_bind 43 NkfpgkngvgelfqsktalrKa 64
                   N++ + n+++ ++++k+ l+  
     EPA05373.1  6 NVIIKLNEITTVVEDKNKLKEE 27
                   7888899999999999999865 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 8e-05
  Aurora-A_bind 27 dvenvDsWFeekANLENkfpg 47
                   dv +++sWFe+     Nk ++
     EPA05373.1 47 DVDDIESWFENEGSWQNKNSR 67
                   999********9999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1386  (0.0773049); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 603.24
//
Query:       EPA05374.1  [L=177]
Description: hypothetical protein BG20_I2149 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-36  125.8   0.1    1.8e-36  125.6   0.1    1.0  1  HD_3      HD domain
      3e-16   59.7   0.7    5.7e-16   58.8   0.7    1.4  1  HD_2      HD containing hydrolase-like enzyme
     0.0046   17.2   0.0       0.01   16.1   0.0    1.6  1  HD        HD domain
  ------ inclusion threshold ------
      0.057   13.3   0.1      0.087   12.7   0.1    1.4  1  BTG       BTG family
      0.068   13.2   0.0      0.089   12.8   0.0    1.3  1  DUF4130   Domain of unknown function (DUF4130


Domain annotation for each model (and alignments):
>> HD_3  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.6   0.1     5e-40   1.8e-36       3     158 ..      11     162 ..       9     173 .. 0.87

  Alignments for each domain:
  == domain 1  score: 125.6 bits;  conditional E-value: 5e-40
        HD_3   3 kLKfqkRqgwlqtg.rvreesvaeHmwrvalmalllseelkekvdiarvikmfLiHDlvEiltgDiispdelakeekeeeekeaaerilkllpeelaee 100
                 +LK ++Rqgw+++  ++++esvaeH++ +a+ ++++s+  k   ++++++k +L+HDl E++ gDi++  ++   +k++ e++a+++il+ lpe+l+ +
  EPA05374.1  11 NLKEVPRQGWIDKLsIEKPESVAEHVFSMAITGMIFSDLKK--YNTEKILKIILLHDLSESIIGDITPG-QIPISKKRNLENNAMKKILSELPESLQSQ 106
                 69*********98747799*****************99998..***********************885.5**************************** PP

        HD_3 101 llalweEFeeretkeakfakdlDklepllqalekegdslaafeaklsqvygvsskela 158
                 ++ lw+E+ ++++ ea+f+++lDkle+ lqa  +  +     + +l+++++++++e++
  EPA05374.1 107 YNRLWDEYIQNTSSEARFVHQLDKLEMALQAKYYLNEGHP--KERLESFFNSAKNEIT 162
                 *******************************988766644..3355555555555443 PP

>> HD_2  HD containing hydrolase-like enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   0.7   1.6e-19   5.7e-16       2     159 ..       5     161 ..       4     173 .. 0.78

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 1.6e-19
        HD_2   2 FfallsrlkyieRwalmrn...treenvaeHslevaliahalalienkkfggkldaerlallalyHDasEiitGDlptpvKyanpeireaykevEeeae 97 
                 F+++  +lk + R +   +    ++e+vaeH +++a+ ++++  +++      +++e+++++ l+HD+sE i+GD+       +  i ++ +++E++a 
  EPA05374.1   5 FLNTAINLKEVPRQGWIDKlsiEKPESVAEHVFSMAITGMIFSDLKK------YNTEKILKIILLHDLSESIIGDITPG----QIPI-SKKRNLENNAM 92 
                 7777778888888666554333689************9998888876......79********************9432....2223.345799***** PP

        HD_2  98 ekllelLpeelreeyeell.adeeaeeeekklvkaaDklsalikcleelkagnke......Feeakkei 159
                 +k+l++Lpe+l+++y++l+ +  + +++e ++v++ Dkl+  +++   l+ g ++      F++ak+ei
  EPA05374.1  93 KKILSELPESLQSQYNRLWdEYIQNTSSEARFVHQLDKLEMALQAKYYLNEGHPKerlesfFNSAKNEI 161
                 *******************4345555779***************9999999876556334444444443 PP

>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   2.8e-06      0.01       3     121 ..      34     133 ..      32     134 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.8e-06
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHH.. CS
          HD   3 eHsleVaklarrlaedlgeeedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgldledvaklirehheswegkkrpr.. 99 
                 eH + +a  + ++  dl+   + e++l++ LlHD+ +  +gd          + ++ + ++    +++++ +     +  k+ +e  es   +++ r  
  EPA05374.1  34 EHVFSMAITG-MIFSDLK-KYNTEKILKIILLHDLSESIIGD----------ITPGQIPISK---KRNLENN-----AMKKILSELPESLQ-SQYNRlw 111
                 6655555544.5555666.68999*****************9..........5566666666...5555555.....45555555555554.5555445 PP

                 HHHCCTSCHHHHHHHHHHHHHH CS
          HD 100 glaerqlslearivklaDrlaa 121
                  +++++ s+ear v  +D+l++
  EPA05374.1 112 DEYIQNTSSEARFVHQLDKLEM 133
                 899****************997 PP

>> BTG  BTG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   2.4e-05     0.087      18      64 ..      83     129 ..      79     161 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.4e-05
                 T..TB-HHHHHHHHHHHHHHHHHHHHTT--TTSTTTTHHHH-E.... CS
         BTG  18 kskklerekveaFaeeLeelLeerykehWypekPerGsayRcirink 64 
                 k+++le++++++  +eL e+L+++y++ W+    +  s  R ++   
  EPA05374.1  83 KKRNLENNAMKKILSELPESLQSQYNRLWDEYIQNTSSEARFVHQLD 129
                 5689**************************99999999999998433 PP

>> DUF4130  Domain of unknown function (DUF4130
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.5e-05     0.089     103     146 .]     100     143 ..      43     143 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.5e-05
     DUF4130 103 lseeedefeelWktyfksiaikeRknpklqrqemPkrywkylpE 146
                  ++ + ++++lW +y+++++ ++R  ++l + em ++   yl E
  EPA05374.1 100 PESLQSQYNRLWDEYIQNTSSEARFVHQLDKLEMALQAKYYLNE 143
                 4555889***************************9998888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       893  (0.0498076); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1271.27
//
Query:       EPA05375.1  [L=196]
Description: ATP:cob(I)alamin adenosyltransferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-53  181.9   0.0    1.1e-53  181.7   0.0    1.0  1  Cob_adeno_trans  Cobalamin adenosyltransferase


Domain annotation for each model (and alignments):
>> Cob_adeno_trans  Cobalamin adenosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.7   0.0   6.4e-58   1.1e-53       1     163 [.      21     182 ..      21     183 .. 0.96

  Alignments for each domain:
  == domain 1  score: 181.7 bits;  conditional E-value: 6.4e-58
                      XXXXXXXXXXXXXXXX.XXXTTHHHHHHHHHHHHHHHHHHHHHHHCTTTTHHHHHHHHHHHHHHHHHHHHHHT.-BTCCG-S--HHHHHHHHHH CS
  Cob_adeno_trans   1 iyTrtGDkGtTslvggervsKddprveayGtvDelnsaiglarallaeeeeelkeaLeeiqneLfdlgaelatpekkkekkkiteeeveeleke 94 
                      iyT+tGD+GtT+l g+ r+sK++pr++ayG+vDe n+++g+++++  e +++++e L+ iqneLf +g++l++p+ k ek+++t + ++++e++
       EPA05375.1  21 IYTKTGDDGTTGLQGNLRISKSHPRISAYGAVDESNAILGIVLSH--ELNDDIRELLNLIQNELFVVGSDLSNPNLKDEKNRVTLSMITNIENN 112
                      9******************************************44..4589***********************9999******888******* PP

                      HHHHHHHS--EESEEES-SSHHHHHHHHHHHHHHHHHHHHHHHHHHS..HHHHHHHHHHHHHHHHHHHHH CS
  Cob_adeno_trans  95 ideleaelpplksfilpggspaaaalhvaRtvcRraERavvelaeee.veeevlkylNRLSDlLfvlarv 163
                      id++e+el+pl++filpgg+ +a++lh+aRtv+Rr E  +v l+e+e +++ +++y+NRLSDl+fvl rv
       EPA05375.1 113 IDKFESELSPLTNFILPGGNLVASQLHHARTVIRRSEICMVILNEQEkINPYCMQYVNRLSDLFFVLGRV 182
                      *********************************************98999*****************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1418.32
//
Query:       EPA05376.1  [L=100]
Description: hypothetical protein BG20_I2538, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 687.96
//
Query:       EPA05377.1  [L=113]
Description: hypothetical protein BG20_I2540, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.4e-40  137.0   0.0    8.1e-40  136.9   0.0    1.0  1  ILVD_EDD  Dehydratase family


Domain annotation for each model (and alignments):
>> ILVD_EDD  Dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.9   0.0   4.5e-44   8.1e-40     411     517 .]       1     107 [.       1     107 [. 0.96

  Alignments for each domain:
  == domain 1  score: 136.9 bits;  conditional E-value: 4.5e-44
    ILVD_EDD 411 mlkptsallgkglgkkvalitDGRfSGaskglvighvsPEAaegGpialvedGDiieidiekrtlelevseeelaaRraawkpekkvktrgllakyakl 509
                 ml++t+al+g+glgkkva++tDGRfSG+++g+++ghv+PEA++gGpialv+++D i+id e++ ++l+vs eel++Rr+ w+p k  +t+g+lakya+l
  EPA05377.1   1 MLSTTAALVGQGLGKKVAMVTDGRFSGGTRGFMVGHVAPEAYVGGPIALVKNDDEITIDTETNIIDLHVSPEELEKRRNLWSPPKPNYTTGALAKYATL 99 
                 899********************************************************************************333345********** PP

    ILVD_EDD 510 vssaseGA 517
                 v sa++GA
  EPA05377.1 100 VGSAAQGA 107
                 *******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 781.61
//
Query:       EPA05378.1  [L=59]
Description: hypothetical protein BG20_I2539 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1265  (0.0705561); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.45
# Mc/sec: 397.28
//
Query:       EPA05379.1  [L=38]
Description: hypothetical protein BG20_I1233 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (38 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.29s 00:00:00.61 Elapsed: 00:00:00.42
# Mc/sec: 273.51
//
Query:       EPA05380.1  [L=176]
Description: hypothetical protein BG20_I1236 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.6e-05   23.2   0.4    6.7e-05   22.7   0.4    1.2  1  DUF4423      Domain of unknown function (DUF4423)
     0.0016   18.3   0.2     0.0036   17.3   0.2    1.5  1  HTH_45       Winged helix-turn-helix
     0.0039   17.4   0.3      0.025   14.8   0.1    2.2  2  Rio2_N       Rio2, N-terminal
  ------ inclusion threshold ------
       0.01   15.7   0.9      0.016   15.0   0.9    1.4  1  TFIIE_alpha  TFIIE alpha subunit
      0.011   15.6   0.1      0.017   15.0   0.1    1.3  1  TrmB         Sugar-specific transcriptional regulator TrmB
      0.017   15.3   0.3      0.032   14.4   0.3    1.3  1  HTH_34       Winged helix DNA-binding domain
      0.091   12.7   0.0       0.14   12.1   0.0    1.2  1  MarR_2       MarR family
       0.16   12.0   3.6        0.2   11.7   3.6    1.3  1  DUF1676      Protein of unknown function (DUF1676)
       0.18   12.0   0.5       0.25   11.6   0.5    1.2  1  Abi_2        Abi-like protein
       0.19   12.0   0.3       0.19   12.0   0.3    2.1  3  DUF3135      Protein of unknown function (DUF3135)


Domain annotation for each model (and alignments):
>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.4   3.8e-08   6.7e-05      28      98 ..      13      81 ..      10      98 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 3.8e-08
     DUF4423 28 ellplkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyrqtekslttssevkseavrsyh 98
                 l ++k+++++ ++++k+ +  i+ ee +++le L++ +l++ +e++ +   +  ++++++ ++e+   +h
  EPA05380.1 13 VLGAIKKGAKKFDKIQKMAQ--IDPEELNSILEKLEERKLIEVEEKKSWLGKKIEIKITEKGSKEVDERIH 81
                5778999*************..***********************************99988888877766 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.2     2e-06    0.0036      11      67 ..      13      77 ..      11      85 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2e-06
      HTH_45 11 ILeaisegeakkTkimykanLsykllnkYLdmLvekgli........kkskekYvlTekGlelle 67
                +L ai++g +k  ki + a ++ + ln+ L++L e++li          +k + ++TekG++ ++
  EPA05380.1 13 VLGAIKKGAKKFDKIQKMAQIDPEELNSILEKLEERKLIeveekkswLGKKIEIKITEKGSKEVD 77
                688999999999***************************88775443336778899999998655 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   1.4e-05     0.025       9      64 ..      11      62 ..       7      73 .. 0.80
   2 ?   -0.3   0.0      0.71   1.3e+03      17      31 ..     134     148 ..     132     153 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.4e-05
      Rio2_N  9 frvLtavEmgmrnhevVptelieeisrlkeeevkkrlsrllkaklisr.ktakydGY 64
                  vL a+  g +++     ++i+++++++ ee+++ l++l ++kli+  +++++ G 
  EPA05380.1 11 VIVLGAIKKGAKKF-----DKIQKMAQIDPEELNSILEKLEERKLIEVeEKKSWLGK 62
                55666666666665.....689************************99666666665 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.71
      Rio2_N  17 mgmrnhevVptelie 31 
                 mgm   ++Vp e i 
  EPA05380.1 134 MGMMMTDYVPAESIP 148
                 899999*****9986 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.9   9.1e-06     0.016      18      63 ..      13      57 ..       6      83 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 9.1e-06
                 HHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEE CS
  TFIIE_alpha 18 vldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrr 63
                 vl ++  kg  + + ++k  +id++el ++L +L e +l+++  ++
   EPA05380.1 13 VLGAIK-KGAKKFDKIQKMAQIDPEELNSILEKLEERKLIEVEEKK 57
                 566655.8888999**************************998776 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   9.5e-06     0.017      19      58 ..      18      57 ..      12      70 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 9.5e-06
                HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
        TrmB 19 klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                k+g ++ d+i +++ ++    +++L++Le++ l+e+e+++
  EPA05380.1 18 KKGAKKFDKIQKMAQIDPEELNSILEKLEERKLIEVEEKK 57
                78999********************************987 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.3   1.8e-05     0.032      16      77 ..      23      84 ..      13      85 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.8e-05
      HTH_34 16 dfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkkyvkaLk 77
                +f ++++  ++   +L + l+kLe+ + iev+ +++   +++ ++iT++G ++ ++ +++L+
  EPA05380.1 23 KFDKIQKMAQIDPEELNSILEKLEERKLIEVEEKKSWLGKKIEIKITEKGSKEVDERIHELQ 84
                688999999999999****************999998889*************999998886 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   7.6e-05      0.14       9      54 ..      12      54 ..       7      58 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.6e-05
                HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
      MarR_2  9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                 vL+a+  +         + +  ++++  ++ il++L+++ L+e +
  EPA05380.1 12 IVLGAIKKGAK---KFDKIQKMAQIDPEELNSILEKLEERKLIEVE 54
                56777777766...677788899********************987 PP

>> DUF1676  Protein of unknown function (DUF1676)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   3.6   0.00011       0.2     110     150 ..      84     137 ..      23     139 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
     DUF1676 110 egR............kkk.kkkkklkkmllplllalklklklLlplalgllall 150
                 +g             k k k+     k++lp++++  ++ ++++ +++ + +++
  EPA05380.1  84 QGKwdqmsmlyksgdKQKlKEYMDDNKSILPMMMFFGIMDMMMFSMMFSMMGMM 137
                 233444444444443333566777889**********9999999****999986 PP

>> Abi_2  Abi-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.5   0.00014      0.25      93     143 ..      78     135 ..      18     151 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00014
       Abi_2  93 k.......liekiekeierskesfikhykkkynkeiPlWvlvevlsfGtlsklykllk 143
                 +         ++++  +++ +++ +k+y++ +++ +P+ +++ ++++  +s +++++ 
  EPA05380.1  78 ErihelqgKWDQMSMLYKSGDKQKLKEYMDDNKSILPMMMFFGIMDMMMFSMMFSMMG 135
                 1212222222333333333335589999988889********************9986 PP

>> DUF3135  Protein of unknown function (DUF3135)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.3   0.00011      0.19       4      29 ..      23      48 ..      21      58 .. 0.83
   2 ?   -2.9   0.0       4.9   8.7e+03      35      47 ..      73      85 ..      64      95 .. 0.65
   3 ?   -6.7   5.3        10   1.8e+04      65      74 ..     120     129 ..     110     139 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
     DUF3135  4 dfdeLvaLakedPealealrqeliee 29
                +fd+  ++a+ dPe+l+++ ++l e+
  EPA05380.1 23 KFDKIQKMAQIDPEELNSILEKLEER 48
                6*****************99988765 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.9
     DUF3135 35 peemqrrLrglqf 47
                ++e  +r+ +lq 
  EPA05380.1 73 SKEVDERIHELQG 85
                5556666666664 PP

  == domain 3  score: -6.7 bits;  conditional E-value: 10
     DUF3135  65 alsrmmqekl 74 
                  ++ mm  ++
  EPA05380.1 120 GIMDMMMFSM 129
                 5566655444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1513  (0.0843884); expected 358.6 (0.02)
Passed bias filter:                      765  (0.0426683); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.59u 0.36s 00:00:00.95 Elapsed: 00:00:00.53
# Mc/sec: 998.82
//
Query:       EPA05381.1  [L=100]
Description: Rieske [2Fe-2S] domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-14   53.7   0.0    1.6e-14   53.6   0.0    1.0  1  Rieske    Rieske [2Fe-2S] domain
    4.4e-13   49.1   0.0    5.1e-13   48.9   0.0    1.1  1  Rieske_2  Rieske-like [2Fe-2S] domain


Domain annotation for each model (and alignments):
>> Rieske  Rieske [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.6   0.0   1.8e-18   1.6e-14       2      89 .]       3      88 ..       2      88 .. 0.93

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 1.8e-18
                EEEEEEGGGC-TTCEEEEEETTEEEEEEE-TTS-EEEEESC-TTTT-BCGGSEEETT.EEE-TTT--EEE.TTSBEEE-TTHHHEEEET CS
      Rieske  2 wvavakesdvpegdpltvkvggeplvvlrdedgevyAlsdvCtHrgaplsegkidekgvleCpcHgwayd.adGkvikgPaprplatyp 89
                w ++a++ ++  g+ +++k+ g+++++++  ++ ++A++d C H+  +++ gk+ e+  +eCp+H w y+ ++G++++  +  +latyp
  EPA05381.1  3 WKKIAEKTEIAAGKGKAFKIDGKQVAIFN--QDGYHAIDDLCVHQDGSIAPGKL-EGDIVECPLHFWHYNiKTGELKDYLKDVKLATYP 88
                99***************************..588**************999***.566*******************998888888886 PP

>> Rieske_2  Rieske-like [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9   0.0   5.6e-17   5.1e-13       2     103 ..       3      98 ..       2      99 .. 0.93

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 5.6e-17
                 EEEEEECCCS-TTB-EEEEETTEEEEEEE-TTS-EEEEESS-TTTSSSTCCCSEEEECTTCEEEE-TTT--EEETTT-BBSS.-TTSB-BEE-EEESTS CS
    Rieske_2   2 wvpvckledlvketgvaalvdgkqvalfrlekeevyAidnldpaseanvlsrGlvgdkkgelvvasPlykqkfdLktGecle.deevslkvypvrvedg 99 
                 w+++++ +++++++g+a  +dgkqva+f +  +  +Aid+l+   +   ++ G+++ +    +v++Pl+  ++++ktGe  +  ++v+l++ypv  +++
  EPA05381.1   3 WKKIAEKTEIAAGKGKAFKIDGKQVAIFNQ--DGYHAIDDLCVH-QDGSIAPGKLEGD----IVECPLHFWHYNIKTGELKDyLKDVKLATYPVEARND 94 
                 ****************************98..999*******99.7889999998877....9*******************5577************9 PP

                 EEEE CS
    Rieske_2 100 kvev 103
                  +++
  EPA05381.1  95 GIYI 98 
                 9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 620.58
//
Query:       EPA05382.1  [L=119]
Description: hypothetical protein BG20_I1238 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00098   19.8   3.3     0.0013   19.5   3.3    1.1  1  AATF-Che1        Apoptosis antagonizing transcription factor
  ------ inclusion threshold ------
      0.013   14.9   2.1      0.016   14.6   2.1    1.0  1  ALIX_LYPXL_bnd   ALIX V-shaped domain binding to HIV
      0.024   14.8   1.9      0.049   13.8   1.5    1.6  2  CREPT            Cell-cycle alteration and expression-elevate
       0.03   14.9   2.3       0.31   11.6   0.7    2.2  2  Syntaxin-6_N     Syntaxin 6, N-terminal
      0.049   13.4   0.5      0.059   13.2   0.5    1.1  1  PH_4             Pleckstrin homology domain
      0.059   13.8   1.5       0.12   12.8   1.1    1.8  1  Snapin_Pallidin  Snapin/Pallidin
      0.062   13.6   0.1        1.9    8.8   0.1    2.1  2  DUF948           Bacterial protein of unknown function (DUF94


Domain annotation for each model (and alignments):
>> AATF-Che1  Apoptosis antagonizing transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   3.3   4.9e-07    0.0013      28     103 ..      37     113 ..      33     119 .] 0.70

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 4.9e-07
   AATF-Che1  28 altaanqLpqpetlkeflesseefeealeeaekalkklleslleLreelleqneikkla...eskeeeekkkskrkrkk 103
                 ++t+an L ++e+l ++ e+++e+ +a+e+ +++l+++ ++++ ++++l  +n +k+++   ++ +++ ++ +k+k  k
  EPA05382.1  37 LITSANLLRSNEHLTKVSEKQSELISAYEQYSNSLEDITKTIFGIQNDL--KNLLKEQSkliSDGKSKVSTPKKKKISK 113
                 5799*********************************************..3333333334433332332222222222 PP

>> ALIX_LYPXL_bnd  ALIX V-shaped domain binding to HIV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   2.1   6.1e-06     0.016      97     194 ..      12     113 ..       8     118 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6.1e-06
  ALIX_LYPXL_bnd  97 ivrqklqenkedlelLsgpeeeleaalp......ssssaaa....sesveeqirklrsllekldelkaereqllkdlkekaendDitpklltekk 181
                     ++r+k+ ++k dl+ L+gp +++ +++       s++   +    se+ +e i+  ++  + l+++ ++   + +dlk+  +++   +kl++  k
      EPA05382.1  12 DLRKKIYDIKLDLDQLGGPIQDMPELITsanllrSNE---HltkvSEKQSELISAYEQYSNSLEDITKTIFGIQNDLKNLLKEQ---SKLISDGK 100
                     79****************9999999988444443222...13356999999999999999999999999999999999888888...89999999 PP

  ALIX_LYPXL_bnd 182 rdiaanefealfe 194
                     +++++ +++++++
      EPA05382.1 101 SKVSTPKKKKISK 113
                     9888888787776 PP

>> CREPT  Cell-cycle alteration and expression-elevated protein in tumour
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1      0.11   2.9e+02      99     138 ..      10      49 ..       7      55 .. 0.78
   2 ?   13.8   1.5   1.9e-05     0.049      37     106 ..      41     110 ..      30     119 .] 0.87

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.11
       CREPT  99 leelkeklekvksvrkelkshiqsLPdLtelpdvtgglap 138
                 +++l++k+  +k   ++l   iq +P+L +  +   + ++
  EPA05382.1  10 INDLRKKIYDIKLDLDQLGGPIQDMPELITSANLLRSNEH 49 
                 6789999999999999999999*99999876665555555 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1.9e-05
       CREPT  37 lekikdkeeaekllkqveealellaeYnkrLeaeleeRkklakmledfleaqkellakaeekleelkekl 106
                 ++ ++++e+ +k +++ +e +++ ++Y ++Le+ ++    +++ l+++l+ q +l+++ ++k++  k+k 
  EPA05382.1  41 ANLLRSNEHLTKVSEKQSELISAYEQYSNSLEDITKTIFGIQNDLKNLLKEQSKLISDGKSKVSTPKKKK 110
                 4456899999****************************************************99988774 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.053   1.4e+02      41      61 ..       8      28 ..       3      39 .. 0.85
   2 ?   11.6   0.7   0.00012      0.31      28      73 ..      45     102 ..      29     118 .. 0.62

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.053
  Syntaxin-6_N 41 etrteLrkalrsiewdledLe 61
                  e  ++Lrk++ +i+ dl++L 
    EPA05382.1  8 EVINDLRKKIYDIKLDLDQLG 28
                  66799*************996 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00012
  Syntaxin-6_N  28 ledtssstseeldetrteLrkalrsiewdledLeetv...............riveknpsk 73 
                   +++   +   +++e ++eL +a+++ ++ led+ +t+               + ++  +sk
    EPA05382.1  45 RSN---EHLTKVSEKQSELISAYEQYSNSLEDITKTIfgiqndlknllkeqsKLISDGKSK 102
                   333...2467899999*********************655555554444444344444444 PP

>> PH_4  Pleckstrin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.5   2.3e-05     0.059      65     136 ..      38     109 ..      35     119 .] 0.78

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.3e-05
        PH_4  65 ltelDLlernktfdeanpgehalprvyaDgwkSseeessrcfvlwfgkkralskakkskkkekekkakekas 136
                 +t+ +Ll++n+++ ++++++++l  +y+   +S e+ +++ f +    k+ l +++k  ++ k+k ++ k++
  EPA05382.1  38 ITSANLLRSNEHLTKVSEKQSELISAYEQYSNSLEDITKTIFGIQNDLKNLLKEQSKLISDGKSKVSTPKKK 109
                 8999*****************************************988887777777666655544433332 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.1   4.8e-05      0.12      35      88 ..      42      94 ..      37      96 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.8e-05
  Snapin_Pallidin 35 qldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqklkkRaek 88
                     +l r ne L++++e q+ e+++  ++y + L  i k +  +++ l++l k  +k
       EPA05382.1 42 NLLRSNEHLTKVSEKQS-ELISAYEQYSNSLEDITKTIFGIQNDLKNLLKEQSK 94
                     56788999999999999.99***********************99999876555 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.051   1.3e+02      24      58 ..       6      43 ..       3      63 .. 0.71
   2 ?    8.8   0.1   0.00075       1.9      28      68 ..      64     104 ..      58     108 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.051
      DUF948 24 lkktldeaaatieele...kqvdpilkevedllakvne 58
                l+++++ +++ i +++   +q+++ ++++ +l++ +n 
  EPA05382.1  6 LGEVINDLRKKIYDIKldlDQLGGPIQDMPELITSANL 43
                67889999999999996666666666777777777765 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00075
      DUF948  28 ldeaaatieelekqvdpilkevedllakvnelledvnekle 68 
                  ++ ++++e+++k + +i +++++ll++  +l +d ++k+ 
  EPA05382.1  64 YEQYSNSLEDITKTIFGIQNDLKNLLKEQSKLISDGKSKVS 104
                 56778888999999999999999999999998888887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1473  (0.0821574); expected 358.6 (0.02)
Passed bias filter:                      605  (0.0337442); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 821.26
//
Query:       EPA05383.1  [L=303]
Description: NAD-binding protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      6e-23   81.5   0.0    7.8e-23   81.2   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
      2e-18   66.9   0.0    4.9e-18   65.6   0.0    1.6  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
      2e-12   46.8   0.0    5.1e-06   25.8   0.0    2.2  2  NAD_binding_4    Male sterility protein
    4.9e-12   45.4   0.4    1.7e-11   43.7   0.4    1.9  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    8.1e-08   31.7   0.0    4.5e-07   29.3   0.0    1.8  2  RmlD_sub_bind    RmlD substrate binding domain
      2e-06   27.2   0.5    0.00024   20.4   0.5    2.9  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    9.2e-06   25.7   0.0    1.5e-05   24.9   0.0    1.3  1  NAD_binding_10   NAD(P)H-binding
    0.00021   20.9   0.1    0.00078   19.1   0.0    1.9  2  NmrA             NmrA-like family
  ------ inclusion threshold ------
      0.019   14.8   0.0      0.039   13.8   0.0    1.5  1  DUF1731          Domain of unknown function (DUF1731)
      0.019   13.0   0.0      0.025   12.7   0.0    1.1  1  PRTP             Herpesvirus processing and transport protein
      0.043   13.5   0.1      0.084   12.6   0.1    1.4  1  Sarcolipin       Sarcolipin
       0.11   11.9   0.0       0.27   10.6   0.0    1.6  1  DUF3798          Protein of unknown function (DUF3798)
       0.12   11.9   0.0       0.21   11.0   0.0    1.4  1  adh_short        short chain dehydrogenase


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.2   0.0   5.6e-26   7.8e-23       1     240 [.       5     219 ..       5     220 .. 0.87

  Alignments for each domain:
  == domain 1  score: 81.2 bits;  conditional E-value: 5.6e-26
                 EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHHHSHHHHHHHHTHHHHHHH CS
   Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggvaassedpadfieknlqgtlnll 99 
                 ilVtGatGfiGs lv+ l +k+y+v  l r+ +++n+ +    +++ +dltd++     ++   ++ v+hlA   ++ +++++  +  + n++gt +l+
  EPA05383.1   5 ILVTGATGFIGSRLVNSLIKKDYDVSSLIRKGNNGNQRS----NIIFGDLTDSTLNISNIE---FQNVFHLAS-HTPLERNKKILE--KVNVEGTKKLF 93 
                 8******************************88887665....89*******997777776...89*****55.444444444344..69********* PP

                 HHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSS CS
   Epimerase 100 eaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklveayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkq 198
                 ++++++    + ++s   vYG+  ++  +et    p  pn+ +    l + k +e+  ++ g+n++++    +yG +        ++  l++++l++  
  EPA05383.1  94 NCIKDKTK-SFTYISGLGVYGETLDKIVDETF---PHDPNTDFVKIRLEAQKFLEKNCKELGINFTVVYFGDVYGSG------GWFYEMLVKRLLKN-- 180
                 ***98877.************99994367777...99****************************************......88888888888876.. PP

                 SEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT-STTEEEEE CS
   Epimerase 199 evtllgdgtalRdflyveDvaeaillvlehvdagdkgeiyni 240
                  + + + g+    f++veD++  ++ + e+   +++g+ y i
  EPA05383.1 181 TFRMPKGGEYYKAFVHVEDAVGSMISIFEK---NPSGGEYII 219
                 59***************************9...666667766 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.6   0.0   3.5e-21   4.9e-18       1     269 [.       6     241 ..       6     247 .. 0.87

  Alignments for each domain:
  == domain 1  score: 65.6 bits;  conditional E-value: 3.5e-21
                    EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHTTSHH CS
  GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevynLAAqshVdvsfekPe 96 
                    L+TG +GfiGs l++ L++k+y+v  ++r+ ++ n                ++ +++ gDltDs+     ++++++++v++LA     ++     +
     EPA05383.1   6 LVTGATGFIGSRLVNSLIKKDYDVSSLIRKGNNGN----------------QRSNIIFGDLTDSTL---NISNIEFQNVFHLASHTPLERNK---K 79 
                    9**************************99988866................1234688*****874...58999*********888887754...5 PP

                    HHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTS CS
  GDP_Man_Dehyd  97 ytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYaaaKlyadwivvnyreayglfavngilfnhesprrgetf 192
                       +vnv Gt +L+++i++    k++ f  +S   vYG++ +  ++Et p +P+  +   +l a+ + ++  ++ g+  ++  +   ++      f
     EPA05383.1  80 ILEKVNVEGTKKLFNCIKD----KTKSFTYISGLGVYGETLDKIVDETFPHDPNTDFVKIRLEAQKFLEKNCKELGINFTVVYFGDVYGSG--GWF 169
                    7899*************98....4578*****************************************************99999999987..579 PP

                    CCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHHHHHHHHCS.S---EEE-TT-EEECHHCHHCCHHCCCHH CS
  GDP_Man_Dehyd 193 vtrkitravarialgkqevlylGnldakRdwghvkDyveamwlmlqqd.kpedyviatgethsvrefvelaflelgkt 269
                     + ++ r + ++ +    +++   ++  + + hv+D v  m  +++++ +  +y+ia++ +++ +efv+ ++ ++g++
     EPA05383.1 170 YEMLVKRLLKNTFR----MPK--GGEYYKAFVHVEDAVGSMISIFEKNpSGGEYIIADNSSVKFKEFVDFTADSIGQN 241
                    99999888877555....333..356689****************98515589*****************99999875 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   1.6e-07   0.00022       1      36 [.       7      40 ..       7      47 .. 0.85
   2 !   25.8   0.0   3.7e-09   5.1e-06      60     157 ..      41     138 ..      35     184 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.6e-07
                   EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSHHH CS
  NAD_binding_4  1 lTGaTGFLGkvLlekLLrttpevkiyllvRaksges 36
                   +TGaTGF+G++L++ L++++    +  l+R+ ++ +
     EPA05383.1  7 VTGATGFIGSRLVNSLIKKDY--DVSSLIRKGNNGN 40
                   7******************98..7999999987644 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 3.7e-09
                    TTEEEEE--TTSGGGG--HHHHHHHHHH--EEEE--SS-S.STTSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H.. CS
  NAD_binding_4  60 erikvveGDlseprlGLseedlqelaeevdviihsaAtvnfdepykellrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeeg 155
                    +r  ++ GDl+++ l +s+ ++q++       +h a  + ++++ k l +vNveGt+++++  k  k + ++ ++S   v+ge  +++ ++++++ 
     EPA05383.1  41 QRSNIIFGDLTDSTLNISNIEFQNV-------FHLASHTPLERNKKILEKVNVEGTKKLFNCIK-DKTK-SFTYISGLGVYGETLDKIVDETFPHD 127
                    6888999999999999999999887.......*****************************888.4444.9******8888888888988888866 PP

                    ........... CS
  NAD_binding_4 156 e.........k 157
                              +
     EPA05383.1 128 PntdfvkirlE 138
                    54555555541 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.7   0.4   1.2e-14   1.7e-11       1     220 [.       6     199 ..       6     249 .. 0.69

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 1.2e-14
   3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslvdvagkltedeimkvnvkGTrnv 99 
                 +vtG++GF+G++lv++L++ +       +D+    ++    +  ++ ++i gD+td  +l+    + + v+hlas +++    +++ + kvnv+GT+++
  EPA05383.1   6 LVTGATGFIGSRLVNSLIKKD-------YDVSSLIRK--GNNGNQRSNIIFGDLTDS-TLNISNIEFQNVFHLASHTPLER--NKKILEKVNVEGTKKL 92 
                 69*****************99.......566554444..33444555589*****96.577777789999********998..88899*********98 PP

   3Beta_HSD 100 leacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKalaEklvlkaNgrtlknggrlyTcaLRpagiyGegdkllvpllkqlak 198
                    c+k   + + Y S ++v g+  + ++i+  dE+ +++++    + + +  a k++ + N    k+ g  +T+ +    +yG g  + + l+k+l+k
  EPA05383.1  93 F-NCIKDKTKSFTYISGLGVYGE--TLDKIV--DETFPHDPN--TDFVKIRLEAQKFL-EKNC---KELGINFTV-VYFGDVYGSGGWFYEMLVKRLLK 179
                 7.59*******************..778888..888888765..34556666666554.3344...444422333.33456777777777777777777 PP

   3Beta_HSD 199 lglalfkigdeevlsdrvYvgN 220
                 +   + k g+    + +v v+ 
  EPA05383.1 180 NTFRMPKGGEYY--KAFVHVED 199
                 777777666543..35666665 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.0   3.3e-10   4.5e-07       2     159 ..       4     170 ..       2     185 .. 0.84
   2 ?    0.1   0.0      0.26   3.5e+02     258     285 ..     269     296 ..     265     298 .. 0.89

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 3.3e-10
                    EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT........T--TTSHHHHHHHHHHH--SEEEE------HHHHHHSHHHHHHHHTHHHHHHHHHH CS
  RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltre........eldltdaeavaellkeakpdvvvnaAAytavDkaEseeeaayavnaeavealAeaa 89 
                     ilvtGa+G +Gs L+++l +++++v +l r+        ++ + d +  +  +++++ + v ++A +t     E +++  ++vn+e++++l +  
     EPA05383.1   4 SILVTGATGFIGSRLVNSLIKKDYDVSSLIRKgnngnqrsNIIFGDLTDSTLNISNIEFQNVFHLASHTP---LERNKKILEKVNVEGTKKLFNCI 96 
                    59***************************9998888886655556666667778999************7...599******************** PP

                    HHCT-EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHHH-S....SEEEEEE-SEESSSSS-H CS
  RmlD_sub_bind  90 aavgalLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavlaagk....kalivRtswvygekgknf 159
                    +     + ++S   V+  + ++   e+ + +P + + + +l+  +  ++++k    ++++v ++ vyg+ g  +
     EPA05383.1  97 KDKTKSFTYISGLGVYGETLDKIVDETFPHDPNTDFVKIRLEAQKFLEKNCKelgiNFTVVYFGDVYGSGGWFY 170
                    ****************9999999999999999999999999998888887763333678888888888865433 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.26
                    B--HHHHHCCT----BHHHHHHHHHHHH CS
  RmlD_sub_bind 258 Ldtekleatfgiklrewrealkevlkel 285
                     +++k+++++ +k +++++++ +v+ el
     EPA05383.1 269 VSNKKISQIYEFKFPSYQQGIPNVISEL 296
                    5899*******************99987 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.5   1.7e-07   0.00024       1     238 [.       5     229 ..       5     278 .. 0.67

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.7e-07
                      EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-SEEEE------HHHHH CS
  Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvdvvfhaAAlKhVPlve 94 
                      +lvtGa+G iGs+lv+ ++kk+     l+ +  +             ++++       + gd++d++   + +e    + vfh A   h Pl e
       EPA05383.1   5 ILVTGATGFIGSRLVNSLIKKDYDVSSLIRKGNN-----------GNQRSN------IIFGDLTDSTLNISNIE---FQNVFHLAS--HTPL-E 75 
                      89***************99987654444433322...........222222......3689**99987666666...99*****97..6775.8 PP

                      HSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEE........GGGSS--SHHHHHHHHHHHHHHHGGG--SSS-......-EEEEEEE-EETTG CS
  Polysacc_synt_2  95 enpleaiktNvlgtenvieaaieagvkkvvliSt........DKAvnPtnvmGatKrlaekllqalakeseekk......tkfvvvRfGNVlgS 174
                      +n     k Nv gt+++ + +i+ + k++ +iS         DK v+ t        +    l a +  +   k       +f+vv fG V gS
       EPA05383.1  76 RNKKILEKVNVEGTKKLFN-CIKDKTKSFTYISGlgvygetlDKIVDETFPHDPNTDFVKIRLEAQKFLE---KnckelgINFTVVYFGDVYGS 165
                      888888899******9987.789999******95444444458888766544433333333332222222...0222444999999*****999 PP

                      TTSSHHHHHHHHHTTSSEEES-TT-EEEEE-HHHHHHHHHHHHHH-.-SS-EEEE--.-EEEHHH CS
  Polysacc_synt_2 175 rGSviplFkkqikeggpvtvTdpemtRyfmtieeavqLvlqalala.kggeifvldmGepvkivd 238
                       G    +  k++ +++       e  + f+ +e+av  +++ +++  +gge  + d   +vk ++
       EPA05383.1 166 GGWFYEMLVKRLLKNTFRMPKGGEYYKAFVHVEDAVGSMISIFEKNpSGGEYIIADN-SSVKFKE 229
                      998877766655554332223344555566777777655555544314455555555.6666655 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   1.1e-08   1.5e-05       1     144 [.       9     160 ..       9     166 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.1e-08
                     TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES-....--TCC........HHHHHHHHHH CS
  NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsal....ggggk........deegaknivd 83 
                     GAtG +G++lv+ l+++ +++v  l+R+ +  +     ++ +++ gd+td+    + ++ +++   a         +        + eg+k++ +
      EPA05383.1   9 GATGFIGSRLVNSLIKK-DYDVSSLIRKGNNGN-----QRSNIIFGDLTDSTLNISNIEFQNVFHLAShtplE---RnkkilekvNVEGTKKLFN 94 
                     9****************.7*********99977.....6889*******999988999988876555533432...1223544444444999997 PP

                     HHHHCT--EEEEEEETTTTSGCGCH......HHHHHHHCCHHHHHHHHHHHHHHHHSSSEEEEEEE- CS
  NAD_binding_10  84 aakeagvkRfvlvsaigvgdevpge......fgewnkellkaylaakraaeellrasgldwTivrpg 144
                        + ++k f ++s++gv+ e+ ++       ++ n++++k  l+a++  e+  ++ g+++T+v  g
      EPA05383.1  95 CI-KDKTKSFTYISGLGVYGETLDKivdetfPHDPNTDFVKIRLEAQKFLEKNCKELGINFTVVYFG 160
                     55.679************987444322222234456678899999999999999999*****99765 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   5.6e-07   0.00078       1      32 [.       5      36 ..       5      57 .. 0.92
   2 ?   -0.9   0.0      0.73     1e+03     126     142 ..     144     160 ..     123     241 .. 0.65

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 5.6e-07
                EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S CS
        NmrA  1 IlviGaTGrqGksvvrallkaghkvralvRdt 32
                Ilv+GaTG +G+ +v+ l+k++++v  l+R+ 
  EPA05383.1  5 ILVTGATGFIGSRLVNSLIKKDYDVSSLIRKG 36
                9*****************************86 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.73
                 HHHHHHCTS-EEEEEE- CS
        NmrA 126 eeyvralgipytfvyag 142
                 e+  ++lgi++t vy g
  EPA05383.1 144 EKNCKELGINFTVVYFG 160
                 77778888888888754 PP

>> DUF1731  Domain of unknown function (DUF1731)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.8e-05     0.039       1      39 [.     246     284 ..     246     288 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.8e-05
     DUF1731   1 vPafalklllG.emaellLegqrVlPkrLleaGFqFrypd 39 
                 +P f+ k++lG +  +ll+++ +V+ k++ +  ++F++p+
  EPA05383.1 246 IPMFIAKAVLGgDLIKLLTTSMKVSNKKISQI-YEFKFPS 284
                 699********99999************9876.7777775 PP

>> PRTP  Herpesvirus processing and transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.8e-05     0.025     463     518 ..      62     117 ..      23     126 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.8e-05
        PRTP 463 alelvdkvlrdvkeRkkaYleklskeglaklqrCireqeellekllsvnvyGevll 518
                  +++ + +++   eR k  lek+  eg +kl +Ci+++ +  + +  + vyGe l 
  EPA05383.1  62 FQNVFHLASHTPLERNKKILEKVNVEGTKKLFNCIKDKTKSFTYISGLGVYGETLD 117
                 67777788888899**************************************9875 PP

>> Sarcolipin  Sarcolipin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   6.1e-05     0.084       2      15 ..     144     157 ..     143     159 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.1e-05
  Sarcolipin   2 erstrElflNFTvV 15 
                 e++ +El +NFTvV
  EPA05383.1 144 EKNCKELGINFTVV 157
                 89***********9 PP

>> DUF3798  Protein of unknown function (DUF3798)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0    0.0002      0.27     136     176 ..     124     167 ..     112     171 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0002
                 ETTGGGSHHHHHH...HHHHHHHHHHCT--EEEEEE---SSTCH CS
     DUF3798 136 fprhlsyellakr...reimektckelGlefvevtapdptsdag 176
                 fp++ ++++++ r   ++ +ek+ckelG++f  v   d+ ++ g
  EPA05383.1 124 FPHDPNTDFVKIRleaQKFLEKNCKELGINFTVVYFGDVYGSGG 167
                 55555555555441115689************999999888776 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00015      0.21       1      37 [.       3      39 ..       3      49 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00015
                SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHH CS
   adh_short  1 kvvlvtGassGIGraiakelakeGakvvvvdrseekl 37
                k +lvtGa++ IG  +++ l+k++++v  + r+ ++ 
  EPA05383.1  3 KSILVTGATGFIGSRLVNSLIKKDYDVSSLIRKGNNG 39
                679************************9977776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 1889.12
//
Query:       EPA05384.1  [L=263]
Description: NAD+ synthetase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-76  256.9   1.4    1.6e-76  256.7   1.4    1.0  1  NAD_synthase     NAD synthase
    0.00044   19.1   0.0      0.028   13.2   0.0    2.4  2  tRNA_Me_trans    tRNA methyl transferase
     0.0034   17.4   0.6        7.1    6.8   0.0    3.3  3  SpoIIID          Stage III sporulation protein D
     0.0051   16.3   0.0      0.012   15.1   0.0    1.7  2  QueC             Queuosine biosynthesis protein QueC
      0.006   16.3   0.0        5.3    7.0   0.0    2.6  2  HTH_23           Homeodomain-like domain
     0.0076   15.9   0.1      0.061   12.9   0.0    2.2  2  ThiI             Thiamine biosynthesis protein (ThiI)
     0.0089   15.7   0.0      0.013   15.2   0.0    1.4  1  Asn_synthase     Asparagine synthase
     0.0092   15.8   3.8        6.5    6.7   0.0    3.4  3  RuvB_C           RuvB C-terminal winged helix domain
  ------ inclusion threshold ------
      0.025   14.3   1.5      0.027   14.1   0.3    1.6  2  DNA_pol_B_exo2   Predicted 3'-5' exonuclease related to the e
      0.041   13.6   0.0      0.072   12.8   0.0    1.5  1  ATP_bind_3       PP-loop family
       0.12   11.5   0.1       0.13   11.4   0.1    1.2  1  Peptidase_C25    Peptidase family C25
       0.27   11.3   1.3        1.3    9.1   0.2    2.5  3  Phage_terminase  Phage terminase small subunit
        1.1    9.3   5.9       0.52   10.4   0.4    2.6  2  AlphaC_C         AlphaC  C-terminal


Domain annotation for each model (and alignments):
>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  256.7   1.4   1.1e-79   1.6e-76       1     241 [.      17     256 ..      17     257 .. 0.98

  Alignments for each domain:
  == domain 1  score: 256.7 bits;  conditional E-value: 1.1e-79
                   HHHHHHHHHHHHHHHCTTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--.SSSTTHHHHHHHHHHHHHHTSEEEE---HHHHHHHHHHHHHHH CS
  NAD_synthase   1 lieelvdflkeyvkkagakgvvlGlSGGvDSslvaalavkalgkenvlalllP.ssvsseedvedalalaenlgievktidikpivrafeqelkeak 96 
                   +i+++++fl ++++k++++gv+lGlSGG+DS++va++++++l ke+ la+++P ++ +++ ++eda++++   g+e+k +dikpiv+ +++ l++++
    EPA05384.1  17 IINKIEEFLVQQLEKSKSNGVILGLSGGIDSAVVAYICKRIL-KEKTLAIIMPdTQITPRTETEDAMKMISLTGLEYKLVDIKPIVNEYSNYLEPNE 112
                   5899**************************************.**********9999***********************************99988 PP

                   -HHHHHHHHHHHHHHHHHHHHHHHTEEEB---BHHHHTTT-S-TTTTT--SBETTTTS-HHHHHHHHHHTT--HHHHCS--B--SSTT-BHHHHHSS CS
  NAD_synthase  97 edlakgNlkaRiRmailyaianklnllvlgTgnksElvvGyfTkyGDgaadlapiaellKtevkeLakelnvPervlkkpPsAdLkpgqtDeeeLgi 193
                      akgNl+aRiR +ily++an+ n+lvlg ++ksE+++GyfTkyGDga d+ pi +l+K +v+e+ak l++P+++++k+ s +L+++   e+e+g 
    EPA05384.1 113 --RAKGNLRARIRTNILYYYANMKNYLVLGSSDKSEYLIGYFTKYGDGASDIVPIISLYKLQVREIAKVLGIPKNIIEKKSSPHLWKEHEAEKEIGA 207
                   ..89********************************************************************************************* PP

                   -HHHHHHHHT.HSSSS...HHHHHTTT--HHHHHHHHHHHHHTGGGGSS CS
  NAD_synthase 194 kYdelDeiLk.lvekkkspeeiikekelpaevvekieklvkksehKrkl 241
                   +Y+e+D iL  ++ekk s e+++++++++++ v k+ kl+  s hKr++
    EPA05384.1 208 QYEEIDSILYcIFEKKLSIEKTAETLQIEKQSVDKVYKLYLDSMHKREM 256
                   *********99************************************97 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0     2e-05     0.028       3      32 ..      37      67 ..      35     136 .. 0.79
   2 ?    3.6   0.0     0.017        23     165     193 ..     162     192 ..     155     196 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2e-05
  tRNA_Me_trans  3 vvvalSgGVDSsvaaallkeqgye.vigvfl 32
                   v+ +lSgG+DS+v+a++ k+  +e + ++++
     EPA05384.1 37 VILGLSGGIDSAVVAYICKRILKEkTLAIIM 67
                   899*************999876541334444 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.017
  tRNA_Me_trans 165 lfPlgeltKeevrkiAkeagla..vaekkdS 193
                    + P+ +l K +vr+iAk  g++  + ekk S
     EPA05384.1 162 IVPIISLYKLQVREIAKVLGIPknIIEKKSS 192
                    68999**************998778888877 PP

>> SpoIIID  Stage III sporulation protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.13   1.8e+02      36      56 ..      10      30 ..       4      40 .. 0.86
   2 !    6.8   0.0    0.0051       7.1      15      42 ..     166     193 ..     157     212 .. 0.82
   3 ?    4.9   0.1      0.02        27      11      40 ..     215     244 ..     208     258 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.13
     SpoIIID 36 vhkDvterLkkinkklakqvk 56
                + +D t++++ki++ l +q+ 
  EPA05384.1 10 INQDYTKIINKIEEFLVQQLE 30
                789*************99965 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0051
     SpoIIID  15 iveskatvRkaakvfgvskstvhkDvte 42 
                 i  +k  vR++akv+g+ k  + k  + 
  EPA05384.1 166 ISLYKLQVREIAKVLGIPKNIIEKKSSP 193
                 5567889*************99987665 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.02
     SpoIIID  11 iakyiveskatvRkaakvfgvskstvhkDv 40 
                 i + i+e+k  + k+a+++++ k  v k  
  EPA05384.1 215 ILYCIFEKKLSIEKTAETLQIEKQSVDKVY 244
                 566799******************998855 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   8.9e-06     0.012       3      64 ..      38     100 ..      36     140 .. 0.82
   2 ?   -3.1   0.0       3.2   4.4e+03     157     177 ..     164     184 ..     162     189 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 8.9e-06
                 EEE--SSHHHHHHHHHHHHH-SE.EEEEEEESS-T.TSHHHHHHHHHHHHT--.-EEEEE-GGG CS
        QueC   3 vvllSGGlDSttvlalakkegke.vealtfdYgqr.hkkeleaakkiakelgveehkildldll 64 
                 ++ lSGG+DS++v+++ k+  ke   a+ +   q   ++e+e a k+++ +g+ e k +d++ +
  EPA05384.1  38 ILGLSGGIDSAVVAYICKRILKEkTLAIIMPDTQItPRTETEDAMKMISLTGL-EYKLVDIKPI 100
                 6779**************988652556666666666999*************9.9999999854 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.2
                 TTTT--HHHHHHHHHHTTHHH CS
        QueC 157 PlidlsKaeivklgkelgvpl 177
                 P+i l K ++ +++k lg+p 
  EPA05384.1 164 PIISLYKLQVREIAKVLGIPK 184
                 899999999999999998765 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0    0.0039       5.3      13      32 ..     168     185 ..     164     189 .. 0.79
   2 !    6.5   0.0    0.0054       7.5      16      41 ..     221     247 ..     214     254 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0039
      HTH_23  13 llaeGlsvreIAreLgvsrr 32 
                 l++  l vreIA+ Lg++++
  EPA05384.1 168 LYK--LQVREIAKVLGIPKN 185
                 555..789*********986 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0054
      HTH_23  16 e.GlsvreIAreLgvsrrTvyrwlkry 41 
                 e +ls+++ A+ L + ++ v+++ k y
  EPA05384.1 221 EkKLSIEKTAETLQIEKQSVDKVYKLY 247
                 5589*********************99 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   4.5e-05     0.061       5      77 ..      36     109 ..      32     135 .. 0.61
   2 ?    0.3   0.1      0.31   4.3e+02     142     167 ..     163     188 ..     160     214 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.5e-05
        ThiI   5 kvlaLlSgGiDSpVaaylllkRGcrvvlv..hlknepgts.eeaiekveklaellaeyqtslevklvvvdfkevlk 77 
                  v++ lSgGiDS V ay+  kR ++ +++   + ++ +t+  e+++ ++++     ey+ ++++k +v ++ ++l+
  EPA05384.1  36 GVILGLSGGIDSAVVAYIC-KRILKEKTLaiIMPDTQITPrTETEDAMKMISLTGLEYK-LVDIKPIVNEYSNYLE 109
                 567779***********75.666655444003433333330444445555555555565.4666666666666654 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.31
        ThiI 142 rPLigldKeeiiklAkeigtyeisie 167
                  P+i+l K ++ ++Ak +g  +  ie
  EPA05384.1 163 VPIISLYKLQVREIAKVLGIPKNIIE 188
                 69**************9997655555 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   9.4e-06     0.013      23      52 ..      40      67 ..      20     131 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 9.4e-06
  Asn_synthase 23 lLSGGlDSSliaalaarqsksplktFsigf 52
                   LSGG+DS+++a++ +r +k   kt +i +
    EPA05384.1 40 GLSGGIDSAVVAYICKRILK--EKTLAIIM 67
                  49***************996..46665555 PP

>> RuvB_C  RuvB C-terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.2     0.013        18      29      51 ..       6      28 ..       3      33 .. 0.90
   2 !    6.7   0.0    0.0047       6.5      25      51 ..     172     198 ..     165     206 .. 0.87
   3 ?    3.3   0.1     0.054        75      15      44 ..     216     244 ..     204     250 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.013
                HHHHTT--HHHHHHTTHHHHHHT CS
      RuvB_C 29 laailgeeketiedviEPyLlke 51
                + +i++ + ++i+++iE +L+++
  EPA05384.1  6 IDEIINQDYTKIINKIEEFLVQQ 28
                77899***************986 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0047
                 -HHHHHHHTT--HHHHHHTTHHHHHHT CS
      RuvB_C  25 glktlaailgeeketiedviEPyLlke 51 
                  ++ +a++lg++k+ ie++  P L ke
  EPA05384.1 172 QVREIAKVLGIPKNIIEKKSSPHLWKE 198
                 6789****************9999876 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.054
                 HHHT.TT--B-HHHHHHHTT--HHHHHHTT CS
      RuvB_C  15 lkekfkggpvglktlaailgeeketiedvi 44 
                 l+  f +++++++  a++l++ek+ + +v+
  EPA05384.1 216 LYCIF-EKKLSIEKTAETLQIEKQSVDKVY 244
                 33333.477888888888888888888776 PP

>> DNA_pol_B_exo2  Predicted 3'-5' exonuclease related to the exonuclease domain of PolB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.5   2.1e+03     178     202 ..       7      31 ..       3      36 .. 0.74
   2 ?   14.1   0.3     2e-05     0.027      74     199 ..     128     251 ..     122     263 .] 0.72

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.5
  DNA_pol_B_exo2 178 gklseeeyaeeiaqvrellekekee 202
                     +++ +++y++ i++++e+l ++ e+
      EPA05384.1   7 DEIINQDYTKIINKIEEFLVQQLEK 31 
                     5667889999999999999766554 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 2e-05
  DNA_pol_B_exo2  74 khgvsapkyfdegdedrekkwnnylsrystrhlDLmdllseygaranakLdelakllglPGKlgvdGskVaelyqegkl.kei.reYcetDvlnT 166
                     ++  ++++y+  g++d+++    y+++y +   D++ ++s y    + ++ e+ak+lg+P K  ++ ++  +l++e +  kei ++Y e+D +  
      EPA05384.1 128 YYYANMKNYLVLGSSDKSEYLIGYFTKYGDGASDIVPIISLY----KLQVREIAKVLGIP-KNIIEKKSSPHLWKEHEAeKEIgAQYEEIDSI-L 216
                     56667788888899888888889*******************....57799*********.888999999****988762567568*****99.5 PP

  DNA_pol_B_exo2 167 Ylvylrlellrgklseeeya.eeiaqv.relleke 199
                     Y+++ +   ++ + ++ + + +++++v + +l + 
      EPA05384.1 217 YCIFEKKLSIEKTAETLQIEkQSVDKVyKLYLDSM 251
                     99998877776655544332022332213344333 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   5.2e-05     0.072       2      51 ..      37      86 ..      36     141 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.2e-05
                EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHH CS
  ATP_bind_3  2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvk 51
                v++++SgG+DS +  ++ ++  k++++ +++   +   r+e+++ +++++
  EPA05384.1 37 VILGLSGGIDSAVVAYICKRILKEKTLAIIMPDTQITPRTETEDAMKMIS 86
                789******************99877666655555555666666666665 PP

>> Peptidase_C25  Peptidase family C25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   9.5e-05      0.13      14      71 ..      79     140 ..      63     245 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.5e-05
                    HHHHHHHHHTTEEEEEEETTSTTT-S............SHHH.......HHHHHHHHHHHHHTT--SEEEEE CS
  Peptidase_C25  14 erlaefrrskGldvkvvtveeiynefs.......aGekdaaa.......irnflkyayknwsasklkYllLv 71 
                    e+  ++ + +Gl+ k v+++ i+ne+s              a       ir  + y+y+n      +Yl+L+
     EPA05384.1  79 EDAMKMISLTGLEYKLVDIKPIVNEYSnylepneR------AkgnlrarIRTNILYYYANM----KNYLVLG 140
                    4444444566*****************65444321......24555667**********99....4889986 PP

>> Phage_terminase  Phage terminase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.2   0.00097       1.3      23      48 ..     171     196 ..     167     204 .. 0.80
   2 ?   -2.1   0.0       2.9     4e+03      21      40 ..     222     241 ..     216     246 .. 0.76
   3 ?   -0.8   0.0       1.1   1.6e+03      10      20 ..     241     251 ..     236     258 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00097
  Phage_terminase  23 lklkdIAkvLdvsestvrkWKakDkW 48 
                      l++++IAkvL+++++ + k      W
       EPA05384.1 171 LQVREIAKVLGIPKNIIEKKSSPHLW 196
                      799**********9999875555555 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.9
  Phage_terminase  21 gtlklkdIAkvLdvsestvr 40 
                      + l + + A+ L++ ++ v 
       EPA05384.1 222 KKLSIEKTAETLQIEKQSVD 241
                      56677788999999888775 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.1
  Phage_terminase  10 DkAyelykEsg 20 
                      Dk y+ly++s 
       EPA05384.1 241 DKVYKLYLDSM 251
                      99*****9986 PP

>> AlphaC_C  AlphaC  C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.7      0.53   7.3e+02      43      58 ..      14      31 ..       3      35 .. 0.76
   2 ?   10.4   0.4   0.00038      0.52      28      65 ..      62      99 ..      57     103 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.53
    AlphaC_C 43 qsdiankiie..vtelek 58
                 ++i nki e  v++lek
  EPA05384.1 14 YTKIINKIEEflVQQLEK 31
                478999999877788988 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00038
    AlphaC_C 28 sleiikkdidnnPktqsdiankiievtelekklvtriP 65
                +l ii  d    P+t ++ a k+i +t le klv   P
  EPA05384.1 62 TLAIIMPDTQITPRTETEDAMKMISLTGLEYKLVDIKP 99
                5789999999************************8776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1189  (0.0663171); expected 358.6 (0.02)
Passed bias filter:                      676  (0.0377043); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 1595.48
//
Query:       EPA05385.1  [L=282]
Description: hypothetical protein BG20_I1228 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-31  108.4  13.4    5.5e-31  107.7  13.4    1.3  1  TackOD1         Thaumarchaeal output domain 1
     0.0004   20.3  19.0       0.07   13.1   2.7    3.8  4  zinc-ribbons_6  zinc-ribbons
    0.00056   19.9  17.6       0.15   12.1   8.7    3.2  3  DZR             Double zinc ribbon
     0.0017   18.5   0.1       0.02   15.1   0.1    2.4  1  Response_reg    Response regulator receiver domain
     0.0073   15.9  19.2        0.5   10.0   0.4    4.8  5  zf_UBZ          Ubiquitin-Binding Zinc Finger
     0.0074   16.6   3.7     0.0074   16.6   3.7    2.6  2  zf-Di19         Drought induced 19 protein (Di19), zinc-bindi
  ------ inclusion threshold ------
      0.015   15.3   2.2      0.015   15.3   2.2    3.2  2  DUF1610         Domain of unknown function (DUF1610)
      0.035   14.1  17.0       0.21   11.6   1.8    3.4  2  HypA            Hydrogenase/urease nickel incorporation, meta
      0.049   13.5  13.2        2.2    8.2   1.0    3.2  3  zf-C3HC4_3      Zinc finger, C3HC4 type (RING finger)
      0.066   13.4  14.1       0.23   11.7   5.2    2.3  2  FYVE_2          FYVE-type zinc finger
      0.089   13.3   0.5       0.18   12.3   0.1    1.8  2  Terminase_2     Terminase small subunit
      0.099   13.2  16.8        4.2    7.9  11.5    3.3  2  zf-CHY          CHY zinc finger
       0.12   13.1  15.7       0.62   10.8   0.2    3.4  3  zinc_ribbon_15  zinc-ribbon family
        0.2   11.8   0.2        0.2   11.8   0.2    3.4  4  Spt4            Spt4/RpoE2 zinc finger
       0.49   10.4  18.0        1.5    8.8   0.4    4.6  4  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
        1.6    8.7  20.7       0.31   11.0   0.3    5.1  5  zinc_ribbon_4   zinc-ribbon domain
        1.8    8.5  17.0        3.9    7.4   0.3    3.4  3  zf-RING_4       RING/Ubox like zinc-binding domain
        1.8    9.2  12.6         33    5.2   0.2    4.5  4  zf-C2H2         Zinc finger, C2H2 type
        3.7    7.6  13.9       0.51   10.4   0.4    3.6  3  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
        5.3    8.1  16.6         27    6.0   0.2    4.8  5  zf-C2H2_4       C2H2-type zinc finger
        5.5    7.0  14.3        6.7    6.7   0.5    3.6  4  Prok-RING_1     Prokaryotic RING finger family 1
        6.2    6.8  10.5         29    4.7   0.0    3.9  3  Zn_ribbon_SprT  SprT-like zinc ribbon domain
        6.6    7.2  15.1         10    6.6   0.1    3.3  3  zf-RING_2       Ring finger domain


Domain annotation for each model (and alignments):
>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.7  13.4   7.1e-34   5.5e-31      22     185 ..     117     277 ..     110     279 .. 0.92

  Alignments for each domain:
  == domain 1  score: 107.7 bits;  conditional E-value: 7.1e-34
     TackOD1  22 eeklepvldpkskelysypllealskekeeseelleelvkrglleeelvdrirlCpsCksghlnvrevCpkCkSidieeqelihhftCgnvgpeeeflk 120
                 ++++ ++l ++ k+    +l e + ++++ ++e+le l++++  ++    +i  C+sCks  ++ +  Cp+C+  +++++ li+h++Cgnv+ e+++ +
  EPA05385.1 117 TQSIIQTLLSTRKNSSVLELSELIGTNSKAIKEFLEFLESNNKAKNIGKIKIISCTSCKSVLVEQHFLCPNCNLEKFSQKDLIEHYSCGNVSLESKYEN 215
                 46667777777777778888888888888********************************************************************87 PP

     TackOD1 121 egkleCpkCktkLrhiGvDYdrplevykCnsCkslfsepevkarClsCekesesddlkvreiysy 185
                 +   +Cp+Ck++L+++GvDY++++e ++C++C++ f+ep+  ++C +C++e++ +++k+ e +++
  EPA05385.1 216 D---ICPNCKKELTALGVDYRKIQEYFICDECNEQFAEPKSTYSCKKCNTEFSLNKAKLIETEKF 277
                 7...5***************************************************999887776 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       2.4   1.9e+03      26      43 ..      10      27 ..       7      31 .. 0.81
   2 !    8.8   2.4     0.002       1.6      15      37 ..     167     190 ..     155     209 .. 0.70
   3 !    8.1   7.9    0.0033       2.6       2      42 ..     184     228 ..     169     230 .. 0.77
   4 !   13.1   2.7     9e-05      0.07       2      28 ..     240     266 ..     239     270 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2.4
                    EEEEEE-SSS-S---EEE CS
  zinc-ribbons_6 26 lkkealCpeCeqelevlk 43
                    ++k ++C++ eq l ++k
      EPA05385.1 10 FNKIKFCENTEQGLHIFK 27
                    678899999999888766 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.002
                     SEEE-TTT--.EEEEEEE-SSS-S CS
  zinc-ribbons_6  15 eqyhCeaCqe.dlkkealCpeCeq 37 
                     + ++C +C++  ++++ lCp+C+ 
      EPA05385.1 167 KIISCTSCKSvLVEQHFLCPNCNL 190
                     5689****9955677789****73 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0033
                     --SSS-S--EE-S...SEEE-TTT--EEE.EEEE-SSS-S---EE CS
  zinc-ribbons_6   2 kCpeCqqelekrg...eqyhCeaCqedlk.kealCpeCeqelevl 42 
                      Cp+C+ e  +++   e+y+C + + + k ++ +Cp+C++el  l
      EPA05385.1 184 LCPNCNLEKFSQKdliEHYSCGNVSLESKyENDICPNCKKELTAL 228
                     5888888777555688999998887655515679******99865 PP

  == domain 4  score: 13.1 bits;  conditional E-value: 9e-05
                     --SSS-S--EE-SSEEE-TTT--EEEE CS
  zinc-ribbons_6   2 kCpeCqqelekrgeqyhCeaCqedlkk 28 
                     +C eC+++  + +++y+C++C+++++ 
      EPA05385.1 240 ICDECNEQFAEPKSTYSCKKCNTEFSL 266
                     6**********9***********9976 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   1.5    0.0016       1.3      29      48 ..     169     188 ..     144     191 .. 0.82
   2 !    9.2   7.5    0.0016       1.2       1      38 [.     171     225 ..     171     230 .. 0.80
   3 !   12.1   8.7   0.00019      0.15       1      41 [.     218     267 ..     218     270 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0016
         DZR  29 drCpsCgekvdpearfCpeC 48 
                 + C sC++ + +++  Cp+C
  EPA05385.1 169 ISCTSCKSVLVEQHFLCPNC 188
                 67888888888888888888 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0016
         DZR   1 CpqCgeelppdarfCseCgtklkavaa.................edrCpsCgekv 38 
                 C +C++ l ++   C++C+ +  ++++                 +d Cp+C++++
  EPA05385.1 171 CTSCKSVLVEQHFLCPNCNLEKFSQKDliehyscgnvsleskyeNDICPNCKKEL 225
                 9*****************9884333336676778888888889899999998876 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 0.00019
         DZR   1 CpqCgee.........lppdarfCseCgtklkavaaedrCpsCgekvdpe 41 
                 Cp+C++e           ++   C+eC+++  ++++ + C +C+++ +++
  EPA05385.1 218 CPNCKKEltalgvdyrKIQEYFICDECNEQFAEPKSTYSCKKCNTEFSLN 267
                 9******9999988865567779********99999*********98877 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   2.5e-05      0.02      15     111 ..       2     102 ..       1     103 [. 0.78

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.5e-05
                   HHHHHHTTEEEEEEESSHHHHHHHHHHHH....ESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEESSTSHHHHHHHHHCTESEEEESSG-HHHH CS
  Response_reg  15 rqlleeegyeevaeaedgkealellkeek....vdlillDinmpgmdGlellkeireedpelpviiltahseeedavealkagaddflsKpfdpeeL 107
                   +++l++ g+++++ +e+ ++ l+++k+ +      +i+l    ++ + ++++  i +++p++++i+l + +e++ +++al  ga+d+l  p+++ ++
    EPA05385.1   2 TSMLKKIGFNKIKFCENTEQGLHIFKQIHenyeEAIIFLSFISDDPSIMKTVLSILDTNPHTKIILLKSPEENNLTNKALVQGAYDVLEMPLSMPKI 98 
                   567888888888888888888877754443433555566555555677788888889999*******************************999999 PP

                   HHHH CS
  Response_reg 108 lkal 111
                   ++++
    EPA05385.1  99 TSII 102
                   8877 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       6.4     5e+03       4      10 ..     170     176 ..     169     179 .. 0.79
   2 ?    5.3   0.3     0.019        15       2      20 ..     182     201 ..     181     202 .. 0.79
   3 ?    3.4   0.1     0.072        56       3      12 ..     216     225 ..     214     228 .. 0.82
   4 !   10.0   0.4   0.00064       0.5       1      15 [.     237     251 ..     237     253 .. 0.87
   5 !    9.2   0.4    0.0012      0.91       1      15 [.     253     267 ..     253     270 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 6.4
      zf_UBZ   4 lCerCgk 10 
                  C  C++
  EPA05385.1 170 SCTSCKS 176
                 6999*97 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.019
      zf_UBZ   2 tylCerCg.keipeselqEH 20 
                 ++lC+ C+ +++++ +l EH
  EPA05385.1 182 HFLCPNCNlEKFSQKDLIEH 201
                 89******556777788888 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.072
      zf_UBZ   3 ylCerCgkei 12 
                  +C+ C+ke+
  EPA05385.1 216 DICPNCKKEL 225
                 68******86 PP

  == domain 4  score: 10.0 bits;  conditional E-value: 0.00064
      zf_UBZ   1 dtylCerCgkeipes 15 
                 ++++C++C++++ e+
  EPA05385.1 237 EYFICDECNEQFAEP 251
                 579********9986 PP

  == domain 5  score: 9.2 bits;  conditional E-value: 0.0012
      zf_UBZ   1 dtylCerCgkeipes 15 
                 +ty C++C++e++ +
  EPA05385.1 253 STYSCKKCNTEFSLN 267
                 59*********9876 PP

>> zf-Di19  Drought induced 19 protein (Di19), zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   3.7   9.5e-06    0.0074       1      42 [.     181     226 ..     181     232 .. 0.78
   2 ?    0.1   2.9       1.3     1e+03       5      14 ..     218     227 ..     216     274 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 9.5e-06
     zf-Di19   1 esftCPyCgk.eltvkeLveHve...deHrveskevvCPvCaekvt 42 
                 + f CP C+  ++++k L+eH +   +   ++ ++ +CP C++++t
  EPA05385.1 181 QHFLCPNCNLeKFSQKDLIEHYScgnVSLESKYENDICPNCKKELT 226
                 579******978*********972223445566689*****98876 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.3
     zf-Di19   5 CPyCgkeltv 14 
                 CP C+kelt+
  EPA05385.1 218 CPNCKKELTA 227
                 7888777764 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   2.2   1.9e-05     0.015       1      22 [.     171     188 ..     171     188 .. 0.98
   2 ?    3.2   1.2      0.11        85      18      22 ..     217     221 ..     212     221 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.9e-05
     DUF1610   1 CtSCGaelaprEravvFpCPNC 22 
                 CtSC  +l++      F+CPNC
  EPA05385.1 171 CTSCKSVLVEQH----FLCPNC 188
                 **********99....****** PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.11
     DUF1610  18 pCPNC 22 
                 +CPNC
  EPA05385.1 217 ICPNC 221
                 6**** PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   6.9     0.035        28      26      93 ..     133     222 ..     113     231 .. 0.44
   2 ?   11.6   1.8   0.00027      0.21      64      95 ..     232     263 ..     225     280 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.035
                 EEEEEEEEETTCT--HHHHHHHHHHHHCC.TTTT.-EEE........EEEE--EEEETTTS-EEECHHHHH..................S-TTTS CS
        HypA  26 vtkvkvevGelsgvepeaLefafellaegtvleg.aeLe........ieevpvkvrCreCgkefeleekal..................rCpkCg 93 
                 v     e+ el g + +a++  +e+l++++ +++  +++           v+ ++ C +C+ e  ++++ l                   Cp+C+
  EPA05385.1 133 VL----ELSELIGTNSKAIKEFLEFLESNNKAKNiGKIKiisctsckSVLVEQHFLCPNCNLEKFSQKD-LiehyscgnvsleskyendICPNCK 222
                 44....444444444444444444444443333101111112222223344555555555533333322.1123455555555555555566665 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00027
                 EEEE--EEEETTTS-EEECHHHHHS-TTTSSS CS
        HypA  64 ieevpvkvrCreCgkefeleekalrCpkCgsa 95 
                 +++++  + C+eC+++f + +++++C+kC+++
  EPA05385.1 232 YRKIQEYFICDECNEQFAEPKSTYSCKKCNTE 263
                 566777899*********8876899****984 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   1.1    0.0042       3.3      24      44 ..     169     189 ..     164     193 .. 0.91
   2 ?    4.6   0.2     0.037        29      35      48 ..     210     226 ..     200     228 .. 0.67
   3 ?    8.2   1.0    0.0028       2.2      24      47 ..     239     264 ..     232     266 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0042
                 EE-HHHHHHHHHTT-B-TTT- CS
  zf-C3HC4_3  24 vlCeeCaekllkrkkkCpiCr 44 
                 + C +C + l +++  Cp C+
  EPA05385.1 169 ISCTSCKSVLVEQHFLCPNCN 189
                 57******************8 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.037
                 H...TT-B-TTT--B-- CS
  zf-C3HC4_3  35 k...rkkkCpiCrrpie 48 
                 +   +++ Cp C+++ +
  EPA05385.1 210 EskyENDICPNCKKELT 226
                 22448999****99865 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0028
                 EE-HHHHHHHHH..TT-B-TTT--B- CS
  zf-C3HC4_3  24 vlCeeCaekllk..rkkkCpiCrrpi 47 
                 ++C eC e++ +  ++ +C  C+++ 
  EPA05385.1 239 FICDECNEQFAEpkSTYSCKKCNTEF 264
                 59********9899999*****9986 PP

>> FYVE_2  FYVE-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   1.7    0.0043       3.3      61     109 ..     148     197 ..      97     203 .. 0.68
   2 ?   11.7   5.2    0.0003      0.23      39     107 ..     200     267 ..     190     273 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0043
      FYVE_2  61 leefkllvnsk..rqCldCklnvCkkCsvenkkekvwlCkiCseaRevkkk 109
                  e +++l +++  ++  + k+  C++C +    e+ +lC +C+ ++  +k 
  EPA05385.1 148 KEFLEFLESNNkaKNIGKIKIISCTSCKSV-LVEQHFLCPNCNLEKFSQKD 197
                 445566665551255666677779999876.56789******998876655 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.0003
      FYVE_2  39 ekskrellgnqaklgethCilCleefkllvnskrqCldCklnvCkkCsve.nkkekvwlCkiCseaRevk 107
                 e+  +  ++ ++k++++ C  C +e++ l    r+ +  ++++C +C  +  + ++++ Ck C+++  + 
  EPA05385.1 200 EHYSCGNVSLESKYENDICPNCKKELTALGVDYRKIQ--EYFICDECNEQfAEPKSTYSCKKCNTEFSLN 267
                 677777788889999**************99999765..79******999789999*******9987765 PP

>> Terminase_2  Terminase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00023      0.18      40      79 ..      93     132 ..      78     205 .. 0.79
   2 ?   -2.0   0.1       5.7   4.4e+03      10      37 ..     236     263 ..     233     273 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00023
  Terminase_2  40 LrkpkIkkaIreakaereertiieadeVlqellkiaraei 79 
                  L+ pkI ++I+++k+e  ++++ +++ ++q ll++ +   
   EPA05385.1  93 LSMPKITSIIEKIKQEYPDDKEYQTQSIIQTLLSTRKNSS 132
                  899*****************************88755444 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 5.7
  Terminase_2  10 deYikd..lNatqAaikAgyskktArsigs 37 
                  +eY+++  +N + A  k  ys k+   +++
   EPA05385.1 236 QEYFICdeCNEQFAEPKSTYSCKK--CNTE 263
                  455555489999999999999887..4444 PP

>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9  11.5    0.0054       4.2      13      74 ..     176     246 ..     150     247 .. 0.75
   2 ?    4.9   0.3     0.046        36      16      42 ..     251     277 ..     246     281 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0054
      zf-CHY  13 apcCkklyaCreCHeeledhelerlevkevlcllCeteq.ekavlCkkCkk..........efaeyf.CpiCkl 74 
                     ++ + C +C  e   +  ++  +++  c + + e   ++ +C +Ckk          +++eyf C+ C+ 
  EPA05385.1 176 SVLVEQHFLCPNCNLE---KFSQKDLIEHYSCGNVSLESkYENDICPNCKKeltalgvdyrKIQEYFiCDECNE 246
                 3445678999999963...22233345555666666655257889****999*******999****88****85 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.046
      zf-CHY  16 CkklyaCreCHeeledhelerlevkev 42 
                  k++y+C++C +e + ++++  e++++
  EPA05385.1 251 PKSTYSCKKCNTEFSLNKAKLIETEKF 277
                 567889999988777666666666655 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2    0.0008      0.62      55      85 ..     158     188 ..     107     189 .. 0.80
   2 ?    1.6   3.8      0.61   4.7e+02      66      73 ..     216     223 ..     190     249 .. 0.55
   3 ?    5.7   8.0     0.031        24       2      55 ..     217     272 ..     216     278 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0008
  zinc_ribbon_15  55 keiekkessekkeCknCgkeveeefkyCpkC 85 
                     ++ ++  +++  +C +C++++ e+   Cp+C
      EPA05385.1 158 NKAKNIGKIKIISCTSCKSVLVEQHFLCPNC 188
                     3334444455999****************** PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.61
  zinc_ribbon_15  66 keCknCgk 73 
                      +C+nC+k
      EPA05385.1 216 DICPNCKK 223
                     33333333 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.031
  zinc_ribbon_15   2 lCpkCgklskaelvkkkkvlklffipvf..kwkkkkpylacskCkslleaskelgk 55 
                     +Cp+C+k  +a  v+++k+ + f +  +  ++ + k  + c+kC++ ++ +k +  
      EPA05385.1 217 ICPNCKKELTALGVDYRKIQEYFICDECneQFAEPKSTYSCKKCNTEFSLNKAKLI 272
                     6*****9999888888888888888755224677788999*******999985544 PP

>> Spt4  Spt4/RpoE2 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   2.3    0.0024       1.9       4      27 ..     171     191 ..     169     203 .. 0.77
   2 ?   11.8   0.2   0.00026       0.2       6      27 ..     203     225 ..     201     240 .. 0.80
   3 ?   -2.5   1.8       7.1   5.6e+03      21      36 ..     241     257 ..     230     265 .. 0.51
   4 ?   -1.6   1.8       3.9   3.1e+03       4      29 ..     241     266 ..     238     277 .. 0.57

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0024
        Spt4   4 CllCklvktedqFeeegCpnCeil 27 
                 C++Ck v  e++     CpnC++ 
  EPA05385.1 171 CTSCKSVLVEQH---FLCPNCNLE 191
                 ************...58****433 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00026
        Spt4   6 lCklvktedqFeeegCpnC.eil 27 
                 +C+ v  e+++e+++CpnC + l
  EPA05385.1 203 SCGNVSLESKYENDICPNCkKEL 225
                 7******************7544 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 7.1
        Spt4  21 CpnC.eilelkgdkekv 36 
                 C+ C e ++  +++ + 
  EPA05385.1 241 CDECnEQFAEPKSTYSC 257
                 55553333322222222 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 3.9
        Spt4   4 CllCklvktedqFeeegCpnC.eilel 29 
                 C +C+    e +  +  C+ C + ++l
  EPA05385.1 241 CDECNEQFAEPK-STYSCKKCnTEFSL 266
                 555544333333.45677777444444 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   3.4       0.4   3.1e+02      18      26 ..     181     189 ..     170     191 .. 0.82
   2 ?    5.6   0.1      0.02        16      21      28 ..     217     224 ..     211     226 .. 0.89
   3 ?    8.8   0.4    0.0019       1.5      19      29 ..     238     248 ..     235     249 .. 0.87
   4 ?    2.5   0.1      0.19   1.5e+02       5      14 ..     257     266 ..     253     277 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.4
  PhnA_Zn_Ribbon  18 allvCpeCa 26 
                     + ++Cp+C 
      EPA05385.1 181 QHFLCPNCN 189
                     578999996 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.02
  PhnA_Zn_Ribbon  21 vCpeCahE 28 
                     +Cp+C+ E
      EPA05385.1 217 ICPNCKKE 224
                     8****998 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0019
  PhnA_Zn_Ribbon  19 llvCpeCahEw 29 
                      ++C+eC +++
      EPA05385.1 238 YFICDECNEQF 248
                     69*******98 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.19
  PhnA_Zn_Ribbon   5 CplCaSeytY 14 
                     C +C+ e+++
      EPA05385.1 257 CKKCNTEFSL 266
                     9999999987 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.3      0.11        85       2      10 ..     168     176 ..     168     178 .. 0.84
   2 ?    1.2   0.2      0.46   3.6e+02       5       9 ..     185     189 ..     183     191 .. 0.81
   3 ?    2.9   0.3      0.14   1.1e+02       5      10 ..     218     223 ..     217     226 .. 0.83
   4 ?    2.1   0.3      0.24   1.8e+02       4      13 ..     240     249 ..     238     253 .. 0.84
   5 ?   11.0   0.3    0.0004      0.31       4      19 ..     256     271 ..     255     276 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.11
  zinc_ribbon_4   2 kitCpsCka 10 
                    +i+C sCk+
     EPA05385.1 168 IISCTSCKS 176
                    699****97 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.46
  zinc_ribbon_4   5 CpsCk 9  
                    Cp+C+
     EPA05385.1 185 CPNCN 189
                    89997 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.14
  zinc_ribbon_4   5 CpsCka 10 
                    Cp+Ck+
     EPA05385.1 218 CPNCKK 223
                    999998 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.24
  zinc_ribbon_4   4 tCpsCkakye 13 
                     C +C+ +++
     EPA05385.1 240 ICDECNEQFA 249
                    7999999996 PP

  == domain 5  score: 11.0 bits;  conditional E-value: 0.0004
  zinc_ribbon_4   4 tCpsCkakyeiddekl 19 
                    +C++C+++++++ +kl
     EPA05385.1 256 SCKKCNTEFSLNKAKL 271
                    7************997 PP

>> zf-RING_4  RING/Ubox like zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   1.1     0.006       4.7      25      44 ..     171     189 ..     168     191 .. 0.81
   2 ?    7.4   0.3     0.005       3.9      36      46 ..     214     224 ..     203     226 .. 0.81
   3 ?    2.4   3.2      0.17   1.3e+02      21      47 ..     237     264 ..     237     265 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.006
   zf-RING_4  25 ClfCyhrileeeegrCPaCr 44 
                 C  C + +l e+++ CP+C 
  EPA05385.1 171 CTSC-KSVLVEQHFLCPNCN 189
                 8999.5566678*******5 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.005
   zf-RING_4  36 eegrCPaCree 46 
                 e+ +CP+C++e
  EPA05385.1 214 ENDICPNCKKE 224
                 6899*****97 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.17
   zf-RING_4  21 gyqiClfCyhrile.eeegrCPaCreeY 47 
                 +y iC  C ++  e +++  C +C +e+
  EPA05385.1 237 EYFICDECNEQFAEpKSTYSCKKCNTEF 264
                 589********999778999****9988 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.2     0.042        33       2      19 ..     184     201 ..     183     203 .. 0.78
   2 ?    1.1   0.1      0.87   6.8e+02       3       9 ..     218     224 ..     216     228 .. 0.82
   3 ?    3.5   0.1      0.15   1.2e+02       1      11 [.     239     249 ..     239     253 .. 0.84
   4 ?    5.0   0.7      0.05        39       1      11 [.     255     265 ..     255     268 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.042
                 EETTTT.EEESSHHHHHHH CS
     zf-C2H2   2 kCpdCg.ksFkrksnLkrH 19 
                  Cp C+ ++F ++ +L  H
  EPA05385.1 184 LCPNCNlEKF-SQKDLIEH 201
                 5*****9999.77777777 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.87
                 ETTTTEE CS
     zf-C2H2   3 CpdCgks 9  
                 Cp C+k 
  EPA05385.1 218 CPNCKKE 224
                 ****996 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.15
                 EEETTTTEEES CS
     zf-C2H2   1 ykCpdCgksFk 11 
                 + C++C++ F 
  EPA05385.1 239 FICDECNEQFA 249
                 78*****9996 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.05
                 EEETTTTEEES CS
     zf-C2H2   1 ykCpdCgksFk 11 
                 y C++C+  F+
  EPA05385.1 255 YSCKKCNTEFS 265
                 89******997 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   1.6      0.15   1.2e+02      17      28 ..     181     192 ..     174     205 .. 0.77
   2 ?   10.4   0.4   0.00065      0.51      20      46 .]     217     247 ..     213     247 .. 0.80
   3 ?    1.5   0.2      0.39   3.1e+02      37      45 ..     254     262 ..     249     263 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.15
  Zn_Tnp_IS1595  17 ngfvCPhCgsrk 28 
                    ++f CP+C  +k
     EPA05385.1 181 QHFLCPNCNLEK 192
                    6799****8765 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00065
  Zn_Tnp_IS1595  20 vCPhCgsr.kayrikt...rglfqCkeCrkq 46 
                    +CP+C+++ +a  +      ++f C eC++q
     EPA05385.1 217 ICPNCKKElTALGVDYrkiQEYFICDECNEQ 247
                    6******99666666555667*******987 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.39
  Zn_Tnp_IS1595  37 lfqCkeCrk 45 
                     + Ck+C++
     EPA05385.1 254 TYSCKKCNT 262
                    699****86 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       8.5   6.7e+03       2       7 ..     170     175 ..     169     182 .. 0.71
   2 ?    5.1   0.2     0.065        51       1      19 [.     183     201 ..     183     203 .. 0.81
   3 ?   -0.1   0.1         3   2.4e+03       2       9 ..     217     224 ..     217     228 .. 0.80
   4 ?    6.0   0.2     0.035        27       1      14 [.     239     252 ..     239     253 .. 0.87
   5 ?    5.8   0.2     0.038        30       1      13 [.     255     267 ..     255     272 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 8.5
   zf-C2H2_4   2 kCpiCg 7  
                  C+ C+
  EPA05385.1 170 SCTSCK 175
                 599995 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.065
   zf-C2H2_4   1 fkCpiCgksFsskkaLlrH 19 
                 f Cp C+    s+k+L  H
  EPA05385.1 183 FLCPNCNLEKFSQKDLIEH 201
                 78****6666699999999 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 3
   zf-C2H2_4   2 kCpiCgks 9  
                 +Cp C+k 
  EPA05385.1 217 ICPNCKKE 224
                 5****886 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.035
   zf-C2H2_4   1 fkCpiCgksFsskk 14 
                 f+C+ C++ F  +k
  EPA05385.1 239 FICDECNEQFAEPK 252
                 89********8876 PP

  == domain 5  score: 5.8 bits;  conditional E-value: 0.038
   zf-C2H2_4   1 fkCpiCgksFssk 13 
                 + C+ C++ Fs +
  EPA05385.1 255 YSCKKCNTEFSLN 267
                 79********733 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   2.4      0.87   6.7e+02       6      26 ..     170     188 ..     165     192 .. 0.81
   2 ?    0.9   0.3      0.58   4.6e+02       6      27 ..     184     205 ..     180     207 .. 0.70
   3 ?    6.4   0.1     0.011       8.5       1      15 [.     212     226 ..     212     232 .. 0.89
   4 ?    6.7   0.5    0.0086       6.7       6      29 ..     240     263 ..     234     267 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.87
  Prok-RING_1   6 kCpvCgkelkeedDiVvCpeC 26 
                  +C+ C+  l e+     Cp+C
   EPA05385.1 170 SCTSCKSVLVEQ--HFLCPNC 188
                  699999988888..6789998 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.58
  Prok-RING_1   6 kCpvCgkelkeedDiVvCpeCg 27 
                   Cp C+ e  +++D++    Cg
   EPA05385.1 184 LCPNCNLEKFSQKDLIEHYSCG 205
                  6999987766666777666666 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.011
  Prok-RING_1   1 nytgkkCpvCgkelk 15 
                  +y++++Cp C+kel+
   EPA05385.1 212 KYENDICPNCKKELT 226
                  599*********997 PP

  == domain 4  score: 6.7 bits;  conditional E-value: 0.0086
  Prok-RING_1   6 kCpvCgkelkeedDiVvCpeCgtp 29 
                  +C  C+++++e +    C +C t 
   EPA05385.1 240 ICDECNEQFAEPKSTYSCKKCNTE 263
                  7********************995 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   2.0      0.61   4.8e+02       7      35 ..     171     194 ..     165     197 .. 0.61
   2 ?    4.7   0.0     0.037        29       9      35 ..     203     226 ..     202     229 .. 0.81
   3 ?    4.5   0.4     0.043        33      25      34 ..     255     264 ..     241     267 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.61
  Zn_ribbon_SprT   7 CtgCgreythhlsirrhnYrCrrCk.gtLr 35 
                     Ct+C+        +  h   C+ C  ++++
      EPA05385.1 171 CTSCK-----SVLVEQHF-LCPNCNlEKFS 194
                     66666.....33445555.66666666655 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.037
  Zn_ribbon_SprT   9 gCgreythhlsirrhnYrCrrCkgtLr 35 
                     +Cg   ++ l ++ +n +C+ Ck +L+
      EPA05385.1 203 SCG---NVSLESKYENDICPNCKKELT 226
                     578...888888888889999999886 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.043
  Zn_ribbon_SprT  25 YrCrrCkgtL 34 
                     Y C++C  ++
      EPA05385.1 255 YSCKKCNTEF 264
                     7788887665 PP

>> zf-RING_2  Ring finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   2.5     0.039        31      26      44 .]     171     189 ..     166     189 .. 0.86
   2 ?    6.6   0.1     0.013        10      26      44 .]     201     222 ..     197     222 .. 0.89
   3 ?    2.9   1.1      0.18   1.4e+02      25      43 ..     240     260 ..     235     264 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.039
   zf-RING_2  26 hreClerwlrssstCPlCr 44 
                 + +C + +++++  CP+C+
  EPA05385.1 171 CTSCKSVLVEQHFLCPNCN 189
                 999*9999999999****5 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.013
   zf-RING_2  26 hreClerwlrssst...CPlCr 44 
                 h++C +  l+s+ +   CP+C+
  EPA05385.1 201 HYSCGNVSLESKYEndiCPNCK 222
                 8999999999999999*****7 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.18
   zf-RING_2  25 fhreClerwlrssst..CPlC 43 
                 ++ eC e++ +++st  C  C
  EPA05385.1 240 ICDECNEQFAEPKSTysCKKC 260
                 678888887777777777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1176  (0.0655921); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); expected 17.9 (0.001)
Passed Fwd filter:                        55  (0.00306766); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.68u 0.32s 00:00:01.00 Elapsed: 00:00:00.53
# Mc/sec: 1593.65
//
Query:       EPA05386.1  [L=124]
Description: response regulator receiver domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-18   67.3   0.5    1.3e-18   67.2   0.5    1.0  1  Response_reg  Response regulator receiver domain
     0.0097   15.5   0.3       0.72    9.4   0.1    2.0  2  PrpR_N        Propionate catabolism activator
  ------ inclusion threshold ------
      0.088   13.2   0.1        4.5    7.6   0.0    2.2  2  Phage_tail_U  Phage minor tail protein U


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.2   0.5   2.2e-22   1.3e-18       1     111 [.       3     114 ..       3     115 .. 0.92

  Alignments for each domain:
  == domain 1  score: 67.2 bits;  conditional E-value: 2.2e-22
                   EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCT.TTSEEEEEESSTS.HHHHHHHHHCTES CS
  Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireed.pelpviiltahse.eedavealkagad 95 
                   +l v+D p++ ++++++l+ ++        d++  ++++++e++dli+lD+ mp+++G+++l+ +++++ ++ ++i++ta +  ++++ +   ++++
    EPA05386.1   3 ILQVEDAPKITDVFSKILTMKKH-AYSYEHDPELGIKKIQNENFDLIFLDLTMPKLSGFDILEDLKQKNfDTSKIIVITASTLsDKELDQLKGYNIH 98 
                   788****************7777.778889***********************************9999899*******6554388899999***** PP

                   EEEESSG-HHHHHHHH CS
  Response_reg  96 dflsKpfdpeeLlkal 111
                   ++++Kp++ ++Ll+ +
    EPA05386.1  99 EIIFKPISLQKLLSTV 114
                   ************9877 PP

>> PrpR_N  Propionate catabolism activator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.9   0.0     0.003        18      77     123 ..       4      48 ..       1      54 [. 0.76
   2 !    9.4   0.1   0.00012      0.72      54     102 ..      56     102 ..      50     122 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.003
      PrpR_N  77 vgfeniikglktlselldldieiytinseeeaeaavkelkaegvevv 123
                 ++ e+++k ++ +s++l ++ + y+++  ++ e  +k++++e+++++
  EPA05386.1   4 LQVEDAPKITDVFSKILTMKKHAYSYE--HDPELGIKKIQNENFDLI 48 
                 567778899999999988887777776..556667888888888876 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00012
      PrpR_N  54 kvsgyDilralkqakklgekialvgfeniikglktlselldldieiyti 102
                 k+sg+Dil+ lkq +  ++ki +++ ++++++  +l++l +++i+ + +
  EPA05386.1  56 KLSGFDILEDLKQKNFDTSKIIVITASTLSDK--ELDQLKGYNIHEIIF 102
                 689**********99999*******9998887..788888888876655 PP

>> Phage_tail_U  Phage minor tail protein U
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0   0.00075       4.5      88     124 ..       5      41 ..       1      49 [. 0.74
   2 ?    4.0   0.0      0.01        62      65     104 ..      75     113 ..      53     120 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00075
                   HHHTC-HHHHTT..SSEEEEEEEEEEE-TTSTTEEEE CS
  Phage_tail_U  88 evleeveeleelesleelvlsgYdYerDeekatWkiA 124
                   +v +  + ++ ++++ +++++ Y+Ye+D e  + ki 
    EPA05386.1   5 QVEDAPKITDVFSKILTMKKHAYSYEHDPELGIKKIQ 41 
                   55455555677999**************987766655 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.01
                   EEEEEEETTS-HHHHHHHHH.HTHHHHTC-HHHHTT..SSE CS
  Phage_tail_U  65 niavylkalaaeseLDelae.kivevleeveeleeleslee 104
                   +i v   ++ +++eLD+l   +i e++ +  +l++l  l++
    EPA05386.1  75 KIIVITASTLSDKELDQLKGyNIHEIIFKPISLQKL--LST 113
                   67777888999******9999999999887777776..444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 921.51
//
Query:       EPA05387.1  [L=413]
Description: adenosylhomocysteinase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.5e-52  176.4   3.9    5.2e-52  176.2   0.8    2.2  2  AdoHcyase_NAD   S-adenosyl-L-homocysteine hydrolase, NAD bind
    9.8e-51  172.7   0.0    1.1e-24   87.1   0.1    2.0  2  AdoHcyase       S-adenosyl-L-homocysteine hydrolase
    1.7e-09   37.3   0.1    4.3e-09   36.0   0.1    1.7  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
    2.1e-06   27.4   0.0    4.2e-06   26.4   0.0    1.5  1  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
     0.0019   18.5   0.0     0.0068   16.7   0.0    1.9  2  TrkA_N          TrkA-N domain
     0.0036   17.4   0.7      0.086   12.9   0.1    2.7  3  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
     0.0082   15.5   2.1      0.044   13.1   2.1    2.1  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
  ------ inclusion threshold ------
      0.015   15.2   1.6      0.036   13.9   0.3    2.3  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
      0.022   14.1   0.2       0.26   10.6   0.5    2.4  2  THF_DHG_CYH_C   Tetrahydrofolate dehydrogenase/cyclohydrolase
      0.068   12.7   0.2       0.15   11.6   0.2    1.6  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
      0.074   12.6   0.0       0.21   11.2   0.0    1.7  1  DUF364          Putative heavy-metal chelation


Domain annotation for each model (and alignments):
>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.2   0.8   3.2e-55   5.2e-52       1     161 [.     184     344 ..     184     345 .. 0.99
   2 ?    0.6   0.1      0.32   5.3e+02     110     138 ..     381     409 ..     358     412 .. 0.68

  Alignments for each domain:
  == domain 1  score: 176.2 bits;  conditional E-value: 3.2e-55
                    HHHHHCCCCCHHHHHHH-S--TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCTT-EE--HHHCTTT-SEEEE-SSSSSSB-HHH CS
  AdoHcyase_NAD   1 nlygcreslvdgikratdvllaGkvavvaGyGdvGkGcaaslkglGarvivtevdPicalqaameGfevvtleevvkkadivvtttGnkdiitleh 96 
                    n yg+ +s +dg  ra ++l+a k +vv+GyG vG+G aa  +g+G++vivte+dP+ al a m+Gfev+ + ++ k +di++t+tG + +i++eh
     EPA05387.1 184 NRYGTGQSTIDGYLRAMNLLMASKRVVVVGYGWVGRGVAARCHGMGSKVIVTEIDPVKALEAHMDGFEVMPMAQACKLGDIFITCTGMTSVIRKEH 279
                    78********************************************************************************************** PP

                    HCCS-TTEEEEE-SSTTTTBTHHHHHTTT-EEEEEETTEEEEE-TTS-EEEEEGGGSBCHHHTS- CS
  AdoHcyase_NAD  97 lkkmkddaivcniGhfdseidvaaleanalkkeevkpqvdrvtlkdgkkiillaeGrllnlgcat 161
                    + +mk+ ai++n+Ghfd eid + l ++++++ +v+p++d++tlk+gk + l+ eGrl nl +a 
     EPA05387.1 280 ILQMKNGAIMGNVGHFDVEIDSKFLLKESKSVRRVRPNLDECTLKNGKYVYLIGEGRLANLVAAE 344
                    *************************************************************9886 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.32
                    SSTTTTBTHHHHHTTT-EEEEEETTEEEE CS
  AdoHcyase_NAD 110 Ghfdseidvaaleanalkkeevkpqvdrv 138
                       d+++ v+al+a+++k++++ pq  ++
     EPA05387.1 381 EEIDKQVAVDALKAMDVKIDKLTPQQVKY 409
                    346777789999*9999999999997665 PP

>> AdoHcyase  S-adenosyl-L-homocysteine hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.1   0.1   6.8e-28   1.1e-24      10     140 ..      11     136 ..       3     142 .. 0.92
   2 !   84.7   0.0   3.8e-27   6.1e-24     173     285 ..     138     410 ..     130     412 .. 0.97

  Alignments for each domain:
  == domain 1  score: 87.1 bits;  conditional E-value: 6.8e-28
                 HHHHHHHHHHHHCC-HHHHHHHHHCTTT-TTTT-EEEEES--SHHHHHHHHHHHHTT-EEEEE-SSTTT--HHHHHHHCCTTEEEE--TT--HHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
   AdoHcyase  10 aefGrkeielaekempglmalreeyaeekplkgariaGslhmtiqtavLietLvalGaevrWasCnifstqdeaaaaiaeagvpvfawkgetleeywwc 108
                  + G+   e a + m  l ++ ++ +++kplkg  +  +lh+t +t+vL+   ++lGa v  +  n   tqd++aa +a++g+ v+aw+g++ +ey wc
  EPA05387.1  11 VQDGKLSYEWARSHMQILDNTINRLKKSKPLKGITLGFCLHITKETSVLLMGAKELGATVACCGGNPLTTQDDIAAFLASQGIHVYAWHGQSVKEYDWC 109
                 566888889999*************************************************************************************** PP

                 HHHCHS-SSTS-S-SEEEESSSHHHHHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
   AdoHcyase 109 ieqalkwaedekepnlilDdGGDltllvhkgv 140
                 i+q+l++     +p ++ DdG D+    h   
  EPA05387.1 110 IDQVLNH-----KPTILTDDGADMNVKAHFDN 136
                 *****65.....79*********998777655 PP

  == domain 2  score: 84.7 bits;  conditional E-value: 3.8e-27
                 HCCCHCC--EEEE-SHHHHHHHHHHHHTT---SEEEESTTSHHHCTTH................................................... CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................................... RF
   AdoHcyase 173 ytellkkikGvseetttGvhrLyelakkgkLlvpainvndsvtkskfD................................................... 220
                 y++   ki G +eett+Gv r+  ++++gkL  p i vn++ tk  fD                                                   
  EPA05387.1 138 YKN--MKILGATEETTAGVTRIRAVENQGKLRYPVILVNEAYTKHMFDnrygtgqstidgylramnllmaskrvvvvgygwvgrgvaarchgmgskviv 234
                 443..3789****************************************************************************************** PP

                 ................................................................................................... CS
                 ................................................................................................... RF
   AdoHcyase 221 ................................................................................................... 220
                                                                                                                    
  EPA05387.1 235 teidpvkaleahmdgfevmpmaqacklgdifitctgmtsvirkehilqmkngaimgnvghfdveidskfllkesksvrrvrpnldectlkngkyvylig 333
                 *************************************************************************************************** PP

                 ............S-HHHHHHHHHHHHHHHHHHHHTTSSS-SSEEE--CHHHHHHHHHCCCCCT-------HHHHHCC CS
                 ............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
   AdoHcyase 221 ............hpsfvmsasftnqvlaqielfkkekkyekkvyvlpkklDekvarlhleklgaklteltkeqaeyi 285
                             hp  vm++sf+nq+l+ + + k+++k  +k+  +p ++D +va   l+++++k+++lt +q +y 
  EPA05387.1 334 egrlanlvaaegHPPEVMAQSFSNQILSVLYILKNHAKIGNKIINVPEEIDKQVAVDALKAMDVKIDKLTPQQVKYA 410
                 ***************************************************************************95 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.1   2.7e-12   4.3e-09      33     128 ..     203     294 ..     176     314 .. 0.87

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 2.7e-12
                   -GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCSTTTEEEEESS- CS
  2-Hacid_dh_C  33 elsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelvsleellaesDivslhlpltpetrhlinaeelakmkkgailiNtaR 128
                    ++ k+v ++G+G +G+ va r++++g kvi+++  + k  e++  g+e++ + ++++  Di + ++ +t     +i +e++ +mk+gai+ N++ 
    EPA05387.1 203 LMASKRVVVVGYGWVGRGVAARCHGMGSKVIVTEIDPVKALEAHMDGFEVMPMAQACKLGDIFITCTGMT----SVIRKEHILQMKNGAIMGNVGH 294
                   5789********************************9988899999***************998887765....69****************9986 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   2.6e-09   4.2e-06       2      99 ..     204     297 ..     203     317 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 2.6e-09
                 HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHHHHHHHHHTGGG--TT-EEEESSSHHH CS
        IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDelqkevyeeeiepnlkegkalafahGfni 99 
                 + +k+++v+GyG  G+  a   +  g +v+v+  +   ++ +A+ +gfev+ +a+a+k  d+ ++ +    +++v+++e   ++k+g+++     f++
  EPA05387.1 204 MASKRVVVVGYGWVGRGVAARCHGMGSKVIVTEIDPV-KALEAHMDGFEVMPMAQACKLGDIFITCT---GMTSVIRKEHILQMKNGAIMGNVGHFDV 297
                 679****************************988877.6778*******************877654...4667777777778888888776666666 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0         4   6.5e+03      44      71 ..      47      74 ..      16      91 .. 0.64
   2 !   16.7   0.0   4.2e-06    0.0068       1      45 [.     209     253 ..     209     259 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 4
                EEES-TTSHHHHHHTTGGGESEEEE-SS CS
      TrkA_N 44 vvvgdatdeevLeeagiekadaviaatg 71
                 ++ + t+e  +  +g+++  a +a++g
  EPA05387.1 47 GFCLHITKETSVLLMGAKELGATVACCG 74
                5666667777777777777766666665 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 4.2e-06
                 EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSEEE CS
      TrkA_N   1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeglevv 45 
                 ++++G+G vGr +a + +  g+ +v+v + d+ ++ e+  +g+ev+
  EPA05387.1 209 VVVVGYGWVGRGVAARCHGmGS-KVIVTEIDPVKALEAHMDGFEVM 253
                 79*****************666.7********99999999998875 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1       6.5   1.1e+04      11      27 ..      54      70 ..      52      71 .. 0.81
   2 !   12.9   0.1   5.3e-05     0.086      10      99 ..     204     284 ..     197     297 .. 0.81
   3 ?    1.7   0.0      0.15   2.5e+02      11      29 ..     325     343 ..     318     349 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 6.5
                  TT-EEEEES-SHHHHHH CS
  Shikimate_DH 11 kekkvlliGaGemaelv 27
                  ke  vll+Ga e++  v
    EPA05387.1 54 KETSVLLMGAKELGATV 70
                  577899***99998877 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 5.3e-05
                   .TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSSSS-SB-HHHHHCCH CS
  Shikimate_DH  10 lkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisataseepilekeeveeal 99 
                   +++k+v+++G G +++ va   +  g k v+v+  +++ +k+l  +++g      ++  + ++ +  d+ i++t+ ++ +++ke++ +++
    EPA05387.1 204 MASKRVVVVGYGWVGRGVAARCHGMGSK-VIVT--EIDPVKALEAHMDGF-----EVMPMAQACKLGDIFITCTGMTS-VIRKEHILQMK 284
                   6799********************9999.6666..688999999999777.....45556677799********9865.66777776665 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.15
                   TT-EEEEES-SHHHHHHHH CS
  Shikimate_DH  11 kekkvlliGaGemaelvak 29 
                   ++k v liG G++a+lva 
    EPA05387.1 325 NGKYVYLIGEGRLANLVAA 343
                   46789***********985 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   2.1   2.7e-05     0.044      28     123 ..     206     288 ..     184     293 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.7e-05
                  --EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHHHHHHHHH-SEEEE---BTTSS---SC-HHHHHTS-TTEE CS
  AlaDh_PNT_C  28 pakvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqeellaeavkeadvvigtvlipGkkaPkLvteemvksMkpgsV 123
                    +v+v+G G +G   +a ++g+g kV v++++p ++ + +  g +           +a+a+k  d+ i++   +G     ++++e++ +Mk+g++
   EPA05387.1 206 SKRVVVVGYGWVGRGVAARCHGMGSKVIVTEIDPVKALEAHMDGFE--------VMPMAQACKLGDIFITC---TG--MTSVIRKEHILQMKNGAI 288
                  568****************************999765544433333........34567788888888887...33..346788888888888876 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1      0.74   1.2e+03      35      35 ..     121     121 ..      70     181 .. 0.52
   2 ?   13.9   0.3   2.2e-05     0.036       2      38 ..     209     245 ..     208     265 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.74
                 H CS
     3HCDH_N  35 l 35 
                 l
  EPA05387.1 121 L 121
                 1 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 2.2e-05
                 EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHH CS
     3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseealeka 38 
                 v v+G G +G+g+aa +   g +V +++i++ ++ +a
  EPA05387.1 209 VVVVGYGWVGRGVAARCHGMGSKVIVTEIDPVKALEA 245
                 89***************************98655444 PP

>> THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       4.5   7.4e+03      96     116 ..      19      39 ..      16      43 .. 0.69
   2 ?   10.6   0.5   0.00016      0.26      27     112 ..     197     297 ..     188     311 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 4.5
                    GGS-TT-EEEE---EEC-TTE CS
  THF_DHG_CYH_C  96 emvkegavviDvGinrvekgk 116
                    e+ ++   ++D  inr++k+k
     EPA05387.1  19 EWARSHMQILDNTINRLKKSK 39 
                    667777778888888886655 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00016
                    HHHCT---TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTS.............CCHHHHHCCSSEEEE-SS-TT-B-GGGS...-TT-EEEE CS
  THF_DHG_CYH_C  27 lketgielegkkvvvvGrsnivgkplallLleknatVtvchskt.............kdlaeitreadivvvavGkpelikaemv...kegavviD 106
                    l++++  ++ k+vvvvG +  vg+ +a+  +  ++ V v++                  +a+ ++  di ++++G  ++i++e++   k+ga++ +
     EPA05387.1 197 LRAMNLLMASKRVVVVGYG-WVGRGVAARCHGMGSKVIVTEIDPvkaleahmdgfevMPMAQACKLGDIFITCTGMTSVIRKEHIlqmKNGAIMGN 291
                    5566677788888888875.6888888888887555555544332112222222323457889999*****************9888899***999 PP

                    ---EEC CS
  THF_DHG_CYH_C 107 vGinrv 112
                    vG+  v
     EPA05387.1 292 VGHFDV 297
                    998655 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   9.2e-05      0.15       2      36 ..     208     242 ..     207     257 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9.2e-05
                     EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHH CS
  UDPG_MGDP_dh_N   2 kisviGlGYvGlvtaavlaeighevigvDideekv 36 
                     +++v+G G+vG   aa    +g +vi+  id  k 
      EPA05387.1 208 RVVVVGYGWVGRGVAARCHGMGSKVIVTEIDPVKA 242
                     89*****************************9875 PP

>> DUF364  Putative heavy-metal chelation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00013      0.21       9      47 ..     204     245 ..     199     270 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00013
      DUF364   9 kkgkkVvvVGy..fap.vlkklkekgaeltvlelnpnlleee 47 
                  ++k+VvvVGy   ++ v+ ++  +g++++v e++p +  e+
  EPA05387.1 204 MASKRVVVVGYgwVGRgVAARCHGMGSKVIVTEIDPVKALEA 245
                 5789*******885555999999*************655444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.68u 0.37s 00:00:01.05 Elapsed: 00:00:00.59
# Mc/sec: 2111.91
//
Query:       EPA05388.1  [L=66]
Description: hypothetical protein BG20_I1232 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.058   12.5   0.1      0.065   12.3   0.1    1.2  1  FUSC-like  FUSC-like inner membrane protein yccS


Domain annotation for each model (and alignments):
>> FUSC-like  FUSC-like inner membrane protein yccS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   3.6e-06     0.065     221     260 ..      20      63 ..       4      65 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.6e-06
   FUSC-like 221 aceeiaqaillnkpyq....hserleraleeleqslellakqnn 260
                 +c eia+ +l++ + +    + +++e+a++el+qsle+++++n+
  EPA05388.1  20 SCSEIANTVLEKWKNNlskkDIDDIEWAIKELHQSLEKIREKNH 63 
                 69999*999988777777778889***************99965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1170  (0.0652574); expected 358.6 (0.02)
Passed bias filter:                      611  (0.0340789); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 455.43
//
Query:       EPA05389.1  [L=136]
Description: CoA binding domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-37  128.3   0.0    2.2e-37  128.1   0.0    1.0  1  CoA_binding_2   CoA binding domain
    4.6e-07   30.4   0.0    8.2e-07   29.6   0.0    1.3  1  CoA_binding     CoA binding domain
  ------ inclusion threshold ------
       0.04   13.1   0.0        0.1   11.8   0.0    1.5  2  Glyco_hydro_57  Glycosyl hydrolase family 57


Domain annotation for each model (and alignments):
>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.1   0.0   3.6e-41   2.2e-37       1     116 []      18     133 ..      18     133 .. 0.98

  Alignments for each domain:
  == domain 1  score: 128.1 bits;  conditional E-value: 3.6e-41
                    --EEEET--S-TTSHHHHHHHHHHHHT--EEEESSS-SEETTEES----T....T--EEEE-S-HHHHGGGHHHHHHH--SEEEE-TT---HHHHH CS
  CoA_binding_2   1 rtiaVvGasdnpgkfgykvlryllehglpvvpVnpkeeeilgekvyaslaedpepvdlvdvftppeatpeivkealalgakavwlqpgsedeeaae 96 
                    +++aVvG+s+n+ k++++v++yl e+g+++vp+np+ +eilg+k+y ++++ ++++d++dvf+p++ ++++v+ea+++++k++wlq+g+ + +a e
     EPA05389.1  18 KRVAVVGMSKNDYKAAHYVPKYLSENGFDIVPINPTTDEILGKKCYDTISDVEGDIDVLDVFRPSDLVLPVVQEAIKKKPKVIWLQEGIHNLQAEE 113
                    689***********************************************847******************************************* PP

                    HHHHTT-EEE.ES-HHHHHH CS
  CoA_binding_2  97 laeeagirvvgdrCilvege 116
                    la+++gi++v +rC+l e++
     EPA05389.1 114 LARKNGIKIVFNRCMLAEHQ 133
                    *****************995 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   1.4e-10   8.2e-07       4      91 ..      18     101 ..      16     103 .. 0.92

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 1.4e-10
                  EEEEEETTTSHHHHHH.HHHHHHHHECEEEEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHHHHHHHHHTT-SEEE CS
  CoA_binding   4 tkviviGagglgiagl.yhfkeklkygikavfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesaqeavdelveagikgiv 91 
                  ++v+v+G++++  + + y+ k   + g+  ++++np+   +e+lg ++y++++++e +  +dv  ++ P++ +  +v+e+++++ k+i+
   EPA05389.1  18 KRVAVVGMSKNDYKAAhYVPKYLSENGFD-IVPINPT--TDEILGKKCYDTISDVEGD--IDVLDVFRPSDLVLPVVQEAIKKKPKVIW 101
                  69**************8888888888876.56*****..*******************..99999999******************998 PP

>> Glyco_hydro_57  Glycosyl hydrolase family 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.22   1.3e+03     186     229 ..      36      48 ..      12      66 .. 0.65
   2 ?   11.8   0.0   1.7e-05       0.1     164     199 ..      89     124 ..      87     128 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.22
                     HHHHHHHTT--EEEE-C------------TTS-EE-TTS.-EEE CS
  Glyco_hydro_57 186 ileilaelGfeylftdelaeiledkskespyrpyllknggiavf 229
                     ++++l e+Gf++                               +
      EPA05389.1  36 VPKYLSENGFDI-------------------------------V 48 
                     444555555544...............................4 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 1.7e-05
                     HHHHHSS--SBEE-GGG-B--SHHHHHHHTT--EEE CS
  Glyco_hydro_57 164 yeeyfgqePrgfwlpElavspeileilaelGfeylf 199
                     ++e + ++P+++wl E + + + +e+ +++G++++f
      EPA05389.1  89 VQEAIKKKPKVIWLQEGIHNLQAEELARKNGIKIVF 124
                     578899***************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 882.67
//
Query:       EPA05390.1  [L=37]
Description: hypothetical protein BG20_I1224 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       260  (0.0145016); expected 358.6 (0.02)
Passed bias filter:                      193  (0.0107647); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.36s 00:00:00.83 Elapsed: 00:00:00.52
# Mc/sec: 213.59
//
Query:       EPA05391.1  [L=920]
Description: PAS domain S-box [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-35  122.0   0.1    6.7e-17   61.7   0.0    3.0  2  PAS_9        PAS domain
    2.9e-31  108.3   4.1    3.8e-31  107.9   0.9    2.8  3  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    1.4e-25   89.3   1.5      1e-12   48.2   0.1    2.8  2  PAS_3        PAS fold
    6.1e-23   81.0   0.0    8.4e-11   41.9   0.0    2.8  2  PAS          PAS fold
    7.1e-20   71.3   0.0    1.8e-09   37.8   0.0    2.5  2  PAS_4        PAS fold
    1.3e-11   44.3   1.7    5.4e-11   42.4   0.0    2.7  3  HisKA        His Kinase A (phospho-acceptor) domain
      5e-10   39.6  22.9    2.8e-09   37.1  10.7    4.4  3  dCache_1     Cache domain
    6.5e-09   35.6   0.0    0.00074   19.5   0.0    2.5  2  PAS_8        PAS domain
    6.5e-08   32.8   0.3    2.5e-07   31.0   0.1    2.1  2  HAMP         HAMP domain
     0.0003   20.9   0.3     0.0015   18.7   0.3    2.2  1  DUF2096      Uncharacterized protein conserved in archaea (DU
    0.00037   20.3   2.2    0.00055   19.8   0.2    2.4  2  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like
      0.006   16.0   0.4      0.012   15.0   0.4    1.4  1  DUF1397      Protein of unknown function (DUF1397)
  ------ inclusion threshold ------
       0.16   12.1   2.0         32    4.7   0.0    4.0  3  PAS_7        PAS fold


Domain annotation for each model (and alignments):
>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.1   0.0   1.3e-18   1.8e-15       4     104 .]     414     514 ..     411     514 .. 0.96
   2 !   61.7   0.0   4.8e-20   6.7e-17       3     104 .]     548     649 ..     545     649 .. 0.93

  Alignments for each domain:
  == domain 1  score: 57.1 bits;  conditional E-value: 1.3e-18
       PAS_9   4 ilidnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetfwvlltaspvkdddgelvgiivilr 100
                 + i++++g+i+y+Ne+++++  y++ee++gk+ + l   ++++e  + ++ ++  g   ++++++ +i k+g+++wv+  ++p+ dd g +  +i+i +
  EPA05391.1 414 VSITDKNGNIIYVNEKFCDVSKYKAEELIGKNHRILKstHHPKEFYSGIWSVISKGG--VWRGDIKNIAKDGSQYWVKSIIAPLLDDYGDIDEYIAIRT 510
                 45799***************************99999999*****************..**************************************** PP

       PAS_9 101 Dite 104
                 Dite
  EPA05391.1 511 DITE 514
                 ***8 PP

  == domain 2  score: 61.7 bits;  conditional E-value: 4.8e-20
       PAS_9   3 gilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk.kerevevvlirkngetfwvlltaspvkdddgelvgiivilr 100
                  ++i++++gri+++N++++++  ys+ee++gk+ + l  ++ +++e++++++e++++ k++++++ +  k+g+++wv+ +++p+   dg+  ++i+i +
  EPA05391.1 548 IVAITDNQGRIISVNDKFCEISKYSREELIGKNHRLLK-SEFHSHEFFKKLWETISSgKVWTGDIKNKAKDGTYYWVKTSITPLLGHDGKPERYIAIRT 645
                 455899***************************99999.88888888888888888888*************************999************ PP

       PAS_9 101 Dite 104
                 Dit+
  EPA05391.1 646 DITK 649
                 **95 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       5.8   8.1e+03      37      51 ..     167     181 ..     111     211 .. 0.59
   2 ?   -0.9   0.0       1.7   2.3e+03      29      61 ..     549     580 ..     529     627 .. 0.51
   3 !  107.9   0.9   2.8e-34   3.8e-31       1     111 [.     784     896 ..     784     897 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 5.8
                 EEEEEEEESSSSSTT CS
   HATPase_c  37 dlvisveDnGiGipk 51 
                   +i+ ++nG  i+ 
  EPA05391.1 167 SWWITARNNGMHISS 181
                 445555555544443 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.7
                 EEEEEEETEEEEEEEESSSSSTTHHHTGTCSTT CS
   HATPase_c  29 veikaseddlvisveDnGiGipkedlkklfekf 61 
                 v i+ +++   isv D  + i+k  +++l +k 
  EPA05391.1 549 VAIT-DNQGRIISVNDKFCEISKYSREELIGKN 580
                 4444.2236666777777777776666444422 PP

  == domain 3  score: 107.9 bits;  conditional E-value: 2.8e-34
                 EHHHHHHHHHHHHHHHHHHH.HSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCH.HCSTCHTSTSSSHHHHHHHHHHHHTTTEEEEEEE CS
   HATPase_c   1 gdekrLrqiisnlvdNavkf.atkageieveikaseddlvisveDnGiGipkedlkklfekfsq.ddstkrggggtGlGlsivkklvelmgGeiwvese 97 
                 gdekr+ qi++n+v N+v+f ++++g+i ++++ + d l +sv+DnGiGi++e++k++f+kf+q d st+r++gg+GlGlsi++ lv  mgG+iw+es+
  EPA05391.1 784 GDEKRIIQILKNMVNNSVDFvSPNDGKIIINVSEKGDSLIFSVRDNGIGISEENQKHVFKKFYQvDTSTTREHGGSGLGLSICQGLVIGMGGNIWFESK 882
                 79******************55578888888874449************************************************8888********** PP

                 TTTEEEEEEEEESS CS
   HATPase_c  98 pgrGttftftlple 111
                  g+Gt f+f+lp++
  EPA05391.1 883 IGEGTVFYFSLPKN 896
                 ***********975 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   0.2   3.6e-13     5e-10       1      88 [.     423     508 ..     423     509 .. 0.91
   2 !   48.2   0.1   7.2e-16     1e-12       1      88 [.     558     643 ..     558     644 .. 0.94

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 3.6e-13
       PAS_3   1 iiyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirdengkpvrvigv 88 
                 iiyv+e+++++  y +eel+gk  +++ l      +++++ ++ +++kg+++ g+++ + kdG+ +wv++ + ++ d+ g ++++i++
  EPA05391.1 423 IIYVNEKFCDVSKYKAEELIGK--NHRILKSTHHPKEFYSGIWSVISKGGVWRGDIKNIAKDGSQYWVKSIIAPLLDDYGDIDEYIAI 508
                 69********************..5665555566778********************************************9999876 PP

  == domain 2  score: 48.2 bits;  conditional E-value: 7.2e-16
       PAS_3   1 iiyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirdengkpvrvigv 88 
                 ii+v+++++ei  ys+eel+gk  +++ l       +++++l+e +++g++++g+++ + kdG+y+wv+++++++   +gkp r+i++
  EPA05391.1 558 IISVNDKFCEISKYSREELIGK--NHRLLKSEFHSHEFFKKLWETISSGKVWTGDIKNKAKDGTYYWVKTSITPLLGHDGKPERYIAI 643
                 589*******************..7777777777889************************************************987 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.0   3.4e-12   4.7e-09      12     109 ..     412     508 ..     406     512 .. 0.89
   2 !   41.9   0.0   6.1e-14   8.4e-11      13     109 ..     548     643 ..     534     647 .. 0.88

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 3.4e-12
                 SEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEECTTSSEEEEEEEEEEEEETTEEEEEEEEE CS
         PAS  12 dpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfklrdgrpihlevraspvrdaggeilgflgv 109
                 + + ++D++g+i+yvN+++++   +++ee++gk+  +l ++ ++ e+++ ++ +++ g  +r+  +++ + dg+ +++    +p++d  g i +++ +
  EPA05391.1 412 SLVSITDKNGNIIYVNEKFCDVSKYKAEELIGKNHRILKSTHHPKEFYSGIWSVISKGGVWRGDIKNIAK-DGSQYWVKSIIAPLLDDYGDIDEYIAI 508
                 56899*****************************99999999899******************6666666.*************99998887776665 PP

  == domain 2  score: 41.9 bits;  conditional E-value: 6.1e-14
                 EEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEECTTSSEEEEEEEEEEEEETTEEEEEEEEE CS
         PAS  13 pifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfklrdgrpihlevraspvrdaggeilgflgv 109
                  + ++D +gri+ vN++++e+  +sree++gk+   l +e +++e+ ++l++ +++g+ +++ +i+ k +dg+++++ +  +p++ ++g++  ++ +
  EPA05391.1 548 IVAITDNQGRIISVNDKFCEISKYSREELIGKNHRLLKSEFHSHEFFKKLWETISSGKVWTG-DIKNKAKDGTYYWVKTSITPLLGHDGKPERYIAI 643
                 566799***************************99888888888****************99.8888888*******************99877766 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.0   1.7e-10   2.3e-07       9     110 .]     415     517 ..     411     517 .. 0.92
   2 !   37.8   0.0   1.3e-12   1.8e-09       6     109 ..     547     651 ..     544     652 .. 0.88

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 1.7e-10
       PAS_4   9 avldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.pgeerhyelrllPlrdesGevigvlvisrDiT 106
                  + d++g+++y+N+ ++++ ++ +eel+Gk  + l ++++  ++ + +  v++ + +++  +     +g++ ++   + Pl+d+ G+++ +++i +DiT
  EPA05391.1 415 SITDKNGNIIYVNEKFCDVSKYKAEELIGKNHRILKSTHHPKEFYSGIWSVISKGGVWRGDIKNIAkDGSQYWVKSIIAPLLDDYGDIDEYIAIRTDIT 513
                 577******************************777777***************9888887777779******************************** PP

       PAS_4 107 errr 110
                 e++r
  EPA05391.1 514 EQKR 517
                 *986 PP

  == domain 2  score: 37.8 bits;  conditional E-value: 1.3e-12
       PAS_4   6 dalavldpdgrvlyaNaaaaelfgappeellGktlaellpee.daarleralrrvlegeepiefleelll.pgeerhyelrllPlrdesGevigvlvis 102
                 +++a+ d +gr++ +N  ++e+ ++++eel+Gk  +  l  e + +++   l + ++++++++  +  +  +g   ++ ++++Pl+ ++G++  +++i 
  EPA05391.1 547 AIVAITDNQGRIISVNDKFCEISKYSREELIGKNHRL-LKSEfHSHEFFKKLWETISSGKVWTGDIKNKAkDGTYYWVKTSITPLLGHDGKPERYIAIR 644
                 678999******************************4.444457777777777777777888888888889**************************** PP

       PAS_4 103 rDiTerr 109
                 +DiT ++
  EPA05391.1 645 TDITKQK 651
                 ****986 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.2       1.2   1.7e+03      32      61 ..     517     545 ..     495     549 .. 0.76
   2 !   42.4   0.0   3.9e-14   5.4e-11       2      65 ..     671     737 ..     670     739 .. 0.95
   3 ?   -2.2   0.1       3.1   4.3e+03      38      58 ..     776     796 ..     770     799 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.2
                 T-HSSCHHHHHHHHHHHHHHHHHHHHHHHH CS
       HisKA  32 klteelkeyletiesearrldhlvedlLdl 61 
                 ++ e+l  +l+++   +  l+++ + l d 
  EPA05391.1 517 RTEEQLSTALASLSHKSSELEKITNAL-DE 545
                 456777778888888888999999987.55 PP

  == domain 2  score: 42.4 bits;  conditional E-value: 3.9e-14
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHC.....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHH CS
       HisKA   2 lgrflagvaHELrtPLsailgnaeaLkre...gklteelkeyletiesearrldhlvedlLdlsrie 65 
                 +++f+ +++HEL+tPL+ i + a aLk+e   gkl+ee+ e+++ti + a+ l+ lv d+ d  +++
  EPA05391.1 671 KEEFMTMISHELKTPLTPITLWAGALKDEnimGKLSEEQLEAINTISNAADELTCLVGDIFDSYKLD 737
                 789*********************************************************9877765 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 3.1
                 HHHHHHHHHHHHHHHHHHHHH CS
       HisKA  38 keyletiesearrldhlvedl 58 
                  +  +t+   ++r+ ++++++
  EPA05391.1 776 SQKMDTMYGDEKRIIQILKNM 796
                 566789999999*****9998 PP

>> dCache_1  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1  10.7     2e-12   2.8e-09      52     247 ..      92     297 ..      40     299 .. 0.68
   2 !    5.4   1.2    0.0096        13      77     218 ..     414     602 ..     377     620 .. 0.47
   3 ?   -0.2   0.1      0.52   7.2e+02      56      88 ..     785     813 ..     744     858 .. 0.57

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 2e-12
    dCache_1  52 a.......................neasreslqallksilksn.pdi.sgvylvdadGqviassdpssppnlegtddpadrdwykealaggggkpvisd 125
                 +                       n+   e+l++ l+ +l+ + ++i  ++++ ++ G ++  +       +   + ++d++w+ +a+++g   ++is 
  EPA05391.1  92 TiesrdeiwrnnfseetnfineviNNPASEALNQKLNFYLNEHeNKIyAEIFVTNSYGVNVGETG------KTSDYLQSDESWWITARNNG---MHISS 181
                 34444444555555556666667788999**********98883344378888888888876442......222469**************...89999 PP

    dCache_1 126 pyvdqtggkpvitiavpiyddsgkfiGvlaadldldnlqd.llsni..klgetgyvfivdsdGniiahpd.kdllgknlrdelkaqealekalakiesg 220
                 +  dq++g++ + i+ +i ddsg+fiGv+ a +d  ++ + l+++    ++e+  ++++d++ nii+ ++ +++    l +               ++ 
  EPA05391.1 182 INYDQSSGVYSLDISQKITDDSGNFIGVIKAVYDSKEFLNiLVKSNehFVSEDIDIYLIDDKKNIIYTTSdHPF-SALLLEGF-------------TNN 266
                 9767777****************************99999788866654567779************8762433.22222221.............112 PP

    dCache_1 221 vssvklngeeylva.yapip....tglgWylv 247
                  +   +++++++v  +++i+    t++g  +v
  EPA05391.1 267 EY-GLIDNDSRFVSiSDKIKinsdTNTGLAIV 297
                 22.22333444455566666665555665555 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0096
    dCache_1  77 vylvdadGqviassdpssppnleg.............................tddpadrdwykealaggg...gkpvisdpyvdqtgg.kpvitiavp 142
                 v++ d++G++i+++ +  + +++                               +  + r+ +k+++++g+    k++i ++  d++ + + +i+i + 
  EPA05391.1 414 VSITDKNGNIIYVNEKFCDVSKYKaeeligknhrilksthhpkefysgiwsviSKGGVWRGDIKNIAKDGSqywVKSIIAPLLDDYG-DiDEYIAIRTD 511
                 444444444444433332222222333333333333333333333333333332222222223444444444444555555555555.54566666666 PP

    dCache_1 143 iyd..dsgkfiGvlaadldl..dnlqdllsniklgetgyvfivdsdGniiahpd..........kdllgknlrdelkaq...ealekalakie 218
                 i    ++ + + ++ a+l+   ++l ++ + +  +e+  v i d++G+ii+ +d          ++l+gkn r  ++++   e+++k    i 
  EPA05391.1 512 ITEqkRTEEQLSTALASLSHksSELEKITNAL--DESAIVAITDNQGRIISVNDkfceiskysrEELIGKNHRLLKSEFhshEFFKKLWETIS 602
                 66543344444444444443223355555544..45567888888888887766444443333333377766666555566655555544444 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.52
    dCache_1  56 sreslqallksilksnpdisgvylvdadGqvia 88 
                 +++++ ++lk+++  n++++ v+   +dG++i 
  EPA05391.1 785 DEKRIIQILKNMV--NNSVDFVS--PNDGKIII 813
                 5667777777766..33333222..34555544 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   4.6e-05     0.063      16      55 ..     416     455 ..     404     465 .. 0.76
   2 !   19.5   0.0   5.4e-07   0.00074      10      46 ..     543     582 ..     535     602 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.6e-05
       PAS_8  16 vvd.lgdrivdvNqaalellGys.adlkgellgqllpvlrpl 55 
                 ++d +g+ i++vN+++++   y+ ++l+g+   ++l+  + +
  EPA05391.1 416 ITDkNGN-IIYVNEKFCDVSKYKaEELIGKNH-RILKSTHHP 455
                 5676888.**************9888888766.555555555 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 5.4e-07
       PAS_8  10 spdgiav..vdlgdrivdvNqaalellGys.adlkgellg 46 
                 ++++ +v  +d+++ri+ vN++++e+  ys ++l+g+  +
  EPA05391.1 543 LDESAIVaiTDNQGRIISVNDKFCEISKYSrEELIGKNHR 582
                 555344333787779**************97777776554 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       4.4   6.1e+03      24      42 ..      55      68 ..      47      69 .. 0.73
   2 !   31.0   0.1   1.8e-10   2.5e-07       1      48 [.     333     380 ..     333     384 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 4.4
                BTSSTCCTTSSSHHHHHHH CS
        HAMP 24 dldtrlpvsgrDEiGeLar 42
                d+++r      DEi eL +
  EPA05391.1 55 DIKYR-----VDEIKELSK 68
                55555.....6***99975 PP

  == domain 2  score: 31.0 bits;  conditional E-value: 1.8e-10
                 HHHHTTHHHHHHHHHHHHHHTTTBTSSTCCTTSSSHHHHHHHHHHHHH CS
        HAMP   1 llarrilrPLrrLaraarriaaGdldtrlpvsgrDEiGeLarafNaMl 48 
                 l++r+i+ PLr L+++ + +a+G ld r+  ++ DE+GeL+  f++M+
  EPA05391.1 333 LISRSIVLPLRVLSKSSDDLASGILDRRISLDTADEFGELGIKFERMR 380
                 689********************************************8 PP

>> DUF2096  Uncharacterized protein conserved in archaea (DUF2096)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.3   1.1e-06    0.0015     126     164 ..     758     796 ..     721     798 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.1e-06
     DUF2096 126 eerlqeiaEyegvIiefeeddvvvvyGdkedikkaLkel 164
                  e  q+i+E +gvI+e+ ++++ ++yGd+++i + Lk++
  EPA05391.1 758 YEQSQKICEKKGVILENTSQKMDTMYGDEKRIIQILKNM 796
                 47889********************************98 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.1       9.6   1.3e+04      91     110 ..     647     666 ..     642     676 .. 0.56
   2 !   19.8   0.2     4e-07   0.00055       7      77 ..     793     863 ..     790     873 .. 0.80

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 9.6
  HATPase_c_3  91 itkkegesstltldvdkidk 110
                  itk+++++++l+++++  +k
   EPA05391.1 647 ITKQKNTEEQLSISLEENKK 666
                  45555555555555554443 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 4e-07
  HATPase_c_3   7 laelvdNsldAdaen...vkievnknrgktgeivieDdGkGmseeelknal.rlatsskeakrkstslGkkGiGl 77 
                  l  +v+Ns+d  + n   + i+v+++ g++  ++++D+G G+see+ k ++ ++ + +++   + + +G  G+Gl
   EPA05391.1 793 LKNMVNNSVDFVSPNdgkIIINVSEK-GDSLIFSVRDNGIGISEENQKHVFkKFYQVDTS---TTREHGGSGLGL 863
                  67899*****5554444499999996.799*******************99457777777...678888888884 PP

>> DUF1397  Protein of unknown function (DUF1397)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.4   8.9e-06     0.012      23     126 ..     711     818 ..     698     831 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8.9e-06
     DUF1397  23 eayekleeaaqelveClkslvdltelq.eeieeakpkgdldtvfkkyCkkleelke....CieevteklkpCldeeekeikkvlkniieelldlvCkkd 116
                 ea++++++aa+el+  + +++d  +l  ++++  ++k d d+++++  ++ +++ e     +e+ ++k++  +  +ek+i ++lkn++++ +d+v  +d
  EPA05391.1 711 EAINTISNAADELTCLVGDIFDSYKLDlNQLKFSHKKIDVDELMNNVYEQSQKICEkkgvILENTSQKMD-TMYGDEKRIIQILKNMVNNSVDFVSPND 808
                 5677777777777766777888888862455556777889999998888877776533323444445554.477899********************** PP

     DUF1397 117 Gdqialfiae 126
                 G++i+++ ++
  EPA05391.1 809 GKIIINVSEK 818
                 ****987644 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.11   1.5e+02      77      93 ..     413     429 ..     362     453 .. 0.57
   2 ?    0.5   0.3      0.46   6.3e+02     101     115 .]     506     520 ..     502     520 .. 0.87
   3 ?    4.7   0.0     0.024        32       9      39 ..     550     579 ..     546     655 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.11
       PAS_7  77 sfererpdgrvievrgn 93 
                  +  + ++g++i v+++
  EPA05391.1 413 LVSITDKNGNIIYVNEK 429
                 44555555555555443 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.46
       PAS_7 101 VttytDiTerrraee 115
                 +++ tDiTe++r+ee
  EPA05391.1 506 IAIRTDITEQKRTEE 520
                 67789*******996 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.024
       PAS_7   9 svfDadlrLvawNrrylelldlpeelvqvgv 39 
                 ++ D+++r++ +N++++e+ ++++e + +g+
  EPA05391.1 550 AITDNQGRIISVNDKFCEISKYSREEL-IGK 579
                 6889***************99998866.555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (920 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1365  (0.0761336); expected 358.6 (0.02)
Passed bias filter:                      623  (0.0347482); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.95u 0.36s 00:00:01.31 Elapsed: 00:00:00.54
# Mc/sec: 5102.31
//
Query:       EPA05392.1  [L=403]
Description: translation-associated GTPase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.8e-32  110.9   0.1    1.3e-31  109.5   0.0    1.7  2  MMR_HSR1_C  GTPase of unknown function C-terminal
    6.3e-19   68.1   0.0    6.4e-18   64.9   0.0    2.3  2  MMR_HSR1    50S ribosome-binding GTPase
    2.5e-07   30.7   0.0    4.9e-07   29.7   0.0    1.5  1  TGS         TGS domain
    5.5e-05   22.7   0.1     0.0025   17.4   0.1    2.7  2  FeoB_N      Ferrous iron transport protein B
    0.00071   19.7   0.1      0.086   12.9   0.0    2.8  3  Dynamin_N   Dynamin family
  ------ inclusion threshold ------
      0.028   14.0   0.8        9.8    5.7   0.0    2.9  2  GTP_EFTU    Elongation factor Tu GTP binding domain


Domain annotation for each model (and alignments):
>> MMR_HSR1_C  GTPase of unknown function C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       2.4   7.1e+03      66      95 ..     142     172 ..      95     190 .. 0.56
   2 !  109.5   0.0   4.2e-35   1.3e-31       1     112 []     224     332 ..     224     332 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.4
  MMR_HSR1_C  66 ldekqkkaLekirdlvlkry.gsTGVqealn 95 
                 l+   +k Le  rd v k + +++G+ +a++
  EPA05392.1 142 LTMWYHKILEGNRDKVSKLIrNGSGIIDAIT 172
                 4444444444444444332234455555554 PP

  == domain 2  score: 109.5 bits;  conditional E-value: 4.2e-35
  MMR_HSR1_C   1 alNKaDlpaadenieklkekypkdkkvvpvsAaaElaLrkaakqglikYepgdedfeikedklkeldekqkkaLekirdlvlkrygsTGVqealnaavf 99 
                 ++NK+D++ ad+n+++l+e+y+++  v+pvs+++E+ Lr+a+++glikY pg+e+fei ++  ++l+ekq +aL+ i++ ++ +y  TGVq a+n avf
  EPA05392.1 224 VANKIDVEGADKNFARLRERYNDSI-VIPVSGDSEFSLRRAEQKGLIKYSPGSEQFEIIKS--EDLNEKQINALDFIKKGIMGEYMRTGVQFAINVAVF 319
                 79********************666.********************************998..56********************************** PP

  MMR_HSR1_C 100 elldlivVYPVed 112
                 +ll++  +YPV d
  EPA05392.1 320 KLLKMNSIYPVAD 332
                 ***********86 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.9   0.0   2.2e-21   6.4e-18       2      87 ..       5     123 ..       4     161 .. 0.77
   2 ?    0.5   0.0       0.2     6e+02      94     114 .]     207     227 ..     166     227 .. 0.75

  Alignments for each domain:
  == domain 1  score: 64.9 bits;  conditional E-value: 2.2e-21
                 EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEE...........ETTEE................EEEEECGGCSSHHHHHHHHHHHHHHH CS
    MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvk...........lkgke................ielvDtpGliegaseekglgkaflal 73 
                  +++G++N+GK+t+ na t +  ++s++p+tT++++ g  +           +   +                +el+D+pGli++a ++kglg++fl++
  EPA05392.1   5 LGLIGKTNTGKTTFYNAATLSSEEISSYPFTTKKPVSGIAHaitlcvhpefkI---QdnpnnskcvegwryipVELIDLPGLIKDAWKGKGLGNQFLSI 100
                 689***********************************877655555555441...03334555566666666***********999***********8 PP

                 HC.TSEEEEEEETT........T CS
    MMR_HSR1  74 ee.adlillvvdas........e 87 
                    +d++l+vvdas         
  EPA05392.1 101 AAqSDALLHVVDASggidssgkI 123
                 8769********99555543330 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.2
                 HHHHHHHHHHTTSEEEEEEES CS
    MMR_HSR1  94 deeleelleeakkplilvlnk 114
                  ++l+ +l++  kp+++v+nk
  EPA05392.1 207 TKKLATYLRKISKPTLIVANK 227
                 3778899999999*****998 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0   1.7e-10   4.9e-07      11      59 ..     345     398 ..     335     399 .. 0.89

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 1.7e-10
                 EE...EETTB-HHHHHHHHSTTHHHHEEEEEECS..EEEETTSBB-SSEEEEEE CS
         TGS  11 pd...lprgatveDfAykIhrslakkfiyAlVnG..qrvgldhvLedgdvveIv 59 
                 pd   l+ gat+ D+A+ Ih++l k ++y++      r + d++L+d dvv++v
  EPA05392.1 345 PDlilLKAGATIADLAKEIHTDLTKGLLYGKDLRynLRLPVDYQLRDRDVVSLV 398
                 347779****************************989**************998 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   8.2e-07    0.0025       2      41 ..       4      43 ..       3     115 .. 0.85
   2 ?   -1.8   0.0      0.68     2e+03      97     118 ..     210     231 ..     205     256 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 8.2e-07
                EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEE CS
      FeoB_N  2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegk 41
                ++ l+G+ n+Gktt+ na t ++++++ +p +t +  +g 
  EPA05392.1  4 KLGLIGKTNTGKTTFYNAATLSSEEISSYPFTTKKPVSGI 43
                6789**************************9986655554 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.68
                 HHHHHHHTTSSEEEEEETHHHH CS
      FeoB_N  97 Ltlqllelgvpvvlalnmidea 118
                 L + l  +++p++++ n+id+ 
  EPA05392.1 210 LATYLRKISKPTLIVANKIDVE 231
                 6677888999999999999974 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1     0.021        64       2      18 ..       6      22 ..       5      41 .. 0.71
   2 !   12.9   0.0   2.9e-05     0.086     102     142 ..      74     117 ..      56     136 .. 0.87
   3 ?   -2.2   0.0       1.3   3.8e+03     146     167 ..     206     227 ..     181     228 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.021
                EEEEBTTTTHHHHHHHH CS
   Dynamin_N  2 avvGsqSsGKSSvlnaL 18
                 ++G+++ GK+++ na 
  EPA05392.1  6 GLIGKTNTGKTTFYNAA 22
                689************84 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 2.9e-05
                 SEEEEE---B-SSSGTTS...HHHHHHHSTTEEEEEEEETTS-C CS
   Dynamin_N 102 gltlvDlPGldsvnkrdq...elvkeyikkadiilavtsanhdl 142
                  ++l+DlPGl++ + + +   +   +++ ++d++l+v++a+  +
  EPA05392.1  74 PVELIDLPGLIKDAWKGKglgNQFLSIAAQSDALLHVVDASGGI 117
                 699*********9999998999999999***********98655 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.3
                 CHHHHHHHHSTTBTTEEEEEE- CS
   Dynamin_N 146 ealflarevdpkgkrtivvltk 167
                 + ++la  +++ +k t++v +k
  EPA05392.1 206 DTKKLATYLRKISKPTLIVANK 227
                 6788999999999999999988 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.2    0.0041        12       5      33 ..       4      32 ..       2     123 .. 0.65
   2 ?    5.7   0.0    0.0033       9.8     109     150 ..     205     248 ..     202     339 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0041
                EEEEEESTTSSHHHHHHHHHHHTTSSCHH CS
    GTP_EFTU  5 nigiighvDhGKtTLtdrLlyktgaiskk 33
                ++g+ig +++GKtT+  + + ++++is+ 
  EPA05392.1  4 KLGLIGKTNTGKTTFYNAATLSSEEISSY 32
                57899*********999999888888873 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0033
                 HHHHHHHHHHHHTTTEEEEEEESCGST..HHHHHHHHHHHHHHH CS
    GTP_EFTU 109 pqteevlrlalkegvpiivfiNKmDrl..kaelkeiveevkqkl 150
                   t++++  ++k   p+ ++ NK+D    ++++ ++ e +++++
  EPA05392.1 205 FDTKKLATYLRKISKPTLIVANKIDVEgaDKNFARLRERYNDSI 248
                 5799999999***************9988899999998888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.54
# Mc/sec: 2238.25
//
Query:       EPA05393.1  [L=295]
Description: biotin-(acetyl-CoA-carboxylase) ligase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.3e-18   64.6   0.1    6.2e-17   61.7   0.0    2.0  2  BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family
    5.2e-08   32.7   0.9      1e-07   31.7   0.9    1.5  1  BPL_C          Biotin protein ligase C terminal domain
     0.0067   15.9   0.1     0.0092   15.4   0.1    1.2  1  Sec15          Exocyst complex subunit Sec15-like
  ------ inclusion threshold ------
      0.038   13.9   0.6       0.14   12.1   0.6    2.0  1  HTH_11         HTH domain


Domain annotation for each model (and alignments):
>> BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.7   0.0   1.4e-20   6.2e-17       2     131 .]      55     178 ..      54     178 .. 0.88
   2 ?    0.5   0.0      0.12   5.2e+02      62     113 ..     210     266 ..     196     272 .. 0.55

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 1.4e-20
                    EEEES-HHH.HHH..GCGGG--TT-EEEEEEESS-B....-B--B-TTSEEEEEEEEESS...-CCGTHHHHHHHHHHHHHHH......HHTT-TT CS
  BPL_LplA_LipB   2 gevikstnt.llkeslnsselesgglvvvrrqtgGr....nvwhspkgeltyslllspeqktfqnrvlelyvsllvlavlealgyrdskpgiegip 92 
                    +e+i+st+  + k     s++++g++ +++ qt+G+    + w+spkg++++s+++    ++f+ + + l+ + ++l    a+       +  gi+
     EPA05393.1  55 FESIDSTQNqAMK---MASDVDDGTIIIAEKQTSGKgrsgRKWVSPKGGIWFSIIMH---PKFDISAITLFPLASSLGLSYAI------EKTLGIK 138
                    7788888553444...45669***********************************9...779*9999999888888888888......6999*** PP

                    EEEETTTEEEETTEEEEEEEEEEEE.TTS-EEEEEEEEEE CS
  BPL_LplA_LipB  93 vfikwpnDlyvngrKlaGiavtstr.gktlhhivigvgvn 131
                     + kwpnD+ ++g+K+aG +v     +++++ +++gvg+n
     EPA05393.1 139 SELKWPNDITIKGKKVAGMLVDASIeSNKIEKLILGVGIN 178
                    *********************9888799**********99 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.12
                    CGTHHH.HHHHHHHHHHHH..........HHTT-TTEEEETTTEEEETTEEEEEEEE CS
  BPL_LplA_LipB  62 rvlely.vsllvlavlealg....yrdskpgiegipvfikwpnDlyvngrKlaGiav 113
                    r+++l+   l++l  + +l     +++ ++++++ +  i    +l  ++rK+ Gia+
     EPA05393.1 210 RPISLLqSFLIELEQVYNLLnsgdSKKIIREYTKRSSTIGQNIELNTDNRKIKGIAI 266
                    556665444555554444433332111333344333333344677889999999987 PP

>> BPL_C  Biotin protein ligase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.9   2.3e-11     1e-07       1      47 [.     247     292 ..     247     293 .. 0.95

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 2.3e-11
                 STTSEEEEEETSCEEEEEEEEE-TTSEEEEEETTE.EEEESSCCEEE CS
       BPL_C   1 hsGqeVtlededgkveGiavGIdddGaLllktddglqpdinsGdisl 47 
                 ++Gq++ l ++++k+ Gia  IdddGaL++ +++     ++sGdi +
  EPA05393.1 247 TIGQNIELNTDNRKIKGIAIKIDDDGALVVSENNK-NIRVTSGDITH 292
                 69****************************99999.********965 PP

>> Sec15  Exocyst complex subunit Sec15-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   2.1e-06    0.0092     245     290 ..     178     236 ..     152     248 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.1e-06
                 HHHTTTSSGGG-.........-----------....-----------TTTT.TTT--S. CS
       Sec15 245 nlelDvkylesf.........akslsvskkee....slestfaelrqlidLllsdnvee 290
                 n+++Dvk++e++         ++sls+++k+      l+s+++el+q+ +Ll s + ++
  EPA05393.1 178 NFNVDVKQIEKIlkdtenfygVASLSEQNKSIrpisLLQSFLIELEQVYNLLNSGDSKK 236
                 9***********88888888888887776544999999*************65887765 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.6   3.2e-05      0.14      37      55 .]       8      26 ..       8      26 .. 0.96

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.2e-05
      HTH_11 37 kaLeelgvpIesepgrGYr 55
                k+++elg++Ies+++ GYr
  EPA05393.1  8 KKIRELGYKIESKQKLGYR 26
                789***************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.62u 0.36s 00:00:00.98 Elapsed: 00:00:00.56
# Mc/sec: 1578.49
//
Query:       EPA05394.1  [L=255]
Description: methionyl-tRNA synthetase domain protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      7e-92  308.2   0.8    7.8e-92  308.0   0.8    1.0  1  tRNA-synt_1g  tRNA synthetases class I (M)
    8.7e-15   54.0   0.9    8.3e-08   30.9   0.1    3.0  2  tRNA-synt_1   tRNA synthetases class I (I, L, M and V)
    4.1e-06   26.3   0.1    8.2e-06   25.4   0.0    1.5  2  tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
  ------ inclusion threshold ------
      0.014   14.3   0.1      0.093   11.6   0.1    2.0  2  tRNA-synt_1f  tRNA synthetases class I (K)
      0.061   11.2   0.3      0.077   10.8   0.3    1.1  1  PolC_DP2      DNA polymerase II large subunit DP2
       0.12   12.7   2.3       0.27   11.5   2.3    1.6  1  zf-Di19       Drought induced 19 protein (Di19), zinc-binding
       0.33   11.5   3.7       0.67   10.5   3.7    1.6  1  zf-CHY        CHY zinc finger
       0.38   10.2   9.2        3.2    7.3   3.0    2.5  3  zf-ribbon_3   zinc-ribbon domain
       0.73    9.9   7.3        3.6    7.7   7.3    2.1  1  DZR           Double zinc ribbon
        3.6    7.7   4.4         47    4.0   0.0    2.2  2  HypA          Hydrogenase/urease nickel incorporation, metall
        8.1    6.7   8.5       0.85    9.8   1.9    2.3  2  Zn-ribbon_8   Zinc ribbon domain


Domain annotation for each model (and alignments):
>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  308.0   0.8   4.8e-95   7.8e-92       2     250 ..       6     254 ..       5     255 .] 0.98

  Alignments for each domain:
  == domain 1  score: 308.0 bits;  conditional E-value: 4.8e-95
                   EEEE--B--SS---HHHHH.HHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHTT---SEEEETTSHHHH CS
  tRNA-synt_1g   2 lvttalpYangklHlGhll.evisaDifaRykrlrgeevlfvcgtDehGtpielkAekegvtpeelvekvheeikelfkklnisfdkygrttseehk 97 
                   ++t+alpYang++HlGh++ ++++aD+ +R+ +l+g e +++c++D +Gtpi ++ ekeg tp+e+v++ +++  ++f+ ++i fd +++t+s+e+ 
    EPA05394.1   6 IITSALPYANGEIHLGHVAsTYLPADVTTRFLKLKGVEAYYFCASDDFGTPILIQSEKEGKTPSEYVAHWNKRDYDDFTAFGIDFDFFYKTSSSENI 102
                   79*****************9***************************************************************************** PP

                   HHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG-EE........-TTS-EE-TTSSB-E................EEE.EEEEEE-GGGGHHH CS
  tRNA-synt_1g  98 elvqeifkklkekgliyekeieqlycpkderflpdryvegtCPkckseeargdqceecgkkleptelinpksaisgskpevketehlffklskfekk 194
                    +vq++fkkl++ g+iyekei q+yc++d++flpdryv+g CP+c++ ++++d ce+cg+   p+e+ +pk++i+g++p+ ++t+h+ffkl++f ++
    EPA05394.1 103 AFVQDVFKKLNNAGHIYEKEIIQFYCNNDKKFLPDRYVKGVCPYCNAIDQYSDLCESCGRV--PEEISDPKCSICGQTPTKEKTTHFFFKLKNFGDA 197
                   ************************************************************8..55******************************** PP

                   HHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS-SSS-EET..TECCEEE-HHHH CS
  tRNA-synt_1g 195 lkewieeeekeleenvkkivkewlkegLkdlaisrdldwGipvP..gaekkvlYVWld 250
                   l +w+  e+++l++ vkk+v++w+k+gL d++i+rd++wG+pvP  +a++kv+Y W+d
    EPA05394.1 198 LYKWL-DENENLQKDVKKYVQNWIKSGLIDWDITRDISWGVPVPvdDAKDKVFYGWFD 254
                   *****.67779**********************************9***********9 PP

>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.1   5.1e-11   8.3e-08      26     170 ..       6     132 ..       2     141 .. 0.85
   2 !   17.7   0.1   5.3e-07   0.00086     363     433 ..     170     241 ..     160     250 .. 0.85

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 5.1e-11
  tRNA-synt_1  26 ilvdgPPyvtGslHiGhalaktl.kdivirykrmkGkevlyvpGwDhaGlaieakvekklgakekkerkklgreefrekvrewkaeyaeeirkqvkrl 122
                  i++   Py++G++H+Gh+  + l  d+ +r+ ++kG e+ y    D  G +i  + ek+ g++                  e++a+  ++  ++++ +
   EPA05394.1   6 IITSALPYANGEIHLGHVASTYLpADVTTRFLKLKGVEAYYFCASDDFGTPILIQSEKE-GKTPS----------------EYVAHWNKRDYDDFTAF 86 
                  567778**************999669**************************9998888.44443................45555566667788999 PP

  tRNA-synt_1 123 GvsvDfdreylTldkeleeavkevfvrladkgliyrgkklvnwstklk 170
                  G  +Dfd  y+T ++e  + v+ vf++l + g+iy+ + + +++++ k
   EPA05394.1  87 G--IDFDFFYKTSSSENIAFVQDVFKKLNNAGHIYEKEIIQFYCNNDK 132
                  9..577778****************************99999998765 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 5.3e-07
  tRNA-synt_1 363 pfcerskkpiiyrateqWfvrvkeladaalkavekvqfvpkskekryaswlen.iqdWciSRqrwWGhripl 433
                  p c+  ++      t+  f ++k++ da+ k +++ +   k  +k  ++w++    dW i R+  WG+++p+
   EPA05394.1 170 PKCSICGQTPTKEKTTHFFFKLKNFGDALYKWLDENENLQKDVKKYVQNWIKSgLIDWDITRDISWGVPVPV 241
                  666666666667788999****************99999999*********96378***************8 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0     5e-09   8.2e-06      21     130 ..      16     125 ..       2     139 .. 0.88
   2 ?   -2.8   0.0       1.9   3.1e+03     226     248 ..     207     226 ..     195     229 .. 0.68

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 5e-09
                   S--BHHH.HHHHHHHHHHHHHHHHTT-EEEEEEEBB--SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHTT----.SB--BGGGGHHHHHHHHHHH CS
  tRNA-synt_1e  21 dashlGh.aRslvafDilrrilqalgYdvqfvqnvtDidDkiikrareeeksvkelaekfieefkkdleaLnvlkp.tleprvsekvdeiielvekl 115
                    ++hlGh a +++  D+  r+l+ +g +  +     D    i+ ++++e+k+ +e ++++ +  ++d++a ++     +++  se+++ + ++ +kl
    EPA05394.1  16 GEIHLGHvASTYLPADVTTRFLKLKGVEAYYFCASDDFGTPILIQSEKEGKTPSEYVAHWNKRDYDDFTAFGIDFDfFYKTSSSENIAFVQDVFKKL 112
                   679****4567999***********************************************************87515688999************* PP

                   HHTTSEEE-TTS-EE CS
  tRNA-synt_1e 116 iekgyaYavsdgdvy 130
                    + g+ Y+ +   ++
    EPA05394.1 113 NNAGHIYEKE--IIQ 125
                   *******987..333 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.9
                   HHHHHHHSS.S--EEEEEEE--EE CS
  tRNA-synt_1e 226 laqseaafd.kqlvkyflhnghlk 248
                   + q+    d k++v+ ++ +g + 
    EPA05394.1 207 NLQK----DvKKYVQNWIKSGLID 226
                   4443....3367888888888775 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.15   2.4e+02      34      71 ..      15      53 ..       3      55 .. 0.79
   2 ?   11.6   0.1   5.7e-05     0.093     104     185 ..      68     152 ..      61     204 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.15
  tRNA-synt_1f 34 SGliHiGnlrev.ltadlvaralrkrgeevrlilisDdm 71
                   G iH+G +  + l ad+  r l+ +g e+  ++ sDd+
    EPA05394.1 15 NGEIHLGHVASTyLPADVTTRFLKLKGVEAYYFCASDDF 53
                  599*****9976155666666677779999999999997 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 5.7e-05
  tRNA-synt_1f 104 hesyaehfnaelvesLdelgievefisatelYksglydeaikealenreki..keilekyrgee.reetyspylpvcekcgrvdt 185
                    ++y+ h+n++  +   ++gi+++f  +t+  ++ ++ + + + l+n  +i  kei++ y +++ +      ++ vc+ c+ +d+
    EPA05394.1  68 PSEYVAHWNKRDYDDFTAFGIDFDFFYKTSSSENIAFVQDVFKKLNNAGHIyeKEIIQFYCNNDkKFLPDRYVKGVCPYCNAIDQ 152
                   468***********************************************96668999998776322222335666666666655 PP

>> PolC_DP2  DNA polymerase II large subunit DP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.3   4.7e-05     0.077     606     697 ..     112     213 ..      96     225 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 4.7e-05
    PolC_DP2 606 akkkgei.eveiarrkCkkCgk....etlearCeeCgekteeklvCkkcee...eveeekcekcekeakavkkkki..dlkellekaleklgereekle 694
                  ++ g+i e ei + +C++ +k    + ++  C+ C++  + +  C++c++   e+++ kc+ c+++ ++ k++++  +lk+  ++ ++ l+e+e+ ++
  EPA05394.1 112 LNNAGHIyEKEIIQFYCNNDKKflpdRYVKGVCPYCNAIDQYSDLCESCGRvpeEISDPKCSICGQTPTKEKTTHFffKLKNFGDALYKWLDENENLQK 210
                 33456666899999999997662222567889*******999999***998654555788999999988887776511566666666666777776666 PP

    PolC_DP2 695 elk 697
                 ++k
  EPA05394.1 211 DVK 213
                 665 PP

>> zf-Di19  Drought induced 19 protein (Di19), zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   2.3   0.00017      0.27       5      49 ..     144     187 ..     141     192 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00017
     zf-Di19   5 CPyCgkeltvkeLveHvedeHrveskevvCPvCaekvtkdlvaHl 49 
                 CPyC+   + + L+e +    ++e     C++C ++ tk+   H+
  EPA05394.1 144 CPYCNAIDQYSDLCESCGR-VPEEISDPKCSICGQTPTKEKTTHF 187
                 ******99999******98.588888999*****99999988887 PP

>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   3.7   0.00041      0.67      36      73 ..     136     176 ..     117     178 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00041
      zf-CHY  36 rlevkevlcllCeteqekavlCkkCkk...efaeyfCpiCk 73 
                   +  + +c  C++ ++ + lC++C++   e+++ +C+iC 
  EPA05394.1 136 PDRYVKGVCPYCNAIDQYSDLCESCGRvpeEISDPKCSICG 176
                 44555668*****************9966666666899996 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   3.0     0.002       3.2       5      23 ..     144     161 ..     142     164 .. 0.94
   2 ?    5.7   4.0    0.0061       9.9       5      24 ..     157     177 ..     156     179 .. 0.92
   3 ?    5.2   0.5    0.0089        15       4      13 ..     171     181 ..     170     185 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.002
  zf-ribbon_3   5 CPnCGaplssddnvCpyCG 23 
                  CP+C+a+ +     C +CG
   EPA05394.1 144 CPYCNAI-DQYSDLCESCG 161
                  *******.**********9 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0061
  zf-ribbon_3   5 CPnCGa.plssddnvCpyCGt 24 
                  C +CG  p + +d++C  CG+
   EPA05394.1 157 CESCGRvPEEISDPKCSICGQ 177
                  889***99999*********6 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.0089
  zf-ribbon_3   4 rCPnCGa.pls 13 
                  +C+ CG+ p +
   EPA05394.1 171 KCSICGQtPTK 181
                  6*****98854 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   7.3    0.0022       3.6       1      39 [.     144     180 ..     120     187 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0022
         DZR   1 CpqCgeelppdarfCseCgtklkavaaedrCpsCgekvd 39 
                 Cp C++ +++ +  C+ Cg  ++ + +  +C+ Cg+  +
  EPA05394.1 144 CPYCNA-IDQYSDLCESCGRVPE-EISDPKCSICGQTPT 180
                 888875.6899999999998886.455678999988744 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.029        47      62      95 ..     117     150 ..      92     155 .. 0.72
   2 ?    4.0   1.9      0.03        49      72      98 ..     156     181 ..     152     191 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.029
                 EEEEEE--EEEETTTS-EEECHHH.HHS-TTTSSS CS
        HypA  62 LeieevpvkvrCreCgkefeleek.alrCpkCgsa 95 
                   +e++ ++++C++ +k    +++ +  Cp C++ 
  EPA05394.1 117 HIYEKEIIQFYCNNDKKFLP-DRYvKGVCPYCNAI 150
                 45788889999998775555.4444779****986 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.03
                 EETTTS-EEECHHHHHS-TTTSSS-EE CS
        HypA  72 rCreCgkefeleekalrCpkCgsadve 98 
                  C++Cg+  e+  ++ +C  Cg++ ++
  EPA05394.1 156 LCESCGRVPEEI-SDPKCSICGQTPTK 181
                 5*****666644.3579*****98765 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.5      0.46   7.5e+02      28      34 ..     143     149 ..     123     154 .. 0.70
   2 ?    9.8   1.9   0.00052      0.85       8      37 ..     157     181 ..     150     183 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.46
  Zn-ribbon_8  28 aCPeCgs 34 
                  +CP C++
   EPA05394.1 143 VCPYCNA 149
                  4999986 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00052
  Zn-ribbon_8   8 CeeCghefevlqsisdapltaCPeCgs.evr 37 
                  Ce+Cg++ e++       +++C  Cg+ +++
   EPA05394.1 157 CESCGRVPEEIS------DPKCSICGQtPTK 181
                  *********887......677*****96654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1065  (0.059401); expected 358.6 (0.02)
Passed bias filter:                      744  (0.041497); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.60u 0.34s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 1491.39
//
Query:       EPA05395.1  [L=94]
Description: hypothetical protein BG20_I1229 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.049   13.5   0.8      0.075   12.9   0.8    1.2  1  DUF2975   Protein of unknown function (DUF2975)


Domain annotation for each model (and alignments):
>> DUF2975  Protein of unknown function (DUF2975)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.8   4.2e-06     0.075      60     112 ..      13      79 ..       9      82 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.2e-06
     DUF2975  60 rriglaliaaalllaagivalallae.lelap.............gvvllllgvafaslvigllvlv 112
                 ++i +++i++a++ +++i+++   a+ +  a+             + v+l+ +v+++++++ +++l+
  EPA05395.1  13 NKILGSIIIIAIIQFIQIPHMIWNADmMLQAGvisrvhpaidwllYGVDLIEIVSIINVGMIMFSLI 79 
                 68999*********************66666699999999999999999999999999999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 586.88
//
Query:       EPA05396.1  [L=388]
Description: tetratricopeptide repeat protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-07   30.2   0.0       0.04   14.0   0.0    3.5  3  TPR_2            Tetratricopeptide repeat
    3.6e-06   26.5   0.2       0.54   10.2   0.0    3.4  3  TPR_1            Tetratricopeptide repeat
     0.0023   17.4   0.1     0.0036   16.8   0.1    1.2  1  Coatomer_E       Coatomer epsilon subunit
     0.0026   17.1   0.2     0.0054   16.1   0.2    1.5  1  Porin_OmpG_1_2   OMPG-porin 1 family
  ------ inclusion threshold ------
      0.015   15.2   0.1      0.096   12.6   0.1    2.1  2  DUF4919          Domain of unknown function (DUF4919)
      0.015   15.8   0.0       0.21   12.1   0.0    2.3  2  TPR_19           Tetratricopeptide repeat
      0.017   15.7   0.9        1.1   10.1   0.0    3.9  4  TPR_6            Tetratricopeptide repeat
       0.04   14.7   0.0        7.3    7.7   0.0    3.1  3  TPR_14           Tetratricopeptide repeat
      0.049   13.7   0.0         28    4.9   0.0    3.2  3  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
        0.1   13.1   0.0       0.24   11.8   0.0    1.6  2  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
        5.6    7.4   5.3         25    5.4   0.0    3.5  4  TPR_8            Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0013       2.1       3      34 .]      25      56 ..      23      56 .. 0.92
   2 ?    3.5   0.0      0.06        98       5      34 .]      61      90 ..      58      90 .. 0.88
   3 !   14.0   0.0   2.5e-05      0.04      11      33 ..     101     123 ..      93     124 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0013
       TPR_2  3 alynlGlayyklgdyeeAleafekAleldPnn 34
                 l+ +++  + +g+y+eA+  ++  l   Pnn
  EPA05396.1 25 TLFKQANQNLLNGKYNEAILIYDDILVKFPNN 56
                689999999***************99999997 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.06
       TPR_2  5 ynlGlayyklgdyeeAleafekAleldPnn 34
                 + + a+ +lg++e+ l  f k l++ P++
  EPA05396.1 61 KMKAIALSNLGEHEKSLLEFFKILQYQPDD 90
                568999***********9999999999986 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 2.5e-05
       TPR_2  11 yyklgdyeeAleafekAleldPn 33 
                   +lg+y+eA ++f++A+   P+
  EPA05396.1 101 FGNLGEYQEANHYFNEAIMKKPD 123
                 5589**************99997 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1      0.01        17       3      34 .]      25      56 ..      23      56 .. 0.77
   2 !    7.3   0.0    0.0027       4.5       3      34 .]      59      90 ..      57      90 .. 0.91
   3 !   10.2   0.0   0.00033      0.54       6      33 ..      96     123 ..      92     124 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.01
                HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1  3 alynlGnayfklgkydeAleyyekALelnPnn 34
                +l+  +n  + +gky+eA+  y+  L   Pnn
  EPA05396.1 25 TLFKQANQNLLNGKYNEAILIYDDILVKFPNN 56
                56777888899********8888777666665 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0027
                HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1  3 alynlGnayfklgkydeAleyyekALelnPnn 34
                +l+ ++ a+ +lg++++ l  + k L+ +P++
  EPA05396.1 59 TLKMKAIALSNLGEHEKSLLEFFKILQYQPDD 90
                577899*********************99996 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.00033
                 HHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
       TPR_1   6 nlGnayfklgkydeAleyyekALelnPn 33 
                 ++G+ + +lg+y+eA  y+++A+   P+
  EPA05396.1  96 GMGVGFGNLGEYQEANHYFNEAIMKKPD 123
                 67888999***************98887 PP

>> Coatomer_E  Coatomer epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   2.2e-06    0.0036     181     277 ..      37     132 ..      17     138 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.2e-06
                 THHHHHHHHHHHHHHHS---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHHHHHHHHHHHH-TT-HHHHHHHH CS
  Coatomer_E 181 ekiqdAyyifqelsekykstplllngkAvvslllgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevsernlsqlklshpehklvkdlne 277
                 +k+++A +i++++  k++++  +l+ kA++   lg++e+      + L+ ++ d  ++  + v   +lg  +   ++++++   ++p+++++k+++e
  EPA05396.1  37 GKYNEAILIYDDILVKFPNNISTLKMKAIALSNLGEHEKSLLEFFKILQYQPDDITAITGMGVGFGNLGEYQ-EANHYFNEAIMKKPDSVIIKNYKE 132
                 69***********************************999999999***********************995.56899999999********99987 PP

>> Porin_OmpG_1_2  OMPG-porin 1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.2   3.3e-06    0.0054      89     130 ..     227     268 ..     219     311 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.3e-06
  Porin_OmpG_1_2  89 telfvgksyenergniGwevklasesideRtkarakvfgdlr 130
                     ++++vg +y +++g iG e+k + e i++  +a+ k+f+ + 
      EPA05396.1 227 KDFVVGIQYMMKNGIIGIEIKKSHEDIQKEKEAELKLFEKYL 268
                     6899***********************************983 PP

>> DUF4919  Domain of unknown function (DUF4919)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   5.9e-05     0.096      54     110 ..      19      76 ..      14     101 .. 0.85
   2 ?    0.2   0.0      0.38   6.2e+02      82     115 ..      82     115 ..      80     120 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.9e-05
     DUF4919  54 deekleel.kldkkelseeelkeiislaeealkknPfdlkqlnllayaykalgkkeea 110
                   +++++l k+++++l + +++e+i +  ++l k+P ++ +l++ a+a+++lg++e++
  EPA05396.1  19 TANDVQTLfKQANQNLLNGKYNEAILIYDDILVKFPNNISTLKMKAIALSNLGEHEKS 76 
                 45666666788999999************************************99875 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.38
     DUF4919  82 ealkknPfdlkqlnllayaykalgkkeeakiysk 115
                 ++l+ +P d+++++ +   +++lg+ +ea++y +
  EPA05396.1  82 KILQYQPDDITAITGMGVGFGNLGEYQEANHYFN 115
                 689999**********************999876 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00013      0.21       2      58 ..      34      90 ..      33      97 .. 0.92
   2 ?    1.0   0.0      0.38   6.2e+02       5      24 ..     105     124 ..     103     129 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
      TPR_19  2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd 58
                l +g+y eA+ ++  +l + p+n   +   A+al +lg+ ++      ++++ +pdd
  EPA05396.1 34 LLNGKYNEAILIYDDILVKFPNNISTLKMKAIALSNLGEHEKSLLEFFKILQYQPDD 90
                568***************************************999999999999997 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.38
      TPR_19   5 gdyaeAlalleqalqedpkn 24 
                 g y+eA  ++ +a+ ++p++
  EPA05396.1 105 GEYQEANHYFNEAIMKKPDS 124
                 67888888888887777765 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00066       1.1       3      33 .]      26      56 ..      24      56 .. 0.89
   2 ?   -1.0   0.0       2.3   3.7e+03       7      32 ..      64      89 ..      62      90 .. 0.81
   3 ?   -0.7   0.0       1.8     3e+03      11      27 ..     102     118 ..      96     124 .. 0.76
   4 ?    0.0   0.0         1   1.7e+03      21      31 ..     132     142 ..     128     142 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00066
                HHHHHHHHHHHHHHHHHHHHHHHHHHH-TT- CS
       TPR_6  3 lyklalsyrklgdtdkAlealerlikeYPdS 33
                l+k+a   +  g++ +A+ ++++++ ++P++
  EPA05396.1 26 LFKQANQNLLNGKYNEAILIYDDILVKFPNN 56
                899998888878*****************95 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.3
                HHHHHHHHHHHHHHHHHHHHHHH-TT CS
       TPR_6  7 alsyrklgdtdkAlealerlikeYPd 32
                a ++ +lg+++k+l  + ++++  Pd
  EPA05396.1 64 AIALSNLGEHEKSLLEFFKILQYQPD 89
                55667788999999999999999998 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.8
                 HHHHHHHHHHHHHHHHH CS
       TPR_6  11 rklgdtdkAlealerli 27 
                  +lg++++A  ++++ i
  EPA05396.1 102 GNLGEYQEANHYFNEAI 118
                 56799****99999877 PP

  == domain 4  score: 0.0 bits;  conditional E-value: 1
                 HHHHHHHHH-T CS
       TPR_6  21 ealerlikeYP 31 
                 e  e++i++YP
  EPA05396.1 132 EFTEKVITKYP 142
                 56699*****9 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0045       7.3       6      42 ..      28      64 ..      23      66 .. 0.85
   2 ?    4.4   0.0      0.05        81       4      41 ..      60      97 ..      57      99 .. 0.85
   3 ?    0.5   0.0      0.89   1.4e+03      13      34 ..     103     124 ..     101     128 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0045
      TPR_14  6 alaeallalGdpdeAiallrralalaPddaeawllla 42
                + a   l +G++ eAi +++++l ++P++  ++ + a
  EPA05396.1 28 KQANQNLLNGKYNEAILIYDDILVKFPNNISTLKMKA 64
                567777889********************99888876 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.05
      TPR_14  4 llalaeallalGdpdeAiallrralalaPddaeawlll 41
                l++ a al +lG++++++  + ++l+ +Pdd +a + +
  EPA05396.1 60 LKMKAIALSNLGEHEKSLLEFFKILQYQPDDITAITGM 97
                56789***********9999999999999999887665 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.89
      TPR_14  13 alGdpdeAiallrralalaPdd 34 
                 +lG+++eA  ++++a+ + Pd+
  EPA05396.1 103 NLGEYQEANHYFNEAIMKKPDS 124
                 5899***********9999997 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.46   7.5e+02      15      38 ..      37      60 ..      33      65 .. 0.84
   2 ?    4.9   0.0     0.017        28       8      34 ..      64      90 ..      62      94 .. 0.93
   3 ?    4.4   0.0     0.024        39       9      33 ..      99     123 ..      97     140 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.46
                T-HHHHHHHHHHHHHHTTS-HHHH CS
  Fis1_TPR_C 15 geYseArryvdalLeiEPenrQaq 38
                g+Y+eA    d +L + P+n   +
  EPA05396.1 37 GKYNEAILIYDDILVKFPNNISTL 60
                89************9999997665 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.017
                HHHHHHHT-HHHHHHHHHHHHHHTTS- CS
  Fis1_TPR_C  8 AlGhyklgeYseArryvdalLeiEPen 34
                A++   lge+++++     +L+ +P+ 
  EPA05396.1 64 AIALSNLGEHEKSLLEFFKILQYQPDD 90
                89999********************85 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.024
                 HHHHHHT-HHHHHHHHHHHHHHTTS CS
  Fis1_TPR_C   9 lGhyklgeYseArryvdalLeiEPe 33 
                 +G   lgeY+eA  y +  + + P+
  EPA05396.1  99 VGFGNLGEYQEANHYFNEAIMKKPD 123
                 566689*********9988888887 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00015      0.24      64     123 ..      18      77 ..      14      80 .. 0.93
   2 ?   -3.8   0.0       9.7   1.6e+04      83     102 ..     105     124 ..     103     137 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                      HHTTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSH CS
  Alkyl_sulf_dimr  64 elmGgaekvlekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesa 123
                      + + +++++ ++a+++l +g+y+ a+ + + ++ + p+n ++ ++ka al +lg++++s 
       EPA05396.1  18 QTANDVQTLFKQANQNLLNGKYNEAILIYDDILVKFPNNISTLKMKAIALSNLGEHEKSL 77 
                      56778999***********************************************99885 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 9.7
                      T-HHHHHHHHHHHHHHSTT- CS
  Alkyl_sulf_dimr  83 gdyrwaaellnhlvfadpen 102
                      g+y+ a +  n +++++p+ 
       EPA05396.1 105 GEYQEANHYFNEAIMKKPDS 124
                      78888888888888888875 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.96   1.6e+03      14      24 ..      36      46 ..      25      50 .. 0.85
   2 ?    1.9   0.0       0.2   3.2e+02       7      33 ..      63      89 ..      62      90 .. 0.82
   3 ?    5.4   0.0     0.015        25      13      29 ..     103     119 ..     101     124 .. 0.88
   4 ?   -3.1   0.3       8.4   1.4e+04      15      28 ..     255     268 ..     253     270 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.96
                TT-HHHHHHHH CS
       TPR_8 14 lgdyeeAkeyy 24
                 g+y+eA+  y
  EPA05396.1 36 NGKYNEAILIY 46
                699****9887 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.2
                HHHHHHHTT-HHHHHHHHHHHHHHHHH CS
       TPR_8  7 lgsiylklgdyeeAkeyyekaleldpd 33
                ++ ++++lg++e++   + k l+++pd
  EPA05396.1 63 KAIALSNLGEHEKSLLEFFKILQYQPD 89
                677899*******98888888888877 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.015
                 HTT-HHHHHHHHHHHHH CS
       TPR_8  13 klgdyeeAkeyyekale 29 
                 +lg+y+eA  y+++a+ 
  EPA05396.1 103 NLGEYQEANHYFNEAIM 119
                 89*************95 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 8.4
                 T-HHHHHHHHHHHH CS
       TPR_8  15 gdyeeAkeyyekal 28 
                 +++e+  + +ek+l
  EPA05396.1 255 KEKEAELKLFEKYL 268
                 56777788899987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       919  (0.0512577); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.63u 0.36s 00:00:00.99 Elapsed: 00:00:00.53
# Mc/sec: 2185.55
//
Query:       EPA05397.1  [L=143]
Description: response regulator receiver domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-25   89.0   0.4    2.5e-25   88.8   0.4    1.1  1  Response_reg  Response regulator receiver domain
  ------ inclusion threshold ------
      0.097   12.9   0.0        6.8    7.0   0.0    2.2  2  Tafi-CsgC     Thin aggregative fimbriae synthesis protein
        1.4    8.9   4.3        2.2    8.3   1.2    2.3  2  AAA_14        AAA domain


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.8   0.4   4.2e-29   2.5e-25       1     111 [.       8     120 ..       8     121 .. 0.94

  Alignments for each domain:
  == domain 1  score: 88.8 bits;  conditional E-value: 4.2e-29
                   EEEESSSHHHHHHHHHHHH..HTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEESSTS.HHHHHHHHHCTE CS
  Response_reg   1 vlivdDdplvrellrqlle..eegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviiltahse.eedavealkaga 94 
                   vli+dD +++re ++ +++   +++ +v +a+dg e l+++++ ++dlillD+nmp++dG+++lk i ++d+++++i+ t++++ +e++++++k+ga
    EPA05397.1   8 VLIIDDAQKFREFCEFVIKrtTKWI-RVYVAKDGLEGLKMYEQYEPDLILLDLNMPKVDGFDVLKYIIKKDKNTKIIVTTSYDDsQENINRVIKLGA 103
                   8******************866777.*****************************************999**********99887899********* PP

                   SEEEESSG-HHHHHHHH CS
  Response_reg  95 ddflsKpfdpeeLlkal 111
                     fl+Kp++   L+k +
    EPA05397.1 104 ISFLAKPMNHIILMKTV 120
                   *******9988887765 PP

>> Tafi-CsgC  Thin aggregative fimbriae synthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0    0.0011       6.8      59      90 ..      59      90 ..      12      95 .. 0.70
   2 ?    4.4   0.0    0.0074        44      61      88 ..      95     122 ..      89     126 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0011
   Tafi-CsgC 59 lsanqpialgklrlnispedkvkivvtvsdGq 90
                l+  +   +  l++ i+ + ++ki+vt s  +
  EPA05397.1 59 LNMPKVDGFDVLKYIIKKDKNTKIIVTTSYDD 90
                44444445667999*************98554 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0074
   Tafi-CsgC  61 anqpialgklrlnispedkvkivvtvsd 88 
                  n+ i+lg +++  +p +++ ++ tvsd
  EPA05397.1  95 INRVIKLGAISFLAKPMNHIILMKTVSD 122
                 68889**********************9 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   1.2   0.00037       2.2      65     101 ..      52      88 ..       2      99 .. 0.65
   2 ?   -3.6   0.1       1.8   1.1e+04      14      22 ..     127     135 ..     126     138 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00037
      AAA_14  65 ktylflDEiqevpewekalkslvdegknldvivtGSn 101
                   +++lD      + +++lk++++++kn ++ivt S 
  EPA05397.1  52 PDLILLDLNMPKVDGFDVLKYIIKKDKNTKIIVTTSY 88 
                 34444443333367789*****************995 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.8
      AAA_14  14 GKTtllkql 22 
                 GKTt l+++
  EPA05397.1 127 GKTTGLNNV 135
                 999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 873.33
//
Query:       EPA05398.1  [L=462]
Description: cysteine--tRNA ligase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   1.2e-125  418.8   1.3   1.2e-125  418.8   1.3    1.7  2  tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
    1.6e-13   50.2   3.0    1.8e-08   33.6   1.2    2.6  2  tRNA-synt_1g  tRNA synthetases class I (M)
    2.5e-08   32.7   0.1    7.7e-06   24.4   0.0    2.3  2  tRNA-synt_1   tRNA synthetases class I (I, L, M and V)
    9.9e-08   32.4   0.1    9.9e-08   32.4   0.1    2.1  2  DALR_2        DALR domain
    7.4e-07   28.4   4.0     0.0014   17.6   0.0    2.6  3  tRNA-synt_1f  tRNA synthetases class I (K)
  ------ inclusion threshold ------
        3.6    6.4  10.1       0.77    8.6   3.1    3.0  3  tRNA-synt_1c  tRNA synthetases class I (E and Q), catalytic d


Domain annotation for each model (and alignments):
>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  418.8   1.3  4.1e-129  1.2e-125       8     298 ..      18     306 ..      12     309 .. 0.98
   2 ?   -1.9   0.2      0.57   1.7e+03      69     117 ..     374     422 ..     363     437 .. 0.80

  Alignments for each domain:
  == domain 1  score: 418.8 bits;  conditional E-value: 4.1e-129
                   TEEEEEEEEEBTTS--BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB--SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHTT----SB--BGGGG CS
  tRNA-synt_1e   8 kkvtlYvCGptvydashlGhaRslvafDilrrilqalgYdvqfvqnvtDidDkiikrareeeksvkelaekfieefkkdleaLnvlkptleprvsek 104
                   k v++Y+CG+tvyd+sh+GhaR++++fD+lr++l+++g +v+f+qn+tD+dDkii+ra+ e+++ +++++k+ie ++kd++ Lnv++++  p+++e+
    EPA05398.1  18 KMVKIYLCGVTVYDESHIGHARTIIIFDVLRKYLESKGVEVKFIQNFTDVDDKIINRAKLENTTAEQISSKYIEGYYKDFDGLNVKRASNYPKATEH 114
                   689********************************************************************************************** PP

                   HHHHHHHHHHHHHTTSEEE-TTS-EEE-GGG-TTTTTTTT--HHHHHHT----S--S-SSTT-EEEEEE--TTS--B--TTSSEEE-SSHHHHHHHH CS
  tRNA-synt_1e 105 vdeiielvekliekgyaYavsdgdvyfdvskkeeYgklskqnleelelgaegevseekkdkkDfaLWkaskegepswdsPwgkGRPGWhieCsvmas 201
                   +++i +++ekli+k +aY+++ + vyf+vsk+++Ygklsk++++el++ga++ev e kkd+ DfaLWk s    p wdsPwgkGRPGWhieCs+m+ 
    EPA05398.1 115 IKDIENFIEKLIQKDIAYVSK-NGVYFSVSKFSQYGKLSKKKIDELQSGARIEVDEAKKDPLDFALWKFSDVK-PVWDSPWGKGRPGWHIECSAMSI 209
                   ********************9.77********************************************99877.*********************** PP

                   HHH-SSEEEEEEEGGGTTTHHHHHHHHHHHHSSS--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHSS-TTS-EEE-HHHHHH CS
  tRNA-synt_1e 202 kllgseidihsGGiDLafPhhenelaqseaafdkqlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRllllsahyrsqldfkeellee 298
                   k+lg+++dih+GG DL+fPhhene+aqse+ + kq++k+++h g+++i+gekmsksL+n+ tik+vl+++ p+++Rl+ ls hy +++d++eell+e
    EPA05398.1 210 KYLGENFDIHGGGRDLIFPHHENEIAQSESFTSKQFAKIWMHVGMVTINGEKMSKSLGNIRTIKHVLENWGPNIIRLFCLSGHYSKPIDYSEELLKE 306
                   **********************************************************************************************997 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.57
                   TS-HHHHHHHHHHHHHHHHHHTT----SB--BGGGGHHHHHHHHHHHHH CS
  tRNA-synt_1e  69 eksvkelaekfieefkkdleaLnvlkptleprvsekvdeiielveklie 117
                   ek +++ a+ +i ef++ l+ L++  p+++    ++++++i+  e+l +
    EPA05398.1 374 EKLTTNDAKIIIPEFERMLKVLGLAIPKITLDEKQEINNLINSREQLRK 422
                   4445556788899999999999999999999999999999988877755 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   1.2   5.9e-12   1.8e-08      12     126 ..      31     144 ..      27     154 .. 0.90
   2 !   15.3   0.0   2.1e-06    0.0062     316     368 ..     250     301 ..     222     311 .. 0.76

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 5.9e-12
                   S---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHTT---.SEEEETTSHHHHHHHHHHHHHH CS
  tRNA-synt_1g  12 gklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAekegvtpeelvekvheeikelfkklnisf.dkygrttseehkelvqeifkkl 107
                   ++ H+Gh++++i+ D++ +y   +g ev f+        +i  +A+ e++t+e++ +k+ e + ++f+ ln++  ++y ++t  eh +  +++++kl
    EPA05398.1  31 DESHIGHARTIIIFDVLRKYLESKGVEVKFIQNFTDVDDKIINRAKLENTTAEQISSKYIEGYYKDFDGLNVKRaSNYPKAT--EHIKDIENFIEKL 125
                   578*****************************9999999*********************************8626777765..688999******* PP

                   HHTT-EEEEEEEEEEETTT CS
  tRNA-synt_1g 108 kekgliyekeieqlycpkd 126
                    +k+  y ++  +++++++
    EPA05398.1 126 IQKDIAYVSKNGVYFSVSK 144
                   ****999999988888776 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 2.1e-06
                   EEE--EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-H CS
  tRNA-synt_1g 316 vaheyltvegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfsw 368
                   +  +++t++g+K+SkS g++ ++k++le+  ++++R + ++ +  +k +d+s+
    EPA05398.1 250 MHVGMVTINGEKMSKSLGNIRTIKHVLENWGPNIIRLFCLS-GHYSKPIDYSE 301
                   445899******************************98776.34445555555 PP

>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0   0.0   0.00099         3      38      66 ..      33      61 ..      27      90 .. 0.92
   2 !   24.4   0.0   2.6e-09   7.7e-06     519     599 ..     218     297 ..     176     300 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.00099
  tRNA-synt_1 38 lHiGhalaktlkdivirykrmkGkevlyv 66
                  HiGha + ++ d++ +y + kG ev++ 
   EPA05398.1 33 SHIGHARTIIIFDVLRKYLESKGVEVKFI 61
                 6*************************986 PP

  == domain 2  score: 24.4 bits;  conditional E-value: 2.6e-09
  tRNA-synt_1 519 mlleGlDiirgWvarlillslaltgsePfkevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltlilsdvgrdi 599
                  +   G D i+   ++ i +s  +t +  f ++ +h  ++  +G KmSKslgN+   ++v+++ g +++Rl+ ++ ++++ i
   EPA05398.1 218 IHGGGRDLIFPHHENEIAQSESFTSK-QFAKIWMHVGMVTINGEKMSKSLGNIRTIKHVLENWGPNIIRLFCLSGHYSKPI 297
                  55667777777777788888777655.5999****999999******************************9988887765 PP

>> DALR_2  DALR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.1   3.3e-11   9.9e-08       2      54 ..     343     397 ..     342     403 .. 0.76
   2 ?   -3.2   0.2       4.2   1.3e+04      25      46 ..     413     437 ..     409     440 .. 0.43

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 3.3e-11
                 HHHHHTBT--HHHHHHHHHHHHHHHHH..HHHTT-HHHHHHHHHHHHHHHGGGT- CS
      DALR_2   2 FeeaMdDDFNTaeAiavlFelakeiNr..alkeedkaaasalkallrelaevLGl 54 
                 F  a++ D+NT  A++++F+l+ke+N   a+++ ++++a+     ++ + +vLGl
  EPA05398.1 343 FDSALESDLNTHLALSAFFKLVKEVNYlaAEEKLTTNDAKIIIPEFERMLKVLGL 397
                 999***********************94333333444444445778888999999 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4.2
                 HHHH...HHHTT-HHHHHHHHHHHH CS
      DALR_2  25 eiNr...alkeedkaaasalkallr 46 
                  iN+     ke++ ++a++ ++ l+
  EPA05398.1 413 LINSreqLRKEKKFQDADRIRDKLN 437
                 5666442223333344444445555 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.1   2.3e-05      0.07      29      73 ..      25      69 ..       4     142 .. 0.82
   2 !   17.6   0.0   4.8e-07    0.0014     273     350 ..     254     332 ..     209     342 .. 0.84
   3 ?   -3.8   0.1       1.5   4.6e+03     147     171 ..     403     427 ..     401     451 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.3e-05
  tRNA-synt_1f 29 sGispSGliHiGnlrevltadlvaralrkrgeevrlilisDdmDg 73
                   G+++    HiG +r ++  d++++ l+++g ev++i    d+D 
    EPA05398.1 25 CGVTVYDESHIGHARTIIIFDVLRKYLESKGVEVKFIQNFTDVDD 69
                  678888889******************************999996 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 4.8e-07
  tRNA-synt_1f 273 lillkggekmssSkGnvltledwlevaepevlrflilrrkPkkakkldldleilrlvdeYdklerkyf...aeqeeeeeke 350
                   +++++g+ kms+S Gn+ t++ +le   p+++r+++l+ +  k ++ + +  + + +  + ++e  y+   ++++e++++ 
    EPA05398.1 254 MVTINGE-KMSKSLGNIRTIKHVLENWGPNIIRLFCLSGHYSKPIDYSEE-LLKENLTKWRQAEICYYeliHANNENHSEI 332
                   5566655.******************************999999999999.8999999****9999995554444444433 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 1.5
  tRNA-synt_1f 147 alenrekikeilekyrgeereetys 171
                    l+++++i++++++  + ++e+++ 
    EPA05398.1 403 TLDEKQEINNLINSREQLRKEKKFQ 427
                   5677777777777665555555544 PP

>> tRNA-synt_1c  tRNA synthetases class I (E and Q), catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   3.1   0.00026      0.77      40      98 ..      77     135 ..      32     138 .. 0.76
   2 ?   -0.7   0.0      0.17   5.1e+02     233     264 ..     251     282 ..     233     321 .. 0.77
   3 ?   -3.6   0.2       1.4   4.1e+03     101     128 ..     417     442 ..     406     454 .. 0.52

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00026
                   E--SSCCC--HHHHHHHHHHHHHTT---SSEEEEGGGGHHHHHHHHHHHHHTTSEEEE- CS
  tRNA-synt_1c  40 ieDTdperekeeaeesiledlkwlgikwdekptyqsdrfdelkkyaeeLikkGkAYvce 98 
                   +e T +e+   +++e  ++d + l++k   +  +++++ + +++++e+Li+k  AYv +
    EPA05398.1  77 LENTTAEQISSKYIEGYYKDFDGLNVKRASNYPKATEHIKDIENFIEKLIQKDIAYVSK 135
                   566777777777888888888888888889999***********************975 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.17
                   EE--EEETTSB-SHHHHHHHHHTTSSSSTT-T CS
  tRNA-synt_1c 233 eylrlnlekkklSKRklsllvdekqvkewddl 264
                    + +++++++k+SK  +++   ++ +++w+ +
    EPA05398.1 251 HVGMVTINGEKMSKSLGNIRTIKHVLENWGPN 282
                   356899999*****999999888888999854 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 1.4
                   HHHHHHHHCCSSHSS-TTTTS-HHHHHH CS
  tRNA-synt_1c 101 keeleeereeqeklgskerdrydeenlk 128
                    e+l++e++ q +     rd+  e n +
    EPA05398.1 417 REQLRKEKKFQDADR--IRDKLNEMNIE 442
                   445555544433222..34444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (462 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1160  (0.0646996); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.69u 0.34s 00:00:01.03 Elapsed: 00:00:00.54
# Mc/sec: 2573.50
//
Query:       EPA05399.1  [L=62]
Description: hypothetical protein BG20_I1230 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0013   18.2   0.6     0.0017   17.8   0.6    1.2  1  TF_Zn_Ribbon    TFIIB zinc-binding
     0.0014   18.3   1.1     0.0022   17.7   1.1    1.4  1  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal
      0.006   16.2   0.9     0.0064   16.2   0.9    1.1  1  DpnI            Dam-replacing family
     0.0074   16.5   0.9     0.0079   16.4   0.9    1.1  1  zf-4CXXC_R1     Zinc-finger domain of monoamine-oxidase A rep
  ------ inclusion threshold ------
      0.015   15.1   1.3      0.022   14.6   1.3    1.2  1  C1_1            Phorbol esters/diacylglycerol binding domain 
      0.017   14.9   3.9       0.18   11.7   0.4    2.1  2  HNH_5           HNH endonuclease
      0.018   15.1   0.9      0.027   14.5   0.9    1.4  1  DZR             Double zinc ribbon
      0.022   15.2   1.4       0.03   14.8   1.4    1.2  1  Enterotoxin_ST  Heat-stable enterotoxin ST
      0.041   13.5   1.0        3.9    7.2   0.1    2.2  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
      0.047   13.3   5.7      0.061   12.9   5.7    1.2  1  GATA            GATA zinc finger
      0.059   13.5   1.3        3.2    8.0   0.1    2.1  2  zf-B_box        B-box zinc finger
      0.079   13.3   1.1       0.94    9.8   0.1    2.0  2  DUF3268         zinc-finger-containing domain
       0.11   12.9   3.2       0.17   12.2   3.3    1.3  1  zf-UBP          Zn-finger in ubiquitin-hydrolases and other p
        0.2   11.6   6.1        4.4    7.3   6.1    2.1  1  PHD             PHD-finger
       0.21   11.9   4.6       0.49   10.7   0.4    2.1  2  Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase
       0.21   11.2   5.3        1.6    8.3   1.5    2.2  2  PHD_2           PHD-finger
       0.41   10.6   5.5       0.94    9.4   5.1    1.7  2  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit


Domain annotation for each model (and alignments):
>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.6   1.6e-06    0.0017       2      30 ..      20      51 ..      19      57 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.6e-06
                  EETTTTCEEC...HEETSTTCEEESSSSBEEE CS
  TF_Zn_Ribbon  2 kCPnCgstnl...veDpergelvCtdCGlVle 30
                   C++C+s++l   v + ++++ +C+ CG+ ++
    EPA05399.1 20 FCKKCNSRRLpkwVKEKNETDWLCETCGNYVD 51
                  6********9******************8776 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   1.1   2.1e-06    0.0022       8      52 ..       7      48 ..       1      50 [. 0.83

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.1e-06
  zinc_ribbon_10  8 vLvGddetsaknryalICskChshnGlapkeeleevkyrCpkCga 52
                    v +G+++   ++ + l C+kC+s      ++e++e+ + C  Cg 
      EPA05399.1  7 VQIGEEK---QSSMSLFCKKCNSRRLPKWVKEKNETDWLCETCGN 48
                    5578888...999*********9975555**************97 PP

>> DpnI  Dam-replacing family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.9     6e-06    0.0064      29      64 ..      16      51 ..       7      60 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 6e-06
                HHH---TTT--SS-EE--------EEE-TTT--EEE CS
        DpnI 29 aknlyCpkCgskklsefennkpvaDfyCesckeefe 64
                +  l+C kC+s++l ++  +k+ +D+ Ce+c +  +
  EPA05399.1 16 SMSLFCKKCNSRRLPKWVKEKNETDWLCETCGNYVD 51
                5678***************************87554 PP

>> zf-4CXXC_R1  Zinc-finger domain of monoamine-oxidase A repressor R1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.9   7.5e-06    0.0079      31      67 ..      16      51 ..       5      60 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 7.5e-06
  zf-4CXXC_R1 31 aklkfCekClknRygeeveevaakkeWvCPkCrgiCn 67
                 +   fC+kC + R  + v+e + +++W C +C +  +
   EPA05399.1 16 SMSLFCKKCNSRRLPKWVKEKN-ETDWLCETCGNYVD 51
                 4567***********9999976.679******88665 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   1.3   2.1e-05     0.022       6      40 ..      13      52 ..      11      53 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.1e-05
                E--SS--B-TTT-SB-.....-SSSS-EEEETTT--EE-C CS
        C1_1  6 rnfkqptfCkhCgefl.....wgkekqglkCswCkllvHk 40
                ++ +++ fCk+C++       ++k+ + + C++C+ +v+ 
  EPA05399.1 13 KQSSMSLFCKKCNSRRlpkwvKEKNETDWLCETCGNYVDS 52
                6778999******99889985559999********99976 PP

>> HNH_5  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.4   0.00017      0.18      28      42 ..      13      27 ..       4      40 .. 0.71
   2 ?    5.3   0.4     0.017        18      32      45 ..      39      52 ..      34      56 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00017
       HNH_5 28 tisnlvtlCkkCNqk 42
                + s++   CkkCN++
  EPA05399.1 13 KQSSMSLFCKKCNSR 27
                4455556******97 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.017
       HNH_5 32 lvtlCkkCNqkkgq 45
                  +lC++C ++  +
  EPA05399.1 39 TDWLCETCGNYVDS 52
                4678****998765 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.9   2.6e-05     0.027      10      43 ..      16      55 ..      10      59 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.6e-05
         DZR 10 pdarfCseCgtk.....lkavaa.....edrCpsCgekvdpear 43
                + + fC++C+++     +    +        C  Cg  vd++ +
  EPA05399.1 16 SMSLFCKKCNSRrlpkwV----KeknetDWLCETCGNYVDSKNN 55
                5577*******9854443....346668899*******999987 PP

>> Enterotoxin_ST  Heat-stable enterotoxin ST
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   1.4   2.9e-05      0.03      14      48 ..      15      48 ..       5      50 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.9e-05
  Enterotoxin_ST 14 ekIaaEvnkkkCdtqkknse.eeendwdyCCelCCN 48
                    + +++    kkC+  + ++  +e+n++d+ Ce C N
      EPA05399.1 15 SSMSLFC--KKCNSRRLPKWvKEKNETDWLCETCGN 48
                    5555555..9***99888667999**********98 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1     0.014        15       3      11 ..      19      27 ..      18      35 .. 0.84
   2 ?    7.2   0.1    0.0037       3.9       2      13 ..      40      51 ..      39      54 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.014
      zf_UBZ  3 ylCerCgke 11
                 +C++C+++
  EPA05399.1 19 LFCKKCNSR 27
                58****985 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0037
      zf_UBZ  2 tylCerCgkeip 13
                 +lCe Cg ++ 
  EPA05399.1 40 DWLCETCGNYVD 51
                699*****9986 PP

>> GATA  GATA zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   5.7   5.8e-05     0.061       1      30 [.      21      50 ..      21      55 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.8e-05
        GATA  1 CsnCgttkTplWRrgpdgnksLCnaCGlyy 30
                C +C+++  p W ++++ +  LC+ CG y 
  EPA05399.1 21 CKKCNSRRLPKWVKEKNETDWLCETCGNYV 50
                9**************************886 PP

>> zf-B_box  B-box zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.1    0.0031       3.2      10      22 ..      13      25 ..      10      27 .. 0.83
   2 ?    4.9   0.1     0.027        29      13      23 ..      38      48 ..      34      51 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0031
    zf-B_box 10 knkpatlfCedCq 22
                k+++++lfC++C+
  EPA05399.1 13 KQSSMSLFCKKCN 25
                56899*******8 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.027
    zf-B_box 13 patlfCedCqq 23
                ++ + Ce+C+ 
  EPA05399.1 38 ETDWLCETCGN 48
                55667777765 PP

>> DUF3268  zinc-finger-containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1      0.14   1.5e+02      23      38 ..      11      26 ..       3      29 .. 0.78
   2 ?    9.8   0.1   0.00089      0.94      24      45 ..      34      55 ..      31      59 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.14
     DUF3268 23 erskgkllylCpkCda 38
                e+++ ++   C+kC++
  EPA05399.1 11 EEKQSSMSLFCKKCNS 26
                4566678888****97 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00089
     DUF3268 24 rskgkllylCpkCdayvgvhkg 45
                ++k+++ +lC++C+ yv  +++
  EPA05399.1 34 KEKNETDWLCETCGNYVDSKNN 55
                5677899**********87765 PP

>> zf-UBP  Zn-finger in ubiquitin-hydrolases and other protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   3.3   0.00016      0.17       1      25 [.      21      54 ..      21      61 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00016
                -TTTH........--..SSEEEETTT--EEE-TT CS
      zf-UBP  1 CseCn........se.nknlWlCLkCghvgCgrk 25
                C++Cn        +e n++ WlC +Cg+++  ++
  EPA05399.1 21 CKKCNsrrlpkwvKEkNETDWLCETCGNYVDSKN 54
                99***99999999555799*********987764 PP

>> PHD  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   6.1    0.0042       4.4      11      50 ..      14      47 ..       7      49 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0042
                TTSCEEEETTTSCEEETTTSSSTHSHHSHHSSTBSSTTTH CS
         PHD 11 eeeelvqCdgCkrwfHqkClkppleseekpegewlCekCk 50
                +++  ++C++C++        +p+  +ek e++wlCe+C 
  EPA05399.1 14 QSSMSLFCKKCNSRR------LPKWVKEKNETDWLCETCG 47
                566667788887765......444445555668******5 PP

>> Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.3     0.074        78      25      32 ..      18      25 ..      11      31 .. 0.79
   2 ?   10.7   0.4   0.00047      0.49      17      33 ..      32      47 ..      26      55 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.074
                    -EEETTTT CS
  Prim_Zn_Ribbon 25 twfCrqCg 32
                    + fC++C+
      EPA05399.1 18 SLFCKKCN 25
                    57*****5 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00047
                    ETT....S-EEETTTTB CS
  Prim_Zn_Ribbon 17 fddkdgrGtwfCrqCgg 33
                    + ++++  +w C +C g
      EPA05399.1 32 WVKEKNETDWLCETC-G 47
                    8889999********.4 PP

>> PHD_2  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1     0.017        18       4      11 ..      18      25 ..      10      27 .. 0.68
   2 ?    8.3   1.5    0.0016       1.6      23      35 ..      34      46 ..      31      47 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.017
       PHD_2  4 llsCdkCs 11
                 l+C+kC+
  EPA05399.1 18 SLFCKKCN 25
                46777775 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0016
       PHD_2 23 kesdgeeWlCrrC 35
                ke+ +++WlC+ C
  EPA05399.1 34 KEKNETDWLCETC 46
                5666779****** PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   5.1   0.00089      0.94       3      28 ..      20      47 ..      19      51 .. 0.90
   2 ?    3.9   0.3     0.046        49       4       9 ..      43      48 ..      41      56 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00089
                    BESTTTSBEEEEECSCCCE..EEESSSS CS
  RNA_POL_M_15KD  3 FCpkCgNlLlpkedkegkn..feCrqCg 28
                    FC kC++  lpk  ke++     C +Cg
      EPA05399.1 20 FCKKCNSRRLPKWVKEKNEtdWLCETCG 47
                    ************99999878999****8 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.046
                    ESTTTS CS
  RNA_POL_M_15KD  4 CpkCgN 9 
                    C +CgN
      EPA05399.1 43 CETCGN 48
                    999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       939  (0.0523733); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.49
# Mc/sec: 383.02
//
Query:       EPA05400.1  [L=305]
Description: 4Fe-4S binding domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.2e-08   32.4  16.0    0.00016   21.4   3.3    2.3  2  Fer4           4Fe-4S binding domain
    1.5e-05   25.1   3.9    2.6e-05   24.3   3.9    1.4  1  Fer4_9         4Fe-4S dicluster domain
    1.7e-05   25.3   4.9    7.8e-05   23.2   5.6    1.8  2  Fer4_7         4Fe-4S dicluster domain
    5.2e-05   23.3   6.1    0.00012   22.2   6.1    1.6  1  Fer4_10        4Fe-4S dicluster domain
    0.00026   21.1   3.7    0.00043   20.3   3.7    1.4  1  Fer4_21        4Fe-4S dicluster domain
    0.00078   19.5   0.6     0.0015   18.7   0.6    1.4  1  ETF_QO         Electron transfer flavoprotein-ubiquinone oxid
     0.0033   17.4  13.1     0.0048   16.9   1.6    2.3  2  Fer4_6         4Fe-4S binding domain
     0.0063   14.5   0.1     0.0088   14.0   0.1    1.1  1  Tenui_PVC2     Tenuivirus PVC2 protein
  ------ inclusion threshold ------
      0.018   15.6   1.6        9.2    6.9   0.9    2.4  2  Fer4_17        4Fe-4S dicluster domain
      0.088   13.3   2.1       0.16   12.5   2.1    1.3  1  Me-amine-dh_L  Methylamine dehydrogenase, L chain
       0.18   12.7   8.1        2.7    9.0   2.6    2.7  2  Fer4_16        4Fe-4S double cluster binding domain
       0.19   12.2   5.1        4.6    7.8   6.1    2.3  2  Fer4_8         4Fe-4S dicluster domain
        1.1    9.5   3.7        5.1    7.3   0.3    2.3  2  Fer4_18        4Fe-4S dicluster domain
        2.3    8.5   9.4        4.7    7.5   0.4    2.4  2  Fer4_2         4Fe-4S binding domain
        2.6    8.7   9.5       0.53   10.9   0.6    2.6  2  Fer4_13        4Fe-4S single cluster domain of Ferredoxin I
        2.6    9.2  14.2         11    7.3   5.3    2.3  2  Fer4_3         4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   3.3   1.4e-07   0.00016       2      23 ..     240     261 ..     239     262 .. 0.91
   2 !   16.6   4.9   4.3e-06    0.0048       7      24 .]     283     300 ..     281     300 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.4e-07
                 EEETTTSSS-THHHHHSTTTEE CS
        Fer4   2 videekCigCGaCvevCPvgAI 23 
                  +d++ Ci+ G C+e+CPvg+ 
  EPA05400.1 240 SVDYDICIADGGCIEACPVGVY 261
                 69*****************985 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 4.3e-06
                 TSSS-THHHHHSTTTEEE CS
        Fer4   7 kCigCGaCvevCPvgAIt 24 
                 +Ci+C aC+ vCP  AI+
  EPA05400.1 283 DCIFCLACEGVCPPQAIK 300
                 6***************96 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   3.9   2.3e-08   2.6e-05       2      51 .]     246     299 ..     245     299 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 2.3e-08
      Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraase....eaCigCgaCveaCpkgai 51 
                 C+  g C+eaCp gv++  + ++  + +++       +Ci+C aC+ +Cp +ai
  EPA05400.1 246 CIADGGCIEACPVGVYEWFDTPGNPASEKKPLmskePDCIFCLACEGVCPPQAI 299
                 556577*************9999999887766999999*************987 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.2   0.00051      0.57      31      52 .]     239     260 ..     221     260 .. 0.86
   2 !   23.2   5.6   6.9e-08   7.8e-05       2      52 .]     246     298 ..     245     298 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00051
      Fer4_7  31 veidpekClgCgaCvavCPtga 52 
                 v +d++ C+  g C+++CP+g+
  EPA05400.1 239 VSVDYDICIADGGCIEACPVGV 260
                 5789999*************96 PP

  == domain 2  score: 23.2 bits;  conditional E-value: 6.9e-08
      Fer4_7   2 CigCgaCvaaCpvkaieldeeenek.gtekveid.pekClgCgaCvavCPtga 52 
                 Ci  g C +aCpv++ e+ +   ++   +k+ ++ + +C++C aC+ vCP +a
  EPA05400.1 246 CIADGGCIEACPVGVYEWFDTPGNPaSEKKPLMSkEPDCIFCLACEGVCPPQA 298
                 777899***********998744442446666651559************765 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   6.1     1e-07   0.00012       2      56 .]     239     295 ..     238     295 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1e-07
     Fer4_10   2 vvidddtCirCgkCvkaCPadl..tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                 v +d d Ci  g C +aCP+ +  + +   + ase+++   k  +C++c aC  +CP
  EPA05400.1 239 VSVDYDICIADGGCIEACPVGVyeWFDTPGNPASEKKPLMSKEPDCIFCLACEGVCP 295
                 57899***************889877777777888888888999************9 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   3.7   3.9e-07   0.00043       3      58 ..     241     300 ..     239     301 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 3.9e-07
     Fer4_21   3 idedkCigCgkCliaCedtshqai.....eidaktvlkvvedeCvGCnlCssvCPvedcie 58 
                 +d d Ci  g C+ aC+ + ++         ++k+ l   e +C+ C  C  vCP  ++i+
  EPA05400.1 241 VDYDICIADGGCIEACPVGVYEWFdtpgnPASEKKPLMSKEPDCIFCLACEGVCP-PQAIK 300
                 78999******************9444322334445556689*************.68886 PP

>> ETF_QO  Electron transfer flavoprotein-ubiquinone oxidoreductase, 4Fe-4S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.6   1.3e-06    0.0015      45      91 ..     251     300 ..     237     304 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.3e-06
                 THHHH-TTS-EEEEETT...TTSSEEEEE-CCC--S--HHHHH-TT--EE CS
      ETF_QO  45 peqryCPagvyeivede...eakekklqinaqnCvhCktCdikdpsqnie 91 
                  +   CP gvye+ ++     +++k l     +C+ C +C+   p q i+
  EPA05400.1 251 GCIEACPVGVYEWFDTPgnpASEKKPLMSKEPDCIFCLACEGVCPPQAIK 300
                 56678*********965323567888999999*********999999987 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   1.6   4.3e-06    0.0048       1      23 [.     238     260 ..     238     261 .. 0.93
   2 ?    5.7   4.2     0.015        17       9      24 .]     284     299 ..     280     299 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.3e-06
      Fer4_6   1 vveidpdkCigCgdCvrvCPega 23 
                 +v +d+d Ci  g C+ +CP g+
  EPA05400.1 238 FVSVDYDICIADGGCIEACPVGV 260
                 689*****************997 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.015
      Fer4_6   9 CigCgdCvrvCPegai 24 
                 Ci C +C+ vCP +ai
  EPA05400.1 284 CIFCLACEGVCPPQAI 299
                 888***********98 PP

>> Tenui_PVC2  Tenuivirus PVC2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.1   7.8e-06    0.0088     427     479 ..     228     280 ..     218     290 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.8e-06
  Tenui_PVC2 427 tdgthsiwgestslsfdycvtdfhifsycpayhynwkrieyeptssractimk 479
                  +g   +wge  s+ +d c++d   +  cp   y+w     +p+s +   + k
  EPA05400.1 228 NNGILGVWGEFVSVDYDICIADGGCIEACPVGVYEWFDTPGNPASEKKPLMSK 280
                 678999******************************99999999987766655 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0    0.0086       9.6      44      60 ..     244     260 ..     221     261 .. 0.89
   2 ?    6.9   0.9    0.0082       9.2      44      57 ..     282     295 ..     265     299 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0086
     Fer4_17  44 slCieCgeCerkCPqgl 60 
                 + Ci  g+C ++CP g+
  EPA05400.1 244 DICIADGGCIEACPVGV 260
                 67************876 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0082
     Fer4_17  44 slCieCgeCerkCP 57 
                  +Ci C  Ce +CP
  EPA05400.1 282 PDCIFCLACEGVCP 295
                 57999999999998 PP

>> Me-amine-dh_L  Methylamine dehydrogenase, L chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   2.1   0.00014      0.16      12      67 ..     237     289 ..     232     300 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
                    GGTT-EEEBGGGGT-BTTBB-TTSEEESEEEEEEEEETTTSEEEEEEEE.EEESS-- CS
  Me-amine-dh_L  12 rycaidGalcaccGGsvtscppGteaskvswvgtcanpadgkdyliayr.dccGkss 67 
                     + ++d  +c + GG++++cp+G       w  t  npa +k+ l++ + dc    +
     EPA05400.1 237 EFVSVDYDICIADGGCIEACPVGV----YEWFDTPGNPASEKKPLMSKEpDCIFCLA 289
                    58899*****************97....57*************99998636654444 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   8.3     0.093     1e+02       6      65 ..     250     295 ..     245     297 .. 0.57
   2 ?    9.0   2.6    0.0024       2.7       2      18 ..     284     300 ..     283     305 .] 0.86

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.093
     Fer4_16   6 gkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCP 65 
                 g C+e+CP+++ +       +++ + ++   ekk l        k++++++C +C+ vCP
  EPA05400.1 250 GGCIEACPVGVYEWF-----DTPGNPAS---EKKPLMS------KEPDCIFCLACEGVCP 295
                 556666666655444.....33333332...3333333......346678*********9 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0024
     Fer4_16   2 CgtCgkCaevCPtnaik 18 
                 C+ C +C  vCP +aik
  EPA05400.1 284 CIFCLACEGVCPPQAIK 300
                 999************98 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.1    0.0067       7.6      48      65 .]     243     260 ..     204     260 .. 0.80
   2 ?    7.8   6.1    0.0041       4.6       4      62 ..     245     295 ..     242     299 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0067
      Fer4_8  48 lwsCttcgaCtevCpvgi 65 
                  + C + g C e+Cpvg+
  EPA05400.1 243 YDICIADGGCIEACPVGV 260
                 567999999******986 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0041
      Fer4_8   4 kCieCgaCqsaCpvlrrtk.khlldargeaaedvqeeqvleeeealwsCttcgaCtevCp 62 
                  Ci  g C +aCpv   +  + + ++  e++    +++          C  c aC+ vCp
  EPA05400.1 245 ICIADGGCIEACPVGVYEWfDTPGNPASEKKP-LMSKEP--------DCIFCLACEGVCP 295
                 69999********7766665777777777666.555544........7***********9 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.3      0.12   1.3e+02      61      75 ..     246     260 ..     237     263 .. 0.79
   2 ?    7.3   0.3    0.0046       5.1      56      73 ..     279     296 ..     268     303 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.12
     Fer4_18  61 cidcescvkvcPtgi 75 
                 ci+ + c++ cP+g+
  EPA05400.1 246 CIADGGCIEACPVGV 260
                 788888888888876 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0046
     Fer4_18  56 kgagdcidcescvkvcPt 73 
                 +++ dci c +c  vcP 
  EPA05400.1 279 SKEPDCIFCLACEGVCPP 296
                 5678************84 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.4    0.0042       4.7       3      21 ..     239     257 ..     237     258 .. 0.85
   2 ?    4.5   3.0     0.037        42       7      21 ..     282     295 ..     276     296 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0042
      Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                 v vd d+Ci+ g C+ aCP
  EPA05400.1 239 VSVDYDICIADGGCIEACP 257
                 56899***98789****** PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.037
      Fer4_2   7 tdrCigCgaCvsaCP 21 
                 +d Ci C aC  +CP
  EPA05400.1 282 PD-CIFCLACEGVCP 295
                 55.999********9 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.6   0.00048      0.53       1      17 [.     241     257 ..     241     266 .. 0.92
   2 ?    1.2   2.7      0.51   5.7e+02       5      17 ..     283     295 ..     281     301 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00048
     Fer4_13   1 VDrdtCiacgaCvelaP 17 
                 VD d Cia+g C e++P
  EPA05400.1 241 VDYDICIADGGCIEACP 257
                 89999************ PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.51
     Fer4_13   5 tCiacgaCvelaP 17 
                  Ci c aC  ++P
  EPA05400.1 283 DCIFCLACEGVCP 295
                 6********9999 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   1.5      0.01        11       6      14 ..     251     259 ..     246     260 .. 0.77
   2 ?    7.3   5.3    0.0096        11       1      15 []     284     298 ..     284     298 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.01
      Fer4_3   6 aCvevCPvg 14 
                  C e+CPvg
  EPA05400.1 251 GCIEACPVG 259
                 5******98 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0096
      Fer4_3   1 CtgCgaCvevCPvgA 15 
                 C+ C aC+ vCP+ A
  EPA05400.1 284 CIFCLACEGVCPPQA 298
                 ************866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.62u 0.36s 00:00:00.98 Elapsed: 00:00:00.55
# Mc/sec: 1677.35
//
Query:       EPA05401.1  [L=512]
Description: hypothetical protein BG20_I0727 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-05   24.9  39.6     0.0064   16.5   1.9    5.9  5  DUF1664          Protein of unknown function (DUF1664)
    2.6e-05   24.6  39.9        0.3   11.6   1.0    6.5  5  NPV_P10          Nucleopolyhedrovirus P10 protein
    0.00028   21.1   2.3    0.00028   21.1   2.3    5.0  5  Fib_alpha        Fibrinogen alpha/beta chain family
    0.00047   20.4  32.4       0.17   12.1   0.8    6.2  4  DUF948           Bacterial protein of unknown function (DUF94
    0.00087   19.7  35.9       0.52   10.8   2.0    6.3  6  Snapin_Pallidin  Snapin/Pallidin
      0.001   19.3  45.1      0.067   13.5   1.6    7.2  7  BLOC1_2          Biogenesis of lysosome-related organelles co
     0.0032   17.5   1.3     0.0032   17.5   1.3    5.0  5  DHR10            Designed helical repeat protein 10 domain
  ------ inclusion threshold ------
      0.028   14.7  28.3        0.5   10.6   7.7    4.3  4  ATG16            Autophagy protein 16 (ATG16)
      0.037   13.9  19.9       0.48   10.3   0.0    6.1  5  HSBP1            Heat shock factor binding protein 1
      0.079   13.3   1.4         18    5.7   0.1    4.1  4  kleA_kleC        Uncharacterized KorC regulated protein A
       0.11   12.5  23.0       0.08   12.9   2.4    4.9  4  Serine_rich      Serine rich protein interaction domain
       0.13   12.0  34.1       0.27   10.9   2.5    4.1  4  Laminin_I        Laminin Domain I
       0.18   11.6   5.7        1.1    9.1   0.3    3.5  3  DUF3540          Protein of unknown function (DUF3540)
        0.2   11.0  35.3       0.31   10.3   9.8    4.6  4  DUF3450          Protein of unknown function (DUF3450)
       0.22   11.4  32.4       0.22   11.4   2.7    6.2  6  Sec34            Sec34-like family
       0.25   11.2  39.8       0.39   10.6   0.4    5.2  5  Cauli_AT         Aphid transmission protein
       0.42   10.1   3.5       0.51    9.9   0.1    2.6  2  DUF4088          Protein of unknown function (DUF4088)
       0.44   10.7  25.3       0.29   11.2   2.8    4.6  3  GIT1_C           G protein-coupled receptor kinase-interactin
       0.51   10.1  38.5       0.73    9.6   3.4    5.3  5  MCPsignal        Methyl-accepting chemotaxis protein (MCP) si
       0.52   10.3  43.0       0.04   13.9  10.2    4.9  4  Laminin_II       Laminin Domain II
       0.64   10.1  19.6        1.3    9.1   0.5    5.8  5  TolA_bind_tri    TolA binding protein trimerisation
       0.86   10.1  34.5        0.4   11.1   0.4    7.8  8  FlaC_arch        Flagella accessory protein C (FlaC)
          1    9.1   6.2       0.53   10.0   0.9    2.9  3  HD_4             HD domain
        1.3    9.4   5.2        9.4    6.6   1.4    3.8  5  HrpB7            Bacterial type III secretion protein (HrpB7)
        1.3    9.3   6.2       0.59   10.4   1.0    3.1  2  Cas_Cmr5         CRISPR-associated protein (Cas_Cmr5)
          2    9.2  22.6        1.5    9.6   0.1    5.2  5  Occludin_ELL     Occludin homology domain
        2.1    8.7  25.2       0.19   12.1   0.4    5.7  6  CCDC-167         Coiled-coil domain-containing protein 167
        2.4    8.4  26.8        6.1    7.1   2.1    4.8  4  SesA             N-terminal domain on NACHT_NTPase and P-loop
        2.8    7.6  26.9        4.7    6.9   1.5    6.0  6  RPW8             Arabidopsis broad-spectrum mildew resistance
        4.6    6.9  24.5       0.35   10.6   1.7    4.2  4  DUF745           Protein of unknown function (DUF745)
        5.5    7.4  28.3        1.2    9.6   4.4    5.1  3  eIF3_N           eIF3 subunit 6 N terminal domain
        6.1    7.1   7.1       0.97    9.7   0.2    2.6  2  DUF3365          Protein of unknown function (DUF3365)
        6.5    6.9  22.7        5.8    7.1   1.2    5.5  6  DUF2730          Protein of unknown function (DUF2730)
        8.2    7.3  14.9        1.4    9.7   3.2    4.8  5  FliT             Flagellar protein FliT
        8.6    6.8  33.7          6    7.3   8.8    3.7  3  Fez1             Fez1
        8.9    6.7  10.3         35    4.7   0.1    5.2  5  Osmo_CC          Osmosensory transporter coiled coil


Domain annotation for each model (and alignments):
>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   3.5    0.0085       4.2      55     107 ..      38      90 ..       2     109 .. 0.84
   2 !    7.5   8.9    0.0081         4      56     123 ..     132     205 ..      91     206 .. 0.70
   3 !   10.7   3.1   0.00083      0.41      65     115 ..     189     242 ..     182     259 .. 0.60
   4 ?    2.2   0.1      0.36   1.8e+02      50     100 ..     257     307 ..     246     314 .. 0.58
   5 !   16.5   1.9   1.3e-05    0.0064      41     112 ..     311     382 ..     305     389 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0085
     DUF1664  55 eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvk 107
                 +++++  + L+++i+++ k   ++++i  ++k  +++++  l++i++++++++
  EPA05401.1  38 AAVTDSSKALQKEIKSMSKIFGDNQKILVSMKGMIDTLSVTLENIQKQSKQIN 90 
                 46777778899999999999999999999999999999999999999988886 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0081
     DUF1664  56 slaat...krhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvk...eaveglesklerieek 123
                 +l++t     +Ls+r++   + + ++++++ +i++ ++evr+dl++++ + +s+    + + +l +++++i++k
  EPA05401.1 132 ELQKTspkTPELSQRVEDSMNAMRNNSQMIIKIAQRIDEVRDDLRKVSGKTDSLAdigKEIDNLRNSIDEINKK 205
                 22222111348*******999**************************988777651115688888999999876 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00083
     DUF1664  65 ssridrvdkkldeqkeiskeik...eevtevredlseigedvesvkeavegles 115
                  ++id++ +++de ++ + +++   + vt+++++l +i++dv+sv+++ ++le+
  EPA05401.1 189 GKEIDNLRNSIDEINKKADNMEvssQIVTSLNQELGKIKDDVNSVSKTSSELEA 242
                 455555555555555444444311134777777888888888888777777764 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.36
     DUF1664  50 leqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseig 100
                 ++++   ++  k++++    + d+  d +++ +ke+  ++++++ ++++++
  EPA05401.1 257 IDSLGGVIEGLKQQFTTIAGKADSASDLSMNSIKEVLGKIDKIETEINSLS 307
                 555555555566666666666666666666666666666666655555544 PP

  == domain 5  score: 16.5 bits;  conditional E-value: 1.3e-05
     DUF1664  41 davesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveg 112
                 d  + v++ l++v+e+ ++ k++  ++ d++++k+ ++++i k  ++  +e +++ ++i e+++svk++ ++
  EPA05401.1 311 DSTAFVGEGLKSVQEDFTNFKKNVFEKTDNIEQKISSVSDILKRQDALTSEFHKKSDKIFEEMQSVKNVTNK 382
                 667889************************************************************998765 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   3.0      0.12        60       9      61 ..      33      89 ..       3      90 .. 0.77
   2 !   10.1   6.3    0.0018      0.89       6      73 ..      75     143 ..      71     145 .. 0.85
   3 !   11.6   1.0   0.00061       0.3      12      62 ..     153     203 ..     149     208 .. 0.88
   4 !   11.2   2.7   0.00076      0.38      17      63 ..     213     259 ..     205     264 .. 0.88
   5 ?    7.0   2.2     0.016       7.8      11      66 ..     287     353 ..     266     383 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.12
     NPV_P10  9 IradikavddkVdalqqqvddvqenlpdvtel....nekLdaqsaqLaeletkvenI 61
                +++ ++av d  +alq++++++++ + d +++    +  +d +s +L++++++ ++I
  EPA05401.1 33 VLKKVAAVTDSSKALQKEIKSMSKIFGDNQKIlvsmKGMIDTLSVTLENIQKQSKQI 89
                678899999999999999988887655544331111566777777777777766555 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0018
     NPV_P10   6 LlvIradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiLnpde.vPdl 73 
                 L v +++i++ +++++ l++  +++ + l+ v   ++ + ++++q + l+++v++I+++  + +  P+l
  EPA05401.1  75 LSVTLENIQKQSKQINILEDDTQKLYAGLNHVRTQSDLVSKINEQTQRLQEEVTKINELQKTSPkTPEL 143
                 677899**************************9999999999999999999999999876654456665 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00061
     NPV_P10  12 dikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIq 62 
                 + ++ ++ +  + q++d+v+++l++v+  ++ L ++ +++++l +++++I+
  EPA05401.1 153 AMRNNSQMIIKIAQRIDEVRDDLRKVSGKTDSLADIGKEIDNLRNSIDEIN 203
                 566777888899999************999***************999997 PP

  == domain 4  score: 11.2 bits;  conditional E-value: 0.00076
     NPV_P10  17 ddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqd 63 
                 ++ V++l+q++ +++++++ v++ +++L+a+  +++++  k ++I++
  EPA05401.1 213 SQIVTSLNQELGKIKDDVNSVSKTSSELEAIKVAIDTIAVKASKIDS 259
                 45589************************************999987 PP

  == domain 5  score: 7.0 bits;  conditional E-value: 0.016
     NPV_P10  11 adikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaelet...........kvenIqdiLn 66 
                 + ik+v  k+d ++++++++++    +  + e L + ++  +++++           k+++++diL 
  EPA05401.1 287 NSIKEVLGKIDKIETEINSLSHRADSTAFVGEGLKSVQEDFTNFKKnvfektdnieqKISSVSDILK 353
                 5699999999999999999999999999999999999999999998888878877778888888876 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   3.8      0.07        35      45     127 ..       7      88 ..       2      97 .. 0.66
   2 ?    4.4   9.6     0.079        40      25     117 ..     115     205 ..     103     205 .. 0.68
   3 !   21.1   2.3   5.6e-07   0.00028      32     124 ..     187     277 ..     181     285 .. 0.89
   4 ?    2.0   3.6      0.43   2.1e+02      36     119 ..     295     356 ..     281     380 .. 0.42
   5 ?    0.5   9.5       1.2   6.2e+02      23     126 ..     324     423 ..     321     431 .. 0.64

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.07
                 CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
   Fib_alpha  45 eeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvlesneqkiqkLeqdidq 127
                 +++s++t++  e +k++++      +  k +  ++++ssk l++ei  + +   ++ + +  ++++++++++ +++++++++q
  EPA05401.1   7 ARVSKKTEKDPEKTKKVTKREPTPAAVLK-KVAAVTDSSKALQKEIKSMSKIFGDNQKILVSMKGMIDTLSVTLENIQKQSKQ 88 
                 45555555555555555544333333333.47788888888888888888888888888888888888888888887776654 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.079
                 CCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHH CS
   Fib_alpha  25 lllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvlesneqk 117
                  ++++ + ++++++k++ el++ s +t e ++ v++ ++ +r++ +   +  + i +++++l+ +++   +++ +  ++i +L+n +++ ++k
  EPA05401.1 115 KINEQTQRLQEEVTKIN-ELQKTSPKTPELSQRVEDSMNAMRNNSQMIIKIAQRIDEVRDDLR-KVSGKTDSLADIGKEIDNLRNSIDEINKK 205
                 45666666677777663.566666666666666666666666666666666888888888888.66666666766668888888888887765 PP

  == domain 3  score: 21.1 bits;  conditional E-value: 5.6e-07
                 CCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHH CS
   Fib_alpha  32 dvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvlesneqkiqkLeqd 124
                 d+ k++++l+n+++ei+++  ++ e++++i +sl+++  + kd  n ++k s+ele  i    +ti  + s+i  L +v+e ++q+ + +  +
  EPA05401.1 187 DIGKEIDNLRNSIDEINKKADNM-EVSSQIVTSLNQELGKIKDDVNSVSKTSSELE-AIKVAIDTIAVKASKIDSLGGVIEGLKQQFTTIAGK 277
                 67799***********8877665.7889999***********9*************.999999******************999998877655 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.43
                 HHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHH CS
   Fib_alpha  36 dlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvlesneqkiq 119
                 +++k+e e++++s++  +                      +  + +  k+++e+ +++k+++ ++  ni++  + +++  ++  
  EPA05401.1 295 KIDKIETEINSLSHRADS----------------------TAFVGEGLKSVQEDFTNFKKNVFEKTDNIEQKISSVSDILKRQD 356
                 333333333333333333......................34444444444444444444444444444433333333333222 PP

  == domain 5  score: 0.5 bits;  conditional E-value: 1.2
                 HHCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHH CS
   Fib_alpha  23 qdlllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvlesneqkiqkL 121
                 q+ +++ +k+v ++ +++e++++++s+  k  + l++e +++  +  ++ +  +nv++k +ke  +e++ l  ++++  snir    + es+  +i++L
  EPA05401.1 324 QEDFTNFKKNVFEKTDNIEQKISSVSDILKRQDALTSEFHKKSDKIFEEMQSVKNVTNKTAKESSKEMMALL-KLSEYQSNIR---MNAESKYGEIKDL 418
                 566667777777777888888888887777777777777777777777777667777777777775555553.3444445554...3555555666666 PP

                 HHHHH CS
   Fib_alpha 122 eqdid 126
                 e+  +
  EPA05401.1 419 ENMAT 423
                 65554 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   7.9     0.097        48      20      88 ..      64     131 ..      31     137 .. 0.69
   2 !   12.1   0.8   0.00035      0.17      21      87 ..     130     195 ..     127     197 .. 0.88
   3 ?    5.9   6.2     0.031        16      22      86 ..     186     232 ..     159     310 .. 0.62
   4 !   10.0   1.3    0.0016      0.78      16      84 ..     315     383 ..     312     387 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.097
      DUF948  20 vllklkktldeaaatieele...kqvdpilkevedllakvnelledvneklekvdplteavadlgesvseln 88 
                 +l+++k ++d ++ t+e+++   kq++ + +++++l a  n     v+ +++ v ++ e+ + l e v ++n
  EPA05401.1  64 ILVSMKGMIDTLSVTLENIQkqsKQINILEDDTQKLYAGLNH----VRTQSDLVSKINEQTQRLQEEVTKIN 131
                 567777777888888888874445555666777777777777....55555555555555555555555444 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00035
      DUF948  21 llklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvsel 87 
                 +++l+kt  ++ +  + +e+ ++++ ++++ +++ +++  ++v++ l kv   t+++ad+g+ + +l
  EPA05401.1 130 INELQKTSPKTPELSQRVEDSMNAMRNNSQMIIKIAQR-IDEVRDDLRKVSGKTDSLADIGKEIDNL 195
                 56789999999999999999999998888877777777.*************************998 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.031
      DUF948  22 lklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvse 86 
                   ++k +d+++++i+e++                  + +++++  ++ v +l ++++++ + v++
  EPA05401.1 186 ADIGKEIDNLRNSIDEIN------------------KKADNMEVSSQIVTSLNQELGKIKDDVNS 232
                 233344444444444444..................32333333333333333333333333222 PP

  == domain 4  score: 10.0 bits;  conditional E-value: 0.0016
      DUF948  16 flivvllklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesv 84 
                 f+   l+++++ ++++++ + e ++++++ +  v d+l+   +l+++ ++k++k+ + +++v++++++ 
  EPA05401.1 315 FVGEGLKSVQEDFTNFKKNVFEKTDNIEQKISSVSDILKRQDALTSEFHKKSDKIFEEMQSVKNVTNKT 383
                 566678999999999999999*******************************************98765 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   2.2    0.0079       3.9      16      82 ..      31      99 ..      25     107 .. 0.83
   2 ?    5.8   7.2     0.036        18      28      88 ..     108     170 ..      90     172 .. 0.73
   3 !   10.8   2.0    0.0011      0.52      15      83 ..     168     241 ..     165     244 .. 0.82
   4 ?    6.0   0.0     0.032        16      37      80 ..     265     311 ..     254     314 .. 0.74
   5 ?    4.3   0.1       0.1        52      54      81 ..     326     354 ..     318     357 .. 0.75
   6 ?    4.8   1.2     0.075        37      15      81 ..     341     382 ..     338     389 .. 0.48

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0079
  Snapin_Pallidin 16 deldeklkelrqsQeeLleqldrlnekLkeleeaqe..aevlpdlkeyakKLvnikkrmsslnerlqkl 82
                      ++ +k++++++s ++L+++++++++ + +++++    + ++ +l   ++ +++  k+++ l++ +qkl
       EPA05401.1 31 AAVLKKVAAVTDSSKALQKEIKSMSKIFGDNQKILVsmKGMIDTLSVTLENIQKQSKQINILEDDTQKL 99
                     567799***************************988666677778888888888888899888888887 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.036
  Snapin_Pallidin  28 sQeeLleqldrlnekLk.eleeaqe.aevlpdlkeyakKLvnikkrmsslnerlqklkkRaek 88 
                      +Q++L +++++++++L+ e+ +++e +++ p+++e  +++    + m + ++ + k+ +R+++
       EPA05401.1 108 TQSDLVSKINEQTQRLQeEVTKINElQKTSPKTPELSQRVEDSMNAMRNNSQMIIKIAQRIDE 170
                      56666666666666665234555555559********************99999999999986 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.0011
  Snapin_Pallidin  15 ldeldeklkelrqsQeeLl...eqldrlnekLkeleeaqe.aevlpdlkeya.kKLvnikkrmsslnerlqklk 83 
                      +de+++ l+++  + + L+   +++d+l+++++e+++ ++  ev +++ + + + L +ik +++s+++++++l+
       EPA05401.1 168 IDEVRDDLRKVSGKTDSLAdigKEIDNLRNSIDEINKKADnMEVSSQIVTSLnQELGKIKDDVNSVSKTSSELE 241
                      667777777777777766533369****************999999998887799************9999876 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.032
  Snapin_Pallidin  37 drlnekLkeleeaqe...aevlpdlkeyakKLvnikkrmsslnerlq 80 
                      + l+++++ ++  ++   + +++ +ke + K+ +i+ +++sl++r  
       EPA05401.1 265 EGLKQQFTTIAGKADsasDLSMNSIKEVLGKIDKIETEINSLSHRAD 311
                      5555666655544443123479********************99865 PP

  == domain 5  score: 4.3 bits;  conditional E-value: 0.1
  Snapin_Pallidin  54 vlpdlkeya.kKLvnikkrmsslnerlqk 81 
                       ++++k+ + +K  ni++++ss++++l++
       EPA05401.1 326 DFTNFKKNVfEKTDNIEQKISSVSDILKR 354
                      35555555559****************98 PP

  == domain 6  score: 4.8 bits;  conditional E-value: 0.075
  Snapin_Pallidin  15 ldeldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqk 81 
                      +++  ++++++ + Q++L+++ ++ ++k+                           +m+s++++++k
       EPA05401.1 341 IEQKISSVSDILKRQDALTSEFHKKSDKI-------------------------FEEMQSVKNVTNK 382
                      34444555555555555555555555554.........................4444444444433 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   2.6    0.0043       2.1      14      77 ..      36      99 ..      29     107 .. 0.82
   2 ?    3.8   1.1      0.15        73      50      72 ..     113     135 ..     103     149 .. 0.66
   3 !   13.5   1.6   0.00013     0.067      30      85 ..     155     210 ..     145     214 .. 0.89
   4 ?    7.3   0.8     0.012       5.8      41      87 ..     214     260 ..     210     270 .. 0.83
   5 !    8.8   0.1    0.0038       1.9      56      81 ..     285     310 ..     264     313 .. 0.73
   6 ?    3.6   1.1      0.17        83      27      67 ..     329     369 ..     310     385 .. 0.64
   7 ?    0.0   2.3       2.1   1.1e+03      32      88 ..     380     436 ..     366     443 .. 0.58

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0043
     BLOC1_2 14 eleatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteL 77
                +++a+++  k L+k  +++s+ + + ++++ s++  ++ l+ + e++q++ +qi+ +e+++++L
  EPA05401.1 36 KVAAVTDSSKALQKEIKSMSKIFGDNQKILVSMKGMIDTLSVTLENIQKQSKQINILEDDTQKL 99
                5667778888888888999999999999999999999999999999999999999999988888 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.15
     BLOC1_2  50 leklnekyeelqpylqqidqiek 72 
                 ++k+ne+ + lq+ +++i++++k
  EPA05401.1 113 VSKINEQTQRLQEEVTKINELQK 135
                 45566666666666666666655 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 0.00013
     BLOC1_2  30 eaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLD 85 
                 ++ s+ + k+++++++++++l k++ k ++l+   ++id++ ++++e+ + ++ ++
  EPA05401.1 155 RNNSQMIIKIAQRIDEVRDDLRKVSGKTDSLADIGKEIDNLRNSIDEINKKADNME 210
                 466778899****************************************9999987 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.012
     BLOC1_2  41 dvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDey 87 
                 +++ sl+++l k++   +++++  +++++i+  ++++   +s++D+ 
  EPA05401.1 214 QIVTSLNQELGKIKDDVNSVSKTSSELEAIKVAIDTIAVKASKIDSL 260
                 67888899999999999999999999999999999999888888875 PP

  == domain 5  score: 8.8 bits;  conditional E-value: 0.0038
     BLOC1_2  56 kyeelqpylqqidqiekqvteLeeav 81 
                   +++++ l +id+ie+++++L + +
  EPA05401.1 285 SMNSIKEVLGKIDKIETEINSLSHRA 310
                 3479*****************98765 PP

  == domain 6  score: 3.6 bits;  conditional E-value: 0.17
     BLOC1_2  27 klNeaasekykklkdvaaslekkleklnekyeelqpylqqi 67 
                 +  +++ ek ++++++++s+++ l++ +++  e++++ ++i
  EPA05401.1 329 NFKKNVFEKTDNIEQKISSVSDILKRQDALTSEFHKKSDKI 369
                 45566777777777777777777777777777777777666 PP

  == domain 7  score: 0.0 bits;  conditional E-value: 2.1
     BLOC1_2  32 asekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeys 88 
                 +++  k+ ++++  l k +e+ ++   + +++  +i+++e+  t+  e+v+  D  s
  EPA05401.1 380 TNKTAKESSKEMMALLKLSEYQSNIRMNAESKYGEIKDLENMATQTAEIVNLFDRLS 436
                 444444444444444445555555555666666777777777777777776666665 PP

>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.82   4.1e+02      11      38 ..      37      64 ..      17      71 .. 0.68
   2 ?    3.9   7.9       0.1        52      22     109 ..      69     159 ..      60     167 .. 0.66
   3 !   17.5   1.3   6.4e-06    0.0032       9      84 ..     166     241 ..     158     243 .. 0.92
   4 ?   -0.5   2.8       2.5   1.3e+03      39      85 ..     324     371 ..     287     394 .. 0.46
   5 ?   -1.1   3.7       3.7   1.8e+03      29      67 ..     367     405 ..     338     442 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.82
       DHR10 11 laelErkarelqakidalqvvekdlrsc 38
                +a+    +++lq+ i++++++  d +++
  EPA05401.1 37 VAAVTDSSKALQKEIKSMSKIFGDNQKI 64
                4455556667777777777666665554 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.1
       DHR10  22 qakidalqvvekdlrsciklleeieaelakleeakkklkelrd...aleekeielrelerkeerlqrqlenaeeklerlreqaeekreaak 109
                 +  id+l+v  + +++  k+++ +e++++kl     ++  ++d   +++e++++l+e  +k+  lq+   +  e  +r++ ++++ r++++
  EPA05401.1  69 KGMIDTLSVTLENIQKQSKQINILEDDTQKLYAGLNHVRTQSDlvsKINEQTQRLQEEVTKINELQKTSPKTPELSQRVEDSMNAMRNNSQ 159
                 5567777777777777777777777777777776666665555222556666777777777777777777777777777777777666665 PP

  == domain 3  score: 17.5 bits;  conditional E-value: 6.4e-06
       DHR10   9 eelaelErkarelqakidalqvvekdlrsciklleeieaelakleeakkklkelrdaleekeielrelerkeerlq 84 
                 + ++e     r+++ k+d+l+++ k++ ++ + ++ei+++   +e +++ +++l+++l + + +++ ++++ + l+
  EPA05401.1 166 QRIDEVRDDLRKVSGKTDSLADIGKEIDNLRNSIDEINKKADNMEVSSQIVTSLNQELGKIKDDVNSVSKTSSELE 241
                 6678888889********************************************************9999887776 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 2.5
       DHR10  39 iklleeieael.akleeakkklkelrdaleekeielrelerkeerlqr 85 
                  +     ++++ +k++  ++k+++ +d l+ + + ++e ++k + +  
  EPA05401.1 324 QEDFTNFKKNVfEKTDNIEQKISSVSDILKRQDALTSEFHKKSDKIFE 371
                 444444333322444444444444444444444444444444443333 PP

  == domain 5  score: -1.1 bits;  conditional E-value: 3.7
       DHR10  29 qvvekdlrsciklleeieaelakleeakkklkelrdale 67 
                 +++ ++++s+ ++ ++ ++e  k+  a  kl+e + ++ 
  EPA05401.1 367 DKIFEEMQSVKNVTNKTAKESSKEMMALLKLSEYQSNIR 405
                 466678888888888888888888888888888777765 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   7.7     0.001       0.5      52     162 ..      15     129 ..       3     132 .. 0.71
   2 ?    9.5   4.5    0.0021         1      71     152 ..     115     195 ..     103     203 .. 0.69
   3 ?    6.9   0.2     0.014       6.8      67     136 ..     207     275 ..     191     310 .. 0.79
   4 ?   -0.9   3.7       3.4   1.7e+03      76     112 ..     345     381 ..     266     431 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.001
       ATG16  52 ksskksakekeasasqsnskqsakiqsleqklaqlreelaelyksrgelaqrlleln...eelqkleeklkedeerlaeleaeraalet...klkdree 144
                 k ++k++k +++++  + ++  +k+++ ++  ++l++e + + k  g++++ l++++   ++l++  e++++++++++ le++ ++l      ++ + +
  EPA05401.1  15 KDPEKTKKVTKREP--TPAAVLKKVAAVTDSSKALQKEIKSMSKIFGDNQKILVSMKgmiDTLSVTLENIQKQSKQINILEDDTQKLYAglnHVRTQSD 111
                 22222222222222..34678*********************************998444677777789999***********9999861114556666 PP

       ATG16 145 elrekeklvqdlqDElsa 162
                  +   ++  q lq+E++ 
  EPA05401.1 112 LVSKINEQTQRLQEEVTK 129
                 666666777788888765 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0021
       ATG16  71 kqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekekl 152
                 k ++++q l++++++++ el+++  +  el+qr+ + +++++   + + + ++r++e++++ ++++ k +++++  +e ++l
  EPA05401.1 115 KINEQTQRLQEEVTKIN-ELQKTSPKTPELSQRVEDSMNAMRNNSQMIIKIAQRIDEVRDDLRKVSGKTDSLADIGKEIDNL 195
                 23344555555555543.3444444567899999999999999999999999999999999999988887777766665554 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.014
       ATG16  67 qsnskqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraale 136
                 ++ +++s+ ++sl+q+l ++++++  + k+ +el+  ++ + ++++++ +k+ +    ++ l+++ +++ 
  EPA05401.1 207 DNMEVSSQIVTSLNQELGKIKDDVNSVSKTSSELEA-IKVAIDTIAVKASKIDSLGGVIEGLKQQFTTIA 275
                 2456778889***********************985.777788888888888777777777777766665 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 3.4
       ATG16  76 iqsleqklaqlreelaelyksrgelaqrllelneelq 112
                 i+s ++ l+++ +  +e +k+  +  +  +++++   
  EPA05401.1 345 ISSVSDILKRQDALTSEFHKKSDKIFEEMQSVKNVTN 381
                 2222222222222222222222222222222222222 PP

>> HSBP1  Heat shock factor binding protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       8.5   4.2e+03      27      41 ..     121     135 ..     110     136 .. 0.54
   2 ?    3.3   0.6      0.15        73       2      33 ..     142     172 ..     141     177 .. 0.88
   3 ?    5.9   0.5     0.023        11      29      50 ..     185     206 ..     182     219 .. 0.85
   4 ?    4.7   0.1     0.053        27      26      48 ..     286     308 ..     262     311 .. 0.70
   5 ?   10.3   0.0   0.00097      0.48       4      36 ..     313     345 ..     310     353 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 8.5
       HSBP1  27 sriDdMssriDdLEk 41 
                 +r+ +  ++i++L+k
  EPA05401.1 121 QRLQEEVTKINELQK 135
                 344444455666655 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.15
       HSBP1   2 eLtavVenlLqqlqdkFqtmsdqilsriDdMs 33 
                 eL++ Ve+ ++ + +  q m  +i +riD+  
  EPA05401.1 142 ELSQRVEDSMNAMRNNSQ-MIIKIAQRIDEVR 172
                 89999**********977.9999******986 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.023
       HSBP1  29 iDdMssriDdLEksiadlmtqa 50 
                 + d+++ iD+L +si+++ ++a
  EPA05401.1 185 LADIGKEIDNLRNSIDEINKKA 206
                 5688999999999999887766 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.053
       HSBP1  26 lsriDdMssriDdLEksiadlmt 48 
                 ++ i +   +iD +E+ i++l  
  EPA05401.1 286 MNSIKEVLGKIDKIETEINSLSH 308
                 66677777788888888887765 PP

  == domain 5  score: 10.3 bits;  conditional E-value: 0.00097
       HSBP1   4 tavVenlLqqlqdkFqtmsdqilsriDdMssri 36 
                 ta+V + L+ +q+ F++  ++++++ D+++++i
  EPA05401.1 313 TAFVGEGLKSVQEDFTNFKKNVFEKTDNIEQKI 345
                 89****************************999 PP

>> kleA_kleC  Uncharacterized KorC regulated protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       9.5   4.7e+03      24      24 ..     131     131 ..      89     170 .. 0.62
   2 ?    5.7   0.1     0.037        18       9      37 ..     182     210 ..     176     216 .. 0.89
   3 ?    2.4   0.0      0.41     2e+02       9      37 ..     257     285 ..     254     301 .. 0.91
   4 ?    0.1   0.0       2.1     1e+03      17      37 ..     360     380 ..     325     394 .. 0.61

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 9.5
   kleA_kleC  24 d 24 
                 +
  EPA05401.1 131 N 131
                 1 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.037
   kleA_kleC   9 iDeLpevatdlvarRdkiAaklaeAeeLv 37 
                  D L ++++++ + R+ i +  ++A++++
  EPA05401.1 182 TDSLADIGKEIDNLRNSIDEINKKADNME 210
                 599**********************9876 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.41
   kleA_kleC   9 iDeLpevatdlvarRdkiAaklaeAeeLv 37 
                 iD L +v + l+ +   iA k  +A +L 
  EPA05401.1 257 IDSLGGVIEGLKQQFTTIAGKADSASDLS 285
                 89*************************96 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 2.1
   kleA_kleC  17 tdlvarRdkiAaklaeAeeLv 37 
                  ++  + dki + +++ ++ +
  EPA05401.1 360 SEFHKKSDKIFEEMQSVKNVT 380
                 455566666666666655555 PP

>> Serine_rich  Serine rich protein interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   2.9    0.0073       3.6      69     131 ..      38     102 ..      31     123 .. 0.84
   2 ?    2.1   2.6      0.36   1.8e+02      75     107 ..     140     172 ..      97     195 .. 0.67
   3 ?   12.9   2.4   0.00016      0.08      25     119 ..     168     256 ..     141     275 .. 0.69
   4 ?   -0.2   0.8       1.8     9e+02      52      85 ..     320     355 ..     287     404 .. 0.58

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0073
  Serine_rich  69 naaklsdknlqtkLrkqlqkledsdqilqetsqeLdsceWslealasdkkqek..pddlDrlvmv 131
                   a+  s k lq+ ++   +   d+++il++++  +d+ + +le + +++kq +  +dd  +l + 
   EPA05401.1  38 AAVTDSSKALQKEIKSMSKIFGDNQKILVSMKGMIDTLSVTLENIQKQSKQINilEDDTQKLYAG 102
                  455666799******************************************99999998888665 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.36
  Serine_rich  75 dknlqtkLrkqlqkledsdqilqetsqeLdsce 107
                    +l+++ ++ +++++++ q++ +++q +d+  
   EPA05401.1 140 TPELSQRVEDSMNAMRNNSQMIIKIAQRIDEVR 172
                  356778888888888888888888888887765 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 0.00016
  Serine_rich  25 lsfvsskWRskenleanlqeirlavdrlrtslrefleFargalanaaklsdknlqtkLrkqlqkledsdqilqetsqeLdsceWslealasdkkq 119
                  ++ v ++ R+ +     l++i + +d+lr+s+ e+ + a+++ ++      +++ t L+++l k++d+ + +++ts+eL++ + +++++a + ++
   EPA05401.1 168 IDEVRDDLRKVSGKTDSLADIGKEIDNLRNSIDEINKKADNMEVS------SQIVTSLNQELGKIKDDVNSVSKTSSELEAIKVAIDTIAVKASK 256
                  333344444444444455555555555555555555544444443......6799*********************************9998866 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 1.8
  Serine_rich  52 lrtslrefleFargalanaaklsd..knlqtkLrkq 85 
                  l++  ++f++F +++     ++++  ++++  L++q
   EPA05401.1 320 LKSVQEDFTNFKKNVFEKTDNIEQkiSSVSDILKRQ 355
                  555555555555555555554444332333333333 PP

>> Laminin_I  Laminin Domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1       2.9   1.4e+03      61      95 ..      21      55 ..      13      68 .. 0.79
   2 ?    7.4  10.1    0.0065       3.3      10     114 ..      82     184 ..      49     193 .. 0.87
   3 ?   10.9   2.5   0.00054      0.27      26     134 ..     193     303 ..     178     315 .. 0.80
   4 ?    6.7   5.7      0.01         5      13     125 ..     288     396 ..     280     406 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.9
   Laminin_I 61 kkatqvlakaqkvnaesertlnnakeLaekikkla 95
                kk+t+       v +++ + + ++k+L+++ik + 
  EPA05401.1 21 KKVTKREPTPAAVLKKVAAVTDSSKALQKEIKSMS 55
                56666666667788888888888999999888875 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0065
   Laminin_I  10 aleapykinanledltkeLqeklskesakkskieilekelesLaqeteeLqkkatqvlakaqkvnaesertlnnakeLaekikkladnikeilekvatl 108
                 + +++++in  led t++L   l+  + ++++++  +++ + L++e+ +   ++++++ k+ ++ +++e+ +n   +  + i k+a+ i e+     ++
  EPA05401.1  82 IQKQSKQINI-LEDDTQKLYAGLNHVRTQSDLVSKINEQTQRLQEEVTKIN-ELQKTSPKTPELSQRVEDSMNAMRNNSQMIIKIAQRIDEVRDDLRKV 178
                 5678999999.9999******************999999999*99999875.69999999999999999999999999999999999999988877777 PP

   Laminin_I 109 neneea 114
                 +++ + 
  EPA05401.1 179 SGKTDS 184
                 776555 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00054
   Laminin_I  26 keLqeklskesakkskieilekelesLaqeteeLqkkatqvlakaqkvnaesertlnnakeLaekikkladnikeilekvatlne...neealpsskls 121
                 ++L+++  ++++k++++e++ + ++sL+qe  +    ++ v++  ++++ +++ ++  + + a ki  l   i+ + ++  t+ +    +++l+ + ++
  EPA05401.1 193 DNLRNSIDEINKKADNMEVSSQIVTSLNQELGKIKDDVNSVSKTSSELE-AIKVAIDTIAVKASKIDSLGGVIEGLKQQFTTIAGkadSASDLSMNSIK 290
                 56788888999999999999999****************9999888875.5777777777777788888777887777777776656667888999999 PP

   Laminin_I 122 eelaeaqrlLeel 134
                 e l +++++  e+
  EPA05401.1 291 EVLGKIDKIETEI 303
                 9999998887666 PP

  == domain 4  score: 6.7 bits;  conditional E-value: 0.01
   Laminin_I  13 apykinanledltkeLqeklskesakkskieilekelesLaqeteeLqkkatqvlakaqkvnaesertlnnakeLaekikkladnikeilekvatlnen 111
                  +++++ ++++ ++e+++     ++++   e+l    +s+++++ ++ k + + +++ ++    ++++l++  +L  + +k  d+i e +++v+++ ++
  EPA05401.1 288 SIKEVLGKIDKIETEINSLSHRADSTAFVGEGL----KSVQEDFTNFKKNVFEKTDNIEQKISSVSDILKRQDALTSEFHKKSDKIFEEMQSVKNVTNK 382
                 566667777777777777777777776666666....9*******************************************************999998 PP

   Laminin_I 112 eealpssklseela 125
                   + +s+++ + l+
  EPA05401.1 383 TAKESSKEMMALLK 396
                 88888888877665 PP

>> DUF3540  Protein of unknown function (DUF3540)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.5      0.55   2.8e+02     107     162 ..     117     172 ..      62     183 .. 0.73
   2 ?    9.1   0.3    0.0022       1.1      90     172 ..     231     312 ..     202     316 .. 0.82
   3 ?    5.1   0.0     0.036        18     113     161 ..     296     344 ..     295     357 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.55
     DUF3540 107 ekaevaveelsllgeeleakvekvrlvaksvesvvdrltqrakrsfRrveeveqvr 162
                 ++++ +++e     +el+ +  k+   +++ve+ ++ +   ++ ++++ +++++vr
  EPA05401.1 117 NEQTQRLQEEVTKINELQKTSPKTPELSQRVEDSMNAMRNNSQMIIKIAQRIDEVR 172
                 44444444445556778888888888888899999999999999999888888887 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0022
     DUF3540  90 aaaeeldlaaerlkvsaekaevaveelsllgeeleakvekvrlvaksvesvvdrltqrakrsfRrveeveqvragridyqaee 172
                 ++ ++ + + e++kv  ++ +v++++++ lg  +e+  ++++++a + +s  d  +  +k+++ +++++e+ +++++ ++a+ 
  EPA05401.1 231 NSVSKTSSELEAIKVAIDTIAVKASKIDSLGGVIEGLKQQFTTIAGKADSASDLSMNSIKEVLGKIDKIET-EINSLSHRADS 312
                 455555666678899999***************************************************85.66777777665 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.036
     DUF3540 113 veelsllgeeleakvekvrlvaksvesvvdrltqrakrsfRrveeveqv 161
                 +++++   ++l+ +++++ +v++ ++sv + +t   k++f +++++eq 
  EPA05401.1 296 IDKIETEINSLSHRADSTAFVGEGLKSVQEDFTNFKKNVFEKTDNIEQK 344
                 6677788899*************************************96 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.2      0.23   1.1e+02      74     110 ..      37      76 ..       8      81 .. 0.59
   2 ?   10.3   9.8   0.00063      0.31      24     113 ..      74     162 ..      67     177 .. 0.89
   3 ?    5.4   0.8     0.019       9.6      47      99 ..     186     241 ..     163     251 .. 0.73
   4 ?    7.6   4.3    0.0042       2.1      14     131 ..     341     457 ..     334     482 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.23
     DUF3450  74 vasqeqeiasleeqieeieei...erelvpllekmidrLe 110
                 va++  + + l+++i+++++i   ++++   ++ mid+L 
  EPA05401.1  37 VAAVTDSSKALQKEIKSMSKIfgdNQKILVSMKGMIDTLS 76 
                 3334444445555555555554445666666666666665 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00063
     DUF3450  24 eaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierelvpllekmidrLeqfv 113
                 + + + ++ ++ +k+i+ l+d++q+l a ++ ++++ +  ++ neq +rl++++ ++i++l++   +  e++++++  +  m +  ++++
  EPA05401.1  74 TLSVTLENIQKQSKQINILEDDTQKLYAGLNHVRTQSDLVSKINEQTQRLQEEV-TKINELQKTSPKTPELSQRVEDSMNAMRNNSQMII 162
                 5556667778999***********************************998887.68*************************98887776 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.019
     DUF3450  47 qellaeyralkeeleslevyneqle...rlvasqeqeiasleeqieeieeierelv 99 
                 +++ +e+ +l++ +++++++ +++e   ++v+s++qe+ +++ + ++++++++el+
  EPA05401.1 186 ADIGKEIDNLRNSIDEINKKADNMEvssQIVTSLNQELGKIKDDVNSVSKTSSELE 241
                 44555666666666666666555542227899999999999999999999999987 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.0042
     DUF3450  14 laatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierelvpllekmidrLeqf 112
                 ++++++++ +  ++  a  ++ +kk dk+ +e q++++  ++  +e ++  +   +l++++++ + + +s   +i+++e+++++   +  ++ drL   
  EPA05401.1 341 IEQKISSVSDILKRQDALTSEFHKKSDKIFEEMQSVKNVTNKTAKESSKEMMALLKLSEYQSNIRMNAESKYGEIKDLENMATQTAEI-VNLFDRLSIE 438
                 57889999**************************************************************************998764.5677777777 PP

     DUF3450 113 veldlPflleeRqarlakL 131
                   + +P   e Rq  + k+
  EPA05401.1 439 AGEKIPLPHEVRQWAVSKI 457
                 7777777777777666665 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   6.1      0.22   1.1e+02       2      54 ..      79     134 ..      60     152 .. 0.57
   2 ?    3.9   2.5     0.088        44      12      67 ..     113     167 ..     103     181 .. 0.50
   3 ?    5.1   3.8     0.038        19      19      76 ..     185     242 ..     130     259 .. 0.61
   4 ?    0.9   0.1      0.75   3.7e+02      10      34 ..     287     311 ..     264     332 .. 0.65
   5 ?   11.4   2.7   0.00043      0.22      13      63 ..     332     382 ..     320     388 .. 0.90
   6 ?    1.2   0.5      0.62   3.1e+02      11      74 ..     372     435 ..     371     438 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.22
       Sec34   2 ldqLeskeeecdelleqtdealeqLeeleek...fksvsektsslheaceqlleeq 54 
                 l+++++++++++ l ++t+++   L++++++   +++++e+t++l+e+  ++ e q
  EPA05401.1  79 LENIQKQSKQINILEDDTQKLYAGLNHVRTQsdlVSKINEQTQRLQEEVTKINELQ 134
                 34455555555555555555555555544441112333445555555555544444 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.088
       Sec34  12 cdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieek 67 
                 + ++ eqt++++e++++++ + ++ s kt +l+++ e+ ++  ++ +++  +i ++
  EPA05401.1 113 VSKINEQTQRLQEEVTKIN-ELQKTSPKTPELSQRVEDSMNAMRNNSQMIIKIAQR 167
                 4444444444444444443.234445555555555555555555555544444443 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.038
       Sec34  19 tdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLkyFeeldp 76 
                 + ++ +++++l+++ +++++k  +++ +++ +++ +++l ++++++++  k  +el+ 
  EPA05401.1 185 LADIGKEIDNLRNSIDEINKKADNMEVSSQIVTSLNQELGKIKDDVNSVSKTSSELEA 242
                 2233445555556666666666666666666666666666666665555555555555 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 0.75
       Sec34  10 eecdelleqtdealeqLeeleekfk 34 
                 ++++e+l ++d++++++++l+++ +
  EPA05401.1 287 NSIKEVLGKIDKIETEINSLSHRAD 311
                 4455566666666665555554433 PP

  == domain 5  score: 11.4 bits;  conditional E-value: 0.00043
       Sec34  13 delleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaee 63 
                 ++++e+td+++++++++++  k+ ++ ts++h+++++++ee +++++++++
  EPA05401.1 332 KNVFEKTDNIEQKISSVSDILKRQDALTSEFHKKSDKIFEEMQSVKNVTNK 382
                 7899***************************************99998876 PP

  == domain 6  score: 1.2 bits;  conditional E-value: 0.62
       Sec34  11 ecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLkyFeel 74 
                 e++++ + t+++ ++ ++      + se  s+++ ++e+ + e k+le++a +  e ++ F+ l
  EPA05401.1 372 EMQSVKNVTNKTAKESSKEMMALLKLSEYQSNIRMNAESKYGEIKDLENMATQTAEIVNLFDRL 435
                 567777778888888888888888999999999999999999999*****99999999999987 PP

>> Cauli_AT  Aphid transmission protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   6.1    0.0062       3.1      73     161 ..      42     130 ..      32     131 .. 0.93
   2 ?    8.6   2.8    0.0032       1.6      98     163 .]     115     180 ..     104     180 .. 0.75
   3 ?    9.0   6.0    0.0024       1.2      87     161 ..     159     233 ..     143     235 .. 0.84
   4 ?   10.6   0.4   0.00079      0.39      86     158 ..     261     334 ..     247     338 .. 0.84
   5 ?   -1.3   7.2       3.7   1.8e+03      92     147 ..     331     391 ..     324     436 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0062
    Cauli_AT  73 DesealsksksPfgsvfkklkkifkeggedkekktklletLkeaqnrikkleeetkklaekivtekllkeevkdlderlseirdslkai 161
                 D s al k+ + ++++f + +ki+ +  +  +  +  le +++ +++i+ le++t+kl   ++  +   + v +++e+ +++++++ +i
  EPA05401.1  42 DSSKALQKEIKSMSKIFGDNQKILVSMKGMIDTLSVTLENIQKQSKQINILEDDTQKLYAGLNHVRTQSDLVSKINEQTQRLQEEVTKI 130
                 8999999999999***********************************************99999999999999999999999999877 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0032
    Cauli_AT  98 eggedkekktklletLkeaqnrikkleeetkklaekivtekllkeevkdlderlseirdslkaiiG 163
                 + +e++++  +++  ++e q+   k  e ++++++ +++ +   +++ ++ +r+ e+rd+l+++ G
  EPA05401.1 115 KINEQTQRLQEEVTKINELQKTSPKTPELSQRVEDSMNAMRNNSQMIIKIAQRIDEVRDDLRKVSG 180
                 4455566666666666777777777777788888888888999999***************99866 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0024
    Cauli_AT  87 svfkklkkifkeggedkekktklletLkeaqnrikkleeetkklaekivtekllkeevkdlderlseirdslkai 161
                 ++  k+ +   e+ +d  k + ++++L ++ + i++l + + ++++k    +   ++v  l+++l +i+d++ ++
  EPA05401.1 159 QMIIKIAQRIDEVRDDLRKVSGKTDSLADIGKEIDNLRNSIDEINKKADNMEVSSQIVTSLNQELGKIKDDVNSV 233
                 44445555558999999*****************************************************99865 PP

  == domain 4  score: 10.6 bits;  conditional E-value: 0.00079
    Cauli_AT  86 gsvfkklkkifkeggedkekktkl.letLkeaqnrikkleeetkklaekivtekllkeevkdlderlseirdsl 158
                 g v + lk+ f    ++ +++++l ++++ke+  +i+k+e+e+++l+++  + + + e +k ++e +++ ++++
  EPA05401.1 261 GGVIEGLKQQFTTIAGKADSASDLsMNSIKEVLGKIDKIETEINSLSHRADSTAFVGEGLKSVQEDFTNFKKNV 334
                 56777888888887777777666427899************************************999988776 PP

  == domain 5  score: -1.3 bits;  conditional E-value: 3.7
    Cauli_AT  92 lkkifkeggedkekktklletLkeaqnrikkleeetkklaeki.....vtekllkeevkdl 147
                  k++f+++++ ++k +   ++Lk+ +   ++ ++++ k+ e++     vt+k  ke  k++
  EPA05401.1 331 KKNVFEKTDNIEQKISSVSDILKRQDALTSEFHKKSDKIFEEMqsvknVTNKTAKESSKEM 391
                 4456666666666666666666666665555555555554443100013344444444443 PP

>> DUF4088  Protein of unknown function (DUF4088)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.3       1.4   6.8e+02     110     174 ..     108     172 ..      97     185 .. 0.72
   2 ?    9.9   0.1     0.001      0.51     147     196 ..     365     414 ..     323     437 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.4
     DUF4088 110 gdaalvealaaqikasaedirvleerlktPawrlaeslrqrvyeakiavetesgeaa..reklGelr 174
                 ++  lv  +  q +   e++ +++e  kt     +  l qrv + + a++++s + +   +++ e+r
  EPA05401.1 108 TQSDLVSKINEQTQRLQEEVTKINELQKTSP--KTPELSQRVEDSMNAMRNNSQMIIkiAQRIDEVR 172
                 5556667777777777777888877777643..3467999999999999988887663356777776 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.001
     DUF4088 147 lrqrvyeakiavetesgeaareklGelrallklaleyGsiqkeeaqqvle 196
                   ++++e + +v+++++++a+e   e+ allkl+    +i+ +++++  e
  EPA05401.1 365 KSDKIFEEMQSVKNVTNKTAKESSKEMMALLKLSEYQSNIRMNAESKYGE 414
                 45799*****************************9999999998887655 PP

>> GIT1_C  G protein-coupled receptor kinase-interacting protein 1 C term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   6.0      0.82   4.1e+02      32      86 ..      80     134 ..      11     151 .. 0.64
   2 ?    6.4   0.7     0.019       9.4      24      96 ..     152     222 ..     139     240 .. 0.76
   3 ?   11.2   2.8   0.00059      0.29       5     101 ..     331     429 ..     328     432 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.82
      GIT1_C  32 esfvpcaerIqsaVqdlvalfpenlseetlrtaLkqLtssaerLqeeCeelqeae 86 
                 e++ + +++I+   +d  +l++   +  t +  +++++++++rLqee ++ +e +
  EPA05401.1  80 ENIQKQSKQINILEDDTQKLYAGLNHVRTQSDLVSKINEQTQRLQEEVTKINELQ 134
                 4445555555555555555665444444444457777777777777777777733 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.019
      GIT1_C  24 qaaqeekkesfvpcaerIqsaVqdlvalfpenlseetlrtaLkqLtssaerLqeeCeelqeaeseskedikke 96 
                 +a+  + ++ ++++a+rI ++ +dl ++  ++ s  ++ +++++L++s   ++++  +++  +s+   ++++e
  EPA05401.1 152 NAM-RNNSQMIIKIAQRIDEVRDDLRKVSGKTDSLADIGKEIDNLRNSIDEINKKADNMEV-SSQIVTSLNQE 222
                 333.35667899************************************9999999998887.44444444444 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.00059
      GIT1_C   5 seeVvrkteqitkriqeLlqaaq..eekkesfvpcaerIqsaVqdlvalfpenlseetlrt.aLkqLtssaerLqeeCeelqeaeseskedikketqqv 100
                 + +V+ kt+ i ++i+++ +  +  ++ +++f + +++I + +q++ ++  ++++e++ +  aL +L++  + ++ + e+    e ++ e+++ +t ++
  EPA05401.1 331 KKNVFEKTDNIEQKISSVSDILKrqDALTSEFHKKSDKIFEEMQSVKNVTNKTAKESSKEMmALLKLSEYQSNIRMNAESKYG-EIKDLENMATQTAEI 428
                 679***************98876337899***************999999977776666666799999999999988877776.556666666666666 PP

      GIT1_C 101 i 101
                 +
  EPA05401.1 429 V 429
                 5 PP

>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   2.3      0.16        81      98     154 ..      33      89 ..       5      97 .. 0.52
   2 ?    9.6   3.4    0.0015      0.73      95     169 ..      79     155 ..      73     158 .. 0.82
   3 ?    7.8   6.4    0.0053       2.6      82     169 ..     118     200 ..     111     214 .. 0.46
   4 ?    5.1  12.2     0.036        18       3     165 ..     208     373 ..     206     380 .. 0.71
   5 ?   -0.8   0.4       2.4   1.2e+03      80     138 ..     379     426 ..     371     442 .. 0.37

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.16
                 ............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHH CS
   MCPsignal  98 iqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeq 154
                 + k++  +++s +  ++++++ s++  + ++ l ++  +++ ++ ++++i++ s+++
  EPA05401.1  33 VLKKVAAVTDSSKALQKEIKSMSKIFGDNQKILVSMKGMIDTLSVTLENIQKQSKQI 89 
                 334444444444444444444455555555555555555555555555554444443 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0015
                 H..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHH CS
   MCPsignal  95 iieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlv...qeiaaaseeqsasieevnqaveeva 169
                 +++iqk++ + +++le+ +q+   g++ v++  + +++i e++++++++v   +e++++s +  + ++ v ++++++ 
  EPA05401.1  79 LENIQKQS-KQINILEDDTQKLYAGLNHVRTQSDLVSKINEQTQRLQEEVtkiNELQKTSPKTPELSQRVEDSMNAMR 155
                 45677766.568999****************************99998751116788999999999999999998886 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0053
                 HHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
   MCPsignal  82 ersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasieevnqaveeva 169
                 e+++   +e++++  e+qk          e  qrve +++ +++  + + +i+++++ev d ++ ++  ++ ++   +e+ +  + ++
  EPA05401.1 118 EQTQRLQEEVTKIN-ELQKT----SPKTPELSQRVEDSMNAMRNNSQMIIKIAQRIDEVRDDLRKVSGKTDSLADIGKEIDNLRNSID 200
                 44444444444432.33332....2333445555555555555555555556666655555555555555544443333333222222 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.036
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH..... CS
   MCPsignal   3 laeeaseeAeeggkevanvvkqmeeieksskeisdiieVideiadQT.NlLALNAaiEAARAGeqGrGFaVVAdEVrkLAersaqaakeiealiieiqk 100
                   e +s+  ++ ++e+ ++ +++++++k s+e++ i   id ia +   +  L   iE  +     + F+ +A+   +  + s+++ ke+   i +i+ 
  EPA05401.1 208 NMEVSSQIVTSLNQELGKIKDDVNSVSKTSSELEAIKVAIDTIAVKAsKIDSLGGVIEGLK-----QQFTTIAGKADSASDLSMNSIKEVLGKIDKIET 301
                 566778888888999999**************************87527889*****9765.....679******9999999***************** PP

                 .........HHHHHHHHHHHHHHHHHCCHHHH........HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
   MCPsignal 101 eindsvesleetrqrveegselveetgealke........iveavaevadlvqeiaaaseeqsasieevnqav 165
                 ein+  +   +++  v eg++ v+e  +++k+        i +++++v+d+++   a ++e  + ++++ + +
  EPA05401.1 302 EINSLSHR-ADSTAFVGEGLKSVQEDFTNFKKnvfektdnIEQKISSVSDILKRQDALTSEFHKKSDKIFEEM 373
                 *9965554.4555667777777777766665421111111445555555555555555555555555555555 PP

  == domain 5  score: -0.8 bits;  conditional E-value: 2.4
                 HHHHHH.HHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHH CS
   MCPsignal  80 LAersa.qaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveava 138
                 + +++a +++ke+ al+ ++           +e ++++   +e      ++l+++++++a
  EPA05401.1 379 VTNKTAkESSKEMMALL-KL-----------SEYQSNIRMNAESKYGEIKDLENMATQTA 426
                 33333212333333333.22...........22222222222222222223333333333 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   3.8      0.11        56      20      97 ..      31     108 ..      10     111 .. 0.77
   2 ?   13.9  10.2     8e-05      0.04       8     112 ..     109     212 ..     103     215 .. 0.87
   3 ?    7.6   4.4    0.0071       3.5       3      91 ..     197     287 ..     196     309 .. 0.80
   4 ?    2.8   6.2      0.22   1.1e+02      43      84 ..     341     382 ..     304     431 .. 0.50

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.11
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH...HHHHHHHHHH CS
  Laminin_II  20 aplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeassslsdniseike 97 
                 a++ +++  + ++ + ++++++ + +   d +k++++ +  + +L  +++++ ++ k+++ le+  + l + ++ ++ 
  EPA05401.1  31 AAVLKKVAAVTDSSKALQKEIKSMSKIFGDNQKILVSMKGMIDTLSVTLENIQKQSKQINILEDDTQKLYAGLNHVRT 108
                 556667777778888888888888888889999999999999999999999999999999999888888777777775 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 8e-05
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH...HHHHHHHHHHHHHHHHHHH CS
  Laminin_II   8 anetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeassslsdniseikelIaqARkaA 106
                  ++ ++++ eq++ l++++ +++e l++   +  e  + v+d+++a+r  ++ + k+ + ++++ d l+++  + +  + ++++i+++++ I    k A
  EPA05401.1 109 QSDLVSKINEQTQRLQEEVTKINE-LQKTSPKTPELSQRVEDSMNAMRNNSQMIIKIAQRIDEVRDDLRKVSGKTDSLADIGKEIDNLRNSIDEINKKA 206
                 566788888999999999988875.66666666899999**************************************999*************999999 PP

                 HT---E CS
  Laminin_II 107 nkikvs 112
                     vs
  EPA05401.1 207 DNMEVS 212
                 998887 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0071
                 XXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH...HHHH CS
  Laminin_II   3 elaaeanetakevl...eqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeassslsdn 91 
                 + ++e+n++a + +   ++++ l+q+l ++k++++++ ++  e  e +k a  +i+   +++  L  +++ L +++ ++  + +  s ls n
  EPA05401.1 197 NSIDEINKKADNMEvssQIVTSLNQELGKIKDDVNSVSKTSSEL-EAIKVAIDTIAVKASKIDSLGGVIEGLKQQFTTIAGKADSASDLSMN 287
                 678999999987653347899*****************995554.55666666666667889999999***********9999987768765 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.22
                 XXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH CS
  Laminin_II  43 tnekvkdankairdArrsvkkLeklapqLldklkelkqleea 84 
                 +++k+++ + +++      ++  k+ +++++ ++++k+  ++
  EPA05401.1 341 IEQKISSVSDILKRQDALTSEFHKKSDKIFEEMQSVKNVTNK 382
                 444444444444444444444444444444444444443332 PP

>> TolA_bind_tri  TolA binding protein trimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.2     0.026        13      27      58 ..      58      89 ..      35     103 .. 0.82
   2 ?    0.7   2.1       1.1   5.5e+02      28      56 ..     107     135 ..      90     137 .. 0.59
   3 ?    9.1   0.5    0.0026       1.3       2      44 ..     143     185 ..     142     187 .. 0.87
   4 ?    3.6   0.1      0.14        70      27      52 ..     185     210 ..     183     232 .. 0.81
   5 ?   -1.1   0.0       4.2   2.1e+03       3      29 ..     342     368 ..     333     382 .. 0.58

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.026
  TolA_bind_tri 27 lealqqelreLRGqiEelqyqleqleerQrdl 58
                     ++q+ l +++G i+ l+  le+++++ +++
     EPA05401.1 58 FGDNQKILVSMKGMIDTLSVTLENIQKQSKQI 89
                   5678888889*******************997 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.1
  TolA_bind_tri  28 ealqqelreLRGqiEelqyqleqleerQr 56 
                     + +  +++++ q+++lq ++ +++e Q+
     EPA05401.1 107 RTQSDLVSKINEQTQRLQEEVTKINELQK 135
                    44444456666677777777777766665 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0026
  TolA_bind_tri   2 ledrvarLErilearsqlllelqqqlealqqelreLRGqiEel 44 
                    l +rv+   +++ ++sq+++++ q++++ + +lr+  G+++ l
     EPA05401.1 143 LSQRVEDSMNAMRNNSQMIIKIAQRIDEVRDDLRKVSGKTDSL 185
                    6788887777888889*********************999876 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.14
  TolA_bind_tri  27 lealqqelreLRGqiEelqyqleqle 52 
                    l +  +e++ LR +i+e + + +++e
     EPA05401.1 185 LADIGKEIDNLRNSIDEINKKADNME 210
                    6677899**********999988886 PP

  == domain 5  score: -1.1 bits;  conditional E-value: 4.2
  TolA_bind_tri   3 edrvarLErilearsqlllelqqqlea 29 
                    e++++++  il+ ++ l  e +++ ++
     EPA05401.1 342 EQKISSVSDILKRQDALTSEFHKKSDK 368
                    444555555555544444444444444 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.5      0.58   2.9e+02       9      27 ..      72      90 ..      65      99 .. 0.77
   2 ?    3.2   1.5      0.24   1.2e+02       2      40 ..      89     130 ..      88     136 .. 0.63
   3 ?   -1.5   0.1         7   3.5e+03      17      27 ..     145     155 ..     128     166 .. 0.45
   4 ?   11.1   0.4    0.0008       0.4       1      36 [.     167     205 ..     167     210 .. 0.91
   5 ?    3.7   0.6      0.17        84       3      26 ..     217     240 ..     208     253 .. 0.67
   6 ?    1.9   0.2       0.6     3e+02       7      34 ..     231     258 ..     225     274 .. 0.79
   7 ?    5.4   0.1     0.048        24       1      37 [.     295     334 ..     295     336 .. 0.65
   8 ?    3.5   1.8      0.19        94       1      38 [.     337     374 ..     337     382 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.58
   FlaC_arch  9 lsklsteletvkkeneels 27
                ++ ls++le+++k+ ++++
  EPA05401.1 72 IDTLSVTLENIQKQSKQIN 90
                5678888888888887774 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.24
   FlaC_arch   2 idelEnklsklsteletvkke...neelsksveelkenVkdl 40 
                 i+ lE + +kl   l+ v+++    ++++++ ++l+e+V ++
  EPA05401.1  89 INILEDDTQKLYAGLNHVRTQsdlVSKINEQTQRLQEEVTKI 130
                 566777777787777777776222355666666666666554 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 7
   FlaC_arch  17 etvkkeneels 27 
                 + v+++++ ++
  EPA05401.1 145 QRVEDSMNAMR 155
                 33333333333 PP

  == domain 4  score: 11.1 bits;  conditional E-value: 0.0008
   FlaC_arch   1 ridelEnklsklst...eletvkkeneelsksveelken 36 
                 ride+  +l k+s    +l+ + ke+++l++s++e++++
  EPA05401.1 167 RIDEVRDDLRKVSGktdSLADIGKEIDNLRNSIDEINKK 205
                 89***********9889999999*************986 PP

  == domain 5  score: 3.7 bits;  conditional E-value: 0.17
   FlaC_arch   3 delEnklsklsteletvkkeneel 26 
                  +l ++l+k++  +++v k+ +el
  EPA05401.1 217 TSLNQELGKIKDDVNSVSKTSSEL 240
                 567788888887666666554444 PP

  == domain 6  score: 1.9 bits;  conditional E-value: 0.6
   FlaC_arch   7 nklsklsteletvkkeneelsksveelk 34 
                 n +sk+s+ele +k  ++ +  +  +++
  EPA05401.1 231 NSVSKTSSELEAIKVAIDTIAVKASKID 258
                 6788888888888888888877666665 PP

  == domain 7  score: 5.4 bits;  conditional E-value: 0.048
   FlaC_arch   1 ridelEnklsklst...eletvkkeneelsksveelkenV 37 
                 +id++E+++++ls    + + v + +++++++ ++ k+nV
  EPA05401.1 295 KIDKIETEINSLSHradSTAFVGEGLKSVQEDFTNFKKNV 334
                 89***********955534445555555555555555554 PP

  == domain 8  score: 3.5 bits;  conditional E-value: 0.19
   FlaC_arch   1 ridelEnklsklsteletvkkeneelsksveelkenVk 38 
                 ++d++E+k+s++s  l+   +  +e  k+ +++ e+ +
  EPA05401.1 337 KTDNIEQKISSVSDILKRQDALTSEFHKKSDKIFEEMQ 374
                 789**********9888888888888888777766554 PP

>> HD_4  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       3.6   1.8e+03      42      72 ..      30      67 ..      18     100 .. 0.61
   2 ?   10.0   0.9    0.0011      0.53      49     126 ..     102     173 ..      90     199 .. 0.74
   3 ?   -0.4   0.1       1.7   8.3e+02      52      88 ..     350     387 ..     344     405 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 3.6
        HD_4 42 iAalLhdvve..d...a..lsleeirerfGeevarLve 72
                 Aa+L +v +  d   a  ++++ +++ fG++   Lv 
  EPA05401.1 30 PAAVLKKVAAvtDsskAlqKEIKSMSKIFGDNQKILVS 67
                57777777652212221224446666777777666665 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0011
        HD_4  49 vvedalsleeirerfGeevarLvegvsklkrlqkvaaadeaeekaeqvenlRkmLlAmveDirvvliklAdrlqtlrs 126
                  +++ ++++++  +++e+  rL e+v+k+++lqk   + ++ e ++ ve       Am +    ++ik+A+r+++ r 
  EPA05401.1 102 GLNHVRTQSDLVSKINEQTQRLQEEVTKINELQKT--SPKTPELSQRVEDSMN---AM-RNNSQMIIKIAQRIDEVRD 173
                 445556678899999********************..5555555555555444...78.455999*******998875 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.7
        HD_4  52 da.lsleeirerfGeevarLvegvsklkrlqkvaaade 88 
                 d  +++++++ +f ++  ++ e+++ +k++++++a+++
  EPA05401.1 350 DIlKRQDALTSEFHKKSDKIFEEMQSVKNVTNKTAKES 387
                 55466789999999999999999999999999942222 PP

>> HrpB7  Bacterial type III secretion protein (HrpB7)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       2.3   1.1e+03      89     137 ..      38      86 ..      31      97 .. 0.69
   2 ?    6.6   1.4     0.019       9.4      36     142 ..      80     187 ..      67     193 .. 0.77
   3 ?    2.7   0.2      0.29   1.5e+02      97     139 ..     166     208 ..     159     222 .. 0.76
   4 ?    1.1   0.0      0.93   4.6e+02      93     140 ..     235     281 ..     182     288 .. 0.58
   5 ?   -0.9   0.0       3.8   1.9e+03      24      63 ..     320     359 ..     289     380 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 2.3
       HrpB7  89 raaeaelaaarqaldaaedavaatarkiaRndaqidacrerierlrraa 137
                 +a+    +a++++++   +     ++ +++++++id    ++e ++++ 
  EPA05401.1  38 AAVTDSSKALQKEIKSMSKIFGDNQKILVSMKGMIDTLSVTLENIQKQS 86 
                 5555555666666665555555556667899999999999999988765 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.019
       HrpB7  36 aalaaaqaqveaardavraheerlddlttgsspfsiadylacrayrdvle..grvraaeaelaaarqaldaaedavaatarkiaRndaqidacrerier 132
                 ++++++++q++  +d+ ++  + l+ + t s  ++ +   + +++ ++++  +++++ + ++  + q++++  +a++   + i +   +id +r  +++
  EPA05401.1  80 ENIQKQSKQINILEDDTQKLYAGLNHVRTQSD-LVSKINEQTQRLQEEVTkiNELQKTSPKTPELSQRVEDSMNAMRNNSQMIIKIAQRIDEVRDDLRK 177
                 55666677777777777777777777777776.666666777777777763357888888999999999999999999999999999999999999999 PP

       HrpB7 133 lrraaerare 142
                 +  +++  ++
  EPA05401.1 178 VSGKTDSLAD 187
                 9888887665 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.29
       HrpB7  97 aarqaldaaedavaatarkiaRndaqidacrerierlrraaer 139
                 +  +++++  ++v+ +   +a    +id  r+ i+ ++++a+ 
  EPA05401.1 166 QRIDEVRDDLRKVSGKTDSLADIGKEIDNLRNSIDEINKKADN 208
                 5556777777888888888888888888888888888887765 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.93
       HrpB7  93 aelaaarqaldaaedavaatarkiaRndaqidacrerierlrraaera 140
                 +    ++ a++ a d +a +a ki ++ + i+  +++   ++ +a+ a
  EPA05401.1 235 KTSSELE-AIKVAIDTIAVKASKIDSLGGVIEGLKQQFTTIAGKADSA 281
                 3333332.3445556666666666666666666666666666666655 PP

  == domain 5  score: -0.9 bits;  conditional E-value: 3.8
       HrpB7  24 leaaraalaaaeaalaaaqaqveaardavraheerlddlt 63 
                 l+  +++  + ++++ ++ +++e++   v ++ +r d+lt
  EPA05401.1 320 LKSVQEDFTNFKKNVFEKTDNIEQKISSVSDILKRQDALT 359
                 5555555555556666666666666666666666666555 PP

>> Cas_Cmr5  CRISPR-associated protein (Cas_Cmr5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.0    0.0012      0.59       7      98 ..      31     121 ..       5     155 .. 0.83
   2 ?   -0.2   0.4       2.4   1.2e+03      55      55 ..     334     334 ..     263     398 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0012
                 HHHHHHHHHHHHHTHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHHHHCTSS...STTTCHHHHHHHHSTH CS
    Cas_Cmr5   7 adayekvkelkekskkkekkykslvkklP....alIltnGLgqalAfllskgkkkkedahkkllehlaewlkkeksaskkkkgendllkelleadl 98 
                 a++++kv++++++sk ++k+ ks+ k ++    +l+ ++G++ +l + l+    +k++++ ++le+ ++ l       +++ ++ dl+ +++e+++
  EPA05401.1  31 AAVLKKVAAVTDSSKALQKEIKSMSKIFGdnqkILVSMKGMIDTLSVTLENI--QKQSKQINILEDDTQKLYAG---LNHVRTQSDLVSKINEQTQ 121
                 5789**********************999777789***************97..66666666666666666666...5666666677777766654 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 2.4
                 S CS
    Cas_Cmr5  55 k 55 
                  
  EPA05401.1 334 V 334
                 2 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.4      0.71   3.5e+02      40      93 ..      46     107 ..      31     111 .. 0.48
   2 ?    3.0   1.2      0.34   1.7e+02      27      73 ..     112     158 ..     107     163 .. 0.76
   3 ?    9.6   0.1    0.0031       1.5      27      97 ..     164     231 ..     159     235 .. 0.79
   4 ?   -0.3   0.0       3.7   1.8e+03      30      71 ..     288     332 ..     279     338 .. 0.64
   5 ?    5.0   3.3     0.082        41      26      81 ..     333     387 ..     320     405 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.71
  Occludin_ELL  40 eLerelkelke...gsk....eykkieeeilqeykklkk.dpeyqekkkrceyLkekLshiK 93 
                    L++e+k++++   +++     +k +++ +  ++++++k +++    +  +++L++ L+h++
    EPA05401.1  46 ALQKEIKSMSKifgDNQkilvSMKGMIDTLSVTLENIQKqSKQINILEDDTQKLYAGLNHVR 107
                   44433333332111111244455555555555555555545555555555666666666655 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.34
  Occludin_ELL  27 lhaeleevskkfseLerelkelkegskeykkieeeilqeykklkkdp 73 
                   l ++++e +++++e  ++++el+++s ++ ++ +++ ++ + +++++
    EPA05401.1 112 LVSKINEQTQRLQEEVTKINELQKTSPKTPELSQRVEDSMNAMRNNS 158
                   55667777777777778888888888899999999988888887765 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0031
  Occludin_ELL  27 lhaeleevskkfseLerelkelkegskeykkieeeilqeykklkkdpeyqekkkrceyLkekLshiKklik 97 
                   + ++++ev++++++++ ++++l++  ke++++ ++ ++e +k+    +     + ++ L+++L  iK  ++
    EPA05401.1 164 IAQRIDEVRDDLRKVSGKTDSLADIGKEIDNLRNS-IDEINKK--ADNMEVSSQIVTSLNQELGKIKDDVN 231
                   56788888888888888888888888888888888.6777766..55566678999***********9987 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 3.7
  Occludin_ELL  30 eleevskkfseLerelkelkegsk...eykkieeeilqeykklkk 71 
                   +++ev  k+ ++e+e+++l+++ +    + +  +++++++ ++kk
    EPA05401.1 288 SIKEVLGKIDKIETEINSLSHRADstaFVGEGLKSVQEDFTNFKK 332
                   456667777777777777776666433444555566666666655 PP

  == domain 5  score: 5.0 bits;  conditional E-value: 0.082
  Occludin_ELL  26 elhaeleevskkfseLerelkelkegskeykkieeeilqeykklkkdpeyqekkkr 81 
                   ++ ++ +++++k+s +++ lk+++  ++e++k  ++i++e +++k+ ++  ++k+ 
    EPA05401.1 333 NVFEKTDNIEQKISSVSDILKRQDALTSEFHKKSDKIFEEMQSVKNVTNK-TAKES 387
                   46688999************************************883333.22332 PP

>> CCDC-167  Coiled-coil domain-containing protein 167
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0       1.4   7.1e+02      29      62 ..      36      69 ..       6      71 .. 0.75
   2 ?    5.5   2.5     0.044        22       4      53 ..      87     136 ..      85     165 .. 0.86
   3 ?   -1.2   0.0       5.3   2.6e+03       7      24 ..     162     179 ..     145     187 .. 0.67
   4 ?   12.1   0.4   0.00037      0.19       8      53 ..     187     232 ..     182     244 .. 0.88
   5 ?    0.3   0.0       1.9   9.2e+02       2      21 ..     292     311 ..     291     325 .. 0.85
   6 ?    1.5   1.6      0.75   3.7e+02       2      50 ..     334     379 ..     333     403 .. 0.60

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 1.4
    CCDC-167 29 keelseeeResleeEeaslkeqleenekeLksLr 62
                k+   ++  ++l++E +s+++   +n+k L s++
  EPA05401.1 36 KVAAVTDSSKALQKEIKSMSKIFGDNQKILVSMK 69
                4444445578999999999999999999998876 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.044
    CCDC-167   4 seIdkleeklascrerLeaverrlrkeelseeeResleeEeaslkeqlee 53 
                 ++I+ le+ +++++  L++v ++   ++  +e+ ++l+eE ++++e  ++
  EPA05401.1  87 KQINILEDDTQKLYAGLNHVRTQSDLVSKINEQTQRLQEEVTKINELQKT 136
                 79999************************************999986544 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 5.3
    CCDC-167   7 dkleeklascrerLeave 24 
                  k+ +++ ++r++L +v 
  EPA05401.1 162 IKIAQRIDEVRDDLRKVS 179
                 344555555555555554 PP

  == domain 4  score: 12.1 bits;  conditional E-value: 0.00037
    CCDC-167   8 kleeklascrerLeaverrlrkeelseeeResleeEeaslkeqlee 53 
                 ++ +++ ++r+++++++++  + e+s++  +sl++E++++k ++++
  EPA05401.1 187 DIGKEIDNLRNSIDEINKKADNMEVSSQIVTSLNQELGKIKDDVNS 232
                 5678999**********************************98876 PP

  == domain 5  score: 0.3 bits;  conditional E-value: 1.9
    CCDC-167   2 vaseIdkleeklascrerLe 21 
                 v  +Idk+e ++ s+ +r +
  EPA05401.1 292 VLGKIDKIETEINSLSHRAD 311
                 66789****99999998866 PP

  == domain 6  score: 1.5 bits;  conditional E-value: 0.75
    CCDC-167   2 vaseIdkleeklascrerLeaverrlrkeelseeeResleeEeaslkeq 50 
                 v+++ d++e+k++s+ + L++ +    + +  +   +++ eE++s+k+ 
  EPA05401.1 334 VFEKTDNIEQKISSVSDILKRQDALTSEFHKKS---DKIFEEMQSVKNV 379
                 567778999999999988888665433322222...2333444444443 PP

>> SesA  N-terminal domain on NACHT_NTPase and P-loop NTPases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.3      0.51   2.5e+02      73     119 ..      31      75 ..       6      77 .. 0.63
   2 ?    5.5   7.5     0.038        19      35     121 ..      72     160 ..      34     161 .. 0.78
   3 ?    7.1   2.1     0.012       6.1       4      82 ..     161     239 ..     159     270 .. 0.72
   4 ?    5.1   1.3     0.051        25       3      84 ..     288     377 ..     286     404 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.51
        SesA  73 atkleeifekvapapadsrl.eryrkavrslgkgskVEtLmkgiledl 119
                 a+ l+++   +   ++++ l ++++++ + +g+++k+ + mkg+ + l
  EPA05401.1  31 AAVLKKVAAVT---DSSKALqKEIKSMSKIFGDNQKILVSMKGMIDTL 75 
                 44444444333...4445555777777777999999999999998876 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.038
        SesA  35 LplvqetLedaksqlesskldedtesaikpvlesckekatkleeifekvapapad.srleryrka.vrslgkgskVEtLmkgiledlql 121
                 + +++ tLe +++q ++ ++ ed++++++  l++++++ + +++i e++++ +++ +++ + +k+  ++    ++VE+ m+++ ++ q+
  EPA05401.1  72 IDTLSVTLENIQKQSKQINILEDDTQKLYAGLNHVRTQSDLVSKINEQTQRLQEEvTKINELQKTsPKTPELSQRVEDSMNAMRNNSQM 160
                 5667889******************************************77777736666666662555677899****9999998776 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.012
        SesA   4 tiaiveaaiklydaikdikglpeaFrevgkrLplvqetLedaksqlesskldedtesaikpvlesckekatkleeifek 82 
                 +i i + + ++ d +++++g   ++ ++gk++  +++  +++++++++ + +++  +++++ l + k+ ++++++   +
  EPA05401.1 161 IIKIAQRIDEVRDDLRKVSGKTDSLADIGKEIDNLRNSIDEINKKADNMEVSSQIVTSLNQELGKIKDDVNSVSKTSSE 239
                 7889999999999999999999999999999999999999999999999988887777444444444444444433333 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.051
        SesA   3 stiaiveaaiklydaikdikglpeaFrevgkrLplvqetLedaksqlesskldedtesa.ikpvlescke....katkleeifekv...a 84 
                 s+  +++++ k+ ++i++++    +   vg+ L  vqe +  +k+++ +++++ +++ + + ++l++ ++      +k ++ife++   +
  EPA05401.1 288 SIKEVLGKIDKIETEINSLSHRADSTAFVGEGLKSVQEDFTNFKKNVFEKTDNIEQKISsVSDILKRQDAltseFHKKSDKIFEEMqsvK 377
                 5667899999***********************************998888887666445666666655422224456666777764431 PP

>> RPW8  Arabidopsis broad-spectrum mildew resistance protein RPW8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.9     0.033        16      12      60 ..      50      98 ..      42     118 .. 0.77
   2 ?    6.9   1.5    0.0095       4.7      13      71 ..      75     133 ..      70     139 .. 0.92
   3 ?    4.8   0.6     0.043        21      17      67 ..     158     208 ..     151     225 .. 0.67
   4 ?    6.8   0.2      0.01       5.1      17      78 ..     223     284 ..     213     290 .. 0.86
   5 ?    1.4   0.0      0.47   2.3e+02      33      61 ..     285     313 ..     275     325 .. 0.62
   6 ?    2.8   1.4      0.18        88      13      70 ..     316     375 ..     312     406 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.033
        RPW8 12 algellkaileakkksldfksilkrLestleritPvvkeieklnkeldr 60
                 ++++ k+  + +k  +++k +++ L  tle+i+   k+i+ l+++ ++
  EPA05401.1 50 EIKSMSKIFGDNQKILVSMKGMIDTLSVTLENIQKQSKQINILEDDTQK 98
                5667777788888889999999999999999999999999988866544 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0095
        RPW8  13 lgellkaileakkksldfksilkrLestleritPvvkeieklnkeldrpreeieeLkkl 71 
                 l++ l+ i +++k+    +   ++L + l+++++  + + k+n++ +r +ee+ ++++l
  EPA05401.1  75 LSVTLENIQKQSKQINILEDDTQKLYAGLNHVRTQSDLVSKINEQTQRLQEEVTKINEL 133
                 7889999********************************************99998765 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.043
        RPW8  17 lkaileakkksldfksilkrLestleritPvvkeieklnkeldrpreeiee 67 
                  ++i++ +++  +++  l++      +++ + kei++l++ +d+ +++ ++
  EPA05401.1 158 SQMIIKIAQRIDEVRDDLRKVSGKTDSLADIGKEIDNLRNSIDEINKKADN 208
                 567777777777777777777777777777777777777777666665544 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.01
        RPW8  17 lkaileakkksldfksilkrLestleritPvvkeieklnkeldrpreeieeLkklLekaekL 78 
                 l  i++  + +++++s l+ ++  + +i+    +i++l  +++  ++++  +  + ++a +L
  EPA05401.1 223 LGKIKDDVNSVSKTSSELEAIKVAIDTIAVKASKIDSLGGVIEGLKQQFTTIAGKADSASDL 284
                 55688999999****************************99999999999888777777665 PP

  == domain 5  score: 1.4 bits;  conditional E-value: 0.47
        RPW8  33 ilkrLestleritPvvkeieklnkeldrp 61 
                 +++++++ l +i  + +ei++l+++ d+ 
  EPA05401.1 285 SMNSIKEVLGKIDKIETEINSLSHRADST 313
                 45555566666666666666666665555 PP

  == domain 6  score: 2.8 bits;  conditional E-value: 0.18
        RPW8  13 lgellkaileakkk.sldfksilkrLestleritPvvkeieklnkel.drpreeieeLkk 70 
                 +ge lk + e + +  +++  + +++e+ +++++ ++k+ + l+ e+ ++ ++ +ee+++
  EPA05401.1 316 VGEGLKSVQEDFTNfKKNVFEKTDNIEQKISSVSDILKRQDALTSEFhKKSDKIFEEMQS 375
                 566677776655441344456789999****************99997777777777654 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   6.0         2   9.9e+02      68     149 ..      48     121 ..       9     136 .. 0.45
   2 ?    2.5   5.4      0.21     1e+02      87     157 ..     105     177 ..      76     190 .. 0.50
   3 ?    3.2   0.3      0.13        66      80     126 ..     197     243 ..     178     271 .. 0.67
   4 ?   10.6   1.7    0.0007      0.35      59     171 ..     276     389 ..     271     394 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 2
      DUF745  68 eqelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektqlleaAkkRve 149
                 ++e++  ++++ + +k l s +  +++ + + +++q+q ++++ l + +++ ++ +++v        + +++l+ + +++ +
  EPA05401.1  48 QKEIKSMSKIFGDNQKILVSMKGMIDTLSVTLENIQKQSKQINILEDDTQKLYAGLNHV--------RTQSDLVSKINEQTQ 121
                 33333333333333333333333333333333333332222222222222222222222........222222222222222 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.21
      DUF745  87 sseanakaaakaakq...aqqqlealkallkaakenlenaeqvaagaqqelaektqlleaAkkRveeLkkqlke 157
                 +  ++ ++++k+++q    q++++ +++l k++ ++ e +++v + + + +++ +q++ +  +R++e++ +l++
  EPA05401.1 105 HVRTQSDLVSKINEQtqrLQEEVTKINELQKTSPKTPELSQRV-EDSMNAMRNNSQMIIKIAQRIDEVRDDLRK 177
                 3333333333333330003333333333333333333333333.344456777788888888888888777765 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.13
      DUF745  80 eekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqv 126
                 +  +++++   n+++ ++++++ +q+l  +k+ +++++++ +++e++
  EPA05401.1 197 NSIDEINKKADNMEVSSQIVTSLNQELGKIKDDVNSVSKTSSELEAI 243
                 33344555566777777777777777777777777777776666655 PP

  == domain 4  score: 10.6 bits;  conditional E-value: 0.0007
      DUF745  59 GKqqlveqle.qelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektqlleaAkkRveeLkkqlk 156
                 GK      l  ++++e    +++++++++s ++ a+++a + +  ++  e ++++ k++ e+ +n+eq  ++++  l+ + +l  + +k+ +++ ++++
  EPA05401.1 276 GKADSASDLSmNSIKEVLGKIDKIETEINSLSHRADSTAFVGEGLKSVQEDFTNFKKNVFEKTDNIEQKISSVSDILKRQDALTSEFHKKSDKIFEEMQ 374
                 5555555554145778888889999999999999999999999999999************************************************** PP

      DUF745 157 earkdlektkkaAyk 171
                 ++++  +kt k+ +k
  EPA05401.1 375 SVKNVTNKTAKESSK 389
                 ****99999998877 PP

>> eIF3_N  eIF3 subunit 6 N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   1.3    0.0056       2.8      55     124 ..      21      97 ..       2     102 .. 0.67
   2 ?    9.6   4.4    0.0024       1.2      56     122 ..     319     383 ..     284     401 .. 0.76
   3 ?    1.6   2.7      0.71   3.5e+02      65     102 ..     360     405 ..     353     435 .. 0.49

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0056
      eIF3_N  55 kelegeeevpeelekkreevleeleeleeeaekvlell.edeevvsnlrs......dkkqnlefLkeehgitpemid 124
                 k++ + e +p+++ kk ++v +  ++l++e++++ +++ +++++  +++          +n++  +++ +i ++  +
  EPA05401.1  21 KKVTKREPTPAAVLKKVAAVTDSSKALQKEIKSMSKIFgDNQKILVSMKGmidtlsVTLENIQKQSKQINILEDDTQ 97 
                 45556667999***************************556666666655443333333444444455555555555 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0024
      eIF3_N  56 elegeeevpeelekkreevleeleeleeeaekvlelledee.vvsnlrsdkkqnlefLkeehgitpem 122
                      ++v+e++++ +++v+e+ +++e+++++v ++l++++  +s+ ++ + +++e +++  ++t ++
  EPA05401.1 319 G---LKSVQEDFTNFKKNVFEKTDNIEQKISSVSDILKRQDaLTSEFHKKSDKIFEEMQSVKNVTNKT 383
                 3...4568899**************************6655055667777777777777777776654 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.71
      eIF3_N  65 eelekkreevleeleeleee........aekvlelledeevvsnlr 102
                 +e+ kk ++++ee++++++         +++++ ll+ +e +sn+r
  EPA05401.1 360 SEFHKKSDKIFEEMQSVKNVtnktakesSKEMMALLKLSEYQSNIR 405
                 4555555555555555555411111111333333333334444433 PP

>> DUF3365  Protein of unknown function (DUF3365)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   2.4       3.2   1.6e+03      51      68 ..     141     172 ..      41     237 .. 0.66
   2 ?    9.7   0.2    0.0019      0.97      12      67 ..     349     435 ..     344     493 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 3.2
                 ...............--GGGGS--SHHHHHHH CS
     DUF3365  51 i..............vpayaareiaeefsekr 68 
                                + ++++ +ia+++ e r
  EPA05401.1 141 PelsqrvedsmnamrNNSQMIIKIAQRIDEVR 172
                 02233333334444555566666666665555 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0019
                 XXXXXXXXX--HHHHHHHHHHHHHHHHHHHHHHTTS-S.................................--GGGGS--SHHHHHH CS
     DUF3365  12 lslrsqkrqaeeealekarllaeqleavreyvakslkp....ti...........................vpayaareiaeefsek 67 
                  ++ +++ ++ +e ++k++ ++e++++v+++++k+ k+    ++                           + a+ + ei + f + 
  EPA05401.1 349 SDILKRQDALTSEFHKKSDKIFEEMQSVKNVTNKTAKEsskeMMallklseyqsnirmnaeskygeikdleNMATQTAEIVNLFDRL 435
                 45566677799************************9954444113344444444445555555566666555555555555555555 PP

>> DUF2730  Protein of unknown function (DUF2730)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   1.2     0.012       5.8      25      95 ..      41     112 ..      30     116 .. 0.87
   2 ?    1.9   0.8      0.47   2.3e+02      38      76 ..     112     151 ..     110     188 .. 0.53
   3 ?    6.3   0.7      0.02       9.8      39      94 ..     158     214 ..     149     223 .. 0.81
   4 ?    2.4   0.1      0.33   1.6e+02      34      81 ..     208     256 ..     203     283 .. 0.73
   5 ?    4.9   0.1     0.055        27      70      94 ..     287     311 ..     243     312 .. 0.79
   6 ?   -1.4   0.3         5   2.5e+03      40      48 ..     374     382 ..     340     431 .. 0.59

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.012
     DUF2730  25 ldskYakredleklaekveendkrlteletkvenLP.takdlekLkllladlrgelkaleaevrqlshqvdL 95 
                  ds  a +++++++ ++  +n+k l +++  +++L  t ++++k +++++ l+ ++++l a ++++++q+dL
  EPA05401.1  41 TDSSKALQKEIKSMSKIFGDNQKILVSMKGMIDTLSvTLENIQKQSKQINILEDDTQKLYAGLNHVRTQSDL 112
                 5666677899999999999****************746788999999************************9 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.47
     DUF2730  38 laekveendkrlteletkvenL....PtakdlekLkllladlr 76 
                 l+ k++e+ +rl+e  tk+++L    P +    +L+  ++d  
  EPA05401.1 112 LVSKINEQTQRLQEEVTKINELqktsPKTP---ELSQRVEDSM 151
                 556677777777777777777732223333...3333333332 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.02
     DUF2730  39 aekveendkrlteletkvenLPtakd.lekLkllladlrgelkaleaevrqlshqvd 94 
                  +++ ++ +r++e+   + ++  + d l+++ +++ +lr  +++++++ ++++  ++
  EPA05401.1 158 SQMIIKIAQRIDEVRDDLRKVSGKTDsLADIGKEIDNLRNSIDEINKKADNMEVSSQ 214
                 4667788899999999999998665549********************999987665 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.33
     DUF2730  34 dleklaekveendkrlteletkvenLP.takdlekLkllladlrgelka 81 
                 ++e   ++v++ ++ l +++  v+++  t ++le++k+ +  +  + ++
  EPA05401.1 208 NMEVSSQIVTSLNQELGKIKDDVNSVSkTSSELEAIKVAIDTIAVKASK 256
                 3444467788888888888888888853677888888888877666555 PP

  == domain 5  score: 4.9 bits;  conditional E-value: 0.055
     DUF2730  70 llladlrgelkaleaevrqlshqvd 94 
                   ++++ g+++++e e+++lsh++d
  EPA05401.1 287 NSIKEVLGKIDKIETEINSLSHRAD 311
                 46899*****************976 PP

  == domain 6  score: -1.4 bits;  conditional E-value: 5
     DUF2730  40 ekveendkr 48 
                 ++v++  ++
  EPA05401.1 374 QSVKNVTNK 382
                 333333333 PP

>> FliT  Flagellar protein FliT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1       3.1   1.5e+03      44      81 ..      51      88 ..      31      91 .. 0.73
   2 ?    9.7   3.2    0.0029       1.4      13      76 ..     116     179 ..     108     184 .. 0.84
   3 ?    0.9   0.0       1.6     8e+02       9      32 ..     181     206 ..     179     239 .. 0.53
   4 ?   -1.4   0.0       8.9   4.4e+03      31      74 ..     300     347 ..     275     357 .. 0.61
   5 ?   -0.5   0.2       4.5   2.2e+03      36      57 ..     407     428 ..     352     444 .. 0.58

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 3.1
                HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHTHHHHHH CS
        FliT 44 rellrrilandaeirallqprldelqkllgalrrqrka 81
                 + +++i  ++++i   ++   d l+  l ++++q k 
  EPA05401.1 51 IKSMSKIFGDNQKILVSMKGMIDTLSVTLENIQKQSKQ 88
                23445899999999999999999999999999999875 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0029
                 HHHHHHHHHHHHHHHHCS-.-ST--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHTH CS
        FliT  13 laaleaerqqlverlreld.aaplspaereekrellrrilandaeirallqprldelqkllgalr 76 
                 ++++ ++ q+ v ++ el+ ++p +p+++++ ++ ++ ++ n + i +++ +r de++++l++++
  EPA05401.1 116 INEQTQRLQEEVTKINELQkTSPKTPELSQRVEDSMNAMRNNSQMIIKIA-QRIDEVRDDLRKVS 179
                 6788888999999999999999**********999998887777777665.69*******99875 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 1.6
                 -HHHHHHHHHHHHHHHHHHHCS-..- CS
        FliT   9 dWdelaaleaerqqlverlreld..a 32 
                 + d+la+  +e  +l ++++e++  a
  EPA05401.1 181 KTDSLADIGKEIDNLRNSIDEINkkA 206
                 56667777777666666666666221 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 8.9
                 -....-ST--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCH CS
        FliT  31 d....aaplspaereekrellrrilandaeirallqprldelqkllga 74 
                 +    +   +++ ++   e l+ ++++    ++ + ++ d +++++++
  EPA05401.1 300 EteinSLSHRADSTAFVGEGLKSVQEDFTNFKKNVFEKTDNIEQKISS 347
                 333344444456666666666666666666666666666666666655 PP

  == domain 5  score: -0.5 bits;  conditional E-value: 4.5
                 -HHHHHHHHHHHHHHHHHHHHH CS
        FliT  36 spaereekrellrrilandaei 57 
                 +++ +    + l+ + ++ aei
  EPA05401.1 407 NAESKYGEIKDLENMATQTAEI 428
                 2333333333333444444444 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6  12.1      0.64   3.2e+02      33     146 ..      65     177 ..       3     184 .. 0.73
   2 ?    7.3   8.8     0.012         6      15     112 ..     143     239 ..     111     283 .. 0.45
   3 ?    3.5   8.0      0.17        86      47     115 ..     320     400 ..     262     442 .. 0.49

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.64
        Fez1  33 ivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelselsleeeeaa.lesdeakaqrqeaeel 130
                 +v++k+ +  l+ +le+ +++ k+++  le+ t++l    n ++ +++ ++ ++e++++l+ee++++ e l+++s+++ e +    d+++a r++++ +
  EPA05401.1  65 LVSMKGMIDTLSVTLENIQKQSKQINI-LEDDTQKLYAGLNHVRTQSDLVSKINEQTQRLQEEVTKINE-LQKTSPKTPELSqRVEDSMNAMRNNSQMI 161
                 566667777777777777776666653.45555666666677777788888888888888888888877.66666665555414445566777888888 PP

        Fez1 131 eelkreverlraeLke 146
                  +  ++++++r  L++
  EPA05401.1 162 IKIAQRIDEVRDDLRK 177
                 8888888888888876 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.012
        Fez1  15 LKqQLkdsqaevtqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelselsleeee 112
                 L q   ds + + +  + i+++  ++ e+r +l++   ++++l +   +  ++l +  +e+++k ++ e+ ++ v++l++el +++++++++s++++e
  EPA05401.1 143 LSQRVEDSMNAMRNNSQMIIKIAQRIDEVRDDLRKVSGKTDSLADIG-KEIDNLRNSIDEINKKADNMEVSSQIVTSLNQELGKIKDDVNSVSKTSSE 239
                 22333333333333344444444444444444444444444433322.22333444444444444444444444444444444444444444433333 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.17
        Fez1  47 leekeeeikeleesleektle....levcenelqrkkseaellrekvekleeelkelreelselsleeeeaa........l 115
                 l++ +e  +++++++ ekt++    +  + + l+r+ + ++ +++k +k+ ee++++++  +++++e+++++        +
  EPA05401.1 320 LKSVQEDFTNFKKNVFEKTDNieqkISSVSDILKRQDALTSEFHKKSDKIFEEMQSVKNVTNKTAKESSKEMmallklseY 400
                 333333344444444444443111122334444455555555555555555555555554444333333333333333221 PP

>> Osmo_CC  Osmosensory transporter coiled coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1       2.3   1.2e+03      21      34 ..     113     129 ..     111     145 .. 0.71
   2 ?   -0.7   0.1       3.5   1.7e+03      17      40 ..     164     187 ..     163     188 .. 0.87
   3 ?    0.1   0.2         2     1e+03      23      33 ..     187     197 ..     182     211 .. 0.54
   4 ?    2.7   0.0       0.3   1.5e+02      20      34 ..     295     309 ..     291     314 .. 0.87
   5 ?    4.7   0.1     0.071        35      12      25 ..     336     349 ..     332     359 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 2.3
                 HHHHHHHHHHHHH...H CS
     Osmo_CC  21 vedideeIaaLee...k 34 
                 v  i+e+ ++L+e   k
  EPA05401.1 113 VSKINEQTQRLQEevtK 129
                 56788888999885553 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 3.5
                 HHHHHHHHHHHHHHHHHHHHHHHH CS
     Osmo_CC  17 IEqkvedideeIaaLeekRqrLvd 40 
                 I q+++++  ++ +   k ++L+d
  EPA05401.1 164 IAQRIDEVRDDLRKVSGKTDSLAD 187
                 889*****9999999999888876 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 2
                 HHHHHHHHHHH CS
     Osmo_CC  23 dideeIaaLee 33 
                 di +eI +L +
  EPA05401.1 187 DIGKEIDNLRN 197
                 55555555543 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.3
                 HHHHHHHHHHHHHHH CS
     Osmo_CC  20 kvedideeIaaLeek 34 
                 k++ i++eI+ L  +
  EPA05401.1 295 KIDKIETEINSLSHR 309
                 89********99877 PP

  == domain 5  score: 4.7 bits;  conditional E-value: 0.071
                 XXXTHHHHHHHHHH CS
     Osmo_CC  12 ehYdnIEqkvedid 25 
                 e+ dnIEqk+  + 
  EPA05401.1 336 EKTDNIEQKISSVS 349
                 5669******8876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (512 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2868  (0.159964); expected 358.6 (0.02)
Passed bias filter:                      588  (0.032796); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        65  (0.00362541); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              36  [number of targets reported over threshold]
# CPU time: 1.36u 0.37s 00:00:01.73 Elapsed: 00:00:00.61
# Mc/sec: 2526.56
//
Query:       EPA05402.1  [L=228]
Description: ERCC4 domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.2e-23   82.3   0.0    6.9e-23   81.6   0.0    1.4  1  ERCC4       ERCC4 domain
    1.8e-09   38.0   0.0    1.9e-08   34.8   0.0    2.2  2  HHH_5       Helix-hairpin-helix domain
    6.1e-07   29.0   0.0     0.0093   15.8   0.0    2.5  2  HHH         Helix-hairpin-helix motif
      4e-05   23.6   0.0    0.00011   22.2   0.0    1.8  2  HHH_2       Helix-hairpin-helix motif
    8.3e-05   22.8   0.0      0.015   15.6   0.0    2.4  2  HHH_3       Helix-hairpin-helix motif
     0.0041   17.7   0.1      0.011   16.3   0.1    1.8  1  5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
  ------ inclusion threshold ------
       0.01   16.2   0.1        1.4    9.4   0.0    2.4  2  HHH_8       Helix-hairpin-helix domain


Domain annotation for each model (and alignments):
>> ERCC4  ERCC4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.6   0.0   2.7e-26   6.9e-23       1     156 []      10     131 ..      10     131 .. 0.92

  Alignments for each domain:
  == domain 1  score: 81.6 bits;  conditional E-value: 2.7e-26
                 EEGGGCTSHHHH..HHTTTSEEEEE--SSSSE.EE...CTT...............EEEEEEEHHHHHHHHCCSHHHHHHHHHHH.H-SEEEEEEES-G CS
       ERCC4   1 iDsrelksgieeylleelgvevvietlpigdyilwrrkvkaeynleldieepceekvlverksaddlvasikdgrleeqvsrlkrngykkpillvegld 99 
                 +D+re ksgi++  l + g++++ +tlpigdy ++    ++                +verks++dl +s+ dgrl++q+srlk+ +++ pi+l eg+ 
  EPA05402.1  10 VDERERKSGIPDL-LTSVGLNIEMKTLPIGDY-IV---APE---------------TVVERKSIRDLMSSVFDGRLFDQCSRLKE-HFEFPIVLMEGNV 87 
                 8****99******.9*****************.77...788...............*****************************.***********66 PP

                 GGTT................THHH.HHHHHHHHHHHHS-EEEEESSHHHHHHHHHHH CS
       ERCC4 100 qykrknknsrnkqykakvrqinrktiesaLvqlqldfgvsilttesanetaewlanl 156
                    + +               n+   ++aL+++ +df+++i+ t sa +ta++l +l
  EPA05402.1  88 DEIEEIT-------------ENPMIFYGALSTVVIDFKIPIIPTPSAIHTAKLLVSL 131
                 6666532.............55557****************************9875 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.41     1e+03      18      41 ..      72      94 ..      70      95 .. 0.83
   2 !   34.8   0.0   7.4e-12   1.9e-08       3      52 ..     159     207 ..     157     213 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.41
                HHTTT--SHHHHHHS-HHHHHTST CS
       HHH_5 18 llsaGiesvedlaaadveeLakip 41
                l ++ +e++  l++ +v+e+ +i+
  EPA05402.1 72 LKEH-FEFPIVLMEGNVDEIEEIT 94
                6667.8899999*******99985 PP

  == domain 2  score: 34.8 bits;  conditional E-value: 7.4e-12
                 HHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHH CS
       HHH_5   3 eLlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAerii 52 
                 +L s++GiG+k A+++l + ++++ ++  a++ eLak+ G+G  +A++i+
  EPA05402.1 159 SLCSLPGIGEKFAVRMLQK-FGTPLKVYTATTSELAKVEGLGDARAKKIK 207
                 5889***************.*****************************6 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0   0.00017      0.43      11      22 ..     158     169 ..     150     171 .. 0.84
   2 !   15.8   0.0   3.6e-06    0.0093       5      28 ..     184     207 ..     181     209 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00017
                 HHHHTSTT-SHH CS
         HHH  11 eeLlalPGVGpk 22 
                   L++lPG+G+k
  EPA05402.1 158 SSLCSLPGIGEK 169
                 68*********9 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 3.6e-06
                 HHTSSHHHHHTSTT-SHHHHHHHH CS
         HHH   5 lipasreeLlalPGVGpktAeaIl 28 
                 + +a+  eL++++G G ++A +I 
  EPA05402.1 184 VYTATTSELAKVEGLGDARAKKIK 207
                 689******************996 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       3.8   9.8e+03      29      41 ..      82      94 ..      72      95 .. 0.65
   2 !   22.2   0.0   4.4e-08   0.00011       7      58 ..     162     213 ..     152     217 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 3.8
       HHH_2 29 LkkasleeLlevd 41
                L++ +++e+ e+ 
  EPA05402.1 82 LMEGNVDEIEEIT 94
                5566666666664 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 4.4e-08
       HHH_2   7 GIrhVGektAklLakrFksldaLkkasleeLlevddiGeeiAqsivefFene 58 
                 +++ +Gek A  + ++F++  +  +a++ eL++v++ G+  A++i+  +e++
  EPA05402.1 162 SLPGIGEKFAVRMLQKFGTPLKVYTATTSELAKVEGLGDARAKKIKHVLESQ 213
                 5799*****************************************9998876 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.015        39      13      31 ..     157     175 ..     151     177 .. 0.84
   2 !   15.6   0.0   5.7e-06     0.015      10      30 ..     186     206 ..     179     212 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.015
       HHH_3  13 aeeLqklpGlgpklAknIv 31 
                 ++ L  lpG+g+k+A +++
  EPA05402.1 157 LSSLCSLPGIGEKFAVRML 175
                 678999*********8875 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 5.7e-06
       HHH_3  10 tAsaeeLqklpGlgpklAknI 30 
                 tA+ +eL+k++Glg++ Ak+I
  EPA05402.1 186 TATTSELAKVEGLGDARAKKI 206
                 9*******************9 PP

>> 5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   4.5e-06     0.011      23      67 ..     163     217 ..     156     226 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.5e-06
  5_3_exonuc  23 vpgiGektAakLlkeygsleeilenld.elke.........kklkekLeenkeea 67 
                  pgiGek A+++l+++g+  +++ ++  el++         kk+k+ Le + +++
  EPA05402.1 163 LPGIGEKFAVRMLQKFGTPLKVYTATTsELAKveglgdaraKKIKHVLESQSKHL 217
                 79*********************98754444444465555566666666665554 PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0    0.0063        16      44      62 ..     154     173 ..     143     178 .. 0.72
   2 ?    9.4   0.0   0.00053       1.4      31      68 .]     171     211 ..     170     211 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0063
                 HHTT..HCTTSTT--HHHHHH CS
       HHH_8  44 slee..eltklpgiGkkiaak 62 
                   ++  +l +lpgiG+k a +
  EPA05402.1 154 K-QQlsSLCSLPGIGEKFAVR 173
                 3.3355699********9865 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00053
                 HHCCCCC-SS-HHHHTT...HCTTSTT--HHHHHHHHHHHH CS
       HHH_8  31 Aaraiealpeeitslee...eltklpgiGkkiaakieeile 68 
                 A+r + + +++++ + +   el k+ g+G++ a+ki+  le
  EPA05402.1 171 AVRMLQKFGTPLKVYTAttsELAKVEGLGDARAKKIKHVLE 211
                 677777777777777333567***************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.58u 0.36s 00:00:00.94 Elapsed: 00:00:00.55
# Mc/sec: 1246.23
//
Query:       EPA05403.1  [L=131]
Description: hypothetical protein BG20_I0709 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.15   13.0   0.9       0.22   12.5   0.1    1.6  2  DUF4284   Immunity protein 22


Domain annotation for each model (and alignments):
>> DUF4284  Immunity protein 22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1      0.62   1.1e+04      79      90 ..      12      21 ..       3      31 .. 0.55
   2 ?   12.5   0.1   1.2e-05      0.22      51     109 ..      45      96 ..      40     102 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.62
     DUF4284 79 klkekklnkana 90
                ++  +++n++n 
  EPA05403.1 12 AC--NQMNQING 21
                33..45555554 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 1.2e-05
     DUF4284  51 fleteaedieellekvsldseiieklkeklkekklnkanavillydkeyseitekkaed 109
                  le+++++ie l+++++ld +    + +++ +++l ++na++ + +k+  +i++ +++d
  EPA05403.1  45 PLEKDQQKIEMLFMEMALDLS----MRKEF-DNTLGSINAIVSYRNKT--NIITIPHQD 96 
                 568899999999999999999....44444.7888***********99..455555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 814.87
//
Query:       EPA05404.1  [L=80]
Description: hypothetical protein BG20_I0717 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-06   27.2   0.0    3.4e-06   27.1   0.0    1.1  1  Pcc1      Transcription factor Pcc1


Domain annotation for each model (and alignments):
>> Pcc1  Transcription factor Pcc1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   1.9e-10   3.4e-06       4      70 ..       6      72 ..       3      76 .. 0.90

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 1.9e-10
                EEEE-SSHHHHHHHHHHHHHHCHC-TTE.CEEEEEEETTEEEEEEEESSHHHHHHHHHHHHHHHHHHH CS
        Pcc1  4 isvpfpterlAsialrtLqvDkelspla.vkrslslegnvLqveykAttnrmLRvavngfleslglvl 70
                 ++ ++ +++ +++++++  D+e  p++ +k  +s ++ +++++++++   +LR+ +n+ l++++   
  EPA05404.1  6 AKIIVDAKEKTKAIFQSINTDNEFYPENpTKTRMSMDD-KITITIESEYIPHLRANLNSTLRLIQASY 72
                56777889999*************************77.***********************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.35s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 471.58
//
Query:       EPA05405.1  [L=187]
Description: tRNA intron endonuclease [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-19   69.7   0.3    3.2e-19   68.8   0.1    1.6  2  tRNA_int_endo    tRNA intron endonuclease, catalytic C-termin
    3.1e-13   49.2   4.5    1.1e-12   47.4   1.1    2.3  2  tRNA_int_endo_N  tRNA intron endonuclease, N-terminal domain


Domain annotation for each model (and alignments):
>> tRNA_int_endo  tRNA intron endonuclease, catalytic C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.57   5.1e+03      24      32 ..      45      53 ..      25      70 .. 0.67
   2 !   68.8   0.1   3.6e-23   3.2e-19       3      85 .]      83     166 ..      81     167 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.57
                   GTSSEEEET CS
  tRNA_int_endo 24 FGadFrvYq 32
                   F + +++Y 
     EPA05405.1 45 FESLYLLYS 53
                   566677773 PP

  == domain 2  score: 68.8 bits;  conditional E-value: 3.6e-23
                    HHHHHHHHHHHTT-EEEECGGGTSSEEEE.TSCTTTSSCSEEEEEEETTSEEEHHHHHHHHHHHHHTTSEEEEEEETTTSCEEE CS
  tRNA_int_endo   3 lkyavyrdLrekGyvvrsGlkFGadFrvY.qrrpslehseylVvvvsedeeldwpdlsaavrlahsvkKklilaivdaegdvty 85 
                    +k+ +yrdL+++Gyvv++G+ FG+dFrvY +++ +++ +++l++ ++e+++ ++  l+++++ ++++ K+ ++a++++ g+v y
     EPA05405.1  83 TKFLIYRDLKTRGYVVKDGFGFGSDFRVYeRGQFGEKGAKFLIFGLNEGQQEKMGALQKKIEQITQMGKEPVIAVIERRGEVIY 166
                    799**************************777889999*****************************************99876 PP

>> tRNA_int_endo_N  tRNA intron endonuclease, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.4   1.1   1.2e-16   1.1e-12       1      67 []       7      71 ..       7      71 .. 0.96
   2 ?    2.8   0.1     0.011        96      20      42 ..     109     130 ..     106     132 .. 0.85

  Alignments for each domain:
  == domain 1  score: 47.4 bits;  conditional E-value: 1.2e-16
                     EEEEEETTEEEESSHHHHHHHHHTTT-SEECCTSSEEEEHHHHHHHHHTTSEEEETTSEEE-HHHHH CS
  tRNA_int_endo_N  1 vegeLsgdrvlvedeeaakrlyekgfYGkplidepLqLslvEAlYLlekGklevvkggeplsfeell 67
                     v+geL++d+ +++++e++++ ++ ++YG+  ++e+L+L+ +E+lYLl+ +kl + kg+++++f++l+
       EPA05405.1  7 VKGELVSDQTCISNKEMIHE-LQLKGYGE-IEKEKLFLKSFESLYLLYSEKLILHKGKRTINFDDLM 71
                     69******************.77888***.***********************************97 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.011
                      HHHHTTT-SEECCTSSEEEEHHH CS
  tRNA_int_endo_N  20 rlyekgfYGkplidepLqLslvE 42 
                      r+ye+g +G+ +  + L   l E
       EPA05405.1 109 RVYERGQFGE-KGAKFLIFGLNE 130
                      79********.999999877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.35s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 1054.82
//
Query:       EPA05406.1  [L=122]
Description: hypothetical protein BG20_I0729 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    0.00022   21.4   1.7    0.00023   21.3   0.8    1.5  2  Spore_YabQ  Spore cortex protein YabQ (Spore_YabQ)


Domain annotation for each model (and alignments):
>> Spore_YabQ  Spore cortex protein YabQ (Spore_YabQ)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.8   1.3e-08   0.00023      28      69 ..      32      73 ..      15      80 .. 0.86
   2 ?   -3.1   0.0      0.55   9.9e+03      56      62 ..     109     115 ..      94     118 .. 0.67

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.3e-08
  Spore_YabQ 28 kvltfieDilfwllaallvflfllrinygelrlylflgillG 69
                    fi+D+ f ++++++  l++++i +  + +ylf g+llG
  EPA05406.1 32 PHTSFITDLAFIMIIGAIATLAFFKIKQPLIIGYLFGGMLLG 73
                44689************************************9 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.55
  Spore_YabQ  56 gelrlyl 62 
                  e+r y+
  EPA05406.1 109 SEIRCYF 115
                 4666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.51
# Mc/sec: 724.88
//
Query:       EPA05407.1  [L=97]
Description: hypothetical protein BG20_I0711 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.048   13.8   0.0       0.05   13.8   0.0    1.1  1  Spore-coat_CotZ  Spore coat protein Z


Domain annotation for each model (and alignments):
>> Spore-coat_CotZ  Spore coat protein Z
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.8e-06      0.05      45     112 ..      25      92 ..       5      97 .] 0.77

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.8e-06
  Spore-coat_CotZ  45 lgekessskadTipfiLyckdgkpfkafgv....sksaddfkcvesiiFrvekvddknCavLelLepkkkld 112
                      +   +++s  +T+   Ly ++ + fk        + +a + +++ s + r++ +  + C  LelL   ++++
       EPA05407.1  25 H---SNTSDLETVLNRLYHRENEIFKRIVIairiNDDA-QSTMLASELLRIRVLKRNICFALELLYNYNTRH 92 
                      2...34778899999***********987776533333.36678*********************6665544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.33s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 588.21
//
Query:       EPA05408.1  [L=169]
Description: ribosomal protein L16 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-24   86.1   0.3    2.3e-24   85.9   0.3    1.1  1  Ribosomal_L16  Ribosomal protein L16p/L10e


Domain annotation for each model (and alignments):
>> Ribosomal_L16  Ribosomal protein L16p/L10e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.9   0.3   1.3e-28   2.3e-24       3     131 ..      11     158 ..       9     159 .. 0.93

  Alignments for each domain:
  == domain 1  score: 85.9 bits;  conditional E-value: 1.3e-28
                    SSXXBSSSXXSSTSXX.XSXXXXXESX.......EEEEESSXEEEEHHHHHHHHHHHCTCCCCTSXC...EEXXSXXXXEEEEE-.....SS-TTT CS
  Ribosomal_L16   3 rkkyrKsrkryirgvs.tkgtklefgd.......ygLvalekgqltaealeaariainrylkkkrgk...klwirvfphhpvtkk.....agedRm 82 
                     +++ +++  +i+g +  k+ k++ g+       ++L ++ek q+++ a+e++r+a+n+ l++++g+     ++r++ph  ++++     ag+dR+
     EPA05408.1  11 GQPFCRKE--FIKGNPqIKIAKFQGGKranydycVQLLINEKVQIRHMAIESCRLAANKLLEQTTGEtgyFSRLRIYPHVLLRENkmvatAGADRI 104
                    56777878..99********************9999**************************999999988899********************** PP

                    SSSS....XEEEEEEEEEXSSCEEEEE..TTXXXSHHHHHHHHHHHHTSSSXEEE CS
  Ribosomal_L16  83 gkGk....Gkpegwvarvkigqiifei..kagvneeiakealrraasKlpiktki 131
                    ++G+    Gk +   arv  gq i+e+  +a  + e+ak+al  a  K+p+ + i
     EPA05408.1 105 SEGMrrawGKATSLGARVARGQCIMEFyvNA-PHLEKAKKALSSACVKIPGTATI 158
                    ***************************7433.59****************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 1029.18
//
Query:       EPA05409.1  [L=212]
Description: RNA polymerase Rpb3/Rpb11 dimerization domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.4e-25   87.5   0.0    1.4e-24   86.6   0.0    1.5  1  RNA_pol_A_bac  RNA polymerase Rpb3/RpoA insert domain
    1.8e-14   52.9   0.0    2.2e-14   52.6   0.0    1.1  1  RNA_pol_L      RNA polymerase Rpb3/Rpb11 dimerisation domain
  ------ inclusion threshold ------
      0.042   13.4   0.2      0.063   12.9   0.2    1.2  1  DUF2401        Putative TOS1-like glycosyl hydrolase (DUF2401


Domain annotation for each model (and alignments):
>> RNA_pol_A_bac  RNA polymerase Rpb3/RpoA insert domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.6   0.0   2.4e-28   1.4e-24       1     112 []      45     157 ..      45     157 .. 0.93

  Alignments for each domain:
  == domain 1  score: 86.6 bits;  conditional E-value: 2.4e-28
                    EEEEECTSSS.HHHHHCHHHCSTCBSSCHHHHHHHHCTT-ETSSSSTTCSEEEEEEEEESSEC...EEGGGCBESSSSCEESSTTSEEEEEETT-E CS
  RNA_pol_A_bac   1 VeieentsvlqDEvvaHrlgliplvsedvleillnlkelveeeeegeeeksvelkLnvkgpge...vtagdlkledadveivnpdilIakLrkgqe 93 
                    V i+en+svl DE +aHrlglipl+++  ++  +   ++  + e+g+++++v l L+   ++    + +++l++ed++v++ +++i+I++L+ gq+
     EPA05409.1  45 VDIIENSSVLPDEGLAHRLGLIPLQTDLSRF--NEPSKCDCKSETGCSNCKVMLVLDSGDSDVtrtILSNELTSEDESVKPTSDKIPIVQLAAGQR 138
                    789**********************888777..778888536799***********9988777788****************************** PP

                    EEEEEEEEEESSEECTTT- CS
  RNA_pol_A_bac  94 leleakvkkGiGkehakfs 112
                    +++e++++ G+G ehak++
     EPA05409.1 139 IKVECYARLGRGTEHAKWN 157
                    ******************7 PP

>> RNA_pol_L  RNA polymerase Rpb3/Rpb11 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.6   0.0   3.7e-18   2.2e-14       3      68 ..      17     199 ..      15     200 .. 0.81

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 3.7e-18
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxx....................................................................... RF
   RNA_pol_L   3 llrgvdhtlgNaLRrillsevpgvaiea....................................................................... 30 
                  l+gv + ++NaLRri+l+ +p +ai++                                                                       
  EPA05409.1  17 KLKGVPLQYANALRRICLNGIPVFAIDTvdiienssvlpdeglahrlgliplqtdlsrfnepskcdcksetgcsnckvmlvldsgdsdvtrtilsnelt 115
                 6899**********************************************9999999999999999999999999999999999999888888888888 PP

                 .........................xxxxxx.........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
   RNA_pol_L  31 .........................pvvkvn.........................tdkdklilevetdgslkPeealkeAlkiLkek 68 
                                               +                         +++d+ il++e++g+lkPe++++ +++ L ++
  EPA05409.1 116 sedesvkptsdkipivqlaagqrikV----EcyarlgrgtehakwnssnisvltetNKDDERILTIESTGALKPEQIVLAGVDELSNR 199
                 88888887777774444444443330....14444444444444555555566777999*************************9886 PP

>> DUF2401  Putative TOS1-like glycosyl hydrolase (DUF2401)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   1.1e-05     0.063     137     182 ..      75     117 ..      68     147 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.1e-05
     DUF2401 137 YpgnaeCsCwk.sgCGelDifEvlesgseklkstlhtaqgaegggss 182
                 +++ ++C C++ +gC +  ++ vl+sg+++++ t+ +++ +    s+
  EPA05409.1  75 FNEPSKCDCKSeTGCSNCKVMLVLDSGDSDVTRTILSNELT----SE 117
                 556689***988**********************9999854....33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       723  (0.0403257); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.34s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 1194.16
//
Query:       EPA05410.1  [L=82]
Description: hypothetical protein BG20_I0734 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.26   11.5   2.7       0.28   11.3   1.9    1.7  2  DUF1492   Protein of unknown function (DUF1492)


Domain annotation for each model (and alignments):
>> DUF1492  Protein of unknown function (DUF1492)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.9   1.6e-05      0.28      32      61 ..       2      31 ..       1      58 [. 0.89
   2 ?   -1.2   0.0      0.13   2.3e+03      42      44 ..      55      57 ..      43      78 .. 0.48

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.6e-05
     DUF1492 32 ediekktaeaikkklelqrlidklensdsr 61
                e+i +k  e+i +k e++++i++l+ +d  
  EPA05410.1  2 EKIKQKIHETISNKDEIRQIIQSLSSIDNS 31
                899********************9998853 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.13
     DUF1492 42 ikk 44
                +++
  EPA05410.1 55 LNR 57
                333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1442  (0.0804284); expected 358.6 (0.02)
Passed bias filter:                      885  (0.0493614); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 468.90
//
Query:       EPA05411.1  [L=271]
Description: NAD(+)/NADH kinase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.1e-35  121.1   0.4      7e-35  120.6   0.4    1.2  1  NAD_kinase     ATP-NAD kinase
    2.7e-06   27.0   0.0    5.1e-06   26.1   0.0    1.4  1  DAGK_cat       Diacylglycerol kinase catalytic domain
     0.0019   18.7   0.0     0.0036   17.8   0.0    1.6  1  CoA_binding_2  CoA binding domain


Domain annotation for each model (and alignments):
>> NAD_kinase  ATP-NAD kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.6   0.4   1.2e-38     7e-35      65     291 ..      37     257 ..       4     258 .. 0.85

  Alignments for each domain:
  == domain 1  score: 120.6 bits;  conditional E-value: 1.2e-38
                 ..........EEECCC-TTTTTSSSEEEEEE-HHHHHHHHHHHHHCT-EEEEEES.SS--SS-SEEGGGHHHHHHHHHHT-SEEEEEEEEEEEEEETTE CS
  NAD_kinase  65 d.........dtrkaleafadagvdliivvGGDGTaldvarllqkaeiPvlgvna.Gvkgfltefepeaaaellekllegeirvekrevldavimrskg 153
                           +  ++l+++ +++ dl++++GGDGT+l+v+r l++ e P+l++n+ G+ g l+e+++e+++e++e++ ++++ ++kr+++ a+   +k+
  EPA05411.1  37 TispievegsKKVESLDELKKEKLDLVVTLGGDGTTLRVFRYLEN-ETPILTINVgGNRGILSEITIEEIDEAIERIEKDKFFLDKRTRVVASC-GGKE 133
                 134444444478889999**************************7.*********8999*****************************998664.4444 PP

                 ......EEEEEEESSEEEEEESSSSS-EEEEEEETTEEEEEEEESEEEEE-TGGGGTHHHHTT--EE-TT---EEEEEESESSS----EEE-TT-EEEE CS
  NAD_kinase 154 eediadiviensvlnevviirgpgstlielelyvdtelleadqldglivstPtGstayslsaGgplisPgvlailivpicPhslssrpiVvssssklri 252
                           + +lne++i r + ++ +e+e++ ++  + ++ +dg+i++tP Gst++s+s Ggp+++ +++ ++i+p+ P  + +  iVv++++ ++i
  EPA05411.1 134 ---------FPPALNEIYICRTNLTKTAEIEIKFQNDTV-KQKMDGVIIATPSGSTGHSFSLGGPILHESLDVLIITPVAPVYRLES-IVVPDEK-IEI 220
                 .........3678**************99***9988766.6799*************************************998876.6777776.665 PP

                 EE-SS--EEEEETTTEEEEE-TT-EEEEEEESSEEEEEE CS
  NAD_kinase 253 rvasrseallaldGseelelspgdevrvtasdkkfklir 291
                    s +++ +++d +    ++ g+ + + + +k++ ++r
  EPA05411.1 221 I--SSHDCSIVMDAQVVKSAGYGEPIIIKKYSKPAVFVR 257
                 5..9*********************99999999999998 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   8.6e-10   5.1e-06       9     113 ..      11     112 ..       5     117 .. 0.73

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 8.6e-10
                 TCTTTTHHHHH.HHCHHHHHHCTCEEEEEE--STTH.HHHHHHHHHHCC-SEEEEEESHHHHHHHHHHHCTHHCTTSEEEEEE-SS--HHHHHCT--SS CS
    DAGK_cat   9 ksGkgkgekll.rkvrelleeagvelelieteepgd.akelakeakeegvdlivvaGGDGtvsevlnglleelatkpplgiiPlGtgNdlaralgigkd 105
                 k G++++e+++ + +++ l+++ + +++   e +g+   e + e+k+e+ dl+v +GGDGt   v+  l +    ++p+ +i +G    +   + i+ +
  EPA05411.1  11 KVGSKDSEDAAkKIAKKFLAKKSIVYTISPIEVEGSkKVESLDELKKEKLDLVVTLGGDGTTLRVFRYLEN----ETPILTINVGGNRGILSEITIE-E 104
                 557777777883555667888888888888885544156779999999********************999....7777777777665555555555.5 PP

                 HHHHHHCH CS
    DAGK_cat 106 ieealesi 113
                 i+ea+e+i
  EPA05411.1 105 IDEAIERI 112
                 66666655 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0     6e-07    0.0036       3     100 ..       6     114 ..       4     135 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 6e-07
                    EEEET--..S-TTSHHHHHHHHHHHHT--EEEESSS-SEETTEES----T.....T--EEEE-S-HHHHGGGHHHHHHH--SEEEE-TT....... CS
  CoA_binding_2   3 iaVvGas..dnpgkfgykvlryllehglpvvpVnpkeeeilgekvyaslae.dpepvdlvdvftppeatpeivkealalgakavwlqpg....... 88 
                    +aVv     ++++ ++ k+++ +l+++  v+ + p   e++g k+++sl+e ++e++dlv+ +    +t+ + ++++ + +   +   g       
     EPA05411.1   6 VAVVSKVgsKDSEDAAKKIAKKFLAKKSIVYTISPI--EVEGSKKVESLDElKKEKLDLVVTLGGDGTTLRVFRYLENETPILTINVGGnrgilse 99 
                    55554433389999***********99999***999..999*********988********99999999999999987754443333336666666 PP

                    ...---HHHHHHHHH CS
  CoA_binding_2  89 ...sedeeaaelaee 100
                       +e +ea+e+ e+
     EPA05411.1 100 itiEEIDEAIERIEK 114
                    666555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.36s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 1532.40
//
Query:       EPA05412.1  [L=271]
Description: 3' exoribonuclease family, domain 1 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-20   74.4   0.0    2.2e-20   73.5   0.0    1.5  1  RNase_PH    3' exoribonuclease family, domain 1
    1.5e-14   53.7   1.9    1.7e-14   53.6   0.1    2.1  2  RNase_PH_C  3' exoribonuclease family, domain 2
  ------ inclusion threshold ------
        9.9    6.3  11.3        8.4    6.5   0.9    3.2  3  SBBP        Beta-propeller repeat


Domain annotation for each model (and alignments):
>> RNase_PH  3' exoribonuclease family, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.5   0.0   3.7e-24   2.2e-20       2     132 .]      33     167 ..      32     167 .. 0.91

  Alignments for each domain:
  == domain 1  score: 73.5 bits;  conditional E-value: 3.7e-24
                 EEEEEEEESSSSTTSEEEEEEECCEEEEEEEEEEEEEE-TCCG.--CCEEEECCCCECCCCEC-C...S...HHHHHHHHHHHHHHCCTC-C....... CS
    RNase_PH   2 lRslsietgvlsqanGSaylelGdtkvlasvtgpieerpseer.ddaegaldveveyapfasgerrregrpsdeeielsrlleralrpsill....... 92 
                  R+l ie + +++anGSa+++lGd +v+++v+ +    p+++  d  +g + +  e+ p++ ++ +  g p+   iel+r+++r +r+s ++       
  EPA05412.1  33 PRQLVIEVNAIPKANGSARVRLGDSEVVCGVKIQPDR-PFPDMgD--KGIFICTAELLPLSHPSVET-GPPGPDVIELARVVDRGIRESHMIdlsqlvi 127
                 599******************************9976.7777545..478***************55.9**********************99999999 PP

                 .CGCCTCEEEEEEEEEECCCS-CHHHCHHHHHHHHHCTCEE CS
    RNase_PH  93 .ekkpkstididitvlssdggslldalinaaslALadagip 132
                  + k+   +  d  v+++dg +l+da+  aa++AL++++ p
  EPA05412.1 128 eKNKSVVGVFADNVVVDYDG-NLFDACAYAATAALLSSKSP 167
                 6666679999999*******.***************99876 PP

>> RNase_PH_C  3' exoribonuclease family, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.4       1.1   6.9e+03       8      18 ..     134     144 ..     132     147 .. 0.89
   2 !   53.6   0.1   2.8e-18   1.7e-14       2      65 ..     191     254 ..     190     256 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.1
                 EEEETTEEEES CS
  RNase_PH_C   8 vgkvddqfvlD 18 
                 vg++ d++v+D
  EPA05412.1 134 VGVFADNVVVD 144
                 89999**9999 PP

  == domain 2  score: 53.6 bits;  conditional E-value: 2.8e-18
                 --EEEEEEEETTEEEES--HHHHHHSSEEEEEEEETTSEEEEEEEECSSCEEHHHHHHHHHHHH CS
  RNase_PH_C   2 pviavtvgkvddqfvlDptkeEedlsegdltlavagtkevvtlmkeggsqldeetlleaielAk 65 
                 ++++vt+gk+++++++Dp+ +E d +++++t++ ++++++++l+k g ++++ e+++++ el+ 
  EPA05412.1 191 IPVSVTMGKIGNHIIVDPNGDEWDSMDARITITTDSNGNICALQKGGIGGFSFEEVIKCGELSV 254
                 89*********************************************************99876 PP

>> SBBP  Beta-propeller repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.3     0.016        96      14      27 ..     137     150 ..     134     150 .. 0.83
   2 ?    2.6   0.2     0.023   1.4e+02      14      24 ..     200     210 ..     198     211 .. 0.87
   3 ?    6.5   0.9    0.0014       8.4      18      26 ..     222     230 ..     220     230 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.016
        SBBP  14 ygngIavDsnGNiY 27 
                 ++ ++ vD +GN +
  EPA05412.1 137 FADNVVVDYDGNLF 150
                 66699*******86 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.023
        SBBP  14 ygngIavDsnG 24 
                 +gn+I vD+nG
  EPA05412.1 200 IGNHIIVDPNG 210
                 599*******9 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.0014
        SBBP  18 IavDsnGNi 26 
                 I++DsnGNi
  EPA05412.1 222 ITTDSNGNI 230
                 9*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       257  (0.0143343); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1627.40
//
Query:       EPA05413.1  [L=306]
Description: transporter, CPA2 family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-38  133.0  43.6    1.4e-38  132.7  43.6    1.0  1  Na_H_Exchanger  Sodium/hydrogen exchanger family


Domain annotation for each model (and alignments):
>> Na_H_Exchanger  Sodium/hydrogen exchanger family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.7  43.6   7.6e-43   1.4e-38      85     380 ..       5     291 ..       1     293 [. 0.87

  Alignments for each domain:
  == domain 1  score: 132.7 bits;  conditional E-value: 7.6e-43
                     HHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC.CCCTSTCCCCCCHHHHHHHHHHHCCCCCHHHHHHTX.XXXXTSSSTSX CS
  Na_H_Exchanger  85 lgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailkeegrvperlgtlllgesvlnDavavvllavllalak.eeaggetslll 178
                     +g++  + ++G ++y++ +lg++  ++l+++a+ls+++++v+++il+e+gr++++  +l+lg+++++D+vav+l+++l+++a  ++++ e+ ++ 
      EPA05413.1   5 VGTIGLFTTLGAIFYAGSLLGLNSMDSLFIAAALSISSTAVIVKILEEMGRIKSESTILVLGILIVEDVVAVILISSLQSIALvGSVSIESIVVV 99 
                     344444444589999877799*************************************************************9999999999999 PP

                     HHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTHHHHHHHHHHHHHHHHHHHHHTSXXXHHHHHHHHHHHHHHHHHHTTHHHH.HHHHHHHHHHHH CS
  Na_H_Exchanger 179 llliflvvavgglllglvigwllrlitrftdddrelevllvlllallaallaellgvsgilgaflaGlvlseyefsnklsek.lesfreglfnpl 272
                     +++++ ++++ + ++ +vi  l  ++ +   ++re+ +l vl ++++ alla ++g+s ++gaflaG++++e++ s+ +s+   +++  + f+ +
      EPA05413.1 100 IIVAIGLIVGTFTIGTRVITPLIDRVAAA--EHREILLLSVLGVCFGYALLANIVGLSVAIGAFLAGVLVAESKSSE-VSKLlASPIK-DMFVAI 190
                     99999998888888888888888888888..****************************************999999.9999455555.****** PP

                     HHHHHHHHSXHHHHHXXHHHHHHHHHHHHHHHTHHHHHHHHHTTTXSSXHHHHHHCC.CCSS.BHHHHHHHHHHHHHHXHHHHTTSSTTTCSTSX CS
  Na_H_Exchanger 273 fFvlvGlsldlkvlnnhlsvlilvllilvaillgrilavflllrllglslrealiig.fgglqrgavalalaalgpalgllarelyallivvvlf 366
                     fF++vG+ +d++ l+   + ++ ++li++ai  +++ + +l   +++ ++   +  + ++ ++rg+++++++  g + g+ ++ l++++ v+ ++
      EPA05413.1 191 FFISVGALMDVSQLQ--NYIVLSIALIILAI-TMKFSGNMLGNFIFRQQRTKGIRSAfTLAAPRGEFSIVIIKTGVDIGAVSAFLFPMIGVISIV 282
                     **********99995..66666666666676.6999999999999965555555444367789******************************** PP

                     HHHHHHHHHHHHHH CS
  Na_H_Exchanger 367 tvlvqGlslkpllk 380
                     t +     l+p++ 
      EPA05413.1 283 TAF-----LTPFMI 291
                     ***.....666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1087  (0.060628); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.35s 00:00:00.95 Elapsed: 00:00:00.52
# Mc/sec: 1774.34
//
Query:       EPA05414.1  [L=51]
Description: hypothetical protein BG20_I0720 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0019   17.7   0.0     0.0023   17.5   0.0    1.2  1  RecR            RecR protein
      0.006   16.6   1.6       0.13   12.3   0.1    2.2  2  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
     0.0065   16.5   2.3      0.014   15.4   2.3    1.4  1  DZR             Double zinc ribbon
     0.0069   16.2   1.1     0.0091   15.8   1.1    1.2  1  zf-C3HC4_3      Zinc finger, C3HC4 type (RING finger)
     0.0082   14.9   0.2     0.0082   14.9   0.2    1.0  1  tRNA-synt_1g    tRNA synthetases class I (M)
  ------ inclusion threshold ------
      0.013   14.8   2.1        2.3    7.6   0.3    2.2  2  zf-TFIIB        Transcription factor zinc-finger
      0.015   15.3   0.2      0.017   15.1   0.2    1.1  1  zinc-ribbons_6  zinc-ribbons
      0.015   15.4   0.4      0.017   15.3   0.4    1.2  1  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like
      0.033   14.4   5.5       0.17   12.1   1.9    2.4  2  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 
      0.039   13.9   0.1      0.039   13.9   0.1    2.4  2  Nudix_N_2       Nudix N-terminal
      0.065   13.0   5.5       0.31   10.8   0.4    2.2  2  zinc_ribbon_2   zinc-ribbon domain
       0.07   13.1   2.0       0.16   11.9   0.8    1.8  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
       0.15   12.2   4.0          2    8.6   0.4    2.3  2  UPF0547         Uncharacterised protein family UPF0547
       0.17   11.8   5.9        1.7    8.6   5.9    2.0  1  Zn_ribbon_SprT  SprT-like zinc ribbon domain
       0.23   11.6   5.0        1.4    9.1   0.4    2.1  2  Zn-ribbon_8     Zinc ribbon domain
       0.31   10.9   0.3       0.31   10.9   0.3    1.7  2  Rad50_zn_hook   Rad50 zinc hook motif
        4.8    7.3  10.2        3.9    7.6   4.1    2.2  2  DUF2752         Protein of unknown function (DUF2752)


Domain annotation for each model (and alignments):
>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   2.2e-06    0.0023       7      37 ..       3      34 ..       1      35 [. 0.84

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.2e-06
                HHHHHHHHH-EE-TTT--E.ESSSS-CCCCST CS
        RecR  7 eaLqeakekvrhCsrCgnl.teedlCaICsdp 37
                ++ q++ + v++C+ C++  t+   C+ C  p
  EPA05414.1  3 NTFQDVGKWVHYCPGCHTNhTTGKECPMCGTP 34
                667889999********88688899****765 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.2     0.055        58       2       7 ..      15      20 ..       7      21 .. 0.76
   2 !   12.3   0.1   0.00012      0.13       1      11 [.      27      37 ..      27      42 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.055
  DNA_ligase_ZBD  2 CPvCGs 7 
                    CP C++
      EPA05414.1 15 CPGCHT 20
                    777775 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00012
  DNA_ligase_ZBD  1 hCPvCGsavvR 11
                    +CP CG+++ +
      EPA05414.1 27 ECPMCGTPLKK 37
                    5*******976 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   2.3   1.3e-05     0.014       1      24 [.      15      37 ..      15      43 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.3e-05
         DZR  1 CpqCgeelppdarfCseCgtklka 24
                Cp C+++++   + C+ Cgt+lk+
  EPA05414.1 15 CPGCHTNHT-TGKECPMCGTPLKK 37
                9***99855.5578********85 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   1.1   8.6e-06    0.0091      24      49 ..      13      37 ..       6      38 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 8.6e-06
                EE-HHHHHHHHHTT-B-TTT--B--E CS
  zf-C3HC4_3 24 vlCeeCaekllkrkkkCpiCrrpiek 49
                 +C  C ++     k+Cp+C +p +k
  EPA05414.1 13 HYCPGCHTNH-TTGKECPMCGTPLKK 37
                57*******9.89*********9876 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.2   7.8e-06    0.0082     138     166 ..      14      41 ..       4      50 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 7.8e-06
                   ........-TTS-EE-TTSSB-E...... CS
  tRNA-synt_1g 138 tCPkckseeargdqceecgkkleptelin 166
                    CP c++++ +g++c  cg+ l+ + l +
    EPA05414.1  14 YCPGCHTNHTTGKECPMCGTPLKKKLL-K 41 
                   6**********************5544.4 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.1    0.0027       2.9      19      26 ..      12      19 ..       9      25 .. 0.76
   2 ?    7.6   0.3    0.0022       2.3       2      11 ..      28      37 ..      27      49 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0027
    zf-TFIIB 19 idyCpqCr 26
                ++yCp C+
  EPA05414.1 12 VHYCPGCH 19
                56777775 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0022
    zf-TFIIB  2 CPkCqdelee 11
                CP C+++l++
  EPA05414.1 28 CPMCGTPLKK 37
                ********95 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.2   1.6e-05     0.017      18      41 ..      14      37 ..       3      42 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.6e-05
                    E-TTT--EEEEEEE-SSS-S---E CS
  zinc-ribbons_6 18 hCeaCqedlkkealCpeCeqelev 41
                     C  C+++ +  + Cp C+ +l++
      EPA05414.1 14 YCPGCHTNHTTGKECPMCGTPLKK 37
                    7*******************9975 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.4   1.6e-05     0.017       3      32 ..       7      34 ..       5      48 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.6e-05
  NOB1_Zn_bind  3 rvkswvlrChaCfkvtkdmtkkFCpkCGnk 32
                   v +wv+ C +C++  +++t k Cp CG +
    EPA05414.1  7 DVGKWVHYCPGCHT--NHTTGKECPMCGTP 34
                  5779********86..6667777*****75 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1     0.079        83      34      39 ..      13      18 ..       2      20 .. 0.72
   2 ?   12.1   1.9   0.00016      0.17      14      27 ..      24      37 ..      24      44 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.079
  Auto_anti-p27 34 vyCvaC 39
                    yC+ C
     EPA05414.1 13 HYCPGC 18
                   477777 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00016
  Auto_anti-p27 14 LaetCpvCgvPLmr 27
                   +++ Cp Cg+PL +
     EPA05414.1 24 TGKECPMCGTPLKK 37
                   5899*******976 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   3.5      0.33   3.4e+02      23      30 ..      13      20 ..      10      22 .. 0.77
   2 ?   13.9   0.1   3.7e-05     0.039       3      17 ..      28      42 ..      26      46 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.33
                EEETTTTE CS
   Nudix_N_2 23 lvCpaCgt 30
                + Cp C+t
  EPA05414.1 13 HYCPGCHT 20
                67888887 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 3.7e-05
                -TTT--B-EEE--TT CS
   Nudix_N_2  3 CsqCGtpvelripdg 17
                C++CGtp++ ++ +g
  EPA05414.1 28 CPMCGTPLKKKLLKG 42
                **********99888 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.5     0.023        24      14      21 ..      13      20 ..      12      24 .. 0.77
   2 ?   10.8   0.4   0.00029      0.31      16      23 .]      28      35 ..      26      38 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.023
  zinc_ribbon_2 14 kFCpyCGt 21
                    +Cp C t
     EPA05414.1 13 HYCPGCHT 20
                   58888876 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00029
  zinc_ribbon_2 16 CpyCGtpl 23
                   Cp CGtpl
     EPA05414.1 28 CPMCGTPL 35
                   77777776 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.4      0.25   2.7e+02      46      55 ..      12      21 ..       3      24 .. 0.72
   2 ?   11.9   0.8   0.00015      0.16      25      41 ..      22      38 ..      18      46 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.25
  OrfB_Zn_ribbon 46 tfkCpnCgfe 55
                    +++Cp C + 
      EPA05414.1 12 VHYCPGCHTN 21
                    5678877765 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00015
  OrfB_Zn_ribbon 25 ayTSktCseCgsknkea 41
                    + T k+C+ Cg  +k++
      EPA05414.1 22 HTTGKECPMCGTPLKKK 38
                    56**********99984 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.2     0.031        33       3       8 ..      15      20 ..      14      21 .. 0.85
   2 ?    8.6   0.4    0.0019         2       1      22 [.      26      33 ..      26      36 .. 0.53

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.031
     UPF0547  3 CPeCea 8 
                CP+C +
  EPA05414.1 15 CPGCHT 20
                ****76 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0019
     UPF0547  1 KvCPeCeakvPvaaqfCphCGy 22
                K+              Cp CG+
  EPA05414.1 26 KE--------------CPMCGT 33
                45..............555554 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   5.9    0.0016       1.7       2      30 ..      10      31 ..      10      39 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0016
  Zn_ribbon_SprT  2 kyvYrCtgCgreythhlsirrhnYrCrrC 30
                    k+v++C+gC+   t h + +     C+ C
      EPA05414.1 10 KWVHYCPGCH---TNHTTGKE----CPMC 31
                    8*********...55555555....5555 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.5     0.015        16      28      35 ..      13      22 ..       3      25 .. 0.77
   2 ?    9.1   0.4    0.0014       1.4      27      39 ..      26      38 ..      20      39 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.015
  Zn-ribbon_8 28 a.CPeCgs.e 35
                 + CP C+  +
   EPA05414.1 13 HyCPGCHTnH 22
                 44****9844 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0014
  Zn-ribbon_8 27 taCPeCgsevrrv 39
                 ++CP Cg ++++ 
   EPA05414.1 26 KECPMCGTPLKKK 38
                 56******99985 PP

>> Rad50_zn_hook  Rad50 zinc hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.2       1.6   1.6e+03      22      27 ..      15      20 ..      13      26 .. 0.84
   2 ?   10.9   0.3    0.0003      0.31      20      30 ..      25      36 ..      19      41 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.6
                   -TTT-- CS
  Rad50_zn_hook 22 CPlCgR 27
                   CP C+ 
     EPA05414.1 15 CPGCHT 20
                   999986 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0003
                   E.E-TTT--EE- CS
  Rad50_zn_hook 20 g.cCPlCgReld 30
                   g  CP+Cg +l 
     EPA05414.1 25 GkECPMCGTPLK 36
                   449*******97 PP

>> DUF2752  Protein of unknown function (DUF2752)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   2.0     0.042        44       9      14 ..      13      18 ..      11      22 .. 0.85
   2 ?    7.6   4.1    0.0037       3.9       1      16 [.      18      33 ..      18      34 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.042
     DUF2752  9 ipCPGC 14
                 +CPGC
  EPA05414.1 13 HYCPGC 18
                59**** PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0037
     DUF2752  1 CpfkaltGipCPGCGl 16
                C   + tG +CP CG+
  EPA05414.1 18 CHTNHTTGKECPMCGT 33
                788899*********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.53
# Mc/sec: 291.02
//
Query:       EPA05415.1  [L=228]
Description: rRNA metabolism protein, SBDS family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.8e-23   80.4   0.1      2e-22   79.1   0.1    1.7  1  SBDS      Shwachman-Bodian-Diamond syndrome (SBDS) protein
    2.2e-18   66.4   0.3    7.3e-18   64.7   0.1    1.8  2  SBDS_C    SBDS protein C-terminal domain
  ------ inclusion threshold ------
      0.031   14.3   0.0      0.056   13.5   0.0    1.4  1  EFG_C     Elongation factor G C-terminus


Domain annotation for each model (and alignments):
>> SBDS  Shwachman-Bodian-Diamond syndrome (SBDS) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.1   0.1   3.3e-26     2e-22       2      88 .]       4      90 ..       3      90 .. 0.98

  Alignments for each domain:
  == domain 1  score: 79.1 bits;  conditional E-value: 3.3e-26
                -EEEEEEETTEEEEEEE-HHHHHHHHCTT---HHHHBSSSS-EEETTTTEE--HHHHHHHHS---HHHHHHHHHHHSEEE--HHHHH CS
        SBDS  2 vsivrykkgkkrFeiavyknklleyregkeidLsevlqsekiFtnaskGetaskselekafgteskdeiikeILkkGeiqvsaeerk 88
                v++vry  ++++Fei+v+++ +l+y+ gk+ d+s +l +++i+t++ kG++ s ++l kaf+te+++ei++++LkkG++++++++r+
  EPA05415.1  4 VTVVRYSYEGEKFEILVKPDPALDYKMGKKKDISSILIADEIYTDSGKGTKPSTEKLLKAFKTEDVNEIAEIMLKKGDLNLTTDQRR 90
                89*********************************************************************************9996 PP

>> SBDS_C  SBDS protein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.26   1.5e+03      41      73 ..      53      87 ..      47      93 .. 0.70
   2 !   64.7   0.1   1.2e-21   7.3e-18       2     107 ..      97     206 ..      96     218 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.26
                TS-CCCCHHHHHHHHT..TTS--EE-EEEEEEEE- CS
      SBDS_C 41 nksaksQalevikaLi..qeipiqrarmrlritcp 73
                +k++ ++ l+++k+    ++ +i+ ++  l++t +
  EPA05415.1 53 TKPSTEKLLKAFKTEDvnEIAEIMLKKGDLNLTTD 87
                57777788888887655355558888888877777 PP

  == domain 2  score: 64.7 bits;  conditional E-value: 1.2e-21
                 HHHHHHHHHHHEEBTTTTB---HHHHHHHHHHTT----TTS-CCCCHHHHHHHHTTTS--EE-EEEEEEEE-...CCCHHHHHHHHHH.....S.EE.. CS
      SBDS_C   2 ekeiieivaeklvnpqtkrpytttmIekalkelgtsvktnksaksQalevikaLiqeipiqrarmrlritcptsikdkilklieqvesqkvaekewe.. 98 
                 +k+ii+++a+  v+p+t+ p+++ +Ie+alk+ ++ ++++ks+++Q+ e++++L+ +i  + ++  l+it+p + +++  +++++v s  ++++ew+  
  EPA05415.1  97 RKQIISFIAKTYVDPRTHLPHPPIRIEQALKDGRITIEPQKSVDEQVPEIVDKLRSIIALKSENLDLEITIPAQYASQSYAVLKSVGS--LKKEEWQnn 193
                 79**********************************************************************8887777777777744..223333322 PP

                 ....EEEEEEGGG CS
      SBDS_C  99 ....vvvliePga 107
                      +  i++ga
  EPA05415.1 194 gslkAILEIPAGA 206
                 2221444465555 PP

>> EFG_C  Elongation factor G C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   9.3e-06     0.056       8      72 ..     162     225 ..     160     227 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.3e-06
                 EEEEEEECCCCCCHHHHHHHCT-EEEEEEEE.TTEEEEEEEEEGGG-TTHHHCHHHCTTTS-EEE CS
       EFG_C   8 kveievpeeyvgkvisdlssrrGeiedmeqdasgrviieaeiPlaeligfateLrslTkGegsfs 72 
                 ++ei++p +y ++ +  l+s     ++  q+ +g  +   eiP+    +  ++L s+TkG ++++
  EPA05415.1 162 DLEITIPAQYASQSYAVLKSVGSLKKEEWQN-NGSLKAILEIPAGARPNVIDRLGSITKGSATVE 225
                 79*************9998887777777777.9999999***********************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.39s 00:00:00.97 Elapsed: 00:00:00.58
# Mc/sec: 1174.74
//
Query:       EPA05416.1  [L=65]
Description: hypothetical protein BG20_I0722 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.048   14.2   0.0      0.058   13.9   0.0    1.1  1  PIN_6     PIN domain of ribonuclease


Domain annotation for each model (and alignments):
>> PIN_6  PIN domain of ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   3.3e-06     0.058       2      46 ..       5      47 ..       5      63 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.3e-06
       PIN_6  2 VlDagaliknslsslqnlaeklyttpeVvaEirdkkare.rlellp 46
                +lDa+a+ +    ++  +a+ +ytt+ V +Ei+  k+++  l +l 
  EPA05416.1  5 ILDASAFYAG--VPF-GSASDCYTTSLVYEEIKHIKKNHdALGTLL 47
                79******99..665.7899*************8665543565555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 397.31
//
Query:       EPA05417.1  [L=680]
Description: glycosyltransferase, group 2 family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-23   81.9   0.0    9.9e-23   81.2   0.0    1.3  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    5.2e-19   68.9   0.6    9.3e-19   68.1   0.6    1.4  1  Glyco_trans_2_3  Glycosyl transferase family group 2
    8.7e-18   64.7   0.0    1.5e-17   63.9   0.0    1.4  1  Glycos_transf_2  Glycosyl transferase family 2
    1.7e-11   43.9   0.1      3e-11   43.1   0.1    1.4  1  Glyco_transf_21  Glycosyl transferase family 21
  ------ inclusion threshold ------
        0.1   13.1   0.0       0.73   10.4   0.0    2.2  2  Glyco_tranf_2_4  Glycosyl transferase family 2


Domain annotation for each model (and alignments):
>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.2   0.0   2.7e-26   9.9e-23       2     228 ..      51     278 ..      50     280 .. 0.93

  Alignments for each domain:
  == domain 1  score: 81.2 bits;  conditional E-value: 2.7e-26
  Glyco_tranf_2_3   2 rdlavlVptfneedvlgevlesllaqeyprvevvvvv.desdaetlevaeelaaalpdvrvrvvvnarnl.gstgksralnealravksdlvll 93 
                      + +++  p +ne  v  ++++++ a +yp  + +++v d sd++t+e +  ++a++++++ ++ +  r + +++ k+ al+ a+ ++++++v++
       EPA05417.1  51 T-ITIQLPIYNEKYVAKRLVDAVCAMDYPKEKMMIMVlDDSDDDTVELLFDVVAKYKKEGFQIEHIRR-GtRKGYKAGALKYAMTITDTEFVAI 142
                      4.7788899**************************************9999******88888655544.5488899****************** PP

  Glyco_tranf_2_3  94 vDdDtvvePdtlkrllqffltpkvgavgtpv.fllnrstlvsalgalefaerhlrflaarralg.vltlnGsgslirrevlkelegldplfllt 185
                      +D+D +    +lk++   f  p++g v+++  +++   +++++++al ++ ++l + +a    + ++ +nG+   +r ++ ++ +g++    l+
       EPA05417.1 143 FDADFIPPNWFLKKAMSHFVKPDIGLVQCRWgHVNENYSAITQAQALSLDFHFLIEQKAKSNSNlFMNFNGTAGIWRSDCIADAGGWHT-ATLV 235
                      *****************999********9987999999****************999999888868***********************.**** PP

  Glyco_tranf_2_3 186 dDyelglrlrragfrtayvpgaavrevfpsslkayikqrnRwv 228
                      +D++l++r+ + g++  ++p+ +v  + p    a+ +q +Rw+
       EPA05417.1 236 EDLDLSYRAQMKGWKCLFLPDIVVDAELPVQMNAAKRQQFRWA 278
                      ******************************************7 PP

>> Glyco_trans_2_3  Glycosyl transferase family group 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.1   0.6   2.6e-22   9.3e-19       2     189 ..     140     351 ..     139     362 .. 0.76

  Alignments for each domain:
  == domain 1  score: 68.1 bits;  conditional E-value: 2.6e-22
  Glyco_trans_2_3   2 illlDaDtvlppdclreiaaelaspevaivqgpvlvm.nvanwleelaalffaedhgkdilvrealgrvvp..svGsgaflrrsalqevggwdg 92 
                      +++ DaD  +p  +l+++ +++  p++++vq+  + + ++ + +++ +al  +  + ++i + +++ + ++  + G   ++r + + ++ggw+ 
       EPA05417.1 140 VAIFDADFIPPNWFLKKAMSHFVKPDIGLVQCRWGHVnENYSAITQAQALSLD--FHFLIEQKAKSNSNLFmnFNGTAGIWRSDCIADAGGWH- 230
                      7899*****************************99652678888888887775..56667777766665552277******************. PP

  Glyco_trans_2_3  93 dessvsEDfdmglrlqrkGyrvrfvpeslvkekspltlraalrQrkRwayGc.......eleklil...................lvrllgylg 160
                       + ++ ED+d++ r+q+kG+++ f p+ +v  + p  + aa rQ  Rwa G        +     +                   l+r++ y+ 
       EPA05417.1 231 -TATLVEDLDLSYRAQMKGWKCLFLPDIVVDAELPVQMNAAKRQQFRWAKGSiqcaiklL-----AdialkrkisveakiqafvqLTRHIVYPL 318
                      .**************************************************765554430.....14444445555565556666889998877 PP

  Glyco_trans_2_3 161 sllwsa....lplhlallllfsllalalvllll 189
                       l+ +     l++++++l+l s+++ ++++ +l
       EPA05417.1 319 MLIQFLtlpvLLAADMNLYLVSFVPALTIATYL 351
                      777555311344566777777777743333332 PP

>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.9   0.0   4.2e-21   1.5e-17       4     151 ..      56     205 ..      53     222 .. 0.85

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 4.2e-21
                      EEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCH....C-TTEEEEEESSS-.HHHHHHHHHHHH--SSEEEEEESSEEE CS
  Glycos_transf_2   4 iptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelak....edprvrvirreenv.GkagalnaglraatgdyilflDaDdep 92 
                       p+yNe+   ++++++++a+d+++++ +i v D S D+tve+l + ++    e+ ++  irr  ++  kagal  ++  +++++++++DaD +p
       EPA05417.1  56 LPIYNEKYVAKRLVDAVCAMDYPKEKMMIMVLDDSDDDTVELLFDVVAkykkEGFQIEHIRRGTRKgYKAGALKYAMTITDTEFVAIFDADFIP 149
                      79******************7777777777777777***9998887777777**************99************************** PP

                      -TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCS CS
  Glycos_transf_2  93 dpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnl 151
                      +  +l+k + ++ k++ ++v + + + + +   i++++     +  +++  +++ k n+
       EPA05417.1 150 PNWFLKKAMSHFVKPDIGLVQCRWGHVNENYSAITQAQA---LSLDFHFLIEQKAKSNS 205
                      ************************************997...55555555555544443 PP

>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   0.1   8.3e-15     3e-11      16     173 .]     122     279 ..     110     279 .. 0.85

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 8.3e-15
  Glyco_transf_21  16 npKvnnllqaleaakydllvisDsdvrvkpdyLeellaaledpkvglVtslpvgsdak.glaaaleaaflntlagvlqa...klsglgfavGks 105
                       +K  +l +a++   ++++ i D+d + +  +L++ + ++ +p++glV++    ++++ ++ ++ +a+ l ++  + q    +   +   +G +
       EPA05417.1 122 GYKAGALKYAMTITDTEFVAIFDADFIPPNWFLKKAMSHFVKPDIGLVQCRWGHVNENySAITQAQALSLDFHFLIEQKaksNSNLFMNFNGTA 215
                      469999********************************************88766666266666666666777655555422345677789*** PP

  Glyco_transf_21 106 malrreaLeaiGGfealadeLAeDyalgkllraaGlkvvlspapiaqtsvprrsslrallaRqlrWar 173
                       ++r + ++++GG      +L eD+ l+ + + +G+k  + p+ +++ ++p    + a  ++q+rWa+
       EPA05417.1 216 GIWRSDCIADAGGWHT--ATLVEDLDLSYRAQMKGWKCLFLPDIVVDAELPV--QMNAAKRQQFRWAK 279
                      ***************9..9*******************************96..6889999*****97 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0    0.0002      0.73       3      81 ..      61     146 ..      59     149 .. 0.69
   2 ?   -0.7   0.0      0.58   2.1e+03      59      89 ..     564     594 ..     544     599 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0002
  Glyco_tranf_2_4   3 eadiLpeflahhlalgf...drilvydndstDgtrail....kel..pevkllhvdksyederrqvellkallaryaeadwvlvvDaD 81 
                      e+ + ++ +++ +a+++   + ++++ +ds+D+t ++l    +++  +  ++ h++   + + ++  +lk ++  + ++++v+ +DaD
       EPA05417.1  61 EKYVAKRLVDAVCAMDYpkeKMMIMVLDDSDDDTVELLfdvvAKYkkEGFQIEHIRRGTR-KGYKAGALKYAM-TITDTEFVAIFDAD 146
                      5555556666666666643245999*************6555333113366888877765.577777777766.67899*******99 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.58
  Glyco_tranf_2_4  59 vellkallaryaeadwvlvvDaDEflvvpds 89 
                       ++  + l + ++  w++   + +fl ++  
       EPA05417.1 564 LAIVMEKLPESKNPVWIFPTESTNFLRIERD 594
                      555566667778999**********988874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (680 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       875  (0.0488036); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.74u 0.34s 00:00:01.08 Elapsed: 00:00:01.11
# Mc/sec: 1852.94
//
Query:       EPA05418.1  [L=169]
Description: rhodanese-like protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.3e-15   57.8   0.0    6.7e-15   55.5   0.0    1.9  2  Rhodanese  Rhodanese-like domain
  ------ inclusion threshold ------
      0.051   13.5   0.0      0.086   12.7   0.0    1.3  1  DUF412     Protein of unknown function, DUF412


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.13   1.2e+03      81      99 ..       7      25 ..       2      33 .. 0.74
   2 !   55.5   0.0   7.5e-19   6.7e-15       3     105 ..      62     162 ..      60     164 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.13
   Rhodanese 81 aaaallkklGyknvsvldG 99
                + a+++ + G++++++ld 
  EPA05418.1  7 RIAWTFLYFGHEKIFLLDA 25
                44778888**666**9985 PP

  == domain 2  score: 55.5 bits;  conditional E-value: 7.5e-19
   Rhodanese   3 kelkellekgkvallDvRppeeYekghIpgAvnv.skdtlsrakkseapllelpeellelgidnkktvvvycdgggraaaaaallkklGyknvsvldGG 100
                 + lke+l++    +lD+R+p+e+  gh+p++  +   + +s+ k  ++++  ++  + + +i +++++v+yc +g+ra+++  +l  +Gy+nv+++dG+
  EPA05418.1  62 DSLKENLDDFV--VLDARTPQEFMGGHLPNSKLIpFTEGISYDKIFQDKSFLQNLFFDN-QIPKESQIVCYCMHGHRASSLFLQLVIAGYENVKLYDGS 157
                 57899997774..*********************7555666666666555555555555.59***************8888555555**999******* PP

   Rhodanese 101 fkawk 105
                 f +w+
  EPA05418.1 158 FVDWY 162
                 ****8 PP

>> DUF412  Protein of unknown function, DUF412
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   9.6e-06     0.086       5      60 ..      95     150 ..      92     158 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.6e-06
      DUF412   5 lkdGqkYlktwPlekeLaalfpenrvikatrfaikvmpalavltlvlqlylagsea 60 
                 +++G +Y k++ +++ L++lf +n++ k  ++++ +m    + +l+lql++ag+e+
  EPA05418.1  95 FTEGISYDKIFQDKSFLQNLFFDNQIPKESQIVCYCMHGHRASSLFLQLVIAGYEN 150
                 679************************************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.35s 00:00:00.83 Elapsed: 00:00:00.52
# Mc/sec: 975.72
//
Query:       EPA05419.1  [L=161]
Description: 3-isopropylmalate dehydratase small subunit [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-20   74.4   0.2    6.8e-20   71.7   0.0    2.2  2  Aconitase_C    Aconitase C-terminal domain
      0.002   17.8   0.2     0.0085   15.7   0.2    1.9  1  Aconitase_2_N  Aconitate hydratase 2 N-terminus


Domain annotation for each model (and alignments):
>> Aconitase_C  Aconitase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.7   0.0   7.6e-24   6.8e-20      58     130 ..      35     107 ..       8     108 .. 0.80
   2 ?   -2.4   0.1      0.63   5.7e+03      37      54 ..     122     139 ..     115     148 .. 0.60

  Alignments for each domain:
  == domain 1  score: 71.7 bits;  conditional E-value: 7.6e-24
                  EEEEHHHHHHHHHHTT--EEEE--SSBTBS---THHHHHHHHTTEEEEEES-B-HHHHHHHHHTT.-EEEEEST CS
  Aconitase_C  58 ekedvvdaaerykkegaklvviagknfGeGSSRehAAkalrllGikaviaeSFerIfennlikng.lLplefke 130
                    ++  d  ++ k+++ ++++++  nfG+GSSRehA+ al++ Gikav+a SF+rIf++n++  + lLp+e+++
   EPA05419.1  35 HAMEGLDPDFHSKVKEGDFILSG-RNFGCGSSREHAPIALSHSGIKAVLALSFARIFYRNAVDGAfLLPIEIDQ 107
                  44566777788888999999999.*************************************9766389**9986 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.63
                  TTCCCCTTTSBBSEEEET CS
  Aconitase_C  37 glgnelveekrankttdl 54 
                  +++ + +++   nkt+++
   EPA05419.1 122 DIKTNQINNLTKNKTYKM 139
                  555555555555555554 PP

>> Aconitase_2_N  Aconitate hydratase 2 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.2   9.5e-07    0.0085      96     165 ..      81     154 ..       5     158 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 9.5e-07
                    EEEEEE-HHHH.HHHHHTT-EEEE---...TT--TT-EEEEETTTTEEEETT--EEEE---S-TCHHHHHHHTS CS
  Aconitase_2_N  96 vlGgkiaPiFf.ntvedsGalpieadv...skletGdvieikpkegkikkeegevvsefklkpetlldevragg 165
                    vl  + a iF+ n v+ +  lpie+d    s++++Gd i+i+ k+++i++ +++   ++k  +e +   + agg
     EPA05419.1  81 VLALSFARIFYrNAVDGAFLLPIEIDQdaySDISEGDQIDIDIKTNQINNLTKNKTYKMKPFSEIIGKIIEAGG 154
                    555567889984677778889***9972225799****************888877788877889999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.35s 00:00:00.90 Elapsed: 00:00:00.55
# Mc/sec: 886.18
//
Query:       EPA05420.1  [L=184]
Description: putative 3-isopropylmalate dehydratase large subunit [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.3e-36  124.4   0.8    1.1e-33  117.0   0.8    2.0  1  Aconitase  Aconitase family (aconitate hydratase)
  ------ inclusion threshold ------
       0.06   12.0   0.0      0.083   11.6   0.0    1.2  1  DUF521     Protein of unknown function (DUF521)


Domain annotation for each model (and alignments):
>> Aconitase  Aconitase family (aconitate hydratase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.0   0.8   1.2e-37   1.1e-33     268     461 .]      15     175 ..       6     175 .. 0.92

  Alignments for each domain:
  == domain 1  score: 117.0 bits;  conditional E-value: 1.2e-37
   Aconitase 268 laadedaeydkvleldlstlepsvagpkrPqdavplselvkkefkeelekeaaekaleyklkegtklkdgkvdiaaigSCTNssnedvraaagllakav 366
                 ++ d+daey+kv+e + s++ep va p++P++   + ++++                            +++d+ +igSCT +++ed+ aaa++l+   
  EPA05420.1  15 VHGDNDAEYEKVYEYEGSEMEPLVAKPFSPENISIV-REAP---------------------------SVELDKSYIGSCTGAKYEDLVAAAKILK--- 82 
                 56799*************************996555.3333...........................23489***********************... PP

   Aconitase 367 ekglkvkpgvktsvaPGSevvkayleaeGlleiLekaGfevvgagCstCig.nsdrleegeaivsssNRNFegRq.gpntrayLaSPelvvaaAlaG 461
                   g+kvk   +t + P+S  + +++ ++Gll+i+ +aG++v  + C+ C+g   + l+++e ++s++NRNF gR+ + ++++yL SP +++a+A++G
  EPA05420.1  83 --GRKVKI--RTEILPASISIYKRAMENGLLTIFLDAGVTVGPPTCGACCGaHMGVLAKDEICISTTNRNFPGRMgHVDSQTYLSSPLVAAASAVTG 175
                 ..*99998..*****************************************999*********************5599999*************98 PP

>> DUF521  Protein of unknown function (DUF521)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   9.2e-06     0.083     298     358 ..      66     125 ..      41     145 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9.2e-06
      DUF521 298 cPhlsleElrelaellkgkkkkvkvelwvttsrevkeeaerlglveklekaGvkvlsdtCm 358
                 c  +++e+l + a++lkg+k+k ++e+ + +s +++++a + gl+ +  +aGv+v   tC 
  EPA05420.1  66 CTGAKYEDLVAAAKILKGRKVKIRTEI-LPASISIYKRAMENGLLTIFLDAGVTVGPPTCG 125
                 6668999*********99999888876.46899**************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.34s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 1045.43
//
Query:       EPA05421.1  [L=245]
Description: exosome complex exonuclease 1 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.1e-34  118.9   0.0    2.8e-34  118.4   0.0    1.2  1  RNase_PH    3' exoribonuclease family, domain 1
    4.4e-12   45.9   0.1      1e-11   44.7   0.1    1.7  1  RNase_PH_C  3' exoribonuclease family, domain 2


Domain annotation for each model (and alignments):
>> RNase_PH  3' exoribonuclease family, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.4   0.0   3.2e-38   2.8e-34       2     132 .]      26     154 ..      25     154 .. 0.95

  Alignments for each domain:
  == domain 1  score: 118.4 bits;  conditional E-value: 3.2e-38
                 EEEEEEEESSSSTTSEEEEEEECCEEEEEEEEEEEEEE-TCCG--CCEEEECCCCECCCCEC-C...S...HHHHHHHHHHHHHHCCTC-CCGCCTCEE CS
    RNase_PH   2 lRslsietgvlsqanGSaylelGdtkvlasvtgpieerpseerddaegaldveveyapfasgerrregrpsdeeielsrlleralrpsillekkpksti 100
                  R++ i+ g l++a+GSay+e+Gd+k+l++v gp+ ++p+ ++++ +g l v++ + pf+ +er++   ps++eie+s+++++al+p ++lek+p++ +
  EPA05421.1  26 PRRIMIKAGGLKNADGSAYIEFGDNKILVGVFGPRDVHPKHMSNTDTGILRVRYHMEPFSVTERKN-PAPSRREIEISKVIKEALEPAVMLEKFPRTAV 123
                 599**********************************99998755569****************65.79****************************** PP

                 EEEEEEEECCCS-CHHHCHHHHHHHHHCTCEE CS
    RNase_PH 101 diditvlssdggslldalinaaslALadagip 132
                 d++i+vl++dg ++  a+  aas+ALadagip
  EPA05421.1 124 DVFIEVLQADG-GTRCAALSAASVALADAGIP 154
                 ***********.*******************9 PP

>> RNase_PH_C  3' exoribonuclease family, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7   0.1   1.1e-15     1e-11       1      64 [.     157     219 ..     157     222 .. 0.97

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 1.1e-15
                 S--EEEEEEEETTEEEES--HHHHHHSSEEEEEEEETTSEEEEEEEECSSCEEHHHHHHHHHHH CS
  RNase_PH_C   1 apviavtvgkvddqfvlDptkeEedlsegdltlavagtkevvtlmkeggsqldeetlleaielA 64 
                 ++v+a++ gk  d+++lD ++eE++ +++d+++ +  + e++tl++++g  l++ + ++++e++
  EPA05421.1 157 DMVAACAAGKAADTIILDVNNEEDQAGQADMPIGYMPSLEKITLLQLDGV-LTPAEYKKCVETG 219
                 69************************************************.***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1532.88
//
Query:       EPA05422.1  [L=236]
Description: hypothetical protein TIGR00266 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-53  181.2   0.2    2.3e-53  181.0   0.2    1.0  1  AIM24     Mitochondrial biogenesis AIM24


Domain annotation for each model (and alignments):
>> AIM24  Mitochondrial biogenesis AIM24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.0   0.2   1.3e-57   2.3e-53       1     200 [.       3     206 ..       3     207 .. 0.97

  Alignments for each domain:
  == domain 1  score: 181.0 bits;  conditional E-value: 1.3e-57
                 EEEESSSS-EEEEEE-TT-EEEE-CCGEEEEETTEEEEE....--------.------EEEEEEES.SS-EEEEE--SSSEEEEEEEGGTT.EEEEEGG CS
       AIM24   1 fevlgepssllsvtLspgeelyaerGalvamsgkvemet....gllkalkr.lltgeslfllkftakissgtvllapklpgtivtlelgggdwlivqkd 94 
                 +++l++p+sll+v+L+++e+++ae+Galv+m+g+++++t    g+lk+lk  +l++es+f++k+tak ++  + l+ +  g+i+++ ++++  +ivq++
  EPA05422.1   3 YQILKNPMSLLEVNLKKDESITAEAGALVFMQGDIQIDTktrsGILKTLKVsILGNESFFVNKYTAKHDGCILGLTGPPVGDIIDIPINSNAGFIVQSG 101
                 89************************************************99***************999******************8888******* PP

                 GEEEEETT-EEEEEEEE--.SSGGGTS-EEEEEEESSSEEEEEEECSEEEEEEE.EEEEEEEGGGEEEEETTEEEEEEEETT---STTTTS-EEEEEEE CS
       AIM24  95 afLAatgnveldikfqkgl.kglfggeglflqkltGrGlvalsgyGaiyeielkageelvvdpghlvafsgslkfdiervgglkrrligGeglflkltG 192
                 +++A+t +v++d+k+q g+ kg+fg ++lf++k tG+G+v+ ++yG+i+++++  ge++v d+ hlva s + ++++++ gglk++++gGegl++k+tG
  EPA05422.1 102 SYIASTPDVDIDTKWQ-GFtKGIFG-SELFMLKATGDGTVFCNAYGGIIKKQILSGETFVLDNYHLVALSINSDYEVTKFGGLKNTILGGEGLVTKITG 198
                 ****************.67799995.59*************************99******************************************** PP

                 EEEEEEES CS
       AIM24 193 pgtvllqs 200
                 p tv+lq+
  EPA05422.1 199 PATVYLQT 206
                 *******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.34s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1388.39
//
Query:       EPA05423.1  [L=226]
Description: KH domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-07   31.2   0.0    3.3e-07   30.5   0.0    1.4  1  KH_6      KH domain
    2.9e-07   30.2   0.2      6e-07   29.2   0.2    1.5  1  KH_1      KH domain
    0.00021   21.0   0.1    0.00042   20.1   0.1    1.5  1  KH_2      KH domain
  ------ inclusion threshold ------
       0.02   14.8   0.1      0.074   12.9   0.0    2.0  2  KH_4      KH domain
      0.065   13.4   0.3        2.3    8.5   0.0    2.3  2  TAF       TATA box binding protein associated factor (TAF)


Domain annotation for each model (and alignments):
>> KH_6  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.0   9.2e-11   3.3e-07       1      45 [.     143     190 ..     143     191 .. 0.89

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 9.2e-11
        KH_6   1 GmlfeVslslvrRll...nhvLeeLgkagpfeiavGlNGriWvksesp 45 
                 G l+++s+s+v+Rl+     +++++++a +  +++G+NG+i v++e+p
  EPA05423.1 143 GTLVKISPSKVPRLIgkrGTMIQMIEMATGAAVTIGQNGWIVVSCETP 190
                 99*************888666677788888***************998 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.2   1.7e-10     6e-07       4      65 ..     146     201 ..     144     202 .. 0.90

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 1.7e-10
                 EEEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEESSTT...T.-EEEEEE.SHHHHHHHHHHHH CS
        KH_1   4 ilvPsslvgriIGkgGsnIkeIreetgakIkvpksedegsderevtisG.speavekAkelie 65 
                 +++  s+v+r+IGk+G +I+ I+  tga +++ +       +  +++s  +pe+  kAk++i+
  EPA05423.1 146 VKISPSKVPRLIGKRGTMIQMIEMATGAAVTIGQ-------NGWIVVSCeTPEGLLKAKKAIQ 201
                 6899999****************99******653.......347****************996 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.1   1.2e-07   0.00042      25      68 ..     142     185 ..     129     191 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.2e-07
                 CEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEE CS
        KH_2  25 nrviiviresqpgivIGkgGsnikkigkelrkdieklegkkVkl 68 
                  ++ + i  s+  ++IGk+G +i++i+ + +  + + +++++ +
  EPA05423.1 142 SGTLVKISPSKVPRLIGKRGTMIQMIEMATGAAVTIGQNGWIVV 185
                 578899***************************99999999877 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.3   4.5e+03      26      43 ..     123     140 ..     107     141 .. 0.73
   2 ?   12.9   0.0   2.1e-05     0.074      33      62 ..     146     175 ..     141     186 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.3
        KH_4  26 eeeveielnvegedlGrv 43 
                 ++++   ++++  dlG++
  EPA05423.1 123 DRTRDPLVTIADRDLGKI 140
                 566666788899999987 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 2.1e-05
        KH_4  33 lnvegedlGrvIGkrGrtldAlqylvsaaa 62 
                 ++++++++ r+IGkrG +++ +   + aa+
  EPA05423.1 146 VKISPSKVPRLIGKRGTMIQMIEMATGAAV 175
                 7899***************98876666665 PP

>> TAF  TATA box binding protein associated factor (TAF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0   0.00064       2.3      10      29 ..      31      50 ..      25      56 .. 0.89
   2 ?    2.7   0.1      0.04   1.4e+02       6      31 ..     197     222 ..     193     225 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00064
                HHHHHHTT---B-HHHHHHH CS
         TAF 10 kviAeslGitnLsdeaaalL 29
                k+iA s+Gi+++ d+  +++
  EPA05423.1 31 KIIATSIGISEIYDDSIKVI 50
                89*************98865 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.04
                 HHHHHHHHHHTT---B-HHHHHHHHH CS
         TAF   6 kesvkviAeslGitnLsdeaaalLae 31 
                 k +++++ e   ++nL d + ++L+ 
  EPA05423.1 197 KKAIQMVDEKAHVANLTDQVKEMLES 222
                 678999999999***********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.35s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 1282.96
//
Query:       EPA05424.1  [L=153]
Description: ribosomal protein L13 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-12   47.0   0.4    3.1e-10   40.4   0.3    2.2  1  Ribosomal_L13  Ribosomal protein L13


Domain annotation for each model (and alignments):
>> Ribosomal_L13  Ribosomal protein L13
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   0.3   1.7e-14   3.1e-10       3     116 ..      14     116 ..      12     124 .. 0.81

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 1.7e-14
                    EEEEETTSBHHHHHHHHHHHHHTTTSTT--TTS--S-EEEEEEGGCBB-SSTHHTT-EEEEE-SSTTSEEEEEHHH..HHCCSHHHHHHHHHHCCS CS
  Ribosomal_L13   3 yviDAegqvlgrlaskiakvLrGkhkptytphvdcGdyvvvinaekvaltgkkleqkvyyrhtgypgglkevtake..llekkpeeilekaVkgmL 96 
                    +v+DA++++ grl+sk+ak+L              G+ v ++n+ek+ l+g++ +  + y++ ++    + ++ ++  +++++p+ i++++V+gmL
     EPA05424.1  14 VVVDATDHIAGRLCSKVAKLLL------------NGNRVSIVNCEKIMLSGTRDN--IIYHYRKFLEVNSVIHPRHgpVHARRPDTIMTRMVRGML 95 
                    69******************96............588899***********9655..555555665555555555444****************** PP

                    -SSHHHHHHG.CTEEEESSST CS
  Ribosomal_L13  97 pknklgrrrl.krLkvyagee 116
                    pk+k +  +  krL+ y g+ 
     EPA05424.1  96 PKKKPSGLMAhKRLRTYIGSP 116
                    *9987666666*****99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.35s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 862.35
//
Query:       EPA05425.1  [L=281]
Description: rhodanese-like protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.4e-35  121.3   0.4    4.6e-18   65.7   0.0    2.1  2  Rhodanese  Rhodanese-like domain


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.0   0.1   1.1e-18     2e-14       3     106 ..      13     121 ..      11     122 .. 0.86
   2 !   65.7   0.0   2.6e-22   4.6e-18       5     105 ..     154     272 ..     152     274 .. 0.86

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 1.1e-18
   Rhodanese   3 kelkellekgkvallDvR..ppeeYekghIpgAvnv.skdtlsrakkseapllelpeellel.gidnkktvvvycdgggr.aaaaaallkklGyknvsv 96 
                 +++ ++  +++ +l+ v   p + Y+kghI+gA  +  k+ ++++  ++   ++++e+l+++ gi+++++v++y+d ++  aa++ + +k++G++n+++
  EPA05425.1  13 EWVSKNPPNENRKLVEVDydPVNGYQKGHINGASLIwWKRDINDPITRDIINKKQFEALMSKnGITKDTEVILYGDFNNWfAAFVFWVFKYYGHENLKI 111
                 677777744444666666437777************98889999999999999***************************99999********888*** PP

   Rhodanese  97 ldGGfkawke 106
                 +dGG k+w  
  EPA05425.1 112 MDGGRKKWEL 121
                 ********86 PP

  == domain 2  score: 65.7 bits;  conditional E-value: 2.6e-22
   Rhodanese   5 lkellekgkvallDvRppeeY...............ek.ghIpgAvnvskdtl.srakkseapllelpeellelgidnkktvvvycdgggraaaaaall 86 
                 + + l++++++ +DvR+p e+               ++ ghIp A n+++ t+ ++a+ + ++ +el + ++++g++++k v++yc+ g+r++ ++  l
  EPA05425.1 154 VSRALGREDTVMVDVRSPKEFsgeitappeypmehaQRgGHIPKANNIPWATAvNDADGTFKSVNELKQNYESKGVTPDKDVICYCRIGERSSHSWFVL 252
                 66788899999*********98888999999999995559********76665155666777788888888888*****************9999**** PP

   Rhodanese  87 kk.lGyknvsvldGGfkawk 105
                 k+ lGy +v+++dG++++w 
  EPA05425.1 253 KYlLGYSKVRNYDGSWTEWG 272
                 *99**999***********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1701.45
//
Query:       EPA05426.1  [L=101]
Description: hypothetical protein BG20_I0725 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.52
# Mc/sec: 586.04
//
Query:       EPA05427.1  [L=149]
Description: ribosomal protein S9 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.6e-34  117.5   0.2    5.3e-34  117.4   0.2    1.0  1  Ribosomal_S9  Ribosomal protein S9/S16
  ------ inclusion threshold ------
      0.024   15.3   0.0      0.034   14.8   0.0    1.2  1  NFACT-R_1     NFACT protein RNA binding domain


Domain annotation for each model (and alignments):
>> Ribosomal_S9  Ribosomal protein S9/S16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.4   0.2   5.9e-38   5.3e-34       2     121 .]      12     149 .]      11     149 .] 0.91

  Alignments for each domain:
  == domain 1  score: 117.4 bits;  conditional E-value: 5.9e-38
                   ECTTEEEEEEEEESSSEEEETTEECCHHSTTSCHHHHHCHHHHHTTTSS.SEEEEEEEESS-HHHHHHHHHHHHHHHHHHHHH............HH CS
  Ribosomal_S9   2 rrKesvArvwikegkgkilvngksleeYfkeeaarekvleplkltgllg.kfdvfvkvkgGGlsgqaeAirlgiaraLvalek............ee 85 
                    rK+s+A+v+i++g+gki++n+ ++e  +++e+are +l+pl++tg l  k+d+ v+v+gGG++gqa A+++gi+raL+ ++k            ++
    EPA05427.1  12 TRKTSSAHVYITKGQGKIRINNIPIEM-IPQETAREVMLAPLEITGDLRdKIDISVRVRGGGFMGQASAAATGISRALTGWTKskkdpkdhpfpkST 107
                   69*************************.*9****************99846******************************8655666666666434 PP

                   HHHHC......TCCCTS-B--------TTSSCTTB----S-- CS
  Ribosomal_S9  86 kkeLk......kaglltrDpRvvErkKtgkkkARkkyqwskR 121
                   ++ L+      ++ l+  D+R++E+kK+g ++AR++ q+s+R
    EPA05427.1 108 REDLRqritdfDKYLISGDARRKEPKKFGGPGARRRKQKSYR 149
                   888887777888****************************99 PP

>> NFACT-R_1  NFACT protein RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   3.8e-06     0.034      30      65 ..       3      45 ..       1      62 [. 0.77

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.8e-06
   NFACT-R_1 30 leesdvwfhvdkessahvylrlsege.......leeipeelle 65
                +++++++f   k ssahvy+ + +g+       +e ip+e+ +
  EPA05427.1  3 TPKTEIYFATRKTSSAHVYITKGQGKirinnipIEMIPQETAR 45
                57889****************8888777444444455555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 916.10
//
Query:       EPA05428.1  [L=145]
Description: prefoldin, beta subunit [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-21   76.3  20.6    1.8e-21   76.1  20.6    1.0  1  Prefoldin_2      Prefoldin subunit
  ------ inclusion threshold ------
        3.7    6.1  11.3          5    5.6  11.3    1.2  1  FapA             Flagellar Assembly Protein A
        6.8    7.5  10.4       0.41   11.4   1.8    2.3  2  Vir_act_alpha_C  Virulence activator alpha C-term
        7.6    5.0  11.9        9.4    4.6  11.9    1.0  1  Macoilin         Macoilin family


Domain annotation for each model (and alignments):
>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.1  20.6   4.1e-25   1.8e-21       1     104 [.      11     114 ..      11     115 .. 0.98

  Alignments for each domain:
  == domain 1  score: 76.1 bits;  conditional E-value: 4.1e-25
                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT--EEEEETTEEEEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
  Prefoldin_2   1 qelinkfqqlqqqlqqlaqqikqletqlkelelvleelelldedtkvyklvGdvlvkqdkeevkeeLeerketlekeiktlekqleklekeleelkee 98 
                  qe+++k+qq+qq lq +++q++ le++  e +++leel+++++d++vyk  G +l+k +k e++++Leerke ++++++ lekq++++++ l+e++++
   EPA05428.1  11 QEQLMKMQQSQQNLQSIMTQKQHLEMERLETDKALEELKKAADDDTVYKHAGSILIKSTKSELIADLEERKEMAKTRLTVLEKQESRIKESLKEQEAK 108
                  89************************************************************************************************ PP

                  HHCCTS CS
  Prefoldin_2  99 lqkklq 104
                  + +++ 
   EPA05428.1 109 ITEMMR 114
                  *99975 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6  11.3    0.0011         5     326     416 ..      17     108 ..       5     115 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0011
        FapA 326 iev.gldepelkeklkeleeeleeleeeleklkkk..ikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeeleskkeeak 416
                  ++   + ++++ + + le e  e+ + le+lkk+   + + k + +  ++s+k+e ++ l+e ke  k++l+ le++  ++ke+l+++  eak
  EPA05428.1  17 MQQsQQNLQSIMTQKQHLEMERLETDKALEELKKAadDDTVYKHAGSILIKSTKSELIADLEERKEMAKTRLTVLEKQESRIKESLKEQ--EAK 108
                 555556667778888999999999999999999997745555544466788999*********************************99..332 PP

>> Vir_act_alpha_C  Virulence activator alpha C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   1.6      0.15   6.9e+02      32      45 ..      18      31 ..       1      68 [. 0.51
   2 ?   11.4   1.8   9.1e-05      0.41      17      46 ..      70     104 ..      65     116 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.15
  Vir_act_alpha_C 32 eekLaeyeeieerl 45
                     ++  +++++i+ + 
       EPA05428.1 18 QQSQQNLQSIMTQK 31
                     33333333322222 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 9.1e-05
  Vir_act_alpha_C  17 pealieeLerrreeheekLaeyeeieerl.....e 46 
                      + +li++Le+r+e ++ +L  +e+ e r+     e
       EPA05428.1  70 KSELIADLEERKEMAKTRLTVLEKQESRIkeslkE 104
                      679********************999999655541 PP

>> Macoilin  Macoilin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6  11.9    0.0021       9.4     453     556 ..       9     112 ..       2     117 .. 0.62

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0021
    Macoilin 453 klhelvsakqkdkqtlqqlekrLkeekearaslekqLaeekkrkkeeeetaara.valaaasrsecteslkskkreleaeikkLekel.klkeeqirel 549
                  l+e + + q+ +q+lq++  + ++ + +r +++k L+e kk+  ++    ++a   l ++++se    l ++k+   + +  Lek+  ++k e ++e 
  EPA05428.1   9 WLQEQLMKMQQSQQNLQSIMTQKQHLEMERLETDKALEELKKAADDD-TVYKHAgSILIKSTKSELIADLEERKEMAKTRLTVLEKQEsRIK-ESLKEQ 105
                 56777777888888888888888888888999999998888876655.34444413445555666666666666666666666665431333.334555 PP

    Macoilin 550 elkvqel 556
                 e+k+ e+
  EPA05428.1 106 EAKITEM 112
                 5555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2545  (0.141949); expected 358.6 (0.02)
Passed bias filter:                      701  (0.0390987); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.34s 00:00:00.95 Elapsed: 00:00:00.53
# Mc/sec: 822.57
//
Query:       EPA05429.1  [L=249]
Description: 3-isopropylmalate dehydratase large subunit domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.6e-54  184.1   0.1    5.9e-54  183.8   0.1    1.0  1  Aconitase  Aconitase family (aconitate hydratase)


Domain annotation for each model (and alignments):
>> Aconitase  Aconitase family (aconitate hydratase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.8   0.1   3.3e-58   5.9e-54      11     247 ..      16     246 ..       5     248 .. 0.86

  Alignments for each domain:
  == domain 1  score: 183.8 bits;  conditional E-value: 3.3e-58
   Aconitase  11 e...egiayv.pdrvllqdvtgvqalvdlaaareavrrlggtlatidhlvpvdlvidhsvgaeealeknledefernkeryefLksaakafgi.rvvpp 104
                 +   +++ +  +d+v+++dv+g+ +l+ +++ +++      +++++    +v++  dh v          +d+++   e++  L++++k++gi + ++ 
  EPA05429.1  16 KvspDDVVFAkVDKVMVHDVSGPGVLKVFDKLKKQG----INVDKLWDPSKVWVAEDHFV--------PSADKVSA--ENIVKLSNFTKNYGIaKHFKY 100
                 133233444469*****************9888877....55555555566666666888........45566666..99999********88666777 PP

   Aconitase 105 g...qGIvHqvnlEyglalpgktvvgtDSHTtmigglGvlaiGvGgieaeavllgqplelkipkvvgvkltGklkegvtakDlvlavigklrkkgvvgk 200
                 g    GI+H    E+ l+lpg++ vg+DSHT++ g+lG +a+G G ++++ vll+ ++++k+p+++ +kl+Gkl+e+v akD +l++ig ++++g+  k
  EPA05429.1 101 GmgqYGICHTLSHEEALVLPGEVYVGGDSHTNTTGALGSFACGLGHTDVAYVLLNGQIWFKVPETLYFKLNGKLPEHVMAKDFILKIIGDITTEGGAYK 199
                 767899********************************************************************************************* PP

   Aconitase 201 vvEffGegvesLsledraTiaNMaaEvGAttglfpvdektleYLkat 247
                 ++ f G+g++++s+e r+T++NM++E+GA+ g++++d+k+++YL+  
  EPA05429.1 200 AMQFGGTGISEMSVESRLTMCNMTTEAGAKNGIVEPDQKVVDYLTSR 246
                 ********************************************954 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 1457.93
//
Query:       EPA05430.1  [L=143]
Description: hypothetical protein BG20_I0731 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.34s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 829.37
//
Query:       EPA05431.1  [L=115]
Description: hypothetical protein BG20_I0706 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-07   30.8   0.0    1.9e-07   30.7   0.0    1.2  1  Ribosomal_L18   Ribosomal protein 60S L18 and 50S L18e
    0.00053   20.7   0.1    0.00073   20.2   0.1    1.4  1  Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27


Domain annotation for each model (and alignments):
>> Ribosomal_L18  Ribosomal protein 60S L18 and 50S L18e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.0   2.1e-11   1.9e-07      54     138 ..      36     114 ..       4     115 .] 0.88

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 2.1e-11
  Ribosomal_L18  54 rinrpplslsrlvkkvkkkeeekkiavvvgtvtdDvrllevPklsvaALrftetararilkaGGeiltlDqLalraPtGkntvLl 138
                     i r+ + l+r+ + +k+    + ++v  g+v+    + +  k++++++ ++++a a++l+ GG+i+++ +L  ++PtGk +vLl
     EPA05431.1  36 SIARRHINLNRIGQLTKE----SDTVVFPGKVLGTGDINH--KITLCSFSISNAAAAKVLERGGKIVSFSDLIEKNPTGKGVVLL 114
                    577888888888888874....589999999988877765..9*****************************************8 PP

>> Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.1   8.1e-08   0.00073      72     127 ..      39      96 ..       7      97 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 8.1e-08
                     --EEEGGGTTTTSSS........SEEEE--S---.--EEEESEE-HHHHHHHHHTT-EEE CS
  Ribosomal_L27A  72 aeeidleelaeaglikk....kdgvKvlgkgeltkklkvkaskfSkkAkekIeaaGGkve 127
                     +  i+l+++   +l+k+        Kvlg+g++++k+++   ++S++A +k+ + GGk++
      EPA05431.1  39 RRHINLNRI--GQLTKEsdtvVFPGKVLGTGDINHKITLCSFSISNAAAAKVLERGGKIV 96 
                     456666666..33333365433344*********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.32s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 716.72
//
Query:       EPA05432.1  [L=242]
Description: nucleotidyl transferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.1e-19   68.0   0.1    1.1e-18   67.7   0.1    1.0  1  NTP_transferase  Nucleotidyl transferase
    3.1e-10   40.6   0.0    3.6e-10   40.4   0.0    1.1  1  NTP_transf_3     MobA-like NTP transferase domain
  ------ inclusion threshold ------
      0.084   12.6   0.0       0.14   11.9   0.0    1.4  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.7   0.1   1.9e-22   1.1e-18       1     231 [.       2     219 ..       2     224 .. 0.83

  Alignments for each domain:
  == domain 1  score: 67.7 bits;  conditional E-value: 1.9e-22
                      EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHH.TT-SEEEEEEETTTHH..HHHHHHTTSGGGTSEEEEEEESS--BGGHHHH CS
  NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlan.sgieeiivvltqehsf..lveeqlkegskfgvevlialepegkgtAdAva 91 
                      kavILaGG+GtR  P t   +k + p+ +  +li++ +  l + s i+e i+++++++     ++++++++++ +      +++++ gt + ++
       EPA05432.1   2 KAVILAGGKGTRGKPYTEYFPKAMTPINDI-PLIDYIVRYLNSfSFIKE-IIIVSDYNGLggQIKNYYSNAKNGK--KITFVQDSQSGTGGDLL 91 
                      79****************999999999888.**********99677777.6666666643126777777776544..5667899999******* PP

                      HTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEECTTSBEEEEECS-SSHSHCSEECCSEEEEETT CS
  NTP_transferase  92 laaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGvieadeegrverfvEKPkeakaselassGiYvfnse 185
                        ++ l+++ +   ++    D l+  ++e++ k ++ek++   ++++++++++++e G + +++ g +++f EKP  +  +     G+Y+  +e
       EPA05432.1  92 HLEDKLKEDTE---FVLWFVDNLCAIDLEKMRKTFKEKNS---IACIATRTKRKEETGFAVVED-GIIKEFREKPVMKL-QLSECLGVYILGKE 177
                      *******9996...666677888999**************...888888888888888888877.79********9977.777788******** PP

                      HHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEE CS
  NTP_transferase 186 vllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsD 231
                      +++++ k ++  +++     dil+++ +egk   af+ +d   W D
       EPA05432.1 178 IIKKI-K-AKTKQKEINLSFDILQQLSQEGKIS-AFDIEDR-DWID 219
                      *****.4.5777777777889*****9999877.5677776.5988 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   0.0   6.1e-14   3.6e-10       1     129 [.       3     140 ..       3     193 .. 0.79

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 6.1e-14
                   EEEEEESS-TTTTT.....THHHHCCCCCCHHHHHHHHHCTT..-CEEEEECSHC....HHHHHH....TTCTS-EEE-TTSS-SHHHHHHHHHHHH CS
  NTP_transf_3   1 aviLAGGrSsRmgg.....dKallplggkpllervldalraag.vdevvvvggde....evlaal....arlgvrvvededpgkgplaslaaalraa 83 
                   aviLAGG+++R +      +Ka+ p+++ pl++++++ l++ + ++e+++v +++    ++++++    +++++++v+d+  + g+++ l++  +++
    EPA05432.1   3 AVILAGGKGTRGKPyteyfPKAMTPINDIPLIDYIVRYLNSFSfIKEIIIVSDYNglggQIKNYYsnakNGKKITFVQDS--QSGTGGDLLHLEDKL 97 
                   79*********98344589***********************856*********83444344333332234467778776..79999*********9 PP

                   .SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESSSEEEE CS
  NTP_transf_3  84 adadavlvlacDmPlltpelverllaaaaasgadvvvptyegergh 129
                   ++++ +++  +D  +  +  +e++++ ++ +++++++++++ +r++
    EPA05432.1  98 KEDTEFVLWFVDNLC--AIDLEKMRKTFK-EKNSIACIATRTKRKE 140
                   999999999999966..778999999997.5556777777777654 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.3e-05      0.14       2      53 ..       2      56 ..       1     106 [. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.3e-05
                EEEEECTTSSCTT-...SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-G CS
        IspD  2 vvvipAAGsGkRmk...aglpKqflelkgqtllehtvdallaskavdkivvvvse 53
                 +vi A G+G+R k   +  pK+   +++ +l+   v+ l + + +++i++v + 
  EPA05432.1  2 KAVILAGGKGTRGKpytEYFPKAMTPINDIPLIDYIVRYLNSFSFIKEIIIVSDY 56
                699********975332678******************************98764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       853  (0.0475766); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 1443.80
//
Query:       EPA05433.1  [L=52]
Description: hypothetical protein BG20_I0708 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.011   15.1   1.8      0.027   13.9   1.9    1.6  2  Vps36-NZF-N  Vacuolar protein sorting 36 NZF-N zinc-finger do
      0.014   15.8   0.5      0.016   15.7   0.5    1.1  1  zf-C4pol     C4-type zinc-finger of DNA polymerase delta
      0.054   13.7   0.2      0.061   13.6   0.2    1.1  1  LIM          LIM domain


Domain annotation for each model (and alignments):
>> Vps36-NZF-N  Vacuolar protein sorting 36 NZF-N zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.4       0.1   6.3e+02      31      39 ..       4      12 ..       2      17 .. 0.82
   2 ?   13.9   1.9   4.5e-06     0.027      22      56 ..      16      50 ..       7      52 .] 0.83

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.1
  Vps36-NZF-N 31 tplPpClaC 39
                 t++ +C +C
   EPA05433.1  4 TKIVICINC 12
                 667789999 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 4.5e-06
  Vps36-NZF-N 22 psnfdpnastplPpClaCGvkpdlelikksikasa 56
                  +++++ ++ + P C +C  + +++++k+ ik+++
   EPA05433.1 16 IGEIELDSTMDNPLCGQCALEESFSMTKSRIKIAQ 50
                 5678888899*********************9876 PP

>> zf-C4pol  C4-type zinc-finger of DNA polymerase delta
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   0.5   2.6e-06     0.016       1      32 [.       9      49 ..       9      52 .] 0.75

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.6e-06
    zf-C4pol  1 ClvCk.........eklkkalCkkCrsdkqesllkllsrlk 32
                C++Ck         ++++++lC +C+ +++ s++k + +++
  EPA05433.1  9 CINCKkpigeieldSTMDNPLCGQCALEESFSMTKSRIKIA 49
                *****8877766654455*******9888888888776665 PP

>> LIM  LIM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2     1e-05     0.061      27      55 ..       7      35 ..       1      38 [. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1e-05
                SB-TTT-SB-CTT.CEEETTEEEEHHHHH CS
         LIM 27 FtCsdCqkeLkegsfyekdgklyCkkdyl 55
                 +C +C+k++ e ++ ++ ++++C ++ l
  EPA05433.1  7 VICINCKKPIGEIELDSTMDNPLCGQCAL 35
                68************9999999*****966 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.32s 00:00:00.70 Elapsed: 00:00:00.47
# Mc/sec: 330.98
//
Query:       EPA05434.1  [L=69]
Description: hypothetical protein BG20_I0716 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-19   68.4   1.9    4.6e-19   68.3   1.9    1.0  1  Ribosomal_L37ae  Ribosomal L37ae protein family
    0.00023   21.1   5.1    0.00028   20.8   3.1    1.9  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
  ------ inclusion threshold ------
      0.014   15.3   2.3      0.018   14.9   2.3    1.2  1  C1_1             Phorbol esters/diacylglycerol binding domain
      0.019   14.9   3.3      0.034   14.1   3.3    1.7  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.044   13.3   1.6      0.075   12.6   1.6    1.4  1  TF_Zn_Ribbon     TFIIB zinc-binding
      0.059   13.5   0.3      0.059   13.5   0.3    2.0  2  Zn-ribbon_8      Zinc ribbon domain
       0.74    9.8   4.1       0.55   10.3   0.8    1.9  2  DUF1451          Zinc-ribbon containing domain


Domain annotation for each model (and alignments):
>> Ribosomal_L37ae  Ribosomal L37ae protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.3   1.9   1.8e-22   4.6e-19      12      68 ..      11      67 ..       3      69 .] 0.95

  Alignments for each domain:
  == domain 1  score: 68.3 bits;  conditional E-value: 1.8e-22
                     TTSS-HHHHHHHHHHHHHHHS-BEESSSSSSEEEEEETTEEEETTTTEEEE-BSSSS CS
  Ribosomal_L37ae 12 gtrYGaslrkrvkkieisqhakytCpfcgktkvkRkavgiwkCkkcgktvaGgAytp 68
                     g+rYG + rk   ki  + ++k tCp+cg+++ +R avgiw+Ckkc+ +vaG Ay +
       EPA05434.1 11 GARYGIKHRKLYSKIHFQLKEKRTCPECGSQQFNRDAVGIWSCKKCSFKVAGTAYDV 67
                     9******************************************************76 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.31   7.9e+02      29      38 ..      13      22 ..       9      23 .. 0.85
   2 !   20.8   3.1   1.1e-07   0.00028      16      44 ..      30      57 ..      26      59 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.31
  Zn_Tnp_IS1595 29 ayriktrglf 38
                    y ik+r+l+
     EPA05434.1 13 RYGIKHRKLY 22
                   5999**9998 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 1.1e-07
  Zn_Tnp_IS1595 16 pngfvCPhCgsrkayriktrglfqCkeCr 44
                   +++++CP Cgs+++ r +  g + Ck+C+
     EPA05434.1 30 KEKRTCPECGSQQFNRDAV-GIWSCKKCS 57
                   6789******999999996.********8 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   2.3   7.1e-06     0.018       5      38 ..      26      60 ..      16      61 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 7.1e-06
                EE--SS--B-TTT-SB--S.SSS-EEEETTT--EE CS
        C1_1  5 hrnfkqptfCkhCgeflwg.kekqglkCswCkllv 38
                h ++k++ +C +Cg++ +   +  +++C+ C+++v
  EPA05434.1 26 HFQLKEKRTCPECGSQQFNrDAVGIWSCKKCSFKV 60
                67999**********998989**********9986 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   3.3   1.3e-05     0.034      30      55 ..      34      59 ..       4      61 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.3e-05
  OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkCpnCgfe 55
                    tC+eCgs++ ++++   + C++C f+
      EPA05434.1 34 TCPECGSQQFNRDAVGIWSCKKCSFK 59
                    8********999***********997 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   1.6   2.9e-05     0.075       2      25 ..      34      56 ..      33      60 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.9e-05
                  EETTTTCEECHEETSTTCEEESSS CS
  TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdC 25
                  +CP+Cgs ++ +D + g   C++C
    EPA05434.1 34 TCPECGSQQFNRD-AVGIWSCKKC 56
                  8******875555.4455599988 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.3   2.3e-05     0.059      23      38 ..      28      45 ..      18      47 .. 0.72
   2 ?    1.4   0.2      0.14   3.6e+02      28      33 ..      51      57 ..      41      61 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.3e-05
  Zn-ribbon_8 23 daplta.CPeCgs.evrr 38
                 + +++  CPeCgs +  r
   EPA05434.1 28 QLKEKRtCPECGSqQFNR 45
                 4455666******88776 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.14
  Zn-ribbon_8 28 a.CPeCg 33
                   C++C 
   EPA05434.1 51 WsCKKCS 57
                 5577773 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.8   0.00022      0.55     133     146 ..      33      46 ..      22      47 .. 0.82
   2 ?    1.2   0.1      0.14   3.5e+02     112     124 ..      48      60 ..      46      65 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00022
     DUF1451 133 ppCpkCgateFrRe 146
                  +Cp+Cg+++F+R 
  EPA05434.1  33 RTCPECGSQQFNRD 46 
                 68***********6 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.14
     DUF1451 112 lGtlvCekCgkel 124
                  G   C+kC  ++
  EPA05434.1  48 VGIWSCKKCSFKV 60 
                 5777899998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 424.57
//
Query:       EPA05435.1  [L=471]
Description: 3-isopropylmalate dehydratase, large subunit [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   2.6e-153  511.3   0.0     3e-153  511.1   0.0    1.0  1  Aconitase  Aconitase family (aconitate hydratase)


Domain annotation for each model (and alignments):
>> Aconitase  Aconitase family (aconitate hydratase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  511.1   0.0  1.7e-157    3e-153       1     461 []       7     460 ..       7     460 .. 0.94

  Alignments for each domain:
  == domain 1  score: 511.1 bits;  conditional E-value: 1.7e-157
   Aconitase   1 ekiwdahlv.eeeg...iayvpdrvllqdvtgvqalvdlaaareavrrlggtlatidhlvpvdlvidhsvgaeealeknledefernkeryefLksaak 95 
                 ekiwdah+v e+e+   + y+ dr+l+++vt++qa+ +l++ +++vrr++ t+at+dh+vp++             ++ l    ++++ ++++L++++k
  EPA05435.1   7 EKIWDAHIVvEKENspsLIYI-DRHLVHEVTSPQAFDGLRMNNRKVRRPDLTIATMDHNVPTN-------------NRTLPILDQTSAVQIQTLEKNCK 91 
                 79*****99533334557777.*****************************************.............2334444444459********** PP

   Aconitase  96 afgirvvppg...qGIvHqvnlEyglalpgktvvgtDSHTtmigglGvlaiGvGgieaeavllgqplelkipkvvgvkltGklk..egvtakDlvlavi 189
                 +fgi++++++   qGIvH+++++ g++lpg+t+v++DSHT+++g++G+la+G+G++e+e+vl+ q+l+l++pk  +++++Gk k  + vtakD++l +i
  EPA05435.1  92 DFGIQLFDIHspnQGIVHVIGPQLGITLPGTTIVCGDSHTSTHGAFGALAFGIGTSEVEHVLASQTLWLEKPKPFEIRVEGKRKnpHAVTAKDIILSII 190
                 **99988877777********************************************************************8752269*********** PP

   Aconitase 190 gklrkkgvvgkvvEffGegvesLsledraTiaNMaaEvGAttglfpvdektleYLkatgreeaavlveaydkaqalf..elaadedaeydkvleldlst 286
                 ++++++g++g v+E++G+g+ +Ls+e+r+Ti+NM++E+GA++gl+++dekt+eYL+  gr++++   ++y++ ++++  +l++d+da+++k ++l++++
  EPA05435.1 191 KNIGTSGGNGTVIEYTGDGICDLSMEQRMTICNMSIEAGARAGLIAPDEKTFEYLR--GRKYTP---KNYESLVDYWreNLKTDSDAKFEKKYTLQIDN 284
                 ********************************************************..******...8*********7569****************** PP

   Aconitase 287 lepsvagpkrPqdavplselvk.k.efk..eelekeaaekaley.klkegtklkdgkvdiaaigSCTNssnedvraaagllakavekglkvkpgvktsv 380
                 ++p+v+++++P ++++++e+v+ + ef+  ++++k+ aekaley +lk+gt ++++k+d ++igSCTN+++ed+ +a ++++     g+kv+++vk++v
  EPA05435.1 285 IAPQVSWGTNPGMTCDVTESVPsPeEFSngDQNQKKGAEKALEYmALKPGTLMTEIKIDRVFIGSCTNARLEDLIEASKVVK-----GKKVSSHVKAMV 378
                 *********************97557774467779999*******9************************************.....************ PP

   Aconitase 381 aPGSevvkayleaeGlleiLekaGfevvgagCstCig.nsdrleegeaivsssNRNFegRqgpntrayLaSPelvvaaAlaG 461
                 +PGS+ vk+++e+ Gl++i+++a fe+++agCs+C+g n+d l++ge+++s+sNRNFegRqg+++r++L+SP +++aaA++G
  EPA05435.1 379 VPGSQMVKKQAEELGLDKIFTDANFEWRDAGCSMCLGmNPDILSPGERCASTSNRNFEGRQGTGGRTHLVSPVMAAAAAIEG 460
                 ********************************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (471 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.36s 00:00:00.98 Elapsed: 00:00:00.54
# Mc/sec: 2647.53
//
Query:       EPA05436.1  [L=222]
Description: hypothetical protein BG20_I0735, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 1316.54
//
Query:       EPA05437.1  [L=54]
Description: hypothetical protein BG20_I0710 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       213  (0.0118802); expected 358.6 (0.02)
Passed bias filter:                      201  (0.0112109); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.32s 00:00:00.79 Elapsed: 00:00:00.51
# Mc/sec: 319.42
//
Query:       EPA05438.1  [L=194]
Description: 3-isopropylmalate dehydratase, small subunit [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.7e-37  127.3   0.0    8.2e-37  126.5   0.0    1.4  1  Aconitase_C    Aconitase C-terminal domain
    0.00013   21.6   0.2     0.0053   16.4   0.2    2.1  1  Aconitase_2_N  Aconitate hydratase 2 N-terminus


Domain annotation for each model (and alignments):
>> Aconitase_C  Aconitase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.5   0.0   9.2e-41   8.2e-37       1     129 [.       1     122 [.       1     124 [. 0.96

  Alignments for each domain:
  == domain 1  score: 126.5 bits;  conditional E-value: 9.2e-41
                  CCCCCCCTT--CHHHHSTGGGCCGHCCHHHCCCGGTTTCCCCTTTSBBSEEEETTTTEEEEHHHHHHHHHHTT--EEEE--SSBTBS---THHHHHHH CS
  Aconitase_C   1 mekllklkGlttedeksnvdtdlkipkqfegtianiglgnelveekrankttdlddgekedvvdaaerykkegaklvviagknfGeGSSRehAAkalr 98 
                  m+ ++k k + t+ +k nvdtd++ pkqf++ +++ g+g+ l++++r+++ ++l    k+d+++++++yk  ++k++v++ +nfG+GSSRehA +al+
   EPA05438.1   1 MQSFKKIKTIVTPFDKVNVDTDQIVPKQFLKLVQKSGFGQFLFYNWRYDEHENL----KPDFILNEPKYK--NSKILVAG-DNFGCGSSREHAVWALL 91 
                  78899************************************************9....789*********..99999999.***************** PP

                  HTTEEEEEES-B-HHHHHHHHHTT-EEEEES CS
  Aconitase_C  99 llGikaviaeSFerIfennliknglLplefk 129
                  ++G+ ++i+ SF++If++n +kng+Lp+ ++
   EPA05438.1  92 DYGFSVIISTSFADIFYSNCFKNGILPIILD 122
                  ***************************9776 PP

>> Aconitase_2_N  Aconitate hydratase 2 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.2     6e-07    0.0053      46     151 ..      60     157 ..      47     187 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6e-07
                    HHHHHTTSS-EEEEEEEEEES---THHHHHHHHHHSEEETTEEEEEE--EEEEEEE-HHHHHHHHHTT-EEEE---TT--...T.T-EEEEETTTT CS
  Aconitase_2_N  46 ieelkkkgvplayvgdvvGtGssRksavnsvlWtigedipyvPnkraggvvlGgkiaPiFfntvedsGalpieadvskle...t.Gdvieikpkeg 137
                    ++e k k  ++   gd  G GssR  av ++l +              +v++ ++ a iF++ +   G lpi +d +++e   +    +e++ +++
     EPA05438.1  60 LNEPKYKNSKILVAGDNFGCGSSREHAVWALLDY------------GFSVIISTSFADIFYSNCFKNGILPIILDDKTVEklqQeTSEVEVDLQNQ 143
                    67788899999999**********9998655532............34799*********************998655541113145799999999 PP

                    EEEETT--EEEE-- CS
  Aconitase_2_N 138 kikkeegevvsefk 151
                    +ik++++++  + +
     EPA05438.1 144 TIKTSSETIHFDID 157
                    99987666555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       966  (0.0538792); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1160.96
//
Query:       EPA05439.1  [L=353]
Description: hypothetical protein BG20_I2491, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.1e-08   34.5   3.2    2.2e-05   23.6   0.0    3.1  3  SBP_bac_5  Bacterial extracellular solute-binding proteins, f


Domain annotation for each model (and alignments):
>> SBP_bac_5  Bacterial extracellular solute-binding proteins, family 5 Middle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   1.2e-09   2.2e-05     269     359 ..      10     109 ..       2     123 .. 0.86
   2 !    4.9   0.1    0.0006        11     141     178 ..     134     175 ..     131     217 .. 0.71
   3 !    5.3   0.2   0.00045       8.1      29      47 ..     322     340 ..     297     351 .. 0.72

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1.2e-09
                 HSHHHHHHHHHHHTT-BCSSTSCEETC........EEEEEEEEETTSHHHHHHHHHHHHHHHHTTEEEEEEEECHH....HHHHHHHHCTTESEEEEEE CS
   SBP_bac_5 269 aydpekAkklLkeaGykdgdggglrek........klkltlllasgspaekaiaeliqqqlkkiGikvevktvdwa....atylervkdgdfdmillgw 355
                  y+p  A++++  a +++g  +    +        + ++t+++ s++p +k i e++ ++lkk G+ v+    d +     +y +  k+ +++++  gw
  EPA05439.1  10 RYNPSLAEEIISNALNEKGAIKS---DgqwkinqkPIEITVFIRSDDPIRKSIGEILSSELKKMGFVVKKDFGDLNkafvVVYGSNPKELKWSLYTEGW 105
                 48999999999988888887543...234578888**************************************8888***999999************* PP

                 ECTT CS
   SBP_bac_5 356 gady 359
                 g + 
  EPA05439.1 106 GRSA 109
                 9875 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0006
                 -TTSTTTSCSSSSEEEEEE-....SHHHHHHHH.HTTSSSEE CS
   SBP_bac_5 141 npdYwgggkpkldriefkvi...pdsdaraaal.qsGeiddv 178
                 np +w+ ++ +ld i+ k++    +s+ ++a+l q+G +d +
  EPA05439.1 134 NPSFWNYKNEYLDNITQKIYsgdFESEEQRAELiQKGIADGI 175
                 889996688899999999997774555555555588877766 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.00045
                 B-TTSSB-SHHHHHHHHHH CS
   SBP_bac_5  29 kFsDGtpltAeDvvfsfer 47 
                  ++DG++++ +D+ +s++ 
  EPA05439.1 322 NWHDGQKMNMDDILHSLYF 340
                 489999********99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.35s 00:00:00.92 Elapsed: 00:00:00.52
# Mc/sec: 2029.68
//
Query:       EPA05440.1  [L=151]
Description: Raf-like protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-38  131.2   0.0    3.3e-38  131.0   0.0    1.0  1  PBP       Phosphatidylethanolamine-binding protein


Domain annotation for each model (and alignments):
>> PBP  Phosphatidylethanolamine-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.0   0.0   1.8e-42   3.3e-38       1     132 []      16     149 ..      16     149 .. 0.93

  Alignments for each domain:
  == domain 1  score: 131.0 bits;  conditional E-value: 1.8e-42
                 B--GGG..CSBGGS-EEEEES--TTSSEEEEEEEETTSCCTCT.TEEEEEEEEEETTSSEE-TTC.....EE-B-TTSSCCCCS---B--STTS..EEE CS
         PBP   1 klpkky..egentsPplswsdvpegtksyalvviDpDapkvse.tflHwvvtnipasvtslpega.....vqgknslgeesesgYlgpcPpkgdgkHrY 91 
                 ++pkky  +++n++Ppl+++++p++tks+al++ DpDa    + +++Hwv++ni++++t+++e++     v+gk+++ge   +gY+gp+Pp+++  H+Y
  EPA05440.1  16 EIPKKYgyKNSNINPPLKIKGIPQNTKSLALIMDDPDAMGAVGkIWVHWVIWNIKPDTTEIKEDSipvnsVEGKTDFGE---IGYGGPAPPDKE--HTY 109
                 58999876777888************************7444446******************9999999*********...************..*** PP

                 EEEEEEESSSG--BGSS-SHHHHHHHHCTTEEEEEEEEEEE CS
         PBP  92 vfllyaldvealdlkagftraelgaaiaghvlakatlagnY 132
                 +f+lyald + l+l++g++++++++ +++h+la+ +l+g+Y
  EPA05440.1 110 IFKLYALDNK-LNLNQGASKSDVEKSMKNHILAESKLTGKY 149
                 ********99.589***99********************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 977.45
//
Query:       EPA05441.1  [L=38]
Description: hypothetical protein BG20_I2319, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (38 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 252.04
//
Query:       EPA05442.1  [L=96]
Description: hypothetical protein BG20_I2317 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-10   40.6   0.0    2.9e-10   40.4   0.0    1.0  1  PIN_9     PIN like domain
    1.6e-05   25.2   0.0      2e-05   24.9   0.0    1.1  1  Fcf1      Fcf1
  ------ inclusion threshold ------
       0.02   15.3   0.4      0.064   13.6   0.1    2.0  2  BRCT      BRCA1 C Terminus (BRCT) domain


Domain annotation for each model (and alignments):
>> PIN_9  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   0.0   4.9e-14   2.9e-10      26     111 ..       3      85 ..       1      89 [. 0.88

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 4.9e-14
       PIN_9  26 lgsvelvvpkavleELerlakagkgkertaakvalsLaerceiveaeeekaDdailelakeldaavlvTnDreLkkrllekgipvi 111
                 +g+v ++vp+ v +EL++l k  ++k+++ ++   +  ++ +i+ ++++ aD  ++++ k+ + a++ T D+eLkk+++e g  ++
  EPA05442.1   3 IGQVSFIVPQVVQNELAKLIK--NPKKNQDITSTIDFIKNFKILPITGNFADKELVDYVKKNH-AIIGTMDKELKKKIKEFGGSIM 85 
                 4899***************55..566677788889************999**********997.6666***********9998887 PP

>> Fcf1  Fcf1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   3.4e-09     2e-05       5      98 ..       4      95 ..       3      96 .] 0.81

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 3.4e-09
                S-EEEEEEHHHHHHHHHCT........-HHHHHHHTTSEEE----SS---HHHHHHHHH-BTB-TT-EEEE-S-HHHHHHHHTSTT--EEEEE--EEEE- CS
        Fcf1  5 akvkpliTqCviaeleklgkk......lkealkiaktferlkCnhkkptsaddClvsvvkkkknkkryivAtqDkdlrrrlrkipgvPilyikrsvmvlE 98
                ++v +++ q v +el kl k+      ++++++++k+f+ l+ +      ad+ lv+ vk    k++ i+ t Dk+l+++++++ g  i+ +++++++lE
  EPA05442.1  4 GQVSFIVPQVVQNELAKLIKNpkknqdITSTIDFIKNFKILPITG---NFADKELVDYVK----KNHAIIGTMDKELKKKIKEFGG-SIMSFSNNKIILE 95
                577888888999999998844333344778888888888888655...79999*******....5799**************9977.6***********9 PP

>> BRCT  BRCA1 C Terminus (BRCT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.44   2.6e+03      16      22 ..      25      31 ..       7      44 .. 0.55
   2 ?   13.6   0.1   1.1e-05     0.064      22      43 ..      70      91 ..      61      94 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.44
                STSSHHH CS
        BRCT 16 vldnftr 22
                +++n + 
  EPA05442.1 25 PKKNQDI 31
                2223333 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 1.1e-05
                HHHHHHHHHHTTCEEESSCSTT CS
        BRCT 22 rdeleelikehGGkvttevskk 43
                 +el+++ike+GG++++  ++k
  EPA05442.1 70 DKELKKKIKEFGGSIMSFSNNK 91
                68*************9877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1043  (0.0581739); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.34s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 559.82
//
Query:       EPA05443.1  [L=275]
Description: putative translation initiation factor IF-2 subunit gamma, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-25   89.2   0.2    1.3e-24   86.3   0.1    2.2  2  eIF2_C        Initiation factor eIF2 gamma, C terminal
    1.4e-06   28.5   0.9    2.7e-06   27.7   0.3    1.8  2  GTP_EFTU_D2   Elongation factor Tu domain 2
     0.0035   17.3   0.0       0.01   15.8   0.0    1.8  2  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
     0.0044   16.6   0.0     0.0063   16.1   0.0    1.2  1  GTP_EFTU      Elongation factor Tu GTP binding domain
  ------ inclusion threshold ------
      0.052   13.0   0.0       0.16   11.4   0.0    1.8  2  ProQ_C        ProQ C-terminal domain


Domain annotation for each model (and alignments):
>> eIF2_C  Initiation factor eIF2 gamma, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.22   7.9e+02      24      49 ..     127     153 ..     112     171 .. 0.77
   2 !   86.3   0.1   3.5e-28   1.3e-24       2      85 ..     190     273 ..     189     274 .. 0.97

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.22
                 ---TTEEEEEEETTEEE.EEEEEEEES CS
      eIF2_C  24 klkkkEvLmlniGsast.ggvvtsvkk 49 
                 k k+ E+L+ +i s+ t  g+v svk 
  EPA05443.1 127 KKKTYEPLLTEITSLGTaAGIVDSVKP 153
                 567889999999998661567777765 PP

  == domain 2  score: 86.3 bits;  conditional E-value: 3.5e-28
                 EEEEEEEE-SBESSSSSCCC-----TTEEEEEEETTEEEEEEEEEEESSEEEEEEEEEEE-STTEEEEEEEEETTSEEEEEEEE CS
      eIF2_C   2 eleieyellerlvgvkeekkveklkkkEvLmlniGsastggvvtsvkkdeakvkLkkPvcaekgekialsRrvekrWrLiGwGe 85 
                 ++ ++++l++  vg+ e++kv +++ +E L lniG+a   g+vt++k+++++v+L++P+c+ +g ++a+sRr+  rWrLiG G+
  EPA05443.1 190 QIILDVNLFDSAVGAAEDTKVLPIQVGELLRLNIGTAPILGKVTKIKSNNIEVELRRPACIFEGGNVAISRRITDRWRLIGAGI 273
                 567899****************************************************************************97 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.3   7.6e-10   2.7e-06       1      62 [.      99     165 ..      99     176 .. 0.92
   2 ?   -2.7   0.0       2.3   8.4e+03      29      42 ..     226     239 ..     213     247 .. 0.63

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 7.6e-10
                  EEEEEEEEEESEEETTEEEEEEC.TCTTSEE....EEEEEEEEEEETEEESEEETTSEEEEEEEESS CS
  GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilg.ndtskke....ivtrissletfhededeavaganaGvivaikg 62 
                  G+v++g++ +Gt+++Gde++i +   ++kk+     +t+i+sl t  + +d + +g+ + +++++++
   EPA05443.1  99 GGVIGGSLTQGTFNVGDEIEIKPgIMDEKKKtyepLLTEITSLGTAAGIVDSVKPGGLVAIGTKLDP 165
                  89*******************99966667778****************************9999875 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.3
                  EEEEEEEEEEEEET CS
  GTP_EFTU_D2  29 keivtrissletfh 42 
                   +i+++++++  ++
   EPA05443.1 226 APILGKVTKIKSNN 239
                  35777888877665 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   2.8e-06      0.01      58     100 ..       8      62 ..       5      68 .. 0.82
   2 ?   -1.7   0.0      0.84     3e+03       8      35 ..      64      93 ..      60      96 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.8e-06
  MMR_HSR1_Xtn  58 clyvlNKiDlisleeldelare............pnsvviSaekelnldeLkeki 100
                    ++v NK+Dlis+ee  + +++              +++iSa+++ln+d+L  +i
    EPA05443.1   8 IVIVQNKVDLISYEEALSNHQDitkfvkgthaakAPIIPISAQSGLNIDALIGAI 62 
                   57899*******999766666456788899888668999***********98766 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.84
  MMR_HSR1_Xtn  8 stvkltklde..etvkkilkeykihnaevl 35
                  st+k+ + de  e ++++l+++ +++  ++
    EPA05443.1 64 STIKTPERDEskEPIMHVLRSFDVNKPGIK 93
                  444444444444899999999988876665 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.8e-06    0.0063     121     192 ..       3      66 ..       1      68 [. 0.78

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.8e-06
                 TTTE.EEEEEESCGST.HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHHS CS
    GTP_EFTU 121 egvp.iivfiNKmDrl.kaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealvell 192
                 +g++ i+++ NK+D +  +e     +++  k+      +  +g+++  + p++++Sa +g ++++l+ a+ + +
  EPA05443.1   3 LGIQqIVIVQNKVDLIsYEEALSNHQDIT-KF------V--KGTHA-AKAPIIPISAQSGLNIDALIGAIESTI 66 
                 6777799999******7777777777777.77......4..44444.368*****************9998766 PP

>> ProQ_C  ProQ C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       1.9   6.9e+03       5      16 ..     111     122 ..     109     122 .. 0.78
   2 ?   11.4   0.0   4.5e-05      0.16       5      36 ..     213     244 ..     211     246 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.9
                 S-TT--B---SS CS
      ProQ_C   5 LkvGqqVkVklG 16 
                   vG+++ +k G
  EPA05443.1 111 FNVGDEIEIKPG 122
                 679999999865 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 4.5e-05
                 S-TT--B---SSSS---EEEEEE-SSSEEEEE CS
      ProQ_C   5 LkvGqqVkVklGkspmpAtileiaKddVrVqL 36 
                 ++vG   + ++G +p+ + ++ i+ +++ V+L
  EPA05443.1 213 IQVGELLRLNIGTAPILGKVTKIKSNNIEVEL 244
                 6999***************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.34s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1591.74
//
Query:       EPA05444.1  [L=160]
Description: universal stress family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-18   66.2   0.0    4.9e-18   66.0   0.0    1.1  1  Usp       Universal stress protein family


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.0   0.0   2.7e-22   4.9e-18       2     141 .]      16     160 .]      15     160 .] 0.88

  Alignments for each domain:
  == domain 1  score: 66.0 bits;  conditional E-value: 2.7e-22
                 -SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH...HHHHHHCTTCEEEEEEEESSHHHHHHH CS
         Usp   2 ykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada...akaaaeaggvkvevvveegdpaeeile 97 
                 +++Il+++D+s+ s+kA+ +A++l  ++++e+ +l v +++  +++     ++++  +++++   +++    +k a++  ++     + + + +e+i+ 
  EPA05444.1  16 FRKILIPFDDSKLSEKAFWYAVNLDMNHKTEILILSVFHSDQLPSSFLDYNAHQTVIEKEKLLNVKLKHnelKKVAEKYNIACNSYMTISSSISESIIS 114
                 79**********************999*****99999998888887766666555555555544444335669************************** PP

                 HHHHTTSSEEEEESCC..SSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
         Usp  98 vaeeedadliVvGsrg..rsglsrlllGSvseyvlrhapcpVlvVr 141
                 +  +   dl+++G+rg   s+ ++l+lGSvs  + +h+p+pVl+V+
  EPA05444.1 115 YIYSTRSDLVIMGTRGnsASTGRKLMLGSVSLEISQHSPVPVLLVK 160
                 ****************88888899*********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       863  (0.0481343); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.35s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 943.39
//
Query:       EPA05445.1  [L=498]
Description: type II secretion system F domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (498 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       908  (0.0506442); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.68u 0.33s 00:00:01.01 Elapsed: 00:00:00.52
# Mc/sec: 2866.28
//
Query:       EPA05446.1  [L=137]
Description: hypothetical protein BG20_I0844 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.066   13.3   0.0       0.11   12.6   0.0    1.4  1  Zf_RING         KIAA1045 RING finger
        1.8    8.5  12.2        3.1    7.7  11.4    1.8  1  HEPN_RiboL-PSP  RiboL-PSP-HEPN


Domain annotation for each model (and alignments):
>> Zf_RING  KIAA1045 RING finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.3e-05      0.11      23      54 ..      67      97 ..      55     100 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.3e-05
     Zf_RING 23 RvCtkvfHegClrklgylqdesalellkrAkt 54
                + C+k fH++C+  ++y+q ++ +++ k  +t
  EPA05446.1 67 KACEKFFHDSCFGTFEYVQ-KTGMSIFKVEHT 97
                57***************99.566666666555 PP

>> HEPN_RiboL-PSP  RiboL-PSP-HEPN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7  11.4   0.00035       3.1      68     133 ..      11      67 ..       2     116 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00035
  HEPN_RiboL-PSP  68 pekllikhllks.salklldwkkknpkkeiikelfklfgenisekinkafidtesnl.kskvleeifk 133
                                + + ++++d++kk+++++ii +++++++e i+e++ + +i+t+s l  sk ++ei+k
      EPA05446.1  11 E----------KpINVNTIDNTKKSKNSTIISRINNSIDEVINEIVLD-LINTNSFLlGSKNIPEIVK 67 
                     3..........3345999******************************.8888887525666777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       748  (0.0417201); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.36s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 808.33
//
Query:       EPA05447.1  [L=165]
Description: response regulator receiver domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.1e-16   58.4   0.2      1e-15   57.9   0.2    1.2  1  Response_reg  Response regulator receiver domain
  ------ inclusion threshold ------
      0.023   14.7   0.6       0.16   12.0   0.0    2.1  2  TIR-like      Predicted nucleotide-binding protein containing
      0.038   14.3   0.1      0.093   13.0   0.0    1.7  1  RNA_binding   RNA binding
      0.062   13.1   0.1      0.089   12.6   0.1    1.3  1  PPP1R35_C     Protein phosphatase 1 regulatory subunit 35 C-t


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.9   0.2   2.3e-19     1e-15       1     111 [.       3     121 ..       3     122 .. 0.89

  Alignments for each domain:
  == domain 1  score: 57.9 bits;  conditional E-value: 2.3e-19
                   EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHH....HHHH......ESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEESSTSHHHHH CS
  Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealell....keek......vdlillDinmpgmdGlellkeireedpelpviiltahseeedav 87 
                   +liv+D+ +++e  +++le+++  +v  a+dg++al+ +    +  +      +d+++lD ++pg +G+++++ei  + p+ ++++ +a+ e++ ++
    EPA05447.1   3 ILIVEDEIDLLEEYQTFLESHKH-TVVLATDGESALKTFfskmQ--SgtntsyFDIVILDYQLPGKNGMDVASEILSKCPDQRILFASAYVEDTLKE 96 
                   8********************99.999**********9986541..2556678*************************************9977777 PP

                   HHHHC.TESEEEESSG-HHHHHHHH CS
  Response_reg  88 ealka.gaddflsKpfdpeeLlkal 111
                       +  +++ l+Kpf+ + +l+++
    EPA05447.1  97 SIKTLkQIVELLQKPFSLQTMLNII 121
                   776442799**********999887 PP

>> TIR-like  Predicted nucleotide-binding protein containing TIR-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   3.5e-05      0.16      12      58 ..      12      58 ..       2      66 .. 0.90
   2 ?    0.7   0.1      0.11   4.9e+02      14      48 ..      92     125 ..      86     131 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.5e-05
    TIR-like 12 aaeevkelLeklglepiileeqvnkgktiiekleealksvdfaivll 58
                + ee +++Le++++++++ +++ +++kt++ k+++ ++++ f iv+l
  EPA05447.1 12 LLEEYQTFLESHKHTVVLATDGESALKTFFSKMQSGTNTSYFDIVIL 58
                567899***************************************98 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.11
    TIR-like  14 eevkelLeklglepiileeqvnkgktiiekleeal 48 
                 +++ke ++    ++++l +++++++t+++ +e+ +
  EPA05447.1  92 DTLKESIK-TLKQIVELLQKPFSLQTMLNIIEDTS 125
                 55666666.33467778888999999999988876 PP

>> RNA_binding  RNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.1e-05     0.093      19      89 ..      35     103 ..      34     132 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.1e-05
                  HHHHTTSTTSE---EEEEEE-CCC-EEEEEEEEESSHHHHHHHHHHHHHHCCCCH....HHHHHCCHCCB-TTSE CS
  RNA_binding  19 ealsnllpeeeveieeeeaeGhygnpitileaelekkkakkvlkkllellreeei....keLlkeleervdekgk 89 
                  +al++++ +     ++ + +++++  i+il ++l +k+  +v++++l++  +++i     +++++l+e +++ ++
   EPA05447.1  35 SALKTFFSKM----QSGTNTSYFD--IVILDYQLPGKNGMDVASEILSKCPDQRIlfasAYVEDTLKESIKTLKQ 103
                  7999999866....4677888998..*****************************9*999999999998775555 PP

>> PPP1R35_C  Protein phosphatase 1 regulatory subunit 35 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1     2e-05     0.089      25      74 ..      88     143 ..      72     164 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2e-05
   PPP1R35_C  25 raveekleksettkksiee......kaaegvNvprdqslYkdLvsldvdeeelisq 74 
                 + ve++l++s +t k+i e      +  + +N+ +d s+Y++L +l+vd ++l + 
  EPA05447.1  88 AYVEDTLKESIKTLKQIVEllqkpfSLQTMLNIIEDTSTYTELEKLNVDIKNLKNI 143
                 5666777777777666666677699999*********************9988655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1269  (0.0707792); expected 358.6 (0.02)
Passed bias filter:                      631  (0.0351944); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.36s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 958.47
//
Query:       EPA05448.1  [L=237]
Description: hypothetical protein BG20_I0864 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-18   67.0   0.7    1.8e-18   66.7   0.7    1.0  1  ATPase           KaiC
    1.5e-06   27.6   0.0    2.2e-06   27.1   0.0    1.3  1  Rad51            Rad51
    0.00022   20.9   2.9    0.00049   19.9   2.9    1.6  1  DUF835           Protein of unknown function (DUF835)
     0.0011   18.2   1.9       0.71    8.9   0.0    2.1  2  PAXNEB           PAXNEB protein
     0.0011   18.9   0.1     0.0077   16.2   0.1    2.0  1  NACHT            NACHT domain
     0.0019   17.5   0.0     0.0024   17.2   0.0    1.2  1  DUF2075          Uncharacterized conserved protein (DUF2075)
     0.0029   17.5   0.8     0.0041   17.1   0.8    1.1  1  ATPase_2         ATPase domain predominantly from Archaea
     0.0036   16.9   0.6     0.0045   16.5   0.6    1.3  1  Elong_Iki1       Elongator subunit Iki1
     0.0036   17.7   0.0     0.0049   17.3   0.0    1.4  1  AAA_16           AAA ATPase domain
     0.0054   16.5   0.0      0.011   15.5   0.0    1.5  1  Sigma54_activat  Sigma-54 interaction domain
     0.0056   17.0   0.0     0.0084   16.4   0.0    1.3  1  AAA_22           AAA domain
     0.0084   15.5   0.0      0.012   15.0   0.0    1.4  1  DnaB_C           DnaB-like helicase C terminal domain
  ------ inclusion threshold ------
      0.012   15.6   2.1       0.41   10.7   2.1    2.3  1  AAA_14           AAA domain
      0.016   14.8   0.0       0.12   11.9   0.0    1.9  1  AAA_25           AAA domain
       0.02   15.5   0.2       0.31   11.6   0.2    2.2  1  AAA_18           AAA domain
      0.041   14.5   0.1       0.11   13.1   0.1    1.7  1  AF2331-like      AF2331-like
      0.042   13.9   2.6      0.072   13.1   2.6    1.4  1  ResIII           Type III restriction enzyme, res subunit
       0.05   13.5   1.0       0.48   10.3   1.0    2.1  1  NTPase_1         NTPase
       0.05   13.8   2.0       0.42   10.8   0.2    2.3  2  Roc              Ras of Complex, Roc, domain of DAPkinase
      0.057   12.8   0.2       0.12   11.7   0.1    1.5  2  FtsK_SpoIIIE     FtsK/SpoIIIE family
       0.08   12.1   0.5       0.13   11.4   0.5    1.6  1  NB-ARC           NB-ARC domain
       0.15   12.5   1.3        0.3   11.5   1.3    1.6  1  AAA              ATPase family associated with various cellul
       0.32   10.6   3.8        2.1    7.9   3.8    2.0  1  EMG1             EMG1/NEP1 methyltransferase


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.7   0.7   2.4e-21   1.8e-18       1     228 [.       5     231 ..       5     233 .. 0.82

  Alignments for each domain:
  == domain 1  score: 66.7 bits;  conditional E-value: 2.4e-21
      ATPase   1 vktgIeglDeilkgGipegrvvlitGepGtGKtifalq....FlikgaekygepgvfvtveepaedlrenakslGwdlekleeegklaiidasesaees 95 
                 ++tg e++D+ + gGip  + v i Ge GtGK+ +a+q    +l +  +k + + ++  +e + ++ ++++ksl  ++ k   +++l+++ ++ ++++ 
  EPA05448.1   5 IPTGNEEFDRQFGGGIPTPSLVFIEGEHGTGKSAIAAQimngYLTTKTKK-NVK-LLCIIENTVTQYIQKMKSLTFNFSKPFVRNQLIFVPIFIKNAKW 101
                 69**********************************99555566666555.444.5556999*********************************9884 PP

      ATPase  96 aeekdkedleelieelaeaikeika..krvviDsitglayeekeavaReilrqlvrvlkklgvTailvsekssseeaaggygveefivdgvivLdlkei 192
                     ++++ e+++  ++e i+++      ++iDsi+++  ++++++    +  + +++  +g T i++s  s+  +++   ++   ++d  ++L    +
  EPA05448.1 102 ----SENNSEKILPAIQEFINQKLTlvDGIIIDSISPM-VINSNNQSIMSFLSFCKQVVSKGKTIIITSHSSDF-SKTANTALIG-ASDVYLKLGTVIV 193
                 ....4677788888888888776554599*********.7777777777888999999999********96655.5555555666.6************ PP

      ATPase 193 eeelvRtleivkmRgtk.hskkehpfeIte.egikvle 228
                  ++ v+tl+i+k+ g+k +    + fe++   gik+++
  EPA05448.1 194 GSREVKTLKIIKLLGAKdTPESGFAFEVDLiFGIKIVP 231
                 ************98876144556778888878888765 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   2.9e-09   2.2e-06      16     141 ..       2     132 ..       1     138 [. 0.72

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 2.9e-09
                 S-EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEESSS---GGGGHHHHHHT...T--HHHHGGGEEEEE- CS
       Rad51  16 llqlttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyidtegtfrperlveiaery...kldkeevlenvayaRa 111
                 + ++ tG++++D+  gGGi+t s+  i Ge+++Gk+ ++ ++     l ++++   +  + i+   t   +++ ++   +    + ++ +   + +  a
  EPA05448.1   2 VFTIPTGNEEFDRQFGGGIPTPSLVFIEGEHGTGKSAIAAQIM-NGYLTTKTKKNVKLLCIIENTVTQYIQKMKSLTFNFskpFVRNQLIFVPIFIKNA 99 
                 56899**********************************9984.5667777766667777777777777777777775553212455556666666666 PP

                 -STTHHHHHHHHTHHHHHHS-EEEE...EEETT CS
       Rad51 112 ytiehqeellqqaaallaedkfall...ivDsv 141
                   +e+ +e +  a +++ ++k++l+   i+Ds+
  EPA05448.1 100 KWSENNSEKILPAIQEFINQKLTLVdgiIIDSI 132
                 666666666666666677777777433377776 PP

>> DUF835  Protein of unknown function (DUF835)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   2.9   6.2e-07   0.00049      47     121 ..      96     167 ..      40     180 .. 0.63

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 6.2e-07
      DUF835  47 ltkveeentvsPtnlekltetivkflkeaekgvvliDgleyLvlengFesvlkflltlkDavllkngtlilvidk 121
                 + +++  +++s + l++++e i+++l+      ++iD++  +v++++ +s++ fl+  k +v   ++t+i++   
  EPA05448.1  96 IKNAKWSENNSEKILPAIQEFINQKLTLVD--GIIIDSISPMVINSNNQSIMSFLSFCKQVVSK-GKTIIITSHS 167
                 333333335555556666666666666666..7**************************87655.5555555444 PP

>> PAXNEB  PAXNEB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0   0.00091      0.71      18      45 ..       4      31 ..       2      43 .. 0.87
   2 !    8.1   1.1    0.0016       1.3     173     262 ..      88     172 ..      46     189 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00091
      PAXNEB 18 ltStGtpsLDklLgGGLplGsillieEd 45
                ++ tG++++D+ +gGG+p  s++ ie +
  EPA05448.1  4 TIPTGNEEFDRQFGGGIPTPSLVFIEGE 31
                788**********************954 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0016
      PAXNEB 173 e........ekeslkespryssllnqiqqllkkesfsaptkknvlRivipsLlspllydyppeeskpedllkFLhsLrallrssnlvalitlplslia 262
                 +        ++++ +e++  +++l  iq+++++    + t   v  i+i s+ sp++      +s+++++++FL   ++++++ +++++ + +++  +
  EPA05448.1  88 QlifvpifiKNAKWSENN-SEKILPAIQEFINQ----KLTL--VDGIIIDSI-SPMVI-----NSNNQSIMSFLSFCKQVVSKGKTIIITSHSSDFSK 172
                 033333333445555566.79************....5555..7889****8.56662.....6899***************9999998888887764 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   9.8e-06    0.0077       2     131 ..      25     169 ..      24     181 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 9.8e-06
                 CEEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-..................-HCHHHCCCCTS--SSS-CCHHHHCCSCCCEE. CS
       NACHT   2 lvilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgna...............rsladllfsqlpepaapvsevwavllelperlL. 84 
                 lv+++Ge G GK++ +++++    + k +++ +kl+  ++   ++ ++++               + +  +  ++ ++++ +++++   ++e  ++ L 
  EPA05448.1  25 LVFIEGEHGTGKSAIAAQIMNGYLTTKTKKN-VKLLCIIENTVTQYIQKMksltfnfskpfvrnqLIFVPIFIKNAKWSENNSEKILPAIQEFINQKLt 122
                 79*******************9999888775.6777666666666666665566666666333332233333344555555555555555555555555 PP

                 ....EEEE-STT-SS-TCH.........HHHHHCTTTTT--EEEEEEECCC CS
       NACHT  85 ....lilDglDelvtdlgqkekqpvrtlLselirkkllpeasllltvrpra 131
                     +i+D++  +v   +   +q++   L + +++ + ++ ++++t++++ 
  EPA05448.1 123 lvdgIIIDSISPMVINSN---NQSIMSFL-SFCKQVVSKGKTIIITSHSSD 169
                 556666666666665333...35666655.677777777777777777665 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   3.1e-06    0.0024       2      51 ..      24      73 ..      23     115 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.1e-06
     DUF2075  2 avvlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlreal 51
                ++v+++G+ GtGK+ ++ ++++ + +++ ++++++l   ++ v  + +++
  EPA05448.1 24 SLVFIEGEHGTGKSAIAAQIMNGYLTTKTKKNVKLLCIIENTVTQYIQKM 73
                689*******************9966666666655554444444444444 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.8   5.3e-06    0.0041      21     167 ..      24     169 ..      21     186 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.3e-06
    ATPase_2  21 eiyfiYGpegsGKtaLlkeiienl.edkdkyviyyialreesiskldefie..eeeekkklekal..giavpkaeleeilkeksklvfkaielllekik 114
                 + +fi G  g GK+a+  +i++     k k+ + +  + e   +++ ++++  +     +++k++  ++ +    + +  k   ++ +k + ++ e i+
  EPA05448.1  24 SLVFIEGEHGTGKSAIAAQIMNGYlTTKTKKNVKLLCIIENTVTQYIQKMKslT----FNFSKPFvrNQLIFVPIFIKNAKWSENNSEKILPAIQEFIN 118
                 679*******************87555555555555554444444444422222....22222223333333333444445556677888888889999 PP

    ATPase_2 115 kkgkk.iiiiiDelqklidlglngaellvkeLlnliesltkekhlcvviclsSe 167
                 +k +    iiiD +  ++   +n++++ + ++l++ ++  ++ +++++   sS+
  EPA05448.1 119 QKLTLvDGIIIDSISPMV---INSNNQSIMSFLSFCKQVVSKGKTIIITSHSSD 169
                 988764359999999888...8888*************9999999999999997 PP

>> Elong_Iki1  Elongator subunit Iki1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.6   5.8e-06    0.0045      29     135 ..      43     170 ..      27     205 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.8e-06
  Elong_Iki1  29 lleelirrakssktkvifvsfetlkk....................pkgvdvfieaterskk.lkelakeiksalspkssekkkkalviiDslnplasl 106
                 +++ +++  +++++k + +  +t+++                       v  fi+ +++s++  +++  +i++ +++k +       +iiDs++p++ +
  EPA05448.1  43 IMNGYLTTKTKKNVKLLCIIENTVTQyiqkmksltfnfskpfvrnqLIFVPIFIKNAKWSENnSEKILPAIQEFINQKLT---LVDGIIIDSISPMVIN 138
                 55556666666666666666666666666666666666664444333445589999999986688888888888855443...45679******99885 PP

  Elong_Iki1 107 ikeeslaafls...sllsspsvslvavYHtdv 135
                  +++s+++fls   +++s+ ++ +++ + +d+
  EPA05448.1 139 SNNQSIMSFLSfckQVVSKGKTIIITSHSSDF 170
                 56666666554222888777888888888887 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   6.3e-06    0.0049      22      51 ..      21      50 ..      12     164 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 6.3e-06
      AAA_16 22 grpelvllsGesGvGKsslvrellralekd 51
                ++p+lv++ Ge G+GKs+++ ++++ + ++
  EPA05448.1 21 PTPSLVFIEGEHGTGKSAIAAQIMNGYLTT 50
                4579*******************9733333 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.4e-05     0.011      20      55 ..      21      57 ..      10      73 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.4e-05
                     TSSS-EEEECSTTSSHHHHHHHHHH.HSTTTTS-EEE CS
  Sigma54_activat 20 ktdlsvlitGesGtGKellaraihe.askrkekpfva 55
                     +t++ v+i+Ge GtGK+ +a +i +   + k+k+ v+
       EPA05448.1 21 PTPSLVFIEGEHGTGKSAIAAQIMNgYLTTKTKKNVK 57
                     677889**************99988533334444444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.1e-05    0.0084       6     104 ..      24     136 ..      21     179 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.1e-05
      AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka..................erlsseellealeqal 86 
                 +++++ Ge GtGK+  ++++++ +   +      ++ v+  +  +++ ++  +++ + + +  k                   ++++se +l a+++ +
  EPA05448.1  24 SLVFIEGEHGTGKSAIAAQIMNGYLTTK-----TKKNVKLLCIIENTVTQYIQKMKSLTFNFSKPfvrnqlifvpifiknakwSENNSEKILPAIQEFI 117
                 678999*****************96443.....34444444444444444444444444432222444777777777777778899************* PP

      AAA_22  87 rarav.ielliiDEaqhlr 104
                 +++ + +  +iiD +  + 
  EPA05448.1 118 NQKLTlVDGIIIDSISPMV 136
                 ***9999999999877654 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.5e-05     0.012       2     108 ..       5     125 ..       4     163 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.5e-05
                 BXSSTHHHHHHCT.SBXTTXEEEEEEXTTSSHHHHHHHHHHHHH.HCSTSEE.EEEESSSXHHHHHHHHHHHHHTXXHHHHHH...........TTSXH CS
                 xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxx RF
      DnaB_C   2 lstgfkdLDklts.GlqkgdliiiAarpsmGktalalniaenaa.vkeklpv.avfslemsaeqlvqRllsseaeidskklrt...........gklke 86 
                 ++tg +++D+ ++ G+    l+ i +  ++Gk+a+a +i++    +k+k++v ++  +e + +q +q++ s + + ++  +r+           +k +e
  EPA05448.1   5 IPTGNEEFDRQFGgGIPTPSLVFIEGEHGTGKSAIAAQIMNGYLtTKTKKNVkLLCIIENTVTQYIQKMKSLTFNFSKPFVRNqlifvpifiknAKWSE 103
                 789999***77751688889********************885525666666155678**********9997776665555443333333333266666 PP

                 HHHHHHHHHHHHHHHSEEEEEE CS
                 xxxxxxxxxxxxxxxxxxxxxx RF
      DnaB_C  87 edweklteaieelseaklfidd 108
                 ++ ek+  ai+e+ ++kl++ d
  EPA05448.1 104 NNSEKILPAIQEFINQKLTLVD 125
                 7777777777777776666655 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   2.1   0.00053      0.41       4     119 ..      25     184 ..      22     190 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00053
      AAA_14   4 ilvitGaRrvGKTtllkqlikell.....................vkkesilyinldderd................kkladpekllelileklkeekk 65 
                 +++i+G   +GK+ ++ q+++ +l                     ++k + l +n+ ++                  + ++++ek+l +i+e +++ k 
  EPA05448.1  25 LVFIEGEHGTGKSAIAAQIMNGYLttktkknvkllciientvtqyIQKMKSLTFNFSKPFVrnqlifvpifiknakwS-ENNSEKILPAIQEFINQ-KL 121
                 678999999999999999999999987777777777766666666666666666666655455666666665443211.11233555555554433.22 PP

      AAA_14  66 ty...lflDEiqev......pewekalkslvdegknldvivtGSnskllskeiatslagrvae 119
                 t+   +++D i+ +      +++ ++l  + +  ++++ i+  S+s++ sk ++t l g  ++
  EPA05448.1 122 TLvdgIIIDSISPMvinsnnQSIMSFLSFCKQVVSKGKTIIITSHSSDFSKTANTALIGASDV 184
                 223558888888778988885555555555554455688999999999999999999987765 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00016      0.12      28     189 ..      18     167 ..      13     170 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00016
      AAA_25  28 gllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgeal...rddarllvldlagv.eslpLfakdrg 122
                 g +p  +l+ + G +gtGK+++a +++  ++t k        +++k l +  E++  +  ++++ +  ++     + +l ++ +  + ++   + ++++
  EPA05448.1  18 GGIPTPSLVFIEGEHGTGKSAIAAQIMNGYLTTKT------KKNVKLLCII-ENTVTQYIQKMKSLTFNFskpFVRNQLIFVPI--FiKNAK-W-SENN 105
                 557888999******************99998662......2566666664.88887888888887777754322333344433..322322.2.2344 PP

      AAA_25 123 gtlltadvdaleaaieevegvrlvviDplsralggdensnsdvgalvealeriarrtgaavllvhHv 189
                 ++++ +++++ +++      v+ ++iD++s ++ +++n    + ++++ ++++   +g +++++ H+
  EPA05448.1 106 SEKILPAIQEFINQKL--TLVDGIIIDSISPMVINSNN--QSIMSFLSFCKQV-VSKGKTIIITSHS 167
                 4444455544444322..23888888888888887766..5567777777776.5777777777776 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2    0.0004      0.31       1      91 [.      26     175 ..      26     192 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0004
      AAA_18   1 IlltGtpGvGKttlakeLskrlgf...............gvnlrdvakenglllevdpe..............aldeskrldedkldklldaleenss. 69 
                 +++ G +G+GK+ +a  +  ++g+                  +++++++  +l+ ++ +              +              + +  e+ns+ 
  EPA05448.1  26 VFIEGEHGTGKSAIAAQI--MNGYlttktkknvkllciiENTVTQYIQKMKSLTFNFSKpfvrnqlifvpifiK--------------NAKWSENNSEk 108
                 799***************..334445555444455666655566666665555555544433333333332221..............22222222223 PP

      AAA_18  70 .............................................aleegknlvidghlaeleseaa 91 
                                                                 +gk+++i +h +++ ++a+
  EPA05448.1 109 ilpaiqefinqkltlvdgiiidsispmvinsnnqsimsflsfckqVVSKGKTIIITSHSSDFSKTAN 175
                 3444444444544555555557777777777777777777777776677777777777777766665 PP

>> AF2331-like  AF2331-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   0.00014      0.11      10      50 ..     146     186 ..     137     204 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00014
                  HHHHHHHCC--TTEEEEEE--EEEEEEEEEEETTEEEEEEE CS
  AF2331-like  10 sflkfleknleedkvvvvssdvtdvdkkesesylGkkeyfl 50 
                  sfl f ++ + ++k ++++s   d+ k    + +G  + +l
   EPA05448.1 146 SFLSFCKQVVSKGKTIIITSHSSDFSKTANTALIGASDVYL 186
                  8***************************99999**999886 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   2.6   9.3e-05     0.072      28      85 ..      27      97 ..      22     178 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.3e-05
                EEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG.................G CS
      ResIII 28 likmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseayke.............i 85
                +i+ + GtGK+ +aa+++  +l+ + ++++ +l+  ++ + q ++++k+++ +  k              +
  EPA05448.1 27 FIEGEHGTGKSAIAAQIMNGYLTTKTKKNVKLLCIIENTVTQYIQKMKSLTFNFSKPfvrnqlifvpifiK 97
                577788**********************9999999999999999888666554433344444444333333 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.0   0.00061      0.48       2     137 ..      26     171 ..      25     204 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00061
                 EEEE--TTSSHHHHHHHHHH....HH...GGGEEEEEEEEE-------EEEEEET.T--EEEEEETT...---SSEETTEEE-HHHHHHHHHHHHHHHH CS
    NTPase_1   2 vfiTGppGvGKtTlvkkvle....llkssgvkvgGfyteevreggrrigFkivdlasgeegiLarve...akreprvgkyvvdvesfeelalealrkal 93 
                 vfi G+ G+GK+ +  ++++    +  +++vk+  ++ + v++  ++    + +l+ +  +++ r++    +  +++ k+  +    +e +l+a+++ +
  EPA05448.1  26 VFIEGEHGTGKSAIAAQIMNgyltTKTKKNVKLLCIIENTVTQYIQK----MKSLTFNFSKPFVRNQlifVPIFIKNAKWSEN---NSEKILPAIQEFI 117
                 78889999999999888876322122455777777777766655544....44555555666666665444455555555544...3333455555554 PP

                 ....HHH-EEEE---STTGGG-HH.....HHHHHHHHHTTTSEEEEE--SS-.- CS
    NTPase_1  94 ....seadviviDEiGkmElkskk.....fkeaveevLksekpvlavihrrk.d 137
                     +  d i+iD i +m  +s++     f +  ++v++++k ++++ h ++ +
  EPA05448.1 118 nqklTLVDGIIIDSISPMVINSNNqsimsFLSFCKQVVSKGKTIIITSHSSDfS 171
                 2111566899********8877643333399999*************9998752 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   0.00053      0.42       4      58 ..      28      78 ..      25      81 .. 0.74
   2 ?    2.2   0.1      0.26     2e+02      10      37 ..     157     184 ..     154     206 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00053
                EESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEE CS
         Roc  4 lvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvkl 58
                + G++g+GK+ ++ +++++  ++k+k+ + +  + ++++  ++    +k+k++++
  EPA05448.1 28 IEGEHGTGKSAIAAQIMNGYLTTKTKKNVKLLCIIENTV--TQ--YIQKMKSLTF 78
                559********************9999998877766542..22..2234555555 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.26
                 SSHHHHHHCHCT-CCC-EEETTTTEEEE CS
         Roc  10 vGKtsllkrfvedkfsekekstigvdfl 37 
                  GKt +++++ +d  ++ +++ ig++ +
  EPA05448.1 157 KGKTIIITSHSSDFSKTANTALIGASDV 184
                 6**********99999999999998644 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00016      0.12      42      78 ..      26      62 ..      18      83 .. 0.87
   2 ?   -3.2   0.0       5.6   4.4e+03      23      48 ..     158     182 ..     153     183 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00016
                  EEEE--TTSSHHHHHHHHHHHHHTT--TTTEEEEEE- CS
  FtsK_SpoIIIE 42 llvaGatgsGKStalntLilSlatthtPeeVqliliD 78
                  + + G  g+GKS     ++ + +tt+t ++V+l++i 
    EPA05448.1 26 VFIEGEHGTGKSAIAAQIMNGYLTTKTKKNVKLLCII 62
                  6789*******************************95 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 5.6
                   EEETTS-EEEEEGGGS-.SEEEE--T CS
  FtsK_SpoIIIE  23 gkeisgnplvldlkkmashllvaGat 48 
                   gk i+   + +d +k a ++ ++Ga+
    EPA05448.1 158 GKTIIITSHSSDFSKTA-NTALIGAS 182
                   56666667888999999.99999986 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.5   0.00017      0.13      22      53 ..      25      56 ..      20     176 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00017
                EEEEEESTTSSHHHHHHHHCCSHCCCCCCBTE CS
      NB-ARC 22 vvalvGmgGvGKttlakqilnksdevegrFds 53
                +v++ G  G GK+ +a+qi+n + +++ + ++
  EPA05448.1 25 LVFIEGEHGTGKSAIAAQIMNGYLTTKTKKNV 56
                79******************986666555444 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.3   0.00038       0.3       2     111 ..      27     167 ..      26     190 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00038
                 EEESSTTSSHHHHHHHHHHHH.......THE...EEEEETTTCSSS............................STTHHHHHHHHHHHHHHHTS.TS.E CS
         AAA   2 llyGppGtGKTllakavakel.......gve...fleisgsellsk............................yvgesekkirelfkeakeka.kp.s 60 
                  + G  GtGK+++a ++++         +v+   ++e  +++ ++k                            + +++++ki   ++e  +++ +   
  EPA05448.1  27 FIEGEHGTGKSAIAAQIMNGYlttktkkNVKllcIIENTVTQYIQKmksltfnfskpfvrnqlifvpifiknakWSENNSEKILPAIQEFINQKlTLvD 125
                 56799**************95444333212243322222223222244444444446666668888888888887777777777777774333344447 PP

                 EEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS CS
         AAA  61 ilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnr 111
                  ++iD i  ++ ++       +++ +  +l++ ++v +k +  ++i+++++
  EPA05448.1 126 GIIIDSISPMVINS-------NNQSIMSFLSFCKQVVSKGK--TIIITSHS 167
                 78888888888777.......56667777777777777544..44444444 PP

>> EMG1  EMG1/NEP1 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   3.8    0.0027       2.1      96     141 ..      42     110 ..      37     210 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0027
                 HHHCCSEEEETTEE.SCEEEECS-HHHHCCC.SEEEEE-TTSEE-......................... CS
        EMG1  96 qLLkklsirategeekLlkviknpitdhlppgskiillsesaekk........................l 141
                 q+++    ++t+++ kLl +i+n++t+++++  k +++++s + +                        l
  EPA05448.1  42 QIMNGYLTTKTKKNVKLLCIIENTVTQYIQK-MKSLTFNFSKPFVrnqlifvpifiknakwsennsekiL 110
                 66666677889999****************9.68888888888444455555554444444444444441 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       772  (0.0430587); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.66u 0.36s 00:00:01.02 Elapsed: 00:00:00.53
# Mc/sec: 1357.04
//
Query:       EPA05449.1  [L=144]
Description: response regulator receiver domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-24   86.8   0.2    1.2e-24   86.6   0.2    1.1  1  Response_reg  Response regulator receiver domain


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.6   0.2   6.9e-29   1.2e-24       1     111 [.       8     120 ..       8     121 .. 0.95

  Alignments for each domain:
  == domain 1  score: 86.6 bits;  conditional E-value: 6.9e-29
                   EEEESSSHHHHHHHHHHHH.HTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEESSTS.HHHHHHHHHCTES CS
  Response_reg   1 vlivdDdplvrellrqlle.eegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviiltahse.eedavealkagad 95 
                   +li+dD++++re  +  ++ + ++ ++ +a++g e l+l+ + k+d+illD++mpg+dGl++l+ i ++dp ++vi+ ta+++ ++ +++++k ga+
    EPA05449.1   8 ILIIDDSKAFREFAKYSIReDIKFVNIFQASTGVEGLQLFLKYKPDVILLDWKMPGIDGLTVLEAIVKDDPATKVIMTTAYDDdQNLINDMMKRGAF 104
                   8******************778889******************************************************9998577788999***** PP

                   EEEESSG-HHHHHHHH CS
  Response_reg  96 dflsKpfdpeeLlkal 111
                    f+ Kp+++ +Llk +
    EPA05449.1 105 SFVPKPMNRINLLKVI 120
                   **********999977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.33s 00:00:00.86 Elapsed: 00:00:00.53
# Mc/sec: 819.01
//
Query:       EPA05450.1  [L=82]
Description: hypothetical protein BG20_I0859 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       987  (0.0550505); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.33s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 484.49
//
Query:       EPA05451.1  [L=481]
Description: PAS domain S-box [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-39  134.5  43.3      1e-37  129.6  24.0    3.6  3  MCPsignal        Methyl-accepting chemotaxis protein (MCP) si
    1.3e-09   38.0   0.3    8.5e-09   35.4   0.0    2.3  2  PAS              PAS fold
    6.6e-09   36.0   0.4    2.9e-08   33.9   0.1    2.3  2  PAS_9            PAS domain
    3.4e-08   33.6   0.1    1.1e-07   32.1   0.1    1.8  1  PAS_3            PAS fold
     0.0005   20.3   0.0      0.002   18.3   0.0    2.0  2  PAS_4            PAS fold
  ------ inclusion threshold ------
      0.033   13.1  25.3      0.031   13.2   3.9    3.2  3  Spc7             Spc7 kinetochore protein
      0.048   13.0   1.0        1.1    8.5   0.1    2.4  2  Stanniocalcin    Stanniocalcin family
      0.076   13.1   0.9         22    5.2   0.0    3.2  2  HisKA            His Kinase A (phospho-acceptor) domain
       0.25   11.0  26.7          1    9.1  12.3    3.0  2  DUF745           Protein of unknown function (DUF745)
       0.26   11.4  20.5        2.1    8.4   1.3    4.6  5  COG2             COG (conserved oligomeric Golgi) complex com
       0.67   10.1  28.0       0.25   11.5   6.6    3.6  4  Fib_alpha        Fibrinogen alpha/beta chain family
       0.79    8.8  21.3         12    4.8  21.0    2.6  1  APG17            Autophagy protein Apg17
        2.5    6.9  29.5        9.5    5.0  11.2    2.3  2  DUF812           Protein of unknown function (DUF812)
        3.1    7.7  20.9      0.061   13.2   3.9    3.7  4  Sec34            Sec34-like family
        4.3    7.5  15.7       0.17   12.1   4.1    3.1  2  COG5             Golgi transport complex subunit 5
        4.8    7.5  32.6          1    9.7   3.1    4.6  4  DUF948           Bacterial protein of unknown function (DUF94
        8.6    6.9  14.1        4.3    7.9   0.0    4.2  6  T7SS_ESX_EspC    Excreted virulence factor EspC, type VII ESX
        8.9    6.5  15.2        3.6    7.7   4.7    2.9  3  CHDCT2           CHDCT2 (NUC038) domain
        9.4    6.3  31.8       0.45   10.5   2.8    4.1  3  Laminin_II       Laminin Domain II
        9.9    6.5  27.3          6    7.2   1.5    4.8  4  BLOC1_2          Biogenesis of lysosome-related organelles co


Domain annotation for each model (and alignments):
>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   4.7   9.7e-05     0.087     107     169 ..      37      94 ..      15      97 .. 0.79
   2 !  129.6  24.0   1.1e-40     1e-37       9     171 ..     130     292 ..      98     293 .. 0.93
   3 ?    1.8   0.6      0.21   1.9e+02     108     139 ..     299     330 ..     289     341 .. 0.43

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.7e-05
                 ...HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
   MCPsignal 107 esleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasieevnqaveeva 169
                 + le+      +g +l+ + +++l e v + ++++d+v e+  a++ q+++ieev+q+++ +a
  EPA05451.1  37 SQLEN-----FTGEKLTTKIQRSLGETVLMSEQLTDTVAELENATKSQTSGIEEVSQSIQSIA 94 
                 33332.....3688999999***************************************9987 PP

  == domain 2  score: 129.6 bits;  conditional E-value: 1.1e-40
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH............ CS
   MCPsignal   9 eeAeeggkevanvvkqmeeieksskeisdiieVideiadQTNlLALNAaiEAARAGeqGrGFaVVAdEVrkLAersaqaakeiealiieiqkeindsve 107
                 ++ ++ +  v++  +++++++k+ +++ +++e i++ia+QTNlLALNAaiEAARAG+ GrGFaVVA+EVr+LAe+s++ a+ei+++i  +++ +++++ 
  EPA05451.1 130 SKMNSMKSIVSESSNDVKKLAKELSKVDNMTEFITQIAEQTNLLALNAAIEAARAGDVGRGFAVVAEEVRRLAENSKKGAEEISDIISSLKESSDKTTI 228
                 44445567788888999999999**************************************************************************** PP

                 ..HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
   MCPsignal 108 sleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasieevnqaveevakv 171
                 s+e+ +  v+ + + + +  +++k i+++++ev +++qei+aa+e+ s++ ee + a ee+ +v
  EPA05451.1 229 SIEKGNIVVQDAYDVITNILNSIKGITTSITEVVSQMQEISAATEQVSSGTEEATAASEEILSV 292
                 *******************************************************999998665 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.21
                 ..HHHHHHHHHHHHHHHHHCCHHHHHHHHHHH CS
   MCPsignal 108 sleetrqrveegselveetgealkeiveavae 139
                 s+e+ ++  ++ ++  ++t++++k++++ v++
  EPA05451.1 299 SFEDIVNAKDKETQNLQNTNKNIKTLTDIVDS 330
                 33333333333333333333333333333332 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1       1.6   1.5e+03       7      31 ..     156     180 ..     155     182 .. 0.92
   2 !   35.4   0.0   9.5e-12   8.5e-09      10     106 ..     333     428 ..     324     431 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.6
                 HHHSSSEEEEEETTSBEEEECHHHH CS
         PAS   7 leslpdpifvvDedgrilyvNaaae 31 
                 +++++++i  + e+++ l  Naa+e
  EPA05451.1 156 VDNMTEFITQIAEQTNLLALNAAIE 180
                 6899******************987 PP

  == domain 2  score: 35.4 bits;  conditional E-value: 9.5e-12
                 SSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEECTTSSEEEEEEEEEEEEETTEEEEEE CS
         PAS  10 lpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfklrdgrpihlevraspvrdaggeilgf 106
                 + ++i ++D dg+i+y N+++ + + ++ ee+ g+ + +  +e +d++++ell++ +++g+ ++++ +++ + dg+++++ +  +p +d+  ++ g+
  EPA05451.1 333 SSTMISILDIDGIINYSNKSFLDYTKFPLEEIHGERYQIIKSEWHDETVHELLWKTINNGNLFQGYLRNRAK-DGSIFWVKTSITPKFDENNTLQGY 428
                 66899****************************975544333333345************************.****************98876665 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       8.7   7.8e+03      37      76 ..      21      59 ..      14      65 .. 0.68
   2 !   33.9   0.1   3.2e-11   2.9e-08       3      96 ..     336     429 ..     333     437 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 8.7
       PAS_9 37 tdlfvtdpeanerlraaleqgrk.kerevevvlirkngetf 76
                t+++  d++ n ++++++ q+++ + +  ++ ++r+ get+
  EPA05451.1 21 TNII--DKKINIKKNDVISQLENfTGEKLTTKIQRSLGETV 59
                5666..77777777777777776666677777777766665 PP

  == domain 2  score: 33.9 bits;  conditional E-value: 3.2e-11
       PAS_9   3 gilidnpdgril.yaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetfwvlltaspvkdddgelvgii 96 
                 +i i + dg i+ y N+++l+ + +  ee+ g ++  +    +d+  +e l++ +++g    +++ + ++ k+g+ fwv+ +++p +d++++l+g+i
  EPA05451.1 336 MISILDIDG-IInYSNKSFLDYTKFPLEEIHGERYQIIKseWHDETVHELLWKTINNGN--LFQGYLRNRAKDGSIFWVKTSITPKFDENNTLQGYI 429
                 4667889**.************************88888*99*****************..********************************9977 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.1   1.2e-10   1.1e-07       3      86 ..     348     429 ..     346     431 .. 0.84

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 1.2e-10
       PAS_3   3 yvserveeilGyspeellgkveswldlvhpeD.rervrealqealkkgepyegeyRirrkdGeyrwveararvirdengkpvrvi 86 
                 y ++++ +++ +  ee+ g     ++++  e   e v e l++ +++g  ++g+ R r kdG+++wv++++++ +den+  + +i
  EPA05451.1 348 YSNKSFLDYTKFPLEEIHGE---RYQIIKSEWhDETVHELLWKTINNGNLFQGYLRNRAKDGSIFWVKTSITPKFDENNTLQGYI 429
                 56777888888888888888...55555555547889*****************************************9988766 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       3.9   3.5e+03       2      30 ..     157     185 ..     156     201 .. 0.76
   2 !   18.3   0.0   2.3e-06     0.002       5     107 ..     334     437 ..     331     439 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3.9
       PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfga 30 
                 d++ + ++ + ++ + l++Naa+++  + 
  EPA05451.1 157 DNMTEFITQIAEQTNLLALNAAIEAARAG 185
                 77788888899999999999998874443 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 2.3e-06
       PAS_4   5 pdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.pgeerhyelrllPlrdesGevigvlvis 102
                 + ++ +ld dg + y N+++ ++ ++p ee+ G++++ + +e + + +++ l + +  +   +     +  +g+  ++ ++++P +de+ + +g++ + 
  EPA05451.1 334 STMISILDIDGIINYSNKSFLDYTKFPLEEIHGERYQIIKSEWHDETVHELLWKTINNGNLFQGYLRNRAkDGSIFWVKTSITPKFDENNTLQGYIRVD 432
                 5678899******************************5444448899999999999999777776655559************************9888 PP

       PAS_4 103 rDiTe 107
                 + iTe
  EPA05451.1 433 TPITE 437
                 88887 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   3.2      0.11        97     190     251 ..      36      98 ..      18     115 .. 0.78
   2 ?    8.0   4.7    0.0013       1.2     140     254 ..     110     223 ..     106     243 .. 0.81
   3 ?   13.2   3.9   3.4e-05     0.031     207     291 ..     260     344 ..     253     357 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.11
        Spc7 190 aeelesidkeeLe.elreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeia 251
                   +le+ + e+L  +++++l e     e++ + +ael++  +++++ iee++++++++  +i+
  EPA05451.1  36 ISQLENFTGEKLTtKIQRSLGETVLMSEQLTDTVAELENATKSQTSGIEEVSQSIQSIAMAIQ 98 
                 566777776676426888888888888999999999999999999999999999999988887 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0013
        Spc7 140 LkegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesid.keeLeelreelaelkaeieekkkelaelqeqleeleekie 237
                 ++++ e++  ++ +d+e+ +++++ +++++ e ++  ++l +el k  ++ e +++i  +++L +l  +++++ a      +  a + e++ +l+e+ +
  EPA05451.1 110 MMKQSEQITRTIGSDAEKGMSKMNSMKSIVSESSNDVKKLAKELSKVDNMTEFITQIAeQTNLLALNAAIEAARAGD--VGRGFAVVAEEVRRLAENSK 206
                 5678899999999***************************************9*9998899*****99999987632..24677777777777777777 PP

        Spc7 238 elkeqkseleeeiaeae 254
                 + +e++s++ + ++e+ 
  EPA05451.1 207 KGAEEISDIISSLKESS 223
                 77777777766666654 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 3.4e-05
        Spc7 207 elaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevkaleeltgwkivslsg 291
                 e++++++ei++  +++++ +e+ ++ +e+i ++++   +  e+i +a++   ++ + +++++++l++ v++l++ t+++i+ ++g
  EPA05451.1 260 EVVSQMQEISAATEQVSSGTEEATAASEEILSVAQTNLKSFEDIVNAKDKETQNLQNTNKNIKTLTDIVDSLDSSTMISILDIDG 344
                 7899****************999999999988888888888888888888999999************************99864 PP

>> Stanniocalcin  Stanniocalcin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1     0.073        65      72     112 ..      72     112 ..      65     157 .. 0.89
   2 ?    8.5   0.1    0.0013       1.1      86     152 ..     247     313 ..     241     339 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.073
  Stanniocalcin  72 lhsaakfdtqGksfvkeslkCiakgitskvfliirrCsalk 112
                    l +a+k +t G   v +s++ ia +i+   + +i+  +++k
     EPA05451.1  72 LENATKSQTSGIEEVSQSIQSIAMAIQGVASNAIKTMEMMK 112
                    889*********************99988888887766665 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0013
  Stanniocalcin  86 vkeslkCiakgitskvfliirrCsalkrmiaevqeeCylkldiCsvakenpeaivevvklkdlfpnr 152
                    + +s+k i+ +it+ v+++    +a +++ +   e    + +i sva++n +   ++v+ kd+ +++
     EPA05451.1 247 ILNSIKGITTSITEVVSQMQEISAATEQVSSGTEEATAASEEILSVAQTNLKSFEDIVNAKDKETQN 313
                    6689*********9999988877777777777777888999******************99876554 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.025        22      25      62 ..     180     223 ..     169     227 .. 0.73
   2 ?    4.9   0.1     0.029        26      17      63 ..     290     335 ..     244     338 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.025
                 HHHHC........T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHC CS
       HisKA  25 eaLkre......gklteelkeyletiesearrldhlvedlLdls 62 
                 ea +        +   ee++++ e  +++a+ ++++++ l + s
  EPA05451.1 180 EAARAGdvgrgfAVVAEEVRRLAENSKKGAEEISDIISSLKESS 223
                 45444455666633459*********************995544 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.029
                 HHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCC CS
       HisKA  17 LsailgnaeaLkregklteelkeyletiesearrldhlvedlLdlsr 63 
                 Ls+ + n++  ++ +++ ++  ++l+   ++++ l+++v+ l d s+
  EPA05451.1 290 LSVAQTNLKSFEDIVNAKDKETQNLQNTNKNIKTLTDIVDSL-DSST 335
                 67778888888887666789999****************998.7665 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1  12.3    0.0011         1      63     179 ..      61     177 ..      56     184 .. 0.88
   2 ?    2.3   9.9      0.14   1.2e+02      91     166 ..     240     315 ..     176     320 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0011
      DUF745  63 lveqleqelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektqlleaAkkRveeLkkqlkearkd 161
                 + eql++ ++e e++ +++++ +++ ++++++ a+a + + +++    +++k++++  +++ + a++  +++++ ++++ ++ + v++L k+l+++ + 
  EPA05451.1  61 MSEQLTDTVAELENATKSQTSGIEEVSQSIQSIAMAIQGVASNAIKTMEMMKQSEQITRTIGSDAEKGMSKMNSMKSIVSESSNDVKKLAKELSKVDNM 159
                 569**********************99999998888888777777777899*********************************************999 PP

      DUF745 162 lektkkaAykAacAAqeA 179
                  e + + A++ +  A +A
  EPA05451.1 160 TEFITQIAEQTNLLALNA 177
                 999999999865444443 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.14
      DUF745  91 nakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektqlleaAkkRveeLkkqlkearkdlektk 166
                 + ++ +++ ++++   +++++++ +++e  + +eqv++g ++  a+ +++l  A++ +++ +  +++  k+ ++ +
  EPA05451.1 240 AYDVITNILNSIKGITTSITEVVSQMQEISAATEQVSSGTEEATAASEEILSVAQTNLKSFEDIVNAKDKETQNLQ 315
                 4444555555666666677788888888888888888888888888888888888887777777666666655554 PP

>> COG2  COG (conserved oligomeric Golgi) complex component, COG2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   1.3    0.0024       2.1      43     108 ..      44     109 ..      22     120 .. 0.82
   2 ?    6.5   1.2     0.009       8.1      69     122 ..     116     169 ..     109     177 .. 0.85
   3 ?    1.0   0.1      0.45     4e+02      79     112 ..     192     225 ..     185     250 .. 0.68
   4 ?    6.7   0.8     0.008       7.2      79     114 ..     255     292 ..     237     311 .. 0.75
   5 ?    1.9   0.3      0.25   2.2e+02      76     124 ..     280     329 ..     269     335 .. 0.61

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0024
        COG2  43 ekellelvnedyadFvslSghLvglqeeleevesplaaarkkvesvreklsereeeveskleeake 108
                  ++l   + + + + v +S++L++  +ele+ +++ ++  ++v++ +++++++++ v s+  +  e
  EPA05451.1  44 GEKLTTKIQRSLGETVLMSEQLTDTVAELENATKSQTSGIEEVSQSIQSIAMAIQGVASNAIKTME 109
                 567777777888888999**************************************9987654443 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.009
        COG2  69 eeleevesplaaarkkvesvreklsereeeveskleeakeleekrellklllkl 122
                 +  +++ s+ ++ ++k++s+++ +se +++v++  +e +++ ++ e++  + + 
  EPA05451.1 116 QITRTIGSDAEKGMSKMNSMKSIVSESSNDVKKLAKELSKVDNMTEFITQIAEQ 169
                 5667888999999*******************************9988766655 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.45
        COG2  79 aaarkkvesvreklsereeeveskleeakeleek 112
                 a + ++v+ + e+ ++  ee+++ ++  ke  +k
  EPA05451.1 192 AVVAEEVRRLAENSKKGAEEISDIISSLKESSDK 225
                 5556666666666666666666666666655444 PP

  == domain 4  score: 6.7 bits;  conditional E-value: 0.008
        COG2  79 aaarkkvesvreklsereeeveskleeakeleekr..e 114
                 ++  ++v s ++++s++ e+v+s  eea+++ e+    
  EPA05451.1 255 TTSITEVVSQMQEISAATEQVSSGTEEATAASEEIlsV 292
                 4556788889999*****************99987532 PP

  == domain 5  score: 1.9 bits;  conditional E-value: 0.25
        COG2  76 splaaarkkvesv.reklsereeeveskleeakeleekrellklllklde 124
                  + +aa +++ sv + +l+  e  v++k +e ++l+++++ +k l ++ +
  EPA05451.1 280 EEATAASEEILSVaQTNLKSFEDIVNAKDKETQNLQNTNKNIKTLTDIVD 329
                 45556666665552456777777777777777777777777776666554 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       4.7   4.2e+03      79     103 ..      17      41 ..      11      53 .. 0.65
   2 ?    7.3   7.9    0.0056         5      38     125 ..      63     153 ..      43     161 .. 0.77
   3 ?   -1.0   0.0       2.1   1.8e+03      45      67 ..     203     225 ..     188     241 .. 0.48
   4 ?   11.5   6.6   0.00028      0.25      35     114 ..     239     321 ..     229     335 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 4.7
                 HHHHHHHHHHCCCHHHHHHHCCHHH CS
   Fib_alpha  79 ikksskeleeeilrlketidaqesn 103
                 + + ++ ++++i+  k+ +++q +n
  EPA05451.1  17 TIQTTNIIDKKINIKKNDVISQLEN 41 
                 5566666676666666666666655 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0056
                 CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHH....HCCHHHHHHHHHHHHHHHHHHHHHHHHH CS
   Fib_alpha  38 ekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketi....daqesnirvLqnvlesneqkiqkLeqdi 125
                 e+l+++++e++n tk+  + ++e+++s+++     ++  +   k  ++++ + +++ +ti     + +s+++ +++++++ +++++kL ++ 
  EPA05451.1  63 EQLTDTVAELENATKSQTSGIEEVSQSIQSIAMAIQGVASNAIKTMEMMK-QSEQITRTIgsdaEKGMSKMNSMKSIVSESSNDVKKLAKEL 153
                 78999999999999999999999999999988888887555555666676.7777777772211344589******************8875 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 2.1
                 CCCCCHHHHHHHHHHHHHHHHHH CS
   Fib_alpha  45 eeisnstkeaeelvkeikdslre 67 
                 e+ ++  +e++++++++k+s  +
  EPA05451.1 203 ENSKKGAEEISDIISSLKESSDK 225
                 22222222333333333333332 PP

  == domain 4  score: 11.5 bits;  conditional E-value: 0.00028
                 HHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HCCCHHHHHHHCCHHHHHHHHHHHHHH CS
   Fib_alpha  35 kdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskele...eeilrlketidaqesnirvLqnvlesn 114
                 +  + ++n l++i+  t+++ e+v++++++ +++++ ++++++++  s++ l    ++   +++ ++a+ ++ ++Lqn+ ++ 
  EPA05451.1 239 DAYDVITNILNSIKGITTSITEVVSQMQEISAATEQVSSGTEEATAASEEILSvaqTNLKSFEDIVNAKDKETQNLQNTNKNI 321
                 555678999****************************9999999999999997111345567788888889999999876554 PP

>> APG17  Autophagy protein Apg17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8  21.0     0.014        12     123     317 ..      60     287 ..      31     334 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.014
                 HHHHHHHHHHHHHHHHHHHHHTTHH..HHHHHHHHHHH.........................-------STCCHHHHHHHHHHHHHHHHHHHHHHHHH CS
       APG17 123 elkealkesidelqaaqkkldssllefdtdlrelkkel.........................sksksksessslipellkelesleeemAslLesLtn 196
                  + e+l++  +el++a k+++s ++e +++++++  ++                         s  +++ ++ ++++++++e ++  +++A+ L+    
  EPA05451.1  60 LMSEQLTDTVAELENATKSQTSGIEEVSQSIQSIAMAIqgvasnaiktmemmkqseqitrtigSDAEKGMSKMNSMKSIVSESSNDVKKLAKELSKV-- 156
                 35566666699999999999999999999999999999999999999999999999999999866677779999******************99998.. PP

                 HHHHHHHH..............................S-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHHHHHHHHH CS
       APG17 197 HfDqcvkAvkltegggal..rraaae............lseeereelleVlekDaaeledVvkelqerleem....ekakkllsekkeeiekllsalkk 277
                   D +++ + ++ ++++l   +aa+e            + +ee + l e  +k a+e++d++ +l+e+ ++     ek +  +++  + i+++l+++k 
  EPA05451.1 157 --DNMTEFITQIAEQTNLlaLNAAIEaaragdvgrgfaVVAEEVRRLAENSKKGAEEISDIISSLKESSDKTtisiEKGNIVVQDAYDVITNILNSIKG 253
                 ..555555555555554444455555888899******9999999999999**************9999999999988888888888888888888888 PP

                 HHHHHH....HHHHHHHHHHHHHHHHHH...HHHHHHHHH CS
       APG17 278 aleeleevgkklpeylaifkaeeeflerweeekekieekl 317
                 + + ++ev ++++e+ a +++ +  +e+        ++  
  EPA05451.1 254 ITTSITEVVSQMQEISAATEQVSSGTEEA------TAASE 287
                 88888888888888888444433333332......22222 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4  16.6     0.065        58     304     421 ..      62     155 ..      15     232 .. 0.54
   2 ?    5.0  11.2     0.011       9.5     316     409 ..     235     332 ..     154     339 .. 0.64

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.065
      DUF812 304 aeklqftkeelakkaeteeelkkkreeeleelqeqieeleskieeleeeikklessikqveeeleeekeeneelekevklkkktlellpdaeeniekLq 402
                 +e+       l+ ++ + e+++k +   +ee+++ i+++   i+ ++++  k  + +kq e+ +++  +  e+  ++++ +k +++             
  EPA05451.1  62 SEQ-------LTDTVAELENATKSQTSGIEEVSQSIQSIAMAIQGVASNAIKTMEMMKQSEQITRTIGSDAEKGMSKMNSMKSIVSES----------- 142
                 222.......223455556666666666666666666666666666655555555555555555555555555555555555555444........... PP

      DUF812 403 alveasaqrlvelakqWek 421
                       ++++++lak+  k
  EPA05451.1 143 ------SNDVKKLAKELSK 155
                 ......4444444444332 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.011
      DUF812 316 kkaeteeelkkkreeeleelqeqieeleskieeleeeikklessikqveeelee....ekeeneelekevklkkktlellpdaeeniekLqalveasa 409
                   +++  ++ ++  ++++ + + i e+ s+++e+++  ++++s +++++ + ee     +++ +  e+ v+ k k  + l+++++ni+ L  +v++  
  EPA05451.1 235 IVVQDAYDVITNILNSIKGITTSITEVVSQMQEISAATEQVSSGTEEATAASEEilsvAQTNLKSFEDIVNAKDKETQNLQNTNKNIKTLTDIVDSLD 332
                 55566677777777888888999999999999988888888877776654444311114555566788899999999999999999999999998765 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   3.9      0.42   3.8e+02      33      98 ..      73     139 ..      45     163 .. 0.57
   2 ?    2.9   1.5       0.1        92       6      62 ..     112     168 ..     107     181 .. 0.59
   3 ?   -1.1   0.0       1.7   1.6e+03      10      41 ..     196     227 ..     192     242 .. 0.75
   4 ?   13.2   3.9   6.8e-05     0.061       8     102 ..     247     341 ..     237     361 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.42
       Sec34  33 fksvsektsslheaceqlleeqkrleelaeeieekLkyFeeldpitrkLnspgss.lvksesFlemL 98 
                  ++ +++ts ++e ++++ +    ++ +a +  + +++ ++ ++itr + s  ++ + k +s+++++
  EPA05451.1  73 ENATKSQTSGIEEVSQSIQSIAMAIQGVASNAIKTMEMMKQSEQITRTIGSDAEKgMSKMNSMKSIV 139
                 2334455555555555555555555555555555666666666666666555555555555554444 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.1
       Sec34   6 eskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelae 62 
                 +++e+ ++++ +++++ +++++++++ +++ s++ ++l ++  ++ + ++ ++++ae
  EPA05451.1 112 KQSEQITRTIGSDAEKGMSKMNSMKSIVSESSNDVKKLAKELSKVDNMTEFITQIAE 168
                 555566666666666666666666666666666666666655555444444444444 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.7
       Sec34  10 eecdelleqtdealeqLeeleekfksvsekts 41 
                 ee+++l e+ ++  e+++++ ++ k+ s+kt+
  EPA05451.1 196 EEVRRLAENSKKGAEEISDIISSLKESSDKTT 227
                 56677777777777888888888888777775 PP

  == domain 4  score: 13.2 bits;  conditional E-value: 6.8e-05
       Sec34   8 keeecdelleqtdealeqLeeleekfksvsektsslheaceqlle.eqkrleelaeeieekLkyFeeldpitrkLnspgsslvksesFlemLkklD 102
                   ++++ + ++++e+ +q++e++   ++vs+ t++  +a+e++l+  q++l+++ + +++k k  ++l+++++++++ +   v+s + ++m++ lD
  EPA05451.1 247 ILNSIKGITTSITEVVSQMQEISAATEQVSSGTEEATAASEEILSvAQTNLKSFEDIVNAKDKETQNLQNTNKNIKTLTDI-VDSLDSSTMISILD 341
                 557788899999999999999999999999999999999999886478999999999999999999999999999988877.77666666666544 PP

>> COG5  Golgi transport complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   4.1   0.00019      0.17      18     120 ..      60     164 ..      52     174 .. 0.86
   2 ?    0.5   2.9      0.73   6.5e+02      34      83 ..     250     299 ..     213     340 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00019
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-TTHHHHHHHHHHHHHHHHHH CS
        COG5  18 lkatnnnddteldlstplkrlnydiqeldkrlrql...itsnhleLlehlskskslssvlselksslesLsasyerlkskvlepyeeaeklqsalkrlh 113
                 l   ++ +dt + l+ + k  +++i+e+ + ++++   i+  +++ ++ ++  k+ ++++ ++ s  e+ ++ ++ +ks v+e  ++++kl ++l+++ 
  EPA05451.1  60 LM-SEQLTDTVAELENATKSQTSGIEEVSQSIQSIamaIQGVASNAIKTMEMMKQSEQITRTIGSDAEKGMSKMNSMKSIVSESSNDVKKLAKELSKVD 157
                 44.677889999999999999********999886222556789999999999*********************************************9 PP

                 HHHHHHH CS
        COG5 114 qtldLlr 120
                 + ++   
  EPA05451.1 158 NMTEFIT 164
                 9887665 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.73
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXX CS
        COG5  34 plkrlnydiqeldkrlrqlitsnhleLlehlskskslss.vlselkssles 83 
                 ++k ++  i e+ ++++ +i++  +++ + +++ + +s+ +ls  +++l+s
  EPA05451.1 250 SIKGITTSITEVVSQMQ-EISAATEQVSSGTEEATAASEeILSVAQTNLKS 299
                 44444444444444442.334444444444444444444444444444443 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   1.6     0.039        35      36      86 ..      49      99 ..      35     104 .. 0.64
   2 ?    9.7   3.1    0.0011         1      22      85 ..     105     171 ..     100     175 .. 0.90
   3 ?    4.0   0.6     0.065        59      31      84 ..     194     247 ..     185     263 .. 0.47
   4 ?    4.2   7.0     0.058        52      22      88 ..     259     325 ..     250     326 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.039
      DUF948 36 eelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvse 86
                +++++ +++++  +e+l+++v el +  ++++  ++++ ++++ ++ +++ 
  EPA05451.1 49 TKIQRSLGETVLMSEQLTDTVAELENATKSQTSGIEEVSQSIQSIAMAIQG 99
                556666666666666666666666666666666666666666666665554 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0011
      DUF948  22 lklkktldeaaatieelekqvdpilkevedllakvnelledvne...klekvdplteavadlgesvs 85 
                 +k  +++++ ++  +++++++++ + +++ + + v e  +dv++   +l kvd++te + +++e+ +
  EPA05451.1 105 IKTMEMMKQSEQITRTIGSDAEKGMSKMNSMKSIVSESSNDVKKlakELSKVDNMTEFITQIAEQTN 171
                 6778999**************************99999999998888*************9999865 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.065
      DUF948  31 aaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesv 84 
                 +a+ ++ l ++ ++  +e+ d+++  +e  +  +  +ek + +++ + d+ +++
  EPA05451.1 194 VAEEVRRLAENSKKGAEEISDIISSLKESSDKTTISIEKGNIVVQDAYDVITNI 247
                 444444444444444444444444444444444444444444444444444433 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.058
      DUF948  22 lklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvseln 88 
                  ++ + ++e++a+ e++ + +++ +  +e++l+ +++ l+  ++ +++ d+ t++++++ +++++l+
  EPA05451.1 259 TEVVSQMQEISAATEQVSSGTEEATAASEEILSVAQTNLKSFEDIVNAKDKETQNLQNTNKNIKTLT 325
                 5566778889999999999999999999999999999999999999999999999999999999987 PP

>> T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX diderm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.2      0.26   2.3e+02      48      76 ..      62      90 ..      47      96 .. 0.59
   2 ?    3.2   0.5      0.14   1.2e+02      16      51 ..      62      97 ..      60     118 .. 0.64
   3 ?    2.7   0.5       0.2   1.8e+02      10      76 ..      88     153 ..      78     171 .. 0.58
   4 ?    0.5   0.1      0.94   8.4e+02      12      59 ..     139     183 ..     129     190 .. 0.68
   5 ?    7.9   0.0    0.0047       4.3       6      48 ..     192     230 ..     189     264 .. 0.70
   6 ?    0.9   1.5      0.73   6.5e+02      11      43 ..     264     295 ..     254     330 .. 0.47

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.26
  T7SS_ESX_EspC 48 caatndavaaaeaarraagealaaasteL 76
                   + +++d+va++e a +++ +++ ++s+ +
     EPA05451.1 62 SEQLTDTVAELENATKSQTSGIEEVSQSI 90
                   44555555555555555555555555444 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.14
  T7SS_ESX_EspC 16 aakhdevaaeiasavaaaagasaavldshGpicaat 51
                   ++++++++ae+++a+++ +   ++v++s  +i +a 
     EPA05451.1 62 SEQLTDTVAELENATKSQTSGIEEVSQSIQSIAMAI 97
                   566667777777777777777777766655555444 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.2
  T7SS_ESX_EspC  10 dhlrelaakhdevaaeiasavaaaagasaavldshGpicaatndavaaaeaarraagealaaasteL 76 
                    + +++ a   ++va+++ +  +++ ++s++++ + G+   +  + +++++   +++ +++++ ++eL
     EPA05451.1  88 QSIQSIAMAIQGVASNAIKTMEMM-KQSEQITRTIGSDAEKGMSKMNSMKSIVSESSNDVKKLAKEL 153
                    334444444455555544455555.566666666666655555555555555555555555555555 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.94
  T7SS_ESX_EspC  12 lrelaakhdevaaeiasavaaaagasaavldshGpicaatndavaaae 59 
                    + e + ++++ a+e++++ +++ +  ++++++  +  +a+n+a++aa+
     EPA05451.1 139 VSESSNDVKKLAKELSKVDNMT-EFITQIAEQ--TNLLALNAAIEAAR 183
                    5677777788888888888877.777777776..44555556655554 PP

  == domain 5  score: 7.9 bits;  conditional E-value: 0.0047
  T7SS_ESX_EspC   6 sVdpdhlrelaakhdevaaeiasavaaaagasaavldshGpic 48 
                     V+++++r+la+  ++ a+ei++  ++ ++ s+     +++  
     EPA05451.1 192 AVVAEEVRRLAENSKKGAEEISDIISSLKESSD----KTTISI 230
                    599********************9999944443....333334 PP

  == domain 6  score: 0.9 bits;  conditional E-value: 0.73
  T7SS_ESX_EspC  11 hlrelaakhdevaaeiasavaaaagasaavlds 43 
                    +++e +a  ++v+++ + a+aa+ ++  +v+++
     EPA05451.1 264 QMQEISAATEQVSSGTEEATAAS-EEILSVAQT 295
                    34444444444444444444444.333333322 PP

>> CHDCT2  CHDCT2 (NUC038) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   4.7     0.004       3.6      64     160 ..      54     163 ..      11     175 .. 0.63
   2 ?    3.3   0.3     0.093        83      95     157 ..     207     269 ..     189     291 .. 0.51
   3 ?    4.1   1.3     0.053        48      84     158 ..     252     326 ..     230     337 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.004
      CHDCT2  64 lleqalvieeqlrraallnlqeekekvgslaqrfaelellaeshqkllkesaagnknanavle.............kvLnqleelLsdmkadvsrlpat 149
                  l +++ + eql  +     + +k+++  +++  ++++ +a + q +++++ +  + +++  +               +n ++ ++s+  +dv++l   
  EPA05451.1  54 SLGETVLMSEQLTDTVAELENATKSQTSGIEEVSQSIQSIAMAIQGVASNAIKTMEMMKQSEQitrtigsdaekgmSKMNSMKSIVSESSNDVKKLAKE 152
                 45667777777765533333444444444555555555555555555555444433333333344477777777777789999**************** PP

      CHDCT2 150 lsrlrpvaeRL 160
                 ls++  ++e +
  EPA05451.1 153 LSKVDNMTEFI 163
                 ****9999865 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.093
      CHDCT2  95 qrfaelellaeshqkllkesaagnknanavlekvLnqleelLsdmkadvsrlpatlsrlrpva 157
                 +   e++ + +s ++ + +++ + ++ n v++   + + ++L+ +k+  + +  ++s+++ ++
  EPA05451.1 207 KGAEEISDIISSLKESSDKTTISIEKGNIVVQDAYDVITNILNSIKGITTSITEVVSQMQEIS 269
                 223333333333333444444444444555555555555555555555555555555555544 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.053
      CHDCT2  84 qeekekvgslaqrfaelellaeshqkllkesaagnknanavlekvLnqleelLsdmkadvsrlpatlsrlrpvae 158
                 +  +++++++ ++++e++  +e+ ++ ++e++a +++  +v ++ L+ +e++++   ++ + l +t + ++++++
  EPA05451.1 252 KGITTSITEVVSQMQEISAATEQVSSGTEEATAASEEILSVAQTNLKSFEDIVNAKDKETQNLQNTNKNIKTLTD 326
                 444556666667777777777777777888888999999999999999999999999999999999988888775 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   9.5      0.02        18       4     103 ..      68     167 ..      63     184 .. 0.74
   2 ?   10.5   2.8   0.00051      0.45       4      84 ..     194     274 ..     192     281 .. 0.93
   3 ?    1.6   2.8      0.29   2.6e+02       6      50 ..     287     331 ..     280     341 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.02
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXX--TTTTTGGGHHHHHHHHHH...HHHHHHHHHHH CS
  Laminin_II   4 laaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankair....dArrsvkkLeklapqLldklkelkqleeassslsdniseikel 98 
                 ++ae ++ +k+  + ++++sq ++ +   ++++++++ +t e +k++ +++r    dA++ ++k++     + +  + +k+l ++   ls +++++ e 
  EPA05451.1  68 TVAELENATKSQTSGIEEVSQSIQSIAMAIQGVASNAIKTMEMMKQSEQITRtigsDAEKGMSKMNSMKSIVSESSNDVKKLAKE---LS-KVDNMTEF 162
                 5677778888888889999999999999999999999999999998887775444478888888888777777777777777777...44.46666666 PP

                 HHHHH CS
  Laminin_II  99 IaqAR 103
                 I q  
  EPA05451.1 163 ITQIA 167
                 66654 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00051
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH CS
  Laminin_II   4 laaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleea 84 
                 +a+e+   a++ ++  +++s  ++ +ke+  +   s+e+ n +v+da  +i    +s+k ++  + +++++++e+    e+
  EPA05451.1 194 VAEEVRRLAENSKKGAEEISDIISSLKESSDKTTISIEKGNIVVQDAYDVITNILNSIKGITTSITEVVSQMQEISAATEQ 274
                 578999999999**************************************************************9887776 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.29
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
  Laminin_II   6 aeanetakevleqlaplsqnlentkeklseinrsveetnekvkda 50 
                 +e+++ a+  l+  +++ +  +++ ++l++ n++++  ++ v+++
  EPA05451.1 287 EEILSVAQTNLKSFEDIVNAKDKETQNLQNTNKNIKTLTDIVDSL 331
                 678888888888888898888899999999998888888877743 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   1.9      0.13   1.2e+02       5      65 ..      49     112 ..      45     127 .. 0.47
   2 ?    7.2   1.5    0.0067         6      33      78 ..     129     174 ..     125     179 .. 0.88
   3 ?    3.2   0.4      0.13   1.1e+02      27      88 ..     232     269 ..     192     278 .. 0.50
   4 ?    6.0   4.9     0.016        15      18      73 ..     279     334 ..     263     337 .. 0.54

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.13
     BLOC1_2   5 ekvskyleaeleatvedyklLeklNeaasekykklkdv...aaslekkleklnekyeelqpylq 65 
                 +k+++ l +++ ++ +  +++ +l +a+ ++   +++v   ++s++  ++ + +   +  ++++
  EPA05451.1  49 TKIQRSLGETVLMSEQLTDTVAELENATKSQTSGIEEVsqsIQSIAMAIQGVASNAIKTMEMMK 112
                 5555555555555555555554444444444444443300033334444444444444444444 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0067
     BLOC1_2  33 sekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLe 78 
                 ++k +++k+++++ +++++kl ++  +++++ + i qi +q++ L 
  EPA05451.1 129 MSKMNSMKSIVSESSNDVKKLAKELSKVDNMTEFITQIAEQTNLLA 174
                 578999*********************************9998776 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.13
     BLOC1_2  27 klNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeys 88 
                 k N +                     ++  y+ + + l++i+ i +++te   +vs++ e+s
  EPA05451.1 232 KGNIV---------------------VQDAYDVITNILNSIKGITTSITE---VVSQMQEIS 269
                 33333.....................333333333333333333333333...333333333 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.016
     BLOC1_2  18 tvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekq 73 
                 t e     e++  +a+++ k+ +d+++   k+ ++l++++++++ + + +d ++ +
  EPA05451.1 279 TEEATAASEEILSVAQTNLKSFEDIVNAKDKETQNLQNTNKNIKTLTDIVDSLDSS 334
                 44444444555555555555555555555555555555555555555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (481 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2437  (0.135925); expected 358.6 (0.02)
Passed bias filter:                      628  (0.0350271); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        45  (0.0025099); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 1.03u 0.39s 00:00:01.42 Elapsed: 00:00:00.56
# Mc/sec: 2590.77
//
Query:       EPA05452.1  [L=512]
Description: ATPase/histidine kinase/DNA gyrase B/HSP90 domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      3e-16   59.9   1.0    6.3e-16   58.9   0.0    2.0  2  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    2.1e-07   30.8   0.0    6.8e-07   29.2   0.0    2.0  1  HisKA        His Kinase A (phospho-acceptor) domain
     0.0069   16.3   0.1     0.0069   16.3   0.1    2.9  3  HATPase_c_5  GHKL domain
  ------ inclusion threshold ------
      0.037   13.9   0.2      0.037   13.9   0.2    2.0  2  LapA_dom     Lipopolysaccharide assembly protein A domain
        4.9    7.5  13.0       0.73   10.1   1.1    3.9  3  AFP_2        Bacterial antifreeze protein repeat


Domain annotation for each model (and alignments):
>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.2         3   1.1e+04      12      44 ..     325     359 ..     323     375 .. 0.57
   2 !   58.9   0.0   1.7e-19   6.3e-16       2      97 ..     384     478 ..     383     492 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3
                 HHHHHHHHHHS.TTTEEEEEEEEEE...TEEEEEEEE CS
   HATPase_c  12 nlvdNavkfat.kageieveikase...ddlvisveD 44 
                 n+  N ++ ++ +++e+e++++  +   +++  +v D
  EPA05452.1 325 NIANNVLDLTKiENNELELHLE--KcsiNNIIQEVVD 359
                 6777777763355566666665..2233444445555 PP

  == domain 2  score: 58.9 bits;  conditional E-value: 1.7e-19
                 HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEE..EETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHHHHHHHHHTTTEEEEEEE CS
   HATPase_c   2 dekrLrqiisnlvdNavkfatkageieveika..seddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsivkklvelmgGeiwvese 97 
                 d++r++q+++n++dN +kf t+ gei+++ +   ++++l++  +D+G+ ip e l+k+f   ++   + ++ +g+GlGl+i+kk+++ ++G+i+  ++
  EPA05452.1 384 DKTRIKQVFRNILDNCIKF-TEVGEISIHTHLlkDQKTLKLFFSDTGPEIPTEVLPKMFNEVVT--MDINKISGFGLGLYISKKIIDAHKGKISAYNN 478
                 789****************.9999999999886544799999******************9999..4566679**************9*****98443 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.0   1.9e-10   6.8e-07       2      66 ..     277     338 ..     276     339 .. 0.93

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 1.9e-10
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHH CS
       HisKA   2 lgrflagvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedlLdlsriea 66 
                 + +f++  +HEL+ PL  i g++e+ k       + +e+le i s a +l+++ +++Ldl++ie+
  EPA05452.1 277 RKEFISIASHELKGPLQPIFGFVELAKT---EIISKQEALEGISSIAFHLENIANNVLDLTKIEN 338
                 689***********************99...4678899*************************97 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.2      0.61   2.2e+03      37      58 ..     247     271 ..     240     286 .. 0.65
   2 ?   -2.6   0.2       1.5   5.2e+03      14      35 ..     323     345 ..     310     357 .. 0.57
   3 !   16.3   0.1   1.9e-06    0.0069       5     100 ..     387     488 ..     383     489 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.61
  HATPase_c_5  37 ekkksliisieNsyegek...kkle 58 
                  +++ +l ++i+N++e+ +   kkl+
   EPA05452.1 247 QTNVNLKLEIKNQTENLNqlnKKLK 271
                  5566788899999988442233333 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.5
  HATPase_c_5  14 LdNAieacskiee.ekrfIrltv 35 
                  L+N  + + ++++ e+ +++l++
   EPA05452.1 323 LENIANNVLDLTKiENNELELHL 345
                  44444444444444455555544 PP

  == domain 3  score: 16.3 bits;  conditional E-value: 1.9e-06
  HATPase_c_5   5 dlcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg.......ek..kklesskskkeehGiGlksireivkkykgnlsieaedgl 93 
                   +  ++ n+LdN+i   +     + +I+ ++ +++k+l + ++ +  +       +   + +    +k +  G+Gl   ++i++ +kg++s  +++++
   EPA05452.1 387 RIKQVFRNILDNCIKFTEVG---EISIHTHLLKDQKTLKLFFSDTGPEiptevlpKMfnEVVTMDINKISGFGLGLYISKKIIDAHKGKISAYNNNNY 481
                  57789*********876653...589****************9997776655444114244445567788999999*****************99998 PP

  HATPase_c_5  94 Ftlsvll 100
                     +++l
   EPA05452.1 482 PMFEITL 488
                  8888877 PP

>> LapA_dom  Lipopolysaccharide assembly protein A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.3       2.2   7.8e+03      17      27 ..      38      48 ..      32      59 .. 0.53
   2 ?   13.9   0.2     1e-05     0.037      22      63 ..     227     270 ..     215     271 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.2
    LapA_dom 17 lpLsllllvaf 27
                +++++++ + +
  EPA05452.1 38 FRIGICISMII 48
                55555553322 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 1e-05
    LapA_dom  22 lllvafgiGallgwllslw..sylrlrrelrrlkkkikklekel 63 
                  +++ +++G++ ++l++++  + + l++e++++++ +++l k+l
  EPA05452.1 227 QIIMIVLLGIITTMLVFFLnqTNVNLKLEIKNQTENLNQLNKKL 270
                 589999************7335569****************997 PP

>> AFP_2  Bacterial antifreeze protein repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   1.1    0.0002      0.73      25      41 ..      73      88 ..      58      93 .. 0.76
   2 ?    1.5   0.9       0.1   3.7e+02      21      39 ..     112     129 ..     108     137 .. 0.87
   3 ?    1.0   0.2      0.14   5.1e+02      21      40 ..     172     189 ..     164     194 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0002
       AFP_2 25 vdniQnkvsnFENIKvs 41
                 +   + +snFENIK s
  EPA05452.1 73 IE-YDQTISNFENIKYS 88
                33.3588********98 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.1
       AFP_2  21 yyanvdniQnkvsnFENIK 39 
                 + +n++ i + +++F N+ 
  EPA05452.1 112 WIYNTE-IKKELKDFNNLV 129
                 899999.**********75 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.14
       AFP_2  21 yyanvdniQnkvsnFENIKv 40 
                 yy  ++  Q+ + +++NIK 
  EPA05452.1 172 YYEGKQ--QDFLREYDNIKY 189
                 444555..999********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (512 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1921  (0.107145); expected 358.6 (0.02)
Passed bias filter:                      614  (0.0342462); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.51
# Mc/sec: 3016.97
//
Query:       EPA05453.1  [L=248]
Description: CheC-like family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-12   45.7   0.0    8.8e-12   44.7   0.0    1.6  1  CheC      CheC-like family
    1.7e-07   31.3   0.0    3.1e-07   30.5   0.0    1.5  1  CheX      Chemotaxis phosphatase CheX


Domain annotation for each model (and alignments):
>> CheC  CheC-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7   0.0   9.8e-16   8.8e-12       1      37 [.     102     138 ..     102     139 .. 0.96

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 9.8e-16
                 HHHHHHHHHHHHHHHHHHHHHHTCCTS-EEE---EEE CS
        CheC   1 melSAlgEigNIlaGsaatalatllnfkidisPPtvv 37 
                 m+ SAl+E++NIl+Gs+ +al++ ++f+id s+P ++
  EPA05453.1 102 MGTSALQEVANILTGSFFNALSENTGFRIDLSTPKFK 138
                 899*******************************986 PP

>> CheX  Chemotaxis phosphatase CheX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.0   3.4e-11   3.1e-07       8      76 ..      68     141 ..      60     157 .. 0.79

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 3.4e-11
        CheX   8 aGdisGliilsadeelalkiasa.lgedeeeieedvndavgEltNmiaGnakskl....geevklspPlvisgk 76 
                 +Gd++  ++ s+    a kias+ lg + +ei+e+  +a++E++N+++G++ + l    g +++ls+P++ +g 
  EPA05453.1  68 KGDLHIELLYSTKLHHAIKIASKlLGTEVNEIDEMGTSALQEVANILTGSFFNALsentGFRIDLSTPKFKEGG 141
                 56666677777777789999**9559998888********************8885444559******998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       689  (0.0384294); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1547.28
//
Query:       EPA05454.1  [L=172]
Description: hypothetical protein BG20_I0865 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.59u 0.35s 00:00:00.94 Elapsed: 00:00:00.58
# Mc/sec: 892.54
//
Query:       EPA05455.1  [L=363]
Description: ATPase/histidine kinase/DNA gyrase B/HSP90 domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.2e-17   62.6   2.0    5.5e-17   62.3   0.3    2.1  2  HATPase_c      Histidine kinase-, DNA gyrase B-, and HSP90-li
    4.9e-10   39.3   2.3    2.2e-08   34.0   0.0    3.2  3  HisKA          His Kinase A (phospho-acceptor) domain
    1.2e-07   31.5   0.1      4e-07   29.9   0.0    2.0  2  HATPase_c_5    GHKL domain
  ------ inclusion threshold ------
       0.01   15.6   0.0      0.051   13.4   0.0    2.2  2  HATPase_c_3    Histidine kinase-, DNA gyrase B-, and HSP90-li
      0.012   15.5   0.0       0.02   14.8   0.0    1.4  1  HATPase_c_2    Histidine kinase-like ATPase domain
       0.61    9.7  15.9       0.11   12.1  12.2    1.6  2  PI3K_P85_iSH2  Phosphatidylinositol 3-kinase regulatory subun


Domain annotation for each model (and alignments):
>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       1.5   4.6e+03      36      62 ..      49      82 ..      26      93 .. 0.57
   2 !   62.3   0.3   1.8e-20   5.5e-17       6     111 ..     263     361 ..     258     362 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.5
                TEEEEEEEE.SS.....SSSTTHHHTGTCS.TTC CS
   HATPase_c 36 ddlvisveD.nG.....iGipkedlkklfe.kfs 62
                + ++is+ D n        i+  + kklf+ +fs
  EPA05455.1 49 KSNSISIDDlNNetqknSKINDVITKKLFQdSFS 82
                4566666664222222234444444466666665 PP

  == domain 2  score: 62.3 bits;  conditional E-value: 1.8e-20
                 HHHHHHHHHHHHHHHHS.TTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHHHHHHHHHTTTEEEEEEETTTEEE CS
   HATPase_c   6 LrqiisnlvdNavkfat.kageieveikaseddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsivkklvelmgGeiwvesepgrGtt 103
                 ++ ++ nl+ N++++ + ++g+i +ei  +   ++i+++D+G G+p e+l+k+f+++ +     ++++gtGlGls v+++++++gG i ++++p   tt
  EPA05455.1 263 MEVVMGNLLLNSIQAIGlEKGQILIEIVETPIAITITIQDSGSGVPNEHLQKIFDPLFT-----TKQEGTGLGLSSVQSIIDQHGGIIDLKNNP---TT 353
                 566889********9445**********6559***********************6666.....699************9999*******9999...** PP

                 EEEEEESS CS
   HATPase_c 104 ftftlple 111
                 +t+tlp++
  EPA05455.1 354 VTITLPKR 361
                 *****975 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.3     0.072   2.2e+02      30      55 ..     102     131 ..      85     143 .. 0.75
   2 !   34.0   0.0   7.3e-12   2.2e-08       3      62 ..     155     216 ..     153     220 .. 0.89
   3 ?    0.5   0.1      0.22   6.5e+02      50      64 ..     227     241 ..     221     244 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.072
                 ......T-HSSCHHHHHHHHHHHHHHHHHH CS
       HisKA  30 e....gklteelkeyletiesearrldhlv 55 
                 e    ++l+e+l e+l +i + +  l +  
  EPA05455.1 102 EkklsEELNEKLHENLSKIAKAESELVKKK 131
                 344445688999999999999888776655 PP

  == domain 2  score: 34.0 bits;  conditional E-value: 7.3e-12
                 HHHHHHHHHHHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHC CS
       HisKA   3 grflagvaHELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedlLdls 62 
                 g++ + v+H+L++PL++i+g++ +Lk +   + ++ +++ le +e ++ r++h+++ +Ld+ 
  EPA05455.1 155 GELSSRVSHDLKNPLTVIKGTVGILKLRkgMPIDDFVMKRLELMEASIFRMTHQIDGVLDYV 216
                 88999********************5545866669************************986 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.22
                 HHHHHHHHHHHHCCH CS
       HisKA  50 rldhlvedlLdlsri 64 
                  l +++e+ L+l +i
  EPA05455.1 227 SLKQIIENSLQLQKI 241
                 678888888888887 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0         4   1.2e+04      41      51 ..     227     237 ..     220     251 .. 0.59
   2 !   29.9   0.0   1.3e-10     4e-07       4      95 ..     261     355 ..     258     359 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 4
  HATPase_c_5  41 sliisieNsye 51 
                  sl  +ieNs +
   EPA05455.1 227 SLKQIIENSLQ 237
                  45555555554 PP

  == domain 2  score: 29.9 bits;  conditional E-value: 1.3e-10
  HATPase_c_5   4 ldlcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg....ekkkle..sskskkeehGiGlksireivkkykgnlsieaedglFt 95 
                  + + v++gnlL N+i+a    e  k  I +++ e+  +++i+i+ s +g    + +k++    ++k+e  G+Gl+s+++i+++++g ++++++ ++ t
   EPA05455.1 261 VKMEVVMGNLLLNSIQAIGL-E--KGQILIEIVETPIAITITIQDSGSGvpneHLQKIFdpLFTTKQEGTGLGLSSVQSIIDQHGGIIDLKNNPTTVT 355
                  56789***********9876.4..689*******************8885544335555444477889********************9998877655 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       3.4     1e+04       6      16 ..     227     237 ..     225     253 .. 0.67
   2 ?   13.4   0.0   1.7e-05     0.051       3      62 ..     263     324 ..     261     336 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 3.4
  HATPase_c_3   6 AlaelvdNsld 16 
                  +l  +++Nsl+
   EPA05455.1 227 SLKQIIENSLQ 237
                  57788899887 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 1.7e-05
  HATPase_c_3   3 lekAlaelvdNsldAdaen...vkievnknrgktgeivieDdGkGmseeelknalrlatsske 62 
                  +e+++  l+ Ns++A   +   + ie+ + +  + +i+i+D G+G+++e l++ + +  ++k+
   EPA05455.1 263 MEVVMGNLLLNSIQAIGLEkgqILIEIVETP-IAITITIQDSGSGVPNEHLQKIFDPLFTTKQ 324
                  5677778999****96555566888888876.5799*******************98887777 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   6.8e-06      0.02      32     123 ..     263     356 ..     237     358 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 6.8e-06
  HATPase_c_2  32 irlaveEactNavehayleapegpvevrlesdeealtvevaDsGpgfdpetlpdpteeepkeslkegGrGlalikglvDev..ey..dgegnvvtm 123
                  ++++++ ++ N +++  le  +g++ +++  ++ a+t++++DsG g + e+l++   +  +++++  G+Gl  ++++ D+    +  +++ ++vt+
   EPA05455.1 263 MEVVMGNLLLNSIQAIGLE--KGQILIEIVETPIAITITIQDSGSGVPNEHLQKIFDPLFTTKQEGTGLGLSSVQSIIDQHggIIdlKNNPTTVTI 356
                  5666666677777777764..679999999****************77777777777777899999999999999999987542244555566665 PP

>> PI3K_P85_iSH2  Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1  12.2   3.7e-05      0.11      41     123 ..      65     150 ..      39     154 .. 0.83
   2 ?   -2.7   0.1       1.3     4e+03      38      42 ..     226     230 ..     192     247 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.7e-05
  PI3K_P85_iSH2  41 nkiseeiqlkrqaleaFneaikmFeeqiklqekfskea...qehEieklqenleqlksrlkelhsskekLeedlkqqkeeereleR 123
                    n+  +++ +k++ ++ F+ ++    ++++l+ k  ++    +e+ +ekl+enl+++ +  +el ++k++Le +lk+++++  e eR
     EPA05455.1  65 NSKINDVITKKLFQDSFSAIEAFNDRKMELIYKQLEDEkklSEELNEKLHENLSKIAKAESELVKKKNNLELELKEKTKKLVESER 150
                    444578999*************9999****99987766332344456********************************9999998 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.3
  PI3K_P85_iSH2  38 eeynk 42 
                    e+ ++
     EPA05455.1 226 ESLKQ 230
                    22221 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1924  (0.107312); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.70u 0.38s 00:00:01.08 Elapsed: 00:00:00.56
# Mc/sec: 1948.68
//
Query:       EPA05456.1  [L=83]
Description: hypothetical protein BG20_I0867, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.038   14.0   0.3      0.042   13.9   0.3    1.2  1  ER        Enhancer of rudimentary


Domain annotation for each model (and alignments):
>> ER  Enhancer of rudimentary
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.3   2.3e-06     0.042      38      76 ..      36      74 ..      13      82 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.3e-06
          ER 38 aLkeanpskksitYdisdLfefidsladlsaLvleketk 76
                +L + + ++++i+Yd ++L +fid+ ++l+  + +++++
  EPA05456.1 36 ELTKIHCKTSKIKYDEKQLKSFIDNKNNLKSDIKKSDSS 74
                478889999****************99999887777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       969  (0.0540465); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.33s 00:00:00.86 Elapsed: 00:00:00.53
# Mc/sec: 470.98
//
Query:       EPA05457.1  [L=159]
Description: hypothetical protein BG20_I0866 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-10   41.0   6.9    2.7e-10   40.7   6.9    1.0  1  Arch_flagellin  Archaebacterial flagellin
  ------ inclusion threshold ------
      0.038   14.7   1.1      0.053   14.2   0.4    1.6  2  Big_5           Bacterial Ig-like domain
       0.67    9.0  10.7          7    5.6  10.3    2.1  1  DUF973          Protein of unknown function (DUF973)


Domain annotation for each model (and alignments):
>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   6.9   4.5e-14   2.7e-10       4     160 ..       4     152 ..       2     155 .. 0.87

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 4.5e-14
                     H.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEEEEE-SSSSSEEEEEEE--TTS--E.EGGG-EEEEEESS- CS
  Arch_flagellin   4 g.igtlIvfIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvgdsatngtineitiyvklnaGsspi.dlnkttisvtddgq 96 
                     g +++ +++IA V+VA +  g++i  +g+ ++ +++t e   +++ +++ei+ +   +++++    + i+vk n+G spi +ln +++ + + ++
      EPA05457.1   4 GiLSEGVLIIASVIVAGIITGIVISKVGTFESTITATTEAQKDKLLNKFEIIHVNK-INSTS----VDIWVK-NTGLSPIqNLNLMDLYFGQINS 92 
                     5478889*********************************************9887.55555....99****.*****77479999999999998 PP

                     -EE--E..................T-EE-TT-EEEEEEE--TTT---TT-EEEEEEE-SSS--E CS
  Arch_flagellin  97 etlltadefgivvisdtdgsltngdevlekgekvelevnvneddgitagdevsvevvpenGast 160
                     ++++ ++++++      dg++tn+   + +g++++++++   ++++t+++ + ++++ +nG+++
      EPA05457.1  93 VQMIGYNDTSTPRWVFGDGTTTNS--DWAQGNTIKITLQD--SSSLTPSTSYLIQIILSNGVTD 152
                     888888766666666667777776..7***********96..699****************975 PP

>> Big_5  Bacterial Ig-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.57   3.4e+03      46      46 ..      50      50 ..      28     108 .. 0.57
   2 ?   14.2   0.4   8.8e-06     0.053      50      89 ..     111     152 ..      84     157 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.57
       Big_5 46 l 46
                 
  EPA05457.1 50 N 50
                1 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 8.8e-06
       Big_5  50 ettavtgsydasgktvtitps..aeLaanttYtvti..tagikD 89 
                  tt+ + +  a+g+t++it++  ++L+++t+Y ++i  ++g++D
  EPA05457.1 111 GTTTNSDW--AQGNTIKITLQdsSSLTPSTSYLIQIilSNGVTD 152
                 34444455..788***999997788***********76777998 PP

>> DUF973  Protein of unknown function (DUF973)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6  10.3    0.0012         7     272     301 ..     121     150 ..       9     155 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0012
      DUF973 272 nNsitinFntvlnLvpgstYtirLlLsngq 301
                  N+i+i  + +++L+p + Y i+++Lsng 
  EPA05457.1 121 GNTIKITLQDSSSLTPSTSYLIQIILSNGV 150
                 49**************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       837  (0.0466841); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 997.19
//
Query:       EPA05458.1  [L=556]
Description: type II/IV secretion system protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-43  149.0   0.0    1.8e-43  148.6   0.0    1.1  1  T2SSE     Type II/IV secretion system protein


Domain annotation for each model (and alignments):
>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.6   0.0     1e-47   1.8e-43       4     259 ..     173     431 ..     170     441 .. 0.93

  Alignments for each domain:
  == domain 1  score: 148.6 bits;  conditional E-value: 1e-47
       T2SSE   4 lleallddekvsdihvekper.vkvrervdgielreveelekaalerlisriaalakldiseerplqdarlpekgvrlrvvllPvvag..ealviRkks 99 
                 lle++l+d++  di +   ++ +++++  +   l+   +l+ +a+  li  +    ++++s+ +p++da+lp +g r+++v+   +    ++++iRk +
  EPA05458.1 173 LLEPFLNDPNLEDISIIGAGNmYIIHKAFGT--LKVPVFLSVDAIDELIVSLSEQFGKTVSHAKPVVDATLP-DGSRINIVFGKDISRkgTNATIRKFA 268
                 7899*****************8888777776..8888899********************************.********98766655799******* PP

       T2SSE 100 akeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderivtvEDpvEiqleganqvqlnak.....kakvtfadllr 193
                 +  l++ ++  ++ l+ + a+ l   +++ +++ v G T sGKtt+l  l ++i+++  ++vt+ED+ E+ l ++n +   ++     + +vt+ dll+
  EPA05458.1 269 STPLSIIQVLSSGVLNFTEAAYLWMMLEAGMSLFVNGETASGKTTTLMGLTAFIPSN-WKVVTIEDTPELTLPHNNWITEATRdtgnkASSVTMDDLLK 366
                 ****************9999999999999***************************9.********************9999999999999******** PP

       T2SSE 194 aaLRlrPDrimvGEiRdketleilkAvnTGHlgslsTlHansaagalerLeqlgaeveaaelkssi 259
                 aaLR+rP  i+vGEiR++e   + +A++TGH++ ++T Ha   +  ++rL++   +++++ +++  
  EPA05458.1 367 AALRQRPNYILVGEIRGAEGNVAFSAMQTGHPV-MATFHAAGMVPLIQRLSNAPINIPKTYMENLN 431
                 *********************************.*****************988888877777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (556 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.71u 0.35s 00:00:01.06 Elapsed: 00:00:00.54
# Mc/sec: 3112.30
//
Query:       EPA05459.1  [L=125]
Description: putative chemotaxis protein Chey [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.4e-28   98.1   0.7    3.8e-28   97.9   0.7    1.0  1  Response_reg  Response regulator receiver domain


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.9   0.7   2.1e-32   3.8e-28       1     106 [.       7     113 ..       7     119 .. 0.95

  Alignments for each domain:
  == domain 1  score: 97.9 bits;  conditional E-value: 2.1e-32
                   EEEESSSHHHHHHHHHHHHHTTE.EEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEESSTSHHHHHHHHHCTESE CS
  Response_reg   1 vlivdDdplvrellrqlleeegy.eevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviiltahseeedavealkagadd 96 
                   +livdD   +r++l+++l+++g+ +++ ea+dg ea++++ ++k+dl+++D+nmp+ dGl++lk i + +p+ +vi++t+ +++  +++a+k ga d
    EPA05459.1   7 ILIVDDASFMRTVLKDILKSNGLcSDTIEAADGVEAVRQYIQHKPDLVTMDVNMPNADGLQALKGIMKINPHARVIMVTSVEQKHIVQDAMKFGARD 103
                   8******************999845666********************************************************************* PP

                   EEESSG-HHH CS
  Response_reg  97 flsKpfdpee 106
                   ++ Kpfd+++
    EPA05459.1 104 YIIKPFDRSN 113
                   *******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 735.64
//
Query:       EPA05460.1  [L=122]
Description: response regulator receiver domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.2e-14   52.6   0.3    5.2e-14   52.4   0.3    1.1  1  Response_reg  Response regulator receiver domain
  ------ inclusion threshold ------
      0.054   13.9   0.3       0.32   11.5   0.1    1.9  2  Toprim_2      Toprim-like


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   0.3   5.8e-18   5.2e-14       1     110 [.       5     121 ..       5     122 .] 0.93

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 5.8e-18
                   EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHH........HHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEESSTSHHHHHHH CS
  Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealell........keekvdlillDinmpgmdGlellkeireedpelpviiltahseeedavea 89 
                   +li++D++   +  ++lle+++   v+ a+dg+e+++++        +e+k+d+i+lD +mp+ +G +++  i   +p+ ++i+ +a++ +++++  
    EPA05460.1   5 ILIAEDNKFTSMQYAKLLESNDH-LVEIATDGDECIKKYtqtltdnsNENKFDVIILDHSMPKRSGADVAIDILSLNPNQKIILASATAISAERTYS 100
                   8******************9998.8************99888887766777***********************************99999999999 PP

                   HHCTESEEEESSG-HHHHHHH CS
  Response_reg  90 lkagaddflsKpfdpeeLlka 110
                      +   fl+Kpf+ +++l+ 
    EPA05460.1 101 KLKNKITFLQKPFELSKILEV 121
                   999999**********99886 PP

>> Toprim_2  Toprim-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   3.5e-05      0.32      36      81 ..      19      63 ..      11      74 .. 0.78
   2 ?    0.6   0.0     0.086   7.7e+02       6      17 ..      73      84 ..      70     111 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.5e-05
    Toprim_2 36 lkllerypekkvvlalDnDkaGrkaakrlaellreagvrekirelp 81
                +klle++ +  v +a+D D+  +k++++l +  +e++++++i+  +
  EPA05460.1 19 AKLLESN-DHLVEIATDGDECIKKYTQTLTDNSNENKFDVIILDHS 63
                5677777.34466************************999998443 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.086
    Toprim_2  6 aiDalSlaqlgi 17
                aiD lSl   ++
  EPA05460.1 73 AIDILSLNPNQK 84
                678888776544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       801  (0.0446762); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.34s 00:00:00.92 Elapsed: 00:00:00.54
# Mc/sec: 685.52
//
Query:       EPA05461.1  [L=39]
Description: hypothetical protein BG20_I0850 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.52
# Mc/sec: 225.53
//
Query:       EPA05462.1  [L=204]
Description: hypothetical protein BG20_I0852 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        1.2    9.3   5.1         18    5.5   0.0    2.9  3  ETRAMP    Malarial early transcribed membrane protein (ETRAMP


Domain annotation for each model (and alignments):
>> ETRAMP  Malarial early transcribed membrane protein (ETRAMP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.001        18      26      72 ..      17      61 ..       9      68 .. 0.70
   2 ?   -1.1   0.0      0.12   2.1e+03      52      66 ..     120     134 ..      95     147 .. 0.59
   3 ?    4.1   1.2    0.0027        48      56      79 ..     175     197 ..     174     201 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.001
      ETRAMP 26 devnkkkekakkaikkiddkiekkkkkkKliiistiatalallvasa 72
                d vn +++ +k ++ +i d+i+  k  k+  iis+++ +++l  +++
  EPA05462.1 17 DYVNLEQKISKREFLEISDEIKPGKFGKR-FIISSMIQGAILT-GLT 61
                4444455889999999******9955555.8999888887554.344 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.12
      ETRAMP  52 kkKliiistiatala 66 
                  +K   ist+ + l 
  EPA05462.1 120 ERKFTKISTMLSWLH 134
                 333444555555555 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.0027
      ETRAMP  56 iiistiatalallvasalGlgiyk 79 
                 +++sti+ a++l++ +++G  + +
  EPA05462.1 175 VYLSTICLAIVLAI-GIIGTLYTS 197
                 67899999999999.777766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       898  (0.0500865); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.36s 00:00:00.94 Elapsed: 00:00:00.54
# Mc/sec: 1131.19
//
Query:       EPA05463.1  [L=42]
Description: hypothetical protein BG20_I0839 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.012   16.1   0.8      0.019   15.4   0.8    1.4  1  zf-C2H2    Zinc finger, C2H2 type
      0.014   16.2   0.7       0.02   15.7   0.7    1.3  1  zf-C2H2_4  C2H2-type zinc finger
      0.026   14.8   0.7      0.026   14.8   0.7    1.0  1  zf-C2H2_2  C2H2 type zinc-finger (2 copies)
      0.038   13.9   0.1      0.043   13.7   0.1    1.1  1  HNH_5      HNH endonuclease
      0.041   13.7   0.4      0.047   13.5   0.1    1.4  2  zf-C2H2_3  zinc-finger of acetyl-transferase ESCO


Domain annotation for each model (and alignments):
>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.8   5.3e-06     0.019       2      23 .]      14      36 ..      13      36 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.3e-06
                EETTTTEEESSHHHHHHHHHC.C CS
     zf-C2H2  2 kCpdCgksFkrksnLkrHirt.H 23
                +C++C++ F+ ++  + H+ + H
  EPA05463.1 14 VCKICNMEFSESHRTQIHMIKaH 36
                7******************9999 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   0.7   5.5e-06      0.02       2      24 .]      14      36 ..      13      36 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5.5e-06
   zf-C2H2_4  2 kCpiCgksFsskkaLlrHlkthH 24
                 C+iC+  Fs +++ + H+ + H
  EPA05463.1 14 VCKICNMEFSESHRTQIHMIKAH 36
                7********98888688**9988 PP

>> zf-C2H2_2  C2H2 type zinc-finger (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.7   7.3e-06     0.026      47      75 ..      11      36 ..       1      42 [] 0.75

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 7.3e-06
   zf-C2H2_2 47 ieekleClyCekefkslealreHmkkkgH 75
                i  +l C +C+ ef++ + ++ Hm k+ H
  EPA05463.1 11 I--GLVCKICNMEFSESHRTQIHMIKA-H 36
                3..569********99********864.4 PP

>> HNH_5  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   1.2e-05     0.043      27      53 ..       6      32 ..       5      35 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.2e-05
       HNH_5 27 ltisnlvtlCkkCNqkkgqkvdaalsk 53
                ++++ ++ +Ck CN ++ +++  ++++
  EPA05463.1  6 KKSQTIGLVCKICNMEFSESHRTQIHM 32
                566777888999999998888877765 PP

>> zf-C2H2_3  zinc-finger of acetyl-transferase ESCO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   1.3e-05     0.047      15      27 ..       9      26 ..       2      32 .. 0.74
   2 ?   -3.4   0.1       2.5   8.8e+03      32      36 ..      34      38 ..      33      38 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.3e-05
   zf-C2H2_3 15 q.....CkeCgMvYnpgs 27
                q     Ck C+M++++++
  EPA05463.1  9 QtiglvCKICNMEFSESH 26
                234566********9986 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.5
   zf-C2H2_3 32 klHkk 36
                k+H+k
  EPA05463.1 34 KAHSK 38
                67865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.42u 0.32s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 267.92
//
Query:       EPA05464.1  [L=458]
Description: NHL repeat protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-11   43.3   8.0      0.061   13.4   0.1    7.3  8  NHL             NHL repeat
    1.7e-08   34.1   1.5      0.043   13.1   0.0    4.6  5  Lactonase       Lactonase, 7-bladed beta-propeller
    0.00014   20.6   3.8        0.1   11.1   0.3    2.6  2  Cytochrom_D1    Cytochrome D1 heme domain
    0.00033   20.8  14.3        4.3    7.6   0.1    5.9  6  Arylesterase    Arylesterase
     0.0042   16.6   4.7       0.19   11.1   1.6    2.6  3  Glu_cyclase_2   Glutamine cyclotransferase
  ------ inclusion threshold ------
      0.028   14.7   1.3        6.1    7.2   0.0    3.3  3  ANAPC4_WD40     Anaphase-promoting complex subunit 4 WD40 dom
      0.032   14.0   0.0      0.098   12.4   0.0    1.7  1  GDPD            Glycerophosphoryl diester phosphodiesterase f
       0.04   13.1   0.4         13    4.9   0.0    3.2  2  SdiA-regulated  SdiA-regulated
        2.1    8.7   5.0         18    5.8   1.1    3.6  3  FHA             FHA domain


Domain annotation for each model (and alignments):
>> NHL  NHL repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.1   3.1e-05     0.061       2      27 ..      36      62 ..      36      63 .. 0.93
   2 ?    4.1   0.0     0.026        52       3      19 ..      82      99 ..      80     107 .. 0.81
   3 !    9.2   0.1   0.00065       1.3       5      22 ..     126     146 ..     123     150 .. 0.84
   4 ?    0.6   0.0      0.36   7.1e+02      12      24 ..     144     156 ..     142     157 .. 0.82
   5 !    7.4   0.0    0.0023       4.7       3      18 ..     166     182 ..     165     182 .. 0.95
   6 ?   -3.5   0.1       6.7   1.3e+04      14      19 ..     188     193 ..     183     195 .. 0.76
   7 ?    5.0   0.0     0.014        28       3      18 ..     208     224 ..     207     224 .. 0.91
   8 ?    1.7   0.0      0.16   3.1e+02       3      19 ..     291     308 ..     289     313 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.1e-05
                SSEEEEEEE.TTTEEEEEECCCTEEEE CS
         NHL  2 nyPhGvavd.snGdiyVaDsenhrvqv 27
                nyP+G+ +d + +++yVa++ + ++ v
  EPA05464.1 36 NYPRGIGIDsQLNNLYVANYDSGTISV 62
                79*****************99999877 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.026
                SEEEEEEE.TTTEEEEEE CS
         NHL  3 yPhGvavd.snGdiyVaD 19
                +P+ ++vd +   ++V+D
  EPA05464.1 82 HPTKLTVDtKHHLVFVSD 99
                799999999999999998 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.00065
                 EEEEEE.TTTEEEEEE..CCC CS
         NHL   5 hGvavd.snGdiyVaD..sen 22 
                 +++ ++ +nG iyV+D  s+n
  EPA05464.1 126 WDLQINsNNGKIYVSDlaSNN 146
                 7888999*********86665 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 0.36
                 TTEEEEEECCCTE CS
         NHL  12 nGdiyVaDsenhr 24 
                 +++i++ Ds+++ 
  EPA05464.1 144 SNNIIIVDSYTME 156
                 799*****99875 PP

  == domain 5  score: 7.4 bits;  conditional E-value: 0.0023
                 SEEEEEEE.TTTEEEEE CS
         NHL   3 yPhGvavd.snGdiyVa 18 
                  P+++++d +++++yVa
  EPA05464.1 166 GPWSITIDhKTNNVYVA 182
                 6***************8 PP

  == domain 6  score: -3.5 bits;  conditional E-value: 6.7
                 EEEEEE CS
         NHL  14 diyVaD 19 
                  iyV D
  EPA05464.1 188 IIYVVD 193
                 599999 PP

  == domain 7  score: 5.0 bits;  conditional E-value: 0.014
                 SEEEEEEE.TTTEEEEE CS
         NHL   3 yPhGvavd.snGdiyVa 18 
                  P+G++++ +++ +yV+
  EPA05464.1 208 KPWGISINeNTDILYVS 224
                 5*********9999995 PP

  == domain 8  score: 1.7 bits;  conditional E-value: 0.16
                 SEEEEEEE.TTTEEEEEE CS
         NHL   3 yPhGvavd.snGdiyVaD 19 
                 +P+++++d +++ ++ a+
  EPA05464.1 291 SPQSIVMDpQSNTVFTAN 308
                 7*************9997 PP

>> Lactonase  Lactonase, 7-bladed beta-propeller
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   2.2e-05     0.043      84     144 ..      34      92 ..      18     109 .. 0.64
   2 ?    1.6   0.0     0.065   1.3e+02      84     114 ..      79     109 ..      65     121 .. 0.66
   3 !    6.3   0.0    0.0025       4.9     245     318 ..     124     192 ..      95     199 .. 0.83
   4 ?    2.9   0.0     0.027        53      85     118 ..     206     239 ..     193     261 .. 0.70
   5 !    7.3   0.1    0.0013       2.5     291     330 ..     290     327 ..     244     337 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.2e-05
                 SSS-EEEEEE-TTSSEEEEEETTTTEEEEEEB.TTSEBESECEEEE.....SSTTT-SSTT CS
   Lactonase  84 egaspchlsvdedgkllavAnYsggsvsvfpldadgslkeasqvlkhegsgpnperqesph 144
                  g+ p  + +d + + l+vAnY +g++sv  +d+++ + + + +++ + s p++   +++h
  EPA05464.1  34 VGNYPRGIGIDSQLNNLYVANYDSGTISV--IDSKNMILKNTIIINEKNSHPTKLTVDTKH 92 
                 57777777888888888888888888888..444556666655666555566654444433 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.065
                 SSS-EEEEEE-TTSSEEEEEETTTTEEEEEE CS
   Lactonase  84 egaspchlsvdedgkllavAnYsggsvsvfp 114
                 + ++p+ l+vd +++l++v++  +g+++v++
  EPA05464.1  79 KNSHPTKLTVDTKHHLVFVSDKISGKLTVID 109
                 5566666666666666666666666666654 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0025
                 -EEEEEE-TTSSEEEEEETSSTEEEEEEE-TTT--EEEEEEEE-SSS.--EEEE-TTSSEEEEEETTTTEEEEE CS
   Lactonase 245 saaeIrlspdgkflyvSnRgadsiavfavdeadgtltlveevstegkfPRdfaldpsgklllvanqksdnvtvf 318
                 s+ ++++ +++  +yvS+  +++i++ +      t++ ++ ++ ++  P ++++d++ + ++va  +s+ + v+
  EPA05464.1 124 SLWDLQINSNNGKIYVSDLASNNIIIVDS----YTMEIITSIPLKTG-PWSITIDHKTNNVYVASGDSEIIYVV 192
                 56688999999999***********9764....589********666.********************999887 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.027
                 SS-EEEEEE-TTSSEEEEEETTTTEEEEEEB.TT CS
   Lactonase  85 gaspchlsvdedgkllavAnYsggsvsvfpldad 118
                 g++p  +s++e+  +l+v+++ ++++++++++++
  EPA05464.1 206 GVKPWGISINENTDILYVSSWDANKITMIDIKNN 239
                 5556666666666666666666666666666654 PP

  == domain 5  score: 7.3 bits;  conditional E-value: 0.0013
                 S.--EEEE-TTSSEEEEEETTTTEEEEEEEETTTTEEEEE CS
   Lactonase 291 kfPRdfaldpsgklllvanqksdnvtvferdaetGkLtel 330
                 + P ++++dp+ + ++ an  s++vt++  d   G+L+++
  EPA05464.1 290 DSPQSIVMDPQSNTVFTANPLSNSVTSITYD--DGNLKNT 327
                 4588888888888888888888888877775..4555544 PP

>> Cytochrom_D1  Cytochrome D1 heme domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.3   0.00012      0.24       4     117 ..      48     163 ..      45     170 .. 0.78
   2 !   11.1   0.3   5.1e-05       0.1       9     102 ..     181     274 ..     172     318 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00012
                   GGEEEEEEGGGTEEEEEETTT-SEEEEEE.-STTEEEEEE-TT.SSEEEEEETT...SEEEEEESSSSSEEEEEE-SSEEEEEEE--TTSEEEEEEE CS
  Cytochrom_D1   4 knlfvvverdagkvalldgdskeilavle.tgyalHisrvfasdgRyvyvigRD...gkvtliDLwakeivaevkiGlnarsvavSqddryvivgnY 96 
                   +nl+ v   d g + ++d+++    +++   + + H +++     ++ +v+  D   gk+t+iD + ++++   kiG     +++  ++  + v+  
    EPA05464.1  48 NNLY-VANYDSGTISVIDSKNMILKNTIIiNEKNSHPTKLTVD-TKHHLVFVSDkisGKLTVIDGLSNKMLDSKKIGQSLWDLQINSNNGKIYVSDL 142
                   4554.5678999******9998777665414555688877665.44444444443459**************************9866666889999 PP

                   ETTEEEEEETTT--EEEEEE- CS
  Cytochrom_D1  97 lPgqlvildaetLelvkvisa 117
                      ++ i+d+ t+e +  i+ 
    EPA05464.1 143 ASNNIIIVDSYTMEIITSIPL 163
                   ****************99985 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 5.1e-05
                   EEEGGGTEEEEEETTT-SEEEEEE-STTE.EEEEE-TT.SSEEEEEETTS.EEEEEESSSSSEEEEEE-SSEEEEEEE--TTSEEEEEEEETTEEE CS
  Cytochrom_D1   9 vverdagkvalldgdskeilavletgyal.HisrvfasdgRyvyvigRDg.kvtliDLwakeivaevkiGlnarsvavSqddryvivgnYlPgqlv 102
                   v   d   + ++dg++ +i+  ++ g     is         +yv + D+ k+t+iD+ +++i+ e+ i + a  +++ q++  +i +n    +l 
    EPA05464.1 181 VASGDSEIIYVVDGTKDTIIDSINPGVKPwGISINEN--TDILYVSSWDAnKITMIDIKNNKIIYEILIHSGAWLMDTNQNNGITIISNEHTNELY 274
                   4556677789**************9998845555555..579*******857*****************999999999988877777775555554 PP

>> Arylesterase  Arylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1     0.023        47      55      78 ..      37      60 ..      24      67 .. 0.82
   2 ?    2.3   0.0       0.1     2e+02      51      77 ..      78     104 ..      70     110 .. 0.80
   3 ?    1.1   0.1      0.23   4.6e+02      61      81 ..     130     150 ..     127     157 .. 0.83
   4 ?    5.2   0.2     0.012        24      56      82 ..     167     193 ..     153     198 .. 0.82
   5 !    7.4   0.5    0.0026       5.2      31      84 ..     181     237 ..     179     239 .. 0.79
   6 !    7.6   0.1    0.0021       4.3      30      78 ..     264     314 ..     252     320 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.023
  Arylesterase 55 sanGInidadkkyiyvadilresi 78
                   + GI+id++   +yva+     i
    EPA05464.1 37 YPRGIGIDSQLNNLYVANYDSGTI 60
                  689**************8765555 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.1
  Arylesterase  51 sglssanGInidadkkyiyvadilres 77 
                   ++ s ++ +++d++++ ++v+d +  +
    EPA05464.1  78 EKNSHPTKLTVDTKHHLVFVSDKISGK 104
                   56678999*************998765 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.23
  Arylesterase  61 idadkkyiyvadilresihvm 81 
                   i++++  iyv+d+  ++i ++
    EPA05464.1 130 INSNNGKIYVSDLASNNIIIV 150
                   6777888**********9775 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.012
  Arylesterase  56 anGInidadkkyiyvadilresihvmk 82 
                   +  I+id +   +yva+   e i+v++
    EPA05464.1 167 PWSITIDHKTNNVYVASGDSEIIYVVD 193
                   4569**************999999986 PP

  == domain 5  score: 7.4 bits;  conditional E-value: 0.0026
  Arylesterase  31 lqlawtavvYyspsevkvvasgls...sanGInidadkkyiyvadilresihvmkkh 84 
                   +  + ++++Y + +   + +++++    + GI i+ +  ++yv++  +++i +++ +
    EPA05464.1 181 VASGDSEIIYVVDGTKDTIIDSINpgvKPWGISINENTDILYVSSWDANKITMIDIK 237
                   666778888888888888888875333799********************9887665 PP

  == domain 6  score: 7.6 bits;  conditional E-value: 0.0021
  Arylesterase  30 slqlawtavvYyspsevkv..vasglssanGInidadkkyiyvadilresi 78 
                   ++    t+ +Y  +++  +   +s ++s+  I++d++   ++ a+ l +s+
    EPA05464.1 264 IISNEHTNELYLISNDYTQykSISLMDSPQSIVMDPQSNTVFTANPLSNSV 314
                   5666777788888887665226899********************999997 PP

>> Glu_cyclase_2  Glutamine cyclotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.9   3.7e+03      89     120 ..      42      73 ..      30      80 .. 0.73
   2 !   11.1   1.6   9.8e-05      0.19      67     232 ..     107     267 ..      98     288 .. 0.79
   3 !    8.3   1.8   0.00069       1.4      92     234 ..     216     357 ..     208     360 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.9
  Glu_cyclase_2  89 Gitvlgdklyqltwkegvafvydaetleeigr 120
                    Gi +  ++ly   + +g++ v d +++  +++
     EPA05464.1  42 GIDSQLNNLYVANYDSGTISVIDSKNMILKNT 73 
                    66666677888888888888888777765555 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 9.8e-05
  Glu_cyclase_2  67 kvdletgkvlkeaeldeelFgEGitvlgdklyqltwkegvafvydaetleeigrvsyegeGWGlttdgk..r.lvmsdGsstltfldpktfaetks 159
                     +d  ++k+l+++++ ++l+   i + ++k+y     ++ ++++d  t+e i+++++++  W +t d k  +  v+s  s+ ++++d ++ +  +s
     EPA05464.1 107 VIDGLSNKMLDSKKIGQSLWDLQINSNNGKIYVSDLASNNIIIVDSYTMEIITSIPLKTGPWSITIDHKtnNvYVASGDSEIIYVVDGTKDTIIDS 202
                    556667788889999999999999999**************************************7754223156666678889999999889999 PP

  Glu_cyclase_2 160 vevtkdgkevsklNELeyvkgeiyaNvwqtdrilridpatGkvtgvidlsalreeaekaakedVlNGiAydpe 232
                    ++   +     ++NE     + +y   w  ++i  id ++ k+  +i +++ +  ++++++    NGi ++++
     EPA05464.1 203 INPGVKPWG-ISINE---NTDILYVSSWDANKITMIDIKNNKIIYEILIHSGAWLMDTNQN----NGITIISN 267
                    886655443.46888...57889*****************999999988776666666554....77765433 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.00069
  Glu_cyclase_2  92 vlgdklyqltwkegvafvydaetleeigrvsyegeGWGlttdgk...rlvmsdGsstltfldpktfaetksvevtkdgkevsklNELeyvkgeiya 184
                    +  d ly   w ++++ + d ++ + i ++ +++  W + t+++   +++  + +++l+ +  +++++ ks++  ++ +++     ++  +++++ 
     EPA05464.1 216 ENTDILYVSSWDANKITMIDIKNNKIIYEILIHSGAWLMDTNQNngiTIISNEHTNELYLIS-NDYTQYKSISLMDSPQSIV----MDPQSNTVFT 306
                    4567799999***********************999*9976544222688888999999998.9999999999998877775....6889999999 PP

  Glu_cyclase_2 185 NvwqtdrilridpatGkvtgvidlsalreeaekaake.dVlNGiAydpetd 234
                        ++++  i  ++G+ +++    +l++++ +++   +VlNGi  +p+++
     EPA05464.1 307 ANPLSNSVTSITYDDGNLKNTSLTGDLNTNSLDDNMIlEVLNGILKIPSNH 357
                    9999***************9999999988887766557******9988775 PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.3   2.5e+03      55      79 ..      53      77 ..      46     125 .. 0.69
   2 ?    7.2   0.0     0.003       6.1      47      81 ..     132     166 ..     117     177 .. 0.88
   3 ?    4.8   0.1     0.018        36      44      81 ..     212     250 ..     170     290 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.3
  ANAPC4_WD40 55 vaysdgevrlldaesgkvvhslsvk 79
                   y+ g+++++d+++  + +++ ++
   EPA05464.1 53 ANYDSGTISVIDSKNMILKNTIIIN 77
                 5567778888877776555544444 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.003
  ANAPC4_WD40  47 kpdgklLavaysdgevrlldaesgkvvhslsvkse 81 
                  +++gk+ +   + +++ ++d+++ +++ s++ k+ 
   EPA05464.1 132 SNNGKIYVSDLASNNIIIVDSYTMEIITSIPLKTG 166
                  4799*************************998876 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.018
  ANAPC4_WD40  44 LaWkpdgklLava.ysdgevrlldaesgkvvhslsvkse 81 
                  ++ +++  +L v+ ++ +++ ++d+++ k++ ++ ++s 
   EPA05464.1 212 ISINENTDILYVSsWDANKITMIDIKNNKIIYEILIHSG 250
                  5556677777775156689************99988876 PP

>> GDPD  Glycerophosphoryl diester phosphodiesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   4.9e-05     0.098     129     197 ..     201     266 ..     190     283 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.9e-05
                 CHHHCCCCCSCHHTT..STTCSCEEEESTHHHHHHHHHTCTCTEEEEEEHHHHHHC-E.EECHCCCCCC CS
        GDPD 129 keilksvdeilkkvlkkadkrkvifssfnpdilkllrekqpklpllflteggteaeadssleraakfak 197
                 + i+  v+ ++  ++ + + + +++ss++++ +++++ k++k+ +  l+++g++ ++   +++ +  ++
  EPA05464.1 201 DSINPGVKPWG--ISINENTDILYVSSWDANKITMIDIKNNKIIYEILIHSGAWLMDT-NQNNGITIIS 266
                 56777778888..67778999***********************************99.5556555555 PP

>> SdiA-regulated  SdiA-regulated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0    0.0064        13     176     205 ..     169     198 ..     136     203 .. 0.92
   2 ?    4.3   0.0      0.01        20     177     240 ..     212     277 ..     210     284 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0064
  SdiA-regulated 176 slefdeetghllvLSdeSrllleldeegev 205
                     s+++d++t++++v S +S+++  +d ++++
      EPA05464.1 169 SITIDHKTNNVYVASGDSEIIYVVDGTKDT 198
                     789**********************99886 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.01
  SdiA-regulated 177 lefdeetghllvLSdeSrllleldeegevlsslsLlkgsngLeedipqaEGvam...DeegnlYivs 240
                     ++++e+t+ l+v S +++ ++ +d + + + +  L +  + L  d +q  G+++   ++ ++lY++s
      EPA05464.1 212 ISINENTDILYVSSWDANKITMIDIKNNKIIYEILIHSGAWL-MDTNQNNGITIisnEHTNELYLIS 277
                     6899*********************99999988888865555.5679999*9974446778999998 PP

>> FHA  FHA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       2.1   4.3e+03      29      54 ..      57      78 ..      48      90 .. 0.59
   2 ?    5.8   1.1     0.009        18      25      61 ..     128     164 ..      70     167 .. 0.75
   3 ?   -1.2   0.1       1.4   2.7e+03      33      48 ..     250     265 ..     232     281 .. 0.65

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.1
                TTCEEEEEEEESSSSSEEETTEEEST CS
         FHA 29 kgsgkvyleDlgSknGtfvNgqrigk 54
                +g  ++ ++D  Skn +  N   i+ 
  EPA05464.1 57 SG--TISVID--SKNMILKNTIIINE 78
                44..777888..55555444433333 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.009
                 EEEETTCEEEEEEEESSSSSEEETTEEESTTSEEEE- CS
         FHA  25 ikfdkgsgkvyleDlgSknGtfvNgqrigkgepveLk 61 
                 +++++++gk+y+ Dl S n + v+   ++  ++++Lk
  EPA05464.1 128 LQINSNNGKIYVSDLASNNIIIVDSYTMEIITSIPLK 164
                 3444446699999999999888887655555555555 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.4
                 EEEEEEESSSSSEEET CS
         FHA  33 kvyleDlgSknGtfvN 48 
                 + +l+D +  nG+ + 
  EPA05464.1 250 GAWLMDTNQNNGITII 265
                 4677888888888763 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (458 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.73u 0.37s 00:00:01.10 Elapsed: 00:00:00.54
# Mc/sec: 2547.56
//
Query:       EPA05465.1  [L=197]
Description: CheW-like protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-33  114.5   0.2    3.4e-33  114.2   0.2    1.1  1  CheW      CheW-like domain


Domain annotation for each model (and alignments):
>> CheW  CheW-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.2   0.2   1.9e-37   3.4e-33       1     136 [.      12     153 ..      12     155 .. 0.96

  Alignments for each domain:
  == domain 1  score: 114.2 bits;  conditional E-value: 1.9e-37
                 EEEEEEETTEE.....EEEEGGGEEEEEECCT.BTTTTSSTTEEEEEEETTEEEEEEEHHHHCTSSSSTT..STCEEEEEEEETTEEEEEEESEEEEEE CS
        CheW   1 qlllfrlgeet.....yaiplakvreilevppitpipgapgavlgvinlrGevipvidLrellglgpees..rentrvivvelgnqvvGllVdevkgiq 92 
                 q++ f+++e       y+i +++v+ei  v+++t+ip+++++v+g++nlrG++ipvid  + lglg++    ++++r++v++++n+  GllVdev++++
  EPA05465.1  12 QVVSFTVAEKSkkkgnYCISIDQVKEIRIVDTVTKIPKSKSYVKGLMNLRGKIIPVIDVNSKLGLGETIIsaNSKQRILVTDVNNTLTGLLVDEVNDVI 110
                 6889999999999999****************************************************9999*************************** PP

                 EEECCGEETTTSSTSSTCCCEEEEEECTTSEEEEEE-CCCHHHH CS
        CheW  93 eivikqiepplglssdlagyisGatklgdgrlvliLDveallrs 136
                 +i+ k+i++ ++     +++++G++k+  +++++iLD+e+ l++
  EPA05465.1 111 KISSKDIDDVPSNMFADNNFFKGIVKI-HDNIIMILDIEKFLNH 153
                 **********8888999**********.667*********9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       782  (0.0436165); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.54
# Mc/sec: 1092.97
//
Query:       EPA05466.1  [L=146]
Description: hypothetical protein BG20_I0842 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.15   12.1   0.0       0.19   11.8   0.0    1.3  1  Peptidase_C31  Porcine arterivirus-type cysteine proteinase a


Domain annotation for each model (and alignments):
>> Peptidase_C31  Porcine arterivirus-type cysteine proteinase alpha
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0     1e-05      0.19      21      62 ..      25      67 ..      11     111 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1e-05
  Peptidase_C31 21 wls.aifpiarmtsgnhnfqqrlvkvaavvyrdgkltskhlke 62
                   +ls ++f i  + sgnh++ +  ++v ++++++g l    l+ 
     EPA05466.1 25 FLSvGLFTIFSIHSGNHDYYDLKQQVIEELHKQGILVDSNLNY 67
                   5553799*****************************9988864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       731  (0.0407719); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 879.33
//
Query:       EPA05467.1  [L=74]
Description: hypothetical protein BG20_I0840 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.34s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 443.10
//
Query:       EPA05468.1  [L=139]
Description: hypothetical protein BG20_I0855 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      3e-15   56.2   0.0    4.3e-15   55.7   0.0    1.2  1  CheD          CheD chemotactic sensory transduction
  ------ inclusion threshold ------
        0.2   11.2   0.0        0.3   10.7   0.0    1.2  1  Cu-oxidase_4  Multi-copper polyphenol oxidoreductase laccase


Domain annotation for each model (and alignments):
>> CheD  CheD chemotactic sensory transduction
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.7   0.0   4.8e-19   4.3e-15       1      80 [.      54     132 ..      54     135 .. 0.89

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 4.8e-19
                 -BS--.....SS-TTSCCCBHHHHHHHHHHHHHTTT--GGG-EEEEEE----S.....---SS-HHHHHHHHHHHHHHHTT CS
        CheD   1 mLPds.keskeksasnpakyadtaielLinellklgakkerleaklaGGAqmfafessksdvlniGerNveavkelLkeeg 80 
                 mLP++ + +++  ++ ++kyad ai+++i+++++       l+ak++GGA++f++   ++++lniG+rNv+a++ +Lke++
  EPA05468.1  54 MLPKNnTGKSTFGTKFEGKYADEAINTIIKKMKEIH-PDIILQAKIVGGAKIFDCID-NNSTLNIGKRNVSAIRLILKEKK 132
                 9**99555666677889****************987.5689*************965.899*****************987 PP

>> Cu-oxidase_4  Multi-copper polyphenol oxidoreductase laccase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   3.3e-05       0.3      85     111 ..      27      53 ..      14      53 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 3.3e-05
                   EEEEEESSSEEEEEEETTSSEEEEEEE CS
  Cu-oxidase_4  85 alavltADCvPvlladpkgkvvaaaHa 111
                    l +++  Cv++ l+d+++k++++aH+
    EPA05468.1  27 RLRTFVGSCVAICLYDKSKKICGMAHV 53 
                   57789999******************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 885.80
//
Query:       EPA05469.1  [L=135]
Description: response regulator receiver domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.4e-24   84.8   0.1    5.5e-24   84.5   0.1    1.1  1  Response_reg  Response regulator receiver domain
  ------ inclusion threshold ------
      0.052   13.8   0.1      0.091   13.0   0.1    1.4  1  THF_DHG_CYH   Tetrahydrofolate dehydrogenase/cyclohydrolase, 
      0.067   13.3   0.2       0.12   12.5   0.2    1.3  1  EcoEI_R_C     EcoEI R protein C-terminal


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.5   0.1   9.1e-28   5.5e-24       1     111 [.       4     114 ..       4     115 .. 0.98

  Alignments for each domain:
  == domain 1  score: 84.5 bits;  conditional E-value: 9.1e-28
                   EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEESSTSHHHHHHHHHCTESEE CS
  Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviiltahseeedavealkagaddf 97 
                   v++vdDd + +e+++++l  +++ +v++a +g e ++l++e ++d+++ Di mp+ dG+ ll+++++ +pel+++++ta  ++e+ ++  +  ad  
    EPA05469.1   4 VIVVDDDFDTAEVFSEFLMLHDIDVVGKAYNGFEGIKLFEELRPDIVFSDIWMPKYDGFYLLNNLKASHPELKIVMITADLSQETYTKLKESKADAL 100
                   89*********************************************************************************************** PP

                   EESSG-HHHHHHHH CS
  Response_reg  98 lsKpfdpeeLlkal 111
                   ++Kpf+++++++ +
    EPA05469.1 101 IFKPFRINQIMETI 114
                   ***********987 PP

>> THF_DHG_CYH  Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   1.5e-05     0.091      21      84 ..      67     120 ..      62     130 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.5e-05
                  HHHHHT---EEEEEEES--HHHHHHHHHHHHHHHHTT-EEEEEEE-TT--HHHHHHHHHHHHH- CS
  THF_DHG_CYH  21 klkekgvkpkLavilvgddpasevYvrnkkkaceevGieseliklpedvseeellklieelned 84 
                  +lk+   +p+L +++++ d ++e+Y + k+ +++++ ++   i+         ++++i++++++
   EPA05469.1  67 NLKA--SHPELKIVMITADLSQETYTKLKESKADALIFKPFRINQ--------IMETIDKISKN 120
                  4555..48**********************999998877555544........33345555444 PP

>> EcoEI_R_C  EcoEI R protein C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   1.9e-05      0.12      11      68 ..      65     122 ..      62     133 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.9e-05
   EcoEI_R_C  11 ieenkdsidaLqiiwsdreltkellkeLeekLkepppgitpealweayellek.kvspq 68 
                 +++ k+s+++L+i+++ ++l++e + +L+e  k++   ++p ++++  e ++k +++++
  EPA05469.1  65 LNNLKASHPELKIVMITADLSQETYTKLKES-KADALIFKPFRINQIMETIDKiSKNDS 122
                 456899*************************.*******************99888555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 804.17
//
Query:       EPA05470.1  [L=351]
Description: putative protein-glutamate methylesterase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-58  197.8   0.0    3.8e-58  196.0   0.0    1.8  2  CheB_methylest  CheB methylesterase
      8e-21   74.3   1.2    1.7e-20   73.2   1.2    1.5  1  Response_reg    Response regulator receiver domain


Domain annotation for each model (and alignments):
>> CheB_methylest  CheB methylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.13   1.2e+03      17      48 ..      72     104 ..      68     151 .. 0.78
   2 !  196.0   0.0   4.3e-62   3.8e-58       1     169 [.     166     341 ..     166     342 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.13
                     GGGS.-TT-SS-EEEEE---TT-HHHHHHHHHH CS
  CheB_methylest  17 laal.pedfpaavvvvqhmppsftsslaelLnr 48 
                     ++++ ++++ ++++vv   +++ t+ + + L++
      EPA05470.1  72 IEKMiKSEVLLPIIVVSSFSQKGTKIVLDALEN 104
                     555557778888888888888888877777765 PP

  == domain 2  score: 196.0 bits;  conditional E-value: 4.3e-62
                     EEEEE-TTHHHHHTTTGGGS-TT-SS-EEEEE---TT-HHHHHHHHHHH-SSEEEE--TT-B--TTEEEE--TTSEEEEE..........EE.-. CS
  CheB_methylest   1 vvigaStGGlealkellaalpedfpaavvvvqhmppsftsslaelLnresslkVkeaedgeelepgrvyvapgdkhllie....lals..ak.kg 88 
                     vvig+StGG+ +l+++l++lp+d+pa +++vqhmp++ft+++a +L+++s +kVkeae+g+ +++g+++vapgd h+ ++    ++l+  +k  g
      EPA05470.1 166 VVIGSSTGGPSTLQKILNDLPRDLPAGILLVQHMPKNFTKQFALRLSENSGFKVKEAEEGDLIKDGEILVAPGDFHMIVQpnkkIHLDcsDKrFG 260
                     89******************************************************************************998866664223244 PP

                     -SS-HHHHHHHHHHHH.GGEEEEE-SBSS-TTHHHHHHHHHTT-EEEEE-GGG-SSBSHHHHHHHTT--SEEE-GGGHHHH CS
  CheB_methylest  89 erpsiDvlfesaaeaygeraigviLtGmgsDGaeGlkaikeaggltiaqdpesavvpgmPkaaieagavdevlpleeiaee 169
                      rps+++++ sa e+yg +++g+iLtGmg+DG  G+k+ik++gg+ti+q++e++v++gmPk++i+ + +d+vlpl++ia +
      EPA05470.1 261 VRPSVNMTMISASEVYGTNLVGIILTGMGHDGGFGMKTIKKRGGRTIVQNKETCVIFGMPKEVIDLKSADFVLPLNKIALK 341
                     5******************************************************************99*********976 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.2   1.2   1.9e-24   1.7e-20       1      99 [.      11     111 ..      11     121 .. 0.94

  Alignments for each domain:
  == domain 1  score: 73.2 bits;  conditional E-value: 1.9e-24
                   EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEESSTS..HHHHHHHHHCTES CS
  Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviiltahse..eedavealkagad 95 
                   v+i+ D+ l+r+ l++l++++++e++ +a dg++a+ +++ +k+d+illD++mp+mdGl++++++ + +  lp+i++++ s+   + + +al+ ga+
    EPA05470.1  11 VCIINDSNLMRKYLSDLVTSDEIEVIFTAIDGEDAISKINLKKPDVILLDLEMPKMDGLTFIEKMIKSEVLLPIIVVSSFSQkgTKIVLDALENGAV 107
                   79***************************************************************99999********87775578999******** PP

                   EEEE CS
  Response_reg  96 dfls 99 
                   df++
    EPA05470.1 108 DFVT 111
                   **98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.36s 00:00:00.99 Elapsed: 00:00:00.54
# Mc/sec: 1954.87
//
Query:       EPA05471.1  [L=120]
Description: hypothetical protein BG20_I0841 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0055   17.0   0.0     0.0062   16.9   0.0    1.2  1  DUF3362          Domain of unknown function (DUF3362)
  ------ inclusion threshold ------
      0.029   14.1   3.6      0.036   13.8   3.6    1.1  1  RNA_pol_Rpc82    RNA polymerase III subunit RPC82
      0.036   12.9   1.4      0.036   12.9   1.4    1.0  1  O-antigen_lig    O-antigen ligase like membrane protein
      0.042   14.3   3.5       0.06   13.7   3.5    1.2  1  PRP1_N           PRP1 splicing factor, N-terminal
       0.11   12.4   2.0       0.11   12.4   0.5    1.7  2  DUF1514          Protein of unknown function (DUF1514)
       0.19   11.1   0.2       0.21   10.9   0.2    1.1  1  Nucleoside_tran  Nucleoside transporter
       0.22   12.1   4.1        0.3   11.6   4.1    1.1  1  Secretin_N_2     Secretin N-terminal domain


Domain annotation for each model (and alignments):
>> DUF3362  Domain of unknown function (DUF3362)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   2.4e-06    0.0062      20      68 ..      33      82 ..      17     115 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.4e-06
     DUF3362 20 tgknpltkvkreeesvdvvrgekerrlhkAllrYhdp.knwpllreALkk 68
                 +k+++++ + e+e+++  ++ek  +++  +l ++d+ + w++++e  k+
  EPA05471.1 33 DNKEARKQAQGESEKINSEKSEKINKIKETFLNFRDAfNSWKVIKETWKS 82
                467888888999************************9456*****98765 PP

>> RNA_pol_Rpc82  RNA polymerase III subunit RPC82
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   3.6   1.4e-05     0.036      21      97 ..      23     104 ..      15     112 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.4e-05
                    S-HHHHHHHHHHHTHTTSSSSSSSSTHHHHHHHHHHHHHHHHHHHHHHHSGT......T..TTCETSSSSSEE......... CS
  RNA_pol_Rpc82  21 rpiedlwnalyeeelkktprssttseikkkaeakekiktelrdlresseslkkkeg..rstadstsngtarKrrk...etea 97 
                    ++++  +n ++ +e +k+ ++++ + + +k+e+ +kik+++ ++r+  +s+k  ++  +s ++s +++t+   +k   e ++
     EPA05471.1  23 SSSHATHNSIDNKEARKQAQGESEKINSEKSEKINKIKETFLNFRDAFNSWKVIKEtwKSIKNSGDENTKLQTKKlldEAKI 104
                    67888999********************************************777789888888899999888776654444 PP

>> O-antigen_lig  O-antigen ligase like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.4   1.4e-05     0.036     250     329 ..       5      87 ..       1     119 [. 0.53

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.4e-05
  O-antigen_lig 250 aiillvligillaiypy..spiyrrkelkekeieiksekkeeeeikneikenykseglk......eavleqyeyandkqfsqellkee 329
                    ++++ v++gi+l+i p+  s  + ++++++ke+ + +++ e+e+i++e  +  k++++k      +     ++ +  k+++++ +++ 
     EPA05471.1   5 FLVITVILGIFLLISPSisSSHATHNSIDNKEARK-QAQGESEKINSE--KSEKINKIKetflnfR--DAFNSWKVIKETWKSIKNSG 87 
                    46677777888888777767777777788777774.556688888888..3333333331133221..11222222333333333332 PP

>> PRP1_N  PRP1 splicing factor, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   3.5   2.4e-05      0.06      85     147 ..      30      91 ..      24      92 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.4e-05
                 -HHHHHHHHHHHHHHTT-------.......-HHHHHHHHHHHHHT..T--HHHHHS----B-SS- CS
      PRP1_N  85 eeiderlderrkkrreakekeelekvreek.pkiqeqFadlkrkLa..evseeeWeniPevgdltr 147
                 ++id++      +++ + e+e++++ ++ek +ki+e+F +++ + +  +v +e W++i ++gd  +
  EPA05471.1  30 NSIDNKE----ARKQAQGESEKINSEKSEKiNKIKETFLNFRDAFNswKVIKETWKSIKNSGDENT 91 
                 4555554....444444444444433333349***********99844699***********9765 PP

>> DUF1514  Protein of unknown function (DUF1514)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.5   4.4e-05      0.11       3      24 ..       6      27 ..       4      34 .. 0.87
   2 ?   -2.3   0.0       1.6   4.1e+03      19      29 ..      48      58 ..      47      66 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.4e-05
     DUF1514  3 ivisivlailLLvllsiisdka 24
                +vi+++l i+LL+  si s +a
  EPA05471.1  6 LVITVILGIFLLISPSISSSHA 27
                79************99998766 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.6
     DUF1514 19 iisdkakeiea 29
                i+s+k  +i+ 
  EPA05471.1 48 INSEKSEKINK 58
                56666666654 PP

>> Nucleoside_tran  Nucleoside transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.2   8.2e-05      0.21      65     147 ..       4      85 ..       1      99 [. 0.63

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 8.2e-05
  Nucleoside_tran  65 YFivsivvvivcvilllvlkklefy.keykqlklegslletkeelrqekeeeseskvkltaekskegeenvfvllkvilakikv 147
                      YF v +v++ + +++ + +  ++   +   +++++ + + + e++ +ek+e + +k+k t+ +     +n ++++k + ++ik+
       EPA05471.1   4 YFLVITVILGIFLLISPSISSSHAThNSIDNKEARKQAQGESEKINSEKSE-KINKIKETFLNF-RDAFNSWKVIKETWKSIKN 85 
                      887766666555555544444443303344444444444444555444444.445688888887.7788999999999999987 PP

>> Secretin_N_2  Secretin N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   4.1   0.00012       0.3      20      86 ..      21      89 ..      15      95 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00012
  Secretin_N_2 20 svtsGsvsssgssssssssssss.sgsssssssssnss....sgtkietesesdfwgeLqkalesmlgpgdG 86
                  s++s+  + ++  +++ +++ +  s++ +s++s+   +    + t+++ ++ ++ w+ ++++ +s+ ++gd+
    EPA05471.1 21 SISSSHATHNSIDNKEARKQAQGeSEKINSEKSE---KinkiKETFLNFRDAFNSWKVIKETWKSIKNSGDE 89
                  4555555544444444444332223333333322...24568************************998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2217  (0.123654); expected 358.6 (0.02)
Passed bias filter:                      737  (0.0411066); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.60u 0.34s 00:00:00.94 Elapsed: 00:00:00.54
# Mc/sec: 667.41
//
Query:       EPA05472.1  [L=515]
Description: putative chemotaxis protein CheA [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-19   70.2   0.1    2.2e-19   69.4   0.1    1.4  1  CheW          CheW-like domain
    1.4e-14   54.1   0.0    2.6e-14   53.2   0.0    1.5  1  Hpt           Hpt domain
    1.4e-14   54.6   6.7    2.8e-14   53.6   3.6    2.5  2  HATPase_c     Histidine kinase-, DNA gyrase B-, and HSP90-lik
    4.8e-09   36.5   0.5    1.7e-08   34.7   0.5    2.0  1  H-kinase_dim  Signal transducing histidine kinase, homodimeri
    0.00066   19.5   1.3     0.0011   18.8   0.5    1.8  2  HATPase_c_3   Histidine kinase-, DNA gyrase B-, and HSP90-lik
  ------ inclusion threshold ------
      0.011   15.7   0.0      0.023   14.7   0.0    1.5  1  HATPase_c_2   Histidine kinase-like ATPase domain


Domain annotation for each model (and alignments):
>> CheW  CheW-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.4   0.1   7.5e-23   2.2e-19       2     134 ..     389     514 ..     388     515 .] 0.95

  Alignments for each domain:
  == domain 1  score: 69.4 bits;  conditional E-value: 7.5e-23
                 EEEEEETTEEEEEEGGGEEEEEECCT.BTTTTSSTTEEEEEEETTEEEEEEEHHHHCTSSSSTT.STCEEEEEEEETTEEEEEEESEEEEEEEEECCGE CS
        CheW   2 lllfrlgeetyaiplakvreilevppitpipgapgavlgvinlrGevipvidLrellglgpees.rentrvivvelgnqvvGllVdevkgiqeivikqi 99 
                 +l++ + ++++++p++++ +++++++  ++   +g    vin ++++ip+i L +ll ++++e+ +++  +i++e +++++Gl++d++++ q++vik++
  EPA05472.1 389 GLIIIVSNQQFVLPISNILTTIKIKS-NDVFSLHGN--KVINFENQIIPLIELDKLLCIDKKEPnKDSVTIIIIENNEKKYGLIIDKFERNQDVVIKKL 484
                 57778899******************.*********..**************************99999****************************** PP

                 ETTTSSTSSTCCCEEEEEECTTSEEEEEE-CCCHH CS
        CheW 100 epplglssdlagyisGatklgdgrlvliLDveall 134
                 +++       +g++s at+l+dg++ l+L +  l+
  EPA05472.1 485 DDN-----TYSGLFSNATILPDGKVSLVLEPSLLI 514
                 ***.....4589*****************999886 PP

>> Hpt  Hpt domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.2   0.0   8.7e-18   2.6e-14       2      79 ..       6     100 ..       5     104 .. 0.90

  Alignments for each domain:
  == domain 1  score: 53.2 bits;  conditional E-value: 8.7e-18
                 HHHHHHHHHHHHHHHHHHHH........SCCHHHHHHHHHHHHHHHHHHTTBHHHHHHHHHHHHHHH..HCTSCHHHHHHHH.......HHHHHH CS
         Hpt   2 llelfleeaeelleqleqal........dqedlqelaraaHtLKGsagmlGltelaelahelEdlld..ragelelepelle.......alkall 79 
                 ++e+++ e+ e+++ ++q l        +   l++++r aHt+KG+a+++G++++ el++ +E+++d  r+g ++l+p   +       +l++++
  EPA05472.1   6 YREMYVSESLEHVTIINQTLlklaekpnEKSYLDQIFRSAHTVKGMASTMGYSDTVELCKNIENVFDnlRNGLEKLTPHITDilftfvnLLQQMI 100
                 689***************999****975555***********************************************99998887666666666 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.092   2.7e+02      35      59 ..     217     244 ..     176     247 .. 0.72
   2 !   53.6   3.6   9.4e-18   2.8e-14       5     111 ..     245     383 ..     241     384 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.092
                 E...TEEEEEEEESSSSSTTHHHTGTCS CS
   HATPase_c  35 e...ddlvisveDnGiGipkedlkklfe 59 
                 +   ++++++  D+Gi +++++l+ + e
  EPA05472.1 217 KrlgKEIHLEMDDSGINLDRSILDSITE 244
                 245569999********99999987765 PP

  == domain 2  score: 53.6 bits;  conditional E-value: 9.4e-18
                 HHHHHHHHHHHHHHHH........HSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHT........................GTCS.TTCHHCSTCHT CS
   HATPase_c   5 rLrqiisnlvdNavkf........atkageieveikaseddlvisveDnGiGipkedlk........................klfe.kfsqddstkrg 70 
                  L +i++n  d+ ++         ++++g+i+++ +++ +++ i+v+D+G+Gi++e++k                        ++++  +s+ +++ ++
  EPA05472.1 245 PLLHILRNCADHGIESaeerkkhkKSEKGNISLTASRKGEHILITVKDDGKGIDEEKVKqkaiekkiitqdeanklnhqeaiqLIGApGLST-SEEITD 342
                 6899***********9888776433355555555554449******************************************7777788888.999999 PP

                 STSSSHHHHHHHHHHHHTTTEEEEEEETTTEEEEEEEEESS CS
   HATPase_c  71 gggtGlGlsivkklvelmgGeiwvesepgrGttftftlple 111
                  +g+G+G+ +v + ve++gG++++ se++ Gtt+++++p++
  EPA05472.1 343 ISGRGVGMDVVISQVETVGGSVKIYSEKNVGTTIILSIPMN 383
                 9************9999********************9985 PP

>> H-kinase_dim  Signal transducing histidine kinase, homodimeric domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.5   5.7e-12   1.7e-08       3      69 .]     138     196 ..     136     196 .. 0.96

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 5.7e-12
  H-kinase_dim   3 tlRVdakrlDyLlnlvGElVitkarLnqsleefrfenglkasvtelksslqnlgrisgeLQegvmki 69 
                   t+RV  + lD+L+n vGEl i+k rL+q +++ +         +e k+ l  ++ ++++LQ   m+i
    EPA05472.1 138 TIRVKMTDLDTLVNSVGELMISKMRLKQTIDDKN--------YEESKQILYDIDHLITDLQHRSMQI 196
                   9*******************************99........999*******************997 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.5   3.7e-07    0.0011       7      78 ..     246     351 ..     241     388 .. 0.65
   2 ?   -3.6   0.0       2.9   8.8e+03      96     122 ..     461     487 ..     454     493 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 3.7e-07
  HATPase_c_3   7 laelvdNsldAdaen..............vkievnknrgktgeivieDdGkGmseeelkn.al..rlatsskeak..r................ksts 69 
                  l+ +++N+ d   e+              ++++++++ g++  i+++DdGkG++ee++k+ a+  ++ t+++ +k  +                + t+
   EPA05472.1 246 LLHILRNCADHGIESaeerkkhkksekgnISLTASRK-GEHILITVKDDGKGIDEEKVKQkAIekKIITQDEANKlnHqeaiqligapglstseEITD 342
                  5666777777555555556677777776688888875.78999****************878754577777776533133333333333333333444 PP

  HATPase_c_3  70 lGkkGiGlk 78 
                  ++ +G+G+ 
   EPA05472.1 343 ISGRGVGMD 351
                  777777764 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2.9
  HATPase_c_3  96 gesstltldvdkidkenekvleeltve 122
                  +++ ++ l +dk +++++ v+++l+ +
   EPA05472.1 461 NNEKKYGLIIDKFERNQDVVIKKLDDN 487
                  556678888888888888888887765 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   7.6e-06     0.023      50     103 ..     269     349 ..     249     378 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 7.6e-06
  HATPase_c_2  50 eapegpvevrlesdeealtvevaDsGpgfdpetlpdpteeep...........................keslkegGrGla 103
                  + ++g +++++++++e + ++v+D+G+g d e+ ++++ e++                           +e  +++GrG+ 
   EPA05472.1 269 KSEKGNISLTASRKGEHILITVKDDGKGIDEEKVKQKAIEKKiitqdeanklnhqeaiqligapglstsEEITDISGRGVG 349
                  3336999999******************99999999999888899999999999999999999888888888888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (515 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1131  (0.0630822); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.72u 0.36s 00:00:01.08 Elapsed: 00:00:00.53
# Mc/sec: 2932.18
//
Query:       EPA05473.1  [L=271]
Description: CheR methyltransferase, SAM binding domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-51  174.1   0.2      3e-51  173.7   0.2    1.1  1  CheR             CheR methyltransferase, SAM binding domain
    1.1e-08   34.6   0.1    3.2e-08   33.2   0.1    1.7  1  CheR_N           CheR methyltransferase, all-alpha domain
    5.7e-07   30.2   0.1    3.3e-05   24.6   0.1    2.4  1  Methyltransf_12  Methyltransferase domain
    8.1e-07   29.0   1.3    1.8e-05   24.6   0.5    2.7  2  Methyltransf_31  Methyltransferase domain
    7.4e-06   26.6   0.0     0.0016   19.1   0.0    2.4  1  Methyltransf_25  Methyltransferase domain
    1.3e-05   25.8   0.0    0.00012   22.6   0.0    2.2  1  Methyltransf_11  Methyltransferase domain
    0.00041   20.2   0.0    0.00059   19.7   0.0    1.2  1  Methyltransf_23  Methyltransferase domain


Domain annotation for each model (and alignments):
>> CheR  CheR methyltransferase, SAM binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.7   0.2   1.2e-54     3e-51       1     184 [.      73     252 ..      73     260 .. 0.95

  Alignments for each domain:
  == domain 1  score: 173.7 bits;  conditional E-value: 1.2e-54
                 SS--TTTTCHHHHHHHHCCH.HHHHHHHTSSSEEEEEES-TTTHHHHHHHHHHHCHSTTTSSS-EEEEEEESSCHHHHHHHHTEEECCHHTTS-HHHHH CS
        CheR   1 neTeffreakhfeelekevlepllakaknekrvriwsagcssGeEpYslAmllketlpkaaklkvkilAtDidlkvlekAkagvykeeeleglseelle 99 
                 n+T+ffr++  ++++e+++l p+  + +n +++ +ws g+++GeE Ys+++ll++ l+k++  k++i++tDi++k++ +Ak+g+yk+e++++++ + l+
  EPA05473.1  73 NVTKFFRDPSVWKTFEHQIL-PNFYNDSNFSSIDLWSCGSATGEEVYSISILLDKHLKKKHM-KYNIIGTDINEKAILTAKQGIYKKEKISNINSQELQ 169
                 79******************.688888889*************************7766666.************************************ PP

                 HHEEEEETTCEEE-HHHHTTEEEEE--TTT-SGGG--EEEEEE-SSGGGC-CHHHHHHHHHHHCCEEEEEEEEE-TTB--SSSCC CS
        CheR 100 ryfekseddsykvkkeikelvkFeklnllekksvlgklDvifcrnvliYfdeetqekvlerfaeklkpgglLllGhsEslkklkd 184
                  yf    d++yk+k+e k++++ e+l+ll+  +  + +D+ifcrnvliY d+ + e + ++f + lk+gg+L+lG+ Es+ + + 
  EPA05473.1 170 TYFDVLPDERYKIKSEFKKNIQLERLDLLQ--TTGKYFDIIFCRNVLIYYDRRAHEILFKKFFSLLKKGGILILGQDESMIGTNG 252
                 ******************************..89999*******************************************96655 PP

>> CheR_N  CheR methyltransferase, all-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.1   1.2e-11   3.2e-08       4      51 ..      11      58 ..       9      59 .. 0.94

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 1.2e-11
                HHHHHHHHHTT-EE--SSTHHHHHTHHHHHHHTTT-SSSHHHHHHTSH CS
      CheR_N  4 erlleliyertGidlsdyKrallkrRlsrRmralglksfeeYldlLrs 51
                e +++l++++tGi+  + K + l+rR+++Rm  lg+ +f+ Y+dlL +
  EPA05473.1 11 ESVISLMKKKTGINIQNFKLTFLERRINHRMCDLGILDFDKYVDLLST 58
                56789****************************************976 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.1   1.3e-08   3.3e-05      13      99 .]     127     239 ..     120     239 .. 0.72

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.3e-08
  Methyltransf_12  13 alleklpdieytgvDispsai.edakeklakrennnnnnvelealdlldldgg.......................ssfDlvvasnvlhhl..k 80 
                      +l +k+   +++g+Di+++ai ++++   +k++  n n  el++  +   d++                       ++fD++++ nvl +   +
       EPA05473.1 127 HLKKKHMKYNIIGTDINEKAIlTAKQGIYKKEKISNINSQELQTYFDVLPDERykiksefkkniqlerldllqttgKYFDIIFCRNVLIYYdrR 220
                      45556577889999999999953333334444444444444444444444444777799999999999999999999**************744 PP

  Methyltransf_12  81 direvldnirklLkpgGrl 99 
                        + +++++ +lLk+gG+l
       EPA05473.1 221 AHEILFKKFFSLLKKGGIL 239
                      4557889**********87 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.32   8.3e+02      92     114 ..       8      33 ..       4      73 .. 0.72
   2 !   24.6   0.5   7.1e-09   1.8e-05       9     109 ..     105     241 ..      97     255 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.32
  Methyltransf_31  92 kileeiervlkpggilliedpr...l 114
                      + +e++++++k+++ + i++++   l
       EPA05473.1   8 QKMESVISLMKKKTGINIQNFKltfL 33 
                      56788999999999998888884432 PP

  == domain 2  score: 24.6 bits;  conditional E-value: 7.1e-09
  Methyltransf_31   9 D...lGCGtGeltfelae.......elgpkae....vvGiDiseeaielAre.naqklgldnveFeq.gdiee.lekl.led............ 72 
                      D   +G++tGe ++ +         +     +    ++G Di+e+ai  A++ + +k +++n++ ++ +  ++ l+   ++             
       EPA05473.1 105 DlwsCGSATGEEVYSISIlldkhlkKK----HmkynIIGTDINEKAILTAKQgIYKKEKISNINSQElQTYFDvLPDErYKIksefkkniqler 194
                      544478888887776665444443333....34555****************999999999998776566677788766665888888999999 PP

  Methyltransf_31  73 ........ekfDlilsnevl..naladpdkileeiervlkpggilli 109
                              + fD+i++++vl  ++  + +  +++ +++lk+ggil++
       EPA05473.1 195 ldllqttgKYFDIIFCRNVLiyYDRRAHEILFKKFFSLLKKGGILIL 241
                      999*999999***********99999999999*************97 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   6.1e-07    0.0016      21      97 .]     134     237 ..     110     237 .. 0.63

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 6.1e-07
                      SSEEEEEESSHHHHHHHH...............HHHHHTTT....................TEEEEESBCCGBSSSTTTEEEEEEESTGGGSSH CS
  Methyltransf_25  21 kakvtgvDiseemleaar...............eraeeegl....................nvefvqgdaedlpfedgsfDlvvssgalhhlsd 79 
                      k++++g+Di+e+++ +a+               e      l                    n+++++ d+  l+   + fD+++++++l ++++
       EPA05473.1 134 KYNIIGTDINEKAILTAKqgiykkekisninsqE------LqtyfdvlpderykiksefkkNIQLERLDL--LQTTGKYFDIIFCRNVLIYYDR 219
                      5777777777777777765555554443333320......122222233332233111122333333333..3456779******999999*** PP

                      HHHHHHHHHHHHHEEEEE CS
  Methyltransf_25  80 edlekalkeiarvLkpgG 97 
                      + +e ++k+++++Lk+gG
       EPA05473.1 220 RAHEILFKKFFSLLKKGG 237
                      *****************9 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   4.8e-08   0.00012      14      96 .]     128     241 ..     110     241 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 4.8e-08
                      HHHTT..SEEEEEES-HHHHHHHHHHCCHHT-.......EEEE......................TTEECCCTSS-TT-EEEEEEES-CCC-.. CS
  Methyltransf_11  14 lakrg..arvvgvDlskemlklakekaseegl.......kvef......................vvadaeklpfednsfDlvvssevlhhv.. 74 
                      l+k+   ++++g+D++++++ +ak+ + +++        +  +                      + +++  l+   ++fD++++++vl +   
       EPA05473.1 128 LKKKHmkYNIIGTDINEKAILTAKQGIYKKEKisninsqE--LqtyfdvlpderykiksefkkniQLERLDLLQTTGKYFDIIFCRNVLIYYdr 219
                      4533347899999999999999987777777666444441..14456667777777777777664556666679999***************77 PP

                      CCHHHHHHHHHHHEEEEEEEEE CS
  Methyltransf_11  75 edpekalkeiaRvLkpgGllvi 96 
                        +e ++k++  +Lk+gG+l++
       EPA05473.1 220 RAHEILFKKFFSLLKKGGILIL 241
                      68899**************985 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   2.3e-07   0.00059      43     117 ..     133     241 ..      81     255 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 2.3e-07
  Methyltransf_23  43 ngfsvtgvDlspeaveiae.........kakkaqkdqfdeqeaae.........pqg...............kfdlIvlrevlehvp..dppel 101
                        ++++g D++++a+  a+         + +++q  q++ +  ++         + +               +fd+I +r+vl   +   ++ l
       EPA05473.1 133 MKYNIIGTDINEKAILTAKqgiykkekiSNINSQELQTYFDVLPDerykiksefK-KniqlerldllqttgkYFDIIFCRNVLIYYDrrAHEIL 225
                      2469********9999999999999877444444444444422222223333331.0334444444444445***********9999545**** PP

  Methyltransf_23 102 lrqiatllkpgGylll 117
                      ++++++llk gG l+l
       EPA05473.1 226 FKKFFSLLKKGGILIL 241
                      ************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       641  (0.0357521); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.63u 0.34s 00:00:00.97 Elapsed: 00:00:00.54
# Mc/sec: 1499.72
//
Query:       EPA05474.1  [L=191]
Description: hypothetical protein BG20_I0838 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.071   13.3   0.7       0.18   11.9   0.0    2.0  2  FUR       Ferric uptake regulator family


Domain annotation for each model (and alignments):
>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0     1e-05      0.18      70     102 ..      44      76 ..      28      97 .. 0.87
   2 ?   -0.7   0.1     0.083   1.5e+03      82      92 ..     142     152 ..     103     177 .. 0.46

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1e-05
                 EEESSSSSEEEEEETTT--EEEE--HHHHHHHH CS
         FUR  70 yelakkehhdhlicekCgkviefkddeiekiqe 102
                 ye++k+  hd   +++ g++ +++d +iek +e
  EPA05474.1  44 YEFVKQASHDETKENSLGNIMDITDRDIEKEKE 76 
                 9****************************9876 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.083
                 EETTT--EEEE CS
         FUR  82 icekCgkvief 92 
                   +k + v+e+
  EPA05474.1 142 TIQKNSMVQEL 152
                 33333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1609  (0.0897429); expected 358.6 (0.02)
Passed bias filter:                      572  (0.0319036); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 1079.78
//
Query:       EPA05475.1  [L=477]
Description: pyridine nucleotide-disulfide oxidoreductase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      7e-44  150.2   0.0    8.6e-44  149.9   0.0    1.1  1  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
    1.3e-09   38.4   0.4    3.3e-07   30.8   0.3    3.0  2  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
  ------ inclusion threshold ------
      0.053   13.9   0.2       0.88    9.9   0.0    2.7  2  Thioredoxin_8    Thioredoxin-like
      0.072   12.8   1.0       0.22   11.2   0.2    2.2  2  DUF835           Protein of unknown function (DUF835)
       0.19   12.0   0.9       0.32   11.3   0.0    1.9  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.9   0.0   2.4e-47   8.6e-44       1     294 []      35     361 ..      35     361 .. 0.89

  Alignments for each domain:
  == domain 1  score: 149.9 bits;  conditional E-value: 2.4e-47
                  CSEEEE--SHHHHHHHHHHHH....HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHHHHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEECTC CS
                  xxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaq....agakvtlvelegtclnggcllskallgvaedaeiasevvkklnqgielllgeevvkidpgkkkvklekkkegd 94 
                  k+++++GgG++G+++ +++ +      +++t++ +++++++++++l++++ g  ++ +i +  ++ + ++ ++l + +v +id +++ v+++ + +++
   EPA05475.1  35 KKILILGGGFGGITTLQNIEKkfanDPVEITII-SNDNFFLFTPMLPQVVSGLIHASNISTP-IRYFCKKAKFLQA-NVESIDLDQQLVTIQRSFDNK 129
                  589****************9988766*******.***********************98873.4556667888888.**************99999** PP

                  EEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-T.................SEEEEES-SHHHHHHHHHHHHHT-......... CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................xxxxxxxxxxxxxxxxxxxxxxxx......... RF
  Pyr_redox_2  95 eekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllp.................krivvvGgGyiGvElAaalaklgk......... 166
                   ++++yd+lvl  G++++ ++ + ++++ + + +++++a a+k +                      +vvvGgG+ GvE+ ++++ +           
   EPA05475.1 130 LHTLEYDYLVLSLGGKSNYFKNENLKKHSFSM-KSIEDAIAVKNHIILmlehaaqtgnyelqknlLTFVVVGGGFAGVETISEINHFVRqsiskfyks 226
                  ********************999997777655.88888888888888788788888777777555777***************977755677778889 PP

                  ......EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEE CS
                  ......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Pyr_redox_2 167 ......evtlveardrllraldkelsaaleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvavGvrpstelleeklglelderggi 258
                        +v l+   dr+l++ ++el++++ + lekeG++v  +++++++  ++    v l++ge+i + ++++  G++ ++ +   +l++e  ++g++
   EPA05475.1 227 inpknvNVILISSKDRILPEINEELANTALRFLEKEGITVLKNSRATDAG-EEF---VLLNNGEKISCATLIWTGGITMKKVI--SELKCEHGDNGRV 318
                  9999989**********************************999996665.333...9**********************988..79*********** PP

                  E--TTSBES.STTEEE-GGGC......TECCSS--HHHHHHHH CS
                  xxxxxxxxx.xxxxxxxxxxx......xxxxxxxxxxxxxxxx RF
  Pyr_redox_2 259 vvdeflrtn.vpgiyaiGDva......ggkggpelaqaAvqqG 294
                  +vde+l+ +  ++++a+GD+a       +   p +aq+A+++G
   EPA05475.1 319 KVDETLKIKnRDNVFALGDCAwipdisTNSIYPSTAQHAIREG 361
                  *******855***************9988899********998 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.017        60       1      38 [.      36      79 ..      36      94 .. 0.73
   2 !   30.8   0.3   9.3e-11   3.3e-07       2      64 ..     196     273 ..     195     279 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.017
                EEEEECSSHHHHHHHHHHHH.TT...SEEEEEESSSSSS..TTS CS
   Pyr_redox  1 kvvvvGgGyiglElAgalae.lg...kkVtvversdkll..rll 38
                k++++GgG+ g+   +++ + ++    ++t++ + + +l  ++l
  EPA05475.1 36 KILILGGGFGGITTLQNIEKkFAndpVEITIISNDNFFLftPML 79
                799*********99999955377555689999998888844444 PP

  == domain 2  score: 30.8 bits;  conditional E-value: 9.3e-11
                 EEEECSSHHHHHHHHHH...............HHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEE CS
   Pyr_redox   2 vvvvGgGyiglElAgal...............aelgkkVtvversdkllrllDeeaskilqeklekngievllntkve 64 
                  vvvGgG+ g+E  +++               +  + +V ++  +d++l+ ++ee+++   + lek+gi+vl n++++
  EPA05475.1 196 FVVVGGGFAGVETISEInhfvrqsiskfyksiNPKNVNVILISSKDRILPEINEELANTALRFLEKEGITVLKNSRAT 273
                 59***************666666666665444444489************************************9987 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.21   7.5e+02      22      45 ..      49      71 ..      46      75 .. 0.87
   2 ?    9.9   0.0   0.00024      0.88      20      74 ..     217     266 ..     204     288 .. 0.69

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.21
                   HHHHHHHHHHHTTSEEEEEEE-SS CS
  Thioredoxin_8 22 klkelyeklkkkkkveivyvsldk 45
                   +l+++++k+  ++ vei  +s+d+
     EPA05475.1 49 TLQNIEKKFA-NDPVEITIISNDN 71
                   7889999997.9**********97 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00024
                    HHHHHHHHHHHHHTTSEEEEEEE-.SS-HHHHHHHGGGS-TTSEE.EE-TT-HHHH CS
  Thioredoxin_8  20 tpklkelyeklkkkkkveivyvsl.dkkeeefekylkknkkpwlsvpfddkkrnkl 74 
                    +++++++y++++ +k+v+++ +s+ d+ + e ++ l+++     +++f +k+  ++
     EPA05475.1 217 RQSISKFYKSIN-PKNVNVILISSkDRILPEINEELANT-----ALRFLEKEGITV 266
                    456899******.9*********9557788888888888.....666666664433 PP

>> DUF835  Protein of unknown function (DUF835)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0         1   3.7e+03     101     117 ..     161     177 ..     155     184 .. 0.79
   2 ?   11.2   0.2   6.3e-05      0.22      22      76 ..     212     263 ..     204     269 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1
      DUF835 101 lltlkDavllkngtlil 117
                 ++++ Da+++kn ++++
  EPA05475.1 161 MKSIEDAIAVKNHIILM 177
                 67788999999987765 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 6.3e-05
      DUF835  22 vlaitRenpkkirekvkienvkviwltkveeentvsPtnlekltetivkflkeae 76 
                 +  ++R++ +k+ + ++++nv+vi ++++++   + P+  e+l +t  +fl++++
  EPA05475.1 212 INHFVRQSISKFYKSINPKNVNVILISSKDR---ILPEINEELANTALRFLEKEG 263
                 5679**********************98766...999999999999999999887 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   8.8e-05      0.32       1      33 [.      37      70 ..      37      74 .. 0.95
   2 ?   -3.5   0.2       3.1   1.1e+04       2      17 ..     197     212 ..     196     214 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.8e-05
                     EEEE--SHHHHHHHHHHHCTCCT-G.EEEEEESS CS
  Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvda.eitvadrs 33
                     +li+G+G+ G  +++ ++++f  d+ eit+++ +
       EPA05475.1 37 ILILGGGFGGITTLQNIEKKFANDPvEITIISND 70
                     89*****************************987 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.1
                      EEE--SHHHHHHHHHH CS
  Sacchrp_dh_NADP   2 liiGaGsvGqavaell 17 
                      +++G+G+ G  ++ ++
       EPA05475.1 197 VVVGGGFAGVETISEI 212
                      89*****998887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (477 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       750  (0.0418317); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.66u 0.33s 00:00:00.99 Elapsed: 00:00:00.50
# Mc/sec: 2874.01
//
Query:       EPA05476.1  [L=108]
Description: GMP synthase (glutamine-hydrolyzing), N-terminal domain protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.7e-23   81.9   0.0    5.2e-23   81.8   0.0    1.0  1  GATase         Glutamine amidotransferase class-I
    0.00049   19.9   0.1    0.00081   19.2   0.1    1.7  1  Peptidase_C26  Peptidase C26


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.8   0.0   5.8e-27   5.2e-23       1      96 [.      13     106 ..      13     108 .] 0.96

  Alignments for each domain:
  == domain 1  score: 81.8 bits;  conditional E-value: 5.8e-27
                 EEEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTTTTTHHHHHHHHCTSTS-EEEETHHHHHHHHHTTTEEEEEE CS
      GATase   1 lliDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspgvegkieaikearenkiPiLGICLGmQllaiefgrkvvkek 96 
                 +++D+++++++ ++++++e+ v+ e+vp+d s+ee +  + np+gi++sgGp s++  +++   +++++ k+P+LGIC+G+Ql++++fg+kv +++
  EPA05476.1  13 VVLDFGSQYSHLICRRIREFSVYAELVPFDISFEELQ--KHNPKGIIFSGGPSSVYNSNAPVPESKIFDMKLPLLGICYGHQLIVNKFGGKVKRAN 106
                 589*********************************5..79***************************************************9887 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1     9e-08   0.00081     101     128 ..      77     104 ..      19     108 .] 0.94

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 9e-08
  Peptidase_C26 101 alergvPilgiCrGlqllnvalGGtlyq 128
                    + + ++P+lgiC G+ql+   +GG++ +
     EPA05476.1  77 IFDMKLPLLGICYGHQLIVNKFGGKVKR 104
                    567899******************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       202  (0.0112667); expected 358.6 (0.02)
Passed bias filter:                      198  (0.0110436); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.34s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 611.69
//
Query:       EPA05477.1  [L=59]
Description: hypothetical protein BG20_I2641, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.34s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 338.59
//
Query:       EPA05478.1  [L=206]
Description: superoxide dismutase, Mn [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-38  131.4   0.1      2e-38  130.6   0.1    1.4  1  Sod_Fe_C  Iron/manganese superoxide dismutases, C-terminal do
    1.9e-29  102.0   1.4    3.3e-29  101.2   1.4    1.4  1  Sod_Fe_N  Iron/manganese superoxide dismutases, alpha-hairpin
  ------ inclusion threshold ------
      0.047   14.2   0.1      0.098   13.2   0.1    1.5  1  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I


Domain annotation for each model (and alignments):
>> Sod_Fe_C  Iron/manganese superoxide dismutases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.6   0.1   3.4e-42     2e-38       1     102 []      99     201 ..      99     201 .. 0.97

  Alignments for each domain:
  == domain 1  score: 130.6 bits;  conditional E-value: 3.4e-42
                 --HHHHHHHHHHHSSHHHHHHHHHHHHHHSSSSEEEEEEEETT.TEEEEEEEETTTBGGGGTTCEEEEEE-SGGGTHHHHTT-HHHHHHHHGGGBBHHH CS
    Sod_Fe_C   1 psgelaeaieedfgslekfkkefkaaalavfgsGwawLvldkk.kkLeivttknqdnplvkeakplLalDvwehAYyldyqnkradYieafwnvvnWke 98 
                 p g++a+ai+++fgs+ +fk++f+++++ ++gsGw+wLv++++ kk+e   ++nq++p +++ +plL++DvwehAYyl+yqnkr+dYi+++wnvvnW+e
  EPA05478.1  99 PGGAIADAIKTSFGSFADFKEKFSSSSAVIQGSGWGWLVYNPStKKVEYKAMPNQTSPRTEGLVPLLGCDVWEHAYYLKYQNKRPDYIASWWNVVNWDE 197
                 6799*************************************98689***************************************************** PP

                 HHHH CS
    Sod_Fe_C  99 veer 102
                 v++r
  EPA05478.1 198 VQNR 201
                 *986 PP

>> Sod_Fe_N  Iron/manganese superoxide dismutases, alpha-hairpin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.2   1.4   5.6e-33   3.3e-29       1      82 []       3      92 ..       3      92 .. 0.92

  Alignments for each domain:
  == domain 1  score: 101.2 bits;  conditional E-value: 5.6e-33
                S------SS-TTTTTTTS-HHHHHHHHHTHHHHHHHHHHHHHHCHHHHCHCCHHHHHH........HHHHHHHHHHHHHHHHHHHHHTB- CS
    Sod_Fe_N  1 kyeLpeLpYaydaLePhisketlelHhdkHhktYvnnlNkalekleeakkkleelvlk........klekalrnnagghvnHslfwknls 82
                ky+Lp++pYaydaLePhi+++t+e+Hh+kHh++Y ++lN+ale+   + ++++ l++         ++++a+++n+gg+ nH+lfw+n++
  EPA05478.1  3 KYTLPQIPYAYDALEPHIDAKTMEIHHTKHHQAYTDKLNAALESCPVEIQSKDILDILaninqvpeAQRGAVNFNGGGYDNHKLFWNNMK 92
                6********************************************8888877776655568999989999******************96 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   1.6e-05     0.098      27      55 ..      23      51 ..      13      52 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.6e-05
     Fer4_13 27 gasvvaeqptseeekadaeeAadaCPves 55
                + + +++ ++ ++ ++++++A+++CPve+
  EPA05478.1 23 KTMEIHHTKHHQAYTDKLNAALESCPVEI 51
                56789999999****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 1228.19
//
Query:       EPA05479.1  [L=312]
Description: signal recognition particle-docking protein FtsY, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-70  235.8   0.6    4.5e-70  235.3   0.6    1.2  1  SRP54            SRP54-type protein, GTPase domain
    1.4e-09   38.1   4.4    1.4e-09   38.1   4.4    2.0  1  SRP54_N          SRP54-type protein, helical bundle domain
    1.8e-07   31.0   0.1    4.1e-07   29.9   0.1    1.5  1  AAA_30           AAA domain
    7.5e-06   25.4   0.1    1.2e-05   24.6   0.1    1.2  1  Zeta_toxin       Zeta toxin
    5.5e-05   23.4   0.1    0.00014   22.1   0.1    1.7  1  AAA_22           AAA domain
    0.00026   21.4   0.0    0.00061   20.2   0.0    1.6  1  AAA_17           AAA domain
    0.00052   19.7   0.9     0.0047   16.5   0.9    2.1  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
    0.00062   20.2   0.1      0.002   18.5   0.1    1.9  1  AAA              ATPase family associated with various cellul
     0.0013   18.9   0.0      0.002   18.3   0.0    1.4  1  AAA_33           AAA domain
     0.0021   17.3   0.1     0.0035   16.6   0.1    1.2  1  DUF2075          Uncharacterized conserved protein (DUF2075)
     0.0031   17.9   0.2     0.0051   17.2   0.2    1.5  1  AAA_19           AAA domain
     0.0042   17.5   0.0     0.0076   16.6   0.0    1.5  1  AAA_16           AAA ATPase domain
     0.0057   16.7   0.1      0.028   14.5   0.0    2.1  2  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
     0.0059   16.5   0.1      0.025   14.5   0.0    2.0  2  APS_kinase       Adenylylsulphate kinase
      0.007   16.1   0.0      0.023   14.3   0.0    1.9  2  Thymidylate_kin  Thymidylate kinase
     0.0089   15.2   0.1      0.014   14.6   0.1    1.2  1  PIF1             PIF1-like helicase
     0.0093   15.7   0.2       0.15   11.8   0.1    2.6  3  TPP_enzyme_M     Thiamine pyrophosphate enzyme, central domai
     0.0096   15.8   0.1      0.019   14.9   0.1    1.4  1  TK               Thymidine kinase
  ------ inclusion threshold ------
      0.011   15.7   0.5       0.91    9.4   0.1    2.4  2  NTPase_1         NTPase
      0.014   15.5   0.6      0.036   14.1   0.0    2.0  2  AAA_14           AAA domain
      0.019   14.5   0.1      0.036   13.5   0.1    1.4  1  KdpD             Osmosensitive K+ channel His kinase sensor d
      0.019   15.5   0.1      0.043   14.3   0.1    1.7  1  ABC_tran         ABC transporter
      0.022   14.0   0.1      0.038   13.2   0.1    1.4  1  DAP3             Mitochondrial ribosomal death-associated pro
      0.032   13.7   0.0      0.062   12.8   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
      0.035   13.8   0.0      0.073   12.8   0.0    1.6  1  AAA_24           AAA domain
      0.036   13.0   0.1       0.13   11.2   0.1    1.9  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
      0.038   13.4   0.2      0.083   12.3   0.0    1.6  2  KTI12            Chromatin associated protein KTI12
      0.045   13.5   0.1       0.11   12.3   0.0    1.6  1  CLP1_P           mRNA cleavage and polyadenylation factor CLP
      0.054   13.5   0.1       0.26   11.2   0.0    1.9  2  SPOUT_MTase      Predicted SPOUT methyltransferase
      0.055   13.5   0.0        0.1   12.6   0.0    1.5  1  AAA_5            AAA domain (dynein-related subfamily)
      0.062   13.3   0.1       0.21   11.6   0.1    1.9  1  B12-binding      B12 binding domain
      0.066   13.4   0.0        0.1   12.8   0.0    1.3  1  AAA_28           AAA domain
      0.089   12.7   0.3       0.32   10.9   0.1    1.9  2  MobB             Molybdopterin guanine dinucleotide synthesis
      0.095   12.7   1.5       0.31   11.0   1.3    2.0  1  ResIII           Type III restriction enzyme, res subunit
        0.1   12.7   2.3       0.39   10.8   0.3    2.6  3  MMR_HSR1         50S ribosome-binding GTPase
       0.11   12.0   0.0       0.22   11.0   0.0    1.5  1  PPK2             Polyphosphate kinase 2 (PPK2)
       0.46   10.5   3.2        1.4    9.0   0.1    3.1  3  Lip_prot_lig_C   Bacterial lipoate protein ligase C-terminus


Domain annotation for each model (and alignments):
>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  235.3   0.6   9.3e-73   4.5e-70       2     195 ..     106     299 ..     105     300 .. 0.99

  Alignments for each domain:
  == domain 1  score: 235.3 bits;  conditional E-value: 9.3e-73
                 EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHHHHHHTTSSEEEEEE--SSTTHHH CS
       SRP54   2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvikkkeeadpaavakeavekakeekidvvlvDTaGrlqndke 100
                  +il+vG++G+GKTt+laK+a++l++ +++++++aaDtfRa+A+eQL++++++l+ ++++++ ++dpaava++av  ak++k+d+vl+DTaGr+q+ k+
  EPA05479.1 106 FLILFVGINGTGKTTSLAKVAHMLQQAKYSLVVAAADTFRAGAIEQLREHTNRLNLKLVAQNYNSDPAAVARDAVLYAKSHKMDCVLIDTAGRMQTSKN 204
                 689************************************************************************************************ PP

                 HHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEESTTSSSSTTHHHHHHHHHTS-EEEEE-SSSTTGEEE--HHHHHHHHH CS
       SRP54 101 lmeelkkikkvvkpdevllvldattgqeavkqakaFkeavgitgviltklDgdakgGaalsiaaelklPikfigvGekiedleefdperlvsrll 195
                 lme+++ki kvv+pd +++v d+++g+++v+qa++F e+v+++g iltk D+da+gGaalsi++ + +P+ ++gvG+++ dl++fd++++++ ++
  EPA05479.1 205 LMEQIAKITKVVNPDFKIFVGDSLAGNDTVNQAREFFEHVKFNGSILTKSDADARGGAALSIVKITSTPVLYLGVGQEYSDLKPFDKQTFLETVF 299
                 ******************************************************************************************99876 PP

>> SRP54_N  SRP54-type protein, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   4.4   2.8e-12   1.4e-09       4      75 .]       4      76 ..       1      76 [. 0.84

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 2.8e-12
                HHHHHHHHHC...CSSCGHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHCTTSS-HHHHHHHHHHHHH CS
     SRP54_N  4 klnsalkkls...gkskideedleealkeleeaLleaDVgvkvvkklienvkkkavgekklkpkqqvkkivkdeL 75
                kl++a+++     g ++++e+d+e +l ele +Lle+DV+ +v +++ +++k++ +g +++ +k +++k vkd+L
  EPA05479.1  4 KLRNAFSNAAkslGEKELNEKDIELILTELEISLLESDVASEVIDSIKSDLKNSLIG-SRV-EKNTIEKFVKDSL 76
                56666655331114557****************************************.777.9**********87 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.1   8.4e-10   4.1e-07      20     124 ..     107     226 ..      97     228 .. 0.67

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 8.4e-10
      AAA_30  20 vavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgieastiakllkrlk.............grarlepgtllivDEagmv..dtk 103
                 + + +G  GtGKtt+l+++++++++a+++++++A     A ++++  + + +   kl+ ++                a+ ++ +++++D ag +  + +
  EPA05479.1 107 LILFVGINGTGKTTSLAKVAHMLQQAKYSLVVAAADTFRAGAIEQLREHTNRLNLKLVAQNYnsdpaavardavlY-AKSHKMDCVLIDTAGRMqtSKN 204
                 66789*********************99999888887777666643332222222333222255567777887752.455666*********9944445 PP

      AAA_30 104 qlaallkaaekag.akvilvGD 124
                  +++++k+ +  +    i+vGD
  EPA05479.1 205 LMEQIAKITKVVNpDFKIFVGD 226
                 5777776666544344466666 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.1   2.6e-08   1.2e-05       5     118 ..      93     210 ..      90     214 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 2.6e-08
  Zeta_toxin   5 lkdkk.ypsqerPklillgGqpGAGKselaellkdele.rqgnvvrldpDdlRe.lhPeyeeilka.dpkkaseltqkdaselvekllqeaiengynii 99 
                 +++++  ++  +P lil +G  G GK++ +++++  l+ ++ + v+  +D++R+  + + +e+ +  + k ++++ ++d   +++ ++ +a +++++ +
  EPA05479.1  93 FEKINeKKKTGQPFLILFVGINGTGKTTSLAKVAHMLQqAKYSLVVAAADTFRAgAIEQLREHTNRlNLKLVAQNYNSDPAAVARDAVLYAKSHKMDCV 191
                 6666656678***************************97777889999*****85688899998877999999************************99 PP

  Zeta_toxin 100 vegtlrspdvvkklaealk 118
                 +  t    ++ k+l+e+++
  EPA05479.1 192 LIDTAGRMQTSKNLMEQIA 210
                 8888888888888877765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.1   2.9e-07   0.00014       7     117 ..     107     214 ..     101     230 .. 0.67

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 2.9e-07
      AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst...sskdllrellralglelka..erlsseellealeqalraravielliiDEa 100
                 +++ +G  GtGKTt+l+++++ l+        ++++ +v ++++t   +  + lre  + l+l+l a  ++ +  ++ +    +++++++  +++iD a
  EPA05479.1 107 LILFVGINGTGKTTSLAKVAHMLQ--------QAKYSLVVAAADTfraGAIEQLREHTNRLNLKLVAqnYNSDPAAVARDAVLYAKSHKM-DCVLIDTA 196
                 57889******************8........5666666666666333344444455555555555566455555555555555555555.79****** PP

      AAA_22 101 qhlr.seealeeLrslln 117
                  ++  s++++e++ ++ +
  EPA05479.1 197 GRMQtSKNLMEQIAKITK 214
                 **9776777777766554 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   1.3e-06   0.00061       1     108 [.     111     224 ..     111     233 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.3e-06
                 EE-TTSSHHHHHHHHHHHH...TEE.EEEHHHHHHHHHHTTTS.HSSHHHHCTSHHHHHHHHHHHHHHHHHHHH..HSSEEEEEE-SEEEETTEEEESS CS
      AAA_17   1 lGgPGsGKgtqceklveky...gft.hlsaGdllreeakrggl.akardemrklpleekkelqkeaaekiaeea..kkkgvlvdghprikeqagfldgl 92 
                 +G+ G GK+t ++k+++ +   +++ ++ a d +r+ a ++    ++r +++ + ++ + +  + a +++  ++  k + vl+d+  r+++++ +++++
  EPA05479.1 111 VGINGTGKTTSLAKVAHMLqqaKYSlVVAAADTFRAGAIEQLReHTNRLNLKLVAQNYNSDPAAVARDAVLYAKshKMDCVLIDTAGRMQTSKNLMEQI 209
                 79*************965544466625688*****9887764324556666666777777777777777755442255669********9999988887 PP

                 HHHHHHHH..SEEEEE CS
      AAA_17  93 pkevleelkpdaiill 108
                  k + + ++pd+ i++
  EPA05479.1 210 AK-ITKVVNPDFKIFV 224
                 75.7789999998876 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.9   9.6e-06    0.0047       3     151 ..     108     255 ..     106     266 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 9.6e-06
                 EEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCHCCCCCCHCCCT.EEEETTTTECCHCTT-HHHHHHH..HHHHHTT-SEEEEEECT.TTTH CS
        cobW   3 tvltGflGsGKTtLlnhll..enraglklavivNefgevsiDaellretgveivelenGciCctlredllkelea..leereerldviliEttG.laeP 96 
                 ++++G  G+GKTt l ++    ++a+++l v   +    +     +++  +++  l+   +  + ++d  +++++  l ++++++d++li t G + + 
  EPA05479.1 108 ILFVGINGTGKTTSLAKVAhmLQQAKYSLVVAAADTFRAGA----IEQLREHTNRLNLKLVAQNYNSDPAAVARDavLYAKSHKMDCVLIDTAGrMQTS 202
                 5789999**********994444455555555555554333....333333344444444555544444444433114455589**********88888 PP

                 HHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HH CS
        cobW  97 apvafteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtD 151
                 + ++ +  ++++ ++ d++++v D+ +  +++ ++++++ +++++   + l+K D
  EPA05479.1 203 KNLMEQIAKITKVVNPDFKIFVGDSLAG-NDTVNQAREFFEHVKFNGSI-LTKSD 255
                 88888899*****************765.78888999999999887664.56666 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   4.2e-06     0.002       1      74 [.     108     203 ..     108     224 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 4.2e-06
                 EEEESSTTSSHHHHHHHHHHHHT...HEEEEEETTTCSSS.....................STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH CS
         AAA   1 vllyGppGtGKTllakavakelg...vefleisgsellsk.....................yvgesekkirelfkeakekakpsilfiDEidalaksr 74 
                 +l++G  GtGKT+    va+ l+    +++   + +++                       y ++ ++  r+ +  ak+++   +++iD + ++ +s+
  EPA05479.1 108 ILFVGINGTGKTTSLAKVAHMLQqakYSLVVAAADTFR-AgaieqlrehtnrlnlklvaqnYNSDPAAVARDAVLYAKSHK-MDCVLIDTAGRMQTSK 203
                 69*******************85322333333333333.235566666667777777666699999999999999999887.8999999999987776 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   4.2e-06     0.002       1      54 [.     107     167 ..     107     242 .. 0.66

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 4.2e-06
      AAA_33   1 lvllvGlpGsGKstlaerllkklg.....avllssdtlrrrlfgtdqqskt..dytrvldr 54 
                 l+l+vG +G+GK+t + +++  l+      v+ + dt+r    ++ +++++  +++ v+++
  EPA05479.1 107 LILFVGINGTGKTTSLAKVAHMLQqakysLVVAAADTFRAGAIEQLREHTNrlNLKLVAQN 167
                 79***************99777777777777778899888555444444432222223333 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   7.2e-06    0.0035       5     117 ..     109     210 ..     106     228 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 7.2e-06
     DUF2075   5 lVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlrealakkeekkkkkeafeklssfinnlsefkkaeekkeepkedvvivDEAhrlltk 103
                 l  G  GtGKt  l ++++ l   ++ +++ ++     +++   e+l++++++ + k ++++++s   ++   ++a   +++ k+d+v++D A r+ t+
  EPA05479.1 109 LFVGINGTGKTTSLAKVAHML---QQAKYSLVVAAADTFRAGAIEQLREHTNRLNLKLVAQNYNSDPAAVA--RDAVLYAKSHKMDCVLIDTAGRMQTS 202
                 556999**************9...88899999999999***999***999966677777777777666666..9999*********************7 PP

     DUF2075 104 sdqaekqseenqlk 117
                 ++  e+      + 
  EPA05479.1 203 KNLMEQ------IA 210
                 665333......33 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.2     1e-05    0.0051      13      69 ..     108     193 ..      97     298 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1e-05
      AAA_19  13 llvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae..............................a 69 
                 +l ++  GtGKT+ l ++ ++l++++  ++   ++ +f   A ++lre ++ l+++                              +
  EPA05479.1 108 ILFVGINGTGKTTSLAKVAHMLQQAK-YSLVVAAADTFRAGAIEQLREHTNRLNLKlvaqnynsdpaavardavlyakshkmdcvlI 193
                 4556778*******987766666666.6556666666777789*******9998887766666665555555444433333333332 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.6e-05    0.0076      18      76 ..      99     152 ..      89     218 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.6e-05
      AAA_16  18 rvrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqal 76 
                 + ++g+p l+l++G  G+GK++ + ++++ l++++  ++ + +d ++     +  +++l
  EPA05479.1  99 KKKTGQPFLILFVGINGTGKTTSLAKVAHMLQQAKYSLVVAAADTFR-----AGAIEQL 152
                 56789999********************8777775444444444441.....1244444 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       1.9   9.1e+02      54      70 ..      67     100 ..      13     114 .. 0.46
   2 !   14.5   0.0   5.8e-05     0.028       9     100 ..     115     244 ..     107     262 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.9
                 H.................CCHCCCHHHHHHCHCH CS
                 x.................xxxxxxxxxxxxxxxx RF
        CbiA  54 p.................dlkrllellealgkkk 70 
                 +                 d    + l+e++ +kk
  EPA05479.1  67 TiekfvkdslissistlfDEAGTIDLFEKINEKK 100
                 0222333333333333332222233333333333 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 5.8e-05
                 TSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH..........................................CCHCCCHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........................................xxxxxxxxxxx RF
        CbiA   9 GvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep..........................................dlkrllellea 65 
                 G+GKTt +a+ a  l+++++  ++  aD+ +  +  +e+l++  ++                                          + k l e +++
  EPA05479.1 115 GTGKTTSLAKVAHMLQQAKYSLVVAAADTFRAGA--IEQLREHTNRlnlklvaqnynsdpaavardavlyakshkmdcvlidtagrmqTSKNLMEQIAK 211
                 9*******************99999999883332..344444444478888888888888888888888888888888888888877766666666666 PP

                 HCHCHHHH..EEEEEEEEESS...-TTCHHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        CbiA  66 lgkkkalllkiagvvlnrvdgeneetllkealeel 100
                 + k+++   +++ +v     g+++ ++ +e++e +
  EPA05479.1 212 ITKVVN--PDFKIFVGDSLAGNDTVNQAREFFEHV 244
                 666644..344444444444444555555555554 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       3.4   1.6e+03      25      79 ..      36      93 ..      28     101 .. 0.59
   2 !   14.5   0.0   5.2e-05     0.025       1      50 [.     104     153 ..     104     168 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 3.4
                HHHHTT--EEEEEHHHHTTTTTTT--SSHHHHHHHHH.....HHHHHHHHHHHTT-EEEE CS
  APS_kinase 25 kLvekgisvylLdGdnvRhgLnkdLgfseedRkenir.....rvaevaklladaglivlv 79
                +L e+ ++ +++  d+++ +L++ L  s+ ++++  +      ++ +++l+ +ag+i l 
  EPA05479.1 36 SLLESDVASEVI--DSIKSDLKNSLIGSRVEKNTIEKfvkdsLISSISTLFDEAGTIDLF 93
                555555555555..4677777777766655554422211111477888888888888765 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 5.2e-05
                 S-EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT-- CS
  APS_kinase   1 rgvvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdLg 50 
                 +++ +++ G+ g+GK+t   +++++L++ ++s ++   d+ R g  ++L 
  EPA05479.1 104 QPFLILFVGINGTGKTTSLAKVAHMLQQAKYSLVVAAADTFRAGAIEQLR 153
                 5789**************************************99888775 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0         6   2.9e+03      57      82 ..      34      57 ..      11      68 .. 0.73
   2 !   14.3   0.0   4.8e-05     0.023       3      28 ..     112     138 ..     110     171 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 6
                     HHHHHHHHHHHTTHHHHHHHHHTT-E CS
  Thymidylate_kin 57 eallfaadriehleekikpalkqgkt 82
                     e  l+  d++ ++ ++ik +lk+   
       EPA05479.1 34 EISLLESDVASEVIDSIKSDLKN--S 57
                     56677788888999999999887..3 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 4.8e-05
                      ESTTSSHHHHHHHHHHHHHHTTE..EE CS
  Thymidylate_kin   3 GlDGaGKttqaellkerlkeegik.vv 28 
                      G++G+GKtt +++++  l++++++ vv
       EPA05479.1 112 GINGTGKTTSLAKVAHMLQQAKYSlVV 138
                      9**********************9655 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   2.9e-05     0.014       9     127 ..      92     214 ..      87     228 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.9e-05
                 HHHHH......HCTS-EEEEESTTSSCHHHHHHHHHHCHCTCCCEEEEESSHHHHHCC.TSEECHHHHT-TTSSS-HHHH..HHHTSCCCHHHHHC-SE CS
        PIF1   9 vfdaiieavlnekgklfFvtGsgGtgKtflwkallkklrsegkivlavAssGvAalllegGrtahsrfkiplekdeestc..kikrgsklaellkktsl 105
                  f++i e  ++ ++ l+ + G  GtgKt  + ++ ++l++ +   ++ A     a  +e+ r    r ++ l +++ ++   +++r+  l  + +k++ 
  EPA05479.1  92 LFEKINEKKKTGQPFLILFVGINGTGKTTSLAKVAHMLQQAKYSLVVAAADTFRAGAIEQLREHTNRLNLKLVAQNYNSDpaAVARDAVLYAKSHKMDC 190
                 57888888888999999**********************988777777777888999999999999999988766554433599*************** PP

                 EEEECGGG..SBHHHHHHHHHHHH CS
        PIF1 106 iiwDEapm..verecfealdrtlr 127
                 +++D a    ++++++e++ ++ +
  EPA05479.1 191 VLIDTAGRmqTSKNLMEQIAKITK 214
                 ****99641246778888777665 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.1    0.0003      0.15       2      44 ..     123     165 ..     122     188 .. 0.91
   2 ?    0.4   0.0         1     5e+02      16      39 ..     222     245 ..     205     248 .. 0.83
   3 ?   -2.0   0.0       5.5   2.6e+03       4      25 ..     263     284 ..     262     287 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0003
                   HHHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEE CS
  TPP_enzyme_M   2 ekaaellkaakrpvilvGggvarsgaseelrelaeklgiPvvt 44 
                   +k+a +l++ak  ++++   + r+ga e+lre  ++l++  v 
    EPA05479.1 123 AKVAHMLQQAKYSLVVAAADTFRAGAIEQLREHTNRLNLKLVA 165
                   79************************************98765 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1
                   EEE-CHHCHTTGHHHHHHHHHHHT CS
  TPP_enzyme_M  16 ilvGggvarsgaseelrelaeklg 39 
                   i+vG   a +++ +++re+ e+++
    EPA05479.1 222 IFVGDSLAGNDTVNQAREFFEHVK 245
                   889999999999999999998876 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 5.5
                   HHHHHHH-SSEEEEE-CHHCHT CS
  TPP_enzyme_M   4 aaellkaakrpvilvGggvars 25 
                   a++++k  + pv+++G g  +s
    EPA05479.1 263 ALSIVKITSTPVLYLGVGQEYS 284
                   5667777889999999987766 PP

>> TK  Thymidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   3.9e-05     0.019       5     107 ..     109     216 ..     106     220 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.9e-05
          TK   5 lilgpmfaGKsteLlrrvkryqlaekkvvvikaakdnRyseg.kvvthd...gisleak...ksktssleeikeeleeedvdvvlvDEaqFfeqdivel 96 
                 l +g   +GK+t+L + ++++q+a+++ vv  a    R ++  ++  h    +++l a+   ++ ++ + + +  ++++++d+vl+D a  ++    +l
  EPA05479.1 109 LFVGINGTGKTTSLAKVAHMLQQAKYSLVVAAAD-TFRAGAIeQLREHTnrlNLKLVAQnynSDPAAVARDAVLYAKSHKMDCVLIDTAGRMQ-TSKNL 205
                 66677779******************98876544.345444335555541114555555333445555666666677889********99888.77788 PP

          TK  97 seklanegkiv 107
                 +e++a+  k+v
  EPA05479.1 206 MEQIAKITKVV 216
                 88888777665 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.1    0.0019      0.91       5      29 ..     111     135 ..     107     147 .. 0.86
   2 ?    4.0   0.0     0.084        41      91     122 ..     183     213 ..     167     245 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0019
                 E--TTSSHHHHHHHHHHHH...GGG CS
    NTPase_1   5 TGppGvGKtTlvkkvlellkssgvk 29 
                  G  G+GKtT + kv+++l++  ++
  EPA05479.1 111 VGINGTGKTTSLAKVAHMLQQAKYS 135
                 5889***************998776 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.084
                 HHHHHH-EEEE---STTGGG-HHHHHHHHHHH CS
    NTPase_1  91 kalseadviviDEiGkmElkskkfkeaveevL 122
                  + ++ d+++iD  G+m   sk++ e++ ++ 
  EPA05479.1 183 AKSHKMDCVLIDTAGRMQT-SKNLMEQIAKIT 213
                 444899***********76.555555555544 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       8.2     4e+03      52      74 ..      68      88 ..      19      98 .. 0.57
   2 ?   14.1   0.0   7.4e-05     0.036       5     105 ..     108     232 ..     104     246 .. 0.62

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 8.2
      AAA_14 52 llelileklkeekktylflDEiq 74
                ++++++++l        ++DE+ 
  EPA05479.1 68 IEKFVKDSLI--SSISTLFDEAG 88
                2222222221..23345666655 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 7.4e-05
      AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderd........kkladpe.kll.elileklke................ekktylflDEiqevp 77 
                 ++ +G+  +GKTt l ++++ l   k s +  + d+ r               + +l+ +l+ +++ +                +k+ ++++D + +++
  EPA05479.1 108 ILFVGINGTGKTTSLAKVAHMLQQAKYSLVVAAADTFRAgaieqlreH-----TnRLNlKLVAQNY-NsdpaavardavlyaksHKMDCVLIDTAGRMQ 200
                 6779**************988775555555555555555444322211.....1222212222222.135666777777778888999*****987775 PP

      AAA_14  78 ewekalkslvd....egknldvivtGSnskll 105
                 + ++ + ++ +     +++++++v  S++++ 
  EPA05479.1 201 TSKNLMEQIAKitkvVNPDFKIFVGDSLAGND 232
                 55555555555322433789999999988765 PP

>> KdpD  Osmosensitive K+ channel His kinase sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   7.4e-05     0.036       7      95 ..     109     200 ..     103     222 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.4e-05
        KdpD   7 iflGaapGvGktyamLeeaqelkeegvdvviglvethgrketeallegleviprkeveyk.gkeleeldldaila...rkpevvlvDelahtn 95 
                 +f+G ++G Gkt ++ + a+ l++    +v+++ +t +   +e+l e+ + ++ k v+++ ++    +  da+l    +k + vl+D  +  +
  EPA05479.1 109 LFVG-INGTGKTTSLAKVAHMLQQAKYSLVVAAADTFRAGAIEQLREHTNRLNLKLVAQNyNSDPAAVARDAVLYaksHKMDCVLIDTAGRMQ 200
                 4555.68*****************************************999999877655144566778888886222456788888776655 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   8.8e-05     0.043      14      80 ..     108     204 ..      93     266 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.8e-05
                 EEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG......B-HHHCCHCEEEE-SS--S-TTSBHHHH........................H CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxx........................x RF
    ABC_tran  14 vaivGenGaGKStLlkllagllkpteGeilldgkdlke......qeleslrkeigvlpqepqlfpeltvren........................e 80 
                 + +vG nG+GK+t l+ +a++l++++ ++ +  +d+ +       +++  r +++ + q+ + +p   +r+                         +
  EPA05479.1 108 ILFVGINGTGKTTSLAKVAHMLQQAKYSLVVAAADTFRagaieqLREHTNRLNLKLVAQNYNSDPAAVARDAvlyakshkmdcvlidtagrmqtskN 204
                 6789******************999988866655555556555355566677888888888888888666668886666666666555555544441 PP

>> DAP3  Mitochondrial ribosomal death-associated protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   7.8e-05     0.038       7      51 ..      89     133 ..      86     159 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.8e-05
                 HHHHHHHHTTS-SSS---EEEEE-SSSSSTTTTHHHHHHHGGGS- CS
        DAP3   7 tlelikklkkadkkkkvkrlvltGekgsGKSvlLlqalayAlekg 51 
                 t++l++k+++++k+++   +++ G +g+GK+++L+++ ++  +++
  EPA05479.1  89 TIDLFEKINEKKKTGQPFLILFVGINGTGKTTSLAKVAHMLQQAK 133
                 899**********************************99966654 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00013     0.062      36      65 ..     108     137 ..      94     146 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00013
       AAA_7  36 vllvGptGtGKtviikdllkkldkekylsl 65 
                 +l+vG  GtGKt+ + ++ + l++ ky+ +
  EPA05479.1 108 ILFVGINGTGKTTSLAKVAHMLQQAKYSLV 137
                 79*********************9999876 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00015     0.073       5      79 ..     108     201 ..     105     267 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00015
      AAA_24   5 iliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdieswedfldevvel......................aaeladyktlviDtidelee 79 
                 il +G +g+GKTt++++    + +++  k +  + a++  ++ ++e++++  + l                      +a+ ++ + + iDt++ +  
  EPA05479.1 108 ILFVGINGTGKTTSLAKV---AHMLQQAKYSLVVAAADTFRAGAIEQLREHTNRLnlklvaqnynsdpaavardavlYAKSHKMDCVLIDTAGRMQT 201
                 6789**************...44455555233333333333446666666666666667777777779999999999**************998843 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00027      0.13      24     141 ..     100     207 ..      82     232 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00027
                 GG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE------------------HCCCTSTTEEEEEE-----HHHHHHHHHHHHHHHHHTT- CS
        MeaB  24 akaGraqvvGltGvPGaGkstlvealglelrrrGkrvavlavDPsspftGGsilGDklRleelavdegvfiRslpsrGalGGlaaktrevvllleaaGf 122
                 +k+G+   + + G+ G+Gk t + +++  l+++ +   v a D   +f  G+i   +lR +    +       l ++      aa +r++vl   +   
  EPA05479.1 100 KKTGQPFLILFVGINGTGKTTSLAKVAHMLQQAKYSLVVAAAD---TFRAGAIE--QLREHTNRLNL-----KLVAQNYNSDPAAVARDAVLYAKSHKM 188
                 57999999************************99999888877...67788873..33322222222.....222333333445666777777777777 PP

                 SEEEEEEESSTTHHHHHHT CS
        MeaB 123 DvvlietvGvGqsevdvae 141
                 D vli+t G  q   +++e
  EPA05479.1 189 DCVLIDTAGRMQTSKNLME 207
                 7777777777776655554 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       7.2   3.5e+03      45      63 ..      61      79 ..      21      84 .. 0.53
   2 ?   12.3   0.0   0.00017     0.083       3      87 ..     107     188 ..     106     221 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 7.2
                SSS--GGGHHHHHHHHHHH CS
       KTI12 45 dsykdsakekalRsslrsa 63
                + ++++  ek +++sl+s+
  EPA05479.1 61 SRVEKNTIEKFVKDSLISS 79
                2245555566666666655 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00017
                 EEEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH.TTSSS--GGGHHHHHHHHHHHHHHHHTT.SEEEE-S---SHHHHH CS
       KTI12   3 LvvltGlPssGKstrakeLakaleeekrsvvviddeslgiekdsykdsakekalRsslrsavkrdLskekvVIvDslnyikgfRY 87 
                 L+++ G+  +GK+t  +++a+ l++ k+s vv   ++++       ++ +e + R +l+  ++   s    V  D++ y k+   
  EPA05479.1 107 LILFVGINGTGKTTSLAKVAHMLQQAKYSLVVAAADTFRAGA---IEQLREHTNRLNLKLVAQNYNSDPAAVARDAVLYAKSHKM 188
                 9**********************************9999433...4567788888888877777777888888888888887665 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00022      0.11      97     163 ..     182     249 ..     160     259 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00022
      CLP1_P  97 enkkakasgliIntpGwvkglg..aellleliealepdvvvvldqeellnelkrdlplskvkvvklpks 163
                   k++k ++++I+t G ++     +e + +++++++pd  ++++++   n+  ++++ ++++ vk++ s
  EPA05479.1 182 YAKSHKMDCVLIDTAGRMQTSKnlMEQIAKITKVVNPDFKIFVGDSLAGNDTVNQAR-EFFEHVKFNGS 249
                 45678999**********97643479****************************999.88887777655 PP

>> SPOUT_MTase  Predicted SPOUT methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       2.3   1.1e+03      63     104 ..      71     112 ..      33     152 .. 0.66
   2 ?   11.2   0.0   0.00054      0.26      58     114 ..     179     235 ..     143     243 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 2.3
                  ..TT-EEEEE-TTSEE--HHHHHHHHHHHHHHT-.-EEEEE- CS
  SPOUT_MTase  63 lkkkayvillderGkelsSeelakkleklaeegkselvfvIG 104
                  + k++ +  ++   +e  + +l +k+++++++g+  l++++G
   EPA05479.1  71 FVKDSLISSISTLFDEAGTIDLFEKINEKKKTGQPFLILFVG 112
                  444555555555555566777777888877777776666666 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00054
                  T--....TT-EEEEE-TTSEE--HHHHHHHHHHHHHHT-.-EEEEE--TT---GGGG CS
  SPOUT_MTase  58 rilkklkkkayvillderGkelsSeelakkleklaeegkselvfvIGGsdGlseevk 114
                  ++l + ++k  ++l+d  G++ +S++l ++++k+++  + ++ +++G s   +++v 
   EPA05479.1 179 AVLYAKSHKMDCVLIDTAGRMQTSKNLMEQIAKITKVVNPDFKIFVGDSLAGNDTVN 235
                  455555677889************************9999*****999876666655 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00021       0.1       2      38 ..     108     145 ..     107     177 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00021
                 EEEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT--H CS
       AAA_5   2 vlLvGppGtgKselaerlaaal.nreveyvqltrdtte 38 
                 +l vG  GtgK++   ++a++l ++++  v   +dt +
  EPA05479.1 108 ILFVGINGTGKTTSLAKVAHMLqQAKYSLVVAAADTFR 145
                 5889******************9999999999888854 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00044      0.21      40      87 ..     172     225 ..     107     236 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00044
  B12-binding  40 n....edivaairaekpdvvglSal..ltsqleavkelvellkrirprvkvvvG 87 
                  +     d v  ++++k d+v++ +   ++++ + ++++++  k ++p++k++vG
   EPA05479.1 172 PaavaRDAVLYAKSHKMDCVLIDTAgrMQTSKNLMEQIAKITKVVNPDFKIFVG 225
                  255556777789**********7766699999999999999************9 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00021       0.1       2      48 ..     108     161 ..     107     200 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00021
      AAA_28   2 ivitGgestGKTtlleaLaar....gypvv...pEaareileeklakgedalpw 48 
                 i ++G  +tGKTt l++ a +    +y+ v   ++++r    e+l+++++ l+ 
  EPA05479.1 108 ILFVGINGTGKTTSLAKVAHMlqqaKYSLVvaaADTFRAGAIEQLREHTNRLNL 161
                 8899***********999944444688866245566665555555555555543 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00066      0.32       2      30 ..     108     136 ..     107     143 .. 0.90
   2 ?   -1.3   0.0       3.7   1.8e+03      54      96 ..     145     193 ..     138     209 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00066
        MobB   2 lgivgksgsGKTtLleklipelkarglrv 30 
                 + +vg +g+GKTt l k+ ++l++ ++++
  EPA05479.1 108 ILFVGINGTGKTTSLAKVAHMLQQAKYSL 136
                 679********************999876 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 3.7
        MobB  54 kAGAkevlvaskerlal..ikel...eeaelsleell.arlsevDlvlv 96 
                 +AGA e l ++ +rl l  + +    + a ++ + +l a+ +++D vl+
  EPA05479.1 145 RAGAIEQLREHTNRLNLklVAQNynsDPAAVARDAVLyAKSHKMDCVLI 193
                 5777777777777766533333333222222222222022244788777 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   1.3   0.00063      0.31      21      80 ..      94     158 ..      44     226 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00063
                 ..........TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG CS
      ResIII  21 s........krdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflse 80 
                 +         +   +l++   GtGKT  +ak++  l+++++    l+++   +    ++e++++ ++ 
  EPA05479.1  94 EkinekkktGQPFLILFVGINGTGKTTSLAKVAHMLQQAKY---SLVVAAADTFRAGAIEQLREHTNR 158
                 03432222133337889****************99999866...688888777777776666554444 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1       1.7   8.1e+02      12      29 ..      51      68 ..      14     104 .. 0.68
   2 ?    2.0   0.4      0.45   2.2e+02       2      14 ..     108     120 ..      51     165 .. 0.52
   3 ?   10.8   0.3    0.0008      0.39       2      94 ..     108     238 ..     107     253 .. 0.52

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.7
                HHHHHHHHHTSTEEESSS CS
    MMR_HSR1 12 KStLinaltgekaivsdk 29
                KS L n+l+g++++ + +
  EPA05479.1 51 KSDLKNSLIGSRVEKNTI 68
                566666666665544433 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.45
                 EEEEESTTSSHHH CS
    MMR_HSR1   2 vaivGrpNvGKSt 14 
                 +++vG   +GK+t
  EPA05479.1 108 ILFVGINGTGKTT 120
                 2333444444443 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.0008
                 EEEEESTTSSHHHHHHHHHT.................STEEESSSTTSSSSEEEEEEEETTEE.......................EEEEECGGCSSHH CS
    MMR_HSR1   2 vaivGrpNvGKStLinaltg.................ekaivsdkpgtTrdinegrvklkgke.......................ielvDtpGliega 60 
                 +++vG   +GK+t + +                    ++  +++    T   n + v+    +                       ++l+Dt+G ++  
  EPA05479.1 108 ILFVGINGTGKTTSLAKVAHmlqqakyslvvaaadtfRAGAIEQLREHTNRLNLKLVA----QnynsdpaavardavlyakshkmdCVLIDTAGRMQ-- 200
                 5678888888888887777544333333333332211122333333333333333333....033334555555555555555555********444.. PP

                 HHHHHHHHHHHHHHC...TSEEEEEEETT..TTCSHHHH CS
    MMR_HSR1  61 seekglgkaflalee...adlillvvdas..eeklkpld 94 
                  ++k+l ++++++ +    d  ++v d+   ++++++ +
  EPA05479.1 201 -TSKNLMEQIAKITKvvnPDFKIFVGDSLagNDTVNQAR 238
                 .44445555554444321699999999435544455544 PP

>> PPK2  Polyphosphate kinase 2 (PPK2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00046      0.22      16      68 ..      90     142 ..      82     169 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00046
                 HHHHHHHHSGGGGG-EEEEEEEESTTS-HHHHHHHHHTTS-GGG-EEEE--S- CS
        PPK2  16 ielvklqekvkaegkklvvifegrDaAGKgGaikrvtealnprvarvvalkaP 68 
                 i+l + ++++k++g+  +++f g ++ GK   +++v + l+ +++  v  +a 
  EPA05479.1  90 IDLFEKINEKKKTGQPFLILFVGINGTGKTTSLAKVAHMLQQAKYSLVVAAAD 142
                 7888999999********************************99988766655 PP

>> Lip_prot_lig_C  Bacterial lipoate protein ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1       1.2     6e+02      47      70 ..      13      36 ..       6      49 .. 0.81
   2 ?    9.0   0.1    0.0029       1.4      43      68 ..      50      76 ..      38      96 .. 0.82
   3 ?   -2.1   0.0       8.1   3.9e+03      33      56 ..     223     247 ..     219     255 .. 0.67

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 1.2
                    HHHHTTSBSSHHHHHHHHHTSCHH CS
  Lip_prot_lig_C 47 eekLigvkyekeaieealekidls 70
                    ++ L  +++++++ie +l ++++s
      EPA05479.1 13 AKSLGEKELNEKDIELILTELEIS 36
                    678999999999**9999998876 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0029
                    C.HHHHHHHTTSBSSHHHHHHHHHTSC CS
  Lip_prot_lig_C 43 i.eeleekLigvkyekeaieealekid 68
                    i ++l++ Lig + ek++ie+++++  
      EPA05479.1 50 IkSDLKNSLIGSRVEKNTIEKFVKDSL 76
                    4579******************99754 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 8.1
                     EEESBSS.SSHCHHHHHHHTTSBSS CS
  Lip_prot_lig_C  33 iyGDffg.pkdieeleekLigvkye 56 
                     + GD++  ++ +++  e ++ vk++
      EPA05479.1 223 FVGDSLAgNDTVNQAREFFEHVKFN 247
                     4588886244457777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       984  (0.0548832); expected 358.6 (0.02)
Passed bias filter:                      696  (0.0388198); expected 358.6 (0.02)
Passed Vit filter:                       107  (0.00596798); expected 17.9 (0.001)
Passed Fwd filter:                        37  (0.0020637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              37  [number of targets reported over threshold]
# CPU time: 0.79u 0.34s 00:00:01.13 Elapsed: 00:00:00.53
# Mc/sec: 1773.98
//
Query:       EPA05480.1  [L=141]
Description: prefoldin, alpha subunit [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.8e-16   58.3   7.7    2.6e-15   56.4   7.7    1.8  1  Prefoldin     Prefoldin subunit
    0.00079   19.4   0.6     0.0012   18.8   0.1    1.5  2  LMP           LMP repeated region
  ------ inclusion threshold ------
      0.038   14.3   0.8       0.15   12.4   0.1    2.4  3  Ribosomal_L5  Ribosomal protein L5
       0.21   11.7   2.6       0.27   11.3   0.2    2.1  2  DUF3848       Protein of unknown function (DUF3848)
       0.21   11.8   8.8       0.64   10.3   0.9    2.2  2  TMF_TATA_bd   TATA element modulatory factor 1 TATA binding
       0.24   11.4  10.5      0.058   13.4   1.3    2.3  2  Prefoldin_2   Prefoldin subunit
       0.32   11.3  13.6       0.55   10.6   2.6    2.1  2  OmpH          Outer membrane protein (OmpH-like)
       0.61    9.6   5.7        3.4    7.2   1.1    2.0  2  Paralemmin    Paralemmin
        1.4    8.0   4.2       0.28   10.3   0.7    1.5  2  Tho2          Transcription factor/nuclear export subunit pro
        1.4    9.2  10.8       0.12   12.7   2.8    2.3  2  ABC_tran_CTD  ABC transporter C-terminal domain
        1.7    9.1  10.2       0.11   12.9   2.2    2.1  2  TSNAXIP1_N    Translin-associated factor X-interacting N-term
        2.9    8.3   7.8        6.5    7.2   1.6    2.3  2  CLZ           C-terminal leucine zipper domain of cyclic nucl
        3.7    7.8   6.9        5.8    7.2   1.6    2.4  2  DUF3947       Protein of unknown function (DUF3947)


Domain annotation for each model (and alignments):
>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.4   7.7   1.9e-18   2.6e-15       4     119 ..      12     133 ..       2     138 .. 0.76

  Alignments for each domain:
  == domain 1  score: 56.4 bits;  conditional E-value: 1.9e-18
                 HHHHHHHHHHHHHHHHHH....HHHHHHHHHHHTT...-TT-EEEEEEETTEEEEEE--STTEEEEEEETTEEEEEEHHHHHHHHHHHHHHHHHHHHHH CS
   Prefoldin   4 eleslqaelaqlkeaiee....lektletlktlkk..edegkevlvplgaglyvkaevkdtdkvlvdlGagyyveksleeAiellkkkleelekqlekl 96 
                 +++ l++ ++ l+++  +    l+++ ++++++k+  ++ + e+lvp+g g +v  ++ +t+k+++++Gag+++eks++ Ai +l+ k++e+e +l++ 
  EPA05480.1  12 QMQMLETYFTDLSQREGTllnvLREAVAAIESIKAirQKSDSETLVPIGMGTFVHTRISSTEKIVLNIGAGVAMEKSYDSAINYLEAKIKEIEVALQDT 110
                 44445555555544433300003444455555555888*******************************************************999998 PP

                 HHHHHHHHHHHHHHHHHHHHHHH CS
   Prefoldin  97 eeeleklkdqittleanlaqlyq 119
                   + +++ +++++ +++l++l q
  EPA05480.1 111 SVKKQQAVARLEQGREQLNMLMQ 133
                 87777777777777777766655 PP

>> LMP  LMP repeated region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       2.5   3.4e+03      98      98 ..      31      31 ..       4      55 .. 0.51
   2 !   18.8   0.1   8.8e-07    0.0012      40      92 ..      87     139 ..      68     140 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.5
         LMP 98 v 98
                +
  EPA05480.1 31 L 31
                2 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 8.8e-07
         LMP  40 asmqsakssLdakvteitkkLekFnkdkeakFkeLeqtRkdieeFlkdvknnp 92 
                 +s +sa + L+ak+ ei+  L++   +k++   +Leq R++++  +++  +np
  EPA05480.1  87 KSYDSAINYLEAKIKEIEVALQDTSVKKQQAVARLEQGREQLNMLMQETSQNP 139
                 68899**************************************9999999888 PP

>> Ribosomal_L5  Ribosomal protein L5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       4.2   5.7e+03      27      37 ..      34      44 ..      24      51 .. 0.62
   2 ?   12.4   0.1   0.00011      0.15       9      36 ..      73      99 ..      68     120 .. 0.85
   3 ?   -1.6   0.0       2.6   3.6e+03      13      23 ..     128     138 ..     127     140 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 4.2
                  HHCCHHHHCCC CS
  Ribosomal_L5 27 lekaakeLaeI 37
                  l++a++ +++I
    EPA05480.1 34 LREAVAAIESI 44
                  55555555554 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00011
                  EEEEEEEE-SSSSSCHHHHHCCHHHHC.C CS
  Ribosomal_L5  9 eKivinmgvGeagedkkllekaakeLa.e 36
                  eKiv+n+g G a e+    ++a++ L+ +
    EPA05480.1 73 EKIVLNIGAGVAMEK--SYDSAINYLEaK 99
                  8*********88887..788888887744 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 2.6
                   EEEE-SSSSSC CS
  Ribosomal_L5  13 inmgvGeaged 23 
                   +nm + e +++
    EPA05480.1 128 LNMLMQETSQN 138
                   79999999998 PP

>> DUF3848  Protein of unknown function (DUF3848)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2    0.0002      0.27      51      89 ..       2      40 ..       1      45 [. 0.92
   2 ?    0.2   0.2       0.6   8.2e+02      40      60 ..     102     122 ..      85     139 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0002
     DUF3848 51 sdeqakaLlksenpLddvyeewekrddsymedlrqtiee 89
                s+eqa+ L+++ + L+  + + ++r+ + ++ lr+++  
  EPA05480.1  2 SEEQAQQLMQQMQMLETYFTDLSQREGTLLNVLREAVAA 40
                799*******************************99875 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.6
     DUF3848  40 dilmsleeeelsdeqakaLlk 60 
                 +i  +l++++ +++qa a l+
  EPA05480.1 102 EIEVALQDTSVKKQQAVARLE 122
                 455666666666555544333 PP

>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.9   0.00046      0.64      56      95 ..       3      42 ..       1      49 [. 0.88
   2 ?    6.0   1.5    0.0095        13      12      56 ..      91     135 ..      83     140 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00046
  TMF_TATA_bd 56 neelkelkkeleelekeleelqeryetlLellGeksEeve 95
                  e+ ++l ++++ le+ +++l++r+ tlL +l e    +e
   EPA05480.1  3 EEQAQQLMQQMQMLETYFTDLSQREGTLLNVLREAVAAIE 42
                 689999**************************99765555 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0095
  TMF_TATA_bd  12 qlverlsseirrlEgElaslkeelerleaerdeareeivklmken 56 
                  + +++l+++i++ E+ l+ +  + ++  a  ++ re++  lm+e+
   EPA05480.1  91 SAINYLEAKIKEIEVALQDTSVKKQQAVARLEQGREQLNMLMQET 135
                  679999999999999999876666666666666666666666655 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   2.0     0.063        86      12      29 ..       4      21 ..       2      44 .. 0.78
   2 ?   13.4   1.3   4.2e-05     0.058      43     104 ..      71     133 ..      67     135 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.063
                 HHHHHHHHHHHHHHHHHH CS
  Prefoldin_2 12 qqlqqlaqqikqletqlk 29
                 +q qql+qq+++let  +
   EPA05480.1  4 EQAQQLMQQMQMLETYFT 21
                 678888888888887555 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 4.2e-05
                  TT--EEEEET.TEEEEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCTS CS
  Prefoldin_2  43 edtkvyklvG.dvlvkqdkeevkeeLeerketlekeiktlekqleklekeleelkeelqkklq 104
                  +++k+  ++G +v ++++ +++++ Le++++++e  ++  + ++++  ++le+ +e+l+ ++q
   EPA05480.1  71 STEKIVLNIGaGVAMEKSYDSAINYLEAKIKEIEVALQDTSVKKQQAVARLEQGREQLNMLMQ 133
                  66788888884588999******************************************8887 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   3.3    0.0072        10      62     105 ..       3      44 ..       1      51 [. 0.77
   2 ?   10.6   2.6    0.0004      0.55       7      71 ..      72     134 ..      68     138 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0072
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
        OmpH  62 eqelqkkeqelqqkqqqkaqelqkkqqellkpildkinkaikev 105
                 e++ q+++q++q  ++  + +l +++  ll+ +l ++ +ai+ +
  EPA05480.1   3 EEQAQQLMQQMQM-LETYFTDLSQREGTLLN-VLREAVAAIESI 44 
                 4557777777777.77788*******99999.888888888776 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0004
                 HHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS.-HHHHHHHHHHHHH CS
        OmpH   7 vqkileespegkaaqeqlekkfkklqaeleakekelqklqeelqkkakklekeekeqelqkkeqe 71 
                 ++ki+ +  +g a+++ +++ ++ l+a++++ e +lq+   + q++ +    e+ +++l+ ++qe
  EPA05480.1  72 TEKIVLNIGAGVAMEKSYDSAINYLEAKIKEIEVALQDTSVKKQQAVAR--LEQGREQLNMLMQE 134
                 7899999999999999999999999999999999999888777744444..34444445555554 PP

>> Paralemmin  Paralemmin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.2     0.011        15      15      67 ..       3      55 ..       1      77 [. 0.86
   2 ?    7.2   1.1    0.0024       3.4      12      62 ..      87     137 ..      83     140 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.011
  Paralemmin 15 EesiqrLekeieeLeseesaisakeevlaeklketeksvedlqksllstdkek 67
                Ee+ q+L ++++ Le+  +  s++e +l + l+e+  ++e+++   +++d e+
  EPA05480.1  3 EEQAQQLMQQMQMLETYFTDLSQREGTLLNVLREAVAAIESIKAIRQKSDSET 55
                8999****************************999999999888887777754 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0024
  Paralemmin  12 rkLEesiqrLekeieeLeseesaisakeevlaeklketeksvedlqkslls 62 
                 ++ + +i+ Le +i+e+e     +s k++++ ++l++ +++++ l +++++
  EPA05480.1  87 KSYDSAINYLEAKIKEIEVALQDTSVKKQQAVARLEQGREQLNMLMQETSQ 137
                 677889*****************************9999999888777665 PP

>> Tho2  Transcription factor/nuclear export subunit protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       1.3   1.8e+03      61      82 ..       8      29 ..       2      56 .. 0.50
   2 ?   10.3   0.7    0.0002      0.28      24      75 ..      86     137 ..      82     140 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.3
        Tho2 61 rlkeliekLeeEkkeqiehvek 82
                +l+++++ Le+ ++  +++   
  EPA05480.1  8 QLMQQMQMLETYFTDLSQREGT 29
                3444444444433333333333 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0002
        Tho2  24 keqYekeieklkseieelakdrsderaaakkkkkekkrlkeliekLeeEkke 75 
                 +++Y++ i+ l+++i+e++ + +d++ ++++  ++ ++ +e+ + L +E ++
  EPA05480.1  86 EKSYDSAINYLEAKIKEIEVALQDTSVKKQQAVARLEQGREQLNMLMQETSQ 137
                 689***************7777776666666677777777777777666654 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   1.1      0.32   4.4e+02      41      55 ..       4      18 ..       1      46 [. 0.57
   2 ?   12.7   2.8   8.4e-05      0.12      15      62 ..      91     133 ..      85     136 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.32
  ABC_tran_CTD 41 eklaelsaeleelea 55
                  e+ ++l+++++ le+
    EPA05480.1  4 EQAQQLMQQMQMLET 18
                  334444444444443 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 8.4e-05
  ABC_tran_CTD  15 aeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLeelye 62 
                   + I+ LE++i+e+e +l+d +      k +++ a+le+ +++L+ l++
    EPA05480.1  91 SAINYLEAKIKEIEVALQDTS-----VKKQQAVARLEQGREQLNMLMQ 133
                   67999*************999.....4556666777777777776665 PP

>> TSNAXIP1_N  Translin-associated factor X-interacting N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   1.1      0.38   5.3e+02      63      98 ..      11      43 ..       1      55 [. 0.40
   2 ?   12.9   2.2   7.6e-05      0.11      48     102 ..      86     137 ..      83     140 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.38
  TSNAXIP1_N 63 reaqylkaklktlsessdkraleleekreelralek 98
                +++q+l++  + ls+++    + l+e+   + a+e+
  EPA05480.1 11 QQMQMLETYFTDLSQREGTLLNVLREA---VAAIES 43
                223333333333444443333334443...444433 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 7.6e-05
  TSNAXIP1_N  48 KkEYelyiahllesqreaqylkaklktlsessdkraleleekreelralekeska 102
                  k Y+ +i+ l+ +++e +     l+ +s ++++ +  le+ re+l++l +e+++
  EPA05480.1  86 EKSYDSAINYLEAKIKEIEVA---LQDTSVKKQQAVARLEQGREQLNMLMQETSQ 137
                 578***************998...877888888888899************9975 PP

>> CLZ  C-terminal leucine zipper domain of cyclic nucleotide-gated channels
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   1.6    0.0047       6.5      30      70 ..       3      43 ..       1      44 [. 0.91
   2 ?    4.8   0.5     0.026        36      38      70 ..      91     123 ..      82     135 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0047
         CLZ 30 eekverLessLeaLqtrlarLlaeyessqrkLkqRitkLEk 70
                ee++++L +++++L+t +  L +   +  + L++ ++++E+
  EPA05480.1  3 EEQAQQLMQQMQMLETYFTDLSQREGTLLNVLREAVAAIES 43
                899******************99999999999999998885 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.026
         CLZ  38 ssLeaLqtrlarLlaeyessqrkLkqRitkLEk 70 
                 s+++ L+ +++ +   ++ +  k +q +++LE+
  EPA05480.1  91 SAINYLEAKIKEIEVALQDTSVKKQQAVARLEQ 123
                 445555555555555666666666666666554 PP

>> DUF3947  Protein of unknown function (DUF3947)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   1.6    0.0042       5.8      32      53 ..       4      25 ..       1      49 [. 0.85
   2 ?    3.5   0.3     0.057        79       6      40 ..      80     116 ..      76     139 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0042
     DUF3947 32 qqalqmqqqaqmqqsqiqPyss 53
                +qa q+ qq+qm    +   s+
  EPA05480.1  4 EQAQQLMQQMQMLETYFTDLSQ 25
                79**********9887766665 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.057
     DUF3947   6 arqvgmrpayGaaitlaGaqstvqavqqalq....mqqq 40 
                 +  v+m  +y +ai +  a+  ++ ++ alq     +qq
  EPA05480.1  80 GAGVAMEKSYDSAINYLEAK--IKEIEVALQdtsvKKQQ 116
                 56789999999999998775..44444444411112233 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1535  (0.0856155); expected 358.6 (0.02)
Passed bias filter:                      709  (0.0395449); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.62u 0.37s 00:00:00.99 Elapsed: 00:00:00.55
# Mc/sec: 769.04
//
Query:       EPA05481.1  [L=38]
Description: hypothetical protein BG20_I2283, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (38 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       127  (0.0070835); expected 358.6 (0.02)
Passed bias filter:                      126  (0.00702772); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.33s 00:00:00.82 Elapsed: 00:00:00.54
# Mc/sec: 212.65
//
Query:       EPA05482.1  [L=320]
Description: putative rusticyanin [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.8e-15   54.8   0.4    2.2e-07   31.2   0.0    2.6  2  Copper-bind   Copper binding proteins, plastocyanin/azurin fa
    6.9e-11   42.2   0.8      3e-05   24.0   0.1    3.1  2  Cu-oxidase_3  Multicopper oxidase
    3.3e-09   36.8   0.0    0.00037   20.6   0.0    2.6  2  Cupredoxin_1  Cupredoxin-like domain
    2.2e-08   33.7   0.5     0.0079   15.7   0.0    2.7  2  SoxE          Sulfocyanin (SoxE) domain
    1.3e-06   28.4   0.0      0.037   14.0   0.0    2.9  2  Cu_bind_like  Plastocyanin-like domain
    2.5e-06   27.3   0.0     0.0043   16.8   0.0    2.7  2  Cu-oxidase_2  Multicopper oxidase
     0.0057   16.8   0.0        5.5    7.3   0.0    2.5  2  DUF2475       Protein of unknown function (DUF2475)
     0.0064   16.5   0.1        1.8    8.7   0.0    2.5  2  CHU_C         C-terminal domain of CHU protein family
  ------ inclusion threshold ------
      0.012   15.3   0.0        1.8    8.1   0.0    2.1  2  PGBA_N        Plasminogen-binding protein pgbA N-terminal
        0.5   11.5   4.5       0.56   11.4   0.3    2.6  2  PPC           Bacterial pre-peptidase C-terminal domain


Domain annotation for each model (and alignments):
>> Copper-bind  Copper binding proteins, plastocyanin/azurin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.1   1.5e-07   0.00027      65      98 ..     147     184 ..      93     185 .. 0.69
   2 !   31.2   0.0   1.2e-10   2.2e-07      17      99 .]     232     320 .]     229     320 .] 0.77

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.5e-07
                  STTEEEEEEEE..SSEEEEEEET.T.TTTTTSEEEEEE CS
  Copper-bind  65 ggGekdsvtfd..eagtYkffCs.P.HaaagMkgkvtv 98 
                   +G + + +f   ++gtY ++C+ P H+ +gM+g+++v
   EPA05482.1 147 KPGMSGTSEFIpsKEGTYYYICTvPgHREQGMVGEIIV 184
                  45666666666568889*******************98 PP

  == domain 2  score: 31.2 bits;  conditional E-value: 1.2e-10
                  SEEEEETTEEEEEEEE....SSSSBEEEEETTSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEE..SSEEEEEEET.T.TTTTTSEEEEEEE CS
  Copper-bind  17 keitvkkgekvtfvnl....avmgHNvvldkdgvpagvdkdkvkaedetkliggGekdsvtfd..eagtYkffCs.P.HaaagMkgkvtve 99 
                   ++tvk+g++vtf  +       +  +v d +  ++ + k+++      +   +G++ svtf+  ++gtY ++C+ P Ha +gMkg  +ve
   EPA05482.1 232 PDFTVKSGDEVTFAAKnagkSFHAFGIVSDPEDFNNILWKSAIATA--SNPLKPGQEGSVTFTagAPGTYYYICTvPgHALQGMKGSFIVE 320
                  578999***9999887554333344566666666666666666664..445789*********99999******************98885 PP

>> Cu-oxidase_3  Multicopper oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.1   1.7e-08     3e-05      26     117 ..      96     187 ..      89     189 .. 0.82
   2 !   15.2   0.1     9e-06     0.016      68     115 ..     275     320 .]     226     320 .] 0.70

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.7e-08
                   S-EEEEETT-EEEEEEEE-SSS-B-EEEET--S-GG.....GS....CSGGG-B-TT-EEEEEEE--S-SEEEEEEE--TTHHHTT-EEEEEEE-H CS
  Cu-oxidase_3  26 gptievregdtvvvnvtNkldentsihwhGlqqrktswmDGvp....gvtqcpiqpgesftyrftvkqqagtlwYhshlslqqaaGlaGaiiiedk 117
                    pti++  gd++v nv+N    + s h  G+  +++ ++  +p      +++p++pg s t +f  ++ +gt++Y   + +++ +G++G ii+ ++
    EPA05482.1  96 NPTINASVGDKIVFNVEND---GKSFHAFGVTADAEGFAGIFPssaiASASNPLKPGMSGTSEFIPSK-EGTYYYICTVPGHREQGMVGEIIVGAP 187
                   69***************96...668888888888884433222111134789****************.***********************9876 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 9e-06
                   SCSGGG-B-TT-EEEEEEE--S-SEEEEEEE--TTHHHTT-EEEEEEE CS
  Cu-oxidase_3  68 pgvtqcpiqpgesftyrftvkqqagtlwYhshlslqqaaGlaGaiiie 115
                   +  +++p++pg++ + +ft+    gt++Y   + ++  +G+ G +i+e
    EPA05482.1 275 A-TASNPLKPGQEGSVTFTAGA-PGTYYYICTVPGHALQGMKGSFIVE 320
                   3.3789****************.*************99********96 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   3.5e-05     0.063      36     104 .]      98     184 ..      93     184 .. 0.85
   2 !   20.6   0.0   2.1e-07   0.00037      37     104 .]     234     319 ..     228     319 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.5e-05
  Cupredoxin_1  36 kievkagekvklkiknkdktpeefesed..............lgeekvlapgktttitiaplkpGeYeftcdmhm...d.akGkliV 104
                   +i++  g k+ ++++n++k+ + f ++                + +  l+pg + t ++ p k+G+Y ++c       + + G++iV
    EPA05482.1  98 TINASVGDKIVFNVENDGKSFHAFGVTAdaegfagifpssaiASASNPLKPGMSGTSEFIPSKEGTYYYICTVPGhreQgMVGEIIV 184
                   688899999***********8888888888889999999988889999***********************9766333556666666 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 2.1e-07
  Cupredoxin_1  37 ievkagekvklkiknkdktpeefesed..............lgeekvlapgktttitiaplkpGeYeftcdmhm...d.akGkliV 104
                    +vk+g +v++  kn +k+ + f + +                 +  l+pg++ ++t+++  pG+Y ++c       + +kG +iV
    EPA05482.1 234 FTVKSGDEVTFAAKNAGKSFHAFGIVSdpedfnnilwksaiATASNPLKPGQEGSVTFTAGAPGTYYYICTVPGhalQgMKGSFIV 319
                   68*****************8888777777888888666665667789***********************9766434556776666 PP

>> SoxE  Sulfocyanin (SoxE) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   4.5e-06    0.0081     101     139 ..     147     185 ..      95     195 .. 0.79
   2 !   15.7   0.0   4.4e-06    0.0079      96     138 ..     277     319 ..     264     320 .] 0.85

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4.5e-06
        SoxE 101 ssGqsasGlledlsaGtywlacgilGhaesGmWvdlivs 139
                   G s +  + +  +Gty+ +c+++Gh e+Gm  ++iv 
  EPA05482.1 147 KPGMSGTSEFIPSKEGTYYYICTVPGHREQGMVGEIIVG 185
                 445555555566678******************999985 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 4.4e-06
        SoxE  96 avsGissGqsasGlledlsaGtywlacgilGhaesGmWvdliv 138
                 a++ +  Gq+ s  +   ++Gty+ +c+++Gha +Gm   +iv
  EPA05482.1 277 ASNPLKPGQEGSVTFTAGAPGTYYYICTVPGHALQGMKGSFIV 319
                 456788899999999999*******************876665 PP

>> Cu_bind_like  Plastocyanin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   2.1e-05     0.037      19      84 .]     102     178 ..      97     178 .. 0.73
   2 !   11.1   0.0   0.00017      0.31      48      84 .]     277     313 ..     233     313 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.1e-05
  Cu_bind_like  19 rvGDtLlFkydsevhsvv...evs.kkeyekCetskpleeft.......tgsdkvtLtkegsnyFisgvpghCkkGq 84 
                   +vGD ++F+ +++ +s +    +   + +     s+ +++ +       +g+++   +keg+ y+i++vpgh ++G+
    EPA05482.1 102 SVGDKIVFNVENDGKSFHafgVTAdAEGFAGIFPSSAIASASnplkpgmSGTSEFIPSKEGTYYYICTVPGHREQGM 178
                   689999999887655544111343467787777666666665677777788888888999************99997 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00017
  Cu_bind_like  48 tskpleefttgsdkvtLtkegsnyFisgvpghCkkGq 84 
                   +s+pl+  ++gs + t   +g+ y+i++vpgh  +G+
    EPA05482.1 277 ASNPLKPGQEGSVTFTAGAPGTYYYICTVPGHALQGM 313
                   3445555558999999999*************99997 PP

>> Cu-oxidase_2  Multicopper oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0    0.0013       2.3      97     134 ..     148     185 ..      93     188 .. 0.89
   2 !   16.8   0.0   2.4e-06    0.0043      78     134 ..     264     320 .]     214     320 .] 0.82

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0013
                   TTEEEEEEEES.S-EEEEEEESSHHHHHTT-EEEEEEE CS
  Cu-oxidase_2  97 pggwvairfkadnpGvwllHCHilwHldqGmalqfvvr 134
                   pg   + +f +   G +++ C +  H +qGm+++++v 
    EPA05482.1 148 PGMSGTSEFIPSKEGTYYYICTVPGHREQGMVGEIIVG 185
                   5566667899999*********************9997 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 2.4e-06
                   TCCSSGCCGSSCBSEEEE-TTEEEEEEEES.S-EEEEEEESSHHHHHTT-EEEEEEE CS
  Cu-oxidase_2  78 dpksynlenpvrrdtvqvppggwvairfkadnpGvwllHCHilwHldqGmalqfvvr 134
                   d +++ ++ ++      ++pg++  + f+a  pG +++ C +  H+ qGm ++f+v+
    EPA05482.1 264 DFNNILWKSAIATASNPLKPGQEGSVTFTAGAPGTYYYICTVPGHALQGMKGSFIVE 320
                   33444457777777888999**********************************985 PP

>> DUF2475  Protein of unknown function (DUF2475)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0031       5.5       4      21 ..      88     105 ..      86     109 .. 0.92
   2 !    6.9   0.0    0.0041       7.3       4      26 ..     223     247 ..     221     256 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0031
     DUF2475   4 lmPGYrGyvPqvkysfGd 21 
                  +PG +G+ P+++ s+Gd
  EPA05482.1  88 ALPGEEGHNPTINASVGD 105
                 58***************8 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0041
     DUF2475   4 lmPGYrGyvPqvkysfGd..tYGnt 26 
                  +PG +G+ P +  + Gd  t+ ++
  EPA05482.1 223 ALPGEEGHNPDFTVKSGDevTFAAK 247
                 58***************98888765 PP

>> CHU_C  C-terminal domain of CHU protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0     0.001       1.8      53      82 ..     152     180 ..     142     184 .. 0.71
   2 ?    5.4   0.0      0.01        19      62      83 ..     295     316 ..     279     319 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.001
       CHU_C  53 GtskgkeklpeGtYfYvlkleegekeekkG 82 
                 Gts+   + +eGtY+Y++++  ++++ + G
  EPA05482.1 152 GTSEF-IPSKEGTYYYICTVPGHREQGMVG 180
                 55554.67889*********5555554555 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.01
       CHU_C  62 peGtYfYvlkleegekeekkGw 83 
                   GtY+Y++++  +  + +kG 
  EPA05482.1 295 APGTYYYICTVPGHALQGMKGS 316
                 57********965555556665 PP

>> PGBA_N  Plasminogen-binding protein pgbA N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0     0.001       1.8      40      91 ..      58     114 ..      46     135 .. 0.80
   2 ?    5.2   0.0     0.008        14      55      90 ..     208     248 ..     175     273 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.001
      PGBA_N  40 saIiaravvisikegvakvrfeefeaLkqkaLP.....tpklvpkkgdevilnelyd 91 
                    +a a+ + i+e+   ++   f +L+ +aLP     +p++ +++gd++++n  +d
  EPA05482.1  58 TESAAVATGKTITENLKFIESPDFRTLSFNALPgeeghNPTINASVGDKIVFNVEND 114
                 44456777788899999****************77777799***********98876 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.008
      PGBA_N  55 vakvrfeefeaLkqkaLP.....tpklvpkkgdevilnely 90 
                 v  ++   f +L+ +aLP     +p  ++k+gdev+++  +
  EPA05482.1 208 VNFIESADFRTLSFNALPgeeghNPDFTVKSGDEVTFAAKN 248
                 55677888999999999966666799***********8766 PP

>> PPC  Bacterial pre-peptidase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.5      0.59   1.1e+03      39      65 ..     140     165 ..      98     167 .. 0.55
   2 ?   11.4   0.3   0.00031      0.56       7      65 ..     234     300 ..     233     302 .. 0.66

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.59
                 S-EE-STT-TTS-TTS-EE-SSSEEEE CS
         PPC  39 aaydansapsgsdeyieftapqaGtYy 65 
                 a+++++  p+ s  + ef + + GtYy
  EPA05482.1 140 ASASNPLKPGMS-GTSEFIPSKEGTYY 165
                 332223343334.66777778999997 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00031
                 EEE-TT-EEEEEES-TT..SEEE..EE-TT.........-SS-EE-STT-TTS-TTS-EE-SSSEEEE CS
         PPC   7 fevpagdsltididggtidldLy..lldsn..gt.....svaaydansapsgsdeyieftapqaGtYy 65 
                 f+v++gd++t +  + + ++  +  ++d++  ++      +a+ + n+ + g   +++fta ++GtYy
  EPA05482.1 234 FTVKSGDEVTFAAKNAGKSFHAFgiVSDPEdfNNilwksAIAT-ASNPLKPGQEGSVTFTAGAPGTYY 300
                 9999999999999888878887756666663333222213333.223334447799***********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.63u 0.37s 00:00:01.00 Elapsed: 00:00:00.54
# Mc/sec: 1779.98
//
Query:       EPA05483.1  [L=77]
Description: hypothetical protein BG20_I0262 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.34s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 433.91
//
Query:       EPA05484.1  [L=54]
Description: hypothetical protein BG20_I0237 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.028   14.5   0.1      0.031   14.3   0.1    1.2  1  HisKA     His Kinase A (phospho-acceptor) domain
      0.089   13.2   0.2       0.11   12.9   0.2    1.2  1  Wbp11     WW domain binding protein 11


Domain annotation for each model (and alignments):
>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   3.4e-06     0.031      37      65 ..      22      50 ..       6      51 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.4e-06
                CHHHHHHHHHHHHHHHHHHHHHHHHCCHH CS
       HisKA 37 lkeyletiesearrldhlvedlLdlsrie 65
                 k++l++iese++ l++lv+  L +  ie
  EPA05484.1 22 NKKNLDIIESEIDKLSQLVNSNLNIKEIE 50
                578*****************999887776 PP

>> Wbp11  WW domain binding protein 11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   1.2e-05      0.11      31      56 ..      18      43 ..      13      53 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.2e-05
       Wbp11 31 eaklakkdpdeleeeiekLeelessg 56
                +   +kk++d +e+ei+kL +l +s+
  EPA05484.1 18 NLTWNKKNLDIIESEIDKLSQLVNSN 43
                556789*************9887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       718  (0.0400469); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 326.66
//
Query:       EPA05485.1  [L=122]
Description: hypothetical protein BG20_I0228 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 719.52
//
Query:       EPA05486.1  [L=471]
Description: amino acid kinase family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.2e-25   89.7   0.4      4e-25   88.8   0.4    1.5  1  AA_kinase  Amino acid kinase family


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.8   0.4   2.3e-29     4e-25       1     241 []       3     299 ..       3     299 .. 0.81

  Alignments for each domain:
  == domain 1  score: 88.8 bits;  conditional E-value: 2.3e-29
                 TEEEEEE-TTCCC.CTCCHHHHHHHHHHHHHHHHTTEEEEEE--H.........HHHHHHHHHTCCCCCHHHC.......................... CS
   AA_kinase   1 krvVvKlGGsslt.dkeeaslrrlaeqiaalkesgnklvvVhGgg.........sftdgllalksglssgelaa........................g 65 
                 k+vV K+GGs+++ d+    +  +++ i +l +++ k++ V ++          s td +l++ ++++ g +a                          
  EPA05486.1   3 KLVVAKFGGSAIGiDGMS--IPLILDRINDL-KKDSKIIAVFSAPltmqnekkcSLTDVILEQGKNVEHGNKADlqvikscyqkilkfvnsenmkdcqN 98 
                 689**********99999..***********.999*********3345566677777777777555555555545666777777766665554444440 PP

                 ..E..HHHHHHHHH...........................HHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE.........HHHTTTCEEECCH CS
   AA_kinase  66 lrstleeagevatr...........................dalaslgerlvaallaaglpavglsaaaldateagr.......degsdgnvesvdaea 130
                                                          ++la  ge+l+++++++ l++ g+++ a+   +  +       +++  +  ++ + e+
  EPA05486.1  99 -------------TideflkkaekaldeglqkkefaeeirsRSLAFSGEILMSHVMNYILRSNGIKSDAVSYDDWPIitdhnieSTNFLASKSRENLEK 184
                 .............1444455556666667777777777777*****************************98887779999888888888888888999 PP

                 HHHHHHTT-EEEEESEEEEETTTE...EEEE-HHHHHHHHHHHCTS..SEEEEEESSSSCESSTTTTCCTT.CECCEEEHHHCHHCSSS.TTTHHHHCH CS
   AA_kinase 131 ieelleagvvpvltgfigldeege...lgrgssDtiaallAealgA..dkliiltdVdGVydadpkkvpda.rllpeisvdeaeesaselatgGmkvkh 223
                  ++l+e+++v+ ++gfig +++g      rg+sD++aa l+ +++   ++ i +   + V +adpk+v+ +   ++++s++ea+      +++Gmk+++
  EPA05486.1 185 TAKLVEDNQVVTMGGFIGKTPDGItttYERGGSDRTAADLGILFHKkyETRIDFEKDSSVVSADPKIVDEGlAEVDQLSYNEARL----AGMFGMKILD 279
                 99**********************99988***************997755666667777*********8889*************....********** PP

                 HHHHHHHHCTT..-EEEEEE CS
   AA_kinase 224 paalaaarrgg..ipvvItn 241
                 p a++ + ++g  +p+++tn
  EPA05486.1 280 PIAIKEIVENGvdMPIIVTN 299
                 ***98766655378888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (471 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       963  (0.0537119); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.69u 0.33s 00:00:01.02 Elapsed: 00:00:00.51
# Mc/sec: 2762.55
//
Query:       EPA05487.1  [L=132]
Description: pyridoxamine 5'-phosphate oxidase family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      9e-16   57.8   0.0    2.1e-15   56.7   0.0    1.6  2  Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
    8.9e-10   38.7   0.0    1.3e-09   38.1   0.0    1.2  1  Pyridox_ox_2    Pyridoxamine 5'-phosphate oxidase
    0.00052   19.4   0.0    0.00063   19.2   0.0    1.2  1  YmdB            YmdB-like protein
     0.0091   15.6   0.1     0.0093   15.6   0.1    1.2  1  Pyrid_ox_like   Pyridoxamine 5'-phosphate oxidase like
  ------ inclusion threshold ------
      0.019   14.7   0.4       0.02   14.6   0.4    1.1  1  DUF2228         Uncharacterised conserved protein (DUF2228)


Domain annotation for each model (and alignments):
>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.7   0.0   5.9e-19   2.1e-15       6      76 ..       5      75 ..       2      87 .. 0.87
   2 ?   -1.9   0.0       1.1     4e+03      43      63 ..      99     119 ..      90     126 .. 0.75

  Alignments for each domain:
  == domain 1  score: 56.7 bits;  conditional E-value: 5.9e-19
                    HHHHHHSSEEEEEEEETTSEEEEEEEEEEEETTTTEEEEEEETTSHHHHHHHHH-EEEEEEEETT..GSEEEE CS
  Putative_PNPOx  6 reflaeskavvlATvdedGrPnvspvllkagdgrdgivfatnadsrklrnleenprvallfldde..lgrgvr 76
                     efl+++k+ +lAT++ + +P+++pv++ +  ++  i++ tn++++k++n+++n++va++++        gv+
      EPA05487.1  5 DEFLKTQKILRLATIGNNKTPHIVPVWYMYSSKK--IYIGTNTKTQKAKNVKKNNKVAFCVDVGInsPIDGVM 75
                    69********************************..************************9976655555555 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.1
                     EEEEETTSHHHHHHHHH-EEE CS
  Putative_PNPOx  43 vfatnadsrklrnleenprva 63 
                      ++ n + + +++l  n  + 
      EPA05487.1  99 RYFKNMENKSAKELLDNTDCI 119
                     567777888888888887765 PP

>> Pyridox_ox_2  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.0   3.8e-13   1.3e-09       5     138 ..       4     128 ..       2     130 .. 0.81

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 3.8e-13
                   HHHHHHC-SEEEEEEEETTE.EEEEEEEEEEETTEEEEEEETTSHCCHCCCT--.ECEEEEEEEEEEE-SEGGEEEEEEEEEEEEEEEE--HHHHHH CS
  Pyridox_ox_2   5 ilalLdegevgrlafvddge.pvilPvnyvvdgdslyfhgakgsrlaaalrgap.vcvvvtevdglvlarsfnslnyrSVvvrGraeevtdeeekae 99 
                    +++L++++++rla+  +++ p+i+Pv y++  +++y+ + +++++a+  ++++ v++ v    g++            V+ +G+a  + +  + ++
    EPA05487.1   4 SDEFLKTQKILRLATIGNNKtPHIVPVWYMYSSKKIYIGTNTKTQKAKNVKKNNkVAFCVDV--GINSPID-------GVMGQGYANIILENNKVKK 91 
                   589**************7777******************************33335555554..5444444.......9**********99999999 PP

                   HCCCHHHHHSTTTGGCSB---CCCCCT..EEEEEEEEEEEE CS
  Pyridox_ox_2 100 alellvekivpgrwenlrpptrkelka..tsvlrlkieevs 138
                   + e+++ ++    ++n + +++kel    + ++++ +e++s
    EPA05487.1  92 IAEKILLRY----FKNMENKSAKELLDntDCIIEIIPEKLS 128
                   999999999....8888877777775545677888887776 PP

>> YmdB  YmdB-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.8e-07   0.00063     161     214 ..      31      84 ..      25     113 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.8e-07
        YmdB 161 lyldgrvsavvGTHthvqTaDerilpkgtayitDvGmtGpedsviGvekeevik 214
                 +y+    ++ +GT t+ q a +   +++ a++ DvG+  p d+v+G  ++++i 
  EPA05487.1  31 WYMYSSKKIYIGTNTKTQKAKNVKKNNKVAFCVDVGINSPIDGVMGQGYANIIL 84 
                 7777788899************************************99998874 PP

>> Pyrid_ox_like  Pyridoxamine 5'-phosphate oxidase like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   2.6e-06    0.0093      18     108 ..      16     106 ..       1     131 [. 0.76

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.6e-06
  Pyrid_ox_like  18 LttteadgklksrPMatqkveedgdlwfltkkdsdkvkeirkdsqvnlafsd..eskkkyvsvsGtaevvedrakieelWspvvkawfpegkd 108
                    L+t+ ++++ +  P        + +++  t+++++k+k+++k+++v +++    +s  + v+ +G a++  +++k+++  ++++  +f++ ++
     EPA05487.1  16 LATIGNNKTPHIVPVWYM--YSSKKIYIGTNTKTQKAKNVKKNNKVAFCVDVgiNSPIDGVMGQGYANIILENNKVKKIAEKILLRYFKNMEN 106
                    566666666666665443..34568************************97611344466888899****************99999987665 PP

>> DUF2228  Uncharacterised conserved protein (DUF2228)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.4   5.6e-06      0.02     119     193 ..      37     111 ..       9     123 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.6e-06
     DUF2228 119 kekeisleqkteklkkRkkkvvaktfhgaGivvpvdkktdvGYReLsesdaelkkllkkieeakneeerekalek 193
                 k+  i +++kt+k k+ kk+        +Gi  p+d     GY ++  +++++kk+ +ki     ++ ++k  ++
  EPA05487.1  37 KKIYIGTNTKTQKAKNVKKNNKVAFCVDVGINSPIDGVMGQGYANIILENNKVKKIAEKILLRYFKNMENKSAKE 111
                 3445556666666666666666666789****************************9998766655555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1230  (0.0686039); expected 358.6 (0.02)
Passed bias filter:                      580  (0.0323498); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 808.86
//
Query:       EPA05488.1  [L=304]
Description: branched-chain-amino-acid transaminase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-48  166.0   0.0    1.4e-48  165.7   0.0    1.1  1  Aminotran_4  Amino-transferase class IV
  ------ inclusion threshold ------
      0.088   13.2   0.1       0.43   11.0   0.0    2.1  2  BRCT         BRCA1 C Terminus (BRCT) domain


Domain annotation for each model (and alignments):
>> Aminotran_4  Amino-transferase class IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.7   0.0   1.5e-52   1.4e-48       2     223 .]      34     265 ..      33     265 .. 0.97

  Alignments for each domain:
  == domain 1  score: 165.7 bits;  conditional E-value: 1.5e-52
  Aminotran_4   2 lfEtmrvy...ngei.ffldeHleRLrksaellglelpfdeeelrkileelleannsengrlrllvsrgggglgaatsepsvavyvsalppgpeseke 95 
                  +fE++r y   ng+  f+l+eH++R+ +sa+l  +++ f+++e++ ++ ++++an+ +++++r+l   g g +g   + ++v+v+++++++++ + k+
   EPA05488.1  34 IFEGIRCYntpNGSAiFRLPEHVDRFFNSAKLYSMKMQFSKKEISDAIIKTVKANGLKECYIRPLAYYGFGTMGLTPTPNKVDVSIACWEWAMGEGKA 131
                  7******99998887355******************************************************************************** PP

  Aminotran_4  96 .....lplvtssdvrrdapsplpgaKtln.yldnvlarreakergadevllvdedgnvtEgstsNvfivkggelitPplssgiLpGitrrallelaka 187
                        ++ +ss+ ++d +s+  +aK  + y++ +lar ea e+g+de+++++ +g v Egs  N+f+vk+g + tPpls g+L+Gitr++++++ ++
   EPA05488.1 132 gkfsgARCKVSSWIKIDSRSQPMQAKAASnYANAALARVEALENGYDEAIMLNIHGKVAEGSAENIFVVKDGIIQTPPLSAGGLEGITRDSIIQIIEE 229
                  ***************************999******************************************************************** PP

  Aminotran_4 188 l.gleveereitlkdleeadeafltntlrgvlpvrsi 223
                    g+ v+er+++ +dl  ade+f+t+t+++v  v++i
   EPA05488.1 230 NgGF-VIERDLERGDLYSADEIFMTGTAAEVKSVTQI 265
                  *666.*****************************987 PP

>> BRCT  BRCA1 C Terminus (BRCT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.42   3.7e+03      60      78 ..      75      93 ..      65      94 .. 0.72
   2 ?   11.0   0.0   4.8e-05      0.43      15      58 ..     213     267 ..     209     288 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.42
                HHHHHTTSEEEETHHHHHH CS
        BRCT 60 lealklnipivheewlldc 78
                +e  +  i++v+ + l++c
  EPA05488.1 75 KEISDAIIKTVKANGLKEC 93
                4555666888888888888 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 4.8e-05
                 ESTSSHHHHHHHHHHHHTTCEE......ESSCSTTSSEEEESSS.....HSHHHH CS
        BRCT  15 gvldnftrdeleelikehGGkv......ttevskktthlvvgep.....esrslk 58 
                 g+l+++trd++ ++i+e+GG v       +++ + + ++ +g+       +   k
  EPA05488.1 213 GGLEGITRDSIIQIIEENGGFVierdleRGDLYSADEIFMTGTAaevksVTQIDK 267
                 68899***************99999888666666666666666644444334444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 1771.61
//
Query:       EPA05489.1  [L=147]
Description: hypothetical protein BG20_I0267 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-18   66.4  15.2    3.2e-14   52.8   8.1    2.0  2  COX15-CtaA     Cytochrome oxidase assembly protein
  ------ inclusion threshold ------
       0.41   10.6   2.6       0.36   10.8   0.6    1.9  2  SLATT_fungal   SMODS and SLOG-associating 2TM effector domain
        1.1    9.4   6.6        1.7    8.8   2.2    2.1  2  DUF2614        Zinc-ribbon containing domain


Domain annotation for each model (and alignments):
>> COX15-CtaA  Cytochrome oxidase assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.4   7.7e-08   0.00046       2      43 ..       5      46 ..       4      48 .. 0.88
   2 !   52.8   8.1   5.3e-18   3.2e-14      74     170 ..      47     137 ..      46     146 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 7.7e-08
  COX15-CtaA  2 rwlllvlllvllvvvlGgltRltdsGlsitdWppctGalppl 43
                +++l++l++++ + ++Gg++   + Gl +++Wp c   ++p 
  EPA05489.1  5 YLALATLIVLYSLMFIGGYISSAGLGLTCPEWPLCPNGIMPN 46
                678999999**************************8877775 PP

  == domain 2  score: 52.8 bits;  conditional E-value: 5.3e-18
  COX15-CtaA  74 aiawiEwiHRllgrllGllilvpllyflakkrisrelkkllllllllvglQGllGwwmVksgLsekprvspyrlaaHLllaflllalllwlalrlla 170
                 ++++iEw+HRl++ ++G l+++ ++ ++ +k++ r++k   ++++ lv+ Q  lG++++ ++L        + +a+HL++++ll++++l++al +++
  EPA05489.1  47 EEYFIEWTHRLVAVTTGSLVIATAVGSWLNKNAGRKIKFTSTFAATLVVTQITLGAIVINLKL------HAVLVAIHLGVGILLFSMVLLTALFAFR 137
                 579************************************************************......9*********************997665 PP

>> SLATT_fungal  SMODS and SLOG-associating 2TM effector domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.6   6.1e-05      0.36       7      37 ..      77     107 ..      74     111 .. 0.92
   2 ?   -1.6   0.1      0.44   2.6e+03      19      38 ..     113     134 ..     105     141 .. 0.50

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 6.1e-05
  SLATT_fungal   7 rkaarkarltslalnlaiglQvllgAlltaL 37 
                   ++a rk ++ts++  ++++ Q++lgA+++ L
    EPA05489.1  77 KNAGRKIKFTSTFAATLVVTQITLGAIVINL 107
                   67899**********************9865 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.44
  SLATT_fungal  19 alnlaiglQvllgA..lltaLg 38 
                   ++ + +g+ +ll +  lltaL 
    EPA05489.1 113 LVAIHLGVGILLFSmvLLTALF 134
                   4444444444444311445554 PP

>> DUF2614  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1     0.019   1.1e+02      42      72 ..       7      35 ..       1      40 [. 0.69
   2 ?    8.8   2.2   0.00028       1.7       4      51 ..      81     128 ..      78     144 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.019
     DUF2614 42 llGlllvlastvvyfwiGllstkavqvvcpe 72
                 l +l+vl    + f+ G +s+  + ++cpe
  EPA05489.1  7 ALATLIVLY--SLMFIGGYISSAGLGLTCPE 35
                344444444..45677899999999999997 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00028
     DUF2614   4 skinkirtfalllvfiglivmyigllfkeselllvlflllGlllvlas 51 
                  ki    tfa +lv + + +  i + +k + +l+++ l +G+ll+ + 
  EPA05489.1  81 RKIKFTSTFAATLVVTQITLGAIVINLKLHAVLVAIHLGVGILLFSMV 128
                 6888899*****************************999998765332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       852  (0.0475208); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.38s 00:00:00.91 Elapsed: 00:00:00.52
# Mc/sec: 846.66
//
Query:       EPA05490.1  [L=508]
Description: putative cytochrome c oxidase, subunit I [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   3.8e-132  441.2  61.7   4.8e-132  440.9  61.7    1.1  1  COX1      Cytochrome C and Quinol oxidase polypeptide I


Domain annotation for each model (and alignments):
>> COX1  Cytochrome C and Quinol oxidase polypeptide I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  440.9  61.7  2.7e-136  4.8e-132       2     432 .]      23     463 ..      22     463 .. 0.98

  Alignments for each domain:
  == domain 1  score: 440.9 bits;  conditional E-value: 2.7e-136
                 HHHHHHHHHHHHHHHHHHHHHHHHHHCTCT......-HHCHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHCTSS-S-HHHHHHHHHHHHHHHHHHH CS
        COX1   2 igllylilalvlllvggllgllirlqlafp......dletynqlrtlHgnlmiflfatpfilgfgnylvplllgardlafprlnalsfwlvvlgvvlll 94 
                 +gllyli+++++l++gg+l+l ir++l++p      d+ t+n+++t+Hg+++iflf++pf+ ++gny+vp++++ +d+a p+lna++fw+++ +++l++
  EPA05490.1  23 VGLLYLITSIAFLFMGGALALAIRAELFLPgsqiiaDSMTFNRIFTVHGTTLIFLFIIPFASAVGNYFVPIMVRYKDMAYPKLNAIAFWMIPPAGALIW 121
                 899*************************9987777788************************************************************* PP

                 HHHHCSS-STTTTTTTC........SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-CCGS-HHHHHHHHHHHHHHHHCHHHHHHHHHCHHHHHC CS
        COX1  95 lsllgaattgwteYapls.......evdlwllglllvvvssllgainfivtilkrrapgmtvaklplfvwavlatailillalpvlalalllllldrsl 186
                 l++   a+  w++ +p+s       + d+w++gl ++++ss+lgainfivtilk + p m++ ++pl++w++la +++il+a+p +a+all+ll+dr  
  EPA05490.1 122 LGF---ADFTWYATPPYSiisapgpAADMWIFGLKILGISSVLGAINFIVTILKCKHPDMSLGQVPLLAWSFLASSLIILVAIPTFAAALLMLLTDRLG 217
                 ***...9******************************************************************************************99 PP

                 T.-SSSC...E-HHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHTSCCCTHHHHHHHHHHHHHHCCCCGGGGTTTSSS-HHHHHHHHHHHHHTHHH CS
        COX1 187 g.kffsp...gdplldqhlfWffgHpeVyililpalgivyyilpkfagrplfsyklsvlafililflsflvwaHHlfttglpewlkalgsvfslliavP 281
                    ff+p   gdp+ ++hlfWf+ HpeVy+l++pa+g++y+i+p+f+++p+fs++  ++af+l+ ++sf  waHH++ tg++ + k+++++ +l+ +  
  EPA05490.1 218 VsGFFNPamgGDPIAYAHLFWFTFHPEVYVLVIPAIGMMYEIIPRFSRKPIFSHSSGIFAFVLLSVVSFSSWAHHMYATGMSFTEKTVFMIGTLAAVPA 316
                 999**999******************************************************************************************* PP

                 HHHCCCHHHHCCTTS-CHCHHHHHHHHHHHHHHHHHHHHHHHHTSHHHHHHHTTBHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHSB--HHHHHHHHH CS
        COX1 282 sglkvfnwlatlwrgsirfktpmlfflgfavlfiigGltGvllalpsvnyvvhntywvvaHfHlvllgavvfllfaaiyyllpkltgrmlserlaklhf 380
                 s+++vfn++at+w+g+irf tpm++++g + lf+ +G+ Gv++a+ ++++++h++ywvv+HfHl ++g+++f+ ++ +yy++p +tgrm++e+++k+hf
  EPA05490.1 317 SAMHVFNFIATMWNGRIRFATPMMWAVGGIALFFSAGAGGVVNAAMPLDFQTHDSYWVVGHFHLFVMGTIAFGSIGYLYYMFPYVTGRMYNEKMGKVHF 415
                 *************************************************************************************************** PP

                 HHHHHHHHHHHHHHHHHHHTTHBSSSST--SCCCCHHHCHHHHHHHHHHHHH CS
        COX1 381 wllfiGlvlmflpmhilGllgmprraadyksfletvpelqplnvlrtiggvl 432
                 ++ fiG+vl+f+++h+lGl+gmprr++dy++     pe+  +n+++++g+++
  EPA05490.1 416 VMSFIGTVLVFFTQHVLGLYGMPRRIFDYPP----IPEWIAMNQIASVGAMI 463
                 *****************************77....79************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (508 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       729  (0.0406604); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.50
# Mc/sec: 3064.81
//
Query:       EPA05491.1  [L=54]
Description: hypothetical protein BG20_I0230 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.093   12.4   0.1       0.14   11.9   0.1    1.3  1  WRC       WRC


Domain annotation for each model (and alignments):
>> WRC  WRC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   7.9e-06      0.14      23      40 ..      23      40 ..      20      43 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.9e-06
         WRC 23 gqklCerHlhrgrkrsrk 40
                 ++lCe+H++  +++++k
  EPA05491.1 23 TRNLCEYHYNLFKNKEEK 40
                579*******99998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.33s 00:00:00.83 Elapsed: 00:00:00.52
# Mc/sec: 314.54
//
Query:       EPA05492.1  [L=215]
Description: hypothetical protein BG20_I0252 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.8e-19   67.8   0.0    1.2e-17   64.3   0.0    1.9  2  adh_short_C2   Enoyl-(Acyl carrier protein) reductase
    1.4e-17   63.9   0.1    1.1e-12   47.8   0.0    2.1  2  adh_short      short chain dehydrogenase
  ------ inclusion threshold ------
      0.015   14.4   0.0       0.03   13.4   0.0    1.4  1  RmlD_sub_bind  RmlD substrate binding domain
      0.039   13.8   0.0      0.056   13.2   0.0    1.2  1  UPF0193        Uncharacterised protein family (UPF0193)


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.026   1.2e+02       3      33 ..      10      40 ..       8      46 .. 0.80
   2 !   64.3   0.0   2.6e-21   1.2e-17      60     231 ..      44     208 ..      36     209 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.026
                  TTSHHHHHHHHHHHTT-EEEEEESSGGHHHH CS
  adh_short_C2  3 asgIGraiAkalaeeGaevvltdlneeakkr 33
                   +gIG+ai  +l++   ev ++  n+ + ++
    EPA05492.1 10 SRGIGKAISNSLKSIDIEVFAASKNDIDTSN 40
                  59***************99999888766555 PP

  == domain 2  score: 64.3 bits;  conditional E-value: 2.6e-21
                   HHHHHHHHSSEEEEEE-----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSCCEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHHH CS
  adh_short_C2  60 veevvekfgklDilvnnagiapklkgpfletsreefdraldvnlyslfllakaalplmkeggsivnlssvgaervvpnynaygaaKaalealtrylA 156
                   v++ v+ +++ D+lv n g  p+  ++f++++ e++++ ++  + ++  +++ +   +++ g i  +ss   +   ++  + +a +aa   + + l 
    EPA05492.1  44 VKKFVQIHNQTDVLVLNTGGPPS--KKFTSITVEDWNKYHNQLFLGFCTILQNI--KINDDGYIFLISSSIIKEPNEKLIISSAYRAAFSEVFKILS 136
                   6778888999*************..**********************9999998..58999********97777777777***************** PP

                   HHHGGGTEEEEEEEE--BHCTGGGGSTTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEEEEST CS
  adh_short_C2 157 velgpkgiRvNavspgpikTlaasgikgfdelleelearaplgrlgtpeevaeaalfLasdeasyitGqtlvvDg 231
                   +e+++k+i +  ++pgpi+T+ ++++    e +ee ++  p++rlg+p+e+++ +  ++ ++ +y +G ++  Dg
    EPA05492.1 137 KEYAAKNISCINIAPGPINTDRTKELV---ENIEEYKKTLPMKRLGEPDEIGNFVKAIIQNKIKYLSGVVINFDG 208
                   **********************99997...7788999**********************************9998 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1     4e-06     0.018       3      34 ..       4      35 ..       2      43 .. 0.88
   2 !   47.8   0.0   2.5e-16   1.1e-12      67     193 ..      43     165 ..      36     167 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4e-06
                EEEESTTSHHHHHHHHHHHHTT-EEEEEESCH CS
   adh_short  3 vlvtGassGIGraiakelakeGakvvvvdrse 34
                +++ G+s+GIG+ai++ l + +++v+++++++
  EPA05492.1  4 AIILGGSRGIGKAISNSLKSIDIEVFAASKND 35
                89***********************9988775 PP

  == domain 2  score: 47.8 bits;  conditional E-value: 2.5e-16
                 HHHHHHHHHSSESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHHHHHHHH CS
   adh_short  67 lvekavkklgkldvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaavagltrslak 165
                  v+k v+ + + dvLv N+G   s++f +++ e+w+++ +  + g   + +     ++ +  G I  +sS + k+p++ ++  sA  aa    ++ l+k
  EPA05492.1  43 SVKKFVQIHNQTDVLVLNTGGPPSKKFTSITVEDWNKYHNQLFLGFCTILQN----IKINDDGYIFLISSSIIKEPNEKLIISSAYRAAFSEVFKILSK 137
                 5788889999****************************99888887766555....56679************************************** PP

                 HHGGGTEEEEEEEESSBSSHHHHHHCTH CS
   adh_short 166 elaptgirvnavaPGlvdTdmakelrek 193
                 e+a ++i+++++aPG+++Td +kel e+
  EPA05492.1 138 EYAAKNISCINIAPGPINTDRTKELVEN 165
                 **********************999876 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   6.7e-06      0.03       2      52 ..       3      53 ..       2      62 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.7e-06
                   EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TTT--TTSHHHHHHHHHHH-- CS
  RmlD_sub_bind  2 kilvtGanGqlGseLakqlaeeglevlaltreeldltdaeavaellkeakp 52
                   + +++G++  +G+++ ++l++ ++ev a +++++d ++ ++v+++++ ++ 
     EPA05492.1  3 RAIILGGSRGIGKAISNSLKSIDIEVFAASKNDIDTSNLDSVKKFVQIHNQ 53
                   5678999999***********************************975543 PP

>> UPF0193  Uncharacterised protein family (UPF0193)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.3e-05     0.056     155     202 ..     153     199 ..     126     205 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.3e-05
     UPF0193 155 vkevDrfeelvkeIeeRkeFLeeMeaLGqgkkYraiIeteIsqklrel 202
                 + ++Dr +elv++Iee k+ L  M+ LG+ ++  + +++ I +k++ l
  EPA05492.1 153 PINTDRTKELVENIEEYKKTL-PMKRLGEPDEIGNFVKAIIQNKIKYL 199
                 5689****************9.5******************9999977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.52
# Mc/sec: 1248.23
//
Query:       EPA05493.1  [L=200]
Description: hypothetical protein BG20_I0268 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.9e-08   32.9   0.0    8.8e-08   32.5   0.0    1.1  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra
    1.7e-07   31.5   0.0    2.7e-07   30.8   0.0    1.4  1  AHSA1            Activator of Hsp90 ATPase homolog 1-like pro
    1.1e-06   28.9   0.0    1.6e-06   28.4   0.0    1.3  1  Polyketide_cyc   Polyketide cyclase / dehydrase and lipid tra


Domain annotation for each model (and alignments):
>> Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.0   1.5e-11   8.8e-08       2     143 .]       2     151 ..       1     151 [. 0.82

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 1.5e-11
                      EEEEEEEEESS-HHHHHHHHTTTTGGG.GT-TTEEEEECS..E.STSSSTTTEEEEECCCS.....SEEEEEEEEEETTTTEEEEEEE.SSS-T CS
  Polyketide_cyc2   2 vkvtvsvviaappekVwalvsdfenwp.rWhpevarvele..g.gggpargvegtvrvggr.....gtvreelvevdpegrllsyrivkpvpva 86 
                      + vt+s++i+ p+e V+ +++ +e+++ + +   + +++   + ++g   gv+ t+r  g          +e +e+  ++r+ + +i    p++
       EPA05493.1   2 TIVTKSIDIKTPVENVFTYFARPEHVSdQIKNDTVGMTVIpmDiKEGM--GVGTTFRIIGDfsgkrLEWDCETTEFVRNERISAKQI--EGPFK 91 
                      569************************656777777764423356777..8888888888778744235778888887788888888..599** PP

                      SEEEEEEEEECCET.EEEEEEEEEEE..E--TT--HHHHHHHHHHHHHHHHHHHHHHHHH CS
  Polyketide_cyc2  87 nyvatwtvtpdggg.trvtwtgefda..gplggpfekpaaakavkgdleagLerLkarle 143
                      + + t +++  g++ t+vt ++++++  gplg+ ++k+ +ak  ++ +e++L + + +le
       EPA05493.1  92 HWKITNEFKSLGANlTKVTMSVDYAMpfGPLGAILDKAKFAKSAERGMETALYNVRGLLE 151
                      99**********999**********77899999999999***********9999887765 PP

>> AHSA1  Activator of Hsp90 ATPase homolog 1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.0   4.6e-11   2.7e-07       1     117 [.      11     143 ..      11     151 .. 0.79

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 4.6e-11
                 SS-HHHHHHHHH-HHHHHHH.....EEEEEEEE--ST....TEEEEEEETTTSEEEEEEEEEEEEETTTEEEEEEEEETSETEEEEEEEEEEEE.ETTE CS
       AHSA1   1 dapperVfraltdpellkrW.....ftlteaemdlrp....Ggkfrlrdspdgkefgnegeylevvpperlvytwrledepeeeestvtielee.eggg 89 
                 ++p+e Vf ++ +pe++          +t++ md+++    G +fr+  +  gk+ ++ +e +e v++er++ + + e  p  +++++t e++    + 
  EPA05493.1  11 KTPVENVFTYFARPEHVSDQikndtVGMTVIPMDIKEgmgvGTTFRIIGDFSGKRLEWDCETTEFVRNERISAK-QIE-GP-FKHWKITNEFKSlGANL 106
                 58****************9889999999999999988777799****8889***********************.444.34.679*********77777 PP

                 EEEEEEE.........EEEEHCHHHHHHHHHHHHHHH CS
       AHSA1  90 Trltlth.........tglprkqkeeegveeGweqsl 117
                 T++t++            + +k+k ++ +e G+e++l
  EPA05493.1 107 TKVTMSVdyampfgplGAILDKAKFAKSAERGMETAL 143
                 *****98777766665333333333333666666655 PP

>> Polyketide_cyc  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   2.7e-10   1.6e-06       4     117 ..      13     129 ..      10     142 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 2.7e-10
                     -HHHHHHHHTTTGGCCSCCCCEE.EEEE.SSSEE....E....EEECSTTSSCEEEEEEEEEEETTT.EEECTTCCCCCEEEEEEEECTECCEEE CS
  Polyketide_cyc   4 padqvyalvadvesypeflphcs.svevleeaes.glsa....dlevgfggltesftarvtldppee.itfklvegdfkslegkWtieslppnsg 91 
                     p++ v+ + a+ e+ ++ +++ +  ++v+  + + g+ +    +    f g + +++ + t+ + +e i  k++eg+fk+ +++ +++sl+    
      EPA05493.1  13 PVENVFTYFARPEHVSDQIKNDTvGMTVIPMDIKeGMGVgttfRIIGDFSGKRLEWDCETTEFVRNErISAKQIEGPFKHWKITNEFKSLG---- 103
                     777777777777777777776442466666665553333444455667999***********999999***********************.... PP

                     CEEEEEEEEEEEE-SSCHHHHHHHHH CS
  Polyketide_cyc  92 gtrtkvalevdfkfaspllgalvgqv 117
                     ++ tkv+++vd+ + +++lga++ ++
      EPA05493.1 104 ANLTKVTMSVDYAMPFGPLGAILDKA 129
                     9*******************999776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1275.85
//
Query:       EPA05494.1  [L=197]
Description: hypothetical protein BG20_I0255 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       863  (0.0481343); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.33s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1202.99
//
Query:       EPA05495.1  [L=214]
Description: CobQ/CobB/MinD/ParA nucleotide binding domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.3e-16   60.0   0.0    3.8e-16   59.3   0.0    1.4  1  CbiA        CobQ/CobB/MinD/ParA nucleotide binding domain
      2e-15   57.2   0.1    1.6e-14   54.2   0.1    1.9  1  AAA_26      AAA domain
    7.1e-05   22.7   0.0     0.0015   18.4   0.0    2.2  2  MobB        Molybdopterin guanine dinucleotide synthesis prot
    0.00037   20.2   0.4       0.39   10.3   0.1    2.2  2  SRP54       SRP54-type protein, GTPase domain
     0.0067   16.3   0.0       0.06   13.3   0.0    2.0  2  NTPase_1    NTPase
  ------ inclusion threshold ------
      0.014   15.9   0.1       0.02   15.4   0.1    1.3  1  AAA_23      AAA domain
      0.015   15.7   0.0      0.016   15.6   0.0    1.3  1  AAA_16      AAA ATPase domain
      0.019   14.5   0.0       0.16   11.5   0.0    2.0  2  CBP_BcsQ    Cellulose biosynthesis protein BcsQ
      0.034   14.1   1.3       0.14   12.0   0.7    2.1  1  AAA_31      AAA domain
      0.042   13.7   0.5      0.042   13.7   0.5    2.0  2  DUF1533     Protein of unknown function (DUF1533)
      0.049   12.6   0.1      0.061   12.3   0.1    1.1  1  SelA        L-seryl-tRNA selenium transferase
      0.065   13.1   0.0      0.089   12.7   0.0    1.2  1  APS_kinase  Adenylylsulphate kinase
       0.07   12.7   0.1       0.81    9.2   0.0    2.1  2  cobW        CobW/HypB/UreG, nucleotide-binding domain
      0.095   12.4   0.2       0.12   12.1   0.2    1.5  1  PRK         Phosphoribulokinase / Uridine kinase family
       0.14   11.4   0.0       0.21   10.9   0.0    1.3  1  VirC1       VirC1 protein
       0.17   11.6   0.0       0.19   11.4   0.0    1.4  1  AAA_30      AAA domain


Domain annotation for each model (and alignments):
>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.3   0.0   3.4e-19   3.8e-16       1     101 [.       4     213 ..       4     214 .] 0.93

  Alignments for each domain:
  == domain 1  score: 59.3 bits;  conditional E-value: 3.4e-19
                 EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH............................................. CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................................. RF
        CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep............................................. 54 
                 ++i++t++G+GKTtl+a+L+r++a++g+ V++++ ++++n +   +  e+ +++                                             
  EPA05495.1   4 LMIQGTSSGSGKTTLVAALCRIFADKGFSVAPFKSQNMSNYAYKTHDFEISRAQaiqaiaarckitsdlnpillkplgnyfsdvylngkkfkkmhasdy 102
                 69************************************8887645566666666999****************************************** PP

                 ..............................................................CCHCCCHHHHHHCHCHHHH.......EEEEEEEEESS CS
                 ..............................................................xxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxx RF
        CbiA  55 ..............................................................dlkrllellealgkkkall.....lkiagvvlnrvdg 86 
                                                                               d++r ++++++++++++ll       i+g+v+n+++g
  EPA05495.1 103 ykkfvntqgikiatkslkslqknydlvilegagspteinldkfdianmkmaeisnssvllvtDIDR-GGSFASIVGTMSLLdkrhqKFIKGFVINKFRG 200
                 **************************************************************9999.8999999999888899998999********** PP

                 ...-TTCHHHHHHHH CS
                 xxxxxxxxxxxxxxx RF
        CbiA  87 eneetllkealeelk 101
                 +  +  lk +++++k
  EPA05495.1 201 D--IDILKPGFKKIK 213
                 *..999999888876 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.2   0.1   1.4e-17   1.6e-14       1     170 [.       2     201 ..       2     213 .. 0.76

  Alignments for each domain:
  == domain 1  score: 54.2 bits;  conditional E-value: 1.4e-17
      AAA_26   1 rtifvtgtdtgvGKTvvslgLvralkrkgvkvgyfKPiqtgie.......ededselikellgldqtyelpeplals...aplspelaarqegedidle 89 
                 +++++ gt+ g+GKT++ ++L+r++ +kg++v+ fK  +  +        e ++++ i+ ++   + +++++p++l+   +++s+  +  ++ ++ + +
  EPA05495.1   2 KSLMIQGTSSGSGKTTLVAALCRIFADKGFSVAPFKSQNMSNYaykthdfEISRAQAIQAIAARCKITSDLNPILLKplgNYFSDVYLNGKKFKKMHAS 100
                 689*********************************976666644544442225555555555445555677777761112334444444443333333 PP

      AAA_26  90 kiv................kelekdadivvVEGagglgvpitee..llnadiaknlgapvilVarggl.gtinqllltiealrqknvr.vlGvilNkvr 168
                 ++                 k+l+k++d+v+ EGag+  +  +++    n ++a+  ++ v+lV+ +++ g+++ ++ t+++l +++ + ++G ++Nk+r
  EPA05495.1 101 DYYkkfvntqgikiatkslKSLQKNYDLVILEGAGSPTEINLDKfdIANMKMAEISNSSVLLVTDIDRgGSFASIVGTMSLLDKRHQKfIKGFVINKFR 199
                 3334445999999999999****************99988777665789*****************9956************8766655********98 PP

      AAA_26 169 np 170
                  +
  EPA05495.1 200 GD 201
                 76 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.3e-06    0.0015       4      37 ..       6      40 ..       3      65 .. 0.84
   2 ?    2.3   0.0      0.13   1.5e+02      81      98 ..     116     133 ..      96     164 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.3e-06
        MobB  4 ivgk.sgsGKTtLleklipelkarglrvgtiKhah 37
                i g+ sgsGKTtL+  l ++++++g++v+  K ++
  EPA05495.1  6 IQGTsSGSGKTTLVAALCRIFADKGFSVAPFKSQN 40
                5554389**********************999865 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.13
        MobB  81 leellarlsevDlvlvEG 98 
                 ++ l +  +++Dlv+ EG
  EPA05495.1 116 TKSLKSLQKNYDLVILEG 133
                 44444444679******9 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.1   0.00035      0.39       4      33 ..       4      34 ..       1      37 [. 0.84
   2 !    8.3   0.1    0.0015       1.7      59     127 ..     102     170 ..      92     201 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00035
                EEEEES.TTSSHHHHHHHHHHHHHHTTS-EE CS
       SRP54  4 illvGl.qGaGKTttlaKLaallkkegkkvl 33
                +++ G+  G+GKTt +a L +++ ++g +v+
  EPA05495.1  4 LMIQGTsSGSGKTTLVAALCRIFADKGFSVA 34
                67777536*****************999875 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0015
                 EEESSTTSCHHHHHHHHHHHHHHTTSSEEEEEE--SSTTHHHHHHHHHHHHHHH.SSSEEEEEEETTBHT CS
       SRP54  59 vikkkeeadpaavakeavekakeekidvvlvDTaGrlqndkelmeelkkikkvv.kpdevllvldattgq 127
                 ++kk  +++ +++a +++++ ++ ++d+v++  aG   + +    +++++k +  ++ +vllv d   g 
  EPA05495.1 102 YYKKFVNTQGIKIATKSLKSLQK-NYDLVILEGAGSPTEINLDKFDIANMKMAEiSNSSVLLVTDIDRGG 170
                 55666677889999999999987.99*********86654444445555554433888999999976665 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   5.3e-05      0.06       7      40 ..      10      43 ..       3      67 .. 0.84
   2 ?    1.2   0.0      0.28   3.1e+02      76     132 ..     107     164 ..      85     195 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.3e-05
                -TTSSHHHHHHHHHHHH...GGGEEEEEEEEE-- CS
    NTPase_1  7 ppGvGKtTlvkkvlellkssgvkvgGfyteevre 40
                ++G+GKtTlv  +++  +++g++v+ f  +++ +
  EPA05495.1 10 SSGSGKTTLVAALCRIFADKGFSVAPFKSQNMSN 43
                57***********************999988875 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.28
                 E-HHHHHHHHHHHHHHHHHHH-EEEE---S.TTGGG-HHHHHHHHHHHT.TTSEEEEE- CS
    NTPase_1  76 vdvesfeelalealrkalseadviviDEiG.kmElkskkfkeaveevLk.sekpvlavi 132
                 v+++   ++a ++l+  +++ d++++   G + E +  kf  a  ++ + s+  vl v 
  EPA05495.1 107 VNTQG-IKIATKSLKSLQKNYDLVILEGAGsPTEINLDKFDIANMKMAEiSNSSVLLVT 164
                 44333.46789999999999999999999855888888888777777777777766664 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.1   1.8e-05      0.02      28      87 ..      11     104 ..       9     168 .. 0.59

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.8e-05
      AAA_23  28 NGaGKTTildAiklaLyget...prlsrks..grgfeksdveiesegkvkay.veltfenkdgry............................t 87 
                  G+GKTT++ A++ ++  +    +++++++  +  ++++d+ei+     +a+ ++++++++ +                              +
  EPA05495.1  11 SGSGKTTLVAALCRIFADKGfsvAPFKSQNmsNYAYKTHDFEISRAQAIQAIaARCKITSDLNPIllkplgnyfsdvylngkkfkkmhasdyyK 104
                 59***********999774322455555556555777999999887555555555554433333244444433333333333333333333333 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.0   1.4e-05     0.016      33      86 ..      11      63 ..       2     148 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.4e-05
      AAA_16 33 sGvGKsslvrellralekdggiflrgkcdqlesaipy.........salaqalareellrqll 86
                sG+GK++lv +l r + ++g+ ++  k +   s+ +y         ++ +qa+         +
  EPA05495.1 11 SGSGKTTLVAALCRIFADKGFSVAPFKSQNM-SNYAYkthdfeisrAQAIQAI---------A 63
                8************999999988888888887.555552222222213444444.........3 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00014      0.16       1      33 [.       1      33 [.       1      66 [. 0.90
   2 ?    0.9   0.0      0.23   2.6e+02     103     140 ..     113     150 ..      94     164 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00014
    CBP_BcsQ  1 mkvlalqGvRGGvGttsllaaLawalhelgesv 33
                mk l++qG   G G+t+l+aaL + +   g sv
  EPA05495.1  1 MKSLMIQGTSSGSGKTTLVAALCRIFADKGFSV 33
                999********************9999888776 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.23
    CBP_BcsQ 103 eallaalkelkeqyrwillDlpagasaltrellaladl 140
                 +  ++ lk+l+++y++++l+    ++++  +    a++
  EPA05495.1 113 KIATKSLKSLQKNYDLVILEGAGSPTEINLDKFDIANM 150
                 5567889999********98777776666666655555 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.7   0.00013      0.14       9     124 ..       9     132 ..       1     142 [. 0.58

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
      AAA_31   9 qKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgiekne.iektlyevlieeknikeaiiktkvenldlipssidLaeaeielvelekk... 103
                    G GKTT + +l+  +a +g  v        +n   +++++  e    + +++++ +++i + ++    + l    s++ L + + + +++++    
  EPA05495.1   9 TSSGSGKTTLVAALCRIFADKGFSVAPFKSQNMSNY--AYKTHDFEiSRAQAIQAIAARCKITSDLNPILLKPLGNYFSDVYLNGKKFKKMHASDYykk 105
                 55699*****************99876555444444..4444333322334444444555555554433333333333444444433333333333333 PP

      AAA_31 104 ......eeilkellekvkdeYDyiiiD 124
                        +i ++ l++++++YD++i+ 
  EPA05495.1 106 fvntqgIKIATKSLKSLQKNYDLVILE 132
                 333333334699*************86 PP

>> DUF1533  Protein of unknown function (DUF1533)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.5   3.7e-05     0.042       9      44 ..      85     125 ..      80     131 .. 0.87
   2 ?   -1.7   0.1       2.6   2.9e+03      29      40 ..     200     211 ..     191     214 .] 0.76

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.7e-05
     DUF1533   9 sevtvNGkkl......ennkyslssigkLklkasvfnkaGen 44 
                 s+v++NGkk       ++ k  ++ +g +k+ ++++++  +n
  EPA05495.1  85 SDVYLNGKKFkkmhasDYYKKFVNTQG-IKIATKSLKSLQKN 125
                 79**************999999*9***.********986544 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.6
     DUF1533  29 gkLklkasvfnk 40 
                 g++++ +  f+k
  EPA05495.1 200 GDIDILKPGFKK 211
                 569999999987 PP

>> SelA  L-seryl-tRNA selenium transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   5.4e-05     0.061     140     208 ..      94     164 ..      80     198 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.4e-05
                 EEEE---SEE...EEES-B---HHHHHHHHHHHT--EEEEEES-B-S-GGGGT-----BHHHHHHTT-SEEE CS
        SelA 140 llkvhtsnyr...ieGftkevelaeLvelgkekglpvleDlGsGllvdlseyglskePtvqealaeGvdlvs 208
                 + k+h s+y+   +     ++ ++ L++l k+++l++le +Gs + ++l+++ + +  ++ e  ++ v lv+
  EPA05495.1  94 FKKMHASDYYkkfVNTQGIKIATKSLKSLQKNYDLVILEGAGSPTEINLDKFDIANM-KMAEISNSSVLLVT 164
                 568999999722222233467899*****************************9874.44555555555555 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   7.9e-05     0.089      10     110 ..      10     110 ..       2     128 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.9e-05
                 STTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT--SSHHHHHHHHHHHHHHHHHHHHTT-EEEEE----SHH...HHHHHHHHHHCHTEEEEE CS
  APS_kinase  10 lsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdLgfseedRkenirrvaevaklladaglivlvafisPyre...eReaarelleealkfiev 105
                  sgsGK+t+  al +   +kg sv     +n+ +  +k   f+   R++ i+ +a   k  +d + i l  +   +++   + ++ +++++   ++++ 
  EPA05495.1  10 SSGSGKTTLVAALCRIFADKGFSVAPFKSQNMSNYAYKTHDFE-ISRAQAIQAIAARCKITSDLNPILLKPLGNYFSDvylNGKKFKKMHA--SDYYKK 105
                 479******************************9999999996.57999999999999999999999887654444441113344444444..356666 PP

                 EEE-- CS
  APS_kinase 106 fvdtp 110
                 fv+t+
  EPA05495.1 106 FVNTQ 110
                 66665 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00072      0.81       7      27 ..       9      29 ..       3      39 .. 0.77
   2 ?    1.4   0.0      0.19   2.1e+02      72      99 ..     115     140 ..     104     195 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00072
                ESTTCCHHHHHHHHHCT--SS CS
        cobW  7 GflGsGKTtLlnhllenragl 27
                 + GsGKTtL+ +l++  a++
  EPA05495.1  9 TSSGSGKTTLVAALCRIFADK 29
                467**********99655544 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.19
                 HHHHHHHHHTT-SEEEEEECTTTTHHHH CS
        cobW  72 elealeereerldviliEttGlaePapv 99 
                 + ++l+++++++d++++E  G   P+++
  EPA05495.1 115 ATKSLKSLQKNYDLVILEGAGS--PTEI 140
                 5566777778899999997774..5555 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   0.00011      0.12       6      53 ..       9      56 ..       5     191 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00011
         PRK  6 gsSGaGkttvarklekifgrekvkaaeiegdsflrldraekdleleer 53
                 sSG+Gktt+ ++l  if+ ++   a  + + + ++    +d e+ ++
  EPA05495.1  9 TSSGSGKTTLVAALCRIFADKGFSVAPFKSQNMSNYAYKTHDFEISRA 56
                58*****************88777554444444444333333333333 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00018      0.21       8      40 ..       8      40 ..       1      77 [. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00018
       VirC1  8 slkGGaGkttalmglcsalasdgkrvalfeade 40
                    G+Gktt + +lc  +a +g  va f++ +
  EPA05495.1  8 GTSSGSGKTTLVAALCRIFADKGFSVAPFKSQN 40
                55679************************9865 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00017      0.19      26      52 ..      10      36 ..       2     167 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00017
      AAA_30 26 pAGtGKttalkalreaweaaggrvigl 52
                  G+GKtt+++al ++++++g++v+ +
  EPA05495.1 10 SSGSGKTTLVAALCRIFADKGFSVAPF 36
                47*******************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.63u 0.37s 00:00:01.00 Elapsed: 00:00:00.56
# Mc/sec: 1145.30
//
Query:       EPA05496.1  [L=79]
Description: hypothetical protein BG20_I0253 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.33s 00:00:00.84 Elapsed: 00:00:00.53
# Mc/sec: 448.90
//
Query:       EPA05497.1  [L=40]
Description: hypothetical protein BG20_I0222, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       222  (0.0123822); expected 358.6 (0.02)
Passed bias filter:                      111  (0.00619109); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.31s 00:00:00.73 Elapsed: 00:00:00.49
# Mc/sec: 247.63
//
Query:       EPA05498.1  [L=339]
Description: hypothetical protein BG20_I0276 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-11   44.3   0.1    9.2e-11   42.0   0.0    2.2  2  Glyco_tran_28_C  Glycosyltransferase family 28 C-terminal dom
    3.3e-07   29.9   0.0    0.00038   19.8   0.0    2.1  2  Glyco_trans_1_3  Glycosyl transferase family 1
  ------ inclusion threshold ------
      0.012   16.0   0.0       0.08   13.4   0.0    2.1  2  Glyco_trans_1_4  Glycosyl transferases group 1
      0.051   13.9   0.4       0.08   13.2   0.4    1.3  1  CCDC117          Coiled-coil domain-containing protein 117


Domain annotation for each model (and alignments):
>> Glyco_tran_28_C  Glycosyltransferase family 28 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.26   1.2e+03      64      77 ..     143     156 ..     107     157 .. 0.84
   2 !   42.0   0.0     2e-14   9.2e-11       5     113 ..     199     295 ..     194     334 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.26
                      SSHHHHHHHH-EEE CS
  Glyco_tran_28_C  64 dkmaeaikaadLvI 77 
                      ++m+++ik+ d+vI
       EPA05498.1 143 KSMQSIIKKCDVVI 156
                      67999999999998 PP

  == domain 2  score: 42.0 bits;  conditional E-value: 2e-14
                      EE-SSSHHHHHCCCTSHHHHHHHHHHHHCHHHCCT-EEC---STT-TTTTCEEEEEESSSSHHHHHHHH-EEEECS-CHHHHHHHHTT--EEEE CS
  Glyco_tran_28_C   5 tGGSqgaeaLnelvlselkllelksrelqvlhqtGkreleevkikveeltlkvevfefidkmaeaikaadLvIsRAGagtiaEllalgkplIlv 98 
                      +GG+   + L+e  l+  ++l++    + v+  +G++ +++ + +  +l+       f++++ e+i aad+++s AG +ti E+ a+g p I++
       EPA05498.1 199 IGGTDAGLFLIEKTLETITKLNQD---VDVIVVSGPSLSKKFDGSIRNLG-------FVNNLHEIIFAADVIVSLAGKSTIDESKAYGTPGIFI 282
                      689999999999999999999998...************99999999995.......************************************* PP

                      --TT....S-HHHHH CS
  Glyco_tran_28_C  99 plpeaaenhqdnNak 113
                      p + +   +q+ Na+
       EPA05498.1 283 PIKGHF--EQEDNAR 295
                      ****99..9999996 PP

>> Glyco_trans_1_3  Glycosyl transferase family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   8.5e-08   0.00038      11     123 ..      12     123 ..       8     161 .. 0.77
   2 !    8.0   0.0   0.00035       1.5     246     292 ..     245     295 ..     236     304 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 8.5e-08
  Glyco_trans_1_3  11 GaGhasRsrvvlehLarghevkvvvsgraldvLeke.fdvneivglsivyeenrvrklktllknlqvaaklaknvkalvelv.edfrpdlvvtD 102
                      G Gh +R  +v+++  ++   k+v+ g a++ L++  f+v + +   +   en v k+ t +  l    +  k+ k++ +++ ed +p++v++D
       EPA05498.1  12 GLGHVTRDIAVANNF-QNISTKFVTGGGATKILKNLeFKVEDKYIPPQFIVENGVLKNSTRW--LWNYYQYYKRCKKIAKKIiEDDNPKIVISD 102
                      89*********9997.66788************87548***999988888889888888754..44444455555555555549********** PP

  Glyco_trans_1_3 103 FealtallakrhkLPvisvdn 123
                       +  +  +a++ k+P + + +
       EPA05498.1 103 EDFASLTIAQKEKMPTVLITD 123
                      999999*********987754 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00035
  Glyco_trans_1_3 246 gFleDLa....taraviagagftLmtealyLkkPlLavPvarqFeqvlnal 292
                      gF+++L     +a  +++ ag + + e+   + P + +P+++ Feq  na+
       EPA05498.1 245 GFVNNLHeiifAADVIVSLAGKSTIDESKAYGTPGIFIPIKGHFEQEDNAR 295
                      6666665222257889999***************************99986 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.21   9.4e+02      63      80 ..     140     159 ..      91     170 .. 0.74
   2 ?   13.4   0.0   1.8e-05      0.08      19     125 ..     207     308 ..     193     317 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.21
                      -..THHHHHHHH-SEEEE-- CS
  Glyco_trans_1_4  63 v..edlaellaaadvfvaPs 80 
                         ++++++++++dv+++P 
       EPA05498.1 140 KmnKSMQSIIKKCDVVIIPE 159
                      34456999999999999995 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 1.8e-05
                      HHHHHH.HHHH.HH..EEEEEES---..HHHHHHHTT-T.TEEEE---THHHHHHHH-SEEEE-----SHHHHHHHHTT-EEEE-TGGGTTT-- CS
  Glyco_trans_1_4  19 llleav.pllrkkd..vrlvivGdgprpeeleelaagleerveftGfvedlaellaaadvfvaPsegfglkllEamaaglpvVatdvggiaevv 109
                      +l+e+  + + k +  v +++v  gp   +l ++ +    +++ +Gfv++l e++ aadv v      + ++ E+ a+g+p +  +++g  e  
       EPA05498.1 207 FLIEKTlETITKLNqdVDVIVVS-GP---SLSKKFD---GSIRNLGFVNNLHEIIFAADVIVSLAG--KSTIDESKAYGTPGIFIPIKGHFEQE 291
                      56666656666332349999999.74...4554443...68*********************9873..67999**************9866622 PP

                      ...TTSSEE--TT-HHHHH CS
  Glyco_trans_1_4 110 ...gengllvppgdpeala 125
                           +g++++  d ++l 
       EPA05498.1 292 dnaRGEGFVFD--DINKLD 308
                      32213468876..555554 PP

>> CCDC117  Coiled-coil domain-containing protein 117
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.4   1.8e-05      0.08      11      62 ..      93     146 ..      83     188 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.8e-05
     CCDC117  11 EiEdRiilEDee..dleadsvsrrPvLvlsDslkeglkrgiddiltkkviesvs 62 
                 + + +i++ De+   l + + ++ P++++ D++++++  gi   + kk+ +s++
  EPA05498.1  93 DDNPKIVISDEDfaSLTIAQKEKMPTVLITDIVQTNFVSGITSFIEKKMNKSMQ 146
                 3445899999998899999******************************99996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1062  (0.0592336); expected 358.6 (0.02)
Passed bias filter:                      628  (0.0350271); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.65u 0.33s 00:00:00.98 Elapsed: 00:00:00.53
# Mc/sec: 1926.82
//
Query:       EPA05499.1  [L=146]
Description: hypothetical protein BG20_I0266 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.059   13.2   0.0        4.5    7.2   0.0    2.4  2  PKD       PKD domain


Domain annotation for each model (and alignments):
>> PKD  PKD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0   0.00025       4.5      45      68 ..      73      96 ..      67      98 .. 0.91
   2 ?    3.6   0.0    0.0034        61      25      51 ..      99     136 ..      97     137 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00025
                EEEEEE-SSEEEEEEEEEE-SS-E CS
         PKD 45 tvthtYlspGeYeVtvtasnavgs 68
                +v +++++pG++ V+v + +++g+
  EPA05499.1 73 EVDYVWKNPGNHIVKVDLYDMDGN 96
                6899*************9999987 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.0034
                 -SEEEEE--SS...........--EEEEETTEEEEEE- CS
         PKD  25 nvtysWdfgdg...........svvqvlseptvthtYl 51 
                 ++tys+++  +           + ++++ +  v+++Yl
  EPA05499.1  99 ILTYSFNMSTQspfgyifiiaiTIGAITLGVVVSYIYL 136
                 589*********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.33s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 841.28
//
Query:       EPA05500.1  [L=69]
Description: hypothetical protein BG20_I0232 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1053  (0.0587317); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.32s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 424.97
//
Query:       EPA05501.1  [L=353]
Description: S-methyl-5-thioribose-1-phosphate isomerase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-86  289.6   1.3      3e-86  289.1   0.8    1.4  2  IF-2B     Initiation factor 2 subunit family


Domain annotation for each model (and alignments):
>> IF-2B  Initiation factor 2 subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0     0.091   1.6e+03      82     126 ..       7      51 ..       3      54 .. 0.79
   2 !  289.1   0.8   1.7e-90     3e-86       2     282 .]      54     340 ..      53     340 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.091
                 HHHHHHHHHHHHHHHHHHHHHTTC-TTEEEEEES--SHHHHHHHH CS
       IF-2B  82 kikelikeieeadekigdiaaelikdgdtilTicnsktvlevlra 126
                 ki++ ++ +e +d+k++ i ++++ ++ + +T+ + + v + +r+
  EPA05501.1   7 KIHSSLRTVEWKDNKVIMIDQTKLPNQLVFVTYDDFNQVADAIRT 51 
                 666777778888999999999999999999999887777777776 PP

  == domain 2  score: 289.1 bits;  conditional E-value: 1.7e-90
                 S-SHHHHHHHHHHHHHHHHHHCCCSTHHHHHHHHHHHHHHHHTSSTS-HHHHHHHHHHHHHHHCCTTTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
       IF-2B   2 vrGspaiaiaalevllevikdaktskvaeLkeelrkaidlLkkarPtavslgnairrllkeiselksssdvkeakksliekikelikeieeadekigdi 100
                 vrG+pai+++++ +l+ +  ++k ++ +eL ++l+ka + L ++rPtav+l + ++ ++k      s ++ +++k+s+i++ k++++e+ e+++ +g++
  EPA05501.1  54 VRGAPAIGVSGAFGLALASLQSKSTTKEELLSDLEKARKILFETRPTAVNLKWGLDKIMK---VARSGNTIEQIKQSVINESKKMAEEDIEINKSMGKN 149
                 79**********************************************************...5699******************************** PP

                 HHTTC-TTEEEEEES--SH........HHHHHHHHHHTTEEEEEEEEEXTTTTHH.HTHHHHHHHTTXEEEEEEGGGHHHHHHC.TESEEEEEXSEEET CS
       IF-2B 101 aaelikdgdtilTicnskt........vlevlraaakekkkfkVivvEsrPrlqG.rltakeLvqagipvtlitdsavayvmse.evdkvivGAdrile 189
                 ++ l+ d+dti+T+cn+++        +l+v+ra ++++k++kVi++E+rP  qG rlta eL+++g +v li+d+av+y m +  v+kvivGAdri++
  EPA05501.1 150 GSVLFDDNDTIMTHCNAGAlatvaygtALGVIRATRESGKNVKVIATETRPIQQGsRLTAFELKHDGFDVSLIPDTAVGYSMANgLVNKVIVGADRIVR 248
                 *************************************************************************************************** PP

                 TSEEEEETTHHHHHHHHHHTTXEEEEEXXGGGBESTSSSGGGSSXXBEXTHHHHEETTEESSTTTEEEEEBSEEEEEGGGXSEEEETTEEEXC CS
       IF-2B 190 nGaiankiGTsslAvlAkefnipvlvvaeslkfservqldedifieerdpeellnitgeriaeeelkvvnpafDvtPpelItliITevGvlpp 282
                  G ++nkiGT+++A +Ak++ ip++v+a++++f+ + +  +d++ie+r+  e++ i ++++a+ +++v+npafD+tPpelI++iITe+Gv +p
  EPA05501.1 249 TGHVFNKIGTYQVATMAKQHGIPFYVAAPLSTFDMK-SDAKDVIIEMRKGVEVTGIGDKKTAPDDINVINPAFDMTPPELISGIITEKGVAKP 340
                 ************************************.66777999*********************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2532.50
//
Query:       EPA05502.1  [L=112]
Description: hypothetical protein BG20_I0223 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.4e-08   33.2   0.1    6.1e-08   32.7   0.1    1.1  1  PAC4       Proteasome assembly chaperone 4
  ------ inclusion threshold ------
      0.029   14.1   0.1      0.039   13.7   0.1    1.3  1  Chlam_vir  Pgp3 C-terminal domain


Domain annotation for each model (and alignments):
>> PAC4  Proteasome assembly chaperone 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.1   6.8e-12   6.1e-08       2      77 ..      19      87 ..      18      89 .. 0.87

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 6.8e-12
        PAC4  2 lhlqltrladsillwvgtasskeasplgslvvAmpsrtnkktptisTtLlgdgsde.aserlAqrLArRlgkqvfvS 77
                + lq++++++ +++ ++++s k    lgs+vv++ + ++   p i+Tt++++ +++ + +  A r++ R++   +vS
  EPA05502.1 19 FSLQILKFENGYFVSITEGSCK----LGSMVVSLATGPS---P-ITTTIIPSRTESlFLKLTAERISTRMKGIAVVS 87
                679***************9855....6*********998...6.9********555599***********8666665 PP

>> Chlam_vir  Pgp3 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   4.3e-06     0.039      25      63 ..      48      87 ..      28     103 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.3e-06
   Chlam_vir 25 llggteigkftvtpdnadsmfl.isadiiasrmegtvvla 63
                l  g    + t+ p  ++s+fl ++a+ i++rm+g  v++
  EPA05502.1 48 LATGPSPITTTIIPSRTESLFLkLTAERISTRMKGIAVVS 87
                55555556789**********9789**********76654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 758.56
//
Query:       EPA05503.1  [L=309]
Description: protoheme IX farnesyltransferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.9e-41  140.2  21.5      9e-41  139.8  21.5    1.1  1  UbiA      UbiA prenyltransferase family


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.8  21.5     5e-45     9e-41       2     249 ..      25     291 ..      24     303 .. 0.89

  Alignments for each domain:
  == domain 1  score: 139.8 bits;  conditional E-value: 5e-45
        UbiA   2 lipalvglalaaggspdl....llllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispk.ealifaivllilgllll.......alll 88 
                 l+++++g++l+a +  ++    ++++l+l+ +++ +aaan+l +y Dr+iDa+mert+nRPl+s ri+p+ +a+ f+++l+ ++l+l+       ++  
  EPA05503.1  25 LVFTAFGATLTASNIYNIeislPTWALMLFSVAAGSAAANTLTNYHDRDIDAIMERTKNRPLPSKRIHPAeKARNFGLALAGISLVLAfaisfttTFEQ 123
                 77888888888888888777889*********************************************7626788*************99999999999 PP

        UbiA  89 npltallgllallly.vvYtglrlKrrtllgtvvggiafglppllgwaa.vtgslsllalllalavflltwaialandlrdregDrkagiktlpvvlGr 185
                 + ++ ++++++l+   +vY+ ++lKr +  ++++gg+++g pp++gw+a +t +l+ + l++a +vf+++  +++a  l+ +e++ k+++++l++v  +
  EPA05503.1 124 GIWATAFIAFGLVNNiLVYS-YMLKRNSRTNIILGGLCGGSPPMIGWVAvTTTDLWTMGLAMAGLVFIWIPMHIWALTLHFKEDYNKVNVPMLTAVQSE 221
                 9999999999999999****.8***************************88889999999999999**********9********************99 PP

        UbiA 186 kaarillalllavllla.......llllllalllllylllalllaalallraarlvrrrdakkaakfflfl 249
                 k++++ +a  ++v++l+        +  +  +++++yl+ a++++al++  +++++++  +k+a+ +f ++
  EPA05503.1 222 KTSARAIAGSTFVMVLFslapfflTTESGEPMVGSVYLWTAIASGALMIGLSVWVIAKPMEKAAWTLF-KF 291
                 99999866666666666655654444555678999*************************99999999.43 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       768  (0.0428356); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 2354.27
//
Query:       EPA05504.1  [L=129]
Description: putative sporulation initiation phosphotransferase F [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-24   86.2   1.1    1.9e-24   86.0   1.1    1.1  1  Response_reg  Response regulator receiver domain
     0.0061   16.6   0.1       0.21   11.7   0.0    2.3  2  HydF_dimer    Hydrogen maturase F dimerization domain


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.0   1.1   2.1e-28   1.9e-24       1     111 [.       5     115 ..       5     116 .. 0.96

  Alignments for each domain:
  == domain 1  score: 86.0 bits;  conditional E-value: 2.1e-28
                   EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEESSTS.HHHHHHHHHCTESE CS
  Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviiltahse.eedavealkagadd 96 
                   +l+v+Dd ++++l +++l+ + y +v +a++g ea+ ++k+ ++dl+++D nm++mdG+e++++i + d++ +v+i+t++s+ ++  ++al+ g   
    EPA05504.1   5 ILVVEDDVDLLDLYEEVLQANAY-NVVKATNGLEAISKYKKAQPDLVVMDGNMSEMDGYEAFSKIIKIDKDARVVIVTGYSNsDPKSKKALEQGLIA 100
                   8**********************.999***************************************************888768999********** PP

                   EEESSG-HHHHHHHH CS
  Response_reg  97 flsKpfdpeeLlkal 111
                   ++sKp+ ++ Ll+ +
    EPA05504.1 101 IISKPVGIDTLLDVV 115
                   ***********9877 PP

>> HydF_dimer  Hydrogen maturase F dimerization domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   2.3e-05      0.21      37      73 ..      20      56 ..      15      64 .. 0.91
   2 ?    2.6   0.0     0.016   1.5e+02       6      31 ..      71      96 ..      67     122 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.3e-05
  HydF_dimer 37 dilDekaiavvvkeseleaalkslkrkpklvitDsqv 73
                ++l ++a++vv   + lea+ k  k +p+lv+ D ++
  EPA05504.1 20 EVLQANAYNVVKATNGLEAISKYKKAQPDLVVMDGNM 56
                7999******************************876 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.016
  HydF_dimer  6 vepgdlvvlvvpidseaPkgRlilpq 31
                ++++  vv+v+   ++ Pk +  l q
  EPA05504.1 71 IDKDARVVIVTGYSNSDPKSKKALEQ 96
                56667788888888888887766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       693  (0.0386525); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1021.25
//
Query:       EPA05505.1  [L=65]
Description: ribosomal protein S27 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.5e-18   64.2   1.2    7.8e-18   63.9   1.2    1.0  1  Ribosomal_S27e  Ribosomal protein S27
    0.00033   20.0   2.3       0.24   10.9   0.2    2.2  2  zf-ribbon_3     zinc-ribbon domain
     0.0014   18.6   0.5     0.0016   18.4   0.5    1.1  1  Zn_Tnp_IS91     Transposase zinc-binding domain
     0.0047   16.4   0.9     0.0058   16.1   0.9    1.2  1  TF_Zn_Ribbon    TFIIB zinc-binding
     0.0076   16.2   2.7       0.04   13.9   2.9    1.9  1  zinc_ribbon_6   Zinc-ribbon
     0.0099   15.7   0.6      0.014   15.3   0.6    1.2  1  C1_1            Phorbol esters/diacylglycerol binding domain 
  ------ inclusion threshold ------
      0.015   15.2   0.9        1.3    9.1   0.0    2.2  2  YhfH            YhfH-like protein
      0.023   14.7   0.3        6.6    6.8   0.0    2.2  2  zf-dskA_traR    Prokaryotic dksA/traR C4-type zinc finger
       0.03   14.3   4.9       0.29   11.2   0.5    2.3  2  zf-BED          BED zinc finger
      0.035   14.2   1.1      0.063   13.4   1.1    1.5  1  Zn-ribbon_8     Zinc ribbon domain
      0.038   14.0   0.5      0.044   13.8   0.5    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.044   13.9   2.4      0.056   13.6   2.4    1.3  1  DUF2318         Predicted membrane protein (DUF2318)
       0.13   12.1   5.7       0.87    9.4   0.4    2.2  2  ZZ              Zinc finger, ZZ type
       0.22   11.2   3.1        6.3    6.6   0.2    2.2  2  Rubredoxin_2    Rubredoxin metal binding domain
        0.4   10.3   4.2        1.5    8.5   0.2    2.2  2  Sgf11           Sgf11 (transcriptional regulation protein)
        0.6   10.0   3.6        4.1    7.3   0.3    2.1  2  zinc_ribbon_12  Probable zinc-ribbon domain
       0.66    9.9   3.5         38    4.2   3.5    2.1  1  TFIIS_C         Transcription factor S-II (TFIIS)
        1.7    8.3   6.3        1.6    8.4   0.6    2.4  2  zf_C2H2_13      Zinc finger domain
        2.9    7.8   5.4        2.4    8.1   0.8    2.2  2  zf-C2H2_3       zinc-finger of acetyl-transferase ESCO


Domain annotation for each model (and alignments):
>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.9   1.2   8.3e-21   7.8e-18       1      51 [.      11      61 ..      11      64 .. 0.96

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 8.3e-21
                    -S--EEEEE-TTTS-EEEEESS-SS-EEESSSTCEEEEECSSSEEESSCEE CS
  Ribosomal_S27e  1 prskFldvkCpdCenetvvFshaatvvkCisCgkvLvePtGGkaklkaqil 51
                    p skF +v C +C++ +vv+sha ++v C sCg+ ++ePtG kak++ +i+
      EPA05505.1 11 PSSKFQKVNCNECGELQVVYSHATQAVVCNSCGNNIAEPTGSKAKINGKIS 61
                    689*******************************************99987 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.2   0.00086      0.81       1      11 [.      16      27 ..      16      29 .. 0.80
   2 !   10.9   0.2   0.00026      0.24       2      12 ..      36      46 ..      32      50 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00086
  zf-ribbon_3  1 stvrCPnCGa.p 11
                 ++v+C++CG+ +
   EPA05505.1 16 QKVNCNECGElQ 27
                 5799*****944 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00026
  zf-ribbon_3  2 tvrCPnCGapl 12
                  v C++CG+++
   EPA05505.1 36 AVVCNSCGNNI 46
                 46788888843 PP

>> Zn_Tnp_IS91  Transposase zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.5   1.7e-06    0.0016      36      69 ..      14      48 ..       6      56 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.7e-06
  Zn_Tnp_IS91 36 GfaryeCeeCghekivyfsCksrh.CpsCqkkate 69
                  f+++ C+eCg+ ++vy    +   C+sC+++ +e
   EPA05505.1 14 KFQKVNCNECGELQVVYSHATQAVvCNSCGNNIAE 48
                 57899***********999988888*****98665 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.9   6.2e-06    0.0058       3      31 ..      20      48 ..      18      58 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 6.2e-06
                  ETTTTCEECHEETSTTCEEESSSSBEEEE CS
  TF_Zn_Ribbon  3 CPnCgstnlveDpergelvCtdCGlVled 31
                  C +Cg  ++v+ +++  +vC +CG+ + +
    EPA05505.1 20 CNECGELQVVYSHATQAVVCNSCGNNIAE 48
                  99***988****************87766 PP

>> zinc_ribbon_6  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   2.9   4.3e-05      0.04      20      54 ..       9      43 ..       2      45 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.3e-05
  zinc_ribbon_6 20 peeyknkkvkilCnDCekksevkfhvl.glkCkeCg 54
                   p+  ++k +k+ Cn C++ + v+ h    + C++Cg
     EPA05505.1  9 PKP-SSKFQKVNCNECGELQVVYSHATqAVVCNSCG 43
                   555.5689***************9986267899997 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.6   1.4e-05     0.014       9      37 ..      15      45 ..      10      49 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.4e-05
                SS--B-TTT-SB-..-SSSS-EEEETTT--E CS
        C1_1  9 kqptfCkhCgefl..wgkekqglkCswCkll 37
                 q+  C++Cge+   + +++q++ C+ C+ +
  EPA05505.1 15 FQKVNCNECGELQvvYSHATQAVVCNSCGNN 45
                57899******987566***********987 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.2     0.027        26      15      21 ..      19      25 ..      13      27 .. 0.86
   2 ?    9.1   0.0    0.0014       1.3      15      25 ..      38      48 ..      30      52 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.027
        YhfH 15 kCteCGk 21
                 C eCG+
  EPA05505.1 19 NCNECGE 25
                6*****8 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0014
        YhfH 15 kCteCGkeieE 25
                +C +CG++i E
  EPA05505.1 38 VCNSCGNNIAE 48
                6********99 PP

>> zf-dskA_traR  Prokaryotic dksA/traR C4-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1    0.0099       9.3       5      11 ..      17      25 ..      13      26 .. 0.79
   2 ?    6.8   0.0     0.007       6.6       6      16 ..      39      49 ..      30      49 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0099
  zf-dskA_traR  5 s..CeeCGE 11
                  +  C eCGE
    EPA05505.1 17 KvnCNECGE 25
                  446*****9 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.007
  zf-dskA_traR  6 CeeCGEpIpea 16
                  C  CG  I+e+
    EPA05505.1 39 CNSCGNNIAEP 49
                  ********996 PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.4     0.019        18      12      24 ..      13      25 ..       3      31 .. 0.80
   2 ?   11.2   0.5   0.00031      0.29      14      28 ..      34      48 ..      27      55 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.019
                GGSS--EETTTTE CS
      zf-BED 12 lkeqkavCryCgk 24
                 k qk+ C+ Cg+
  EPA05505.1 13 SKFQKVNCNECGE 25
                688********95 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00031
                SS--EETTTTEE--- CS
      zf-BED 14 eqkavCryCgkilsr 28
                 q +vC+ Cg++++ 
  EPA05505.1 34 TQAVVCNSCGNNIAE 48
                4899********986 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   1.1   6.7e-05     0.063       7      35 ..      19      45 ..      14      48 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.7e-05
  Zn-ribbon_8  7 rCeeCghefevlqsisdaplta.CPeCgse 35
                  C+eCg e  v+ s   a + + C +Cg +
   EPA05505.1 19 NCNECG-ELQVVYS--HATQAVvCNSCGNN 45
                 4*****.8887774..3445555****986 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.5   4.7e-05     0.044      69     102 ..      16      51 ..       4      58 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.7e-05
                 -EEEETTTS-EEECHH..H.HHS-TTTSSS-EEEEES CS
        HypA  69 vkvrCreCgkefelee..k.alrCpkCgsadveivsG 102
                  kv C+eCg+   + +  + a+ C++Cg++  e  +G
  EPA05505.1  16 QKVNCNECGELQVVYShaTqAVVCNSCGNNIAEP-TG 51 
                 5799*****65443333325789*****965444.44 PP

>> DUF2318  Predicted membrane protein (DUF2318)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   2.4     6e-05     0.056      36      64 ..      19      49 ..       5      59 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6e-05
     DUF2318 36 aCevC..ekkgYvqegeelvCknCgvrfald 64
                 C+ C   +  Y +  +++vC++Cg+++a +
  EPA05505.1 19 NCNECgeLQVVYSHATQAVVCNSCGNNIAEP 49
                5999*65567899*************99865 PP

>> ZZ  Zinc finger, ZZ type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.4   0.00092      0.87       3      21 ..      16      31 ..      14      34 .. 0.81
   2 ?    5.6   0.7     0.015        14       3      12 ..      35      44 ..      33      49 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00092
                S-EE-TTT-S..EESSEEE CS
          ZZ  3 kkytCdgCseapligvRyh 21
                +k+ C++C+e    +v+y+
  EPA05505.1 16 QKVNCNECGE---LQVVYS 31
                589******9...777775 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.015
                S-EE-TTT-S CS
          ZZ  3 kkytCdgCse 12
                +++ C+ C++
  EPA05505.1 35 QAVVCNSCGN 44
                6789*****9 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.3     0.017        16       3       8 ..      20      25 ..      19      30 .. 0.79
   2 ?    6.6   0.2    0.0066       6.3       2       9 ..      38      45 ..      38      51 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.017
  Rubredoxin_2  3 CsqCGf 8 
                  C++CG 
    EPA05505.1 20 CNECGE 25
                  999997 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0066
  Rubredoxin_2  2 vCsqCGfe 9 
                  vC++CG+ 
    EPA05505.1 38 VCNSCGNN 45
                  7****986 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.5     0.063        59       3      11 ..      16      24 ..      14      25 .. 0.86
   2 ?    8.5   0.2    0.0015       1.5       2      15 ..      34      47 ..      33      48 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.063
                -EEE-TTTS CS
       Sgf11  3 eyvtCpnCg 11
                + v+C+ Cg
  EPA05505.1 16 QKVNCNECG 24
                679*****8 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0015
                C-EEE-TTTSSEEE CS
       Sgf11  2 seyvtCpnCgRqia 15
                ++ v+C+ Cg +ia
  EPA05505.1 34 TQAVVCNSCGNNIA 47
                789*******9997 PP

>> zinc_ribbon_12  Probable zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.3    0.0044       4.1      26      40 ..      12      26 ..       6      31 .. 0.80
   2 ?    4.0   0.2     0.046        43       7      16 ..      37      46 ..      33      59 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0044
  zinc_ribbon_12 26 kkkqqklrCGaCsev 40
                    + k qk+ C +C e+
      EPA05505.1 12 SSKFQKVNCNECGEL 26
                    557899******985 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.046
  zinc_ribbon_12  7 vvCsnCfelL 16
                    vvC++C + +
      EPA05505.1 37 VVCNSCGNNI 46
                    7899997665 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   3.5      0.04        38      25      36 ..      33      44 ..      18      47 .. 0.62

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.04
     TFIIS_C 25 mtvfykCtkCgh 36
                +t  ++C++Cg+
  EPA05505.1 33 ATQAVVCNSCGN 44
                466677777776 PP

>> zf_C2H2_13  Zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.7     0.078        74      20      24 ..      20      24 ..      12      32 .. 0.90
   2 ?    8.4   0.6    0.0017       1.6      19      27 ..      38      46 ..      28      50 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.078
  zf_C2H2_13 20 CnkCG 24
                Cn+CG
  EPA05505.1 20 CNECG 24
                ***** PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0017
  zf_C2H2_13 19 vCnkCGkPi 27
                vCn+CG  i
  EPA05505.1 38 VCNSCGNNI 46
                9*****866 PP

>> zf-C2H2_3  zinc-finger of acetyl-transferase ESCO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.8    0.0025       2.4       8      20 ..      12      24 ..       5      36 .. 0.85
   2 ?    2.6   0.4      0.13   1.2e+02      15      20 ..      35      43 ..      26      43 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0025
   zf-C2H2_3  8 qksfgasqCkeCg 20
                 ++f+++ C+eCg
  EPA05505.1 12 SSKFQKVNCNECG 24
                57899999****8 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.13
   zf-C2H2_3 15 q...CkeCg 20
                q   C+ Cg
  EPA05505.1 35 QavvCNSCG 43
                2344****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.33u 0.25s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 503.41
//
Query:       EPA05506.1  [L=152]
Description: transcriptional regulator, AsnC family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.6e-13   47.9   0.1    1.7e-12   47.1   0.1    1.4  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
  ------ inclusion threshold ------
      0.014   15.5   0.1      0.029   14.5   0.1    1.6  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
      0.031   14.2   0.1      0.068   13.1   0.1    1.5  1  MarR            MarR family
       0.06   12.9   0.3       0.17   11.5   0.1    1.8  2  HTH_24          Winged helix-turn-helix DNA-binding
       0.12   12.3   0.8          3    7.9   0.2    2.2  2  SAM_LFY         Floricaula / Leafy protein SAM domain


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   0.1   4.9e-16   1.7e-12       3      74 ..      69     137 ..      67     138 .. 0.94

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 4.9e-16
                     EEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEE CS
  AsnC_trans_reg   3 vslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivle 74 
                     ++++ ++    + ++e+l +++ V+e+  vtG +d+l+ +++++l+++++ ++ek+++++g++++e++i ++
      EPA05506.1  69 INMDTKK---RDHIIEELFKIDGVREIAEVTGRFDILVTMYAKSLDQMHKMVSEKIGRIEGIQSSESFIEMK 137
                     7788777...99********************************************************9887 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1     8e-06     0.029      22      55 ..      21      56 ..      18      96 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 8e-06
  B-block_TFIIIC 22 sdLakeskqdprslfyrlksLekkgLIvkqsii..d 55
                    +d  k ++  ++ +++r+k L k +LI++ +i+  d
      EPA05506.1 21 QDYQKKINVNSSVVYSRIKRLVKRKLIERFTIVvnD 56
                    677899999***********************5440 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   1.9e-05     0.068      24      50 ..      24      50 ..      13      55 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.9e-05
                HHHHTS-HHHHHHHHHHHHHTTSEEEE CS
        MarR 24 akklgvskstvtrvldrLekkGlieRs 50
                +kk++v++s v   ++rL+k+ lieR 
  EPA05506.1 24 QKKINVNSSVVYSRIKRLVKRKLIERF 50
                79************************7 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   4.7e-05      0.17      24      48 .]      24      48 ..      20      48 .. 0.90
   2 ?   -2.0   0.0      0.76   2.7e+03      21      28 ..      90      97 ..      89      97 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.7e-05
      HTH_24 24 AerlglSpstvnrrlkrLeeeGlIk 48
                 +++++ +s v  r+krL++  lI+
  EPA05506.1 24 QKKINVNSSVVYSRIKRLVKRKLIE 48
                589*****************99996 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.76
      HTH_24 21 reLAerlg 28
                re+Ae +g
  EPA05506.1 90 REIAEVTG 97
                8****987 PP

>> SAM_LFY  Floricaula / Leafy protein SAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1    0.0042        15      16      49 ..      49      84 ..      38      87 .. 0.82
   2 ?    7.9   0.2   0.00082         3       5      50 ..      79     119 ..      75     129 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0042
     SAM_LFY 16 ryltvakiaelGftvstl..vnmkeeelddmmksls 49
                r++ v   ae+G+ v++l  +nm  +  d +++ l 
  EPA05506.1 49 RFTIVVNDAEIGYGVKALtgINMDTKKRDHIIEELF 84
                777888899****99977557999999999998775 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00082
     SAM_LFY   5 gleelfeayGvryltvakiaelGftvstlvnmkeeelddmmkslse 50 
                  +eelf+  Gvr      iae+    + lv m  + ld+m k +se
  EPA05506.1  79 IIEELFKIDGVR-----EIAEVTGRFDILVTMYAKSLDQMHKMVSE 119
                 579999999998.....689999999**************999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1021  (0.0569468); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1055.36
//
Query:       EPA05507.1  [L=207]
Description: phosphoglycerate mutase family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.5e-50  171.6   0.0    1.7e-50  171.4   0.0    1.0  1  His_Phos_1  Histidine phosphatase superfamily (branch 1)
  ------ inclusion threshold ------
      0.061   12.5   0.3       0.14   11.3   0.1    1.7  2  CRM1_C      CRM1 C terminal


Domain annotation for each model (and alignments):
>> His_Phos_1  Histidine phosphatase superfamily (branch 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.4   0.0   1.9e-54   1.7e-50       1     192 [.       4     196 ..       4     198 .. 0.97

  Alignments for each domain:
  == domain 1  score: 171.4 bits;  conditional E-value: 1.9e-54
                 EEEEE---BTTB--.....TT----B-HHHHHHHHHHHHHHTTS---EEEE-SSHHHHHHHHHHHHCTT--EEE-GGGS----GGGTT-B.HHHHHH.. CS
  His_Phos_1   1 lyLvRHGetewnaegr.lqgrtdvpLteeGreqAealaerlagepidaiysSplkRarqTaeliaealglpveldegLrEidfGdweglttaeiaeeyp 98 
                 ++++RHG+ ++n e++  ++   vpLte+G+eqAe++a++l++++i+aiysSp++Ra++Tae+++++  l+v++d++L E+d+G++ g +++ei +++ 
  EPA05507.1   4 VIFLRHGQAKNNIERIlTGRTPGVPLTEKGIEQAEKAAKFLEHMNISAIYSSPIERAKHTAEIVGKHNSLDVIIDDRLIELDMGKFTGVPYDEIFSSHG 102
                 689*************5555689********************************************99****************************** PP

                 HSHHHHHHHHH-GGG-BS-BHHHHHHHHHHHHHHHHHHTTTSEEEEEE-HHHHHHHHHHHHT--GGGGGGB---TT-EEEEEE-SS-EEEEEEE CS
  His_Phos_1  99 eeleawlrdpadvrppggEsledvaaRvaaaleelaarhegetvlvVsHggvirallarllglpleelrrleldnaslsvlefdeggwrlvrln 192
                 + + ++ +++ + + +g E++ +v +Rv  ++++++++h++++v++V+H  +i+a+l+++++l +e+l +l ++nasl++++ +++++++  ln
  EPA05507.1 103 NVFMKFYNGELEIAHNGVETFSEVKKRVLGIVDHVVENHPDQNVVLVTHMDPIKAMLSTIVDLTPENLFELIIANASLNIFREHKRKFSISGLN 196
                 ***************************************************************************************9998877 PP

>> CRM1_C  CRM1 C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0      0.46   4.1e+03       6      35 ..      43      71 ..      41      74 .. 0.73
   2 ?   11.3   0.1   1.6e-05      0.14      27      71 ..     110     154 ..     100     169 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 0.46
      CRM1_C  6 yldllklyklvseliseavaaegeiatktp 35
                +l+ +++  ++s+ i++  +++ ei+ k++
  EPA05507.1 43 FLEHMNISAIYSSPIER-AKHTAEIVGKHN 71
                77788889999999988.566666666665 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 1.6e-05
      CRM1_C  27 egeiatktpkvrllrtvkkeiLkLietyiekaedleevlnnlvep 71 
                 +ge ++ ++ v ++  vkk +L +++ ++e+ +d++ vl + + p
  EPA05507.1 110 NGELEIAHNGVETFSEVKKRVLGIVDHVVENHPDQNVVLVTHMDP 154
                 7899999*****************************976544433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.34s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 1205.58
//
Query:       EPA05508.1  [L=37]
Description: hypothetical protein BG20_I0240 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-06   27.9   0.2    2.4e-06   27.9   0.2    1.0  1  CobS      Cobalamin-5-phosphate synthase


Domain annotation for each model (and alignments):
>> CobS  Cobalamin-5-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.2   1.3e-10   2.4e-06     176     204 .]       4      32 ..       1      32 [. 0.82

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 1.3e-10
        CobS 176 rrlarrklggvtGDvlGavieltellvll 204
                   l+ r++gg+tGD++Ga++elt+l+ ll
  EPA05508.1   4 VGLTSRSFGGITGDIMGATNELTRLTSLL 32 
                 3456677******************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       168  (0.00937029); expected 358.6 (0.02)
Passed bias filter:                      116  (0.00646996); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.32s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 231.11
//
Query:       EPA05509.1  [L=223]
Description: NADPH-dependent F420 reductase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.7e-17   61.7   0.1    1.2e-16   61.1   0.1    1.3  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
      0.002   18.6   0.0     0.0031   17.9   0.0    1.3  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
      0.007   16.6   0.0     0.0099   16.1   0.0    1.4  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
  ------ inclusion threshold ------
      0.023   14.4   0.0       0.04   13.5   0.0    1.4  1  ApbA             Ketopantoate reductase PanE/ApbA
      0.026   14.6   0.1      0.045   13.9   0.1    1.3  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
      0.029   13.4   0.0       0.04   12.9   0.0    1.3  1  PDH              Prephenate dehydrogenase
      0.054   13.5   0.0      0.099   12.6   0.0    1.6  2  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
      0.077   12.4   0.1       0.13   11.7   0.1    1.2  1  adh_short        short chain dehydrogenase


Domain annotation for each model (and alignments):
>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.1   0.1   5.2e-20   1.2e-16       1      96 [.       2     104 ..       2     105 .. 0.96

  Alignments for each domain:
  == domain 1  score: 61.1 bits;  conditional E-value: 5.2e-20
                    EEEEE.TTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC...........-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHHCGHH CS
  F420_oxidored   1 kigii.GaGnmgealasgllaagaqpheivvansrnpekaeelaeelg...........vkvtavdneeaaeeadvvvlavkpedveevlselakd 84 
                    kigii G+G mg+++a++++++    h+++++ sr+  +a e+a+e+             ++t+ dn  +a+e+dv++l++++e++++v+s + ++
     EPA05509.1   2 KIGIIgGTGGMGKGFALRWSQN----HNVIIG-SRDAARASEAAKEYTdlanesfgkinGTITGNDNVSVAKESDVLILSIPYENIDSVCSGILPA 92 
                    7********************9....9***88.*************************999********************************999 PP

                    HHTTSEEEEESS CS
  F420_oxidored  85 alkgklvisvla 96 
                     +   +v+s  +
     EPA05509.1  93 VKDSCVVVSPIV 104
                    999999999876 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.4e-06    0.0031       1      83 [.       2      86 ..       2     101 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.4e-06
                    EEEEETTTSHHHHHH.HHHHHCTSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGC.TT-SEEEE-SCHHHHHHHH CS
  Semialdhyde_dh  1 kvaivGatGyvGqel.lrlLeehpevelvvllsssrsaGkklaeavkaleegkdlkvedvdeeel.kevdivflalpagvskela 83
                    k++i+G+tG +G+ + lr  ++h  +  ++ ++++++a k++++++++  ++ + +++  d+ ++ ke d+++l+ p +   ++ 
      EPA05509.1  2 KIGIIGGTGGMGKGFaLRWSQNHNVIIGSRDAARASEAAKEYTDLANESFGKINGTITGNDNVSVaKESDVLILSIPYENIDSVC 86
                    79*************555555599999999999999***********9999999999997777777*********9987665554 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   4.4e-06    0.0099       1      74 [.       3      74 ..       3     110 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.4e-06
                     EEEE--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH...TTTCEEEEE--TTTHHHHHHHHHTTSSEEE CS
  Sacchrp_dh_NADP  1 vliiGa.GsvGqavaellarhfdvdaeitvadrskeklealaaka...lgvrfeaialdaenyeavLaallkegdlvv 74
                     + iiG+ G++G+++a   +++++    +++ +r+ +++ ++a++    ++++f +i  ++   +   +++ ke d+++
       EPA05509.1  3 IGIIGGtGGMGKGFALRWSQNHN----VIIGSRDAARASEAAKEYtdlANESFGKINGTITGNDN--VSVAKESDVLI 74
                     689******************95....69********8888876688877777777777666666..55556666666 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.8e-05      0.04       3     100 ..       6     101 ..       3     102 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.8e-05
                 EES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETT.CEEEEEECEEECCHSCCCCS-ESEEEE-SSGGGHHHHHHHHGGGECTCEEEE CS
        ApbA   3 ilGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseg.geeilrppealsaeekselepidlvivtvKayqteealeeikplldpntvvl 99 
                 i G+G++G  +a + ++ +++v++  r++ r+ +  k+  +l  e+ g+ +   + + +    s +++ d++i++++    +++++ i p++++ +vv+
  EPA05509.1   6 IGGTGGMGKGFALRWSQ-NHNVIIGSRDAaRASEAAKEYTDLANESfGKINGTITGNDNV---SVAKESDVLILSIPYENIDSVCSGILPAVKDSCVVV 100
                 5699***********66.999*******99999999999999999954444444444444...5999****************************9998 PP

                 E CS
        ApbA 100 l 100
                 +
  EPA05509.1 101 S 101
                 5 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1     2e-05     0.045       1      72 [.       1      74 [.       1      79 [. 0.77

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2e-05
                EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS..--S-BEB.SSHHHHHHH-SEEE CS
      DapB_N  1 ikvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglg..klgvavt.ddleevlekadvli 72
                +k++++G +G mGk  +   +++ ++ +++   ++  +  +k+  +l++ +  k++ ++t +d  +v++++dvli
  EPA05509.1  1 MKIGIIGGTGGMGKGFALRWSQNHNVIIGSRDAARA-SEAAKEYTDLANESfgKINGTITgNDNVSVAKESDVLI 74
                89********************99999988766655.444455555554433599999995666666677***98 PP

>> PDH  Prephenate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.8e-05      0.04      35      76 ..      59     100 ..      17     111 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.8e-05
                 EEES-GGGGCCGSEEEE-S-GGGHHHHHHHHHHHS-TT-EEE CS
         PDH  35 eatddieavkeadivvlavPvevilevlkelaphlkedalit 76 
                 + +d+++ +ke d+ +l++P e i  v   + p++k +++++
  EPA05509.1  59 TGNDNVSVAKESDVLILSIPYENIDSVCSGILPAVKDSCVVV 100
                 455569*******************************99986 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   4.4e-05     0.099       2     101 ..       3     101 ..       2     141 .. 0.81
   2 ?   -3.0   0.0       2.8   6.3e+03      97     108 ..     176     187 ..     164     218 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.4e-05
                     EEEE-.-SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHHSSBTTTBTT----TTEEEES-HHHHHTT--EEEE---HHHHHHHHHHHCCC--T CS
  NAD_Gly3P_dh_N   2 iavlG.aGswGtalAkvlaenghevrlwvreeelieeineehenvkyLpgiklpenlvattdlaealkgadiivlvvPsqalrevlkklkgllkk 95 
                     i+++G +G  G  +A   ++n  +v + +r+++ + e  +e ++ +     k++ +++ + d  +++k++d+++l +P + + +v+  + + +k+
      EPA05509.1   3 IGIIGgTGGMGKGFALRWSQNH-NVIIGSRDAARASEAAKEYTDLANESFGKINGTITGN-DNVSVAKESDVLILSIPYENIDSVCSGILPAVKD 95 
                     6777525888888888887764.8888888887777777776666655556677777665.66688999**********************9999 PP

                     T-EEEE CS
  NAD_Gly3P_dh_N  96 kailvs 101
                       ++vs
      EPA05509.1  96 SCVVVS 101
                     999887 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.8
                     -EEEE---SEET CS
  NAD_Gly3P_dh_N  97 ailvsliKGiee 108
                       l++ iKG+ +
      EPA05509.1 176 NGLINEIKGLRP 187
                     455666666633 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   5.7e-05      0.13       5      64 ..       5      64 ..       2      70 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.7e-05
                EESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT.TSEEEEEE-TTTSHHHH CS
   adh_short  5 vtGassGIGraiakelakeGakvvvvdrseekleevakelkee.gakalaiqvDvtdreev 64
                ++G+++G+G+ +a +  + + +v++ +r ++++ e+ake  ++ ++++  i++++t  ++v
  EPA05509.1  5 IIGGTGGMGKGFALRWSQ-NHNVIIGSRDAARASEAAKEYTDLaNESFGKINGTITGNDNV 64
                99*************866.599999***************999888888888888766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1428.36
//
Query:       EPA05510.1  [L=594]
Description: putative adenine deaminase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-46  157.6   0.1    4.1e-46  156.4   0.0    1.6  2  Adenine_deam_C  Adenine deaminase C-terminal domain
    1.9e-16   60.3   0.0    2.3e-15   56.8   0.0    2.1  1  Amidohydro_1    Amidohydrolase family
    4.9e-08   32.9   0.0     0.0012   18.4   0.0    2.1  2  Amidohydro_3    Amidohydrolase family
  ------ inclusion threshold ------
      0.069   12.3   0.1       0.28   10.3   0.1    2.0  2  DUF2099         Uncharacterized protein conserved in archaea 
       0.12   12.2   0.0       0.46   10.3   0.0    1.8  2  NMT             Myristoyl-CoA:protein N-myristoyltransferase,


Domain annotation for each model (and alignments):
>> Adenine_deam_C  Adenine deaminase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       1.2   4.2e+03      56      78 ..      12      32 ..       8      33 .. 0.78
   2 !  156.4   0.0   1.1e-49   4.1e-46       2     168 ..     421     587 ..     420     588 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.2
                    EEES--TTT--EEEEESSHHHHH CS
  Adenine_deam_C 56 iAssvahDshniivvGtndedma 78
                    +A s++    n +++G++++d++
      EPA05510.1 12 LANSISS--LNSVAMGDKKADLI 32
                    5666665..999*****999986 PP

  == domain 2  score: 156.4 bits;  conditional E-value: 1.1e-49
                     SS-EEEEEEEEEETTEEE-..-TTEEEEEEE--SSSS--EEEEEEESS--BSSEEEES--TTT--EEEEESSHHHHHHHHHHHHHTTSEEEEEET CS
  Adenine_deam_C   2 liTkelevelpvkdgvvvadlekdllkiavveRhgktgnvgvgfvkgfglkkgAiAssvahDshniivvGtndedmalAvnrvielgGGivvved 96 
                     +iTk  +vel  kdg v+a+ +kd++k+a ++R ++t++ ++gf+++fg + gA+As+++  ++++iv+G+nd+dm +A+n++i+++GG+vv++ 
      EPA05510.1 421 IITKLGSVELVSKDGSVHASFDKDVWKVAAFDRIRGTNKHSIGFLENFGADIGALASTWSFHENDMIVIGSNDSDMSIAANTLIKNQGGLVVIKS 515
                     89********************************************************************************************* PP

                     TEEEEEEE-TBTTTBBSS-HHHHHHHHHHHHHHHHTTS-TTTBSGGGGGSTT-TTSSSEEEETTSEEETTTT CS
  Adenine_deam_C  97 gkvlaelpLpiaGlmSdepaeevaekleeleaalkelgvkledpfmtlsflalpviPelkltdkGlvdvkkf 168
                     gk++a+lpL++aG++S++++e+v +++e++++   + g+k+++p +   fl ++ +P+ ++t  G+vdvk++
      EPA05510.1 516 GKIIASLPLQLAGIVSTDSFENVLSNFEQINKSIVDSGCKFSRPHLIPLFLPFLALPSARITSGGIVDVKRR 587
                     *******************************88888*********************************985 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.8   0.0   6.4e-19   2.3e-15       1     344 []      83     368 ..      83     368 .. 0.83

  Alignments for each domain:
  == domain 1  score: 56.8 bits;  conditional E-value: 6.4e-19
                   EEEE-EEEEEEECETTECSSSGHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHHHHHHHHHHTSSSEEEEEEESSEGGSGCCCSHHHH CS
  Amidohydro_1   1 ivlPGlIDaHvHleqsllrgatledwlvppetaaealesgiktalksGtttvadmgattstgiealleaaeelplglrilggkvsldrgsaetskas 97 
                   +v PG+ D H+H+           ++++p e a+  l  g++ ++++++ +v  +g++   g++  l+  e+lp+ +  +++++ +  +++++ k +
    EPA05510.1  83 YVSPGFADPHLHID----------QFVLPSELAKKSLLCGVTSLFSDPIDIVSVSGYK---GFQEFLKLGEDLPIRIFQVVPGGLPVDRKFSHGKSL 166
                   689**********5..........3459*****************************8...***************999999888866444444433 PP

                   HHHHHHHHHHHHHHCTTTCEE.EEEEECGTCCSHHHHHHHHHHHHHHHTTEEEEEE..TSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEE CS
  Amidohydro_1  98 reklkagaaetikgkadgvvk.valapheapafsdeelkealkeakkrdlpvaiHa..letkgevedaeaafgetiehgthlevaeslglldeikli 191
                       ++     + +k++ v+   ++  +  +++ d+   + l    ++d  +  H+  +++k+ ++++  ++ + +e   +  v+e           
    EPA05510.1 167 SLSQEK-----LAIKHPNVLGlGEVFSWTKVTLRDSKTMQSLYSMLEKDCVINGHTagASEKKLNAYVASGILSCHEPINFEQVLER---------- 248
                   333333.....335566777767777777777777755555556667899999999999*************988888888888777.......... PP

                   EHCTCEEEHHHHHHHHHHHHHHCEEHHHHHHHHSEHHHHHHHHHHHH.TSC...EEEEEECT........TSSCCGGHHHHHHHHHHHHHHCCTTTT CS
  Amidohydro_1 192 lahgvhltpteaellkerlkeagvahcpfsnsilrsgrealrkalde.Gvk...vglgtDga........asgnslnlleelrlalklqrgllyede 276
                   l  g++++                      + ++r ++  +  ++ + G++    ++++Dg         ++++ +     +r  +           
    EPA05510.1 249 LRLGMWIMIR--------------------EGSIRRDLKEIISCVMSnGINldrLMFCSDGLdpldivkyGHIDHC-----VRESI----------- 309
                   ********77....................456888999999998888999999******7777777777777777.....78888........... PP

                   HCHCHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECCCTCGGGTTTCTSEEEEEEEETTEEE CS
  Amidohydro_1 277 egglslkealrmaTingAkalglddkvGsievGkdADlvvvdldilaafvglkkdgnvkkvivkGklv 344
                   + gl + +a++ma+ n  +++++++++G i++Gk AD+ ++          + ++ ++ kv+v+Gklv
    EPA05510.1 310 KLGLHPIDAISMASKNCFDYYNMSKDLGGIAPGKLADILIF---------DDLNSIKPNKVFVGGKLV 368
                   999**************************************.........8888888999*****997 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   3.4e-07    0.0012       2      25 ..      76      99 ..      75     131 .. 0.87
   2 !   12.6   0.0     2e-05      0.07     412     469 ..     317     372 ..     267     376 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 3.4e-07
  Amidohydro_3  2 viDakGrlvlPGFvDsHtHlaggg 25
                  viD k ++v PGF D+H+H++   
    EPA05510.1 76 VIDIKEKYVSPGFADPHLHIDQFV 99
                  8******************99876 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 2e-05
  Amidohydro_3 412 ealalyTrgpAkalgledrkGtLevGadADlvvldadpldvdppelaearvrltvvdG 469
                   +a+ + +++    +++++  G++++G+ AD+ ++d d+  ++p++++  + +l+v +G
    EPA05510.1 317 DAISMASKNCFDYYNMSKDLGGIAPGKLADILIFD-DLNSIKPNKVFV-GGKLVVSNG 372
                   68888888889999999999**************7.888888775544.355555555 PP

>> DUF2099  Uncharacterized protein conserved in archaea (DUF2099)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.44   1.6e+03     168     209 ..     192     229 ..     185     236 .. 0.65
   2 ?   10.3   0.1   7.8e-05      0.28      90     144 ..     498     552 ..     477     555 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.44
     DUF2099 168 vtvaeaedakklrelekeegvkilifavhttgiskeeaeelv 209
                 vt+ +++++++l ++ +    k +++  ht+g s+++ + +v
  EPA05510.1 192 VTLRDSKTMQSLYSMLE----KDCVINGHTAGASEKKLNAYV 229
                 45555555544444444....667778899999999887776 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 7.8e-05
     DUF2099  90 idaavivcdgaGtvivtnpelvqglggrisGlveTePieevierieeeggivldk 144
                 i a  ++ +  G v++++ +++ +l  +++G+v+T+ +e+v+++ e+ +  ++d+
  EPA05510.1 498 IAANTLIKNQGGLVVIKSGKIIASLPLQLAGIVSTDSFENVLSNFEQINKSIVDS 552
                 5566666677899**********************************99999985 PP

>> NMT  Myristoyl-CoA:protein N-myristoyltransferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00013      0.46      16      48 ..     181     213 ..     169     219 .. 0.85
   2 ?   -1.5   0.0      0.57     2e+03     111     154 ..     240     281 ..     220     284 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00013
                 ---STTEEEEE--TTSHHHHHHHHHHHHHHSSC CS
         NMT  16 lklpkgfewvtvdledeeelkevyelLsenYve 48 
                 l l + f+w++v l+d+++++ +y++L+++ v 
  EPA05510.1 181 LGLGEVFSWTKVTLRDSKTMQSLYSMLEKDCVI 213
                 567889**********************98876 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.57
                 EEEEEE-GGGTTSSHHHHHHHHHHHHHHTTT--EEEEEESSTSS CS
         NMT 111 infLcvhkklRskrlapvlikEitRrvnlkgifqavytagvvlp 154
                 inf  v  +lR      ++i+E + r  lk+i + v + g+ l 
  EPA05510.1 240 INFEQVLERLRLGM--WIMIREGSIRRDLKEIISCVMSNGINLD 281
                 67777766666543..5899999999999999999999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (594 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.25s 00:00:00.85 Elapsed: 00:00:00.42
# Mc/sec: 4241.47
//
Query:       EPA05511.1  [L=227]
Description: hypothetical protein BG20_I0227 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1161  (0.0647554); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1546.04
//
Query:       EPA05512.1  [L=194]
Description: hypothetical protein BG20_I0242 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-13   50.1   0.0    4.9e-13   49.7   0.0    1.1  1  NTP_transf_3     MobA-like NTP transferase domain
    9.9e-08   32.0   0.0    1.3e-07   31.6   0.0    1.1  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
    0.00075   19.1   0.0    0.00097   18.8   0.0    1.4  1  NTP_transferase  Nucleotidyl transferase
  ------ inclusion threshold ------
      0.017   14.9   1.3        0.4   10.4   0.3    2.3  2  NIF              NLI interacting factor-like phosphatase


Domain annotation for each model (and alignments):
>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.7   0.0   1.1e-16   4.9e-13       1     121 [.       3     123 ..       3     136 .. 0.88

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 1.1e-16
                   EEEEEESS-TTTT..TTHHHHCCCCCCHHHHHHHHHCTT.-.CEEEEECSH..CHHHHHHTTCTS-EEE-TTSS-SHHHHHHHHHHHH.SSSCEEEE CS
  NTP_transf_3   1 aviLAGGrSsRmg..gdKallplggkpllervldalraagv.devvvvggd..eevlaalarlgvrvvededpgkgplaslaaalraaadadavlvl 92 
                   a+++AGG++sRm+  ++K+ll+++ k l+ +v+dal+ +++ ++++ v+ +  ++ ++ l++ ++++++ +  g g ++ l   l+++  +d v+++
    EPA05512.1   3 AIVMAGGKGSRMNldEEKLLLKYK-KHLILHVIDALENSKCfSKILAVTSSnsPKTEKLLKENNIELFHTS--GVGYVEDLNLVLKSL--NDFVFIT 94 
                   79**********954599999986.66999*********755****9985544899999***********8..9************98..7****** PP

                   ETT-TT--HHHHHHHHHCHHHHTSSEEEE CS
  NTP_transf_3  93 acDmPlltpelverllaaaaasgadvvvp 121
                   ++D+P+l+ ++++ +++++++++  ++++
    EPA05512.1  95 SADLPYLDGDIINDIINQYDSKNIWTTIL 123
                   *****************998777666555 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0   2.8e-11   1.3e-07       1     118 [.       1     114 [.       1     130 [. 0.82

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 2.8e-11
                 EEEEEECTTSSCTT-SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHHGGCCEEEEE.--SSHHHHHHHHHHTTSSTTSEEEE- CS
        IspD   1 vvvvipAAGsGkRmkaglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqllldksiqlva.GGdeRaesVlnglkalegeakfVLvH 98 
                 +++++ A G+G+Rm+ + +K++l+ k + l+ h +dal +sk  +ki+ v s +  +++e+ll +++i+l +  G    e  +  lk l   ++fV + 
  EPA05512.1   1 MIAIVMAGGKGSRMNLDEEKLLLKYK-KHLILHVIDALENSKCFSKILAVTSSNS-PKTEKLLKENNIELFHtSGVGYVEDLNLVLKSL---NDFVFIT 94 
                 689*********************87.568889*************987777776.*************98625666777777766664...4679998 PP

                 -TT-TT--HHHHHHHHHHHH CS
        IspD  99 DaARpllkaadiaellaaae 118
                  a  p l  + i++++++ +
  EPA05512.1  95 SADLPYLDGDIINDIINQYD 114
                 88888888888888887765 PP

>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   2.2e-07   0.00097       2      69 ..       3      65 ..       2     127 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.2e-07
                     EEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSG CS
  NTP_transferase  2 avILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegs 69
                     a+++aGG+G+R+    +    kl+++++k  li +++ +l ns++ + i+ +t+ +s+  e+ lke++
       EPA05512.1  3 AIVMAGGKGSRM----NLDEEKLLLKYKK-HLILHVIDALENSKCFSKILAVTSSNSPKTEKLLKENN 65
                     8**********8....567899*******.************999999*************9999875 PP

>> NIF  NLI interacting factor-like phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.013        58      66     110 ..      33      93 ..      23     102 .. 0.56
   2 ?   10.4   0.3     9e-05       0.4      69     121 ..     131     184 ..     103     188 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.013
         NIF  66 vidildpekkllshrlyrescv..kkkg...............eyvKdLsllgrdlsrvviv 110
                 vid+l++ k+ +s+ l   s+   k+++                yv dL+l+ ++l+++v++
  EPA05512.1  33 VIDALENSKC-FSKILAVTSSNspKTEKllkennielfhtsgvGYVEDLNLVLKSLNDFVFI 93 
                 5555555554.555533333321111112222222222233357779999999999999988 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 9e-05
         NIF  69 ildpekkllshrlyrescv.kk.kgeyvKdLsllgrdlsrvvivDdspdsfelqp 121
                 +l+ + +  +  +  ++c+ +  +    K++s+l++  ++++i+Dd++ +f l+ 
  EPA05512.1 131 SLHLTSN-YNFSFNNQQCCyTGiSLVNAKNISTLDNVIEEFIILDDKRVAFNLNT 184
                 4444443.33334455554122233667***********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1326.14
//
Query:       EPA05513.1  [L=68]
Description: hypothetical protein BG20_I0274 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 508.19
//
Query:       EPA05514.1  [L=75]
Description: hypothetical protein BG20_I0259 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.016   15.6   0.8      0.021   15.2   0.8    1.3  1  YfzA             YfzA-like protein
      0.021   14.4   0.3      0.025   14.1   0.3    1.0  1  L6_membrane      L6 membrane protein
      0.023   14.6   1.7       0.76    9.8   0.1    2.1  2  Gram_pos_anchor  LPXTG cell wall anchor motif
      0.024   15.1   1.5      0.058   13.8   1.1    1.7  2  DUF202           Domain of unknown function (DUF202)
       0.13   11.8   0.2       0.13   11.8   0.2    1.1  1  DUF334           Domain of unknown function (DUF334)


Domain annotation for each model (and alignments):
>> YfzA  YfzA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.8   5.9e-06     0.021       6      53 ..       8      52 ..       3      71 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.9e-06
        YfzA  6 lkrtwlksigv.fllvqlifiilevtawiPnfkeGglydrvvnseffte 53
                + r+w+ +ig+ fl++  i ++ ++  w P+f e    d +vnsef  e
  EPA05514.1  8 RGRNWYTAIGAlFLIMAGIVLVRQLILWGPDFVE----DFIVNSEFTNE 52
                569******974778899999***********66....67888887655 PP

>> L6_membrane  L6 membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.3     7e-06     0.025       5      62 ..      11      67 ..       9      73 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7e-06
  L6_membrane  5 kcakclGlsLlplallsivaNilllfpngkteylkeekiskevwlfgGilGgGllvll 62
                 ++ + +G + l++a + +v  ++l+ p++ ++ + +++ ++e ++  G++G G+++++
   EPA05514.1 11 NWYTAIGALFLIMAGIVLVRQLILWGPDFVEDFIVNSEFTNE-KVSIGMIGFGIFMIV 67
                 788899***************************999999996.56779*******997 PP

>> Gram_pos_anchor  LPXTG cell wall anchor motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00021      0.76      18      37 ..      11      30 ..       9      31 .. 0.87
   2 ?    4.4   0.3      0.01        36      14      31 ..      52      69 ..      50      70 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00021
                     XXXXXXXXXXXXXXXXXXXX CS
  Gram_pos_anchor 18 ifltaaGllallggllLlvk 37
                     +++ta G+l l+ ++ +lv+
       EPA05514.1 11 NWYTAIGALFLIMAGIVLVR 30
                     899****9999999999887 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.01
                     XXXXXXXXXXXXXXXXXX CS
  Gram_pos_anchor 14 engnifltaaGllallgg 31
                     e+ +i++  +G++++++g
       EPA05514.1 52 EKVSIGMIGFGIFMIVLG 69
                     6779999********998 PP

>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.6     0.026        92      37      56 ..      11      29 ..       6      36 .. 0.55
   2 ?   13.8   1.1   1.6e-05     0.058      18      62 ..      19      73 ..      18      75 .] 0.76

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.026
      DUF202 37 salgkilglilivlgiltll 56
                +++++i +l+li +gi+ l+
  EPA05514.1 11 NWYTAIGALFLIMAGIV-LV 29
                45544444445555554.44 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1.6e-05
      DUF202 18 lalialglallrffl............tgepsalgkilglilivlgiltllvglvry 62
                l li++g++l+r                +e +  +  +++++i++gi+++++g++ y
  EPA05514.1 19 LFLIMAGIVLVRQLIlwgpdfvedfivNSEFT--NEKVSIGMIGFGIFMIVLGFRKY 73
                77899999999853367788887765533333..47799****************99 PP

>> DUF334  Domain of unknown function (DUF334)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   3.5e-05      0.13     139     185 ..       2      46 ..       1      73 [. 0.65

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.5e-05
      DUF334 139 shehyqkrqkqlftgigamllvfmlfali...mtigrdfmsflhvdvlqn 185
                 she+y +r ++ +t iga++l++  + l+   +  g df+  +    + n
  EPA05514.1   2 SHEYY-RRGRNWYTAIGALFLIMAGIVLVrqlILWGPDFVEDF----IVN 46 
                 89877.588999********99865555411155688887533....333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 525.94
//
Query:       EPA05515.1  [L=93]
Description: ribosomal protein L44 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.1e-24   84.5   9.0    5.1e-24   84.5   9.0    1.4  2  Ribosomal_L44  Ribosomal protein L44
     0.0055   17.1   4.1       0.25   11.8   1.1    2.6  2  Ribosomal_L33  Ribosomal protein L33


Domain annotation for each model (and alignments):
>> Ribosomal_L44  Ribosomal protein L44
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1      0.44   3.9e+03      52      60 ..       7      15 ..       5      16 .. 0.74
   2 !   84.5   9.0   5.7e-28   5.1e-24       1      75 [.      16      90 ..      16      91 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.44
                   EEEEETTT- CS
  Ribosomal_L44 52 lrleCteCk 60
                   +r  C +Ck
     EPA05515.1  7 MRKYCATCK 15
                   677799998 PP

  == domain 2  score: 84.5 bits;  conditional E-value: 5.7e-28
                   EEEEEEEEE-------SSSHHHHHHHH.H-SSSGGGGS----.--SSBB--EEEEETTT--EEE----BBS--EE CS
  Ribosomal_L44  1 kHtehkveqykkgkdselaqgkRrydrkqsgygGqtkpvfkkkaKttKKivlrleCteCkkkrlkalkRakkfel 75
                   +Hte+kv+ yk+gk++  a+g+Rr++++++gygGq+ p++ k aK+tKK+++ ++Ct Ckkk  k ++R+kkfel
     EPA05515.1 16 THTEQKVSIYKAGKRRGSARGERRHAERKRGYGGQKFPKLAKPAKVTKKVTPIMTCTVCKKKYNKIGIRIKKFEL 90
                   6*************************************************************************9 PP

>> Ribosomal_L33  Ribosomal protein L33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   1.1   2.8e-05      0.25      30      43 ..       7      20 ..       6      21 .. 0.88
   2 !    5.6   0.1    0.0025        22       4      15 ..      68      78 ..      65      89 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.8e-05
                   EEEEETTTTEEEEE CS
  Ribosomal_L33 30 lkKYcprcrkhtlh 43
                   ++KYc +c+ ht  
     EPA05515.1  7 MRKYCATCKTHTEQ 20
                   89**********75 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0025
                   EEEET......E CS
  Ribosomal_L33  4 tLeCtecksrnY 15
                   ++ Ct ck++ Y
     EPA05515.1 68 IMTCTVCKKK-Y 78
                   699*****97.7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       934  (0.0520944); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 586.55
//
Query:       EPA05516.1  [L=166]
Description: cyclic phosphodiesterase-like protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-09   36.5   2.6    2.1e-08   34.1   2.6    2.0  1  CPDase           Cyclic phosphodiesterase-like protein
      2e-07   31.0   0.0    2.8e-07   30.6   0.0    1.1  1  2_5_RNA_ligase2  2'-5' RNA ligase superfamily
  ------ inclusion threshold ------
       0.01   16.0   0.1        4.3    7.6   0.0    2.2  2  LigT_PEase       LigT like Phosphoesterase
      0.019   14.4   1.9      0.063   12.7   1.9    1.9  1  HVSL             Uncharacterised conserved protein
        1.2    9.3   7.9          5    7.3   4.6    2.8  2  KaiA             KaiA C-terminal domain


Domain annotation for each model (and alignments):
>> CPDase  Cyclic phosphodiesterase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   2.6   5.8e-12   2.1e-08       4     148 ..       3     127 ..       1     164 [. 0.75

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 5.8e-12
      CPDase   4 sLWlcPpanspeyetlktlIqsLqtlfpdsevFePHvTltselsvdskddvekvldsavaalksvrsglaalvkfegvsvgkkYfkkvvlevkkdkell 102
                 ++Wl  ++   + e lk +I  +++ +  ++ FePH+T+   ++++  d +++v+++  +  +s        vk + +   ++ +k v++e k +++l+
  EPA05516.1   3 AIWLTFSK--SDREYLKNVIDVISEKYH-APKFEPHITVYGLINLK-LDLIDNVINEVAHNCNSF------IVKKSDILQSEELWKTVYIELKMNQQLK 91 
                 78998888..55666999*****99995.79*********999886.467788888844444443......578889999999**************** PP

      CPDase 103 slaqlireafveaedeasqraaewvkeefePHvSLlYsDislvdq.a 148
                 s+ + ++++f           ++ +k ef+PH+SL+Y  +++ ++ +
  EPA05516.1  92 SVNENLKKHF-----------EKTLKYEFNPHISLIYKILPKEEKiK 127
                 *998887776...........455689**********9776655532 PP

>> 2_5_RNA_ligase2  2'-5' RNA ligase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.0   7.8e-11   2.8e-07      20     145 ..      28     145 ..      14     148 .. 0.88

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 7.8e-11
  2_5_RNA_ligase2  20 ayprwppHitLlypfvededladlaellsrlaketepfevrldgfgvFehkksvvylsvsdsealqalraallealpeagdkedsgeftPHlTi 113
                      + p+ +pHit++++   +   + +++++ ++a+++  f v    +   e+  ++vy++ +  ++l+ +++ l ++++++       ef+PH+++
       EPA05516.1  28 HAPKFEPHITVYGLINLKL--DLIDNVINEVAHNCNSFIVKKSDILQSEELWKTVYIELKMNQQLKSVNENLKKHFEKTLK----YEFNPHISL 115
                      578889********99998..79****************999888888864449**********************99975....78******* PP

  2_5_RNA_ligase2 114 aqsadstsaaelleklaqalpplefevdeval 145
                       ++  +++  e ++ ++++++  ef++d++ +
       EPA05516.1 116 IYKILPKE--EKIKIVNELNLKNEFTIDKIVV 145
                      ****7777..677888999*********9976 PP

>> LigT_PEase  LigT like Phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0012       4.3      31      59 ..      30      58 ..      13      75 .. 0.80
   2 ?    6.5   0.0    0.0026       9.3       9      75 ..      88     144 ..      82     147 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0012
                SGGGSEEEEEEEEEESHHHHHHHHHHHHH CS
  LigT_PEase 31 rpfnpHiTLaflgevdeekvpellealae 59
                ++f pHiT+  l + + + ++++++++a+
  EPA05516.1 30 PKFEPHITVYGLINLKLDLIDNVINEVAH 58
                89********9999999999999888875 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0026
                 HHHHHHHHHHHHHHCCTTEEETSGGGSEEEEEEEEEESHHHHHHHHHHHHHHHHTSBEEEEEEEEEE CS
  LigT_PEase   9 eelarlaaeleralaklglkpvrpfnpHiTLaflgevdeekvpellealaeiasgaepfelkvdgvg 75 
                 ++l ++ ++l++++ ++ lk +  fnpHi L      +eek++ ++++l+ +     +  +++d+++
  EPA05516.1  88 QQLKSVNENLKKHF-EKTLKYE--FNPHISLIYKILPKEEKIK-IVNELN-LKN---E--FTIDKIV 144
                 57888888888555.4566666..*****99988766555555.778875.422...2..7777665 PP

>> HVSL  Uncharacterised conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.9   1.7e-05     0.063     154     204 ..      85     133 ..       5     163 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.7e-05
        HVSL 154 eLkklleavnkvleefglpplykdeaFHiSiawslgepseeekeellsele 204
                 +++++l+ vn+ l+++  ++l ++  +HiS+   +  +  eek ++ +el+
  EPA05516.1  85 KMNQQLKSVNENLKKHFEKTLKYEFNPHISLIYKILPK--EEKIKIVNELN 133
                 68899999999999999999999999999999888843..33434444443 PP

>> KaiA  KaiA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1     0.058   2.1e+02      56      87 ..      25      56 ..       3      76 .. 0.70
   2 ?    7.3   4.6    0.0014         5       7      76 ..      79     161 ..      74     165 .. 0.64

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.058
                HHHHHHHHHTT--HHHHHHHHHHHHHHHHHHH CS
        KaiA 56 defvnkaffadlsvskileihmelldefskql 87
                +++    f   ++v  +++++++l+d+  +++
  EPA05516.1 25 EKYHAPKFEPHITVYGLINLKLDLIDNVINEV 56
                34445566778999999999999999877665 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0014
                 ECEEE--GGGSCCCSTHHHHHHHHHHHHHHHH.HHHHHC..TSTTSSH...HH.......HHHHHHHHHHHTT--HHHHHHHH CS
        KaiA   7 gvyykrdpkkflrnlskeekkelleelkseyr.eivley..fkddsev...nq.......kidefvnkaffadlsvskileih 76 
                 +vy + + ++ l+ ++++ kk++ ++lk e+  +i l y  + +++++   n+       +id++v + ff+d+   ki++i 
  EPA05516.1  79 TVYIELKMNQQLKSVNENLKKHFEKTLKYEFNpHISLIYkiLPKEEKIkivNElnlknefTIDKIVVQEFFSDIEKWKIVKIQ 161
                 67777777777888888888888888887775333333321434333211121111222369******************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1718  (0.0958224); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1082.10
//
Query:       EPA05517.1  [L=154]
Description: hypothetical protein BG20_I0254 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.01   15.8   0.0      0.014   15.4   0.0    1.2  1  EMP24_GP25L  emp24/gp25L/p24 family/GOLD
      0.011   16.0   0.1      0.019   15.3   0.1    1.3  1  Invasin_D3   Invasin, domain 3
      0.063   13.6   0.1       0.26   11.6   0.2    1.9  2  Big_3        Bacterial Ig-like domain (group 3)
        0.1   12.8   0.7       0.19   11.9   0.6    1.4  1  SdrD_B       SdrD B-like domain
       0.23   11.2   0.1       0.23   11.2   0.1    2.0  2  Spore_YhaL   Sporulation protein YhaL


Domain annotation for each model (and alignments):
>> EMP24_GP25L  emp24/gp25L/p24 family/GOLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.0   3.8e-06     0.014      26     100 ..      45     114 ..      35     147 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.8e-06
  EMP24_GP25L  26 gsyqvtdgg.aaldvdlsvkdpdgngerlvkkkdresegdfsftakesgeykvCfdnsfstksskkvsfdievgse 100
                  g+y+v   +  + +v +++   d++++++ ++  + +++  +f  ++sg+y+v ++n+     +k+v++++e+g++
   EPA05517.1  45 GYYKVFIPEfTGDQVFIQIL--DKSQNIISEEMVQTKMSVGYFDFEQSGTYTVKITNPT----EKQVDIELELGDA 114
                  7788885555589*******..5555777777555566777888899**********74....4788888888754 PP

>> Invasin_D3  Invasin, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.1   5.2e-06     0.019      25      82 ..      60     113 ..      56     120 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.2e-06
  Invasin_D3  25 tvtlkDangnpvsgltvtfsttsagtlsavtdngdGtytatLtattagtatitptvnG 82 
                  +++ D+++n +s++ v+ +++    ++  + +++Gtyt+++t  t++++ i+ +++ 
  EPA05517.1  60 FIQILDKSQNIISEEMVQTKMS----VGYFDFEQSGTYTVKITNPTEKQVDIELELGD 113
                 57899*********99999988....556778899*****************999953 PP

>> Big_3  Bacterial Ig-like domain (group 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       0.7   2.5e+03      36      55 ..      32      51 ..      27      52 .. 0.85
   2 ?   11.6   0.2   7.3e-05      0.26      29      57 ..      68      99 ..      54     110 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.7
       Big_3 36 dvevsgsvdstkaGeytvtv 55
                 +++++ ++ +  G y+v++
  EPA05517.1 32 SYDLKLNFNGEGNGYYKVFI 51
                68999999999999999986 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 7.3e-05
       Big_3 29 dae.vpfddvevsg...svdstkaGeytvtvty 57
                + + ++++ v+ +    ++d+++ G+ytv +t 
  EPA05517.1 68 Q-NiISEEMVQTKMsvgYFDFEQSGTYTVKITN 99
                3.2388888888888899************996 PP

>> SdrD_B  SdrD B-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.6   5.4e-05      0.19      26      74 ..      58     107 ..      43     119 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.4e-05
      SdrD_B  26 gvtVtLkdakgevv..atttTd.asGkYkFtnltpGeYkVeftapagytvta 74 
                  v +++ d++++++  + + T+ + G++ F+  ++G+Y+V++t+p++ +v  
  EPA05517.1  58 QVFIQILDKSQNIIseEMVQTKmSVGYFDFE--QSGTYTVKITNPTEKQVDI 107
                 5778888999999853344454466999998..79*********99877655 PP

>> Spore_YhaL  Sporulation protein YhaL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.5         2     7e+03       3       9 ..       9      15 ..       5      18 .. 0.63
   2 ?   11.2   0.1   6.3e-05      0.23       9      30 ..     130     151 ..     125     153 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2
  Spore_YhaL  3 wWvYlvi 9 
                +W+ +v 
  EPA05517.1  9 IWISFVF 15
                5666654 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 6.3e-05
  Spore_YhaL   9 iagIlfSgymavktakeEreld 30 
                  + I+fS ym +k  k E+  +
  EPA05517.1 130 AVMIIFSSYMKLKNYKIEHPEE 151
                 578*************999776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       839  (0.0467957); expected 358.6 (0.02)
Passed bias filter:                      603  (0.0336327); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1026.83
//
Query:       EPA05518.1  [L=288]
Description: ROK family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.3e-70  237.4   0.2    2.6e-70  237.2   0.2    1.0  1  ROK          ROK family
     0.0012   18.5   0.2     0.0055   16.2   0.1    2.1  2  BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
  ------ inclusion threshold ------
       0.01   15.6   0.0      0.018   14.8   0.0    1.4  1  Hydant_A_N   Hydantoinase/oxoprolinase N-terminal region
       0.05   13.2   0.0        0.1   12.1   0.0    1.5  1  FGGY_N       FGGY family of carbohydrate kinases, N-terminal 


Domain annotation for each model (and alignments):
>> ROK  ROK family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  237.2   0.2   5.8e-74   2.6e-70       2     290 ..       5     288 .]       4     288 .] 0.95

  Alignments for each domain:
  == domain 1  score: 237.2 bits;  conditional E-value: 5.8e-74
                 EEEEE-SSEEEEEEEETTS-EEEEEEEEEHCCHHCCHHHHHHHHHHCCCHCCHTEEEEEEEEESSEEETTCCEBSSGGCGCC.CCTTHHHHHHHHHTS- CS
         ROK   2 igidiGgtkialalvdeegeilarekvetptetteetlvdaiaelvdeaerkadeliavgigspGlisdksgkivstpnitw.enfdlvekleerlnvp 99 
                 +g+d+Ggtk++++l+d + +  +r++v+tp++++  +l ++i +l  ++ +   e  ++gi+ pG i +k+++++++ n +    + l+e+le++++  
  EPA05518.1   5 LGVDLGGTKTEAILLDTNLKLIKRKRVPTPQNNYDAIL-NTIFTLSVDLLDGI-EDYSIGICTPGAI-SKKTGLIKNSNTQClIGKSLKEDLEKKFGKN 100
                 69*****************************9998888.99999999998866.578**********.778888888999998**************** PP

                 EEEEEHHHHHHHHHHHHCTTTTTS-EEEEEESSSEEEEEEETTEEE--TTS-TT-GGGSBS-TTS-B-TTS-BSBHHHCCSHHHHHHCHTC.CGTTS-H CS
         ROK 100 vevenDvnaaalaEavfgaskdvenviyvtvgtGvGaGviingklitGrnGvagelGHiqldpegekcgCGnqgClEtlasgralekraqq.kgeklea 197
                 + +enD+n+++ aE+ +g +++++ v+ v++gtGvG+G++i+ kl++Gr+ +age+GH +l+ +g  c+CG+qgC+Et++sg++lekr+++ +g+  ++
  EPA05518.1 101 ISMENDANCFTIAESTIGSANGYDVVFGVIMGTGVGGGIVIDKKLHQGRTNIAGEWGHHTLHLNGNNCYCGKQGCVETYISGPSLEKRWKElTGKSQTM 199
                 ******************************************************************************************999999999 PP

                 HHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHHHHHH--SEEEEEHCCCTSTTHHHHHHHHHHHCCTTTTCCCT-EEEE-S-STTHHHHHHHHH CS
         ROK 198 keiiklaekgdevaeevverlaeylakaiadlinlfdpqaivlgGgvseadklleairklvkkylnkklevpvveivaaklgdkagllGaaaL 290
                  ei++  +  d++a++  +++ e+ ++++a++i ++dp+aivlgGg+s+ d l+ + +++v + +++ l  ++  i++ klgd+ag+ Gaa+L
  EPA05518.1 200 PEIVE--NTDDPNATKWKNEFLENFGIGLANVIDILDPDAIVLGGGLSNIDFLYTEGKNSVYHKVFSDLVDTP--ILKNKLGDSAGVFGAALL 288
                 99965..4567*******************************************9999999999999999999..9***************87 PP

>> BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   1.2e-06    0.0055       1      26 [.       5      30 ..       5     158 .. 0.91
   2 ?    0.0   0.0      0.11   4.9e+02     217     266 ..     235     288 .]     227     288 .] 0.69

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.2e-06
                 EEEEE-SSEEEEEEEETTTEEEEEEE CS
  BcrAD_BadFG  1 vGiDgGsTttkavlmdekgevlgrgi 26
                 +G+D+G+T+t a+l+d + ++++r  
   EPA05518.1  5 LGVDLGGTKTEAILLDTNLKLIKRKR 30
                 8****************999887754 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.11
                  SS.EEEESGGGG-HHHHHHH.....HHHH....-S-EE--GGGGGHHHHHHHHH CS
  BcrAD_BadFG 217 tdevtltGGvakneaavkelrklvkenyg....evkininpdsiytgalGAalf 266
                  +d ++l GG+++   ++ e ++ v  ++     + +i  n+  + +g+ GAal+
   EPA05518.1 235 PDAIVLGGGLSNIDFLYTEGKNSVYHKVFsdlvDTPILKNKLGDSAGVFGAALL 288
                  566888888888887777777776665541111456667888899999999985 PP

>> Hydant_A_N  Hydantoinase/oxoprolinase N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0     4e-06     0.018       1      44 [.       4      46 ..       4      63 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4e-06
  Hydant_A_N  1 rigIDvGGTfTDavaldekeeevavlKllstpdavaegireale 44
                ++g+D GGT T a++ld +  ++++ K + tp++   +i++ + 
  EPA05518.1  4 KLGVDLGGTKTEAILLDTN-LKLIKRKRVPTPQNNYDAILNTIF 46
                589**************88.667777777777888888888765 PP

>> FGGY_N  FGGY family of carbohydrate kinases, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.3e-05       0.1       1      34 [.       3      36 ..       3      42 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.3e-05
                EEEEEEEESSEEEEEEEETTS-EEEEEEEE--EB CS
      FGGY_N  1 lilglDcGttstkaivldekgkvvasaqaelels 34
                + lg+D+G+t+t ai+ld + k++++++++ +++
  EPA05518.1  3 YKLGVDLGGTKTEAILLDTNLKLIKRKRVPTPQN 36
                569************************9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1895.00
//
Query:       EPA05519.1  [L=323]
Description: cobalamin biosynthesis protein CobD [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.9e-85  284.2   0.0    1.1e-84  283.9   0.0    1.2  1  CobD_Cbib     CobD/Cbib protein
  ------ inclusion threshold ------
        0.1   11.7   0.0       0.15   11.2   0.0    1.2  1  AAA_9         ATP-binding dynein motor region
        1.3    8.5   6.0       0.18   11.3   1.2    1.9  2  E1-E2_ATPase  E1-E2 ATPase


Domain annotation for each model (and alignments):
>> CobD_Cbib  CobD/Cbib protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  283.9   0.0   1.8e-88   1.1e-84       2     272 ..      10     291 ..       9     318 .. 0.86

  Alignments for each domain:
  == domain 1  score: 283.9 bits;  conditional E-value: 1.8e-88
   CobD_Cbib   2 llAlllDlllgdprrllhPvvligklisalekrlrk..akkerlaGvllalllvllallvalllllla..laall........glvlealllkltlalr 88 
                 ++Al+lD+ lgdpr+ +hP  +ig+li++l+ ++++  +k e++ G+l++l+ +l+++ +++ l + +  +             +++ ++llk+t+a++
  EPA05519.1  10 FFALALDFTLGDPRNKFHPTSWIGSLIAKLTPYTKNssEKLEKFGGILIILISCLVVASLIISLNVGIklI---TfdylhliiSIIVGGILLKTTIAVK 105
                 78*****************************9885334667888998887776666655444444433331...13344555577999*********** PP

   CobD_Cbib  89 sLleevrkvakal.kgdleaaReavsmiVgRdtseldeeeiarAavEsvaENlsDgvvaPlfyflllglpgalaykavnTlDsmvGYkneryedfGwaa 186
                  +++++ +v +al +++l++aR ++smiV+R+t++ld++++ + ++Es++EN++Dg+++Plfyf+++glpga++++++nT+Dsm+GYk++ ++++Gw+ 
  EPA05519.1 106 GMEKHALAVVTALeQNNLSSARDNLSMIVKRNTKNLDKNHVFSGVLESISENTVDGITSPLFYFAFFGLPGAFVFRVINTADSMIGYKTDIFKNVGWFG 204
                 *************5599********************************************************************************** PP

   CobD_Cbib 187 ArlDDllnyiPARltalllala.........aalriarrdarkhpSpNsgwpeaalAgalgvrLggpnvY.lgkleekptlgdkkrpleaediera 272
                 A +D +lnyiP+Rlt+++++l+         ++++i++rd+rk++SpN+g+p+aa+Agal+ ++++ ++Y lg+ +          ++++e+++ a
  EPA05519.1 205 ANCDKILNYIPSRLTGFIMILSsmilgnnwkKSYQIMMRDGRKTQSPNAGYPMAAIAGALEAKFEKLDHYsLGDGS---------ISFTKEHVKSA 291
                 *********************755556555566*************************************777432.........22344444444 PP

>> AAA_9  ATP-binding dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   2.4e-05      0.15     138     184 ..      97     143 ..      67     162 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.4e-05
                 EEE---SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
       AAA_9 138 linFtvteeGLedqlLaevvkkerpeleekkeeliqeeaenkkqlke 184
                 l++ t+  +G+e+  La v + e+++l + +++l    ++n+k+l++
  EPA05519.1  97 LLKTTIAVKGMEKHALAVVTALEQNNLSSARDNLSMIVKRNTKNLDK 143
                 56669999**************************9999999998875 PP

>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.2   2.9e-05      0.18      98     159 ..      33      96 ..      29     104 .. 0.87
   2 ?   -1.8   0.3      0.32   1.9e+03     114     135 ..     293     314 ..     282     322 .. 0.51

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.9e-05
                   STTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTT..HHHHHHHHHHHHHS CS
  E1-E2_ATPase  98 arlveeakskktplqkkldklgkvlvpvvlliallvflialllgksla..eallralallvaai 159
                    +l+++ ++ +++  +kl+k+g++l++++ +++++ ++i l +g +l+  ++l  +++++v+ i
    EPA05519.1  33 GSLIAKLTPYTKNSSEKLEKFGGILIILISCLVVASLIISLNVGIKLItfDYLHLIISIIVGGI 96 
                   567777778889999***************************9999988778888999998765 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.32
                   HHHHHHHHHHHHHHHHHHHHHH CS
  E1-E2_ATPase 114 kldklgkvlvpvvlliallvfl 135
                    + k++++l++ ++++ ++++l
    EPA05519.1 293 SIMKVTSILFCGIVVVPIVLLL 314
                   3444455544444444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       954  (0.0532099); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 2098.39
//
Query:       EPA05520.1  [L=156]
Description: pyridoxamine 5'-phosphate oxidase family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-13   51.0   0.0    3.7e-13   49.5   0.0    1.6  2  Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
  ------ inclusion threshold ------
      0.012   15.5   1.3      0.012   15.5   1.3    1.5  2  GatB_Yqey       GatB domain


Domain annotation for each model (and alignments):
>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.5   0.0   4.1e-17   3.7e-13       2      87 ..       5      89 ..       4      90 .. 0.97
   2 ?   -1.2   0.0      0.27   2.4e+03      47      70 ..     106     129 ..     103     135 .. 0.78

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 4.1e-17
                    HHHHHHHHHHSSEEEEEEEETTSEEEEEEEEEEEETTTTEEEEEEETTSHHHHHHHHH-EEEEEEEETTGSEEEEEEEEEEEESCH CS
  Putative_PNPOx  2 deelreflaeskavvlATvdedGrPnvspvllkagdgrdgivfatnadsrklrnleenprvallflddelgrgvrieGtaelvsdg 87
                    + e++ef++e+ +++++T + ++ Pnvsp+ + + d++ +i++    +++ +rn ++np v++ ++++e+ +g++++G + +++++
      EPA05520.1  5 PNEIKEFIEEQGIFAVGTTGVNNLPNVSPRIFFRIDED-VIYWLDFFKHKSHRNFKANPWVTIAVFNKENLKGFQFRGIVSFITEE 89
                    679***********************************.*****************************************999987 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.27
                     ETTSHHHHHHHHH-EEEEEEEETT CS
  Putative_PNPOx  47 nadsrklrnleenprvallfldde 70 
                      + s+k++ l e   v +  ++++
      EPA05520.1 106 TNSSEKVKKLSEKKDVEVIQFEPK 129
                     578999999999999988777665 PP

>> GatB_Yqey  GatB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.52   4.6e+03      75      87 ..       7      19 ..       3      23 .. 0.76
   2 ?   15.5   1.3   1.3e-06     0.012      36      89 ..      70     125 ..      64     131 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.52
                XHHHHHHHCTXXX CS
   GatB_Yqey 75 speeiieekgLkq 87
                +++e iee+g+++
  EPA05520.1  7 EIKEFIEEQGIFA 19
                5788888888876 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.3e-06
                 TCSSTTHHHHHHHHHHHHTTSSGHHHHHHHHHHHH.HH.TXXHHHHHHHCTXXXXX CS
   GatB_Yqey  36 eelkltpeqlaellkliaegkIskkiakevleell.ee.gkspeeiieekgLkqis 89 
                 ++ +l+  q+  ++ +i e+ I +ki + +++++l ++ +++++++ e+k+ + i+
  EPA05520.1  70 NKENLKGFQFRGIVSFITEEPIKSKIKESIIKKILeTNsSEKVKKLSEKKDVEVIQ 125
                 5678999****************************64468999*******998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1057  (0.0589548); expected 358.6 (0.02)
Passed bias filter:                      572  (0.0319036); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1098.91
//
Query:       EPA05521.1  [L=443]
Description: UbiD family decarboxylase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-92  311.1   0.1    1.2e-92  311.0   0.1    1.0  1  UbiD             3-octaprenyl-4-hydroxybenzoate carboxy-lyase
  ------ inclusion threshold ------
      0.029   14.0   0.6       0.59    9.7   0.1    2.3  2  PGP_phosphatase  Mitochondrial PGP phosphatase


Domain annotation for each model (and alignments):
>> UbiD  3-octaprenyl-4-hydroxybenzoate carboxy-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  311.0   0.1   1.3e-96   1.2e-92       2     406 .]       9     392 ..       8     392 .. 0.95

  Alignments for each domain:
  == domain 1  score: 311.0 bits;  conditional E-value: 1.3e-96
                 HHCCCTTSEEEEESEB-TBTHHHHHHHHHHHHT--EEEEEEBTTB.TT-EEEE-TTS-HCHHHHHHTS-GHHHHHHHHHHHHHS..----EE--GCG-G CS
        UbiD   2 ealekagelvrikeevdpelEiaeiarrvleeggpallFenvkgkgskfpvltnlfgtrervalalglssleeileklaellepkppippkvvesekap 100
                 + ++k gel+++k++v++ +Eia i+ ++   g  a+lFen+   +s+f +++nl+gtr+r+a+a+g ss e+i + + +++++    +pk +   +++
  EPA05521.1   9 SLIKKSGELKTVKKQVSTTYEIAGITAKID--GSSAVLFENIV--ESNFHLISNLVGTRKRFAQAIG-SSEEQIHQTMISAIKK--AKKPKIIP--TGK 98 
                 67899************************9..899*******6..358*******************.888************7..379****5..577 PP

                 GGSEEECCCCC--HHHS---BSSTTSSS-EEECEEEEEE-TTTT-EEEEEEEEEEEETTEEEE--TTTHCHHHHHHHHHHCCT--EEEEEEES--HHHH CS
        UbiD 101 cqeevvlegddvdLskLPvltlwpgDgGpyitlglvitrdpetgkrnlgiyRmqvldknklglhwqihkggaehlrkakkkggeplpvavaiGvdPalt 199
                 ++e+        d+s +P++t+++++ Gp+it+ + ++++petg++n +++Rm+ +dk+++ ++++++++ ++ + +ak+ + e+l++av+iGv+Pa+ 
  EPA05521.1  99 FMENK-----SKDISIMPIVTHFEKESGPFITSSIAYVKNPETGEQNSSFHRMMPIDKTHFSIRMVEGRHLHRCFINAKEHH-EDLKIAVTIGVHPAIS 191
                 88555.....4689999**************************************************************999.9*************** PP

                 HHCTS--TTT-TCHHHHHHHHTS--EEEE-SSSSSEEETT-SEEEEEEEECCEEEECTTTC-TTSCEEC--CCEEEEEEEEEEE-TT-EEEE-SSSCCS CS
        UbiD 200 laAvaplPeglsElefaGalrgepvelvkcetvdlevpadAEivleGeidpgetapEGPfgdhtGyysevrdefpvfkVtaithRkdpiypttvvgkpp 298
                 +a++ ++  g +E+++a  l g+++ l k + ++l+vp+  Eiv+eG i  ++t+pE  +++++ +y++ r+ +p+f++++ + R++pi++ ++ g   
  EPA05521.1 192 IAGAYQAEWGKDEIDIANSLLGSKLTLSKLPYTGLHVPSGTEIVMEGKILQDKTHPEW-MVEMLQTYDHHRS-QPIFELESLYSRNNPIFHDILSGFS- 287
                 *********************************************************9.99******76655.7*****************9977776. PP

                 HHHHCHHHHHHHHHHHHHHCCSTTEEEEEE-GGGTTTCEEEEECHHHTCCHHHHHHHHHHCCTTGGC-SEEEEEEETTS-TTSHHHHHHHHHHC--CCC CS
        UbiD 299 eedallgkalealflpllkkqvpevkdvhlpeeggfhllavvsikkrypghakkvmealwalkqqlsltKlvivvDedvdvrdlkevlwaiatrvdpdr 397
                 e+ +l+g+++e+ +   lkk++p+ k+v ++  g+ +l+avv+ikk+++ + kk+++  ++ ++  sl K v vvDed+d+++ + v++a+atr+++d+
  EPA05521.1 288 EHRLLMGMPIESKLNGELKKTFPQTKKVSMTNGGCNWLHAVVQIKKKTDADPKKIIKKTFESHR--SL-KQVTVVDEDIDPNNAESVEYAMATRFQADK 383
                 **************************************************************99..99.****************************** PP

                 CEEEECCCE CS
        UbiD 398 Dlviiegtr 406
                 Dlvii+++r
  EPA05521.1 384 DLVIIKNVR 392
                 ******985 PP

>> PGP_phosphatase  Mitochondrial PGP phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1     0.013   1.2e+02      77     118 ..      50      92 ..      25     105 .. 0.77
   2 ?    9.7   0.1   6.6e-05      0.59      73     119 ..     378     424 ..     337     429 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.013
  PGP_phosphatase  77 eksilivSNsaGssddkdaekaealekktg..ipVlrhkekKPg 118
                      e++  ++SN  G++++  +   +++e+  +  i+ +  k kKP 
       EPA05521.1  50 ESNFHLISNLVGTRKRFAQAIGSSEEQIHQtmISAI-KKAKKPK 92 
                      457789**********99999999998777324443.3478885 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 6.6e-05
  PGP_phosphatase  73 evypeksilivSNsaGssddkdaekaealekktgipVlrhkekKPgc 119
                      +   +k+++i+ N  Gss d+++ +++   +k+gi   r   k+P +
       EPA05521.1 378 RFQADKDLVIIKNVRGSSLDPSSDQKNLKTAKIGIDATRSLLKRPEG 424
                      4456779********************************99999965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 3109.80
//
Query:       EPA05522.1  [L=533]
Description: thermosome, subunit [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   1.2e-177  591.5  19.3   1.4e-177  591.3  19.3    1.0  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  591.3  19.3  7.6e-182  1.4e-177       1     488 [.      38     526 ..      38     528 .. 0.99

  Alignments for each domain:
  == domain 1  score: 591.3 bits;  conditional E-value: 7.6e-182
                 HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHHHHHHHCTXXHHHHHHHHHHHHH CS
  Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleeaekliaagvhpttiiegyekale 99 
                 +a++v+++lGP+G+dKmlv++ g+v++TnDGatilke++++hPaak++ve++++ d+evGDGTt+ v++ g+Ll +ae+l++++vh ++ii+gy+ a+e
  EPA05522.1  38 VAELVRSSLGPRGLDKMLVDSLGDVTITNDGATILKEIDVQHPAAKMMVEISKTVDNEVGDGTTSSVVFGGALLARAEDLLKKDVHASVIIDGYQAAAE 136
                 689************************************************************************************************ PP

                 HHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHH.HCHCCCS..EECSCCCEECCCCEECECTTSEEESEEEESS--SSTTS CS
  Cpn60_TCP1 100 kaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAv.klieene..keldlgrikvvkieggsledselveGlvldkgvlspdm 195
                 k+le+ +e+a++i+   +dre+Llk+a ts++skl+s++++ lsk vvdA+ k+ ++++  +++dl++ikv+k+ ggs++d+++++G+vldk+v+++ m
  EPA05522.1 137 KTLEIYSEMAKKIKP--DDRETLLKIAITSMQSKLISEDSDILSKVVVDAIlKIATKKAetYSVDLENIKVEKKAGGSITDTQIIKGIVLDKEVVHSGM 233
                 *********888875..59********************************7777666699************************************** PP

                 SCEEECEEEEEESS-BS--HHCCHHHCCCCSCCHHHHHHHHHHHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT CS
  Cpn60_TCP1 196 pkklenakvllldvsLeiektetkttvvlsdaeeleklekaeekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatG 294
                 p+k+e+ak++ll+  Leiekte++++++++d+++++ ++++e+++l+ +++k++  gvnv++cqkgidd+a+h+lak+gi+a+rrvk++d+ +l katG
  EPA05522.1 234 PTKIEKAKIALLNSALEIEKTEMSSEIRITDPTQMQMFLEEENRMLKTMVDKLHHVGVNVLICQKGIDDIAQHYLAKYGIMAVRRVKESDMIKLGKATG 332
                 *************************************************************************************************** PP

                 --EBSCGGGGGCGC-EEEEEEEECCETTCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHHHHHHHHCCCCT CS
  Cpn60_TCP1 295 atavssledltpeelGtakkveeekigsekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatelelakklkeyaks 393
                 ++++s+l+dl++++lGta+  +++k++s+k+++ie++k+++++t+l+rg ++ v+de+ r+i+d+l vvk +ie++++v+GGGa e ++a+ lke+a+s
  EPA05522.1 333 GRVISNLDDLSEKDLGTADLAHQKKVESDKWVFIEGCKNPQSVTLLIRGGSQRVVDEVDRSIHDSLMVVKDVIEKPEIVAGGGAPESYAASLLKEWADS 431
                 *************************************************************************************************** PP

                 SXCCHHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTCEEECCCCTXEEEHHHHHHHHHHHHHHHHHHHCEEEEEX CS
  Cpn60_TCP1 394 vsgeeqlaieafakALevipktLaeNaGldpievlaklraahnkgekelgidvesgeiidlveagvvDplkvkrqalksAteaastiLrideiik 488
                  +g+eqlai+++a+ALe+ip t+aeNaG+dpi+++a lr ++n+g+k++gid+++ +i d+++  vv+pl+vk+q++ksAteaa++iLrid++i+
  EPA05522.1 432 FDGREQLAIKKYAEALEIIPLTIAENAGMDPIDTMATLRVKQNQGRKWTGIDARNTRIADMLSIDVVEPLAVKEQIIKSATEAACMILRIDDVIS 526
                 *********************************************************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (533 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       863  (0.0481343); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.46
# Mc/sec: 3518.05
//
Query:       EPA05523.1  [L=360]
Description: aspartate-semialdehyde dehydrogenase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.5e-36  124.4   0.0    8.2e-36  123.8   0.0    1.2  1  Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation dom
    1.1e-28  100.1   0.0      2e-28   99.2   0.0    1.4  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
  ------ inclusion threshold ------
      0.011   14.9   0.1      0.017   14.3   0.1    1.3  1  Paramyxo_PNT     Phosphoprotein P region PNT disordered
      0.047   13.3   0.6       0.88    9.2   0.2    2.5  2  Gp_dh_C          Glyceraldehyde 3-phosphate dehydrogenase, C-
       0.18   12.0   0.0       0.37   11.0   0.0    1.5  1  PilN             Fimbrial assembly protein (PilN)


Domain annotation for each model (and alignments):
>> Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.8   0.0   2.3e-39   8.2e-36       1     181 [.     166     338 ..     166     339 .. 0.91

  Alignments for each domain:
  == domain 1  score: 123.8 bits;  conditional E-value: 2.3e-39
                      HHHHHHCTT.EEEEEEEEEEEGGGCHHHHHHHHHHHHHHHHHSTTS.CTTTSSHHTTSEESTCSTBTTTTCHCBHHHHHHHHHHHHHCTESCSE CS
  Semialdhyde_dhC   1 LkPLldalgelervivatyqavSGaGkkgvreLlkqvaelqrsdeakpgvfgvpiagNlipyidkeedkgepetreelkavaetkkileftekv 94 
                      LkPL+++ ++ ++v+++++qa+SGaG++                   pgv+ ++i +N+ipyi kee+k  +etr++l+++++ k + ++ + v
       EPA05523.1 166 LKPLYEK-YGAKKVMMTSMQAISGAGRA-------------------PGVSAMNITDNIIPYIAKEEEKVRIETRKILGKLKNGKIEDANIK-V 238
                      8*****9.88*****************7...................************************************888777776.* PP

                      EEEEEEESBSSEEEEEEEEEES..SSHHHHHHHHHHHHCS.........TTEEEEESSHCHHSSHHHHTTC..SSSEEEEEEEEETTCTTEEEE CS
  Semialdhyde_dhC  95 satcvrVPvlrGhseavtiklk..lkdveveeveellaaa.........pevkvvvneeedrPtpaavagg..tnsvsVGRirkdemgdeglkl 175
                      s tc+rVPv++Gh+e+v+++++   ++  +++v++   ++         pe+    +e + rP+p++ +    ++++++GR++k e +d+glk+
       EPA05523.1 239 SCTCTRVPVIDGHTESVFVETDkdIDPLIAKQVYDDANSEstvsglpssPEKYYAFHEDPTRPQPRMERSVgdGMTTTIGRVEKEELFDHGLKY 332
                      *********************8665666677788877777*******9977777777789******9997778********************* PP

                      EEEEET CS
  Semialdhyde_dhC 176 vvvgDN 181
                      v  ++N
       EPA05523.1 333 VLFSHN 338
                      *****9 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.2   0.0   5.7e-32     2e-28       1     117 [.       5     134 ..       5     138 .. 0.98

  Alignments for each domain:
  == domain 1  score: 99.2 bits;  conditional E-value: 5.7e-32
                     EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSG..............GGTTTECEBEEEGGGGGCTT-SEEEE-SCHHHHHH CS
  Semialdhyde_dh   1 kvaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavk..............aleegkdlkvedvdeeelkevdivflalpagvske 81 
                     +vaivG tG vGqe++  L++hp++e++ +++s+rsaGkk+ ea +              ++e++k+++v+++de +l+++d+vf+a++++++++
      EPA05523.1   5 RVAIVGVTGSVGQEFVLSLNNHPWFEVTQIAASERSAGKKYLEAIRdpnsgiiswevegqIPEYIKEMTVKNIDELDLSQLDLVFSAVESKAARD 99 
                     7*******************************************999************************************************ PP

                     HHHHHHHTTSEEEESSSTTTTSTTSEBE-HHHHGGG CS
  Semialdhyde_dh  82 lapklaeagvkviDlssdfRlkddavyvlpevnrea 117
                     ++ k+ +a++ vi+ ss++R++dd+++ +p +n e+
      EPA05523.1 100 IETKI-AAQLPVISTSSAYRYEDDVPILIPGINDEQ 134
                     *****.899************************987 PP

>> Paramyxo_PNT  Phosphoprotein P region PNT disordered
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   4.9e-06     0.017      34      73 ..     260     299 ..     232     316 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.9e-06
  Paramyxo_PNT  34 diqldpmvtdvvyhdhggectghgpssspergwsyhmsgt 73 
                   d ++dp+++  vy d   e t  g  sspe+ +++h   t
    EPA05523.1 260 DKDIDPLIAKQVYDDANSESTVSGLPSSPEKYYAFHEDPT 299
                   6678********************************8766 PP

>> Gp_dh_C  Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       1.8   6.5e+03      85     106 ..      83     104 ..      80     114 .. 0.64
   2 ?    9.2   0.2   0.00024      0.88      65      97 ..     231     263 ..     162     285 .. 0.66

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.8
                 EEEEEEEEESSTS-HHHHHHHH CS
     Gp_dh_C  85 svvdlvvelekevtveevnaal 106
                 s+ dlv+   ++  + ++   +
  EPA05523.1  83 SQLDLVFSAVESKAARDIETKI 104
                 6666666666666666665554 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00024
                 SGGGTTTEEEEEEEESSSSEEEEEEEEEESSTS CS
     Gp_dh_C  65 lpelkgkldglAvrVPtpnvsvvdlvvelekev 97 
                 + + ++k++ +  rVP+++++  ++ ve++k+ 
  EPA05523.1 231 IEDANIKVSCTCTRVPVIDGHTESVFVETDKDI 263
                 445578999999*****************9986 PP

>> PilN  Fimbrial assembly protein (PilN)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0    0.0001      0.37      23      63 ..       3      41 ..       1      59 [. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0001
        PilN 23 gnqltitGsAvsndeVaefmrnLegspffknidlksaeqkt 63
                ++++ i+G++ s     ef+++L++ p+f+ +++  +e+  
  EPA05523.1  3 KKRVAIVGVTGSVG--QEFVLSLNNHPWFEVTQIAASERSA 41
                56788888884444..69************99999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 2190.31
//
Query:       EPA05524.1  [L=534]
Description: ATPase/histidine kinase/DNA gyrase B/HSP90 domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.6e-22   77.9   0.1    1.4e-21   77.1   0.1    1.5  1  HATPase_c      Histidine kinase-, DNA gyrase B-, and HSP90-li
    8.5e-12   44.9   0.5    1.7e-11   44.0   0.1    1.7  2  HisKA          His Kinase A (phospho-acceptor) domain
    1.5e-05   24.8   0.0    3.7e-05   23.5   0.0    1.6  1  HATPase_c_5    GHKL domain
     0.0033   17.3   0.1     0.0092   15.8   0.1    1.7  1  HATPase_c_3    Histidine kinase-, DNA gyrase B-, and HSP90-li
  ------ inclusion threshold ------
      0.022   14.6   0.0      0.052   13.4   0.0    1.6  1  MAPKK1_Int     Mitogen-activated protein kinase kinase 1 inte
      0.041   13.9   0.0      0.069   13.1   0.0    1.3  1  HATPase_c_2    Histidine kinase-like ATPase domain
        0.1   11.8   0.0       0.22   10.7   0.0    1.5  1  CobD_Cbib      CobD/Cbib protein
        8.7    5.2   8.5        6.8    5.5   1.1    2.8  3  ASC            Amiloride-sensitive sodium channel


Domain annotation for each model (and alignments):
>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.1   0.1   6.1e-25   1.4e-21       5     110 ..     433     530 ..     429     532 .. 0.92

  Alignments for each domain:
  == domain 1  score: 77.1 bits;  conditional E-value: 6.1e-25
                 HHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHHHHHHHHHTTTEEEEEEETTTEEE CS
   HATPase_c   5 rLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsivkklvelmgGeiwvesepgrGtt 103
                 ++  +++nl+ N++++++++g+ie++ik++ d++v+   D+G Gip e ++klfe++ +     ++++gtGlGl+ +k++vel++G+i+v+++p   tt
  EPA05524.1 433 KIDAAFINLILNSIQANPEGGTIEIKIKSDHDNVVVDFIDSGSGIPDEVMDKLFEPLFT-----TKQQGTGLGLASCKNIVELHKGKITVKNNP---TT 523
                 5667899*********99**********7669***********************6666.....699***********************9999...** PP

                 EEEEEES CS
   HATPase_c 104 ftftlpl 110
                 ft++lp+
  EPA05524.1 524 FTVRLPK 530
                 ****997 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0         4     9e+03      34      45 ..     296     307 ..     288     315 .. 0.61
   2 !   44.0   0.1   7.7e-15   1.7e-11       3      63 ..     324     388 ..     322     391 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 4
                 HSSCHHHHHHHH CS
       HisKA  34 teelkeyletie 45 
                  ee+k +l  i+
  EPA05524.1 296 LEEQKNNLTHII 307
                 456666555544 PP

  == domain 2  score: 44.0 bits;  conditional E-value: 7.7e-15
                 HHHHHHHHHHHHHHHHHHHHHHHHHHC.......T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCC CS
       HisKA   3 grflagvaHELrtPLsailgnaeaLkre.....gklteelkeyletiesearrldhlvedlLdlsr 63 
                 g++   +aH+Lr+PLs+i+  +++Lk +     +  ++   + le ies+++r++h+++d+Ld+ r
  EPA05524.1 324 GELSGRLAHDLRNPLSVIKISLDLLKQSpadtkI-SDDVTTKRLELIESSVERISHQIDDVLDYVR 388
                 6777789******************998888853.35677779********************987 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   1.7e-08   3.7e-05       9      97 ..     437     527 ..     430     529 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.7e-08
  HATPase_c_5   9 ilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg...ek.kkle..sskskkeehGiGlksireivkkykgnlsieaedglFtls 97 
                   + nl+ N+i+a  +       I+++++++++++++ +  s +g   e  +kl+    ++k++  G+Gl s ++iv+ +kg+++++++ ++Ft+ 
   EPA05524.1 437 AFINLILNSIQANPEGG----TIEIKIKSDHDNVVVDFIDSGSGipdEVmDKLFepLFTTKQQGTGLGLASCKNIVELHKGKITVKNNPTTFTVR 527
                  67888889888877755....7*****************9988855522455443444778899****************************986 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   4.1e-06    0.0092       5      63 ..     436     495 ..     432     515 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.1e-06
  HATPase_c_3   5 kAlaelvdNsldAdaen..vkievnknrgktgeivieDdGkGmseeelknalrlatsskea 63 
                   A + l+ Ns++A+ e   ++i+++ ++ ++  + + D G+G++ e +++ +++  ++k++
   EPA05524.1 436 AAFINLILNSIQANPEGgtIEIKIKSDH-DNVVVDFIDSGSGIPDEVMDKLFEPLFTTKQQ 495
                  68899*********99755556655553.5789999***************9998888874 PP

>> MAPKK1_Int  Mitogen-activated protein kinase kinase 1 interacting
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.3e-05     0.052      23      84 ..     461     522 ..     442     531 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.3e-05
  MAPKK1_Int  23 tDrDGvvllkvgddss.adsalrpslistfvlatdQasKLdlgknksiislyedyqvvqfnkl 84 
                 +D+D vv+  +   s  +d+++++ + + f+ + +Q+  L+l++ k+i+ l++ ++ v+ n  
  EPA05524.1 461 SDHDNVVVDFIDSGSGiPDEVMDKLFEPLFT-TKQQGTGLGLASCKNIVELHKGKITVKNNPT 522
                 8*******99999999899999999988886.679*******************999988754 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   3.1e-05     0.069      40     109 ..     438     508 ..     432     527 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.1e-05
  HATPase_c_2  40 ctNavehayleap.egpvevrlesdeealtvevaDsGpgfdpetlpdpteeepkeslkegGrGlalikglv 109
                  ++N +    + +p  g++e++++sd++ ++v + DsG g + e  ++  e+  +++++  G+Gla  k++v
   EPA05524.1 438 FINLILNSIQANPeGGTIEIKIKSDHDNVVVDFIDSGSGIPDEVMDKLFEPLFTTKQQGTGLGLASCKNIV 508
                  55555555566666899**********************77777777777777899999999998777776 PP

>> CobD_Cbib  CobD/Cbib protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   9.6e-05      0.22      44     127 ..     229     318 ..     179     325 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 9.6e-05
   CobD_Cbib  44 aGvllalllvllallvalllllla....laall..glvle..alllkltlalrsLleevrkvakalk.gdleaaReavsmiVgRdtseldeee 127
                  G+ l+l++  l+++++l+ ++++        +   +v+   ++++ + +a+  +l++ +  + ++k ++le+ ++++ +i+ ++t++l ++e
  EPA05524.1 229 FGIPLTLMMFSLIVIISLISAFYYnfdnQ---FsaDYVVPgvIVMITIFFAIIFILNKNMTRFVQMKtKELEEQKNNLTHIIDKKTQDLLKAE 318
                 56555555555554444444443332221...13322333336666677777776666666555664489*****************998776 PP

>> ASC  Amiloride-sensitive sodium channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.2     0.016        36      17      51 ..      79     112 ..      70     126 .. 0.81
   2 ?    5.5   1.1    0.0031       6.8      22      49 ..     149     176 ..     137     181 .. 0.82
   3 ?   -1.3   0.1      0.36   8.1e+02      29      88 ..     236     298 ..     231     390 .. 0.59

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.016
                 SXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
         ASC  17 rsllrrlfWlllllvslilfiiqivllvekylsyp 51 
                 ++ +++ +Wl  +++s++++i +i+  +   ++++
  EPA05524.1  79 KN-ISKKIWLFSFILSFAFCIPSIIACLDSLQTND 112
                 34.5688**************99998888777765 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0031
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
         ASC  22 rlfWlllllvslilfiiqivllvekyls 49 
                  +fW+lll+++li++i   ++l+++ ++
  EPA05524.1 149 SYFWMLLLFGFLIYCISDTFFLFSQLNN 176
                 58********************999887 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.36
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
         ASC  29 llvslilfiiqivllvekylsypvitsiels....veevpFPavTiCnlnpfkksavreldaek 88 
                 +++sli+ i +i+ ++ ++ ++ +  ++ +     + ++ F  + i n n+ +  +++  + e+
  EPA05524.1 236 MMFSLIVIISLISAFYYNFDNQFS-ADYVVPgvivMITIFFAIIFILNKNMTRFVQMKTKELEE 298
                 455555555555555555533322.222111122244566666666666666544333333322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (534 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1604  (0.089464); expected 358.6 (0.02)
Passed bias filter:                      696  (0.0388198); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.72u 0.34s 00:00:01.06 Elapsed: 00:00:00.50
# Mc/sec: 3221.75
//
Query:       EPA05525.1  [L=144]
Description: cytochrome C oxidase subunit II, periplasmic domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      3e-14   52.9   1.2    5.3e-10   39.2   0.0    2.1  2  COX2          Cytochrome C oxidase subunit II, periplasmic do
      6e-05   23.1   0.0    7.4e-05   22.8   0.0    1.3  1  Cupredoxin_1  Cupredoxin-like domain


Domain annotation for each model (and alignments):
>> COX2  Cytochrome C oxidase subunit II, periplasmic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.2   7.5e-06     0.068       2      20 ..      43      61 ..      42      74 .. 0.86
   2 !   39.2   0.0     6e-14   5.3e-10      55     113 ..      74     132 ..      65     138 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.5e-06
        COX2  2 tikaiGhqwywsyeytdfe 20
                +ik  G+qw+ws+e++d +
  EPA05525.1 43 VIKVTGQQWFWSFEHEDGT 61
                6999**********99865 PP

  == domain 2  score: 39.2 bits;  conditional E-value: 6e-14
        COX2  55 kirllvtaedvlhsfavpslgvkvdavpGrlnqvsllidreGvfyGqcselcGvnhssm 113
                   ++ + ++dv hsf +  + v +davpGr+n v++     G +  qc e cG  h  m
  EPA05525.1  74 AYKFEIMSKDVNHSFNIHDYVVLMDAVPGRVNTVWFAPMEVGEHDIQCREYCGLIHYNM 132
                 568899**************************************************988 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   8.3e-09   7.4e-05      28     102 ..      58     136 ..      15     138 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 8.3e-09
  Cupredoxin_1  28 kdggfePskievkagekvklkiknkdktpeefesedlgeekvlapgktttitiaplkpGeYeftcd.....mhmdakGkl 102
                   +dg+ e  +++vk+g   k++i  kd   ++f ++d  +  +  pg  +t+++ap + Ge+++ c+     +h +++Gkl
    EPA05525.1  58 EDGTKEIGELHVKKGHAYKFEIMSKDV-NHSFNIHDYVVLMDAVPGRVNTVWFAPMEVGEHDIQCReycglIHYNMRGKL 136
                   566777889*************98875.69******99999************************986665555688887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 954.38
//
Query:       EPA05526.1  [L=212]
Description: hypothetical protein BG20_I0251 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-17   63.7   0.1    2.4e-17   62.8   0.1    1.5  1  FeS_assembly_P  Iron-sulfur cluster assembly protein
    1.5e-10   41.2   0.1    2.6e-10   40.5   0.1    1.3  1  PqqD            Coenzyme PQQ synthesis protein D (PqqD)
  ------ inclusion threshold ------
      0.013   15.5   0.5      0.025   14.6   0.5    1.4  1  HemN_C          HemN C-terminal domain
      0.096   13.0   0.2       0.21   11.9   0.2    1.6  1  DUF4777         Domain of unknown function (DUF4777)
       0.17   11.9   0.0       0.32   11.0   0.0    1.4  1  HTH_46          Winged helix-turn-helix DNA binding


Domain annotation for each model (and alignments):
>> FeS_assembly_P  Iron-sulfur cluster assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.8   0.1   6.8e-21   2.4e-17       2      73 ..       7      79 ..       6      80 .. 0.95

  Alignments for each domain:
  == domain 1  score: 62.8 bits;  conditional E-value: 6.8e-21
                    HHHHHHHTT-B-TTTSSBCCCCT---EEEE-T.-EEEEEE--SSTT-TTHHHHHHHHHHHHC.STT--EEEEE CS
  FeS_assembly_P  2 eavlaaLrtVtDPelgvdlvslglvreidieg.gkVsvditltypacslaeairadaeaalralpgvevveVe 73
                    +a+ + L++ +DPe ++++v++gl+++id+ + ++V++++t+t+ +c+l e + +d+ + ++++pgv+ v+V+
      EPA05526.1  7 QAIKDSLKQCMDPEVPLNIVEMGLIYGIDVVEnNNVNIKMTMTTQGCPLHETLVQDVTRYAKKVPGVNNVKVD 79
                    89***************************9999*********************************8888876 PP

>> PqqD  Coenzyme PQQ synthesis protein D (PqqD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.5   0.1   7.1e-14   2.6e-10       4      67 .]     134     197 ..     131     197 .. 0.93

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 7.1e-14
                 EE-SS-..EEE--CHHHHHHHH-SSSS-HHHHHHHHHHHCT--HHHHHHHHHHHHHHHHCTT-- CS
        PqqD   4 lldpetgkyisLnetgafiWklldgersveeivaalaeeydvdeeeaeadvlafldqLrekgli 67 
                 +l+ e  + ++ n+   + Wk+++g+r+v e+v+++a++++  ++++e+ v ++l+qLre gli
  EPA05526.1 134 VLANEHEQGFMVNQAIVDFWKSCNGQRKVTELVEIFAQQTGLQRNQVEKEVMQLLQQLREGGLI 197
                 6666677789****************************************************98 PP

>> HemN_C  HemN C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.5     7e-06     0.025      24      55 ..     167     201 ..     165     202 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 7e-06
      HemN_C  24 aafeqrfgld...leellaaaleklqeqGLLeldg 55 
                 + f+q++gl+   +e+++++ l++l+e GL+ +++
  EPA05526.1 167 EIFAQQTGLQrnqVEKEVMQLLQQLREGGLIAIQN 201
                 689****************************9987 PP

>> DUF4777  Domain of unknown function (DUF4777)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   5.9e-05      0.21      23      51 ..     163     191 ..     161     202 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.9e-05
     DUF4777  23 dEivervaerydlseeelkkvVkntLeaA 51 
                  E+ve +a+ ++l+ ++++k+V ++L++ 
  EPA05526.1 163 TELVEIFAQQTGLQRNQVEKEVMQLLQQL 191
                 69************************975 PP

>> HTH_46  Winged helix-turn-helix DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   8.9e-05      0.32       5      57 ..     145     201 ..     143     203 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8.9e-05
      HTH_46   5 iralLleLielpeelreninvlkyIqkrtnLSrSs....imkvLseLkkggyIeier 57 
                 + + + + ++  +  r+ ++ ++   ++t L r      +m+ L++L++gg I i++
  EPA05526.1 145 VNQAIVDFWKSCNGQRKVTELVEIFAQQTGLQRNQvekeVMQLLQQLREGGLIAIQN 201
                 666677777777778888888888889999999752333799************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1143  (0.0637515); expected 358.6 (0.02)
Passed bias filter:                      797  (0.0444531); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1348.01
//
Query:       EPA05527.1  [L=323]
Description: putative histidinol-phosphate transaminase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-51  175.3   0.0    2.4e-51  175.1   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
     0.0066   15.5   0.0      0.017   14.1   0.0    1.6  2  Aminotran_5      Aminotransferase class-V
  ------ inclusion threshold ------
      0.047   12.2   0.0      0.073   11.6   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.1   0.0   3.9e-55   2.4e-51       2     310 ..      27     304 ..      26     319 .. 0.92

  Alignments for each domain:
  == domain 1  score: 175.1 bits;  conditional E-value: 3.9e-55
                    EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEE CS
  Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeil 97 
                    d+++++sn  + +    +++ v+k+ k       ++++y++++ + +l+++l  +l+        +++++v g+Ga+++i  + +++ l  ++ +l
     EPA05527.1  27 DILDFSSNISPLG----PSQMVRKTIKN---HLDSVKIYPDSE-STTLKKNLQNYLK-------IPSSQIVIGNGATEIIYNFCQAF-LSNKTSVL 106
                    7899*********....99988888865...8889********.*************.......8999*******************.******** PP

                    EEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTC CS
  Aminotran_1_2  98 vpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagf 193
                    +p pt+++y+ +++lsg++v  ++            +le++++e+ ++ + + +i++++p+NPtG+++++++l+k+++ a+k++ l+fvDe + ++
     EPA05527.1 107 IPIPTFGEYESAAKLSGSKVSFFK----------TMNLEQDIDEFISKFPFNGCIFICNPNNPTGQLMKKQTLQKIIRSAHKKKTLVFVDECFIEL 192
                    ************************..........33455555555555557789****************************************** PP

                    BSSSSHTHHH.HGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
  Aminotran_1_2 194 vfgsldavat.ranveeepnllivgslsKafGlaGeRvGyilgnaavvsqlrklsrpflsssllqaavaaalsdallkqseleemrqrlqkrrkel 288
                    v +   +++t + +v++  nl++++sl K+f+laG+R+Gy +g++ ++s l+ ++ p+++s ++q+a+++al+d+     +l++  + ++k++ +l
     EPA05527.1 193 VPD---YNETiIELVKKFSNLFVLRSLTKSFALAGLRIGYGIGSKQIISVLNTIKIPWNVSGIAQYAASTALDDPT----YLNKVNKIIKKESSYL 281
                    **9...66775778888888********************************************************....**************** PP

                    HHHHHHS.TEEEECCSCSSEEEE CS
  Aminotran_1_2 289 rdeLael.glkvlasqsgmfllt 310
                     d++ +  ++++++  ++++l+ 
     EPA05527.1 282 IDRISKFnNFQCIPTSTNFILIK 304
                    ****888************9875 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   2.9e-06     0.017      47     176 ..      65     187 ..      50     189 .. 0.85
   2 ?   -2.1   0.0      0.24   1.4e+03     271     301 ..     265     295 ..     248     318 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.9e-06
                  HHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEE CS
  Aminotran_5  47 earekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklva 144
                  + ++++++ ++++s ++i+   G+te i  + +++   l++++++++  +   ++    + +ak  g kv +++   + e d+de+ ++  +    ++
   EPA05527.1  65 TLKKNLQNYLKIPS-SQIVIGNGATEIIYNFCQAF---LSNKTSVLIP-IPTFGEY---ESAAKLSGSKVSFFKT-MNLEQDIDEFISKF-PFNGCIF 152
                  568999999****8.9*********8777777777...8999998885.6778888...6777778****99987.88999999**9999.7778899 PP

                  EESBETTTTE...B--HHHHHHHHHHTT-EEEEE- CS
  Aminotran_5 145 ithvsnvtGt...iqpveeigklakkkgalvlvDa 176
                  i+  +n tG     q +++i++ a+kk+ lv+vD 
   EPA05527.1 153 ICNPNNPTGQlmkKQTLQKIIRSAHKKKTLVFVDE 187
                  *********953347899****************6 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.24
                  HHHHHHHHHHHHHHHHHHHHHCTSTTEEEES CS
  Aminotran_5 271 igleaiekhekelaeyllerlkslpgvrlyg 301
                  + l++++k  k+ ++yl +r+++ ++++++ 
   EPA05527.1 265 TYLNKVNKIIKKESSYLIDRISKFNNFQCIP 295
                  5578888999999999999999999998854 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   1.2e-05     0.073     115     177 ..     122     190 ..      93     197 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.2e-05
                      TTCEEEEESTTSH.HHHHHHCCT..TEEEEEEESS-TTT...T----HHHHHHHHHHTT-EEEEEGTTT CS
  Cys_Met_Meta_PP 115 lgievkfvdtsdl.eelekaike..ntklvylEtptnpl...lkvvDiekiaklakkagvlvvvDntfa 177
                      +g +v+f+ t +l +++ + i++     ++++  p np+   +k   ++ki++ a+k+++lv+vD +f+
       EPA05527.1 122 SGSKVSFFKTMNLeQDIDEFISKfpFNGCIFICNPNNPTgqlMKKQTLQKIIRSAHKKKTLVFVDECFI 190
                      556666666654413466666554356799999999997333666789*******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       826  (0.0460706); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2080.05
//
Query:       EPA05528.1  [L=391]
Description: alanine transaminase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-56  191.7   0.0    2.4e-56  191.5   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    3.2e-07   30.0   0.0    5.1e-07   29.3   0.0    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    6.5e-06   25.3   0.0    1.3e-05   24.4   0.0    1.4  1  Aminotran_5      Aminotransferase class-V
    0.00031   19.4   0.0    0.00041   19.0   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
  ------ inclusion threshold ------
       0.12   11.6   0.0       0.24   10.7   0.0    1.4  1  Beta_elim_lyase  Beta-eliminating lyase


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.5   0.0   6.7e-60   2.4e-56       6     354 ..      34     376 ..      30     385 .. 0.94

  Alignments for each domain:
  == domain 1  score: 191.5 bits;  conditional E-value: 6.7e-60
                    SSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEES CS
  Aminotran_1_2   6 LgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdp 101
                    L+++++ +  g  ++++v++a++   +  ++ n+y+ ++glpel+ ++ak  +  ++l++  +  ++ ++G +++++++i  + ++ gde+l+p p
     EPA05528.1  34 LNIGDPVQF-GFQPPDNVKEAMIN--AIRKGENFYSSSEGLPELRAEIAKKEN-VKGLSISSD-DILITNGVSEGLDMVISSI-VEEGDEVLLPGP 123
                    778888888.667999******98..999999*******************99.889999999.*******************.9*********** PP

                    S-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSS CS
  Aminotran_1_2 102 tyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgs 197
                    +y++y  ++rl+gg  v++ ++  ++ + d+++++ +++       kt  i++ sp+NPtG+v+++  l+kl+++a+++nl++++De+Y    f+ 
     EPA05528.1 124 YYPPYASYVRLHGGIPVEFGVD-LDNSTPDIDDIKSKISP------KTVAICLISPNNPTGVVFNESSLKKLVEIANQHNLYIICDEIYDQIIFD- 211
                    ********************55.7888************9......999*********************************************9. PP

                    SHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEH.....HHHHHHHHHHHHHTS.SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
  Aminotran_1_2 198 ldavatranveeepnllivgslsKafGlaGeRvGyilgna.....avvsqlrklsrpfls.ssllqaavaaalsdallkqseleemrqrlqkrrke 287
                    +++v  + +v+ +  +++++++sK   + G+R+Gyi+ n+     a+++ l kl+r  +    ++q+a++++l+ ++    +++e +++l+krr+ 
     EPA05528.1 212 QKFVG-IGKVAGDSPVIVLNGFSKVHLMSGWRIGYIAFNQssqldALRENLPKLARVRIAtNLPVQYAALESLRGPQG---YISEFVSELKKRRDL 303
                    67888.********************************999***************9999899**************8...89************* PP

                    HHHHHHHS.TEEEECCSCSSEEEEEETHH...CHHHHHHHHHHTCTEEEEEGGGGTS...TTEEEEECTTS-HH CS
  Aminotran_1_2 288 lrdeLael.glkvlasqsgmflltdlsae...takelskkLleevgvyvtpgtsftv...pgrlRitvAgltee 354
                    ++++L+   gl++  ++++++ +  ++     ++ke+ +kLle +gv+ ++g+ f+    +g++R+ +   + e
     EPA05528.1 304 VVKRLNTMpGLSCPNPKGAFYAFPKIEDNrfgNDKEFVQKLLETKGVLTVHGSGFGEqygKGHFRLVY-LPSLE 376
                    *****999*********************************************************998.44444 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.0   1.4e-10   5.1e-07      60     144 ..     112     202 ..      91     203 .. 0.83

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 1.4e-10
                      TTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTEEEEEEB...-GGGB--...-HHHHHHHHHHCT-EEEEE CS
  DegT_DnrJ_EryC1  60 vgpgdeVIvpsltFvatanavlelgakpvfvDvdpdtynidpaaieaaitertkaIlpV...hlyGqva...dmdalkaiaakhglkvieD 144
                      v++gdeV+ p   +   a+ v+  g  pv   vd d  ++d ++i+++i ++t aI ++   +  G v+    +++l +ia++h+l++i D
       EPA05528.1 112 VEEGDEVLLPGPYYPPYASYVRLHGGIPVEFGVDLDNSTPDIDDIKSKISPKTVAICLIspnNPTGVVFnesSLKKLVEIANQHNLYIICD 202
                      678**************************************************99886522256788774336999999**********88 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   3.6e-09   1.3e-05      58     175 ..      89     202 ..      56     205 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 3.6e-09
                  -STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB CS
  Aminotran_5  58 aeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtGti 155
                  ++ +++i+ t G +e++ +v+ s+   +++gde+++    +       ++l    g+ v++    ++ + d+d++++++++kt ++++   +n tG++
   EPA05528.1  89 IS-SDDILITNGVSEGLDMVISSI---VEEGDEVLLPGPYYPPYA-SYVRL--HGGIPVEFGVDLDNSTPDIDDIKSKISPKTVAICLISPNNPTGVV 179
                  34.489******************...*********999888777.55555..59*****99999********************************7 PP

                  --...HHHHHHHHHHTT-EEEEE CS
  Aminotran_5 156 qp...veeigklakkkgalvlvD 175
                  +    +++++++a +++ ++++D
   EPA05528.1 180 FNessLKKLVEIANQHNLYIICD 202
                  64233889999999********9 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.2e-07   0.00041      75     175 ..      98     204 ..      50     212 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.2e-07
                      SHHH.HHHHHHHTTS-TTEEEEEESTSSHHHHHHHH...HTHHHTTCEEEEESTTSHHHHHHHCCTTEEEEEEESS-TTTT--...--HHHHHH CS
  Cys_Met_Meta_PP  75 sGma.AiaaailallkaGdeivvsddlYggtqrllk...kvlkklgievkfvdtsdleelekaikentklvylEtptnpllkv...vDiekiak 161
                       G++  ++++i +++++Gde+++    Y +  ++++    +  ++g++ +   + d+++++++i+++t ++ l +p np+  v     ++k+++
       EPA05528.1  98 NGVSeGLDMVISSIVEEGDEVLLPGPYYPPYASYVRlhgGIPVEFGVDLDNSTP-DIDDIKSKISPKTVAICLISPNNPTGVVfneSSLKKLVE 190
                      44442578999**************99977655544111456678888887665.89**********************9655111679***** PP

                      HHHHTT-EEEEEGT CS
  Cys_Met_Meta_PP 162 lakkagvlvvvDnt 175
                      +a ++++ ++ D  
       EPA05528.1 191 IANQHNLYIICDEI 204
                      *********99975 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   6.6e-05      0.24     108     167 ..     150     202 ..     130     203 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 6.6e-05
                      BE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEE CS
  Beta_elim_lyase 108 kmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlD 167
                      + d+++++++i +      k+ +i+l   nn   G v    +l+++ +ia+++++ +++D
       EPA05528.1 150 TPDIDDIKSKISP------KTVAICLISPNNP-TGVVFNESSLKKLVEIANQHNLYIICD 202
                      5677777777766......7999***999995.9**********************9999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2498.68
//
Query:       EPA05529.1  [L=167]
Description: thioesterase family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-14   54.0   0.1    2.5e-14   53.4   0.1    1.3  1  4HBT             Thioesterase superfamily
     0.0002   20.9   0.2    0.00032   20.2   0.2    1.3  1  MaoC_dehydratas  MaoC like domain
  ------ inclusion threshold ------
      0.025   14.8   0.1      0.039   14.2   0.1    1.3  1  OspE             Borrelia outer surface protein E


Domain annotation for each model (and alignments):
>> 4HBT  Thioesterase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   0.1   4.2e-18   2.5e-14       2      77 ..      35     109 ..      34     111 .. 0.97

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 4.2e-18
                 SSB-HHHHHHHHHHHHHHHHHHTTSTTEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEEEEEEEETTSCE CS
        4HBT   2 GvvhgGvylallDeaagaalrslggrgilvvvvelsidflrpvrlgdeltvearvlrlgrtsavvevevrdedgrl 77 
                 G+v+gG +l+ +D +ag+++ ++  +  +v+v+ +s++f++pv +g++l + ar++++ ++s+++ev+  +ed ++
  EPA05529.1  35 GNVFGGEILKHIDMVAGIVAQRHSQS-NAVTVSMDSVNFIKPVFVGNVLKLNARINYVHNSSMEIEVKAEAEDIVT 109
                 9*************************.********************************************99876 PP

>> MaoC_dehydratas  MaoC like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.2   5.4e-08   0.00032      62     118 ..      49     105 ..      45     110 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 5.4e-08
                      HHHHHHHHHSTTEGGGEEEEEEEE-S--BTTCEEEEEEEEEEEEEEEEEEEEEEEEE CS
  MaoC_dehydratas  62 vaklveeelgdnvvarvgeikvrFtkpVlpgdtlkvelevvgkrdvrktkkvevtke 118
                      va++v+++  ++++  v +++v F+kpV++g+ lk  +  + + +  ++++v+++ e
       EPA05529.1  49 VAGIVAQRHSQSNAVTVSMDSVNFIKPVFVGNVLKLNARINYVHNSSMEIEVKAEAE 105
                      778888999999999*********************999999999888888877655 PP

>> OspE  Borrelia outer surface protein E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   6.5e-06     0.039      50     106 ..      66     124 ..      41     125 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.5e-06
                 GGGHHHHHHHHHHS-EEE-SEE---..TTBGGGTT-EET-EEEEEEEESSSSEEEEEEE CS
        OspE  50 eseinnfikamikggsfktslyygy..keeesdknviknkeiktkiekindaefitflg 106
                   +  nfik +  g  +k +    y  ++  + +   +  +i t i+++ ++ f+tf+g
  EPA05529.1  66 SMDSVNFIKPVFVGNVLKLNARINYvhNSSMEIEVKAEAEDIVTGIKTVTGTAFVTFVG 124
                 344568********998766555550055555555566789****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1059.16
//
Query:       EPA05530.1  [L=173]
Description: adenosylcobinamide-GDP ribazoletransferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.7e-33  115.4   8.1    4.3e-33  115.2   8.1    1.0  1  CobS          Cobalamin-5-phosphate synthase
  ------ inclusion threshold ------
      0.021   14.8   1.5      0.021   14.8   1.5    2.1  2  RseC_MucC     Positive regulator of sigma(E), RseC/MucC
       0.51   10.1   3.5       0.22   11.3   0.5    1.7  2  TMEM208_SND2  SRP-independent targeting protein 2/TMEM208


Domain annotation for each model (and alignments):
>> CobS  Cobalamin-5-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.2   8.1   7.2e-37   4.3e-33       2     145 ..       9     166 ..       8     172 .. 0.85

  Alignments for each domain:
  == domain 1  score: 115.2 bits;  conditional E-value: 7.2e-37
        CobS   2 lsflTrlPvp.....elaralaffPlvGlllGlll.llallllllll.llaallavaalvlltgglHlDGlaDtaDglgsgrdrerrleImkDsrvGaf 93 
                 +sflT+lP        +a+ +++fP+vG+++Gl++  + + l+l+l  l+ +ll+va  +++tg++H DGlaD+aDgl++++++e++l++mkD ++G+ 
  EPA05530.1   9 FSFLTILPTSnsnleTIAKYMYLFPIVGAVIGLVVgSIGFGLSLFLDpLIVSLLVVASFAIITGIHHTDGLADFADGLMAKGTKEKKLAAMKDLSTGSA 107
                 89*******8664434488****************88888888877755588888999999*****************9999***************** PP

        CobS  94 Gvlalvlvlllkvaa..laala........lllapvlsRlaallaiallpyaeeglgalfae 145
                 G++++vl+++  ++a  l   +        +ll+++l++++++l+++++++a+ g  ++f+e
  EPA05530.1 108 GIVTIVLYIVGLIIAisL---StgyqlflaILLSEILAKFSMVLMASIGKSASLGSNSPFVE 166
                 *************99432...2234555667899****************997677777765 PP

>> RseC_MucC  Positive regulator of sigma(E), RseC/MucC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   1.5   3.5e-06     0.021      59     114 ..      18      73 ..      14      82 .. 0.82
   2 ?    1.0   1.7     0.063   3.8e+02      76     112 ..     113     150 ..     101     165 .. 0.52

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.5e-06
   RseC_MucC  59 eeksllkaallvYllPllllilgallgsallgssellaalgallglvlgflivrll 114
                 ++++l + a ++Yl+P+++ ++g+++gs+ +g s +l  l+  l++v++f i++ +
  EPA05530.1  18 SNSNLETIAKYMYLFPIVGAVIGLVVGSIGFGLSLFLDPLIVSLLVVASFAIITGI 73 
                 67778888999******************997888888888888888888887655 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.063
   RseC_MucC  76 lllilgallgsall.gssellaalgallglvlgflivr 112
                 +l i+g++++ +l+ g + +la+l++ +++ ++++++ 
  EPA05530.1 113 VLYIVGLIIAISLStGYQLFLAILLSEILAKFSMVLMA 150
                 33444444444444333333344444444434433333 PP

>> TMEM208_SND2  SRP-independent targeting protein 2/TMEM208
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1      0.23   1.4e+03      12      38 ..      20      46 ..      17      76 .. 0.53
   2 ?   11.3   0.5   3.7e-05      0.22       6      70 ..      88     155 ..      86     162 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.23
  TMEM208_SND2 12 eNkatLknlrlislavnalylllrlll 38
                  +N +t+ ++ +++ +v a+  l+   +
    EPA05530.1 20 SNLETIAKYMYLFPIVGAVIGLVVGSI 46
                  666677777666666666665554444 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 3.7e-05
  TMEM208_SND2   6 aKkiaeeNkatLknlrlislavnalylllrlll...rsslrprslllylllslpalllyyvlekmgrp 70 
                   aK ++e+  a++k l+++s+++ +++l +  l+   + s+ ++ +l +ll++++a +++ +++++g+ 
    EPA05530.1  88 AKGTKEKKLAAMKDLSTGSAGIVTIVLYIVGLIiaiSLSTGYQLFLAILLSEILAKFSMVLMASIGKS 155
                   577788888999******99999888877766666455555566667778889999999999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       759  (0.0423336); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1182.20
//
Query:       EPA05531.1  [L=145]
Description: hypothetical protein BG20_I0226 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00028   21.1   6.5    0.00041   20.5   6.5    1.4  1  Spore_III_AB     Stage III sporulation protein AB (spore_III_
      0.005   16.3   0.9      0.042   13.3   0.0    2.0  2  HBM              Helical bimodular sensor domain
     0.0062   16.4   1.7     0.0062   16.4   1.7    2.1  2  Sec5             Exocyst complex component Sec5
  ------ inclusion threshold ------
      0.013   15.5   1.5       0.07   13.1   0.8    2.0  2  RRF              Ribosome recycling factor
      0.038   13.7  11.1       0.14   11.9   0.3    2.1  2  DDE_Tnp_ISL3     Transposase
      0.062   13.2   0.0       0.21   11.5   0.0    1.8  2  Dak2             DAK2 domain
       0.11   12.5   2.1       0.19   11.6   1.9    1.6  1  HNOB             Haem-NO-binding
       0.16   12.3   2.0       0.92    9.8   0.5    2.4  2  DUF1722          Protein of unknown function (DUF1722)
       0.22   11.9   8.5       0.33   11.3   4.3    2.1  2  OmpH             Outer membrane protein (OmpH-like)
       0.24   11.3   3.4         31    4.5   0.1    3.5  4  HU-CCDC81_bac_2  CCDC81-like prokaryotic HU domain 2
       0.26   11.7   9.7        4.5    7.7   0.2    2.8  3  DASH_Dad2        DASH complex subunit Dad2
       0.34   10.8   3.2       0.51   10.2   0.9    2.1  2  Sec34            Sec34-like family
       0.48   10.6   5.3        1.2    9.3   3.9    2.2  1  Ribonuc_2-5A     Ribonuclease 2-5A
        0.5   10.1   5.2       0.36   10.5   1.6    1.9  2  DUF745           Protein of unknown function (DUF745)
       0.53   10.6   5.4        4.6    7.6   3.4    2.9  2  FCH              Fes/CIP4, and EFC/F-BAR homology domain
       0.55   10.8   2.7        4.6    7.8   2.7    2.3  1  YtxH             YtxH-like protein
        1.5    8.3  11.0        2.6    7.5  11.0    1.3  1  DUF2884          Protein of unknown function (DUF2884)
        1.5    9.4   5.9         23    5.6   0.7    3.4  3  BrnA_antitoxin   BrnA antitoxin of type II toxin-antitoxin sy
        3.8    6.6   8.3         43    3.2   1.1    2.5  3  JHBP             Haemolymph juvenile hormone binding protein 


Domain annotation for each model (and alignments):
>> Spore_III_AB  Stage III sporulation protein AB (spore_III_AB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   6.5   4.3e-07   0.00041      53     148 ..      26     123 ..       5     133 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 4.3e-07
                   HHHHHHH...HCS-TTHHHHHHHHHHHHH.STSS-HHHHHHHHHHHHGGGS---HHHHHHHHHHHHHHT--SHHHHHHHHHHHHHHHHHHHHHHHHH CS
  Spore_III_AB  53 ealekla...eksesplseffeevaerleekegesfeeaweeavekllkklaLkkedkeilkelgeslgysdregqlkalelaleeleeeieearee 146
                    ++e+++   ++++s++++++e++ ++ + ++ ++f+e w++a+ ++++k a++++ ++ +ke+ges  +s  e++  a++ ++e+ ++ +     e
    EPA05531.1  26 TMFEQIQnatNEMQSKFNDVWEKATKESSVDTMKQFSENWQKALGENWQK-AINDAGMKSFKEFGESWQKSLNETNTVAFKQFMENWQNSLNSSGME 121
                   4777777333566668888899999998889***************9866.***********************************99999877655 PP

                   HH CS
  Spore_III_AB 147 ak 148
                   + 
    EPA05531.1 122 QM 123
                   54 PP

>> HBM  Helical bimodular sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   4.4e-05     0.042     195     234 ..       8      47 ..       2      52 .. 0.85
   2 ?    2.2   0.2      0.11     1e+02      44     121 ..      52     132 ..      46     139 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.4e-05
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
         HBM 195 qqlesalskYRaaleqfkaavaaieqarkemteqgdeivk 234
                 ++  s  ++Y ++le++k+ +++i++a +em+++++++ +
  EPA05531.1   8 NEWDSLWQEYSKSLENWKTMFEQIQNATNEMQSKFNDVWE 47 
                 566666799*************************998765 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.11
                 HHHHHHHHHHHHH.HHHHHHH--SHHHHHHHHHHHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
         HBM  44 aavqkkldelkaq.lqklkakfkspenvrlLqeqlalvqeyrksfnelraay..esrnaaRqeldsaaeraleaideleae 121
                 +   ++++++++  +++l ++ +++ n   +++  +  +  +ks+ne++ +   +  ++  ++l+s++ +  +a +el ++
  EPA05531.1  52 ESSVDTMKQFSENwQKALGENWQKAINDAGMKSFKEFGESWQKSLNETNTVAfkQFMENWQNSLNSSGMEQMKAYGELMKK 132
                 445567777776624556678899999999999999999999999998865311334666666777776666666666655 PP

>> Sec5  Exocyst complex component Sec5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   1.7   6.5e-06    0.0062      39      84 ..      15      66 ..       1      70 [. 0.81
   2 ?    1.1   0.2      0.31   2.9e+02      23      50 ..      82     116 ..      62     136 .. 0.45

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.5e-06
        Sec5 39 d......slveeLeeslneairkttllfkpvlenkekadklraaleviernk 84
                +       +++++ e++++a+++ +++f++v e+++k++++ +++++ e ++
  EPA05531.1 15 QeyskslENWKTMFEQIQNATNEMQSKFNDVWEKATKESSVDTMKQFSENWQ 66
                044455578999**********************************988765 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.31
        Sec5  23 dqiykefseskteaqed.......slveeLeesln 50 
                 ++  kef es +++ ++       + +e+ ++sln
  EPA05531.1  82 MKSFKEFGESWQKSLNEtntvafkQFMENWQNSLN 116
                 33334443333333333223333333333333333 PP

>> RRF  Ribosome recycling factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.8   7.4e-05      0.07      95     149 ..      21      76 ..      11      88 .. 0.79
   2 ?    1.5   0.0      0.27   2.6e+02      96     126 ..      83     114 ..      77     142 .. 0.51

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.4e-05
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCS-HHHHHHHHHHHHHHH.HHHHHH CS
         RRF  95 vkeakkaaekakvairniRrdankklkklekkiseDdvkkaekeiqklt.dkyike 149
                  ++ k+++e++++a +++++++n+  +k+ k+ s D +k++ ++ qk   ++ +k 
  EPA05531.1  21 LENWKTMFEQIQNATNEMQSKFNDVWEKATKESSVDTMKQFSENWQKALgENWQKA 76 
                 56778999999999999999999999999999889**********99751344444 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.27
                 HHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHC CS
         RRF  96 keakkaaekakvairniRrdankkl.kklekk 126
                 k  k+ +e +++++++  + a k++ ++++++
  EPA05531.1  83 KSFKEFGESWQKSLNETNTVAFKQFmENWQNS 114
                 66666677777776666666666652223222 PP

>> DDE_Tnp_ISL3  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   6.4    0.0082       7.7     110     197 ..       7      96 ..       1     101 [. 0.73
   2 ?   11.9   0.3   0.00014      0.14     159     202 ..      96     139 ..      87     144 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0082
  DDE_Tnp_ISL3 110 rkklkrsrrlllknpenlteeqkqrldelleaspelekaYe..lkeelrevfrkk.dkeearkalkewiekaersglkefkklaktlknhr 197
                    +++   +  + k+ en++   +q  +++ e++++++ ++e  +ke+ ++ ++ + ++++ +++ ++w + ++++g+k+fk+++++ ++  
    EPA05531.1   7 SNEWDSLWQEYSKSLENWKTMFEQIQNATNEMQSKFNDVWEkaTKESSVDTMK-QfSENWQKALGENWQKAINDAGMKSFKEFGESWQKSL 96 
                   55556666667777777777666665667799999999998324555555555.3588888899999***************999988765 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00014
  DDE_Tnp_ISL3 159 frkkdkeearkalkewiekaersglkefkklaktlknhreeIln 202
                   +++++  ++++++++w +++++sg++++k  ++ +k+ +e  + 
    EPA05531.1  96 LNETNTVAFKQFMENWQNSLNSSGMEQMKAYGELMKKFAETWTT 139
                   44346788999********************9999998876655 PP

>> Dak2  DAK2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00022      0.21      87     168 ..      15      88 ..       9      94 .. 0.80
   2 ?    2.1   0.0      0.17   1.6e+02      35      38 ..      86      89 ..      57     140 .. 0.49

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00022
                 HHHH---TTSSSTHHHHHHHHHHHHT...........T---HHHHHHHHHHCCS---SSGGGGGGGGGT.TS--HHHHHHHHH CS
        Dak2  87 qavgkarpgdkTmlDvlrpavealekakdgedlkealekaakaaekgaeaTkellaklgrAsylgersl.gvvDpGAvglali 168
                 q+++k+    kTm   ++ a ++++++     +++++eka+k++   ++  k+  ++ ++A  lge+ +  + D+G +++  +
  EPA05531.1  15 QEYSKSLENWKTMFEQIQNATNEMQSK-----FNDVWEKATKES--SVDTMKQFSENWQKA--LGENWQkAINDAGMKSFKEF 88 
                 667777778889999888888888884.....559999999865..677888889999999..9999886799***9998665 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.17
                HHHH CS
        Dak2 35 kala 38
                k+++
  EPA05531.1 86 KEFG 89
                2222 PP

>> HNOB  Haem-NO-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.9    0.0002      0.19      25     101 ..      28     113 ..       7     126 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0002
                 HHHTTSTTSS--TTSBTTHH...........HHHHHHHHHHHHHTS-HHHHHHHHHHHHHHHHHHHHTHHHHTHTTCSHHHHHHHHHH CS
        HNOB  25 leeagleekvftthetYdds...........lllklveaaskvlglsadelleafGeyfvkffsekgydkllrvlgrnlfeFLknldn 101
                  e+++  + + +++ +++d             ++++ e+  k lg + ++ ++++G   +k f e++ ++l ++    +++F++n +n
  EPA05531.1  28 FEQIQ--NATNEMQSKFNDVwekatkessvdTMKQFSENWQKALGENWQKAINDAGMKSFKEFGESWQKSLNETNTVAFKQFMENWQN 113
                 44443..222222222222233334444555888888889999999999999999999999999444444444444466777666555 PP

>> DUF1722  Protein of unknown function (DUF1722)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.5   0.00098      0.92      20      84 ..       3      64 ..       1      70 [. 0.81
   2 ?    1.9   0.1      0.28   2.7e+02      23      42 ..      81     100 ..      66     139 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00098
     DUF1722 20 anakkepleelaeeYeellmealskpatrkkhinvlqhilgyfkkklsaeekqelleliekYreg 84
                +++k++++++l +eY++ l++  +   ++++ +   + ++  f++  +++ k+   ++++++ e+
  EPA05531.1  3 SEEKSNEWDSLWQEYSKSLENWKTMFEQIQNAT---NEMQSKFNDVWEKATKESSVDTMKQFSEN 64
                567788999999*****9999877766666555...57888999999999999999999999886 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.28
     DUF1722  23 kkepleelaeeYeellmeal 42 
                 + ++++e+ e++++ l+e+ 
  EPA05531.1  81 GMKSFKEFGESWQKSLNETN 100
                 55555555555555555443 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   4.3   0.00035      0.33      13      86 ..       6      76 ..       4     101 .. 0.64
   2 ?    4.4   1.6     0.046        43      29      95 ..      71     134 ..      54     140 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00035
                HSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS.-HHHHHHHHHHHHHHHHHHHHHH.HHHHHH CS
        OmpH 13 espegkaaqeqlekkfkklqaeleakekelqklqeelqkkakklekeekeqelqkkeqelqqkqqqka.qelqkk 86
                +s+e+ +  +++ k  +++++ +e+ +++ +++q +++     +ek++ke  +++++q  ++  q++  ++ qk+
  EPA05531.1  6 KSNEWDSLWQEYSKSLENWKTMFEQIQNATNEMQSKFN---DVWEKATKESSVDTMKQFSEN-WQKALgENWQKA 76
                78899999999999999999999999999999999996...443456666665555555555.444443333333 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.046
                 HHHHHHHHHHH.HHHHHHHHHHHHHTTTS.-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
        OmpH  29 kklqaeleake.kelqklqeelqkkakklekeekeqelqkkeqelqqkqqqkaqelqkkqqellkpil 95 
                 +++q+++++ + k++++  e  q   k+l +e+   ++++ ++++q++++    e +k+  el+k++ 
  EPA05531.1  71 ENWQKAINDAGmKSFKEFGESWQ---KSL-NETNTVAFKQFMENWQNSLNSSGMEQMKAYGELMKKFA 134
                 44444444332134444444444...332.55555558888888888777777777777777777665 PP

>> HU-CCDC81_bac_2  CCDC81-like prokaryotic HU domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       2.3   2.1e+03      18      32 ..      27      41 ..      15      44 .. 0.69
   2 ?    4.5   0.1     0.033        31      12      45 ..      48      81 ..      46      87 .. 0.82
   3 ?    3.7   0.0     0.061        58      23      43 ..      86     106 ..      82     107 .. 0.87
   4 ?    3.2   0.0     0.084        79      23      48 ..     105     130 ..     103     137 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2.3
  HU-CCDC81_bac_2 18 Alqkiekeveelkqe 32
                     + ++i+++++e++++
       EPA05531.1 27 MFEQIQNATNEMQSK 41
                     445677777777665 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.033
  HU-CCDC81_bac_2 12 gisyeeAlqkiekeveelkqeLeeegrveleniG 45
                     + + e+ +   +++ e+++++L e+ +  +++ G
       EPA05531.1 48 KATKESSVDTMKQFSENWQKALGENWQKAINDAG 81
                     56678888999***********999877777666 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.061
  HU-CCDC81_bac_2  23 ekeveelkqeLeeegrvelen 43 
                      +++ e++++ L+e+++v +++
       EPA05531.1  86 KEFGESWQKSLNETNTVAFKQ 106
                      57889***********99985 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.084
  HU-CCDC81_bac_2  23 ekeveelkqeLeeegrveleniGeLs 48 
                      ++++e++++ L++ g  +++  GeL 
       EPA05531.1 105 KQFMENWQNSLNSSGMEQMKAYGELM 130
                      689**********9999999888886 PP

>> DASH_Dad2  DASH complex subunit Dad2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   3.1     0.008       7.5      49      82 ..      21      53 ..       4      69 .. 0.71
   2 ?    0.9   0.2      0.66   6.2e+02      37      63 ..      57      84 ..      49      98 .. 0.56
   3 ?    7.7   0.2    0.0048       4.5      37      65 ..      96     124 ..      83     136 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.008
   DASH_Dad2 49 lanWqnvlraismaslkllqkaee...eaeeeeedee 82
                l+nW++ ++ i+ a+ ++++k ++   +    +++e+
  EPA05531.1 21 LENWKTMFEQIQNATNEMQSKFNDvweK----ATKES 53
                89***************98655554431....22222 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.66
   DASH_Dad2 37 tladgteavasVl.anWqnvlraismas 63
                t+++ +e  ++ l +nWq+ ++ + m s
  EPA05531.1 57 TMKQFSENWQKALgENWQKAINDAGMKS 84
                4444444444433245665555555544 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0048
   DASH_Dad2  37 tladgteavasVlanWqnvlraismaslk 65 
                   +++t a ++ ++nWqn l++  m ++k
  EPA05531.1  96 LNETNTVAFKQFMENWQNSLNSSGMEQMK 124
                 4567999999**********999998877 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.9   0.00054      0.51       9      58 ..       7      53 ..       2      88 .. 0.77
   2 ?    1.1   0.1      0.34   3.2e+02      73      98 ..     107     130 ..      55     137 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00054
       Sec34  9 eeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrle 58
                ++e+d+l ++     ++Le+ ++ f+++++ t++++++ +++ e+ ++ +
  EPA05531.1  7 SNEWDSLWQE---YSKSLENWKTMFEQIQNATNEMQSKFNDVWEKATKES 53
                5555555554...5567888888999999999999999999998877644 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.34
       Sec34  73 eldpitrkLnspgsslvksesFlemL 98 
                  +++ +++Lns+g++  + +++ e++
  EPA05531.1 107 FMENWQNSLNSSGME--QMKAYGELM 130
                 356677777777777..555555555 PP

>> Ribonuc_2-5A  Ribonuclease 2-5A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   3.9    0.0013       1.2       7     104 ..      41     143 ..      36     143 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0013
  Ribonuc_2-5A   7 dvSdrfeiekrdpesellkkLeseasevvksdWtkkldkelvdslgkyr.....kYkgdsvrdLLRaiRNkkeHyeelpedvkeilgelpegflsYf 98 
                   ++ d +e+ +++++ +++k+++++ +++++++W+k ++++ ++s +++      + ++++     +++ N ++  +    +  +++gel ++f + +
    EPA05531.1  41 KFNDVWEKATKESSVDTMKQFSENWQKALGENWQKAINDAGMKSFKEFGeswqkSLNETNTVAFKQFMENWQNSLNSSGMEQMKAYGELMKKFAETW 137
                   5668889999888889****************************98665444436788888888889999999988888888888899999999988 PP

  Ribonuc_2-5A  99 tkrFPk 104
                   t+ +Pk
    EPA05531.1 138 TTMWPK 143
                   888885 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.6   0.00038      0.36      68     137 ..       4      72 ..       2      84 .. 0.83
   2 ?    0.3   0.1      0.53     5e+02     104     137 ..      99     132 ..      91     134 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00038
      DUF745  68 eqelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaek 137
                 e++ +e ++  qe +ksl++ ++  +  ++a +++q++++ + +   + ++++++++q+++++q+ l e 
  EPA05531.1   4 EEKSNEWDSLWQEYSKSLENWKTMFEQIQNATNEMQSKFNDVWEKA-TKESSVDTMKQFSENWQKALGEN 72 
                 5677888999999999999999999999999999999998876643.34568999*********999885 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.53
      DUF745 104 qqlealkallkaakenlenaeqvaagaqqelaek 137
                 ++  a+k+++++++++l+++   +++a  el++k
  EPA05531.1  99 TNTVAFKQFMENWQNSLNSSGMEQMKAYGELMKK 132
                 4555678888888888888888888888887776 PP

>> FCH  Fes/CIP4, and EFC/F-BAR homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   3.4    0.0049       4.6      31      65 ..      15      50 ..      15     106 .. 0.86
   2 ?   -1.1   0.0       2.5   2.3e+03      11      26 ..     118     133 ..     104     137 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0049
                HHHHHHHHHHCT----TT.-.....HHHHHHHHHHH CS
         FCH 31 keYakkLqkLakkylkrr.kkkseestlvtawtvll 65
                +eY+k+L+++   +++ +  +++ +s ++++w++  
  EPA05531.1 15 QEYSKSLENWKTMFEQIQnATNEMQSKFNDVWEKAT 50
                79**************98777778888888888654 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.5
                 HHHHHHHHHHHHHHHH CS
         FCH  11 qgialledlqeflkeR 26 
                 +g+++++ + e++k+ 
  EPA05531.1 118 SGMEQMKAYGELMKKF 133
                 5666666666666664 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   2.7    0.0049       4.6      28      68 ..      29      66 ..      15     139 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0049
        YtxH 28 kdlkekaddlkekakelleeakekakekaedlkekvkekad 68
                +++++++++++ k++++ e+a    ke++ d +++++e  +
  EPA05531.1 29 EQIQNATNEMQSKFNDVWEKAT---KESSVDTMKQFSENWQ 66
                5666666666666666665553...4555555555554433 PP

>> DUF2884  Protein of unknown function (DUF2884)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5  11.0    0.0027       2.6      92     192 ..      25     124 ..      10     140 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0027
     DUF2884  92 sevaeklktkldelkarvkekfykdgdklvlgaqslesldeafdkefeqeieelveesiGsilsalgsemlesegdn.leafeqrmeklgekieeevee 189
                 ++ +e+++++ +e++++ ++  +k+  +   + +++++++e+++k + ++ ++++++   + +++ g++ ++s +++   af+q me+ +++++++  e
  EPA05531.1  25 KTMFEQIQNATNEMQSKFNDVWEKATKES--SVDTMKQFSENWQKALGENWQKAINDAGMKSFKEFGESWQKSLNETnTVAFKQFMENWQNSLNSSGME 121
                 33445555555555555555555544422..35666668888888888888888888888888888877777655545889999999999999876555 PP

     DUF2884 190 qak 192
                 q k
  EPA05531.1 122 QMK 124
                 544 PP

>> BrnA_antitoxin  BrnA antitoxin of type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.7     0.024        23      50      65 ..      65      80 ..      18      80 .. 0.87
   2 ?    4.5   0.0     0.052        49      49      64 ..      83      98 ..      82      99 .. 0.88
   3 ?   -1.7   0.1       4.6   4.3e+03      50      63 ..     103     116 ..     102     117 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.024
  BrnA_antitoxin 50 aFkatGkgwQtriNea 65
                    + ka G+ wQ  iN+a
      EPA05531.1 65 WQKALGENWQKAINDA 80
                    55999*********97 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.052
  BrnA_antitoxin 49 eaFkatGkgwQtriNe 64
                    + Fk+ G+ wQ  +Ne
      EPA05531.1 83 KSFKEFGESWQKSLNE 98
                    68*********99997 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 4.6
  BrnA_antitoxin  50 aFkatGkgwQtriN 63 
                     aFk+  + wQ  +N
      EPA05531.1 103 AFKQFMENWQNSLN 116
                     68888899*98887 PP

>> JHBP  Haemolymph juvenile hormone binding protein (JHBP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   1.1     0.045        43     201     229 ..      29      57 ..       8      64 .. 0.57
   2 ?    2.7   7.3     0.063        59     182     231 ..      59     109 ..      23     114 .. 0.62
   3 ?    1.7   0.4      0.13   1.2e+02     190     226 ..      98     134 ..      85     140 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.045
        JHBP 201 enwrellnelkpaieealskiftdilnki 229
                 e ++  +ne++ +++++++k+ ++ + + 
  EPA05531.1  29 EQIQNATNEMQSKFNDVWEKATKESSVDT 57 
                 33444555555555555555555544444 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.063
        JHBP 182 dnlfng.nkelgdainkflnenwrellnelkpaieealskiftdilnkifk 231
                 +++  + +k+lg+++ k +n+   + ++e+ ++ +++l ++ t  ++++++
  EPA05531.1  59 KQFSENwQKALGENWQKAINDAGMKSFKEFGESWQKSLNETNTVAFKQFME 109
                 333333356777777777777777777777777777776666666666655 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.13
        JHBP 190 elgdainkflnenwrellnelkpaieealskiftdil 226
                 e + ++ k + enw+  ln    +  +a ++++++++
  EPA05531.1  98 ETNTVAFKQFMENWQNSLNSSGMEQMKAYGELMKKFA 134
                 5567777888999999999888888888888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2409  (0.134363); expected 358.6 (0.02)
Passed bias filter:                      716  (0.0399353); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.44
# Mc/sec: 987.64
//
Query:       EPA05532.1  [L=184]
Description: methyltransferase domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-16   60.3   0.0    4.2e-16   59.4   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    1.1e-14   54.8   0.0    1.9e-14   54.1   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    4.6e-12   46.0   0.1    6.3e-12   45.5   0.1    1.1  1  Methyltransf_31  Methyltransferase domain
    3.8e-08   33.3   0.0    5.3e-08   32.9   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
    4.5e-07   30.5   0.0    7.9e-07   29.7   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
    5.8e-05   22.5   0.1    7.6e-05   22.2   0.1    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    0.00054   19.6   0.0    0.00089   18.9   0.0    1.3  1  MetW             Methionine biosynthesis protein MetW
     0.0013   18.2   0.0     0.0015   18.0   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
     0.0033   17.1   0.0     0.0073   16.0   0.0    1.7  2  TPMT             Thiopurine S-methyltransferase (TPMT)
  ------ inclusion threshold ------
       0.01   16.7   4.3       0.36   11.8   0.4    2.3  2  Ribosomal_L18_c  Ribosomal L18 C-terminal region
      0.064   12.8   0.0       0.11   12.1   0.0    1.4  1  MTS              Methyltransferase small domain


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.4   0.0   2.6e-19   4.2e-16       1      92 [.      39     123 ..      39     126 .. 0.96

  Alignments for each domain:
  == domain 1  score: 59.4 bits;  conditional E-value: 2.6e-19
                      EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHHHHHHHHHHHHH CS
  Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsdedlekalkeiarv 92 
                      vL++GcGtG +++ +++     +v gvD+++ +l +a+++     ++++f + ++++lpf+d+s+D+v+  + l++l+d+ lek ++e++r+
       EPA05532.1  39 VLEIGCGTGIDLRLFSET---VDVFGVDLNDMALSIAKKNG----PKFNFNKSSITNLPFKDSSVDFVFTHQLLNYLDDDILEKGISEMYRI 123
                      9***************98...69****************99....9************************766*****************97 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.1   0.0   1.2e-17   1.9e-14       1      87 [.      40     123 ..      40     126 .. 0.93

  Alignments for each domain:
  == domain 1  score: 54.1 bits;  conditional E-value: 1.2e-17
                      EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-..CCHHHHHHHHHHH CS
  Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhv..edpekalkeiaRv 87 
                      L++GcGtG+ ++ + +++ +v+gvDl++ +l +ak+++++     +f ++++++lpf+d+s+D+v+ ++ l+++  + +ek ++e++R+
       EPA05532.1  40 LEIGCGTGIDLRLFSETV-DVFGVDLNDMALSIAKKNGPKF----NFNKSSITNLPFKDSSVDFVFTHQLLNYLddDILEKGISEMYRI 123
                      89*************888.***************9999985....589**************************866789999999997 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   0.1   3.9e-15   6.3e-12       6     137 ..      38     162 ..      35     178 .. 0.80

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 3.9e-15
  Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnevlnaladpdkileeier 99 
                      +vl++GCGtG ++  +  e     +v+G+D +  a++ A++n    g + ++F +++i++l+  ++d+++D+++++++ln+l d d   ++i++
       EPA05532.1  38 SVLEIGCGTGIDLRLFS-E---TVDVFGVDLNDMALSIAKKN----GPK-FNFNKSSITNLP--FKDSSVDFVFTHQLLNYLDD-DILEKGISE 119
                      79*******87766655.5...467***************97....776.99**********..***************88765.334457888 PP

  Methyltransf_31 100 vlkpggilliedprllaelpakveeeskay...evvegak...i 137
                        +  g ++++  +  +el +++ ++sk++   + + ++k   i
       EPA05532.1 120 MYRIAGKYIMNCEK-YDELEKQIDDNSKFRnmqKRWMHHKvrvI 162
                      88889999988777.89999999999998777767777766663 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.0   3.3e-11   5.3e-08       8     107 ..      22     122 ..       7     173 .. 0.69

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 3.3e-11
  Methyltransf_23   8 elsdklerllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae..kakkaqkdqfdeqeaaepqgkfdlIvlrevlehvpd.. 97 
                      e+s+++  l+    +  +vL+iGcGtGi l++++e  ++v gvDl+++a +ia+  + +k ++ +    + ++++ + d++   ++l+ ++d  
       EPA05532.1  22 EFSKFIRDLA-ISLRCTSVLEIGCGTGIDLRLFSET-VDVFGVDLNDMALSIAKknG-PKFNFNKSSITNLPFKDSSVDFVFTHQLLNYLDDdi 112
                      4444444444.2444559***************887.8**************97742.222222232446666888999999999999998755 PP

  Methyltransf_23  98 ppellrqiat 107
                      +++ ++ +++
       EPA05532.1 113 LEKGISEMYR 122
                      5555555555 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0   4.9e-10   7.9e-07       1      91 [.      40     122 ..      40     126 .. 0.76

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 4.9e-10
  Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhl.kdir.evldnirk 91 
                      LeiGcGtG  lr + e    +++ gvD++  a+  ak+      + ++n+++   ++l  +d  ss+D v+ +++l++l +di  + ++++++
       EPA05532.1  40 LEIGCGTGIDLRLFSET---VDVFGVDLNDMALSIAKKN-----GPKFNFNKSSITNLPFKD--SSVDFVFTHQLLNYLdDDILeKGISEMYR 122
                      8*************999...*************444444.....444444555555544444..4**************86665477777776 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.1   4.6e-08   7.6e-05      35     142 ..      23     123 ..      15     152 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 4.6e-08
                      HHHHHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES-GGG CS
  Ubie_methyltran  35 WkkfveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtvsfGlrn 128
                      + kf+ +l  ++r ++vl++ +Gtg + ++      e+ +v ++D+n++ L++++k        + +f +++  +Lpf+d s D+v   + l n
       EPA05532.1  23 FSKFIRDLAISLRCTSVLEIGCGTG-IDLR---LFSETVDVFGVDLNDMALSIAKKNG-----PKFNFNKSSITNLPFKDSSVDFVFT-HQLLN 106
                      67899*******************9.3444...456778999***********98753.....3578999**************9865.55666 PP

                      -S-...HHHHHHHHHHH CS
  Ubie_methyltran 129 vtD...klkaLkeayrv 142
                        D    +k++ e+yr+
       EPA05532.1 107 YLDddiLEKGISEMYRI 123
                      65523336999999997 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   5.5e-07   0.00089      15     108 ..      37     130 ..      25     141 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 5.5e-07
        MetW  15 srvldlGcGdGellellkeekqvdgrGleldeegvaecvakGlsviqgdldkdlenfedksfdyvvlsqtlqatrnp..kevldellrigrraivs 108
                 + vl++GcG G  l+l+ e   vd  G++l++ ++  + + G +   +        f+d+s d+v   q l  + +   ++ ++e+ ri+ + i+ 
  EPA05532.1  37 TSVLEIGCGTGIDLRLFSE--TVDVFGVDLNDMALSIAKKNGPKFNFNKSSITNLPFKDSSVDFVFTHQLLNYLDDDilEKGISEMYRIAGKYIMN 130
                 569**************88..67778899999999999999988877777777778**************99887642266788999999998875 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   9.4e-07    0.0015     163     232 ..      37     101 ..      29     162 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 9.4e-07
        PrmA 163 eevlDvGtGSGi.LaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellkeekadviva 232
                 ++vl +G+G+Gi L + +    + +v++vD++++A+++ak+N  + + +++  ++l+   +k++++d ++ 
  EPA05532.1  37 TSVLEIGCGTGIdLRLFSE---TVDVFGVDLNDMALSIAKKNGPKFNFNKSSITNLP---FKDSSVDFVFT 101
                 68*********96666554...5689****************877666664423332...23345666655 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   4.5e-06    0.0073       3      75 ..       5      72 ..       3     104 .. 0.77
   2 ?   -2.1   0.0       1.5   2.4e+03     191     214 ..     138     161 ..     114     164 .. 0.55

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.5e-06
                HHHHHHHHHTT--TT--SS--HHHHHHHHT..T-S--EEEEEET-TT-HHHHHH-BTTEEEEEE-S-HHHHHHH CS
        TPMT  3 edfWekrweeeqipfhqeevnpllkkflda.lkakaglrvlvPlCGkaldlvwlAeqgrevvGvelselAvekf 75
                ++fW+   +e++  f+       ++kf+ + + + +  +vl  +CG ++dl  ++e   +v Gv+l ++A++ +
  EPA05532.1  5 KEFWDTYANENEAKFNE-----EFSKFIRDlAISLRCTSVLEIGCGTGIDLRLFSE-TVDVFGVDLNDMALSIA 72
                56777777777666655.....677777774456777899999********99987.589**********9874 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.5
                 TT--TT.................. CS
        TPMT 191 edaleeevrkkaagvealeekvyv 214
                 e  ++ + +++++  +++++kv v
  EPA05532.1 138 EKQIDDNSKFRNMQKRWMHHKVRV 161
                 223333345555556666666655 PP

>> Ribosomal_L18_c  Ribosomal L18 C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.3     0.011        19      15      38 ..       6      29 ..       2      34 .. 0.86
   2 ?   11.8   0.4   0.00022      0.36      28      83 ..     100     159 ..      92     172 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.011
  Ribosomal_L18_c 15 eYmeeLkeedeekykkqFskyikk 38
                     e+  + ++e+e k++++Fsk+i++
       EPA05532.1  6 EFWDTYANENEAKFNEEFSKFIRD 29
                     66777889*************986 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00022
  Ribosomal_L18_c  28 ykkqFskyikkgieaddleelykkahaaIredpvkk....ek.kekkevkkeskkykkkkl 83 
                      +++q  +y++++i  + + e+y+ a + I +  + +    ++  ++++  + +k++ ++k+
       EPA05532.1 100 FTHQLLNYLDDDILEKGISEMYRIAGKYIMNCEK-YdeleKQiDDNSKFRNMQKRWMHHKV 159
                      789999***********************86555.42442223444444446666666664 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   6.5e-05      0.11      33      80 ..      37      81 ..      25     105 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.5e-05
                SEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTG CS
         MTS 33 gkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankl 80
                 +vl +GcG+G   + l  +s++++v  vd + +Al +ak+n  + ++
  EPA05532.1 37 TSVLEIGCGTG---IDLRLFSETVDVFGVDLNDMALSIAKKNGPKFNF 81
                469*******8...57888888999***************98655444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       790  (0.0440627); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1318.35
//
Query:       EPA05533.1  [L=158]
Description: hypothetical protein BG20_I0229 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0097   15.6   0.5        6.6    6.5   0.1    3.2  3  TPR_11         TPR repeat
  ------ inclusion threshold ------
      0.049   13.8   0.9         38    4.6   0.0    3.4  3  YozE_SAM_like  YozE SAM-like fold
      0.099   11.8   7.8        2.4    7.3   7.7    2.2  1  DUF3080        Protein of unknown function (DUF3080)
       0.11   11.2   5.0       0.13   11.0   5.0    1.2  1  UPF0061        Uncharacterized ACR, YdiU/UPF0061 family
        1.6    8.4   8.9        1.9    8.1   4.6    2.0  2  DDE_Tnp_ISL3   Transposase
        1.8    8.9   6.0       0.55   10.6   2.1    1.9  2  Muted          Organelle biogenesis, Muted-like protein
        4.4    7.5   8.5    1.1e+03   -0.1   8.5    2.8  1  CTK3_C         CTD kinase subunit gamma CTK3 C-terminus
        5.4    7.6   6.9    1.8e+02    2.7   6.9    3.0  1  RPAP3_C        Potential Monad-binding region of RPAP3


Domain annotation for each model (and alignments):
>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.027        62       9      22 ..      33      46 ..      29      47 .. 0.88
   2 ?    2.0   0.0     0.076   1.7e+02      10      22 ..      48      60 ..      48      62 .. 0.87
   3 !    6.5   0.1     0.003       6.6      12      22 ..     136     146 ..     135     152 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.027
      TPR_11  9 kyeeAieaYkkAlk 22
                ++e+A ++Y+ Al 
  EPA05533.1 33 EFEKAWKEYNSALS 46
                79**********95 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.076
      TPR_11 10 yeeAieaYkkAlk 22
                ++e++++++kA +
  EPA05533.1 48 WKESLAQWQKATN 60
                679********86 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.003
      TPR_11  12 eAieaYkkAlk 22 
                 ++i+aY++A+k
  EPA05533.1 136 DSIKAYQEAIK 146
                 67888888887 PP

>> YozE_SAM_like  YozE SAM-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.017        38      49      65 ..      26      42 ..       9      43 .. 0.85
   2 ?    1.2   0.0      0.19   4.3e+02      52      65 ..     117     130 ..      97     131 .. 0.76
   3 ?    4.6   0.0     0.017        38      49      62 ..     140     153 ..     133     155 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.017
                   HHHTTHHHHHHHHHHHH CS
  YozE_SAM_like 49 eylssmeifdeaweeYl 65
                   + + s   f++aw+eY+
     EPA05533.1 26 KSSTSKPEFEKAWKEYN 42
                   56677788********7 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.19
                    TTHHHHHHHHHHHH CS
  YozE_SAM_like  52 ssmeifdeaweeYl 65 
                     s++ f+e we++l
     EPA05533.1 117 GSIKKFNEQWEKFL 130
                    57899999999997 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.017
                    HHHTTHHHHHHHHH CS
  YozE_SAM_like  49 eylssmeifdeawe 62 
                    +y++++++f+eaw+
     EPA05533.1 140 AYQEAIKQFNEAWQ 153
                    6999*********8 PP

>> DUF3080  Protein of unknown function (DUF3080)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   7.7    0.0011       2.4     258     307 ..     104     154 ..       8     155 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0011
     DUF3080 258 lpllkqlaekase.epealaayfqayleeqasslwqqyrqamkrHvkaWQk 307
                 ++ +++++++++    +++++ ++++l+++ +++ ++y++a+k++ +aWQ 
  EPA05533.1 104 TKMIENIFKETNIgSIKKFNEQWEKFLKTSGDDSIKAYQEAIKQFNEAWQS 154
                 344555566666656889********************************5 PP

>> UPF0061  Uncharacterized ACR, YdiU/UPF0061 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   5.0   5.9e-05      0.13     314     436 ..      33     151 ..       7     157 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5.9e-05
     UPF0061 314 eleealeeykevyttkYaqlmlkkLGleklsekekefdselleellelLqetqvdYneffveLaeskskkwrdeaesileesekeleeekleeWrelYk 412
                 e+e+a +ey++ ++   ++l + +   +++ ++ ++ +++ le+  elL++ +++++++++e+  +  k+ ++      e++ ke++  +++++ e ++
  EPA05533.1  33 EFEKAWKEYNSALSVWKESLAQWQKATNDTLMTYHDACQRALESDTELLKKVSASWDNTWQEIGPEYIKQQTKMI----ENIFKETNIGSIKKFNEQWE 127
                 5555556666555443333333344445666777888**********************9998766555544444....5555556668899******* PP

     UPF0061 413 klleeleedeleeraerlkkvNpk 436
                 k+l++  +d++++ +e +k++N +
  EPA05533.1 128 KFLKTSGDDSIKAYQEAIKQFNEA 151
                 *********************976 PP

>> DDE_Tnp_ISL3  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   4.6   0.00085       1.9     137     200 ..      26      95 ..       3     105 .. 0.76
   2 ?    2.7   0.2     0.039        88     154     196 ..     106     148 ..      99     155 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00085
  DDE_Tnp_ISL3 137 elleaspelekaYelkeelrevfrkk..dkeeark....alkewiekaersglkefkklaktlknhreeI 200
                   +   ++pe+eka++ +++  +v++++  ++++a++    ++++ +++a +s+ + +kk+ ++ +n ++eI
    EPA05533.1  26 KSSTSKPEFEKAWKEYNSALSVWKESlaQWQKATNdtlmTYHDACQRALESDTELLKKVSASWDNTWQEI 95 
                   3457899****************97776566665555556777888888999999***********9999 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.039
  DDE_Tnp_ISL3 154 elrevfrkkdkeearkalkewiekaersglkefkklaktlknh 196
                   ++ ++f++++  + +k+ ++w + +++sg +++k   +++k+ 
    EPA05533.1 106 MIENIFKETNIGSIKKFNEQWEKFLKTSGDDSIKAYQEAIKQF 148
                   5678888777888888888888888888888877666666654 PP

>> Muted  Organelle biogenesis, Muted-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1      0.58   1.3e+03      92     115 ..      20      43 ..       3      51 .. 0.50
   2 ?   10.6   2.1   0.00024      0.55      39     119 ..      50     135 ..      47     156 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.58
       Muted  92 ekrkseqlqekeeerkaeweeflk 115
                 +  k+++ ++++ e ++ w+e+ +
  EPA05533.1  20 KPIKQTKSSTSKPEFEKAWKEYNS 43 
                 222333334444555555555544 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00024
       Muted  39 elLenikklvnelkeqllpkclesmkenLselnkkleaalekverllqkeleeekrkseqlqeke.....eerkaeweeflkelqe 119
                 e+L + +k +n++  ++++ c ++++++ + l+k      ++ +++  +  +++ +  e++ ++      ++ +++we+flk   +
  EPA05533.1  50 ESLAQWQKATNDTLMTYHDACQRALESDTELLKKVSASWDNTWQEIGPEYIKQQTKMIENIFKETnigsiKKFNEQWEKFLKTSGD 135
                 5799999999***99*99999999988855554444455677899999999999998888877666888899********875443 PP

>> CTK3_C  CTD kinase subunit gamma CTK3 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   8.5      0.48   1.1e+03      34      60 ..     116     142 ..      14     152 .. 0.58

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.48
      CTK3_C  34 lateaEfenlWeetsdlneddeeeale 60 
                 + + + f+++We++ +++ dd  +a++
  EPA05533.1 116 IGSIKKFNEQWEKFLKTSGDDSIKAYQ 142
                 222455666666666665555555544 PP

>> RPAP3_C  Potential Monad-binding region of RPAP3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   6.9     0.082   1.8e+02       6      40 ..      32     132 ..      27     156 .. 0.66

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.082
     RPAP3_C   6 yeFeklwrklkredkdlkavllqinp..................................................................kqlpkiF 38 
                  eFek+w+++++  + +k  l q ++                                                                  +q++k++
  EPA05533.1  32 PEFEKAWKEYNSALSVWKESLAQWQKatndtlmtyhdacqralesdtellkkvsaswdntwqeigpeyikqqtkmienifketnigsikkfnEQWEKFL 130
                 69********77777777788885544666787777777777777777777777777777777777777666655555555555555555555555555 PP

     RPAP3_C  39 kn 40 
                 k+
  EPA05533.1 131 KT 132
                 55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1998  (0.11144); expected 358.6 (0.02)
Passed bias filter:                      639  (0.0356406); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1115.96
//
Query:       EPA05534.1  [L=86]
Description: hypothetical protein BG20_I0248 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-34  118.2   2.8    1.2e-34  118.1   2.8    1.0  1  DUF2024         Domain of unknown function (DUF2024)
     0.0072   15.8   0.1     0.0073   15.8   0.1    1.1  1  Ribonuc_red_sm  Ribonucleotide reductase, small chain
  ------ inclusion threshold ------
      0.094   11.8   0.2        0.1   11.7   0.2    1.1  1  Plant_NMP1      Plant nuclear matrix protein 1 (NMP1)


Domain annotation for each model (and alignments):
>> DUF2024  Domain of unknown function (DUF2024)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.1   2.8   1.9e-38   1.2e-34       1      81 []       1      81 [.       1      81 [. 0.99

  Alignments for each domain:
  == domain 1  score: 118.1 bits;  conditional E-value: 1.9e-38
                -EEEEEEEEE--SSS--EEEEEEES---HHHHHHHHHHHHHHHT---S---TTTEEEEEEEE--HHHHHHHHHHSEEEE-- CS
     DUF2024  1 mkvavfDtyvkkkdGkvlHFDvlvdekdeekaleyakeyLkskgeeeakvtskeCkfCHseeaeeeveeaikkqGyyiiel 81
                m+++vfDtyvk+k+G+++HFDv++d+k+ e+a+e+ak++L+s+ge++ak+t++eCkfCHs++++ee+e +i+++Gy+i ++
  EPA05534.1  1 MDFHVFDTYVKSKSGQTMHFDVITDKKNVENAIEFAKKWLESIGEKDAKITTEECKFCHSQSVSEEIEIDIMTDGYFIAKM 81
                999****************************************************************************98 PP

>> Ribonuc_red_sm  Ribonucleotide reductase, small chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   1.2e-06    0.0073     101     142 ..       4      45 ..       3      79 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.2e-06
                     HHHHHHT.-HHHHHHHHCHHHH-HHHHHHHHHHHHHHCTTTS CS
  Ribonuc_red_sm 101 llletlvkdekekdelfnaieenpalqkkaewikkwyeskkd 142
                     ++++t+vk++  +++ f+ i++ +++++ +e++kkw+es  +
      EPA05534.1   4 HVFDTYVKSKSGQTMHFDVITDKKNVENAIEFAKKWLESIGE 45 
                     58***********************************97663 PP

>> Plant_NMP1  Plant nuclear matrix protein 1 (NMP1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   1.7e-05       0.1     120     150 ..      28      58 ..      17      71 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.7e-05
  Plant_NMP1 120 svdeqvakdiqlldaiaekqaqifseecklf 150
                  v++ ++   + l++i ek+a+i +eeck+ 
  EPA05534.1  28 NVENAIEFAKKWLESIGEKDAKITTEECKFC 58 
                 466777777789*****************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       977  (0.0544927); expected 358.6 (0.02)
Passed bias filter:                      605  (0.0337442); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 564.34
//
Query:       EPA05535.1  [L=539]
Description: putative chaperone protein DnaK, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   2.3e-196  653.6  12.9     3e-196  653.2  12.9    1.1  1  HSP70          Hsp70 protein
    1.8e-16   59.9   2.4    1.8e-16   59.9   2.4    1.9  2  MreB_Mbl       MreB/Mbl protein
    0.00043   20.1   0.0    0.00082   19.1   0.0    1.5  1  FGGY_C         FGGY family of carbohydrate kinases, C-termina
  ------ inclusion threshold ------
      0.013   15.2   0.0      0.059   13.0   0.0    2.2  1  Raco_middle    RACo middle region
      0.077   12.7   0.0        0.2   11.3   0.0    1.6  1  Peptidase_M22  Glycoprotease family
       0.14   12.2   1.5       0.25   11.5   1.5    1.4  1  DUF1885        Domain of unknown function (DUF1885)
        1.2    9.2   5.0       0.48   10.5   0.9    2.3  2  DUF1664        Protein of unknown function (DUF1664)
        3.4    8.3  12.6       0.14   12.7   5.6    2.2  3  TetR_C_19      Tetracyclin repressor-like, C-terminal domain
         10    6.2  10.1       0.59   10.2   3.7    2.0  2  RP-C_C         Replication protein C C-terminal region


Domain annotation for each model (and alignments):
>> HSP70  Hsp70 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  653.2  12.9  1.5e-199    3e-196     103     598 ..       4     500 ..       2     501 .. 0.99

  Alignments for each domain:
  == domain 1  score: 653.2 bits;  conditional E-value: 1.5e-199
                 ETTEEEEHHHHHHHHHHHHHHHHHHHHTSBEEEEEEEEXTTXXHHHHHHHHHHHHHTTXEEEEEEEHHHHHHHHHHTCCSSSCEEEEEEEEXSSXEEEE CS
       HSP70 103 aagekftpeqisamvLkklketaeaylgkkvtdavitvPaYfndaqRqatkdAgkiAGLnvlRivNepTAaalaYGldkkdkernvlvyDlGggtfdvS 201
                 +++++++p+qisa++L+k+k++aea++g++v++avitvPaYf+d+qRqatkdAg+iAGL+v+Ri+NepTAa+la+Gldk++++ ++lv+D+Gggt dv 
  EPA05535.1   4 IQDKNYKPQQISAFILQKIKKDAEAFIGEPVDKAVITVPAYFDDNQRQATKDAGTIAGLDVVRIINEPTAASLAFGLDKTKQDMKILVFDFGGGTLDVT 102
                 6799*********************************************************************************************** PP

                 EEEEETTEEEEEEEEEETTXSHHHHHHHHHHHHHHHHHHHHSXXGGGSHHHHHHHHHHHHHHHHHTTTSSCSEEEEEEEEEETTT..EEEEEEEEHHHH CS
       HSP70 202 ilelekGvfevkaTagDthlGGedfDealvehlveefkkkegidlskdkkalqrlkeaaekaKkeLSsskqteinleietvdedg..kdlseklsRakf 298
                 i+e++ Gvfev +T+gDt+lGG d+D+++++++++efkkkegidlskd+ a+ r++eaaekaK+eLS+ ++t+inl++++ d +   k+l+ +l+Rak+
  EPA05535.1 103 IMEMGGGVFEVMSTSGDTQLGGTDMDKVVINYILDEFKKKEGIDLSKDSTAMARIREAAEKAKIELSTIMETDINLPFISHDPSSgaKNLELRLTRAKL 201
                 *********************************************************************************986559************ PP

                 HHHHHHHHHHTHHHHHHHHHHCTEEGGGCSEEEEESGGGGSHHHHHHHHHHTTCHHBSSSHTTTHHHHHHHHHHHHHCTCGCSHCCEEEEBESS-EEEE CS
       HSP70 299 eelvedllertlepvekalkdaklkkeeidevvlvGGstRiPkvqelvkelfgkepsktvnpDeavaiGAAvqagvlsgeeevkdllllDvtpLslgie 397
                 +el+++++er++ ++ekal+dak++k++i+++v+vGG tRiP v++ v e++gkep+++++p eava+GAA+qag+ +g   ++d++llDvtpL+lgie
  EPA05535.1 202 DELIRPIIERCKPSIEKALEDAKISKSDISKIVMVGGPTRIPLVKKFVGEVLGKEPESGIDPMEAVAMGAAIQAGIIAG-DVTSDIVLLDVTPLTLGIE 299
                 *******************************************************************************.6789*************** PP

                 ETTTEEEEEESTTCBSSEEEEEEEEESSTTSSSEEEEEEESSSSBGGGSEEEEEEEEECESSCSTTCSEEEEEEEEETTSCEEEEEEETTTCCEEEEEE CS
       HSP70 398 tlggvmtkliernttiptkksqvfstaadnqtaveievlqgerelvkdnkllgsfeldgippaprGvpqieVtfdidanGiltvsakdketgkeeeiti 496
                 tlggv + liernttipt+ks+vf+taadnqtav+i+v+qger +++dn +lgsf+l+++ppaprG pqieV+fdidanGi++v+akd +t+ke++iti
  EPA05535.1 300 TLGGVREPLIERNTTIPTSKSKVFTTAADNQTAVTIHVVQGERPMASDNVSLGSFNLTDLPPAPRGIPQIEVKFDIDANGIINVAAKDLGTKKEAKITI 398
                 *************************************************************************************************** PP

                 ECCSSSBHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.GGGSTHHHHHHHHHHHHHHHCHTTSSCHHHHHHHHHHHHHHHHHHH CS
       HSP70 497 easeglseeeiekmvkdaeesaeedkkkkeaieakneaeelvyslekkleee.aekvseaekekvesaieeLkeeleeeekeeieakteelkkvvekia 594
                 +++++ls+eeiek+ +dae++++edkkkke+i+ +neae+++y++ek ++++ ++k+s+++  kv++a++e+ke+l ++e++ ++ k+++lk++v++i+
  EPA05535.1 399 TSNSKLSKEEIEKLKQDAEKFSDEDKKKKEKIDLRNEAESFIYTVEKLVNHDlKDKISQEQGIKVTDAVKEVKESL-DKEIDVLKPKLDTLKSLVNEIT 496
                 **************************************************999**********************8.8899*****************9 PP

                 HHHH CS
       HSP70 595 ekly 598
                 ++ly
  EPA05535.1 497 TELY 500
                 9987 PP

>> MreB_Mbl  MreB/Mbl protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.9   2.4   9.1e-20   1.8e-16      82     317 ..      19     273 ..       4     279 .. 0.75
   2 ?   -3.2   1.0       1.4   2.9e+03     196     264 ..     404     474 ..     381     485 .. 0.60

  Alignments for each domain:
  == domain 1  score: 59.9 bits;  conditional E-value: 9.1e-20
                 HHHHHT.SS-S...S--EEEEEE-SS--HHHHHHHHHHHHHTT-SEEEEEEHHHHHHHHTT--TTSSS-E.EEEEE-SS-EEEEEEETTEEE.....EE CS
    MreB_Mbl  82 ikkvkk.kksl...skprvvicvPsgiteverrAvkeaakkaGarevllieeplaAAiGaglpveepsgn.mvvdiGggttevavislggiv.....ts 170
                 ++k+kk ++++   + ++ vi+vP   ++ +r+A k+a + aG + v +i+ep aA +  gl+ ++   + +v d Gggt +v+++ +gg v     ts
  EPA05535.1  19 LQKIKKdAEAFigePVDKAVITVPAYFDDNQRQATKDAGTIAGLDVVRIINEPTAASLAFGLDKTKQDMKiLVFDFGGGTLDVTIMEMGGGVfevmsTS 117
                 3344442122212266799*******************************************987766552789**************98552222245 PP

                 EEES-SHHHHHHHHHHHHHHHHSEE--H.............HHHHHHHHHH-BSS--HHHHEEEEEEEETTTTCEE.EEEEEHHHHHHHHHHHHHHHHH CS
    MreB_Mbl 171 ksvrvaGdeldeaiikyirkkynlliGe.............rtaekikieigsavkeeeeekmeikGrdlvtglpk.evevsseevrealkepvsaive 255
                    +++G ++d+ +i+yi  +++   G              + aek kie++++++++ +  +    +d  +g    e++++ +++ e ++  +++   
  EPA05535.1 118 GDTQLGGTDMDKVVINYILDEFKKKEGIdlskdstamarirEAAEKAKIELSTIMETDIN--LPFISHDPSSGAKNlELRLTRAKLDELIRPIIERCKP 214
                 5689**************888876544311111111111113355555555555544443..3445566677754337899999999999999999999 PP

                 HHHHHHHTS-HHHHHHHHHH-EEEESGGGGSBTHHHHHHHHHSS-EEE-SSTTTHHHHHHHH CS
    MreB_Mbl 256 avkevLektppeLaadivdrgivltGGgallkgldkllseetglpvkvaedpltcvakGtgk 317
                 +++++Le+++    +di +  iv++GG + +  ++k++ e +g + + + dp+++va G+++
  EPA05535.1 215 SIEKALEDAKIS-KSDISK--IVMVGGPTRIPLVKKFVGEVLGKEPESGIDPMEAVAMGAAI 273
                 9*****998865.678875..9999**********************************976 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.4
                 --HHHHHHHHHHH-BSS--HHHHEEEEEEEETTTTCEEEEE.EEHHHHHHHH.HHHHHHHHHHHHHHHHTS CS
    MreB_Mbl 196 iGertaekikieigsavkeeeeekmeikGrdlvtglpkeve.vsseevreal.kepvsaiveavkevLekt 264
                 + +++ ek+k++  +   e++++k +i  r+ ++    +ve + ++++++ + +e+  ++++avkev e+ 
  EPA05535.1 404 LSKEEIEKLKQDAEKFSDEDKKKKEKIDLRNEAESFIYTVEkLVNHDLKDKIsQEQGIKVTDAVKEVKESL 474
                 45556666666666666666666666666666665554443244555554441334455666666665554 PP

>> FGGY_C  FGGY family of carbohydrate kinases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   4.1e-07   0.00082     125     196 ..     206     277 ..     123     279 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 4.1e-07
      FGGY_C 125 rAaleavalqlrailealekdsgkpldrlavdGGgskndllmqllAdilg.vpVerpktaeatalGaAilAav 196
                 r ++e +  ++   le  +  s++++++++++GG ++ +l+ ++ +++lg  p    ++ ea+a+GaAi A++
  EPA05535.1 206 RPIIERCKPSIEKALEDAKI-SKSDISKIVMVGGPTRIPLVKKFVGEVLGkEPESGIDPMEAVAMGAAIQAGI 277
                 45555555555555555544.5999*************************777667777************86 PP

>> Raco_middle  RACo middle region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     3e-05     0.059      52     111 ..     198     257 ..     193     292 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3e-05
  Raco_middle  52 eegleklqkavveeinelieelleeagiekeeiyevvvagNttMlhlllgldpkslakap 111
                  + +l++l + ++e  +  ie++le+a+i+k++i+++v++g  t + l+ ++  + l+k+p
   EPA05535.1 198 RAKLDELIRPIIERCKPSIEKALEDAKISKSDISKIVMVGGPTRIPLVKKFVGEVLGKEP 257
                  567899999********************************9999999888888888887 PP

>> Peptidase_M22  Glycoprotease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   9.9e-05       0.2      30      60 ..     209     239 ..     203     242 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 9.9e-05
                    HHHHHHHHHHHHHHHTSTGGGEEEEEEEEES CS
  Peptidase_M22  30 serllplieealaeaglsledldaIavtkgP 60 
                     er+ p ie+al++a++s++d+++I++  gP
     EPA05535.1 209 IERCKPSIEKALEDAKISKSDISKIVMVGGP 239
                    5899**********************99998 PP

>> DUF1885  Domain of unknown function (DUF1885)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.5   0.00012      0.25       2      72 ..     393     460 ..     392     506 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00012
     DUF1885   2 sayiklveasaketvtlddvkellerykeitaktGeqldweYadaafPYeieekeedkwlyLkgkddrYka 72 
                 +a i++ ++s+ ++  ++++k+  e++ +  +k  e++d   +  +f Y++e+  +     Lk k ++ + 
  EPA05535.1 393 EAKITITSNSKLSKEEIEKLKQDAEKFSDEDKKKKEKIDLRNEAESFIYTVEKLVN---HDLKDKISQEQG 460
                 6899999********************************************98776...234444444444 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.2      0.86   1.7e+03      81     104 ..     401     424 ..     386     434 .. 0.69
   2 ?   10.5   0.9   0.00024      0.48      52      91 ..     462     501 ..     438     514 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.86
     DUF1664  81 iskeikeevtevredlseigedve 104
                  sk  kee++++++d ++++++ +
  EPA05535.1 401 NSKLSKEEIEKLKQDAEKFSDEDK 424
                 455667788888888888777654 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00024
     DUF1664  52 qvseslaatkrhLssridrvdkkldeqkeiskeikeevte 91 
                 +v ++++++k+ L ++id +  kld  k + +ei+ e+ +
  EPA05535.1 462 KVTDAVKEVKESLDKEIDVLKPKLDTLKSLVNEITTELYK 501
                 6899******************************999876 PP

>> TetR_C_19  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       8.3   1.6e+04      10      27 ..     132     149 ..     129     166 .. 0.64
   2 ?   12.7   5.6   7.2e-05      0.14      35     114 ..     398     482 ..     393     483 .. 0.92
   3 ?   -1.4   0.2       1.7   3.5e+03      14      53 ..     488     527 ..     486     537 .. 0.70

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 8.3
   TetR_C_19  10 feklldeiseeenakffk 27 
                  +++lde++++e +++ k
  EPA05535.1 132 INYILDEFKKKEGIDLSK 149
                 566677777766666555 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 7.2e-05
   TetR_C_19  35 ykiekkftkefkkkkkkerlkelyelidkskLnieseeelklllkilmavtfqtiveyfakelse......eeakenfkkeldwLk 114
                 + +++k++ke  +k k+++ +++ +  +k+k +i+ + e +++++ + +++++ + +++++e+        +e+ke ++ke+d Lk
  EPA05535.1 398 ITSNSKLSKEEIEKLKQDA-EKFSDEDKKKKEKIDLRNEAESFIYTVEKLVNHDLKDKISQEQGIkvtdavKEVKESLDKEIDVLK 482
                 5678888888888888777.9******************************************999******************98 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1.7
   TetR_C_19  14 ldeiseeenakffkniflnmnykiekkftkefkkkkkker 53 
                 l+ + +e   +++kn+    n + +++ + + +++++ ++
  EPA05535.1 488 LKSLVNEITTELYKNAASQSNSDQQNAGQGDSQNDSNSQQ 527
                 6667777788899999999888777766666666655555 PP

>> RP-C_C  Replication protein C C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.4      0.95   1.9e+03      61      93 ..     394     427 ..     377     445 .. 0.48
   2 ?   10.2   3.7    0.0003      0.59       6      79 ..     464     536 ..     461     539 .] 0.75

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.95
      RP-C_C  61 rhiqnsnpdsssese.pasekereekeaaaasae 93 
                 ++i+ + + + s++e ++ ++++e+  +++++++
  EPA05535.1 394 AKITITSNSKLSKEEiEKLKQDAEKFSDEDKKKK 427
                 4444333322222221222222222222222222 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0003
      RP-C_C   6 eqrfralverlprkatlaeleelleelealreevenal.esalkaenssanesqnerhiqnsnpdsssesepase 79 
                 +++++++ e+l   ++++ l++ l++l++l +e+++ l ++a++++ns+ +++ +++ +++sn++++ses+   e
  EPA05535.1 464 TDAVKEVKESLD--KEIDVLKPKLDTLKSLVNEITTELyKNAASQSNSDQQNAGQGDSQNDSNSQQNSESSTTDE 536
                 566777777774..88999***************99997777778888888777777777888766666544333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (539 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2578  (0.143789); expected 358.6 (0.02)
Passed bias filter:                      721  (0.0402142); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.72u 0.34s 00:00:01.06 Elapsed: 00:00:00.49
# Mc/sec: 3286.95
//
Query:       EPA05536.1  [L=57]
Description: DnaJ domain protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.5e-22   77.1   0.1    9.4e-22   76.9   0.1    1.0  1  DnaJ      DnaJ domain


Domain annotation for each model (and alignments):
>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.9   0.1   5.3e-26   9.4e-22       1      53 [.       6      57 .]       6      57 .] 0.98

  Alignments for each domain:
  == domain 1  score: 76.9 bits;  conditional E-value: 5.3e-26
                HHHHHHTSSTTG-HHHHHHHHHHHHHHHSTTTSCCHHHHHHHHHHHHHHHHHH CS
        DnaJ  1 dyYeiLgvskdasedeIkkaYrklalkyHPDknpkdpeaeekFkeineAyevL 53
                dyYe+Lgvsk++ +deIk++Yrklalk+HPD+n k+ ea e+Fkei+eAy vL
  EPA05536.1  6 DYYEVLGVSKTSGSDEIKAQYRKLALKFHPDRN-KSAEAGEHFKEISEAYAVL 57
                8********************************.8889*************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 365.02
//
Query:       EPA05537.1  [L=157]
Description: hypothetical protein BG20_I2080 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-09   37.0   0.0    5.8e-09   35.8   0.0    1.6  2  PUA       PUA domain
    1.2e-07   31.7   0.0      2e-07   31.0   0.0    1.3  1  TGT_C2    Patch-forming domain C2 of tRNA-guanine transglycos


Domain annotation for each model (and alignments):
>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.56     5e+03      36      47 ..      37      48 ..      13      50 .. 0.62
   2 !   35.8   0.0   6.5e-13   5.8e-09       4      73 ..      79     147 ..      77     148 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.56
                EEEEEETTSCEE CS
         PUA 36 vVaivdedgelv 47
                 ++ v+++g+l+
  EPA05537.1 37 RIRTVTHEGKLL 48
                345555555555 PP

  == domain 2  score: 35.8 bits;  conditional E-value: 6.5e-13
                 EE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEEEE CS
         PUA   4 vvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveierv 73 
                  v++ A+ ++++g+s++++ vv ++++++      ++   ++++avG+a +sse + ++++g+++++++ 
  EPA05537.1  79 EVNQDAAPFVKEGKSVFCKHVVWCGKNIRIASDTPVLYD-NKVIAVGKAILSSEMISDFNRGMAIRVRDS 147
                 799*************************77666666666.7**************************976 PP

>> TGT_C2  Patch-forming domain C2 of tRNA-guanine transglycosylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.0   2.2e-11     2e-07       7      68 ..      11      71 ..       6      74 .. 0.88

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 2.2e-11
      TGT_C2  7 adYqFGagagdaLfpedvtitrs.atgrirqvlvdgerlatlraqdgrltLsleGarrlhesl 68
                +d +FG+g+ + L + ++++t s +tgrir+v ++g+ l+tlr  dg l +s + a++l +s 
  EPA05537.1 11 LDALFGNGVSKYLPK-NIEMTFSrKTGRIRTVTHEGKLLCTLR-IDGGLAISPYFAQLLLKSK 71
                6668******99986.5*************************6.99*9**9999999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1104.98
//
Query:       EPA05538.1  [L=188]
Description: hypothetical protein BG20_I2083 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0019   17.9   0.0     0.0031   17.2   0.0    1.3  1  DUF460    Protein of unknown function (DUF460)
  ------ inclusion threshold ------
      0.055   13.9   0.0       0.28   11.6   0.0    2.0  2  RuvX      Holliday junction resolvase


Domain annotation for each model (and alignments):
>> DUF460  Protein of unknown function (DUF460)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   3.4e-07    0.0031      26      50 ..      59      83 ..      45     107 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.4e-07
      DUF460 26 kkrkkklivGiDPGittgiavldld 50
                   +++li+GiDPG  tgi++  + 
  EPA05538.1 59 LGYEEELIIGIDPGQRTGISIFYFG 83
                456899**************98664 PP

>> RuvX  Holliday junction resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.15   1.3e+03       3      15 ..      66      77 ..      64      96 .. 0.82
   2 ?   11.6   0.0   3.1e-05      0.28      71     131 ..     122     174 ..     100     175 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.15
                EEEEEESSSEEEE CS
        RuvX  3 ilglDvGtkriGv 15
                i+g+D G++ +G+
  EPA05538.1 66 IIGIDPGQR-TGI 77
                89*****75.565 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 3.1e-05
                 SSTTHHHHHHHHHT...T-EEEEE--S----XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
        RuvX  71 akkvrkfaeeLakrl.kklpvelvDErlttveaerilresglsrkkrkkvvDklaAviiLqs 131
                 +k +++++  L+ ++ ++++ e+vDEr t+ + ++           ++++ D l+A +iLq+
  EPA05538.1 122 MKIAKEIVTMLNLTFcSSFELEFVDERKTSLKIKNFN---------QRGKRDMLSAKYILQR 174
                 56667777777766657889**********9999665.........67888999*****996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1272.81
//
Query:       EPA05539.1  [L=113]
Description: putative alpha-NAC protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-14   53.7   1.7    1.5e-14   53.7   1.7    1.6  2  NAC       NAC domain
  ------ inclusion threshold ------
      0.011   15.6   0.1      0.015   15.1   0.1    1.2  1  UBA_4     UBA-like domain


Domain annotation for each model (and alignments):
>> NAC  NAC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.7   1.7   1.7e-18   1.5e-14       2      51 ..       7      59 ..       6      65 .. 0.92
   2 ?   -1.7   0.0      0.32   2.9e+03      21      40 ..      69      88 ..      69      96 .. 0.62

  Alignments for each domain:
  == domain 1  score: 53.7 bits;  conditional E-value: 1.7e-18
         NAC  2 kKlrkalkklgl..keipgieeVtirksdgkvlvfdnPkVq..kspgsntyvvf 51
                +++r+++ k+gl  keip+++eV+i++++ k++++++P+V+  k++ + +++v+
  EPA05539.1  7 REMRRMMDKMGLdmKEIPNVQEVIIKTDK-KEIIVSKPSVTemKAKDNSIFTVT 59
                79***************************.***********8888889999998 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.32
         NAC 21 eVtirksdgkvlvfdnPkVq 40
                eV i+ +++  lv +++ V 
  EPA05539.1 69 EVPIFSDEDIQLVSQQAGVD 88
                56677777777777777665 PP

>> UBA_4  UBA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.1   1.7e-06     0.015      11      33 ..      85     107 ..      75     109 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.7e-06
       UBA_4  11 TGadeekArqlLeannWdLerAi 33 
                 +G+deekA+  Le + +dL rAi
  EPA05539.1  85 AGVDEEKAKNALEEAKGDLARAI 107
                 699*******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       863  (0.0481343); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.34s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 633.00
//
Query:       EPA05540.1  [L=347]
Description: SpoVT/AbrB-like protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-24   86.1  16.2    4.7e-17   62.2   2.6    2.4  2  PhoU             PhoU domain
    1.1e-07   31.6   0.1    7.5e-07   28.9   0.0    2.5  2  MazE_antitoxin   Antidote-toxin recognition MazE, bacterial a
  ------ inclusion threshold ------
      0.042   14.4   0.1      0.084   13.4   0.1    1.6  1  WAC_Acf1_DNA_bd  ATP-utilising chromatin assembly and remodel


Domain annotation for each model (and alignments):
>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.2   2.6   7.9e-21   4.7e-17       1      88 [.     147     238 ..     147     239 .. 0.89
   2 !   29.3   5.9   1.5e-10   8.7e-07       1      89 []     254     334 ..     254     334 .. 0.92

  Alignments for each domain:
  == domain 1  score: 62.2 bits;  conditional E-value: 7.9e-21
                 HHHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SH....HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
        PhoU   1 lrrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplae....dlrellsllriardlERigDhavniaer 88 
                 ++rm  ++++m +da+ a +e++ ela+evi+ dde+dr+ + i+r+l  a+ ++  l e    + r+ l+++ +++++ER gDha  ia+ 
  EPA05540.1 147 IKRMIHLAKSMSSDAILAMSENNLELAQEVINTDDEVDRFGFYIIRQLKIAIQNEHMLKEmgfrNARDCLGYRLVVKNIERTGDHASFIAND 238
                 68*********************************************6666654333333789************************99975 PP

  == domain 2  score: 29.3 bits;  conditional E-value: 1.5e-10
                 HHHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
        PhoU   1 lrrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERigDhavniaerv 89 
                 +++m e +++ ldd++ al+++d   a++ ie+ ++i ++ek+i++s  + l+ ++++ +       ++ri+ ++ R++ +a +iae+v
  EPA05540.1 254 IQDMNEFALSVLDDSCLALFKEDYMQAEKTIEKTNDIIKYEKKIRDS-SKSLKDEEEMYR-------VRRITENIRRVAEYASDIAEIV 334
                 579*****************************************999.777766777766.......7789****************86 PP

>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   1.3e-10   7.5e-07       1      42 [.      12      54 ..      12      58 .. 0.89
   2 ?   -1.3   0.0      0.38   2.3e+03      24      41 ..     119     136 ..     112     148 .. 0.72

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 1.3e-10
                    EEETTEEEEEE-CCCHHHCCEECTCEEEEEECTT.CCCCCCCH CS
  MazE_antitoxin  1 fkvGnsgavriPkevrfelgireGdevelevdgd.kiilrplk 42
                    f++ +s++v++Pk ++ +lg+++Gd + +++++   + ++p+k
      EPA05540.1 12 FTGKSSYIVSLPKQWVMDLGLKQGDQIRMIRKDSqTLEIYPPK 54
                    8999*************************99987777777766 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.38
                     TCEEEEEECTTCCCCCCC CS
  MazE_antitoxin  24 Gdevelevdgdkiilrpl 41 
                     G+e++    +++ii +++
      EPA05540.1 119 GSEIISDSSNGIIIQVLV 136
                     777777777777776655 PP

>> WAC_Acf1_DNA_bd  ATP-utilising chromatin assembly and remodelling N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   1.4e-05     0.084      59     100 ..     241     282 ..     171     283 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.4e-05
  WAC_Acf1_DNA_bd  59 kfpealkkpvlelvqfstrsrlddLvedvyeelkerffvgEe 100
                      +f+++lkk+++e +q  ++  l+ L +++++ +ke++++ E+
       EPA05540.1 241 EFKKPLKKEIVEKIQDMNEFALSVLDDSCLALFKEDYMQAEK 282
                      49*************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1010  (0.0563333); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.34s 00:00:00.98 Elapsed: 00:00:00.54
# Mc/sec: 1948.06
//
Query:       EPA05541.1  [L=93]
Description: hypothetical protein BG20_I2085, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       897  (0.0500307); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 665.38
//
Query:       EPA05542.1  [L=111]
Description: hypothetical protein BG20_I2082 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00018   21.6   6.4    0.00023   21.3   6.4    1.1  1  DivIVA          DivIVA protein
     0.0039   17.7   3.4      0.005   17.3   3.4    1.3  1  V-ATPase_G      Vacuolar (H+)-ATPase G subunit
     0.0087   16.5   6.2       0.27   11.7   0.4    2.3  1  V-ATPase_G_2    Vacuolar (H+)-ATPase G subunit
  ------ inclusion threshold ------
      0.015   15.2   2.4       0.02   14.7   2.4    1.2  1  Apolipoprotein  Apolipoprotein A1/A4/E domain
      0.042   12.1   5.3       0.13   10.4   4.9    1.7  1  COG6            Conserved oligomeric complex COG6
      0.043   12.5   0.8      0.048   12.3   0.8    1.1  1  CsoSCA          Carboxysome Shell Carbonic Anhydrase
      0.046   14.0   3.7       0.58   10.5   3.7    2.1  1  DUF948          Bacterial protein of unknown function (DUF948
      0.051   14.0   4.6        1.2    9.6   4.6    2.3  1  NPV_P10         Nucleopolyhedrovirus P10 protein
      0.057   14.1   4.3       0.18   12.5   4.3    1.7  1  YabA            Initiation control protein YabA
       0.14   12.2   0.5          1    9.4   0.2    2.1  2  TFIIA_gamma_N   Transcription initiation factor IIA, gamma su
        1.1    9.8   8.8         62    4.2   8.8    2.1  1  YtxH            YtxH-like protein


Domain annotation for each model (and alignments):
>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   6.4   1.4e-07   0.00023      36     117 ..      11      94 ..       5     103 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.4e-07
                 HHHHHHHHHHHHHHCCCCTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXXXXXXXX CS
      DivIVA  36 allkeneelkekvkeleeklkeykeleetLkktlvvaqetaeevkanakkeaeliik....eAekkaekiveeaeeeakkiaeeie 117
                  +++  + l+++++ l++k+ ++k++ +   k+l    +  e++++ a+keaelii+    +A+ +++ki +e ++++ +i+++i+
  EPA05542.1  11 GIIQSLNGLEDNLDSLNSKVGDMKKQLNV--KALNEIDKLLEKTREMATKEAELIINasksKATTESTKITKEGQQKVSEIQSNID 94 
                 577888999****************9999..*************************822223555567899999999999999987 PP

>> V-ATPase_G  Vacuolar (H+)-ATPase G subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   3.4   3.1e-06     0.005      32     103 ..      35     110 ..      11     111 .] 0.74

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.1e-06
                 HHHHHHHHHHHHHHHHH.HHHHHHHHH...HHHHSHHHHHHHHHHHHSSHHHHHHHHHHHHHHHHHHHHHHHHHTS CS
  V-ATPase_G  32 kqAkeeAekEieeyrak.kekefkeke...aeklgseeelekkieketeekikelkesvkknkeavvkellklvld 103
                 kq   +A +Ei++  +k +e   ke e   ++  ++  + ++ki ke ++k++e++++++++ ++ vk+++++vl+
  EPA05542.1  35 KQLNVKALNEIDKLLEKtREMATKEAEliiNASKSKATTESTKITKEGQQKVSEIQSNIDAHFDEAVKHVVSTVLK 110
                 5566677777777643313333333331114444557778899*****************************9986 PP

>> V-ATPase_G_2  Vacuolar (H+)-ATPase G subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.4   0.00016      0.27      69     103 ..      75     109 ..      70     110 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00016
                   HHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHH- CS
  V-ATPase_G_2  69 reeararaeaeaqavrkraearlqqAvelilkaVl 103
                     ++ +++++++ +++ +  a+ ++Av++++  Vl
    EPA05542.1  75 STKITKEGQQKVSEIQSNIDAHFDEAVKHVVSTVL 109
                   56788999999*********************998 PP

>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   2.4   1.3e-05      0.02       2      85 ..      19     103 ..      18     109 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.3e-05
                     HHHCCCCHHHHHCCHHHCHHCHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHCCCHHHHHHHHHCCHHHHHHHHH CS
  Apolipoprotein   2 leesldelkayaeeleeqlaplaq.elrdrlskeleelrarlraeleevrarlepyrdevqeqlgqnleelrqrlapyteelrer 85 
                     le++ld+l++++ ++++ql+  a  e+ + l+k  e ++++ +  +++ +++ ++    + ++ +q++ e+++ ++++ +e  + 
      EPA05542.1  19 LEDNLDSLNSKVGDMKKQLNVKALnEIDKLLEKTREMATKEAELIINASKSKATTESTKITKEGQQKVSEIQSNIDAHFDEAVKH 103
                     7999**************9987665677777888888888888889999999999999999999999999999999999887665 PP

>> COG6  Conserved oligomeric complex COG6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   4.9   8.2e-05      0.13      41     132 ..      11     104 ..       6     106 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 8.2e-05
        COG6  41 pvaeqLkriesdveklnelcdemkkkls.sakeetsdlleeaeeLkeekkklelkqkllkaflkkFtLseeEeaaLtsgee.vddeFFkaLakv 132
                  + ++L+ +e+++++ln+ + +mkk+l+ +a +e ++lle++ e+ +++++l +     ka ++  ++++e  +  ++ ++ +d++F +a+++v
  EPA05542.1  11 GIIQSLNGLEDNLDSLNSKVGDMKKQLNvKALNEIDKLLEKTREMATKEAELIINASKSKATTESTKITKEGQQKVSEIQSnIDAHFDEAVKHV 104
                 57899**********************94556777**************999999988888888888888888888887777888888888887 PP

>> CsoSCA  Carboxysome Shell Carbonic Anhydrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.8   2.9e-05     0.048     241     311 ..      16      85 ..       9     107 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.9e-05
      CsoSCA 241 LiGldtDtDairvHvpdakgeveleryvdaaelyretleldaeeArariaeaveaaaekegagkaeegmrr 311
                 L Gl+ + D++   v d+k +++++   +  +l ++t+e++++eA+  i+++ ++a++++ ++ ++eg ++
  EPA05542.1  16 LNGLEDNLDSLNSKVGDMKKQLNVKALNEIDKLLEKTREMATKEAELIINASKSKATTES-TKITKEGQQK 85 
                 669999*****************************************9998877766665.3345555444 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   3.7   0.00036      0.58      16      62 ..      11      58 ..       8     108 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00036
      DUF948 16 flivvllklkktldeaaatieelekqvd.pilkevedllakvnelled 62
                 +i  l+ l++ ld++++ + +++kq++ + l+e+++ll+k++e++  
  EPA05542.1 11 GIIQSLNGLEDNLDSLNSKVGDMKKQLNvKALNEIDKLLEKTREMATK 58
                578899999*****************9746899*********997654 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   4.6   0.00075       1.2      20      68 ..       9      40 ..       2     109 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00075
     NPV_P10 20 VdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiLnpd 68
                V+                  + + L+++ ++L++l++kv + ++ Ln +
  EPA05542.1  9 VT-----------------GIIQSLNGLEDNLDSLNSKVGDMKKQLNVK 40
                33.................333334444444444444333333333322 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   4.3   0.00011      0.18       5      78 ..      25      98 ..       8     108 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                HHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXXXXXXXXXXXX CS
        YabA  5 elfdkleeleeqle.elleeleelkeelaelleenaeLeleneklrerleeeekkekekkkelsegkenLarlYe 78
                +l +k+ ++++ql+ + l+e+++l e++ e+  ++aeL ++ +k + +  e++k +ke ++++se ++n+   ++
  EPA05542.1 25 SLNSKVGDMKKQLNvKALNEIDKLLEKTREMATKEAELIINASKSKATT-ESTKITKEGQQKVSEIQSNIDAHFD 98
                3444555555555423455555555555555555555555555555554.5666666666677777777666555 PP

>> TFIIA_gamma_N  Transcription initiation factor IIA, gamma subunit, helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.2   0.00062         1      14      45 ..      19      51 ..      17      52 .. 0.88
   2 ?    0.7   0.0      0.33   5.4e+02      36      46 ..      94     104 ..      75     106 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00062
  TFIIA_gamma_N 14 LtdaLDeliqe.gkIspqlamkVLeqFDksine 45
                   L+d LD l ++ g++++ql  k L++ Dk +++
     EPA05542.1 19 LEDNLDSLNSKvGDMKKQLNVKALNEIDKLLEK 51
                   8999****87659****************9877 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.33
  TFIIA_gamma_N  36 LeqFDksinea 46 
                     ++FD++++++
     EPA05542.1  94 DAHFDEAVKHV 104
                    57999999876 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   8.8     0.038        62      35      70 ..      24     100 ..      15     105 .. 0.51

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.038
        YtxH  35 ddlkekakelleeakeka.........................................kekaedlkekvkekadel 70 
                 d l  k+ +++++++ ka                                         ++k+++++++++  +de+
  EPA05542.1  24 DSLNSKVGDMKKQLNVKAlneidkllektrematkeaeliinaskskattestkitkegQQKVSEIQSNIDAHFDEA 100
                 55555555555555555544444444444444444444555555444433444444455666666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2368  (0.132077); expected 358.6 (0.02)
Passed bias filter:                      693  (0.0386525); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 760.32
//
Query:       EPA05543.1  [L=109]
Description: hypothetical protein BG20_I1863 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.049   13.7   1.3      0.073   13.2   1.3    1.2  1  ARL2_Bind_BART  The ARF-like 2 binding protein BART


Domain annotation for each model (and alignments):
>> ARL2_Bind_BART  The ARF-like 2 binding protein BART
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.3   4.1e-06     0.073       2      68 ..      17      89 ..      16      93 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.1e-06
                    HHHHHHHHHHHTS-HHHHHHHHHHHHHHHHTT--S.....S-SSTT.HHHHHHHHHHHHHHHHHHHHTT-SSS CS
  ARL2_Bind_BART  2 edwivesleeflaspefkspvqeFidencivFdde.....eenkle.ytdihkeYkklveklleslleeigis 68
                    +++i+ +l+ + +sp  + pv+ F++e+ i+ dd      + n+++   d + +Y k    l++slle+++++
      EPA05543.1 17 FETILIKLLRYNMSPIVEVPVRYFLQEYIIIRDDFwiefrKSNSFDmAFDKYYQYAKNKCMLIDSLLENLNFT 89
                    789999***********************66666344444445444135667778888888899999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 728.31
//
Query:       EPA05544.1  [L=66]
Description: hypothetical protein BG20_I1862 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       820  (0.045736); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 442.83
//
Query:       EPA05545.1  [L=321]
Description: hypothetical protein BG20_I1858 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1929.35
//
Query:       EPA05546.1  [L=52]
Description: hypothetical protein BG20_I1861 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.069   13.3   0.0      0.082   13.0   0.0    1.3  1  DUF3785   Protein of unknown function (DUF3785)
      0.081   12.8   1.4        1.2    9.1   0.0    2.3  2  zf-LSD1   LSD1 zinc finger
       0.13   12.3   1.6          1    9.4   0.2    2.1  2  XPA_N     XPA protein N-terminal
       0.21   11.8   2.2       0.37   11.0   2.2    1.4  1  DUF2685   Protein of unknown function (DUF2685)
       0.57    9.8   2.6        7.2    6.3   0.4    2.1  2  zf_UBZ    Ubiquitin-Binding Zinc Finger


Domain annotation for each model (and alignments):
>> DUF3785  Protein of unknown function (DUF3785)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.3e-05     0.082      44      77 ..      19      52 .]       5      52 .] 0.94

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.3e-05
     DUF3785 44 eevdfskeyykekceeckegveekkksfafleyh 77
                 evd++ e  + kc +c + + + k   ++l yh
  EPA05546.1 19 GEVDYDAELIRPKCGQCSNPIPDSKDKMPYLIYH 52
                58*****************************998 PP

>> zf-LSD1  LSD1 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0   0.00033       1.2      14      23 ..       6      15 ..       3      16 .. 0.84
   2 ?    2.7   0.4     0.031   1.1e+02       1       6 [.      32      37 ..      32      39 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00033
     zf-LSD1 14 ApsVrCalCq 23
                 ++VrC +C+
  EPA05546.1  6 TKTVRCVICD 15
                679******8 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.031
     zf-LSD1  1 CggCrt 6 
                Cg+C  
  EPA05546.1 32 CGQCSN 37
                ****75 PP

>> XPA_N  XPA protein N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1     0.052   1.9e+02       4      10 ..      11      17 ..       8      20 .. 0.70
   2 ?    9.4   0.2   0.00029         1       1      15 [.      29      43 ..      29      43 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.052
       XPA_N  4 CdeCgke 10
                C  C+k+
  EPA05546.1 11 CVICDKP 17
                7777776 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00029
       XPA_N  1 apkCdeCgkefldSy 15
                +pkC +C+ ++ dS+
  EPA05546.1 29 RPKCGQCSNPIPDSK 43
                59***********95 PP

>> DUF2685  Protein of unknown function (DUF2685)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   2.2    0.0001      0.37       3      33 ..      10      38 ..       8      43 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0001
     DUF2685  3 iCvvCKqPideadvtvdtdkGtvHaGqCyqy 33
                 Cv+C +Pi e d   d +      GqC + 
  EPA05546.1 10 RCVICDKPIGEVDY--DAELIRPKCGQCSNP 38
                6********99887..777777778899875 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1     0.011        40       2      14 ..       8      20 ..       7      24 .. 0.80
   2 ?    6.3   0.4     0.002       7.2       5      15 ..      32      42 ..      30      46 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.011
      zf_UBZ  2 tylCerCgkeipe 14
                t+ C  C+k+i e
  EPA05546.1  8 TVRCVICDKPIGE 20
                789******9965 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.002
      zf_UBZ  5 CerCgkeipes 15
                C +C  +ip+s
  EPA05546.1 32 CGQCSNPIPDS 42
                *********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.32s 00:00:00.81 Elapsed: 00:00:00.52
# Mc/sec: 300.35
//
Query:       EPA05547.1  [L=148]
Description: acetyltransferase, GNAT family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.4e-18   65.1   0.0    7.6e-18   64.9   0.0    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
      1e-14   54.7   0.1    1.4e-14   54.3   0.1    1.2  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    6.6e-14   51.9   0.0    8.9e-14   51.5   0.0    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    4.2e-07   30.2   0.2    5.2e-07   29.9   0.2    1.1  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    0.00023   21.0   0.0    0.00036   20.5   0.0    1.3  1  FR47             FR47-like protein
    0.00073   19.3   0.0    0.00088   19.0   0.0    1.2  1  PanZ             Acetyltransferase (GNAT) domain, PanZ
    0.00074   19.6   0.0     0.0013   18.8   0.0    1.4  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
     0.0017   18.4   0.0     0.0026   17.9   0.0    1.3  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
  ------ inclusion threshold ------
      0.018   14.5   1.0      0.078   12.4   1.0    2.0  1  Acetyltransf_15  Putative acetyl-transferase
      0.059   13.1   0.0      0.094   12.4   0.0    1.2  1  Acetyltransf_8   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.9   0.0   4.2e-21   7.6e-18       5     117 .]      21     136 ..      13     136 .. 0.82

  Alignments for each domain:
  == domain 1  score: 64.9 bits;  conditional E-value: 4.2e-21
                     HHHHHHHTHHHHHHHHHHH......HHHHHHSTTCEEEEEEETTEEEEEEEEEEEET..TSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHH CS
  Acetyltransf_1   5 vellvesffppnedaseee......feesfsleaegllvaeedgeliGfisllkipd..ekggvayieslaVspeyrgkGlGsaLlealeerare 91 
                     +el+++      + +s e         +++ ++ +++lva+e+ ++iG +s+  i     ++ ++yi +l+Vs+e+r++G+G +L++++ e  ++
      EPA05547.1  21 YELERPK-----PIDSNELkifknkIDDYLADPQKEILVAKENSKIIGVASIVFIRRlnRAKLEMYIPELVVSKEFRNQGIGEKLIQHCTELSKK 110
                     3333333.....22222222233455666888888**********************99888999999*************************** PP

                     TTESEEEEEEETTEHHHHHHHHHTTE CS
  Acetyltransf_1  92 egikkivlaveedndaairlYeklGF 117
                     + +++i l+  +  + ++++Y+k+GF
      EPA05547.1 111 KKCYRIRLESGNQRKDSHKFYKKMGF 136
                     ********99999********88**9 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.3   0.1   7.6e-18   1.4e-14       2      75 ..      49     137 ..      48     138 .. 0.75

  Alignments for each domain:
  == domain 1  score: 54.3 bits;  conditional E-value: 7.6e-18
                     TEEEEEEEETTEEEEEEEEEEES........TCTEEEEE-GGGTTSSHHHHHHHH.....TTSEEEEEEEEE...THH..HHHHHHHHTTEE CS
  Acetyltransf_7   2 kgevfVaeddgkivGfialslld........aeitrlaVdpeyrgkGiGraLlea.....aekgiileqlel...nae..kaikfYeklGFe 75 
                     ++e++Va+++ ki+G ++++ +          +i +l+V++e+r++GiG +L+++     ++k++  +  +l   n +   ++kfY+k+GFe
      EPA05547.1  49 QKEILVAKENSKIIGVASIVFIRrlnrakleMYIPELVVSKEFRNQGIGEKLIQHctelsKKKKCYRI--RLesgN-QrkDSHKFYKKMGFE 137
                     6789***********999888889999877777777******************86654321334322..332232.1347899*******9 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.5   0.0     5e-17   8.9e-14      20     115 ..      39     145 ..      24     147 .. 0.82

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 5e-17
  Acetyltransf_10  20 ealrerieegealllvaeeggkivGvi......elrdgs.......hisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yav 98 
                      ++++++++++++ +lva+e+ ki+Gv+      +            +i  l+V++e+r qGig++L++++ e  +k++    +l+   ++    
       EPA05547.1  39 NKIDDYLADPQKEILVAKENSKIIGVAsivfirR----LnraklemYIPELVVSKEFRNQGIGEKLIQHCTELSKKKKCYRiRLESGNQRkDSH 128
                      5678888999*****************5543332....14666899***************************988877766777767777999 PP

  Acetyltransf_10  99 pfYeklGFkavgeeqee 115
                      +fY+k+GF++    +++
       EPA05547.1 129 KFYKKMGFEQSALSFTK 145
                      *********98776665 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.2   2.9e-10   5.2e-07       1     135 [.       5     137 ..       5     144 .. 0.82

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 2.9e-10
  Acetyltransf_4   1 iraateeDakeilaiyaeyvvntaitfeyevssveefekfleal.dsekeyvflvaesdrivGyaylgqfkkr..akdwkaelsvylaerdnnke 92 
                     +r a+ +D k il+i+ e +     +++ + + ++ f+  ++++   +++ ++ + e+ +i+G a ++ ++    ak +  + +  +  +  +++
      EPA05547.1   5 VRRAQDKDVKDILEILYELE---RPKPI-DSNELKIFKNKIDDYlADPQKEILVAKENSKIIGVASIVFIRRLnrAKLEMYIPELVV-SKEFRNQ 94 
                     688999*********99833...34444.3568999********7799999999999**********96665222444444444444.58899** PP

  Acetyltransf_4  93 glgrelidaleqvlkeqnienllaeiaspnensiqfhkalGFe 135
                     g+g +li+++ +  k+    ++  e   +++ s +f+k++GFe
      EPA05547.1  95 GIGEKLIQHCTELSKKKKCYRIRLESGNQRKDSHKFYKKMGFE 137
                     ***************************9**************8 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0     2e-07   0.00036      24      80 ..      82     139 ..      69     144 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2e-07
                 EEEEEE-GGG-SSSHHHHHHHHHHHHHHH.S-S-EEEEEETT-HHHHHHHHHHT-EEE CS
        FR47  24 lgalqvlpehrrrGlgsrlvkalakeiae.rgktvllvvvasNtpsirlyeklGfeki 80 
                 +  l v +e+r++G g +l++  ++   + + + + l  + + + s ++y+k+Gfe+ 
  EPA05547.1  82 IPELVVSKEFRNQGIGEKLIQHCTELSKKkKCYRIRLESGNQRKDSHKFYKKMGFEQS 139
                 56789*****************99876665666777777777789**********975 PP

>> PanZ  Acetyltransferase (GNAT) domain, PanZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   4.9e-07   0.00088      12     123 ..      28     139 ..       4     144 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 4.9e-07
        PanZ  12 aqdkiDLakIypaqsaealeaalteegalfaarFNdRlLgAvkv......eledkeaelsdlcVRevTRrRGVgsyLleearrqaPevkswvlaeedvk 104
                 + d   L kI+ ++ ++ l    + ++++++a+ N + +g + +      ++ + e  + +l+V ++ R+ G+g++L++++ +   + k++++  e ++
  EPA05547.1  28 PIDSNEL-KIFKNKIDDYLA---DPQKEILVAKENSKIIGVASIvfirrlNRAKLEMYIPELVVSKEFRNQGIGEKLIQHCTELSKKKKCYRIRLESGN 122
                 4444444.677777777776...7788999999999999987542222115566688899*********************999989999999998876 PP

        PanZ 105 eldlavlqaflealgfaae 123
                   +++  ++f +++gf+++
  EPA05547.1 123 --QRKDSHKFYKKMGFEQS 139
                 ..67788999999999765 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   7.2e-07    0.0013       2     127 ..       5     138 ..       4     139 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 7.2e-07
                     EEEE-GGGHHHHHHHHHHHTT----H..HHHHHHHHHHT......TSEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEEEEE-CCGTTS-H CS
  Acetyltransf_9   2 irelteedldevlellkyaFqdeespleeireyfrklle......esrvlgaedngelvgqlallplelnvpGktlkaagvtgVavapehrgrgv 90 
                     +r+++++d++++le+l +    ++ + +e+ + f+++++      ++++l+a +n +++g++ ++    +++ ++l+++ +    v  e r++g+
      EPA05547.1   5 VRRAQDKDVKDILEILYELERPKPIDSNEL-KIFKNKIDdyladpQKEILVAKENSKIIGVASIVFI-RRLNRAKLEMY-IPELVVSKEFRNQGI 96 
                     89**************99877666665244.56666666566666689************9876644.46777888886.55666899******* PP

                     HHHHHHHHHHHHHHTT--EEEE--.....SSHHHHHTTT-EE CS
  Acetyltransf_9  91 lskLlaraleemreegqplsllfP.....ssipiYrrfGyei 127
                      +kL+++  e  ++++   + l        s ++Y+++G+e+
      EPA05547.1  97 GEKLIQHCTELSKKKKCYRIRLESgnqrkDSHKFYKKMGFEQ 138
                     **********99999876666666677776689999999986 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.4e-06    0.0026      20      56 ..      75     111 ..      53     119 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.4e-06
  Acetyltransf_CG  20 rkegvldfthTeVpeelrGkGiAkkLvkaalddaree 56 
                      r + ++ +   +V++e+r +Gi++kL++++ +  +++
       EPA05547.1  75 RAKLEMYIPELVVSKEFRNQGIGEKLIQHCTELSKKK 111
                      344489999********************99877665 PP

>> Acetyltransf_15  Putative acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.0   4.4e-05     0.078      71     138 ..      76     138 ..      13     146 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.4e-05
  Acetyltransf_15  71 nvleiY..tlyvsekyrgkGlakklLeeslkelk..knYkvdnelllaLHlnpkDksMnisfalYyslgFrk 138
                      + le+Y  +l+vs+++r++G+  kl+++ ++  k  k Y ++      L   ++ ++ + s  +Y ++gF +
       EPA05547.1  76 AKLEMYipELVVSKEFRNQGIGEKLIQHCTELSKkkKCYRIR------L---ESGNQRKDSHKFYKKMGFEQ 138
                      344555448*****************9996555411333333......3...33444455666777777766 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   5.2e-05     0.094      86     139 ..      86     138 ..      82     141 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.2e-05
                     ESSHHHCTTTCHHHHHHHHHHHHHCCTT--EEEE--BTT-HHHHHHHHHTT-EE CS
  Acetyltransf_8  86 igeaeargkglttallralvhylfadprtrrvvvEPdvrNerairllekaGfek 139
                     +  +e+r++g++ +l+++++++  ++ ++ r+ +E   + + ++++++k+Gfe+
      EPA05547.1  86 VVSKEFRNQGIGEKLIQHCTELSKKK-KCYRIRLESGNQRKDSHKFYKKMGFEQ 138
                     556899***********999876555.9************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 990.02
//
Query:       EPA05548.1  [L=633]
Description: peptidase families S8 and S53 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.7e-21   74.3   7.7    2.1e-14   53.5   0.5    3.1  2  Peptidase_S8  Subtilase family


Domain annotation for each model (and alignments):
>> Peptidase_S8  Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   1.7     5e-09     9e-05       1     169 [.     245     380 ..     245     416 .. 0.74
   2 !   53.5   0.5   1.2e-18   2.1e-14     179     298 .]     514     622 ..     497     622 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 5e-09
                   -TT-EEEEECS-B-TT-TTTGGGEEE..EEEE---TTSG.GGEETT-SS-TT-SC-SSS....HHHHHHHHHH-B..SSSSSB-SSTTSEEEEEE-S CS
                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Peptidase_S8   1 gkgvlvavlDtGvdpshpdlsvttdgerklvdvideegagfngadsettstnwarddngnsieHGthvAGiaaanapeegekngvapgakilsvkvl 97 
                   gk+++vavlD  + +++p++s+++ +           ++ f++  ++++s ++ ++++   i HGt vA i+            vap+ k++ +++ 
    EPA05548.1 245 GKDIKVAVLDMLFYTDNPKISDNIVN-----------FKSFRNSFENSMSAQSITNEEN--ISHGTAVAEIITD----------VAPNSKLYLYEMN 318
                   89*******************55333...........3336666666666666555543..55******88865..........69****9944444 PP

                   STTSB-HH..HHHHHHHHHHHHCT-SEEEE-EE.SCETTCHHCHHHHHHHHHHHH.CCT-EEEEE--SS-T-H CS
                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Peptidase_S8  98 dtsggsmetgteliraieeaaedkvdvinmslg.estslpktgrsiealainravnkkgvlvviSaGNngktg 169
                           t  e  rai+ea+ ++vd+i+m  g    s++ ++++++   +++a+ ++g+ v++ +GN  +++
    EPA05548.1 319 --------TDVEFGRAIDEAISNDVDIIAMAAGwPNLSTDGSSQITK--KVEEAI-NHGISVIVPSGNFAQKH 380
                   ........3356779999999999**999999944444555555555..999999.89999999999988443 PP

  == domain 2  score: 53.5 bits;  conditional E-value: 1.2e-18
                   ECTTTSTTCEEEEEES.TTSSB-TT--B-TT.......-EEEE-S-CCCCCCCCCHHHTTTHHEEEE-SHHHCHHHHHHHHHHHHHHHTT--HHHHH CS
                   xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Peptidase_S8 179 gtpstsknvitvgayt.tegkiapfSsrGpssdgklkpdivapGgnivstwsrqsnnsaglssyqsmsGTSmAsPnaagaaAlllsalpkltpetvr 274
                     ps +k+vi vga++ ++g + +fSs+Gp+ +gk  p +v p g    t+  ++         ++++GTS+ +P +ag+aAl+l+a+p+l+p ++ 
    EPA05548.1 514 VVPSDAKGVIVVGAVNnKDGVLESFSSHGPTNNGKSVPNVVGPNGV--TTIAYNG---------NLFYGTSATTPYVAGIAALMLDANPNLSPSQLL 599
                   469999*********955677889*****************99886..5555555.........689****************************** PP

                   HHHHCCS-EE......SSSSSSTT CS
                   xxxxxxxxxxxxxxxxxxxxxxxx RF
  Peptidase_S8 275 aallntAqdlgkadniesfaqGaG 298
                     +++ A++  ++ +  ++++G+G
    EPA05548.1 600 NQIEQHAKPKHME-TNYKNEYGFG 622
                   *******996555.7778899988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (633 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       974  (0.0543254); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.73u 0.32s 00:00:01.05 Elapsed: 00:00:00.51
# Mc/sec: 3764.65
//
Query:       EPA05549.1  [L=83]
Description: hypothetical protein BG20_I1860 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.017   15.2   0.9      0.022   14.8   0.9    1.1  1  DZR            Double zinc ribbon
      0.018   12.9   0.0      0.018   12.9   0.0    1.0  1  PolC_DP2       DNA polymerase II large subunit DP2
      0.031   14.3   0.1      0.032   14.2   0.1    1.1  1  HypA           Hydrogenase/urease nickel incorporation, metal
      0.064   13.1   1.2      0.089   12.7   1.2    1.2  1  zf-C3HC4_3     Zinc finger, C3HC4 type (RING finger)
      0.081   11.4   0.0      0.081   11.4   0.0    1.0  1  FHIPEP         FHIPEP family
       0.17   11.6   2.6        6.7    6.6   0.1    2.2  2  zinc_ribbon_2  zinc-ribbon domain


Domain annotation for each model (and alignments):
>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.9   7.4e-06     0.022      13      37 ..      59      79 ..      51      82 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 7.4e-06
         DZR 13 rfCseCgtklkavaaedrCpsCgek 37
                 +C eCg+k+      ++Cp+C++ 
  EPA05549.1 59 GMCLECGAKIY----DQKCPNCDSL 79
                58*******99....8******876 PP

>> PolC_DP2  DNA polymerase II large subunit DP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   6.1e-06     0.018     609     641 ..      49      81 ..      24      83 .] 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.1e-06
    PolC_DP2 609 kgeieveiarrkCkkCgketlearCeeCgekte 641
                 k++ie e+++  C +Cg++ + ++C++C++  e
  EPA05549.1  49 KKSIEKELGEGMCLECGAKIYDQKCPNCDSLNE 81 
                 7899************************98765 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   1.1e-05     0.032      63      96 ..      51      80 ..      30      83 .] 0.84

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.1e-05
                EEEEE--EEEETTTS-EEECHHHHHS-TTTSSS- CS
        HypA 63 eieevpvkvrCreCgkefeleekalrCpkCgsad 96
                +ie++  + +C eCg+++  +    +Cp+C+s +
  EPA05549.1 51 SIEKELGEGMCLECGAKIYDQ----KCPNCDSLN 80
                588999999******888754....7****9976 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.2     3e-05     0.089      25      45 ..      60      78 ..      58      83 .] 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3e-05
                E-HHHHHHHHHTT-B-TTT-- CS
  zf-C3HC4_3 25 lCeeCaekllkrkkkCpiCrr 45
                +C eC  k+   ++kCp C +
  EPA05549.1 60 MCLECGAKI--YDQKCPNCDS 78
                8********..89******86 PP

>> FHIPEP  FHIPEP family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   2.7e-05     0.081     254     297 ..       4      48 ..       2      75 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.7e-05
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXX CS
      FHIPEP 254 anpkalliaagvllllalvpglpklvflllaallalla.yllkkk 297
                 +++ ++li++++l++++l+p +  +  +l+a+++ +   +++  +
  EPA05549.1   4 EKRDIILIVGLLLFMIGLIPFMAPIYAVLIAIAMYFGIkFYVGVR 48 
                 678899****************99988888877765440333333 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1    0.0022       6.7       2      11 ..      61      70 ..      60      71 .. 0.83
   2 ?    5.1   0.6    0.0066        20       1       5 [.      72      76 ..      72      82 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0022
  zinc_ribbon_2  2 CpnCGaelqd 11
                   C +CGa++ d
     EPA05549.1 61 CLECGAKIYD 70
                   8899999966 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0066
  zinc_ribbon_2  1 fCpnC 5 
                   +CpnC
     EPA05549.1 72 KCPNC 76
                   79999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1052  (0.0586759); expected 358.6 (0.02)
Passed bias filter:                      622  (0.0346924); expected 358.6 (0.02)
Passed Vit filter:                       103  (0.00574488); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 527.82
//
Query:       EPA05550.1  [L=133]
Description: hypothetical protein BG20_I1856, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
          2    8.4  14.3        2.6    8.0  14.3    1.3  1  FAM60A          Protein Family FAM60A
        2.6    7.0  17.2        2.8    6.9  17.2    1.0  1  SLC12           Solute carrier family 12
        3.8    7.0  10.1        4.7    6.7  10.1    1.2  1  ASD2            Apx/Shroom domain ASD2
        4.3    5.6  13.1        4.7    5.5  13.1    1.1  1  SID-1_RNA_chan  dsRNA-gated channel SID-1
        4.4    7.1  29.9        4.6    7.1  29.9    1.0  1  SPX             SPX domain
        6.9    5.5  10.0        8.8    5.1  10.0    1.3  1  CSG2            Ceramide synthase regulator
        7.8    5.2  27.8          9    5.0  27.8    1.0  1  Apt1            Golgi-body localisation protein domain
        9.1    4.9  22.7        9.5    4.9  22.7    1.1  1  Presenilin      Presenilin
        9.1    5.5  15.2         10    5.4  15.2    1.2  1  FAM76           FAM76 protein
        9.2    4.9  19.0         11    4.6  19.0    1.3  1  NPR3            Nitrogen Permease regulator of amino acid tra
        9.4    6.4  14.8         12    6.2  14.8    1.2  1  PNISR           Arginine/serine-rich protein PNISR


Domain annotation for each model (and alignments):
>> FAM60A  Protein Family FAM60A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0  14.3    0.0016       2.6     102     179 ..      21      98 ..       2     119 .. 0.51

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0016
      FAM60A 102 kieekfekklkkkkklkktkakasdasssereaspassdsasedsdesedeeekkrkkllekkkkrsaeklvsfldls 179
                   ++ +++ ++    ++++++++s+++s+++++s+++s+s+s+++++s+++++++++++++++++++++++++f+ ++
  EPA05550.1  21 AASNAASNAASTTISVNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNFISKQ 98 
                 222222222222222222333333334444444444444444444444444445555666677777777888888765 PP

>> SLC12  Solute carrier family 12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9  17.2    0.0017       2.8     148     247 ..      20     104 ..       1     125 [. 0.31

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0017
       SLC12 148 sekeeeekkkakkkklleekskekeekekleekdsnlslseekk.eeekekkkekkkkkekkeklkkkekslllkeaskeekevleeitqfqkkqkkgt 245
                 ++ +++++                + ++++ + +sn++ +++++ +++++++++++++++++++++++++s++++++++++++ +++ ++f +kq++ +
  EPA05550.1  20 NAASNAAS----------------NAASTTISVNSNSNSNSNSNsNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNFISKQSTVV 102
                 11111111................111111111111111111110111111111111111112222222222222222222333344444444444444 PP

       SLC12 246 iD 247
                 +D
  EPA05550.1 103 VD 104
                 44 PP

>> ASD2  Apx/Shroom domain ASD2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7  10.1    0.0029       4.7      54     131 ..      26     111 ..       3     130 .. 0.42

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0029
        ASD2  54 k.........eeeekkeeeekseasslesssayystsaakaelltklkdeteleekdeeeek.seeeedldlkekkeeLieslskkle 131
                 +          +++++++++++++s+++s+s++ s s+++++ ++  +++++++++++++++ +++ +++ ++++    ++++ k +e
  EPA05550.1  26 AsnaasttisVNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNS--NSNSNSNSNSNSNSNsNSNSNSNFISKQSTVVVDAIVKAVE 111
                 122223333322222222222222222222222222222222222..22222222222222213333334666666666666666655 PP

>> SID-1_RNA_chan  dsRNA-gated channel SID-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5  13.1    0.0029       4.7     140     221 ..      33     114 ..       5     122 .. 0.60

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0029
  SID-1_RNA_chan 140 vvivekvresseekrvkessssesaseslesvssavrsesessveeesdydtleeiesdknvirtkkvlvvsdlsrkdkrvl 221
                     ++ v+++++s+++++ +++s+s+s+s+s+++ +s+ +s+s+s+++++s+ ++ ++ +s++n i +++ +vv  + +  ++++
      EPA05550.1  33 TISVNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNFISKQSTVVVDAIVKAVEEIV 114
                     2333333434444444444444444444555555566667777777777777777777888888888888866665555554 PP

>> SPX  SPX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1  29.9    0.0028       4.6      64     162 ..      11     108 ..       1     132 [. 0.33

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0028
         SPX  64 tepstsaaadesgnsaadasssepkdeae......slprrsplsrssrssssygglvssppsansssssddssesnpadssssssssesesssssspsl 156
                 + ++ s+aa++++++aa +++s      +      +++++s+++++s+s+s+ ++ ++s++++ns+s+s+++s+sn++++s+s+s+s+s+  s++s+ +
  EPA05550.1  11 S-NAASNAASNAASNAASNAAS------TtisvnsNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNFISKQSTVV 102
                 1.11111111111111111112......12222222222222222222222222222222222222222222222222344555555555555555556 PP

         SPX 157 lrrlfs 162
                 +  + +
  EPA05550.1 103 VDAIVK 108
                 555554 PP

>> CSG2  Ceramide synthase regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1  10.0    0.0054       8.8      89     152 ..      42     106 ..       5     115 .. 0.44

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0054
        CSG2  89 kenklesnsessleleek.vesdeeleekteeeklekvaekekkllsvstlkyvakllilslllv 152
                 ++++ +sns+s+++++++ ++++++ ++ +++++ ++ ++ +++  s+s+ ++++k +++ + ++
  EPA05550.1  42 SNSNSNSNSNSNSNSNSNsNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNFISKQSTVVVDAI 106
                 11111111111111111101111111112222222222223444444455555555544444433 PP

>> Apt1  Golgi-body localisation protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0  27.8    0.0055         9     317     401 ..      22     119 ..       2     131 .. 0.27

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0055
        Apt1 317 ddesdeesessssss......ssssssassssssssrssslelrlkptsstssssssessssssskkrsseesslessaservkssr............ 397
                  ++  ++       s      s+s+s+++s+s+s+s+s+s+++++++++s+s+s+s+++s+s+s ++++s+++s ++  s+++   +            
  EPA05550.1  22 ASNAASNAA-----SttisvnSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNFISKQS---Tvvvdaivkavee 112
                 111111111.....112233322222222222222222222222111111122212222222222222222222222222222...0222333333334 PP

        Apt1 398 ...asdd 401
                    +sdd
  EPA05550.1 113 ivdNSDD 119
                 4444554 PP

>> Presenilin  Presenilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9  22.7    0.0058       9.5     228     306 ..      13      90 ..       1     123 [. 0.34

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0058
  Presenilin 228 kkaevaeseeeeeaekkkeeasesskeeeseeesseksaqsseseeeseeesseaessaeesseekeseessesseeee 306
                  ++++a+++ +++a+++++++ + +++++s+++s+++s+++s+s+++s+++s+++++s+++s+++++s+++s+s+++ +
  EPA05550.1  13 AASNAASNAASNAASNAASTTISVNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSN-S 90 
                 12222222222222222222222222222222222222222222222222222222222221111111111111111.1 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4  15.2    0.0062        10     152     217 ..      40     105 ..       4     132 .. 0.36

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0062
       FAM76 152 kkskskkskkskekskekkaskkkskkhkkrssrlevskleeeklaeekesnetskksldsnssdh 217
                 ++s+s+++++s+++s+++++s+++s+++++++s++++ + ++++ +++++sn++  ++ ++ + d 
  EPA05550.1  40 SNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNFISKQSTVVVDA 105
                 111111111111111111111111111111111111111111111112222222222333333333 PP

>> NPR3  Nitrogen Permease regulator of amino acid transport activity 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6  19.0     0.007        11      68     122 ..      36      87 ..       3     126 .. 0.39

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.007
        NPR3  68 kesskksesssksesseekksskeseeseekesneeeeeeededdeesekeeeek 122
                  +s+++s+s+s+s+s+++++s+++s+++++++sn++++++++++++++++   ++
  EPA05550.1  36 VNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSN---SN 87 
                 22222222211111111111111111111111111111111111111111...11 PP

>> PNISR  Arginine/serine-rich protein PNISR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2  14.8    0.0071        12      42     113 ..      21      92 ..       2     131 .. 0.40

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0071
       PNISR  42 rkeekkesskeeeeaknprnlakskfdsedeksdeeeeegaegedsesqekasskksevdeqespeeeeaar 113
                 ++++ +++   ++ ++n +++++s+++s+++++++ + + + + +s+s+++++s+++  ++++s+++++++ 
  EPA05550.1  21 AASNAASNAASTTISVNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNSNS 92 
                 222222222222222333333333333332222222221122222222222222222222222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2664  (0.148586); expected 358.6 (0.02)
Passed bias filter:                      593  (0.0330749); expected 358.6 (0.02)
Passed Vit filter:                       247  (0.0137766); expected 17.9 (0.001)
Passed Fwd filter:                        89  (0.00496402); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.93u 0.37s 00:00:01.30 Elapsed: 00:00:00.50
# Mc/sec: 795.73
//
Query:       EPA05551.1  [L=175]
Description: hypothetical protein BG20_I2670, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.32s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1093.13
//
Query:       EPA05552.1  [L=101]
Description: NADH dehydrogenase subunit K [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.1e-22   77.8   6.1    5.4e-22   77.4   6.1    1.1  1  Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase cha
  ------ inclusion threshold ------
        1.6    8.6   5.6         16    5.4   0.0    2.8  3  VPDSG-CTERM  VPDSG-CTERM motif


Domain annotation for each model (and alignments):
>> Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase chain 4L
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.4   6.1     6e-26   5.4e-22       3     104 ..       9      97 ..       7      99 .. 0.96

  Alignments for each domain:
  == domain 1  score: 77.4 bits;  conditional E-value: 6e-26
                  HHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHHHHHHHC.............TTSCGGHHHHHHHHHHHHHHHHHHHHHHHHHHHSSS-BC CS
  Oxidored_q2   3 llliallfliGlygvllrrnllkvliglelisnavnlllvlagvftegtlvitnpatefadplpqalvLtaivigaaetavgLallvrlyreygtddv 100
                   l++++l +iG+yg+ ++rn++++l+++e+i na+nl+lv++g+f               +  +q+l+L+ i+i+aae+avgL+l++ +yr y+++d+
   EPA05552.1   9 VLVSVALLGIGIYGLSVKRNAIRMLFAVEIIINAANLNLVAFGRFI-------------PNSGGQTLALFSIAIAAAEVAVGLSLIIVAYRMYQNIDI 93 
                  6899*****************************************9.............99************************************9 PP

                  CG-- CS
  Oxidored_q2 101 qelr 104
                   ++r
   EPA05552.1  94 ADFR 97 
                  9875 PP

>> VPDSG-CTERM  VPDSG-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0    0.0018        16       9      19 ..      13      23 ..      12      27 .. 0.86
   2 ?    5.0   0.4    0.0024        22       7      18 ..      60      71 ..      58      71 .. 0.85
   3 ?   -1.1   0.1       0.2   1.8e+03      14      22 ..      76      84 ..      75      86 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0018
  VPDSG-CTERM  9 laLLglgLlgL 19
                 +aLLg+g+ gL
   EPA05552.1 13 VALLGIGIYGL 23
                 89*****9988 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0024
  VPDSG-CTERM  7 STlaLLglgLlg 18
                  TlaL+++++++
   EPA05552.1 60 QTLALFSIAIAA 71
                 59*******987 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.2
  VPDSG-CTERM 14 lgLlgLlgl 22
                  gL++++++
   EPA05552.1 76 VGLSLIIVA 84
                 578888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 636.78
//
Query:       EPA05553.1  [L=236]
Description: NADH dehydrogenase, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.7e-65  219.6  13.6    6.4e-65  219.4  13.6    1.0  1  NADHdh    NADH dehydrogenase


Domain annotation for each model (and alignments):
>> NADHdh  NADH dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  219.4  13.6   3.6e-69   6.4e-65     113     297 ..       2     220 ..       1     222 [. 0.98

  Alignments for each domain:
  == domain 1  score: 219.4 bits;  conditional E-value: 3.6e-69
                 HHHHHHHHTSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-SS-HHHHHHCCCTT.-CCCCHHHHHHHHHHHHHHCCTCTTBTTTTSTTSSSSCCCT CS
      NADHdh 113 illaGwasnskYallGalRsaaqmisyEvalglsllavvllagslslseiveaqeei.wfillqllafiifliallaetnraPFDlpeaesELvaGfht 210
                 ++l++w+snsk++++G++R++ qm+s+E++l+lsll+vv+l+g+l+lseiv +q++  w+i+l ++++iif+i++lae++r+PFDlpeaesE+vaG+ t
  EPA05553.1   2 TILSAWSSNSKFPFIGGIRALHQMVSFEIPLILSLLGVVILTGTLNLSEIVVSQTNFpWIIFL-PIGAIIFFITILAELERIPFDLPEAESEIVAGWLT 99 
                 6899**************************************************988888887.*********************************** PP

                 T-HCHHHHHHHHHHHHHHHHHHHHHHHHCT.SS-HCCS..................................HHHHHHHHHHHHHHHHHHHHHC----T CS
      NADHdh 211 EYsgmkfalfflaeyanmvlvsalavllFlgGwllpfs..................................gllwfllKvllllflfiwiratlpRlR 275
                 E+sgm ++l+ l+ y+++++++al+v+lFlgGw++p++                                  g++wf+lK++ ++f++++ r ++pR+R
  EPA05553.1 100 EFSGMIYGLVQLGTYLKLYAFAALFVVLFLGGWTGPMIwppfpeeiitdgivmgpitakipglpvfsqemlnGVVWFVLKTVGVIFFILLPRGVFPRIR 198
                 ***********************************999999********************************************************** PP

                 CHHHHHHHCCTCHHHHHHHHHH CS
      NADHdh 276 ydqlmklgwkvllplalanlll 297
                 +d l++lgw  l+ la++n+++
  EPA05553.1 199 IDMLLSLGWYKLIGLAFVNIFI 220
                 ********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1661.31
//
Query:       EPA05554.1  [L=592]
Description: proton-translocating NADH-quinone oxidoreductase, chain L, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.4e-59  199.8  31.0    1.2e-54  185.5  30.5    3.0  3  Proton_antipo_M  Proton-conducting membrane transporter
    2.1e-13   50.1   2.0    2.1e-13   50.1   2.0    2.6  2  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 
     0.0075   15.9   0.1      0.014   15.1   0.1    1.4  1  Proton_antipo_C  NADH-dehyrogenase subunit F, TMs, (complex I
  ------ inclusion threshold ------
      0.055   13.1   0.3      0.055   13.1   0.3    4.7  4  Oxidored_q2      NADH-ubiquinone/plastoquinone oxidoreductase
        3.9    7.5   6.2        2.6    8.1   1.3    2.6  2  PsbW             Photosystem II reaction centre W protein (Ps


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -5.4   5.2       4.9   1.8e+04      81     125 ..      43      88 ..      18     132 .. 0.60
   2 !   21.0   0.0   4.3e-08   0.00015       1      31 [.     140     170 ..     140     176 .. 0.92
   3 !  185.5  30.5   3.3e-58   1.2e-54      32     292 ..     190     468 ..     179     469 .. 0.87

  Alignments for each domain:
  == domain 1  score: -5.4 bits;  conditional E-value: 4.9
  Proton_antipo_M  81 lllllllllvgllvKsaqvplhlWlpdayveaPtpvsall.Aatlv 125
                       +++  + l+++l  ++++p+ l   +++ + ++ +s+ l A++l 
       EPA05554.1  43 GFVAVGFALMSALSALSLLPMALEAHEVHDQISWINSIGLkAGVLA 88 
                      3344444444555556777777777777777777777766555443 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 4.3e-08
  Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpks 31 
                      +++Ll++++g+E+v+l++y Li +w++++k+
       EPA05554.1 140 SDNLLQVFFGWEGVGLASYALISFWYRDKKK 170
                      79************************99876 PP

  == domain 3  score: 185.5 bits;  conditional E-value: 3.3e-58
  Proton_antipo_M  32 leAslklflltllgsliLLlgilllynltgtlefeelskal...elglnslelllllllllvgllvKsaqvplhlWlpdayveaPtpvsall.A 121
                      ++A++k+f++t +g+++++ g+ll++ ++gt  f+el+  +   +++ ++  l  +++ll+ g++ Ksaq+pl+ Wl +a + +Pt+vsal+ A
       EPA05554.1 190 THAGMKAFIMTKVGDVMMIAGMLLIFLFAGTFGFRELMHDTawaTTMSAQGLLIPAFVLLFGGAVGKSAQFPLNEWLLEA-MTGPTAVSALIhA 282
                      68***********************************9988888888888888999************************.************* PP

  Proton_antipo_M 122 atlvkagvlllirllllla......vssneisqlllilaiismllgslvalaqtdiKrllAySsishlGymlialav.....atqygveaaiih 204
                      at+vkagv+l++rl +l++      + + +   ++l+++++++ll +l +++ ++iK++lAyS+ s++Gym++ l++     + + g++a ++h
       EPA05554.1 283 ATMVKAGVFLVMRLAPLVFalsaagILADQFFEIILLVGATTALLLGLQGMVNSEIKKVLAYSTGSQIGYMMMVLGIaglsqQFVNGYTAGFFH 376
                      ***************999877522223333445677889**********************************99994443334679******* PP

  Proton_antipo_M 205 llthalfkallFllagsviyerektrdirayggLakkmPilalvllvlllslaGlPpt.agFlskfliLeaavavslillvla....vvasvl 292
                      l++ha+fka+lF++ags+ +  + +r ++++ggL+k+m  ++l +  + l+l+G P+  +gF+sk++i+ a++  ++ +++ +    v+++v+
       EPA05554.1 377 LISHAMFKASLFMAAGSLLH-VVGSRFMTDMGGLRKHMKKTYLFMWAAGLGLMGAPFItTGFWSKDSIFGAIYTSGHEWAMPVfaiaVLTAVI 468
                      *****************955.569********************************9669**********99987766655431112555555 PP

>> Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.1   2.0   5.8e-17   2.1e-13       3      57 ..      75     127 ..      73     128 .. 0.90
   2 ?   -2.6   0.1       1.7   6.1e+03      25      43 ..     352     370 ..     349     373 .. 0.66

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 5.8e-17
  Proton_antipo_N   3 tWlsvgglsieigfllDklsalmllvvtfvsllvhlYSigYMaddegyqRFfayl 57 
                      +W++  ++ ++ g+l D+l ++m+ vv ++s+l+++YS+gYM++d++++RF + +
       EPA05554.1  75 SWIN--SIGLKAGVLADPLAVIMANVVGWISFLIMIYSTGYMKGDKSITRFWFWM 127
                      6877..344899***************************************8765 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.7
  Proton_antipo_N  25 mllvvtfvsllvhlYSigY 43 
                      ++++v +++ l + +  gY
       EPA05554.1 352 YMMMVLGIAGLSQQFVNGY 370
                      5677777777666666665 PP

>> Proton_antipo_C  NADH-dehyrogenase subunit F, TMs, (complex I) C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   3.8e-06     0.014      89     150 ..     495     556 ..     473     588 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.8e-06
  Proton_antipo_C  89 tlsyPhEsdntmlfpllvLvlftlfvGliGipfnqegidldilskwLtps..inllhknsnesv 150
                      + +  hE++++m +p  +L+++t+ +G++G +f+ +    ++++++L  +  i+ +h++ ++s+
       EPA05554.1 495 EGHHIHEAPSSMWIPYGILAVLTIGIGIVGLSFEGG--LHELFTNYLEETfgIHSIHHEIENSI 556
                      456679***************************954..45677777766522556677777644 PP

>> Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase chain 4L
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.3   1.5e-05     0.055       7      48 ..     126     168 ..     121     250 .. 0.87
   2 ?   -1.8   2.1      0.64   2.3e+03      64      88 ..     309     331 ..     274     343 .. 0.50
   3 ?    2.1   0.1     0.041   1.5e+02      54      88 ..     440     480 ..     376     493 .. 0.72
   4 ?   -1.2   0.5      0.45   1.6e+03       4      19 ..     512     527 ..     509     531 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.5e-05
                  HHHHHHHHHHHHH.SSCCHHHHHHHHHHHHHHHHHHHHHHHHC CS
  Oxidored_q2   7 allfliGlygvll.rrnllkvliglelisnavnlllvlagvft 48 
                   ++f+iG + +++ ++nll+v++g e +++a + l+  + + +
   EPA05554.1 126 WMMFFIGSMQLIVlSDNLLQVFFGWEGVGLASYALISFWYRDK 168
                  57999999999999*******************9999886665 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.64
                  SCGGHHHHHHHHHHHHHHHHHHHHH CS
  Oxidored_q2  64 plpqalvLtaivigaaetavgLall 88 
                  ++ q + ++++v   a+ta++L+l 
   EPA05554.1 309 LADQFFEIILLVG--ATTALLLGLQ 331
                  3334444444433..3555555554 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.041
                  ...............TTSCGGHHHHHHHHHHHHHHHHHHHHH CS
  Oxidored_q2  54 i.......tnpatefadplpqalvLtaivigaaetavgLall 88 
                           ++ +e a p+  + vLta vi+a  t  +L+l+
   EPA05554.1 440 KdsifgaiYTSGHEWAMPVFAIAVLTA-VITAFYTTRMLGLV 480
                  144445555667777888888888888.55666666666665 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 0.45
                  HHHHHHHHHHHHHHHH CS
  Oxidored_q2   4 lliallfliGlygvll 19 
                  +l++l ++iG++g+ +
   EPA05554.1 512 ILAVLTIGIGIVGLSF 527
                  6788999999999865 PP

>> PsbW  Photosystem II reaction centre W protein (PsbW)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.3      0.11   3.8e+02      84     111 ..       1      30 [.       1      35 [. 0.81
   2 ?    8.1   1.3   0.00072       2.6      54     126 ..      42     117 ..      31     121 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.11
        PsbW  84 lsteGtGLpl..GlsnnllgwiLlgvfgli 111
                 ++te  GL+l  G s   l wiL  + +li
  EPA05554.1   1 MATEMLGLSLeaGASSAWLIWILPFIAALI 30 
                 6788777775559**********9998888 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00072
        PsbW  54 esklgmgasllaaaaaatvsspalAl....vDeRls.teGtGLplGlsnnllgwiLlgvfgliwalyfvytstleeDe 126
                 +  + +g +l++a++a ++    +Al    v + +s  +  GL  G+  + l++i++ v g i  l ++y++   + +
  EPA05554.1  42 TGFVAVGFALMSALSALSLL--PMALeaheVHDQISwINSIGLKAGVLADPLAVIMANVVGWISFLIMIYSTGYMKGD 117
                 45566788888877665554..4444445588888846899*****************************98665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (592 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       764  (0.0426125); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 3743.16
//
Query:       EPA05555.1  [L=517]
Description: proton-translocating NADH-quinone oxidoreductase, chain M [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.5e-61  206.1  24.6    6.5e-61  206.1  24.6    1.9  2  Proton_antipo_M  Proton-conducting membrane transporter
    1.6e-05   24.9   0.3    0.00029   20.8   0.0    3.0  2  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 
  ------ inclusion threshold ------
       0.15   12.1   1.3        1.2    9.2   0.4    2.3  2  DUF1515          Protein of unknown function (DUF1515)


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  206.1  24.6   1.1e-64   6.5e-61       1     279 [.     156     430 ..     156     445 .. 0.94
   2 ?   -1.1   0.2      0.14   8.4e+02      39      95 ..     439     495 ..     429     500 .. 0.72

  Alignments for each domain:
  == domain 1  score: 206.1 bits;  conditional E-value: 1.1e-64
  Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskalelglnslelllllllllvgllv 94 
                      +++L+ +y+++E++l+p ++L++lw++ p++ + +l +++ t +g ++LLlg+l++    g+ +f ++ +     +    lll ++++ +gl v
       EPA05555.1 156 STNLIEFYVFFEVMLIPGFFLVALWGAGPRR-KIGLMFLFWTHAGAVVLLLGFLMIGLSIGSFDFADIEES---KIPHDILLLSAIAISIGLGV 245
                      78************************99665.679999999*****************************9...7788889999********** PP

  Proton_antipo_M  95 KsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla.vssneisqlllilaiismllgslvalaqtdiKrllAySsishlGyml 187
                      K+a++++h Wlp ++  aPtp+sall+  +  +g+++++rl++ l      ++s+++ i ++++m++g+ +al q diKrllAySsis++Gy+l
       EPA05555.1 246 KLAVFMFHIWLPWVHGSAPTPISALLSPAMIGIGAYGIFRLIVELLpNTFADLSIWFHIWGLVTMIYGGAMALMQDDIKRLLAYSSISQMGYIL 339
                      **************************888************9988879999******************************************* PP

  Proton_antipo_M 188 ialavatqygveaaiihllthalfkallFllagsviyerektrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavs 279
                       +++ +++ g+++a +  +thal k  lF++ag +   ++ tr+i ++ggLa kmPi+a++ ++++l+++G+Ppt+gF+++++++++a++  
       EPA05555.1 340 FGIGSMSVLGLSGAEMMYVTHALGKGILFMMAGIL-IVKVGTRSISQLGGLAGKMPITAVCTVIGALTIMGVPPTSGFMGEWTLFYGALETA 430
                      ********************************666.5566**********************************************998865 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.14
  Proton_antipo_M  39 flltllgsliLLlgilllynltgtlefeelskalelglnslelllllllllvgllvK 95 
                      ++++ lg ++  l +++++++   + f +l  +le++++ +  + + +++l+g+ + 
       EPA05555.1 439 AVTFGLGLVATALTMSYILWMLKRVFFGKLPVNLENVKEGSWYMTAPMMVLAGFTIV 495
                      667777788888888888888888888888888877777777777777777777654 PP

>> Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   4.9e-08   0.00029       8      46 ..      66     100 ..      58     112 .. 0.83
   2 ?    0.1   0.1      0.15   8.7e+02      21      41 ..     234     254 ..     217     255 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 4.9e-08
  Proton_antipo_N   8 gglsieigfllDklsalmllvvtfvsllvhlYSigYMad 46 
                      g    e+gfllD+l   +++++ ++s++  lYS  YM +
       EPA05555.1  66 G----EFGFLLDGLASPFAIMIYVLSTILVLYSKPYMIH 100
                      4....89******************************65 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.15
  Proton_antipo_N  21 lsalmllvvtfvsllvhlYSi 41 
                      lsa+ + +  +v l v ++ i
       EPA05555.1 234 LSAIAISIGLGVKLAVFMFHI 254
                      99*************999866 PP

>> DUF1515  Protein of unknown function (DUF1515)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0     0.073   4.4e+02      78     101 ..     275     298 ..     272     308 .. 0.90
   2 ?    9.2   0.4   0.00019       1.2      53      99 ..     313     361 ..     303     372 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.073
     DUF1515  78 lmGlGalGviGiaaaalavtfadv 101
                 ++G+Ga G+  +    l  tfad+
  EPA05555.1 275 MIGIGAYGIFRLIVELLPNTFADL 298
                 68********************97 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00019
     DUF1515  53 egsvvklkaditsvkevte.dvkkwklmGlGalGviGiaaaala.vtfa 99 
                  g+++++++di  +   +      + l G+G++ v+G+++a +  vt+a
  EPA05555.1 313 GGAMALMQDDIKRLLAYSSiSQMGYILFGIGSMSVLGLSGAEMMyVTHA 361
                 47899999999998776651345689***************98878876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (517 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       784  (0.043728); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.49
# Mc/sec: 3186.62
//
Query:       EPA05556.1  [L=170]
Description: NADH-ubiquinone/plastoquinone oxidoreductase chain 6 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-22   79.0  14.2    4.1e-22   78.4  14.2    1.3  1  Oxidored_q3    NADH-ubiquinone/plastoquinone oxidoreductase c
  ------ inclusion threshold ------
      0.067   12.4   4.8      0.083   12.1   4.1    1.5  1  MIG-14_Wnt-bd  Wnt-binding factor required for Wnt secretion


Domain annotation for each model (and alignments):
>> Oxidored_q3  NADH-ubiquinone/plastoquinone oxidoreductase chain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.4  14.2   4.6e-26   4.1e-22       1     144 []      16     157 ..      16     157 .. 0.84

  Alignments for each domain:
  == domain 1  score: 78.4 bits;  conditional E-value: 4.6e-26
                  HHHHHHH-SBHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHIIIIIHHHHHHHHHHHSSTTS----TTCHHHHHHHHHHHHHHHHHHHTT--.... CS
  Oxidored_q3   1 gallvitsknpvysalfLilsfvgvaglfillgaeFlallqilvYvGAilvlflFvimllesaeeeepeslsrslalaalligllllallllllless 98 
                  +a++++ +++++y  ++L+ ++ g+ag+f+ll+ +F+a++q+ vYvG i+vl+lF++ml++++   ++ + +r++ ++ ++++l++++ l  +++ s 
   EPA05556.1  16 SAIAALEMRSLIYGSIALMGTLGGIAGFFLLLDSPFVAMFQLAVYVGSIAVLILFTVMLVKRELIFKKIEDKRRKFVG-IALMLVFMVALGSIIMDSG 112
                  5889999****************************************************9666665555555555555.7777777777777777653 PP

                  ..--------TT-HHHHHHHHTTTTHHHHHHHHHHHHHHHHHHHHC CS
  Oxidored_q3  99 ssavdaqvadvsnieaigsllftkyllpfelasllLLvaligaivl 144
                   +   ++++   + ++ig  ++t+y+ +++l++l+L   + ga+vl
   EPA05556.1 113 IKS-ITTNEPAVDFRNIGADFLTYYWPALILMALILTGSVTGALVL 157
                  333.33445567*******************************997 PP

>> MIG-14_Wnt-bd  Wnt-binding factor required for Wnt secretion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   4.1   9.2e-06     0.083     108     207 ..      43     151 ..      39     161 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.2e-06
  MIG-14_Wnt-bd 108 lellfnswflllldiifqsiFlsvLllFwlvff..eslrdeqnrrktlsfylpklllvlllwlvllvlalyerleqlkdpfysiwss...al.... 194
                    + ll +s+f+ +++  +++  ++vL+lF ++++  e + ++ ++ k+ +f    l+lv+++ l  +++++  +  ++++p +++ +    +l    
     EPA05556.1  43 FFLLLDSPFVAMFQLAVYVGSIAVLILFTVMLVkrELIFKKIED-KRRKFVGIALMLVFMVALGSIIMDSGIKSITTNEPAVDFRNIgadFLtyyw 137
                    568899***************************85444455544.899********************************9999765654114456 PP

  MIG-14_Wnt-bd 195 .ilkilaiilavly 207
                     +l+++a+il++  
     EPA05556.1 138 pALILMALILTGSV 151
                    76777777666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       826  (0.0460706); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1089.80
//
Query:       EPA05557.1  [L=165]
Description: 4Fe-4S binding domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.6e-12   44.5  10.8    3.2e-09   36.2   2.1    2.3  2  Fer4      4Fe-4S binding domain
    4.4e-09   36.3  16.8      3e-05   24.0  11.1    2.0  2  Fer4_10   4Fe-4S dicluster domain
      1e-08   35.6   9.4    1.6e-08   35.0   9.4    1.3  1  Fer4_7    4Fe-4S dicluster domain
      2e-08   34.2  20.1    4.2e-06   26.8  10.6    2.0  2  Fer4_21   4Fe-4S dicluster domain
    1.3e-07   31.6   6.2    2.3e-07   30.9   6.2    1.4  1  Fer4_9    4Fe-4S dicluster domain
    9.1e-06   25.5   9.8     0.0014   18.6   1.6    2.4  2  Fer4_2    4Fe-4S binding domain
    1.9e-05   24.5  11.8    4.3e-05   23.4   1.7    2.3  2  Fer4_6    4Fe-4S binding domain
     0.0001   22.6   8.1      0.012   16.0   0.9    2.2  2  Fer4_4    4Fe-4S binding domain
    0.00022   21.6   9.5      0.012   16.0   1.1    2.2  2  Fer4_8    4Fe-4S dicluster domain
    0.00098   20.0   9.7     0.0047   17.8   0.2    2.4  3  Fer4_16   4Fe-4S double cluster binding domain
     0.0012   19.4  10.2      0.028   14.9   0.8    2.3  3  Fer4_17   4Fe-4S dicluster domain
     0.0022   18.7   5.0       0.26   12.1   0.4    2.4  2  Fer4_15   4Fe-4S single cluster domain
     0.0041   17.6   4.2       0.21   12.2   0.1    2.4  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
  ------ inclusion threshold ------
      0.011   16.6   4.1      0.011   16.6   4.1    2.3  2  Fer4_3    4Fe-4S binding domain
       0.21   11.8   9.4       0.18   12.0   1.2    2.2  2  Fer4_18   4Fe-4S dicluster domain
        1.7    9.5  10.9       0.58   11.0   0.8    2.2  2  Fer4_22   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   1.7     5e-05     0.056       6      18 ..      61      73 ..      58      77 .. 0.89
   2 !   36.2   2.1   2.9e-12   3.2e-09       1      23 [.      98     120 ..      98     121 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5e-05
                TTSSS-THHHHHS CS
        Fer4  6 ekCigCGaCvevC 18
                + C+gC +C  +C
  EPA05557.1 61 DHCTGCQLCSIAC 73
                89*********** PP

  == domain 2  score: 36.2 bits;  conditional E-value: 2.9e-12
                 EEEETTTSSS-THHHHHSTTTEE CS
        Fer4   1 vvideekCigCGaCvevCPvgAI 23 
                 ++id+ kC++CG+Cv++CP+ A+
  EPA05557.1  98 PQIDYGKCVFCGLCVDACPFYAL 120
                 68******************998 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0  11.1   2.7e-08     3e-05       7      56 .]      61     116 ..      56     116 .. 0.83
   2 !   22.2   0.3   9.7e-08   0.00011       3      24 ..      99     129 ..      97     160 .. 0.73

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2.7e-08
     Fer4_10   7 dtCirCgkCvkaCPadl........tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                 d C++C+ C  aC            +  +  +++++  + +++++kC +cg Cv+aCP
  EPA05557.1  61 DHCTGCQLCSIAC--EGvaeaiamvKVPEEHKQNKKAIMPQIDYGKCVFCGLCVDACP 116
                 78***********..5569**977655556666666777899***************9 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 9.7e-08
     Fer4_10   3 vidddtCirCgkCvkaCPadl.........t 24 
                 +id  +C+ Cg Cv+aCP+++         +
  EPA05557.1  99 QIDYGKCVFCGLCVDACPFYAlymtndyelS 129
                 789999************9776655444441 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   9.4   1.5e-11   1.6e-08       1      50 [.      62     117 ..      62     119 .. 0.79

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 1.5e-11
      Fer4_7   1 rCigCgaCvaaCp..vkaieldee.enekgtekv...eidpekClgCgaCvavCPt 50 
                 +C+gC+ C  aC   ++ai + ++ e++k+++k+   +id+ kC++Cg Cv++CP+
  EPA05557.1  62 HCTGCQLCSIACEgvAEAIAMVKVpEEHKQNKKAimpQIDYGKCVFCGLCVDACPF 117
                 6***********999899998876233344444345599****************8 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   1.9   6.9e-07   0.00077      33      59 .]      55      82 ..      46      82 .. 0.80
   2 !   26.8  10.6   3.8e-09   4.2e-06       5      53 ..      60     117 ..      57     122 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 6.9e-07
     Fer4_21 33 vlkvvedeCvGCnlCssvC.Pvedciem 59
                ++ + +d+C+GC+lCs+ C  v ++i+m
  EPA05557.1 55 RHMLFHDHCTGCQLCSIACeGVAEAIAM 82
                456779*************447888877 PP

  == domain 2  score: 26.8 bits;  conditional E-value: 3.8e-09
     Fer4_21   5 edkCigCgkCliaCedtshqai.........eidaktvl.kvvedeCvGCnlCssvCPv 53 
                 +d+C gC++C iaCe +  +ai         + ++k+++ ++   +Cv C lC++ CP 
  EPA05557.1  60 HDHCTGCQLCSIACE-GVAEAIamvkvpeehKQNKKAIMpQIDYGKCVFCGLCVDACPF 117
                 689************.68899977777665333333444344578*************6 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   6.2     2e-10   2.3e-07       2      48 ..      63     117 ..      53     120 .. 0.79

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 2e-10
      Fer4_9   2 CtgCgaCveaC........pagvvvedaaerkarlraaseeaCigCgaCveaCpk 48 
                 CtgC+ C  aC          +v +e+++++ka + + ++ +C++Cg Cv+aCp 
  EPA05557.1  63 CTGCQLCSIACegvaeaiaMVKVPEEHKQNKKAIMPQIDYGKCVFCGLCVDACPF 117
                 ***********9977665555555555556666666666699***********95 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   1.4   0.00023      0.26       8      20 ..      61      73 ..      56      74 .. 0.93
   2 !   18.6   1.6   1.3e-06    0.0014       3      21 ..      98     116 ..      95     117 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00023
      Fer4_2  8 drCigCgaCvsaC 20
                d+C+gC  C  aC
  EPA05557.1 61 DHCTGCQLCSIAC 73
                89********999 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 1.3e-06
      Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                 +++d  +C+ Cg Cv+aCP
  EPA05557.1  98 PQIDYGKCVFCGLCVDACP 116
                 899**************** PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   2.8      0.01        12       9      21 ..      63      77 ..      60      80 .. 0.81
   2 !   23.4   1.7   3.9e-08   4.3e-05       2      24 .]      98     120 ..      97     120 .. 0.94

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.01
      Fer4_6  9 CigCgdCvrvCP..e 21
                C+gC  C ++C   +
  EPA05557.1 63 CTGCQLCSIACEgvA 77
                ***********7554 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 3.9e-08
      Fer4_6   2 veidpdkCigCgdCvrvCPegai 24 
                 ++id+ kC+ Cg Cv++CP++a+
  EPA05557.1  98 PQIDYGKCVFCGLCVDACPFYAL 120
                 78******************996 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   1.2   0.00069      0.77       2      15 ..      61      74 ..      60      87 .. 0.91
   2 !   16.0   0.9   1.1e-05     0.012       3      16 ..     104     117 ..     102     126 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00069
      Fer4_4  2 erCigCgsCvaaCP 15
                + C+gC  C +aC+
  EPA05557.1 61 DHCTGCQLCSIACE 74
                56***********8 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1.1e-05
      Fer4_4   3 rCigCgsCvaaCPq 16 
                 +C+ Cg Cv+aCP+
  EPA05557.1 104 KCVFCGLCVDACPF 117
                 8999*********6 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   1.8   0.00091         1       3      16 ..      61      74 ..      60     102 .. 0.59
   2 !   16.0   1.1   1.1e-05     0.012       4      20 ..     104     120 ..     101     137 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00091
      Fer4_8  3 ekCieCgaCqsaCp 16
                ++C++C++C  aC 
  EPA05557.1 61 DHCTGCQLCSIACE 74
                57899999988885 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1.1e-05
      Fer4_8   4 kCieCgaCqsaCpvlrr 20 
                 kC+ Cg+C +aCp++  
  EPA05557.1 104 KCVFCGLCVDACPFYAL 120
                 8************8864 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   3.4     0.043        49      52      64 ..      61      73 ..      51      76 .. 0.76
   2 !   10.7  12.3   0.00071       0.8       1      66 [.      62     117 ..      62     118 .. 0.69
   3 !   17.8   0.2   4.2e-06    0.0047       1      26 [.     104     129 ..     104     158 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.043
     Fer4_16 52 eaitgCdiCqdvC 64
                 ++tgC+ C  +C
  EPA05557.1 61 DHCTGCQLCSIAC 73
                6788888888877 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00071
     Fer4_16   1 rCgtCgkCaevCPt..naikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCPa 66 
                 +C++C+ C  +C    +ai      +++ +e+   ++++kk + +++   k    + +C+ C+d+CP+
  EPA05557.1  62 HCTGCQLCSIACEGvaEAIA-----MVKVPEE---HKQNKKAIMPQIDYGK----CVFCGLCVDACPF 117
                 7***********65113333.....3344444...4456677777766555....99**********8 PP

  == domain 3  score: 17.8 bits;  conditional E-value: 4.2e-06
     Fer4_16   1 rCgtCgkCaevCPtnaikekkekeie 26 
                 +C+ Cg C+++CP  a+ +++++e+ 
  EPA05557.1 104 KCVFCGLCVDACPFYALYMTNDYELS 129
                 59**************9998776654 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   2.7    0.0029       3.2      43      57 ..      60      74 ..      38      78 .. 0.82
   2 !   10.1  12.2   0.00081       0.9       2      57 ..      63     116 ..      62     119 .. 0.71
   3 !   14.9   0.8   2.5e-05     0.028       1      22 [.     104     125 ..     104     155 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0029
     Fer4_17 43 aslCieCgeCerkCP 57
                 + C++C++C+ +C 
  EPA05557.1 60 HDHCTGCQLCSIACE 74
                578999999999996 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00081
     Fer4_17   2 CiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCP 57 
                 C++C+ C  +C   ++     k + +  ++  +++++ +   ++C+ Cg+C+ +CP
  EPA05557.1  63 CTGCQLCSIACEGVAEAIAMVKVPEEHKQN--KKAIMPQIDYGKCVFCGLCVDACP 116
                 *********999877755544444444222..23334446889************9 PP

  == domain 3  score: 14.9 bits;  conditional E-value: 2.5e-05
     Fer4_17   1 rCiqCgyClpeCpsyeaydnep 22 
                 +C  Cg C+++Cp+y+ y ++ 
  EPA05557.1 104 KCVFCGLCVDACPFYALYMTND 125
                 6999**********99966543 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.5     0.003       3.3       5      22 ..      60      77 ..      59      94 .. 0.87
   2 !   12.1   0.4   0.00023      0.26       3      19 ..     100     116 ..      99     130 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.003
     Fer4_15  5 rdaCigcglCvaeapevf 22
                +d C+gc lC  +++ v 
  EPA05557.1 60 HDHCTGCQLCSIACEGVA 77
                699********9998765 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00023
     Fer4_15   3 vDrdaCigcglCvaeap 19 
                 +D  +C  cglCv+++p
  EPA05557.1 100 IDYGKCVFCGLCVDACP 116
                 8999************9 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.9    0.0094        11       4      17 ..      61      74 ..      60      95 .. 0.90
   2 !   12.2   0.1   0.00019      0.21       1      17 [.     100     116 ..     100     145 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0094
     Fer4_13  4 dtCiacgaCvelaP 17
                d C++c++C  ++ 
  EPA05557.1 61 DHCTGCQLCSIACE 74
                78********9996 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00019
     Fer4_13   1 VDrdtCiacgaCvelaP 17 
                 +D  +C+ cg+Cv+++P
  EPA05557.1 100 IDYGKCVFCGLCVDACP 116
                 68889************ PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   5.6     0.034        38       1      11 [.      63      73 ..      63      74 .. 0.96
   2 ?   16.6   4.1     1e-05     0.011       1      15 []     105     119 ..     105     119 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.034
      Fer4_3  1 CtgCgaCvevC 11
                CtgC++C  +C
  EPA05557.1 63 CTGCQLCSIAC 73
                ********999 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 1e-05
      Fer4_3   1 CtgCgaCvevCPvgA 15 
                 C+ Cg+Cv++CP  A
  EPA05557.1 105 CVFCGLCVDACPFYA 119
                 ************765 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   2.0      0.05        56      84     103 ..      62      81 ..      46      86 .. 0.82
   2 ?   12.0   1.2   0.00016      0.18      45      72 ..      89     116 ..      81     119 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.05
     Fer4_18  84 eciscllcidacdkvmeklg 103
                 +c  c+lc  ac+ v e++ 
  EPA05557.1  62 HCTGCQLCSIACEGVAEAIA 81 
                 69999999999999988776 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00016
     Fer4_18  45 kalkekeerkekgagdcidcescvkvcP 72 
                 +++++k    + + g+c+ c+ cv+ cP
  EPA05557.1  89 HKQNKKAIMPQIDYGKCVFCGLCVDACP 116
                 4455555666777888899999998888 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   3.5      0.16   1.8e+02      80      93 ..      61      74 ..      52      80 .. 0.80
   2 ?   11.0   0.8   0.00052      0.58      70      93 ..      93     116 ..      78     119 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.16
     Fer4_22 80 sgCvGCgRCieacp 93
                 +C+GC  C+ ac 
  EPA05557.1 61 DHCTGCQLCSIACE 74
                57888888888886 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00052
     Fer4_22  70 lsefkekfgesgCvGCgRCieacp 93 
                  + ++ +++  +Cv Cg C++acp
  EPA05557.1  93 KKAIMPQIDYGKCVFCGLCVDACP 116
                 35677889999************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1000.17
//
Query:       EPA05558.1  [L=167]
Description: hypothetical protein BG20_I0439 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.044   14.1   0.1         14    6.1   0.0    2.3  2  SQAPI        Aspartic acid proteinase inhibitor
      0.056   13.4   0.0        0.1   12.5   0.0    1.4  1  EMP24_GP25L  emp24/gp25L/p24 family/GOLD
        0.2   11.7   0.6        1.5    8.8   0.0    2.1  2  DUF4366      Domain of unknown function (DUF4366)


Domain annotation for each model (and alignments):
>> SQAPI  Aspartic acid proteinase inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1    0.0028        16      27      48 ..      27      48 ..      24      72 .. 0.81
   2 ?    6.1   0.0    0.0023        14      21      55 ..      82     116 ..      70     122 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0028
       SQAPI 27 nLvfvkvvkGetQvvsgtnYrL 48
                + +f+ ++kGe Qv  g+n   
  EPA05558.1 27 QVIFEDLIKGEGQVKLGKNLIV 48
                6789*************98655 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0023
       SQAPI  21 nkqskanLvfvkvvkGetQvvsgtnYrLviaakdg 55 
                 +++++++ + ++v +G+ ++    +Y+Lvi+  d+
  EPA05558.1  82 DREIESQVINQEVFEGRFKIEEPGTYKLVIENPDE 116
                 7899999999********************98776 PP

>> EMP24_GP25L  emp24/gp25L/p24 family/GOLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.8e-05       0.1      26      83 ..      62     115 ..      42     126 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.8e-05
  EMP24_GP25L  26 gsyqvtdggaaldvdlsvkdpdgngerlvkkkdresegdfsftakesgeykvCfdnsf 83 
                  + +q++d +  +++ +++ dp++  +++ ++ ++++  + +f+ +e+g+yk+ ++n++
   EPA05558.1  62 YAIQIIDFK--KEITAKILDPSD--REIESQVINQEVFEGRFKIEEPGTYKLVIENPD 115
                  334455555..99******6666..******999999999***************985 PP

>> DUF4366  Domain of unknown function (DUF4366)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1     0.064   3.8e+02      21      42 ..      51      72 ..      35      79 .. 0.85
   2 ?    8.8   0.0   0.00025       1.5     108     145 ..     127     164 ..      75     165 .. 0.63

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.064
     DUF4366 21 qfitvttksgntFYivIDrdee 42
                +f tv+t +g +   +ID ++e
  EPA05558.1 51 EFETVQTHAGVYAIQIIDFKKE 72
                799*******999999998754 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00025
     DUF4366 108 peeepekksnnglllvvlavaligg.gaayyfkvlkpkk 145
                 pe++  kk + g++ + ++v+++gg g++ ++ ++  kk
  EPA05558.1 127 PEPDAGKK-SIGFISLYILVIGLGGmGGVTIYAIKNRKK 164
                 45554444.589999999999999965555555544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       671  (0.0374254); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1041.86
//
Query:       EPA05559.1  [L=213]
Description: putative isopentenyl-diphosphate delta-isomerase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.2e-18   64.7   0.0    1.1e-17   64.3   0.0    1.2  1  NUDIX     NUDIX domain


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.3   0.0   6.2e-22   1.1e-17       1     123 [.      30     154 ..      30     162 .. 0.85

  Alignments for each domain:
  == domain 1  score: 64.3 bits;  conditional E-value: 6.2e-22
                 EEEEEEEEEEEETTSEEEEEEES..SSSTTT.EE.SSEEECBTTSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEECSG CS
       NUDIX   1 klrravgvvllnekgevLlvrrs..kkpfpg.We.lPgGkvepgEtpeeAArREleEEtGleaellellgrlhylapydgpygdeheilyvfleevege 95 
                 kl+ra+ ++l+++kg+++l++r+  k  +p+ W+ +++ + ++gEt+   A R++ EE+G+++  +++l +++y  py+++   e+ei+ ++ + v++ 
  EPA05559.1  30 KLHRAFTALLFDKKGRLVLTKRAkeKMLWPEdWDgTVASHPREGETYISSAERRMPEELGVSC-KMDYLMKFEYHVPYKDVGS-ENEICGTLIGIVDES 126
                 589********************99999999**88**************************99.6699999********9999.899997888444444 PP

                 CSST.STTTEEEEEEEEHHHHHHHHTHCT CS
       NUDIX  96 lepn.denevsevrwvpleellkeklaae 123
                  + +  e+e++e++wv+++el   +++++
  EPA05559.1 127 TKFKiVEDEIDEIKWVSVNEL-ISEIKNN 154
                 444457***************.4444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1451.40
//
Query:       EPA05560.1  [L=50]
Description: hypothetical protein BG20_I0440 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       851  (0.047465); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.25s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 381.89
//
Query:       EPA05561.1  [L=250]
Description: amino acid kinase family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-30  106.8   0.0    1.5e-30  106.6   0.0    1.0  1  AA_kinase    Amino acid kinase family
  ------ inclusion threshold ------
      0.035   14.0   0.0      0.061   13.2   0.0    1.4  1  RsgA_GTPase  RsgA GTPase
      0.071   13.1   0.0        1.3    9.0   0.0    2.4  2  DUF1967      Domain of unknown function (DUF1967)


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.6   0.0   2.5e-34   1.5e-30       3     241 .]       2     223 ..       1     223 [. 0.93

  Alignments for each domain:
  == domain 1  score: 106.6 bits;  conditional E-value: 2.5e-34
                 EEEEE-TTCCCCTCC......HHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC....E..HHHHHHHHHHHHHHHHHHHHHHHHH CS
   AA_kinase   3 vVvKlGGssltdkee......aslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaaglrstleeagevatrdalaslgerlvaalla 95 
                 + +KlGGs++t+ke+      ++++++++ ++ l   +++++vVhGggsf+++ + + ++++ ++++       + +g ++ + ++  l++++++ +++
  EPA05561.1   2 ILIKLGGSIITNKEKplsprkKVIENIVKKLKHL---KEPIIVVHGGGSFGHFWSVK-YDMHTKPKK------YDMHGVAIVKNSMIDLNKIILEIFVK 90 
                 89********************************...999*****************.9***99998......5778888888**************** PP

                 TTHGEEEE-GGGTCEECCCE..HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEETTTEEEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCC CS
   AA_kinase  96 aglpavglsaaaldateagrdegsdgnvesvdaeaieelleagvvpvltgfigldeegelgrgssDtiaallAealgAdkliiltdVdGVydadpkkvp 194
                 + l+ + l++ ++ + ++ +           + ++ie++ ++g +p++ g++    +++ +++s+D i +ll + l+++ +i++ + dG+y++   k  
  EPA05561.1  91 NKLNPYALPPTDFMSGNKSI---------TTKVKEIENIAKSGLIPITYGDALWYGNKKTYILSGDKIMTLLSKILKPRLIIFALNEDGLYSDLTTK-- 178
                 *************9988888.........88999******************777777778******************************998655.. PP

                 TTCECCEEEHHHCHH.CSSS.TTTHHHHCHHHHHHHHHCTT-EEEEEE CS
   AA_kinase 195 darllpeisvdeaee.saselatgGmkvkhpaalaaarrggipvvItn 241
                   +l++e++ +  +  +++ ++tgGm  k+++a ++a+ g ++v+ +n
  EPA05561.1 179 --KLIRELKGENPKIsENKMDVTGGMSRKVEEATNIAKMG-MNVFFVN 223
                 ..8*****888888877888********************.*999877 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0     1e-05     0.061      20     104 ..     161     244 ..     156     250 .] 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1e-05
                  EEEEESTTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTTSEEEE CS
  RsgA_GTPase  20 livvslkepelslnlldrfLvlaeekgiepvivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelkellkdktsvl 104
                  li+++l+e+ l ++l ++ L+  e kg +p i  nK+D++  +++  e +++++++g++v++v+ ++ e + +  ++ k + +++
   EPA05561.1 161 LIIFALNEDGLYSDLTTKKLIR-ELKGENPKISENKMDVTGGMSRKVEEATNIAKMGMNVFFVNGNKPERILKAIKNKKYEGTLF 244
                  79*****************986.778889**************98888889999*********9998877765555545455555 PP

>> DUF1967  Domain of unknown function (DUF1967)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0     0.059   3.6e+02       9      26 ..     139     156 ..     135     158 .. 0.85
   2 ?    9.0   0.0   0.00023       1.3       7      33 ..     215     241 ..     206     244 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.059
                 TTEEEEE-HHHHHHHTTE CS
     DUF1967   9 egvfvVeGekierlvkqt 26 
                 +++++++G+ki  l++++
  EPA05561.1 139 KKTYILSGDKIMTLLSKI 156
                 579********9998875 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00023
                 EETTEEEEE-HHHHHHHTTEEE-TGGG CS
     DUF1967   7 deegvfvVeGekierlvkqtnfeneea 33 
                    +vf V+G+k+er++k ++ +++e+
  EPA05561.1 215 MGMNVFFVNGNKPERILKAIKNKKYEG 241
                 45689*************999888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1474.51
//
Query:       EPA05562.1  [L=47]
Description: hypothetical protein BG20_I0430 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
        3.7    7.8   5.8        3.9    7.7   5.1    1.6  1  HHV-5_US34A  Herpesvirus US34A protein family


Domain annotation for each model (and alignments):
>> HHV-5_US34A  Herpesvirus US34A protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   5.1   0.00022       3.9      21      35 ..      20      34 ..      12      46 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00022
  HHV-5_US34A 21 vrfivyvvlftvavq 35
                 + fiv vvl tvav 
   EPA05562.1 20 IAFIVTVVLITVAVI 34
                 67***********94 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1250  (0.0697194); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 330.07
//
Query:       EPA05563.1  [L=207]
Description: putative ribosomal protein S2 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.9e-20   72.0   0.4    8.2e-11   41.5   0.6    2.1  2  Ribosomal_S2  Ribosomal protein S2


Domain annotation for each model (and alignments):
>> Ribosomal_S2  Ribosomal protein S2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   4.9e-11   8.8e-07      16      95 ..      27     105 ..      14     108 .. 0.84
   2 !   41.5   0.6   4.6e-15   8.2e-11     148     212 ..     113     177 ..     110     179 .. 0.95

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 4.9e-11
  Ribosomal_S2  16 npkmkpyIyger.ngihiidlektlaalrraykvvkevaakggkilfvgtk.kqakeavkeaakrangyyvnerWlgGtLTN 95 
                   ++ m p+I ++  +g +++d++ tl+++++a+k+++++  ++   l+v++  + a+  +++ +++ ++  +  r+++GtLTN
    EPA05563.1  27 TKFMTPFITKASpEGLYMLDIDITLEKIKTAAKFINRLGTDK---LIVCSArQYANTPIEKFCEMLGSKKLLGRFMPGTLTN 105
                   5679****977658**********************997665...555554179999************************* PP

  == domain 2  score: 41.5 bits;  conditional E-value: 4.6e-15
  Ribosomal_S2 148 lPdlvvvldpkkekiavkEakklgipviaivDtnvdpdlvdypIpaNddsirsiklilgvladai 212
                    P++v++ dp+ +  a++Ea+++gipvi+i +t+  ++++d +IpaN+   +++  ++ +l ++i
    EPA05563.1 113 EPKVVLISDPQVDVQAITEATNAGIPVIGISNTDNITSKLDVIIPANNRGRKALATVYWLLVRQI 177
                   59*****************************************************9999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1352.90
//
Query:       EPA05564.1  [L=364]
Description: hypothetical protein BG20_I0433 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.8e-05   23.1   2.5    5.8e-05   23.1   2.5    1.9  2  Trypan_PARP      Procyclic acidic repetitive protein (PARP)
     0.0019   18.4   4.1        4.7    7.6   0.3    4.6  3  EB               EB module
  ------ inclusion threshold ------
      0.021   15.3   0.0      0.036   14.5   0.0    1.4  1  MG2              MG2 domain
      0.041   13.1   0.2      0.067   12.4   0.2    1.3  1  SPESP1           Sperm equatorial segment protein 1
      0.061   13.5   1.9       0.15   12.2   1.9    1.7  1  Big_3_5          Bacterial Ig-like domain (group 3)
      0.063   13.6   0.3       0.14   12.4   0.3    1.6  1  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
      0.071   13.1   1.7       0.15   12.1   0.6    2.1  2  Neocarzinostat   Neocarzinostatin family
       0.11   12.8   0.0       0.21   11.9   0.0    1.5  1  HTH_55           RctB helix turn helix domain


Domain annotation for each model (and alignments):
>> Trypan_PARP  Procyclic acidic repetitive protein (PARP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1      0.88     2e+03      19      55 ..       5      41 ..       3      48 .. 0.78
   2 !   23.1   2.5   2.6e-08   5.8e-05      93     115 ..     198     220 ..     153     229 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.88
  Trypan_PARP 19 fagvgfaaaaegpedkgltkggkgkekgtkvsdddtn 55
                 f g   aa+ ++ +d  l + g   + g   ++   n
   EPA05564.1  5 FVGSAHAATQDDCADGQLFQNGECIDTGCTADQVYQN 41
                 7788889999999999999999988777766555555 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 2.6e-08
  Trypan_PARP  93 pepepepepepepepepepgaat 115
                   epepepepepepep+p  ga t
   EPA05564.1 198 SEPEPEPEPEPEPEPQPTCGAGT 220
                  56777777777777777777766 PP

>> EB  EB module
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1      0.23   5.1e+02       1      13 [.      17      29 ..      17      32 .. 0.85
   2 ?    4.6   0.0     0.018        40       1      15 [.      33      47 ..      33      83 .. 0.85
   3 !    7.6   0.3    0.0021       4.7       1      22 [.     166     195 ..     166     249 .. 0.68

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.23
          EB  1 CpsgqvlingyCl 13
                C++gq   ng+C+
  EPA05564.1 17 CADGQLFQNGECI 29
                8999999999997 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.018
          EB  1 CpsgqvlingyClkk 15
                C+ +qv+ ng+C+  
  EPA05564.1 33 CTADQVYQNGQCVAV 47
                999*********854 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0021
          EB   1 CpsgqvlingyClkk........vapgssC 22 
                 Cpsgq+l++g+C  k        + +  +C
  EPA05564.1 166 CPSGQILVDGKCTVKpvtcnageKLVDGKC 195
                 999999999999744444333333333333 PP

>> MG2  MG2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.6e-05     0.036       6      80 ..      59     133 ..      54     155 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.6e-05
                 ES-SEE-TT-EEEEEEEEESTTCSB---EEEEEEEE-TTSSEEEEEEEEE-CTTEEEEEEE-..-TT--SEEEEEEE CS
         MG2   6 tDRglYrPgetVslkallrdetlqglaklplkltirdpdgkevkelplatdetggaesefal..peaaklGeysvel 80 
                 +D+ lY  g  V +++l+++ +   + +  +++ +r pd++ v   ++  +++g+++ +f+   p+    G y+v +
  EPA05564.1  59 SDKSLYAQGGLVTVTGLVKNFDTAVPGD--VSVIVRAPDNNIVAIDQIHPNADGSFQLSFKAdgPQFKTAGAYTVHA 133
                 79****************9888888887..******************************9755788899***9998 PP

>> SPESP1  Sperm equatorial segment protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2     3e-05     0.067     122     140 ..     197     215 ..     192     268 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3e-05
      SPESP1 122 ekePepepePelepeveee 140
                   ePepepePe+epe++ +
  EPA05564.1 197 MSEPEPEPEPEPEPEPQPT 215
                 4578887777777777433 PP

>> Big_3_5  Bacterial Ig-like domain (group 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.9   6.8e-05      0.15      10      70 ..      70     138 ..      62     161 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.8e-05
                 EEEEEE--CCCCTTS--EEEEEE...TTEE-.SS-EE--TTSEEEEEEE-.....SS-EEEEEEEEEE-T CS
     Big_3_5  10 vtltatVtaasggtptGtVtftd...ggttl.gtavllsanGtAtltvsa.....laaGthsitAtYsGd 70 
                 vt+t  V+    +++ G V++ +   +++ +  +++  +a+G+ +l+++a      +aG+++++A++sG 
  EPA05564.1  70 VTVTGLVKNF-DTAVPGDVSVIVrapDNNIVaIDQIHPNADGSFQLSFKAdgpqfKTAGAYTVHAVFSGL 138
                 5555555555.467778888887565333331355555679******9885554456***********95 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.3   6.4e-05      0.14       1      63 [.      71     142 ..      71     160 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.4e-05
  CarboxypepD_reg   1 tisGrVtdasgapiagatVtvtnadtg..tvastttdadGafrlrglpp.......gtysvtvsapGyatat 63 
                      t++G V++ + a+   ++V+v++ d++  +  +   +adG+f+l++ +        g y+v++ ++G ++  
       EPA05564.1  71 TVTGLVKNFDTAVPGDVSVIVRAPDNNivAIDQIHPNADGSFQLSFKADgpqfktaGAYTVHAVFSGLKSDI 142
                      799****99999999*******9999944479************9774344455569999999999988765 PP

>> Neocarzinostat  Neocarzinostatin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.6   6.5e-05      0.15      19      76 ..      30      86 ..      11     116 .. 0.78
   2 ?   -1.7   0.0       1.2   2.8e+03      54      75 ..     117     141 ..      97     145 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.5e-05
  Neocarzinostat 19 gtGftagstlalgeCvavapggvaCnkaagavvtadasGkisasltvaksFegvlsdG 76
                     tG ta+ +++ g+Cvav +++   + + +++    a+G++ +   + k+F++ ++  
      EPA05564.1 30 DTGCTADQVYQNGQCVAV-TKQLRNDLNLKSDKSLYAQGGLVTVTGLVKNFDTAVPGD 86
                    49****************.777788888888888999999988888889998775543 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.2
  Neocarzinostat  54 dasG...kisasltvaksFegvlsd 75 
                      a+G   k++   tv+  F+g  sd
      EPA05564.1 117 KADGpqfKTAGAYTVHAVFSGLKSD 141
                     3333222445566777777776655 PP

>> HTH_55  RctB helix turn helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   9.5e-05      0.21      14      62 ..      33      81 ..      15      93 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.5e-05
      HTH_55 14 ssvdwieqyqhfkgvtksilellnlislkglsskdglvsttelieatdg 62
                 ++d + q  +   vtk + + lnl s k l ++ glv+ t l++  d 
  EPA05564.1 33 CTADQVYQNGQCVAVTKQLRNDLNLKSDKSLYAQGGLVTVTGLVKNFDT 81
                35677778888889******************************98775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 2719.11
//
Query:       EPA05565.1  [L=204]
Description: translin family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.3e-11   42.4   0.3    5.6e-09   36.3   0.1    2.3  2  Translin  Translin family


Domain annotation for each model (and alignments):
>> Translin  Translin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.7   0.1    0.0015        26       1      48 [.      22      70 ..      22      92 .. 0.80
   2 !   36.3   0.1   3.1e-13   5.6e-09      89     186 ..      84     174 ..      65     183 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0015
                HHHHHHHHHHHHHHHHHHHHHHHHHTTGSSTTTHHHHHHH.H.HHHHHH CS
    Translin  1 drreriikasrditaaskkiifllhrvrsekteaqdkkakik.keakek 48
                d re + k  r+i ++  + i+++h+ + + ++++ ++a++  k+ k+k
  EPA05565.1 22 DAREFLLKNTREIIILCSRSIMAVHNGDMKLAKNNLSQADVLlKKYKKK 70
                78***********************988555666666666665555544 PP

  == domain 2  score: 36.3 bits;  conditional E-value: 3.1e-13
                 HHHHHHSS---HHHHHHHTT.---SSSSSS---HHHHHHHHHHHHHHHHHHHHHHHCTT--S.HHHHHHHHHHHHHHHHHTS----HH...HHHHHTT CS
    Translin  89 ahYletqtLitleevqkilealkeneedafhltpedYllGlfdLtgELmRfainsvalgdkeekplqilkflrelragfellnlkndsakdlrkKldv 186
                 ++Y+e  +Li + e ++i +       +++ + pe Y+lGl+d++gEL R+   ++  gd + ++++i + +++l+ ++  +++  +  k+ r+K+dv
  EPA05565.1  84 QEYVEAASLIAIVEKKEIPS------DKKLGVLPESYVLGLMDCVGELKRMIFDKIRIGDID-NASRIFQIMENLYLELYPFSMYDKVLKEARRKIDV 174
                 46666666776666665544......5799******************************88.9********************966699******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       797  (0.0444531); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1362.26
//
Query:       EPA05566.1  [L=450]
Description: cation diffusion facilitator family transporter [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.4e-49  164.0  20.0    4.4e-19   68.4   0.2    3.2  3  ZT_dimer         Dimerisation domain of Zinc Transporter
    3.2e-40  138.0  17.8    4.2e-40  137.6  17.8    1.1  1  Cation_efflux    Cation efflux family
  ------ inclusion threshold ------
       0.16   12.1   5.8        8.8    6.5   0.4    3.9  4  Fe_dep_repr_C    Iron dependent repressor, metal binding and 
          1    9.7   9.4        1.9    8.9   1.5    3.1  3  AMP-binding_C_2  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> ZT_dimer  Dimerisation domain of Zinc Transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.4   0.2   9.8e-23   4.4e-19       3      78 ..     208     282 ..     206     283 .. 0.96
   2 !   65.5   3.4   7.8e-22   3.5e-18       7      78 ..     291     362 ..     288     363 .. 0.97
   3 !   39.0   3.8   1.5e-13   6.5e-10       5      78 ..     377     449 ..     374     450 .] 0.96

  Alignments for each domain:
  == domain 1  score: 68.4 bits;  conditional E-value: 9.8e-23
                 ..HHHHHHHHHTT-SS-EEEEEEEEE-S----EEEEEEEE-TTS-HHHHHHHHHHHHHHHHHH-TT--EEEEEEEE CS
    ZT_dimer   3 eeeeeeireiiksvpgvkgvhdlrtrksGskifvdlhievdgdlsvkeaHeiadevekrikeefpgvadvliHveP 78 
                 +e ++++r+ii++++gv++v ++ +r+sG+++f d++i + gd+s  +aHei+++ve++ik+++p+v  +++H eP
  EPA05566.1 208 PELVKNVRKIIADTEGVIDVGEILMRRSGNTLFTDVTISLRGDTSFDRAHEISNRVENNIKNRIPNV-SITVHFEP 282
                 68999*************************************************************6.89****** PP

  == domain 2  score: 65.5 bits;  conditional E-value: 7.8e-22
                 HHHHHHHTT-SS-EEEEEEEEE-S----EEEEEEEE-TTS-HHHHHHHHHHHHHHHHHH-TT--EEEEEEEE CS
    ZT_dimer   7 eeireiiksvpgvkgvhdlrtrksGskifvdlhievdgdlsvkeaHeiadevekrikeefpgvadvliHveP 78 
                 ++i +i+ksv gvkgvh++ ++k   k + +lh+ v++++++  aH+i++eve++i+e++p++++v+iH+eP
  EPA05566.1 291 AKINDIAKSVAGVKGVHNIISHKTKGKTYSNLHVMVEREINLDLAHKISEEVEQKIQENIPEIEHVTIHLEP 362
                 79********************9999********************************************** PP

  == domain 3  score: 39.0 bits;  conditional E-value: 1.5e-13
                 HHHHHHHHHTT-SS-EEEEEEEEE-S----EEEEEEEE-TTS-HHHHHHHHHHHHHHHHHH-TT--EEEEEEEE CS
    ZT_dimer   5 eeeeireiiksvpgvkgvhdlrtrksGskifvdlhievdgdlsvkeaHeiadevekrikeefpgvadvliHveP 78 
                 +ee+irei+k++  +k++ ++ + ++ + + +d++  +d+++s+++ H+++ e+e++i++++++ a ++iH eP
  EPA05566.1 377 TEEKIREILKKYSTIKKIGRIVSLNFENILKIDIDCSFDKEISIEKVHDMTSEIEHAIRAQIKN-AVITIHPEP 449
                 789***********************************************************88.778****** PP

>> Cation_efflux  Cation efflux family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.6  17.8   9.4e-44   4.2e-40       1     198 [.       9     202 ..       9     203 .. 0.97

  Alignments for each domain:
  == domain 1  score: 137.6 bits;  conditional E-value: 9.4e-44
  Cation_efflux   1 lilsllanlilalvelivglltnSlalladafhslsdlvsllllllalklsrkppderfpfGygrlevlgalvsgllllglavfllleaiqklike 96 
                    l +sl+a ++ ++vel++gl++nSl l+ d++h+l+d v + +llla +++ kppde++++G+g++e+lg+++ g+ ++++avf ++eaiq+l ++
     EPA05566.1   9 LQISLIAIFSAFVVELVFGLISNSLGLITDSVHALLDSVVTAILLLAARMAIKPPDEDHTYGHGKIESLGGMIGGIAIFLIAVFFIYEAIQRLQSP 104
                    5699******************************************************************************************99 PP

  Cation_efflux  97 gereihaglalvvalvslvvnlalllilrragrklrsaalkaaalhvlgDaltslgvlvsalvillfnlksgplaDpvaslligliilysalkllk 192
                     + + +   a++++l  +++ ++ +++l ++ +k++ ++lka+++h+++D+ ++++++v+++++ ++ ++     D +a+l++g+++++ +l+l+ 
     EPA05566.1 105 APTVLPGMFAIIGGLYTIGIDIFRIILLQKSIKKIGGTTLKADFYHAFMDLGSTVIAIVGIILVSYGFYN----GDFAAALILGVLLVILSLRLIH 196
                    999999999*********************************************************9444....7********************* PP

  Cation_efflux 193 eslseL 198
                    ++ ++L
     EPA05566.1 197 KTALDL 202
                    *99988 PP

>> Fe_dep_repr_C  Iron dependent repressor, metal binding and dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.025   1.1e+02      31      57 ..     193     219 ..     182     224 .. 0.86
   2 ?   -2.3   0.0       1.1   4.8e+03      33      54 ..     256     269 ..     252     282 .. 0.63
   3 ?    2.2   0.3     0.044     2e+02      40      56 ..     334     350 ..     327     362 .. 0.77
   4 ?    6.5   0.4     0.002       8.8      28      51 ..     418     441 ..     415     448 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.025
                    CCHHHHCCCCGGGS-HHHHHHHHHHCT CS
  Fe_dep_repr_C  31 eeaheeAerlEhalseelierldellg 57 
                      +h+ A  l  ++s+el++++++++ 
     EPA05566.1 193 RLIHKTALDLTDIISPELVKNVRKIIA 219
                    679*******************99986 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.1
                    HHHHCCCCGGGS-HHHHHHHHH CS
  Fe_dep_repr_C  33 aheeAerlEhalseelierlde 54 
                    a        h +s ++++++ +
     EPA05566.1 256 A--------HEISNRVENNIKN 269
                    4........5555555555544 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.044
                    CGGGS-HHHHHHHHHHC CS
  Fe_dep_repr_C  40 lEhalseelierldell 56 
                    l h +see+++++ e +
     EPA05566.1 334 LAHKISEEVEQKIQENI 350
                    56888888888887765 PP

  == domain 4  score: 6.5 bits;  conditional E-value: 0.002
                    --CCCHHHHCCCCGGGS-HHHHHH CS
  Fe_dep_repr_C  28 vdweeaheeAerlEhalseelier 51 
                    ++ e++h+  +++Eha+  ++ ++
     EPA05566.1 418 ISIEKVHDMTSEIEHAIRAQIKNA 441
                    7889************98887665 PP

>> AMP-binding_C_2  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.035   1.6e+02      10      74 ..     215     278 ..     212     283 .. 0.71
   2 ?    8.9   1.5   0.00042       1.9       8      74 ..     292     360 ..     290     380 .. 0.69
   3 ?    1.5   0.5     0.084   3.8e+02       9      69 ..     381     439 ..     378     448 .. 0.64

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.035
                      HHHHHT-TTEEEEEEEEEEEETTEEEEEEEEEE-TT----HHHHHHHHHHHHHHHHHHH.SS--EE CS
  AMP-binding_C_2  10 eevlkeieevepeYqivvtregelDelevkvEvkegfsdelkelealekkiakklkskl.gvsvkv 74 
                       +++ ++e+v +  +i ++r+g+     v++ ++ ++  ++++ +++++++++++k+++ +vs++v
       EPA05566.1 215 RKIIADTEGVIDVGEILMRRSGNTLFTDVTISLRGDT--SFDRAHEISNRVENNIKNRIpNVSITV 278
                      5666777777777778888888877788888888854..345789999999999999863455555 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00042
                      HHHHHHHT-TTEEEEEEEEEEEET..TEEEEEEEEEE-TT----HHHHHHHHHHHHHHHHHHHSS--EE CS
  AMP-binding_C_2   8 qieevlkeieevepeYqivvtreg..elDelevkvEvkegfsdelkelealekkiakklksklgvsvkv 74 
                      +i+++ k++++v++ ++i+ ++++  +  +l+v vE++ ++    k  e++e+ki++++ +   v++++
       EPA05566.1 292 KINDIAKSVAGVKGVHNIISHKTKgkTYSNLHVMVEREINLDLAHKISEEVEQKIQENIPEIEHVTIHL 360
                      6899999************99986225677788888777775555556777777777776655555443 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.084
                      HHHHHHT-TTEEEEEEEEEEEETTEEEEEEEEEE-TT----HHHHHHHHHHHHHHHHHHHS CS
  AMP-binding_C_2   9 ieevlkeieevepeYqivvtregelDelevkvEvkegfsdelkelealekkiakklksklg 69 
                      i e+lk+++++++  +iv  + ++  ++ +    ++++  ++++ ++++++i+++++++++
       EPA05566.1 381 IREILKKYSTIKKIGRIVSLNFENILKIDIDCSFDKEI--SIEKVHDMTSEIEHAIRAQIK 439
                      66677777777777777766666666666666666655..456777777777777766654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1174  (0.0654805); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.44
# Mc/sec: 3067.46
//
Query:       EPA05567.1  [L=260]
Description: hypothetical protein BG20_I0426 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.3e-15   55.6   4.1    8.4e-15   54.6   4.1    1.5  1  AIRC            AIR carboxylase
     0.0059   15.8   0.0      0.013   14.7   0.0    1.6  1  NAD_kinase      ATP-NAD kinase
  ------ inclusion threshold ------
      0.015   14.9   1.6       0.18   11.4   0.2    2.4  2  PrpR_N          Propionate catabolism activator
       0.65   10.5   2.4         14    6.3   2.4    2.3  1  HSCB_C          HSCB C-terminal oligomerisation domain
       0.81    9.8   5.1          2    8.6   5.1    1.7  1  Ribosomal_L38e  Ribosomal L38e protein family


Domain annotation for each model (and alignments):
>> AIRC  AIR carboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.6   4.1   2.4e-18   8.4e-15       1     129 [.     122     252 ..     122     260 .] 0.83

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 2.4e-18
                 EEEEEESSGGGHHHHHHHHHHHHHTT-EEEEEE--TTTSHHHHHHHHHHCHTTTEEEEEEEEESS--HHHHHHHHSSS-EEEEEE--...STTCCHHHH CS
        AIRC   1 kVgiimGSdsDlevmkkaaeilkelgveyevrvvSahrtpeelleyaeeaeerglkviIagAGgaahLpgvvaslttlPVigvPvks...kalkgldsl 96 
                 kVgi+ + +sD+ v+++a  + ++++ ++  +        ++++ +++e+ ++++++iI++AG++ +L+ +v+s++++PVig+P++       kg+ +l
  EPA05567.1 122 KVGILAAGTSDIGVAEEARLMSEAMNCKCISSYDVGVAGIQRIFPILKEMISEDVDCIIVVAGMEGALATLVSSMVDIPVIGIPTSIgygYGGKGIAAL 220
                 69**********************999765555445556777888888888999********************************63224589***** PP

                 HHHHT--T.TS--EE-SSTHHHHHHHHHHHHHTT CS
        AIRC  97 lSivqmPs.gvpvatvaigkaknAallAaqilal 129
                  S++q +s g++v  v+i+++ +A+ ++a+i  +
  EPA05567.1 221 ASMLQSCSlGLSV--VNIDNGIAAGAISANIANR 252
                 ******9856665..5666999999999999765 PP

>> NAD_kinase  ATP-NAD kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   3.5e-06     0.013      65     110 ..     111     206 ..      18     212 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.5e-06
                 ....................................................EEECCC-TTTTTSSSEEEEE.E-HHHHHHHHHHHHHCT-EEEEEES CS
  NAD_kinase  65 d...................................................dtrkaleafadagvdliivv.GGDGTaldvarllqkaeiPvlgvna 110
                                                                     +    l++++ ++vd+iivv G  G+    ++ +   +iPv+g+++
  EPA05567.1 111 LykkpiifkggkvgilaagtsdigvaeearlmseamnckcissydvgvagiqRIFPILKEMISEDVDCIIVVaGMEGALATLVSSMV--DIPVIGIPT 206
                 155556666666666666666666666666666666666666666677777777788999********9887255888777777777..7*******8 PP

>> PrpR_N  Propionate catabolism activator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1     0.033   1.2e+02       9      40 ..      54      85 ..      50      91 .. 0.83
   2 ?   11.4   0.2     5e-05      0.18       9      56 ..     156     207 ..     152     209 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.033
      PrpR_N  9 vvegdleeavelakeleaegvdviiSrGgtae 40
                +++++l+e  +++++  ++   v++Sr + ++
  EPA05567.1 54 AESKKLDEIKKIIQKTLEKTNSVVVSRINKGD 85
                5678999999999999999999***9966655 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 5e-05
      PrpR_N   9 vvegdleeavelakeleaegvdviiS....rGgtaellrkhvsvPVveikvs 56 
                 v ++++++   ++ke+++e+vd ii      G+ a+l+++ v++PV+ i+ s
  EPA05567.1 156 VGVAGIQRIFPILKEMISEDVDCIIVvagmEGALATLVSSMVDIPVIGIPTS 207
                 567788899999**********988533335888999************987 PP

>> HSCB_C  HSCB C-terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   2.4    0.0038        14      20      70 ..      52     101 ..       1     105 [. 0.84

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0038
                 GGSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
      HSCB_C  20 eeaadkeeleelkaeveerieeleaeleeafekkdleaaadllrrlrYlek 70 
                  +a +  +l+e+k+ +++ +e++ + + + ++k d++++ + + + ++ +k
  EPA05567.1  52 IFA-ESKKLDEIKKIIQKTLEKTNSVVVSRINKGDYAKILAFAKKSKFKVK 101
                 445.4599***********************888*****999999998666 PP

>> Ribosomal_L38e  Ribosomal L38e protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   5.1   0.00055         2       2      50 ..      57     114 ..      56     119 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00055
  Ribosomal_L38e   2 keikdiKeFLeiarrkDaksvkikknk.........kdntKfKvRcsryLYTLvvkdk 50 
                     k+ ++iK+ ++ + +k  + v    nk         +++ KfKv++ +   TLv+  k
      EPA05567.1  57 KKLDEIKKIIQKTLEKTNSVVVSRINKgdyakilafAKKSKFKVKTGKNSSTLVLYKK 114
                     7899*******99988666444444447799999999****************99766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1172  (0.065369); expected 358.6 (0.02)
Passed bias filter:                      684  (0.0381505); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 1891.53
//
Query:       EPA05568.1  [L=78]
Description: DNA-directed RNA polymerase subunit N family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      1e-28   99.4   0.3    1.4e-28   98.9   0.3    1.2  1  RNA_pol_N    RNA polymerases N / 8 kDa subunit
  ------ inclusion threshold ------
      0.065   12.3   0.0      0.074   12.1   0.0    1.0  1  tRNA-synt_2  tRNA synthetases class II (D, K and N)


Domain annotation for each model (and alignments):
>> RNA_pol_N  RNA polymerases N / 8 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.9   0.3   1.6e-32   1.4e-28       1      58 [.       1      58 [.       1      59 [. 0.98

  Alignments for each domain:
  == domain 1  score: 98.9 bits;  conditional E-value: 1.6e-32
                ----SS-TTT--B-STHHHHHHHHHHTT--HHHHHHHHT--SHHHHHHHHTB--THHH CS
   RNA_pol_N  1 MiiPVrCFtCGkvigekweeylellekgeepkdaLdaLglkryCCrrmllthvdliek 58
                M+iPVrCFtCG++i++k+eey+++++ ge+p++ Ld+Lg++ryCCrrmllt+v++i++
  EPA05568.1  1 MLIPVRCFTCGNLIADKYEEYQNKVKSGEDPAKGLDSLGIHRYCCRRMLLTTVETIQQ 58
                9******************************************************987 PP

>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   8.2e-06     0.074     267     310 ..      15      62 ..       6      65 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.2e-06
                  GGGGHHHHHHHHCT--SEEEE.EEEHHHHH...HHHCT-SSGGGCSSS CS
                  xxxxxxxxxxxxxxxxxxxxx.xxxxxxxx...xxxxxxxxxxxxxxx RF
  tRNA-synt_2 267 eekfswylealeyGapphgGl.glGldRlv...mlllgsesIrdviaF 310
                   +k+++y + ++ G  p  Gl  lG+ R++   mll+  e I++vi+F
   EPA05568.1  15 ADKYEEYQNKVKSGEDPAKGLdSLGIHRYCcrrMLLTTVETIQQVIPF 62 
                  689*****************9558****876669************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       797  (0.0444531); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.51
# Mc/sec: 461.40
//
Query:       EPA05569.1  [L=332]
Description: multicopper oxidase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-22   80.2   6.5    8.6e-20   70.9   0.9    2.5  2  Cu-oxidase_3  Multicopper oxidase
    2.4e-21   75.9  10.1    5.2e-11   42.4   0.4    3.2  2  Cu-oxidase_2  Multicopper oxidase


Domain annotation for each model (and alignments):
>> Cu-oxidase_3  Multicopper oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.9   0.9   9.6e-24   8.6e-20      15     117 ..      98     196 ..      87     197 .. 0.89
   2 !   11.8   0.5   2.1e-05      0.19      28     118 ..     236     330 ..     228     331 .. 0.75

  Alignments for each domain:
  == domain 1  score: 70.9 bits;  conditional E-value: 9.6e-24
                   EEEEEECTSSBS-EEEEETT-EEEEEEEE-SSS-B-EEEET--S-GG.....GSCSGGG-B-TT-EEEEEEE--S-SEEEEEEE--TT..HHH.TT- CS
  Cu-oxidase_3  15 revitvNgqfpgptievregdtvvvnvtNkldentsihwhGlqqrktswmDGvpgvtqcpiqpgesftyrftvkqqagtlwYhshlsl..qqa.aGl 108
                    +v+t+Ng++pgpti+++egd v+++++N+ +++ ++h+hG++  +    DGv  +   + + g +fty+f +   +g + Yh h++   ++  +Gl
    EPA05569.1  98 YTVWTFNGTVPGPTIRATEGDLVRIHFINNGSKPHTMHFHGIHPAEM---DGVFEI---VGAGGGQFTYEFVAGP-IGVHPYHCHVMPleEHIsHGL 187
                   589***************************************96665...999884...44679*******9998.**********99985557*** PP

                   EEEEEEE-H CS
  Cu-oxidase_3 109 aGaiiiedk 117
                   +G++i+++k
    EPA05569.1 188 YGVFIVDPK 196
                   ******986 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 2.1e-05
                   EEEEETT-EEEEEEEE-S..SS-B-EEEET.--S-GG.....GSCSGGG-B-TT-EEE..EEEE--S-SEEEEEEE--TTHHHTT-EEEEEEE-HH CS
  Cu-oxidase_3  28 tievregdtvvvnvtNkl..dentsihwhG.lqqrktswmDGvpgvtqcpiqpgesft..yrftvkqqagtlwYhshlslqqaaGlaGaiiiedke 118
                    i++++++ +++ v+N +  d     h+hG l q   +    vp   +++i+  ++ +   +f+ +   g +++h+h      +G +G+++++dk+
    EPA05569.1 236 PIQINTNELIRIYVVNMVefDPINNFHLHGnLYQYFPTGTSLVPSTYTDMITLSQTERgiMEFQYQY-PGKYLFHAHKVEFSEKGWVGLFLVKDKS 330
                   58999999999*****997555578999994344444344445666667777766654226777777.9*********99888**********985 PP

>> Cu-oxidase_2  Multicopper oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   4.0   7.3e-11   6.5e-07      31     135 ..     108     195 ..      85     196 .. 0.84
   2 !   42.4   0.4   5.9e-15   5.2e-11      23     136 ..     218     329 ..     200     330 .. 0.87

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 7.3e-11
                   SSEEEEEETTEEEEEEEEE-SSS-EEEEESS-EEEEEEEEECCCCCCTCCSSGCCGSSCBSEEEE-TTEEEEEEEES.S-EEEEEEESSH...HHHH CS
  Cu-oxidase_2  31 ntnvitlpkgevveiviqnntklpHPfHlHGhdfqvlgrgpgndpeedpksynlenpvrrdtvqvppggwvairfkadnpGvwllHCHil...wHld 124
                     ++i++ +g+ v+i + nn++ pH++H+HG + + +                    +    v   +gg+++++f a   Gv  +HCH+    +H +
    EPA05569.1 108 PGPTIRATEGDLVRIHFINNGSKPHTMHFHGIHPAEM-------------------DGVFEIVGA-GGGQFTYEFVAGPIGVHPYHCHVMpleEHIS 184
                   46789999***********************944333...................222355666.69********************99999**** PP

                   TT-EEEEEEEC CS
  Cu-oxidase_2 125 qGmalqfvvrp 135
                   +G++++f+v+p
    EPA05569.1 185 HGLYGVFIVDP 195
                   *********97 PP

  == domain 2  score: 42.4 bits;  conditional E-value: 5.9e-15
                   E.......ETCCTTTSSEEEEEETTEEEEEEEEE-SSS..-EEEEESS-EEEEEEEEECCCCCCTCCSSGCCGSSCBSEEEE-TTEEEEEEEES.S- CS
  Cu-oxidase_2  23 t.......ngeefsentnvitlpkgevveiviqnntkl..pHPfHlHGhdfqvlgrgpgndpeedpksynlenpvrrdtvqvppggwvairfkadnp 110
                   t       n  +f  + ++i+++ +e ++i++ n+ ++     fHlHG+  q   +g++            +  +  d +++   ++ +++f++++p
    EPA05569.1 218 TennfyaaNTIPFYYQHHPIQINTNELIRIYVVNMVEFdpINNFHLHGNLYQYFPTGTSL-----------VPSTYTDMITLSQTERGIMEFQYQYP 303
                   12223456888999**********************999889***********9888888...........99999********************* PP

                   EEEEEEESSHHHHHTT-EEEEEEECH CS
  Cu-oxidase_2 111 GvwllHCHilwHldqGmalqfvvrpd 136
                   G +l+H H  +  ++G ++ f+v+++
    EPA05569.1 304 GKYLFHAHKVEFSEKGWVGLFLVKDK 329
                   *********************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2569.39
//
Query:       EPA05570.1  [L=48]
Description: hypothetical protein BG20_I0432 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-05   23.5   4.4    3.2e-05   23.5   4.4    2.1  2  TSP_3     Thrombospondin type 3 repeat


Domain annotation for each model (and alignments):
>> TSP_3  Thrombospondin type 3 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   4.4   1.8e-09   3.2e-05      15      34 ..      12      31 ..      11      33 .. 0.92
   2 !    2.8   0.2    0.0055        99      17      24 ..      37      44 ..      34      45 .. 0.67

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.8e-09
       TSP_3 15 DfDnDgvqddlDNCprnani 34
                D+DnDg++d++D Cp+ +++
  EPA05570.1 12 DTDNDGIPDSSDSCPNDPET 31
                9***************9985 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.0055
       TSP_3 17 DnDgvqdd 24
                D Dg +d+
  EPA05570.1 37 DSDGCPDV 44
                66777664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       194  (0.0108205); expected 358.6 (0.02)
Passed bias filter:                      154  (0.00858944); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.26s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 357.23
//
Query:       EPA05571.1  [L=107]
Description: hypothetical protein BG20_I0428 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.019   15.1   0.1      0.023   14.8   0.1    1.2  1  TerY_C    TerY-C metal binding domain


Domain annotation for each model (and alignments):
>> TerY_C  TerY-C metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   1.3e-06     0.023      13      55 ..      47      90 ..      37     105 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.3e-06
      TerY_C 13 ktkrpYllkyerelqevaleelkleveeyrlagay.pidedYfe 55
                +t  +Yl+ y++ + e+ + e+++++++y+ ++a  + d++Yf 
  EPA05571.1 47 STGDTYLMIYAKGTLESGIYEFDVNSKSYKKVNAIeRADKNYFV 90
                57789************************977776268999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.32s 00:00:00.79 Elapsed: 00:00:00.51
# Mc/sec: 636.63
//
Query:       EPA05572.1  [L=203]
Description: metallo-beta-lactamase domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.3e-22   78.2   3.7      9e-20   71.5   3.7    2.0  1  Lactamase_B    Metallo-beta-lactamase superfamily
    2.1e-05   24.2   0.1    3.2e-05   23.5   0.1    1.5  1  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.011   15.5   0.3      0.017   14.9   0.3    1.3  1  COR            C-terminal of Roc, COR, domain
      0.055   12.8   0.0       0.11   11.8   0.0    1.5  1  DUF1776        Fungal family of unknown function (DUF1776)


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.5   3.7     2e-23     9e-20       4     197 .]      11     169 ..       8     169 .. 0.79

  Alignments for each domain:
  == domain 1  score: 71.5 bits;  conditional E-value: 2e-23
                  CSSEEEEEE..ETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHHHHCCHHTT CS
  Lactamase_B   4 dpvnsylie..gdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmeeaddaasrkgllla 99 
                   + ++y++e  + ++ i+iD+ ++ ++   +     ++++ ++++++i+TH+H+DH+ g++g+++ t+++++ +++ + ++                 
   EPA05572.1  11 MQNFTYVVEdeNTDEGIIIDPSWDLDEIERV-----IKRNNLKIKYIINTHHHFDHTLGNEGIAKSTNAKIIQHEKSELKHDIS-------------- 89 
                  5778999999999*****************9.....9********************************998776655444333.............. PP

                  CHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEE.S CS
  Lactamase_B 100 gvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetgridltlrgaevrdpsdaekyldsllklaglkaevlvp.g 196
                              + dg++ + ++ + t+ +++gh+  + ++ g++ +f+GD+l++g+ gridl+++ a+ +++s+ + +         l+++++++ g
   EPA05572.1  90 ------------VKDGDVIEFGESKLTVLHTPGHSKDSMCLIGDGKIFSGDTLFVGNCGRIDLPGGSAKELYHSLFDVLH-------SLNDDLVLYcG 168
                  ............44555555555555555555555556666667779****************88888888888776666.......66666666667 PP

                  S CS
  Lactamase_B 197 H 197
                  H
   EPA05572.1 169 H 169
                  7 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.1   7.2e-09   3.2e-05       3      63 ..      27      79 ..      26     155 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 7.2e-09
                   EEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEE CS
  Lactamase_B_2  3 iLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyap 63
                   i+iD+++dl +  +r      +r++  +i+ ++ th H+DH+ g   +++ ++  ++++ +
     EPA05572.1 27 IIIDPSWDLDEI-ERVI----KRNN-LKIKYIINTHHHFDHTLGNEGIAKSTN--AKIIQH 79
                   89******8766.8887....4444.79****************999999544..455555 PP

>> COR  C-terminal of Roc, COR, domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.3   3.9e-06     0.017      51     118 ..       8      78 ..       4      96 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.9e-06
         COR  51 lGvvlyFqd...deglrdiviLnpeWltnavyrvldskkvankkGilkredlekiwkekeypaeehdllle 118
                 +G++++F+    de + + +i++p+W  + + rv+++++++ k  i ++ ++++ + ++   ++    +++
  EPA05572.1   8 VGNMQNFTYvveDENTDEGIIIDPSWDLDEIERVIKRNNLKIKYIINTHHHFDHTLGNEGIAKSTNAKIIQ 78 
                 688888877665779999************************999999*9999999998877766666665 PP

>> DUF1776  Fungal family of unknown function (DUF1776)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.5e-05      0.11     241     278 ..     131     169 ..     120     186 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.5e-05
     DUF1776 241 kaisaksir.rgsslreLhnalfdllegsskkrvvyvGk 278
                    ++++i   g s++eL++ lfd+l++     v+y+G 
  EPA05572.1 131 FVGNCGRIDlPGGSAKELYHSLFDVLHSLNDDLVLYCGH 169
                 5556788888899**************999********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1387.57
//
Query:       EPA05573.1  [L=189]
Description: ribosomal protein S4 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-10   40.2   0.1    8.2e-10   38.3   0.0    2.0  2  S4        S4 domain


Domain annotation for each model (and alignments):
>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.17   3.1e+03       3      14 ..      73      84 ..      73      86 .. 0.85
   2 !   38.3   0.0   4.6e-14   8.2e-10       1      46 [.     103     148 ..     103     150 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.17
                HHHHHHHTTSSS CS
          S4  3 Ldkvlarlglas 14
                L k l+r+gl+s
  EPA05573.1 73 LMKSLSRIGLVS 84
                67889****987 PP

  == domain 2  score: 38.3 bits;  conditional E-value: 4.6e-14
                 EEHHHHHHHTTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-TTC CS
          S4   1 rRLdkvlarlglassrreArqlIehGrVlVNGkvvkdpsyrVkpgD 46 
                 rRL++++ +++  ++  +Arq++ hG++ +  ++v++psy+V+ ++
  EPA05573.1 103 RRLQTLVTKKLGFKTPYQARQAVIHGHIMIGDRKVNIPSYIVTLEE 148
                 8******99999999***************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1199.00
//
Query:       EPA05574.1  [L=407]
Description: hypothetical protein TIGR00299 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     2e-100  336.5   0.6   2.2e-100  336.3   0.6    1.0  1  DUF111           Protein of unknown function DUF111
  ------ inclusion threshold ------
      0.049   14.2   0.1       0.15   12.7   0.1    1.8  1  Scaffolding_pro  Phi29 scaffolding protein


Domain annotation for each model (and alignments):
>> DUF111  Protein of unknown function DUF111
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  336.3   0.6  2.5e-104  2.2e-100       2     371 ..       4     393 ..       3     395 .. 0.92

  Alignments for each domain:
  == domain 1  score: 336.3 bits;  conditional E-value: 2.5e-104
      DUF111   2 yldcs.sGisGDmllgALldlgadkeeleealeklgl.....eeveleiekvkksgisatkvdveeeehehehrs...laeieeiieaaslsekvkeka 91 
                 ++d++ +G+sGDmll +L+d+ga+k ++ + ++  +         +++++k +k+gi+at++ +e +eh he +     + i ++ ++  lsek+k  a
  EPA05574.1   4 VIDPQiAGVSGDMLLCSLVDIGANKIKIIDGVKLSEKflsdsVIKKIDFQKIDKHGINATELILEIDEHVHERKGieiKNAIINLTKEIGLSEKAKIFA 102
                 6888889*******************9999887644446644345899**************9976555555544222345666667999********* PP

      DUF111  92 laiferlaeAeakvhgvpleevhfhEvGavDaivdivgaalaldeLgv..ekvvasplalGsGtvrcahGilPvPaPAvlellkelklkl..gevegEl 186
                  +++++l ++e+k+hg p+++vhfhE  ++D+++divg+a+a+d+Lg+  e++++ p+a+G+G v+++hGi++ Pa A+le+l++++l++  g+v+ El
  EPA05574.1 103 ESCIDTLISSESKIHGLPIDSVHFHEASSIDTLIDIVGTAIAIDDLGMldEEIICMPVAVGGGNVSFSHGIMSNPASAILEILRDSNLSIhgGHVKDEL 201
                 ************************************************9999***********************************9999999***** PP

      DUF111 187 vTPTGaAilaalaeefg.slpamkvekiGyGaGkrdleeipnvlRvlleeeeeelekeevvvletniDDlspevlgyvlerLleaGAlDvfltpilmKK 284
                 +TPTGa il +l+++    +p+mk+++iGyGaG+++++ + nvl+++ ++++++ + +++ +letn+DD+ +e+lg+++e+++e+GA Dv++   ++KK
  EPA05574.1 202 TTPTGASILVNLSKTSAeYYPSMKITSIGYGAGQKNFDGFSNVLKIVKGTQTNSFQIDSIKILETNVDDVPGEILGNMIEKIMENGAKDVSIYHGITKK 300
                 ************998887999****************************************************************************** PP

      DUF111 285 gRpavllsvlckeedaeeleellfretttlGvReseverlvlereietvetelg....evrvKva..eevvkvkpEyedvkkiAeetglplke 371
                 gRp+ l++v+c++++++++ ++l++et+tlG+R s+ +r++++r+ ++ ++ l+     v+ Kv+  +++ ++k+E++d+k i+++ + ++ke
  EPA05574.1 301 GRPTNLITVICDNASMHDIMDILVTETGTLGIRISTSDRFIVPRTSHNAKLILDgkefVVKYKVStfKGKDHFKIEFDDLKLISNKLNKSIKE 393
                 ***********************************************9999888787778888888877********************9997 PP

>> Scaffolding_pro  Phi29 scaffolding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   1.6e-05      0.15      23      70 ..     343     391 ..     335     397 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.6e-05
                      HHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHH CS
  Scaffolding_pro  23 ertealqtlrvdyvevvveysdlt.ksieklkvekddlivsnsklfrki 70 
                       rt +  +l  d  e+vv+y+  t k ++++k+e ddl+    kl + i
       EPA05574.1 343 PRTSHNAKLILDGKEFVVKYKVSTfKGKDHFKIEFDDLKLISNKLNKSI 391
                      6999****************99886889**********99988998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.52
# Mc/sec: 2342.36
//
Query:       EPA05575.1  [L=103]
Description: hypothetical protein BG20_I0438 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       729  (0.0406604); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 598.99
//
Query:       EPA05576.1  [L=192]
Description: ribosomal protein S13p/S18e [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.9e-38  130.1   0.0      7e-38  129.9   0.0    1.1  1  Ribosomal_S13  Ribosomal protein S13/S18
  ------ inclusion threshold ------
      0.048   13.9   0.0      0.078   13.2   0.0    1.5  1  HHH_6          Helix-hairpin-helix motif
      0.093   12.2   0.0       0.12   11.8   0.0    1.1  1  DUF4238        Protein of unknown function (DUF4238)


Domain annotation for each model (and alignments):
>> Ribosomal_S13  Ribosomal protein S13/S18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.9   0.0   1.2e-41     7e-38       1     128 []      11     139 ..      11     139 .. 0.99

  Alignments for each domain:
  == domain 1  score: 129.9 bits;  conditional E-value: 1.2e-41
  Ribosomal_S13   1 RilgtdidgkkkveialtaikGiGrrkakiilkkadvdedkrigelteeeiekieeivenkaqykipnwi.nrqkdikdGkdshvvendlrrklre 95 
                    Ri+g di+g +kv + lt+ikGiG++ a++il  +++++++ ig l+e +++ ie+++ n++  + p w+ nr+kdi++G ++h++++d+ ++lr+
     EPA05576.1  11 RIVGNDIPGARKVIVGLTQIKGIGYNFATAILDTLKINTNTNIGFLSESDVQSIEKLITNPIAGNFPPWFlNRRKDIETGSNMHLLTSDIPFTLRN 106
                    9********************************************************************99************************* PP

  Ribosomal_S13  96 dieRlkkirsyrGlRHkrGlkvRGQrTkttgRt 128
                    dieR++  +s+rG RH+ GlkvRGQ T+ttgR+
     EPA05576.1 107 DIERERITNSWRGYRHMYGLKVRGQCTRTTGRK 139
                    *******************************95 PP

>> HHH_6  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.3e-05     0.078      22      46 ..      20      44 ..       3      84 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.3e-05
       HHH_6 22 dgairlGLaaikglgeaaaerivae 46
                 +++++GL++ikg+g + a +i+++
  EPA05576.1 20 ARKVIVGLTQIKGIGYNFATAILDT 44
                356*******************985 PP

>> DUF4238  Protein of unknown function (DUF4238)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0     2e-05      0.12     139     218 ..      41     124 ..      26     125 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2e-05
     DUF4238 139 lldelkvildtkvdle.....etllqeafeddaewfikhleelywalleassdedFitsDnPvflrndestgeeglsayseyhil 218
                 +ld+lk++ +t++ +      + + + +++ +a  f +++ ++   + + s+   ++tsD P +lrnd ++++ ++s+ ++ h++
  EPA05576.1  41 ILDTLKINTNTNIGFLsesdvQSIEKLITNPIAGNFPPWFLNRRKDIETGSNMH-LLTSDIPFTLRNDIERERITNSWRGYRHMY 124
                 555555555555555566677678888888899999999999999887777777.***********************9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 1151.17
//
Query:       EPA05577.1  [L=62]
Description: hypothetical protein BG20_I0422, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       754  (0.0420548); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.35s 00:00:00.87 Elapsed: 00:00:00.54
# Mc/sec: 344.14
//
Query:       EPA05578.1  [L=357]
Description: hypothetical protein TIGR00303 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-13   51.2   0.1    1.6e-13   50.6   0.1    1.2  1  DBI_PRT   Phosphoribosyltransferase


Domain annotation for each model (and alignments):
>> DBI_PRT  Phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.6   0.1   8.8e-18   1.6e-13     114     260 ..     121     260 ..      95     278 .. 0.78

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 8.8e-18
                 -SSSSB--TTTS-SS-HHHHHHHHHHHHHHHHHHHCTTECEEEEEEE-TTCHHHHHHHHHHHHT--HHHH---TTT--HHHHHHHHHHHHHHHHCH-TT CS
     DBI_PRT 114 kvrrgtaniakepAmtreeaeaaleaGieladeladagadllalGemGigNttaaaallaallglepeevvGrGtglddeglarKiavieqalarhaek 212
                  + +g +ni++++Am+++++ +a+++G+ + ++l ++ +++l++Ge   g tt+a a+l  l     ++ v   + + ++ ++ K +++++al+r ++k
  EPA05578.1 121 GLSYG-RNISVDSAMNDTQVSQAVDYGRMVGRNL-ASMTNCLIIGESIPGGTTTALAVLRGL---GFNAKV--SSSIPNNPVELKNQIVNSALERLTSK 212
                 55554.89********************999997.557*****************9987654...333333..5689*******************878 PP

                 .HHHHHHHHS-HHHHHHHHHHHHHHHTT--EEE-SHHHHHHHHHHHHH CS
     DBI_PRT 213 dplevLakvGGleiaalaGailgAaarripvvlDGfistaAalvAvrl 260
                 dp +v+++vG   ia +aG++ +A +   +++  G  +ta  + A+++
  EPA05578.1 213 DPYHVISQVGDPMIAFVAGMLSAASEVTKVMLAGGTQMTAVLAFASKI 260
                 *******************77666666666666666666666667776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 2101.63
//
Query:       EPA05579.1  [L=265]
Description: hypothetical protein TIGR00268 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.8e-09   35.5   0.4    4.1e-08   33.0   0.2    2.2  3  QueC             Queuosine biosynthesis protein QueC
    4.1e-08   33.2   0.1      3e-07   30.4   0.1    2.0  1  ATP_bind_3       PP-loop family
    6.9e-08   31.9   0.0    1.1e-07   31.2   0.0    1.2  1  NAD_synthase     NAD synthase
    1.5e-07   30.5   0.3    2.5e-06   26.5   0.2    2.2  2  tRNA_Me_trans    tRNA methyl transferase
    2.9e-07   30.5   0.0    9.1e-07   28.8   0.0    1.7  2  Asn_synthase     Asparagine synthase
    9.3e-05   22.1   0.1    0.00017   21.2   0.1    1.5  1  ThiI             Thiamine biosynthesis protein (ThiI)
  ------ inclusion threshold ------
      0.034   13.4   0.3      0.067   12.5   0.1    1.5  2  Arginosuc_synth  Arginosuccinate synthase


Domain annotation for each model (and alignments):
>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.2   1.6e-11   4.1e-08       2      65 ..      17      80 ..      16      90 .. 0.87
   2 ?   -1.6   0.0      0.63   1.6e+03     107     129 ..     105     127 ..     102     134 .. 0.88
   3 ?   -1.0   0.0      0.41   1.1e+03     154     185 ..     139     174 ..     121     183 .. 0.76

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 1.6e-11
                EEEE--SSHHHHHHHHHHHHH.-SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-GGGG CS
        QueC  2 avvllSGGlDSttvlalakke.gkevealtfdYgqrhkkeleaakkiakelgveehkildldllk 65
                +++ lSGG+DS+ v++ a ++ g+  +a+t dY+   k+ele+ak+i++e+g+ ++  +d d l+
  EPA05579.1 17 VMIALSGGVDSALVAYAAFQKlGNSAIAVTADYKTLSKEELETAKQICSEIGI-KQILVDYDELQ 80
                6788**********999966527999***************************.99999988665 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.63
                 HHHHHHT-SEEEE---S-STT-- CS
        QueC 107 syaealgaeaiiiGvneedfsgY 129
                 s+a++ ++e i+ G n  d   Y
  EPA05579.1 105 SLAKQHNVEVIVDGTNLDDLGEY 127
                 79999999999999999998877 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.41
                 EE-TTTT..--HHHHHHHHHHTT..HHHHH-B-STT CS
        QueC 154 ieaPlid..lsKaeivklgkelg..vpleetlsCYe 185
                 i  Pl++  ++K+ei  ++k +g  +  + + sC +
  EPA05579.1 139 ICSPLVEtrFTKNEIRSTAKFVGlsIYDKPSNSCLA 174
                 677887522689999999999995445567888866 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.1   1.2e-10     3e-07       1     111 [.      16     126 ..      16     175 .. 0.87

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 1.2e-10
                 EEEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--H..HHCTTSTCCCHHHHHHHHH...HHHCHHC CS
  ATP_bind_3   1 kvlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklnikleiekvdv..akkkgknleeaARelRYev...lkealkk 94 
                 kv++A+SgG+DS +  +++ ++   lg +++a++ d++  + skee e+ k++c++++ik +  + d   +++  kn  ++  ++R e+   l +++k+
  EPA05579.1  16 KVMIALSGGVDSALVAYAAFQK---LGNSAIAVTADYK--TLSKEELETAKQICSEIGIKQILVDYDElqNEEFVKNSSDRCFHCRLELgdhLISLAKQ 109
                 589*********9988887776...4557788888886..5789999*************99999998877777899999999999976333777899* PP

                 CT.CEEE---BHHHHHH CS
  ATP_bind_3  95 egievlllAhhadDqaE 111
                 +++ev++ + + dD  E
  EPA05579.1 110 HNVEVIVDGTNLDDLGE 126
                 **************987 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0   4.3e-11   1.1e-07      18      84 ..      14      79 ..       6      96 .. 0.89

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 4.3e-11
                  TSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE---HHH CS
  NAD_synthase 18 akgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievktidikpi 84
                   ++v++ lSGGvDS+lva+ a + lg + ++a+    ++ s+e++e a++++ ++gi+   +d ++ 
    EPA05579.1 14 KNKVMIALSGGVDSALVAYAAFQKLG-NSAIAVTADYKTLSKEELETAKQICSEIGIKQILVDYDEL 79
                  589**********************6.67899***99*********************999997765 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.2   9.8e-10   2.5e-06       2      79 ..      16      85 ..      15      92 .. 0.77
   2 ?    1.6   0.0     0.038        96     170     192 ..     147     169 ..     135     177 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 9.8e-10
  tRNA_Me_trans  2 kvvvalSgGVDSsvaaal.lkeqgyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfekeykekvf 79
                   kv++alSgGVDS+++a+  +++ g + i+v+            +  ++e+l++a+++++++gi+   vd+ +   e+ +
     EPA05579.1 16 KVMIALSGGVDSALVAYAaFQKLGNSAIAVTADY---------KTLSKEELETAKQICSEIGIKQILVDYDELQNEEFV 85
                   8************998861555566666665433.........2357899********************987666655 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.038
  tRNA_Me_trans 170 eltKeevrkiAkeaglavaekkd 192
                    ++tK+e+r+ Ak  gl++ +k+ 
     EPA05579.1 147 RFTKNEIRSTAKFVGLSIYDKPS 169
                    579**************999974 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0   3.6e-10   9.1e-07      19      83 ..      16      78 ..      11     119 .. 0.82
   2 ?   -1.2   0.0      0.49   1.3e+03     132     188 ..     159     218 ..     158     234 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 3.6e-10
  Asn_synthase 19 pvGalLSGGlDSSliaalaarqsksplktFsigfeekgsdeakyakevaehlgtehtelvlteee 83
                  +v + LSGG+DS+l+a+ a +++ +++ ++++++++ + +e++ ak+++ ++g++++ + +  +e
    EPA05579.1 16 KVMIALSGGVDSALVAYAAFQKLGNSAIAVTADYKTLSKEELETAKQICSEIGIKQILVDY--DE 78
                  67789****************999**********99*******************865543..33 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.49
  Asn_synthase 132 fgGYpyfykaalsrsrefeklp.....larslrasllarklrklaellelaeardleelael 188
                   f G + +y+++ s+s  ++++p     ++++l + +l++ + k+ + l++++ rdl+ +a++
    EPA05579.1 159 FVGLS-IYDKP-SNSCLASRIPwgqrvTSEKLTRIELGETIVKQITNLKQVRVRDLDGNAKI 218
                   66777.77777.56677788888888889999999999999999999999988888776554 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.1   6.8e-08   0.00017       4     160 ..      15     161 ..      12     191 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 6.8e-08
        ThiI   4 gkvlaLlSgGiDSpVaaylllkR.GcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlkeilekvkekltivllkrkmlriAe 101
                 +kv+  lSgG+DS   ay ++++ G  + +v+ + + + s+e+ e  ++   + +e +    +k + vd++e+++e   k     ++  ++  +     
  EPA05579.1  15 NKVMIALSGGVDSALVAYAAFQKlGNSAIAVTAD-YKTLSKEELETAKQ---ICSEIG----IKQILVDYDELQNEEFVKN-SSDRCFHCRLELGDHLI 104
                 79999**************998757778888775.66666666655555...556655....67899******98865553.4568999***9988777 PP

        ThiI 102 kvaeeegakalvtGesLgqVaSqtleNlrvisavvnllilrPLig..ldKeeiiklAkeig 160
                  +a++++++ +v+G +L             i+a  +  i +PL+   + K+ei  +Ak +g
  EPA05579.1 105 SLAKQHNVEVIVDGTNLDDLGEY----RPGIEALKKNGICSPLVEtrFTKNEIRSTAKFVG 161
                 7***************9876533....2335555556677777652245777777777665 PP

>> Arginosuc_synth  Arginosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   2.6e-05     0.067       2      66 ..      19      87 ..      18      98 .. 0.82
   2 ?   -3.9   0.0       2.5   6.5e+03     333     360 ..     206     233 ..     198     238 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.6e-05
  Arginosuc_synth  2 LaysGGlDtsviikllkeklgeeviavavdvGq.eeedldevkekalklgavksvvvDa....keefved 66
                     +a sGG+D + +     +klg+  iav++d     +e+l+++k+   ++g  k+++vD     +eefv++
       EPA05579.1 19 IALSGGVDSALVAYAAFQKLGNSAIAVTADYKTlSKEELETAKQICSEIGI-KQILVDYdelqNEEFVKN 87
                     799******999999999999*********8653679*************9.777888522225678875 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 2.5
  Arginosuc_synth 333 tvrvklfkGsvvvlgReseeslYdeela 360
                      +vrv+   G+++++  +   s+++ ++ 
       EPA05579.1 206 QVRVRDLDGNAKIEVEKDRISIFEDDIL 233
                      5788888888888888888888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       909  (0.0507); expected 358.6 (0.02)
Passed bias filter:                      714  (0.0398237); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 1814.68
//
Query:       EPA05580.1  [L=304]
Description: malate dehydrogenase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-36  124.1   0.5    8.4e-36  123.2   0.5    1.5  1  Ldh_1_N   lactate/malate dehydrogenase, NAD binding domain
    2.9e-28   98.9   0.1      5e-28   98.1   0.1    1.4  1  Ldh_1_C   lactate/malate dehydrogenase, alpha/beta C-terminal


Domain annotation for each model (and alignments):
>> Ldh_1_N  lactate/malate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.2   0.5   9.4e-40   8.4e-36       3     141 .]       2     140 ..       1     140 [. 0.99

  Alignments for each domain:
  == domain 1  score: 123.2 bits;  conditional E-value: 9.4e-40
                 EEEETTTSHHHHHHHHHHHHTTSSSEEEEE-SSHHHHHHHHHHHHHCHCCSTS-EEEEE.SSGGGGTTESEEEE--S-SS-TTTTHHHHHHHHHHHHHH CS
     Ldh_1_N   3 vavvGaaGgiGqslalllankkladelaLlDiakekleGvaldlshistflsvkvkvse.keeealkdadvvvitagvprkpGetRddLlkvNakIvke 100
                 ++++G+ G++G   al  a k l d++ LlD+a    +G+a+d++h+     ++v+v++ ++ e++k++++vv++ag  rkpG+tR dLlk+Na+Ivk+
  EPA05580.1   2 ITIIGS-GKVGGDAALFSALKRLDDQILLLDVAAGLPQGEAMDINHMLSEQGIDVEVKGsNNFEDMKGSNIVVVVAGSGRKPGMTRMDLLKINATIVKS 99 
                 89****.**************************************************998999************************************ PP

                 HHHHHHHHTTTSEEEE-SSSHHHHHHHHHHHHTS-GGGEEE CS
     Ldh_1_N 101 iveaiakvapnaivlvvsNPvdiltevlkkasglpkkrvig 141
                 +ve+i+k+a++ +++ v+NP d ++++++k+sg++++r++g
  EPA05580.1 100 VVENIKKYASDSMIIPVTNPLDPMAYITYKVSGFDRSRIFG 140
                 ***************************************98 PP

>> Ldh_1_C  lactate/malate dehydrogenase, alpha/beta C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.1   0.1   5.6e-32     5e-28       3     160 ..     145     299 ..     143     303 .. 0.95

  Alignments for each domain:
  == domain 1  score: 98.1 bits;  conditional E-value: 5.6e-32
                 HHHHHHHHHHHHHHTS-GGGEE--EEBSSST..........ETTEEHHHHHTTSTTSTHHHHHHHHHHHHHHHHHHHHHHTTSSSS-HHHHHHHHHHHH CS
     Ldh_1_C   3 LDivRaktflaekagvtprsvkvtViGgHsg..........vtiipllsqvkellklsekqleeliervqnggdevvkakkGagsatlsmAvAgakfve 91 
                 LD+ R+++f+ e +g + +s ++ ViG+H++          v +ipl      +  l +++l+el++++++ +++v++ k   g++  + ++A+  ++e
  EPA05580.1 145 LDLSRFRQFIHEATGYSRDSIRALVIGEHGEnmlplprfssVSGIPL------NTILPKQKLDELVQNTKQVAAKVIELK---GATVHAPGNAISAMIE 234
                 9******************************9999888888888888......667889*********************...9*************** PP

                 HHHTTHTEEEEEEEEEESCCCECCSSEEEEEEEEEEETTEEEEE-------HHHHHHHHHHHHHHHHHH CS
     Ldh_1_C  92 allrdtkeilsagvyldgevglkdqeieyfsvPvvlgknGvekvleilklndfeeekleksvkeLkkei 160
                 +++rd k+++++++yldge+g +d   + ++vP+v+gk+Gvek++e l ln++e++ ++++++  k+ i
  EPA05580.1 235 SVVRDRKQVIPVSTYLDGEYGYSD---VTIGVPAVIGKKGVEKIIE-LDLNAEEKQVFDTAIQSVKSAI 299
                 ************************...9******************.****************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 1909.76
//
Query:       EPA05581.1  [L=390]
Description: putative membrane protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.6e-06   25.2  19.0    8.6e-06   25.2  19.0    2.5  2  Zip       ZIP Zinc transporter
  ------ inclusion threshold ------
       0.91    7.7  21.4       0.08   11.2   6.0    2.5  3  DUF2070   Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> Zip  ZIP Zinc transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   2.9     0.014   1.3e+02       7      92 ..     146     229 ..     140     245 .. 0.61
   2 !   25.2  19.0   9.6e-10   8.6e-06     184     298 ..     247     357 ..     230     387 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.014
         Zip   7 aiiaililsllgllgpllvpkiskllsklllslllafavGvllgtaflhLlPealealeesqleee.hthplagllvllGflllllv 92 
                 aii + +  + +++g+l +p+i++   k+ ++++la+ vG l+  ++  +l e++e  +e  l+++ ++++l   ++ll+fl l+ +
  EPA05581.1 146 AIIGTYVGIIPVMIGLLWLPFIKR-IGKNKYNFFLALTVGLLFFLGIDAML-EGFEVSKE-NLSANfNGELLIITVALLSFLGLYYT 229
                 444444444444455555554444.58999999999999999877777666.55553333.34455455577777777887766544 PP

  == domain 2  score: 25.2 bits;  conditional E-value: 9.6e-10
         Zip 184 vraiilllglilHsfidGLAlG.vssssstgislfiAv..llHelpeelglgaiLlkaglsrkkavllnllfaltaplGiliGilvrsisessgaeivs 279
                 ++++++ +g++lH++ +GLA+G +    + ++s+f+ v   lH+  e++++ ++++k++ ++ k+vll l+ ++ ++lG+ iG +        ++ +++
  EPA05581.1 247 AIGLMIAIGIGLHNLGEGLAIGaAIGLGQVALSTFLIVgfALHNTTEGIAIASPVAKSKSPVLKIVLLGLIAGAPTILGTWIGGF-------FYSPFTA 338
                 5699******************75555566666666552278****************************************999.......8****** PP

         Zip 280 gillalsaGtflYvalvel 298
                  i+la+ aG    valv l
  EPA05581.1 339 IIFLAIGAGAIFQVALVIL 357
                 ****************955 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.16   1.4e+03     409     448 ..      41      78 ..      36      79 .. 0.77
   2 ?   11.2   6.0   8.9e-06      0.08      30     172 ..     134     279 ..     125     289 .. 0.75
   3 ?    2.4   8.2    0.0042        37      38     146 ..     278     386 ..     264     389 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.16
     DUF2070 409 varsetpkltpe.eglGdlgiqvlvlevdgqktayvliDgN 448
                 va   +p++t e  ++ d++i v+v +++   +++v++D N
  EPA05581.1  41 VA---LPEITIEkVEFVDSEIHVTVRNTGPISVVIVMADVN 78 
                 55...333444448999999999999999999999999987 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 8.9e-06
     DUF2070  30 llaflssklfgillfglp..alvaflltlpvlrilggrltykrslflalltelivviisllaillsall..qalvllalvls..lalvfalrllvlvav 122
                 +l ++s+ l g+++++ +   ++ +++ l +l +++++ + k ++flal+  l++++   + ++l  +   ++ ++  +     ++ v+ l++l l+ +
  EPA05581.1 134 ALKSDSE-LAGFFAIIGTyvGIIPVMIGLLWLPFIKRIGKNKYNFFLALTVGLLFFL--GIDAMLEGFEvsKENLSANFNGEllIITVALLSFLGLYYT 229
                 5555666.778888877766689999999999999888888999******9999999..666676666666333333333335466689999******* PP

     DUF2070 123 sdesllkavlpaliqpllailllvlyfspesfllllllslifalavylfi 172
                 +++ +++a+l a+  p+++ l++ + ++ ++    l++ ++++l+ +++ 
  EPA05581.1 230 AEKLTSRATLSASSKPFAIGLMIAIGIGLHNLGEGLAIGAAIGLGQVALS 279
                 ************************99777777777777777776655544 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.0042
     DUF2070  38 lfgillfglpalvaflltlpvlrilggrltykrslflalltelivviisllaillsallqalvllalvlslalvfalrllvlvavsdesllkavlpali 136
                 l ++l++g+ +  ++     +  +++++ ++ + ++l l++  + ++ ++++ +++  ++a+++la+  + ++ +al++l ++  s+++l + ++++ i
  EPA05581.1 278 LSTFLIVGFALHNTTEGIAIASPVAKSKSPVLKIVLLGLIAGAPTILGTWIGGFFYSPFTAIIFLAIGAGAIFQVALVILKWIYQSEQKLVQTSIISGI 376
                 4445555555444444444444444455666667999***************999998899999999999************************99999 PP

     DUF2070 137 qpllailllv 146
                  + ++i++l+
  EPA05581.1 377 GSGMLIMYLT 386
                 9999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       779  (0.0434492); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.26s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2455.68
//
Query:       EPA05582.1  [L=60]
Description: hypothetical protein BG20_I0431 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 381.27
//
Query:       EPA05583.1  [L=1061]
Description: hypothetical protein BG20_I0434 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00042   20.7   0.0     0.0056   17.1   0.0    2.9  3  MG2            MG2 domain
  ------ inclusion threshold ------
       0.11   12.5   0.3       0.52   10.3   0.2    2.1  2  STI1           STI1 domain
       0.16   11.8   0.1         16    5.4   0.0    2.5  2  HTH_10         HTH DNA binding domain
       0.21   11.6   0.3       0.42   10.6   0.3    1.4  1  Tachystatin_B  Antimicrobial chitin binding protein tachystat


Domain annotation for each model (and alignments):
>> MG2  MG2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.3   5.8e+03      33      45 ..     748     760 ..     725     767 .. 0.77
   2 ?   -3.0   0.0       2.4   1.1e+04      54      69 ..     824     839 ..     818     841 .. 0.80
   3 !   17.1   0.0   1.3e-06    0.0056      28      88 ..     914     971 ..     904     993 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.3
                 -EEEEEEEE-TTS CS
         MG2  33 klplkltirdpdg 45 
                 ++p+++t++dpd 
  EPA05583.1 748 GQPVTITLNDPDL 760
                 3899****99985 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.4
                 EE-CTTEEEEEEE--T CS
         MG2  54 atdetggaesefalpe 69 
                 +  +tg++e++f+ p+
  EPA05583.1 824 TGPSTGVFEGSFKMPS 839
                 5678999*****9997 PP

  == domain 3  score: 17.1 bits;  conditional E-value: 1.3e-06
                 CSB---EEEEEEEE-TTSSEEEEEEEEE-CTTEEEEEEE--TT--SEEEEEEEEECSTTT- CS
         MG2  28 lqglaklplkltirdpdgkevkelplatdetggaesefalpeaaklGeysvelsadsaees 88 
                 +++ ++ pl++ +++pd+ + +++  + +++g +   f ++e++  G y+++l   +++ +
  EPA05583.1 914 SNPKNSVPLTIILTRPDNVV-QNFAATVSNSGAYRAAFSINENSVPGIYKIQL--YHNGVN 971
                 4555569*********9765.556669999***********************..444444 PP

>> STI1  STI1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.3   5.9e+03      19      30 ..     680     691 ..     677     693 .. 0.75
   2 ?   10.3   0.2   0.00012      0.52       8      33 ..     987    1012 ..     984    1014 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.3
        STI1  19 sDPefvakleei 30 
                 sDP f + ++ i
  EPA05583.1 680 SDPNFIKSIRAI 691
                 789988888776 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00012
        STI1    8 laanPetrellsDPefvakleeiqsN 33  
                  +++n + r ++sDPef ++l+++ ++
  EPA05583.1  987 IKNNKKQRSIISDPEFINMLNQLVKD 1012
                  6789999***************9775 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.012        53      24      44 ..     510     530 ..     509     533 .. 0.89
   2 ?    5.4   0.0    0.0036        16      28      50 ..     672     694 ..     671     696 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.012
      HTH_10  24 vtlkeLAkelGIskstlsehL 44 
                 ++ k++++ lGI++s+l+  L
  EPA05583.1 510 ANFKQISMNLGITASSLQSVL 530
                 6789*************9877 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0036
      HTH_10  28 eLAkelGIskstlsehLrkaesk 50 
                 ++A++l+Is++++ + +r++ + 
  EPA05583.1 672 AIANQLNISDPNFIKSIRAIDNE 694
                 59****************99776 PP

>> Tachystatin_B  Antimicrobial chitin binding protein tachystatin B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.3   9.4e-05      0.42      15      36 ..     115     136 ..     112     140 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 9.4e-05
  Tachystatin_B  15 sGrsCCfGyyCrrdfPGsifGt 36 
                    sG+   fG +C rd P  +fG 
     EPA05583.1 115 SGKGLDFGVFCSRDTPSNVFGV 136
                    899999**************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1061 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.76u 0.29s 00:00:01.05 Elapsed: 00:00:00.47
# Mc/sec: 6741.13
//
Query:       EPA05584.1  [L=157]
Description: hypothetical protein BG20_I0429 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 1038.02
//
Query:       EPA05585.1  [L=412]
Description: enolase, C-terminal TIM barrel domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.3e-57  195.3   0.1    1.8e-57  194.9   0.1    1.1  1  Enolase_C  Enolase, C-terminal TIM barrel domain
    3.2e-21   75.9   0.0    8.9e-21   74.4   0.0    1.8  1  Enolase_N  Enolase, N-terminal domain
    8.3e-05   22.3   0.0    0.00025   20.7   0.0    1.7  2  MR_MLE_C   Enolase C-terminal domain-like
  ------ inclusion threshold ------
       0.09   12.9   0.0       0.24   11.5   0.0    1.6  1  DUF155     Uncharacterised ACR, YagE family COG1723


Domain annotation for each model (and alignments):
>> Enolase_C  Enolase, C-terminal TIM barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  194.9   0.1   3.9e-61   1.8e-57       3     279 ..     132     402 ..     130     407 .. 0.95

  Alignments for each domain:
  == domain 1  score: 194.9 bits;  conditional E-value: 3.9e-61
                 EE-EE-EEEEE-GGGSS.SS--SSEEEEE-TT-SSHHHHHHHHHHHHHHHHHHHHHCC.GGGG-B-TTS-B----SSHHHHHHHHHHHHHHCT-TC..T CS
   Enolase_C   3 vlPvPalnvinGGshag.nklalqefmilPvgassfkealrlGaevyhklksvlkkkygksatnvGdeGGfaPnlqsnkealdliveaiekaGykg..k 98 
                  +P P+ n++ GG hag ++ ++qe +i  vga+++++a+ +   v+++l+++l+k+  + +   GdeGG+aP+l+ n++al+l ++a e+ G++   +
  EPA05585.1 132 KFPFPLGNILGGGAHAGpGTPDIQEILICAVGAKTIRDAIETNLSVHKELRRILEKEDPSFTNGRGDEGGWAPKLK-NEKALELSAKACENLGFTLgkE 229
                 579*************95678*************************************9999999*********97.678**************98889 PP

                 BEEEEE--GGGCEETCTTEEECTTTTTT..GGCEEEHHHHHHHHHHHHHHS-EEEEES-S-TT-HHHHHHHHHHHTTTSEEEESTTTTT-HHHHHHHHH CS
   Enolase_C  99 vkialdvassefykekdkkydldfkeeesdkskkltseqladlykelvkkyPivsiedpldeddweawkklteelgdkvqivGddltvtnpkrlkeaie 197
                 v +++d ass  ++e+++ky  +  +       + +seq  ++  ++++ky ++  ed++ e+ ++  ++lt++   +  + Gddltvtn ++l++ai+
  EPA05585.1 230 VALGVDFASSTQWNEEKQKYVYQRGG------FVNSSEQQIEFAANIINKYKLIYAEDAVHEEAFSDMAELTAKFP-NTLVTGDDLTVTNKDILSKAIK 321
                 ********************999888......778899999**********************************9.67799***************** PP

                 CT--SEEEE-HHHH-SHHHHHHHHHHHHHTT-EEEEE--SC--S--HHHHHHHHCT-SEEE---S-SHHHHHHHHHHHHHHH CS
   Enolase_C 198 kkaanalllkvnqiGsltesleavklakeagygvvvshrsGetedttiadlavglsaGqiktGaparserlakynqllriee 279
                  k++na +lkvnq Gsl +++e +k+a+++    + shrsGe+ d+ i+++ +++++  +k G +   er+ak+n+l+r+ e
  EPA05585.1 322 LKSCNAAILKVNQAGSLYDAFEFAKVASQNNIKLITSHRSGESTDSHISHIGLATKSKMLKVGVV-GGERVAKLNELIRLSE 402
                 ***************************************************************86.58***********977 PP

>> Enolase_N  Enolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.4   0.0     2e-24   8.9e-21       1     130 [.       4     124 ..       4     125 .. 0.92

  Alignments for each domain:
  == domain 1  score: 74.4 bits;  conditional E-value: 2e-24
                 EEEEEEEEEE-TTS-EEEEEEEEETTC-EEEEE--B-BSSSSSS-B----SSTTSGGGT--HHHHHHHHHTHHHHHTTSBTT-HHHHHHHHHHHH-STT CS
   Enolase_N   1 IkkvkareildSrGnpTvevevttedgalgraavpsGaStgekealelrDgdkkrylgkgvekavenvnekiapaligldvtdqeeiDkllielDgten 99 
                 I+++k+r i++SrG++T+ev++  e++ lgr ++psGaS+g++ea+ + +        +  e++++  ne+ a++ igl+ +d +++ ++l ++D+++n
  EPA05585.1   4 ITSIKGRIIYNSRGSKTIEVDILSENKFLGRVCAPSGASVGKYEAVSFPN--------EKPEESLRILNEN-AQKFIGLESSDLKTVHDTLRSIDQSPN 93 
                 899*******************************************6555........5778888877776.55667********************** PP

                 -TTT-HHHHHHHHHHHHHHHHHHHTS-HHHH CS
   Enolase_N 100 ksklGaNailavSlAvakaaAkakelplyry 130
                  +++G+  ++av++A ++ a+ka++ pl++ 
  EPA05585.1  94 YENIGGGLAFAVTIASMESASKALDKPLFQI 124
                 ****************************996 PP

>> MR_MLE_C  Enolase C-terminal domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   5.5e-08   0.00025      26     155 ..     211     358 ..     196     381 .. 0.80
   2 ?   -1.3   0.0       0.3   1.3e+03      97     119 ..     380     403 ..     363     406 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 5.5e-08
                 HHHHHHHHHHHHHHHHTTTSTSEEEEE-TTTS..................BHHHHHHHHHHH.GGGTESEEESSSSTTTHHHHHHHHHHHH.SSEEEES CS
    MR_MLE_C  26 dvaedvervravreavgpgddvdlmvDanqaw..................dlatAirvarel.eeldllwlEEPvppeddleglaelrara.sipiaag 104
                  ++  ++ ++ +  ++  g++v l vD+  +                   + ++ i++a  + ++++l + E+ v+ e    ++ael+ ++ +  +++g
  EPA05585.1 211 ALELSAKACENLGFTL--GKEVALGVDFASSTqwneekqkyvyqrggfvnSSEQQIEFAANIiNKYKLIYAEDAVHEE-AFSDMAELT-AKfPNTLVTG 305
                 4666666677777777..446699999888844488888889999999988999********556***********95.6********.6666678888 PP

                 TTS..SSHHHHHHHHHHTSESEEEEBHHHHTSHHHHHHHHHHHHHTT-EEEEB CS
    MR_MLE_C 105 Esl..ysradfrelleagavdivqpdvsrvgGitearkvaalaeafgvpvapH 155
                  +l  ++   + ++++ + + ++ ++v+++g +  a ++a++a++++++++  
  EPA05585.1 306 DDLtvTNKDILSKAIKLKSCNAAILKVNQAGSLYDAFEFAKVASQNNIKLITS 358
                 765115689999***********************************997654 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.3
                 H.SSEEEESTTSSSHHHHHHHHHH CS
    MR_MLE_C  97 a.sipiaagEslysradfrellea 119
                   ++ +++gE+++ + ++ +l e 
  EPA05585.1 380 MlKVGVVGGERVAKLNELIRLSEH 403
                 35789*******999999888665 PP

>> DUF155  Uncharacterised ACR, YagE family COG1723
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   5.4e-05      0.24      89     136 ..     282     329 ..     280     350 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.4e-05
      DUF155  89 dvlEesldellestekipkelakkgklklsrkellkktgellslrinl 136
                 +v+Ee++++++e t k+p++l ++ +l++++k++l+k  +l s  + +
  EPA05585.1 282 AVHEEAFSDMAELTAKFPNTLVTGDDLTVTNKDILSKAIKLKSCNAAI 329
                 69********************99999************998876554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.52
# Mc/sec: 2366.47
//
Query:       EPA05586.1  [L=216]
Description: GHMP kinase, N-terminal domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-17   63.2   0.2    3.3e-17   62.5   0.2    1.4  1  GHMP_kinases_N   GHMP kinases N terminal domain
      0.003   17.1   0.0     0.0076   15.8   0.0    1.7  1  GalKase_gal_bdg  Galactokinase galactose-binding signature


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.5   0.2   3.7e-21   3.3e-17       1      66 []      91     157 ..      91     157 .. 0.92

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 3.7e-21
                     EEEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHH.HH.HHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
  GHMP_kinases_N   1 divikseiPvgaGLGSSAAlavalvaAllallglsl.ee.aklaleaerlaqggngsggDvaasvyGg 66 
                     +i ++seiP g GLGSS+A++va++aA+ +l++ s  +e +++a+eaer +   n+sg D +++++Gg
      EPA05586.1  91 KIIVESEIPSGVGLGSSSACCVAGAAAISRLFEESTkKEiLEMAIEAERTIF-QNTSGADCTVCTFGG 157
                     5899****************************87764337********9986.7*************8 PP

>> GalKase_gal_bdg  Galactokinase galactose-binding signature
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   8.5e-07    0.0076      14      47 ..       5      38 ..       3      40 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 8.5e-07
                     EEEEEEEEEE--S-TTTT-EEEEEEEEEEEEEEE CS
  GalKase_gal_bdg 14 asAPGRvnLiGEHtDYngGfVlpmAieqdiyiav 47
                     asAPG   L GEH    g + + +Ai++++++ +
       EPA05586.1  5 ASAPGKAILFGEHFVVYGIKAILCAINKRVTVTA 38
                     79****************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       819  (0.0456802); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1326.46
//
Query:       EPA05587.1  [L=586]
Description: glutamine-fructose-6-phosphate transaminase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-50  168.9   3.6    3.2e-25   88.5   2.6    2.6  2  SIS       SIS domain
      1e-21   77.6   0.0    5.2e-21   75.2   0.0    2.1  2  GATase_6  Glutamine amidotransferase domain
    4.8e-16   58.8   0.4    2.2e-15   56.7   0.0    2.3  3  GATase_7  Glutamine amidotransferase domain
    1.1e-06   28.7   3.3    0.00039   20.4   0.6    3.6  3  SIS_2     SIS domain
    8.1e-05   21.7   0.0    0.00013   21.0   0.0    1.2  1  GATase_4  Glutamine amidotransferases class-II


Domain annotation for each model (and alignments):
>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.5   2.6   8.8e-29   3.2e-25       2     126 ..     281     404 ..     280     408 .. 0.97
   2 !   78.8   0.0   8.6e-26   3.1e-22       4     130 ..     445     568 ..     442     569 .. 0.93

  Alignments for each domain:
  == domain 1  score: 88.5 bits;  conditional E-value: 8.8e-29
                 HCTSSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHHTTSEEEEEESSTTSHHHHHSSE CS
         SIS   2 LakakriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelakergakiiaITdskgsplareadl 100
                 + ++++iy++G+Gtsy++a+ ++  l++ ++i v++  +sel+ +  ++i+++  +i+is+sge++d+++a++ ak+ + +ii+I +s +s+lare+ +
  EPA05587.1 281 IKNSNNIYITGSGTSYNAALIAKQVLAKYAKIKVDAIISSELQFS-SDTIEPNSTLIAISQSGESADVLDAVNIAKKVNCNIISIVNSLTSSLARESNI 378
                 67899****************************************.***************************************************** PP

                 EEEEEEECHCSSSHCHHHHHHHHHHH CS
         SIS 101 alyinaepetlvastksltaqlaald 126
                 ++ +n +pe++va+tks+t+q+++++
  EPA05587.1 379 VIGMNCGPEIGVAATKSFTSQMIVIY 404
                 ***********************986 PP

  == domain 2  score: 78.8 bits;  conditional E-value: 8.6e-26
                 TSSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHH.HHHHHHHHHHHHTTSEEEEEESSTTSHHHHHSSEE CS
         SIS   4 kakriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsget.kdlvaaaelakergakiiaITdskgsplareadla 101
                 +   iyvlG+G +y+ia e+alkl+e+++i++e+ + +elkhg+lal+d++  vi+i +++ t +d++ +a++ k+rgakii+I d+k++      d++
  EPA05587.1 445 EISDIYVLGRGIHYPIAIESALKLKELTYIHAEGIPGGELKHGPLALMDSNVFVIIINPNDSTySDTLTSAREIKARGAKIIGISDQKSDVY----DYW 539
                 5568******************************************************99999568999999*************9987754....899 PP

                 EEEEEECHCSSSHCHHHHHHHHHHHHHHH CS
         SIS 102 lyinaepetlvastksltaqlaaldalav 130
                 ++i++ +e  +++  +++ ql++++a++ 
  EPA05587.1 540 IEIPKTNELAYPISETIPIQLLSYYAALE 568
                 *************************9975 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.2   0.0   1.5e-24   5.2e-21      11     128 ..      64     186 ..      51     192 .. 0.79
   2 ?   -1.1   0.0      0.57     2e+03      42      62 ..     220     242 ..     213     252 .. 0.75

  Alignments for each domain:
  == domain 1  score: 75.2 bits;  conditional E-value: 1.5e-24
    GATase_6  11 edevalaHvRlaivglaeeegaqPfpsedgrlllvhNGeiynykelreelpalkglafrsrsDtevllall......eelG......eevlerlrGmfa 97 
                  ++++++H+R+a++g  +++ a+P ps++g+l++vhNG i+n+++l+ el++ +g+ f+s++Dtev+++ll                 +++++l+G +a
  EPA05587.1  64 PGKIGIGHTRWATHGKVTDANAHPHPSNSGKLAIVHNGIIENFEQLKIELEE-DGYVFKSETDTEVIANLLqknyenV--KnvkdaiIKTVSELEGHYA 159
                 5679************966666******************************.****************998666440..256566688888******* PP

    GATase_6  98 faiwdkrentlilardrlgvkplyyavdesg 128
                 f+++  ++++  la+ r+  +pl++++ ++ 
  EPA05587.1 160 FVAMF-ENGQ--LAAARFH-EPLIVGIGKDS 186
                 98765.3444..4444666.78888876443 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.57
    GATase_6  42 lllvhNGeiynyk..elreelpa 62 
                  +l +NGei + +  ++++e+++
  EPA05587.1 220 QILDFNGEIVKQQitKVSKEFAD 242
                 67779****99987766666655 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.7   0.0   6.1e-19   2.2e-15       8     116 ..      80     191 ..      71     196 .. 0.87
   2 ?   -2.5   0.0       1.3   4.5e+03      25      35 ..     221     231 ..     207     255 .. 0.64
   3 ?   -2.9   0.1       1.6   5.9e+03      20      46 ..     283     309 ..     279     316 .. 0.78

  Alignments for each domain:
  == domain 1  score: 56.7 bits;  conditional E-value: 6.1e-19
    GATase_7   8 dseagaQPmvssedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllallea.........ewgeealerlnGmfAfaiwdeeekrlllaRDrl 97 
                  ++a+a P   s++g+l+iv+nG i N+++l+ eLe+ g+ f++++Dtev+++ll++         + + +++++l+G +Af+ + e+  +l +aR + 
  EPA05587.1  80 VTDANAHPHP-SNSGKLAIVHNGIIENFEQLKIELEEDGYVFKSETDTEVIANLLQKnyenvknvkDAIIKTVSELEGHYAFVAMFENG-QLAAARFH- 175
                 4567777888.689*************************************************9999999***************9988.99999985. PP

    GATase_7  98 GikPLyygedkgdallfaS 116
                    PL++g  k d+++++S
  EPA05587.1 176 --EPLIVGIGK-DSYFLSS 191
                 ..899999886.5766666 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.3
    GATase_7  25 vivfnGeiyNy 35 
                 ++ fnGei+ +
  EPA05587.1 221 ILDFNGEIVKQ 231
                 55567776543 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.6
    GATase_7  20 edgrlvivfnGeiyNykelreeLeakg 46 
                 +++++ i+ +G+ yN   + ++  ak 
  EPA05587.1 283 NSNNIYITGSGTSYNAALIAKQVLAKY 309
                 567899999999999999988877764 PP

>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.1    0.0028       9.9      20      73 ..     269     324 ..     252     328 .. 0.70
   2 !   20.4   0.6   1.1e-07   0.00039      98     137 ..     326     365 ..     301     366 .. 0.81
   3 ?    1.1   0.0     0.099   3.6e+02     120     137 ..     512     529 ..     492     530 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0028
                 HHHHHHHHHHHHHHTT--EEEEESGGG...HHHHHHTSSSTT-BTTEEEE--GGGSS CS
       SIS_2  20 aiekaaeliadslenggkvlvfGsGhS...aalaeelaaragglaeferialpalal 73 
                 +  +a++  a+ ++n + +++ GsG S   a++a+++ a++ + +++++i+  +l +
  EPA05587.1 269 NTGNAIKNAAEYIKNSNNIYITGSGTSynaALIAKQVLAKYAK-IKVDAIISSELQF 324
                 44567888889999***********884335566666666655.3666666666665 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 1.1e-07
                 HTT--TT-EEEEE-SS--SHHHHHHHHHHHHHT-EEEEEE CS
       SIS_2  98 lvrlkpgDvLlviSnsGnnavvveaaeaakergmkviAlt 137
                 +  ++p+ +L+ iS+sG++a v++a++ ak++ +++i ++
  EPA05587.1 326 SDTIEPNSTLIAISQSGESADVLDAVNIAKKVNCNIISIV 365
                 34689********************************997 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.099
                 HHHHHHHHHHT-EEEEEE CS
       SIS_2 120 veaaeaakergmkviAlt 137
                 +  a++ k+rg+k+i+++
  EPA05587.1 512 LTSAREIKARGAKIIGIS 529
                 66799***********95 PP

>> GATase_4  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   3.7e-08   0.00013      72     188 ..      66     176 ..      55     187 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3.7e-08
    GATase_4  72 knvvaHiRkatqGevklenthpFvRelwgrewifAHnGdlkeykpkl....egrfePvGsTDsElafCelleelasrfekaepsaeeleralaelakei 166
                 k+ + H R at+G+v+++n+hp   + +  +  + HnG ++++++      e+ +    +TD+E++   l   l++++    ++++++++a+ + ++e+
  EPA05587.1  66 KIGIGHTRWATHGKVTDANAHPHPSNSG--KLAIVHNGIIENFEQLKieleEDGYVFKSETDTEVIA-NL---LQKNY----ENVKNVKDAIIKTVSEL 154
                 67799*****************976655..56667*****99988766667778888899***9763.34...44455....46788999999999999 PP

    GATase_4 167 aelGvfnlllsdgralfahast 188
                 + +  f  ++ +g+   a+ ++
  EPA05587.1 155 EGHYAFVAMFENGQLAAARFHE 176
                 9999999999999987776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (586 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       916  (0.0510904); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.66u 0.27s 00:00:00.93 Elapsed: 00:00:00.46
# Mc/sec: 3841.74
//
Query:       EPA05588.1  [L=277]
Description: memo-like protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-82  275.5   0.0    4.1e-82  275.4   0.0    1.0  1  Memo      Memo-like protein
     0.0034   16.5   0.0     0.0044   16.1   0.0    1.2  1  LigB      Catalytic LigB subunit of aromatic ring-opening dio


Domain annotation for each model (and alignments):
>> Memo  Memo-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  275.4   0.0   4.6e-86   4.1e-82       2     270 ..       6     274 ..       5     275 .. 0.97

  Alignments for each domain:
  == domain 1  score: 275.4 bits;  conditional E-value: 4.6e-86
        Memo   2 aavAGsfYpedeeelkkqleeflekntgkkei........arviisPHagyvysgevaakayaelesskvervvilGpsHtilgskvsvlaaseleTPl 92 
                 +avAG fY+ +++elkk ++ ++++++g+++i           +i+PHagy ysg++a+++++e++s+ +e ++i+Gp+H ++gs v+ ++ s+++TPl
  EPA05588.1   6 PAVAGMFYSGEKKELKKSINDCFLHKFGPGKIppsdnkkkIFGVICPHAGYAYSGPIACHSFYEISSNLPELFIIVGPNHWGIGSSVATMKDSKWQTPL 104
                 89********************************997422223466***************************************************** PP

        Memo  93 GdlkvDeelveeLvkkeeiadldetaalaEHSlEvqlpfLkellkekkfkivPilvsaqseetakevgealakvikdesnlviiSsDlsHygrrFgspq 191
                 G+++vD+e +ee+ + ++i+++d+ ++  EHSlEvq+p+L+e+ k+  f+i+Pi++  qs+e+a ++g+a+a++++++++++i SsD++Hy+     p+
  EPA05588.1 105 GEVEVDSETAEEISNITKIIEVDNFSHSREHSLEVQIPILQEISKK--FRILPIVLINQSKEVAIQLGSAIANIARKKKVMIIGSSDFTHYE-----PN 196
                 *******************************************999..********************************************.....** PP

        Memo 192 eiaesieDrevikaleelneeelkeylektnnticGekpiavilkalkklgakkakllkYaqssdvtsdtdsvVsyasl 270
                 e a+++ D+ +i+ + +l+ + ++++l+k++++ cG++ ia+++ a k+lga+k++llkYa+s+d+t+dt+svV+y+s+
  EPA05588.1 197 EFAHEQ-DAALIEPILKLDVDRFYDVLNKKDISACGYGAIASTMIACKELGATKGELLKYATSGDITGDTSSVVGYGSI 274
                 *****9.*********************************************************************997 PP

>> LigB  Catalytic LigB subunit of aromatic ring-opening dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   4.9e-07    0.0044      63     200 ..      86     208 ..      68     254 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.9e-07
        LigB  63 lgvaeefeaiddfgkflprleyelkgnpeLaekiaealkksgidlavesnsmklDHGtlvPLelmlpdeakvpvikvslntvaypllsferlykLGeAl 161
                  g ++   +++d++     + +e++++ e ae+i + +k  ++d      s   +H + v + ++ + + k + ++++l+       s e   +LG A+
  EPA05588.1  86 WGIGSSVATMKDSK--WQTPLGEVEVDSETAEEISNITKIIEVDN-F---SHSREHSLEVQIPILQEISKKFRILPIVLIN-----QSKEVAIQLGSAI 173
                 44455556667766..77788999999999999999999888884.3...3444666666666666644589999999999.....89*********** PP

        LigB 162 rkaveeldknvlilgsGglsHqlegdeaakadaqtllln 200
                 +++     k+v+i+gs +++H+ +++ a ++da   l++
  EPA05588.1 174 ANIA--RKKKVMIIGSSDFTHYEPNEFAHEQDAA--LIE 208
                 *987..58*************9888888877774..233 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1996.15
//
Query:       EPA05589.1  [L=374]
Description: hypothetical protein BG20_I0427 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.1e-09   36.1   0.0    1.8e-08   35.0   0.0    1.5  1  Radical_SAM  Radical SAM superfamily
  ------ inclusion threshold ------
      0.056   13.5   0.1       0.17   11.9   0.0    1.8  1  B12-binding  B12 binding domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.0     2e-12   1.8e-08       1     122 [.     217     351 ..     217     368 .. 0.80

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 2e-12
                  EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS...........TTHHHHHHHHHHTC...CCTEEEEEEE CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxxx...xxxxxxxxxx RF
  Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly...........pdfvellerlakla...vpgiritvet 84 
                  ++ +rgC ++C fC++++     +  ++l++e++ +e+k++  + g + ++l+++e lly           + ++el++ l+ l        ++t+++
   EPA05589.1 217 IEAMRGCGRGCDFCDVNK-----RSKKDLPLERLQHEAKIN-LDYGFDSIWLHSDEMLLYgcdnrdfipnrDAITELWKGLKSLGanfIGTTHMTFSA 308
                  5789*************5.....9*****************.8*************************999888888888888856444444444444 PP

                  CSSCHG.HHHHHHHHHTT....-SEEEEEEBSSSHHHHHHHHT CS
                  xxxxxx.xxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM  85 ngtlpd.eeklerllelg....vdrvslgleaaddekvlklmn 122
                   +  p+  +++  + +      +   +lg+e++ + +v+k+++
   EPA05589.1 309 VAADPElMRQISSINKQDetgrWLATNLGIETVAPNMVKKHLG 351
                  444444644444444444777999999********99999985 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.9e-05      0.17      68     117 ..     132     179 ..     120     183 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.9e-05
  B12-binding  68 vkelvellkrirprvkvvvGGahp.sldpeetleak...lgiddvvvgegedal 117
                  ++++++l+k++  +++vvvGG ++ +l+  +    +    gid vvvge+++ +
   EPA05589.1 132 CANIIQLKKKY--DFHVVVGGNGAwELAKSD----RmqiHGIDTVVVGEADELA 179
                  46788888888..8899***98852334444....2447**********98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2682.33
//
Query:       EPA05590.1  [L=323]
Description: polyprenyl synthetase, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-70  237.3   0.1    1.7e-70  237.0   0.1    1.1  1  polyprenyl_synt  Polyprenyl synthetase
    0.00092   18.6   0.0     0.0017   17.8   0.0    1.4  1  Terpene_synth_C  Terpene synthase family, metal binding domai


Domain annotation for each model (and alignments):
>> polyprenyl_synt  Polyprenyl synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  237.0   0.1   1.9e-74   1.7e-70       3     254 ..      28     277 ..      26     279 .. 0.94

  Alignments for each domain:
  == domain 1  score: 237.0 bits;  conditional E-value: 1.9e-74
                      HHHHHHHHHHHSSS--HHHHHHHHHHHHHSCGHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEETTEE-HHHCTCHHHHHHHHHHHHHHHHH CS
  polyprenyl_synt   3 lleealeylveagGKrlRpllvllaaealkeeeeelekaavlawivellhaasLvhDDimDdsetRRGqpcahrlvGnklAindgdfllarafe 96 
                       l++a+++l+ +gGKrlRp +v++++++l+    ++ +a  +a +ve++h+++LvhDDimD++e+R G p++h+++G+++Ai++gd+l+++a++
       EPA05590.1  28 SLYDAASHLIVHGGKRLRPYMVIKSCQILG---GNTATAMPAASAVEMIHNFTLVHDDIMDNDEMRHGVPTVHKKFGMPIAILAGDVLFSKAYQ 118
                      57778888888*******************...35589******************************************************** PP

                      HHHHHH..STT.HHHHHHHHHHHHHHHHHHHHHHHHTTTTTCCC.SHHHHHHHHHHHTHHHCHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH CS
  polyprenyl_synt  97 llaklf..eks.lellelfsevllqtveGqlldleeekdddlskfsleeyleivkyKTaylfalpvalaallagasdeelealkdiglelGlaF 187
                      ++++ +  ++s ++l++ +++++++++eGqlld++ ++++ +  ++ +ey +++ +KTa+lf +++ ++a++a  +++++ +l+++g++lG+aF
       EPA05590.1 119 IISESNisKDStVQLVSRLAKACVDVCEGQLLDVKMAEEKRI--PTQKEYIAMIGKKTAALFDVSCSMGAICATNNQKDILNLSNFGKNLGIAF 210
                      ***999986667**********************66643444..599***************************999***************** PP

                      HHHHHHHHHHS-HHHHSS-TSHHHHTT---HHHHHHHHCT-HHHHHHHHHHTTSSHHHHHHHHHHHH CS
  polyprenyl_synt 188 QiqDDylDlfgdpevlgKpagtDiqegkctlpilkalelaspeqrkvlkeilgkkaekeedvkeale 254
                      Qi DD++ ++gd++ + Kp+g+D++egk +lpil a++l++ +++k++ +++g+ +++++d+k+a++
       EPA05590.1 211 QITDDLIGVMGDSKITKKPVGNDLREGKKSLPILMAIKLSKGKDHKIILKAFGNPKATKNDLKNAVD 277
                      *****************************************************9999*****99986 PP

>> Terpene_synth_C  Terpene synthase family, metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.9e-07    0.0017     114     229 ..     113     222 ..     108     230 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.9e-07
  Terpene_synth_C 114 ykallntfneledelekeeksdrvskylkeawkelvkaylkeakWreekyvPsfeEylenslvssglpllllaalvgmgdevtkeafewvasyp 207
                      +++ +++++e   +++k+    ++++ l +a+ ++++  l  +k++eek++P+ +Ey+ +   +  +++l+ +++  mg ++ +++ + +++ +
       EPA05590.1 113 FSKAYQIISES--NISKDSTV-QLVSRLAKACVDVCEGQLLDVKMAEEKRIPTQKEYIAMIGKK--TAALFDVSC-SMGAICATNNQKDILNLS 200
                      66666666654..56664444.56689999***************************9874444..445555555.667765665568899999 PP

  Terpene_synth_C 208 klvkalstilRLlnDiasyere 229
                      ++ k l + + +++D+ +  ++
       EPA05590.1 201 NFGKNLGIAFQITDDLIGVMGD 222
                      ***************9877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2182.82
//
Query:       EPA05591.1  [L=106]
Description: GHMP kinase C-terminal domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-14   53.8   0.1    2.3e-14   53.5   0.1    1.1  1  GHMP_kinases_C  GHMP kinases C terminal


Domain annotation for each model (and alignments):
>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.5   0.1   1.3e-18   2.3e-14       5      83 ..      16      90 ..       7      92 .. 0.93

  Alignments for each domain:
  == domain 1  score: 53.5 bits;  conditional E-value: 1.3e-18
  GHMP_kinases_C  5 lergdlellgellnlsqrselkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqvaralreef 83
                    l+++dle lg+ ++++ +   ++ +gi+++ l+++++++ e+  +gak++GaGgG++++al+ d+++ e+ +++lre  
      EPA05591.1 16 LKNNDLEGLGKSMHENEEY--LEILGISNDKLRDMVKIAGEAS-FGAKITGAGGGGCIIALT-DESNLEKTILKLRERN 90
                    578***************6..778******************9.*****************9.************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 785.10
//
Query:       EPA05592.1  [L=385]
Description: putative cysteine desulfurase NifS [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.7e-91  305.0   0.1    7.9e-91  304.8   0.1    1.0  1  Aminotran_5      Aminotransferase class-V
    2.1e-07   30.5   0.0    3.4e-07   29.8   0.0    1.3  1  Beta_elim_lyase  Beta-eliminating lyase
    0.00016   21.1   0.0    0.00029   20.2   0.0    1.4  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
     0.0027   16.3   0.0      0.004   15.7   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
  ------ inclusion threshold ------
      0.054   12.2   0.0       0.12   11.0   0.0    1.6  2  Pyridoxal_deC    Pyridoxal-dependent decarboxylase conserved 


Domain annotation for each model (and alignments):
>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  304.8   0.1   2.2e-94   7.9e-91       1     369 [.       2     360 ..       2     362 .. 0.93

  Alignments for each domain:
  == domain 1  score: 304.8 bits;  conditional E-value: 2.2e-94
                  EEEBTTTS----HHHHHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSH CS
  Aminotran_5   1 iyldsaAttqkpqeVldalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaeh 98 
                  iyld+aA+tq+ ++Vl+++  y+++ ++n+ +s+h++g  a+ka+e+ar+++a+linaes +ei+ftsG+te++n++++++ +  +p  +i+++++eh
   EPA05592.1   2 IYLDNAASTQIHENVLESMLPYLKEQYGNP-SSIHRYGRLAHKAIEKARKQIAQLINAES-SEILFTSGGTESNNTALYGISE-KRPNSQIITSSIEH 96 
                  8*****************************.****************************9.********************54.9************* PP

                  GGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEE CS
  Aminotran_5  99 hanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavghipidvkklgvDfla 196
                   a l p ++la + g++v++ip+d++g+++l+ le+ l+++t+lv+i+ ++n+ Gti+p+ +i+kl+ +k++ +++Da qavg+ipidvkklg+D+l+
   EPA05592.1  97 DAILEPSKRLA-KNGYDVVYIPVDDKGTVNLEVLENSLSDNTCLVSIMFANNEVGTIEPISKITKLCNEKNIPFHTDAIQAVGKIPIDVKKLGIDLLS 193
                  **********9.67************************************************************************************ PP

                  EETTTTTSSTT-EEEEEEHHHHHTS..SS.STTSEEEEETTEEEEHCTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHH.HHHHHHCT CS
  Aminotran_5 197 fsghKllgPtGiGvlyvrkellekleplllggemveevsleettfaeapskfeaGTpnvagiiglgaaleyleeigleaiekhekelae.yllerlks 293
                  +s+hK++gP+GiG+lyvrk     + p+ lgg+       +e +       +++GT+nva+i+g+g+a e+  +++l++   h k+l++  +l+ lk+
   EPA05592.1 194 ISSHKINGPKGIGALYVRK--GIDIDPIILGGG-------QENG-------LRSGTENVANIVGFGKACEIA-NLNLSENIFHMKKLRDiLVLKILKE 274
                  *******************..8899********.......8888.......99******************9.5555555555555555166789999 PP

                  STTEEEES.-B-CTCBSEEEEEETTCSHHHHHHHHHHTTEEEEEE-TTT....HHHHHHTT.S.............-EEEEE--TTS-HHHHH CS
  Aminotran_5 294 lpgvrlygpdkaerrasivsfnfkgvhaedvatlLdeegIavrsGhhca....qplmkrlale.............gtvRaSlyiynteeevd 369
                  +pgv l+g ++++r ++   f+f gv  ed+   Lde+gIa ++G++c+    + +      +             g++R+ l++ynte ++d
   EPA05592.1 275 IPGVSLNG-HPENRLPNNAHFTFLGVAGEDLIIKLDEYGIAASTGSACSvhtqKAS------HvlkamgysyeqitGSLRLTLGLYNTESQID 360
                  ******99.79**************************************6665333......33444448888888***************98 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0   9.5e-11   3.4e-07      34     168 ..      45     173 ..      27     215 .. 0.80

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 9.5e-11
                      HHHHHHHHHHHTT-S..EEEEES-HHHHHHHHHHHH-..-TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHHHHHHS--S-T CS
  Beta_elim_lyase  34 vnrLedavaelfgke..aalfvpqGtaAnsillkill..qrgeevivtepahihfdetgaiaelagvklrdlknkeaGkmdlekleaaikevga 123
                      +++  +++a+l+ +e   +lf+  Gt +n+ +l  +   ++++++i ++  h    e     + +g  ++ ++ +++G+++le le+ + +   
       EPA05592.1  45 IEKARKQIAQLINAEssEILFTSGGTESNNTALYGISekRPNSQIITSSIEHDAILEPSKRLAKNGYDVVYIPVDDKGTVNLEVLENSLSD--- 135
                      56667778888777654789***********9955554344555555555999999998888889************************99... PP

                      TS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEE CS
  Beta_elim_lyase 124 heekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDg 168
                         ++ l+s+  +nn    +v ++e + ++++++++++ip+h D+
       EPA05592.1 136 ---NTCLVSIMFANN----EVGTIEPISKITKLCNEKNIPFHTDA 173
                      ...799*********....5889999******************8 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   8.2e-08   0.00029      39     151 ..      61     179 ..      39     189 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 8.2e-08
                      SEEEEESSHHHHHHHHHHHTTTT.TT-EEEEESSS-THHHHH...HHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTE..EEEEEB.-GGGB-- CS
  DegT_DnrJ_EryC1  39 khaiavssGtaAlhlaLralgvg.pgdeVIvpsltFvatana...vlelgakpvfvDvdpdtynidpaaieaaitert..kaIlpV.hlyGqva 125
                         + +s Gt+++  aL  ++ + p+ ++I+ s+   a  ++    +++g+++v++ vd d  +++ + +e+ +  +t    I+ + + +G + 
       EPA05592.1  61 SEILFTSGGTESNNTALYGISEKrPNSQIITSSIEHDAILEPskrLAKNGYDVVYIPVD-DKGTVNLEVLENSLSDNTclVSIMFAnNEVGTIE 153
                      456778999********99777779************998763337789**********.8999**************996777762569**** PP

                      -HHHHHHHHHHCT-EEEEE-TT-TT- CS
  DegT_DnrJ_EryC1 126 dmdalkaiaakhglkvieDaAhAlGa 151
                       +++++++++++++++  Da +A+G 
       EPA05592.1 154 PISKITKLCNEKNIPFHTDAIQAVGK 179
                      ************************95 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.1e-06     0.004      41     198 ..      32     198 ..       8     205 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.1e-06
                      SSS-SBTTT--HHHHHHHHHHHHHHT-SEE..EEESSHHHHHHHHHHTTS-T..TEE....EEEESTSSHHHHHHHHHTHHHTTCEEEEESTTS CS
  Cys_Met_Meta_PP  41 ekgyeYsRsgnptrsvleeriaaLeggeaa..lavssGmaAiaaailallka..Gde....ivvsddlYggtqrllkkvlkklgievkfvdtsd 126
                      ++ + Y+R+     +   ++ia+L ++e++  l +s G+ + ++a+  + ++   ++     + +d + ++++rl k+ +  + i v+   t +
       EPA05592.1  32 SSIHRYGRLAHKAIEKARKQIAQLINAESSeiLFTSGGTESNNTALYGISEKrpNSQiitsSIEHDAILEPSKRLAKNGYDVVYIPVDDKGTVN 125
                      444899999999999999********96543155555666777788888876533442222334467788888888888888888888888899 PP

                      HHHHHHHCCTTEEEEEEESS-TTTT----HHHHHHHHHHTT-EEEEEGTTTHT.TTS-GGGGT-SEEEEETTT CS
  Cys_Met_Meta_PP 127 leelekaikentklvylEtptnpllkvvDiekiaklakkagvlvvvDntfasp.llqrplklgaDivvhSaTK 198
                      le le+ +++nt lv +    n +  +  i ki+kl+ +++++   D+  a + + +   klg+D+   S  K
       EPA05592.1 126 LEVLENSLSDNTCLVSIMFANNEVGTIEPISKITKLCNEKNIPFHTDAIQAVGkIPIDVKKLGIDLLSISSHK 198
                      999********************************************99988856666667888877666555 PP

>> Pyridoxal_deC  Pyridoxal-dependent decarboxylase conserved domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   3.4e-05      0.12     169     238 ..     113     176 ..      87     208 .. 0.81
   2 ?   -2.8   0.0      0.55     2e+03     330     359 ..     350     379 ..     346     380 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.4e-05
                    EEEE--BTTTBB-HHHHHHHHHHHHCTT.EEEEEEEEBS-TTT-BB--HHHHHHHHHHCT-EEEEE-TTG CS
  Pyridoxal_deC 169 lrvipldengklrgaalekaieedkekGlipffvvatlGttvlgaFddlkelgdicekydlwlHvDAAya 238
                    + +ip+d++g++  + le+ + ++         v   +    +g  + ++++ ++c++ +++ H DA  a
     EPA05592.1 113 VVYIPVDDKGTVNLEVLENSLSDNTCL------VSIMFANNEVGTIEPISKITKLCNEKNIPFHTDAIQA 176
                    678999999988888888777655444......55556666677789********************655 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.55
                    HHHHHHHHHHHHHHHHHHHHHHHHHTTTTE CS
  Pyridoxal_deC 330 lGveglqnqirksvelakyleklirkderf 359
                    lG  + + qi+++v++ k++++++r  ++f
     EPA05592.1 350 LGLYNTESQIDETVNILKKVTAELRSVSPF 379
                    7999999*************9999988877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 2382.48
//
Query:       EPA05593.1  [L=215]
Description: YjeF N-terminal domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-46  158.5   0.0    1.6e-46  158.3   0.0    1.0  1  YjeF_N    YjeF-related protein N-terminus


Domain annotation for each model (and alignments):
>> YjeF_N  YjeF-related protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.3   0.0   9.1e-51   1.6e-46       3     171 .]      24     188 ..      22     188 .. 0.94

  Alignments for each domain:
  == domain 1  score: 158.3 bits;  conditional E-value: 9.1e-51
      YjeF_N   3 eLmenagravaevlrallgnspaekkvlvlvGsgnnGgdglaaArhLaqegakVtv.llleeeekldedaeralellkka.ggkvveekpeedleekls 99 
                  +menag+a+++ l ++l +++++kk+l+ vG gnnGgdgl++ArhLa  ga+Vtv ll ++++  +e+  +++++l+k+  +k+++  +++++     
  EPA05593.1  24 FMMENAGAAAVKRLVEKL-GNVESKKILIYVGMGNNGGDGLVMARHLAGYGANVTVhLLGTPDKIKTEESSWNWSILEKMpSVKLLTGGKFDYDF---- 117
                 69**********777777.59***********************************888888889**************9457888888888874.... PP

      YjeF_N 100 apvdlviDAllGiglrgelreelaeliewlnsseapvlavDiPSGldadtGavsgtavkadvtvtfgapkrg 171
                  ++d+++D++lG+g++g++re++ ++i+ +n+++ + ++vD+PSGld++tG+ ++++vk+d+tvtf+ +k+g
  EPA05593.1 118 -TPDVIVDGILGTGISGDIREPYVSAINFINNAKCFKFSVDVPSGLDPQTGETANIYVKSDMTVTFHKMKQG 188
                 .6********************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1531.16
//
Query:       EPA05594.1  [L=182]
Description: hypothetical protein BG20_I2598 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.9e-09   36.1   0.4    1.5e-08   35.2   0.4    1.4  1  CxxCxxCC  Putative zinc- or iron-chelating domain


Domain annotation for each model (and alignments):
>> CxxCxxCC  Putative zinc- or iron-chelating domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.4   8.1e-13   1.5e-08       1      84 [.      12     120 ..      12     121 .. 0.87

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 8.1e-13
    CxxCxxCC   1 eCkeC.gaCCkelkvklteedlerlkaaevaeeeeeskkiak....................adgrCvfldeetk..lCkiYeeRpkicrlfpas..ek 74 
                 +C +C  +CCke+ + ++++d+ rl+       +++ + +                      ++g C+fl+e+ +  +C++   +p +c+ +p+   + 
  EPA05594.1  12 PCVSChTNCCKEYVIFVNAHDIYRLSVGLGLPPDNFLEIYGAkdyslgikvkeglldlalkqKNGGCTFLEETGDifRCTVNDFKPGVCKSYPFQmkDG 110
                 5****99*******************999999999888887789***************************998899*****************86433 PP

    CxxCxxCC  75 eellaraetC 84 
                 + ++  +++C
  EPA05594.1 111 KLTQMDEKMC 120
                 3333344455 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1313.78
//
Query:       EPA05595.1  [L=37]
Description: hypothetical protein BG20_I2597, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.30s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 247.27
//
Query:       EPA05596.1  [L=77]
Description: hypothetical protein BG20_I1064 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1021  (0.0569468); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 555.54
//
Query:       EPA05597.1  [L=92]
Description: hypothetical protein BG20_I1048 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-06   26.6   0.1    5.4e-06   26.4   0.1    1.0  1  TMEM51           Transmembrane protein 51
     0.0021   17.8   0.1     0.0027   17.4   0.1    1.1  1  Oxidored_q3      NADH-ubiquinone/plastoquinone oxidoreductase
     0.0028   17.4   0.3     0.0034   17.1   0.3    1.0  1  Tetraspanin      Tetraspanin family
     0.0065   16.8   0.1       0.12   12.7   0.0    2.0  2  MnhB             Domain related to MnhB subunit of Na+/H+ ant
  ------ inclusion threshold ------
      0.032   14.4   0.1        1.3    9.3   0.0    2.0  2  COX2_TM          Cytochrome C oxidase subunit II, transmembra
      0.067   12.6   0.0      0.084   12.3   0.0    1.2  1  SfLAP            Sap, sulfolipid-1-addressing protein
      0.095   12.4   0.0       0.11   12.2   0.0    1.0  1  7tm_3            7 transmembrane sweet-taste receptor of 3 GC
      0.095   12.8   0.3        0.2   11.8   0.0    1.7  2  OSTbeta          Organic solute transporter subunit beta prot
       0.16   10.7   0.0       0.21   10.3   0.0    1.1  1  DUF2207          Predicted membrane protein (DUF2207)
       0.17   12.4   0.7       0.36   11.3   0.5    1.6  1  DUF202           Domain of unknown function (DUF202)
       0.49   10.4   7.0       0.64   10.0   0.4    2.3  2  Gram_pos_anchor  LPXTG cell wall anchor motif
       0.59    9.6   0.0       0.59    9.6   0.0    2.1  2  ATP1G1_PLM_MAT8  ATP1G1/PLM/MAT8 family
          1    9.9   4.0         18    5.9   0.0    2.2  2  DUF3899          Domain of unknown function (DUF3899)
        1.7    8.8   4.8         12    6.1   0.1    2.1  2  DUF872           Eukaryotic protein of unknown function (DUF8
        3.2    8.1   9.3         49    4.3   9.0    2.0  1  DUF4064          Protein of unknown function (DUF4064)


Domain annotation for each model (and alignments):
>> TMEM51  Transmembrane protein 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.1   4.6e-09   5.4e-06      19      94 ..      11      86 ..       6      92 .] 0.68

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 4.6e-09
      TMEM51 19 givmivWsvvPg.eseadkpkasanssskpdkdsgkeek.ksktssvAyVLvGaGvalLlLsicLgirdkkrarqeee 94
                gi+m+v  +v   + +ad p  +++++++   d   +++ ++   ++A +L+G+G +l+l+s  +g r k++ + e+ 
  EPA05597.1 11 GIIMLVVGIVLIiFINADVPVGQSGMTEEEVIDLMIKQQeNKDMNTLAGILIGVGFMLILIS--FGARRKRKDSPEKV 86
                5555555555431344578888888888877776666662445689*********9999977..68999999876554 PP

>> Oxidored_q3  NADH-ubiquinone/plastoquinone oxidoreductase chain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   2.3e-06    0.0027      44      95 ..       7      75 ..       6      91 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.3e-06
                 IIIIIHHHHHHHHHHHS..................STTS----TTCHHHHHHHHHHHHHHHHHHHTT--. CS
  Oxidored_q3 44 vYvGAilvlflFvimll..................esaeeeepeslsrslalaalligllllalllllll 95
                 +++G+i++l++ +++++                    + + ++++ + +++la++lig++++++l+ +  
   EPA05597.1  7 IFAGGIIMLVVGIVLIIfinadvpvgqsgmteeevI-DLMIKQQENKDMNTLAGILIGVGFMLILISFGA 75
                 89*******99999999**************99852.35566778899999999******9999987744 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.3   2.9e-06    0.0034      14      65 ..       9      73 ..       5      79 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.9e-06
                 XXXXXXXXXXXXXXX.............XXX.....................XXXXXXXXXXXXX CS
                 xxxxxxxxxxxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Tetraspanin 14 ligivllavGvwlrl.............khaeaalacllsesaedpailaillivvGvllfllgf 65
                   gi++l+vG+ l++              ++e  +   ++++++d ++la +li vG++l+l++f
   EPA05597.1  9 AGGIIMLVVGIVLIIfinadvpvgqsgmTEEEVIDLMIKQQENKDMNTLAGILIGVGFMLILISF 73
                 4566666666555555666678888888666667777778899999999999**********998 PP

>> MnhB  Domain related to MnhB subunit of Na+/H+ antiporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1      0.15   1.9e+02      32      47 ..       8      23 ..       5      46 .. 0.65
   2 !   12.7   0.0   9.9e-05      0.12      34      62 ..      58      86 ..      57      91 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.15
        MnhB 32 FqgGlilaaalillyl 47
                F+gG+i+ +  i+l++
  EPA05597.1  8 FAGGIIMLVVGIVLII 23
                5555554444333333 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 9.9e-05
        MnhB 34 gGlilaaalillylafgleelekllrvkl 62
                +G++++++++l++++fg+++++k ++ k+
  EPA05597.1 58 AGILIGVGFMLILISFGARRKRKDSPEKV 86
                9*******************888776664 PP

>> COX2_TM  Cytochrome C oxidase subunit II, transmembrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.3     0.071        85      33      68 ..      11      43 ..       2      46 .. 0.66
   2 ?    9.3   0.0    0.0011       1.3      23      59 ..      49      85 ..      43      90 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.071
     COX2_TM 33 lililVlyilvlilvefrrrknkitakylvhgqeiE 68
                 i++lV++i+++i ++      ++ ++ +++ ++i+
  EPA05597.1 11 GIIMLVVGIVLIIFIN---ADVPVGQSGMTEEEVID 43
                5667777776666666...56677777777777666 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0011
     COX2_TM 23 lhdyilliltlililVlyilvlilvefrrrknkitak 59
                 +++ +  l+ ili V ++l+li +  rr++++ ++k
  EPA05597.1 49 QENKDMNTLAGILIGVGFMLILISFGARRKRKDSPEK 85
                56778999***************99988877777766 PP

>> SfLAP  Sap, sulfolipid-1-addressing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   7.1e-05     0.084      36      99 ..       9      86 ..       7      92 .] 0.75

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.1e-05
       SfLAP 36 vgwlvvlvalglivlfvlrslls.............gasaa......pssaikalqivlGvlllllaaveavrrpkassrsel 99
                +g++++lv+++++++f+ ++++                            ++  + i++G +l+l+++   ++r  ++s++++
  EPA05597.1  9 AGGIIMLVVGIVLIIFINADVPVgqsgmteeevidlM---IkqqenkDMNTLAGILIGVGFMLILISFGARRKR--KDSPEKV 86
                799*******************877766555555551...0555555889999999**********99888888..4444444 PP

>> 7tm_3  7 transmembrane sweet-taste receptor of 3 GCPR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   9.5e-05      0.11      98     172 ..       7      80 ..       2      89 .. 0.51

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.5e-05
       7tm_3  98 llllvlllvlvqviillvwtlidplstrek..seeereevileC....ssssysdiffllllgykglllllgtflafktrk 172
                 ++   ++++lv  i+l++   i+ + +  +  +  ++eevi  +    +  + ++   ++l+g +g++l+l  f a++ rk
  EPA05597.1   7 IFA-GGIIMLVVGIVLIIF--INADVPVGQsgM--TEEEVIDLMikqqE-NKDMNTLAGILIG-VGFMLILISFGARRKRK 80 
                 444.455555555555555..332222121222..23334333357433.4677777788777.66666666666666555 PP

>> OSTbeta  Organic solute transporter subunit beta protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.2       2.6   3.1e+03      42      53 ..      11      22 ..       5      28 .. 0.64
   2 ?   11.8   0.0   0.00017       0.2      37      69 ..      53      85 ..      48      92 .] 0.83

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2.6
     OSTbeta 42 savvvvisvvLL 53
                 ++ +v+++vL+
  EPA05597.1 11 GIIMLVVGIVLI 22
                456666777765 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00017
     OSTbeta 37 siLvLsavvvvisvvLLarsiqanRnrKiqpqe 69
                 + +L+ + + ++++L+ +s  a R+rK  p++
  EPA05597.1 53 DMNTLAGILIGVGFMLILISFGARRKRKDSPEK 85
                677899**********************99544 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00017      0.21     382     435 ..       6      77 ..       3      89 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00017
     DUF2207 382 klsalglgliilglilillallllvll.....................lvfllilllillliaiivlllfsrllg 435
                 k+ a g++ +++g++li+++++ + ++                     ++ l+ +l+++++++i++ + +    +
  EPA05597.1   6 KIFAGGIIMLVVGIVLIIFINADVPVGqsgmteeevidlmikqqenkdMNTLAGILIGVGFMLILISFGA---RR 77 
                 56677888888888888888888777799****************7654444444444444444333333...22 PP

>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.5    0.0003      0.36      18      64 ..      12      78 ..      10      82 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0003
      DUF202 18 lalialglallrffl.....................tgepsalgkilglilivlgiltllvglvrylr 64
                + ++++g++l+ f +                     ++e+++++ ++g ili++g++++l+++   ++
  EPA05597.1 12 IIMLVVGIVLIIFINadvpvgqsgmteeevidlmikQQENKDMNTLAG-ILIGVGFMLILISFGARRK 78
                789999999999888999999999999999999998778888666666.8999999999988766555 PP

>> Gram_pos_anchor  LPXTG cell wall anchor motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   1.3     0.061        73      22      34 ..       9      21 ..       8      26 .. 0.82
   2 ?   10.0   0.4   0.00054      0.64      21      42 ..      56      80 ..      55      82 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.061
                     XXXXXXXXXXXXX CS
  Gram_pos_anchor 22 aaGllallggllL 34
                     a+G+++l++g++L
       EPA05597.1  9 AGGIIMLVVGIVL 21
                     6899999999998 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00054
                     XXXXXXXXXXXXXX...XXXXXXXX CS
  Gram_pos_anchor 21 taaGllallggllL...lvkrRKke 42
                     t+aG+l+ +g +l+   ++ rRK++
       EPA05597.1 56 TLAGILIGVGFMLIlisFGARRKRK 80
                     7888888888888888844444444 PP

>> ATP1G1_PLM_MAT8  ATP1G1/PLM/MAT8 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   4.9         6   7.2e+03      20      32 ..       8      22 ..       7      24 .. 0.68
   2 ?    9.6   0.0   0.00049      0.59      20      46 ..      57      84 ..      56      85 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 6
                     HHH..HHHHHHHHHH CS
  ATP1G1_PLM_MAT8 20 fAg..lLfivGilii 32
                     fAg  ++ +vGi++i
       EPA05597.1  8 FAGgiIMLVVGIVLI 22
                     555447788999887 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00049
                     HHHHHHHHHHH.HHHCCHHHCCCS--TT CS
  ATP1G1_PLM_MAT8 20 fAglLfivGil.iilSkkckCkfkqkkr 46
                     +Ag+L  vG++ i++S   ++k+k +++
       EPA05597.1 57 LAGILIGVGFMlILISFGARRKRKDSPE 84
                     8********9725568888888888876 PP

>> DUF3899  Domain of unknown function (DUF3899)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   2.9      0.12   1.4e+02       5      21 ..       8      24 ..       6      26 .. 0.83
   2 ?    5.9   0.0     0.015        18      51      80 ..      46      73 ..      31      75 .. 0.66

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.12
     DUF3899  5 Fllglllliigillivl 21
                F  g+++l++gi+li++
  EPA05597.1  8 FAGGIIMLVVGIVLIIF 24
                77899999999999986 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.015
     DUF3899 51 yeykekkkesskkstrplliiGlllivlsi 80
                ++++e+ k+  ++ + +l+++G++li++s+
  EPA05597.1 46 IKQQEN-KD-MNTLAGILIGVGFMLILISF 73
                333333.23.78888888888888888875 PP

>> DUF872  Eukaryotic protein of unknown function (DUF872)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   1.4     0.036        43      44      62 ..       6      24 ..       3      42 .. 0.71
   2 ?    6.1   0.1      0.01        12      40      67 ..      49      76 ..      43      85 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.036
      DUF872 44 kvvlaallLlllGlvLlll 62
                k  +  +++l++G+vL++ 
  EPA05597.1  6 KIFAGGIIMLVVGIVLIIF 24
                5667788999999998753 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.01
      DUF872 40 kknrkvvlaallLlllGlvLlllgvvil 67
                ++n+    +a +L+ +G +L+l+++   
  EPA05597.1 49 QENKDMNTLAGILIGVGFMLILISFGAR 76
                67777778899************99765 PP

>> DUF4064  Protein of unknown function (DUF4064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   9.0     0.041        49      12      69 ..      10      73 ..       8      76 .. 0.61

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.041
     DUF4064 12 Ggilgillglllllflfllssgefsqeltee........qalsgedasavleflstllivlgvial 69
                Ggi+ ++ g++l++f  ++ + +  q+ ++e        ++++ +d ++ +++l +++++l++i++
  EPA05597.1 10 GGIIMLVVGIVLIIF--INADVPVGQSGMTEeevidlmiKQQENKDMNTLAGILIGVGFMLILISF 73
                555555555555555..3333333444444346666788888888888888888888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1020  (0.0568911); expected 358.6 (0.02)
Passed bias filter:                      730  (0.0407162); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 649.28
//
Query:       EPA05598.1  [L=147]
Description: transcriptional regulator, AsnC family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-12   46.3   2.3    2.2e-12   46.3   2.3    2.0  2  HTH_24          Winged helix-turn-helix DNA-binding
      3e-12   46.2   1.3    4.6e-12   45.6   1.3    1.3  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    1.5e-11   44.1   0.1    2.4e-11   43.4   0.1    1.3  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    4.1e-05   23.4   0.4    4.1e-05   23.4   0.4    1.8  2  HTH_11          HTH domain
    0.00074   19.5   0.2     0.0014   18.5   0.2    1.5  1  HTH_Crp_2       Crp-like helix-turn-helix domain
     0.0013   18.3   0.1     0.0048   16.5   0.1    2.0  2  HTH_50          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.011   15.8   0.0      0.018   15.1   0.0    1.3  1  HTH_20          Helix-turn-helix domain
      0.014   15.2   1.1       0.02   14.7   0.3    1.7  2  HTH_10          HTH DNA binding domain
      0.017   15.3   0.1        2.4    8.5   0.0    2.5  2  NUMOD1          NUMOD1 domain
      0.021   14.4   0.7      0.049   13.2   0.2    1.7  2  DDRGK           DDRGK domain
      0.021   14.7   0.1      0.035   14.0   0.1    1.3  1  MarR_2          MarR family
      0.048   13.3   0.2      0.078   12.6   0.2    1.3  1  GntR            Bacterial regulatory proteins, gntR family
      0.052   13.5   0.2        0.1   12.5   0.2    1.5  1  MarR            MarR family
       0.19   11.8   1.9       0.73    9.9   0.1    2.7  3  HTH_3           Helix-turn-helix


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.3   2.3   1.7e-15   2.2e-12       1      48 []       3      50 ..       3      50 .. 0.98
   2 ?   -1.6   0.1       1.6     2e+03       7      17 ..      67      77 ..      60      78 .. 0.75

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 1.7e-15
      HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                ld+td +IL+ L+ ++r+s r+LA +lg+S  tv+ r+k+Le+e +Ik
  EPA05598.1  3 LDKTDERILKNLMVDARLSARQLALKLGISTVTVLSRIKKLEKEKIIK 50
                79********************************************97 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.6
      HTH_24  7 kILelLqknpr 17
                +I+e++ k+ +
  EPA05598.1 67 AIIEIIAKKDK 77
                69999988765 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   1.3   3.6e-15   4.6e-12       1      42 []       3      44 ..       3      44 .. 0.99

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 3.6e-15
  HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                   LD++D +IL+ L+ daR+s ++LA ++G+S+ tvl R+++Le
     EPA05598.1  3 LDKTDERILKNLMVDARLSARQLALKLGISTVTVLSRIKKLE 44
                   8****************************************8 PP

>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.4   0.1   1.9e-14   2.4e-11      11      75 .]      76     139 ..      69     139 .. 0.92

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 1.9e-14
                     THHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEEE CS
  AsnC_trans_reg  11 eqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivlet 75 
                     + + ++e++l +l++V  +y +tG  d l+++++++ ++l++f++  +as+ ++++t t++vl+t
      EPA05598.1  76 DKIIDIEAELSKLENVCGVYDITGNTDTLVIAKFKSRNELSEFVKG-IASIQNIENTITHVVLNT 139
                     458899**************************************99.****************86 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.4   3.2e-08   4.1e-05       4      42 ..       9      46 ..       7      63 .. 0.85
   2 ?   -2.2   0.1       3.3   4.3e+03       3      14 ..      66      76 ..      64      83 .. 0.59

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 3.2e-08
      HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeel 42
                 il+ L   +  +s+ +LA +L++S+ tv  +Ik+Le+ 
  EPA05598.1  9 RILKNL-MVDARLSARQLALKLGISTVTVLSRIKKLEKE 46
                577777.55666************************986 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.3
      HTH_11  3 lqilelLlearg 14
                ++i+e++ + ++
  EPA05598.1 66 TAIIEIIAK-KD 76
                567777733.33 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.2   1.1e-06    0.0014      17      64 ..      15      60 ..       1      62 [. 0.78

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.1e-06
                EEEEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETEEEEES-HHH CS
   HTH_Crp_2 17 eielpltqeelAsmlGltretvsrilseLkreglisrgrririldlea 64
                 ++ +l+ ++lA  lG++ +tv   +++L++e++i+      + d e+
  EPA05598.1 15 MVDARLSARQLALKLGISTVTVLSRIKKLEKEKIIKGY--TALIDHEK 60
                67889******************************943..34555555 PP

>> HTH_50  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   3.8e-06    0.0048      24      46 ..      20      42 ..       3      44 .. 0.79
   2 ?   -2.4   0.0         3   3.9e+03      32      42 ..      60      70 ..      59      74 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.8e-06
      HTH_50 24 pStRklAkrLGvShtaianklrk 46
                 S+R lA +LG+S  +++ +++k
  EPA05598.1 20 LSARQLALKLGISTVTVLSRIKK 42
                59*******************98 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3
      HTH_50 32 rLGvShtaian 42
                +LG   tai+ 
  EPA05598.1 60 KLGYNLTAIIE 70
                78888899985 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   1.4e-05     0.018      14      56 ..       9      51 ..       3      54 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.4e-05
                HHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
      HTH_20 14 rilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                ril+ L+ ++ l+a +la  l++s  t+  ++++Le+  ++++
  EPA05598.1  9 RILKNLMVDARLSARQLALKLGISTVTVLSRIKKLEKEKIIKG 51
                89**********************************9999876 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.3   1.5e-05      0.02      23      49 ..      19      45 ..      16      50 .. 0.87
   2 ?   -3.2   0.0       6.2   7.9e+03      30      46 ..     123     139 ..     120     142 .. 0.54

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.5e-05
      HTH_10 23 rvtlkeLAkelGIskstlsehLrkaes 49
                r ++++LA +lGIs  t++ +++k e+
  EPA05598.1 19 RLSARQLALKLGISTVTVLSRIKKLEK 45
                7899********************986 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 6.2
      HTH_10  30 AkelGIskstlsehLrk 46 
                 A + +I ++ ++  L+ 
  EPA05598.1 123 ASIQNIENTITHVVLNT 139
                 55555555555555555 PP

>> NUMOD1  NUMOD1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.041        53      18      33 ..      21      36 ..      21      39 .. 0.89
   2 ?    8.5   0.0    0.0019       2.4       5      27 ..      94     120 ..      93     121 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.041
      NUMOD1 18 SireAakyLgishntI 33
                S r++a +Lgis  t+
  EPA05598.1 21 SARQLALKLGISTVTV 36
                7899********9885 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0019
      NUMOD1   5 vYDlntkt....igkFsSireAakyLg 27 
                 vYD++++t    i kF S +e++++++
  EPA05598.1  94 VYDITGNTdtlvIAKFKSRNELSEFVK 120
                 9********9999********998875 PP

>> DDRGK  DDRGK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   3.9e-05     0.049     117     145 ..      23      51 ..       8      59 .. 0.90
   2 ?   -1.3   0.0       1.1   1.3e+03     126     148 ..      74      96 ..      59     101 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.9e-05
                 HHHHHHH-S-HHHHHHHHHHHHHHSSS-E CS
       DDRGK 117 eelavkfklktqevierikeLeeqgsltG 145
                  +la k++++t  v +rik+Le+++ ++G
  EPA05598.1  23 RQLALKLGISTVTVLSRIKKLEKEKIIKG 51 
                 579************************99 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.1
                 -HHHHHHHHHHHHHHSSS-EEE- CS
       DDRGK 126 ktqevierikeLeeqgsltGvlD 148
                 k +++i+   eL + +++ Gv D
  EPA05598.1  74 KKDKIIDIEAELSKLENVCGVYD 96 
                 44455555556666666666666 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   2.8e-05     0.035       9      51 ..       9      49 ..       2      58 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.8e-05
                HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSE CS
      MarR_2  9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLv 51
                r+L +L    +  l++++la +lg+s  +v  ++k+L++   +
  EPA05598.1  9 RILKNLMVDAR--LSARQLALKLGISTVTVLSRIKKLEKEKII 49
                67777777776..*************************99877 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   6.1e-05     0.078      12      54 ..       9      49 ..       4      51 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.1e-05
                HHHTTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
        GntR 12 dIlsgelrpGdkLPsereLaaefgVsrttvReALrrLeaeglv 54
                +Il+ +l+  ++L s r+La ++g+s+ tv   +++Le e+++
  EPA05598.1  9 RILK-NLMVDARL-SARQLALKLGISTVTVLSRIKKLEKEKII 49
                5555.899999**.**************************997 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2     8e-05       0.1       8      47 ..      10      49 ..       4      52 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8e-05
                HHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
        MarR  8 iLrilyeqgplsvseLakklgvskstvtrvldrLekkGli 47
                iL +l     ls  +La klg+s+ tv   +++Lek+  i
  EPA05598.1 10 ILKNLMVDARLSARQLALKLGISTVTVLSRIKKLEKEKII 49
                66666666778999**********************8665 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00057      0.73       2      26 ..      12      36 ..      11      48 .. 0.80
   2 ?   -0.3   0.0      0.87   1.1e+03      40      50 ..      84      94 ..      59      97 .. 0.77
   3 ?   -1.2   0.0       1.7   2.2e+03      14      30 ..     114     129 ..     110     134 .. 0.48

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00057
                HHHHHHTTHHHHHHHHHHTSSHHHH CS
       HTH_3  2 kelRkqlglsqeeLAeklGvsrsti 26
                k l+  + ls ++LA klG+s  t+
  EPA05598.1 12 KNLMVDARLSARQLALKLGISTVTV 36
                666777789**********877765 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.87
                HHHHHHHHHTS CS
       HTH_3 40 tlkklakaLgv 50
                 l kl++++gv
  EPA05598.1 84 ELSKLENVCGV 94
                46777777776 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.7
                 HHHHHHTSSHHHHHHHH CS
       HTH_3  14 eLAeklGvsrstisriE 30 
                 eL+e +    ++i++iE
  EPA05598.1 114 ELSEFV-KGIASIQNIE 129
                 333333.2334555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       849  (0.0473534); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 954.62
//
Query:       EPA05599.1  [L=51]
Description: hypothetical protein BG20_I1050 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.014   15.7   0.4      0.014   15.7   0.4    1.0  1  Sec3_C_2  Sec3 exocyst complex subunit
      0.032   14.5   2.4      0.038   14.3   2.4    1.1  1  TcdB_N    TcdB toxin N-terminal helical domain
      0.059   13.5   0.5      0.064   13.4   0.5    1.1  1  DpnI_C    Dam-replacing HTH domain


Domain annotation for each model (and alignments):
>> Sec3_C_2  Sec3 exocyst complex subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   0.4   2.3e-06     0.014      19      56 ..       5      42 ..       1      51 [] 0.89

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.3e-06
    Sec3_C_2 19 lkelefsldeaiiesveelaeekielkevkdilqdsil 56
                 k+++f l+e ii   +el e ++e k++ ++++d i 
  EPA05599.1  5 DKRTLFVLKENIIMCFNELKETDFEDKNILKQINDLIE 42
                5899*******************************986 PP

>> TcdB_N  TcdB toxin N-terminal helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   2.4   6.3e-06     0.038       8      44 ..      14      49 ..      12      51 .] 0.87

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.3e-06
                HHHHHHHHTTTTS-HHHHHHHHHHHHHHHHHHHHHST CS
      TcdB_N  8 enleeklnklseeqskkkyellkklkkeidnYnnlyk 44
                en+  ++n l e+ +++ ++ lk+++++i +Y +l k
  EPA05599.1 14 ENIIMCFNELKETDFED-KNILKQINDLIEEYKALKK 49
                68888998999888888.999*************955 PP

>> DpnI_C  Dam-replacing HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.5   1.1e-05     0.064       8      38 ..      15      45 ..       6      49 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.1e-05
                HHHHHHHHS-SSEEEHHHHHTTHHHHHHHST CS
      DpnI_C  8 dilkcidklekkeFtlediykfeeeLkekhp 38
                +i++c ++l++++F+ ++i+k++++L e++ 
  EPA05599.1 15 NIIMCFNELKETDFEDKNILKQINDLIEEYK 45
                69************************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1000  (0.0557756); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.28s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 361.67
//
Query:       EPA05600.1  [L=123]
Description: hypothetical protein BG20_I1040 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 929.75
//
Query:       EPA05601.1  [L=359]
Description: hypothetical protein BG20_I1066 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.037   14.1   0.4       0.82    9.8   0.0    2.6  2  Zincin_1  Zincin-like metallopeptidase


Domain annotation for each model (and alignments):
>> Zincin_1  Zincin-like metallopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   4.6e-05      0.82      23      72 ..     181     230 ..     173     233 .. 0.90
   2 ?    1.5   0.1     0.018   3.3e+02      42      73 ..     249     280 ..     237     291 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 4.6e-05
                 T-B-.-EEEE---S-BTTB-.-GGG--EEEEEHHHHHHH--TT--HHHHH CS
    Zincin_1  23 depellGlyegvpltersaedagslpdrivlyrrpllavaetreeleeev 72 
                 ++ el+Glye +  +e+s ++ +++  +i + r  l++ + +r+e e++v
  EPA05601.1 181 KSDELTGLYEKIKTEEESLKEHKKIHSEIEIQRSKLAQLILNRKEYENQV 230
                 5679*********************************9998998888887 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.018
                 -.-GGG--EEEEEHHHHHHH--TT--HHHHHH CS
    Zincin_1  42 edagslpdrivlyrrpllavaetreeleeevr 73 
                 +++ +l ++i+l ++ +++v  +r+el ++++
  EPA05601.1 249 QEQTKLSEQIILQKAEIEKVKTERNELMKKIT 280
                 4578999*****************99999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3048  (0.170004); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.24s 00:00:00.88 Elapsed: 00:00:00.43
# Mc/sec: 2504.40
//
Query:       EPA05602.1  [L=42]
Description: hypothetical protein BG20_I1051 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       128  (0.00713927); expected 358.6 (0.02)
Passed bias filter:                      102  (0.00568911); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.26s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 313.36
//
Query:       EPA05603.1  [L=95]
Description: hypothetical protein BG20_I1053 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 652.20
//
Query:       EPA05604.1  [L=140]
Description: hypothetical protein BG20_I1037 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.021   15.0   0.0      0.032   14.4   0.0    1.2  1  Transglut_C  Transglutaminase family, C-terminal ig like doma
      0.065   13.5   0.2        0.1   12.8   0.2    1.3  1  ASH          Abnormal spindle-like microcephaly-assoc'd, ASPM


Domain annotation for each model (and alignments):
>> Transglut_C  Transglutaminase family, C-terminal ig like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   3.6e-06     0.032       4      87 ..      34     110 ..      32     121 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.6e-06
                  EEEESSCEBTTSEEEEEEEEEE-SSS-BEEEEEEEEEEEEECTTTEEEEEEEEEEEEEE-TTEEEEEEEEE-HHSHEEECCEEE CS
  Transglut_C   4 kievlesavlgqdltvsvllkNplseelkdvklnlcaqtveynGvlaaefkkksleltLePkeeksvrlkilpskyGerkllve 87 
                   ++++++ +++q +++++ +kN+ +++ ++      +q+   +Gv+++  +   + l+L+P+++ s  l+ +p ++   +++ve
   EPA05604.1  34 GVKISNQVNVNQHVQITADIKNNQDKA-QK--FVYIVQVKNQQGVVVSLGW--INGLSLDPEQTFSPALSWTPLES--DEYTVE 110
                  68999******************9999.77..445599999****986666..566899*******9999999999..899988 PP

>> ASH  Abnormal spindle-like microcephaly-assoc'd, ASPM-SPD-2-Hydin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   1.1e-05       0.1      18      79 ..      40     104 ..      34     115 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.1e-05
                 ----EEEEEEE-EEESS-SS-.-EEEEEEEE--XXXXXXXXXX...XXXXXXXXXXXXXXXXXXXX CS
         ASH  18 dvkvGssaerlLtveNpseep.aevkvskvpaaekgfsveete...levqpgesvtltvtwtPtee 79 
                 +v+v++  + + +++N+++++   v + +v   ++g+ v+  +   l ++p+++++  ++wtP+e+
  EPA05604.1  40 QVNVNQHVQITADIKNNQDKAqKFVYIVQVK-NQQGVVVSLGWingLSLDPEQTFSPALSWTPLES 104
                 6999999999***********5555555555.88888888777779*****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       955  (0.0532657); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 881.75
//
Query:       EPA05605.1  [L=84]
Description: hypothetical protein BG20_I1054 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0098   15.8   2.2      0.017   15.1   2.2    1.4  1  Sec2p         GDP/GTP exchange factor Sec2p
  ------ inclusion threshold ------
      0.052   13.8   6.2      0.079   13.3   6.2    1.3  1  ATP-synt_E_2  ATP synthase epsilon subunit


Domain annotation for each model (and alignments):
>> Sec2p  GDP/GTP exchange factor Sec2p
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   2.2   1.9e-06     0.017      10      51 ..      43      84 .]      34      84 .] 0.82

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.9e-06
                HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
       Sec2p 10 eeaekekkklekEledLtasLFeeANkmVaaarkekealekk 51
                e  ++  +++++E+  L+++ F+e N++  + +ke+  +ekk
  EPA05605.1 43 EMGKEIGENINQEISKLSKKNFDELNEISEDIKKERSMFEKK 84
                444555689***************************999986 PP

>> ATP-synt_E_2  ATP synthase epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   6.2   8.8e-06     0.079      19      56 .]      40      77 ..      31      77 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.8e-06
  ATP-synt_E_2 19 kLdeKKsElLkkiNmEYEKlLKqRLdeLeklKrkvLKE 56
                  k++e   E+ ++iN E  Kl K+  deL+++  ++ KE
    EPA05605.1 40 KIEEMGKEIGENINQEISKLSKKNFDELNEISEDIKKE 77
                  7889999***************************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1364  (0.0760779); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 535.45
//
Query:       EPA05606.1  [L=279]
Description: hypothetical protein BG20_I1061 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.8e-80  268.4   0.0    7.6e-80  268.2   0.0    1.0  1  VitK2_biosynth  Menaquinone biosynthesis
  ------ inclusion threshold ------
      0.043   14.1   0.0      0.085   13.1   0.0    1.5  1  Imm26           Immunity protein 26
      0.062   13.1   0.0       0.11   12.3   0.0    1.3  1  SCAB_CC         Coiled-coil regions of plant-specific actin-b


Domain annotation for each model (and alignments):
>> VitK2_biosynth  Menaquinone biosynthesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  268.2   0.0   1.3e-83   7.6e-80       1     265 [.       3     260 ..       3     261 .. 0.97

  Alignments for each domain:
  == domain 1  score: 268.2 bits;  conditional E-value: 1.3e-83
                     EEEEEESSHHHHHHHHHHHTTSS..SGCCEEEEEE-HHHHHHHHHTTS-SEEEEEHHHHTTCTTTEEEESEESCEEEESSSSEEEEESS-CCC-S CS
  VitK2_biosynth   1 lrlGhspylNdlflfyaLvegkvdsegleveivledpetlnrallegelDvakiSsaayariaddyalLpdlsisalGrvygvllvskvpleele 95 
                     +++Gh+p+++d+f+fy++++gkv+s+ ++v++v+ed+e+lnr++ + elDv+++S++a+a+i   y++L+  s++++G +yg+++ +k++++ +e
      EPA05606.1   3 ITVGHTPDSDDAFMFYGMFTGKVSSRDFTVTHVIEDIEKLNRKATNPELDVTAVSVHACAYIPG-YTILR--SGGSFGIGYGPIVTAKKQMSIDE 94 
                     68***********************************************************776.*****..***************99887776 PP

                     SS.T.EEEESTTTSHHHHHHHHHHCSTS----EEEEE-GGGHHHHHHTTS.SEEEEECCHHHTGGGGTTEEEEEHHHHHHHHH.SS-EEEEEEEE CS
  VitK2_biosynth  96 gelgkrvalpgestTsvlLlrlllaeryglkprlvevpfdeieaavlege.dagLlIgesaltyaeeglkkvlDLgelWeelt.glPlvlglwvv 188
                      + + ++a+pg++t+++lLl+l++ ++     ++ve++f++i++av++g+ dagL+I+e +l y++eg +k+lD ge+W ++t glP++lg++v+
      EPA05606.1  95 IK-KCKIAIPGKMTSAFLLLQLMIGKF-----DYVEMNFSDIPEAVKKGKvDAGLVIHETQLSYEQEGNVKILDVGEWWDKETgGLPVPLGINVM 183
                     55.99*********************9.....9**************************************************77********** PP

                     ECCCHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHCCSTTS.HHHHHHHHHHHCSHHHHS-CHHHHHHHHHHHHHHH CS
  VitK2_biosynth 189 rrdlaaeaakeleealreSveyalahldevaeyaaeraqemddevlekhlelYvnelsydlgeegragleeflelaa 265
                     + +l++++++++++ l++S+ey+l++ld+++eya+++++ + +e +ek++++Yvn++++++g++g++++++ +e+a+
      EPA05606.1 184 KTSLGEDTIHKFDKYLQASIEYGLKNLDDALEYAMQYSRGKPRELIEKFVKMYVNKVTINMGDKGEESIRRVFEMAK 260
                     *****************************************99********************************97 PP

>> Imm26  Immunity protein 26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.4e-05     0.085      14      62 ..      29     107 ..      20     129 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.4e-05
       Imm26  14 kyafGrvisder..............................lmggglvieiydivseneeidleeitnssllfepiii 62 
                  +++ +vi+d++                                gg + i +++iv+ +++++++ei++++++++  ++
  EPA05606.1  29 DFTVTHVIEDIEklnrkatnpeldvtavsvhacayipgytilRSGGSFGIGYGPIVTAKKQMSIDEIKKCKIAIPGKMT 107
                 56666666666666666666666666777777777777777667999**************************998876 PP

>> SCAB_CC  Coiled-coil regions of plant-specific actin-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.8e-05      0.11      10      63 ..     207     261 ..     201     269 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.8e-05
     SCAB_CC  10 lkkLrdvLeslrgrvaGknkddveesism.veaLavqLtkregellqekaevkkl 63 
                 lk+L d+Le+  +   Gk ++ +e+ + m v+ +++++  + +e +++ +e++k 
  EPA05606.1 207 LKNLDDALEYAMQYSRGKPRELIEKFVKMyVNKVTINMGDKGEESIRRVFEMAKQ 261
                 8**************************9989****************99999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2176.32
//
Query:       EPA05607.1  [L=410]
Description: hypothetical protein BG20_I1038 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0072   16.5   0.0      0.015   15.5   0.0    1.5  1  HD        HD domain
  ------ inclusion threshold ------
      0.022   14.5   1.3      0.046   13.5   0.4    1.9  2  PDEase_I  3'5'-cyclic nucleotide phosphodiesterase
      0.042   13.6   0.2       0.78    9.5   0.0    2.3  2  HD_2      HD containing hydrolase-like enzyme
      0.052   14.0   0.1       0.14   12.6   0.1    1.7  1  DUF1091   Protein of unknown function (DUF1091)


Domain annotation for each model (and alignments):
>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   3.3e-06     0.015       7      98 ..      32     119 ..      24     159 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.3e-06
                 HHHHHHHHHHHHHHH..HHHHHHHHHHHHHTTTTHHHHTS..HHHHHH.CTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHH CS
          HD   7 eVaklarrlaedlge..eedrellllaaLlHDiGkgpfgdafekkeee.fekflaHekvgaeilrevekrlgldledvaklirehheswegkkrp 98 
                  Va l++ l ++ ++   +d   l++aaL+HD    ++ d   k +ee + kf +     ++++  ++++    le++  li++ + +w gk ++
  EPA05607.1  32 YVALLSANLNNSSKKfsITDLKYLYTAALFHDFDPQKSVD---KPHEEsVLKFISMDRKLRKLIDVAGLD----LEIIKVLILRTTYPWSGKLKE 119
                 3666666666666669*****************9999777...333333455444444444444444444....699************988655 PP

>> PDEase_I  3'5'-cyclic nucleotide phosphodiesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.4     1e-05     0.046       1      45 [.      21      65 ..      21      67 .. 0.96
   2 ?   -1.7   0.0      0.45     2e+03     121     197 ..     117     146 ..      99     156 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1e-05
                SSSHHHHHHHHHHHHHHHHCCHCCCCS-HHHHHHHHHHHHHTTTT CS
    PDEase_I  1 YHNfrHAadVlqalfyllkkeklkeeltpleilalliaalcHDvd 45
                YHN +H ++V+ +  +  + ++ +++++  +   l++aal HD+d
  EPA05607.1 21 YHNINHELEVTYVALLSANLNNSSKKFSITDLKYLYTAALFHDFD 65
                ***************99999999999*****************97 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.45
                 HHHHHHHHCCTTS-TTTCT.-HHHHHHHHHHHHHHHHTGCCCS-HHHHHHHHHHHHHHHHHHHHHHHHCT----GGG CS
    PDEase_I 121 lleklkelvkkkeknslnkeeeedkklllsllikaaDisnptkpweiskkwaelvleEffeqgdeekelglpvsplm 197
                 l                                               k+ ae+ ++E f+ ++  k+++ ++  +m
  EPA05607.1 117 L-----------------------------------------------KENAERQIKECFNNSEITKNNKAKQDHFM 146
                 3...............................................45556666666666666666655555554 PP

>> HD_2  HD containing hydrolase-like enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00017      0.78      28      66 ..      25      64 ..      18      68 .. 0.88
   2 ?    1.5   0.0      0.05   2.2e+02      92     118 ..     201     228 ..     188     258 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00017
        HD_2 28 eHslevaliahalalienkkfgg.kldaerlallalyHDa 66
                +H lev+++a + a ++n   +    d++ l+++al+HD 
  EPA05607.1 25 NHELEVTYVALLSANLNNSSKKFsITDLKYLYTAALFHDF 64
                7*****************88655578*************6 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.05
        HD_2  92 vEeeaeekllelLpeelreeyeell.ad 118
                  E+e  + +le+Lp+++r+++ + + + 
  EPA05607.1 201 KETEMCRFILESLPKHMRKNFFDTVlGF 228
                 58888999***********998776323 PP

>> DUF1091  Protein of unknown function (DUF1091)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   3.1e-05      0.14       6      68 ..     188     250 ..     184     267 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.1e-05
     DUF1091   6 fkrsngykpflynitldfCkfl.knpnnnplfkifykslkkysnl.nhtCPypkgdyilknlrld 68 
                  ++s  y   l n  + +C+f+ ++  +  + k f++++  + n+ +++  + + +y+++nl+l 
  EPA05607.1 188 VRSSVAYFEELLNKETEMCRFIlESLPK-HMRKNFFDTVLGFMNIrQQEITI-QANYTYDNLKLV 250
                 4555668899***********8544444.6***************7888999.99******9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       676  (0.0377043); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 2425.55
//
Query:       EPA05608.1  [L=97]
Description: hypothetical protein BG20_I1060 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 684.14
//
Query:       EPA05609.1  [L=71]
Description: hypothetical protein BG20_I1065 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.032   14.1   1.2      0.035   14.1   1.2    1.0  1  YliH      Biofilm formation protein (YliH/bssR)
      0.051   13.7   5.3       0.05   13.7   5.3    1.1  1  COG2      COG (conserved oligomeric Golgi) complex component,
       0.38   10.7   6.0       0.57   10.1   5.4    1.6  2  Nas2_N    Nas2 N_terminal domain
       0.96    9.8   8.0       0.97    9.8   8.0    1.0  1  Tli4_N    Tle cognate immunity protein 4 N-terminal domain
        1.1    8.5   6.6        1.2    8.5   6.6    1.0  1  DUF4407   Domain of unknown function (DUF4407)
        2.4    5.9  13.1        2.3    5.9  13.1    1.0  1  Nup88     Nuclear pore component
        2.8    6.0   5.9        3.3    5.8   5.9    1.0  1  YfhO      Bacterial membrane protein YfhO
        3.6    6.5  12.8        3.8    6.4  12.8    1.0  1  eIF-4B    Plant specific eukaryotic initiation factor 4B
        3.7    6.3   4.4        3.7    6.3   4.4    1.1  1  MscS_TM   Mechanosensitive ion channel inner membrane domain 
        5.1    7.3  14.6        5.4    7.3  14.6    1.0  1  MSV199    MSV199 domain
        6.6    5.7  17.8        6.7    5.7  17.8    1.0  1  Atg14     Vacuolar sorting 38 and autophagy-related subunit 1


Domain annotation for each model (and alignments):
>> YliH  Biofilm formation protein (YliH/bssR)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   1.2   2.1e-05     0.035      10      67 ..       2      59 ..       1      69 [. 0.91

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.1e-05
        YliH 10 llnklinaridlaaylqlrkakGymsvsesdhlrdnlfelnrelrdkalrlqlaldqe 67
                l +++i+ +i l+   q rk       se+++l+++ +++ +e+ +k  +l+l +++ 
  EPA05609.1  2 LAKQIIDEKIALEEIKQKRKKIQNEIKSEKQKLKEQQIKIKKEISEKKKQLKLSINKS 59
                56789***************999999***********************999999875 PP

>> COG2  COG (conserved oligomeric Golgi) complex component, COG2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   5.3   3.1e-05      0.05      62     109 ..       4      51 ..       1      67 [. 0.87

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.1e-05
        COG2  62 ghLvglqeeleevesplaaarkkvesvreklsereeeveskleeakel 109
                 ++ ++ + +lee++++ ++++++++s ++kl+e++ +++++++e+k+ 
  EPA05609.1   4 KQIIDEKIALEEIKQKRKKIQNEIKSEKQKLKEQQIKIKKEISEKKKQ 51 
                 5666777789*********************************99874 PP

>> Nas2_N  Nas2 N_terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   5.4   0.00035      0.57       1      33 [.      13      45 ..      13      51 .. 0.90
   2 ?    4.7   1.1     0.018        29       2      23 ..      32      53 ..      31      63 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00035
      Nas2_N  1 lkeLekkkdeiekeieelsevLesqnvgmdgpl 33
                l+e+++k+++i++ei++  + L++q+++++++ 
  EPA05609.1 13 LEEIKQKRKKIQNEIKSEKQKLKEQQIKIKKEI 45
                57899**********************999876 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.018
      Nas2_N  2 keLekkkdeiekeieelsevLe 23
                ++L++++ +i+kei+e  ++L+
  EPA05609.1 32 QKLKEQQIKIKKEISEKKKQLK 53
                689999**********999998 PP

>> Tli4_N  Tle cognate immunity protein 4 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   8.0   0.00059      0.97      30      94 ..       5      68 ..       1      71 [] 0.89

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00059
      Tli4_N 30 kieskrvspeafrqriakreqeLkaekrikekdepllkkavslpdnkgrifirnesvskedaare 94
                +i+ ++++ e+ +q+ +k+++e+k+ek++ +++++ +kk +s ++++ ++ i++++ + ++++++
  EPA05609.1  5 QIIDEKIALEEIKQKRKKIQNEIKSEKQKLKEQQIKIKKEISEKKKQLKLSINKSKPK-KSSKIK 68
                68999999*********************9************9999999999999998.766665 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   6.6   0.00071       1.2     116     160 ..      12      56 ..       3      69 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00071
     DUF4407 116 qqeeakelkeqlaaaltaelaeleaqiaalqaeidaaearldalr 160
                 + ee+k+ +++++++ ++e ++l++q+ ++++ei++++++l+   
  EPA05609.1  12 ALEEIKQKRKKIQNEIKSEKQKLKEQQIKIKKEISEKKKQLKLSI 56 
                 567888888888888899999999999999999999888876554 PP

>> Nup88  Nuclear pore component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9  13.1    0.0014       2.3     630     682 ..       9      60 ..       1      70 [. 0.84

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0014
       Nup88 630 mkkelekikeklkslknalkqvkkkldkqrkqiakskeeekksslelsekqkk 682
                  k  le+ik+k k+++n++k  k+kl++q+ +i+k+ +e kk++l+ls +++k
  EPA05609.1   9 EKIALEEIKQKRKKIQNEIKSEKQKLKEQQIKIKKEISE-KKKQLKLSINKSK 60 
                 56689*****************************99888.7888888766655 PP

>> YfhO  Bacterial membrane protein YfhO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   5.9    0.0021       3.3     630     691 ..       5      67 ..       2      70 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0021
        YfhO 630 tlnltkiklqniteknkkltvtl..kqkenktatitltvt.ptanselYlelpsknsksdknvsi 691
                 ++ ++ki l++i++k kk+++++  ++++ k+ +i+++ + ++++++l l++++  sk +k+++i
  EPA05609.1   5 QIIDEKIALEEIKQKRKKIQNEIksEKQKLKEQQIKIKKEiSEKKKQLKLSINK--SKPKKSSKI 67 
                 566789999***********8887878888999999999999999999999998..777777666 PP

>> eIF-4B  Plant specific eukaryotic initiation factor 4B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4  12.8    0.0024       3.8     375     427 ..       8      57 ..       3      68 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0024
      eIF-4B 375 eekllkeeieelkkelekeaaenkesqqessedqnslkelisekekdlellir 427
                 +ek+  eei++ +k++++e   ++e+ q+ +e+q ++k++isek+k+l+l i+
  EPA05609.1   8 DEKIALEEIKQKRKKIQNE--IKSEK-QKLKEQQIKIKKEISEKKKQLKLSIN 57 
                 799**************99..45555.556677888************99876 PP

>> MscS_TM  Mechanosensitive ion channel inner membrane domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   4.4    0.0023       3.7     255     289 ..       9      45 ..       3      67 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0023
     MscS_TM 255 RRlayerakekRaaalaqrakeeeeeeekkesae...v 289
                  ++a+e+ k+kR++++++ + e+++ +e++ +     +
  EPA05609.1   9 EKIALEEIKQKRKKIQNEIKSEKQKLKEQQIK-IkkeI 45 
                 699************95554444444333222.12332 PP

>> MSV199  MSV199 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3  14.6    0.0033       5.4      60     122 ..       8      68 ..       1      70 [. 0.88

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0033
      MSV199  60 rnnieykelkykdeeielypslkeeikllkknaiaqkkWlilevkdfKkailrlntknsekir 122
                  ++i  +e+k+k ++i   +++k+e ++lk+++i+ kk +  + k++K +i + + k+s ki+
  EPA05609.1   8 DEKIALEEIKQKRKKI--QNEIKSEKQKLKEQQIKIKKEISEKKKQLKLSINKSKPKKSSKIK 68 
                 5689999999666655..579*****************************************9 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7  17.8    0.0041       6.7      60     131 ..       4      65 ..       1      71 [] 0.45

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0041
       Atg14  60 dkiknkkakleelksliadlrer....lqelkdklsqlkkeieekkkklaklsdklkkRrsdleslqneleerrkk 131
                 ++i  +k +lee+k+++ +++++    +q+lk+++ + kkei ekkk+l+   +k k               ++ +
  EPA05609.1   4 KQIIDEKIALEEIKQKRKKIQNEikseKQKLKEQQIKIKKEISEKKKQLKLSINKSK--------------PKKSS 65 
                 455555555555555555555443333444444444555555555555544444444..............33222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      4690  (0.261587); expected 358.6 (0.02)
Passed bias filter:                      963  (0.0537119); expected 358.6 (0.02)
Passed Vit filter:                       133  (0.00741815); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 461.15
//
Query:       EPA05610.1  [L=91]
Description: hypothetical protein BG20_I1052 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.013   14.9   2.6        3.3    7.3   0.0    2.4  2  zf-ribbon_3  zinc-ribbon domain
      0.017   15.2   1.0      0.025   14.7   1.0    1.4  1  zf-UDP       Zinc-binding RING-finger
      0.021   15.5   0.6        2.6    8.8   0.0    2.3  2  zf-ISL3      zinc-finger of transposase IS204/IS1001/IS1096/I
       0.14   12.0   4.6       0.24   11.3   4.6    1.3  1  C1_1         Phorbol esters/diacylglycerol binding domain (C1
       0.15   11.9   8.6       0.79    9.6   8.9    1.8  2  zf-RING_4    RING/Ubox like zinc-binding domain


Domain annotation for each model (and alignments):
>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.7   0.00099       3.5      18      26 .]      20      28 ..      20      28 .. 0.69
   2 ?    7.3   0.0   0.00092       3.3       4      11 ..      42      49 ..      41      55 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00099
  zf-ribbon_3 18 vCpyCGtkl 26
                 +Cp CG k+
   EPA05610.1 20 KCPACGFKI 28
                 488888775 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00092
  zf-ribbon_3  4 rCPnCGap 11
                 +CP+C+++
   EPA05610.1 42 FCPQCKTL 49
                 6****984 PP

>> zf-UDP  Zinc-binding RING-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   1.0     7e-06     0.025      30      61 ..      21      51 ..      15      65 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 7e-06
      zf-UDP 30 cnecafpvcrpcyeyerkdgnqsCPqCktryk 61
                c  c+f ++  c ++    g   CPqCkt   
  EPA05610.1 21 CPACGFKIIIECCSFIEGRG-WFCPQCKTLSV 51
                899**********9988888.8*******755 PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.2     0.012        41       2       9 ..      18      25 ..      17      29 .. 0.85
   2 ?    8.8   0.0   0.00071       2.6       3      16 ..      41      54 ..      39      60 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.012
     zf-ISL3  2 phrCPnCg 9 
                p +CP Cg
  EPA05610.1 18 PGKCPACG 25
                789****9 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00071
     zf-ISL3  3 hrCPnCgsktvvkh 16
                + CP+C+  +v++ 
  EPA05610.1 41 WFCPQCKTLSVYDE 54
                89*******99986 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   4.6   6.6e-05      0.24       4      36 ..      11      48 ..       9      50 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.6e-05
                EEE--SS--B-TTT-SB-.....-SSSS-EEEETTT-- CS
        C1_1  4 vhrnfkqptfCkhCgefl.....wgkekqglkCswCkl 36
                v+   k+p++C  Cg  +     ++ e +g+ C +Ck 
  EPA05610.1 11 VKYINKEPGKCPACGFKIiieccSFIEGRGWFCPQCKT 48
                5555599********9999999888***********96 PP

>> zf-RING_4  RING/Ubox like zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.3     0.002       7.1      31      43 ..      12      24 ..       6      25 .. 0.77
   2 ?    9.6   8.9   0.00022      0.79      18      45 ..      21      48 ..      15      53 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.002
   zf-RING_4 31 rileeeegrCPaC 43
                + +++e g+CPaC
  EPA05610.1 12 KYINKEPGKCPAC 24
                5566789****** PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00022
   zf-RING_4 18 C.eCgyqiClfCyhrileeeegrCPaCre 45
                C  Cg++i   C++ i    +  CP+C++
  EPA05610.1 21 CpACGFKIIIECCSFIE-GRGWFCPQCKT 48
                757*********99776.689******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 621.92
//
Query:       EPA05611.1  [L=77]
Description: hypothetical protein BG20_I1059 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0013   18.3   4.7     0.0016   18.0   4.7    1.1  1  PI3K_P85_iSH2  Phosphatidylinositol 3-kinase regulatory subun
     0.0018   19.0   3.5     0.0021   18.8   3.5    1.0  1  DUF4472        Domain of unknown function (DUF4472)
     0.0024   17.4   4.5     0.0027   17.2   4.5    1.0  1  Flagellar_rod  Paraflagellar rod protein
     0.0028   18.0   5.1      0.022   15.1   1.4    2.1  2  CLZ            C-terminal leucine zipper domain of cyclic nuc
     0.0036   15.6   3.0     0.0042   15.4   3.0    1.0  1  COG6           Conserved oligomeric complex COG6
     0.0045   17.2   3.3       0.07   13.4   3.3    2.0  1  ABC_tran_CTD   ABC transporter C-terminal domain
     0.0082   16.0   4.4     0.0084   15.9   4.4    1.1  1  DUF724         Protein of unknown function (DUF724)
  ------ inclusion threshold ------
      0.011   15.0   5.6      0.016   14.5   5.6    1.4  1  GAS            Growth-arrest specific micro-tubule binding
      0.019   14.3   2.8       0.02   14.1   2.8    1.0  1  TMPIT          TMPIT-like protein
      0.026   14.6   4.6      0.029   14.5   4.6    1.0  1  ADIP           Afadin- and alpha -actinin-Binding
       0.03   14.8   5.1      0.033   14.7   5.1    1.1  1  APG6_N         Apg6 coiled-coil region
      0.034   14.4   1.4      0.034   14.4   1.4    1.1  1  GLTP           Glycolipid transfer protein (GLTP)
      0.037   14.4   4.6      0.048   14.0   4.6    1.2  1  CCDC-167       Coiled-coil domain-containing protein 167
      0.053   13.8   3.5       0.17   12.2   0.4    2.1  2  BLOC1_2        Biogenesis of lysosome-related organelles comp
      0.054   13.5   3.1      0.058   13.4   3.1    1.1  1  Laminin_II     Laminin Domain II
      0.069   13.2   3.1       0.12   12.4   3.1    1.4  1  DUF1664        Protein of unknown function (DUF1664)
      0.074   13.7   3.9        1.1    9.9   3.9    2.0  1  SlyX           SlyX
      0.092   12.4   5.9        2.6    7.7   4.9    2.1  2  Vac_Fusion     Chordopoxvirus multifunctional envelope protei
       0.11   10.3   6.0       0.13   10.1   6.0    1.0  1  Nup88          Nuclear pore component
       0.11   12.5   2.7       0.71   10.0   0.4    2.3  2  Exog_C         Endo/exonuclease (EXOG) C-terminal domain
       0.12   12.4   2.9        0.2   11.6   2.9    1.5  1  EMP24_GP25L    emp24/gp25L/p24 family/GOLD
       0.17   11.3   2.4       0.22   11.0   2.4    1.2  1  Allexi_40kDa   Allexivirus 40kDa protein
       0.18   11.7   2.6       0.22   11.4   2.6    1.2  1  ACCA           Acetyl co-enzyme A carboxylase carboxyltransfe
        0.2   11.2   0.6       0.19   11.2   0.6    1.0  1  Inositol_P     Inositol monophosphatase family
       0.22   11.3   6.8         29    4.5   6.8    2.1  1  DivIC          Septum formation initiator
       0.42   11.0   5.3        1.7    9.1   3.4    2.1  2  FlaC_arch      Flagella accessory protein C (FlaC)
        1.7    8.9   9.4        6.1    7.1   7.6    2.0  2  XhlA           Haemolysin XhlA
          2    7.9   4.5        1.7    8.1   1.3    1.9  2  BRI3BP         Negative regulator of p53/TP53


Domain annotation for each model (and alignments):
>> PI3K_P85_iSH2  Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   4.7   2.6e-06    0.0016      81     139 ..       5      63 ..       3      76 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.6e-06
  PI3K_P85_iSH2  81 hEieklqenleqlksrlkelhsskekLeedlkqqkeeereleReinalkpellqLqkrk 139
                    ++ie l++ + ++ +r+k+l+  k+++++++++ k++++++   + +l  +l +L+k++
     EPA05611.1   5 NDIEALETAILEVDQRIKKLEVHKDSVNKEIREGKSDNKTVTETLRRLERNLKELHKKQ 63 
                    6899***********************************99999999999999999865 PP

>> DUF4472  Domain of unknown function (DUF4472)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   3.5   3.3e-06    0.0021      26      95 ..       3      72 ..       2      76 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 3.3e-06
     DUF4472 26 heaekfelknkvlalenrvlelelerekaaeeiqslrerlaeleeekkeleeeyvvlkknyqalekefek 95
                +e+++  l++ +l+ ++r+  le++++  ++ei++ ++  +++ e  ++le +++ l+k+   l ke ++
  EPA05611.1  3 FENDIEALETAILEVDQRIKKLEVHKDSVNKEIREGKSDNKTVTETLRRLERNLKELHKKQVFLIKERDS 72
                57888899********************************************999999998877777665 PP

>> Flagellar_rod  Paraflagellar rod protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   4.5   4.2e-06    0.0027      17      88 ..       3      70 ..       1      74 [. 0.88

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.2e-06
  Flagellar_rod 17 veeDlekikekreeeaaadekqrkrykaqreesdkflqeneeqqeklvreieelereLqklaeerrelvedr 88
                   +e+D+e ++ ++ e+++      k+ ++++  ++k ++e ++  + + + +++ler+L++l +++ +l+++r
     EPA05611.1  3 FENDIEALETAILEVDQ----RIKKLEVHKDSVNKEIREGKSDNKTVTETLRRLERNLKELHKKQVFLIKER 70
                   57788877777777765....578899******************************************997 PP

>> CLZ  C-terminal leucine zipper domain of cyclic nucleotide-gated channels
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.2     0.021        14      28      61 ..       2      35 ..       1      37 [. 0.73
   2 !   15.1   1.4   3.5e-05     0.022      18      58 ..      34      74 ..      27      77 .] 0.86

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.021
         CLZ 28 eleekverLessLeaLqtrlarLlaeyessqrkL 61
                ++e+ +e Le+++   ++r+++L    +s+++++
  EPA05611.1  2 DFENDIEALETAILEVDQRIKKLEVHKDSVNKEI 35
                5677888888888888888888877777777665 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 3.5e-05
         CLZ 18 eaakagaeqkeleekverLessLeaLqtrlarLlaeyessq 58
                e ++ ++++k++ e ++rLe +L+ L+++   L++e +s  
  EPA05611.1 34 EIREGKSDNKTVTETLRRLERNLKELHKKQVFLIKERDSKS 74
                5678889**********************999999988865 PP

>> COG6  Conserved oligomeric complex COG6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   3.0   6.5e-06    0.0042      38      99 ..       6      67 ..       2      72 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 6.5e-06
        COG6 38 efqpvaeqLkriesdveklnelcdemkkklssakeetsdlleeaeeLkeekkklelkqkllk 99
                + +++++++ +++++++kl+   d+++k++++ k+++++++e+  +L++++k+l +kq  l 
  EPA05611.1  6 DIEALETAILEVDQRIKKLEVHKDSVNKEIREGKSDNKTVTETLRRLERNLKELHKKQVFLI 67
                677889999************************************************98775 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   3.3   0.00011      0.07      12      57 ..      16      59 ..       2      63 .. 0.50

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00011
  ABC_tran_CTD 12 eleaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeL 57
                  e++++I +LE  + ++++e+ +    sd ++++e+ ++le+  +eL
    EPA05611.1 16 EVDQRIKKLEVHKDSVNKEIREGK--SDNKTVTETLRRLERNLKEL 59
                  344555555555555555555555..55555555555555555555 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   4.4   1.3e-05    0.0084      96     156 ..      13      73 ..       2      77 .] 0.82

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.3e-05
      DUF724  96 kLlslkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaa 156
                  +l++ ++ +kl+ ++  ++k+i+e +s+++ + e ++ le++ +el+++++ l ++++++
  EPA05611.1  13 AILEVDQRIKKLEVHKDSVNKEIREGKSDNKTVTETLRRLERNLKELHKKQVFLIKERDSK 73 
                 5788899999999999999999999999999999999999999999999998877666655 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   5.6   2.6e-05     0.016      34      85 ..      20      71 ..       5      76 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.6e-05
         GAS 34 eieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkq 85
                 i++l+  +++ +ke+ e +++nk  +e+L+++e++++eL+k+  +  k++ 
  EPA05611.1 20 RIKKLEVHKDSVNKEIREGKSDNKTVTETLRRLERNLKELHKKQVFLIKERD 71
                577788888899999999999*******************999988877765 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   2.8   3.2e-05      0.02       7      73 ..       3      69 ..       1      75 [. 0.90

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.2e-05
       TMPIT  7 lekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelke 73
                +e+++++le++  e+ q++++l+ +++++ kei++ k + k ++++l++l++++ke ++++v  +ke
  EPA05611.1  3 FENDIEALETAILEVDQRIKKLEVHKDSVNKEIREGKSDNKTVTETLRRLERNLKELHKKQVFLIKE 69
                789999***********************************************99999888876665 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   4.6   4.5e-05     0.029      73     140 ..       4      71 ..       2      77 .] 0.89

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.5e-05
        ADIP  73 qskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlknalqqiktqyahelkkkd 140
                 +++ie l+t   + +++++ ++  + + +k++++ ++ +k+ +e l+rl+++l+++ +++   +k +d
  EPA05611.1   4 ENDIEALETAILEVDQRIKKLEVHKDSVNKEIREGKSDNKTVTETLRRLERNLKELHKKQVFLIKERD 71 
                 6899999999999999***999999***************************9999999877777776 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   5.1   5.2e-05     0.033      54     121 ..       5      72 ..       1      77 [] 0.50

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.2e-05
      APG6_N  54 eeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelqlelleleeelds 121
                 +++e+le +  e  + +k+le +++++++e+++ ++  + + e  +r  r  +el+ ++  l +e+ds
  EPA05611.1   5 NDIEALETAILEVDQRIKKLEVHKDSVNKEIREGKSDNKTVTETLRRLERNLKELHKKQVFLIKERDS 72 
                 44555555555555555555555555555555555555555555555555555555555545444444 PP

>> GLTP  Glycolipid transfer protein (GLTP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   1.4   5.4e-05     0.034      30      85 ..       2      57 ..       1      76 [. 0.78

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.4e-05
                HTHHHHHHHHHHTT....T-SBHH...HHHHHHHHTT-TT..STT-HHHHHHHHHHHHH CS
        GLTP 30 Dvegniekleeaykknpeeystle...slveaEkeeglakkkkkesatrallwLkRgLe 85
                D e++ie le+a+++ ++++++le   + v++E++eg  +   +++ t++l +L R L+
  EPA05611.1  2 DFENDIEALETAILEVDQRIKKLEvhkDSVNKEIREGKSD---NKTVTETLRRLERNLK 57
                89999********999887776652227788888776555...78***********997 PP

>> CCDC-167  Coiled-coil domain-containing protein 167
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   4.6   7.4e-05     0.048       5      64 ..       6      62 ..       2      67 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.4e-05
    CCDC-167  5 eIdkleeklascrerLeaverrlrkeelseeeResleeEeaslkeqleenekeLksLrke 64
                +I+ le +++++ +r++++e   +k+++ +e Re+     ++++e l++ e++Lk+L+k+
  EPA05611.1  6 DIEALETAILEVDQRIKKLEV--HKDSVNKEIREGK-SDNKTVTETLRRLERNLKELHKK 62
                688888888888888888875..5566667777775.58899****************96 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.4   0.00027      0.17      69      93 ..       2      26 ..       1      29 [. 0.92
   2 ?    3.1   0.1      0.18   1.1e+02      31      55 ..      44      61 ..      27      71 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00027
     BLOC1_2 69 qiekqvteLeeavseLDeyskeLEa 93
                ++e++++ Le+a+ e+D+ +k+LE+
  EPA05611.1  2 DFENDIEALETAILEVDQRIKKLEV 26
                5799********************7 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.18
     BLOC1_2 31 aasekykklkdvaaslekkleklne 55
                +       +++ +  le++l++l +
  EPA05611.1 44 T-------VTETLRRLERNLKELHK 61
                2.......23333333333333333 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   3.1   9.1e-05     0.058      23      83 ..       4      64 ..       1      75 [. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.1e-05
                XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHH CS
  Laminin_II 23 sqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqlee 83
                ++++e ++  + e+++ +++ + + ++ nk ir+ ++  k++++++ +L+  lkel ++++
  EPA05611.1  4 ENDIEALETAILEVDQRIKKLEVHKDSVNKEIREGKSDNKTVTETLRRLERNLKELHKKQV 64
                6778888888888888888888888899999999999999999999999999999999875 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   3.1   0.00019      0.12      64     124 .]       3      63 ..       1      63 [. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00019
     DUF1664  64 LssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerieekQ 124
                 ++++i+ +++ + e+ + +k+++ + ++v+++++e ++d ++v e+ + le +l+++ +kQ
  EPA05611.1   3 FENDIEALETAILEVDQRIKKLEVHKDSVNKEIREGKSDNKTVTETLRRLERNLKELHKKQ 63 
                 5677888888888888888888888888999999999999999999999999999999888 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   3.9    0.0017       1.1      16      55 ..       4      43 ..       1      74 [. 0.65

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0017
                HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXX CS
        SlyX 16 edtieeLndvvaeqqqqidrlqrqlrllaerlkeleessg 55
                e+ ie+L  ++ e +q+i++l+ + + ++++++e +++++
  EPA05611.1  4 ENDIEALETAILEVDQRIKKLEVHKDSVNKEIREGKSDNK 43
                5556666666666666666666666666666665555543 PP

>> Vac_Fusion  Chordopoxvirus multifunctional envelope protein A27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.2    0.0067       4.3      13      42 ..       4      33 ..       1      37 [. 0.80
   2 ?    7.7   4.9    0.0041       2.6       2      49 ..      21      68 ..      20      72 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0067
                HHHHHHHHHHHHHHHHHHHHHH-XXXXXXX CS
  Vac_Fusion 13 ekdfqlvikcckrvnealkRlEnHleTlRk 42
                e+d + ++    +v++++k lE H + + k
  EPA05611.1  4 ENDIEALETAILEVDQRIKKLEVHKDSVNK 33
                56667777778899**********998866 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0041
                HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-XXXXXXXXXXXXXX CS
  Vac_Fusion  2 lkdleerllvlekdfqlvikcckrvnealkRlEnHleTlRkamlaLak 49
                +k+le    +++k+  +  +  k+v e l+RlE+ l  l k  + L k
  EPA05611.1 21 IKKLEVHKDSVNKEIREGKSDNKTVTETLRRLERNLKELHKKQVFLIK 68
                6777777778889999999999************99999888777766 PP

>> Nup88  Nuclear pore component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   6.0    0.0002      0.13     549     607 ..      10      68 ..       4      74 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0002
       Nup88 549 qelvreeiekrvkllkkqkeqqleelqsleeerkslseraeklAekyeeikdkQeklvr 607
                  e++  e+++r+k l+ +k+   +e+++ + + k+++e+  +l  ++ e ++kQ  l++
  EPA05611.1  10 LETAILEVDQRIKKLEVHKDSVNKEIREGKSDNKTVTETLRRLERNLKELHKKQVFLIK 68 
                 5778889***********************************************88876 PP

>> Exog_C  Endo/exonuclease (EXOG) C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1      0.21   1.3e+02      28      45 ..       7      24 ..       3      30 .. 0.81
   2 ?   10.0   0.4    0.0011      0.71      18      36 ..      46      64 ..      44      69 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.21
      Exog_C 28 mkeLkeagiepDeyLlkl 45
                ++ L+ a +e D+ + kl
  EPA05611.1  7 IEALETAILEVDQRIKKL 24
                578999999999999886 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0011
      Exog_C 18 ArtlkRLekvmkeLkeagi 36
                + tl+RLe+ +keL ++ +
  EPA05611.1 46 TETLRRLERNLKELHKKQV 64
                67************99876 PP

>> EMP24_GP25L  emp24/gp25L/p24 family/GOLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   2.9   0.00031       0.2      98     139 ..      27      68 ..       1      74 [. 0.70

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00031
  EMP24_GP25L  98 gseasdykdsak.kekletleselkkleekldsikreqkylre 139
                  ++++ + k++   k++ +t++++l++le++l++++++q +l +
   EPA05611.1  27 HKDSVN-KEIREgKSDNKTVTETLRRLERNLKELHKKQVFLIK 68 
                  222222.333335788899*******************99865 PP

>> Allexi_40kDa  Allexivirus 40kDa protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   2.4   0.00034      0.22      81     141 ..       8      70 ..       2      76 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00034
  Allexi_40kDa  81 selrdalrtltklldklksvekklelsae..tasdskllkklesietsleelhakldelssse 141
                     l +a+ ++++ ++kl+  +++++++++  + +++ ++++l  +e++l+elh+k   l+++ 
    EPA05611.1   8 EALETAILEVDQRIKKLEVHKDSVNKEIRegKSDNKTVTETLRRLERNLKELHKKQVFLIKER 70 
                   56677788888888888777777666654114555667789999*********9976666655 PP

>> ACCA  Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   2.6   0.00035      0.22       3      61 ..       2      66 ..       1      74 [. 0.63

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00035
        ACCA  3 dfekpiaeleekieelkklaee...sevdlseeiekle...kkleklkkeiyknltpwqkvqlaR 61
                dfe++i+ le+ i e+++  ++   ++ ++++ei++ +   k+++++ +++ +nl+++ k q+  
  EPA05611.1  2 DFENDIEALETAILEVDQRIKKlevHKDSVNKEIREGKsdnKTVTETLRRLERNLKELHKKQVFL 66
                78888888888888877776663334444777776554111445555567778888888887755 PP

>> Inositol_P  Inositol monophosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.6   0.00029      0.19      10      62 ..       7      64 ..       2      76 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00029
                HHHHHHHHHHHHHHTT.....TSEEEESTTTCCHHHHHHHHHHHHHHHHHHHHHHHHS CS
  Inositol_P 10 velaakagevlreefs.....enelvieekskegeedlvtaadeaveelilealaekf 62
                +e+   a+  ++++++     +++++ e  ++++++ +vt++ +++e++++e  ++++
  EPA05611.1  7 IEALETAILEVDQRIKklevhKDSVNKEIREGKSDNKTVTETLRRLERNLKELHKKQV 64
                4444455555555554222235555555555899999**************9866654 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   6.8     0.045        29      19      28 ..      28      37 ..       1      71 [. 0.49

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.045
                HHHHHHHHHH CS
       DivIC 19 ykqlkqeiaa 28
                  ++++ei +
  EPA05611.1 28 KDSVNKEIRE 37
                2233333333 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   1.6     0.013       8.1       5      38 ..       3      36 ..       1      37 [. 0.77
   2 ?    9.1   3.4    0.0027       1.7       1      40 [.      20      59 ..      14      61 .. 0.62

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.013
   FlaC_arch  5 lEnklsklsteletvkkeneelsksveelkenVk 38
                +En+++ l+t +  v + +++l+   + ++++++
  EPA05611.1  3 FENDIEALETAILEVDQRIKKLEVHKDSVNKEIR 36
                7888888888888888888888888888877776 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0027
   FlaC_arch  1 ridelEnklsklsteletvkkeneelsksveelkenVkdl 40
                ri++lE   +++  e+   k++n+ + +++ +l++n k+l
  EPA05611.1 20 RIKKLEVHKDSVNKEIREGKSDNKTVTETLRRLERNLKEL 59
                4555555555555577777777777777777777777665 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   7.6    0.0095       6.1       8      49 ..      16      57 ..       2      67 .. 0.52
   2 ?    5.0   0.5     0.044        28       3      30 ..      46      74 ..      44      76 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0095
        XhlA  8 rietkldnleervdkleekaaeaeekiknleedlkklesnqk 49
                ++++++++le   d +++  +e ++  k ++e+l +le n+k
  EPA05611.1 16 EVDQRIKKLEVHKDSVNKEIREGKSDNKTVTETLRRLERNLK 57
                334444444442234444444444444555555555555554 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.044
        XhlA  3 kerlerietkldnlee.rvdkleekaaea 30
                 e l r+e++l++l + +v  ++e+ ++ 
  EPA05611.1 46 TETLRRLERNLKELHKkQVFLIKERDSKS 74
                68899999999999987888888877765 PP

>> BRI3BP  Negative regulator of p53/TP53
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1      0.32     2e+02     159     178 ..       8      27 ..       2      33 .. 0.74
   2 ?    8.1   1.3    0.0027       1.7     151     179 ..      35      63 ..      28      64 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.32
      BRI3BP 159 asleakvrsLerqvrelnkr 178
                 + le+++ + ++++++l+  
  EPA05611.1   8 EALETAILEVDQRIKKLEVH 27 
                 56788888888888888765 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0027
      BRI3BP 151 aksseesgasleakvrsLerqvrelnkrq 179
                 +++++++++++ + +r Ler ++el+k+q
  EPA05611.1  35 IREGKSDNKTVTETLRRLERNLKELHKKQ 63 
                 5777899*******************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2174  (0.121256); expected 358.6 (0.02)
Passed bias filter:                      974  (0.0543254); expected 358.6 (0.02)
Passed Vit filter:                       161  (0.00897987); expected 17.9 (0.001)
Passed Fwd filter:                        28  (0.00156172); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              28  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 494.81
//
Query:       EPA05612.1  [L=578]
Description: CBS domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.8e-24   84.2  23.7    1.4e-17   63.3   6.6    2.3  2  TrkH      Cation transport protein
      1e-17   64.3   3.0    1.8e-10   41.1   0.2    2.5  2  CBS       CBS domain


Domain annotation for each model (and alignments):
>> TrkH  Cation transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   9.4   2.8e-10   2.5e-06      27     241 ..     183     378 ..     157     395 .. 0.81
   2 !   63.3   6.6   1.6e-21   1.4e-17     317     491 ..     414     574 ..     391     577 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 2.8e-10
        TrkH  27 kyplalkddfqivkaaeialsvdgtlklll....esaslaf.ldalfeavsgltttglsvivveeslprsgltlraqlqqiGglgvvvlaylslptlgr 120
                 k  l+l+++++ v+++   l+ +gt++ l     e+++ ++ ++a f++  g+tt g+s++++ e+lp+s +++r+++q +Gg   +++ yl++  +  
  EPA05612.1 183 KASLNLHQASILVVSSLFLLTLIGTIPYLYvlpyEGSNTEIfANAFFSSAAGFTTGGISLFDQPENLPQSFTFYRSFTQLVGG---MSFIYLIITAFY- 277
                 56789999999999************98778998666666559****************************************...9999***98882. PP

        TrkH 121 gsaflylseaqkeelggkelrslselikilvvyyvgleilafvllvvliytakaysevvdstgvsplwwaffhsmSafnnlGfsltpnSlasfnknivi 219
                    +l++    + + +gk l   ++ ++i +++++ + i+a +l+         ++e        ++ + +  +mS++ ++Gf  +p S    n  i+ 
  EPA05612.1 278 PESKLQS---MRGFISGKTLHMRELFATITIIFILYISIIASLLY--------LFGER-------NIIDNVSLAMSTVATGGF--IPTSTILHNL-IWE 355
                 2223332...35578888887777788888888888899999999........35555.......778999999********9..6777777777.665 PP

        TrkH 220 .llvaiifiilGnigFpillrvi 241
                  ++v+i  +ilG+  F+ ++++ 
  EPA05612.1 356 eKMVLIGGMILGALPFTFHYSLV 378
                 15778889999999999999876 PP

  == domain 2  score: 63.3 bits;  conditional E-value: 1.6e-21
        TrkH 317 lkalFqsvstrta.GFsvvdlsnlhpaikvllvlmmyigglpgStaggIrrtnvyeefslgkyeieqekepkavskksidgkhlerqllvdlwslflvl 414
                 l ++F  vs++t+ G+++  ls    +  ++l++ m+igg++ StaggI++ +++ + + +k  i+++k+ +   +  ++++ +   +++  + l+  l
  EPA05612.1 414 LTSVFYTVSASTTaGLQSDNLSDFNGSAHLILIILMFIGGCGFSTAGGIKIFRLMHL-KDIKKIIDKQKKSE--LSPELKKELIVTLIIIIAFPLVASL 509
                 66789999998888***************************************8765.67788888888855..5555555555555555566666666 PP

        TrkH 415 liilileglklsdvqepdfsffdiLfevvSaygtvGLSlGaknaslsaqlttisklvlialmirGrlrglpvlldra 491
                  +++++    l+dv     +f d++ e++  ++t GLS G    ++  q  + +k+++++lmi Grl+++ ++  ++
  EPA05612.1 510 SAVYLMV---LEDV-----NFQDAFLESTGVITTGGLSAG----IIDLQTDPTAKIIFSFLMIFGRLEIIAIIYIFV 574
                 6666665...5555.....59*******************....9**************************998887 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.3   6.8e-09   6.1e-05      18      56 ..       8      46 ..       1      47 [. 0.85
   2 !   41.1   0.2     2e-14   1.8e-10       2      55 ..      58     111 ..      57     113 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 6.8e-09
                HHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
         CBS 18 leealelmrekgvsrlPVVdedgklvGivtlrDllrall 56
                 ++a++l+ +++ + + V+de++ +vGivt++D++r+++
  EPA05612.1  8 TRDAARLLQHYETDDIIVTDENNIPVGIVTDEDIIRKVS 46
                5899****77779999788*****************875 PP

  == domain 2  score: 41.1 bits;  conditional E-value: 2e-14
                 HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEE.EEEEHHHHHHHH CS
         CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklv.GivtlrDllral 55 
                 +dim+++++t+++ ++l +al +mr+++v+ lPVV + + lv Gi+ +  +++++
  EPA05612.1  58 KDIMNTPLITINEKASLQDALHKMRDNNVRKLPVVSKKN-LViGIIYQVTIANVI 111
                 79*********************************5444.555***887777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (578 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       868  (0.0484132); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.68u 0.30s 00:00:00.98 Elapsed: 00:00:00.51
# Mc/sec: 3430.45
//
Query:       EPA05613.1  [L=46]
Description: hypothetical protein BG20_I1058 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 321.52
//
Query:       EPA05614.1  [L=80]
Description: hypothetical protein BG20_I1035 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 569.60
//
Query:       EPA05615.1  [L=730]
Description: translation elongation factor aEF-2 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      4e-60  202.7   0.6    6.4e-60  202.0   0.6    1.3  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    2.8e-21   75.3   0.0    9.2e-21   73.7   0.0    2.0  1  EFG_C        Elongation factor G C-terminus
    1.2e-20   73.5   0.0    6.1e-20   71.2   0.0    2.2  2  EFG_IV       Elongation factor G, domain IV
    1.2e-20   73.4   0.7    3.2e-20   72.0   0.7    1.8  1  EFG_II       Elongation Factor G, domain II
    2.1e-12   47.2   0.1    8.7e-12   45.3   0.1    2.2  1  GTP_EFTU_D2  Elongation factor Tu domain 2
  ------ inclusion threshold ------
      0.027   14.6   0.0      0.061   13.4   0.0    1.6  1  MMR_HSR1     50S ribosome-binding GTPase
      0.041   13.7   0.0      0.091   12.6   0.0    1.6  1  RF3_C        Class II release factor RF3, C-terminal domain
      0.057   13.2   0.0       0.13   12.1   0.0    1.5  1  DUF4393      Domain of unknown function (DUF4393)


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.0   0.6   2.8e-63   6.4e-60       2     193 ..      19     256 ..      18     257 .. 0.89

  Alignments for each domain:
  == domain 1  score: 202.0 bits;  conditional E-value: 2.8e-63
                 CEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE..TTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEE CS
    GTP_EFTU   2 rirnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle..ketkkylinliDtPGHvdFskevirglrvlDgav 98 
                 +irn+++i+hvDhGKtT++d+Ll+++g+i+   + a+++ ++D+ keE+ergiTi  a+++l+  +++k+y in+iDtPGHvdFs  vir+lr++Dga 
  EPA05615.1  19 QIRNFSVIAHVDHGKTTMSDSLLAASGIIAP--SAAGKALAMDFDKEEQERGITIYQANVTLFftQKEKEYVINMIDTPGHVDFSGRVIRSLRAIDGAT 115
                 79*****************************..66777899*********************9877********************************* PP

                 EEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGSTHHHHHHHHHHHHHHHHHH..........HHHHHHHHHTTT............TTEEEEEEBT CS
    GTP_EFTU  99 lvvdaveGvepqteevlrlalkegvpiivfiNKmDrlkaelkeiveevkqklsrk..........eeklekygekge............kevpvvfgSa 175
                 +v+daveG+++qte+v r+al+e+v++++fiNK+Drl++el+ ++e+++++l  +                                  +e +v fgSa
  EPA05615.1 116 VVCDAVEGIMTQTETVTRMALEERVRPVLFINKVDRLIKELRLTPEKMQETLAGVvssfnqlvetY----------AepeykdkwkvsiQEASVTFGSA 204
                 ****************************************************77766664444330..........23334556667777889****** PP

                 TTTBTHH..................................HHHHHHHHHSH CS
    GTP_EFTU 176 lkgegvk..................................tllealvellp 193
                 +++++++                                  ++l ++v+++p
  EPA05615.1 205 KDKWAFNvdimkekgitfkdvidayknekvddlvarapladAVLGMVVKHVP 256
                 ****888888888888899889999999999999999888888888888887 PP

>> EFG_C  Elongation factor G C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.7   0.0   4.1e-24   9.2e-21       2      86 ..     620     703 ..     619     706 .. 0.97

  Alignments for each domain:
  == domain 1  score: 73.7 bits;  conditional E-value: 4.1e-24
                 EEEEEEEEEEEEECCCCCCHHHHHHHCT-EEEEEEEE.TTEEEEEEEEEGGG-TTHHHCHHHCTTTS-EEEEEEEEEEE--HHHH CS
       EFG_C   2 llEPivkveievpeeyvgkvisdlssrrGeiedmeqdasgrviieaeiPlaeligfateLrslTkGegsfsmefsgYeevpgdkl 86 
                 +lEP+  +e++vp+++vg+v + +s +rG+++dm+q+ ++  ii +eiP+ae++++++++r  T+G+++++++f+ + e+p++++
  EPA05615.1 620 ILEPMLAIEVRVPTDLVGNVATVISGKRGKVLDMQQK-GAASIIVGEIPAAETFTLSEAMRGQTAGRATWNTSFKAWTELPKSIA 703
                 8************************************.******************************************99876 PP

>> EFG_IV  Elongation factor G, domain IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.86   1.9e+03       3      41 ..     462     494 ..     460     504 .. 0.59
   2 !   71.2   0.0   2.7e-23   6.1e-20      12     120 ..     510     616 ..     501     617 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.86
                 CESCEE.SS-CCHCCCCCCCHTSSSHCCCCCEEEECCTT CS
      EFG_IV   3 VayrEtirkpvkereeklkkqsggdgqyakvileiePle 41 
                 ++yrEt++  ++    ++ k     +   k+ +++ePle
  EPA05615.1 462 INYRETVKGSCE---PIMSKS---PNRHNKIFMKVEPLE 494
                 889998887777...333332...223345666666665 PP

  == domain 2  score: 71.2 bits;  conditional E-value: 2.7e-23
                 -CCHCCCCCCCHTSSSHCCCCCEEEECCTTTTSSEEEEE--STCCCHCCCCHHHHCCCCCCTTS-TTTS--EESEEEEEEEEE--T..TTC-HHHHHHH CS
      EFG_IV  12 pvkereeklkkqsggdgqyakvileiePleegsgnefvdetkggqvpkeyieavekGfqealkeGplagepvtdvkvtLldgslhe..vdsseaafkpa 108
                 + k+++  l k +g+d +  k i++++P     gn++++ tkg+q  +e  ++++ Gf+e++keGpl++e+++d+k+ ++  + he   +++ +++ pa
  EPA05615.1 510 KDKKVVSDLLKGAGWDTDTIKRIMKMDPR----GNVMINGTKGVQFIQESTDSINSGFEEVMKEGPLCKEQMRDCKFIFTHFVPHEdtAHRGLSQLGPA 604
                 445588888888****************5....9***************************************************************** PP

                 HCHHHHHHHHCC CS
      EFG_IV 109 arralkeallkA 120
                 +rra++ all+A
  EPA05615.1 605 SRRACMGALLTA 616
                 *********998 PP

>> EFG_II  Elongation Factor G, domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.0   0.7   1.4e-23   3.2e-20       1      73 [.     386     457 ..     386     459 .. 0.95

  Alignments for each domain:
  == domain 1  score: 72.0 bits;  conditional E-value: 1.4e-23
      EFG_II   1 fPePvislaiepkskadedklskaLarlleEDptlrverdeeTketilsGmGelHleivverlkreykvevel 73 
                 ++ePv+++aiepk  +d  kl ++L++l+ EDp l v+ dee++et+++GmG lHl++++ r++   kve+ +
  EPA05615.1 386 VSEPVVQIAIEPKHPKDLPKLVEVLKQLTIEDPNLVVKIDEESGETLVAGMGVLHLDVATHRIQDA-KVEIIT 457
                 689************************************************************985.888776 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   0.1   3.9e-15   8.7e-12       1      73 [.     305     371 ..     305     372 .. 0.96

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 3.9e-15
                  EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEE CS
  GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtl 73 
                  G va gr++sGt+k G+++ i   d +++   +r++s+  f+++++e+v +  aG+i a+ gl +a ++G+t+
   EPA05615.1 305 GPVAIGRLFSGTIKDGQTINI--IDAKRE---GRVQSVNFFMGNQREQVGELGAGNIPALLGLTEA-RAGNTI 371
                  679******************..999888...*********************************8.*****9 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.7e-05     0.061      10     113 ..      31     147 ..      22     148 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.7e-05
                 SSHHHHHHHHHT.......................STEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHCTSEEEEEEET CS
    MMR_HSR1  10 vGKStLinaltg.......................ekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkaflaleeadlillvvda 85 
                  GK+t+  +l+                        e+ i+  ++ +T+  ++++    +  i+++DtpG ++        g+ +++l+  d + +v+da
  EPA05615.1  31 HGKTTMSDSLLAasgiiapsaagkalamdfdkeeqERGITIYQANVTLFFTQKEK---EYVINMIDTPGHVD------FSGRVIRSLRAIDGATVVCDA 120
                 5777777777742222222222222222222111123334444444444444433...3569*******666......4667777767789*******9 PP

                 TTTCSHHHHHHHHHHHHHTTSEEEEEEE CS
    MMR_HSR1  86 seeklkpldeeleelleeakkplilvln 113
                   e++  + e++ ++  e++ + +l +n
  EPA05615.1 121 V-EGIMTQTETVTRMALEERVRPVLFIN 147
                 8.66878878888887665544455555 PP

>> RF3_C  Class II release factor RF3, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0     4e-05     0.091      15      70 ..     395     450 ..     376     491 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4e-05
                 EEESSGGGHHHHHHHHHHHHHCTSSEEEEET.TSS-EEEEESSTHHHHHHHHHHHH CS
       RF3_C  15 vrlkdplkrkqlrkgleqLaeEGavqvfkeeeageelilgaVGqLQfeVveeRlkn 70 
                 ++ k p    +l + l+qL+ E    v k +e++ e++++ +G+L ++V ++R+++
  EPA05615.1 395 IEPKHPKDLPKLVEVLKQLTIEDPNLVVKIDEESGETLVAGMGVLHLDVATHRIQD 450
                 566777777789999**************99999*******************985 PP

>> DUF4393  Domain of unknown function (DUF4393)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   5.6e-05      0.13      56     143 ..     404     516 ..     398     556 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.6e-05
     DUF4393  56 paFveIikqLspdeAklLkilk.............................sgeeipiidiklekeeikeskesiknsfsdlhekvvlenpekvkasld 125
                 p  ve++kqL+ ++++l  ++                                ++ p+i+++ + +   +s+e i+ ++ + h+k++++  e +++ + 
  EPA05615.1 404 PKLVEVLKQLTIEDPNLVVKIDeesgetlvagmgvlhldvathriqdakveIITSEPLINYRETVK---GSCEPIMSKSPNRHNKIFMK-VEPLEPAIA 498
                 7789************************************99999999887777888888887777...99999999999999996655.5999***** PP

     DUF4393 126 nLerlgLiklsekqklte 143
                 n+ r+g i  ++++k+ +
  EPA05615.1 499 NMLRTGEISDMKDKKVVS 516
                 ******999999888554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (730 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.68u 0.30s 00:00:00.98 Elapsed: 00:00:00.46
# Mc/sec: 4720.31
//
Query:       EPA05616.1  [L=165]
Description: tetratricopeptide repeat protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.3e-23   80.5   8.3    2.1e-06   27.3   0.1    4.2  4  TPR_1       Tetratricopeptide repeat
    3.2e-21   73.7   4.2    5.4e-05   23.0   0.1    4.2  4  TPR_2       Tetratricopeptide repeat
    2.3e-14   52.3   4.3    0.00029   20.8   0.0    3.6  3  TPR_8       Tetratricopeptide repeat
    1.4e-13   50.3   4.0     0.0016   18.1   0.0    4.1  4  TPR_11      TPR repeat
    1.3e-10   41.2   0.0      0.094   13.6   0.0    4.1  4  TPR_14      Tetratricopeptide repeat
    2.1e-10   40.3   2.5       0.08   13.4   0.0    4.0  4  TPR_17      Tetratricopeptide repeat
    3.1e-10   40.2   1.5    4.4e-05   23.7   0.2    3.7  3  TPR_12      Tetratricopeptide repeat
    3.8e-09   36.5   0.0    0.00029   20.9   0.0    2.3  2  TPR_9       Tetratricopeptide repeat
    6.9e-09   35.1   0.4      0.015   15.3   0.0    4.1  4  TPR_7       Tetratricopeptide repeat
    8.3e-09   36.0   0.0     0.0029   18.2   0.0    2.5  2  TPR_16      Tetratricopeptide repeat
    8.9e-08   32.5   0.5     0.0019   18.7   0.1    3.0  3  TPR_19      Tetratricopeptide repeat
    2.7e-07   30.7   0.6    4.3e-05   23.6   0.1    2.2  2  ANAPC3      Anaphase-promoting complex, cyclosome, subunit 3
    5.2e-07   29.6   0.4       0.58   10.3   0.0    4.1  4  Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
    1.4e-06   28.0   0.0       0.64   10.0   0.0    3.7  4  TPR_10      Tetratricopeptide repeat
      2e-06   27.7   2.9    3.6e-05   23.7   0.1    3.4  3  TPR_3       Tetratricopeptide repeat
    0.00012   22.4   0.6        1.4    9.7   0.0    3.7  4  TPR_6       Tetratricopeptide repeat
     0.0002   21.4   0.0        4.7    7.3   0.0    3.3  3  DUF3856     Domain of Unknown Function (DUF3856)
    0.00023   21.1   1.3       0.68   10.0   0.1    4.0  4  MIT         MIT (microtubule interacting and transport) domai
  ------ inclusion threshold ------
      0.084   12.9   0.0        1.1    9.4   0.0    2.2  2  CODH_A_N    Carbon monoxide dehydrogenase subunit alpha N-ter
       0.12   12.5   0.0       0.14   12.3   0.0    1.1  1  DUF531      Protein of unknown function (DUF531)
       0.12   12.6   0.1        8.4    6.9   0.1    3.0  2  PPR         PPR repeat


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.4     0.058        50      13      34 .]      17      38 ..       9      38 .. 0.85
   2 !   26.5   0.0   4.4e-09   3.8e-06       3      34 .]      41      72 ..      39      72 .. 0.94
   3 !   27.3   0.1   2.4e-09   2.1e-06       2      33 ..      74     105 ..      73     106 .. 0.94
   4 !   25.5   0.2   8.8e-09   7.5e-06       3      34 .]     109     140 ..     107     140 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.058
                HTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1 13 klgkydeAleyyekALelnPnn 34
                + g++ +Al+ y+  L+ +P+n
  EPA05616.1 17 EDGNFLDALKLYDLILKKEPQN 38
                569999**********999987 PP

  == domain 2  score: 26.5 bits;  conditional E-value: 4.4e-09
                HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1  3 alynlGnayfklgkydeAleyyekALelnPnn 34
                al  +G+++++lg++++ ++yy+k++ l+P n
  EPA05616.1 41 ALLDKGVTLQNLGRLKQSIKYYDKVIHLDPRN 72
                8889**************************87 PP

  == domain 3  score: 27.3 bits;  conditional E-value: 2.4e-09
                 HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
       TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPn 33 
                 +al n+G+ +++ +ky +A+ +y+ AL+++ +
  EPA05616.1  74 QALINKGASLHSSKKYHDAIHCYDLALKIDKK 105
                 699**************************975 PP

  == domain 4  score: 25.5 bits;  conditional E-value: 8.8e-09
                 HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                 al  +G+ + +lg++++Al++++kAL+++ ++
  EPA05616.1 109 ALAYKGLSLGELGNLNDALKHFKKALSIEKDY 140
                 8899***********************99875 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.2    0.0014       1.2       8      34 .]      12      38 ..       8      38 .. 0.91
   2 !   20.3   0.0   4.7e-07    0.0004       3      34 .]      41      72 ..      40      72 .. 0.93
   3 !   20.1   0.0   5.2e-07   0.00044       2      33 ..      74     105 ..      73     106 .. 0.94
   4 !   23.0   0.1   6.3e-08   5.4e-05       3      33 ..     109     139 ..     107     140 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0014
       TPR_2  8 GlayyklgdyeeAleafekAleldPnn 34
                ++ + + g++ +Al++++  l+ +P+n
  EPA05616.1 12 AYELCEDGNFLDALKLYDLILKKEPQN 38
                7788899******************97 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 4.7e-07
       TPR_2  3 alynlGlayyklgdyeeAleafekAleldPnn 34
                al   G  + +lg++++ +++++k++ ldP+n
  EPA05616.1 41 ALLDKGVTLQNLGRLKQSIKYYDKVIHLDPRN 72
                567789************************87 PP

  == domain 3  score: 20.1 bits;  conditional E-value: 5.2e-07
       TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPn 33 
                 +al n G ++  +++y +A+++++ Al++d +
  EPA05616.1  74 QALINKGASLHSSKKYHDAIHCYDLALKIDKK 105
                 5899*************************976 PP

  == domain 4  score: 23.0 bits;  conditional E-value: 6.3e-08
       TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                 al + Gl++ +lg++++Al++f+kAl+++ +
  EPA05616.1 109 ALAYKGLSLGELGNLNDALKHFKKALSIEKD 139
                 8999***********************9876 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   3.4e-07   0.00029       3      33 ..      41      71 ..      39      72 .. 0.93
   2 !   16.7   0.3   7.1e-06    0.0061       2      33 ..      74     105 ..      73     106 .. 0.94
   3 !   14.5   0.4   3.7e-05     0.031       7      33 ..     113     139 ..     109     140 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3.4e-07
                HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
       TPR_8  3 ayynlgsiylklgdyeeAkeyyekaleldpd 33
                a++ +g ++++lg+++++++yy k++ ldp 
  EPA05616.1 41 ALLDKGVTLQNLGRLKQSIKYYDKVIHLDPR 71
                67889************************97 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 7.1e-06
                 CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
       TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                 +a+ n+g  +++ ++y+ A+ +y  al++d++
  EPA05616.1  74 QALINKGASLHSSKKYHDAIHCYDLALKIDKK 105
                 7999**************************97 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 3.7e-05
                 HHHHHHHTT-HHHHHHHHHHHHHHHHH CS
       TPR_8   7 lgsiylklgdyeeAkeyyekaleldpd 33 
                 +g+ + +lg+++ A + ++kal++++d
  EPA05616.1 113 KGLSLGELGNLNDALKHFKKALSIEKD 139
                 688999******************997 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0      0.03        25       3      42 .]      14      53 ..      12      53 .. 0.91
   2 !   18.1   0.0   1.8e-06    0.0016       7      39 ..      52      84 ..      51      87 .. 0.94
   3 !   17.8   0.0   2.3e-06     0.002       3      42 .]      82     121 ..      80     121 .. 0.91
   4 !   15.6   0.0   1.1e-05    0.0096       6      28 ..     119     141 ..     114     144 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.03
      TPR_11  3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42
                +++e G++ +A++ Y   lk  P+n  a++  G++++++G
  EPA05616.1 14 ELCEDGNFLDALKLYDLILKKEPQNIVALLDKGVTLQNLG 53
                788999999************************9999988 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 1.8e-06
      TPR_11  7 qGkyeeAieaYkkAlkldPdnaeayynLGlayy 39
                +G+++++i+ Y k + ldP n  a+ n G+ ++
  EPA05616.1 52 LGRLKQSIKYYDKVIHLDPRNIQALINKGASLH 84
                69***************************9887 PP

  == domain 3  score: 17.8 bits;  conditional E-value: 2.3e-06
      TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                  +++  ky +Ai +Y  Alk+d +++ a+   Gl + ++G
  EPA05616.1  82 SLHSSKKYHDAIHCYDLALKIDKKSPMALAYKGLSLGELG 121
                 678999**********************999999988887 PP

  == domain 4  score: 15.6 bits;  conditional E-value: 1.1e-05
      TPR_11   6 eqGkyeeAieaYkkAlkldPdna 28 
                 e+G++++A++++kkAl +  d+ 
  EPA05616.1 119 ELGNLNDALKHFKKALSIEKDYD 141
                 89******************996 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   0.00028      0.24       5      40 ..       7      44 ..       3      48 .. 0.83
   2 !   13.6   0.0   0.00011     0.094       3      41 ..      41      79 ..      39      82 .. 0.90
   3 ?    4.6   0.0     0.083        71      11      41 ..      83     113 ..      79     116 .. 0.85
   4 !    9.4   0.0    0.0025       2.1       8      36 ..     114     142 ..     107     145 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00028
      TPR_14  5 lalaeall..alGdpdeAiallrralalaPddaeawll 40
                ++l +a++  + G++ +A++l++ +l++ P++ +a+l 
  EPA05616.1  7 RMLSQAYElcEDGNFLDALKLYDLILKKEPQNIVALLD 44
                6788888744679********************99986 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 0.00011
      TPR_14  3 allalaeallalGdpdeAiallrralalaPddaeawlll 41
                all+ +  l +lG+++++i+++++++ l+P + +a++  
  EPA05616.1 41 ALLDKGVTLQNLGRLKQSIKYYDKVIHLDPRNIQALINK 79
                6788889999**********************9999866 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.083
      TPR_14  11 llalGdpdeAiallrralalaPddaeawlll 41 
                 l  + ++ +Ai +++ al+ + +++ a+ + 
  EPA05616.1  83 LHSSKKYHDAIHCYDLALKIDKKSPMALAYK 113
                 55677899*****************998775 PP

  == domain 4  score: 9.4 bits;  conditional E-value: 0.0025
      TPR_14   8 aeallalGdpdeAiallrralalaPddae 36 
                 +  l +lG++ +A++++++al+   d + 
  EPA05616.1 114 GLSLGELGNLNDALKHFKKALSIEKDYDL 142
                 5556689***************9998776 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   9.3e-05      0.08       2      33 ..      28      59 ..      27      60 .. 0.89
   2 !   13.0   0.0   0.00012       0.1       1      33 [.      61      93 ..      61      94 .. 0.95
   3 !   11.5   0.2   0.00035       0.3       1      33 [.      95     127 ..      95     128 .. 0.95
   4 ?   -1.9   0.0       6.8   5.8e+03       2      12 ..     130     140 ..     129     143 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.3e-05
      TPR_17  2 ylkaleldPnnadaynnLAelllknGdlmtAr 33
                y   l+++P n +a+  ++++l ++G+l++ +
  EPA05616.1 28 YDLILKKEPQNIVALLDKGVTLQNLGRLKQSI 59
                666799*********************99876 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00012
      TPR_17  1 lylkaleldPnnadaynnLAelllknGdlmtAr 33
                +y k++ ldP n  a+ n++  l++ +++ +A+
  EPA05616.1 61 YYDKVIHLDPRNIQALINKGASLHSSKKYHDAI 93
                69**************************99996 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.00035
      TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtAr 33 
                 +y  al++d++++ a+ +++  l ++G+l +A+
  EPA05616.1  95 CYDLALKIDKKSPMALAYKGLSLGELGNLNDAL 127
                 7999*************************9997 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 6.8
      TPR_17   2 ylkaleldPnn 12 
                 ++kal +++++
  EPA05616.1 130 FKKALSIEKDY 140
                 78999887765 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1      0.36   3.1e+02      13      28 ..      15      30 ..       6      33 .. 0.77
   2 !   21.6   0.1   2.3e-07   0.00019       5      77 .]      41     105 ..      37     105 .. 0.88
   3 !   23.7   0.2   5.1e-08   4.4e-05       4      68 ..      74     137 ..      71     140 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.36
      TPR_12 13 lrrlgrydeAlellek 28
                l++ g++ +Al+l++ 
  EPA05616.1 15 LCEDGNFLDALKLYDL 30
                5778999999999875 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 2.3e-07
      TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiaek 77 
                 al   +++l+ lgr+ +++++++k++ +      p     +++l+n g  ++ +++y +A+  +  al+i++k
  EPA05616.1  41 ALLDKGVTLQNLGRLKQSIKYYDKVIHLD-----PR---NIQALINKGASLHSSKKYHDAIHCYDLALKIDKK 105
                 455799*******************4333.....65...69****************************9986 PP

  == domain 3  score: 23.7 bits;  conditional E-value: 5.1e-08
      TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlell 68 
                 +al n +a l+  ++y++A+ +++ al i ++++    ++   +l  Lg l +al+++++Al++ 
  EPA05616.1  74 QALINKGASLHSSKKYHDAIHCYDLALKIDKKSPMA-LAYKGLSLGELGNLNDALKHFKKALSIE 137
                 5788**************************999987.5588999999999999999999998875 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   3.4e-07   0.00029      10      65 ..      20      75 ..       9      77 .. 0.93
   2 !   13.5   0.0   7.2e-05     0.061       5      60 ..      83     138 ..      80     149 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 3.4e-07
       TPR_9 10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65
                ++  al+ ++++l   P+ +  ++d G+ l+ lG+l++ ++  +  ++l+p + +a
  EPA05616.1 20 NFLDALKLYDLILKKEPQNIVALLDKGVTLQNLGRLKQSIKYYDKVIHLDPRNIQA 75
                6789***********************************************98877 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 7.2e-05
       TPR_9   5 aireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalap 60 
                 + +++++  a+ ++++ l ++ ++p  +   Gl l +lG+l+ Al+ +  +l+++ 
  EPA05616.1  83 LHSSKKYHDAIHCYDLALKIDKKSPMALAYKGLSLGELGNLNDALKHFKKALSIEK 138
                 567889999***************************************99997765 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.73   6.2e+02      10      31 ..      16      35 ..       9      39 .. 0.74
   2 !   15.3   0.0   1.8e-05     0.015       1      34 [.      41      72 ..      41      74 .. 0.90
   3 !    7.0   0.0     0.008       6.8       2      30 ..      76     104 ..      75     107 .. 0.79
   4 !    7.2   0.1    0.0065       5.6       6      31 ..     114     139 ..     109     144 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.73
       TPR_7 10 srlGdyeeAielyeqsLaltkd 31
                +++G++ +A++ly     l k+
  EPA05616.1 16 CEDGNFLDALKLYDL--ILKKE 35
                568999999999987..55555 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1.8e-05
       TPR_7  1 aLlnLarlysrlGdyeeAielyeqsLaltkdped 34
                aLl  +++ ++lG+ ++ i++y +  +++ dp +
  EPA05616.1 41 ALLDKGVTLQNLGRLKQSIKYYDK--VIHLDPRN 72
                677889******************..99999976 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.008
       TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltk 30 
                 L n +   ++  +y +Ai +y  +L ++k
  EPA05616.1  76 LINKGASLHSSKKYHDAIHCYDLALKIDK 104
                 6677777778899**********887765 PP

  == domain 4  score: 7.2 bits;  conditional E-value: 0.0065
       TPR_7   6 arlysrlGdyeeAielyeqsLaltkd 31 
                 +    +lG+  +A+++++++L ++kd
  EPA05616.1 114 GLSLGELGNLNDALKHFKKALSIEKD 139
                 5556689************9999887 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   3.4e-06    0.0029       1      66 [.       9      71 ..       9      73 .. 0.94
   2 !   15.4   0.0   2.6e-05     0.023      10      61 ..      86     134 ..      77     141 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.4e-06
      TPR_16  1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66
                l +a+++ + g++ dA+++++  lk+    P++  All +g+ +  +grl+  + +y++ +  +p 
  EPA05616.1  9 LSQAYELCEDGNFLDALKLYDLILKKE---PQNIVALLDKGVTLQNLGRLKQSIKYYDKVIHLDPR 71
                57899999*******************...*****************************9988886 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 2.6e-05
      TPR_16  10 agdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraal 61 
                 +++y dA++ ++ alk d++sP    Al ++g+++ ++g+l +A+  +++al
  EPA05616.1  86 SKKYHDAIHCYDLALKIDKKSPM---ALAYKGLSLGELGNLNDALKHFKKAL 134
                 789***************88888...********************999998 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   2.2e-06    0.0019       3      64 ..      17      76 ..      15      80 .. 0.92
   2 ?   -1.0   0.0       3.1   2.7e+03       5      27 ..      87     109 ..      83     114 .. 0.69
   3 !   10.6   0.0   0.00075      0.64       5      28 ..     121     144 ..     118     147 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.2e-06
      TPR_19  3 aegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryasL 64
                ++g++ +Al+l+  +l+++p+n  a+l+    l +lg+l++ ++  d++   dp   ++++L
  EPA05616.1 17 EDGNFLDALKLYDLILKKEPQNIVALLDKGVTLQNLGRLKQSIKYYDKVIHLDPR--NIQAL 76
                789**********************************************999998..66665 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.1
      TPR_19   5 gdyaeAlalleqalqedpknaea 27 
                 ++y +A+  +  al+ d k++ a
  EPA05616.1  87 KKYHDAIHCYDLALKIDKKSPMA 109
                 56777777777777777776655 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00075
      TPR_19   5 gdyaeAlalleqalqedpknaear 28 
                 g++ +Al+++++al+ + +++ a 
  EPA05616.1 121 GNLNDALKHFKKALSIEKDYDLAS 144
                 899***************998775 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.1   5.1e-08   4.3e-05       3      79 ..      19      96 ..      17      99 .. 0.95
   2 ?    6.3   0.1     0.013        11      42      81 ..      95     132 ..      94     133 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 5.1e-08
                T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH CS
      ANAPC3  3 nnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaL 79
                +n+ +A+ l++++l++e+++  +++ ++ +l ++g+ k+ +++++k   l+++++++++ ++ +l   kky++Ai ++
  EPA05616.1 19 GNFLDALKLYDLILKKEPQNIVALLDKGVTLQNLGRLKQSIKYYDKViHLDPRNIQALINKGASLHSSKKYHDAIHCY 96
                57779*********9999999999999************************************************986 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.013
                 HHHHHHCTSHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
      ANAPC3  42 AyellrkaklnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                 +y+l+ k   ++ks+ ++  ++ +l +L+++++A+++++k
  EPA05616.1  95 CYDLALKI--DKKSPMALAYKGLSLGELGNLNDALKHFKK 132
                 56666666..778888888899999999999999999987 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0    0.0009      0.77      15      34 ..      19      38 ..      18      43 .. 0.91
   2 !   10.3   0.0   0.00068      0.58      14      38 ..      52      76 ..      47      77 .. 0.93
   3 ?    0.6   0.0       0.7     6e+02      15      31 ..      87     103 ..      85     111 .. 0.87
   4 ?    3.4   0.0     0.097        82      14      33 ..     120     139 ..     114     145 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0009
                T-HHHHHHHHHHHHHHTTS- CS
  Fis1_TPR_C 15 geYseArryvdalLeiEPen 34
                g++ +A+++ d +L++EP+n
  EPA05616.1 19 GNFLDALKLYDLILKKEPQN 38
                78899**************9 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00068
                HT-HHHHHHHHHHHHHHTTS-HHHH CS
  Fis1_TPR_C 14 lgeYseArryvdalLeiEPenrQaq 38
                lg+ +++ +y d +++++P+n Qa+
  EPA05616.1 52 LGRLKQSIKYYDKVIHLDPRNIQAL 76
                8999*******************96 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.7
                 T-HHHHHHHHHHHHHHT CS
  Fis1_TPR_C  15 geYseArryvdalLeiE 31 
                 ++Y +A  + d  L+i+
  EPA05616.1  87 KKYHDAIHCYDLALKID 103
                 78999999999999997 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.097
                 HT-HHHHHHHHHHHHHHTTS CS
  Fis1_TPR_C  14 lgeYseArryvdalLeiEPe 33 
                 lg+ ++A++  +  L+iE +
  EPA05616.1 120 LGNLNDALKHFKKALSIEKD 139
                 89***************976 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       3.1   2.6e+03      12      26 ..      15      29 ..      12      33 .. 0.78
   2 !    8.1   0.0    0.0028       2.4       7      29 ..      44      66 ..      39      68 .. 0.87
   3 ?    5.5   0.0      0.02        17       4      31 ..      75     102 ..      73     106 .. 0.89
   4 !   10.0   0.0   0.00075      0.64       9      31 ..     114     136 ..     108     139 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 3.1
      TPR_10 12 lrqrgrydeAealle 26
                l++ g++ +A++l++
  EPA05616.1 15 LCEDGNFLDALKLYD 29
                677889999999986 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0028
      TPR_10  7 NLanalrqrgrydeAealleeal 29
                + +++l+++gr++++ +++++++
  EPA05616.1 44 DKGVTLQNLGRLKQSIKYYDKVI 66
                5699****************998 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.02
      TPR_10   4 slnNLanalrqrgrydeAealleealai 31 
                 +l N ++ l++ ++y++A   ++ al i
  EPA05616.1  75 ALINKGASLHSSKKYHDAIHCYDLALKI 102
                 78899******************99988 PP

  == domain 4  score: 10.0 bits;  conditional E-value: 0.00075
      TPR_10   9 analrqrgrydeAealleealai 31 
                 +  l ++g++++A++++++al+i
  EPA05616.1 114 GLSLGELGNLNDALKHFKKALSI 136
                 778999***************98 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.53   4.5e+02       8      25 ..      12      29 ..       9      35 .. 0.74
   2 ?    0.8   0.0      0.59     5e+02       9      25 ..      47      63 ..      41      65 .. 0.87
   3 !   23.7   0.1   4.2e-08   3.6e-05       8      35 ..      80     105 ..      75     106 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.53
                HHHHHHTT-HHHHHHH.. CS
       TPR_3  8 AaefynkkkyqeArelfs 25
                A+e+   +++ +A+ l++
  EPA05616.1 12 AYELCEDGNFLDALKLYD 29
                666667788889999977 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.59
                HHHHHTT-HHHHHHH.. CS
       TPR_3  9 aefynkkkyqeArelfs 25
                 +++n +++ + + +++
  EPA05616.1 47 VTLQNLGRLKQSIKYYD 63
                689******99999977 PP

  == domain 3  score: 23.7 bits;  conditional E-value: 4.2e-08
                 HHHHHHTT-HHHHHHH..HHHHHHH-TT CS
       TPR_3   8 AaefynkkkyqeArelfsYallaildke 35 
                 +a+++++kky +A++ ++  l+ ++dk+
  EPA05616.1  80 GASLHSSKKYHDAIHCYD--LALKIDKK 105
                 79**************77..******97 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0      0.17   1.4e+02      10      32 ..      13      37 ..       3      38 .. 0.75
   2 !    9.7   0.0    0.0017       1.4       2      32 ..      41      71 ..      40      72 .. 0.90
   3 ?   -2.0   0.0       8.9   7.6e+03       2      24 ..      75      97 ..      74     102 .. 0.61
   4 ?    5.5   0.0     0.036        30       2      27 ..     109     134 ..     108     137 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.17
                HHH.H.HHHHHHHHHHHHHHHH-TT CS
       TPR_6 10 yrk.l.gdtdkAlealerlikeYPd 32
                y+    g+  +Al++++ ++k+ P+
  EPA05616.1 13 YELcEdGNFLDALKLYDLILKKEPQ 37
                33333578999***********997 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0017
                HHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
       TPR_6  2 AlyklalsyrklgdtdkAlealerlikeYPd 32
                Al+  +  +++lg+  +++++++++i   P 
  EPA05616.1 41 ALLDKGVTLQNLGRLKQSIKYYDKVIHLDPR 71
                889999999**99*************98885 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 8.9
                HHHHHHHHHHHHHHHHHHHHHHH CS
       TPR_6  2 AlyklalsyrklgdtdkAleale 24
                Al + + s+ + +++ +A+  ++
  EPA05616.1 75 ALINKGASLHSSKKYHDAIHCYD 97
                55555556666457888877765 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.036
                 HHHHHHHHHHHHHHHHHHHHHHHHHH CS
       TPR_6   2 AlyklalsyrklgdtdkAlealerli 27 
                 Al + +ls+ +lg+  +Al+ +++ +
  EPA05616.1 109 ALAYKGLSLGELGNLNDALKHFKKAL 134
                 6778899999999*********9987 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0055       4.7      98     126 ..      37      65 ..      28      69 .. 0.88
   2 ?    3.7   0.0     0.069        59     100     127 ..      73     100 ..      67     107 .. 0.88
   3 !    6.6   0.0    0.0087       7.4     102     127 ..     109     134 ..     103     141 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0055
                 HHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
     DUF3856  98 lWiaavfsravaleelGrkdealkafrma 126
                 + i a+++++v+l++lGr ++++k++ ++
  EPA05616.1  37 QNIVALLDKGVTLQNLGRLKQSIKYYDKV 65 
                 568999*******************9886 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.069
                 HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
     DUF3856 100 iaavfsravaleelGrkdealkafrmag 127
                 i+a+++++++l++  ++++a++ +  a 
  EPA05616.1  73 IQALINKGASLHSSKKYHDAIHCYDLAL 100
                 8999*****************9998875 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.0087
                 HHHHHHHHHHHTT-HHHHHHHHHHHH CS
     DUF3856 102 avfsravaleelGrkdealkafrmag 127
                 a+  ++ +l elG+ ++alk+f++a 
  EPA05616.1 109 ALAYKGLSLGELGNLNDALKHFKKAL 134
                 56679999***************986 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0       0.1        89       8      28 ..       9      29 ..       7      30 .. 0.88
   2 ?    0.5   0.0      0.78   6.6e+02       6      29 ..      41      64 ..      40      68 .. 0.82
   3 !   10.0   0.1    0.0008      0.68       6      32 ..      75     101 ..      74     102 .. 0.91
   4 ?    3.1   0.0      0.12     1e+02      17      31 ..     120     134 ..     108     160 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.1
         MIT  8 vkkAveeDnagnyeeAlelYk 28
                +++A e+ + gn+ +Al+lY 
  EPA05616.1  9 LSQAYELCEDGNFLDALKLYD 29
                689999999***********5 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.78
         MIT  6 elvkkAveeDnagnyeeAlelYke 29
                +l+ k v + n g  +  +++Y +
  EPA05616.1 41 ALLDKGVTLQNLGRLKQSIKYYDK 64
                577889999999999999999987 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.0008
         MIT   6 elvkkAveeDnagnyeeAlelYkeale 32 
                 +l++k + + ++++y +A+++Y  al+
  EPA05616.1  75 ALINKGASLHSSKKYHDAIHCYDLALK 101
                 5899999999*************9986 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.12
         MIT  17 agnyeeAlelYkeal 31 
                  gn  +Al+ +k+al
  EPA05616.1 120 LGNLNDALKHFKKAL 134
                 566666666666665 PP

>> CODH_A_N  Carbon monoxide dehydrogenase subunit alpha N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.41   3.5e+02      34      69 ..      46      82 ..      38      94 .. 0.77
   2 ?    9.4   0.0    0.0012       1.1      27      59 ..     107     139 ..     105     158 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.41
    CODH_A_N 34 GekvktlgdleevLerarsllkeeet.LedaldaGla 69
                G   ++lg l++ ++ + + ++ +++ ++   ++G +
  EPA05616.1 46 GVTLQNLGRLKQSIKYYDKVIHLDPRnIQALINKGAS 82
                7788999999999999999999888766666666655 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0012
    CODH_A_N  27 PviyaltGekvktlgdleevLerarsllkeeet 59 
                 P+  a++G +  +lg+l+++L++ ++ l+ e++
  EPA05616.1 107 PMALAYKGLSLGELGNLNDALKHFKKALSIEKD 139
                 8999**********************9876665 PP

>> DUF531  Protein of unknown function (DUF531)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00016      0.14      21     147 ..       7     136 ..       2     152 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00016
      DUF531  21 RaiARaapicyafdf..nLalldFplkkeekelvdvvaekttiGesGkylkelaeknrllvldlpkkgfpaqfGevvattskpdekkaitpeevaeeil 117
                 R +  a ++c   +f   L l+d  lkke++++v  + +  t+ + G+  ++++  +++  ld   ++++a + +     s  + + ai+  ++a +i 
  EPA05616.1   7 RMLSQAYELCEDGNFldALKLYDLILKKEPQNIVALLDKGVTLQNLGRLKQSIKYYDKVIHLD--PRNIQALINKGASLHSSKKYHDAIHCYDLALKID 103
                 777888888886555327999***********************************9998888..78999999998888888889999*********99 PP

      DUF531 118 rkksvlll...iGlGrkGlPkellklakyhldi 147
                 +k+++ l    + lG+ G  ++ lk  k  l i
  EPA05616.1 104 KKSPMALAykgLSLGELGNLNDALKHFKKALSI 136
                 999998853334567777777777766666655 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1    0.0098       8.4      10      29 ..      15      34 ..      14      35 .. 0.90
   2 ?    2.2   0.0      0.32   2.7e+02      10      25 ..     117     132 ..     116     136 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0098
         PPR 10 ycknGkleeAlelfkeMkek 29
                +c  G++ +Al+l++ +++k
  EPA05616.1 15 LCEDGNFLDALKLYDLILKK 34
                799************98876 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.32
         PPR  10 ycknGkleeAlelfke 25 
                 ++  G+l +Al+ fk+
  EPA05616.1 117 LGELGNLNDALKHFKK 132
                 6789********9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       780  (0.0435049); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1139.97
//
Query:       EPA05617.1  [L=310]
Description: hypothetical protein BG20_I1062 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-10   40.0   3.0    3.6e-08   33.3   0.0    3.0  2  SIS       SIS domain


Domain annotation for each model (and alignments):
>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.2   1.5    0.0021        37      50     104 ..      79     129 ..      38     155 .. 0.59
   2 !   33.3   0.0     2e-12   3.6e-08       6      78 ..     181     251 ..     180     269 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0021
                 G-STTCEEEEEESSSHHHHHHHHHHHHHHTTSEEEEEESSTTSHHHHHSSEEEEE CS
         SIS  50 lideddlvilisfsgetkdlvaaaelakergakiiaITdskgsplareadlalyi 104
                  i ++ ++ ++s sg+t + ++aa+  k+      aIT+ + s la+ +   +++
  EPA05617.1  79 SIVKNKIIYFVSISGNTISNIKAAKITKKS----TAITSVPQSKLANVCNSSIIL 129
                 566777888999999999999999988854....568888888888776444443 PP

  == domain 2  score: 33.3 bits;  conditional E-value: 2e-12
                 SEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHH CS
         SIS   6 kriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelake 78 
                 kr++vlG+G+ ++ia++ a+k+ e+ g+ v+++  +++ h+ l  i+++d vi++  ++   + +++ + +k+
  EPA05617.1 181 KRLFVLGSGYTFPIAMYCAAKFYEVLGYDVHFQRIEQFSHMELFSIKKGDTVIIFEENN--YHAKQLSRNLKN 251
                 89*****************************************************9444..444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2018.73
//
Query:       EPA05618.1  [L=57]
Description: hypothetical protein BG20_I1045 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0011   18.9   0.3     0.0014   18.6   0.3    1.2  1  OTT_1508_deam  OTT_1508-like deaminase
  ------ inclusion threshold ------
      0.026   14.8   0.6      0.026   14.8   0.6    2.0  2  zf-C2H2_jaz    Zinc-finger double-stranded RNA-binding
      0.093   13.2   2.6        0.1   13.1   1.3    1.7  2  zf-C2H2        Zinc finger, C2H2 type


Domain annotation for each model (and alignments):
>> OTT_1508_deam  OTT_1508-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.3   2.4e-07    0.0014      29      56 ..      10      37 ..       6      48 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.4e-07
  OTT_1508_deam 29 KpaCylCelylrahgkatlkvreshgkl 56
                   Kp CylC+l +++++k + +   +h+++
     EPA05618.1 10 KPKCYLCHLGFENIEKLREHQNTTHKEF 37
                   9***********9995555444444433 PP

>> zf-C2H2_jaz  Zinc-finger double-stranded RNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.6   4.4e-06     0.026       3      23 ..      12      32 ..      10      35 .. 0.90
   2 ?    0.6   0.3      0.12   7.4e+02      16      25 ..      37      46 ..      33      46 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.4e-06
                 BBTTTTBBBSSHHHHHCCTTS CS
  zf-C2H2_jaz  3 YCvlCdKyFksenaldnHlkS 23
                  C lC   F++ + l++H+++
   EPA05618.1 12 KCYLCHLGFENIEKLREHQNT 32
                 7******************98 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.12
                 HHHCCTTSHH CS
  zf-C2H2_jaz 16 aldnHlkSKk 25
                  l+ H+k  k
   EPA05618.1 37 FLESHEKNNK 46
                 5899999765 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.3   1.7e-05       0.1       2      23 .]      12      34 ..      12      34 .. 0.97
   2 ?   -1.5   0.0      0.76   4.5e+03      15      20 ..      37      42 ..      35      44 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.7e-05
                EETTTTEEESSHHHHHHHHHC.C CS
     zf-C2H2  2 kCpdCgksFkrksnLkrHirt.H 23
                kC  C+  F + + L+ H++t H
  EPA05618.1 12 KCYLCHLGFENIEKLREHQNTtH 34
                7********************99 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.76
                HHHHHH CS
     zf-C2H2 15 nLkrHi 20
                 L++H 
  EPA05618.1 37 FLESHE 42
                589996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       985  (0.0549389); expected 358.6 (0.02)
Passed bias filter:                      612  (0.0341346); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 389.14
//
Query:       EPA05619.1  [L=106]
Description: hypothetical protein BG20_I1057 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        2.7    7.7   5.9        7.1    6.3   0.1    3.2  3  CagY_M    DC-EC Repeat


Domain annotation for each model (and alignments):
>> CagY_M  DC-EC Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1     0.014   2.6e+02       2       8 ..      43      49 ..      42      51 .. 0.88
   2 ?    1.2   0.2     0.016   2.9e+02       4       7 ..      72      75 ..      60      77 .. 0.61
   3 ?    6.3   0.1    0.0004       7.1       4      11 ..      96     103 ..      95     104 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.014
      CagY_M  2 ykDCLkn 8 
                y +C++n
  EPA05619.1 43 YQNCISN 49
                89****9 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.016
      CagY_M  4 DCLk 7 
                DCL+
  EPA05619.1 72 DCLS 75
                5555 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0004
      CagY_M   4 DCLknAkd 11 
                 DC+++Ak+
  EPA05619.1  96 DCIDQAKN 103
                 9******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 727.06
//
Query:       EPA05620.1  [L=149]
Description: universal stress family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-26   94.0   0.0    1.4e-26   93.7   0.0    1.1  1  Usp              Universal stress protein family
     0.0011   19.6   0.1     0.0021   18.8   0.1    1.5  1  GARS_N           Phosphoribosylglycinamide synthetase, N doma
  ------ inclusion threshold ------
       0.14   12.7   0.1       0.32   11.5   0.1    1.6  1  Peptidase_M15_4  D-alanyl-D-alanine carboxypeptidase


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.7   0.0   2.3e-30   1.4e-26       2     141 .]       7     149 .]       6     149 .] 0.85

  Alignments for each domain:
  == domain 1  score: 93.7 bits;  conditional E-value: 2.3e-30
                 -SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCC..CCCHHHHHHHHHHHHHHHHHHHH...HHHHHHCTTCEEEEEEEESSHHHHH CS
         Usp   2 ykrIlVavDgseeskkAlewAlelakargaelillhvidprasgav..sdadeeaeeeeleleeaeleada...akaaaeaggvkvevvveegdpaeei 95 
                 +k+IlV+ Dgs+ s +A++ Al+ ak++++++ ++h+i  +a+     +da  + +   ++ + ae+e         a+++g+ +  +v+   +    i
  EPA05620.1   7 FKNILVPWDGSNPSLHAFKIALDIAKKYDSKISVIHCIQNEAYRGQwfPDAGYSKAVIKKQTKSAEAE--IdklVVLAKNKGIQISATVLAAPSIVKQI 103
                 79************************************998875441133333333333333444444..25588999********************* PP

                 HHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
         Usp  96 levaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                 + +++++++dl+++Gs+gr+g s+ l GSv++ v ++ +cpVl+Vr
  EPA05620.1 104 VTYVKSKKIDLVIMGSHGRTGWSKTLYGSVANGVSQNIHCPVLIVR 149
                 *********************************************8 PP

>> GARS_N  Phosphoribosylglycinamide synthetase, N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   3.5e-07    0.0021      13      59 ..      61     119 ..      56     140 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 3.5e-07
                 HHHHHHHTTS..TTESEEEEEE--CGG..........TTHHHHHHHHHHCTESEEEE-S CS
      GARS_N  13 halawklaqs..pkvekvyvapgNagt..........edlealvefakeekidlvvvGp 59 
                 +a+++k ++s   +++k++v+ +N+g+          + ++++v+++k++kidlv++G 
  EPA05620.1  61 KAVIKKQTKSaeAEIDKLVVLAKNKGIqisatvlaapSIVKQIVTYVKSKKIDLVIMGS 119
                 5666776666224567***********888877776644568***************97 PP

>> Peptidase_M15_4  D-alanyl-D-alanine carboxypeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   5.3e-05      0.32       7      49 ..      19      86 ..      15      90 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.3e-05
  Peptidase_M15_4  7 lSnHsyGlAiDinplvnpyw.....kalkpengeaya....................devvkifkklG 49
                      S H++ +A+Di+ ++++ +      + + ++g+++                     d++v ++k+ G
       EPA05620.1 19 PSLHAFKIALDIAKKYDSKIsvihcIQNEAYRGQWFPdagyskavikkqtksaeaeiDKLVVLAKNKG 86
                     599**********9976644234443344444444446666655555555555566666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       723  (0.0403257); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1037.71
//
Query:       EPA05621.1  [L=305]
Description: putative transcription initiation factor IIB [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.2e-31  105.7   6.1    4.4e-16   58.7   0.4    2.2  2  TFIIB          Transcription factor TFIIB repeat
    3.8e-10   39.1   1.1    6.2e-10   38.4   1.1    1.4  1  TF_Zn_Ribbon   TFIIB zinc-binding
     0.0022   18.1   0.0        2.7    8.1   0.0    2.3  2  Cyclin_C       Cyclin, C-terminal domain
     0.0045   16.5   0.0       0.45   10.1   0.0    3.5  4  Sigma70_r4     Sigma-70, region 4
     0.0064   16.2   0.1      0.012   15.2   0.1    1.4  1  RPW8           Arabidopsis broad-spectrum mildew resistance p
     0.0066   16.2   0.8      0.061   13.1   0.2    2.1  2  Cyclin_N       Cyclin, N-terminal domain
     0.0084   16.0   1.1      0.092   12.7   0.0    2.7  3  HTH_11         HTH domain
     0.0093   15.8   0.0       0.24   11.3   0.0    2.8  3  HTH_AsnC-type  AsnC-type helix-turn-helix domain
  ------ inclusion threshold ------
      0.011   15.8   0.1       0.02   14.9   0.1    1.5  1  RB_B           Retinoblastoma-associated protein B domain
      0.043   13.3   2.7       0.22   11.0   2.7    2.1  1  zf-ribbon_3    zinc-ribbon domain
       0.19   11.4   1.5        5.4    6.8   0.0    3.2  3  Sigma70_r4_2   Sigma-70, region 4
       0.25   11.1   1.5        1.4    8.6   0.2    2.4  2  zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
        1.2    9.0   4.1        0.7    9.7   0.3    2.2  2  zinc_ribbon_2  zinc-ribbon domain


Domain annotation for each model (and alignments):
>> TFIIB  Transcription factor TFIIB repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.7   0.4   3.2e-19   4.4e-16       2      71 .]     127     196 ..     126     196 .. 0.96
   2 !   49.9   0.9   1.8e-16   2.4e-13       2      71 .]     221     290 ..     220     290 .. 0.98

  Alignments for each domain:
  == domain 1  score: 58.7 bits;  conditional E-value: 3.2e-19
                 HHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
       TFIIB   2 krfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                 +r+ d+l L++ V ++A +++++a e+k++ Grs  +++A++ly Acr  e+ rt+ ++ + ++ ++k i
  EPA05621.1 127 NRLKDKLSLSDAVIEKAAYIYRKAIEKKLVRGRSISAMIASALYAACRDTETPRTLNDVGEAANLKKKDI 196
                 68889**********************************************************9999876 PP

  == domain 2  score: 49.9 bits;  conditional E-value: 1.8e-16
                 HHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
       TFIIB   2 krfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                  r+a+++++ ek ++ A +++k + e +  +G+ p g+aAA+ly+Ac k+++  tq++i++ + V+e+ti
  EPA05621.1 221 ARIASRIGITEKTKRYAAKVLKISQEHEESAGKDPMGLAAAALYLACVKNGEDITQRDIAEAASVTEVTI 290
                 589*****************************************************************98 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   1.1   4.5e-13   6.2e-10       3      43 .]      11      51 ..      10      51 .. 0.97

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 4.5e-13
                  ETTTTCEECHEETSTTCEEESSSSBEEEECCCCCCCHHHHH CS
  TF_Zn_Ribbon  3 CPnCgstnlveDpergelvCtdCGlVlednsidegpewref 43
                  CP C   +l++D  +ge +C++CG+V+ + s ++gpewr f
    EPA05621.1 11 CPRCAKNSLLTDDVTGERFCGKCGYVISEKSQESGPEWRSF 51
                  *****999*******************************87 PP

>> Cyclin_C  Cyclin, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0026       3.6      46      88 ..     164     205 ..     158     212 .. 0.81
   2 !    8.1   0.0    0.0019       2.7       3      58 ..     216     269 ..     214     298 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0026
                 HHHHHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHHHHHH CS
    Cyclin_C  46 liAaaalllarstlnspewtetlehytgyskedlkpcvelile 88 
                 +i a+al++a++  ++p   + + +   ++k+d+  c++l++ 
  EPA05621.1 164 MI-ASALYAACRDTETPRTLNDVGEAANLKKKDIARCYRLLHR 205
                 44.5666666666699999999999999************997 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0019
                 HHHHHHHH.HCCSSHT.-HCCHHCHHCHHHHHHCSCCHCCS-HHHHHHHHHHHCCHH CS
    Cyclin_C   3 plsFlrrf.lkaadasedselrtlakylleltlldydflsyppSliAaaalllarst 58 
                 p+++l r+ ++++    + +++  a  +l ++  + ++++ +p  +Aaaal+la+  
  EPA05621.1 216 PIQCLARIaSRIGIT--E-KTKRYAAKVLKISQEHEESAGKDPMGLAAAALYLACVK 269
                 899999998888334..6.888899999****99999*****************987 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.29     4e+02      18      32 ..     177     191 ..     169     197 .. 0.81
   2 ?   -0.9   0.0       0.9   1.2e+03      23      35 ..     220     232 ..     219     235 .. 0.87
   3 ?   -0.5   0.0      0.67   9.2e+02      26      36 ..     237     247 ..     223     247 .. 0.72
   4 !   10.1   0.0   0.00033      0.45      17      42 ..     269     295 ..     261     296 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.29
                 TTT--HHHHHHHHTS CS
  Sigma70_r4  18 geglTleEIgerlgi 32 
                 + ++Tl ++ge  ++
  EPA05621.1 177 ETPRTLNDVGEAANL 191
                 789********8876 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.9
                 HHHHHHHHTS-HH CS
  Sigma70_r4  23 leEIgerlgiSre 35 
                 l+ I+ r gi++ 
  EPA05621.1 220 LARIASRIGITEK 232
                 688*******986 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.67
                 HHHHHTS-HHH CS
  Sigma70_r4  26 IgerlgiSrer 36 
                  +++l iS+e+
  EPA05621.1 237 AAKVLKISQEH 247
                 68889999886 PP

  == domain 4  score: 10.1 bits;  conditional E-value: 0.00033
                 H.TTT--HHHHHHHHTS-HHHHHHHHH CS
  Sigma70_r4  17 f.geglTleEIgerlgiSrerVrqiek 42 
                   ge+ T+ +I+e   +++ ++r + k
  EPA05621.1 269 KnGEDITQRDIAEAASVTEVTIRNRYK 295
                 2699*******************9975 PP

>> RPW8  Arabidopsis broad-spectrum mildew resistance protein RPW8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1     9e-06     0.012      15     103 ..      73     164 ..      61     174 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 9e-06
        RPW8  15 ellkaileakkksldfksilkrLestleritP..vvkei.eklnkeldrpreeieeLkklLekaekLVekcsklkrynvlkkyrYkkklkeL 103
                 + l  i++  +k ++ k+   +++st+er+++  ++ ++ e++  +l +  +e+++Lk++L      +ek + + r ++ kk    + + ++
  EPA05621.1  73 MGLSTIINPMNKDASGKPLTASMKSTIERLRTwdSRSQVhESVDRNLRQALSELNRLKDKLSLSDAVIEKAAYIYRKAIEKKLVRGRSISAM 164
                 56889999**********************9833466774667777799999******************************9988888765 PP

>> Cyclin_N  Cyclin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.2   4.5e-05     0.061      23     123 ..     112     208 ..      92     212 .. 0.81
   2 ?    1.5   0.0      0.16   2.3e+02      53      85 ..     235     267 ..     216     295 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.5e-05
                 TSSS-HHHHHHHHHHHHHHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHHHSSS---HHHHHHHTTTSS-HHHHHHHHHHHHHH CS
    Cyclin_N  23 qpelnpemRailidwlvevaekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAaKveeisppkledlvyitdeafteeeilemErliLet 121
                 +++++ + R+ +++ l ++  k++l+  ++  a+ ++ + ++kk v+ + +  + a++L+ A++  e+ p +l+d+  +++   ++++i +  rl+ ++
  EPA05621.1 112 HESVDRNLRQ-ALSELNRLKDKLSLSDAVIEKAAYIYRKAIEKKLVRGRSISAMIASALYAACRDTET-PRTLNDVGEAAN--LKKKDIARCYRLLHRE 206
                 4445556666.5556999***********************************************999.999999887754..7777777777777666 PP

                 TT CS
    Cyclin_N 122 Ln 123
                 L+
  EPA05621.1 207 LE 208
                 66 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.16
                 HHHHHHHHHHHHHS---CCCHHHHHHHHHHHHH CS
    Cyclin_N  53 flavnyldRflskksvpkdklqlvgatcLllAa 85 
                   a+++l    ++++   ++   ++a++L+lA+
  EPA05621.1 235 RYAAKVLKISQEHEESAGKDPMGLAAAALYLAC 267
                 45555554444444555557777999******9 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0       0.4   5.5e+02      19      34 ..     127     142 ..     119     143 .. 0.85
   2 ?   -2.4   0.0       3.4   4.6e+03      19      31 ..     221     233 ..     220     233 .. 0.86
   3 !   12.7   0.0   6.7e-05     0.092       9      40 ..     268     298 ..     262     300 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.4
      HTH_11  19 eeLAeeLnvSrrtvrr 34 
                 ++L+++L++S +++ +
  EPA05621.1 127 NRLKDKLSLSDAVIEK 142
                 68999****9999865 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.4
      HTH_11  19 eeLAeeLnvSrrt 31 
                 +++A +++++++t
  EPA05621.1 221 ARIASRIGITEKT 233
                 5799*****9987 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 6.7e-05
      HTH_11   9 LleargpisgeeLAeeLnvSrrtvrrdIkaLe 40 
                 + ++ ++i+  ++Ae  +v++ t+r++ k L+
  EPA05621.1 268 V-KNGEDITQRDIAEAASVTEVTIRNRYKGLK 298
                 5.77788*******************977775 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       3.6     5e+03      18      35 ..     180     197 ..     175     202 .. 0.75
   2 ?    0.8   0.0      0.32   4.4e+02      21      33 ..     221     233 ..     215     235 .. 0.86
   3 !   11.3   0.0   0.00017      0.24      17      41 ..     273     297 ..     265     298 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.6
  HTH_AsnC-type  18 isyaeLAervGlSestvl 35 
                    ++  +++e+ +l    ++
     EPA05621.1 180 RTLNDVGEAANLKKKDIA 197
                    677889999888766655 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.32
  HTH_AsnC-type  21 aeLAervGlSest 33 
                    a++A r+G++e t
     EPA05621.1 221 ARIASRIGITEKT 233
                    789*****99976 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.00017
  HTH_AsnC-type  17 RisyaeLAervGlSestvlrRvrrL 41 
                     i+ +++Ae+  ++e t+++R++ L
     EPA05621.1 273 DITQRDIAEAASVTEVTIRNRYKGL 297
                    6899*****************9976 PP

>> RB_B  Retinoblastoma-associated protein B domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.1   1.4e-05      0.02      10      90 ..     119     197 ..     111     249 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.4e-05
        RB_B  10 yklaavrlrdLcerLklsselrekiwtlfehvlveetellkdRhlDqillcavYvvakvtkeelsFkeiikaYrkqpqass 90 
                 ++ a + l++L ++L+ls+ + ek+  + ++++  e++l++ R +  ++ +a+Y+ ++ t++ ++++++ +a + +++  +
  EPA05621.1 119 LRQALSELNRLKDKLSLSDAVIEKAAYIYRKAI--EKKLVRGRSISAMIASALYAACRDTETPRTLNDVGEAANLKKKDIA 197
                 6678899************99999888888887..568********************99776666666554444444333 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   2.7   0.00016      0.22       4      26 .]      10      37 ..       7      37 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00016
  zf-ribbon_3  4 rCPnCGa.p.lssdd...nvCpyCGtkl 26
                 +CP+C +   l++d+   ++C +CG+++
   EPA05621.1 10 NCPRCAKnSlLTDDVtgeRFCGKCGYVI 37
                 7*****9877887652226*******97 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0         2   2.7e+03       3      11 ..     118     126 ..     114     129 .. 0.65
   2 ?    1.8   0.1      0.14   1.9e+02      30      42 ..     221     233 ..     220     239 .. 0.86
   3 ?    6.8   0.0    0.0039       5.4      25      47 ..     272     294 ..     270     295 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2
                   HHHHHHTTS CS
  Sigma70_r4_2   3 alrealaeL 11 
                    lr+al+eL
    EPA05621.1 118 NLRQALSEL 126
                   566777766 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.14
                   HHHHHHHT--HHH CS
  Sigma70_r4_2  30 kEIAellgisegt 42 
                   + IA+++gi+e+t
    EPA05621.1 221 ARIASRIGITEKT 233
                   57*********99 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0039
                   S---HHHHHHHHT--HHHHHHHH CS
  Sigma70_r4_2  25 eglsykEIAellgisegtVksrl 47 
                   e+ ++++IAe   ++e+t+++r+
    EPA05621.1 272 EDITQRDIAEAASVTEVTIRNRY 294
                   567899***************98 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1      0.35   4.9e+02       6      10 ..      11      15 ..      11      22 .. 0.86
   2 ?    8.6   0.2     0.001       1.4       4      10 ..      28      34 ..      27      40 .. 0.96

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.35
  zf-NADH-PPase  6 CgrCG 10
                   C+rC+
     EPA05621.1 11 CPRCA 15
                   99997 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.001
  zf-NADH-PPase  4 rFCgrCG 10
                   rFCg+CG
     EPA05621.1 28 RFCGKCG 34
                   9*****9 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.4      0.67   9.2e+02       2       5 ..      11      14 ..       8      17 .. 0.75
   2 ?    9.7   0.3   0.00051       0.7      12      21 ..      26      35 ..      24      37 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.67
  zinc_ribbon_2  2 CpnC 5 
                   Cp+C
     EPA05621.1 11 CPRC 14
                   6766 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00051
  zinc_ribbon_2 12 nakFCpyCGt 21
                   +++FC +CG+
     EPA05621.1 26 GERFCGKCGY 35
                   789******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       897  (0.0500307); expected 358.6 (0.02)
Passed bias filter:                      636  (0.0354733); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 1828.93
//
Query:       EPA05622.1  [L=365]
Description: radical SAM domain protein, CofH family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-17   64.6   0.0      3e-17   63.5   0.0    1.6  1  Radical_SAM  Radical SAM superfamily
     0.0061   16.7   0.0      0.012   15.8   0.0    1.5  1  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.5   0.0   3.3e-21     3e-17       2     159 ..      63     228 ..      62     236 .. 0.89

  Alignments for each domain:
  == domain 1  score: 63.5 bits;  conditional E-value: 3.3e-21
                  EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTC........CCTEEEEEEECSSCHG CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxx RF
  Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlakla........vpgiritvetngtlpd 90 
                  + t+ C+  C  Ca++++    +++++l++e+i++ v ++ + +g +++ i+gg +p+l  +++e++ + +k+             +i++ +  t+ +
   EPA05622.1  63 NYTNVCAASCQMCAFYRK-DGAEDAYTLTPEQIEQRVGIA-ETMGaTEVHIVGGFHPTLPLEYYEDMVKVIKKNhpqlkikaLTAAEIFFLSKLTKNS 158
                  67999************7.9********************.9***9999999999******************9999999998888888888888877 PP

                  .HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHH CS
                  .xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM  91 .eeklerllelg.vdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGendee 159
                   +e+l rl+++g       g+e +++e+  k+++++ t +e+l+++e ++++gik++v++++g+  e  ++
   EPA05622.1 159 tKEILSRLKDAGlDSMPGGGAELFHPEVRGKIVRGKCTGQEWLDTIEQAHNLGIKSNVTMLYGHI-EKPSH 228
                  9***********77788999*******8889999*********************6666665554.55555 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.3e-06     0.012       4     109 ..      64     164 ..      60     173 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.3e-06
     Fer4_14   4 rlsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGG.ePLhyenkkellklvkrlkeeypekkiwletngtleielektpdl 101
                  ++ C  sC++C    +   e     t e++eq++    ++ + + ++ ++GG  P ++   +   ++vk +k++ p++ki+  t + +    +     
  EPA05622.1  64 YTNVCAASCQMCAFYRKDGAEDAYTLTPEQIEQRV--GIAETMGATEVHIVGGfHPTLP--LEYYEDMVKVIKKNHPQLKIKALTAAEIFFLSK--LTK 156
                 5799********95554455555555666667777..5666777899*****9666644..666889999999************998874433..344 PP

     Fer4_14 102 kekleals 109
                 ++++e+ls
  EPA05622.1 157 NSTKEILS 164
                 45566665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 2249.07
//
Query:       EPA05623.1  [L=47]
Description: hypothetical protein BG20_I1036 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.022   14.6   1.5        1.7    8.6   0.1    2.1  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain
      0.054   13.7   1.6       0.52   10.5   0.0    2.2  2  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 
       0.11   12.5   0.2       0.51   10.3   0.0    1.9  2  VP_N-CPKC       Virion protein N terminal domain


Domain annotation for each model (and alignments):
>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1    0.0022        13       5      14 ..       4      13 ..       3      16 .. 0.80
   2 ?    8.6   0.1   0.00029       1.7       5      22 ..      32      46 ..      31      47 .] 0.84

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0022
  Zn_ribbon_SprT  5 YrCtgCgrey 14
                     +C+ C+++ 
      EPA05623.1  4 GYCVKCRDKR 13
                    59*****875 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00029
  Zn_ribbon_SprT  5 YrCtgCgreythhlsirr 22
                     +C+ C    t++++i r
      EPA05623.1 32 GTCPKCS---TAIFRIGR 46
                    58*****...*****965 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.3     0.027   1.6e+02      35      39 ..       5       9 ..       2      10 .. 0.88
   2 ?   10.5   0.0   8.7e-05      0.52      14      27 ..      30      43 ..      21      46 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.027
  Auto_anti-p27 35 yCvaC 39
                   yCv C
     EPA05623.1  5 YCVKC 9 
                   9***9 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 8.7e-05
  Auto_anti-p27 14 LaetCpvCgvPLmr 27
                   L  tCp+C++ ++r
     EPA05623.1 30 LKGTCPKCSTAIFR 43
                   5669******9998 PP

>> VP_N-CPKC  Virion protein N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.16   9.5e+02      15      22 ..       2       9 ..       1      11 [. 0.76
   2 ?   10.3   0.0   8.6e-05      0.51      19      30 ..      34      45 ..      32      46 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.16
   VP_N-CPKC 15 tFEECPKC 22
                t   C KC
  EPA05623.1  2 TIGYCVKC 9 
                66679999 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 8.6e-05
   VP_N-CPKC 19 CPKCsALqYRnG 30
                CPKCs   +R G
  EPA05623.1 34 CPKCSTAIFRIG 45
                *****9888866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.50
# Mc/sec: 282.06
//
Query:       EPA05624.1  [L=188]
Description: DnaJ domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.7e-21   75.4   7.4    2.7e-21   75.4   7.4    2.0  2  DnaJ        DnaJ domain
  ------ inclusion threshold ------
      0.025   15.0   1.8      0.038   14.4   0.6    1.9  1  HSP9_HSP12  Heat shock protein 9/12
      0.035   14.2   0.0       0.07   13.2   0.0    1.6  1  CD20        CD20-like family
      0.061   13.4   0.2       0.17   12.0   0.2    1.7  1  SUIM_assoc  Unstructured region C-term to UIM in Ataxin3


Domain annotation for each model (and alignments):
>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   1.8         1   4.7e+03      22      33 ..      81      92 ..      64     116 .. 0.50
   2 !   75.4   7.4     6e-25   2.7e-21       1      63 []     121     182 ..     121     182 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1
                HHHHHHHSTTTS CS
        DnaJ 22 rklalkyHPDkn 33
                 k   kyH D +
  EPA05624.1 81 DKTYEKYHSDWS 92
                555566666633 PP

  == domain 2  score: 75.4 bits;  conditional E-value: 6e-25
                 HHHHHHTSSTTG-HHHHHHHHHHHHHHHSTTTSCCHHHHHHHHHHHHHHHHHHTSHHHHHHHH CS
        DnaJ   1 dyYeiLgvskdasedeIkkaYrklalkyHPDknpkdpeaeekFkeineAyevLsdpekRkqYD 63 
                 dyY+ L +s++a++deIk++Yr+la+k+HPDkn kd ++ee   +in+AyevLs++e Rk+YD
  EPA05624.1 121 DYYKTLDISQEATQDEIKNKYRELAKKIHPDKN-KDDKSEEIMVKINKAYEVLSNEELRKKYD 182
                 8********************************.77779999********************9 PP

>> HSP9_HSP12  Heat shock protein 9/12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.6   8.5e-06     0.038       7      51 ..     108     155 ..     104     159 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 8.5e-06
                 SCHHHHHHHHCS--SSHC...HHHHHHHHHHHHHHHHHHCS-TTCHHC CS
  HSP9_HSP12   7 kdftdkakeevtPDsqKS...tlekaketvtdaaDklarklqpddqKs 51 
                 k+f +  +++v PD  K+    +e +++++++++ +la+k++pd++K+
  EPA05624.1 108 KEFREAFQNSVLPDYYKTldiSQEATQDEIKNKYRELAKKIHPDKNKD 155
                 88999999*********944459************************8 PP

>> CD20  CD20-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.6e-05      0.07      65     121 ..      42      98 ..      10     111 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.6e-05
        CD20  65 llnlvslvlalaGiillilslalltsaeelkesesdltsstsrcsskesseeeesra 121
                 ++  +s++la++Gi+++    + l++  ++ ++e+d+ + + +++++++++++ + +
  EPA05624.1  42 IILFASFALAVIGIFVYLARDIILRKKTSYDSKEFDSKNDKTYEKYHSDWSDDYEEF 98 
                 56789*********9999999999999999899999999999999999999887655 PP

>> SUIM_assoc  Unstructured region C-term to UIM in Ataxin3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   3.7e-05      0.17      14      29 ..     172     187 ..     165     188 .] 0.92

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.7e-05
  SUIM_assoc  14 ltsEeLrkrreaYFEK 29 
                 l+ EeLrk+ +aY+ K
  EPA05624.1 172 LSNEELRKKYDAYYDK 187
                 899***********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2037  (0.113615); expected 358.6 (0.02)
Passed bias filter:                      645  (0.0359752); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.67u 0.36s 00:00:01.03 Elapsed: 00:00:00.58
# Mc/sec: 976.32
//
Query:       EPA05625.1  [L=75]
Description: tetratricopeptide repeat protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.5e-16   57.4   0.1    3.4e-09   36.1   0.0    2.1  2  TPR_1       Tetratricopeptide repeat
    1.7e-14   52.7   0.0    9.8e-08   31.6   0.0    2.1  2  TPR_2       Tetratricopeptide repeat
    5.8e-12   44.8   0.0    3.7e-08   32.9   0.0    2.1  2  TPR_8       Tetratricopeptide repeat
    7.6e-11   41.5   0.0    0.00012   21.6   0.0    2.1  2  TPR_11      TPR repeat
    7.1e-10   39.4   0.0      8e-10   39.2   0.0    1.0  1  TPR_16      Tetratricopeptide repeat
    6.1e-09   35.3   0.0    0.00012   21.8   0.0    2.1  2  TPR_7       Tetratricopeptide repeat
    4.1e-08   33.2   0.1    4.9e-08   33.0   0.1    1.1  1  TPR_9       Tetratricopeptide repeat
    1.7e-07   31.7   0.0    1.8e-07   31.5   0.0    1.1  1  TPR_19      Tetratricopeptide repeat
    5.9e-07   29.7   0.2    0.00053   20.2   0.0    2.1  2  TPR_12      Tetratricopeptide repeat
      2e-06   27.7   0.1    7.7e-06   25.9   0.1    1.9  2  TPR_17      Tetratricopeptide repeat
    3.8e-06   27.3   0.1      0.011   16.5   0.0    2.1  2  TPR_14      Tetratricopeptide repeat
    0.00031   20.9   0.0    0.00033   20.8   0.0    1.1  1  ANAPC3      Anaphase-promoting complex, cyclosome, subunit 3
     0.0011   18.7   0.0       0.28   11.1   0.0    2.2  2  TPR_10      Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.015   15.5   0.0       0.56   10.5   0.0    2.1  2  NRBF2_MIT   MIT domain of nuclear receptor-binding factor 2
       0.02   15.0   0.0        1.3    9.1   0.0    2.1  2  MIT         MIT (microtubule interacting and transport) domai
      0.032   13.2   0.0      0.035   13.0   0.0    1.0  1  NARP1       NMDA receptor-regulated protein 1
      0.034   14.8   0.0       0.97   10.2   0.0    2.2  2  TPR_6       Tetratricopeptide repeat
      0.041   14.0   0.0      0.047   13.8   0.0    1.1  1  DUF3856     Domain of Unknown Function (DUF3856)
      0.066   13.3   0.1       0.37   10.9   0.0    2.0  3  Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
      0.069   12.6   0.0       0.13   11.6   0.0    1.4  1  Coatomer_E  Coatomer epsilon subunit
       0.14   12.4   0.2        1.8    9.0   0.0    2.2  2  PPR         PPR repeat


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.2   6.7e-07   0.00057      16      34 .]      19      37 ..      10      37 .. 0.89
   2 !   36.1   0.0     4e-12   3.4e-09       2      34 .]      39      71 ..      38      71 .. 0.95

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 6.7e-07
                -HHHHHHHHHHHHHHSTTH CS
       TPR_1 16 kydeAleyyekALelnPnn 34
                ++++Al+++e+AL ln n+
  EPA05625.1 19 NFEDALACFEQALLLNQND 37
                8***************996 PP

  == domain 2  score: 36.1 bits;  conditional E-value: 4e-12
                HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1  2 kalynlGnayfklgkydeAleyyekALelnPnn 34
                + ++ +++ +++lg+y+eA+e+++k L ++P +
  EPA05625.1 39 ELWNLKAVSLRSLGRYEEAVECFNKSLGIDPRD 71
                78*****************************75 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   7.8e-07   0.00067       7      34 .]      10      37 ..       5      37 .. 0.86
   2 !   31.6   0.0   1.1e-10   9.8e-08       1      34 []      38      71 ..      38      71 .. 0.96

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 7.8e-07
       TPR_2  7 lGlayyklgdyeeAleafekAleldPnn 34
                 G+  + + ++e+Al++fe+Al l+ n+
  EPA05625.1 10 KGKNFLDSLNFEDALACFEQALLLNQND 37
                577777888****************986 PP

  == domain 2  score: 31.6 bits;  conditional E-value: 1.1e-10
       TPR_2  1 aealynlGlayyklgdyeeAleafekAleldPnn 34
                +e+++  + +++ lg+yeeA+e+f+k+l +dP++
  EPA05625.1 38 PELWNLKAVSLRSLGRYEEAVECFNKSLGIDPRD 71
                699****************************986 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   0.00081      0.69      16      34 .]      19      37 ..       8      37 .. 0.88
   2 !   32.9   0.0   4.4e-11   3.7e-08       2      33 ..      39      70 ..      38      71 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00081
                -HHHHHHHHHHHHHHHHH. CS
       TPR_8 16 dyeeAkeyyekaleldpdn 34
                ++e A +++e+al l++++
  EPA05625.1 19 NFEDALACFEQALLLNQND 37
                7899***********9985 PP

  == domain 2  score: 32.9 bits;  conditional E-value: 4.4e-11
                CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
       TPR_8  2 eayynlgsiylklgdyeeAkeyyekaleldpd 33
                e++++++  +++lg+yeeA+e+++k l +dp 
  EPA05625.1 39 ELWNLKAVSLRSLGRYEEAVECFNKSLGIDPR 70
                79****************************96 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   1.2e-06     0.001       9      33 ..      19      43 ..      11      48 .. 0.88
   2 !   21.6   0.0   1.4e-07   0.00012       4      27 ..      48      71 ..      45      75 .] 0.91

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.2e-06
      TPR_11  9 kyeeAieaYkkAlkldPdnaeayyn 33
                ++e+A++++++Al l+++++e+++ 
  EPA05625.1 19 NFEDALACFEQALLLNQNDPELWNL 43
                68********************986 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 1.4e-07
      TPR_11  4 yyeqGkyeeAieaYkkAlkldPdn 27
                ++++G+yeeA+e+++k l +dP +
  EPA05625.1 48 LRSLGRYEEAVECFNKSLGIDPRD 71
                799*******************87 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   0.0   9.3e-13     8e-10       4      67 ..      11      71 ..      10      72 .. 0.94

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 9.3e-13
      TPR_16  4 araalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67
                ++ +l++ +++dA+a +e+al ++     ++e ++l+++++  +gr++eA++ +++ l+ +p +
  EPA05625.1 11 GKNFLDSLNFEDALACFEQALLLN---QNDPELWNLKAVSLRSLGRYEEAVECFNKSLGIDPRD 71
                67899*******************...88888***************************99975 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   0.00022      0.19      14      35 ..      19      38 ..      16      39 .. 0.82
   2 !   21.8   0.0   1.5e-07   0.00012       3      34 ..      42      73 ..      40      75 .] 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00022
       TPR_7 14 dyeeAielyeqsLaltkdpeda 35
                ++e+A+ ++eq  al   ++d+
  EPA05625.1 19 NFEDALACFEQ--ALLLNQNDP 38
                79*********..777666665 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 1.5e-07
       TPR_7  3 lnLarlysrlGdyeeAielyeqsLaltkdped 34
                +  a+  ++lG+yeeA+e++ +sL+++ ++ +
  EPA05625.1 42 NLKAVSLRSLGRYEEAVECFNKSLGIDPRDRN 73
                6678899*****************99988766 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.1   5.8e-11   4.9e-08      10      65 ..      19      74 ..      15      75 .] 0.95

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 5.8e-11
       TPR_9 10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65
                ++e ala+ e  lll+ +dpe++   ++ l  lG++++A+++++  l ++p ++ a
  EPA05625.1 19 NFEDALACFEQALLLNQNDPELWNLKAVSLRSLGRYEEAVECFNKSLGIDPRDRNA 74
                5899***********************************************99876 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.0   2.2e-10   1.8e-07       6      59 ..      19      72 ..      14      75 .] 0.91

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 2.2e-10
      TPR_19  6 dyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdda 59
                ++++Ala +eqal  + +++e++ l A  l +lg+++eA ++ ++ +  dp d 
  EPA05625.1 19 NFEDALACFEQALLLNQNDPELWNLKAVSLRSLGRYEEAVECFNKSLGIDPRDR 72
                799*****************************************9999988864 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.1     0.004       3.4      18      34 ..      19      35 ..      13      39 .. 0.81
   2 !   20.2   0.0   6.2e-07   0.00053       5      32 ..      40      67 ..      36      71 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.004
      TPR_12 18 rydeAlellekaleiar 34
                ++++Al+++e+al + +
  EPA05625.1 19 NFEDALACFEQALLLNQ 35
                68899999999998766 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 6.2e-07
      TPR_12  5 alnnlaavlrrlgrydeAlellekalei 32
                ++n  a+ lr lgry+eA e+++k+l i
  EPA05625.1 40 LWNLKAVSLRSLGRYEEAVECFNKSLGI 67
                67779999999************99965 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.1   9.1e-09   7.7e-06       1      34 []      26      59 ..      26      59 .. 0.97
   2 ?   -1.0   0.0       3.5     3e+03       1      12 [.      60      71 ..      60      71 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 9.1e-09
      TPR_17  1 lylkaleldPnnadaynnLAelllknGdlmtArq 34
                ++++al l+ n+++++n++A+ l+++G++++A++
  EPA05625.1 26 CFEQALLLNQNDPELWNLKAVSLRSLGRYEEAVE 59
                89******************************75 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.5
      TPR_17  1 lylkaleldPnn 12
                ++ k+l +dP +
  EPA05625.1 60 CFNKSLGIDPRD 71
                799999999975 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.1   0.00018      0.15      16      42 ..      19      45 ..      13      48 .. 0.92
   2 !   16.5   0.0   1.3e-05     0.011       1      35 [.      38      72 ..      38      74 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00018
      TPR_14 16 dpdeAiallrralalaPddaeawllla 42
                ++++A+a++++al l+ +d+e+w l a
  EPA05625.1 19 NFEDALACFEQALLLNQNDPELWNLKA 45
                79*********************8876 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 1.3e-05
      TPR_14  1 peallalaeallalGdpdeAiallrralalaPdda 35
                pe++ + a  l+ lG+++eA++++++ l  +P d+
  EPA05625.1 38 PELWNLKAVSLRSLGRYEEAVECFNKSLGIDPRDR 72
                6889999999**********************986 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   3.9e-07   0.00033      36      81 ..      17      63 ..       3      73 .. 0.63

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3.9e-07
                TT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
      ANAPC3 36 ngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81
                + +++ A+  +++a  ln ++++ + l+A +l  L++yeeA+ ++ k
  EPA05625.1 17 SLNFEDALACFEQAlLLNQNDPELWNLKAVSLRSLGRYEEAVECFNK 63
                45566666666666666666666666666666666666666665544 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.016        14      17      30 ..      19      32 ..      15      36 .. 0.79
   2 !   11.1   0.0   0.00033      0.28       9      29 ..      45      65 ..      42      68 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.016
      TPR_10 17 rydeAealleeala 30
                ++++A+a +e+al 
  EPA05625.1 19 NFEDALACFEQALL 32
                78899999999985 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00033
      TPR_10  9 analrqrgrydeAealleeal 29
                a+ lr++gry+eA++ + ++l
  EPA05625.1 45 AVSLRSLGRYEEAVECFNKSL 65
                7789***********998877 PP

>> NRBF2_MIT  MIT domain of nuclear receptor-binding factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.092        79      18      34 ..      14      30 ..       7      40 .. 0.81
   2 ?   10.5   0.0   0.00066      0.56      14      34 ..      44      64 ..      34      67 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.092
   NRBF2_MIT 18 llaaGkyeeaischkka 34
                +l +  +e+a++c ++a
  EPA05625.1 14 FLDSLNFEDALACFEQA 30
                667778*******9987 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00066
   NRBF2_MIT 14 kadrllaaGkyeeaischkka 34
                ka  l + G+yeea+ c +k+
  EPA05625.1 44 KAVSLRSLGRYEEAVECFNKS 64
                78888999*********9996 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.061        52      15      31 ..      15      31 ..       3      36 .. 0.78
   2 ?    9.1   0.0    0.0015       1.3      10      32 ..      44      66 ..      43      67 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.061
         MIT 15 DnagnyeeAlelYkeal 31
                  + n+e+Al ++++al
  EPA05625.1 15 LDSLNFEDALACFEQAL 31
                56789999*99999998 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0015
         MIT 10 kAveeDnagnyeeAlelYkeale 32
                kAv + + g yeeA+e++ ++l+
  EPA05625.1 44 KAVSLRSLGRYEEAVECFNKSLG 66
                79999999**********99986 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   4.1e-05     0.035     207     260 ..      19      72 ..       7      74 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.1e-05
                 -SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT-H CS
       NARP1 207 srekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaDR 260
                 + e Al + ++a+  + +  el+  Ka  l+  G  ++A+e+ +++  +D +DR
  EPA05625.1  19 NFEDALACFEQALLLNQNDPELWNLKAVSLRSLGRYEEAVECFNKSLGIDPRDR 72 
                 5679*************************************************9 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.29   2.5e+02      13      27 ..      18      31 ..      11      35 .. 0.81
   2 ?   10.2   0.0    0.0011      0.97       7      25 ..      45      63 ..      43      70 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.29
                HHHHHHHHHHHHHHH CS
       TPR_6 13 lgdtdkAlealerli 27
                l + ++Al+ +e+ +
  EPA05625.1 18 L-NFEDALACFEQAL 31
                6.8899*****9975 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0011
                HHHHHHHHHHHHHHHHHHH CS
       TPR_6  7 alsyrklgdtdkAlealer 25
                a s+r+lg++++A+e +++
  EPA05625.1 45 AVSLRSLGRYEEAVECFNK 63
                88999*99*********87 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   5.5e-05     0.047      78     126 ..      20      64 ..       4      71 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.5e-05
                 HHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
     DUF3856  78 adkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrma 126
                  + al  f++   l+q++ +lW      +av+l +lGr++ea++ f+++
  EPA05625.1  20 FEDALACFEQALLLNQNDPELWN----LKAVSLRSLGRYEEAVECFNKS 64 
                 47799999999999********5....699***************9975 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1       1.2   9.8e+02      22      38 ..      25      31 ..       9      36 .. 0.52
   2 ?    0.5   0.1      0.79   6.7e+02      17      31 ..      20      34 ..      15      51 .. 0.61
   3 ?   10.9   0.0   0.00043      0.37      14      37 ..      51      74 ..      43      75 .] 0.91

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.2
                HHHHHHHHHTTS-HHHH CS
  Fis1_TPR_C 22 ryvdalLeiEPenrQaq 38
                 +           +Qa+
  EPA05625.1 25 ACF----------EQAL 31
                333..........3444 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.79
                HHHHHHHHHHHHHHT CS
  Fis1_TPR_C 17 YseArryvdalLeiE 31
                +++A+ + ++ L + 
  EPA05625.1 20 FEDALACFEQALLLN 34
                556666665555433 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00043
                HT-HHHHHHHHHHHHHHTTS-HHH CS
  Fis1_TPR_C 14 lgeYseArryvdalLeiEPenrQa 37
                lg+Y+eA ++ +  L i+P+ r+a
  EPA05625.1 51 LGRYEEAVECFNKSLGIDPRDRNA 74
                89*******************998 PP

>> Coatomer_E  Coatomer epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00015      0.13     183     236 ..      20      73 ..      13      74 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00015
                 HHHHHHHHHHHHHHS---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HH CS
  Coatomer_E 183 iqdAyyifqelsekykstplllngkAvvslllgryeeAeslLkeaLdkdakdee 236
                 ++dA+  f++     ++ p l n kAv    lgryeeA +  +++L  d++d +
  EPA05625.1  20 FEDALACFEQALLLNQNDPELWNLKAVSLRSLGRYEEAVECFNKSLGIDPRDRN 73 
                 567888887766666788999999999999999999999999999999988875 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.61   5.2e+02      15      25 ..      19      29 ..      14      32 .. 0.86
   2 ?    9.0   0.0    0.0021       1.8      12      25 ..      50      63 ..      46      66 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.61
         PPR 15 kleeAlelfke 25
                ++e+Al +f++
  EPA05625.1 19 NFEDALACFEQ 29
                799*****986 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0021
         PPR 12 knGkleeAlelfke 25
                + G++eeA+e+f++
  EPA05625.1 50 SLGRYEEAVECFNK 63
                68**********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.48u 0.33s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 456.60
//
Query:       EPA05626.1  [L=48]
Description: hypothetical protein BG20_I1056 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      193  (0.0107647); expected 358.6 (0.02)
Passed Vit filter:                         3  (0.000167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 350.73
//
Query:       EPA05627.1  [L=42]
Description: hypothetical protein BG20_I1055 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 299.92
//
Query:       EPA05628.1  [L=201]
Description: imidazole glycerol phosphate synthase, glutamine amidotransferase subunit [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-25   90.1   0.0    1.8e-25   89.8   0.0    1.0  1  GATase         Glutamine amidotransferase class-I
    1.2e-05   25.2   0.0     0.0004   20.2   0.0    2.7  1  Peptidase_C26  Peptidase C26
    0.00032   20.6   0.0     0.0033   17.3   0.0    2.0  1  SNO            SNO glutamine amidotransferase family
     0.0012   18.5   0.0     0.0022   17.6   0.0    1.4  2  GATase_3       CobB/CobQ-like glutamine amidotransferase doma


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.8   0.0   4.1e-29   1.8e-25       2     186 ..       6     195 ..       5     198 .. 0.86

  Alignments for each domain:
  == domain 1  score: 89.8 bits;  conditional E-value: 4.1e-29
                 EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT.....TTTHHHHHHHHCTSTS-EEEETHHHHHHHHHTTT..... CS
      GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg.....vegkieaikearenkiPiLGICLGmQllaiefgr..... 90 
                 + D++++++ +l+++l + g++v+v+  d ++ +i          l+ +G+g+       ++++ ++ +++ + ++P+LGICLGm + ++++ +     
  EPA05628.1   6 IFDYGAGNIFSLKNSLEKSGATVDVIT-DFDKPNI-------YSGLLLPGVGNFDpaiksITKSKTNFHNYVKDNTPVLGICLGMEMFFEKSEEgkekg 96 
                 689*********************998.6555555.......45566688999888899967777777777777*******************989998 PP

                 ......EEE....EEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEEEEEEETTTEEEESSBTTSTTSTTH CS
      GATase  91 ......kvv....kekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeelmeiiekknpfvgvQFHPEststpeg 179
                       +v+    ++k  +h+g++    +++ +ll+g k+   +++ H+y v+p     ++ ++ta+s+ + ++ +++ek+n f+g+QFHPE++ + + 
  EPA05628.1  97 lgiiqgDVIilppSMK-VPHMGWNNLEIKKPGRLLEGIKDNTWVYFVHSYRVKP----VDNSVITAESDYGIKVPAVVEKRN-FFGTQFHPEKSGKVG- 188
                 88777766699*7777.******999999899*********************9....6667899****************9.**********99988. PP

                 HHHHHHH CS
      GATase 180 pellfnf 186
                 + +++nf
  EPA05628.1 189 KIMIQNF 195
                 5555555 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   8.9e-08    0.0004      99     216 .]      66     182 ..      36     182 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 8.9e-08
  Peptidase_C26  99 raalergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhrehe.......q...saashavkvekgsllaellgseeievnslHhqaikelaee 184
                    ++ ++ ++P+lgiC+G++++            e +++     + +                +++++k + l e ++ +++ v  +H+  +k ++++
     EPA05628.1  66 HNYVKDNTPVLGICLGMEMFFEKSE-------EGKEKGLGIIQGDviilppsMkvpHMGWNNLEIKKPGRLLEGIK-DNTWVYFVHSYRVKPVDNS 153
                    567899************9933322.......22222222222222222222234466678999997776666666.79*************9986 PP

  Peptidase_C26 185 lrveAvaeDgviEaieseeakafvlgvQwHPE 216
                    + ++A ++ g i    + e k  ++g Q+HPE
     EPA05628.1 154 V-ITAESDYG-IKVPAVVE-KRNFFGTQFHPE 182
                    4.56666555.44444444.33799******9 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   7.3e-07    0.0033      10     177 ..      16     189 ..      10     201 .] 0.70

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 7.3e-07
                 HHHHHHHHTTSEEEEE-SGGGGCC-SEEEE-S.S-.HHHHHHHHHHTT-HHHHHHHHHTT.--EEEETHHHHHHCCEETTBSS-SS--CCEEEETTTT- CS
         SNO  10 ehveaikkclaenktvkrkedlaevdaliiPG.Ge.stamskliertglyedllefvknsekvvlGtCaGlillskelenelvktlellkvkvkrnafG 106
                    + ++k++a   ++ + ++ +   +l++PG G+   a++ + +      +++++vk++  +vlG C G+ ++ ++ e+ + k l++++ +v      
  EPA05628.1  16 SLKNSLEKSGATVDVITDFDKPNIYSGLLLPGvGNfDPAIKSITKSKT---NFHNYVKDN-TPVLGICLGMEMFFEKSEEGKEKGLGIIQGDVIILPPS 110
                 556788999999999999999999999****94442457777776655...788899887.9*********99999999999999***99887666655 PP

                 SCCGEE.EEEEEETTTC.......SEEEEEESS--EEEEE-.TTTCEEEEECT.T.EEEEEEET.TEEEESS-GGGSTTHCH CS
         SNO 107 rqvdsf.ekeldfknli.......ekftavfiraPvieeilddeavkvlyeld.g.eivvakqk.kilatsfhPelaeddir 177
                  +v  +  ++l++k+ +       ++    f+ +  ++ +    + ++  e d g ++ ++  k ++++t fhPe + +  +
  EPA05628.1 111 MKVPHMgWNNLEIKKPGrllegikDNTWVYFVHSYRVKPVD---NSVITAESDyGiKVPAVVEKrNFFGTQFHPEKSGKVGK 189
                 55554414566666544344344467777777777776664...666666666677887777555**********8876333 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   4.9e-07    0.0022      15     107 ..      13     102 ..       3     116 .. 0.70
   2 ?   -3.5   0.0       1.4   6.5e+03     178     188 ..     170     180 ..     153     181 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.9e-07
    GATase_3  15 dldpLeaepevrvrfvplkdeslg..edadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmLGeeiedpegvegeageveg 107
                 ++  L++  e+ +  v+   ++++  + +  ++lpG  +     a++  ++ + + ++++++++pvlgiC G+ m+ e+ e+  g+e+  g ++g
  EPA05628.1  13 NIFSLKNSLEKSGATVD-VITDFDkpNIYSGLLLPGVGNFD--PAIKSITKSKTNFHNYVKDNTPVLGICLGMEMFFEKSEE--GKEKGLGIIQG 102
                 66667776666666666.33333323557788999988755..555555668999*********************999654..55555444444 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.4
    GATase_3 178 edgnvlGtYlH 188
                 e++n +Gt +H
  EPA05628.1 170 EKRNFFGTQFH 180
                 46799999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1176.24
//
Query:       EPA05629.1  [L=130]
Description: Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.2e-41  139.9   0.2      9e-41  139.8   0.2    1.0  1  His_biosynth  Histidine biosynthesis protein
  ------ inclusion threshold ------
       0.11   11.7   0.1        3.6    6.8   0.0    1.9  2  ThiG          Thiazole biosynthesis protein ThiG


Domain annotation for each model (and alignments):
>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.8   0.2     1e-44     9e-41       2     129 ..       3     128 ..       2     130 .] 0.98

  Alignments for each domain:
  == domain 1  score: 139.8 bits;  conditional E-value: 1e-44
                   EEEEEEEETTEEEEECTTCSTCEEEETTSHHHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SE CS
  His_biosynth   2 iipalDlkdGkvVrlvkGdrfqelryagdpvelakryeeegadelhvvDldaakegreanldlveeiaeevfipvqvGGGIrsledveelleagadk 98 
                   +ipa+Dl+dGkvVrl+kG+ +q+++y+++pve+ak+++++gad+lh+vDlda+  gr+ nl  +++i+e+++ip+q+ GG r+ ++++++ ++ +++
    EPA05629.1   3 VIPAIDLMDGKVVRLYKGNPDQKTVYSDNPVEVAKKWQSNGADMLHLVDLDATL-GRGSNLLTIKKIVEQISIPIQIAGGLRDESTITDVSKI-CNR 97 
                   9**************************************************996.**********************************9999.*** PP

                   EEESHHHHH-THHHHHHHHHHCGGGEEEEEE CS
  His_biosynth  99 viigtaavknpelikelaekfgsqkivvaiD 129
                   v++gt a+k+++++k+l+++ gs+kiv+++D
    EPA05629.1  98 VVLGTLAFKDKSMLKKLLKFLGSEKIVISVD 128
                   ******************************* PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0    0.0004       3.6     129     192 ..      28      90 ..      24      95 .. 0.73
   2 ?    3.7   0.0    0.0037        33       6      40 ..      93     127 ..      88     130 .] 0.87

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0004
                 EE-S-HHHHHHHHHTT-SEB..EEBSSSTTS----S-HHHHHHHHHH-SS-BEEES---SHHHHHH CS
        ThiG 129 YvsdDlvlarrleevGcaav..mPlaapiGsglGllnkealkiiieeakvPvivDAGigspsdaaq 192
                 Y  + + +a++ +  G+  +  + l a +G g    n  ++k i+e++++P+ +  G++  s ++ 
  EPA05629.1  28 YSDNPVEVAKKWQSNGADMLhlVDLDATLGRGS---NLLTIKKIVEQISIPIQIAGGLRDESTITD 90 
                 555555678888888877541156667776664...5667999***************99888765 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.0037
                 EES--EEEE-STSSSHHHHHHHHHHHT-SEEEEEC CS
        ThiG   6 efksrlllGtgkykslevlkeaveasgaeivtval 40 
                 ++ +r++lGt  +k++++lk+ ++  g+e + +++
  EPA05629.1  93 KICNRVVLGTLAFKDKSMLKKLLKFLGSEKIVISV 127
                 56789******************999998887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 803.06
//
Query:       EPA05630.1  [L=113]
Description: putative imidazoleglycerol-phosphate dehydratase, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-26   93.1   0.0    2.1e-26   92.9   0.0    1.0  1  IGPD          Imidazoleglycerol-phosphate dehydratase
  ------ inclusion threshold ------
      0.051   12.7   0.0      0.059   12.5   0.0    1.1  1  ANF_receptor  Receptor family ligand binding region


Domain annotation for each model (and alignments):
>> IGPD  Imidazoleglycerol-phosphate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.9   0.0   2.4e-30   2.1e-26      52     143 ..       1      92 [.       1      93 [. 0.98

  Alignments for each domain:
  == domain 1  score: 92.9 bits;  conditional E-value: 2.4e-30
                 S..-SSB--EEEEEEEETTEEEEEEEE--SS-EEE--..-SB--TT.--HHHHHHHHHHHHHHHT-EEEEEEEE--BHHHHHHHHHHHHHHH CS
        IGPD  52 lgdkrgikRfgsallpmDealaevaldlsgrpylvleaelkrekigeldtelveeffeslaeaagitlhvkvlrgenahhivealfKafara 143
                 lg+++gi+Rf  a +pmDe+lae+++dl +rp+++l  ++kr++i  ++ e +e+ff+sl ++ + ++h++v++g+n+hh+vea++K++a a
  EPA05630.1   1 LGTRSGITRFSYASVPMDESLAEASIDLVKRPFWKLVLSIKRNTIEGISKEDLEHFFQSLLQNLNSCVHLTVKYGDNDHHKVEAAIKSLAVA 92 
                 7899*******************************999****************************************************98 PP

>> ANF_receptor  Receptor family ligand binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   6.6e-06     0.059      97     170 ..      12      86 ..       4     101 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.6e-06
                   EESS--CHHHHHHHHHHHHHTT--EEEEEEESS...HHHHHHHHHHHHHHHHTT-EEEEEEEESTCHHHCHHHHHHH CS
  ANF_receptor  97 lrtvpsdtsqaqAivdilkhfgWkkvaliysdd...dygesglqaleeeleergicvalkekipessnddevvrkll 170
                      vp d+s+a+A +d++k+  Wk v  i  +       e + + ++  l++ + cv l  k+    nd + v++  
    EPA05630.1  12 YASVPMDESLAEASIDLVKRPFWKLVLSIKRNTiegISKEDLEHFFQSLLQNLNSCVHLTVKYG--DNDHHKVEAAI 86 
                   6789*****************************654455667777777999999*********9..34445555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.30s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 743.18
//
Query:       EPA05631.1  [L=100]
Description: hypothetical protein BG20_I2145, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      4e-12   45.9   0.0    4.6e-12   45.7   0.0    1.0  1  DNase-RNase     Bifunctional nuclease
  ------ inclusion threshold ------
       0.11   12.6   0.2       0.63   10.1   0.0    2.1  3  HTH_19          Helix-turn-helix domain
       0.16   11.7   0.5       0.29   10.9   0.3    1.5  2  Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 famil


Domain annotation for each model (and alignments):
>> DNase-RNase  Bifunctional nuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.7   0.0   7.7e-16   4.6e-12      36     124 ..       9      96 ..       5     100 .] 0.91

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 7.7e-16
                  HHHHHHHHCT---SS--HHHHHHHHHHHTTEEEEEEEEEEEETTEEEEEEEEEET---EEEEE-HHHHHHHHHHHT--EEEEHHHHHHH CS
  DNase-RNase  36 aqaialalegeeppRPlthDLlasllealgakvervvItdledgtfyAelvlrkeeeeleidaRpSDaiaLAlrtgapIyveeevleea 124
                  a+ i+  leg++ + P+ + L+ +++e+ ++++ +v I++   g+f A+l+++ +++ +  + R+SDaiaLA  +++pI+v +++l++ 
   EPA05631.1   9 ARYISNFLEGKREEPPTIYKLVEQICEENEMHLVKVKIYE-SGGIFRANLYFTGKKDMILRNFRASDAIALATYYSIPILVRKSLLKKI 96 
                  8899999********************************8.589*********965448889***********************9986 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0    0.0001      0.63      27      51 ..      10      36 ..       3      42 .. 0.89
   2 ?   -2.3   0.0      0.79   4.7e+03      35      42 ..      61      72 ..      58      87 .. 0.57
   3 ?   -0.5   0.0      0.22   1.3e+03      24      34 ..      88      98 ..      85     100 .] 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0001
      HTH_19 27 skisaiEngkkdvps..aelllkiaea 51
                ++is++  gk+++p+  ++l+ +i+e+
  EPA05631.1 10 RYISNFLEGKREEPPtiYKLVEQICEE 36
                79***********************97 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.79
      HTH_19 35 gkkdvps....a 42
                gkkd++     a
  EPA05631.1 61 GKKDMILrnfrA 72
                677777644444 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.22
      HTH_19 24 isrskisaiEn 34
                +++s + +iEn
  EPA05631.1 88 VRKSLLKKIEN 98
                67899999998 PP

>> Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.3   4.9e-05      0.29      41      65 ..      21      45 ..      19      49 .. 0.91
   2 ?   -3.2   0.0       1.2   7.4e+03      52      62 ..      77      87 ..      72      91 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.9e-05
                    SSSGGHHHHHHHHHHHTTEEEEEES CS
  Ribosomal_L7Ae 41 vepeekkkllealckekevpyvkvk 65
                     ep+++ kl+e++c+e+e ++vkvk
      EPA05631.1 21 EEPPTIYKLVEQICEENEMHLVKVK 45
                    589999****************997 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.2
                    HHHHHTTEEEE CS
  Ribosomal_L7Ae 52 alckekevpyv 62
                    al+ ++++p++
      EPA05631.1 77 ALATYYSIPIL 87
                    67777888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 752.66
//
Query:       EPA05632.1  [L=59]
Description: hypothetical protein BG20_I2141 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       983  (0.0548274); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.40
# Mc/sec: 443.76
//
Query:       EPA05633.1  [L=263]
Description: CBS domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-37  127.2   1.6    8.2e-10   39.0   0.0    4.1  4  CBS       CBS domain
  ------ inclusion threshold ------
      0.058   11.2   0.0       0.07   11.0   0.0    1.1  1  DUF5521   Family of unknown function (DUF5521)


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   0.0   9.1e-14   8.2e-10       1      56 [.      10      65 ..      10      66 .. 0.92
   2 !   32.6   0.0     9e-12   8.1e-08       3      55 ..      77     128 ..      75     130 .. 0.90
   3 !   22.3   0.1   1.5e-08   0.00014       3      55 ..     139     190 ..     137     192 .. 0.91
   4 !   30.1   0.0   5.6e-11     5e-07       8      55 ..     207     253 ..     201     255 .. 0.88

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 9.1e-14
                HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEE.ETTTBEEEEEEHHHHHHHHH CS
         CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVV.dedgklvGivtlrDllrall 56
                Vg +mt  +++v p+ +l+e+++ m+++g++ l +V  e+g ++G++t+rD+l+ ++
  EPA05633.1 10 VGNYMTAYPISVLPEVSLSECINFMARRGIGNL-IVsTEEGDPLGVLTERDILKQIV 65
                7889*********************9999****.66678999***********9876 PP

  == domain 2  score: 32.6 bits;  conditional E-value: 9e-12
                 HHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
         CBS   3 dimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                 +i  +++  v+pd ++  a+el+++k+  rl+V  e +k vGi+t +Dllra 
  EPA05633.1  77 EIILTPFEKVSPDISIQSAAELIISKK-ARLLVFAEPNKMVGIITPSDLLRAF 128
                 56778999**************99988.5**999999**************96 PP

  == domain 3  score: 22.3 bits;  conditional E-value: 1.5e-08
                 HHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEE.EEEEHHHHHHHH CS
         CBS   3 dimtrdvvtvppdttleealelmrekgvsrlPVVdedgklv.GivtlrDllral 55 
                 d+ +++v  v  d ++ +  +lm ek+++++ +Vd+ +    G++t+rDl+ ++
  EPA05633.1 139 DVISKKVYHVGYDNSIFDTCKLMYEKRIGSV-IVDGKN-SEfGMFTERDLVFKV 190
                 899****************************.**8777.788********9876 PP

  == domain 4  score: 30.1 bits;  conditional E-value: 5.6e-11
                 SCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
         CBS   8 dvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                  ++   p+    ea+ +m+++++ rl V+ ++gk+ Givt rD+++a 
  EPA05633.1 207 FPLITAPEILANEAASMMAQHHIKRL-VLQDQGKISGIVTVRDIIDAY 253
                 566777888899******9999****.**99**************985 PP

>> DUF5521  Family of unknown function (DUF5521)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   7.8e-06      0.07     105     147 ..     129     171 ..      74     190 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 7.8e-06
     DUF5521 105 ekcyldpslnslvyknilkvgielrisrvsclynekrlgqgil 147
                  k yl p l+ +++k + +vg +  i+    l  ekr+g  i+
  EPA05633.1 129 RKTYLAPILDDVISKKVYHVGYDNSIFDTCKLMYEKRIGSVIV 171
                 699************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1643.79
//
Query:       EPA05634.1  [L=327]
Description: hypothetical protein BG20_I2142 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0056   16.6   0.0      0.016   15.1   0.0    1.7  1  RMMBL     Zn-dependent metallo-hydrolase RNA specificity doma


Domain annotation for each model (and alignments):
>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   8.9e-07     0.016      11      57 ..     271     313 ..     266     317 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 8.9e-07
       RMMBL  11 idfSgHadknellelirklkprnvilvHGeeeatsalarllkeeegi 57 
                 i +S H d+nel +++ +   ++v+ +HG  e+    a++l ++ gi
  EPA05634.1 271 ITMSDHCDFNELVDMVVRSGAEQVYTIHGFVEEF---AEHL-RKIGI 313
                 6689*************************99655...4555.44455 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2069.53
//
Query:       EPA05635.1  [L=89]
Description: hypothetical protein BG20_I2140, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-16   60.7   0.1    1.5e-16   60.6   0.1    1.0  1  Response_reg  Response regulator receiver domain
  ------ inclusion threshold ------
      0.059   12.9   0.0      0.062   12.8   0.0    1.1  1  DUF1188       Protein of unknown function (DUF1188)


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.6   0.1   1.6e-20   1.5e-16       1      79 [.       6      84 ..       6      88 .. 0.94

  Alignments for each domain:
  == domain 1  score: 60.6 bits;  conditional E-value: 1.6e-20
                  EEEESSSHHHHHHHHHHHH.HTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEES CS
  Response_reg  1 vlivdDdplvrellrqlle.eegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviilta 79
                  v+i+ D++ +r  l+++++  +++e +++  dg+ al+ l+++k+d+illD++mp+mdGl++l+++ +++ + p iil+ 
    EPA05635.1  6 VMIINDSRSMRLFLEEVIKsFADFEIIGSYFDGNLALDALRTKKPDVILLDLEMPNMDGLTFLEKLSQDQ-KYPTIILSN 84
                  89*****************559*********************************************988.888888886 PP

>> DUF1188  Protein of unknown function (DUF1188)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   6.9e-06     0.062      32      76 ..      15      61 ..       4      83 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.9e-06
                HHHHHTT--E..EEEEEES-CCCHHHHHHHHCCC.EEEEEEESS.GG CS
     DUF1188 32 vleyleeeeleeknvlviGaYltGaaiakkLskk.eevtlvDie.ph 76
                ++ +lee   +  +  +iG+Y+ G+   ++L+ k  +v+l+D e p+
  EPA05635.1 15 MRLFLEEVIKSFADFEIIGSYFDGNLALDALRTKkPDVILLDLEmPN 61
                55666655555577789**************99889******86344 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 571.86
//
Query:       EPA05636.1  [L=81]
Description: transcriptional regulator, AsnC family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.4e-11   42.1   0.1    7.2e-11   41.9   0.1    1.0  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
  ------ inclusion threshold ------
      0.019   14.5   0.2       0.02   14.5   0.2    1.1  1  RimK            RimK-like ATP-grasp domain
       0.09   12.6   0.7        5.9    6.8   0.0    2.1  2  ACT_5           ACT domain
       0.12   11.8   0.0       0.14   11.5   0.0    1.1  1  GCV_T           Aminomethyltransferase folate-binding domain


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   0.1   1.6e-14   7.2e-11       1      69 [.       6      71 ..       6      75 .. 0.94

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 1.6e-14
                    EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEE CS
  AsnC_trans_reg  1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartet 69
                    +l++++ g+    e+++ ++ ++peV+e+  + G yd ++kv + + ++l++++ +k++++  +++t t
      EPA05636.1  6 ILIQCDLGS---EEQIINQIMQIPEVKEVRGTYGIYDVFCKVQADSKDSLDKVITNKIRKIQKIRSTIT 71
                    678999889...9***************************************************99976 PP

>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.2   4.5e-06      0.02      29      76 ..      14      60 ..       2      79 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.5e-06
                -HHHHHHTT-.-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHH.GGG-- CS
        RimK 29 daekliekiklrfPvvvKsvegsqGikvvlakkeqklkqvlea.lkeai 76
                  e++i++i ++ P  vK+v g++Gi+ v++k + + k+ l+  ++++i
  EPA05636.1 14 SEEQIINQI-MQIPE-VKEVRGTYGIYDVFCKVQADSKDSLDKvITNKI 60
                66899****.7***8.6***************99888888887666666 PP

>> ACT_5  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0    0.0013       5.9      47      62 .]      16      31 ..      10      31 .. 0.92
   2 ?    4.5   0.1    0.0069        31      36      57 ..      42      64 ..      39      68 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0013
       ACT_5 47 elLsnQleKLidVlkV 62
                e+++nQ+ ++++V++V
  EPA05636.1 16 EQIINQIMQIPEVKEV 31
                78***********998 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0069
       ACT_5 36 ieltVes.ersvelLsnQleKLi 57
                ++++ +s +     ++n+++K+ 
  EPA05636.1 42 CKVQADSkDSLDKVITNKIRKIQ 64
                67899995555556*******85 PP

>> GCV_T  Aminomethyltransferase folate-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   3.1e-05      0.14      31      83 ..      26      73 ..      20      80 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.1e-05
       GCV_T 31 aehlavreaaglfDvShmgkievsGpdaaalLqrlltndisklkpgkatytll 83
                 e++ vr + g++Dv  + k++ +    ++ L++++tn+i+k++++++t tl 
  EPA05636.1 26 PEVKEVRGTYGIYDV--FCKVQADS---KDSLDKVITNKIRKIQKIRSTITLH 73
                588999999999998..67766555...559*****************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       882  (0.049194); expected 358.6 (0.02)
Passed bias filter:                      589  (0.0328518); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 598.88
//
Query:       EPA05637.1  [L=303]
Description: hypothetical protein BG20_I0303 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.026   14.8   0.1       0.06   13.6   0.1    1.6  1  CARDB     CARDB
      0.046   13.5   0.2       0.11   12.3   0.2    1.7  1  Big_4     Bacterial Ig-like domain (group 4)


Domain annotation for each model (and alignments):
>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   6.7e-06      0.06      10      72 ..      28      95 ..      22     117 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.7e-06
                EC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE.....EEEEESEE-CTEEEEEEEEEE-S CS
       CARDB 10 lnpseafvgeentitvtvkNqGtaasgatkvalyldgelv.....gtvtvpsLaagesttvsftwtte 72
                + p+e   g++++i++ +kN+G ++ ++++  ++  ++       +++t+++L+ g+s   ++ ++++
  EPA05637.1 28 THPDESIIGRTISISILIKNNGWEDKKDISFVFTSQDNALipvsnNNITIEKLSQGGSFGGNVDFKIS 95
                678889999************************999999899999999*********98777766665 PP

>> Big_4  Bacterial Ig-like domain (group 4)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   1.2e-05      0.11       8      31 ..     211     235 ..     169     238 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.2e-05
       Big_4   8 vt.vgtspnLPttVeatysdgseee 31 
                 ++ v+++++LP +V++ty+d+  ee
  EPA05637.1 211 IKeVNSEYKLPFEVIVTYTDDIGEE 235
                 3336999***********9986655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2217.41
//
Query:       EPA05638.1  [L=171]
Description: adenylyl-sulfate kinase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.5e-50  171.2   0.0    1.8e-50  170.9   0.0    1.0  1  APS_kinase  Adenylylsulphate kinase
    1.5e-06   28.4   0.0    2.2e-06   27.9   0.0    1.2  1  AAA_33      AAA domain
    7.9e-05   23.2   0.0    0.00017   22.1   0.0    1.7  1  AAA_18      AAA domain
    0.00011   21.6   0.0    0.00036   19.9   0.0    1.8  2  Zeta_toxin  Zeta toxin
    0.00081   19.8   0.0     0.0016   18.8   0.0    1.5  1  AAA_17      AAA domain
      0.001   18.6   0.0     0.0015   18.1   0.0    1.3  1  KTI12       Chromatin associated protein KTI12
  ------ inclusion threshold ------
      0.013   15.8   0.0      0.023   15.0   0.0    1.4  1  AAA_28      AAA domain
      0.049   13.5   0.1        6.3    6.6   0.0    2.3  2  CPT         Chloramphenicol phosphotransferase-like protein
       0.12   11.8   0.0       0.22   10.9   0.0    1.4  1  Arf         ADP-ribosylation factor family


Domain annotation for each model (and alignments):
>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.9   0.0   8.8e-54   1.8e-50       1     156 [.       2     152 ..       2     154 .. 0.95

  Alignments for each domain:
  == domain 1  score: 170.9 bits;  conditional E-value: 8.8e-54
                 S-EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT--SSHHHHHHHHHHHHHHHHHHHHTT-EEEEE----SHHHHHHHHHHHHCH CS
  APS_kinase   1 rgvvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdLgfseedRkenirrvaevaklladaglivlvafisPyreeReaarelleea 99 
                 +++v+w+tGl +sGK+ti ++l+k +     +  +LdGd++R+  + +  fs++ R+e+ +rva++akll ++g+ + v+++sPy+e+R++are+++++
  EPA05638.1   2 KPFVLWMTGLPCSGKTTIVKELQKDI----PNLAMLDGDELREWFSPK-DFSKAGRDEHNKRVAHLAKLLLKHGVPSAVSLVSPYKENRDNAREIINSG 95 
                 589***************98887665....57899*******988765.8************************************************* PP

                 TEEEEEEEE--HHHHHHHTTTSHHHHHHTTSSSSHTTTSS-----SS-SEEEETTTS CS
  APS_kinase 100 lkfievfvdtplevceerDpkglYkkareGeikeftGidspYeaPenpelvvdtdke 156
                  +f e +v++++e ce+rD+kg+Y+kar+Geik+ftGid+pY+aP+np+l +dt++e
  EPA05638.1  96 DQFAECYVKCSVEKCEQRDVKGMYAKARKGEIKGFTGIDDPYDAPQNPDLLIDTEHE 152
                 *****************************************************9876 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   1.1e-09   2.2e-06       1     117 [.       5     116 ..       5     129 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 1.1e-09
      AAA_33   1 lvllvGlpGsGKstlaerllkklg.avllssdtlrrrlfgtdqqsktdytrvldrlyqilnelarkalsagrnvildatnlsrrerarflklarrlgvp 98 
                 ++++ Glp+sGK+t +++l k  +    l+ d+lr+   ++d  +       +d+ +++++ la+  l++g +  +      +++r++ +++ +  + +
  EPA05638.1   5 VLWMTGLPCSGKTTIVKELQKDIPnLAMLDGDELREWFSPKDFSK-----AGRDEHNKRVAHLAKLLLKHGVPSAVSLVSPYKENRDNAREIINSGD-Q 97 
                 789*******************999********999999876644.....46788999999***********98887777778999999***99777.9 PP

      AAA_33  99 vrivvvetdeetlkeRlak 117
                 ++  +v+++ e++++R  k
  EPA05638.1  98 FAECYVKCSVEKCEQRDVK 116
                 999*************877 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   8.6e-08   0.00017       3      44 ..       8      54 ..       6     113 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 8.6e-08
      AAA_18  3 ltGtpGvGKttlakeLskrl.gf....gvnlrdvakenglllevdpe 44
                 tG p++GKtt+ keL+k   ++    g++lr+ ++ ++ +    +e
  EPA05638.1  8 MTGLPCSGKTTIVKELQKDIpNLamldGDELREWFSPKDFSKAGRDE 54
                59****************98666888888888887777766655555 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   1.8e-07   0.00036      15      75 ..       2      59 ..       1      71 [. 0.80
   2 ?   -1.1   0.0      0.48   9.6e+02     133     157 ..     103     128 ..      98     133 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.8e-07
  Zeta_toxin 15 rPklillgGqpGAGKselaellkdelerqgnvvrldpDdlRelhPeyeeilka.dpkkasel 75
                +P ++ + G p +GK+++ ++l++++    n   ld+D+lRe +   ++  ka +++++ ++
  EPA05638.1  2 KPFVLWMTGLPCSGKTTIVKELQKDI---PNLAMLDGDELREWFSP-KDFSKAgRDEHNKRV 59
                799999*******************9...7************8833.444454355555554 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.48
  Zeta_toxin 133 kelSrlgvldRyeeevae.gRlvpke 157
                  + S++++++R  + +++ +R+ +++
  EPA05638.1 103 VKCSVEKCEQRDVKGMYAkARKGEIK 128
                 5789999****999966646886665 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   8.2e-07    0.0016       1      50 [.       9      55 ..       9      77 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 8.2e-07
                EE-TTSSHHHHHHHHHHHH.TEEEEEHHHHHHHHHHTTTSHSSHHHHCTSH CS
      AAA_17  1 lGgPGsGKgtqceklveky.gfthlsaGdllreeakrgglakardemrklp 50
                +G+P sGK+t++++l++++ ++ +l  Gd lre  +++  +   ++ r++ 
  EPA05638.1  9 TGLPCSGKTTIVKELQKDIpNLAMLD-GDELREWFSPKDFS---KAGRDEH 55
                7******************6777777.******99988753...3333333 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   7.3e-07    0.0015       6      25 ..       8      27 ..       3      62 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 7.3e-07
                EE--TTSSHHHHHHHHHHHH CS
       KTI12  6 ltGlPssGKstrakeLakal 25
                +tGlP+sGK+t++keL+k +
  EPA05638.1  8 MTGLPCSGKTTIVKELQKDI 27
                8***************9976 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   1.1e-05     0.023       4      60 ..       8      67 ..       6      76 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.1e-05
      AAA_28  4 itGgestGKTtlleaLaar..gypvv.pEaareileeklakgedalpwv.edllafaervl 60
                +tG +++GKTt++++L+++  +  ++  +  re ++ k +++ +  + + +++ ++a+++l
  EPA05638.1  8 MTGLPCSGKTTIVKELQKDipNLAMLdGDELREWFSPKDFSKAGRDE-HnKRVAHLAKLLL 67
                6999*************998888888888888888888866665333.3367777777666 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0031       6.3       6      27 ..       8      29 ..       4      57 .. 0.78
   2 ?    4.6   0.0     0.013        26     116     173 ..     103     165 ..      77     166 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0031
                EEE-TTSSHHHHHHHHHHHSSS CS
         CPT  6 LnGgsssGKsslaralqevlde 27
                + G + sGK+++++ lq+ +++
  EPA05638.1  8 MTGLPCSGKTTIVKELQKDIPN 29
                68999************97765 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.013
                 EE--HHHHHHHHHH......HTSSSTTHHHHHTTGGGTT---SEEEETTSS-HHHHHHHHHTT- CS
         CPT 116 vrcplevlerRele......rgdRepGlaalqaeavHagaeyDlevDtsaktpeecArairerl 173
                 v+c++e  e+R+++      r +   G +  +     a++  Dl +Dt ++  +++A++++e+l
  EPA05638.1 103 VKCSVEKCEQRDVKgmyakaRKGEIKGFTGIDDP-YDAPQNPDLLIDTEHESLTDSAKKVKEFL 165
                 7788888888876422111133344455544443.5678888999************9999876 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00011      0.22      17      37 ..       6      26 ..       1      31 [. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00011
                EEEEESTTSSHHHHHHHHHHS CS
         Arf 17 illlGLDnaGKtTilkklkle 37
                + + GL ++GKtTi+k+l+++
  EPA05638.1  6 LWMTGLPCSGKTTIVKELQKD 26
                5588**************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1095.74
//
Query:       EPA05639.1  [L=76]
Description: hypothetical protein BG20_I0319 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 511.39
//
Query:       EPA05640.1  [L=90]
Description: hypothetical protein BG20_I0311 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 694.98
//
Query:       EPA05641.1  [L=435]
Description: ammonium transporter [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   2.2e-113  378.9  29.1   2.5e-113  378.8  29.1    1.0  1  Ammonium_transp  Ammonium Transporter Family
  ------ inclusion threshold ------
      0.079   12.7   0.1      0.079   12.7   0.1    3.6  3  DUF3188          Protein of unknown function (DUF3188)


Domain annotation for each model (and alignments):
>> Ammonium_transp  Ammonium Transporter Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  378.8  29.1  2.8e-117  2.5e-113       1     399 []       9     407 ..       9     407 .. 0.96

  Alignments for each domain:
  == domain 1  score: 378.8 bits;  conditional E-value: 2.8e-117
                      HHHHHHHHHHHHHHHHHHHHHHHHSSGGGHHHHHHHHHHHHHHHHHHHHHTHHHHHHSSCBSSSSSCE-.TTTTSCCGCCTTCCHHH....... CS
  Ammonium_transp   1 aflllsaalvifmqagfalleaglvrsknvlnilvknlldlavvvllyvlfGyslafgkskgvsgfign.lglsaagvqdetlldgl....... 86 
                      a++l++  lv++m + ++l+e+gl r+kn+++++++ ++ la+ ++++++fG+slafg + +++g+ign   ++++gv++++ ld++       
       EPA05641.1   9 AWMLVAGSLVLLMIPALGLFESGLLRKKNAVSVFMQIFFGLALLSVMWFVFGFSLAFGPD-ESGGLIGNmDWVFLKGVPWDEALDYAptipgvl 101
                      7*********************************************************99.999999995345678999999999999999999 PP

                      HHHHHHHHHHHHHHHHHHHCTTTB-HHHHHHHHHHHHHHTHHHHHHHHHS.SSHHHHTT--.-SSSTTTTHHHHHHHHHHHHHHHS-STTTTGT CS
  Ammonium_transp  87 fflfqlafaataitivsgavaerikfsayllfsallgtlvyppvahwvwgeggwlaklgvliDfAgstvVHlvggvagLaaalvlgkregrfeg 180
                      f+ fql+faa++  + +g +aer+kfs++++f+a ++ l+y p++hwvwg ggwla+lgv+ DfAg++v+H+  g+ +Laaa+vlg+r+  +  
       EPA05641.1 102 FVKFQLMFAAITPLLLTGTIAERMKFSSFIIFIASWSILIYYPLVHWVWG-GGWLAELGVV-DFAGGIVIHTSVGMGALAAAIVLGRRRFFG-- 191
                      **************************************************.**********.***************************766.. PP

                      TTSS--GSBHHHHHHHHHHHHHHHHHHHHGGGSSSSHHHHH.HHHHHHHHHHHHHHHHHHHHHHHCSS-BHHHHHHHHHHHHHHHTTTTTTS-H CS
  Ammonium_transp 181 keeaikghnlpfavlGtllLwfgWfgFNaGsaltankrararaavtTllAaaagaltallisrlkegkinvlglanGilAGlVAiTaacavvep 274
                       +    +h++p+av G +lLw+gWfgFNaGsal+  + a + ++++T +A++++al+++ +s++++gk++v+ ++nG++AGl++iT+a ++v++
       EPA05641.1 192 -PAIEIPHSIPLAVTGSALLWLGWFGFNAGSALASGSLAGN-TVIVTHMASSVSALIWVGLSWMRTGKPSVVAAVNGAIAGLAGITPASGYVSV 283
                      .777889**********************************.**************************************************** PP

                      HHHHHHHHHHHHHHHHHHHHHHHHHTC-CTTHHHHHHHHHHHHHHHHHHHHTSHHHCSSHSSTTGGGT-CHHHHHHHHHHHHHHHHHHHHHHHH CS
  Ammonium_transp 275 wgAliiGlvAgvlsvlgvkklkeklkidDsldvvavHgvgGiwGllavgifaaekvvaskisggllsgegkqlvvqligilvilayafvvtlil 368
                       ++++iG+  g+ s+ g+  +keklkidD+ldv +vHgv+Gi+G+la gifa + v+  +  +gll g+ +ql++q+ig+ v++a+ f+ t+i+
       EPA05641.1 284 EHSFVIGIAIGIASYSGIIIFKEKLKIDDALDVSSVHGVAGIIGSLAIGIFASKLVN-PGGPNGLLFGNPEQLGIQAIGVGVAAALGFCGTWII 376
                      ******************************************************998.5555668888899*********************** PP

                      HHHHHHHTTSB--HHHHHHSHHHHHHSSSSB CS
  Ammonium_transp 369 llllklllgLrvseeeeevglDvaehgetay 399
                      +++l++l+g rvs+e e +glD++eh+e ay
       EPA05641.1 377 MKVLDFLVGVRVSPEVEDAGLDISEHAERAY 407
                      ****************************998 PP

>> DUF3188  Protein of unknown function (DUF3188)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   1.2       0.4   3.6e+03      30      44 ..      45      59 ..      15      60 .. 0.71
   2 ?   12.7   0.1   8.8e-06     0.079      26      45 ..     199     218 ..     198     221 .. 0.93
   3 ?   -0.7   0.1      0.14   1.2e+03      17      34 ..     350     364 ..     346     370 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.4
     DUF3188 30 llvGlgLivsgavgr 44
                ++ Gl+L+++ ++++
  EPA05641.1 45 IFFGLALLSVMWFVF 59
                567888888888777 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 8.8e-06
     DUF3188  26 slPallvGlgLivsgavgrg 45 
                 s+P++++G++L+ +g++g++
  EPA05641.1 199 SIPLAVTGSALLWLGWFGFN 218
                 9*****************97 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.14
     DUF3188  17 qrqgsdrlqslPallvGl 34 
                  ++++ ++q++   +vG 
  EPA05641.1 350 GNPEQLGIQAI---GVGV 364
                 4799999***9...7775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 2612.52
//
Query:       EPA05642.1  [L=237]
Description: radical SAM domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.8e-13   50.3   0.7    1.3e-12   48.2   0.1    1.9  2  Fer4_12      4Fe-4S single cluster domain
    7.3e-13   48.7   1.2    1.5e-12   47.7   0.3    2.0  2  Fer4_14      4Fe-4S single cluster domain
    1.8e-08   35.0   0.0    2.5e-08   34.5   0.0    1.2  1  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.2   0.1   2.1e-16   1.3e-12       2     100 ..      13     113 ..      12     134 .. 0.84
   2 ?    0.5   0.0      0.11   6.7e+02      68     105 ..     145     183 ..     140     200 .. 0.66

  Alignments for each domain:
  == domain 1  score: 48.2 bits;  conditional E-value: 2.1e-16
     Fer4_12   2 nGeGvrl.....slfvsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekdiwlytgyt 95 
                 +GeG+ +     +++++gC++ C +C  ke    +sg+e++ e +  +i++  k++  ++ ++GG+Pl   + ea+++l+k+++++k+ ++ ++++ + 
  EPA05642.1  13 EGEGILYgtktlFVRLAGCPFTCFYCDTKESLPLDSGQEYSIEEACTLIDSNLKNQTYKVNFTGGDPLI--QHEAVAKLAKHIQTKKI-PTYLESSCFD 108
                 788855444533888**************************777778888877999*************..****************9.7888888887 PP

     Fer4_12  96 leels 100
                  + ++
  EPA05642.1 109 SDRFN 113
                 77775 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.11
     Fer4_12  68 naeallelvkevkeekpekdiwlytgytleelskk..eke 105
                 na ++l+l    k++ +  +i++++ ++le++++   +  
  EPA05642.1 145 NAMKCLKLSVGSKKTTY-IKIVVSSKTKLEDFKDLvnKIF 183
                 56666677666666666.6789999999999874333333 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.7   0.3   2.5e-16   1.5e-12       1      88 [.      24     105 ..      24     157 .. 0.89
   2 ?   -0.6   0.0      0.23   1.4e+03      79     112 ..     160     190 ..     135     193 .. 0.63

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 2.5e-16
     Fer4_14   1 lfvrlsgCnlsCkgCdnketwkselgkpqteelleqilk.dlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekkiwletn 88 
                 lfvrl+gC++ C  Cd+ke+   ++g++++ e+  + ++ +lk++ +k   + +tGG+PL   +++++ kl k++++++  ++  le++
  EPA05642.1  24 LFVRLAGCPFTCFYCDTKESLPLDSGQEYSIEEACTLIDsNLKNQTYK---VNFTGGDPL--IQHEAVAKLAKHIQTKK--IPTYLESS 105
                 7******************************99999999788888884...67*******..6699*********9998..66666665 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.23
     Fer4_14  79 pekkiwletngtleielektpdlkeklealskid 112
                 + +ki + +  +le +++  +  +++++++sk d
  EPA05642.1 160 TYIKIVVSSKTKLE-DFK--DLVNKIFNIISKKD 190
                 34777777777777.777..45566677776544 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.0   4.2e-12   2.5e-08       2     162 ..      26     177 ..      25     188 .. 0.71

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 4.2e-12
                  EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHH CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritvetngtlpdeeklerlle 99 
                  v + gC++ C +C+++e+  + + g++ s+ee   +++++  ++++  v ++gg+pl + + v +l++ ++   ++i + +e++ +    +     l+
   EPA05642.1  26 VRLAGCPFTCFYCDTKES-LPLDSGQEYSIEEACTLIDSN-LKNQTYKVNFTGGDPLIQHEAVAKLAKHIQT--KKIPTYLESSCFDS--DRFNHVLP 117
                  5689*************7.99*******************.5667**************************9..79999999999986..33333333 PP

                  TT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET.EEEEEEEBTTTSHHHHHH CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
  Radical_SAM 100 lgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikr.vvdrivglpGendeelee 162
                    +d + +  ++ d++ + +l +    ++  +++l++   +   + +++ iv+      e++++
   EPA05642.1 118 F-FDIIKIEFKTKDSD-FIDLKHYERLIDNAMKCLKLSVGS-K-KtTYIKIVVSSKTKLEDFKD 177
                  2.35566666665555.333333444444444444433333.1.12555555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       779  (0.0434492); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1529.76
//
Query:       EPA05643.1  [L=155]
Description: universal stress family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-28   98.3   0.0    6.5e-28   98.0   0.0    1.1  1  Usp       Universal stress protein family
  ------ inclusion threshold ------
       0.06   13.1   0.2       0.11   12.3   0.2    1.3  1  DnaB_2    Replication initiation and membrane attachment


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.0   0.0   7.3e-32   6.5e-28       1     141 []       5     155 .]       5     155 .] 0.94

  Alignments for each domain:
  == domain 1  score: 98.0 bits;  conditional E-value: 7.3e-32
                 S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH.........HHHHHHCTTCEEEEEEEESS CS
         Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada.........akaaaeaggvkvevvveegd 90 
                 m  +IlV++Dgs++s kAl +A ela++ ++e++l  v++ +  ++ + +  +  ++e++  ++  +            a +++++ g++    + +g+
  EPA05643.1   5 MLSKILVPYDGSKYSIKALSRAMELAHNLDSEIFLFSVVHQSYISPPGILGLTRTKSEKDAIKKWIKTIRkdtetmlkmAVKRCDENGITASYNISQGN 103
                 6789************************************999999999999999888888888887766999************************** PP

                 HHHHHHHHHHHTTSSEEEEESCCSSTTTTCS.SBHHHHHHHHHTSSEEEEEE CS
         Usp  91 paeeilevaeeedadliVvGsrgrsglsrll.lGSvseyvlrhapcpVlvVr 141
                 +a eil +a++++++liV+Gs g++g+++l+ lGSvs++v ++a+cpVl+V+
  EPA05643.1 104 VANEILNFAKKKNISLIVIGSQGLHGVEKLMtLGSVSRRVSEQAKCPVLLVK 155
                 *****************************555*******************8 PP

>> DnaB_2  Replication initiation and membrane attachment
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   1.2e-05      0.11       9      64 ..      55     117 ..      53     118 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.2e-05
                 -.S--HHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHH......T--SHHHHHHHHHHHHHHT- CS
      DnaB_2   9 grplspseletilywlddl.glspevilllleyavek......gkrnlrYiekilknWaekgi 64 
                 g + ++se + i++w+++  + ++ +++++++++ e+      + ++ +  + il+  ++k+i
  EPA05643.1  55 GLTRTKSEKDAIKKWIKTIrKDTETMLKMAVKRCDENgitasyNISQGNVANEILNFAKKKNI 117
                 556699*************65669999*******77744433444466788888888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1000  (0.0557756); expected 358.6 (0.02)
Passed bias filter:                      761  (0.0424452); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1066.98
//
Query:       EPA05644.1  [L=165]
Description: hypothetical protein BG20_I0328 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.6e-06   28.2   4.4    3.1e-05   24.0   4.4    2.1  1  HSP20       Hsp20/alpha crystallin family
    0.00013   22.3   0.2    0.00018   21.8   0.2    1.2  1  PIH1_CS     PIH1 CS-like domain
     0.0013   18.3   0.1     0.0021   17.6   0.1    1.4  1  ArsA_HSP20  HSP20-like domain found in ArsA


Domain annotation for each model (and alignments):
>> HSP20  Hsp20/alpha crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   4.4   5.2e-09   3.1e-05       4     101 ..      82     164 ..      78     165 .] 0.80

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 5.2e-09
                 SSEEEEEEEEE-TT--CCCEEEEEETTEEEEEEE--..---TT----SS---EEEEEE--STTB-TTT-EEEEETTEEEEEEEBSS--..-------- CS
       HSP20   4 eeeeefevkldvpglkkeelkvkvednrvlvkgeheeeeedekglikerssrkFsrkftLPenvdadkvkaslkdGvLtvtvpkkepekkkkerkiqi 101
                 e+e+  ++ +++pg++k ++k+ v+d+ v +++eh   e++ ++ +          k+     vd+++ kas+k+G+L++  +  e e k+k +k+++
  EPA05644.1  82 EKEKLVKLVAEIPGVEKTDVKILVQDKIVDISAEHG--EKKYHVRVP--------IKY----KVDENSAKASYKNGILELVFKLIEDE-KPKGKKVEV 164
                 556668999***************************..333333333........344....56****************77776666.5699*9998 PP

>> PIH1_CS  PIH1 CS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.2   3.1e-08   0.00018      37      89 ..      91     144 ..      77     152 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 3.1e-08
     PIH1_CS  37 ielPllksikevklrvgerrleleskk..akyfLslkLpYpvdedkveAkFvkkt 89 
                  e+P++ + ++vk+ v+ + +++ +++  +ky  ++++ Y+vde++++A +++  
  EPA05644.1  91 AEIPGV-EKTDVKILVQDKIVDISAEHgeKKYHVRVPIKYKVDENSAKASYKNGI 144
                 478999.6678************9988889*********************8765 PP

>> ArsA_HSP20  HSP20-like domain found in ArsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   3.6e-07    0.0021       5      63 .]      88     149 ..      84     149 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.6e-07
  ArsA_HSP20   5 vlkldLPfvdkeeidlsrsgdeLtIkig..nfrRqitLPsvla.rkevtsAkfedgvLeIrF 63 
                 +l++++P+v+k ++++  +++   I+++    + ++  P + + +++ ++A++++g Le  F
  EPA05644.1  88 KLVAEIPGVEKTDVKILVQDKIVDISAEhgEKKYHVRVPIKYKvDENSAKASYKNGILELVF 149
                 799****************998888888445555688887766233466*********9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       750  (0.0418317); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1110.52
//
Query:       EPA05645.1  [L=69]
Description: hypothetical protein BG20_I0310 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 472.81
//
Query:       EPA05646.1  [L=123]
Description: universal stress family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.3e-20   72.1   0.0      7e-20   72.0   0.0    1.0  1  Usp       Universal stress protein family


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.0   0.0   3.9e-24     7e-20      18     141 .]       3     123 .]       1     123 [] 0.95

  Alignments for each domain:
  == domain 1  score: 72.0 bits;  conditional E-value: 3.9e-24
                 HHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSST CS
         Usp  18 AlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggvkvevvveegdpaeeilevaeeedadliVvGsrgrsg 116
                  l+ A+ la++ +a+++ l++++   + + s+    ++      ++  ++a+    +a++ g++ +  +  gd +++i+ + +++  d+iV+Gsrg+++
  EPA05646.1   3 GLDEAIYLARQCHATITGLYIVPLAKPVTDSQISYIEKHLLNNASKFMSKAK---IRAAQNGIVFDDAIDYGDEGPKIINYSNKKLFDIIVIGSRGMGS 98 
                 5899********************9999999999999999999999999875...7******************************************* PP

                 TTTCSSBHHHHHHHHHTSSEEEEEE CS
         Usp 117 lsrlllGSvseyvlrhapcpVlvVr 141
                 +++ +lGS+s+yvl+++++pVl+V+
  EPA05646.1  99 IKETFLGSTSNYVLHKSQIPVLIVK 123
                 ************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 774.77
//
Query:       EPA05647.1  [L=252]
Description: hypothetical protein BG20_I0282 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      4e-56  190.5   0.0    4.4e-56  190.4   0.0    1.0  1  ATP_bind_1  Conserved hypothetical ATP binding protein
     0.0031   17.9   0.0     0.0045   17.4   0.0    1.4  1  AAA_16      AAA ATPase domain
     0.0039   16.2   0.0     0.0072   15.3   0.0    1.4  1  MeaB        Methylmalonyl Co-A mutase-associated GTPase MeaB
     0.0046   16.2   0.0     0.0094   15.2   0.0    1.5  2  DUF2075     Uncharacterized conserved protein (DUF2075)
     0.0077   16.8   0.0      0.012   16.1   0.0    1.4  1  AAA_18      AAA domain
     0.0097   15.7   0.1       0.29   10.9   0.1    2.1  1  CLP1_P      mRNA cleavage and polyadenylation factor CLP1 P-l
  ------ inclusion threshold ------
      0.015   15.3   0.1      0.023   14.7   0.1    1.3  1  CbiA        CobQ/CobB/MinD/ParA nucleotide binding domain
      0.017   14.7   0.2        1.3    8.6   0.2    3.0  1  GTP_EFTU    Elongation factor Tu GTP binding domain
      0.025   14.2   0.1        1.5    8.4   0.0    2.2  2  SRP54       SRP54-type protein, GTPase domain
      0.065   13.3   0.1       0.89    9.7   0.1    2.3  1  MMR_HSR1    50S ribosome-binding GTPase
      0.079   12.9   0.1          1    9.3   0.0    2.2  2  NTPase_1    NTPase
      0.095   12.4   0.0       0.14   11.9   0.0    1.3  1  AAA_24      AAA domain
      0.095   13.0   0.1       0.16   12.2   0.1    1.6  1  AAA_22      AAA domain


Domain annotation for each model (and alignments):
>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.4   0.0   3.2e-59   4.4e-56       1     236 [.       6     241 ..       6     246 .. 0.95

  Alignments for each domain:
  == domain 1  score: 190.4 bits;  conditional E-value: 3.2e-59
  ATP_bind_1   1 vvGpaGsGKttfvgalseilelrgrsvavvNLDPAaeelpYeaavdirelitledvmedlglgpngalvvaleflresldwldeelekeeddyllfDtP 99 
                 v+G+aG+GK+ ++++l+e+++++    av+NLDP++++lpY +++d+r+++++ d+m++++lgpnga+v+a +++++++d+++e+++k + dyl++DtP
  EPA05647.1   6 VTGTAGAGKSLLTSKLYEYYTKNSAFAAVLNLDPGVQNLPYTCDIDVRDYVNVIDIMQQYDLGPNGAVVMANDLIASKIDEIQEQINKVNPDYLIVDTP 104
                 89************************************************************************************888********** PP

  ATP_bind_1 100 GQielfthseslakiveeLesefalvvvyLvDsqrltdptkfisgllsalsamlrlelPhvvvlnkfDllkeklekeleffedvealslllekee.eky 197
                 GQielf +++s++ +ve+++s  +  +++L+D   +t+p++f+s +l+a s+ lrl+lP+++v++k+Dl+ +kl+  +++ ++++ l++++  e+ + +
  EPA05647.1 105 GQIELFAYRSSGRFVVENISS-EEKTSIFLFDGALVTTPVNFVSIALLATSIKLRLGLPTINVITKTDLIGTKLRNIIDWSSNIKLLENAIAAETdGET 202
                 ********************6.677799*******************************************99**************999887777888 PP

  ATP_bind_1 198 kklaeaiaelleefalvlrflplssekeesiedllslid 236
                  +l+ +i + l++ +  + ++p+s+ +++++ +l  ++ 
  EPA05647.1 203 YSLTTNILRGLNLGGFAQGLIPVSNVTGNGLVNLEGALS 241
                 99**************999*****999999988876665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   3.3e-06    0.0045      26      70 ..       3      52 ..       1     137 [. 0.77

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.3e-06
      AAA_16 26 lvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipy.....s 70
                +++++G +G GKs l  +l+++++k+ ++++  + d   +++py     +
  EPA05647.1  3 SIFVTGTAGAGKSLLTSKLYEYYTKNSAFAAVLNLDPGVQNLPYtcdidV 52
                79***********************9665566666666666888554442 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   5.3e-06    0.0072      32      69 ..       4      41 ..       1      45 [. 0.93

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.3e-06
                EEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE---- CS
        MeaB 32 vGltGvPGaGkstlvealglelrrrGkrvavlavDPss 69
                + +tG+ GaGks l+++l + ++++    avl +DP+ 
  EPA05647.1  4 IFVTGTAGAGKSLLTSKLYEYYTKNSAFAAVLNLDPGV 41
                679*********************************86 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   6.8e-06    0.0094       3      25 ..       3      25 ..       1      44 [. 0.83
   2 ?   -2.9   0.0       2.2     3e+03     111     132 ..     115     136 ..     108     139 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 6.8e-06
     DUF2075  3 vvlVtGvaGtGKtvvllnllael 25
                 ++VtG aG+GK+++ ++l   +
  EPA05647.1  3 SIFVTGTAGAGKSLLTSKLYEYY 25
                58***************998877 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.2
     DUF2075 111 seenqlkelmkrakvvvalvDe 132
                 s++  ++++ +++k +++l+D+
  EPA05647.1 115 SGRFVVENISSEEKTSIFLFDG 136
                 4555566777779999999997 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   8.9e-06     0.012       1      80 [.       4     102 ..       4     133 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 8.9e-06
      AAA_18   1 IlltGtpGvGKttlakeLskrl.gf....................gvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleegknlv 78 
                 I++tGt+G+GK+ l+  L +   ++                     + +rd++   ++   +d    +   ++  d  ++ +d+++e+++   +++ l+
  EPA05647.1   4 IFVTGTAGAGKSLLTSKLYEYYtKNsafaavlnldpgvqnlpytcDIDVRDYVNVIDIMQQYDLG-PNGAVVMANDLIASKIDEIQEQIN-KVNPDYLI 100
                 99****************66533334557777778887888888877777777776666666655.233344444555555555555554.45566666 PP

      AAA_18  79 id 80 
                 +d
  EPA05647.1 101 VD 102
                 65 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.1   0.00021      0.29       1     119 [.       8     112 ..       8     119 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00021
      CLP1_P   1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvGqseispPgtislalverpidveegfsldaplvyffGdtspsdnpslylalvkelareveekleenk 99 
                 G   +GKS l+  L +y ++++   ++++lD+G +++ + + i +  + + id +++++             p++++   ++l+++ ++e++e++   +
  EPA05647.1   8 GTAGAGKSLLTSKLYEYYTKNSAFAAVLNLDPGVQNLPYTCDIDVRDYVNVIDIMQQYD-----------LGPNGAVVMANDLIASKIDEIQEQI---N 92 
                 66788999999999999999999999999999999976666666666666666544432...........3455556666666777777777433...3 PP

      CLP1_P 100 kakasgliIntpGwvkglga 119
                 k++ + li++tpG ++ +++
  EPA05647.1  93 KVNPDYLIVDTPGQIELFAY 112
                 68999999999999987776 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   1.7e-05     0.023       3     117 ..       5     172 ..       3     180 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.7e-05
                 EEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH.HTTEB-HHHH.............................................. CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx.............................................. RF
        CbiA   3 iastkGGvGKTtlaanLaralarrglrVllvDaDpqannlai.leglendiep.............................................. 54 
                 ++ ++ G+GK+ l+ +L  +  ++    +++ +Dp   nl +  + ++ d  +                                              
  EPA05647.1   5 FVTGTAGAGKSLLTSKLYEYYTKNSAFAAVLNLDPGVQNLPYtCDIDVRDYVNvidimqqydlgpngavvmandliaskideiqeqinkvnpdylivdt 103
                 678899*****************999999999999999999775555555555788899**************************************99 PP

                 ........CCHCCCHHHHHHCHCHHHH...EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CC CS
                 ........xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        CbiA  55 ........dlkrllellealgkkkall.lkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdea 117
                          ++++  ++e+++ + +   +++ g +++ + +  +++ll  +++ ++   g+p ++vi +++ 
  EPA05647.1 104 pgqielfaYRSSGRFVVENISSEEKTSiFLFDGALVTTPVNFVSIALLATSIKLRL---GLPTINVITKTDL 172
                 99999998777777888999999888899999999999999999999999999988...9999999988775 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.2   0.00092       1.3      66     146 ..      92     184 ..       1     244 [. 0.55

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00092
                 TCSSEEEEEEEESSSGG.G.............HHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHH..HHTTTEEEEEEESCGSTHHHHHHHHHHH CS
    GTP_EFTU  66 etkkylinliDtPGHvd.F.............skevirglrvlDgavlvvdaveGvepqteevlrla..lkegvpiivfiNKmDrlkaelkeiveev 146
                 ++ +  + ++DtPG ++ F             s+e  +++   Dga++       v+  +  +l     l++g+p+i +i+K D ++++l++i++  
  EPA05647.1  92 NKVNPDYLIVDTPGQIElFayrssgrfvveniSSEEKTSIFLFDGALVTTP----VNFVSIALLATSikLRLGLPTINVITKTDLIGTKLRNIIDWS 184
                 555566667777776653211111111111111222223344444443333....333333333333004556779999999999988888887644 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0    0.0011       1.5       3      35 ..       3      35 ..       1      39 [. 0.83
   2 ?    3.7   0.0     0.029        40      73      95 ..      84     107 ..      70     138 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0011
                EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEE CS
       SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllv 35
                 i + G+ GaGK   ++KL ++++k+   +++ 
  EPA05647.1  3 SIFVTGTAGAGKSLLTSKLYEYYTKNSAFAAVL 35
                68899*******************996655554 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.029
                 HHHH.HHHHHTTSSEEEEEE--SS CS
       SRP54  73 keav.ekakeekidvvlvDTaGrl 95 
                  +++ e+ ++ + d+++vDT G+ 
  EPA05647.1  84 IDEIqEQINKVNPDYLIVDTPGQI 107
                 4444045566689********986 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1   0.00064      0.89       2      72 ..       4     125 ..       3     169 .. 0.54

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00064
                 EEEEESTTSSHHHHHHHHHT......S.TEEESSSTTSSSSEEEEEEEETTEE..........................................EEEE CS
    MMR_HSR1   2 vaivGrpNvGKStLinaltg......e.kaivsdkpgtTrdinegrvklkgke..........................................ielv 51 
                 + + G   +GKS L ++l +      + +a  +  pg+   + +  +++++                                            + +v
  EPA05647.1   4 IFVTGTAGAGKSLLTSKLYEyytknsAfAAVLNLDPGVQNLPYTCDIDVRD-YvnvidimqqydlgpngavvmandliaskideiqeqinkvnpdYLIV 101
                 567788888888888888754433321222223344444444444444322.01233344444455555555555555555555555555555669*** PP

                 ECGGCSS...HHHHHHHHHHHHHH CS
    MMR_HSR1  52 DtpGlie...gaseekglgkafla 72 
                 DtpG ie     s+++ + +++ +
  EPA05647.1 102 DTPGQIElfaYRSSGRFVVENISS 125
                 ****76543333333334444443 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00073         1       2      23 ..       4      25 ..       3      32 .. 0.87
   2 ?    1.2   0.0      0.22     3e+02      87     112 ..      85     112 ..      63     136 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00073
                EEEE--TTSSHHHHHHHHHHHH CS
    NTPase_1  2 vfiTGppGvGKtTlvkkvlell 23
                +f+TG  G GK+ l +k++e  
  EPA05647.1  4 IFVTGTAGAGKSLLTSKLYEYY 25
                9****************99876 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.22
                 HHHHHHH..HHH-EEEE---STTGGG-H CS
    NTPase_1  87 ealrkal..seadviviDEiGkmElksk 112
                 + +++++   ++d +++D  G++El++ 
  EPA05647.1  85 DEIQEQInkVNPDYLIVDTPGQIELFAY 112
                 4455554446789999*******99874 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0    0.0001      0.14       3      76 ..       2     106 ..       1     117 [. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0001
      AAA_24   3 lkiliyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdieswedfldevvel........................aaeladyktlv 70 
                 ++i+++G +g+GK+ l ++l          +++++++ G+++l  +   d++ + +++d +++                         + ++ + + l+
  EPA05647.1   2 KSIFVTGTAGAGKSLLTSKLyeyytknSAFAAVLNLDPGVQNLPYTCDIDVRDYVNVIDIMQQYdlgpngavvmandliaskideiqeQINKVNPDYLI 100
                 5799******************9*8666667899*********99999999955555555554444477777777777777777777655555566777 PP

      AAA_24  71 iDtide 76 
                 +Dt ++
  EPA05647.1 101 VDTPGQ 106
                 777665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00012      0.16       7      32 ..       3      28 ..       1     102 [. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00012
      AAA_22  7 ilvvtGesGtGKTtllrrlleqldee 32
                +++vtG +G+GK++l  +l e +++ 
  EPA05647.1  3 SIFVTGTAGAGKSLLTSKLYEYYTKN 28
                799*************9998877654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1551.25
//
Query:       EPA05648.1  [L=142]
Description: universal stress family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.6e-28   97.8   0.0    9.4e-28   97.5   0.0    1.1  1  Usp       Universal stress protein family


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.5   0.0   5.3e-32   9.4e-28       2     141 .]       6     142 .]       5     142 .] 0.90

  Alignments for each domain:
  == domain 1  score: 97.5 bits;  conditional E-value: 5.3e-32
                 -SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTCEEEEEEEESSHHHHHHHHHH CS
         Usp   2 ykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggvkvevvveegdpaeeilevae 100
                 +k+IlV++Dgs++s + l+ A+ la++ +a+++ l+vi+  +   ++  ++      +  ++  + a   k+ ++++g+  + ++ +g+p  ei  +a+
  EPA05648.1   6 IKKILVPLDGSKNSLRGLDEAIYLARQCHATITGLYVIPIYPRNFTDIIMPYQIHLTKSAKKFMESA---KTTCAQKGIMFKSKIIFGSPIMEIDYMAK 101
                 69*************************************9998888877766555554444444443...489************************** PP

                 HTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
         Usp 101 eedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                 +++ d+iV+Gsrg+sgl++++lGSv++++++++ +pVlv++
  EPA05648.1 102 NKGFDIIVIGSRGQSGLKEAFLGSVAKAIIHKSRIPVLVIK 142
                 ***************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 868.49
//
Query:       EPA05649.1  [L=83]
Description: hypothetical protein BG20_I0285 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.059   13.4   0.4      0.059   13.4   0.4    1.6  2  Phage_holin_2_1  Bacteriophage P21 holin S


Domain annotation for each model (and alignments):
>> Phage_holin_2_1  Bacteriophage P21 holin S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.5      0.26   4.6e+03      32      45 ..      17      30 ..      13      35 .. 0.64
   2 ?   13.4   0.4   3.3e-06     0.059      32      59 ..      52      79 ..      39      83 .] 0.88

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.26
  Phage_holin_2_1 32 Wsaigvlgglvigl 45
                     W   ++  g+vi++
       EPA05649.1 17 WTWYAIEFGIVIAV 30
                     55555556666665 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 3.3e-06
  Phage_holin_2_1 32 WsaigvlgglvigllTyltnlYFKrket 59
                       ++g++gg++++   ++ n+ FKrk  
       EPA05649.1 52 YVFMGIVGGIFFIWYMIIRNFVFKRKIL 79
                     5689*********************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 495.59
//
Query:       EPA05650.1  [L=222]
Description: hypothetical protein BG20_I0329 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.3e-07   28.6   0.1    1.8e-06   27.6   0.1    1.5  1  ACT_7     ACT domain
  ------ inclusion threshold ------
      0.014   15.9   0.1       0.03   14.8   0.0    1.6  2  SecD-TM1  SecD export protein N-terminal TM region
      0.034   14.1   0.0       0.16   12.0   0.0    2.1  1  Pox_A3L   Poxvirus A3L Protein


Domain annotation for each model (and alignments):
>> ACT_7  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.1     3e-10   1.8e-06       5      64 ..     156     215 ..     153     216 .. 0.91

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 3e-10
                 EEEEEEE-S-.---SS--HHHHHHHHHHTTT---EEEE.-SS-EEEEEEGGGHHHHHHHHH CS
       ACT_7   5 gwiklsvvgsglpfdvtGivaklaspLaeagIsifqiS.tyrtdyiLVpeedlekAveaLh 64 
                 g +k++++ +  + +++ +v+ +a+ L e+gI++     ++++++i+ +e+d+ +A+e+L+
  EPA05650.1 156 GLAKIRISIP-TNQNQSDVVSYVAEILHENGIELVNAYfSQDSIIIILNEKDASRAYEILR 215
                 6789999999.44479*****************999999*********************8 PP

>> SecD-TM1  SecD export protein N-terminal TM region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.8   1.1e+04      82      92 ..      65      75 ..      49      89 .. 0.49
   2 ?   14.8   0.0     5e-06      0.03      40      93 ..     166     216 ..     151     220 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.8
    SecD-TM1 82 dqqlkAkdvle 92
                 ++++ kd+++
  EPA05650.1 65 ADSFENKDAIK 75
                33333333333 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 5e-06
    SecD-TM1  40 katlkvdeatlskveqaLkeagievksielenesllvrfestdqqlkAkdvlek 93 
                 ++  + +++++s+v ++L+e+gie  ++ ++++s+++ ++++d+  +A ++l++
  EPA05650.1 166 TN--QNQSDVVSYVAEILHENGIELVNAYFSQDSIIIILNEKDA-SRAYEILRS 216
                 33..35677899*************************9988776.578888876 PP

>> Pox_A3L  Poxvirus A3L Protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.6e-05      0.16      18      52 ..     127     161 ..     125     163 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.6e-05
     Pox_A3L  18 nlveylkeDretikmilesqpkklkilkeFLaavr 52 
                 + +++l+eD e i+ i e+ p+++++    La +r
  EPA05650.1 127 DSFRFLTEDVESIREIFENMPNRENMFSTGLAKIR 161
                 6799********************99887777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1574.76
//
Query:       EPA05651.1  [L=153]
Description: CBS domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-25   88.6   3.9    1.1e-12   48.2   0.1    2.2  2  CBS       CBS domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   0.9   8.5e-15   1.5e-10       1      55 [.       9      62 ..       9      64 .. 0.91
   2 !   48.2   0.1   6.3e-17   1.1e-12       1      54 [.      73     125 ..      73     127 .. 0.93

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 8.5e-15
                HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
         CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55
                V+ +mt+ v+ v+ + t+ ea++lm++++v+++ V+ e++  +Givt+rD + ++
  EPA05651.1  9 VRNVMTKSVIAVDSSLTVNEAAKLMEDARVGAVIVM-ENNSAIGIVTDRDFAVKI 62
                789**********************9999****666.8999*********98665 PP

  == domain 2  score: 48.2 bits;  conditional E-value: 6.3e-17
                 HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
         CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54 
                 V++im+++++ + pd++++ +++lm  +g++ lPV+ ed++++Gi+t +Dl++ 
  EPA05651.1  73 VKQIMSSPLLAIGPDESVWMVADLMYTRGIRKLPVI-EDDQVIGIITATDLVNQ 125
                 89***********************8888*******.7888**********976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.53
# Mc/sec: 866.30
//
Query:       EPA05652.1  [L=287]
Description: CBS domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-47  158.9  13.2    5.5e-14   52.4   0.6    4.1  4  CBS       CBS domain
  ------ inclusion threshold ------
      0.066   12.2   0.5       0.86    8.6   0.1    2.1  2  PhnJ      Phosphonate metabolism protein PhnJ


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.4   1.1e-13   9.5e-10       6      55 ..      13      62 ..       7      64 .. 0.89
   2 !   43.8   0.0   2.8e-15   2.5e-11       1      53 [.      75     127 ..      75     130 .. 0.88
   3 !   30.7   0.2   3.7e-11   3.3e-07       1      51 [.     139     188 ..     139     192 .. 0.93
   4 !   52.4   0.6   6.1e-18   5.5e-14       3      56 ..     233     285 ..     231     286 .. 0.94

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 1.1e-13
                BSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
         CBS  6 trdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55
                 ++ vt++p+t++ +a + + ++++ rl V+d+ +++vGi+t++D+++ +
  EPA05652.1 13 IKKTVTISPNTSILDARQVLLRHNLKRLVVIDSKKHPVGIITEKDVAKTI 62
                57789**************99*******77799999**********9866 PP

  == domain 2  score: 43.8 bits;  conditional E-value: 2.8e-15
                 HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
         CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53 
                 V+ +m+++++t++ ++++ ++++lm+++++s++ V+ ++g l Gi+t++Dl++
  EPA05652.1  75 VSGFMSKKLITIKKTDSIYDCAKLMKKNHISSIIVLGNNGVLEGIITKTDLAS 127
                 6779*********************5555****7778899888********87 PP

  == domain 3  score: 30.7 bits;  conditional E-value: 3.7e-11
                 HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHH CS
         CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDl 51 
                 V+ imtr+v+t+ p ++l  +  l++++++ r+ V+  +  +vGi+t rD 
  EPA05652.1 139 VSKIMTRNVITAMPGDSLLYVESLLIHNRIARI-VIQRNRIPVGIITFRDF 188
                 789*********************99999****.**87888*********7 PP

  == domain 4  score: 52.4 bits;  conditional E-value: 6.1e-18
                 HHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
         CBS   3 dimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                 dim++++vt+  d++++ a+ lm+++g+s+lPVV +  klvGi+t++D+++a++
  EPA05652.1 233 DIMSSNPVTIEADEDVGVAVLLMIRNGISGLPVV-KKSKLVGIITKTDIVNAIA 285
                 89********************************.5666************996 PP

>> PhnJ  Phosphonate metabolism protein PhnJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.1   9.6e-05      0.86      54     102 ..      51     101 ..      47     116 .. 0.81
   2 ?    1.7   0.0     0.012     1e+02      97     174 ..     169     243 ..     160     249 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 9.6e-05
        PhnJ  54 sligkddvlkvidqGsddsvnavnirkliekta.gvettektee.atliqt 102
                  +i+++dv k i    d+s+n+v++  +++k    ++ t++  + a+l++ 
  EPA05652.1  51 GIITEKDVAKTIYALGDKSINTVKVSGFMSKKLiTIKKTDSIYDcAKLMKK 101
                 79**************************98765488888876652455554 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.012
        PhnJ  97 atliqtrhriPeeklkedqilvlqvPipeplrvvepseaetkklhaeedysklwvklyedivrfgeiatsadyPvlvn 174
                 a ++  r riP   ++ ++ +  ++P     +  +p+e+e+ k+ ++ d  ++ v+  +++++f+ + + ++ Pv+++
  EPA05652.1 169 ARIVIQRNRIPVGIITFRDFVPAKLPFWI-SQSADPKEVENYKMKSNVD--EFRVNQMNHLLHFKAVDIMSSNPVTIE 243
                 77778888999888888888777777653.4667899999998887766..678899999999*99999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1990.20
//
Query:       EPA05653.1  [L=306]
Description: putative transcription initiation factor IIB [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-32  111.5   3.0    2.2e-15   56.4   0.1    2.2  2  TFIIB         Transcription factor TFIIB repeat
    3.6e-06   26.4   0.2    7.8e-06   25.3   0.2    1.5  1  TF_Zn_Ribbon  TFIIB zinc-binding
    1.5e-05   24.8   1.4     0.0069   16.3   0.1    2.6  2  HTH_11        HTH domain
     0.0016   18.2   0.2       0.67    9.7   0.0    2.2  2  Cyclin_N      Cyclin, N-terminal domain
  ------ inclusion threshold ------
      0.067   12.9   0.2       0.34   10.6   0.0    2.0  2  Herpes_UL51   Herpesvirus UL51 protein
      0.069   13.3   0.3       0.57   10.4   0.0    2.5  2  DUF2543       Protein of unknown function (DUF2543)


Domain annotation for each model (and alignments):
>> TFIIB  Transcription factor TFIIB repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.4   0.1   7.5e-19   2.2e-15       2      66 ..     128     192 ..     127     196 .. 0.94
   2 !   55.5   0.5   1.5e-18   4.4e-15       1      71 []     221     291 ..     221     291 .. 0.98

  Alignments for each domain:
  == domain 1  score: 56.4 bits;  conditional E-value: 7.5e-19
                 HHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS- CS
       TFIIB   2 krfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqV 66 
                 +++  +l++p+ V ++A +++++a++ k++ Gr +a++++A+ly Acr ++  rt+ +i++  ++
  EPA05653.1 128 NAMKTKLGIPDNVIENAAYIYRKAVNSKLTRGRTMASLISASLYAACRENNIPRTLDDIADAGNI 192
                 567789*****************************************************998776 PP

  == domain 2  score: 55.5 bits;  conditional E-value: 1.5e-18
                 HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
       TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                 i++++++++L+ek +++A+ ++k++  +++++G+ p + aAA+lyiAc  +++k +qk +ss + Vs++ti
  EPA05653.1 221 ISKISNNMNLKEKTKRDAFDILKRCELKEITAGKHPVAQAAASLYIACMINNEKISQKKFSSEAGVSDVTI 291
                 7899*****************************************************************98 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.2   2.6e-09   7.8e-06       6      29 ..      18      41 ..      17      51 .. 0.91

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 2.6e-09
                  TTCEECHEETSTTCEEESSSSBEE CS
  TF_Zn_Ribbon  6 CgstnlveDpergelvCtdCGlVl 29
                  C+++ +++D erge++C+ CGlVl
    EPA05653.1 18 CKTYPIITDSERGEMFCGGCGLVL 41
                  99988******************8 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.1    0.0021       6.3      13      45 ..     178     211 ..     169     214 .. 0.84
   2 !   16.3   0.1   2.3e-06    0.0069      10      43 ..     270     302 ..     263     305 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0021
      HTH_11  13 rgpisgeeLAeeLnvSrrtvrrdIkaL.eelgvp 45 
                 + p + +++A+  n+ rr   rd++++ ++lg++
  EPA05653.1 178 NIPRTLDDIADAGNIERRILSRDLRTIiKKLGLK 211
                 5567999*******************97777766 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 2.3e-06
      HTH_11  10 leargpisgeeLAeeLnvSrrtvrrdIkaLeelg 43 
                 ++++ +is ++ + e +vS  t+r+++  +++++
  EPA05653.1 270 INNE-KISQKKFSSEAGVSDVTIRNRVTLIKKTL 302
                 3444.5*************************997 PP

>> Cyclin_N  Cyclin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.0    0.0021       6.3      29     101 ..     118     189 ..      92     213 .. 0.77
   2 !    9.7   0.0   0.00022      0.67      36      91 ..     219     274 ..     213     294 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0021
                 HHHHHHHHHHHHHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHHHSSS---HHHHHHH CS
    Cyclin_N  29 emRailidwlvevaekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAaKveeisppkledlvyi 101
                    + + + l  + +k+ +  +++  a+ ++ + + +k ++ +++  +  ++L+ A++ ++i p +l+d++ +
  EPA05653.1 118 VALSKAFTLLNAMKTKLGIPDNVIENAAYIYRKAVNSKLTRGRTMASLISASLYAACRENNI-PRTLDDIADA 189
                 555677888999999999999***************9999999***************9888.8999988755 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00022
                 HHHHHHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHHHSSS CS
    Cyclin_N  36 dwlvevaekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAaKveeis 91 
                 +++ +++++++l+++t   a ++l R   k+++  ++    +a++L++A+ +++ +
  EPA05653.1 219 SFISKISNNMNLKEKTKRDAFDILKRCELKEITAGKHPVAQAAASLYIACMINNEK 274
                 799***********************************************997765 PP

>> Herpes_UL51  Herpesvirus UL51 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1      0.28   8.5e+02      55      66 ..     153     164 ..      91     186 .. 0.44
   2 ?   10.6   0.0   0.00011      0.34      61      95 ..     258     292 ..     252     302 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.28
  Herpes_UL51  55 trrlvraqalar 66 
                    +l r++++a 
   EPA05653.1 153 NSKLTRGRTMAS 164
                  235556665543 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00011
  Herpes_UL51  61 aqalartyaaclrnleclkrhhpgeenPgldavve 95 
                  aqa a  y ac+ n e++++ +++ e+   d  ++
   EPA05653.1 258 AQAAASLYIACMINNEKISQKKFSSEAGVSDVTIR 292
                  899*********************99977776665 PP

>> DUF2543  Protein of unknown function (DUF2543)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.39   1.2e+03      39      54 ..     220     235 ..     175     240 .. 0.56
   2 ?   10.4   0.0   0.00019      0.57      37      69 ..     263     292 ..     248     300 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.39
     DUF2543  39 litrltnneeiseeaq 54 
                 +i++++nn +++e+++
  EPA05653.1 220 FISKISNNMNLKEKTK 235
                 4566666666666665 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00019
     DUF2543  37 qllitrltnneeiseeaqkemareagideqrid 69 
                  l i+++ nne is   qk+ ++eag+ +  i 
  EPA05653.1 263 SLYIACMINNEKIS---QKKFSSEAGVSDVTIR 292
                 588**********8...99********998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       746  (0.0416086); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1857.60
//
Query:       EPA05654.1  [L=117]
Description: nitrogen regulatory protein P-II [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-12   47.3   0.5    3.2e-12   47.0   0.5    1.1  1  P-II      Nitrogen regulatory protein P-II


Domain annotation for each model (and alignments):
>> P-II  Nitrogen regulatory protein P-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.0   0.5   1.8e-16   3.2e-12       1     102 []      12     110 ..      12     110 .. 0.84

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 1.8e-16
                 EEEEEEGGGHHHHHHHHHHTTGGCEEEEEEEEEESTCCEEEECTTE...EEEEEEEEEEEEEEEEEGGGHHHHHHHHHHHH-SSSTTSEEEEEEEESEE CS
        P-II   1 ieaiirpekleevkeaLekagvkgltvtevkGrGkqkghtelyrga...eyevellpkvkleivvsdedvekvveaiikaaktgeiGDGkiFvlpveev 96 
                 iea++  +++ ++ eaL+k+++ gltv +v+GrGk    +e++  +     + ++ +k ++ +++++++ e+v+++i ++   g++  GkiFv+p+ ++
  EPA05654.1  12 IEAMLGNNDVMAISEALRKIEIGGLTVGKVRGRGKRP-PAEIHAAKgsaIFQPQFSEKYVIVVIIPESKEEEVINIIKTK---GTV--GKIFVSPILRA 104
                 789999999*************************987.4444443333367778********************988764...443..68********* PP

                 EETTTT CS
        P-II  97 irirtg 102
                 i i tg
  EPA05654.1 105 IDIGTG 110
                 ***997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 797.36
//
Query:       EPA05655.1  [L=64]
Description: hypothetical protein BG20_I0324 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.1e-08   33.0   0.1    7.7e-08   32.4   0.1    1.3  1  DUF1059    Protein of unknown function (DUF1059)
  ------ inclusion threshold ------
      0.017   15.0   0.1      0.021   14.8   0.1    1.1  1  AAA_lid_9  AAA lid domain


Domain annotation for each model (and alignments):
>> DUF1059  Protein of unknown function (DUF1059)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.1   8.6e-12   7.7e-08       4      49 ..       5      50 ..       3      56 .. 0.90

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 8.6e-12
     DUF1059  4 fkCgDvgpdCgfeitaeteeEvlrkvaeHakaaHglteippelvek 49
                ++C D g++C+f  ++ ++  +l+k++eH  ++Hg+   ++++ + 
  EPA05655.1  5 LRCEDYGFECDFVLEGAKNIGLLEKLREHFAEEHGIDYTTEAITQM 50
                79*********************************88888777655 PP

>> AAA_lid_9  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   2.3e-06     0.021       6      33 ..      24      51 ..      19      54 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.3e-06
   AAA_lid_9  6 ieiLrglkekyekhHgvkisdealeaav 33
                i +L++l+e++ + Hg+ ++ ea+++++
  EPA05655.1 24 IGLLEKLREHFAEEHGIDYTTEAITQMI 51
                778*********************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.32s 00:00:00.76 Elapsed: 00:00:00.49
# Mc/sec: 395.36
//
Query:       EPA05656.1  [L=247]
Description: oxidoreductase, short chain dehydrogenase/reductase family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-72  244.4   0.0    1.3e-72  244.1   0.0    1.0  1  adh_short_C2   Enoyl-(Acyl carrier protein) reductase
    4.3e-61  205.8   0.5      5e-61  205.6   0.5    1.0  1  adh_short      short chain dehydrogenase
      7e-08   32.6   0.0    1.1e-07   32.0   0.0    1.2  1  KR             KR domain
  ------ inclusion threshold ------
      0.014   14.8   0.4      0.019   14.4   0.0    1.5  2  Epimerase      NAD dependent epimerase/dehydratase family
      0.028   14.1   0.0      0.056   13.1   0.0    1.4  1  ATP-synt_ab    ATP synthase alpha/beta family, nucleotide-bin
      0.028   14.3   0.2      0.045   13.6   0.2    1.3  1  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
      0.059   12.7   0.1        0.1   11.9   0.1    1.4  1  THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase,


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  244.1   0.0   5.2e-76   1.3e-72       3     232 ..      14     243 ..      10     245 .. 0.97

  Alignments for each domain:
  == domain 1  score: 244.1 bits;  conditional E-value: 5.2e-76
                   TTSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEE.EE--TTSHHHHHHHHHHHHHHHSSEEEEEE-----EGCSS-GGGH-HHHHHHH CS
  adh_short_C2   3 asgIGraiAkalaeeGaevvltdlneeakkrveelaeelgaev.lecDVtdeeqvealveevvekfgklDilvnnagiapklkgpfletsreefdra 98 
                    +gIG+a+Ak +ae+Ga+vv+t  + ++   +e++++e++++v + +D+++e++v+++ve++v+kfgklDil+nnagi pk  ++++e+++ e++++
    EPA05656.1  14 SRGIGFATAKIFAENGANVVITAKDSKR---LENAVNEIPNSVgITADIRNENDVKKVVEQTVKKFGKLDILINNAGIFPK-IKQLHEIEEFEWNEV 106
                   59********************988887...8999999999999*************************************.*************** PP

                   HHHHTHHHHHHHHHHHHHCTSC.CEEEEEEEGGGTSBSTTTT..HHHHHHHHHHHHHHHHHHHHGGGTEEEEEEEE--BHCTGGGGSTTHHHHHHHH CS
  adh_short_C2  99 ldvnlyslfllakaalplmkeg.gsivnlssvgaervvpnyn..aygaaKaalealtrylAvelgpkgiRvNavspgpikTlaasgikgfdelleel 192
                   ldvnl++ f+++k a+p++k++ gsivn+ss ++ ++ ++ n  ay+a+Ka+++ lt+++A e+++++iRvN+++pg+++T++++ + ++++ ++ +
    EPA05656.1 107 LDVNLTGQFRFTKVAIPYLKKTsGSIVNISSDAGLKAYQGFNadAYSASKAGMIILTKCWALEYAKDKIRVNCICPGVVDTDMTKPFLKTEKDRDFM 203
                   *****************888888**************9999999***************************************************** PP

                   HHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEEEESTT CS
  adh_short_C2 193 earaplgrlgtpeevaeaalfLasdeasyitGqtlvvDgG 232
                   ++++plgr+g+p+eva+a+l+++sd+a+++tG++l vDgG
    EPA05656.1 204 NNEHPLGRIGQPDEVAKAILYFVSDDAAWTTGAILTVDGG 243
                   ***************************************9 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.6   0.5     2e-64     5e-61       1     193 [.       6     196 ..       6     198 .. 0.95

  Alignments for each domain:
  == domain 1  score: 205.6 bits;  conditional E-value: 2e-64
                 SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEEE---S.S--SSGGGCSH CS
   adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldvLvnNAGi.tgsgpfselse 98 
                 kv++vtG+s+GIG a+ak +a++Ga+vv++++ +++le++++e+ +     + i++D++++++v+++ve+ vkk+gkld+L+nNAGi  + ++ +e++e
  EPA05656.1   6 KVAIVTGGSRGIGFATAKIFAENGANVVITAKDSKRLENAVNEIPN----SVGITADIRNENDVKKVVEQTVKKFGKLDILINNAGIfPKIKQLHEIEE 100
                 89*******************************************9....69***********************************9999******** PP

                 HHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBH..HHHHHHHHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHHCTH CS
   adh_short  99 eewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagva..aYsAsKaavagltrslakelaptgirvnavaPGlvdTdmakelrek 193
                  ew++v++vNltg f  t+ ++p+ lk+ sG+Ivn+sS ag++++ g+   aYsAsKa+++ lt+++a e+a+++irvn+++PG+vdTdm+k+  ++
  EPA05656.1 101 FEWNEVLDVNLTGQFRFTKVAIPY-LKKTSGSIVNISSDAGLKAYQGFNadAYSASKAGMIILTKCWALEYAKDKIRVNCICPGVVDTDMTKPFLKT 196
                 ************************.669*************99988765237***************************************987665 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.0   4.2e-11   1.1e-07       4     140 ..       9     141 ..       7     159 .. 0.78

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 4.2e-11
                 EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS---EEEE------.---TTT-- CS
          KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppikGvihaAgvlr.dklleemt 101
                 ++tGG  g+G ++a+  ae+ga+ +v+++++      sk+l +++++   +v  + aD+ ++++v++++e+  ++++++   i+ Ag++   k+l e +
  EPA05656.1   9 IVTGGSRGIGFATAKIFAENGAN-VVITAKD------SKRLENAVNEIPNSVG-ITADIRNENDVKKVVEQTVKKFGKLDILINNAGIFPkIKQLHEIE 99 
                 8********************96.5666666......2223333444444554.567******************************9962699***** PP

                 HHHHHHHHTTTTHHHHHHHHHTTT...S--SEEEEEEEHHHH CS
          KR 102 aedleqvlapKvkGawnLhelled...esldffvlfSSiagl 140
                 + ++++vl   ++G     ++  +   ++   +v +SS agl
  EPA05656.1 100 EFEWNEVLDVNLTGQFRFTKVAIPylkKTSGSIVNISSDAGL 141
                 **************9988887665455666667777776665 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   7.3e-06     0.019       2      62 ..       9      71 ..       8     140 .. 0.78
   2 ?   -3.5   0.1       2.3   5.8e+03     141     161 ..     151     171 ..     148     179 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7.3e-06
                EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC...EEEE--TT-HHHHHHHHHH CS
   Epimerase  2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl...elveldltdrsalerlfke 62
                +VtG++  iG a++k ++e+g +v+  +++s++ ++a +e +     +++d+++++++++++++
  EPA05656.1  9 IVTGGSRGIGFATAKIFAENGANVVITAKDSKRLENAVNE-IpnsVGITADIRNENDVKKVVEQ 71
                8********************9977776664433333322.2467999********99988875 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.3
                 HHHHHHHHHHHHHHHHHHHHT CS
   Epimerase 141 pYaaaKlageklveayaaqyg 161
                 +Y+a+K+ +  l++ +a +y 
  EPA05656.1 151 AYSASKAGMIILTKCWALEYA 171
                 799999999888888888884 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.2e-05     0.056      92     128 ..      17      53 ..       6      61 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.2e-05
                  HHHHHHHHHHHTTSEEEEEEETHHHHHHHHHHHHHHT CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  ATP-synt_ab  92 tgitlAEyfrdqgknvlliadslsrwaeAlreislrl 128
                  +g ++A  f+++g nv++ a ++ r  +A++ei  ++
   EPA05656.1  17 IGFATAKIFAENGANVVITAKDSKRLENAVNEIPNSV 53 
                  6999*****************************8766 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   1.7e-05     0.045       1      48 [.       6      55 ..       6      84 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.7e-05
                EEEEE--SC..CHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHC CS
     3HCDH_N  1 kvaviGaGt..mGagiaavfasagleVvlvdiseealekalekiekslek 48
                kva++  G   +G   a++fa++g +Vv++  ++++le+a ++i +s+  
  EPA05656.1  6 KVAIVTGGSrgIGFATAKIFAENGANVVITAKDSKRLENAVNEIPNSVGI 55
                6888888872255556789************************9985543 PP

>> THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1     4e-05       0.1      33      78 ..       2      47 ..       1      62 [. 0.94

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4e-05
                   --TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTSCCHHHHHC CS
  THF_DHG_CYH_C 33 elegkkvvvvGrsnivgkplallLleknatVtvchsktkdlaeitr 78
                   +l+gk ++v G s+ +g + a +++e++a V ++ + +k l++ ++
     EPA05656.1  2 KLSGKVAIVTGGSRGIGFATAKIFAENGANVVITAKDSKRLENAVN 47
                   789*************************************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       701  (0.0390987); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1738.63
//
Query:       EPA05657.1  [L=208]
Description: oxidoreductase, short chain dehydrogenase/reductase family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.2e-57  191.8   0.3    9.3e-57  191.6   0.3    1.0  1  adh_short        short chain dehydrogenase
    2.8e-39  135.1   0.0    3.3e-39  134.8   0.0    1.0  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    4.5e-16   59.3   0.2    5.3e-16   59.0   0.2    1.1  1  KR               KR domain
    0.00051   19.5   0.0     0.0014   18.0   0.0    1.7  1  DUF1776          Fungal family of unknown function (DUF1776)
     0.0014   17.8   0.1     0.0016   17.6   0.1    1.2  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
     0.0022   17.5   0.0     0.0029   17.1   0.0    1.2  1  Epimerase        NAD dependent epimerase/dehydratase family
  ------ inclusion threshold ------
       0.02   14.8   0.0      0.025   14.5   0.0    1.4  1  NAD_binding_10   NAD(P)H-binding
      0.027   14.3   0.0      0.068   13.0   0.0    1.6  1  DFP              DNA / pantothenate metabolism flavoprotein
       0.15   12.2   0.0       0.25   11.5   0.0    1.3  1  F420H2_quin_red  F420H(2)-dependent quinone reductase


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.6   0.3   4.7e-60   9.3e-57       1     188 [.       6     193 ..       6     200 .. 0.98

  Alignments for each domain:
  == domain 1  score: 191.6 bits;  conditional E-value: 4.7e-60
                 SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEEE---SS--SSGGGCSHH CS
   adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldvLvnNAGitgsgpfselsee 99 
                 kvvl+tGassGIGr++a ++ak+G ++++v+r++ekle++ + lk  + + l++++Dv+d+ +ve++ + + +k+g++d+L+nNAG +  g++s+l+ +
  EPA05657.1   6 KVVLITGASSGIGRETAVQFAKKGSNLILVARRKEKLEQLDNALKTYQISTLVCECDVSDKLQVENMSKLVLEKFGHVDILINNAGFAIYGSVSDLTID 104
                 89************************************************************************************************* PP

                 HHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHH CS
   adh_short 100 ewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaavagltrslakelaptgirvnavaPGlvdTdmak 188
                 e+e+ +++N++g++ +++ +lp m++++sG+Ivnv+Sva+  +++g a+Y+AsK+a+ g+++ l++el+ +g+ +++v P +v+T++  
  EPA05657.1 105 EIESQMATNYFGMIYCIKNFLPSMIQKKSGHIVNVASVAASIGLPGIASYCASKFAMLGFSEGLKHELKGSGVGITVVSPIMVRTNFFD 193
                 *************************************************************************************9865 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.8   0.0   1.7e-42   3.3e-39       1     181 [.      12     194 ..      12     204 .. 0.94

  Alignments for each domain:
  == domain 1  score: 134.8 bits;  conditional E-value: 1.7e-42
                   TTTTSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTT.SE.EEE--TTSHHHHHHHHHHHHHHHSSEEEEEE-----EGCSS-GGGH-HHHH CS
  adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneeakkrveelaeelg.ae.vlecDVtdeeqvealveevvekfgklDilvnnagiapklkgpfletsreef 95 
                   Ga sgIGr++A ++a++G +++l+ +++e+ ++++++ + ++ ++ v+ecDV+d+ qve++ + v ekfg++Dil+nnag+a    g++ +++ +e+
    EPA05657.1  12 GASSGIGRETAVQFAKKGSNLILVARRKEKLEQLDNALKTYQiSTlVCECDVSDKLQVENMSKLVLEKFGHVDILINNAGFAIY--GSVSDLTIDEI 106
                   899***************************89999999988855557*************************************..*********** PP

                   HHHHHHHTHHHHHHHHHHHH.HCTSC.CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHHHHHHGGGTEEEEEEEE--BHCTGGGG CS
  adh_short_C2  96 draldvnlyslfllakaalp.lmkeg.gsivnlssvgaervvpnynaygaaKaalealtrylAvelgpkgiRvNavspgpikTlaasg 181
                   +  +++n  ++++++k +lp +++++ g ivn++sv+a++++p+ + y+a+K a+ +++  l +el   g+ + +vsp +++T+  ++
    EPA05657.1 107 ESQMATNYFGMIYCIKNFLPsMIQKKsGHIVNVASVAASIGLPGIASYCASKFAMLGFSEGLKHELKGSGVGITVVSPIMVRTNFFDN 194
                   ********************8666667********************************************************97655 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.0   0.2   2.7e-19   5.3e-16       2     154 ..       7     159 ..       6     182 .. 0.88

  Alignments for each domain:
  == domain 1  score: 59.0 bits;  conditional E-value: 2.7e-19
                 EEEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS---EEEE---------TTT- CS
          KR   2 tylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppikGvihaAgvlrdklleem 100
                 ++litG+  g+G+e+a + a+kg  +l+l++R+   +e+ ++l ++l+ ++++  v+++Dvsdk +ve++ + + ++++ +   i+ Ag++  + ++++
  EPA05657.1   7 VVLITGASSGIGRETAVQFAKKGS-NLILVARR---KEKLEQLDNALKTYQISTLVCECDVSDKLQVENMSKLVLEKFGHVDILINNAGFAIYGSVSDL 101
                 579*******************95.79999999...4555668899***************************************************** PP

                 -HHHHHHHHTTTTHHHHHHHHHTTT....S--SEEEEEEEHHHHH--TT-HHHHHHHH CS
          KR 101 taedleqvlapKvkGawnLhelled....esldffvlfSSiagllgsagqanYaaaNa 154
                 t +++e+ +a    G+    + + +    ++  ++v ++S+a+ +g +g a+Y a   
  EPA05657.1 102 TIDEIESQMATNYFGMIYCIKNFLPsmiqKKSGHIVNVASVAASIGLPGIASYCASKF 159
                 ************99987644443333666999*********************99755 PP

>> DUF1776  Fungal family of unknown function (DUF1776)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   7.3e-07    0.0014      96     191 ..      85     178 ..       4     201 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 7.3e-07
     DUF1776  96 ilvPslsy.ptgpietiplsswaselnerllspiltlqallplltsrakqkakiivvnpsissslnlpfhapEalvssalsalfevLkrelrphnid 191
                 il+ +  +  +g +  +++++++s++ ++ + +i  ++++lp + +   +k+  iv  +s+ +s+ lp  a       a+  + e Lk+el+  ++ 
  EPA05657.1  85 ILINNAGFaIYGSVSDLTIDEIESQMATNYFGMIYCIKNFLPSMIQ---KKSGHIVNVASVAASIGLPGIASYCASKFAMLGFSEGLKHELKGSGVG 178
                 78888889899**********************************9...9999999***********************************955444 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   8.1e-07    0.0016       1      74 [.       8      74 ..       8     140 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 8.1e-07
                     EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT CS
  Polysacc_synt_2  1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekale 74
                     vl+tGa+  iG+e   q++kk  + i++  r   kl ++++ l ++++ ++l +e     +dv dk ++e++ +
       EPA05657.1  8 VLITGASSGIGRETAVQFAKKGSNLILVARR-KEKLEQLDNAL-KTYQISTLVCE-----CDVSDKLQVENMSK 74
                     89****************9988766655555.55899999998.34555555444.....89999988887644 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.5e-06    0.0029       1      59 [.       8      72 ..       8     114 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.5e-06
                EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC........EEEE--TT-HHHHHHH CS
   Epimerase  1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl........elveldltdrsalerl 59
                +l+tGa+  iG+ ++ ++++kg ++i ++r+++  + ++l+++         ++e+d+ d+ ++e++
  EPA05657.1  8 VLITGASSGIGRETAVQFAKKGSNLILVARRKE--KLEQLDNAlktyqistLVCECDVSDKLQVENM 72
                79***************************9944..4444444457999*99899*****99877654 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.2e-05     0.025       1      56 [.      12      71 ..      12     196 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.2e-05
                    TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCE.....EEE--TT-CCHHHH CS
  NAD_binding_10  1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeegle.....vvegdvtdvedlae 56
                    GA+ ++Gr+ + + +++g  ++ +++R++ekl++l ++ ++      v+e dv+d+ ++++
      EPA05657.1 12 GASSGIGRETAVQFAKKG-SNLILVARRKEKLEQLDNALKTYqistlVCECDVSDKLQVEN 71
                    9****************5.9*************9963321111222356677777655555 PP

>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.4e-05     0.068      18      94 ..       5      94 ..       2     113 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.4e-05
                CTTEEEEE----HHHHHHHHHHHHTT-EEEEEE-S-.SS--.............-TT-EEEE--SHHHHHHHHHHHHTT-SEEEE---S-- CS
         DFP 18 DpVRfisNrSSGkmGyalAeaaaarGaeVtlvsgpv.slet.............pegvevvkvesaeemleaveealkeadivimaAAvaD 94
                D+V +i+  SSG  G + A ++a++G +  lv+    +le+               +++v +  ++e+m + v e++ + di+i  A  a 
  EPA05657.1  5 DKVVLITGASSG-IGRETAVQFAKKGSNLILVARRKeKLEQldnalktyqistlVCECDVSDKLQVENMSKLVLEKFGHVDILINNAGFAI 94
                9999********.6******************99853776544444433332211223444445678999999999999999999997664 PP

>> F420H2_quin_red  F420H(2)-dependent quinone reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00013      0.25      30      57 ..      10      37 ..       2      44 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                     EE-TTT-SEEEEEEEEEEETTEEEEE-S CS
  F420H2_quin_red 30 ttGrktgkprktplgfvrdgdsylvvas 57
                      tG+ +g  r+t++ f+++g ++++va 
       EPA05657.1 10 ITGASSGIGRETAVQFAKKGSNLILVAR 37
                     68************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       757  (0.0422221); expected 358.6 (0.02)
Passed bias filter:                      580  (0.0323498); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 1565.91
//
Query:       EPA05658.1  [L=156]
Description: hypothetical protein BG20_I0294 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.6e-05   23.4  10.9    3.6e-05   23.4  10.9    1.4  2  HMMR_N         Hyaluronan mediated motility receptor N-termin
     0.0002   21.5  16.2    0.00082   19.6  14.7    2.0  2  Tropomyosin_1  Tropomyosin like
    0.00047   19.1  10.5    0.00061   18.8  10.5    1.1  1  Spc7           Spc7 kinetochore protein
    0.00082   19.4   6.5    0.00088   19.3   5.0    1.5  1  DUF1664        Protein of unknown function (DUF1664)
      0.002   18.3   3.1     0.0024   18.0   3.1    1.3  1  CREPT          Cell-cycle alteration and expression-elevated 
     0.0038   16.6   2.7     0.0059   15.9   2.7    1.3  1  DUF3450        Protein of unknown function (DUF3450)
     0.0045   17.0   7.0     0.0065   16.5   7.0    1.3  1  Laminin_II     Laminin Domain II
     0.0056   15.9   8.6     0.0056   15.9   8.6    1.5  2  Taxilin        Myosin-like coiled-coil protein
  ------ inclusion threshold ------
      0.023   13.4   5.2      0.023   13.4   5.2    1.1  1  AAA_13         AAA domain
      0.029   14.4   0.2      0.042   13.9   0.2    1.2  1  Baculo_PEP_C   Baculovirus polyhedron envelope protein, PEP, 
      0.039   13.8   7.8       0.06   13.2   7.3    1.5  1  DUF724         Protein of unknown function (DUF724)
      0.059   13.7   5.6       0.46   10.8   5.6    2.0  2  THOC7          Tho complex subunit 7
      0.059   12.2   5.0      0.072   11.9   4.5    1.3  1  Fmp27_WPPW     RNA pol II promoter Fmp27 protein domain
      0.066   12.1   1.4      0.086   11.7   1.4    1.1  1  FemAB          FemAB family
      0.069   13.2   5.4      0.048   13.8   3.1    1.8  2  GldM_N         GldM N-terminal domain
      0.073   13.0   7.6       0.15   12.0   1.8    2.5  3  Prefoldin      Prefoldin subunit
      0.075   11.5   2.7      0.083   11.4   2.7    1.0  1  Baculo_F       Baculovirus F protein
      0.099   13.1  10.7       0.29   11.6   4.7    2.4  2  DUF16          Protein of unknown function DUF16
       0.12   12.7   3.5       0.19   12.0   3.5    1.5  1  Rx_N           Rx N-terminal domain
       0.14   12.7   6.8       0.76   10.3   1.6    2.3  2  NPV_P10        Nucleopolyhedrovirus P10 protein
       0.15   10.0   3.0       0.17    9.8   3.0    1.0  1  Prominin       Prominin
       0.22   11.7   7.1        0.6   10.3   6.9    1.8  2  Fib_alpha      Fibrinogen alpha/beta chain family
       0.42    9.8   3.3       0.54    9.4   3.3    1.2  1  TMPIT          TMPIT-like protein
       0.44   11.2   6.6        1.5    9.5   6.4    1.9  2  YabA           Initiation control protein YabA
       0.44   11.1   6.7        1.9    9.0   5.2    2.3  2  Spectrin       Spectrin repeat
       0.48   10.8   7.4         26    5.3   7.4    2.5  1  Syntaxin_2     Syntaxin-like protein
       0.49    9.4   7.1       0.59    9.2   7.1    1.2  1  Atg14          Vacuolar sorting 38 and autophagy-related subu
       0.49   10.2  12.3        3.8    7.3  12.3    2.0  1  Mei5           Double-strand recombination repair protein
       0.84    9.9   2.5        7.2    6.9   2.5    2.1  1  DUF948         Bacterial protein of unknown function (DUF948)
       0.94    9.6   9.6        1.3    9.0   9.6    1.4  1  UPF0242        Uncharacterised protein family (UPF0242) N-ter
       0.94    9.9  12.2        1.5    9.2   4.0    2.9  3  FlaC_arch      Flagella accessory protein C (FlaC)
        1.3    8.3   7.6        1.5    8.1   7.6    1.1  1  FAM76          FAM76 protein
        3.5    7.9   8.2        5.5    7.2   8.2    1.3  1  zf-C4H2        Zinc finger-containing protein
        5.2    7.1   8.4        5.6    7.0   0.2    3.4  3  Nas2_N         Nas2 N_terminal domain
        9.4    6.5  12.8        4.7    7.5   4.7    2.6  3  XhlA           Haemolysin XhlA


Domain annotation for each model (and alignments):
>> HMMR_N  Hyaluronan mediated motility receptor N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.2       7.6   3.9e+03      29      55 ..       4      30 ..       3      36 .. 0.47
   2 !   23.4  10.9     7e-08   3.6e-05     204     297 ..      61     154 ..      42     156 .] 0.93

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 7.6
      HMMR_N 29 Rfkkqk..esqqnlssskdasttaaarkv 55
                +fkk++  e    +++s d   t  +r v
  EPA05658.1  4 KFKKEEggE--MTQERSPDEQNTMKSRDV 30
                677777433..333333333333444544 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 7e-08
      HMMR_N 204 kvaqLkeklvslekekieekseteklleyieelsnvseqlekykldiaqleellkekndeiesLkssLeekeqelskqvkdlnekckllekeke 297
                  + +Lk+k + lek+ +ee  ++++l e  e++s+ +e+ ++   ++aq ++ +++++de+ sL ++L++k   +++ +++  +k+k++ +++e
  EPA05658.1  61 MIKNLKDKRTVLEKDIEEESVDIKNLKEKLEKVSQYIEEENRGIRELAQKRQQVENEADEVGSLINNLRDKLSGIDRIIDNEGSKVKQIKESRE 154
                 589*************************************9*************************************************9998 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.2     0.088        45      10      64 ..      12      68 ..       4      70 .. 0.74
   2 !   19.6  14.7   1.6e-06   0.00082      37     125 ..      62     154 ..      50     156 .] 0.92

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.088
  Tropomyosin_1 10 eeaqekaeeleekvKeleq..enlekeqeiksLtkknqqleeevekleeklkeakek 64
                   e  qe+  + ++ +K+ +   +++  e  i +L  k  +lee v+ +   +k+ k+k
     EPA05658.1 12 EMTQERSPDEQNTMKSRDVspNETVGEIGIVELMGKRAKLEEAVDYVGLMIKNLKDK 68
                   5567777666777766655115556688899**************998888888776 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 1.6e-06
  Tropomyosin_1  37 iksLtkknqqleeevekleeklkeakekaeesekkktnne....altrkiqlLEeeleesdkkLkettekLretdvkaeelERkvkaLeqerd 125
                    ik+L+ k  +le+++e+ + ++k+ kek+e+ ++   + +    +l +k q++E+e++e  + +++  +kL+ +d   ++   kvk++ ++r+
     EPA05658.1  62 IKNLKDKRTVLEKDIEEESVDIKNLKEKLEKVSQYIEEENrgirELAQKRQQVENEADEVGSLINNLRDKLSGIDRIIDNEGSKVKQIKESRE 154
                    99****************************999887776678999******************************************999887 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8  10.5   1.2e-06   0.00061     158     273 ..      44     154 ..      42     156 .] 0.90

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.2e-06
        Spc7 158 LekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaerv 256
                 L+ ++++l+e+++ +    ++l+++ + l++  ee    ++ ++++l+e+l+++++ iee ++ + el ++++++e++ +e+ + +++l+++++  +r+
  EPA05658.1  44 LMGKRAKLEEAVDYVGLMIKNLKDKRTVLEKDIEE----ESVDIKNLKEKLEKVSQYIEEENRGIRELAQKRQQVENEADEVGSLINNLRDKLSGIDRI 138
                 77788899999999999999999999999998887....67789******************************************************* PP

        Spc7 257 leeckgwsesevsrlke 273
                 ++ ++g++ +++++ +e
  EPA05658.1 139 ID-NEGSKVKQIKESRE 154
                 99.77888888887766 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   5.0   1.7e-06   0.00088      36     121 ..      48     136 ..      41     139 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.7e-06
     DUF1664  36 krslsdavesvskqleqvses...laatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                 +  l++av+ v+  +++++++   l++  ++ s +i+++ +kl+++++ ++e ++ + e+ ++ ++++++ ++v +++++l  kl+ i+
  EPA05658.1  48 RAKLEEAVDYVGLMIKNLKDKrtvLEKDIEEESVDIKNLKEKLEKVSQYIEEENRGIRELAQKRQQVENEADEVGSLINNLRDKLSGID 136
                 66799999999977777775511166666666778*************************************************99885 PP

>> CREPT  Cell-cycle alteration and expression-elevated protein in tumour
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   3.1   4.7e-06    0.0024      31     125 ..      36     130 ..      16     152 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4.7e-06
       CREPT  31 vsdvsllekikdkeeaekllkqveealellaeYnkrLeaeleeRkklakmledfleaqkellakaeekleelkeklekvksvrkelkshiqsLPd 125
                 v ++ ++e +  +++ e+ ++ v   ++ l++  + Le+++ee +   k+l++ le + + ++++++ ++el +k ++v+++ +e+ s i++L d
  EPA05658.1  36 VGEIGIVELMGKRAKLEEAVDYVGLMIKNLKDKRTVLEKDIEEESVDIKNLKEKLEKVSQYIEEENRGIRELAQKRQQVENEADEVGSLINNLRD 130
                 667778888889999999999999999******************************************************************77 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   2.7   1.1e-05    0.0059      39     110 ..      62     133 ..      46     137 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.1e-05
     DUF3450  39 idklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierelvpllekmidrLe 110
                 i++l+d+++ l++++++ +  +++l+ + e++++++++ ++ i +l ++ +++e+ ++e+  l+ ++ d+L 
  EPA05658.1  62 IKNLKDKRTVLEKDIEEESVDIKNLKEKLEKVSQYIEEENRGIRELAQKRQQVENEADEVGSLINNLRDKLS 133
                 7899********************************************************999999888875 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   7.0   1.3e-05    0.0065       6      97 ..      63     151 ..      48     154 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.3e-05
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH...HHHHHHHHHH CS
  Laminin_II   6 aeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeassslsdniseike 97 
                 ++ +++ +  ++++++ s++++n+kekl+++ + +ee n  ++++ +  ++++++  ++  l+++L dkl+ ++   ++++    ++++ike
  EPA05658.1  63 KNLKDKRTVLEKDIEEESVDIKNLKEKLEKVSQYIEEENRGIRELAQKRQQVENEADEVGSLINNLRDKLSGIDRIIDNEG---SKVKQIKE 151
                 555556666677888888888999999999999989999999988888889999999999999999999999988888844...67777776 PP

>> Taxilin  Myosin-like coiled-coil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.4      0.95   4.9e+02     239     291 ..       2      58 ..       1      72 [. 0.52
   2 !   15.9   8.6   1.1e-05    0.0056      23     134 ..      44     154 ..      38     156 .] 0.79

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.95
     Taxilin 239 FatFkkE.mekmtkktkklEketnlwkskfektnka.....llemaeertekkkeiekl 291
                 F++FkkE   +mt++     +e+n++ks+  + n++     ++e++ +r + ++ ++  
  EPA05658.1   2 FDKFKKEeGGEMTQER--SPDEQNTMKSRDVSPNETvgeigIVELMGKRAKLEEAVDYV 58 
                 8888776135666554..44455555555444443311112556666666666666555 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.1e-05
     Taxilin  23 LvkkyaelleerkrlqkqlkklkkkleqlqkekeqlqaelskaalaksKLekLcRelqkqnkklkeeskqrareeeekrk..elaekfqakLkdiqaqi 119
                 L+ k a+l e +  +  ++k lk k   l k+    ++e  + +++k+KLek ++ + ++n+ ++e  ++r++ e+e+ +  +l + +++kL+ i+  i
  EPA05658.1  44 LMGKRAKLEEAVDYVGLMIKNLKDKRTVLEKDI---EEESVDIKNLKEKLEKVSQYIEEENRGIRELAQKRQQVENEADEvgSLINNLRDKLSGIDRII 139
                 666667777777777777777777777776665...5899999**********************988777766655553229**************** PP

     Taxilin 120 eekserneklreena 134
                 +++ ++ ++ +e  +
  EPA05658.1 140 DNEGSKVKQIKESRE 154
                 *99999998887655 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   5.2   4.5e-05     0.023     372     462 ..      49     141 ..      17     156 .] 0.53

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.5e-05
      AAA_13 372 aeineliakhNekvanleeekeeakkklelhlv..eeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaee 462
                 a+++e +     +++nl+++++ ++k++e   v  ++l+++l++  + +++ ++ i +l ++ ++ e+e+ ++   i++L+ +l+ + +++++
  EPA05658.1  49 AKLEEAVDYVGLMIKNLKDKRTVLEKDIEEESVdiKNLKEKLEKVSQYIEEENRGIRELAQKRQQVENEADEVGSLINNLRDKLSGIDRIIDN 141
                 445555555555555666666666666555443224444444444444444444444444444444444444444444444444444444443 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   8.3e-05     0.042      35     110 ..      64     141 ..      46     153 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.3e-05
  Baculo_PEP_C  35 qlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq...dtlrneLtnlnsiltnLlssvtNinstLnn 110
                   +l+   + +e+ +++ s d+k+l ++l+ ++++ +++ ++ + +l+   ++++ne + + s ++nL  ++ +i   + n
    EPA05658.1  64 NLKDKRTVLEKDIEEESVDIKNLKEKLE-KVSQYIEEENRGIRELAqkrQQVENEADEVGSLINNLRDKLSGIDRIIDN 141
                   4444444455555555555555333332.44445555555555555777888888888888888888888888777666 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   7.3   0.00012      0.06      99     185 ..      64     150 ..      60     153 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00012
      DUF724  99 slkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaekleeeledveqeFeava 185
                 +lkd++t l++ +++   +i++ +++ +k+++ i+e ++ i+el ++++++ ++ ++  + i +l+ + + +++ +++  +++++++
  EPA05658.1  64 NLKDKRTVLEKDIEEESVDIKNLKEKLEKVSQYIEEENRGIRELAQKRQQVENEADEVGSLINNLRDKLSGIDRIIDNEGSKVKQIK 150
                 589999999999999999999999999999999999999999999999999999999999999999999999999999888888775 PP

>> THOC7  Tho complex subunit 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.9     0.023        12      69     102 ..      61      94 ..      43      98 .. 0.87
   2 ?   10.8   5.6   0.00089      0.46      39     101 ..      73     135 ..      61     142 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.023
       THOC7  69 ereryeaekeeieseieavreeieelkaqLeear 102
                  ++++++++  +e+ ie+   +i++lk++Le+  
  EPA05658.1  61 MIKNLKDKRTVLEKDIEEESVDIKNLKEKLEKVS 94 
                 688999************************9875 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00089
       THOC7  39 eqlkedllldfaafelsierlqllakanerereryeaekeeieseieavreeieelkaqLeea 101
                 e++ e+  +d+ +++  +e++    +   r +++++++++++e+e+ +v + i +l+++L+  
  EPA05658.1  73 EKDIEEESVDIKNLKEKLEKVSQYIEEENRGIRELAQKRQQVENEADEVGSLINNLRDKLSGI 135
                 5566677789999999999999999999*******************************9876 PP

>> Fmp27_WPPW  RNA pol II promoter Fmp27 protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   4.5   0.00014     0.072     159     240 ..      69     146 ..      62     155 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00014
  Fmp27_WPPW 159 dCilgkendpervqkelleeRleeleeqiekleekleelelksekedeelkeeieelekeikelkeklefletlledlkese 240
                 + +l+k+ + e+v  + l+e le++++ ie+ ++ ++el +k+++    +++e +e+ + i++l++kl+ +++++++  ++ 
  EPA05658.1  69 RTVLEKDIEEESVDIKNLKEKLEKVSQYIEEENRGIRELAQKRQQ----VENEADEVGSLINNLRDKLSGIDRIIDNEGSKV 146
                 56889999999*****************************99999....99********************99998765554 PP

>> FemAB  FemAB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.4   0.00017     0.086     239     301 ..      64     128 ..      55     141 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00017
       FemAB 239 nlaeylkelqekleklekklakleekleknpe..kkkkkklkelekqlaslekelkeaeefiekd 301
                 nl+++++ l++++e+ + ++++l+eklek  +  +++++ ++el ++ +++e+e +e+ ++i++ 
  EPA05658.1  64 NLKDKRTVLEKDIEEESVDIKNLKEKLEKVSQyiEEENRGIRELAQKRQQVENEADEVGSLINNL 128
                 89999999*********************9999999999999*****999999999998888765 PP

>> GldM_N  GldM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.3      0.85   4.4e+02     111     143 ..      49      81 ..       7      90 .. 0.64
   2 ?   13.8   3.1   9.4e-05     0.048      19      86 ..      80     148 ..      70     155 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.85
      GldM_N 111 kkineyreellklvndlakdaklieselstedp 143
                 +k++e  +++  ++++l+++++++e++++ e  
  EPA05658.1  49 AKLEEAVDYVGLMIKNLKDKRTVLEKDIEEESV 81 
                 455555555555666555555555555554443 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 9.4e-05
      GldM_N  19 nasekN.aalyasleakaeenpekakewlekAkevkkksdelynyiealKeeivkeaggkdedvgeika 86 
                 +++ kN ++ +++ ++ +ee++   +e+++k ++v++++de+ + i++l++++       d++  ++k+
  EPA05658.1  80 SVDIKNlKEKLEKVSQYIEEENRGIRELAQKRQQVENEADEVGSLINNLRDKLSGIDRIIDNEGSKVKQ 148
                 55556658899999**************************************96655555555444444 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.8   0.00029      0.15      74     119 ..      50      95 ..      48      96 .. 0.95
   2 ?    7.6   2.5    0.0067       3.5      79     117 ..      83     121 ..      78     124 .. 0.91
   3 ?    3.5   0.2      0.12        63      89     113 ..     107     131 ..     101     152 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00029
                 EHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
   Prefoldin  74 sleeAiellkkkleelekqlekleeeleklkdqittleanlaqlyq 119
                 +leeA++++   +++l++ +++le+++e+ +  i++l ++l++++q
  EPA05658.1  50 KLEEAVDYVGLMIKNLKDKRTVLEKDIEEESVDIKNLKEKLEKVSQ 95 
                 589**************************************99987 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0067
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
   Prefoldin  79 iellkkkleelekqlekleeeleklkdqittleanlaql 117
                 i+ lk+kle++++ +e+ +  +++l+++ +++e++++++
  EPA05658.1  83 IKNLKEKLEKVSQYIEEENRGIRELAQKRQQVENEADEV 121
                 56799*****************************99987 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.12
                 HHHHHHHHHHHHHHHHHHHHHHHHH CS
   Prefoldin  89 lekqlekleeeleklkdqittlean 113
                 l + ++++e+e+++  + i++l+++
  EPA05658.1 107 LAQKRQQVENEADEVGSLINNLRDK 131
                 3333333444433333333333333 PP

>> Baculo_F  Baculovirus F protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   2.7   0.00016     0.083     137     241 ..      31     141 ..       4     151 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00016
    Baculo_F 137 kkrkkRg..gllnfvGrvdky.....lfGvmDdkDAelLhklaksenslneqvkqltdeliklseyveskkqeieeqkedkCeyieaklnllkdqldei 228
                 ++++  g  g+++ +G+  k        G+m ++  +    l k  ++    +k+l+++l k+s+y+e++ ++  ++ ++k++++e++ + + + ++++
  EPA05658.1  31 SPNETVGeiGIVELMGKRAKLeeavdYVGLMIKNLKDKRTVLEKDIEEESVDIKNLKEKLEKVSQYIEEE-NRGIRELAQKRQQVENEADEVGSLINNL 128
                 4444444566666666666666666666777665555555577777788889******************.5555666999999***999999999999 PP

    Baculo_F 229 eslytkldravdd 241
                     + +dr++d+
  EPA05658.1 129 RDKLSGIDRIIDN 141
                 9999999999997 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   1.0     0.038        20      45      79 ..      43      77 ..       1      84 [. 0.66
   2 ?   11.6   4.7   0.00057      0.29      37     100 ..      77     140 ..      72     143 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.038
                ...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH... CS
       DUF16 45 klgeqinkleqkvekqgekikelkveqkaqgeeln 79
                 l  + +kle++v+  g  ik+lk +    +++++
  EPA05658.1 43 ELMGKRAKLEEAVDYVGLMIKNLKDKRTVLEKDIE 77
                56667788999999999999999988888888776 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00057
                 HHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHHHHH CS
       DUF16  37 kkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletLqkinkRlD 100
                 ++    ++ l+e+++k+ q +e+ +  i+el ++ ++ ++e ++v++ ++ + + L  i+  +D
  EPA05658.1  77 EEESVDIKNLKEKLEKVSQYIEEENRGIRELAQKRQQVENEADEVGSLINNLRDKLSGIDRIID 140
                 4445568899*************************999999**********9999999987766 PP

>> Rx_N  Rx N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   3.5   0.00038      0.19      17      74 ..      73     141 ..      48     155 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00038
        Rx_N  17 akllkgvkeeleklkdeLesiqavLedaee........rqi.kd..eavkeWlkelrdlaydaeDvlDe 74 
                  k +++   ++++lk++Le++ +++e+  +        rq+ ++  ++v   +++lrd    ++ ++D+
  EPA05658.1  73 EKDIEEESVDIKNLKEKLEKVSQYIEEENRgirelaqkRQQvENeaDEVGSLINNLRDKLSGIDRIIDN 141
                 455566666788899999999999887777777777664443442377889****************97 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.6    0.0015      0.76      13      54 ..      62     100 ..      58     110 .. 0.81
   2 ?    5.5   0.4     0.046        23      13      62 ..     104     150 ..     101     152 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0015
     NPV_P10  13 ikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLael 54 
                 ik+++dk ++l++   d++e++ d+++l+ekL++ s+ ++e 
  EPA05658.1  62 IKNLKDKRTVLEK---DIEEESVDIKNLKEKLEKVSQYIEEE 100
                 8999999999996...56667777777********9988775 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.046
     NPV_P10  13 ikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIq 62 
                 i+++ +k + ++++ d+v + +++   l +kL ++   +++  +kv++I+
  EPA05658.1 104 IRELAQKRQQVENEADEVGSLINN---LRDKLSGIDRIIDNEGSKVKQIK 150
                 666777777777777777776666...77888888888887777888776 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   3.0   0.00033      0.17     315     416 ..      53     154 ..      38     156 .] 0.71

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00033
    Prominin 315 dqlpnvdevlealeevletnlssivkeglarlneipekvknqtaevvp..dlkkalakgreqikklakkiprealdavisdlenterssktfddvveky 411
                 ++++ v  ++++l++  +t l++ ++e+  ++++++ek+++  + + +    +++la++r+q++++a ++  + ++++ ++l+ + r +++   +v++ 
  EPA05658.1  53 EAVDYVGLMIKNLKDK-RTVLEKDIEEESVDIKNLKEKLEKVSQYIEEenRGIRELAQKRQQVENEADEV-GSLINNLRDKLSGIDRIIDNEGSKVKQI 149
                 4555556666666665.67778888888888888888887655554443357788888888888888888.8888888888888888888888888888 PP

    Prominin 412 ekyrw 416
                  + r+
  EPA05658.1 150 KESRE 154
                 77775 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   1.5     0.017       8.6      72     119 ..      52      98 ..      19     101 .. 0.73
   2 ?   10.3   6.9    0.0012       0.6      26     110 ..      72     152 ..      61     156 .] 0.65

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.017
                 HHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHH CS
   Fib_alpha  72 kkdndnvikksskeleeeilrlketidaqesnirvLqnvlesneqkiq 119
                 ++    ++  + k+l+++ + l++ i ++   i++L++ le+ +q i+
  EPA05658.1  52 EE-AVDYVGLMIKNLKDKRTVLEKDIEEESVDIKNLKEKLEKVSQYIE 98 
                 33.456666777788888888888888888888888888888877765 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0012
                 CCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHH CS
   Fib_alpha  26 llkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnv 110
                 l+k  ++ + d+++l+++le++s+  +e ++    i++  +++q+ +++    + ++ ++l+++ + +++ id++ s+++++++ 
  EPA05658.1  72 LEKDIEEESVDIKNLKEKLEKVSQYIEEENRG---IRELAQKRQQVENE-ADEVGSLINNLRDKLSGIDRIIDNEGSKVKQIKES 152
                 44555555566777777777776666655555...55555666666664.44566666777777778999999888998888876 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   3.3    0.0011      0.54      14      88 ..      51     124 ..      41     154 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0011
       TMPIT  14 leetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlkevesl 88 
                 lee+ + +   +++l+   + + k+i++++ ++k+lk++l+k+++ + eee++ ++el+++ ++ ++  +ev sl
  EPA05658.1  51 LEEAVDYVGLMIKNLKDKRTVLEKDIEEESVDIKNLKEKLEKVSQYI-EEENRGIRELAQKRQQVENEADEVGSL 124
                 55555555555566666666666666666666666666666666554.455555555555555555555544443 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   2.1     0.022        12      13      63 ..      51     101 ..      42     110 .. 0.52
   2 ?    9.5   6.4     0.003       1.5       2      70 ..      82     153 ..      61     156 .] 0.63

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.022
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXX CS
        YabA  13 leeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekk 63 
                 lee ++ +   +++lk++ + l ++ +e +++ ++l+e+le+ ++  +e++
  EPA05658.1  51 LEEAVDYVGLMIKNLKDKRTVLEKDIEEESVDIKNLKEKLEKVSQYIEEEN 101
                 555555555556666665555555555555556666666644433333333 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.003
                 -HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...XXXXXXXXXXXXXXXXXX CS
        YabA   2 dkkelfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerl...eeeekkekekkkelsegk 70 
                 d k+l +kle++++ +ee ++ ++el ++ +++ +e +e+    ++lr++l   ++  ++e +k k+++e++
  EPA05658.1  82 DIKNLKEKLEKVSQYIEEENRGIRELAQKRQQVENEADEVGSLINNLRDKLsgiDRIIDNEGSKVKQIKESR 153
                 456667777777777777777777777777777777777777777777777665333444444445555555 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   5.2    0.0037       1.9      36     101 ..      62     130 ..      44     133 .. 0.73
   2 ?    4.4   0.4     0.099        51      29      66 ..     114     155 ..     104     156 .] 0.51

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0037
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTTH...HHHHHHHHHHHHHHHHHHHHHHHHHH CS
    Spectrin  36 vqallkkhkaleaelaaqqervkalnelaeklldeghsas...eeieerleelnerWeeLkelaaerkq 101
                 +++l +k + le++++++   +k+l+e  ek+ ++ ++++    e+ ++ +++++  +e+ +l++  ++
  EPA05658.1  62 IKNLKDKRTVLEKDIEEESVDIKNLKEKLEKVSQYIEEENrgiRELAQKRQQVENEADEVGSLINNLRD 130
                 577888999999999999999999998888887776555544466666666776666666666665555 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.099
                 CSSSHHHHHHHHH....HHHHHHHHHHHHHHHHHHHHHHHHH CS
    Spectrin  29 lgkdleevqallk....khkaleaelaaqqervkalnelaek 66 
                 ++++ +ev +l++    k+ ++ + ++++  +vk+++e  e+
  EPA05658.1 114 VENEADEVGSLINnlrdKLSGIDRIIDNEGSKVKQIKESRES 155
                 234444444444433346666666666677777776666554 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   7.4      0.05        26      28      63 ..      83     118 ..      43     156 .] 0.51

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.05
  Syntaxin_2  28 teelreklhelieeinelikktnellkklsqldnss 63 
                  ++l+ekl+++ ++i e  + + el +k +q++n  
  EPA05658.1  83 IKNLKEKLEKVSQYIEEENRGIRELAQKRQQVENEA 118
                 333333333333333333333333333333333322 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   7.1    0.0012      0.59      22      98 ..      74     150 ..      43     156 .] 0.51

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0012
       Atg14  22 erlyelrerlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeie 98 
                 ++++e+ +++++lk++ e + + ie++  g +e  q++++++n+++ + +l +  +d+ + + ++ d   +  k+i+
  EPA05658.1  74 KDIEEESVDIKNLKEKLEKVSQYIEEENRGIRELAQKRQQVENEADEVGSLINNLRDKLSGIDRIIDNEGSKVKQIK 150
                 35666666666666666666666665555555333333333333333333333333333333333333333333333 PP

>> Mei5  Double-strand recombination repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3  12.3    0.0074       3.8      83     165 ..      15     129 ..       3     134 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0074
                 .XXXXXXXXXXXXXXXXXXX.........................XXXXHHHHHHHHHHHHHHH....................HHHHHHHHHHHHHHH CS
        Mei5  83 eeeskllkstiknrdvckse.....sslilnslkekie.......lekkeLeeekakLekqvre....................keelLrrLklvkkye 149
                 +e s   ++t+k rdv+  e       ++l ++++k+e       l +k+L+ +++ Lek+++e                    +e+  +r   +k+++
  EPA05658.1  15 QERSPDEQNTMKSRDVSPNEtvgeiGIVELMGKRAKLEeavdyvgLMIKNLKDKRTVLEKDIEEesvdiknlkeklekvsqyieEENRGIRELAQKRQQ 113
                 45566678888888888888888885667777777777777788899*****************77777777777666666664333333333445566 PP

                 HH--HHHHHHHHHHHH CS
        Mei5 150 skndlseLqllikkwr 165
                 ++n+ +e  +li+ +r
  EPA05658.1 114 VENEADEVGSLINNLR 129
                 7777777777777666 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   2.5     0.014       7.2      22      74 ..      84     139 ..      43     155 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.014
      DUF948  22 lklkktldeaaatieelekqvdpilkevedllakvne...lledvneklekvdplt 74 
                 ++lk+ l+++++ iee ++ ++++ ++ +++ +++ e   l +++++kl  +d+++
  EPA05658.1  84 KNLKEKLEKVSQYIEEENRGIRELAQKRQQVENEADEvgsLINNLRDKLSGIDRII 139
                 44455555555555555544444444444444444442223444444555555554 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   9.6    0.0026       1.3      57     176 ..       5     129 ..       1     151 [. 0.52

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0026
     UPF0242  57 wekalkeklekskleekeaklteld..eglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelkleleeq...Laekqel 150
                 ++k++  ++ ++  + +++ +++ d  ++ ++ e  + el  +  +L+e +d+    +++lk +   L++  e+ + d+++lk +le+    ++e++  
  EPA05658.1   5 FKKEEGGEMTQERSPDEQNTMKSRDvsPNETVGEIGIVELMGKRAKLEEAVDYVGLMIKNLKDKRTVLEKDIEEESVDIKNLKEKLEKVsqyIEEENRG 103
                 555555555556666666666666655333444445666666666666666666666666666666666666666666655555554321113444444 PP

     UPF0242 151 lqeyqetieeqrsvlekrqdqieqLe 176
                 + e++++ ++  ++ ++    i++L 
  EPA05658.1 104 IRELAQKRQQVENEADEVGSLINNLR 129
                 44444433333333333333333333 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.2      0.23   1.2e+02       4      32 ..      50      78 ..      47      78 .. 0.91
   2 ?    9.2   4.0     0.003       1.5       5      40 ..      72     107 ..      68     109 .. 0.92
   3 ?    5.0   0.6     0.065        33       4      32 ..     113     141 ..     110     153 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.23
   FlaC_arch  4 elEnklsklsteletvkkeneelsksvee 32
                +lE+ ++ +  +++++k++   l+k++ee
  EPA05658.1 50 KLEEAVDYVGLMIKNLKDKRTVLEKDIEE 78
                799*****************999999996 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.003
   FlaC_arch   5 lEnklsklsteletvkkeneelsksveelkenVkdl 40 
                 lE+++++ s+ ++++k+++e++s+ +ee ++ +++l
  EPA05658.1  72 LEKDIEEESVDIKNLKEKLEKVSQYIEEENRGIREL 107
                 9**************************999988876 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.065
   FlaC_arch   4 elEnklsklsteletvkkeneelsksvee 32 
                 ++En+ +++ + +++++++++ +   +++
  EPA05658.1 113 QVENEADEVGSLINNLRDKLSGIDRIIDN 141
                 68999999999999999999999877765 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   7.6    0.0029       1.5     185     294 ..      33     134 ..       3     154 .. 0.45

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0029
       FAM76 185 rlevskleeeklaeekesnetskksldsnssdhlvavtqLkeeiaslkkqleqkdqellekdkkitelkaellekekelreklkelekeakekieklek 283
                 +  v ++    ++e ++++    ++l+ ++    +++++Lk++ + l+k +e+  +++ + + k+ ++    +e+e++  + l + +++++++ +++ +
  EPA05658.1  33 NETVGEIG---IVELMGKR----AKLEEAVDYVGLMIKNLKDKRTVLEKDIEEESVDIKNLKEKLEKVSQ-YIEEENRGIRELAQKRQQVENEADEVGS 123
                 12222222...22222221....12333333333566666666666666666666666666666655543.3333333333445555555666666666 PP

       FAM76 284 kirellkevae 294
                  i++l+ +++ 
  EPA05658.1 124 LINNLRDKLSG 134
                 66666555544 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   8.2     0.011       5.5      12     121 ..      44     151 ..      39     155 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.011
     zf-C4H2  12 leklknklakevealekeekcleeykkelelLeqEkmaHveeLrlIhaDinalEsvikeaeeekekslekakklyeeykklkeevnelrse.lglekle 109
                 l  +++kl ++v+ +     ++++ k + + Le++ ++ + +++ +++ ++++ + i+e +   ++  +k +++ +e +++ + +n+lr + +g++++ 
  EPA05658.1  44 LMGKRAKLEEAVDYV---GLMIKNLKDKRTVLEKDIEEESVDIKNLKEKLEKVSQYIEEENRGIRELAQKRQQVENEADEVGSLINNLRDKlSGIDRII 139
                 555566666655555...566777777777788888888888999999999999999999999999999999*******************999*9999 PP

     zf-C4H2 110 dleeeeeellke 121
                 d+e ++ + +ke
  EPA05658.1 140 DNEGSKVKQIKE 151
                 977776666665 PP

>> Nas2_N  Nas2 N_terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       1.9   9.7e+02       2      16 ..      42      56 ..      41      61 .. 0.84
   2 ?    1.8   1.8      0.44   2.3e+02       2      23 ..      63      84 ..      62     106 .. 0.63
   3 ?    7.0   0.2     0.011       5.6       1      38 [.     104     143 ..     104     144 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.9
      Nas2_N  2 keLekkkdeiekeie 16
                 eL+ k++++e+ ++
  EPA05658.1 42 VELMGKRAKLEEAVD 56
                589*******99875 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.44
      Nas2_N  2 keLekkkdeiekeieelsevLe 23
                k+L++k++ +ek+iee s  ++
  EPA05658.1 63 KNLKDKRTVLEKDIEEESVDIK 84
                6677777777777776554444 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.011
      Nas2_N   1 lkeLekkkdeiekeieelsevLe..sqnvgmdgplvDeeg 38 
                 ++eL +k++++e+e +e+ + ++  ++++   ++ +D+eg
  EPA05658.1 104 IRELAQKRQQVENEADEVGSLINnlRDKLSGIDRIIDNEG 143
                 689**************99999965555555567777776 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   4.7    0.0091       4.7      12      44 ..      61      93 ..      49      98 .. 0.81
   2 ?    3.7   0.4      0.14        71      14      44 ..     105     135 ..      93     140 .. 0.73
   3 ?    1.0   0.1      0.97     5e+02       3      25 ..     129     151 ..     127     154 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0091
        XhlA 12 kldnleervdkleekaaeaeekiknleedlkkl 44
                +++nl+++ + le++ +e    iknl e+l+k 
  EPA05658.1 61 MIKNLKDKRTVLEKDIEEESVDIKNLKEKLEKV 93
                689999966999999999999999999999886 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.14
        XhlA  14 dnleervdkleekaaeaeekiknleedlkkl 44 
                  +l ++ +++e+ a+e+ + i nl ++l+ +
  EPA05658.1 105 RELAQKRQQVENEADEVGSLINNLRDKLSGI 135
                 4566644788889999999999999888876 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.97
        XhlA   3 kerlerietkldnleervdklee 25 
                 +++l  i++ +dn +++v++++e
  EPA05658.1 129 RDKLSGIDRIIDNEGSKVKQIKE 151
                 78899999999999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2183  (0.121758); expected 358.6 (0.02)
Passed bias filter:                      896  (0.0499749); expected 358.6 (0.02)
Passed Vit filter:                       177  (0.00987227); expected 17.9 (0.001)
Passed Fwd filter:                        35  (0.00195214); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              35  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.46
# Mc/sec: 1026.10
//
Query:       EPA05659.1  [L=241]
Description: hypothetical protein BG20_I0313 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.8e-32  111.4   0.0    6.6e-32  111.3   0.0    1.0  1  PAC2      PAC2 family


Domain annotation for each model (and alignments):
>> PAC2  PAC2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.3   0.0   3.7e-36   6.6e-32       1     206 [.      13     211 ..      13     218 .. 0.90

  Alignments for each domain:
  == domain 1  score: 111.3 bits;  conditional E-value: 3.7e-36
                 EEEESSCGGGHHHHHHHHHHHHTTEEEEEEEEHCCHSBCCCC.SEEEEETTEEE-SEEEEEETTT.SEEEEEEE...E-HSCHHHHHHHHHHHHHHHTT CS
        PAC2   1 LilGfpgiGnVgqlavdlLiesleaekvgeidsdyllpfvgprpvvlveegrelepprlyakdsgsrdllvlqg...repilqyeefakalldwaeelg 96 
                 Li+Gfp+ G++g+ ++++Li+ l+++++ge+d ++ lp     p+ +ve+g+ l p+r+y ++    ++ ++ +    +p l y+ fa   l++++ + 
  EPA05659.1  13 LIVGFPSNGLIGTFSISYLIHALDMKQIGELDHPD-LP-----PTLFVEDGEILAPIRIYKRN----NIFAIISdlpFDPYLAYD-FAGLTLEYCKTNM 100
                 89*********************************.99.....9*9**************665....799999956666666666.************* PP

                 ESEEEEEEEEEESS-ES..TTS-.EEEEEESSHHHHHHH.HCT....-CEEEEHHHHHHHHHHHHTT-EEEEEEEEEECCC--HHHHHHHHHHHHHHHT CS
        PAC2  97 vkevvvLggldageradvphtrpekvtgaatdeelleel.ees....eyggivgitglLlsaakergipavgllaevphylpdPkaaaalleflskllg 190
                 +k++++++g+ + ++     ++  k++g +t+++l e l +++     +g i+g  ++++s +++++ipa+ l+ae+++ +pdP+a+++ +  l+++l+
  EPA05659.1 101 IKKIIIVSGMETINKD----SKMPKIYGLVTHQSLEETLyTNQiskfLAGSIFGTDAAIISVFRKSKIPALILYAECHPFFPDPEASIVSIITLAQILN 195
                 **********977663....4555************9997533567888999*********************************************** PP

                 ---HCHHHHHHHHHHH CS
        PAC2 191 levdtedLeedaeele 206
                 +++dt+d +++ e l+
  EPA05659.1 196 IKIDTTDIQKKMEYLR 211
                 *********9999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1563.62
//
Query:       EPA05660.1  [L=70]
Description: hypothetical protein BG20_I0299 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.053   13.5   2.7      0.059   13.4   2.7    1.1  1  CRPA        Chlamydia 15 kDa cysteine-rich outer membrane pro
        7.2    6.2   8.4      1e+02    2.4   8.4    2.0  1  Saf_2TM     SAVED-fused 2TM effector domain
        7.9    6.5  11.7        3.4    7.7   2.0    2.1  2  Holin_BlyA  holin, BlyA family


Domain annotation for each model (and alignments):
>> CRPA  Chlamydia 15 kDa cysteine-rich outer membrane protein (CRPA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   2.7   9.9e-06     0.059      68     108 ..      13      53 ..       2      66 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.9e-06
        CRPA  68 lvvlGilLviaglallfilqaqlganafylliPaviGlvkl 108
                 ++ lG++ v+++l l ++++    + + + +i a+iG++ +
  EPA05660.1  13 IILLGVIWVVITLPLPWVVNNPQVSATQFNIILAIIGIMSI 53 
                 4679****************9999999999*******9987 PP

>> Saf_2TM  SAVED-fused 2TM effector domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   8.4     0.017     1e+02      61      88 ..      38      65 ..       1      70 [] 0.76

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.017
     Saf_2TM 61 seipeivlaiilvigvllivvGavllil 88
                +  ++i+laii + ++ +iv+G+v+ ++
  EPA05660.1 38 ATQFNIILAIIGIMSIPFIVLGVVWTLK 65
                3368899999999************876 PP

>> Holin_BlyA  holin, BlyA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   2.3    0.0047        28      16      29 ..      10      23 ..       5      39 .. 0.80
   2 ?    7.7   2.0   0.00057       3.4      15      40 ..      42      68 ..      37      70 .] 0.81

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0047
  Holin_BlyA 16 iKLiilgiFvvllv 29
                 KLiil + + +++
  EPA05660.1 10 AKLIILLGVIWVVI 23
                79****99998877 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00057
  Holin_BlyA 15 eiKLiilgiF.vvllvlgvllllKPll 40
                +i L i+gi  +  +vlgv+  lKP l
  EPA05660.1 42 NIILAIIGIMsIPFIVLGVVWTLKPEL 68
                56677777764889***********87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.28s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 507.36
//
Query:       EPA05661.1  [L=338]
Description: putative membrane protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.8e-23   81.5  15.5      1e-22   81.0  15.5    1.2  1  LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
  ------ inclusion threshold ------
      0.038   13.8   0.0      0.068   13.0   0.0    1.4  1  SIS              SIS domain


Domain annotation for each model (and alignments):
>> LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.0  15.5   1.2e-26     1e-22      36     300 ..      37     319 ..       7     320 .. 0.83

  Alignments for each domain:
  == domain 1  score: 81.0 bits;  conditional E-value: 1.2e-26
  LPG_synthase_TM  36 lllalllallsvllralrWrlllrsl.garislrrllrayliglfvnnvtPgalgGevvrayllkrkegvslskalasvvverlldllalvllg 128
                      ++la++ +++ + l +++++++ ++  g+  s+++l  +   ++f+  +tP+ +g e+v +y+l++ +gv+ sk++++ +++ + +++a +ll 
       EPA05661.1  37 FVLAVVSMIIKLGLQGIKFAYIAQKYlGKFDSFWKLCGVRVGSEFIKFTTPMFVGAEFVVIYYLHK-KGVAPSKSTWIAIMDIVTEVFAGGLLS 129
                      4667776666666999988777766559999***********************************.**********************99998 PP

  LPG_synthase_TM 129 llallllggllaegaavllllalallllavlalllllllrrrlarlarvlkrlarllarfarklasakr...............klvlasprrl 207
                      + a ++ +   a+    +l+l++++++  +  + l++l+ rr + + +v+ rl+ ++++ ++ +    +                +  +s++ +
       EPA05661.1 130 IMAGIFALMNGAYVI-GALILGISITITSLWMV-LFFLSSRRTFQVPKVFVRLVKKFSKEKGVKYID-QtnswmeevctmsrknLRTSESKKVF 220
                      887777666555544.66666666666555555.566666666777777777777776666544433.259***********99889999**** PP

  LPG_synthase_TM 208 llafllslliwllealtlylllralgvdvslallllillaltlvgalpplPgGlGvrEaalalllall.....Gvsaaeala.aallyrlitly 295
                       ++fl+sl+ w +++  +++++++ g+ ++++ ++ +++ ++++g lp++ gG+G++E++ ++ l++l      +++++ +  a++ +r++t+y
       EPA05661.1 221 TVSFLFSLASWSFYGISFMIIAMGTGYIIDTFHSIMAVMGANAIGNLPITVGGSGLAEFGIIAYLNNLdpfnlTIPQGTVTWdAVIGWRIATYY 314
                      *******************************************************************97776667776666558899******* PP

  LPG_synthase_TM 296 lllll 300
                      +++l+
       EPA05661.1 315 VPILV 319
                      **997 PP

>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   7.6e-06     0.068      56     125 ..     160     231 ..     142     237 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.6e-06
                 EEEEEESSSHHHHH....HHHHH.HHHHTTSEEEEEESSTTSHHHHHSSEEEEEEEECHCSSSHCHHHHHHHHHH CS
         SIS  56 lvilisfsgetkdl....vaaae.lakergakiiaITdskgsplareadlalyinaepetlvastksltaqlaal 125
                  v+++  s++t+++    v++++   ke+g+k i  T+s++  ++++++ +l++ +++++   +t s++ +la+ 
  EPA05661.1 160 MVLFFLSSRRTFQVpkvfVRLVKkFSKEKGVKYIDQTNSWMEEVCTMSRKNLRTSESKKV---FTVSFLFSLASW 231
                 5666666888888633336788888899********************************...999999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1094  (0.0610185); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 2323.88
//
Query:       EPA05662.1  [L=271]
Description: putative 3'(2'),5'-bisphosphate nucleotidase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.4e-48  164.5   0.1    3.8e-48  164.3   0.1    1.0  1  Inositol_P  Inositol monophosphatase family
     0.0096   15.4   0.1      0.017   14.6   0.1    1.4  1  FBPase      Fructose-1-6-bisphosphatase, N-terminal domain
  ------ inclusion threshold ------
       0.05   13.1   0.0       0.17   11.3   0.0    1.8  2  MTBP_N      MDM2-binding


Domain annotation for each model (and alignments):
>> Inositol_P  Inositol monophosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.3   0.1   6.4e-52   3.8e-48       6     268 ..      13     268 ..       8     271 .] 0.86

  Alignments for each domain:
  == domain 1  score: 164.3 bits;  conditional E-value: 6.4e-52
                 HHHHHHHHHHHHHHHHHHTTTSEEEESTTTCCHHHHHHHHHHHHHHHHHHHHHHHHSTTSEEEHHCHHHHCCCT.SSSSSEEEEEEEEETHHHHHHT-S CS
  Inositol_P   6 tkaavelaakagevlreefsenelvieekskegeedlvtaadeaveelilealaekfpshkilgeetlakgekseltedgltwivDPiDGTknFvrgip 104
                 ++ a+e+a +ag+ + e ++  +    +ks   +  ++t+ad +++e+i++ l+++   hkil+ee++++ +  +l e+  +wivDP+DGT+ F+ ++ 
  EPA05662.1  13 LDLAIEAAYEAGKSILEIYE-SKYETFTKS---DDSPITEADLKSNEIIKTILSKTN--HKILSEEDKDDLK--RLAEE-TIWIVDPLDGTSDFIDKTG 102
                 567999999********998.555555555...888****************99987..*************..88888.******************* PP

                 G-EEEEEEEETTEEEEEEEEETTTTEEECEETTTEEEETC....EEEEECTTSEGGGTEEEEEESSSSSSHHHHCHHHHHHHCCCCCHEEEBESSHHHH CS
  Inositol_P 105 qvaVsigllvegkpvlGviaqPllgqlysaakgkGaflng....eklplsrappiseallvtlfavssrkdtseasllekvesavsaegvrsvgssalk 199
                  ++V+i+l++++kp++Gvi+ P+++ ++ a+kg+Gaf ++    e + + + +++s++ +v+   ++++ + +e+++++k+    ++    s+gss lk
  EPA05662.1 103 EFTVMIALVKNKKPIIGVIGWPTEKIIFAAQKGCGAFRFSkgrwEEIAVTKVSDLSKCKVVG---SRHHLSEKEKMFIKKL--GIRDF--TSIGSS-LK 193
                 *************************************9998899999999999888888866...6666777776667666..44444..567666.9* PP

                 HHHHHHTSTSEEEEEC..EBHHHHHHHHHHHHHTTEEEEESSSC.....SSSTTSS.EEEEESCHHHHHHHHHHHC CS
  Inositol_P 200 laavaeGkadaylefg.rekkWDhAAGeaileeaGGvvtdakge.....grlllar.giiaanqkelaellaaave 268
                 +  + +G+a+ay++ + ++k+WD AA  +++ eaGG++td++g+     ++ ++++ gi+++n + +++ ++++++
  EPA05662.1 194 VGKISSGEAEAYITTTnKMKEWDSAASYCLISEAGGKMTDMSGNditynNKIVNHQnGILVTN-GLIHDEIVKEFK 268
                 ****************9***************************8888755554441555555.999999988876 PP

>> FBPase  Fructose-1-6-bisphosphatase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   2.8e-06     0.017      63     116 ..      48      96 ..      36     115 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.8e-06
      FBPase  63 klDvladeiliealkaseevkvlvSEEeeelivlerekegkyvvafDPlDGSSn 116
                 + D+ ++ei++  l++  + k+l  E++++l+ l   +e   + ++DPlDG S 
  EPA05662.1  48 EADLKSNEIIKTILSKT-NHKILSEEDKDDLKRL--AEE--TIWIVDPLDGTSD 96 
                 6799*******999887.7788877778889999..333..45567*****995 PP

>> MTBP_N  MDM2-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   2.9e-05      0.17      52      91 ..     117     155 ..     103     172 .. 0.81
   2 ?   -2.0   0.0      0.32   1.9e+03     173     185 ..     207     219 ..     197     237 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.9e-05
      MTBP_N  52 acsllgspaskrwffavqailgsfQfcsSdWeelsadsek 91 
                    + g p++ ++ fa q+ +g f f+   Wee++ +   
  EPA05662.1 117 IIGVIGWPTE-KIIFAAQKGCGAFRFSKGRWEEIAVTKVS 155
                 5567777875.6889*******************776554 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.32
      MTBP_N 173 galkhlkeWhsak 185
                   + ++keW sa 
  EPA05662.1 207 TTTNKMKEWDSAA 219
                 4566778887654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1672.59
//
Query:       EPA05663.1  [L=185]
Description: GTP cyclohydrolase I [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-64  216.9   0.1    1.6e-64  216.7   0.1    1.0  1  GTP_cyclohydroI  GTP cyclohydrolase I
  ------ inclusion threshold ------
      0.013   15.7   0.0      0.025   14.7   0.0    1.5  1  QueF             QueF-like protein
      0.035   13.9   0.1        1.5    8.7   0.0    2.3  2  OST-HTH          OST-HTH/LOTUS domain


Domain annotation for each model (and alignments):
>> GTP_cyclohydroI  GTP cyclohydrolase I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  216.7   0.1   2.6e-68   1.6e-64       2     178 ..       7     176 ..       6     177 .. 0.93

  Alignments for each domain:
  == domain 1  score: 216.7 bits;  conditional E-value: 2.6e-68
                      HHHHHHHHHHTT--TTSTTTTTHHHHHHHHHHHHTGGGGS-G.GGGGSSEEETT--S-EEEEEEEEEEEETTT--EEEEEEEEEEE-TTEEE-H CS
  GTP_cyclohydroI   2 eeavreiLealgedpereglketpkRvakayeelfkgleedpkekvlkkvfeeekdemvlvkdiefsSlCeHHllpfigkahvaYiPkkkviGl 95 
                      ++ vre++ ++gedp+reglk+tp+R+a++y+e+f g+e+d+    l+ +f+ e +++v+ ++i+f+S+CeHH+lpf+gk+h+aY P+++v+G+
       EPA05663.1   7 KKLVRELIIEIGEDPTREGLKDTPERIANMYKEIFGGYESDS---ELSVQFS-EDSDVVVARNIQFYSMCEHHMLPFFGKIHIAYSPNGRVFGI 96 
                      6789*************************************9...3666676.689************************************** PP

                      HHHHHHHHHHHSSEE-HHHHHHHHHHHHHHHH--SEEEEEEEEEEHHHHSSTT--TT-EEEEEEEEEHHHH-HHHHHHHHHHH CS
  GTP_cyclohydroI  96 SklaRivdvvarrlqvQErlteqiadaleevlkpkgvavvieaehlCmtmrgvkkkesktvtsalrGefkedaalreefleli 178
                      Skl+R+v+ +++rlq+QErlt++iad+l  + + kgv+v+ +aehlCm+mrgv++ +++++tsa+rG + e+++ +e ++++i
       EPA05663.1  97 SKLVRLVEKYSKRLQIQERLTKNIADELFVQ-GVKGVVVLADAEHLCMKMRGVRN-DATLTTSAYRGIY-ENKEEKESIMTMI 176
                      ****************************866.99*******************75.6788999******.7777778888776 PP

>> QueF  QueF-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   4.1e-06     0.025       1      48 [.      78     125 ..      78     139 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.1e-06
        QueF   1 PDfatlvirYvpdkkvvelkslklYlisfrnrgifhEevvnrilddlv 48 
                 P f++++i Y p+ +v     l + +  + +r + +E  +++i+d+l+
  EPA05663.1  78 PFFGKIHIAYSPNGRVFGISKLVRLVEKYSKRLQIQERLTKNIADELF 125
                 669******************************************986 PP

>> OST-HTH  OST-HTH/LOTUS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.017     1e+02       5      35 ..       5      41 ..       2      48 .. 0.66
   2 ?    8.7   0.0   0.00025       1.5      42      66 ..      92     116 ..      86     120 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.017
                HHHHHHHHHHHH.....TTTT.SBEHHHHHHHHHHHH CS
     OST-HTH  5 klkkeirelLrs.....dpdg.wvslsrlgslykkky 35
                 +kk +rel+++      ++g   +  r+ ++yk+ +
  EPA05663.1  5 RVKKLVRELIIEigedpTREGlKDTPERIANMYKEIF 41
                5789999999998776655552233555555555555 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00025
                 CCCTSSSHHHHHHTSTTTEEEEEET CS
     OST-HTH  42 rkyGfskLseLlkalpdvveveerg 66 
                 r +G skL +L++++++ ++++er 
  EPA05663.1  92 RVFGISKLVRLVEKYSKRLQIQERL 116
                 679*******************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1391.42
//
Query:       EPA05664.1  [L=452]
Description: pyridine nucleotide-disulfide oxidoreductase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-49  168.8   0.0    1.9e-49  168.5   0.0    1.1  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    6.7e-17   61.8   2.0    4.9e-11   43.0   0.7    3.5  4  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    2.7e-08   33.8   0.2        1.5    8.3   0.0    4.1  4  DAO             FAD dependent oxidoreductase
      0.003   16.9   0.0        0.1   11.8   0.0    2.4  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
     0.0046   16.1   0.1        1.8    7.6   0.0    2.5  2  GIDA            Glucose inhibited division protein A
  ------ inclusion threshold ------
      0.032   14.2   0.1        8.4    6.4   0.1    3.1  3  NAD_binding_9   FAD-NAD(P)-binding
      0.043   13.0   0.0       0.55    9.3   0.0    2.6  3  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
      0.063   12.1   0.0        1.4    7.7   0.0    2.4  2  Trp_halogenase  Tryptophan halogenase
       0.11   12.8   0.1         13    6.1   0.0    2.5  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
       0.11   12.3   0.1       0.29   10.8   0.0    1.7  2  T4-gp15_tss     T4-like virus Myoviridae tail sheath stabilis


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.5   0.0     1e-52   1.9e-49       1     292 [.       6     342 ..       6     344 .. 0.87

  Alignments for each domain:
  == domain 1  score: 168.5 bits;  conditional E-value: 1e-52
                  CSEEEE--SHHHHHHHHHHHH.....HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHHHHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEECT CS
                  xxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaq.....agakvtlvelegtclnggcllskallgvaedaeiasevvkklnqgielllgeevvkidpgkkkvklekkkeg 93 
                  k++v++GgG+AG+++a++l       ++++ +++ +e+++l+++++l++++ g+ e ++i+   ++++ ++ +++ g  v ++dp  k v+l  + ++
   EPA05664.1   6 KKIVILGGGFAGVECARQLESdfgdnSEIELVMI-SEDNFLLFTPMLPQVASGMIETRHIVMP-IREICKKTKFYEG-RVKNVDPFGKLVTLWGTADK 100
                  589******************9998889999999.***********************99885.5778889999999.9*****9999********** PP

                  CEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-T.................SEEEEES-SHHHHHHHHHHHHHT-........ CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................xxxxxxxxxxxxxxxxxxxxxxxx........ RF
  Pyr_redox_2  94 deekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllp.................krivvvGgGyiGvElAaalaklgk........ 166
                   + +i yd+lv+A Gs+++ +g+  v++n++++ +tl++a  l+    +                   +vvvGgG+ G+E+A++l +l          
   EPA05664.1 101 RGISIHYDYLVVALGSETNFFGMADVEKNAYTM-KTLNDAVVLRNRAIDmleqaenetdvilrdsfLTFVVVGGGFAGIETAGELLDLLLdarkhyht 197
                  **************************8888777.*************999999*999998888877778***************85553344556667 PP

                  ......EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE.......EEE.EEETTSCE....EEESEEEE-S-EEES-HHCSH CS
                  ......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxx.xxxxxxxx....xxxxxxxxxxxxxxxxxxxxx RF
  Pyr_redox_2 167 ......evtlveardrllraldkelsaaleealekeGvevklgtsvkeidgnge.......kle.vvledgee....idadlvvvavGvrpstellee 246
                        +v ++ea++ +l++++++l+++ +e++ ++G++++l+t v+ +dg +        +l+  v++        i ++++++ +Gv+p +++  +
   EPA05664.1 198 ihkediRVIVLEALPMILPGFNEKLAKFSKEKMIERGIDIRLKTAVTSFDGIEVnvksldeNLKdSVDK---NgidsIRTKTLIWTAGVTPVNTI--K 290
                  777888999*****************************************9999666544433344444...14447***************988..7 PP

                  CCT-EEEETTEEE--TTSBES.STTEEE-GGGC......TECCSS--HHHHHH CS
                  xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx......xxxxxxxxxxxxxx RF
  Pyr_redox_2 247 klglelderggivvdeflrtn.vpgiyaiGDva......ggkggpelaqaAvq 292
                  ++ l++ ++g++ v++fl+++  pg++aiGD+a       ++    +aq A +
   EPA05664.1 291 RSMLKT-DKGKVIVNDFLEVTeFPGVFAIGDCAlfmdpqTNRPYAPTAQLAEA 342
                  889999.999999*****9877***********99965544444455555555 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   7.7e-06     0.014       1      35 [.       7      45 ..       7      70 .. 0.68
   2 ?   -3.2   0.0       7.2   1.3e+04      52      67 ..     100     115 ..      98     119 .. 0.78
   3 !   43.0   0.7   2.7e-14   4.9e-11       2      75 ..     168     255 ..     167     263 .. 0.90
   4 ?   -2.2   0.0       3.5   6.2e+03      42      58 ..     256     272 ..     253     277 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 7.7e-06
                EEEEECSSHHHHHHHHHH.HHTT..SEE.EEEESSSSSS CS
   Pyr_redox  1 kvvvvGgGyiglElAgal.aelg..kkV.tvversdkll 35
                k+v++GgG+ g+E+A  l +++g  +++  v+  +d++l
  EPA05664.1  7 KIVILGGGFAGVECARQLeSDFGdnSEIeLVMISEDNFL 45
                79****************555985556633334445555 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 7.2
                 HTTEEEECSEEEEEEE CS
   Pyr_redox  52 kngievllntkveeie 67 
                 k+gi ++++  v+++ 
  EPA05664.1 100 KRGISIHYDYLVVALG 115
                 789***9999888775 PP

  == domain 3  score: 43.0 bits;  conditional E-value: 2.7e-14
                 EEEECSSHHHHHHHHHH..............HHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEE CS
   Pyr_redox   2 vvvvGgGyiglElAgal..............aelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedgves 75 
                  vvvGgG+ g+E Ag+l              ++   +V v+e+ +++l++++e+++k  +ek+ ++gi+++l+t v++++g e +v+s
  EPA05664.1 168 FVVVGGGFAGIETAGELldllldarkhyhtiHKEDIRVIVLEALPMILPGFNEKLAKFSKEKMIERGIDIRLKTAVTSFDGIEVNVKS 255
                 59***************9999998877765555558********************************************99987665 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 3.5
                 HHHHHHHHHHHTTEEEE CS
   Pyr_redox  42 askilqeklekngievl 58 
                 + ++l++++ kngi+ +
  EPA05664.1 256 LDENLKDSVDKNGIDSI 272
                 56789999999999865 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0   0.00086       1.5       1      20 [.       7      26 ..       7      46 .. 0.74
   2 !    6.6   0.0    0.0028       5.1     161     210 ..      75     124 ..      54     160 .. 0.74
   3 !    6.3   0.1    0.0035       6.3       2      27 ..     168     209 ..     167     213 .. 0.66
   4 !    7.9   0.0    0.0011       2.1     147     203 ..     221     284 ..     219     360 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00086
                EEEEECTSHHHHHHHHHHHH CS
         DAO  1 dvviiGGGiiGlstAyeLar 20
                ++vi GGG +G+ +A++L  
  EPA05664.1  7 KIVILGGGFAGVECARQLES 26
                59****************43 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0028
                 -EEEESECEEEEEEEETCEEEEE.EECT.EEEEEEEEEEE--GGGHHHHHTT CS
         DAO 161 veilegtevtgleeedgkvwgve.rttp.gendaadavVnaaGawsdllgll 210
                  +++eg +v+++ ++ gk++++  ++ + g+  ++d++V+a G  ++++g++
  EPA05664.1  75 TKFYEG-RVKNV-DPFGKLVTLWgTADKrGISIHYDYLVVALGSETNFFGMA 124
                 389999.****9.678999999995666698866799********9977444 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0035
                 EEEECTSHHHHHHHHHH......HHTT..........EEEEE CS
         DAO   2 vviiGGGiiGlstAyeL......arrg..........Vtlle 27 
                  v++GGG +G+ tA eL      ar++          V++le
  EPA05664.1 168 FVVVGGGFAGIETAGELldllldARKHyhtihkedirVIVLE 209
                 69************9995555543332233334455555555 PP

  == domain 4  score: 7.9 bits;  conditional E-value: 0.0011
                 HHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEE.........EECTEEEEEEEE..EEE--GGG CS
         DAO 147 kltaalaraaealGveilegtevtgleeedgkvwgve.........rttpgendaada..vVnaaGaw 203
                 kl+++  +++ ++G++i+++t vt+++      ++v+         ++++g+  ++++  ++ +aG+ 
  EPA05664.1 221 KLAKFSKEKMIERGIDIRLKTAVTSFDGI---EVNVKsldenlkdsVDKNGID-SIRTktLIWTAGVT 284
                 788888999*****************432...233334445556643444665.33444599999965 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.045        81       1      17 [.       9      25 ..       5      36 .. 0.88
   2 !   11.8   0.0   5.6e-05       0.1     166     305 .]     167     319 ..     161     319 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.045
  Pyr_redox_3  1 iIiGaGPaGlaaaielk 17
                 +I G+G aG+++a +l+
   EPA05664.1  9 VILGGGFAGVECARQLE 25
                 699*********99886 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 5.6e-05
  Pyr_redox_3 166 kvvViGgknSavDaAlelvrk....gaeVtvvtrgseiekeesdpsyslkpdienrleelvke....ekikvlfnaevkeikekeeeykvktedgk.k 254
                   +vV+Gg+  ++++A el +      ++ + + +++ i+    +    + p  +++l++ +ke    + i++  ++ v++ +  e+++k   e+ k +
   EPA05664.1 167 TFVVVGGGFAGIETAGELLDLlldaRKHYHTI-HKEDIRVIVLEALPMILPGFNEKLAKFSKEkmieRGIDIRLKTAVTSFDGIEVNVKSLDENLKdS 263
                  589************99998744213333333.34457777777788899999999999988888864499999999999888777776554443203 PP

  Pyr_redox_3 255 vev......kddvvlatGykpdlsflkkslfeldedgrpvlteeteetnvpglflaG 305
                  v++      +++ ++ t     ++ +k+s++++ ++g++ +++  e t +pg+f +G
   EPA05664.1 264 VDKngidsiRTKTLIWTAGVTPVNTIKRSMLKT-DKGKVIVNDFLEVTEFPGVFAIG 319
                  333444445667777776667799999999998.999*****************998 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0   0.00099       1.8       1      18 [.       7      24 ..       7      46 .. 0.88
   2 !    5.9   0.1    0.0033       5.9       2      17 ..     168     183 ..     167     192 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00099
                CEEEE-SSHHHHHHHHHH CS
        GIDA  1 dviViGgGhAGceAAlaa 18
                +++++GgG AG+e+A ++
  EPA05664.1  7 KIVILGGGFAGVECARQL 24
                589************887 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0033
                 EEEE-SSHHHHHHHHH CS
        GIDA   2 viViGgGhAGceAAla 17 
                  +V+GgG AG+e A +
  EPA05664.1 168 FVVVGGGFAGIETAGE 183
                 58**********9965 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.053        95       1      28 [.       9      36 ..       9      47 .. 0.75
   2 ?    0.7   0.0      0.27   4.8e+02     118     155 ..      76     116 ..      64     117 .. 0.73
   3 ?    6.4   0.1    0.0047       8.4       1      27 [.     169     197 ..     169     213 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.053
  NAD_binding_9  1 aivGaGprGlavlerLlarakkksplei 28
                   +i G+G++G+ ++++L +   + s++e+
     EPA05664.1  9 VILGGGFAGVECARQLESDFGDNSEIEL 36
                   699************9888634444444 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.27
  NAD_binding_9 118 evhraevvdleeradgqavll...adgaslaadaVvLAlGh 155
                    ++++++v ++++ ++ +++     ++g s+++d++v+AlG 
     EPA05664.1  76 KFYEGRVKNVDPFGKLVTLWGtadKRGISIHYDYLVVALGS 116
                    677888889988887764332222455689*********95 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0047
  NAD_binding_9   1 aivGaGprGlavlerLlara..kkksple 27 
                    ++vG+G++G+ ++ +Ll+    ++k+ ++
     EPA05664.1 169 VVVGGGFAGIETAGELLDLLldARKHYHT 197
                    69***************998764444444 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00031      0.55     189     227 ..       3      42 ..       1      51 [. 0.85
   2 ?   -0.2   0.0      0.24   4.4e+02     193     212 ..     167     186 ..     136     209 .. 0.79
   3 ?   -1.8   0.0      0.73   1.3e+03      88     128 ..     402     437 ..     397     448 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00031
  K_oxygenase 189 lakkriaVvGsGqSaaeifedllrr.qkkvelklvtrsea 227
                  ++kk+i++ G+G  + e +++l ++  +++e++lv+ se 
   EPA05664.1   3 KNKKKIVILGGGFAGVECARQLESDfGDNSEIELVMISED 42 
                  6899*********************555699999987765 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.24
  K_oxygenase 193 riaVvGsGqSaaeifedllr 212
                  +++VvG+G  + e + +ll+
   EPA05664.1 167 TFVVVGGGFAGIETAGELLD 186
                  679*****998888877765 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.73
  K_oxygenase  88 letflpsRkefedYlrWvasqleeqvrfgeeveevepdeee 128
                  l++ +++ k+f  +l Wv++ l     f+ ++ +++  ++e
   EPA05664.1 402 LSKVALPNKKFRIFLDWVIDIL-----FDRDISRLKLMKRE 437
                  5667778899999999999755.....44555555555554 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0   0.00079       1.4       1      32 [.       7      38 ..       7      44 .. 0.90
   2 ?    1.9   0.0     0.043        77       2      37 ..     168     204 ..     167     247 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00079
                    EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE CS
  Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlve 32
                    kivi+GGG aG   A  l+  + ++ e++lv 
      EPA05664.1  7 KIVILGGGFAGVECARQLESDFGDNSEIELVM 38
                    79********************7779999985 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.043
                     EEEE--SHHHHHHHHHHHHHT.TTSSEEEEEE-SSS- CS
  Trp_halogenase   2 ivivGGGtaGwlaAaalakal.kgklevtlveseeig 37 
                      v+vGGG aG  +A  l   l + + +   + +e+i 
      EPA05664.1 168 FVVVGGGFAGIETAGELLDLLlDARKHYHTIHKEDIR 204
                     69********988876654440444666666666665 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0    0.0071        13       1      18 [.      10      27 ..      10      39 .. 0.82
   2 ?    4.1   0.0     0.031        55       1      16 [.     170     185 ..     170     214 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0071
                   EE--SHHHHHHHHHHHCC CS
  NAD_binding_8  1 IvGaGlsGlvaAylLaka 18
                   I+G+G++G  +A+ L  +
     EPA05664.1 10 ILGGGFAGVECARQLESD 27
                   89************9875 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.031
                    EE--SHHHHHHHHHHH CS
  NAD_binding_8   1 IvGaGlsGlvaAylLa 16 
                    +vG+G++G  +A +L 
     EPA05664.1 170 VVGGGFAGIETAGELL 185
                    8*******98886654 PP

>> T4-gp15_tss  T4-like virus Myoviridae tail sheath stabiliser
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.5   4.5e+03      12      34 ..       6      28 ..       4      47 .. 0.69
   2 ?   10.8   0.0   0.00016      0.29     123     187 ..     196     257 ..     190     267 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.5
                 HHHHHHHHHTSS-EEEEE-SSSE CS
  T4-gp15_tss 12 kyvllmGdlfsniqvkrqlesgd 34
                 k ++++G  f+ +   rqles  
   EPA05664.1  6 KKIVILGGGFAGVECARQLESDF 28
                 66788899999999999999853 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00016
                  EESSHHHHHHHHHHHGGG-SSEEEEEEEEEETTS--EEEEEEEEEEEEEEEEE---------EEE CS
  T4-gp15_tss 123 ytryeddafqiveqilpyfqpqfnttikeldenevvvkrdikivlesavieeaieGdaldrrrie 187
                  +t +++d+  iv + lp + p fn  + + +  e +++r i+i l++av  ++++G +++ + ++
   EPA05664.1 196 HTIHKEDIRVIVLEALPMILPGFNEKLAK-FSKEKMIERGIDIRLKTAV--TSFDGIEVNVKSLD 257
                  6889*********************9975.6778889***********9..57888877776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3237.90
//
Query:       EPA05665.1  [L=146]
Description: universal stress family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.3e-31  107.4   0.0      1e-30  107.1   0.0    1.1  1  Usp       Universal stress protein family
  ------ inclusion threshold ------
      0.019   14.5   0.0      0.021   14.3   0.0    1.1  1  PRORP     Protein-only RNase P
      0.054   12.3   0.5      0.069   12.0   0.1    1.3  2  DLIC      Dynein light intermediate chain (DLIC)


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.1   0.0   1.7e-34     1e-30       2     141 .]      10     146 .]       9     146 .] 0.96

  Alignments for each domain:
  == domain 1  score: 107.1 bits;  conditional E-value: 1.7e-34
                 -SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTCEEEEEEEESSHHHHHHHHHH CS
         Usp   2 ykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggvkvevvveegdpaeeilevae 100
                 y +IlV++Dgs++s+kAl +A ++ak+++++lill+v++ + +    d +e  e  ++   +   + +   +++ ++gv+ +++ +eg+   ei+++a+
  EPA05665.1  10 YMNILVPLDGSKYSEKALLHACDMAKNYQSHLILLYVVEKSLPINLLDKKEYLEILRKFGNKVLIKGK---DMTVQHGVDSTIIMKEGNIVNEIIKLAK 105
                 779**************************************999999999999999999999888765...8*************************** PP

                 HTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
         Usp 101 eedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                 +++++li++Gs+g+++ +r++lGSvs+++++++pc+ l+++
  EPA05665.1 106 NKKCNLIILGSKGMGATARFFLGSVSNKLANNSPCSILIIK 146
                 ***************************************97 PP

>> PRORP  Protein-only RNase P
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   3.6e-06     0.021      43     113 ..      48     121 ..      32     140 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.6e-06
       PRORP  43 kkttPeelerfqkfvektlpf..diviDglnvaklvkkkkesivkaqallevvrqlakq.klrllvlgrkhmlk 113
                 +k+ P +l   ++++e    f  +++i g  ++   +  ++ i+k  ++++ + +lak+ k +l++lg k m  
  EPA05665.1  48 EKSLPINLLDKKEYLEILRKFgnKVLIKGKDMTVQHGVDSTIIMKEGNIVNEIIKLAKNkKCNLIILGSKGMGA 121
                 689999*********9988885579*******999999999999999999888888887699********9944 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   1.2e-05     0.069      80     142 ..      17      80 ..       7      93 .. 0.83
   2 ?   -3.4   0.0      0.54   3.2e+03      21      39 ..     102     122 ..      94     124 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.2e-05
        DLIC  80 ldGdlyh.kgllkfaleaeslkdtlvil.vvdlsrPwtileslqkwasvlrehidklkiepeekr 142
                 ldG  y  k+ll+    a++++  l++l vv+ s P  +l++ +++ ++lr++ +k+ i+ +++ 
  EPA05665.1  17 LDGSKYSeKALLHACDMAKNYQSHLILLyVVEKSLPINLLDK-KEYLEILRKFGNKVLIKGKDMT 80 
                 8999996256777666789999999865399*********98.6799************999986 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 0.54
        DLIC  21 klPsgk..svlvlGedgsGkt 39 
                 kl  +k  ++++lG +g G t
  EPA05665.1 102 KLAKNKkcNLIILGSKGMGAT 122
                 555555346889999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 978.80
//
Query:       EPA05666.1  [L=37]
Description: hypothetical protein BG20_I0293 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.50
# Mc/sec: 222.09
//
Query:       EPA05667.1  [L=192]
Description: nitrogen regulatory protein P-II [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-08   34.8   0.9    3.5e-08   34.0   0.9    1.4  1  P-II      Nitrogen regulatory protein P-II


Domain annotation for each model (and alignments):
>> P-II  Nitrogen regulatory protein P-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.9   1.9e-12   3.5e-08       1     101 [.       4     103 ..       4     104 .. 0.87

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 1.9e-12
                 EEEEEEGGGHHHHHHHHHHTTGGCEEEEEEEEEESTCCEEEECTTEEEEEEEEEEEEEEEEEEGGGHHHHHHHHHHHH-.SSSTTSEEEEEEEESEEEE CS
        P-II   1 ieaiirpekleevkeaLekagvkgltvtevkGrGkqkghtelyrgaeyevellpkvkleivvsdedvekvveaiikaak.tgeiGDGkiFvlpveevir 98 
                 ieaii+ +++  +  +L+++g++ +   + +      ++t++  g++   + +p  k+e+vvs++d+ kv++ i k+   t + G GkiF++++eev+ 
  EPA05667.1   4 IEAIIKRSTYPIIIAELSSMGYSIMDKRNLEDSKIFDKQTSVKVGSTGI-KSIPLSKIELVVSEKDARKVINLISKKSGyTANHG-GKIFISEMEEVVD 100
                 89************************99999877777788888887776.55**********************98775156655.***********98 PP

                 TTT CS
        P-II  99 irt 101
                 + t
  EPA05667.1 101 MET 103
                 766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       679  (0.0378716); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1249.58
//
Query:       EPA05668.1  [L=83]
Description: hypothetical protein BG20_I0292 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-07   31.3   0.0    1.8e-07   31.0   0.0    1.1  1  HTH_45         Winged helix-turn-helix
    8.6e-06   25.6   0.0    1.2e-05   25.1   0.0    1.3  1  MarR_2         MarR family
     0.0002   21.8   0.0    0.00027   21.4   0.0    1.2  1  HTH_27         Winged helix DNA-binding domain
     0.0029   17.4   0.0     0.0036   17.1   0.0    1.1  1  DUF4364        Domain of unknown function (DUF4364)
     0.0057   16.7   0.0      0.027   14.6   0.0    1.9  2  Mrr_N          Mrr N-terminal domain
     0.0098   15.9   0.0      0.014   15.4   0.0    1.3  1  HTH_20         Helix-turn-helix domain
  ------ inclusion threshold ------
      0.019   14.7   0.0      0.035   13.9   0.0    1.5  1  DUF1495        Winged helix DNA-binding domain (DUF1495)
      0.024   14.0   0.0       0.03   13.7   0.0    1.1  1  RNA_pol_Rpc34  RNA polymerase Rpc34 subunit
       0.03   14.2   0.1      0.051   13.5   0.1    1.4  1  TrmB           Sugar-specific transcriptional regulator TrmB
       0.06   13.5   0.0      0.077   13.1   0.0    1.3  1  DUF2250        Uncharacterized protein conserved in archaea (
      0.067   12.8   0.1      0.075   12.6   0.1    1.0  1  DDRGK          DDRGK domain
       0.13   12.6   0.0       0.19   12.1   0.0    1.3  1  Rrf2           Transcriptional regulator


Domain annotation for each model (and alignments):
>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.0   1.2e-10   1.8e-07      10      75 ..       3      75 ..       1      77 [. 0.83

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 1.2e-10
      HTH_45 10 dILeaisegeak...kTkimykanLsykllnkYLdmLvekgli....kkskekYvlTekGlelleklkeleel 75
                dIL+++ +g+ +    ++i  kanLs   +    ++Lve gl+    ++++  + +TekGl++ +++k+++ l
  EPA05668.1  3 DILDVTADGGRSgviVSAISRKANLSHYAVLDKCEKLVEAGLVesvkNDRNRVFLITEKGLQFFQEFKRFQGL 75
                88888876554422279*********99999999********98885558899****************9865 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   8.1e-09   1.2e-05       9      60 ..       3      52 ..       2      54 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 8.1e-09
                HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSS CS
      MarR_2  9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDk 60
                ++L + +++++  + v+++ r+ +ls+ av   +++Lv+aGLve +++  D+
  EPA05668.1  3 DILDVTADGGRSGVIVSAISRKANLSHYAVLDKCEKLVEAGLVESVKN--DR 52
                56777777777689********************************98..55 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   1.8e-07   0.00027      14      68 .]      11      62 ..       4      62 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.8e-07
      HTH_27 14 hrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                + r +++ ++++++ n++  ++    +kL+e+GLve+    +++r++ + +T+kG
  EPA05668.1 11 GGRSGVIVSAISRKANLSHYAVLDKCEKLVEAGLVESV---KNDRNRVFLITEKG 62
                5566667799*************999*********555...999**********9 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   2.4e-06    0.0036      23      74 ..      19      70 ..      13      72 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.4e-06
     DUF4364 23 eiileneytnYfdlqqalseLvesglieeeekenktlykiTekGketlelfe 74
                  i  +  ++   + +  ++Lve+gl+e+ +++ + ++ iTekG +  ++f+
  EPA05668.1 19 SAISRKANLSHYAVLDKCEKLVEAGLVESVKNDRNRVFLITEKGLQFFQEFK 70
                55555555555556666699**************************999997 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.32   4.8e+02       7      37 ..       3      31 ..       1      38 [. 0.75
   2 !   14.6   0.0   1.8e-05     0.027      58      86 ..      36      67 ..      22      68 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.32
       Mrr_N  7 plLealadgsehrlkeirervaerfglseee 37
                 +L + adg  +    i+++++++++ls ++
  EPA05668.1  3 DILDVTADGGRSG--VIVSAISRKANLSHYA 31
                6788888865554..7899999999998776 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 1.8e-05
       Mrr_N 58 rtyLkkagllespk...rgvwkiTekGrevlk 86
                + +L++agl+es k   + v+ iTekG ++ +
  EPA05668.1 36 CEKLVEAGLVESVKndrNRVFLITEKGLQFFQ 67
                6789*******999887899********9876 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   9.5e-06     0.014      21      58 ..      12      49 ..       3      52 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 9.5e-06
                TCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
      HTH_20 21 raegltaselaerldlskntlsyHLrvLeeagLvevvr 58
                ++ g+ +s++ +   ls   + +  ++L+eagLve+v+
  EPA05668.1 12 GRSGVIVSAISRKANLSHYAVLDKCEKLVEAGLVESVK 49
                56788899***************************997 PP

>> DUF1495  Winged helix DNA-binding domain (DUF1495)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.4e-05     0.035      56      87 ..      36      66 ..      28      69 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.4e-05
     DUF1495 56 essLielGLveeeeeseglklYklteeGieiv 87
                 + L+e GLve   +++  +++ +te+G ++ 
  EPA05668.1 36 CEKLVEAGLVE-SVKNDRNRVFLITEKGLQFF 66
                567*******7.57777889********9875 PP

>> RNA_pol_Rpc34  RNA polymerase Rpc34 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0     2e-05      0.03      91     138 ..       4      51 ..       4      58 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2e-05
                    HHHHHHHHXSSXEEHHHHHHTTGX.XHHHHHHHHHHHHHTTXXEEEEXS CS
  RNA_pol_Rpc34  91 VysiIeesGneGIwsrtiksklnL.hksvvkkcLksLeskkyiksvksv 138
                    ++++  + G++G+   +i +k nL h +v++kc k L+  +++ svk+ 
     EPA05668.1   4 ILDVTADGGRSGVIVSAISRKANLsHYAVLDKCEK-LVEAGLVESVKND 51 
                    57788899***************956678888876.6667999999985 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   3.4e-05     0.051      25      59 ..      18      52 ..      13      60 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.4e-05
                HCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTT CS
        TrmB 25 adeiaeelgvprskvYevLrsLedkGlVerekgrp 59
                ++ i++++++++  v +  ++L+++GlVe +k  +
  EPA05668.1 18 VSAISRKANLSHYAVLDKCEKLVEAGLVESVKNDR 52
                789**************************999764 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   5.1e-05     0.077      28      57 ..      21      50 ..      18      70 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.1e-05
     DUF2250 28 iakeleipleevrellkkLeelGLlerveg 57
                i+++ +++   v ++++kL e+GL+e v++
  EPA05668.1 21 ISRKANLSHYAVLDKCEKLVEAGLVESVKN 50
                77888999999****************997 PP

>> DDRGK  DDRGK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1     5e-05     0.075     114     176 ..      16      78 ..      13      82 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5e-05
                 E-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EEE-TT--EEE---XXXXXXXXXXXXXXXXXX CS
       DDRGK 114 vlleelavkfklktqevierikeLeeqgsltGvlDdrGkyiyitdeEleavakyikkkGrvsi 176
                 v +  ++ k +l++  v ++ ++L e g ++ v  dr ++  it++ l+  +++ + +G v+ 
  EPA05668.1  16 VIVSAISRKANLSHYAVLDKCEKLVEAGLVESVKNDRNRVFLITEKGLQFFQEFKRFQGLVES 78 
                 56788999**************************************99999999888887754 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00013      0.19      21      59 ..      11      49 ..       4      57 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                STCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
        Rrf2 21 eeeepvsseeiaerqnispsylekilakLrkaglvksvr 59
                 +++ v +++i+++ n+s+  +    +kL +aglv+sv+
  EPA05668.1 11 GGRSGVIVSAISRKANLSHYAVLDKCEKLVEAGLVESVK 49
                455558899****************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 531.10
//
Query:       EPA05669.1  [L=715]
Description: AAA family ATPase, CDC48 family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   7.1e-100  330.6   0.0    9.3e-51  171.7   0.0    2.5  2  AAA              ATPase family associated with various cellul
    2.1e-27   94.6   0.9    9.3e-13   47.8   0.2    2.7  2  AAA_lid_3        AAA+ lid domain
      2e-23   82.3   0.0    5.4e-23   81.0   0.0    1.8  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal
    3.1e-16   60.0   0.1    3.8e-07   30.4   0.0    2.9  2  AAA_2            AAA domain (Cdc48 subfamily)
    2.3e-14   53.4   0.0    1.3e-07   31.5   0.0    2.9  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    3.5e-14   53.5   0.0      6e-06   26.7   0.0    3.4  3  AAA_16           AAA ATPase domain
    5.1e-12   46.0   2.5    0.00026   21.0   0.0    4.0  2  AAA_5            AAA domain (dynein-related subfamily)
    2.8e-10   40.6   1.9     0.0051   17.1   0.0    4.3  4  AAA_22           AAA domain
    3.2e-10   39.7   0.3    0.00079   18.7   0.0    2.8  2  TIP49            TIP49 P-loop domain
    6.2e-10   39.4   0.0    0.00018   21.7   0.0    2.5  2  AAA_33           AAA domain
    8.1e-10   38.8   0.0    0.00041   20.4   0.0    3.4  3  AAA_14           AAA domain
    1.2e-09   37.8   0.6    3.2e-09   36.4   0.6    1.8  1  CDC48_2          Cell division protein 48 (CDC48), domain 2
    1.5e-08   34.3   0.3     0.0018   17.7   0.0    2.6  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    6.8e-08   32.4   0.1      0.014   15.2   0.0    2.5  2  IstB_IS21        IstB-like ATP binding protein
    1.5e-07   32.0   0.1     0.0082   16.7   0.0    2.7  2  AAA_18           AAA domain
    5.7e-07   29.4   0.0       0.01   15.6   0.0    2.7  2  AAA_24           AAA domain
      6e-07   29.2   1.2       0.11   12.0   0.0    3.5  3  AAA_25           AAA domain
    1.2e-06   28.3   0.3       0.19   11.4   0.0    4.1  2  Sigma54_activat  Sigma-54 interaction domain
    1.5e-06   28.6   0.0      0.068   13.6   0.0    2.6  2  RNA_helicase     RNA helicase
    1.7e-06   27.5   0.2      0.012   14.9   0.0    2.5  2  Zeta_toxin       Zeta toxin
      2e-06   27.4   0.1      0.058   12.9   0.0    2.7  2  AAA_7            P-loop containing dynein motor region
    2.9e-06   27.6   0.1      0.099   12.9   0.0    2.4  2  AAA_28           AAA domain
    6.1e-06   26.8   0.1       0.21   12.1   0.0    3.0  2  ABC_tran         ABC transporter
    1.2e-05   25.1   0.0      0.034   14.0   0.0    2.6  2  AAA_3            ATPase family associated with various cellul
    3.3e-05   23.8   0.0      0.085   12.6   0.0    2.6  2  AAA_11           AAA domain
    4.2e-05   22.8   0.0       0.27   10.4   0.0    2.7  2  DUF815           Protein of unknown function (DUF815)
    5.3e-05   23.2   0.2       0.49   10.4   0.1    2.7  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    6.7e-05   22.1   0.2       0.16   11.1   0.1    2.4  2  Parvo_NS1        Parvovirus non-structural protein NS1
    8.3e-05   22.4   0.3       0.17   11.6   0.0    2.9  2  AAA_30           AAA domain
    0.00011   22.2   1.1        0.6   10.0   0.1    3.7  3  NACHT            NACHT domain
    0.00015   21.3   0.4       0.48    9.8   0.1    2.7  2  PhoH             PhoH-like protein
    0.00046   19.5   0.0       0.48    9.6   0.0    2.3  2  DUF2075          Uncharacterized conserved protein (DUF2075)
     0.0011   19.3   2.9        1.4    9.3   0.0    3.7  3  AAA_19           AAA domain
     0.0014   18.7   0.0        2.2    8.4   0.0    2.8  2  Sigma54_activ_2  Sigma-54 interaction domain
     0.0017   17.8   0.0       0.65    9.4   0.0    3.1  3  TniB             Bacterial TniB protein
     0.0017   18.1   0.5        5.6    6.6   0.0    4.2  4  Guanylate_kin    Guanylate kinase
     0.0018   17.8   0.1     0.0034   16.9   0.1    1.4  1  UFD1             Ubiquitin fusion degradation protein UFD1
     0.0023   16.9   0.0       0.78    8.6   0.0    2.4  2  AFG1_ATPase      AFG1-like ATPase
     0.0039   17.2   0.1       0.75    9.8   0.0    2.9  2  ResIII           Type III restriction enzyme, res subunit
     0.0043   16.9   0.1       0.15   11.9   0.0    2.6  2  CPT              Chloramphenicol phosphotransferase-like prot
     0.0049   17.3   0.0        3.5    8.1   0.0    2.9  2  AAA_17           AAA domain
     0.0059   16.5   0.0       0.44   10.4   0.0    2.7  2  Bac_DnaA         Bacterial dnaA  protein
     0.0096   15.1   0.2        4.1    6.5   0.0    2.5  2  NB-ARC           NB-ARC domain
  ------ inclusion threshold ------
       0.01   15.7   2.8        4.9    7.0   0.0    4.1  3  NTPase_1         NTPase
      0.019   14.1   0.0        2.2    7.3   0.0    2.7  2  T2SSE            Type II/IV secretion system protein
       0.02   14.6   1.6        5.3    6.7   0.0    3.1  3  Cytidylate_kin   Cytidylate kinase
      0.025   14.3   0.0       0.26   11.0   0.0    2.5  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.028   14.1   0.0        7.4    6.4   0.0    2.8  2  AAA_29           P-loop containing region of AAA domain
      0.033   13.6   0.5          2    7.7   0.1    2.5  2  IPT              Isopentenyl transferase
      0.042   13.0   0.0        4.7    6.3   0.0    2.9  2  PIF1             PIF1-like helicase
      0.055   12.8  10.7       0.54    9.6   0.1    4.2  4  ATPase           KaiC
      0.065   13.1   2.6       0.67    9.8   0.1    3.3  3  ATPase_2         ATPase domain predominantly from Archaea
      0.066   13.3   0.1        2.5    8.2   0.0    2.6  2  Torsin           Torsin
      0.075   13.0   0.3         11    5.9   0.0    2.9  3  Rad17            Rad17 P-loop domain
      0.082   12.9   4.5       0.76    9.8   0.1    3.3  3  Vps4_C           Vps4 C terminal oligomerisation domain
       0.24   11.7   1.2          1    9.6   0.1    2.3  2  Hydin_ADK        Hydin Adenylate kinase-like domain
        2.8    8.4   7.4        2.6    8.5   0.2    3.6  2  AAA_23           AAA domain


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.7   0.0     3e-53   9.3e-51       1     131 [.     216     345 ..     216     346 .. 0.98
   2 !  156.6   0.0   1.4e-48   4.4e-46       1     131 [.     489     620 ..     489     621 .. 0.96

  Alignments for each domain:
  == domain 1  score: 171.7 bits;  conditional E-value: 3e-53
                 EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS CS
         AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkk 99 
                 vllyGppGtGKTllakava e++++f+++sg+e++ ky gese+k+re+fk+a+e++ psi+fiDEid++a++r++ + e+e+r+v+qLlt +dg+k++
  EPA05669.1 216 VLLYGPPGTGKTLLAKAVAGETSAHFISLSGPEIMGKYYGESEEKLREIFKQAEENS-PSIVFIDEIDSIAPKRDEVSGEVEKRIVSQLLTLMDGMKSR 313
                 79******************************************************9.****************************************6 PP

                 SSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
         AAA 100 eskvivigatnrpdkldpallr.gRfdrkieie 131
                  +kv+vi+atnrpd++dpal+r gRfdr+iei+
  EPA05669.1 314 -GKVVVIAATNRPDSIDPALRRpGRFDREIEIG 345
                 .77***************************986 PP

  == domain 2  score: 156.6 bits;  conditional E-value: 1.4e-48
                 EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH..TTCCCHHHHHHHHHHHHHHHHTT CS
         AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr..sgseseeeervvnqLlteldgvk 97 
                 +ll+GppGtGKT++aka+a+ ++++f++i+g+ellsk+vgesek +re+f++a++ a p+i+f+DE+dal+++r   +s s ++e+vv+q+lte+dg++
  EPA05669.1 489 ILLHGPPGTGKTMIAKALATMTDSNFISIKGPELLSKWVGESEKGVREIFRKARQAA-PCIIFLDEVDALVPRRgsGDSGSHVTENVVSQILTEIDGLE 586
                 69******************************************************9.****************96666999***************** PP

                 TSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
         AAA  98 kkeskvivigatnrpdkldpallr.gRfdrkieie 131
                 +  ++v++igatnr d +d+allr gRfdr+ie++
  EPA05669.1 587 EL-HNVLIIGATNRLDIVDEALLRpGRFDRIIEVP 620
                 *7.66***************************998 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.9   0.0   2.3e-14   7.3e-12       2      40 ..     369     407 ..     368     429 .. 0.76
   2 !   47.8   0.2     3e-15   9.3e-13       1      43 [.     643     694 ..     643     696 .. 0.84

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 2.3e-14
   AAA_lid_3   2 vdlkeLAerTeGySGADlaalcreAallAlrrgikeitm 40 
                 vdlk++A+ T+G++GADl+ l +eAa++ lrr ++ i+ 
  EPA05669.1 369 VDLKQIAKITHGFVGADLEMLSKEAAMRSLRRILPDINL 407
                 9*******************************6443332 PP

  == domain 2  score: 47.8 bits;  conditional E-value: 3e-15
   AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrr.......gik..eitmedf 43 
                 dvd+ +++e+T+G+SGA++aa+ ++Aa+lAl+r       +ik  +it++d+
  EPA05669.1 643 DVDITKVVELTNGFSGAEIAAIANRAAILALKRhvntkskNIKdiKITQQDI 694
                 9********************************7766665444545888887 PP

>> CDC48_N  Cell division protein 48 (CDC48), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.0   0.0   1.7e-25   5.4e-23       2      84 ..       6      88 ..       5      90 .. 0.97

  Alignments for each domain:
  == domain 1  score: 81.0 bits;  conditional E-value: 1.7e-25
                EEEECCSS-CSSTTEEEE-HHHHHHHTS-TTSEEEEECCCCEEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEEEEEEE- CS
     CDC48_N  2 LrVaeapqedvgrgivridpedmeelglepgdvveiegkrkTvaivwpaepedegkgiIrmdgvtRknagvsiGdkVtVrkae 84
                L+V e+pq++vgrg++++dp+ +ee +++pg+++e++ ++kT+++ wp+ +e+ g g+I++dg+tR+n+g++iGdk++++++e
  EPA05669.1  6 LKVIEIPQQHVGRGRAIVDPKIIEETKWKPGQILELTYNKKTHVKLWPGSTEEYGSGTIKIDGMTRQNIGAGIGDKISIKSVE 88
                89**************************************************99**************************997 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.0   1.2e-09   3.8e-07       6     105 ..     216     309 ..     213     320 .. 0.88
   2 !   26.2   0.0   2.3e-08   7.3e-06       6     100 ..     489     580 ..     486     586 .. 0.87

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 1.2e-09
                 EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG-------------H...HHHHHH CS
       AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpkessgadvSre...gVqrdL 99 
                 +ll gp g+Gkt+laka+a   ++    ++i +   e++     + + ++++  ++  ++aee+   iv++DEid i+p   ++ +vS+e    ++  L
  EPA05669.1 216 VLLYGPPGTGKTLLAKAVAGETSA----HFISLSGPEIMG----KYYGESEEKLREIFKQAEENSpsIVFIDEIDSIAP---KRDEVSGEvekRIVSQL 303
                 5789****************9996....************....********************99*************...55555554333677888 PP

                 HHHHH- CS
       AAA_2 100 Lqileg 105
                 L +++g
  EPA05669.1 304 LTLMDG 309
                 999997 PP

  == domain 2  score: 26.2 bits;  conditional E-value: 2.3e-08
                 EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG----...---------HHHHHHH CS
       AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpk...essgadvSregVqrdL 99 
                 ill gp g+Gkt++akala + +    +++i +   ell     + + ++++g ++   +a +    i++lDE+d   p+   + sg+ v ++ V ++L
  EPA05669.1 489 ILLHGPPGTGKTMIAKALATMTD----SNFISIKGPELLS----KWVGESEKGVREIFRKARQAApcIIFLDEVDALVPRrgsGDSGSHVTENVVSQIL 579
                 7999******************9....5************....999999*************9999************97766666667666666666 PP

                 H CS
       AAA_2 100 L 100
                  
  EPA05669.1 580 T 580
                 4 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.0   4.2e-10   1.3e-07      32     103 ..     212     291 ..     205     334 .. 0.86
   2 !   18.5   0.0   4.1e-06    0.0013      31      69 ..     484     522 ..     448     560 .. 0.69

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 4.2e-10
      RuvB_N  32 aldhvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrlsraveev 103
                 a   vllyGpPG Gkt lak +a e  +++ + sgP +      e +  l  ++++ ee+   ++fidei  ++++ +ev
  EPA05669.1 212 APKGVLLYGPPGTGKTLLAKAVAGETSAHFISLSGPEImgkyygESEEKLREIFKQAEENspSIVFIDEIDSIAPKRDEV 291
                 66779*******************************995555555678899999999877336**********9999887 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 4.1e-06
      RuvB_N  31 ealdhvllyGpPGlGkttlakiiakelgvklkitsgPvl 69 
                 ea   +ll+GpPG Gkt +ak +a+  ++++ +  gP l
  EPA05669.1 484 EAPKGILLHGPPGTGKTMIAKALATMTDSNFISIKGPEL 522
                 445568*************************99999976 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   1.9e-08     6e-06      22     140 ..     211     319 ..     181     320 .. 0.79
   2 !   18.9   0.0   5.1e-06    0.0016      15      56 ..     477     515 ..     473     528 .. 0.76
   3 ?    3.6   0.0      0.24        75     123     146 ..     534     556 ..     530     594 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 1.9e-08
      AAA_16  22 grpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekleealaavpelagaeasrll 120
                   p  vll+G++G+GK+ l+++++    ++ ++f++    +  ++  y    + l r e+++q +++   +    + +++++ +   +e++g+ ++r+ 
  EPA05669.1 211 EAPKGVLLYGPPGTGKTLLAKAVAG---ETSAHFISLSGPEI-MGKYYGESEEKL-R-EIFKQAEEN---SPSIVFIDEIDSIAPKRDEVSGEVEKRIV 300
                 44599*******************5...33477999999999.777776688888.6.888888777...6668888889999999999****99**** PP

      AAA_16 121 ellkrllallsrderplvlv 140
                  +l  l++ ++++++ +v++
  EPA05669.1 301 SQLLTLMDGMKSRGK-VVVI 319
                 *******99999888.6654 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 5.1e-06
      AAA_16  15 alervrsgrpelvllsGesGvGKsslvrellralekdggifl 56 
                 a+e v+   p  +ll+G++G+GK+ ++++l++ +++++  f+
  EPA05669.1 477 AFEYVNVEAPKGILLHGPPGTGKTMIAKALAT-MTDSN--FI 515
                 566666667899*****************994.55554..44 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.24
      AAA_16 123 lkrllallsrderplvlvlDdlqw 146
                 ++++++++++ + p +++lD+++ 
  EPA05669.1 534 VREIFRKARQ-AAPCIIFLDEVDA 556
                 5678899999.999********94 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.4   1.4e-06   0.00043       1     136 [.     215     334 ..     215     335 .. 0.74
   2 !   21.0   0.0   8.3e-07   0.00026       2      75 ..     489     555 ..     488     560 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.4e-06
                 EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG--...HHHHHHHHHHHHSSEE CS
       AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEverae...sevlnsLlslleerrl 94 
                 +vlL GppGtgK+ la+ +a  + + +    +++      + g++    g+ + +  ++ ++a+  +++i+++DE++ +    +ev +++ + +  + l
  EPA05669.1 215 GVLLYGPPGTGKTLLAKAVAGETSAHFISLSGPE------IMGKYY---GESEEKLREIFKQAEenSPSIVFIDEIDSIApkrDEVSGEVEKRIVSQLL 304
                 59*****************999988887776665......888887...445555555555666689**********9983234566666555555555 PP

                 E..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHT CS
       AAA_5  95 lleeggelvkaknddllerfrviatanpldrslnelspalrs 136
                  l++g +  ++        + via++n++d    +++palr+
  EPA05669.1 305 TLMDGMKSRGK--------VVVIAATNRPD----SIDPALRR 334
                 55555555544........99*********....99999987 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 8.3e-07
                 EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGG CS
       AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEve 75 
                 +lL GppGtgK+++a+ la ++ +++  + +++      l+ ++    g+ +    ++ r+ar   ++i++lDEv+
  EPA05669.1 489 ILLHGPPGTGKTMIAKALATMTDSNFISIKGPE------LLSKWV---GESEKGVREIFRKARqaAPCIIFLDEVD 555
                 89**********************999998887......777777...3444444445555555777888888887 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1     3e-05    0.0095       8      60 ..     216     268 ..     211     273 .. 0.77
   2 ?    4.0   0.0      0.18        57      73     119 ..     256     312 ..     245     324 .. 0.66
   3 !   17.1   0.0   1.6e-05    0.0051       8      42 ..     489     514 ..     483     544 .. 0.78
   4 ?    0.9   0.0       1.7   5.2e+02      84     105 ..     539     561 ..     528     601 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3e-05
      AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevv.fvtlpsstsskdllrel 60 
                 ++++G++GtGKT+l++ ++ +  +  ++   +pe++ +++  s++++++++++ 
  EPA05669.1 216 VLLYGPPGTGKTLLAKAVAGETSA-HFISLSGPEIMgKYYGESEEKLREIFKQA 268
                 689****************99843.34444777777888888888888887765 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.18
      AAA_22  73 lsseellealeqalraravielliiDEaqhlr....s......eealeeLrsllnl..s 119
                  s+e l+e + qa ++     ++ iDE++ +     +      ++++++L +l++   s
  EPA05669.1 256 ESEEKLREIFKQAEENSPS--IVFIDEIDSIApkrdEvsgeveKRIVSQLLTLMDGmkS 312
                 4556666666666666655..**********8865415566778888888888876433 PP

  == domain 3  score: 17.1 bits;  conditional E-value: 1.6e-05
      AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpev 42 
                 ++++G++GtGKT+ ++ l+   d         + +
  EPA05669.1 489 ILLHGPPGTGKTMIAKALATMTD---------SNF 514
                 89****************99984.........333 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 1.7
      AAA_22  84 qalraravielliiDEaqhlr..s 105
                 + +r++a + ++ +DE++ l   +
  EPA05669.1 539 RKARQAA-PCIIFLDEVDALVprR 561
                 3344444.48********996541 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0     4e-06    0.0013      50     104 ..     213     266 ..     206     315 .. 0.80
   2 !   18.7   0.0   2.5e-06   0.00079      50     106 ..     486     541 ..     480     544 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 4e-06
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXX CS
       TIP49  50 GravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkt.evltqalr 104
                  ++vLl Gp+gtGkt la a++ e +   +f++lsg e+       + e l + ++
  EPA05669.1 213 PKGVLLYGPPGTGKTLLAKAVAGETS--AHFISLSGPEIMGKYYGESeEKLREIFK 266
                 699*******************9987..89********987655544134444444 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 2.5e-06
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXX CS
       TIP49  50 GravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkktev.ltqalrks 106
                  +++Ll Gp+gtGkt +a a++    +d  f++++g e+ s  v  +e  + + +rk+
  EPA05669.1 486 PKGILLHGPPGTGKTMIAKALATM--TDSNFISIKGPELLSKWVGESEKgVREIFRKA 541
                 599*****************9975..5789************9999986467788886 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   5.6e-07   0.00018       2      80 ..     216     324 ..     216     344 .. 0.85
   2 !   15.1   0.0     6e-05     0.019       2      41 ..     489     530 ..     489     599 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 5.6e-07
      AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt............................dytrvldrlyqilnelarkalsag 70 
                 vll G+pG+GK+ la+ ++ ++   ++ ls ++++ +++g+ +++++                             + +v++r+  +l  l + + s+g
  EPA05669.1 216 VLLYGPPGTGKTLLAKAVAGETSahFISLSGPEIMGKYYGESEEKLReifkqaeenspsivfideidsiapkrdeVSGEVEKRIVSQLLTLMDGMKSRG 314
                 7899***************999999999*****999999977776667777777888889999999999988776556688999999999999999999 PP

      AAA_33  71 rnvildatnl 80 
                 + v++ atn+
  EPA05669.1 315 KVVVIAATNR 324
                 9999999986 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 6e-05
      AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtd 41 
                 +ll+G+pG+GK+  a+ l+  ++  ++ +  ++l+++ +g+ 
  EPA05669.1 489 ILLHGPPGTGKTMIAKALATMTDsnFISIKGPELLSKWVGES 530
                 689***************988887788888888877777644 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0       1.6     5e+02      48     106 ..     106     163 ..      79     175 .. 0.69
   2 !   20.4   0.0   1.3e-06   0.00041       4      80 ..     215     300 ..     212     337 .. 0.72
   3 !   13.2   0.0   0.00021     0.067       4      75 ..     488     556 ..     485     601 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 1.6
      AAA_14  48 dpekllelileklkeekktylflDEiqevpewekalkslvdeg.knldvivtGSnsklls 106
                 d+e+l++++  ++  +++ + + D iq  +++   ++ ++ ++ +   vivt S    l 
  EPA05669.1 106 DEEQLHDVMITNF--QNHVFTVHDSIQLPTQMGGKIQFIITNTkPSKPVIVTESTIFKLG 163
                 2234445555544..46888999999999********99998856678999999877665 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 1.3e-06
      AAA_14   4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev............pewe 80 
                  +++ G+  +GKT l+k ++ e      +++ ++  +   k + ++e+ l++i+++++e+  +++f+DEi  +            +++ 
  EPA05669.1 215 GVLLYGPPGTGKTLLAKAVAGETS---AHFISLSGPEIMGKYYGESEEKLREIFKQAEENSPSIVFIDEIDSIapkrdevsgeveKRIV 300
                 57899**************98888...77777777777667666666555566665556699*********995555555544444444 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 0.00021
      AAA_14   4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqe 75 
                  +++ G+  +GKT+++k l+       ++++ i+  +   k   ++ek  ++i++k+++    ++flDE+  
  EPA05669.1 488 GILLHGPPGTGKTMIAKALATMTD---SNFISIKGPELLSKWVGESEKGVREIFRKARQAAPCIIFLDEVDA 556
                 57899**************96655...8999998888888777776655666666555558899*****976 PP

>> CDC48_2  Cell division protein 48 (CDC48), domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.6     1e-11   3.2e-09       2      59 ..     105     166 ..     104     170 .. 0.87

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 1e-11
                 .SCCCCH.HHHCCCTTEEE-TTEEEEECC.TCCCEEEEEEEECCCCSCEEECTSCCEEE..S CS
     CDC48_2   2 idgdema.ylkrqFlgrpvtkGdlvvfef.kgqeiklvVvstePkgpvgitetTeielg..t 59 
                 id++++    + +F+++++t+ d ++ +  +g+ i++ +++t+P+ pv++te+T+ +lg  t
  EPA05669.1 105 IDEEQLHdVMITNFQNHVFTVHDSIQLPTqMGGKIQFIITNTKPSKPVIVTESTIFKLGsmT 166
                 666777778899***************7747************************9998444 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.1   8.7e-05     0.027      24      43 ..     215     234 ..     206     239 .. 0.87
   2 !   17.7   0.0   5.7e-06    0.0018      24      45 ..     488     509 ..     472     516 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.7e-05
  Mg_chelatase  24 nlllvGppGsGKtmlakrlp 43 
                    +ll+GppG+GKt+lak+++
    EPA05669.1 215 GVLLYGPPGTGKTLLAKAVA 234
                   589*************9976 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 5.7e-06
  Mg_chelatase  24 nlllvGppGsGKtmlakrlpsl 45 
                    +ll GppG+GKtm+ak+l+++
    EPA05669.1 488 GILLHGPPGTGKTMIAKALATM 509
                   689***************9876 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   6.8e-05     0.021      44      71 ..     210     237 ..     199     246 .. 0.85
   2 !   15.2   0.0   4.4e-05     0.014      44      69 ..     483     508 ..     464     524 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.8e-05
   IstB_IS21  44 iekkenivllGpsGvGKshlaialgvea 71 
                 +e+ ++++l Gp+G+GK+ la a++ e+
  EPA05669.1 210 VEAPKGVLLYGPPGTGKTLLAKAVAGET 237
                 5677899****************98765 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 4.4e-05
   IstB_IS21  44 iekkenivllGpsGvGKshlaialgv 69 
                 +e+ ++i+l Gp+G+GK+ +a al++
  EPA05669.1 483 VEAPKGILLHGPPGTGKTMIAKALAT 508
                 567789******************97 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   0.00045      0.14       1      22 [.     216     237 ..     216     324 .. 0.62
   2 !   16.7   0.0   2.6e-05    0.0082       1      28 [.     489     514 ..     489     597 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00045
      AAA_18   1 IlltGtpGvGKttlakeLskrl 22 
                 +ll G+pG+GKt lak+++ ++
  EPA05669.1 216 VLLYGPPGTGKTLLAKAVAGET 237
                 799***************7665 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 2.6e-05
      AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvnl 28 
                 Ill G+pG+GKt +ak+L+ ++    n 
  EPA05669.1 489 ILLHGPPGTGKTMIAKALATMT--DSNF 514
                 89****************9998..3333 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   3.2e-05      0.01       4      77 ..     215     284 ..     212     298 .. 0.78
   2 !   11.2   0.0   0.00071      0.22       4      23 ..     488     511 ..     485     596 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.2e-05
      AAA_24   4 kiliyGpsgiGKTtlakel..gpkplfidtekGlksldadkfpdieswedfldevvelaaeladyktlviDtidel 77 
                  +l+yGp+g+GKT lak    + ++ fi + +   ++ ++ +   es e++++ +++ +++ +  ++++iD id +
  EPA05669.1 215 GVLLYGPPGTGKTLLAKAVagETSAHFISLSG--PEIMGKYYG--ESEEKLREIFKQAEENSP--SIVFIDEIDSI 284
                 589***************99878888888877..556666655..578888888888877777..78888888876 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00071
      AAA_24   4 kiliyGpsgiGKTtlakel....g 23 
                  il+ Gp+g+GKT++ak l     
  EPA05669.1 488 GILLHGPPGTGKTMIAKALatmtD 511
                 699**************9865543 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.2    0.0031      0.99      36      54 ..     216     234 ..     209     241 .. 0.86
   2 ?    4.6   0.0     0.065        21     128     176 ..     259     307 ..     255     327 .. 0.80
   3 !   12.0   0.0   0.00035      0.11      36     142 ..     489     587 ..     469     606 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0031
      AAA_25  36 allaGapgtGKttlaldla 54 
                 +ll+G+pgtGKt la  +a
  EPA05669.1 216 VLLYGPPGTGKTLLAKAVA 234
                 69************97766 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.065
      AAA_25 128 advdaleaaieevegvrlvviDplsralgg.densnsdvgalvealeria 176
                 ++++++ +++ee + +  v iD ++++ +  de s + ++++v++l  + 
  EPA05669.1 259 EKLREIFKQAEE-NSPSIVFIDEIDSIAPKrDEVSGEVEKRIVSQLLTLM 307
                 567888899999.78***************56665555599999998775 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 0.00035
      AAA_25  36 allaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgealrddarllvldlagveslpLfakdrggtlltadvdale 134
                 +ll G+pgtGKt++a    la++t++++  +  pe    ++   E +  e+ r++r++   + + +++++l   +       + d+g+++++ +v ++ 
  EPA05669.1 489 ILLHGPPGTGKTMIAKA--LATMTDSNFISIKGPELLSKWVGESEKGVREIFRKARQAAPCIIFLDEVDALVPRR------GSGDSGSHVTENVVSQIL 579
                 79***********9865..55677777777555677777777777777666666666554443333333332111......122344444555666666 PP

      AAA_25 135 aaieeveg 142
                  +i+  e+
  EPA05669.1 580 TEIDGLEE 587
                 66666655 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.1    0.0015      0.48      21      45 ..     212     236 ..     202     329 .. 0.89
   2 !   11.4   0.0   0.00061      0.19      20      53 ..     484     514 ..     471     599 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0015
                      SSS-EEEECSTTSSHHHHHHHHHHH CS
  Sigma54_activat  21 tdlsvlitGesGtGKellaraihea 45 
                       +  vl+ G  GtGK+lla+a+  +
       EPA05669.1 212 APKGVLLYGPPGTGKTLLAKAVAGE 236
                      56789***************98654 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00061
                      TSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-E CS
  Sigma54_activat  20 ktdlsvlitGesGtGKellaraiheaskrkekpf 53 
                      + +  +l++G  GtGK+++a+a+ + ++   ++f
       EPA05669.1 484 EAPKGILLHGPPGTGKTMIAKALATMTD---SNF 514
                      455779***************9976544...445 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   0.00022     0.068       1      27 [.     216     247 ..     216     320 .. 0.72
   2 !   12.3   0.0   0.00052      0.16       1      25 [.     489     513 ..     489     533 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00022
  RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl.....k 27 
                   ++lyGp+g+GK++lak +a + + ++      
    EPA05669.1 216 VLLYGPPGTGKTLLAKAVAGETSAHFislsgP 247
                   689**************999988887555431 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00052
  RNA_helicase   1 iwlyGpsgeGKStlakeLakallkk 25 
                   i+l+Gp+g+GK+++ak La+   ++
    EPA05669.1 489 ILLHGPPGTGKTMIAKALATMTDSN 513
                   689**************99876655 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.1    0.0014      0.45      13      44 ..     210     239 ..     202     249 .. 0.83
   2 !   14.9   0.0   3.8e-05     0.012       9      51 ..     478     519 ..     473     523 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0014
  Zeta_toxin  13 qerPklillgGqpGAGKselaellkdelerqg 44 
                  e Pk +ll G pG GK+ la++++ e+    
  EPA05669.1 210 VEAPKGVLLYGPPGTGKTLLAKAVAGET--SA 239
                 489*********************9997..44 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 3.8e-05
  Zeta_toxin   9 k.ypsqerPklillgGqpGAGKselaellkdelerqgnvvrldp 51 
                   y++ e Pk ill G pG GK+ +a++l++ +  ++n++ +++
  EPA05669.1 478 FeYVNVEAPKGILLHGPPGTGKTMIAKALATMT--DSNFISIKG 519
                 4478889**********************9998..899998875 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   0.00049      0.15      30      58 ..     210     238 ..     200     292 .. 0.86
   2 !   12.9   0.0   0.00018     0.058      30      63 ..     483     515 ..     477     520 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00049
       AAA_7  30 lknkkpvllvGptGtGKtviikdllkkld 58 
                 +++ k vll+Gp GtGKt+++k +  + +
  EPA05669.1 210 VEAPKGVLLYGPPGTGKTLLAKAVAGETS 238
                 677899**************999776665 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00018
       AAA_7  30 lknkkpvllvGptGtGKtviikdllkkldkekyl 63 
                 +++ k +ll Gp GtGKt+i+k l +  d ++++
  EPA05669.1 483 VEAPKGILLHGPPGTGKTMIAKALATMTD-SNFI 515
                 5667889**************99887777.5555 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   0.00031     0.099       2      45 ..     216     264 ..     215     283 .. 0.79
   2 !   12.4   0.0   0.00045      0.14       2      23 ..     489     513 ..     488     547 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00031
      AAA_28   2 ivitGgestGKTtlleaLa....argypvv.pEaareileeklakgeda 45 
                 + + G+++tGKT l++a a    a+ ++   pE++ +++ e  +k +++
  EPA05669.1 216 VLLYGPPGTGKTLLAKAVAgetsAHFISLSgPEIMGKYYGESEEKLREI 264
                 6799***************876666777778998888887776665554 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00045
      AAA_28   2 ivitGgestGKTtlleaLaar...g 23 
                 i + G+++tGKT +++aLa +   +
  EPA05669.1 489 ILLHGPPGTGKTMIAKALATMtdsN 513
                 7899***************754343 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0    0.0011      0.35       8      37 ..     210     239 ..     207     324 .. 0.74
   2 !   12.1   0.0   0.00066      0.21       8      67 ..     483     540 ..     480     597 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0011
                 EETTSEEEEEESTTSSHHHHHHHHTTSS-- CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkp 37 
                 +++ + v + G+ G+GK+ L+k++ag+++ 
  EPA05669.1 210 VEAPKGVLLYGPPGTGKTLLAKAVAGETSA 239
                 566677899*****************9874 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00066
                 EETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe 67 
                 +++ + + + G+ G+GK+ ++k+la +++  +  i ++g +l ++   +++k ++ ++ +
  EPA05669.1 483 VEAPKGILLHGPPGTGKTMIAKALATMTD--SNFISIKGPELLSKWVGESEKGVREIFRK 540
                 566667889*****************986..67788888888887777777777777666 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0052       1.6       2      28 ..     216     242 ..     215     327 .. 0.74
   2 !   14.0   0.0   0.00011     0.034       2      31 ..     489     518 ..     488     559 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0052
       AAA_3   2 vllegvPGlaktllvkalakaldlefk 28 
                 vll g PG++ktll+ka+a   +++f 
  EPA05669.1 216 VLLYGPPGTGKTLLAKAVAGETSAHFI 242
                 7999***************99888875 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 0.00011
       AAA_3   2 vllegvPGlaktllvkalakaldlefkriq 31 
                 +ll+g PG++kt+++kala++ d +f  i+
  EPA05669.1 489 ILLHGPPGTGKTMIAKALATMTDSNFISIK 518
                 79**********************998876 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0    0.0054       1.7      17      35 ..     213     231 ..     204     274 .. 0.78
   2 !   12.6   0.0   0.00027     0.085      16      41 ..     485     510 ..     459     550 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0054
      AAA_11  17 seitliqGPPGtgKTktiv 35 
                 ++ +l+ GPPGtgKT    
  EPA05669.1 213 PKGVLLYGPPGTGKTLLAK 231
                 556899*********5433 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00027
      AAA_11  16 eseitliqGPPGtgKTktivellsql 41 
                  ++  l++GPPGtgKT    +l  + 
  EPA05669.1 485 APKGILLHGPPGTGKTMIAKALATMT 510
                 333679**********6655555444 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   0.00085      0.27      54     116 ..     214     281 ..     174     334 .. 0.70
   2 !    9.5   0.0    0.0016      0.49      22      81 ..     446     514 ..     430     555 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00085
      DUF815  54 nnvLLwGarGtGKSslvkallneyaeegLrli..evekedl....kelpklvellrerperfilfvDDL 116
                 + vLL+G  GtGK  l ka+  e++++ + l   e+  +      ++l +++++  e++   i+f+D +
  EPA05669.1 214 KGVLLYGPPGTGKTLLAKAVAGETSAHFISLSgpEIMGKYYgeseEKLREIFKQA-EENSPSIVFIDEI 281
                 679********************99998655322666554410004444444443.3345567887764 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0016
      DUF815  22 vdevklddLvgidkqkealvente.........qfleglpannvLLwGarGtGKSslvkallneyaeeg 81 
                 + +v++dd+ g+d+ ke+l e +e         ++++ ++ + +LL G  GtGK  + kal + + ++ 
  EPA05669.1 446 IPNVNWDDVGGLDELKEELREAIEwpikhkeafEYVNVEAPKGILLHGPPGTGKTMIAKALATMTDSNF 514
                 56778888888888888887766511111111145666666789****************998777665 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0    0.0025      0.78      13      44 ..     207     238 ..     190     259 .. 0.77
   2 !   10.4   0.1    0.0016      0.49      19      47 ..     486     516 ..     458     522 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0025
                 HHHHCHTEEEEEEESTTSSHHHHHHHHHHHTT CS
        TsaE  13 klakalgdvilLeGdLGaGKTtlvrglakalg 44 
                 k++ ++ + +lL+G+ G+GKT l++++a +  
  EPA05669.1 207 KIGVEAPKGVLLYGPPGTGKTLLAKAVAGETS 238
                 4444345569****************997765 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0016
                 TEEEEEEESTTSSHHHHHHHHHHHTT--..- CS
        TsaE  19 gdvilLeGdLGaGKTtlvrglakalgve..e 47 
                  + ilL+G+ G+GKT+++++la   + +  +
  EPA05669.1 486 PKGILLHGPPGTGKTMIAKALATMTDSNfiS 516
                 3349*****************9987665555 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0031      0.98     117     135 ..     216     234 ..     213     241 .. 0.90
   2 !   11.1   0.1    0.0005      0.16     117     138 ..     489     510 ..     485     513 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0031
   Parvo_NS1 117 vwfyGpantGktnlaeaIa 135
                 v++yGp+ tGkt la+a a
  EPA05669.1 216 VLLYGPPGTGKTLLAKAVA 234
                 899*************987 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0005
   Parvo_NS1 117 vwfyGpantGktnlaeaIakav 138
                 ++++Gp+ tGkt++a+a+a+ +
  EPA05669.1 489 ILLHGPPGTGKTMIAKALATMT 510
                 7899***************976 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.1    0.0088       2.8      21      39 ..     216     234 ..     203     244 .. 0.83
   2 !   11.6   0.0   0.00054      0.17      20      43 ..     488     511 ..     474     519 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0088
      AAA_30  21 avltGpAGtGKttalkalr 39 
                 ++l Gp+GtGKt + ka++
  EPA05669.1 216 VLLYGPPGTGKTLLAKAVA 234
                 6899*********999986 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00054
      AAA_30  20 vavltGpAGtGKttalkalreawe 43 
                   +l+Gp+GtGKt++ kal+ + +
  EPA05669.1 488 GILLHGPPGTGKTMIAKALATMTD 511
                 5689**************998766 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.1    0.0085       2.7       3      21 ..     216     234 ..     214     240 .. 0.88
   2 ?   -0.3   0.0       2.8   8.9e+02      62     130 ..     254     323 ..     245     345 .. 0.65
   3 !   10.0   0.1    0.0019       0.6       3      22 ..     489     508 ..     487     513 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0085
                 EEEEC-TTTCHHHHHHHHH CS
       NACHT   3 vilqGeaGsGKTtLlqkla 21 
                 v+l G++G GKT L++ +a
  EPA05669.1 216 VLLYGPPGTGKTLLAKAVA 234
                 799************9987 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 2.8
                 CTS--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH.............HHHHHCTTTTT--EEEEEEECC CS
       NACHT  62 lpepaapvsevwavllelperlLlilDglDelvtdlgq....kekqpvrtlLselirkkllpeasllltvrpr 130
                 + e++++ +e+++   e+  ++++ +D +D ++ + ++     ek+ v +lL +l+ + + ++ ++++++ ++
  EPA05669.1 254 YGESEEKLREIFKQAEENSPSIVF-IDEIDSIAPKRDEvsgeVEKRIVSQLL-TLMDG-MKSRGKVVVIAATN 323
                 566777777877777778888887.599999998888888844444444444.77766.44444444444443 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.0019
                 EEEEC-TTTCHHHHHHHHHH CS
       NACHT   3 vilqGeaGsGKTtLlqklal 22 
                 ++l+G++G GKT+ ++ la+
  EPA05669.1 489 ILLHGPPGTGKTMIAKALAT 508
                 789*************9986 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.1    0.0015      0.48      22      40 ..     216     234 ..     204     241 .. 0.85
   2 !    8.6   0.0    0.0037       1.2      22      41 ..     489     508 ..     473     515 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0015
                 EEEE--TTSSTTHHHHHHH CS
        PhoH  22 vfaiGpaGtGKtylavala 40 
                 v   Gp GtGKt+la a+a
  EPA05669.1 216 VLLYGPPGTGKTLLAKAVA 234
                 7789***********9998 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0037
                 EEEE--TTSSTTHHHHHHHH CS
        PhoH  22 vfaiGpaGtGKtylavalav 41 
                 +   Gp GtGKt++a ala 
  EPA05669.1 489 ILLHGPPGTGKTMIAKALAT 508
                 6678***********99985 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0    0.0015      0.48       4      61 ..     216     266 ..     213     298 .. 0.67
   2 !    7.6   0.0    0.0061       1.9       4      25 ..     489     510 ..     486     532 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0015
     DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvl.vlrealakkeekkkkk 61 
                 vl  G +GtGKt+++ +++ e        +a+++s ++p+++ +++ + ++k  ++ +k
  EPA05669.1 216 VLLYGPPGTGKTLLAKAVAGET-------SAHFISLSGPEIMgKYYGESEEKL-REIFK 266
                 6789************999998.......667777777766546666666666.33333 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0061
     DUF2075   4 vlVtGvaGtGKtvvllnllael 25 
                 +l +G +GtGKt+++ +l++  
  EPA05669.1 489 ILLHGPPGTGKTMIAKALATMT 510
                 7889***********9988765 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       5.1   1.6e+03      86     118 ..      85     115 ..      25     133 .. 0.47
   2 ?    7.4   0.2     0.017       5.2      11      30 ..     214     233 ..     207     245 .. 0.82
   3 !    9.3   0.0    0.0044       1.4      11      31 ..     487     507 ..     476     523 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 5.1
      AAA_19  86 ealelleeaeeekklqeeellivDEfqdvdelq 118
                 + +e+    +e+ +l  +e l +DE q  d ++
  EPA05669.1  85 KSVEA--ADAEQITLSPTEKLAIDEEQLHDVMI 115
                 22222..33344445444478888877665544 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.017
      AAA_19  11 kvllvtaGpGtGKTrvlkhi 30 
                 k +l+ ++pGtGKT + k++
  EPA05669.1 214 KGVLLYGPPGTGKTLLAKAV 233
                 55899*********877665 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0044
      AAA_19  11 kvllvtaGpGtGKTrvlkhiv 31 
                 k +l+ ++pGtGKT + k+  
  EPA05669.1 487 KGILLHGPPGTGKTMIAKALA 507
                 56899*********9877654 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0     0.016       5.2      22      46 ..     214     238 ..     205     313 .. 0.68
   2 !    8.4   0.0    0.0069       2.2      23      46 ..     488     511 ..     476     560 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.016
                      S-EEEEEETT--HHHHHHCC--TTS CS
  Sigma54_activ_2  22 lpvfltGekGsgkelvArlLhknsg 46 
                        v+l G++G+gk+l A++ + + +
       EPA05669.1 214 KGVLLYGPPGTGKTLLAKAVAGETS 238
                      569***************9875544 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0069
                      -EEEEEETT--HHHHHHCC--TTS CS
  Sigma54_activ_2  23 pvfltGekGsgkelvArlLhknsg 46 
                       ++l G++G+gk+++A++L+    
       EPA05669.1 488 GILLHGPPGTGKTMIAKALATMTD 511
                      589****************97654 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.066        21      25      55 ..     203     233 ..     192     243 .. 0.83
   2 ?   -2.2   0.0       7.1   2.2e+03     106     132 ..     259     285 ..     252     293 .. 0.76
   3 !    9.4   0.0    0.0021      0.65      27      58 ..     478     509 ..     466     518 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.066
        TniB  25 eLleypkrkrmpnlllvGdsnnGKtmivekF 55 
                 eL+e+   + ++ +ll+G++ +GKt +++  
  EPA05669.1 203 ELFEKIGVEAPKGVLLYGPPGTGKTLLAKAV 233
                 5666777778899************998865 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 7.1
        TniB 106 kleqqvlrllrelkvrvLiiDEihnll 132
                 ++ +++ +  +e ++ ++ iDEi+++ 
  EPA05669.1 259 EKLREIFKQAEENSPSIVFIDEIDSIA 285
                 4555566677778899999****9885 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0021
        TniB  27 leypkrkrmpnlllvGdsnnGKtmivekFarl 58 
                 +ey + + ++ +ll+G++ +GKtmi++  a +
  EPA05669.1 478 FEYVNVEAPKGILLHGPPGTGKTMIAKALATM 509
                 56677778899***************987766 PP

>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.37   1.2e+02       3      30 ..     214     241 ..     212     249 .. 0.84
   2 ?    4.0   0.0      0.11        35      74      95 ..     249     270 ..     238     288 .. 0.79
   3 ?    6.6   0.0     0.018       5.6       3      30 ..     487     514 ..     485     520 .. 0.86
   4 ?   -1.2   0.0       4.5   1.4e+03      81     120 ..     529     551 ..     523     597 .. 0.56

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.37
                    SEEEEESTTTSSHHHHHHHHHHHSTTTE CS
  Guanylate_kin   3 rpvvlvgpsgaGksslkkaLlselpekf 30 
                    + v l gp g+Gk  l ka+  e + +f
     EPA05669.1 214 KGVLLYGPPGTGKTLLAKAVAGETSAHF 241
                    66899**************998888777 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.11
                    ETTEEEEEEHHHHHHHHHTTSE CS
  Guanylate_kin  74 fsgnlygtsveaieevlekgki 95 
                      g++yg+s e+ +e+++++ +
     EPA05669.1 249 IMGKYYGESEEKLREIFKQAEE 270
                    6799**************9976 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.018
                    SEEEEESTTTSSHHHHHHHHHHHSTTTE CS
  Guanylate_kin   3 rpvvlvgpsgaGksslkkaLlselpekf 30 
                    + + l gp g+Gk ++ kaL +   ++f
     EPA05669.1 487 KGILLHGPPGTGKTMIAKALATMTDSNF 514
                    66899***************99888887 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 4.5
                    EEHHHHHHHHHTTSEEEEE--CHHHHHHHHTTTTEEEEEE CS
  Guanylate_kin  81 tsveaieevlekgkiviLDvdiqavkqlrkaelspiivFi 120
                    +s + ++e++ k+++                  +p i+F+
     EPA05669.1 529 ESEKGVREIFRKARQ-----------------AAPCIIFL 551
                    555555555555555.................44444444 PP

>> UFD1  Ubiquitin fusion degradation protein UFD1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   1.1e-05    0.0034      68     164 ..      61     157 ..      34     160 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.1e-05
        UFD1  68 egtvylPewmmenlgleegdlveiesvslpkgkfvklqpqsedfldisdpkavLekaLrnfatLtkgdvieikyn.dkvyelkvlevkpesavsiiet 164
                  gt+ +  +  +n+g   gd ++i+sv+   ++ ++l p ++  +d ++   v+ ++++n+ + t+ d i++  +   + ++ ++++kp++ v + e 
  EPA05669.1  61 SGTIKIDGMTRQNIGAGIGDKISIKSVEAADAEQITLSPTEKLAIDEEQLHDVMITNFQNH-VFTVHDSIQLPTQmGGKIQFIITNTKPSKPVIVTES 157
                 4788888888999999*******************************************98.689******98862578************9999885 PP

>> AFG1_ATPase  AFG1-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.019       5.9      52      78 ..     205     229 ..     177     235 .. 0.78
   2 !    8.6   0.0    0.0025      0.78      57      78 ..     481     502 ..     437     511 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.019
  AFG1_ATPase  52 fgrkrksvepvrglYlwGgvGrGKtyl 78 
                  f  k   ve+++g+ l+G+ G GKt l
   EPA05669.1 205 FE-K-IGVEAPKGVLLYGPPGTGKTLL 229
                  44.3.2578****************98 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0025
  AFG1_ATPase  57 ksvepvrglYlwGgvGrGKtyl 78 
                   +ve+++g+ l+G+ G GKt++
   EPA05669.1 481 VNVEAPKGILLHGPPGTGKTMI 502
                  4689*****************8 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0      0.13        41      21      44 ..     207     233 ..     165     243 .. 0.76
   2 !    9.8   0.0    0.0024      0.75      21      46 ..     466     508 ..     409     530 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.13
                 .....TTSEEEEEESTTSTHHHHHHHH CS
      ResIII  21 s...krdkrglikmaTGtGKTlvaakl 44 
                 +   +  k +l+  + GtGKTl+a ++
  EPA05669.1 207 KigvEAPKGVLLYGPPGTGKTLLAKAV 233
                 1444778899999*********98655 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0024
                 ...................TTSEEEEEESTTSTHHHHHHHHHH CS
      ResIII  21 s.................krdkrglikmaTGtGKTlvaaklie 46 
                 +                 +  k +l++ + GtGKT++a +l+ 
  EPA05669.1 466 EaiewpikhkeafeyvnvEAPKGILLHGPPGTGKTMIAKALAT 508
                 1444444445566667668889999************977665 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.52   1.6e+02       4      32 ..     216     244 ..     214     319 .. 0.89
   2 !   11.9   0.0   0.00049      0.15       4      33 ..     489     518 ..     487     537 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.52
                 EEEEE-TTSSHHHHHHHHHHHSSS-EEEE CS
         CPT   4 ilLnGgsssGKsslaralqevldepwlhl 32 
                 +lL G + +GK+ la+a+   + + ++ l
  EPA05669.1 216 VLLYGPPGTGKTLLAKAVAGETSAHFISL 244
                 89***************998888888776 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00049
                 EEEEE-TTSSHHHHHHHHHHHSSS-EEEEE CS
         CPT   4 ilLnGgsssGKsslaralqevldepwlhlg 33 
                 ilL+G + +GK+ +a+al +++d  ++ ++
  EPA05669.1 489 ILLHGPPGTGKTMIAKALATMTDSNFISIK 518
                 9************************99886 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0     0.011       3.5       1      26 [.     219     244 ..     219     304 .. 0.75
   2 ?    6.2   0.0     0.042        13       2      25 ..     493     516 ..     492     554 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.011
                 EE-TTSSHHHHHHHHHHHHTEEEEEH CS
      AAA_17   1 lGgPGsGKgtqceklvekygfthlsa 26 
                 +G+PG GK+ +++ ++ +   +++s 
  EPA05669.1 219 YGPPGTGKTLLAKAVAGETSAHFISL 244
                 7***********99998886666664 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.042
                 E-TTSSHHHHHHHHHHHHTEEEEE CS
      AAA_17   2 GgPGsGKgtqceklvekygfthls 25 
                 G+PG GK+ +++ l+   +  ++s
  EPA05669.1 493 GPPGTGKTMIAKALATMTDSNFIS 516
                 9***********999877555555 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0    0.0014      0.44      37     176 ..     216     357 ..     207     379 .. 0.72
   2 ?    2.9   0.0      0.27        84      37      63 ..     489     515 ..     480     561 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0014
                 EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHT.T-SEEEEE-GGGGTT-H.........HHHHHHHHHHHH CS
    Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklr.kvDvLliDDiqflagke.........ktqeelfhtfna 125
                 +++yg+ G Gkt L ka++ e+ +++     + l++ e + +     ++k  e fk+    +  ++ iD+i  +a k          ++  +l+++++ 
  EPA05669.1 216 VLLYGPPGTGKTLLAKAVAGETSAHF-----ISLSGPEIMGKYYGESEEKLREIFKQAEEnSPSIVFIDEIDSIAPKRdevsgevekRIVSQLLTLMDG 309
                 89***************998876655.....56788888888888888888888998766356789999999999885222221111344566777777 PP

                 HHTTT-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHHHH CS
    Bac_DnaA 126 lleegkqvvlssDrsPkeleeledrlrsrfeaGlvvdieppdletrlailk 176
                 +   gk vv+++   P +++    r   rf++ +  +i  pd e r +il 
  EPA05669.1 310 MKSRGKVVVIAATNRPDSIDPAL-RRPGRFDREI--EIGIPDDEGRHEILS 357
                 77889999999999999886543.3356777754..445577777877775 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.27
                 EEEE-SSSSSHHHHHHHHHHHHHHHSS CS
    Bac_DnaA  37 lfiygevGlGktHLlkaignevlenap 63 
                 ++++g+ G Gkt + ka++  + +n+ 
  EPA05669.1 489 ILLHGPPGTGKTMIAKALATMTDSNFI 515
                 79****************998887765 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0     0.013       4.1      23      43 ..     216     236 ..     203     243 .. 0.83
   2 ?    5.9   0.0      0.02       6.4      23      41 ..     489     507 ..     481     517 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.013
                 EEEEESTTSSHHHHHHHHCCS CS
      NB-ARC  23 valvGmgGvGKttlakqilnk 43 
                 v l+G +G GKt lak +  +
  EPA05669.1 216 VLLYGPPGTGKTLLAKAVAGE 236
                 789************998765 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.02
                 EEEEESTTSSHHHHHHHHC CS
      NB-ARC  23 valvGmgGvGKttlakqil 41 
                 + l+G +G GKt +ak   
  EPA05669.1 489 ILLHGPPGTGKTMIAKALA 507
                 679***********98764 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.096        30       2      23 ..     216     237 ..     215     247 .. 0.81
   2 ?    1.2   0.1      0.95     3e+02      73     120 ..     252     297 ..     245     321 .. 0.72
   3 ?    7.0   0.0     0.016       4.9       2      32 ..     489     519 ..     488     554 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.096
                 EEEE--TTSSHHHHHHHHHHHH CS
    NTPase_1   2 vfiTGppGvGKtTlvkkvlell 23 
                 v++ GppG+GKt l k v+ + 
  EPA05669.1 216 VLLYGPPGTGKTLLAKAVAGET 237
                 6788*********999998766 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.95
                 TEEE-HHHHHHHHHHHHHHHH.HHH-EEEE---STTGGG-HHHHHHHHH CS
    NTPase_1  73 kyvvdvesfeelalealrkal.seadviviDEiGkmElkskkfkeavee 120
                 ky+ +    ee   e++++a  +++ ++ iDEi ++  k  +++ +ve+
  EPA05669.1 252 KYYGE---SEEKLREIFKQAEeNSPSIVFIDEIDSIAPKRDEVSGEVEK 297
                 55544...455556666666646777*******8877776666666665 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.016
                 EEEE--TTSSHHHHHHHHHHHH...GGGEEE CS
    NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgG 32 
                 +++ GppG+GKt + k ++ + +s+ ++++G
  EPA05669.1 489 ILLHGPPGTGKTMIAKALATMTDSNFISIKG 519
                 6899*******98888888777777667776 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.077        24     128     154 ..     212     238 ..     170     244 .. 0.84
   2 ?    7.3   0.0     0.007       2.2     125     154 ..     482     511 ..     368     520 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.077
       T2SSE 128 erglilvsGgTgsGKttllyallkein 154
                 + + +l+ G+ g+GKt l+ a+  e  
  EPA05669.1 212 APKGVLLYGPPGTGKTLLAKAVAGETS 238
                 55678999**********999887765 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.007
       T2SSE 125 avrerglilvsGgTgsGKttllyallkein 154
                  v++ + il+ G+ g+GKt ++ al ++ +
  EPA05669.1 482 NVEAPKGILLHGPPGTGKTMIAKALATMTD 511
                 34456789************9999877654 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1      0.04        13       4      28 ..     219     243 ..     216     246 .. 0.90
   2 ?   -1.2   0.0       4.5   1.4e+03     136     181 ..     389     436 ..     377     442 .. 0.67
   3 ?    6.7   0.0     0.017       5.3       2      27 ..     490     515 ..     489     518 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.04
                     E-STTSSHHHHHHHHHHHHT-EEEE CS
  Cytidylate_kin   4 DGPagsGKssvaralaeklglkyld 28 
                      GP g+GK  +a+a+a + ++++++
      EPA05669.1 219 YGPPGTGKTLLAKAVAGETSAHFIS 243
                     6*******************99986 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 4.5
                     EE--HHHHHHHHHHHHHHTT----HHHHHHHHH..HHHHHHHCTSSS- CS
  Cytidylate_kin 136 ldAsveeRakRRlkqlkakgtsvsleellaeik..eRDklDkerevgp 181
                     l   + +R  RR+    + + ++   e+l++ik    D +D  +e+ p
      EPA05669.1 389 LSKEAAMRSLRRILPDINLSEEKVSTEILQKIKitSDDFRDALKEIRP 436
                     556677888899887777777777778888765225677777776655 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.017
                     EEE-STTSSHHHHHHHHHHHHT-EEE CS
  Cytidylate_kin   2 aiDGPagsGKssvaralaeklglkyl 27 
                      + GP g+GK  +a+ala+  + +++
      EPA05669.1 490 LLHGPPGTGKTMIAKALATMTDSNFI 515
                     578***************98887776 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       2.2   6.8e+02       5      71 ..     220     281 ..     216     284 .. 0.58
   2 ?   11.0   0.0   0.00082      0.26       1      71 [.     489     554 ..     489     559 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 2.2
  Viral_helicase1   5 GvpGcGKStlirkllrts..liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                      G pG GK+ l + ++ +   + ++ + p  e+  +   +++ +  + +++++++        i+++DE+
       EPA05669.1 220 GPPGTGKTLLAKAVAGETsaHFISLSGP--EIMGKYYGESEEKLREIFKQAEENSP-----SIVFIDEI 281
                      779*****99999998866433332222..33333334555555555565555542.....37777775 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00082
  Viral_helicase1   1 ivvhGvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                      i+ hG pG GK+ + + l+ +   ++ +++   ell++++ ++++   + ++++ +a+ +     i++lDE 
       EPA05669.1 489 ILLHGPPGTGKTMIAKALATMTdSNFISIKG-PELLSKWVGESEKGVREIFRKARQAAPC-----IIFLDEV 554
                      678**********999999999988888998.9*******88888888888888887764.....8999986 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.089        28      21      38 ..     213     229 ..     204     235 .. 0.80
   2 ?    6.4   0.0     0.024       7.4      21      44 ..     486     508 ..     466     513 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.089
      AAA_29  21 lkgatlltGpsGsGKSTl 38 
                 +kg +ll Gp G+GK+ l
  EPA05669.1 213 PKG-VLLYGPPGTGKTLL 229
                 467.9**********866 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.024
      AAA_29  21 lkgatlltGpsGsGKSTllDAiqa 44 
                 +kg +ll Gp G+GK+ +  A+++
  EPA05669.1 486 PKG-ILLHGPPGTGKTMIAKALAT 508
                 466.9**********999888776 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1    0.0064         2       5      32 ..     217     244 ..     213     246 .. 0.93
   2 ?    3.5   0.1      0.12        39       5      31 ..     490     516 ..     487     518 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0064
         IPT   5 lifGatttGKtaeaiklaketgapvivl 32 
                 l++G+ +tGKt  a ++a et+a  i+l
  EPA05669.1 217 LLYGPPGTGKTLLAKAVAGETSAHFISL 244
                 89*********************99987 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.12
         IPT   5 lifGatttGKtaeaiklaketgapviv 31 
                 l++G+ +tGKt  a +la  t    i+
  EPA05669.1 490 LLHGPPGTGKTMIAKALATMTDSNFIS 516
                 799***************999877665 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.12        39      17      43 ..     208     234 ..     201     241 .. 0.81
   2 ?    6.3   0.0     0.015       4.7      12      47 ..     476     511 ..     472     517 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.12
                 ...HCTS-EEEEESTTSSCHHHHHHHH CS
        PIF1  17 vlnekgklfFvtGsgGtgKtflwkall 43 
                 +  e +k + ++G  GtgKt l ka+ 
  EPA05669.1 208 IGVEAPKGVLLYGPPGTGKTLLAKAVA 234
                 45577888999***********99876 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.015
                 HH......HCTS-EEEEESTTSSCHHHHHHHHHHCH CS
        PIF1  12 aiieavlnekgklfFvtGsgGtgKtflwkallkklr 47 
                 ++ e v+ e +k + ++G  GtgKt++ kal ++  
  EPA05669.1 476 EAFEYVNVEAPKGILLHGPPGTGKTMIAKALATMTD 511
                 45677888999*******************998765 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1    0.0017      0.54      15      37 ..     209     231 ..     202     241 .. 0.83
   2 ?    1.3   0.1      0.56   1.8e+02     110     155 ..     260     311 ..     248     326 .. 0.63
   3 ?    6.0   0.0     0.021       6.7      22      37 ..     489     504 ..     482     512 .. 0.87
   4 ?   -1.3   0.3       3.5   1.1e+03     112     138 ..     681     708 ..     644     714 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0017
      ATPase  15 GipegrvvlitGepGtGKtifal 37 
                 G+   + vl++G pGtGKt++a+
  EPA05669.1 209 GVEAPKGVLLYGPPGTGKTLLAK 231
                 67777889*************97 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.56
      ATPase 110 elaeaikeika...krvviDsitgl...ayeekeavaReilrqlvrvlkklg 155
                 +l+e+ k+ ++   + v iD i+++     e + +v ++i+ ql++ + +++
  EPA05669.1 260 KLREIFKQAEEnspSIVFIDEIDSIapkRDEVSGEVEKRIVSQLLTLMDGMK 311
                 4444444444333377888888888321233344556778888888886654 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.021
      ATPase  22 vlitGepGtGKtifal 37 
                 +l+ G pGtGKt++a+
  EPA05669.1 489 ILLHGPPGTGKTMIAK 504
                 899**********997 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 3.5
      ATPase 112 aeaikeika.krvviDsitglayeekea 138
                  + ik+ik+ ++ ++Dsi+ ++ ++ke+
  EPA05669.1 681 SKNIKDIKItQQDILDSIDKVKPRKKEM 708
                 4677888876777999999995555555 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1    0.0021      0.67      22     122 ..     215     319 ..     203     323 .. 0.59
   2 ?    0.8   0.0       1.2   3.8e+02      16      43 ..     482     509 ..     475     518 .. 0.77
   3 ?   -1.0   0.0       4.4   1.4e+03     107     131 ..     531     558 ..     499     595 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0021
    ATPase_2  22 iyfiYGpegsGKtaLlkeiienledkdk.......yviyyialreesiskldefieeeeekkklekal..........giavpkaeleeilkeksklvf 103
                  +++YGp g GKt L k ++ + + +            yy + +e+  + +++                          i+    + +e++ e  k + 
  EPA05669.1 215 GVLLYGPPGTGKTLLAKAVAGETSAHFIslsgpeiMGKYYGESEEKLREIFKQA-------------EenspsivfidEIDSIAPKRDEVSGEVEKRIV 300
                 5789***********999998884422233433323333333333333333333.............12333333333334444445566778888888 PP

    ATPase_2 104 kaielllekikkkgkkiii 122
                 +++  l++ +k +gk ++i
  EPA05669.1 301 SQLLTLMDGMKSRGKVVVI 319
                 8888888888888886666 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 1.2
    ATPase_2  16 erepneiyfiYGpegsGKtaLlkeiien 43 
                 + e  + +++ Gp g GKt + k +++ 
  EPA05669.1 482 NVEAPKGILLHGPPGTGKTMIAKALATM 509
                 55666678999********999887665 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 4.4
    ATPase_2 107 elllekikkkgkk...iiiiiDelqkli 131
                 e+  ++i +k+++    ii++De+  l+
  EPA05669.1 531 EKGVREIFRKARQaapCIIFLDEVDALV 558
                 455566777777778789999**98876 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.68   2.1e+02      56      76 ..     216     236 ..     205     242 .. 0.83
   2 ?    8.2   0.0    0.0079       2.5      50      75 ..     483     508 ..     472     516 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.68
                 EEEEE-TTSSHHHHHHHHHHH CS
      Torsin  56 lsfhGwtGtGknfvaeiiaen 76 
                 + ++G +GtGk  +a+ +a +
  EPA05669.1 216 VLLYGPPGTGKTLLAKAVAGE 236
                 5589***********999865 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0079
                 -SS-EEEEEEE-TTSSHHHHHHHHHH CS
      Torsin  50 pkkpLvlsfhGwtGtGknfvaeiiae 75 
                 ++ p  + +hG +GtGk  +a+ +a 
  EPA05669.1 483 VEAPKGILLHGPPGTGKTMIAKALAT 508
                 455666789*************9986 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0      0.24        76      48      76 ..     216     244 ..     204     265 .. 0.83
   2 ?   -2.0   0.0       8.9   2.8e+03     140     178 ..     248     284 ..     229     291 .. 0.73
   3 ?    5.9   0.0     0.035        11      48      73 ..     489     514 ..     475     540 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.24
       Rad17  48 LLisGPsGCgkstvvkvLskelgiklrew 76 
                 +L+ GP+G gk+   k ++ e + +++  
  EPA05669.1 216 VLLYGPPGTGKTLLAKAVAGETSAHFISL 244
                 5789********99999998887777665 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 8.9
       Rad17 140 dlPnkfyrds.dalrevirkylrssealplilviteiesl 178
                 ++  k+y++s ++lre+ +++   s +   i+ i ei+s+
  EPA05669.1 248 EIMGKYYGESeEKLREIFKQAEENSPS---IVFIDEIDSI 284
                 555678888878899999887655544...6667777765 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.035
       Rad17  48 LLisGPsGCgkstvvkvLskelgikl 73 
                 +L+ GP+G gk+ + k L+     ++
  EPA05669.1 489 ILLHGPPGTGKTMIAKALATMTDSNF 514
                 5789*************998766555 PP

>> Vps4_C  Vps4 C terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1    0.0024      0.76      19      44 ..     412     437 ..     403     441 .. 0.80
   2 ?   -1.4   0.0       7.8   2.4e+03      36      60 ..     632     656 ..     627     656 .. 0.82
   3 ?    2.7   0.3       0.4   1.3e+02      20      43 ..     680     703 ..     674     706 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0024
      Vps4_C  19 ipsdkllePpvtlkDflkalkkarpt 44 
                 + ++ l + ++t +Df +alk+ rp+
  EPA05669.1 412 VSTEILQKIKITSDDFRDALKEIRPS 437
                 555556666****************8 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 7.8
      Vps4_C  36 kalkkarptVskeDLekheeFTkef 60 
                 k+ +k +p  ++ D++k  e T+ f
  EPA05669.1 632 KIHSKKKPLSNDVDITKVVELTNGF 656
                 666788999999******9999866 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.4
      Vps4_C  20 psdkllePpvtlkDflkalkkarp 43 
                 +s+ ++  ++t +D+l+++ k++p
  EPA05669.1 680 KSKNIKDIKITQQDILDSIDKVKP 703
                 47788899***************9 PP

>> Hydin_ADK  Hydin Adenylate kinase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1       3.1   9.6e+02       2      25 ..     216     239 ..     215     245 .. 0.79
   2 ?    9.6   0.1    0.0032         1       2      30 ..     489     517 ..     488     520 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 3.1
   Hydin_ADK   2 iivhGaPlsGKtatavtLakkYea 25 
                 +++ G+P +GKt  a ++a +  a
  EPA05669.1 216 VLLYGPPGTGKTLLAKAVAGETSA 239
                 5789********999998866555 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0032
   Hydin_ADK   2 iivhGaPlsGKtatavtLakkYeaAllti 30 
                 i++hG+P +GKt +a +La   +  +++i
  EPA05669.1 489 ILLHGPPGTGKTMIAKALATMTDSNFISI 517
                 889****************9988888777 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   2.6       3.2     1e+03      23      39 ..     217     233 ..     206     469 .. 0.86
   2 ?    8.5   0.2    0.0082       2.6      21     154 ..     489     669 ..     472     709 .. 0.49

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 3.2
      AAA_23  23 lItGpNGaGKTTildAi 39 
                 l++Gp G+GKT +  A+
  EPA05669.1 217 LLYGPPGTGKTLLAKAV 233
                 78899999998887775 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0082
      AAA_23  21 ltlItGpNGaGKTTildAiklaL.ygetprlsrks...............grgfeksdveiesegkvkayveltfenkdgry.trsiererelskkkgk 102
                 + l++Gp G+GKT i  A+  ++  ++ +  +++                 r++ ++ + i + ++v+a v ++ + ++g   t+++  ++ +  +   
  EPA05669.1 489 I-LLHGPPGTGKTMIAKALATMTdSNFISIKGPELlskwvgesekgvreiFRKARQAAPCIIFLDEVDALVPRRGSGDSGSHvTENVVSQILTEIDG-- 584
                 4.99***************998833333333332255544333322222222222222222222444444444444444422333332222222221.. PP

      AAA_23 103 ttkkaklelleideleqfisellgskki...ilnlilflgqerfeefelkdkke..............................r 154
                      +  +++ +++ ++++e l +  +   i+++     ++r++ f+  +kk+                              +
  EPA05669.1 585 LEELHNVLIIGATNRLDIVDEALLRPGRfdrIIEVPNPDSKGREQIFKIHSKKKplsndvditkvveltngfsgaeiaaianraA 669
                 1122344444446666666665554444444666666666666666666555555666666666666666666665555554442 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (715 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                       102  (0.00568911); expected 17.9 (0.001)
Passed Fwd filter:                        57  (0.00317921); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              57  [number of targets reported over threshold]
# CPU time: 0.93u 0.38s 00:00:01.31 Elapsed: 00:00:00.60
# Mc/sec: 3599.16
//
Query:       EPA05670.1  [L=194]
Description: hypothetical protein BG20_I0305 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00029   21.3   0.6     0.0014   19.1   0.2    2.2  2  CopG_antitoxin  CopG antitoxin of type II toxin-antitoxin sys


Domain annotation for each model (and alignments):
>> CopG_antitoxin  CopG antitoxin of type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.2   7.8e-08    0.0014      36      78 ..      11      53 ..       2      54 .. 0.88
   2 ?   -0.6   0.0      0.11   2.1e+03      48      67 ..      68      87 ..      63      94 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 7.8e-08
  CopG_antitoxin 36 peLkkktksislrlpedlLealkekAnkrdvpyqslikellee 78
                    p  k  t+si+ rlp +++e+l  +A +++++ + l+k++le+
      EPA05670.1 11 PSKKDPTRSITYRLPTKIVEELETEAMNKNISQNVLVKQILEK 53
                    55577799********************************986 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.11
  CopG_antitoxin 48 rlpedlLealkekAnkrdvp 67
                     +p+ +L++l ++ n +d++
      EPA05670.1 68 PIPKGILNSLGMEMNGQDIN 87
                    58999*****9999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       760  (0.0423894); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.55
# Mc/sec: 1065.23
//
Query:       EPA05671.1  [L=58]
Description: hypothetical protein BG20_I0289 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.034   14.3   0.3      0.038   14.1   0.3    1.2  1  DUF4363         Domain of unknown function (DUF4363)
      0.039   13.9   0.1       0.05   13.5   0.1    1.2  1  Arm-DNA-bind_2  Arm DNA-binding domain
       0.16   11.1   1.4       0.17   11.1   1.4    1.0  1  GLE1            GLE1-like protein


Domain annotation for each model (and alignments):
>> DUF4363  Domain of unknown function (DUF4363)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.3   6.4e-06     0.038       4      43 ..      14      53 ..      11      58 .] 0.82

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.4e-06
     DUF4363  4 qnylkkstdelsekleeleeaienedweeakekleeleke 43
                 + +k+  ++ +++l+++++++ ++d ++a+e +++l   
  EPA05671.1 14 DKLTKSELENAKKTLQTIKRQLAQGDFDSANELIRSLATL 53
                5678888999999999999999999999999999888665 PP

>> Arm-DNA-bind_2  Arm DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   8.3e-06      0.05      31      57 ..      16      42 ..       4      45 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.3e-06
  Arm-DNA-bind_2 31 dtpanrKkaerllaeIeeeIalGtFdY 57
                     t++ ++ a+++l++I+++ a+G Fd 
      EPA05671.1 16 LTKSELENAKKTLQTIKRQLAQGDFDS 42
                    6999*********************95 PP

>> GLE1  GLE1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.4   2.8e-05      0.17       5      58 ..       2      56 ..       1      58 [] 0.94

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.8e-05
        GLE1  5 qikknlleqvkedkelkkllgdlkrkInpkvgQltnss.eqlkkitkelkelles 58
                q++k+ll+ +++dk +k+ l ++k+  ++   Ql++ + ++ +++++ l  ll++
  EPA05671.1  2 QVEKTLLKLSNSDKLTKSELENAKKTLQTIKRQLAQGDfDSANELIRSLATLLDQ 56
                78899********************************************999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1700  (0.0948185); expected 358.6 (0.02)
Passed bias filter:                      902  (0.0503096); expected 358.6 (0.02)
Passed Vit filter:                       109  (0.00607954); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 390.00
//
Query:       EPA05672.1  [L=213]
Description: hypothetical protein BG20_I0295 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.1e-06   26.9   4.9    5.2e-06   26.2   4.9    1.4  1  Snf7           Snf7
  ------ inclusion threshold ------
      0.033   14.2   0.9      0.033   14.2   0.9    2.4  2  TMF_DNA_bd     TATA element modulatory factor 1 DNA binding
      0.038   12.8   0.1      0.044   12.6   0.1    1.1  1  RHSP           Retrotransposon hot spot protein
      0.057   13.7   1.2       0.39   11.0   0.2    2.5  2  RVT_N          N-terminal domain of reverse transcriptase
      0.067   13.2   4.6       0.87    9.6   4.6    2.2  1  Baculo_PEP_C   Baculovirus polyhedron envelope protein, PEP, 
       0.15   12.1   0.5       0.15   12.1   0.5    2.5  3  BRE1           BRE1 E3 ubiquitin ligase
       0.18   11.9   1.4        2.6    8.2   1.4    2.2  1  V-ATPase_H_C   V-ATPase subunit H
       0.19   12.2   2.1        2.9    8.4   1.8    2.3  2  GPS2_interact  G-protein pathway suppressor 2-interacting dom


Domain annotation for each model (and alignments):
>> Snf7  Snf7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   4.9   2.3e-09   5.2e-06       3     171 ..      38     203 ..      36     205 .. 0.92

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 2.3e-09
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCT CS
        Snf7   3 irsLrkaerkldkkqeslekkikkleaelkklakkgnkdralllLKqkkryekqldqldnqlanleqvslaienlksnkevlnamkqgakamkamnkkv 101
                 i++L++++ kld+ + +l ++ +kl + + +  ++ ++ + ++l K++++ +k  + l+n ++ leq+ l + + ++  +++ +   +   mk+ ++ +
  EPA05672.1  38 IKKLQTQIAKLDSMITKLNERDSKLFKRIVEATQSHDMNTSRVLSKELVEVRKTTKILSNARIALEQIELRLTTYHDLGDTVVTIMPTIGLMKNLKSSL 136
                 689********************************************************************************************9988 PP

                 CCHHHHHHHHHHHHHH.HHHTCHHHHHHHHHTT-.GGTTHHHHHHHHHHHHHHHHHCSH.HHHHHHHTXXXS CS
        Snf7 102 didkidklmdeiedqm.ekaeeisEalsrsldda.deedEeeleaeLdaLeqelgdeelldesvklpevPse 171
                       k m +  +++ ++a+++   + +s+ +  +  ++e ++ e ++++qe ++  +++ ++  p+ P +
  EPA05672.1 137 L-----KFMPNADQEInQMAQMLGGFMTDSFSSDaTFGMDETTNSESEKILQEATAVAESSVGNRFPSTPAT 203
                 7.....78877765551567899999***998877999***************9999988999999999987 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.9   1.5e-05     0.033      33      70 ..      36      73 ..      32      77 .. 0.91
   2 ?   -2.9   0.1       3.2   7.1e+03      42      52 ..     175     185 ..     172     193 .. 0.53

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.5e-05
  TMF_DNA_bd 33 ntikkLrkknkelekeikelkkkleklekeleeleerl 70
                n ikkL+ ++++l++ i++l+++ +kl k + e ++++
  EPA05672.1 36 NGIKKLQTQIAKLDSMITKLNERDSKLFKRIVEATQSH 73
                77*************************99999999876 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.2
  TMF_DNA_bd  42 nkelekeikel 52 
                 n+e+ek ++e 
  EPA05672.1 175 NSESEKILQEA 185
                 45555544443 PP

>> RHSP  Retrotransposon hot spot protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1     2e-05     0.044     291     364 ..      18      92 ..       3     140 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2e-05
        RHSP 291 qeikgrikkvGPllrqile.eesykrrvakieeavdeissvdkesyakvlqtaaeWetdkvserlarvvrvkken 364
                  +i++ ik  GPl  +il+  ++ ++++ak++ ++ ++ + d + + +++++++  + +        +v v+k  
  EPA05672.1  18 DKINDTIKPKGPLKPKILNgIKKLQTQIAKLDSMITKLNERDSKLFKRIVEATQSHDMNTSRVLSKELVEVRKTT 92 
                 589****************8899***********************99999888877776655556688888875 PP

>> RVT_N  N-terminal domain of reverse transcriptase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.37   8.3e+02      11      22 ..      36      47 ..      32      53 .. 0.79
   2 ?   11.0   0.2   0.00018      0.39       9      43 ..      55      89 ..      51     104 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.37
       RVT_N 11 kkVfkLqkrIyk 22
                + ++kLq++I+k
  EPA05672.1 36 NGIKKLQTQIAK 47
                568999999988 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00018
       RVT_N  9 vekkVfkLqkrIykAsqegdikkvkkLqklLtkSl 43
                ++++  kL krI+ A+q+ d+++ + L k L++  
  EPA05672.1 55 LNERDSKLFKRIVEATQSHDMNTSRVLSKELVEVR 89
                5566689*********************9998754 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   4.6   0.00039      0.87      21     133 ..      34     172 ..      30     183 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00039
  Baculo_PEP_C  21 vLnairlqnvqilaqlatlldaietqLnalsedlksllaeldt..................rldtlltnLtdalnalq..........dtlrneLtn 89 
                   +Ln i+ +++qi a+l +++++++++ ++l +++ ++ ++ d                    l+++  +L++     +          dt+ + + +
    EPA05672.1  34 ILNGIKKLQTQI-AKLDSMITKLNERDSKLFKRIVEATQSHDMntsrvlskelvevrkttkILSNARIALEQI----ElrlttyhdlgDTVVTIMPT 125
                   89**********.************999999999988777666668888888885554444222222223322....23333665555666666655 PP

  Baculo_PEP_C  90 lnsiltnLlss....vtNinstLnnllqalnnldlgalsqeledaldt 133
                   +   + nL ss    ++N  + +n + q l ++ ++++s+ ++  +d+
    EPA05672.1 126 IG-LMKNLKSSllkfMPNADQEINQMAQMLGGFMTDSFSSDATFGMDE 172
                   42.344444442222688888888888888888888777776655555 PP

>> BRE1  BRE1 E3 ubiquitin ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       2.2     5e+03       7      17 ..       3      13 ..       1      21 [. 0.68
   2 ?   12.1   0.5   6.8e-05      0.15      57      93 ..      34      70 ..      30      72 .. 0.88
   3 ?   -1.6   0.1       1.3   2.9e+03       9      33 ..      82     106 ..      79     111 .. 0.52

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.2
        BRE1  7 klekafeelse 17
                +l++ ++++++
  EPA05672.1  3 NLQNKWNKQQK 13
                56666666654 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 6.8e-05
        BRE1 57 lenelkkLnkllsKsselieqLkelekefvrklkele 93
                + n +kkL+++++K  ++i++L+e+++++ +++ e+ 
  EPA05672.1 34 ILNGIKKLQTQIAKLDSMITKLNERDSKLFKRIVEAT 70
                67889*******************9999999888875 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1.3
        BRE1   9 ekafeelseqlskkvkeltileekk 33 
                 +k+  e++++++ + +   +le+  
  EPA05672.1  82 SKELVEVRKTTKILSNARIALEQIE 106
                 4444455555555555555555555 PP

>> V-ATPase_H_C  V-ATPase subunit H
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   1.4    0.0011       2.6      33      83 ..      52     104 ..      48     159 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0011
  V-ATPase_H_C  33 aekleeknfkllkkLiklleeskdktvlavalnDigelvkl...lpegkkvlek 83 
                   ++kl+e++ kl+k++++   +s+d ++  v+ +++ e+ k    l++ +  le+
    EPA05672.1  52 ITKLNERDSKLFKRIVEAT-QSHDMNTSRVLSKELVEVRKTtkiLSNARIALEQ 104
                   6899999999999999999.4777666666666666554440004444444444 PP

>> GPS2_interact  G-protein pathway suppressor 2-interacting domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   1.8    0.0013       2.9      28      67 ..      30      69 ..      12      93 .. 0.76
   2 ?    1.6   0.0      0.17   3.9e+02      26      48 ..     130     152 ..     125     155 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0013
  GPS2_interact 28 sKdeLlqnidkvDREiakveqqiskLkkkqkeleeeaakp 67
                    K ++l+ i k    iak ++ i kL ++  +l ++ ++ 
     EPA05672.1 30 LKPKILNGIKKLQTQIAKLDSMITKLNERDSKLFKRIVEA 69
                   57889999*******************9999886655444 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.17
  GPS2_interact  26 rlsKdeLlqnidkvDREiakveq 48 
                    +  K  Ll+ +   D Ei ++ q
     EPA05672.1 130 KNLKSSLLKFMPNADQEINQMAQ 152
                    667999************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1051  (0.0586201); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 1435.78
//
Query:       EPA05673.1  [L=247]
Description: hypothetical protein BG20_I0290 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.019   14.2   4.0      0.026   13.8   0.8    2.0  2  GlcNAc_2-epim  N-acylglucosamine 2-epimerase (GlcNAc 2-epimer
      0.042   14.2   3.5        3.8    8.0   0.3    3.0  3  DUF1957        Domain of unknown function (DUF1957)
       0.32   10.4  11.6       0.42   10.0   2.1    2.3  2  DDE_Tnp_IS66   Transposase IS66 family
       0.97   10.4  10.9        1.8    9.5   1.9    3.0  2  ERp29          Endoplasmic reticulum protein ERp29, C-termina
        1.4    9.2   6.5          2    8.7   0.2    2.6  2  DUF4695        Domain of unknown function (DUF4695)
        5.4    7.6  10.6        2.4    8.8   0.6    3.6  2  YtxH           YtxH-like protein
        7.9    6.5  13.9        1.4    9.0   1.5    2.7  3  Prp18          Prp18 domain
        7.9    7.0  18.7       0.72   10.3   0.2    3.9  4  Wbp11          WW domain binding protein 11


Domain annotation for each model (and alignments):
>> GlcNAc_2-epim  N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.8   1.2e-05     0.026     114     180 ..      24      91 ..       6     105 .. 0.73
   2 ?    1.4   0.1     0.068   1.5e+02      97     134 ..     181     218 ..     175     228 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.2e-05
                    HHTEETTT.TEE--EE-TTSS-BEEHHHHHHHHHHHHHHHHTT-BTHHHHHHHHHHHHHTTTTGGGGT CS
  GlcNAc_2-epim 114 khlweeka.glvkeesdkefsklrgsnpnMhlleAmLalaeatgdkeyleraeeiaelvisefadaes 180
                    k+ +++ + ++ +++sdk+ +  r    +M++le  La ++++  k+y   +++i++ v +++ +++s
     EPA05673.1  24 KQAQNQLEnQINQDSSDKAKQLFREGTQQMKALEESLANNDVESAKKYFLSTMRIFKEVSQQLTNNKS 91 
                    33333333034445555555555877888*****************************9987776654 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.068
                    T-TTHHHHHHHHHHHHHHHTEETTTTEE--EE-TTSS- CS
  GlcNAc_2-epim  97 geeeakdlldetlavlekhlweekaglvkeesdkefsk 134
                     + +akd +++ l++l++ +++ k +++ e+  ++ + 
     EPA05673.1 181 EQSRAKDYAQKYLEQLDRLIENAKNQGLSENIIQKLES 218
                    46788999999999999999999999999987766655 PP

>> DUF1957  Domain of unknown function (DUF1957)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1    0.0077        17      49      96 ..      36      82 ..      30      87 .. 0.80
   2 ?    0.8   0.0      0.28   6.3e+02      53      87 ..      66     100 ..      65     106 .. 0.77
   3 ?    8.0   0.3    0.0017       3.8      52      90 ..     182     220 ..     170     229 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0077
                TSSHHHHHHHHHHHHHHHHHHHHHHHHS---HHHHHHHHHHS---S-- CS
     DUF1957 49 gtaveYAekrikehlerftelyealesgeideelleeleekdniFpei 96
                +   + A++ ++e ++++++l e+l++++++ +  +   ++  iF+e+
  EPA05673.1 36 QDSSDKAKQLFREGTQQMKALEESLANNDVESA-KKYFLSTMRIFKEV 82
                556799***********************8876.55555666666665 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.28
                 HHHHHHHHHHHHHHHHHHHHHHHS---HHHHHHHH CS
     DUF1957  53 eYAekrikehlerftelyealesgeideelleele 87 
                 e A+k + + ++ f+e+ ++l++++  ++ +++l+
  EPA05673.1  66 ESAKKYFLSTMRIFKEVSQQLTNNKSPQTEMATLK 100
                 5688889999999********99987666566555 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0017
                 HHHHHHHHHHHHHHHHHHHHHHHHS---HHHHHHHHHHS CS
     DUF1957  52 veYAekrikehlerftelyealesgeideelleeleekd 90 
                 +  A++ +++ le++++l e+++++ ++e+++++le+++
  EPA05673.1 182 QSRAKDYAQKYLEQLDRLIENAKNQGLSENIIQKLESAR 220
                 455777788999************************965 PP

>> DDE_Tnp_IS66  Transposase IS66 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   2.2    0.0045        10     165     247 ..      37     116 ..      21     119 .. 0.82
   2 ?   10.0   2.1   0.00019      0.42     162     243 ..     144     225 ..     138     246 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0045
  DDE_Tnp_IS66 165 kksqaaaealar.igklyaiereareaeaeerlalrqeesrpllaeleawleeqlkkvlpksklgkairyllkrweallrfled 247
                   + s++a++  ++  ++++a+e+++    a++  + ++++    ++ ++++ ++  ++++p+++++++ +++ +  ++llr  ++
    EPA05673.1  37 DSSDKAKQLFREgTQQMKALEESL----ANNDVESAKKYFLSTMRIFKEVSQQLTNNKSPQTEMATLKATTEDPSADLLRLQDY 116
                   2388999999999999999**999....567888888888889999999888888999********999999999999998776 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00019
  DDE_Tnp_IS66 162 eakkksqaaaealarigklyaiereareaeaeerlalrqeesrpllaeleawleeqlkkvlpksklgkairyllkrweallr 243
                   +++ ++++ ++al++ig++++i+ +++++ +e + +++q+++++  +++ ++l+   ++++++   ++ i++l + +e+l  
    EPA05673.1 144 KKQIRAKQFDDALQTIGQIKQITIDLNNKIREYASQQEQSRAKDYAQKYLEQLDRLIENAKNQGLSENIIQKLESARESLSS 225
                   3333488999***********9999985556777777777777777777777777777888888888899998888888765 PP

>> ERp29  Endoplasmic reticulum protein ERp29, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   1.8     0.024        55      17      59 ..      42      84 ..      22     109 .. 0.70
   2 ?    9.5   1.9   0.00079       1.8       4      59 ..     150     204 ..     148     226 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.024
       ERp29 17 akaereelleeakkaaeklksekekkaaeyYvkvmekiaekge 59
                ak+  +e  +++k++ e+l++++ ++a +y+++ m+ ++e ++
  EPA05673.1 42 AKQLFREGTQQMKALEESLANNDVESAKKYFLSTMRIFKEVSQ 84
                2444555667777777777788888999999999987777654 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00079
       ERp29   4 eeldelaaefvaaakaereelleeakkaaeklksekekkaaeyYvkvmekiaekge 59 
                 +++d+ ++ + + + +   +l ++++++a++ +++++k++a+ Y++ +++++e+++
  EPA05673.1 150 KQFDDALQTIGQIK-QITIDLNNKIREYASQQEQSRAKDYAQKYLEQLDRLIENAK 204
                 56777666655544.77788999****************************99986 PP

>> DUF4695  Domain of unknown function (DUF4695)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.2   0.00089         2      58     100 ..      57     100 ..      50     109 .. 0.79
   2 ?    2.8   1.0     0.058   1.3e+02      58      90 ..     174     206 ..     144     228 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00089
     DUF4695  58 deGvskeeeekarksllqsleslrrsakkldlqrg.slkssklk 100
                 +e  ++++ e a+k +l +++ +++ +++l +++  + + + lk
  EPA05673.1  57 EESLANNDVESAKKYFLSTMRIFKEVSQQLTNNKSpQTEMATLK 100
                 678899999*********************99975234444455 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.058
     DUF4695  58 deGvskeeeekarksllqsleslrrsakkldlq 90 
                  e +s++e+ +a+   ++ le l r  ++ ++q
  EPA05673.1 174 REYASQQEQSRAKDYAQKYLEQLDRLIENAKNQ 206
                 466899999999998888888887766655544 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   9.0       1.8   4.1e+03      29      74 ..     161     203 ..      17     204 .. 0.77
   2 ?    8.8   0.6    0.0011       2.4      28      65 ..     183     225 ..     171     238 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.8
        YtxH  29 dlkekaddlkekakelleeakeka....kekaedlkekvkekadelkekv 74 
                 ++k+ + dl +k+ e+       a    +++a+d+++k  e+ d+l e++
  EPA05673.1 161 QIKQITIDLNNKIREY-------AsqqeQSRAKDYAQKYLEQLDRLIENA 203
                 3333333444444333.......144446667777777777777776655 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0011
        YtxH  28 kdlkekaddlkekakelleeakeka.....kekaedlkekvke 65 
                  ++k++a+++ e++++l+e+ak+++      +k e ++e++++
  EPA05673.1 183 SRAKDYAQKYLEQLDRLIENAKNQGlseniIQKLESARESLSS 225
                 578999***************9999865553344444444444 PP

>> Prp18  Prp18 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   3.2     0.032        71       9      56 ..      20      67 ..      16      91 .. 0.76
   2 ?   -0.4   0.1      0.47   1.1e+03      29      48 ..     107     126 ..      69     162 .. 0.45
   3 ?    9.0   1.5   0.00061       1.4       9      65 ..     163     219 ..     158     227 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.032
       Prp18  9 kewekeleerseeekksvegkkesatlkqtkedlkpLlkklkkkklee 56
                 + +k+ +++ e++ ++ ++ k+++ +++ ++++k L ++l ++++e+
  EPA05673.1 20 LKIAKQAQNQLENQINQDSSDKAKQLFREGTQQMKALEESLANNDVES 67
                45566666777777777888999999*****************99986 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.47
       Prp18  29 kkesatlkqtkedlkpLlkk 48 
                 +++  +l++ ++++k++ kk
  EPA05673.1 107 SADLLRLQDYSDNIKTIAKK 126
                 23333344444444444444 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.00061
       Prp18   9 kewekeleerseeekksvegkkesatlkqtkedlkpLlkklkkkkleedileklvei 65 
                 k+   +l+++ +e  +++e+++++   ++  e+l +L+++ k++ l+e+i++kl++ 
  EPA05673.1 163 KQITIDLNNKIREYASQQEQSRAKDYAQKYLEQLDRLIENAKNQGLSENIIQKLESA 219
                 66667888888888888888888888899999*********************9875 PP

>> Wbp11  WW domain binding protein 11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.7     0.082   1.8e+02      34      74 ..      22      61 ..      20      63 .. 0.74
   2 ?    5.0   1.9     0.014        32      14      70 ..      40     100 ..      35     121 .. 0.73
   3 ?    1.1   4.8      0.24   5.3e+02      22      73 ..     171     223 ..     143     225 .. 0.75
   4 ?   10.3   0.2   0.00032      0.72      27      54 ..     217     244 ..     213     246 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.082
       Wbp11 34 lakkdpdeleeeiekLeelessgkldaadkkklekLekelk 74
                +ak+  ++le++i++ ++ +++++l ++ +++++ Le+ l+
  EPA05673.1 22 IAKQAQNQLENQINQ-DSSDKAKQLFREGTQQMKALEESLA 61
                566667788888877.4677777888889999999998875 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.014
       Wbp11  14 qrkkelkKnKkerqkareaklakkdpdelee....eiekLeelessgkldaadkkklekLe 70 
                 +++k+l +  ++++ka e+ la+ d+++ ++     ++  +e++++ + ++  + +++ L+
  EPA05673.1  40 DKAKQLFREGTQQMKALEESLANNDVESAKKyflsTMRIFKEVSQQLTNNKSPQTEMATLK 100
                 799***********************99776111133334444444455555555555555 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.24
       Wbp11  22 nKkerqkareaklakkdp.deleeeiekLeelessgkldaadkkklekLekel 73 
                 nK +  + ++++ + kd  ++  e++++L e ++++ l+++  +kle  ++ l
  EPA05673.1 171 NKIREYASQQEQSRAKDYaQKYLEQLDRLIENAKNQGLSENIIQKLESARESL 223
                 45555555556555555415677888888888888888888888888777665 PP

  == domain 4  score: 10.3 bits;  conditional E-value: 0.00032
       Wbp11  27 qkareaklakkdpdeleeeiekLeeles 54 
                 + are+  ++ dp+e+ ++i+kL +l++
  EPA05673.1 217 ESARESLSSTTDPHEIINQIKKLYQLKN 244
                 57899999***************87765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2947  (0.164371); expected 358.6 (0.02)
Passed bias filter:                      652  (0.0363657); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 1620.89
//
Query:       EPA05674.1  [L=37]
Description: hypothetical protein BG20_I0331 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.47
# Mc/sec: 235.89
//
Query:       EPA05675.1  [L=222]
Description: putative protein ExsB [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-47  162.3   0.0    1.2e-47  162.1   0.0    1.0  1  QueC             Queuosine biosynthesis protein QueC
    0.00015   21.2   0.0    0.00018   20.9   0.0    1.1  1  Arginosuc_synth  Arginosuccinate synthase
    0.00044   20.0   0.0     0.0006   19.6   0.0    1.1  1  Asn_synthase     Asparagine synthase
     0.0071   15.5   0.0     0.0092   15.1   0.0    1.2  1  NAD_synthase     NAD synthase
  ------ inclusion threshold ------
       0.05   13.4   0.0      0.082   12.7   0.0    1.4  1  ATP_bind_3       PP-loop family


Domain annotation for each model (and alignments):
>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.1   0.0   3.4e-51   1.2e-47       1     209 [.       3     214 ..       3     215 .. 0.91

  Alignments for each domain:
  == domain 1  score: 162.1 bits;  conditional E-value: 3.4e-51
                 EEEEE--SSHHHHHHHHHHHHH-SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-GGGGGGS..CGGG-----------...--------TTH CS
        QueC   1 kavvllSGGlDSttvlalakkegkevealtfdYgqrhkkeleaakkiakelgveehkildldllkelg..gsaLtdeeievpkeeleeeelpntfVpaR 97 
                 kav+++SGG+DS ++++  +k+ + ++ ++f+Ygq++++e+++ak++ak+lg+++hki+d+ ++kel   ++ Lt+++ ++p+     +   +  Vp R
  EPA05675.1   3 KAVIVFSGGIDS-VCMVSHLKSKYDLYGISFSYGQKANREINSAKAFAKKLGLKQHKIIDIGFMKELYgdSNVLTSSKRKIPS-----AFDYSIVVPIR 95 
                 79*********9.677777777899******************************************8445668888888998.....4456789**** PP

                 HHHHHHHHHHHHHHHT-SEEEE---S-STT--GGGSHHHHHHHHHHHHHH........HTS--EEE-TTTT.--HHHHHHHHHH.TTHHHHH-B-STTS CS
        QueC  98 NliflslaasyaealgaeaiiiGvneedfsgYPDcrdefvkalnkalnlg........edkkieieaPlid.lsKaeivklgke.lgvpleetlsCYeg 186
                 N++fls+a+++a++l+a+ +++G+++ d + YPDcr+ f k+l++a nlg          k+i+i  P  + +sK++ +k+g + l+  + +t+sCY++
  EPA05675.1  96 NAVFLSIASAWAYTLNASLVAYGAHTGD-KHYPDCRPIFTKKLESAFNLGeidginsgLRKNIQIWSPYREgISKSDLLKIGFKmLDDSIFKTWSCYSN 193
                 ****************************.89************************999789*******97549********9762679999******** PP

                 .-BTTTTSSSHHHHHHHHHHHHH CS
        QueC 187 eeegkaCgeCdaCalRkkgfeea 209
                   ++ +Cg C++C+ Rk++f++a
  EPA05675.1 194 --QKFHCGVCESCNNRKTAFQKA 214
                 ..557***************986 PP

>> Arginosuc_synth  Arginosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0     5e-08   0.00018       1      59 [.       5      62 ..       5     123 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 5e-08
  Arginosuc_synth  1 vLaysGGlDtsviikllkeklgeeviavavdvGqe.eedldevkekalklgavksvvvDa 59
                     v+ +sGG+D  ++++ lk k+  +   ++   Gq+ + +++++k+ a+klg +++ ++D+
       EPA05675.1  5 VIVFSGGIDSVCMVSHLKSKY--DLYGISFSYGQKaNREINSAKAFAKKLGLKQHKIIDI 62
                     678*****************9..6677777889983469********************7 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   1.7e-07    0.0006      22      77 ..       6      59 ..       2      62 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.7e-07
  Asn_synthase 22 alLSGGlDSSliaalaarqsksplktFsigfeekgsdeakyakevaehlgtehtel 77
                  +++SGG+DS   ++ ++ + +    +Fs g   k++ e+  ak+ a++lg++++++
    EPA05675.1  6 IVFSGGIDSVCMVSHLKSKYDLYGISFSYGQ--KANREINSAKAFAKKLGLKQHKI 59
                  679******9999999998876777777777..*******************9987 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.6e-06    0.0092      19      88 ..       2      69 ..       1     103 [. 0.82

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.6e-06
                  SEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE.---HHHHHHH CS
  NAD_synthase 19 kgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievkt.idikpivraf 88
                  k++v+  SGG+DS    ++  ++  k    ++ +   ++ +++++ a+a+a++lg++ ++ idi  + + +
    EPA05675.1  2 KKAVIVFSGGIDSV---CMVSHLKSKYDLYGISFSYGQKANREINSAKAFAKKLGLKQHKiIDIGFMKELY 69
                  789999*******6...344455567799******99******************9987626776655555 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.3e-05     0.082       2      59 ..       4      54 ..       3      69 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.3e-05
                EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT- CS
  ATP_bind_3  2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklni 59
                +++ +SgG+DS++++  l+++ +       +  + ++  +++++e +  k+++kkl++
  EPA05675.1  4 AVIVFSGGIDSVCMVSHLKSKYD-------LYGISFSYGQKANREINSAKAFAKKLGL 54
                6899***********99998855.......3444444455666666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1539.37
//
Query:       EPA05676.1  [L=131]
Description: hypothetical protein BG20_I0297 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 846.74
//
Query:       EPA05677.1  [L=304]
Description: putative transcription initiation factor IIB [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      7e-33  112.5   6.2    8.5e-16   57.8   0.4    2.3  2  TFIIB            Transcription factor TFIIB repeat
    8.1e-10   38.1   0.4    1.4e-09   37.3   0.4    1.4  1  TF_Zn_Ribbon     TFIIB zinc-binding
     0.0067   16.2   0.3      0.075   12.8   0.1    2.0  2  Cyclin_N         Cyclin, N-terminal domain
     0.0083   15.6   0.0      0.024   14.2   0.0    1.8  1  Sigma70_r4       Sigma-70, region 4
     0.0086   16.0   0.2       0.33   10.9   0.0    2.8  3  HTH_11           HTH domain
  ------ inclusion threshold ------
      0.016   15.8   0.0      0.046   14.3   0.0    1.9  1  RPA_interact_C   Replication protein A interacting C-terminal
      0.016   15.0   0.0       0.19   11.6   0.0    2.3  2  HTH_AsnC-type    AsnC-type helix-turn-helix domain
      0.021   14.5   0.2       0.28   10.9   0.0    2.4  2  Sigma70_r4_2     Sigma-70, region 4
      0.026   14.2   1.9      0.068   12.9   0.1    2.2  2  zinc_ribbon_2    zinc-ribbon domain
      0.032   14.1   0.3        0.5   10.3   0.1    2.5  2  zf-FPG_IleRS     Zinc finger found in FPG and IleRS
      0.055   13.5   0.2        1.4    9.0   0.0    2.8  3  Phage_terminase  Phage terminase small subunit
        0.1   11.8   0.1       0.16   11.2   0.1    1.3  1  Baculo_ME53      Baculoviridae ME53
       0.11   12.6   0.1       0.21   11.6   0.1    1.5  1  RB_B             Retinoblastoma-associated protein B domain
       0.17   12.0   1.4       0.49   10.6   1.4    1.8  1  zf-piccolo       Piccolo Zn-finger
        0.2   11.8   0.3        8.2    6.5   0.0    2.3  2  Cyclin_C         Cyclin, C-terminal domain
       0.22   11.4   1.8       0.54   10.1   0.0    2.5  2  HTH_23           Homeodomain-like domain
       0.24   11.6   1.4       0.44   10.7   1.4    1.4  1  Auto_anti-p27    Sjogren's syndrome/scleroderma autoantigen 1
       0.26   11.0   1.1       0.55   10.0   1.1    1.5  1  A2L_zn_ribbon    A2L zinc ribbon domain
       0.27   10.7   1.4        1.4    8.5   1.4    2.1  1  zf-ribbon_3      zinc-ribbon domain
        1.7    8.4   5.5       0.76    9.5   0.3    2.6  2  zf-CCHC_5        GAG-polyprotein viral zinc-finger


Domain annotation for each model (and alignments):
>> TFIIB  Transcription factor TFIIB repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.8   0.4   9.5e-19   8.5e-16       2      71 .]     128     197 ..     127     197 .. 0.96
   2 !   57.6   0.9   1.1e-18   9.9e-16       2      71 .]     222     291 ..     221     291 .. 0.98

  Alignments for each domain:
  == domain 1  score: 57.8 bits;  conditional E-value: 9.5e-19
                 HHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
       TFIIB   2 krfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                 +r+ d+l +++ V ++A +++++al+++++ Grs  +++A++ly Acr  e+ r +k++ + ++++ k i
  EPA05677.1 128 NRLKDKLAISDAVIEKAAYIYRKALDKGLVRGRSISALMASALYAACRDTETPRNLKDVEQAANIKRKDI 197
                 68889************************************************************99876 PP

  == domain 2  score: 57.6 bits;  conditional E-value: 1.1e-18
                 HHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
       TFIIB   2 krfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                  r+a+++++ ek ++ A++++k+a e++v +G+ p g+aAA+ly+ c k+++ +tq++i++ ++V+e+ti
  EPA05677.1 222 ARIASRIGIAEKTKRYAVNVLKQAQENEVSAGKDPMGLAAAALYLSCVKNGEDKTQRDIAEAANVTEVTI 291
                 799*****************************************************************98 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.4   1.6e-12   1.4e-09       3      43 .]      12      52 ..      11      52 .. 0.98

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 1.6e-12
                  ETTTTCEECHEETSTTCEEESSSSBEEEECCCCCCCHHHHH CS
  TF_Zn_Ribbon  3 CPnCgstnlveDpergelvCtdCGlVlednsidegpewref 43
                  CP C   +lv+D+e+ge++C++CG V+ +   ++gpewr f
    EPA05677.1 12 CPRCAQGKLVTDNESGEMFCSKCGFVMSEKLQESGPEWRSF 52
                  ******99*******************************87 PP

>> Cyclin_N  Cyclin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.1   8.3e-05     0.075      30     126 ..     120     212 ..      94     213 .. 0.85
   2 ?    1.4   0.0      0.27   2.4e+02      39      85 ..     222     268 ..     215     294 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.3e-05
                 HHHHHHHHHHHHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHHHSSS---HHHHHHHTTTSS-HHHHHHHHHHHHHHTTT-- CS
    Cyclin_N  30 mRailidwlvevaekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAaKveeisppkledlvyitdeafteeeilemErliLetLnfdl 126
                 +R+ + + l ++  k+ ++  ++  a+ ++ + l k  v+ + +  ++a++L+ A++  e+ p +l+d+  +++  +++++i +  rl++++L+ ++
  EPA05677.1 120 FRQ-AFSELNRLKDKLAISDAVIEKAAYIYRKALDKGLVRGRSISALMASALYAACRDTET-PRNLKDVEQAAN--IKRKDIARCYRLLIKELDLKM 212
                 444.44448899999999999*************************************999.99****999965..9**************998765 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.27
                 HHHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHH CS
    Cyclin_N  39 vevaekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAa 85 
                  ++a++  + ++t   avn+l +  +++    ++   ++a++L+l++
  EPA05677.1 222 ARIASRIGIAEKTKRYAVNVLKQAQENEVSAGKDPMGLAAAALYLSC 268
                 56777777888888899999999999888888899999*******98 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   2.7e-05     0.024      17      42 ..     268     296 ..     261     302 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.7e-05
                 H...TTT--HHHHHHHHTS-HHHHHHHHH CS
  Sigma70_r4  17 f...geglTleEIgerlgiSrerVrqiek 42 
                     ge+ T+ +I+e  ++++ ++r + k
  EPA05677.1 268 CvknGEDKTQRDIAEAANVTEVTIRNRYK 296
                 34479*********************987 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.35   3.1e+02      19      34 ..     128     143 ..     126     145 .. 0.87
   2 ?   -1.9   0.0       3.6   3.3e+03       6      19 ..     239     253 ..     235     254 .. 0.80
   3 !   10.9   0.0   0.00037      0.33      14      42 ..     273     301 ..     265     303 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.35
      HTH_11  19 eeLAeeLnvSrrtvrr 34 
                 ++L+++L +S +++ +
  EPA05677.1 128 NRLKDKLAISDAVIEK 143
                 689********99966 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.6
      HTH_11   6 lelLleargp.isge 19 
                 +  L++a+++ +s+ 
  EPA05677.1 239 VNVLKQAQENeVSAG 253
                 667999999999985 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00037
      HTH_11  14 gpisgeeLAeeLnvSrrtvrrdIkaLeel 42 
                 ++ +  ++Ae  nv++ t+r++ k L+++
  EPA05677.1 273 EDKTQRDIAEAANVTEVTIRNRYKGLRDS 301
                 5568899***************9999876 PP

>> RPA_interact_C  Replication protein A interacting C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   5.1e-05     0.046       1      28 [.      11      41 ..      11      84 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.1e-05
  RPA_interact_C  1 lCPvCkkrklkets..evifCe.Cglrlets 28
                    lCP C ++kl  ++    +fC+ Cg+ ++ +
      EPA05677.1 11 LCPRCAQGKLVTDNesGEMFCSkCGFVMSEK 41
                    6*********99763466***99***99885 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.65   5.9e+02      21      33 ..     222     234 ..     216     239 .. 0.88
   2 ?   11.6   0.0   0.00021      0.19      19      42 .]     276     299 ..     267     299 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.65
  HTH_AsnC-type  21 aeLAervGlSest 33 
                    a++A r+G++e t
     EPA05677.1 222 ARIASRIGIAEKT 234
                    89******99876 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00021
  HTH_AsnC-type  19 syaeLAervGlSestvlrRvrrLe 42 
                    + +++Ae+ +++e t+++R++ L+
     EPA05677.1 276 TQRDIAEAANVTEVTIRNRYKGLR 299
                    689*****************9875 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1      0.48   4.3e+02      30      42 ..     222     234 ..     221     239 .. 0.85
   2 ?   10.9   0.0   0.00031      0.28      25      47 ..     273     295 ..     270     299 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.48
                   HHHHHHHT--HHH CS
  Sigma70_r4_2  30 kEIAellgisegt 42 
                   + IA+++gi e+t
    EPA05677.1 222 ARIASRIGIAEKT 234
                   67*********98 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00031
                   S---HHHHHHHHT--HHHHHHHH CS
  Sigma70_r4_2  25 eglsykEIAellgisegtVksrl 47 
                   e++++++IAe  +++e+t+++r+
    EPA05677.1 273 EDKTQRDIAEAANVTEVTIRNRY 295
                   789******************98 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.2       0.8   7.1e+02      16      19 ..      12      15 ..       9      18 .. 0.72
   2 ?   12.9   0.1   7.5e-05     0.068       8      21 ..      23      36 ..      22      38 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.8
  zinc_ribbon_2 16 CpyC 19
                   Cp+C
     EPA05677.1 12 CPRC 15
                   6666 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 7.5e-05
  zinc_ribbon_2  8 elqdnakFCpyCGt 21
                    ++ ++ FC++CG+
     EPA05677.1 23 DNESGEMFCSKCGF 36
                   5899*********7 PP

>> zf-FPG_IleRS  Zinc finger found in FPG and IleRS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00055       0.5      14      29 ..       2      17 ..       1      18 [. 0.84
   2 ?    1.3   0.0      0.36   3.3e+02      16      27 ..      23      34 ..      19      34 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00055
                  EECTTEEEEE-TTTT. CS
  zf-FPG_IleRS 14 vgqagrstyfCprCqk 29
                  v++a + +++CprC++
    EPA05677.1  2 VSKAKNPKELCPRCAQ 17
                  67788899******96 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.36
                  CTTEEEEE-TTT CS
  zf-FPG_IleRS 16 qagrstyfCprC 27
                   ++ + +fC  C
    EPA05677.1 23 DNESGEMFCSKC 34
                  577899****99 PP

>> Phage_terminase  Phage terminase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0       0.5   4.5e+02      18      30 ..     187     199 ..     185     207 .. 0.87
   2 ?   -2.4   0.0       5.4   4.9e+03      27      38 ..     223     234 ..     217     237 .. 0.80
   3 ?    9.0   0.0    0.0016       1.4      19      41 ..     271     293 ..     254     297 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.5
  Phage_terminase  18 EsggtlklkdIAk 30 
                      E++ ++k kdIA 
       EPA05677.1 187 EQAANIKRKDIAR 199
                      7899*******97 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.4
  Phage_terminase  27 dIAkvLdvsest 38 
                       IA  ++++e+t
       EPA05677.1 223 RIASRIGIAEKT 234
                      699999999998 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0016
  Phage_terminase  19 sggtlklkdIAkvLdvsestvrk 41 
                      +g  +  +dIA+  +v e t+r+
       EPA05677.1 271 NGEDKTQRDIAEAANVTEVTIRN 293
                      5778999**************98 PP

>> Baculo_ME53  Baculoviridae ME53
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00018      0.16     262     295 ..       4      39 ..       1      53 [. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00018
  Baculo_ME53 262 lkkedkeycklckktklytkn..PvlscskcGftnv 295
                  + k+ ke c  c ++kl+t+n    ++cskcGf   
   EPA05677.1   4 KAKNPKELCPRCAQGKLVTDNesGEMFCSKCGFVMS 39 
                  567889************77622569******9765 PP

>> RB_B  Retinoblastoma-associated protein B domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00024      0.21      11      91 ..     121     199 ..     116     250 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00024
        RB_B  11 klaavrlrdLcerLklsselrekiwtlfehvlveetellkdRhlDqillcavYvvakvtkeelsFkeiikaYrkqpqassk 91 
                 + a + l++L ++L +s+ + ek+  + +++l  ++ l++ R +  ++ +a+Y+ ++ t++ +++k++ +a + + +  ++
  EPA05677.1 121 RQAFSELNRLKDKLAISDAVIEKAAYIYRKAL--DKGLVRGRSISALMASALYAACRDTETPRNLKDVEQAANIKRKDIAR 199
                 6788999***********99999888888887..568********************997666666665554444333333 PP

>> zf-piccolo  Piccolo Zn-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.4   0.00055      0.49      28      50 ..      28      51 ..      10      56 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00055
  zf-piccolo 28 kqvCnlCGFnptphlte.kkeWlc 50
                ++ C++CGF ++ +l+e + eW +
  EPA05677.1 28 EMFCSKCGFVMSEKLQEsGPEWRS 51
                578**************899**76 PP

>> Cyclin_C  Cyclin, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0    0.0091       8.2      45      90 ..     163     208 ..     152     226 .. 0.86
   2 ?    3.0   0.0      0.12   1.1e+02      47      80 ..     259     292 ..     251     302 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0091
                 HHHHHHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHHHHHHHH CS
    Cyclin_C  45 SliAaaalllarstlnspewtetlehytgyskedlkpcvelilell 90 
                 S + a+al++a++  ++p   + +e+   ++ +d+  c++l+ + l
  EPA05677.1 163 SALMASALYAACRDTETPRNLKDVEQAANIKRKDIARCYRLLIKEL 208
                 556689999999999999999*******************997755 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.12
                 HHHHHHHHCCHHHHS--S-HHHHHHC---HHHHH CS
    Cyclin_C  47 iAaaalllarstlnspewtetlehytgyskedlk 80 
                 +Aaaal+l++   ++ + ++ + +   +++  ++
  EPA05677.1 259 LAAAALYLSCVKNGEDKTQRDIAEAANVTEVTIR 292
                 8********9987666666666666666665555 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1         2   1.8e+03      19      33 ..     220     234 ..     216     234 .. 0.84
   2 ?   10.1   0.0    0.0006      0.54      13      41 ..     266     295 ..     259     302 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2
      HTH_23  19 svreIAreLgvsrrT 33 
                 +v++IA + g+ + T
  EPA05677.1 220 CVARIASRIGIAEKT 234
                 6899***99998876 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0006
      HTH_23  13 llae....GlsvreIAreLgvsrrTvyrwlkry 41 
                 l  +     +++r+IA++ +v++ T+++    y
  EPA05677.1 266 LSCVkngeDKTQRDIAEAANVTEVTIRNR---Y 295
                 4443456689****************954...3 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.4    0.0005      0.44      16      40 .]      10      35 ..       9      35 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0005
  Auto_anti-p27 16 etCpvC.gvPLmrdrkggkvyCvaCd 40
                   e Cp+C +  L+ d ++g+++C  C+
     EPA05677.1 10 ELCPRCaQGKLVTDNESGEMFCSKCG 35
                   67*************99********6 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   1.1   0.00061      0.55       6      30 ..      12      37 ..       9      38 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00061
  A2L_zn_ribbon  6 CsvCggngiln.seqgylvCieCgas 30
                   C  C   +++   e+g+++C +Cg++
     EPA05677.1 12 CPRCAQGKLVTdNESGEMFCSKCGFV 37
                   556666777766789*********97 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   1.4    0.0015       1.4       5      25 ..      12      37 ..       9      38 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0015
  zf-ribbon_3  5 CPnCGa.pl....ssddnvCpyCGtk 25
                 CP+C + +l    +s+ ++C +CG +
   EPA05677.1 12 CPRCAQgKLvtdnESGEMFCSKCGFV 37
                 77777776434446899*******87 PP

>> zf-CCHC_5  GAG-polyprotein viral zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.3   0.00085      0.76       1      12 [.       8      19 ..       8      23 .. 0.87
   2 ?    1.0   0.0       0.4   3.6e+02      23      34 ..      86      97 ..      84      99 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00085
                ---B-TTT-SSB CS
   zf-CCHC_5  1 ppglCpRCkkgk 12
                p +lCpRC +gk
  EPA05677.1  8 PKELCPRCAQGK 19
                678******998 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.4
                EGGGEE---XXX CS
   zf-CCHC_5 23 dknGnpLsaneg 34
                d  G+pLsa  +
  EPA05677.1 86 DATGKPLSASMK 97
                678*****9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       757  (0.0422221); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1911.23
//
Query:       EPA05678.1  [L=306]
Description: homoserine kinase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-13   50.7   1.5    3.6e-13   49.5   1.5    1.6  1  GHMP_kinases_N  GHMP kinases N terminal domain
    2.5e-08   34.2   0.0    5.2e-08   33.1   0.0    1.5  1  GHMP_kinases_C  GHMP kinases C terminal


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.5   1.5   4.1e-17   3.6e-13       2      66 .]      79     145 ..      78     145 .. 0.93

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 4.1e-17
                     EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHH..HH.HHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
  GHMP_kinases_N   2 ivikseiPvgaGLGSSAAlavalvaAllallglsl..ee.aklaleaerlaqggngsggDvaasvyGg 66 
                     i+ik+ +P g G+GSSAA a+a+v A+ +++gl+l  ++ ++ a ++e++ + g  + ++vaasv+Gg
      EPA05678.1  79 IKIKKGVPAGFGMGSSAASAAATVIAFDKMYGLKLdgNTlVEFAGTGEKASA-GTIHYDNVAASVLGG 145
                     89********************************865448********9998.999***********8 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.0   5.8e-12   5.2e-08      24      83 ..     229     284 ..     206     286 .. 0.83

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 5.8e-12
  GHMP_kinases_C  24 elkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqvaralreef 83 
                     e+   +  + p + +++e ++++Ga+g+ +sGa  Gp+v+a+ ++  + +++ +a+++ f
      EPA05678.1 229 EP--ARQHMIPGFAKVKENAMKAGAFGVTISGA--GPSVIAFSDSLGDLKKISLAMSKGF 284
                     66..66678999*********************..*********************8876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2266.13
//
Query:       EPA05679.1  [L=39]
Description: hypothetical protein BG20_I0278 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       204  (0.0113782); expected 358.6 (0.02)
Passed bias filter:                      175  (0.00976072); expected 358.6 (0.02)
Passed Vit filter:                         3  (0.000167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.45
# Mc/sec: 262.33
//
Query:       EPA05680.1  [L=99]
Description: hypothetical protein BG20_I0304 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0019   18.5   0.1     0.0022   18.2   0.1    1.1  1  IL5             Interleukin 5
     0.0072   15.1   0.0     0.0083   14.9   0.0    1.0  1  Alginate_exp    Alginate export
  ------ inclusion threshold ------
      0.016   14.4   0.0      0.017   14.3   0.0    1.0  1  RE_Alw26IDE     Type II restriction endonuclease (RE_Alw26IDE
      0.018   14.5   0.8      0.026   14.0   0.8    1.2  1  Pneumovirus_M2  Pneumovirus matrix protein 2 (M2)
      0.019   14.7   1.8        2.9    7.7   0.2    2.3  2  S_100           S-100/ICaBP type calcium binding domain


Domain annotation for each model (and alignments):
>> IL5  Interleukin 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   6.2e-07    0.0022      36     107 ..      28      95 ..      12      98 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 6.2e-07
                 SS-GGGGHHHHHHHHHHHHTTS--SSTHHHHHHHHHHHHHHHHHHHHTTTSSEEEHHHHHHHHHHHHHCCTS CS
         IL5  36 hknhqlcieeifqGidtlknqtvqgeaveklfqnlslikkyidlqkkkcgeerrrvkqfldylqeflgvint 107
                 +k  +l  +e  + i+ lk+qt   + ++kl++n  +  k i+ +    +  + +++ f dy q+++++in 
  EPA05680.1  28 TK--NLLEKEFQNLINELKSQTK--DDLKKLLDNQLIADKQINSRPGAMALAQDKIRLFSDYNQKYIQIINE 95 
                 33..35556666679******96..569******************************************96 PP

>> Alginate_exp  Alginate export
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   2.3e-06    0.0083      25      66 ..      46      87 ..      35      97 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.3e-06
                  SS--EEEEEEEEEEEEEEEETTEEEEEEEESSS---STTGGG CS
  Alginate_exp 25 sngddnyllrrlrvhadleigdavraaveltDareydkdlns 66
                  +++dd + l++++++ad++i+ +++a++ ++D++++++d+n+
    EPA05680.1 46 QTKDDLKKLLDNQLIADKQINSRPGAMALAQDKIRLFSDYNQ 87
                  56799999*******************************986 PP

>> RE_Alw26IDE  Type II restriction endonuclease (RE_Alw26IDE)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   4.7e-06     0.017     127     186 ..      29      87 ..       3      95 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.7e-06
  RE_Alw26IDE 127 eslgesvleelkeilkvkdeledllawleefiikeeksllspGamsnaPDRldGfHsynk 186
                  ++l e+++++l + lk  ++ +dl++ l++++i++++    pGam+ a D++  f  yn+
   EPA05680.1  29 KNLLEKEFQNLINELKS-QTKDDLKKLLDNQLIADKQINSRPGAMALAQDKIRLFSDYNQ 87 
                  45567889999999999.8889999999***************************99997 PP

>> Pneumovirus_M2  Pneumovirus matrix protein 2 (M2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.8   7.1e-06     0.026     112     145 ..      34      67 ..      29      79 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.1e-06
  Pneumovirus_M2 112 ktnkslinllkklpkeklkklikntliieksiiv 145
                     k+ ++lin lk   k+ lkkl+ n li +k i  
      EPA05680.1  34 KEFQNLINELKSQTKDDLKKLLDNQLIADKQINS 67 
                     67789**********************9998865 PP

>> S_100  S-100/ICaBP type calcium binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.2    0.0008       2.9      31      42 ..      29      40 ..      26      41 .. 0.88
   2 ?    6.3   0.1    0.0022       7.7      26      38 ..      47      59 ..      47      60 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0008
                HHHHHHHSTTTS CS
       S_100 31 keLlekElpnfl 42
                k+LlekE+ n++
  EPA05680.1 29 KNLLEKEFQNLI 40
                9********986 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0022
                EHHHHHHHHHHHS CS
       S_100 26 sKkELkeLlekEl 38
                +K++Lk+Ll ++l
  EPA05680.1 47 TKDDLKKLLDNQL 59
                79*******9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1453  (0.0810419); expected 358.6 (0.02)
Passed bias filter:                      653  (0.0364214); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.34s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 567.05
//
Query:       EPA05681.1  [L=37]
Description: hypothetical protein BG20_I0307 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); expected 358.6 (0.02)
Passed Vit filter:                         4  (0.000223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.44
# Mc/sec: 253.39
//
Query:       EPA05682.1  [L=343]
Description: hypothetical protein BG20_I0291 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    0.00046   19.1   0.2    0.00064   18.7   0.2    1.2  1  HTH_micro  HTH-like
     0.0056   16.2   0.0      0.032   13.8   0.0    2.2  2  HTH_24     Winged helix-turn-helix DNA-binding


Domain annotation for each model (and alignments):
>> HTH_micro  HTH-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.2   7.1e-08   0.00064      95     155 ..     281     340 ..     267     343 .] 0.84

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 7.1e-08
   HTH_micro  95 kivdflvkakdyvkaaelraklnidpK.klfYvikkLakkglieqktkeeakivikinkDes 155
                 +iv f+  +   v  ++lr+k+ + p+ ++  ++k+L++ g+ie ++k++ + ++k++kD +
  EPA05682.1 281 EIVKFIFDNGGQVLESDLRKKF-LQPRtTMWRAVKRLERLGVIE-IDKKDLQNLVKLKKDLE 340
                 799****************888.5665167789***********.9999999999****865 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.13   1.2e+03       4      17 ..     128     141 ..     127     142 .. 0.90
   2 !   13.8   0.0   3.5e-06     0.032       5      48 .]     279     323 ..     276     323 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.13
      HTH_24   4 tdrkILelLqknpr 17 
                 +d++I  l+ k++r
  EPA05682.1 128 IDYDIHDLISKEGR 141
                 89*********998 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 3.5e-06
      HTH_24   5 drkILelLqknpr.isqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                 d++I + + +n++    ++L ++   +++t +r +krLe+ G+I+
  EPA05682.1 279 DKEIVKFIFDNGGqVLESDLRKKFLQPRTTMWRAVKRLERLGVIE 323
                 6677777777777777788888888999****************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2190.44
//
Query:       EPA05683.1  [L=126]
Description: putative CrcB protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-19   69.0   4.5      4e-19   68.7   4.5    1.1  1  CRCB      CrcB-like protein, Camphor Resistance (CrcB)
     0.0032   17.7   1.4     0.0045   17.2   0.9    1.5  1  DUF2104   Predicted membrane protein (DUF2104)


Domain annotation for each model (and alignments):
>> CRCB  CrcB-like protein, Camphor Resistance (CrcB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.7   4.5   4.5e-23     4e-19       2      92 ..       8     114 ..       7     117 .. 0.87

  Alignments for each domain:
  == domain 1  score: 68.7 bits;  conditional E-value: 4.5e-23
                 HHHHHHHHHHHHHHHH.HHHHBE......BHHHHHHHHHHHHHHHHHHH.............HHTTTHHHHHS-SHHHHHHHHHHHHHT-HHHHHHHHH CS
        CRCB   2 lvalggalGallRyllssllnkr......plgtlavNvlGsfllgllla.............llttGflGglTTfStfvlelvslleegellaallyvl 81 
                 ++a+g+++Ga+lRy +++           pl++l+vN++G+f+lg+++              l + Gf+G+lTT+S+f+l+  +ll+++++ + +++++
  EPA05683.1   8 FLAVGSVIGAFLRYKITES---PllfnalPLNVLIVNIIGAFILGMFVIvseqwnldgryslLAAIGFCGSLTTMSSFALDSSNLLDNHHYGTLAINLV 103
                 789*************553...133466889***************99988888888888766889********************999********** PP

                 HHHHHHHHHHH CS
        CRCB  82 lsvvlgllavv 92 
                 +++ l++ a++
  EPA05683.1 104 ANTGLSIGALI 114
                 *****998876 PP

>> DUF2104  Predicted membrane protein (DUF2104)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.9     5e-07    0.0045       7      55 ..       6      53 ..       3      79 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5e-07
     DUF2104  7 viafivGsilGLlysYkkysepyvekkidklalvlaviGwllllnvsll 55
                 i + vGs++G  + Yk  ++p   + +   +l++ +iG+++ l + ++
  EPA05683.1  6 FIFLAVGSVIGAFLRYKITESPLLFNALPLNVLIVNIIGAFI-LGMFVI 53
                57889**********************************999.444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 785.90
//
Query:       EPA05684.1  [L=145]
Description: prevent-host-death family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-26   92.2   1.9    7.6e-13   48.7   0.1    2.1  2  CBS       CBS domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   0.2   2.3e-15   4.2e-11       1      56 [.       6      60 ..       6      61 .. 0.91
   2 !   48.7   0.1   4.3e-17   7.6e-13       2      53 ..      71     121 ..      70     124 .. 0.93

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 2.3e-15
                HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
         CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56
                V+d+m +d+  ++ +t++++a++lm ek+v+++ +V +++ ++Gi+t+rD ++ ++
  EPA05684.1  6 VKDVMISDLAALDSSTSIRDAAKLMDEKNVGCI-IVTKNKLPIGILTERDFVKRIA 60
                89***********************99******.775666699********99886 PP

  == domain 2  score: 48.7 bits;  conditional E-value: 4.3e-17
                 HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
         CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53 
                 +++m+++++ ++p++t++ea+++m+ k+++ lPV  +d++++Givt +Dl++
  EPA05684.1  71 EEVMSSPIIEIDPNETVWEAAQIMKTKNIHKLPV-KKDNQIIGIVTTTDLVK 121
                 79**********************8888******.69999**********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1094.14
//
Query:       EPA05685.1  [L=131]
Description: hypothetical protein BG20_I0312 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.9e-13   50.4   0.0    2.7e-13   49.9   0.0    1.2  1  HSP20       Hsp20/alpha crystallin family
    7.3e-10   38.3   0.0    9.6e-10   37.9   0.0    1.2  1  ArsA_HSP20  HSP20-like domain found in ArsA
    0.00066   20.6   0.9    0.00066   20.6   0.9    1.5  2  CS          CS domain
  ------ inclusion threshold ------
      0.028   14.8   0.0      0.058   13.8   0.0    1.6  1  PIH1_CS     PIH1 CS-like domain


Domain annotation for each model (and alignments):
>> HSP20  Hsp20/alpha crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.9   0.0     6e-17   2.7e-13       9      92 ..      44     126 ..      38     131 .] 0.91

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 6e-17
                 EEEEEE-TT--CCCEEEEEETTEEEEEEE--..---TT----SS---EEEEEE--STTB-TTT-EEEEETTEEEEEEEBSS--. CS
       HSP20   9 fevkldvpglkkeelkvkvednrvlvkgeheeeeedekglikerssrkFsrkftLPenvdadkvkaslkdGvLtvtvpkkepek 92 
                 + +++d+p ++k+++k++ ++n+++v+++ +e   +ek+ +k  + + F+++++LP  +d +k++a++++G L++ +pk+++ +
  EPA05685.1  44 WLLEFDLPLVNKKDIKITSDENSISVEAKLKETYFEEKFGRK-AEFEYFKKSISLPGKIDSKKITAKFEKGRLEIIIPKTTSSN 126
                 5689***************************77778888887.999*********************************98874 PP

>> ArsA_HSP20  HSP20-like domain found in ArsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.0   2.1e-13   9.6e-10       6      61 ..      46     117 ..      41     119 .. 0.96

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 2.1e-13
  ArsA_HSP20   6 lkldLPfvdkeeidlsrsgdeLtIkig.................nfrRqitLPsvlarkevtsAkfedgvLeI 61 
                 l  dLP v+k++i+++ +++ ++++++                  f+++i+LP +++ k++  Akfe+g+LeI
  EPA05685.1  46 LEFDLPLVNKKDIKITSDENSISVEAKlketyfeekfgrkaefeYFKKSISLPGKIDSKKI-TAKFEKGRLEI 117
                 789**********************************************************.**********9 PP

>> CS  CS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       2.7   1.2e+04      24      38 ..       5      19 ..       3      29 .. 0.64
   2 !   20.6   0.9   1.5e-07   0.00066      20      76 .]      52     121 ..      46     121 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.7
                TTTCEEEEEETTEEE CS
          CS 24 kkkdvkvefkerslk 38
                k+k++++++ ++s++
  EPA05685.1  5 KQKEFEIRIIPSSIS 19
                556666666665554 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 1.5e-07
                 TCTTTTTCEEEEEETTEEEEEETS.CEEEEECE...............BSS-BETTTEEEEEETTEEEEEEEB CS
          CS  20 kvnikkkdvkvefkerslkvkigk.eklliege...............LfgpIdpeesswtieskkveitLkK 76 
                  v  +kkd+k++  e+s++v+  k ++ + e++               L g+Id ++ + ++e+ ++ei++ K
  EPA05685.1  52 LV--NKKDIKITSDENSISVEA-KlKETYFEEKfgrkaefeyfkksisLPGKIDSKKITAKFEKGRLEIIIPK 121
                 44..99***************8.77788889889***********************************9987 PP

>> PIH1_CS  PIH1 CS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.3e-05     0.058      31      88 ..      42     113 ..      23     121 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.3e-05
     PIH1_CS  31 kelaieielPllksikevklrvgerrlel...............eskkakyfLslkLpYpvdedkveAkFvkk 88 
                 ++  +e++lPl+   k++k+  +e+++++               +++ + ++ s++Lp ++d +k+ AkF+k 
  EPA05685.1  42 TYWLLEFDLPLV-NKKDIKITSDENSISVeaklketyfeekfgrKAEFEYFKKSISLPGKIDSKKITAKFEKG 113
                 5778899***99.77999999999999999999999999998865455667778****************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 800.21
//
Query:       EPA05686.1  [L=64]
Description: hypothetical protein BG20_I0288 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.042   13.3   0.0       0.05   13.0   0.0    1.0  1  Ceramidase       Ceramidase
      0.045   13.2   0.7      0.045   13.2   0.7    2.0  2  SKG6             Transmembrane alpha-helix domain
        1.5    8.6   6.6        1.3    8.8   1.0    2.0  2  Phage_holin_2_4  Bacteriophage holin family, superfamily II-l
          7    6.2   7.0         12    5.5   0.8    2.0  2  Saf_2TM          SAVED-fused 2TM effector domain


Domain annotation for each model (and alignments):
>> Ceramidase  Ceramidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.1e-05      0.05      86     136 ..      12      64 .]      11      64 .] 0.69

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.1e-05
  Ceramidase  86 lsmiyatalvlyavfsekksrstrv.llgvll.talavvvtllylvlkepvlh 136
                 ++mi++ al+++++ +++   +++v ++g l+ ++ +v++    +++kepv+h
  EPA05686.1  12 IPMIVVGALMAWLMAPFQGDMQNTVeFVGSLIgILGVVFFISGLFYTKEPVMH 64 
                 79***************666654441444444144455555556679****98 PP

>> SKG6  Transmembrane alpha-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.7     1e-05     0.045      10      28 ..       4      22 ..       1      25 [. 0.86
   2 ?    0.7   0.7      0.08   3.6e+02      18      27 ..      43      52 ..      39      58 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1e-05
        SKG6 10 vaIavaVaVPVaViiivLl 28
                 aI ++V++P +V+ ++ +
  EPA05686.1  4 KAITAGVGIPMIVVGALMA 22
                59************99865 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.08
        SKG6 18 VPVaViiivL 27
                +++  +++ +
  EPA05686.1 43 IGILGVVFFI 52
                4444444444 PP

>> Phage_holin_2_4  Bacteriophage holin family, superfamily II-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   1.0   0.00028       1.3      29      51 ..       1      23 [.       1      29 [. 0.93
   2 ?    3.6   0.4     0.012        54      33      48 ..      34      49 ..      25      60 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00028
  Phage_holin_2_4 29 lasselialvGlavAliGlLvnW 51
                     +as  + a vG+ + ++G+L+ W
       EPA05686.1  1 MASKAITAGVGIPMIVVGALMAW 23
                     8899999**************** PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.012
  Phage_holin_2_4 33 elialvGlavAliGlL 48
                     + + +vG ++ ++G++
       EPA05686.1 34 NTVEFVGSLIGILGVV 49
                     5566677777776653 PP

>> Saf_2TM  SAVED-fused 2TM effector domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.8    0.0026        12      70      88 ..       6      24 ..       2      30 .. 0.86
   2 ?    4.9   0.7    0.0041        18      60      84 ..      32      56 ..      26      60 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0026
     Saf_2TM 70 iilvigvllivvGavllil 88
                i   +g+ +ivvGa++++l
  EPA05686.1  6 ITAGVGIPMIVVGALMAWL 24
                66789************97 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0041
     Saf_2TM 60 sseipeivlaiilvigvllivvGav 84
                +++++e+v  +i ++gv++++ G++
  EPA05686.1 32 MQNTVEFVGSLIGILGVVFFISGLF 56
                6778999999999999999999965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       842  (0.046963); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 462.27
//
Query:       EPA05687.1  [L=303]
Description: putative transcription initiation factor IIB [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.4e-33  113.5   1.6    8.8e-16   57.7   0.4    2.3  2  TFIIB           Transcription factor TFIIB repeat
    1.1e-07   31.3   0.8      2e-07   30.4   0.8    1.4  1  TF_Zn_Ribbon    TFIIB zinc-binding
    0.00048   19.6   0.0      0.048   13.2   0.0    2.5  2  Sigma70_r4      Sigma-70, region 4
     0.0013   18.4   0.0      0.019   14.7   0.0    2.1  2  Cyclin_N        Cyclin, N-terminal domain
     0.0022   17.6   0.6     0.0042   16.8   0.6    1.5  1  A2L_zn_ribbon   A2L zinc ribbon domain
     0.0045   17.1   0.0        3.6    7.7   0.0    2.3  2  Cyclin_C        Cyclin, C-terminal domain
  ------ inclusion threshold ------
      0.047   13.8   0.5       0.12   12.5   0.5    1.6  1  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like
      0.074   12.7   0.0       0.18   11.5   0.0    1.7  1  Sigma70_r4_2    Sigma-70, region 4
      0.077   13.2   0.3        0.2   11.8   0.3    1.8  1  Ribosomal_L37e  Ribosomal protein L37e
      0.082   12.9   1.5        1.5    8.8   0.0    2.8  3  HTH_11          HTH domain


Domain annotation for each model (and alignments):
>> TFIIB  Transcription factor TFIIB repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.9   0.0   3.6e-18   6.5e-15       3      71 .]     128     196 ..     126     196 .. 0.95
   2 !   57.7   0.4   4.9e-19   8.8e-16       1      71 []     220     290 ..     220     290 .. 0.99

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 3.6e-18
                 HHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
       TFIIB   3 rfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                 r+  +l L+++V ++  +++++al+++++ Grs  g++AA+ly Acr  e+ rt++++++ ++++ k i
  EPA05687.1 128 RLKTKLALSDTVIEKTAYIYRKALDKGLVRGRSIPGLIAASLYAACRNTETPRTLSDVANSINIKRKDI 196
                 56679***********************************************************99876 PP

  == domain 2  score: 57.7 bits;  conditional E-value: 4.9e-19
                 HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
       TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                 i+r++++++L+ek +++A e++++a++ ++ +G+ p g+aAA+ly+ c k+++ +tqk+i+  + V+e+ti
  EPA05687.1 220 ISRISSNAGLSEKTKRKAIEILDQAAKIELSAGKDPMGLAAAALYLSCVKNGEDKTQKDIAVAAGVTEVTI 290
                 899******************************************************************98 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.8   1.1e-10     2e-07       3      43 .]      11      51 ..      10      51 .. 0.96

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 1.1e-10
                  ETTTTCEECHEETSTTCEEESSSSBEEEECCCCCCCHHHHH CS
  TF_Zn_Ribbon  3 CPnCgstnlveDpergelvCtdCGlVlednsidegpewref 43
                  C  C+   +++D ++ge++C++CG V  d+   egpewr f
    EPA05687.1 11 CQRCNRGAILTDSNTGEMFCSKCGFVATDRVEQEGPEWRSF 51
                  999**988*******************************87 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.025        46      18      37 ..     177     196 ..     169     207 .. 0.80
   2 !   13.2   0.0   2.7e-05     0.048      17      42 ..     267     295 ..     260     301 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.025
                 TTT--HHHHHHHHTS-HHHH CS
  Sigma70_r4  18 geglTleEIgerlgiSrerV 37 
                 + ++Tl+++++  +i r  +
  EPA05687.1 177 ETPRTLSDVANSINIKRKDI 196
                 679************99766 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 2.7e-05
                 H...TTT--HHHHHHHHTS-HHHHHHHHH CS
  Sigma70_r4  17 f...geglTleEIgerlgiSrerVrqiek 42 
                     ge+ T+++I+   g+++ ++r + k
  EPA05687.1 267 CvknGEDKTQKDIAVAAGVTEVTIRNRYK 295
                 34479********************9986 PP

>> Cyclin_N  Cyclin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.1e-05     0.019      38     126 ..     126     211 ..      93     212 .. 0.87
   2 ?    1.7   0.0      0.11     2e+02      37      85 ..     219     267 ..     215     292 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.1e-05
                 HHHHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHHHSSS---HHHHHHHTTTSS-HHHHHHHHHHHHHHTTT-- CS
    Cyclin_N  38 lvevaekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAaKveeisppkledlvyitdeafteeeilemErliLetLnfdl 126
                 l ++ +k+ l+  ++  ++ ++ + l k  v+ + +  + a++L+ A++  e+ p +l+d++  ++  +++++i +  rl+L++L+ ++
  EPA05687.1 126 LDRLKTKLALSDTVIEKTAYIYRKALDKGLVRGRSIPGLIAASLYAACRNTET-PRTLSDVANSIN--IKRKDIARCYRLLLRELDLKM 211
                 678899999999*****************************************.9******99977..9****************9765 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.11
                 HHHHHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHH CS
    Cyclin_N  37 wlvevaekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAa 85 
                  + +++++  l+++t   a+++ld+  + +    ++   ++a++L+l++
  EPA05687.1 219 CISRISSNAGLSEKTKRKAIEILDQAAKIELSAGKDPMGLAAAALYLSC 267
                 57788889999999999999999999999988888999999******98 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.6   2.3e-06    0.0042       5      31 ..      10      37 ..       6      38 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.3e-06
  A2L_zn_ribbon  5 vCsvCggngiln.seqgylvCieCgasf 31
                    C  C++  il  s+ g+++C +Cg+++
     EPA05687.1 10 RCQRCNRGAILTdSNTGEMFCSKCGFVA 37
                   5999**********************97 PP

>> Cyclin_C  Cyclin, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0     0.002       3.6      44      88 ..     162     205 ..     158     213 .. 0.86
   2 !    7.0   0.0    0.0032       5.7       2      89 ..     215     300 ..     214     302 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.002
                 HHHHHHHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHHHHHH CS
    Cyclin_C  44 pSliAaaalllarstlnspewtetlehytgyskedlkpcvelile 88 
                 p liAa+ ++++r+t ++p   + + + + ++ +d+  c++l+l 
  EPA05687.1 162 PGLIAASLYAACRNT-ETPRTLSDVANSINIKRKDIARCYRLLLR 205
                 667888888888888.9999999999999************9986 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0032
                 -HHHHHHHHHCCSSHT.-HCCHHCHHCHHHHHHCSCCHCCS-HHHHHHHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHHHHHHH CS
    Cyclin_C   2 tplsFlrrflkaadasedselrtlakylleltlldydflsyppSliAaaalllarstlnspewtetlehytgyskedlkpcvelilel 89 
                  p+ +++r++ +a+  ++ +++  a  +l+ ++    +++ +p  +Aaaal+l++   ++ + ++ +    g+++  +++ ++ ++e+
  EPA05687.1 215 NPVKCISRISSNAGL-SE-KTKRKAIEILDQAAKIELSAGKDPMGLAAAALYLSCVKNGEDKTQKDIAVAAGVTEVTIRNRYKGLKEA 300
                 577777777666554.23.56667777777777777788888999**********998888888888888899999988888877766 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.5   6.8e-05      0.12       9      37 ..       9      41 ..       5      47 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.8e-05
  NOB1_Zn_bind  9 lrChaCfk....vtkdmtkkFCpkCGnktLkrv 37
                   rC+ C +    + +++  +FC+kCG    +rv
    EPA05687.1  9 SRCQRCNRgailTDSNTGEMFCSKCGFVATDRV 41
                  69****997754447899********8776666 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0    0.0001      0.18      25      48 ..     272     295 ..     269     301 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0001
                   S---HHHHHHHHT--HHHHHHHHH CS
  Sigma70_r4_2  25 eglsykEIAellgisegtVksrls 48 
                   e++++k+IA   g++e+t+++r++
    EPA05687.1 272 EDKTQKDIAVAAGVTEVTIRNRYK 295
                   799*******************95 PP

>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.3   0.00011       0.2      13      43 ..       5      40 ..       1      50 [. 0.70

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
  Ribosomal_L37e 13 kktHilCrrCgkrsy....hvqkktCascGy.psak 43
                      +  +C+rC++ +     ++ +  C++cG+  + +
      EPA05687.1  5 VDSTSRCQRCNRGAIltdsNTGEMFCSKCGFvATDR 40
                    456689******9972222555667******66666 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       1.5   2.7e+03      20      34 ..     128     142 ..     126     143 .. 0.83
   2 ?    1.7   0.1      0.14   2.5e+02      21      52 ..     223     253 ..     220     258 .. 0.81
   3 ?    8.8   0.0   0.00083       1.5      12      43 ..     270     301 ..     263     302 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.5
      HTH_11  20 eLAeeLnvSrrtvrr 34 
                 +L+ +L +S +++ +
  EPA05687.1 128 RLKTKLALSDTVIEK 142
                 79999****999865 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.14
      HTH_11  21 LAeeLnvSrrtvrrdIkaLeelgvpIesepgr 52 
                 ++   ++S++t r+ I++L  + ++Ie ++g+
  EPA05687.1 223 ISSNAGLSEKTKRKAIEILDQA-AKIELSAGK 253
                 666778999999*******988.589888886 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.00083
      HTH_11  12 argpisgeeLAeeLnvSrrtvrrdIkaLeelg 43 
                 + ++ + +++A   +v++ t+r++ k L+e++
  EPA05687.1 270 NGEDKTQKDIAVAAGVTEVTIRNRYKGLKEAL 301
                 55556999******************999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1910.78
//
Query:       EPA05688.1  [L=46]
Description: hypothetical protein BG20_I0281 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       859  (0.0479112); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 308.36
//
Query:       EPA05689.1  [L=72]
Description: hypothetical protein BG20_I0326 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.012   16.1   0.1      0.013   15.9   0.1    1.1  1  Evr1_Alr         Erv1 / Alr family
      0.069   13.0   0.0       0.11   12.3   0.0    1.4  1  dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-
       0.14   12.4   0.0       0.15   12.3   0.0    1.1  1  Pox_vIL-18BP     Orthopoxvirus interleukin 18 binding protein


Domain annotation for each model (and alignments):
>> Evr1_Alr  Erv1 / Alr family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.9   0.1   2.2e-06     0.013      34      87 ..       2      59 ..       1      70 [. 0.68

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.2e-06
                HHHHHHSSCHHHHHHHHHHHH.HCH.....CCCGSSHHHHHHHHHHHHHHHHHHTT... CS
    Evr1_Alr 34 kliakfypCeeCaehfekvla.enp....pekevesrdelvlWlweaHNeVnkrlakee 87
                kl   f pC+eC   ++++ + e       +k+ ++  ++ + l   HNeV + + ++ 
  EPA05689.1  2 KLYLDFEPCKECNVMMNELSSpE-MlfadAKKRADESAKFLRHLTYNHNEVVQAVMEDL 59
                5667899***********43332.2343334666777789999999*****99998543 PP

>> dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.9e-05      0.11      75      99 ..       3      27 ..       1      29 [. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.9e-05
                     EEEEE--BHHHHHHHHHHT-SEEEE CS
  dCMP_cyt_deam_1 75 lyvtlePCsmCakaiiqsgikkvvv 99
                     ly  +ePC++C  +++++   ++ +
       EPA05689.1  3 LYLDFEPCKECNVMMNELSSPEMLF 27
                     899************9998776655 PP

>> Pox_vIL-18BP  Orthopoxvirus interleukin 18 binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.5e-05      0.15      39      74 ..      10      47 ..       5      63 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.5e-05
  Pox_vIL-18BP 39 csgcvkfmpkfsy..mywlakdmksdedakfiehlgeg 74
                  c  c  +m ++s   m +     ++de akf+ hl   
    EPA05689.1 10 CKECNVMMNELSSpeMLFADAKKRADESAKFLRHLTYN 47
                  8899999999996225555555789*********9754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       857  (0.0477997); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 518.28
//
Query:       EPA05690.1  [L=388]
Description: CBS domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-25   87.9   2.1    1.6e-07   31.6   0.1    4.4  4  CBS       CBS domain
  ------ inclusion threshold ------
      0.015   15.8   0.8        5.2    7.7   0.0    3.1  3  NLE       NLE (NUC135) domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.5   0.0    0.0053        47      10      31 ..      26      48 ..      11      58 .. 0.73
   2 !   31.6   0.1   1.8e-11   1.6e-07       8      56 ..      82     129 ..      73     130 .. 0.90
   3 !   29.9   0.1   6.5e-11   5.8e-07       5      55 ..     142     191 ..     138     193 .. 0.91
   4 !   18.3   0.0   2.7e-07    0.0024       4      56 ..     217     268 ..     214     269 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0053
                EEEETTSBHHHHHHHHHHHT.SS CS
         CBS 10 vtvppdttleealelmrekg.vs 31
                  + p++tl+ +++++++++ ++
  EPA05690.1 26 TIIEPTDTLSHVINKITKNNsYD 48
                4899************8877675 PP

  == domain 2  score: 31.6 bits;  conditional E-value: 1.8e-11
                 SCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
         CBS   8 dvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                 +++ v+ ++++ ++++++++++++ +PVVd  +k++G+vt   ++++l+
  EPA05690.1  82 PIPHVTQNDSVQKVANIITHYRIREVPVVD-KNKIIGVVTAQRIIKLLS 129
                 6789**************9999*******6.666***********9985 PP

  == domain 3  score: 29.9 bits;  conditional E-value: 6.5e-11
                 SBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
         CBS   5 mtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                  t +++tvp d+t++ a ++m+ k++++lPV++ ++k+  ++t  ++l+ +
  EPA05690.1 142 YTQNPITVPSDETISNARRIMTTKRIDHLPVLN-QDKIKQVITSYHILQSI 191
                 5789*****************9999*******6.777**********9876 PP

  == domain 4  score: 18.3 bits;  conditional E-value: 2.7e-07
                 HSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
         CBS   4 imtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                 i +++++ ++ +++l ++++ m +++ ++   V+ +g l Gi+t rD+l +l+
  EPA05690.1 217 IGSTRIPQCSANDDLNKIINSMLKADTTCC-LVNLQGTLQGIITFRDILGLLA 268
                 55788999*************998887666.66789*9***********9886 PP

>> NLE  NLE (NUC135) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1    0.0037        34      30      63 ..      32      64 ..      30      66 .. 0.82
   2 ?   -2.3   0.0      0.76   6.8e+03      17      26 ..     143     152 ..     137     158 .. 0.78
   3 ?    7.7   0.0   0.00058       5.2      21      42 ..     220     242 ..     213     250 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0037
         NLE 30 kqLselvnkLlkeekpvpFd.Flidgel.lrtsLee 63
                + Ls ++nk+ k +   ++d F+i+++  l t++++
  EPA05690.1 32 DTLSHVINKITK-N--NSYDvFYIKDKKiLSTNIRA 64
                579*******99.3..478889***98889999876 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.76
         NLE  17 pgtplsvPas 26 
                 +++p++vP++
  EPA05690.1 143 TQNPITVPSD 152
                 5799****97 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.00058
         NLE  21 lsvPasltrkqLselvnkLlk.e 42 
                  ++P+ +  ++L++++n++lk +
  EPA05690.1 220 TRIPQCSANDDLNKIINSMLKaD 242
                 579999999***********943 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1076  (0.0600145); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 2723.35
//
Query:       EPA05691.1  [L=68]
Description: hypothetical protein BG20_I2324 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.011   15.9   1.6      0.027   14.6   1.6    1.6  1  zinc_ribbon_13   Nucleic-acid-binding protein containing Zn-r
       0.02   15.3   0.1      0.023   15.1   0.1    1.2  1  Lar_restr_allev  Restriction alleviation protein Lar
      0.023   14.4   1.3      0.054   13.2   1.3    1.6  1  DUF2225          Uncharacterized protein conserved in bacteri
      0.063   12.8   0.3        7.5    6.2   0.0    2.2  2  TF_Zn_Ribbon     TFIIB zinc-binding
       0.14   12.2   1.1        1.8    8.6   0.2    2.0  2  HypA             Hydrogenase/urease nickel incorporation, met


Domain annotation for each model (and alignments):
>> zinc_ribbon_13  Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   1.6   7.6e-06     0.027       2      50 ..       8      56 ..       7      62 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 7.6e-06
  zinc_ribbon_13  2 CpKCgnteaev..kevaatGsglskifdvqnkkfitvsCknCgYtelYkae 50
                    Cp C++++ae+  ++v+ +G + +k f   +   ++  C++CgY  ++++ 
      EPA05691.1  8 CPVCQSNKAEIagENVKLSGRFEDKEFL--TTPLTVLRCTRCGYYMFFDNM 56
                    9999998877633689999998888774..5678999**********9975 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.1   6.4e-06     0.023       4      42 ..       6      60 ..       3      68 .] 0.75

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 6.4e-06
  Lar_restr_allev  4 kpCPfCggravlersqrvvaeigq............cvyCadCga.....stpwfk 42
                     + CP C + +  +  ++v+ ++              +  C+ Cg+     +  +f+
       EPA05691.1  6 LSCPVCQSNKAEIAGENVKLSG-RfedkeflttpltVLRCTRCGYymffdNMAQFT 60
                     78******99999998887554.459*******************55554333333 PP

>> DUF2225  Uncharacterized protein conserved in bacteria (DUF2225)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.3   1.5e-05     0.054       3      68 ..       3      61 ..       1      66 [. 0.78

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.5e-05
     DUF2225  3 kkkieCPvCeekfkkkkvkssslrlikrdsdlnakYeevnplfYevvvCpkCgYaalkkdfeklsk 68
                +k ++CPvC+++  k ++  ++++l  r +d+      +  +   v  C++CgY  + ++ +++++
  EPA05691.1  3 QKALSCPVCQSN--KAEIAGENVKLSGRFEDKE-----FLTTPLTVLRCTRCGYYMFFDNMAQFTT 61
                6899*****985..7899999999999999864.....44455579*******9888776766655 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1    0.0038        14       2       9 ..       7      14 ..       6      25 .. 0.86
   2 ?    6.2   0.0    0.0021       7.5      20      27 ..      42      49 ..      26      60 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0038
                  EETTTTCE CS
  TF_Zn_Ribbon  2 kCPnCgst 9 
                   CP+C s 
    EPA05691.1  7 SCPVCQSN 14
                  5****996 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0021
                  EEESSSSB CS
  TF_Zn_Ribbon 20 lvCtdCGl 27
                  l+Ct+CG+
    EPA05691.1 42 LRCTRCGY 49
                  57888886 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.2   0.00049       1.8      85     107 ..       4      25 ..       1      30 [. 0.79
   2 ?    3.3   0.0     0.023        81      69      80 ..      40      51 ..      23      63 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00049
                 HHHS-TTTSSS-EEEEESSSEEE CS
        HypA  85 kalrCpkCgsadveivsGeellv 107
                 kal+Cp C+s++ ei +Ge++++
  EPA05691.1   4 KALSCPVCQSNKAEI-AGENVKL 25 
                 4689********998.6887765 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.023
                -EEEETTTS-EE CS
        HypA 69 vkvrCreCgkef 80
                 ++rC++Cg+ +
  EPA05691.1 40 TVLRCTRCGYYM 51
                456788887654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 459.38
//
Query:       EPA05692.1  [L=81]
Description: hypothetical protein BG20_I2323, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.019   14.3   0.4      0.047   13.1   0.2    1.8  2  P3A       Poliovirus 3A protein like


Domain annotation for each model (and alignments):
>> P3A  Poliovirus 3A protein like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0     0.084   1.5e+03      31      36 ..      41      46 ..      35      62 .. 0.67
   2 ?   13.1   0.2   2.6e-06     0.047      17      35 ..      62      80 ..      50      81 .] 0.90

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.084
                HHHHHH CS
         P3A 31 qEvrdY 36
                +++rdY
  EPA05692.1 41 KDIRDY 46
                456666 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 2.6e-06
                SS-TTHHHHHHH--HHHHH CS
         P3A 17 PPeaiaDLLravdsqEvrd 35
                 Pe i DLL+ vd+q +++
  EPA05692.1 62 TPEEIQDLLKQVDTQPIIE 80
                599************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 528.72
//
Query:       EPA05693.1  [L=442]
Description: putative dihydroxy-acid dehydratase, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   7.4e-160  533.0   2.8   8.4e-160  532.8   2.8    1.0  1  ILVD_EDD        Dehydratase family
  ------ inclusion threshold ------
      0.014   15.4   0.4        8.3    6.4   0.1    2.8  3  Ribosomal_S24e  Ribosomal protein S24e


Domain annotation for each model (and alignments):
>> ILVD_EDD  Dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  532.8   2.8  9.4e-164  8.4e-160       1     408 [.      33     442 .]      33     442 .] 0.98

  Alignments for each domain:
  == domain 1  score: 532.8 bits;  conditional E-value: 9.4e-164
    ILVD_EDD   1 kpiigiansyselvpchvhlkelaeavkegveeaggvpaefntigvsDgiamgeegmrysLpsReliadsvetmleaqllDalvlisgCDKivPgllma 99 
                 k+++g++++ +e +pc+ hl +la ++kegv++ag++p ef+ti+vsDgiamg+egm++sL+sRe+iads+e m++a+++Dalv i+gCDK++Pg++ma
  EPA05693.1  33 KAFVGVCHTGNEATPCNIHLPRLALKAKEGVSDAGATPREFSTIAVSDGIAMGHEGMKSSLISREVIADSIELMVRAHQYDALVGIAGCDKSLPGTMMA 131
                 789************************************************************************************************ PP

    ILVD_EDD 100 aarlniPaifvsgGpmeagkkk..kldlssvfeavgalaagkiseeeleeleeaacpgaGsCsgmgTAntmaclaealGlslpgsasipatsaerkela 196
                 +arlniP++fv+gG++++g  +  +l++++v+eavga+ ag++s e l+++e++acp aGsC+gm+TAntma++ ea+Gl+lpgsas pa++++r++++
  EPA05693.1 132 MARLNIPSVFVYGGTIMPGILNgqELTVVDVYEAVGAYDAGQLSLEALKNIENTACPNAGSCGGMFTANTMASISEAIGLALPGSASPPAEDDRREKMV 230
                 ******************77444599************************************************************************* PP

    ILVD_EDD 197 eeagkrivelvekdlkprdiltkeafeNAivvllalGGStNavlHllAiAreagveltlddfdelsrkvpllaklkPsgkydmedlhraGGvpavlkeL 295
                 +++g + v+l+e++++pr+ilt eafeNAi++l a+GGStN +lHllA+ +e+g++lt+ddf+++ +k+p+la++kP g+y m++l+++GG+p+vlk+L
  EPA05693.1 231 YDTGIACVRLLEQNIRPREILTFEAFENAITMLNAVGGSTNGILHLLALSNEVGIKLTYDDFERVRKKTPHLADMKPGGNYVMNSLDKIGGIPFVLKKL 329
                 *************************************************************************************************** PP

    ILVD_EDD 296 lkagllhgdvltvtgktlaenleeaev..keqdvirplekplskegglavLkGnLapeGavvKtsaveeellkfegpArvfdseeeaveailkgkikag 392
                 ++++l+h ++ltvtgkt++enl++ ++    q++i+++++p+++ g+  +LkG+LapeGav+Kt++ve  ++kf+g+Arv+d+ee a++a++kg++++g
  EPA05693.1 330 AERKLIHDNCLTVTGKTIRENLASMNIpePVQQIIKSVDNPIHSVGTAVILKGSLAPEGAVIKTAGVE--MTKFTGKARVYDREEYAFDAVAKGEVEEG 426
                 **********************996665688************************************9..***************************** PP

    ILVD_EDD 393 dvvviryeGPkGgpGm 408
                 +vvviryeGPkGgpGm
  EPA05693.1 427 HVVVIRYEGPKGGPGM 442
                 ***************9 PP

>> Ribosomal_S24e  Ribosomal protein S24e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       1.3   1.2e+04      51      64 ..     287     300 ..     284     301 .. 0.76
   2 ?    6.0   0.0    0.0013        11       4      25 ..     334     355 ..     332     370 .. 0.83
   3 ?    6.4   0.1   0.00093       8.3      43      59 ..     398     414 ..     394     422 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 1.3
                     EEES-HHHHHHHS- CS
  Ribosomal_S24e  51 kiYdsleaakkfEp 64 
                     + Yd+ e+ +k  p
      EPA05693.1 287 LTYDDFERVRKKTP 300
                     57999999988655 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0013
                     EE-SSS-S--HHHHHHHHHHHH CS
  Ribosomal_S24e   4 vlHpgkatpskteireklakmy 25 
                     ++H+++ t++ + ire la+m 
      EPA05693.1 334 LIHDNCLTVTGKTIRENLASMN 355
                     79*****************996 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.00093
                     SSEEEEEEEEES-HHHH CS
  Ribosomal_S24e  43 ggkttGfakiYdsleaa 59 
                     ++k tG+a++Yd +e+a
      EPA05693.1 398 MTKFTGKARVYDREEYA 414
                     7899***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (442 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       293  (0.0163422); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 3099.24
//
Query:       EPA05694.1  [L=92]
Description: hypothetical protein BG20_I1881, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0057   16.6   0.6     0.0057   16.6   0.6    1.9  2  T2SSF     Type II secretion system (T2SS), protein F


Domain annotation for each model (and alignments):
>> T2SSF  Type II secretion system (T2SS), protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.6   3.2e-07    0.0057      79     124 ..       1      46 [.       1      47 [. 0.95
   2 ?   -2.7   3.6      0.29   5.2e+03     106     123 ..      68      85 ..      62      90 .. 0.55

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.2e-07
                 HHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXXXX CS
       T2SSF  79 evLerlaeyleeerelrrkllaallepllllvvallvllillaill 124
                 e++++ a+ + ee ++  ++ +++l+ +++++++ll++++lla+++
  EPA05694.1   1 EYFNATAKVQLEEKKMLLQKTTESLGSVAEIYTILLIVFPLLAVIM 46 
                 678899**************************************98 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.29
                 XXXXXXXXXXXXXXXXXX CS
       T2SSF 106 llllvvallvllillail 123
                 +l+++v+ l ++++l+++
  EPA05694.1  68 ILTFAVIPLSGVLMLVMM 85 
                 445555555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       873  (0.0486921); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 621.12
//
Query:       EPA05695.1  [L=131]
Description: pyridoxamine 5'-phosphate oxidase family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.9e-12   45.4   0.0    8.6e-12   45.1   0.0    1.1  1  Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
      6e-07   29.5   0.0    7.3e-07   29.3   0.0    1.1  1  Pyridox_ox_2    Pyridoxamine 5'-phosphate oxidase
  ------ inclusion threshold ------
      0.028   14.2   0.0      0.028   14.2   0.0    1.2  1  DUF447          Protein of unknown function (DUF447)


Domain annotation for each model (and alignments):
>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.1   0.0   1.4e-15   8.6e-12       6      86 ..       7      86 ..       2      88 .. 0.91

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 1.4e-15
                    HHHHHHSSEEEEEEEETTSEEEEEEEEEEEETTTTEEEEEEETTSHHHHHHHHH-EEEEEEEETT..GSEEEEEEEEEEEESC CS
  Putative_PNPOx  6 reflaeskavvlATvdedGrPnvspvllkagdgrdgivfatnadsrklrnleenprvallfldde..lgrgvrieGtaelvsd 86
                    ++fl++ + +++AT  +d  P+v+pv+++++ g   i +at++++r+++n++ np+va++++ +e  + + v i+G+a +++ 
      EPA05695.1  7 EKFLHSIEEARIATS-HDDIPHVKPVSFIYHEGA--IFIATDYHTRTFKNVKINPHVAISIDIYElgKHKAVIIQGKAIILEK 86
                    67888888899***9.7777**************..*****************************9999********998876 PP

>> Pyridox_ox_2  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.0   1.2e-10   7.3e-07       7     114 ..       8     104 ..       6     122 .. 0.80

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 1.2e-10
                   HHHHC-SEEEEEEEETTEEEEEEEEEEEETTEEEEEEETTSHCCHCCC...T--ECEEEEEEEEEEE-SEGGEEEEEEEEEEEEEEEE--HHHHHHH CS
  Pyridox_ox_2   7 alLdegevgrlafvddgepvilPvnyvvdgdslyfhgakgsrlaaalr...gapvcvvvtevdglvlarsfnslnyrSVvvrGraeevtdeeekaea 100
                   ++L + e +r+a++ d+ p++ Pv++ ++++++++ +  ++r ++  +   ++ +++ ++e+              + V+++G+a  ++  +e   +
    EPA05695.1   8 KFLHSIEEARIATSHDDIPHVKPVSFIYHEGAIFIATDYHTRTFKNVKinpHVAISIDIYELGK-----------HKAVIIQGKAIILEKGKEFLDI 93 
                   578888889***************************************7533337777777666...........699********99999998888 PP

                   CCCHHHHHSTTTGG CS
  Pyridox_ox_2 101 lellvekivpgrwe 114
                    + + +k++   w 
    EPA05695.1  94 YKIFEKKFA---WV 104
                   888777662...33 PP

>> DUF447  Protein of unknown function (DUF447)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   4.7e-06     0.028       5      51 ..      18      64 ..      14     114 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.7e-06
                EEEE-TT-EEEEEEEEEESSSE.EEEEEETTSHHHHHHHHHSEEEEEE CS
      DUF447  5 vtTksekrpnaaPiGvivkgdk.vvlrlfkgsrTleNllengelvinv 51
                + T++++ p+++P+  i+++   +++  ++ +rT++N++ n++++i++
  EPA05695.1 18 IATSHDDIPHVKPVSFIYHEGAiFIATDYH-TRTFKNVKINPHVAISI 64
                44555567**********666615555566.9***********99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 898.70
//
Query:       EPA05696.1  [L=48]
Description: hypothetical protein BG20_I1874 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 326.24
//
Query:       EPA05697.1  [L=92]
Description: PPIC-type PPIASE domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    8.9e-26   90.7   0.2    1.5e-25   90.0   0.2    1.3  1  Rotamase_3  PPIC-type PPIASE domain
    5.2e-23   81.8   0.1    6.2e-23   81.6   0.1    1.1  1  Rotamase    PPIC-type PPIASE domain
    1.7e-07   32.1   0.0      2e-07   31.8   0.0    1.0  1  Rotamase_2  PPIC-type PPIASE domain
     0.0041   16.9   0.0     0.0054   16.5   0.0    1.1  1  NTPase_I-T  Protein of unknown function DUF84
  ------ inclusion threshold ------
      0.036   14.4   0.0      0.048   14.0   0.0    1.2  1  PapD_C      Pili assembly chaperone PapD, C-terminal domain


Domain annotation for each model (and alignments):
>> Rotamase_3  PPIC-type PPIASE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.0   0.2   4.2e-29   1.5e-25      14     111 ..       3      89 ..       1      91 [. 0.93

  Alignments for each domain:
  == domain 1  score: 90.0 bits;  conditional E-value: 4.2e-29
  Rotamase_3  14 dsvkvshIlistkgkesrseeeakakadsllaalkegadFaalAkeySdDpaskenGGelgwftkgqmvkeFedavfslkkgeiskvvktdfGyHiik 111
                 +++k shIl++            ++ a  +++++k+g++F +lAke S D++s+++ G+lg+ftkg+mvk+Fe+a+f+l++ge+s++vk++fGyHiik
  EPA05697.1   3 NKIKCSHILVEK-----------QSEAIAICERIKKGEKFGKLAKELSIDTGSAKKDGSLGYFTKGMMVKPFEEAAFKLQIGEMSEPVKSEFGYHIIK 89 
                 678888888864...........668889********************************************************************8 PP

>> Rotamase  PPIC-type PPIASE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.6   0.1   1.7e-26   6.2e-23      19      95 ..      15      90 ..       6      92 .] 0.95

  Alignments for each domain:
  == domain 1  score: 81.6 bits;  conditional E-value: 1.7e-26
                HHHHHHHHCCTCCCHHHHHHHHCCC-.-CHHHCCTTEEECEETTTS-CCCHHHHCCS-CT-B-S-EEETTEEEEEEE CS
    Rotamase 19 kakaeeileqlksgedtFeelArkySddknsakngGdlgwvekgqlppefekaafslkkGeisepvetkfGfhiikl 95
                + +a +i e++k+ge+ F +lA++ S d++sak++G+lg+++kg +++ fe+aaf+l+ Ge+sepv+++fG+hiik+
  EPA05697.1 15 QSEAIAICERIKKGEK-FGKLAKELSIDTGSAKKDGSLGYFTKGMMVKPFEEAAFKLQIGEMSEPVKSEFGYHIIKR 90
                56788999*******9.**********************************************************96 PP

>> Rotamase_2  PPIC-type PPIASE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.0   5.7e-11     2e-07      27     104 ..       9      89 ..       3      91 .. 0.79

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 5.7e-11
  Rotamase_2  27 lavvkdqvaaeaalalakagaekdfaalakgnskkaadlgifesasnlpe.....elakaafalkpgevsgpvetdngyyivk 104
                 ++ v  q +a a+ ++ k+g  ++f +lak+ s++++++  + s  ++ +     ++++aaf+l+ ge s+pv++++gy+i+k
  EPA05697.1   9 HILVEKQSEAIAICERIKKG--EKFGKLAKELSIDTGSAKKDGSLGYFTKgmmvkPFEEAAFKLQIGEMSEPVKSEFGYHIIK 89 
                 56677788888898999988..589999999999866666444444444444444**************************98 PP

>> NTPase_I-T  Protein of unknown function DUF84
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.5e-06    0.0054     107     145 ..      21      59 ..      17      67 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.5e-06
                 HHHHHCTT--HHHHHHHHHTHCCHHHTTHHHHHHTTTSS CS
  NTPase_I-T 107 vveevkegeelgevmdelfgtenikqkeGaigllTkglv 145
                 ++e++k+ge++g+  +el+ ++++++k G  g++Tkg++
  EPA05697.1  21 ICERIKKGEKFGKLAKELSIDTGSAKKDGSLGYFTKGMM 59 
                 789*********************************986 PP

>> PapD_C  Pili assembly chaperone PapD, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.3e-05     0.048      27      59 ..      51      92 .]      36      92 .] 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.3e-05
                E......EEE-TTEEEEE...TT--S--TT-EEEEEEE-TTS CS
      PapD_C 27 a......gmvaPfssatf...akkaapaagatvsftvINDyG 59
                       +mv+Pf++a f    + ++ +  +++ + +I  yG
  EPA05697.1 51 LgyftkgMMVKPFEEAAFklqIGEMSEPVKSEFGYHIIKRYG 92
                24455669**********999999999999999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.32u 0.25s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 759.98
//
Query:       EPA05698.1  [L=92]
Description: hypothetical protein BG20_I1877 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.029   14.5   0.0      0.031   14.4   0.0    1.1  1  DUF2407_C  DUF2407 C-terminal domain


Domain annotation for each model (and alignments):
>> DUF2407_C  DUF2407 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.7e-06     0.031      79     126 ..      26      75 ..       1      79 [. 0.69

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.7e-06
   DUF2407_C  79 e...nsvdseeskanedlliGlliGfflglfalllllkeegllnkrqkmav 126
                 e   ++ +s + +  +++++G+++G+ lg+ +  +l ++e + +   +m v
  EPA05698.1  26 EdikQNQESLKVGNPQEFVYGMIMGMALGMSG-AILSAQEEMPTAEDQMKV 75 
                 0333445677888899**************88.777777778888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       703  (0.0392102); expected 358.6 (0.02)
Passed bias filter:                      568  (0.0316805); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 604.25
//
Query:       EPA05699.1  [L=280]
Description: sugar-specific transcriptional regulator TrmB [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-14   52.3   0.1    7.9e-14   51.3   0.1    1.6  1  TrmB      Sugar-specific transcriptional regulator TrmB
    2.8e-05   23.9   0.0    5.4e-05   23.0   0.0    1.4  1  MarR_2    MarR family
     0.0013   18.8   0.0     0.0028   17.7   0.0    1.6  1  HTH_20    Helix-turn-helix domain
     0.0029   17.5   0.0     0.0072   16.2   0.0    1.7  1  MarR      MarR family
  ------ inclusion threshold ------
      0.016   15.5   0.0      0.033   14.4   0.0    1.6  1  RisS_PPD  Periplasmic domain of Sensor histidine kinase RisS
      0.069   13.1   0.6       0.37   10.8   0.1    2.4  2  HTH_11    HTH domain


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.3   0.1   2.6e-17   7.9e-14       1      67 [.      14      81 ..      14      82 .. 0.96

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 2.6e-17
                HH.HCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE--H CS
        TrmB  1 Lq.klGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravdp 67
                L+  l+L e EakvYl Ll+ gp ta+ +a+el+++r++ Y+++ +L+++ ++ +  ++pkl  av+p
  EPA05699.1 14 LEeILNLDEIEAKVYLNLLRVGPVTASALAKELDIDRARMYRTVDKLVSRNIISITLSSPKLCMAVEP 81
                56689*********************************************************999998 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   1.8e-08   5.4e-05      12      51 ..      29      66 ..      19      75 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1.8e-08
                HHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSE CS
      MarR_2 12 aaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLv 51
                ++L r ++  +t+++la++l+++++++ r++++Lv++  +
  EPA05699.1 29 LNLLRVGP--VTASALAKELDIDRARMYRTVDKLVSRNII 66
                57888888..**************************9987 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   9.4e-07    0.0028      19      55 ..      31      67 ..      20      73 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 9.4e-07
                HSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
      HTH_20 19 LaraegltaselaerldlskntlsyHLrvLeeagLve 55
                L r +++tas+la++ld++++ +++ +++L++  ++ 
  EPA05699.1 31 LLRVGPVTASALAKELDIDRARMYRTVDKLVSRNIIS 67
                55779**************************988876 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   2.4e-06    0.0072      14      48 ..      33      67 ..      25      69 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.4e-06
                HSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
        MarR 14 eqgplsvseLakklgvskstvtrvldrLekkGlie 48
                + gp + s Lak l ++++ + r++d+L+ ++ i+
  EPA05699.1 33 RVGPVTASALAKELDIDRARMYRTVDKLVSRNIIS 67
                5699***************************9986 PP

>> RisS_PPD  Periplasmic domain of Sensor histidine kinase RisS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.1e-05     0.033      28      83 ..      73     130 ..      49     139 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.1e-05
    RisS_PPD  28 vaLlkeLaekegirilprepsDkiepleddr..ltrliaeevrerlgektivassvng 83 
                 ++L + ++ +e+++i  r+++D+++++++d   ++++i++e++++ g +t   + v+g
  EPA05699.1  73 PKLCMAVEPQEALKIALRKKEDEVNKIKKDGeaIIEKINSEISTKHGRNTPTFRVVQG 130
                 68899999*******************9986569***************987777766 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00012      0.37      14      39 ..      35      60 ..      24      71 .. 0.84
   2 ?   -0.7   0.0      0.48   1.4e+03      32      45 ..     134     147 ..     131     152 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00012
      HTH_11 14 gpisgeeLAeeLnvSrrtvrrdIkaL 39
                gp++++ LA+eL++ r+  +r +++L
  EPA05699.1 35 GPVTASALAKELDIDRARMYRTVDKL 60
                57**************9999999988 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.48
      HTH_11  32 vrrdIkaLeelgvp 45 
                 ++ dI++L e   +
  EPA05699.1 134 IYADIAQLIENSTD 147
                 89999999776544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       806  (0.0449551); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1839.82
//
Query:       EPA05700.1  [L=281]
Description: type II secretion system F domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.3e-18   65.2   0.3    1.6e-17   63.7   0.3    1.9  1  T2SSF         Type II secretion system (T2SS), protein F
     0.0074   16.1   2.1       0.03   14.2   0.3    2.7  3  MtrG          Tetrahydromethanopterin S-methyltransferase, su
  ------ inclusion threshold ------
      0.023   14.8   1.5      0.064   13.4   0.0    2.1  2  Spore_III_AB  Stage III sporulation protein AB (spore_III_AB)
        6.8    7.4  11.5         33    5.2   0.1    3.5  3  Rab5ip        Rab5-interacting protein (Rab5ip)


Domain annotation for each model (and alignments):
>> T2SSF  Type II secretion system (T2SS), protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.7   0.3   3.5e-21   1.6e-17       1     123 [.      72     197 ..      72     199 .. 0.96

  Alignments for each domain:
  == domain 1  score: 63.7 bits;  conditional E-value: 3.5e-21
                 HHHHHHHHHHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTSSHHHHHC....T-TT.TS-HHHHHHHHHHHHHT-HHHHHHHHHHHHHHHHHHH CS
       T2SSF   1 flrqlatllsaGvplveaLellaeeaengplaeelkriarrlraGgslseale....rtpssefpelvvqlirageeggnLaevLerlaeyleeerelr 95 
                 fl  l + +++G +l +a+e +ae    g+l++elk++++++++G+++++a+e    rt++ + +++ v l  a + gg+++e Le +++++ e+++++
  EPA05700.1  72 FLLALLSSVQSGSNLIKAIEQAAERN-LGALTPELKNLKANISWGTPIEDAFEnfakRTGTRVSRRVTVLLEMAMKIGGDVSENLEMIQKHVSEMQNIE 169
                 788999********************.*****************************98888666*********************************** PP

                 HHHHHHHHTTXXXXXXXXXXXXXXXXXX CS
       T2SSF  96 rkllaallepllllvvallvllillail 123
                 + +++al  +  ++++ ++v+l++ + l
  EPA05700.1 170 KSRKSALQPYTYTIYISFAVFLAVSVLL 197
                 **********************998766 PP

>> MtrG  Tetrahydromethanopterin S-methyltransferase, subunit G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.3   6.8e-06      0.03      40      60 ..      33      53 ..      19      56 .. 0.80
   2 ?    0.1   0.0      0.17   7.4e+02      27      48 ..     119     140 ..     116     148 .. 0.78
   3 ?   -3.1   0.1       1.6   7.2e+03      15      27 ..     151     163 ..     150     172 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.8e-06
        MtrG 40 kvGRdiGilYGlviGliillv 60
                ++ Rd+Gi++G+++G+i l +
  EPA05700.1 33 SMIRDVGIIFGIMVGIIPLTI 53
                566*************97665 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.17
        MtrG  27 efvnsEiaqriGkkvGRdiGil 48 
                 e +    a+r+G +v R + +l
  EPA05700.1 119 EDAFENFAKRTGTRVSRRVTVL 140
                 555566889*******999887 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 1.6
        MtrG  15 vkkrLdeieekve 27 
                 v + L+ i+++v 
  EPA05700.1 151 VSENLEMIQKHVS 163
                 5677777777774 PP

>> Spore_III_AB  Stage III sporulation protein AB (spore_III_AB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.3       0.2   9.2e+02     152     168 ..      33      49 ..      27      49 .. 0.89
   2 ?   13.4   0.0   1.4e-05     0.064       6     110 ..      73     176 ..      70     184 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.2
                   XXXXXXXXXXXXXXXXX CS
  Spore_III_AB 152 klyrtlGvlaGlflvil 168
                    ++r +G++ G+++ i+
    EPA05700.1  33 SMIRDVGIIFGIMVGII 49 
                   69999********9997 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 1.4e-05
                   XXXXXXXXXXXXXXXXXX.XHHHHHHHHHHHHHHHHHHHHHH-SS-HHHHHHHHHHCS-TTHHHHHHHHHHHHH.STSS-HHHHHHHHHHHHGGGS- CS
  Spore_III_AB   6 llillactgiGfalakrl.krrlkeleelkralellegeirygatpLpealeklaeksesplseffeevaerleekegesfeeaweeavekllkkla 101
                   ll ll+++  G  l k + +  +++l +l   l+ l++ i++g tp+++a+e++a++++ ++s+ +  + e +  k g++++e +e   ++  +  +
    EPA05700.1  73 LLALLSSVQSGSNLIKAIeQAAERNLGALTPELKNLKANISWG-TPIEDAFENFAKRTGTRVSRRVTVLLE-MAMKIGGDVSENLEMIQKHVSEMQN 167
                   6777888888888777773556789*****************5.9*************9988776443333.2333666666665555555555566 PP

                   --HHHHHHH CS
  Spore_III_AB 102 Lkkedkeil 110
                   ++k+ k  l
    EPA05700.1 168 IEKSRKSAL 176
                   666666555 PP

>> Rab5ip  Rab5-interacting protein (Rab5ip)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1    0.0074        33      10      23 ..      39      52 ..      32      54 .. 0.89
   2 ?    3.6   0.1     0.023     1e+02      25      46 ..     184     204 ..     180     230 .. 0.80
   3 ?    2.9   2.8     0.037   1.7e+02       2      44 ..     237     279 ..     236     281 .] 0.87

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0074
      Rab5ip 10 alllGvvaGilgLe 23
                ++++G+++Gi++L+
  EPA05700.1 39 GIIFGIMVGIIPLT 52
                79**********97 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.023
      Rab5ip  25 lsGflfylllsllvsllfyalk 46 
                 ++ f+++l++s+l++  f++ +
  EPA05700.1 184 YISFAVFLAVSVLLTTSFFS-E 204
                 7789********99999984.3 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.037
      Rab5ip   2 lsnlrsltalllGvvaGilgLeslsGflfylllsllvsllfya 44 
                 l n+  + a++ Gv+aG +g  s+ + +  ++++++++++ ++
  EPA05700.1 237 LFNMAIIEAVFGGVAAGKIGSGSYVAGTKHVVVMIIMAVIAFN 279
                 567778889****************999999999999988774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       901  (0.0502538); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1848.16
//
Query:       EPA05701.1  [L=133]
Description: hypothetical protein BG20_I1878 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.4e-36  123.2   0.1    1.1e-35  123.1   0.1    1.0  1  DUF2203   Uncharacterized conserved protein (DUF2203)
  ------ inclusion threshold ------
      0.088   13.1   1.1       0.13   12.6   0.1    1.8  2  GCR1_C    Transcriptional activator of glycolytic enzymes


Domain annotation for each model (and alignments):
>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.1   0.1   1.2e-39   1.1e-35       2     122 .]       4     125 ..       3     125 .. 0.97

  Alignments for each domain:
  == domain 1  score: 123.1 bits;  conditional E-value: 1.2e-39
     DUF2203   2 lFtleeAnalLpllkelleelralrkeleeleeeleeakaeaekse.aaeleaeleeleaeieelveeieelGvevkdleaglvDFpakldgeevllCW 99 
                 +Ft +eAn+ Lp + +++e + a+++e+ ++e+el+ + +++++ e +  l+++l+++ +++ e+ve +e++Gv+vk++e+gl+DFp+k+ ++ev+lCW
  EPA05701.1   4 YFTTNEANQSLPDVIKKFEFALAKKNEVSKIEQELQMSLSTTNSFEtYVVLKQKLNSAITRFYEAVELLENTGVVVKSIEQGLLDFPSKRFDDEVWLCW 102
                 8***********************************99999887777999************************************************* PP

     DUF2203 100 klgEeeieywHeleeGfagRkpi 122
                 k+gE+ei++wHe ++Gf+gRkpi
  EPA05701.1 103 KYGETEIKFWHEKDSGFMGRKPI 125
                 **********************8 PP

>> GCR1_C  Transcriptional activator of glycolytic enzymes
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   1.5e-05      0.13       1      64 [.       5      68 ..       5      84 .. 0.88
   2 ?   -1.2   0.1       0.3   2.7e+03      33      46 ..      97     110 ..      92     124 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.5e-05
      GCR1_C  1 fklsreiktVedlwnEykeglngkpsikslekkygkrWrkdskesklfsrRkkiidfierliee 64
                f+ ++++++  d+++ ++  l++k ++ ++e++ + ++ +++ +++++  ++k+ ++i r  e 
  EPA05701.1  5 FTTNEANQSLPDVIKKFEFALAKKNEVSKIEQELQMSLSTTNSFETYVVLKQKLNSAITRFYEA 68
                678999***********************************99999999999999999888765 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.3
      GCR1_C  33 kygkrWrkdskesk 46 
                 + + +W+ +++e k
  EPA05701.1  97 EVWLCWKYGETEIK 110
                 44445555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       782  (0.0436165); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 857.88
//
Query:       EPA05702.1  [L=505]
Description: DEAD/DEAH box helicase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.8e-24   84.4   0.1      2e-23   82.9   0.1    1.8  1  Helicase_C    Helicase conserved C-terminal domain
    8.9e-20   71.4   0.0    2.7e-19   69.8   0.0    1.8  2  ResIII        Type III restriction enzyme, res subunit
    5.9e-18   65.2   0.1    3.3e-17   62.8   0.0    1.9  2  DEAD          DEAD/DEAH box helicase
     0.0034   17.4   0.0     0.0078   16.2   0.0    1.6  1  Flavi_DEAD    Flavivirus DEAD domain
  ------ inclusion threshold ------
       0.03   14.5   0.0        0.7   10.0   0.0    2.4  2  Helicase_C_2  Helicase C-terminal domain
      0.067   12.5   0.0       0.13   11.5   0.0    1.4  1  DUF3638       Protein of unknown function (DUF3638)
       0.12   12.5   0.0        1.1    9.4   0.0    2.5  2  DUF2007       Putative prokaryotic signal transducing protein


Domain annotation for each model (and alignments):
>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.9   0.1   7.6e-27     2e-23       2     110 ..     337     448 ..     336     449 .. 0.92

  Alignments for each domain:
  == domain 1  score: 82.9 bits;  conditional E-value: 7.6e-27
                 HHHHHHHHHHHTTTTSEEEEEESSHHHHHHHHHHHHHT..TSTEEEESTT.....STHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEESSS CS
  Helicase_C   2 kleallellkleeeggkilifvntidrlekvklllekk..gikvavlhge.....lpqnereeileqfnkgesdvLiatdvaerGidipkvnlVinfdl 93 
                 k+++l+e++  e++ gk+lif+ ++d+++   ++++    gi++a+l g+     l+q++++e++++f++g ++vL+at+v+e+G+di +vn Vi++d 
  EPA05702.1 337 KILKLKEII--ESVPGKALIFTSYRDSVD--VIFNKLTemGISAAILIGKsgdtgLKQKKQIETVQNFRDGLFRVLVATRVGEEGLDISEVNQVIFYDN 431
                 788999998..89***************8..5552222469********999999******************************************** PP

                 SSSHHHHHHHHTTSSST CS
  Helicase_C  94 prnvtsyiqriGRtgRa 110
                   +  +++qr+GRtgR 
  EPA05702.1 432 VPSSIRFVQRRGRTGRK 448
                 ****************5 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.8   0.0     1e-22   2.7e-19      13     170 ..      29     172 ..       6     173 .. 0.85
   2 ?   -2.5   0.0       1.8   4.5e+03      39      71 ..     275     307 ..     274     359 .. 0.67

  Alignments for each domain:
  == domain 1  score: 69.8 bits;  conditional E-value: 1e-22
                 HHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B--.......-SEEEEEH CS
      ResIII  13 enlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseaykeigkkvsgdkkkakekdstnkkilvtti 111
                 ++         +++ +++++TG GKT +a+++i+++l+ g+   +lfl+p++ l++q ++ +kk l  +       ++g+  ++k+ +  n +++ +t 
  EPA05702.1  29 NQ-------AIQENCIVVLPTGLGKTAIALQVIAEYLSRGS-GGVLFLAPTRVLVNQHYDFLKKNLTLD---DISLITGEDSIQKRTKLWNGSVICATP 116
                 22.......3466889*********************9765.6*****************999999877...578888888888899999********* PP

                 HHHHHTH........HHHTTT-SEEEEETGGGTTS.TTTHHHHHT-..--SEEEEEESS-S CS
      ResIII 112 qsldadseeeeeeseellrdrfdviiiDEaHrlgakkswreilekf..keavllglTATpe 170
                 +  ++d+     +++  ++++f ++i DE+Hr+ ++ ++  i+e f  +++ +lg+TAT++
  EPA05702.1 117 EITKNDL-----DRDIVSPNQFSLVIYDEVHRTVGDYAYSGIAERFasSNSRILGMTATLP 172
                 *******.....9999*******************99*****99996677*********86 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.8
                 HHHHHHHHHH-S.....-EEEEESSHHHHHHHH CS
      ResIII  39 lvaaklierllkkgkeekflflvprkslleqtl 71 
                  + ++ + ++l+++++  fl +++r ++ + + 
  EPA05702.1 275 AIRIHYALNILEAHGITSFLKFCDRAKIKKGAG 307
                 566777778888888888888888888877664 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.8   0.0   1.3e-20   3.3e-17       2     173 ..      22     175 ..      14     178 .. 0.81
   2 ?   -0.1   0.0      0.27   6.9e+02      48      95 ..     350     398 ..     236     427 .. 0.73

  Alignments for each domain:
  == domain 1  score: 62.8 bits;  conditional E-value: 1.3e-20
                 HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHHHHHHHTTCSE CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        DEAD   2 diQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaardqlskldngvdi 100
                 d+Q +  ++++ +++++v  +TG GKT+++l  + + ++    +    +l+++Ptr L++q+++ lkk +        ++i+g++  ++++kl  +  +
  EPA05702.1  22 DYQVNLANQAI-QENCIVVLPTGLGKTAIALQVIAEYLS----RGSGGVLFLAPTRVLVNQHYDFLKKNLTL---DDISLITGEDSIQKRTKL-WNGSV 111
                 56777777777.67***************9999999994....55667********************9994...344445555555777778.57789 PP

                 EEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHT.TTHHHHHHHHHHSHHHCTTSTTTSEEEEEESSBSHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        DEAD 101 vvgtpgrlddllstgklnlsqvrflVlDEadrlldq.gfsdfinrilnqlpqitcdgklqrqvivlSATlpkdv 173
                 + +tp+   + l++  ++ +q+++++ DE++r   +  +s   +r +++           ++++ ++ATlp++ 
  EPA05702.1 112 ICATPEITKNDLDRDIVSPNQFSLVIYDEVHRTVGDyAYSGIAERFASSN----------SRILGMTATLPSEK 175
                 99**********999999**************999856666666644444..........56********9654 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.27
                 -EEEEEESSHHHHHHHHHHHHHHTTTSTSEEE.EEETTSSHHHHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
        DEAD  48 pkalivePtreLaeqtlnnlkkfkkyidlrvl.liiggvaardqlskld 95 
                  kali +  r  +  ++n+l++++  + + +  +  +g ++++q+++++
  EPA05702.1 350 GKALIFTSYRDSVDVIFNKLTEMGISAAILIGkSGDTGLKQKKQIETVQ 398
                 5888888888888888888888888644222112233455555555553 PP

>> Flavi_DEAD  Flavivirus DEAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   3.1e-06    0.0078      10     144 ..      39     179 ..      31     181 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.1e-06
                 E--TTS-TTTTHHHHHHHHHHHTT--EEEEESSHHHHHHHHHHTTTS-EEE--------...-----SE..EEEEHH.HHHHHHHH..T------SEEE CS
  Flavi_DEAD  10 dlhPGaGktrkvlpelvkeaierrlrtlvLaPtrvvlaemeealkglevryktsavkee...ktgrelv..dvmcha.tftkrlls..pvrkknyelii 100
                  l  G Gkt   l  + +   +     l LaPtrv ++  ++ lk+     + s+++ e   ++ ++l    v+c +  +tk+ l    v  +++ l+i
  EPA05702.1  39 VLPTGLGKTAIALQVIAEYLSRGSGGVLFLAPTRVLVNQHYDFLKKNLTLDDISLITGEdsiQKRTKLWngSVICATpEITKNDLDrdIVSPNQFSLVI 137
                 455699***98887666666666677889********9988877765433333333322000222333312577755247888888534556679**** PP

                 EETTT--SHHHHHHHHHHHHHHHTTS-EEEEEESS-TT---SS- CS
  Flavi_DEAD 101 mDeahflDPasiaarGyletkaeegeaalilltatPPGtsdpfp 144
                  De h +     a  G++e+ a+++ + ++ +tat P ++d+ +
  EPA05702.1 138 YDEVHRTVG-DYAYSGIAERFASSN-SRILGMTATLPSEKDKAT 179
                 *****9865.578999988888777.89999******9998765 PP

>> Helicase_C_2  Helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0       0.1   2.6e+02       2      44 ..      55      97 ..      54     111 .. 0.80
   2 ?   10.0   0.0   0.00027       0.7       2      82 ..     342     422 ..     341     433 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.1
  Helicase_C_2  2 lellevvpggvlvffpSyklleevverlkeeleskkieifvee 44
                  +e+l+   ggvl + p   l+++ +++lk++l+ ++i++++ e
    EPA05702.1 55 AEYLSRGSGGVLFLAPTRVLVNQHYDFLKKNLTLDDISLITGE 97
                  567777889**********************999999887743 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00027
  Helicase_C_2   2 lellevvpggvlvffpSyklleevverlkeeleskkieifvee....keesrekvleeykekkkkgaillavcrGklsEGidfsd 82 
                    e++e+vpg++l+f++  + ++ ++++l e + s  i i ++     k++++ ++++++++  +   +l+a+      EG+d+s+
    EPA05702.1 342 KEIIESVPGKALIFTSYRDSVDVIFNKLTEMGISAAILIGKSGdtglKQKKQIETVQNFRD--GLFRVLVATR--VGEEGLDISE 422
                   5799**********99999*************999888888778999999999999***99..8888888888..5579999884 PP

>> DUF3638  Protein of unknown function (DUF3638)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   5.2e-05      0.13      20      92 ..      17      86 ..      13      89 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.2e-05
     DUF3638 20 niliReeQaevAkemispssgensvlQLnmGeGKssvIvPivaaaladgk.kLvrvivlkpllkqmaqlLvskL 92
                +i  R+ Q++ A++ i+    en ++ L  G GK+++ + ++a +l+ g+  ++ +  ++ l++q +++L+++L
  EPA05702.1 17 SIEKRDYQVNLANQAIQ----ENCIVVLPTGLGKTAIALQVIAEYLSRGSgGVLFLAPTRVLVNQHYDFLKKNL 86
                56679999999999996....9*************************999456666667889999999999887 PP

>> DUF2007  Putative prokaryotic signal transducing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.87   2.2e+03      36      52 ..      60      76 ..      45      79 .. 0.71
   2 ?    9.4   0.0   0.00045       1.1      10      30 ..     275     295 ..     272     313 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.87
     DUF2007 36 sileGalgelpvrilVa 52
                +   G l+  p+r+lV+
  EPA05702.1 60 RGSGGVLFLAPTRVLVN 76
                33444578888****97 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00045
     DUF2007  10 pveaelikslLeeagIeavvk 30 
                 +++++++ ++Le +gI +++k
  EPA05702.1 275 AIRIHYALNILEAHGITSFLK 295
                 699****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (505 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3381.93
//
Query:       EPA05703.1  [L=1112]
Description: BNR/Asp-box repeat protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.021   15.3   0.0      0.095   13.2   0.0    2.2  1  MG2       MG2 domain
        3.3    8.1  11.5        3.1    8.2   0.4    4.4  4  BNR       BNR/Asp-box repeat


Domain annotation for each model (and alignments):
>> MG2  MG2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.1e-05     0.095       8      86 ..       2      79 ..       2      90 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.1e-05
                -SEE-TT-EEEEEEEEESTTCSB---EEEEEEEE-TTSS..EEEEEEEEE-CTTEEEEEEE--TT--SEEEEEEEEECSTT CS
         MG2  8 RglYrPgetVslkallrdetlqglaklplkltirdpdgk..evkelplatdetggaesefalpeaaklGeysvelsadsae 86
                + +Y+Pge   l +++++ t+ ++  ++++++i+dp+    + ++  + +++ g++  ++++   +  G+y+++++a++ +
  EPA05703.1  2 KSIYKPGELAALDIVVLNGTGAPVCPANITMQITDPNFSltVLSSDNVIQSSCGLYLANYPT---TIAGNYTINIQAETGN 79
                68**********************************97632334444466666666666554...5679999998665554 PP

>> BNR  BNR/Asp-box repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.4   0.00035       3.1       2      11 ..     258     267 ..     257     268 .. 0.90
   2 ?    5.4   0.1    0.0029        26       3      10 ..     376     383 ..     374     384 .. 0.91
   3 ?   -2.3   0.2         1     9e+03       6      11 ..     490     495 ..     490     496 .. 0.84
   4 ?   -2.6   0.1       1.2   1.1e+04       2       9 ..    1098    1105 ..    1097    1105 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00035
                 EESSTTSS-E CS
         BNR   2 yStDgGktWs 11 
                 ySt+gG +W+
  EPA05703.1 258 YSTNGGLSWN 267
                 9********7 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0029
                 ESSTTSS- CS
         BNR   3 StDgGktW 10 
                 S DgG tW
  EPA05703.1 376 SIDGGTTW 383
                 99****** PP

  == domain 3  score: -2.3 bits;  conditional E-value: 1
                 TTSS-E CS
         BNR   6 gGktWs 11 
                 +G +W+
  EPA05703.1 490 NGASWN 495
                 79***7 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 1.2
                  EESSTTSS CS
         BNR    2 yStDgGkt 9   
                  +St+ Gkt
  EPA05703.1 1098 VSTNTGKT 1105
                  8***9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.75u 0.30s 00:00:01.05 Elapsed: 00:00:00.47
# Mc/sec: 7069.68
//
Query:       EPA05704.1  [L=354]
Description: hypothetical protein BG20_I1971, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.4e-11   44.0   0.4      1e-09   38.7   0.4    2.6  1  Laminin_G_3   Concanavalin A-like lectin/glucanases superfami
  ------ inclusion threshold ------
       0.11   12.6   2.4         15    5.8   0.1    2.7  2  DUF2802       Protein of unknown function (DUF2802)
       0.12   11.6   0.0       0.18   10.9   0.0    1.3  1  DUF2099       Uncharacterized protein conserved in archaea (D
        0.2   11.9   5.2         10    6.4   0.3    3.5  4  Tn7_TnsC_Int  Tn7 transposition regulator TnsC


Domain annotation for each model (and alignments):
>> Laminin_G_3  Concanavalin A-like lectin/glucanases superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7   0.4   2.2e-13     1e-09      25     150 ..       1     146 [.       1     148 [. 0.74

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 2.2e-13
  Laminin_G_3  25 vkpdslpsaaqi.iissssdgrgfelgl...dgsgrlrfsvnagngaeesvtsgasvpageWtHvavtydggtlrlYvNGvevgsatltgg....... 111
                  vkpd +++++ + +i  s++  +f+l++   ++s++  fs+ +g  ++ +v+s++++ + eWtH+++ ++++t+++YvNG + g+++l          
   EPA05704.1   1 VKPDYSHGSKEFtVI--SKEK-SFSLTVnnyASSHTAKFSIFDG-IKWVQVDSKSEI-PQEWTHLTASFSNKTISIYVNGSLEGTKQLEKIpslslig 93 
                  688888888777355..7777.*****84434666999999999.699999999998.789************************9985554455555 PP

  Laminin_G_3 112 .......llsatsgplviGrdp..gg.....ddpfdGlidevriynralsaae 150
                             + +++v+G+    +g     ++ f Gl+d+v +++++ls  +
   EPA05704.1  94 klesvdvEHISSENDIVVGAYIstKGsftqtNNLFSGLVDDVLLFDTPLSILQ 146
                  55555543335566667776654422345558888899999999999988655 PP

>> DUF2802  Protein of unknown function (DUF2802)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.4    0.0034        15      15      39 ..     184     208 ..     165     210 .. 0.84
   2 ?    5.8   0.1    0.0034        15      13      37 ..     214     238 ..     213     240 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0034
     DUF2802  15 qleerleeleqqdpqsklYsqAikl 39 
                 ++++ +e+l+ +d+ + +YsqA+  
  EPA05704.1 184 NTQSLQEQLSLSDTLTFSYSQAQNT 208
                 678899****************865 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0034
     DUF2802  13 lkqleerleeleqqdpqsklYsqAi 37 
                 l++l++ +e+l+ +d+ + +YsqA+
  EPA05704.1 214 LSSLNSLQEQLSLSDTLTFSYSQAQ 238
                 6789999*****************7 PP

>> DUF2099  Uncharacterized protein conserved in archaea (DUF2099)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   4.1e-05      0.18     113     172 ..     154     211 ..     134     243 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.1e-05
     DUF2099 113 glggrisGlveTePieevierieeeggivldketaeidqveGvkkAiekgykkiavtvae 172
                 g++    Gl +T+ i+e++++ie+e g+ ++++t ++++   ++  ++ +y++   tv  
  EPA05704.1 154 GIS--THGLTQTKSIDEILKEIEREAGLYVQNNTQSLQEQLSLSDTLTFSYSQAQNTVNP 211
                 444..45******************************99999999999999998888865 PP

>> Tn7_TnsC_Int  Tn7 transposition regulator TnsC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       2.1   9.4e+03      20      40 ..     123     140 ..     121     142 .. 0.75
   2 ?   -2.8   0.0       1.7   7.8e+03      20      32 ..     162     174 ..     161     177 .. 0.81
   3 ?    5.7   0.1    0.0038        17      11      24 ..     195     208 ..     193     211 .. 0.90
   4 ?    6.4   0.3    0.0022        10      11      25 ..     227     241 ..     225     246 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.1
  Tn7_TnsC_Int  20 QasseedfyeeLkqkglifdl 40 
                   Q+++   ++  L+   l+fd+
    EPA05704.1 123 QTNN---LFSGLVDDVLLFDT 140
                   5544...78888999999997 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.7
  Tn7_TnsC_Int  20 QasseedfyeeLk 32 
                   Q++s +++ +e+ 
    EPA05704.1 162 QTKSIDEILKEIE 174
                   9999999998875 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.0038
  Tn7_TnsC_Int  11 sddLRFvySQasse 24 
                   sd L F ySQa+++
    EPA05704.1 195 SDTLTFSYSQAQNT 208
                   899********995 PP

  == domain 4  score: 6.4 bits;  conditional E-value: 0.0022
  Tn7_TnsC_Int  11 sddLRFvySQassee 25 
                   sd L F ySQa++++
    EPA05704.1 227 SDTLTFSYSQAQNTT 241
                   899*********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2485.02
//
Query:       EPA05705.1  [L=139]
Description: CBS domain protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-16   60.7   0.4    2.8e-07   30.9   0.0    2.1  2  CBS          CBS domain
  ------ inclusion threshold ------
      0.021   14.4   0.1      0.034   13.7   0.1    1.4  1  NPR1_like_C  NPR1/NIM1 like defence protein C terminal
      0.095   13.7   0.2       0.78   10.7   0.2    2.0  1  FKBP_N       Domain amino terminal to FKBP-type peptidyl-prol


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.1   3.2e-10   1.9e-06       2      56 ..      18      72 ..      16      73 .. 0.91
   2 !   30.9   0.0   4.7e-11   2.8e-07       2      37 ..      84     119 ..      83     126 .. 0.89

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 3.2e-10
                HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
         CBS  2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56
                g++m++d++ ++ +t ++ a++++ +++ + + V+de++ ++Givt++D++++++
  EPA05705.1 18 GAYMSKDFLLLNQNTLIRGAAKMLQDSDRDDIIVIDENNLPIGIVTDEDIINKMS 72
                789*********************9888789979999999***********9875 PP

  == domain 2  score: 30.9 bits;  conditional E-value: 4.7e-11
                 HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEE CS
         CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVVd 37 
                 +dim+ +++t+++ ttl eal +mr+++++ lPV+ 
  EPA05705.1  84 KDIMSAPLITINEKTTLQEALHKMRDSKIRKLPVLS 119
                 79***********************999******93 PP

>> NPR1_like_C  NPR1/NIM1 like defence protein C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   5.6e-06     0.034     105     141 ..      95     131 ..      63     137 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.6e-06
  NPR1_like_C 105 ltevDlnetpfkikekllsRleaLskTVelGkrfFpr 141
                   +++ l+e+ +k+++ +  +l  Lsk  e+G+ +Fp+
   EPA05705.1  95 NEKTTLQEALHKMRDSKIRKLPVLSKKKEVGRNYFPE 131
                  3445799*****************************6 PP

>> FKBP_N  Domain amino terminal to FKBP-type peptidyl-prolyl isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2   0.00013      0.78       2      40 ..       7      45 ..       6     135 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00013
      FKBP_N  2 dkvsYalGlsigqqlkaqgkeldkdavlaGlkdalkgks 40
                 +vsY+l   ig ++++++  l+++++++G +++l++++
  EPA05705.1  7 RSVSYVLSKHIGAYMSKDFLLLNQNTLIRGAAKMLQDSD 45
                689******************************998754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 920.69
//
Query:       EPA05706.1  [L=70]
Description: hypothetical protein BG20_I2418 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.047   12.5   0.0      0.047   12.5   0.0    1.0  1  Nup188_C  Nuclear pore protein NUP188 C-terminal domain
      0.077   12.7   0.0       0.09   12.5   0.0    1.1  1  TFB6      Subunit 11 of the general transcription factor TFII


Domain annotation for each model (and alignments):
>> Nup188_C  Nuclear pore protein NUP188 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.2e-06     0.047     298     338 ..      22      62 ..       2      68 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.2e-06
                 SS--------HHHHHHHHHHHHT-HHHHHHHB---SHHHHH CS
    Nup188_C 298 ardipevewdaasvkedvefwlssrklLrerlvplgerele 338
                  r++++ +wd+ ++k+++  +l+ r  L ++l++ +e++++
  EPA05706.1  22 VRTLHQNNWDSGNLKQQIADLLKIRDDLVDKLMSFKEHDAN 62 
                 57788899**************************9998875 PP

>> TFB6  Subunit 11 of the general transcription factor TFIIH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     1e-05      0.09      10      50 ..      20      60 ..      12      63 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1e-05
        TFB6 10 kdldklvdvlWvSgtpslqipyLlniaselldylekfppsp 50
                  + +l ++ W Sg  + qi  Ll+i ++l+d l +f+ ++
  EPA05706.1 20 DCVRTLHQNNWDSGNLKQQIADLLKIRDDLVDKLMSFKEHD 60
                5566777788************************9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.32s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 437.36
//
Query:       EPA05707.1  [L=38]
Description: hypothetical protein BG20_I2419, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (38 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1801  (0.100452); expected 358.6 (0.02)
Passed bias filter:                      918  (0.051202); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 264.03
//
Query:       EPA05708.1  [L=120]
Description: hypothetical protein BG20_I2417 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-07   31.1   0.0    1.5e-07   31.1   0.0    1.0  1  DNase-RNase  Bifunctional nuclease


Domain annotation for each model (and alignments):
>> DNase-RNase  Bifunctional nuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.0   8.2e-12   1.5e-07      16     124 ..      10     117 ..       1     120 [] 0.83

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 8.2e-12
                  EEEEETTSSEEEEEE--HHHHHHHHHHHCT---SS--HHHHHHHHHHHTTEEEEEEEEEEEETTEEEEEEEEEET---.EEEEE-HHHHHHHHHHHT- CS
  DNase-RNase  16 vlLreeegrrvlpIwigaaeaqaialalegeeppRPlthDLlasllealgakvervvItdledgtfyAelvlrkeeee.leidaRpSDaiaLAlrtga 112
                  ++L+ ++g+++       + a++i+  +++e+ + P  + ++ +++e+ ++ + +v I++   ++  A+l+++ + ++ +  + R+SDa+aL + +++
   EPA05708.1  10 LVLKGDDGKEFHMRAFSGEVARHISSFVDSESDSVPSIYKMMEEICEENELILVKVKIYES-GEVLRANLYFTGK-KDiVLRNYRASDAMALGALYNI 105
                  566666664443334445569999999********************************96.6799*******95.44477799************** PP

                  -EEEEHHHHHHH CS
  DNase-RNase 113 pIyveeevleea 124
                  pI+v +++l+e+
   EPA05708.1 106 PILVRKNLLKEH 117
                  ********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 816.47
//
Query:       EPA05709.1  [L=71]
Description: hypothetical protein BG20_I1991 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      6e-13   48.7   2.3    8.6e-13   48.2   2.3    1.3  1  CbtB      Probable cobalt transporter subunit (CbtB)


Domain annotation for each model (and alignments):
>> CbtB  Probable cobalt transporter subunit (CbtB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.2   2.3   4.8e-17   8.6e-13      11      51 .]      18      71 .]       9      71 .] 0.91

  Alignments for each domain:
  == domain 1  score: 48.2 bits;  conditional E-value: 4.8e-17
        CbtB 11 lqlvaAllLGlllvylvgfsqaaa..............lHnaaHDtRHaagfPCH 51
                + +++A++++++l ++vgf+q+ +              +H+++HD+RHaagfPCH
  EPA05709.1 18 AIVALAIIFAAGL-FVVGFDQGHIfslvygdqayqdlyIHELTHDMRHAAGFPCH 71
                5678888888885.9**************************************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       676  (0.0377043); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.30s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 464.97
//
Query:       EPA05710.1  [L=135]
Description: histidine triad domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.5e-23   82.7   1.7    3.2e-23   82.3   1.7    1.2  1  HIT        HIT domain
    4.3e-11   43.3   0.6    5.4e-11   43.0   0.6    1.1  1  DcpS_C     Scavenger mRNA decapping enzyme C-term binding
  ------ inclusion threshold ------
       0.07   13.0   1.0       0.11   12.4   1.0    1.3  1  CwfJ_C_1   Protein similar to CwfJ C-terminus 1
       0.11   12.8   0.0       0.16   12.3   0.0    1.2  1  SMC_hinge  SMC proteins Flexible Hinge Domain
       0.13   12.1   0.5       0.31   10.9   0.1    1.8  2  MarB       MarB protein


Domain annotation for each model (and alignments):
>> HIT  HIT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.3   1.7     9e-27   3.2e-23       3      98 .]      12     107 ..      10     107 .. 0.98

  Alignments for each domain:
  == domain 1  score: 82.3 bits;  conditional E-value: 9e-27
                 CC-CCEEEE-SSEEEEE-SS-SSSSEEEEEESSTGCSGGGCCHHHHHHHHHHHHHHHHHHHTCTTCCCEEEEEEESGGGT-SSSS-EEEEEEC-TT CS
         HIT   3 eipstvvyeddlvlafldidpkapghlLvipkkhlselhdlteeelakllsavkkvakalqkkfknkglrvvinngahagqsvahlHiHviprreh 98 
                 + +s+++yed   +afld+ p   gh Lv+pk+h ++++d+++e +++++s+v k+a+a+ +   ++++ ++ nng++a q ++h+HiH+ipr++h
  EPA05710.1  12 VRDSHMIYEDASHVAFLDKYPIDVGHSLVVPKNHHERITDMNHESVGNMFSIVPKIANAVLTATGADAFSLAQNNGRAAKQIIPHVHIHIIPRYNH 107
                 6799*****************************************************************************************986 PP

>> DcpS_C  Scavenger mRNA decapping enzyme C-term binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.0   0.6   1.5e-14   5.4e-11       1     101 [.       2     103 ..       2     116 .. 0.89

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 1.5e-14
                 T-HHHHHHTTSS-B-EEEE-SSEEEEE-SS-SSSEEEEEEESS---SGGG--TTTTTHHHHHHHHHHHHHHHTT-T.-EEEEE--SCCCT--S-S--EE CS
      DcpS_C   1 kwvfnilakgkepervvyedekfvvlkDikpkaklhllvipkrdikslrdLtkehlpllkemrekakkvieekyne.vdaeelrvgvhyqPsvyhlHlH 98 
                 +++f+++ +g   + ++yed + v++ D++p +  h lv+pk++ + ++d+++e +  + +++ k+ +++     +   +   + g  +++ + h+H+H
  EPA05710.1   2 SCIFCDILSGVRDSHMIYEDASHVAFLDKYPIDVGHSLVVPKNHHERITDMNHESVGNMFSIVPKIANAVLTATGAdAFSLAQNNGRAAKQIIPHVHIH 100
                 69******************************************************9999999998887766664457788899*************** PP

                 EEE CS
      DcpS_C  99 vis 101
                 +i 
  EPA05710.1 101 IIP 103
                 *97 PP

>> CwfJ_C_1  Protein similar to CwfJ C-terminus 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.0   3.1e-05      0.11      13     108 ..       2     103 ..       1     111 [. 0.72

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.1e-05
                 H-S--.--SS---SS--S-B-SSEEEE---S-SSTT-EEEEESS--SSTTSS-HHHHHHHHHHHHHHH.HHHHHTT--EEEEEE-.....SSS-----E CS
    CwfJ_C_1  13 sClfC.lsnpklekhlivsignkvYlalpkgpLssgHvliipieHisallsldeevldeirkfrkalv.kmykkqdkdavvfEis.....sersvHlai 104
                 sC fC + +  +++h+i   + +  + l k p++ gH l++p +H +  + +++e   ++      ++ ++ ++++ da  +  +     ++  +H++i
  EPA05710.1   2 SCIFCdILSGVRDSHMIYEDA-SHVAFLDKYPIDVGHSLVVPKNHHERITDMNHESVGNMFSIVPKIAnAVLTATGADAFSLAQNngraaKQIIPHVHI 99 
                 688885444455566665433.333557789*********************99988887666555550558899999988876666655666789999 PP

                 EEEE CS
    CwfJ_C_1 105 qvip 108
                 ++ip
  EPA05710.1 100 HIIP 103
                 9998 PP

>> SMC_hinge  SMC proteins Flexible Hinge Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.4e-05      0.16       6      49 ..      55      98 ..      52     121 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.4e-05
   SMC_hinge  6 GrladlievdegyekAveaalgnrlqalvvedeetakkiieflk 49
                  +++++++ ++   Av +a g+++++l   +  +ak+ii +++
  EPA05710.1 55 ESVGNMFSIVPKIANAVLTATGADAFSLAQNNGRAAKQIIPHVH 98
                56899***********************************8865 PP

>> MarB  MarB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   8.6e-05      0.31      30      51 ..      38      59 ..      33      62 .. 0.91
   2 ?   -1.4   0.0      0.61   2.2e+03      44      44 ..     105     105 ..      74     125 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 8.6e-05
        MarB 30 vmllPsehdespfDlnhmsags 51
                 +++P +h+e+  D+nh s+g+
  EPA05710.1 38 SLVVPKNHHERITDMNHESVGN 59
                689***************9986 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.61
        MarB  44 l 44 
                  
  EPA05710.1 105 Y 105
                 3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 884.88
//
Query:       EPA05711.1  [L=252]
Description: peptide chain release factor 1, archaeal and eukaryotic form [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-18   67.2   0.1    2.8e-18   66.5   0.1    1.4  1  eRF1_3    eRF1 domain 3
    2.4e-11   44.1   0.0    1.2e-10   41.8   0.0    2.2  3  eRF1_2    eRF1 domain 2


Domain annotation for each model (and alignments):
>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.5   0.1   3.1e-22   2.8e-18       2     112 ..     105     243 ..     104     244 .. 0.89

  Alignments for each domain:
  == domain 1  score: 66.5 bits;  conditional E-value: 3.1e-22
                 HHHHHHHHHHHHHHHCTCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSH.HHHHS............................-HHH-HHHHHHHH CS
      eRF1_3   2 iqekklleefleelakdtgkavYGveevlkalemgAvetLLvseelersrdt.lkekv............................ketgeelelveli 71 
                 ++ekkl+e++++e++  +g+ vYG ++v + l+ + v+ L+++++ + +r++  ++++                            ++  +e+++ +++
  EPA05711.1 105 VEEKKLIEDLFREINSHSGLGVYGLQDVIELLKNNVVKVLIITDDTNLNRVEgKCRRCehlqeeiverrevipkktqytsnpcpgcNSMEVEANEQDIV 203
                 89************************************************9954444599*********************997654444444444588 PP

                 HHHHHHHHHTT-EEEEE-TTSHHHHHHHHHTTTEEEEESS- CS
      eRF1_3  72 eelvenveesgakveiisseseeGeqlvkafgGiaaiLRyk 112
                 + l   + ++g+++e++s + e+G +l +++g ++aiLRy+
  EPA05711.1 204 DYLELLAAKVGTRLEVVSGSAEHGVML-SSLGKVGAILRYN 243
                 88888999*******************.************7 PP

>> eRF1_2  eRF1 domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   0.0   1.4e-14   1.2e-10      76     133 .]      44     101 ..      14     101 .. 0.91
   2 ?   -2.8   0.0       0.8   7.1e+03     116     128 ..     125     137 ..     106     143 .. 0.68
   3 ?   -1.6   0.0      0.34     3e+03      54      90 ..     213     249 ..     199     251 .. 0.74

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 1.4e-14
                 TESEEEEEESSTHHHHHHHHHHHHHHHHTCCEEEEE-S-TSCHHHHHHHHCCHHHHCC CS
      eRF1_2  76 klkgiilagpgfvkeefldkdlldaelkkkviklvdvsyggesglnevlekaaevlkd 133
                 + kg+i+ gpg++ke+f+++++l+++l++ +i ++d+sy g +g++e+  k+ e l+d
  EPA05711.1  44 QSKGLIISGPGPTKEDFINGNYLEYRLQNMIINTIDASYSGAEGIREAFAKSGELLSD 101
                 569**********************************************999888876 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.8
                 SCHHHHHHHHCCH CS
      eRF1_2 116 gesglnevlekaa 128
                 g +gl++v+e  +
  EPA05711.1 125 GVYGLQDVIELLK 137
                 5678888888744 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.34
                 HHHHHHHHHHHHHHHHHHCHTTTESEEEEEESSTHHH CS
      eRF1_2  54 leeflkkvaeaankafllvdkdklkgiilagpgfvke 90 
                 +   l+ v  +a++  +l   +k+ +i+   pg++k+
  EPA05711.1 213 VGTRLEVVSGSAEHGVMLSSLGKVGAILRYNPGHTKQ 249
                 5556677777888887888899999999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       751  (0.0418874); expected 358.6 (0.02)
Passed bias filter:                      598  (0.0333538); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1655.23
//
Query:       EPA05712.1  [L=184]
Description: peptide chain release factor 1, archaeal and eukaryotic form [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.8e-10   39.5   0.0    6.7e-10   39.1   0.0    1.2  1  eRF1_1          eRF1 domain 1
  ------ inclusion threshold ------
       0.16   11.8   0.0       0.17   11.7   0.0    1.1  1  RNA_pol_Rpb1_6  RNA polymerase Rpb1, domain 6


Domain annotation for each model (and alignments):
>> eRF1_1  eRF1 domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   0.0   7.5e-14   6.7e-10       2     128 ..      19     143 ..      18     144 .. 0.91

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 7.5e-14
                 EEEEE..CTBTTSCCEEEEEE-SCHHHHHHHHHCHTTHEEEEEEEECHHH.......--CEEEEEEEEEEEEEEECTT...SSEEEEEEEEEEGGGG.- CS
      eRF1_1   2 kllkr..dlekdgsgsvtLipeddedlwhlynliapgdsvrastvrkvqresstgsreservklkLtikvekvdfdkd...agvlrisGkvieeneh.v 94 
                 k+l++  + +++g++++++++++ ++l ++   ++++++++ ++++  +r         ++v   L   v+++++ k+    g++ ++G    e +   
  EPA05712.1  19 KMLEElsQKSGRGTELISVYIPKGKQLHEIISTLQQEQGTADNIKSDLTR---------SHVVDSLGKVVQRLKLLKKtpeRGLVMFCGALPPEGGGpL 108
                 77777767889*************************************99.........89999***********9997778************99644 PP

                 -TTSEEEEEE-TTSEEEEEECE.ESHHHHHHHHHH CS
      eRF1_1  95 klgafhtldlelkrpftiikee.wdsfalerLkea 128
                   +    ++++++++++ + ++ +d+f++++Lk++
  EPA05712.1 109 GSEVVKVWEIDPPKDLKQYLYRcDDHFHVDILKDM 143
                 44557789************999**********98 PP

>> RNA_pol_Rpb1_6  RNA polymerase Rpb1, domain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   1.9e-05      0.17      65     137 ..      13      87 ..       8     141 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.9e-05
                     HHHHHHHHHHHTT-T..T---EEE..EES..-HHHHHHHHHHHTT--SSS-B---HHHHHHHHHHHHTT--SS-S CS
  RNA_pol_Rpb1_6  65 qLkedRellrkeifpdeekdekvklqLPv..NikRlienaqkefkidkrkesdlspveviekvkelldklvvvrg 137
                     +L + R++l +   ++++++e +++++P    ++ +i++ q+e +  ++ +sdl+  +v++++ +++++l ++++
      EPA05712.1  13 KLYKIRKMLEELSQKSGRGTELISVYIPKgkQLHEIISTLQQEQGTADNIKSDLTRSHVVDSLGKVVQRLKLLKK 87 
                     57788888888777767788889999995337999***********************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      598  (0.0333538); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1175.16
//
Query:       EPA05713.1  [L=214]
Description: DSBA-like thioredoxin domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-32  113.3   0.0    1.6e-32  113.0   0.0    1.0  1  Thioredoxin_4  Thioredoxin
    8.8e-16   58.3   0.0    9.3e-15   54.9   0.0    1.9  1  DSBA           DSBA-like thioredoxin domain
    1.8e-09   38.0   0.1      3e-09   37.3   0.1    1.3  1  Thioredoxin_2  Thioredoxin-like domain
    2.2e-05   24.2   0.0    2.8e-05   23.9   0.0    1.2  1  Thioredoxin_5  Thioredoxin
  ------ inclusion threshold ------
      0.087   12.8   0.1       0.34   10.9   0.0    1.9  2  Thioredoxin    Thioredoxin


Domain annotation for each model (and alignments):
>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.0   0.0   4.3e-36   1.6e-32       4     166 .]      43     213 ..      41     213 .. 0.85

  Alignments for each domain:
  == domain 1  score: 113.0 bits;  conditional E-value: 4.3e-36
                    SSEEES-TT-SEEEEEEE-TT-HHHHHHHHHHH.HHHHHHHHTTSEEEEEEE-..---STTTHHHHHHHTT--TTHHHHHHHHHHHHTH.....HH CS
  Thioredoxin_4   4 tdiviGnpdApvtvieyedlrCphCakfeeeve.klleeyidtGkvkfiirdfpldkekeslkaamaarcageespeaflaikallysq.....qe 93 
                    +++++Gnp+A++t+ e+ d++C  C kf++ ++  ++ ++idtGkvk++++dfpl++   s+ aa+ a ca++++  +++ +++ +y++       
     EPA05713.1  43 GSPILGNPSASITILEFGDYQCTFCYKFHQGTLnTIKHDFIDTGKVKLVFKDFPLNGSD-SILAAQGAYCAQDQE--KYWQYHDEIYKNwagerT- 134
                    6799***************************9989***********************8.***********9997..667777768887454433. PP

                    HTTS-......HHHHH.....HHHHHTS-------HHHHHHHHHHHHHHT--SS-EEEE..TTEE..E-TT--HHHHHHHHT- CS
  Thioredoxin_4  94 ewaes......lkelaaealdkdekfeacleeekldalveaeskeakkagiestPtfii..ngek..veepqtyeelkalida 166
                               l+++a+    +  kf++cl+++k+ ++v +     kk g+ +tP+f++  n+++  ++++q+ e + + id+
     EPA05713.1 135 ----GwitrdsLDKFASTVNLNLDKFNECLDSQKYLEKVNQLYDFGKKIGVDATPSFFVfnNEKIikITGNQPLEVFLKTIDE 213
                    ....334444677777777777999**************8877777**************6566555699*******999995 PP

>> DSBA  DSBA-like thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.9   0.0   2.6e-18   9.3e-15       1     192 [.      55     211 ..      55     212 .. 0.93

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 2.6e-18
                 EEEEEEBTTBHHHHHHHHHHHHHHHHC....CTEEEEEEE-SSSCHHHHCT.S.GGGSHHHHHHHHHHHHHHHHHHT....GGSSHHHHHHHHHHHHHH CS
        DSBA   1 tvdeffDvlCPyCylgkerleklaars....pdvkvvlrpfelagakkasgnvgpselpeklkylledlkrlaeaegiplrfpkdklknstraarllla 95 
                 t+ ef D++C +Cy + +     ++ +     +vk+v+++f+l g+                                          +s  aa+ ++ 
  EPA05713.1  55 TILEFGDYQCTFCYKFHQGTLNTIKHDfidtGKVKLVFKDFPLNGS------------------------------------------DSILAAQGAYC 111
                 789*************997766666666*9777*************..........................................*********** PP

                 HHHHHGHHHHHHHHHHHHHTSSS-TSSHHHHHHHHHHTTS.HHHHHHHHTSHHHHHHHHHHHHHHHHTT-SSSSEEEE.TTC..EEEESSSSHHHHHHH CS
        DSBA  96 agaeglaekvvrelfealwsegqaitddqellevaekaGldaeeldealeseavkeavrentaaaqslgvtGvPtvvv.dgk..rmvfGadrldtlada 191
                 a+ ++++ ++  e+++   +e++   ++++l+++a+ + l+ +++ e l+s+++ e+v++  + ++++gv  +P ++v +++    ++G+++l+ + + 
  EPA05713.1 112 AQDQEKYWQYHDEIYKNWAGERTGWITRDSLDKFASTVNLNLDKFNECLDSQKYLEKVNQLYDFGKKIGVDATPSFFVfNNEkiIKITGNQPLEVFLKT 210
                 ********************9999999999************************************************96666999*********9987 PP

                 H CS
        DSBA 192 l 192
                 +
  EPA05713.1 211 I 211
                 6 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.1   8.3e-13     3e-09       7     107 ..      54     209 ..      49     211 .. 0.90

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 8.3e-13
  Thioredoxin_2   7 pvlvvftdpdCpyCkklkk.elkel.......ddvtvrvllfp.lkpsfepkavaiwcakekkkafkd............................ 65 
                     +++ f d +C +C k+++ +l ++        +v+    +fp  ++++  +a+  +ca++++k ++                             
     EPA05713.1  54 ITILEFGDYQCTFCYKFHQgTLNTIkhdfidtGKVKLVFKDFPlNGSDSILAAQGAYCAQDQEKYWQYhdeiyknwagertgwitrdsldkfastv 149
                    67889**************666666**9**7767777777788888899**************99999999************************* PP

  Thioredoxin_2  66 ...................ieenvelarkygvrgtPtivfldgkeivarlpGyvpaeelea 107
                                       +++ +++++k gv++tP++++++ + ++ +++G  p e +++
     EPA05713.1 150 nlnldkfnecldsqkylekVNQLYDFGKKIGVDATPSFFVFNNE-KIIKITGNQPLEVFLK 209
                    *************************************9988888.56699**999998876 PP

>> Thioredoxin_5  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   7.9e-09   2.8e-05     100     184 ..     126     207 ..      93     209 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 7.9e-09
  Thioredoxin_5 100 qealflekkniskeellleiaekaglDveefkeDlesklakkafqcDlklakemgvtevPtlvffneneeeeglkveglksyevy 184
                     ++   e++   + + l + a++++l++++f+e l s+   ++ ++   + k +gv+ +P++++fn   +e+ +k++g++++ev+
     EPA05713.1 126 YKNWAGERTGWITRDSLDKFASTVNLNLDKFNECLDSQKYLEKVNQLYDFGKKIGVDATPSFFVFN---NEKIIKITGNQPLEVF 207
                    555555566666669999************************************************...999********99986 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.47   1.7e+03      19      52 ..      53      89 ..      47      95 .. 0.70
   2 ?   10.9   0.0   9.5e-05      0.34      60     102 ..     171     212 ..     149     213 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.47
                 SEEEEEEE-TTSHHHHCH.HHHHHHHHHHCTT..TSE CS
  Thioredoxin 19 klvlveFyApwCghCkal.aPeleklaeelkd..kvk 52
                 +  ++eF    C+ C ++ +++l+++++++ d  kvk
   EPA05713.1 53 SITILEFGDYQCTFCYKFhQGTLNTIKHDFIDtgKVK 89
                 5678888888999995552677777777777655555 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 9.5e-05
                  TSHHHHHHTT-SSSSEEEEEETTEEEEEEESS-HHHHHHHHHH CS
  Thioredoxin  60 enedlakkyevegiPtlklfkngkevkkyegarekeklaaflk 102
                  +  d  kk++v++ P + +f+n+k + k++g+++ e + ++++
   EPA05713.1 171 QLYDFGKKIGVDATPSFFVFNNEK-IIKITGNQPLEVFLKTID 212
                  5567899**********9998887.88999**99999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1325.60
//
Query:       EPA05714.1  [L=109]
Description: sugar-specific transcriptional regulator TrmB, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      5e-07   29.7   0.0    7.3e-07   29.2   0.0    1.2  1  HTH_20          Helix-turn-helix domain
    1.4e-06   28.1   0.6    2.6e-06   27.2   0.4    1.6  1  TrmB            Sugar-specific transcriptional regulator TrmB
    2.1e-05   24.3   0.7    2.5e-05   24.1   0.7    1.1  1  TFIIE_alpha     TFIIE alpha subunit
    0.00022   21.0   0.8    0.00045   20.0   0.5    1.7  2  HTH_5           Bacterial regulatory protein, arsR family
     0.0015   18.3   0.0     0.0019   18.0   0.0    1.2  1  DUF742          Protein of unknown function (DUF742)
     0.0025   17.6   0.0     0.0039   17.0   0.0    1.4  1  HTH_IclR        IclR helix-turn-helix domain
     0.0036   17.2   0.9     0.0067   16.3   0.9    1.5  1  HTH_11          HTH domain
  ------ inclusion threshold ------
      0.013   16.0   2.2       0.12   13.0   0.5    2.1  2  Mga             Mga helix-turn-helix domain
      0.016   14.4   0.0      0.018   14.3   0.0    1.0  1  SdiA-regulated  SdiA-regulated
      0.025   14.7   0.5      0.035   14.2   0.4    1.4  1  DUF2250         Uncharacterized protein conserved in archaea 
      0.035   14.0   0.0      0.052   13.4   0.0    1.4  1  MarR_2          MarR family
      0.037   13.6   1.0      0.076   12.6   0.3    2.0  2  HTH_24          Winged helix-turn-helix DNA-binding
      0.039   13.8   0.1      0.082   12.7   0.1    1.6  1  YycC            YycC-like protein
      0.047   13.7   0.1      0.088   12.8   0.1    1.4  1  PadR            Transcriptional regulator PadR-like family


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.0   5.7e-10   7.3e-07       2      58 ..      18      73 ..      17      73 .. 0.90

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 5.7e-10
                HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
      HTH_20  2 qiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvr 58
                +++eALa+   r+il  +  ++  tasel e l ++ +++++ L  Lee  L+ev++
  EPA05714.1 18 KVIEALADSESRAILFTI-IKKSKTASELSEKLKIPLSSVYKKLSDLEELTLIEVEK 73
                799*****7777777777.7**********************************986 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.4     2e-09   2.6e-06      14      56 ..      31      73 ..      22      88 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 2e-09
                CHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
        TrmB 14 YlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerek 56
                 l  + ++++ta+e++e+l++p s+vY+ L+ Le+  l+e+ek
  EPA05714.1 31 ILFTIIKKSKTASELSEKLKIPLSSVYKKLSDLEELTLIEVEK 73
                444456899*******************************997 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.7   1.9e-08   2.5e-05       4      81 ..      17      93 ..      14     101 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.9e-08
                 HHHHHHCS-HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEEEECCCH CS
  TFIIE_alpha  4 kevvrkfygeeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywrinyekl 81
                 + v+   ++ e   +l+ +++k++++  +l+++lki l  + k L +L e  l+++ ++   +k+ +   ++    k+
   EPA05714.1 17 QKVIEALADSESRAILFTIIKKSKTAS-ELSEKLKIPLSSVYKKLSDLEELTLIEVEKWMISDKGRKFKMYKSRISKA 93
                 789999**************9999875.6*****************************98877777766666665555 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.5   3.5e-07   0.00045       6      46 ..      30      70 ..      25      71 .. 0.92
   2 ?   -3.1   0.0         6   7.7e+03      24      33 ..      82      91 ..      81      92 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 3.5e-07
                HHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
       HTH_5  6 kILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                 IL+   +++++++el+e+l+++ s v   L+ L+e+ L+e
  EPA05714.1 30 AILFTIIKKSKTASELSEKLKIPLSSVYKKLSDLEELTLIE 70
                699999******************************98886 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 6
                HHTS-HHHHH CS
       HTH_5 24 elglsqstvS 33
                ++++ +s +S
  EPA05714.1 82 KFKMYKSRIS 91
                5788889888 PP

>> DUF742  Protein of unknown function (DUF742)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.4e-06    0.0019      41      93 ..      24      77 ..       4      87 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.4e-06
      DUF742 41 lqpehrail.rLcreplsVaelaAelklPvgvvrvLlsdLldaglltvrapvtd 93
                + +e rail  +++++++  el+ +lk+P++ v   lsdL +  l++v++ ++ 
  EPA05714.1 24 ADSESRAILfTIIKKSKTASELSEKLKIPLSSVYKKLSDLEELTLIEVEKWMIS 77
                5678888873566669*******************************9986665 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0     3e-06    0.0039      10      49 ..      21      70 ..      15      73 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3e-06
                CT-CTTBSS..........-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
    HTH_IclR 10 dalaeapqe..........ltlselArrtglpkStvhRlLqtLvelGyve 49
                +ala    +           t sel++++ +p S+v+  L+ L+el ++e
  EPA05714.1 21 EALADSESRailftiikksKTASELSEKLKIPLSSVYKKLSDLEELTLIE 70
                5555555555555555554489***********************98887 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.9   5.2e-06    0.0067       3      45 ..      29      70 ..      27      73 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.2e-06
      HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg.vp 45
                ++il  ++++ +  +++eL+e+L++  + v++ + +Leel  ++
  EPA05714.1 29 RAILFTIIKKSK--TASELSEKLKIPLSSVYKKLSDLEELTlIE 70
                567777777776..9***********************987444 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.5   9.1e-05      0.12      13      57 ..      23      66 ..      11      72 .. 0.84
   2 ?    2.9   0.0      0.13   1.7e+02      49      67 ..      81      99 ..      71     104 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.1e-05
                HHHSHHHHHHHHHHHHSEEEHHHHHHHCT--HHHHHHHHHHHHHH CS
         Mga 13 lkeslkyqllkflfeeeevsieelaqelyiSestlkrkikelnkl 57
                l++s++  +l +++ +++++  el+++l i  s++++k+ +l++l
  EPA05714.1 23 LADSESRAILFTII-KKSKTASELSEKLKIPLSSVYKKLSDLEEL 66
                66677778888888.99999*********************9985 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.13
                HHHHHHHHHCHCCT-EEET CS
         Mga 49 rkikelnklLkefdleltk 67
                rk k  + ++++ d++++k
  EPA05714.1 81 RKFKMYKSRISKADISIKK 99
                889999***********43 PP

>> SdiA-regulated  SdiA-regulated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.4e-05     0.018      25     101 ..      20      97 ..       3     106 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.4e-05
  SdiA-regulated  25 lSgltydpdtktLfavtnkpeelveLskeGevlrriplkgfkdpEaveylgdgrlaivdE.reqalvvvkvdadtksl 101
                     + +l+ ++++  Lf+++ k ++  eLs++ ++  +   k ++d E ++ ++ ++ +i+d  r+ ++++ ++ ++  s+
      EPA05714.1  20 IEALADSESRAILFTIIKKSKTASELSEKLKIPLSSVYKKLSDLEELTLIEVEKWMISDKgRKFKMYKSRISKADISI 97 
                     6677778999************************************************96477789998887766555 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.4   2.7e-05     0.035      25      69 ..      42      85 ..      20      92 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.7e-05
     DUF2250 25 aksiakeleipleevrellkkLeelGLlervegktikrteaklKk 69
                a  ++++l+ipl+ v ++l +Leel L+e ve+ +i  + +k+K 
  EPA05714.1 42 ASELSEKLKIPLSSVYKKLSDLEELTLIE-VEKWMISDKGRKFKM 85
                667899**********************7.788899999999986 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   4.1e-05     0.052      18      54 ..      27      72 ..      11      81 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.1e-05
                TTS..........EEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
      MarR_2 18 pgr..........dltvgelarrlglsksavsrilkrLvaaGLverr 54
                + r          + t++el ++l+++ s+v + l +L++  L+e +
  EPA05714.1 27 ESRailftiikksK-TASELSEKLKIPLSSVYKKLSDLEELTLIEVE 72
                44444444444333.*****************************987 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.3   5.9e-05     0.076       6      43 ..      29      65 ..      28      70 .. 0.84
   2 ?   -2.2   0.0       2.5   3.2e+03      16      24 ..      88      96 ..      87      97 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.9e-05
      HTH_24  6 rkILelLqknprisqreLAerlglSpstvnrrlkrLee 43
                r+IL ++ k  + + +eL+e+l +++s v + l  Lee
  EPA05714.1 29 RAILFTIIK-KSKTASELSEKLKIPLSSVYKKLSDLEE 65
                567777777.556899********************98 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.5
      HTH_24 16 prisqreLA 24
                +ris ++++
  EPA05714.1 88 SRISKADIS 96
                689999986 PP

>> YycC  YycC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   6.4e-05     0.082       9      24 ..      40      55 ..      38      65 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.4e-05
        YycC  9 eTAvkLskkLnvPLEh 24
                 TA +Ls+kL++PL  
  EPA05714.1 40 KTASELSEKLKIPLSS 55
                6************976 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   6.9e-05     0.088      22      64 ..      45      87 ..      33      88 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.9e-05
                CSTT-CCTTHHHHHHHHHHHHHTTSEEEE.EE-STSSS-EEEEE CS
        PadR 22 lsegllelseGslYpaLkrLekeglvese.weesgegpprkyYr 64
                lse  l++  +s+Y+ L++Le+  l+e e w  s++g++ k+Y+
  EPA05714.1 45 LSEK-LKIPLSSVYKKLSDLEELTLIEVEkWMISDKGRKFKMYK 87
                4333.677789***************965267779999999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       775  (0.0432261); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 727.08
//
Query:       EPA05715.1  [L=241]
Description: putative membrane protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.6e-50  169.9   1.1    9.4e-50  169.6   1.1    1.0  1  CbtA      Probable cobalt transporter subunit (CbtA)
  ------ inclusion threshold ------
       0.18   12.2   3.8       0.48   10.8   0.2    2.9  3  Romo1     Reactive mitochondrial oxygen species modulator 1
        3.4    6.2   8.5        2.4    6.7   6.9    1.5  2  EMP70     Endomembrane protein 70


Domain annotation for each model (and alignments):
>> CbtA  Probable cobalt transporter subunit (CbtA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.6   1.1   1.6e-53   9.4e-50       5     242 ..       7     228 ..       5     229 .. 0.95

  Alignments for each domain:
  == domain 1  score: 169.6 bits;  conditional E-value: 1.6e-53
        CbtA   5 llrgllaGllAGllaflvqrlvvePlilaAeayEeaaaaaeaaeaaaeHehaeaeepelvsrgvqrtlgtvlanvltgvalglllaavfallegrlgkl 103
                 +++ +++G+ AG+++++++ ++veP +++A+ +E+++  ++++e+++     e  ++   +r +q++ g++la+v++g+++g l++++fa+ ++ l++ 
  EPA05715.1   7 VIIVIVSGATAGVIHGGLNLIFVEPSLDQAIGIENQHLFESGEEKET----PEFYAQFDSYRYWQKG-GQILAGVILGISIGSLFGIIFAFSRNTLPGK 100
                 778899*******************************9999988877....2344445678******.******************************* PP

        CbtA 104 saralalllalagflavvlvPflklPpepPgvgaadtieaRqalylatvalsavalalavflarrlaargwnavlaaavaflvlvavallalPhvveaP 202
                 s  +++l+la++++l+++++Pflk+P++pP vg+++t+  R +lyl+++a+s++++++++ ++++l     ++ l+a+v++++ ++++++ +P+    P
  EPA05715.1 101 SYLQKSLVLAGIMWLTIYFIPFLKYPANPPTVGDPETVVLRGILYLTFIAISGFGALGFYKIYQKL----KTKKLIAMVGYVAFIGIVFVTMPQN---P 192
                 ******************************************************************....778**********************...9 PP

        CbtA 203 qpeaaesgfpaallaqFrvaslltqavlWavlGlvfgalv 242
                 +      ++p +l+ +Fr++s++t  ++W++lGl++g l+
  EPA05715.1 193 DLI----TAPMSLVDSFRMVSAFTVSLFWISLGLILGSLW 228
                 965....9*****************************998 PP

>> Romo1  Reactive mitochondrial oxygen species modulator 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0     0.078   4.6e+02      17      36 ..      14      33 ..       9      49 .. 0.71
   2 ?   10.8   0.2     8e-05      0.48       7      31 ..      73      93 ..      67     110 .. 0.57
   3 ?   -2.4   0.1       1.1   6.5e+03      41      44 ..     173     176 ..     151     188 .. 0.55

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.078
       Romo1 17 GlaiGllfGtfsalryglrg 36
                G+++G++ G+++++   +  
  EPA05715.1 14 GATAGVIHGGLNLIFVEPSL 33
                88999999999988766655 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 8e-05
       Romo1  7 kmGalmGaaVGlaiGllfGtfsalr 31
                 +G+++G  +G  +G++f    a++
  EPA05715.1 73 LAGVILGISIGSLFGIIF----AFS 93
                455555555555555555....443 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.1
       Romo1  41 rtlg 44 
                  ++g
  EPA05715.1 173 AMVG 176
                 3332 PP

>> EMP70  Endomembrane protein 70
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1      0.19   1.1e+03     297     347 ..      70     121 ..      58     128 .. 0.59
   2 ?    6.7   6.9    0.0004       2.4     304     394 ..     143     232 ..     108     240 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.19
       EMP70 297 slltvalllyvllgliaGYvsarlyktfgge.kwkkntlltalllpgllflv 347
                 + + ++++l + +g + G + a   +t+ g+ + +k+++l +++  ++ f+ 
  EPA05715.1  70 GQILAGVILGISIGSLFGIIFAFSRNTLPGKsYLQKSLVLAGIMWLTIYFIP 121
                 4445555555555555555555555666555366666666666666666654 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0004
       EMP70 304 llyvllgliaGYvsarlyktfggekwkkntllta.lllpgllflvffllnlilwakessgalpfgtlvlllllwflisvPlvliGsllgfkk 394
                 +ly+ +  i+G+ +  +yk +++ k kk + +++ +++ g++f v++  n  l++  +s   +f ++ ++ +  f is+ l ++Gsl+++ +
  EPA05715.1 143 ILYLTFIAISGFGALGFYKIYQKLKTKKLIAMVGyVAFIGIVF-VTMPQNPDLITAPMSLVDSFRMVSAFTVSLFWISLGL-ILGSLWSHYR 232
                 7999*****************9657666666555145555555.6778899999999999999****************99.7888877664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       693  (0.0386525); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1687.44
//
Query:       EPA05716.1  [L=208]
Description: hypothetical protein BG20_I1990 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.7e-05   23.3   0.0    8.5e-05   22.7   0.0    1.2  1  DUF4443         Domain of unknown function (DUF4443)
  ------ inclusion threshold ------
       0.01   15.8   0.1      0.024   14.6   0.1    1.7  1  HTH_45          Winged helix-turn-helix
       0.17   11.6   0.1       0.47   10.2   0.1    1.8  1  Ribosomal_S19e  Ribosomal protein S19e


Domain annotation for each model (and alignments):
>> DUF4443  Domain of unknown function (DUF4443)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   1.4e-08   8.5e-05      16     105 ..     111     202 ..     104     208 .] 0.86

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.4e-08
     DUF4443  16 yaivvknppqf.k.sielrdeairffakgamilivkngepvfpederplrdtmeelamnieevlnfsdgdlivvtwaenpsdamksayhval 105
                 +ai++kn  ++ k  +e rd ai + ++g++ ++ kn + +fp +++       +    i e l   +gd+i+++ +++p  a  sa   al
  EPA05716.1 111 HAILIKNYSKMiKtGLEQRDYAILYGSEGCITVVCKNKKLIFPGEDKECFIGDSKTRDYILEKLSPDEGDVIIISSSDDPFVAEISAKNSAL 202
                 799999998763325899*************************8888777777777889999*******************99999988887 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1     4e-06     0.024      35      73 ..      55      93 ..      28      96 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4e-06
      HTH_45 35 llnkYLdmLvekglikkskekYvlTekGlelleklkele 73
                 ++  + +L e g+++ +k+   lTekG +l e+l++++
  EPA05716.1 55 SVKTLILHLKETGIVDSTKSGTFLTEKGHKLTEQLQKII 93
                56777889*******99999999************9986 PP

>> Ribosomal_S19e  Ribosomal protein S19e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   7.8e-05      0.47      95     132 ..      55      91 ..      38      96 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 7.8e-05
                     TTSSS--SSS---SS-HHHHHTHHHHH--SS--S--XX CS
  Ribosomal_S19e  95 virkilqqLeklglvkkekkkgrrltkkGqrlldriae 132
                      +++++ +L++ g+v ++ k+g  lt+kG++l +++ +
      EPA05716.1  55 SVKTLILHLKETGIVDST-KSGTFLTEKGHKLTEQLQK 91 
                     45667778*******777.66**********9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      590  (0.0329076); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1376.29
//
Query:       EPA05717.1  [L=52]
Description: hypothetical protein BG20_I2114, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       224  (0.0124937); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.44
# Mc/sec: 354.58
//
Query:       EPA05718.1  [L=40]
Description: hypothetical protein BG20_I2112 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       114  (0.00635841); expected 358.6 (0.02)
Passed bias filter:                       90  (0.0050198); expected 358.6 (0.02)
Passed Vit filter:                         4  (0.000223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 276.03
//
Query:       EPA05719.1  [L=571]
Description: hypothetical protein BG20_I2111, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.76    9.8   7.9       0.41   10.7   1.0    2.5  2  TMEMspv1-c74-12  Plectrovirus spv1-c74 ORF 12 transmembrane p


Domain annotation for each model (and alignments):
>> TMEMspv1-c74-12  Plectrovirus spv1-c74 ORF 12 transmembrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.0   2.3e-05      0.41      14      42 ..     447     475 ..     438     482 .. 0.79
   2 ?    2.3   1.0    0.0092   1.7e+02      29      44 ..     516     531 ..     514     534 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 2.3e-05
  TMEMspv1-c74-12  14 vLgiFlyiGLsiyqKikqirgkkkDKKei 42 
                      +++  + iGL iy+Kik   +kk  +K+ 
       EPA05719.1 447 IMSSAAIIGLIIYKKIKNGSRKKIPQKNT 475
                      5666688***********99999877765 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.0092
  TMEMspv1-c74-12  29 ikqirgkkkDKKeier 44 
                      ik i++kk   Ke+e+
       EPA05719.1 516 IKEIERKKIAEKELEK 531
                      8999999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (571 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3832.33
//
Query:       EPA05720.1  [L=470]
Description: transporter, CPA2 family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.9e-35  120.5  46.8    9.4e-35  120.1  46.8    1.1  1  Na_H_Exchanger  Sodium/hydrogen exchanger family


Domain annotation for each model (and alignments):
>> Na_H_Exchanger  Sodium/hydrogen exchanger family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.1  46.8   5.3e-39   9.4e-35       7     375 ..      76     446 ..      69     448 .. 0.84

  Alignments for each domain:
  == domain 1  score: 120.1 bits;  conditional E-value: 5.3e-39
                     HHHHHHH...HHHHTTSXHHHHHHHHHHHHTTTTTS.......HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCTHHHHHHHHHHHHHHHHHHHHH CS
  Na_H_Exchanger   7 lallvgl...larrlklpeivgliiaGlllGpsglglieps..eedlevlselglilllFlaGleldlrelrknlksilllallgvlitvvliGl 96 
                     +++++ +   ++++ ++p++ +l+i+G+++Gp+ lgli+p     ++ +++ l li+++++ Gl+ldl+++ +    +++l+++g+++++ +++ 
      EPA05720.1  76 VIFFGVVgeaFFKKTGIPDVAFLMILGIIIGPI-LGLIQPEvvLQVVPYFAALALIIIMYDGGLNLDLKSVASTAHFAIILSIVGFAASIGIVAA 169
                     34444446746*********************9.889***988888899********************************************** PP

                     HHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC.CCCTSTCCCCCCHHHHHHHHHHHC.CCCCHHHHHHTXXXXXTSSSTSXHHHHHHHHHHHH CS
  Na_H_Exchanger  97 llylllilgiplleallfgailsatdpvvvlailkeegrvperlgtlllgesvlnDava.vvllavllalakeeaggetslllllliflvvavgg 190
                     ++++  +lg++++e++l+g+i+  ++ ++v  ++ ++ +++ +  +ll  es l+D++a v++++++ a++  + + +++ +   ++ +v+++++
      EPA05720.1 170 FAHY--GLGWEWIEGVLLGSIVGGSSSAIVFGLV-RNLKISDSAKSLLSFESALTDILAtVIAFVLFGAVL--SGTLNVDFMGTTIENAVIVGLV 259
                     ***8..8999************************.99999****************986266777777777..8999****************** PP

                     HHHHHHHHHHHHHHHHHSCTHHHHHHHHHHHHHHHHHHHHHTSXXXHHHHHHHHHHHHH.HHHHHTTHHHH.........HHHHHHHHHHHHHHH CS
  Na_H_Exchanger 191 lllglvigwllrlitrftdddrelevllvlllallaallaellgvsgilgaflaGlvls.eyefsnklsek.........lesfreglfnplfFv 275
                     l lg+ i+w++  +      +++   +l+l++++++++ a +lg sg+l a++ Gl+l+ + ++++ l+           +++ +++l+ ++fFv
      EPA05720.1 260 LGLGVGIPWMYVTTKLA---SSKHSYMLTLAILFILYFMANSLGESGALTALVFGLMLGnKRRLAKYLRFPlpkidtddpTHNQITFLVRTFFFV 351
                     ********998666665...8999999********************************655555544444555566578666666********* PP

                     HHHHHSXHHHHHXXHHHHHHHHHHHHHHHTHHHHHHHHHTTTX.SSXHHHHHHCCCCSS.BHHHHHHHHHHHHHHXHHHHTT.SSTTTCSTSXHH CS
  Na_H_Exchanger 276 lvGlsldlkvlnnhlsvlilvllilvaillgrilavflllrll.glslrealiigfgglqrgavalalaalgpalgllarel.yallivvvlftv 368
                     +vGl   +  +   ++ ++ v++++++++++ i++ ++l+ ++ +l+ +      + +++rg  a++la +  + gl++++    +++ +++ +v
      EPA05720.1 352 FVGLLASFGNI---EYIVFGVVAAIAIYVARTIIVKMTLTQRFsQLDKKVT----TIMIPRGLAAAVLATFPITMGLPNADAySQIVFSIIMASV 439
                     *******6666...6777777777777766666666777776623444433....34667999*******************8888888999999 PP

                     HHHHHHH CS
  Na_H_Exchanger 369 lvqGlsl 375
                     ++ +l+l
      EPA05720.1 440 IITTLGL 446
                     9777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (470 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       930  (0.0518713); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 3099.63
//
Query:       EPA05721.1  [L=47]
Description: hypothetical protein BG20_I2617, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.33s 00:00:00.81 Elapsed: 00:00:00.51
# Mc/sec: 276.74
//
Query:       EPA05722.1  [L=132]
Description: hypothetical protein BG20_I2616 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-12   47.4   0.2    8.7e-12   45.4   0.2    1.8  1  RNA_binding   RNA binding
     0.0014   17.5   0.0     0.0015   17.3   0.0    1.0  1  tRNA-synt_1g  tRNA synthetases class I (M)


Domain annotation for each model (and alignments):
>> RNA_binding  RNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   0.2   9.7e-16   8.7e-12       1     117 [.       9     116 ..       9     118 .. 0.80

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 9.7e-16
                  EEEEEEEE-TTC-HHHHHHHHHTTSTTSE---EEEEEE-CCC-EEEEEEEEESS.HHHHHHHHHHHHHHCCCCH.HHHHHCCHCCB-TTSEEEEEEEH CS
  RNA_binding   1 kievrafvhaTEdeekVlealsnllpeeeveieeeeaeGhygnpitileaelek.kkakkvlkkllellreeei.keLlkeleervdekgklylrldK 96 
                  kie+   v+++Ed +kV++a+ n++++ +               i+   + + + ++++++l+k+++ + +++  ++ +++le+ ++ ++++ + l+K
   EPA05722.1   9 KIEIISNVNPSEDLKKVETAILNIFQNAK---------------IKSDDFSVMSnSRDLHLLEKIYDVIHSNRSqNIYRRQLEKNLE-NDSTWFYLNK 90 
                  689999********************773...............444444333303559**********999995444556666665.89******** PP

                  HHHHTT---BESSSS.....EEEEEE CS
  RNA_binding  97 Qaaylgklslvegdd.....vIkvki 117
                  Qaa++g+ +l+e+ +     +Ikv++
   EPA05722.1  91 QAAFVGTAALCEEAEesplgPIKVTL 116
                  ***********998888888888875 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.7e-07    0.0015      60     134 ..      15      91 ..       9     120 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.7e-07
                   TS-HHHHHHHHHHHHHHHHHHTT---SEEEETTSHHHHHHHHHHHHHHHHT..T-EEEEEEEEEEETTTTEEE-GGG CS
  tRNA-synt_1g  60 gvtpeelvekvheeikelfkklnisfdkygrttseehkelvqeifkklkek..gliyekeieqlycpkderflpdry 134
                   +v+p+e  +kv+++i ++f++ +i+ d+++  +++++ +l ++i+  ++++    iy+++ e+   ++   f+ +++
    EPA05722.1  15 NVNPSEDLKKVETAILNIFQNAKIKSDDFSVMSNSRDLHLLEKIYDVIHSNrsQNIYRRQLEKNLENDSTWFYLNKQ 91 
                   79999*****************************************998773368********99999999988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       898  (0.0500865); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.34s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 784.73
//
Query:       EPA05723.1  [L=39]
Description: hypothetical protein BG20_I2615, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.29u 0.24s 00:00:00.53 Elapsed: 00:00:00.37
# Mc/sec: 315.68
//
Query:       EPA05724.1  [L=40]
Description: hypothetical protein BG20_I1926 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00051   20.6   0.0    0.00052   20.6   0.0    1.0  1  SAF       SAF domain
     0.0084   16.0   0.0     0.0084   16.0   0.0    1.0  1  DUF3284   Domain of unknown function (DUF3284)


Domain annotation for each model (and alignments):
>> SAF  SAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   5.8e-08   0.00052      22      62 ..       2      39 ..       1      40 [] 0.90

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 5.8e-08
                EEECECGGCCTSCCCGGHHHHTTEEESS-B-TT-B-BGGGE CS
         SAF 22 tlkrpiashkigllpiaygeviGkratrdikaGepvhahnl 62
                t+krp+     ++ ++++  +iGk+a+rdi+++  +  +++
  EPA05724.1  2 TTKRPN---TGQIQAKDFYKIIGKKAKRDIPKNKQLLYSDI 39
                899998...8999999999*************999988887 PP

>> DUF3284  Domain of unknown function (DUF3284)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   9.4e-07    0.0084       6      30 ..       8      32 ..       1      38 [. 0.88

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 9.4e-07
     DUF3284  6 tlnvsaeefFdkliksvleDikqat 30
                t +++a++f++++ k+++ Di +++
  EPA05724.1  8 TGQIQAKDFYKIIGKKAKRDIPKNK 32
                789*******************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       261  (0.0145574); expected 358.6 (0.02)
Passed bias filter:                      184  (0.0102627); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.31s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 260.61
//
Query:       EPA05725.1  [L=234]
Description: glycosyltransferase, group 1 family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-33  116.3   0.2    1.6e-33  115.7   0.2    1.2  1  Glycos_transf_1  Glycosyl transferases group 1
    2.4e-27   96.0   0.0    4.1e-27   95.2   0.0    1.4  1  Glyco_trans_1_4  Glycosyl transferases group 1
    4.3e-12   46.2   0.0    8.3e-12   45.4   0.0    1.4  1  Glyco_trans_1_2  Glycosyl transferases group 1
  ------ inclusion threshold ------
      0.015   15.0   0.0       0.11   12.2   0.0    2.0  2  Peptidase_S51    Peptidase family S51
       0.02   14.9   0.0      0.089   12.8   0.0    2.0  3  Glyco_transf_4   Glycosyltransferase Family 4
      0.061   13.4   0.0       0.15   12.1   0.0    1.7  1  DUF3880          DUF based on E. rectale Gene description (DU


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.7   0.2   5.3e-37   1.6e-33      15     170 ..      62     210 ..      55     212 .. 0.94

  Alignments for each domain:
  == domain 1  score: 115.7 bits;  conditional E-value: 5.3e-37
                      -EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHHHCESEEEEEESSBSS-HH CS
  Glycos_transf_1  15 kkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleellknadifvlpsisEgfGiv 108
                      +k i++ grl+keKg+ ++++ ++ l+    ++v+l+i+G g+ee+ + +     ++ dnv+flg++ +e+ + l++ + ++++ps  Eg   +
       EPA05725.1  62 EKQIIFAGRLSKEKGILTILETAKNLP----KDVHLIIVGAGPEENVVVEF---VKNIDNVHFLGYQTKEKTIPLIRGSILLIQPSFAEGISAT 148
                      689**********************97....57***********9888877...566788********************************** PP

                      HHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHHHHHHHHH CS
  Glycos_transf_1 109 llEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelrerlgenar 170
                      llE+ma+++p+ia+n+gg++e++++++tG+l++p+n  +l ++i ++l+d++lre++ + a+
       EPA05725.1 149 LLESMACKTPIIATNVGGNKELFVHNKTGILIEPGNSNELLKEIMRMLNDQNLREEIARSAY 210
                      ********************************************************999886 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.2   0.0   1.4e-30   4.1e-27       2     134 .]      63     198 ..      62     198 .. 0.93

  Alignments for each domain:
  == domain 1  score: 95.2 bits;  conditional E-value: 1.4e-30
                      EEEEEES---GG.GTHHHHHHHHHHHH.HHEEEEEES---..HHHHHHHTT-T.TEEEE---..THHHHHHHH-SEEEE--..---SHHHHHHH CS
  Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkkdvrlvivGdgprpeeleelaagleerveftGfv..edlaellaaadvfvaPs..egfglkllEam 91 
                      + i+f Grl  ++kg+  +le ++ l  kdv+l+ivG gp+++ + e ++++ ++v+f+G+   e+  +l++ + +++ Ps  eg++ +llE+m
       EPA05725.1  63 KQIIFAGRL-SKEKGILTILETAKNLP-KDVHLIIVGAGPEENVVVEFVKNI-DNVHFLGYQtkEKTIPLIRGSILLIQPSfaEGISATLLESM 153
                      789******.566**************.66*********9555777788899.7********9777**************************** PP

                      HTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHHH- CS
  Glyco_trans_1_4  92 aaglpvVatdvggiaevv..gengllvppgdpealaeailrLled 134
                      a+++p++at+vgg +e+   +++g+l++pg++++l ++i r+l+d
       EPA05725.1 154 ACKTPIIATNVGGNKELFvhNKTGILIEPGNSNELLKEIMRMLND 198
                      ****************99999*********************997 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   0.0   2.8e-15   8.3e-12       5      85 ..     139     220 ..     129     227 .. 0.90

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 2.8e-15
  Glyco_trans_1_2   5 psrsespnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarervlaehtydh 85 
                      ps +e+++  l+E +ac ++++++   g  elf  +k++il+e  + +el++ i ++l++  +r++ia+ a+  v+ ++++ +
       EPA05725.1 139 PSFAEGISATLLESMACKTPIIATNVGGNKELFVHNKTGILIEpgNSNELLKEIMRMLNDQNLREEIARSAYDAVQ-KYDWSN 220
                      566689999*****************************************************************65.667776 PP

>> Peptidase_S51  Peptidase family S51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.14   4.2e+02      27      39 ..      35      47 ..      24      96 .. 0.76
   2 ?   12.2   0.0   3.6e-05      0.11      56     116 ..     150     208 ..     139     210 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.14
                   --TT-EEEEE-GG CS
  Peptidase_S51 27 gksekkvlFiPtA 39
                   +k + kv F+P A
     EPA05725.1 35 SKLGTKVFFVPNA 47
                   4556788999988 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 3.6e-05
                    HHHTT-EEEE--TTTS-HHHHHHHHHHSSEEEE--S-HHHHHHHHHHTTHHHHHHHHHHTT CS
  Peptidase_S51  56 leklglevdeLelskdpeeeieeklleadviyvgGGntfrLlkllketgldkllreavqqg 116
                    le++ +++ ++ ++   ++e+   ++++++i+++ Gn  +Llk++ ++ +d+ lre+++++
     EPA05725.1 150 LESMACKTPIIATNVGGNKELF--VHNKTGILIEPGNSNELLKEIMRMLNDQNLREEIARS 208
                    5566666666666666666664..599*****************************99765 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     3e-05     0.089     125     168 ..      11      50 ..       3      52 .. 0.87
   2 ?   -1.7   0.0      0.85   2.5e+03       8      51 ..      80     120 ..      79     138 .. 0.53
   3 ?   -2.8   0.0       1.9   5.6e+03      60      76 ..     197     213 ..     168     226 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3e-05
  Glyco_transf_4 125 alerrllrradrviavSeatadelrerygvppekitVipnGvDl 168
                     +  + ++++ad+v+a S+++ d++ + +g    k+  +pn++D+
      EPA05725.1  11 NSKKNAFKWADAVTAGSKEAFDYYSK-LG---TKVFFVPNAIDI 50 
                     5567789*******************.**...99*********8 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.85
  Glyco_transf_4   8 vleLaraLarrGheVtvvtpgddgpleeevelvvrvprvplpll 51 
                     +le a++L+++   V+++  g ++++   ve v+++  v ++++
      EPA05725.1  80 ILETAKNLPKD---VHLIIVGAGPEENVVVEFVKNIDNVHFLGY 120
                     56777778777...555544444444444324444444444444 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 1.9
  Glyco_transf_4  60 flrrlrrllkrekpDvv 76 
                     + + lr+ + r  +D v
      EPA05725.1 197 NDQNLREEIARSAYDAV 213
                     44567777777777776 PP

>> DUF3880  DUF based on E. rectale Gene description (DUF3880)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   5.1e-05      0.15      11      76 ..      12      71 ..       4      73 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.1e-05
     DUF3880 11 ysksiandcnyiftfDkeqyeelkelGvknvyylPLAanverldpleaeaekeekyrsdisFvGsl 76
                 +k+ ++  +++    ke ++++ +lG ++v+++P A +++ l pl +++    +y+++i F G+l
  EPA05725.1 12 SKKNAFKWADAVTAGSKEAFDYYSKLG-TKVFFVPNAIDIKSL-PLGNDK----RYEKQIIFAGRL 71
                44666666777777778889*******.69************9.888888....9*********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1576.37
//
Query:       EPA05726.1  [L=40]
Description: hypothetical protein BG20_I1922 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-06   28.3   0.0    1.6e-06   28.2   0.0    1.0  1  Glyco_transf_4   Glycosyltransferase Family 4
     0.0003   21.3   0.0    0.00031   21.2   0.0    1.0  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
     0.0004   20.2   0.0    0.00041   20.1   0.0    1.0  1  Glyco_transf_5   Starch synthase catalytic domain
     0.0072   16.4   0.0     0.0073   16.3   0.0    1.0  1  Glyco_trans_4_2  Glycosyl transferase 4-like
  ------ inclusion threshold ------
       0.12   12.4   0.0       0.14   12.3   0.0    1.1  1  EFP              Elongation factor P (EF-P) OB domain


Domain annotation for each model (and alignments):
>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   4.5e-10   1.6e-06       1      31 [.       4      34 ..       4      39 .. 0.90

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 4.5e-10
  Glyco_transf_4  1 vGGverhvleLaraLarrGheVtvvtpgddg 31
                    +GG++ hv++L++ L ++Gh+V+v++++  +
      EPA05726.1  4 IGGIAQHVRDLIKFLKEHGHQVDVISSENTP 34
                    7************************987765 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   8.6e-08   0.00031       1      30 [.       5      34 ..       5      38 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 8.6e-08
  Glyco_trans_4_4  1 gGigryvaelaraLaarGheVtvltpapap 30
                     gGi+++v++l++ L ++Gh+V+v+ ++ +p
       EPA05726.1  5 GGIAQHVRDLIKFLKEHGHQVDVISSENTP 34
                     9***********************988766 PP

>> Glyco_transf_5  Starch synthase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   1.1e-07   0.00041      15      41 ..       4      30 ..       2      39 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.1e-07
  Glyco_transf_5 15 tGGLadvvgaLpkaLaklghdvrvilP 41
                     GG+a++v++L k L+++gh+v+vi+ 
      EPA05726.1  4 IGGIAQHVRDLIKFLKEHGHQVDVISS 30
                    6***********************985 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0     2e-06    0.0073      12      35 ..      10      33 ..       5      39 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2e-06
  Glyco_trans_4_2 12 htlrlakeLakrgyeVhvitpkkg 35
                     h++ l+k+L+++g++V+vi++++ 
       EPA05726.1 10 HVRDLIKFLKEHGHQVDVISSENT 33
                     8999****************9764 PP

>> EFP  Elongation factor P (EF-P) OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   3.8e-05      0.14      31      54 .]      11      35 ..       7      35 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.8e-05
                HTTGCGG--T.T-EEEEEEETTEEE CS
         EFP 31 lgdaakfLkE.gmevtvllyegepi 54
                + d +kfLkE g +v+v++ e+ pi
  EPA05726.1 11 VRDLIKFLKEhGHQVDVISSENTPI 35
                66788*****9999********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 296.27
//
Query:       EPA05727.1  [L=344]
Description: UDP-N-acetyl-D-glucosamine 2-epimerase, UDP-hydrolysing [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-71  239.9   1.1    3.9e-71  239.7   1.1    1.0  1  Epimerase_2      UDP-N-acetylglucosamine 2-epimerase
    0.00026   21.1   2.4      0.039   14.1   0.0    3.1  4  MGDG_synth       Monogalactosyldiacylglycerol (MGDG) synthase
  ------ inclusion threshold ------
       0.19   11.9   0.9        4.8    7.4   0.0    2.2  2  Ribonuclease_T2  Ribonuclease T2 family


Domain annotation for each model (and alignments):
>> Epimerase_2  UDP-N-acetylglucosamine 2-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  239.7   1.1   6.5e-75   3.9e-71      15     346 ..       1     328 [.       1     329 [. 0.93

  Alignments for each domain:
  == domain 1  score: 239.7 bits;  conditional E-value: 6.5e-75
                  EE-S--SGGGTHHHHH....HTT-.---SEEE-..--S.--HHHHHHHHHHHHHHHHHHH--SEEEEESSSHHHHHHHHHHHHTT-EEEEET-----S CS
  Epimerase_2  15 vtGqHldremgdtvfe....elei.ekpdydln..sds.qslakstgrvligleevleeekpDlvlvlGDtnetlagalaAfklripvaHveAGlRsf 104
                  +tG+Hl ++ g+t++e    +++i +k +++ +  +d+ ++++  +gr++ +l+++++++kpD+++   D    +a+a+ +++++i vaH+e+G    
   EPA05727.1   1 MTGSHLLKKHGYTINEikkdGFRIyKKFNMFYEneEDTsSTMTMAFGRAIFSLTKIIKSLKPDIIFSGFDLGGNFAAAIIGAHMNIHVAHLEGG---- 94 
                  59****************************9997755559999***************************************************.... PP

                  -TT..SHHHHHHHHHHHT-SEEEESSHHHHHHHHHTT--GGGEEE---HHHHHH....HHHHHHHH...T-HHHHHH--SS-EEEEE---HHHHTSHH CS
  Epimerase_2 105 dltegmpeEinRhlidklsdlhfapteearenLlkegeeeerifvvGntviDal....llskeeieeklkaseilkelkekkyvlvtlHrrenedepe 198
                  ++t g+++E +Rh+i+k +++hf++++ea+++L+k+ge++++if+vGn+ +D +    +  k+e+e+++   +i  +  +k+++lv+ H +++e  ++
   EPA05727.1  95 EVT-GTIDEPIRHAISKFAHIHFTSNQEATKRLVKMGEDRRNIFTVGNPSLDVIksikFIPKTELEKEF---KI--N-LQKPFLLVVQHTVTTEI-KD 184
                  ***.**************************************************554444444444444...44..5.9***************9.77 PP

                  HHHHHHHHHHHHHHHH--EEEEE--..HHHHHHHHHHHHH-TTEEEE----HHHHHHHHHC-SEEEES-H.HHHHHHHHCT--EEESSSS-S-THHHH CS
  Epimerase_2 199 rlkeilealkalakekdvevvvpvhnnprtrkrlleeleelenvtlieplgyldflsllknaklvltdSg.GiqeEapslgvpvvnlReeteRpegve 295
                    k +le+++a+++  d++ ++++ n +++++++++++++ +++  +e+l +++++sll ++ +++++S+ Gi  Eap+l+vp +n+   ++R+eg++
   EPA05727.1 185 IDKYFLETINAIKEL-DMQSIIIAGNIDAGSQKIRKIIKD-SKISYYENLPFVKYISLLYHSSAIIGNSSsGIM-EAPFLHVPSINI---GTRQEGRS 276
                  99************9.8999999************99998.79*******************************.************...******** PP

                  TTSEEE.-TT-HHHHHHHHHHHCT-..--......--TT-SS-HHHHHHHHH CS
  Epimerase_2 296 agtnvl.vgtdkeeIvaaleklledkkelekmanaknpYgdGkaseriveil 346
                  + ++++ v +dk+eI +a++k++++kk +  ++++kn  g+G a+++i  il
   EPA05727.1 277 KTKSIInVRYDKKEIKKAINKAITNKKFHTLIKKQKNQHGNGTAAKKIKIIL 328
                  ***********************99777788899**************8777 PP

>> MGDG_synth  Monogalactosyldiacylglycerol (MGDG) synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   6.4e-06     0.039      50     102 ..      22      74 ..       5      86 .. 0.81
   2 !    5.4   0.0    0.0031        18     141     168 ..     115     142 ..     106     142 .. 0.91
   3 ?   -1.9   0.0      0.51     3e+03     136     152 ..     183     199 ..     170     207 .. 0.82
   4 ?   -3.3   0.1       1.4   8.6e+03      66      88 ..     288     311 ..     282     313 .. 0.56

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.4e-06
                 ----------------------------HHHHHHHHHHH--SEEEE-STTTTH CS
  MGDG_synth  50 salyrllyygteekiqkksilaklatflakelaalleeeqPDiiisthplvae 102
                 +++y+++  + e++   +s + + +     +l +++++ +PDii+s + l+ +
  EPA05727.1  22 FRIYKKFNMFYENEEDTSSTMTMAFGRAIFSLTKIIKSLKPDIIFSGFDLGGN 74 
                 388888877777777788888899999999******************98655 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0031
                 EEESSHHHHHHHHHCT--GGGEEE--S- CS
  MGDG_synth 141 yyvaskevkkealekGidksnikvtGiP 168
                 ++++++e++k++++ G d+ ni ++G P
  EPA05727.1 115 HFTSNQEATKRLVKMGEDRRNIFTVGNP 142
                 89***********************976 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.51
                 TT-SEEEESSHHHHHHH CS
  MGDG_synth 136 keidryyvaskevkkea 152
                 k+id+y++ + +++ke+
  EPA05727.1 183 KDIDKYFLETINAIKEL 199
                 67899999988888886 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 1.4
                 ------------HH.HHHHHHHHH CS
  MGDG_synth  66 kksilaklatflak.elaalleee 88 
                 kk+i +++++ +++ ++++l++++
  EPA05727.1 288 KKEIKKAINKAITNkKFHTLIKKQ 311
                 444555555555543666666654 PP

>> Ribonuclease_T2  Ribonuclease T2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0008       4.8     101     133 ..     183     215 ..       5     227 .. 0.89
   2 ?    3.3   0.4     0.014        83     134     173 ..     284     328 ..     276     337 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0008
                      -SHHHHHHHHHHHHTT--HHHHHHHTT--S.SS CS
  Ribonuclease_T2 101 ksehkYFqkalelrkkldlkkvLakagIvPskt 133
                      k+  kYF ++++  k+ld+++++ + +I + ++
       EPA05727.1 183 KDIDKYFLETINAIKELDMQSIIIAGNIDAGSQ 215
                      44589******************9999988655 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.014
                      -EEEHHHHHHHHHHHHSS--EEEE..EE..-.....-EEEEEEEEEE CS
  Ribonuclease_T2 134 ksyslseikdalkkaigvkpkieC..skdsk.....eqalsevelcl 173
                        y+++eik+a++kai +k+ ++   +k +k      +a +++++ l
       EPA05727.1 284 VRYDKKEIKKAINKAITNKK-FHTliKK-QKnqhgnGTAAKKIKIIL 328
                      579*************6555.3331222.222234445556666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1059  (0.0590663); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2253.28
//
Query:       EPA05728.1  [L=251]
Description: NeuB family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.6e-68  228.7   0.1    8.2e-68  228.4   0.1    1.0  1  NeuB      NeuB family
  ------ inclusion threshold ------
      0.065   13.3   0.2       0.23   11.5   0.0    2.0  3  Band_7_C  C-terminal region of band_7


Domain annotation for each model (and alignments):
>> NeuB  NeuB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  228.4   0.1   9.1e-72   8.2e-68       1     208 [.      38     239 ..      38     246 .. 0.95

  Alignments for each domain:
  == domain 1  score: 228.4 bits;  conditional E-value: 9.1e-72
                 HHHHHHHHT-SEEEEEE--HHHH--GGGGG--......TT-S-HHHHHHHH---HHHHHHHHHHHHHTT-EEEEEE-SHHHHHHHHHHT-S-EEE-GGG CS
        NeuB   1 lieaAaeagadavKfQtfkaeelvskeakkaeyqkkekekeesqlellkklelseeehkelkeyceekgieflstpfdlesvdlleslgveayKiaSge 99 
                 li++A++agad++KfQt+ +ee ++k++         k +++ +++++k++el+ ee ++l++yc+ k+i flstpf+  +vd le+++++ayKi+Sge
  EPA05728.1  38 LIDMAKKAGADCIKFQTHITEEEMTKTNI-----LPGKISKTPLWDIIKNCELTGEEEAKLSKYCKGKKIIFLSTPFSIPAVDRLEKIKMPAYKIGSGE 131
                 79*****************9999999653.....334566779******************************************************** PP

                 TT-HHHHHHHHTT-S-EEEE-TT--HHHHHHHHHHH.HHHT--EEEEE----SS--GGG--THHHHHHHHH-TSEEEEE--SSSSHHHHHHHHHT--EE CS
        NeuB 100 ltnlpllekiaktgkpvilStGmatleeieeavevlreagaeklvllhCtseYPapledvnLkaietlkeafgvpvGySDHtlgiavaiaAvalGAkvi 198
                 ltn+p+l++iak+gk vilS+Gm++++ei++av+++ ++++  l+ll+ tseYP+ ++d+nL +i+++k+ f++pvG SDH+lgi +a+ A+a GA+++
  EPA05728.1 132 LTNIPFLKHIAKKGKSVILSSGMSNMNEIKAAVTLF-KKSRIPLALLQTTSEYPCDYKDINLGVIDKYKKLFNIPVGISDHSLGIYTALGAIAKGACIV 229
                 ************************************.78899********************************************************* PP

                 EEEB-S-TT- CS
        NeuB 199 EkHftldrnl 208
                 EkH+tld++ 
  EPA05728.1 230 EKHITLDKKY 239
                 *******985 PP

>> Band_7_C  C-terminal region of band_7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0      0.95   8.5e+03      17      28 ..      31      42 ..      29      44 .. 0.77
   2 ?   -3.6   0.0       1.4   1.2e+04      36      45 ..      63      72 ..      61      73 .. 0.78
   3 ?   11.5   0.0   2.6e-05      0.23      29      60 ..     139     169 ..     135     171 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.95
    Band_7_C 17 sLrvAeqYveaF 28
                s+++A++ +++ 
  EPA05728.1 31 SFSIAKKLIDMA 42
                578999998875 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.4
    Band_7_C 36 ntvilPanvg 45
                +t ilP++++
  EPA05728.1 63 KTNILPGKIS 72
                7889999876 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 2.6e-05
    Band_7_C  29 gkLAkesntvilPanvgdvssmvaqalsiykk 60 
                 +++Ak++++vil + ++++++ ++ a +++kk
  EPA05728.1 139 KHIAKKGKSVILSSGMSNMNE-IKAAVTLFKK 169
                 78*****************98.5566666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1734.77
//
Query:       EPA05729.1  [L=109]
Description: hypothetical protein BG20_I1929, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-18   66.0   0.0    3.6e-18   65.7   0.0    1.1  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
  ------ inclusion threshold ------
       0.03   14.6   0.0      0.037   14.3   0.0    1.1  1  RNase_Zc3h12a_2  Zc3h12a-like Ribonuclease NYN domain


Domain annotation for each model (and alignments):
>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.7   0.0   4.1e-22   3.6e-18     189     292 ..      14     104 ..       5     106 .. 0.91

  Alignments for each domain:
  == domain 1  score: 65.7 bits;  conditional E-value: 4.1e-22
                      TSSEEES-TT-EEEEE-HHHHHHHHHHHHHH--SS-EEEE--.-EEEHHHHHHHH..........SSSS-EEE----TT--SS-EEE-GGGGGG CS
  Polysacc_synt_2 189 ggpvtvTdpemtRyfmtieeavqLvlqalalakggeifvldmGepvkivdlakalielsgleekkeedieikitGlRpGEklyEeLlieeesve 282
                      ++p+++T+p+m Ryf+ +++ v+++l++l lak+geif+ +m + ++i++la  +            + + +i+GlR GEkl E Ll++ee+++
       EPA05729.1  14 NKPLSITEPSMQRYFINVNDVVDFILNSLLLAKTGEIFIPKM-KKYNIKKLADGI------------SKSQRIIGLRRGEKLDEILLNSEEKAN 94 
                      489***************************************.**********99............235689********************* PP

                      EEE-SSEEEE CS
  Polysacc_synt_2 283 etelekilra 292
                      + e +++ ++
       EPA05729.1  95 ALEKSDMWII 104
                      9999888776 PP

>> RNase_Zc3h12a_2  Zc3h12a-like Ribonuclease NYN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   4.1e-06     0.037       7      66 ..      29      91 ..      23     102 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.1e-06
  RNase_Zc3h12a_2  7 lpvkalvdiillflirghktkvylpkyyedfvsd..cgvskvddlvafqklidldfikf.ite 66
                     + v+ +vd il+ l+  +   +++pk  +  + +   g+sk + ++ +++  +ld i+  ++e
       EPA05729.1 29 INVNDVVDFILNSLLLAKTGEIFIPKMKKYNIKKlaDGISKSQRIIGLRRGEKLDEILLnSEE 91
                     57899********************9877666542269************9999999652443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 752.08
//
Query:       EPA05730.1  [L=50]
Description: hypothetical protein BG20_I1927 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-06   27.1   0.0    2.9e-06   26.9   0.0    1.0  1  NeuB      NeuB family


Domain annotation for each model (and alignments):
>> NeuB  NeuB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   1.6e-10   2.9e-06     208     241 .]       1      34 [.       1      34 [. 0.96

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 1.6e-10
                 --STTGGG-B-HHHHHHHHHHHHHHHHHSS--TT CS
        NeuB 208 legpDhkaSlepeelkelveairnvekalgegek 241
                 ++gpD+k+Slep+el+elv+++r+++ alg+ +k
  EPA05730.1   1 MPGPDQKLSLEPHELAELVRGCRAIKLALGDTKK 34 
                 79****************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 355.56
//
Query:       EPA05731.1  [L=118]
Description: hypothetical protein BG20_I1921, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 876.72
//
Query:       EPA05732.1  [L=281]
Description: NAD-binding protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-39  135.3   0.0    2.9e-39  135.0   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    3.9e-35  121.8   0.5    2.1e-33  116.1   0.0    2.2  2  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    3.9e-18   65.4   1.2    1.9e-15   56.6   0.0    2.3  2  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    6.5e-18   64.8   0.1    9.4e-16   57.8   0.0    2.8  2  NAD_binding_4    Male sterility protein
    8.7e-18   64.5   0.4    1.5e-15   57.1   0.0    2.7  2  Polysacc_synt_2  Polysaccharide biosynthesis protein
    2.7e-15   56.2   0.0    3.5e-15   55.8   0.0    1.1  1  RmlD_sub_bind    RmlD substrate binding domain
    3.3e-06   27.1   0.0    7.8e-06   25.9   0.0    1.6  1  NAD_binding_10   NAD(P)H-binding


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.0   0.0   1.1e-42   2.9e-39       1     241 []       4     212 ..       4     212 .. 0.91

  Alignments for each domain:
  == domain 1  score: 135.0 bits;  conditional E-value: 1.1e-42
                 EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHHHSHHHHHHHHTHHHHHHH CS
   Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggvaassedpadfieknlqgtlnll 99 
                 il+tG +GfiG  +vk+l +    +i+ +++               ++dl +r+++ +l +   +d+vihl   g  +++  + ++++++n++gtln+l
  EPA05732.1   4 ILITGSSGFIGGEIVKRLDKLE--IITDSND-------------SEHIDLQNREQVMKL-D--SADIVIHL--GGKTPQRELKWSEYFDNNVIGTLNVL 82 
                 8******************975..4444444.............3489***99988886.4..79******..55666667777889************ PP

                 HHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSS CS
   Epimerase 100 eaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklveayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkq 198
                 e++ +++vk+++++sS  vYG+++  p +e+    p+ p+++Y  +K++ge+l+e y +  +l+ +ilr+fn++G      ++  +i+ li++i++gk 
  EPA05732.1  83 EYCIQKKVKKMIYVSS-YVYGNPKYCPVDENH---PISPHNAYTESKYLGERLCEFYCKRSDLSLTILRPFNIFGGS---MKEGFLITNLINSIKTGK- 173
                 ****************.****99999999999...*****************************************9...78999*************. PP

                 SEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT-STTEEEEES CS
   Epimerase 199 evtllgdgtalRdflyveDvaeaillvlehvdagdkgeiyniG 241
                 +vt+++  +++Rdfl+v+D +++i  +++    + k e++n+G
  EPA05732.1 174 KVTIVN-KNSKRDFLHVDDFVDLITKLIDC---NFKFEVFNVG 212
                 ****95.999*******************8...5678899998 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.2     0.011        29       1      17 [.       5      21 ..       5      32 .. 0.90
   2 !  116.1   0.0   8.2e-37   2.1e-33      63     331 ..      37     274 ..      22     275 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.011
                   EEETTTSHHHHHHHHHH CS
  GDP_Man_Dehyd  1 LiTGiaGfiGsylaelL 17
                   LiTG +GfiG  ++++L
     EPA05732.1  5 LITGSSGFIGGEIVKRL 21
                   9*********9999887 PP

  == domain 2  score: 116.1 bits;  conditional E-value: 8.2e-37
                    -HHHHHHHHHHHT-SEEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHHHHHH CS
  GDP_Man_Dehyd  63 DssslerllaevqpdevynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYaaaKl 158
                    D ++ e++++    d v++L+++   ++ ++ +ey +++nv+Gtl++Le + + +    v+ ++  +s vYG+++  p++E++p++P++ Y  +K 
     EPA05732.1  37 DLQNREQVMKLDSADIVIHLGGKT-PQRELKWSEY-FDNNVIGTLNVLEYCIQKK----VKKMIYVSSYVYGNPKYCPVDENHPISPHNAYTESKY 126
                    45556678888889*******976.5677777666.5999***********7644....4444555689*************************** PP

                    HHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHHHHHHHHCSS---EEE-TT-EEE CS
  GDP_Man_Dehyd 159 yadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyveamwlmlqqdkpedyviatgeths 254
                      + +++ y +  +l  ++ + fn  +  ++e f    it+ +  i+ gk+  +++ n ++kRd++hv+D+v+ + +++  +        + e+++
     EPA05732.1 127 LGERLCEFYCKRSDLSLTILRPFNIFGGSMKEGFL---ITNLINSIKTGKK--VTIVNKNSKRDFLHVDDFVDLITKLIDCNF-------KFEVFN 210
                    ******************************99987...99*********95..456799******************999764.......688888 PP

                    CHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB--B-THHHHHHH----SS-HHHHHHH CS
  GDP_Man_Dehyd 255 vrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdlllgdaskakeeLgWkpkvsfeelvre 331
                    v+     +f+e++k+ie  +           sg  +++vd++ ++++    ++ d+sk+k+ ++W+pk++f+e++++
     EPA05732.1 211 VGAGESYSFEEIVKKIEIIT-----------SG--KINVDYEENKETFIVDIASDISKIKNIINWQPKIKFNEGLEK 274
                    88888888888888887643...........34..4788888889999999***********************987 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.2   0.00056       1.4       1      20 [.       5      24 ..       5      31 .. 0.87
   2 !   56.6   0.0   7.5e-19   1.9e-15      50     222 ..      34     193 ..      22     199 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00056
   3Beta_HSD  1 vvtGgaGFlGralvkeLvrl 20
                ++tG++GF+G ++vk+L +l
  EPA05732.1  5 LITGSSGFIGGEIVKRLDKL 24
                69*************99665 PP

  == domain 2  score: 56.6 bits;  conditional E-value: 7.5e-19
   3Beta_HSD  50 iegDvtdkdkleealegvdvvihlaslvdvagkltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaype 148
                  + D+++ +++ + l+++d+vihl + ++ +  l+  e+ + nv GT nvle c+++ v++++Y+Ss+  v++n +  ++   dE+  ++ ++++ay+e
  EPA05732.1  34 EHIDLQNREQVMK-LDSADIVIHLGGKTPQRE-LKWSEYFDNNVIGTLNVLEYCIQKKVKKMIYVSSY--VYGNPKYCPV---DEN--HPISPHNAYTE 123
                 4679999999876.8*********99888887.77777*****************************9..4554444455...565..667899***** PP

   3Beta_HSD 149 sKalaEklvlkaNgrtlknggrlyTcaLRpagiyGegdk..llvpllkqlaklglalfkigdeevlsdrvYvgNva 222
                 sK l E+l            ++l    LRp  i+G   k  +l + l +++k+g +++ i++++++ d+  v+  +
  EPA05732.1 124 SKYLGERLCEFYCK-----RSDLSLTILRPFNIFGGSMKegFLITNLINSIKTG-KKVTIVNKNSKRDFLHVDDFV 193
                 ********976666.....56899999********86542279999********.89999999999**99998765 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.4   0.1    0.0071        18       1      16 [.       6      21 ..       6      26 .. 0.93
   2 !   57.8   0.0   3.7e-19   9.4e-16      61     255 ..      23     194 ..      20     196 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0071
                   EE-TTSHHHHHHHHHH CS
  NAD_binding_4  1 lTGaTGFLGkvLlekL 16
                   +TG++GF+G  ++++L
     EPA05732.1  6 ITGSSGFIGGEIVKRL 21
                   8************998 PP

  == domain 2  score: 57.8 bits;  conditional E-value: 3.7e-19
                    TEEEEE--TTSGGGG--HHHHHHHHHH--EEEE--SS-S.ST.TSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H.. CS
  NAD_binding_4  61 rikvveGDlseprlGLseedlqelaeevdviihsaAtvnfde.pykellrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeeg 155
                    ++++++     +++ L++++     ++ d++ih ++++   e + +e ++ Nv Gt +vle + + k +  +++vS+ +  + ++  v        
     EPA05732.1  23 KLEIITDSNDSEHIDLQNREQVMKLDSADIVIHLGGKTPQRElKWSEYFDNNVIGTLNVLEYCIQKKVK-KMIYVSSYVYGNPKYCPV-------- 109
                    6666666667788899998888888*************988879********************88877.9*****754444444444........ PP

                    ....HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE--SSST---TTSHHHHHHHHHHHH-EEES-SB---TT--EEEHH CS
  NAD_binding_4 156 ekeekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitgesktGwingsdlgirgllgliakgvlpeilgdkeavldlvpvD 251
                             ++++  + +n+Y+ sK+l+E+l++ + +rs+l ++i+Rp +i g    G++++   +i+ l+ +i++g+  +i+++ +++ d++ vD
     EPA05732.1 110 ---------DENHPISPHNAYTESKYLGERLCEFYCKRSDLSLTILRPFNIFG----GSMKEGF-LITNLINSIKTGKKVTIVNK-NSKRDFLHVD 190
                    .........567889999*********************************99....6666666.78888899999988866666.6788888888 PP

                    HHHH CS
  NAD_binding_4 252 yvan 255
                      ++
     EPA05732.1 191 DFVD 194
                    6665 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.5   0.2    0.0062        16       1      21 [.       4      24 ..       4      30 .. 0.88
   2 !   57.1   0.0   5.8e-19   1.5e-15      67     246 ..      39     229 ..      21     250 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0062
                     EEEETTTSHHHHHHHHHHHHH CS
  Polysacc_synt_2  1 vlvtGagGsiGselvrqilkk 21
                     +l+tG++G iG e+v+++ k 
       EPA05732.1  4 ILITGSSGFIGGEIVKRLDKL 24
                     89*************998665 PP

  == domain 2  score: 57.1 bits;  conditional E-value: 5.8e-19
                      HHHHHHTT..T-SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEE.............GGGSS--SHHHHHHHHHHH CS
  Polysacc_synt_2  67 erlekaleelkvdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliSt.............DKAvnPtnvmGatKrlaek 147
                      ++ e++++  + d+v+h     + P  e ++ e +++Nv+gt nv+e +i+++vkk++++S+                ++P n++  +K l e 
       EPA05732.1  39 QNREQVMKLDSADIVIHLGG--KTPQRELKWSEYFDNNVIGTLNVLEYCIQKKVKKMIYVSSyvygnpkycpvdeNHPISPHNAYTESKYLGER 130
                      344678888899*****986..68*************************************8555555555553335789************** PP

                      HHHHGGG--SSS--EEEEEEE-EETTGT...TSSHHHHHHHHHTTSSEEES-TT-EEEEE-HHHHHHHHHHHHHH--SS-EEEE--.-EEEHHH CS
  Polysacc_synt_2 148 llqalakeseekktkfvvvRfGNVlgSr...GSviplFkkqikeggpvtvTdpemtRyfmtieeavqLvlqalalakggeifvldmGepvkivd 238
                      l+  + k+s   +  +++ R  N++g +   G +i+   + ik+g++vt+ +++  R f+ +++ v+L+ + +    + e+f + +Ge+++  +
       EPA05732.1 131 LCEFYCKRS---DLSLTILRPFNIFGGSmkeGFLITNLINSIKTGKKVTIVNKNSKRDFLHVDDFVDLITKLIDCNFKFEVFNVGAGESYSFEE 221
                      ***999998...8999999999999864444*************************************************************** PP

                      HHHHH... CS
  Polysacc_synt_2 239 lakaliel 246
                      ++k++  +
       EPA05732.1 222 IVKKIEII 229
                      **998333 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.8   0.0   1.4e-18   3.5e-15       2     198 ..       3     201 ..       2     230 .. 0.83

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 1.4e-18
                    EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TTT--TTSHHHHHHHHHHH--SEEEE------HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-.EE CS
  RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltreeldltdaeavaellkeakpdvvvnaAAytavDkaEseeeaayavnaeavealAeaaaavga.lL 96 
                    kil+tG++G +G e++k+l++ ++ + + ++e++dl+++e+v++l ++   d+v++++  t   + E +  + +  n+ ++ ++ e++ + ++ ++
     EPA05732.1   3 KILITGSSGFIGGEIVKRLDKLEIITDSNDSEHIDLQNREQVMKLDSA---DIVIHLGGKTP--QRELKWSEYFDNNVIGTLNVLEYCIQKKVkKM 93 
                    79*********************999999*************998766...9******9775..889999******************99988358 PP

                    EEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHHH-S....SEEEEEE-SEE.SSSSS-HHHH.HHHHHHH-SEEEEESS-EE--.EE CS
  RmlD_sub_bind  97 ihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavlaagk....kalivRtswvy.gekgknfvkt.mlrlakereelkvvaDqlgsP.Ts 185
                    i+vS+ yV+   k  p  e+++ sP n+Y ++K++GE+  + ++k      +i+R   ++ g+ ++ f+ t +++  k+ +++++v+    +   +
     EPA05732.1  94 IYVSS-YVYGNPKYCPVDENHPISPHNAYTESKYLGERLCEFYCKrsdlSLTILRPFNIFgGSMKEGFLITnLINSIKTGKKVTIVNKNSKRDfLH 188
                    99987.9**999**************************99887762222579********55578888765388889********99776543145 PP

                    HHHHHHHHHHHHH CS
  RmlD_sub_bind 186 ardlAevllqlle 198
                    ++d  + +++l++
     EPA05732.1 189 VDDFVDLITKLID 201
                    5566666655555 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0     3e-09   7.8e-06      46     150 ..      36     155 ..       8     178 .. 0.74

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 3e-09
                     --TT-CCHHHHHHTT-SEEEES---TCC.........HHHH..HHHHHHHHHHCT--EEEEEEETTTTSGCGCHHHHHHH.HCCHHHHHHHHHHH CS
  NAD_binding_10  46 gdvtdvedlaealkgadaVvsalggggk.........deeg..aknivdaakeagvkRfvlvsaigvgdevpgefgewnk.ellkaylaakraae 128
                     +d+++ e++   l+ ad+V+  +g++ +         d+++  + n+++ + +++vk++++vs+   g+    +++e    +  +ay + k+  e
      EPA05732.1  36 IDLQNREQVM-KLDSADIVIHLGGKTPQrelkwseyfDNNVigTLNVLEYCIQKKVKKMIYVSSYVYGNPKYCPVDENHPiSPHNAYTESKYLGE 129
                     5666666654.47899999999988887666666665444499***********************99855445444333234567777777777 PP

                     HH....HHHSSSEEEEEEE-CEE-ST CS
  NAD_binding_10 129 el....lrasgldwTivrpggLtdep 150
                     +l     ++s+l  Ti+rp  +  + 
      EPA05732.1 130 RLcefyCKRSDLSLTILRPFNIFGGS 155
                     763322688**********8776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.61u 0.35s 00:00:00.96 Elapsed: 00:00:00.53
# Mc/sec: 1593.50
//
Query:       EPA05733.1  [L=341]
Description: leucyl-tRNA synthetase domain protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.9e-16   57.4   0.2    2.5e-15   55.8   0.2    1.6  1  tRNA-synt_1   tRNA synthetases class I (I, L, M and V)
    2.4e-10   39.8   0.0    3.8e-10   39.1   0.0    1.3  1  tRNA-synt_1g  tRNA synthetases class I (M)
    8.9e-07   28.5   0.0    1.3e-06   28.0   0.0    1.3  1  tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
  ------ inclusion threshold ------
       0.14   12.1   0.0       0.27   11.2   0.0    1.5  1  CHB_HEX_C     Chitobiase/beta-hexosaminidase C-terminal domai


Domain annotation for each model (and alignments):
>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.8   0.2   5.7e-19   2.5e-15     321     601 ..      25     301 ..      22     302 .. 0.85

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 5.7e-19
  tRNA-synt_1 321 gtlteeaaefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkpiiyrateqWfvrvke..ladaalkavekvqfvpkskekryaswleni 416
                  g+l+ ++++f+g+kv  a++++ e l ++       + + +   c  + + ++  + +qWf +  +   ++ a k  +++++ p+  +++++  +   
   EPA05733.1  25 GKLKANTEQFSGIKVAYAKDTIKEWLIKNKHADILLELTNTPVRCRCGAECVVKVLNNQWFLNYGDkdWKELATKCFDEMSILPQEIRSEFNYVIGWL 122
                  88999*******************99877655555555555555667778899999******9855459999999999******************** PP

  tRNA-synt_1 417 qdWciSRqrwWGhripl...fvsketeevvvreelkelvagreeeeaekkalekeakdklkkekgelekdedvlDvWFsSgswpfstlgypeedteel 511
                  ++ +  Rq   G+++p    ++ ++  + v+      + +  ++ + ++++l+ e+ d +  +kg+++ ++ +       g++  ++     + ++e+
   EPA05733.1 123 RERACARQHGLGTKLPWdkdWIVESLSDSVIYMAYYTISKYVNNGTLHAEKLSGEFFDYIFLGKGNVNNVSTIT------GLSGDTIN----KIKKEF 210
                  ****************7666888888888777777788888888888888889999999988999988887774......44333332....34789* PP

  tRNA-synt_1 512 kkffpadmlleGlDiirgWvarlillslaltgsePf.kevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltli.lsdvgrdinl 601
                  + f+p d   +G D +   ++  +l  +a++ ++ + ke++v+g v+  +G KmSKs+gN+i   + i+ ygad +Rl++i +++ ++d ++
   EPA05733.1 211 DYFYPVDSRHSGRDLVPNHLTFFVLNHVAIFPESNWpKEIVVNGSVL-MNGSKMSKSMGNIIPLRKAIQDYGADPIRLAIIiSAELLQDADF 301
                  *****************************99877554999****998.57******************************988899988765 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   0.0   8.6e-14   3.8e-10     289     376 ..     222     311 ..     188     318 .. 0.90

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 8.6e-14
                   EGGGHHHHHTHHHHHHHH..TT----S-EEEE--EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HHHHHHHHH CS
  tRNA-synt_1g 289 gkdiikFHtifwPaillg..aelklpkkvvaheyltvegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfswedfvervN 376
                   g+d ++ H  f+     +   e + pk++v+++ + ++g+K+SkS g+++  ++a++ + ad +R  ++ +a+  +D+df++e++    N
    EPA05733.1 222 GRDLVPNHLTFFVLNHVAifPESNWPKEIVVNGSVLMNGSKMSKSMGNIIPLRKAIQDYGADPIRLAIIISAELLQDADFNMESVSGIQN 311
                   99**********999999888999**********************************************************99887777 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   2.9e-10   1.3e-06     211     295 ..     219     305 ..     206     311 .. 0.84

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 2.9e-10
                   EEEEGGGTTTHHHHHHHHHHHHSS.S--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHH.HSS-TTS-EEE-HHH CS
  tRNA-synt_1e 211 hsGGiDLafPhhenelaqseaafd.kqlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRlll.lsahyrsqldfkeel 295
                      G DL+  h    +  + a f  +++ k  + ng + ++g kmsks++n+i ++++++ + +  +Rl++ +sa+  +  df+ e 
    EPA05733.1 219 RHSGRDLVPNHLTFFVLNHVAIFPeSNWPKEIVVNGSVLMNGSKMSKSMGNIIPLRKAIQDYGADPIRLAIiISAELLQDADFNMES 305
                   556889988888888889999998799*****************************************9861566777777777665 PP

>> CHB_HEX_C  Chitobiase/beta-hexosaminidase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   6.1e-05      0.27      18      52 ..      19      54 ..      16      71 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.1e-05
   CHB_HEX_C 18 GAkvengkLeanv.alPGltieYsldggetwqkyta 52
                G ++  gkL+an+ ++ G+++ Y  d  ++w   ++
  EPA05733.1 19 GKEFYGGKLKANTeQFSGIKVAYAKDTIKEWLIKNK 54
                566778******956****************87664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 2026.52
//
Query:       EPA05734.1  [L=133]
Description: low molecular weight phosphotyrosine protein phosphatase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-23   82.7   0.2    6.6e-23   81.7   0.2    1.5  1  LMWPc     Low molecular weight phosphotyrosine protein phosph


Domain annotation for each model (and alignments):
>> LMWPc  Low molecular weight phosphotyrosine protein phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.7   0.2   3.7e-27   6.6e-23       1     141 [.       5     127 ..       5     128 .. 0.91

  Alignments for each domain:
  == domain 1  score: 81.7 bits;  conditional E-value: 3.7e-27
                 EEEEESSSSSHHHHHHHHHHHHHHHTT-CCCEEEEEEESTSTTT-B--HHHHHHHHHTTS--TT-BB-BS-HHHHHHSSEEEESSHHHHHHHHHHCCTT CS
       LMWPc   1 vlfvClgNicRSpmAealfrkelekagleekvevdSaGtgalvgkradpravevlkekgislsghvarqlskeelaelDlilamdeenkreleslapek 99 
                 +lfvC+ N++RS+mAea+frk+l+       +e  SaGt+  ++++++p +++++ke gi++++  ++++s+++++e+   + m    k++  +l  + 
  EPA05734.1   5 ILFVCVENAGRSQMAEAFFRKYLPA-----GFEPISAGTK--PASKVNPIVAQAMKEIGIDIENNHPQNISQQMMDEAENTINMGCIDKESCPALFLK- 95 
                 89********************665.....7899******..******************************************77777455555555. PP

                 GGGGEEEGGGGSSTSS---HTTSSHHHHHHHHHHHHHHHHHH CS
       LMWPc 100 ekakvkllgeyteqldieDPyygeieafeevldeieeavkkl 141
                 +           +++++ DP++ +ie+++e++d+ie++vk+l
  EPA05734.1  96 N----------VDDWQVLDPKGRSIEEVREIRDQIEKKVKDL 127
                 3..........479*************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       822  (0.0458475); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 885.96
//
Query:       EPA05735.1  [L=139]
Description: putative chemotaxis protein Chey [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      3e-24   85.3   0.9    3.5e-24   85.1   0.9    1.0  1  Response_reg  Response regulator receiver domain


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.1   0.9   1.9e-28   3.5e-24       1     112 []       8     121 ..       8     121 .. 0.93

  Alignments for each domain:
  == domain 1  score: 85.1 bits;  conditional E-value: 1.9e-28
                   EEEESSSHHHHHHHHHHHH.HTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEESSTSHHHHHHHH.HCTES CS
  Response_reg   1 vlivdDdplvrellrqlle.eegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviiltahseeedaveal.kagad 95 
                   +livdD++++re  + +++ + ++ +v +a++g e l+++k+ k+d+i+lD++mp mdG+++lk + ++dp ++vi+ ta++e++ + + +  +ga 
    EPA05735.1   8 ILIVDDSQAFREFAQLVIKdDLKFVTVITASNGMEGLQMYKKYKPDVIILDWKMPVMDGMQVLKAVMKDDPRTKVIMTTAYTEDQLLLNEMkALGAL 104
                   8******************889999999***************************************************999988766555389*** PP

                   EEEESSG-HHHHHHHHH CS
  Response_reg  96 dflsKpfdpeeLlkale 112
                    f+ Kp ++  Llka++
    EPA05735.1 105 CFVPKPTQRLLLLKAIN 121
                   ******99999999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 890.39
//
Query:       EPA05736.1  [L=55]
Description: hypothetical protein BG20_I2464, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00045   20.1   0.0    0.00063   19.6   0.0    1.3  1  ADH_N     Alcohol dehydrogenase GroES-like domain


Domain annotation for each model (and alignments):
>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   3.5e-08   0.00063       1      23 [.      33      55 .]      33      55 .] 0.92

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 3.5e-08
                TTEEEEEEEEEEE-HHHHHHHTT CS
       ADH_N  1 pgevlikvkaagiCgsDlhilkg 23
                p+e+l+k++a+g+C+s lh ++g
  EPA05736.1 33 PNEILLKIEACGVCHSQLHGIEG 55
                689****************8876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 391.63
//
Query:       EPA05737.1  [L=125]
Description: hypothetical protein BG20_I2450 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.015   14.5   1.9      0.018   14.2   1.7    1.3  1  ATG19_autophagy  Autophagy protein Atg19, Atg8-binding
      0.054   13.7   0.2      0.064   13.5   0.2    1.1  1  DUF3958          Protein of unknown function (DUF3958)


Domain annotation for each model (and alignments):
>> ATG19_autophagy  Autophagy protein Atg19, Atg8-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   1.7   2.1e-06     0.018      13      75 ..      21      90 ..      18     105 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.1e-06
  ATG19_autophagy 13 dFFskikTesqLeevmngYekYekllqkfdgkkkeles......vnevealkqiasdesskea.keelat 75
                      FF ++  +s+ ++v+n+Y +Y +ll + ++  k++         +  +++     + +ske  +++l++
       EPA05737.1 21 AFFGHLIFVSDTQQVINKYSVYVHLLSEWNSSSKNIIFevtnswYKSDKSHVTTGFNSESKEYnTNQLQK 90
                     6*****************************9999875456666744445555556666666541444444 PP

>> DUF3958  Protein of unknown function (DUF3958)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   7.2e-06     0.064      21     104 ..      33     117 ..      29     120 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.2e-06
     DUF3958  21 ekelkkqeqlkeeyeehfnqskrlfdelletfrkdeeshlfeklrdevqrlsrklredLE.eeeeeLkrekrqLedqeeelyyek 104
                 ++ ++k       + e+++ sk  + e+   ++k+++sh+  +++ e  +++ +  +++  +++ eLk e  + +++ + +++ek
  EPA05737.1  33 QQVINKYSVYVHLLSEWNSSSKNIIFEVTNSWYKSDKSHVTTGFNSESKEYNTNQLQKINgKSYVELKHEFSDCQEEWQPISIEK 117
                 555666666666678999*******************************999988888864678899988888888777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1225  (0.0683251); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 864.72
//
Query:       EPA05738.1  [L=99]
Description: hypothetical protein BG20_I2451 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.8e-16   59.2   0.0    6.6e-16   58.8   0.0    1.2  1  DM13             Electron transfer DM13
  ------ inclusion threshold ------
       0.17   11.7   0.0        6.7    6.6   0.0    2.1  2  ThiC-associated  ThiC-associated domain


Domain annotation for each model (and alignments):
>> DM13  Electron transfer DM13
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   0.0   7.4e-20   6.6e-16       4     104 .]       7      98 ..       4      98 .. 0.91

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 7.4e-20
        DM13   4 sde.hgtsGtvsivd..d.ktlelegfatdgkgpdlkvwlgkseapsskkgfkipdedgvtlgplkaykgeq.ytlelpagvdladyksvsvWcerfnv 97 
                   + h+  G ++i++  d ++l++e+f++  +gpdl+v+++ + +           ++gv l++lk+ kg+q y l   +++dl  y++v+++c+ f+v
  EPA05738.1   7 GLAgHNAMGVAKIIQvnDmTFLRFENFEV-TNGPDLRVYITSGGDI----------HKGVHLEKLKGSKGDQnYLL---ENIDLGVYDTVVIYCQPFGV 91 
                 555599*********9559*********9.9************963..........5699************9*99...******************** PP

        DM13  98 nFGaakl 104
                  FG+a+l
  EPA05738.1  92 YFGKAPL 98 
                 ****986 PP

>> ThiC-associated  ThiC-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0    0.0059        53      35      51 ..      32      48 ..      13      62 .. 0.72
   2 ?    6.6   0.0   0.00075       6.7      24      56 ..      55      88 ..      51      91 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.0059
                     ....G----EEEE---G CS
  ThiC-associated 35 kekeeenepvrvYDtSG 51
                     + + ++ +++rvY tSG
       EPA05738.1 32 NFEVTNGPDLRVYITSG 48
                     445578899*******9 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.00075
                     E---GG..........G----EEEE---GGGG-T CS
  ThiC-associated 24 iklsptvlketkeke.eenepvrvYDtSGpYtdp 56
                     ++l++ + ++++++   en ++ vYDt   Y +p
       EPA05738.1 55 VHLEKLKGSKGDQNYlLENIDLGVYDTVVIYCQP 88
                     555655555554444479*********9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 698.31
//
Query:       EPA05739.1  [L=110]
Description: hypothetical protein BG20_I2449, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 657.18
//
Query:       EPA05740.1  [L=36]
Description: hypothetical protein BG20_I2531, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (36 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       234  (0.0130515); expected 358.6 (0.02)
Passed bias filter:                      150  (0.00836633); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 264.77
//
Query:       EPA05741.1  [L=168]
Description: hypothetical protein BG20_I2532 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0097   16.4   0.5       0.13   12.8   0.2    2.5  2  DUF3644   Protein of unknown function (DUF3644)


Domain annotation for each model (and alignments):
>> DUF3644  Protein of unknown function (DUF3644)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0     0.031   5.5e+02      58      72 ..      91     105 ..      73     106 .. 0.87
   2 !   12.8   0.2   7.1e-06      0.13       4      27 ..     137     161 ..     135     168 .] 0.84

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.031
     DUF3644  58 vrkNleaLielRnki 72 
                   +N+  L e Rn+ 
  EPA05741.1  91 YTRNMSRLFEVRNDT 105
                 579**********85 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 7.1e-06
     DUF3644   4 mvnAWelLLkakllkk.giksiykk 27 
                 m+ AW  LLk +l+++ +i+ i  +
  EPA05741.1 137 MCKAWDDLLKIYLNQQaNIDWIALS 161
                 9***************99**99833 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1126.18
//
Query:       EPA05742.1  [L=170]
Description: adenine phosphoribosyltransferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.6e-14   53.0   0.0    3.2e-14   52.8   0.0    1.1  1  Pribosyltran  Phosphoribosyl transferase domain
     0.0079   15.7   0.0     0.0098   15.3   0.0    1.1  1  UPRTase       Uracil phosphoribosyltransferase


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.8   0.0   3.5e-18   3.2e-14      22     125 ..      39     149 ..      26     168 .. 0.86

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 3.5e-18
                   EEEE..--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE.............EE----TTSEEEEE-SEESSSHHHHHHHHHHH CS
  Pribosyltran  22 ilee..yngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdes.....rlledpagkkVliVDDildtGgTllaalelLk 111
                    +e+   +   d+++gi+ +G+ +a  la++ +  +++vrk  + p+++++ + +++  +     ++ ++ +g+k++i+DD+l+tGgT +a ++l++
    EPA05742.1  39 EFEKyfHPKDVDLFAGIEARGFLLACVLASRYNKGMVMVRKAGKLPGKTTKLSYKIEYGQdtiemQKDIIDKGQKIIICDDLLATGGTAKASAKLIE 135
                   4444233455679***************************************9766555599*********************************** PP

                   CC-BSEEEEEEEEE CS
  Pribosyltran 112 ekgpeevriavlvd 125
                   ++g ++ ++a +++
    EPA05742.1 136 KVGGKVTGFAFIIE 149
                   ******99998874 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.1e-06    0.0098     115     168 ..     103     158 ..      76     165 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.1e-06
     UPRTase 115 LPkki..aertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlaseegvkr 168
                 ++k+i  + ++++++D ++aTGg+a a  +l+ + g ++    ++  l   +g+k 
  EPA05742.1 103 MQKDIidKGQKIIICDDLLATGGTAKASAKLIEKVGGKVTGFAFIIELTELNGIKG 158
                 45566566678***********************9998888777777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 1078.55
//
Query:       EPA05743.1  [L=120]
Description: hypothetical protein BG20_I1768 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0067   16.3   0.0     0.0082   16.0   0.0    1.2  1  MRF_C2    Myelin gene regulatory factor C-terminal domain 2


Domain annotation for each model (and alignments):
>> MRF_C2  Myelin gene regulatory factor C-terminal domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   4.6e-07    0.0082      44     111 ..       8      75 ..       2      96 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.6e-07
      MRF_C2  44 ltlelnsseslvvklCgltkgrkCeeeeselsskeskstestqgtehlwslpvasfqesaYhFRvals 111
                 +++  ++  s+ v++Cg+ k+r Cee++ ++++ ++     +   + +w + v ++q+  Y++++   
  EPA05743.1   8 INIAERTIGSVDVWRCGVCKKRFCEEKQLGIEELADLVGMPKIDPDAKWGVVVCKLQQGKYRWKLVRL 75 
                 444446667899**************87788777777766666789****************987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 857.29
//
Query:       EPA05744.1  [L=173]
Description: hypothetical protein BG20_I1772 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-11   43.0   0.0    4.5e-06   27.0   0.0    2.5  2  MG2       MG2 domain
    2.6e-06   27.2   0.2      0.012   15.5   0.1    2.7  2  FlgD_ig   FlgD Ig-like domain
  ------ inclusion threshold ------
      0.018   15.3   0.0        1.4    9.2   0.0    2.4  2  DUF4625   Domain of unknown function (DUF4625)


Domain annotation for each model (and alignments):
>> MG2  MG2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0   7.5e-10   4.5e-06      33      83 ..      18      69 ..       3      84 .. 0.79
   2 !   13.7   0.0   1.1e-05     0.066      34      87 ..     113     163 ..      95     172 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 7.5e-10
                -EEEEEEEE-TTSSEEEEEEE.EE-CTTEEEEEEE--TT--SEEEEEEEEEC CS
         MG2 33 klplkltirdpdgkevkelpl.atdetggaesefalpeaaklGeysvelsad 83
                +  l++++ dp+gk vk+++   +++  + ++e+++p++ak G++ ++++  
  EPA05744.1 18 NSFLTIELFDPNGKIVKTKETfSDKNGKISNNELRIPSDAKVGTWAINVKSG 69
                46799***********9999845555556999*****************433 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 1.1e-05
                 EEEEEEEE-TTSSEEEEEEEEE-CTTEEEEEEE--TT--SEEEEEEEEECSTTT CS
         MG2  34 lplkltirdpdgkevkelplatdetggaesefalpeaaklGeysvelsadsaee 87 
                 +++ + i++++g ++++l++ ++ +g +++ + +p++   G+y +++   ++++
  EPA05744.1 113 QKVDMIITTSEGIVIQKLSFPASGKGEIKQPWFIPSNVVPGTYILKV---TDAK 163
                 68999******************************************...2222 PP

>> FlgD_ig  FlgD Ig-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0   0.00021       1.3      20      49 ..      16      45 ..       8      49 .. 0.85
   2 !   15.5   0.1   1.9e-06     0.012      11      76 ..     101     162 ..      92     165 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00021
                SSSEEEEEEEE-SS--EEEEEEEEESSSEE CS
     FlgD_ig 20 eaadevtvtikDasGevVrtidlgaqsaGv 49
                ++ + +t+++ D +G++V+t +  + + G 
  EPA05744.1 16 NPNSFLTIELFDPNGKIVKTKETFSDKNGK 45
                677889**************9988888776 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.9e-06
                 -EEEEEE.ESSSEEEEEEEE-SS--EEEEEEEEESSSEEEEEEE-SB-TTS-B--SEEEEEEEEEE CS
     FlgD_ig  11 eaplgvelpeaadevtvtikDasGevVrtidlgaqsaGvvsftWdGtdndGnkladGaYtvkvtat 76 
                 ++++++++++aa++v + i+ ++G v++++++ a+ +G+ +  W       +++ +G+Y +kvt +
  EPA05744.1 101 GKSIDITVSNAAQKVDMIITTSEGIVIQKLSFPASGKGEIKQPWF--IP--SNVVPGTYILKVTDA 162
                 4688999********************************999997..23..346777777777765 PP

>> DUF4625  Domain of unknown function (DUF4625)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0    0.0074        44      87     112 ..      40      65 ..      24      69 .. 0.81
   2 ?    9.2   0.0   0.00023       1.4      92     123 ..     138     167 ..      71     172 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0074
     DUF4625  87 gskkeyelheeieiPadaeaGdYhlv 112
                   k+ ++ ++e++iP+da+ G + + 
  EPA05744.1  40 SDKNGKISNNELRIPSDAKVGTWAIN 65 
                 4567788999**********988665 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00023
     DUF4625  92 yelheeieiPadaeaGdYhlvirvtDasGnet 123
                  e+++   iP+++ +G Y  +++vtDa+G  +
  EPA05744.1 138 GEIKQPWFIPSNVVPGTY--ILKVTDAKGSAE 167
                 56788889**********..67899***9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1220.98
//
Query:       EPA05745.1  [L=94]
Description: hypothetical protein BG20_I1770 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.063   12.5   0.0      0.067   12.4   0.0    1.2  1  DUF4882   Domain of unknown function (DUF4882)


Domain annotation for each model (and alignments):
>> DUF4882  Domain of unknown function (DUF4882)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   3.8e-06     0.067      44      95 ..      32      84 ..       7      87 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.8e-06
     DUF4882 44 lplkifpiidGqkfslkvepvteeeygyidyiaksk.aklnstndeGdfslpk 95
                +    f  i Gq ++ k++ +te e  ++ y+       l+s   +Gd++lp+
  EPA05745.1 32 FNAIAFGRIGGQNIGAKISKITERELEKLGYNVDEViDSLQSNLLQGDLTLPE 84
                55567899***********************98765167999999******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 687.66
//
Query:       EPA05746.1  [L=697]
Description: hypothetical protein BG20_I1774 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.3e-25   88.7   4.3    6.3e-25   88.7   4.3    2.4  2  AAA_15           AAA ATPase domain
    6.6e-13   49.1  12.8    1.2e-11   45.0   5.4    3.6  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
     0.0019   17.6   0.1        1.8    7.8   0.0    3.4  4  DUF2813          Protein of unknown function (DUF2813)
     0.0022   18.5   1.1     0.0073   16.8   0.1    2.4  2  ABC_tran         ABC transporter
     0.0058   16.3   0.1      0.039   13.7   0.0    2.3  2  AAA_29           P-loop containing region of AAA domain
     0.0058   16.2   0.1      0.032   13.8   0.0    2.1  2  AAA_27           AAA domain
  ------ inclusion threshold ------
       0.14   11.9   0.1       0.82    9.4   0.0    2.1  2  Glyco_hydro_42C  Beta-galactosidase C-terminal domain
       0.16   11.4   0.1        1.3    8.5   0.1    2.3  1  SMC_N            RecF/RecN/SMC N terminal domain
        3.6    8.0  24.4       0.14   12.6  14.1    3.4  2  AAA_23           AAA domain


Domain annotation for each model (and alignments):
>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.7   4.3   3.1e-28   6.3e-25       1     369 []       1     421 [.       1     421 [. 0.61
   2 ?   -2.4   4.3       1.5   3.1e+03     117     182 ..     616     679 ..     493     695 .. 0.43

  Alignments for each domain:
  == domain 1  score: 88.7 bits;  conditional E-value: 3.1e-28
      AAA_15   1 MkIkkikikNFRslkd.veidlseeltvliGkNnsGKSsilealdlFlnnkekkn................................kkvikiekedle 66 
                 M+++k++++ +R++ d  ei + + l  ++G+N sGK++il+al l+   +e+ +                                            
  EPA05746.1   1 MRLRKFRVRAYRCIHDsGEITVGD-LAAFVGRNESGKTTILQALTLLNR-DERVSdldlcdelseelkgeirivegefelssneiqlL----------- 86 
                 9***************99******.*******************65555.65666555655555555555555555555554444442........... PP

      AAA_15  67 ifeniseskdikIdvef......................aek.ekakeyektlkskekkkadlllkkkesdlkktikdkklklkknelsdekisvekkk 142
                                                          + e++++ +++++++e ++ ++  k++ + l+++ +   ++++       +       
  EPA05746.1  87 ----------------KqlfpglpeikkiklfrtnkkpkV-QyEFEDIQISEERNRELNSWENFSKQILNFLDTIPNHLRIQID------TRLFEGPPP 162
                 ................044555555554444443322210.1222444444444444443333333333333333333333332......222222222 PP

      AAA_15 143 skkelpkekeeklekekeelkidkedlkklikkleeslkkee.........................elknvlksaiiklllisakRnvsdedsekkss 216
                 +++e +++   +  ++   + i+  ++ + ++k++e+ + +                          + ++ +k+ +  + l++  R+ + e+  +++ 
  EPA05746.1 163 KNQEMFDSGMAEFSNQFHVIAIQEPKVIEEWEKIYENPENQFskllsgeseksaldnfiasdlhprfVYFSDYKKIYGNINLNEYLREEKGERASSIEF 261
                 344555555555555566666666666666666666655555666666555553333333334333333444444443344443333333333333333 PP

      AAA_15 217 llgklkekileealqekl..........eeelteklkeiqeklkeidkklaeelkkilkkkid..kik.kfnykgkkneeieik.......ddeelpln 295
                 + +  k +                    +++l ++ ke+ +k  ++ ++ +++l+++l++ ++   i  ++ y++ +     i+         +   ln
  EPA05746.1 262 VEEFDKAE---------TvrnlfylaelDIKLLDDVKETPSKCIKLLNTASNRLTRKLNPAWKgdPIHvDLRYNPGNIMSLVISdvhrdgtVTNTGLLN 351
                 33333333.........033334778888899999999999999999999999998888877522555588888888888888899998887788889* PP

      AAA_15 296 knGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSphii 369
                 ++  G++ ++++i+  +   ++   e k +ill++EP  +LHp +q+ + +llk la +n  Qv++ THSp++i
  EPA05746.1 352 RRAEGFKWTFSFIVNFAAETQR--AELKEAILLLDEPARNLHPTQQRGISDLLKGLAGSN--QVLYATHSPFMI 421
                 **********999876666655..7999********************************..***********8 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.5
      AAA_15 117 ktikdkklklkknelsdekisvekkkskkelpkekeeklekekeelkidkedlkklikkleeslkk 182
                 k + d+  k+  +e +d+    +++++    ++ ++  le+ +   +++k+  ++l++ + e + +
  EPA05746.1 616 KGVLDNLKKIW-EEHKDDDWGQFDNEE-ITRYICEKITLEETEFLSDKTKDQFRSLYRLIAERIRQ 679
                 22222222221.111222222222221.11222233344444444444444444444444444444 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.0   5.4   6.1e-15   1.2e-11       1     302 [.      25     421 ..      25     421 .. 0.65
   2 ?    2.2   0.7     0.067   1.3e+02      39     111 ..     558     640 ..     545     666 .. 0.81

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 6.1e-15
      AAA_21   1 lnvliGpNgsGKSnLLdaldllarl..............................drdvegltdelsggggirkipslldlydpeipfefeieeflsqg 69 
                 l++++G+N sGK+++L+al ll r                                ++++ l+  ++g  +i+ki  + +++ p+   efe+++  ++ 
  EPA05746.1  25 LAAFVGRNESGKTTILQALTLLNRDervsdldlcdelseelkgeirivegefelsSNEIQLLKQLFPGLPEIKKIKLFRTNKKPKVQYEFEDIQISEER 123
                 5789******************65555555554444444444444444444444433333333333333344444444444444444444444444444 PP

      AAA_21  70 vryryglrlersqveeklssvetllesgllldkrsleeedvfnpeargirggvsvfslkelsvsepndlqfgkaltditsrawsllllldglrkerigl 168
                 +r   + +   +q+                                                           +l+ i+++++   +           +
  EPA05746.1 124 NRELNSWENFSKQI---------------------------------------------------------LNFLDTIPNHLRI--Q--------IDTR 155
                 44444444444444.........................................................3333333333332..1........3333 PP

      AAA_21 169 lnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrer................................................ 219
                 l+      ++ +    + +++++++ + i   +  e +e+i+++ e +  +                                                
  EPA05746.1 156 LFEGPPPKNQEMFDSGMAEFSNQFHVIAIQEPKVIEEWEKIYENPENQFSKllsgeseksaldnfiasdlhprfvyfsdykkiygninlneylreekge 254
                 333333333444444444445555555555555544444444444444444555555555555555555555555555555555555555556666666 PP

      AAA_21 220 ..............................................................................gvvflengdgqelparel... 237
                                                                                                v+  ++ dg  ++   l   
  EPA05746.1 255 rassiefveefdkaetvrnlfylaeldikllddvketpskcikllntasnrltrklnpawkgdpihvdlrynpgnimsLVISDVHRDGTVTNTGLLnrr 353
                 6666666666666666666666777****************************************************8888888888888888888*** PP

      AAA_21 238 SdGtkrllalltallralkkg....sllliDEpEngLHPkllrrllellkelsrngaQviltTHSplll 302
                  +G+k  + +++ +++  + +    ++ll+DEp  +LHP  +r + +llk l+    Qv+ +THSp+ +
  EPA05746.1 354 AEGFKWTFSFIVNFAAETQRAelkeAILLLDEPARNLHPTQQRGISDLLKGLAG-SNQVLYATHSPFMI 421
                 ********99999999998889999************************88877.89*********975 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.067
      AAA_21  39 gggirkipslldlydpeipfefeieeflsqgvryryglrlersqv..........eeklssvetllesgllldkrsleeedvf 111
                 +++i+ i ++ d+++ e+   + + e  ++ v+ +y++rl ++++          +ek++++++l+++++ +++++  ++d+ 
  EPA05746.1 558 FSPIQTIFFERDGKNLESIEDYIVLEDYLHAVNQTYEIRLRKEGYsnltapevtlREKKGVLDNLKKIWEEHKDDDWGQFDNE 640
                 44555566666666666666666666668888999999999999888999999999************999999999988875 PP

>> DUF2813  Protein of unknown function (DUF2813)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0   0.00088       1.8       1      49 [.       1      49 [.       1      63 [. 0.85
   2 !    5.1   0.0    0.0057        11     275     309 ..     369     403 ..     356     420 .. 0.76
   3 ?   -1.8   0.0      0.72   1.4e+03     254     292 ..     450     488 ..     434     492 .. 0.79
   4 ?   -1.1   0.1      0.43   8.5e+02     178     213 ..     638     673 ..     540     692 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00088
     DUF2813  1 myLerieisGFRGinrL.SlsleentvLiGENaWGKSSLldALslilnve 49
                m L++  +  +R i+    +++ ++ +++G N  GK  +l+AL+l+ n +
  EPA05746.1  1 MRLRKFRVRAYRCIHDSgEITVGDLAAFVGRNESGKTTILQALTLL-NRD 49
                78999999999999865269***********************974.555 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0057
     DUF2813 275 gkvelkriarPilllEdpearLHPtmlaiaWelle 309
                 ++++  + +  illl++p  +LHPt+   + +ll+
  EPA05746.1 369 AETQRAELKEAILLLDEPARNLHPTQQRGISDLLK 403
                 44555667889*************98766666665 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.72
     DUF2813 254 eeekslrllllgllatllqakgkvelkriarPilllEdp 292
                 +++k l  +l gl   l+++  ++e+   +rP++++E +
  EPA05746.1 450 ADDKTLTPILYGLSRGLVESIVDREVGTNSRPVIIVETM 488
                 56677778888888999999999999999******9965 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 0.43
     DUF2813 178 rlerrlenllrrllskpqklsedelkselqalssll 213
                   e+ +  ++++++ +++++ +d++k+++++l  l+
  EPA05746.1 638 DNEEITRYICEKITLEETEFLSDKTKDQFRSLYRLI 673
                 445555556666666666666666666666666655 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   3.7e-06    0.0073       7      72 ..      19      80 ..      15     177 .. 0.68
   2 ?   -1.1   0.1       1.2   2.5e+03     126     136 ..     377     387 ..     375     388 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.7e-06
                EEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-T CS
                xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  7 klkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfp 72
                ++  g + a+vG+n +GK+t+l++l+ l +++   +   + dl ++  e+l+ ei++++ e +l +
  EPA05746.1 19 EITVGDLAAFVGRNESGKTTILQALTLLNRDER--V--SDLDLCDELSEELKGEIRIVEGEFELSS 80
                6778999*******************9987643..3..2333444444455555555555533333 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.2
                 TSSEEEEESTT CS
                 xxxxxxxxxxx RF
    ABC_tran 126 kpkllllDEpt 136
                 k  +lllDEp 
  EPA05746.1 377 KEAILLLDEPA 387
                 5689******6 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   1.9e-05     0.039      20      45 ..      21      46 ..      12      49 .. 0.83
   2 ?   -1.7   0.0       1.2   2.5e+03       8      17 ..     633     642 ..     633     650 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.9e-05
      AAA_29 20 dlkgatlltGpsGsGKSTllDAiqal 45
                ++ +   ++G+++sGK+T+l A++ l
  EPA05746.1 21 TVGDLAAFVGRNESGKTTILQALTLL 46
                44457899*************99865 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.2
      AAA_29   8 NWgtfdghti 17 
                 +Wg fd+++i
  EPA05746.1 633 DWGQFDNEEI 642
                 6*****9766 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   1.6e-05     0.032       1      48 [.       1      45 [.       1      47 [. 0.86
   2 ?   -0.7   0.0      0.46   9.2e+02     108     132 ..     655     679 ..     649     688 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.6e-05
      AAA_27  1 MrlerLdLeryGkftdr.sldfsaeeadlhliyGpNEAGKstalrAisd 48
                Mrl+++++++y  + d+ +++ +    dl   +G NE+GK+t+l+A++ 
  EPA05746.1  1 MRLRKFRVRAYRCIHDSgEITVG----DLAAFVGRNESGKTTILQALTL 45
                89999999999888887567776....99999**************975 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.46
      AAA_27 108 aallggldretFealFgLdherLre 132
                 +++l   ++++F++l+ L +er+r+
  EPA05746.1 655 TEFLSDKTKDQFRSLYRLIAERIRQ 679
                 6799999**************9997 PP

>> Glyco_hydro_42C  Beta-galactosidase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.75   1.5e+03      17      57 ..      45      87 ..      44      88 .. 0.67
   2 ?    9.4   0.0   0.00041      0.82       6      30 ..     352     377 ..     350     384 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.75
                     EEE-SSS-EE----TT-EEEES-........SEE-TTEEEEEE CS
  Glyco_hydro_42C 17 vlNfsneevtvtlpasagdlltge..laeggvtlePygvaVlr 57
                     +lN+ + +  ++l ++  + l+ge  ++eg+++l  ++++ l+
       EPA05746.1 45 LLNRDERVSDLDLCDELSEELKGEirIVEGEFELSSNEIQLLK 87
                     5788888888888555555555541156777888888887776 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00041
                      E.....ETTEEEEEE-SSS-EE---- CS
  Glyco_hydro_42C   6 rR.engegrylFvlNfsneevtvtlp 30 
                      rR e+ ++++ F++Nf +e+++++l+
       EPA05746.1 352 RRaEGFKWTFSFIVNFAAETQRAELK 377
                      6778889****************995 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.1   0.00063       1.3       6      45 ..       7      44 ..       2     426 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00063
                EEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHH CS
                xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       SMC_N  6 eienFksyagktvilpfsksftaivGpNGSGKsnlldAil 45
                +++ ++ ++ ++ ++ + + + a vG+N SGK+ +l+A+ 
  EPA05746.1  7 RVRAYRCIH-DSGEITVGD-LAAFVGRNESGKTTILQALT 44
                555555553.333444433.7899**************93 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6  14.1   7.1e-05      0.14      13     170 ..      18     273 ..       5     311 .. 0.63
   2 ?   -1.1   2.5       1.1   2.2e+03      75     123 ..     593     628 ..     533     695 .. 0.40

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.1e-05
      AAA_23  13 qeidFskgltlItGpNGaGKTTildAiklaLygetprlsrks...........grgfeksdveiese......................gkvkayvelt 78 
                  ei  +  l +++G N++GKTTil+A++l    e  r s+ +           + +++++++e++s+                      +++k+ v+ +
  EPA05746.1  18 GEITVG-DLAAFVGRNESGKTTILQALTLLNRDE--RVSDLDlcdelseelkgEIRIVEGEFELSSNeiqllkqlfpglpeikkiklfrTNKKPKVQYE 113
                 566666.6899*****************987665..444444667877777765566666666666688899999988888888888876666667777 PP

      AAA_23  79 fenkdgry................................................................trsiererelskkkgkttkkakle.ll 112
                 fe+++  +                                                                  ++ +e e+++++ +++  + l+ + 
  EPA05746.1 114 FEDIQISEernrelnswenfskqilnfldtipnhlriqidtrlfegpppknqemfdsgmaefsnqfhviaiqEPKVIEEWEKIYENPENQFSKLLSgES 212
                 777655445566677777777777777777777777777777777777777777777777777776666666444545555555555444444333133 PP

      AAA_23 113 eideleqfisellgskkiil.nlilflgqerfeefelkdkkerleel..ekeleeledekk 170
                 e+++l++fi + l+ ++  + ++  ++g  + +e ++++k er  ++   +e++++e++++
  EPA05746.1 213 EKSALDNFIASDLHPRFVYFsDYKKIYGNINLNEYLREEKGERASSIefVEEFDKAETVRN 273
                 4466666666666666663325556666666666666666664444311444555555444 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.1
      AAA_23  75 veltfenkdgry..........trsiererelskkkgkttkkaklelleideleqfise 123
                 +e+++++++  +          +            kg+            d+l+++++e
  EPA05746.1 593 YEIRLRKEGYSNltapevtlreK------------KGVL-----------DNLKKIWEE 628
                 22222222222112222222221............1111...........111111111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (697 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       633  (0.0353059); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.72u 0.33s 00:00:01.05 Elapsed: 00:00:00.48
# Mc/sec: 4354.96
//
Query:       EPA05747.1  [L=152]
Description: hypothetical protein BG20_I1775 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1079.52
//
Query:       EPA05748.1  [L=557]
Description: hypothetical protein BG20_I1773 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-07   30.4   0.2       0.18   12.3   0.0    4.0  4  MG2              MG2 domain
     0.0019   18.4   8.9      0.016   15.5   0.2    3.5  4  Big_6            Bacterial Ig domain
     0.0047   16.8   2.7       0.62   10.0   0.1    3.9  3  FlgD_ig          FlgD Ig-like domain
     0.0086   16.1   0.1       0.89    9.6   0.0    3.3  4  FixH             FixH
  ------ inclusion threshold ------
      0.021   14.9   0.4        1.5    8.9   0.1    3.0  3  bMG3             Bacterial alpha-2-macroglobulin MG3 domain
      0.062   13.9   0.1       0.62   10.7   0.0    2.8  2  YtkA             YtkA-like
      0.096   13.0  14.8       0.45   10.9   2.9    3.9  4  Invasin_D3       Invasin, domain 3
       0.11   12.6   2.3       0.33   11.0   1.2    2.6  2  TIG              IPT/TIG domain
        0.2   11.7   0.9        4.2    7.4   0.1    3.3  3  CE2_N            Carbohydrate esterase 2 N-terminal
       0.87    9.9  12.9       0.22   11.8   1.1    4.3  4  CarboxypepD_reg  Carboxypeptidase regulatory-like domain


Domain annotation for each model (and alignments):
>> MG2  MG2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.94   1.7e+03      52      86 ..     203     237 ..     196     245 .. 0.64
   2 !   12.3   0.0    0.0001      0.18      29      92 ..     280     343 ..     268     346 .. 0.82
   3 !   12.3   0.0    0.0001      0.18      27      87 ..     369     428 ..     351     436 .. 0.85
   4 ?   -1.4   0.0       1.9   3.3e+03      13      54 ..     467     509 ..     465     533 .. 0.54

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.94
                 EEEE-CTTEEEEEEE--TT--SEEEEEEEEECSTT CS
         MG2  52 platdetggaesefalpeaaklGeysvelsadsae 86 
                 +++tde g + +++++p+++ + +   ++++++ +
  EPA05748.1 203 TFQTDEGGHFITTVTVPKTQNTDRVDFSIRDNDGN 237
                 56788888888888888877765555555444444 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.0001
                 SB---EEEEEEEE-TTSSEEEEEEEEE-CTTEEEEE.EE--TT--SEEEEEEEEECSTTT-EEEE CS
         MG2  29 qglaklplkltirdpdgkevkelplatdetggaese.falpeaaklGeysvelsadsaeeslssg 92 
                 ++ ++  +++t++++ + ++++ + ++d++g  + e +++p +a+ G+y++ + +d++e+++ s+
  EPA05748.1 280 TAQPSSGVTITVQNAADATINTRTANADAKGNWSIEpITVPGDAEFGDYTAII-TDGKEQKTLSW 343
                 44445679*****************9999999776549**************9.77777766655 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.0001
                 TCSB---EEEEEEEE-TTSSEEEEEEEEE-CTTEEEEEEE--TT-.-SEEEEEEEEECSTTT CS
         MG2  27 tlqglaklplkltirdpdgkevkelplatdetggaesefalpeaa.klGeysvelsadsaee 87 
                 ++++l+++ l+l + +p g+e +++++  d +g++e++++++ +  + G++++e+ +  a++
  EPA05748.1 369 NGTALPNKDLELILLNPLGEEKHSESILVDGSGIVEFQYPTKVNVdMEGTWTLEATQ--AGD 428
                 56788999**********************************996368*******33..222 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 1.9
                 TT-EEEEEEEEESTTCSB---..EEEEEEEE-TTSSEEEEEEEE CS
         MG2  13 PgetVslkallrdetlqglak..lplkltirdpdgkevkelpla 54 
                 Pg+++s+ ++   ++ + + +   ++ +t+++ dg++ ++l+l+
  EPA05748.1 467 PGDKISMIIVDPSDKQKIFSDgtNEIFITLEQ-DGRKDYSLSLT 509
                 67777666555555555555544444444443.33333444444 PP

>> Big_6  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   0.7    0.0055       9.9      33      73 ..     197     238 ..     172     242 .. 0.70
   2 !   15.5   0.2   8.7e-06     0.016      16      52 ..     276     316 ..     267     344 .. 0.73
   3 ?   -3.9   0.0        10   1.8e+04      40      53 ..     411     424 ..     408     431 .. 0.61
   4 ?   -3.2   0.0       5.9   1.1e+04      46      60 ..     514     528 ..     503     538 .. 0.50

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0055
       Big_6  33 dgtvlgtgtadadGeFsvtlepaq.angetlsvvatDaagnt 73 
                 d  ++gt + d+ G+F  t++ ++ +n  ++  +  D++gn+
  EPA05748.1 197 DRDQVGTFQTDEGGHFITTVTVPKtQNTDRVDFSIRDNDGNE 238
                 4556788899******8888655537888999********97 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 8.7e-06
       Big_6  16 tltGkaeagatVtv..kdadgtvl..gtgtadadGeFsvtl 52 
                 +++G+a++ + Vt+  ++a+++++   t+ ada+G++s++ 
  EPA05748.1 276 KVSGTAQPSSGVTItvQNAADATIntRTANADAKGNWSIEP 316
                 59*****9886655227788888744567779******975 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 10
       Big_6  40 gtadadGeFsvtle 53 
                 + +d +G+++++ +
  EPA05748.1 411 VNVDMEGTWTLEAT 424
                 45677777766554 PP

  == domain 4  score: -3.2 bits;  conditional E-value: 5.9
       Big_6  46 GeFsvtlepaqange 60 
                 G ++  +++a+a+ +
  EPA05748.1 514 GVYTAIIKKANAKTT 528
                 334444433333222 PP

>> FlgD_ig  FlgD Ig-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.061   1.1e+02       8      41 ..     208     242 ..     202     245 .. 0.62
   2 !   10.0   0.1   0.00034      0.62      14      51 ..     275     313 ..     267     338 .. 0.89
   3 ?    0.9   0.1      0.23   4.2e+02      39      57 ..     418     436 ..     416     438 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.061
                 SS--EEEEEE...ESSSEEEEEEEE-SS--EEEEEE CS
     FlgD_ig   8 gdgeaplgve..lpeaadevtvtikDasGevVrtid 41 
                 ++g    +v+   +++ d v ++i+D  G++ ++i+
  EPA05748.1 208 EGGHFITTVTvpKTQNTDRVDFSIRDNDGNE-KKIS 242
                 3444333333336777888888888888887.6665 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00034
                 EEEE..ESSSEEEEEEEE-SS--EEEEEEEEESSSEEEE CS
     FlgD_ig  14 lgve.lpeaadevtvtikDasGevVrtidlgaqsaGvvs 51 
                 ++v+  +++++ vt+t+++a+  +++t ++ a ++G  s
  EPA05748.1 275 IKVSgTAQPSSGVTITVQNAADATINTRTANADAKGNWS 313
                 666677999**************************9866 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.23
                 EEEEEESSSEEEEEEE-SB CS
     FlgD_ig  39 tidlgaqsaGvvsftWdGt 57 
                 t +l+a +aG+ +f+  G 
  EPA05748.1 418 TWTLEATQAGDTEFSYAGL 436
                 56899*********99886 PP

>> FixH  FixH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       1.1     2e+03      41     111 ..     184     205 ..     178     245 .. 0.59
   2 ?   -3.3   0.0       4.5   8.1e+03     112     132 ..     293     314 ..     280     322 .. 0.59
   3 !    9.6   0.0    0.0005      0.89      57     145 ..     336     433 ..     327     436 .. 0.73
   4 ?    2.2   0.0     0.093   1.7e+02      94     123 ..     492     521 ..     448     530 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.1
        FixH  41 dyYkkGkainqelarakaaqalglsadvaldegeltitlrdaagkpveaaaltlslshptdagkDkklkLt 111
                 d ++++ ++n  ++r+                                                 +  +++
  EPA05748.1 184 DNFEASTQYNIFIDRD-------------------------------------------------QVGTFQ 205
                 5555555555555554.................................................444444 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4.5
        FixH 112 eaangvYrapleal.lkGrWyv 132
                 +aa+ +  +  ++  +kG+W +
  EPA05748.1 293 NAADATINTRTANAdAKGNWSI 314
                 4444444443333346777776 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0005
        FixH  57 kaaqalglsadvalde..........geltitlrdaagkpveaaaltlslshptdagkDkklkLteaang..vYrapleal..lkGrWyvqlaaeegge 141
                 k+++ l ++ + + +               i++   +g  + ++ l+l+l +p  ++k ++  L+ ++ g  +++ p +    ++G W ++  ++ g++
  EPA05748.1 336 KEQKTLSWKLETSKTIsltasavqftPGDVIKF---NGTALPNKDLELILLNPLGEEKHSESILV-DGSGivEFQYPTKVNvdMEGTWTLEA-TQAGDT 429
                 666666666655555555555555556666777...8999*************************.66665755554444477********8.888888 PP

        FixH 142 awrl 145
                 ++ +
  EPA05748.1 430 EFSY 433
                 8876 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.093
        FixH  94 lslshptdagkDkklkLteaangvYraple 123
                 +++    d +kD +l Lt  a gvY+a  +
  EPA05748.1 492 IFITLEQDGRKDYSLSLTGYASGVYTAIIK 521
                 55555667899***************9554 PP

>> bMG3  Bacterial alpha-2-macroglobulin MG3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       2.6   4.7e+03      42      64 ..     200     222 ..     197     235 .. 0.73
   2 ?    8.9   0.1   0.00081       1.5      24      99 ..     280     359 ..     276     363 .. 0.75
   3 ?    2.3   0.0     0.091   1.6e+02      49      82 ..     398     433 ..     372     445 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.6
        bMG3  42 vlaegtTDaqGvarfaallargk 64 
                 ++++ +TD+ G+   + + ++++
  EPA05748.1 200 QVGTFQTDEGGHFITTVTVPKTQ 222
                 68899999999977666655544 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00081
        bMG3  24 sgkPvagaeVrlldkkgevlae..gtTDaqGvarfaallargkegaapylvsAr.kdedlaf.lkldwergldlsrfdvp 99 
                 +++P +g+++++ ++ ++++ +  +++Da+G  ++++    g+ +   y  + + ++e+ ++  kl++++ ++l+ + v+
  EPA05748.1 280 TAQPSSGVTITVQNAADATINTrtANADAKGNWSIEPITVPGDAEFGDYTAIITdGKEQKTLsWKLETSKTISLTASAVQ 359
                 789*****************8622668999******99888999999998888853333333145566777777766665 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.091
        bMG3  49 DaqGvarfaallargkegaapylvsAr..kdedlaf 82 
                 D +G+++f+ + + + + +    + A+  +d ++++
  EPA05748.1 398 DGSGIVEFQYPTKVNVDMEGTWTLEATqaGDTEFSY 433
                 99*********8889999999999999444555555 PP

>> YtkA  YtkA-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00035      0.62       3      85 ..     337     423 ..     335     424 .. 0.78
   2 ?   -1.5   0.0       2.3   4.1e+03      15      33 ..     482     501 ..     474     502 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00035
        YtkA   3 esddlevelvspeepkagentivvt....vtqggkpVedadvkvefwmpameGmeemttkvelkesedG....vYeaevnfsmeGtWqvql 85 
                 e+++l  +l+++++++    ++++t     + +g++++++d ++    p   G e ++++  l + + G    +Y ++vn  meGtW++++
  EPA05748.1 337 EQKTLSWKLETSKTISLTASAVQFTpgdvIKFNGTALPNKDLELILLNPL--GEE-KHSESILVD-GSGivefQYPTKVNVDMEGTWTLEA 423
                 56778888888888888888888844444889999999999999999996..666.567777777.7775555799***********9875 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.3
        YtkA  15 eep.kagentivvtvtqggk 33 
                 +++ ++g n+i +t +q+g 
  EPA05748.1 482 QKIfSDGTNEIFITLEQDGR 501
                 444599*******9999885 PP

>> Invasin_D3  Invasin, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1     0.038        67      36      84 ..     181     235 ..     170     245 .. 0.67
   2 ?   10.9   2.9   0.00025      0.45      21      95 ..     284     362 ..     276     363 .. 0.75
   3 ?   -2.7   0.0       4.1   7.4e+03      63      76 ..     418     431 ..     407     437 .. 0.70
   4 ?    4.7   0.3     0.021        37      18      76 ..     465     530 ..     454     541 .. 0.65

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.038
  Invasin_D3  36 vsgltvtfsttsag.......tlsavtdngdGtytatLta.ttagtatitptvnGva 84 
                 v+g++ + st+          ++++ ++++ G  ++t+t  +t  t  + +++  ++
  EPA05748.1 181 VTGDNFEASTQ--YnifidrdQVGTFQTDEGGHFITTVTVpKTQNTDRVDFSIRDND 235
                 44555555544..023455568889999999******99999999999999886544 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00025
  Invasin_D3  21 tstltvtlkDangnpvsgltvtfsttsag..tlsavt...dngdGtytatLta.ttagtatitptvnG.vaiaatat.vtlta 95 
                 +s +t+t+++a++  +   t +  ++  g  +++ +t   d + G yta++t  ++ +t  ++ +++  ++i+ ta+ v++t+
  EPA05748.1 284 SSGVTITVQNAADATINTRTANADAK--GnwSIEPITvpgDAEFGDYTAIITDgKEQKT--LSWKLETsKTISLTASaVQFTP 362
                 5779***********99999888866..5467777774456666*******98565555..5555554478888888799987 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 4.1
  Invasin_D3  63 tatLtattagtati 76 
                 t tL at+ag + +
  EPA05748.1 418 TWTLEATQAGDTEF 431
                 44677777776665 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.021
  Invasin_D3  18 GkststltvtlkDangnp...vsglt.vtfsttsag....tlsavtdngdGtytatLtattagtati 76 
                 Gk    +++ + D +++      g + + ++ +++g    +l ++t  ++G+yta+++ ++a+t+ i
  EPA05748.1 465 GKPGDKISMIIVDPSDKQkifSDGTNeIFITLEQDGrkdySL-SLTGYASGVYTAIIKKANAKTTEI 530
                 555556666666666666665555333555555566665444.4788899******99988888765 PP

>> TIG  IPT/TIG domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   1.2   0.00019      0.33      13      60 ..     173     221 ..     168     304 .. 0.82
   2 ?   -2.3   0.0       2.8     5e+03      27      27 ..     387     387 ..     350     425 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00019
         TIG  13 asgGttititGtnFgtnssdssvtiggtpctvtasvssttl....vcttPpg 60 
                 +s+G+t+ +tG+nF   s+++++ i+ +++ +   +++       ++t+P +
  EPA05748.1 173 PSAGSTVRVTGDNF-EASTQYNIFIDRDQVGTF--QTDEGGhfitTVTVPKT 221
                 678***********.************999665..44443323334444444 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.8
         TIG  27 g 27 
                 g
  EPA05748.1 387 G 387
                 2 PP

>> CE2_N  Carbohydrate esterase 2 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1    0.0024       4.2      28      72 ..     176     218 ..     174     242 .. 0.82
   2 ?   -0.8   0.0       0.8   1.4e+03      44      69 ..     327     353 ..     287     359 .. 0.76
   3 ?   -0.5   0.0      0.65   1.2e+03      30      82 ..     458     508 ..     452     525 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0024
                 EEEEEEEEEE..SSS-EEEEEEETTS--EEEEE-SS-EEEEEEEE CS
       CE2_N  28 GtslsvrlkdkedkgknrlaviiDgkrvkdlkldgeektytlaeg 72 
                 G++++v+ ++   + +++++++iD ++v ++++d+ ++ +t+++ 
  EPA05748.1 176 GSTVRVTGDN--FEASTQYNIFIDRDQVGTFQTDEGGHFITTVTV 218
                 6777777777..99*******************888887777654 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.8
                 EEEEEEETTS--EEEEE.-SS-EEEEE CS
       CE2_N  44 nrlaviiDgkrvkdlkl.dgeektytl 69 
                  + a+i Dgk++k+l+   ++ kt++l
  EPA05748.1 327 DYTAIITDGKEQKTLSWkLETSKTISL 353
                 678899999999988875444444544 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.65
                 EEEEEEEE..SSS-EEEEEEETTS--EEEEE-SS-EEEEEEEEEEEEEEEEEE CS
       CE2_N  30 slsvrlkdkedkgknrlaviiDgkrvkdlkldgeektytlaeglepgehtvrl 82 
                 s++++l++  + g++  ++i+D + ++++  dg+++++ ++e++ ++  ++ l
  EPA05748.1 458 SAQISLSG--KPGDKISMIIVDPSDKQKIFSDGTNEIFITLEQDGRKDYSLSL 508
                 66777777..7788888899999999999889999988888888777766665 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.7      0.15   2.7e+02      19      41 ..     179     213 ..     170     230 .. 0.52
   2 ?   11.8   1.1   0.00012      0.22      10      48 ..     280     321 ..     272     356 .. 0.76
   3 ?    0.6   0.0      0.39     7e+02      32      55 ..     411     434 ..     402     470 .. 0.71
   4 ?   -2.5   0.0       3.7   6.7e+03      43      63 ..     509     529 ..     496     537 .. 0.55

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.15
  CarboxypepD_reg  19 Vtvtnadtg..............tvastttdadGafr 41 
                      V+vt   ++              +v + +td+ G+f 
       EPA05748.1 179 VRVTG--DNfeastqynifidrdQVGTFQTDEGGHFI 213
                      44432..111122222232222266677777777775 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00012
  CarboxypepD_reg  10 sgapiagatVtvtnadtgt..vastttdadGafrlrglpp.g 48 
                      + +p +g+t+tv+na++ t  ++++  da+G+++++ ++  g
       EPA05748.1 280 TAQPSSGVTITVQNAADATinTRTANADAKGNWSIEPITVpG 321
                      67899*********88776557999**********9776652 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.39
  CarboxypepD_reg  32 tttdadGafrlrglppgtysvtvs 55 
                      +  d +G+++l++ ++g+ +    
       EPA05748.1 411 VNVDMEGTWTLEATQAGDTEFSYA 434
                      566777888887777776655444 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 3.7
  CarboxypepD_reg  43 rglppgtysvtvsapGyatat 63 
                      +g + g y+  + +++ +t++
       EPA05748.1 509 TGYASGVYTAIIKKANAKTTE 529
                      233335555555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (557 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 3886.48
//
Query:       EPA05749.1  [L=263]
Description: methylthioadenosine phosphorylase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.6e-42  144.2   0.0      4e-42  144.1   0.0    1.0  1  PNP_UDP_1  Phosphorylase superfamily


Domain annotation for each model (and alignments):
>> PNP_UDP_1  Phosphorylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.1   0.0   2.2e-46     4e-42       2     233 ..       7     243 ..       6     244 .. 0.95

  Alignments for each domain:
  == domain 1  score: 144.1 bits;  conditional E-value: 2.2e-46
                 EEEEESSH....HHHHHHHHHEEEEEEEEEE.TTEEEEEEEETTEEE.EEEE--....SSHHHHHHHHHHHHHHHC--SEEEEEEEEEESSTTT-TT-E CS
   PNP_UDP_1   2 iaiivgsp....gevellaespleetpfgregrgfkfvtGtlkgkpv.vivstG....iGkpnaavvaeirllkefgvkaiiriGtaGglnpdlkvGDv 91 
                 i+i +g++    g +e+ +e    +tp+g++  +  +++G  kg+++ ++ ++G    + ++ +++ a+i++ ke+g+ +ii+ +++G+l++++++G++
  EPA05749.1   7 IGIFGGTGiydsGILEDAKEI-SIDTPYGKP--SDSITVGIFKGRKIaFLPRHGkkhtVPPHLINYKANIWAFKELGITRIIAPSAVGSLKEEIEPGHF 102
                 899999999887666666666.99*******..*********8888769************************************************** PP

                 EEEEEEEESSSCCGCCTHHCCTCCCCTTSSEE--HHHHHHHHHCHHTTTTTEEE.EEEEEESESS-CHHHHHHHHHHTC-CEEESSHHHHHHHHHHTT- CS
   PNP_UDP_1  92 vipddainfdgrsplygpkeegqyfpdsydapadpelrallkeaaealgikvhr.GvvatadgfyaeteaelrllrrlgadaveMEtaavaqlArelgi 189
                 ++p+++++f+  ++  + +++ + ++ ++d+ ++pel + + +++++++  +h   ++++ +g++++t+ae++++r+ ga +++M+ ++++qlAre+++
  EPA05749.1 103 ALPTQFLDFTKSRDGSFSENGRVIHISVADP-FCPELQSSILKVVKEQNFHIHKdCTYVCIEGPRFSTKAESKFYRSTGAGIIGMTLVPECQLAREAQM 200
                 **********999999988888999999999.*******************9999******************************************** PP

                 -EEEEEEEEETTTBETTCTCH.HCCCHHHHHHHHHHHHHHHHHH CS
   PNP_UDP_1 190 pfaairvvsdlaaggadaeatheeveefaqeaaknaaalllall 233
                 ++a+i++v+d ++ +a+++ t +ev e++ +++++++++l+ l+
  EPA05749.1 201 CYASISTVTD-YDVWAEKPVTAKEVLETLSKNVERTKKVLTDLI 243
                 **********.899**************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       767  (0.0427799); expected 358.6 (0.02)
Passed bias filter:                      680  (0.0379274); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 1684.29
//
Query:       EPA05750.1  [L=39]
Description: hypothetical protein BG20_I2489 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0002   21.0  10.1      0.009   15.7   1.3    2.3  3  zinc_ribbon_2    zinc-ribbon domain
      0.005   16.6   7.5        0.4   10.5   0.5    2.3  2  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
     0.0062   15.9  10.3      0.064   12.7   1.8    2.2  2  zf-ribbon_3      zinc-ribbon domain
     0.0081   16.7   4.9     0.0086   16.6   4.9    1.0  1  RPA_interact_C   Replication protein A interacting C-terminal
  ------ inclusion threshold ------
       0.01   15.9   2.9          1    9.5   0.4    2.3  2  zf-ACC           Acetyl-coA carboxylase zinc finger domain
      0.011   16.5   2.9      0.012   16.3   2.9    1.0  1  FYDLN_acid       Protein of unknown function (FYDLN_acid)
      0.013   15.5   7.0      0.023   14.7   6.9    1.5  1  zinc-ribbons_6   zinc-ribbons
      0.016   15.2   6.9       0.07   13.2   7.2    1.4  1  DZR              Double zinc ribbon
       0.02   15.0   2.4       0.02   15.0   2.4    1.0  1  zf-RRPl_C4       Putative ribonucleoprotein zinc-finger pf C4
      0.023   14.4   5.0      0.063   13.0   5.0    1.7  1  A2L_zn_ribbon    A2L zinc ribbon domain
      0.029   13.7   7.2       0.36   10.2   1.6    2.1  2  zf-TFIIB         Transcription factor zinc-finger
      0.032   13.8   8.2       0.49   10.0   2.0    2.2  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
      0.075   12.6   6.3       0.13   11.9   6.3    1.5  1  TF_Zn_Ribbon     TFIIB zinc-binding
      0.088   12.7   4.0        4.1    7.4   0.3    2.4  2  DUF1936          Domain of unknown function (DUF1936)
      0.094   13.0   0.9       0.43   10.9   0.1    1.8  2  DUF555           Protein of unknown function (DUF555)
      0.098   12.6   5.2       0.12   12.4   5.2    1.1  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
        0.1   12.7   6.4       0.13   12.4   6.4    1.1  1  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
       0.14   12.2   4.9        4.5    7.3   0.7    2.2  2  Ogr_Delta        Ogr/Delta-like zinc finger
       0.16   12.0   5.9       0.17   11.9   5.9    1.1  1  Zn_Tnp_IS91      Transposase zinc-binding domain
       0.17   11.6   5.2       0.27   11.0   5.2    1.4  1  Ribosomal_S27e   Ribosomal protein S27
       0.19   11.8   5.5       0.22   11.6   5.5    1.1  1  HypA             Hydrogenase/urease nickel incorporation, met
       0.19   11.3   8.5        1.1    8.9   0.4    2.4  2  zf_C2H2_10       C2H2 type zinc-finger
       0.24   11.3   8.1        1.5    8.8   8.2    2.0  2  zf-FPG_IleRS     Zinc finger found in FPG and IleRS
       0.26   11.0   6.9       0.35   10.6   2.5    2.2  2  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
       0.28   11.4   6.6        0.8    9.9   6.6    1.7  1  NOB1_Zn_bind     Nin one binding (NOB1) Zn-ribbon like
       0.29   10.9   8.2        9.4    6.1   8.2    2.1  1  Cys_rich_KTR     Cysteine-rich KTR
       0.53   11.0   7.7        2.8    8.7   0.5    2.2  2  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
       0.75    9.3   9.4       0.48    9.9   1.3    2.1  2  Mu-like_Com      Mu-like prophage protein Com
       0.75   10.4   6.1         64    4.2   6.1    2.1  1  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
       0.81    9.6   9.8       0.21   11.5   1.5    2.3  2  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
        1.1    9.4  11.8         32    4.7  11.9    2.6  1  UPF0547          Uncharacterised protein family UPF0547
        1.2    9.1   9.1          3    7.8   0.6    2.3  2  zf-HIT           HIT zinc finger
        2.5    8.1   8.1        2.2    8.2   1.1    2.2  2  DUF3797          Domain of unknown function (DUF3797)
        2.5    7.8   6.6        2.7    7.7   6.6    1.0  1  Rep_fac-A_C      Replication factor-A C terminal domain


Domain annotation for each model (and alignments):
>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.5    0.0064       3.4       1      11 [.       5      15 ..       5      18 .. 0.85
   2 !   15.7   1.3   1.7e-05     0.009      14      23 .]      21      30 ..      15      30 .. 0.83
   3 !   14.7   2.0   3.6e-05     0.019       1      10 [.      22      31 ..      22      35 .. 0.60

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0064
  zinc_ribbon_2  1 fCpnCGaelqd 11
                   +Cp+C ++  d
     EPA05750.1  5 KCPRCENKMVD 15
                   8****999765 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1.7e-05
  zinc_ribbon_2 14 kFCpyCGtpl 23
                    FCp+CG++l
     EPA05750.1 21 MFCPKCGAHL 30
                   6999999987 PP

  == domain 3  score: 14.7 bits;  conditional E-value: 3.6e-05
  zinc_ribbon_2  1 fCpnCGaelq 10
                   fCp+CGa l+
     EPA05750.1 22 FCPKCGAHLD 31
                   5666666665 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   1.4   0.00092      0.49       2      12 ..       4      14 ..       3      19 .. 0.88
   2 !   10.5   0.5   0.00075       0.4       4      11 ..      23      30 ..      20      38 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00092
                    EE-SSS--EEE CS
  zf-C4_Topoisom  2 ekCPkCggdLv 12
                    +kCP C +++v
      EPA05750.1  4 IKCPRCENKMV 14
                    79********9 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00075
                    -SSS--EE CS
  zf-C4_Topoisom  4 CPkCggdL 11
                    CPkCg++L
      EPA05750.1 23 CPKCGAHL 30
                    ******98 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   1.6    0.0023       1.2       2      19 ..       3      19 ..       2      20 .. 0.75
   2 !   12.7   1.8   0.00012     0.064       4      13 ..      22      31 ..      20      35 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0023
  zf-ribbon_3  2 tvrCPnCGaplssddnvC 19
                 +++CP+C ++   d+++C
   EPA05750.1  3 EIKCPRCENK-MVDMQAC 19
                 6889999887.6666666 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00012
  zf-ribbon_3  4 rCPnCGapls 13
                 +CP+CGa+l+
   EPA05750.1 22 FCPKCGAHLD 31
                 7999999777 PP

>> RPA_interact_C  Replication protein A interacting C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   4.9   1.6e-05    0.0086       2      28 ..       6      33 ..       5      38 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.6e-05
  RPA_interact_C  2 CPvCkkrklketsevifCe.Cglrlets 28
                    CP C+++ + ++ +++fC  Cg +l+ s
      EPA05750.1  6 CPRCENKMVDMQACHMFCPkCGAHLDCS 33
                    ******************99*****985 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.4    0.0019         1       2       9 ..       4      11 ..       4      14 .. 0.89
   2 ?    6.9   0.1     0.012       6.5       4       9 ..      23      28 ..      21      30 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0019
      zf-ACC  2 tKCpsCge 9 
                +KCp+C++
  EPA05750.1  4 IKCPRCEN 11
                8*****96 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.012
      zf-ACC  4 CpsCge 9 
                Cp+Cg+
  EPA05750.1 23 CPKCGA 28
                999987 PP

>> FYDLN_acid  Protein of unknown function (FYDLN_acid)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.3   2.9   2.2e-05     0.012      12      39 ..       6      33 ..       4      37 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.2e-05
  FYDLN_acid 12 CpscgakFYDLnkdPivcpkcgeefepe 39
                Cp c++k  D++   + cpkcg+  + +
  EPA05750.1  6 CPRCENKMVDMQACHMFCPKCGAHLDCS 33
                **********************998765 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   6.9   4.4e-05     0.023       2      27 ..       5      31 ..       4      37 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.4e-05
                    --SSS-S--E.E-SSEEE-TTT--EEE CS
  zinc-ribbons_6  2 kCpeCqqele.krgeqyhCeaCqedlk 27
                    kCp+C+++++  +  +++C +C ++l+
      EPA05750.1  5 KCPRCENKMVdMQACHMFCPKCGAHLD 31
                    799999999988889999999999876 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   7.2   0.00013      0.07       1      23 [.       6      31 ..       6      35 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00013
         DZR  1 CpqCgee...lppdarfCseCgtklk 23
                Cp+C+++   +++   fC++Cg++l+
  EPA05750.1  6 CPRCENKmvdMQACHMFCPKCGAHLD 31
                77887775444455558888887775 PP

>> zf-RRPl_C4  Putative ribonucleoprotein zinc-finger pf C4 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   2.4   3.8e-05      0.02       2      33 ..       4      35 ..       3      39 .] 0.89

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.8e-05
  zf-RRPl_C4  2 kkCkyClskklknlnetvyCeaCeiyfkvkne 33
                 kC+ C +k +++   +++C++C  ++   ++
  EPA05750.1  4 IKCPRCENKMVDMQACHMFCPKCGAHLDCSDK 35
                59***********************9987776 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   5.0   0.00012     0.063       1      29 [.       1      28 [.       1      29 [. 0.93

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00012
  A2L_zn_ribbon  1 snlkvCsvCggngilnseqgylvCieCga 29
                   +++++C  C + ++      +++C++Cga
     EPA05750.1  1 MDEIKCPRCENKMVD-MQACHMFCPKCGA 28
                   7999********999.9999********8 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.6   0.00068      0.36       1      13 [.       5      17 ..       5      20 .. 0.90
   2 ?    7.2   0.4    0.0059       3.1       2      11 ..      23      32 ..      22      38 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00068
    zf-TFIIB  1 kCPkCqdeleese 13
                kCP+C + +++++
  EPA05750.1  5 KCPRCENKMVDMQ 17
                8********9886 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0059
    zf-TFIIB  2 CPkCqdelee 11
                CPkC++ l  
  EPA05750.1 23 CPKCGAHLDC 32
                ****998765 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   1.4    0.0067       3.5       2      13 ..       3      14 ..       2      21 .. 0.76
   2 ?   10.0   2.0   0.00094      0.49       4      17 ..      22      35 ..      19      36 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0067
      zf_UBZ  2 tylCerCgkeip 13
                 + C+rC  ++ 
  EPA05750.1  3 EIKCPRCENKMV 14
                689****98875 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00094
      zf_UBZ  4 lCerCgkeipesel 17
                +C++Cg+++  s++
  EPA05750.1 22 FCPKCGAHLDCSDK 35
                8*******999886 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   6.3   0.00024      0.13       2      29 ..       5      30 ..       4      34 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00024
                  EETTTTCEECHEETSTTCEEESSSSBEE CS
  TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGlVl 29
                  kCP C +++  +D     ++C++CG+ l
    EPA05750.1  5 KCPRCENKM--VDMQACHMFCPKCGAHL 30
                  9*******5..9*999999******855 PP

>> DUF1936  Domain of unknown function (DUF1936)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.3     0.013       6.8      19      29 ..       3      13 ..       2      20 .. 0.82
   2 ?    7.4   0.3    0.0077       4.1       2       7 ..      23      28 ..      22      30 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.013
                -EEEEEES-TT CS
     DUF1936 19 EIKvFRCdred 29
                EIK  RC++  
  EPA05750.1  3 EIKCPRCENKM 13
                89999999975 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0077
                -TTTSS CS
     DUF1936  2 CPKCnv 7 
                CPKC+ 
  EPA05750.1 23 CPKCGA 28
                ****95 PP

>> DUF555  Protein of unknown function (DUF555)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.2      0.13        68      46      56 ..       3      13 ..       1      19 [. 0.82
   2 ?   10.9   0.1   0.00081      0.43      38      58 ..      12      32 ..      10      34 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.13
      DUF555 46 etecPkcgeel 56
                e++cP+c++++
  EPA05750.1  3 EIKCPRCENKM 13
                789*****998 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00081
      DUF555 38 dfveievgetecPkcgeeles 58
                ++v++++ ++ cPkcg++l++
  EPA05750.1 12 KMVDMQACHMFCPKCGAHLDC 32
                7899***************98 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   5.2   0.00022      0.12      30      57 ..       5      31 ..       4      36 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00022
  OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkCpnCgfead 57
                    +C++C  k+ +  +   + Cp+Cg+++d
      EPA05750.1  5 KCPRCENKMVD-MQACHMFCPKCGAHLD 31
                    8**********.9************987 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   6.4   0.00024      0.13       1      30 [.       5      34 ..       5      36 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00024
    zf-Mss51  1 lCPvpkhkqtapkhvdfeCpdCGiptycse 30
                +CP +++k+ + +  ++ Cp+CG    cs 
  EPA05750.1  5 KCPRCENKMVDMQACHMFCPKCGAHLDCSD 34
                6*************************9997 PP

>> Ogr_Delta  Ogr/Delta-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.2    0.0094         5       1      10 [.       5      14 ..       5      17 .. 0.90
   2 ?    7.3   0.7    0.0085       4.5       2       9 ..      23      30 ..      22      37 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0094
   Ogr_Delta  1 rCPhCgapaa 10
                +CP C+++++
  EPA05750.1  5 KCPRCENKMV 14
                6*******96 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0085
   Ogr_Delta  2 CPhCgapa 9 
                CP+Cga+ 
  EPA05750.1 23 CPKCGAHL 30
                *****986 PP

>> Zn_Tnp_IS91  Transposase zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   5.9   0.00033      0.17      39      66 ..       3      29 ..       1      34 [. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00033
  Zn_Tnp_IS91 39 ryeCeeCghekivyfsCksrhCpsCqkk 66
                 +++C+ C+++ +v ++  + +Cp+C+++
   EPA05750.1  3 EIKCPRCENK-MVDMQACHMFCPKCGAH 29
                 689****975.555555589*****987 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   5.2   0.00051      0.27       7      36 ..       3      30 ..       2      36 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00051
                    EEE-TTTS-EEEEESS-SS-EEESSSTCEE CS
  Ribosomal_S27e  7 dvkCpdCenetvvFshaatvvkCisCgkvL 36
                    ++kCp Cen+ v  +  a  + C +Cg  L
      EPA05750.1  3 EIKCPRCENKMV--DMQACHMFCPKCGAHL 30
                    69*******987..77778899****9876 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   5.5   0.00041      0.22      70      95 ..       3      29 ..       2      37 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00041
                EEEETTTS-EEECHHH.HHS-TTTSSS CS
        HypA 70 kvrCreCgkefeleek.alrCpkCgsa 95
                +++C +C++++   ++ ++ CpkCg++
  EPA05750.1  3 EIKCPRCENKMVDMQAcHMFCPKCGAH 29
                589*****999966656889*****96 PP

>> zf_C2H2_10  C2H2 type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.4    0.0021       1.1       5      15 ..       6      16 ..       3      21 .. 0.88
   2 ?    5.1   3.7     0.031        16       5      11 ..      23      29 ..      19      32 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0021
  zf_C2H2_10  5 CPKCqeklPDi 15
                CP+C+ k+ D+
  EPA05750.1  6 CPRCENKMVDM 16
                *******9998 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.031
  zf_C2H2_10  5 CPKCqek 11
                CPKC+  
  EPA05750.1 23 CPKCGAH 29
                ****865 PP

>> zf-FPG_IleRS  Zinc finger found in FPG and IleRS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   8.2    0.0028       1.5       3      27 ..       5      26 ..       3      28 .. 0.95
   2 ?    5.1   0.6     0.041        21       4      10 ..      23      29 ..      22      31 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0028
                  B-TTT--BBEEEECTTEEEEE-TTT CS
  zf-FPG_IleRS  3 pCpRCwryiervgqagrstyfCprC 27
                  +CpRC +  +++       +fCp C
    EPA05750.1  5 KCPRCENKMVDMQA---CHMFCPKC 26
                  9*******999999...*******9 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.041
                  -TTT--B CS
  zf-FPG_IleRS  4 CpRCwry 10
                  Cp C+ +
    EPA05750.1 23 CPKCGAH 29
                  8888877 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1      0.16        82      24      27 ..       6       9 ..       4      13 .. 0.66
   2 ?   10.6   2.5   0.00066      0.35       3      11 ..      20      28 ..      18      35 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.16
  zf-NADH-PPase 24 CpaC 27
                   Cp C
     EPA05750.1  6 CPRC 9 
                   5555 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00066
  zf-NADH-PPase  3 hrFCgrCGa 11
                   h FC++CGa
     EPA05750.1 20 HMFCPKCGA 28
                   77******8 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   6.6    0.0015       0.8      10      32 ..       5      29 ..       2      31 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0015
  NOB1_Zn_bind 10 rChaCfkvtkd..mtkkFCpkCGnk 32
                  +C  C + + d     +FCpkCG +
    EPA05750.1  5 KCPRCENKMVDmqACHMFCPKCGAH 29
                  79999998866235689******75 PP

>> Cys_rich_KTR  Cysteine-rich KTR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   8.2     0.018       9.4       4      33 ..       4      26 ..       2      30 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.018
  Cys_rich_KTR  4 vlcPvCgnkTRlkiredTvLknfpLfCPKC 33
                  + cP C+nk          ++   +fCPKC
    EPA05750.1  4 IKCPRCENKMV-------DMQACHMFCPKC 26
                  67999999864.......467888****** PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.5    0.0052       2.8       3      14 ..       4      14 ..       2      21 .. 0.80
   2 ?    6.0   2.4     0.037        20       3      12 ..      21      31 ..      19      39 .] 0.72

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0052
     zf-ISL3  3 hrCPnCgsktvv 14
                ++CP+C +k+ v
  EPA05750.1  4 IKCPRCENKM-V 14
                79******97.4 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.037
     zf-ISL3  3 hrCPnCgsk.t 12
                + CP+Cg+   
  EPA05750.1 21 MFCPKCGAHlD 31
                58*****9754 PP

>> Mu-like_Com  Mu-like prophage protein Com
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.3    0.0009      0.48      21      30 ..       2       9 ..       1      16 [. 0.86
   2 ?    5.0   1.3     0.031        16      25      32 ..      21      28 ..      11      34 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0009
  Mu-like_Com 21 DeltiKCPRC 30
                 D  +iKCPRC
   EPA05750.1  2 D--EIKCPRC 9 
                 5..69***** PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.031
  Mu-like_Com 25 iKCPRCGt 32
                 + CP+CG 
   EPA05750.1 21 MFCPKCGA 28
                 56*****6 PP

>> Zn_ribbon_recom  Recombinase zinc beta ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   6.1      0.12        64       6      21 ..       4      19 ..       3      37 .. 0.62

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.12
  Zn_ribbon_recom  6 lrCgeCGspmtrrkrk 21
                     ++C +C ++m+  ++ 
       EPA05750.1  4 IKCPRCENKMVDMQAC 19
                     6788888888876653 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   1.6      0.16        87       4      11 ..       6      13 ..       5      19 .. 0.87
   2 ?   11.5   1.5   0.00041      0.21       3      11 ..      22      30 ..      21      37 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.16
                    ESTTTSBE CS
  RNA_POL_M_15KD  4 CpkCgNlL 11
                    Cp C N +
      EPA05750.1  6 CPRCENKM 13
                    *****977 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00041
                    BESTTTSBE CS
  RNA_POL_M_15KD  3 FCpkCgNlL 11
                    FCpkCg +L
      EPA05750.1 22 FCPKCGAHL 30
                    ******998 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7  11.9     0.061        32       2      21 ..       5      27 ..       5      29 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.061
     UPF0547  2 vCPeCeakvPvaaqfC....phCG 21
                +CP+Ce k  v++q+C    p CG
  EPA05750.1  5 KCPRCENKM-VDMQAChmfcPKCG 27
                7*******8.******99999999 PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   2.5     0.029        15      15      22 ..       5      12 ..       2      19 .. 0.84
   2 ?    7.8   0.6    0.0057         3      16      23 ..      23      30 ..      22      34 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.029
                E-TTT--E CS
      zf-HIT 15 kCpkCntr 22
                kCp+C+ +
  EPA05750.1  5 KCPRCENK 12
                9****865 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0057
                -TTT--EE CS
      zf-HIT 16 CpkCntry 23
                CpkC++++
  EPA05750.1 23 CPKCGAHL 30
                ******94 PP

>> DUF3797  Domain of unknown function (DUF3797)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   1.1    0.0042       2.2      15      25 ..       5      15 ..       3      21 .. 0.86
   2 ?    5.5   1.1      0.03        16      11      21 ..      18      28 ..      12      37 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0042
     DUF3797 15 qCPeCgNnkvl 25
                +CP C N+ v 
  EPA05750.1  5 KCPRCENKMVD 15
                8******9885 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.03
     DUF3797 11 ekYvqCPeCgN 21
                   + CP+Cg 
  EPA05750.1 18 ACHMFCPKCGA 28
                44778****95 PP

>> Rep_fac-A_C  Replication factor-A C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   6.6    0.0052       2.7      21      47 ..       6      30 ..       4      35 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0052
                 --STT---B-EEETTTEEEETTTTEEE CS
  Rep_fac-A_C 21 CpsedCnkKvveeedgewrCekCdkev 47
                 Cp   C+ K+v+ +  ++ C kC  ++
   EPA05750.1  6 CP--RCENKMVDMQACHMFCPKCGAHL 30
                 99..9******************8775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       882  (0.049194); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                        34  (0.00189637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              34  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 276.04
//
Query:       EPA05751.1  [L=57]
Description: hypothetical protein BG20_I2490 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0005   19.9   3.4     0.0032   17.4   3.4    2.0  1  zinc_ribbon_4   zinc-ribbon domain
     0.0014   18.8   1.0     0.0024   18.1   1.0    1.3  1  IBR             IBR domain, a half RING-finger domain
     0.0042   17.0   0.4     0.0053   16.7   0.4    1.2  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
     0.0055   16.7   2.6       0.03   14.3   0.0    2.0  2  CpXC            CpXC protein
  ------ inclusion threshold ------
      0.017   14.8   0.3        3.2    7.6   0.0    2.2  2  YacG            DNA gyrase inhibitor YacG
      0.021   14.4   1.7        1.4    8.5   0.2    2.3  2  zf_C2H2_10      C2H2 type zinc-finger
      0.024   14.6   0.3        3.3    7.7   0.0    2.1  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
      0.037   14.1   0.1       0.04   14.0   0.1    1.1  1  Zn_Tnp_IS91     Transposase zinc-binding domain
      0.053   13.6   0.2      0.054   13.5   0.2    1.2  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.064   13.3   0.4        9.8    6.2   0.0    2.2  2  Ogr_Delta       Ogr/Delta-like zinc finger
      0.065   13.0   0.4      0.065   13.0   0.4    1.6  2  zf-H2C2_5       C2H2-type zinc-finger domain
      0.086   12.6   3.3       0.25   11.1   3.3    1.7  1  Ribosomal_S27e  Ribosomal protein S27
       0.12   12.4   2.9       0.15   12.0   2.9    1.2  1  Prok-RING_1     Prokaryotic RING finger family 1
       0.16   12.0   1.6        0.8    9.8   0.1    2.1  2  zf-BED          BED zinc finger
       0.27   11.5   3.8       0.95    9.8   0.4    2.1  2  zf-Di19         Drought induced 19 protein (Di19), zinc-bindi
        0.3   10.6   7.4          5    6.7   7.4    2.2  1  zf-ribbon_3     zinc-ribbon domain
       0.53   10.3   4.7        1.3    9.0   0.1    2.2  2  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
        1.5    9.2   6.2         27    5.1   6.6    2.1  2  zinc_ribbon_9   zinc-ribbon
        1.7    8.5   5.2        5.3    6.9   5.2    1.7  1  zinc_ribbon_5   zinc-ribbon domain


Domain annotation for each model (and alignments):
>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   3.4   3.4e-06    0.0032       1      32 [.       1      27 [.       1      29 [. 0.94

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.4e-06
  zinc_ribbon_4  1 MkitCpsCkakyeiddeklpakgvkvrCskCg 32
                   M+ +Cp+C+++  +dd     ++++v+C++C+
     EPA05751.1  1 MDARCPKCEKVAILDD-----DITNVKCPHCN 27
                   9**********99999.....6*********6 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   1.0   2.5e-06    0.0024      20      47 ..       4      29 ..       2      31 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.5e-06
         IBR 20 wCprpdCeaiieksegcksvtCskCgfe 47
                 Cp  +Ce+++  +++ ++v+C++C+fe
  EPA05751.1  4 RCP--KCEKVAILDDDITNVKCPHCNFE 29
                6*9..***********999*******97 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.4   5.6e-06    0.0053      30      59 ..       4      33 ..       3      40 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.6e-06
  OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkCpnCgfeadrD 59
                    +C++C ++   +++  ++kCp+C+fead D
      EPA05751.1  4 RCPKCEKVAILDDDITNVKCPHCNFEADYD 33
                    6*********99**************9977 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.4     0.022        21      37      49 ..       2      14 ..       1      17 [. 0.77
   2 !   14.3   0.0   3.2e-05      0.03      29      58 ..      12      41 ..      10      54 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.022
        CpXC 37 eatCpkCgatakl 49
                +a+CpkC++ a l
  EPA05751.1  2 DARCPKCEKVAIL 14
                5789999987766 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 3.2e-05
        CpXC 29 klldgslfeatCpkCgatakleapllyhdp 58
                ++ld+++++++Cp+C+ +a ++  l + + 
  EPA05751.1 12 AILDDDITNVKCPHCNFEADYDSYLEIMKD 41
                799*************99999888776554 PP

>> YacG  DNA gyrase inhibitor YacG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1     0.012        11       2      10 ..       4      12 ..       3      19 .. 0.79
   2 ?    7.6   0.0    0.0034       3.2       1      13 [.      21      33 ..      21      39 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.012
        YacG  2 kCPtCkkev 10
                +CP+C+k  
  EPA05751.1  4 RCPKCEKVA 12
                8****9966 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0034
        YacG  1 vkCPtCkkevews 13
                vkCP+C+ e  ++
  EPA05751.1 21 VKCPHCNFEADYD 33
                89****9888776 PP

>> zf_C2H2_10  C2H2 type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.2    0.0015       1.4       5      12 ..       5      12 ..       2      15 .. 0.87
   2 ?    5.4   0.1     0.014        13       5      12 ..      23      30 ..      20      38 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0015
  zf_C2H2_10  5 CPKCqekl 12
                CPKC+ ++
  EPA05751.1  5 CPKCEKVA 12
                ****9876 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.014
  zf_C2H2_10  5 CPKCqekl 12
                CP C+  +
  EPA05751.1 23 CPHCNFEA 30
                ****9876 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1     0.019        18      20      26 ..       4      10 ..       2      15 .. 0.82
   2 ?    7.7   0.0    0.0035       3.3      19      27 ..      21      29 ..      16      38 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.019
  Zn_Tnp_IS1595 20 vCPhCgs 26
                   +CP+C++
     EPA05751.1  4 RCPKCEK 10
                   7****85 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0035
  Zn_Tnp_IS1595 19 fvCPhCgsr 27
                   + CPhC  +
     EPA05751.1 21 VKCPHCNFE 29
                   67****865 PP

>> Zn_Tnp_IS91  Transposase zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   4.2e-05      0.04      40      84 ..       3      48 ..       1      51 [. 0.82

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.2e-05
  Zn_Tnp_IS91 40 yeCeeCghekivyfsCksrhCpsCqkkat.eewlekqqeellpvpy 84
                  +C++C++  i+     +  Cp+C+ +a  + +le ++++ ++++y
   EPA05751.1  3 ARCPKCEKVAILDDDITNVKCPHCNFEADyDSYLEIMKDQAINMSY 48
                 68**********************9776526677888888887777 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   5.7e-05     0.054      70      94 ..       2      28 ..       1      47 [. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.7e-05
                EEEETTTS-EEECHHH..HHS-TTTSS CS
        HypA 70 kvrCreCgkefeleek..alrCpkCgs 94
                 +rC +C+k   l+++  +++Cp+C+ 
  EPA05751.1  2 DARCPKCEKVAILDDDitNVKCPHCNF 28
                589*****999888856789*****85 PP

>> Ogr_Delta  Ogr/Delta-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1     0.015        15       1       9 [.       4      12 ..       4      15 .. 0.86
   2 ?    6.2   0.0      0.01       9.8       1       8 [.      22      29 ..      22      41 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.015
   Ogr_Delta  1 rCPhCgapa 9 
                rCP+C++ a
  EPA05751.1  4 RCPKCEKVA 12
                7****9987 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.01
   Ogr_Delta  1 rCPhCgap 8 
                +CPhC  +
  EPA05751.1 22 KCPHCNFE 29
                6****855 PP

>> zf-H2C2_5  C2H2-type zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   1.0       6.4   6.1e+03       2       6 ..       4       8 ..       4       9 .. 0.66
   2 ?   13.0   0.4   6.9e-05     0.065       2      16 ..      22      36 ..      22      37 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 6.4
   zf-H2C2_5 2 KCsqC 6
               +C+ C
  EPA05751.1 4 RCPKC 8
               67766 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 6.9e-05
   zf-H2C2_5  2 KCsqCDYstawksnL 16
                KC++C++ + + s L
  EPA05751.1 22 KCPHCNFEADYDSYL 36
                9******99987765 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   3.3   0.00027      0.25       6      32 ..       1      26 [.       1      30 [. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00027
                    EEEE-TTTS-EEEEESS-SS-EEESSS CS
  Ribosomal_S27e  6 ldvkCpdCenetvvFshaatvvkCisC 32
                    +d +Cp+Ce+  +  +   t vkC  C
      EPA05751.1  1 MDARCPKCEKVAI-LDDDITNVKCPHC 26
                    7889****99865.68899******99 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   2.9   0.00016      0.15       5      27 ..       3      27 ..       1      33 [. 0.91

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00016
  Prok-RING_1  5 kkCpvCgkelkeedDi..VvCpeCg 27
                  +Cp C+k    +dDi  V Cp+C 
   EPA05751.1  3 ARCPKCEKVAILDDDItnVKCPHCN 27
                 68*************99999****5 PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.3      0.25   2.3e+02      17      25 ..       3      11 ..       2      12 .. 0.87
   2 ?    9.8   0.1   0.00085       0.8      13      29 ..      17      33 ..      11      41 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.25
                -EETTTTEE CS
      zf-BED 17 avCryCgki 25
                a+C  C+k+
  EPA05751.1  3 ARCPKCEKV 11
                79*****97 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00085
                GSS--EETTTTEE---- CS
      zf-BED 13 keqkavCryCgkilsrg 29
                + ++++C +C+++ +++
  EPA05751.1 17 DITNVKCPHCNFEADYD 33
                5699*******998775 PP

>> zf-Di19  Drought induced 19 protein (Di19), zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.2     0.096        90       4      12 ..       4      13 ..       1      20 [. 0.70
   2 ?    9.8   0.4     0.001      0.95       2      19 ..      20      37 ..      19      44 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.096
     zf-Di19  4 tCPyCgk.el 12
                 CP C+k ++
  EPA05751.1  4 RCPKCEKvAI 13
                7999988654 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.001
     zf-Di19  2 sftCPyCgkeltvkeLve 19
                +++CP+C+ e + ++ +e
  EPA05751.1 20 NVKCPHCNFEADYDSYLE 37
                689*****9887776665 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   7.4    0.0053         5       4      22 ..       4      26 ..       2      28 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0053
  zf-ribbon_3  4 rCPnCGap.lssddn...vCpyC 22
                 rCP+C ++ + +dd+   +Cp+C
   EPA05751.1  4 RCPKCEKVaILDDDItnvKCPHC 26
                 8******546555542227**** PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   1.0       0.1        98       5       8 ..       5       8 ..       3      10 .. 0.65
   2 ?    9.0   0.1    0.0014       1.3       4      14 ..      22      32 ..      20      50 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.1
  PhnA_Zn_Ribbon 5 CplC 8
                   Cp+C
      EPA05751.1 5 CPKC 8
                   6666 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0014
  PhnA_Zn_Ribbon  4 kCplCaSeytY 14
                    kCp+C+ e  Y
      EPA05751.1 22 KCPHCNFEADY 32
                    8****988877 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.6      0.23   2.2e+02      23      28 ..       4       9 ..       1      10 [. 0.75
   2 ?    5.1   6.6     0.028        27      11      28 ..      10      27 ..       5      29 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.23
  zinc_ribbon_9 23 lCPhCg 28
                    CP C+
     EPA05751.1  4 RCPKCE 9 
                   4****6 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.028
  zinc_ribbon_9 11 fVsvspdedsdvlCPhCg 28
                    V +  d+  +v CPhC+
     EPA05751.1 10 KVAILDDDITNVKCPHCN 27
                   5666655555579****8 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   5.2    0.0057       5.3       3      31 ..       3      26 ..       1      28 [. 0.88

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0057
  zinc_ribbon_5  3 irCpdCdtkFklvdsklKksgkkVrCakC 31
                    rCp+C+    l+d+        V+C +C
     EPA05751.1  3 ARCPKCEKVAILDDDI-----TNVKCPHC 26
                   69*****999999999.....89****** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.43
# Mc/sec: 401.45
//
Query:       EPA05752.1  [L=134]
Description: ribosomal protein S6e [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.8e-25   87.7   0.1    6.8e-25   87.5   0.1    1.0  1  Ribosomal_S6e  Ribosomal protein S6e


Domain annotation for each model (and alignments):
>> Ribosomal_S6e  Ribosomal protein S6e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.5   0.1   3.8e-29   6.8e-25       1     111 [.      11     116 ..      11     124 .. 0.96

  Alignments for each domain:
  == domain 1  score: 87.5 bits;  conditional E-value: 3.8e-29
                    -EEEEEETTTTEEEEEE-CHHHCTTCTT-BSSEEEECCTTTSSSTS-EEEEEEEEETTC-BB-TTS-SSSEEEEEEETTSSSS-SSSSS-EEEEEE CS
  Ribosomal_S6e   1 mklnisdpatgkqklievdekklrtligkrigeevdgdalGeelkgyvlkitggsdkqGfpmkqgvltpgrvrlLlskggvgyrprrkGerkrksv 96 
                    +kl isd + gk+ + e+++++++ l+g ++g+  d++++G  l+g +lk+tggsdk+G+pm+++++++ r+ +Llsk gvg +  ++G+r rk +
     EPA05752.1  11 FKLTISDTK-GKSITKELKDSDANPLLGLQLGSDADASVVG--LQG-KLKLTGGSDKSGVPMRNDIHGSARKYILLSK-GVGLQAAETGQRVRKLM 101
                    79*****88.9******************************..998.79*****************************.***************** PP

                    E-SB--SSEEEEEEE CS
  Ribosomal_S6e  97 rGcivsadisqlnlv 111
                    rG++vs++i q+n++
     EPA05752.1 102 RGNTVSEEIYQINCK 116
                    *************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       234  (0.0130515); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 910.29
//
Query:       EPA05753.1  [L=74]
Description: hypothetical protein BG20_I2487, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.5e-08   32.0   1.0    3.4e-07   30.0   1.0    1.8  1  GTP_EFTU  Elongation factor Tu GTP binding domain
     0.0033   17.5   0.0     0.0036   17.4   0.0    1.1  1  MMR_HSR1  50S ribosome-binding GTPase
  ------ inclusion threshold ------
       0.11   12.1   0.0       0.12   11.9   0.0    1.1  1  FeoB_N    Ferrous iron transport protein B


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   1.0   5.7e-11   3.4e-07       3      36 ..      20      53 ..      18      72 .. 0.80

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 5.7e-11
                EEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHH CS
    GTP_EFTU  3 irnigiighvDhGKtTLtdrLlyktgaiskkgek 36
                 +nig++ghvDhGKtTL+ +L+ +   +++++ k
  EPA05753.1 20 CVNIGTAGHVDHGKTTLIQALTGSWTSVHSQELK 53
                68*******************9877777775544 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   6.1e-07    0.0036       2      34 ..      23      58 ..      22      71 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 6.1e-07
                EEEEESTTSSHHHHHHHHHTS.TEEESSST..TSSS CS
    MMR_HSR1  2 vaivGrpNvGKStLinaltge.kaivsdkp..gtTr 34
                ++ +G+   GK+tLi+altg+ ++  s++   g T+
  EPA05753.1 23 IGTAGHVDHGKTTLIQALTGSwTSVHSQELkrGITI 58
                7899****************9533223332125555 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.9e-05      0.12       2      27 ..      22      47 ..      21      63 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.9e-05
                EEEEEESTTSSHHHHHHHHHTTSEEE CS
      FeoB_N  2 tvalvGnpnvGkttlfnaltgakqkv 27
                ++ ++G  + Gkttl+ altg+ ++v
  EPA05753.1 22 NIGTAGHVDHGKTTLIQALTGSWTSV 47
                57789****************98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 514.47
//
Query:       EPA05754.1  [L=71]
Description: hypothetical protein BG20_I2248 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1605  (0.0895198); expected 358.6 (0.02)
Passed bias filter:                      614  (0.0342462); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 562.01
//
Query:       EPA05755.1  [L=250]
Description: hypothetical protein BG20_I2249, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-42  144.8   5.2    5.5e-42  144.5   5.2    1.1  1  SIMPL     Protein of unknown function (DUF541)
  ------ inclusion threshold ------
      0.064   13.2   0.1       0.13   12.2   0.1    1.5  1  DUF1657   Protein of unknown function (DUF1657)


Domain annotation for each model (and alignments):
>> SIMPL  Protein of unknown function (DUF541)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.5   5.2   6.2e-46   5.5e-42       1     200 []      37     245 ..      37     245 .. 0.87

  Alignments for each domain:
  == domain 1  score: 144.5 bits;  conditional E-value: 6.2e-46
       SIMPL   1 ItVtGsaevevapDqatltlsvesegkdaaeakaevaekmnavlealkklgikekdiqtsslslkpeysy......engknkitgyeasqsltvkfrdl 93 
                 I+VtG a+++v+pDq  ++++ve+++k+a++a +++++ m+++++a+k++gi+e++i+tss++++p+y+          ++++ gy++s+ +tv++ +l
  EPA05755.1  37 ISVTGMASASVKPDQLNINFGVETQEKTAKAALDSNSADMDKIISAIKSAGISESEISTSSFNISPVYNSyenkttGMWTQELVGYRVSNIVTVSTAKL 135
                 89**********************************************99*******************9888888778888888************** PP

       SIMPL  94 dklgevldaavka.aneingvsfsls..dedelrdeareeAvkdArakAealAkalgvklgkv..vsise.sgsnpyappapamaaaaaa.aasaatpf 185
                 d++++++d av+a +n++++v f ls  ++++l+d+++ +Av +A+ kAe + + l+ k+ +v  vs++e +    +++p+    a ++  a++a+tp+
  EPA05755.1 136 DSAASIIDNAVNAgTNRVDNVYFALSpaKQQSLKDDLLGKAVTNAKSKAEMALAPLDHKIIGVkmVSLNEfA----MPQPMYGGVAYSMSeAVRAPTPV 230
                 *************999**********6555999***********************9999755338888842....22222223333333577888888 PP

       SIMPL 186 epgeievtasVtvvf 200
                  +++++vt sV+vvf
  EPA05755.1 231 FSSDQDVTTSVNVVF 245
                 88888*********9 PP

>> DUF1657  Protein of unknown function (DUF1657)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   1.4e-05      0.13      18      46 ..      56      84 ..      55      85 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.4e-05
     DUF1657 18 FaLqTedeeAKqmYeqaaeqleeviqdLe 46
                F  +T+ ++AK++   ++ +++++i  ++
  EPA05755.1 56 FGVETQEKTAKAALDSNSADMDKIISAIK 84
                8899********************97665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       778  (0.0433934); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1795.04
//
Query:       EPA05756.1  [L=473]
Description: transporter, major facilitator family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-49  168.7  75.7    1.9e-45  155.3  45.4    2.0  2  MFS_1     Major Facilitator Superfamily
    7.4e-09   35.0  12.3    7.4e-09   35.0  12.3    3.5  3  Sugar_tr  Sugar (and other) transporter
     0.0017   16.9  12.6     0.0017   16.9  12.6    1.5  2  TRI12     Fungal trichothecene efflux pump (TRI12)
  ------ inclusion threshold ------
       0.11   11.8   0.2       0.11   11.8   0.2    1.9  2  DUF1523   Protein of unknown function (DUF1523)
       0.45   10.4   2.7         13    5.8   0.1    3.7  3  DUF2631   Protein of unknown function (DUF2631)
        2.9    6.4  45.1       0.47    8.9   4.3    4.5  4  MFS_2     MFS/sugar transport protein


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.3  45.4   6.4e-49   1.9e-45       2     353 .]      20     416 ..      19     416 .. 0.91
   2 !   27.4  22.3     5e-10   1.5e-06      40     169 ..     314     462 ..     302     470 .. 0.86

  Alignments for each domain:
  == domain 1  score: 155.3 bits;  conditional E-value: 6.4e-49
       MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslwlllvlrvlqGlgag 100
                 ++++++++++ ++l+pa+p al ed+ i   +  ++l++y+++ ava++++G lsd +Gr++vll+ + ++++g+l++ fa s++++l++r+ qG+g  
  EPA05756.1  20 SCLGLIAMYGETMLLPAIP-ALIEDFEIPYNTSAWILSTYMIAGAVATPIAGKLSDVYGRKKVLLIVMSIYSAGILAGGFADSFPFMLAARAAQGIGI- 116
                 78999**************.999***************************************************66666977777************6. PP

       MFS_1 101 alfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpeepperkrkspkeee........... 188
                 a+fp++  +i+++ p+++ + + +++s++f +Ga +g l g+ +++++gW+a+f+ + ++++l+++++l ++ ++p +++ ++++              
  EPA05756.1 117 AMFPIAFGIIREVLPEKKLAVGQSIFSSTFPAGATIGLLMGANIVQHYGWHATFFTVFPIAVLLGIFILKFIHVTPLPNSSEKKISIDikgsiflsiti 215
                 ******************************************************************87788877666666665555558999******* PP

       MFS_1 189 .....................................kgtgpaplvpawkallkdpvlw...illialllfffgfsglltllplylqevlgls.gllla 246
                                                      +++ ++pl++ +k+l+++  l+   illi+ l++f++++++ +++ +   + lg++ + l++
  EPA05756.1 216 isflvgisyiqnsegeiyeslaffattiislfvfiiiEKRTESPLID-LKLLKNKMLLFgimILLIVGLCTFMVYQTIPIMIQS--PQPLGFGgTELTT 311
                 ***********************************************.777776666645667777777777777776666666..6677777857889 PP

       MFS_1 247 glllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGfglgfvfpsllalasdlappeeagtasglfntag 345
                 +++ + ++++++++++ +g+ + ++g++r  l++ +l+++++l+++l+  +   ++l + l++i  gl+++f+  ++++  ++p + ag a+g + +++
  EPA05756.1 312 AAIQMPFMIIFLVGSISSGFALEKIGNKRLVLIGTILGSIGFLSILLFHSS--DFMLTVTLAVIAAGLSLAFIGGFNVVLLSTPIQFAGIALGMTLLLN 408
                 99999999999999************************************9..777777899999999999999999999999**************** PP

       MFS_1 346 slggalgp 353
                  +g ++gp
  EPA05756.1 409 LIGQSIGP 416
                 ******98 PP

  == domain 2  score: 27.4 bits;  conditional E-value: 5e-10
       MFS_1  40 l...yalgaavaslplGrlsdrfGrrrvlllglllfalg.lllllfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGa 134
                 +   +++ ++v+s+  G+  +++G +r++l+g +l ++g l +llf+ss ++l v  ++ ++g +++f +g  ++   +p +  g a+g+  + + +G 
  EPA05756.1 314 IqmpFMIIFLVGSISSGFALEKIGNKRLVLIGTILGSIGfLSILLFHSSDFMLTVTLAVIAAGLSLAFIGGFNVVLLSTPIQFAGIALGMTLLLNLIGQ 412
                 1445999********************************566666978888************************************************ PP

       MFS_1 135 ilgpllgglla.sslg..............Wravfyilaivsllafvlfl 169
                  +gp ++g++   + g              + ++f+ + ++sl ++v+++
  EPA05756.1 413 SIGPSIAGMFQqMHRGtvtgisgsfptpeaYNLIFLTAFAISLTSVVFAI 462
                 ********998444448888888999999999999999999999988543 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0  12.3   2.5e-12   7.4e-09      47     189 ..      50     185 ..      41     193 .. 0.88
   2 !    5.8   3.2    0.0018       5.3      44      97 ..     135     189 ..     119     226 .. 0.81
   3 ?   -0.0  13.9       0.1   3.1e+02     255     344 ..     271     362 ..     252     437 .. 0.59

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 2.5e-12
                 HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHH CS
    Sugar_tr  47 lsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyql 145
                 +s +i+s +++ +++   +ag+l+d++GRkk+lli+  ++++g++  ++a+   s+  ++++R   Gig+ ++ +     i E+ p+k+     s++ +
  EPA05756.1  50 TSAWILSTYMIAGAVATPIAGKLSDVYGRKKVLLIVMSIYSAGILAGGFAD---SFPFMLAARAAQGIGIAMFPIAFG-IIREVLPEKKLAVGQSIFSS 144
                 578************************************************...****************98876665.69******998888888888 PP

                 HHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGG CS
    Sugar_tr 146 aitfGilvaaifglglnktsnadgwrillglqlvpallllilll 189
                    +G  ++  +g+++ +  +   w+ +++  + +a+ll i++l
  EPA05756.1 145 TFPAGATIGLLMGANIVQHYG---WHATFFTVFPIAVLLGIFIL 185
                 888888777777776655555...************99988876 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0018
                 ...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHH.HHHHHHHHHHHHH-TT CS
    Sugar_tr  44 ssvlsglivsiflvGaiiGslfagllgdrfGRkkslli.aavlfvigavlqaaak 97 
                 ++v ++++ s f +Ga+iG l++  +++ +G   ++ + + + ++ g+++  +++
  EPA05756.1 135 LAVGQSIFSSTFPAGATIGLLMGANIVQHYGWHATFFTvFPIAVLLGIFILKFIH 189
                 5677899************************999999834455556777777776 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.1
                 HHHHHHHHHHHHHTTHHHHHHHTTTHH..HHSS-THH....HHHHHHHHHHHHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHH....HHHHTTS CS
    Sugar_tr 255 lligvvlqifqqltGinaimyysptif..enlglsks....llvtiivgvvnfvatfvaiflvdrfGRRtllllGaagmaicfvilg..ivalllvak 344
                 ll g+++ ++  l++ ++   ++ +i   + lg+  +    +++ + ++++  v ++ + f  +++G ++l+l+G++ ++i f+ +          ++
  EPA05756.1 271 LLFGIMILLIVGLCTFMVYQTIPIMIQspQPLGFGGTelttAAIQMPFMIIFLVGSISSGFALEKIGNKRLVLIGTILGSIGFLSILlfH------SS 362
                 556666666666666555555555554223456665552333344444444444455555888888888888888888888777774221......22 PP

>> TRI12  Fungal trichothecene efflux pump (TRI12)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9  12.6   5.7e-07    0.0017      66     325 ..      36     287 ..      21     311 .. 0.77
   2 ?   -3.6   1.1      0.87   2.6e+03     104     146 ..     335     376 ..     319     411 .. 0.56

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5.7e-07
       TRI12  66 alpnilqdvgqsenss..lfstlwttgqavsilvmgrltdrfgrrpfvilthilglvgaivgctatkfntllaamtllgvaagpagasplfvgelmsnk 162
                 a+p +++d     n+s  ++st + +  av+  + g+l+d +gr+ ++++   +   g + g  a+ f  +laa +  g+       +  ++ e++ +k
  EPA05756.1  36 AIPALIEDFEIPYNTSawILST-YMIAGAVATPIAGKLSDVYGRKKVLLIVMSIYSAGILAGGFADSFPFMLAARAAQGIGIAMFPIAFGIIREVLPEK 133
                 7788888887777766224555.55666999****************999999999******************99998888777778889******** PP

       TRI12 163 tkflgllivsipvvvtsglspylgqrlaiqgswrwifyiyiitsaiavlliv...vwyyppsfaqlhgkkvrkreelakldwigiilvivgvslfllgv 258
                    +g  i s    + ++++  +g  +     w   f+       iavll +    + +   + +   kk         +d  g i++++ +  fl+g+
  EPA05756.1 134 KLAVGQSIFSSTFPAGATIGLLMGANIVQHYGWHATFFTVF---PIAVLLGIfilKFIHVTPLPNSSEKK-------ISIDIKGSIFLSITIISFLVGI 222
                 **********999999999******9999999998888655...45555544000444444444433343.......569999*999999999****** PP

       TRI12 259 swggkpnspwnsakviglissglgslvvfalyevygkpvrpivppalfkdtrgfvc..illissimgam 325
                 s+  +     +    + ++++ + sl vf + e   + + p++   l+k+   +    illi  +   m
  EPA05756.1 223 SYIQNS--EGEIYESLAFFATTIISLFVFIIIE--KRTESPLIDLKLLKNKMLLFGimILLIVGLCTFM 287
                 **8655..4555566889999999999999988..57899*********98765440044444443333 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 0.87
       TRI12 104 rfgrrpfvilthilglvgaivgctatkfntllaamtllgvaag 146
                 ++g + +v++  ilg +g +        + ++ ++tl  +aag
  EPA05756.1 335 KIGNKRLVLIGTILGSIGFLSILLFHSSD-FMLTVTLAVIAAG 376
                 55555555555555555544332222222.2223333333333 PP

>> DUF1523  Protein of unknown function (DUF1523)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   3.7e-05      0.11     120     139 ..     161     180 ..     157     229 .. 0.84
   2 ?   -3.8   0.4       2.3   6.9e+03     152     170 ..     272     290 ..     267     292 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.7e-05
     DUF1523 120 ikyYGWriellsifpNavsi 139
                 +++YGW  +++++fp av +
  EPA05756.1 161 VQHYGWHATFFTVFPIAVLL 180
                 89*************99854 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 2.3
     DUF1523 152 wfniillvvlllllllliq 170
                 +f i++l+++ l++++++q
  EPA05756.1 272 LFGIMILLIVGLCTFMVYQ 290
                 5667777777777777766 PP

>> DUF2631  Protein of unknown function (DUF2631)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.22   6.6e+02      28      48 ..       8      28 ..       6      31 .. 0.87
   2 ?    5.8   0.1    0.0042        13      22      44 ..     163     185 ..     162     193 .. 0.87
   3 ?    1.2   0.1      0.11   3.3e+02      33      54 ..     394     415 ..     390     453 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.22
     DUF2631 28 espkttriaGlisvlallaml 48
                +++ ++ i G +s l l+am 
  EPA05756.1  8 INRSAWLILGTLSCLGLIAMY 28
                6889999************96 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0042
     DUF2631  22 aWGWsgespkttriaGlisvlal 44 
                 ++GW+ ++   + ia l+ +++l
  EPA05756.1 163 HYGWHATFFTVFPIAVLLGIFIL 185
                 59************999988887 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.11
     DUF2631  33 triaGlisvlallamliGnhqG 54 
                 ++ aG+   + ll+ liG   G
  EPA05756.1 394 IQFAGIALGMTLLLNLIGQSIG 415
                 7899999999999999998777 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   4.3   0.00016      0.47     262     334 ..      52     122 ..      18     135 .. 0.88
   2 ?    3.3   3.3     0.008        24     262     309 ..     140     187 ..     127     226 .. 0.84
   3 ?    2.2   3.1     0.017        52     266     316 ..     236     294 ..     211     301 .. 0.77
   4 ?    8.7  12.2   0.00018      0.54     262     336 ..     312     387 ..     303     466 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00016
       MFS_2 262 svfllvvtisallgiplwqplakrlgkkntyllgalltivllvlvlllqpsnlllflvllviagfgvgvaall 334
                 +++l + +i++++++p++ +l   +g+k++ l+ ++++ ++ +   ++   +  ++l++ ++ g+g++++ ++
  EPA05756.1  52 AWILSTYMIAGAVATPIAGKLSDVYGRKKVLLIVMSIYSAGILAGGFA--DSFPFMLAARAAQGIGIAMFPIA 122
                 4556666*********************************99999999..89999999999999998877555 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.008
       MFS_2 262 svfllvvtisallgiplwqplakrlgkkntyllgalltivllvlvlll 309
                 s+f+ ++ ++a++g+++ +++++++g ++t++  + ++++l++++l +
  EPA05756.1 140 SIFSSTFPAGATIGLLMGANIVQHYGWHATFFTVFPIAVLLGIFILKF 187
                 6777888899*****************************999998866 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.017
       MFS_2 266 lvvtisallgiplwqplakrlg.........kkntyllgalltivllvlvlllqpsnlll 316
                 l++++ ++++++++  + kr           k ++ l+g++++++ +++++++  + + +
  EPA05756.1 236 LAFFATTIISLFVFIIIEKRTEsplidlkllKNKMLLFGIMILLIVGLCTFMV-YQTIPI 294
                 56677777888888888887777777777779999999999999999999988.555544 PP

  == domain 4  score: 8.7 bits;  conditional E-value: 0.00018
       MFS_2 262 svfllvvtisallgiplwqplakrlgkkntyllgalltivllvlvlllqpsnlllflvllv.iagfgvgvaallpw 336
                 +++ + ++i  l+g++    +  ++g+k+++l+g++l  ++++ +ll++ s+ +l+++l+v +ag+++++++ +  
  EPA05756.1 312 AAIQMPFMIIFLVGSISSGFALEKIGNKRLVLIGTILGSIGFLSILLFHSSDFMLTVTLAViAAGLSLAFIGGFNV 387
                 455666799999************************************7777666655554045666665555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (473 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       872  (0.0486363); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.46
# Mc/sec: 3122.14
//
Query:       EPA05757.1  [L=404]
Description: putative membrane protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-27   96.8  20.9    1.4e-27   96.8  20.9    2.0  2  STT3      Oligosaccharyl transferase STT3 subunit


Domain annotation for each model (and alignments):
>> STT3  Oligosaccharyl transferase STT3 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.8  20.9   7.7e-32   1.4e-27      30     273 ..       3     238 ..       1     277 [. 0.85
   2 !    3.1   5.7     0.002        35     158     217 ..     322     386 ..     313     400 .. 0.78

  Alignments for each domain:
  == domain 1  score: 96.8 bits;  conditional E-value: 7.7e-32
                 --SSCHHHHHHHCCCHHHT-C.....CCHHSSEETTSSTTT-EEESTTCCHCCC.CHHHHHHCCHHC..HHHHHHHHCCHHHHHHHHCHHHHHHHHHHS CS
        STT3  30 lsefDpYYnyRltenllnnGfpGdvvikkknwfdhsqyyPpGsrvdygplivlLamlasaiinhsld..vsirevclwlpallgsLlaIpiyflvrelk 126
                 l efDp++nyR+t+++++nG+      +   w d+ ++yP G r    ++ ++L  l++a++++++   +++ + ++++p ++gsL +I+i+ lvr++ 
  EPA05757.1   3 LNEFDPFFNYRATQYIVDNGI-----NAYYQWNDNLSWYPHG-RDVSQTSQITL-HLTAALTYWIFGggMQLYDFAILFPVIFGSLSGIVIFALVRVIG 94 
                 68*******************.....99999***********.55568888999.99999999999999****************************** PP

                 -CCCHHHHHHHCCC-CCCCCTTSTT--STCCCCHHHHHHHHHHHHHHHHCCSTTCHH..HHHHHHHHHHHHTTSCCGGHHHHCCHHHHHHHHHCTTTS- CS
        STT3 127 sdiaGllAAlllaiaPgYlsrtvaGfyDtdmfeivlllfvlffflkaiktksnkisl..aviaaliiflivlaWggyailiyallllfilalLiigrfe 223
                 +  aGl++All +++   + r   G++  + + +++ l++l+f+l +i +k++ki+   + +a++++ l +++Wgg   ++++ + +f+l l       
  EPA05757.1  95 GTTAGLFSALLFSVSLPMILRGTIGWFKSEPLGLFFGLLALYFLLSGIISKNKKIAIvkLIAAGITVPLSISSWGGS-QFFIIPIGIFFLTLPFLRTDH 192
                 **************99999*********************************88776215678899**********8.788888888877766666677 PP

                 CCHHHHHHHHHHHHHHH..CCCCCCCTTCHHHSTTTCHHCCCCHHHHHHH CS
        STT3 224 lklkiavtfsviiaflviaiivllflgfqvvavseiigalgifgllqlva 273
                 ++l++++ ++++++flv    +l+f  +++   ++++g+ +i+++++++ 
  EPA05757.1 193 KFLLWSIPLFTATVFLV----SLNFERLASSFIFGLGGISLIVPTIFVIS 238
                 77788888888888888....666666666569999***99999998763 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.002
                 CCHHHHHHHHHHHHHHHHCCS......TTCHHHHHHHHHHHHHHTTSCCGGHHHHCCHHHHHHHHH CS
        STT3 158 feivlllfvlffflkaiktks......nkislaviaaliiflivlaWggyailiyallllfilalL 217
                 + i++ l  +++++k  ktk+         s+++i++li  ++++a++   +++   l++  +++L
  EPA05757.1 322 LMIFAGLG-IWLIIKNNKTKEssfiknDMLSFSLIIGLIGIYVSSAFVRLEVFASLSLIILSSIGL 386
                 44444443.6****************66678999****************9998776666555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       948  (0.0528752); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.51
# Mc/sec: 2405.92
//
Query:       EPA05758.1  [L=146]
Description: hypothetical protein BG20_I2362, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-06   27.8   0.1    1.4e-06   27.5   0.1    1.2  1  STT3      Oligosaccharyl transferase STT3 subunit
  ------ inclusion threshold ------
      0.036   12.3   0.1      0.062   11.5   0.1    1.3  2  Dpy19     Q-cell neuroblast polarisation


Domain annotation for each model (and alignments):
>> STT3  Oligosaccharyl transferase STT3 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.1   1.6e-10   1.4e-06     440     485 ..      40      89 ..       2      91 .. 0.81

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 1.6e-10
                 H...HHHHCT.TTTTHHH.TTHHHCHHHHHHHHHHHHHHHHHHHHHHHHH CS
        STT3 440 v...aptksnglkeslew.kantnrdsvvitwwdyghilaveadrpVtfd 485
                 +    p+  + + e +ew k+nt++d+vv +wwdyg+ + +  +r +++d
  EPA05758.1  40 GgssYPVSTDDWLETMEWiKNNTPKDAVVASWWDYGYWISTLGERATIAD 89 
                 044489999******************************99999988887 PP

>> Dpy19  Q-cell neuroblast polarisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   6.9e-06     0.062     502     525 ..      46      70 ..      37      75 .. 0.87
   2 ?   -3.6   0.0      0.25   2.3e+03     566     585 ..     107     126 ..      98     126 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.9e-06
       Dpy19 502 snpdt.eeLleWIksntekdavfaG 525
                  ++d+  e +eWIk+nt+kdav a+
  EPA05758.1  46 VSTDDwLETMEWIKNNTPKDAVVAS 70 
                 567788999*************997 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 0.25
       Dpy19 566 ksaedvyktleklkvnYlil 585
                  s+++ ++ l++++++Y+++
  EPA05758.1 107 SSPDKGWQMLNDMQADYVVV 126
                 56778889999999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 828.33
//
Query:       EPA05759.1  [L=70]
Description: hypothetical protein BG20_I2556 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.47
# Mc/sec: 443.93
//
Query:       EPA05760.1  [L=171]
Description: hypothetical protein BG20_I2555, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.6e-05   22.3   1.8    0.00016   21.3   1.8    1.5  1  TSP_3         Thrombospondin type 3 repeat
     0.0034   17.5   0.0     0.0057   16.7   0.0    1.6  1  Cupredoxin_1  Cupredoxin-like domain
  ------ inclusion threshold ------
      0.057   13.9   0.0       0.12   12.9   0.0    1.6  1  Copper-bind   Copper binding proteins, plastocyanin/azurin fa


Domain annotation for each model (and alignments):
>> TSP_3  Thrombospondin type 3 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   1.8   2.6e-08   0.00016      14      34 ..     144     164 ..     143     166 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2.6e-08
       TSP_3  14 kDfDnDgvqddlDNCprnani 34 
                 kD+D+Dg+ d++D Cp+ +++
  EPA05760.1 144 KDTDGDGISDSVDKCPTDPET 164
                 7****************9975 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   9.5e-07    0.0057      27     104 .]      56     136 ..       8     136 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 9.5e-07
  Cupredoxin_1  27 vkdggfePskievkagekvklkiknkdktpeefesed.....lg..eekvlapgktttitiaplkpGeYeftcdmhmdakGkliV 104
                    +dg + P+k  ++ g   k+ + n d+  ++f+++      lg   +  +  g++++ ++ p + Ge++++c  h+ +kG++ V
    EPA05760.1  56 TTDGCYIPKKAIIPIGG--KVIFSNIDAVEHTFTADIttdgmLGifDSGLISAGSSYE-WV-PTDVGEFPYHCTVHPWMKGTIFV 136
                   468899**********8..88************9998889996621346788888888.55.99*************99***977 PP

>> Copper-bind  Copper binding proteins, plastocyanin/azurin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.9e-05      0.12      29      99 .]      76     137 ..      52     137 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.9e-05
                  EEEESSSSBEEEEETTSSTTTGGGTTSCTTC....EEEEBSTTEEEEEEEESSEEEEEEETTTTTTTSEEEEEEE CS
  Copper-bind  29 fvnlavmgHNvvldkdgvpagvdkdkvkaed....etkliggGekdsvtfdeagtYkffCsPHaaagMkgkvtve 99 
                  f n +++ H   +++d   +g              +  li++G +++   ++ g++ ++C+ H    Mkg++ ve
   EPA05760.1  76 FSNIDAVEHT--FTADITTDG---------MlgifDSGLISAGSSYEWVPTDVGEFPYHCTVHP--WMKGTIFVE 137
                  4444444442..333333222.........122334459999**********************..69****986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.34s 00:00:00.86 Elapsed: 00:00:00.53
# Mc/sec: 978.94
//
Query:       EPA05761.1  [L=99]
Description: 6-O-methylguanine DNA methyltransferase, DNA binding domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-29  101.2   0.0    3.1e-29  100.9   0.0    1.1  1  DNA_binding_1  6-O-methylguanine DNA methyltransferase, DNA b


Domain annotation for each model (and alignments):
>> DNA_binding_1  6-O-methylguanine DNA methyltransferase, DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.9   0.0   1.7e-33   3.1e-29       3      81 .]       4      82 ..       2      82 .. 0.98

  Alignments for each domain:
  == domain 1  score: 100.9 bits;  conditional E-value: 1.7e-33
                   HHHHHHHHTTS-TT-BEEHHHHHHHTT.TSCHHHHHHHHHTSSBTTTSGGGGEEBTTSBCCTTTTCHHHHHHHHHHTTS CS
  DNA_binding_1  3 qqrVwellrqIpyGkvttYgeiAkllgkpkaaraVgqalaanplailvPcHRVvgadgklggyagglerkralLeaEgv 81
                    +++++ l ++p+Gk+ttYge+Ak++g++++ raVg+++++np+++++PcHRVv++dgk+ggya g e+k ++L  Eg+
     EPA05761.1  4 DKKIYKKLLEVPKGKITTYGELAKAVGMKNGQRAVGKIMNKNPFPVIIPCHRVVKSDGKVGGYAYGEEIKSSMLTLEGI 82
                   589**************************************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 558.43
//
Query:       EPA05762.1  [L=57]
Description: protein translocase SEC61 complex gamma subunit, archaeal and eukaryotic [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-07   29.7   0.0    5.3e-07   29.5   0.0    1.1  1  SecE      SecE/Sec61-gamma subunits of protein translocation 
  ------ inclusion threshold ------
      0.026   14.1   0.0      0.028   13.9   0.0    1.0  1  Frag1     Frag1/DRAM/Sfk1 family


Domain annotation for each model (and alignments):
>> SecE  SecE/Sec61-gamma subunits of protein translocation complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.0   5.9e-11   5.3e-07       3      48 ..       6      51 ..       4      55 .. 0.92

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 5.9e-11
                CHHHHHHHHHCCCCCHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
        SecE  3 FfkevkaElkKVtWPtrkEllkttvvVlvfvvimglflflvDlvfs 48
                 +k++ + +k   +P+r+E+++    Vl++++ +g+++f + +vfs
  EPA05762.1  6 TLKNMANTMKMAKKPDRDEYTQHLRLVLLGIAGVGAIGFTIQFVFS 51
                5899999**************************************5 PP

>> Frag1  Frag1/DRAM/Sfk1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   3.1e-06     0.028     138     181 ..       9      50 ..       5      56 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.1e-06
       Frag1 138 qtalyykmgrhyvwnkstisfrlkvvllilavvlailfgvffvr 181
                 ++a ++km++++  ++++ + +l++vll +a v ai+f + fv+
  EPA05762.1   9 NMANTMKMAKKP--DRDEYTQHLRLVLLGIAGVGAIGFTIQFVF 50 
                 78999*****96..*************************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 378.05
//
Query:       EPA05763.1  [L=135]
Description: ribosomal protein L32 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.2e-31  108.0   0.0    3.8e-31  107.7   0.0    1.1  1  Ribosomal_L32e  Ribosomal protein L32
  ------ inclusion threshold ------
       0.11   12.9   0.0       0.23   11.8   0.0    1.5  1  Mnd1            Mnd1 HTH domain


Domain annotation for each model (and alignments):
>> Ribosomal_L32e  Ribosomal protein L32
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.7   0.0   4.3e-35   3.8e-31       2     108 .]      19     125 ..      18     125 .. 0.94

  Alignments for each domain:
  == domain 1  score: 107.7 bits;  conditional E-value: 4.3e-35
                     -----TTTTT-TTS-SS------TT-TTTTT-..TTS-----GGG---TTTTT--TTS-EEEEESSGGGGTT--TTTE..EEEE-TTS-HHHHHH CS
  Ribosomal_L32e   2 kkFirhqsdryvklkeswrkprGidnrvrrrf..kgqilmpkiGYgspkktrgllpsGfkkvlVhnvkeLevllmenksyaaeiahsVsskkrke 94 
                     ++F r +s+ryv+l+++wrkp+G+d+++r+    +g++ ++k+GYg pk  +gl+psGf++ lV+++++Le+l+++++   ++ +hsV++kkrke
      EPA05763.1  19 PDFVRPESWRYVRLETNWRKPKGVDHHQRKLKggRGRPGLVKVGYGGPKIAKGLHPSGFTDNLVYTLNDLEKLNPKTD--GVRFGHSVGTKKRKE 111
                     78************************9987551157799***************************************..*************** PP

                     HHHHHHHTT-EBSS CS
  Ribosomal_L32e  95 iverAaelgikVtN 108
                     i+++A e ++k++N
      EPA05763.1 112 IMAKALENKFKIFN 125
                     ************98 PP

>> Mnd1  Mnd1 HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.6e-05      0.23       9      28 ..      80      99 ..      77     104 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.6e-05
        Mnd1  9 kefytlKeleklapkekgiv 28
                + +ytl++lekl pk  g++
  EPA05763.1 80 NLVYTLNDLEKLNPKTDGVR 99
                679************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       258  (0.0143901); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1025.99
//
Query:       EPA05764.1  [L=152]
Description: ribosomal protein L24 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-20   72.1   0.0    4.1e-20   71.5   0.0    1.3  1  Spt5-NGN  Early transcription elongation factor of RNA pol II
    1.7e-05   24.6   0.3    3.3e-05   23.7   0.3    1.5  1  KOW       KOW motif


Domain annotation for each model (and alignments):
>> Spt5-NGN  Early transcription elongation factor of RNA pol II, NGN section
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.5   0.0   4.5e-24   4.1e-20       2      84 .]       9      87 ..       8      87 .. 0.97

  Alignments for each domain:
  == domain 1  score: 71.5 bits;  conditional E-value: 4.5e-24
    Spt5-NGN  2 iwavkctagqErevalslmkkilelakkenleIkSvfapdelkGyiyvEAdrkaaveralegipnvrgvvqglvpikEvedll 84
                ++a+++t gqE+ v++ l++k    a++++l+I+Sv+ +d+lkGy+++EA +++++  a+eg++++rg  +g++++k++e +l
  EPA05764.1  9 LFAIRTTGGQEKIVMRLLEAK----ANTNKLNIQSVLLVDNLKGYVVIEAINPSDAYMAVEGVRHIRGQLRGELEFKDIEGYL 87
                8********************....99*9**************************************************9876 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.3   3.7e-09   3.3e-05       1      29 [.      98     128 ..      98     132 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 3.7e-09
                 TTSEEEESSSTTTTCEEEEEEEETTT..TEE CS
         KOW   1 pGdhVkVvsGphkGktGkVvkvdqhk..vrV 29 
                 ++d+ ++++Gp+kG +++++++d +k  ++V
  EPA05764.1  98 VDDVIEITGGPFKGMKATITRIDVDKeeATV 128
                 689***********************66554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1141.86
//
Query:       EPA05765.1  [L=160]
Description: ribosomal protein L11, N-terminal domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.6e-23   79.8   1.3    1.7e-22   79.0   0.7    1.8  2  Ribosomal_L11_N  Ribosomal protein L11, N-terminal domain
      1e-19   70.8   1.2      2e-19   69.9   1.2    1.5  1  Ribosomal_L11    Ribosomal protein L11, RNA binding domain
  ------ inclusion threshold ------
       0.11   12.7   0.3       0.17   12.1   0.3    1.3  1  Hom_end          Homing endonuclease


Domain annotation for each model (and alignments):
>> Ribosomal_L11_N  Ribosomal protein L11, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.0   0.7   2.9e-26   1.7e-22       4      63 ..       3      62 ..       1      64 [. 0.94
   2 ?   -1.8   0.0      0.49   2.9e+03      33      43 ..     137     152 ..     121     153 .. 0.70

  Alignments for each domain:
  == domain 1  score: 79.0 bits;  conditional E-value: 2.9e-26
  Ribosomal_L11_N  4 vvkvvklrvpaGkAtpaPplGpaLGplGlnikkfckefnkaTkdkkglripVkitvyqdr 63
                     ++++v   v++G A+++PplGpaLGplG+ni++++k++n++Tkd++g+++pV+++v++d 
       EPA05765.1  3 EAQKVSSLVTGGAASAGPPLGPALGPLGVNIMEIIKAINDKTKDFEGMKVPVTVSVFPDT 62
                     56788999************************************************9885 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.49
  Ribosomal_L11_N  33 n.....ikkfckefnk 43 
                      +     +k+++ e+n+
       EPA05765.1 137 KvegktPKEITAEINE 152
                      4444447777888876 PP

>> Ribosomal_L11  Ribosomal protein L11, RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.9   1.2   3.3e-23     2e-19       2      70 .]      71     138 ..      70     138 .. 0.96

  Alignments for each domain:
  == domain 1  score: 69.9 bits;  conditional E-value: 3.3e-23
                    --SHHHHHHHHHTXSSXXSSTTTSXXEEEEHHHHHHHHHHHGGGHTXS.SHHHHHHHHHHHHCTTTEEE CS
  Ribosomal_L11   2 tPptsylLkkaagiekgsgkpgketvGtvslkqvyeIAkiKksdlnaalsleaavksilgtArsmGikV 70 
                     P++++lL+k+ag++kg+g+pg+  vG+++++ v+++Ak+K +++ a+ sl++++k+i+gt+ s+GikV
     EPA05765.1  71 IPSAAALLLKEAGVQKGTGTPGTAWVGDITIDSVVKVAKTKLEKSYAS-SLKSVAKTIVGTCLSLGIKV 138
                    59****************************************777788.*******************9 PP

>> Hom_end  Homing endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.3   2.9e-05      0.17      22      68 ..     101     146 ..     100     157 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.9e-05
     Hom_end  22 vdsdgyvkkekedsatvktedksvmegivklarsLGikasvktkeek 68 
                 +ds   v k+k  + +  ++ ksv + iv    sLGik++ kt +e 
  EPA05765.1 101 IDSVVKVAKTKL-EKSYASSLKSVAKTIVGTCLSLGIKVEGKTPKEI 146
                 566666666633.77778999*********************94443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1031.36
//
Query:       EPA05766.1  [L=502]
Description: phosphoenolpyruvate carboxykinase (ATP) [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   3.5e-215  715.0   0.0     4e-215  714.9   0.0    1.0  1  PEPCK_ATP  Phosphoenolpyruvate carboxykinase


Domain annotation for each model (and alignments):
>> PEPCK_ATP  Phosphoenolpyruvate carboxykinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  714.9   0.0  2.2e-219    4e-215       9     464 ..       3     455 ..       1     456 [. 0.99

  Alignments for each domain:
  == domain 1  score: 714.9 bits;  conditional E-value: 2.2e-219
                 HHHHHHHHHHTTS-EE-TTS-EEE--TT--S--GGGEEEE--TTTTTTS-BTTTBEEE-HHHHHHHHHHHHHHHHTS-EEEEEEEE-SSTTT-EEEEEE CS
   PEPCK_ATP   9 vaeLveealkreegkltstgalvvetgkktgRspkdkfiVedeetedkiwWgkvnkpiseekfealkekvleylkekelyvvdafagadpkyrlkvrvi 107
                 v+eLv+ a++r+eg+++stg+l+v+tgk+tgRsp+d+fiV d++t+++i+Wgkvn+++ ++kfe+l ek+ +++++k+l+v+d+f+g+d+++rl++rvi
  EPA05766.1   3 VDELVKLAVERKEGVVNSTGSLSVNTGKYTGRSPDDRFIVLDDKTRNTIDWGKVNHQFPSDKFEKLLEKMKRFVENKDLFVFDGFVGSDKDTRLPIRVI 101
                 789************************************************************************************************ PP

                 ES-HHHHHHHHHHSBGGS-S-TTT---SEEEEEETT----HHHH--SSS-EEEEETTTTEEEEES---THHHHHHHHHHHHHHHHHTT-EEEEEEEEE- CS
   PEPCK_ATP 108 terawqalfvknllirpteeeleefepdftilnapefkadpekdglnsetvvalnlekklvlilgteYaGEikKsifsvmnyllpkkgvlsmhcsanvg 206
                 +++awq+lf +nl+irpt++elee++p+ft++++ +f+a p++dg++s+ +++++l++k+vli+gt+YaGE+kKs+fsvmn+llp+kgv++mhcsan+g
  EPA05766.1 102 NDHAWQSLFGRNLFIRPTAKELEEHTPEFTVMCINNFEAIPAEDGTRSNVFIIIDLTRKIVLIGGTQYAGEMKKSMFSVMNFLLPEKGVFPMHCSANIG 200
                 *************************************************************************************************** PP

                 T.TS-EEEEEE-TTSSHHHHH-BTTB-EEESSEEEE-SS-EEES-SEEEEE-TT--TTTSHHHHHHHSTT-EEES-EE-TTT--EETT--SS-S--EEE CS
   PEPCK_ATP 207 ekkgdvalfFGLSGtGKTtLsadperkligdDehgwsdegvfniegGcYaKtidLskekepeiynairfgavlENvvldeetrevdfddtslteNtrva 305
                  k+gd++lfFGLSGtGKTtLsadp+r+ligdDehgwsd+g fn+egGcYaK+i+Ls+e+epei+nair+gavlENvv++  ++++d+dd++lteNtrva
  EPA05766.1 201 -KNGDTSLFFGLSGTGKTTLSADPNRNLIGDDEHGWSDNGTFNFEGGCYAKCINLSQEAEPEIWNAIRPGAVLENVVVN--NGVPDYDDNTLTENTRVA 296
                 .677**************************************************************************5..78**************** PP

                 EEGGGSSSB-TTSEE--EEEEEEEE--TTS-S-SEEEE-HHHHHHHHHH-EEEE-----------EEEE-GGG-GGG-SS-HHHHHHHHHHHHHHH--E CS
   PEPCK_ATP 306 ypiehienakeesvaghpkniifLtadafgvlPpvskLtkeqamyhFlsGytakvaGtergvtepeatFsacfgapFlplhpteyaelLaeklekhnak 404
                 yp+e+i+ a+ +sv+ghpk i+fLtada gvlPp+s+Ltke amyhF+sGyt+k+aGterg++ep++ Fs cfgapF+p+++++ya++L+ek+++hn+ 
  EPA05766.1 297 YPLEFIPGAVIPSVGGHPKVIVFLTADALGVLPPISRLTKEGAMYHFMSGYTSKLAGTERGIKEPKSVFSECFGAPFMPRPAAVYAKILGEKITQHNTV 395
                 *************************************************************************************************** PP

                 EEEEE-SEESSSTTTSEE--HHHHHHHHHHHHTTCCCTS-EEE-TTT--EEES-BTTC-G CS
   PEPCK_ATP 405 vyLvNtGwtggaygvgkrislkatraiikaildgeleavefekdpvfglevptevpgvps 464
                 vyLvNtGw+gg+ygvgkri++k++ra+++a+l+g+l++v++++d+ f+l++ptev++vp 
  EPA05766.1 396 VYLVNTGWSGGPYGVGKRIKIKYSRAMVTAALTGKLDNVKYNHDHLFNLDIPTEVSDVPP 455
                 **********************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (502 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.50
# Mc/sec: 3042.15
//
Query:       EPA05767.1  [L=258]
Description: D-aminoacyl-tRNA deacylase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.1e-59  199.5   0.0    5.1e-59  199.3   0.0    1.1  1  tRNA_deacylase  D-aminoacyl-tRNA deacylase


Domain annotation for each model (and alignments):
>> tRNA_deacylase  D-aminoacyl-tRNA deacylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.3   0.0   2.8e-63   5.1e-59       3     205 .]      55     256 ..      53     256 .. 0.98

  Alignments for each domain:
  == domain 1  score: 199.3 bits;  conditional E-value: 2.8e-63
                     ---SEEEEEEEEE-TT---EEEEE--B-SS--TTSS-TT-B--B-HHHHHHHHHHHHGGGGGSTT-EEEE--S-SS-----S-EEEEEEEESHHH CS
  tRNA_deacylase   3 edvdliiflSrHssesgkplLTvHvtGnlgeaelGGkpeelapaaPrllkallralkkiaekleefevtlEatHHGPtelkvPslFvEiGSteee 97 
                      d+d ++flS+H++esg+ +LT+H tGn+++a++GG+p+++a+++P ++k++l+ l k +++ ++f++t+EatHHGPt+lk+P++F+EiG+te++
      EPA05767.1  55 YDYDGFVFLSKHAAESGVLALTCHSTGNFSDAKFGGNPKQVAIPHPFIQKKYLQVLWKNKSNFSDFQITIEATHHGPTALKKPAIFIEIGTTEKQ 149
                     6899******************************************************************************************* PP

                     HT-HHHHHHHHHHHHHHHH------EEEEEE-S-TT-HHHHHHHHHBSEEEEEEE-GGGGGG--HHHHHHHHHHH.T-SEEEE-TTT--HHHHHH CS
  tRNA_deacylase  98 WkdedaaeavaeavlelleseeekekvlvgiGGgHYaprftklvletevavGhilskyaleelkeevikqaleksegadvalidkkslkseqkea 192
                     W+d   ++ +a++v +++ ++  + +v++++GG+HY ++ft+ +l+ ++++G +++k+ale+++++++ ++le+++ a++al+d+ ++ + +k++
      EPA05767.1 150 WTDVSLCNSIASLVHQVMIEKIPSSPVAICFGGTHYPDKFTDEILDGKYSLGTVVPKHALENIDKNLFLHILEQNKIAKTALLDWGGM-GPNKQK 243
                     *********************9***************************************************************887.999*** PP

                     HHHHHHHHT-EEE CS
  tRNA_deacylase 193 ieelleelgievl 205
                     i ell+++++ev+
      EPA05767.1 244 IVELLKDTDLEVI 256
                     *********9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1732.85
//
Query:       EPA05768.1  [L=517]
Description: PA domain protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.1e-29  101.8   0.0      6e-29  101.2   0.0    1.2  1  Peptidase_S8  Subtilase family
    1.8e-11   43.9   0.6    5.7e-11   42.3   0.0    2.2  2  PA            PA domain


Domain annotation for each model (and alignments):
>> Peptidase_S8  Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.2   0.0   6.7e-33     6e-29     146     287 ..       6     276 ..       1     289 [. 0.95

  Alignments for each domain:
  == domain 1  score: 101.2 bits;  conditional E-value: 6.7e-33
                   HHHHHH.CCT-EEEEE--SS-T-HHEEE-TTCEECTTTSTTCEEEEEES................................................ CS
                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................................ RF
  Peptidase_S8 146 ainravnkkgvlvviSaGNngktgsslqagspvgtpstsknvitvgayt................................................ 194
                   a+++a   k+++vv++aGN+g      +  +++g+p+  +++itvga+                                                 
    EPA05768.1   6 AVDKAL-AKNIFVVTAAGNDG------PLPQTIGSPGRNEESITVGATYnnltsslvatlevneksytvipmvgsskldepivgkiifgkygkqedl 95 
                   899999.89************......9999****************999*********************************************** PP

                   ................................................................................................T CS
                   ................................................................................................x RF
  Peptidase_S8 195 ................................................................................................t 195
                                                                                                                   +
    EPA05768.1  96 kdinatgaivivergsdnkddrlyfslkeknavnagakalivynnepgiflgelihdfiepgyvpqipvvsidrddgleiiekikeknnamihlfyN 192
                   ************************************************************************************************* PP

                   TSSB-TT--B-TT.......-EEEE-S-CCCCCCCCCHHHTTTHHEEEE-SHHHCHHHHHHHHHHHHHHHTT--HHHHHHHHHCCS-EE... CS
                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Peptidase_S8 196 egkiapfSsrGpssdgklkpdivapGgnivstwsrqsnnsaglssyqsmsGTSmAsPnaagaaAlllsalpkltpetvraallntAqdlgka 287
                   ++ +a fSsrGp+s   +kpdivapG+      ++q n +     y+  sGTS+A+P+++gaaAll++++p++ +++++++l++t +++++a
    EPA05768.1 193 PDFVAHFSSRGPVSPFYIKPDIVAPGAY---INTTQRNGG-----YNFTSGTSFAAPHVSGAAALLIEKYPSIGNQEIKSLLMTTSEPVSDA 276
                   ****************************...666666555.....9****************************************998665 PP

>> PA  PA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.0   6.3e-15   5.7e-11       3      89 .]      82     175 ..      56     175 .. 0.88
   2 ?   -3.0   0.1      0.83   7.4e+03      45      52 ..     502     509 ..     497     513 .. 0.81

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 6.3e-15
          PA   3 gplVyscfagygisadfegvdvkGkivLvqr.........tfaeKarnAqaaGAagviivndge...lgaatgasgnegepdgitiPavgvsredgeal 89 
                 g+++   f  yg+++d++ ++ +G iv+v+r          f  K +nA +aGA+++i++n+++   lg+  +   + g+    +iP+v+++r+dg ++
  EPA05768.1  82 GKII---FGKYGKQEDLKDINATGAIVIVERgsdnkddrlYFSLKEKNAVNAGAKALIVYNNEPgifLGELIHDFIEPGYV--PQIPVVSIDRDDGLEI 175
                 4444...88899999999999********9887777766777******************88888**99999999999999..*************875 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.83
          PA  45 aGAagvii 52 
                  GA+gvi 
  EPA05768.1 502 IGAVGVIT 509
                 59****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (517 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.47
# Mc/sec: 3335.11
//
Query:       EPA05769.1  [L=151]
Description: ribosomal protein L19e [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.8e-39  132.7   8.4    1.2e-38  132.5   8.4    1.0  1  Ribosomal_L19e  Ribosomal protein L19e


Domain annotation for each model (and alignments):
>> Ribosomal_L19e  Ribosomal protein L19e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.5   8.4   6.4e-43   1.2e-38       1     142 [.       4     144 ..       4     146 .. 0.96

  Alignments for each domain:
  == domain 1  score: 132.5 bits;  conditional E-value: 6.4e-43
                     -THHHHHHHHHHTTS-GGGEEE-GGGHHHHHH--SHHHHHHHHHTTSEEE-------THHHHHHHHHHHTT-S-SGGG--S-HHHHS-HHHHHHH CS
  Ribosomal_L19e   1 dlklqkrlaasvlkvGknrvwldpeeleeiaeAitredirklikdglIikkpkkgnsrararerkekkrkgrrrgsGkrkGtkeaRlpekelWik 95 
                     +l+++k+l a+v++vG++rv+ld+++l+++a+Aitre+ir+li+ + I+ kp  g+s++ra+++k++k+k r + +G++kG+k+aR+ +k+++++
      EPA05769.1   4 NLRAKKKLVARVTGVGVHRVRLDSDHLDDVADAITRENIRSLITAKKITIKPIVGTSKGRAQTKKAQKNK-RGTTQGSKKGRKGARVGKKDVYVS 97 
                     5899*********************************************************998888776.78889******************* PP

                     HHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHTT--SSHHHHHHHHT- CS
  Ribosomal_L19e  96 riRalRrlLkelrekkkidkktYrelYrkakGgefknkavLkeyiek 142
                     ++R+lRrlLk  +++k++++ +++ lY+k+ G++++nka+L+  +e+
      EPA05769.1  98 KVRSLRRLLKIAKDRKELTNPEFWALYKKVGGNTVRNKAHLRLLMEE 144
                     *****************************************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       794  (0.0442858); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.33s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 870.76
//
Query:       EPA05770.1  [L=166]
Description: hypothetical protein BG20_I2230 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.1e-06   26.3  13.5    7.1e-06   26.1  13.5    1.1  1  SpoIIM    Stage II sporulation protein M


Domain annotation for each model (and alignments):
>> SpoIIM  Stage II sporulation protein M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1  13.5     4e-10   7.1e-06      36     151 ..      36     149 ..       1     152 [. 0.73

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 4e-10
      SpoIIM  36 lflaifanNlrvalllfllGllllgiptilvl.linGfvlGav.aalvaefgglllflllilPhgilelpaiiiagaaglrlgkalrsrrkalkeakre 132
                   + if++Nl++al +f+ G+   g++  l+  + +Gf   a+ +++ a  +   l++l++ P gi+el a+ ++++ ++ + +a+ ++r  + ++   
  EPA05770.1  36 DGFGIFVHNLTIALPMFIPGF---GLVWGLFAgWSTGFAFAAIvTSIPALANFPPLAILYLSPFGIMELVAYSLGISRSYMIIYAIIKHRSIKPQLLIT 131
                 4689****************5...999998888*****999662555555577899******************************6444444444444 PP

      SpoIIM 133 llklllllvp.llliAaliE 151
                 ++++ ++  + llli++ +E
  EPA05770.1 132 SVEIGIV--VaLLLIGGYLE 149
                 4443333..25888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.36s 00:00:00.92 Elapsed: 00:00:00.55
# Mc/sec: 911.19
//
Query:       EPA05771.1  [L=125]
Description: nitrite/sulfite reductase ferredoxin domain protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.2e-17   61.0   0.0    1.1e-16   60.4   0.0    1.3  1  NIR_SIR_ferr  Nitrite/Sulfite reductase ferredoxin-like half 


Domain annotation for each model (and alignments):
>> NIR_SIR_ferr  Nitrite/Sulfite reductase ferredoxin-like half domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.4   0.0   6.2e-21   1.1e-16       7      69 .]      62     124 ..      56     124 .. 0.95

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 6.2e-21
  NIR_SIR_ferr   7 kgyymvrlrvpnGritaeqlraladiaekygsgeirlTtrQnlqlhgvpeedleeileeLaea 69 
                     y+mvr+++p+G i + ql+++ +++e++++g ++++tr n+qlh+v  ed+ eil+ Lae+
    EPA05771.1  62 SDYAMVRIKLPAGEIYPNQLEKISQLSEQFSIGSAHFSTRENIQLHWVILEDVSEILRGLAEV 124
                   4689********************************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.59
# Mc/sec: 642.20
//
Query:       EPA05772.1  [L=260]
Description: hypothetical protein BG20_I2233, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.41   10.7   4.1       0.42   10.6   0.2    2.5  2  DUF1910   Domain of unknown function (DUF1910)


Domain annotation for each model (and alignments):
>> DUF1910  Domain of unknown function (DUF1910)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.6     0.029   5.3e+02      20      43 ..      33      61 ..      14      92 .. 0.69
   2 ?   10.6   0.2   2.3e-05      0.42      54      85 ..     161     192 ..     151     237 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.029
     DUF1910 20 riaklkekieelsedeeksiqae.....i 43
                +++k+++ ++ +++d +k i++      i
  EPA05772.1 33 QVEKRENILKYSKKDTAKKIASCrifnlI 61
                45666666666677777666655433333 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 2.3e-05
     DUF1910  54 kleliiakYSlGesieeleadyeelikeleel 85 
                 ++ +++a+Y++G ++++++++y+ ++ e+++ 
  EPA05772.1 161 YYLELMANYTQGINVDTIKQKYKGTYLEYNDS 192
                 556789****************9998888654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       884  (0.0493056); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1825.89
//
Query:       EPA05773.1  [L=37]
Description: hypothetical protein BG20_I2229 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       185  (0.0103185); expected 358.6 (0.02)
Passed bias filter:                      151  (0.00842211); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.47
# Mc/sec: 239.16
//
Query:       EPA05774.1  [L=280]
Description: thiazole biosynthesis enzyme [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.8e-64  215.5   0.1    7.2e-64  215.2   0.1    1.1  1  Thi4            Thi4 family
    4.7e-15   55.6   0.2    9.7e-07   28.2   0.0    3.0  3  FAD_binding_2   FAD binding domain
    9.6e-11   41.7   0.0    2.2e-10   40.5   0.0    1.5  1  FAD_oxidored    FAD dependent oxidoreductase
    5.8e-08   32.3   0.0    7.6e-08   31.9   0.0    1.2  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
      2e-07   31.1   0.0    4.2e-07   30.1   0.0    1.6  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
      1e-06   28.6   0.2    0.00028   20.6   0.1    2.2  2  DAO             FAD dependent oxidoreductase
    1.9e-06   27.3   0.0    3.3e-06   26.6   0.0    1.3  1  FAD_binding_3   FAD binding domain
    2.8e-06   26.3   0.0    4.1e-06   25.8   0.0    1.2  1  HI0933_like     HI0933-like protein
    4.9e-05   22.5   0.3     0.0019   17.3   0.0    2.3  2  Lycopene_cycl   Lycopene cyclase protein
    9.9e-05   21.7   0.0    0.00015   21.1   0.0    1.2  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    0.00029   20.0   0.1     0.0005   19.3   0.1    1.3  1  GIDA            Glucose inhibited division protein A
      0.004   16.1   0.0        1.3    7.8   0.0    2.1  2  Trp_halogenase  Tryptophan halogenase
     0.0067   15.7   0.1      0.025   13.9   0.1    1.8  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
  ------ inclusion threshold ------
       0.01   15.2   0.0      0.016   14.5   0.0    1.3  1  Amino_oxidase   Flavin containing amine oxidoreductase
      0.011   16.3   0.1      0.064   13.8   0.0    2.3  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
      0.046   12.2   0.0        0.1   11.1   0.0    1.5  2  GDI             GDP dissociation inhibitor
      0.064   13.2   0.1       0.14   12.2   0.1    1.5  1  NAD_binding_9   FAD-NAD(P)-binding
       0.11   12.7   0.0       0.25   11.6   0.0    1.6  1  TrkA_N          TrkA-N domain


Domain annotation for each model (and alignments):
>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  215.2   0.1   7.2e-67   7.2e-64       1     235 []      31     257 ..      31     257 .. 0.97

  Alignments for each domain:
  == domain 1  score: 215.2 bits;  conditional E-value: 7.2e-67
                 HHHHHHHHHHHHHHHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTTBSEEEEETTTHHHHHHTT---EEESSEEEESEHHHH CS
        Thi4   1 sraiveryfedllkyaesDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGqlfsaivvrkpakelLdelgikyedegdyvvvkdaalf 99 
                 +rai ++    l++ a+sDv+i+GaG++GLta++ l++  ++kv+++e++  +GGG wlGG + + + vr+pa+++ delg++y++  ++++      +
  EPA05774.1  31 TRAIANEWHAVLIDRAQSDVIIIGAGPAGLTASRDLSNM-GFKVLVVEQNNYLGGGYWLGGYMMNPVTVREPAQKIWDELGVPYKKVSEGLYLTPGPHA 128
                 699999999*****************************9.*********************************************************** PP

                 HHHHHHHHHTSTTEEEEESEEEEEEEEETBTEEEEEEEEEHHHHTCTTTSS.-B-EEEEEEEEEE--GSSSTTTTHHHHHHHHCTTTS-----ECB-HH CS
        Thi4 100 tstllskvlqlanvkllnavaveDlivregegvaGvvinwtlvelahdtqscvDPlvirakvvvdatGhdgeivavvvkkikleakiekvkgeksldae 198
                 +s+l++++++ a+vk ln +  +Dl++++  +v+G+v+nw+ v+    + +cvDP  ++ak+v+da+Ghd+    v+vk++++     + kg+ +++++
  EPA05774.1 129 VSKLIAAACD-AGVKFLNLTKFDDLVMKN-GRVTGIVVNWMPVSALPRNITCVDPIALEAKMVIDASGHDS----VAVKRLVDRG-LVEWKGMNPMYVN 220
                 **********.******************.8***************999*********************6....7889998888.55689******** PP

                 HHHHHHHHHECEEETTEEE-THHHHHHHT-EB--SB- CS
        Thi4 199 kaedaivkktrevvpnlyvaGmevaevdganRmGpif 235
                 ++e+++v+kt ev+p+l++aGm v+e +g+ RmGp++
  EPA05774.1 221 EGEEHVVHKTGEVYPGLVAAGMSVTETHGLARMGPTY 257
                 ***********************************96 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   9.7e-10   9.7e-07       1      36 [.      49      84 ..      49     108 .. 0.92
   2 !   22.4   0.0   5.8e-08   5.8e-05     136     203 ..     121     197 ..     111     225 .. 0.84
   3 ?    1.8   0.1       0.1     1e+02     383     413 ..     225     254 ..     218     256 .. 0.89

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 9.7e-10
                   SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
  FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36
                   Dvi+iG+G AGL+A+  +++ G kv+vve+ ++ gg
     EPA05774.1 49 DVIIIGAGPAGLTASRDLSNMGFKVLVVEQNNYLGG 84
                   9******************************99887 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 5.8e-08
                    ...HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEET.........TTTCEEEEEESEEEE-----G CS
  FAD_binding_2 136 tlvtghallarlvesarkagvdfqerteadeLivedgrvtGavvenp.........esgrevrirakavvlatgGfg 203
                     l++g++ +  l+++a +agv+f++ t+ d+L++++grvtG+vv+ +         +     +++ak v++a+g  +
     EPA05774.1 121 YLTPGPHAVSKLIAAACDAGVKFLNLTKFDDLVMKNGRVTGIVVNWMpvsalprniTCVDPIALEAKMVIDASGHDS 197
                    5789*****************************************88999766544444444999999999999765 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.1
                    BESTTEEESSBTEEE-STCEESSSSTTS--T CS
  FAD_binding_2 383 rvldadgqpipGLYAaGevaaggvhganrlg 413
                    +v  ++g++ pGL AaG    +  hg  r+g
     EPA05774.1 225 HVVHKTGEVYPGLVAAGMSV-TETHGLARMG 254
                    567899***********999.9****99987 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.5   0.0   2.2e-13   2.2e-10       1     145 [.      49     195 ..      49     201 .. 0.73

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 2.2e-13
  FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsgl.vatdignkaeeqvvtgiareflerlrq.rggarlkkrskwntfepevakavlee 95 
                   Dv+++G+gpaG++A     ++G kvl+ve++++lGG    g+ ++++++ +   + +++i++e+    ++  +g          t  p+++ +++ +
    EPA05774.1  49 DVIIIGAGPAGLTASRDLSNMGFKVLVVEQNNYLGGGYWLGGyMMNPVTVR---EPAQKIWDELGVPYKKvSEGL----Y---LTPGPHAVSKLIAA 135
                   9*********************************99765444034444433...566777777777775521111....1...3689********** PP

  FAD_oxidored  96 mlaeagvtvllntrlvevekegkriesvtve.........ske.g.rktirAkvfiDATgd 145
                    ++  gv+ l  t++++ +++++r+++++v+         + +    ++++Ak++iDA+g 
    EPA05774.1 136 ACDA-GVKFLNLTKFDDLVMKNGRVTGIVVNwmpvsalprNITcVdPIALEAKMVIDASGH 195
                   **88.***************99888888875222222211222213678899999999986 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0   7.7e-11   7.6e-08       2      70 ..      49     116 ..      48     169 .. 0.79

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 7.7e-11
                  SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHHHHHHCHHHHCCCC CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeiasevvkklnqgiell 70 
                  dv++iG+GpAGl+a+++l++ g+kv++v ++++ l+gg +l   + +    +e a++  ++l+  ++++
   EPA05774.1  49 DVIIIGAGPAGLTASRDLSNMGFKVLVV-EQNNYLGGGYWLGGYMMNPVTVREPAQKIWDELGVPYKKV 116
                  8***************************.8888999998888888777777777775555555444444 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.0   4.2e-10   4.2e-07       1      33 [.      52      84 ..      52     108 .. 0.93

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 4.2e-10
                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSG CS
  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGG 33
                   I+GaG +Gl+a + L++ gf+vl++e++++lGG
     EPA05774.1 52 IIGAGPAGLTASRDLSNMGFKVLVVEQNNYLGG 84
                   9*******************************8 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.1   2.8e-07   0.00028       1      35 [.      49      84 ..      49     110 .. 0.89
   2 !    6.6   0.0    0.0052       5.1     147     222 ..     127     213 ..      99     280 .] 0.62

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.8e-07
                EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSS CS
         DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiagsg 35
                dv+iiG+G +Gl++ ++L+  g  V+++e+++ +g g
  EPA05774.1 49 DVIIIGAGPAGLTASRDLSNMGfkVLVVEQNNYLG-G 84
                9*****************9999*********9999.5 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0052
                 HHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEE..........EECTEEEE.......EEEE..EEE--GGGHHHHHTTCTT.TSEEEEEEE CS
         DAO 147 kltaalaraaealGveilegtevtgleeedgkvwgve..........rttpgend.......aada..vVnaaGawsdllgllkel.dlpispvrg 222
                 +++  l +aa ++Gv++l+ t+  +l  ++g+v+g+           r   ++ +       +  a  v+ a G+ s  +   k+l d+ ++  +g
  EPA05774.1 127 HAVSKLIAAACDAGVKFLNLTKFDDLVMKNGRVTGIVvnwmpvsalpR---NI-TcvdpialE--AkmVIDASGHDSVAV---KRLvDRGLVEWKG 213
                 4566788888899************988999*****987777643221...33.133566444..355999999998655...3333333333333 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   3.3e-09   3.3e-06       2      33 ..      48      79 ..      47      82 .. 0.94

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 3.3e-09
                   EEEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
  FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekr 33
                    dV+I+GaGpaGl++++ Ls+ G +v++ve+ 
     EPA05774.1 48 SDVIIIGAGPAGLTASRDLSNMGFKVLVVEQN 79
                   69****************************86 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   4.1e-09   4.1e-06       2      36 ..      49      83 ..      48     107 .. 0.93

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 4.1e-09
                 SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
  HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36
                 dvi+iG+G+AGl a+  +++ g +Vl++e+++ lg
   EPA05774.1 49 DVIIIGAGPAGLTASRDLSNMGFKVLVVEQNNYLG 83
                 8******************************9887 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.9e-06    0.0019       1      36 [.      49      82 ..      49     121 .. 0.84
   2 ?    3.2   0.0     0.036        36     113     143 ..     167     197 ..     142     218 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.9e-06
  Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieaspsl 36
                   Dv++iGaGpAgl     l  +++g kv+++e  + l
     EPA05774.1 49 DVIIIGAGPAGLTASRDL--SNMGFKVLVVEQNNYL 82
                   9*****************..**********976655 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.036
  Lycopene_cycl 113 eeeeageslvvleggrkirarlvvdarglas 143
                    ++++a  + +++ +   ++a++v+da+g  s
     EPA05774.1 167 MPVSALPRNITCVDPIALEAKMVIDASGHDS 197
                    555556678999999*************443 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   1.5e-07   0.00015       1      31 [.      51      80 ..      51      83 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.5e-07
  Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgn 31
                 iIiGaGPaGl+a   l ++g+ ++l++E++n
   EPA05774.1 51 IIIGAGPAGLTASRDLSNMGF-KVLVVEQNN 80
                 8********************.7*****987 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1     5e-07    0.0005       1      31 [.      49      79 ..      49      85 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 5e-07
                CEEEE-SSHHHHHHHHHHHHTT--EEEEES- CS
        GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithk 31
                dvi+iG+G AG+ A+  ++++G+kvl + ++
  EPA05774.1 49 DVIIIGAGPAGLTASRDLSNMGFKVLVVEQN 79
                8************************998655 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0013       1.3       1      34 [.      49      79 ..      49      83 .. 0.92
   2 !    6.2   0.0     0.004       3.9     197     227 ..     183     213 ..     154     219 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0013
                    EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-S CS
  Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlvese 34
                    +++i+G+G+aG +a   l++++   ++v++ve++
      EPA05774.1 49 DVIIIGAGPAGLTASRDLSNMG---FKVLVVEQN 79
                    699****************999...899999986 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.004
                     EEE-SEEEE-SGGG-IIIIIIT---EEE-TT CS
  Trp_halogenase 197 eveadlfiDcsGfrgllieqaLktgfedwsd 227
                      +ea ++iD+sG+ +  +++ ++ g  +w+ 
      EPA05774.1 183 ALEAKMVIDASGHDSVAVKRLVDRGLVEWKG 213
                     699***************9999999999876 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.1   2.5e-05     0.025      28      60 ..      47      79 ..      40      82 .. 0.91
   2 ?   -1.6   0.0       1.3   1.3e+03     128     166 ..     136     173 ..     130     178 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.5e-05
                 --EEEEESTSHHHHHHHHHHHHTT-EEEEEESS CS
  AlaDh_PNT_C 28 pakvlviGgGvaGlqAiatakglgakVtvlDvr 60
                 ++ v++iG+G aGl A +  +++g kV v++ +
   EPA05774.1 47 QSDVIIIGAGPAGLTASRDLSNMGFKVLVVEQN 79
                 578*************************99987 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.3
                  TGGGT-SBTT--TBBTTSEEEEETTEEEEEBSTGG.GGSH CS
  AlaDh_PNT_C 128 AidqGGnvetsrltthgepvveekgvvhygvanlp.gavp 166
                  A+d+G  +   +lt+ ++ v+++  v+ + v+ +p +a+p
   EPA05774.1 136 ACDAGVKFL--NLTKFDDLVMKNGRVTGIVVNWMPvSALP 173
                  777777776..89999999999999999999999834555 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.6e-05     0.016       2      28 ..      58      84 ..      57      87 .. 0.96

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.6e-05
                   HHHHHHHHHHHTTEEEEEEESSSSSBT CS
  Amino_oxidase  2 aGLaaArqLlsaGfdVtvlEardrvGG 28
                   aGL+a r L++ Gf+V+v+E ++ +GG
     EPA05774.1 58 AGLTASRDLSNMGFKVLVVEQNNYLGG 84
                   9*************************9 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   6.5e-05     0.064       2      35 ..      50      83 ..      49      97 .. 0.92
   2 ?   -1.5   0.0       3.8   3.8e+03      52      78 ..     138     164 ..     126     166 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.5e-05
                EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
   Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35
                v+++G+G  gl +   l+++g kV vve ++ l 
  EPA05774.1 50 VIIIGAGPAGLTASRDLSNMGFKVLVVEQNNYLG 83
                89**************************999886 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.8
                 HTTEEEECSEEEEEEEEETTSEEEEEE CS
   Pyr_redox  52 kngievllntkveeiegsedgvesvkl 78 
                 + g+++l  tk   ++ ++  v+++++
  EPA05774.1 138 DAGVKFLNLTKFDDLVMKNGRVTGIVV 164
                 568999999999988855544888876 PP

>> GDI  GDP dissociation inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0    0.0001       0.1       5      41 ..      48      84 ..      44      87 .. 0.94
   2 ?   -3.1   0.0       2.1   2.1e+03     242     269 ..     136     163 ..     121     180 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0001
                ECEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSSCG CS
         GDI  5 ydvivlGtGlkecilsGllsvdgkkvlhldrndyyGg 41
                 dvi++G+G      s  ls  g kvl++++n+y Gg
  EPA05774.1 48 SDVIIIGAGPAGLTASRDLSNMGFKVLVVEQNNYLGG 84
                69*********************************98 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.1
                 HHTT-EEETS--.ECEEEE-TTS-EEEEE CS
         GDI 242 aiyGGtymlnkp.vdevvldedgkvvGvk 269
                 a   G   ln    d++v+ ++g+v+G+ 
  EPA05774.1 136 ACDAGVKFLNLTkFDDLVM-KNGRVTGIV 163
                 4456666666540555666.888888875 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00014      0.14       2      42 ..      52      87 ..      51      97 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
  NAD_binding_9  2 ivGaGprGlavlerLlarakkkspleitlfdpsep.gagrvw 42
                   i+GaGp+Gl++ + L +       +++ +++++++ g g+ w
     EPA05774.1 52 IIGAGPAGLTASRDLSNM-----GFKVLVVEQNNYlG-GGYW 87
                   9**************999.....6********88856.9888 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00025      0.25       1      30 [.      50      79 ..      50      82 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00025
                EEEES-SHHHHHHHHHHHH.TTEEEEEEESS CS
      TrkA_N  1 iiiiGlGrvGrslaeeLse.ggkdvvvidkd 30
                +iiiG+G  G +  + Ls+ g  +v+v++++
  EPA05774.1 50 VIIIGAGPAGLTASRDLSNmGF-KVLVVEQN 79
                79*****************666.6*****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 1778.22
//
Query:       EPA05775.1  [L=97]
Description: hypothetical protein BG20_I2057, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       817  (0.0455686); expected 358.6 (0.02)
Passed bias filter:                      608  (0.0339115); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.33s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 588.24
//
Query:       EPA05776.1  [L=405]
Description: hypothetical protein BG20_I2052 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.035   13.9   0.5      0.035   13.9   0.5    1.8  2  SH3BP5           SH3 domain-binding protein 5 (SH3BP5)
      0.039   14.3   4.4        1.4    9.3   1.0    2.4  2  CC2-LZ           Leucine zipper of domain CC2 of NEMO, NF-kap
      0.044   12.9   0.0       0.96    8.5   0.0    2.5  2  Polysacc_synt_2  Polysaccharide biosynthesis protein
       0.12   11.5  10.8       0.06   12.4   4.3    2.1  2  Atg14            Vacuolar sorting 38 and autophagy-related su
       0.15   12.1  20.3       0.17   11.9   8.6    3.0  3  FlxA             FlxA-like protein
        0.3   11.5  10.0      0.097   13.1   3.9    2.5  2  Snapin_Pallidin  Snapin/Pallidin
        0.3   11.3   3.6        6.9    6.9   0.1    2.5  2  I_LWEQ           I/LWEQ domain
       0.63   10.1   7.4      0.087   12.9   2.8    1.9  2  LidA_Long_CC     LidA long coiled-coil domain
       0.75   10.7   4.3        4.9    8.1   0.8    2.6  2  Pilin            Pilin (bacterial filament)
       0.85    9.9   6.9        1.1    9.5   2.0    2.7  2  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
       0.98    9.8   6.6        4.5    7.6   0.2    2.3  2  OmpH             Outer membrane protein (OmpH-like)
        2.2    8.1   6.1         13    5.5   0.1    2.5  2  DUF724           Protein of unknown function (DUF724)
        3.1    8.1   8.1        4.5    7.6   0.5    2.9  2  ABC_tran_CTD     ABC transporter C-terminal domain
        7.7    7.2   8.2         32    5.2   0.1    2.6  2  BST2             Bone marrow stromal antigen 2
        8.4    6.6  12.4    1.3e+02    2.7   8.4    3.3  3  TolA_bind_tri    TolA binding protein trimerisation


Domain annotation for each model (and alignments):
>> SH3BP5  SH3 domain-binding protein 5 (SH3BP5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       1.4   1.7e+03     186     199 ..     203     216 ..     166     241 .. 0.56
   2 ?   13.9   0.5   2.9e-05     0.035     136     209 ..     324     399 ..     258     401 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.4
      SH3BP5 186 eqkekveelekevk 199
                 +q +k+ el+k+++
  EPA05776.1 203 SQSSKIIELRKQIN 216
                 23333333333333 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 2.9e-05
      SH3BP5 136 keaeeehqrktkkleeaekkvqqlekklk..rsikkskpYfelkaklnkqleeqkekveelekevkeaKaeYseaL 209
                  + +++ ++  +k+ ++e+++ ql+k+l+  r+  +s     +k+ +n+qle + +k+ el+ +++  K++Y++ L
  EPA05776.1 324 IKIDTAGNTDSNKIPNIENQLIQLQKQLNdeRNTIRSLIHDTKKSDYNEQLEMHSAKIIELRGQISLLKEQYNQIL 399
                 44555666677888899**********98667888899999999****************************9876 PP

>> CC2-LZ  Leucine zipper of domain CC2 of NEMO, NF-kappa-B essential modulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1     0.016        19      13      51 ..     177     222 ..     166     230 .. 0.73
   2 ?    9.3   1.0    0.0012       1.4       6      60 ..     327     394 ..     322     402 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.016
      CC2-LZ  13 keeieeLkaqlqaaeealaakq.......eeidelkeeikkkeeel 51 
                 +++i +L+++l+ a +al +k+       ++i el+++i++++e+l
  EPA05776.1 177 EAKIASLQQELDIAKKALGDKSspdtsqsSKIIELRKQINNEKEDL 222
                 788999**********998775222222267888888888888877 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0012
      CC2-LZ   6 keaekvkkeeieeLkaqlqaaeealaakqeeidelkeeikkkee............ele.tisvlkaQ 60 
                 + a +++ ++i ++++ql + +++l+++++ i  l ++ kk +             el+ +is+lk Q
  EPA05776.1 327 DTAGNTDSNKIPNIENQLIQLQKQLNDERNTIRSLIHDTKKSDYneqlemhsakiiELRgQISLLKEQ 394
                 55666778999************************999988877777766666666666666666666 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0    0.0008      0.96       7      45 ..     103     141 ..      95     165 .. 0.83
   2 ?    1.5   0.0      0.11   1.3e+02      38      92 ..     228     284 ..     210     316 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0008
                      TSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH... CS
  Polysacc_synt_2   7 gGsiGselvrqilkkkpkkiillerdElklyeiekelee 45 
                      g s+G e++  +l+  +  +++ + +E++ yei ++++ 
       EPA05776.1 103 GYSFGFEVCASFLRIYVPDVLIKSDSETQRYEIPQNVDP 141
                      459******************************998754 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.11
                      HHHHH......-TTEEEE....E--TT-HHHHHHHTT...T-SEEEE-.-----HHH CS
  Polysacc_synt_2  38 eiekeleeelkkkklkveivpvigdvrdkerlekale.elkvdvvfha.AAlKhVPl 92 
                      +i  e +e+++ +kl+++ +p+ g+ ++   ++k l+ e + dvvf a AA K++ l
       EPA05776.1 228 TIYAEPKEKYNIQKLTFTGIPITGESTEIIAVKKSLSaENTFDVVFEAcAADKQISL 284
                      5667777888999999999999999999999998886246789***98577788754 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.5     0.038        46      46     104 ..     170     222 ..     126     242 .. 0.69
   2 ?   12.4   4.3     5e-05      0.06      33     133 ..     288     382 ..     280     398 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.038
       Atg14  46 ekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkkl 104
                 +k+l+  e      +ki ++++ l+  k+   d+++     + k+ +l+k+i++ k+ l
  EPA05776.1 170 SKLLSDGE------AKIASLQQELDIAKKALGDKSSPDTSQSSKIIELRKQINNEKEDL 222
                 44444444......445555555555555555555555555555555555555555444 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 5e-05
       Atg14  33 klksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklkkRrsdleslqneleerrkk 131
                 ++ s+ e+   ki ++++ ++ ++ +++ki +k+ +  ++ +     ++++ +++ +l ql+k++++ ++++++l +++k  +sd    +++le   +k
  EPA05776.1 288 RISSDTETTNVKIGDKISPNT-CQMTSTKITSKNPDTIKIDTAGNTDSNKIPNIENQLIQLQKQLNDERNTIRSLIHDTK--KSD---YNEQLEMHSAK 380
                 677889999999999999999.888999999999999999999999999*****************************97..555...44555544444 PP

       Atg14 132 qi 133
                 +i
  EPA05776.1 381 II 382
                 44 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   3.8     0.059        70      16      60 ..     177     217 ..     169     225 .. 0.58
   2 ?    6.0   0.4      0.01        12      10      36 ..     199     225 ..     195     242 .. 0.78
   3 ?   11.9   8.6   0.00014      0.17      10      73 ..     328     396 ..     322     398 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.059
        FlxA  16 asqiasLqkQiknlqkqLkelsesdeltkeekkkqqqliqaQIqq 60 
                 +++iasLq++++ ++k L + s+ d+ ++   + ++ ++ +QI++
  EPA05776.1 177 EAKIASLQQELDIAKKALGDKSSPDT-SQ---SSKIIELRKQINN 217
                 56677777777777766666555522.22...2455555555554 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.01
        FlxA  10 ssssgsasqiasLqkQiknlqkqLkel 36 
                 s +++ +s+i +L+kQi+n ++ L  l
  EPA05776.1 199 SPDTSQSSKIIELRKQINNEKEDLYRL 225
                 55678899************9999877 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.00014
        FlxA  10 ssssgsasqiasLqkQiknlqkqLkelses.....deltkeekk....kqqqliqaQIqqlqaQIaqlqqqqa 73 
                 + +++ +++i ++++Q+ +lqkqL++  ++          + kk    +q ++ +a+I  l+ QI  l++q +
  EPA05776.1 328 TAGNTDSNKIPNIENQLIQLQKQLNDERNTirsliH----DTKKsdynEQLEMHSAKIIELRGQISLLKEQYN 396
                 567788899*******************99955543....444444449999999999999999999988865 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.4       0.4   4.8e+02      35      78 ..     179     221 ..     177     226 .. 0.66
   2 ?   13.1   3.9   8.1e-05     0.097      30      87 ..     345     403 ..     334     404 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.4
  Snapin_Pallidin  35 qldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslner 78 
                      ++ +l+++L+ +++a  +++ pd+ +   K+++++k++++ +e 
       EPA05776.1 179 KIASLQQELDIAKKALGDKSSPDT-SQSSKIIELRKQINNEKED 221
                      677888888755555545666666.5677888888888876555 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 8.1e-05
  Snapin_Pallidin  30 eeLleqldrlnekLkeleeaqe.aevlpdlkeyakKLvnikkrmsslnerlqklkkRae 87 
                       +L++ql+ +++ +++l ++++ +++ ++l+ + +K+++++ ++s l+e+ +++  Ra 
       EPA05776.1 345 IQLQKQLNDERNTIRSLIHDTKkSDYNEQLEMHSAKIIELRGQISLLKEQYNQILYRAF 403
                      68**************************************************9999885 PP

>> I_LWEQ  I/LWEQ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1    0.0058       6.9     104     147 ..     182     225 ..     163     230 .. 0.84
   2 ?    4.5   0.7     0.031        37      76     133 ..     332     393 ..     294     397 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0058
      I_LWEQ 104 seeeeldisklslvqakrqemeaqvkilklekeLeearkkLaei 147
                 s ++eldi k+ l ++      + +ki++l k+++++++ L ++
  EPA05776.1 182 SLQQELDIAKKALGDKSSPDTSQSSKIIELRKQINNEKEDLYRL 225
                 3568999999999999999********************99875 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.031
      I_LWEQ  76 aaskaVkkatkelvkavkeakekqeeees...eeeeld.isklslvqakrqemeaqvkilkl 133
                 + s+++ +  ++l++  k+ ++++++ +s   ++++ d  ++l++++ak  e+  q + lk 
  EPA05776.1 332 TDSNKIPNIENQLIQLQKQLNDERNTIRSlihDTKKSDyNEQLEMHSAKIIELRGQISLLKE 393
                 44667777777788888888877777663345666777567788888888888888888775 PP

>> LidA_Long_CC  LidA long coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.2       2.2   2.6e+03       9      27 ..     178     196 ..     172     223 .. 0.57
   2 ?   12.9   2.8   7.3e-05     0.087       3      61 ..     336     391 ..     334     400 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2.2
                   HHHHHHHHHHHHHHHHHHH CS
  LidA_Long_CC   9 eriaklekkldkqaeeIne 27 
                   ++ia+l+++ld  ++++ +
    EPA05776.1 178 AKIASLQQELDIAKKALGD 196
                   5566666655555544443 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 7.3e-05
                   HHHHHHHHHHHHHHHHHHHHHHHHHHHH-S-HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
  LidA_Long_CC   3 kiekieeriaklekkldkqaeeIneliesgsdgkeeearkllhelnglnlqvaglkdml 61 
                   ki  ie+++ +l+k+l+ ++++I  li ++++++    +++l+++ ++ ++++g   +l
    EPA05776.1 336 KIPNIENQLIQLQKQLNDERNTIRSLIHDTKKSD---YNEQLEMHSAKIIELRGQISLL 391
                   7889*************************77777...6679999999888888876666 PP

>> Pilin  Pilin (bacterial filament)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1      0.17     2e+02      30      85 ..      11      73 ..       3      94 .. 0.74
   2 ?    8.1   0.8    0.0041       4.9      29      85 ..     292     352 ..     272     370 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.17
                CTCCCCCTTBSTCSCCTCEEEEECCCEEC.......CEEEEEECCCSSTC.CTTEEEEEEEECT CS
       Pilin 30 pttaaadiGlasstaicgvisvtveaatg.......gtitatfggnaaak.ikgktltltrtad 85
                p++++a +G++s+  +c++ + +v  + +        + +++f +++ ak i++ktl+ +++ d
  EPA05776.1 11 PKKQTA-LGISSDDISCETGTYKVIRDRTntpacvkISHVIKFVTSGWAKpIDQKTLESQTKLD 73
                455555.99999999999555555555555699988555667777776667*****99877755 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0041
                 SCTCCCCCTTBSTCSCCTCEEEEECCCEECCEEEEEECCCSSTC....CTTEEEEEEEECT CS
       Pilin  29 tpttaaadiGlasstaicgvisvtveaatggtitatfggnaaak....ikgktltltrtad 85 
                  ++t++ +iG + s ++c+ +s ++++++  ti++  +gn+ ++    i ++ ++l+ + +
  EPA05776.1 292 DTETTNVKIGDKISPNTCQMTSTKITSKNPDTIKIDTAGNTDSNkipnIENQLIQLQKQLN 352
                 344444459**********88888888888999999998888878999*****99998866 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.2      0.19   2.3e+02       7      34 ..     183     211 ..     149     226 .. 0.57
   2 ?    9.5   2.0   0.00092       1.1      40      93 ..     343     398 ..     307     401 .. 0.67

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.19
                   HHH-HHHHHHHHCCCT.CCCHHHHHHHHH CS
  Seryl_tRNA_N   7 irenpeavkeklkkRg.edkadvdellel 34 
                   ++++++  k++l  +   d+++  +++el
    EPA05776.1 183 LQQELDIAKKALGDKSsPDTSQSSKIIEL 211
                   34444444444444432222333333333 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00092
                   HHHHHHHHHHHHHHHHHHHCCCCCCTT..S-TCCCCCCCHHHHHHHHHHHHHHHHH CS
  Seryl_tRNA_N  40 elqveleelqaerNelskeIgkakkkk..edaeeliaevkelkeelkaleaelkel 93 
                   +l++   +l+ erN++   I+  kk++  e+ e   a++ el  +++ l+++ +++
    EPA05776.1 343 QLIQLQKQLNDERNTIRSLIHDTKKSDynEQLEMHSAKIIELRGQISLLKEQYNQI 398
                   44455567777888888888888877766666777777777777777777776665 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.2    0.0037       4.5      29     116 ..     174     274 ..     164     289 .. 0.61
   2 ?    4.6   1.6     0.033        39      24      77 ..     340     393 ..     313     405 .] 0.54

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0037
                 HHHHHHHHHHHHHHHHHHHHHHHHTTTS.-HHHHHHHHHHHHHHHHHHHHHH...........HHHHHHHHHHHH.HHHHHHHHHH...HHHHHHTT-S CS
        OmpH  29 kklqaeleakekelqklqeelqkkakklekeekeqelqkkeqelqqkqqqka...........qelqkkqqellk.pildkinkai...kevakekgyd 112
                 ++ +a+++++++el+ ++++l +k++    + +  ++ +++++++++++  +           ++++ ++  ++  pi+ + +++i   k + +e+ +d
  EPA05776.1 174 SDGEAKIASLQQELDIAKKALGDKSSP--DTSQSSKIIELRKQINNEKEDLYrlyftiyaepkEKYNIQKLTFTGiPITGESTEIIavkKSLSAENTFD 270
                 556889999999999999999744433..4445555777777777755555522222223332222222222333556666666557778899999999 PP

                 EEEE CS
        OmpH 113 lvld 116
                 +v++
  EPA05776.1 271 VVFE 274
                 9998 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.033
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS.-HHHHHH........HHHHHHHHHHHHH CS
        OmpH  24 lekkfkklqaeleakekelqklqeelqkkakklekeekeqe........lqkkeqelqqkqq 77 
                 +e++  +lq++l+++++ +++l+ + +k+  +        e        + +++ ++  +++
  EPA05776.1 340 IENQLIQLQKQLNDERNTIRSLIHDTKKSDYN--------EqlemhsakIIELRGQISLLKE 393
                 44455566666666666666666666644444........2211112233333333333333 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.011        13     124     179 ..     165     220 ..     154     228 .. 0.67
   2 ?    3.4   1.7      0.05        60     104     153 ..     348     395 ..     334     400 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.011
      DUF724 124 ekrkleeeidelekkilelerqlallk.......ekkeaadkeiarlkseaekleeeledveq 179
                 +k  +++ +++ e ki+ l+++l+ +k       +          + +s+  +l++++++ ++
  EPA05776.1 165 NKGDISKLLSDGEAKIASLQQELDIAKkalgdksS-------PDTSQSSKIIELRKQINNEKE 220
                 5667788899999**************55554444.......444444444444444444444 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.05
      DUF724 104 qtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekk 153
                 q++l +er+ + + i   +++k+ ++e+++  + ki+el+ q  llke+ 
  EPA05776.1 348 QKQLNDERNTIRSLIH--DTKKSDYNEQLEMHSAKIIELRGQISLLKEQY 395
                 4555556555555554..44556678999999999999999999999775 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.5    0.0038       4.5      14      61 ..     177     226 ..     170     228 .. 0.77
   2 ?    2.9   1.9      0.11   1.3e+02      15      35 ..     335     355 ..     334     397 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0038
  ABC_tran_CTD  14 eaeIeaLEeeiaeleaeladpely..sdpeklaelsaeleeleaeLeely 61 
                   ea+I++L++e+    ++l d +    s++ k+ el +++++ +++L +ly
    EPA05776.1 177 EAKIASLQQELDIAKKALGDKSSPdtSQSSKIIELRKQINNEKEDLYRLY 226
                   99**************9999886532333778888888888777776665 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.11
  ABC_tran_CTD  15 aeIeaLEeeiaeleaeladpe 35 
                   ++I  +E+++ +l+++l+d+ 
    EPA05776.1 335 NKIPNIENQLIQLQKQLNDER 355
                   6899**************985 PP

>> BST2  Bone marrow stromal antigen 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1     0.027        32      33      82 ..     173     222 ..     168     228 .. 0.85
   2 ?    4.0   3.1     0.065        78      22      83 ..     340     396 ..     329     402 .. 0.62

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.027
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
        BST2  33 lreaeaqaatcnqtvvtLkasLekekaqsqkqqakvqelqgeikkLnqkL 82 
                 l + ea++a+ +q +   k++L  + +    q +k+ el+++i++ ++ L
  EPA05776.1 173 LSDGEAKIASLQQELDIAKKALGDKSSPDTSQSSKIIELRKQINNEKEDL 222
                 66778888999999999999999999999999999999999999988877 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.065
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
        BST2  22 LerqLtqaqeslreaeaqaatcnqtvvtLkasLekekaqsqkqqakvqelqgeikkLnqkLq 83 
                 +e+qL q q++l++     +t  + + + k+s  +e+ +   + ak+ el+g+i  L+++ +
  EPA05776.1 340 IENQLIQLQKQLNDER---NTIRSLIHDTKKSDYNEQLE--MHSAKIIELRGQISLLKEQYN 396
                 5566666666555433...33444444444444444444..3456899******99999865 PP

>> TolA_bind_tri  TolA binding protein trimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       4.5   5.3e+03      25      35 ..     178     188 ..     170     195 .. 0.66
   2 ?   -0.3   0.0      0.96   1.1e+03      15      37 ..     203     225 ..     199     226 .. 0.82
   3 ?    2.7   8.4      0.11   1.3e+02       6      54 ..     344     401 ..     340     402 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 4.5
  TolA_bind_tri  25 qqlealqqelr 35 
                     ++ +lqqel+
     EPA05776.1 178 AKIASLQQELD 188
                    45566666665 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.96
  TolA_bind_tri  15 arsqlllelqqqlealqqelreL 37 
                    ++s+ ++el +q+++ +++l +L
     EPA05776.1 203 SQSSKIIELRKQINNEKEDLYRL 225
                    45588999999999999998877 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.11
  TolA_bind_tri   6 varLErilears.........qlllelqqqlealqqelreLRGqiEelqyqleqleer 54 
                    + +L ++l+ +              +  +qle  ++ + eLRGqi  l+ q +q++ r
     EPA05776.1 344 LIQLQKQLNDERntirslihdTKKSDYNEQLEMHSAKIIELRGQISLLKEQYNQILYR 401
                    55555555554455555555577889999*************************9866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1257  (0.0701099); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.49
# Mc/sec: 2482.78
//
Query:       EPA05777.1  [L=146]
Description: CBS domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-26   92.1   3.8    1.4e-14   54.2   1.0    2.1  2  CBS       CBS domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6   0.1     6e-14   1.1e-09       4      55 ..      14      64 ..      10      65 .. 0.92
   2 !   54.2   1.0   7.9e-19   1.4e-14       1      55 [.      75     128 ..      75     130 .. 0.95

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 6e-14
                HSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
         CBS  4 imtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55
                +mtr++ ++  +t++++a ++m e+++ +l VV ++++++Givt +D++ al
  EPA05777.1 14 FMTRNIKSIQSNTSVKDASKIMYESHIPSL-VVQDSEEILGIVTYEDIAVAL 64
                7*********************99889999.9988999**********9776 PP

  == domain 2  score: 54.2 bits;  conditional E-value: 7.9e-19
                 HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
         CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                 +++im++++++v+ d+++ +a+elm  k+++ lPV+ +dgk+ Gi++ +Dl+ +l
  EPA05777.1  75 IKEIMSSPIISVKSDASILDAVELMLAKKIHELPVI-DDGKIKGIISSTDLIVLL 128
                 589*********************************.6*************9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 989.15
//
Query:       EPA05778.1  [L=420]
Description: hypothetical protein BG20_I2055 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00033   20.4   3.8      0.058   13.3   0.3    3.2  3  HSBP1            Heat shock factor binding protein 1
    0.00046   20.6   9.6      0.044   14.2   0.9    4.0  3  DUF4140          N-terminal domain of unknown function (DUF41
    0.00065   20.0   6.3       0.28   11.4   0.8    2.4  2  ATG16            Autophagy protein 16 (ATG16)
    0.00067   19.7   8.2      0.055   13.5   2.8    2.6  2  TcpS             Toxin-coregulated pilus protein S
    0.00094   19.2  10.6      0.019   15.1   0.8    3.0  2  Med9             RNA polymerase II transcription mediator com
    0.00098   19.2   8.6       0.12   12.4   0.9    2.3  2  ADIP             Afadin- and alpha -actinin-Binding
     0.0027   17.6   9.7       0.18   11.8   0.4    4.1  4  Prefoldin_2      Prefoldin subunit
     0.0039   17.1  10.6       0.84    9.5   0.5    3.4  3  NleF_casp_inhib  NleF caspase inhibitor
     0.0063   16.6   5.3       0.56   10.3   1.2    2.4  2  DUF848           Gammaherpesvirus protein of unknown function
     0.0066   16.8   7.2       0.17   12.3   0.5    2.6  2  Snapin_Pallidin  Snapin/Pallidin
  ------ inclusion threshold ------
      0.011   16.3   1.1          1    9.9   0.1    2.6  2  Spectrin         Spectrin repeat
      0.015   15.6   6.2        0.2   11.9   0.1    3.1  2  ABC_tran_CTD     ABC transporter C-terminal domain
      0.017   15.5   3.9         11    6.5   0.3    4.2  3  LPP              Lipoprotein leucine-zipper
      0.022   14.6  11.8      0.027   14.4   0.3    4.0  4  Shugoshin_N      Shugoshin N-terminal coiled-coil region
      0.023   14.1   0.7       0.83    9.0   0.1    2.2  2  TraF_2           F plasmid transfer operon, TraF, protein
      0.042   13.5   8.5        2.7    7.6   0.2    3.2  2  PI3K_P85_iSH2    Phosphatidylinositol 3-kinase regulatory sub
      0.049   13.7  12.0       0.41   10.7   1.5    2.9  3  DUF1664          Protein of unknown function (DUF1664)
      0.064   13.5   0.6        0.6   10.4   0.1    2.3  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
       0.07   13.6   7.8          2    8.9   1.1    2.3  2  Fez1             Fez1
      0.072   13.5  11.7       0.37   11.2   1.4    3.5  3  FlaC_arch        Flagella accessory protein C (FlaC)
      0.073   12.6   6.7       0.88    9.1   0.7    2.3  2  Filament         Intermediate filament protein
      0.073   13.1   0.2        5.3    7.1   0.0    2.8  2  DUF1137          Protein of unknown function (DUF1137)
       0.08   12.9   1.5        0.3   11.1   0.2    2.2  2  ApoO             Apolipoprotein O
       0.11   11.4   7.3       0.27   10.1   0.8    2.3  2  Spc7             Spc7 kinetochore protein
       0.13   12.1   7.1          2    8.3   0.5    2.7  2  ACCA             Acetyl co-enzyme A carboxylase carboxyltrans
       0.14   11.6   9.8       0.32   10.5   1.5    2.2  2  Leu_zip          Leucine zipper
       0.17   11.7   1.6          8    6.2   0.3    2.4  2  USP8_interact    USP8 interacting
       0.22   11.6   6.3       0.32   11.1   2.3    2.4  2  DUF148           Domain of unknown function DUF148
       0.23   11.5  14.4       0.63   10.1   2.2    2.7  2  Laminin_II       Laminin Domain II
       0.23   11.7   2.0        6.6    7.0   0.0    2.7  2  FliJ             Flagellar FliJ protein
       0.24   11.7   9.7        3.8    7.8   1.4    3.2  2  THOC7            Tho complex subunit 7
       0.29   11.6  12.1        0.6   10.6   0.4    3.5  3  DUF4094          Domain of unknown function (DUF4094)
       0.39   10.9   9.1         10    6.3   0.3    3.2  3  Cnn_1N           Centrosomin N-terminal motif 1
       0.55   10.7  11.2        1.2    9.6   0.6    3.4  2  NPV_P10          Nucleopolyhedrovirus P10 protein
       0.72    9.8   9.0        2.7    7.9   1.8    2.4  2  Ax_dynein_light  Axonemal dynein light chain
       0.72    9.9  13.5          1    9.4   2.5    3.3  2  FlxA             FlxA-like protein
        0.9    9.3   8.9        5.7    6.7   0.7    2.3  2  DUF724           Protein of unknown function (DUF724)
       0.94    9.9  13.0        2.8    8.3   2.2    2.5  2  Syntaxin_2       Syntaxin-like protein
        1.2    9.7  14.6        1.7    9.3   0.5    4.1  4  BST2             Bone marrow stromal antigen 2
        1.3    9.1  11.0        1.5    9.0   0.5    2.7  2  Tropomyosin_1    Tropomyosin like
        1.4    8.6   6.7        1.1    8.8   1.2    2.3  2  LUC7             LUC7 N_terminus
        1.5    8.9   6.8         25    5.0   0.5    4.2  4  DUF1192          Protein of unknown function (DUF1192)
        1.5    8.9   4.0        2.5    8.2   0.2    2.6  2  DUF1515          Protein of unknown function (DUF1515)
        1.5    8.9  12.8        4.7    7.2   4.0    2.5  2  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
        1.6    9.4   7.0         20    5.9   1.6    3.1  2  HIP1_clath_bdg   Clathrin-binding domain of Huntingtin-intera
        1.8    8.9   9.8        1.9    8.9   1.3    3.1  3  Uso1_p115_C      Uso1 / p115 like vesicle tethering protein, 
        2.1    8.6  11.5        9.7    6.5   3.0    3.2  2  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
        2.1    8.3   7.6       0.48   10.4   0.2    3.1  2  DUF5001          Ig-like domain
        2.3    8.2  11.4        4.7    7.2   0.7    4.1  4  Prefoldin        Prefoldin subunit
        3.3    7.0   9.0        1.2    8.5   1.1    2.3  2  FAM76            FAM76 protein
        3.6    7.2  10.5        3.5    7.3   0.5    2.6  2  Lebercilin       Ciliary protein causing Leber congenital ama
        3.8    7.9   9.6        1.1    9.7   1.8    2.9  3  T4SS             Type IV secretion system proteins
        3.9    7.4  12.2        9.6    6.2   1.3    3.3  3  MIP-T3_C         Microtubule-binding protein MIP-T3 C-termina
        4.1    7.5  12.0       0.37   10.9   1.1    2.7  2  TssO             Type VI secretion system, TssO
        5.1    6.8   8.9        1.5    8.5   0.3    2.9  2  Lectin_N         Hepatic lectin, N-terminal domain
        6.8    7.1  15.6        1.3    9.4   0.3    4.0  4  DUF4200          Domain of unknown function (DUF4200)
        9.6    6.9   9.3         19    5.9   2.6    3.2  2  YabA             Initiation control protein YabA


Domain annotation for each model (and alignments):
>> HSBP1  Heat shock factor binding protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.034        11      25      45 ..     174     194 ..     166     199 .. 0.86
   2 ?    0.5   0.1       1.8   5.7e+02      17      46 ..     198     227 ..     196     231 .. 0.86
   3 !   13.3   0.3   0.00018     0.058      31      49 ..     349     367 ..     338     369 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.034
       HSBP1  25 ilsriDdMssriDdLEksiad 45 
                 i+ +i  ++++i  LE++ia+
  EPA05778.1 174 ITAKITSLENKISGLEQNIAS 194
                 999****************86 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.8
       HSBP1  17 kFqtmsdqilsriDdMssriDdLEksiadl 46 
                 k + ++++ +s i d +++i +L ++i++ 
  EPA05778.1 198 KLSGVTNDTTSTISDTTQKIVELRNNITKT 227
                 77889999999**************99875 PP

  == domain 3  score: 13.3 bits;  conditional E-value: 0.00018
       HSBP1  31 dMssriDdLEksiadlmtq 49 
                 d+ss iD+LEk ++dl ++
  EPA05778.1 349 DISSSIDELEKKVSDLQEK 367
                 89**************875 PP

>> DUF4140  N-terminal domain of unknown function (DUF4140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   1.0     0.041        13      34      83 ..     159     233 ..     132     248 .. 0.56
   2 !   14.2   0.9   0.00014     0.044      32      98 .]     307     378 ..     303     378 .. 0.86
   3 ?    1.6   0.0       1.2   3.8e+02      66      87 ..     391     412 ..     379     419 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.041
     DUF4140  34 ldedSlrVega..ga..atildvqvervpnreaeee.....................elkalraeleeledelaa 83 
                 ++++S++++ +  g+  a+i++++ + +  +++ ++                     ++ +lr+ +++ +del++
  EPA05778.1 159 ANPESIKATMTnkGGitAKITSLENKISGLEQNIASeraklsgvtndttstisdttqKIVELRNNITKTKDELNR 233
                 455666666332222335555555555444443333455666666666653344443344444444444444444 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 0.00014
     DUF4140  32 ptldedSlrVe...gagaatildvqvervpnreaeee..elkalraeleeledelaaledelaaaearlafl 98 
                 ++ +++S+r     ++++++i +vq++++  +++  +      + ++++ele++ ++l++++++ ++rl++l
  EPA05778.1 307 SDFETQSVRLAddiSPNSCQINSVQISTENPQSISISlkNKGDISSSIDELEKKVSDLQEKIKTEKQRLEIL 378
                 567889999997766688**********8888888887448899************************9987 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 1.2
     DUF4140  66 elkalraeleeledelaalede 87 
                 e+ +l++ +e l+ +l++++ e
  EPA05778.1 391 EVTKLTENIEHLRNDLNRAKVE 412
                 7999************999876 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.8   0.00088      0.28      92     167 ..     166     238 ..     114     243 .. 0.80
   2 !   11.1   0.5    0.0011      0.33      93     132 ..     343     382 ..     322     416 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00088
       ATG16  92 elyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLqlql 167
                 ++   +g  + ++++l+++++ le+++ +++++l  ++++    +  ++d ++++ e+++ + + +DEl+  +l+l
  EPA05778.1 166 ATMTNKGGITAKITSLENKISGLEQNIASERAKLSGVTNDT---TSTISDTTQKIVELRNNITKTKDELNRYKLAL 238
                 445678999999999*********99999999999888765...568999*******************9988876 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0011
       ATG16  93 lyksrgelaqrllelneelqkleeklkedeerlaeleaer 132
                 ++k +g+ ++++ el++++++l+ek+k++++rl+ l ++ 
  EPA05778.1 343 SLKNKGDISSSIDELEKKVSDLQEKIKTEKQRLEILIHQT 382
                 6899*****************************9886554 PP

>> TcpS  Toxin-coregulated pilus protein S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.3    0.0052       1.6      43     101 ..     178     237 ..     153     276 .. 0.78
   2 !   13.5   2.8   0.00018     0.055      21      97 ..     327     406 ..     317     417 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0052
        TcpS  43 qLeLkkkileveieikeaedklqPkvskaipvlskp.kavvkvellkeiesfdekL..vkLl 101
                 +  L+ ki  +e +i  ++ kl    +++ +++s++ + +v  el ++i +  ++L   kL+
  EPA05778.1 178 ITSLENKISGLEQNIASERAKLSGVTNDTTSTISDTtQKIV--ELRNNITKTKDELnrYKLA 237
                 456889******************99999999985414444..6667766666666444454 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00018
        TcpS  21 adelevyennyksie.sLknkle....qLeLkkkileveieikeaedklqPkvskaipvlskpkavvkvellkeiesfdekL 97 
                  + ++++ +n +si  sLknk +    + eL+kk+ +++ +ik ++++l+  ++++   l        ++l ++ie++ ++L
  EPA05778.1 327 INSVQISTENPQSISiSLKNKGDisssIDELEKKVSDLQEKIKTEKQRLEILIHQTPRSLTY--DLEVTKLTENIEHLRNDL 406
                 57899999999999769****76222256**********************99999444443..333346788888887776 PP

>> Med9  RNA polymerase II transcription mediator complex subunit 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.8   5.9e-05     0.019      19      77 ..     176     235 ..     155     237 .. 0.89
   2 !    8.0   1.8    0.0096         3      43      74 ..     345     376 ..     338     382 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.9e-05
        Med9  19 lsskdletktgelrhkLkkarelirelpg.idrsveeqeaeieeleeqlakKrelLkkyk 77 
                   ++ le+k+++l + + + r+ ++ + +    ++ +  ++i el+++++k ++ L++yk
  EPA05778.1 176 AKITSLENKISGLEQNIASERAKLSGVTNdTTSTISDTTQKIVELRNNITKTKDELNRYK 235
                 567899********************9877*****************************8 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0096
        Med9  43 relpgidrsveeqeaeieeleeqlakKrelLk 74 
                 ++  +i+ s++e e+++ +l+e++++ ++ L+
  EPA05778.1 345 KNKGDISSSIDELEKKVSDLQEKIKTEKQRLE 376
                 55567899999999999999999988888775 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.9   0.00039      0.12      65     124 ..     174     237 ..     154     241 .. 0.80
   2 !   10.7   1.5    0.0013      0.41      65     123 ..     350     411 ..     333     417 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00039
        ADIP  65 leaeierlqskierlktqleqlerelalvqakerq....lekklktleqklknekeelqrlkna 124
                 ++a i++l++ki+ l+++ ++ + +l+ v++++++    +++k+ +l + + ++k+el+r k a
  EPA05778.1 174 ITAKITSLENKISGLEQNIASERAKLSGVTNDTTStisdTTQKIVELRNNITKTKDELNRYKLA 237
                 578999*********************9998876522226788888888888889999888765 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0013
        ADIP  65 leaeierlqskierlktqleqlerela.lvqakerqlekkl..ktleqklknekeelqrlkn 123
                 ++++i+ l++k++ l+++ +  +++l+ l +++ r+l+ +l  ++l++ +  ++ +l+r k 
  EPA05778.1 350 ISSSIDELEKKVSDLQEKIKTEKQRLEiLIHQTPRSLTYDLevTKLTENIEHLRNDLNRAKV 411
                 678999*********************9********9976522789999999******9985 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.089        28      60      99 ..     160     199 ..     153     205 .. 0.83
   2 ?    2.7   0.3      0.37   1.2e+02       8      35 ..     211     238 ..     204     240 .. 0.76
   3 !   11.8   0.4   0.00058      0.18      50     105 ..     326     381 ..     313     382 .. 0.83
   4 ?    1.7   0.0      0.79   2.5e+02      74      98 ..     388     412 ..     384     418 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.089
                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
  Prefoldin_2  60 keevkeeLeerketlekeiktlekqleklekeleelkeel 99 
                   +e ++   ++k  ++++i++le++++ le++++  +++l
   EPA05778.1 160 NPESIKATMTNKGGITAKITSLENKISGLEQNIASERAKL 199
                  567778888999999************9999998877776 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.37
                  HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
  Prefoldin_2   8 qqlqqqlqqlaqqikqletqlkelelvl 35 
                  ++++q++ +l ++i++ + +l++ +l+l
   EPA05778.1 211 SDTTQKIVELRNNITKTKDELNRYKLAL 238
                  6778888888888888888888887775 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 0.00058
                  EETTEEEEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCTS- CS
  Prefoldin_2  50 lvGdvlvkqdkeevkeeLeerketlekeiktlekqleklekeleelkeelqkklqq 105
                  ++  v ++++ ++ ++   ++k +++  i++lek+ ++l+++++  k+ l ++++q
   EPA05778.1 326 QINSVQISTENPQSISISLKNKGDISSSIDELEKKVSDLQEKIKTEKQRLEILIHQ 381
                  55666666777777777779999***************************999876 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.79
                  HHHHHHHHHHHHHHHHHHHHHHHHH CS
  Prefoldin_2  74 lekeiktlekqleklekeleelkee 98 
                  ++ e+++l++++e+l+++l+  k e
   EPA05778.1 388 YDLEVTKLTENIEHLRNDLNRAKVE 412
                  6789999999999999999998876 PP

>> NleF_casp_inhib  NleF caspase inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1     0.067        21      33      67 ..     174     208 ..     142     214 .. 0.72
   2 !    9.5   0.5    0.0027      0.84      31      61 ..     211     241 ..     197     302 .. 0.82
   3 !    9.0   1.3    0.0039       1.2       4      63 ..     359     418 ..     356     420 .] 0.92

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.067
  NleF_casp_inhib  33 aeekikElsdkltklknsvlseredlYevedykle 67 
                         ki  l +k+  l +++ ser +l  v +  ++
       EPA05778.1 174 ITAKITSLENKISGLEQNIASERAKLSGVTNDTTS 208
                      456788899****************9888776665 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0027
  NleF_casp_inhib  31 tTaeekikElsdkltklknsvlseredlYev 61 
                      + + +ki+El++++tk k++++ ++  lY  
       EPA05778.1 211 SDTTQKIVELRNNITKTKDELNRYKLALYVE 241
                      335689********************99954 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0039
  NleF_casp_inhib   4 kiteetektlkdIkdklklifereiastTaeekikElsdkltklknsvlseredlYeved 63 
                      k+  + ++ +k  k++l+  +++   s+T + ++  l++++++l n+++  + +++ v++
       EPA05778.1 359 KKVSDLQEKIKTEKQRLEILIHQTPRSLTYDLEVTKLTENIEHLRNDLNRAKVEMFSVLN 418
                      6667899********************************************999998877 PP

>> DUF848  Gammaherpesvirus protein of unknown function (DUF848)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.2      0.01       3.2      54     115 ..     177     235 ..     143     247 .. 0.77
   2 !   10.3   1.2    0.0018      0.56      55     105 ..     354     407 ..     329     417 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.01
      DUF848  54 rtkeikalveavdteieakkkelslLkklnrkkvarveeLtdkvlelkeevsleldsleeaq 115
                 + ++++++++ ++++i     e+++L+ +      ++ + t+k+ el+++++   d+l+ ++
  EPA05778.1 177 KITSLENKISGLEQNIA---SERAKLSGVTNDTTSTISDTTQKIVELRNNITKTKDELNRYK 235
                 44455566666665554...577778889999999*****************9999999876 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0018
      DUF848  55 tkeikalveavdteieakkkelslLkklnrkkva...rveeLtdkvlelkeevs 105
                   e++++v+ ++++i+++k+ l++L++  ++ ++   +v +Lt++++ l+++++
  EPA05778.1 354 IDELEKKVSDLQEKIKTEKQRLEILIHQTPRSLTydlEVTKLTENIEHLRNDLN 407
                 568999*********************9999997544689***********996 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.5   0.00055      0.17      19      82 ..     175     234 ..     173     236 .. 0.91
   2 ?    7.2   1.3     0.022       6.8      19      83 ..     351     410 ..     348     416 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00055
  Snapin_Pallidin  19 deklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqkl 82 
                      ++k+ +l+++ + L +++ ++++kL  + +++     +++    +K+v++++++++ ++ l++ 
       EPA05778.1 175 TAKITSLENKISGLEQNIASERAKLSGVTNDTT----STISDTTQKIVELRNNITKTKDELNRY 234
                      6788899999999*************9999888....99*******************999886 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.022
  Snapin_Pallidin  19 deklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqklk 83 
                       +++ el+++ ++L+e++++++++L+ +  +q     p+  +y   ++++  +++ l + l+++k
       EPA05778.1 351 SSSIDELEKKVSDLQEKIKTEKQRLE-ILIHQT----PRSLTYDLEVTKLTENIEHLRNDLNRAK 410
                      678999999999*************7.666666....5666777777788888888888887776 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1      0.16        51      33      70 ..     175     212 ..     145     234 .. 0.67
   2 ?    9.9   0.1    0.0032         1      46     104 ..     316     376 ..     304     377 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.16
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
    Spectrin  33 leevqallkkhkaleaelaaqqervkalnelaekllde 70 
                  +++ +l++k  +le+++a+++ ++  ++   ++ ++ 
  EPA05778.1 175 TAKITSLENKISGLEQNIASERAKLSGVTNDTTSTISD 212
                 56677888888888888888888888888444433333 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0032
                 HHHHHHHHHHHHHHHH...HHHHHHHHTTHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
    Spectrin  46 leaelaaqqervkaln...elaeklldeghsaseeieerleelnerWeeLkelaaerkqkLe 104
                 l ++++ +  ++++++   e  +++ + + + + +i+++++el+++  +L+e++++ kq+Le
  EPA05778.1 316 LADDISPNSCQINSVQistENPQSI-SISLKNKGDISSSIDELEKKVSDLQEKIKTEKQRLE 376
                 6677888888888888654333444.333477899**************************7 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00064       0.2      10      57 ..     178     224 ..     174     233 .. 0.82
   2 ?    3.6   2.0      0.25        77      16      33 ..     353     370 ..     345     412 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00064
  ABC_tran_CTD  10 leeleaeIeaLEeeiaeleaeladpelysdp.eklaelsaeleeleaeL 57 
                   +  le++I  LE+ ia+  a+l+  +  +d   +++++++++ el++ +
    EPA05778.1 178 ITSLENKISGLEQNIASERAKLSGVT--NDTtSTISDTTQKIVELRNNI 224
                   5689*******************554..888788999999988887765 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.25
  ABC_tran_CTD  16 eIeaLEeeiaeleaelad 33 
                    I++LE++ ++l++++  
    EPA05778.1 353 SIDELEKKVSDLQEKIKT 370
                   455555555555555543 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.3       0.6   1.9e+02       8      31 ..     177     200 ..     173     235 .. 0.63
   2 ?    6.5   0.3     0.034        11       5      26 ..     350     371 ..     348     377 .. 0.81
   3 ?    3.6   0.0      0.29        90      16      34 ..     392     410 ..     386     414 .. 0.58

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.6
         LPP   8 qVsqLkskvdqlssdvnsakaaaq 31 
                  + +L++k++ l+++++s +a + 
  EPA05778.1 177 KITSLENKISGLEQNIASERAKLS 200
                 555666666666666555444443 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.034
         LPP   5 LssqVsqLkskvdqlssdvnsa 26 
                 +ss + +L++kv+ l+++++  
  EPA05778.1 350 ISSSIDELEKKVSDLQEKIKTE 371
                 8999999999999999998765 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.29
         LPP  16 vdqlssdvnsakaaaqaak 34 
                 v +l++++++++++++ ak
  EPA05778.1 392 VTKLTENIEHLRNDLNRAK 410
                 4555555555555555555 PP

>> Shugoshin_N  Shugoshin N-terminal coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.3   8.4e-05     0.027      15      44 ..     170     199 ..     164     200 .. 0.85
   2 ?    0.3   0.1         2   6.4e+02      21      32 ..     215     226 ..     211     231 .. 0.89
   3 ?    4.8   0.2     0.079        25      19      37 ..     350     367 ..     344     369 .. 0.80
   4 ?   -0.8   0.1       4.6   1.4e+03      23      41 ..     392     408 ..     388     411 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 8.4e-05
  Shugoshin_N  15 sNsalslkirelekevseLlsENlnLReli 44 
                  ++  +++ki +le+++s L + + + R+++
   EPA05778.1 170 NKGGITAKITSLENKISGLEQNIASERAKL 199
                  5556899********************997 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 2
  Shugoshin_N  21 lkirelekevse 32 
                  +ki el++ +++
   EPA05778.1 215 QKIVELRNNITK 226
                  89*******997 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.079
  Shugoshin_N  19 lslkirelekevseLlsEN 37 
                  +s  i elek+vs+L +E+
   EPA05778.1 350 ISSSIDELEKKVSDL-QEK 367
                  567799*********.876 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 4.6
  Shugoshin_N  23 irelekevseLlsENlnLR 41 
                  +  l+  +++L++    +R
   EPA05778.1 392 VTKLTENIEHLRND--LNR 408
                  55566666666543..555 PP

>> TraF_2  F plasmid transfer operon, TraF, protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0      0.14        43      24      80 ..     162     222 ..     148     255 .. 0.76
   2 ?    9.0   0.1    0.0026      0.83      23      81 ..     337     405 ..     325     416 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.14
      TraF_2  24 lsvgvevgdvdnlvDkiDdlsdildgleaavnaasad.......etqvdeaaddlnalLedlgg 80 
                  s+ + ++++ +++ ki +l++++ gle++++++ a+       +   ++ + d ++ + +l++
  EPA05778.1 162 ESIKATMTNKGGITAKITSLENKISGLEQNIASERAKlsgvtndT---TSTISDTTQKIVELRN 222
                 58899999********************99999888877654431...3333333333333333 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0026
      TraF_2  23 plsvgvevgdvdnlvDkiDdlsdildgleaavnaasad............etqvdeaaddlnalLedlggd 81 
                 p s+ ++++++ +++  iD+l++++ +l++ +++++++            +   d ++++l++ +e l++d
  EPA05778.1 337 PQSISISLKNKGDISSSIDELEKKVSDLQEKIKTEKQRleilihqtprslT--YDLEVTKLTENIEHLRND 405
                 67999*********************9999999988888888887766441..444444444444444433 PP

>> PI3K_P85_iSH2  Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.2    0.0086       2.7      61     119 ..     142     200 ..     137     236 .. 0.81
   2 ?    6.5   3.2     0.018       5.8      70     118 ..     327     375 ..     317     411 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0086
  PI3K_P85_iSH2  61 ikmFeeqiklqekfskeaqehEieklqenleqlksrlkelhsskekLeedlkqqkeeer 119
                    +++  + +++ +  +k a+++ i+  ++n   +++++ +l+++ + Le+++ ++ ++  
     EPA05778.1 142 ERIEIDTCQTTAVQIKSANPESIKATMTNKGGITAKITSLENKISGLEQNIASERAKLS 200
                    556668899999999999*********************************99887665 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.018
  PI3K_P85_iSH2  70 lqekfskeaqehEieklqenleqlksrlkelhsskekLeedlkqqkeee 118
                    ++   ++  +++ i+   +n  ++ s ++el+++ ++L+e++k++k++ 
     EPA05778.1 327 INSVQISTENPQSISISLKNKGDISSSIDELEKKVSDLQEKIKTEKQRL 375
                    4555555668999999999999*********************999865 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.3     0.094        29      60     118 ..     136     193 ..     129     198 .. 0.78
   2 ?    8.4   1.1    0.0066       2.1      46     105 ..     174     233 ..     166     244 .. 0.69
   3 ?   10.7   1.5    0.0013      0.41      38     106 ..     349     416 ..     343     419 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.094
     DUF1664  60 tkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskle 118
                  + +L++ri+ +d+ +    +i+++  e +++   +   i  +++s+++ ++gle++++
  EPA05778.1 136 KRVKLAERIE-IDTCQTTAVQIKSANPESIKATMTNKGGITAKITSLENKISGLEQNIA 193
                 4567888885.777788888888888888888888889999999999999999998886 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0066
     DUF1664  46 vskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedves 105
                 ++ +++++ ++++   ++++s+ +++    ++++ +++++++++ e+r+++++++++++ 
  EPA05778.1 174 ITAKITSLENKISGLEQNIASERAKLSGVTNDTTSTISDTTQKIVELRNNITKTKDELNR 233
                 556666666777777777777777777777777777777777777777777777777664 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.0013
     DUF1664  38 slsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesv 106
                  +s+ ++++ k++ +++e++++ k++L+  i++  ++l    e++k + e+++++r+dl++ + ++ sv
  EPA05778.1 349 DISSSIDELEKKVSDLQEKIKTEKQRLEILIHQTPRSLTYDLEVTKLT-ENIEHLRNDLNRAKVEMFSV 416
                 567889999**********************************99876.679*******9999988776 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1    0.0019       0.6      12      69 ..     112     171 ..     108     178 .. 0.78
   2 ?    0.8   0.0       1.7   5.5e+02      15      69 ..     290     346 ..     286     354 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0019
                      HHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH..TTTCEEEEE--TTTHHHHHHHHHTT CS
  Sacchrp_dh_NADP  12 avaellarhfdvdaeitvadrskeklealaaka..lgvrfeaialdaenyeavLaallke 69 
                      +++e +a++   ++ei+v++ s++k  +la+ +     + +a+++  +n+e++ a + ++
       EPA05778.1 112 VILEACAKSTVRSPEIVVVSDSEAKRVKLAERIeiDTCQTTAVQIKSANPESIKATMTNK 171
                      68899999987766***********99999988777777777777888888854455544 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 1.7
                      HHHHCTCCT-G.EEEEEESSHHHHHHHHCHH..TTTCEEEEE--TTTHHHHHHHHHTT CS
  Sacchrp_dh_NADP  15 ellarhfdvda.eitvadrskeklealaaka..lgvrfeaialdaenyeavLaallke 69 
                      + +a+ + + a ei v +  +++  +la+++  ++ +++++++  en+++ ++  lk 
       EPA05778.1 290 QICAKDKAIHApEILVTSDFETQSVRLADDIspNSCQINSVQISTENPQS-ISISLKN 346
                      67899999988999999999999999999998888888899999999998.4444443 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.9    0.0086       2.7      44     147 ..     137     241 ..     115     251 .. 0.64
   2 ?    8.9   1.1    0.0062         2      35     102 ..     343     412 ..     308     419 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0086
        Fez1  44 rakleekeeeikeleesleektlelevcenelqrk...kseaellrekvekleeelkelreelselsleeeeaalesdeakaqrqeaeeleelkrever 139
                 r kl e+ e  +   ++++ k+++ e +++ + +k   +++ + l++k++ le+++++ r +ls ++++++++++++++ k  +  ++++++ k e++r
  EPA05778.1 137 RVKLAERIEIDTCQTTAVQIKSANPESIKATMTNKggiTAKITSLENKISGLEQNIASERAKLSGVTNDTTSTISDTTQ-KIVEL-RNNITKTKDELNR 233
                 4455554433333344556677777777777777777778888899999999999999999999887766665544444.32222.3567777777777 PP

        Fez1 140 lraeLkee 147
                  + +L  e
  EPA05778.1 234 YKLALYVE 241
                 77766665 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0062
        Fez1  35 alkaqlrelrakleekeeeikeleesleektlelevcenelqrk...kseaellrekvekleeelkelree 102
                 +lk++  +++++++e e+++++l+e++++ ++ le + ++  r+     e++ l e++e+l ++l++ + e
  EPA05778.1 343 SLKNK-GDISSSIDELEKKVSDLQEKIKTEKQRLEILIHQTPRSltyDLEVTKLTENIEHLRNDLNRAKVE 412
                 55544.47888999999999999999999999999999998888554445666666666666666666554 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.4    0.0012      0.37       1      48 [.     177     225 ..     177     232 .. 0.86
   2 ?    7.4   0.7     0.019       5.9       2      24 ..     354     376 ..     349     381 .. 0.84
   3 ?   -1.3   0.1       9.2   2.9e+03       2      10 ..     399     407 ..     389     416 .. 0.49

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0012
   FlaC_arch   1 ridelEnklsklsteletvkkeneels.ksveelkenVkdllsLYEvVs 48 
                 +i +lEnk+s l+ ++++ +++++ +  ++  ++ ++ +++++L   ++
  EPA05778.1 177 KITSLENKISGLEQNIASERAKLSGVTnDTTSTISDTTQKIVELRNNIT 225
                 899**********************971567789999999999866655 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.019
   FlaC_arch   2 idelEnklsklsteletvkkene 24 
                 idelE+k+s+l+ +++t k+ +e
  EPA05778.1 354 IDELEKKVSDLQEKIKTEKQRLE 376
                 79999999999999999887776 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 9.2
   FlaC_arch   2 idelEnkls 10 
                 i+ l n+l+
  EPA05778.1 399 IEHLRNDLN 407
                 233333343 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.7    0.0028      0.88     206     280 ..     159     233 ..     141     240 .. 0.82
   2 ?    6.7   0.7     0.015       4.7      22      77 ..     356     413 ..     310     419 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0028
                 XXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
    Filament 206 knsealrsakeeitelrrqiqsleieleslkkqkasleaqlaeleerleaeleklqeklseleeelaeireemar 280
                  n e+++++ ++   +  +i sle +++ l+++ as +a+l+ + +   + ++++ +k+ el ++++++++e++r
  EPA05778.1 159 ANPESIKATMTNKGGITAKITSLENKISGLEQNIASERAKLSGVTNDTTSTISDTTQKIVELRNNITKTKDELNR 233
                 455666777777777788999999999999999999999999999999999999999999999999999999887 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.015
                 XXXXXXXXXXXXXXXXXXXX..XXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
    Filament  22 aLEqenkeLeakieeleekk..saevsklkelyekeleelrkqldeltkerarlqlel 77 
                  LE++ ++L+ ki+  +++     +++  + +y  e+++l +++++l ++ +r+++e+
  EPA05778.1 356 ELEKKVSDLQEKIKTEKQRLeiLIHQTPRSLTYDLEVTKLTENIEHLRNDLNRAKVEM 413
                 4666666666666666666423233333455666666666666666666666666665 PP

>> DUF1137  Protein of unknown function (DUF1137)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.33   1.1e+02      31      55 ..      18      42 ..       4      63 .. 0.82
   2 ?    7.1   0.0     0.017       5.3       9      51 ..     263     305 ..     256     330 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.33
     DUF1137 31 dkscmelhlsdaslackellsklsg 55
                 k  m+l +s  ++ cke l +++ 
  EPA05778.1 18 PKKQMKLNFSSDDVVCKEGLIRVTN 42
                5788**************9988875 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.017
     DUF1137   9 ikklgvrkriispekqlfyctvdkscmelhlsdaslackells 51 
                 + kl v+k  i p+ ql +  +  s +++   d +++  e+l 
  EPA05778.1 263 LTKLSVHKSNIQPQTQLKNILMYNSLFQICAKDKAIHAPEILV 305
                 579**********************************999985 PP

>> ApoO  Apolipoprotein O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   0.00095       0.3       9      61 ..     180     233 ..     157     241 .. 0.88
   2 ?    0.2   0.1       2.1   6.8e+02      26      51 ..     356     381 ..     340     409 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00095
        ApoO   9 s.eeptdrLeegvrslRkslepytsavqdelnkvkskvetaeqsvtdtiasLke 61 
                 s e++ + Le++++s R  l+  t+ ++++++++++k+ ++ +++t+t ++L+ 
  EPA05778.1 180 SlENKISGLEQNIASERAKLSGVTNDTTSTISDTTQKIVELRNNITKTKDELNR 233
                 25889999****************************************999986 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 2.1
        ApoO  26 slepytsavqdelnkvkskvetaeqs 51 
                 +le+++s +q+++++ k+++e + ++
  EPA05778.1 356 ELEKKVSDLQEKIKTEKQRLEILIHQ 381
                 44555555555555555555544444 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.8   0.00085      0.27     182     273 ..     145     236 ..     128     255 .. 0.82
   2 ?    4.6   0.8      0.04        13     167     192 ..     352     377 ..     308     416 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00085
        Spc7 182 eleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlke 273
                 e+++ q+ a +++s ++e+++++  +   + a+i +++++++ l++++++ ++k++ +++  +++ +++ ++   l+++   +++e++r+k 
  EPA05778.1 145 EIDTCQTTAVQIKSANPESIKATMTNKGGITAKITSLENKISGLEQNIASERAKLSGVTNDTTSTISDTTQKIVELRNNITKTKDELNRYKL 236
                 67788999999999999999999999999999999999999999999999999999999999999998887777777777777888888875 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.04
        Spc7 167 ellpeleeekaeleeeleklqeaaee 192
                 +  +ele++ ++l+e++++++++ e 
  EPA05778.1 352 SSIDELEKKVSDLQEKIKTEKQRLEI 377
                 22233333333333333333332222 PP

>> ACCA  Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.5    0.0063         2       4      60 ..     181     237 ..     176     241 .. 0.88
   2 ?    6.1   1.2      0.03       9.3      22      55 ..     343     376 ..     323     410 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0063
        ACCA   4 fekpiaeleekieelkklaeesevdlseeieklekkleklkkeiyknltpwqkvqla 60 
                  e++i+ le++i++ ++  +  + d++++i+++ +k+ +l+++i+k+ +++++ +la
  EPA05778.1 181 LENKISGLEQNIASERAKLSGVTNDTTSTISDTTQKIVELRNNITKTKDELNRYKLA 237
                 68899999999999888888899999******************9999999998887 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.03
        ACCA  22 aeesevdlseeieklekkleklkkeiyknltpwq 55 
                 + +++ d+s++i++lekk+++l+++i+++ ++++
  EPA05778.1 343 SLKNKGDISSSIDELEKKVSDLQEKIKTEKQRLE 376
                 4557778888888888888888888875544433 PP

>> Leu_zip  Leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.5     0.001      0.32     157     245 ..     151     233 ..     126     246 .. 0.52
   2 ?    5.8   1.6     0.026       8.3     159     230 ..     343     414 ..     305     419 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.001
     Leu_zip 157 tsaleeksklekalkelqkelgekkdekenskeiskleeklaelkldlektleektasaksleedlastkhelLkvqeqLelaekeLek 245
                 t+a++ ks+  +++k++ ++ g        +++i++le+k++ l++++ ++  + +  +++ ++ + +t +++++++++++ ++ eL++
  EPA05778.1 151 TTAVQIKSANPESIKATMTNKGG------ITAKITSLENKISGLEQNIASERAKLSGVTNDTTSTISDTTQKIVELRNNITKTKDELNR 233
                 34444444444444444332222......233455555555555555555555555555555555555555555555555555555543 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.026
     Leu_zip 159 aleeksklekalkelqkelgekkdeke.nskeiskleeklaelkldlektleektasaksleedlastkhelL 230
                 +l++k  ++++++el+k++++ +++ + ++++++ l  + +   l ++ ++++ t++ ++l++dl  +k e+ 
  EPA05778.1 343 SLKNKGDISSSIDELEKKVSDLQEKIKtEKQRLEILI-HQTPRSLTYDLEVTKLTENIEHLRNDLNRAKVEMF 414
                 4455555555555555555554444331233333222.22222233333344455555556666655555555 PP

>> USP8_interact  USP8 interacting
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1      0.11        35      12      66 ..     177     234 ..     168     247 .. 0.49
   2 ?    6.2   0.3     0.025         8      10      60 ..     351     401 ..     346     417 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.11
  USP8_interact  12 kiaelkkevaeqkqqlseqkrelell.keyiralrstnpvlraladqler..devlrW 66 
                    ki++l+++++  +q++++++ +l+ + +++  ++  t++++ +l +++++  de+ r+
     EPA05778.1 177 KITSLENKISGLEQNIASERAKLSGVtNDTTSTISDTTQKIVELRNNITKtkDELNRY 234
                    4555555555555555555555543313333444444444444444442222444333 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.025
  USP8_interact  10 qqkiaelkkevaeqkqqlseqkrelellkeyiralrstnpvlraladqler 60 
                    +++i el+k+v++ +++++++k+ le+l +      + + ++++l++++e+
     EPA05778.1 351 SSSIDELEKKVSDLQEKIKTEKQRLEILIHQTPRSLTYDLEVTKLTENIEH 401
                    567889999999999999999999998877665554555555555544443 PP

>> DUF148  Domain of unknown function DUF148
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   2.3     0.001      0.32      44      95 ..     174     225 ..     159     232 .. 0.88
   2 ?    1.8   0.1      0.81   2.6e+02      34      56 ..     351     373 ..     341     411 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.001
      DUF148  44 vkaqkeevkknvtavisnLssvqekleaIldnkslTrkeqkeaieelkkqyp 95 
                 ++a+ ++++++++   +n++s  +kl+ ++++++ T+ +++++i el+++  
  EPA05778.1 174 ITAKITSLENKISGLEQNIASERAKLSGVTNDTTSTISDTTQKIVELRNNIT 225
                 68888999999999999******************************99865 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.81
      DUF148  34 tdeykefeakvkaqkeevkknvt 56 
                 ++ + e+e+kv++ +e++k + +
  EPA05778.1 351 SSSIDELEKKVSDLQEKIKTEKQ 373
                 33444444444444444443332 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   2.2     0.002      0.63      11      69 ..     177     232 ..     155     236 .. 0.88
   2 ?    6.5   4.3     0.025       7.8      17     111 ..     311     411 ..     293     415 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.002
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTT CS
  Laminin_II  11 takevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklap 69 
                 ++++ ++++ +l+qn+  +++kls++ ++   t+  ++d ++ i++ r+++ k + +++
  EPA05778.1 177 KITSLENKISGLEQNIASERAKLSGVTND---TTSTISDTTQKIVELRNNITKTKDELN 232
                 56777889999****************99...999*********999999988777766 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.025
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH..........HHHHHHHHHHHHHHHHHHHHT CS
  Laminin_II  17 eqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeasss.......lsdniseikelIaqARkaAnk 108
                  q   l+ +++  + ++++++ s  e  + ++ + k   d ++s+ +Lek++ +L +k+k+ kq+ e              ++ ++ e I+  R+  n+
  EPA05778.1 311 TQSVRLADDISPNSCQINSVQIS-TENPQSISISLKNKGDISSSIDELEKKVSDLQEKIKTEKQRLEILIHqtprsltYDLEVTKLTENIEHLRNDLNR 408
                 55556778888888899999988.7778888888899999999999**********9999999887643223344433333444555555555555555 PP

                 --- CS
  Laminin_II 109 ikv 111
                  kv
  EPA05778.1 409 AKV 411
                 555 PP

>> FliJ  Flagellar FliJ protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0     0.021       6.6      12      71 ..     176     234 ..     168     239 .. 0.85
   2 ?    2.5   0.8       0.5   1.6e+02      14      70 ..     354     408 ..     345     415 .. 0.46

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.021
        FliJ  12 relqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqa 71 
                 +++++ e+k+  leq++++ + +lsg + + + + +  + + i  l++ i+++k el++ 
  EPA05778.1 176 AKITSLENKISGLEQNIASERAKLSGVT-NDTTSTISDTTQKIVELRNNITKTKDELNRY 234
                 678999*******************998.7777888888888899999999998888775 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.5
        FliJ  14 lqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaq 70 
                 +++ e+k+  l++ ++  +++l+      +  +  +y     +l e i++++++l++
  EPA05778.1 354 IDELEKKVSDLQEKIKTEKQRLEILI--HQTPRSLTYDLEVTKLTENIEHLRNDLNR 408
                 33344444444444444444443333..33334444444444555555555555554 PP

>> THOC7  Tho complex subunit 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   1.7     0.028       8.8      58     106 ..     184     232 ..     133     237 .. 0.79
   2 ?    7.8   1.4     0.012       3.8      77     122 ..     354     399 ..     328     412 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.028
       THOC7  58 rlqllakanerereryeaekeeieseieavreeieelkaqLeearatra 106
                 ++  l++  + er+++   ++++ s+i+++ ++i+el++ +++ + +++
  EPA05778.1 184 KISGLEQNIASERAKLSGVTNDTTSTISDTTQKIVELRNNITKTKDELN 232
                 6677778888888888888899999999999999999999999888765 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.012
       THOC7  77 keeieseieavreeieelkaqLeearatranrkeydelaekItsnp 122
                  +e+e++ ++++e+i+ +k++Le    +  +  +yd +++k+t+n 
  EPA05778.1 354 IDELEKKVSDLQEKIKTEKQRLEILIHQTPRSLTYDLEVTKLTENI 399
                 579999************************************9985 PP

>> DUF4094  Domain of unknown function (DUF4094)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.4    0.0019       0.6      43      88 .]     147     198 ..     120     198 .. 0.67
   2 ?    0.4   0.1       2.8   8.7e+02      55      83 ..     204     232 ..     199     236 .. 0.82
   3 ?    7.1   0.4     0.023       7.3      54      87 ..     340     373 ..     299     374 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0019
     DUF4094  43 edcds.....kdaesr.skdilgevskthkaiqtLdktissLemeLaaarae 88 
                 + c++     k a+ +  k  + + +     i++L+++is Le+ +a++ra+
  EPA05778.1 147 DTCQTtavqiKSANPEsIKATMTNKGGITAKITSLENKISGLEQNIASERAK 198
                 455554543322222255566666677777899*****************85 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 2.8
     DUF4094  55 kdilgevskthkaiqtLdktissLemeLa 83 
                 +d  + +s+t + i  L + i +   eL 
  EPA05778.1 204 NDTTSTISDTTQKIVELRNNITKTKDELN 232
                 56777899999999999999999998886 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.023
     DUF4094  54 skdilgevskthkaiqtLdktissLemeLaaara 87 
                  +  l++ ++ ++ i  L+k++s L+ ++ ++++
  EPA05778.1 340 ISISLKNKGDISSSIDELEKKVSDLQEKIKTEKQ 373
                 3355667778888999***********9999886 PP

>> Cnn_1N  Centrosomin N-terminal motif 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.3     0.033        10      21      63 ..     183     235 ..     174     239 .. 0.79
   2 ?   -0.7   0.0       5.3   1.7e+03      37      54 ..     264     281 ..     247     286 .. 0.79
   3 ?    5.9   3.1     0.046        14       6      64 ..     351     411 ..     349     416 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.033
      Cnn_1N  21 LriyfLeerleklse..........eqkeellkenielkveveslqkelkekk 63 
                  +i  Le+++   +           +++ ++ ++ +el+ ++ + ++el+++k
  EPA05778.1 183 NKISGLEQNIASERAklsgvtndttSTISDTTQKIVELRNNITKTKDELNRYK 235
                 466666666555555677777788899***********************998 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 5.3
      Cnn_1N  37 qkeellkenielkveves 54 
                 +k +++k+ni+ ++++++
  EPA05778.1 264 TKLSVHKSNIQPQTQLKN 281
                 566789999999999987 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.046
      Cnn_1N   6 eeqidkLkKENFdLKLriyfLeerleklseeqkeellk..enielkveveslqkelkekkk 64 
                 +++id+L+K   dL+ +i++ ++rle l  ++ ++l    e ++l +++e+l+++l++ k 
  EPA05778.1 351 SSSIDELEKKVSDLQEKIKTEKQRLEILIHQTPRSLTYdlEVTKLTENIEHLRNDLNRAKV 411
                 679***********************99998888887533678999999999999988775 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.6    0.0039       1.2       9      66 ..     174     232 ..     173     245 .. 0.88
   2 ?    5.5   1.9     0.073        23      40      59 ..     350     369 ..     314     416 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0039
     NPV_P10   9 IradikavddkVdalqqqvddvqenlpdvte.lnekLdaqsaqLaeletkvenIqdiLn 66 
                 I a i+ +++k++ l+q++++ +++l  vt+  ++ + + ++++ el +++++ +d Ln
  EPA05778.1 174 ITAKITSLENKISGLEQNIASERAKLSGVTNdTTSTISDTTQKIVELRNNITKTKDELN 232
                 778899*******************9999852678899999***********9999999 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.073
     NPV_P10  40 lnekLdaqsaqLaeletkve 59 
                 +++ +d++ +++ +l++k++
  EPA05778.1 350 ISSSIDELEKKVSDLQEKIK 369
                 44444444444444444433 PP

>> Ax_dynein_light  Axonemal dynein light chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.9     0.036        11     120     169 ..     170     219 ..     148     235 .. 0.59
   2 ?    7.9   1.8    0.0087       2.7     129     186 ..     348     407 ..     330     411 .. 0.62

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.036
  Ax_dynein_light 120 gkselekkikeLeeekeelekqvaelkaklealekrekerrqeeekkhee 169
                      +k  +++ki++Le++ + le+++a+ +akl+ + ++ +   +  ++k  e
       EPA05778.1 170 NKGGITAKITSLENKISGLEQNIASERAKLSGVTNDTTSTISDTTQKIVE 219
                      33344555777777777777777777777776666666555555544444 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0087
  Ax_dynein_light 129 keLeeekeelekqvaelkaklealekrekerrqeeek..kheeeieflkksnqqlkeqle 186
                       ++ +  +elek+v++l++k++++++r +   ++  +   ++ e+++l ++ ++l++ l+
       EPA05778.1 348 GDISSSIDELEKKVSDLQEKIKTEKQRLEILIHQTPRslTYDLEVTKLTENIEHLRNDLN 407
                      455666667777777777777777777665544443311455566666677777776665 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   2.5    0.0032         1       8      67 ..     174     233 ..     160     236 .. 0.65
   2 ?    4.9   2.6     0.079        25       7      39 ..     342     374 ..     334     413 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0032
        FlxA   8 ssssssgsasqiasLqkQiknlqkqLkelsesdeltkeekkkqqqliqaQIqqlqaQIaq 67 
                  +++ ++ +++i+ L++ i++   +L+ ++++++ t  +  +++ ++ + I++ + ++ +
  EPA05778.1 174 ITAKITSLENKISGLEQNIASERAKLSGVTNDTTSTISDTTQKIVELRNNITKTKDELNR 233
                 333444555666666666666666666777777888888888888888888877766655 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.079
        FlxA   7 sssssssgsasqiasLqkQiknlqkqLkelses 39 
                  s +++ +++s i +L+k +++lq+++k  ++ 
  EPA05778.1 342 ISLKNKGDISSSIDELEKKVSDLQEKIKTEKQR 374
                 566778889999999999999999999987765 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   2.1     0.023       7.4      98     182 ..     144     232 ..     133     238 .. 0.67
   2 ?    6.7   0.7     0.018       5.7     125     180 ..     347     412 ..     308     419 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.023
      DUF724  98 lslkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallk...........ekkeaadkeiarlkseaekleeeledveqeFe 182
                 +++ + qt + + +++  ++i+   ++k  + ++i  le+ki+ le++ a+ +           +        i++  ++  +l++++ ++++e +
  EPA05778.1 144 IEIDTCQTTAVQIKSANPESIKATMTNKGGITAKITSLENKISGLEQNIASERaklsgvtndttS-------TISDTTQKIVELRNNITKTKDELN 232
                 56666677777777777788888888999999999999999999999998888778755444444.......444444444444444444444443 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.018
      DUF724 125 krkleeeidelekkilelerqlallk..........ekkeaadkeiarlkseaekleeeledveqe 180
                 k  ++++idelekk+++l+++ ++ k           +  + d e+ +l  + e+l+++l++++ e
  EPA05778.1 347 KGDISSSIDELEKKVSDLQEKIKTEKqrleilihqtPRSLTYDLEVTKLTENIEHLRNDLNRAKVE 412
                 445566666777777777766666665565655555445555666666666666666666666655 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   2.2     0.009       2.8       8      67 ..     174     231 ..     170     240 .. 0.80
   2 ?    6.3   3.3     0.038        12      28      89 ..     347     409 ..     320     413 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.009
  Syntaxin_2   8 insnvstleklvkqLgtkkdteelreklhelieeinelikktnellkklsqldnsssdsq 67 
                 i+ ++++le++++ L+ +      r kl  ++++++ +i++t++++ +l +++ +++d+ 
  EPA05778.1 174 ITAKITSLENKISGLEQN--IASERAKLSGVTNDTTSTISDTTQKIVELRNNITKTKDEL 231
                 566788888888888776..5666899999999999999999999999999999997653 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.038
  Syntaxin_2  28 teelreklhelieeinelikktnellkklsqldnsssds.qqklqkekLkkdfkealqeFqki 89 
                   ++ ++++el +++++l +k++   ++l+ l+++++ s +  l+  kL++ ++++ + ++++
  EPA05778.1 347 KGDISSSIDELEKKVSDLQEKIKTEKQRLEILIHQTPRSlTYDLEVTKLTENIEHLRNDLNRA 409
                 455778889999999999999999999999999998887877778888888877777766665 PP

>> BST2  Bone marrow stromal antigen 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.5    0.0054       1.7      35      89 ..     141     199 ..     133     201 .. 0.78
   2 ?    1.7   0.1       1.3   4.1e+02      60      84 ..     209     233 ..     202     238 .. 0.75
   3 ?    4.6   1.5      0.15        48      60      83 ..     353     376 ..     321     384 .. 0.63
   4 ?    0.7   0.1       2.7   8.4e+02      67      88 ..     391     412 ..     376     414 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0054
                 HHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
        BST2  35 eaeaqaatcnqtvvtLk....asLekekaqsqkqqakvqelqgeikkLnqkLqdaeaev 89 
                     ++ tc+ t v++k    +s++   +++    ak+  l+++i  L+q++   +a++
  EPA05778.1 141 AERIEIDTCQTTAVQIKsanpESIKATMTNKGGITAKITSLENKISGLEQNIASERAKL 199
                 5567889*********93333356666777777899****************9998876 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 1.3
                 HHHHHHHHHHHHHHHHHHHHHHHHH CS
        BST2  60 qsqkqqakvqelqgeikkLnqkLqd 84 
                    +  +k+ el+++i+k +++L+ 
  EPA05778.1 209 TISDTTQKIVELRNNITKTKDELNR 233
                 4556677889999999999998875 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.15
                 HHHHHHHHHHHHHHHHHHHHHHHH CS
        BST2  60 qsqkqqakvqelqgeikkLnqkLq 83 
                    + ++kv +lq++ik+ +q+L+
  EPA05778.1 353 SIDELEKKVSDLQEKIKTEKQRLE 376
                 234445566666666666666664 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 2.7
                 HHHHHHHHHHHHHHHHHHHHHH CS
        BST2  67 kvqelqgeikkLnqkLqdaeae 88 
                 +v +l ++i++L + L+ a+ e
  EPA05778.1 391 EVTKLTENIEHLRNDLNRAKVE 412
                 6778888888888888888766 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.5    0.0047       1.5       7      74 ..     144     215 ..     139     239 .. 0.59
   2 ?    3.0   4.5      0.33     1e+02      36      92 ..     353     409 ..     335     417 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0047
  Tropomyosin_1   7 leaeeaqekaeele....ekvKeleqenlekeqeiksLtkknqqleeevekleeklkeakekaeesekkktn 74 
                    +e ++ q+ a +++    e++K+   ++     +i+sL++k++ le+++    +kl+ +++   ++ ++ t+
     EPA05778.1 144 IEIDTCQTTAVQIKsanpESIKATMTNKGGITAKITSLENKISGLEQNIASERAKLSGVTNDTTSTISDTTQ 215
                    555555555555551111334555555555567788888888888888888888887777666555444444 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.33
  Tropomyosin_1  36 eiksLtkknqqleeevekleeklkeakekaeesekkktnnealtrkiqlLEeelees 92 
                     i +L+kk++ l+e++ + +++l+   ++   s + + +  +lt  i+ L ++l+++
     EPA05778.1 353 SIDELEKKVSDLQEKIKTEKQRLEILIHQTPRSLTYDLEVTKLTENIEHLRNDLNRA 409
                    455666666666666666666666666666666666666667777777777776666 PP

>> LUC7  LUC7 N_terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.4      0.34   1.1e+02      87     141 ..     179     230 ..     140     239 .. 0.78
   2 ?    8.8   1.2    0.0036       1.1      86     142 ..     354     406 ..     347     413 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.34
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXX CS
        LUC7  87 rfleklledvdrkiqkgkqrleltqeekeeeeeakakkqeqlkeleekiekllae 141
                 + le+ ++ +++ i+  +++l+  +++++++ +    +++++ el ++i+k+ +e
  EPA05778.1 179 TSLENKISGLEQNIASERAKLSGVTNDTTSTISD---TTQKIVELRNNITKTKDE 230
                 5677778888888999999998877777666655...488888888888887665 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0036
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXX CS
        LUC7  86 lrfleklledvdrkiqkgkqrleltqeekeeeeeakakkqeqlkeleekiekllaea 142
                 +++lek ++d+++ki++ kqrle   +++ ++ +     + ++ +l+e+ie+l ++ 
  EPA05778.1 354 IDELEKKVSDLQEKIKTEKQRLEILIHQTPRSLT----YDLEVTKLTENIEHLRNDL 406
                 67899******************77766654443....3677888888887776554 PP

>> DUF1192  Protein of unknown function (DUF1192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.66   2.1e+02      27      51 ..     176     200 ..     173     204 .. 0.72
   2 ?    0.1   0.0       2.8   8.8e+02      23      42 ..     218     237 ..     213     239 .. 0.80
   3 ?    5.0   0.5     0.079        25      21      37 ..     353     369 ..     345     381 .. 0.86
   4 ?    1.1   0.1       1.4   4.3e+02      20      40 ..     390     410 ..     379     414 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.66
     DUF1192  27 erIalLeaEIaRleaaiakkkasra 51 
                 + I+ Le  I  le+ ia+ +a+ +
  EPA05778.1 176 AKITSLENKISGLEQNIASERAKLS 200
                 6777788888888888887777765 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 2.8
     DUF1192  23 eELeerIalLeaEIaRleaa 42 
                  EL++ I++ ++E  R + a
  EPA05778.1 218 VELRNNITKTKDELNRYKLA 237
                 58999999999999887765 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.079
     DUF1192  21 SveELeerIalLeaEIa 37 
                 S++ELe+ +++L++ I+
  EPA05778.1 353 SIDELEKKVSDLQEKIK 369
                 9************9775 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 1.4
     DUF1192  20 LSveELeerIalLeaEIaRle 40 
                 L v+ L+e I++L+    R++
  EPA05778.1 390 LEVTKLTENIEHLRNDLNRAK 410
                 567777788888877777765 PP

>> DUF1515  Protein of unknown function (DUF1515)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.2     0.008       2.5       9      78 ..     170     236 ..     163     239 .. 0.88
   2 ?    0.6   0.5       1.8   5.7e+02       8      34 ..     352     378 ..     346     411 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.008
     DUF1515   9 qlgtllaevkelredlkrsedrsdasrakmyrkmdelvervtalegsvvklkaditsvkevtedvkkwkl 78 
                 + g + a+++ l +++   e+  ++ rak+   +++    ++ +   +v+l+++it+ k+   +++++kl
  EPA05778.1 170 NKGGITAKITSLENKISGLEQNIASERAKLSGVTNDTTSTISDTTQKIVELRNNITKTKD---ELNRYKL 236
                 4577899*************************************************9984...6666665 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1.8
     DUF1515   8 qqlgtllaevkelredlkrsedrsdas 34 
                  ++++l ++v +l+e++k  ++r ++ 
  EPA05778.1 352 SSIDELEKKVSDLQEKIKTEKQRLEIL 378
                 566777888888888888777776654 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   4.0     0.015       4.7      34      95 ..     172     232 ..     150     238 .. 0.67
   2 ?    6.3   1.6      0.03       9.3      34      88 ..     348     407 ..     323     418 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.015
  Baculo_PEP_C  34 aqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnlnsilt 95 
                   + +++ ++++e++++ l++++ s  a+l+   ++++++++d+ +++  +lrn++t ++ +l+
    EPA05778.1 172 GGITAKITSLENKISGLEQNIASERAKLSGVTNDTTSTISDTTQKIV-ELRNNITKTKDELN 232
                   55666677777777777777777666666666666666666666666.56666666666655 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.03
  Baculo_PEP_C  34 aqlatlldaietqLnalsedlksllaeldtrldtlltnLtdaln..alq...dtlrneLt 88 
                   +++++ +d++e+++++l+e++k   + l+  ++++   Lt  l   +l+   + lrn+L+
    EPA05778.1 348 GDISSSIDELEKKVSDLQEKIKTEKQRLEILIHQTPRSLTYDLEvtKLTeniEHLRNDLN 407
                   667777777777777777777776666666555555555544330033344444444444 PP

>> HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interacting protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.2       0.1        33      33      75 ..     196     238 ..     166     249 .. 0.81
   2 ?    5.9   1.6     0.063        20      21      70 ..     364     415 ..     333     419 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.1
  HIP1_clath_bdg  33 eeelerlkeeaerkleeqkeelekLkreleakraelarlkssL 75 
                       +l  +++++++ +++ ++++ +L+++++++++el+r k +L
      EPA05778.1 196 RAKLSGVTNDTTSTISDTTQKIVELRNNITKTKDELNRYKLAL 238
                     567888889999999999999999************9999887 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.063
  HIP1_clath_bdg  21 aqeeverekkeleeelerlkeeaerkle..eqkeelekLkreleakraelar 70 
                      qe +++ek++le  +++  ++ +  le  + +e++e+L+++l++ + e+ +
      EPA05778.1 364 LQEKIKTEKQRLEILIHQTPRSLTYDLEvtKLTENIEHLRNDLNRAKVEMFS 415
                     5889999999999999999888777666547789999999999999998755 PP

>> Uso1_p115_C  Uso1 / p115 like vesicle tethering protein, C terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0       1.3   4.1e+02      87     104 ..     128     145 ..     127     162 .. 0.88
   2 ?    2.7   0.5      0.51   1.6e+02      22      72 ..     176     228 ..     157     238 .. 0.55
   3 ?    8.9   1.3     0.006       1.9      13      72 ..     350     410 ..     333     413 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 1.3
  Uso1_p115_C  87 lllgDleeKvekykarLk 104
                  ++++D e+K+ k+ +r++
   EPA05778.1 128 VVVSDSEAKRVKLAERIE 145
                  899***********9987 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.51
  Uso1_p115_C  22 aelqslskalesleqk..eakkaaesqakeleaenkklekeleklraelkeek 72 
                  a++ sl++++  leq   ++ ++ + + +++ ++++ +++++ +lr ++ + k
   EPA05778.1 176 AKITSLENKISGLEQNiaSERAKLSGVTNDTTSTISDTTQKIVELRNNITKTK 228
                  55555666666666664444444444444444444444444444444444333 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.006
  Uso1_p115_C  13 lkdeneklkaelqslskalesleqk.eakkaaesqakeleaenkklekeleklraelkeek 72 
                  +++   +l++++++l+++++ ++q  e + +++ ++ +++ e+ kl++++e lr  l+ +k
   EPA05778.1 350 ISSSIDELEKKVSDLQEKIKTEKQRlEILIHQTPRSLTYDLEVTKLTENIEHLRNDLNRAK 410
                  45556677777777777777777779999999**********************9998776 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   1.3     0.086        27      10      88 ..     160     236 ..     154     244 .. 0.66
   2 ?    6.5   3.0     0.031       9.7      38     101 ..     354     417 ..     329     419 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.086
                   -HHHHHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT.S-TCCCCCCCHHHHHHHHHHHH CS
  Seryl_tRNA_N  10 npeavkeklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkk.edaeeliaevkelkeelkalea 88 
                   npe +k+ + ++g+     +++ +l++k   l++ + + +a+   +++   + + +  +++ el++ + + k+el++++ 
    EPA05778.1 160 NPESIKATMTNKGG---ITAKITSLENKISGLEQNIASERAKLSGVTNDTTSTISDTtQKIVELRNNITKTKDELNRYKL 236
                   89999999998884...566666666666666666666666555555444444444445688888888888888887765 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.031
                   HHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH CS
  Seryl_tRNA_N  38 rrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaelekll 101
                     el++++ +lq++ ++  +  + ++ +         ev +l e++++l ++l+ ++ e+ ++l
    EPA05778.1 354 IDELEKKVSDLQEKIKTEKQRLEILIHQTPRSLTYDLEVTKLTENIEHLRNDLNRAKVEMFSVL 417
                   3355566666666666666666666666666667888888888888888888888888877665 PP

>> DUF5001  Ig-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.2    0.0015      0.48      32      82 ..     133     182 ..     130     186 .. 0.86
   2 ?    1.1   0.3       1.1   3.6e+02       8      25 ..     334     351 ..     326     395 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0015
                 S--TTEE--SEEEE-TTEEEEEEEEE-TT---EEEEEEEEEEEEETTEEEE CS
     DUF5001  32 seytfynypevitipanstttvviktkekkesidlkfeVlNaliapdkhle 82 
                 se++ ++ +e+i+i   +tt v+ik  +++esi+ +++  + ++a  ++le
  EPA05778.1 133 SEAKRVKLAERIEIDTCQTTAVQIK-SANPESIKATMTNKGGITAKITSLE 182
                 566778999****************.********99998888888766665 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 1.1
                 ...TTEEEEEEEE-SSS- CS
     DUF5001   8 ytetkvleveikNkSdid 25 
                 +++ +++++++kNk di 
  EPA05778.1 334 TENPQSISISLKNKGDIS 351
                 334888999999998885 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0       1.8   5.6e+02      89     116 ..     174     201 ..     159     205 .. 0.62
   2 ?    3.3   0.3      0.23        73      88     116 ..     205     233 ..     199     235 .. 0.85
   3 ?    7.2   0.7     0.015       4.7      80     111 ..     341     372 ..     329     379 .. 0.84
   4 ?    1.8   0.1       0.7   2.2e+02      93     115 ..     392     414 ..     387     419 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 1.8
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
   Prefoldin  89 lekqlekleeeleklkdqittleanlaq 116
                 +++ +++le+++  l ++i + +a+l+ 
  EPA05778.1 174 ITAKITSLENKISGLEQNIASERAKLSG 201
                 5556666666666666666665555555 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.23
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
   Prefoldin  88 elekqlekleeeleklkdqittleanlaq 116
                 + ++++ + ++++ +l+++it++ ++l++
  EPA05778.1 205 DTTSTISDTTQKIVELRNNITKTKDELNR 233
                 66788899999999999999999999876 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.015
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
   Prefoldin  80 ellkkkleelekqlekleeeleklkdqittle 111
                  +  k++ ++++++++le+++ +l+++i+t  
  EPA05778.1 341 SISLKNKGDISSSIDELEKKVSDLQEKIKTEK 372
                 555689999*******************9865 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.7
                 HHHHHHHHHHHHHHHHHHHHHHH CS
   Prefoldin  93 lekleeeleklkdqittleanla 115
                 ++kl+e++e l++ ++ + +++ 
  EPA05778.1 392 VTKLTENIEHLRNDLNRAKVEMF 414
                 56788888888888888877775 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   1.1    0.0037       1.2     189     277 ..     147     234 ..     116     256 .. 0.62
   2 ?    2.9   1.5      0.18        57     211     256 ..     351     399 ..     261     416 .. 0.56

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0037
       FAM76 189 skleeeklaeekesnetskksldsnssdhlvavtqLkeeiaslkkqleqkdqellekdkkitelkaellekekelreklkelekeakek 277
                    + +++++ k++n +s k++ +n+     ++t L+++i  l++++++   +l+      t+  +++++k  elr+ +++++ e ++ 
  EPA05778.1 147 DTCQ-TTAVQIKSANPESIKATMTNKGGITAKITSLENKISGLEQNIASERAKLSGVTNDTTSTISDTTQKIVELRNNITKTKDELNRY 234
                 3333.223333444444444555555666677777777777777777777777777777777777777777777777777777766654 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.18
       FAM76 211 dsnssdhlvavtqLkeeiaslkkqle...qkdqellekdkkitelkael 256
                 +s+  +   +v++L+e+i++ k++le   ++    l+ d ++t+l+ + 
  EPA05778.1 351 SSSIDELEKKVSDLQEKIKTEKQRLEiliHQTPRSLTYDLEVTKLTENI 399
                 2222222233333444443333333211111222222333333333222 PP

>> Lebercilin  Ciliary protein causing Leber congenital amaurosis disease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.5     0.011       3.5     138     188 ..     176     226 ..     149     238 .. 0.68
   2 ?    3.2   3.9       0.2        62     120     146 ..     355     381 ..     350     413 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.011
  Lebercilin 138 ekikeLerkleleeksfrrqlaaekkktkeaqeevkalqeeierlkqklke 188
                  ki +Le+k+  +e++ + + a+ +  t+++ +++++++++i +l++++ +
  EPA05778.1 176 AKITSLENKISGLEQNIASERAKLSGVTNDTTSTISDTTQKIVELRNNITK 226
                 456666666666666666666666666666666666666666666666532 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.2
  Lebercilin 120 eeLqkkLeeleakleekeekikeLerk 146
                 +eL+kk+++l++k+++++++++ L ++
  EPA05778.1 355 DELEKKVSDLQEKIKTEKQRLEILIHQ 381
                 566777777777777766666666554 PP

>> T4SS  Type IV secretion system proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   1.8    0.0034       1.1     103     154 ..     178     230 ..     131     238 .. 0.76
   2 ?    2.1   0.5       0.7   2.2e+02      15      42 ..     352     379 ..     262     385 .. 0.80
   3 ?    2.1   0.4      0.69   2.2e+02      15      44 ..     352     381 ..     342     410 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0034
        T4SS 103 ltskeqaskaceqaankaaqd.kalaeqaydkankrlkqiqkLadqinnatDp 154
                 +ts e++ + +eq++ ++ ++  ++++++ +++++++++i +L++ i++++D 
  EPA05778.1 178 ITSLENKISGLEQNIASERAKlSGVTNDTTSTISDTTQKIVELRNNITKTKDE 230
                 4444555577888877665541689**************************96 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.7
        T4SS  15 kqvkeaaqqltqlkqqleqakqqleslt 42 
                  +++e+++ ++ l++ +++ kq le+l 
  EPA05778.1 352 SSIDELEKKVSDLQEKIKTEKQRLEILI 379
                 4556667777777777777777777665 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.69
        T4SS  15 kqvkeaaqqltqlkqqleqakqqlesltga 44 
                  +++e+++ ++ l++ +++ kq le+l  +
  EPA05778.1 352 SSIDELEKKVSDLQEKIKTEKQRLEILIHQ 381
                 566778888888888888888888777655 PP

>> MIP-T3_C  Microtubule-binding protein MIP-T3 C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.2     0.069        22      95     140 ..     154     199 ..     143     207 .. 0.70
   2 ?    2.4   0.5      0.42   1.3e+02     124     147 ..     208     231 ..     202     238 .. 0.68
   3 ?    6.2   1.3      0.03       9.6     111     139 ..     346     374 ..     328     380 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.069
    MIP-T3_C  95 rqqaeelaeerrateealeplkaqlaeleeaIkdqkekisnvraki 140
                  q + +  e  +at+ +   + a++  le++I+  +++i   rak+
  EPA05778.1 154 VQIKSANPESIKATMTNKGGITAKITSLENKISGLEQNIASERAKL 199
                 5556666666777888888888888888888888888777777664 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.42
    MIP-T3_C 124 eaIkdqkekisnvrakilkNeaki 147
                 ++I+d+ +ki ++r++i k + ++
  EPA05778.1 208 STISDTTQKIVELRNNITKTKDEL 231
                 467777777777777777665554 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.03
    MIP-T3_C 111 aleplkaqlaeleeaIkdqkekisnvrak 139
                 +  ++   + ele++++d +eki++ +++
  EPA05778.1 346 NKGDISSSIDELEKKVSDLQEKIKTEKQR 374
                 55678889999999999999999998886 PP

>> TssO  Type VI secretion system, TssO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   1.1    0.0012      0.37      60     145 ..     145     235 ..     119     238 .. 0.87
   2 ?    1.3   2.3       1.1   3.4e+02      52     144 ..     356     409 ..     346     413 .. 0.44

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0012
        TssO  60 lkkkvdsiykkIdsLkpevnavflene..Ikkdlndiknty...gknssdeRykmyaqiakfykmlledKkelksvseniklfkkqLeece 145
                  +++++++  +I+s +pe  ++  +n+  I+ ++ ++ n++   ++n   eR k+  ++ ++  ++ ++ ++++++++ni++ k  L++++
  EPA05778.1 145 EIDTCQTTAVQIKSANPESIKATMTNKggITAKITSLENKIsglEQNIASERAKLSGVTNDTTSTISDTTQKIVELRNNITKTKDELNRYK 235
                 567899999******98876666555444************98889******************************************997 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 1.1
        TssO  52 kfeekqkelkkkvdsiykkIdsLkpevnavfleneIkkdlndikntygknssdeRykmyaqiakfykmlledKkelksvseniklfkkqLeec 144
                 ++e+k  +l++k+++ +++++ L                                       + +    l+   e+ +++eni++++++L++ 
  EPA05778.1 356 ELEKKVSDLQEKIKTEKQRLEIL---------------------------------------IHQTPRSLTYDLEVTKLTENIEHLRNDLNRA 409
                 33333333333333333333333.......................................3333333333345556666666666666654 PP

>> Lectin_N  Hepatic lectin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.3    0.0049       1.5      54     110 ..     143     199 ..     127     203 .. 0.84
   2 ?    1.5   1.9      0.72   2.3e+02      82     119 ..     347     384 ..     309     414 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0049
    Lectin_N  54 qreLetLketfsnfssstlaeiqalssqggslsekvtsleaklekkqqdlkadhsel 110
                 + e+ t ++t   + s     i+a  ++ g +  k+tsle k+   +q++  + ++l
  EPA05778.1 143 RIEIDTCQTTAVQIKSANPESIKATMTNKGGITAKITSLENKISGLEQNIASERAKL 199
                 5688999999999999999*****************************999988876 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.72
    Lectin_N  82 ggslsekvtsleaklekkqqdlkadhselllhvkqlvk 119
                  g++s  +  le k+   q+++k+++  l + + q + 
  EPA05778.1 347 KGDISSSIDELEKKVSDLQEKIKTEKQRLEILIHQTPR 384
                 45555566666666666666666665555544444443 PP

>> DUF4200  Domain of unknown function (DUF4200)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.3       1.7   5.3e+02      82     104 ..     171     193 ..     130     201 .. 0.65
   2 ?    9.4   0.3    0.0041       1.3      78     113 ..     206     254 ..     197     259 .. 0.79
   3 ?    2.7   1.8      0.52   1.6e+02      70     104 ..     342     376 ..     331     382 .. 0.72
   4 ?    1.2   0.1       1.5   4.7e+02      78     100 ..     388     410 ..     381     415 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 1.7
     DUF4200  82 ikklkaeietlkseiekleekle 104
                    ++a+i+ l+++i+ le++++
  EPA05778.1 171 KGGITAKITSLENKISGLEQNIA 193
                 34455666666666666666554 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0041
     DUF4200  78 keaeikklkaeietlkseiekleekleeykk.............YeefL 113
                  ++ i + +++i++l++ i+k++++l++yk              ++ fL
  EPA05778.1 206 TTSTISDTTQKIVELRNNITKTKDELNRYKLalyvepteisglkFKPFL 254
                 66789999*********************97665555555555555555 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.52
     DUF4200  70 eerklkkekeaeikklkaeietlkseiekleekle 104
                 +  k+k +  + i +l++++++l+++i+  +++le
  EPA05778.1 342 ISLKNKGDISSSIDELEKKVSDLQEKIKTEKQRLE 376
                 55677778888888888888888887777666665 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 1.5
     DUF4200  78 keaeikklkaeietlkseiekle 100
                 ++ e+ kl+++ie+l++++++ +
  EPA05778.1 388 YDLEVTKLTENIEHLRNDLNRAK 410
                 67899999999999999887765 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.6      0.39   1.2e+02      18      40 ..     186     208 ..     168     295 .. 0.51
   2 ?    5.9   2.6     0.061        19       3      54 ..     347     401 ..     345     418 .. 0.65

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.39
                 HHHHHHHHHHHHHHHHHHHHHHH CS
        YabA  18 eelleeleelkeelaelleenae 40 
                 + l +++++ +++l+ ++++ ++
  EPA05778.1 186 SGLEQNIASERAKLSGVTNDTTS 208
                 44433333333333333322221 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.061
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHH..HHHHHHHHXX CS
        YabA   3 kkelfdkleeleeqleelleeleelkeelaelleen.aeLele..neklrerlee 54 
                 k ++ ++++ele+++++l+e++++ k++l+ l+++  ++L+ +   +kl e++e+
  EPA05778.1 347 KGDISSSIDELEKKVSDLQEKIKTEKQRLEILIHQTpRSLTYDleVTKLTENIEH 401
                 6788899999999999999999999999988887652334432224444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1706  (0.0951531); expected 358.6 (0.02)
Passed bias filter:                      847  (0.0472419); expected 358.6 (0.02)
Passed Vit filter:                       130  (0.00725082); expected 17.9 (0.001)
Passed Fwd filter:                        66  (0.00368119); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              57  [number of targets reported over threshold]
# CPU time: 0.95u 0.34s 00:00:01.29 Elapsed: 00:00:00.52
# Mc/sec: 2409.00
//
Query:       EPA05779.1  [L=58]
Description: hypothetical protein BG20_I2054 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 390.01
//
Query:       EPA05780.1  [L=168]
Description: hypothetical protein BG20_I2321 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00014   21.7  44.5     0.0011   18.8  16.3    3.6  3  STI1             STI1 domain
     0.0033   17.6   5.0        0.3   11.3   0.0    2.5  2  Bep_C_terminal   BID domain of Bartonella effector protein (B
     0.0042   17.0  37.8     0.0053   16.7  16.2    2.9  3  GerD             Spore germination GerD central core domain
  ------ inclusion threshold ------
       0.02   15.3   3.4       0.02   15.3   3.4    1.6  2  Sulfotransfer_3  Sulfotransferase family
      0.035   13.8   0.1      0.058   13.1   0.1    1.4  1  DUF3172          Protein of unknown function (DUF3172)
      0.061   13.4  11.1       0.53   10.3   2.8    2.6  2  PutA_N           Proline utilization A N-terminal domain
       0.11   12.0   2.8       0.13   11.8   2.8    1.3  1  DUF1221          Protein of unknown function (DUF1221)
       0.33   10.4   8.0       0.55    9.6   8.0    1.5  1  Cupin_4          Cupin superfamily protein
          3    7.7  19.2        6.3    6.6   7.3    3.6  3  XPC-binding      XPC-binding domain
        8.2    6.5   8.3         44    4.2   0.6    3.7  4  DUF2065          Uncharacterized protein conserved in bacteri
         10    5.9   6.8         37    4.1   2.0    2.6  2  Spore_YhaL       Sporulation protein YhaL


Domain annotation for each model (and alignments):
>> STI1  STI1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.7   3.7    0.0084        14      28      47 ..      44      63 ..      37      65 .. 0.53
   2 !   18.8  16.3   6.8e-07    0.0011      15      54 ..      66     107 ..      64     108 .. 0.95
   3 !    6.5  13.2     0.005       8.1      14      55 .]     103     150 ..     102     150 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0084
        STI1 28 eeiqsNPqalqqymsDprim 47
                +++++N  +++q++ D ++m
  EPA05780.1 44 NQMMANNPKMSQHWMDSDMM 63
                44444433445555555555 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 6.8e-07
        STI1  15 rellsDPef.vakleeiqsNPqalqqym.sDprimtvlsvLm 54 
                 +++++DP+f +++l+++++NP  +++ m  +p+  + +s++m
  EPA05780.1  66 QQMMNDPQFkQQMLQQMMQNPDDMMEWMaTNPKHVEQMSKIM 107
                 79*******668*****************************9 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.005
        STI1  14 trells.DPefvak.leeiqsNPq...alqqym.sDprimtvlsvLmg 55 
                 ++++++ D  f++k +  + ++P    +++ +m  +p++ + ++ +m+
  EPA05780.1 103 MSKIMKeDHVFMSKmMSAMINDPDlrlQMMGHMsENPEVFKEMMNMMN 150
                 666777677777650556667**777799****9************96 PP

>> Bep_C_terminal  BID domain of Bartonella effector protein (Bep)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   2.0    0.0044       7.1      33      55 ..      62      87 ..      38      92 .. 0.85
   2 !   11.3   0.0   0.00018       0.3      13      57 ..      98     142 ..      91     146 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0044
  Bep_C_terminal 33 i...davlkdpalakellqkiaaepe 55
                    +   +++++dp++ +++lq++ ++p 
      EPA05780.1 62 MmnqQQMMNDPQFKQQMLQQMMQNPD 87
                    3477899*****************97 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00018
  Bep_C_terminal  13 eeisrlsklVYadpeaafkaidavlkdpalakellqkiaaepesi 57 
                     + ++++sk+  +d   ++k+++a+++dp+l+ +++  + ++pe +
      EPA05780.1  98 KHVEQMSKIMKEDHVFMSKMMSAMINDPDLRLQMMGHMSENPEVF 142
                     789999999999999999999*********************987 PP

>> GerD  Spore germination GerD central core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   4.2      0.53   8.6e+02      40      61 ..      33      55 ..      23      68 .. 0.61
   2 ?    2.7  16.5     0.071   1.2e+02      24      72 ..      43      88 ..      33      95 .. 0.60
   3 !   16.7  16.2   3.3e-06    0.0053      24     100 ..      89     168 .]      87     168 .] 0.83

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.53
        GerD 40 ksmkkenekllkdLmkD.peYqk 61
                 smk +n++l+ ++m + p+  +
  EPA05780.1 33 MSMKFQNQELFNQMMANnPKMSQ 55
                58999999999999964144433 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.071
        GerD 24 fwkklfkdpkfaealaksmkkenekllkdLmkDpeYqkmll.eilkdpem 72
                f + + ++pk +++  +s   +     +++m+Dp++++++l +++++p+ 
  EPA05780.1 43 FNQMMANNPKMSQHWMDSDMMN----QQQMMNDPQFKQQMLqQMMQNPDD 88
                3333445666666665554443....3579******77665278999973 PP

  == domain 3  score: 16.7 bits;  conditional E-value: 3.3e-06
        GerD  24 fwkklfkdpkfaealaksmkken...ekllkdLmkDpeYqkmlleil.kdpemekqllellkskeyrkqlekviqetlesP 100
                 +++ + ++pk +e+++k mk+++    k++ ++++Dp+ + +++  + ++pe+ k+++++++s+ + +++ + +++ +  P
  EPA05780.1  89 MMEWMATNPKHVEQMSKIMKEDHvfmSKMMSAMINDPDLRLQMMGHMsENPEVFKEMMNMMNSN-MTNHMGSEMNQQMMHP 168
                 5677889***************9555699999********8777666379************97.6678888888888766 PP

>> Sulfotransfer_3  Sulfotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   3.4   1.2e-05      0.02      51     121 ..      38     108 ..      21     113 .. 0.75
   2 ?   -1.4   0.0       1.5   2.5e+03      25      35 ..     139     149 ..     109     167 .. 0.45

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.2e-05
                      -S...TTTHHHHHHHHHH....T--HHHHHHHHHHHHHTT-BHHHHHHHHHHHTTTSEEEEEESSGGG-HHHHHH CS
  Sulfotransfer_3  51 elrrlldagltqeeaelp....hledaeepeedlqllraalasvilealarvpsyarwlvdKsPshlfrldllle 121
                      ++++l +++++ +    p    h++d + +++++ + ++++++++l+++++ p+    ++  +P h++++  +++
       EPA05780.1  38 QNQELFNQMMANN----PkmsqHWMDSDMMNQQQMMNDPQFKQQMLQQMMQNPDDMMEWMATNPKHVEQMSKIMK 108
                      2333333333333....24445************9*****************9888766779********99987 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.5
                      EE--S--.--T CS
  Sulfotransfer_3  25 vripeetlfva 35 
                      ++++ e+++++
       EPA05780.1 139 PEVFKEMMNMM 149
                      22222222222 PP

>> DUF3172  Protein of unknown function (DUF3172)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   3.5e-05     0.058       5      64 ..       8      69 ..       5     121 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.5e-05
     DUF3172  5 lailagvlvlGigiGva.lsstanldpenvasreaidr.aaPnaelCvqyGasaivvdlrvf 64
                +ai+ gv+ +Gig+  a + st +  + + +++e +++ +a n+++ +++  s ++ ++++ 
  EPA05780.1  8 IAIVIGVFFVGIGVSYAhFASTYDPMSMKFQNQELFNQmMANNPKMSQHWMDSDMMNQQQMM 69
                799***********976478877777788888888876268899*********999888875 PP

>> PutA_N  Proline utilization A N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   2.8   0.00033      0.53       8      47 ..      39      79 ..      34      82 .. 0.85
   2 ?    8.1   0.4    0.0016       2.7      15      47 ..     100     132 ..      97     147 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00033
      PutA_N  8 grellaaleeerpklfdrrwwddklle..wamkdeelkvqlf 47
                 +el++++ +++pk+  ++w+d  +++   +m+d+++k q++
  EPA05780.1 39 NQELFNQMMANNPKMS-QHWMDSDMMNqqQMMNDPQFKQQML 79
                699*******999998.59999999973358*********98 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0016
      PutA_N  15 leeerpklfdrrwwddkllewamkdeelkvqlf 47 
                 +e+ ++ +++ + +  k+++ +++d++l+ q++
  EPA05780.1 100 VEQMSKIMKEDHVFMSKMMSAMINDPDLRLQMM 132
                 555556666778899****************98 PP

>> DUF1221  Protein of unknown function (DUF1221)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   2.8   7.8e-05      0.13     113     178 ..      58     124 ..      45     168 .] 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.8e-05
     DUF1221 113 ldedelqkkrlvlakkYdkelldpklfqwkfgkqylvtr.elcarlesawkeDrwlllellkekkks 178
                 +d+d +++++++   ++++++l++ + +     ++++t+ + ++++ +++keD+ +++++++ + + 
  EPA05780.1  58 MDSDMMNQQQMMNDPQFKQQMLQQMMQNPDDMMEWMATNpKHVEQMSKIMKEDHVFMSKMMSAMIND 124
                 799*******************99999999999***9974789****************99988754 PP

>> Cupin_4  Cupin superfamily protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   8.0   0.00034      0.55     214     292 ..      65     148 ..      19     167 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00034
                 HCCHHH..CHHHHHHHHHHHH...HHHCTSCHHCTCGTTTGGGTTS-HHHHHHHHHHHHHHHHHHHCS-HHHHCCHHHHHHHHS CS
     Cupin_4 214 aaelle..svldllldklpei...derlrdallravqargeidsdsidalaaqlsellrdpalleeflgqlltsssrekdiaqs 292
                 ++++++  ++ +++l++++++     ++ +  ++ v+++ +i ++    +++++s++++dp+l+ +++g++ ++++  k++++ 
  EPA05780.1  65 QQQMMNdpQFKQQMLQQMMQNpddMMEWMATNPKHVEQMSKIMKEDHVFMSKMMSAMINDPDLRLQMMGHMSENPEVFKEMMNM 148
                 455554224666667777666654478889999999******999999***************************877775543 PP

>> XPC-binding  XPC-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.8      0.11   1.7e+02      44      55 ..      38      49 ..      37      52 .. 0.84
   2 ?    6.6   7.3    0.0038       6.3      15      52 ..      66     103 ..      55     110 .. 0.82
   3 ?    5.6   0.1     0.008        13      37      54 ..     130     147 ..     115     150 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.11
  XPC-binding 44 qnqeeFlqlLne 55
                 qnqe F q++ +
   EPA05780.1 38 QNQELFNQMMAN 49
                 899999999975 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0038
  XPC-binding  15 qlvqqnPqlLqplLqqlaqsnPqllqlIqqnqeeFlql 52 
                  q +  +Pq  q++Lqq+ q   +++++++ n+ +  q+
   EPA05780.1  66 QQMMNDPQFKQQMLQQMMQNPDDMMEWMATNPKHVEQM 103
                  45567899999999999998889999999999876555 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.008
  XPC-binding  37 qllqlIqqnqeeFlqlLn 54 
                  q++  +++n+e F +++n
   EPA05780.1 130 QMMGHMSENPEVFKEMMN 147
                  567788999999999998 PP

>> DUF2065  Uncharacterized protein conserved in bacteria (DUF2065)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       0.8   1.3e+03       4      13 ..      11      20 ..       7      39 .. 0.60
   2 ?    4.2   0.6     0.027        44      20      41 ..      72      93 ..      69      95 .. 0.84
   3 ?    4.1   0.2     0.028        46      23      44 ..     114     135 ..     113     136 .. 0.91
   4 ?   -0.8   0.0      0.96   1.6e+03      20      31 ..     139     150 ..     138     156 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.8
     DUF2065  4 AlGLvlviEG 13
                ++G+ +v  G
  EPA05780.1 11 VIGVFFVGIG 20
                3444444444 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.027
     DUF2065 20 PerwrralrqlaelpdrqlRli 41
                P+  +++l+q+++ pd ++ ++
  EPA05780.1 72 PQFKQQMLQQMMQNPDDMMEWM 93
                67779***********987655 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.028
     DUF2065  23 wrralrqlaelpdrqlRliGlv 44 
                 + +++  +++ pd +l+++G +
  EPA05780.1 114 MSKMMSAMINDPDLRLQMMGHM 135
                 789*****************76 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 0.96
     DUF2065  20 Perwrralrqla 31 
                 Pe  +++++++ 
  EPA05780.1 139 PEVFKEMMNMMN 150
                 899999999885 PP

>> Spore_YhaL  Sporulation protein YhaL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   2.0     0.023        37       1      17 [.       4      19 ..       4      25 .. 0.80
   2 ?    3.8   0.2     0.029        48      27      46 ..      98     118 ..      89     122 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.023
  Spore_YhaL  1 iPwWvYlviagIlfSgy 17
                +P+W+ ++++g++f g+
  EPA05780.1  4 TPIWI-AIVIGVFFVGI 19
                6***9.67779999886 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.029
  Spore_YhaL  27 reldq.efIEkEGevylerle 46 
                 ++++q + I kE  v++ ++ 
  EPA05780.1  98 KHVEQmSKIMKEDHVFMSKMM 118
                 56676468*********9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2670  (0.148921); expected 358.6 (0.02)
Passed bias filter:                      740  (0.0412739); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.61u 0.25s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 1139.25
//
Query:       EPA05781.1  [L=266]
Description: hypothetical protein BG20_I2320, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      5e-72  243.0   0.1    5.8e-72  242.8   0.1    1.0  1  GSDH            Glucose / Sorbosone dehydrogenase
     0.0025   17.4   1.1       0.12   12.1   0.1    2.7  2  Proteasome_A_N  Proteasome subunit A N-terminal signature
  ------ inclusion threshold ------
       0.03   14.6   2.1       0.49   10.7   2.3    3.0  3  DUF5122         Domain of unknown function (DUF5122) beta-pro
      0.085   12.4   0.0         13    5.3   0.0    2.3  2  SGL             SMP-30/Gluconolactonase/LRE-like region


Domain annotation for each model (and alignments):
>> GSDH  Glucose / Sorbosone dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  242.8   0.1   1.3e-75   5.8e-72       1     228 [.      39     257 ..      39     265 .. 0.93

  Alignments for each domain:
  == domain 1  score: 242.8 bits;  conditional E-value: 1.3e-75
                 -S-EEEEEE-TTS-EEEEETTTEEEEEE.TTEE.EEEEE-.----STT-SEEEEEE-TTTTTS-EEEEEEEE-...TTSSEEEEEEEEE-SS..-EEEE CS
        GSDH   1 lehPwslaflpdgrlLvtersGrlrlvkadgklkepiagvpevvakgqgGlldvalhpdfaenrlvYltyaeaeeekggagtavararlsedeaaledl 99 
                 l++Pw++ f pdgr+++ter G+lr++++ +   epia +   v  g+gGll++al+p+f+en+++Yl+ + +  e   + ++v+r++ s++  +l+++
  EPA05781.1  39 LHIPWEIVFSPDGRIFFTERVGNLRVIENWQLNPEPIASF--SVGGGEGGLLGIALDPNFKENHYLYLYQTYN--ELFSTFNKVVRYKESDN--KLSEE 131
                 578*************************5555599***99..579**************************55..7777789*******999..***** PP

                 EEEEEEE---TT-------EEE-TTS-EEEE---TT-GGGGG-TT-SSSEEEEE-TTSSB-TT-TTTT-TTS-TTEEEE--SCE---EE-TTT--EEEE CS
        GSDH 100 evifrqepkvesgahfGsrlafgpdgtLfvtvGdrskreeaqdlsselGkilrlnkdGsvpadnpfvgkagakpeiwsyGhRnpqGlaldpdtgeLwes 198
                 + +++++p    + h G+r+ fgpdg+L++t+Gd+++ + aqd++s++Gkilr+n+dGs+p+dnpf      ++ ++syGhRnpqG+ ++p+tg+L+es
  EPA05781.1 132 KILVDKIPG--ASYHDGGRIKFGPDGKLYITTGDAGNYNLAQDINSNAGKILRINSDGSIPQDNPFE-----NSLVFSYGHRNPQGIDWEPNTGKLFES 223
                 *********..789****************************************************5.....799************************ PP

                 EE--SSS.....EEEEEE-TT-B--TTT-S..... CS
        GSDH 199 EhGprgg.....DelnlieaGknYGWplvsygeeY 228
                 EhGp+g+     De+n+ie+GknYGWp +  g+e 
  EPA05781.1 224 EHGPSGErgvahDEINVIEKGKNYGWPDII-GDET 257
                 ******999******************998.4443 PP

>> Proteasome_A_N  Proteasome subunit A N-terminal signature
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.1   2.7e-05      0.12       7      15 ..      46      54 ..      45      54 .. 0.93
   2 ?    3.3   0.1     0.015        67       8      15 ..     151     158 ..     151     158 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.7e-05
  Proteasome_A_N  7 tFSPdGRLf 15
                    +FSPdGR+f
      EPA05781.1 46 VFSPDGRIF 54
                    8*******9 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.015
  Proteasome_A_N   8 FSPdGRLf 15 
                     F PdG+L+
      EPA05781.1 151 FGPDGKLY 158
                     89*****8 PP

>> DUF5122  Domain of unknown function (DUF5122) beta-propeller
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.94   4.2e+03       2       7 ..      49      54 ..      49      55 .. 0.86
   2 ?   -2.5   0.0       1.4   6.5e+03      21      27 ..     116     122 ..     113     125 .. 0.77
   3 ?   10.7   2.3   0.00011      0.49       2      32 ..     153     189 ..     152     189 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.94
     DUF5122  2 pDGKIl 7 
                pDG+I+
  EPA05781.1 49 PDGRIF 54
                8***95 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.4
     DUF5122  21 falvRLn 27 
                 + +vR+ 
  EPA05781.1 116 NKVVRYK 122
                 7899*96 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00011
     DUF5122   2 pDGKI.lVaGsftsy.....ngssdfalvRLnaDGsl 32 
                 pDGK+ +  G+ ++y      +s++  ++R+n+DGs+
  EPA05781.1 153 PDGKLyITTGDAGNYnlaqdINSNAGKILRINSDGSI 189
                 9****99999999888988889999**********96 PP

>> SGL  SMP-30/Gluconolactonase/LRE-like region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0    0.0042        19     125     150 ..      31      56 ..      23      68 .. 0.86
   2 ?    5.3   0.0    0.0029        13      91     126 ..     149     189 ..     116     221 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0042
         SGL 125 klervlddltipNGlawspdgktlYl 150
                 k+e v+d+l+ip  + +spdg+ +++
  EPA05781.1  31 KVETVADNLHIPWEIVFSPDGRIFFT 56 
                 799999***************99975 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0029
         SGL  91 gvvdpdGrlwfGtmgdeeakgeev.....galyrldpdgkl 126
                 +++ pdG+l+++t + ++ +  +      g+++r++ dg++
  EPA05781.1 149 IKFGPDGKLYITTGDAGNYNLAQDinsnaGKILRINSDGSI 189
                 46778888888877666554444455677888888887664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 1735.54
//
Query:       EPA05782.1  [L=61]
Description: hypothetical protein BG20_I2322 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.024   14.6   0.4      0.024   14.6   0.4    1.9  3  PriA_CRR         PriA DNA helicase Cys-rich region (CRR) doma
      0.035   13.8   1.2      0.038   13.7   1.2    1.0  1  Cytochrom_NNT    NapC/NirT cytochrome c family, N-terminal re
       0.77    9.7   8.2       0.21   11.5   5.2    1.6  2  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
        1.1    8.6  10.0      0.077   12.3   3.8    2.2  2  zf-RanBP         Zn-finger in Ran binding protein and others
        3.2    7.5   7.7        4.2    7.1   7.7    1.3  1  Rep_fac-A_C      Replication factor-A C terminal domain


Domain annotation for each model (and alignments):
>> PriA_CRR  PriA DNA helicase Cys-rich region (CRR) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.3       1.7   6.1e+03       1       5 [.      27      31 ..      27      34 .. 0.57
   2 ?   14.6   0.4   6.8e-06     0.024      14      24 ..      39      49 ..      37      50 .. 0.84
   3 ?   -3.1   0.3       2.3   8.3e+03       1       2 [.      56      57 ..      54      60 .. 0.51

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.7
    PriA_CRR  1 CpnCd 5 
                C  C+
  EPA05782.1 27 CGKCQ 31
                55554 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 6.8e-06
    PriA_CRR 14 rnrLrCHyCgy 24
                ++r  CHyCgy
  EPA05782.1 39 EGRWTCHYCGY 49
                67778*****9 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 2.3
    PriA_CRR  1 Cp 2 
                C 
  EPA05782.1 56 CE 57
                33 PP

>> Cytochrom_NNT  NapC/NirT cytochrome c family, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   1.2   1.1e-05     0.038      14      71 ..       2      59 ..       1      60 [. 0.95

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.1e-05
  Cytochrom_NNT 14 vgvvvgvvflggfntaleatsteeFCvsCHemednveeykesiHysnrsgvraeCsdC 71
                    g+v+g++fl++++++++     e C +C +  ++++e + + Hy +    + +C+ C
     EPA05782.1  2 GGIVLGIIFLMITAAMVKSRYGWETCGKCQKRVKTFDEGRWTCHYCGYFNGQTNCEGC 59
                   5899*******************************************999999**999 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   5.2   5.9e-05      0.21      22      55 ..      18      50 ..      12      56 .. 0.87
   2 ?    1.8   2.9     0.064   2.3e+02      30      51 ..      43      58 ..      43      60 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.9e-05
  OrfB_Zn_ribbon 22 vnpayTSktCseCgsknkealsgrtfkCpnCgfe 55
                    v+ +y   tC +C +++k+  ++ +++C  Cg+ 
      EPA05782.1 18 VKSRYGWETCGKCQKRVKT-FDEGRWTCHYCGYF 50
                    667777789**********.************85 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.064
  OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkCpn 51
                    tC+ Cg+ n +       +C+ 
      EPA05782.1 43 TCHYCGYFNGQ------TNCEG 58
                    7*****99988......45555 PP

>> zf-RanBP  Zn-finger in Ran binding protein and others
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.4      0.46   1.7e+03       7      10 ..      27      30 ..      25      33 .. 0.66
   2 ?   12.3   3.8   2.1e-05     0.077       2      16 ..      39      53 ..      39      60 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.46
                -SSS CS
    zf-RanBP  7 CskC 10
                C kC
  EPA05782.1 27 CGKC 30
                6677 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 2.1e-05
                SSSEE-SSS--EEES CS
    zf-RanBP  2 egdWdCskClvqNfa 16
                eg+W+C+ C++ N +
  EPA05782.1 39 EGRWTCHYCGYFNGQ 53
                79***********65 PP

>> Rep_fac-A_C  Replication factor-A C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   7.7    0.0012       4.2      15      44 ..      21      48 ..      10      59 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0012
                 TTEEEB--STT---B-EEETTTEEEETTTT CS
  Rep_fac-A_C 15 nlvYkACpsedCnkKvveeedgewrCekCd 44
                 +  ++ C   +C+k+v + ++g+w+C+ C 
   EPA05782.1 21 RYGWETCG--KCQKRVKTFDEGRWTCHYCG 48
                 45578899..*******************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1142  (0.0636957); expected 358.6 (0.02)
Passed bias filter:                      649  (0.0361983); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 385.19
//
Query:       EPA05783.1  [L=139]
Description: putative chemotaxis protein Chey [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.5e-24   84.5   1.1    6.3e-24   84.3   1.1    1.0  1  Response_reg  Response regulator receiver domain


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.3   1.1   3.5e-28   6.3e-24       1     112 []       8     121 ..       8     121 .. 0.93

  Alignments for each domain:
  == domain 1  score: 84.3 bits;  conditional E-value: 3.5e-28
                   EEEESSSHHHHHHHHHHHH.HTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEESSTSHHHHHHHH.HCTES CS
  Response_reg   1 vlivdDdplvrellrqlle.eegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviiltahseeedaveal.kagad 95 
                   +livdD++++re  + +++ + ++ ++ +a++g e l+++k+ k+d+i+lD++mp mdG+++lk++ ++dp ++vi+ ta++e++ + + +  +ga 
    EPA05783.1   8 ILIVDDSQAFREFAQLVIKdDLKFVTIITATNGMEGLQMYKKYKPDVIILDWKMPVMDGMQVLKTVMKDDPRTKVIMTTAYTEDQLLLNEMkALGAL 104
                   8******************889999999***************************************************999988766555389*** PP

                   EEEESSG-HHHHHHHHH CS
  Response_reg  96 dflsKpfdpeeLlkale 112
                    f+ Kp ++  Llka++
    EPA05783.1 105 CFVPKPTQRLLLLKAIN 121
                   ******99999999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 915.62
//
Query:       EPA05784.1  [L=133]
Description: low molecular weight phosphotyrosine protein phosphatase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-24   85.5   0.2    9.2e-24   84.4   0.2    1.5  1  LMWPc     Low molecular weight phosphotyrosine protein phosph


Domain annotation for each model (and alignments):
>> LMWPc  Low molecular weight phosphotyrosine protein phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.4   0.2   5.1e-28   9.2e-24       1     141 [.       5     127 ..       5     128 .. 0.91

  Alignments for each domain:
  == domain 1  score: 84.4 bits;  conditional E-value: 5.1e-28
                 EEEEESSSSSHHHHHHHHHHHHHHHTT-CCCEEEEEEESTSTTT-B--HHHHHHHHHTTS--TT-BB-BS-HHHHHHSSEEEESSHHHHHHHHHHCCTT CS
       LMWPc   1 vlfvClgNicRSpmAealfrkelekagleekvevdSaGtgalvgkradpravevlkekgislsghvarqlskeelaelDlilamdeenkreleslapek 99 
                 +lfvC+ N++RS+mAea+frk+l+       +e  SaGt+  ++++++p +++v+ke gi++++  ++++s+++++e+   + m    k++  +l  + 
  EPA05784.1   5 ILFVCVENAGRSQMAEAFFRKYLPS-----GFEPISAGTK--PASKVNPIVAQVMKEVGIDIENNHPQNISQQMMDEAENTINMGCIDKESCPALFLK- 95 
                 89********************776.....7899******..******************************************77777455555555. PP

                 GGGGEEEGGGGSSTSS---HTTSSHHHHHHHHHHHHHHHHHH CS
       LMWPc 100 ekakvkllgeyteqldieDPyygeieafeevldeieeavkkl 141
                 +           ++++i DP++ +ie+++e++d+ie++vk+l
  EPA05784.1  96 N----------VDDWQILDPKGRSIEEVREIRDQIEKKVKDL 127
                 3..........479*************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       881  (0.0491383); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 868.40
//
Query:       EPA05785.1  [L=73]
Description: hypothetical protein BG20_I2463, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00074   19.4   0.0     0.0011   18.8   0.0    1.3  1  ADH_N     Alcohol dehydrogenase GroES-like domain
  ------ inclusion threshold ------
      0.011   14.6   0.1      0.013   14.5   0.1    1.0  1  AAA_PrkA  PrkA AAA domain


Domain annotation for each model (and alignments):
>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.3e-07    0.0011       1      23 [.      51      73 .]      51      73 .] 0.91

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.3e-07
                TTEEEEEEEEEEE-HHHHHHHTT CS
       ADH_N  1 pgevlikvkaagiCgsDlhilkg 23
                p+e+l+k++a+g+C+s lh ++g
  EPA05785.1 51 PNEILLKIEACGVCHSQLHGIEG 73
                689****************8876 PP

>> AAA_PrkA  PrkA AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   1.4e-06     0.013     104     161 ..      11      68 ..       7      73 .] 0.86

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.4e-06
    AAA_PrkA 104 lverlkklleaapiyal.egsPvfeePlhlipeelrkkleeeygirlegllsPlatkrl 161
                 +  ++kk ++++ + +l + +P++ +Pl+l  e +r+++++  +i l+ + + +++ +l
  EPA05785.1  11 ITSKIKKNMQKMKVMMLsKCAPIETNPLKLT-EIDRHEINKPNEILLKIEACGVCHSQL 68 
                 6789*************5566********95.778999999999999999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       939  (0.0523733); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 490.60
//
Query:       EPA05786.1  [L=609]
Description: excinuclease ABC, A subunit [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.8e-17   62.8   0.1    6.3e-10   39.7   0.0    3.2  2  ABC_tran         ABC transporter
      8e-16   58.4   0.1    1.5e-13   51.1   0.0    3.6  4  UvrA_DNA-bind    UvrA DNA-binding domain
    1.2e-08   35.1   0.6      0.077   12.8   0.0    3.3  3  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    1.4e-08   34.5   0.3      0.067   12.6   0.0    3.1  3  SMC_N            RecF/RecN/SMC N terminal domain
    1.5e-05   24.9   1.8      0.051   13.3   0.2    3.2  3  AAA_15           AAA ATPase domain
    0.00022   21.5   1.7      0.013   15.8   0.4    2.4  2  DnaJ_CXXCXGXG    DnaJ central domain
    0.00033   20.6   0.3    0.00098   19.1   0.3    1.7  1  RsgA_GTPase      RsgA GTPase
    0.00066   20.1   0.0      0.014   15.8   0.0    2.6  3  AAA_16           AAA ATPase domain
     0.0034   16.6   0.0      0.037   13.2   0.0    2.5  3  NB-ARC           NB-ARC domain
     0.0067   16.2   0.1      0.016   14.9   0.1    1.6  1  AAA_29           P-loop containing region of AAA domain
  ------ inclusion threshold ------
       0.01   15.9   0.1       0.06   13.4   0.0    2.2  2  MMR_HSR1         50S ribosome-binding GTPase
       0.01   15.6   0.1      0.029   14.1   0.1    1.8  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.016   15.5   0.3       0.33   11.2   0.0    2.9  3  AAA_22           AAA domain
      0.016   15.0   0.1        5.4    7.0   0.0    2.9  3  RACo_linker      RACo linker region
      0.063   13.3   0.0        1.3    9.1   0.0    2.9  3  AAA_14           AAA domain
      0.065   12.8   0.2       0.22   11.1   0.1    1.9  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
      0.068   12.7   0.1       0.36   10.3   0.0    1.9  2  AAA_7            P-loop containing dynein motor region
       0.08   12.8   0.2       0.26   11.2   0.0    1.9  1  DUF2972          Protein of unknown function (DUF2972)
      0.083   12.8   0.0       0.21   11.5   0.0    1.7  1  ATPase_2         ATPase domain predominantly from Archaea
      0.091   12.9   0.0       0.24   11.6   0.0    1.7  1  T4_Rnl2_C        T4 RNA ligase 2 C-terminal
       0.13   11.2   0.2       0.39    9.7   0.0    1.8  2  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
       0.29   10.8   1.7         17    5.1   0.0    2.8  3  AAA_24           AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0     2e-06    0.0016      74     136 ..     115     185 ..      48     186 .. 0.71
   2 !   39.7   0.0   7.7e-13   6.3e-10       1     136 [.     290     526 ..     290     527 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2e-06
                 SBHHHH.........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSS..EEEEESTT CS
                 xxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx RF
    ABC_tran  74 ltvren.........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpk..llllDEpt 136
                 l++ en         +   ei++ l+ l +++l+  ++++  s+LSgG+ qr+ la  + ++ +  l++lDEpt
  EPA05786.1 115 LKLTENeqyiardvlK---EIKERLEFLMNVGLNYLTLNRLSSTLSGGESQRIRLATQIGSNLTgvLYVLDEPT 185
                 4444445555553332...34444444444445555555558****************9998755599*****9 PP

  == domain 2  score: 39.7 bits;  conditional E-value: 7.7e-13
                 EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--...SEEEE..................EETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxx..................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp...teGei..................lldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                 lkn+++++  g  v ++G +G+GKStL++ ++ ++      + ++                   +d+ ++ +++++     igv+++  +l  ++++ +
  EPA05786.1 290 LKNIDVEIPLGLFVSVTGVSGSGKSTLINDILLKSLEshfYSTTVkpgrhteiiglenidkviAIDQSPIGRTPRSNPATYIGVFTHIRELYANTELSK 388
                 79**************************96655443334666666888889999999999999999999999***************999999999555 PP

                 H.............................................................................HHHTC...HHHHHHHSTTGGT CS
                 x.............................................................................xxxxx...xxxxxxxxxxxxx RF
    ABC_tran  79 n.............................................................................esdee...iekalsklglkel 97 
                 +                                                                             e   +   i++ l+++ +++l
  EPA05786.1 389 ErgysmgqfsfnvadgrcfacdgdgvkqiemqflsdvyvkcdeckgkrynsetlsvlykgknisdildmtvfealeffE---NipsIKRKLQTIFDVGL 484
                 56******************************************99999988888887777777766666655553332...23336666666666668 PP

                 TCBGESTTSGGS-HHHHHHHHHHHHHHHT...SSEEEEESTT CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxx RF
    ABC_tran  98 kdtvvksspssLSgGqkqrvalarallkk...pkllllDEpt 136
                    ++++s ++LSgG+ qrv+la  l k+   +++++lDEpt
  EPA05786.1 485 GYIKLGQSSTTLSGGEAQRVKLASELSKRgtgKTFYILDEPT 526
                 999999999*****************98644478*******9 PP

>> UvrA_DNA-bind  UvrA DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.1   0.0   1.8e-16   1.5e-13      45     110 .]       2      68 ..       1      68 [. 0.93
   2 ?    1.3   0.0      0.54   4.4e+02      23      71 ..     119     167 ..     110     179 .. 0.86
   3 ?   -1.5   0.0         4   3.2e+03      82     105 ..     239     262 ..     228     264 .. 0.80
   4 ?    0.4   0.0         1   8.4e+02      74     101 ..     358     386 ..     340     392 .. 0.78

  Alignments for each domain:
  == domain 1  score: 51.1 bits;  conditional E-value: 1.8e-16
                    ---------S-THHHHH----.....................---HHHHHHHHHH-------HHHHHH CS
  UvrA_DNA-bind  45 dtpfkeLpeeqkdilLyGsgeekikveyks..ggrkrsyektfeGvipnlerryreteSeavreelek 110
                     tp+++++++++ i+L+Gs++  i ++y+s  g  +++y+  feGv+ nl+r + et+Se+ re+l++
     EPA05786.1   2 MTPIEKISPKHLRIILHGSND-LIDFKYQSksGDSSWQYTDAFEGVLVNLQRSFMETDSESKREWLKQ 68 
                    69******************9.7777777778999******************************985 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.54
                    .TT-HHHHHHHHHHHTTTS------------S-THHHHH----...... CS
  UvrA_DNA-bind  23 skkssyyrqlleavaehygidldtpfkeLpeeqkdilLyGsgeekikve 71 
                    ++++ + r +l+++ e++++ +++ ++ L+ + +   L G ++++i+  
     EPA05786.1 119 ENEQYIARDVLKEIKERLEFLMNVGLNYLTLNRLSSTLSGGESQRIRLA 167
                    4556669999******************************999988765 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 4
                    ...---HHHHHHHHHH-------H CS
  UvrA_DNA-bind  82 ektfeGvipnlerryreteSeavr 105
                    +  feG i+++ +  ++ + ++ +
     EPA05786.1 239 NVVFEGTINQILKSTKSVTGNYLK 262
                    66799*999999988888877776 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 1
                    ............---HHHHHHHHHH---- CS
  UvrA_DNA-bind  74 s.ggrkrsyektfeGvipnlerryreteS 101
                      g++ rs  +t+ Gv +++++ y +te 
     EPA05786.1 358 PiGRTPRSNPATYIGVFTHIRELYANTEL 386
                    356777888899*************9985 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0    0.0002      0.17     231     302 ..     150     220 ..      58     221 .. 0.84
   2 !    7.5   0.1    0.0039       3.2       4      44 ..     305     344 ..     302     352 .. 0.84
   3 !   12.8   0.0   9.4e-05     0.077     244     298 ..     503     557 ..     460     562 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0002
      AAA_21 231 elparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSplll 302
                 ++ ++ lS G  + ++l+t + + l    l+++DEp  gLH +  +rl++ l +l++ g  vi++ H+ +++
  EPA05786.1 150 NRLSSTLSGGESQRIRLATQIGSNLTG-VLYVLDEPTIGLHQRDNERLIKTLTKLRNLGNTVIVVEHDEEIM 220
                 455667799999999**********99.9*************999999999999999999999987776665 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0039
      AAA_21   4 liGpNgsGKSnLLdaldllarldrdvegltdelsggggirk 44 
                 ++G  gsGKS+L+  + ll++l +++ ++t +++++ +i++
  EPA05786.1 305 VTGVSGSGKSTLINDI-LLKSLESHFYSTTVKPGRHTEIIG 344
                 7999************.889989999999998888777665 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 9.4e-05
      AAA_21 244 llalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                   +l++ l  +    +++++DEp +gLH + + +ll++l++l + g  v++  H+
  EPA05786.1 503 RVKLASELSKRGTGKTFYILDEPTTGLHFADVQKLLDVLNRLVNLGNTVLVIEHN 557
                 447777777777777************************9999988888876555 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   0.00014      0.11     135     208 ..     120     226 ..      38     232 .. 0.75
   2 !    6.5   0.1    0.0059       4.8      20      44 ..     297     320 ..     282     343 .. 0.80
   3 !   12.6   0.0   8.2e-05     0.067     135     209 ..     463     568 ..     367     575 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00014
                 T..................................CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SS CS
                 x..................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
       SMC_N 135 e..................................lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislr 198
                 +                                  +LSgGe + + la    i +     ly+lDe    L ++  +++ + l + ++    +iv+ ++
  EPA05786.1 120 NeqyiardvlkeikerleflmnvglnyltlnrlssTLSGGESQRIRLATQ--IGSNLTGVLYVLDEPTIGLHQRDNERLIKTLTKLRNLgNTVIVVEHD 216
                 144444444444555555555555555566666669*****998777766..67777889***********************9999876899****** PP

                 HHHCCC-SCE CS
                 xxxxxxxxxx RF
       SMC_N 199 eemlekadkl 208
                 ee+++++d +
  EPA05786.1 217 EEIMRNSDWI 226
                 ****998865 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0059
                 EETTSSEEEEEESTTSSHHHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxx RF
       SMC_N  20 lpfsksftaivGpNGSGKsnlldAi 44 
                 +p+   f +++G  GSGKs l++ i
  EPA05786.1 297 IPLGL-FVSVTGVSGSGKSTLINDI 320
                 44444.899************9988 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 8.2e-05
                 T...............................CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHH CS
                 x...............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
       SMC_N 135 e...............................lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreem 201
                                                 +LSgGe + v la  ++  +   + +y+lDe    L ++ v+k+ ++l++  +    ++vi ++ ++
  EPA05786.1 463 LeffenipsikrklqtifdvglgyiklgqsstTLSGGEAQRVKLASELSK-RGTGKTFYILDEPTTGLHFADVQKLLDVLNRLVNLgNTVLVIEHNLDV 560
                 155555555555555555555556666666669************99875.556789************************998765889999999999 PP

                 CCC-SCEE CS
                 xxxxxxxx RF
       SMC_N 202 lekadklv 209
                 ++++d l+
  EPA05786.1 561 IKNSDWLI 568
                 99998776 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.2   6.3e-05     0.051     199     367 ..      47     218 ..       4     220 .. 0.62
   2 ?    4.7   0.0     0.026        21      11      61 ..     290     355 ..     288     441 .. 0.79
   3 ?    4.7   0.0     0.025        21     318     357 ..     511     550 ..     448     561 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.3e-05
      AAA_15 199 lisakRnvsdedsekkssllgklkekileealqekl........eeelteklkeiqeklkeidkklaeelkkilkkkidkikkfnykgkkneeieik.. 287
                 l + +R++ ++dse+k+++l + ++++  ++ + k         +     + k i +  +  +++      ++++  ++  ++++y   ++ + eik  
  EPA05786.1  47 LVNLQRSFMETDSESKREWLKQFMRDTPCTSCNGKKlkpeslavK----INDKGIMDVCDLSIDQC-----YDFFATLKLTENEQYIARDVLK-EIKer 135
                 345566666666666666666665555443333222344422222....22222222222222222.....6666777777777776666555.44447 PP

      AAA_15 288 .......ddeelplnknGs....GvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSph 367
                          ++l+ln+ +s    G ++ + l+++i ++  +       v+++++EP + LH    + lik+l +l n ++  vi+  H + 
  EPA05786.1 136 leflmnvGLNYLTLNRLSStlsgGESQRIRLATQIGSNLTG-------VLYVLDEPTIGLHQRDNERLIKTLTKLRNLGN-TVIVVEHDEE 218
                 77777887777777777665555899999999999999999.......******************************99.7888777765 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.026
      AAA_15  11 FRslkdveidlseeltvliGkNnsGKSsilealdlFlnnkekkn...................kkvikie 61 
                  + ++ vei+l   +  + G  +sGKS++++ +  +l+  e+++                   +kvi i+
  EPA05786.1 290 LKNID-VEIPLGL-FVSVTGVSGSGKSTLINDI--LLKSLESHFysttvkpgrhteiigleniDKVIAID 355
                 55555.8999999.99999************77..66666677756666666666666665554444444 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.025
      AAA_15 318 dekeeknvilliEEPEahLHpqaqkvlikllkelandnkt 357
                 +++ +   +++++EP + LH    + l + l +l+n ++t
  EPA05786.1 511 SKRGTGKTFYILDEPTTGLHFADVQKLLDVLNRLVNLGNT 550
                 555666889***************************9984 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.065        53      41      50 ..      72      81 ..      56      93 .. 0.65
   2 !   15.8   0.4   1.6e-05     0.013      16      51 ..     405     436 ..     393     442 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.065
  DnaJ_CXXCXGXG 41 qstCpeCeGt 50
                    ++C++C+G+
     EPA05786.1 72 DTPCTSCNGK 81
                   3344444443 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 1.6e-05
  DnaJ_CXXCXGXG  16 tCktCkGsGvvreeqktlgpfvqqsqstCpeCeGtG 51 
                    +C +C+G Gv++ e+    +f + +  +C+eC+G+ 
     EPA05786.1 405 RCFACDGDGVKQIEM----QFLSDVYVKCDECKGKR 436
                    7********644443....36677889*******86 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.3   1.2e-06   0.00098      88     140 ..     288     340 ..     263     344 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.2e-06
                  TTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S------------ CS
  RsgA_GTPase  88 egleelkellkd.ktsvlvGqSGvGKStLinallpelelktgevseklgrGkhT 140
                  ++l+++  ++    ++ + G SG GKStLin +l + +l+ +  s++ + G+hT
   EPA05786.1 288 NNLKNIDVEIPLgLFVSVTGVSGSGKSTLINDILLK-SLESHFYSTTVKPGRHT 340
                  5555565555543556789***************99.9999************9 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       7.6   6.2e+03     116     141 ..     184     213 ..     116     216 .. 0.53
   2 !   15.8   0.0   1.7e-05     0.014      25      59 ..     301     335 ..     288     356 .. 0.75
   3 ?    1.0   0.0       0.6   4.9e+02      56     164 ..     425     547 ..     414     566 .. 0.48

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 7.6
      AAA_16 116 a.....srllellkrllallsrderplvlvl 141
                 +     +r +e l + l +l++ +  +v+v+
  EPA05786.1 184 PtiglhQRDNERLIKTLTKLRNLGN-TVIVV 213
                 0333334445555555555555455.55555 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 1.7e-05
      AAA_16  25 elvllsGesGvGKsslvrellralekdggiflrgk 59 
                   v ++G sG+GKs+l++ +l    +++++ ++ k
  EPA05786.1 301 LFVSVTGVSGSGKSTLINDILLKSLESHFYSTTVK 335
                 6799*************887754444445555544 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.6
      AAA_16  56 lrgkcdqlesaipy.salaqalareellrqlldeaesaeleawrekleeala............................................... 106
                 ++ kcd++ ++ +y s  +++l + + + ++ld++   e+ ++ e +++  +                                               
  EPA05786.1 425 VYVKCDEC-KGKRYnSETLSVLYKGKNISDILDMTVF-EALEFFENIPSIKRklqtifdvglgyiklgqssttlsggeaqrvklaselskrgtgktfyi 521
                 67777777.6666633366666666777777777444.3333333333333344444445555665655333333333333333333333333333333 PP

      AAA_16 107 ...avpelagaeasrllellkrllallsrderplvlvlDdlqwadeaslqllaaLlrlles 164
                    ++  l+ a+ + ll++l+rl+                                   + 
  EPA05786.1 522 ldePTTGLHFADVQKLLDVLNRLV-----------------------------------NL 547
                 333333333333355555555555...................................33 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.76   6.2e+02     154     191 ..      98     133 ..      87     137 .. 0.70
   2 !   13.2   0.0   4.6e-05     0.037      21      51 ..     301     329 ..     285     334 .. 0.85
   3 ?   -2.0   0.0         2   1.6e+03      85     135 ..     530     582 ..     522     600 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.76
                 EEESS--HHHHHHHHHHCCTS-GGCHH..CHHHHHHHH CS
      NB-ARC 154 ievelLekdeawellenkvfekkleekesleevakeiv 191
                 + v  L++d++++++      ++ +     ++v+kei 
  EPA05786.1  98 MDVCDLSIDQCYDFFATLKLTENEQYI--ARDVLKEIK 133
                 667779999999999887666665533..677777765 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 4.6e-05
                 EEEEEEESTTSSHHHHHHHHCCSHCCCCCCB CS
      NB-ARC  21 lvvalvGmgGvGKttlakqilnksdevegrF 51 
                 l+v++ G  G+GK+tl+++il k  ++e++F
  EPA05786.1 301 LFVSVTGVSGSGKSTLINDILLK--SLESHF 329
                 79*******************99..777777 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 2
                 SS-STTSHHHHHHHHCCCTTEEEEEE...EE-SHHHH.....HHHHCHTTSEEE CS
      NB-ARC  85 ekeeveslkrklvrlLltkrfllvlD...DVweeedwdkigvvlparenrlrvl 135
                 ++++v++l + l rl +  +++lv+    DV ++ dw  i +     +++ +++
  EPA05786.1 530 HFADVQKLLDVLNRLVNLGNTVLVIEhnlDVIKNSDW-LIDLGPEGGDEGGQIV 582
                 6677777888888888888999999888899999999.6766666555555555 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1     2e-05     0.016      23      39 ..     300     317 ..     288     326 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2e-05
      AAA_29  23 g.atlltGpsGsGKSTll 39 
                 g ++ +tG sGsGKSTl+
  EPA05786.1 300 GlFVSVTGVSGSGKSTLI 317
                 447789***********9 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       2.1   1.7e+03      48      84 ..     178     214 ..     144     229 .. 0.62
   2 ?   13.4   0.0   7.3e-05      0.06       2      37 ..     303     337 ..     302     417 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 2.1
                 EEEEECGGCSS.HHHHHHHHHHHHHHHHCTSEEEEEEE CS
    MMR_HSR1  48 ielvDtpGlie.gaseekglgkaflaleeadlillvvd 84 
                 ++++D p  i   ++++++l k++ +l++    ++vv+
  EPA05786.1 178 LYVLDEPT-IGlHQRDNERLIKTLTKLRNLGNTVIVVE 214
                 55666665.43224444467777777777666666665 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 7.3e-05
                 EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEE CS
    MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdin 37 
                 v + G + +GKStLin ++ + +  s++  tT ++ 
  EPA05786.1 303 VSVTGVSGSGKSTLINDILLK-SLESHFYSTTVKPG 337
                 7899**************974.56667777777773 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   3.6e-05     0.029       3      22 ..     305     324 ..     303     343 .. 0.81
   2 ?   -3.2   0.0         7   5.7e+03     116     133 ..     508     525 ..     497     544 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.6e-05
  Viral_helicase1   3 vhGvpGcGKStlirkllrts 22 
                      v Gv G+GKStli ++l +s
       EPA05786.1 305 VTGVSGSGKSTLINDILLKS 324
                      99**************9985 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 7
  Viral_helicase1 116 sslshrvgrrttyllpsd 133
                      s+ls+r + +t y+l + 
       EPA05786.1 508 SELSKRGTGKTFYILDEP 525
                      444444444444444433 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1       1.5   1.2e+03      50     103 ..     118     188 ..     106     214 .. 0.61
   2 ?   11.2   0.0   0.00041      0.33       7      30 ..     302     325 ..     300     355 .. 0.80
   3 ?   -0.6   0.0       1.9   1.5e+03      89     115 ..     513     547 ..     477     589 .. 0.65

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.5
      AAA_22  50 stsskdllrellralglelka..................erlsseellealeqalraravielliiDEaqh.l 103
                  ++ + ++r++l++++++l+                   ++++s++++ a +  ++ ++v  l ++DE    l
  EPA05786.1 118 TENEQYIARDVLKEIKERLEFlmnvglnyltlnrlsstlSGGESQRIRLATQIGSNLTGV--LYVLDEPTIgL 188
                 446677888888888888888888888777777777775445555554444444444444..77777754444 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00041
      AAA_22   7 ilvvtGesGtGKTtllrrlleqld 30 
                 ++ vtG sG+GK+tl++ +l +  
  EPA05786.1 302 FVSVTGVSGSGKSTLINDILLKSL 325
                 6789************99887754 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.9
      AAA_22  89 rav.ielliiDEaqh.lrs.......eealeeLrsl 115
                 r++ + + i+DE    l +        ++l+ L++l
  EPA05786.1 513 RGTgKTFYILDEPTTgL-HfadvqklLDVLNRLVNL 547
                 44455666666655555.322232234444444443 PP

>> RACo_linker  RACo linker region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       4.4   3.6e+03      33      62 ..     131     160 ..     124     162 .. 0.77
   2 ?    7.0   0.0    0.0066       5.4      17      63 ..     179     225 ..     166     228 .. 0.77
   3 ?    4.5   0.0     0.038        31      14      50 ..     517     560 ..     512     575 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 4.4
  RACo_linker  33 RLkeaLekqwdleidlsvLrkLpevLrkgn 62 
                   +ke Le  +++  ++ +L++L+++L  g+
   EPA05786.1 131 EIKERLEFLMNVGLNYLTLNRLSSTLSGGE 160
                  567777777789999999999999998776 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0066
  RACo_linker  17 veleePtledpsgDleRLkeaLekqwdleidlsvLrkLpevLrkgnw 63 
                    l+ePt+  +  D eRL++ L+k  +l   + v+ +  e++r ++w
   EPA05786.1 179 YVLDEPTIGLHQRDNERLIKTLTKLRNLGNTVIVVEHDEEIMRNSDW 225
                  5699******************9988766666666666666666655 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.038
  RACo_linker  14 kvyveleePtledpsgDleRLkeaLekqwd.......leidlsv 50 
                  k +  l+ePt   + +D+++L + L++ ++       +e +l v
   EPA05786.1 517 KTFYILDEPTTGLHFADVQKLLDVLNRLVNlgntvlvIEHNLDV 560
                  778889********************999633344434444444 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       9.2   7.5e+03      91     106 ..      11      26 ..       8      33 .. 0.76
   2 ?    9.1   0.0    0.0016       1.3       5      36 ..     303     331 ..     300     356 .. 0.81
   3 ?    0.1   0.0      0.96   7.8e+02      59      89 ..     513     547 ..     482     556 .. 0.62

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 9.2
      AAA_14  91 knldvivtGSnsklls 106
                 k+l++i+ GSn ++  
  EPA05786.1  11 KHLRIILHGSNDLIDF 26 
                 57899*****988765 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0016
      AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyi 36 
                 + +tG+  +GK+tl+++++ ++l   es +y 
  EPA05786.1 303 VSVTGVSGSGKSTLINDILLKSL---ESHFYS 331
                 789***************99999...666654 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.96
      AAA_14  59 klkeekktylflDEiqev......pewekalkslvde 89 
                 +  + +kt+ +lDE          +++ ++l++lv+ 
  EPA05786.1 513 R--GTGKTFYILDEPTTGlhfadvQKLLDVLNRLVNL 547
                 2..2578888888865443333336666666666665 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.8   2.3e+03      36      78 ..     210     251 ..     196     258 .. 0.74
   2 ?   11.1   0.1   0.00027      0.22       3      23 ..     303     323 ..     301     334 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.8
                 -SSCHCCCCCCHCCCT.EEEETTTTECCHCTT-HHHHHHHHHH CS
        cobW  36 fgevsiDaellretgveivelenGciCctlredllkelealee 78 
                 +  v++D+e++r+++  i++l  G   +  +  +  +++++++
  EPA05786.1 210 VIVVEHDEEIMRNSD-WILDLGPGAGVHGGNVVFEGTINQILK 251
                 555889999999994.588888888888777666666666665 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00027
                 EEEEESTTCCHHHHHHHHHCT CS
        cobW   3 tvltGflGsGKTtLlnhllen 23 
                 + +tG  GsGK+tL+n +l +
  EPA05786.1 303 VSVTGVSGSGKSTLINDILLK 323
                 579**************9944 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00044      0.36      36      65 ..     303     332 ..     297     343 .. 0.82
   2 ?   -0.8   0.0       1.1   9.2e+02      42      58 ..     513     530 ..     510     564 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00044
       AAA_7  36 vllvGptGtGKtviikd.llkkldkekylsl 65 
                 v ++G +G+GK+++i+d llk+l++ ++ s+
  EPA05786.1 303 VSVTGVSGSGKSTLINDiLLKSLES-HFYST 332
                 5689*************99999995.44444 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.1
       AAA_7  42 tGtGKtviikd.llkkld 58 
                  GtGKt +i d  ++ l+
  EPA05786.1 513 RGTGKTFYILDePTTGLH 530
                 79*****99876666665 PP

>> DUF2972  Protein of unknown function (DUF2972)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00031      0.26     124     176 ..     436     488 ..     426     492 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00031
     DUF2972 124 eyllelieeLkkqkeiekkkklsekdvLeylkkhkkvaleaKaildeeLvylk 176
                  y  e+++ L k k+i +   +++ + Le++++ ++++++ + i+d  L y+k
  EPA05786.1 436 RYNSETLSVLYKGKNISDILDMTVFEALEFFENIPSIKRKLQTIFDVGLGYIK 488
                 566789999*******************************************8 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00025      0.21      22      66 ..     302     346 ..     289     383 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00025
    ATPase_2  22 iyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskld 66 
                 ++ ++G  gsGK++L++ i+ +++++++y   + + r  +i  l+
  EPA05786.1 302 FVSVTGVSGSGKSTLINDILLKSLESHFYSTTVKPGRHTEIIGLE 346
                 67799********************99999888888877765555 PP

>> T4_Rnl2_C  T4 RNA ligase 2 C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0    0.0003      0.24       2      28 ..     131     157 ..     130     171 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0003
                 TS-TTTHHHHHHHGGG--HHHHHHHHH CS
   T4_Rnl2_C   2 klseeleelleeierYvtenRLnNviS 28 
                 +++e le+l++  ++Y+t nRL +++S
  EPA05786.1 131 EIKERLEFLMNVGLNYLTLNRLSSTLS 157
                 568999*******************99 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.8   2.3e+03     160     175 ..      92     107 ..      89     135 .. 0.67
   2 ?    9.7   0.0   0.00048      0.39      29      50 ..     300     321 ..     270     329 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.8
                 T--CCCHHH-SEEEEE CS
        MeaB 160 gikkGileiaDiivvn 175
                  + kGi+++ D+ +  
  EPA05786.1  92 INDKGIMDVCDLSIDQ 107
                 5678999999987644 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00048
                 SEEEEEEE-TTSSHHHHHHHHH CS
        MeaB  29 aqvvGltGvPGaGkstlvealg 50 
                    v +tGv G+Gkstl++ + 
  EPA05786.1 300 GLFVSVTGVSGSGKSTLINDIL 321
                 56799*************9875 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.048        39     109     133 ..     194     218 ..     187     223 .. 0.85
   2 ?    5.1   0.0      0.02        17       6      22 ..     304     320 ..     300     361 .. 0.83
   3 ?   -2.8   0.1       5.5   4.5e+03     110     130 ..     536     556 ..     534     558 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.048
      AAA_24 109 eefrrllkklqelrknvifiahekt 133
                 e+++++l+kl++l+++vi++ h ++
  EPA05786.1 194 ERLIKTLTKLRNLGNTVIVVEHDEE 218
                 678899999999999*****99775 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.02
      AAA_24   6 liyGpsgiGKTtlakel 22 
                  ++G sg+GK+tl++ +
  EPA05786.1 304 SVTGVSGSGKSTLINDI 320
                 589**********9877 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 5.5
      AAA_24 110 efrrllkklqelrknvifiah 130
                 ++ ++l++l +l+++v +i h
  EPA05786.1 536 KLLDVLNRLVNLGNTVLVIEH 556
                 56788999*********9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (609 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      623  (0.0347482); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.74u 0.33s 00:00:01.07 Elapsed: 00:00:00.48
# Mc/sec: 3779.93
//
Query:       EPA05787.1  [L=48]
Description: hypothetical protein BG20_I2285, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.056   13.8   0.0      0.067   13.5   0.0    1.1  1  UvrA_DNA-bind  UvrA DNA-binding domain


Domain annotation for each model (and alignments):
>> UvrA_DNA-bind  UvrA DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.8e-06     0.067       1      16 [.      21      36 ..      21      41 .. 0.96

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.8e-06
                   -S----.--------- CS
  UvrA_DNA-bind  1 Dpdlvvpdpslslaeg 16
                   D dlv+pd+s+s+ eg
     EPA05787.1 21 DADLVIPDKSKSILEG 36
                   99************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 339.73
//
Query:       EPA05788.1  [L=102]
Description: GIY-YIG catalytic domain protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.7e-12   47.5   0.7    2.2e-12   47.1   0.7    1.1  1  GIY-YIG      GIY-YIG catalytic domain
  ------ inclusion threshold ------
      0.084   13.0   0.2       0.18   11.9   0.1    1.4  1  Codanin-1_C  Codanin-1 C-terminus


Domain annotation for each model (and alignments):
>> GIY-YIG  GIY-YIG catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   0.7   2.4e-16   2.2e-12       2      78 .]      14      88 ..      13      89 .. 0.91

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 2.4e-16
                -EEEEEEETTT--EEEEEESSHHHHHHHHHHHHHHT--S-HS.STEEEEEEEE----HHHHHHHHHHHHHHTTSSSS CS
     GIY-YIG  2 ggvYiirskenkliYvGstknlekRlkqHnagkkakytrkkgkkpfeliileifptksealelEkklikkyksnkyn 78
                 g+Y++++ ++k+iY+G++knl++R ++++ ++ +  t+ k +++   i +   +++sea  lE   ikk+++ k n
  EPA05788.1 14 PGIYLMKDCDGKIIYIGKAKNLKNRVRSYFLKNQNYKTQ-KLVENISDIEFVLTDNESEAFLLESNMIKKHRP-KFN 88
                69***************************9998655555.479*****************************9.665 PP

>> Codanin-1_C  Codanin-1 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1     2e-05      0.18      64      93 ..      32      61 ..      28      65 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2e-05
  Codanin-1_C 64 rkqlqlqLeeaFlhsqpaslrrtveFVser 93
                 +k+l+ +    Fl++q+ ++ ++ve +s++
   EPA05788.1 32 AKNLKNRVRSYFLKNQNYKTQKLVENISDI 61
                 67889999999****************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1084  (0.0604607); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 649.22
//
Query:       EPA05789.1  [L=191]
Description: type I secretion target GGXGXDXXX repeat (2 copies) [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.9e-38  128.0  79.2      5e-10   39.2  10.3    4.5  4  HemolysinCabind  RTX calcium-binding nonapeptide repeat (4 co


Domain annotation for each model (and alignments):
>> HemolysinCabind  RTX calcium-binding nonapeptide repeat (4 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1  11.0   2.2e-12   3.9e-08       1      34 [.      11      44 ..      11      46 .. 0.98
   2 !   36.5  17.1     2e-13   3.5e-09       1      36 []      47      82 ..      47      82 .. 0.96
   3 !   38.0  16.8   6.5e-14   1.2e-09       1      36 []      83     118 ..      83     118 .. 0.98
   4 !   39.2  10.3   2.8e-14     5e-10       2      36 .]     120     154 ..     119     154 .. 0.98

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 2.2e-12
  HemolysinCabind  1 yGgdGnDtlvGgaGnDtiyGgaGnDtlyGGaGnD 34
                     +G+ GnD l G++GnD i G +G+D ++G +GnD
       EPA05789.1 11 IGTLGNDNLKGTNGNDLIRGLDGDDKINGKKGND 44
                     599******************************9 PP

  == domain 2  score: 36.5 bits;  conditional E-value: 2e-13
  HemolysinCabind  1 yGgdGnDtlvGgaGnDtiyGgaGnDtlyGGaGnDtl 36
                     +Gg G+D ++Gg+G+Dti G++G+D ++ G+GnD +
       EPA05789.1 47 IGGLGDDKIHGGDGDDTIEGNEGDDKINSGKGNDNI 82
                     69********************************76 PP

  == domain 3  score: 38.0 bits;  conditional E-value: 6.5e-14
  HemolysinCabind   1 yGgdGnDtlvGgaGnDtiyGgaGnDtlyGGaGnDtl 36 
                      +GgdG+D ++Gg  nDti Gg GnD ++G +G+Dtl
       EPA05789.1  83 FGGDGDDKINGGKDNDTISGGLGNDKIHGASGDDTL 118
                      7**********************************8 PP

  == domain 4  score: 39.2 bits;  conditional E-value: 2.8e-14
  HemolysinCabind   2 GgdGnDtlvGgaGnDtiyGgaGnDtlyGGaGnDtl 36 
                      G+dGnD+++Gg GnD+i+Gg   D+  GG+Gn+t+
       EPA05789.1 120 GDDGNDRIHGGKGNDIIDGGPQTDRCTGGSGNNTI 154
                      99*******************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1186.90
//
Query:       EPA05790.1  [L=485]
Description: glycine--tRNA ligase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.2e-17   61.3   0.3    2.1e-16   59.8   0.1    1.8  2  HGTP_anticodon  Anticodon binding domain
    2.9e-12   46.9   0.5    5.9e-11   42.7   0.5    2.4  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
  ------ inclusion threshold ------
       0.13   11.6   0.7        8.3    5.8   0.1    2.6  2  zf-TFIIB        Transcription factor zinc-finger
       0.26   12.1   2.2        0.5   11.1   0.8    2.2  3  zinc_ribbon_15  zinc-ribbon family
       0.48   10.4   4.2        9.7    6.2   0.5    2.8  2  zinc_ribbon_4   zinc-ribbon domain
        1.1    9.1   7.4        2.9    7.7   1.4    3.0  3  zinc_ribbon_5   zinc-ribbon domain


Domain annotation for each model (and alignments):
>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       4.4   1.3e+04      45      65 ..     136     156 ..     133     157 .. 0.80
   2 !   59.8   0.1   7.1e-20   2.1e-16       2      91 ..     392     478 ..     391     480 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 4.4
                     HHHHHHTT-SEEEEE-HHHHH CS
  HGTP_anticodon  45 ireadllgipfavvvGekele 65 
                     ++ a++ +  f v +G++e e
      EPA05790.1 136 FESAKKFNMMFKVGIGPEEEE 156
                     667888888899999999975 PP

  == domain 2  score: 59.8 bits;  conditional E-value: 7.1e-20
                     EEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTCEEEEEETTHHHHHH CS
  HGTP_anticodon   2 vvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtreqervsldelvekl 91 
                     v v+ l +k+  l+e  ++++ +L+++ +++ ld  ++ ig+++r+ d++g pfav+++++++e++tvt+r+rd+++qer++++e+ ++l
      EPA05790.1 392 VGVLSLIKKDG-LKEKTDEIYLQLKRK-YDAFLD-HSGAIGRRYRRLDEIGAPFAVTIDYQSMEDNTVTIRKRDSMSQERIKISEIDSIL 478
                     66777777455.99999********99.777776.89************************************************97765 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.7   0.5     2e-14   5.9e-11       7     178 ..     153     368 ..     146     369 .. 0.67

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 2e-14
                   TSEEEEE-SSSHHHHHHHHHHHEE...EBGGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGGHHHH..HHHHHHHHHHHHHHTT.SC CS
                   xxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxx RF
  tRNA-synt_2b   7 ndreyiLkPtneetfvelirdevl...rskrLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfhaeasldds..lrdlikaisriferlglef 98 
                   +++e +L+P+ ++ +   +        r k LPl ++q++  +R+E s  + LlR+reF q + ++f+ + +ldd+  + +++++i r+  +  +  
    EPA05790.1 153 EEEEAYLRPETCQSIFVDFPRL-YktmRGK-LPLGIAQVGKSFRNEISPRQSLLRLREFYQAEIEIFCNPTKLDDIekFTEIENTIIRVQTDSEIVA 247
                   67999*******9977555433.3111545.****************9556*******************999986225566666666655554443 PP

                   EEEEEEGTTSC.........................................BTTSEEEEEEEEETTTSEEEEEEEEEEEET..HHHHHTTE..EEE CS
                   xxxxxxxxxxx.........................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx..xxx RF
  tRNA-synt_2b  99 raiielmsaks.........................................adykdkkefeavsesltkgieigtiqklgt..rlserlga..tvl 150
                      ++     +                                         + ++   +fe+ +      +e++ ++ + +    s + +   ++ 
    EPA05790.1 248 MTCKKAV---EsgvvpnkfvayylailtefyektgidvtksrfrklgdkekaFYAQVAFDFEVETT--IGWLELVACNYRSDydLSSHAVKSkeKFE 339
                   3222222...13456677778888888888888888888888888888887333344556666555..34456666665544314455555555444 PP

                   CTTS.SEEEEEEEEEEEEHHHHHHHHHHH CS
                   xxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
  tRNA-synt_2b 151 denn.reksvimicaaigveRllsaileq 178
                    ++n  +  +++   ++g+ R l  ile+
    EPA05790.1 340 VMDNeDKVLPHVFEISMGIDRSLYTILEH 368
                   44551344688888888888888888886 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1     0.016        47       1      19 [.      87     109 ..      87     112 .. 0.81
   2 ?    5.8   0.1    0.0028       8.3       1      11 [.     128     138 ..     128     146 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.016
    zf-TFIIB   1 kCPkCqdele....eserggvei 19 
                 kC kC+++++    ++e ++vei
  EPA05790.1  87 KCTKCKSTFRadriIAEISKVEI 109
                 8*******997777777777776 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0028
    zf-TFIIB   1 kCPkCqdelee 11 
                 kCPkC+ ++e 
  EPA05790.1 128 KCPKCKGDFES 138
                 79999887775 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.8   0.00017       0.5      35      79 ..      83     140 ..      79     145 .. 0.79
   2 ?    3.5   0.3      0.04   1.2e+02       1      50 [.     127     171 ..     126     181 .. 0.72
   3 ?   -4.0   0.0         6   1.8e+04      30      45 ..     238     252 ..     229     257 .. 0.51

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00017
  zinc_ribbon_15  35 kpylacskCkslleaskelgkeiekkesse..............kkeCknCgkeveeef 79 
                     +p+++c+kCks++ a++    ei+k e  e              + +C++C+   e+  
      EPA05790.1  83 DPIIKCTKCKSTFRADR-IIAEISKVEIPEsadlsefdnailqnNIKCPKCKGDFESAK 140
                     799*************8.77888877777767788888888887778888887766655 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.04
  zinc_ribbon_15   1 ilCpkCgklskaelvkkkkvlklffipvfkwkkkkpylacskCkslleas 50 
                     i+CpkC+     ++   kk+  +f + + + ++ ++yl  ++C+s++ + 
      EPA05790.1 127 IKCPKCK----GDFESAKKFNMMFKVGIGPEEE-EAYLRPETCQSIFVDF 171
                     5799998....4555666666677777777776.9999999999988665 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 6
  zinc_ribbon_15  30 kwkkkkpylacskCks 45 
                     ++++++ ++   +Ck+
      EPA05790.1 238 RVQTDSEIV-AMTCKK 252
                     444433333.333444 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.5    0.0032       9.7      26      36 .]      86      96 ..      85      98 .. 0.74
   2 ?    4.4   0.2     0.012        35       3       9 ..     127     133 ..     124     137 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0032
  zinc_ribbon_4 26 vrCskCghvFr 36
                   ++C+kC+ +Fr
     EPA05790.1 86 IKCTKCKSTFR 96
                   67888877775 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.012
  zinc_ribbon_4   3 itCpsCk 9  
                    i Cp+Ck
     EPA05790.1 127 IKCPKCK 133
                    5566665 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   1.4   0.00099       2.9       2      14 ..      85      97 ..      85     100 .. 0.87
   2 ?    3.5   0.1      0.02        59       3      12 ..     127     136 ..     123     140 .. 0.77
   3 ?   -2.8   0.0       1.9   5.5e+03      31      36 ..     164     169 ..     160     169 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00099
  zinc_ribbon_5  2 iirCpdCdtkFkl 14
                   ii+C +C+++F+ 
     EPA05790.1 85 IIKCTKCKSTFRA 97
                   8999999999996 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.02
  zinc_ribbon_5   3 irCpdCdtkF 12 
                    i+Cp+C+  F
     EPA05790.1 127 IKCPKCKGDF 136
                    7888887766 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 1.9
  zinc_ribbon_5  31 CaevFd 36 
                    C ++F+
     EPA05790.1 164 CQSIFV 169
                    888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (485 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 2992.84
//
Query:       EPA05791.1  [L=35]
Description: hypothetical protein BG20_I2156, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (35 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       122  (0.00680462); expected 358.6 (0.02)
Passed bias filter:                       93  (0.00518713); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.29s 00:00:00.65 Elapsed: 00:00:00.45
# Mc/sec: 231.64
//
Query:       EPA05792.1  [L=279]
Description: apurinic endonuclease (APN1) [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-34  119.6   0.0    2.5e-34  118.6   0.0    1.5  2  AP_endonuc_2  Xylose isomerase-like TIM barrel
  ------ inclusion threshold ------
       0.12   12.0   0.0       0.13   11.8   0.0    1.3  1  DUF3445       Protein of unknown function (DUF3445)


Domain annotation for each model (and alignments):
>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.6   0.0   2.8e-38   2.5e-34       4     210 .]      20     237 ..      17     237 .. 0.95
   2 ?   -2.3   0.0      0.27   2.4e+03     112     131 ..     241     260 ..     240     272 .. 0.86

  Alignments for each domain:
  == domain 1  score: 118.6 bits;  conditional E-value: 2.8e-38
                   HHHCT-SEEEEECCTCSHHHHC..HHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCS.HHHHHHHHHHHHHHHHHHTBSEEEEEBCCGBCT CS
  AP_endonuc_2   4 aaeaGfdgvElfgrdlvpvsel..sdeelrelrkaldelglriaslslftrfgypdederear.reesvdalkraielaaaLGapllvlhpGtagag 97 
                   a e    ++++f+r+++ + ++  s+ ++  ++  l++  +  ++ ++++ +   +    +++  e+svd l +++ ++a+LG+p+l++h G   ++
    EPA05792.1  20 AVERECSAFQIFTRNPRGWNAKdlSENDITNFKTKLKASKIDKFATCAHMPYLPNLST-PKSDgFEKSVDTLISEMSRCAQLGIPYLITHLG---SH 112
                   55666789**********************************9999999999996653.44449****************************...** PP

                   TTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTSSSTC..HHHHHHHHHHTTTT.EEEEEEHHHHHHH......TTTHHHHHHHHHGG... CS
  AP_endonuc_2  98 pkgseeeawerlaeslneladyaekegvklalEtlagsgvelgd..eelarlldavdspn.vgvclDtgHllia......eedvddalraladr... 182
                    +++ee+ +++l+++ln++++   k++v+++lE++ag+ ++ g   e+l+++++++++++ +g+c+Dt+H++        e  v d++++++d    
    EPA05792.1 113 LGSGEEAGIKQLVKGLNKAGQT--KNDVMILLENTAGQKNSVGAgfEQLEEIFNQLKPTKkFGICIDTCHAFVSgydlrtEKSVKDTFAKFDDVigf 207
                   **********************..****************9999***************************************************** PP

                   ..EEEEEE.EESSTTTTSSTTEESTTSSSS CS
  AP_endonuc_2 183 ..ikhvHikDakgdlgagrdrhvpigeGei 210
                     +k++H++Dakg+ g++ drh  ig G+i
    EPA05792.1 208 enLKILHLNDAKGEIGCNLDRHYHIGLGNI 237
                   **************************9986 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.27
                   HHHHHHHHHHHHTSEEEEE- CS
  AP_endonuc_2 112 slneladyaekegvklalEt 131
                   +l e+++ a k+ + ++lEt
    EPA05792.1 241 GLSEVVKTANKKKIPIILET 260
                   68899999999999999998 PP

>> DUF3445  Protein of unknown function (DUF3445)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.5e-05      0.13      93     156 ..     133     201 ..      24     204 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.5e-05
     DUF3445  93 lvqeDllillen..dgeyyleAgvvcfpagwd...lreklgkpLseiHepVpgykekleksmerffarl 156
                 ++++D++illen   ++  + Ag   +   ++   + +k+g  +++ H+ V gy+ + eks++  fa+ 
  EPA05792.1 133 QTKNDVMILLENtaGQKNSVGAGFEQLEEIFNqlkPTKKFGICIDTCHAFVSGYDLRTEKSVKDTFAKF 201
                 6789999999996433477788877777666433399*****************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1927.84
//
Query:       EPA05793.1  [L=286]
Description: hypothetical protein BG20_I2560, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 2001.92
//
Query:       EPA05794.1  [L=287]
Description: hypothetical protein BG20_I2558, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1829.49
//
Query:       EPA05795.1  [L=32]
Description: hypothetical protein BG20_I2668, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (32 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       141  (0.00786435); expected 358.6 (0.02)
Passed bias filter:                      136  (0.00758548); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 228.94
//
Query:       EPA05796.1  [L=133]
Description: hypothetical protein BG20_I2666, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-08   32.6   0.2      8e-08   31.9   0.2    1.4  1  CbiD      CbiD
  ------ inclusion threshold ------
       0.11   11.4   0.1       0.12   11.2   0.1    1.1  1  DUF917    Protein of unknown function (DUF917)


Domain annotation for each model (and alignments):
>> CbiD  CbiD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.2   8.9e-12     8e-08     214     252 .]       2      40 ..       1      40 [. 0.97

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 8.9e-12
        CbiD 214 alvkvsnfvgealeeaaekgvkkvllvghiGKlvKlagG 252
                 ++v++++f g++++++a+k++kk ++vg+iGKl+K+a+G
  EPA05796.1   2 CFVQMGDFSGYTIQQCARKEIKKAYVVGFIGKLAKMAAG 40 
                 79***********************************99 PP

>> DUF917  Protein of unknown function (DUF917)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   1.3e-05      0.12     173     237 ..       3      71 ..       1      96 [. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 1.3e-05
                 CTTTTTEEEEEEEEE-HHHHHH--SBSHHHHHHHHHHHHHTT--.......-SHHHHHHHHHH-EEEEEE CS
      DUF917 173 lvemgsfagvaaypmtgaelkraavpgtlslalriGravaearea.k....dvveailealgggakvlfk 237
                  v+mg f+g   + +  +e+k+a+v g + +  ++   v++ +++ +    + +++i+++++ + k+++ 
  EPA05796.1   3 FVQMGDFSGYTIQQCARKEIKKAYVVGFIGKLAKMAAGVKQTHVKgSkvdmNFLAEIAKKCN-ADKMIID 71 
                 68*****************************************9973577777899999999.7776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.56
# Mc/sec: 713.61
//
Query:       EPA05797.1  [L=154]
Description: hypothetical protein BG20_I2661, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-35  120.9   0.0      4e-35  120.7   0.0    1.0  1  DUF3473   Domain of unknown function (DUF3473)


Domain annotation for each model (and alignments):
>> DUF3473  Domain of unknown function (DUF3473)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.7   0.0   2.2e-39     4e-35       1     129 [.      16     151 ..      16     152 .. 0.96

  Alignments for each domain:
  == domain 1  score: 120.7 bits;  conditional E-value: 2.2e-39
     DUF3473   1 SSvfPvrhdlyGipdaprkpfrikkekgk.......llElPvstlklggrnlplaGGgyfRlfPyalikallrrlnregrpavlYfHpwEldpdq.prv 91 
                 SS++P++++lyGi +a++kp++i++++ +       +lE+P+ ++k++g+++p+aGG+y+R +P+++i++++r++n+e+ pa +Y+H wEl p+  p++
  EPA05797.1  16 SSIVPAKTKLYGIDNAETKPYKITSSSIEknnpdgkILEFPLLVTKIFGKTIPAAGGFYLRTLPLKIIERAIRKYNDESIPATFYIHSWELTPEYmPKI 114
                 9***********************998778999999*********************************************************962699 PP

     DUF3473  92 kgaslksrfrhylnlkrteerlrrllsdfeFttveell 129
                 + +sl+ +f +y+nl++t+++++++l++f+Ft++e++l
  EPA05797.1 115 P-LSLMDSFITYHNLNSTFSKMDKILKKFKFTSFEQYL 151
                 5.9********************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 999.99
//
Query:       EPA05798.1  [L=231]
Description: hypothetical protein BG20_I2522, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.7e-05   25.0   0.1    2.8e-05   24.3   0.1    1.6  1  HAD_2       Haloacid dehalogenase-like hydrolase
    0.00015   22.1   0.0    0.00021   21.6   0.0    1.2  1  Hydrolase   haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.092   12.6   0.0       0.19   11.6   0.0    1.6  1  Hypoth_Ymh  Protein of unknown function (Hypoth_ymh)


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.1   4.6e-09   2.8e-05      86     171 ..      97     183 ..      16     192 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 4.6e-09
       HAD_2  86 elLeeL.keagyklgivTsksreaveekleqlgiesyFdvivtsedvekk..KPdpeviekaleklklkkeeviyvGDsptDieaakka 171
                 +l+e+L k+   k+ iv+ + +e+v+ +l+ +  +  ++     ed +++  KP+pe++ + ++ + ++   +iyvGDs  D++ akka
  EPA05798.1  97 NLIEKLtKKFTDKISIVSGRGKESVRYSLKSILDKFDLKNSAFLEDESRElaKPNPESLIRSIRGMACT--CCIYVGDSMEDLIMAKKA 183
                 6788884455669****************99864433444444555555455********999987775..7***************98 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   3.5e-08   0.00021     126     209 ..      98     183 ..      91     184 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 3.5e-08
                 HHHHHHHTTE.EEEEEESSEHHHHH.HHHHHTT.GGGE.SEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHT CS
                 xxxxxxxxxx.xxxxxxxxxxxxxx.xxxxxxx.xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
   Hydrolase 126 avasLkaagi.evvlltgdnpetae.raanqlG.ddyf.daviasdietvakpspegkvaaireLqgkpeevamVGDgvnDaaalaaA 209
                 ++++L ++   ++ +++g  +e ++ ++ + l+ +d   +a ++ +  + akp+pe + + ir +      ++ VGD++ D+ ++++A
  EPA05798.1  98 LIEKLTKKFTdKISIVSGRGKESVRySLKSILDkFDLKnSAFLEDESRELAKPNPESLIRSIRGMACTC--CIYVGDSMEDLIMAKKA 183
                 566677665557999**********666666996555535555555555****************8777..***************98 PP

>> Hypoth_Ymh  Protein of unknown function (Hypoth_ymh)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   3.2e-05      0.19      68      93 ..     179     204 ..     103     207 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.2e-05
  Hypoth_Ymh  68 etekseqeGlknLlaGivsaiRNpka 93 
                  ++k+ ++G+k+++ Gi+++ +Np+a
  EPA05798.1 179 MAKKATEQGYKTIFCGIIGTSKNPQA 204
                 467899******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1466.75
//
Query:       EPA05799.1  [L=85]
Description: imidazoleglycerol-phosphate dehydratase domain protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-13   51.1   1.3    3.8e-13   50.0   1.2    1.5  2  IGPD      Imidazoleglycerol-phosphate dehydratase


Domain annotation for each model (and alignments):
>> IGPD  Imidazoleglycerol-phosphate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.15   2.7e+03      68      82 ..      15      29 ..       6      35 .. 0.66
   2 !   50.0   1.2   2.1e-17   3.8e-13       1      51 [.      36      85 .]      36      85 .] 0.96

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.15
                ETTEEEEEEEE--SS CS
        IGPD 68 mDealaevaldlsgr 82
                  e+ ++v+++l g+
  EPA05799.1 15 TKETTVSVSVNLDGT 29
                456777777777665 PP

  == domain 2  score: 50.0 bits;  conditional E-value: 2.1e-17
                ....HHHHHHHHHHHHHT--EEEEEEESSH...HHHHHHHHHHHHHHHHHH CS
        IGPD  1 TgigfldhmLdqlakhggfdlkvkvkgdlevddHhtvedvgialGqalkea 51
                Tgi fldh+++++ khg +dlkv++k + ++ +Hh++ed++i++G a+++a
  EPA05799.1 36 TGISFLDHLITAFGKHGMMDLKVNAKSNDKI-EHHLIEDTAITIGLAIDKA 85
                9*************************99998.79**************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 541.96
//
Query:       EPA05800.1  [L=137]
Description: hypothetical protein BG20_I1962, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.044   14.1   0.4        6.5    7.1   0.0    2.4  2  DUF948     Bacterial protein of unknown function (DUF948)
      0.084   12.7   0.6        0.2   11.5   0.1    1.9  3  DASH_Duo1  DASH complex subunit Duo1
      0.091   12.3   2.5        0.2   11.2   2.5    1.6  1  Snf7       Snf7


Domain annotation for each model (and alignments):
>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0    0.0011       6.5      47      87 ..      12      52 ..       3      54 .. 0.85
   2 ?    5.0   0.1    0.0047        28      24      61 ..      66     113 ..      55     127 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0011
      DUF948 47 kevedllakvnelledvneklekvdplteavadlgesvsel 87
                ++v+++l +++  le+v+ +l ++  l +a+  +g ++s++
  EPA05800.1 12 RKVTKMLGNARMSLEQVQLRLTTIHDLGDAMVAIGPAMSTM 52
                67999999999999999999999999999998888887765 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0047
      DUF948  24 lkktldeaaatieele..........kqvdpilkevedllakvnelle 61 
                 + + l+++++t+++l+           ++++ ++e+e++l+++ +++e
  EPA05800.1  66 ADSELNSMTQTLNGLMmdslagdsfsMETGASSEETERILQEASAVAE 113
                 455667777777777788888888888888888888888888877654 PP

>> DASH_Duo1  DASH complex subunit Duo1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   3.3e-05       0.2       2      34 ..       4      36 ..       3      42 .. 0.93
   2 ?   -3.2   0.0       1.3   7.7e+03      10      15 ..      71      76 ..      65      83 .. 0.48
   3 ?   -3.1   0.0       1.1   6.8e+03      55      62 ..      99     106 ..      95     113 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.3e-05
   DASH_Duo1  2 LekEleqLrkinevienviesLkkaksniervk 34
                L +El ++rk+ +++ n + sL++++  + +++
  EPA05800.1  4 LSNELAEIRKVTKMLGNARMSLEQVQLRLTTIH 36
                889***********************9999998 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.3
   DASH_Duo1 10 rkinev 15
                +++ ++
  EPA05800.1 71 NSMTQT 76
                222222 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 1.1
   DASH_Duo1  55 ehtqrlll 62 
                 e+t r+l+
  EPA05800.1  99 EETERILQ 106
                 44555544 PP

>> Snf7  Snf7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   2.5   3.3e-05       0.2      48     171 ..       6     126 ..       1     128 [. 0.62

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.3e-05
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTCCHHHHHHHHHHHHHHHHHTC.HHHHHHHHHTT-......GGTTH CS
        Snf7  48 Kqkkryekqldqldnqlanleqvslaienlksnkevlnamkqgakamkamnkkvdidkidklmdeiedqmekaee.isEalsrsldda......deedE 139
                 +++ +++k  ++l n + +leqv+l + + ++  + + a + + ++mk  ++ +      + m e   ++  + + ++  + +sl  +      +  + 
  EPA05800.1   6 NELAEIRKVTKMLGNARMSLEQVQLRLTTIHDLGDAMVAIGPAMSTMKGLKSSLG-----RFMPEADSELNSMTQtLNGLMMDSLA-GdsfsmeTGASS 98 
                 6677788888888888888888888888888888888888888888888887765.....77777665554443314444444442.212222244444 PP

                 HHHHHHHHHHHHHHHHCSH.HHHHHHHTXXXS CS
        Snf7 140 eeleaeLdaLeqelgdeelldesvklpevPse 171
                 ee+e++L++  +  +++     + k p+vP+ 
  EPA05800.1  99 EETERILQEASAVAEQQ----IGDKFPSVPTS 126
                 44444444444444444....49999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 916.37
//
Query:       EPA05801.1  [L=287]
Description: hypothetical protein BG20_I1961 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.027   14.0   6.4      0.067   12.7   6.4    1.6  1  DUF1189   Protein of unknown function (DUF1189)
       0.27   11.0   1.3       0.48   10.2   1.3    1.4  1  SpoIIIAH  SpoIIIAH-like protein


Domain annotation for each model (and alignments):
>> DUF1189  Protein of unknown function (DUF1189)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   6.4   7.5e-06     0.067      21     130 ..       2     120 ..       1     130 [. 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.5e-06
     DUF1189  21 gigkailYlllLslilalpisiiifyefnskinqleeliee...........eipdFtiedGelqieekepiiiqedgitiifDtsgetdeedlekynn 108
                 +i k i+++l+ +l++++++ + ++   n+k + +  +i++           +i +++  +Ge+ ++e+     q +  ++ fD++++ + ++l ++++
  EPA05801.1   2 SINKKIIFVLIAVLLISVIYYYNFMD-NNQKQQFFDFNINTsqadleqleidSIFKISGGKGEFILDEEAR-LKQYTRLYFEFDEKNQATYDQLMNNDE 98 
                 68999*************99666665.66666666666655667777787777777777889999999965.4489999******************99 PP

     DUF1189 109 gililkdkiviknggttqsysy 130
                   ++    ++ ++++++  y+y
  EPA05801.1  99 KTVVIYPIFTASAYNQPGFYNY 120
                 9999999999999999999988 PP

>> SpoIIIAH  SpoIIIAH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.3   5.4e-05      0.48       1      28 [.       5      37 ..       5     100 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 5.4e-05
                XXXXXXXXXXXXXXXXXXXXXXXXX.......X CS
    SpoIIIAH  1 knqiiitaLalmiavagYlnftedsgk.....k 28
                k++i ++  +l+i v+ Y+nf+++++k      
  EPA05801.1  5 KKIIFVLIAVLLISVIYYYNFMDNNQKqqffdF 37
                7888899999*************9865444431 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       963  (0.0537119); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1952.49
//
Query:       EPA05802.1  [L=217]
Description: hypothetical protein BG20_I1958 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 1238.98
//
Query:       EPA05803.1  [L=270]
Description: hypothetical protein BG20_I1960 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1549.97
//
Query:       EPA05804.1  [L=253]
Description: precorrin-4 C(11)-methyltransferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.1e-46  158.0   0.0    3.7e-46  157.8   0.0    1.1  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
      0.004   17.2   0.1       0.09   12.9   0.0    2.4  2  UvrA_inter    UvrA interaction domain
     0.0098   16.3   0.1      0.017   15.5   0.1    1.5  1  Radical_SAM   Radical SAM superfamily
  ------ inclusion threshold ------
      0.014   14.8   0.1       0.03   13.7   0.1    1.5  1  Aldolase      KDPG and KHG aldolase


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.8   0.0   8.2e-50   3.7e-46       1     211 [.       3     207 ..       3     209 .. 0.94

  Alignments for each domain:
  == domain 1  score: 157.8 bits;  conditional E-value: 8.2e-50
  TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealragkdVvllvsGDPlvygtgs 97 
                   ++y+VG GpGdpel+T++A +++++ad+v++++s+ +  +l+l+++        g+  + ++ + eei + l + ++++k V++l+ GDP++yg+  
    EPA05804.1   3 RIYFVGCGPGDPELITIKAKKLIQKADIVVYSGSLIPPPILKLCKK--------GELHNAAGLVREEIFDLLYKNAKNDKLVIRLHDGDPSIYGAIK 91 
                   69*******************************9999999999976........5666677777********************************* PP

  TP_methylase  98 elvealrareagieveviPGvsslqaaaarlgiplteggevlsvl....lpglakeeereleallangdtlvllkaprklaelaelLkea.lyddtt 189
                   e ++ l++  +gie  v+PG++++ a aa+lg+ lt  g++++++    + +++ ++++++++l++++ tl+++ +++ l++++++  +  ++ + t
    EPA05804.1  92 EQIDNLKE--KGIESVVVPGITAFLASAAALGTQLTLPGVTQTIIvtraESRTKVPKREKISELAKHKATLIFYLSVHLLSNIVKEAVAGgYK-KST 185
                   ********..9**************************************99999*********************************999555.567 PP

  TP_methylase 190 pvavveragtedervvrgtlee 211
                   pvavv ra+++d+++++gtl  
    EPA05804.1 186 PVAVVYRASWDDQKIIKGTLDN 207
                   *******************986 PP

>> UvrA_inter  UvrA interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.043   1.9e+02      31      58 ..      88     115 ..      60     155 .. 0.84
   2 !   12.9   0.0     2e-05      0.09       2      48 ..     204     251 ..     203     253 .] 0.90

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.043
  UvrA_inter  31 gefkkllenlkkkGfvrvriDgeiydld 58 
                 g +k+ ++nlk+kG   v++ g +  l 
  EPA05804.1  88 GAIKEQIDNLKEKGIESVVVPGITAFLA 115
                 7889999*******99999988766555 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 2e-05
  UvrA_inter   2 sveqIvdqilklee.gtkllilaPvvrerkgefkkllenlkkkGfvrv 48 
                 ++++Iv+++ + +  +t ++i++ v+ +   e++kl ++  ++G++++
  EPA05804.1 204 TLDNIVKKVRDEKItRTAIVIISNVIDSTDYEYSKLYDKNFSHGYRKI 251
                 7899*****987651679***************************998 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   3.9e-06     0.017      32     127 ..      60     183 ..      51     239 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.9e-06
                  HHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC........................CCTEEEEEEECSSCHG..............H CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................xxxxxxxxxxxxxxxx..............x RF
  Radical_SAM  32 eeileevkelkaekgvkevilgggepllypdfvellerlakla........................vpgiritvetngtlpd..............e 91 
                  eei +++ ++ a++++ ++ l+ g+p+ y  + e +++l+++                                   +g++ +              +
   EPA05804.1  60 EEIFDLLYKN-AKNDKLVIRLHDGDPSIYGAIKEQIDNLKEKGiesvvvpgitaflasaaalgtqltL---------PGVTQTiivtraesrtkvpkR 147
                  8899999888.6777**************************99*****88888888885544455442.........33333355555555678999* PP

                  HHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHTCTSHH CS
                  xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM  92 eklerllelg.vdrvslgleaaddekvlklmnrghtf 127
                  ek+ +l++   +  ++l+++ +++  v++ + +g+  
   EPA05804.1 148 EKISELAKHKaTLIFYLSVHLLSNI-VKEAVAGGYKK 183
                  ********9999999****999999.99888766655 PP

>> Aldolase  KDPG and KHG aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   6.7e-06      0.03      70     112 ..      91     133 ..      88     140 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.7e-06
                 HHHHHHHHHCT-SEEEESS--HHHHHHHHHTTS-EEEEESSHH CS
    Aldolase  70 aeqlaeakeaGaqfvvsPGltadllkaavdlkipllPGvstps 112
                 +eq+++ ke G + vv PG+ta l+ aa   +   lPGv+++ 
  EPA05804.1  91 KEQIDNLKEKGIESVVVPGITAFLASAAALGTQLTLPGVTQTI 133
                 57999**********************************8765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       821  (0.0457917); expected 358.6 (0.02)
Passed bias filter:                      564  (0.0314574); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1518.71
//
Query:       EPA05805.1  [L=40]
Description: hypothetical protein BG20_I1955, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       236  (0.013163); expected 358.6 (0.02)
Passed bias filter:                      142  (0.00792013); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 260.01
//
Query:       EPA05806.1  [L=240]
Description: precorrin-2 C(20)-methyltransferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.9e-56  190.8   0.0    3.2e-56  190.6   0.0    1.0  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.6   0.0   1.8e-60   3.2e-56       2     212 ..       4     222 ..       3     223 .. 0.96

  Alignments for each domain:
  == domain 1  score: 190.6 bits;  conditional E-value: 1.8e-60
  TP_methylase   2 lylVGvGpGdpellTvrAlralktadvvlgddsr......aleilldllaeel.....eleapmgkekepleeayeeiaealaealragkdVvllvs 87 
                   l+++GvGpGdpellTv+A++a+++ad +++++s+      al+i+  l+++ +     +l +pm+k+k++le++++++a+++ae++ +gk+Vv+l++
    EPA05806.1   4 LIGIGVGPGDPELLTVKAAKAIQNADTIMCPASNedrpsiALSIVSSLIDKSKnqeiiKLIFPMTKDKDVLEATWKKNAKIMAEKVLTGKNVVYLTI 100
                   89**************************9999656778899999999999999******************************************** PP

  TP_methylase  88 GDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvllpglakeeereleallangdtlvllkaprklaelaelLkea. 183
                   GDP++y+t++++++ ++ ++++i++ viPG+ s+ + aa++g++++eg e+++++ p+++  + + ++++++n +t+v+lk++r +++++e+Lkea 
    EPA05806.1 101 GDPYLYSTWIYMHKDIEMNHPEIKISVIPGIVSMFTFAAKVGVSIAEGAEKVAII-PSCY--DLSSVKEIAKNSETMVFLKDGRYFDKVIEVLKEAg 194
                   *******************************************************.9999..**********************************8 PP

  TP_methylase 184 lyddttpvavveragtedervvrgtleel 212
                   ++d+    a+++++gte+e +++ tl+e+
    EPA05806.1 195 FPDNS-IFAIGQDLGTENEIIRKLTLGEV 222
                   88855.********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1966.99
//
Query:       EPA05807.1  [L=60]
Description: hypothetical protein BG20_I1959 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.032   13.8   0.8      0.041   13.4   0.8    1.1  1  4HB_MCP_1  Four helix bundle sensory module for signal transd


Domain annotation for each model (and alignments):
>> 4HB_MCP_1  Four helix bundle sensory module for signal transduction
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.8   2.3e-06     0.041      13      43 ..       5      35 ..       2      36 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.3e-06
   4HB_MCP_1 13 lllallliivGvvGlyslkkinknletmYed 43
                +++ ++++iv ++G +sl +in+n et+  d
  EPA05807.1  5 IIIGIIIVIVISIGAVSLAQINQNDETVNAD 35
                5677788888888999999999999998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1073  (0.0598472); expected 358.6 (0.02)
Passed bias filter:                      810  (0.0451782); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 406.27
//
Query:       EPA05808.1  [L=224]
Description: CobB/CobQ-like glutamine amidotransferase domain protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.5e-41  141.0   0.2    4.1e-41  140.8   0.2    1.0  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
    2.7e-05   24.1   0.0    2.7e-05   24.1   0.0    1.2  1  SNO            SNO glutamine amidotransferase family
  ------ inclusion threshold ------
      0.032   14.3   0.7      0.057   13.5   0.7    1.5  1  DUF1836        Domain of unknown function (DUF1836)
      0.037   13.7   0.0      0.047   13.3   0.0    1.2  1  Peptidase_S51  Peptidase family S51


Domain annotation for each model (and alignments):
>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.8   0.2   9.1e-45   4.1e-41       1     195 [.      18     209 ..      18     210 .. 0.89

  Alignments for each domain:
  == domain 1  score: 140.8 bits;  conditional E-value: 9.1e-45
    GATase_3   1 kiavirlpaisnyt..dldpLeaepevrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmLGeeiedpeg 97 
                 +ia++ + ++++y+  +l++L++e+++  +f+p+++++l+e  d ++++Gg+++i  + l++++ +++ ik+++e+ +p++++CGGl++L ++i   + 
  EPA05808.1  18 TIAIALDGSFNFYYrdNLNALRREGANLKFFSPINNKKLPE-SDGIYIGGGFPEILGNLLEKNHVMKKTIKKLSEDSAPIYAECGGLMYLTKSIDYGN- 114
                 69*************************************66.***************************************************97654. PP

    GATase_3  98 vegeageveglglLdietefekekltgqvegevel....aaegeevkGyEiHsGrtilkekakpllkvkv..ggnng.ekdGavkksedgnvlGtYlHg 189
                 +     + +++gl+d++t+++k+  ++ ++g++ l    ++++ e++G+E+H+++  +  + +  ++++   g +++ +kdG+++     n+l++Y H+
  EPA05808.1 115 K-----KFKMIGLFDADTKMTKKMKLNYTKGKIVLkntiTNKTHELRGHEFHYSELDSV-SSDSKFAYELdiGLGIKnQKDGLIQY----NTLASYGHL 203
                 3.....8***************877778888877799988889***********66554.455555555545666667******99....********* PP

    GATase_3 190 lfdnrn 195
                  fd+++
  EPA05808.1 204 YFDSSD 209
                 **9975 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   6.1e-09   2.7e-05      27     101 ..      52     128 ..      21     219 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 6.1e-09
                 SGGGGCC-SEEEE-SS-HHHHHHHHHHTT-HHHHHHHHHTT.--EEEETHHHHHHCCEETTB..SS-SS--CCEEEE CS
         SNO  27 rkedlaevdaliiPGGestamskliertglyedllefvknsekvvlGtCaGlillskelene..lvktlellkvkvk 101
                 ++++l e d++ i GG    ++ l+e+  ++++  +++ + + +++  C Gl++l+k ++    + k ++l++ + k
  EPA05808.1  52 NNKKLPESDGIYIGGGFPEILGNLLEKNHVMKKTIKKLSEDSAPIYAECGGLMYLTKSIDYGnkKFKMIGLFDADTK 128
                 4568999**************************************************99744338888888887655 PP

>> DUF1836  Domain of unknown function (DUF1836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.7   1.3e-05     0.057      11      51 ..     104     145 ..      76     154 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.3e-05
     DUF1836  11 Lyldqvvelvnqvleslkrned.kvltktminNYvKkkllek 51 
                 +yl + +++ n++++ +   +  +++tk m  NY+K k++ k
  EPA05808.1 104 MYLTKSIDYGNKKFKMIGLFDAdTKMTKKMKLNYTKGKIVLK 145
                 799999**********9998777**************98765 PP

>> Peptidase_S51  Peptidase family S51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.1e-05     0.047      78     140 ..      54     117 ..      26     151 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.1e-05
                    HHHHHSSEEEE--S-HHHHHHHHHHTTHHHHHHHHH.HTT-EEEEETHHHHTTSSB-GGGTTTS CS
  Peptidase_S51  78 eklleadviyvgGGntfrLlkllketgldkllreav.qqglvyiGvSAGaivagesiettsysd 140
                    +kl e+d+iy+gGG    L +ll+++++ k  ++++ +++ ++     G +  ++si + + + 
     EPA05808.1  54 KKLPESDGIYIGGGFPEILGNLLEKNHVMKKTIKKLsEDSAPIYAECGGLMYLTKSIDYGNKKF 117
                    47899*******************999988777776699*****99999999999999988544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1424.53
//
Query:       EPA05809.1  [L=70]
Description: hypothetical protein BG20_I2212 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-16   59.7   0.2    3.1e-16   59.6   0.2    1.0  1  CbiC      Precorrin-8X methylmutase


Domain annotation for each model (and alignments):
>> CbiC  Precorrin-8X methylmutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.6   0.2   1.7e-20   3.1e-16       2      59 ..       9      68 ..       8      70 .] 0.94

  Alignments for each domain:
  == domain 1  score: 59.6 bits;  conditional E-value: 1.7e-20
                HHHHHHHHHHCHC-TT.S-CHHHHHHHHHHHHHT-CCHH..HHEEE-TTHHHHHHHHHHC CS
        CbiC  2 IeaeSfaiideelgeeelseeeeevvrRvihatadfela..ellrfspdaveaglealka 59
                Ie+ S+++idee+g+++++e+e+++vrR+ih+tadf++a  + + f+++a+e+g++alk+
  EPA05809.1  9 IEDASMQMIDEEIGTHQYNEKEWPIVRRIIHSTADFDFAkeNRVIFHKKAIESGINALKK 68
                99************************************9445789*************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 491.31
//
Query:       EPA05810.1  [L=250]
Description: sirohydrochlorin cobaltochelatase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      4e-36  123.6   0.0    3.4e-17   62.7   0.0    2.1  2  CbiX            CbiX
      1e-09   38.1   1.5    1.2e-09   37.9   1.5    1.1  1  CbiK            Cobalt chelatase (CbiK)
    2.5e-07   30.1   0.1    0.00069   18.8   0.0    2.0  2  Ferrochelatase  Ferrochelatase


Domain annotation for each model (and alignments):
>> CbiX  CbiX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.7   0.0   5.8e-21   3.4e-17       1     106 [.      10     112 ..      10     113 .. 0.91
   2 !   59.2   0.0   7.1e-20   4.2e-16       1     106 [.     138     240 ..     138     241 .. 0.96

  Alignments for each domain:
  == domain 1  score: 62.7 bits;  conditional E-value: 5.8e-21
                 -STSSCCHHHHHHHHHHHHHHHCCSCCCEECESCCCECCSCCSSHHHHC-SBSEEEEEEESSSSSHHHHTHHHHHCT--SSSS-TTEEEEE---CCCSC CS
        CbiX   1 HGSrdpesneeveklaeelrekgpfkpvelgfleleepsleealrelaeqgvkrivvvPlflfaGvhvkeDIpeeleeaeeahpkdveieytepLGthp 99 
                 +GSr++e++ee+e +++++++k++++  e++fle+e p++e++++++ +q +++ ++vP+fl +G  vk+     ++ ++ +++ +v++++t+p++ h+
  EPA05810.1  10 RGSREREASEELEIICDAIKAKRDYVFTEYCFLEVEPPYIEDGIKRCLKQDIDHLTIVPYFLYPGKKVKN---AVTDVMKFQKDTKVKFVVTKPMSMHK 105
                 7*********************************************************************...55555555555568************ PP

                 CHHHHHH CS
        CbiX 100 lvaevlk 106
                  ++ +++
  EPA05810.1 106 TLISLVE 112
                 9998875 PP

  == domain 2  score: 59.2 bits;  conditional E-value: 7.1e-20
                 -STSSCCHHHHHHHHHHHHHHHCCSCCCEECESCCCECCSCCSSHHHHC-SBSEEEEEEESSSSSHHHHTHHHHHCT--SSSS-TTEEEEE---CCCSC CS
        CbiX   1 HGSrdpesneeveklaeelrekgpfkpvelgfleleepsleealrelaeqgvkrivvvPlflfaGvhvkeDIpeeleeaeeahpkdveieytepLGthp 99 
                 HGS+dp+++  +  +++ l++  +++ v  ++le+e+p++ e+++++++++ +  v+v +fl +G hvk+DI + l+ a e+     + ++t++LG ++
  EPA05810.1 138 HGSKDPNAQLSLDYVVDGLKN--NYRNVNRCWLEIEQPDIVEGIKTCEKNKPQVLVIVFYFLHEGAHVKTDINNDLKPALENSS-IKKAYITKHLGVDE 233
                 *********************..556***************************************************9888888.789*********** PP

                 CHHHHHH CS
        CbiX 100 lvaevlk 106
                 +++++++
  EPA05810.1 234 KMIDLII 240
                 ****997 PP

>> CbiK  Cobalt chelatase (CbiK)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   1.5     2e-13   1.2e-09      62     260 ..      51     246 ..      18     248 .. 0.84

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 2e-13
                 HHHHHHHHCT--EEEEEE--SCSSHHHHHHHHHHHHHGGGSS.EEEEE--SCS......SH.HHHHHHHHHHHTTS----TTEEEEEEE---SCHHHHH CS
        CbiK  62 ealeklkeegykevivqplhiipGeeyeklkreVkkfkkkfe.kiklgrPlldykGvedst.eDykevvealkdeierarkdealvfvgHGtehesnav 158
                 + +++  ++   ++ + p +++pG++  + ++ V kf+k+ + k ++++P+   k + +   + + + ++   ++i+  +kd  ++ +gHG++ + ++ 
  EPA05810.1  51 DGIKRCLKQDIDHLTIVPYFLYPGKKVKNAVTDVMKFQKDTKvKFVVTKPMSMHKTLISLVeNRIATTLQE--NQITIPKKDVDVLIIGHGSKDPNAQ- 146
                 567777788889999**********************999764679*****99888775540444444444..45555589999********998776. PP

                 HHHHHHHHHH..CT-S.EEEEETT.SSS-HHHHHHHHHHHT--EEEEEE-SSS--HHHHCCCCSSSTTSHHHHHHHTT--EEE----GGGSHHHHHHHH CS
        CbiK 159 yaeldkvlke..kdfkqvvvgtve.gyPeveevieelkkkgikevkliPlmlvAGdHaknDmasdeedswkealeaaGikveiilkgLGeieeirsifi 254
                    ld+v++   +++++v  + +e  +P++ e i++ +k++ +   ++ ++l  G H+k D+    +++ k ale+  ik   i k LG +e++ ++ i
  EPA05810.1 147 -LSLDYVVDGlkNNYRNVNRCWLEiEQPDIVEGIKTCEKNKPQVLVIVFYFLHEGAHVKTDI----NNDLKPALENSSIKKAYITKHLGVDEKMIDLII 240
                 .467777764447799*****999558***************99999999************....6789***************************** PP

                 HHHHHH CS
        CbiK 255 khikea 260
                 ++ ke+
  EPA05810.1 241 ERAKEV 246
                 *99986 PP

>> Ferrochelatase  Ferrochelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.1e-07   0.00069      87     193 ..      34     140 ..       7     165 .. 0.82
   2 !    9.8   0.0   6.5e-05      0.39     241     314 ..     172     244 ..     161     247 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.1e-07
                     --EEEEEEESSSSSBHHHHHHHHHCTT-SEEEEEES-SS--TTTHHHHHHHHHHHHHHTT-SSEEEEE---TT-HHHHHHHHHHHHHHHTTS-.. CS
  Ferrochelatase  87 idvkvylamrywePsiedaleelkadgvervvvlplyPqysasttgssleeleralkkkreapevrvirqfydhpgyiealaesikealeelp.. 179
                       +  y+  +  +P+ied +++  ++++++++++p +  y    +++++ ++++  k    ++++ v +    h+++i+ + ++i  +l+e++  
      EPA05810.1  34 YVFTEYCFLEVEPPYIEDGIKRCLKQDIDHLTIVPYFL-YPGKKVKNAVTDVMKFQKD--TKVKFVVTKPMSMHKTLISLVENRIATTLQENQit 125
                     5566677778899*********************9775.5556688888888888766..5899***************************9999 PP

                     .HC.C-EEEEEEE-- CS
  Ferrochelatase 180 .eekkakllfsaHgl 193
                      ++k +++l+  Hg 
      EPA05810.1 126 iPKKDVDVLIIGHGS 140
                     955569999999995 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 6.5e-05
                     SSBHHHHHHHHCCC.-S-EEEE-TT-SS--HHHHIIIIIIIITTSTT..CCCEEE----TT-HHHHHHHHHHHH CS
  Ferrochelatase 241 ePdtddtleelaekgvkaivvvpigFvsDhlEtleeldiearelaeeaggekfvrvptlndspafiealadlve 314
                     +Pd+ + ++ +++++  +++v+   F  +   ++ +++  ++ ++e+++++k    + l+ ++++i+++ + ++
      EPA05810.1 172 QPDIVEGIKTCEKNK-PQVLVIVFYFLHEGAHVKTDINNDLKPALENSSIKKAYITKHLGVDEKMIDLIIERAK 244
                     699999999999887.9**************************************************9988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1771.97
//
Query:       EPA05811.1  [L=318]
Description: protein CbiG, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.5e-34  115.3   0.2    1.5e-33  114.6   0.2    1.3  1  CbiG_N         Cobalamin synthesis G N-terminal
    6.3e-27   94.4   0.4    1.3e-26   93.5   0.2    1.6  2  CbiG_C         Cobalamin synthesis G C-terminus
    5.8e-15   55.2   0.0    1.9e-14   53.5   0.0    1.9  2  CbiG_mid       Cobalamin biosynthesis central region
  ------ inclusion threshold ------
       0.12   12.7   0.0       0.49   10.7   0.0    2.0  2  SpoU_sub_bind  RNA 2'-O ribose methyltransferase substrate bi


Domain annotation for each model (and alignments):
>> CbiG_N  Cobalamin synthesis G N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.6   0.2   3.4e-37   1.5e-33       4      82 .]      22     100 ..      19     100 .. 0.97

  Alignments for each domain:
  == domain 1  score: 114.6 bits;  conditional E-value: 3.4e-37
                 HHHCCC-SEEEEES-HHHHHHHHHHH---TTT--EEEEE-TT--EEEEEE-TT.TTHHHHHHHHHHHTT-EE-XXXXX. CS
      CbiG_N   4 relfkeydalvfilaaGivvRliapllkdKktDpaVvvvdeagrfvisllsGhlggAnelAeeiaallgaepviTtatd 82 
                  elfk++ al++i+++G+v+Rliap+lkdKktDpaV+v+d++++fvis+lsGhlggAnel++ ia+ l+a+pviTta d
  EPA05811.1  22 VELFKNNTALICIFSLGAVIRLIAPYLKDKKTDPAVIVIDDKANFVISMLSGHLGGANELTQIIAQKLDAKPVITTAAD 100
                 589**************************************************************************97 PP

>> CbiG_C  Cobalamin synthesis G C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.7   7.6e+03      63      87 ..      84     108 ..      56     112 .. 0.67
   2 !   93.5   0.2   2.8e-30   1.3e-26       1     116 []     197     314 ..     197     314 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.7
                 E-HHHHHCHHCSCT-CHHHCCCSSS CS
      CbiG_C  63 fsaeeLaavevpnpsefvkkevGvp 87 
                 + a++L a +v ++ + v+k++ v+
  EPA05811.1  84 IIAQKLDAKPVITTAADVNKTIAVD 108
                 4455666666666666666666655 PP

  == domain 2  score: 93.5 bits;  conditional E-value: 2.8e-30
                 EEEEEEE-SS--HHHHHHHHHHHHHHCT--GGGEEEEEESSCCSHHHHHHHHHHHCTSTEEEE-HHHHHCHHCSCT-CHHHCCCSSS-HHHHHHHHHC. CS
      CbiG_C   1 lvvGiGcrrgtsaeeieeaieealeeaglseeavaalatidlKadepgllelaeklglplktfsaeeLaavevpnpsefvkkevGvpsVaEaaAllaa. 98 
                 lvvGiG + +ts+++i+e i+ +l++ +lse+++a+la+i++ +d +gl+++ +++g++++++++eeLa+++ pnps++vk+  G+ sV+EaaA+  + 
  EPA05811.1 197 LVVGIGLHWDTSKQTIKEGIDVCLQKFKLSEKSIAKLASIKKSEDVKGLIDIGKEMGVNVEYVNREELAEISAPNPSDTVKAFEGTSSVSEAAAIKVSr 295
                 79*********************************************************************************************8764 PP

                 .EECSCEEEE.TTEEEEEE CS
      CbiG_C  99 arllvpKqak.ggvTvAia 116
                 ++l+v+Kq+   + T+A+a
  EPA05811.1 296 GELIVEKQKFpPNLTIAVA 314
                 7******87799*****98 PP

>> CbiG_mid  Cobalamin biosynthesis central region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.96   4.3e+03      46      67 ..      13      34 ..       4      63 .. 0.78
   2 !   53.5   0.0   4.2e-18   1.9e-14       1      84 []     105     194 ..     105     194 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.96
    CbiG_mid 46 rlertlpehvdveykekaliwi 67
                + e+t  ++v++++++ ali+i
  EPA05811.1 13 YTESTSEKIVELFKNNTALICI 34
                5677777888888887777776 PP

  == domain 2  score: 53.5 bits;  conditional E-value: 4.2e-18
    CbiG_mid   1 palDilgrpfGwriegegaltevsaalvngepvavlqdvrlegterlertlpehvdveyk.e.......kaliwitprqlrfseesd.lqlhP 84 
                 +a+D++g++fGw+i++++ +t+vsa++vn+e ++v+q     g+++  ++lp+ v+++ + e       k  ++i+++ l+++  ++ ++++P
  EPA05811.1 105 IAVDLVGKEFGWKIDDDSTVTKVSAHMVNEESIGVYQ---EAGKKNWVKELPKNVKNYPSlEeminsnsKGYLIISDKILEGDFLKNsVVYRP 194
                 69***********************************...79999999999*******99889*****************99999888***99 PP

>> SpoU_sub_bind  RNA 2'-O ribose methyltransferase substrate binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00011      0.49      28      58 ..     238     268 ..     215     276 .. 0.81
   2 ?   -3.2   0.0       2.4   1.1e+04       3      13 ..     280     290 ..     279     303 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00011
  SpoU_sub_bind  28 adkrleellklakkrgikvelvdkekLdkls 58 
                    + ++++ l++  k+ g+ ve+v++e+L ++s
     EPA05811.1 238 KSEDVKGLIDIGKEMGVNVEYVNREELAEIS 268
                    35667799999*****************998 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.4
  SpoU_sub_bind   3 yGlhaVleaLk 13 
                    +G+ +V ea +
     EPA05811.1 280 EGTSSVSEAAA 290
                    78999999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2384.38
//
Query:       EPA05812.1  [L=109]
Description: putative precorrin-8X methylmutase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-38  132.5   0.6    1.6e-38  132.4   0.6    1.0  1  CbiC      Precorrin-8X methylmutase
  ------ inclusion threshold ------
       0.01   13.9   0.0      0.011   13.8   0.0    1.0  1  DUF4958   Domain of unknown function (DUF4958)


Domain annotation for each model (and alignments):
>> CbiC  Precorrin-8X methylmutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.4   0.6   1.8e-42   1.6e-38      97     195 ..       2     101 ..       1     102 [. 0.97

  Alignments for each domain:
  == domain 1  score: 132.4 bits;  conditional E-value: 1.8e-42
                 HHHHHHTS-HHHHHHHHHHHCTTTCEEEESS-HHHHHHHHHHHHHS..HTSEEEE----SCCHHHHHHHHHCSS.S-EEEESSS---HHHHHHHHHHHH CS
        CbiC  97 elakekgitrsaaamekaaeelegaivviGnAPtALlellelieegkvkpalvigvPvGFvgaaesKealaese.vpyitveGrkGGsavAaaivnaLl 194
                 e+ak++++trs+++m+ a ++ +g+iv++GnAPtALle++ +++eg vkpal+ig+PvGF+ aaesKe+l+++e +p+it+ GrkGGs+ A ai+naL+
  EPA05812.1   2 EIAKKENKTRSQVSMRIASSDIDGGIVAVGNAPTALLEVIGMVKEGIVKPALIIGIPVGFICAAESKEELSKLEeTPFITNIGRKGGSSSASAIINALY 100
                 789********************************************************************9656***********************8 PP

                 H CS
        CbiC 195 e 195
                 +
  EPA05812.1 101 K 101
                 7 PP

>> DUF4958  Domain of unknown function (DUF4958)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.2e-06     0.011     505     595 ..       6      99 ..       1     104 [. 0.66

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.2e-06
                 EE-TTT-EEEE-TTT--E..EEES--.TTBE...EEEEEEEEESSGGG-EEEEEEEEEEE----.GGG---B-SSSEEEE-TTT-EE----B--TT- CS
     DUF4958 505 kyeklstkvtinektgki..tlsglkdeaks...nvvlvtatagegkeavslkvPvffhfsnis.kdnvkieytPfvlqvnPkkGGesvaPkiisgi 595
                 k++k+ ++v + + +++i   + ++ ++ ++   ++++v+   g  k a+ + +Pv f  +  s ++  k+e tPf+ ++  +kGG s a  ii++ 
  EPA05812.1   6 KENKTRSQVSMRIASSDIdgGIVAVGNAPTAlleVIGMVKE--GIVKPALIIGIPVGFICAAESkEELSKLEETPFITNIG-RKGGSSSASAIINAL 99 
                 55666666665555555522355555555551114455544..44578999*****8887776636779********9996.799999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 882.81
//
Query:       EPA05813.1  [L=151]
Description: hypothetical protein BG20_I2625, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0032   17.5   0.0     0.0044   17.1   0.0    1.2  1  DNA_primase_S  DNA primase small subunit


Domain annotation for each model (and alignments):
>> DNA_primase_S  DNA primase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   2.5e-07    0.0044     131     171 ..      26      83 ..       2      88 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.5e-07
                    ................................-----------------....----- CS
  DNA_primase_S 131 w.................eakedivlvllyprldeqvtkgikhllkapfcihgktgnv 171
                                        + + v +++ +++d +vt +i++ +++p++++ k+g +
     EPA05813.1  26 SkrskiitelitngyssfQKTLENVSDSIGVKIDPNVTMDIHRIFRLPGSLNSKSGLT 83 
                    04444456666666666677888999***************************99966 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1109.33
//
Query:       EPA05814.1  [L=46]
Description: hypothetical protein BG20_I2624, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.28s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 328.29
//
Query:       EPA05815.1  [L=120]
Description: hypothetical protein BG20_I2650, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.9e-10   38.6   0.4    1.7e-09   37.3   0.4    1.7  1  AAA_lid_3  AAA+ lid domain


Domain annotation for each model (and alignments):
>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.4   9.6e-14   1.7e-09       2      45 .]      39      97 ..      38      97 .. 0.86

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 9.6e-14
   AAA_lid_3  2 vdlkeLAerTeGySGADlaalcreAallAlrr..............gik.eitmedfee 45
                vd++++Ae+T+G SGAD aa+ + A+ l + +              + + ++tm++fe+
  EPA05815.1 39 VDIDKIAELTDGLSGADTAAIANTAVSLVIHEfldahpdvkdieksSADaKVTMKHFEA 97
                9*****************************998888888776665444445******95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       922  (0.0514251); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 882.44
//
Query:       EPA05816.1  [L=66]
Description: hypothetical protein BG20_I2651, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.2e-17   60.5   0.2    9.3e-17   60.1   0.2    1.2  1  GatD_N    GatD N-terminal domain


Domain annotation for each model (and alignments):
>> GatD_N  GatD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.1   0.2   5.2e-21   9.3e-17       1      47 [.      20      65 ..      20      66 .] 0.93

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 5.2e-21
                --TT-EEEEE-SS-EEEEEE----TTS-SSEEEEEETTS-EEEEE-T CS
      GatD_N  1 ievGDlikvekkgreyeGilmPrselsdddiivlKLdnGYNiGikie 47
                i+vGD +k+   + +y Gi+mPr+e sdd+++vlKL++GYN+G++ie
  EPA05816.1 20 ISVGDSVKIL-SDLSYFGIIMPRYEHSDDKHLVLKLKSGYNVGLEIE 65
                579*****95.689******************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       194  (0.0108205); expected 358.6 (0.02)
Passed bias filter:                      173  (0.00964917); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 493.58
//
Query:       EPA05817.1  [L=103]
Description: hypothetical protein BG20_I2395 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.093   12.3   0.1        1.6    8.3   0.0    2.0  2  Cu_bind_CorA  Copper(I)-binding protein CorA


Domain annotation for each model (and alignments):
>> Cu_bind_CorA  Copper(I)-binding protein CorA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0   8.8e-05       1.6     128     159 ..      10      41 ..       6      46 .. 0.93
   2 ?    2.2   0.1     0.007   1.3e+02      59      84 ..      60      84 ..      52      97 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 8.8e-05
  Cu_bind_CorA 128 lsetydqseinkvldGvaGklelsfkatksrf 159
                   +s+tyd  ++    d v   ++l f+  k++f
    EPA05817.1  10 VSKTYDLRDVKDASDAVEDMVKLGFTNRKEGF 41 
                   899**************************998 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.007
  Cu_bind_CorA 59 hpGvtvwlrrkddrtapikyvvdhsy 84
                    Gvt+ lr+k++ +  i+y + h+ 
    EPA05817.1 60 TTGVTYALRQKNE-VRDIRYWTYHYD 84
                  579******9999.899999888854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 796.02
//
Query:       EPA05818.1  [L=101]
Description: hypothetical protein BG20_I2396, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-17   63.2   0.9    2.3e-17   63.1   0.9    1.0  1  PAP2      PAP2 superfamily
    7.3e-10   38.8   1.5    8.8e-10   38.6   1.5    1.1  1  PAP2_3    PAP2 superfamily
    4.8e-06   27.0   0.2    6.4e-06   26.6   0.2    1.1  1  PAP2_C    PAP2 superfamily C-terminal
  ------ inclusion threshold ------
      0.042   14.0   0.7          2    8.5   0.1    2.1  2  DUF212    Divergent PAP2 family


Domain annotation for each model (and alignments):
>> PAP2  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.1   0.9   5.1e-21   2.3e-17      52     128 ..      16      87 ..       3      94 .. 0.90

  Alignments for each domain:
  == domain 1  score: 63.1 bits;  conditional E-value: 5.1e-21
        PAP2  52 akesfPSgHsafafalalllalllrrkrkkiglvllalillllavlvalsRlylgvHflsDvlaGlliGialaalay 128
                 ++ s+PSgH+a++  +a+++ + l +++++      a +l+l+ vlv+lsR+y+  H+++Dv++G+++Gi+la ++ 
  EPA05818.1  16 FNASYPSGHAARTIIFAIVIGYALSERFPR-----GAYLLFLYPVLVSLSRVYVLQHYPMDVIGGTILGIMLAGVLA 87 
                 35689*************************.....89***********************************98765 PP

>> PAP2_3  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6   1.5     2e-13   8.8e-10     125     188 ..      18      83 ..       8      85 .. 0.88

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 2e-13
      PAP2_3 125 aafPSlHvawallvalalwrlrrkr..llrvlalllnvlmivatvatgnHYlvDviaGvalalvai 188
                 a+ PS H+a ++++a+++ +  + r  +  +l+ l++vl+ ++ v+   HY +Dvi+G +l+++ +
  EPA05818.1  18 ASYPSGHAARTIIFAIVIGYALSERfpRGAYLLFLYPVLVSLSRVYVLQHYPMDVIGGTILGIMLA 83 
                 569***********99999999998556678999**************************998865 PP

>> PAP2_C  PAP2 superfamily C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.2   1.4e-09   6.4e-06       8      69 ..      22      83 ..      20      88 .. 0.95

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 1.4e-09
      PAP2_C  8 SGHtvvltlavlfileyspkklailkvillllallglfliiasrkHYtvDVllglyittlvf 69
                SGH++ +++++++i +  ++++    ++l+l+ +l +++ ++  +HY +DV+ g ++ +++ 
  EPA05818.1 22 SGHAARTIIFAIVIGYALSERFPRGAYLLFLYPVLVSLSRVYVLQHYPMDVIGGTILGIMLA 83
                9*******************************************************999875 PP

>> DUF212  Divergent PAP2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.009        40      41      59 ..      19      37 ..       3      57 .. 0.67
   2 ?    8.5   0.1   0.00045         2     110     127 ..      64      81 ..      55      82 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.009
      DUF212 41 gmPSsHsalvtalatavgl 59
                 +PS H+a  +  a+++g+
  EPA05818.1 19 SYPSGHAARTIIFAIVIGY 37
                4589999876555555554 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00045
      DUF212 110 llGHtpleVlvGallGii 127
                 +l H p++V++G++lGi+
  EPA05818.1  64 VLQHYPMDVIGGTILGIM 81 
                 577*************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 701.56
//
Query:       EPA05819.1  [L=222]
Description: hypothetical protein BG20_I2397 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0025   16.7  23.0     0.0025   16.7  23.0    3.0  3  Spc7            Spc7 kinetochore protein
  ------ inclusion threshold ------
       0.13   11.8  42.0      0.028   14.0  22.8    2.2  2  MscS_porin      Mechanosensitive ion channel porin domain
       0.32   10.2  32.1       0.93    8.7  18.5    2.2  2  TMPIT           TMPIT-like protein
        0.7    9.7  48.8       0.58    9.9  30.7    2.0  2  ERM             Ezrin/radixin/moesin family
       0.98    9.3   2.4          2    8.3   0.8    2.4  2  MtrG            Tetrahydromethanopterin S-methyltransferase, 
        1.3    7.6  40.1      0.067   11.8  31.7    2.2  2  AAA_13          AAA domain
        4.5    7.0  37.1        1.2    8.8  11.2    2.4  2  DUF745          Protein of unknown function (DUF745)
        4.6    5.3  43.5         32    2.5  43.5    1.9  1  FPP             Filament-like plant protein, long coiled-coil
        9.7    6.9  33.6        2.8    8.7   5.0    4.4  5  DUF4404         Domain of unknown function (DUF4404)
        9.7    4.4  45.8         69    1.6  45.9    1.8  1  MAD             Mitotic checkpoint protein


Domain annotation for each model (and alignments):
>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8  15.9    0.0015       2.7     165     262 ..       4     104 ..       1     108 [. 0.87
   2 !   16.7  23.0   1.4e-06    0.0025     138     256 ..      44     163 ..      43     171 .. 0.93
   3 ?    0.1   9.9      0.17     3e+02     204     255 ..     167     218 ..     165     221 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0015
        Spc7 165 ldellpeleeeka...eleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleec 260
                 l++l+ +l+++k+   +l++++e++ +++++le+  +  L++l +++++ k+++   +  l+++++qle+++  +++++e+  + ++++  ae+ le  
  EPA05819.1   4 LEKLVIQLRQKKQkaaNLRKKAERQLQQVRSLEKRSSSGLHSLDRKIESEKENVTDVSGVLTQKTSQLESIQRLVASANERLIRENQALVDAEQELEFA 102
                 55666666666555559*******9999*****************************************************999999999999988877 PP

        Spc7 261 kg 262
                 k+
  EPA05819.1 103 KN 104
                 66 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 1.4e-06
        Spc7 138 egLkegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesid.keeLeelreelaelkaeieekkkelaelqeqleeleek 235
                 ++L  ++e++ e++++ + +L+++ ++l+++   + +  ++l +e + l +a++ele  + +ee ++++++la ++++i+e++ e++++++  ++++e+
  EPA05819.1  44 HSLDRKIESEKENVTDVSGVLTQKTSQLESIQRLVASANERLIRENQALVDAEQELEFAKnPEEENTAKSKLAIINEKIQELESEIKNREKTAKKITEE 142
                 5788899999999999999**************************************8776************************************** PP

        Spc7 236 ieelkeqkseleeeiaeaerv 256
                 +++++e ks+++++i+++ + 
  EPA05819.1 143 VSKISEIKSKINTQIQKQTKS 163
                 ****************98876 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.17
        Spc7 204 lreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaer 255
                 lre+++e ++  +++ kel+++ +  e+ ++++e+++ q +el ++ ++ ++
  EPA05819.1 167 LRETMSESHKAAQKFAKELEQKAKAEESAKKALEKVTLQLQELLAKKRKLQK 218
                 6777777777777777777777777777777777777777777766665554 PP

>> MscS_porin  Mechanosensitive ion channel porin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0  22.8   1.6e-05     0.028      41     174 ..      10     138 ..       3     144 .. 0.87
   2 ?    2.6  12.8     0.047        85      97     165 ..     146     211 ..     133     222 .] 0.65

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.6e-05
  MscS_porin  41 elqkaiddaPkelrelqqelealqkkkeeaskeilaklsleeLeqrllqtssqlqelqeqlaqlnsqlvelqtrperaqqqltearqrlqeirnrLnst 139
                 +l+++ ++a ++ ++++++l++        s e+ ++  l  L ++++++++++ +++  l+q  sql ++q   + a ++l   +q+l + +++L+  
  EPA05819.1  10 QLRQKKQKAANLRKKAERQLQQV------RSLEKRSSSGLHSLDRKIESEKENVTDVSGVLTQKTSQLESIQRLVASANERLIRENQALVDAEQELEFA 102
                 78999999999999999999999......999999*************************************************************444 PP

  MscS_porin 140 aaage.alsqaqrtalqaelaaleaqieeleqells 174
                 + ++e + ++++ +  + + + le++i+ +e+ ++ 
  EPA05819.1 103 KNPEEeNTAKSKLAIINEKIQELESEIKNREKTAKK 138
                 434444888888888888888888888888887665 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.047
  MscS_porin  97 lqeqlaqlnsqlvelqtrperaqqqltearqrlqeirnrLnstaaagealsqaqrtalqaelaaleaqi 165
                  +e  +++n+q++++  +  +++++++e  ++ q+  ++L+++a+a+   + a++++ ++ l++ e+  
  EPA05819.1 146 ISEIKSKINTQIQKQTKSKPTLRETMSESHKAAQKFAKELEQKAKAE---ESAKKALEKVTLQLQELLA 211
                 55556789999999999999999999999999999999997774433...3344444444444433333 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   5.7     0.001       1.9      18      93 ..       8      82 ..       1     106 [. 0.49
   2 ?    8.7  18.5   0.00052      0.93       2      92 ..     120     213 ..     119     221 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.001
       TMPIT 18 akeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlkevesllpkkn 93
                  +++qk ++ ++l +k  +++++ +   k+ +s l++l++++ e+e+e+v++++  l +++++l++++ l  + n
  EPA05819.1  8 VIQLRQKKQKAANLRKKAERQLQQVRSLEKRSSSGLHSLDRKI-ESEKENVTDVSGVLTQKTSQLESIQRLVASAN 82
                3333344444444444444444444444444444444444443.34444555555555555555555554444444 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00052
       TMPIT   2 eeweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk..eeeeeeveelkeelkerkkvlk.evesllpkk 92 
                 e+++ele+e+k+ e+tak++++++ ++s+ +sk+ ++i+kq+k    l++++++ +k+++  ++e e+ ++ +e+ k++ + +  ++++ll kk
  EPA05819.1 120 EKIQELESEIKNREKTAKKITEEVSKISEIKSKINTQIQKQTKSKPTLRETMSESHKAAQkfAKELEQKAKAEESAKKALEKVTlQLQELLAKK 213
                 7899************************************************999998764533444444444444444333334666666655 PP

>> ERM  Ezrin/radixin/moesin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4  16.7     0.063   1.1e+02      38     146 ..       4     109 ..       1     114 [. 0.79
   2 ?    9.9  30.7   0.00032      0.58      13     125 ..     100     212 ..      94     221 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.063
         ERM  38 LaekarraeeeaelLeqkaaeaeeeiqrlkesaekeeeekeklerklreaeleaarleeeserkeeeaerLkeeleeareaeeeakekllealstpsks 136
                 L++   ++++++++ ++ +++ae++ q+++  ++++ +  ++l rk++  +++++++    ++k ++ e  ++ +  a+e++ +++++l +a ++ +  
  EPA05819.1   4 LEKLVIQLRQKKQKAANLRKKAERQLQQVRSLEKRSSSGLHSLDRKIESEKENVTDVSGVLTQKTSQLESIQRLVASANERLIRENQALVDAEQELEF- 101
                 444455566666666777778899999999999999999*******************************************9999999998887732. PP

         ERM 137 eseenveese 146
                   ++n+ee++
  EPA05819.1 102 --AKNPEEEN 109
                 ..23333333 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00032
         ERM  13 rLkqlqeeaekaqeaLreseetaelLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeeeekeklerklreaeleaarleeeserkeeeaerLkee 111
                 +  +  ee + a+ +L   +e++++L+ + +  e+ a++ +++ +++ e +++++ + +k+ ++k  l + + e    a+++++e e+k++  e  k+ 
  EPA05819.1 100 EFAKNPEEENTAKSKLAIINEKIQELESEIKNREKTAKKITEEVSKISEIKSKINTQIQKQTKSKPTLRETMSESHKAAQKFAKELEQKAKAEESAKKA 198
                 455666899999*************************************************************************************** PP

         ERM 112 leeareaeeeakek 125
                 le++  +++e  +k
  EPA05819.1 199 LEKVTLQLQELLAK 212
                 ***99998875443 PP

>> MtrG  Tetrahydromethanopterin S-methyltransferase, subunit G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       2.1   3.7e+03      19      32 ..      43      56 ..      37      63 .. 0.72
   2 ?    8.3   0.8    0.0011         2       8      36 ..     104     132 ..     100     144 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.1
        MtrG 19 LdeieekvefvnsE 32
                L  +++k+e  +  
  EPA05819.1 43 LHSLDRKIESEKEN 56
                78899999976655 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0011
        MtrG   8 dpddfnevkkrLdeieekvefvnsEiaqr 36 
                 +p++ n++k++L  i+ek++  +sEi +r
  EPA05819.1 104 NPEEENTAKSKLAIINEKIQELESEIKNR 132
                 57788999******************987 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8  31.7   3.7e-05     0.067     309     468 ..      15     186 ..       2     188 .. 0.75
   2 ?    2.4  13.4     0.027        49     367     452 ..     139     219 ..     138     221 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.7e-05
      AAA_13 309 vsdeasensafeedkeelkaeaealeeqLkglqraleaKrkepfksve.lesvkakiesikklvaeineliakhNekvanleeekeeakkklelhlv.. 404
                   ++a++++++e++ +++++  +  ++ L +l r++e  ++++      l++ ++++esi+ lva++ne   + N+   + e+e e ak+  e   +  
  EPA05819.1  15 KQKAANLRKKAERQLQQVRSLEKRSSSGLHSLDRKIESEKENVTDVSGvLTQKTSQLESIQRLVASANERLIRENQALVDAEQELEFAKNPEEENTAks 113
                 2334667777888899999999999999************999996655799*****************999999999888877666655444444333 PP

      AAA_13 405 .........eeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeLk 468
                          +elese+++ +k+ kk++++++k  + +++++++++k  +    L++++++ ++aa++++keL+
  EPA05819.1 114 klaiinekiQELESEIKNREKTAKKITEEVSKISEIKSKINTQIQKQTKSKPTLRETMSESHKAAQKFAKELE 186
                 444444444777777777777777777777777777777777888888888899**************99997 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.027
      AAA_13 367 ikklvaeineliakhNekvanleeekeeakkklelhl..veeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekq 452
                 i+++v++i e+ +k N ++++ +++k ++++ +  +   ++++ +el++         ka e+++k+l++ + +l++l ++ + L+k+
  EPA05819.1 139 ITEEVSKISEIKSKINTQIQKQTKSKPTLRETMSESHkaAQKFAKELEQKA-------KAEESAKKALEKVTLQLQELLAKKRKLQKN 219
                 788899999999999999999999999988888764312344444444433.......444555555555555555555555555554 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8  11.2   0.00068       1.2      78     166 ..      15     103 ..       1     116 [. 0.83
   2 ?    3.1  18.7     0.037        67      68     165 ..     119     216 ..     112     221 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00068
      DUF745  78 vqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektqlleaAkkRveeLkkqlkearkdlektk 166
                  q+  +  +++e++++ +++  k   + l++l + +++ ken++++  v ++  ++l++ + l+++A++R+ + ++ l +a ++le  k
  EPA05819.1  15 KQKAANLRKKAERQLQQVRSLEKRSSSGLHSLDRKIESEKENVTDVSGVLTQKTSQLESIQRLVASANERLIRENQALVDAEQELEFAK 103
                 45555666789999999999999999999999999999999999999999999999999999999999999999999999999998666 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.037
      DUF745  68 eqelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektqlleaAkkRveeLkkqlkearkdlekt 165
                 +++++e e+ +++ +k  ++  + ++  +++++++++q++  ++   + +e++++++++a++ ++el++k++  e+Akk +e+++ ql+e  +  +k 
  EPA05819.1 119 NEKIQELESEIKNREKTAKKITEEVSKISEIKSKINTQIQKQTKSKPTLRETMSESHKAAQKFAKELEQKAKAEESAKKALEKVTLQLQELLAKKRKL 216
                 5678999999999999999999999999************************************************************9987665555 PP

>> FPP  Filament-like plant protein, long coiled-coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5  43.5     0.018        32     602     816 ..       3     213 ..       2     221 .. 0.60

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.018
         FPP 602 dledfvleLssvldeiselkfslldvssmeeeikksddidkvalsenkvaqkges.snecaeisklssekeipselplvsgsnesk.....keenkllk 694
                 +le++v +L +  +++ +l+ +  ++ ++    +k  + +    ++ k+ +++e+ ++ +  + +++s+ e ++   lv+++ne       + +   ++
  EPA05819.1   3 SLEKLVIQLRQKKQKAANLRKKAERQLQQVRSLEKRSSSGL-HSLDRKIESEKENvTDVSGVLTQKTSQLESIQ--RLVASANERLirenqALVDAEQE 98 
                 56777777777777777766655544444444444444443.22222331222221222222222222222222..22222233332222133334445 PP

         FPP 695 eeleelksekenlevelksatenleslkaqlqesEqllaelkseLeslkeskslaetqlkcmkesyesletrateleaelnelkqkieaLeveLeeekk 793
                  e+ +   e ++ + +l+  +e++++l + +++ E++ +++++e++++ e ks+++tq+++++ s+ +l   ++       e ++ +++  +eLe++ k
  EPA05819.1  99 LEFAKNPEEENTAKSKLAIINEKIQELESEIKNREKTAKKITEEVSKISEIKSKINTQIQKQTKSKPTLRETMS-------ESHKAAQKFAKELEQKAK 190
                 5666667788899999*************************************************997755444.......444445556677777777 PP

         FPP 794 sheeleakckelqeqlervekke 816
                 + e ++ + +++ +ql+   +k+
  EPA05819.1 191 AEESAKKALEKVTLQLQELLAKK 213
                 77777777777777777654444 PP

>> DUF4404  Domain of unknown function (DUF4404)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       1.8   3.3e+03       4      18 ..       3      17 ..       2      27 .. 0.66
   2 ?    6.9   1.5    0.0054       9.7       9      39 ..      26      56 ..      19      80 .. 0.81
   3 ?   -0.5   0.5       1.1     2e+03      21      32 ..      87      98 ..      59     116 .. 0.47
   4 ?    8.5   4.0    0.0017         3       1      55 [.     118     173 ..     118     183 .. 0.66
   5 ?    8.7   5.0    0.0015       2.8       6      44 ..     179     217 ..     175     221 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.8
     DUF4404  4 lLekLheeLeqnesl 18
                +LekL  +L+q+++ 
  EPA05819.1  3 SLEKLVIQLRQKKQK 17
                578888888877654 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0054
     DUF4404  9 heeLeqnesldeetralLeslaedieellae 39
                + +L+q+ sl++ + + L+sl+++ie   ++
  EPA05819.1 26 ERQLQQVRSLEKRSSSGLHSLDRKIESEKEN 56
                579**********************965444 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 1.1
     DUF4404 21 etralLeslaed 32
                 +++ L +++++
  EPA05819.1 87 RENQALVDAEQE 98
                223333333333 PP

  == domain 4  score: 8.5 bits;  conditional E-value: 0.0017
     DUF4404   1 LkelLekLheeLeqneslde...etralLeslaedieellaeedaaaeeeelaerlne 55 
                 ++e++++L++e+++ e++ +   e+ +++++++++i+ +++++++ +++  l e++ e
  EPA05819.1 118 INEKIQELESEIKNREKTAKkitEEVSKISEIKSKINTQIQKQTKSKPT--LRETMSE 173
                 5788999999999777666512245567778888888888888888877..5555544 PP

  == domain 5  score: 8.7 bits;  conditional E-value: 0.0015
     DUF4404   6 ekLheeLeqnesldeetralLeslaedieellaeedaaa 44 
                 +k  +eLeq+ +++e+ ++ Le++  +++ella++ + +
  EPA05819.1 179 QKFAKELEQKAKAEESAKKALEKVTLQLQELLAKKRKLQ 217
                 67789****************************998765 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6  45.9     0.038        69      33     239 ..      12     218 ..       2     219 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.038
         MAD  33 ekkasalkrqleeesdrnqelqkrikllekreeekeealreqiElarlkkknlealnkkekekesklaearevisalknelaelkrqiekqelels..e 129
                  +k    k++ ++ +++ +  +++++ lekr +   ++l  +iE ++    n + ++  + +k+s+l++++ +  + +++l + ++ + ++e+el+  +
  EPA05819.1  12 RQK----KQKAANLRKKAERQLQQVRSLEKRSSSGLHSLDRKIESEK---ENVTDVSGVLTQKTSQLESIQRLVASANERLIRENQALVDAEQELEfaK 103
                 333....56666667777778899********************999...899999999******************9999888888877776665215 PP

         MAD 130 keseleelqerldllkkklseleqliqqlekkqkelaeaeqrikeLefeiqs....qeddslivknsksel.aripelekelerlreenkklnelkenk 223
                 + +e +  + +l + ++k++ele  i++ ek  k+ +e+  +i e++ +i+     q++++  +++  se      +  kele++ +  +  ++  e +
  EPA05819.1 104 NPEEENTAKSKLAIINEKIQELESEIKNREKTAKKITEEVSKISEIKSKINTqiqkQTKSKPTLRETMSEShKAAQKFAKELEQKAKAEESAKKALEKV 202
                 66677889999**********************************998876645448888888888887774666789999999999999999888888 PP

         MAD 224 elLkEevedlkkkLer 239
                  l   e+   k+kL++
  EPA05819.1 203 TLQLQELLAKKRKLQK 218
                 8877777777788776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      4380  (0.244297); expected 358.6 (0.02)
Passed bias filter:                      691  (0.0385409); expected 358.6 (0.02)
Passed Vit filter:                       171  (0.00953762); expected 17.9 (0.001)
Passed Fwd filter:                        71  (0.00396006); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 1.19u 0.38s 00:00:01.56 Elapsed: 00:00:00.57
# Mc/sec: 1173.35
//
Query:       EPA05820.1  [L=534]
Description: CTP synthase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   3.4e-117  390.4   0.3   4.8e-117  390.0   0.3    1.2  1  CTP_synth_N    CTP synthase N-terminus
    1.1e-54  185.1   0.0    1.9e-54  184.4   0.0    1.4  1  GATase         Glutamine amidotransferase class-I
    1.3e-12   47.9   0.0    3.9e-11   43.1   0.0    2.3  2  Peptidase_C26  Peptidase C26
  ------ inclusion threshold ------
      0.014   15.4   0.0       0.04   14.0   0.0    1.8  1  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
      0.041   13.7   0.0      0.094   12.5   0.0    1.6  1  DJ-1_PfpI      DJ-1/PfpI family
      0.093   12.6   0.1       0.46   10.4   0.0    2.2  3  AAA_31         AAA domain


Domain annotation for each model (and alignments):
>> CTP_synth_N  CTP synthase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  390.0   0.3  1.6e-120  4.8e-117       1     263 [.       4     266 ..       4     268 .. 0.99

  Alignments for each domain:
  == domain 1  score: 390.0 bits;  conditional E-value: 1.6e-120
                  EEEEEEE--STTTTHHHHHHHHHHHHHCTT--EEEEEEE-SSSSSSTT--CCCC--EEE-TT--EEETHHHHHHHHHT----GGGEEEHHHHHHHHHH CS
  CTP_synth_N   1 kyilvtGGvvSglGkGiiaaslgallksrglkvtlikiDPYlnvdagtlsplehGEvfvlddGaetDlDlGnYeRfldikltkennittGkiyksvie 98 
                  k+i+vtGGv+SglGkG++++s+++ll+  + kv+++kiDPYln+dagt++p+ hGEvfv++dG+e+D+D+GnYeRfl++++ k++nitt ++y++vie
   EPA05820.1   4 KFIFVTGGVMSGLGKGVTTSSIAKLLQLADQKVSCVKIDPYLNYDAGTMNPVAHGEVFVTEDGGECDMDIGNYERFLNQNIPKSHNITTAQVYSTVIE 101
                  8************************************************************************************************* PP

                  HHHTTTTTT----CCCHHHHHHHHHHHHHH.HCT-SEEEEEE-S-TTSGGGHHHHHHHHHHHHHH-TTTEEEEEEEE--B-TTTSSB-HHHHHHHHHH CS
  CTP_synth_N  99 kerrGdylGktvqviphvtdeikeriekvakkveadvviveigGtvgdieslpfleairqlklelgkenvllihvtlvpvlkaagelktkptqhsvke 196
                   er+G+ylG++vq+iph+tdeik+ri+k+ak+++ d++ive gGtvgdieslpflea+rq+++e g +nv+++hvtl p l+  ge+ktkptqhs +e
   EPA05820.1 102 AERKGEYLGACVQIIPHITDEIKNRIRKIAKEEKLDFLIVECGGTVGDIESLPFLEALRQMRVEEGPQNVIFVHVTLAPSLDVVGEQKTKPTQHSAQE 199
                  *******************************999**************************************************************** PP

                  HHHHT---SEEEEEESS---HHHHHHHHHHCT--GGGEEEEE--S-GGGHHHHHHHCTHHHHHHHHT CS
  CTP_synth_N 197 lrslGiqpdiivcrsekeleeevkekialfcnvekeavisvkdvesiyevpllleeqglaelilekl 263
                  lr++Giqpd++++r++++lee++k+kialf+nv+ ++v+s++dv+si++vp++l +qg+++++ +k+
   EPA05820.1 200 LRRIGIQPDFLAVRCSTPLEESTKKKIALFTNVTANDVLSCHDVKSIFQVPQILYDQGIMDSLFTKF 266
                  ************************************************************9998876 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.4   0.0   6.2e-58   1.9e-54       2     190 .]     307     529 ..     306     529 .. 0.95

  Alignments for each domain:
  == domain 1  score: 184.4 bits;  conditional E-value: 6.2e-58
                 EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTTTTTHHHHHHHHCTSTS-EEEETHHHHHHHHHTTTEEE....... CS
      GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspgvegkieaikearenkiPiLGICLGmQllaiefgrkvv....... 93 
                 l D+y sv+++l+ha+++lg ++ +++id++    +++l+++dgilv+gG+g +g+eg i+++++are++iP+LGIC+G+Ql+ai+fgr+v        
  EPA05820.1 307 LADSYVSVNHALKHAGAKLGKSIIIDWIDSESISDYSILSKYDGILVPGGFGVRGAEGIIKTANYAREKNIPYLGICFGFQLAAIAFGRNVLklddans 405
                 78***************************977777668***************************************************9999999999 PP

                 ................EEECEEEEEEEEEEEETTT........CGGTTTTSEEEEEEEEEEEEESG...CHHHTTEEEEEEEETTEEEEEEEEETT.T. CS
      GATase  94 ................kekekehhggtmrlgddet........allyglknevierhrHryevnpk...elepaglevtakseddeelmeiiekkn.p. 163
                                 ++k+ +++gg+ rlg+++         +++y+  +++  rhrHrye+n+k   e+e++gl+++a+s+++ ++me+ e ++ + 
  EPA05820.1 406 teikpetknpvvdllpEQKTISDMGGSLRLGANDIeikpntisHKIYNA-ERISKRHRHRYEINKKyipEFEKNGLIFSAESDNG-KRMEMLEIPShKf 502
                 999999999999****9999************6669************9.99******************************888.8*********999 PP

                 EEEESSBTTSTTSTTHHHHHHHHHHHH CS
      GATase 164 fvgvQFHPEststpegpellfnflika 190
                 ++gvQFHPE+ s+p+ pe +f+ ++ka
  EPA05820.1 503 YIGVQFHPEFNSRPGYPEQVFEAFVKA 529
                 **********************99985 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.039   1.2e+02      37      70 ..     325     359 ..     293     364 .. 0.62
   2 !   43.1   0.0   1.3e-14   3.9e-11      99     216 .]     370     511 ..     363     511 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.039
  Peptidase_C26  37 gglpvll.pieedeedvkaildkldgllltGgqdv 70 
                     g ++++ +i++++ +  +il+k dg+l++Gg  v
     EPA05820.1 325 LGKSIIIdWIDSESISDYSILSKYDGILVPGGFGV 359
                    34566662555555555679***********9655 PP

  == domain 2  score: 43.1 bits;  conditional E-value: 1.3e-14
  Peptidase_C26  99 raalergvPilgiCrGlqllnvalGGtlyq..dieeqsgltdhrehe............q......saashavkvekgsllaellgseeievnslH 174
                    + a e+++P lgiC G+ql ++a+G ++ +  d+++++ + + +  +            +         + +++++++++ ++++++e+i+    H
     EPA05820.1 370 NYAREKNIPYLGICFGFQLAAIAFGRNVLKldDANSTEIKPETK--NpvvdllpeqktiSdmggslRLGANDIEIKPNTISHKIYNAERISKRHRH 463
                    567899******************99876511344433333333..2468888886655156666777899************************* PP

  Peptidase_C26 175 hqaike......laeelrveAvae.DgviEaieseeakafvlgvQwHPE 216
                    +  i++        ++l  +A ++    +E +e++++k f++gvQ+HPE
     EPA05820.1 464 RYEINKkyipefEKNGLIFSAESDnGKRMEMLEIPSHK-FYIGVQFHPE 511
                    *****99999966677777777773447********87.*********9 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.3e-05      0.04       7      55 ..      13     307 ..       6     434 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.3e-05
                 STTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH................................................... CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................................... RF
        CbiA   7 kGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep................................................... 54 
                  +G GK +++ ++a++l+ +  +V  v+ Dp  n +a   g+ n ++                                                    
  EPA05820.1  13 MSGLGKGVTTSSIAKLLQLADQKVSCVKIDPYLNYDA---GTMNPVAHgevfvtedggecdmdignyerflnqnipkshnittaqvystvieaerkgey 108
                 69******************************88887...77777777888888888888888888888888888888888877777777777777777 PP

                 ................................................................................................... CS
                 ................................................................................................... RF
        CbiA  55 ................................................................................................... 54 
                                                                                                                    
  EPA05820.1 109 lgacvqiiphitdeiknrirkiakeekldflivecggtvgdieslpflealrqmrveegpqnvifvhvtlapsldvvgeqktkptqhsaqelrrigiqp 207
                 777777777777777777777777777777777777666666666666666666666666666666666666666666666666666666666666666 PP

                 ................................................................................................... CS
                 ................................................................................................... RF
        CbiA  55 ................................................................................................... 54 
                                                                                                                    
  EPA05820.1 208 dflavrcstpleestkkkialftnvtandvlschdvksifqvpqilydqgimdslftkfgkvgmvnasanwdkwntiaesminhedqkvriamvgkyvt 306
                 666666666666666666666666666666666655555555555555555555555555555555555555555555555555555555555555555 PP

                 C CS
                 x RF
        CbiA  55 d 55 
                  
  EPA05820.1 307 L 307
                 0 PP

>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.1e-05     0.094      60     106 ..     346     388 ..     287     397 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.1e-05
                 CG-SEEEE--BHHHHHHHHTSHHHHHHHHHHHHTT-EEEEETTTHHH CS
   DJ-1_PfpI  60 aeyDalvlpGGragperlrenekvvelvkefaekgklvaaICagpql 106
                 ++yD +++pGG      +r  e +++++  + ek+ ++  IC g ql
  EPA05820.1 346 SKYDGILVPGGFG----VRGAEGIIKTANYAREKNIPYLGICFGFQL 388
                 59***********....99999*********************9665 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00015      0.46      12      50 ..      15      53 ..       5     152 .. 0.60
   2 ?   -3.1   0.0       2.1   6.3e+03     121     162 ..     329     367 ..     307     378 .. 0.66
   3 ?   -1.9   0.0      0.92   2.7e+03      48      86 ..     440     483 ..     401     503 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00015
      AAA_31 12 GvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgi 50
                G GK  t+  +a+ l  +++kv  v +Dp  n   g+  
  EPA05820.1 15 GLGKGVTTSSIAKLLQLADQKVSCVKIDPYLNYDAGTMN 53
                88****************************998774433 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.1
      AAA_31 121 iiiDcpPsLglltenaLvasdsviipvqaeayaleGleqllk 162
                 iiiD   s ++   ++L   d +++p     +  eG   ++k
  EPA05820.1 329 IIIDWIDSESISDYSILSKYDGILVPGGFGVRGAEG---IIK 367
                 666666666666666677777777765544444444...344 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.92
      AAA_31  48 lgiekneiektlyevl......ieeknikeaiiktkvenldlips 86 
                 ++i+ n+i++++y++        ++++i++ +i  ++e++ li s
  EPA05820.1 440 IEIKPNTISHKIYNAEriskrhRHRYEINKKYI-PEFEKNGLIFS 483
                 455556666777776433333234555555555.44555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (534 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      619  (0.0345251); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.47
# Mc/sec: 3411.57
//
Query:       EPA05821.1  [L=89]
Description: hypothetical protein BG20_I0779 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.45
# Mc/sec: 595.52
//
Query:       EPA05822.1  [L=74]
Description: zinc finger, C2H2 type [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00072   20.2  11.8      0.047   14.5   1.2    2.4  2  zf-C2H2_4       C2H2-type zinc finger
     0.0017   18.7  13.9        0.1   13.1   3.7    2.3  2  zf-C2H2         Zinc finger, C2H2 type
     0.0048   17.1   2.6       0.03   14.6   0.2    2.2  2  zinc_ribbon_9   zinc-ribbon
     0.0057   16.6   4.9          1    9.3   0.2    2.3  2  Prok-RING_1     Prokaryotic RING finger family 1
     0.0073   17.0   6.3      0.012   16.3   6.3    1.4  1  zf-C2H2_3rep    Zinc finger C2H2-type, 3 repeats
      0.008   16.6   5.3      0.008   16.6   5.3    2.8  2  zf-H2C2_2       Zinc-finger double domain
  ------ inclusion threshold ------
      0.014   15.7   5.0      0.014   15.7   5.0    2.0  2  zf-C2H2_2       C2H2 type zinc-finger (2 copies)
      0.019   15.7   2.6      0.023   15.4   2.6    1.4  1  zinc_ribbon_15  zinc-ribbon family
      0.022   15.0  16.5       0.34   11.3   4.9    2.5  2  zf-C2H2_jaz     Zinc-finger double-stranded RNA-binding
      0.047   13.7   0.9          2    8.5   0.1    2.2  2  zf-CHCC         Zinc-finger domain
       0.05   12.1  16.7        0.1   11.1   4.7    2.0  2  DUF629          Protein of unknown function (DUF629)
      0.082   12.7   1.8       0.15   11.8   1.2    1.6  2  zf-CSL          CSL zinc finger
        0.1   12.4   5.3       0.24   11.2   1.1    2.3  2  zf-HYPF         HypF finger
       0.15   12.1   8.8        8.5    6.5   1.4    2.4  2  zf-BED          BED zinc finger
       0.16   11.7   3.8       0.42   10.4   3.8    1.8  1  Ribosomal_S27e  Ribosomal protein S27
       0.38   10.7   4.7        5.4    7.0   4.7    2.1  1  zinc_ribbon_4   zinc-ribbon domain
       0.44   10.5   6.1       0.12   12.3   1.3    2.0  2  PyrI_C          Aspartate carbamoyltransferase regulatory cha
        0.5   10.6  10.2       0.53   10.6   9.2    1.5  2  LIM             LIM domain
       0.58   10.3   5.6        1.9    8.6   0.4    2.2  2  XPA_N           XPA protein N-terminal
          1    9.2   6.1        4.5    7.1   6.1    1.9  1  zinc_ribbon_5   zinc-ribbon domain
          2    8.2   6.3       0.98    9.2   0.8    2.2  3  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
        2.2    9.0  12.5         13    6.5   8.5    2.3  2  FOXP-CC         FOXP coiled-coil domain
        2.4    8.4   9.0        7.5    6.8   4.8    2.3  2  Ribosomal_L37e  Ribosomal protein L37e
        2.7    8.2   5.8        3.6    7.8   1.0    2.0  2  Zn-ribbon_8     Zinc ribbon domain
        4.8    7.4  10.8         87    3.4  10.8    2.1  1  FYVE            FYVE zinc finger


Domain annotation for each model (and alignments):
>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   1.2   6.6e-05     0.047       3      24 .]      11      32 ..      10      32 .. 0.96
   2 !   10.5   3.6    0.0013      0.91       2      24 .]      38      60 ..      37      60 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.6e-05
   zf-C2H2_4  3 CpiCgksFsskkaLlrHlkthH 24
                C +C++ F ++++L +H++  H
  EPA05822.1 11 CIQCDAKFDNHEDLVKHVRHEH 32
                99*****************988 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0013
   zf-C2H2_4  2 kCpiCgksFsskkaLlrHlkthH 24
                kC +Cgk F   k+ l+H +  H
  EPA05822.1 38 KCQHCGKEFIHEKDRLHHAREEH 60
                8*********7777799988877 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   2.6   0.00057      0.41       5      23 .]      13      32 ..      10      33 .. 0.92
   2 !   13.1   3.7   0.00015       0.1       2      23 .]      38      60 ..      37      60 .. 0.96

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00057
                TTTEEESSHHHHHHHHHC.C CS
     zf-C2H2  5 dCgksFkrksnLkrHirt.H 23
                 C+ +F + ++L++H r  H
  EPA05822.1 13 QCDAKFDNHEDLVKHVRHeH 32
                6****************997 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00015
                EETTTTEEESSHHHHHHHHHC.C CS
     zf-C2H2  2 kCpdCgksFkrksnLkrHirt.H 23
                kC +Cgk F +  +  +H r  H
  EPA05822.1 38 KCQHCGKEFIHEKDRLHHAREeH 60
                8*******************988 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.2      0.24   1.7e+02      24      31 ..      11      18 ..       5      18 .. 0.78
   2 !   14.6   0.2   4.2e-05      0.03      11      34 ..      27      49 ..      25      49 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.24
  zinc_ribbon_9 24 CPhCgggF 31
                   C +C+  F
     EPA05822.1 11 CIQCDAKF 18
                   9***9988 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 4.2e-05
  zinc_ribbon_9 11 fVsvspdedsdvlCPhCgggFVEe 34
                   +V+ ++++  +v C hCg  F++e
     EPA05822.1 27 HVR-HEHHKTIVKCQHCGKEFIHE 49
                   666.466777778*********98 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.9    0.0018       1.3       3      21 ..       7      25 ..       5      28 .. 0.91
   2 !    9.3   0.2    0.0014         1       4      19 ..      36      51 ..      31      53 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0018
  Prok-RING_1  3 tgkkCpvCgkelkeedDiV 21
                 +++ C  C+ ++++ +D+V
   EPA05822.1  7 KKNDCIQCDAKFDNHEDLV 25
                 6889*************99 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0014
  Prok-RING_1  4 gkkCpvCgkelkeedD 19
                   kC+ Cgke+ +e+D
   EPA05822.1 36 IVKCQHCGKEFIHEKD 51
                 579*******999988 PP

>> zf-C2H2_3rep  Zinc finger C2H2-type, 3 repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   6.3   1.7e-05     0.012      34      94 ..      10      70 ..       4      74 .] 0.82

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.7e-05
  zf-C2H2_3rep 34 qcipcgshfgnaeelwlhvlsvhpsdfklskvaqkknlsasedssqklelsksasvennse 94
                   ci c ++f n+e+l +hv   h + + + +   k+ +++++  ++  e++k a  e + +
    EPA05822.1 10 DCIQCDAKFDNHEDLVKHVRHEHHKTIVKCQHCGKEFIHEKDRLHHAREEHKHALEERSRK 70
                  6***********************9999999999888888887777777777766555444 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.3     0.034        25       9      26 .]       5      20 ..       1      20 [. 0.73
   2 !   16.6   5.3   1.1e-05     0.008       1      26 []      23      48 ..      23      48 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.034
   zf-H2C2_2  9 HtgekpyeCplCdkaFkt 26
                H +++   C  Cd +F +
  EPA05822.1  5 HNKKN--DCIQCDAKFDN 20
                66666..6999**99976 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 1.1e-05
   zf-H2C2_2  1 nLrrHir.kHtgekpyeCplCdkaFkt 26
                +L++H r +H+ +++++C  C+k F +
  EPA05822.1 23 DLVKHVRhEHH-KTIVKCQHCGKEFIH 48
                69*****5588.79**********965 PP

>> zf-C2H2_2  C2H2 type zinc-finger (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   5.0     2e-05     0.014      49      78 ..       7      36 ..       1      38 [. 0.89
   2 ?    3.5   5.3      0.13        91      52      82 ..      38      67 ..      36      74 .] 0.58

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2e-05
   zf-C2H2_2 49 ekleClyCekefkslealreHmkkkgHcki 78
                +k+ C+ C+ +f++ e+l +H+++++H++i
  EPA05822.1  7 KKNDCIQCDAKFDNHEDLVKHVRHEHHKTI 36
                5799***********************987 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.13
   zf-C2H2_2 52 eClyCekefkslealreHmkkkgHckineee 82
                +C +C+kef + ++ r H + ++H+   ee+
  EPA05822.1 38 KCQHCGKEFIHEKD-RLHHAREEHKHALEER 67
                79999999844444.4455555666654433 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   2.6   3.3e-05     0.023      39      77 ..      10      48 ..       2      70 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.3e-05
  zinc_ribbon_15 39 acskCkslleaskelgkeiekkessekkeCknCgkevee 77
                     c +C +++ ++++l k+++++++++  +C++Cgke  +
      EPA05822.1 10 DCIQCDAKFDNHEDLVKHVRHEHHKTIVKCQHCGKEFIH 48
                    6999*****************************998655 PP

>> zf-C2H2_jaz  Zinc-finger double-stranded RNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   4.9   0.00047      0.34       4      22 ..      11      29 ..       8      34 .. 0.92
   2 ?    9.4   3.7    0.0018       1.3       3      18 ..      38      53 ..      37      62 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00047
                 BTTTTBBBSSHHHHHCCTT CS
  zf-C2H2_jaz  4 CvlCdKyFksenaldnHlk 22
                 C+ Cd  F ++++l +H++
   EPA05822.1 11 CIQCDAKFDNHEDLVKHVR 29
                 *****************86 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0018
                 BBTTTTBBBSSHHHHH CS
  zf-C2H2_jaz  3 YCvlCdKyFksenald 18
                  C++C K F+ e++  
   EPA05822.1 38 KCQHCGKEFIHEKDRL 53
                 5**********99765 PP

>> zf-CHCC  Zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.067        48      21      37 .]       2      18 ..       1      18 [. 0.84
   2 ?    8.5   0.1    0.0028         2      24      37 .]      33      46 ..      30      46 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.067
                E--TTSEEEETTTTEEE CS
     zf-CHCC 21 eldkkgpvdCgYCglrF 37
                +l +++ +dC  C+ +F
  EPA05822.1  2 KLFHNKKNDCIQCDAKF 18
                5668899*******998 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0028
                TTSEEEETTTTEEE CS
     zf-CHCC 24 kkgpvdCgYCglrF 37
                +k+ v+C+ Cg+ F
  EPA05822.1 33 HKTIVKCQHCGKEF 46
                6889*******998 PP

>> DUF629  Protein of unknown function (DUF629)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   4.1    0.0012      0.89      59      83 ..      11      35 ..       7      38 .. 0.92
   2 ?   11.1   4.7   0.00014       0.1      57      92 ..      37      72 ..      35      74 .] 0.91

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0012
      DUF629 59 CrtCsekfsdaeeckqHlvqeHvak 83
                C +C+ kf + e+ ++H+ +eH ++
  EPA05822.1 11 CIQCDAKFDNHEDLVKHVRHEHHKT 35
                **********************876 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00014
      DUF629 57 WvCrtCsekfsdaeeckqHlvqeHvaklkpklqkvl 92
                 +C+ C ++f++ ++ ++H  +eH + l+ +++k+l
  EPA05822.1 37 VKCQHCGKEFIHEKDRLHHAREEHKHALEERSRKKL 72
                58***************************9998876 PP

>> zf-CSL  CSL zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.2   0.00022      0.15      20      50 ..      10      42 ..       7      44 .. 0.91
   2 ?    6.2   0.4     0.012       8.3      20      39 ..      38      58 ..      36      66 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00022
                EE.TTSSEEEEEHHHHHTT.....--EEEETTS CS
      zf-CSL 20 pC.RCgdeFelteedleegae.gaevvvqCssC 50
                +C  C  +F+  e+ +++ ++ +++++v+C+ C
  EPA05822.1 10 DCiQCDAKFDNHEDLVKHVRHeHHKTIVKCQHC 42
                7999*********999997668*********** PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.012
                EE.TTSSEEEEEHHHHHTT.. CS
      zf-CSL 20 pC.RCgdeFelteedleegae 39
                +C  Cg+eF  +++ l++ +e
  EPA05822.1 38 KCqHCGKEFIHEKDRLHHARE 58
                7999*********99998755 PP

>> zf-HYPF  HypF finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.2      0.11        77       2      18 ..      11      32 ..       4      37 .. 0.76
   2 ?   11.2   1.1   0.00033      0.24       2      19 ..      39      56 ..      38      58 .. 0.95

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.11
                -HHHHHHHC-TTS.....TTTT CS
     zf-HYPF  2 CedClrEykdpld.....RRfh 18
                C +C +++++ +d     R  h
  EPA05822.1 11 CIQCDAKFDNHEDlvkhvRHEH 32
                8899999999988665555555 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00033
                -HHHHHHHC-TTSTTTT- CS
     zf-HYPF  2 CedClrEykdpldRRfha 19
                C+ C +E+   +dR +ha
  EPA05822.1 39 CQHCGKEFIHEKDRLHHA 56
                *****************9 PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   1.4     0.012       8.5      15      43 ..       7      32 ..       4      33 .. 0.91
   2 ?    5.9   6.6     0.018        13      12      26 ..      32      46 ..      26      50 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.012
                S--EETTTTEE----SSTHHHHHHHHHS- CS
      zf-BED 15 qkavCryCgkilsrgggttnLkrHLrrkH 43
                +k  C+ C ++++++     L +H r+ H
  EPA05822.1  7 KKNDCIQCDAKFDNH---EDLVKHVRHEH 32
                7889**********9...99*******99 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.018
                GGSS--EETTTTEE- CS
      zf-BED 12 lkeqkavCryCgkil 26
                  ++ ++C +Cgk++
  EPA05822.1 32 HHKTIVKCQHCGKEF 46
                4699*********85 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   3.8   0.00058      0.42      20      35 ..      30      45 ..       6      49 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00058
                    ESS-SS-EEESSSTCE CS
  Ribosomal_S27e 20 FshaatvvkCisCgkv 35
                     +h +t+vkC+ Cgk 
      EPA05822.1 30 HEHHKTIVKCQHCGKE 45
                    6899**********95 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   4.7    0.0076       5.4       5      35 ..      11      46 ..       8      47 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0076
  zinc_ribbon_4  5 CpsCkakyeiddeklpa.....kgvkvrCskCghvF 35
                   C +C ak+   ++ ++      +++ v+C +Cg+ F
     EPA05822.1 11 CIQCDAKFDNHEDLVKHvrhehHKTIVKCQHCGKEF 46
                   778888887777765422222255689999999887 PP

>> PyrI_C  Aspartate carbamoyltransferase regulatory chain, metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.3      0.61   4.4e+02      32      46 ..       7      21 ..       2      22 .. 0.69
   2 ?   12.3   1.3   0.00016      0.12      26      46 ..      28      49 ..      16      50 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.61
                TEEEETTT--EEEHH CS
      PyrI_C 32 vklkCkYCekeisee 46
                 k  C  C+ +++++
  EPA05822.1  7 KKNDCIQCDAKFDNH 21
                455688888888765 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00016
                E.EETTTTEEEETTT--EEEHH CS
      PyrI_C 26 v.edkekvklkCkYCekeisee 46
                v  +++k+++kC+ C+ke+ +e
  EPA05822.1 28 VrHEHHKTIVKCQHCGKEFIHE 49
                226899***********99765 PP

>> LIM  LIM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.4      0.02        15      20      40 ..       2      22 ..       2      28 .. 0.83
   2 ?   10.6   9.2   0.00074      0.53       1      40 [.      11      50 ..      11      63 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.02
                EEEETTTSB-TTT-SB-CTT. CS
         LIM 20 kvwHeeCFtCsdCqkeLkegs 40
                k +H +   C +C+ ++++++
  EPA05822.1  2 KLFHNKKNDCIQCDAKFDNHE 22
                679999999******999876 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00074
                -TTT--BE-TTTEEEEETTEEEETTTSB-TTT-SB-CTT. CS
         LIM  1 CagCnkkiadrelvlkaldkvwHeeCFtCsdCqkeLkegs 40
                C +C+ k+ ++e ++k   +  H+   +C++C+ke+ +++
  EPA05822.1 11 CIQCDAKFDNHEDLVKHVRHEHHKTIVKCQHCGKEFIHEK 50
                99*******999999*******************997765 PP

>> XPA_N  XPA protein N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.7     0.068        49       2      12 ..       9      19 ..       8      20 .. 0.85
   2 ?    8.6   0.4    0.0027       1.9       3      11 ..      38      46 ..      37      48 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.068
       XPA_N  2 pkCdeCgkefl 12
                ++C +C+ +f+
  EPA05822.1  9 NDCIQCDAKFD 19
                68*****9996 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0027
       XPA_N  3 kCdeCgkef 11
                kC++Cgkef
  EPA05822.1 38 KCQHCGKEF 46
                7*******9 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   6.1    0.0063       4.5       5      35 ..      11      46 ..       8      48 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0063
  zinc_ribbon_5  5 CpdCdtkFklvdsklKk.....sgkkVrCakCaevF 35
                   C +Cd kF   ++ +K          V+C +C++ F
     EPA05822.1 11 CIQCDAKFDNHEDLVKHvrhehHKTIVKCQHCGKEF 46
                   99******999999886222113456******9765 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.6      0.33   2.4e+02      13      20 ..       7      14 ..       4      17 .. 0.77
   2 ?    1.1   0.4      0.44   3.2e+02       2      10 ..      10      18 ..       9      26 .. 0.75
   3 ?    9.2   0.8    0.0014      0.98      14      24 ..      33      43 ..      25      48 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.33
                    -SSS---- CS
  DNA_RNApol_7kD 13 kkgdpiRC 20
                    kk+d i+C
      EPA05822.1  7 KKNDCIQC 14
                    67888888 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.44
                    B-SSS--B- CS
  DNA_RNApol_7kD  2 iCgeCgaev 10
                    +C +C+a++
      EPA05822.1 10 DCIQCDAKF 18
                    588888775 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0014
                    SSS----SSS- CS
  DNA_RNApol_7kD 14 kgdpiRCkeCG 24
                    ++ +++C++CG
      EPA05822.1 33 HKTIVKCQHCG 43
                    6779******9 PP

>> FOXP-CC  FOXP coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   8.5     0.018        13      11      33 ..      13      35 ..       3      55 .. 0.82
   2 ?    3.1   2.4      0.21   1.5e+02      12      33 ..      42      63 ..      38      73 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.018
     FOXP-CC 11 gCekvledveeflkhlnseHald 33
                 C++ ++++e+++kh+++eH+ +
  EPA05822.1 13 QCDAKFDNHEDLVKHVRHEHHKT 35
                6*******************864 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.21
     FOXP-CC 12 CekvledveeflkhlnseHald 33
                C k +   ++ l+h+++eH++ 
  EPA05822.1 42 CGKEFIHEKDRLHHAREEHKHA 63
                6666666677777887777653 PP

>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1     0.094        68      26      37 ..       3      14 ..       1      19 [. 0.89
   2 ?    6.8   4.8      0.01       7.5      10      28 ..      30      48 ..      27      56 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.094
  Ribosomal_L37e 26 syhvqkktCasc 37
                     +h +k+ C +c
      EPA05822.1  3 LFHNKKNDCIQC 14
                    59*******999 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.01
  Ribosomal_L37e 10 rqkkktHilCrrCgkrsyh 28
                    ++++kt ++C++Cgk+  h
      EPA05822.1 30 HEHHKTIVKCQHCGKEFIH 48
                    7899**********98766 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   4.9    0.0097         7       8      34 ..      11      44 ..       4      46 .. 0.71
   2 ?    7.8   1.0     0.005       3.6       7      16 ..      38      47 ..      36      66 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0097
  Zn-ribbon_8  8 CeeCghefe......vlqsisdaplta.CPeCgs 34
                 C +C+ +f+      + ++    + ++ C +Cg+
   EPA05822.1 11 CIQCDAKFDnhedlvKHVRHEHHKTIVkCQHCGK 44
                 8899999999998763332234445666999997 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.005
  Zn-ribbon_8  7 rCeeCghefe 16
                 +C+ Cg+ef 
   EPA05822.1 38 KCQHCGKEFI 47
                 8*****9995 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4  10.8      0.12        87      10      37 ..       9      48 ..       3      67 .. 0.53

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.12
                SB-TTT--B--.......SSS--EE.....-TTT--EE-S CS
        FYVE 10 kkCeiCakkFs.......llrrrhh.....CrlCGkvvCe 37
                + C +C++kF         +r  hh     C++CGk + +
  EPA05822.1  9 NDCIQCDAKFDnhedlvkHVRHEHHktivkCQHCGKEFIH 48
                5666666666423333222344444444446666655543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1490  (0.0831056); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 481.78
//
Query:       EPA05823.1  [L=110]
Description: hypothetical protein BG20_I0781 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 741.26
//
Query:       EPA05824.1  [L=158]
Description: hypothetical protein BG20_I0784 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       819  (0.0456802); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1114.62
//
Query:       EPA05825.1  [L=45]
Description: hypothetical protein BG20_I0775 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.018   14.8   0.1      0.023   14.4   0.1    1.2  1  YdjO      Cold-inducible protein YdjO


Domain annotation for each model (and alignments):
>> YdjO  Cold-inducible protein YdjO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   1.3e-06     0.023      32      56 ..       6      31 ..       4      34 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.3e-06
        YdjO 32 dnFsfeeePtCplCkseMvk.evrmL 56
                d+Fs e++ tCp Ck   +k ++++L
  EPA05825.1  6 DDFSDEDKGTCPNCKHTIKKhSNKEL 31
                89*************99987245665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       828  (0.0461822); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.46
# Mc/sec: 295.12
//
Query:       EPA05826.1  [L=449]
Description: chorismate binding enzyme [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.8e-92  308.2   0.0    2.2e-91  306.0   0.0    2.0  3  Chorismate_bind  chorismate binding enzyme
    7.6e-22   78.1   0.4    6.8e-19   68.5   0.1    3.0  3  Anth_synt_I_N    Anthranilate synthase component I, N termina
  ------ inclusion threshold ------
      0.084   12.5   0.0       0.38   10.4   0.0    2.1  2  FlbD             Flagellar and Swarming motility proteins


Domain annotation for each model (and alignments):
>> Chorismate_bind  chorismate binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       0.2   1.2e+03      37      83 ..      17      67 ..       7      97 .. 0.69
   2 ?   -2.2   0.0       0.4   2.4e+03     185     215 ..      82     112 ..      77     115 .. 0.86
   3 !  306.0   0.0   3.7e-95   2.2e-91       2     258 .]     183     436 ..     182     436 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.2
                     -B-HHHHHHHHHCTBSSSEEEEE...EETT....EEEEEEESSEEEEEETTSEE CS
  Chorismate_bind 37 avdplalyralrarnpapysfll...eled....sellgaSPElllkveggrri 83
                       +++++y+++ +++++++ f        +    ++++g+ P +++k   + ++
       EPA05826.1 17 TENQFQIYNKISRNYSHSFLFESltgP--EvlaeTSVMGFDPKIIFKGYTD-KV 67
                     456789999999998888877664440..1444467899999998875534.33 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.4
                      ESHHHHHHHHHHHSSS--TTTTSEEEEEETT CS
  Chorismate_bind 185 aPkkrameiidelEearRgvYaGavgyldad 215
                       P k+  +++ + E ++ ++ +Gavg+++ d
       EPA05826.1  82 EPFKEIKKLLGKSEDQSYRYLGGAVGVVNYD 112
                      57788889999999*9**********99976 PP

  == domain 3  score: 306.0 bits;  conditional E-value: 3.7e-95
                      HCHHHHHHHHHHHHHHTTS-SEEEEEEEEEECESS-B-HHHHHHHHHCTBSSSEEEEEEETTEEEEEEESSEEEEEETTSEEEEECEEEEEEHS CS
  Chorismate_bind   2 redYaeavekvkeeiragdlykvvlsrrlkaeleaavdplalyralrarnpapysflleledsellgaSPElllkveggrrietepiaGTrarg 95 
                      +e++ + v+k+k++i++gd+++vvlsr++ +   ++ d l+ly++lr+ np+py++ l+ ++++++gaSPE+l+++ ++ ++et piaGTr+ +
       EPA05826.1 183 KEKFSNIVNKAKQYIHDGDIFQVVLSRKFIFD--KKGDDLTLYKTLRKLNPSPYMYHLKQDTKTIIGASPEMLVRITND-KVETFPIAGTRKIT 273
                      799*****************************..99*****************************************66.************** PP

                      SSHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCBSCCEEEEECCEEEEEETTEEEEEEEEEEEESTT--HHHHHHHCSS-CCCSEESHHH CS
  Chorismate_bind  96 ktpeedealeeelledeKeraEhlmivdlirndLgkvakpgsvkvpelfkverysevlhlvstiegelkedvslldllkalfPtgavtGaPkkr 189
                      +++e++++l+ ell+deKe+aEh m+vdl rnd+g+v+k g+v+++el++++r+s+v+h+ +++ g+l+++ +++d++ka+fP+g+v+GaPk r
       EPA05826.1 274 DDEEKNKQLAYELLHDEKELAEHTMLVDLGRNDIGRVCKYGTVHTEELMEIKRFSHVQHIITHVVGNLAPENDMFDAFKAVFPAGTVSGAPKVR 367
                      ********************************************************************************************** PP

                      HHHHHHHHSSS--TTTTSEEEEEETTS-EEEEEE-SEEEEETTEEEEEEEEEEETT--HHHHHHHHHHH CS
  Chorismate_bind 190 ameiidelEearRgvYaGavgyldadgeaelavvIRtavvkdkelrlgaGaGIvadSdpeaEyeEtlaK 258
                      ameii+elE ++Rg+YaGavgy++++g +++a++IR+++++ ++  +++GaGIv dS +e+E+ Et++K
       EPA05826.1 368 AMEIIEELELESRGPYAGAVGYFSFNGCCDFAIAIRSIFIDGNKGFVQSGAGIVSDSVAENEFIETEHK 436
                      ****************************************9999***********************99 PP

>> Anth_synt_I_N  Anthranilate synthase component I, N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.5   0.1   1.1e-22   6.8e-19       4     141 ..      19     150 ..      16     151 .. 0.86
   2 ?   -0.3   0.0      0.19   1.1e+03      35      56 ..     245     273 ..     239     299 .. 0.73
   3 !    5.9   0.0    0.0023        14      18     102 ..     297     394 ..     283     411 .. 0.68

  Alignments for each domain:
  == domain 1  score: 68.5 bits;  conditional E-value: 1.1e-22
  Anth_synt_I_N   4 tplsvylklaeee.hkflLeSaeneggegrySfigldpflelkskngeveveg.pegeeleeeepldalrellerfrsaedseptelpfvgGlvGy 97 
                    +  ++y k++ +  h+fl+eS  + +  ++ S++g+dp++ +k  +++ve+++  + e  +++ep++ +++ll + ++      ++ +  gG+vG 
     EPA05826.1  19 NQFQIYNKISRNYsHSFLFESLTGPEVLAETSVMGFDPKIIFKGYTDKVEITKdGKTETIKTNEPFKEIKKLLGKSED------QSYRYLGGAVGV 108
                    567899*****99*********966666***********************9944455555566*************3......45789******* PP

  Anth_synt_I_N  98 lgYDlvreieklpksakddln.lpdarlilydtlivfDhkerrly 141
                    + YD++r +e++p+   ++ +  p +++ +yd+ i++D++ ++l+
     EPA05826.1 109 VNYDAIRLVENIPD---THNSpQPLMEFGIYDDGILYDNIHKKLF 150
                    *************5...44555899*****************997 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.19
  Anth_synt_I_N  35 figldpflelkskngeveveg.......p 56 
                    +ig++p + +++ n++ve+         +
     EPA05826.1 245 IIGASPEMLVRITNDKVETFPiagtrkiT 273
                    89*********999999987755554442 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.0023
  Anth_synt_I_N  18 kflLeSaenegge.grySfigldpflelk..skngevevegpegeeleeeepldalrellerfrsaedse............ptelp...fvgGlv 95 
                    ++l + ++n+ g+ ++y  + +++ +e+k  s+ + + +++  g  + e++++da ++++     ++ +                      + G+v
     EPA05826.1 297 TMLVDLGRNDIGRvCKYGTVHTEELMEIKrfSHVQHIITHV-VGNLAPENDMFDAFKAVFPAGT-VSGAPkvrameiieeleL---EsrgPYAGAV 387
                    55555555555556777777777777777654444444444.6788888889999999988888.434445888888776542...2334899*** PP

  Anth_synt_I_N  96 GylgYDl 102
                    Gy++++ 
     EPA05826.1 388 GYFSFNG 394
                    ****975 PP

>> FlbD  Flagellar and Swarming motility proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   6.3e-05      0.38       7      28 ..     102     123 ..     100     124 .. 0.87
   2 ?   -2.7   0.0      0.77   4.6e+03      41      54 ..     183     196 ..     182     198 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 6.3e-05
        FlbD   7 lngeefvlNadlIetieetPDT 28 
                 l g   v+N d I+ +e +PDT
  EPA05826.1 102 LGGAVGVVNYDAIRLVENIPDT 123
                 5677789*************** PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.77
        FlbD  41 kEsvdevierviey 54 
                 kE+ ++++++ ++y
  EPA05826.1 183 KEKFSNIVNKAKQY 196
                 799999**999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (449 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.52
# Mc/sec: 2603.20
//
Query:       EPA05827.1  [L=40]
Description: hypothetical protein BG20_I0777 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      151  (0.00842211); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.35s 00:00:00.83 Elapsed: 00:00:00.55
# Mc/sec: 219.12
//
Query:       EPA05828.1  [L=319]
Description: NAD(+)/NADH kinase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-30  106.7   0.3    2.2e-30  105.9   0.3    1.4  2  NAD_kinase      ATP-NAD kinase
    4.2e-05   23.0   0.6     0.0002   20.9   0.0    2.4  3  HTH_24          Winged helix-turn-helix DNA-binding
    0.00013   21.7   0.8      0.013   15.4   0.1    2.8  2  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0017   18.3   0.9     0.0054   16.6   0.1    2.2  3  MarR            MarR family
  ------ inclusion threshold ------
       0.01   15.2   0.2      0.016   14.6   0.2    1.2  1  RNA_pol_Rpc34   RNA polymerase Rpc34 subunit
      0.013   15.0   0.0      0.021   14.3   0.0    1.3  1  TPALS           TIR- and PNP-associating SLOG family
      0.014   15.2   0.0      0.048   13.6   0.0    1.9  2  MarR_2          MarR family
        3.4    7.9   4.7        7.5    6.8   0.1    2.9  4  B-block_TFIIIC  B-block binding subunit of TFIIIC


Domain annotation for each model (and alignments):
>> NAD_kinase  ATP-NAD kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.9   0.3   9.7e-34   2.2e-30      73     274 ..      35     228 ..      11     235 .. 0.92
   2 ?   -3.4   0.0       1.9   4.2e+03     162     195 ..     255     288 ..     239     292 .. 0.63

  Alignments for each domain:
  == domain 1  score: 105.9 bits;  conditional E-value: 9.7e-34
                 TTTTTSSSEEEEEE-HHHHHHHHHHHHHCT-EEEEEESSS-.-SS-SEEGGGHHHHHHHHHHT-SEEEEEEEEEEEEEETTE......EEEEEEESSEE CS
  NAD_kinase  73 afadagvdliivvGGDGTaldvarllqkaeiPvlgvnaGvk.gfltefepeaaaellekllegeirvekrevldavimrskgeediadiviensvlnev 170
                 +   + vd+i+v+GGD  ++  ++   + + Pvlg++ G + gfl++++ +++ +  + l +++++ve+  ++ ++i  ++           + vln+v
  EPA05828.1  35 KSKSRLVDCILVLGGDKGVRNYFHRSFDSTTPVLGISEGEAsGFLAQIDLREFSSHVKILKKQNYTVEEVPRIGVKIDGKNV----------YPVLNDV 123
                 566789****************9999999**********8659***************9999************99977766..........789**** PP

                 EEEESSSSS-EEEEEEETTEEEEEEEESEEEEE-TGGGGTHHHHTT--EE-TT---EEEEEESESSS----EEE-TT-EEEEEE-.SS--EEEEETTTE CS
  NAD_kinase 171 viirgpgstlielelyvdtelleadqldglivstPtGstayslsaGgplisPgvlailivpicPhslssrpiVvssssklrirva.srseallaldGse 268
                  +   + + l e  l v++e +  d +dg+ivstP+Gs ays+saGgp++ P+   + i  ++ +  + rpi+vs+ s+++i    +r  + ++ldG +
  EPA05828.1 124 AVFSSRSAMLMEHTLRVNDEEVWHDNSDGIIVSTPIGSSAYSMSAGGPMLFPDSGVFEIISVNSLDITRRPIIVSNTSSIQISDIsARLHCEVVLDGLD 222
                 *********************************************************************************98447***********99 PP

                 EEEE-T CS
  NAD_kinase 269 elelsp 274
                 +++++ 
  EPA05828.1 223 RYKVTN 228
                 988765 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.9
                 EEEEESSEEEEEESSSSS-EEEEEEETTEEEEEE CS
  NAD_kinase 162 iensvlnevviirgpgstlielelyvdtellead 195
                 +++  l e+++ + p s+l+ + l+++++l ++d
  EPA05828.1 255 AKKVHLAEELLSMPPSSKLLLKTLEYEGALTQKD 288
                 3333477888888888888888888888777665 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       2.8   6.3e+03      16      27 ..     201     212 ..     197     213 .. 0.76
   2 ?   -1.6   0.0      0.93   2.1e+03      19      30 ..     250     261 ..     244     263 .. 0.77
   3 !   20.9   0.0   8.8e-08    0.0002       8      48 .]     274     314 ..     269     314 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.8
      HTH_24  16 prisqreLAerl 27 
                 ++i +++++ rl
  EPA05828.1 201 SSIQISDISARL 212
                 568889999887 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.93
      HTH_24  19 sqreLAerlglS 30 
                  ++ LA++++l 
  EPA05828.1 250 AISALAKKVHLA 261
                 57899**99985 PP

  == domain 3  score: 20.9 bits;  conditional E-value: 8.8e-08
      HTH_24   8 ILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                 +L++L+ ++ ++q++LA ++ l+  tv+  l  L ++G++k
  EPA05828.1 274 LLKTLEYEGALTQKDLANKTLLPDRTVRLALSHLLKKGYVK 314
                 799************************************97 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.024        53       9      44 ..      85     121 ..      66     124 .. 0.87
   2 !   15.4   0.1   5.7e-06     0.013      17      55 ..     278     316 ..     271     319 .] 0.89

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.024
                 HCCCHCHHHHHHCCCHHCHHCCC.TTSSCHCHHHHHH CS
        TrmB   9 yEakvYlaLlklgpatadeiaee.lgvprskvYevLr 44 
                  E++  +++lk+++ t++e+ ++ ++++  +vY vL+
  EPA05828.1  85 REFSSHVKILKKQNYTVEEVPRIgVKIDGKNVYPVLN 121
                 577788899999*******998658999999999997 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 5.7e-06
                 HHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
        TrmB  17 LlklgpatadeiaeelgvprskvYevLrsLedkGlVere 55 
                 L  +g +t +++a+++ +p  +v  +L+ L++kG+V++e
  EPA05828.1 278 LEYEGALTQKDLANKTLLPDRTVRLALSHLLKKGYVKKE 316
                 447899*******************************98 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.6   3.6e+03      13      30 ..     198     215 ..     196     216 .. 0.78
   2 ?   -3.0   0.0       3.4   7.5e+03      20      29 ..     251     260 ..     246     262 .. 0.74
   3 !   16.6   0.1   2.4e-06    0.0054       7      50 ..     273     316 ..     268     318 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.6
                 HHSTTEEHHHHHHHHTS- CS
        MarR  13 yeqgplsvseLakklgvs 30 
                 ++  ++ +s++  +l+++
  EPA05828.1 198 SNTSSIQISDISARLHCE 215
                 566788999999999875 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.4
                 HHHHHHHHTS CS
        MarR  20 vseLakklgv 29 
                 +s Lakk+++
  EPA05828.1 251 ISALAKKVHL 260
                 6789999886 PP

  == domain 3  score: 16.6 bits;  conditional E-value: 2.4e-06
                 HHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
        MarR   7 viLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50 
                 ++L +l+++g+l++++La+k  +   tv  +l +L kkG+++++
  EPA05828.1 273 LLLKTLEYEGALTQKDLANKTLLPDRTVRLALSHLLKKGYVKKE 316
                 589**************************************986 PP

>> RNA_pol_Rpc34  RNA polymerase Rpc34 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.2     7e-06     0.016      37     134 ..     221     315 ..     202     317 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 7e-06
                    STTSHHHHHHHHHHHHHHCTSEECCC.STTSCECEE--CCCHHHHHTSXHHHHHHHHHHHHHXSSXEEHHHHHHTTGXXHHHHHHHHHHHHHTTXX CS
  RNA_pol_Rpc34  37 ipslslklllsavqeLldkkllvllknsndeLvyravsreeAkkktslsedeslVysiIeesGneGIwsrtiksklnLhksvvkkcLksLeskkyi 132
                    +++ ++++ ++++q L   k ++l k + + ++  a++ + A+ + s++ + +l +++ e  G+    ++++ +k+ L++  v+  L  L +k+y+
     EPA05828.1 221 LDRYKVTNTVECTQFLPPAKIIRLKK-NSTAISALAKKVHLAEELLSMPPSSKLLLKTLEYEGA--LTQKDLANKTLLPDRTVRLALSHLLKKGYV 313
                    56778889999999999999999999.5556688899999*********************998..79**************************** PP

                    EE CS
  RNA_pol_Rpc34 133 ks 134
                    k+
     EPA05828.1 314 KK 315
                    96 PP

>> TPALS  TIR- and PNP-associating SLOG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   9.3e-06     0.021     110     162 ..      13      68 ..      10      71 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 9.3e-06
       TPALS 110 selvkiesieddn.mtgkri..eaqarvgdalialGGgkGVsylAnkyhkagkPvi 162
                 s  + i++i dd+ + +  i    + r+ d +++lGG+kGV    ++ +++  Pv+
  EPA05828.1  13 SAAITIKKILDDAeIESFVItsKSKSRLVDCILVLGGDKGVRNYFHRSFDSTTPVL 68 
                 5667788888887778877766678899***************************8 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       3.4   7.7e+03      24      32 ..     205     213 ..     201     214 .. 0.84
   2 ?   13.6   0.0   2.1e-05     0.048       3      54 ..     267     316 ..     265     319 .] 0.89

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.4
                 HHHHHHHHT CS
      MarR_2  24 vgelarrlg 32 
                 ++++ +rl+
  EPA05828.1 205 ISDISARLH 213
                 799999998 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 2.1e-05
                 --HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
      MarR_2   3 ltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54 
                 ++p+   +L  L  ++   lt+++la ++ l+  +v  +l  L ++G+v ++
  EPA05828.1 267 MPPSSKLLLKTLEYEGA--LTQKDLANKTLLPDRTVRLALSHLLKKGYVKKE 316
                 66777778888888888..******************************987 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1      0.11   2.6e+02      29      48 ..      81     100 ..      74     105 .. 0.87
   2 ?   -2.1   0.0         2   4.6e+03      28      40 ..     109     121 ..     103     124 .. 0.88
   3 ?   -3.7   0.2       6.4   1.4e+04      48      64 ..     190     206 ..     190     208 .. 0.74
   4 ?    6.8   0.1    0.0033       7.5      19      53 ..     284     318 ..     280     319 .] 0.92

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.11
  B-block_TFIIIC  29 kqdprslfyrlksLekkgLI 48 
                      +d r + +++k L+k+++ 
      EPA05828.1  81 QIDLREFSSHVKILKKQNYT 100
                     6999************9985 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2
  B-block_TFIIIC  28 skqdprslfyrlk 40 
                     +k+d+++++ +l+
      EPA05828.1 109 VKIDGKNVYPVLN 121
                     589******9988 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 6.4
  B-block_TFIIIC  48 Ivkqsiidsatkksist 64 
                     I++++ii s+t +++ +
      EPA05828.1 190 ITRRPIIVSNTSSIQIS 206
                     78899988888777665 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.0033
  B-block_TFIIIC  19 itqsdLakeskqdprslfyrlksLekkgLIvkqsi 53 
                     +tq+dLa+ +    r +   l +L kkg+++k s+
      EPA05828.1 284 LTQKDLANKTLLPDRTVRLALSHLLKKGYVKKESL 318
                     589*****************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.68u 0.33s 00:00:01.01 Elapsed: 00:00:00.56
# Mc/sec: 1722.53
//
Query:       EPA05829.1  [L=49]
Description: hypothetical protein BG20_I0785 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 333.59
//
Query:       EPA05830.1  [L=116]
Description: hypothetical protein BG20_I0792 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.02   14.4   0.0      0.025   14.1   0.0    1.2  1  Hint      Hint module
      0.085   12.5   0.0        0.1   12.3   0.0    1.1  1  DUF4956   Domain of unknown function (DUF4956)


Domain annotation for each model (and alignments):
>> Hint  Hint module
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.8e-06     0.025     149     208 ..      39     108 ..      14     112 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.8e-06
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..............XXXXXXXXXXXXXXXXXX CS
        Hint 149 vVdgvlaScYavieshslahtafapvrllsslssllas..........eeeneasqtegihwYskllykl 208
                  Vdgvl  c+a++es++la+  ++ + +l ++  +  +          ++e +  + ++ h+Y +l+  l
  EPA05830.1  39 WVDGVLFACFAMTESEELAKKEMQGMTYLDKVVFAKYDkysktaklstNMEINVLNMQKSHLYRDLISWL 108
                 59*******************9999988887443333344444444444444555555556666666555 PP

>> DUF4956  Domain of unknown function (DUF4956)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.1e-05       0.1      82     156 ..      27      95 ..      18     106 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.1e-05
     DUF4956  82 glinglaslslvellvlnvlivlvlallesprllkkerrklvtldrieliapedeeeliadleerlglkvtevev 156
                 ++++   sl+   +  ++ ++ +++a+ es+ l+kke + +  ld++   ++++ ++ +a+l++ ++++v +   
  EPA05830.1  27 SMMA---SLESGSAYWVDGVLFACFAMTESEELAKKEMQGMTYLDKVVFAKYDKYSK-TAKLSTNMEINVLN--M 95 
                 4444...4456678999*****************************55555553333.45555555555544..4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 760.62
//
Query:       EPA05831.1  [L=266]
Description: tryptophan synthase, alpha subunit [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.4e-83  277.2   1.4    9.3e-83  277.0   1.4    1.0  1  Trp_syntA       Tryptophan synthase alpha chain
    4.5e-08   32.8   0.3    1.7e-07   31.0   0.1    1.9  2  His_biosynth    Histidine biosynthesis protein
    3.5e-07   29.7   1.1    4.8e-07   29.3   1.1    1.3  1  DHO_dh          Dihydroorotate dehydrogenase
    4.1e-05   22.8   0.1     0.0003   19.9   0.0    2.3  3  FMN_dh          FMN-dependent dehydrogenase
    4.1e-05   22.9   0.5    0.00058   19.1   0.1    2.7  3  NanE            Putative N-acetylmannosamine-6-phosphate epim
    6.6e-05   22.5   2.4    0.00052   19.5   2.4    2.2  1  PcrB            PcrB family
    0.00024   20.2   0.6      0.001   18.1   0.2    2.1  2  IMPDH           IMP dehydrogenase / GMP reductase domain
     0.0016   17.8   0.1     0.0034   16.7   0.0    1.6  2  ThiG            Thiazole biosynthesis protein ThiG
     0.0032   16.7   0.0      0.024   13.8   0.0    2.0  2  IGPS            Indole-3-glycerol phosphate synthase
     0.0066   15.6   0.0       0.04   13.0   0.0    2.0  2  Dus             Dihydrouridine synthase (Dus)
     0.0093   15.4   0.0      0.018   14.5   0.0    1.5  1  NMO             Nitronate monooxygenase
  ------ inclusion threshold ------
      0.012   14.9   0.6       0.04   13.2   0.6    2.0  1  TMP-TENI        Thiamine monophosphate synthase
      0.015   14.7   1.7       0.12   11.8   0.6    2.3  3  BtpA            BtpA family
      0.038   13.1   0.0       0.11   11.6   0.0    1.7  2  TGT             Queuine tRNA-ribosyltransferase
      0.057   12.8   0.3      0.088   12.2   0.3    1.5  1  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family


Domain annotation for each model (and alignments):
>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  277.0   1.4   7.8e-86   9.3e-83       1     250 [.       8     259 ..       8     266 .] 0.94

  Alignments for each domain:
  == domain 1  score: 277.0 bits;  conditional E-value: 7.8e-86
                 HHHHHCTTB-EEEEEEETTSS-HHHHHHHHHHHHHCT-SSEEEE---S--TTS-HHHHHHHHCCCCTT--HHHHHHHHHHHHHHCSSS-EEEEE-CHHH CS
   Trp_syntA   1 faklkaenraafvpyvtagdpdleqsleilkalekagadviElGlpfsdPladGPvIqaanlraLakgvtlekvlelveevrkkevevPivlltylnlv 99 
                 fa+l a+n++a+++y+++g+p+ + ++  +++l ++gad+iElG+pfsdPladGP+Iq+a++++L++g++++k++e+v+++r ke+++P++l+ty n++
  EPA05831.1   8 FAALSAKNEKALIAYIMVGYPNEAATMASVRGLIQGGADIIELGFPFSDPLADGPIIQNASTISLQNGAKISKFFEIVKKIR-KETDIPLILMTYTNIL 105
                 89999*****************************************************************************.**************** PP

                 CCC-HHHHCHHHHHCTEEEEEETTSBCCCHHHHHHHHHHTT-EEEEEE-TTS-HHHHHHHHHH--S-EEEESTTC-SSTTSSB-TTHHHHHHHHHHCT. CS
   Trp_syntA 100 lsygeerflaelkeagvdglivpDlPleeaeelveaakkkglelvflvapttsderlkevveqaegfvYvvsraGvTgaenavaaevdelverlkklt. 197
                 +++g+++f+ e+k+ag+dgli+pD+  ee++e+ + a+k+ ++++fl++p+t++ r++++++ ++gf Y+v++ G+Tg+++ +++ + ++++++kk+t 
  EPA05831.1 106 YHKGYQKFIIEAKNAGIDGLILPDMSIEESKEYLA-ATKNKIDTIFLISPNTTKTRIEKIAKLSSGFLYLVAVYGTTGVKTGIKNYTLKAIKEVKKITk 203
                 ********************************986.67789*******************************************************997 PP

                 .SS-EEEESSS-SHHHHHHHH.TT-SEEEE-HHHHHHHHCTTTSH.HHHHHHHHHH CS
   Trp_syntA 198 .avPvavGFGistkeqvkqva.kvadGvivGSalvkkieeeaeek.eqalekleel 250
                  + Pv vGFG+st+e+vk+ + ++ad+vivGSa +k ie++ ++k e++++k++ +
  EPA05831.1 204 eKIPVGVGFGVSTPEDVKKYIkTGADAVIVGSAFLKLIEKTPQNKlESNISKFTRS 259
                 789****************9989****************86655425555555544 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.96   1.1e+03      62     195 ..      82      97 ..      73      99 .. 0.61
   2 !   31.0   0.1   1.4e-10   1.7e-07      55     108 ..     188     240 ..     179     254 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.96
                   HHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEECEEEEETTTTEEEEEEHHHHHHHHHH CS
  His_biosynth  62 ldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarrgykvaikgwreetgldavelakklee 158
                    ++v++i++e++ip+                                                                                  
    EPA05831.1  82 FEIVKKIRKETDIPL---------------------------------------------------------------------------------- 96 
                   455556666655555.................................................................................. PP

                   TT-SEEEEEETTTTTTSS---HHHHHHHHHHHSSEEE CS
  His_biosynth 159 lgageilltdidrdGtlsGpdleltkelaeavkipvi 195
                                                       i
    EPA05831.1  97 ------------------------------------I 97 
                   ....................................4 PP

  == domain 2  score: 31.0 bits;  conditional E-value: 1.4e-10
                   CTTHHHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH- CS
  His_biosynth  55 kegreanldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavkn 108
                   k+ + + ++ v++i++e +ipv vG G+++ edv+++++ gad vi+g+a +k 
    EPA05831.1 188 KNYTLKAIKEVKKITKE-KIPVGVGFGVSTPEDVKKYIKTGADAVIVGSAFLKL 240
                   55556677788999999.9******************************98875 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   1.1     4e-10   4.8e-07     169     278 ..     126     239 ..      68     254 .. 0.83

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 4e-10
                 E-SSSSHHHHHHHHHHHH.HHTECEEEE...BSEE--CTTCCGCCCCTT.SSEEEEEGG..GHHHHHHHHHHHHHHTTT.S-EEEES.S--SHHHHHHH CS
      DHO_dh 169 laPdltdeekkdiadvll.elkldgiivtNttvqrlaidlkseknvkan.ktGGlsGka..lkdialkvirelykrlkkeipiIgvG.GiesgeDalek 262
                 + Pd++ ee k+  +  + +     +i+ Ntt  r  +  k  +         G  G +  +k+  lk i e++k +k++ip+ gvG G+++ eD+  +
  EPA05831.1 126 ILPDMSIEESKEYLAATKnKIDTIFLISPNTTKTRIEKIAKLSSGFLYLvAVYGTTGVKtgIKNYTLKAIKEVKKITKEKIPV-GVGfGVSTPEDVKKY 223
                 67999988888887776657777778999***99997777777777665644445554334*********************7.7777*********** PP

                 HHHTECEEEESHHHHH CS
      DHO_dh 263 ieaGAslvqvytalvf 278
                 i+ GA +v v++a+ +
  EPA05831.1 224 IKTGADAVIVGSAFLK 239
                 ************9864 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.65   7.7e+02     205     221 ..      82      98 ..      64     128 .. 0.83
   2 ?   -2.1   0.0       1.2   1.5e+03     302     320 ..     170     188 ..     163     191 .. 0.83
   3 !   19.9   0.0   2.5e-07    0.0003     257     306 ..     191     240 ..     187     264 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.65
                 HHHHHHHHHHHSSEEEE CS
      FMN_dh 205 wddikwlreqtklplvv 221
                 ++ +k++r++t++pl++
  EPA05831.1  82 FEIVKKIRKETDIPLIL 98 
                 56689999999999986 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.2
                 HHHHHHHHHHHHHHHHHHH CS
      FMN_dh 302 pflyglaagGeeGvervle 320
                  fly +a++G+ Gv+  ++
  EPA05831.1 170 GFLYLVAVYGTTGVKTGIK 188
                 68999*********98665 PP

  == domain 3  score: 19.9 bits;  conditional E-value: 2.5e-07
                 HHHCHHHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHHHH CS
      FMN_dh 257 tidvLpeiveavggrievlvDgGirrGsDvlkAlalGAdavllGRpflyg 306
                 t++++ e+ +  +++i+v v  G+++ +Dv k +  GAdav++G +fl  
  EPA05831.1 191 TLKAIKEVKKITKEKIPVGVGFGVSTPEDVKKYIKTGADAVIVGSAFLKL 240
                 78999999************************************999865 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.56   6.7e+02      51      70 ..      31      50 ..      25      54 .. 0.89
   2 ?    0.3   0.1      0.28   3.3e+02      23      37 ..      84      98 ..      62     149 .. 0.74
   3 !   19.1   0.1   4.9e-07   0.00058     132     181 ..     193     242 ..     157     251 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.56
                S-SHHHHHHHHTTT-SEEEE CS
        NanE 51 tatlkdideLaaagadiial 70
                +at+  +  L++ gadii l
  EPA05831.1 31 AATMASVRGLIQGGADIIEL 50
                58999************976 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.28
                HHHHHHTT--S-EEE CS
        NanE 23 dikaikavvdlPiiG 37
                 +k+i++++d+P+i 
  EPA05831.1 84 IVKKIRKETDIPLIL 98
                468888888888885 PP

  == domain 3  score: 19.1 bits;  conditional E-value: 4.9e-07
                 --HHHHHHHHHTT--EEEES---SHHHHHHHHTT--SEEEE-HHHH-HHH CS
        NanE 132 pDfalvkalseaglkviaeGrintPekakkaieiGvdavvvGsaitrlee 181
                   ++ vk+++++++ v +   + tPe  kk i++G+dav+vGsa  +l e
  EPA05831.1 193 KAIKEVKKITKEKIPVGVGFGVSTPEDVKKYIKTGADAVIVGSAFLKLIE 242
                 4556699999******99999***********************987755 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   2.4   4.3e-07   0.00052     133     211 ..     153     237 ..      63     256 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 4.3e-07
                 -B-TTHHHHHHHHHHHHHHTT-SEEEEE-...TTSSS-H.HHHHHHHHHHSSSE..EEEESS--SHHHHHHHHCC.SSEEEE-CHH CS
        PcrB 133 kvdlnkediaayallaakllglrliYlEa...sGaledv.eevialkkklekar..livGGGirsaEkAkevvea.ADvivvGnvv 211
                 + +  k  i  +a l++ +l l  +Y       G+++   ++++++kk ++k++  + vG G+  +E+ k++++  AD+++vG + 
  EPA05831.1 153 SPNTTKTRIEKIAKLSSGFLYLVAVYGTTgvkTGIKNYTlKAIKEVKK-ITKEKipVGVGFGVSTPEDVKKYIKTgADAVIVGSAF 237
                 556778899999999*******99996543345655555355666655.4444401557789*********************864 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.32   3.8e+02     153     173 ..      31      51 ..      12      53 .. 0.86
   2 !   18.1   0.2   8.7e-07     0.001     181     244 ..     180     242 ..     104     259 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.32
                 E-SHHHHHHHHHTT-SEEEE- CS
                 xxxxxxxxxxxxxxxxxxxxx RF
       IMPDH 153 vataegakaLieagadavkvG 173
                  at + ++ Li+ gad++  G
  EPA05831.1  31 AATMASVRGLIQGGADIIELG 51 
                 589999999********9988 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 8.7e-07
                 HHHHHCSB---HHHHHHHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-SEEEESCCCTTBTT CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       IMPDH 181 ttrvvagvGvpqltAvaevaeaakkagvpviaDGGikysgdivkAlaaGadavmlGsllagteE 244
                 tt v +g+    l A+ ev +++k  ++pv    G+++ +d+ k +  Gadav++Gs +    E
  EPA05831.1 180 TTGVKTGIKNYTLKAIKEVKKITK-EKIPVGVGFGVSTPEDVKKYIKTGADAVIVGSAFLKLIE 242
                 788888888889999999988765.569999999999999999999999999999998866554 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       2.3   2.7e+03     165     180 ..      83      98 ..      63     100 .. 0.64
   2 !   16.7   0.0   2.8e-06    0.0034     145     207 ..     171     237 ..     121     243 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.3
                 HHHHHHHHH-SS-BEE CS
        ThiG 165 ealkiiieeakvPviv 180
                 e +k i++e+++P+i+
  EPA05831.1  83 EIVKKIRKETDIPLIL 98 
                 3456688899999996 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 2.8e-06
                 -SEBEEBSSSTTS----S-HH..HHHHH..HHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHH CS
        ThiG 145 caavmPlaapiGsglGllnke..alkii..ieeakvPvivDAGigspsdaaqamelGadavllntav 207
                    ++ +    G   G++n +  a+k +  i + k+Pv v  G+ +p+d+ + ++ Gadav++ +a 
  EPA05831.1 171 FLYLVAVYGTTGVKTGIKNYTlkAIKEVkkITKEKIPVGVGFGVSTPEDVKKYIKTGADAVIVGSAF 237
                 55555555667778888774311444442223459****************************9985 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.24   2.9e+02      92     154 ..     105     168 ..      90     188 .. 0.65
   2 !   13.8   0.0     2e-05     0.024     200     243 ..     196     239 ..     185     249 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.24
                 CCC---CCHHHHHHHH.-SS-EEEES---S.HHHHHHHHHCT-SEEEEECCCS-HHHHHHHHHHH CS
        IGPS  92 kyFqGsledLrevrqa.vslpvlrKdFiid.eyqieearalgadaiLLivkvledeeleelaeaa 154
                  y +G  +++ e+++a ++  +l  d  i+ +++  +a +   d+i Li    +++++e++a+ +
  EPA05831.1 105 LYHKGYQKFIIEAKNAgIDGLILP-DMSIEeSKEYLAATKNKIDTIFLISPNTTKTRIEKIAKLS 168
                 566666666666665523444443.4444304445566777888888888888888888877765 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 2e-05
                 HHHCHCC-TTSEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC CS
        IGPS 200 eeLaklvpkdvllvaeSGiktredveklkeegvnafLvGeslmr 243
                 +e++k  ++++ +    G++t+edv+k+ ++g++a++vG+++++
  EPA05831.1 196 KEVKKITKEKIPVGVGFGVSTPEDVKKYIKTGADAVIVGSAFLK 239
                 55555445455555667************************987 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.29   3.5e+02     110     156 ..      81     126 ..      76     127 .. 0.74
   2 !   13.0   0.0   3.3e-05      0.04     154     217 ..     174     238 ..     141     254 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.29
                 HHHHHHHHHCCSSS-EEEEEESESSTTTC.HHHHHHHHHHCT-SEEE CS
         Dus 110 vaqivkavvkaveiPvtvkirigiddeeenalelakiveaaGaqalt 156
                 + +ivk+++k ++iP+ + + + i   ++   +++  +++aG++ l+
  EPA05831.1  81 FFEIVKKIRKETDIPLILMTYTNIL-YHKGYQKFIIEAKNAGIDGLI 126
                 6789999999999999988887776.444456777778888877665 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 3.3e-05
                 EEEEESSECCCTT-CG--CHHHHHHHHH-S..S-EEEESS--SHHHHHHHHHHH--SEEEESCHHC CS
         Dus 154 altvHgRtraqnyegtadweaIkevkqavs..ipviaNGdIkdaedaqaileetGadgvmigrgal 217
                  ++v g t  +   ++  ++aIkevk+  +  ipv +  ++ ++ed+++ ++  Gad+v++g + l
  EPA05831.1 174 LVAVYGTTGVKTGIKNYTLKAIKEVKKITKekIPVGVGFGVSTPEDVKKYIKT-GADAVIVGSAFL 238
                 5677777777777778899********99999******************987.********8765 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   1.5e-05     0.018     172     231 ..     182     243 ..     137     257 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.5e-05
         NMO 172 Gtpevgd.kglfaLvpqvldavd..iPviAaGGiidrrgvaaaLalGAsgvqigtrfLltkes 231
                 G +++g  + +++ +++v++  +  iPv    G+ + ++v+  +  GA +v +g++fL   e 
  EPA05831.1 182 G-VKTGIkNYTLKAIKEVKKITKekIPVGVGFGVSTPEDVKKYIKTGADAVIVGSAFLKLIEK 243
                 4.33333345778888888888889***9999*************************976665 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.6   3.3e-05      0.04     104     180 ..     155     236 ..      73     237 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.3e-05
    TMP-TENI 104 hslee.aeeaealgadYigvGpifpTdtKkda.eplgleglkelaeale..iPv.vaiGGitlenvaevleagadgvavvsa 180
                 ++ +  +e++++l   ++ + +++ T+  k   +   l+ +ke+++ ++  iPv v  G  t+e+v++ +++gad v v sa
  EPA05831.1 155 NTTKTrIEKIAKLSSGFLYLVAVYGTTGVKTGiKNYTLKAIKEVKKITKekIPVgVGFGVSTPEDVKKYIKTGADAVIVGSA 236
                 4444448889999999999999998886555559999999999999999999985677888999999999999999999887 PP

>> BtpA  BtpA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0         2   2.4e+03      63      83 ..      76      96 ..      56     115 .. 0.77
   2 ?    0.7   0.0      0.24   2.9e+02     172     225 ..     121     172 ..      97     179 .. 0.72
   3 ?   11.8   0.6   9.8e-05      0.12     179     231 ..     181     238 ..     175     261 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2
        BtpA 63 etvaamtvivkevksdvsipl 83
                ++++    ivk+++++  ipl
  EPA05831.1 76 AKISKFFEIVKKIRKETDIPL 96
                456777788888888888887 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.24
        BtpA 172 ladavilsGkatGgevdleelklaketvkvkvlvgsGvseenlekllsiadGvi 225
                  +d++il  ++   e + e l + k+ +++  l+   +++  +ek+ +++ G++
  EPA05831.1 121 GIDGLILPDMS--IEESKEYLAATKNKIDTIFLISPNTTKTRIEKIAKLSSGFL 172
                 45555555443..34566778888888888888888888888888888888875 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 9.8e-05
        BtpA 179 sGkatG.gevdleelklaketvk..vkvlvgsGvse.enlekllsi.adGvivgtsik 231
                 +G +tG ++  l+ +k +k++ k  ++v vg Gvs+ e+++k++++ ad vivg+ + 
  EPA05831.1 181 TGVKTGiKNYTLKAIKEVKKITKekIPVGVGFGVSTpEDVKKYIKTgADAVIVGSAFL 238
                 78888844567899999999999899********86589*****9769******9874 PP

>> TGT  Queuine tRNA-ribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.78   9.3e+02     198     227 ..      72      99 ..       7     123 .. 0.69
   2 ?   11.6   0.0   9.2e-05      0.11     148     245 ..     132     230 ..     129     238 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.78
                 SSSSSHHHHHHHHHHHHGGGS-TTS-EEET CS
         TGT 198 lsvgeekeellevveavtellpedkprylm 227
                 l+ g + ++++e+v++++++   d p +lm
  EPA05831.1  72 LQNGAKISKFFEIVKKIRKET--DIPLILM 99 
                 344555666666666666666..5555555 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 9.2e-05
                 HHHHHHHHHHHHHHHSEEEEEE--TT-HHHHHHHHHHHHHH--SEEEE-SSSSSS..HHHHHHHHHHHHGGGS-TTS-EE.ETTB-SHHHHHHHHHTT- CS
         TGT 148 verTlrwldrcleahqalfgivqGglyedlreesaeelakrdfdgyaigGlsvge..ekeellevveavtellpedkpry.lmGvgtPedlleavalGv 243
                 +e++ ++l   +++ +++f i      ++ r e + +l++  +  +a+ G ++ +   k+  l+ +++v++   e+ p+   +Gv tPed+ + ++ G+
  EPA05831.1 132 IEESKEYLAATKNKIDTIFLISPN--TTKTRIEKIAKLSSGFLYLVAVYGTTGVKtgIKNYTLKAIKEVKKITKEKIPVGvGFGVSTPEDVKKYIKTGA 228
                 566677777777766777766654..4556777777776533344555554422224488999**********999999846***************** PP

                 -E CS
         TGT 244 Dm 245
                 D 
  EPA05831.1 229 DA 230
                 *7 PP

>> Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.3   7.4e-05     0.088     109     197 ..     149     237 ..      82     238 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.4e-05
                     EEEE-TT--GGGGTTTCCC-SEEE.EESS-TT-SS----.CCHHHHHHHHHHHHHHHT---EEEEESS--.TTTCHHHHHHT--EEEESHHH CS
  Ribul_P_3_epim 109 glvlnpatplealeyllekldlvl.lmsvePgfgGQkFi.pevlekikkvrklidekeldlkievDGGvk.ldnieqiaeagadvlVagsav 197
                     +  + p+t  + +e++++     l l +v    g +  i + +l+ ik+v+k+++e   ++ + v  Gv+  + +++ ++ gad++++gsa+
      EPA05831.1 149 IFLISPNTTKTRIEKIAKLSSGFLyLVAVYGTTGVKTGIkNYTLKAIKEVKKITKE---KIPVGVGFGVStPEDVKKYIKTGADAVIVGSAF 237
                     5556677777777777665443330444444444444441457899********99...899999999972589****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       883  (0.0492498); expected 358.6 (0.02)
Passed bias filter:                      597  (0.033298); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1949.49
//
Query:       EPA05832.1  [L=396]
Description: tryptophan synthase, beta subunit [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.4e-45  153.8   0.8    7.6e-45  153.6   0.8    1.1  1  PALP          Pyridoxal-phosphate dependent enzyme
  ------ inclusion threshold ------
      0.063   13.1   0.1       0.14   11.9   0.1    1.5  1  Succ_CoA_lig  Succinyl-CoA ligase like flavodoxin domain


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.6   0.8   8.4e-49   7.6e-45       3     294 .]      52     377 ..      50     377 .. 0.85

  Alignments for each domain:
  == domain 1  score: 153.6 bits;  conditional E-value: 8.4e-49
                 GCSSS--EEEECCTCCCCCCE.EEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-EEEEEEETTS-...HHHHHHH CS
        PALP   3 lgigpTPlvrlprlskelgvp.lflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallGlkvtivvpadas...pekvall 97 
                 ++ +pTPl  +++ls+++g++ ++lK+E+l ++g++K++      + +k+ ++++ ++e+++G+hg+a+A+a+a+lG+k+++++  +++   + +v ++
  EPA05832.1  52 YAGRPTPLYYAKNLSEKCGGAkIYLKREDLLHGGAHKINNTLGQALLAKKMNKKRIIAETGAGQHGVATAMACAVLGIKSEVYMGYKDTirqKLNVYRM 150
                 5789****************9********************97777777777*************************************77779***** PP

                 HHTT-EEEEECCHHHHHHHHHHHHHHH.....STTCEE--TTT..SHH...HHHHHHTHHHHHHHHTT....TTEEEEEEE-SSSHHHHHHHHHHHHHS CS
        PALP  98 rllGaevvevggdydeavaaaaelaae.....gegaylvsqfd..npt...viegygtiglEileqlg....gkpdavvvpvGgGgliaGiaaglkerr 182
                  +lG +v+ v+++ ++ ++a++e++++     +  +yl+ ++   +p+   v + ++ ig Ei+ q++    ++pd+v+++vGgG+++ G+  +l + +
  EPA05832.1 151 NMLGSKVHPVKSGSKTLKDAINEAIRDwitnvESTYYLLGSTVgpHPYpvmVRDFQSVIGEEIKVQMKkitnKVPDTVIACVGGGSNAIGTFYPLVDTN 249
                 **********999999999999999999999755555555555564447656666*********88888889************************965 PP

                 TT-EEEEEEEC..TTCGGTTCC..S..S.SS..B................SSS.CCSTCSCGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB- CS
        PALP 183 pdvrvigvepe..gsdalarsl..ragrrvtvpvs...............dtiadglavgspselafelldrlvdeivtvsdeealeamrllarregiv 262
                    ++igve++  g  + ++s+   ag+   ++ +               ++i  gl+ + +++++  l d +  ++ + +d+e+++a   l r+egi+
  EPA05832.1 250 --AEIIGVEAAgkGLKSKYHSAtlSAGSKGVLHGMmtyllqdeegqitetHSISAGLDYPGVGPEHSYLKDIKRVKYHSATDAEVIDAFLMLTRTEGII 346
                 ..57*******664444444443444444444444888888888888888**********99999988888888899********************** PP

                 B-HHHHHHHHHHHHHHHHCCTTCEEEEEEE-B CS
        PALP 263 vepssaaalaalklreagelkegdrvvviltg 294
                 +   sa+a+a + ++ a++ k+++++vv l+g
  EPA05832.1 347 PALESAHAIAEA-MKIAKKSKKSESIVVTLSG 377
                 ************.888888888888****998 PP

>> Succ_CoA_lig  Succinyl-CoA ligase like flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   1.6e-05      0.14      43      98 ..     330     385 ..     325     392 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.6e-05
  Succ_CoA_lig  43 adlleylaedpetkvillylEsirdgrkflsaarraarkkpvvvlksGrseagara 98 
                   a++++++   ++t+ i+  lEs +  ++ +++a++ +++  +vv  sGr ++  + 
    EPA05832.1 330 AEVIDAFLMLTRTEGIIPALESAHAIAEAMKIAKKSKKSESIVVTLSGRGDKDVEE 385
                   7999*********************************************8877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       792  (0.0441742); expected 358.6 (0.02)
Passed bias filter:                      600  (0.0334653); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 2564.66
//
Query:       EPA05833.1  [L=226]
Description: hypothetical protein BG20_I0790 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-26   93.1   0.0    2.6e-26   92.9   0.0    1.0  1  PAC2      PAC2 family
  ------ inclusion threshold ------
      0.047   13.6   0.0      0.083   12.8   0.0    1.5  1  LpxI_N    LpxI N-terminal domain


Domain annotation for each model (and alignments):
>> PAC2  PAC2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.9   0.0     3e-30   2.6e-26       2     208 ..      17     223 ..      16     226 .] 0.81

  Alignments for each domain:
  == domain 1  score: 92.9 bits;  conditional E-value: 3e-30
                 EEESSCGGGHHHHHHHHHHHHTTEEEEEEEEHCCHSBCCCC.SEEEEETT..EEE-SEEE..EEE.TTT.SEEEEEEE..E-HSCHHH..HHHHHHHHH CS
        PAC2   2 ilGfpgiGnVgqlavdlLiesleaekvgeidsdyllpfvgprpvvlveeg..relepprl..yak.dsgsrdllvlqg..repilqye..efakalldw 91 
                 i+++ ++GnVg+++v+++ +sl  +k+    ++y        p+ +v+ g   el p++   y k +     l+v+ g   +p+  +e  ++++ ++d+
  EPA05833.1  17 IAAMQDMGNVGSIVVNFINDSLRTKKFRIAKTPY--------PTYVVDIGghIEL-PNESweY-KyS---DGLIVFGGgtGQPQDSQElyALCQDVIDI 102
                 78999**********************9999999........4444444423222.2233443.322...479999999945555555579******** PP

                 HHHTTESEEEEEEEEEESS-ES..TTS-.EEEEEESSHHHHHHHH....CT..-CEEEEHHHHHHHHHHHHTT-EEEEEEEEEEC.CC--HHHHHHHHH CS
        PAC2  92 aeelgvkevvvLggldageradvphtrpekvtgaatdeelleele....es..eyggivgitglLlsaakergipavgllaevph.ylpdPkaaaalle 183
                  +++  k +++Lgg+++++     +++p k++++ t+ el ++++     +  + ++i+g++gl+l+ ak++gi+++g+++e +h ++p  +aa+++++
  EPA05833.1 103 SKKYSAKFIYTLGGFHTNRV---LDKNP-KTFVTTTSSELTKQMQglgvFTtpQRSIITGFNGLILGFAKQNGIQGMGMYGELNHpEIPQYRAAISIIK 197
                 ****************7644...56777.99**********99974555115799******************************555*********** PP

                 HHHHHHT--.-HCHHHHHHHHHHHHH CS
        PAC2 184 flskllgle.vdtedLeedaeeleeq 208
                  l+kl+  +  dt +Le +a+ +e+ 
  EPA05833.1 198 TLEKLTYRNlGDTGKLEMMAQDIEKN 223
                 ******99945577*********986 PP

>> LpxI_N  LpxI N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   9.2e-06     0.083      55     114 ..     161     222 ..     125     224 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.2e-06
      LpxI_N  55 gklikaLkregvtevvmaGkvekpklldlrpDlralkllak..lkdrgddalLravveelek 114
                 g ++ + k++g++ + m G++++p++ + r  ++++k+l k  +++ gd   L+  ++ +ek
  EPA05833.1 161 GLILGFAKQNGIQGMGMYGELNHPEIPQYRAAISIIKTLEKltYRNLGDTGKLEMMAQDIEK 222
                 56778889*********************************5555999*****999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1437.17
//
Query:       EPA05834.1  [L=228]
Description: hypothetical protein BG20_I0791 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-07   29.9   0.0    1.1e-06   28.7   0.0    1.4  1  PDDEXK_1  PD-(D/E)XK nuclease superfamily
  ------ inclusion threshold ------
      0.013   14.8   0.3        1.2    8.3   0.2    2.4  1  DUF2800   Protein of unknown function (DUF2800)
      0.028   14.6   0.0      0.044   13.9   0.0    1.4  1  Cas_Cas4  Domain of unknown function DUF83


Domain annotation for each model (and alignments):
>> PDDEXK_1  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0   1.9e-10   1.1e-06      87     180 ..      86     177 ..      44     187 .. 0.69

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 1.9e-10
    PDDEXK_1  87 rylaeklkevleklverlaeeleakrgfrpvalelefggekvrLkGriDrvddkegelriiDyKtgsappkskelaelkegl.QlllYllalaeg 180
                 +  +++  ++ ++ +e+l+ +l++  +++ ++l   f+  ++++ G +D++ + +g+l iiD+Kt++++  ++ + ++++ + Q ++Y l+ +e 
  EPA05834.1  86 KESNGDFLDIPKNHFEKLKPYLHKMNNIQGIELP-LFS-DEFKIAGTCDCIAEYNGDLSIIDFKTSRSRLMEHYD-KVQKYFmQATAYSLMWKER 177
                 4444555556666666677777777775555555.444.5799*********99999**********99777764.4555555********9986 PP

>> DUF2800  Protein of unknown function (DUF2800)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.2    0.0002       1.2     113     134 ..     127     148 ..      44     161 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0002
     DUF2800 113 gfGtaDvviiaddvLeviDlKy 134
                   Gt+D++   ++ L++iD+K 
  EPA05834.1 127 IAGTCDCIAEYNGDLSIIDFKT 148
                 6799999999999999999996 PP

>> Cas_Cas4  Domain of unknown function DUF83
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   7.3e-06     0.044      49     109 ..     125     190 ..      97     224 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.3e-06
    Cas_Cas4  49 velsesikiDvvekekeklvvvEvKkskkk.......eeaaklQllyYlllLe.kkgveikeGvleypk 109
                 +++   + +D + +++++l ++++K s+++        ++  +Q ++Y l+ + ++g++i++ ++ + +
  EPA05834.1 125 FKI--AGTCDCIAEYNGDLSIIDFKTSRSRlmehydkVQKYFMQATAYSLMWKeRTGIDIDQ-IVIIGS 190
                 333..899********************998888875555589**********99*****93.333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1496.88
//
Query:       EPA05835.1  [L=89]
Description: hypothetical protein BG20_I0783 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       858  (0.0478554); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 559.55
//
Query:       EPA05836.1  [L=475]
Description: putative membrane protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.4e-08   34.4  19.1    2.4e-08   34.4  19.1    3.4  4  PMT_2         Dolichyl-phosphate-mannose-protein mannosyltran
  ------ inclusion threshold ------
       0.22   11.5   0.5       0.48   10.4   0.5    1.5  1  SLATT_fungal  SMODS and SLOG-associating 2TM effector domain
        3.8    8.0   8.8       0.62   10.6   0.7    3.3  4  DUF3681       Protein of unknown function (DUF3681)


Domain annotation for each model (and alignments):
>> PMT_2  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4  19.1     4e-12   2.4e-08      25     154 ..      93     221 ..      85     226 .. 0.84
   2 ?   -1.3   0.6      0.37   2.2e+03     118     155 ..     262     293 ..     251     303 .. 0.53
   3 ?    0.5   3.4       0.1   6.1e+02      75     117 ..     303     346 ..     280     355 .. 0.65
   4 ?   -0.1   0.0      0.16   9.7e+02      71     101 ..     368     399 ..     359     405 .. 0.68

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 4e-12
       PMT_2  25 rlvsalagvltilllyllarrlfgkraallaalllavvplfvalsalftpdaplvllwalalylllraleknklkyw.llagvlfGlgflsKytaalll 122
                 r++  +++v+ ++l+y++++ ++g+  a+l+a+l av+p+  +    + +d++l++l++ a+++ l  ++++  + +  ++g+l+Gl++++K  a+ ++
  EPA05836.1  93 RIFMGILAVVDTFLIYKIVQIRYGTISAFLSAALFAVLPFTWIFK-RILLDSILIPLILGAILIALYSAKTKHSSILiTFSGALMGLAVFTKIPAFTMI 190
                 89999**********************************433333.6788*********999988888776664555489******************* PP

       PMT_2 123 iaallyllisarrilkekkpylalllalllfs 154
                 + +++++++++r+++ + +++l+ +l + l+ 
  EPA05836.1 191 F-VVAWIVYNNRKKFSDVILLLIPFLLIPLIW 221
                 *.888888886779999999987666665555 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.37
       PMT_2 118 aallliaallyllisarrilkekkpylalllalllfsp 155
                 +++l+++ +++++++      ++k++l  ++ +++f++
  EPA05836.1 262 MFVLGLSGIVFAVLR------KDKFLLFWFIPFVVFLS 293
                 555555555555555......44444444444444443 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.1
       PMT_2  75 daplvllwalalylllrale.knklkywllagvlfGlgflsKyt 117
                   + v+++++++ ++++ ++ ++k+k ++++g++ ++ ++    
  EPA05836.1 303 WMMIVPVLCISAGIWIESIHkEGKMKKYVYFGIISAVFVFGFTS 346
                 45678888888888888887345699998888887776654444 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 0.16
       PMT_2  71 lftpdaplvllwalalylllraleknk.lkyw 101
                 ++  d++ vl+    +++l+ + +k++ ++++
  EPA05836.1 368 NNYDDNVTVLASPVYTWILYDVFKKENvPEDY 399
                 33348888888888888888888887755555 PP

>> SLATT_fungal  SMODS and SLOG-associating 2TM effector domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.5     8e-05      0.48      23      55 ..     143     175 ..     132     179 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 8e-05
  SLATT_fungal  23 aiglQvllgAlltaLgalssgrtqvaitvLGal 55 
                    i++ ++lgA+l+aL ++++++++++it  Gal
    EPA05836.1 143 SILIPLILGAILIALYSAKTKHSSILITFSGAL 175
                   688899************99999******9998 PP

>> DUF3681  Protein of unknown function (DUF3681)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.13     8e+02      36      81 ..     163     210 ..     139     220 .. 0.70
   2 ?   -1.7   0.0      0.69   4.1e+03      83      96 ..     257     270 ..     252     273 .. 0.84
   3 ?   -1.5   0.2      0.61   3.6e+03      47      62 ..     303     315 ..     271     322 .. 0.59
   4 ?   10.6   0.7    0.0001      0.62      34      59 ..     322     347 ..     304     359 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.13
     DUF3681  36 hgkallylYYgiLvavvvfGlaeasvgfWvsgd..perrravGktvlw 81 
                 +++ +l+++ g+L++ +vf  + a++ ++v      ++r+    ++l+
  EPA05836.1 163 KHSSILITFSGALMGLAVFTKIPAFTMIFVVAWivYNNRKKFSDVILL 210
                 445567778888999999988888888777665444556666665554 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.69
     DUF3681  83 svlplvlvaalGGf 96 
                  + pl++v++l G+
  EPA05836.1 257 VIDPLMFVLGLSGI 270
                 5779*******996 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.61
     DUF3681  47 iLvavvvfGlaeasvg 62 
                     ++++ +  +s+g
  EPA05836.1 303 W---MMIVPVLCISAG 315
                 2...223333334445 PP

  == domain 4  score: 10.6 bits;  conditional E-value: 0.0001
     DUF3681  34 lrhgkallylYYgiLvavvvfGlaea 59 
                 +++gk+  y+Y+gi+ av+vfG+   
  EPA05836.1 322 HKEGKMKKYVYFGIISAVFVFGFTST 347
                 45789999**************9754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       996  (0.0555525); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.66u 0.33s 00:00:00.99 Elapsed: 00:00:00.50
# Mc/sec: 2858.39
//
Query:       EPA05837.1  [L=199]
Description: hypothetical protein BG20_I0776 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1194.41
//
Query:       EPA05838.1  [L=39]
Description: hypothetical protein BG20_I0788 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.052   13.1   0.0      0.059   12.9   0.0    1.2  1  RecR      RecR protein


Domain annotation for each model (and alignments):
>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   3.3e-06     0.059      28      39 ..      23      34 ..      12      34 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.3e-06
                SSS-CCCCSTTS CS
        RecR 28 edlCaICsdprR 39
                + lC IC+d++R
  EPA05838.1 23 NYLCGICRDKKR 34
                559********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.30s 00:00:00.71 Elapsed: 00:00:00.47
# Mc/sec: 251.54
//
Query:       EPA05839.1  [L=197]
Description: glutamine amidotransferase, class I [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.4e-53  178.8   0.0    1.1e-52  178.6   0.0    1.0  1  GATase         Glutamine amidotransferase class-I
    3.8e-09   36.6   0.9    1.9e-08   34.3   0.9    1.9  1  Peptidase_C26  Peptidase C26
    5.3e-05   23.1   0.1    0.00019   21.3   0.0    1.8  2  SNO            SNO glutamine amidotransferase family


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.6   0.0   1.8e-56   1.1e-52       2     188 ..       5     191 ..       4     193 .. 0.96

  Alignments for each domain:
  == domain 1  score: 178.6 bits;  conditional E-value: 1.8e-56
                 EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT....TTTHHHHHHHHCTSTS-EEEETHHHHHHHHHTTTEEEEEE CS
      GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg....vegkieaikearenkiPiLGICLGmQllaiefgrkvvkek 96 
                 +iDnyds+++n++++l elgv+ +v+++d+   e+++ ++++d+i++s+Gpg+p+     + + ++ik +    +PiLG+CLG+Q ++++fg+kv ++ 
  EPA05839.1   5 IIDNYDSFVYNIAQYLGELGVDSDVIRNDKITVEQIK-QNKYDAIIISPGPGTPSdrkyFGVCGDVIKDIGP-ITPILGVCLGHQGIIEAFGGKVTNAG 101
                 89***************************98888874.89***************99999999999**9998.9************************* PP

                 CEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEEEEEEETTTEEEESSBTTSTTSTTHHHHHHHHHH CS
      GATase  97 ekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeelmeiiekknpfvgvQFHPEststpegpellfnfli 188
                     hg+t+++g+++++l+++ kn+++++++H+++ ++  + p+ levta+ +dd+e+m++++kk+ + gvQFHPEs++t+ g+++l+nf+ 
  EPA05839.1 102 -CVRHGKTSPVGHTNSELFKDVKNPFRATRYHSLVGDK-TIIPDALEVTAVAADDGEVMAVRHKKYLIEGVQFHPESIMTEDGKRILANFIK 191
                 .9***********************************8.**************************************************965 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.9   3.2e-12   1.9e-08     106     216 .]      77     175 ..      70     175 .. 0.83

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 3.2e-12
  Peptidase_C26 106 vPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkvekgsllaellgseeievnslHhqaike..laeelrveAvae.DgviEa 198
                    +Pilg+C+G+q +  a+GG++ ++       ++h       ++  v  +++ l++++ +   ++ + +H+   ++  + + l+v+Ava+ Dg + a
     EPA05839.1  77 TPILGVCLGHQGIIEAFGGKVTNAGC-----VRH------GKTSPVGHTNSELFKDVKN--PFRATRYHSLVGDKtiIPDALEVTAVAAdDGEVMA 159
                    7******************9987766.....344......3456777777888887755..9********999988889*********97887777 PP

  Peptidase_C26 199 ieseeakafvlgvQwHPE 216
                    +++++  + + gvQ+HPE
     EPA05839.1 160 VRHKK--YLIEGVQFHPE 175
                    77776..99********9 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.18   1.1e+03      31      46 ..      42      57 ..      25      93 .. 0.61
   2 !   21.3   0.0   3.2e-08   0.00019     118     187 ..     119     194 ..     106     195 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.18
                GCC-SEEEE-SS-HHH CS
         SNO 31 laevdaliiPGGesta 46
                 ++ da+ii  G  t 
  EPA05839.1 42 QNKYDAIIISPGPGTP 57
                2567888886666554 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 3.2e-08
                 ETTTCSEEEEEESS--EEEEE-.TTTCEE..EEECTTEEEEEEETTEE..EESS-GG..GSTTHCHHHHHHHHHHC CS
         SNO 118 fknliekftavfiraPvieeilddeavkv..lyeldgeivvakqkkil..atsfhPe..laeddirvhdyfveevv 187
                 fk+++++f a+   + v ++ + ++a +v  +   dge+++++ kk+l  ++ fhPe  ++ed++r+   f+++v 
  EPA05839.1 119 FKDVKNPFRATRYHSLVGDKTIIPDALEVtaVAADDGEVMAVRHKKYLieGVQFHPEsiMTEDGKRILANFIKQVK 194
                 8999999999999999999988777665511556679******9998845689****888*************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1359.59
//
Query:       EPA05840.1  [L=56]
Description: hypothetical protein BG20_I0789 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 410.55
//
Query:       EPA05841.1  [L=51]
Description: hypothetical protein BG20_I0780 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0017   18.4   0.8     0.0031   17.6   0.8    1.7  1  zf-met2    Zinc-binding
  ------ inclusion threshold ------
      0.038   14.8   4.3       0.14   13.1   4.3    1.9  1  zf-C2H2_4  C2H2-type zinc finger


Domain annotation for each model (and alignments):
>> zf-met2  Zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.8   3.4e-07    0.0031       1      26 [.       7      32 ..       7      48 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.4e-07
     zf-met2  1 iCkiCrqtFmcTtkevlLkeHaenKH 26
                +CkiC ++  +  + ++L+eH++  H
  EPA05841.1  7 QCKICGTPLGKEPTTQQLYEHWKKHH 32
                8*********************9766 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   4.3   1.5e-05      0.14       2      24 .]       7      32 ..       6      32 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.5e-05
   zf-C2H2_4  2 kCpiCgksFsskka...LlrHlkthH 24
                +C+iCg++     +   L  H+k+hH
  EPA05841.1  7 QCKICGTPLGKEPTtqqLYEHWKKHH 32
                8****999964444799********* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.49
# Mc/sec: 314.80
//
Query:       EPA05842.1  [L=116]
Description: hypothetical protein BG20_I0786 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0058   17.4   0.2     0.0075   17.0   0.2    1.2  1  zinc_ribbon_15  zinc-ribbon family
     0.0068   16.6   0.5       0.65   10.3   0.0    2.2  2  zf-LITAF-like   LITAF-like zinc ribbon domain
  ------ inclusion threshold ------
      0.041   13.4   4.0       0.52    9.9   4.0    2.2  1  TF_Zn_Ribbon    TFIIB zinc-binding


Domain annotation for each model (and alignments):
>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.2   1.3e-06    0.0075      21      75 ..      30      94 ..      17     101 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.3e-06
  zinc_ribbon_15 21 lklffipvfkwkkkk.pylacskCkslleaskelgkeiekkesse.........kkeCknCgkev 75
                     klf  p+ k+++ k +  +c++C++ +++  + + e +++e+++         +++C++C++ +
      EPA05842.1 30 GKLFLAPIGKLEEGKmKKHYCKNCETEFGNPPKIHLEENTNEQVSdnlilvergQYTCEKCSSII 94
                    57888888888875515689**********99777766666666689**************9877 PP

>> zf-LITAF-like  LITAF-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   0.00011      0.65      52      67 ..      43      58 ..      30      59 .. 0.84
   2 !    4.8   0.1    0.0057        34      56      70 .]      84      98 ..      80      98 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00011
  zf-LITAF-like 52 lkdvehyCpnCgallg 67
                    k ++hyC+nC++  g
     EPA05842.1 43 GKMKKHYCKNCETEFG 58
                   57899******98766 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0057
  zf-LITAF-like 56 ehyCpnCgallgtyk 70
                   +++C +C + +g y+
     EPA05842.1 84 QYTCEKCSSIIGEYR 98
                   579********9985 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   4.0   8.6e-05      0.52       3      38 ..      50     103 ..      48     108 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 8.6e-05
                   ETTTTCEEC..............HEE....TSTTCEEESSSSBEEEECCCCCCC CS
  TF_Zn_Ribbon   3 CPnCgstnl..............veD....pergelvCtdCGlVlednsidegp 38 
                   C+nC +++               v D     erg ++C++C +++ +  + ++ 
    EPA05842.1  50 CKNCETEFGnppkihleentneqVSDnlilVERGQYTCEKCSSIIGEYRVFKKQ 103
                   77777664257777777777777777677789**********999988777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 812.96
//
Query:       EPA05843.1  [L=384]
Description: glycosyltransferase, group 2 family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-34  117.9   0.0    8.7e-34  116.8   0.0    1.6  2  Glycos_transf_2  Glycosyl transferase family 2
    2.8e-24   85.6  11.4    4.6e-23   81.7  12.3    2.2  1  GtrA             GtrA-like protein
    2.1e-10   40.9   0.0    3.1e-10   40.3   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
     0.0065   16.0   0.0      0.013   15.0   0.0    1.5  1  Glyco_transf_21  Glycosyl transferase family 21
  ------ inclusion threshold ------
      0.032   14.6   0.0      0.048   14.0   0.0    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
      0.038   13.5   0.0       0.06   12.8   0.0    1.3  1  Glyco_tranf_2_2  Glycosyltransferase like family 2


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.8   0.0   2.9e-37   8.7e-34       1     166 [.      10     179 ..      10     182 .. 0.97
   2 ?   -3.2   0.0       2.1   6.3e+03     134     159 ..     235     260 ..     209     267 .. 0.59

  Alignments for each domain:
  == domain 1  score: 116.8 bits;  conditional E-value: 2.9e-37
                      EEEEEESS-TTTHHHHHHHHHHH.GGCCEEEEEEEEES-SSCHHHHHGGGCH.....C-TTEEEEEESSS-HHHHHHHHHHHH--SSEEEEEES CS
  Glycos_transf_2   1 svviptyNeektlletlesllaq.dpypdfeiivvDDgStDetveileelak.....edprvrvirreenvGkagalnaglraatgdyilflDa 88 
                      s+viptyNe+++++  l+ +++  +    +e ivvDD+S+D+t +i+e++ +      +  v vi r+ ++G+++a+ +g+++a+g++i+++D+
       EPA05843.1  10 SIVIPTYNESENIKGILHLIKEHlPINTAVEAIVVDDNSPDGTGKIAEDYFEslkekTRYTVSVINRKTREGLSSAILNGIQQAKGKIIIVMDS 103
                      8*****************66666********************************99999********************************** PP

                      SEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTCSTCCCEEEEHHH CS
  Glycos_transf_2  89 Ddepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfeigsaallrreal 166
                      D  ++p+ ++klv+ l++  +d+v+++r+ ++g+   ++  ++    +++ + + k+ l+++ s+  +++++++++++
       EPA05843.1 104 DFSHPPQLIPKLVDVLKQSKTDIVVASRYLNGGSIQGWSLKRK--MISKVATVIAKQGLGIKESDPMSGFFAFNKDII 179
                      ****************************************998..6****************************9987 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.1
                      EEECCHCCCCHCCCCCCSTTCSTCCC CS
  Glycos_transf_2 134 enerlyfkerkrslkgnlsfeigsaa 159
                        +r+ +ke+++++  ++ f++  a+
       EPA05843.1 235 NLYRYGKKEQRNEKRTSVRFVSKAAR 260
                      33444555555555555555555555 PP

>> GtrA  GtrA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.7  12.3   1.5e-26   4.6e-23       1     117 []     260     378 ..     260     378 .. 0.98

  Alignments for each domain:
  == domain 1  score: 81.7 bits;  conditional E-value: 1.5e-26
        GtrA   1 rFlivGvlgtlvdlallllllellglsyllAnaiafivailfnFilnrrwtFkdrekakl..lkqflkFvlvsllglllnllilwllveklgleallak 97 
                 rF  vG++g lv++++ +l+++ +++ yl A+++++iv+i +nF+ln++wtF+dre +++  ++q+ kF+ +s +g+l++l+++++lv+ +++++ +a 
  EPA05843.1 260 RFFSVGASGLLVNYLMSMLFTTSFNMWYLHATILGIIVSISSNFVLNKYWTFEDREFTPKrtIIQYGKFAGFSSIGALVQLGLVYYLVDEISISYPIAL 358
                 79*******************99*********************************999899************************************* PP

        GtrA  98 lvgiivalvlnyvlsklfvF 117
                 + +++ a++ n++l+k+++F
  EPA05843.1 359 VSAVATAAFSNFILNKKWTF 378
                 *******************9 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.0     1e-13   3.1e-10       4     127 ..       9     134 ..       6     153 .. 0.79

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 1e-13
  Glyco_tranf_2_3   4 lavlVptfneedvlgevlesll.aqe.yprvevvvvvdesdaetlevaeelaaalp...dvrvrvvvnarnlgstgksralnealravksdlvl 92 
                      +++++pt+ne++ +  +l+ +    + + +ve +vv+d+s ++t + ae   + l+   +  v+v+   ++ ++ g s a+ ++++++k+++++
       EPA05843.1   9 VSIVIPTYNESENIKGILHLIKeHLPiNTAVEAIVVDDNSPDGTGKIAEDYFESLKektRYTVSVI---NRKTREGLSSAILNGIQQAKGKIII 99 
                      89********99666655555522242688***********9998877776666664222235554...33466789999************** PP

  Glyco_tranf_2_3  93 lvDdDtvvePdtlkrllqffltpkvgavgtpvfll 127
                      ++D+D    P ++++l+ +++++k ++v ++++l+
       EPA05843.1 100 VMDSDFSHPPQLIPKLVDVLKQSKTDIVVASRYLN 134
                      ********************999999998777665 PP

>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   4.3e-06     0.013      21      86 ..      85     150 ..      70     179 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.3e-06
  Glyco_transf_21  21 nllqaleaakydllvisDsdvrvkpdyLeellaaledpkvglVtslpvgsdakglaaaleaaflnt 86 
                      ++l+++++ak +++++ Dsd   +p+ + +l+  l+++k+ +V++  +  + +  +  l++ +++ 
       EPA05843.1  85 AILNGIQQAKGKIIIVMDSDFSHPPQLIPKLVDVLKQSKTDIVVASRYLNGGSIQGWSLKRKMISK 150
                      57999***************************************9888665553333355555555 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.6e-05     0.048      57     124 ..      66     132 ..      27     163 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.6e-05
                   TCTS-E.EE-TTSS-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESS CS
  NTP_transf_3  57 rlgvrv.vededpgkgplaslaaalraaadadavlvlacDmPlltpelverllaaaaasgadvvvptye 124
                   +++++v v +++  +g +++++ ++++a + + ++v+  D  + +p+l+ +l++ +++s+ d+vv+++ 
    EPA05843.1  66 KTRYTVsVINRKTREGLSSAILNGIQQA-KGKIIIVMDSDFSH-PPQLIPKLVDVLKQSKTDIVVASRY 132
                   3344445778889**************9.9***********88.9******************999764 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     2e-05      0.06       1     104 [.      10     117 ..      10     147 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2e-05
  Glyco_tranf_2_2   1 svviplraseerhyieervlqkakyy..deeielivvddgSsekfleev....ssiidl.nllvylkdeddkayslaaarNrGaskaesdlvlF 87 
                      s+vip +++ e+  i+  + +++ +   +  +e ivvdd S++ + +      +s++++ +  v++ +  ++  +l+ a   G+++a++ +++ 
       EPA05843.1  10 SIVIPTYNESEN--IKGILHLIKEHLpiNTAVEAIVVDDNSPDGTGKIAedyfESLKEKtRYTVSVINR-KTREGLSSAILNGIQQAKGKIIIV 100
                      79**********..99999888888777999***********987665410014444431334454555.457788999999************ PP

  Glyco_tranf_2_2  88 lDaDcfissDkfekilk 104
                      +D+D    +  + k++ 
       EPA05843.1 101 MDSDFSHPPQLIPKLVD 117
                      ***98777766666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       754  (0.0420548); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2676.48
//
Query:       EPA05844.1  [L=56]
Description: hypothetical protein BG20_I0795 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       232  (0.0129399); expected 358.6 (0.02)
Passed bias filter:                      188  (0.0104858); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 402.04
//
Query:       EPA05845.1  [L=115]
Description: hypothetical protein BG20_I0778 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       756  (0.0421663); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 829.43
//
Query:       EPA05846.1  [L=61]
Description: hypothetical protein BG20_I0798 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0096   15.5   3.0      0.012   15.2   3.0    1.2  1  RecR             RecR protein
  ------ inclusion threshold ------
      0.041   14.2   2.6      0.067   13.5   2.6    1.4  1  C1_2             C1 domain
       0.09   13.2   7.3       0.16   12.4   7.3    1.4  1  FeoB_associated  FeoB-associated Cys-rich membrane protein
       0.97    9.5   3.9         22    5.2   3.9    2.1  1  YyzF             YyzF-like protein


Domain annotation for each model (and alignments):
>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   3.0   2.6e-06     0.012      14      36 ..      33      55 ..      27      57 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.6e-06
                HH-EE-TTT--EESSSS-CCCCS CS
        RecR 14 ekvrhCsrCgnlteedlCaICsd 36
                +k ++C  Cgn t + +C++C+ 
  EPA05846.1 33 NKTKQCIACGNKTNSLICEFCKK 55
                689******************85 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   2.6   1.5e-05     0.067      11      39 ..      28      54 ..      15      59 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.5e-05
        C1_2 11 kgedssesfnCsaCgrkidgffYsCseCd 39
                +g++ +++++C aCg+k++    +C+ C+
  EPA05846.1 28 IGKNTNKTKQCIACGNKTN--SLICEFCK 54
                7889999**********74..47997795 PP

>> FeoB_associated  FeoB-associated Cys-rich membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   7.3   3.5e-05      0.16       3      43 ..       5      50 ..       4      56 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.5e-05
  FeoB_associated  3 iIVgliiaaavafvirrlikk...kkkGsCg..ggCsgCsssssg..C 43
                     +I+++ ia++v+++i++l ++   +k+   +    C  C+++ ++  C
       EPA05846.1  5 VIITVGIAVVVVLIIIKLLRDpniGKNT--NktKQCIACGNKTNSliC 50
                     69*******************9997777..233567899887666775 PP

>> YyzF  YyzF-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   3.9     0.005        22      32      44 ..      46      58 ..      24      60 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.005
        YyzF 32 lsktCefCekpAt 44
                 s  CefC+k+A+
  EPA05846.1 46 NSLICEFCKKNAK 58
                5667999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1616  (0.0901333); expected 358.6 (0.02)
Passed bias filter:                      859  (0.0479112); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 451.91
//
Query:       EPA05847.1  [L=73]
Description: hypothetical protein BG20_I0793 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.019   14.7   0.1       0.02   14.6   0.1    1.1  1  DUF4292   Domain of unknown function (DUF4292)


Domain annotation for each model (and alignments):
>> DUF4292  Domain of unknown function (DUF4292)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   1.1e-06      0.02      52      99 ..      15      65 ..       9      73 .] 0.84

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.1e-06
     DUF4292 52 alitpdsvlvydklnkryfvgdfsnLskllgvelsfellqnlllGq...ll 99
                 ++  d+++++d+l+ r   +  ++++ + + ++ fe++q ++l++   ++
  EPA05847.1 15 TEFPKDGFSLVDQLQGRVQFAILDQIKLMKTSGIEFEEIQKIILNNvqrII 65
                57788****************************************955444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       764  (0.0426125); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 468.95
//
Query:       EPA05848.1  [L=289]
Description: kinase, PfkB family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.3e-12   45.4   0.1    7.8e-11   41.8   0.1    2.0  1  PfkB      pfkB family carbohydrate kinase
  ------ inclusion threshold ------
       0.13   12.7   0.2       0.33   11.4   0.1    1.7  2  HMA       Heavy-metal-associated domain


Domain annotation for each model (and alignments):
>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   0.1   8.7e-15   7.8e-11     177     295 ..     153     262 ..       3     268 .. 0.67

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 8.7e-15
                 HHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSEEEEEEGGGEEEEEETTEEEEEEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHH CS
        PfkB 177 llellaladllkpneeElealtgekledieealaalhklkakgaktvvvtlGkeGalvvekdgelkvpavpkvkvvDttGAGDsfvggflaallegksl 275
                  l+ l++++++k+n eE + l++ +   ++e ++al+k   kg+++v++t   e +l+v kd+ +  +  p ++v+DttG GD f++ f    l++k++
  EPA05848.1 153 ELD-LSGVNAIKVNPEESQMLVDGN---HDEMMKALQK---KGVEHVIMTNKTEVSLLV-KDKIYSLTL-PNKEVYDTTGLGDIFCATFCCTMLKEKDF 242
                 233.679************999999...8999***999...**********99999999.777777666.99*************************** PP

                 HHHHHHHHHHHHHHHTSSSS CS
        PfkB 276 eealrfanavAalvvqkkga 295
                   al fa   A++++ +k++
  EPA05848.1 243 LWALCFAGGSAQAALDSKQV 262
                 *******9999999888766 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       1.8   1.7e+04      26      36 ..      11      21 ..      10      22 .. 0.80
   2 ?   11.4   0.1   3.7e-05      0.33      22      54 ..     155     186 ..     150     192 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.8
         HMA 26 Vesvkvdlatk 36
                ++s+++d  t+
  EPA05848.1 11 IDSITIDGTTH 21
                78999998887 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 3.7e-05
         HMA  22 elpgVesvkvdlatktvtVegdaes.tklrkiie 54 
                  l+gV+++kv+ +++++ V+g+ ++ +  +++++
  EPA05848.1 155 DLSGVNAIKVNPEESQMLVDGNHDEmM--KALQK 186
                 589******************888744..44444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 1889.34
//
Query:       EPA05849.1  [L=346]
Description: anthranilate phosphoribosyltransferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-78  262.6   1.1    5.4e-78  262.1   1.1    1.2  1  Glycos_transf_3  Glycosyl transferase family, a/b domain
    5.5e-09   35.8   0.0    1.2e-08   34.7   0.0    1.6  1  Glycos_trans_3N  Glycosyl transferase family, helical bundle 


Domain annotation for each model (and alignments):
>> Glycos_transf_3  Glycosyl transferase family, a/b domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  262.1   1.1     6e-82   5.4e-78       3     252 ..      75     325 ..      73     326 .. 0.99

  Alignments for each domain:
  == domain 1  score: 262.1 bits;  conditional E-value: 6e-82
                      TBEEEEESS-SSSTHHHHHHHHHHHHHHTT-BEEEEE-STCTTCS-HHHHHCTST--ST--HHHHHHHHHHHSEEEEEHHSSSSHHHHHHHHHH CS
  Glycos_transf_3   3 dlvDivgTGGdgantfNiStaaaivvAaaGvkvakhgnrsvssksGsaDvLealgvnleltpeeveklleevgvgflfapeyhkamkhvapvrr 96 
                      +++D++gTGGd+ +tfNiStaa++vv aaG  vakhgnrs+s  sGsaDv e +g++l+ +p +++++le+ +++f+fa+++h+amk+v+++r+
       EPA05849.1  75 RVIDMCGTGGDNLQTFNISTAASFVVTAAGGIVAKHGNRSSSGVSGSADVFEYFGYDLNAEPTKIAQILEKHNICFMFAQKFHPAMKYVVNARK 168
                      799******************************************************************************************* PP

                      HHTT.-SSHHHCHHHHHT..SEEEEHHHHHHHHTCHSEEEEEEEESTTSSCCS.TSHHHHHHHHHHHHHHHHTTEEEEEEEEEGSSTSSSEEES CS
  Glycos_transf_3  97 elgirTvfnlLGPLinparvkkqllgvyskelaeklaevlkelgveralvvhg.dGldevsllakttvaelkdgeiteytlepedfglkraele 189
                      +l  r+ fnlLGPL npa+vk+q++gvys e++e l  +lk+ g e+ + v + dG+de+s+ ak+ v  l ++++ + +++pe +gl++++l+
       EPA05849.1 169 QLAKRSAFNLLGPLSNPANVKNQMIGVYSVEFLERLPLILKRNGAENIMTVRSdDGMDEFSTSAKNRVCILRNDKVLMNSIDPEVVGLHKSKLK 262
                      ********************************************************************************************** PP

                      HHHHSSHHHHHHHHTTHHTSCHHHHHHHHHHHHHHHHHHHTTSSSSHHHHHHHHHHHHHTSHH CS
  Glycos_transf_3 190 aleggepkenaeilkavlegkksaakrdlvllnagaalvlagkadslkegvakaeevidsGkA 252
                      +++ ++ +e+++   +vl+++ +++  ++++lna+  l++ag  ++ +egv+ a+++i++GkA
       EPA05849.1 263 DIQIKTKEEAIKSFVKVLNNTANQSMIETTALNAAGGLIVAGISNNFEEGVELALNTIKDGKA 325
                      **************************************************************9 PP

>> Glycos_trans_3N  Glycosyl transferase family, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.0   1.3e-12   1.2e-08       2      62 ..       4      64 ..       3      65 .. 0.96

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 1.3e-12
                     HHHHHHHTT.---HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHH---HHHHHHHHHHHHHH CS
  Glycos_trans_3N  2 diikklrdgeeLtaeeirfaihgilkgevtdaqiaAfLmAlrlkGetaeEiaalaeAmres 62
                     ++i kl ++ +Lt++++  ++++il+g+ +d +   fL++l  kGet +E+ ++ + mr++
       EPA05849.1  4 ELISKLEQKTDLTYDQMNLVMKEILSGKTNDKENFDFLSSLTEKGETDDELLGMLDKMRAF 64
                     6889999999*************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2562.06
//
Query:       EPA05850.1  [L=223]
Description: nitroreductase family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.7e-24   85.4   0.2    1.3e-12   48.1   0.0    2.2  2  Nitroreductase  Nitroreductase family
    3.4e-10   39.8   0.7      9e-05   22.1   0.0    3.1  3  TM1586_NiRdase  Putative TM nitroreductase
  ------ inclusion threshold ------
      0.065   12.0   0.0      0.099   11.4   0.0    1.2  1  DUF1157         Protein of unknown function (DUF1157)


Domain annotation for each model (and alignments):
>> Nitroreductase  Nitroreductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.1   0.0   2.3e-16   1.3e-12       2      61 ..      62     121 ..      61     126 .. 0.95
   2 !   36.2   0.0     1e-12     6e-09      89     170 .]     124     202 ..     118     202 .. 0.88

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 2.3e-16
                     HH--B---B-S----HHHHHHHHHHHHTS--GGG---EEEEEE.-CCCHHHHHHHHHHHH CS
  Nitroreductase   2 rkRrSiRkFddepvpkeelekileaarraPsagnlqpwrfvvvqdkelryklaeaalell 61 
                      kRrS+RkF+d+ v+  +++ki++aa +aP+agn q ++++ v++ e++++l ea++++ 
      EPA05850.1  62 SKRRSTRKFTDKIVETVKIDKIIAAADTAPTAGNFQGFEIFYVKSPEKKQQLIEACNNQP 121
                     79******************************************************9985 PP

  == domain 2  score: 36.2 bits;  conditional E-value: 1e-12
                     HSSEEEEE---TTS--.-HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGGGGHHHHHHHHT-S..SEEEEEEEEE- CS
  Nitroreductase  89 gapvlivivatldkse.rkaaerayryalldagaaaqnllLaAtalGlgscpiggfdeaaeevrkllglpdeeeivvliavGy 170
                     +ap+++v+ +++++ + + ++e    +a++da +aa   +LaA+alGl s++ig+fde++  v+k+++ +    +  +++vGy
      EPA05850.1 124 NAPLVLVFCKNPSRVKmNFPEEILKKFAIQDATLAAAYSQLAAQALGLSSIWIGMFDEQK--VMKVINTD--LIPSSILCVGY 202
                     7888888855555554256788999***********************************..********..99999999998 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.2   0.00036       2.2       2      27 ..      57      82 ..      56      83 .. 0.84
   2 !    8.5   0.0   0.00022       1.3     159     185 ..      79     105 ..      75     123 .. 0.85
   3 !   22.1   0.0   1.5e-08     9e-05      93     150 ..     164     220 ..     160     223 .] 0.92

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00036
                    HHHHHHH--B---B--S---HHHHHH CS
  TM1586_NiRdase  2 lyeaiekRhsvRkYkdealeeellee 27
                    l+  + kR+s Rk++d+ +e  ++++
      EPA05850.1 57 LFTVMSKRRSTRKFTDKIVETVKIDK 82
                    7889*************998877665 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00022
                     HHHHHHHHHHTS--GGG----EEE.E- CS
  TM1586_NiRdase 159 wfkeileaarlAPsAlNqqpwrfelkd 185
                     ++++i+ aa  AP+A N q +++ +++
      EPA05850.1  79 KIDKIIAAADTAPTAGNFQGFEIFYVK 105
                     6899*****************987665 PP

  == domain 3  score: 22.1 bits;  conditional E-value: 1.5e-08
                     HHHHHTT-EEEEES--SST...........T-S-EEEEE-BS----.-----HHHHBS CS
  TM1586_NiRdase  93 LkltalGlgtcWvggtykkkkakvelkkgeklvivIalGyaktklveakrkpleelce 150
                     L ++alGl++ W+g+ ++++k+   ++ +     ++ +Gy+k++++++ r++l+e+++
      EPA05850.1 164 LAAQALGLSSIWIGM-FDEQKVMKVINTDLIPSSILCVGYPKQNKFPKPRRNLKEIVH 220
                     89************7.8888998999999999***********************986 PP

>> DUF1157  Protein of unknown function (DUF1157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   1.7e-05     0.099     195     242 ..      39      86 ..      24      92 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.7e-05
     DUF1157 195 eilgkillyikknvikdkkfiisgetGlnskyiqlaietifldeviss 242
                 ++l +il    +++i+ ++f ++++     k+ + ++et+ +d++i++
  EPA05850.1  39 QLLNQILKSSPTEFINTDLFTVMSKRRSTRKFTDKIVETVKIDKIIAA 86 
                 6788999999***********************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1618.09
//
Query:       EPA05851.1  [L=76]
Description: hypothetical protein BG20_I0782 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.29s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 505.60
//
Query:       EPA05852.1  [L=331]
Description: oxidoreductase, aldo/keto reductase family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.9e-56  189.8   0.0    6.7e-56  189.6   0.0    1.0  1  Aldo_ket_red  Aldo/keto reductase family


Domain annotation for each model (and alignments):
>> Aldo_ket_red  Aldo/keto reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.6   0.0   3.7e-60   6.7e-56       2     291 ..      17     311 ..      16     314 .. 0.94

  Alignments for each domain:
  == domain 1  score: 189.6 bits;  conditional E-value: 3.7e-60
                   EEEE-SSS-ST..TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH.-TTTGGG-EEEEEE--SSSTTSSSS-HHHHHHHHHHHHHH CS
  Aldo_ket_red   2 lglGtwqlgsk.eeiskeealellrraleaGinffDtAevYgkgqseellGealkk.srkkreeviiatKvdlrdaeiksglskeniresleeslkr 96 
                   +  G+wq+++  ++i++e+a+  +  + +aG++++D+A++Y  g++e ++Ge+ k+ s k+ ++    tK      +++  ++k+ ++  +++slk+
    EPA05852.1  17 ILNGMWQVSGShGQINRESAISEMLEYHKAGFTTWDLADIY--GPAESFVGEFRKRlSTKELKNSQSLTKF----VPNPGPMTKSIVEYYVDQSLKK 107
                   778******99******************************..**************99************....89999999999999******** PP

                   HT-S-EEEEEE-S--TTS-.HHHHHHHHHHHHHTTSEEEEEEES--HHHHHHHHHTTT--EEEEE-B-BTT-HHHHTTHHHHHHHTT-EEEEBSTTG CS
  Aldo_ket_red  97 LgtdyvDllllHrpdpslpsieevldaleelvkeGkiraiGvSnfsveqlekakkkkkvkivavqveynllreleeegllelckkkgvpliaysplg 193
                   ++td +Dl+++H++d++  +++++l +l ++++eGki+++G++nf+ ++++ +  +k++k+v++q++y++l++++e+ ++++c+k+g+ l +y++l 
    EPA05852.1 108 MNTDSLDLIQFHWWDYNNLNYLDALNHLSKMHDEGKIKHLGLTNFDTQRIKIM-IDKGIKLVSNQIQYSILDQRAEKSMVPFCQKHGISLLTYGTLL 203
                   ***************************************************88.******************************************* PP

                   GGTTGTTTSS---SSSCCC-------............TS-HHHHHHHHHHHHHHHHTT--HHHHHHHHHTTSTT-SEEEE--SS..HHHHHHHHGG CS
  Aldo_ket_red 194 gGlltgkyqseedkedkeprkdlkrd............ertsknldaaeelselakehgvslaqlalryalsqpavgivipgasn..ieqlednlda 276
                   gG++++ky +++++ + +                      ++ ++++++ ls++ k+h+ s++ +a +++l +pav  +i+g++   +e+ ednl++
    EPA05852.1 204 GGFFSEKYLDSPEPRRSDLIT----AslqkyydminawGGWALFQELLSVLSKISKKHDSSISNVAAKFILDKPAVAGIIIGTRLgiSEHREDNLRV 296
                   *********999987443333....2466699***************************************************75449********* PP

                   GG----HHHHHHHHH CS
  Aldo_ket_red 277 lelklseeevaelde 291
                   + ++l++e++  +++
    EPA05852.1 297 FGVNLDSEDLILINS 311
                   ********9987776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 1943.30
//
Query:       EPA05853.1  [L=258]
Description: indole-3-glycerol phosphate synthase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-70  237.0   0.8    2.1e-70  236.8   0.8    1.0  1  IGPS          Indole-3-glycerol phosphate synthase
      5e-06   26.4   0.0    1.1e-05   25.3   0.0    1.5  1  QRPTase_C     Quinolinate phosphoribosyl transferase, C-termi
    0.00033   19.9   0.1    0.00084   18.6   0.1    1.8  1  NanE          Putative N-acetylmannosamine-6-phosphate epimer
    0.00069   18.7   0.0      0.012   14.6   0.0    2.0  2  FMN_dh        FMN-dependent dehydrogenase
     0.0048   16.1   0.4       0.17   11.0   0.0    2.3  3  DHO_dh        Dihydroorotate dehydrogenase
     0.0087   15.5   0.0      0.018   14.5   0.0    1.6  1  His_biosynth  Histidine biosynthesis protein
  ------ inclusion threshold ------
      0.016   14.7   0.0      0.023   14.1   0.0    1.3  1  Cellulase     Cellulase (glycosyl hydrolase family 5)
      0.063   12.6   0.0       0.15   11.3   0.0    1.6  1  ThiG          Thiazole biosynthesis protein ThiG
      0.078   12.4   0.0        0.2   11.1   0.0    1.6  1  AP_endonuc_2  Xylose isomerase-like TIM barrel


Domain annotation for each model (and alignments):
>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  236.8   0.8   1.1e-73   2.1e-70      26     254 .]      24     254 ..       4     254 .. 0.93

  Alignments for each domain:
  == domain 1  score: 236.8 bits;  conditional E-value: 1.1e-73
                 CG..-SS-SS-HHHHCHCHTTS-EEEEEE-SEETTTEESBSS--HHHHHHHHTTT.-SEEEEE--CCCC---CCHHHHHHHH-SS-EEEES---SHHHH CS
        IGPS  26 aavklakpkrsfaeaLresekklaliaEvKkaSPskgliredfdpaeiAkkyeeagAsaiSVLteekyFqGsledLrevrqavslpvlrKdFiideyqi 124
                  ++kl+k++++f + +++ +++++l++E+K  SPs g ir+ ++pa+iAk++ ++gA+a+S+Lt+++ F+Gs +++ +vrqav++p l+Kd +id+ qi
  EPA05853.1  24 LDIKLEKSNKDFLQIIKS-NNHATLLTEIKFSSPSLGKIRTLTNPASIAKQMIAGGAKALSILTQPHLFNGSPDYFIQVRQAVDVPLLMKDIMIDTIQI 121
                 45588999********99.9999**************************************************************************** PP

                 HHHHHCT-SEEEEECCCS-HHHHHHHHH...HHCCTT-EEEEEESSHHHHHHHHHTT-SEEEEESEETTTTEE-CHHHHHHCHCC-TTSEEEEESSS-S CS
        IGPS 125 eearalgadaiLLivkvledeeleelae...aakslglevLvEvhdeeeleralklgakiiGvNnRnLktlevdlntteeLaklvpkdvllvaeSGikt 220
                 ++a ++gad +L+i +++++e l+++ e   + ++ gl++L Evh+++e++ alk +a++iG+NnRnL tle+dl+tte++ + ++k + +++eSGi+t
  EPA05853.1 122 DAAEKIGADYMLVIQSLFDQEFLKDIDEfigYGHKKGLKILLEVHTKQEFQNALKTEADLIGINNRNLDTLEIDLKTTERVLEGYKKTRPIISESGIET 220
                 ********************997765443339******************************************************************* PP

                 HHHHHHHCCTT-SEEEESHHHHC-TTHHHHHHHH CS
        IGPS 221 redveklkeegvnafLvGeslmrqedvekairel 254
                 +ed++ lk+ g++afL+G+s+m++++ e+++r+l
  EPA05853.1 221 PEDIQYLKKCGADAFLIGSSIMKSDNIEENVRKL 254
                 *******************************987 PP

>> QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   5.4e-09   1.1e-05      78     161 ..     156     244 ..     133     249 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 5.4e-09
                 TTTSEEEEEESSHHHHHHHHHHT-SEEEEES--HHHHHHHHHHH.....HHHSTTSEEEEESS--TTTHHHHHCTT-SEEEECHHCHTB CS
   QRPTase_C  78 dkevkievevesleeleevleaeadiimLDnfsveelkkaveel.....keknkrvlievSGgvtlenveeyaksgvdvisvgalthsv 161
                 +k +ki +ev++++e++++l++ead+i + n + ++l+  ++++       k+ r +i+ SG  t e+++ ++k g d++ +g+ + ++
  EPA05853.1 156 KKGLKILLEVHTKQEFQNALKTEADLIGINNRNLDTLEIDLKTTervleGYKKTRPIISESGIETPEDIQYLKKCGADAFLIGSSIMKS 244
                 45566**********************99998665554333333100113344559**************************9987765 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.1   4.2e-07   0.00084      79     186 ..     145     251 ..      98     257 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 4.2e-07
                 --HHHHHHHHHHH--EEEEE-SSHHHHHHHHHTT-SEEE-TTTTSSTTS-.SS--HHHHHHHHHTT--EEEES---SHHHHHHHHTT--SEEEE-HHHH CS
        NanE  79 vtieelikkikekyqllmaDistleeglvakklGvdivGttlsGytkeeekaepDfalvkalseaglkviaeGrintPekakkaieiGvdavvvGsait 177
                  +i+e+i   ++k++ ++ ++ t +e  +a k  +d++G       + e + +   ++++ +++    +i e  i+tPe  +   ++G+da  +Gs+i 
  EPA05853.1 145 KDIDEFIGYGHKKGLKILLEVHTKQEFQNALKTEADLIGINNRNLDTLEIDLKTTERVLEGYKK-TRPIISESGIETPEDIQYLKKCGADAFLIGSSIM 242
                 78999999999999999999******************98766555555554444445555443.4469****************************** PP

                 -HHHHHHHH CS
        NanE 178 rleeiakkf 186
                 + ++i +  
  EPA05853.1 243 KSDNIEENV 251
                 *99998765 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.033        66     193     241 ..      80     132 ..      18     136 .. 0.70
   2 !   14.6   0.0   6.2e-06     0.012     223     304 ..     164     242 ..     144     257 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.033
                 HHCCCHB-TC-...-HHHHHHHHHHHSSEEEEEEE-.SHHHHHHHHHTTESEE CS
      FMN_dh 193 efvgkqldpsl...twddikwlreqtklplvvKGvl.taedakraveaGvdgi 241
                 + ++   +p+l   + d   ++r+++++pl++K ++ +   ++ a ++G+d  
  EPA05853.1  80 KALSILTQPHLfngSPDYFIQVRQAVDVPLLMKDIMiDTIQIDAAEKIGADYM 132
                 4444444555555577788899*************615556777777788765 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 6.2e-06
                 EE-SHHHHHHHHHTTESEEEE--GGGTSSTT---HHHCHHHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHH CS
      FMN_dh 223 GvltaedakraveaGvdgivvSNHGGRqldgapatidvLpeiveavggrievlvDgGirrGsDvlkAlalGAdavllGRpfl 304
                 +v t+++ ++a++  +d i + N   R+ld+    +++  ++ e  ++  +++  +Gi + +D+     +GAda l+G  ++
  EPA05853.1 164 EVHTKQEFQNALKTEADLIGINN---RNLDTLEIDLKTTERVLEGYKKTRPIISESGIETPEDIQYLKKCGADAFLIGSSIM 242
                 789999***************99...****************************************************8776 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1     0.027        55     103     178 ..      28     102 ..       2     144 .. 0.64
   2 ?   -0.1   0.0      0.21   4.3e+02     184     215 ..     174     204 ..     162     207 .. 0.65
   3 !   11.0   0.0   8.7e-05      0.17     233     280 ..     198     245 ..     191     256 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.027
                 E-TTSS.HHHHHHHHHHHHGGGESEEEEES-SCTCCTSCCCGCHHHHHHHHHHHHHHHH...SSEEEEEE-SSSSHHHH CS
      DHO_dh 103 kakktenavddyvevvrkigpfadilelNvSsPntpglrdlqekeelkaillkvvkevs...kvpvlvKlaPdltdeek 178
                      e+   d+ ++++  ++   ++e+  SsP     r+l +  ++++++++  +++    ++p l   +Pd++ ++ 
  EPA05853.1  28 L----EKSNKDFLQIIKSNNHATLLTEIKFSSPSLGKIRTLTNPASIAKQMIAGGAKALsilTQPHLFNGSPDYFIQVR 102
                 2....234578888888888888899********999999999999988877654444335544444445555554444 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.21
                 HHH.HHTECEEEE...BSEE--CTTCCGCCCCT CS
      DHO_dh 184 vll.elkldgiivtNttvqrlaidlkseknvka 215
                  l+ e  l gi+  N  +  l idlk+++ v +
  EPA05853.1 174 ALKtEADLIGIN--NRNLDTLEIDLKTTERVLE 204
                 233355555555..8889999999999998875 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 8.7e-05
                 HHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHG CS
      DHO_dh 233 virelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfeg 280
                 +  ++ +  kk+ piI+  Gie+ eD     ++GA +  +++ +++++
  EPA05853.1 198 TTERVLEGYKKTRPIISESGIETPEDIQYLKKCGADAFLIGSSIMKSD 245
                 4444445555555**************9999***********997765 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   9.2e-06     0.018     180     225 ..     196     243 ..     165     256 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 9.2e-06
                   HHHHHHHHHHH..SSEEEEESS--SHHHHHHHHHTTCSEEEESHHHHT CS
  His_biosynth 180 leltkelaeav..kipviasGGvgsledlkelksegvdavivgsalye 225
                   l+ t+++ e +  + p+i   G++++ed++ lk+ g+da+++gs + +
    EPA05853.1 196 LKTTERVLEGYkkTRPIISESGIETPEDIQYLKKCGADAFLIGSSIMK 243
                   444444444443234555556666666666666666666666655433 PP

>> Cellulase  Cellulase (glycosyl hydrolase family 5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.2e-05     0.023      53      86 ..     136     173 ..     103     214 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.2e-05
                 TTGCTHHHHHHHHHHHHHHHHTT-EEEEEEESS....T CS
   Cellulase  53 dykvdenslerveevvkyakenglyvildiHse....e 86 
                 + ++d++ l++++e++ y  ++gl+++l++H +    +
  EPA05853.1 136 QSLFDQEFLKDIDEFIGYGHKKGLKILLEVHTKqefqN 173
                 4489****************************844431 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   7.6e-05      0.15     176     213 ..     210     247 ..     196     255 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7.6e-05
                 S-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSH CS
        ThiG 176 vPvivDAGigspsdaaqamelGadavllntavaeakdp 213
                  P+i + Gi +p+d+    + Gada l+ +++ +++++
  EPA05853.1 210 RPIISESGIETPEDIQYLKKCGADAFLIGSSIMKSDNI 247
                 5*******************************999886 PP

>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   9.9e-05       0.2      76     141 ..     121     175 ..     119     191 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.9e-05
                   HHHHHHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTSSSTC CS
  AP_endonuc_2  76 ielaaaLGapllvlhpGtagagpkgseeeawerlaeslneladyaekegvklalEtlagsgvelgd 141
                   i++a+++Ga+++ +                 + + ++++e + y++k+g k++lE +++++ ++  
    EPA05853.1 121 IDAAEKIGADYMLVI-----------QSLFDQEFLKDIDEFIGYGHKKGLKILLEVHTKQEFQNAL 175
                   566666666665555...........223457899************************9987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       693  (0.0386525); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 1501.75
//
Query:       EPA05854.1  [L=64]
Description: hypothetical protein BG20_I0799 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.11   12.4   0.5       0.16   11.8   0.5    1.3  1  Rad50_zn_hook  Rad50 zinc hook motif


Domain annotation for each model (and alignments):
>> Rad50_zn_hook  Rad50 zinc hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.5   9.2e-06      0.16       6      30 ..      13      39 ..      11      43 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.2e-06
                   HHHHHHHHHHTT-SE..E-TTT--EE- CS
  Rad50_zn_hook  6 eelnkkieelkeakg..cCPlCgReld 30
                   +++ kki e+k++     C+ Cg+ + 
     EPA05854.1 13 DLYFKKIPEVKSSVSevECYICGKGIQ 39
                   6899******9998889******9775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 415.48
//
Query:       EPA05855.1  [L=214]
Description: kazal-type serine protease inhibitor domain protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-11   43.7   0.3    4.2e-11   42.7   0.3    1.5  1  Kazal_1   Kazal-type serine protease inhibitor domain
    3.6e-07   30.2   0.3    6.5e-07   29.4   0.3    1.4  1  Kazal_2   Kazal-type serine protease inhibitor domain


Domain annotation for each model (and alignments):
>> Kazal_1  Kazal-type serine protease inhibitor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.7   0.3   4.6e-15   4.2e-11       8      49 .]      38      73 ..      29      73 .. 0.87

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 4.6e-15
                S-TSSS--EEETTSEEESSHHHHHHHHHTTSSS--EEECS-- CS
     Kazal_1  8 aCpreyepvCGtDgkTYsneCllCaengkkgtklqlehdGeC 49
                aC++ey pvCG Dg+TY n+C+l        +k+ql+h GeC
  EPA05855.1 38 ACTMEYAPVCGVDGITYGNSCMLN------AAKVQLDHTGEC 73
                7**********************6......678999999999 PP

>> Kazal_2  Kazal-type serine protease inhibitor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.3   7.3e-11   6.5e-07       5      35 ..      38      67 ..      35      80 .. 0.86

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 7.3e-11
                GCCT-----EEETTTEEESSHHHHHHHCCCC CS
     Kazal_2  5 kCpeleydpVCGsDgktYtseCkLqaagCll 35
                +C+  ey+pVCG Dg+tY + C+L+aa+ +l
  EPA05855.1 38 ACT-MEYAPVCGVDGITYGNSCMLNAAKVQL 67
                688.8999**************999998754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1383.96
//
Query:       EPA05856.1  [L=53]
Description: hypothetical protein BG20_I2578, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0016   18.7   0.0     0.0016   18.7   0.0    1.1  1  HEAT_2    HEAT repeats
     0.0055   17.2   0.0     0.0069   16.9   0.0    1.2  1  HEAT_EZ   HEAT-like repeat
     0.0076   16.4   0.0      0.012   15.8   0.0    1.3  1  HEAT      HEAT repeat
  ------ inclusion threshold ------
      0.012   15.6   0.0      0.012   15.6   0.0    1.0  1  Cnd1      non-SMC mitotic condensation complex subunit 1


Domain annotation for each model (and alignments):
>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   3.7e-07    0.0016      24      59 ..       1      36 [.       1      51 [. 0.84

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 3.7e-07
      HEAT_2 24 LgrignpealpaLvellededpavRraaaeaLgaig 59
                Lg ig++ea + L ++l+d++p v + a+ aL+ i 
  EPA05856.1  1 LGVIGSKEAKAVLEKALNDPEPPVVESAVVALSNIE 36
                678999999999999999999999999999999875 PP

>> HEAT_EZ  HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.5e-06    0.0069      31      55 .]      11      35 ..       6      35 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.5e-06
     HEAT_EZ 31 paLlalLnddsdeVRaaAagaLgnl 55
                + L ++Lnd++++V + A+ aL+n+
  EPA05856.1 11 AVLEKALNDPEPPVVESAVVALSNI 35
                7899*******************98 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   2.7e-06     0.012       4      27 ..      12      35 ..      11      36 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.7e-06
                HHHHHHT-SSHHHHHHHHHHHHHH CS
        HEAT  4 lllkllsDpspeVReaAakaLgal 27
                +l k+l+Dp+p V e+A+ aL ++
  EPA05856.1 12 VLEKALNDPEPPVVESAVVALSNI 35
                5889*****************987 PP

>> Cnd1  non-SMC mitotic condensation complex subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.0   2.7e-06     0.012      59      89 ..       9      39 ..       2      51 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.7e-06
        Cnd1 59 flselaklleDenprVvanalaalteiseks 89
                  + l+k+l+D++p Vv++a+ al++i  ++
  EPA05856.1  9 AKAVLEKALNDPEPPVVESAVVALSNIEFME 39
                5567999*****************9998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 359.73
//
Query:       EPA05857.1  [L=286]
Description: CBS domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.6e-42  143.1   4.1    4.3e-11   43.1   0.0    4.2  4  CBS        CBS domain
  ------ inclusion threshold ------
        8.4    6.1   8.8        6.3    6.5   0.1    3.7  4  PduV-EutP  Ethanolamine utilisation - propanediol utilisation


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.0   9.3e-12   8.4e-08       9      51 ..      15      56 ..       8      61 .. 0.85
   2 !   41.2   0.2   1.9e-14   1.7e-10       7      55 ..      79     126 ..      71     128 .. 0.88
   3 !   25.1   0.0     2e-09   1.8e-05      15      54 ..     150     189 ..     136     192 .. 0.81
   4 !   43.1   0.0   4.8e-15   4.3e-11       1      56 [.     228     283 ..     228     284 .. 0.96

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 9.3e-12
                CEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHH CS
         CBS  9 vvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDl 51
                + t++ +++l+++l+++++++ sr++V+ e++k+vGivt++Dl
  EPA05857.1 15 PKTIKYESSLADILKKIIDEKKSRILVT-ENDKVVGIVTEKDL 56
                459*************8866658**888.8999*********8 PP

  == domain 2  score: 41.2 bits;  conditional E-value: 1.9e-14
                 SSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
         CBS   7 rdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                 ++++tv+++t+l+e++e+m +k +++l V  +++ +vGi+t++Dl+r+ 
  EPA05857.1  79 KKIITVDENTSLAECAEIMLRKSIGSLAV-KSNDDVVGIITKTDLVRYF 126
                 789************************66.56666***********985 PP

  == domain 3  score: 25.1 bits;  conditional E-value: 2e-09
                 TSBHHHHHHHHHHHTSSEEEEE.ETTTBEEEEEEHHHHHHH CS
         CBS  15 dttleealelmrekgvsrlPVV.dedgklvGivtlrDllra 54 
                 dt l +++++m+++++sr+ ++ d d+ +vGi+t rDl+++
  EPA05857.1 150 DTQLYQVVKKMIDEKISRI-ILrDHDETPVGIITFRDLFEL 189
                 56699**************.99888888**********986 PP

  == domain 4  score: 43.1 bits;  conditional E-value: 4.8e-15
                 HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
         CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                 ++dim++d+v+v+ d++l++a +l+ ek++++  V+ + g+++Gi++++D+++al+
  EPA05857.1 228 ASDIMSKDIVSVDYDEDLAKAGKLLLEKNINGAGVLSGHGNIIGIISKTDIVKALA 283
                 58**********************99*********999***************996 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1     0.027   2.4e+02      88     101 ..      43      56 ..       4      97 .. 0.73
   2 ?    6.5   0.1    0.0007       6.3      89     103 ..     110     124 ..      82     136 .. 0.83
   3 ?   -2.6   0.2      0.46   4.1e+03      27      42 ..     147     162 ..     144     164 .. 0.87
   4 ?    1.6   0.0     0.024   2.1e+02      91     103 ..     268     280 ..     254     285 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.027
   PduV-EutP  88 fnkeviGiitkidl 101
                  n +v+Gi+t  dl
  EPA05857.1  43 ENDKVVGIVTEKDL 56 
                 46689999999987 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0007
   PduV-EutP  89 nkeviGiitkidlae 103
                 n +v+Giitk+dl++
  EPA05857.1 110 NDDVVGIITKTDLVR 124
                 679*********985 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 0.46
   PduV-EutP  27 kYkktqaiefsdeviD 42 
                 +Y  tq  ++ +++iD
  EPA05857.1 147 QYLDTQLYQVVKKMID 162
                 6899999999999999 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.024
   PduV-EutP  91 eviGiitkidlae 103
                 ++iGii k+d+++
  EPA05857.1 268 NIIGIISKTDIVK 280
                 69********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 2287.60
//
Query:       EPA05858.1  [L=130]
Description: hypothetical protein BG20_I2254, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-15   56.4  10.9    3.9e-15   56.2  10.9    1.0  1  EamA      EamA-like transporter family
  ------ inclusion threshold ------
      0.013   15.7  10.9      0.022   14.9  10.7    1.5  1  DUF1097   Protein of unknown function (DUF1097)
      0.065   13.4   6.1       0.15   12.3   1.6    2.2  2  DMT_6     Putative member of DMT superfamily (DUF486)
      0.098   11.6   6.5       0.11   11.4   6.5    1.2  1  CRT-like  CRT-like, chloroquine-resistance transporter-like


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.2  10.9   8.7e-19   3.9e-15      21     136 ..       6     121 ..       4     122 .. 0.88

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 8.7e-19
        EamA  21 skillrkvspltltfvrfliagilllii.allkegklaklslkdwllllllgllgtvlafllffyalkktsasnaslitslePvftlilsvlllgeklt 118
                 s++l +k++   ++ + + i+g +ll+i +l+++  + +l  ++++ +l+lg +g+++  ++f+++lk+++  +   i+s++ vf l+ ++++lge+++
  EPA05858.1   6 SRYLAQKMDVANIVQIKSAIGGGVLLVIaLLIFRVDI-NLQAEHIIPILVLGSVGFAASLFFFLQGLKRIGTVRTITIFSMSAVFGLVAASVFLGEQIS 103
                 6778888888888888888776666555156666666.999999******************************************************* PP

        EamA 119 lkqllgivlillGvllil 136
                 ++q+ +++++++Gv+l++
  EPA05858.1 104 WTQITAAGIMIFGVYLVS 121
                 ****************97 PP

>> DUF1097  Protein of unknown function (DUF1097)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9  10.7   4.9e-06     0.022      20      93 ..      53     123 ..      24     129 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.9e-06
     DUF1097  20 elpvWagFigwasffaaGggkkgllkslltnllGvvwAllaillisllggnlgllalllvvgivaflmvllaki 93 
                  +++ +gF +   ff +G +  g+++++  + + +v++l+a+ ++    +++++++++ + gi++f + l+++ 
  EPA05858.1  53 LVLGSVGFAASLFFFLQGLKRIGTVRTITIFSMSAVFGLVAASVFLG--EQISWTQIT-AAGIMIFGVYLVSRR 123
                 5899*************************************999865..889*****9.999999999998875 PP

>> DMT_6  Putative member of DMT superfamily (DUF486)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.5     0.017        78      54      97 ..      11      55 ..       4      67 .. 0.71
   2 ?   12.3   1.6   3.3e-05      0.15      59     104 ..      68     120 ..      57     121 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.017
       DMT_6 54 eenlslaqlkiiqevitlvvfvlfsvlllk..eklklnhlvaflll 97
                ++ +++a++  i+ +i   v+ ++++l+++   +l+++h++ +l+l
  EPA05858.1 11 QK-MDVANIVQIKSAIGGGVLLVIALLIFRvdINLQAEHIIPILVL 55
                33.8888899999999999999999999984345566666665544 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 3.3e-05
       DMT_6  59 laqlkiiqevitlvvfvlfsv.......lllkeklklnhlvaflllvlavyfv 104
                 l  lk i  v t+++f + +v       ++l+e++++++++a+ +++ +vy+v
  EPA05858.1  68 LQGLKRIGTVRTITIFSMSAVfglvaasVFLGEQISWTQITAAGIMIFGVYLV 120
                 55678888888887776544311111126789*******************98 PP

>> CRT-like  CRT-like, chloroquine-resistance transporter-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   6.5   2.5e-05      0.11      72     143 ..      53     125 ..      12     129 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.5e-05
    CRT-like  72 aimgaLDavsgilvvigavstsGslqvl.lnqaiipitllasllllkerysliqylGAlviilgvvvvlipsl 143
                 +++g++   ++++ ++ + +  G++ ++ +  ++ ++ l+a++++l e+ s++q++ A ++i gv +v   ++
  EPA05858.1  53 LVLGSVGFAASLFFFLQGLKRIGTVRTItIFSMSAVFGLVAASVFLGEQISWTQITAAGIMIFGVYLVSRREI 125
                 688888888899999999999999987625678899*****************************98876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       915  (0.0510346); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 904.58
//
Query:       EPA05859.1  [L=51]
Description: hypothetical protein BG20_I2257 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       239  (0.0133304); expected 358.6 (0.02)
Passed bias filter:                      146  (0.00814323); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 368.25
//
Query:       EPA05860.1  [L=64]
Description: hypothetical protein BG20_I2255 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.075   13.1   0.1      0.075   13.1   0.1    1.0  1  PAPS_reduct  Phosphoadenosine phosphosulfate reductase family


Domain annotation for each model (and alignments):
>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   4.2e-06     0.075      28      71 ..      19      62 ..       5      64 .] 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.2e-06
                 EEEEE-STB-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHH CS
  PAPS_reduct 28 vvfvdtghefpetiefvdeleeryglrlkvyepeeevaekinae 71
                 ++ + + ++f+e +++v ++++++++ l +++ ++++ +k++++
   EPA05860.1 19 LILAIQNDKFDEAMDYVSKMTHQLKIVLTYVKMKKSIPKKVKKK 62
                 56677899*******************99999999988887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1307  (0.0728987); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.22s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 538.66
//
Query:       EPA05861.1  [L=188]
Description: hypothetical protein BG20_I2258 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00017   21.4   3.7    0.00053   19.8   3.7    1.8  1  HTH_AsnC-type  AsnC-type helix-turn-helix domain
    0.00035   20.1   3.1      0.059   12.9   0.6    2.4  2  HTH_24         Winged helix-turn-helix DNA-binding


Domain annotation for each model (and alignments):
>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   3.7   5.9e-08   0.00053       1      25 [.      15      39 ..      15      61 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 5.9e-08
  HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAe 25
                   LD+iDr+IL++L ++aR s + + +
     EPA05861.1 15 LDAIDRQILNLLIANARDSTRTIVK 39
                   8**************9999887744 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.6   6.6e-06     0.059       1      17 [.      15      31 ..      15      42 .. 0.83
   2 !    7.4   0.1   0.00035       3.2      35      47 ..      54      66 ..      45      67 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.6e-06
      HTH_24  1 ldetdrkILelLqknpr 17
                ld +dr+IL+lL +n+r
  EPA05861.1 15 LDAIDRQILNLLIANAR 31
                799*************9 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00035
      HTH_24 35 nrrlkrLeeeGlI 47
                 +r+ rLe++G+I
  EPA05861.1 54 GKRIARLEKMGVI 66
                58**********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1323.31
//
Query:       EPA05862.1  [L=177]
Description: hypothetical protein BG20_I1462 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1270.95
//
Query:       EPA05863.1  [L=131]
Description: hypothetical protein BG20_I1451, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.03   14.5   0.1       0.47   10.6   0.0    2.4  2  Ribosomal_L37e  Ribosomal protein L37e


Domain annotation for each model (and alignments):
>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   2.6e-05      0.47      32      45 ..      47      60 ..      43      65 .. 0.84
   2 ?    1.1   0.0     0.025   4.4e+02      14      45 ..      96     127 ..      90     130 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 2.6e-05
  Ribosomal_L37e 32 ktCascGypsaklr 45
                    k+C+scG+++++  
      EPA05863.1 47 KVCSSCGFKDERAL 60
                    89********9975 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.025
  Ribosomal_L37e  14 ktHilCrrCgkrsyhvqkktCascGypsaklr 45 
                        +lC  C++    v k+++ +   p++k r
      EPA05863.1  96 DLRVLCLNCNEIRQPVTKTEYKKPKNPNKKSR 127
                     56689****98777777766666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.34s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 788.95
//
Query:       EPA05864.1  [L=41]
Description: hypothetical protein BG20_I1466, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 264.75
//
Query:       EPA05865.1  [L=545]
Description: phenylalanyl-tRNA synthetase, beta subunit [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-39  134.4   0.0    1.3e-38  132.6   0.0    1.7  2  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
    3.1e-18   65.8   0.0    1.6e-11   44.3   0.0    3.3  3  B5               tRNA synthetase B5 domain
    2.7e-12   46.7   0.3    4.8e-12   45.9   0.3    1.3  1  B3_4             B3/4 domain
  ------ inclusion threshold ------
      0.079   12.8   0.0       0.26   11.2   0.0    1.8  1  DUF3215          Protein of unknown function (DUF3215)


Domain annotation for each model (and alignments):
>> tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.27   1.2e+03      14      35 ..     233     254 ..     223     273 .. 0.64
   2 !  132.6   0.0   2.8e-42   1.3e-38      14     214 .]     355     539 ..     345     539 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.27
  tRNA_synthFbeta  14 elnkeqklrrklrdllagaGln 35 
                      ++n+++++   ++++l+ aG++
       EPA05865.1 233 NKNDAEDMLSIVATILQTAGFS 254
                      4555555555555555555554 PP

  == domain 2  score: 132.6 bits;  conditional E-value: 2.8e-42
  tRNA_synthFbeta  14 elnkeqklrrklrdllagaGlnEvitysfvsekeldklleddderkavelanPlsedqsvlRtsLlpglLevlarNlargnedvrlFEigkvfl 107
                      + n+     + l+ +++g+G++Ev+++s++s+k+l ++  + +  +++ ++   s+++++lR s++p lLe+l+rN++ + +  ++FE+g+vf 
       EPA05865.1 355 QTNSISVKLKSLSLIMIGLGYTEVLNSSLTSKKVLYEM-TNREPVNMISVLDSKSQEHTILRDSIIPELLENLSRNIHASYP-QKIFETGSVFS 446
                      456666666778899***********************.6889***************************************.*********** PP

  tRNA_synthFbeta 108 kdseeelpeeerhlaivltgkreeeswsekaravdfydlkgivealles.lgiekvefepaehpalhpgrsAeikvdgkevGvlGelhpevlea 200
                           + ++e + +a++ ++++           ++f ++k i+++ l++ +++ ++e ++ +hp+++ gr+A+i+v+gk++Gv+Ge++ ++ e+
       EPA05865.1 447 RG---NPINEATSFAVISAHQD-----------ASFTEIKSILQSALKTgFNL-EIETKTFTHPTFEEGRTASISVNGKTIGVIGEINSKTIEN 525
                      *9...67999999999999999...........***********988742666.999999********************************** PP

  tRNA_synthFbeta 201 fdlkqrvyvfEldl 214
                      ++++ +v++fE++l
       EPA05865.1 526 YKIRVPVVGFEISL 539
                      ************87 PP

>> B5  tRNA synthetase B5 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   7.4e-07    0.0033       1      51 [.       4      53 ..       4      59 .. 0.94
   2 ?   -2.6   0.0       1.6   7.1e+03      21      36 ..     244     259 ..     229     269 .. 0.74
   3 !   44.3   0.0   3.5e-15   1.6e-11       7      66 ..     281     339 ..     275     340 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 7.4e-07
                EEEEHHHHHHHHTS---HHHHHHHHHHTT-E.EESSTTCEEEE--TT-TT- CS
                xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
          B5  1 vslrvekinkllGidlseeeiikiLkrlgceriekdkdlllVtvPswRsDl 51
                v+l++ +++kllG ++s+++i + L  lg++++++d+d+++++  + R+D 
  EPA05865.1  4 VELSYTRLQKLLG-KISKKQISDNLPFLGLDIESEDNDKVRIEYSPNRPDY 53
                689999*******.9*********************************996 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.6
                 HHHHHHHTT-E.EESS CS
                 xxxxxxxxxxxxxxxx RF
          B5  21 iikiLkrlgceriekd 36 
                 +++iL+  g+  i+++
  EPA05865.1 244 VATILQTAGFSLISTK 259
                 5689999999876655 PP

  == domain 3  score: 44.3 bits;  conditional E-value: 3.5e-15
                 HHHHHHTS---HHHHHHHHHHTT-E.EESSTTCEEEE--TT-TT--SHHHHHHHHHHHH- CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
          B5   7 kinkllGidlseeeiikiLkrlgceriekdkdlllVtvPswRsDlereeDliEEvaRlyG 66 
                  in++lG++l++++ii  Lk+  +++i+k+k+ + +t+P++R D+  + Dl+EEva  yG
  EPA05865.1 281 LINQMLGTNLTNSQIIASLKKSRLDAILKGKN-IICTIPPYRFDIFGPMDLVEEVALGYG 339
                 69***********************9777776.999***********************9 PP

>> B3_4  B3/4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.9   0.3   1.1e-15   4.8e-12      41     129 ..     120     234 ..      84     241 .. 0.88

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 1.1e-15
                 HHHHHHHHHT-.....-EEEEEGGGTBTEEEEEE--TTEEEEBTTS-EEEE-T.....................TSEEEETEEEEE.EETTTEEBTTTB CS
        B3_4  41 itNyvmlelgq.....PlhafDldkiqgdivvrlakegeklvtldgkerelde.....................edlviadsekpv.slagvmggeesk 112
                 +++ +++ +g+      ++++Dldki+ +++  +++++ k+++l  +++el+                      + +vi ds+k+  s +++++ + + 
  EPA05865.1 120 MQEDLHFGIGRkrkksSIGIHDLDKISFPLTYTTSNKDHKFIPLH-SDKELSIsqilettdigkeygsiiknstQVPVILDSKKQTvSFPPIINAAITT 217
                 56666777777777889***************************8.5566644469****************************999************ PP

                 --TT--EEEEEEEE--H CS
        B3_4 113 vsedTknvfleaaafdp 129
                 v+ +T+n f+e++++++
  EPA05865.1 218 VTTKTRNLFVEVTGINK 234
                 *************9876 PP

>> DUF3215  Protein of unknown function (DUF3215)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   5.8e-05      0.26       5      51 ..     211     257 ..     209     261 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.8e-05
                 HHH-SEEEEEETTS-EEEEEEGGGCTHHHHHHHCCHH-STCCEEEEE CS
     DUF3215   5 lpkaiGtltfDennnlvdasGiGkerieDilelsqveldkeGyavle 51 
                 ++ ai t+t  ++n  v+ +Gi k+  eD l +    l   G+++++
  EPA05865.1 211 INAAITTVTTKTRNLFVEVTGINKNDAEDMLSIVATILQTAGFSLIS 257
                 677888999999999****************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (545 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.21s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 4280.67
//
Query:       EPA05866.1  [L=93]
Description: hypothetical protein BG20_I1452 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       778  (0.0433934); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 686.26
//
Query:       EPA05867.1  [L=139]
Description: hypothetical protein BG20_I1456 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-40  137.2   0.4    4.3e-40  137.1   0.4    1.0  1  EVE       EVE domain


Domain annotation for each model (and alignments):
>> EVE  EVE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.1   0.4   2.4e-44   4.3e-40       1     144 [.       3     135 ..       3     136 .. 0.96

  Alignments for each domain:
  == domain 1  score: 137.1 bits;  conditional E-value: 2.4e-44
                 -EEEEEEBHHT...SHHHHHCHHHCEEE-EE-GHHHHHHHCC--TT-EEEEEETSSSS-EEEEEEEEECEEEE-GGGG-TTSTT--TTTBTTS--EEEE CS
         EVE   1 ayWllksepde...fsiddlkrkkeegWdgvrnyqarnllramkkGDlvlfYhsgeklqaivgiaeVvseaypdetqfdpkskyydpkskkekpwlrvd 96 
                 +yWl+k ep+    ++++ lk++k+++Wdgv+n+ a +++r+mkkGDlvlfYh+g++ ++ vgi+eVvse+yp++++ +++             + ++d
  EPA05867.1   3 NYWLAKQEPSGprgYNFETLKKDKKTVWDGVHNNLALKHMREMKKGDLVLFYHTGDE-RQAVGIMEVVSEPYPNPKEDNKR-------------FIVFD 87 
                 7*********7777*******************************************.***************99777555.............99*** PP

                 EEEEEEEEEEEEHHHHTTHGTCTTSHHHHCCT-SEEEE-HHHHHHHHH CS
         EVE  97 vkpvkklkrplslkelkaepelegmkllrkgrlsvrpvteedwelile 144
                  k+ k lkrp++l+e+k+++++++++llr +rlsv+pv+++ w++il+
  EPA05867.1  88 GKYKKSLKRPVTLDEMKKQKKFQNWELLRISRLSVMPVPKDIWNTILD 135
                 **********************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1042.84
//
Query:       EPA05868.1  [L=322]
Description: putative pyridoxal 5'-phosphate synthase, synthase subunit Pdx1 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-98  328.6   3.2    2.1e-98  328.2   3.2    1.2  1  SOR_SNZ       SOR/SNZ family
    3.3e-07   29.9   1.4    1.3e-05   24.6   0.1    2.3  2  ThiG          Thiazole biosynthesis protein ThiG
    5.6e-05   22.7   0.4      0.013   15.0   0.0    3.1  2  His_biosynth  Histidine biosynthesis protein
     0.0012   18.0   0.3        1.2    8.1   0.0    2.2  2  Dus           Dihydrouridine synthase (Dus)
     0.0024   17.1   0.0       0.05   12.8   0.0    2.3  2  IGPS          Indole-3-glycerol phosphate synthase
     0.0024   17.3   5.3       0.15   11.4   0.1    2.3  2  NMO           Nitronate monooxygenase
     0.0086   15.7   0.4        1.1    8.9   0.1    2.5  2  OMPdecase     Orotidine 5'-phosphate decarboxylase / HUMPS fa
  ------ inclusion threshold ------
      0.018   14.2   3.0        0.7    9.0   0.0    3.3  3  NanE          Putative N-acetylmannosamine-6-phosphate epimer


Domain annotation for each model (and alignments):
>> SOR_SNZ  SOR/SNZ family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  328.2   3.2  9.3e-102   2.1e-98       2     207 .]      29     238 ..      28     238 .. 0.99

  Alignments for each domain:
  == domain 1  score: 328.2 bits;  conditional E-value: 9.3e-102
                 THHHHHHHHTTTSSEEEEESSHHHHHHHHHHT-SEEEE-SS-HHHHHHH-S------HHHHHHHHHH-SS-EEEEEETT-HHHHHHHHHTT-SEEEEET CS
     SOR_SNZ   2 lkvkaglaemlkgGvimdvvnaeqakiaeeaGavavmalervpadirkeggvarmsdpklikeikeavsipvmakvriGhfveaqilealgvdyiDese 100
                  ++k+g+a+mlk+Gv+mdv+++eqa+iaeeaGav+vm+l+++p+d+rk+ggvar++++++i++i+++v+ipvmak+riGh+ ea++le+ +vd+iDese
  EPA05868.1  29 STLKRGFAHMLKNGVVMDVTTVEQAQIAEEAGAVSVMVLDKLPSDVRKAGGVARTASIRIIEDIMDSVTIPVMAKCRIGHVYEAKVLEETDVDMIDESE 127
                 578************************************************************************************************ PP

                 TS--S-SS----GGG-SS-EEEEESSHHHHHHHHHHT-SEEEEES-TTS--THHHHHHHHHHHHHHHHHTTS....-HHHHHHHHHHHHGGGHHHHHHH CS
     SOR_SNZ 101 vltpadeeahidkkkfkvpfvcGarnlgealrriaeGaamirtkGeagtGdvveavrhvrkikeeirklksl....seeelvalakelkaplelvkeva 195
                 vltpade++hi k++f++pfv+Gar+l+ealrri+eGaamirtkGe+gtG+v+eav+h++k+++e+r++ks+    ++++lv++a+e+k+++++v+e+a
  EPA05868.1 128 VLTPADEHHHIWKWDFTTPFVNGARSLSEALRRIEEGAAMIRTKGEPGTGNVAEAVTHIKKVNDELRTIKSIydsgDNQDLVRIAREFKVSYDIVEETA 226
                 **********************************************************************998888999******************** PP

                 HHTTS-S---T. CS
     SOR_SNZ 196 elgrlpvvnfaa 207
                 +lgrlpvvnfaa
  EPA05868.1 227 KLGRLPVVNFAA 238
                 **********98 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.3   0.2    0.0098        22     137     194 ..      53     116 ..      20     134 .. 0.75
   2 !   24.6   0.1     6e-09   1.3e-05     175     224 ..     230     281 ..     215     296 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0098
                 HHHHHHTT-SEBEEB...SSSTTS----S-HHHHHHH...HHH-SS-BEEES---SHHHHHHHH CS
        ThiG 137 arrleevGcaavmPl...aapiGsglGllnkealkii...ieeakvPvivDAGigspsdaaqam 194
                 a+  ee+G+ +vm l    + +  + G++ ++ ++ii   ++++++Pv+    ig+  +a    
  EPA05868.1  53 AQIAEEAGAVSVMVLdklPSDVRKAGGVARTASIRIIediMDSVTIPVMAKCRIGHVYEAKVLE 116
                 5556899999999652227899999999999988886222667799**9999999988876555 PP

  == domain 2  score: 24.6 bits;  conditional E-value: 6e-09
                 SS-BEEES..---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHHHHHHHHHH CS
        ThiG 175 kvPvivDA..GigspsdaaqamelGadavllntavaeakdpvamArafklav 224
                 ++Pv+  A  Gi +p daa  m lG+d++++ + + +a+d  + Ara+ la+
  EPA05868.1 230 RLPVVNFAagGIATPADAAYLMSLGCDGIFVGSGIFNADDAQERARAIVLAT 281
                 56777543349*************************************9997 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1     0.087   1.9e+02      32      78 ..      50     102 ..      31     127 .. 0.59
   2 !   15.0   0.0   5.7e-06     0.013      59     132 ..     216     310 ..     206     321 .. 0.65

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.087
                   HHHHHHHHHHT-SEEEEEEHHHHC......TTHHHHHHHHHHHHHH-SSEEEE CS
  His_biosynth  32 velakryeeegadelhvvDldaak......egreanldlveeiaeevfipvqv 78 
                   ve+a+  ee+ga  ++v+D   +         r+a + ++e i+++v+ipv+ 
    EPA05868.1  50 VEQAQIAEEAGAVSVMVLDKLPSDvrkaggVARTASIRIIEDIMDSVTIPVMA 102
                   55555556666666666552222222222245566666777777777777655 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 5.7e-06
                   HHHHHHHHHHHHH-SSEE..EEESSSSSHHHHHHHHHCT-S...................EEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEE CS
  His_biosynth  59 eanldlveeiaeevfipv..qvGGGIrsledveelleagad...................kviigtaavknpelikelaekfgsqkivvaiDarr 132
                   ++ +d+vee+a+  ++pv     GGI +  d++ l+++g+d                    ++++t   ++pe +k++ + + + + ++++D++ 
    EPA05868.1 216 KVSYDIVEETAKLGRLPVvnFAAGGIATPADAAYLMSLGCDgifvgsgifnaddaqerarAIVLATTFWNEPEKVKDAQKMIDERQSMLGLDVKT 310
                   56677888888887777733478888888888888888866333333333333333433367777777777777777777777777777777765 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.1   0.00055       1.2     139     202 ..      48     115 ..      41     197 .. 0.83
   2 !    8.1   0.0   0.00054       1.2     181     224 ..     230     272 ..     211     318 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00055
                 .HHHHHHHHHHCT-SEEEEESS....ECCCTT-C.G--CHHHHHHHHH-SS-EEEESS--SHHHHHHHH CS
         Dus 139 nalelakiveaaGaqaltvHgR....traqnyeg.tadweaIkevkqavsipviaNGdIkdaedaqail 202
                 +++e a+i+e+aGa  ++v       +r+ +  + ta ++ I+++ ++v+ipv+a   I ++ +a+ +l
  EPA05868.1  48 TTVEQAQIAEEAGAVSVMVLDKlpsdVRKAGGVArTASIRIIEDIMDSVTIPVMAKCRIGHVYEAK-VL 115
                 578999999999999999999888776666666679999999999999999999988888877765.34 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00054
                 H-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTHHH CS
         Dus 181 avsipviaNGdIkdaedaqaileetGadgvmigrgalgnPwlfa 224
                 +++++ +a G+I ++ da   ++  G+dg+ +g g  +     +
  EPA05868.1 230 RLPVVNFAAGGIATPADAAYLMSL-GCDGIFVGSGIFNADDAQE 272
                 355666899*********999998.********99877655555 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.047     1e+02      63      88 ..      42      67 ..      39     104 .. 0.89
   2 !   12.8   0.0   2.2e-05      0.05     190     252 ..     213     275 ..     205     277 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.047
                ESBSS--HHHHHHHHTTT.-SEEEEE CS
        IGPS 63 liredfdpaeiAkkyeeagAsaiSVL 88
                 + +d+  +e+A+  eeagA  + VL
  EPA05868.1 42 GVVMDVTTVEQAQIAEEAGAVSVMVL 67
                5778999*************999988 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 2.2e-05
                 TTTEE-CHHHHHHCHCC-TTSEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC-TTHHHHHH CS
        IGPS 190 ktlevdlntteeLaklvpkdvllvaeSGiktredveklkeegvnafLvGeslmrqedvekair 252
                 ++++v+ + +ee akl +  v+  a  Gi+t++d+  l + g +++ vG+ + +++d+++  r
  EPA05868.1 213 REFKVSYDIVEETAKLGRLPVVNFAAGGIATPADAAYLMSLGCDGIFVGSGIFNADDAQERAR 275
                 57899999999999988888999*********************************9998776 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   1.3     0.001       2.3     140     198 ..      44     102 ..      36     109 .. 0.74
   2 !   11.4   0.1   6.9e-05      0.15     183     232 ..     220     271 ..     172     282 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.001
         NMO 140 iptissvkearkvearGaDalivqGpeaGGhqGtpevgdkglfaLvpqvldavdiPviA 198
                 ++ +++v++a+++e++Ga ++ v  +     +    v+ +  +++++ ++d v iPv+A
  EPA05868.1  44 VMDVTTVEQAQIAEEAGAVSVMVLDKLPSDVRKAGGVARTASIRIIEDIMDSVTIPVMA 102
                 56799************76555544443333332344446689***************9 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 6.9e-05
         NMO 183 aLvpqvldavdiPvi..AaGGiidrrgvaaaLalGAsgvqigtrfLltkesd 232
                  +v++ ++   +Pv+  AaGGi +  + a  ++lG  g+ +g+    +++++
  EPA05868.1 220 DIVEETAKLGRLPVVnfAAGGIATPADAAYLMSLGCDGIFVGSGIFNADDAQ 271
                 44555555555999777**************************999998876 PP

>> OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       2.3   5.1e+03       8      28 ..      46      66 ..      36      78 .. 0.61
   2 !    8.9   0.1   0.00047       1.1      81     159 ..     159     240 ..     151     277 .. 0.57

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.3
                -SSSHHHHHHHHHHHGG.GSSE CS
   OMPdecase  8 Dvatarelleladkvgp.sivv 28
                Dv+t  e  ++a+++g+ s++v
  EPA05868.1 46 DVTTV-EQAQIAEEAGAvSVMV 66
                44444.2334555555544443 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00047
                 HHHHTTESEEEEEGTGHHHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHH..H..SHHHHHHHHHHHHHHHTTESEEECCC CS
   OMPdecase  81 arikewadivtvhavaGkasvkalaeaaekwgnrgllilaqmsskgnlmlqe..k..gytqacveaarehkaedfvmGfvaqe 159
                  ri+e+a ++   + +G++ v+++++ ++k ++    i   + s +n++l +  +  ++ +++ve+ ++  +   v+ f a+ 
  EPA05868.1 159 RRIEEGAAMIRTKGEPGTGNVAEAVTHIKKVNDELRTIKSIYDSGDNQDLVRiaRefKVSYDIVEETAKLGRL-PVVNFAAGG 240
                 5777777777777777777777777777777644444444555555666655642567777777777776643.333333332 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.5      0.03        66      97     170 ..      45     123 ..      29     141 .. 0.65
   2 ?    9.0   0.0   0.00031       0.7     147     177 ..     235     265 ..     212     275 .. 0.82
   3 ?    1.1   0.0     0.087     2e+02      61     103 ..     270     312 ..     266     319 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.03
                 EE-SSHHHHHHHHHTT-S..EEE-TTTTSSTTS-...SS--HHHHHHHHHT.T--EEEES---SHHHHHHHHTT--SEE CS
        NanE  97 aDistleeglvakklGvd..ivGttlsGytkeeek..aepDfalvkalsea.glkviaeGrintPekakkaieiGvdav 170
                  D+ t+e++ +a+++G+   +v   l   + ++        ++++++++++  + v+a  ri    +ak   e+ vd++
  EPA05868.1  45 MDVTTVEQAQIAEEAGAVsvMVLDKLPSDVRKAGGvaRTASIRIIEDIMDSvTIPVMAKCRIGHVYEAKVLEETDVDMI 123
                 4777777777777777531133344544444444444566677777777652456888888887777777777777665 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00031
                 EEEES---SHHHHHHHHTT--SEEEE-HHHH CS
        NanE 147 viaeGrintPekakkaieiGvdavvvGsait 177
                   a G i tP+ a+  + +G d + vGs i 
  EPA05868.1 235 NFAAGGIATPADAAYLMSLGCDGIFVGSGIF 265
                 46899***********************986 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.087
                 HTTT-SEEEEE--SS--T--HHHHHHHHHHH--EEEEE-SSHH CS
        NanE  61 aaagadiialDatdrerpvtieelikkikekyqllmaDistle 103
                 a++ a  i l +t+ + p+++++  k i e+  +l  D+ tle
  EPA05868.1 270 AQERARAIVLATTFWNEPEKVKDAQKMIDERQSMLGLDVKTLE 312
                 667788899999*******************999999999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2008.22
//
Query:       EPA05869.1  [L=210]
Description: hypothetical protein BG20_I1460 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.039   13.9   0.1       0.48   10.4   0.1    2.1  1  F-box-like_2  F-box-like domain


Domain annotation for each model (and alignments):
>> F-box-like_2  F-box-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   2.7e-05      0.48      23      60 ..      24      98 ..      17     109 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 2.7e-05
  F-box-like_2 23 lDlPdellelifkgCk.....................................dpayeplspslakayrrkrkhi 60
                    lPd +l li k+Ck                                     + a + +  ++   y ++   +
    EPA05869.1 24 YNLPDFILVLIAKECKsellergriddrlqsmndealellhkvfvgceedgagKYAQYRFYAYVSSMYHKCEVLV 98
                  579*************88888888888888888777777777777777776655555557777777777776555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1375.52
//
Query:       EPA05870.1  [L=463]
Description: phenylalanyl-tRNA synthetase, alpha subunit [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-82  277.1   0.0      2e-82  276.4   0.0    1.3  1  tRNA-synt_2d     tRNA synthetases class II core domain (F)
    3.6e-06   26.6   0.0    0.00049   19.6   0.0    2.3  2  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
     0.0067   16.7   0.0       0.02   15.2   0.0    1.8  1  PheRS_DBD3       PheRS DNA binding domain 3
     0.0082   15.3   0.1      0.029   13.5   0.0    1.9  2  tRNA-synt_2      tRNA synthetases class II (D, K and N)
  ------ inclusion threshold ------
      0.013   15.4   0.0      0.039   13.9   0.0    1.8  2  tRNA-synt_2b     tRNA synthetase class II core domain (G, H, 
       0.18   11.9   0.0       0.48   10.6   0.0    1.8  1  HTH_9            RNA polymerase III subunit RPC82 helix-turn-


Domain annotation for each model (and alignments):
>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  276.4   0.0   6.7e-86     2e-82       2     244 ..     194     458 ..     193     459 .. 0.96

  Alignments for each domain:
  == domain 1  score: 276.4 bits;  conditional E-value: 6.7e-86
                   .-TSSCTSCTSHSB-SHHHHHHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-...................... CS
  tRNA-synt_2d   2 idvtlpgkrieagklhpltkvleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpeka...................... 76 
                   idv+ + + +  +++hpl+++++ei+eif+ lgf+ev g+  + +f+nfdaL++pqdhpaR++qdtFyl+  + +                      
    EPA05870.1 194 IDVESKVPGVFVARTHPLKDTIDEIREIFVTLGFTEVIGEFTQPSFWNFDALFTPQDHPARELQDTFYLDGISAKkigtveqirkiseshkknwryy 290
                   799999999999*********************************************************66555589******************** PP

                   ....ECESEEE-SSTHHHHHHHH.TTS-SSEEEEEEEEEEBSST-SSSB-SEEEEEEEEEEETT--HHHHHHHHHHHHHHHCTSTEEEEEEECEETT CS
  tRNA-synt_2d  77 ....veekllLRthttavqirtl.ekkkppikiisigrvfRrdavDathlaeFhqveglvvdenvsladlkgvleellkklfgaevkvrfrpsyfpf 168
                       +++k++LRthtt+v+i++l e+k    +i+s+grvfR+++v ++hl+eF+q+eg+vv++n +l+dl+g+ +e+++++ g + k++f p++fp+
    EPA05870.1 291 wdinEARKMVLRTHTTCVTIKHLaETKPDESRIFSLGRVFRNEKVSYKHLVEFNQIEGVVVGKNATLRDLMGIQREFYRRI-GIT-KIKFWPTFFPY 385
                   ****999****************55566789**************************************************.**9.*********** PP

                   EEEEEEEEEEECCSSSSEEEEEEEEEE-HHHHHHTT-.TTSEEEEEEEEHHHHHHHHHT-SSGHHHHTT.HHHHGG CS
  tRNA-synt_2d 169 tePsaevdvylvekkkkwlEllgaGmvrpevleavgideevsgfafGlGveRlamlkygieDiRelvendlrflrq 244
                   tePs+++ vy  ++ +kw+El+g+G++rpev++++gi   ++++a+G G+eR+amlkyg++D+Re+++n+l +lr+
    EPA05870.1 386 TEPSLQTMVYN-DRLGKWVELFGMGIFRPEVTKPLGI--TKPVLAWGGGIERIAMLKYGLDDVREFYNNNLSWLRS 458
                   ***********.9************************..**********************************986 PP

>> tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.5   0.0     0.007        21      15      38 ..     208     231 ..     197     242 .. 0.85
   2 !   19.6   0.0   1.6e-07   0.00049      94     209 ..     318     427 ..     297     428 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.007
  tRNA_synthFbeta  15 lnkeqklrrklrdllagaGlnEvi 38 
                       ++ +++ +++r++ + +G++Evi
       EPA05870.1 208 THPLKDTIDEIREIFVTLGFTEVI 231
                      57889999***************8 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 1.6e-07
  tRNA_synthFbeta  94 nedvrlFEigkvflkd.seeelpeeerhlaivltgkreeeswsekaravdfydlkgivealleslgiekvefepaehpalhpgrsAeikvdgk. 185
                       ++ r+F +g+vf+++  + +   e +++ +v++gk+           +   dl gi +++ +++gi+k++f p+  p+ +p  +  ++ d+  
       EPA05870.1 318 PDESRIFSLGRVFRNEkVSYKHLVEFNQIEGVVVGKN-----------ATLRDLMGIQREFYRRIGITKIKFWPTFFPYTEPSLQTMVYNDRLg 400
                      45689***********888899***************...........**********************************999988876646 PP

  tRNA_synthFbeta 186 ...evGvlGelhpevleafdlkqrvyv 209
                         e+  +G + pev + +++ ++v +
       EPA05870.1 401 kwvELFGMGIFRPEVTKPLGITKPVLA 427
                      66788889*************999875 PP

>> PheRS_DBD3  PheRS DNA binding domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   6.8e-06      0.02       2      52 ..      76     123 ..      76     128 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 6.8e-06
  PheRS_DBD3   2 hEarvfaavppeggisqkelkklggdpvakiGfskAmknkWikkdkgdgkv 52 
                 +E r+ + ++  ++ +++el+k +g +v+  +++ A kn+W+  d+++  +
  EPA05870.1  76 PERRLLELLKN-ESKNLQELQKELG-SVFGPAMGLARKNNWVDTDDDKV-I 123
                 78899999955.669*****99889.68****************76542.3 PP

>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   9.6e-06     0.029      92     119 ..     321     347 ..     317     369 .. 0.88
   2 ?   -2.5   0.0       0.7   2.1e+03     287     306 ..     428     447 ..     426     449 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.6e-06
                  SEEEEEEEEE--S--BTTB-S-CEEEEE CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  tRNA-synt_2  92 drvfqiaraFRaEdsrtdrhlaEFtqie 119
                  +r+f+++r+FR+E+++ + hl EF qie
   EPA05870.1 321 SRIFSLGRVFRNEKVSYK-HLVEFNQIE 347
                  699************965.555*****9 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.7
                  EEEEHHHHHHHHCT-SSGGG CS
                  xxxxxxxxxxxxxxxxxxxx RF
  tRNA-synt_2 287 lglGldRlvmlllgsesIrd 306
                  +g G++R+ ml  g++++r+
   EPA05870.1 428 WGGGIERIAMLKYGLDDVRE 447
                  5789************9997 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.7   5.1e+03      80     100 ..     211     230 ..     208     251 .. 0.79
   2 ?   13.9   0.0   1.3e-05     0.039      25     130 ..     312     404 ..     289     442 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.7
                   HHHHHHHHHHHHHHTT.SCEE CS
                   xxxxxxxxxxxxxxxxxxxxx RF
  tRNA-synt_2b  80 lrdlikaisriferlglefra 100
                   l+d i +i +if +lg+ + +
    EPA05870.1 211 LKDTIDEIREIFVTLGFTE-V 230
                   5789999999**9999752.3 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 1.3e-05
                   HHHHEEEB.GGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGGHHHHHHHHHHHHHHHHHHTT.SCEEEEEEGTTSCBTTSEEEEEEE CS
                   xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  tRNA-synt_2b  25 irdevlrs.krLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfhaeaslddslrdlikaisriferlglefraiielmsaksadykdkkefea 120
                   +  e  ++ +    +++ +++++R+Ek + +    + eF+q +g+v++++a     lrdl+    ++++r+g+ + +       + +  +++++ ++
    EPA05870.1 312 HLAE-TKPdE---SRIFSLGRVFRNEKVSYKH---LVEFNQIEGVVVGKNA----TLRDLMGIQREFYRRIGITKIKFWPT---FFPYTEPSLQTMV 394
                   3333.34434...699***********95667...66************99....8999*************986543333...2345667777777 PP

                   EETTTSEEEE CS
                   xxxxxxxxxx RF
  tRNA-synt_2b 121 vsesltkgie 130
                   +   l+k +e
    EPA05870.1 395 YNDRLGKWVE 404
                   7776666665 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00016      0.48       9      47 ..       3      41 ..       1      45 [. 0.93

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00016
                HCSTTHHHHHHHHHHHHSSBEHHHHHHHHSSTHHHHHHH CS
       HTH_9  9 ehFGevvakVvetLlrkgrltlrelvkktkLsldqVkks 47
                ++F e+ +k+++ L ++  +t  +l k+t+Ls+dq++++
  EPA05870.1  3 QIFHEIEKKIITSLQNNPIQTPEKLEKSTNLSPDQIRRG 41
                7899999*****************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.70u 0.35s 00:00:01.04 Elapsed: 00:00:00.55
# Mc/sec: 2528.96
//
Query:       EPA05871.1  [L=79]
Description: transcriptional regulator, AsnC family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.3e-11   42.3   0.0    6.1e-11   42.1   0.0    1.0  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
     0.0019   18.2   0.0     0.0022   18.0   0.0    1.1  1  NapD            NapD protein


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   0.0   6.8e-15   6.1e-11       1      71 [.       6      73 ..       6      76 .. 0.95

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 6.8e-15
                    EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEE CS
  AsnC_trans_reg  1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsi 71
                    vl+++e g+    e+++++l+ l+ V+e++ + G yd+l+k+ +  +e l++ +  k+++++ +++t t++
      EPA05871.1  6 VLINCELGS---EESIIQQLKGLDGVKEVHGTFGAYDILAKIESDTVEKLRETITWKIRKIEKIRSTLTLM 73
                    789999999...9******************************************************9987 PP

>> NapD  NapD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.5e-07    0.0022       6      67 ..       6      69 ..       4      73 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.5e-07
        NapD  6 lvVqarperlaavkaalaalpgv.EvhasdeegklVvviEaesedeladtiea.iealpgVlsa 67
                +++++  ++ +++ ++l+ l+gv Evh++ ++  +   iE++++++l +ti+  i++++++ s+
  EPA05871.1  6 VLINCELGSEESIIQQLKGLDGVkEVHGTFGAYDILAKIESDTVEKLRETITWkIRKIEKIRST 69
                6899******************99***************************9779999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.33s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 481.89
//
Query:       EPA05872.1  [L=753]
Description: aconitate hydratase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   2.9e-146  488.1   0.0   5.5e-146  487.2   0.0    1.4  2  Aconitase    Aconitase family (aconitate hydratase)
    4.3e-35  120.9   0.1    1.6e-34  119.1   0.0    2.0  2  Aconitase_C  Aconitase C-terminal domain
  ------ inclusion threshold ------
      0.032   13.0   0.0      0.052   12.2   0.0    1.3  1  DUF521       Protein of unknown function (DUF521)


Domain annotation for each model (and alignments):
>> Aconitase  Aconitase family (aconitate hydratase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  487.2   0.0  9.2e-150  5.5e-146       2     461 .]      37     477 ..      36     477 .. 0.91
   2 ?   -3.6   0.0      0.71   4.2e+03      48      87 ..     703     738 ..     696     745 .. 0.68

  Alignments for each domain:
  == domain 1  score: 487.2 bits;  conditional E-value: 9.2e-150
   Aconitase   2 kiwdahlv...ee...egiayv...pdrvllqdvtgvqalvdlaaareavrrlggtlatidhlvpvdlvidhsvgaeealeknledefernkeryefLk 91 
                 ki++ h +   ++   +g++yv   pdrv+lqdvtg++++ ++++a+ ++           ++ p+++++dh+++a+ + +++++ ++++n+e+++fL+
  EPA05872.1  37 KILAGHFEqvtDKnidDGKNYVfliPDRVALQDVTGQMVMLQFMQAELQK-----------TALPTTVHCDHLIRAQIEGDADMKIALDENSEVFKFLQ 124
                 6666554433312454455666668***********************99...........9************************************* PP

   Aconitase  92 saakafgirvvppgqGIvHqvnlEyglalpgktvvgtDSHTtmigglGvlaiGvGgieaeavllgqplelkipkvvgvkltGklkegvtakDlvlavig 190
                 saa++fg+ +++pg+GI+Hqv+lE+ +a+pg +++gtDSHT+++gglG++aiGvGg +a++ ++g+p+el +pk +gvkltG l+ ++ +kD++l+v++
  EPA05872.1 125 SAAAKFGCGFWKPGAGIIHQVVLEN-YAFPGGLMIGTDSHTPNAGGLGMIAIGVGGLDAAETMAGMPWELLYPKRIGVKLTGALNGWTAPKDIILKVAE 222
                 *************************.************************************************************************* PP

   Aconitase 191 klrkkgvvgkvvEffGegvesLsledraTiaNMaaEvGAttglfpvdektleYLkatgreeaavlveaydkaqalf..elaadedaeydkvleldlstl 287
                 +l+++g+++ +vE+fG+g++++s++++aTi+NM+aE+GAt+++fp+d+++ +YLk t+re+ a   ++ +k+  +   e+++++++ +dk++e++ls+l
  EPA05872.1 223 ELTVSGGTNSIVEYFGPGTNTISCTGKATITNMGAEIGATCSIFPYDQRMETYLKSTNREKIAE-LANQNKELLVAdpEVESNPEKFFDKIIEINLSKL 320
                 ***********************************************************99995.3333332222234799****************** PP

   Aconitase 288 epsvagpkrPqdavplselvkkefkeelekeaaekaleyklkegtklkdgkvdiaaigSCTNssnedvraaagllakavekglkvkpgvktsvaPGSev 386
                 ep++ gp++P+ a p+s+l+     +++             k+++ ++  ++++a+igSCTNss+ed+++aa+l+++a+ kg  +k++++++v+PGSe+
  EPA05872.1 321 EPHIVGPHTPDLARPISNLA-----DDV-------------KSNQYID--PISVALIGSCTNSSYEDMSRAASLAEQAKLKG--IKSKIPLLVTPGSEQ 397
                 ****************6666.....444.............3445566..79************************999999..66667********** PP

   Aconitase 387 vkayleaeGlleiLekaGfevvgagCstCignsdrle...egeaivsssNRNFegRq..gpntrayLaSPelvvaaAlaG 461
                 ++ ++e++G +++L+++G++v++++C++Cig++dr e   e+++iv+s+NRNF gR+  ++nt +++ SPe+++a Al G
  EPA05872.1 398 IRSTIERDGQMKSLKEIGATVLANACGPCIGQWDRPElndEKNTIVTSFNRNFPGRNdgHRNTLNFIGSPEMIIALALGG 477
                 ***********************************88777888**************65578888************976 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 0.71
   Aconitase  48 tlatidhlvpvdlvidhsvgaeealeknledefernkery 87 
                 +l+ ++++ pv++vi+h+ g++++++ n     + n+ ++
  EPA05872.1 703 DLKNLEPQKPVRCVIKHKDGTKDEISLN----HSYNQSQI 738
                 5677889999999999988666555444....44444444 PP

>> Aconitase_C  Aconitase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.1   0.0   2.6e-38   1.6e-34       4     130 ..     560     686 ..     557     687 .. 0.97
   2 ?   -1.8   0.0      0.61   3.6e+03      36      76 ..     702     740 ..     691     744 .. 0.70

  Alignments for each domain:
  == domain 1  score: 119.1 bits;  conditional E-value: 2.6e-38
                  CCCCTT--CHHHHSTGGGCCGHCCHHHCCCGGTTTCCCCTTTSBBSEEEETTTTEEEEHHHHHHHHHHTT--EEEE--SSBTBS---THHHHHHHHTT CS
  Aconitase_C   4 llklkGlttedeksnvdtdlkipkqfegtianiglgnelveekrankttdlddgekedvvdaaerykkegaklvviagknfGeGSSRehAAkalrllG 101
                  + k+kG++t+d++s ++ +l  ++++++ ++n+ lg+ ++ + + +k ++l + + e++ + a++yk++g ++v+++++n+GeGSSRehAA+ +r lG
   EPA05872.1 560 IVKAKGKCTTDHISPAGAWLSLRGHLDNLSDNMLLGAVNAFNDEIGKGKNLLNDKLESFSKIAREYKEKGMRWVIVGDNNYGEGSSREHAAMTPRYLG 657
                  5789***********************************************999999***************************************** PP

                  EEEEEES-B-HHHHHHHHHTT-EEEEEST CS
  Aconitase_C 102 ikaviaeSFerIfennliknglLplefke 130
                    avi++S +rI+e+nl+k+g+L l+f++
   EPA05872.1 658 CAAVITKSLARIHETNLKKQGILALTFSN 686
                  ***************************87 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.61
                  TTTCCCCTTTSBBSEEEETTTTEEEEHHHHHHHHHHTT--E CS
  Aconitase_C  36 iglgnelveekrankttdlddgekedvvdaaerykkegakl 76 
                  i+l+n l ++k ++++++ +dg k ++ ++   y++ ++++
   EPA05872.1 702 IDLKN-LEPQKPVRCVIKHKDGTKDEISLNH-SYNQSQIEW 740
                  44443.5556888999999998887776665.666688887 PP

>> DUF521  Protein of unknown function (DUF521)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   8.7e-06     0.052     298     361 ..     360     432 ..     331     447 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.7e-06
      DUF521 298 cPhlsleElrelaell...kgkkkkvkvelwvttsre.vkeeaerlglveklekaGvkvlsdtC.mvv....s 361
                 c   s+e++ + a+l    k k+ k+k++l+vt + e +++++er g ++ l++ G++vl++ C +++    +
  EPA05872.1 360 CTNSSYEDMSRAASLAeqaKLKGIKSKIPLLVTPGSEqIRSTIERDGQMKSLKEIGATVLANACgPCIgqwdR 432
                 66677777777666664337788899******9865449*************************434454443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (753 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 4919.34
//
Query:       EPA05873.1  [L=370]
Description: tryptophan--tRNA ligase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.4e-29  101.4   0.0    8.7e-29  100.8   0.0    1.3  1  tRNA-synt_1b  tRNA synthetases class I (W and Y)
  ------ inclusion threshold ------
      0.051   12.5   0.2       0.46    9.3   0.0    2.1  2  tRNA-synt_1f  tRNA synthetases class I (K)


Domain annotation for each model (and alignments):
>> tRNA-synt_1b  tRNA synthetases class I (W and Y)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.8   0.0   9.7e-33   8.7e-29       3     292 ..      71     348 ..      69     349 .. 0.85

  Alignments for each domain:
  == domain 1  score: 100.8 bits;  conditional E-value: 9.7e-33
                   HS--EEEEEEETSSS-BGGGHHHHHHHHHHHH.TTSEEEEEEEHHHHHTTTTT-SSHHHHHHHHHHHHHHHHHHHHHTCHTTTEEEEETHHHHTTHH CS
  tRNA-synt_1b   3 erplrvysGidPTgklHlGylvplkklvelqk.aghevffliaDlhAiigdpskaeerklrkreevlenaikaqlakgldpekaevvlqsewlehle 98 
                    +++ +y+G  P+g  H+G+lvp     +lq+  g++++f + D + +  +++  ++++  k + + +      +a g++p++++++++++ +++l 
    EPA05873.1  71 GKKFFLYTGRGPSGHTHIGHLVPWVFSKWLQDkFGVNMYFQLTDDEKFFSKQN-LTLEETSKFAYENALD---FIALGFNPKNTKIIINTKNIQTL- 162
                   578889*****************999999998679******************.6677777777666666...****************9998876. PP

                   HHHHHHHHHTTCBHHHHHHHHHCCHHCSSSC--BHHHHHHHHHHHHHHHHTCHS.EEEEEGGGHHHHHHHHHHHHHHHHHSTTSS-EEEEET-BBST CS
  tRNA-synt_1b  99 laellrdlgklgslnrmlqfksvkkrleegegislgeftYplLqaaDilllkad.lvpgGsDQkqnielgrdlarrfnkkevfkkpegltvplltgl 194
                      + ++++k       ++f   k  +  +++ ++g + Y  Lq+a  +  ++  l p G DQ+ +++l+rd+a++++k     kp  + + +++gl
    EPA05873.1 163 -YPIAAQVAK------KINFSNTKAVFGFTNETNIGMIFYTSLQSAPCFIEDKPvLIPLGVDQDPHFRLTRDIAPKIGKP----KPALIHNIMIPGL 248
                   .333444444......3344443444444346799***********998776667**********************997....99999999****9 PP

                   TSSS.BTTCETTCGC-BTTCCHHHHHHHHHH.CHCSTTC..SHHHHHHHHHTHHHCHHHHHHHHCCSEEESSHHHHHHHHHCCCCHHHHHHHHHHHH CS
  tRNA-synt_1b 195 dGek.KmSKSagnsaIfLddekesvkkkiqk.avtdsde..evekllklktelsnelierleavsgkkpkreaeellaeevtklvhggdlkkalaea 287
                   +G   KmS S++n++I+ +d+++ vkkki+k a++  ++  e ++ + +++ ++   +++l  + + ++ ++++ +  +++++++  g+lk  l e+
    EPA05873.1 249 SGPGgKMSASDENGTIYTTDSPNVVKKKINKhAFSGGKQdiEQHRKYGGNPDIDV-SYQYLRIFFEPND-NKLKSIHDDYKSGKMLTGELKAILIEK 343
                   98666************************874677777777778899999****9.9999999999998.9************************** PP

                   HHHHH CS
  tRNA-synt_1b 288 lnell 292
                   +ne+l
    EPA05873.1 344 INEFL 348
                   ***98 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   5.1e-05      0.46      21      43 ..      70      92 ..      58     108 .. 0.78
   2 ?    0.7   0.0     0.021   1.9e+02     289     329 ..     123     163 ..     107     180 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 5.1e-05
  tRNA-synt_1f 21 ekdevvvesGispSGliHiGnlr 43
                  + ++  + +G +pSG+ HiG l 
    EPA05873.1 70 KGKKFFLYTGRGPSGHTHIGHLV 92
                  34578899************975 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.021
  tRNA-synt_1f 289 vltledwlevaepevlrflilrrkPkkakkldldleilrlv 329
                    ltle+  ++a ++ l f+ l  +Pk+ k +    +i+ l+
    EPA05873.1 123 NLTLEETSKFAYENALDFIALGFNPKNTKIIINTKNIQTLY 163
                   589**********************9988877776888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2297.55
//
Query:       EPA05874.1  [L=86]
Description: hypothetical protein BG20_I1459 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.51
# Mc/sec: 507.51
//
Query:       EPA05875.1  [L=205]
Description: pyridoxal 5'-phosphate synthase, glutaminase subunit Pdx2 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.1e-50  169.5   0.1    8.1e-50  169.3   0.1    1.0  1  SNO            SNO glutamine amidotransferase family
    1.8e-12   47.3   0.0    2.5e-12   46.8   0.0    1.2  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
    2.1e-11   43.9   0.0    2.7e-10   40.3   0.0    2.0  1  GATase         Glutamine amidotransferase class-I
    6.1e-07   29.4   0.0    1.8e-05   24.6   0.0    2.6  1  Peptidase_C26  Peptidase C26
    1.8e-06   27.8   0.0    3.1e-06   27.1   0.0    1.4  1  DJ-1_PfpI      DJ-1/PfpI family
      3e-06   27.0   0.1    4.2e-06   26.6   0.1    1.2  1  Peptidase_S51  Peptidase family S51


Domain annotation for each model (and alignments):
>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.3   0.1   2.7e-53   8.1e-50       1     186 [.       7     200 ..       7     202 .. 0.90

  Alignments for each domain:
  == domain 1  score: 169.3 bits;  conditional E-value: 2.7e-53
                 EESSSSSHHHHHHHHHHTTSEE......EEE-SGGGGCC-SEEEE-SS-HHHHHHHHHHTT-HHHHHHHHHTT.--EEEETHHHHHHCCEETTB..... CS
         SNO   1 vlalqGaveehveaikkclaen......ktvkrkedlaevdaliiPGGestamskliertglyedllefvknsekvvlGtCaGlillskelene..... 88 
                 +la+qG+v+e +   + +l e         vk++ed+ ++d+liiPGGest++++l      ++ ++e+++++  +v+G CaG+i+lsk  +       
  EPA05875.1   7 ILAIQGDVQENILSTETALKELgvegkvVSVKTTEDISKLDGLIIPGGESTTIGQLSLVNSSLKLMKEKIEKG-MPVFGICAGMIMLSKTADDRvvgkt 104
                 69********986655555554444566679*************************9999999*********9.9**************9776655555 PP

                 SS-SS--CCEEEETTTT-SCCGEEEEEEEETTTC.SEEEEEESS--EEEEE-.TTTCEEEEECTTEEEEEEETTEEEESS-GGGSTTHCHHHHHHHHHH CS
         SNO  89 lvktlellkvkvkrnafGrqvdsfekeldfknli.ekftavfiraPvieeilddeavkvlyeldgeivvakqkkilatsfhPelaeddirvhdyfveev 186
                 + + l+ll++k++rn+fGrq +sfe+++ ++ ++  kf++vfiraP +  ++    v+vl + + +i+++k++++l++sfhPel++d + +h+yf++ +
  EPA05875.1 105 DQPLLDLLDIKLERNSFGRQKESFEANISMNPIDiPKFKGVFIRAPSVSDVG--PGVDVLAKFNEKIIAVKKDNMLGVSFHPELTKD-VSLHKYFINLI 200
                 7889****************************9989****************..78999**************************99.9*******865 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   0.0   8.2e-16   2.5e-12      23     119 ..      29     120 ..      16     145 .. 0.77

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 8.2e-16
    GATase_3  23 pevrvrfvpl.kdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmLGeeiedpegvegeageveglglLdietefek 119
                 + v++++v++ ++e++ +++d +i+pGg++t+  + +l +s+  + +ke++e+g+pv+giC+G++mL+++  d   v   ++  + l+lLdi+ e ++
  EPA05875.1  29 G-VEGKVVSVkTTEDI-SKLDGLIIPGGESTTIGQLSLVNSS-LKLMKEKIEKGMPVFGICAGMIMLSKTADDRV-V--GKTDQPLLDLLDIKLERNS 120
                 3.44444444055667.66***********998888888855.5789***********************87754.3..567999*******988765 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.0   9.2e-14   2.7e-10      13     185 ..      21     198 ..      13     202 .. 0.72

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 9.2e-14
                 HHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT.....TTTHHHHHHHHCTSTS-EEEETHHHHHHHHHTTTEEE............. CS
      GATase  13 lvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg.....vegkieaikearenkiPiLGICLGmQllaiefgrkvv............. 93 
                  + al elgv+ +vv ++++ +++     + dg++++gG  +       v  ++++ ke +e+++P++GIC Gm +l +     vv             
  EPA05875.1  21 TETALKELGVEGKVVSVKTTEDIS-----KLDGLIIPGGESTTIgqlslVNSSLKLMKEKIEKGMPVFGICAGMIMLSKTADDRVVgktdqplldlldi 114
                 567899************865555.....79********887767888*******************************99999996555555444433 PP

                 EEECEEEEEEEEEEEETTT........CGGTTTTSEEEEEEEEEEEEESG..CHHHTTEEEEEEEETTEEEEEEEEETTTEEEESSBTTSTTSTTHHHH CS
      GATase  94 kekekehhggtmrlgddet........allyglknevierhrHryevnpk..elepaglevtakseddeelmeiiekknpfvgvQFHPEststpegpel 182
                 k               +++         +++ + n+++     +  +     + +  g++v+ak ++  +++++ ++  ++ gv FHPE t     +++
  EPA05875.1 115 K--------------LERNsfgrqkesFEANISMNPIDIPKFKGVFIRAPsvSDVGPGVDVLAKFNE--KIIAVKKD--NMLGVSFHPELTKDVSLHKY 195
                 2..............2222233333334445555677777777777776655557778888888833..34444333..38*********999887777 PP

                 HHH CS
      GATase 183 lfn 185
                 + n
  EPA05875.1 196 FIN 198
                 665 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   6.1e-09   1.8e-05      93     216 .]      67     185 ..      31     185 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 6.1e-09
  Peptidase_C26  93 lelaLiraalergvPilgiCrGlqllnvalGGtlyqdiee.qsgltdhreheqsaashavkvekgsllaellgseeievnslHhqaikelaeelrv 187
                     +l+L+++ +e+g+P++giC G+ +l  +   +++ + ++   +l d + +++s+ +++ ++e +  ++ + +  +++   +   +++++++++ v
     EPA05875.1  67 SSLKLMKEKIEKGMPVFGICAGMIMLSKTADDRVVGKTDQpLLDLLDIKLERNSFGRQKESFEANISMNPIDI-PKFKGVFIRAPSVSDVGPGVDV 161
                    5799**********************99988888888876345667776677788888888888888877777.666666777888888******* PP

  Peptidase_C26 188 eAvaeDgviEaieseeakafvlgvQwHPE 216
                     A  +  +i a++  +    +lgv +HPE
     EPA05875.1 162 LAKFNEKII-AVKKDN----MLGVSFHPE 185
                    **9998877.565555....89******9 PP

>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0     1e-09   3.1e-06      59     110 ..      43      95 ..      10     101 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 1e-09
                 CCG-SEEEE--BHHHH.HHHHTSHHHHHHHHHHHHTT-EEEEETTTHHHHHHT CS
   DJ-1_PfpI  59 aaeyDalvlpGGragp.erlrenekvvelvkefaekgklvaaICagpqlLaaa 110
                  ++ D l++pGG++    +l+  +  ++l+ke  ekg +v+ ICag ++L+++
  EPA05875.1  43 ISKLDGLIIPGGESTTiGQLSLVNSSLKLMKEKIEKGMPVFGICAGMIMLSKT 95 
                 4578********98532688999999************************987 PP

>> Peptidase_S51  Peptidase family S51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.1   1.4e-09   4.2e-06      43     134 ..      12      97 ..       8     114 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 1.4e-09
                    -S--HHHHHHHHHHHHTT-EEEE--TTTS-HHHHHHHHHHSSEEEE--S-HHHHHHHHHHTTHHHHHHHHHHTT-EEEEETHHHHTTSSB-G CS
  Peptidase_S51  43 gdddeyvekvrkaleklglevdeLelskdpeeeieeklleadviyvgGGntfrLlkllketgldkllreavqqglvyiGvSAGaivagesie 134
                    gd++e + ++++al++lg+e ++++++  ++e+i +     d++++ GG+   + +l   +   kl++e++++g++++G+ AG i+ +++  
     EPA05875.1  12 GDVQENILSTETALKELGVEGKVVSVK--TTEDISK----LDGLIIPGGESTTIGQLSLVNSSLKLMKEKIEKGMPVFGICAGMIMLSKTAD 97 
                    678888899999*******99999988..6788888....*******************************************999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1418.69
//
Query:       EPA05876.1  [L=49]
Description: hypothetical protein BG20_I1458 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0017   18.5   0.2     0.0018   18.4   0.2    1.1  1  DUF2315   Apoptogenic protein 1


Domain annotation for each model (and alignments):
>> DUF2315  Apoptogenic protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.2   9.8e-08    0.0018      73     101 ..      19      47 ..       4      48 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 9.8e-08
     DUF2315  73 keelsaeemseFYkeFldknakkhlaYna 101
                  e    ++m++FYk +++kn +k l Yna
  EPA05876.1  19 PEFEYVKQMANFYKVWIKKNLTKILIYNA 47 
                 33445789*******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       799  (0.0445647); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 347.09
//
Query:       EPA05877.1  [L=301]
Description: hypothetical protein BG20_I2495, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.014   15.5   1.5      0.032   14.3   1.5    1.6  1  Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C
      0.041   13.9   0.1      0.086   12.9   0.1    1.5  1  DUF1664       Protein of unknown function (DUF1664)
      0.071   13.4   0.4       0.17   12.2   0.4    1.6  1  BLOC1_2       Biogenesis of lysosome-related organelles compl
      0.085   13.7   0.0       0.26   12.1   0.0    1.8  2  Filamin       Filamin/ABP280 repeat
       0.35   11.4   2.2         25    5.4   0.2    2.5  2  NPV_P10       Nucleopolyhedrovirus P10 protein
        1.3    9.5   4.6        3.5    8.1   2.0    2.7  2  FlaC_arch     Flagella accessory protein C (FlaC)


Domain annotation for each model (and alignments):
>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   1.5   1.1e-05     0.032      11     119 ..     215     269 ..     199     289 .. 0.39

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.1e-05
  Baculo_PEP_C  11 ggnqfldLtnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnlnsil....tnLlssvtN 103
                    +nq + L+ vL                                                          ++ ++eLt+l+s++    ++L s  +N
    EPA05877.1 215 ISNQIIKLNSVL----------------------------------------------------------EETSTELTTLKSEIsgfgNTLESASGN 253
                   222222222222..........................................................222223333333222222222333333 PP

  Baculo_PEP_C 104 instLnnllqalnnld 119
                   i ++++++ +++nn++
    EPA05877.1 254 IDKSVTSVSKSVNNIE 269
                   3333333333333322 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   2.9e-05     0.086      39     110 ..     208     279 ..     202     293 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.9e-05
     DUF1664  39 lsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeav 110
                 ls+ +  +s+q+ ++ + l++t  +L+    ++    +  + +s +i++ vt+v++ +++i+e ++++++++
  EPA05877.1 208 LSQDLGGISNQIIKLNSVLEETSTELTTLKSEISGFGNTLESASGNIDKSVTSVSKSVNNIEEASSQLNSLF 279
                 556666678888888777777777776554555555555556788889999999999999998888888766 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.4   5.7e-05      0.17      33      93 ..     216     277 ..     204     279 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.7e-05
     BLOC1_2  33 sekykklkdvaaslekkleklnekyeelqpylqqid.qiekqvteLeeavseLDeyskeLEa 93 
                 s+++ kl++v+++++++l  l+++   + + l++   +i+k+vt+  + v+ ++e s++L +
  EPA05877.1 216 SNQIIKLNSVLEETSTELTTLKSEISGFGNTLESASgNIDKSVTSVSKSVNNIEEASSQLNS 277
                 56678899999999999999999999999888776438999999999999999999999975 PP

>> Filamin  Filamin/ABP280 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       3.2   9.7e+03      65      75 ..      47      57 ..      17      60 .. 0.69
   2 ?   12.1   0.0   8.7e-05      0.26      59      91 ..     120     191 ..      72     200 .. 0.57

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.2
                EEEE-SSSEEE CS
     Filamin 65 evvdnedgtyt 75
                +++ nedgt++
  EPA05877.1 47 QFETNEDGTFE 57
                47888999875 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 8.7e-05
                 .........................................EEEEEEEE-SSSEEEEEE--SSSCEEEEEEE CS
     Filamin  59 k..............................s.........svkievvdnedgtytvsYtpeepgtyrvsvk 91 
                                                +          +  +++  ++g y   Y p+e+gty  +v 
  EPA05877.1 120 AainipfrvfvqvtsdglligddpakllqttHvhlpsgkveTLANNFSTLHQGLYYTDYVPKEEGTYVFHVV 191
                 0444444444444444444443333333333033333433345568*********************99974 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.2    0.0083        25      30      65 ..     212     247 ..     201     252 .. 0.75
   2 ?    5.2   0.3      0.01        30      23      46 ..     254     277 ..     245     279 .. 0.66

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0083
     NPV_P10  30 vqenlpdvtelnekLdaqsaqLaeletkvenIqdiL 65 
                 +   ++++ +ln+ L++ s++L++l+++++   ++L
  EPA05877.1 212 LGGISNQIIKLNSVLEETSTELTTLKSEISGFGNTL 247
                 444456777899999999999999999998776666 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.01
     NPV_P10  23 lqqqvddvqenlpdvtelnekLda 46 
                 ++++v++v++ +++++e +++L++
  EPA05877.1 254 IDKSVTSVSKSVNNIEEASSQLNS 277
                 566666666666666666666654 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       5.3   1.6e+04      19      30 ..      80      91 ..      76      92 .. 0.51
   2 ?    8.1   2.0    0.0012       3.5       4      38 ..     221     255 ..     218     279 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 5.3
   FlaC_arch 19 vkkeneelsksv 30
                + ++++ lsk++
  EPA05877.1 80 ISTQQNGLSKKI 91
                444555555555 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0012
   FlaC_arch   4 elEnklsklsteletvkkeneelsksveelkenVk 38 
                 +l + l+++stel+t+k+e++   +++e    n+ 
  EPA05877.1 221 KLNSVLEETSTELTTLKSEISGFGNTLESASGNID 255
                 57788999*****************9998888774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       745  (0.0415528); expected 358.6 (0.02)
Passed bias filter:                      617  (0.0344135); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 2122.49
//
Query:       EPA05878.1  [L=37]
Description: hypothetical protein BG20_I2494, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 257.36
//
Query:       EPA05879.1  [L=126]
Description: HAD ATPase, P-type, family IC domain protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.3e-10   39.5   0.5    1.6e-09   38.4   0.2    1.6  2  Hydrolase    haloacid dehalogenase-like hydrolase
    0.00042   20.1   0.3    0.00052   19.8   0.3    1.2  1  Hydrolase_3  haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.2   1.8e-13   1.6e-09     175     209 ..       1      35 [.       1      36 [. 0.96
   2 ?   -1.2   0.0      0.23     2e+03      42      62 ..      44      64 ..      40     113 .. 0.62

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 1.8e-13
                 SHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHT CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
   Hydrolase 175 spegkvaaireLqgkpeevamVGDgvnDaaalaaA 209
                 +pe+kv a+++L+++  +v+mVGDg+nDa+ala+A
  EPA05879.1   1 LPEQKVIAVKKLKEEYGQVVMVGDGINDAPALAMA 35 
                 59*******************************98 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.23
                HHHHHHHHHHHHHHHHHHHHH CS
                xxxxxxxxxxxxxxxxxxxxx RF
   Hydrolase 42 igkalvaaakarsgaltgfat 62
                +g a+ a+a ++ + ++++a+
  EPA05879.1 44 HGTAISAEAADVVFLVDDIAK 64
                566666666666555555444 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.3   5.8e-08   0.00052     191     241 ..       8      55 ..       4      81 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 5.8e-08
                  HHHHHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHH.HSSE CS
  Hydrolase_3 191 alkklakelnisleeviafGDgeNDieMLeaaglgvAmgnaseevkk.aAdy 241
                  a+kkl +e+     +v+ +GDg ND + L +a +g+Amg     + + aAd 
   EPA05879.1   8 AVKKLKEEY----GQVVMVGDGINDAPALAMATTGIAMGAHGTAISAeAADV 55 
                  555555444....59***********************96555554404444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 938.23
//
Query:       EPA05880.1  [L=139]
Description: universal stress family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-30  105.5   0.0    3.5e-30  105.3   0.0    1.0  1  Usp       Universal stress protein family


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.3   0.0     2e-34   3.5e-30       1     141 []       1     139 []       1     139 [] 0.95

  Alignments for each domain:
  == domain 1  score: 105.3 bits;  conditional E-value: 2e-34
                 S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTCEEEEEEEESSHHHHHHHHH CS
         Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggvkvevvveegdpaeeileva 99 
                 m k+IlV++Dgs++s + le+A+e+ak++++ ++llh+   ++    + ++++++++ ++ +++  + + + +  ++ +  ++  v + dp   i ++a
  EPA05880.1   1 M-KKILVPIDGSPNSVRGLEKAIEFAKNDNSSITLLHIATLPPVHVIGHSKDKVKKSLAKNAQKFIKDA-EDRCINQSIQFTTKLVYGSDPPYDIEQFA 97 
                 5.9************************************************************988765.588888888888888999999******** PP

                 HHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
         Usp 100 eeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                 ++++ dliV+G++g+s+l+rl+lGSvs+y+++ a+ pV+v++
  EPA05880.1  98 KKYKHDLIVIGAKGKSTLKRLFLGSVSSYLVETAKTPVTVIK 139
                 ****************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 869.13
//
Query:       EPA05881.1  [L=468]
Description: amino acid permease [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.6e-54  184.2  54.3    4.4e-54  183.9  54.3    1.0  1  AA_permease_2   Amino acid permease
    2.7e-35  121.9  48.5    3.5e-35  121.5  48.5    1.1  1  AA_permease     Amino acid permease
     0.0011   17.9  25.6     0.0011   17.9  25.6    2.4  2  Spore_permease  Spore germination protein


Domain annotation for each model (and alignments):
>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.9  54.3   7.4e-58   4.4e-54       1     404 [.      10     401 ..      10     421 .. 0.87

  Alignments for each domain:
  == domain 1  score: 183.9 bits;  conditional E-value: 7.4e-58
  AA_permease_2   1 lsllsafalvigsvigsgifvkn..laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkvaflsawfnwfayvpvlas 94 
                    ls+++++ ++igs++g+ i++++   a+ +gp++i++++ia +   + ++lv+a  s+  p+ gG + ++++af ++ +fl++w+ w+a + +l++
     EPA05881.1  10 LSFFDLTNIIIGSIVGADIYIASaiTAGLVGPIAIFVWVIAGGFA-IVLALVFAYSSYYVPKVGGPFAFVSKAFDNFYGFLTGWSMWIAEMMALPV 104
                    79********************9988888*******999999988.89******99999************************************* PP

  AA_permease_2  95 ilsvaasyllnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgilkillpliiliilglitvdgggfsslstetdt...ffpngw 187
                     ++++++yl +++  ++    w+ +l+  ++l++++++ni+++k  ++++ il+i+k+  pl+ilii g++++ ++       ++++    +p g 
     EPA05881.1 105 FAIAFTQYLHYFVELNF----WQDVLVKGVFLLGLTMVNIISVKAAGRLNDILTIVKL-APLVILIISGIVFFVIHPEA----IQKNytpLMPLGL 191
                    ***********997655....67777777*****************************.6************9776665....2333112455566 PP

  AA_permease_2 188 pgvllgllivlwsfdGfesaanvseevkk..kdvpkaifigllivlvlyllvniaflgvvpddeianlsnlgsvaalffeavggkvvaiivvilia 281
                    + +  +l  ++w+++Gfe+ +  ++evk+  k++pkai++g+l+v+v+yl +n++++gv++++ ++++++   ++ l+   + g+++aii+ +++ 
     EPA05881.1 192 DNFGTALVLIFWAYVGFEMGTLPASEVKNpkKNIPKAIIVGILVVIVFYLITNFVLFGVSSWEDLSKTQT---PLVLVSTITLGSIGAIIIGVGAL 284
                    668999999*****************8877589*********************************9876...58899999999************ PP

  AA_permease_2 282 lsllgaintavigssrvlealardgvlPrffakvn.kfgspiraiiltaivslillllfllassaaynfllsvsslgliisyllliigalilrkkr 376
                    ls+ g+  + ++g++r+ +a++  g +P+ f+k++ k+++p+ a+i++ ++++ l+ ++       ++ l s s++ l +s+ll+ +++++l+k++
     EPA05881.1 285 LSVSGSNESGTLGIARLSYAMSIKGLFPKIFSKTHpKYKTPYMALIIQGVIAFSLS-IYG-----GISELISFSVFNLSFSFLLVCFSLIVLKKNS 374
                    ***************************************************95443.333.....4789**************************9 PP

  AA_permease_2 377 phlkrpgkilvaiigalfllfllvalff 404
                    +h+   g  ++ ++g+ ++l+ll+ + f
     EPA05881.1 375 EHK-LHGQSILPWLGIGICLYLLYSTSF 401
                    995.344445666666666666654444 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.5  48.5   5.8e-39   3.5e-35       3     434 ..      16     404 ..      14     422 .. 0.88

  Alignments for each domain:
  == domain 1  score: 121.5 bits;  conditional E-value: 5.8e-39
  AA_permease   3 lvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGlnylfswitvlaleltaasil 100
                  + i +g+++G+ ++++++++++ +Gp+++  ++++ag + +  +l +++ + ++pk+gg  +++s+  +   Gf +G++ ++ + ++l++  +a   +
   EPA05881.1  16 TNIIIGSIVGADIYIASAITAGLVGPIAI-FVWVIAGGFAIVLALVFAYSSYYVPKVGGPFAFVSKAFDNFYGFLTGWSMWIAEMMALPVFAIAFTQY 112
                  5688**********************766.67777777777788999999*****************************9999999999888888888 PP

  AA_permease 101 iqfwelvtdlpkawvt..gavflvvlliinlvgvkvygeaefilalikiiaiiafiivgiillaggkpnkgagfrflgdngsifknnlppgfakeeeg 196
                  +++   v+ ++ ++v   g vfl+ l+++n+++vk+ g+   il+++k+  ++++ii gi++ +    + +       +n++     +p g       
   EPA05881.1 113 LHYF--VELNFWQDVLvkG-VFLLGLTMVNIISVKAAGRLNDILTIVKLAPLVILIISGIVFFVIHPEAIQ-------KNYT---PLMPLG------- 190
                  8888..7766666666744.9**************************************999998888877.......4444...345666....... PP

  AA_permease 197 afknfisvfvivvfaftGielvaiiagEvkdPeksiPkailqvviritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplina 294
                   + nf  ++v ++ a+ G+e++++ a+Evk+P+k+iPkai+  ++ +++fY++  +++  + ++ dl+ ++       p+v++ + +  s+ a +i +
   EPA05881.1 191 -LDNFGTALVLIFWAYVGFEMGTLPASEVKNPKKNIPKAIIVGILVVIVFYLITNFVLFGVSSWEDLSKTQ------TPLVLVSTITLGSIGAIIIGV 281
                  .99***************************************************************88888......5899999999999******** PP

  AA_permease 295 viltaalssansslysasRvlyslakdglaPkvl.kkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisaliglivwlliilsylrfR 391
                  + l+++ +s  s++    R+ y+++  gl+Pk++ k + k++ P++a+++  +i++ + +  +++          +++s +   + +ll+++s+++++
   EPA05881.1 282 GALLSVSGSNESGTLGIARLSYAMSIKGLFPKIFsKTHPKYKTPYMALIIQGVIAFSLSIYGGISEL--------ISFSVFNLSFSFLLVCFSLIVLK 371
                  *******************************77725689**************99999988888877........88888888899999999999998 PP

  AA_permease 392 kalkyqgrsieelgfkaallplgvilvlaaliiillilalyay 434
                  k    +++       k+++++ +++l++ +++ +l  +++++ 
   EPA05881.1 372 KN---SEH-------KLHGQSILPWLGIGICLYLLYSTSFFDK 404
                  88...444.......7789999999999999888877777654 PP

>> Spore_permease  Spore germination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9  25.6   1.8e-07    0.0011       2     247 ..      10     264 ..       9     279 .. 0.80
   2 !    4.6   4.7     0.002        12     111     179 ..     323     395 ..     318     424 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.8e-07
  Spore_permease   2 istkqlfvlivsfqlGvgiltlprsvaeqatpdg.WisvllagiiililvllmlkllkkfpektliellkkilgkwLGslls....ilfil...y 88 
                     +s++ l+ +i+  ++G+ i ++ ++ a   +p +  + v+ +g++i++++++++  ++  +    +++++k +  + G+l +    i+ ++   +
      EPA05881.1  10 LSFFDLTNIIIGSIVGADIYIASAITAGLVGPIAiFVWVIAGGFAIVLALVFAYSSYYVPKVGGPFAFVSKAFDNFYGFLTGwsmwIAEMMalpV 104
                     78899999*********************966552667788888888888888888887778999***999998887766551111333332235 PP

  Spore_permease  89 FlllaafelRefseliqvfl.ledtplwiiilllllvilYlvvkGieslareflfiivilliilllillfslklaeiknlrPvlgngikpvlksl 182
                     F++  +  l  f+el +++  +    ++++ l+++ +i   + + ++++   + ++ +++lii  ++++++  +a  kn +P++  g+ ++  +l
      EPA05881.1 105 FAIAFTQYLHYFVEL-NFWQdVLVKGVFLLGLTMVNIISVKAAGRLNDILTIVKLAPLVILIISGIVFFVIHPEAIQKNYTPLMPLGLDNFGTAL 198
                     776667777777775.44441333346777788999999999999999998777777788888888888888888889***************** PP

  Spore_permease 183 kttslsflgveillllvpflkdkk.kvkkaallgvlistllyllttlivilvlsveqlkkatwptl 247
                       +  +++g+e+ +l    +k++k ++ ka+++g+l+++++yl+t ++ ++v s e l+k++ p++
      EPA05881.1 199 VLIFWAYVGFEMGTLPASEVKNPKkNIPKAIIVGILVVIVFYLITNFVLFGVSSWEDLSKTQTPLV 264
                     ****************999998651678**********************************9987 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.002
  Spore_permease 111 dtplwiiilllllvilYlvvkGieslareflfiivilliilllillfslkl.....aeiknlrPvlgngikpvl 179
                     +tp +++i+  ++ + + +++Gi++l+  f ++ + + + l+ ++l++lk       + + ++P lg gi   l
      EPA05881.1 323 KTPYMALIIQGVIAFSLSIYGGISELI-SFSVFNLSFSFLLVCFSLIVLKKnsehkLHGQSILPWLGIGICLYL 395
                     69999**********************.5666666666666666666655311111455667777777776555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (468 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       920  (0.0513135); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.44
# Mc/sec: 3190.22
//
Query:       EPA05882.1  [L=48]
Description: hypothetical protein BG20_I2181, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.6e-06   26.1   0.0    7.6e-06   26.1   0.0    1.0  1  MOFRL     MOFRL family
  ------ inclusion threshold ------
      0.021   14.5   0.3      0.021   14.5   0.3    1.0  1  DUF4940   Domain of unknown function (DUF4940)


Domain annotation for each model (and alignments):
>> MOFRL  MOFRL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   8.5e-10   7.6e-06      74     109 .]       7      42 ..       1      42 [. 0.88

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 8.5e-10
                 TT--HHHHHHTT-HHHHHHHTT-EE-----S----E CS
       MOFRL  74 agldakeaLanndsyeffeklgallktgpTgtNVnD 109
                  +  +ke+L+n+ds +ff+k +  +kt+ T+tN++D
  EPA05882.1   7 DESIIKEFLKNSDSGRFFQKQKCNIKTDFTHTNLMD 42 
                 455689**************9**************9 PP

>> DUF4940  Domain of unknown function (DUF4940)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.3   2.4e-06     0.021     155     193 ..       3      41 ..       2      48 .] 0.91

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.4e-06
     DUF4940 155 niqldekliesklrssDleklsellskdveevynkllkl 193
                 ni++de +i+++l+ sD  ++ ++ + +++  + +++ +
  EPA05882.1   3 NIKIDESIIKEFLKNSDSGRFFQKQKCNIKTDFTHTNLM 41 
                 89*****************************99888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 335.67
//
Query:       EPA05883.1  [L=122]
Description: hypothetical protein BG20_I2179 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.075   13.0   0.8        2.1    8.4   0.2    2.1  2  FlxA      FlxA-like protein
        0.2   12.2   2.1        2.8    8.4   0.1    2.4  2  NPV_P10   Nucleopolyhedrovirus P10 protein


Domain annotation for each model (and alignments):
>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0    0.0084        75      18      40 ..      11      33 ..       2      47 .. 0.83
   2 ?    8.4   0.2   0.00024       2.1      34      66 ..      86     120 ..      81     122 .] 0.81

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.0084
        FlxA 18 qiasLqkQiknlqkqLkelsesd 40
                +i+ +++ ++ ++k+Lk+l+e++
  EPA05883.1 11 NIRVINRALDYYSKSLKNLKENE 33
                57789999999*********993 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00024
        FlxA  34 kelses..deltkeekkkqqqliqaQIqqlqaQIa 66 
                  else+  + +++ee kk  +l++++I ++   I+
  EPA05883.1  86 AELSEDleELEDTEENKKNMNLLEEEIGKITETIQ 120
                 57888885556678889999*********999887 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1   0.00032       2.8      33      57 ..       8      48 ..       3      83 .. 0.79
   2 ?    3.7   0.3      0.01        89      26      52 ..      94     120 ..      68     122 .] 0.81

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00032
     NPV_P10 33 nlpdvtelnekLdaqsaqLaelet................k 57
                +++++  +n  Ld  s++L++l++                +
  EPA05883.1  8 EIENIRVINRALDYYSKSLKNLKEneiedsmplfngqideS 48
                568999****************9876777666666666663 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.01
     NPV_P10  26 qvddvqenlpdvtelnekLdaqsaqLa 52 
                 +++d +en ++++ l+e++ +++++++
  EPA05883.1  94 ELEDTEENKKNMNLLEEEIGKITETIQ 120
                 567778888888888888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1105  (0.061632); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 770.12
//
Query:       EPA05884.1  [L=59]
Description: hypothetical protein BG20_I2349, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0003   20.4   0.0    0.00033   20.3   0.0    1.1  1  GATase_3  CobB/CobQ-like glutamine amidotransferase domain


Domain annotation for each model (and alignments):
>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   1.9e-08   0.00033       1      37 [.      18      56 ..      18      59 .] 0.94

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.9e-08
    GATase_3  1 kiavirlpaisnyt..dldpLeaepevrvrfvplkdesl 37
                +ia++ + ++++y+  +l++L++e+++  +f+p+++++ 
  EPA05884.1 18 TIAIALDGSFNFYYsdNLNALRREGANLKFFSPINNKKT 56
                69*******************************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 468.79
//
Query:       EPA05885.1  [L=94]
Description: putative precorrin-8X methylmutase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-34  119.0   0.4    2.2e-34  118.9   0.4    1.0  1  CbiC      Precorrin-8X methylmutase
  ------ inclusion threshold ------
      0.045   11.7   0.0      0.047   11.7   0.0    1.0  1  DUF4958   Domain of unknown function (DUF4958)


Domain annotation for each model (and alignments):
>> CbiC  Precorrin-8X methylmutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.9   0.4   2.4e-38   2.2e-34     111     196 .]       1      87 [.       1      87 [. 0.96

  Alignments for each domain:
  == domain 1  score: 118.9 bits;  conditional E-value: 2.4e-38
                 HHHHHHCTTTCEEEESS-HHHHHHHHHHHHHS..HTSEEEE----SCCHHHHHHHHHCSS.S-EEEESSS---HHHHHHHHHHHHHH CS
        CbiC 111 mekaaeelegaivviGnAPtALlellelieegkvkpalvigvPvGFvgaaesKealaese.vpyitveGrkGGsavAaaivnaLlel 196
                 m++a ++ +g+ivviGnAPtALle++e++++g vkpal+ig+PvGF+ aaesKe+l+++e +p+it+ GrkGGs+ A ai+naL+++
  EPA05885.1   1 MRAAYSDIDGGIVVIGNAPTALLEVIEMVKDGVVKPALIIGIPVGFICAAESKEELSKLEeTPFITNIGRKGGSSSASAIINALYKM 87 
                 7889999**************************************************9656***********************975 PP

>> DUF4958  Domain of unknown function (DUF4958)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   5.3e-06     0.047     536     595 ..      27      84 ..       4      89 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.3e-06
                 EEEEEEESSGGG-EEEEEEEEEEE----.GGG---B-SSSEEEE-TTT-EE----B--TT- CS
     DUF4958 536 vlvtatagegkeavslkvPvffhfsnis.kdnvkieytPfvlqvnPkkGGesvaPkiisgi 595
                  +v+      k a+ + +Pv f  +  s ++  k+e tPf+ ++  +kGG s a  ii++ 
  EPA05885.1  27 EMVKDG--VVKPALIIGIPVGFICAAESkEELSKLEETPFITNIG-RKGGSSSASAIINAL 84 
                 444443..346788999***8887776636779********9996.799999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 622.52
//
Query:       EPA05886.1  [L=65]
Description: hypothetical protein BG20_I2346 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-13   50.0   0.5    2.9e-13   49.9   0.5    1.0  1  CbiC      Precorrin-8X methylmutase


Domain annotation for each model (and alignments):
>> CbiC  Precorrin-8X methylmutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.9   0.5   1.6e-17   2.9e-13       2      46 ..       9      53 ..       8      62 .. 0.93

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 1.6e-17
                HHHHHHHHHHCHC-TT.S-CHHHHHHHHHHHHHT-CCHHHHEEE- CS
        CbiC  2 IeaeSfaiideelgeeelseeeeevvrRvihatadfelaellrfs 46
                Ie+ S+++idee+g+++++e+e+++vrR+ih+tadf++a+ +++s
  EPA05886.1  9 IEDASMQMIDEEIGTHQYNEKEWHIVRRIIHSTADFDFAKEIELS 53
                99**************************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 435.81
//
Query:       EPA05887.1  [L=148]
Description: sirohydrochlorin cobaltochelatase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.7e-17   62.3   0.0    6.1e-17   61.9   0.0    1.1  1  CbiX            CbiX
    1.6e-06   27.7   0.2    1.8e-06   27.5   0.2    1.0  1  CbiK            Cobalt chelatase (CbiK)
  ------ inclusion threshold ------
      0.036   13.1   0.1       0.14   11.2   0.1    1.7  2  Ferrochelatase  Ferrochelatase


Domain annotation for each model (and alignments):
>> CbiX  CbiX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.9   0.0     1e-20   6.1e-17       1     106 [.      36     138 ..      36     139 .. 0.96

  Alignments for each domain:
  == domain 1  score: 61.9 bits;  conditional E-value: 1e-20
                 -STSSCCHHHHHHHHHHHHHHHCCSCCCEECESCCCECCSCCSSHHHHC-SBSEEEEEEESSSSSHHHHTHHHHHCT--SSSS-TTEEEEE---CCCSC CS
        CbiX   1 HGSrdpesneeveklaeelrekgpfkpvelgfleleepsleealrelaeqgvkrivvvPlflfaGvhvkeDIpeeleeaeeahpkdveieytepLGthp 99 
                 HGS+dp+++  +  +++ l++  +++ v  ++le+e+p++ e+++++++++ +  v+v +fl +G hvk+DI + l+ a e+     + ++t++LG ++
  EPA05887.1  36 HGSKDPNAQLSLDYVVDGLKN--NYRNVNRCWLEIEQPDIVEGIKTCEKNKPEVLVIVFYFLHEGAHVKTDINNDLKPALENSS-IKKAYITKHLGVDE 131
                 *********************..556***************************************************9888888.789*********** PP

                 CHHHHHH CS
        CbiX 100 lvaevlk 106
                 +++++++
  EPA05887.1 132 KMIDLII 138
                 ****997 PP

>> CbiK  Cobalt chelatase (CbiK)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.2   3.1e-10   1.8e-06     130     260 ..      17     144 ..       7     146 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 3.1e-10
                 HHHTTS----TTEEEEEEE---SCHHHHHHHHHHHHHHH..CT-S.EEEEETT.SSS-HHHHHHHHHHHT--EEEEEE-SSS--HHHHCCCCSSSTTSH CS
        CbiK 130 alkdeierarkdealvfvgHGtehesnavyaeldkvlke..kdfkqvvvgtve.gyPeveevieelkkkgikevkliPlmlvAGdHaknDmasdeedsw 225
                 + +++++  +kd  ++ +gHG++ + ++    ld+v++   +++++v  + +e  +P++ e i++ +k++ +   ++ ++l  G H+k D+    +++ 
  EPA05887.1  17 LQENQVTIPKKDVDVLIIGHGSKDPNAQ--LSLDYVVDGlkNNYRNVNRCWLEiEQPDIVEGIKTCEKNKPEVLVIVFYFLHEGAHVKTDI----NNDL 109
                 445566666799999*******998776..467777764447799*****999558**************9999999999***********....6789 PP

                 HHHHHHTT--EEE----GGGSHHHHHHHHHHHHHH CS
        CbiK 226 kealeaaGikveiilkgLGeieeirsifikhikea 260
                 k ale+  ik   i k LG +e++ ++ i++ ke+
  EPA05887.1 110 KPALENSSIKKAYITKHLGVDEKMIDLIIERAKEV 144
                 ******************************99986 PP

>> Ferrochelatase  Ferrochelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0     0.059   3.5e+02     160     193 ..       2      38 ..       1      63 [. 0.84
   2 ?   11.2   0.1   2.3e-05      0.14     241     314 ..      70     142 ..      59     145 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.059
                     -HHHHHHHHHHHHHHHTTS-...HC.C-EEEEEEE-- CS
  Ferrochelatase 160 hpgyiealaesikealeelp...eekkakllfsaHgl 193
                     h+++i+ + ++i  +l+e++   ++k +++l+  Hg 
      EPA05887.1   2 HKTLINLVENRIAITLQENQvtiPKKDVDVLIIGHGS 38 
                     8899999999999999999899855569999999995 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 2.3e-05
                     SSBHHHHHHHHCCC.-S-EEEE-TT-SS--HHHHIIIIIIIITTSTT..CCCEEE----TT-HHHHHHHHHHHH CS
  Ferrochelatase 241 ePdtddtleelaekgvkaivvvpigFvsDhlEtleeldiearelaeeaggekfvrvptlndspafiealadlve 314
                     +Pd+ + ++ +++++  +++v+   F  +   ++ +++  ++ ++e+++++k    + l+ ++++i+++ + ++
      EPA05887.1  70 QPDIVEGIKTCEKNK-PEVLVIVFYFLHEGAHVKTDINNDLKPALENSSIKKAYITKHLGVDEKMIDLIIERAK 142
                     699999999999887.9**************************************************9988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1060.00
//
Query:       EPA05888.1  [L=109]
Description: CobB/CobQ-like glutamine amidotransferase domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-17   63.5   0.2    2.1e-17   63.4   0.2    1.0  1  GATase_3  CobB/CobQ-like glutamine amidotransferase domain
  ------ inclusion threshold ------
       0.01   15.9   0.6      0.014   15.4   0.6    1.2  1  DUF1836   Domain of unknown function (DUF1836)


Domain annotation for each model (and alignments):
>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.4   0.2   2.3e-21   2.1e-17      64     154 ..       1      89 [.       1     108 [. 0.82

  Alignments for each domain:
  == domain 1  score: 63.4 bits;  conditional E-value: 2.3e-21
    GATase_3  64 ldeaikeaaeaggpvlgiCGGlqmLGeeiedpegvegeageveglglLdietefekekltgqvegevel....aaegeevkGyEiHsGrtilkek 154
                 ++  ik++ae+ +p++++CGGl++L ++i   + +     + +++gl+d++t+++k+  ++ ++g++ l    ++++ e+ G+E+H+++  +  +
  EPA05888.1   1 MKTTIKKLAEDCAPIYAECGGLMYLTKSIDYGN-K-----KFKMIGLFDADTKMTKKMKLNYTKGKIVLknsiTNKTHELHGHEFHYSELDSVSP 89 
                 6889************************97654.3.....8***************877778888877799998899***********7665443 PP

>> DUF1836  Domain of unknown function (DUF1836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.6   1.6e-06     0.014      11      51 ..      23      64 ..      20      75 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.6e-06
     DUF1836 11 Lyldqvvelvnqvleslkrned.kvltktminNYvKkkllek 51
                +yl + +++ n++++ +   +  +++tk m  NY+K k++ k
  EPA05888.1 23 MYLTKSIDYGNKKFKMIGLFDAdTKMTKKMKLNYTKGKIVLK 64
                799999**********9998777**************98755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 694.62
//
Query:       EPA05889.1  [L=33]
Description: hypothetical protein BG20_I2469, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (33 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      183  (0.0102069); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.29u 0.24s 00:00:00.53 Elapsed: 00:00:00.37
# Mc/sec: 268.84
//
Query:       EPA05890.1  [L=51]
Description: hypothetical protein BG20_I2470 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.06   13.1   0.0       0.06   13.1   0.0    1.0  1  CAP_assoc_N  CAP-associated N-terminal


Domain annotation for each model (and alignments):
>> CAP_assoc_N  CAP-associated N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   3.4e-06      0.06      18      60 ..       3      46 ..       1      50 [. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.4e-06
  CAP_assoc_N 18 kdpseygyewwvYnedykeyiqvgvedgkVvtlytngeeia.ik 60
                 ++p++ ++++  Y++ ++ey+ +  edg++v++++  + +   +
   EPA05890.1  3 ESPEKIEFKMLDYKRIENEYVSFELEDGTIVKVKVDLDRVGiAT 46
                 57889999*************************99877776555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.43
# Mc/sec: 358.66
//
Query:       EPA05891.1  [L=257]
Description: hypothetical protein BG20_I1658 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-05   25.1   0.0        0.2   11.7   0.0    2.4  2  tRNA_anti-codon  OB-fold nucleic acid binding domain
  ------ inclusion threshold ------
      0.021   14.7   0.0       0.47   10.3   0.0    2.2  2  POT1PC           ssDNA-binding domain of telomere protection 
      0.086   12.2   0.1       0.13   11.6   0.1    1.3  1  RNA_pol_Rpb1_1   RNA polymerase Rpb1, domain 1


Domain annotation for each model (and alignments):
>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   3.3e-05       0.2      18      70 ..      94     148 ..      69     163 .. 0.72
   2 !   11.1   0.0   4.9e-05      0.29       5      56 ..     191     247 ..     188     256 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.3e-05
                      EEEEEEEETTEEEEEEEET.HHHHHHHTTS-TTSEEEEE.EEEEECTTSSEEEEE CS
  tRNA_anti-codon  18 vifidlrDgtgriqvvlfr.eeatklaenlkeGdvvrvt.Grvkrrpggelelkv 70 
                      + ++++ D   +  v l++ ++     e++k+Gd++++   +vk++ +g +++++
       EPA05891.1  94 LRTMTVYDANSTASVKLWDdKANLPGIEDIKPGDLIKIIkAYVKSDLNGSPTINI 148
                      456889*************6666667899****************9777455544 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 4.9e-05
                      EEEEEEE....EEEETTEEEEEEEETT.EEEEEEEETHHHHHHHTTS-TTSEEEEEE CS
  tRNA_anti-codon   5 Grvtsis....drsggkvifidlrDgt.griqvvlfreeatklaenlkeGdvvrvtG 56 
                      G v+s++    +++ gk++ + l+ +  g+++vvl+ ++ t++ + +  +  vr  G
       EPA05891.1 191 GNVSSMEftnsRGQPGKALRMRLKGKDgGMMRVVLWGKDETDIPNMISQNAKVRLLG 247
                      666666677777999************99*************999999999999986 PP

>> POT1PC  ssDNA-binding domain of telomere protection protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   7.8e-05      0.47      76     115 ..     103     143 ..      75     182 .. 0.82
   2 ?    2.5   0.0      0.02   1.2e+02      78     110 ..     220     252 ..     194     257 .] 0.86

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 7.8e-05
                 S-EEEEEE-HHHHHHHTTT.--TT-EEEEEEEEEEE-TTS. CS
      POT1PC  76 kltlqitlydehaefaren.lkpgdfvrLrNvhiklgrkgs 115
                 + t+ + l+d+ a++   + +kpgd++++    +k + +gs
  EPA05891.1 103 NSTASVKLWDDKANLPGIEdIKPGDLIKIIKAYVKSDLNGS 143
                 56899**********99988*********998888777775 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.02
                 EEEEEE-HHHHHHHTTT--TT-EEEEEEEEEEE CS
      POT1PC  78 tlqitlydehaefarenlkpgdfvrLrNvhikl 110
                 ++ ++l+++  + +++ +++++ vrL  v+ik 
  EPA05891.1 220 MMRVVLWGKDETDIPNMISQNAKVRLLGVNIKK 252
                 689************99*************985 PP

>> RNA_pol_Rpb1_1  RNA polymerase Rpb1, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   2.1e-05      0.13     271     306 ..     184     218 ..     145     225 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.1e-05
                     HHHHCC-TTSSSSSEEBSTTSSS--THHHHHTSSSS CS
                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  RNA_pol_Rpb1_1 271 hvatlfdneisglkpatqkskrplkslsqrLkGKeG 306
                      +  ++d ++s+  ++t++ ++p k+l+ rLkGK G
      EPA05891.1 184 VISGIIDGNVSS-MEFTNSRGQPGKALRMRLKGKDG 218
                     467789999999.556999***************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       735  (0.040995); expected 358.6 (0.02)
Passed bias filter:                      604  (0.0336884); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 1716.12
//
Query:       EPA05892.1  [L=303]
Description: hypothetical protein BG20_I1653 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.9e-46  156.9   3.3      8e-46  156.6   3.3    1.0  1  DUF354    Protein of unknown function (DUF354)
    0.00054   18.9   0.1    0.00076   18.4   0.1    1.3  1  LpxB      Lipid-A-disaccharide synthetase
  ------ inclusion threshold ------
      0.046   13.4   0.7      0.066   12.8   0.7    1.2  1  AAA_12    AAA domain


Domain annotation for each model (and alignments):
>> DUF354  Protein of unknown function (DUF354)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.6   3.3   1.3e-49     8e-46       1     300 [.       1     298 [.       1     302 [. 0.91

  Alignments for each domain:
  == domain 1  score: 156.6 bits;  conditional E-value: 1.3e-49
      DUF354   1 ldvwidltnaphvryfrdlikkfekeGievlltardsGdlaklvklynfvfksiGkhGvtlk.ekliesakrvinlskliaevkpdvalakhsvelprv 98 
                 +++wid+     + +   +i+k+ k+  +vl t r + +++kl k+ nf+  siGkhG t k  kl  s +r+ +ls li +  pd+ ++  s e  rv
  EPA05892.1   1 MKIWIDILTPKQLLFSEPIIEKLGKK-HNVLCTSRSYDEVTKLAKIRNFNLISIGKHGGTEKyGKLEASIDRIKKLSLLINKFSPDLVISFCSPEAARV 98 
                 59*****9988888889999999886.78******************************988469999******************************* PP

      DUF354  99 afGlnipvvyvldnehaeaankltlpladeiikpividendlkktGadpnrirryeGtsevinvqsyeideeilkdlnlkledektilmrpepslasyl 197
                 +fG++i  +   d  ha+a  kltlpl ++++ p vi ++++ k+G d   i +y+     + ++   i+++  + l +k +++k il+r e  +a+y 
  EPA05892.1  99 SFGMGIKHIAFCDSPHANAVMKLTLPLIQKLLIPSVIPKKEFSKYGIDSKNIIQYKAIDAAVTIKR-RINQK--DPLPFKNNHKKNILIRVEEEQAAYT 194
                 ************************************************999999**9888887776.34443..56788889****************9 PP

      DUF354 198 dadchkdvltkiveklkdrid..ilviprdeeqkeiyeev..dnviviketvdalsllkrsdlviGaGGtmnreaallGipvvscypqkllsvdkylie 292
                      k +++ i e + ++ +  i+++ r+ eq +  +++  +++ +ik + d   ll ++++ +G+GGtm  e+allG+p++s y   +  v+kyl++
  EPA05892.1 195 TK--SKRIIPIIKEIVDEFGEenIVILGRYSEQIKNLKKLfgKKAKIIKMSFDGKHLLSETNVFLGSGGTMTAESALLGVPTIS-YNAVPNIVEKYLVK 290
                 98..8999999999999876556**********8777765345699*************************************9.8999999******* PP

      DUF354 293 kdlmirst 300
                 k+l+ + +
  EPA05892.1 291 KNLVKKGN 298
                 *9988766 PP

>> LpxB  Lipid-A-disaccharide synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   1.3e-07   0.00076     227     306 ..     218     294 ..     159     298 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.3e-07
                 SSHHHHHHHHHHHHHH-TT---EEEES-HHHHHHH-SEEEESSTTHHHHHHHTT--EEE-----HHHHHHHHHHHHHS-- CS
        LpxB 227 vnkkyeeqileikaeenldvqllllsgealealaaadlaliksGTaaLEaalaktPmvvayrvkpltfflakrlvkikyv 306
                 +   y eqi ++k+++ ++ +++ +s + +++l + ++ l   GT++ E al+++P++ +     +  ++ k+lvk ++v
  EPA05892.1 218 ILGRYSEQIKNLKKLFGKKAKIIKMSFDGKHLLSETNVFLGSGGTMTAESALLGVPTISYNA---VPNIVEKYLVKKNLV 294
                 45679999************************************************985543...445677777776665 PP

>> AAA_12  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.7   1.1e-05     0.066      58     136 ..     163     238 ..     133     256 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.1e-05
      AAA_12  58 ealeepleplvfidvekseeekekkeksyiNeeEaelvvklvekllkkgseeerkkigvitpYraqvellkkklkekee 136
                 ++  +++ pl f + +k++   + +e++ +  +  + ++ +++++++++ ee   +i ++  Y++q++ lkk + +k++
  EPA05892.1 163 KRRINQKDPLPFKNNHKKNILIRVEEEQAAYTTKSKRIIPIIKEIVDEFGEE---NIVILGRYSEQIKNLKKLFGKKAK 238
                 55566677777777777777766666777888889999************99...9****************9987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       701  (0.0390987); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2020.68
//
Query:       EPA05893.1  [L=312]
Description: ABC transporter, ATP-binding protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.6e-29  101.4   0.0    9.8e-29  100.6   0.0    1.4  1  ABC_tran      ABC transporter
    2.2e-13   50.7   0.1    5.8e-07   29.6   0.0    2.3  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    5.1e-06   27.1   1.4    1.7e-05   25.5   1.2    2.0  2  DUF4162       Domain of unknown function (DUF4162)
    7.1e-06   26.0   0.1    0.00036   20.4   0.1    3.0  1  AAA_15        AAA ATPase domain
      0.006   16.3   0.3      0.012   15.4   0.3    1.4  1  AAA_29        P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.042   13.2   0.0      0.067   12.6   0.0    1.4  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.061   13.8   8.0       0.24   11.9   8.0    2.2  1  AAA_23        AAA domain
      0.078   13.2   0.0       0.13   12.5   0.0    1.3  1  SbcCD_C       Putative exonuclease SbcCD, C subunit
      0.094   12.1   1.0         11    5.4   0.0    2.5  3  SMC_N         RecF/RecN/SMC N terminal domain
       0.15   11.7   0.0       0.23   11.1   0.0    1.4  1  AAA_30        AAA domain
        1.1    9.3   5.9        7.4    6.6   0.3    2.5  2  DUF87         Helicase HerA, central domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.6   0.0     6e-32   9.8e-29       2     136 ..      20     162 ..      19     163 .. 0.95

  Alignments for each domain:
  == domain 1  score: 100.6 bits;  conditional E-value: 6e-32
                 EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.............HHHTCHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............xxxxxxxx RF
    ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.............esdeeiek 87 
                 ++v l++k g++ +++G+nGaGKSt +kll+ l  p +G++++ g +  e +  + r++igv+ q+p+  p+ltv+++             e+++++e+
  EPA05893.1  20 DDVVLSVKSGQVFGFLGPNGAGKSTTIKLLTTLIPPSSGSLTILGINAIE-NPLEIRHKIGVILQQPSYEPTLTVEKSldkygmmwnvpknERKKRMEQ 117
                 7899****************************************988888.45567999****************999***********9999999*** PP

                 HHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  88 alsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                 +l+ ++l+++++++     + LS Gq++rv++ar ++ + +ll+lDEpt
  EPA05893.1 118 LLKDFDLVDIRKKRN----EDLSIGQRRRVQVAREFMHDMELLFLDEPT 162
                 *********999998....*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.1   2.5e-07   0.00041       2     106 ..      32     122 ..      31     149 .. 0.82
   2 !   29.6   0.0   3.6e-10   5.8e-07     189     297 ..     119     192 ..     105     196 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.5e-07
      AAA_21   2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrlersqv.eeklssvetllesgll 99 
                  ++ GpNg+GKS+ +++l  l               + ++ +  +  ++ ++   ++++ i  + +q + y+  l++e+s   + +  +v++++++  +
  EPA05893.1  32 FGFLGPNGAGKSTTIKLLTTL--------------IPPSSGSLTILGINAIENPLEIRHKIG-VILQQPSYEPTLTVEKSLDkYGMMWNVPKNERKKRM 115
                 5789**************666..............89999999*******************.*****************9996666666666666655 PP

      AAA_21 100 ldkrsle 106
                  + + ++
  EPA05893.1 116 EQLLKDF 122
                 5555444 PP

  == domain 2  score: 29.6 bits;  conditional E-value: 3.6e-10
      AAA_21 189 vrslklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr 287
                 ++ ++lv+i+   ++                                +lS G++r   ++  +  +     ll++DEp  gL+P++ r+ll+ lk++ +
  EPA05893.1 119 LKDFDLVDIRKKRNE--------------------------------DLSIGQRRRVQVAREFMHDM---ELLFLDEPTVGLDPSARRKLLDYLKNKVK 182
                 555555555555553................................44666666655555555555...89*************************** PP

      AAA_21 288 ngaQviltTH 297
                 +g  ++ tTH
  EPA05893.1 183 TGLTIFYTTH 192
                 ********** PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       4.5   7.4e+03      47      61 ..     167     181 ..     162     184 .. 0.80
   2 !   25.5   1.2     1e-08   1.7e-05       2      81 .]     217     305 ..     217     305 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 4.5
                 --------------- CS
     DUF4162  47 eeaanellkaltsgv 61 
                  +a+++ll++l+++v
  EPA05893.1 167 PSARRKLLDYLKNKV 181
                 578899999998877 PP

  == domain 2  score: 25.5 bits;  conditional E-value: 1e-08
                 -HHHHHTTS.-SSEEEEE..-------..--.-EEEE-T.T..S-EEEEE--.-----------.----EEEEEEEE---HHHHHHHHH CS
     DUF4162   2 tleeiKrsy.gknrieve..adaeelleepg.veeveee.g..gelelkled.eeaanellkal.tsgveirsFeeeePsLndIFiekv 81 
                 t+e +K+++ ++++i+++  +++ e+ ++ + + + + + +  ++++++ e+ e +  ++l+ l ++++ei+ ++ ++  L++IF++ v
  EPA05893.1 217 TPEALKNKFgKEKTIKIHllEKQNEITKLLSgIADCKVDfDngTNIVIHSEQsELVLLHILRILnENQIEIEDLSAVPTNLEEIFLKMV 305
                 5789*****7777888**9866777777744488884441334558888887799999******66********************987 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.1   2.2e-07   0.00036      26     211 ..      32     285 ..      13     311 .. 0.54

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.2e-07
      AAA_15  26 tvliGkNnsGKSsilealdlFlnnkekkn....................................kkvikiekedleifeniseskdikIdvef..... 83 
                   + G+N++GKS+ +++l  ++  +   +                                    +k +++    +++ +n+ ++++ ++ + f     
  EPA05893.1  32 FGFLGPNGAGKSTTIKLLTTLIPPS---SgsltilginaienpleirhkigvilqqpsyeptltvEKSLDKYGMMWNVPKNERKKRMEQLLKDFdlvdi 127
                 5589*******************88...22245666666666666666666666666666666664444444455555555555555555555555555 PP

      AAA_15  84 .........................aek.ekakeyektlkskekkkadlllkkkesdlkktikdkklklkknelsdekisvekkks....kkelpkeke 152
                                          + +  + +e  + l++++++k   +lk+k +   +++ + ++  ++++l de+  ++k k     + e  k+k 
  EPA05893.1 128 rkkrnedlsigqrrrvqvarefmhdM-ElLFLDEPTVGLDPSARRKLLDYLKNKVKTGLTIFYTTHILSEAEYLCDEIAIIDKGKIltvdTPEALKNKF 225
                 55555555555555555555544431.134555555555566666555555555554444444444444433333333333333335555555555555 PP

      AAA_15 153 eklekekeelkidkedlkklikkleeslkkee.elknvlksaiiklllisakRnvsdeds 211
                  k+++ k +l  ++++++kl++ +  ++   +   + v+ s++ +l l +  R  ++++ 
  EPA05893.1 226 GKEKTIKIHLLEKQNEITKLLSGIADCKVDFDnGTNIVIHSEQSELVLLHILRILNENQI 285
                 555555555555566666665555544433334444444444444444444444444433 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.3   7.1e-06     0.012      13      49 ..      20      56 ..      17      61 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 7.1e-06
      AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiqalLvpa 49
                d+ +++++  +++ + Gp+G+GKST +  +++l+ p+
  EPA05893.1 20 DDVVLSVKSGQVFGFLGPNGAGKSTTIKLLTTLIPPS 56
                556677774448999************8777777665 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   4.1e-05     0.067      11      81 ..      18      89 ..       8      97 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.1e-05
  Mg_chelatase 11 akraleiaaaGgHnlllvGppGsGKtmlakrlpsllpplsee.ealevakiasvagkkeeekllkrrpfrap 81
                  a   + +++  g  + ++Gp G+GK+  +k l++l+pp s +  +l +++i+   + +++ +++ ++p  +p
    EPA05893.1 18 AVDDVVLSVKSGQVFGFLGPNGAGKSTTIKLLTTLIPPSSGSlTILGINAIENPLEIRHKIGVILQQPSYEP 89
                  555555666666667799*******************98864255666666666666666666666666665 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   8.0   0.00015      0.24      15     176 ..      24     240 ..       4     300 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00015
      AAA_23  15 idF.skgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiese....gkvkay.veltfenkdgrytrsiererelskkkgkttkka 107
                 +   s  ++ + GpNGaGK+T +  ++      ++   +  g ++ ++  ei ++     ++++y  +lt+e+  +  ++ + ++ ++++ k++  +  
  EPA05893.1  24 LSVkSGQVFGFLGPNGAGKSTTIKLLTTLIPPSSG-SLTILGINAIENPLEIRHKigviLQQPSYePTLTVEKSLD--KYGMMWNVPKNERKKRMEQLL 119
                 444456799**************999987655433.3333455555555555555545444444444444444444..356777777777666555544 PP

      AAA_23 108 .klellei.deleqfisellgskki.ilnlilflgqer..................feefelkdkke................................ 153
                  +++l++i +++++ +s  +g++ + +  + ++++ e                             +                                
  EPA05893.1 120 kDFDLVDIrKKRNEDLS--IGQRRRvQVAREFMHDMELlfldeptvgldpsarrklL---------Dylknkvktgltifytthilseaeylcdeiaii 207
                 14555555444444444..33333334455555544444444445554444322221.........122233336677777777777777777766666 PP

      AAA_23 154 .........rleelekeleeled.ekkllekle 176
                            e+l++++ ++++ ++ llek++
  EPA05893.1 208 dkgkiltvdTPEALKNKFGKEKTiKIHLLEKQN 240
                 666666666666666666555552333555443 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     8e-05      0.13      62      89 ..     151     178 ..     138     179 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8e-05
     SbcCD_C  62 palrlvfLDEAFsklDeesiatllelle 89 
                 ++++l+fLDE   +lD+  +++ll++l+
  EPA05893.1 151 HDMELLFLDEPTVGLDPSARRKLLDYLK 178
                 6799*********************997 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0    0.0095        15      28      41 ..      33      46 ..      16      53 .. 0.80
   2 ?    5.4   0.0    0.0065        11     156     190 ..     150     184 ..      84     206 .. 0.73
   3 ?   -2.6   0.1       1.8     3e+03     106     138 ..     257     291 ..     223     300 .. 0.57

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0095
                EEEESTTSSHHHHH CS
                xxxxxxxxxxxxxx RF
       SMC_N 28 aivGpNGSGKsnll 41
                  +GpNG+GKs  +
  EPA05893.1 33 GFLGPNGAGKSTTI 46
                468********866 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0065
                 CS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTS CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       SMC_N 156 vkpaplyllDeidaaLDeknvkkvaellkekskna 190
                 ++   l +lDe    LD + ++k+ ++lk+k k+ 
  EPA05893.1 150 MHDMELLFLDEPTVGLDPSARRKLLDYLKNKVKTG 184
                 45566899*********************998763 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.8
                 TSEEEEEETTEEE-H..HHHHHHHHCTT-STTCS- CS
                 xxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxx RF
       SMC_N 106 kgeseykingkevtk..kevsellesagiskelLS 138
                 ++ +++ i  ++ +     + ++l++ +i++e LS
  EPA05893.1 257 DNGTNIVIHSEQSELvlLHILRILNENQIEIEDLS 291
                 33344444333333322455556666666666555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00014      0.23      15      47 ..      27      58 ..      17     128 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00014
      AAA_30 15 tsgdrvavltGpAGtGKttalkalreaweaagg 47
                +sg +v    Gp G+GK+t++k l+ ++  + g
  EPA05893.1 27 KSG-QVFGFLGPNGAGKSTTIKLLTTLIPPSSG 58
                455.488899**************998876644 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.3    0.0045       7.4      26      46 ..      32      52 ..      14      63 .. 0.83
   2 ?    5.4   0.8      0.01        17     154     224 ..     235     306 ..     117     309 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0045
       DUF87 26 lAilgsTGsGKSntvavLlee 46
                ++ lg  G+GKS+t+++L   
  EPA05893.1 32 FGFLGPNGAGKSTTIKLLTTL 52
                6778999**********9865 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.01
       DUF87 154 keelrklknqaiarlldkledllrkggsf.snsstdliallleklekegkitiidlsgvdelaqqlvvsvil 224
                  +e +++ +++ +++ d + d+++ ++   ++++++l+ l    + +e++i i dls v+ +  +++  +++
  EPA05893.1 235 LLEKQNEITKLLSGIADCKVDFDNGTNIViHSEQSELVLLHILRILNENQIEIEDLSAVPTNLEEIFLKMVS 306
                 337778888888889999999999888888777777777777788899***************999988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       767  (0.0427799); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 1981.24
//
Query:       EPA05894.1  [L=212]
Description: nucleic acid-binding domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.1e-06   25.5   0.1    1.8e-05   24.5   0.0    1.5  2  CDC24_OB3        Cell division control protein 24, OB domain 
    1.8e-05   24.6   0.2    0.00082   19.3   0.0    2.6  3  tRNA_anti-codon  OB-fold nucleic acid binding domain


Domain annotation for each model (and alignments):
>> CDC24_OB3  Cell division control protein 24, OB domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0      0.61   5.5e+03      37      37 ..      53      53 ..      25      75 .. 0.50
   2 !   24.5   0.0   2.1e-09   1.8e-05      17      74 ..     133     192 ..     124     209 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.61
   CDC24_OB3 37 e 37
                +
  EPA05894.1 53 D 53
                2 PP

  == domain 2  score: 24.5 bits;  conditional E-value: 2.1e-09
   CDC24_OB3  17 ai..freknsek.kkmdryslrieDttGaidatlweeagklhfkrlrvGhlvllsgLatse 74 
                 +i   re+++++ +++  + + +eD+tG+i++  w++ ++l++k +++G+++ ++g++ ++
  EPA05894.1 133 KIpeRREIQTKSgESILLSEMFVEDDTGQIWVKGWRNQARLIDK-CELGEIISITGVNAKS 192
                 555433666677789999**************************.***********98775 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0         1     9e+03      60      75 ..       6      20 ..       4      21 .. 0.72
   2 ?    2.7   0.0     0.014   1.3e+02       3      36 ..      32      65 ..      32      94 .. 0.81
   3 !   19.3   0.0   9.2e-08   0.00082      21      72 ..     153     204 ..     138     208 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1
                     ECTTSSEEEEEEEEEE CS
  tRNA_anti-codon 60 rrpggelelkveeiel 75
                       ++g le++ ++ ++
       EPA05894.1  6 NGNQG-LEIHGNDSTI 20
                     56788.9999988665 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.014
                     EEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET CS
  tRNA_anti-codon  3 vaGrvtsisdrsggkvifidlrDgtgriqvvlfr 36
                     v +r+ si ++++gk + + ++++  + +++ f+
       EPA05894.1 32 VIARILSITTTESGKNMILGVDNKKNIYNITDFS 65
                     6799*****999****999999998877777666 PP

  == domain 3  score: 19.3 bits;  conditional E-value: 9.2e-08
                      EEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEEEEEEEC..TTSSEEEEEEE CS
  tRNA_anti-codon  21 idlrDgtgriqvvlfreeatklaenlkeGdvvrvtGrvkrr..pggelelkvee 72 
                      + ++D+tg+i v  +r ++ +l ++ + G ++ +tG   ++  +g+ +el+ + 
       EPA05894.1 153 MFVEDDTGQIWVKGWR-NQARLIDKCELGEIISITGVNAKSglEGR-IELTLTA 204
                      5589************.******************99888887777.8887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1354.97
//
Query:       EPA05895.1  [L=250]
Description: hypothetical protein BG20_I1656 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.1e-07   29.5   0.5     0.0061   16.1   0.0    2.3  2  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
    6.4e-06   26.4   0.0    1.3e-05   25.4   0.0    1.5  1  TrkA_N          TrkA-N domain
      0.001   19.2   0.0     0.0024   18.0   0.0    1.7  1  UDPG_MGDP_dh    UDP-glucose/GDP-mannose dehydrogenase family,
  ------ inclusion threshold ------
      0.026   14.7   0.0        0.2   11.8   0.0    2.3  2  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
      0.034   12.9   0.0      0.048   12.4   0.0    1.2  1  OKR_DC_1        Orn/Lys/Arg decarboxylase, major domain
      0.056   12.8   0.0      0.098   12.0   0.0    1.4  1  GDP_Man_Dehyd   GDP-mannose 4,6 dehydratase
       0.06   12.9   0.0      0.092   12.3   0.0    1.4  1  DUF166          Domain of unknown function


Domain annotation for each model (and alignments):
>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   2.4e-06    0.0061       5      47 ..       5      47 ..       1      59 [. 0.89
   2 !   11.4   0.1   6.6e-05      0.17     103     131 ..      65      93 ..      56      99 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.4e-06
                    EE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS- CS
  UDPG_MGDP_dh_N  5 viGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiy 47
                    ++G+G vG +   +l e+g++ +g+D+d++k ++  ++++ i 
      EPA05895.1  5 ILGMGEVGSTLYELLVERGFDCVGIDNDKSKCRNYSENESIIK 47
                    89******************************99999888775 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 6.6e-05
                     HHHHHHHHHHCEEEEEE-S---TTHHHHC CS
  UDPG_MGDP_dh_N 103 aarsiaealkkgkvvvvkSTvpvgtaeel 131
                     ++ +  + +k+ +vvv+ STv +gt++ l
      EPA05895.1  65 ITSKWINKIKDLQVVVIHSTVRPGTTKSL 93 
                     445555678999**************965 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   5.2e-09   1.3e-05       2      40 ..       4      42 ..       4      52 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 5.2e-09
                EEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHT CS
      TrkA_N  2 iiiGlGrvGrslaeeLseggkdvvvidkdeerveelree 40
                ii+G+G+vG++l+e L e+g d+v+id+d++++++++e+
  EPA05895.1  4 IILGMGEVGSTLYELLVERGFDCVGIDNDKSKCRNYSEN 42
                8*****************7768************99876 PP

>> UDPG_MGDP_dh  UDP-glucose/GDP-mannose dehydrogenase family, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   9.4e-07    0.0024       1      64 [.     153     218 ..     153     247 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 9.4e-07
  UDPG_MGDP_dh   1 etAEliKl.aaNaflatkIsfiNelanlcealgidveeVieavgldpr.igpkf.lkpglGvGGscl 64 
                   +tAEl+K+ ++ ++    I ++   +++c++  id +e ++ +   ++ +g++  ++pg+ +GG+c+
    EPA05895.1 153 KTAELAKIlVDTTYYGWLINYAQITKMICDKEKIDFDEMWKFADEIHEnLGNRPkMYPGI-IGGHCV 218
                   59*****73688999***************************9886444888877****9.*****7 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   7.8e-05       0.2       5      42 ..       6      43 ..       4     108 .. 0.80
   2 ?   -1.8   0.0       1.2   3.2e+03      69     104 ..     162     198 ..     115     202 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.8e-05
                   E--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT CS
  NAD_binding_2  5 iGlGvMGsnmalnllkagykvavynrtkekveelvaeg 42
                   +G+G+ Gs + + l+++g++ ++++ +k+k+++  +++
     EPA05895.1  6 LGMGEVGSTLYELLVERGFDCVGIDNDKSKCRNYSENE 43
                   7******************************9998877 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.2
                    HHHHHHS.HCCC--TT-EEEE-S---HHHHHHHHHHH CS
  NAD_binding_2  69 vdevieg.llealkkgdilidgstsspedtrelakel 104
                    vd+++ g l+++++  +++ d   +++++  ++a+e+
     EPA05895.1 162 VDTTYYGwLINYAQITKMICDKEKIDFDEMWKFADEI 198
                    3444444677777777777777777777766666665 PP

>> OKR_DC_1  Orn/Lys/Arg decarboxylase, major domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.9e-05     0.048     158     212 ..     144     198 ..     122     226 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.9e-05
                 HHHHHSTTTGSESE.EEEESS-TTSEEE-HHHHHHHHTTSESEEEEE-TT-TTGGG CS
    OKR_DC_1 158 ekikevpdakaprl.avitnsTYdGvlynakeivdkleklsdrilfDeAwvgyeqf 212
                 +ki+ ++ +k+  l  ++  +TY+G l n  +i++ +  +  +i fDe w    ++
  EPA05895.1 144 QKIQWMSTTKTAELaKILVDTTYYGWLINYAQITKMICDKE-KIDFDEMWKFADEI 198
                 45555555555444158889****************99887.9*******765555 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   3.8e-05     0.098       5      35 ..       7      37 ..       4      55 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.8e-05
                   TTSHHHHHHHHHHHHCT-CCEEEEEEESS-T CS
  GDP_Man_Dehyd  5 iaGfiGsylaelLlekgyevhgivrrsssfn 35
                   + G +Gs l elL+e+g++++gi++++s+ +
     EPA05895.1  7 GMGEVGSTLYELLVERGFDCVGIDNDKSKCR 37
                   6799*********************998753 PP

>> DUF166  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   3.6e-05     0.092       2      73 ..       5      96 ..       4     136 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.6e-05
      DUF166  2 vltsgeyGervvenilnepdfersl...................ivavvevpeeldefiedpeelLpelkeaDivia.ytlhpDlllelaek 73
                +l  ge G++++e + +++  ++ +                    + +v +p+el+efie++++ ++++k+  +v+   t+ p  + +l +k
  EPA05895.1  5 ILGMGEVGSTLYELLVERGFDCVGIdndkskcrnysenesiikpEYLHVCLPGELNEFIEITSKWINKIKDLQVVVIhSTVRPGTTKSLQDK 96
                56667888888888888877776668888888888999987777777888899******************998764155666666555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       840  (0.0468515); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1749.50
//
Query:       EPA05896.1  [L=266]
Description: DEAD/DEAH box helicase, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.5e-28   99.0   0.1    4.3e-28   98.3   0.1    1.4  1  DEAD        DEAD/DEAH box helicase
    1.3e-11   44.8   0.0    1.9e-11   44.3   0.0    1.3  1  ResIII      Type III restriction enzyme, res subunit
    2.2e-06   28.0   0.1     0.0027   18.0   0.0    2.4  2  Helicase_C  Helicase conserved C-terminal domain
    0.00057   18.7   0.0    0.00079   18.2   0.0    1.2  1  SNF2_N      SNF2 family N-terminal domain
  ------ inclusion threshold ------
      0.044   13.5   0.0      0.066   12.9   0.0    1.2  1  SWI2_SNF2   SWI2/SNF2 ATPase
      0.068   13.5   0.1       0.16   12.3   0.1    1.6  1  AAA_19      AAA domain
       0.12   12.7   0.1       0.98    9.7   0.0    2.4  2  OKR_DC_1_N  Orn/Lys/Arg decarboxylase, N-terminal domain


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.3   0.1   1.7e-31   4.3e-28      19     170 ..       1     151 [.       1     156 [. 0.88

  Alignments for each domain:
  == domain 1  score: 98.3 bits;  conditional E-value: 1.7e-31
                 EEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHHHHHHHTT.CSEEEEEHHHHHHHH.HCT CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx.xxx RF
        DEAD  19 vaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaardqlskldng.vdivvgtpgrlddll.stg 115
                 v a+TGsGKT++ +ip+++ v ++k+  + k+l+++P+r+L ++++++++k+ +  +l+++ i +g++++  ++k++++ +d++++tp+ l+ ll + +
  EPA05896.1   1 VIAPTGSGKTECSVIPIFSLVKKSKKIGKIKVLYITPLRALNRDVFRRITKYAQSNELSIE-IRHGDTTQTARRKISENpPDVLITTPETLVILLtQIK 98 
                 579***************999988******************************9888887.566788888888886556*************884555 PP

                 SSH.CTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEEEEEESSBS CS
                 xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        DEAD 116 kln.lsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrqvivlSATlp 170
                  ln ls+++++++DE+++ll ++++ +++  +++l q +++ +l+   i lSAT+ 
  EPA05896.1  99 MLNaLSELEWIIIDEVHELLGSERGSQLSLSIERL-QLNSKFSLT--KIGLSATVG 151
                 5779*******************************.677777766..9******86 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   0.0   7.4e-15   1.9e-11      30     169 ..       2     150 ..       1     152 [. 0.84

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 7.4e-15
                 EESTTSTHHHHHHHHHHHH-S........-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B--.........-SEEEEEHHHHHHTH..... CS
      ResIII  30 kmaTGtGKTlvaaklierllkkgkee...kflflvprkslleqtleefkkflseaykeigkkvsgdkkka..kekdstnkkilvttiqsldadseeeee 123
                  ++TG+GKT +++  i +l kk k+    k+l + p ++l     ++++k+++++     ++ +gd+ +   ++++++  ++l+tt ++l   +   ++
  EPA05896.1   2 IAPTGSGKTECSVIPIFSLVKKSKKIgkiKVLYITPLRALNRDVFRRITKYAQSNEL-SIEIRHGDTTQTarRKISENPPDVLITTPETLVILL---TQ 96 
                 579*********88888888876654799***********************99976.6777788887777778889999**************...99 PP

                 ...HHHTTT-SEEEEETGGGTTS.T.......TTHHH..HHT---SEEEEEESS- CS
      ResIII 124 eseellrdrfdviiiDEaHrlgakk.......swrei..lekfkeavllglTATp 169
                  +  +  ++ + iiiDE+H l +++       s++++  + kf+  +++gl+AT 
  EPA05896.1  97 IKMLNALSELEWIIIDEVHELLGSErgsqlslSIERLqlNSKFS-LTKIGLSATV 150
                 99999999999***********9855556667777755355555.99*******6 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0    0.0015       3.9      31      72 ..      43      85 ..      14     123 .. 0.73
   2 !   18.0   0.0   1.1e-06    0.0027      10      66 ..     201     257 ..     191     264 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0015
                H......HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEE CS
  Helicase_C 31 k......vklllekkgikvavlhgelpqnereeileqfnkgesdvLia 72
                +      +k+  +++++++ + hg+++q  r++i e+      dvLi+
  EPA05896.1 43 RdvfrriTKYA-QSNELSIEIRHGDTTQTARRKISENPP----DVLIT 85
                22333334555.5668******************99874....35554 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 1.1e-06
                 HHHTTTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTS CS
  Helicase_C  10 lkleeeggkilifvntidrlek.vklllekkgikvavlhgelpqnereeileqfnkge 66 
                 l + + ++ +l+f+nt+ ++e  +++l+ek+ i++  +hg+l+++ re++  + ++g+
  EPA05896.1 201 L-ELNLDSPVLLFTNTRGEAEFlASILKEKSTISIELHHGSLSKEVREDTELSLREGT 257
                 3.45678899********9988899999999******************999888876 PP

>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   3.1e-07   0.00079      99     211 ..      32     141 ..       5     144 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.1e-07
                 EEEE--H.HHHHHHHHHHHHH-TTS-EEE--SSHHHH-----------------EEEE-HHHHHHHT......TTS-S-S-SEEEES-GGGT--T..TS CS
                 xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xx RF
      SNF2_N  99 tLivvPa.slldqWeneierhvsssalrvlvyggqkkmkkkntkvapklladydvvittYdvlsreaelqkkrsvlkqvewkrvvlDEghtlkns..ts 194
                 +L + P  +l +   + i ++++s +l + + +g+++++ +     +   +  dv+itt ++l       k  ++l+++ew  +++DE h l  s   s
  EPA05896.1  32 VLYITPLrALNRDVFRRITKYAQSNELSIEIRHGDTTQTAR----RKISENPPDVLITTPETLVILLTQIKMLNALSELEW--IIIDEVHELLGSerGS 124
                 66677776777777889***************998754444....34445578***********99966677777777777..9******987664668 PP

                 HHHHHHHH---S-EEEE CS
                 xxxxxxxxxxxxxxxxx RF
      SNF2_N 195 kaaeavskLstsnrwil 211
                 +++  +++L+ + +  l
  EPA05896.1 125 QLSLSIERLQLNSKFSL 141
                 99999988887766655 PP

>> SWI2_SNF2  SWI2/SNF2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.6e-05     0.066      27     130 ..       5     115 ..       2     142 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.6e-05
   SWI2_SNF2  27 qGSGKsltmvflakklle.e.elknpkvvvvtDRkdLdkQlsktfakageekp.....kqaesrkeLkellekesekiifttiqKfe...eeekeklev 115
                 +GSGK+  +v+   +l++ + +  + kv+ +t  + L++ +++ ++k  ++++     ++ +++++ +++++++ +++++tt + +    + + + l++
  EPA05896.1   5 TGSGKTECSVIPIFSLVKkSkKIGKIKVLYITPLRALNRDVFRRITKYAQSNElsieiRHGDTTQTARRKISENPPDVLITTPETLVillT-QIKMLNA 102
                 7*********99999988534779********************9998544431222257778889999**999*******9999976532.3334567 PP

   SWI2_SNF2 116 lsereniivlvDEaH 130
                 lse e   +++DE H
  EPA05896.1 103 LSELE--WIIIDEVH 115
                 77766..88999999 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   6.2e-05      0.16      15     114 ..       1     117 [.       1     128 [. 0.65

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.2e-05
      AAA_19  15 vtaGpGtGKTrvlkh.ivallvelggvkpeeillvaftgrAakelrerlaalgae............atTiHrlal..........ldfddlltealel 90 
                 v+a+ G+GKT++ +  i +l+++ +++   ++l +++ +   + +  r++++ ++            ++T                + ++++  + + l
  EPA05896.1   1 VIAPTGSGKTECSVIpIFSLVKKSKKIGKIKVLYITPLRALNRDVFRRITKYAQSnelsieirhgdtTQTAR---RkisenppdvlI-TTPE--TLVIL 93 
                 79********98665155666667777778899999877777777777766666667777777766644444...033345554321.1111..12334 PP

      AAA_19  91 leeaeeekklqeeellivDEfqdv 114
                 l + +  + l e e++i+DE+ ++
  EPA05896.1  94 LTQIKMLNALSELEWIIIDEVHEL 117
                 44777788886667******9875 PP

>> OKR_DC_1_N  Orn/Lys/Arg decarboxylase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.36   9.3e+02      74      93 ..      37      56 ..      13      73 .. 0.66
   2 ?    9.7   0.0   0.00038      0.98      44      86 ..     187     229 ..     146     241 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.36
  OKR_DC_1_N 74 tsedvpadvlreidgfiell 93
                  +++++dv+r+i+++ + +
  EPA05896.1 37 PLRALNRDVFRRITKYAQSN 56
                34556666666666666555 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00038
  OKR_DC_1_N  44 lsvddeaaelldeirernedlPvFllaetrtsedvpadvlrei 86 
                  +++d a+++++ + e+n d Pv l+++tr + ++ a +l+e 
  EPA05896.1 187 GTISDVAEKIIEYVLELNLDSPVLLFTNTRGEAEFLASILKEK 229
                 456699************************9999988888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.69u 0.33s 00:00:01.02 Elapsed: 00:00:00.56
# Mc/sec: 1427.10
//
Query:       EPA05897.1  [L=379]
Description: hypothetical protein BG20_I1652 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.042   13.8   0.0       0.11   12.5   0.0    1.6  1  DUF3783   Domain of unknown function (DUF3783)


Domain annotation for each model (and alignments):
>> DUF3783  Domain of unknown function (DUF3783)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.9e-06      0.11      13      44 ..     271     302 ..     267     303 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.9e-06
     DUF3783  13 ldklldalkkaglpiplkAvlTptNinWtlke 44 
                 ++kl+d+++++  + +lkA+ T+  ++Wtl++
  EPA05897.1 271 IKKLIDEIRSTLKKNDLKASRTKIALSWTLDQ 302
                 789********999***************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.66u 0.33s 00:00:00.99 Elapsed: 00:00:00.53
# Mc/sec: 2155.07
//
Query:       EPA05898.1  [L=253]
Description: ABC-2 type transporter [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.8e-21   74.5  21.2    7.8e-21   74.5  21.2    1.4  2  ABC2_membrane    ABC-2 type transporter
    4.4e-14   52.3  35.7    1.2e-13   50.9  25.4    2.0  2  ABC2_membrane_3  ABC-2 family transporter protein
     0.0036   16.6  19.2     0.0057   16.0  19.2    1.4  1  ABC2_membrane_2  ABC-2 family transporter protein
  ------ inclusion threshold ------
        0.2   11.8   7.4      0.073   13.2   3.5    2.3  2  Phage_holin_4_1  Bacteriophage holin family
       0.38   10.7  17.7       0.02   14.8  10.8    2.0  2  ABC2_membrane_4  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.5  21.2   2.2e-24   7.8e-21      16     210 .]      16     219 ..       4     219 .. 0.83
   2 ?   -3.3   0.6       1.4   4.9e+03     147     160 ..     230     243 ..     222     249 .. 0.43

  Alignments for each domain:
  == domain 1  score: 74.5 bits;  conditional E-value: 2.2e-24
  ABC2_membrane  16 rdpslgllwrliqplllalvfgtvfgnlgnsedglnr..............pgllffsvlflafsaltsvapvferergvlerelvsplyslsayv 97 
                     +p  + +w++i+pl++++v g+++ +l ++                     g+++f +++ +  +++++++  +r++g++e+ ++ p+ ++ +y+
     EPA05898.1  16 INPGFL-IWQVIFPLIYIFVAGFAYTSLIDQ-----VpfgdknidyptflaTGMIGFNIMNST--LISGIIIWNDRRHGMFEQIMSGPF-TRTDYI 102
                    456555.9******************74322.....122344566677788888888888888..999998888999999999999999.****** PP

  ABC2_membrane  98 lakvlvelpvsllqalifllivyflv..gldls..rfflflllllltalaasslgllisalapsfedasqlaslvllpllllsGffipidsmpkwl 189
                    l+++++  +v+l+ a ++ l+ y+++  +++ +   + ++++++++ ++++ s++ +is+ ++s e ++++++ v+l+l ++s +f+p +  p+ l
     EPA05898.1 103 LSNICTIGIVGLASASLIALVGYPVFfdSIEFTiiTIPMIVFAAIVGSVLFGSIASIISTRLRSSEGFNVIINTVFLFLAFVSTAFYPASGSPEPL 198
                    ************************975544443333366777777778888889999999********************************99** PP

  ABC2_membrane 190 qwiaylnPltyavealrsnlf 210
                    +   ylnPlty+v+++r+++f
     EPA05898.1 199 RTAFYLNPLTYLVDVIRAGIF 219
                    *****************9986 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.4
  ABC2_membrane 147 lgllisalapsfed 160
                    +g+l++a ++ f  
     EPA05898.1 230 MGILVAAASVLFII 243
                    33333333333333 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   3.2   0.00046       1.7       2      30 ..      19      44 ..      18      61 .. 0.76
   2 !   50.9  25.4   3.5e-17   1.2e-13     158     344 ..      54     245 ..      43     246 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00046
  ABC2_membrane_3  2 sfliitlllPiilvlllglifsnsvedde 30
                     +fli+++++P+i+++++g+++ +     +
       EPA05898.1 19 GFLIWQVIFPLIYIFVAGFAYTSLI---D 44
                     69*****************965333...3 PP

  == domain 2  score: 50.9 bits;  conditional E-value: 3.5e-17
  ABC2_membrane_3 158 nvasflvg.liliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilll....afglgipfg..nlglllll 244
                      ++  fl++ +i + ++  + ++    i +++++++ e++++ + +++ y+ls+i+++++v+l ++ li l+    +f+ +i+f+   +  +++ 
       EPA05898.1  54 DYPTFLATgMIGFNIM-NSTLISGIIIWNDRRHGMFEQIMSGPFTRTDYILSNICTIGIVGLASASLIALVgypvFFD-SIEFTiiTIPMIVFA 145
                      5556677745555544.44444555789************************************98888753353555.666665588888899 PP

  ABC2_membrane_3 245 fllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwifsiiPffapglgllrlitgdplwe.illsliilalfav 337
                       ++++ ++ +++  +s+  ++se  +++i  v+l+l +++++++p +  p++l+++f+++P++++ +++   i+g+ + e +++ ++il++ a 
       EPA05898.1 146 AIVGSVLFGSIASIISTRLRSSEGFNVIINTVFLFLAFVSTAFYPASGSPEPLRTAFYLNPLTYLVDVIRAGIFGN-ITEfVIMEMGILVAAAS 238
                      999999999999999*******************9**********************************9999***.888566*********** PP

  ABC2_membrane_3 338 vylllal 344
                      v++++a+
       EPA05898.1 239 VLFIIAA 245
                      *****98 PP

>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0  19.2   1.6e-06    0.0057      85     287 ..      67     252 ..      17     253 .] 0.75

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.6e-06
  ABC2_membrane_2  85 ipviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaigla.iavallatvllalaiilalgivlaledllllvvasvlllllvvf 177
                        +  +l++  +i  ++  g  ++ +s P +R +++l+++    ++gla   +++l+++ +        +i++++  +  +v+a++ ++ +  f
       EPA05898.1  67 NIMNSTLISGIIIWNDRRHGMFEQIMSGPFTRTDYILSNICTIGIVGLAsASLIALVGYPV-----FFDSIEFTIITIPMIVFAAI-VGSV-LF 153
                      3344677788889999999999***************************999999999666.....66788888888877777766.4443.48 PP

  ABC2_membrane_2 178 lalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavpqeindflsllsptsayntllneilagsdlnalgstatnllillll 271
                       +++  +S+ +rss+    +   +f++la++++ +  + ++++   ++         +    ++ ++l++ i ag   n        ++il++ 
       EPA05898.1 154 GSIASIISTRLRSSEGFNVIINTVFLFLAFVSTAFYPASGSPEPLRTA--------FY---LNPLTYLVDVIRAGIFGNITEFVIMEMGILVAA 236
                      ************777777777777777777777777666666665555........55...5555556666666653222334456799999** PP

  ABC2_membrane_2 272 lavllvlgyvlFkrkD 287
                      + vl+++++ l+ + D
       EPA05898.1 237 ASVLFIIAAKLLTKLD 252
                      ********99999887 PP

>> Phage_holin_4_1  Bacteriophage holin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.2      0.41   1.5e+03      33      33 ..      91      91 ..      21     139 .. 0.60
   2 ?   13.2   3.5     2e-05     0.073      15      79 ..     141     227 ..     127     249 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.41
  Phage_holin_4_1 33 i 33
                     i
       EPA05898.1 91 I 91
                     3 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 2e-05
  Phage_holin_4_1  15 tallllmviDyltGllaaivegklsskkglkgiikkvlilllvlvah......................llDvllgknletlrtlvi 79 
                      +++++++v  +l+G +a+i++ +l+s+ g++ ii  v+ +l+ +  +                      l+Dv+   ++ +++++vi
       EPA05898.1 141 MIVFAAIVGSVLFGSIASIISTRLRSSEGFNVIINTVFLFLAFVSTAfypasgspeplrtafylnpltyLVDVIRAGIFGNITEFVI 227
                      6788999999**************************998876554444888888888888888888888555555544443333333 PP

>> ABC2_membrane_4  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8  10.8   5.7e-06      0.02      15     178 ..      22     181 ..      19     182 .. 0.76
   2 ?   -0.2   0.6      0.23   8.2e+02     140     157 ..     226     243 ..     203     251 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.7e-06
  ABC2_membrane_4  15 vwllvlaallvpllallyfnllgktgldpaefyslsvfgftlllllplilgiiasylifrEeqndtlknLltiPvsrtklllaKlivllllsvl 108
                      +w +++ ++ + + +++y  l+++  + +++    + + ++++ +  +  ++i++++i + +  +++ +++  P +rt ++l+ ++++ ++ ++
       EPA05898.1  22 IWQVIFPLIYIFVAGFAYTSLIDQVPFGDKNIDYPTFLATGMIGFNIMNSTLISGIIIWNDRRHGMFEQIMSGPFTRTDYILSNICTIGIVGLA 115
                      4555554444444455565566665554444444455566777888889999************************************997555 PP

  ABC2_membrane_4 109 lmlvtflitvlfallsgfvgfsvklvlellkkclelgllvffavlpiialvllkksyvlpliltlvytia 178
                             + +l++  + f +++++ +++ +  +  ++  v+f +++ i+ + l +s  + +i++ v+ ++
       EPA05898.1 116 SA----SLIALVGYPVFFDSIEFTIITIPMIVFAAIVGSVLFGSIASIISTRLRSSEGFNVIINTVFLFL 181
                      54....4556677777777788888888888889999999999999999999***********9999885 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.23
  ABC2_membrane_4 140 kclelgllvffavlpiia 157
                       ++e+g+lv++a++  i+
       EPA05898.1 226 VIMEMGILVAAASVLFII 243
                      245666666655443222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       832  (0.0464053); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 1527.05
//
Query:       EPA05899.1  [L=601]
Description: DEAD/H associated [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-26   93.1   0.0    3.9e-26   92.0   0.0    1.6  1  DEAD_assoc    DEAD/H associated
    0.00011   22.5   0.1    0.00042   20.6   0.1    2.1  1  Helicase_C    Helicase conserved C-terminal domain
  ------ inclusion threshold ------
       0.34   11.5   3.6       0.62   10.6   3.6    1.4  1  Secretin_N_2  Secretin N-terminal domain


Domain annotation for each model (and alignments):
>> DEAD_assoc  DEAD/H associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.0   0.0   6.5e-30   3.9e-26       1     191 []     265     439 ..     265     439 .. 0.92

  Alignments for each domain:
  == domain 1  score: 92.0 bits;  conditional E-value: 6.5e-30
  DEAD_assoc   1 lPtdrtllvErfrdelgdwrlvvhspfGrrvnealalllaarlsrrfgidvqvaanDdgivlll..pleerlpllldellellspd.eleedleaalna 96 
                 +P+++++++E+ r +     +vvhs+fG+++n +l++ll++++s+ +g+ v    + ++ivl++  + +e+l      +l+ ++ d +l +++ a+l +
  EPA05899.1 265 IPDENNIVIESSRSQG---SIVVHSCFGTKINSTLSALLSSMISSMLGSMVDSRSDGYRIVLSSrsRISEKL------FLDVINDDyDLYSLVSASLVG 354
                 7************999...*******************************************8854444443......3455666669*********** PP

  DEAD_assoc  97 selfkrrFrevAaralllprrypgkrkplwqqrlraaqLldvareypdfpllleavrevledqlDlerlaellrriaageirvvevetprpSpfA 191
                 ++ ++++   vA++++++ r+          ++ +a+ L++ ++   ++ l++ea+re ++d++Dle++ ++l++i++++i ++  e +++S +A
  EPA05899.1 355 THNVNWKTWCVAKKFGVVGRGAIY-------EKKSARFLYERYA---KTSLVKEALRELFHDKYDLENTNKILKKIRDNKILIKWLEIDKFSKLA 439
                 **********************99.......8888999998777...*********************************************998 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.1   7.1e-08   0.00042      79     107 ..       2      30 ..       1      33 [. 0.94

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 7.1e-08
                 SSTSTTESEEEESSSSSSHHHHHHHHTTS CS
  Helicase_C  79 GidipkvnlVinfdlprnvtsyiqriGRt 107
                 G+di +++lVi+++ pr+v++++qriGR 
  EPA05899.1   2 GLDIGSIELVIHYGSPRQVSKLVQRIGRS 30 
                 9***************************6 PP

>> Secretin_N_2  Secretin N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   3.6    0.0001      0.62       3      93 ..     227     325 ..     226     327 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0001
  Secretin_N_2   3 tFpinylamkrsGlsntsvtsGsvsssgssssssssssss.sgsssssssssnss......sgtkietesesdfwgeLqkalesmlg.pgdGrsviv 91 
                    +pi+y   k+ G+  ++v+ Gs +  +++ ++ s ++   +++   +ss+s+ s       gtki+++ +  + + + ++l sm+   +dG  ++ 
    EPA05899.1 227 SIPIDYNTAKKVGSFRSKVKNGSLKLINKTIEELSFNEIPdENNIVIESSRSQGSivvhscFGTKINSTLSALLSSMISSMLGSMVDsRSDGYRIVL 323
                   79****************************99999999666666666776666668889999*************************9999988887 PP

  Secretin_N_2  92 sp 93 
                   s+
    EPA05899.1 324 SS 325
                   76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (601 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.68u 0.27s 00:00:00.95 Elapsed: 00:00:00.47
# Mc/sec: 3864.21
//
Query:       EPA05900.1  [L=52]
Description: ribosomal L39 protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-16   59.9   7.7    1.6e-16   59.7   7.7    1.1  1  Ribosomal_L39  Ribosomal L39 protein
  ------ inclusion threshold ------
      0.094   12.7   2.6        0.1   12.6   2.6    1.1  1  REV            REV protein (anti-repression trans-activator p


Domain annotation for each model (and alignments):
>> Ribosomal_L39  Ribosomal L39 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.7   7.7   1.7e-20   1.6e-16       1      41 [.       9      49 ..       9      50 .. 0.97

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 1.7e-20
  Ribosomal_L39  1 kKlrLaKalkqNrpvPaWvrlktdrkvrynpkrRhWRrtkL 41
                   +K+rL ++++q +pvPaW++l+t+r+vr+npkrR WR+t+ 
     EPA05900.1  9 RKIRLLRKTRQTSPVPAWIILRTKRTVRSNPKRRAWRSTDV 49
                   7*************************************985 PP

>> REV  REV protein (anti-repression trans-activator protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   2.6   1.1e-05       0.1      14      50 ..       9      45 ..       2      51 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.1e-05
         REV 14 rklrllkllyqsnPyPqgeGtasarrnrrrrrrerql 50
                rk+rll+   q+ P P     + +r  r   +r+ ++
  EPA05900.1  9 RKIRLLRKTRQTSPVPAWIILRTKRTVRSNPKRRAWR 45
                89***************99888888877777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       202  (0.0112667); expected 358.6 (0.02)
Passed bias filter:                      128  (0.00713927); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.30u 0.23s 00:00:00.53 Elapsed: 00:00:00.36
# Mc/sec: 437.95
//
Query:       EPA05901.1  [L=162]
Description: hydrolase, NUDIX family, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-11   43.8   0.0    2.7e-11   43.6   0.0    1.2  1  NUDIX     NUDIX domain


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   0.0   1.5e-15   2.7e-11       4      73 ..       7      80 ..       4     131 .. 0.75

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 1.5e-15
                EEEEEEEEETTSEEEEEEES..SSSTTT.EESSEEECBTTS.HHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEE CS
       NUDIX  4 ravgvvllnekgevLlvrrs..kkpfpg.WelPgGkvepgE.tpeeAArREleEEtGleaellellgrlhylap 73
                ++v vv++ ++  +++++     k ++g  ++PgGk++p++ ++ e+A+RE++EE+Gl+    +++g+l+ + +
  EPA05901.1  7 ASVLVVIYGKEPIIVMTEKPenLKFHAGeISFPGGKLDPDDsDLLETALRETREEIGLRISKNQVIGQLKPVMT 80
                6799999999954777777797555555588**************************98877788887665544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 922.27
//
Query:       EPA05902.1  [L=108]
Description: ribosomal protein L31e, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.8e-19   67.5   0.3    1.3e-18   67.0   0.3    1.3  1  Ribosomal_L31e  Ribosomal protein L31e


Domain annotation for each model (and alignments):
>> Ribosomal_L31e  Ribosomal protein L31e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.0   0.3   7.4e-23   1.3e-18       5      72 ..       7      73 ..       3      77 .. 0.94

  Alignments for each domain:
  == domain 1  score: 67.0 bits;  conditional E-value: 7.4e-23
  Ribosomal_L31e  5 reytInihkrihgvgfkkraprAlkeikkfamkemgtpdvridtrLnkavwakgirnvpyrirvrlsr 72
                    r ytIn+ k + +v+ + raprA+++ik+fa+ +m+t++ +i+ +L   +w++g+r++p++irvr+s+
      EPA05902.1  7 RVYTINLGKVLLSVDTH-RAPRAINMIKEFARHHMKTEEIKIEEDLAHIIWSRGVRSPPRKIRVRMSK 73
                    88***********9975.69**********************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.33s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 632.28
//
Query:       EPA05903.1  [L=227]
Description: rhodanese-like protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.1e-30  106.3   0.0    2.9e-18   66.4   0.0    2.1  2  Rhodanese  Rhodanese-like domain


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.4   0.0   1.6e-22   2.9e-18       3     106 ..      14     114 ..      12     115 .. 0.93
   2 !   38.2   0.0   8.9e-14   1.6e-09       4      78 ..     145     219 ..     142     227 .] 0.85

  Alignments for each domain:
  == domain 1  score: 66.4 bits;  conditional E-value: 1.6e-22
   Rhodanese   3 kelkellekgkvallDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellel....gidnkktvvvycdgggr.aaaaaallkklGyknvsv 96 
                 + l+  + +++v+++DvR +++Y+++hIp Avn+           +  ++++pe++l+l    gi+++++vvvy+d+ g  a+++a++l++lG+ +vs+
  EPA05903.1  14 DSLRSEIRDKSVRVIDVRREDDYKQSHIPTAVNL--------PLANLLSDDTPERVLKLvnamGISDETPVVVYDDTFGAlASRVAWTLEYLGHSDVSL 104
                 6788889999999*********************........78899999999999999*********************99999********777*** PP

   Rhodanese  97 ldGGfkawke 106
                 l+  f++wk+
  EPA05903.1 105 LETTFSKWKS 114
                 ********96 PP

  == domain 2  score: 38.2 bits;  conditional E-value: 8.9e-14
   Rhodanese   4 elkellekgkvallDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycdgggr 78 
                  l+   ek +v+l+D R++  Y ++hIpgA++++ +tl +++k  +p +++   l+++gi+ ++++++yc + g 
  EPA05903.1 145 YLETSKEKSDVILIDNRERLNYLEQHIPGAISLPYRTLATSDKILRPKDDMKRLLENRGISGNSEIITYCGSVGT 219
                 455566888889*********************9999999999999999999888888************88766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1499.80
//
Query:       EPA05904.1  [L=279]
Description: tetratricopeptide repeat protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.1e-21   73.0   3.9    6.7e-07   29.0   0.1    5.4  5  TPR_2         Tetratricopeptide repeat
    9.6e-20   69.5   5.2    6.4e-07   28.9   0.1    4.8  5  TPR_1         Tetratricopeptide repeat
    4.6e-14   52.7   1.5    1.3e-08   35.2   0.1    2.7  2  TPR_19        Tetratricopeptide repeat
    1.6e-13   50.0   0.2     0.0014   18.8   0.0    3.8  3  TPR_17        Tetratricopeptide repeat
    5.8e-13   49.2   0.0    0.00049   20.7   0.0    3.0  4  TPR_16        Tetratricopeptide repeat
    6.3e-13   47.8   6.0    0.00074   19.5   0.1    5.6  6  TPR_8         Tetratricopeptide repeat
    1.8e-12   46.7   6.6    0.00035   20.2   0.2    4.8  4  TPR_11        TPR repeat
    2.3e-11   43.5   0.9     0.0033   18.1   0.0    4.9  5  TPR_14        Tetratricopeptide repeat
    5.2e-09   36.3   3.6    3.9e-06   27.0   0.2    4.7  5  TPR_12        Tetratricopeptide repeat
    6.1e-09   36.0   0.2    1.5e-08   34.7   0.2    1.7  1  ANAPC3        Anaphase-promoting complex, cyclosome, subunit 
    9.5e-07   28.8   0.2      0.071   13.2   0.0    3.8  3  Fis1_TPR_C    Fis1 C-terminal tetratricopeptide repeat
    1.2e-06   28.5   0.0    0.00051   20.1   0.0    2.5  2  TPR_9         Tetratricopeptide repeat
    5.2e-06   26.8   3.1        5.3    7.9   0.0    4.8  4  TPR_6         Tetratricopeptide repeat
    5.4e-05   22.9   1.5        5.9    6.9   0.0    4.4  4  TPR_10        Tetratricopeptide repeat
    0.00024   20.9   0.6         22    5.4   0.0    4.8  5  TPR_7         Tetratricopeptide repeat
    0.00037   20.9   0.3     0.0015   18.9   0.2    2.1  1  HTH_27        Winged helix DNA-binding domain
     0.0004   20.4   1.2    0.00074   19.5   0.5    1.9  2  SRP_TPR_like  Putative TPR-like repeat
     0.0028   17.1   1.1      0.049   13.1   0.2    2.5  3  Coatomer_E    Coatomer epsilon subunit
     0.0073   15.3   3.0       0.14   11.0   0.0    2.5  3  NARP1         NMDA receptor-regulated protein 1
  ------ inclusion threshold ------
      0.012   15.9   0.5        1.6    9.1   0.0    3.1  3  TPR_20        Tetratricopeptide repeat
      0.019   14.9   2.6        7.5    6.7   0.3    3.9  4  TPR_3         Tetratricopeptide repeat
      0.032   14.1   0.0        4.6    7.2   0.0    3.0  3  TrmB          Sugar-specific transcriptional regulator TrmB


Domain annotation for each model (and alignments):
>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.3e-05     0.011       4      34 .]      36      66 ..      34      66 .. 0.95
   2 !   15.9   0.0   1.2e-05      0.01       2      31 ..      68      97 ..      67     100 .. 0.92
   3 !   29.0   0.1   8.2e-10   6.7e-07       1      34 []     101     134 ..     101     134 .. 0.96
   4 !    7.9   0.0    0.0047       3.8       3      31 ..     137     165 ..     135     168 .. 0.94
   5 ?    0.7   0.3      0.89   7.3e+02      17      29 ..     217     229 ..     216     230 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.3e-05
       TPR_2  4 lynlGlayyklgdyeeAleafekAleldPnn 34
                l+  G  +++  ++e+A+  fe+Al+++P+n
  EPA05904.1 36 LFKKGVNLMADEKLEDAAVIFEQALRIEPDN 66
                7999*************************98 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.2e-05
       TPR_2  2 ealynlGlayyklgdyeeAleafekAleld 31
                e l+ lG++ ++l +y eAl+ ++k l +d
  EPA05904.1 68 ETLMKLGYVRFHLEEYGEALKIYDKILDID 97
                67899**********************998 PP

  == domain 3  score: 29.0 bits;  conditional E-value: 8.2e-10
       TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                 +ea++  +l++y++++y +Al+a ekA+e dP++
  EPA05904.1 101 PEAWNLKALVHYEQKNYSKALDAVEKAVESDPTY 134
                 69******************************85 PP

  == domain 4  score: 7.9 bits;  conditional E-value: 0.0047
       TPR_2   3 alynlGlayyklgdyeeAleafekAleld 31 
                 a+yn ++ +   ++  e lea+++++e+d
  EPA05904.1 137 AWYNKACFLSLVNQVPESLEALKRSIEID 165
                 8**************************98 PP

  == domain 5  score: 0.7 bits;  conditional E-value: 0.89
       TPR_2  17 yeeAleafekAle 29 
                  ++Al+a++k le
  EPA05904.1 217 KADALDALRKLLE 229
                 689*******998 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   0.00032      0.26       5      34 .]      37      66 ..      34      66 .. 0.88
   2 !   15.5   0.0   1.4e-05     0.012       2      31 ..      68      97 ..      67     100 .. 0.92
   3 !   28.9   0.1   7.9e-10   6.4e-07       1      34 []     101     134 ..     101     134 .. 0.96
   4 !   13.0   0.0   8.7e-05     0.071       3      31 ..     137     165 ..     136     168 .. 0.95
   5 ?   -2.7   0.1       7.5   6.1e+03      18      28 ..     218     228 ..     216     229 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00032
                HHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1  5 ynlGnayfklgkydeAleyyekALelnPnn 34
                + +G+ ++  +k+++A   +e+AL+++P+n
  EPA05904.1 37 FKKGVNLMADEKLEDAAVIFEQALRIEPDN 66
                56778888889*****************98 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.4e-05
                HHHHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
       TPR_1  2 kalynlGnayfklgkydeAleyyekALeln 31
                ++l  lG++ f+l++y eAl+ y+k L ++
  EPA05904.1 68 ETLMKLGYVRFHLEEYGEALKIYDKILDID 97
                67899***********************98 PP

  == domain 3  score: 28.9 bits;  conditional E-value: 7.9e-10
                 HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                 ++a++ ++++++++++y +Al++ ekA+e +P++
  EPA05904.1 101 PEAWNLKALVHYEQKNYSKALDAVEKAVESDPTY 134
                 68******************************97 PP

  == domain 4  score: 13.0 bits;  conditional E-value: 8.7e-05
                 HHHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
       TPR_1   3 alynlGnayfklgkydeAleyyekALeln 31 
                 a+yn++  +   ++  e le+ ++ +e++
  EPA05904.1 137 AWYNKACFLSLVNQVPESLEALKRSIEID 165
                 9***************************9 PP

  == domain 5  score: -2.7 bits;  conditional E-value: 7.5
                 HHHHHHHHHHH CS
       TPR_1  18 deAleyyekAL 28 
                  +Al++ +k L
  EPA05904.1 218 ADALDALRKLL 228
                 58999999866 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.1   1.6e-11   1.3e-08       1      67 [.      43     109 ..      43     110 .. 0.98
   2 !   16.2   0.0   1.4e-05     0.011       2      58 ..     112     168 ..     111     172 .. 0.93

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 1.6e-11
      TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryasLlAk 67 
                 l+a++++++A+ ++eqal  +p+n e ++ L  + + l ++ eA ++ d++++ d  ++++++L+A 
  EPA05904.1  43 LMADEKLEDAAVIFEQALRIEPDNIETLMKLGYVRFHLEEYGEALKIYDKILDIDVTNPEAWNLKAL 109
                 7999*************************************************************95 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1.4e-05
      TPR_19   2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd 58 
                 +++++y  Al++ e+a + dp ++ a+++ A  l   +q+ e  ++L++  e d ++
  EPA05904.1 112 YEQKNYSKALDAVEKAVESDPTYGMAWYNKACFLSLVNQVPESLEALKRSIEIDVKN 168
                 689**********************************************99988775 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   7.9e-05     0.064       2      33 ..      56      87 ..      55      88 .. 0.94
   2 !   13.4   0.1   9.3e-05     0.076       2      33 ..      90     121 ..      89     122 .. 0.94
   3 !   18.8   0.0   1.8e-06    0.0014       3      29 ..     125     151 ..     123     163 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.9e-05
      TPR_17  2 ylkaleldPnnadaynnLAelllknGdlmtAr 33
                +++al+++P+n + +  L+++  ++ ++++A+
  EPA05904.1 56 FEQALRIEPDNIETLMKLGYVRFHLEEYGEAL 87
                89**************************9997 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 9.3e-05
      TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                 y k l++d +n++a+n++A ++++++++ +A+
  EPA05904.1  90 YDKILDIDVTNPEAWNLKALVHYEQKNYSKAL 121
                 999************************99986 PP

  == domain 3  score: 18.8 bits;  conditional E-value: 1.8e-06
      TPR_17   3 lkaleldPnnadaynnLAelllknGdl 29 
                 +ka+e dP++  a++n+A +l+  ++ 
  EPA05904.1 125 EKAVESDPTYGMAWYNKACFLSLVNQV 151
                 89*******************998885 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0     6e-07   0.00049       4      64 ..      40      97 ..      37     101 .. 0.90
   2 !   19.0   0.0     2e-06    0.0017      33      66 ..     100     133 ..      96     134 .. 0.93
   3 !   20.1   0.0   9.3e-07   0.00076       3      63 ..     107     164 ..     105     169 .. 0.91
   4 ?   -1.1   0.1       3.8   3.1e+03      14      26 ..     218     230 ..     216     231 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 6e-07
      TPR_16  4 araalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraa 64
                +  +++  + +dAa  +e+al+     Pd+ e l+ lg +++++ ++ eA+  y++ l+ +
  EPA05904.1 40 GVNLMADEKLEDAAVIFEQALRIE---PDNIETLMKLGYVRFHLEEYGEALKIYDKILDID 97
                556788999***************...****************************999876 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 2e-06
      TPR_16  33 aaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                 ++eA++l+++++++q+++ +A++++++a++ +p 
  EPA05904.1 100 NPEAWNLKALVHYEQKNYSKALDAVEKAVESDPT 133
                 578**************************99996 PP

  == domain 3  score: 20.1 bits;  conditional E-value: 9.3e-07
      TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalra 63 
                 +a+ ++++++y +A+ a e a+++d   P    A+++++  +   + ++e ++++++ ++ 
  EPA05904.1 107 KALVHYEQKNYSKALDAVEKAVESD---PTYGMAWYNKACFLSLVNQVPESLEALKRSIEI 164
                 6899*********************...***********9999999999999999987765 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 3.8
      TPR_16  14 ddAaaaleaalkr 26 
                 +dA+ al+ +l++
  EPA05904.1 218 ADALDALRKLLEK 230
                 6788888888776 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0027       2.2       5      34 .]      37      66 ..      36      66 .. 0.88
   2 !   11.7   0.1    0.0003      0.25       2      31 ..      68      97 ..      67      98 .. 0.94
   3 !   19.5   0.1     9e-07   0.00074       2      33 ..     102     133 ..     101     134 .. 0.96
   4 ?    5.2   0.0     0.035        28       3      31 ..     137     165 ..     137     168 .. 0.95
   5 ?   -2.3   0.0       8.9   7.2e+03       6      25 ..     216     225 ..     213     229 .. 0.46
   6 ?    0.7   0.0      0.96   7.9e+02       2      27 ..     246     271 ..     245     273 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0027
                HHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
       TPR_8  5 ynlgsiylklgdyeeAkeyyekaleldpdn 34
                +++g  ++  +++e A   +e+al+++pdn
  EPA05904.1 37 FKKGVNLMADEKLEDAAVIFEQALRIEPDN 66
                677888888899****************97 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.0003
                CHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
       TPR_8  2 eayynlgsiylklgdyeeAkeyyekaleld 31
                e +++lg++ + l++y eA + y k l++d
  EPA05904.1 68 ETLMKLGYVRFHLEEYGEALKIYDKILDID 97
                6899***********************997 PP

  == domain 3  score: 19.5 bits;  conditional E-value: 9e-07
                 CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
       TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                 ea++++++++ ++++y +A  + eka+e dp+
  EPA05904.1 102 EAWNLKALVHYEQKNYSKALDAVEKAVESDPT 133
                 89****************************97 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.035
                 HHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
       TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleld 31 
                 a+yn+++ ++  ++  e+ e++++ +e+d
  EPA05904.1 137 AWYNKACFLSLVNQVPESLEALKRSIEID 165
                 7**************************98 PP

  == domain 5  score: -2.3 bits;  conditional E-value: 8.9
                 HHHHHHHHTT-HHHHHHHHH CS
       TPR_8   6 nlgsiylklgdyeeAkeyye 25 
                  ++++++           ++
  EPA05904.1 216 DKADALDA----------LR 225
                 44444444..........44 PP

  == domain 6  score: 0.7 bits;  conditional E-value: 0.96
                 CHHHHHHHHHHHTT-HHHHHHHHHHH CS
       TPR_8   2 eayynlgsiylklgdyeeAkeyyeka 27 
                 ++y + +++ +k+g+ e  +  y+ka
  EPA05904.1 246 PIYDLAADVAEKMGKEERIVWNYKKA 271
                 6788899*******998766555555 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0     2e-06    0.0016       8      38 ..      47      77 ..      42      80 .. 0.90
   2 !   20.2   0.2   4.3e-07   0.00035       1      41 [.      74     114 ..      74     115 .. 0.96
   3 !   11.2   0.3   0.00028      0.23       3      33 ..     110     140 ..     108     143 .. 0.93
   4 ?    5.8   0.0     0.014        11       8      28 ..     149     169 ..     149     170 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2e-06
      TPR_11  8 GkyeeAieaYkkAlkldPdnaeayynLGlay 38
                 k+e+A   +++Al++ Pdn e + +LG++ 
  EPA05904.1 47 EKLEDAAVIFEQALRIEPDNIETLMKLGYVR 77
                699*************************986 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 4.3e-07
      TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykq 41 
                 G++ + + +y eA++ Y k l++d +n+ea++  +l++y+q
  EPA05904.1  74 GYVRFHLEEYGEALKIYDKILDIDVTNPEAWNLKALVHYEQ 114
                 78899999*******************************98 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.00028
      TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayyn 33 
                 + yeq +y +A+ a +kA++ dP++  a+yn
  EPA05904.1 110 VHYEQKNYSKALDAVEKAVESDPTYGMAWYN 140
                 68***********************999998 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.014
      TPR_11   8 GkyeeAieaYkkAlkldPdna 28 
                 ++ +e++ea+k+ +++d +na
  EPA05904.1 149 NQVPESLEALKRSIEIDVKNA 169
                 6889*************9998 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0    0.0004      0.33      11      42 ..      43      74 ..      39      76 .. 0.91
   2 !   18.1   0.0     4e-06    0.0033       2      42 ..      68     108 ..      67     109 .. 0.93
   3 !   15.8   0.0   2.2e-05     0.018       1      41 [.     101     141 ..     101     142 .. 0.95
   4 ?   -0.6   0.0       4.2   3.4e+03      19      35 ..     153     169 ..     146     170 .. 0.79
   5 ?    0.7   0.0       1.6   1.3e+03      18      30 ..     218     230 ..     212     237 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0004
      TPR_14 11 llalGdpdeAiallrralalaPddaeawllla 42
                l+a +++++A+ ++++al+  Pd+ e+++ l+
  EPA05904.1 43 LMADEKLEDAAVIFEQALRIEPDNIETLMKLG 74
                6788899********************99987 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 4e-06
      TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawllla 42 
                 e l++l+ + ++l+++ eA+++++++l+ + +++eaw l a
  EPA05904.1  68 ETLMKLGYVRFHLEEYGEALKIYDKILDIDVTNPEAWNLKA 108
                 67899********************************7765 PP

  == domain 3  score: 15.8 bits;  conditional E-value: 2.2e-05
      TPR_14   1 peallalaeallalGdpdeAiallrralalaPddaeawlll 41 
                 pea+ + a +++++ ++ +A+++ ++a++ +P+   aw+  
  EPA05904.1 101 PEAWNLKALVHYEQKNYSKALDAVEKAVESDPTYGMAWYNK 141
                 799***********************************876 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 4.2
      TPR_14  19 eAiallrralalaPdda 35 
                 e++++l+r ++ + ++a
  EPA05904.1 153 ESLEALKRSIEIDVKNA 169
                 78899999999888776 PP

  == domain 5  score: 0.7 bits;  conditional E-value: 1.6
      TPR_14  18 deAiallrralal 30 
                 ++A+++lr++l++
  EPA05904.1 218 ADALDALRKLLEK 230
                 5788888888875 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1      0.27   2.2e+02      59      74 ..      47      62 ..      36      65 .. 0.65
   2 !   27.0   0.2   4.8e-09   3.9e-06       5      73 ..      69     129 ..      65     133 .. 0.88
   3 !   13.1   0.1   0.00011      0.09       5      31 ..     103     129 ..      99     165 .. 0.71
   4 ?   -1.4   0.0       3.6     3e+03      50      72 ..     205     228 ..     203     230 .. 0.60
   5 ?    0.9   0.0      0.68   5.6e+02      23      63 ..     225     263 ..     213     273 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.27
      TPR_12 59 gryeeAlelleealai 74
                +++e+A  ++e+al+i
  EPA05904.1 47 EKLEDAAVIFEQALRI 62
                4566666666666665 PP

  == domain 2  score: 27.0 bits;  conditional E-value: 4.8e-09
      TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73 
                 +l +l+ v ++l++y eAl++++k l+i   + +p+      + +  + +++++++y +Al++ e+a++
  EPA05904.1  69 TLMKLGYVRFHLEEYGEALKIYDKILDID--VTNPE------AWNLKALVHYEQKNYSKALDAVEKAVE 129
                 6669*************************..53344......6899999******************98 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 0.00011
      TPR_12   5 alnnlaavlrrlgrydeAlellekale 31 
                 a+n  a+v++++++y +Al+  eka+e
  EPA05904.1 103 AWNLKALVHYEQKNYSKALDAVEKAVE 129
                 677789999999999999999888866 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 3.6
      TPR_12  50 nLgrlyral.gryeeAlelleeal 72 
                 +Lg + + +  + ++Al++l++ l
  EPA05904.1 205 TLGAIVWTTyLDKADALDALRKLL 228
                 555555533357777888877766 PP

  == domain 5  score: 0.9 bits;  conditional E-value: 0.68
      TPR_12  23 lellekaleiarrllGpdhpltattlrnLgrlyralgryee 63 
                 ++llek l ++ +    d +  + ++   +++ +++g+ e 
  EPA05904.1 225 RKLLEKGLIVQHEK--RDGLSKIPIYDLAADVAEKMGKEER 263
                 56777777777777..7788888899999999999988776 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.2   1.8e-11   1.5e-08       4      82 .]      48     127 ..      45     127 .. 0.96

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 1.8e-11
                 -HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-SS CS
      ANAPC3   4 nyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLekl 82 
                 ++++A  ++e +l  e+++ e ++ l+++ +++++y +A+++++k  +++ ++++++ l+A + +++k+y +A++a ek+
  EPA05904.1  48 KLEDAAVIFEQALRIEPDNIETLMKLGYVRFHLEEYGEALKIYDKIlDIDVTNPEAWNLKALVHYEQKNYSKALDAVEKA 127
                 6789999******99*************************************************************9985 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.11        86      19      35 ..      51      67 ..      47      71 .. 0.79
   2 !   13.2   0.0   8.7e-05     0.071      13      45 ..      79     111 ..      72     113 .. 0.90
   3 !   10.1   0.1    0.0008      0.66       8      33 ..     108     133 ..     108     135 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.11
                HHHHHHHHHHHHTTS-H CS
  Fis1_TPR_C 19 eArryvdalLeiEPenr 35
                +A    ++ L+iEP+n 
  EPA05904.1 51 DAAVIFEQALRIEPDNI 67
                566678999******95 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 8.7e-05
                 HHT-HHHHHHHHHHHHHHTTS-HHHHHHHHHHH CS
  Fis1_TPR_C  13 klgeYseArryvdalLeiEPenrQaqsLkelie 45 
                  l eY eA++  d +L i+  n  a +Lk+l++
  EPA05904.1  79 HLEEYGEALKIYDKILDIDVTNPEAWNLKALVH 111
                 489**************************9986 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.0008
                 HHHHHHHT-HHHHHHHHHHHHHHTTS CS
  Fis1_TPR_C   8 AlGhyklgeYseArryvdalLeiEPe 33 
                 Al hy +++Ys+A+  v+   e +P 
  EPA05904.1 108 ALVHYEQKNYSKALDAVEKAVESDPT 133
                 6679*****************99995 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   0.00031      0.25       7      53 ..      45      91 ..      42      97 .. 0.87
   2 !   20.1   0.0   6.3e-07   0.00051      10      60 ..      82     132 ..      81     138 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00031
       TPR_9  7 reedweralavverllllaPddpeerrdRGlllaqlGclsaAladLe 53
                  e+ e a  + e  l + Pd +e ++  G ++++l+ + +Al+  +
  EPA05904.1 45 ADEKLEDAAVIFEQALRIEPDNIETLMKLGYVRFHLEEYGEALKIYD 91
                56788999999*******************************98665 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 6.3e-07
       TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalap 60 
                 ++ +al++++ +l ++   pe +   +l+++++ ++s+Al++ e +++ +p
  EPA05904.1  82 EYGEALKIYDKILDIDVTNPEAWNLKALVHYEQKNYSKALDAVEKAVESDP 132
                 5678********************************************999 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0      0.11        93       3      32 ..      36      65 ..      36      66 .. 0.81
   2 !    7.9   0.0    0.0066       5.3       2      28 ..      69      95 ..      68      97 .. 0.91
   3 !    7.8   0.0     0.007       5.7       7      31 ..     108     132 ..     106     134 .. 0.91
   4 ?    3.7   0.2      0.14   1.1e+02      15      29 ..     216     230 ..     213     230 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.11
                HHHHHHHHHH.HHHHHHHHHHHHHHHHH-TT CS
       TPR_6  3 lyklalsyrk.lgdtdkAlealerlikeYPd 32
                l+k +  + +   + ++A  ++e+ ++  Pd
  EPA05904.1 36 LFKKGVNLMAdE-KLEDAAVIFEQALRIEPD 65
                567776666645.999***********9999 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0066
                HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
       TPR_6  2 AlyklalsyrklgdtdkAlealerlik 28
                 l+kl++ ++ l ++ +Al++++++++
  EPA05904.1 69 TLMKLGYVRFHLEEYGEALKIYDKILD 95
                589********88***********986 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.007
                 HHHHHHHHHHHHHHHHHHHHHHH-T CS
       TPR_6   7 alsyrklgdtdkAlealerlikeYP 31 
                 al ++++++++kAl+a e+ +++ P
  EPA05904.1 108 ALVHYEQKNYSKALDAVEKAVESDP 132
                 899*************999999988 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.14
                 HHHHHHHHHHHHHHH CS
       TPR_6  15 dtdkAlealerlike 29 
                 d+++Al+al++l+++
  EPA05904.1 216 DKADALDALRKLLEK 230
                 8899********986 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.1     0.053        43      12      31 ..      43      62 ..      40      63 .. 0.84
   2 ?    6.3   0.0     0.011       8.9       4      31 ..      69      96 ..      67      97 .. 0.89
   3 !    6.9   0.0    0.0072       5.9       9      30 ..     108     129 ..     105     130 .. 0.93
   4 ?    0.6   0.0      0.68   5.5e+02       8      31 ..     141     164 ..     139     166 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.053
      TPR_10 12 lrqrgrydeAealleealai 31
                l +  ++++A  ++e+al+i
  EPA05904.1 43 LMADEKLEDAAVIFEQALRI 62
                6677899***********97 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.011
      TPR_10  4 slnNLanalrqrgrydeAealleealai 31
                +l  L+ + +++ +y eA++++++ l+i
  EPA05904.1 69 TLMKLGYVRFHLEEYGEALKIYDKILDI 96
                7888999999*************99876 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0072
      TPR_10   9 analrqrgrydeAealleeala 30 
                 a +++++++y +A++  e+a++
  EPA05904.1 108 ALVHYEQKNYSKALDAVEKAVE 129
                 789*****************97 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 0.68
      TPR_10   8 LanalrqrgrydeAealleealai 31 
                  a+ l+ +++  e+++ l+++++i
  EPA05904.1 141 KACFLSLVNQVPESLEALKRSIEI 164
                 588899999************997 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.15   1.3e+02      14      33 ..      48      65 ..      43      68 .. 0.72
   2 ?    5.4   0.0     0.027        22       2      29 ..      70      97 ..      69     102 .. 0.82
   3 ?    5.1   0.0     0.033        27       1      32 [.     103     132 ..     103     133 .. 0.88
   4 ?   -0.5   0.0       2.1   1.7e+03       1      30 [.     137     166 ..     137     175 .. 0.79
   5 ?    0.5   0.0      0.97   7.9e+02       5      32 ..     251     276 ..     248     279 .] 0.81

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.15
       TPR_7 14 dyeeAielyeqsLaltkdpe 33
                + e+A+ ++eq+L+++  p+
  EPA05904.1 48 KLEDAAVIFEQALRIE--PD 65
                6799*******55554..43 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.027
       TPR_7  2 LlnLarlysrlGdyeeAielyeqsLalt 29
                L  L+ +++ l +y eA+++y + L ++
  EPA05904.1 70 LMKLGYVRFHLEEYGEALKIYDKILDID 97
                5669999999************977766 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.033
       TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdp 32 
                 a++  a ++ ++ +y++A++  e+  a+++dp
  EPA05904.1 103 AWNLKALVHYEQKNYSKALDAVEK--AVESDP 132
                 56777899999*************..999998 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 2.1
       TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltk 30 
                 a++n a   s +++  e +e +++s++++ 
  EPA05904.1 137 AWYNKACFLSLVNQVPESLEALKRSIEIDV 166
                 567778888888888899999999888874 PP

  == domain 5  score: 0.5 bits;  conditional E-value: 0.97
       TPR_7   5 LarlysrlGdyeeAielyeqsLaltkdp 32 
                  a++ +++G+ e+ ++ y++  a+tk  
  EPA05904.1 251 AADVAEKMGKEERIVWNYKK--ATTKTN 276
                 578888999999999*****..999865 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.2   1.9e-06    0.0015       5      56 ..     192     240 ..     190     245 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.9e-06
      HTH_27   5 qalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdead 56 
                 +++vL++ir  ++  +l +++ +++++++ +  +l+kL ekGL+++ ++ +d
  EPA05904.1 192 EVVVLESIR--QGYHTLGAIVWTTYLDKADALDALRKLLEKGLIVQHEK-RD 240
                 899******..999******************************77777.45 PP

>> SRP_TPR_like  Putative TPR-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.5   9.1e-07   0.00074       5     104 ..      21     130 ..      17     161 .. 0.75
   2 ?   -2.3   0.0       5.4   4.4e+03      32      75 ..     219     262 ..     203     266 .. 0.63

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 9.1e-07
  SRP_TPR_like   5 yekilrlegkelkkf....kvvaliklekyeeaLkllkkgsal...sedvrfEkaYvlYklkkykkalkilkkveaee....kvkvlksqvlYrlgs 90 
                   +e+ + l ++ +++     k v l+  ek e+a  + +++  +   + ++ +   Yv ++l++y +alki +k+ + +    ++  lk+ v Y  ++
    EPA05904.1  21 HEETS-LVDPDYNRKklfkKGVNLMADEKLEDAAVIFEQALRIepdNIETLMKLGYVRFHLEEYGEALKIYDKILDIDvtnpEAWNLKALVHYEQKN 116
                   55543.4445566555566788899999999988888877644111445678889999999999999999988755432214667899999999999 PP

  SRP_TPR_like  91 yekAYklLskekke 104
                   y+kA + + k  ++
    EPA05904.1 117 YSKALDAVEKAVES 130
                   99998887665554 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 5.4
  SRP_TPR_like  32 eaLkllkkgsalsedvrfEkaYvlYklkkykkalkilkkveaee 75 
                   +aL +l+k  +    v+ Ek   l k+  y  a+ + +k+ +ee
    EPA05904.1 219 DALDALRKLLEKGLIVQHEKRDGLSKIPIYDLAADVAEKMGKEE 262
                   55555555544445566666666666666666777766666665 PP

>> Coatomer_E  Coatomer epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.19   1.5e+02     205     241 ..      37      73 ..      29      82 .. 0.81
   2 !   13.1   0.2     6e-05     0.049     181     274 ..      81     177 ..      79     195 .. 0.75
   3 ?   -1.2   0.0       1.3   1.1e+03     104     127 ..     203     226 ..     175     231 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.19
                 HHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHH CS
  Coatomer_E 205 ngkAvvslllgryeeAeslLkeaLdkdakdeetLiNl 241
                   k v  ++ ++ e+A  + ++aL  ++ + etL+ l
  EPA05904.1  37 FKKGVNLMADEKLEDAAVIFEQALRIEPDNIETLMKL 73 
                 5677888999999999999999*99999999999876 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 6e-05
                 THHHHHHHHHHHHHHHS---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--H...HHHHHHHHHHHHH-TT-HHHHH CS
  Coatomer_E 181 ekiqdAyyifqelsekykstplllngkAvvslllgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkda...evsernlsqlklshpehklvkd 274
                 e++ +A+ i++ + +   ++p   n kA v+  +++y +A    ++a ++d+ +  +  N      ++++ +   e+ +r+++   ++ +++   kd
  EPA05904.1  81 EEYGEALKIYDKILDIDVTNPEAWNLKALVHYEQKNYSKALDAVEKAVESDPTYGMAWYNKACFLSLVNQVPeslEALKRSIEIDVKNARKSIRDKD 177
                 67889***********9999**********************************9999998766655554430114556666655555555555555 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.3
                 HHHHHHHHHHHTT-HHHHHHHHTT CS
  Coatomer_E 104 lrllaaivflkegdfddalkllkk 127
                  ++l+aiv++   d  dal++l+k
  EPA05904.1 203 YHTLGAIVWTTYLDKADALDALRK 226
                 789999999999999999998876 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   1.2     0.045        37     437     493 ..       9      71 ..       1      90 [. 0.66
   2 ?    2.1   0.1     0.087        71      18      67 ..      47      96 ..      35     105 .. 0.60
   3 !   11.0   0.0   0.00017      0.14     201     258 ..     111     167 ..     101     170 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.045
                 -.......-------------S-SSSTTTT-......S-HHHHHHHHHTTTGGGTTT-THHHH CS
       NARP1 437 ekkaaekkakkedeeakkededplgekLvkt......eepLeeAlkflkpLlklaaeniethl 493
                  k+++ + + k++ee++ +d+d + +kL k+      +e Le+A   +++ l+  ++niet +
  EPA05904.1   9 PKEEEIEAKIKDHEETSLVDPDYNRKKLFKKgvnlmaDEKLEDAAVIFEQALRIEPDNIETLM 71 
                 222222333344556667777777777765422222267999999999999999999999965 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.087
                THHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
       NARP1 18 gkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLler 67
                +kle+A   +e++ +   D+++ + + + + ++L+++ eA ++y ++l+ 
  EPA05904.1 47 EKLEDAAVIFEQALRIEPDNIETLMKLGYVRFHLEEYGEALKIYDKILDI 96
                44555555555555555566666666666666677777777777666665 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00017
                 HHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT CS
       NARP1 201 hydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDla 258
                 hy+  ++++kAl+ ++ka+e++pt    +++Ka +l    ++ +  e+++++ ++D +
  EPA05904.1 111 HYE-QKNYSKALDAVEKAVESDPTYGMAWYNKACFLSLVNQVPESLEALKRSIEIDVK 167
                 555.47899*************************999999999999999988888865 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0       0.1        85      11      43 ..      56      88 ..      31     104 .. 0.89
   2 ?    9.1   0.0    0.0019       1.6       3      62 ..     116     175 ..     114     179 .. 0.92
   3 ?   -1.8   0.1       5.2   4.2e+03      38      51 ..     217     230 ..     214     240 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.1
      TPR_20 11 leaalaanpddldarldlAlallaagryeeAle 43
                +e+al  +pd++++ ++l  + ++ ++y eAl+
  EPA05904.1 56 FEQALRIEPDNIETLMKLGYVRFHLEEYGEALK 88
                689999*****************9999999997 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0019
      TPR_20   3 adapelaeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrkweddaark 62 
                 + ++ l+++e+a++++p+   a ++ A  l   +++ e+le+L + ++ d k +++++r+
  EPA05904.1 116 NYSKALDAVEKAVESDPTYGMAWYNKACFLSLVNQVPESLEALKRSIEIDVKNARKSIRD 175
                 5578899*******************************************9999999886 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 5.2
      TPR_20  38 yeeAleqLleilkr 51 
                 +++Al++L ++l++
  EPA05904.1 217 KADALDALRKLLEK 230
                 56788888777776 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       1.5   1.2e+03      15      36 .]      47      66 ..      45      66 .. 0.83
   2 ?    4.2   0.0     0.053        43       2      25 ..      68      91 ..      67      94 .. 0.91
   3 ?    6.7   0.3    0.0092       7.5       8      23 ..     108     123 ..     106     123 .. 0.88
   4 ?   -0.1   0.0       1.2   9.8e+02       4      14 ..     247     257 ..     247     257 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.5
                T-HHHHHHH..HHHHHHH-TT- CS
       TPR_3 15 kkyqeArelfsYallaildken 36
                +k+++A+    ++++  ++++n
  EPA05904.1 47 EKLEDAAVI--FEQALRIEPDN 66
                6999*****..77999888776 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.053
                HHHHHHHHHHHHTT-HHHHHHH.. CS
       TPR_3  2 dylysyAaefynkkkyqeArelfs 25
                + l++++++ +  ++y eA+  ++
  EPA05904.1 68 ETLMKLGYVRFHLEEYGEALKIYD 91
                779****************99976 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0092
                 HHHHHHTT-HHHHHHH CS
       TPR_3   8 AaefynkkkyqeArel 23 
                 A + y +k+y++A+++
  EPA05904.1 108 ALVHYEQKNYSKALDA 123
                 6778*********986 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 1.2
                 HHHHHHHHHHT CS
       TPR_3   4 lysyAaefynk 14 
                 +y++Aa++  k
  EPA05904.1 247 IYDLAADVAEK 257
                 8*****99876 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       6.7   5.5e+03      44      54 ..      68      78 ..      66      90 .. 0.77
   2 ?    3.4   0.0     0.085        70       4      43 ..     134     173 ..     132     185 .. 0.88
   3 ?    7.2   0.0    0.0056       4.6      34      58 ..     215     239 ..     199     258 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 6.7
                HHHHHCTSEEE CS
        TrmB 44 rsLedkGlVer 54
                + L++ G+V+ 
  EPA05904.1 68 ETLMKLGYVRF 78
                67999999975 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.085
                 CHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHH CS
        TrmB   4 lGLseyEakvYlaLlklgpatadeiaeelgvprskvYevL 43 
                 +G+  y   ++l L+++ p + + + + ++++  ++ +++
  EPA05904.1 134 YGMAWYNKACFLSLVNQVPESLEALKRSIEIDVKNARKSI 173
                 677889999*******************999987777665 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0056
                 SSCHCHHHHHHHHHHCTSEEEESST CS
        TrmB  34 vprskvYevLrsLedkGlVerekgr 58 
                 ++++ + ++Lr+L++kGl+   ++r
  EPA05904.1 215 LDKADALDALRKLLEKGLIVQHEKR 239
                 67888899**********9877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       753  (0.041999); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 1673.70
//
Query:       EPA05905.1  [L=37]
Description: hypothetical protein BG20_I2075 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.45
# Mc/sec: 247.51
//
Query:       EPA05906.1  [L=477]
Description: nitrite/sulfite reductase ferredoxin domain protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.4e-42  143.3   0.0    4.1e-32  110.9   0.0    2.2  2  NIR_SIR       Nitrite and sulphite reductase 4Fe-4S domain
    3.8e-12   45.9   0.0    6.7e-12   45.1   0.0    1.4  1  NIR_SIR_ferr  Nitrite/Sulfite reductase ferredoxin-like half 


Domain annotation for each model (and alignments):
>> NIR_SIR  Nitrite and sulphite reductase 4Fe-4S domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.9   0.0   4.6e-36   4.1e-32       2     153 ..       8     160 ..       7     164 .. 0.94
   2 !   30.2   0.0   3.1e-11   2.7e-07       7     142 ..     290     422 ..     285     428 .. 0.85

  Alignments for each domain:
  == domain 1  score: 110.9 bits;  conditional E-value: 4.6e-36
                 SSSCCCCCCSTCCCTBSS-SS-THHHHHHHHHHHCTCCCCTSSSS-BEEEEESSTCSTSSGGGSSEEEEEEEETTCEE...EEEEEE--B-SSSTC-TC CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxx RF
     NIR_SIR   2 ganlrnvtlcpgaglceeallDttelakaiedelepeygetylPrKfKiavsgcpnncvaveanDiglvgvkkdekei...gfnilvGGglgrthgakk 97 
                 g+++rnv+++p +g+c+++ +D+t++a a  + +  ++  ++lPrKfK+++++c++  + v++ D+gl++ ++d       gf+i++GGglg++   + 
  EPA05906.1   8 GNSVRNVMCSPLSGVCPDEEFDSTPYALATARFFLRNPLSQNLPRKFKFNFTCCEK-HGMVRMVDVGLIPQTRDLNGTlqkGFKIFLGGGLGNKSFVGH 105
                 899***************************************************76.5678999*********97776788****************** PP

                 EEEEEEEEEGGGHHHHHHHHHHHHHHHS-CSSGGG-SHHHHHHHHHHHHHHHHH.HH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
     NIR_SIR  98 tsarlgfvpeeevlevveaivevyrdhgdrknrkkeRlkylverlGvekFrekv.ee 153
                  +    f+pee++l +  a+++++++ gdrkn ++ R++ylv+++G+ekF + v +e
  EPA05906.1 106 QLE--EFTPEEDLLHTSIAVLRIFDRMGDRKNMARNRMRYLVNDMGWEKFQNLVlKE 160
                 **9..7**********************************************99444 PP

  == domain 2  score: 30.2 bits;  conditional E-value: 3.1e-11
                 CCCCSTCCCTBSS-SS-THHHHHHHHHHH.CTCCCCTSSSS-BEEEEESSTCSTSSGGGSSEEEEEEEETTCEE...EEEEEE--B-SSSTC-TCEEEE CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxx RF
     NIR_SIR   7 nvtlcpgaglceeallDttelakaiedel.epeygetylPrKfKiavsgcpnncvaveanDiglvgvkkdekei...gfnilvGGglgrthgakktsar 101
                 ++ +c g++ c  al+++  lak+i++++ e ++++ +  r   i++sgcpn c+++ +  ig+ g     + +    +++ +GG+   + + ++t  r
  EPA05906.1 290 APIGCSGTTSCNLALTNSHRLAKEIQRKFlELKLDQDDDLRDSSIKISGCPNSCGQHGIATIGFFGGGARIGTEmypNYQMSLGGRSDGETMLGATCHR 388
                 67789*********************6551666677777799*********************999877555555667888888888888888888877 PP

                 EEEEEGGGHHHHHHHHHHHHHHHS-CSSGGG-SHHHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
     NIR_SIR 102 lgfvpeeevlevveaivevyrdhgdrknrkkeRlkylverl 142
                    +p++ v++v+ +i+e+++    ++++ +  l+++++r+
  EPA05906.1 389 ---IPAKRVIPVILKIIELFK----QNKKSNDTLRDWIHRI 422
                 ...8*****************....9999*********997 PP

>> NIR_SIR_ferr  Nitrite/Sulfite reductase ferredoxin-like half domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.1   0.0   7.5e-16   6.7e-12       2      68 ..     211     277 ..     210     278 .. 0.94

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 7.5e-16
  NIR_SIR_ferr   2 kqkdgkgyymvrlrvpnGritaeqlraladiaekygs.geirlTtrQnlqlhgvpeedleeileeLae 68 
                   kqk+  +y++v +++++G+it+ q  ala i+++++s g++r    Qn+ l++v+++dl+ ++++L e
    EPA05906.1 211 KQKQ-SEYNSVFITLEAGDITSSQIAALATIIQEFSSeGHARAGFVQNIALRYVHDDDLPRLYSKLLE 277
                   6888.6789***************************66***************************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (477 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.51
# Mc/sec: 2824.28
//
Query:       EPA05907.1  [L=102]
Description: hypothetical protein BG20_I2078, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 639.52
//
Query:       EPA05908.1  [L=108]
Description: hypothetical protein BG20_I2076 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0022   18.2   1.3     0.0025   18.0   1.0    1.3  1  DUF2666   Protein of unknown function (DUF2666)
  ------ inclusion threshold ------
      0.039   13.9   0.1      0.064   13.3   0.1    1.4  1  Vps4_C    Vps4 C terminal oligomerisation domain
      0.099   12.1   0.4       0.18   11.3   0.4    1.4  1  NMD3      NMD3 family


Domain annotation for each model (and alignments):
>> DUF2666  Protein of unknown function (DUF2666)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   1.0   4.2e-07    0.0025      52     127 ..      12      86 ..       5      94 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4.2e-07
                 -HHHHHHHTTT--S--S....HHHHHHHHHHHHT-.............---HHHHHHHHHHHHHTTT--SS--HHH CS
     DUF2666  52 DlekleeiadeikkkkkgrvkeedisevleklkspattkklnkitdskegkeilkvilarivLerlGiktkveskl 127
                  +++l+ei ++i+ ++   ++eed+ + +  ++++    k ++   ++ ++e+ ++ l +i L+  G+   +e k+
  EPA05908.1  12 PIKNLKEISQAIQAVRE-SIEEEDVDKTMDLFEEFIDPTKSGEQMIEQFFEEHREIRLWKIRLKDRGVDYLIENKT 86 
                 57899**********99.9****************9999999999999********************99999875 PP

>> Vps4_C  Vps4 C terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   1.1e-05     0.064      19      55 ..       4      40 ..       1      45 [. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.1e-05
      Vps4_C 19 ipsdkllePpvtlkDflkalkkarptVskeDLekhee 55
                i+ ++l +P  +lk + +a++ +r ++ +eD++k  +
  EPA05908.1  4 ITRKQLPKPIKNLKEISQAIQAVRESIEEEDVDKTMD 40
                67889999999*********************99765 PP

>> NMD3  NMD3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.4     3e-05      0.18     150     213 ..      25      99 ..      13     106 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3e-05
        NMD3 150 QvRqkrelteeehkrtfelleqli.............lkhdahafiskikevkeGlDfyfgsksaArklveflksev 213
                  vR++  ++ee+ ++t++l+e++i              +++++  + ki  ++ G+D+ + +k++  +l ++++ ++
  EPA05908.1  25 AVRES--IEEEDVDKTMDLFEEFIdptksgeqmieqfFEEHREIRLWKIRLKDRGVDYLIENKTKMLNLFDNVEVTI 99 
                 47777..889999999999999999999998888888566899999******************9999998887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1260  (0.0702772); expected 358.6 (0.02)
Passed bias filter:                      665  (0.0370907); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 706.25
//
Query:       EPA05909.1  [L=254]
Description: hypothetical protein BG20_I1334 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-09   37.2   0.0    5.1e-09   35.7   0.0    1.8  1  PHP_C            PHP-associated
  ------ inclusion threshold ------
      0.013   15.8   1.3      0.016   15.5   1.3    1.3  1  PHP              PHP domain
      0.027   14.0   0.0      0.064   12.8   0.0    1.6  2  CNPase           2',3'-cyclic nucleotide 3'-phosphodiesterase
        0.1   13.1   0.2       0.72   10.4   0.1    2.3  2  Glyco_tranf_2_4  Glycosyl transferase family 2


Domain annotation for each model (and alignments):
>> PHP_C  PHP-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.0   1.1e-12   5.1e-09       3      55 ..     152     203 ..     151     204 .. 0.92

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 1.1e-12
       PHP_C   3 aNrrArrfAeklglpgtgGSDAHrleeVGrayTefeepiatpdelleairegr 55 
                 +N rA +fA  ++   + GSD+H+l ++Gr+++++e++++  d++l++++ g+
  EPA05909.1 152 SNIRATQFAVDNNMIQVSGSDSHVLSTLGRCVNMIESENN-LDSILQSMKHGK 203
                 6889*******************************55555.8********997 PP

>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   1.3   3.5e-06     0.016       1      65 [.       6      79 ..       6     243 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.5e-06
                EEEE--CCC.........--.S-H..HHHHHHHHHCT-SEEEEEEEEBTTHHHHHHHHHHHHTTTTSEEEEEEE CS
                xxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
         PHP  1 dlHvHteys.........lldgalsieelvkkakelglkaiaiTDhgnlfgyvefykaakkkykagikpiiGle 65
                +lH+H ++s           d ++si e +++  +lgl+ai +T h+ l+gy +  ++ k+++k +  +++ +e
  EPA05909.1  6 ELHCHNSFSnfhvgedeaPYDCNVSIREQLERSYNLGLDAIFVTNHNTLDGYEQLLHYKKDHKKFQNIAVYPAE 79
                7999999998888555444456799*****************************99999998875444555555 PP

>> CNPase  2',3'-cyclic nucleotide 3'-phosphodiesterase (CNP or CNPase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.4e-05     0.064      62     110 ..       5      53 ..       3     119 .. 0.70
   2 ?   -2.6   0.0      0.75   3.4e+03     140     172 ..     170     202 ..     161     214 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.4e-05
                 T--EEEEEE-TTTTSSSHHHHHT-HHHHHHTT-EEEEEEEEEEE-SS-E CS
      CNPase  62 gvlhcttkfcdyGkaeGaeeyaqqevvkksygkafelsisalfvtprtv 110
                 + lhc   f+++   e    y  +  +++ + ++++l + a+fvt + +
  EPA05909.1   5 TELHCHNSFSNFHVGEDEAPYDCNVSIREQLERSYNLGLDAIFVTNHNT 53 
                 679******************************************8643 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.75
                 -SSSEEE----TT--HHHHHHHHHHHHHHHHTT CS
      CNPase 140 GsrahvtlGcaedveavqtGldlleilklekgG 172
                 Gs +hv     + v+ + +  +l  il+  k G
  EPA05909.1 170 GSDSHVLSTLGRCVNMIESENNLDSILQSMKHG 202
                 677777433334444555555555555555555 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00016      0.72       7      49 ..      31      79 ..      25     153 .. 0.77
   2 ?    0.2   0.0      0.24   1.1e+03      29      76 ..     188     233 ..     182     237 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00016
  Glyco_tranf_2_4  7 LpeflahhlalgfdrilvydndstDgtrail......kelpevkllhvd 49
                     + e l+  ++lg d+i+v++++  Dg  ++l      k+ +++ +++ +
       EPA05909.1 31 IREQLERSYNLGLDAIFVTNHNTLDGYEQLLhykkdhKKFQNIAVYPAE 79
                     777788889**********************554222223445555544 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.24
  Glyco_tranf_2_4  29 stDgtrailkelpevkllhvdksyederrqvellkallar.yaeadwvl 76 
                      s+ + + il+++++ k+   ++ y+    q+e l++l  + ++ +d+++
       EPA05909.1 188 SENNLDSILQSMKHGKIEILQTGYA---LQNETLDHLKYKiHNSKDYLI 233
                      6777888888888888777777775...666666666665234467765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       766  (0.0427241); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1595.38
//
Query:       EPA05910.1  [L=303]
Description: putative methyltransferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   4.8e-101  338.0   0.8   5.4e-101  337.8   0.8    1.0  1  Methyltransf_33  Histidine-specific methyltransferase, SAM-de
  ------ inclusion threshold ------
       0.01   15.6   0.0       0.13   12.1   0.0    2.2  1  Methyltransf_23  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltransf_33  Histidine-specific methyltransferase, SAM-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  337.8   0.8    6e-105  5.4e-101      10     308 ..       2     297 ..       1     298 [. 0.98

  Alignments for each domain:
  == domain 1  score: 337.8 bits;  conditional E-value: 6e-105
  Methyltransf_33  10 sskpktlpskllYDarGselFeeitelpeYyptrtEiaiLqehaaeiaaaipaa.tlvelGsGsseKtrlLLealeaaekeltYvplDvseeaL 102
                      ++++k +++k++YD++Gs+lFe+i++lpeYyptrtEi+iL++ ++e+   ++++ +lvelGsGss Ktrl+L+ l++ +++++Y+p+D+s e+L
       EPA05910.1   2 NQSSKFINPKFFYDQKGSKLFEKICDLPEYYPTRTEISILKRLKDELPPYLNDSfRLVELGSGSSVKTRLILDVLNQIQEKIEYFPIDIS-EIL 94 
                      5788*********************************************997777*********************999**********9.79* PP

  Methyltransf_33 103 eealealaaeypsleveglvgdyedglewlaslpeaederrlvlflGssigNlepeeaaafLrklraalgpgdllLlGvDlvkdeekleaAYnd 196
                      +e++++l++ey++l ++g++ +ye gle+l++ ++   +++l++flGss+gN++p + ++fL+k+++++++gdl+L+G+Dlvk++++le+AYnd
       EPA05910.1  95 TESSSELQQEYDDLFITGIIDSYEGGLEFLKNYDD---TKNLIVFLGSSFGNFTPVNGKEFLKKINSTMKDGDLFLIGLDLVKSKTILEDAYND 185
                      ********************************995...99****************************************************** PP

  Methyltransf_33 197 sagvtaaFnlnllerinrelgadfdledfehvaewnaeegriemylrskrdqtvrvealdltvafkagekirteiSyKyteeevrelleaagle 290
                      s+gvta+Fnln+l+r+n el+++f+l++f+h+a +n++ +riemyl+s +dq+v + + +l++ +k++e i+te+S+K++ +++++l++++g++
       EPA05910.1 186 SQGVTAQFNLNVLSRLNDELDSNFNLNNFSHYALYNEHDQRIEMYLKSLEDQSVVISKSNLSIMLKKNELIHTEHSHKFKISQIKDLMHDTGFK 279
                      *********************************************************99*********************************** PP

  Methyltransf_33 291 vlkvWtdeksdfalyllq 308
                      +++ W de+s+fal+ll+
       EPA05910.1 280 IETIWLDENSYFALTLLS 297
                      ***************996 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   1.5e-05      0.13       9     163 ..      41     281 ..      32     283 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.5e-05
  Methyltransf_23   9 lsdklerllpklraggrvLdiGcGtGillevl....rengf..svtgvDlspeaveiaekakkaqkdqfdeq............eaaepqgkfd 84 
                      l+++ ++l+p+l+ + r++++G G+   ++++     + +   ++  +D+s+++ e  ++ ++  +d f  +            + ++ +++ +
       EPA05910.1  41 LKRLKDELPPYLNDSFRLVELGSGSSVKTRLIldvlNQIQEkiEYFPIDISEILTESSSELQQEYDDLF--ItgiidsyeggleFLKNYDDTKN 132
                      567778889999999999999999986555543432333333588899999888886543333333333..13333333333333333444666 PP

  Methyltransf_23  85 lIvlre.vlehvp..dppellrqiatllkpgGylllseplasl................................................... 124
                      lIv    +++++   +  e l++i++ +k+g ++l+   l+++                                                   
       EPA05910.1 133 LIVFLGsSFGNFTpvNGKEFLKKINSTMKDGDLFLIGLDLVKSktiledayndsqgvtaqfnlnvlsrlndeldsnfnlnnfshyalynehdqr 226
                      6666542567776556779999999999988777777766666678888888888888888888888877777777666666666666655544 PP

  Methyltransf_23 125 ....kedrllld....................wlylvpagrhisffsarslkelleeaGlevv 163
                                 +                    ++++ +  +h++ f  +++k+l+++ G+++ 
       EPA05910.1 227 iemyL------KsledqsvvisksnlsimlkkNELIHT--EHSHKFKISQIKDLMHDTGFKIE 281
                      44440......144444444444433332211444443..799*****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       792  (0.0441742); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1953.77
//
Query:       EPA05911.1  [L=241]
Description: gamma-glutamyl ligase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.9e-56  190.1   1.4    4.8e-56  189.8   1.4    1.0  1  F420_ligase  F420-0:Gamma-glutamyl ligase


Domain annotation for each model (and alignments):
>> F420_ligase  F420-0:Gamma-glutamyl ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.8   1.4   2.7e-60   4.8e-56       6     244 .]      11     218 ..       7     218 .. 0.98

  Alignments for each domain:
  == domain 1  score: 189.8 bits;  conditional E-value: 2.7e-60
                  ---TT--HHHHHHCCS-.....--TT-EEEEEHHHHHHHTT-EEEGGGS---HHHHHHHHHH.TS-H..................HHHHHHHHTEEEE CS
  F420_ligase   6 likegddlaeivvesvkkagleledgDivvvtekvvakaegnyvsledikpsekAeeiaeklkvidpilSrnrfsliLkalakatrkvevvlsepsde 103
                  +i++gdd+ +++++s +     ++dgDi+vv++k+++k eg++v+l+++ ps  Ae i++++ +++p                  r ve++l+e++++
   EPA05911.1  11 EIEPGDDISKLILDSAE-----IHDGDILVVAQKIISKQEGRIVELSSVIPSLLAEGISSEY-QKNP------------------RIVELILNESKQI 84 
                  79**************9.....9***************************************.****..................************* PP

                  EE-...S-EEEE.......TTS-EEEGGG-B-TTS-TTEEE---S-HHHHHHHHHHHHHHHHS---EEEE..EEEEEETTEECEEEEEEEEESB-SEE CS
  F420_ligase 104 vgn...qlidekytdevlvklGllgsnagidesnveegllkllPedpdksaeeikkklkertgkdveVliygkDpegriweladpvvaigtsglealr 198
                  ++     li+e+       k G++++nagidesnv++g+++llP ++d sae+i +++ ++tg dv+V+i   D++gr+++++++++aig+sg++++ 
   EPA05911.1  85 IRMnngILIVET-------KNGFICANAGIDESNVKHGFVTLLPINADLSAEKICNRILKNTGNDVSVVI--ADTFGRPFRMGQTNCAIGISGMRPIL 173
                  *99899999999.......***************************************************..************************** PP

                  E-TT-B-TTS-B-S--EEEHHHHHHHHHHHHC-SSSS---EEEEES CS
  F420_ligase 199 dlrgkkdldgkelgttpravtdelgsladLvsGsadegtPvvlvrg 244
                  d+ g+ d+++k+l++t  av+de++s+a+Lv+ ++  ++Pvv++rg
   EPA05911.1 174 DYAGTLDSFEKTLRITAIAVADEICSAAELVMQKT-TNCPVVIIRG 218
                  ********************************988.99*******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1440.78
//
Query:       EPA05912.1  [L=222]
Description: phosphoserine phosphatase SerB [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.6e-10   39.9   0.0    6.9e-10   39.6   0.0    1.2  1  HAD          haloacid dehalogenase-like hydrolase
    9.1e-10   39.2   0.0    1.2e-08   35.5   0.0    2.1  1  Hydrolase    haloacid dehalogenase-like hydrolase
    8.5e-05   22.4   0.7    0.00079   19.2   0.5    2.2  2  Hydrolase_3  haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   0.0   1.2e-13   6.9e-10       1     187 [.       9     173 ..       9     174 .. 0.74

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 1.2e-13
         HAD   1 alfDfDgTLldgdslelllrfllrrgaprlwralreklllalfrellrldraglaelleallaglseelaaelerfvaevirpklldpgalellaahra 99 
                 a+fD+ g L d + l+ l++ +l +      +++ e +++ +  ++ ++ ++gl+  +e +l+gl+    +e+++++     p ++  ga+e+++  +a
  EPA05912.1   9 AIFDVEGVLYDAEYLPILAE-KLNK-----EAEIWEITKKGI--QGVINWEDGLRTRVE-ALKGLDYNTCKEIADAL-----P-IM-TGAKEACRVLKA 91 
                 57777777777777767777.5555.....566666666666..555555666666666.58999955556666666.....3.45.9*********** PP

         HAD 100 aGdrvvvvSgglrplvepllaelgadevlatelevdd.rltgelglegkpvrgegkvaalrewlaaegegidleevvayGDspsDlpll 187
                 aG+++  +Sgg+ +++ +l +el+ d++ ++el ++d +l+g   + +++  +++k+ +++e      ++ + e+++ + D+ +D++l+
  EPA05912.1  92 AGWKLMAISGGFTIMTDRLQKELNLDYIFSNELIFKDgKLDGVTLHVDSDKSKSAKI-KIAE------WNEKKENIICVVDGANDVKLF 173
                 *******************************************55555555554443.5555......55555679**********986 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.0     2e-12   1.2e-08     107     205 ..      66     172 ..       7     177 .. 0.76

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 2e-12
                 HHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT.GGGESEEEEHHCESSTTT.......SHHHHHHHHHHHTSTGGGEEEEE CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxx RF
   Hydrolase 107 alavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG.ddyfdaviasdietvakp.......spegkvaaireLqgkpeevamVG 197
                 +    +iad l+++ +a+ea++ Lkaag+++  ++g++  + +r+ ++l+ d +f++++   + +  ++       + +  + +i e ++k+e+++ V 
  EPA05912.1  66 YNTCKEIADALPIMTGAKEACRVLKAAGWKLMAISGGFTIMTDRLQKELNlDYIFSNELIFKDGKLDGVtlhvdsdKSKSAKIKIAEWNEKKENIICVV 164
                 344445666666**************************************988889999999988666666667335555555555667********** PP

                 SSHHHHHH CS
                 xxxxxxxx RF
   Hydrolase 198 DgvnDaaa 205
                 Dg+nD++ 
  EPA05912.1 165 DGANDVKL 172
                 *****985 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0     0.075   4.5e+02      20      59 ..      82     120 ..      75     131 .. 0.87
   2 !   19.2   0.5   1.3e-07   0.00079     185     246 ..     139     199 ..     134     208 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.075
                  HHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEEE CS
  Hydrolase_3  20 tkeaikklkekgikvviATGRslravlpvleelgldlpvi 59 
                  +kea++ lk++g k++  +G  + ++ ++ +el+ld ++ 
   EPA05912.1  82 AKEACRVLKAAGWKLMAISGGFTIMTDRLQKELNLD-YIF 120
                  79999***************9999999999999999.443 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 1.3e-07
                  T-SHHHHHHHHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--G CS
  Hydrolase_3 185 gvsKgtalkklakelnisleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksn 246
                  + +K ++ k  + e+n ++e++i + Dg ND++++  aglg+A   a++ vk  A+ + + +
   EPA05912.1 139 DSDKSKSAKIKIAEWNEKKENIICVVDGANDVKLFDIAGLGIAY-RAQDVVKDLATTTLEEK 199
                  56888888888999*****************************7.59999999999887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.34s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1332.41
//
Query:       EPA05913.1  [L=265]
Description: deoxyhypusine synthase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-53  181.8   0.1    1.9e-53  181.6   0.1    1.0  1  DS        Deoxyhypusine synthase


Domain annotation for each model (and alignments):
>> DS  Deoxyhypusine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.6   0.1   1.1e-57   1.9e-53       3     210 ..      23     229 ..      21     232 .. 0.95

  Alignments for each domain:
  == domain 1  score: 181.6 bits;  conditional E-value: 1.1e-57
          DS   3 lesyeki.gfqatslgeaidilnkmrkdekctiflgltsnlissGlreiiadlvkeklvdvivtTaggieeDlikalgkktylgdfelddeeLrekgin 100
                 +++ +k+ gf++ +l++++dil  m +d++c  f+++ ++++s+Glr+ii+d++k+k++dv +tT+g +++D+++ +++ +  g+f++dd eL +++i+
  EPA05913.1  23 FDEISKSgGFESVNLSDGLDILTAMISDQECLKFISFVGAVVSTGLRGIIKDMIKNKWFDVAITTCGALDHDIARHFSN-YKEGSFTMDDGELADQHIH 120
                 56677777*********************************************************************99.999**************** PP

          DS 101 Rignllvpneny.ckfedwvreildkleeeq.kvwspselikelGkeindeeSilywAykndipvfcpaltDgslGdqlllfhsvkekkklkldivkDi 197
                 R+gn+lvp e+y   +e+ ++++l++  ++  k++s+ e++k +Gk++  e+S+lywAykn+i+v +p+++Dg++G q++lf+  ++++++kl+++ D 
  EPA05913.1 121 RLGNILVPMESYgPLIEEKMQSFLEEEYKNGiKEMSTVEICKMIGKHLG-ENSFLYWAYKNNIDVVVPGIMDGAVGSQIWLFT--QKHNDFKLNLAGDA 216
                 ************99***********9998653577*************5.9********************************..58889********* PP

          DS 198 relndialkakkt 210
                 + l+ +++kakk 
  EPA05913.1 217 DLLSGLIFKAKKI 229
                 **********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 1527.52
//
Query:       EPA05914.1  [L=321]
Description: ABC transporter, ATP-binding protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-33  116.7   0.1    1.5e-33  116.2   0.1    1.2  1  ABC_tran         ABC transporter
    2.3e-17   63.3   0.3    5.4e-17   62.1   0.1    1.7  1  oligo_HPY        Oligopeptide/dipeptide transporter, C-termin
    3.1e-05   23.5   0.7    5.4e-05   22.7   0.7    1.3  1  SMC_N            RecF/RecN/SMC N terminal domain
      8e-05   23.1   0.0    0.00013   22.4   0.0    1.5  1  AAA_16           AAA ATPase domain
    0.00018   21.8   0.7     0.0031   17.8   0.7    2.2  1  AAA_22           AAA domain
    0.00034   20.5   0.2    0.00065   19.6   0.2    1.5  1  RsgA_GTPase      RsgA GTPase
    0.00066   20.1   0.4      0.012   16.0   0.4    2.4  1  AAA              ATPase family associated with various cellul
      0.001   18.9   0.4          1    9.1   0.1    2.2  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
     0.0012   18.6   0.1     0.0027   17.4   0.1    1.5  1  AAA_29           P-loop containing region of AAA domain
     0.0016   17.8   0.0     0.0027   17.0   0.0    1.4  1  Zeta_toxin       Zeta toxin
     0.0019   18.0   0.0     0.0038   17.0   0.0    1.4  1  AAA_15           AAA ATPase domain
     0.0026   16.9   0.0     0.0038   16.3   0.0    1.3  1  T2SSE            Type II/IV secretion system protein
     0.0072   15.5   0.2     0.0095   15.1   0.2    1.2  1  G-alpha          G-protein alpha subunit
  ------ inclusion threshold ------
      0.013   15.9   0.0      0.027   14.8   0.0    1.6  1  RNA_helicase     RNA helicase
      0.013   15.0   0.1      0.033   13.7   0.1    1.7  1  AAA_7            P-loop containing dynein motor region
      0.014   14.8   0.0      0.023   14.1   0.0    1.4  1  DnaB_C           DnaB-like helicase C terminal domain
      0.014   15.1   0.1      0.032   13.9   0.1    1.7  1  Sigma54_activat  Sigma-54 interaction domain
      0.017   15.7   0.0      0.032   14.8   0.0    1.5  1  AAA_18           AAA domain
      0.018   14.4   0.4       0.11   11.8   0.1    2.1  2  ATPase           KaiC
      0.036   14.5   0.1      0.094   13.2   0.1    1.7  1  Phage_TAC_13     Phage tail assembly chaperone, TAC
      0.039   14.0   1.8      0.054   13.6   0.3    1.9  2  DUF87            Helicase HerA, central domain
      0.047   12.7   0.1      0.063   12.3   0.1    1.1  1  Membralin        Tumour-associated protein
       0.05   13.3   0.1       0.21   11.3   0.0    1.9  2  IstB_IS21        IstB-like ATP binding protein
      0.055   13.1   0.0      0.082   12.6   0.0    1.2  1  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
      0.085   12.9   0.0       0.28   11.2   0.0    1.8  2  AAA_5            AAA domain (dynein-related subfamily)
      0.094   12.7   0.0       0.17   11.8   0.0    1.5  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.097   12.6   0.0       0.19   11.6   0.0    1.5  1  APS_kinase       Adenylylsulphate kinase
       0.11   12.2   0.0       0.26   11.0   0.0    1.6  2  AAA_30           AAA domain
       0.12   11.7   0.2       0.24   10.7   0.0    1.5  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
       0.13   12.4   0.0       0.52   10.5   0.0    2.0  1  AAA_33           AAA domain
       0.29   11.6   5.7        2.9    8.3   5.7    2.3  1  AAA_23           AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.2   0.1   2.6e-36   1.5e-33       2     136 ..      31     182 ..      30     183 .. 0.96

  Alignments for each domain:
  == domain 1  score: 116.2 bits;  conditional E-value: 2.6e-36
                 EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG..B-HHHCCHCEEEE-SS..--S-TTSBHHHH..............HHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx..xxxxxxxxxxxx..............xxx RF
    ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke..qeleslrkeigvlpqe..pqlfpeltvren..............esd 82 
                 ++vs+ +k+ge+ ++ Ge+G+GKSt++kl+++  + ++G+il++++++k+  ++l++ r + ++++q+  ++++p++t+++               e++
  EPA05914.1  31 DDVSFAVKKGEIFVLAGESGSGKSTIAKLILKSIESDSGKILFENQEIKNdkESLKKIRMNCQMIHQDpyDSVNPRMTIADIisepleihkmgnkdERK 129
                 89************************************************99999*************999**********9***********988888 PP

                 TCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  83 eeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                 +++ ++l++++l+   ++++k+ p+ LSgGq+qrv+laral  kpk++l+DEp 
  EPA05914.1 130 KRVIEVLREVKLEP-VEEILKKYPHMLSGGQRQRVVLARALTLKPKIILADEPV 182
                 88*********999.889999********************************7 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.1   0.1   9.3e-20   5.4e-17       1      65 []     234     299 ..     234     299 .. 0.98

  Alignments for each domain:
  == domain 1  score: 62.1 bits;  conditional E-value: 9.3e-20
   oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekd.klekikgeapslerldeGCpFapRCpfaleeC 65 
                 +E+g++++++ +p+HPYT+aL++++ ++d+e+  + +ki+ ++p+  +  eGC+F+ RCp+a e+C
  EPA05914.1 234 IEIGTTNDVLLRPKHPYTQALIDAISEPDPENLdRERKIRINEPLDINVYEGCRFRARCPYAIEKC 299
                 79*****************************9999******************************* PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.7   9.4e-08   5.4e-05      25     201 ..      41     217 ..      20     232 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 9.4e-08
                 SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--...BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEETTSEEEEEETTEEE-H CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk...skekasvkkaeveitfdnedkklkiekeevsisrrvkrkgeseykingkevtk 120
                 ++ ++ G+ GSGKs +   il  +         s++ + l  +   +++k+s+kk +++  + ++d      +++++i   +++  e  +k+ +k+ +k
  EPA05914.1  41 EIFVLAGESGSGKSTIAKLILKSI--------ESDSGKILFENqeiKNDKESLKKIRMNCQMIHQDPY-DSVNPRMTIADIISEPLE-IHKMGNKDERK 129
                 456789************994444........444444444444333455666666665555455554.456778888877777666.89999****** PP

                 HHHHHHHHCTT-STT.........CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSE..EEEE-SSHHH CS
                 xxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxx RF
       SMC_N 121 kevsellesagiske.........lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQ..fivislreem 201
                 k v e+l+++++++          +LSgG+++ v la  + +   kp+ + l De  + LD + ++++ el++e +k+ Q  f+ i+++  +
  EPA05914.1 130 KRVIEVLREVKLEPVeeilkkyphMLSGGQRQRVVLARALTL---KPK-IILADEPVSMLDVSIRAEMLELMHELQKKYQisFLYITHDLAT 217
                 *************9999**************98888876554...554.7789************************999446777776555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   2.2e-07   0.00013      19      57 ..      37      77 ..      20     186 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 2.2e-07
      AAA_16 19 vrsgrpelvllsGesGvGKsslvrellralekd..ggif..lr 57
                v++g  e+ +l GesG+GKs++++ +l+++e d  +++f   +
  EPA05914.1 37 VKKG--EIFVLAGESGSGKSTIAKLILKSIESDsgKILFenQE 77
                5555..899**********************996424443333 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.7   5.4e-06    0.0031       4     128 ..      39     211 ..      36     218 .. 0.56

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 5.4e-06
      AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee...................................erpevvfvtlpsstsskdllrellralgle 67 
                 +  i v+ GesG+GK+t ++ +l++ + ++                                                       +d+ +e l+     
  EPA05914.1  39 KGEIFVLAGESGSGKSTIAKLILKSIESDSGKILfenqeikndkeslkkirmncqmihqdpydsvnprmT--------------IADIISEPLE----- 118
                 567899******************9976544443777777777766666664333333333333322220..............2222222222..... PP

      AAA_22  68 lka............................erlsseell.ealeqalrarav.........ielliiDEaqh.lr...seealeeLrsllnlsrkgvq 124
                                                  +  + l   + ++      v         +++++ DE    l+   ++e+le  ++l++  +++++
  EPA05914.1 119 --IhkmgnkderkkrvievlrevklepveeiLKKYPHMLSgGQRQR------VvlaraltlkPKIILADEPVSmLDvsiRAEMLELMHELQK--KYQIS 207
                 ..12223333555555555555543333354222222222233333......2333344788888889988775667544888888888888..88888 PP

      AAA_22 125 liLv 128
                 ++++
  EPA05914.1 208 FLYI 211
                 8665 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.2   1.1e-06   0.00065      84     130 ..      24      71 ..       7      96 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.1e-06
                  TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S-- CS
  RsgA_GTPase  84 aktkegleelkellkd.ktsvlvGqSGvGKStLinallpelelktgev 130
                  +++ +++++++ ++k+ ++ vl+G+SG GKSt+ + +l + e   g++
   EPA05914.1  24 TTKIKAVDDVSFAVKKgEIFVLAGESGSGKSTIAKLILKSIESDSGKI 71 
                  44457899999999988******************9999877766665 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.4   2.1e-05     0.012       2     110 ..      44     240 ..      43     250 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.1e-05
                 EEESSTTSSHHHHHHHHHHHHTHE...................EEEEETTTCSSS............................................ CS
         AAA   2 llyGppGtGKTllakavakelgve...................fleisgsellsk............................................ 37 
                 +l G  G GK+++ak + k+++++                    +++++  + ++                                            
  EPA05914.1  44 VLAGESGSGKSTIAKLILKSIESDsgkilfenqeikndkeslkKIRMNCQMIHQDpydsvnprmtiadiisepleihkmgnkderkkrvievlrevkle 142
                 699*****************8433333333333333333443356666666664477777777777777777888888888888888888888888888 PP

                 ..........STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS..........................S CS
         AAA  38 ..........yvgesekkirelfkeakekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkk..........................e 100
                           ++  + ++ r ++++a + + p+i++ DE  ++   +          + +++l+ + +++kk                           
  EPA05914.1 143 pveeilkkypHMLSGGQRQRVVLARALTLK-PKIILADEPVSMLDVS----------IRAEMLELMHELQKKyqisflyithdlataryfgqrigilyL 230
                 888888887777777777777777776665.8999999988887777..........778888888888887555555555555555555555555554 PP

                 STEEEEEEES CS
         AAA 101 skvivigatn 110
                 +k+i ig+tn
  EPA05914.1 231 GKIIEIGTTN 240
                 4555555555 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.1    0.0018         1       1      35 [.      42      70 ..      42      93 .. 0.67
   2 !    8.2   0.0    0.0032       1.9     238     299 ..     156     215 ..      99     218 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0018
      AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltde 35
                + vl G  gsGKS++ +++  l+++    e++  +
  EPA05914.1 42 IFVLAGESGSGKSTIAKLI--LKSI----ESDSGK 70
                679****************..4444....333333 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0032
      AAA_21 238 SdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSp 299
                 S G+++   +++a + +lk+ +++l DEp + L+ ++ ++ lel+ el++   + ++  TH+ 
  EPA05914.1 156 SGGQRQR--VVLARALTLKP-KIILADEPVSMLDVSIRAEMLELMHELQKkYQISFLYITHDL 215
                 5555554..33333444444.9***********************66655488899*****96 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   4.6e-06    0.0027      13      38 ..      31      56 ..      27      59 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.6e-06
      AAA_29 13 dghtieidlkgatlltGpsGsGKSTl 38
                d+ ++ ++  ++++l+G+sGsGKST+
  EPA05914.1 31 DDVSFAVKKGEIFVLAGESGSGKSTI 56
                55667777555**************8 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   4.7e-06    0.0027      14      55 ..      38      79 ..      23      93 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.7e-06
  Zeta_toxin 14 erPklillgGqpGAGKselaellkdelerqgnvvrldpDdlR 55
                ++  + +l+G +G+GKs++a+l+ +++e++++ + ++  +++
  EPA05914.1 38 KKGEIFVLAGESGSGKSTIAKLILKSIESDSGKILFENQEIK 79
                5567889********************988888777776666 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   6.6e-06    0.0038      24      84 ..      40     113 ..      23     156 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.6e-06
      AAA_15  24 e.ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifeniseskdikIdvef..................a 84 
                   + vl G+ +sGKS+i++++  +++  e+ +  +i +e++++++   ++  k+i+ +++                   +
  EPA05914.1  40 GeIFVLAGESGSGKSTIAKLI--LKS-IESDS-GKILFENQEIKND--KESLKKIRMNCQMihqdpydsvnprmtiadiI 113
                 358899***************..444.33333.5566666666555..78888899888885555555555555544441 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   6.6e-06    0.0038     122     171 ..      33      80 ..       5     118 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 6.6e-06
       T2SSE 122 lrkavrerglilvsGgTgsGKttllyallkeinksderivtvEDpvEiql 171
                 ++ av++  +++++G  gsGK+t++  +lk i++++ +i+      Ei+ 
  EPA05914.1  33 VSFAVKKGEIFVLAGESGSGKSTIAKLILKSIESDSGKILFE--NQEIKN 80 
                 567899999**************************8888753..344444 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.2   1.6e-05    0.0095      26     144 ..      43     207 ..      19     231 .. 0.54

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.6e-05
                 EEEEESTTSSHHHHHHHHH.HHCS--....--HHHHHCCHHHHHHHHHHHHHHHHHHHHHTT.........................HHHC-SS-SCCC CS
     G-alpha  26 llllGqseSGKsTilkqlk.llykkg....fseeelatwraviqlnivrsiktilealesleselsesf..................elqelkerldpl 101
                 ++l G+s+SGKsTi k +   ++ ++    f+++e+++ ++      +++i++ ++ + +   ++ ++                   +++  k+ ++ l
  EPA05914.1  43 FVLAGESGSGKSTIAKLILkSIESDSgkilFENQEIKNDKE-----SLKKIRMNCQMIHQDPYDSVNPRmtiadiisepleihkmgnKDERKKRVIEVL 136
                 6899**********998763666555889*****9988555.....33334444444433211111111233334444455555554222222222333 PP

                 S-HCHHHH.......................................HHCCHHC..........-HCHHHHHHHHCCSHHHH CS
     G-alpha 102 kkveasliaklssateee.............................qeiefnp..........raevgedikaLwndpgiq 144
                 ++v+ +  +++                                          +          rae+ e +++L +++ i+
  EPA05914.1 137 REVKLEPVEEI------LkkyphmlsggqrqrvvlaraltlkpkiilA-----DepvsmldvsiRAEMLELMHELQKKYQIS 207
                 33333322222......1223333444444446666555555333331.....13333344455556666666666666555 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   4.7e-05     0.027       2      58 ..      44     112 ..      43     144 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.7e-05
  RNA_helicase   2 wlyGpsgeGKStlakeLakallkkl..........klkkkdsvys.rnpeddfwdgYt.gqevvvidDf 58 
                   +l G+sg GKSt+ak + k++++++          k++k++   +  n++  + d Y+  ++ + i D+
    EPA05914.1  44 VLAGESGSGKSTIAKLILKSIESDSgkilfenqeiKNDKESLKKIrMNCQMIHQDPYDsVNPRMTIADI 112
                   689*************99999977766677766652222222222144444444666655555555555 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   5.7e-05     0.033      28      77 ..      35      84 ..      21      97 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.7e-05
       AAA_7 28 lllknkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanq 77
                  +k++  ++l G++G+GK++i+k +lk++++++ ++l+ n   + + ++
  EPA05914.1 35 FAVKKGEIFVLAGESGSGKSTIAKLILKSIESDSGKILFENQEIKNDKES 84
                5688899999********************99887777766655555555 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   3.9e-05     0.023       4      64 ..      25      84 ..      24     141 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.9e-05
                SSTHHHHHHCTSBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHH CS
                xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
      DnaB_C  4 tgfkdLDkltsGlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlv 64
                t+ k +D++   ++kg+++++A+ ++ Gk+++a  i +++   ++ ++++ + e ++++  
  EPA05914.1 25 TKIKAVDDVSFAVKKGEIFVLAGESGSGKSTIAKLILKSIES-DSGKILFENQEIKNDKES 84
                6788999******************************99986.445788888887765543 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   5.5e-05     0.032      11      53 ..      29      71 ..      18      98 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.5e-05
                     HHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-E CS
  Sigma54_activat 11 lleqikkvaktdlsvlitGesGtGKellaraiheaskrkekpf 53
                     +++ ++ ++k+    ++ GesG+GK+++a++i ++ + +++++
       EPA05914.1 29 AVDDVSFAVKKGEIFVLAGESGSGKSTIAKLILKSIESDSGKI 71
                     455556666666777899**************99766655544 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   5.5e-05     0.032       3      67 ..      45     103 ..      44     167 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.5e-05
      AAA_18   3 ltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpealdeskrldedkldklldaleen 67 
                 l+G +G+GK+t+ak + k+      ++++++en+    + +    + k+++++ ++ ++d  +  
  EPA05914.1  45 LAGESGSGKSTIAKLILKSI--ESDSGKILFENQEIKNDKE----SLKKIRMNCQMIHQDPYDSV 103
                 89**************9997..8999999999664444444....47778888777777665555 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1    0.0002      0.11       3      97 ..      25     121 ..      23     147 .. 0.65
   2 ?    0.4   0.0      0.59   3.4e+02     139     160 ..     188     209 ..     177     225 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0002
      ATPase   3 tgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepa.....edlrenakslGwdlekleeegklaiidasesaeesa 96 
                 t I+  D++    + +g++  ++Ge+G+GK+++a+  ++k++e+   + +f   e ++     +++r n++++  d  +  +  +++i d+ ++  e++
  EPA05914.1  25 TKIKAVDDVS-FAVKKGEIFVLAGESGSGKSTIAK-LILKSIESDSGKILFENQEIKNdkeslKKIRMNCQMIHQDPYDSVNP-RMTIADIISEPLEIH 120
                 7788888886.67899****************986.67788888444444433333325555666777777776666555555.566666666665544 PP

      ATPase  97 e 97 
                 +
  EPA05914.1 121 K 121
                 4 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.59
      ATPase 139 vaReilrqlvrvlkklgvTail 160
                  +R+++ +l+++l+k+++ + l
  EPA05914.1 188 SIRAEMLELMHELQKKYQISFL 209
                 68***********666666554 PP

>> Phage_TAC_13  Phage tail assembly chaperone, TAC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   0.00016     0.094      31      86 ..      12      85 ..       6      95 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00016
  Phage_TAC_13 31 tvyvrklsfktaeadlkalkkked...................kvAariaaSicdekGkpvftvdditgeldpsl 86
                  +++++k  fk+  +++ka+ + +                     +A+ i+ Si  + Gk +f+ ++i  + ++sl
    EPA05914.1 12 KTFIKKGRFKSKTTKIKAVDDVSFavkkgeifvlagesgsgksTIAKLILKSIESDSGKILFENQEIK-NDKESL 85
                  67888888888888888887777678888888888888888889***********************9.665555 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.3   9.3e-05     0.054      30      56 ..      47      72 ..      32      73 .. 0.88
   2 ?   -0.9   0.1       2.5   1.4e+03     151     180 ..     121     152 ..      76     210 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.3e-05
       DUF87 30 gsTGsGKSntvavLleellekkgatil 56
                g++GsGKS+ ++++l+++  +++++il
  EPA05914.1 47 GESGSGKSTIAKLILKSIE-SDSGKIL 72
                89***************98.7777775 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.5
       DUF87 151 k..kekeelrklknqaiarlldkledllrkgg 180
                 k  +++e  ++  + +++ +l+++e++l+k+ 
  EPA05914.1 121 KmgNKDERKKRVIEVLREVKLEPVEEILKKYP 152
                 33344445555555555555555555555544 PP

>> Membralin  Tumour-associated protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00011     0.063     133     239 ..     113     234 ..      51     243 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
   Membralin 133 eaeeeekessslkkeeelrsveliensslktnlklledleiseleede.......................evkpeee..yiveYsleygfLrlspstr 206
                  +e  e +++  k e++ r +e++++ +l+   + l+          +                       + +  +e   +++ s++ ++L+l ++ +
  EPA05914.1 113 ISEPLEIHKMGNKDERKKRVIEVLREVKLEPVEEILK----------KyphmlsggqrqrvvlaraltlkpKIILADEpvSMLDVSIRAEMLELMHELQ 201
                 2222222222222333333333333333332222222..........022233333334456666677777555444445999**************** PP

   Membralin 207 erlnipvllvaLdpekdkCfgdslsrflLkefl 239
                 ++++i++l+++ d+++ + fg+++  ++L + +
  EPA05914.1 202 KKYQISFLYITHDLATARYFGQRIGILYLGKII 234
                 ***********************9999998766 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00036      0.21      30      80 ..      22      73 ..       6      95 .. 0.77
   2 ?   -0.8   0.0       1.9   1.1e+03     107     154 ..     171     220 ..     156     225 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00036
   IstB_IS21 30 ldkrkvkeLatlsf.iekkenivllGpsGvGKshlaialgveavraglsvlf 80
                ++ +k+k++   sf ++k e +vl G sG GKs +a  + ++   +  ++lf
  EPA05914.1 22 SKTTKIKAVDDVSFaVKKGEIFVLAGESGSGKSTIAKLILKSIESDSGKILF 73
                4567788888899956788999*************97654443334455555 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.9
   IstB_IS21 107 lkvdllilDd.lgllpld.qaeaellfeviekryerrsiiitsnlpfaew 154
                 lk+++++ D+ +++l+++ +ae  +l++ ++k+y+ + + it +l  a++
  EPA05914.1 171 LKPKIILADEpVSMLDVSiRAEMLELMHELQKKYQISFLYITHDLATARY 220
                 45566666664455666533455567777888999998899988877765 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00014     0.082       6      65 ..      32     138 ..      27     184 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00014
                  HHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSS.EEEEEE..............................................ESEEHHHH CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx..............................................xxxxxxxx RF
  ATP-synt_ab   6 DalfpivqGqrtlipgafgvGktvisqslskqsnsdd.aiiyvg..............................................iGergnev 56 
                  D+ f + +G+  ++ g++g Gk++i++ ++k  +sd+  i +                                                +G++ +  
   EPA05914.1  32 DVSFAVKKGEIFVLAGESGSGKSTIAKLILKSIESDSgKILFENqeikndkeslkkirmncqmihqdpydsvnprmtiadiisepleihkMGNKDERK 129
                  6779999**************************99985555555777777777777777777777777777777777777777777777755444444 PP

                  HHHHHHCHH CS
                  xxxxxxxxx RF
  ATP-synt_ab  57 aevleefpe 65 
                  ++v+e ++e
   EPA05914.1 130 KRVIEVLRE 138
                  444444444 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00048      0.28       2      24 ..      43      65 ..      42      81 .. 0.84
   2 ?   -1.9   0.0       5.3     3e+03      55      91 ..     161     199 ..     143     214 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00048
                EEEE--SSSSHHHHHHHGGGGBS CS
       AAA_5  2 vlLvGppGtgKselaerlaaaln 24
                ++L G++G+gKs++a+ +++ ++
  EPA05914.1 43 FVLAGESGSGKSTIAKLILKSIE 65
                689**************999884 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5.3
                 ..--------.G-SEEEEES.GGG--HHHHHHHHHHHHS CS
       AAA_5  55 vdsplvraar.egeilvlDE.veraesevlnsLlsllee 91 
                 +  +l ra + +++i++ DE v +++ ++ +++l l++e
  EPA05914.1 161 QRVVLARALTlKPKIILADEpVSMLDVSIRAEMLELMHE 199
                 455667777677777777765666667777777776665 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0    0.0003      0.17      14      45 ..      37      66 ..      21     135 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0003
                HHHCHTEEEEEEESTTSSHHHHHHHHHHHTT- CS
        TsaE 14 lakalgdvilLeGdLGaGKTtlvrglakalgv 45
                ++k  g++++L G+ G+GK+t+++ ++k+++ 
  EPA05914.1 37 VKK--GEIFVLAGESGSGKSTIAKLILKSIES 66
                222..789*******************99865 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00033      0.19       2      29 ..      40      67 ..      39      81 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00033
                -EEEEEESSTTSSHHHHHHHHHHHHHHT CS
  APS_kinase  2 gvvvwltGlsgsGKstianalekkLvek 29
                g ++ l+G sgsGKstia+ + k+++++
  EPA05914.1 40 GEIFVLAGESGSGKSTIAKLILKSIESD 67
                667889*************998887765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00045      0.26      15      49 ..      37      71 ..      29      98 .. 0.83
   2 ?   -2.4   0.0       5.8   3.4e+03      86     114 ..     169     199 ..     128     204 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00045
      AAA_30 15 tsgdrvavltGpAGtGKttalkalreaweaaggrv 49
                 ++  + vl G  G+GK+t+ k + + +e++ g++
  EPA05914.1 37 VKKGEIFVLAGESGSGKSTIAKLILKSIESDSGKI 71
                3445699*****************99999886565 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.8
      AAA_30  86 lepg.tllivDE.agmvdtkqlaallkaaek 114
                 l+ + ++++ DE ++m+d +  a++l+ +++
  EPA05914.1 169 LTLKpKIILADEpVSMLDVSIRAEMLELMHE 199
                 3334467777775678777777777776655 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00042      0.24      18      80 ..      36     102 ..      22     120 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00042
  Mg_chelatase  18 aaaGgHnlllvGppGsGKtmlakrlpsllpplseeealevakia....svagkkeeekllkrrpfra 80 
                   a+  g  ++l+G +GsGK+ +ak + + + + s +  +e ++i+    s+++ + + +++++ p+ +
    EPA05914.1  36 AVKKGEIFVLAGESGSGKSTIAKLILKSIESDSGKILFENQEIKndkeSLKKIRMNCQMIHQDPYDS 102
                   5555666899*************98877777777777777666422226777777777778877765 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00089      0.52       2      24 ..      43      65 ..      42     220 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00089
      AAA_33  2 vllvGlpGsGKstlaerllkklg 24
                ++l G +GsGKst a+ +lk   
  EPA05914.1 43 FVLAGESGSGKSTIAKLILKSIE 65
                5789************9987644 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   5.7    0.0051       2.9      18      39 ..      39      60 ..      20     151 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0051
      AAA_23 18 skgltlItGpNGaGKTTildAi 39
                +  ++++ G+ G+GK+Ti   i
  EPA05914.1 39 KGEIFVLAGESGSGKSTIAKLI 60
                4469**************8766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       876  (0.0488594); expected 358.6 (0.02)
Passed bias filter:                      664  (0.037035); expected 358.6 (0.02)
Passed Vit filter:                       109  (0.00607954); expected 17.9 (0.001)
Passed Fwd filter:                        31  (0.00172904); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              31  [number of targets reported over threshold]
# CPU time: 0.68u 0.34s 00:00:01.02 Elapsed: 00:00:00.51
# Mc/sec: 1901.71
//
Query:       EPA05915.1  [L=30]
Description: hypothetical protein BG20_I1333, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (30 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      208  (0.0116013); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.47
# Mc/sec: 193.68
//
Query:       EPA05916.1  [L=66]
Description: hypothetical protein BG20_I1338 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       743  (0.0414412); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 443.94
//
Query:       EPA05917.1  [L=454]
Description: proline--tRNA ligase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-18   67.1   0.0    3.1e-18   66.4   0.0    1.3  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
    1.4e-16   60.4   0.2    1.4e-16   60.4   0.2    2.1  2  HGTP_anticodon  Anticodon binding domain


Domain annotation for each model (and alignments):
>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.4   0.0   3.5e-22   3.1e-18       5     176 ..     106     277 ..      98     280 .. 0.85

  Alignments for each domain:
  == domain 1  score: 66.4 bits;  conditional E-value: 3.5e-22
                   ETTSEEEEE-SSSHHHHHHHHHHHEEEB.GGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEES.GGGHHHHHHHHHHHHHHHHHHTT..SC CS
                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx.xxx RF
  tRNA-synt_2b   5 drndreyiLkPtneetfvelirdevlrs.krLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfha.easlddslrdlikaisriferlg.lef 98 
                   ++ +++++L+Pt+e+  + +++++ ++s ++LPlk+    t  R E +++++ lR  eF +++g+ +ha +++++ ++ ++++ +++  e+ + ++ 
    EPA05917.1 106 NEVGDRLALRPTSETLAYTMYSKW-IQSwRDLPLKINFWNTALRAEIKATKPFLRTSEFLWQEGHTVHAvQEEAEKEVMKILEIYKKTVEDELaIP- 200
                   455899****************99.***888**************************************999999999999999988888765044. PP

                   EEEEEE..GTTSCBTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHTTEEEECTTSSEEEEEEEEEEEEHHHHHHHHH CS
                   xxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  tRNA-synt_2b  99 raiiel..msaksadykdkkefeavsesltkgieigtiqklgtrlserlgatvldennreksvimicaaigveRllsail 176
                    +i +    ++k + + +++ +e +++  +k++++gt ++lg+++s  ++++++d++n e++   +  +++  Rl++a++
    EPA05917.1 201 -VITGKksEKEKFVGAVYTTTMESIMP-DGKALQMGTSHFLGQNFSIPFEVKFADKDNVEQFAWQTSWGVS-WRLIGAMI 277
                   .45555223334477889999999999.9*******************************99977777766.69988876 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.4   0.2   1.6e-20   1.4e-16       1      88 [.     296     387 ..     296     390 .. 0.92
   2 ?   -2.6   0.2      0.72   6.5e+03      67      80 ..     437     450 ..     434     452 .. 0.82

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 1.6e-20
                     SEEEEESSSS...HHHHH...HHHHHHHHHHHTTTSEEEEES.SSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTCEEEEEETTHHH CS
  HGTP_anticodon   1 qvvviplnek...aeele...eyakklaeeLraagirveldd.snesigkkireadllgipfavvvGekelekgtvtvrdrdtreqervsldelv 88 
                     qvv++p+ +    +       +  ++++e+L+   irv++dd ++ ++g+k+++++l+g+p+++++G+k++ek+++ + +r +re++++ ++e++
      EPA05917.1 296 QVVIVPIYKSddaK---NivfPKLNEIKEQLETTKIRVHVDDrNELTPGYKFNDWELKGVPLRIEIGPKDIEKQQIVLAKRYNREKINLGFNEIE 387
                     8******9985543...2446*********************9999******************************************9999875 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.72
                     TEEEEEETTTCEEE CS
  HGTP_anticodon  67 gtvtvrdrdtreqe 80 
                     +++ vr+r +++q+
      EPA05917.1 437 EKLDVRKRSKKRQV 450
                     57899999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 2923.14
//
Query:       EPA05918.1  [L=39]
Description: hypothetical protein BG20_I1345 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.39   10.2   0.4       0.39   10.2   0.4    2.4  3  DUF4462   Domain of unknown function (DUF4462)


Domain annotation for each model (and alignments):
>> DUF4462  Domain of unknown function (DUF4462)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.4   2.2e-05      0.39      12      21 ..       5      15 ..       2      15 .. 0.88
   2 ?   -2.2   0.0      0.16   2.9e+03      14      17 ..      17      20 ..      17      25 .. 0.71
   3 ?    0.1   2.2     0.033   5.9e+02       4       9 ..      32      37 ..      32      38 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 2.2e-05
     DUF4462 12 pRAGsIGIG.C 21
                +R+G++GIG C
  EPA05918.1  5 IRVGLVGIGnC 15
                5********66 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.16
     DUF4462 14 AGsI 17
                AG+I
  EPA05918.1 17 AGLI 20
                7888 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.033
     DUF4462  4 SrfnWN 9 
                S +nWN
  EPA05918.1 32 SGSNWN 37
                669**9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       244  (0.0136092); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.43
# Mc/sec: 271.66
//
Query:       EPA05919.1  [L=205]
Description: translocator protein, LysE family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.5e-31  108.2  15.5    4.5e-31  107.8  15.5    1.0  1  LysE        LysE type translocator
  ------ inclusion threshold ------
      0.075   13.0   0.5       0.23   11.4   0.5    1.8  1  TNFR_16_TM  Tumor necrosis factor receptor member 16 trans-me
        1.4    9.1   6.7        5.2    7.2   6.7    1.9  1  GWT1        GWT1


Domain annotation for each model (and alignments):
>> LysE  LysE type translocator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.8  15.5   7.6e-35   4.5e-31       2     190 ..      17     201 ..      16     203 .. 0.96

  Alignments for each domain:
  == domain 1  score: 107.8 bits;  conditional E-value: 7.6e-35
        LysE   2 slllspGpqnllvlkqgikrgfkggilvalgvligdavlillgllGlalLlkaapivlsilrllGgayLlwlgvlalrdakekkveaeksveaslvkpf 100
                 s++++pGp +++ ++qg++ g k+gi +a+g++i++  l++l+ +G+  +    p + + +++lG+++L+ ++  ++r+a++k+ +++ +     ++p+
  EPA05919.1  17 SGVMAPGPLFAANVSQGLRGGGKAGIKMAIGHTIVEFPLVILLGMGVFSFEV-FPEFRTYVSILGAVVLFVFAGIQIRSALQKNKSNNFNL---KHSPI 111
                 899***********************************************99.******************************97555555...5**** PP

        LysE 101 lkglllslsNPkailfwlsvisallaka.eqygdagrlilaaglvvasliwfsllaflaarlsrrlsskkvlriinvvvgvlligfavkll 190
                 ++g+ll+ +NP++i++wlsv+  l+++a   +  +g+l+ ++ +++ +++w++ +++la+  s+ ls + ++ i+++ ++v+l +f++ ++
  EPA05919.1 112 ITGVLLTGLNPFFIVWWLSVGFKLISDAvLIWAFTGILFVFLFHIWMDFAWLYSVGHLASKSSKILSNRNYK-ILMISLSVMLAYFGITFI 201
                 *********************************************************************977.***************998 PP

>> TNFR_16_TM  Tumor necrosis factor receptor member 16 trans-membrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.5   3.9e-05      0.23      10      22 ..      75      87 ..      74      91 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.9e-05
  TNFR_16_TM 10 YcSILaaVvvgLl 22
                Y+SIL+aVv++  
  EPA05919.1 75 YVSILGAVVLFVF 87
                **********976 PP

>> GWT1  GWT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   6.7   0.00087       5.2       7     100 ..      76     195 ..      74     204 .. 0.51

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00087
        GWT1   7 fsliGylaiyll.gvslgkyvlkrekeae..eee.............kkkkkkkkesketlkllikllllsilllllllllelyvef............ 77 
                 +s++G + ++++ g+++ + + k+++++   + +                         +l++  kl++ ++l+++++ +l +++              
  EPA05919.1  76 VSILGAVVLFVFaGIQIRSALQKNKSNNFnlK-HspiitgvlltglnP------FFIVWWLSVGFKLISDAVLIWAFTGILFVFLFHiwmdfawlysvg 167
                 57777777775426666666664444433441.134444443333220......223333333333333333333333222222222233335555666 PP

        GWT1  78 .....vSRrlaNlpYvlwvvalnltlll 100
                      +S++l N +Y +++++l+++l  
  EPA05919.1 168 hlaskSSKILSNRNYKILMISLSVMLAY 195
                 667778*************999887654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       866  (0.0483016); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:01.08
# Mc/sec: 573.90
//
Query:       EPA05920.1  [L=307]
Description: inositol-3-phosphate synthase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.7e-30  103.5   0.4    2.2e-28   98.6   0.0    2.2  2  Inos-1-P_synth  Myo-inositol-1-phosphate synthase
  ------ inclusion threshold ------
      0.041   13.4   0.1       0.85    9.1   0.0    2.2  2  RexA            Intracellular sensor of Lambda phage, Abi com
      0.057   13.0   0.0       0.13   11.8   0.0    1.6  1  CobU            Cobinamide kinase / cobinamide phosphate guan
       0.17   11.6   0.1        9.3    5.9   0.0    2.7  3  Raco_middle     RACo middle region


Domain annotation for each model (and alignments):
>> Inos-1-P_synth  Myo-inositol-1-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1     0.024   1.1e+02      38      65 ..      62      89 ..      54     135 .. 0.69
   2 !   98.6   0.0     5e-32   2.2e-28       1     108 [.     142     249 ..     142     250 .. 0.96

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.024
                    TSHHHHHHHHHHHHHHHHHHHSS--EEE CS
  Inos-1-P_synth 38 seeerfksKkisKssvvddivkanelly 65
                    +e+ + + Kki K++ v+ iv++ ++ +
      EPA05920.1 62 HEQITEEVKKIIKENNVEIIVSYLPVGS 89
                    5556677888888888888887766554 PP

  == domain 2  score: 98.6 bits;  conditional E-value: 5e-32
                     SHHHHHHHHHHHHHHTT-EEEEEEEEEEE-HHHHHHTTSHHHHHHHHHHHHHHHHHHHSS--EEE....EEE...EE-GGGTTEEEEEEEEEEEE CS
  Inos-1-P_synth   1 GqTklksvLaellverglkvksivslNilGnnDgknlseeerfksKkisKssvvddivkanellyvdhevvi...kYvpylgDsKvaldeiesei 92 
                     G+T+++++La+l+ +rg k+++++++N++Gn+D++n++e++r++sK+isK++ v++++k++     d ++++   +++p+lg++K ++++ie++ 
      EPA05920.1 142 GATIVHRTLAKLCSDRGTKIEKTYQINVGGNTDFLNMKEQDRLASKRISKTESVQSQLKERLA---DDQIYVgpsDFIPFLGNTKLMFMRIEGRQ 233
                     9**********************************************************9554...5679999********************** PP

                     GGGEEEEEEEEEEEEH CS
  Inos-1-P_synth  93 flggkntielkleceD 108
                     + +++ ++e++le++D
      EPA05920.1 234 WANIPYNMEVRLEVDD 249
                     **************99 PP

>> RexA  Intracellular sensor of Lambda phage, Abi component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.027   1.2e+02     183     215 ..      35      75 ..      28     117 .. 0.70
   2 ?    9.1   0.0   0.00019      0.85      48     106 ..     162     222 ..     145     234 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.027
        RexA 183 nsvdaelleslei....tlKP.klkk...nikkaakniikn 215
                 +++++ ll+++ i    ++KP ++kk   +i++++k iik+
  EPA05920.1  35 KVYESPLLDGVGIwvenRIKPlETKKtheQITEEVKKIIKE 75 
                 56677777776554444788875554222577777777765 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00019
        RexA  48 dkiylvkvdgnt.ylfiktrdnelvkkinratlkvedlkkkLgede.siGfaSyifvepdr 106
                 +k y ++v gnt +l +k +d+ + k+i +++   ++lk++L++d+  +G + +i + +++
  EPA05920.1 162 EKTYQINVGGNTdFLNMKEQDRLASKRISKTESVQSQLKERLADDQiYVGPSDFIPFLGNT 222
                 789999****885888999999999*******************98458999999888776 PP

>> CobU  Cobinamide kinase / cobinamide phosphate guanyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.9e-05      0.13      73     111 ..      37      75 ..      25      97 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.9e-05
        CobU  73 kevvLvDcltlwltnllleeeaekveekleeeveellea 111
                  e  L+D +++w++n +   e++k++e+++eev+++++ 
  EPA05920.1  37 YESPLLDGVGIWVENRIKPLETKKTHEQITEEVKKIIKE 75 
                 5778***************99887888888888777653 PP

>> Raco_middle  RACo middle region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       0.3   1.4e+03      56      77 ..      59      76 ..      49     108 .. 0.67
   2 ?    5.9   0.0    0.0021       9.3      66      94 ..     146     174 ..     135     179 .. 0.87
   3 ?    2.4   0.0     0.026   1.1e+02      62     131 ..     191     258 ..     175     273 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.3
  Raco_middle 56 eklqkavveeinelieelleea 77
                 +k ++ ++ee++++i+e    +
   EPA05920.1 59 KKTHEQITEEVKKIIKE----N 76
                 44444444444444443....3 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0021
  Raco_middle  66 inelieelleeagiekeeiyevvvagNtt 94 
                  +++ +++l+++ g + e+ y++ v+gNt 
   EPA05920.1 146 VHRTLAKLCSDRGTKIEKTYQINVGGNTD 174
                  567899*********************95 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.026
  Raco_middle  62 vveeinelieelleeagiekeeiyevvvagNttMlhlllgldpkslakapyvpvvseavelkakelglki 131
                   +e++++ ++e l++ +i       + + gNt +  +++ ++ ++ a+ py++ v+  v+ ka++ g+ i
   EPA05920.1 191 KTESVQSQLKERLADDQIYVGPSDFIPFLGNTKL--MFMRIEGRQWANIPYNMEVRLEVDDKANSAGIVI 258
                  5566667777777777777777777888899965..78999**************999999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1075  (0.0599587); expected 358.6 (0.02)
Passed bias filter:                      760  (0.0423894); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 1953.49
//
Query:       EPA05921.1  [L=237]
Description: hypothetical protein BG20_I1348 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-22   79.5   0.0    4.4e-22   79.1   0.0    1.0  1  PAC2      PAC2 family


Domain annotation for each model (and alignments):
>> PAC2  PAC2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.1   0.0   2.5e-26   4.4e-22       1     211 [.      20     223 ..      20     224 .. 0.95

  Alignments for each domain:
  == domain 1  score: 79.1 bits;  conditional E-value: 2.5e-26
                 EEEESSCGGGHHHHHHHHHHHHTTEEEEEEEEHCCHSBCCCC.SEEEEETTEEE-SEEEEEETTT.SEEEEEEE...E-HSCHHHHHHHHHHHHHHHTT CS
        PAC2   1 LilGfpgiGnVgqlavdlLiesleaekvgeidsdyllpfvgprpvvlveegrelepprlyakdsgsrdllvlqg...repilqyeefakalldwaeelg 96 
                 Li Gfp++G +  +a++ +i+  +++  g +dsd  +p     p+ +++egr+  p r++++d  + ++ ++ +   ++ +l+   +ak++l+wa++ +
  EPA05921.1  20 LIDGFPSMGFASAIATESMIQISQFKIAGIVDSDR-FP-----PISVIKEGRPNYPTRIFVND--DLKVSIFLSyltIDESLHRV-VAKTMLNWAKKQK 109
                 89*********************************.**.....*****************995..499******99999999999.************* PP

                 ESEEEEEEEEEESS-ES..TTS-.EEEEEESSHHHHHHHHCT.....-CEEEEHHHHHHHHHHHHTT-EEEEEEEEEECCC--HHHHHHHHHHHHHHH. CS
        PAC2  97 vkevvvLggldageradvphtrpekvtgaatdeelleelees.....eyggivgitglLlsaakergipavgllaevphylpdPkaaaalleflskll. 189
                 ++ +v   ++ ++          e++++++++e+ +++l+es     ++g+i gi g Ll+++   + +++++l ++++  pd +++a l   +s+l+ 
  EPA05921.1 110 IQLIVSSVAVKSMGG-------LEGMMAVGNTESARKKLKESglkvlQHGTIPGIPGMLLNEGTLTNQDVIVILFQSDGTGPDFRSSAQLCTGISQLIp 201
                 *****8888887765.......4699*************86668899***************************************************9 PP

                 T---HCHHHHHHHHHHHHHHHH CS
        PAC2 190 glevdtedLeedaeeleeqlee 211
                 g+++d   L+++ae+ e+ ++e
  EPA05921.1 202 GTSCDIPLLQKEAEKAEQSIKE 223
                 9*****************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1883.56
//
Query:       EPA05922.1  [L=80]
Description: hypothetical protein BG20_I1349 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       980  (0.05466); expected 358.6 (0.02)
Passed bias filter:                      671  (0.0374254); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 607.70
//
Query:       EPA05923.1  [L=65]
Description: hypothetical protein BG20_I1337 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.24   11.5   4.6       0.24   11.4   4.6    1.0  1  VGLL4     Transcription cofactor vestigial-like protein 4


Domain annotation for each model (and alignments):
>> VGLL4  Transcription cofactor vestigial-like protein 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   4.6   1.4e-05      0.24      48     108 ..       3      62 ..       1      65 [] 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.4e-05
       VGLL4  48 sPsKRKlseeqgdddlddeehvakmsRlfatqlaresagdsrkeaaersrspieratapst 108
                 +P  RK s+e+ ++ l+++e+v  + R  a ++ ++  +d+ k +++++  p  ++t + +
  EPA05923.1   3 TPKTRKISSEELKK-LQKNEKVRIIARRKAQKVGKSIVTDKSKPKTTKPTRPARKVTKKRA 62 
                 799********998.**************************99999999999988877654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1152  (0.0642534); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 460.93
//
Query:       EPA05924.1  [L=1174]
Description: RecF/RecN/SMC N-terminal domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-55  187.9  33.6    1.1e-32  113.3   0.1    3.5  2  SMC_N         RecF/RecN/SMC N terminal domain
    2.3e-18   66.6   0.0      1e-17   64.5   0.0    2.2  1  SMC_hinge     SMC proteins Flexible Hinge Domain
      3e-09   37.1  25.0    9.6e-06   25.6   4.2    4.7  3  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    3.9e-07   30.1  25.8    3.9e-07   30.1  25.8    4.4  2  AAA_15        AAA ATPase domain
    4.2e-06   27.4 120.4     0.0002   21.9  63.2    7.3  2  AAA_23        AAA domain
    4.4e-06   26.3   0.0      1e-05   25.2   0.0    1.5  1  AAA_29        P-loop containing region of AAA domain
     0.0016   18.2   0.1     0.0097   15.6   0.1    2.4  1  Tubulin_3     Tubulin domain
     0.0064   16.7   7.7     0.0064   16.7   7.7    6.8  6  ATG16         Autophagy protein 16 (ATG16)
  ------ inclusion threshold ------
      0.051   13.8   0.2       0.35   11.1   0.0    2.6  3  SbcCD_C       Putative exonuclease SbcCD, C subunit
       0.73   10.4 113.5       0.08   13.5  11.5    9.0  9  APG6_N        Apg6 coiled-coil region
        1.9    8.2   4.0        9.3    5.9   0.0    3.3  3  CT_C_D        Carboxyltransferase domain, subdomain C and D


Domain annotation for each model (and alignments):
>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.3   0.1   6.6e-36   1.1e-32       1     129 [.       3     132 ..       3     142 .. 0.97
   2 !   73.4  30.4     1e-23   1.7e-20      63     218 ..     378    1157 ..     210    1159 .. 0.89

  Alignments for each domain:
  == domain 1  score: 113.3 bits;  conditional E-value: 6.6e-36
                 EEEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--.BTTCSSTTEEEEEEEEEETTEESSSSSSCEE CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       SMC_N   1 vlkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk.skekasvkkaeveitfdnedkklkiekeevs 98 
                 ++k++ei +Fks+  k++++ f++++ +i GpNGSGKsn+ldAi F LGe++ k +r +kl++lih  + +++  k a+ +++fdn+d+k+++++++v+
  EPA05924.1   3 HIKKVEIFGFKSFGFKNTTVMFEPGLVSISGPNGSGKSNILDAIIFALGENKPKMMRVDKLRSLIHDiEGNRHGPKLARSSVHFDNSDRKIPVDADSVE 101
                 599****************************************************************999999************************** PP

                 EEEEEETTSEEEEEETTEEE-HHHHHHHHHC CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       SMC_N  99 isrrvkrkgeseykingkevtkkevselles 129
                 i+r++  kge++y++n+k  +++++ +ll  
  EPA05924.1 102 ITREMDDKGENNYYLNKKPTNRSQILDLLDV 132
                 ***************************9975 PP

  == domain 2  score: 73.4 bits;  conditional E-value: 1e-23
                  CCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHC.TT-STT....................... CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx....................... RF
       SMC_N   63 dlihkskekasvkkaeveitfdnedkklkiekeevsisrrvkrkgeseykingkevtkkevselles.agiske....................... 135 
                  +++++ ++ a++kk e++  ++  +++   ++ ++++s+   +k+es++ki+ ++++ +e+++ + + + ++                         
  EPA05924.1  378 KILTE-QSVAASKKSEIDNKIKLLSDQ--LNQAKLKLSKAENEKEESQIKIKSNTAKLSELEQDVVKlSALKLRlesiinnhnasiselqsrisrln 471 
                  44444.444555555555544444444..55556666666666666666666666666666553222022222255888888888888888888888 PP

                  ................................................................................................. CS
                  ................................................................................................. RF
       SMC_N  136 ................................................................................................. 135 
                                                                                                                   
  EPA05924.1  472 skksktlndleeldlileksskaaaqyeskiktvkgimhedytvaklkedadklgivglvyemiswdkqyersvlavssdwikaivvpdfatllsia 568 
                  8888999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 PP

                  ................................................................................................. CS
                  ................................................................................................. RF
       SMC_N  136 ................................................................................................. 135 
                                                                                                                   
  EPA05924.1  569 evarsknlpklkiipldaipkfkldlpkdsgvigvlsdyvkcdpshialktflfgnvvlvesrdtayriskmghkavtingeyfeakggavvidins 665 
                  9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 PP

                  ................................................................................................. CS
                  ................................................................................................. RF
       SMC_N  136 ................................................................................................. 135 
                                                                                                                   
  EPA05924.1  666 kiskltkiismstdidgllesisllkkyvlkkkhslkkledsiqgyakrlslseqglasteenhshlqsrissainmkqqlseriselnqrhetllv 762 
                  9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 PP

                  ................................................................................................. CS
                  ................................................................................................. RF
       SMC_N  136 ................................................................................................. 135 
                                                                                                                   
  EPA05924.1  763 evssseshieslnsritiveenyasgeqtrianelsrvnakksdleklyttimneyrdkdsqltaiqveenrkqsqikglydeisslnsqhqelenk 859 
                  9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 PP

                  ................................................................................................. CS
                  ................................................................................................. RF
       SMC_N  136 ................................................................................................. 135 
                                                                                                                   
  EPA05924.1  860 ikeleirkesktatlvtlrekeqelistsgssigqlkeyddklkvlsekdkeltkeinslerqsdsltrdlrdlienetklqtlltsfgfdknmetf 956 
                  999999999**************************************************************************************** PP

                  ................................................................................................. CS
                  ................................................................................................. RF
       SMC_N  136 ................................................................................................. 135 
                                                                                                                   
  EPA05924.1  957 dvdsivhgltteynslnalnakapetylevsygyrsmsvrknsleeernsivkfiediekdkrqtfldafdkvdkeirlifskmtggnawlelqned 1053
                  ************************************************************************************************* PP

                  ......................CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEE CS
                  ......................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       SMC_N  136 ......................lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadklvg 210 
                                        ++SgGektL+a+ +++A+qk kp+p+yl+De+da+LD+ n +++a++l+e+s+++Qfi++sl++ +++ka+ ++g
  EPA05924.1 1054 difnsgisymiqfpskpkrestSISGGEKTLAAIVFVLALQKLKPSPFYLFDEVDAHLDAPNSERLAKILEERSQESQFIMVSLKDSVVQKAKLIYG 1150
                  ************************************************************************************************* PP

                  EEEEETTE CS
                  xxxxxxxx RF
       SMC_N  211 vtkvengv 218 
                  v+  +ngv
  EPA05924.1 1151 VYP-KNGV 1157
                  **9.6665 PP

>> SMC_hinge  SMC proteins Flexible Hinge Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.5   0.0   6.3e-21     1e-17       3     116 ..     526     637 ..     524     638 .. 0.95

  Alignments for each domain:
  == domain 1  score: 64.5 bits;  conditional E-value: 6.3e-21
   SMC_hinge   3 gvlGrladlievdegyekAveaalgnrlqalvvedeetakkiieflkkknagratflpldrikqknkadgandknsgavplidlvevddelrkalryll 101
                 g++G + ++i+ d++ye  v a+  + ++a+vv d +t  +i e  ++kn+ ++ ++pld i +++ +  ++     ++ l+d+v++d+++ ++  +l+
  EPA05924.1 526 GIVGLVYEMISWDKQYERSVLAVSSDWIKAIVVPDFATLLSIAEVARSKNLPKLKIIPLDAIPKFKLDLPKDSG--VIGVLSDYVKCDPSHIALKTFLF 622
                 79***************************************************************887777665..8*************999999*** PP

   SMC_hinge 102 gdtlvvdsldeAeel 116
                 g++++v+s d+A ++
  EPA05924.1 623 GNVVLVESRDTAYRI 637
                 ************987 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   8.5   2.7e-05     0.044       5      26 ..      32      70 ..      28     375 .. 0.78
   2 ?    0.7   1.5      0.23   3.7e+02      82     195 ..     331     446 ..     278     494 .. 0.71
   3 !   25.6   4.2   5.9e-09   9.6e-06     182     296 ..    1016    1136 ..     697    1136 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.7e-05
      AAA_21  5 iGpNgsGKSnLLdaldllarl.................d 26
                 GpNgsGKSn+Lda+ ++ +                  +
  EPA05924.1 32 SGPNGSGKSNILDAIIFALGEnkpkmmrvdklrslihdI 70
                5**************998877777777774444443332 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.23
      AAA_21  82 qv.eeklssvetllesgllldkrsleeedvfnpeargirggvsvfslkelsvsepndlqfgkaltditsrawsllllldglrke.rigllnifadyfgf 178
                     e+ +s +++ +s++l+  +s +e++ + ++  +  ++++ +++k l+  +  + ++++  ++i+   ++l++ + +l k+ +    +  +   + 
  EPA05924.1 331 KNeIETMQSTGQDIQSRILQIQESINETNIKKNKINDDLELLDAERNKILTEQSVAASKKSEIDNKIKLLSDQLNQAKLKLSKAeNEKEESQIKIKSNT 429
                 334566677788888888888888888888888888888888888888888888888888888888888888888888777777666655555666666 PP

      AAA_21 179 akekrllqrlvrslklv 195
                 ak+ +l q+ v+ + l 
  EPA05924.1 430 AKLSELEQDVVKLSALK 446
                 66666665555554444 PP

  == domain 3  score: 25.6 bits;  conditional E-value: 5.9e-09
      AAA_21  182 krllqrlvrslklveielsdlgegeeliasvderlrer......gvvflengdgqelparelSdGtkrllalltallralkkg.sllliDEpEngLH 271 
                  k+ +q +++ +++v+ e++++  +    + + e+++e        ++    ++  ++ ++++S G k l+a++  l+ +  k+ +++l+DE++++L+
  EPA05924.1 1016 KDKRQTFLDAFDKVDKEIRLIFSKMTGGNAWLELQNEDdifnsgISYMIQFPSKPKRESTSISGGEKTLAAIVFVLALQKLKPsPFYLFDEVDAHLD 1112
                  3333334444444444444444444444444444444477778899999999999999***********988888888888888************* PP

      AAA_21  272 PkllrrllellkelsrngaQviltT 296 
                      +rl+++l+e s+  +Q+i+++
  EPA05924.1 1113 APNSERLAKILEERSQ-ESQFIMVS 1136
                  ***********88888.8****986 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1  25.8   2.4e-10   3.9e-07       3     281 ..       4     365 ..       3     382 .. 0.53
   2 ?   -0.9  37.6      0.62     1e+03      72     361 ..     771    1134 ..     616    1136 .. 0.74

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 2.4e-10
      AAA_15   3 IkkikikNFRs..lkdveidlseeltvliGkNnsGKSsilealdlFlnnkekkn............................................. 54 
                 Ikk++i  F+s  +k++++ +++ l  + G+N+sGKS+il+a+ + l ++++k                                              
  EPA05924.1   4 IKKVEIFGFKSfgFKNTTVMFEPGLVSISGPNGSGKSNILDAIIFALGENKPKMmrvdklrslihdiegnrhgpklarssvhfdnsdrkipvdadsvei 102
                 99********84459****************************66566554444888888899999999888888888666666666666655555555 PP

      AAA_15  55 ......kkvikiekedleifeniseskdikIdvef..............................................................ae 85 
                       k                                                                                          + 
  EPA05924.1 103 tremddK---------------------------GennyylnkkptnrsqildlldvanaglgqlnavqqgtvtriseftseekrktiedliglsyfD- 173
                 4444440...........................1444444444444444444555666666666666666666655555555555555554444331. PP

      AAA_15  86 kekakeyektlkskekkk..adlllkkkesdlkktikdkklklkknelsdekisvekkks....kkelpkekeeklekekeelkid.kedlkklikkle 177
                  ek+ e +k l++ +++   a   + +++++++++ +++++kl ++ l  e   ++ + +    +++   +++++++ +k + +i+ ++d +++i++ +
  EPA05924.1 174 -EKKTEAIKQLDDADRRLeiALAKMGEIKKRIDELEEERNQKLRHDILERELNRYKAIAAsnklRVITSQKSSKEETFQKITNEIKaFDDERNTIRTEI 271
                 .33333333333332222002223334444444444445555444444444444444444222233333333333444444444446777777777777 PP

      AAA_15 178 eslkkee...............elknvlksaiiklllisakRnvsdedsekkssllgklkekileealqekleeelteklkeiqeklkeidkklaeelk 261
                 +sl+ e+                +++ l+sa+++++++++   +s+++ ++++  + ++k++i     q+   +++++ + +iqe+++e++ k      
  EPA05924.1 272 NSLENEKsklmtaandysqakaAIDSELSSAMEQYEIDNSAIVASTKRLQQIEIRIPEIKNEIETM--QST-GQDIQSRILQIQESINETNIK------ 361
                 777777755555555555555556666666666666666666666666555555555555555332..111.222333333333333333333...... PP

      AAA_15 262 kilkkkidkikkfnykgkkn 281
                                 ++k 
  EPA05924.1 362 ----------------KNKI 365
                 ................2222 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.62
      AAA_15   72 seskdikIdvefaekekakeyektlkskekkkadlllkkkesdlkktikdkklklkknelsdekisvekkks.........kkelpkekeeklekek 159 
                   es + +I++ +      ++y + ++++ +++    ++ k+sdl k++++ + ++  ++ +   i+ve++ +         + +  ++++ +le+++
  EPA05924.1  771 IESLNSRITIVE------ENYASGEQTRIANELS-RVNAKKSDLEKLYTTIMNEYRDKDSQLTAIQVEENRKqsqikglydEISSLNSQHQELENKI 860 
                  334444444444......2222222222222222.33334444444444444444444444444444433334444444444555667788888899 PP

      AAA_15  160 eelkidkedlkklikkleeslkkee.....elknvlksaiiklllisakRnvsd..edsekkssllgklkekileealqekl............... 234 
                  +el+i ke+++ ++ +l+e+ ++       +++++ +   ++  l +++++ ++  +  e +s++l++ +++++e+  +  l               
  EPA05924.1  861 KELEIRKESKTATLVTLREKEQELIstsgsSIGQLKEYDDKLKVLSEKDKELTKeiNSLERQSDSLTRDLRDLIENETK--Lqtlltsfgfdknmet 955 
                  9999999999999998887775555888888888888888888899999999997778899999999999999997544..4459999999999999 PP

      AAA_15  235 .........................................eeelteklkeiqeklkeidkklaeelk...........kilkkkidkikkfnykgk 279 
                                                           +      l+e  +++ ++++++++++            k++  +++k+  +n+  +
  EPA05924.1  956 fdvdsivhgltteynslnalnakapetylevsygyrsmsvrK----NSLEEERNSIVKFIEDIEKDKRqtfldafdkvdKEIRLIFSKMTGGNAWLE 1048
                  999999999999999988888888888888888888755543....444555555555555555555545556777777777777777777777777 PP

      AAA_15  280 kneeieik...........ddeelplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQvii 361 
                   ++e++i+           ++ + + +  + G + l  +++ ++  + k     ++ ++l++E +ahL   + + l+k l e ++++  Q i+
  EPA05924.1 1049 LQNEDDIFnsgisymiqfpSKPKRESTSISGGEKTLAAIVFVLALQKLK-----PSPFYLFDEVDAHLDAPNSERLAKILEERSQES--QFIM 1134
                  77777777*****************************************.....*************************99999998..7775 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9  63.2   1.2e-07    0.0002       1     194 [.       6     259 ..       6     525 .. 0.77
   2 ?   -1.1   0.9       1.4   2.2e+03      93     135 ..    1003    1037 ..     949    1138 .. 0.54

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.2e-07
      AAA_23   1 kLkienfrsf..rdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkayveltfenkdgry...trsierer 94 
                 k++i +f+sf  +++++ F++gl+ I+GpNG+GK+ ildAi +aL++ +p++ r ++ ++  +d+e +  g + a  ++ f n d++         ++ 
  EPA05924.1   6 KVEIFGFKSFgfKNTTVMFEPGLVSISGPNGSGKSNILDAIIFALGENKPKMMRVDKLRSLIHDIEGNRHGPKLARSSVHFDNSDRKIpvdA----DSV 100
                 68999***************************************************999999999988887777778888877666533331....233 PP

      AAA_23  95 elskkkgkttkkaklelleideleqfisellgskkiilnlilflgqer................feefelkdkke........................ 153
                 e ++++ ++  ++   + +++++ q+++ ll++ ++ l ++   +q+                 +         +                        
  EPA05924.1 101 EITREMDDKGENNYYLNKKPTNRSQILD-LLDVANAGLGQLNAVQQGTvtriseftseekrktiE---------Dliglsyfdekkteaikqlddadrr 189
                 3333433333334444444455444444.456666666666666666555544442222222220.........1333333333333344446666674 PP

      AAA_23 154 ......rleelekeleeledekkllekl..............................eqekekekeleeleeelee 194
                       ++ e++k ++e       le++                               q+ +ke++++++ +e++ 
  EPA05924.1 190 leialaKMGEIKKRIDE-------LEEErnqklrhdilerelnrykaiaasnklrvitSQKSSKEETFQKITNEIKA 259
                 44444444444444444.......33333333333455555566666666666556554555555555555555544 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.4
      AAA_23   93 erelskkkgkttkkaklelleideleqfisellgskkiilnli 135 
                  er+ + k          e +e+d+++ f++   +++k+i  ++
  EPA05924.1 1003 ERNSIVK--------FIEDIEKDKRQTFLDAFDKVDKEIRLIF 1037
                  2222222........2223333333444443222222222222 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   6.3e-09     1e-05      12      46 ..      17      50 ..       5      57 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 6.3e-09
      AAA_29 12 fdghtieidlkgatlltGpsGsGKSTllDAiqalL 46
                f+++t+++++   + ++Gp+GsGKS +lDAi++ L
  EPA05924.1 17 FKNTTVMFEPG-LVSISGPNGSGKSNILDAIIFAL 50
                77889999855.6******************9887 PP

>> Tubulin_3  Tubulin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1     6e-06    0.0097      23      91 ..     890     957 ..     885    1007 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 6e-06
   Tubulin_3  23 rsivqlneyelnskllpfedwsvGeeLfeeldkehdlldrdlrpfaeecdqlrglqvftgvddaWGGfa 91 
                  si ql+ey+ + k+l+ +d ++ +e+ ++l+++ d l rdlr ++e+  +l++l    g d     f 
  EPA05924.1 890 SSIGQLKEYDDKLKVLSEKDKELTKEI-NSLERQSDSLTRDLRDLIENETKLQTLLTSFGFDKNMETFD 957
                 599**************9999999986.89***********************9988888887766665 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9  13.8         4   6.5e+03      77     155 ..     205     287 ..     168     307 .. 0.54
   2 !    6.5  22.0    0.0053       8.6      31     176 ..     271     420 ..     265     434 .. 0.84
   3 ?    0.4   6.9      0.39   6.4e+02      98     154 ..     433     489 ..     419     525 .. 0.73
   4 !    8.6   6.6    0.0013       2.1      68     141 ..     714     787 ..     671     793 .. 0.77
   5 ?    1.8   7.5      0.15   2.4e+02     130     178 ..     823     864 ..     787     870 .. 0.51
   6 !   16.7   7.7   3.9e-06    0.0064      77     153 ..     868     944 ..     864     979 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4
       ATG16  77 qsleqkl.aqlreel..aelyksrgela.qrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqd 155
                  +le+++ ++lr++    el + ++  a ++l+  +++ + +ee+ ++ ++++++  +er++++t+++++e+e   + ++ +d
  EPA05924.1 205 DELEEERnQKLRHDIleRELNRYKAIAAsNKLRVITSQKSSKEETFQKITNEIKAFDDERNTIRTEINSLENEKSKLMTAAND 287
                 33333321234444311233444433321355556666666666666666666666666666666666666666655555555 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0053
       ATG16  31 tsaleaenaklekaaasaks......sksskksakekeasasq......snskqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleek 117
                 +++le e++kl +aa++ ++      s+ s++ +        q         ++++++q+ e ++ ++++e ++++ + ++ ++r+l+ +e++ + + k
  EPA05924.1 271 INSLENEKSKLMTAANDYSQakaaidSELSSAME--------QyeidnsAIVASTKRLQQIEIRIPEIKNEIETMQSTGQDIQSRILQIQESINETNIK 361
                 6788999999988877777754443322222222........234444455788999****************************************** PP

       ATG16 118 lkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLqlqlnqaEeklrk 176
                  ++ +  l+ l aer+++ t+ +  + +  e ++ ++ l D l++ +l+l++aE ++++
  EPA05924.1 362 KNKINDDLELLDAERNKILTEQSVAASKKSEIDNKIKLLSDQLNQAKLKLSKAENEKEE 420
                 ******************************************************99986 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.39
       ATG16  98 gelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvq 154
                 +el+q +++l++   +le+ +++ ++++ el++++++l+ k ++  + l+e++  ++
  EPA05924.1 433 SELEQDVVKLSALKLRLESIINNHNASISELQSRISRLNSKKSKTLNDLEELDLILE 489
                 577788888888888888888888888888888888888888877777777776655 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.0013
       ATG16  68 snskqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkd 141
                 + s +++ ++s+e++ + l++  + +   +++l++r+ eln+ +++l  + ++ e+ +++l+++++ +e+++++
  EPA05924.1 714 RLSLSEQGLASTEENHSHLQSRISSAINMKQQLSERISELNQRHETLLVEVSSSESHIESLNSRITIVEENYAS 787
                 2334567899******************************************************9999987765 PP

  == domain 5  score: 1.8 bits;  conditional E-value: 0.15
       ATG16 130 aeraaletklkdreeelrekeklvqdlqDElsaLqlqlnqaEeklrkle 178
                 ++ +a        + e + k+  ++ l DE+s+L+ q + +E k ++le
  EPA05924.1 823 SQLTA-------IQVEENRKQSQIKGLYDEISSLNSQHQELENKIKELE 864
                 22222.......2222334455555678888888888888888888776 PP

  == domain 6  score: 16.7 bits;  conditional E-value: 3.9e-06
       ATG16  77 qsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklv 153
                 +s +++l++lre  +el  + g +  +l+e  ++l++l ek ke ++++++le++  +l++ l+d+ e+   +++l+
  EPA05924.1 868 ESKTATLVTLREKEQELISTSGSSIGQLKEYDDKLKVLSEKDKELTKEINSLERQSDSLTRDLRDLIENETKLQTLL 944
                 678899***********************************************************999888777776 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       4.4   7.1e+03      12      50 ..     411     449 ..     402     461 .. 0.69
   2 ?   -3.8   0.1       9.9   1.6e+04      70      79 ..    1024    1032 ..    1019    1034 .. 0.78
   3 ?   11.1   0.0   0.00021      0.35      27      89 ..    1071    1124 ..    1064    1125 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 4.4
     SbcCD_C  12 fevevrdedgkekelsrssgtlSGGekqflaylalaaal 50 
                 ++  ++++++++ ++++++++lS  e+ ++   al + l
  EPA05924.1 411 LSKAENEKEESQIKIKSNTAKLSELEQDVVKLSALKLRL 449
                 444455677777789999999998888777666665555 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 9.9
     SbcCD_C   70 DEAFsklDee 79  
                  D AF+k+D+e
  EPA05924.1 1024 D-AFDKVDKE 1032
                  4.9*****97 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00021
     SbcCD_C   27 srssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89  
                  +r+s++ SGGek +la++++++al  l  s         + ++DE  + lD+ ++++l ++le
  EPA05924.1 1071 KRESTSISGGEK-TLAAIVFVLALQKLKPS--------PFYLFDEVDAHLDAPNSERLAKILE 1124
                  789999******.99999999999887666........4889999999999999999999887 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   8.3      0.38   6.3e+02      45     111 ..     155     223 ..     115     237 .. 0.74
   2 ?   13.5  11.5   4.9e-05      0.08      14     126 ..     213     327 ..     211     334 .. 0.84
   3 ?   -0.8  10.0       1.3   2.1e+03      50     125 ..     321     396 ..     295     405 .. 0.37
   4 ?   -0.9  20.3       1.4   2.2e+03      45     132 ..     344     431 ..     318     442 .. 0.73
   5 ?    2.1   6.3      0.16   2.5e+02      32      93 ..     446     504 ..     429     512 .. 0.72
   6 ?    9.9   6.2   0.00064         1      25     127 ..     680     779 ..     669     785 .. 0.87
   7 ?    4.5  15.2     0.029        48      26      94 ..     816     884 ..     782     899 .. 0.55
   8 ?    6.8   8.3    0.0055         9      48     100 ..     894     946 ..     879     961 .. 0.84
   9 ?    0.6   0.1      0.45   7.4e+02      18      56 ..     997    1033 ..     991    1041 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.38
      APG6_N  45 qdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreyne..lqle 111
                 + ee +++ e+l  l+   e++ e +k+l++++++le +la+  e +++++e ee+  ++ +   l++e
  EPA05924.1 155 TSEEKRKTIEDLIGLSYFDEKKTEAIKQLDDADRRLEIALAKMGEIKKRIDELEEERNQKLRHdiLERE 223
                 456777777887778888888888999999999999999988888888888877776666555234444 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 4.9e-05
      APG6_N  14 ldkqleqaekerdaYeeflkklkkekkeeek..qdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelql 110
                  + + + +e+e + Y++  +  k +  +++k  ++e  +++ +e+++ ++e+++  +e++ le+e+++l  + +++++ ++a++ e    +++y   + 
  EPA05924.1 213 QKLRHDILERELNRYKAIAASNKLRVITSQKssKEETFQKITNEIKAFDDERNTIRTEINSLENEKSKLMTAANDYSQAKAAIDSELSSAMEQYEIDNS 311
                 567889999999999998776664432222234678999*******************************************************99999 PP

      APG6_N 111 elleleeeldsleaqy 126
                       ++l+++e ++
  EPA05924.1 312 AIVASTKRLQQIEIRI 327
                 9999999999988876 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.3
      APG6_N  50 eeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelqlelleleeeldsleaq 125
                 +++e ++ ++++e e++++  +++++   ++++ +++   ++++++++ e    e+n+  +e++    ++  ++++
  EPA05924.1 321 QQIEIRIPEIKNEIETMQSTGQDIQSRILQIQESINETNIKKNKINDDLELLDAERNKILTEQSVAASKKSEIDNK 396
                 2222223333333333333333333333333333333333333333333333333333333333333333333333 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 1.4
      APG6_N  45 qdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelqlelleleeeldsleaqyehaqnq 132
                  ++ + +++e++ +++ ++++    L+ l++er ++  e + +++++++++++ +    + n+ +l+l++ e+e++  + +++ ++++
  EPA05924.1 344 IQSRILQIQESINETNIKKNKINDDLELLDAERNKILTEQSVAASKKSEIDNKIKLLSDQLNQAKLKLSKAENEKEESQIKIKSNTAK 431
                 3456667778888888888888888888888888888888888888888888888888888888888888888888887777766554 PP

  == domain 5  score: 2.1 bits;  conditional E-value: 0.16
      APG6_N  32 lkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelea 93 
                   +l++    ++ ++ ++ el+ ++++l++++++ l+ L+el+   e+  ++ a++e++ + 
  EPA05924.1 446 KLRLESI--INN-HNASISELQSRISRLNSKKSKTLNDLEELDLILEKSSKAAAQYESKIKT 504
                 3333333..322.6789999999999999999999999999999888888888888887765 PP

  == domain 6  score: 9.9 bits;  conditional E-value: 0.00064
      APG6_N  25 rdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelqlelleleeeldsle 123
                 +d ++e  + lkk+  ++   +++l++le++++   k  +  ++ L+ +e++++ l++ ++++ + +++l e   +  +++  l +e+++ e   +sl+
  EPA05924.1 680 IDGLLESISLLKKYVLKK---KHSLKKLEDSIQGYAKRLSLSEQGLASTEENHSHLQSRISSAINMKQQLSERISELNQRHETLLVEVSSSESHIESLN 775
                 555566666667775444...5799************************************************************************** PP

      APG6_N 124 aqye 127
                 ++++
  EPA05924.1 776 SRIT 779
                 9986 PP

  == domain 7  score: 4.5 bits;  conditional E-value: 0.029
      APG6_N  26 daYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeeleal 94 
                 ++Y++  ++l++ ++ee++++++++ l +e++ l+++ +el++++kele  +e+  a l +l+e++++l
  EPA05924.1 816 NEYRDKDSQLTAIQVEENRKQSQIKGLYDEISSLNSQHQELENKIKELEIRKESKTATLVTLREKEQEL 884
                 223333333333333333355556666666666666666666666666666666666666666666655 PP

  == domain 8  score: 6.8 bits;  conditional E-value: 0.0055
      APG6_N  48 eleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeer 100
                 +l+e +++l+ l+++ +el +e++ le++ ++l ++l++l e + +l+   + 
  EPA05924.1 894 QLKEYDDKLKVLSEKDKELTKEINSLERQSDSLTRDLRDLIENETKLQTLLTS 946
                 56677888999********************************9999986655 PP

  == domain 9  score: 0.6 bits;  conditional E-value: 0.45
      APG6_N   18 leqaekerdaYeeflkklkkekkeeekqdeeleeleeel 56  
                   +++e+er++  +f + ++k+k+++    +  ++ ++e+
  EPA05924.1  997 KNSLEEERNSIVKFIEDIEKDKRQTF--LDAFDKVDKEI 1033
                  56788999999999999999988876..45555555555 PP

>> CT_C_D  Carboxyltransferase domain, subdomain C and D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.2       2.8   4.5e+03      15      74 ..     200     258 ..     197     277 .. 0.67
   2 ?    1.3   0.3      0.14   2.4e+02      30      82 ..     738     790 ..     713     803 .. 0.76
   3 ?    5.9   0.0    0.0057       9.3      32      79 ..     973    1020 ..     958    1044 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.8
                 E-SS--HHHHHHHHHHHHHHHT..STTECEEEE-SSEEEEEESCCCCHHHHHH.HHHHHH CS
      CT_C_D  15 fgeeisealskrvlalaaalrakalpgvvelvpayrsllvefdpealdaaellaalkall 74 
                 ++++i+e   +r ++l++++ +++l++   ++ a ++l v   +++ + +++++  +++ 
  EPA05924.1 200 IKKRIDELEEERNQKLRHDILERELNRY-KAIAASNKLRVITSQKSSKEETFQKITNEIK 258
                 6677888888888888888888888777.6777888888877777765555554444443 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.14
                 HHHHHHT..STTECEEEE-SSEEEEEESCCCCHHHHHH.HHHHHHHH.----- CS
      CT_C_D  30 laaalrakalpgvvelvpayrsllvefdpealdaaellaalkalleeaeeeaa 82 
                  a +++++  +++ el +  ++llve+   +   ++l+++++ ++e+ ++ ++
  EPA05924.1 738 SAINMKQQLSERISELNQRHETLLVEVSSSESHIESLNSRITIVEENYASGEQ 790
                 334456667999*****************************988888544443 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.0057
                  HHHHT..STTECEEEE-SSEEEEEESCCCCHHHHHH.HHHHHHHH.-- CS
      CT_C_D   32 aalrakalpgvvelvpayrsllvefdpealdaaellaalkalleeaee 79  
                  +al+aka +  +e+  +yrs+ v+ +  + ++++++++++++++++ +
  EPA05924.1  973 NALNAKAPETYLEVSYGYRSMSVRKNSLEEERNSIVKFIEDIEKDKRQ 1020
                  6899999**********************************9988433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2526  (0.140889); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                       157  (0.00875676); expected 17.9 (0.001)
Passed Fwd filter:                       108  (0.00602376); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 2.85u 0.39s 00:00:03.24 Elapsed: 00:00:00.71
# Mc/sec: 5020.37
//
Query:       EPA05925.1  [L=43]
Description: hypothetical protein BG20_I1347 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-07   31.0   0.0    1.6e-07   30.9   0.0    1.0  1  DS        Deoxyhypusine synthase


Domain annotation for each model (and alignments):
>> DS  Deoxyhypusine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.0   8.8e-12   1.6e-07     255     287 ..       2      34 ..       1      35 [. 0.95

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 8.8e-12
          DS 255 ldEavSwgkikaeaksvkvyaDaTivlPLlvaa 287
                 ++Ea+Swgk++++a++++ +a++T +lP+++aa
  EPA05925.1   2 VREAISWGKVTQQARQATLHAEVTTILPFIYAA 34 
                 68****************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (43 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 263.82
//
Query:       EPA05926.1  [L=96]
Description: putative DNA-binding protein Alba, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.9e-13   48.4   1.3    7.7e-13   48.1   1.3    1.2  1  Alba             Alba
  ------ inclusion threshold ------
      0.019   14.5   0.6       0.02   14.4   0.6    1.0  1  Methyltrn_RNA_3  Putative RNA methyltransferase


Domain annotation for each model (and alignments):
>> Alba  Alba
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.1   1.3   8.6e-17   7.7e-13       2      64 ..      11      70 ..      10      73 .. 0.93

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 8.6e-17
                EEEE-STS-HHHHHHHHHHHHTHTTESEEEEEEETTHHHHHHHHHHHHHHHTCTT.EEEEEEE CS
        Alba  2 eiyVsskspimsyvkralklLsnkkeeeVvlkatGraIskAvsvaeilkrrfgkglyqvnvlt 64
                +i+V++ +p+m+yv+++l++L  ++ ++V++ka+G+ I+ Av+v +++ +r+++  y v ++ 
  EPA05926.1 11 VIFVGT-KPVMTYVSATLTQL--STRKTVTIKARGKRITQAVDVSQMIVKRMNAVGYVVSDVR 70
                799***.**************..9****************************98668888765 PP

>> Methyltrn_RNA_3  Putative RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.6   2.3e-06      0.02     121     194 ..       8      81 ..       1      92 [. 0.79

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.3e-06
  Methyltrn_RNA_3 121 kkklVniGlkkevklel.kqevpegtRVtVklsseesveakvVspsepreeaglywGYsVrlakslsavftespf 194
                      +++++ +G  k+v     ++  +  tR tV ++++ ++  ++V+ s+  ++    +GY V  ++ ls+ +t +  
       EPA05926.1   8 ERDVIFVG-TKPVMTYVsATLTQLSTRKTVTIKARGKRITQAVDVSQMIVKRMNAVGYVVSDVRILSDSLTSQDG 81 
                      23588899.88886555445558999******99***********************************998754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.34u 0.27s 00:00:00.61 Elapsed: 00:00:00.42
# Mc/sec: 681.84
//
Query:       EPA05927.1  [L=414]
Description: hypothetical protein TIGR03440 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-41  141.9   5.3    4.7e-41  141.1   5.3    1.3  1  FGE-sulfatase   Sulfatase-modifying factor enzyme 1
    3.9e-08   33.8   0.0    1.7e-07   31.8   0.0    2.1  2  DinB_2          DinB superfamily
  ------ inclusion threshold ------
      0.088   12.7   0.2       0.27   11.1   0.2    1.9  1  DinB            DinB family
       0.26    9.4   1.0       0.42    8.7   1.0    1.2  1  E3_UbLigase_R4  E3 ubiquitin-protein ligase UBR4


Domain annotation for each model (and alignments):
>> FGE-sulfatase  Sulfatase-modifying factor enzyme 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.1   5.3   1.1e-44   4.7e-41       4     221 ..     178     398 ..     175     409 .. 0.85

  Alignments for each domain:
  == domain 1  score: 141.1 bits;  conditional E-value: 1.1e-44
                    TEEEE-SEEEEES-.TSTTGGCCC-S-EEEEES-EEEESS--BHHHHHHHHHHH....H................SSETTEEEEETSCTTBCCTTC CS
  FGE-sulfatase   4 emvlipgGsfemGs.eektandeeapahevtvraFaidkteVTnaqyaafveatgyete................aasqwwaeveganvrhpegrk 82 
                    + + i+gG f +G+ +    +d e p h+v ++++ +d++++Tn+qy +f+++ gy+t                 +a+  w+++eg++  +     
     EPA05927.1 178 KSIKIKGGIFSVGYnDVGYCYDIELPEHKVYLDDYTMDEFPITNEQYLKFMNDGGYDTYkywlsdgwekvkknewKAPMYWEKIEGQWKVRDFL-- 271
                    6799**********777899*************************************9999888888888888777778888888887666554.. PP

                    -SSTT-TTSB--S--HHHHHHHHHHHCHHHTS-EE---HHHHHHHHHTT-...SSSSCTTBSTTSCCGB...SSTTTTB--TTCGGS-SS.---TT CS
  FGE-sulfatase  83 sdikkradhPvvhVsweDavaYArwlgkktgegyrLPteaEweyAArggk...kgreypwgdelkpakniwqGslakfekeaaaadsqngrtspvg 175
                      +k ++++Pv h+s+++a aY++w+ k      rLPteaEwe+AA + +   +++ +pwg++               e++a+  +s+++  + +g
     EPA05927.1 272 GIRKINPKEPVCHISYYEADAYCKWAQK------RLPTEAEWEKAACWNEekqQKTIFPWGNQMP------------TEQNANLLESYHWGCTAIG 349
                    3567899*********************......**************99776777899999966............46777888999999***** PP

                    -S-B..-TTS-B-TTCSSEEEEEEE--THCCH-.SSCS----SS-SSEE CS
  FGE-sulfatase 176 sfpp..nalGlyDmaGNvwEWtsdwykkyalap.aeelsqeaekgelrv 221
                    s+p+  ++ G+++m+G+vwEWts+++ +y   +   e  ++++ ++++v
     EPA05927.1 350 SYPNgvSPSGCHQMIGDVWEWTSSEFIGYPGFKtGFEEYNDKWFTNQKV 398
                    **************************94443331334444445555555 PP

>> DinB_2  DinB superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.0   3.7e-11   1.7e-07       1     126 [.      16     147 ..      16     149 .. 0.79
   2 ?   -2.6   0.0       1.6   7.3e+03      36      56 ..     282     302 ..     276     337 .. 0.66

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 3.7e-11
      DinB_2   1 qlerararllalledlteeelnrqpspgkwsiawllaHlgnveelllerlr...........geeaprpgldpltp......................p 66 
                 q+ ++r r+l+l+++l  +++  q + + +++ w+++H+ +  e +  ++            +            +                      p
  EPA05927.1  16 QFKETRGRTLELVKTLEKDDFVVQTAFFTSPPKWHIGHVSWIYEAIMSKIDknyefystefsE------------YlnsyyqqfgiphdkgergvisrP 102
                 799************************************************444443332220............22333345666666666677777* PP

      DinB_2  67 saaealaylaevrarllallealtdadldrpltaphpglgkltlgdvllfvlqHeqhHle 126
                 + +++ +y++ v +r+++++e+++                  ++  ++ +  +He +H e
  EPA05927.1 103 TTEQIFQYFNTVSQRVNHFIESTSL---------------SNDVIKLITMGFHHECQHQE 147
                 **********************877...............23677888888888888877 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.6
      DinB_2  36 laHlgnvee.lllerlrgeeap 56 
                 ++H+  +e   ++  + ++  p
  EPA05927.1 282 VCHISYYEAdAYCKWAQKR-LP 302
                 7899999986777777642.22 PP

>> DinB  DinB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   6.1e-05      0.27       9      65 ..      12      86 ..       1     157 [. 0.69

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 6.1e-05
                HHHHHHHHHHHHHHHHHCT--CCCTT--SSTTS--HHHHHHHHHHHHHHHHHHHHH................... CS
        DinB  9 ellqynqwardrtldaiaaLpdeelkaengegfqsvkqtlnHvldveelwlsrleg..................e 65
                 ll+ ++++r+rtl+++++L ++++  + + +    k ++ Hv   +e+ +s ++                   +
  EPA05927.1 12 PLLEQFKETRGRTLELVKTLEKDDFVVQTAFFTSPPKWHIGHVSWIYEAIMSKIDKnyefystefseylnsyyqQ 86
                6899**********************7666666667889999999999999999887666666666666555551 PP

>> E3_UbLigase_R4  E3 ubiquitin-protein ligase UBR4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   1.0   9.3e-05      0.42     541     589 ..     303     350 ..     281     367 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 9.3e-05
  E3_UbLigase_R4 541 pkeEWesaalrNaetkCNgllPlwgpkvsesafascldryntnlqeltr 589
                     +  EWe aa  N+e +  +++P wg++++ ++ a+ l+ y   + ++++
      EPA05927.1 303 TEAEWEKAACWNEEKQQKTIFP-WGNQMPTEQNANLLESYHWGCTAIGS 350
                     346*******************.****************9988888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       756  (0.0421663); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.54
# Mc/sec: 2325.22
//
Query:       EPA05928.1  [L=135]
Description: Mov34/MPN/PAD-1 family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.9e-20   71.2   0.0    6.7e-20   71.0   0.0    1.0  1  Prok-JAB    Prokaryotic homologs of the JAB domain
    5.8e-07   29.5   0.0    7.5e-07   29.1   0.0    1.1  1  JAB         JAB1/Mov34/MPN/PAD-1 ubiquitin protease
    0.00012   22.0   0.2    0.00024   21.1   0.2    1.4  1  RadC        RadC-like JAB domain
     0.0024   18.2   0.3      0.035   14.4   0.1    2.1  2  Toxin-JAB1  JAB-like toxin  1
  ------ inclusion threshold ------
      0.052   12.8   0.0      0.087   12.1   0.0    1.4  1  TylF        Macrocin-O-methyltransferase (TylF)
       0.06   13.1   0.0        0.1   12.3   0.0    1.3  1  Sda         Sporulation inhibitor A


Domain annotation for each model (and alignments):
>> Prok-JAB  Prokaryotic homologs of the JAB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.0   0.0   2.2e-23   6.7e-20       6     107 ..      12     112 ..       7     123 .. 0.86

  Alignments for each domain:
  == domain 1  score: 71.0 bits;  conditional E-value: 2.2e-23
    Prok-JAB   6 salvaharrahpeEtcGlllgkeseseevivvplvnewsn......rfeipdpedslarlkfearerglevvgiwHSHpggsarPSetDrrdaaalarv 98 
                   lv h  +++p+E c++l+g+   +e+v+ v++v  ++n      +f+i + e+ +   k  a++r+++vvgi+HSHp+++a+PS+tD + ++ +   
  EPA05928.1  12 KILVNHTNNEKPNESCAILFGSV--KEQVASVKEVFLANNieespvNFTI-SNEQLIEIYK-TAEDRKTDVVGIFHSHPNSEAYPSSTDKKFMQSN--- 103
                 57899****************98..777777777888999999*99****.999999*999.*********************************8... PP

    Prok-JAB  99 kalliivgd 107
                 +++++i + 
  EPA05928.1 104 PVVWVIYSG 112
                 677777766 PP

>> JAB  JAB1/Mov34/MPN/PAD-1 ubiquitin protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   2.5e-10   7.5e-07       8     110 ..       6     101 ..       1     104 [. 0.85

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 2.5e-10
                 EEHHHHHHHHHHHHHHHHHTS--EEEEEEEESSSEEEEEEEEEEESEEEESSECEEEEEHHHHHHHHHHHHHHHCTT.SEEEEEEEESSSS-SS--HHH CS
         JAB   8 leslvllkildhalrtekeeeevmGlliGelnddttveitnvfalpfeetekdvdavsldqeylekksellkklrgr.ervvGWYhshpditvwlsevd 105
                 +  +     ++h ++++ +  e + +l G+++++ + ++ +vf     e++    ++s +q      +e +k  + r   vvG +hshp+ ++++s+ d
  EPA05928.1   6 ITEDQKKILVNHTNNEKPN--ESCAILFGSVKEQ-VASVKEVFLANNIEESPVNFTISNEQL-----IEIYKTAEDRkTDVVGIFHSHPNSEAYPSSTD 96 
                 5555555678999999999..999**********.9*******9988888888778888777.....99999999999*******************99 PP

                 HHHHH CS
         JAB 106 vrtqa 110
                  + ++
  EPA05928.1  97 KKFMQ 101
                 77665 PP

>> RadC  RadC-like JAB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.2   7.9e-08   0.00024       8      89 ..      11     101 ..       5     103 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 7.9e-08
                 HHHHTTTSS-T.TS-EEEEEEE-TTSBEEEEEEE.EESTT-.......GGGCSHHHHHHHHHHTT-SEEEEEEE-TTS--S--HHHHHHHH CS
        RadC   8 aeylkeeladl.eqEefvvllLdsknrliadeel.seGtln.......stlvdprevfkealklnAaavilaHnhPsgdlepSeeDieltk 89 
                 +++l ++ +++ ++E +++l+   k ++ + +e+    +++        ++ +  e++k+a +++   v ++H hP+ ++ pS+ D+++++
  EPA05928.1  11 KKILVNHTNNEkPNESCAILFGSVKEQVASVKEVfLANNIEespvnftISNEQLIEIYKTAEDRKTDVVGIFHSHPNSEAYPSSTDKKFMQ 101
                 56666676666357****************99995234455111112234445679*******************************9987 PP

>> Toxin-JAB1  JAB-like toxin  1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.057   1.7e+02      31      59 ..       8      36 ..       2      44 .. 0.75
   2 !   14.4   0.1   1.2e-05     0.035      35      86 .]      42      99 ..      31      99 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.057
  Toxin-JAB1 31 engkkglvvsTsheknsvsgtyllskllk 59
                e+ kk lv +T++ek ++s + l+ ++++
  EPA05928.1  8 EDQKKILVNHTNNEKPNESCAILFGSVKE 36
                455666699******99988888877776 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 1.2e-05
  Toxin-JAB1 35 kglvvsTsheknsvsgtyllskllkagytirel........iHsHpdggtkkpsdaDkgf 86
                k+++++ + e+  v    + +++l + y+++e+         HsHp+ + ++ps  Dk+f
  EPA05928.1 42 KEVFLANNIEESPV-NFTISNEQLIEIYKTAEDrktdvvgiFHSHPN-SEAYPSSTDKKF 99
                55666555555555.667788888899999999999999999*****.99*******986 PP

>> TylF  Macrocin-O-methyltransferase (TylF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.9e-05     0.087     108     165 ..      70     125 ..      58     130 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.9e-05
        TylF 108 gvedRkvwvaDsFeglPkpdeeklaedagdklkeleevlavseeevrenFrrygLldd 165
                  +edRk  v+  F+  P++  e++++ +++k  + + v+ v +  v++nFr y L  d
  EPA05928.1  70 TAEDRKTDVVGIFHSHPNS--EAYPSSTDKKFMQSNPVVWVIYSGVSKNFRAYVLESD 125
                 5689999999999999887..78******************************99876 PP

>> Sda  Sporulation inhibitor A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   3.5e-05       0.1       3      17 ..      58      72 ..      57      77 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.5e-05
         Sda  3 kLsDelLieaYekAl 17
                ++s+e+Lie+Y++A 
  EPA05928.1 58 TISNEQLIEIYKTAE 72
                58***********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 842.63
//
Query:       EPA05929.1  [L=302]
Description: protoheme IX farnesyltransferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-50  171.5  22.5    2.6e-50  171.1  22.5    1.1  1  UbiA      UbiA prenyltransferase family
  ------ inclusion threshold ------
        1.5    8.3   9.2        2.8    7.4   0.4    2.4  2  DUF1129   Protein of unknown function (DUF1129)


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.1  22.5   2.9e-54   2.6e-50       2     246 ..      28     277 ..      27     291 .. 0.92

  Alignments for each domain:
  == domain 1  score: 171.1 bits;  conditional E-value: 2.9e-54
        UbiA   2 lipalvglalaaggspdl.....llllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllilgllllalllnpltall 95 
                 +i+a+ ++ +a++ +p+         l ++++++la+a++ alN+y+D +iD +m rt  RP++sGr+   +++i++++   ++++ ++++lnp++a++
  EPA05929.1  28 VITAVTSMYAASKLVPNVphldyIAYLHIIIAGALASAGSSALNHYYDKDIDPKMTRTSTRPIPSGRMAASHVMIYGLAVSCISVIYGYFTLNPVSAFF 126
                 7888999999988888888888777888889999***************************************************************** PP

        UbiA  96 gllallly.vvYtglrlKrrtllgtvvggiafglppllgwaavtgslsllalllalavflltwaialandlrdregDrkagiktlpvvlGrkaaril.. 191
                 ++l+++ y ++Yt ++lKr    ++v+ggia+  ++++gw a+tgs++ll +l++++vf++t +++++ +++ ++++++a+i++lpvv+G +++  +  
  EPA05929.1 127 IALGIFSYvIIYT-VWLKRLNTSNIVIGGIAGSAAAWAGWSAATGSMDLLGFLVGFLVFVWTPSHFWCLAMKIKDEYAQANIPMLPVVIGMQRTSKYil 224
                 *************.9**************************************************************************9999999755 PP

        UbiA 192 .lalllavlllallllllalllllylllalllaalallraarlvrrrdakkaakff 246
                   +l+l+      l+l++++++l+y+++a+++++l+l+++++l+++ +++ a+k++
  EPA05929.1 225 gNTLILLPY---SLILPAFGMGLVYTVIAAVSGGLMLAYHYKLTKTPTSEFAWKAY 277
                 433333333...4579*********************************9999998 PP

>> DUF1129  Protein of unknown function (DUF1129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   2.9    0.0026        24      86     199 ..      26     144 ..      18     158 .. 0.65
   2 ?    7.4   0.4   0.00031       2.8     111     159 ..     242     286 ..     233     300 .. 0.64

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0026
     DUF1129  86 LlllalfallfgilalfskkkqtasiGlitlllvalvgGlamvlvyrlltre.....kkkkkrpplwkrllilllllvvwlvlftlvallpaviNpvLp 179
                 Ll++  ++ +++  +l+ +  +  +i  + +++ ++++ +    ++++ +++      +++ rp    r++++ +++  + v ++ v     ++Npv  
  EPA05929.1  26 LLVITAVTSMYAASKLVPNVPHLDYIAYLHIIIAGALASAGSSALNHYYDKDidpkmTRTSTRPIPSGRMAASHVMIYGLAVSCISVIYGYFTLNPVSA 124
                 788888999999999999988888999999999999999999999999988884333333334433444444433333333333333334445566655 PP

     DUF1129 180 plvliiigviafvvryylkk 199
                  ++ + i    ++  ++lk+
  EPA05929.1 125 FFIALGIFSYVIIYTVWLKR 144
                 55444444444444455554 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00031
     DUF1129 111 iGlitlllvalvgGlamvlvyrlltrekkkkkrpplwkrllilllllvv 159
                 +Gl++ ++ a+ gGl++ + y+l++  + ++    +wk   +++  l +
  EPA05929.1 242 MGLVYTVIAAVSGGLMLAYHYKLTKT-PTSE---FAWKAYKVTAPYLTI 286
                 79******999999999999999875.2222...233333333222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       761  (0.0424452); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 2165.35
//
Query:       EPA05930.1  [L=85]
Description: hypothetical protein BG20_I0679 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-37  126.4   1.7    3.2e-37  126.3   1.7    1.0  1  DUF2024   Domain of unknown function (DUF2024)
  ------ inclusion threshold ------
      0.036   14.0   0.1       0.04   13.9   0.1    1.1  1  Haem_bd   Haem-binding domain


Domain annotation for each model (and alignments):
>> DUF2024  Domain of unknown function (DUF2024)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.3   1.7   3.6e-41   3.2e-37       1      81 []       1      81 [.       1      81 [. 0.99

  Alignments for each domain:
  == domain 1  score: 126.3 bits;  conditional E-value: 3.6e-41
                -EEEEEEEEE--SSS--EEEEEEES---HHHHHHHHHHHHHHHT---S---TTTEEEEEEEE--HHHHHHHHHHSEEEE-- CS
     DUF2024  1 mkvavfDtyvkkkdGkvlHFDvlvdekdeekaleyakeyLkskgeeeakvtskeCkfCHseeaeeeveeaikkqGyyiiel 81
                m+++v+Dtyvk+kdG+++HFDv++ ek+++ka++y+ke+Lk++ge +a++t++eC+fCHs+ a+e ve+aik++Gy+i+++
  EPA05930.1  1 MEIHVYDTYVKAKDGHTMHFDVITGEKNHDKAIQYGKEWLKTVGEANATMTTNECQFCHSQGAPEPVERAIKEKGYFIQKM 81
                9******************************************************************************99 PP

>> Haem_bd  Haem-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   4.5e-06      0.04      12      59 ..      26      72 ..      16      81 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.5e-06
     Haem_bd 12 ekneen.ltaeadvkaelkapkevkkiL.eksCydCHsnetelpwYakia 59
                ekn+++ ++  +++ +   +  e+++++ +++C+ CHs+ +  p    i+
  EPA05930.1 26 EKNHDKaIQYGKEWLK---TVGEANATMtTNECQFCHSQGAPEPVERAIK 72
                4555555666666644...6667777777**********99888766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 564.64
//
Query:       EPA05931.1  [L=60]
Description: hypothetical protein BG20_I0681 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       892  (0.0497518); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.32s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 402.54
//
Query:       EPA05932.1  [L=207]
Description: aspartate dehydrogenase, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-32  111.9   1.1    2.3e-32  111.2   1.1    1.3  1  DUF108         Domain of unknown function DUF108
    1.8e-08   35.1   0.1    3.7e-08   34.0   0.1    1.5  1  NAD_binding_3  Homoserine dehydrogenase, NAD binding domain


Domain annotation for each model (and alignments):
>> DUF108  Domain of unknown function DUF108
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.2   1.1   2.6e-36   2.3e-32       2      89 .]     105     192 ..     104     192 .. 0.97

  Alignments for each domain:
  == domain 1  score: 111.2 bits;  conditional E-value: 2.6e-36
                 SS-EEEEEEEHHHHHHHSTTS-CHHHHHHHHHH.CCGEEEEEEEETT-SSEEEEEEEEETTEEEEEEEEE-EETTEEEEEHHHHHHHH CS
      DUF108   2 teptvlFeGsareaikkfPknvNvaaalaLaalgfdrvkvelvadpnldkniheieveGsfgefslevenkpspenPktsalaalsvi 89 
                 ++ t++FeG+a++a+ +fP+n+Nvaa l+La+lg ++++v++vadpn +kn+h+i ++G+fg+++l++en+p+++nPkts la ls+i
  EPA05932.1 105 NTTTTIFEGTAKQAVSLFPANINVAALLSLAGLGSEKTMVKIVADPNTTKNTHNIVAQGKFGKMNLSIENVPDETNPKTSSLAILSAI 192
                 5789*********************************************************************************986 PP

>> NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.1   4.1e-12   3.7e-08      61     117 .]       1      57 [.       1      57 [. 0.96

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 4.1e-12
                    EEEEE-S--HHHHTTHHHHHHTTEEEE-S--CGGG-HHHHHHHTSSSTTS--.EE-G CS
  NAD_binding_3  61 dvvVEcasseavaelvlkaLkagkdvvtankgaladealyeeLreaaeangakiyve 117
                    d++VE+as+eav++++ ++L+++ d++++++gal de+ ++ L ea e  +++iy++
     EPA05932.1   1 DIIVEAASQEAVRNVAHSVLQNKRDLMIMSVGALLDETIFDILSEACEHFHKTIYLP 57 
                    89***************************************9999999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1351.46
//
Query:       EPA05933.1  [L=67]
Description: hypothetical protein BG20_I0666 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.3e-05   23.1   9.5    5.3e-05   23.1   9.5    3.0  4  DUF1610         Domain of unknown function (DUF1610)
  ------ inclusion threshold ------
      0.037   14.5  17.1      0.042   14.3  17.1    1.2  1  zf-CHY          CHY zinc finger
      0.058   12.8   0.2      0.058   12.8   0.2    3.7  4  zf-ribbon_3     zinc-ribbon domain


Domain annotation for each model (and alignments):
>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   1.3      0.85   5.1e+03      21      23 ..       6       8 ..       6       8 .. 0.91
   2 !   23.1   9.5   8.9e-09   5.3e-05       1      24 []      18      41 ..      18      41 .. 0.99
   3 ?   -4.0   1.2       2.6   1.6e+04       1       4 [.      47      50 ..      47      50 .. 0.81
   4 !    4.4   0.6    0.0064        38       1       5 [.      59      63 ..      59      65 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.85
     DUF1610 21 NCG 23
                NCG
  EPA05933.1  6 NCG 8 
                999 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 8.9e-09
     DUF1610  1 CtSCGaelaprEravvFpCPNCGE 24
                C+ C + + p  + v+F CPNCGE
  EPA05933.1 18 CSCCHRHIMPNDKCVKFNCPNCGE 41
                9**********************9 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 2.6
     DUF1610  1 CtSC 4 
                C SC
  EPA05933.1 47 CESC 50
                8899 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.0064
     DUF1610  1 CtSCG 5 
                C+SC+
  EPA05933.1 59 CSSCN 63
                ****9 PP

>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3  17.1     7e-06     0.042      21      74 ..      17      64 ..       5      65 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7e-06
      zf-CHY 21 aCreCHeeledhelerlevkevlcllCeteqekavlCkkCkkefaeyfCpiCkl 74
                +C  CH+    h + + +  ++ c +C ++   +  C++C++ +++y+C+ C++
  EPA05933.1 17 KCSCCHR----HIMPNDKCVKFNCPNCGEV--LVWRCESCREAARTYTCSSCNF 64
                7******....*****************97..999*****************96 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.6   5.1         3   1.8e+04       8      10 ..       7       9 ..       5      21 .. 0.54
   2 ?   12.8   0.2   9.8e-06     0.058       4      25 ..      35      42 ..      32      44 .. 0.60
   3 ?   -3.0   0.8      0.91   5.4e+03       5       8 ..      47      50 ..      46      50 .. 0.52
   4 ?    4.6   0.3    0.0037        22       2       9 ..      56      63 ..      55      64 .. 0.87

  Alignments for each domain:
  == domain 1  score: -4.6 bits;  conditional E-value: 3
  zf-ribbon_3  8 CGa 10
                 CG 
   EPA05933.1  7 CGM 9 
                 443 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 9.8e-06
  zf-ribbon_3  4 rCPnCGaplssddnvCpyCGtk 25
                 +CPnCG+              +
   EPA05933.1 35 NCPNCGE--------------V 42
                 5666665..............4 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 0.91
  zf-ribbon_3  5 CPnC 8 
                 C +C
   EPA05933.1 47 CESC 50
                 5555 PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.0037
  zf-ribbon_3  2 tvrCPnCG 9 
                 t++C++C+
   EPA05933.1 56 TYTCSSCN 63
                 899****6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       911  (0.0508115); expected 358.6 (0.02)
Passed bias filter:                      200  (0.0111551); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 481.41
//
Query:       EPA05934.1  [L=317]
Description: quinolinate synthetase complex, A subunit [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   5.7e-113  377.0   1.8   6.5e-113  376.8   1.8    1.0  1  NadA      Quinolinate synthetase A protein


Domain annotation for each model (and alignments):
>> NadA  Quinolinate synthetase A protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  376.8   1.8  3.6e-117  6.5e-113       1     299 []      10     315 ..      10     315 .. 0.98

  Alignments for each domain:
  == domain 1  score: 376.8 bits;  conditional E-value: 3.6e-117
                 HHHHHHHHHHTEEEEEETTS-HHHHHH-SEEE-HHHHHHHCCC-SSSEEEEES-HHHHHHHHHHSTTSEEE-SSTT---HHHCT--HHHHHHHHHHSTT CS
        NadA   1 eeikelkkeknavilaHnYqedeiqeiadfvGDSleLarkaaeteaevivfcGVhFMaetakiLspekkvllpdleagCsladmitaeeveelkeelpd 99 
                 eei +lkkek++vilaHnYq +++q+iadf+GDSl L+r+aa++ +++i+fcGVhFMaeta+i++p+k+vl+pdleagCsl+d+ita+e++++k+++p+
  EPA05934.1  10 EEIMRLKKEKDVVILAHNYQIPDVQDIADFTGDSLGLSRQAAKVPQKTILFCGVHFMAETAAIICPDKRVLIPDLEAGCSLSDSITADELRNWKKQHPG 108
                 589************************************************************************************************ PP

                 S-EEEESSS-HHHHTT-SEEE-TTTHHHHHHHSS.-SEEEEES-HHHHHHHHHHH.SEEEEESSSS-GCGGG--CHHHHHHHHCSTT-EEEE-TTS... CS
        NadA 100 aavvtYvNssaevKalsdivcTSsnavkvvealk.ekkilflPDqnLgryvakklgekkiilwkgaCsvHeefkaeeveelkeehpdakvlvHPEc... 194
                 a+ v YvN++ae+K++ d++cTS+nav+vv+a++ +k+ilflPD +Lg+yvak +g+k++ +w+g+C+vH+ +k+e++++  ++ +da++l+HPEc   
  EPA05934.1 109 AIAVGYVNTTAEIKSELDYCCTSANAVNVVKAIPaDKEILFLPDMFLGSYVAKVTGRKNMFIWAGECHVHAGIKPEDITNKLNSLKDAEFLIHPECsct 207
                 *********************************77**************************************************************** PP

                 ........-HHHHHCSSEE--HHHHCCCCGTTSSSCEEEES-THHHHHHHHH-TTSEEE.....ECSSSSSTTGGG--HHHHHHHHHHT-S.B----HH CS
        NadA 195 ........keevveaadvvgSTsqiikavkeseakefiigTelglverlkkeapekefialsaeaaeeavCetMkkitleklleaLeeleeeeikvdee 285
                         + +  +++  + ST+++++++++s++k+f+++Te+g+++++++++p+k+fi +    +e+a C++Mk+itl+k+++aL ++++ ++ v++e
  EPA05934.1 208 tpmmydaaSGSFDDQKVSILSTEGMLNHAHDSKSKNFVVATEIGILYKMRQQNPGKNFIPA----SEKAECQYMKMITLDKVYNALVQEKN-QVVVPKE 301
                 *****99999999999*******************************************33....33789****************99999.9****** PP

                 HHHHHHHHHHHHHH CS
        NadA 286 vaekAkkalermle 299
                 +a+kA+ a+erml+
  EPA05934.1 302 IADKARLAIERMLA 315
                 ************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       633  (0.0353059); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2027.06
//
Query:       EPA05935.1  [L=203]
Description: O-methyltransferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.3e-37  126.6   0.8    1.6e-36  125.5   0.8    1.6  1  Methyltransf_3   O-methyltransferase
      2e-13   51.3   0.0    3.6e-13   50.4   0.0    1.4  1  Methyltransf_24  Methyltransferase domain
    8.4e-08   32.2   0.1    3.7e-07   30.1   0.1    1.9  2  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    4.5e-06   26.5   0.1    7.1e-06   25.9   0.1    1.4  1  Methyltransf_31  Methyltransferase domain
    2.8e-05   23.9   0.0    3.7e-05   23.5   0.0    1.2  1  CmcI             Cephalosporin hydroxylase
    5.3e-05   23.8   0.0    0.00016   22.3   0.0    1.8  2  Methyltransf_25  Methyltransferase domain
    0.00015   21.1   0.1    0.00019   20.9   0.1    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
    0.00031   20.4   0.0    0.00048   19.8   0.0    1.4  1  Cons_hypoth95    Conserved hypothetical protein 95
    0.00065   19.3   0.0     0.0012   18.5   0.0    1.4  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
     0.0023   17.6   0.0      0.004   16.8   0.0    1.3  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
  ------ inclusion threshold ------
      0.038   13.7   0.0      0.049   13.3   0.0    1.2  1  GCD14            tRNA methyltransferase complex GCD14 subunit
      0.038   13.7   0.0      0.064   12.9   0.0    1.4  1  UPF0020          Putative RNA methylase family UPF0020
       0.05   12.8   0.0      0.069   12.3   0.0    1.2  1  TRM              N2,N2-dimethylguanosine tRNA methyltransfera
      0.052   13.4   0.0      0.067   13.0   0.0    1.3  1  Methyltransf_23  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.5   0.8   1.3e-39   1.6e-36      22     166 ..      24     170 ..       6     200 .. 0.90

  Alignments for each domain:
  == domain 1  score: 125.5 bits;  conditional E-value: 1.3e-39
                     TST...TGGGS--HHHHHHHHHHHHHHT--EEEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHHHTT-GGGEEEEES-HHHHHHH CS
  Methyltransf_3  22 kktd..lsemevsvdegqfLslLvklvnakrvleiGvftGyslLatalalPeDGkilaididreayeialkfiqkagvaekieliegdalkvLee 114
                     +k +     + +++d g f +lL++  + k++leiG+  Gys L  a ++ +  ki++i++++++ e a+  ++kagv + i++++g a+ vL +
      EPA05935.1  24 HKVErdQRMLAITKDTGIFYNLLLNTHQPKKILEIGMSVGYSTLWFAGSISKKSKIITIEQNPQKIEQAKINFKKAGVSKMIDIKQGVAKDVLTK 118
                     444322566789*********************************************************************************** PP

                     HHTSSS---EEEEEE-S-GGGHHHHHHHHHHTEEEEEEEEEE-TTGGGGGG- CS
  Methyltransf_3 115 lvkdkklpefDfifvDaDkssyvnyyeklleLvkvGgliaiDntLWeGkvve 166
                     l k k++ +fDfif+DaDk++y  y++ ++ L+k+ g+ia Dn+L+    ++
      EPA05935.1 119 LSKSKSREQFDFIFIDADKEQYSLYFDLCVPLLKKDGIIAADNILYPTRFTK 170
                     *********************************************9776655 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.4   0.0   2.8e-16   3.6e-13       1     106 []      56     162 ..      56     162 .. 0.93

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 2.8e-16
  Methyltransf_24   1 vEiGvysGvstlwllralrrngagrlvavdhdpg.aeeaaalareaglddrvrlikadseealasla....agsiDllfiDgghaaeavledle 89 
                      +EiG++ G+stlw++  + +    ++++++ +p+  e+a+ ++++ag+++ +++ ++ ++++l++l+    ++++D++fiD++  +e++  +++
       EPA05935.1  56 LEIGMSVGYSTLWFAGSISKKS--KIITIEQNPQkIEQAKINFKKAGVSKMIDIKQGVAKDVLTKLSksksREQFDFIFIDAD--KEQYSLYFD 145
                      7**************9999887..5********876778888999**********************9999999*******87..89999999* PP

  Methyltransf_24  90 allprlapggvvlfdDi 106
                      ++ p+l+++g++  d+i
       EPA05935.1 146 LCVPLLKKDGIIAADNI 162
                      *************9986 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.1   2.9e-10   3.7e-07      20     127 ..       4     105 ..       1     114 [. 0.70
   2 ?   -0.9   0.0      0.89   1.1e+03      10      57 ..     151     199 ..     147     201 .. 0.69

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 2.9e-10
                 HHHHHHHHS-GGG.GSSCGGGGGTTSSS-EEEETTEEE--HHHHHHHHHHTT.--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHH CS
        PCMT  20 kvaealeevdRee.fvpesfkekaYedaplsigynatiSaphmvalalelle.lkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakr 116
                 k+a +l++ +R + + ++++++   ++  l i  +         +++ +ll   ++ +++Le+G   Gy t  +a  + +k ++++ie+ ++ +e+ak 
  EPA05935.1   4 KIASVLRSLERRStYEEKNYHKVERDQRMLAITKD--------TGIFYNLLLnTHQPKKILEIGMSVGYSTLWFAGSISKKSKIITIEQNPQKIEQAKI 94 
                 66666666665431333333333333333333333........344555544388899***************************************** PP

                 HHHHCTTCSEE CS
        PCMT 117 nlkkldlenvi 127
                 n kk +++++i
  EPA05935.1  95 NFKKAGVSKMI 105
                 *****998654 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.89
                 HHHTTS---HHHHHHHHHS-G.GGGSSCGGGGGTTSSS-EEEETTEEE- CS
        PCMT  10 lkkkgviksdkvaealeevdR.eefvpesfkekaYedaplsigynatiS 57 
                 lkk+g+i+ d+++   + ++  ++++++ +k+k ++  ++++g ++  S
  EPA05935.1 151 LKKDGIIAADNILYPTRFTKYiQKYLNHIHKNKRFDSVTVPVGNGQELS 199
                 6777888887777665555432677887777788888888888877665 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.1   5.6e-09   7.1e-06       3      82 ..      51     135 ..      49     197 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 5.6e-09
  Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdiee.lekl.led..ekfDlilsne 82 
                      + +++l++G   G+ t+ +a  + +k++++ i+ +++ ie+A+ n +k g++  +  +qg + + l kl  ++  e+fD+i+ ++
       EPA05935.1  51 QPKKILEIGMSVGYSTLWFAGSISKKSKIITIEQNPQKIEQAKINFKKAGVSkMIDIKQGVAKDvLTKLsKSKsrEQFDFIFIDA 135
                      668999**************99999**************************988899997666665554433366*******982 PP

>> CmcI  Cephalosporin hydroxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   2.9e-08   3.7e-05      23     122 ..      42     138 ..      23     151 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 2.9e-08
        CmcI  23 ayQeliwelkPdliietGiahGGsalfsasllallkskrkvlaididireknrqaieahplasrielie.gssvdpeiveqvkslakekekvlvilDsd 120
                  y  l+   +P+ i+e+G+  G s l++a    ++++k k+++i+ + ++ ++++i+ +  a   ++i   ++v+ +++ + ++ +++++  ++ +D+d
  EPA05935.1  42 FYNLLLNTHQPKKILEIGMSVGYSTLWFAG---SISKKSKIITIEQNPQKIEQAKINFK-KAGVSKMIDiKQGVAKDVLTKLSKSKSREQFDFIFIDAD 136
                 466677889*******************96...566789*******9999999888874.444444554146799999999999999999989999988 PP

        CmcI 121 Ht 122
                  +
  EPA05935.1 137 KE 138
                 66 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       8.2     1e+04      20      38 ..      19      37 ..       7      40 .. 0.63
   2 !   22.3   0.0   1.2e-07   0.00016       1      97 []      55     155 ..      55     155 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 8.2
                     TSSEEEEEESSHHHHHHHH CS
  Methyltransf_25 20 gkakvtgvDiseemleaar 38
                     ++++++ v+ +++ml++++
       EPA05935.1 19 EEKNYHKVERDQRMLAITK 37
                     3567777777788887765 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 1.2e-07
                      EEEET-TTSHHHHHHHCTS.TSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCG....BS..SSTTTEEEEEEESTGGGSSHHHHHHH CS
  Methyltransf_25   1 vLdlGcGtGrltlalakrl.gkakvtgvDiseemleaareraeeegl..nvefvqgdaed....lp..fedgsfDlvvssgalhhlsdedleka 85 
                      +L++G   G  tl++a  + +k+k++ ++ +++ +e+a+ +++++g+   +++ qg a+d    l+     ++fD++++  a    ++e++  +
       EPA05935.1  55 ILEIGMSVGYSTLWFAGSIsKKSKIITIEQNPQKIEQAKINFKKAGVskMIDIKQGVAKDvltkLSksKSREQFDFIFID-A----DKEQYSLY 143
                      8*****************9669**********************9999988888877755311254335888******93.3....45666666 PP

                      HHHHHHHEEEEE CS
  Methyltransf_25  86 lkeiarvLkpgG 97 
                      ++ +  +Lk++G
       EPA05935.1 144 FDLCVPLLKKDG 155
                      777777777666 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.1   1.4e-07   0.00019      58     175 ..      47     170 ..      16     187 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.4e-07
                 TT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHH..HHHTS-SSS-EEEEES-GGG-----SEEEEES-GGGT....SGGGHHHHHH CS
        CMAS  58 lelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakk..rvdeldlerkvevklldyedldekvdrvvsvgafehv....gkenydtffk 150
                 l+ ++ +++L+iG   G+ +   +     k   +T+ ++ +k  ++  +++++++++  ++k    +d+  k+ +  s + f+ +     ke+y  +f+
  EPA05935.1  47 LNTHQPKKILEIGMSVGYSTLWFAGSISKKSKIITIEQNPQKIEQAkiNFKKAGVSKMIDIKQGVAKDVLTKLSKSKSREQFDFIfidaDKEQYSLYFD 145
                 45567789*****99999998888888888999999999887666511567899999999999999*****************9989999********* PP

                 HHHHHS-TT-EEEEEEEEE--HHHH CS
        CMAS 151 klkkllkedGllllhtitslhkkel 175
                  +  llk+dG+++   i  +++ ++
  EPA05935.1 146 LCVPLLKKDGIIAADNILYPTRFTK 170
                 **************99988776544 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   3.8e-07   0.00048      61     152 ..      74     167 ..      42     192 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 3.8e-07
                    HTT-SEEEEEES-HHHHHHHHHHHCCCT--T..TTEE.EEES-HHHHCTS--SS-EEEEEEE--SSSTTCH..HHHHHHHHHTT-EEEEEEEEEEE CS
  Cons_hypoth95  61 SRgakkavlvekdkeavkilkenleelklee..etae.lkedaleallklakkkeefdivflDPPyakell.ieevlelleekkllkenalvvvet 152
                    S + +k++ +e++++ +++ k n ++ ++++   +++ + +d l +l +++k  e+fd++f+D   ++  l +  ++ ll++ ++++ + +++  +
     EPA05935.1  74 SKK-SKIITIEQNPQKIEQAKINFKKAGVSKmiDIKQgVAKDVLTKL-SKSKSREQFDFIFIDADKEQYSLyFDLCVPLLKKDGIIAADNILYPTR 167
                    554.78999*******************9986633330334444444.4457889********876665554666777777777777777766544 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   9.1e-07    0.0012      23      77 ..      77     133 ..      54     137 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 9.1e-07
  Methyltransf_15  23 ekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklkleki..kvdlvfl 77 
                      +k+i+ie n++k+++a+ N +  gvs+ i++++g  +++l kl  +k   ++d++f+
       EPA05935.1  77 SKIITIEQNPQKIEQAKINFKKAGVSKMIDIKQGVAKDVLTKLSKSKSreQFDFIFI 133
                      68*******************************977777766665555456999996 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   3.1e-06     0.004       2      87 ..      45     135 ..      44     137 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.1e-06
                      HHH---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEE.EEES-C....TCCHHHHCC..EEEEEEEE CS
  Methyltr_RsmB-F   2 llLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtnti.vleaDa....rkidkvlggelfDriLlDa 87 
                      llL+ ++ ++il++  + G  T + a  +++k++++ +++n +++++ + n k+ gv ++i + ++ a    +k +k  + e+fD i +Da
       EPA05935.1  45 LLLNTHQPKKILEIGMSVGYSTLWFAGSISKKSKIITIEQNPQKIEQAKINFKKAGVSKMIdIKQGVAkdvlTKLSKSKSREQFDFIFIDA 135
                      579999999************************************************965424444330001455555555*********8 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.8e-05     0.049      39     120 ..      50     134 ..      27     146 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.8e-05
       GCD14  39 kpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvtvth...rDvckeGfdeevsgkvDavfLD 120
                 ++  +++e G   g  +  +a +++ + ++ t+e   q++e+a+ +f++ ++s+++ +++   +Dv ++  +++  ++ D +f+D
  EPA05935.1  50 HQPKKILEIGMSVGYSTLWFAGSISKKSKIITIEQNPQKIEQAKINFKKAGVSKMIDIKQgvaKDVLTKLSKSKSREQFDFIFID 134
                 55567888888888888889999*********************************99854448998888888889999999998 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     5e-05     0.064      75     116 ..      75     116 ..      59     134 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5e-05
                 HH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG-- CS
     UPF0020  75 aelklygsDldrrvvqgareNaekagvgdliefsqadaakLr 116
                 ++ k++ ++ +++ +++a+ N +kagv++ i+++q  a+++ 
  EPA05935.1  75 KKSKIITIEQNPQKIEQAKINFKKAGVSKMIDIKQGVAKDVL 116
                 567799*****************************9998865 PP

>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   5.4e-05     0.069      46     128 ..      49     135 ..      16     160 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.4e-05
                 HH-S-EEEEESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHHHHHHHHHTT--GGEEEE-S-HHHHHC.....--SS-EEEEEE-- CS
         TRM  46 klgekikvldaLsasGlRaiRfalEvpgvkevlaNDisekAvelikeNvklneveeivvineddAnvlla.....ekkkrfdviDlDP 128
                    ++ k+l+   + G  ++ fa  ++++++++  + +++ +e  k N+k   v++++ i+++ A+ +l+     + +++fd+i +D 
  EPA05935.1  49 T-HQPKKILEIGMSVGYSTLWFAGSISKKSKIITIEQNPQKIEQAKINFKKAGVSKMIDIKQGVAKDVLTklsksKSREQFDFIFIDA 135
                 2.45568888888899999***********************************************9999888877778899988774 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   5.3e-05     0.067      19      86 ..      48     131 ..      28     189 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.3e-05
  Methyltransf_23  19 klraggrvLdiGcGtGillevlrengf...svtgvDlspeaveiae..........................kakkaqkdqfdeqeaaepqgkf 83 
                      +  +++++L+iG  +G+ +  ++       +++ ++++p+++e a+                          +              +++ ++f
       EPA05935.1  48 NTHQPKKILEIGMSVGYSTLWFAGSISkksKIITIEQNPQKIEQAKinfkkagvskmidikqgvakdvltklS-------------KSKSREQF 128
                      578899***********99999776433579************997877777666666555444444333221.............22233355 PP

  Methyltransf_23  84 dlI 86 
                      d+I
       EPA05935.1 129 DFI 131
                      554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1021  (0.0569468); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1261.41
//
Query:       EPA05936.1  [L=123]
Description: aminoacyl-tRNA hydrolase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-40  136.7   0.0    4.6e-40  136.6   0.0    1.0  1  PTH2      Peptidyl-tRNA hydrolase PTH2


Domain annotation for each model (and alignments):
>> PTH2  Peptidyl-tRNA hydrolase PTH2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.6   0.0   2.6e-44   4.6e-40       2     117 .]      11     123 .]      10     123 .] 0.98

  Alignments for each domain:
  == domain 1  score: 136.6 bits;  conditional E-value: 2.6e-44
                 EEEEEEESSSSS-HHHHHHHHHHHHHHHHHHHHHH.CHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHHHTT-SEEEEEETSSSSSSTTCEEEEEEE CS
        PTH2   2 kmvlvvrkDLkmskGkiaaqcahAavalvkkllkesnekellkeWeeegqkkivlkveseeeLlelaakakalglpaalirDagrtqiepgtkTvlaig 100
                 k+v+v+r+DL+m+kGkiaaq++hA+v  +++++k+ ++ e++++W   gq+k+vlkv+  +eL+e++++a +l+lp + ++Dag+tqi+pgt T++ ig
  EPA05936.1  11 KQVIVIRTDLEMGKGKIAAQVGHACVLGAEHVRKS-HP-EWFEQW-WGGQEKVVLKVSGLKELQEVKRHAIDLNLPWSEVTDAGHTQIAPGTITCISIG 106
                 9*********************************8.88.8*****.89*************************************************** PP

                 EEEHHHHHHHHTTSEB- CS
        PTH2 101 PapksivdkvtgkLkll 117
                 Pap++++dk+tg+Lkll
  EPA05936.1 107 PAPENLIDKITGDLKLL 123
                 ***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.32s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 770.00
//
Query:       EPA05937.1  [L=202]
Description: proline dehydrogenase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.6e-25   88.1   0.0    1.1e-24   87.5   0.0    1.1  1  Pro_dh           Proline dehydrogenase
  ------ inclusion threshold ------
      0.068   12.8   0.4       0.22   11.2   0.1    1.8  2  Peptidase_M15_2  Bacterial protein of unknown function (DUF88
       0.15   12.5   0.0       0.64   10.5   0.0    1.9  2  Telomere_reg-2   Telomere length regulation protein


Domain annotation for each model (and alignments):
>> Pro_dh  Proline dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.5   0.0   1.8e-28   1.1e-24      79     288 ..       7     186 ..       3     190 .. 0.92

  Alignments for each domain:
  == domain 1  score: 87.5 bits;  conditional E-value: 1.8e-28
                 HHHHHHHHHHHHHHHTT-EEEE----GGGHHHHHHHHHHHHHSCCTTT---EEEEEETTBTTHHHHHHHHHHHHHHTTS-EEEEEE--S-HHHHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
      Pro_dh  79 elverlrtlakeakelgvrlliDaEeaklqeltlelfrklnkepelkdwevvgntyQaYlkdalevlqkllelAeregfrlgvkLVrGAYldsErkraq 177
                  ++ ++++l++ a +  v ++iD+E ++  + t+el+ +l++     ++e +g+++Qa lk++ e++q+l+++        ++++V+GAY ++ +    
  EPA05937.1   7 TCLANFERLIDSASKSHVFVWIDMESSEHTDETIELYYALFS-----RYERLGIAIQANLKRSHEDIQDLVRHGG------KIRIVKGAYRENSKI--- 91 
                 5678999*********************************96.....4556******************997654......79*******988777... PP

                 HTT-S-SB-SSHHHHHHHHHHHHHHHHHTTTTEEEEEE-S-HHHHHHHHHHHHHT..T--GGGEEEEEETTSSHHHHHHHHHTTS-EEEEEEECEHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
      Pro_dh 178 elgyespifdtkeeTDanYdavaelllenrdeiypavAsHNaesvakalalaeelgqekeksevefqqLlGMadnlsfalakagynvrkYlPvGpveev 276
                         f+t +e D+nY ++++ l++  +e  +++A+H  + +++a++l ++       +++efq L+G  d+l+  l k+g+ +  Y+P+G+  + 
  EPA05937.1  92 -------AFKTRKEVDENYLNIMKTLFKDANE--FGIATHDSKLINHAVELSKKY-----PKKFEFQLLKGIRDELKPDLVKQGFIISDYIPYGT--NW 174
                 .......69*****************976665..679******************.....9*********************************7..89 PP

                 HHHHHHHHHHHH CS
                 xxxxxxxxxxxx RF
      Pro_dh 277 lpYLvRRleENt 288
                 lpY +RRl E +
  EPA05937.1 175 LPYSIRRLRERK 186
                 *********976 PP

>> Peptidase_M15_2  Bacterial protein of unknown function (DUF882)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.15   9.2e+02      14      39 ..      34      59 ..      27      70 .. 0.78
   2 ?   11.2   0.1   3.7e-05      0.22      15      81 ..      84     150 ..      72     160 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.15
  Peptidase_M15_2 14 lhtgekaeivykengkylsealkkld 39
                      ht+e++e  y   ++y++ +++   
       EPA05937.1 34 EHTDETIELYYALFSRYERLGIAIQA 59
                     5999****999999999988776554 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 3.7e-05
  Peptidase_M15_2  15 htgekaeivykengkylsealkkldkllrdfrrnevtrmdkrlfdlllqvkrklgskeeiqvvsgyr 81 
                        +e+ +i++k+ ++ +++ l+ +++l++d  +  ++  d +l+++ +++ +k   k e+q++ g r
       EPA05937.1  84 AYRENSKIAFKTRKEVDENYLNIMKTLFKDANEFGIATHDSKLINHAVELSKKYPKKFEFQLLKGIR 150
                      568999*************************************************999999999988 PP

>> Telomere_reg-2  Telomere length regulation protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.31   1.9e+03      21      40 ..       6      25 ..       3      53 .. 0.72
   2 ?   10.5   0.0   0.00011      0.64      19      80 ..      80     141 ..      66     151 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.31
  Telomere_reg-2 21 eaaLksaeeLirrkadevee 40
                    +++L + e Li ++++  + 
      EPA05937.1  6 KTCLANFERLIDSASKSHVF 25
                    67899999999977774333 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00011
  Telomere_reg-2  19 kieaaLksaeeLirrkadeveenaveLataLltledkfdienfeelrlnalvallvatpekv 80 
                      ++ a ++ +++  + ++ev+en  +++++L +  ++f i + +++ +n  v+l  + p+k 
      EPA05937.1  80 IVKGAYRENSKIAFKTRKEVDENYLNIMKTLFKDANEFGIATHDSKLINHAVELSKKYPKKF 141
                     556666667777778899**************************************999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1326.19
//
Query:       EPA05938.1  [L=122]
Description: hypothetical protein BG20_I0664 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0021   18.3   0.1     0.0044   17.2   0.1    1.6  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
     0.0034   16.2   0.8      0.011   14.5   0.0    1.8  2  HI0933_like    HI0933-like protein
  ------ inclusion threshold ------
      0.013   14.7   0.0      0.013   14.7   0.0    1.1  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
      0.014   14.7   0.0      0.014   14.7   0.0    1.2  1  Thi4           Thi4 family
      0.015   14.4   0.0      0.015   14.4   0.0    1.2  1  FAD_binding_2  FAD binding domain
      0.023   14.0   0.0      0.039   13.2   0.0    1.3  1  Amino_oxidase  Flavin containing amine oxidoreductase
      0.027   13.8   0.3      0.042   13.2   0.2    1.3  1  FAD_oxidored   FAD dependent oxidoreductase
       0.19   10.7   0.0       0.21   10.6   0.0    1.0  1  Lycopene_cycl  Lycopene cyclase protein


Domain annotation for each model (and alignments):
>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1     2e-06    0.0044       1      32 [.       2      33 ..       2      56 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2e-06
                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSS CS
  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlG 32
                   + G+ ++Gl +A+++a ++++vl++e    +G
     EPA05938.1  2 VAGGSVAGLICAREIASNNHSVLVIEEDYEIG 33
                   5699**********************987777 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   4.9e-06     0.011       5      36 ..       2      33 ..       1      37 [. 0.93
   2 ?    0.2   0.2      0.11   2.4e+02     105     312 ..      79     104 ..      60     120 .. 0.50

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.9e-06
                 EE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
  HI0933_like  5 viGgGaAGlmaAisaakrgkrVlllekakklg 36
                 v Gg  AGl +A ++a+++++Vl++e+  ++g
   EPA05938.1  2 VAGGSVAGLICAREIASNNHSVLVIEEDYEIG 33
                 78999*********************998887 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.11
                  T.-CHHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----SS-GGGT--SHHHHHHHHTT--EEEEEEES--EE--HH CS
  HI0933_like 105 sdkaedivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGlSiPklGstgkgyklaeqfghtivplrpalvpltlkes 202
                  + k                                                                                               
   EPA05938.1  79 NSKK---------------------------------------------------------------------------------------------- 82 
                  3333.............................................................................................. PP

                  HHHCGGGTT-EEEEEEE...ECTTEEEEEEEEE-SSEEESHHHHHHTTT-......-TT--EEEECSTTS-...HHHHHHHHHHHTTTSBHHHHHTTT CS
  HI0933_like 203 klklkelsGvslkavvlslkkkkkatekgellfThrGlsGpailqlSsyvakalekkeeetleidllPdldaeelkaalekekekeskkslknalael 300
                                                                                                          ++++++ ++ 
   EPA05938.1  83 ----------------------------------------------------------------------------------------QKVAEISRRE 92 
                  ........................................................................................3333333333 PP

                  S-HHHHHHHHHC CS
  HI0933_like 301 lpkrlvevllee 312
                  l k+++++ +++
   EPA05938.1  93 LDKQIAHQSQKK 104
                  333333333333 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   5.8e-06     0.013       4      39 ..       1      40 [.       1     120 [. 0.59

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.8e-06
                 EEE--SHHHHHHHHHHHHHTS-EEEEE....TTHCHHHCS CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxx RF
  Pyr_redox_2  4 vviGgGpAGlaaaltlaqagakvtlve....legtclngg 39
                 +v Gg +AGl +a+++a +++ v+++e     ++  + gg
   EPA05938.1  1 MVAGGSVAGLICAREIASNNHSVLVIEedyeIGTPEHCGG 40
                 688***********************76664333333333 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   6.2e-06     0.014      22      63 ..       2      42 ..       1      97 [. 0.90

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 6.2e-06
                EE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTT CS
        Thi4 22 ivGaGssGLtaayylakkpdlkvailersvspGGGawlGGql 63
                + G+  +GL +a+ +a + +  v+++e+   +G     GG +
  EPA05938.1  2 VAGGSVAGLICAREIASN-NHSVLVIEEDYEIGTPEHCGGLV 42
                678889************.**************999999976 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   6.8e-06     0.015       4      49 ..       2      46 ..       1     106 [. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 6.8e-06
                   EE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-EE-TT CS
  FAD_binding_2  4 ViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgidavl 49
                   V G+ +AGL +A e+a ++++v+v+e   e  g+   ++G +  ++
     EPA05938.1  2 VAGGSVAGLICAREIASNNHSVLVIEEDYE-IGTPEHCGGLVSTAG 46
                   88999*********************9998.556666777766665 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.8e-05     0.039       1      27 [.       7      33 ..       7      34 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.8e-05
                   HHHHHHHHHHHHTTEEEEEEESSSSSB CS
  Amino_oxidase  1 laGLaaArqLlsaGfdVtvlEardrvG 27
                   +aGL++Ar+ +s++++V+v+E +  +G
     EPA05938.1  7 VAGLICAREIASNNHSVLVIEEDYEIG 33
                   69*******************987777 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   1.9e-05     0.042       3      41 ..       1      45 [.       1      66 [. 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.9e-05
  FAD_oxidored  3 vVvGGgpaGvaAAiaAaraGakvlLveer......gvlGGlltsg 41
                  +V GG +aG+++A   a +  +vl++ee+      +++GGl++ +
    EPA05938.1  1 MVAGGSVAGLICAREIASNNHSVLVIEEDyeigtpEHCGGLVSTA 45
                  69*************************872222224556666555 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   9.5e-05      0.21       4      97 ..       2     101 ..       1     117 [. 0.84

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 9.5e-05
  Lycopene_cycl   4 viGaGpAglslAarlteakpglkvvlieaspsllfpnny.vWsdefedlga.....leecvehsWsgtivylddgkkillg...raYgrvsskrlk 90 
                    v G+  Agl  A ++  a  + +v++ie   ++  ++++       ++l++     + +  +h  + +++++++gk+ +++    + + +s+++l 
     EPA05938.1   2 VAGGSVAGLICAREI--ASNNHSVLVIEEDYEI-GTPEHcGGLVSTAGLEElgvlpFRKTFDHLIETAEIHAPNGKSFTINskkQKVAEISRRELD 94 
                    77999**********..99999*****988888.666665777777777777778899*******************9999777788899999999 PP

  Lycopene_cycl  91 eellerl 97 
                    ++++++ 
     EPA05938.1  95 KQIAHQS 101
                    9998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1141  (0.0636399); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 779.41
//
Query:       EPA05939.1  [L=120]
Description: hypothetical protein BG20_I0682 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0015   18.4   0.2     0.0024   17.7   0.2    1.4  1  SprT-like      SprT-like family
  ------ inclusion threshold ------
      0.011   15.8   0.0      0.025   14.6   0.0    1.5  2  DUF45          Protein of unknown function DUF45
      0.032   14.0   0.0      0.035   13.9   0.0    1.1  1  Peptidase_M76  Peptidase M76 family


Domain annotation for each model (and alignments):
>> SprT-like  SprT-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.2     4e-07    0.0024      48      96 ..      64     104 ..      41     111 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4e-07
   SprT-like  48 sIeLseklldsrsedrllntLaHElcHlalfvisgvrnnpHGaeFkawa 96 
                  + ++ + + +  e+ l+ntL+HEl+H+ +          HG++F ++ 
  EPA05939.1  64 LVFINVRKIPD--EKTLENTLVHELIHMRFP------YLAHGKRFNKLV 104
                 55556555666..89************9872......234677777665 PP

>> DUF45  Protein of unknown function DUF45
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.63   3.7e+03     110     136 ..       5      31 ..       3      35 .. 0.74
   2 ?   14.6   0.0   4.2e-06     0.025     166     192 ..      78     106 ..      68     110 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.63
       DUF45 110 keakeeleerlaklaaklgvkprsvsi 136
                 +e+k ++ e + ++++++ ++ +++ +
  EPA05939.1   5 SELKLQILEKVGIYSNRFSIPEPKILL 31 
                 577888888888888888888877755 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 4.2e-06
       DUF45 166 idYVvvHElaHllek..nHskrFwalvek 192
                 ++  +vHEl+H++ +   H+krF +lv +
  EPA05939.1  78 LENTLVHELIHMRFPylAHGKRFNKLVRQ 106
                 55668********87447********987 PP

>> Peptidase_M76  Peptidase M76 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   5.9e-06     0.035      54      79 ..      64      89 ..      11      93 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.9e-06
  Peptidase_M76 54 gillcenrlrskehledtlahElvha 79
                    + +   ++ ++++le+tl+hEl+h+
     EPA05939.1 64 LVFINVRKIPDEKTLENTLVHELIHM 89
                   3555556679***************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 856.57
//
Query:       EPA05940.1  [L=679]
Description: V-type H(+)-translocating pyrophosphatase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.3e-221  737.7  50.8   1.5e-221  737.6  50.8    1.0  1  H_PPase   Inorganic H+ pyrophosphatase


Domain annotation for each model (and alignments):
>> H_PPase  Inorganic H+ pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  737.6  50.8  8.3e-226  1.5e-221       2     650 .]      14     669 ..      13     669 .. 0.97

  Alignments for each domain:
  == domain 1  score: 737.6 bits;  conditional E-value: 8.3e-226
                 HHHHHHHHHHHHHHTS--SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT...HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
     H_PPase   2 lallfalvllkkvlkedegtekmkeiaeaikegaeaflkrqykviailvvvlavlllllallsvltaiaflvGallSalagyigmkvavranvrtakaa 100
                 +++++al ++++++k+++gt++m ei++a+k ga+afl+r++k+i+ ++++l +++ +  ++++   +af vGa+lSa+ag+i++k++v+a vr+a+ +
  EPA05940.1  14 ASFIVALGIVSWISKQPSGTKEMMEISNAVKVGAAAFLRREMKIIIPIAIALSIIIGY--FIGFSNGLAFAVGATLSAVAGLISLKITVKAAVRAAHLS 110
                 578999*************************************************999..6889*********************************** PP

                 HHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTS-EE-HHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHTCHHHHTS---TT-TT-TT CS
     H_PPase 101 rkslkkalkvafrsGavmgllvvglallgvsllllllkaaalelekllellvgfglGaslvalfarvgGGiytKaADvGaDLvGKveagipEDdprnpa 199
                 +++l k++++afr+Ga +gl+v ++all ++ l++++ +        + +++g g+Gasl+alf r+gGGi+tKaAD+GaDLvGKve +ipEDdprnpa
  EPA05940.1 111 SSGLGKTFAMAFRGGATVGLAVPAMALLAITGLYMVYPN--------PITIAGVGIGASLIALFIRIGGGIFTKAADMGADLVGKVESNIPEDDPRNPA 201
                 ***************************************........999************************************************* PP

                 HHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHH....SHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHSS--HHHHHHHHHHHHHHHHHHHHH CS
     H_PPase 200 viADnvGDnvGDvaGmgADlfesyvasivaamvlg...aavklvllpllvaavgilasiigillvktkedasskkkeellkaLkkgllvsavlsvvlva 295
                 +iADnvGDnvGD aGmg+D++esy+++i+a+++++    a +++++p+l+ + g++asiigi++v+       ++ ++++k L+ +++vsa++++++ +
  EPA05940.1 202 TIADNVGDNVGDAAGMGSDVYESYIVTILASLLIAaliGAPEIFMYPILIGTSGMIASIIGIVIVRS------TNLTDVMKPLNLSFYVSATIAIIINF 294
                 ***********************************6543999***********************43......34678****************99999 PP

                 HHHH-S..-TTTTSHHHHHHHHHHHHHHHHHHHHHHHH-TTSHHHHHHHHHGGG-HHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHH.......... CS
     H_PPase 296 llslll..keaaalklflavlvGlvagllivllteyytsteykpvkeiaeasetGaatniisGlavgmestvlpvlviavaillsylla.......... 382
                 ++++++   +  a++lf ++++G+++  +i+++t+ yt+++ykpv+ei+e+++ G a   + G+  gm+st   +++++vai+ls+++a          
  EPA05940.1 295 VFTYYFmgPTPIAYALFGTTVIGVILVPVIQKITDRYTNYKYKPVQEIVESAKWGYASLTLMGIIKGMQSTGPFMIALIVAIILSFSIAsnaapegadp 393
                 9999776755678999************************************************************************98999999999 PP

                 ...HHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHT--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT.......HHCS CS
     H_PPase 383 ...glygialaavgmLstlgitlavdayGPiaDNAggiaemseleeevreitdklDavGNttkAitKgfaigsAalaalaLfaaylee.......akle 471
                    g++g++l+a++mLs++gi+l++da+GPiaDNAggi+em+++ ee r++td++DavGNttkA+tKgfai+sA+laala+++a+  e         + 
  EPA05940.1 394 vlyGIFGTSLTAMAMLSLAGIVLSIDAFGPIADNAGGIVEMTGMGEENRKVTDEIDAVGNTTKAVTKGFAIASAGLAALAMIQAFQFEaahifegVLAL 492
                 9999**********************************************************************************9999999885567 PP

                 --BTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTTTTTTSS---HHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHH CS
     H_PPase 472 kvdllnpevlvglliGamlvflfsaltmkaVgkaAeevveevrrqfkeipgilegkekpdykkcveistkaalkemilpgllavlapivvglllgaeal 570
                 + +l+n +v+vgll+G++++f++++  ++ V++aA ++v+evrrqfk ++gil+g++kpdy+kcv+i+t a++ke+++p+++a+++pi++g+llg++a+
  EPA05940.1 493 NYSLTNVTVIVGLLVGGLIPFIITGQLINGVSRAAGKMVDEVRRQFKADSGILAGTSKPDYAKCVDIATAASIKELWKPAVIAIISPIILGILLGPTAV 591
                 89************************************************************************************************* PP

                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSTT.SSSHHHHHHHHHHHHHHHHHCTHHHHHHHHHHHHHHHHHHH CS
     H_PPase 571 agllagalvsgvllAifmanaGgawDNAKkyiEegelggkgseahkaaVvGDtVGDPfKDtagpslniliklmsivslvi 650
                 agll+ga+v+g+ lA  +an+GgawDNAKk++E   +g kg+e hk aVvGD +GDP+KDtagp+ln +ikl++++++v+
  EPA05940.1 592 AGLLMGAVVTGIPLAYHLANTGGAWDNAKKLVEM--QGDKGTEIHKVAVVGDIIGDPYKDTAGPALNTVIKLLNTIAIVF 669
                 *********************************9..689***************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (679 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1000  (0.0557756); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.72u 0.30s 00:00:01.02 Elapsed: 00:00:00.48
# Mc/sec: 4214.77
//
Query:       EPA05941.1  [L=38]
Description: hypothetical protein BG20_I0691 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (38 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       202  (0.0112667); expected 358.6 (0.02)
Passed bias filter:                      171  (0.00953762); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 272.03
//
Query:       EPA05942.1  [L=431]
Description: multicopper oxidase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.7e-43  146.8   1.1    1.7e-34  118.3   0.0    2.3  2  Cu-oxidase_3  Multicopper oxidase
    5.1e-33  113.7   1.1    6.9e-24   84.1   0.7    3.9  3  Cu-oxidase_2  Multicopper oxidase
    7.8e-17   61.8   0.0    3.5e-16   59.7   0.0    1.9  2  Cu-oxidase    Multicopper oxidase
    2.9e-16   59.4   0.8    2.1e-10   40.6   0.1    4.0  3  Cupredoxin_1  Cupredoxin-like domain
    4.7e-08   33.4   0.3     0.0019   18.6   0.1    3.5  3  Copper-bind   Copper binding proteins, plastocyanin/azurin fa
    3.2e-05   23.4   0.1     0.0014   18.1   0.0    2.7  2  SoxE          Sulfocyanin (SoxE) domain
  ------ inclusion threshold ------
       0.21   10.8   0.0       0.43    9.8   0.0    1.4  1  DUF2310       Zn-ribbon-containing, possibly nucleic-acid-bin
        3.9    7.3   5.3       0.32   10.8   0.4    1.6  2  RPAP1_N       RPAP1-like, N-terminal


Domain annotation for each model (and alignments):
>> Cu-oxidase_3  Multicopper oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.3   0.0   7.8e-38   1.7e-34      17     118 ..     207     308 ..     192     309 .. 0.94
   2 !   27.0   0.3   1.6e-09   3.5e-06      18     112 ..     325     425 ..     312     431 .] 0.76

  Alignments for each domain:
  == domain 1  score: 118.3 bits;  conditional E-value: 7.8e-38
                   EEEECTSSBS-EEEEETT-EEEEEEEE-SSS-B-EEEET--S-GG.....GSCSGGG-B-TT-EEEEEEE--S-SEEEEEEE--TT.HHH.TT-EEE CS
  Cu-oxidase_3  17 vitvNgqfpgptievregdtvvvnvtNkldentsihwhGlqqrktswmDGvpgvtqcpiqpgesftyrftvkqqagtlwYhshlsl.qqa.aGlaGa 111
                      +Ngq+pgp+i+v++gd+v+v ++N+l+e+tsih+hGl+++ +  +DGvp+++q+p++pge+f+y+ft+ +  gt+ Yh+hl++ qq+ +Gl+G+
    EPA05942.1 207 SYSYNGQIPGPEIRVKQGDKVKVVLKNNLPESTSIHFHGLDLPFS--QDGVPFISQDPVRPGETFEYNFTIIDTPGTFIYHPHLNAeQQVdKGLFGT 301
                   5689*****************************************..***************************************88889****** PP

                   EEEE-HH CS
  Cu-oxidase_3 112 iiiedke 118
                   +i+e ++
    EPA05942.1 302 FIVEGEK 308
                   ***9875 PP

  == domain 2  score: 27.0 bits;  conditional E-value: 1.6e-09
                   EEECTS.SBS.-EEEEETT-EEEEEEEE-SSS-B-EEEET--S-GG.....GSCS..GGG..-B-TT-EEEEEEE--S-SEEEEEEE--TT..HHHT CS
  Cu-oxidase_3  18 itvNgq.fpg.ptievregdtvvvnvtNkldentsihwhGlqqrktswmDGvpgv..tqc..piqpgesftyrftvkqqagtlwYhshlsl..qqaa 106
                    t Ng+ fp+   i v+++++v v+++N+ ++   +h+hG++ +    +DG p    t +   ++pge+++  ft+++  g   +h h+ +  +  +
    EPA05942.1 325 YTLNGKeFPAtAPIIVQKDQKVLVRIVNAGSQLHPMHLHGFDFQVI-AQDGKPTTayTRDtiTVAPGERYDILFTASK-TGIWPFHCHILShvESEH 419
                   556654256424699**************************99887.9***987422444225689************.99999**99988774446 PP

                   T-EEEE CS
  Cu-oxidase_3 107 GlaGai 112
                   G++G+ 
    EPA05942.1 420 GMHGMA 425
                   666653 PP

>> Cu-oxidase_2  Multicopper oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.31   6.9e+02     111     134 ..     115     138 ..      98     141 .. 0.83
   2 !   22.4   0.0   3.6e-08   8.1e-05      31     134 ..     215     305 ..     190     308 .. 0.85
   3 !   84.1   0.7   3.1e-27   6.9e-24      23     132 ..     326     429 ..     310     431 .] 0.86

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.31
                   EEEEEEESSHHHHHTT-EEEEEEE CS
  Cu-oxidase_2 111 GvwllHCHilwHldqGmalqfvvr 134
                   G + + C +  Hl++Gm +++vv 
    EPA05942.1 115 GIYEIGCYLPGHLEAGMKGKLVVG 138
                   66666788889********99987 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 3.6e-08
                   SSEEEEEETTEEEEEEEEE-SSS-EEEEESS-EEEEEEEEECCCCCCTCCSSGCCGSSCBSEEEE-TTEEEEEEEES..S-EEEEEEESSH..HHHH CS
  Cu-oxidase_2  31 ntnvitlpkgevveiviqnntklpHPfHlHGhdfqvlgrgpgndpeedpksynlenpvrrdtvqvppggwvairfka.dnpGvwllHCHil..wHld 124
                     + i++++g+ v++v++nn +   ++H+HG d    + g                 +++d   v+pg+++ + f+  d pG +++H H+   + +d
    EPA05942.1 215 PGPEIRVKQGDKVKVVLKNNLPESTSIHFHGLDLPFSQDGVPF--------------ISQD--PVRPGETFEYNFTIiDTPGTFIYHPHLNaeQQVD 295
                   457899***************************9998555555..............3334..3559********999************99999** PP

                   TT-EEEEEEE CS
  Cu-oxidase_2 125 qGmalqfvvr 134
                   +G+ ++f+v+
    EPA05942.1 296 KGLFGTFIVE 305
                   *******997 PP

  == domain 3  score: 84.1 bits;  conditional E-value: 3.1e-27
                   E.ETCCTTTSSEEEEEETTEEEEEEEEE-SSS-EEEEESS-EEEEEEEEECCCCCCTCCSSGCCGSSCBSEEEE-TTEEEEEEEES.S-EEEEEEES CS
  Cu-oxidase_2  23 t.ngeefsentnvitlpkgevveiviqnntklpHPfHlHGhdfqvlgrgpgndpeedpksynlenpvrrdtvqvppggwvairfkadnpGvwllHCH 118
                   t ng+ef+  t +i ++k++ v + i n ++  HP+HlHG+dfqv+++++++           +++  rdt++v pg++  i f+a  +G w +HCH
    EPA05942.1 326 TlNGKEFP-ATAPIIVQKDQKVLVRIVNAGSQLHPMHLHGFDFQVIAQDGKP-----------TTAYTRDTITVAPGERYDILFTASKTGIWPFHCH 410
                   25899999.99*****************************************...........8899****************************** PP

                   SH.....HHHHTT-EEEEE CS
  Cu-oxidase_2 119 il.....wHldqGmalqfv 132
                   il     +H  +Gma++++
    EPA05942.1 411 ILshvesEHGMHGMATAVI 429
                   **55555555566666665 PP

>> Cu-oxidase  Multicopper oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.2   2.7e+03      55      76 ..     212     234 ..     192     248 .. 0.70
   2 !   59.7   0.0   1.5e-19   3.5e-16      39     155 ..     315     430 ..     305     431 .] 0.94

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.2
                 TTTTSGGGEEEEETTEEEEEE.E CS
  Cu-oxidase  55 dgaslatltvepgktyrlrii.n 76 
                 ++   ++++v++g+++++ +  n
  EPA05942.1 212 GQIPGPEIRVKQGDKVKVVLKnN 234
                 35667899999999999877644 PP

  == domain 2  score: 59.7 bits;  conditional E-value: 1.5e-19
                 EEETTBSS.......CTTTTSGGGEEEEETTEEEEEEEESSS-BEEEEETSB-EEEEEETCETTSEEEESCEEE-TTEEEEEEEEE-SSSEEEEEEEE. CS
  Cu-oxidase  39 vlingkggfnatladkdgaslatltvepgktyrlriinvsaddslnfsIeGHkltVvevDgvyvepvevdsldIavGqrysvlvtanqapgnYwivas. 136
                 +li g+g   +tl+ k+  ++a + v++ +++++ri+n++  + +++ ++G  ++V++ Dg++++ ++ d++ +a+G+ry++l+ta++ +g + ++++ 
  EPA05942.1 315 TLIPGDGSHGYTLNGKEFPATAPIIVQKDQKVLVRIVNAGS-QLHPMHLHGFDFQVIAQDGKPTTAYTRDTITVAPGERYDILFTASK-TGIWPFHCHi 411
                 7999999999999999999*******************986.689******************************************8.********** PP

                 GSSSCHHHHTTSEEEEEEE CS
  Cu-oxidase 137 grsnlieafengtaaailr 155
                  +++ +e++  g+a+a+++
  EPA05942.1 412 LSHVESEHGMHGMATAVIV 430
                 99999***********997 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.1   9.3e-14   2.1e-10       5     104 .]      21     137 ..      15     137 .. 0.78
   2 !    5.6   0.1    0.0075        17      36      64 ..     218     246 ..     209     295 .. 0.74
   3 !    8.7   0.0   0.00083       1.9      37      96 ..     338     413 ..     333     424 .. 0.75

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 9.3e-14
  Cupredoxin_1   5 lavllllsskaa......aaaekt.....veitvkdggfePskievkagekvklkiknkdktpeefesed.......lgeekvlapgktttitiapl 83 
                   ++vl++++ +++       +   +     +++++k+ +++Ps+i++k g  vk+++kn ++ ++ef++ +       +++ k+++ g++++ ++ +l
    EPA05942.1  21 ILVLIYVQDSSQmmskdnIQ---EmpvelISVELKEFKISPSEINIKPGN-VKFEVKNIGSVAHEFSVFEpgntipiVSV-KNIENGQSKESNVVML 112
                   33333333333366533322...24457799******************8.****************9999***995555.**************** PP

  Cupredoxin_1  84 kpGeYeftcdmhm...d.akGkliV 104
                   k+G Ye+ c +       +kGkl+V
    EPA05942.1 113 KEGIYEIGCYLPGhleAgMKGKLVV 137
                   *********9655444689****98 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0075
  Cupredoxin_1  36 kievkagekvklkiknkdktpeefesedl 64 
                   +i vk+g kvk+ +kn+ ++++++ ++ l
    EPA05942.1 218 EIRVKQGDKVKVVLKNNLPESTSIHFHGL 246
                   79**************9998877777764 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.00083
  Cupredoxin_1  37 ievkagekvklkiknkdkt.....peefesed...........lgeekvlapgktttitiaplkpGeYeftcdmhm 96 
                   i v++++kv ++i+n +++      + f ++             +   ++apg+ + i +++ k G ++f+c + +
    EPA05942.1 338 IIVQKDQKVLVRIVNAGSQlhpmhLHGFDFQViaqdgkpttayTRDTITVAPGERYDILFTASKTGIWPFHCHILS 413
                   67899999999999999996655413333333555577777755566789**********************9765 PP

>> Copper-bind  Copper binding proteins, plastocyanin/azurin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.1   8.3e-07    0.0019       8      98 ..      50     137 ..      44     138 .. 0.66
   2 ?    4.4   0.0     0.022        49      18      88 ..     218     288 ..     213     294 .. 0.80
   3 !    6.3   0.0     0.006        13      59      96 ..     382     428 ..     338     431 .] 0.68

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 8.3e-07
                  TTETSEEESSEEEEETTEEEEEEEE.SSSSBEEEEETTSST.TTGGGTTSCTTCEEEEBSTTEEEEEEEESSEEEEEEET.T.TTTTTSEEEEEE CS
  Copper-bind   8 esgdlqFetkeitvkkgekvtfvnl.avmgHNvvldkdgvp.agvdkdkvkaedetkliggGekdsvtfdeagtYkffCs.P.HaaagMkgkvtv 98 
                  e ++++ +++ei++k+g+  + v++  +++H   + + g     v  ++++       +g+ ++++v + ++g Y+  C  P H  agMkgk++v
   EPA05942.1  50 ELKEFKISPSEINIKPGNVKFEVKNiGSVAHEFSVFEPGNTiPIVSVKNIE-------NGQSKESNVVMLKEGIYEIGCYlPgHLEAGMKGKLVV 137
                  555677788888898888777766657788887666544320222222222.......2344445555557888*******************98 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.022
                  EEEEETTEEEEEEEESSSSBEEEEETTSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEESSEE.EEEEETTTT CS
  Copper-bind  18 eitvkkgekvtfvnlavmgHNvvldkdgvpagvdkdkvkaedetkliggGekdsvtfdeagt.YkffCsPHa 88 
                  ei+vk+g+kv+ v ++  +    ++  g++  + +d v    ++  + +Ge+++ +f+  +t  +f+  PH 
   EPA05942.1 218 EIRVKQGDKVKVVLKNNLPESTSIHFHGLDLPFSQDGVPFISQD-PVRPGETFEYNFTIIDTpGTFIYHPHL 288
                  899*********99999999998888888888888888887666.456899999999955555667777886 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.006
                  CEEEEBSTTEEEEEEEESSEE..EEEEET..TT.....TTTTSEEEE CS
  Copper-bind  59 detkliggGekdsvtfdeagt..YkffCs..PH.....aaagMkgkv 96 
                  ++t  +++Ge + + f++++t  + f+C    H      + gM  +v
   EPA05942.1 382 RDTITVAPGERYDILFTASKTgiWPFHCHilSHvesehGMHGMATAV 428
                  367789***********555556*****6533511100444555555 PP

>> SoxE  Sulfocyanin (SoxE) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   6.3e-07    0.0014      89     145 ..      88     144 ..      65     147 .. 0.87
   2 ?    2.3   0.0     0.047   1.1e+02      81     132 ..     366     421 ..     322     430 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 6.3e-07
        SoxE  89 GattsnyavsGissGqsasGlledlsaGtywlacgilGhaesGmWvdlivssnvtvP 145
                 G+t    +v+ i  Gqs++  +  l +G y + c ++Gh e+Gm  +l+v ++ + P
  EPA05942.1  88 GNTIPIVSVKNIENGQSKESNVVMLKEGIYEIGCYLPGHLEAGMKGKLVVGTAASQP 144
                 5555556778899*************************************9988877 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.047
        SoxE  81 dGkillivGattsnyavsGi..ssGqsasGlledlsaGtywlacgilGhaes..Gm 132
                 d +++ + G+ t++y+ + i  + G+    l+    +G + + c il h es  Gm
  EPA05942.1 366 DFQVIAQDGKPTTAYTRDTItvAPGERYDILFTASKTGIWPFHCHILSHVESehGM 421
                 556788888888999877652157899999999999999999****9998763344 PP

>> DUF2310  Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00019      0.43      25      63 ..     203     242 ..     194     246 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00019
     DUF2310  25 qlldalrynGQilgrefpvavkeq.efavrvvcpeqdsLe 63 
                 +++d++ ynGQi g e+ v   ++ +++++  +pe++s++
  EPA05942.1 203 KFIDSYSYNGQIPGPEIRVKQGDKvKVVLKNNLPESTSIH 242
                 689***************9999888999999999999987 PP

>> RPAP1_N  RPAP1-like, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.6       3.2   7.2e+03      14      26 ..      34      46 ..      32      48 .. 0.75
   2 ?   10.8   0.4   0.00014      0.32      11      25 ..     146     160 ..     143     167 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.2
     RPAP1_N 14 MspeEIeeereeL 26
                Ms++ I+e   eL
  EPA05942.1 34 MSKDNIQEMPVEL 46
                9999999976666 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00014
     RPAP1_N  11 LasMspeEIeeeree 25 
                 ++sMs eEIe++ ee
  EPA05942.1 146 MKSMSNEEIEKAHEE 160
                 79**********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       786  (0.0438396); expected 358.6 (0.02)
Passed bias filter:                      662  (0.0369234); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.48
# Mc/sec: 2705.34
//
Query:       EPA05943.1  [L=165]
Description: hypothetical protein BG20_I0684 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-34  116.6   0.0    8.4e-34  115.9   0.0    1.3  1  DUF359    Protein of unknown function (DUF359)


Domain annotation for each model (and alignments):
>> DUF359  Protein of unknown function (DUF359)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.9   0.0   4.7e-38   8.4e-34       1     126 []      46     165 .]      46     165 .] 0.93

  Alignments for each domain:
  == domain 1  score: 115.9 bits;  conditional E-value: 4.7e-38
      DUF359   1 vtknllkagikPdlaivDgktkReeveeeekeeekekekekevievkNpaGtiteelieaikealeseekvlilVdGEEDLavlpaillapegsvvvYG 99 
                 +++++++ g++P+l i+D++ kR   ++e ++    + ++++++ ++Npa++it + ie ik+a+es+ +v++++ GEEDL+vlp+++ ape+s+v+YG
  EPA05943.1  46 TSEKMVDFGFIPSLQIIDNQEKRV--KREPTK----NIHGYTELVCENPAAEITPQSIEIIKKAFESKPPVRLTIIGEEDLLVLPVCVHAPENSLVMYG 138
                 68999*******************..223333....4588*********************************************************** PP

      DUF359 100 qpdeGvvlvkvteeakeeaeellekfe 126
                 qp+eG+vlv++t e++++++ ll+ +e
  EPA05943.1 139 QPNEGLVLVHITPEIRNKTQGLLDLME 165
                 **********************99885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1051.29
//
Query:       EPA05944.1  [L=137]
Description: hypothetical protein BG20_I0659, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-24   85.9   0.4    2.6e-24   85.8   0.4    1.0  1  TruD      tRNA pseudouridine synthase D (TruD)


Domain annotation for each model (and alignments):
>> TruD  tRNA pseudouridine synthase D (TruD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.8   0.4   1.5e-28   2.6e-24       2     133 ..       9     137 .]       8     137 .] 0.92

  Alignments for each domain:
  == domain 1  score: 85.8 bits;  conditional E-value: 1.5e-28
        TruD   2 lgielyvtdtegigGrlrespeDFiVeEieef.sgeeeadegeylvlrvekrnwdtldlvrelaralgisrkrvgfaGtKDkrAvTtQlisirkvepee 99 
                 +gi+++ t  +gigG++r+++eDF V+E+    s ++ +++  y v++++kr++dt+++++++ r++gi   r++  G+KD+ AvT Q+++ ++ + ++
  EPA05944.1   9 IGISVFSTTFNGIGGQIRSEAEDFQVSEVISDkSLKSISTQEGYAVYKLKKRKIDTNHALSDIFRKTGI---RLKALGLKDAFAVTEQFVC-SDSRGKS 103
                 89***************************777544467777889*************************...677779************9.6677789 PP

        TruD 100 lealeikdvelevvgrarrklrlGdLaGNkFeir 133
                 +e+ + ++ ++e++g  +++l+  d++ N+F+i+
  EPA05944.1 104 IENYSSDKYSIEKIGFVKKPLSKKDMIANHFNIK 137
                 9*******************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.53
# Mc/sec: 772.75
//
Query:       EPA05945.1  [L=98]
Description: hypothetical protein BG20_I0669 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       763  (0.0425568); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.50
# Mc/sec: 589.70
//
Query:       EPA05946.1  [L=172]
Description: quinolinate phosphoribosyl transferase, C-terminal domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      8e-56  188.4   1.1    8.9e-56  188.3   1.1    1.0  1  QRPTase_C       Quinolinate phosphoribosyl transferase, C-ter
     0.0077   15.6   0.2      0.015   14.7   0.1    1.5  1  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
  ------ inclusion threshold ------
      0.018   14.2   0.1       0.12   11.5   0.0    2.0  2  Glu_synthase    Conserved region in glutamate synthase
      0.041   13.9   0.1      0.093   12.7   0.1    1.6  2  AAA_5           AAA domain (dynein-related subfamily)
      0.087   12.6   0.0        0.1   12.4   0.0    1.3  1  Ssl1            Ssl1-like


Domain annotation for each model (and alignments):
>> QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.3   1.1   2.5e-59   8.9e-56       1     169 []       4     171 ..       4     171 .. 0.97

  Alignments for each domain:
  == domain 1  score: 188.3 bits;  conditional E-value: 2.5e-59
                 HHHHHHHHHHHHHCTSSEEEE-S---TTTHHHHHHHHHHTTSB--TSSTTTSEEE-HHHHHHHSSHHHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHH CS
   QRPTase_C   1 iAtltarmveaaksakvrildTRkttPglrllekyAvliGGgdnhrlgLsdmvlikdnhiaaagsiveavksvreavdkevkievevesleeleevlea 99 
                 iAt+t+ +v++++++k+++ +TRkt+Pglr+++k Av iGGg++hrl+L++mv+ikdnhia+a s+ + +k ++ + +   k eveve+  ++  ++++
  EPA05946.1   4 IATQTEYLVRKISNKKTKLYATRKTAPGLRYFDKEAVEIGGGKKHRLRLDEMVMIKDNHIAVANSLLSLIKDAKRKYK---KFEVEVENTSDAVLAAKE 99 
                 9***********************************************************************999884...469*************** PP

                 T-SEEEEES--HHHHHHHHHHHHHHSTT..SEEEEESS--TTTHHHHHCTT-SEEEECHHCHTB----EEEE CS
   QRPTase_C 100 eadiimLDnfsveelkkaveelkeknkr..vlievSGgvtlenveeyaksgvdvisvgalthsvkalDislk 169
                 +a iimLDnfs+ +++k++++lke++ r  vl+e+SGg++ +n+++y  +gvd+isvg++t+svk +D+sl+
  EPA05946.1 100 GATIIMLDNFSPSQIRKTIQTLKEQKLRnkVLLEASGGINAKNIAKYGGTGVDIISVGSITNSVKGIDMSLE 171
                 **********************98888888****************************************95 PP

>> Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   4.1e-06     0.015     145     195 ..     109     158 ..     104     160 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.1e-06
                     --CCHHHH.HHHHHHHHHHHT---EEEEESS--TTTCHHHHHHT--EEEESH CS
  Ribul_P_3_epim 145 Fipevlek.ikkvrklidekeldlkievDGGvkldnieqiaeagadvlVags 195
                     F p+++ k i+++++   +   ++ +e+ GG++++ni++    g+d++ +gs
      EPA05946.1 109 FSPSQIRKtIQTLKEQKLR--NKVLLEASGGINAKNIAKYGGTGVDIISVGS 158
                     5555554425555554444..7899***********************9998 PP

>> Glu_synthase  Conserved region in glutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0     0.093   3.4e+02     325     342 ..       2      19 ..       1      26 [. 0.74
   2 ?   11.5   0.0   3.3e-05      0.12     259     303 ..     114     157 ..     111     165 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.093
                   TSSS---HHHH..TT--- CS
  Glu_synthase 325 vGvatqdpeLrkrlkvee 342
                    G+atq ++L ++ + ++
    EPA05946.1   2 SGIATQTEYLVRKISNKK 19 
                   59********96554443 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 3.3e-05
                   HHHHHHHHHHTT-GGG-EEEEESS--SHHHHHHHHHHT-SEEE-S CS
  Glu_synthase 259 laevdqtlkeeglrdrvsliadGglktgadvvkalalGAdavgig 303
                   + ++ qtlke++lr++v l+a+Gg+ + ++++k    G d +++g
    EPA05946.1 114 IRKTIQTLKEQKLRNKVLLEASGGINA-KNIAKYGGTGVDIISVG 157
                   56788*******************975.56776666666666655 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   2.6e-05     0.093      53     121 ..      33     108 ..       5     121 .. 0.66
   2 ?    0.8   0.0      0.13   4.5e+02      58      92 ..      92     124 ..      86     143 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.6e-05
                 ....--------.G-SEEEEESGGG--HH...HHHHHHHHHHSSEEE..-SSSEEE---.............-EEEEEES CS
       AAA_5  53 slvdsplvraar.egeilvlDEveraese...vlnsLlslleerrllleeggelvkakndd...ller....frviatan 121
                 ++ d+++v+ +  +++ l+lDE  +++++   v+nsLlsl+ + ++     +++v ++n++   l  +     ++i++ n
  EPA05946.1  33 RYFDKEAVEIGGgKKHRLRLDEMVMIKDNhiaVANSLLSLIKDAKRK--YKKFEVEVENTSdavL--AakegATIIMLDN 108
                 344445554444699*******999985423388999999*999999..6666666666542222..1356666666655 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.13
                 -------.G-SEEEEESGGG--.HHHHHHHHHHHHSS CS
       AAA_5  58 plvraar.egeilvlDEverae.sevlnsLlslleer 92 
                  +v aa+  + i++lD +   + ++++++L     e+
  EPA05946.1  92 DAVLAAKeGATIIMLDNFSPSQiRKTIQTL----KEQ 124
                 445566624567788888844444444444....333 PP

>> Ssl1  Ssl1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.9e-05       0.1     111     140 ..     106     135 ..      55     156 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.9e-05
                 S----SS-HHHHHHHHHHTT-EEEEEEESS CS
        Ssl1 111 lstcDPgdiyetidelkkekirvsvigLsa 140
                 l    P++i +ti++lk++k+r +v+  ++
  EPA05946.1 106 LDNFSPSQIRKTIQTLKEQKLRNKVLLEAS 135
                 55678*******************985444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       785  (0.0437838); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 989.64
//
Query:       EPA05947.1  [L=58]
Description: putative DNA-directed RNA polymerase subunit E'' [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-13   50.7   0.5    1.8e-13   50.4   0.5    1.1  1  Spt4      Spt4/RpoE2 zinc finger
     0.0029   17.2   0.7     0.0035   16.9   0.7    1.1  1  RecR      RecR protein


Domain annotation for each model (and alignments):
>> Spt4  Spt4/RpoE2 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.4   0.5     2e-17   1.8e-13       3      77 .]       2      58 .]       1      58 [] 0.97

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 2e-17
        Spt4  3 ACllCklvktedqFeeegCpnCeilelkgdkekvsectseefeGlvaildpekSwvAkwqrldkkvpglYAlkve 77
                AC++Ck+v+t +      Cp+C            s++++++++G+v ++dp++S+v k   l+ k++g+YA+kv+
  EPA05947.1  2 ACRKCKFVTTGKV-----CPVC-----------KSSDLTPDWSGIVLVVDPTNSQVSKT--LGIKQKGKYAIKVT 58
                9*********999.....****...........899***********************..************95 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.7   3.9e-07    0.0035      19      37 ..       3      21 ..       1      22 [. 0.92

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.9e-07
                -TTT--EESSSS-CCCCST CS
        RecR 19 CsrCgnlteedlCaICsdp 37
                C++C  +t+  +C++C+++
  EPA05947.1  3 CRKCKFVTTGKVCPVCKSS 21
                ****************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.35s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 339.63
//
Query:       EPA05948.1  [L=374]
Description: NHL repeat protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-09   38.2   0.9       0.16   11.5   0.0    4.2  4  SGL              SMP-30/Gluconolactonase/LRE-like region
    8.6e-06   25.5   0.0    0.00053   19.9   0.0    2.9  2  NHL              NHL repeat
    2.6e-05   24.2   0.7        2.1    8.4   0.1    3.7  3  DUF5074          Domain of unknown function (DUF5074)
     0.0054   16.8   3.9         18    6.0   0.0    4.6  4  Reg_prop         Two component regulator propeller
     0.0059   16.7   0.0         12    6.1   0.0    4.0  4  Str_synth        Strictosidine synthase
     0.0063   16.5   0.1          1    9.2   0.0    2.4  2  Phytase-like     Esterase-like activity of phytase
  ------ inclusion threshold ------
       0.23   11.3   0.0        1.5    8.7   0.0    2.3  2  Biotin_lipoyl_2  Biotin-lipoyl like


Domain annotation for each model (and alignments):
>> SGL  SMP-30/Gluconolactonase/LRE-like region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   6.2e-05      0.16     188     216 ..      85     113 ..      61     121 .. 0.86
   2 !    5.2   0.0    0.0054        14     188     225 ..     132     169 ..     121     175 .. 0.81
   3 !    6.4   0.1    0.0023       5.9     186     215 ..     220     252 ..     176     266 .. 0.68
   4 !   10.7   0.0   0.00011      0.29     129     214 ..     275     310 ..     258     325 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.2e-05
         SGL 188 GlavDaeGnvwvAvwgggkvvrfdpdGkl 216
                  +a+D +Gnvw A+ ++g +++fdp  + 
  EPA05948.1  85 AIATDYSGNVWFAQTNTGNIAKFDPTTES 113
                 5899*********************8665 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0054
         SGL 188 GlavDaeGnvwvAvwgggkvvrfdpdGklieeiklpak 225
                 G+    +G vw +  + + +++f+++ +  ++i++pa+
  EPA05948.1 132 GMDYSPDGSVWFTDESYDSIWQFTTQDEKYHRIAFPAT 169
                 66667789999999999999999999999999999976 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0023
         SGL 186 pDGlavDaeGnvwvAvw...gggkvvrfdpdGk 215
                    +++D+++nvw + w   +gg +v+fd++G 
  EPA05948.1 220 TGAFTIDSSKNVWYTNWifqKGGVLVKFDQEGY 252
                 44579************9988889999**9996 PP

  == domain 4  score: 10.7 bits;  conditional E-value: 0.00011
         SGL 129 vlddltipNGlawspdgktlYlaDsltrkiwaydvdaeggklsnrrvfadlkkgegepDGlavDaeGnvwvAvwgggkvvrfdpdG 214
                 +  dl                                                    p G+a   +G++w+A  + + +  fdp  
  EPA05948.1 275 LPFDLLT--------------------------------------------------PNGIAASDDGKIWIADTSRSAIFSFDPTT 310
                 3344444..................................................55555555555555555555555555554 PP

>> NHL  NHL repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.07   1.8e+02       4      20 ..     130     147 ..     128     154 .. 0.80
   2 !   19.9   0.0   2.1e-07   0.00053       3      26 ..     281     304 ..     279     306 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.07
                 EEEEEEETTTEEEEEE.C CS
         NHL   4 PhGvavdsnGdiyVaD.s 20 
                  +G  ++++G ++ +D s
  EPA05948.1 130 IWGMDYSPDGSVWFTDeS 147
                 69***********88843 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 2.1e-07
                 SEEEEEEETTTEEEEEECCCTEEE CS
         NHL   3 yPhGvavdsnGdiyVaDsenhrvq 26 
                  P+G+a++++G i++aD+ ++ ++
  EPA05948.1 281 TPNGIAASDDGKIWIADTSRSAIF 304
                 6*****************999886 PP

>> DUF5074  Domain of unknown function (DUF5074)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.1   0.00084       2.1       2      31 ..      87     118 ..      86     131 .. 0.86
   2 ?    3.8   0.0     0.022        56       4      34 ..     136     213 ..     134     274 .. 0.64
   3 !    8.4   0.0   0.00086       2.2       1      27 [.     285     313 ..     285     365 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00084
     DUF5074   2 vqskDGnvWaa..sgtkLvkinpktlevktve 31 
                 +  + GnvW a  ++ ++ k++p+t + k+ +
  EPA05948.1  87 ATDYSGNVWFAqtNTGNIAKFDPTTESFKEFN 118
                 66788******888889********9999876 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.022
     DUF5074   4 skDGnvWaa.............................................sgtkLvkinpktle..vktvelpe 34 
                 s DG+vW +                                             +g+k++ ++p++     k ++lp 
  EPA05948.1 136 SPDGSVWFTdesydsiwqfttqdekyhriafpatgdtlpqklkvdgsqiiindfTGNKITFLDPTQTAdnLKYLNLPS 213
                 689999999997777777777777777777777777666666666666666666677777777644332444555554 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.00086
     DUF5074   1 vvqskDGnvWaa..sgtkLvkinpktlev 27 
                 ++ s+DG++W+a  s  ++  ++p+t   
  EPA05948.1 285 IAASDDGKIWIAdtSRSAIFSFDPTTEIF 313
                 5789********88889999999977654 PP

>> Reg_prop  Two component regulator propeller
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0   0.0    0.0072        18       8      21 ..      84      97 ..      79     100 .. 0.85
   2 ?    2.0   0.1      0.14   3.6e+02       8      21 ..     131     144 ..     126     147 .. 0.77
   3 ?    1.7   0.1      0.18   4.6e+02       5      19 ..     217     232 ..     214     236 .. 0.86
   4 ?    4.5   0.0     0.022        55      10      21 ..     285     296 ..     280     299 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0072
                EEEEE-TTSCEEEE CS
    Reg_prop  8 taileDsdGrlWvG 21
                 ai+ D  G++W++
  EPA05948.1 84 LAIATDYSGNVWFA 97
                4899********97 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.14
                 EEEEE-TTSCEEEE CS
    Reg_prop   8 taileDsdGrlWvG 21 
                 + + + +dG +W+ 
  EPA05948.1 131 WGMDYSPDGSVWFT 144
                 5556789*****96 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.18
                 SCEE.EEEE-TTSCEE CS
    Reg_prop   5 nnvt.aileDsdGrlW 19 
                 ++vt a+  Ds  ++W
  EPA05948.1 217 GSVTgAFTIDSSKNVW 232
                 578989999******* PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.022
                 EEE-TTSCEEEE CS
    Reg_prop  10 ileDsdGrlWvG 21 
                 i+   dG++W++
  EPA05948.1 285 IAASDDGKIWIA 296
                 77789******8 PP

>> Str_synth  Strictosidine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.0    0.0046        12      33      64 ..      98     129 ..      89     136 .. 0.88
   2 ?   -0.5   0.0      0.54   1.4e+03       3      19 ..     133     148 ..     131     157 .. 0.80
   3 ?    4.3   0.0     0.017        43      55      72 ..     278     295 ..     266     311 .. 0.83
   4 ?   -0.5   0.0      0.54   1.4e+03       4      23 ..     344     363 ..     342     371 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0046
   Str_synth  33 gdktGrllkydkstkvvkvlldkLyfanGial 64 
                 + +tG + k+d++t + k   + L   nG ++
  EPA05948.1  98 QTNTGNIAKFDPTTESFKEFNNSLWPKNGRSM 129
                 5689**************99999999998665 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.54
   Str_synth   3 ldvdeetgvlyftdsSs 19 
                 +d  ++ g ++ftd S+
  EPA05948.1 133 MDYSPD-GSVWFTDESY 148
                 666777.99*****996 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.017
   Str_synth  55 kLyfanGialsedgsfvl 72 
                 +L  +nGia s+dg+  +
  EPA05948.1 278 DLLTPNGIAASDDGKIWI 295
                 7889**********9765 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.54
   Str_synth   4 dvdeetgvlyftd.sSskydr 23 
                  +++e g l f++ +S++y+ 
  EPA05948.1 344 KIAPE-GQLVFNEqTSTTYQY 363
                 57777.777776526777875 PP

>> Phytase-like  Esterase-like activity of phytase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0    0.0004         1      72     110 ..     132     170 ..     130     195 .. 0.84
   2 ?    4.5   0.0     0.011        28      70     100 ..     282     312 ..     256     329 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0004
  Phytase-like  72 giavapdgtfwvssEggpfilefdadGkllrelplpael 110
                   g+ ++pdg++w+++E   +i++f+ + +   +++ pa  
    EPA05948.1 132 GMDYSPDGSVWFTDESYDSIWQFTTQDEKYHRIAFPATG 170
                   566789******************998888888888765 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.011
  Phytase-like  70 pEgiavapdgtfwvssEggpfilefdadGkl 100
                   p gia ++dg++w+++  + +i  fd++ ++
    EPA05948.1 282 PNGIAASDDGKIWIADTSRSAIFSFDPTTEI 312
                   559***********************98665 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.63   1.6e+03      27      43 ..     191     207 ..     190     210 .. 0.86
   2 ?    8.7   0.0   0.00058       1.5      25      48 ..     239     262 ..     238     271 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.63
  Biotin_lipoyl_2  27 GdvLaelDsralqlala 43 
                      G+ +  lD++++++ l+
       EPA05948.1 191 GNKITFLDPTQTADNLK 207
                      99999******998876 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00058
  Biotin_lipoyl_2  25 kaGdvLaelDsralqlalaqaeaq 48 
                      ++G vL+  D++ +++ala a+++
       EPA05948.1 239 QKGGVLVKFDQEGYRNALANAKGD 262
                      5899*****************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.51
# Mc/sec: 2190.45
//
Query:       EPA05949.1  [L=355]
Description: copper binding protein, plastocyanin/azurin family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.1e-16   58.3   0.6    8.8e-08   32.5   0.1    2.7  2  Copper-bind   Copper binding proteins, plastocyanin/azurin fa
    1.2e-12   47.9   0.1    1.3e-06   28.5   0.0    2.4  2  Cupredoxin_1  Cupredoxin-like domain


Domain annotation for each model (and alignments):
>> Copper-bind  Copper binding proteins, plastocyanin/azurin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.1   6.7e-09     6e-05      13      98 ..     180     255 ..     170     256 .. 0.83
   2 !   32.5   0.1   9.9e-12   8.8e-08       7      99 .]     273     355 .]     268     355 .] 0.89

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 6.7e-09
                  EEESSEEEEETTEEEEEEEESSSSBEEEEETTSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEE..SSEEEEEEETTTTTTTSEEEEEE CS
  Copper-bind  13 qFetkeitvkkgekvtfvnlavmgHNvvldkdgvpagvdkdkvkaedetkliggGekdsvtfd..eagtYkffCsPHaaagMkgkvtv 98 
                   +e+   +v kg+ ++++n + ++H v  + d      d++++++      + +Gek+++  +  ++g+Y+++C  H    M++++++
   EPA05949.1 180 DYEPDVAHVPKGDVIEWINEDTVPHTVTSSVDFG----DTFNSNM------MNAGEKYTLDTSklASGEYEYMCMVHP--WMVATLII 255
                  6999999**********************99995....4455555......4579***99888777788********9..58988876 PP

  == domain 2  score: 32.5 bits;  conditional E-value: 9.9e-12
                  ETTETSEEESSEEEEETTEEEEEEEESSSSBEEEEETTSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEESSEEEEEEETTTTTTTSEEEEEEE CS
  Copper-bind   7 vesgdlqFetkeitvkkgekvtfvnlavmgHNvvldkdgvpagvdkdkvkaedetkliggGekdsvtfdeagtYkffCsPHaaagMkgkvtve 99 
                   ++g+l +++ +itv  g+ v++ n + + H v   kd+ p+g  ++         li +G++++ tf+ +g+ ++fC  H    M+g v+ve
   EPA05949.1 273 QKEGQLYYDPTTITVPVGTPVVWDNVDNVVHTVTSGKDATPDGTFDS--------GLIDAGKTFKFTFSSPGKVDYFCMVHP--WMVGSVEVE 355
                  57889**********************************98875433........26668**********************..69****996 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0   1.4e-10   1.3e-06      30     104 .]     172     255 ..     130     255 .. 0.82
   2 !   17.3   0.0   4.3e-07    0.0039      31     101 ..     279     351 ..     257     354 .. 0.84

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1.4e-10
  Cupredoxin_1  30 g.......gfePskievkagekvklkiknkdktpeefesed....lgeekvlapgktttitiaplkpGeYeftcdmhmdakGkliV 104
                   +        +eP++ +v++g    +++ n+d+ p++++s         +   + g+++t++ ++l  GeYe+ c  h+ + ++li+
    EPA05949.1 172 DsaiqgnpDYEPDVAHVPKGD--VIEWINEDTVPHTVTSSVdfgdTFNSNMMNAGEKYTLDTSKLASGEYEYMCMVHPWMVATLII 255
                   445555559***********9..69********9888776555545567999*************************988888875 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 4.3e-07
  Cupredoxin_1  31 gfePskievkagekvklkiknkdktpeefesed......lgeekvlapgktttitiaplkpGeYeftcdmhmdakGk 101
                    ++P +i+v+ g++v   ++n d+ +++++s +         +  ++ gkt+++t+   +pG+ +++c  h+ + G 
    EPA05949.1 279 YYDPTTITVPVGTPV--VWDNVDNVVHTVTSGKdatpdgTFDSGLIDAGKTFKFTF--SSPGKVDYFCMVHPWMVGS 351
                   79**********966..9*************999999953334789**********..***********99876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 2194.02
//
Query:       EPA05950.1  [L=128]
Description: tetratricopeptide repeat protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-13   49.1   1.1    4.6e-05   23.1   0.0    3.1  3  TPR_1            Tetratricopeptide repeat
    9.1e-12   44.1   0.0    0.00021   21.2   0.0    3.1  3  TPR_2            Tetratricopeptide repeat
    1.3e-10   40.6   1.6    0.00011   22.1   0.0    2.8  3  TPR_8            Tetratricopeptide repeat
    2.5e-10   40.7   0.0    5.8e-08   33.1   0.0    2.1  2  TPR_19           Tetratricopeptide repeat
    9.5e-09   35.4   0.1    1.2e-08   35.0   0.1    1.2  1  ANAPC3           Anaphase-promoting complex, cyclosome, subun
    3.3e-06   27.3   0.0     0.0047   17.2   0.0    2.7  2  TPR_12           Tetratricopeptide repeat
    4.1e-05   23.3   0.0       0.05   13.6   0.0    2.5  2  TPR_7            Tetratricopeptide repeat
    4.4e-05   24.0   0.0    6.7e-05   23.5   0.0    1.3  1  TPR_16           Tetratricopeptide repeat
    0.00013   22.1   0.2       0.05   14.0   0.0    3.2  4  TPR_17           Tetratricopeptide repeat
    0.00034   21.1   0.0       0.22   12.2   0.0    3.2  3  TPR_6            Tetratricopeptide repeat
     0.0012   18.9   0.7        1.1    9.4   0.0    3.1  3  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
     0.0015   18.5   1.3      0.033   14.1   0.6    2.0  2  DUF4919          Domain of unknown function (DUF4919)
  ------ inclusion threshold ------
      0.022   14.8   0.8      0.089   12.8   0.4    1.8  2  SRP_TPR_like     Putative TPR-like repeat
      0.023   14.7   4.8      0.046   13.7   0.3    2.4  2  TPR_3            Tetratricopeptide repeat
      0.026   15.3   0.0         18    6.5   0.0    2.9  3  TPR_14           Tetratricopeptide repeat
      0.029   13.4   0.1      0.032   13.3   0.1    1.1  1  ChAPs            ChAPs (Chs5p-Arf1p-binding proteins)
      0.044   14.7   0.7       0.17   12.8   0.2    2.0  2  DUF4284          Immunity protein 22
      0.057   14.1   0.0        0.1   13.3   0.0    1.4  1  DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomer
      0.072   13.2   0.5        1.6    8.8   0.2    2.1  2  Rapsyn_N         Rapsyn N-terminal myristoylation and linker 
       0.32   11.8   4.8       0.74   10.6   0.4    2.9  3  FIVAR            FIVAR domain
       0.46   10.2   2.5        3.1    7.5   0.4    2.8  3  TPR_11           TPR repeat


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1      0.11        96      13      22 ..      25      34 ..      23      34 .. 0.88
   2 !   20.3   0.0     4e-07   0.00034       3      30 ..      49      76 ..      48      78 .. 0.91
   3 !   23.1   0.0   5.4e-08   4.6e-05       3      34 .]      83     114 ..      81     114 .. 0.94

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.11
                HTT-HHHHHH CS
       TPR_1 13 klgkydeAle 22
                k+++yd+Al+
  EPA05950.1 25 KKKQYDDALK 34
                89******97 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 4e-07
                HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
       TPR_1  3 alynlGnayfklgkydeAleyyekALel 30
                +l+ +G +y+ +++y+ A+ y+ek L++
  EPA05950.1 49 VLFIIGGIYYMKNQYQTAISYFEKSLKI 76
                5777899*******************97 PP

  == domain 3  score: 23.1 bits;  conditional E-value: 5.4e-08
                 HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                 +l  ++na++ lg+ ++A+ +++k  e++P+n
  EPA05950.1  83 VLILKANAHHFLGQSKQAISCCNKIKEIDPKN 114
                 67889*************************98 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.044        37      12      32 ..      24      44 ..      21      46 .. 0.83
   2 !   21.2   0.0   2.4e-07   0.00021       2      30 ..      48      76 ..      47      78 .. 0.93
   3 !   15.0   0.0   2.3e-05      0.02       3      34 .]      83     114 ..      81     114 .. 0.94

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.044
       TPR_2 12 yklgdyeeAleafekAleldP 32
                 k+++y++Al+   + l+  P
  EPA05950.1 24 VKKKQYDDALKIGTEILKKVP 44
                5899******99888888777 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 2.4e-07
       TPR_2  2 ealynlGlayyklgdyeeAleafekAlel 30
                ++l+ +G +yy +++y+ A+ +fek+l++
  EPA05950.1 48 DVLFIIGGIYYMKNQYQTAISYFEKSLKI 76
                67999**********************97 PP

  == domain 3  score: 15.0 bits;  conditional E-value: 2.3e-05
       TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                 +l   ++a+  lg+ ++A+ +++k  e+dP+n
  EPA05950.1  83 VLILKANAHHFLGQSKQAISCCNKIKEIDPKN 114
                 68899*************************97 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       4.1   3.5e+03      13      22 ..      25      34 ..      23      35 .. 0.71
   2 !   16.7   0.1   7.2e-06    0.0061       3      30 ..      49      76 ..      48      76 .. 0.94
   3 !   22.1   0.0   1.3e-07   0.00011       2      34 .]      82     114 ..      81     114 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 4.1
                HTT-HHHHHH CS
       TPR_8 13 klgdyeeAke 22
                k+++y+ A +
  EPA05950.1 25 KKKQYDDALK 34
                7888888765 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 7.2e-06
                HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
       TPR_8  3 ayynlgsiylklgdyeeAkeyyekalel 30
                +++ +g iy  +++y+ A++y+ek l++
  EPA05950.1 49 VLFIIGGIYYMKNQYQTAISYFEKSLKI 76
                78999*********************97 PP

  == domain 3  score: 22.1 bits;  conditional E-value: 1.3e-07
                 CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
       TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                 +++ +++++++ lg+ ++A+++++k  e+dp+n
  EPA05950.1  82 DVLILKANAHHFLGQSKQAISCCNKIKEIDPKN 114
                 57899**************************97 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0094         8       2      40 ..      24      62 ..      23      63 .. 0.74
   2 !   33.1   0.0   6.8e-11   5.8e-08       4      68 .]      60     124 ..      57     124 .. 0.96

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0094
      TPR_19  2 laegdyaeAlalleqalqedpknaearllLAeallalgq 40
                ++ ++y++Al++ +++l++ p+  +++     +++  +q
  EPA05950.1 24 VKKKQYDDALKIGTEILKKVPEENDVLFIIGGIYYMKNQ 62
                677899999999999999999877776656666666655 PP

  == domain 2  score: 33.1 bits;  conditional E-value: 6.8e-11
      TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryasLlAkl 68 
                  ++y+ A++++e+ l+    + ++++l A+a+  lgq ++A+ +++++ e dp++ +++ Ll k+
  EPA05950.1  60 KNQYQTAISYFEKSLKIGSYDTDVLILKANAHHFLGQSKQAISCCNKIKEIDPKNKAVSELLSKI 124
                 679**********************************************************9997 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.1   1.4e-11   1.2e-08       2      79 ..      26     104 ..      25     120 .. 0.96

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 1.4e-11
                 TT-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH CS
      ANAPC3   2 qnnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaL 79 
                 +++y++A+ ++  +l++ +e ++ ++  +  +y  +qy++A+ +++k+ k+ s +  +++l+A +   L++ ++Ai++ 
  EPA05950.1  26 KKQYDDALKIGTEILKKVPEENDVLFIIGGIYYMKNQYQTAISYFEKSlKIGSYDTDVLILKANAHHFLGQSKQAISCC 104
                 79*************999999999****************************************************975 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   5.5e-06    0.0047      19      74 ..      29      76 ..      23      78 .. 0.70
   2 !    7.0   0.0    0.0081       6.9       6      32 ..      84     110 ..      80     124 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5.5e-06
      TPR_12 19 ydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74
                yd+Al++  + l           p++  +l+ +g +y++ ++y+ A++++e++l+i
  EPA05950.1 29 YDDALKIGTEILKK--------VPEENDVLFIIGGIYYMKNQYQTAISYFEKSLKI 76
                44444444444333........3334448899999******************987 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0081
      TPR_12   6 lnnlaavlrrlgrydeAlellekalei 32 
                 l   a++++ lg+  +A+++++k  ei
  EPA05950.1  84 LILKANAHHFLGQSKQAISCCNKIKEI 110
                 45789****************999887 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   5.9e-05      0.05       5      28 ..      53      76 ..      49      82 .. 0.78
   2 !    7.2   0.0    0.0066       5.7       4      23 ..      86     105 ..      83     117 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.9e-05
       TPR_7  5 LarlysrlGdyeeAielyeqsLal 28
                ++ +y   ++y++Ai+++e+sL +
  EPA05950.1 53 IGGIYYMKNQYQTAISYFEKSLKI 76
                566666679***********9954 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0066
       TPR_7   4 nLarlysrlGdyeeAielye 23 
                   a++++ lG+ ++Ai+++ 
  EPA05950.1  86 LKANAHHFLGQSKQAISCCN 105
                 5699*************985 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   7.8e-08   6.7e-05       7      67 ..      23      80 ..      18      81 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 7.8e-08
      TPR_16  7 alragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67
                +++ ++yddA++  ++ lk+    P+  + l+  g +++ ++ ++ A+ ++++ l+ ++++
  EPA05950.1 23 LVKKKQYDDALKIGTEILKKV---PEENDVLFIIGGIYYMKNQYQTAISYFEKSLKIGSYD 80
                78899****************...*****************************99988775 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       5.2   4.4e+03      25      33 ..      25      33 ..      20      34 .. 0.78
   2 ?    4.4   0.0     0.068        58      16      33 ..      50      67 ..      40      68 .. 0.84
   3 !   14.0   0.0   5.9e-05      0.05       1      33 [.      69     101 ..      69     102 .. 0.96
   4 ?   -1.4   0.0       4.8   4.1e+03       7      12 ..     109     114 ..     103     121 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 5.2
      TPR_17 25 knGdlmtAr 33
                k++++++A+
  EPA05950.1 25 KKKQYDDAL 33
                778999997 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.068
      TPR_17 16 ynnLAelllknGdlmtAr 33
                ++  + +++++++++tA+
  EPA05950.1 50 LFIIGGIYYMKNQYQTAI 67
                5556669**********7 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 5.9e-05
      TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtAr 33 
                 +++k+l++   + d++ ++A++++ +G++++A+
  EPA05950.1  69 YFEKSLKIGSYDTDVLILKANAHHFLGQSKQAI 101
                 599****************************97 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 4.8
      TPR_17   7 eldPnn 12 
                 e+dP+n
  EPA05950.1 109 EIDPKN 114
                 789999 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1       1.1   9.5e+02      13      22 ..      26      35 ..      12      45 .. 0.65
   2 !   12.2   0.0   0.00026      0.22       1      25 [.      48      72 ..      48      76 .. 0.91
   3 ?    4.2   0.0     0.092        79       5      32 ..      86     113 ..      82     114 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 1.1
                HHHHHHHHHH CS
       TPR_6 13 lgdtdkAlea 22
                 +++d+Al++
  EPA05950.1 26 KKQYDDALKI 35
                2588888775 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00026
                HHHHHHHHHHHHHHHHHHHHHHHHH CS
       TPR_6  1 dAlyklalsyrklgdtdkAlealer 25
                d+l+ ++  y++ +++++A+ ++e+
  EPA05950.1 48 DVLFIIGGIYYMKNQYQTAISYFEK 72
                789********988*********98 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.092
                 HHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
       TPR_6   5 klalsyrklgdtdkAlealerlikeYPd 32 
                 + a ++  lg++ +A+   +++ +  P+
  EPA05950.1  86 LKANAHHFLGQSKQAISCCNKIKEIDPK 113
                 5677888889********9999998887 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.025        21      13      36 ..      25      48 ..      22      52 .. 0.87
   2 ?    2.0   0.1      0.26   2.2e+02      12      30 ..      58      76 ..      47      92 .. 0.75
   3 !    9.4   0.0    0.0013       1.1      10      45 ..      90     125 ..      81     127 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.025
                HHT-HHHHHHHHHHHHHHTTS-HH CS
  Fis1_TPR_C 13 klgeYseArryvdalLeiEPenrQ 36
                k ++Y++A++    +L++ Pe + 
  EPA05950.1 25 KKKQYDDALKIGTEILKKVPEEND 48
                789**************9998765 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.26
                HHHT-HHHHHHHHHHHHHH CS
  Fis1_TPR_C 12 yklgeYseArryvdalLei 30
                y   +Y++A  y +  L+i
  EPA05950.1 58 YMKNQYQTAISYFEKSLKI 76
                5556899999999999987 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0013
                 HHHHHT-HHHHHHHHHHHHHHTTS-HHHHHHHHHHH CS
  Fis1_TPR_C  10 GhyklgeYseArryvdalLeiEPenrQaqsLkelie 45 
                 +h  lg+ ++A  +++ + ei+P+n+ + +L + i 
  EPA05950.1  90 AHHFLGQSKQAISCCNKIKEIDPKNKAVSELLSKIT 125
                 6666788899*********************99986 PP

>> DUF4919  Domain of unknown function (DUF4919)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.6   3.8e-05     0.033      59     117 ..      14      73 ..       2      78 .. 0.79
   2 !    7.7   0.1    0.0036       3.1      70     120 ..      60     110 ..      57     112 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.8e-05
     DUF4919  59 eel.kldkkelseeelkeiislaeealkknPfdlkqlnllayaykalgkkeeakiyskrl 117
                 ++  k+ +k ++++++++++++++e+lkk P +   l+++  +y  +++ + a +y ++ 
  EPA05950.1  14 SQKkKELRKLVKKKQYDDALKIGTEILKKVPEENDVLFIIGGIYYMKNQYQTAISYFEKS 73 
                 1113567999******************************99999999998887777665 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0036
     DUF4919  70 eeelkeiislaeealkknPfdlkqlnllayaykalgkkeeakiyskrlnkl 120
                 +++++++is+ e++lk    d   l l a+a++ lg++++a +  ++++++
  EPA05950.1  60 KNQYQTAISYFEKSLKIGSYDTDVLILKANAHHFLGQSKQAISCCNKIKEI 110
                 6899*************************************9999999886 PP

>> SRP_TPR_like  Putative TPR-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.4    0.0001     0.089      57     100 ..      25      72 ..       7      88 .. 0.78
   2 ?    2.9   0.1      0.13   1.1e+02      30      75 ..      63     111 ..      63     125 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.0001
  SRP_TPR_like  57 klkkykkalk....ilkkveaeekvkvlksqvlYrlgsyekAYklLsk 100
                   k k+y +alk    ilkkv +e+ v  +   ++Y++++y++A ++  k
    EPA05950.1  25 KKKQYDDALKigteILKKVPEENDVLFIIGGIYYMKNQYQTAISYFEK 72 
                   7789999987333369999999999999**************666533 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.13
  SRP_TPR_like  30 yeeaLkllkkgs...alsedvrfEkaYvlYklkkykkalkilkkveaee 75 
                   y+ a+++ +k     + + dv   ka ++  l + k+a +  +k+++ +
    EPA05950.1  63 YQTAISYFEKSLkigSYDTDVLILKANAHHFLGQSKQAISCCNKIKEID 111
                   5666666666553334556777778888888888888888777776655 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.6      0.19   1.6e+02      14      21 ..      26      33 ..      25      35 .. 0.88
   2 ?   13.7   0.3   5.4e-05     0.046      11      36 .]      57      80 ..      54      80 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.19
                TT-HHHHH CS
       TPR_3 14 kkkyqeAr 21
                kk+y++A+
  EPA05950.1 26 KKQYDDAL 33
                9******7 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 5.4e-05
                HHHTT-HHHHHHH..HHHHHHH-TT- CS
       TPR_3 11 fynkkkyqeArelfsYallaildken 36
                +y+k +yq+A+ +  ++ + ++ +++
  EPA05950.1 57 YYMKNQYQTAISY--FEKSLKIGSYD 80
                9************..66888887776 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0       1.2     1e+03      15      34 ..      27      46 ..      21      53 .. 0.77
   2 ?    6.2   0.0     0.026        22       8      42 ..      54      88 ..      47      90 .. 0.83
   3 ?    6.5   0.0     0.021        18       7      42 ..      87     122 ..      81     124 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 1.2
      TPR_14 15 GdpdeAiallrralalaPdd 34
                 ++d+A+++  ++l++ P++
  EPA05950.1 27 KQYDDALKIGTEILKKVPEE 46
                68999999888888888865 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.026
      TPR_14  8 aeallalGdpdeAiallrralalaPddaeawllla 42
                + +++   ++++Ai ++++ l+ +  d ++++l a
  EPA05950.1 54 GGIYYMKNQYQTAISYFEKSLKIGSYDTDVLILKA 88
                667888899*************9998888887776 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.021
      TPR_14   7 laeallalGdpdeAiallrralalaPddaeawllla 42 
                  a a+  lG+ ++Ai +++++ + +P++ ++  ll 
  EPA05950.1  87 KANAHHFLGQSKQAISCCNKIKEIDPKNKAVSELLS 122
                 5888999********************998877665 PP

>> ChAPs  ChAPs (Chs5p-Arf1p-binding proteins)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   3.7e-05     0.032     176     266 ..      24     113 ..       6     126 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.7e-05
                 HHHHHHHT-HHHHHHHHHHHHTT-GGGHHHHHHHHHHTT-HHHHHHHHHHHH-SSS-HHHHHHHHHHHHHHSS--HHHHHHHHHHHHH-TT CS
       ChAPs 176 lklvrltkrydralellekLkeeepevvillarvllladeEvdavkllneeleeeekdaelLllqaefllskkkeelAlevakravksaPs 266
                 +k  +    ++ ++e+l+k+ ee  +v  ++  ++ ++++   a+   +++l+  + d+++L+l+a+      +++ A+++ ++  ++ P 
  EPA05950.1  24 VKKKQYDDALKIGTEILKKVPEE-NDVLFIIGGIYYMKNQYQTAISYFEKSLKIGSYDTDVLILKANAHHFLGQSKQAISCCNKIKEIDPK 113
                 44444455566677777777654.5899************************999999988888887655556666677777666666665 PP

>> DUF4284  Immunity protein 22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0       1.8   1.6e+03      50      80 ..      12      39 ..       7      58 .. 0.58
   2 ?   12.8   0.2    0.0002      0.17      17      72 ..      58     107 ..      51     128 .] 0.68

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 1.8
     DUF4284 50 kfleteaedieellekvsldseiieklkekl 80
                k   ++++++++l++k ++d +   k+ +++
  EPA05950.1 12 KT-SQKKKELRKLVKKKQYDDA--LKIGTEI 39
                44.5566666777777777776..3444444 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.0002
     DUF4284  17 YldqsydedgkelssqFckdlgleeyDeDfleikfleteaedieellekvsldsei 72 
                 Y++++y+  +    s F+k+l++ +yD D+l++k   ++   + +  +++s+ ++i
  EPA05950.1  58 YMKNQYQTAI----SYFEKSLKIGSYDTDVLILKA--NAHHFLGQSKQAISCCNKI 107
                 5555554444....9****************9999..4444445555566665553 PP

>> DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   0.00012       0.1      47      99 ..       5      57 ..       2      72 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00012
                     T-SEEEESSHHHHHHHHHHHHHTTSSSEEEESHHHHHHHHCHTT-SEEEE--S CS
  DXP_reductoisom 47 kpklvavadeeaaeelkealkekelktevlvGeealkelaeeeeadvvvaaiv 99
                     kpk+  v+ +++++el++ +k+k+++  + +G+e lk++ ee+++ +++ +i 
       EPA05950.1  5 KPKTTEVKTSQKKKELRKLVKKKQYDDALKIGTEILKKVPEENDVLFIIGGIY 57
                     799999*************************************9999998875 PP

>> Rapsyn_N  Rapsyn N-terminal myristoylation and linker region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.2    0.0019       1.6       8      52 ..      15      59 ..       9      76 .. 0.79
   2 ?    4.8   0.0     0.034        29      17      64 ..      58     102 ..      53     111 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0019
    Rapsyn_N  8 rkiekGLklyesndtekalrvWrkvLkktsdregkfrvLGcLita 52
                +k +   kl ++ + + al++ +++Lkk  ++++ + ++G ++  
  EPA05950.1 15 QKKKELRKLVKKKQYDDALKIGTEILKKVPEENDVLFIIGGIYYM 59
                44444447999999********************99999988754 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.034
    Rapsyn_N  17 yesndtekalrvWrkvLkktsdregkfrvLGcLitahsemGkykeale 64 
                 y +n+ + a+  + k Lk  s   +   vL    +ah  +G+ k+a+ 
  EPA05950.1  58 YMKNQYQTAISYFEKSLKIGSYDTD---VLILKANAHHFLGQSKQAIS 102
                 899**************99988777...55566788888888888876 PP

>> FIVAR  FIVAR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.4   0.00087      0.74      28      56 ..      25      49 ..       4      50 .. 0.75
   2 ?   -0.1   0.0       1.9   1.6e+03      29      42 ..      60      73 ..      59      82 .. 0.75
   3 ?    1.5   0.1      0.59     5e+02      42      66 ..     107     127 ..      94     128 .] 0.70

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00087
                HHHHHHHHHHHHHHHC...TSTTTTCCCH CS
       FIVAR 28 kkdaynnalsaAnailnktnnpnatveqV 56
                kk++y++al++ ++il+k+    + +++V
  EPA05950.1 25 KKKQYDDALKIGTEILKKV----PEENDV 49
                789*************999....666655 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.9
                HHHHHHHHHHHHHH CS
       FIVAR 29 kdaynnalsaAnai 42
                k++y++a+s  ++ 
  EPA05950.1 60 KNQYQTAISYFEKS 73
                68899988865555 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.59
                 HC...TSTTTTCCCHHHHHHHHHHH CS
       FIVAR  42 ilnktnnpnatveqVnqalanlnqa 66 
                 i    +  ++  ++V + l+++++a
  EPA05950.1 107 I----KEIDPKNKAVSELLSKITSA 127
                 3....55578888888888888887 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.31   2.7e+02       4      15 ..      23      34 ..      21      34 .. 0.84
   2 ?    7.5   0.4    0.0037       3.1       2      38 ..      55      91 ..      54      95 .. 0.76
   3 ?   -0.1   0.0      0.91   7.8e+02       3      26 ..      90     113 ..      88     117 .. 0.57

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.31
      TPR_11  4 yyeqGkyeeAie 15
                ++++ +y++A++
  EPA05950.1 23 LVKKKQYDDALK 34
                78999*****86 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0037
      TPR_11  2 dayyeqGkyeeAieaYkkAlkldPdnaeayynLGlay 38
                 +yy +++y  Ai  ++k lk+ + + +++   ++a+
  EPA05950.1 55 GIYYMKNQYQTAISYFEKSLKIGSYDTDVLILKANAH 91
                59***********999999998666666655555555 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.91
      TPR_11   3 ayyeqGkyeeAieaYkkAlkldPd 26 
                 a + +G+ ++Ai + +k  ++dP+
  EPA05950.1  90 AHHFLGQSKQAISCCNKIKEIDPK 113
                 445556666666555554456665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1524  (0.085002); expected 358.6 (0.02)
Passed bias filter:                      676  (0.0377043); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 803.26
//
Query:       EPA05951.1  [L=157]
Description: hypothetical protein BG20_I0661 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.012   14.9   0.0      0.017   14.5   0.0    1.1  1  alpha-hel2  Alpha-helical domain 2


Domain annotation for each model (and alignments):
>> alpha-hel2  Alpha-helical domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   9.3e-07     0.017      17      70 ..      24      87 ..      15      94 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 9.3e-07
  alpha-hel2 17 aslvdlsaeavqlqlagwierqvgalrvllPldlAIsaesee..........vefiakaradap 70
                a+++d s  +++  + +w+e+ +g +   +Pl +AI++es++          ++fi   ++d+p
  EPA05951.1 24 AQIFDFSIYKNKIWFTEWVENNIGVVDTSVPLPFAIDLESKDitlkpgeskaTSFIISSQKDIP 87
                6899999999********************************8888888888777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1080.70
//
Query:       EPA05952.1  [L=93]
Description: translation elongation factor aEF-1 beta [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.1e-19   67.6   0.2    9.1e-19   67.4   0.2    1.0  1  EF1_GNE   EF-1 guanine nucleotide exchange domain
  ------ inclusion threshold ------
        0.1   12.6   0.1       0.27   11.3   0.1    1.6  2  BofC_C    BofC C-terminal domain


Domain annotation for each model (and alignments):
>> EF1_GNE  EF-1 guanine nucleotide exchange domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.4   0.2     1e-22   9.1e-19       2      90 .]       6      88 ..       5      88 .. 0.95

  Alignments for each domain:
  == domain 1  score: 67.4 bits;  conditional E-value: 1e-22
                EEEEEEESSS---HHHHHHHHHH.HS-TSEE--.--EEE-SSS-EEEEEEEEESSS-GGGGHHHHHHTTS-S.....SEEEEEEEEEE- CS
     EF1_GNE  2 vvlevkPeddetdleelekkvksikleglvwgeasklepiafGlkkLqiscvieddkvstdeleekieeiegeledlVqsveivsfnkl 90
                +v ++ P   ++dl++l + +ks   eg+++++ + +ep+afGl+ L+ ++v ed+++++d le++++++eg     V++ e+ +++++
  EPA05952.1  6 LVTKILPTGMDVDLDKLSETIKSALKEGIQMKR-HAKEPLAFGLEFLKAEFVLEDKEGQMDSLEDAVKSVEG-----VSEFEVLNMSRM 88
                689********************66677****6.**************************************.....*********995 PP

>> BofC_C  BofC C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1     3e-05      0.27      32      61 ..       9      38 ..       7      42 .. 0.87
   2 ?   -1.7   0.0      0.35   3.1e+03      32      45 ..      75      88 ..      58      92 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3e-05
                -BS-------TTTS-HHHHHHHHH--S--- CS
      BofC_C 32 kviksffqidveklesslkeqLkkGIrves 61
                k++ + +++d +kl++  k++Lk+GI+++ 
  EPA05952.1  9 KILPTGMDVDLDKLSETIKSALKEGIQMKR 38
                67778899******************9976 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.35
                -BS-------TTTS CS
      BofC_C 32 kviksffqidvekl 45
                + + +f  ++++++
  EPA05952.1 75 EGVSEFEVLNMSRM 88
                33445555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.32s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 568.16
//
Query:       EPA05953.1  [L=127]
Description: hypothetical protein BG20_I0672 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-37  128.4   0.0    1.5e-37  128.1   0.0    1.0  1  Cyclophil_like   Cyclophilin-like
    8.3e-08   32.2   0.0      1e-07   31.9   0.0    1.2  1  Cyclophil_like2  Cyclophilin-like family
  ------ inclusion threshold ------
       0.18   12.1   0.0       0.23   11.8   0.0    1.1  1  NSP2_assoc       Non-essential region of nsp2 of arterivirus 


Domain annotation for each model (and alignments):
>> Cyclophil_like  Cyclophilin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.1   0.0   2.4e-41   1.5e-37       3     113 ..       5     119 ..       3     124 .. 0.94

  Alignments for each domain:
  == domain 1  score: 128.1 bits;  conditional E-value: 2.4e-41
                     EEEEETTEEEEEEEETT...HHHHHHHHC-SEEEEEEECTTEEEEE-S-----SSSEESSB-TTEEEEECCCTEEEEESS--TT-.TTSB--SSS CS
  Cyclophil_like   3 ikidiesseveveLddt...etaraikealPiesrvntWgeEiYfstpvklekeenakevveagdiaywppGkalclffGktPis.ddeirpasp 93 
                     i ++i+++ v++eLdd+   +t+++++e lP++++++ Wg+EiY+s +    +eena++ v+++d+aywp+Gka+clf+G+tPi+ +++i+pasp
      EPA05953.1   5 IILKIKNTDVSLELDDKfspKTVKEFVERLPFTVKLHIWGDEIYSSESPIDVTEENAQSPVSLNDVAYWPTGKAICLFYGPTPIGkKGDITPASP 99 
                     6688999*************************************987655555****************************************** PP

                     EEEEEEEEC-GGGGGG--TT CS
  Cyclophil_like  94 vnviGrivedlellkkvkdg 113
                     vnviG+i+ ++++++k++dg
      EPA05953.1 100 VNVIGKIITPDKSVLKIADG 119
                     ************99999887 PP

>> Cyclophil_like2  Cyclophilin-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0   1.7e-11     1e-07       2      88 ..       8      95 ..       7     125 .. 0.80

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 1.7e-11
  Cyclophil_like2  2 tiggqtftatLedn...aaaralleklPltltmedyngnEkiaylpeklptddapegssikaGdlayyapwgnlvlfykdfeesysyglt 88
                     +i +++++ +L+d    +++++++e+lP+t+++   +  E i++ +++++ ++++++s ++  d+ay++ ++ ++lfy+ + ++ + ++t
       EPA05953.1  8 KIKNTDVSLELDDKfspKTVKEFVERLPFTVKLHIWG-DE-IYSSESPIDVTEENAQSPVSLNDVAYWPTGKAICLFYGPTPIGKKGDIT 95
                     6889999999998655589**************9998.44.444477888888877888888*****************99877666666 PP

>> NSP2_assoc  Non-essential region of nsp2 of arterivirus polyprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.9e-05      0.23     111     169 ..      17      75 ..       6      80 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.9e-05
  NSP2_assoc 111 gsdagalpvtvrefvptglilrhvehcGtesgdsssPLdlsdaqtldqPLnLs.LaaWPv 169
                 + d +  p tv+efv   + + +    G e   s+sP+d+ + ++ + P+ L  +a WP 
  EPA05953.1  17 ELDDKFSPKTVKEFVERLPFTVKLHIWGDEIYSSESPIDVTEENA-QSPVSLNdVAYWPT 75 
                 567777899*******************************98765.56888853788995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 870.15
//
Query:       EPA05954.1  [L=367]
Description: ATP-binding protein, Mrp/Nbp35 family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-99  331.9   0.2    2.8e-99  331.5   0.2    1.1  1  ParA            NUBPL iron-transfer P-loop NTPase
    5.4e-18   64.9   0.1    1.9e-17   63.2   0.1    2.0  2  FeS_assembly_P  Iron-sulfur cluster assembly protein
    1.2e-13   51.2   0.0    5.5e-13   49.1   0.0    2.0  1  CbiA            CobQ/CobB/MinD/ParA nucleotide binding domain
    1.1e-09   38.5   1.5    9.2e-08   32.2   0.8    2.3  2  AAA_31          AAA domain
      8e-08   31.9   0.0    1.3e-07   31.2   0.0    1.3  1  MipZ            ATPase MipZ
    7.9e-07   29.1   0.8     0.0073   16.1   0.0    2.4  2  AAA_26          AAA domain
    6.7e-06   25.5   0.8    3.1e-05   23.3   0.7    2.0  2  ArsA_ATPase     Anion-transporting ATPase
    9.4e-06   25.3   0.2    0.00047   19.7   0.1    2.3  2  Fer4_NifH       4Fe-4S iron sulfur cluster binding proteins, 
     0.0024   17.2   0.0     0.0062   15.9   0.0    1.7  1  VirC1           VirC1 protein
     0.0035   17.1   0.0     0.0078   16.0   0.0    1.6  1  CLP1_P          mRNA cleavage and polyadenylation factor CLP1
     0.0038   16.7   0.1      0.017   14.6   0.1    1.9  1  CBP_BcsQ        Cellulose biosynthesis protein BcsQ
  ------ inclusion threshold ------
      0.018   14.1   0.4      0.028   13.4   0.4    1.2  1  MeaB            Methylmalonyl Co-A mutase-associated GTPase M
      0.026   14.1   0.7      0.053   13.1   0.7    1.4  1  AAA_25          AAA domain
      0.087   12.7   0.1       0.18   11.7   0.1    1.5  1  APS_kinase      Adenylylsulphate kinase


Domain annotation for each model (and alignments):
>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  331.5   0.2  2.2e-102   2.8e-99       2     245 ..      96     339 ..      95     340 .. 0.99

  Alignments for each domain:
  == domain 1  score: 331.5 bits;  conditional E-value: 2.2e-102
        ParA   2 vkkviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqsekkliPveakgikvmSigfllesedeavvwrGpmkskai 100
                 vk++i v+SgKGGVGKStv+ nlAlaL+++g+kvgllDaDiyGpsip +lg++++++e++++kl+P +++g++v+S+gf+ e++++a ++rGp++s+++
  EPA05954.1  96 VKNIIGVASGKGGVGKSTVSLNLALALSQTGAKVGLLDADIYGPSIPLMLGMKSAHMEVDNNKLQPAKSNGLQVVSFGFFAEQSHQAAIYRGPIISGIL 194
                 9***********************************************************99************************************* PP

        ParA 101 kqllkdvewgelDyLiiDlPPGtgDeqltvaqklplagaviVttpqevaladvkkaiemfkkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklae 199
                 kq+l d++w++lDyLi+DlPPGtgD+ lt+aq++p++g+++Vttpq+va +++ kai mf+k++v+++GvveNms+f+cp+c+ek++ifg+gg++k++e
  EPA05954.1 195 KQFLVDTNWSDLDYLIVDLPPGTGDIPLTLAQTIPITGILVVTTPQDVASNVAVKAIGMFEKLNVPIIGVVENMSHFICPSCSEKHYIFGDGGAKKISE 293
                 *************************************************************************************************** PP

        ParA 200 elgvpllgeipldpeireasdegkplvlkepeseaakaleeiaekv 245
                 ++++p+lgeipl++ i++ sd gkp+++++p+s+ a a+++ a+++
  EPA05954.1 294 QFKIPFLGEIPLNSGIMSGSDLGKPIMITNPDSPSAIAFRSTAKNI 339
                 ****************************************999987 PP

>> FeS_assembly_P  Iron-sulfur cluster assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.2   0.1   1.5e-20   1.9e-17       2      66 ..       5      69 ..       4      74 .. 0.96
   2 ?   -3.5   0.0       9.9   1.3e+04      16      29 ..     238     251 ..     236     255 .. 0.75

  Alignments for each domain:
  == domain 1  score: 63.2 bits;  conditional E-value: 1.5e-20
                    HHHHHHHTT-B-TTTSSBCCCCT---EEEE-T-EEEEEE--SSTT-TTHHHHHHHHHHHHC.STT CS
  FeS_assembly_P  2 eavlaaLrtVtDPelgvdlvslglvreidieggkVsvditltypacslaeairadaeaalralpg 66
                    ++vl+ L+tV+DP l +d+vs+g+++++++++++ +++++lt+pac++  +i++d+++a++ +++
      EPA05954.1  5 DQVLEKLSTVIDPDLKKDIVSMGMIKDLELNDNNLKFTLELTTPACPFNVEIEDDVRKAIAEIKE 69
                    79**********************************************************99887 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 9.9
                     TSSBCCCCT---EE CS
  FeS_assembly_P  16 lgvdlvslglvrei 29 
                     +++d+ s+ +v++i
      EPA05954.1 238 TPQDVASNVAVKAI 251
                     66888888888877 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   0.0   4.3e-16   5.5e-13       2     124 ..     101     315 ..     100     319 .. 0.84

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 4.3e-16
                 EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH.............................................. CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............................................. RF
        CbiA   2 aiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep.............................................. 54 
                  +as+kGGvGK+t+++nLa al++ g +V l+DaD  +++  +  g +  + +                                              
  EPA05954.1 101 GVASGKGGVGKSTVSLNLALALSQTGAKVGLLDADIYGPSIPLMLGMKSAHMEvdnnklqpaksnglqvvsfgffaeqshqaaiyrgpiisgilkqflv 199
                 59***************************************99555555555556688899************************************** PP

                 ..............................................CCHCCCHHHHHHCHCHHHH..EEEEEEEEES......S...-TTCHHHHHHHH CS
                 ..............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxx RF
        CbiA  55 ..............................................dlkrllellealgkkkalllkiagvvlnrvd......geneetllkealeelk 101
                                                                + + ++++e+l  +      i+gvv n+        +e+++     + +++ 
  EPA05954.1 200 dtnwsdldylivdlppgtgdipltlaqtipitgilvvttpqdvasnVAVKAIGMFEKLNVP------IIGVVENMSHficpscSEKHYIFGDGGAKKIS 292
                 ********************************99999999988888555668888888855......78888777533333335666777777788888 PP

                 HHCTS-EEEEEE--CCHCCCCHH CS
                 xxxxxxxxxxxxxxxxxxxxxxx RF
        CbiA 102 qrygvpvlgviprdeavaeapar 124
                 +++++p+lg+ip +++++     
  EPA05954.1 293 EQFKIPFLGEIPLNSGIMSGSDL 315
                 88899999999999888766555 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.8   7.2e-11   9.2e-08       2      40 ..      98     136 ..      97     152 .. 0.94
   2 ?    4.8   0.0     0.019        24      78     131 ..     154     219 ..     143     258 .. 0.66

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 7.2e-11
      AAA_31   2 kvIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDp 40 
                  +I +a  KGGvGK+T s+nla al+++g kv l D+D 
  EPA05954.1  98 NIIGVASGKGGVGKSTVSLNLALALSQTGAKVGLLDADI 136
                 5899*********************************95 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.019
      AAA_31  78 venldlipssid.Laeaeielvelekk..........eeilkellekvk.deYDyiiiDcpPsLgl 131
                 v+n++l p++ + L+ ++  ++  +++            ilk++l + + ++ Dy i+D pP  g 
  EPA05954.1 154 VDNNKLQPAKSNgLQVVSFGFFAEQSHqaaiyrgpiiSGILKQFLVDTNwSDLDYLIVDLPPGTGD 219
                 5666777777666666776666655554455555444555888875554278**********8764 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0     1e-10   1.3e-07       2      72 ..      99     169 ..      98     237 .. 0.73

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 1e-10
                 EEEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHHHHHHHHHHHHT------EEE-SSS CS
        MipZ   2 vivlgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtlarylenraataerkglsLplpealalse 72 
                 +i ++  kGG Gkst+++ +a aL+++Ga+v+ +d d+   ++   l+ ++a +e  + +L+ ++   l+ 
  EPA05954.1  99 IIGVASGKGGVGKSTVSLNLALALSQTGAKVGLLDADIYGPSIPLMLGMKSAHMEVDNNKLQPAKSNGLQV 169
                 688999********************************999999999999988887777776665554443 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.5   0.00024       0.3       5      33 ..     102     130 ..      98     132 .. 0.89
   2 !   16.1   0.0   5.7e-06    0.0073     121     195 ..     222     310 ..     211     313 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00024
      AAA_26   5 vtgtdtgvGKTvvslgLvralkrkgvkvg 33 
                 v++   gvGK++vsl L+ al+++g+kvg
  EPA05954.1 102 VASGKGGVGKSTVSLNLALALSQTGAKVG 130
                 6777789********************98 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 5.7e-06
      AAA_26 121 adiaknlgapvilVargglg.tinqllltiealrqknvrvlGvilNk....vrnp...e........nvetlekksgipvlGvvPylpdle 195
                   +a+++ +  ilV+++ ++ + n ++ +i ++ + nv+++Gv+ N     +  p   e          ++++++++ip lG++P ++ ++
  EPA05954.1 222 LTLAQTIPITGILVVTTPQDvASNVAVKAIGMFEKLNVPIIGVVENMshfiC--PscsEkhyifgdgGAKKISEQFKIPFLGEIPLNSGIM 310
                 66788888887888877666266888899***************99844332..24451566666679*****************998766 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.7   2.4e-08   3.1e-05       6      38 ..     103     135 ..      98     141 .. 0.90
   2 ?   -0.6   0.0      0.46   5.9e+02     118     137 ..     199     219 ..     150     305 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 2.4e-08
                  EEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
  ArsA_ATPase   6 vgGKGGVGKttvsaatavklsekgkkvllistD 38 
                   +GKGGVGK+tvs  +a+ ls++g kv l+  D
   EPA05954.1 103 ASGKGGVGKSTVSLNLALALSQTGAKVGLLDAD 135
                  58************************9887665 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.46
                  HHHHCSSSSEEEEESBS.CCH CS
  ArsA_ATPase 118 kyvkeeeydvvvlDtaP.TGh 137
                    ++ ++ d++++D +P TG+
   EPA05954.1 199 VDTNWSDLDYLIVDLPPgTGD 219
                  455566788999999885554 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1   3.7e-07   0.00047       7      53 ..     105     151 ..      99     174 .. 0.86
   2 ?    3.4   0.0     0.033        43     191     251 ..     286     346 ..     227     359 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 3.7e-07
   Fer4_NifH   7 GkGGiGksttsqnlsaalaemgkkvlivGCDPkaDstrlllggkaqe 53 
                 GkGG+Gkst s nl+ al+++g kv ++  D    s  l+lg k  +
  EPA05954.1 105 GKGGVGKSTVSLNLALALSQTGAKVGLLDADIYGPSIPLMLGMKSAH 151
                 9************************9999999999998888877665 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.033
   Fer4_NifH 191 eliekfaeelgtkvlevvPrdeivrkaelrkktvieyapeseqakeyrelarkilenkklv 251
                 + ++k+ e+ +++ l  +P++  +   +   k ++  +p+s+ a  +r  a++i+ +   +
  EPA05954.1 286 GGAKKISEQFKIPFLGEIPLNSGIMSGSDLGKPIMITNPDSPSAIAFRSTAKNIAAQCSIL 346
                 5578899999**********99998888777888888999999***********9887443 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   4.8e-06    0.0062       2      40 ..      98     136 ..      97     143 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.8e-06
       VirC1   2 klitfcslkGGaGkttalmglcsalasdgkrvalfeade 40 
                 ++i ++s kGG Gk+t  + l  al + g +v+l++ad 
  EPA05954.1  98 NIIGVASGKGGVGKSTVSLNLALALSQTGAKVGLLDADI 136
                 68999********************************95 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   6.1e-06    0.0078       1      58 [.     105     160 ..     105     186 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 6.1e-06
      CLP1_P   1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvGqseispPgtislalverpidveegf 58 
                 G+  +GKST++ +L+  + + g k+ ++D+D+  ++  +P ++++   ++++d+++  
  EPA05954.1 105 GKGGVGKSTVSLNLALALSQTGAKVGLLDADIYGPS--IPLMLGMKSAHMEVDNNKLQ 160
                 66789***************************9987..78888888888888664443 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   1.3e-05     0.017       4     153 ..     100     246 ..      97     259 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.3e-05
    CBP_BcsQ   4 lalqGvRGGvGttsllaaLawalhelgesvlviDlspdnlLrlhFnvdieqregwaraeld..gapwrqaaleyapgldllPfGelnveekenlqq.la 99 
                 + +   +GGvG+++++  La al + g +v ++D+    +   +  +      g+  a+++  +++++       +gl+++ fG  +++ +++      
  EPA05954.1 100 IGVASGKGGVGKSTVSLNLALALSQTGAKVGLLDAD---IYGPSIPLM----LGMKSAHMEvdNNKLQP---AKSNGLQVVSFGFFAEQSHQAAIYrGP 188
                 5556668***************************74...444444333....44445555400444444...45799*******998887775444133 PP

    CBP_BcsQ 100 ekaeallaalkelk.eqyrwillDlpagasaltrellaladlv..llvvep.danchv 153
                   ++ l+++l   + ++ +++++Dlp g+ ++  +l ++  ++  l v++p d+++ v
  EPA05954.1 189 IISGILKQFLVDTNwSDLDYLIVDLPPGTGDIPLTLAQTIPITgiLVVTTPqDVASNV 246
                 447778888888888999********99988766666554332214444443555555 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.4   2.2e-05     0.028      25      66 ..      90     135 ..      75     147 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.2e-05
                 G-S-SEE...EEE.EE-TTSSHHHHHHHHHHHHHCTT--EEEEEE- CS
        MeaB  25 kaGraqv...vGl.tGvPGaGkstlvealglelrrrGkrvavlavD 66 
                 ++G a+v   +G+  G  G+Gkst+  +l+l l + G +v++l  D
  EPA05954.1  90 DSGMATVkniIGVaSGKGGVGKSTVSLNLALALSQTGAKVGLLDAD 135
                 556555422277734889***********************99877 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.7   4.1e-05     0.053      34      61 ..      99     127 ..      94     135 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.1e-05
      AAA_25  34 elallaGapgtGKttlaldlalava.tGk 61 
                  +++  G +g+GK+t+ l+lala++ tG 
  EPA05954.1  99 IIGVASGKGGVGKSTVSLNLALALSqTGA 127
                 567889*****************997775 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00014      0.18       8      42 ..     104     138 ..      97     160 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00014
                 ESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHT CS
  APS_kinase   8 tGlsgsGKstianalekkLvekgisvylLdGdnvR 42 
                 +G  g GKst++ +l+ +L ++g +v lLd d   
  EPA05954.1 104 SGKGGVGKSTVSLNLALALSQTGAKVGLLDADIYG 138
                 78999*************************99655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.47
# Mc/sec: 2326.18
//
Query:       EPA05955.1  [L=87]
Description: quinolinate phosphoribosyl transferase, N-terminal domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    8.5e-19   67.4   0.1    1.1e-18   67.1   0.1    1.0  1  QRPTase_N  Quinolinate phosphoribosyl transferase, N-terminal
     0.0004   20.4   0.1    0.00047   20.2   0.1    1.1  1  Ufm1       Ubiquitin fold modifier 1 protein
  ------ inclusion threshold ------
      0.085   12.3   0.0      0.085   12.3   0.0    1.1  1  Ppx-GppA   Ppx/GppA phosphatase family


Domain annotation for each model (and alignments):
>> QRPTase_N  Quinolinate phosphoribosyl transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.1   0.1   1.8e-22   1.1e-18       1      71 [.      17      84 ..      17      86 .. 0.97

  Alignments for each domain:
  == domain 1  score: 67.1 bits;  conditional E-value: 1.8e-22
                CTT--HHHHHHGCTTSEEEEEEEESSSEEE-SHHHHHHHHHHHTTTEEEESS-TT-EEETTEEEEEEEEEH CS
   QRPTase_N  1 igrgDlttealipeekkakaeiiakeegvvaGlevaeevfellpglevellvkDGervekgdvlleieGna 71
                ig+gD+t+  +++++++++a+ii++e+++vaG+++a+e+f+l  g+++ + +kDG++v+++d++++i+Gna
  EPA05955.1 17 IGKGDITS--TLLPKRNITAKIISREKAIVAGTKYAKEIFKLK-GCNAIIVKKDGSKVKPNDTIMTISGNA 84
                689*****..999****************************99.**************************8 PP

>> Ufm1  Ubiquitin fold modifier 1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.1   7.8e-08   0.00047      21      64 ..      37      80 ..      21      85 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 7.8e-08
        Ufm1 21 vpeeapftavlkfaaeeFkvpaatsaiitndGvginpqqtagnv 64
                ++ e ++ a  k+a e Fk++  +++i+++dG+ + p++t+ ++
  EPA05955.1 37 ISREKAIVAGTKYAKEIFKLKGCNAIIVKKDGSKVKPNDTIMTI 80
                45677788999*****************************9876 PP

>> Ppx-GppA  Ppx/GppA phosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.4e-05     0.085     128     171 ..       3      46 ..       1      82 [. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.4e-05
                 EEETTEEEEEEEES--CCHHHHHHSGCCC--HHHHHHHHHHHHH CS
    Ppx-GppA 128 lgeekevsklvSlplGavrlterfltddpltkeeveaarkavek 171
                 +  +k+ ++ +S ++G + +t + l+++++t++++++ +++v+ 
  EPA05955.1   3 FNSKKQLQDFLSEDIGKGDITSTLLPKRNITAKIISREKAIVAG 46 
                 6678999*******************************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 582.83
//
Query:       EPA05956.1  [L=722]
Description: AAA family ATPase, CDC48 family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-91  303.4   0.1      5e-48  162.9   0.0    3.1  2  AAA              ATPase family associated with various cellul
    4.9e-32  109.5   3.6    3.5e-15   55.5   0.1    2.6  2  AAA_lid_3        AAA+ lid domain
    1.6e-27   95.5   0.8    6.2e-27   93.6   0.8    2.1  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal
    1.2e-15   57.6   1.3    1.1e-08   35.0   0.0    3.5  3  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    3.6e-13   50.0   0.0    1.4e-07   31.8   0.0    2.5  2  AAA_2            AAA domain (Cdc48 subfamily)
    1.2e-12   48.5   0.2     0.0032   17.9   0.0    4.8  4  AAA_16           AAA ATPase domain
      1e-11   45.0   0.0    3.7e-06   27.0   0.0    2.5  2  AAA_14           AAA domain
    1.2e-10   41.6   0.4    0.00038   20.5   0.0    4.5  2  AAA_5            AAA domain (dynein-related subfamily)
    1.9e-10   41.1   0.1       0.03   14.6   0.0    4.4  4  AAA_22           AAA domain
    1.7e-09   38.0   0.0     0.0017   18.7   0.0    3.0  2  RNA_helicase     RNA helicase
    2.6e-09   36.7   0.2    1.1e-08   34.8   0.1    2.0  2  CDC48_2          Cell division protein 48 (CDC48), domain 2
    9.5e-09   35.5   0.0     0.0041   17.1   0.0    3.5  3  ATPase_2         ATPase domain predominantly from Archaea
    1.2e-08   34.7   1.0       0.22   11.0   0.0    4.8  5  AAA_25           AAA domain
      2e-08   34.9   0.1      0.011   16.3   0.0    3.5  2  ABC_tran         ABC transporter
    2.3e-08   34.3   0.0     0.0041   17.3   0.0    2.5  2  AAA_33           AAA domain
    2.5e-08   34.5   0.0     0.0042   17.6   0.0    3.0  2  AAA_18           AAA domain
    1.1e-07   32.0   0.4       0.03   14.3   0.0    3.3  2  Rad17            Rad17 P-loop domain
    7.2e-07   29.1   0.1       0.11   12.2   0.0    3.7  3  AAA_24           AAA domain
      8e-07   28.6   0.4      0.018   14.4   0.0    2.5  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    8.3e-07   29.4   0.0      0.077   13.2   0.0    2.7  2  AAA_28           AAA domain
    1.5e-06   28.3   0.0       0.11   12.7   0.0    3.2  2  Sigma54_activ_2  Sigma-54 interaction domain
    2.9e-06   27.1   0.0       0.13   12.0   0.0    2.8  2  IstB_IS21        IstB-like ATP binding protein
    5.9e-06   25.7   0.0       0.02   14.1   0.0    2.6  2  TIP49            TIP49 P-loop domain
    1.1e-05   25.2   0.0        1.1    9.0   0.0    3.9  3  Sigma54_activat  Sigma-54 interaction domain
    4.8e-05   23.0   0.2       0.15   11.6   0.0    3.2  3  AAA_7            P-loop containing dynein motor region
    5.8e-05   22.5   0.6       0.49    9.7   0.0    3.6  3  ATPase           KaiC
    6.6e-05   22.3   0.0       0.15   11.3   0.0    2.6  2  Zeta_toxin       Zeta toxin
    8.2e-05   22.6   0.3        2.1    8.3   0.0    3.4  3  NACHT            NACHT domain
    0.00024   21.0   0.0       0.12   12.1   0.0    2.7  2  AAA_11           AAA domain
    0.00025   21.0   0.0       0.34   10.9   0.0    2.6  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    0.00039   19.8   0.0       0.61    9.3   0.0    2.6  2  DUF2075          Uncharacterized conserved protein (DUF2075)
    0.00039   20.2   0.0       0.17   11.6   0.0    2.4  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
    0.00052   19.5   0.5        2.2    7.7   0.1    3.7  3  PhoH             PhoH-like protein
     0.0008   19.8   0.0        2.3    8.7   0.0    2.7  2  AAA_17           AAA domain
     0.0013   18.5   0.1        1.7    8.2   0.0    3.2  3  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
     0.0015   18.3   0.0        3.7    7.4   0.0    3.2  2  AAA_3            ATPase family associated with various cellul
     0.0016   17.9   0.0        2.3    7.6   0.0    3.3  3  SRPRB            Signal recognition particle receptor beta su
     0.0022   17.1   0.1        1.8    7.6   0.0    2.3  2  Parvo_NS1        Parvovirus non-structural protein NS1
     0.0034   16.6   0.3        2.7    7.1   0.0    3.2  3  NB-ARC           NB-ARC domain
     0.0067   15.6   0.0        5.8    6.0   0.0    2.8  3  DUF815           Protein of unknown function (DUF815)
  ------ inclusion threshold ------
      0.013   14.9   0.1      0.028   13.9   0.1    1.5  1  UFD1             Ubiquitin fusion degradation protein UFD1
      0.022   14.7   0.2        7.1    6.7   0.0    2.8  2  Vps4_C           Vps4 C terminal oligomerisation domain
      0.032   14.3   0.1        8.5    6.5   0.0    2.7  2  SKI              Shikimate kinase
      0.038   13.2   0.3        5.2    6.2   0.0    3.0  3  KAP_NTPase       KAP family P-loop domain
      0.043   14.2   1.1         13    6.2   0.0    2.8  2  AAA_19           AAA domain
      0.049   13.4   1.5         14    5.3   0.0    3.2  3  Cytidylate_kin   Cytidylate kinase
      0.059   12.8   0.1       0.62    9.4   0.1    2.3  2  IPT              Isopentenyl transferase
      0.061   13.6   2.1         13    6.0   0.0    3.7  3  Hydin_ADK        Hydin Adenylate kinase-like domain
      0.065   12.0   0.1        5.7    5.6   0.0    2.3  2  Adeno_IVa2       Adenovirus IVa2 protein
      0.068   12.9   0.2         24    4.5   0.0    3.0  2  AAA_30           AAA domain
      0.087   13.3   0.1        4.3    7.8   0.1    2.6  2  AAA_23           AAA domain
       0.11   12.7   0.0        9.6    6.3   0.0    2.4  2  Cytidylate_kin2  Cytidylate kinase-like family


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.9   0.0   1.5e-50     5e-48       1     131 [.     217     346 ..     217     347 .. 0.98
   2 !  137.1   0.0   1.3e-42   4.5e-40       2     131 ..     491     617 ..     490     618 .. 0.97

  Alignments for each domain:
  == domain 1  score: 162.9 bits;  conditional E-value: 1.5e-50
                 EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS CS
         AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkk 99 
                 +llyGppG+GKTl+ak +a+e+++++++i+g+e+++ky ge+e+k+r++fkeak ++ psi+fiDEida+a++r+++  ++e+rvv+qLl+ +dg++++
  EPA05956.1 217 ILLYGPPGCGKTLIAKVLASESEANMFSINGPEIMNKYYGETEAKLRDIFKEAKDNS-PSIIFIDEIDAIAPKREEAYGDVEKRVVAQLLALMDGLNDR 314
                 69******************************************************9.****************************************7 PP

                 SSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
         AAA 100 eskvivigatnrpdkldpallr.gRfdrkieie 131
                  ++viv+gatnrp+++dpal+r gRfdr++ei+
  EPA05956.1 315 -GNVIVLGATNRPESIDPALRRpGRFDREFEIS 346
                 .66***************************986 PP

  == domain 2  score: 137.1 bits;  conditional E-value: 1.3e-42
                 EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSS CS
         AAA   2 llyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkke 100
                 l+yGppG+GKTl+a+a+a+e+g++++ ++g+e+lsk++gesek +re+f++ak+++ p+++++DE+d+la+ +  +e +++e+v++qLlte+++ ++  
  EPA05956.1 491 LIYGPPGCGKTLIARALATETGANMILVKGPEILSKWIGESEKAVREIFRKAKTSS-PCVVIFDELDSLARLK-VGEGGVGETVLSQLLTEIEEGTS-- 585
                 89*****************************************************9.************9999.8899*******************.. PP

                 STEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
         AAA 101 skvivigatnrpdkldpallr.gRfdrkieie 131
                 s+v+vig+tnrpd ld+ llr gR+d +++++
  EPA05956.1 586 SRVVVIGITNRPDVLDNSLLRtGRLDLVLYVP 617
                 59*************************99986 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.5   0.1     1e-17   3.5e-15       1      41 [.     369     409 ..     369     413 .. 0.93
   2 !   54.1   0.6   2.8e-17   9.6e-15       1      43 [.     640     682 ..     640     684 .. 0.98

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 1e-17
   AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeitme 41 
                 dvdlk+LA++ +Gy+GAD+++lcreAal A+rr ++ei+ e
  EPA05956.1 369 DVDLKDLASELHGYTGADIKSLCREAALKAIRRYLPEIDLE 409
                 9*********************************9998765 PP

  == domain 2  score: 54.1 bits;  conditional E-value: 2.8e-17
   AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeitmedf 43 
                 dv l+e+A +T++y+GADlaalcreAa  A+r +  +it +df
  EPA05956.1 640 DVKLEEIAVATQNYTGADLAALCREAAVQAMRNNSAKITNSDF 682
                 8*****************************************9 PP

>> CDC48_N  Cell division protein 48 (CDC48), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.6   0.8   1.8e-29   6.2e-27       1      84 [.       9      92 ..       9      93 .. 0.98

  Alignments for each domain:
  == domain 1  score: 93.6 bits;  conditional E-value: 1.8e-29
                CEEEECCSS-CSSTTEEEE-HHHHHHHTS-TTSEEEEECCCCEEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEEEEEEE- CS
     CDC48_N  1 rLrVaeapqedvgrgivridpedmeelglepgdvveiegkrkTvaivwpaepedegkgiIrmdgvtRknagvsiGdkVtVrkae 84
                ++rV ea+q+dvg++++ri pe+m+ l++ pgd++e+ g+r+++a+vwp +++++ ++iIr+dg tRkn+g+s++d V++rka+
  EPA05956.1  9 QMRVGEAKQRDVGKKRARIGPEAMDFLKVTPGDIIEVMGSRTSCAVVWPVDEDEKTPDIIRIDGQTRKNVGASLNDIVKIRKAS 92
                69***************************************************99***************************85 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.0   3.2e-11   1.1e-08      34     105 ..     215     293 ..     207     334 .. 0.80
   2 !   19.5   0.1   1.8e-06   0.00063      34      69 ..     488     523 ..     447     561 .. 0.84
   3 ?   -1.6   0.0       5.8     2e+03      39      58 ..     563     583 ..     551     625 .. 0.72

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 3.2e-11
      RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrlsraveevly 105
                   +llyGpPG Gkt +ak++a+e ++++ +  gP +      e ++ l  ++++ +++   ++fidei  ++++ ee  y
  EPA05956.1 215 SGILLYGPPGCGKTLIAKVLASESEANMFSINGPEImnkyygETEAKLRDIFKEAKDNspSIIFIDEIDAIAPKREEA-Y 293
                 569*******************************993322222345566666666554336***********999986.4 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 1.8e-06
      RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvklkitsgPvl 69 
                    l+yGpPG Gkt +a+ +a+e g+++    gP +
  EPA05956.1 488 KGALIYGPPGCGKTLIARALATETGANMILVKGPEI 523
                 5679*****************************987 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 5.8
      RuvB_N  39 yGpPGlGkttlakiiak.elg 58 
                 +G  G+G t l++++++ e g
  EPA05956.1 563 VGEGGVGETVLSQLLTEiEEG 583
                 678888888888887652333 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.0     4e-10   1.4e-07       2     105 ..     213     310 ..     212     314 .. 0.90
   2 !   15.5   0.0   4.1e-05     0.014       7     107 ..     491     584 ..     485     595 .. 0.83

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 4e-10
                 ----EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG----.---------HHHHH CS
       AAA_2   2 piisilllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpk.essgadvSregVqr 97 
                 p + ill gp g+Gkt++ak la+  ++    ++  ++  e++     + + + +   ++  ++a+++   i+++DEid i+pk e++  dv +  V+ 
  EPA05956.1 213 PHSGILLYGPPGCGKTLIAKVLASESEA----NMFSINGPEIMN----KYYGETEAKLRDIFKEAKDNSpsIIFIDEIDAIAPKrEEAYGDVEKR-VVA 302
                 567799******************9985....************....99999999999999999999999*************99999999876.667 PP

                 HHHHHHH- CS
       AAA_2  98 dLLqileg 105
                  LL +++g
  EPA05956.1 303 QLLALMDG 310
                 78888887 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 4.1e-05
                 EEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG-------------HHHHHHHHHHH CS
       AAA_2   7 lllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpkessgadvSregVqrdLLqil 103
                 l+ gp g+Gkt++a+ala    +    ++i +   e+l     + + ++++  ++   +a+ +   +v +DE+d  ++  + g+   +e V+  LL  +
  EPA05956.1 491 LIYGPPGCGKTLIARALATETGA----NMILVKGPEILS----KWIGESEKAVREIFRKAKTSSpcVVIFDELDSLAR-LKVGEGGVGETVLSQLLTEI 580
                 789****************9996....9*********99....55555555555555555555599************.88888888999*99999999 PP

                 H--E CS
       AAA_2 104 eggt 107
                 e+gt
  EPA05956.1 581 EEGT 584
                 9987 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   9.3e-06    0.0032      24     132 ..     213     313 ..     205     320 .. 0.56
   2 !   16.8   0.0     2e-05    0.0069      25      51 ..     488     514 ..     480     532 .. 0.82
   3 ?    5.9   0.0     0.045        16     122     164 ..     534     582 ..     529     591 .. 0.71
   4 ?   -0.5   0.0         4   1.4e+03      30      61 ..     563     598 ..     561     677 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 9.3e-06
      AAA_16  24 p.elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekleealaavpelagaeasrlle 121
                 p + +ll+G++G+GK+ +++ l+ + e++ ++ ++g    +     y+  ++a  r +++++ +d+   +    + +++++ +    e+ g+ ++r+ +
  EPA05956.1 213 PhSGILLYGPPGCGKTLIAKVLASESEAN-MFSINGPEIMN----KYYGETEAKLR-DIFKEAKDN---SPSIIFIDEIDAIAPKREEAYGDVEKRVVA 302
                 45789**************9999877777.44466655555....44343333324.555555555...222233333333333333333344466666 PP

      AAA_16 122 llkrllallsr 132
                 +l +l++ l  
  EPA05956.1 303 QLLALMDGLND 313
                 66666655555 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 2e-05
      AAA_16  25 elvllsGesGvGKsslvrellralekd 51 
                    l++G++G+GK+ ++r+l+++  ++
  EPA05956.1 488 KGALIYGPPGCGKTLIARALATETGAN 514
                 788*****************9876665 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.045
      AAA_16 122 llkrllallsrderplvlvlDdlqwade.......aslqllaaLlrlles 164
                 +++++++++++ ++p v+++D+l+ +            ++l++Ll++ e 
  EPA05956.1 534 AVREIFRKAKT-SSPCVVIFDELDSLARlkvgeggVGETVLSQLLTEIEE 582
                 57788899999.999*********76665556665555556777666555 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 4
      AAA_16  30 sGesGvGKsslvrellralekd...ggif..lrgkcd 61 
                 +Ge GvG + l + l + +e+    ++++  ++ + d
  EPA05956.1 563 VGEGGVGETVLSQLLTE-IEEGtssRVVVigITNRPD 598
                 59999999999877774.4444354455534444444 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0   1.1e-08   3.7e-06       5     103 ..     217     325 ..     214     346 .. 0.82
   2 !   15.3   0.0   4.5e-05     0.015       6      76 ..     491     558 ..     487     593 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 1.1e-08
      AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe.kllelileklkeekktylflDEiqev............pewekalkslvd.. 88 
                 +++ G+  +GKT ++k l++e+     +++ in  +  +k + ++e kl ++++e  k++  +++f+DEi  +            +++   l  l+d  
  EPA05956.1 217 ILLYGPPGCGKTLIAKVLASESE---ANMFSINGPEIMNKYYGETEaKLRDIFKEA-KDNSPSIIFIDEIDAIapkreeaygdveKRVVAQLLALMDgl 311
                 6899***************9998...**********99998887764666666665.56699***********99999999999988888888888853 PP

      AAA_14  89 egknldvivtGSnsk 103
                 + ++++viv G  + 
  EPA05956.1 312 N-DRGNVIVLGATNR 325
                 3.4789999998766 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 4.5e-05
      AAA_14   6 vitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev 76 
                 +i G+  +GKT +++ l+ e      +++ ++  +   k + ++ek  ++i++k+k++   ++++DE   +
  EPA05956.1 491 LIYGPPGCGKTLIARALATETG---ANMILVKGPEILSKWIGESEKAVREIFRKAKTSSPCVVIFDELDSL 558
                 799***************9999...9*********999999988877877777766668999*****9876 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   1.1e-06   0.00038       2      80 ..     217     288 ..     216     335 .. 0.77
   2 !   15.3   0.1   4.3e-05     0.015       3      46 ..     491     528 ..     489     605 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.1e-06
                 EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG--HH CS
       AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEveraese 80 
                 +lL GppG+gK+ +a+ la+  +++++ +++++ +++      +    g+t+ +   + ++a+  +++i+++DE++ + ++
  EPA05956.1 217 ILLYGPPGCGKTLIAKVLASESEANMFSINGPEIMNK------YY---GETEAKLRDIFKEAKdnSPSIIFIDEIDAIAPK 288
                 89*****************************996654......33...455556677777777889999999999987765 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 4.3e-05
                 EEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B- CS
       AAA_5   3 lLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrre 46 
                 l+ GppG+gK+ +a+ la  +++++  v +++      ++ ++ 
  EPA05956.1 491 LIYGPPGCGKTLIARALATETGANMILVKGPE------ILSKWI 528
                 899******************99999998876......444454 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   8.8e-05      0.03       7      58 ..     216     267 ..     211     273 .. 0.72
   2 ?    2.8   0.0      0.39   1.3e+02      83     115 ..     263     307 ..     252     325 .. 0.62
   3 !   13.5   0.0   0.00019     0.067       8      29 ..     490     511 ..     485     523 .. 0.85
   4 ?    5.6   0.0     0.053        18      81     132 ..     534     595 ..     529     600 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8.8e-05
      AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaee...erpevv.fvtlpsstsskdllr 58 
                  ++++G++G+GKT+ ++ l+++ ++     +   ++pe++ +++   + +++d+++
  EPA05956.1 216 GILLYGPPGCGKTLIAKVLASESEAN----MfsiNGPEIMnKYYGETEAKLRDIFK 267
                 589****************9997533....24445666666666666666777666 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.39
      AAA_22  83 eqalrarav..ielliiDEaqhlr..s........eealeeLrsl 115
                 ++ ++++++  ++++ iDE++ +   +        ++++ +L  l
  EPA05956.1 263 RDIFKEAKDnsPSIIFIDEIDAIApkReeaygdveKRVVAQLLAL 307
                 4444444446678*********98753334444444444444444 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 0.00019
      AAA_22   8 lvvtGesGtGKTtllrrlleql 29 
                  +++G++G+GKT+ +r l+ + 
  EPA05956.1 490 ALIYGPPGCGKTLIARALATET 511
                 589**************99875 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.053
      AAA_22  81 aleqalrarav..ielliiDEaqhlr....s.....eealeeL.rsllnlsrkgvqliLvGtpe 132
                 a+++ +r++++  + ++i DE + l           e++l++L  ++   + ++ +++++G ++
  EPA05956.1 534 AVREIFRKAKTssPCVVIFDELDSLArlkvGeggvgETVLSQLlTEIE--EGTSSRVVVIGITN 595
                 455566666667779*********986755156777888888833344..48888888888766 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   4.9e-06    0.0017       1      68 [.     217     275 ..     217     292 .. 0.70
   2 !   15.9   0.0   3.8e-05     0.013       2      44 ..     491     539 ..     490     558 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 4.9e-06
  RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgqevvvidDfgqvkdeenps 68 
                   i+lyGp+g+GK+++ak La++ + ++       + s  +  +++++Y g++     D+ +  ++++ps
    EPA05956.1 217 ILLYGPPGCGKTLIAKVLASESEANM-------F-S-INGPEIMNKYYGETEAKLRDIFKEAKDNSPS 275
                   789**************777666444.......2.2.2566777777777777777777776664444 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 3.8e-05
  RNA_helicase   2 wlyGpsgeGKStlakeLakallkkl.....klkkkdsvys.rnpeddfw 44 
                   ++yGp+g+GK+++a+ La++   ++      ++ ++++    ++  +++
    EPA05956.1 491 LIYGPPGCGKTLIARALATETGANMilvkgPEILSKWIGEsEKAVREIF 539
                   69*****************999887666664444455544344444444 PP

>> CDC48_2  Cell division protein 48 (CDC48), domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       8.8     3e+03      19      28 ..      37      46 ..      36      54 .. 0.83
   2 !   34.8   0.1   3.1e-11   1.1e-08       3      60 ..     111     168 ..     109     172 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 8.8
                E-TTEEEEEC CS
     CDC48_2 19 vtkGdlvvfe 28
                vt+Gd++ ++
  EPA05956.1 37 VTPGDIIEVM 46
                7999999876 PP

  == domain 2  score: 34.8 bits;  conditional E-value: 3.1e-11
                 SCCCCHHHHCCCTTEEE-TTEEEEECCTCCCEEEEEEEECCCCSCEEECTSCCEEEST CS
     CDC48_2   3 dgdemaylkrqFlgrpvtkGdlvvfefkgqeiklvVvstePkgpvgitetTeielgtk 60 
                 d ++ + +k+++ g p+t Gd + ++ +g+ +++++ +t+Pk +v+i+++T  +++ +
  EPA05956.1 111 DKEFTDFVKNRLKGLPITHGDEISVMILGNSMDFKISKTSPKHIVKIDRATTLTISAG 168
                 6777789********************************************9998754 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.2e-05    0.0041      18     118 ..     212     316 ..     204     321 .. 0.68
   2 !    9.0   0.0    0.0035       1.2      23      42 ..     490     509 ..     481     518 .. 0.84
   3 ?    4.9   0.0      0.06        21     103     152 ..     532     583 ..     513     594 .. 0.64

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.2e-05
    ATPase_2  18 epneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekal..........giavpkaeleeilkeksklvfkai 106
                 ep + +++YGp g+GKt + k +++++e      ++ i+  e+ ++++ e+  e + ++ +++a+           i+    + ee + +  k v +++
  EPA05956.1 212 EPHSGILLYGPPGCGKTLIAKVLASESE----ANMFSINGPEIMNKYYGET--EAKLRDIFKEAKdnspsiifidEIDAIAPKREEAYGDVEKRVVAQL 304
                 6778899**********99998888884....579***************9..7777777777776665555555333333333334445555555555 PP

    ATPase_2 107 elllekikkkgk 118
                  +l++ ++++g 
  EPA05956.1 305 LALMDGLNDRGN 316
                 555555555555 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0035
    ATPase_2  23 yfiYGpegsGKtaLlkeiie 42 
                  +iYGp g+GKt + + +++
  EPA05956.1 490 ALIYGPPGCGKTLIARALAT 509
                 58**********98887765 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.06
    ATPase_2 103 fkaielllekikkkgkk...iiiiiDelqklidlgln...gaellvkeLlnliesl 152
                 +ka+ ++++k k         ++i+Del  l  l++      e ++++Ll+ ie+ 
  EPA05956.1 532 EKAVREIFRKAK----TsspCVVIFDELDSLARLKVGeggVGETVLSQLLTEIEEG 583
                 444555555544....44559***********988883333455666666666554 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       9.4   3.2e+03      20      52 ..     149     180 ..     142     182 .. 0.77
   2 !   10.6   0.0   0.00089      0.31      31      54 ..     212     235 ..     189     238 .. 0.77
   3 ?    6.8   0.0     0.013       4.4     127     177 ..     259     309 ..     250     322 .. 0.85
   4 !   11.0   0.0   0.00065      0.22      12      55 ..     467     509 ..     460     517 .. 0.77
   5 ?   -0.8   0.0       2.7   9.3e+02     128     156 ..     533     560 ..     528     592 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 9.4
      AAA_25  20 pprrwlvkgllpagelallaGapgtGKttlald 52 
                 ++++++vk   +a +l++ aG +g  K+ ++++
  EPA05956.1 149 TSPKHIVKID-RATTLTISAGETGERKSRVTYE 180
                 5666777755.37899***********998875 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00089
      AAA_25  31 pagelallaGapgtGKttlaldla 54 
                   ++ +ll+G+pg+GKt +a  la
  EPA05956.1 212 EPHSGILLYGPPGCGKTLIAKVLA 235
                 567889*************98887 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.013
      AAA_25 127 tadvdaleaaieevegvrlvviDplsralggdensnsdv.galvealeriar 177
                 +a+++++ +++++ + +  + iD ++++ +  e++  dv +++v++l  + +
  EPA05956.1 259 EAKLRDIFKEAKD-NSPSIIFIDEIDAIAPKREEAYGDVeKRVVAQLLALMD 309
                 5677889999999.88**********************99999999877654 PP

  == domain 4  score: 11.0 bits;  conditional E-value: 0.00065
      AAA_25  12 vadlaapppprrwlvkgllpagelallaGapgtGKttlaldlal 55 
                 ++ + a  +p +   +g++p +  al++G+pg+GKt +a  la 
  EPA05956.1 467 DNLIVAMKEPTKFTKMGIRPPK-GALIYGPPGCGKTLIARALAT 509
                 4446667777888888887755.4799************99986 PP

  == domain 5  score: -0.8 bits;  conditional E-value: 2.7
      AAA_25 128 advdaleaaieevegvrlvviDplsralg 156
                  +v+++ ++++    + +v++D l+++ +
  EPA05956.1 533 KAVREIFRKAKT-SSPCVVIFDELDSLAR 560
                 578899999999.7799*****9998876 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   3.1e-05     0.011       4      68 ..     207     269 ..     206     319 .. 0.77
   2 !   13.2   0.2   0.00027     0.094       7      68 ..     483     542 ..     478     697 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.1e-05
                 EEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS- CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran   4 vslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqep 68 
                 v l +++ + + + G+ G+GK+ ++k+la +++ ++ +i  +g ++ ++   +++++++ +++e+
  EPA05956.1 207 VRLGVEPHSGILLYGPPGCGKTLIAKVLASESEANMFSI--NGPEIMNKYYGETEAKLRDIFKEA 269
                 5688999999*********************98876666..777777766777777777666664 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00027
                 EEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS- CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran   7 klkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqep 68 
                  +++ +   i G+ G+GK+ ++++la ++   +  il++g ++ ++ + +++k ++ ++ ++
  EPA05956.1 483 GIRPPKGALIYGPPGCGKTLIARALATETG--ANMILVKGPEILSKWIGESEKAVREIFRKA 542
                 5666677789****************9986..678888999999988888888888777773 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.2e-05    0.0041       2      80 ..     217     325 ..     217     353 .. 0.79
   2 !   14.5   0.0   8.5e-05     0.029       4      39 ..     492     529 ..     490     562 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.2e-05
      AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt............................dytrvldrlyqilnelarkalsag 70 
                 +ll G+pG+GK+  a+ l+ +    ++ ++ ++++++++g+ + +++                             y +v++r+ ++l +l +    +g
  EPA05956.1 217 ILLYGPPGCGKTLIAKVLASESEanMFSINGPEIMNKYYGETEAKLRdifkeakdnspsiifideidaiapkreeAYGDVEKRVVAQLLALMDGLNDRG 315
                 6789***************999999999*****999999955555555666666666778888888888888887888889998888888887666666 PP

      AAA_33  71 rnvildatnl 80 
                 + ++l atn+
  EPA05956.1 316 NVIVLGATNR 325
                 6667788876 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 8.5e-05
      AAA_33   4 lvGlpGsGKstlaerllkklg..avllssdtlrrrlfg 39 
                 + G+pG+GK+  a+ l+ ++g  ++l+  ++++++  g
  EPA05956.1 492 IYGPPGCGKTLIARALATETGanMILVKGPEILSKWIG 529
                 67*******************99999999997766555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.2e-05    0.0042       1      44 [.     217     278 ..     217     330 .. 0.66
   2 !   13.5   0.0   0.00023     0.079       2      27 ..     491     514 ..     491     556 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.2e-05
      AAA_18   1 IlltGtpGvGKttlakeLskrl.gf.................gvnlrdvakenglllevdpe 44 
                 Ill G+pG+GKt +ak L+++  ++                   +lrd++ke     +   +
  EPA05956.1 217 ILLYGPPGCGKTLIAKVLASESeANmfsingpeimnkyygetEAKLRDIFKEAKDNSPSIIF 278
                 99****************66543334777777777777777766666666665555544444 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00023
      AAA_18   2 lltGtpGvGKttlakeLskrlgfgvn 27 
                 l+ G+pG+GKt +a++L+ ++  g n
  EPA05956.1 491 LIYGPPGCGKTLIARALATET--GAN 514
                 689**************9997..333 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   8.6e-05      0.03      44      74 ..     213     243 ..     207     270 .. 0.78
   2 !   13.3   0.1   0.00017     0.059      48      81 ..     490     523 ..     462     558 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.6e-05
       Rad17  44 kkriLLisGPsGCgkstvvkvLskelgiklr 74 
                 ++  +L+ GP+GCgk+ + kvL+ e   ++ 
  EPA05956.1 213 PHSGILLYGPPGCGKTLIAKVLASESEANMF 243
                 66768999***************99776654 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00017
       Rad17  48 LLisGPsGCgkstvvkvLskelgiklrewlnpvs 81 
                  Li GP+GCgk+ + + L+ e g +++    p  
  EPA05956.1 490 ALIYGPPGCGKTLIARALATETGANMILVKGPEI 523
                 69********************999886666654 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   0.00031      0.11       5      77 ..     217     285 ..     215     332 .. 0.74
   2 !   11.8   0.0   0.00042      0.15       5      82 ..     490     563 ..     487     567 .. 0.68
   3 ?   -1.2   0.0       4.2   1.4e+03      86     122 ..     668     704 ..     657     712 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00031
      AAA_24   5 iliyGpsgiGKTtlakel..gpkplfidtekGlksldadkfpdieswedfldevvelaaeladyktlviDtidel 77 
                 il+yGp+g GKT +ak l  + ++ ++ +++   ++ ++ +   e+ ++++d ++e +++ +  ++++iD id +
  EPA05956.1 217 ILLYGPPGCGKTLIAKVLasESEANMFSING--PEIMNKYYG--ETEAKLRDIFKEAKDNSP--SIIFIDEIDAI 285
                 89**************997744444444444..122222222..255777777777766666..78888888876 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00042
      AAA_24   5 iliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdie.swedfldevvel...aaeladyktlviDtideleelcl 82 
                  liyGp+g GKT +a+ l        te G+ ++   k+p+i  +w+   +++v     +a+ +   ++++D +d l +l++
  EPA05956.1 490 ALIYGPPGCGKTLIARAL-------ATETGA-NMILVKGPEILsKWIGESEKAVREifrKAKTSSPCVVIFDELDSLARLKV 563
                 58*************999.......888888.55555566664445444444443356655555556888888888887765 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 4.2
      AAA_24  86 irqnekaeskedkgdgkGygelaeefrrllkklqelr 122
                 + + ++  +++   +++G +++++ +++ +++ +++ 
  EPA05956.1 668 QAMRNNSAKITNSDFANGMKQVRPSITKEVDQWYNTI 704
                 4444444455667788888888887777777655443 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   5.4e-05     0.018      25      43 ..     217     235 ..     207     249 .. 0.89
   2 !   11.6   0.1   0.00038      0.13      26      43 ..     491     508 ..     485     516 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.4e-05
  Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                   +ll+GppG+GKt++ak l+
    EPA05956.1 217 ILLYGPPGCGKTLIAKVLA 235
                   89*************9886 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00038
  Mg_chelatase  26 llvGppGsGKtmlakrlp 43 
                   l++GppG+GKt++a++l+
    EPA05956.1 491 LIYGPPGCGKTLIARALA 508
                   899************996 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   0.00022     0.077       2      49 ..     217     269 ..     216     302 .. 0.78
   2 !   13.2   0.0   0.00022     0.077       4      32 ..     492     525 ..     490     548 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00022
      AAA_28   2 ivitGgestGKTtlleaLaar...gypvv..pEaareileeklakgedalpwv 49 
                 i + G++++GKT +++ La++   ++  +  pE++ +++ e  ak +d+ +++
  EPA05956.1 217 ILLYGPPGCGKTLIAKVLASEseaNMFSIngPEIMNKYYGETEAKLRDIFKEA 269
                 7899***************6554554444599999999998888888776655 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00022
      AAA_28   4 itGgestGKTtlleaLaar.gypvv....pEaar 32 
                 i G++++GKT +++aLa + g +++    pE+  
  EPA05956.1 492 IYGPPGCGKTLIARALATEtGANMIlvkgPEILS 525
                 89***************65555443125555555 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   0.00031      0.11      21      80 ..     214     284 ..     208     291 .. 0.67
   2 !   10.9   0.0     0.001      0.36      25     110 ..     491     595 ..     488     607 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00031
                      SS-EEEEEETT--HHHHHHCC--TTS-EE--SSTTHHHH-H..........HHHHHHT...TTSEEEEEE-TT CS
  Sigma54_activ_2  21 klpvfltGekGsgkelvArlLhknsgpwleifvverlaklp..........ldlleqa...kggtLylkdiad 80 
                      ++ ++l G++G+gk+l+A++L+++s+   ++f ++ +  ++           d++++a   ++ ++++ +i+ 
       EPA05956.1 214 HSGILLYGPPGCGKTLIAKVLASESEA--NMFSINGPEIMNkyygeteaklRDIFKEAkdnSPSIIFIDEIDA 284
                      67799*****************99998..44444444433333333344446666665444566777777765 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.001
                      EEEEETT--HHHHHHCC--TTS-EE--SSTTHHHH-H.........HHHHHHT...TTSEEEEEE-TT--HHH.......HHHHHHHHHHHT.T CS
  Sigma54_activ_2  25 fltGekGsgkelvArlLhknsgpwleifvverlaklp.........ldlleqa...kggtLylkdiadlskae.......qkeLlellakae.k 98 
                      ++ G++G+gk+l+Ar+L+ + g ++ +++  +  +            +++ +a   ++ + ++ ++++l + +        + L +ll + e +
       EPA05956.1 491 LIYGPPGCGKTLIARALATETGANMILVKGPEILS-KwigesekavREIFRKAktsSPCVVIFDELDSLARLKvgeggvgETVLSQLLTEIEeG 583
                      799***************99998776654322221.1122333333666666544477788888888887766222222224466666665556 PP

                      TT-EEEEEEEE- CS
  Sigma54_activ_2  99 sslrlVstsskd 110
                       s+r+V ++ ++
       EPA05956.1 584 TSSRVVVIGITN 595
                      777777766665 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   0.00037      0.13      44      73 ..     211     240 ..     204     282 .. 0.90
   2 !   11.9   0.0    0.0004      0.14      49      71 ..     489     511 ..     480     559 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00037
   IstB_IS21  44 iekkenivllGpsGvGKshlaialgveavr 73 
                 +e + +i+l Gp+G GK+ +a  l+ e  +
  EPA05956.1 211 VEPHSGILLYGPPGCGKTLIAKVLASESEA 240
                 567899****************99988655 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.0004
   IstB_IS21  49 nivllGpsGvGKshlaialgvea 71 
                 + ++ Gp+G GK+ +a al++e+
  EPA05956.1 489 GALIYGPPGCGKTLIARALATET 511
                 6789***************9875 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0027      0.92      52     100 ..     216     262 ..     207     272 .. 0.83
   2 !   14.1   0.0   5.8e-05      0.02      51     106 ..     488     542 ..     468     545 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0027
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
       TIP49  52 avLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkktevlt 100
                 ++Ll Gp+g Gkt +a  ++ e        +++g e+       te+ +
  EPA05956.1 216 GILLYGPPGCGKTLIAKVLASESE--ANMFSINGPEIMNKYYGETEAKL 262
                 79***************9999865..55678999999999888888754 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 5.8e-05
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXX CS
       TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte.vltqalrks 106
                 ++ L+ Gp+g Gkt +a a++ e g+++  + ++g e+ s  +  +e ++ + +rk+
  EPA05956.1 488 KGALIYGPPGCGKTLIARALATETGANM--ILVKGPEILSKWIGESEkAVREIFRKA 542
                 789*********************9765..6789*******9999884677889987 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0031       1.1      23      48 ..     215     240 ..     206     293 .. 0.86
   2 !    8.8   0.0    0.0036       1.3       8      45 ..     473     510 ..     470     519 .. 0.81
   3 ?    2.1   0.0       0.4   1.4e+02      25      65 ..     560     600 ..     530     606 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0031
                      S-EEEECSTTSSHHHHHHHHHHHSTT CS
  Sigma54_activat  23 lsvlitGesGtGKellaraiheaskr 48 
                      + +l+ G  G+GK+l+a+ + ++s+ 
       EPA05956.1 215 SGILLYGPPGCGKTLIAKVLASESEA 240
                      679****************9887763 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0036
                      HHHHHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHH CS
  Sigma54_activat   8 lkelleqikkvaktdlsvlitGesGtGKellaraihea 45 
                      +ke ++ +k+ ++ +   li G  G+GK+l+ara+ ++
       EPA05956.1 473 MKEPTKFTKMGIRPPKGALIYGPPGCGKTLIARALATE 510
                      666666677777778889***************98764 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.4
                      EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTC CS
  Sigma54_activat  25 vlitGesGtGKellaraiheaskrkekpfvavncaaipeel 65 
                       l +Ge G+G ++l++++ e ++ +++++v + +++ p+ l
       EPA05956.1 560 RLKVGEGGVGETVLSQLLTEIEEGTSSRVVVIGITNRPDVL 600
                      5668***************9999999999988887766655 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   0.00043      0.15      25      63 ..     206     244 ..     202     295 .. 0.84
   2 !    7.5   0.0    0.0077       2.7      27      57 ..     481     511 ..     467     519 .. 0.80
   3 ?   -1.7   0.0       5.3   1.8e+03      37      55 ..     561     579 ..     558     596 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00043
       AAA_7  25 llelllknkkpvllvGptGtGKtviikdllkkldkekyl 63 
                 +++l ++ +  +ll+Gp G+GKt+i+k l ++ + + ++
  EPA05956.1 206 FVRLGVEPHSGILLYGPPGCGKTLIAKVLASESEANMFS 244
                 66777888999***************9988887755554 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0077
       AAA_7  27 elllknkkpvllvGptGtGKtviikdllkkl 57 
                 ++ ++  k  l++Gp G+GKt+i++ l ++ 
  EPA05956.1 481 KMGIRPPKGALIYGPPGCGKTLIARALATET 511
                 5566667889*************99977665 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 5.3
       AAA_7  37 llvGptGtGKtviikdllk 55 
                 l vG+ G+G tv+ + l++
  EPA05956.1 561 LKVGEGGVGETVLSQLLTE 579
                 679********98775544 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0038       1.3      15      38 ..     210     233 ..     189     247 .. 0.84
   2 ?   -0.1   0.0       1.4   4.8e+02     107     152 ..     258     309 ..     233     327 .. 0.66
   3 !    9.7   0.0    0.0014      0.49      13      39 ..     481     507 ..     455     519 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0038
      ATPase  15 GipegrvvlitGepGtGKtifalq 38 
                 G+   + +l++G pG+GKt++a+ 
  EPA05956.1 210 GVEPHSGILLYGPPGCGKTLIAKV 233
                 66667889************9975 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.4
      ATPase 107 lieelaeaikeika...krvviDsitglayeeke...avaReilrqlvrvlk 152
                   ++l+++ ke k    + + iD i+++a + +e   +v ++ + ql+  + 
  EPA05956.1 258 TEAKLRDIFKEAKDnspSIIFIDEIDAIAPKREEaygDVEKRVVAQLLALMD 309
                 4556666666666544488999999999333333111345566666666665 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.0014
      ATPase  13 kgGipegrvvlitGepGtGKtifalqF 39 
                 k Gi   +  li+G pG+GKt++a   
  EPA05956.1 481 KMGIRPPKGALIYGPPGCGKTLIARAL 507
                 5789999999************99765 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0046       1.6      19      51 ..     217     247 ..     212     265 .. 0.87
   2 !   11.3   0.0   0.00043      0.15      14      50 ..     485     519 ..     473     523 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0046
  Zeta_toxin  19 illgGqpGAGKselaellkdelerqgnvvrldp 51 
                 ill G pG+GK+ +a+ l+ e   + n+  +++
  EPA05956.1 217 ILLYGPPGCGKTLIAKVLASES--EANMFSING 247
                 7899****************98..788877775 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00043
  Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrld 50 
                 + Pk  l+ G pG+GK+ +a++l++e+  + n++ ++
  EPA05956.1 485 RPPKGALIYGPPGCGKTLIARALATET--GANMILVK 519
                 5689999*******************9..89998776 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0096       3.3       3      23 ..     217     237 ..     215     242 .. 0.88
   2 !    8.3   0.0     0.006       2.1       4      23 ..     491     510 ..     489     516 .. 0.89
   3 ?    2.6   0.0      0.33   1.1e+02      63     132 ..     529     600 ..     521     617 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0096
                 EEEEC-TTTCHHHHHHHHHHH CS
       NACHT   3 vilqGeaGsGKTtLlqklala 23 
                 ++l G++G+GKT  ++ la++
  EPA05956.1 217 ILLYGPPGCGKTLIAKVLASE 237
                 7899***********999986 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.006
                 EEEC-TTTCHHHHHHHHHHH CS
       NACHT   4 ilqGeaGsGKTtLlqklala 23 
                 ++ G++G+GKT  ++ la++
  EPA05956.1 491 LIYGPPGCGKTLIARALATE 510
                 699**************987 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.33
                 TS--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH............HHHHHCTTTTT--EEEEEEECCCH CS
       NACHT  63 pepaapvsevwavllelperlLlilDglDelvtdlgq...kekqpvrtlLselirkkllpeasllltvrpral 132
                  e++++v+e +   ++     + i+D lD l++        +++ + +lL+e+ ++++ + + + +t rp+ l
  EPA05956.1 529 GESEKAVRE-IFRKAKTSSPCVVIFDELDSLARLKVGeggVGETVLSQLLTEIEEGTSSRVVVIGITNRPDVL 600
                 556666666.3334566677889********984443444455555555555555566666666666666655 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.026         9      20      38 ..     217     235 ..     200     274 .. 0.78
   2 !   12.1   0.0   0.00035      0.12      18      76 ..     488     544 ..     472     714 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.026
      AAA_11  20 tliqGPPGtgKTktivell 38 
                  l+ GPPG+gKT     l 
  EPA05956.1 217 ILLYGPPGCGKTLIAKVLA 235
                 6999********5544444 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00035
      AAA_11  18 eitliqGPPGtgKTktivellsqllsrrkseeeksakpriLv..CapSNaAvDellerllr 76 
                 + +li GPPG+gKT    +l  +       ++   ++p+iL    ++S++Av e+  +  +
  EPA05956.1 488 KGALIYGPPGCGKTLIARALATET----GANMILVKGPEILSkwIGESEKAVREIFRKAKT 544
                 4589**********9999999999....567889999999953379999999999888666 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00099      0.34      19      62 ..     214     257 ..     181     280 .. 0.80
   2 ?    7.1   0.0     0.014         5      22      49 ..     490     519 ..     461     524 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00099
                 TEEEEEEESTTSSHHHHHHHHHHHTT--..----TTTTSEEEEEE. CS
        TsaE  19 gdvilLeGdLGaGKTtlvrglakalgve..evkSPTFtlveeYele 62 
                 ++ ilL+G+ G+GKT +++ la++ + +  +++ P   ++++Y  e
  EPA05956.1 214 HSGILLYGPPGCGKTLIAKVLASESEANmfSINGP--EIMNKYYGE 257
                 3459********************99987888888..688888654 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.014
                 EEEEESTTSSHHHHHHHHHHHTT--..--- CS
        TsaE  22 ilLeGdLGaGKTtlvrglakalgve..evk 49 
                  l++G+ G+GKT ++r+la + g +   vk
  EPA05956.1 490 ALIYGPPGCGKTLIARALATETGANmiLVK 519
                 6889****************9998755565 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0    0.0018      0.61       4      67 ..     217     273 ..     214     301 .. 0.69
   2 !    7.9   0.0    0.0046       1.6       4      25 ..     490     511 ..     487     554 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0018
     DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhpl.vlvlrealakkeekkkkkeafekl 67 
                 +l  G +G GKt+++  l+ e        +a+++s N+p+ +++++ + + k  +  +kea  ++
  EPA05956.1 217 ILLYGPPGCGKTLIAKVLASES-------EANMFSINGPEiMNKYYGETEAKL-RDIFKEAKDNS 273
                 6789***********9999998.......777888888772568888888887.44444443333 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0046
     DUF2075   4 vlVtGvaGtGKtvvllnllael 25 
                  l+ G +G GKt+++ +l++e 
  EPA05956.1 490 ALIYGPPGCGKTLIARALATET 511
                 589**************99987 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.021       7.3       4      71 ..     220     282 ..     217     287 .. 0.60
   2 !   11.6   0.0   0.00049      0.17       2      71 ..     491     555 ..     490     562 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.021
  Viral_helicase1   4 hGvpGcGKStlirkllrts..liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                       G pGcGK+ + + l+++s    +++n p  e+ ++   +++++    ++++  +        i+++DE+
       EPA05956.1 220 YGPPGCGKTLIAKVLASESeaNMFSINGP--EIMNKYYGETEAKLRDIFKEAKDNS-----PSIIFIDEI 282
                      588*****987777776657433433333..5666655555555555555444433.....347888876 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00049
  Viral_helicase1   2 vvhGvpGcGKStlirkllrts...liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                      ++ G pGcGK+ + r l+ +    +il  ++   e+l+++  ++++   + ++++  +  +     ++i+DE 
       EPA05956.1 491 LIYGPPGCGKTLIARALATETganMIL--VKG-PEILSKWIGESEKAVREIFRKAKTSSPC-----VVIFDEL 555
                      57799******9999999888964443..333.67*****977777766666666665543.....8999996 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.018       6.2      22      41 ..     217     236 ..     209     243 .. 0.84
   2 ?    0.6   0.0      0.92   3.2e+02      68     105 ..     413     450 ..     399     458 .. 0.85
   3 !    7.7   0.1    0.0065       2.2      23      42 ..     491     510 ..     478     519 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.018
                 EEEE--TTSSTTHHHHHHHH CS
        PhoH  22 vfaiGpaGtGKtylavalav 41 
                 +   Gp G+GKt++a +la 
  EPA05956.1 217 ILLYGPPGCGKTLIAKVLAS 236
                 5678***********99986 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.92
                 S---------TTTHHHHHHHTTTS-TTCHHHHHHTTSE CS
        PhoH  68 lpgdleekvdpylrplydaLkdllgaekvekllekgki 105
                  p d+ + +++ l  +yda++d++ ++  e ++e+ k+
  EPA05956.1 413 IPSDVLQSMQIKLIDFYDAMHDVIPTAMREFYVERPKV 450
                 68899999****************99988888887665 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0065
                 EEE--TTSSTTHHHHHHHHH CS
        PhoH  23 faiGpaGtGKtylavalave 42 
                  + Gp G+GKt++a ala e
  EPA05956.1 491 LIYGPPGCGKTLIARALATE 510
                 578*************9976 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0065       2.3       1      26 [.     220     245 ..     220     296 .. 0.73
   2 !    8.4   0.0    0.0079       2.7       1      23 [.     493     515 ..     493     553 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0065
                 EE-TTSSHHHHHHHHHHHHTEEEEEH CS
      AAA_17   1 lGgPGsGKgtqceklvekygfthlsa 26 
                 +G+PG+GK+ +++ l+ + +  ++s 
  EPA05956.1 220 YGPPGCGKTLIAKVLASESEANMFSI 245
                 7************9999887777664 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0079
                 EE-TTSSHHHHHHHHHHHHTEEE CS
      AAA_17   1 lGgPGsGKgtqceklvekygfth 23 
                 +G+PG+GK+ +++ l+ + g  +
  EPA05956.1 493 YGPPGCGKTLIARALATETGANM 515
                 7***************9987665 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.048        16      18      64 ..     218     270 ..     215     301 .. 0.74
   2 !    8.2   0.0    0.0051       1.7      18      65 ..     491     544 ..     487     563 .. 0.79
   3 ?    0.8   0.0      0.95   3.3e+02      20      53 ..     563     597 ..     559     609 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.048
                  EEEESTTSSHHHHHHHHHHHSSTS.....S.EEEEEEESEEHHHHHHHHHHCH CS
                  xxxxxxxxxxxxxxxxxxxxxxxx.....x.xxxxxxxxxxxxxxxxxxxxxx RF
  ATP-synt_ab  18 lipgafgvGktvisqslskqsnsd.....d.aiiyvgiGergnevaevleefp 64 
                  l+ g  g+Gkt i++ l+ +s+++        i     Ge + +++++++e +
   EPA05956.1 218 LLYGPPGCGKTLIAKVLASESEANmfsinGpEIMNKYYGETEAKLRDIFKEAK 270
                  678999**************977655554234445556666666666666655 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0051
                  EEEESTTSSHHHHHHHHHHHSSTSSEEEEEE........ESEEHHHHHHHHHHCHH CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxx RF
  ATP-synt_ab  18 lipgafgvGktvisqslskqsnsddaiiyvg........iGergnevaevleefpe 65 
                  li g  g+Gkt i+++l+ ++ ++  +i+v         iGe ++ v+e++++ ++
   EPA05956.1 491 LIYGPPGCGKTLIARALATETGAN--MILVKgpeilskwIGESEKAVREIFRKAKT 544
                  799*****************8666..333333666666699999999999887765 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.95
                  EESTTSSHHHHHHHHHHHSSTSS.EEEEEEESEEH CS
                  xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
  ATP-synt_ab  20 pgafgvGktvisqslskqsnsdd.aiiyvgiGerg 53 
                  +g+ gvG tv+sq l++  + ++  ++++gi +r 
   EPA05956.1 563 VGEGGVGETVLSQLLTEIEEGTSsRVVVIGITNRP 597
                  5889********99998876665588888888875 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0     0.011       3.7       2      29 ..     217     244 ..     216     294 .. 0.86
   2 ?    7.1   0.0     0.013       4.5       3      27 ..     491     515 ..     489     528 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.011
       AAA_3   2 vllegvPGlaktllvkalakaldlefkr 29 
                 +ll g PG +ktl++k la+  ++++  
  EPA05956.1 217 ILLYGPPGCGKTLIAKVLASESEANMFS 244
                 7999***************998887655 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.013
       AAA_3   3 llegvPGlaktllvkalakaldlef 27 
                 l+ g PG +ktl+++ala+  ++++
  EPA05956.1 491 LIYGPPGCGKTLIARALATETGANM 515
                 8999**************9988876 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.58     2e+02     121     176 ..      90     148 ..      78     152 .. 0.73
   2 !    7.6   0.0    0.0067       2.3       6      49 ..     217     260 ..     213     266 .. 0.75
   3 ?    4.5   0.0     0.061        21       7      30 ..     491     514 ..     487     536 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.58
                 -TTSTT---HHHH....HHHHHHHHHHHHHCHHHHHH------T....T--------GGG CS
       SRPRB 121 Kqelflakspkli....kdaLEkElnkiierrskalkeldeeedksavlakkgkdFkfdq 176
                 K  + +aks  li       ++kE +  +++r k l  + ++e  s+ +  ++ dFk ++
  EPA05956.1  90 KASSKIAKSVMLIpvndSVTVDKEFTDFVKNRLKGLPITHGDEI-SVMILGNSMDFKISK 148
                 666667777766633112357999**********9999966555.666778999999875 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0067
                 EEEE-STTSSHHHHHHHHHHSS---B---S.S-EEETTG...GGT CS
       SRPRB   6 vllvGlsdsGKTslftrLttdsvkktvtSq.essaalkvksekgs 49 
                 +ll G+  +GKT++ + L ++s    + S+  +++ +k+ +e + 
  EPA05956.1 217 ILLYGPPGCGKTLIAKVLASESE-ANMFSInGPEIMNKYYGETEA 260
                 89**********99888887765.556677688888888555544 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.061
                 EEE-STTSSHHHHHHHHHHSS--- CS
       SRPRB   7 llvGlsdsGKTslftrLttdsvkk 30 
                 l+ G+  +GKT++   L t++  +
  EPA05956.1 491 LIYGPPGCGKTLIARALATETGAN 514
                 899**************9987655 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0075       2.6     117     136 ..     217     236 ..     210     243 .. 0.88
   2 !    7.6   0.0    0.0052       1.8     118     136 ..     491     509 ..     465     517 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0075
   Parvo_NS1 117 vwfyGpantGktnlaeaIak 136
                 +++yGp+ +Gkt +a+ +a 
  EPA05956.1 217 ILLYGPPGCGKTLIAKVLAS 236
                 89**************9986 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0052
   Parvo_NS1 118 wfyGpantGktnlaeaIak 136
                 ++yGp+ +Gkt +a+a+a+
  EPA05956.1 491 LIYGPPGCGKTLIARALAT 509
                 689**************97 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0078       2.7      23      43 ..     217     237 ..     206     244 .. 0.82
   2 ?    4.6   0.1     0.044        15      25      40 ..     492     507 ..     488     513 .. 0.86
   3 ?    0.2   0.0      0.98   3.4e+02      26      38 ..     563     575 ..     552     585 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0078
                 EEEEESTTSSHHHHHHHHCCS CS
      NB-ARC  23 valvGmgGvGKttlakqilnk 43 
                 + l+G +G+GKt +ak   ++
  EPA05956.1 217 ILLYGPPGCGKTLIAKVLASE 237
                 679*********999877766 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.044
                 EEESTTSSHHHHHHHH CS
      NB-ARC  25 lvGmgGvGKttlakqi 40 
                 ++G +G+GKt +a+  
  EPA05956.1 492 IYGPPGCGKTLIARAL 507
                 89**********9875 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.98
                 EESTTSSHHHHHH CS
      NB-ARC  26 vGmgGvGKttlak 38 
                 vG gGvG t+l++
  EPA05956.1 563 VGEGGVGETVLSQ 575
                 8*********987 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.017       5.8      52     115 ..     213     281 ..     204     327 .. 0.67
   2 ?    6.0   0.0     0.017       5.8      28      81 ..     453     515 ..     444     557 .. 0.64
   3 ?   -1.3   0.0       2.8   9.7e+02     173     226 ..     597     649 ..     576     666 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.017
      DUF815  52 pannvLLwGarGtGKSslvkallneyaeeg..Lrlievekedlkelp.klvellr..erperfilfvDD 115
                 p + +LL+G  G+GK  + k l +e +++   +   e+ ++   e + kl ++ +  + +   i+f+D 
  EPA05956.1 213 PHSGILLYGPPGCGKTLIAKVLASESEANMfsINGPEIMNKYYGETEaKLRDIFKeaKDNSPSIIFIDE 281
                 55679***********99999999988877333334665554433321233333311223446777775 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.017
      DUF815  28 ddLvgidkqkealvent.......eqfleg..lpannvLLwGarGtGKSslvkallneyaeeg 81 
                 +d+ g+d+ k+al++n        ++f +   +p + +L++G  G+GK  + +al +e+ ++ 
  EPA05956.1 453 HDVGGLDNVKKALTDNLivamkepTKFTKMgiRPPKGALIYGPPGCGKTLIARALATETGANM 515
                 5666677777777666511111112333322357889******************99987766 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 2.8
      DUF815 173 seaveeklsLsdRFGlwlgFykldqeeYleiveklakklglelekeeleeeAle 226
                  +++++ l  + R  l+l   ++d +  lei++ l kk+ l+ +  +lee A++
  EPA05956.1 597 PDVLDNSLLRTGRLDLVLYVPPPDDKGRLEIIKILTKKMPLASDV-KLEEIAVA 649
                 577777777788999999999**************9999887764.55555544 PP

>> UFD1  Ubiquitin fusion degradation protein UFD1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   8.1e-05     0.028      78     161 ..      75     157 ..      32     165 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.1e-05
        UFD1  78 menlgleegdlveiesvslpkgkfvklqpqsedfldisdpkavLekaLrnfatLtkgdvieikyndkvyelkvlevkpesavsi 161
                  +n+g + +d+v+i+++s + +k+v l p + +    ++   + +++L+    +t+gd i++    +++++k++++ p++ v+i
  EPA05956.1  75 RKNVGASLNDIVKIRKASSKIAKSVMLIPVNDSVTVDKEFTDFVKNRLKGLP-ITHGDEISVMILGNSMDFKISKTSPKHIVKI 157
                 577888899**********************99999999*********9976.7*************************98887 PP

>> Vps4_C  Vps4 C terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0      0.02       7.1      16      45 ..     410     439 ..     404     456 .. 0.84
   2 ?    5.0   0.0     0.069        24      28      48 ..     676     696 ..     666     698 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.02
      Vps4_C  16 wmdipsdkllePpvtlkDflkalkkarptV 45 
                  ++ipsd l   +++l Df +a++ + pt 
  EPA05956.1 410 TEKIPSDVLQSMQIKLIDFYDAMHDVIPTA 439
                 5789*********************99995 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.069
      Vps4_C  28 pvtlkDflkalkkarptVske 48 
                 ++t +Df + +k++rp+++ke
  EPA05956.1 676 KITNSDFANGMKQVRPSITKE 696
                 7999**************986 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.073        25       1      21 [.     223     243 ..     223     272 .. 0.77
   2 ?    6.5   0.0     0.025       8.5       1      21 [.     496     516 ..     496     544 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.073
                 TTSSHHHHHHHHHHHHTSEEE CS
         SKI   1 mGaGKstvGkllAkklglefi 21 
                 +G+GK+ ++k lA + + +++
  EPA05956.1 223 PGCGKTLIAKVLASESEANMF 243
                 6************98876655 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.025
                 TTSSHHHHHHHHHHHHTSEEE CS
         SKI   1 mGaGKstvGkllAkklglefi 21 
                 +G+GK+ ++++lA + g ++i
  EPA05956.1 496 PGCGKTLIARALATETGANMI 516
                 6*************9987665 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.27        93      18      45 ..     212     239 ..     190     245 .. 0.81
   2 ?    6.2   0.0     0.015       5.2     140     189 ..     241     289 ..     230     301 .. 0.83
   3 ?    0.9   0.0      0.61   2.1e+02     160     185 ..     534     558 ..     463     563 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.27
  KAP_NTPase  18 atpivvgLygkWGsGKssllnkledelk 45 
                 ++ + + Lyg+ G+GK+ + + l +e +
  EPA05956.1 212 EPHSGILLYGPPGCGKTLIAKVLASESE 239
                 5667799**********99888887755 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.015
  KAP_NTPase 140 raaklkeeaplkklqteveelladmektLdalqkrlVvviDdLDrcetee 189
                 +++  +  + + k   e e++l d++k+ ++ +++ +++iD++D + +++
  EPA05956.1 241 NMFSINGPEIMNKYYGETEAKLRDIFKEAKD-NSPSIIFIDEIDAIAPKR 289
                 666677777888888899999********99.************988776 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.61
  KAP_NTPase 160 lladmektLdalqkrlVvviDdLDrc 185
                    +++++ +  +++ Vv+ D+LD++
  EPA05956.1 534 AVREIFRKAKT-SSPCVVIFDELDSL 558
                 44555555555.88999999999997 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.036        13      11      30 ..     215     234 ..     210     246 .. 0.80
   2 ?    5.5   0.2     0.058        20      12      30 ..     489     507 ..     483     525 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.036
      AAA_19  11 kvllvtaGpGtGKTrvlkhi 30 
                 + +l+ ++pG+GKT + k  
  EPA05956.1 215 SGILLYGPPGCGKTLIAKVL 234
                 56899*********987765 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.058
      AAA_19  12 vllvtaGpGtGKTrvlkhi 30 
                   l+ ++pG+GKT + ++ 
  EPA05956.1 489 GALIYGPPGCGKTLIARAL 507
                 5799*********987765 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.067        23       3      27 ..     219     243 ..     217     247 .. 0.87
   2 ?    5.3   0.0     0.041        14       3      26 ..     492     515 ..     491     518 .. 0.90
   3 ?   -0.0   0.2       1.8   6.1e+02      40     109 ..     630     700 ..     624     708 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.067
                     EE-STTSSHHHHHHHHHHHHT-EEE CS
  Cytidylate_kin   3 iDGPagsGKssvaralaeklglkyl 27 
                     + GP g GK  +a+ la++ +++++
      EPA05956.1 219 LYGPPGCGKTLIAKVLASESEANMF 243
                     67****************9998876 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.041
                     EE-STTSSHHHHHHHHHHHHT-EE CS
  Cytidylate_kin   3 iDGPagsGKssvaralaeklglky 26 
                     i GP g GK  +arala++ g+++
      EPA05956.1 492 IYGPPGCGKTLIARALATETGANM 515
                     66*****************99886 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 1.8
                     HHHTT--TT-HHHHHHHHHT--EEEEEEEEEETTEE-TTGGGSHHHHHHHHHHTT.SHHHHHHHHHHHHTT CS
  Cytidylate_kin  40 alrrkvdlldeaalvelakevelsfeaekvllngedveeelrsdevekavSavaa.ipavRailvkklrel 109
                     +l +k++l++  +l+e+a  ++    a+ + l  e   +++r++  + + S +a+ +++vR  ++k + + 
      EPA05956.1 630 ILTKKMPLASDVKLEEIAVATQNYTGADLAALCREAAVQAMRNNSAKITNSDFANgMKQVRPSITKEVDQW 700
                     67888999999999999999999888887777777778889999999999999865889999999887765 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0         1   3.6e+02       5      28 ..     218     241 ..     216     246 .. 0.85
   2 ?    9.4   0.1    0.0018      0.62       5      31 ..     491     517 ..     487     520 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1
         IPT   5 lifGatttGKtaeaiklaketgap 28 
                 l++G+ + GKt  a  la e  a 
  EPA05956.1 218 LLYGPPGCGKTLIAKVLASESEAN 241
                 89*************999987765 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0018
         IPT   5 lifGatttGKtaeaiklaketgapviv 31 
                 li+G+ + GKt  a +la etga +i 
  EPA05956.1 491 LIYGPPGCGKTLIARALATETGANMIL 517
                 9**********************9885 PP

>> Hydin_ADK  Hydin Adenylate kinase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.038        13       2      31 ..     217     246 ..     216     250 .. 0.93
   2 ?    4.1   0.1      0.14        48       3      29 ..     491     517 ..     490     524 .. 0.89
   3 ?   -0.8   0.1       4.6   1.6e+03      43      77 ..     652     685 ..     641     715 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.038
   Hydin_ADK   2 iivhGaPlsGKtatavtLakkYeaAlltiD 31 
                 i++ G+P  GKt +a  La + ea +++i 
  EPA05956.1 217 ILLYGPPGCGKTLIAKVLASESEANMFSIN 246
                 7889**********************9996 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.14
   Hydin_ADK   3 ivhGaPlsGKtatavtLakkYeaAllt 29 
                 ++ G+P  GKt +a +La + +a ++ 
  EPA05956.1 491 LIYGPPGCGKTLIARALATETGANMIL 517
                 589***************999998765 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 4.6
   Hydin_ADK  43 ssaGlrArelCaeaaieqaekekeeaaeeaekkeg 77 
                 + +G     lC eaa++   ++++ + ++++  +g
  EPA05956.1 652 NYTGADLAALCREAAVQAM-RNNSAKITNSDFANG 685
                 4556666679999996554.444444444333333 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0      0.06        21      81     109 ..     207     236 ..     184     247 .. 0.75
   2 ?    5.6   0.0     0.016       5.7      85     108 ..     484     508 ..     473     522 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.06
  Adeno_IVa2  81 lnyglqPviGv.iyGPtGsGksqllrnlis 109
                 + +g +P  G+ +yGP G+Gk+ + + l s
  EPA05956.1 207 VRLGVEPHSGIlLYGPPGCGKTLIAKVLAS 236
                 5678899999846********977776665 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.016
  Adeno_IVa2  85 lqPviG.viyGPtGsGksqllrnli 108
                  +P  G +iyGP G+Gk+ + r+l 
  EPA05956.1 484 IRPPKGaLIYGPPGCGKTLIARALA 508
                 55554437***********999996 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.071        24      22      45 ..     218     241 ..     205     248 .. 0.81
   2 ?    4.5   0.3     0.073        25      21      40 ..     490     509 ..     485     595 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.071
      AAA_30  22 vltGpAGtGKttalkalreaweaa 45 
                 +l Gp+G GKt + k+l+   ea+
  EPA05956.1 218 LLYGPPGCGKTLIAKVLASESEAN 241
                 789***********9998766665 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.073
      AAA_30  21 avltGpAGtGKttalkalre 40 
                 a++ Gp+G GKt + +al+ 
  EPA05956.1 490 ALIYGPPGCGKTLIARALAT 509
                 5789*********9998864 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.56   1.9e+02      23      36 ..     218     231 ..     206     235 .. 0.83
   2 ?    7.8   0.1     0.012       4.3      23      40 ..     491     508 ..     486     512 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.56
      AAA_23  23 lItGpNGaGKTTil 36 
                 l++Gp G+GKT i 
  EPA05956.1 218 LLYGPPGCGKTLIA 231
                 99*********885 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.012
      AAA_23  23 lItGpNGaGKTTildAik 40 
                 lI+Gp G+GKT i +A+ 
  EPA05956.1 491 LIYGPPGCGKTLIARALA 508
                 9**************986 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0      0.16        55       8      91 ..     223     303 ..     217     323 .. 0.57
   2 ?    6.3   0.0     0.028       9.6       8      52 ..     496     540 ..     492     572 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.16
  Cytidylate_kin2   8 yGsgGetigeaLAekLglpfydr...eiieevakelglseeev.eevdersrlssflskllaarvagdtldeklddelfeaqervire 91 
                       G+g++ i++ LA + + ++++    ei+++   e++ +   + +e++++s++  f++++ a   + ++ + + +++       v+ +
       EPA05956.1 223 PGCGKTLIAKVLASESEANMFSIngpEIMNKYYGETEAKLRDIfKEAKDNSPSIIFIDEIDAIAPKREEAYGDVEKR-------VVAQ 303
                      6*************999998887223555555555555544445555556666666666655533333333333333.......3333 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.028
  Cytidylate_kin2   8 yGsgGetigeaLAekLglpfydreiieevakelglseeeveevde 52 
                       G+g++ i++aLA++ g +++  + +e ++k  g se+ v+e+  
       EPA05956.1 496 PGCGKTLIARALATETGANMILVKGPEILSKWIGESEKAVREIFR 540
                      6*****************999999999999999998888855444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (722 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                        52  (0.00290033); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              52  [number of targets reported over threshold]
# CPU time: 0.90u 0.33s 00:00:01.23 Elapsed: 00:00:00.50
# Mc/sec: 4321.89
//
Query:       EPA05957.1  [L=519]
Description: aldehyde dehydrogenase (NAD) family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   2.8e-138  461.3   0.0   3.5e-138  461.0   0.0    1.0  1  Aldedh    Aldehyde dehydrogenase family
  ------ inclusion threshold ------
       0.11   12.8   0.1        6.4    7.1   0.0    3.0  3  DUF4806   Domain of unknown function (DUF4806)


Domain annotation for each model (and alignments):
>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  461.0   0.0  3.9e-142  3.5e-138       6     461 ..      51     514 ..      47     515 .. 0.96

  Alignments for each domain:
  == domain 1  score: 461.0 bits;  conditional E-value: 3.9e-142
                 SSEEEEEETT.TCEEEEEEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHH CS
      Aldedh   6 setievinPa.tgeviakvpaataedvdaavaaAkeafkawaklpaeeRaeiLrkaadlleerkeelaeletletGkplaearaeveeaidvlryyael 103
                 ++t++v +P+ t+ +++++p+ ++++ ++a+ aAk+af +w++++ +eRa+i++++ad + + k ela++++ e+Gk+  ea ++v+e+id++r+y  +
  EPA05957.1  51 ENTFDVRSPSdTRIILGTFPKLDESQTNEAILAAKDAFAKWSHVSYQERAKIFKQTADEFSKIKFELAAWMSFENGKTRIEAINDVDESIDFMRFYSFQ 149
                 368*******889999*********************************************************************************** PP

                 HHHHSE..EEEEE.CTTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHHTT-EEEEEE-TTSHHHHHHHHHHHHHTTS-TTSEEE--SSTCCHHHH CS
      Aldedh 104 aekleg..evlps.segklalvrrePlGvvgaItPWNfPlllaawklapalaaGNtvvlKPaeetplsalllaelfeeaglPkgvlnvvtgsgsevgea 199
                 +e+ eg  + +p  ++++++ ++ +P+Gv+g+I+P+NfP ++a++++  al++GNt vlKPa+ tpls++ +a++++  ++P+g++n+vtg+g  vg++
  EPA05957.1 150 LEENEGfcKQTPHpNPHEKTKSVLKPYGVWGIIAPFNFPSAIAIGMTTGALLTGNTAVLKPASATPLSSYFFANIIKS-KIPSGAINFVTGDGGIVGRT 247
                 ****997666777669*************************************************************9.******************** PP

                 HHH-TTESEEEEES-HHHHHHHHHH.HHCTTSEEEEEE---EEEEE-TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT-- CS
      Aldedh 200 lvehpevdkvsftGstevgrkiaka.aaknlkrvtlElGGknplivledaDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklk 297
                 ++e+ +vd ++ftGs++vg++  k+  +++ k++++E+GGknp+iv+++a+l+ka e+++++afg+ GQ+C+a+sr++vq+++++ef++klve+ k+lk
  EPA05957.1 248 IIESSNVDGIAFTGSQKVGMDSFKKfTETTAKPFIAEMGGKNPVIVTKNANLEKASEGVMRAAFGFGGQKCSACSRVYVQKDVAEEFIKKLVEKSKSLK 346
                 *************************666889******************************************************************** PP

                 BS-TTSTT-SB---SSHHHHHHHHHHHHHHHHTTSEEEE-TTE.SB-SSSTTEE--EEEES-TTTSHHHHS---SSEEEEEEESSHHHHHHHHHSSSEE CS
      Aldedh 298 vgdpldedtdvGPliseaqlekvekyveeakeegaklllGgereeaglekgyfvePtvlanvtpdmriaqeEiFGPVlsvikfkdeeeaieiaNdteyG 396
                 +  p   dt +GP+i+ ++++k+e+ v+ a++ g k++lGge + +++e+gyfv+Pt+++n+++d+++++eE+F P l++ +f+d++eai++aN++eyG
  EPA05957.1 347 IDMPWSADTFLGPVINDESVSKFENAVNLARKYG-KIILGGE-KIKEYEHGYFVQPTIVTNLPKDHKLITEELFLPFLCIDTFDDFDEAIKLANKSEYG 443
                 ********************************88.9999995.5789**************************************************** PP

                 SEEEEE-SBHHHHHHHHHHS-SSEEEESSS...ST--TTT.SEB--CGGGEES..-BSHHHHHHHTEEEEE CS
      Aldedh 397 LaagvftkdleraervaerleaGnvyiNds...ttgaaea.lpfgGvkqSglG..reggkegleeytevkt 461
                 L+ag+f++d +++e++ e+++aG+vy N+    tt+a  + +pf G+k Sg+     gg+++l+++++ +t
  EPA05957.1 444 LTAGIFSEDKKQLEEFFEKIQAGTVYANREssaTTAALVQsQPFVGWKGSGITgkGAGGEYYLQQFLRSQT 514
                 ****************************99776666667779*********86566677*******98775 PP

>> DUF4806  Domain of unknown function (DUF4806)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.65   5.8e+03      27      55 ..      22      50 ..      17      54 .. 0.64
   2 ?    7.1   0.0   0.00071       6.4      51      85 ..     241     275 ..     221     278 .. 0.81
   3 ?    2.0   0.0     0.029   2.6e+02       3      27 ..     354     378 ..     352     417 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.65
     DUF4806 27 kirqqyvnyLrkikgkkadlkkvfdklft 55
                k +++ v+y rk+ gkk     + +++f+
  EPA05957.1 22 KKFENAVEYVRKKFGKKYPCIINGKQVFS 50
                55778899999999964433333355555 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.00071
     DUF4806  51 dklftdealvnynwtGksrkskkKkamkkykiftd 85 
                   ++ ++++ + n++G+  ++++K  m ++k+ft+
  EPA05957.1 241 GGIVGRTIIESSNVDGIAFTGSQKVGMDSFKKFTE 275
                 568889999************************97 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.029
     DUF4806   3 kgfefPvsseeelerLEaavrtdek 27 
                 + f  Pv + e ++++E+av+  +k
  EPA05957.1 354 DTFLGPVINDESVSKFENAVNLARK 378
                 56778***************95444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (519 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       859  (0.0479112); expected 358.6 (0.02)
Passed bias filter:                      693  (0.0386525); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.66u 0.36s 00:00:01.02 Elapsed: 00:00:00.51
# Mc/sec: 3050.05
//
Query:       EPA05958.1  [L=257]
Description: hypothetical protein BG20_I0665 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0056   16.0   0.0     0.0078   15.5   0.0    1.3  1  FAD_binding_3  FAD binding domain
  ------ inclusion threshold ------
       0.05   12.5   0.2      0.068   12.1   0.2    1.1  1  Peptidase_C6   Helper component proteinase
       0.18   10.8   0.0        2.3    7.2   0.0    2.0  2  Lycopene_cycl  Lycopene cyclase protein


Domain annotation for each model (and alignments):
>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.3e-06    0.0078     278     337 ..     118     176 ..      57     187 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.3e-06
                    ESSSEETTEEE-GGGTEEE-STTSHHHHHHHHHHHHHHHHHHHHHTTSS-GGGGHHHHHH CS
  FAD_binding_3 278 aekyrkgrvflaGDAaHihpPtgGqGlNtaiqDavnLawkLaavlkGeAkeelLdtYeee 337
                     +k+ +gr  ++GDAa    Pt++ G+ ++ +   + + ++ + l+ + ++e L+ Y+++
     EPA05958.1 118 IDKFIDGRTVIVGDAAGQAKPTTAGGIYSSGMGGLYAGQAISKYLE-TEDRENLEEYQKR 176
                    68999****************************************9.9999******976 PP

>> Peptidase_C6  Helper component proteinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   1.1e-05     0.068      58     133 ..     170     244 ..     155     248 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.1e-05
  Peptidase_C6  58 lrkakrrgllelGkekdrfiadekvlikLlelseppsldletiseitkiigekddepFkrirvlnkvllegkladv 133
                   l++ ++r  +++Gke ++  + +k+l++L + +    l  ++  eitk i+e++d  F+   +++ + ++g  +++
    EPA05958.1 170 LEEYQKRWTKRFGKEFEKQLFARKILERLDNNTVNK-LFESVTPEITKEISENEDFDFHTGSIVKLLGIKGSIKTA 244
                   6667778889******************98877554.55567778*************987776666577766665 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.022   1.3e+02     127     149 ..      10      32 ..       2      40 .. 0.75
   2 ?    7.2   0.0   0.00038       2.3     244     340 ..     111     208 ..      88     214 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.022
  Lycopene_cycl 127 grkirarlvvdarglaslkkarr 149
                    + +i++++ vdarg+ sl ++ r
     EPA05958.1  10 DGEIKCKIFVDARGVSSLIHKDR 32 
                    448***********888765544 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00038
  Lycopene_cycl 244 Pvtlggslpr.leqkvlaiGaaaglvhPaTGYsvarslaeapllasaiaaalresslsara.watlwprerkrqreffrllglalllkldiegrrr 337
                    P+   g++ + ++ +++ +G aag  +P+T   +  s        +ai+++l+++++++ +  ++ w +   ++ e  +l+ +++l +ld++  ++
     EPA05958.1 111 PIWIKGPIDKfIDGRTVIVGDAAGQAKPTTAGGIYSSGMGGLYAGQAISKYLETEDRENLEeYQKRWTKRFGKEFEK-QLFARKILERLDNNTVNK 205
                    555555555514566999************8777777766666779*******886555440344444443333333.378999999999998888 PP

  Lycopene_cycl 338 fld 340
                    +++
     EPA05958.1 206 LFE 208
                    876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       889  (0.0495845); expected 358.6 (0.02)
Passed bias filter:                      705  (0.0393218); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1855.50
//
Query:       EPA05959.1  [L=196]
Description: DNA-directed RNA polymerase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.4e-15   56.6   0.0    5.7e-15   55.4   0.0    1.6  2  SHS2_Rpb7-N  SHS2 domain found in N terminus of Rpb7p/Rpc25p/
    4.5e-14   52.6   0.0    7.6e-14   51.8   0.0    1.4  1  S1           S1 RNA binding domain
  ------ inclusion threshold ------
      0.012   15.7   0.0      0.024   14.7   0.0    1.6  1  S1_2         S1 domain
       0.03   14.2   0.0      0.069   13.1   0.0    1.6  1  BPL_C        Biotin protein ligase C terminal domain


Domain annotation for each model (and alignments):
>> SHS2_Rpb7-N  SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.4   0.0   1.3e-18   5.7e-15       2      70 .]       9      77 ..       8      77 .. 0.98
   2 ?   -3.0   0.0       2.2     1e+04      21      36 ..     111     125 ..     101     129 .. 0.53

  Alignments for each domain:
  == domain 1  score: 55.4 bits;  conditional E-value: 1.3e-18
                 EEEEE-GGGTTSTHHHHHHHHHHHHHTTBEETTTEEEEEEEEEEEECCEEE-TTTSSEEEEEEEEEEEE CS
  SHS2_Rpb7-N  2 dtvrlePsylgstledallerllekyegkvvpslGvivavldiaeysegkvlggsGsvyvrVtfralvF 70
                 d+vr++Ps +g  l++a++ +l++kye  ++ +lG+i+ +ld + ++ gk + g+G+++++V+f+al F
   EPA05959.1  9 DVVRIPPSLFGTALKKAATNILKDKYESMINAELGYIIMILDAKVDEMGKMIAGDGGTFHKVEFEALTF 77
                 9******************************************************************99 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.2
                  HHHHHHHTTBEETTTE CS
  SHS2_Rpb7-N  21 erllekyegkvvpslG 36 
                   ++ ++y+   v+s G
   EPA05959.1 111 SQVMDDYLKSDVKS-G 125
                  34555555555544.5 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.8   0.0   1.7e-17   7.6e-14       2      68 ..      79     154 ..      78     160 .. 0.93

  Alignments for each domain:
  == domain 1  score: 51.8 bits;  conditional E-value: 1.7e-17
                 STTTCEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSS..........CEESCHHHCEETTEEEEEEEEEEETTTT CS
          S1   2 pekgevveGeVtsvtkgGafVelgngvegfvpaselsrd..........arvedpdevlkvGdevkvkvlkvdkdrr 68 
                 p+  e+v+Ge++++t++GafV++g + ++++++s++++d              +++++lkvG +++++++ v   ++
  EPA05959.1  79 PKLQEIVQGEIVDITDFGAFVRIG-PTDALLHLSQVMDDylksdvksgmILANQSGRTLKVGSTLRARITAVSLGKA 154
                 67789*******************.************************8889******************987766 PP

>> S1_2  S1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   5.4e-06     0.024       4      36 ..      84     115 ..      83     135 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.4e-06
        S1_2   4 intlkvlretdfgyfLqkdesgevlLpkkevpe 36 
                 i++ +++++tdfg+f+  +  ++ lL+ ++v +
  EPA05959.1  84 IVQGEIVDITDFGAFVRIGP-TDALLHLSQVMD 115
                 78899***************.******999964 PP

>> BPL_C  Biotin protein ligase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.5e-05     0.069      12      28 ..      82      98 ..      79      99 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.5e-05
                SCEEEEEEEEE-TTSEE CS
       BPL_C 12 dgkveGiavGIdddGaL 28
                +++v+G +v+I+d+Ga 
  EPA05959.1 82 QEIVQGEIVDITDFGAF 98
                6799***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1327.40
//
Query:       EPA05960.1  [L=278]
Description: putative agmatinase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-59  202.0   0.0    1.6e-59  201.7   0.0    1.0  1  Arginase  Arginase family


Domain annotation for each model (and alignments):
>> Arginase  Arginase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.7   0.0     9e-64   1.6e-59       2     277 ..      15     273 ..      14     275 .. 0.90

  Alignments for each domain:
  == domain 1  score: 201.7 bits;  conditional E-value: 9e-64
                 EEEEEEEE--T.TTSSSGGGGGHHHHHHHHHHTSBTHCHEETTTTESCCSEEEEEEEEE--SSCHHH.HHHHHHHHHHHHHHTTCEEEEEESSGGGHHH CS
    Arginase   2 dvallGvPfda.agsgrpGarfGPraireasarleealeynlelgvleelkivdlgdvavtpvdnee.vleqieeavaeilkagklpivlGGDHsialg 98 
                 +v+++G+P ++ + s r+G++++P+ ir+ s+  ++   yn  +g +++l +  l  ++ +++d  + + +qi e++++i+k+ k+pi +GGDHs++  
  EPA05960.1  15 NVVIIGIPDESqSHSLREGTSEAPERIRKISNLADS---YNR-DG-KKSLGF-PLNGISKKVFDYGDiTRKQIPETFEKIIKDFKVPISIGGDHSLSAT 107
                 699*****99944677**************887776...665.33.344443.344455556677774589**************************** PP

                 HHHHHHHHHSTTEEEEEESSS----SSCTTTBSSSTTSHHHHHHHHTSECGCEEEEEEE-STCSHHHHHHHHTTSEEEEHHHHHHHHHHHHHHHHHHHH CS
    Arginase  99 ilralaekygkplgvihfDAHaDlrtpetegsgnshGtpfrraaeegllkpkklvqiGirsvdneeyelakelgirvitmreidelglkavveeilerv 197
                 i++ +++  g +l+++ fDAH D+ t+     +n  G++f  ++  ++++ k+++qiGir++++ee++ +k+ +i vi+  +i e+g+ ++ e+i++ +
  EPA05960.1 108 IIKQFSKT-G-KLSLVYFDAHPDFITSI----KNYYGSVFGDVI--EVIDVKTSMQIGIRTPEKEEMDNLKKFQILVISPFDIAEKGIVKISEQIMSTL 198
                 ******97.6.6*************976....79**********..89*************************************************** PP

                 TCTTSEEEEEEEGGGBBTTTSTSSSS-BSS-B-HHHHHHHHHHHHCHSEEEEEEEE-B-GGGSSTTTHHHHHHHHHHHHH CS
    Arginase 198 gaeedpvylSfDiDvlDpavaPGtGtpepgGltlrellallrelaeklnlvgaDvvEvnPaldteaeqtarlaarlvrel 277
                 g   d+vy+SfD+D++Dp+ aPG++ p+p G+++ +++ ll+++a+ + +vg+D+vEv Pa+d ++ +t++la r++ e+
  EPA05960.1 199 G---DNVYVSFDMDCIDPSHAPGVSVPVPFGISSVDAILLLKKIAN-HGIVGMDIVEVCPAYDVKD-RTSHLASRMIGEV 273
                 7...68**************************************99.88***************66.*********9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1742.47
//
Query:       EPA05961.1  [L=204]
Description: putative membrane protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-05   23.8   8.6    5.7e-05   22.5   8.5    1.6  1  UbiA      UbiA prenyltransferase family
  ------ inclusion threshold ------
        8.2    7.2  14.7      0.086   13.6   0.6    3.5  3  PrgI      PrgI family protein


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   8.5   6.3e-09   5.7e-05      55     201 ..      55     197 ..       6     203 .. 0.66

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 6.3e-09
        UbiA  55 pnRPlvsGrispkealifaivllilgllll...alllnpltallgllalllyvvYt.glrlKrrtllgtvvggiafglppllgwaavtgslsllallla 149
                 p+  l+     +++ + +ai +l++ + ++   a+l +pl++ +g++  +++++Y+ +l+ ++++  +  ++   + lp+++g a++++s+s++++ll+
  EPA05961.1  55 PWGDLP-----KRKIVSIAISSLVVVFTIGfyyAFLDSPLLIPIGIAEGFFLFAYNlELFGGKFHN-NSSTIISWGILPVFAGSAIQSNSISIETILLS 147
                 555455.....445555555555555555555348888******************6666666666.666666666677777777799*********** PP

        UbiA 150 lavflltwaialandlrdregDrkagiktlpvvlGrkaarillalllavlll 201
                 ++ +  t+ ++++   r ++  ++ g+    ++  ++  + + + ++a++ l
  EPA05961.1 148 IISASITYLLITT--SRKYKHLKREGVDLDGIKNKERILKLITIGVIAITGL 197
                 *955555555555..9999999999999988888888888764434444333 PP

>> PrgI  PrgI family protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   1.2      0.31   2.8e+03      32      57 ..      18      40 ..       7      46 .. 0.55
   2 ?   13.6   0.6   9.6e-06     0.086      10      79 ..      52     149 ..      46     157 .. 0.75
   3 ?   -1.6   0.6       0.5   4.5e+03      25      40 ..     187     202 ..     182     204 .] 0.58

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.31
        PrgI 32 aiglylllrafleelasvlvillavP 57
                ++g +++l +++   a+ ++++lav 
  EPA05961.1 18 SLGGVFVLDRLV---AIGVIYFLAVG 40
                455666666666...55555555554 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 9.6e-06
        PrgI  10 eekiffgLtlRQliflvlallvaiglylllrafleelasvlvill...............................avPvaalgfykkdglplekylka 77 
                 ++k ++ L +R ++ +++  lv++ ++ + +afl    s+l+i++                               ++Pv+a   ++ + +++e++l+ 
  EPA05961.1  52 KTKPWGDLPKRKIVSIAISSLVVVFTIGFYYAFL---DSPLLIPIgiaegfflfaynlelfggkfhnnsstiiswgILPVFAGSAIQSNSISIETILLS 147
                 899******************9999999999999...78888777556666666666666666666666666666666666666667777777777776 PP

        PrgI  78 ii 79 
                 ii
  EPA05961.1 148 II 149
                 66 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.5
        PrgI  25 lvlallvaiglylllr 40 
                 + +++++  gl+++l+
  EPA05961.1 187 ITIGVIAITGLFFILK 202
                 4455555566666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       739  (0.0412181); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1296.18
//
Query:       EPA05962.1  [L=145]
Description: hypothetical protein BG20_I0677 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      8e-07   29.7   0.0      9e-07   29.5   0.0    1.0  1  Usp              Universal stress protein family
     0.0092   14.4   1.0      0.011   14.2   1.0    1.1  1  MAD              Mitotic checkpoint protein
  ------ inclusion threshold ------
      0.049   12.5   0.1      0.058   12.3   0.1    1.2  1  DUF711           Uncharacterised ACR (DUF711)
      0.068   13.0   1.2      0.088   12.6   1.2    1.2  1  Selenoprotein_S  Selenoprotein S (SelS)


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.0     2e-10     9e-07       1     138 [.       1     140 [.       1     143 [. 0.84

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 2e-10
                 S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH..HHHHHHCTTCEEEEEEEESSHHHHHHH CS
         Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada..akaaaeaggvkvevvveegdpaeeile 97 
                 m+ +I Va+   +++kk ++ ++++ak++++el+++ ++    ++    + ++ ++  ++++e+ +++++  ++ a+ +g+++ +   +  + ae  ++
  EPA05962.1   1 MFNNIAVAIITPTHTKKSFDIGIQMAKKFESELTVIECVYKIQPKFYFFETKSDKKILEKQKEKMKKELEnwEEIALGKGIKIKTKFALTDSIAEWVID 99 
                 899******9999999******************99766665555555555555555555555555545559*************************** PP

                 HHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEE CS
         Usp  98 vaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVl 138
                 +++e++++l+++   ++s ++     +  + + ++a+c  l
  EPA05962.1 100 YVKEHKINLLIMDYPKLSMVEATHYDDIINMIHHKAKCNIL 140
                 *************9999999999999999999999999887 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   1.0   2.4e-06     0.011     226     286 ..      35      94 ..      23     105 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.4e-06
         MAD 226 LkEevedlkkkLereEkareelvkLelekekleqeLksWeklaqdtgLnlrsPealsrkie 286
                 + E v  ++ k + +E   ++ + Le +kek+++eL++We++a  +g+++++  al   i 
  EPA05962.1  35 VIECVYKIQPKFYFFETKSDKKI-LEKQKEKMKKELENWEEIALGKGIKIKTKFALTDSIA 94 
                 56778888999999998877776.9*************************99999888775 PP

>> DUF711  Uncharacterised ACR (DUF711)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   1.3e-05     0.058      27      84 ..      51     108 ..      34     136 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.3e-05
      DUF711  27 eklaekiyekiikkaaklvktveeieeeyGievvtkRisvtpisellaeasaeeavel 84 
                 +k  +ki ek+ +k++k +++ eei   +Gi++ tk   +++i+e++ +  +e++++l
  EPA05962.1  51 TKSDKKILEKQKEKMKKELENWEEIALGKGIKIKTKFALTDSIAEWVIDYVKEHKINL 108
                 467799*****************************************99887777554 PP

>> Selenoprotein_S  Selenoprotein S (SelS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   1.2     2e-05     0.088     105     138 ..      55      88 ..      41     108 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2e-05
  Selenoprotein_S 105 ekkkqleeekRrqkiemWesmkeGksykgkakla 138
                      +k  + + ek ++++e+We    Gk+ k k+k a
       EPA05962.1  55 KKILEKQKEKMKKELENWEEIALGKGIKIKTKFA 88 
                      3445677899*******************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1454  (0.0810977); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1025.98
//
Query:       EPA05963.1  [L=133]
Description: hypothetical protein BG20_I0675 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.012   15.8   0.0      0.014   15.6   0.0    1.3  1  ARD       ARD/ARD' family
      0.089   12.5   0.0       0.14   11.9   0.0    1.3  1  Cupin_2   Cupin domain


Domain annotation for each model (and alignments):
>> ARD  ARD/ARD' family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.0   1.6e-06     0.014      60     136 ..      37     112 ..       3     128 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.6e-06
         ARD  60 eekkdidvevlkestpnfdeklekFfeEhlhedeeirlive.Gt.gyFdvrskdeawirvlvekGDLivlPagiyhrFt 136
                 + + d ++++  +  + +++k+ k+   h h+ +e+ +i++ G+  ++ ++  de++    v++   i++P+g+ h  +
  EPA05963.1  37 KTIPDSNIHAAVHIVDVKNKKISKYSTLHKHNADEVNIILSqGKkLVYEIQLGDETYK---VRSPATIFIPKGVMHKAD 112
                 44444456666667788899*******************95475258**********9...99999**********865 PP

>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.5e-05      0.14      11      57 ..      62     111 ..      51     123 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.5e-05
                 EEEECSSSEEEEEEEEESE.EEEE..ECTEEEEEETTEEEEE-TT-EEEE CS
     Cupin_2  11 apshrHpgedeffyVleGe.gelt..vdgeeveleaGdsvyfpagtpHrf 57 
                 +  h H   +  ++  +G+ ++++  +++e+++++   ++++p+g+ H+ 
  EPA05963.1  62 STLHKHNADEVNIILSQGKkLVYEiqLGDETYKVRSPATIFIPKGVMHKA 111
                 5689999985666666799866653367********************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 848.47
//
Query:       EPA05964.1  [L=301]
Description: putative membrane protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-30  105.4  17.0    2.5e-30  105.4  17.0    2.4  3  DUF389    Domain of unknown function (DUF389)
  ------ inclusion threshold ------
        0.2   11.0  11.3       0.34   10.2   2.3    2.2  2  TssN      Type VI secretion system, TssN


Domain annotation for each model (and alignments):
>> DUF389  Domain of unknown function (DUF389)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0     0.083   7.4e+02      63      93 ..      73     107 ..      21     115 .. 0.56
   2 !  105.4  17.0   2.8e-34   2.5e-30       1     142 []     116     254 ..     116     254 .. 0.94
   3 ?   -1.5   0.1      0.27   2.4e+03      19      47 ..     271     299 ..     260     300 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.083
      DUF389  63 semlsrtepn.....lvdllvAlasGaagalallsg 93 
                 +e +s++ep+      + +++ +a+G+a++  l  +
  EPA05964.1  73 EEYQSIIEPSvkfnrNLLFMIVIAAGVAVV-GLFAN 107
                 455555555544444344444555555543.33444 PP

  == domain 2  score: 105.4 bits;  conditional E-value: 2.8e-34
      DUF389   1 MlisPlmgpilaiafglvigdrkllrrglknlliglllallvgflfglllplkvlgeeelptsemlsrtepnlvdllvAlasGaagalallsgnssslv 99 
                 MlisPl+gpi a++f +++g+++ + +++++ li ll ++ +g+l+++++ l+ + ++   t+e+lsrte++ v l vA+a G+ag +a++s+  + lv
  EPA05964.1 116 MLISPLLGPISAFSFNTAVGKTDKMLKSFVSGLILLLSVIGTGALLTAIA-LQ-F-TDLPMTNEILSRTEMSPVFLGVAIALGIAGGIAMSSNIPGILV 211
                 ***********************************************544.32.2.345667************************************* PP

      DUF389 100 GvaIaaaLlPPavnaGlglalgewalalgslllllvNivgIvl 142
                 GvaIaaaL+PPa +aG+g+al ++++++++l l++ Ni+g+vl
  EPA05964.1 212 GVAIAAALVPPATVAGIGIALLDFDIFANALTLTAANIIGLVL 254
                 ***************************************9985 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.27
      DUF389  19 igdrkllrrglknlliglllallvgflfg 47 
                  ++ k +++  +++++ + l++l+gfl++
  EPA05964.1 271 FEKEKAQQHMTFTIIAFIGLSVLLGFLLF 299
                 55666666777777777888888888765 PP

>> TssN  Type VI secretion system, TssN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   2.3   3.8e-05      0.34      36     121 ..      88     171 ..      63     196 .. 0.76
   2 ?    6.1   1.9   0.00068       6.1      61     111 ..     243     299 ..     213     301 .] 0.62

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 3.8e-05
        TssN  36 yiLlaglvlalpgllgflknefvpygyillqilylllGilhlylllkkffkelkekkilfeilltlivillglvlfvlvfnllsel 121
                  +L+++++ a ++++g++ n+      i +++++ llG + ++ +++ + k+ k+ k +++ l++l++++   +l + +   + +l
  EPA05964.1  88 NLLFMIVIAAGVAVVGLFANNAS--LVIGAMLISPLLGPISAFSFNTAVGKTDKMLKSFVSGLILLLSVIGTGALLTAIALQFTDL 171
                 47999999999*****9999888..689************************9999966666666655555555555554444444 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.00068
        TssN  61 gyillqilylllGilhlylll....kkffkelkekk.ilfeil.ltlivillglvlf 111
                  + +++i+ l+lG++ ++ +     ++ff++ k ++ ++f+i+ ++ +++llg++lf
  EPA05964.1 243 TLTAANIIGLVLGMMIVFFISgvspRTFFEKEKAQQhMTFTIIaFIGLSVLLGFLLF 299
                 445566777777777777544333345665555555555555425567788888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1273  (0.0710023); expected 358.6 (0.02)
Passed bias filter:                      594  (0.0331307); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.52
# Mc/sec: 1752.81
//
Query:       EPA05965.1  [L=230]
Description: prephenate dehydratase, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.1e-59  198.3   0.1    1.1e-58  198.0   0.1    1.1  1  PDT       Prephenate dehydratase
     0.0019   17.9   0.0     0.0034   17.1   0.0    1.4  1  ACT       ACT domain


Domain annotation for each model (and alignments):
>> PDT  Prephenate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.0   0.1   1.3e-62   1.1e-58       1     182 [.       4     179 ..       4     180 .. 0.97

  Alignments for each domain:
  == domain 1  score: 198.0 bits;  conditional E-value: 1.3e-62
                 EEEES-TTSHHHHHHCCCS.....EEEEES-HHHHHHHHCTTS-SEEEEEEEESSS-B-HHHHHHHHH.SSEEEEEEEEEE---EEEE-TT--TTT--E CS
         PDT   1 vaylGpegtyshqAalkvfkaedvelipvasieevfeavekgeadyavvPiENsteGsVnetlDlLlkesdlkivgEvvlpiehcLlakpktkleeikk 99 
                 v+++G++g+ys+ Aa+++f ++d++++p +++ ev+e+   g+++y ++P+ENs+eGsV e++DlL++ ++l+ +gE++ +iehcL+++    l+ei +
  EPA05965.1   4 VSFQGERGAYSEAAARAFF-NSDIQTVPLPTFAEVLENTTAGKTEYCILPVENSLEGSVGESYDLLYS-TPLNAIGEIYHRIEHCLIGNG-V-LDEIDT 98 
                 78*****************.************************************************.99***************8765.4.6***** PP

                 EEE-HHHHHHTHHHHHH-.TTSEEEE-S-HHHHHHHHHHCT-TTEEEEE-HHHHHHTT-EEEECS-SS-S--EEEEEEEEETT CS
         PDT 100 vyShpqalgQcrkfLeehlpqvervavestaeAakkveassdkdaaaiasevaaelyglkvleeniedkknntTRFlvlakee 182
                 vyShpqalgQcr+f+e+h  +++ v++++ta +++++++ ++k++a+ias+ a e+y++ v++e+i +++nn+TRFl+lak++
  EPA05965.1  99 VYSHPQALGQCRNFIEKH--NMKTVPTYDTAGSVEIIKKVNKKNVACIASKDASEIYKVPVIAEKIANNSNNYTRFLILAKNN 179
                 ******************..***********************************************************9986 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   3.8e-07    0.0034       1      38 [.     188     225 ..     188     230 .] 0.91

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.8e-07
                 EEEEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEEST CS
         ACT   1 tvlrvgvpDrPGlLarvfgaladrgiNidsieqrssed 38 
                 t+++++ + +PG L+r+   + ++++N+++ie+r+++ 
  EPA05965.1 188 TSIIFSIKHEPGSLHRIIENFYNYNVNLTKIESRPTKT 225
                 578999999***************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1442.12
//
Query:       EPA05966.1  [L=59]
Description: hypothetical protein BG20_I2557, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.013   15.6   0.3      0.016   15.3   0.3    1.1  1  Ribosomal_L37e  Ribosomal protein L37e
      0.014   15.3   0.5      0.017   15.1   0.5    1.1  1  Prok-RING_1     Prokaryotic RING finger family 1
       0.19   11.4   8.0        2.9    7.6   8.0    2.1  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
       0.31   11.1   4.7        4.6    7.4   0.5    2.2  2  zf-ACC          Acetyl-coA carboxylase zinc finger domain


Domain annotation for each model (and alignments):
>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.3   3.6e-06     0.016      16      48 ..      15      48 ..      10      53 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.6e-06
  Ribosomal_L37e 16 HilCrrCgkrsyhvqkk.tCascGypsaklrkyn 48
                    +++Cr+Cg +   ++   +C +c++ ++++ + n
      EPA05966.1 15 FTKCRKCGGKVVQMRDAiKCTECAWIDERKLSTN 48
                    799*****99999987648******888876655 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.5   3.7e-06     0.017       5      27 ..      16      38 ..      14      49 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.7e-06
  Prok-RING_1  5 kkCpvCgkelkeedDiVvCpeCg 27
                 +kC  Cg ++ +  D++ C+eC 
   EPA05966.1 16 TKCRKCGGKVVQMRDAIKCTECA 38
                 69********************6 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   8.0   0.00066       2.9       2      23 ..      17      37 ..      17      39 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00066
                    B-SSS--B----SSS----SSS CS
  DNA_RNApol_7kD  2 iCgeCgaevslkkgdpiRCkeC 23
                    +C +Cg +v  + +d+i+C+eC
      EPA05966.1 17 KCRKCGGKVV-QMRDAIKCTEC 37
                    6999**9995.7789******* PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.5     0.001       4.6       1       8 [.      15      22 ..      15      25 .. 0.90
   2 ?    5.7   0.3    0.0036        16       2       9 ..      32      39 ..      32      40 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.001
      zf-ACC  1 WtKCpsCg 8 
                +tKC +Cg
  EPA05966.1 15 FTKCRKCG 22
                89*****9 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0036
      zf-ACC  2 tKCpsCge 9 
                +KC++C +
  EPA05966.1 32 IKCTECAW 39
                8*****86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 356.23
//
Query:       EPA05967.1  [L=41]
Description: hypothetical protein BG20_I2633, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       238  (0.0132746); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 263.80
//
Query:       EPA05968.1  [L=155]
Description: hypothetical protein BG20_I2632 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.016   14.0   0.5       0.12   11.1   0.5    1.9  1  ResB        ResB-like family
      0.086   13.0   0.0       0.12   12.6   0.0    1.2  1  ChapFlgA_N  FlgA N-terminal domain


Domain annotation for each model (and alignments):
>> ResB  ResB-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.5   1.3e-05      0.12     243     314 ..      31     148 ..      25     154 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 1.3e-05
        ResB 243 ktikVNhPlrykgvriYqssfgdggklelklvllk................gksaqelelpgtvslslra.lelane...................... 302
                 +tikVN+ + ++ ++ Yq+s +++ ++++ ++  k                +++a+e++l+ +  ++ ++  +l+n+                      
  EPA05968.1  31 HTIKVNETFAVGEATSYQISANEHAHQHMVITGEKfdiklsspgdglqipkTSHAKEVTLDWVHLKDGKTiINLQNTgsselkvdatlqvttdpilfty 129
                 79******************9555566666655556666555554444443222222333333322222223333333333333344444444555555 PP

        ResB 303 .......elrnvgpavqfk 314
                         +  +g+++ f+
  EPA05968.1 130 hivvitsGMVIIGFSMGFT 148
                 5555555555555555555 PP

>> ChapFlgA_N  FlgA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.3e-05      0.12       5      72 ..      51     117 ..      48     125 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.3e-05
  ChapFlgA_N   5 vedflqqqtaglpgkveikvgnldprlrlpacdeaLevelpsgsrplGrtsvkvrcngpeppwtvyvp 72 
                 +++++ q++   ++k +ik  ++ + l++p  ++a ev+l+  + ++G+t + ++ +g +   +v  +
  EPA05968.1  51 ANEHAHQHMVITGEKFDIKLSSPGDGLQIPKTSHAKEVTLDWVHLKDGKTIINLQNTGSSE-LKVDAT 117
                 89*************************************************9999999886.344333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1055.61
//
Query:       EPA05969.1  [L=341]
Description: eukaryotic-type DNA primase, large subunit [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.3e-27   94.2   0.0      2e-26   93.0   0.0    1.7  1  DNA_primase_lrg  Eukaryotic and archaeal DNA primase, large s
     0.0014   16.6   0.1     0.0017   16.3   0.1    1.1  1  Med5             Mediator complex subunit Med5


Domain annotation for each model (and alignments):
>> DNA_primase_lrg  Eukaryotic and archaeal DNA primase, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.0   0.0   2.2e-30     2e-26       2     195 ..     145     319 ..     144     337 .. 0.85

  Alignments for each domain:
  == domain 1  score: 93.0 bits;  conditional E-value: 2.2e-30
                      EEEEEHHHHH.HHTT..-G.....GS-EETTEEEE-HHHHHHHHHHHHHHHHHH..........HHGGGSSS---HHHHHHHCT--........ CS
  DNA_primase_lrg   2 fykvpfedvl.dlvk..rr.....rvllkkGyaylpkeeleslllekfrkrlekalestkeslpeleeeikederekleellealsesyvaedv 87 
                      f+ +p++d+l   ++  +r     ++ +++G+++l+ +e ++l++++    ++ ++ ++k   p++ + ++e  + kl ++ ++++        
       EPA05969.1 145 FFVIPVSDYLrHSINfhERewkliNRHVENGFVFLTPHETVRLIRKELGTYISSKIINAKTP-PMI-TGFEEPVN-KLISMSKKFT-------- 227
                      67788888883333354337999999*************************99988885544.344.45555555.6888888888........ PP

                      .....TTSSTTGGSHHHHTT--HHHHCCHHHHCCCSS--CHHHHHHHHHHHHCT--CHHHHCCCHCHST..HHHHHH.HTHCHCHHHCC-STT- CS
  DNA_primase_lrg  88 qeeedskisaknidklakesfPpCmrelleglkknghlkhegrlqltlFlkdiglsldeilelwkeaftrteekFdk.eyrynirhnyGkegkr 180
                                  +++++ + +PpC++++++ l+k+++l+h+gr+ l++Fl + g +++ei +l+k+a     +++++  + y+ +h +G +g++
       EPA05969.1 228 ------------TYTVTTGEYPPCIKHAIDVLEKGENLPHSGRFMLATFLLSKGQTVEEIAPLFKNA-----PDYNErVTLYQLNHLAGTSGSG 304
                      ............689999************************************************9.....*****7788************* PP

                      -------HHHHHHS. CS
  DNA_primase_lrg 181 tnyspysCekiltkp 195
                      t ys++sCek++t++
       EPA05969.1 305 THYSCPSCEKLKTQN 319
                      ***********7665 PP

>> Med5  Mediator complex subunit Med5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   1.9e-07    0.0017     124     220 ..     116     211 ..      73     253 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.9e-07
        Med5 124 klvidqlskdlskviipsiLsadvnslanelvvaiakvlqavlklsespiklesvnlreslaiLlsrlskinklLekklsqtldsklelkesksvv.l 220
                   + d+ +k+l+  +i  ++s++++++++  v+ ++++l+++++++e + kl + ++++ + +L     ++ +l++k+l+  ++sk++  ++ +++  
  EPA05969.1 116 ANISDESKKQLAIRVIDDLFSVQIKKQDDFFVIPVSDYLRHSINFHEREWKLINRHVENGFVFLT-PH-ETVRLIRKELGTYISSKIINAKTPPMItG 211
                 45778899999999**************************************9999988876665.44.4559*************998777665542 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2551.31
//
Query:       EPA05970.1  [L=222]
Description: hypothetical protein BG20_I2340, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.4e-11   43.1   1.4      5e-09   36.4   1.4    2.4  1  DNA_primase_S  DNA primase small subunit
  ------ inclusion threshold ------
      0.018   13.0   4.2      0.022   12.6   4.2    1.1  1  PolC_DP2       DNA polymerase II large subunit DP2
       0.21   11.6   9.4        2.3    8.3   9.3    2.4  2  HypA           Hydrogenase/urease nickel incorporation, metal


Domain annotation for each model (and alignments):
>> DNA_primase_S  DNA primase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   1.4   8.4e-13     5e-09      12      80 ..     137     207 ..      94     219 .. 0.90

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 8.4e-13
                    TT--HHHHHHHHHHHHHHHHHHHH-----GG..GEEEEE--SEEEEEEE--TTEEES-HHHHHHHHHH... CS
  DNA_primase_S  12 seatvcekcwkfvsvavkvldellredfgfk..dilwvfsgrrGfHcwvsdkdarpltdeeraaivnylnl 80 
                    ++ + c+ c    ++ v++l e l+edf+ +  +i+++fsg+ GfH++v d +++ l+++er+++++y+ +
     EPA05970.1 137 KKSLPCKNCIGASKNEVSKLSEILIEDFDVQknNIHVYFSGNEGFHVYVYDSQFQQLGSRERSELTDYIMF 207
                    556669999999******************999*********************************98755 PP

>> PolC_DP2  DNA polymerase II large subunit DP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   4.2   3.7e-06     0.022     623     667 ..     104     151 ..      88     176 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.7e-06
    PolC_DP2 623 kCgketlearCeeCgekteeklvCkkceeeveeek...cekcekeaka 667
                 +C k+ + ++C+eC+e  + +++C+kc++++ e+k   c++c   +k+
  EPA05970.1 104 ECRKNHMVSKCSECNEISTDSVKCNKCNSSKLEKKslpCKNCIGASKN 151
                 79**************************97665553667777544333 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.55   3.3e+03      62      78 ..      59      75 ..      39      86 .. 0.71
   2 ?    8.3   9.3   0.00038       2.3      58      98 ..      99     136 ..      91     166 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.55
                EEEEEE--EEEETTTS- CS
        HypA 62 LeieevpvkvrCreCgk 78
                L ++++p  v+C++  +
  EPA05970.1 59 LLMKNIPSDVYCSNACY 75
                44889999999987554 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00038
                 TT-EEEEEEE--EEEETTTS-EEECHHHHHS-TTTSSS-EE CS
        HypA  58 egaeLeieevpvkvrCreCgkefeleekalrCpkCgsadve 98 
                 ++ +Le+++ +++ +C+eC+ e++++  +++C+kC+s+++e
  EPA05970.1  99 KDLNLECRKNHMVSKCSECN-EISTD--SVKCNKCNSSKLE 136
                 66789999999999999999.44444..4689999998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       925  (0.0515924); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1422.35
//
Query:       EPA05971.1  [L=222]
Description: hypothetical protein BG20_I2344, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      4e-11   43.3   0.9    6.3e-09   36.1   0.9    2.4  1  DNA_primase_S  DNA primase small subunit
  ------ inclusion threshold ------
      0.017   13.0   5.4      0.022   12.7   5.4    1.1  1  PolC_DP2       DNA polymerase II large subunit DP2
       0.26   11.7   2.3       0.53   10.7   2.3    1.5  1  DUF3624        Protein of unknown function (DUF3624)
        8.3    6.5  12.1         30    4.7  12.1    2.1  1  HypA           Hydrogenase/urease nickel incorporation, metal


Domain annotation for each model (and alignments):
>> DNA_primase_S  DNA primase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.9   1.4e-12   6.3e-09      12      80 ..     137     207 ..      94     220 .. 0.90

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 1.4e-12
                    TT--HHHHHHHHHHHHHHHHHHHH-----GG..GEEEEE--SEEEEEEE--TTEEES-HHHHHHHHHH... CS
  DNA_primase_S  12 seatvcekcwkfvsvavkvldellredfgfk..dilwvfsgrrGfHcwvsdkdarpltdeeraaivnylnl 80 
                    ++ + c+ c +  ++ v++l e l+ed++ +  +i+++fsg+ GfH++v d +++ l+++er+++++y+ +
     EPA05971.1 137 KKSLPCKNCIDTSKNEVSKLSEILTEDLDVQqnNIHVYFSGNEGFHVYVYDSQFQQLGSRERSELTDYIMF 207
                    5566799***********************************************************98765 PP

>> PolC_DP2  DNA polymerase II large subunit DP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   5.4   4.8e-06     0.022     623     677 ..     104     158 ..      85     180 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.8e-06
    PolC_DP2 623 kCgketlearCeeCgekteeklvCkkceeeveeek...cekcekeakavkkkkidlke 677
                 kC k+ + ++C+eC e   e+++C+kc++++ e+k   c++c  ++k   ++  +l+e
  EPA05971.1 104 KCRKNHTVSKCSECSEVSAESMKCNKCNSSKLEKKslpCKNCIDTSK---NEVSKLSE 158
                 7999999*********************9776555355666654433...33333333 PP

>> DUF3624  Protein of unknown function (DUF3624)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   2.3   0.00012      0.53       1      24 [.     125     148 ..     125     157 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00012
     DUF3624   1 maCkeckesvfkkKlGRCkrCmkq 24 
                 m C++c++s+++kK   Ck+C++ 
  EPA05971.1 125 MKCNKCNSSKLEKKSLPCKNCIDT 148
                 99*******************985 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7  12.1    0.0067        30      57      98 ..      98     136 ..      40     166 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0067
                 TTT-EEEEEEE--EEEETTTS-EEECHHHHHS-TTTSSS-EE CS
        HypA  57 legaeLeieevpvkvrCreCgkefeleekalrCpkCgsadve 98 
                 +++ +L++++ + + +C+eC+ e++ e  +++C+kC+s+++e
  EPA05971.1  98 AKDLNLKCRKNHTVSKCSECS-EVSAE--SMKCNKCNSSKLE 136
                 56778999999*********9.44444..468*****99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1159  (0.0646439); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1442.67
//
Query:       EPA05972.1  [L=150]
Description: hypothetical protein BG20_I2342 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1017.25
//
Query:       EPA05973.1  [L=134]
Description: eukaryotic-type DNA primase, large subunit [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-24   86.3   0.1    3.3e-24   85.7   0.1    1.3  1  DNA_primase_lrg  Eukaryotic and archaeal DNA primase, large s


Domain annotation for each model (and alignments):
>> DNA_primase_lrg  Eukaryotic and archaeal DNA primase, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.7   0.1   1.9e-28   3.3e-24      98     195 ..      18     112 ..       5     130 .. 0.89

  Alignments for each domain:
  == domain 1  score: 85.7 bits;  conditional E-value: 1.9e-28
                      TGG.SHHHHTT--HHHHCCHHHHCCCSS--CHHHHHHHHHHHHCT--CHHHHCCCHCHST..HHHHHH.HTHCHCHHHCC-STT--------HH CS
  DNA_primase_lrg  98 kni.dklakesfPpCmrelleglkknghlkhegrlqltlFlkdiglsldeilelwkeaftrteekFdk.eyrynirhnyGkegkrtnyspysCe 189
                      k   ++++ + +PpC+++++e l+k+++l+h+gr+ l++Fl + g +++ei +l+k+a     +++++  + y+ +h +G +g++t ys++sCe
       EPA05973.1  18 KFAtYTVTTGEYPPCIKHAIEVLEKGENLPHSGRFMLATFLLSKGQTVEEIAPLFKNA-----PDYNErVTLYQLNHLAGTSGSGTHYSCPSCE 106
                      33348899999**********************************************9.....*****7788********************** PP

                      HHHHS. CS
  DNA_primase_lrg 190 kiltkp 195
                      k++t++
       EPA05973.1 107 KLKTQN 112
                      **6665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 939.81
//
Query:       EPA05974.1  [L=357]
Description: ATPase/histidine kinase/DNA gyrase B/HSP90 domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.3e-17   62.3   0.0    1.5e-16   60.8   0.0    1.8  1  HATPase_c     Histidine kinase-, DNA gyrase B-, and HSP90-lik
      8e-09   35.4   0.3      8e-09   35.4   0.3    2.3  2  HisKA         His Kinase A (phospho-acceptor) domain
    8.2e-07   28.9   2.4    1.1e-06   28.5   0.0    2.4  2  HATPase_c_5   GHKL domain
     0.0023   17.9   0.0     0.0057   16.6   0.0    1.6  1  HATPase_c_2   Histidine kinase-like ATPase domain
  ------ inclusion threshold ------
          1    9.7   7.6       0.09   13.0   1.0    2.6  3  GlcNAc-1_reg  Putative GlcNAc-1 phosphotransferase regulatory


Domain annotation for each model (and alignments):
>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.8   0.0   4.3e-20   1.5e-16       2     106 ..     249     345 ..     248     356 .. 0.87

  Alignments for each domain:
  == domain 1  score: 60.8 bits;  conditional E-value: 4.3e-20
                 HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHHHHHHHHHTTTEEEEEEETTT CS
   HATPase_c   2 dekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsivkklvelmgGeiwvesepgr 100
                 d ++L+ ++ nl++N++++  ++g ++++i +s+  ++i  eD+G Gi++  + ++fe++ +     +++ g+GlGl+i+k ++e++gG++++++ p  
  EPA05974.1 249 DDRKLQAVFVNLIKNSLEAIHNQGYVTIKILSSSTGVEIYFEDSGEGISPVVQSRMFEPLFT-----TKQNGSGLGLAICKMIIEQHGGRLEYKNHP-- 340
                 7889**************97799999999997779***********************6666.....699***********************8877.. PP

                 EEEEEE CS
   HATPase_c 101 Gttftf 106
                  + f +
  EPA05974.1 341 -SAFSV 345
                 .33433 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.3      0.54   1.9e+03      18      18 ..      67      67 ..      21     120 .. 0.63
   2 !   35.4   0.3   2.2e-12     8e-09       2      65 ..     145     209 ..     144     211 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.54
                H CS
       HisKA 18 s 18
                s
  EPA05974.1 67 S 67
                2 PP

  == domain 2  score: 35.4 bits;  conditional E-value: 2.2e-12
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHH.HHHHHHHHHHHHHHHHHHHHHHCCHH CS
       HisKA   2 lgrflagvaHELrtPLsailgnaeaLkregklteelke.yletiesearrldhlvedlLdlsrie 65 
                  g++++ +aH++r+PLs i +  ++L  +++l+ + k  + ++i se+  ++h++ed+L++ r+ 
  EPA05974.1 145 IGQLTSKLAHDIRNPLSKINLSHDILCQSQNLNVMDKIkNRNRIDSEITNITHIIEDVLEFVRMS 209
                 589***********************5543444444437**********************9986 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   1.3      0.98   3.5e+03      43      43 ..      66      66 ..      22     118 .. 0.59
   2 !   28.5   0.0   3.1e-10   1.1e-06       3      96 ..     250     345 ..     248     348 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.98
  HATPase_c_5 43 i 43
                 i
   EPA05974.1 66 I 66
                 1 PP

  == domain 2  score: 28.5 bits;  conditional E-value: 3.1e-10
  HATPase_c_5   3 dldlcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg.....ekkkle.sskskkeehGiGlksireivkkykgnlsieaedglF 94 
                  d  l +++ nl+ N++ea +++     ++++++ +++  + i +e s eg     +++ +e   ++k++  G+Gl   + i+++++g l+++++   F
   EPA05974.1 250 DRKLQAVFVNLIKNSLEAIHNQG----YVTIKILSSSTGVEIYFEDSGEGispvvQSRMFEpLFTTKQNGSGLGLAICKMIIEQHGGRLEYKNHPSAF 343
                  667999*************9977....9*********************966654334444444677899*************************999 PP

  HATPase_c_5  95 tl 96 
                  ++
   EPA05974.1 344 SV 345
                  86 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.6e-06    0.0057      41     110 ..     258     328 ..     256     339 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.6e-06
  HATPase_c_2  41 tNavehayleap.egpvevrlesdeealtvevaDsGpgfdpetlpdpteeepkeslkegGrGlalikglvD 110
                  +N ++   +  + +g v++++ s+++ +++ ++DsG+g  p  + +  e+  ++++  +G+Gla+ k++ +
   EPA05974.1 258 VNLIKNSLEAIHnQGYVTIKILSSSTGVEIYFEDSGEGISPVVQSRMFEPLFTTKQNGSGLGLAICKMIIE 328
                  56666666666669************************99999999999999*************999875 PP

>> GlcNAc-1_reg  Putative GlcNAc-1 phosphotransferase regulatory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.2      0.71   2.6e+03      50      73 ..      17      41 ..      12      49 .. 0.73
   2 ?   13.0   1.0   2.5e-05      0.09      38      85 ..      78     125 ..      52     127 .. 0.81
   3 ?   -2.0   0.0       1.3   4.5e+03      25      62 ..     147     181 ..     141     198 .. 0.60

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.71
  GlcNAc-1_reg 50 alldlndfkdldeLlkd.dkknvti 73
                  a + +n  kdl+   k+ + +++ i
    EPA05974.1 17 AQISINALKDLEMAKKQlQENDLRI 41
                  6778899999999988855555555 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 2.5e-05
  GlcNAc-1_reg  38 vkllelylekrvalldlndfkdldeLlkddkknvtidndelrLtaasL 85 
                    k ++l  + +  +++  +++ l+eLlk d +nv   ++el+++ a+L
    EPA05974.1  78 EKNIQLQNDVKSVIVEKSNYRKLNELLKSDLQNVIKKEKELTVKQAFL 125
                   35788888888899999***************************9988 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.3
  GlcNAc-1_reg  25 elkskLeeklaekvkllelylekrvalldlndfkdlde 62 
                   +l skL   +++  + ++l  +    l + ++ + +d+
    EPA05974.1 147 QLTSKLAHDIRNPLSKINLSHD---ILCQSQNLNVMDK 181
                   6777777777777777666443...2344444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1887  (0.105248); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2517.49
//
Query:       EPA05975.1  [L=132]
Description: hypothetical protein BG20_I1489 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-05   24.8  37.4     0.0044   16.9   8.8    3.8  3  STI1             STI1 domain
      5e-05   23.2  24.0    0.00026   20.9  11.3    2.1  2  GerD             Spore germination GerD central core domain
     0.0093   16.0   9.4        0.3   11.1   0.4    2.9  3  PutA_N           Proline utilization A N-terminal domain
  ------ inclusion threshold ------
      0.014   15.6   1.8       0.21   11.8   0.1    2.2  2  Bep_C_terminal   BID domain of Bartonella effector protein (B
      0.015   15.7   1.3      0.021   15.2   0.8    1.4  1  Sulfotransfer_3  Sulfotransferase family
      0.043   13.6  11.3          1    9.2   0.2    3.3  2  XPC-binding      XPC-binding domain
       0.12   12.3   0.0        2.2    8.2   0.0    2.1  2  DUF4934          Domain of unknown function (DUF4934)
       0.15   11.5   3.6       0.18   11.2   3.0    1.4  1  Cupin_4          Cupin superfamily protein
       0.27   11.7   5.0         38    4.8   4.8    2.8  1  EF-hand_3        EF-hand
        4.3    7.5   8.5        5.9    7.1   8.5    1.5  1  HmuY             HmuY protein


Domain annotation for each model (and alignments):
>> STI1  STI1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   8.2     0.002       3.7      25      48 ..      16      40 ..       6      42 .. 0.83
   2 !   16.9   8.8   2.5e-06    0.0044      24      54 ..      40      71 ..      40      72 .. 0.97
   3 !   10.8   6.9    0.0002      0.35      14      42 ..      82     111 ..      77     130 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.002
        STI1 25 akleeiqs.NPqalqqymsDprimt 48
                +++++++  NPqa+  +m+Dp++ +
  EPA05975.1 16 NMFNQMMGqNPQAMTWMMDDPQVRQ 40
                566666655*************987 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 2.5e-06
        STI1 24 vakleeiqsNPqalqqym.sDprimtvlsvLm 54
                ++++ ++++NP+++++ m +Dp+  + +s++m
  EPA05975.1 40 QQMFYQMMQNPNNMMEWMaKDPKNVEQMSKIM 71
                79*****************************9 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.0002
        STI1  14 trellsDPefv.akleeiqsNPqalqqyms 42 
                 ++ +++DP+++ +++  +++NP al q+ms
  EPA05975.1  82 MSTMMNDPDLRlQMIGHMSENPEALKQMMS 111
                 56799****9659*********99999996 PP

>> GerD  Spore germination GerD central core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   6.7    0.0013       2.3      36      72 ..      15      52 ..       5      57 .. 0.80
   2 !   20.9  11.3   1.5e-07   0.00026      23      84 ..      52     117 ..      49     132 .] 0.82

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0013
        GerD 36 ealaksmkkenekllkdLmkDpeYqkml.leilkdpem 72
                +++ + m  +n + +  +m+Dp+ ++++  +++++p+ 
  EPA05975.1 15 QNMFNQMMGQNPQAMTWMMDDPQVRQQMfYQMMQNPNN 52
                67888999***************976652689999974 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 1.5e-07
        GerD  23 kfwkklfkdpkfaealaksmkken...ekllkdLmkDpeYqkmlleil.kdpemekqllellkske 84 
                 ++++ + kdpk +e+++k mk+++    k++ ++m+Dp+ + +++  + ++pe  kq++++l s+ 
  EPA05975.1  52 NMMEWMAKDPKNVEQMSKIMKEDHvfmSKMMSTMMNDPDLRLQMIGHMsENPEALKQMMSMLGSNM 117
                 6778899****************955569999*********9999877368*********998864 PP

>> PutA_N  Proline utilization A N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.6   0.00038      0.69      26      47 ..      22      43 ..       4      47 .. 0.76
   2 ?   -1.1   0.1         1   1.8e+03      31      41 ..      52      62 ..      47      63 .. 0.85
   3 !   11.1   0.4   0.00017       0.3      16      47 ..      65      96 ..      61     111 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00038
      PutA_N 26 rwwddkllewamkdeelkvqlf 47
                +  + ++++w+m d++++ q+f
  EPA05975.1 22 MGQNPQAMTWMMDDPQVRQQMF 43
                4445689**************9 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1
      PutA_N 31 kllewamkdee 41
                 ++ew+ kd++
  EPA05975.1 52 NMMEWMAKDPK 62
                699***99985 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00017
      PutA_N 16 eeerpklfdrrwwddkllewamkdeelkvqlf 47
                e+ ++ +++ + +  k+++ +m+d++l+ q++
  EPA05975.1 65 EQMSKIMKEDHVFMSKMMSTMMNDPDLRLQMI 96
                45555566778899****************86 PP

>> Bep_C_terminal  BID domain of Bartonella effector protein (Bep)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.3      0.05        90      32      56 ..      28      52 ..       5      55 .. 0.80
   2 ?   11.8   0.1   0.00012      0.21      10      58 ..      59     107 ..      54     118 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.05
  Bep_C_terminal 32 aidavlkdpalakellqkiaaepes 56
                    a+  +++dp++++++  ++ ++p+ 
      EPA05975.1 28 AMTWMMDDPQVRQQMFYQMMQNPNN 52
                    5577889999999999999999975 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00012
  Bep_C_terminal  10 kqweeisrlsklVYadpeaafkaidavlkdpalakellqkiaaepesig 58 
                     k  ++++++sk+  +d   ++k+++ +++dp+l+ +++  + ++pe++ 
      EPA05975.1  59 KDPKNVEQMSKIMKEDHVFMSKMMSTMMNDPDLRLQMIGHMSENPEALK 107
                     566899999999999999999999*********************9975 PP

>> Sulfotransfer_3  Sulfotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.8   1.2e-05     0.021      57     121 ..      10      72 ..       2      77 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.2e-05
                      TTHHHHHHHHHHT--HHHHHHHHHHHHHTT-BHHHHHHHHHHHTTTSEEEEEESSGGG-HHHHHH CS
  Sulfotransfer_3  57 dagltqeeaelphledaeepeedlqllraalasvilealarvpsyarwlvdKsPshlfrldllle 121
                      +a  ++++ ++++++ ++ +++ + + +++++++++ ++++ p++   ++ K+P +++++  +++
       EPA05975.1  10 NA--FHNQNMFNQMMGQNPQAMTWMMDDPQVRQQMFYQMMQNPNNMMEWMAKDPKNVEQMSKIMK 72 
                      33..4444567789999999999********************99987888*********99987 PP

>> XPC-binding  XPC-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   4.9    0.0036       6.5      25      56 ..      15      50 ..      10      51 .. 0.80
   2 ?    9.2   0.2   0.00056         1      12      33 ..      94     115 ..      82     127 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0036
  XPC-binding 25 qplLqqlaqsnPqllqlIqqn....qeeFlqlLnep 56
                 q + +q+  +nPq + ++ ++    q+ F+q++++p
   EPA05975.1 15 QNMFNQMMGQNPQAMTWMMDDpqvrQQMFYQMMQNP 50
                 678899999*********776222267899999987 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00056
  XPC-binding  12 qlRqlvqqnPqlLqplLqqlaq 33 
                  q+   + +nP++L++++ +l+ 
   EPA05975.1  94 QMIGHMSENPEALKQMMSMLGS 115
                  66677899*********99986 PP

>> DUF4934  Domain of unknown function (DUF4934)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.087   1.6e+02      46      89 ..      17      62 ..       9      70 .. 0.64
   2 ?    8.2   0.0    0.0012       2.2      46      76 ..      85     114 ..      63     128 .. 0.69

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.087
     DUF4934 46 lfdketGkflasvGhiGedPegysev..agwlndatgllyf.srkpd 89
                +f++  G+  + +  + +dP+  +++  ++++n+ ++++ +  ++p+
  EPA05975.1 17 MFNQMMGQNPQAMTWMMDDPQVRQQMfyQMMQNP-NNMMEWmAKDPK 62
                6778888888888888899998888742333444.444444044444 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0012
     DUF4934  46 lfdketGkflasvGhiGedPegysevagwln 76 
                 +++  + + l+ +Gh+ e+Pe+ ++++++l 
  EPA05975.1  85 MMNDPDLR-LQMIGHMSENPEALKQMMSMLG 114
                 44444444.789***********99977664 PP

>> Cupin_4  Cupin superfamily protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   3.0    0.0001      0.18     226     293 ..      43     113 ..      23     129 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0001
                 HHHHHHH...HHHCTSCHHCTCGTTTGGGTTS-HHHHHHHHHHHHHHHHHHHCS-HHHHCCHHHHHHHHS- CS
     Cupin_4 226 ldklpei...derlrdallravqargeidsdsidalaaqlsellrdpalleeflgqlltsssrekdiaqsl 293
                  ++++++     ++ ++++++v+++ +i ++    +++++s +++dp+l+ ++ g++ +++++ k++++ l
  EPA05975.1  43 FYQMMQNpnnMMEWMAKDPKNVEQMSKIMKEDHVFMSKMMSTMMNDPDLRLQMIGHMSENPEALKQMMSML 113
                 444444443347888999**********999999***************************8888877655 PP

>> EF-hand_3  EF-hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   4.8     0.021        38      18      50 ..      32      65 ..       2     100 .. 0.53

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.021
   EF-hand_3 18 lldqkkl.gllLeellqvprqvgEsaaFggsnve 50
                ++d  ++ +++ ++++q p++++E  a   +nve
  EPA05975.1 32 MMDDPQVrQQMFYQMMQNPNNMMEWMAKDPKNVE 65
                3333333134555555555555555555555555 PP

>> HmuY  HmuY protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   8.5    0.0033       5.9      36     124 ..       4      81 ..       1     130 [. 0.75

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0033
                 SS-EEEE..-S-SSHHHHCSS--.-S--EE-EEEEE-TTCCCTT-EEE...EEEE-TTCCGGE.....S-EEEE--......-EEEEE- CS
        HmuY  36 NggavlaaatdktdidavtselpangeyvdDevsydmsdmvasnvggqiktktdvnpilsswltegskpptyalsnasikknrvfvlkd 124
                 N+  +++a  +++ +++++ ++p+ ++++ D+      ++ +++++++    ++ n+ + +w+   ++p+++   ++ +k+++vf+ k+
  EPA05975.1   4 NSNQSMNAFHNQNMFNQMMGQNPQAMTWMMDD-----PQVRQQMFYQM---MQNPNN-MMEWMA--KDPKNVEQMSKIMKEDHVFMSKM 81 
                 88899995599********99********999.....45555555544...223333.444652..33555555555788888887664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1698  (0.0947069); expected 358.6 (0.02)
Passed bias filter:                      612  (0.0341346); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.60u 0.34s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 774.88
//
Query:       EPA05976.1  [L=70]
Description: hypothetical protein BG20_I1484 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-38  130.1   2.9    2.3e-38  129.9   2.9    1.0  1  NitrOD1   Nitrosopumilus output domain 1


Domain annotation for each model (and alignments):
>> NitrOD1  Nitrosopumilus output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.9   2.9   1.3e-42   2.3e-38       2      66 ..       3      67 ..       2      69 .. 0.98

  Alignments for each domain:
  == domain 1  score: 129.9 bits;  conditional E-value: 1.3e-42
     NitrOD1  2 navkiryklkGdkqyttcvvtriqyenfkilPvvkvceiverdvsisGdeieqinqklveaikke 66
                navkirykl Gdkqyttc+vtr+qyenfkilP++k+cei++rdvsi+ ++i+ +nq lveai+ke
  EPA05976.1  3 NAVKIRYKLEGDKQYTTCIVTRVQYENFKILPIIKECEIIQRDVSITDEQIDVANQSLVEAIRKE 67
                9***************************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 449.12
//
Query:       EPA05977.1  [L=148]
Description: hypothetical protein BG20_I1474, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-42  145.5   5.2    1.7e-42  145.3   5.2    1.0  1  Topoisom_I_N  Eukaryotic DNA topoisomerase I, DNA binding fra
  ------ inclusion threshold ------
       0.16   12.3   5.2        6.9    7.1   0.3    2.9  3  DUF1947       Domain of unknown function (DUF1947)


Domain annotation for each model (and alignments):
>> Topoisom_I_N  Eukaryotic DNA topoisomerase I, DNA binding fragment
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.3   5.2   1.9e-46   1.7e-42       1     145 [.       1     147 [.       1     148 [] 0.98

  Alignments for each domain:
  == domain 1  score: 145.3 bits;  conditional E-value: 1.9e-46
                   ---S-EE----B---------TT--EEETTEEE---HHHHHHHHHHHHTTTSSGGG-HHHHHHHHHHHHHHHHHTT----GGGEE-HHHHHHHHHHH CS
  Topoisom_I_N   1 vkWktLehnGvlfppeYeplpknvklkydgkpvkLspeaEEvatfyaamletdyakkevFqknffkdfkkvlkekekikelekcdFskikeylekek 97 
                   +kWktL+hnG+lfpp+Ye   +++k+k++g++v+++ ++EE+++ +a++++t ya+++vFqknf++df k+l  k k  ++e++dFs+ ++ ++kek
    EPA05977.1   1 MKWKTLQHNGILFPPAYE--AHGIKIKIKGENVDIDLNQEEMIYQWAKKKDTPYAQDKVFQKNFTSDFAKTLPAKFKNISYEDIDFSHAYKIVDKEK 95 
                   69****************..***************************************************************************** PP

                   HHHTT-----HHHH....HHHHHHHHHHHHEEEETTEEEEEE--B----EE- CS
  Topoisom_I_N  98 ekkkaltkeekkkl....keekekleekygyalldgrkekvgnfrvepPgLf 145
                   + ++ +tkeekk+l    k+ +ekl +kyg a++dg++ +v+n++ epPg+f
    EPA05977.1  96 DIREMMTKEEKKALalkrKQLREKLVQKYGKAIMDGKEVDVANYMAEPPGIF 147
                   ************9877778899999**************************9 PP

>> DUF1947  Domain of unknown function (DUF1947)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.3   0.00077       6.9      20      43 ..      20      43 ..      17      59 .. 0.89
   2 ?   -1.9   0.1      0.47   4.3e+03       7      16 ..      94     103 ..      91     112 .. 0.62
   3 ?    6.8   0.3   0.00091       8.1      10      36 ..     113     139 ..     100     143 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00077
                TT---TT--..-EEEE-SS-EEEE CS
     DUF1947 20 kyisislesdkiEieeekkeklYl 43
                 +i+i++++++++i+ +++e +Y 
  EPA05977.1 20 HGIKIKIKGENVDIDLNQEEMIYQ 43
                6899*****99********99995 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.47
                 HHHHHHHHHH CS
     DUF1947   7 kKeakeilek 16 
                 +K+++e++ k
  EPA05977.1  94 EKDIREMMTK 103
                 5666666554 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.00091
                 HHHHHHHHHTTT---TT--..-EEEE- CS
     DUF1947  10 akeileklkekyisislesdkiEieee 36 
                 +k++ ekl +ky ++ +++++++++ +
  EPA05977.1 113 RKQLREKLVQKYGKAIMDGKEVDVANY 139
                 799****************98*99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1447  (0.0807072); expected 358.6 (0.02)
Passed bias filter:                      576  (0.0321267); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 985.07
//
Query:       EPA05978.1  [L=130]
Description: hypothetical protein BG20_I1492, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0061   16.7   0.3        4.3    7.6   0.0    2.1  2  AzlD      Branched-chain amino acid transport protein (AzlD)
     0.0098   15.8   2.2     0.0098   15.8   2.2    1.4  2  DsbD      Cytochrome C biogenesis protein transmembrane regio
  ------ inclusion threshold ------
      0.021   14.5   1.3        5.9    6.7   0.0    3.0  3  DUF3188   Protein of unknown function (DUF3188)
      0.041   14.1   0.6       0.11   12.7   0.1    1.8  2  DUF2304   Uncharacterized conserved protein (DUF2304)
      0.047   13.7   2.1      0.086   12.9   2.1    1.3  1  DUF2892   Protein of unknown function (DUF2892)


Domain annotation for each model (and alignments):
>> AzlD  Branched-chain amino acid transport protein (AzlD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.4    0.0015       5.5      32      79 ..       6      53 ..       3      59 .. 0.77
   2 !    7.6   0.0    0.0012       4.3      35      55 ..     101     121 ..      84     129 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0015
        AzlD 32 lqrllryvPiavLaaliapellaetgklsaslglarllaalvavlval 79
                ++ ++r++P+ ++++l +  +  ++g  +  +++ + ++ +++v+ a+
  EPA05978.1  6 VHGVGRAIPLILMSVLAILGISVTKGLTTKRVKIENATGWMLIVIGAF 53
                6678999***99999999999999999888887777776655555443 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0012
        AzlD  35 llryvPiavLaaliapellae 55 
                  ++yvPi +++++++p ++  
  EPA05978.1 101 PMDYVPIVLFGLVVFPIIWYR 121
                 589**************9965 PP

>> DsbD  Cytochrome C biogenesis protein transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   2.2   2.7e-06    0.0098     162     212 ..       5      55 ..       1      56 [. 0.93
   2 ?   -3.5   0.1       2.2     8e+03     172     178 ..     107     113 ..     101     120 .. 0.56

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.7e-06
        DsbD 162 lvyvlGlaipfllvglllellkkklkslkkyskaveiaggvllvllGvlll 212
                 lv+ +G aip++l+++l+ l   ++k l     ++e a+g +l+++G +l+
  EPA05978.1   5 LVHGVGRAIPLILMSVLAILGISVTKGLTTKRVKIENATGWMLIVIGAFLI 55 
                 7899***************9999************************9887 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.2
        DsbD 172 fllvgll 178
                 ++l+gl+
  EPA05978.1 107 IVLFGLV 113
                 3333332 PP

>> DUF3188  Protein of unknown function (DUF3188)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.2      0.12   4.3e+02       5      15 ..      15      26 ..      12      37 .. 0.72
   2 ?    3.8   0.5     0.014        48      29      40 ..      47      58 ..      42      59 .. 0.70
   3 ?    6.7   0.0    0.0017       5.9      24      47 ..     102     125 ..      93     127 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.12
     DUF3188  5 Lillgllill.y 15
                Lil ++l++l  
  EPA05978.1 15 LILMSVLAILgI 26
                788888888844 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.014
     DUF3188 29 allvGlgLivsg 40
                ++++G++Li+ g
  EPA05978.1 47 LIVIGAFLIING 58
                367777777766 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0017
     DUF3188  24 lqslPallvGlgLivsgavgrgrr 47 
                 + ++P++l Gl++  + ++ + ++
  EPA05978.1 102 MDYVPIVLFGLVVFPIIWYRFHKK 125
                 789*********999888877665 PP

>> DUF2304  Uncharacterized conserved protein (DUF2304)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1     3e-05      0.11       4      44 ..      15      55 ..      12      69 .. 0.88
   2 ?   -0.7   0.0      0.45   1.6e+03      69      80 ..     109     120 ..     104     128 .. 0.44

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3e-05
     DUF2304  4 iiliivsvllllliirlvrkkklkleysllwlllalilivl 44
                +il+ v+++l + + + +  k++k+e++  w+l++++++++
  EPA05978.1 15 LILMSVLAILGISVTKGLTTKRVKIENATGWMLIVIGAFLI 55
                688888888999999********************999876 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.45
     DUF2304  69 llgivfllvilf 80 
                 l+g+v++ +i +
  EPA05978.1 109 LFGLVVFPIIWY 120
                 233333333332 PP

>> DUF2892  Protein of unknown function (DUF2892)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   2.1   2.4e-05     0.086       5      48 ..       6      59 ..       6      60 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.4e-05
     DUF2892  5 vgtldRilrivvGlvllllallglsggw..........gwllglvGavllltgl 48
                v+++ R++ +++ +vl++l++  + g +          gw+l+++Ga+l++ gl
  EPA05978.1  6 VHGVGRAIPLILMSVLAILGISVTKGLTtkrvkienatGWMLIVIGAFLIINGL 59
                677889999***9**********999999*********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       754  (0.0420548); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 925.83
//
Query:       EPA05979.1  [L=92]
Description: hypothetical protein BG20_I1488 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.029   14.4   0.0       0.13   12.3   0.0    1.9  2  YpmT         Uncharacterized YmpT-like
        1.5    8.9   5.7        8.5    6.5   2.2    2.3  2  Insulin_TMD  Insulin receptor trans-membrane segment


Domain annotation for each model (and alignments):
>> YpmT  Uncharacterized YmpT-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.12   1.1e+03      47      53 ..      24      30 ..      10      40 .. 0.68
   2 ?   12.3   0.0   1.5e-05      0.13      28      61 ..      53      87 ..      48      88 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.12
        YpmT 47 simvftl 53
                si v+++
  EPA05979.1 24 SIFVYLF 30
                5666665 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 1.5e-05
        YpmT 28 vaenmDkvYLnigYCaLFL.simvftldmkdekkt 61
                +ae  D   +nig C  F   ++v t+d+k +k+t
  EPA05979.1 53 IAETHDGFAVNIGPCDAFPgEVIVATFDVKSKKQT 87
                7899999********99963699**********98 PP

>> Insulin_TMD  Insulin receptor trans-membrane segment
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   2.2   0.00095       8.5      13      30 ..       6      23 ..       1      32 [. 0.66
   2 ?    3.6   0.1    0.0078        70      31      44 ..      74      87 ..      72      88 .. 0.93

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.00095
  Insulin_TMD 13 nivkIvigPviciillll 30
                 ++ kIvig +i +i+ + 
   EPA05979.1  6 KNNKIVIGVIIGVIMTVS 23
                 5679****9999887443 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.0078
  Insulin_TMD 31 vigavfvvvkKrQt 44
                 vi+a+f v  K+Qt
   EPA05979.1 74 VIVATFDVKSKKQT 87
                 89***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       877  (0.0489152); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 631.82
//
Query:       EPA05980.1  [L=169]
Description: hypothetical protein BG20_I1479 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.11   12.9   0.0       0.18   12.2   0.0    1.3  1  Myb_DNA-bind_4  Myb/SANT-like DNA-binding domain


Domain annotation for each model (and alignments):
>> Myb_DNA-bind_4  Myb/SANT-like DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   9.9e-06      0.18      33      74 ..      47      90 ..      40     110 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.9e-06
                    -HHHHHHHHHHHHHHC----HH..HHHHHHHHHHHHHHCSSSSS CS
  Myb_DNA-bind_4 33 nkklWeevaeamaergykrspe..qCkeKienLkkrYkkekere 74
                    +kk++ +v e++++ +++++p+   C  K+++Lk  Y +++   
      EPA05980.1 47 AKKVFTDVRENVNTLQITVTPScpGCPCKWRSLKVGYIRVHTGH 90
                    5679*****************9889*************999854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 1251.51
//
Query:       EPA05981.1  [L=39]
Description: hypothetical protein BG20_I1485 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-06   28.2   0.0    1.7e-06   28.2   0.0    1.0  1  DUF1059   Protein of unknown function (DUF1059)
  ------ inclusion threshold ------
      0.053   13.8   0.1      0.056   13.8   0.1    1.1  1  MAP       MAP domain


Domain annotation for each model (and alignments):
>> DUF1059  Protein of unknown function (DUF1059)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   1.9e-10   1.7e-06      11      49 ..       1      39 []       1      39 [] 0.96

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 1.9e-10
     DUF1059 11 pdCgfeitaeteeEvlrkvaeHakaaHglteippelvek 49
                ++C++++ a +  ++++kv  H  ++Hg++ ++ +l +k
  EPA05981.1  1 MKCDWSVMAISIRDLMNKVTSHLEKEHGIQALTYDLKKK 39
                89*******************************999886 PP

>> MAP  MAP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   6.2e-06     0.056      25      48 ..       9      32 ..       6      39 .] 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.2e-06
         MAP 25 kisykdlsskvKsvlksdrGitee 48
                 is++dl +kv s l++++Gi   
  EPA05981.1  9 AISIRDLMNKVTSHLEKEHGIQAL 32
                699******************865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.33s 00:00:00.78 Elapsed: 00:00:00.50
# Mc/sec: 233.95
//
Query:       EPA05982.1  [L=74]
Description: glutaredoxin [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-16   59.3   0.2    3.2e-16   59.1   0.2    1.1  1  Thioredoxin_3  Thioredoxin domain
    1.7e-10   41.0   0.0    2.3e-10   40.5   0.0    1.2  1  Glutaredoxin   Glutaredoxin
    0.00021   21.6   0.0    0.00022   21.6   0.0    1.1  1  DUF836         Glutaredoxin-like domain (DUF836)
    0.00035   20.9   0.0    0.00045   20.6   0.0    1.1  1  GST_N_3        Glutathione S-transferase, N-terminal domain
     0.0059   16.3   0.0       0.01   15.5   0.0    1.4  1  KaiB           KaiB domain
  ------ inclusion threshold ------
       0.02   14.9   0.1       0.98    9.4   0.0    2.0  2  DUF1223        Protein of unknown function (DUF1223)
      0.074   13.4   0.0      0.091   13.1   0.0    1.2  1  GST_N          Glutathione S-transferase, N-terminal domain


Domain annotation for each model (and alignments):
>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.1   0.2   1.2e-19   3.2e-16       2      75 ..       3      73 ..       2      74 .] 0.93

  Alignments for each domain:
  == domain 1  score: 59.1 bits;  conditional E-value: 1.2e-19
                   EEEE.ESSSSTTCHHHHHHHHHHCHCCTCECEEECCTTHHHH.HHCT-SSSSEEECTTCEEEESS---CCHHHHHH CS
  Thioredoxin_3  2 eikv.lgpgCakCpklekavkeaaaekgikaevekvtdfeei.ekygVmsvPalvidgkvvvsGkvpseeeirkll 75
                   +i++  +pgC +C     +v+++++e+++++++++vt+ +e  eky +++ P++vidgk++++G vp+++e+ + l
     EPA05982.1  3 KIEIlTTPGCSNCS----VVERMLDELNFSYDIIDVTEKPEYlEKYPIYTAPGVVIDGKLEFTG-VPKKQELVEKL 73
                   89**55999****9....999999************9999999*********************.******98765 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.5   0.0     9e-14   2.3e-10       1      59 [.       4      58 ..       4      59 .. 0.93

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 9e-14
                  EEEEESTSSHHHHHHHHHHHHTTGGEEEEEGCCSHHHHHHHHHHHTSSSSSEEEETTEE CS
  Glutaredoxin  1 vvlftkptCpyCkkakrlLkelgvkfeeidvdkdeeireelkelsgvrtvPqvfidgkh 59
                  +++ t+p+C  C+ + r L+el++++++idv++ +e+ e+     ++ t P v+idgk+
    EPA05982.1  4 IEILTTPGCSNCSVVERMLDELNFSYDIIDVTEKPEYLEKY----PIYTAPGVVIDGKL 58
                  7899*****************************98887777....8899********96 PP

>> DUF836  Glutaredoxin-like domain (DUF836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   8.5e-08   0.00022       1      57 [.       3      56 ..       3      74 .] 0.79

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 8.5e-08
                -EEEEE-TT-HHHHHHHHHHHHHCCCTTEEEEEEETTT-CCCHCCCC.TTTTEEEECT CS
      DUF836  1 kltLyskpgChlCeqakekLkelkleegleleviDIakdeeleakYg.leipvlaleg 57
                k+ ++++pgC+ C  ++  L el+    ++ + iD+++++e  +kY  ++ p ++++g
  EPA05982.1  3 KIEILTTPGCSNCSVVERMLDELN----FSYDIIDVTEKPEYLEKYPiYTAPGVVIDG 56
                6899*****************665....66779********99999537778887777 PP

>> GST_N_3  Glutathione S-transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   1.8e-07   0.00045       4      55 ..       9      57 ..       7      63 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.8e-07
                -TTSHHHHHHHHHHHHHT--EEEE---TTTTHHHHHHH-TT--SSEEETTS- CS
     GST_N_3  4 fpaSpyarrvrlaLnekglpvevvevtpgehdeellaknplgkvPvLeddge 55
                +p++ ++ +v  +L+e++ ++ + +v  +e ++e+l+k+p +++P  ++dg+
  EPA05982.1  9 TPGCSNCSVVERMLDELNFSYDIIDV--TE-KPEYLEKYPIYTAPGVVIDGK 57
                79*********************887..44.478***********9998876 PP

>> KaiB  KaiB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0     4e-06      0.01      21      54 ..      18      51 ..      12      54 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4e-06
                HCCCHCTTTEEEEEEETTTSHCHHCCTCEESCCC CS
        KaiB 21 leeedlgfqyeLqvvdvleqPelaeedrlvatPa 54
                +e+   + +++  ++dv+e+Pe +e++ +   P 
  EPA05982.1 18 VERMLDELNFSYDIIDVTEKPEYLEKYPIYTAPG 51
                5555566778889**************9998885 PP

>> DUF1223  Protein of unknown function (DUF1223)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00038      0.98       2      36 ..       4      37 ..       4      45 .. 0.79
   2 ?    4.9   0.0    0.0093        24      65      88 ..      41      65 ..      35      74 .] 0.78

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00038
                EEEEE-TT-TT-HHHHHHHHHH.HHHTSSEEEEEE CS
     DUF1223  2 vELFtSqGCssCPpAdallselaaedkdvvaLalh 36
                +E+ t  GCs C   +++l el + + d++ ++ +
  EPA05982.1  4 IEILTTPGCSNCSVVERMLDEL-NFSYDIIDVTEK 37
                69999*****************.555577666655 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0093
                TT-S---S.SEEEETTTEEEETT-H CS
     DUF1223 65 lglrsvYT.PqvvvnGreevvgsde 88
                l++  +YT P vv++G+ e++g  +
  EPA05982.1 41 LEKYPIYTaPGVVIDGKLEFTGVPK 65
                567789999*********9999764 PP

>> GST_N  Glutathione S-transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   3.5e-05     0.091       5      62 ..       6      57 ..       2      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.5e-05
                EESSSTSHTHHHHHHHHHHTT-EEEEEEECSTTTCGGCHHHHHHCTTS-SSEEEETTE CS
       GST_N  5 lysirgsprahrirlllaakgveyevvpldfeageekspellklnplgkvPaLedngk 62
                 ++ +g+++  +++ +l++++++y +++++      ++pe+l + p+  +P ++++gk
  EPA05982.1  6 ILTTPGCSNCSVVERMLDELNFSYDIIDVT------EKPEYLEKYPIYTAPGVVIDGK 57
                5677899999999****************9......259***************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.39u 0.29s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 516.60
//
Query:       EPA05983.1  [L=364]
Description: hypothetical protein BG20_I1487 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      0.002   18.7   0.2     0.0071   16.9   0.2    2.0  1  SlyX             SlyX
  ------ inclusion threshold ------
      0.023   15.0   1.6      0.023   15.0   1.6    2.6  3  CLZ              C-terminal leucine zipper domain of cyclic n
       0.11   12.9   0.2       0.11   12.9   0.2    2.2  2  Arm-DNA-bind_5   Arm DNA-binding domain
       0.15   12.5   0.3       0.15   12.5   0.3    2.3  2  RIC3             Resistance to inhibitors of cholinesterase h
       0.22   11.5  17.9       0.42   10.6  17.9    1.4  1  Trypan_PARP      Procyclic acidic repetitive protein (PARP)
       0.22   11.3   0.8       0.53   10.1   0.8    1.6  1  Methyltransf_14  C-methyltransferase C-terminal domain
        6.9    6.7  11.5      0.039   14.0   2.4    1.9  2  Laminin_II       Laminin Domain II
        9.2    5.5  29.3         12    5.0  29.3    1.1  1  BUD22            BUD22


Domain annotation for each model (and alignments):
>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.2   3.2e-06    0.0071      21      56 ..     189     224 ..     177     231 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.2e-06
                 HHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXX CS
        SlyX  21 eLndvvaeqqqqidrlqrqlrllaerlkeleessga 56 
                 + +d+v + qq+id+l+++l+ l ++l++ e   + 
  EPA05983.1 189 TADDTVLQLQQKIDQLEQRLKDLLNKLENGEYFGPV 224
                 5589***********************998876654 PP

>> CLZ  C-terminal leucine zipper domain of cyclic nucleotide-gated channels
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.0         8   1.8e+04      20      34 ..      31      45 ..      28      47 .. 0.74
   2 ?   -7.4   7.5         8   1.8e+04      16      18 ..      83      85 ..      55     112 .. 0.60
   3 ?   15.0   1.6     1e-05     0.023      20      56 ..     181     217 ..     172     220 .. 0.84

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 8
         CLZ 20 akagaeqkeleekve 34
                a+ g++ ++ e+k++
  EPA05983.1 31 AEDGEDGEDDEDKIK 45
                667788888888875 PP

  == domain 2  score: -7.4 bits;  conditional E-value: 8
         CLZ 16 Dee 18
                De+
  EPA05983.1 83 DET 85
                222 PP

  == domain 3  score: 15.0 bits;  conditional E-value: 1e-05
         CLZ  20 akagaeqkeleekverLessLeaLqtrlarLlaeyes 56 
                 + +++ +k++++ v +L++++++L++rl+ Ll+++e+
  EPA05983.1 181 KHENDAKKTADDTVLQLQQKIDQLEQRLKDLLNKLEN 217
                 344488999************************9987 PP

>> Arm-DNA-bind_5  Arm DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.9   3.6         8   1.8e+04      57      57 ..      73      73 ..      43     121 .. 0.58
   2 ?   12.9   0.2   5.1e-05      0.11      40      81 ..     184     226 ..     153     231 .. 0.78

  Alignments for each domain:
  == domain 1  score: -4.9 bits;  conditional E-value: 8
  Arm-DNA-bind_5 57 l 57
                    +
      EPA05983.1 73 T 73
                    1 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 5.1e-05
  Arm-DNA-bind_5  40 wdkkkgkvkerepn.tlelnskirqerekledivrklrqkek.....t 81 
                      d k     ++  +  l+l++ki+q +++l+d+++kl++ e+     t
      EPA05983.1 184 NDAK-----KTADDtVLQLQQKIDQLEQRLKDLLNKLENGEYfgpvtT 226
                     3333.....6666679**********************9888655543 PP

>> RIC3  Resistance to inhibitors of cholinesterase homologue 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.8   8.9         8   1.8e+04      98     137 ..      66     105 ..      39     110 .. 0.51
   2 ?   12.5   0.3   6.5e-05      0.15     101     144 ..     168     212 ..     116     213 .. 0.79

  Alignments for each domain:
  == domain 1  score: -4.8 bits;  conditional E-value: 8
        RIC3  98 kkkeksk.eakakkkakenakkkteteeeLeeLqerLaeTE 137
                 +++++++ e +++++++ +++ +t ++e   e +++L+eTE
  EPA05983.1  66 HDDNEDEtEDETEDETEDETEDET-EDETEDETEDHLNETE 105
                 222222212222222222222222.3445567788888888 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 6.5e-05
        RIC3 101 e.kskeakakkkakenakkkteteeeLeeLqerLaeTEramekil 144
                 + k++++++++ +k++++ k++++  + +Lq+++ + E+ ++ +l
  EPA05983.1 168 SgKNDSQASENIVKHENDAKKTADDTVLQLQQKIDQLEQRLKDLL 212
                 223337777777777777777799***************999987 PP

>> Trypan_PARP  Procyclic acidic repetitive protein (PARP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6  17.9   0.00019      0.42      30     104 ..      37     109 ..      22     118 .. 0.52

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00019
  Trypan_PARP  30 gpedkgltkggkgkekgtkvsdddtngtdpepepepepepepepepepepetepeeepepepepepepepepepe 104
                  g +d+  +k        tk + dd n  + + ++e+e e e e e+e e e e e+e+e+e+e     e+e e e
   EPA05983.1  37 GEDDEDKIKTPDQSTSETKHNTDDKNKNNHD-DNEDETEDETEDETEDETEDETEDETEDETEDH-LNETEIEVE 109
                  3444555666666667788888888776433.344444444444444444444455555555443.223333332 PP

>> Methyltransf_14  C-methyltransferase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.8   0.00024      0.53      13      66 ..     164     217 ..     160     220 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00024
  Methyltransf_14  13 kkeeakkevseavaellaeEkaagldeletyaeFaervekvkeellalllelka 66 
                      +k+++ k+ s+a ++++++E++a+ +  +t  +++++++++ ++l +ll++l++
       EPA05983.1 164 HKDSSGKNDSQASENIVKHENDAKKTADDTVLQLQQKIDQLEQRLKDLLNKLEN 217
                      6677888899999************************************99875 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   1.9       4.4   9.9e+03      43      43 ..      73      73 ..      41     115 .. 0.55
   2 ?   14.0   2.4   1.7e-05     0.039      17      84 ..     152     217 ..     136     220 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 4.4
                X CS
  Laminin_II 43 t 43
                t
  EPA05983.1 73 T 73
                1 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 1.7e-05
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH CS
  Laminin_II  17 eqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleea 84 
                 ++ a+ + n+e  k++  + +++    ++ vk  n a + A + v +L+++++qL+++lk l ++ e+
  EPA05983.1 152 QIRADWDFNTEDHKDSSGKNDSQ--ASENIVKHENDAKKTADDTVLQLQQKIDQLEQRLKDLLNKLEN 217
                 44567778888888888777777..7778999****************************99887776 PP

>> BUD22  BUD22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0  29.3    0.0056        12     148     270 ..      43     185 ..      24     218 .. 0.45

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0056
       BUD22 148 kkkkkkkkkkkkkkeeeeeeesdkeeesedsedeekeeseddeeeeeededdedaeedeedeeaeerelaqydglla............sddeded... 231
                 k k+ +++ +++k++++++++++ ++++++ ede+++e+ed+ e+e+ede+++++e+   +e ++e e+++ +++++            +d +++    
  EPA05983.1  43 KIKTPDQSTSETKHNTDDKNKNNHDDNEDETEDETEDETEDETEDETEDETEDETED-HLNETEIEVEVKNDKAIVKihlngdkyrfvvNDTSESAiia 140
                 222222222222222222233333333333333233344444444444444333333.44455555555555555556776777777765555555899 PP

       BUD22 232 ...................eyneetdeesseesdssdssesasesesessek....kkkkkk 270
                                    +                 +++++s+ +++s+++    k  ++ 
  EPA05983.1 141 aiidktglteeqiradwdfN----------------TEDHKDSSGKNDSQASenivK-HEND 185
                 98866665544444433222................222222222222222211111.1111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2579  (0.143845); expected 358.6 (0.02)
Passed bias filter:                      806  (0.0449551); expected 358.6 (0.02)
Passed Vit filter:                       215  (0.0119917); expected 17.9 (0.001)
Passed Fwd filter:                        73  (0.00407162); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 1.16u 0.37s 00:00:01.52 Elapsed: 00:00:00.54
# Mc/sec: 2024.09
//
Query:       EPA05984.1  [L=51]
Description: hypothetical protein BG20_I1486 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       193  (0.0107647); expected 358.6 (0.02)
Passed bias filter:                      132  (0.00736237); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.29s 00:00:00.65 Elapsed: 00:00:00.45
# Mc/sec: 340.01
//
Query:       EPA05985.1  [L=58]
Description: hypothetical protein BG20_I1483 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 450.62
//
Query:       EPA05986.1  [L=45]
Description: YHS domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-17   63.9   0.6    1.1e-17   63.8   0.6    1.0  1  YHS       YHS domain
    7.7e-05   22.6   0.4    9.5e-05   22.3   0.4    1.2  1  zf-FCS    MYM-type Zinc finger with FCS sequence motif
  ------ inclusion threshold ------
      0.016   14.6   0.1       0.02   14.4   0.1    1.2  1  zf-FLZ    zinc-finger of the FCS-type, C2-C2
      0.046   13.2   0.1       0.05   13.1   0.1    1.0  1  FAP206    Domain of unknown function
        0.1   12.6   1.3       0.77    9.8   1.3    1.9  1  DUF2116   Uncharacterized protein containing a Zn-ribbon (DUF


Domain annotation for each model (and alignments):
>> YHS  YHS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.8   0.6   3.2e-21   1.1e-17       1      47 [.       1      44 [.       1      45 [] 0.93

  Alignments for each domain:
  == domain 1  score: 63.8 bits;  conditional E-value: 3.2e-21
         YHS  1 vtdPvcgmkvdkekaeekseYkGkeYyFcSegCkdkFedePekYata 47
                ++dPvcgm++   ++ e++++kGk+Y FcS++C+++Fe +P++++ +
  EPA05986.1  1 MKDPVCGMDI---QKGEEITHKGKQYKFCSAACRWAFESNPDQFVED 44
                69********...466****************************975 PP

>> zf-FCS  MYM-type Zinc finger with FCS sequence motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.4   2.7e-08   9.5e-05       9      38 ..       6      31 ..       5      34 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 2.7e-08
      zf-FCS  9 CkkyikgkpeftyvlendgvvgqFCStsCl 38
                C+ +i+ ++e    ++++g++++FCS  C+
  EPA05986.1  6 CGMDIQKGEE----ITHKGKQYKFCSAACR 31
                9999*****8....***************8 PP

>> zf-FLZ  zinc-finger of the FCS-type, C2-C2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   5.5e-06      0.02      18      45 ..       5      32 ..       4      39 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.5e-06
      zf-FLZ 18 lCkkkLgegkDiymYrGdkaFCSeeCRq 45
                +C  ++++g++i     +  FCS+ CR+
  EPA05986.1  5 VCGMDIQKGEEITHKGKQYKFCSAACRW 32
                69999******987777789*******8 PP

>> FAP206  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   1.4e-05      0.05     227     253 ..      17      43 ..      13      45 .] 0.94

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.4e-05
      FAP206 227 kykdkyyaFsseeaareFaadpdrfie 253
                  +k+k y F s+ +  +F+++pd+f+e
  EPA05986.1  17 THKGKQYKFCSAACRWAFESNPDQFVE 43 
                 79***********************98 PP

>> DUF2116  Uncharacterized protein containing a Zn-ribbon (DUF2116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   1.3   0.00021      0.77       8      33 ..       5      39 ..       3      44 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00021
     DUF2116  8 vCGkaIplde.........sfCsekCqeeyekkrk 33
                vCG  I ++e         +fCs  C+ ++e++  
  EPA05986.1  5 VCGMDIQKGEeithkgkqyKFCSAACRWAFESNPD 39
                677777666533333333369*********98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.50
# Mc/sec: 268.97
//
Query:       EPA05987.1  [L=835]
Description: DEAD/DEAH box helicase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-33  115.8   0.1    4.9e-33  114.3   0.0    1.8  2  DEAD            DEAD/DEAH box helicase
    1.3e-17   64.1   2.3    2.3e-13   50.5   0.5    3.5  4  Helicase_C      Helicase conserved C-terminal domain
    1.7e-09   38.3   0.1    5.3e-09   36.7   0.1    1.9  1  DUF1998         Domain of unknown function (DUF1998)
  ------ inclusion threshold ------
      0.019   13.7   0.0       0.03   13.0   0.0    1.3  1  SNF2_N          SNF2 family N-terminal domain
       0.12   12.2   2.4       0.31   10.9   2.4    1.7  1  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
        1.3    9.0  13.1       0.29   11.1   4.7    2.9  2  zinc_ribbon_4   zinc-ribbon domain


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.3   0.0   1.7e-36   4.9e-33       2     173 ..     142     310 ..     141     313 .. 0.90
   2 ?   -2.4   0.0       1.1   3.4e+03      43      59 ..     407     423 ..     343     445 .. 0.67

  Alignments for each domain:
  == domain 1  score: 114.3 bits;  conditional E-value: 1.7e-36
                 HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHHHHHHHTTCSE CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        DEAD   2 diQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaardqlskldngvdi 100
                 + Q+eai+++l g++++++a+T+sGKT+aflipv+q++ + +++ g  al+v Pt++L ++++ ++ k+ ++i+++v+++ g++++ + ++ l+n +++
  EPA05987.1 142 KFQQEAIEEVLFGENIVIEAPTASGKTEAFLIPVIQKIKK-ESTGGVFALFVYPTKALSRDQYPKILKLAEKIGISVQVFDGDTEQIERREILENPPQV 239
                 68************************************76.999*********************************9887777777777777788*** PP

                 EEEEHHHHHHHH.HCTSSH..CTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEEEEEESSBSHHH CS
                 xxxxxxxxxxxx.xxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        DEAD 101 vvgtpgrlddll.stgkln..lsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrqvivlSATlpkdv 173
                 ++++ + l+ +l ++ k++  ls+vr+lV+DEa+ ++   f+  ++ i+++l++i++  k   q+i+ SATl+ d 
  EPA05987.1 240 LITNFDVLHYHLwHQTKFSslLSSVRILVVDEAHVYSGI-FGSNVHYIVKRLKRICS-NK--IQFIAASATLE-DA 310
                 **********99766777779*****************9.************87755.46..56********8.54 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.1
                 TTSTS-EEEEEESSHHH CS
                 xxxxxxxxxxxxxxxxx RF
        DEAD  43 kgktgpkalivePtreL 59 
                  ++++ +a+  +Pt eL
  EPA05987.1 407 FKDDKLQAISCTPTLEL 423
                 34444555555555555 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   0.00017      0.52      11      63 ..     180     237 ..     170     247 .. 0.69
   2 !   50.5   0.5   7.6e-17   2.3e-13       8     111 .]     352     454 ..     345     454 .. 0.89
   3 ?   -3.2   0.0       3.5   1.1e+04       5      30 ..     546     571 ..     542     604 .. 0.63
   4 ?   -1.7   0.0       1.2   3.5e+03      42      71 ..     796     825 ..     783     830 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00017
                 HHTTTTSEEEEEESSHHHHHH...HHHH..HHHTTSTEEEESTTSTHHHHHHHHHHHH CS
  Helicase_C  11 kleeeggkilifvntidrlek...vkll..lekkgikvavlhgelpqnereeileqfn 63 
                 k+e+ gg   +fv  ++ l++    k+l   ek gi+v v++g+++q er+eile+  
  EPA05987.1 180 KKESTGGVFALFVYPTKALSRdqyPKILklAEKIGISVQVFDGDTEQIERREILENPP 237
                 5666666666666666655444564444224666********************9865 PP

  == domain 2  score: 50.5 bits;  conditional E-value: 7.6e-17
                 HHH.HHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEESSSSSSHHHHHHHHT CS
  Helicase_C   8 ell.kleeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVinfdlprnvtsyiqriG 105
                 +l  k++e+++k++if n+  + e + +  +k++i++ v+ + l +n r+ + ++f++++ + + +t  +e Gid+ +v++Vi   +p  + ++ qriG
  EPA05987.1 352 DLTkKMTEKNHKTMIFNNSHLNSELLAIQAKKQKINIKVHRAGLMANYRKSVEQEFKDDKLQAISCTPTLELGIDVGNVDCVISSTIP--INRLTQRIG 448
                 44468899*************8854555577889******************************************************..669****** PP

                 TSSSTT CS
  Helicase_C 106 RtgRag 111
                 R++R g
  EPA05987.1 449 RAARKG 454
                 ****76 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 3.5
                 HHHHHHHHTTTTSEEEEEESSHHHHH CS
  Helicase_C   5 allellkleeeggkilifvntidrle 30 
                 +ll+ ++ + +g+ i if+n ++  +
  EPA05987.1 546 TLLNDYSIRGIGKSIDIFLNEKKVGD 571
                 55555466777888888888887333 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 1.2
                 TEEEESTTSTHHHHHHHHHHHHTTSSSEEE CS
  Helicase_C  42 kvavlhgelpqnereeileqfnkgesdvLi 71 
                 ++   +  l + + +eil++ nkge + Li
  EPA05987.1 796 RCGNNNEFLHKHSALEILQRINKGEETKLI 825
                 555556668888999*******99987665 PP

>> DUF1998  Domain of unknown function (DUF1998)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.1   1.8e-12   5.3e-09       2      82 ..     717     791 ..     716     792 .. 0.88

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 1.8e-12
     DUF1998   2 ehalinalplflqcdesdlgteckapedeprkrpariliydavpgGaGiaekaaelleellraalelieecdCee.aGCpaC 82 
                 eh++i++  +  +  ++dlg+ +             i+iyd++ gG G ++++++ +e+ l++ + +++ec+C++ aGCp+C
  EPA05987.1 717 EHVVIEGSNMITGGVSQDLGGISL-------GTSGLIFIYDGAIGGNGASKALFDRFESALERSMFIVKECPCKNeAGCPRC 791
                 678888888888888888888887.......25789*************************************6579***** PP

>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     1e-05      0.03      99     203 ..     189     290 ..      64     298 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1e-05
                 EEEE--H.HHHHHHHHHHHHH-TTS-EEE--SSHHHH-----------------EEEE-HHHHHHHT......TTS-S-S-SEEEES-GGGT--T.TSH CS
                 xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx RF
      SNF2_N  99 tLivvPa.slldqWeneierhvsssalrvlvyggqkkmkkkntkvapklladydvvittYdvlsreaelqkkrsvlkqvewkrvvlDEghtlkns.tsk 195
                 +L v P+ +l +  + +i + +++  + v v +g++++ ++     + l +  +v+it++dvl  +   q+k s l + + + +v+DE+h       s+
  EPA05987.1 189 ALFVYPTkALSRDQYPKILKLAEKIGISVQVFDGDTEQIER----REILENPPQVLITNFDVLHYHLWHQTKFSSLLS-SVRILVVDEAHVYSGIfGSN 282
                 67788887888888889999999999999999998743333....455566789**********88855555555543.456799*****876556666 PP

                 HHHHHHH- CS
                 xxxxxxxx RF
      SNF2_N 196 aaeavskL 203
                 ++ +v++L
  EPA05987.1 283 VHYIVKRL 290
                 66666666 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   2.4    0.0001      0.31       1      28 [.       1      30 [.       1      33 [. 0.90

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0001
                    EEB.ESTTTSBEEEEECSCCCE.EEESSSS CS
  RNA_POL_M_15KD  1 lkF.CpkCgNlLlpkedkegkn.feCrqCg 28
                    +kF CpkC++ L++++   +k  + C +Cg
      EPA05987.1  1 MKFsCPKCKSKLEIQKTFNKKMhVSCEKCG 30
                    5666****************99*******8 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   4.7   9.7e-05      0.29       1      32 [.       1      30 [.       1      31 [. 0.89
   2 ?    1.6   1.2     0.087   2.6e+02       5      13 ..     788     796 ..     785     799 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.7e-05
  zinc_ribbon_4  1 MkitCpsCkakyeiddeklpakgvkvrCskCg 32
                   Mk++Cp+Ck+k ei+      k++ v C kCg
     EPA05987.1  1 MKFSCPKCKSKLEIQKT--FNKKMHVSCEKCG 30
                   **************994..56669*******8 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.087
  zinc_ribbon_4   5 CpsCkakye 13 
                    Cp+C + y+
     EPA05987.1 788 CPRCTFSYR 796
                    ******997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (835 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1111  (0.0619666); expected 358.6 (0.02)
Passed bias filter:                      664  (0.037035); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.81u 0.35s 00:00:01.16 Elapsed: 00:00:00.54
# Mc/sec: 4681.74
//
Query:       EPA05988.1  [L=143]
Description: response regulator receiver domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-25   89.6   0.7    3.8e-25   88.2   0.7    1.6  2  Response_reg  Response regulator receiver domain
  ------ inclusion threshold ------
       0.02   15.2   0.0      0.053   13.8   0.0    1.7  2  DUF5475       Family of unknown function (DUF5475)


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.2   0.7   4.2e-29   3.8e-25       2     111 ..       9     120 ..       8     121 .. 0.94
   2 ?   -1.6   0.0      0.32   2.9e+03      90     101 ..     128     139 ..     122     142 .. 0.79

  Alignments for each domain:
  == domain 1  score: 88.2 bits;  conditional E-value: 4.2e-29
                   EEESSSHHHHHHHHHHHH.HTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEESSTS.HHHHHHHHHCTESE CS
  Response_reg   2 livdDdplvrellrqlle.eegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviiltahse.eedavealkagadd 96 
                   livdD+  +re  r  ++ + ++ ++  a++g e+l+++k++k+d+illD++mpg+dG+++lk i ++d  ++vi+ ta++e +e +++++ +ga+ 
    EPA05988.1   9 LIVDDSDSFREFARHHIKtDIKFITILLAKNGVECLQMYKQHKPDVILLDWKMPGLDGIQVLKAIMRDDARTKVIMTTAYTEdQELLNQMMVLGAFS 105
                   9*****************878888999***************************************************8877488889999****** PP

                   EEESSG-HHHHHHHH CS
  Response_reg  97 flsKpfdpeeLlkal 111
                   f+ Kp+++ +Llk +
    EPA05988.1 106 FVPKPMQRVNLLKVV 120
                   **********99876 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.32
                   HHCTESEEEESS CS
  Response_reg  90 lkagaddflsKp 101
                    ++g+++ + Kp
    EPA05988.1 128 KNIGMYGQIPKP 139
                   6789*******9 PP

>> DUF5475  Family of unknown function (DUF5475)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   5.9e-06     0.053      41      64 ..      25      48 ..      16      55 .. 0.86
   2 ?   -3.3   0.0       1.3   1.2e+04      34      41 ..      90      97 ..      79     106 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.9e-06
     DUF5475 41 qktnikevavmlskktteclqlkr 64
                 kt+ik ++++l+k   eclq+ +
  EPA05988.1 25 IKTDIKFITILLAKNGVECLQMYK 48
                59*******************965 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.3
     DUF5475 34 enlellrq 41
                e+ ell q
  EPA05988.1 90 EDQELLNQ 97
                55566655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.32s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 889.32
//
Query:       EPA05989.1  [L=276]
Description: putative short chain dehydrogenase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-50  170.7   0.1    3.5e-50  170.2   0.1    1.1  1  adh_short       short chain dehydrogenase
    6.2e-37  127.4   0.0    8.3e-37  127.0   0.0    1.1  1  adh_short_C2    Enoyl-(Acyl carrier protein) reductase
    5.3e-09   36.2   0.0    7.7e-09   35.7   0.0    1.2  1  KR              KR domain
    4.9e-08   32.7   0.1    5.4e-07   29.3   0.1    2.1  1  DUF1776         Fungal family of unknown function (DUF1776)
     0.0044   16.6   0.1      0.016   14.7   0.1    1.8  2  NmrA            NmrA-like family
  ------ inclusion threshold ------
      0.043   13.7   0.1      0.088   12.7   0.1    1.7  1  NAD_binding_10  NAD(P)H-binding


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.2   0.1   1.2e-53   3.5e-50       1     189 [.       3     191 ..       3     196 .. 0.98

  Alignments for each domain:
  == domain 1  score: 170.2 bits;  conditional E-value: 1.2e-53
                 SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEEE---SS--SSGGGCSHH CS
   adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldvLvnNAGitgsgpfselsee 99 
                 kv++vtG ssG+G +++ +la++G+ ++++ r+ +k  ++++  k+e+ ++ +i++Dv ++++++ ++ek+ +k +++dvLvnNAG   +g+++++  +
  EPA05989.1   3 KVAVVTGSSSGMGFETSLALARDGFYTFATVRNVKKSDKILQIAKKEKLNLEIIELDVDNEKSISSAIEKILAKKQRIDVLVNNAGWGLFGSVEDVPLK 101
                 89************************************************************************************************* PP

                 HHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHH CS
   adh_short 100 ewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaavagltrslakelaptgirvnavaPGlvdTdmake 189
                 e+++ +e+N++g++++++ v+p m kq sG Ivn+sSvagk +++g +aY +sK+a++gl++sl+ el + g++v+++ PG+v+T++  +
  EPA05989.1 102 EFRAQFETNFFGIISIIQKVAPVMRKQGSGIIVNISSVAGKIGFPGSPAYISSKFALEGLSESLRYELGQFGVKVIIIEPGVVKTNFFSS 191
                 *************************************************************************************98765 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.0   0.0   2.8e-40   8.3e-37       1     186 [.       9     196 ..       9     245 .. 0.88

  Alignments for each domain:
  == domain 1  score: 127.0 bits;  conditional E-value: 2.8e-40
                   TTTTSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSE..EEE--TTSHHHHHHHHHHHHHHHSSEEEEEE-----EGCSS-GGGH-HHHH CS
  adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneeakkrveelaeelgae..vlecDVtdeeqvealveevvekfgklDilvnnagiapklkgpfletsreef 95 
                   G  sg+G+++  ala+ G    +t +n ++ +++ ++a++ + +  ++e+DV +e+++ +++e++ +k +++D+lvnnag+     g++++++ +ef
    EPA05989.1   9 GSSSGMGFETSLALARDGFYTFATVRNVKKSDKILQIAKKEKLNleIIELDVDNEKSISSAIEKILAKKQRIDVLVNNAGWGLF--GSVEDVPLKEF 103
                   5679**************************99999999987755347************************************9..*********** PP

                   HHHHHHHTHHHHHHHHHHHHHCTSC..CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHHHHHHGGGTEEEEEEEE--BHCTGGGGSTTHH CS
  adh_short_C2  96 draldvnlyslfllakaalplmkeg..gsivnlssvgaervvpnynaygaaKaalealtrylAvelgpkgiRvNavspgpikTlaasgikgfd 186
                   +  +++n+ +++++++ ++p+m+++  g ivn+ssv++++++p+  ay  +K ale+l+ +l +elg+ g++v  + pg++kT+  s++k ++
    EPA05989.1 104 RAQFETNFFGIISIIQKVAPVMRKQgsGIIVNISSVAGKIGFPGSPAYISSKFALEGLSESLRYELGQFGVKVIIIEPGVVKTNFFSSMKVAE 196
                   ********************999995666*******************************************************988877533 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.0   2.6e-12   7.7e-09       4     164 ..       6     166 ..       4     185 .. 0.86

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 2.6e-12
                 EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS---EEEE---------TTT--H CS
          KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppikGvihaAgvlrdklleemta 102
                 ++tG   g+G e++  la++g  + + + R+    ++s++ ++  ++   + e++++Dv +++++++++e+i a++++i   ++ Ag    + +e++  
  EPA05989.1   6 VVTGSSSGMGFETSLALARDGFYTFATV-RN---VKKSDKILQIAKKEKLNLEIIELDVDNEKSISSAIEKILAKKQRIDVLVNNAGWGLFGSVEDVPL 100
                 89*******************9998765.66...2334445666677799************************************************* PP

                 HHHHHHHTTTTHHHHHHHHHTTT....S--SEEEEEEEHHHHH--TT-HHHHHHHHHHHHHHHHHH CS
          KR 103 edleqvlapKvkGawnLhelled....esldffvlfSSiagllgsagqanYaaaNaflDalaeyrr 164
                 +++++ ++  + G+  + + +++    +   ++v +SS+ag +g +g  +Y +    l++l e+ r
  EPA05989.1 101 KEFRAQFETNFFGIISIIQKVAPvmrkQGSGIIVNISSVAGKIGFPGSPAYISSKFALEGLSESLR 166
                 ************9877665444334438999********************999999998887654 PP

>> DUF1776  Fungal family of unknown function (DUF1776)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.1   1.8e-10   5.4e-07      21     202 ..      19     186 ..       2     254 .. 0.82

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 1.8e-10
     DUF1776  21 alDLerrGFiVfvtvesaeeeklv....esed.redIrplsvdddpssieasleefaqslesphvalpgakphvlrLkgvilvPslsy.ptgpietipl 113
                 +l L r GF  f tv++ +++ ++    ++e+ + +I +l vd+ ++si++++e+++ + ++                  +lv +  +  +g +e +pl
  EPA05989.1  19 SLALARDGFYTFATVRNVKKSDKIlqiaKKEKlNLEIIELDVDN-EKSISSAIEKILAKKQRI----------------DVLVNNAGWgLFGSVEDVPL 100
                 5679999*******999888766522224455566677777776.999999999999988853................4789999999********** PP

     DUF1776 114 sswaselnerllspiltlqallplltsrakqkakiivvnpsissslnlpfhapEalvssalsalfevLkrelrphnidvtqikLGnldl 202
                 ++++ +++++++  i+++q+  p +++   q + iiv   s+  ++  p ++  +    al+ l e+L+ el++ +++v+ i  G ++ 
  EPA05989.1 101 KEFRAQFETNFFGIISIIQKVAPVMRK---QGSGIIVNISSVAGKIGFPGSPAYISSKFALEGLSESLRYELGQFGVKVIIIEPGVVKT 186
                 **************************8...99**************99998888888889*********************99888765 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   5.5e-06     0.016       3      64 ..       7      72 ..       5      75 .. 0.78
   2 ?   -0.9   0.0      0.32   9.6e+02      89     106 ..     178     196 ..     161     239 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.5e-06
                ESSTTSHHHHHHHHHHHHHT-EEEEEES-S.-SHHHHHHH...HSTTEEEES-TT-HHHHHHHHTT CS
        NmrA  3 viGaTGrqGksvvrallkaghkvralvRdt.kselakslk...eaGvelvkgdlddkeslvealkg 64
                v+G++  +G     al+++g+ ++a vR++ ks+++ +++   +   e+++ d+d+++s+++a+++
  EPA05989.1  7 VTGSSSGMGFETSLALARDGFYTFATVRNVkKSDKILQIAkkeKLNLEIIELDVDNEKSISSAIEK 72
                667777777777889999************755665555411156789***************986 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.32
                 HHHHS.-SEEEEEE---GG CS
        NmrA  89 akeaG.vkhfiySslgddn 106
                 + e G vk  ++Ss+  ++
  EPA05989.1 178 IIEPGvVKTNFFSSMKVAE 196
                 5566777777777776655 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   2.9e-05     0.088      13      60 ..      20      72 ..      16     238 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.9e-05
                    HHHHC-T-EEEEEETTHHHCH...HHH..CTTTCEEEE--TT-CCHHHHHHTT CS
  NAD_binding_10 13 ellargghevtalvRnpekla...ele..aeeglevvegdvtdvedlaealkg 60
                     +lar+g+ + a vRn +k +   +++  ++ +le++e+dv +++++ +a++ 
      EPA05989.1 20 LALARDGFYTFATVRNVKKSDkilQIAkkEKLNLEIIELDVDNEKSISSAIEK 72
                    5788888999999**97666622245433456999****************94 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1944.73
//
Query:       EPA05990.1  [L=143]
Description: response regulator receiver domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-24   86.5   0.1    1.6e-24   86.2   0.1    1.1  1  Response_reg  Response regulator receiver domain


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.2   0.1   8.9e-29   1.6e-24       1     111 [.       8     120 ..       8     121 .. 0.95

  Alignments for each domain:
  == domain 1  score: 86.2 bits;  conditional E-value: 8.9e-29
                   EEEESSSHHHHHHHHHHHH.HTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEESSTS.HHHHHHHHHCTES CS
  Response_reg   1 vlivdDdplvrellrqlle.eegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviiltahse.eedavealkagad 95 
                   vli+dD+p++r+  +  ++ + ++ ++ +a+d+ e l+l+k+ k+d++llD++mpg+dG+ +lk i ++dp+++vi+ ta+++ ++ +++ +k ga+
    EPA05990.1   8 VLIIDDSPAFRDFAKYSIRtDIKFVNIFQAADAIEGLKLYKKYKPDVVLLDWKMPGIDGMSTLKAIITNDPDVKVIMTTAYDDnQNLLNDFMKFGAF 104
                   8******************888999******************************************************9999677889999***** PP

                   EEEESSG-HHHHHHHH CS
  Response_reg  96 dflsKpfdpeeLlkal 111
                    f+ Kp+++ +Llk +
    EPA05990.1 105 SFVPKPMNRINLLKVV 120
                   **********999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1016.73
//
Query:       EPA05991.1  [L=57]
Description: hypothetical protein BG20_I1482 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       230  (0.0128284); expected 358.6 (0.02)
Passed bias filter:                      172  (0.0095934); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.35s 00:00:00.83 Elapsed: 00:00:00.54
# Mc/sec: 318.02
//
Query:       EPA05992.1  [L=50]
Description: hypothetical protein BG20_I1996 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.26s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 379.35
//
Query:       EPA05993.1  [L=240]
Description: precorrin-2 C(20)-methyltransferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-56  191.6   0.0    1.8e-56  191.4   0.0    1.0  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.4   0.0     1e-60   1.8e-56       2     212 ..       4     222 ..       3     223 .. 0.96

  Alignments for each domain:
  == domain 1  score: 191.4 bits;  conditional E-value: 1e-60
  TP_methylase   2 lylVGvGpGdpellTvrAlralktadvvlgddsr......aleilldllaeel.....eleapmgkekepleeayeeiaealaealragkdVvllvs 87 
                   l+++GvGpGdpellTv+A++a+++ad +++++s+      al+i+  l+++ +     +l +pm+k+k++le++++++a+++ae++ +gk+Vv+l++
    EPA05993.1   4 LIGIGVGPGDPELLTVKAAKAIQNADTIMCPASNedrpsiALSIVSSLIDKSKnqeiiKLIFPMTKDKDVLEATWKKNAKIMAEKVLTGKNVVYLTI 100
                   89**************************9999656778899999999999999******************************************** PP

  TP_methylase  88 GDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvllpglakeeereleallangdtlvllkaprklaelaelLkea. 183
                   GDP++y+t++++++ ++ ++++i++ viPG+ s+ + aa++gi+++eg e+++++ p+++  + + ++++++n +t+v+lk++r +++++e+Lkea 
    EPA05993.1 101 GDPYLYSTWIYMHKDIEMNHPEIKISVIPGIVSMFTFAAKVGISIAEGAEKVAII-PSCY--DLSSVKEIAKNSETMVFLKDGRYFDKVIEVLKEAg 194
                   *******************************************************.9999..**********************************8 PP

  TP_methylase 184 lyddttpvavveragtedervvrgtleel 212
                   ++d+    a+++++gte+e +++ tl+e+
    EPA05993.1 195 FPDNS-IFAIGQDLGTENEIIRKLTLGEV 222
                   88855.********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1497.55
//
Query:       EPA05994.1  [L=218]
Description: hypothetical protein BG20_I1997 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1611.75
//
Query:       EPA05995.1  [L=264]
Description: hypothetical protein BG20_I1995 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.63u 0.35s 00:00:00.98 Elapsed: 00:00:00.56
# Mc/sec: 1416.45
//
Query:       EPA05996.1  [L=287]
Description: hypothetical protein BG20_I1994 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 1700.90
//
Query:       EPA05997.1  [L=40]
Description: hypothetical protein BG20_I2000, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       236  (0.013163); expected 358.6 (0.02)
Passed bias filter:                      142  (0.00792013); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 276.34
//
Query:       EPA05998.1  [L=250]
Description: precorrin-4 C(11)-methyltransferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.8e-47  159.6   0.1    1.2e-46  159.4   0.1    1.1  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
  ------ inclusion threshold ------
      0.024   15.0   0.0      0.042   14.2   0.0    1.5  1  Radical_SAM   Radical SAM superfamily
      0.033   13.6   0.1      0.073   12.5   0.1    1.5  1  Aldolase      KDPG and KHG aldolase
      0.042   13.1   0.5       0.12   11.6   0.0    1.9  3  V-ATPase_H_N  V-ATPase subunit H
      0.059   13.5   0.0          1    9.5   0.0    2.4  2  UvrA_inter    UvrA interaction domain
        0.1   12.0   0.1       0.41   10.1   0.1    1.7  2  ESAG1         ESAG protein
       0.19   11.4   0.1       0.35   10.6   0.1    1.5  1  PPR_1         PPR repeat


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.4   0.1   4.6e-50   1.2e-46       1     212 [.       3     208 ..       3     209 .. 0.94

  Alignments for each domain:
  == domain 1  score: 159.4 bits;  conditional E-value: 4.6e-50
  TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealragkdVvllvsGDPlvygtgs 97 
                   ++y+VG GpGdpel+T++A +++++ad+v++++s+ +  +l+l+++        g+  + ++ + eei + l + ++++k Vv+l+ GDP++yg+  
    EPA05998.1   3 RVYFVGCGPGDPELITIKAKKLIQKADIVVYSGSLIPPPILKLCKK--------GELHDAAGLVREEIFDLLYKNAKNDKLVVRLHDGDPSIYGAIK 91 
                   69*******************************9999999999976........5666677777********************************* PP

  TP_methylase  98 elvealrareagieveviPGvsslqaaaarlgiplteggevlsvl....lpglakeeereleallangdtlvllkaprklaelaelLkea.lyddtt 189
                   e ++ l++  +gie  v+PG++++ a aa+lg+ lt  g +++++    + +++ ++++++++l++++ tl+++ +++ l++++++  +  ++ + t
    EPA05998.1  92 EQIDNLQE--KGIESVVVPGITAFLASAAALGMQLTLPGITQTIIvtraESRTKVPKREKISELAKHKATLIFYLSVHLLSNIVKEAVAGgYK-KST 185
                   ********..9**************************************99999*********************************999555.567 PP

  TP_methylase 190 pvavveragtedervvrgtleel 212
                   pvavv ra+++d+++++gtl ++
    EPA05998.1 186 PVAVVYRASWDDQKIIKGTLNDI 208
                   ********************875 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.6e-05     0.042      31     127 ..      59     183 ..      46     236 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.6e-05
                  HHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC........................CCTEEEEEEECSSCHG.............. CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................xxxxxxxxxxxxxxxx.............. RF
  Radical_SAM  31 veeileevkelkaekgvkevilgggepllypdfvellerlakla........................vpgiritvetngtlpd.............. 90 
                   eei +++ ++ a++++ +v l+ g+p+ y  + e +++l ++                                   +g++ +              
   EPA05998.1  59 REEIFDLLYKN-AKNDKLVVRLHDGDPSIYGAIKEQIDNLQEKGiesvvvpgitaflasaaalgmqltL---------PGITQTiivtraesrtkvpk 146
                  58999999899.6777**************999999999999999999988888888886666666663.........33333344444444478888 PP

                  HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHTCTSHH CS
                  xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM  91 eeklerllelg.vdrvslgleaaddekvlklmnrghtf 127
                  +ek+ +l++   +  ++l+++ +++  v++ + +g+  
   EPA05998.1 147 REKISELAKHKaTLIFYLSVHLLSNI-VKEAVAGGYKK 183
                  *********99999999999999999.98888766655 PP

>> Aldolase  KDPG and KHG aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   2.8e-05     0.073      70     112 ..      91     133 ..      88     140 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.8e-05
                 HHHHHHHHHCT-SEEEESS--HHHHHHHHHTTS-EEEEESSHH CS
    Aldolase  70 aeqlaeakeaGaqfvvsPGltadllkaavdlkipllPGvstps 112
                 +eq+++ +e G + vv PG+ta l+ aa       lPG++++ 
  EPA05998.1  91 KEQIDNLQEKGIESVVVPGITAFLASAAALGMQLTLPGITQTI 133
                 57999************************999999****8765 PP

>> V-ATPase_H_N  V-ATPase subunit H
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.75   1.9e+03      68     111 ..      50      92 ..      20     125 .. 0.58
   2 ?   -2.1   0.1      0.72   1.8e+03     232     255 ..     151     176 ..     137     178 .. 0.65
   3 ?   11.6   0.0   4.8e-05      0.12     243     272 ..     204     233 ..     193     245 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.75
  V-ATPase_H_N  68 skedtlqyiLvlidDllsedksrvelflslakkeeqdpwkpflk 111
                   +  d    +   i Dll ++ +  +l+  l +  + ++++ + +
    EPA05998.1  50 ELHDAAGLVREEIFDLLYKNAKNDKLVVRLHD-GDPSIYGAIKE 92 
                   44555555556667777777777777777555.33345555544 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.72
  V-ATPase_H_N 232 eelvkkk.eli.pllvdilrdsvKEK 255
                    el k+k +li  l v++l+++vKE 
    EPA05998.1 151 SELAKHKaTLIfYLSVHLLSNIVKEA 176
                   45556666555134567777777775 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 4.8e-05
  V-ATPase_H_N 243 llvdilrdsvKEKvtRvilatlrNllekae 272
                   +l di++++  EK+tR ++ ++ N++++  
    EPA05998.1 204 TLNDIVKKVRDEKITRTAIVIISNVIDSTD 233
                   688***********************8876 PP

>> UvrA_inter  UvrA interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0       0.1   2.6e+02      31      57 ..      88     114 ..      60     155 .. 0.85
   2 ?    9.5   0.0   0.00039         1       2      46 ..     204     249 ..     203     250 .] 0.88

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.1
  UvrA_inter  31 gefkkllenlkkkGfvrvriDgeiydl 57 
                 g +k+ ++nl++kG   v++ g +  l
  EPA05998.1  88 GAIKEQIDNLQEKGIESVVVPGITAFL 114
                 778999999999999999988766555 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00039
  UvrA_inter   2 sveqIvdqilklee.gtkllilaPvvrerkgefkkllenlkkkGfv 46 
                 ++++Iv+++ + +  +t ++i++ v+ +   e++kl ++  ++G++
  EPA05998.1 204 TLNDIVKKVRDEKItRTAIVIISNVIDSTDYEYSKLYDKNFSHGYR 249
                 678999999987651679***************************7 PP

>> ESAG1  ESAG protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.31     8e+02     105     185 ..      62     144 ..      50     159 .. 0.68
   2 ?   10.1   0.1   0.00016      0.41      35      86 ..     165     219 ..     162     229 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.31
       ESAG1 105 vsestlkkykdgcleinvlkg..svskClnlprdnLyksGavknssdvleWreeeatffqLklkvqeifspLiapfaaGkpps 185
                 + +   k+ k++ l + + +g  s+   ++ + dnL ++G++      +     +a+ + ++l++  i +++i++ a  ++  
  EPA05998.1  62 IFDLLYKNAKNDKLVVRLHDGdpSIYGAIKEQIDNLQEKGIESVVVPGITAFLASAAALGMQLTLPGITQTIIVTRAESRTKV 144
                 55555677788888888888511444567788888888888887777766666777777788888888888887776666555 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00016
       ESAG1  35 svravrkelpdaLikankyytaiaeitrtvWddvkaveadee...akCkeeelkk 86 
                 sv  + + +++a+    k  t +a++ r+ Wdd+k ++   +   +k ++e++++
  EPA05998.1 165 SVHLLSNIVKEAVAGGYKKSTPVAVVYRASWDDQKIIKGTLNdivKKVRDEKITR 219
                 77788899999999999******************99876543446666666655 PP

>> PPR_1  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00014      0.35      17      32 ..      45      60 ..      42      60 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00014
                HHHTS-HHHHHHHHHH CS
       PPR_1 17 lCkaGrvdeAfelfde 32
                lCk+G++++A  l++e
  EPA05998.1 45 LCKKGELHDAAGLVRE 60
                9***********9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       796  (0.0443973); expected 358.6 (0.02)
Passed bias filter:                      564  (0.0314574); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 1478.57
//
Query:       EPA05999.1  [L=431]
Description: citrate transporter [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-38  132.3  41.7    3.2e-38  131.6  36.5    2.2  2  CitMHS    Citrate transporter
    9.4e-07   28.5  32.9    1.7e-06   27.6  32.9    1.4  1  ArsB      Arsenical pump membrane protein
  ------ inclusion threshold ------
        7.8    6.4   5.2         17    5.3   0.9    2.7  2  DUF3767   Protein of unknown function (DUF3767)


Domain annotation for each model (and alignments):
>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.6  36.5   5.4e-42   3.2e-38       3     299 ..      20     370 ..      18     371 .. 0.78
   2 !    5.3   0.6    0.0016       9.8     118     169 ..     367     425 ..     357     431 .] 0.83

  Alignments for each domain:
  == domain 1  score: 131.6 bits;  conditional E-value: 5.4e-42
                 xxxxxx...xxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
      CitMHS   3 llilek...lrldvvallvlvll......vltieealsgiaspiillllgamiigaaleetGlfdrlaakllrlaggkrd.llvllvlltallsafvsn 91 
                 l+i+ +   +++++ a +v  ++      +lt+e+a+s+i ++++++llg++i++++le++G+ + +++++l++a++ ++ +l+++ ++++llsaf+ n
  EPA05999.1  20 LIIFRNvrgVNIPIWASMVFGAVsvlvlqILTPEDAFSAINFDVVFFLLGMFILVSGLESSGMLNQMVTRILSFAKT-PNqILFFILFVMGLLSAFLIN 117
                 66776677755555555554444557888***********************************************9.6769999************** PP

                 xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
      CitMHS  92 dgvvlimipivlslakrlkklppl.lliplalaaniggaltpiGtpttraaarpglslpnlll........lalllvgllplvllfmfgvalalpvnap 181
                 d+ +l+ +piv+ l k  ++ +p+ +li la++  ig+++tp+G+p            +nll+        +  ++   l+l ++ +  v + ++  + 
  EPA05999.1 118 DTIALVATPIVIGLTKP-MNVRPApMLICLAFGITIGSMMTPMGNP------------QNLLIslhsgmefPLFTFLRYLFLPTITCLLVTFFILKRYY 203
                 ****************8.5555555*********************............*****999999985555555566666666666666777777 PP

                 xxxxxxxxxxxxxxxxxxx...............xxxxxxx........................................xxxxxxxxxxxxxxxxxx RF
      CitMHS 182 kvkkqkaiieaiarsllpv...............atillla........................................ykkveWsvlllfaGvfll 225
                 k++  +a++ ++++s +                 +     +                                        +k ++W+++++f+++f++
  EPA05999.1 204 KKEFSNAVMLQLTSSEIVLdsslakkssiltmitV-----IgffvvgviklfgistelnfshvamfgglallvignkrkqiVKGINWQIIVFFVAMFVF 297
                 77777777777766555336666666555333330.....25557777777777777777777777777888899************************ PP

                 xxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
      CitMHS 226 vgaleqtGilealadllga...ggplvalalvlglial.lsafisnvavaalmapialgmapalgllspsplalalav 299
                 ++++ + Gi+e++ +ll     +++ ++ ++ ++ +++  s+++snv+++a+ +pi+ +     g+++++p++++ ++
  EPA05999.1 298 MQGVWNGGIIELFQALL-PfdqNPNSATASINIIGTSIlTSQIVSNVPFVAISIPILQN----YGFSEIDPIPWIALA 370
                 *****************.444534444444444445555***********999999877....234567777776554 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0016
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...................xxxxxxxxxxxxxxxx RF
      CitMHS 118 iplalaaniggaltpiGtpttraaarpglslpnlll...................lalllvgllplvllfm 169
                 i+la ++ i g+lt+ G               n+++                   ++++++++ + +l+f 
  EPA05999.1 367 IALAAGSTIAGTLTILGAA------------SNVIIletaerrhnvtftfkeffrIGIIVTAANTTILIFF 425
                 7899***************............**9999******9999999999998888887766666662 PP

>> ArsB  Arsenical pump membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6  32.9   2.9e-10   1.7e-06       2     414 ..      12     421 ..       9     428 .. 0.75

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 2.9e-10
        ArsB   2 avfiflltlvlvi.wqpknlsigwsacggavlaliagvvnfhdvltvtgivwnatlafvaiilislildnigffewaalhmakaakgygvrmfvyvsll 99 
                  vfi++  l++    +  n+ i  s + gav  l+  ++   d ++   i ++  + ++ + ++   l+  g+++    ++   ak     +f  + ++
  EPA05999.1  12 IVFIIVYGLIIFRnVRGVNIPIWASMVFGAVSVLVLQILTPEDAFS--AINFDVVFFLLGMFILVSGLESSGMLNQMVTRILSFAKTPNQILFFILFVM 108
                 455555555443213567899999999***************9875..678888888887777777899*****************9988888777777 PP

        ArsB 100 gaivaalfandgaaliltpivlamvralhfneklvfpfiiasgfiadttslpfvvsn....lvnivsadyfhitfidyasrmvvpylfsllasiivlyl 194
                 g +++a++ nd  al+ tpiv+ + + + +      p++i+  f     s+   + n    l+ + s   f   +  +   + +p +  ll +  +l  
  EPA05999.1 109 G-LLSAFLINDTIALVATPIVIGLTKPMNVRP---APMLICLAFGITIGSMMTPMGNpqnlLISLHSGMEF--PLFTFLRYLFLPTITCLLVTFFILKR 201
                 7.5677889****************9998765...455555555555555555555500113444444333..33444455899*************** PP

        ArsB 195 ffrksipkrydltevkkpveaikdqnmfrlswyilgllligyfas...effsipvsvvagsiaiifliaaqkspavhtkkvvkeapwaivffsigmyvv 290
                 +++k   +   l       e + d  + + s  +  + +ig+f     ++f i   +    +a+     a      + k++vk   w i++f + m+v 
  EPA05999.1 202 YYKKEFSNAVMLQL--TSSEIVLDSSLAKKSSILTMITVIGFFVVgviKLFGISTELNFSHVAMF-GGLALLVIGNKRKQIVKGINWQIIVFFVAMFVF 297
                 ****9998877654..4578999****999999999999***98622267888888777777765.444556667789********************* PP

        ArsB 291 vygvrnagltdvlsdviqaaadqglfagtigmgfi..aailssimnnlptvmidalaiagtdthgmmrealiyanvigsdlgpkitpigslatllwlhv 387
                 + gv n g+ +++  ++    dq   + t  + +i  + + s i+ n+p v i    i     +  +      a   gs +   +t +g+ + ++ l  
  EPA05999.1 298 MQGVWNGGIIELFQALLPF--DQNPNSATASINIIgtSILTSQIVSNVPFVAISI-PILQNYGFSEIDPIPWIALAAGSTIAGTLTILGAASNVIILET 393
                 ***********99988865..66666666666666214455779******98864.444444455555566678899*****************99998 PP

        ArsB 388 lsh.kgmkiswgtyfktgiiltiptlli 414
                   + + +  ++  +f+ gii+t     i
  EPA05999.1 394 AERrHNVTFTFKEFFRIGIIVTAANTTI 421
                 7651578999***********9864433 PP

>> DUF3767  Protein of unknown function (DUF3767)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.2      0.03   1.8e+02      35      65 ..      35      70 ..      27      74 .. 0.76
   2 ?    5.3   0.9    0.0028        17      33      66 ..     258     295 ..     237     300 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.03
     DUF3767 35 agavvGglrfvlkk.....nvakaaNWavgafllgs 65
                a +v+G++ +++ +     ++ +a+N+ v  fllg 
  EPA05999.1 35 ASMVFGAVSVLVLQiltpeDAFSAINFDVVFFLLGM 70
                6667777766666666666999**********9986 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0028
     DUF3767  33 igagavvGglrfvlkk....nvakaaNWavgafllgsi 66 
                 ++  a++Ggl +++ +    ++ k +NW + +f+++ +
  EPA05999.1 258 FSHVAMFGGLALLVIGnkrkQIVKGINWQIIVFFVAMF 295
                 667788888888775556679************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       864  (0.0481901); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.50
# Mc/sec: 2585.97
//
Query:       EPA06000.1  [L=135]
Description: anticodon binding domain protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-10   40.3   0.3    3.9e-10   39.7   0.3    1.2  1  HGTP_anticodon  Anticodon binding domain
  ------ inclusion threshold ------
      0.032   14.1   1.0      0.047   13.6   0.5    1.4  1  RcpB            Rough colony protein B, tight adherence - tad
        0.1   11.9   0.6        0.2   10.9   0.6    1.5  1  tRNA-synt_His   Histidyl-tRNA synthetase


Domain annotation for each model (and alignments):
>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   0.3   6.6e-14   3.9e-10       2      88 ..      46     127 ..      45     129 .. 0.95

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 6.6e-14
                     EEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTCEEEEEETTHHH CS
  HGTP_anticodon   2 vvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtreqervsldelv 88 
                     v v+ +ne   e++++a+++ + Lr ++i + +d s+++++k++++a      f+++v +kele+ +v +r+++++ + ++++++l 
      EPA06000.1  46 VSVLYINE---EMQKVAMSITSLLRLNNIPTNIDLSGKNLKKQMEQASDS--KFCIIVAPKELEQSKVVLRNMQDGTESQIEIEKLT 127
                     8899****...9*********************************99876..59*****************************9985 PP

>> RcpB  Rough colony protein B, tight adherence - tad - subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.5   7.9e-06     0.047      74     120 ..      40      85 ..      24      88 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.9e-06
        RcpB  74 sdkdkqihiissdkeakklakkirkrLkakgvkaksiklekkatknk 120
                   k+ ++ +++ ++e +k a++i   L+ +++ + +i l  k+ k++
  EPA06000.1  40 ESKQIRVSVLYINEEMQKVAMSITSLLRLNNIPT-NIDLSGKNLKKQ 85 
                 33555699************************99.****99998886 PP

>> tRNA-synt_His  Histidyl-tRNA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.6   3.3e-05       0.2     284     310 .]       1      28 [.       1      28 [. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 3.3e-05
                    EEEECTTTGGGT-.--EEEEEEEEHHHH CS
  tRNA-synt_His 284 GGrYdelgaafgr.arpAtGfsldleal 310
                    GGrYd l +afgr    AtG +  +e++
     EPA06000.1   1 GGRYDSLTKAFGReDIGATGVAGGVERI 28 
                    9**********7636799**99888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 962.05
//
Query:       EPA06001.1  [L=180]
Description: 4Fe-4S binding domain protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.7e-10   38.0  11.9    6.4e-06   25.8   1.3    2.2  2  Fer4      4Fe-4S binding domain
    1.2e-09   38.6   2.7    7.9e-05   23.2   0.8    2.3  2  Fer4_7    4Fe-4S dicluster domain
    5.3e-08   33.7   3.9    0.00034   21.5   0.9    2.3  2  Fer4_16   4Fe-4S double cluster binding domain
    6.9e-08   32.5  15.3    4.2e-07   30.0   5.1    1.7  2  Fer4_10   4Fe-4S dicluster domain
    2.9e-07   30.5   6.4    1.6e-06   28.2   6.8    1.9  2  Fer4_9    4Fe-4S dicluster domain
    4.5e-07   29.9   4.6     0.0009   19.3   0.7    2.2  2  Fer4_21   4Fe-4S dicluster domain
    7.8e-07   29.5   0.7      0.017   15.6   0.1    2.2  2  Fer4_8    4Fe-4S dicluster domain
      6e-06   26.1  12.5       0.01   15.9   3.8    2.3  2  Fer4_6    4Fe-4S binding domain
    0.00024   21.7   4.0      0.027   15.2   0.3    2.6  2  Fer4_15   4Fe-4S single cluster domain
    0.00045   20.5   6.0      0.036   14.6   1.2    2.4  2  Fer4_4    4Fe-4S binding domain
    0.00049   20.3   5.9    0.00056   20.1   4.0    1.9  2  Fer4_18   4Fe-4S dicluster domain
    0.00078   19.4  11.6      0.055   13.6   3.6    2.4  2  Fer4_2    4Fe-4S binding domain
     0.0014   19.2   5.7       0.11   13.0   7.9    2.2  2  Fer4_17   4Fe-4S dicluster domain
  ------ inclusion threshold ------
       0.01   16.3  13.8       0.18   12.4   2.6    2.6  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
      0.012   16.5   0.7        6.1    7.8   0.1    2.2  2  Fer4_22   4Fe-4S dicluster domain
      0.078   14.0  14.9        1.8    9.7   6.4    2.3  2  Fer4_3    4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   1.3   5.7e-09   6.4e-06       2      22 ..      72      92 ..      71      94 .. 0.90
   2 !   17.4   3.5   2.6e-06    0.0029       4      24 .]     134     154 ..     132     154 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 5.7e-09
                EEETTTSSS-THHHHHSTTTE CS
        Fer4  2 videekCigCGaCvevCPvgA 22
                 +d++ C++ GaC+e+CPv +
  EPA06001.1 72 AVDWDSCVADGACIEACPVQV 92
                69****************986 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 2.6e-06
                 ETTTSSS-THHHHHSTTTEEE CS
        Fer4   4 deekCigCGaCvevCPvgAIt 24 
                  e +Ci C+aCv+vCP  AI+
  EPA06001.1 134 REHDCIWCMACVSVCPPQAIK 154
                 5678999************96 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.9e-05     0.021      31      52 .]      71      92 ..      39     111 .. 0.79
   2 !   23.2   0.8     7e-08   7.9e-05       2      26 ..     138     162 ..     137     176 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.9e-05
      Fer4_7 31 veidpekClgCgaCvavCPtga 52
                v++d ++C+  gaC+++CP+++
  EPA06001.1 71 VAVDWDSCVADGACIEACPVQV 92
                4677788888888888888875 PP

  == domain 2  score: 23.2 bits;  conditional E-value: 7e-08
      Fer4_7   2 CigCgaCvaaCpvkaieldeeenek 26 
                 Ci C aCv++Cp +ai++d+++ e+
  EPA06001.1 138 CIWCMACVSVCPPQAIKVDQSNLEA 162
                 ******************9875443 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.1   0.00013      0.14       2      33 ..      78     110 ..      77     134 .. 0.61
   2 !   21.5   0.9   3.1e-07   0.00034       2      30 ..     138     165 ..     137     176 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00013
     Fer4_16   2 CgtCgkCaevCPtnaikek.kekeiearecisy 33 
                 C+  g+C+e+CP+++++   ++k i + e  ++
  EPA06001.1  78 CVADGACIEACPVQVFQWYrTDKDIPNTEALNA 110
                 88889**********996623333433333333 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 3.1e-07
     Fer4_16   2 CgtCgkCaevCPtnaikekkekeiearec 30 
                 C+ C +C++vCP +aik + + ++ea+e+
  EPA06001.1 138 CIWCMACVSVCPPQAIKVD-QSNLEAHEK 165
                 9****************99.677777765 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   5.1   3.7e-10   4.2e-07       3      56 .]      72     149 ..      70     149 .. 0.95
   2 !   14.8   2.5     2e-05     0.023       6      31 ..     135     160 ..     131     169 .. 0.69

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 3.7e-10
     Fer4_10   3 vidddtCirCgkCvkaCPadl........................tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                  +d d+C+  g+C +aCP+++                        +sv+ + ++  ++a+ +   +C+ c aCv++CP
  EPA06001.1  72 AVDWDSCVADGACIEACPVQVfqwyrtdkdipntealnatfkgtgSSVKEERKDLTDKADPIREHDCIWCMACVSVCP 149
                 67889**************99**********************9999999999999999999***************9 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 2e-05
     Fer4_10   6 ddtCirCgkCvkaCPadltsvgakge 31 
                 +  Ci C +Cv++CP ++ +v++++ 
  EPA06001.1 135 EHDCIWCMACVSVCPPQAIKVDQSNL 160
                 568************96644444433 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.3   0.00056      0.63      30      49 ..      74      91 ..      51      93 .. 0.71
   2 !   28.2   6.8   1.4e-09   1.6e-06       2      51 .]      78     153 ..      76     153 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00056
      Fer4_9 30 aaseeaCigCgaCveaCpkg 49
                   +++C+  gaC+eaCp +
  EPA06001.1 74 D--WDSCVADGACIEACPVQ 91
                2..25799999999999987 PP

  == domain 2  score: 28.2 bits;  conditional E-value: 1.4e-09
      Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraase..........................eaCigCgaCveaCpkgai 51 
                 C+  gaC+eaCp +v++  +  + + +++a +                           +Ci C+aCv +Cp +ai
  EPA06001.1  78 CVADGACIEACPVQVFQWYRTDKDIPNTEALNatfkgtgssvkeerkdltdkadpireHDCIWCMACVSVCPPQAI 153
                 666689************999999988766558*************************99*************987 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.2   0.00014      0.16      31      54 ..      68      91 ..      56      94 .. 0.85
   2 !   19.3   0.7     8e-07    0.0009      35      58 ..     132     154 ..     117     165 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00014
     Fer4_21 31 ktvlkvvedeCvGCnlCssvCPve 54
                 t+++v  d+Cv+   C++ CPv+
  EPA06001.1 68 GTMVAVDWDSCVADGACIEACPVQ 91
                577889999*************94 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 8e-07
     Fer4_21  35 kvvedeCvGCnlCssvCPvedcie 58 
                 +++e++C+ C  C+svCP  ++i+
  EPA06001.1 132 PIREHDCIWCMACVSVCP-PQAIK 154
                 667778888888888888.56665 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   0.00013      0.14      45      65 .]      72      92 ..      33      92 .. 0.71
   2 !   15.6   0.1   1.5e-05     0.017       4      16 ..     137     149 ..     103     175 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00013
      Fer4_8 45 eealwsCttcgaCtevCpvgi 65
                +  ++sC++ gaC e+Cpv++
  EPA06001.1 72 AVDWDSCVADGACIEACPVQV 92
                66789*************975 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 1.5e-05
      Fer4_8   4 kCieCgaCqsaCp 16 
                 +Ci C+aC s Cp
  EPA06001.1 137 DCIWCMACVSVCP 149
                 5777777777776 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   1.5   1.2e-05     0.014       2      23 ..      71      92 ..      70      93 .. 0.90
   2 !   15.9   3.8   9.2e-06      0.01       9      24 .]     138     153 ..     133     153 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.2e-05
      Fer4_6  2 veidpdkCigCgdCvrvCPega 23
                v++d d+C+  g+C+ +CP ++
  EPA06001.1 71 VAVDWDSCVADGACIEACPVQV 92
                678889*************998 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 9.2e-06
      Fer4_6   9 CigCgdCvrvCPegai 24 
                 Ci C++Cv+vCP +ai
  EPA06001.1 138 CIWCMACVSVCPPQAI 153
                 999***********98 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.3   2.4e-05     0.027       1      23 [.      71      94 ..      71     131 .. 0.72
   2 !    7.5   0.3    0.0061       6.9       7      28 ..     137     159 ..     133     174 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.4e-05
     Fer4_15  1 VvvDrdaCigcglCvaeap.evfe 23
                V vD+d C  +g+C++++p +vf+
  EPA06001.1 71 VAVDWDSCVADGACIEACPvQVFQ 94
                89****************734555 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0061
     Fer4_15   7 aCigcglCvaea.pevfeldedg 28 
                  Ci c +Cv ++ p+ ++ d+  
  EPA06001.1 137 DCIWCMACVSVCpPQAIKVDQSN 159
                 7***********66677666655 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.3    0.0037       4.1       2      17 .]      76      91 ..      74      96 .. 0.89
   2 !   14.6   1.2   3.2e-05     0.036       4      15 ..     138     149 ..     129     159 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0037
      Fer4_4  2 erCigCgsCvaaCPqg 17
                ++C+  g+C+ aCP++
  EPA06001.1 76 DSCVADGACIEACPVQ 91
                789999********75 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 3.2e-05
      Fer4_4   4 CigCgsCvaaCP 15 
                 Ci C++Cv++CP
  EPA06001.1 138 CIWCMACVSVCP 149
                 999********* PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.5     0.017        19      58      75 ..      75      92 ..      40     109 .. 0.81
   2 !   20.1   4.0     5e-07   0.00056       4      73 ..      82     150 ..      79     161 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.017
     Fer4_18 58 agdcidcescvkvcPtgi 75
                   c++ ++c++ cP+++
  EPA06001.1 75 WDSCVADGACIEACPVQV 92
                567888899999999876 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 5e-07
     Fer4_18   4 dvcvyvcPyarvqsvlydeet..llvvydakrGekiagrkkekkalkekeerkekgagdcidcescvkvcPt 73 
                   c+ +cP   +q    d++     +   + +G +++ ++++k+ + + +      + dci c +cv+vcP 
  EPA06001.1  82 GACIEACPVQVFQWYRTDKDIpnTEALNATFKGTGSSVKEERKDLTDKADPI---REHDCIWCMACVSVCPP 150
                 57************99999852145566677888877777777666666654...678************95 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   1.0    0.0005      0.56       3      21 ..      71      89 ..      69      90 .. 0.87
   2 !   13.6   3.6   4.9e-05     0.055      10      21 ..     138     149 ..     132     150 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0005
      Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                v+vd d+C++ gaC+ aCP
  EPA06001.1 71 VAVDWDSCVADGACIEACP 89
                67999999987******** PP

  == domain 2  score: 13.6 bits;  conditional E-value: 4.9e-05
      Fer4_2  10 CigCgaCvsaCP 21 
                 Ci C aCvs+CP
  EPA06001.1 138 CIWCMACVSVCP 149
                 ***********9 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.1    0.0006      0.67      41      59 ..      73      91 ..      36      93 .. 0.81
   2 !   13.0   7.9    0.0001      0.11       2      57 ..      78     149 ..      77     152 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0006
     Fer4_17 41 ekaslCieCgeCerkCPqg 59
                  +++C+  g C ++CP +
  EPA06001.1 73 VDWDSCVADGACIEACPVQ 91
                479**************76 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.0001
     Fer4_17   2 CiqCgyClpeCps..yeaydnepkkllraakl..............glleeaeke.......ekaslCieCgeCerkCP 57 
                 C   g+C+++Cp   +++y+++++ +  +a +              +       +        + ++Ci C  C+++CP
  EPA06001.1  78 CVADGACIEACPVqvFQWYRTDKDIPNTEALNatfkgtgssvkeerK-------DltdkadpIREHDCIWCMACVSVCP 149
                 666789******65577788876654444433355777754433221.......234344435789************9 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   2.6   0.00016      0.18       1      17 [.      73      89 ..      73     130 .. 0.90
   2 ?    9.3   3.5    0.0015       1.7       4      17 ..     136     149 ..     133     151 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00016
     Fer4_13  1 VDrdtCiacgaCvelaP 17
                VD d+C+a+gaC e++P
  EPA06001.1 73 VDWDSCVADGACIEACP 89
                899************** PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0015
     Fer4_13   4 dtCiacgaCvelaP 17 
                 + Ci c+aCv+++P
  EPA06001.1 136 HDCIWCMACVSVCP 149
                 67***********9 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0072         8      70      95 ..      66      91 ..      35      92 .. 0.77
   2 ?    7.8   0.1    0.0054       6.1       2      14 ..     138     150 ..     118     172 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0072
     Fer4_22 70 lsefkekfgesgCvGCgRCieacpvk 95
                +s ++  ++  +Cv  g Cieacpv+
  EPA06001.1 66 VSGTMVAVDWDSCVADGACIEACPVQ 91
                555666778899************97 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0054
     Fer4_22   2 ClsCgaCtlvCpt 14 
                 C+ C aC  vCp 
  EPA06001.1 138 CIWCMACVSVCPP 150
                 7778888888874 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   1.3    0.0021       2.4       4      13 ..      78      90 ..      76      92 .. 0.76
   2 ?    9.7   6.4    0.0016       1.8       1      15 []     138     152 ..     138     152 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0021
      Fer4_3  4 C...gaCvevCPv 13
                C   gaC e+CPv
  EPA06001.1 78 CvadGACIEACPV 90
                533379******7 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0016
      Fer4_3   1 CtgCgaCvevCPvgA 15 
                 C+ C+aCv vCP+ A
  EPA06001.1 138 CIWCMACVSVCPPQA 152
                 666*********866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1207.39
//
Query:       EPA06002.1  [L=221]
Description: putative translation initiation factor eIF-6 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-62  211.0   1.2    1.2e-62  210.8   1.2    1.1  1  eIF-6     eIF-6 family


Domain annotation for each model (and alignments):
>> eIF-6  eIF-6 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.8   1.2   6.8e-67   1.2e-62       1     196 [.       5     200 ..       5     201 .. 0.99

  Alignments for each domain:
  == domain 1  score: 210.8 bits;  conditional E-value: 6.8e-67
                 .E-BTTB--HHHH-EE-SSEEEE-TTS-HHHHHHHHHHHT-EEEE--BTTBS-HHHH-EE-SSEEEEETT--HHHHHHHHHHHH---EEE--SS--HHH CS
       eIF-6   1 rlsiegsseiGvfarltnkyalvpegveeefvkaieeeLkvevvettiagsrlvGslvvgNsngllvpstvtdeeleklkeslkleverleekltAlGN 99 
                 ++++++ ++iG+++ +++++++vp+g+++++ +++ + Lk +vv   ia++rl+G+l+v+N+ng+l+p+t++ +e+e lk+++k+e+ +l++k+tAlGN
  EPA06002.1   5 KFDVYRGPNIGIYINTNDSFVFVPMGFAQTKAEKLGDYLKAQVVYSAIANTRLLGALMVMNNNGILLPKTAYMDEYEFLKKETKMEIGVLDSKYTALGN 103
                 5689999******************************************************************************************** PP

                 HEEE-SSEEEE-GGGGG.GHHHHHHHHTSEEEE--BTTBS-TTTSEEE-SSEEEE-TT--HHHHHHHHHHHT-SEEE--BTTTBS-GGGTEEE-SS- CS
       eIF-6 100 vilaNDkvAlvhpdlsketveiiadvLgvevvrgtiagiktvGsaavvtnkgllvhpkateeeleeleellkveveagTvNrGsklvgsglvaNdkg 196
                 +i+aNDk+A+v+p lske +++i++vLgvev +++iag ++ G ++v++n+g+ +hp+a+ee+++  +++++v++e  T+N+G ++v+sg+++N+++
  EPA06002.1 104 IICANDKGAIVSPWLSKEDCQTIEQVLGVEVLQKRIAGFNQTGAVMVANNSGAAIHPEADEEDMKIFANVMGVNIEPTTINNGIPYVKSGMLVNNHS 200
                 **********************************************************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1409.31
//
Query:       EPA06003.1  [L=269]
Description: RIO1 family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-52  176.8   0.0    4.2e-52  176.5   0.0    1.1  1  RIO1            RIO1 family
     0.0092   14.8   0.0      0.013   14.3   0.0    1.2  1  Pkinase_fungal  Fungal protein kinase
  ------ inclusion threshold ------
       0.01   15.8   0.0        3.9    7.3   0.0    2.6  2  APH             Phosphotransferase enzyme family
      0.026   14.6   0.0      0.052   13.6   0.0    1.4  1  BBS2_Mid        Ciliary BBSome complex subunit 2, middle regi
      0.094   12.1   0.0        2.7    7.3   0.0    2.1  2  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family


Domain annotation for each model (and alignments):
>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.5   0.0   1.2e-55   4.2e-52       2     186 ..      82     261 ..      81     263 .. 0.96

  Alignments for each domain:
  == domain 1  score: 176.5 bits;  conditional E-value: 1.2e-55
                 EEEEEETTTEEEEEEEE-S---SS-HHHHCTTTSTTSTCG--GS-HHHHHHHHHHHHHHHHHHHHHTT--S--EEEEETTEEEEE--EETTEEGGBHHH CS
        RIO1   2 VyhavsedgkevaiKiyktstteFkkrkkyvsgekrfkdrksktnprklvklwaekEfrnLkrleeagvpvPkpielkrhvlvmefigedgvaapklkd 100
                  ++av+e++++va+Kiy +st++Fkkr++y++g++rf +   k+ +++l+ lwa+kE+rnL++ ++ g+pvP+p+ l ++vl ++f+ge+g +a  l d
  EPA06003.1  82 LFWAVDEKNNDVALKIYLISTSNFKKREQYITGDPRFLKL--KKGTKNLIYLWAKKEYRNLTQCYKCGIPVPRPLYLSNNVLALDFVGEKGSPAHILLD 178
                 5899********************************9965..99******************************************************* PP

                 CG-HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETTEEEE--GTTEEETTSTTHHHHHHHHHHHHHHHHHTTC-----HH CS
        RIO1 101 veeeeeaeelyeevleemrklykeaglvHaDLSeyNvlvdedkvviIDvsQaveldhpnalefLerDveniikfFrrkgvekvdee 186
                  e    +++ y + ++ + +ly++a+lvH+D SeyN++ + +++v++D++ av+l+hpna+efL+rD++ni++fF+++g++  d +
  EPA06003.1 179 SE---VDQNDYSQAISIITRLYQKAKLVHGDYSEYNIFKTPKGLVLFDLGSAVDLRHPNAQEFLKRDINNIVRFFSKRGISVEDPN 261
                 99...677889999******************************************************************976665 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   3.7e-06     0.013     314     369 ..     188     237 ..     185     251 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.7e-06
  Pkinase_fungal 314 DaIkghrsLflkagiLHrDiSenNilitdskkegerkglLiDLDlakelsddsses 369
                     +aI +  +L++ka+++H D Se+Ni  t       +  +L DL  a++l ++++++
      EPA06003.1 188 QAISIITRLYQKAKLVHGDYSEYNIFKT------PKGLVLFDLGSAVDLRHPNAQE 237
                     799**********************988......5667899999999998877665 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0011       3.9      38      89 ..     134     180 ..      73     198 .. 0.70
   2 ?    6.3   0.0    0.0022       7.9     165     196 ..     199     227 ..     176     229 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0011
                 HHHHHHHHHHHHTT-B--B-CTTBS-EEETTEEEEEEE----EE-SSHHHHH CS
         APH  38 rrevallrlLakagvpvPevlagdtddeeigllfalieyvpgrsllrklsaa 89 
                  +e++ l++  k g+pvP++l+   +++++ l f+   + p+++ll+    +
  EPA06003.1 134 KKEYRNLTQCYKCGIPVPRPLY--LSNNVLALDFVGEKGSPAHILLD---SE 180
                 4677799999999*********..68888888888888888888777...33 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0022
                 -EEEE-SS-SGGGEEEC..TTEEEEE---TT- CS
         APH 165 ptvllHgDlhpgNllvdpddgrvtGviDfeda 196
                 ++ l+HgD++  N+  +p  g v  ++D++ a
  EPA06003.1 199 KAKLVHGDYSEYNIFKTPK-GLV--LFDLGSA 227
                 5779**********99944.666..8888866 PP

>> BBS2_Mid  Ciliary BBSome complex subunit 2, middle region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.5e-05     0.052      27      91 ..      40     103 ..      38     115 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.5e-05
    BBS2_Mid  27 fkeeelvaeitetekvvslarlekerfayaleNGtvgvyekkerlWrvksknevvalaaydingd 91 
                 fk++++++e+  +  v++l ++ ++++ +a  NG v   +++   W v +kn+ val+ y i+ +
  EPA06003.1  40 FKKGKVINEVLDKPTVMTLYKMISDHI-IAYVNGPVSAGKESVLFWAVDEKNNDVALKIYLISTS 103
                 8999******************98876.5778*********************999999877643 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0   0.00075       2.7      56      81 ..     131     156 ..     116     165 .. 0.86
   2 ?    2.6   0.0     0.021        75     117     199 ..     179     259 ..     170     265 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00075
         Kdo  56 travrEfrllkrLeeagvavpkpvaa 81 
                 + a +E+r+l + ++ g++vp+p++ 
  EPA06003.1 131 LWAKKEYRNLTQCYKCGIPVPRPLYL 156
                 56789******************986 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.021
         Kdo 117 eelkrallkavgrliakl.hragvnHadlyaknillqqeeeeeaeiwliDldkar.lrlr.adrwrekdLarLkrsflkieltead 199
                  e+ ++ + +   +i +l  +a++ H+d    ni+   ++     ++l Dl  a  lr + a+   ++d++++ r f k++++  d
  EPA06003.1 179 SEVDQNDYSQAISIITRLyQKAKLVHGDYSEYNIFKTPKG-----LVLFDLGSAVdLRHPnAQEFLKRDINNIVRFFSKRGISVED 259
                 566666666655666666257999**********988888.....99999988752677767777888999998888877776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 1983.96
//
Query:       EPA06004.1  [L=368]
Description: type IIB DNA topoisomerase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-15   55.3   0.1    7.6e-15   54.6   0.1    1.4  1  TP6A_N    Type IIB DNA topoisomerase
  ------ inclusion threshold ------
      0.048   13.9   0.0       0.11   12.8   0.0    1.7  1  Toprim    Toprim domain


Domain annotation for each model (and alignments):
>> TP6A_N  Type IIB DNA topoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.6   0.1   8.5e-19   7.6e-15       1      62 []      80     144 ..      80     144 .. 0.95

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 8.5e-19
                 HHHHHHHHHHHHHHHHHHTT--EEHHHHHHH...GGGS-SSHHHHHHHHHHHHHHHTS-GGGGTE CS
      TP6A_N   1 rkfaqllkvlelihelleegkvvTkRdiYYr...dvelFksQaesdrliddievllgvsReeLnv 62 
                 r+f+ql++++ + ++l +e+k++T+Rd+YY+    +  F++Q+esd++i d+e++l+ +Re++++
  EPA06004.1  80 RSFTQLMWLAFFANRLTQEKKSSTLRDVYYSsqaFEIEFEDQSESDNIIVDLEAVLSKPREDFHI 144
                 68*****************************6655999**************************8 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.2e-05      0.11      56      84 ..     238     267 ..     152     280 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.2e-05
                 HHHHHHHHS.EEEEECSSSHHHHHHHHHHH CS
      Toprim  56 lkelakrad.eiilatDpDreGeaiawell 84 
                 lk+l  +    +i++tD+D+ Ge+ia+ + 
  EPA06004.1 238 LKRLHDEMGlPVIVLTDGDVYGEHIAMVIK 267
                 45555333369***************8776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2243.39
//
Query:       EPA06005.1  [L=213]
Description: putative membrane protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 1385.97
//
Query:       EPA06006.1  [L=139]
Description: copper binding protein, plastocyanin/azurin family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-10   41.0   0.0      2e-10   40.7   0.0    1.3  1  Cupredoxin_1  Cupredoxin-like domain
    5.8e-09   36.3   0.0    1.1e-08   35.4   0.0    1.5  1  Copper-bind   Copper binding proteins, plastocyanin/azurin fa


Domain annotation for each model (and alignments):
>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   0.0   2.2e-14     2e-10      28     104 .]      60     138 ..      19     138 .. 0.94

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 2.2e-14
  Cupredoxin_1  28 kdggfePskievkagekvklkiknkdktpeefesed......lgeekvlapgktttitiaplkpGeYeftcdmhmdakGkliV 104
                   +d  + Pskie+k+ge  +++++n+d+  +++++ +      l  ++ l+p++++t+ +  ++ G+Y+++c +h+ +kG++iV
    EPA06006.1  60 TDSCYIPSKIEIKKGE--SVNWVNQDAAFHSVTAGSygepsgLFDSTYLDPEESFTFIF--ENVGTYDYFCTLHPWMKGQVIV 138
                   567899**********..78*************9999999999999*************..**************99*****9 PP

>> Copper-bind  Copper binding proteins, plastocyanin/azurin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   0.0   1.2e-12   1.1e-08       8      99 .]      58     139 .]      52     139 .] 0.89

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 1.2e-12
                  TTETSEEESSEEEEETTEEEEEEEESSSSBEEEEETTSSTTT.GGGTTSCTTCEEEEBSTTEEEEEEEESSEEEEEEETTTTTTTSEEEEEEE CS
  Copper-bind   8 esgdlqFetkeitvkkgekvtfvnlavmgHNvvldkdgvpag.vdkdkvkaedetkliggGekdsvtfdeagtYkffCsPHaaagMkgkvtve 99 
                  e++d  + +++i++kkge+v++vn+++  H v   + g p+g +d++++++e         e+++  f++ gtY++fC+ H    Mkg+v+v+
   EPA06006.1  58 ENTDSCYIPSKIEIKKGESVNWVNQDAAFHSVTAGSYGEPSGlFDSTYLDPE---------ESFTFIFENVGTYDYFCTLHP--WMKGQVIVQ 139
                  56667899**************************998888883588999997.........99*******************..69****996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 930.20
//
Query:       EPA06007.1  [L=224]
Description: undecaprenyl pyrophosphate synthetase 1 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.9e-63  211.7   0.0    1.1e-62  211.5   0.0    1.0  1  Prenyltransf  Putative undecaprenyl diphosphate synthase


Domain annotation for each model (and alignments):
>> Prenyltransf  Putative undecaprenyl diphosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  211.5   0.0   6.1e-67   1.1e-62      11     224 .]       8     223 ..       3     223 .. 0.91

  Alignments for each domain:
  == domain 1  score: 211.5 bits;  conditional E-value: 6.1e-67
                   HTT.S-HHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEEGGGGGS-HHHHHHHHHHHH...HHHHHHHHHHHHHTTEEEEEESSGGGS-HHHHHHHH CS
  Prenyltransf  11 krgleereeGhkaGaealkeilelclelgvkvvtvYafSteNfkRskeevdalmellk...eellkeelkellkegvrvrviGdlellpedvleale 104
                   kr+l+  ++Gh +Ga+a++++l++c e+++k++t+Ya+S eN+ R++ee+++l+el++   e+l ++   +++k+++rv+ iG++ellpe+++e l+
    EPA06007.1   8 KRHLTIPKTGHWKGADAVENLLDWCEEFDIKIITLYALSAENLDRDDEELKHLYELIRirlEKLYNDP--RIHKNKMRVKGIGRIELLPESIREILD 102
                   444455556************************************************87766566555..9************************** PP

                   HHHHHHT.TTTSEEEEEEEEE-HHHHHHHHHHHHHHTT..SSSG.GGHSHHHHHCTSTT..T.SSS-SEEEEESS--S-TTSSTTTTTT-EEEEESS CS
  Prenyltransf 105 kaeeatkknnkklvlniavnYgsrdeiveavrelvkekseekkk.eeideetlekhlytaka.lpdpDlliRtsGeeRlSnFllwqlayselyfldv 199
                   ++  atk n ++  lnia++Yg+++e+v+av++++++ +  + + ++i+++++e++lyt++  + +pD+++RtsGe+RlS+Fl+wq+aysel+f+d 
    EPA06007.1 103 RLDVATK-NYDNHFLNIALAYGGQNELVDAVKKIAEKIKVGTLDvKDISKKEIESNLYTSHLpQSSPDMILRTSGEKRLSGFLMWQSAYSELIFMDI 198
                   *******.6666**********************9988766655567889********97778899******************************* PP

                   SGGG--HHHHHHHHHHHHHCHHHTT CS
  Prenyltransf 200 lWPdfskedllealleyqkrerrfg 224
                   +WP+f+k dl++a++++q+r+rr+g
    EPA06007.1 199 FWPEFRKIDLMRAIRTFQERKRRLG 223
                   **********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1635.42
//
Query:       EPA06008.1  [L=47]
Description: hypothetical protein BG20_I1197 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0021   17.7   1.5       0.13   12.0   0.2    2.3  2  zinc_ribbon_2   zinc-ribbon domain
     0.0037   17.2   0.8     0.0053   16.8   0.8    1.2  1  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.019   15.0   0.7      0.021   14.8   0.7    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.027   15.2   0.8      0.032   15.0   0.8    1.1  1  zinc_ribbon_15  zinc-ribbon family
      0.056   12.9   2.6       0.26   10.7   0.3    2.1  2  zf-ribbon_3     zinc-ribbon domain
      0.074   13.0   2.2        6.3    6.8   0.1    2.1  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain
        0.1   13.0   2.3        0.3   11.5   2.3    1.7  1  GFA             Glutathione-dependent formaldehyde-activating
       0.16   12.1   3.3       0.47   10.6   3.3    1.7  1  Zn-ribbon_8     Zinc ribbon domain
       0.16   11.9   6.9       0.77    9.7   6.9    1.9  1  zinc_ribbon_4   zinc-ribbon domain
       0.18   12.0   4.2        1.1    9.5   0.1    2.2  2  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 


Domain annotation for each model (and alignments):
>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.4   0.1    0.0089        16      15      22 ..       5      12 ..       2      16 .. 0.72
   2 !   12.0   0.2   7.1e-05      0.13      16      22 ..      34      40 ..      21      41 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0089
  zinc_ribbon_2 15 FCpyCGtp 22
                   +C +C+++
     EPA06008.1  5 YCVKCRAK 12
                   67777664 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 7.1e-05
  zinc_ribbon_2 16 CpyCGtp 22
                   Cp+CGt+
     EPA06008.1 34 CPKCGTN 40
                   8888886 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.8     3e-06    0.0053      13      38 ..       4      41 ..       2      44 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3e-06
         DZR 13 rfCseCgtk..lkavaa..........edrCpsCgekv 38
                 +C +C++k  +k +++          + +Cp+Cg+ v
  EPA06008.1  4 AYCVKCRAKreVKDPKEtklkngrpavKGTCPKCGTNV 41
                69******966555555999***************975 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.7   1.2e-05     0.021      69      99 ..       2      44 ..       1      46 [. 0.81

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.2e-05
                -EEEETTTS-EEECHH.HHH...........S-TTTSSS-EEE CS
        HypA 69 vkvrCreCgkefelee.kal...........rCpkCgsadvei 99
                v+++C +C+++ e+++ k++           +CpkCg++ ++i
  EPA06008.1  2 VEAYCVKCRAKREVKDpKETklkngrpavkgTCPKCGTNVFRI 44
                6789*****999988643336799*************987765 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.8   1.8e-05     0.032      39      75 ..       5      41 ..       2      44 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.8e-05
  zinc_ribbon_15 39 acskCkslleaskelgkeiekkessekkeCknCgkev 75
                    +c kC+++ e ++ +++++++++ + k +C++Cg++v
      EPA06008.1  5 YCVKCRAKREVKDPKETKLKNGRPAVKGTCPKCGTNV 41
                    899**********9********************987 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1     0.056     1e+02       2       8 ..       3       9 ..       2      14 .. 0.86
   2 ?   10.7   0.3   0.00015      0.26       4      11 ..      33      40 ..      31      43 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.056
  zf-ribbon_3 2 tvrCPnC 8
                + +C +C
   EPA06008.1 3 EAYCVKC 9
                679*999 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00015
  zf-ribbon_3  4 rCPnCGap 11
                 +CP+CG++
   EPA06008.1 33 TCPKCGTN 40
                 47777764 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.3    0.0046       8.3       5      14 ..       4      13 ..       3      16 .. 0.78
   2 ?    6.8   0.1    0.0035       6.3       5      13 ..      32      40 ..      31      44 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0046
  Zn_ribbon_SprT  5 YrCtgCgrey 14
                    ++C+ C+ + 
      EPA06008.1  4 AYCVKCRAKR 13
                    89*****765 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0035
  Zn_ribbon_SprT  5 YrCtgCgre 13
                     +C+ Cg++
      EPA06008.1 32 GTCPKCGTN 40
                    58****976 PP

>> GFA  Glutathione-dependent formaldehyde-activating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   2.3   0.00017       0.3      36      61 ..      17      43 ..       2      47 .] 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00017
         GFA 36 eykkt.adsgnkvtrsfCpeCgsplys 61
                  k+t  ++g+++ +  Cp+Cg++++ 
  EPA06008.1 17 DPKETkLKNGRPAVKGTCPKCGTNVFR 43
                3333336899**************994 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   3.3   0.00026      0.47       8      38 ..       6      43 ..       3      44 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00026
  Zn-ribbon_8  8 CeeCghefe.......vlqsis.daplta.CPeCgsevrr 38
                 C +C  + e       +l   + +++ +  CP+Cg +v r
   EPA06008.1  6 CVKCRAKREvkdpketKLK--NgRPAVKGtCPKCGTNVFR 43
                 5556655555556543343..235555556*****99866 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   6.9   0.00043      0.77       4      33 ..       5      39 ..       3      43 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00043
  zinc_ribbon_4  4 tCpsCkakyeiddek.lp.akgv...kvrCskCgh 33
                    C +C ak+e+ d k  + ++g+   k +C+kCg+
     EPA06008.1  5 YCVKCRAKREVKDPKeTKlKNGRpavKGTCPKCGT 39
                   69*********997765556665423567****97 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.7     0.035        62      33      39 ..       3       9 ..       1      10 [. 0.78
   2 ?    9.5   0.1   0.00061       1.1      17      27 ..      33      43 ..      30      47 .] 0.86

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.035
  Auto_anti-p27 33 kvyCvaC 39
                   + yCv C
     EPA06008.1  3 EAYCVKC 9 
                   5699999 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00061
  Auto_anti-p27 17 tCpvCgvPLmr 27
                   tCp+Cg+  +r
     EPA06008.1 33 TCPKCGTNVFR 43
                   8******9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 309.12
//
Query:       EPA06009.1  [L=71]
Description: DNA-binding protein HMf-1 family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-13   51.3   0.5    1.2e-13   51.1   0.5    1.0  1  CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) a
    4.9e-05   23.6   0.0    5.7e-05   23.4   0.0    1.2  1  CENP-S         CENP-S protein
    6.3e-05   23.3   0.2    7.4e-05   23.1   0.2    1.1  1  Histone        Core histone H2A/H2B/H3/H4
    0.00013   22.0   0.1    0.00015   21.8   0.1    1.1  1  CENP-T_C       Centromere kinetochore component CENP-T histon
    0.00074   19.5   0.0    0.00087   19.3   0.0    1.1  1  Bromo_TP       Bromodomain associated
    0.00092   19.3   0.0     0.0011   19.0   0.0    1.0  1  TFIID-31kDa    Transcription initiation factor IID, 31kD subu
     0.0014   19.1   0.0     0.0017   18.8   0.0    1.1  1  TFIID_20kDa    Transcription initiation factor TFIID subunit 
     0.0067   16.6   0.5     0.0078   16.4   0.5    1.1  1  TAF            TATA box binding protein associated factor (TA
     0.0069   16.5   0.2     0.0077   16.3   0.2    1.0  1  DUF1931        Domain of unknown function (DUF1931)
  ------ inclusion threshold ------
      0.017   15.3   0.2      0.021   14.9   0.2    1.3  1  DUF2120        Uncharacterized protein conserved in archaea (
      0.029   14.4   0.0      0.031   14.3   0.0    1.1  1  TFIID-18kDa    Transcription initiation factor IID, 18kD subu
      0.065   13.3   0.1      0.094   12.8   0.1    1.3  1  TFIIB          Transcription factor TFIIB repeat
      0.089   13.0   0.1      0.099   12.9   0.1    1.1  1  MR_MLE_N       Mandelate racemase / muconate lactonizing enzy


Domain annotation for each model (and alignments):
>> CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) and archaeal histone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.1   0.5   8.9e-17   1.2e-13       2      64 ..       5      66 ..       4      66 .. 0.96

  Alignments for each domain:
  == domain 1  score: 51.1 bits;  conditional E-value: 8.9e-17
                   XXXHHHHHHHHHCCTTXS-B-HHHHHHHHHHHHHHHHHHHHHHHHHHCCTTSSCE-HHHHHHH CS
  CBFD_NFYB_HMF  2 eLPiarvkkImksdpdarkiakdAkeliaecveefieelaseAaeickkekrKtikaehiklA 64
                   eL i+++ +I+k++ +a+++++++ e +  ++ee ++ +a+ A++ +++++rKtikae+iklA
     EPA06009.1  5 ELGISAMYRILKKA-GAERVSDESAEELRGIIEELANNIAKSAVDMASHAGRKTIKAEDIKLA 66
                   57789999******.**********************************************98 PP

>> CENP-S  CENP-S protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   4.1e-08   5.7e-05      27      71 ..      24      68 ..       7      69 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 4.1e-08
      CENP-S 27 tkqfiaaltelvykqlenlakDLeaFakHAkRstittdDvlLlaR 71
                + +  + l  ++ + ++n+ak     a HA+R+ti+++D++L ++
  EPA06009.1 24 SDESAEELRGIIEELANNIAKSAVDMASHAGRKTIKAEDIKLASK 68
                444444555555556667777777789***************875 PP

>> Histone  Core histone H2A/H2B/H3/H4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.2   5.3e-08   7.4e-05      79     128 ..      18      67 ..       2      68 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 5.3e-08
                 SSSXEEXHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTXSEEXHHHHHHHH CS
     Histone  79 kedlrisaeavlalqealEallvelfeeAnllakhaKRvTitpkDiqlAr 128
                     r+s e+ + l  ++E l   +++ A  +a ha R+Ti ++Di+lA 
  EPA06009.1  18 AGAERVSDESAEELRGIIEELANNIAKSAVDMASHAGRKTIKAEDIKLAS 67 
                 4557999999999***********************************95 PP

>> CENP-T_C  Centromere kinetochore component CENP-T histone fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.1   1.1e-07   0.00015      24      72 ..      17      65 ..       5      68 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.1e-07
    CENP-T_C 24 sgskaklekealkalekasdkffeqvgeDLeayakHagRKtidesDvil 72
                ++  ++++ e+ + l  + ++  + +++     a+HagRKti+++D+ l
  EPA06009.1 17 KAGAERVSDESAEELRGIIEELANNIAKSAVDMASHAGRKTIKAEDIKL 65
                467889****************************************975 PP

>> Bromo_TP  Bromodomain associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   6.3e-07   0.00087      15      66 ..      14      65 ..       5      68 .. 0.95

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 6.3e-07
                HHHHHT-SEE-HHHHHHHHHHHHHHHHHHHHHHHHHHTTSS-SS--HHHHHH CS
    Bromo_TP 15 ileeaGfdsaeesaLEtLteiaqkYirelgeqaksfaehagRseptlkDvvl 66
                il++aG +++ ++  E L++i+++  ++++++a   a hagR + + +D+ l
  EPA06009.1 14 ILKKAGAERVSDESAEELRGIIEELANNIAKSAVDMASHAGRKTIKAEDIKL 65
                89***********************************************986 PP

>> TFIID-31kDa  Transcription initiation factor IID, 31kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   8.2e-07    0.0011      10      66 ..      10      66 ..       6      69 .. 0.95

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 8.2e-07
  TFIID-31kDa 10 lihliLaslgvteyeerVvlqLldfayrytssvLedAkvlaehakkkevslddvrlA 66
                  +  iL++ g + ++++  + L  ++     ++ + A  +a+ha++k+++++d++lA
   EPA06009.1 10 AMYRILKKAGAERVSDESAEELRGIIEELANNIAKSAVDMASHAGRKTIKAEDIKLA 66
                 5778****************************************************9 PP

>> TFIID_20kDa  Transcription initiation factor TFIID subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.2e-06    0.0017      10      60 ..      16      65 ..       9      68 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.2e-06
                 HCC-SS----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHH CS
  TFIID_20kDa 10 qqvdsetkldedvedlLleiaddFvesvtkfacklakhRksdklevrDiql 60
                 ++  +e + de  e+ L  i+++  +++ k+a+ +a h   +++ + Di+l
   EPA06009.1 16 KKAGAERVSDESAEE-LRGIIEELANNIAKSAVDMASHAGRKTIKAEDIKL 65
                 555555555655555.799*******************************9 PP

>> TAF  TATA box binding protein associated factor (TAF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.5   5.6e-06    0.0078      11      64 ..      13      66 ..       4      68 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5.6e-06
                HHHHHTT---B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHH CS
         TAF 11 viAeslGitnLsdeaaalLaedveyrlkeivqeaakfmrhskRqkLtvaDvdsA 64
                 i    G + +sde a++L   +e+   +i++ a+    h+ R+++ ++D+  A
  EPA06009.1 13 RILKKAGAERVSDESAEELRGIIEELANNIAKSAVDMASHAGRKTIKAEDIKLA 66
                5566679999*****************************************876 PP

>> DUF1931  Domain of unknown function (DUF1931)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.2   5.6e-06    0.0077       3      55 ..      13      65 ..      11      68 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.6e-06
                HHHHHHHS----HHHHHHHHHHHHHHHHHCCCCHHHHHHHTT-SEE-GGGS-- CS
     DUF1931  3 rlfreaagLdvdkedlkrisdfVekklydLllvaeenAkangrdviepaDLPi 55
                r++++a    v +e +++++ ++e+  ++++  a + A+  gr++i+ +D+ +
  EPA06009.1 13 RILKKAGAERVSDESAEELRGIIEELANNIAKSAVDMASHAGRKTIKAEDIKL 65
                7889999999****************************************987 PP

>> DUF2120  Uncharacterized protein conserved in archaea (DUF2120)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.2   1.5e-05     0.021      33      73 ..      22      63 ..       7      69 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.5e-05
     DUF2120 33 rkkee.leeleskleellekldaeevdleseeakklieklde 73
                r ++e +eel++++eel +++ +  vd++s+ ++k i+  d 
  EPA06009.1 22 RVSDEsAEELRGIIEELANNIAKSAVDMASHAGRKTIKAEDI 63
                5555559****************************9987765 PP

>> TFIID-18kDa  Transcription initiation factor IID, 18kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   2.3e-05     0.031      21      62 ..      24      65 ..       8      68 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.3e-05
                 -HHHHHHHHHHHHHHHHHHHHHHHC-XXXX...XXXXXXXXX CS
  TFIID-18kDa 21 lqetvqlledlvrgyliellqqaakvaklrgsrkitlEDllf 62
                  +e+++ l  ++++   ++ + a+++a + g++ i+ ED++ 
   EPA06009.1 24 SDESAEELRGIIEELANNIAKSAVDMASHAGRKTIKAEDIKL 65
                 5788999999*****************************985 PP

>> TFIIB  Transcription factor TFIIB repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   6.8e-05     0.094       9      37 ..      30      58 ..      21      61 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.8e-05
                T--HHHHHHHHHHHHHHTTSTTTTSGCTT CS
       TFIIB  9 eLpekVadaAkelaklaleekvlkGrspa 37
                eL  ++++ A+++ak a+++  ++Gr+ +
  EPA06009.1 30 ELRGIIEELANNIAKSAVDMASHAGRKTI 58
                788899********************975 PP

>> MR_MLE_N  Mandelate racemase / muconate lactonizing enzyme, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   7.2e-05     0.099      70     101 ..      18      52 ..       4      61 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.2e-05
                 SBTTHHHHHHHHHHHHCSS...CHHHHHHHHHHHH CS
    MR_MLE_N  70 kdaanisdlaqllkravlg...nmsAkaaidmAlw 101
                   a+++sd+  ++ r ++    n  Ak+a+dmA +
  EPA06009.1  18 AGAERVSDESAEELRGIIEelaNNIAKSAVDMASH 52 
                 56899***********999899***********87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       810  (0.0451782); expected 358.6 (0.02)
Passed bias filter:                      589  (0.0328518); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 479.54
//
Query:       EPA06010.1  [L=83]
Description: hypothetical protein BG20_I1188, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    0.00022   21.1   0.0    0.00027   20.8   0.0    1.2  1  TrmB        Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
       0.13   11.8   0.0       0.27   10.8   0.0    1.5  1  Sigma70_r4  Sigma-70, region 4


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0     3e-08   0.00027       4      59 ..      14      74 ..      10      82 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3e-08
                CHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.....T CS
        TrmB  4 lGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.....p 59
                + L+   akv+l + ++g++t ++i+e+ g++   + ++ + L++ G    + ++      
  EPA06010.1 14 IKLKPLQAKVFLLVTCYGKMTSTTISEKMGISFDEALKTAKDLMQLGAFIDISETefeamH 74
                568999****************************************976666555455443 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0     3e-05      0.27       4      33 ..      15      45 ..      15      46 .. 0.96

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3e-05
                HS-HHHHHHHHHHH.TTT--HHHHHHHHTS- CS
  Sigma70_r4  4 sLpererevlelrf.geglTleEIgerlgiS 33
                +L + + +v+ l+  + ++T   I+e++giS
  EPA06010.1 15 KLKPLQAKVFLLVTcYGKMTSTTISEKMGIS 45
                69999*************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 600.82
//
Query:       EPA06011.1  [L=98]
Description: hypothetical protein BG20_I1195 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-22   79.7   0.5    1.7e-22   79.5   0.5    1.0  1  DUF424    Protein of unknown function (DUF424)


Domain annotation for each model (and alignments):
>> DUF424  Protein of unknown function (DUF424)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.5   0.5   9.5e-27   1.7e-22       3      92 .]      10      98 .]       8      98 .] 0.97

  Alignments for each domain:
  == domain 1  score: 79.5 bits;  conditional E-value: 9.5e-27
                ETTE.EEEEEEEGGGTT-EEEETTEEEE--HHHH--EEE-HHHHHHHHHHHEEEEEESHHHHHHHHHTTSS-GGG-EEETTEEEEEEEE- CS
      DUF424  3 tddllklvavcdkellgktfkegelllnvsegfyggelaseeeaikeLekatiaNivgeeavvlavkaGlvdpdsVlvidgvphaqigkl 92
                ++++  ++++cd++llgk ++++el++++s+++yg ++ +e+ea k Le+ ti+N+vg+++++l ++ G+  ++ + +i+gvp+ +++k+
  EPA06011.1 10 YQKN-LMLNICDADLLGKNIVQNELTMTISKSYYGDQIIEEDEAKKLLENSTIINMVGKNTISLSLELGIGSENGIKKISGVPFLIVFKM 98
                6777.8*********************************************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 654.53
//
Query:       EPA06012.1  [L=333]
Description: adenylosuccinate synthase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-83  280.2   1.1    3.9e-40  138.1   0.0    3.0  3  Adenylsucc_synt  Adenylosuccinate synthetase


Domain annotation for each model (and alignments):
>> Adenylsucc_synt  Adenylosuccinate synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.3   0.1   5.3e-39   9.6e-35       1     142 [.       4     138 ..       4     145 .. 0.94
   2 !  138.1   0.0   2.2e-44   3.9e-40     192     332 ..     146     284 ..     138     289 .. 0.92
   3 !   20.0   0.0   1.5e-08   0.00027     380     419 .]     290     329 ..     285     329 .. 0.91

  Alignments for each domain:
  == domain 1  score: 120.3 bits;  conditional E-value: 5.3e-39
                      .EEEE-SSS-S-HHHHHHHHHT..T-SEEEE-SB-TTSSEEEEETTEEEEESSS-GGGGSTT-EEEE-TTBEE-HHHHHHHHTTSS-TT..... CS
  Adenylsucc_synt   1 vvvvGaqwGDEGKGkivDllae..eadvvvRfqGGanAGHtvvvdgkkyklhllpSGilnpgvvnviGngvvvdpealleEieeleakgvelsk 92 
                      +vvvG  +GDEGKGki+ +la   + +++vR   G nAGHt+  ++k yk+++lpSG ln++++ +iG+gvv++p++ll+Ei++++a+g     
       EPA06012.1   4 TVVVGGFFGDEGKGKIISYLAMkdNPKIIVRGGAGPNAGHTIRDGDKIYKVRMLPSGFLNKNARVLIGPGVVINPSVLLKEIQDFDASG----- 92 
                      69******************662269***********************************************************9964..... PP

                      .TEEEETTSEE--HHHHHHHHHHHHH----------TTHHHHHHHHHTT- CS
  Adenylsucc_synt  93 erllisdrahlvlpyhkalDkleeaakgkkkiGtTkkGiGpayadkvarr 142
                       r +i++++ ++ + h + D+  e +   +kiG+T++G Gpa ad+++r 
       EPA06012.1  93 -RAFIDKHCGIIEESHLTRDSKGELK---EKIGSTGSGTGPANADRAMRV 138
                      .789********************93...59****************996 PP

  == domain 2  score: 138.1 bits;  conditional E-value: 2.2e-44
                      HHHGGGEE-HHHHHHHHHHTT--EEEE--S-GGG-TTTSSTTSS-SS--SHHHHHHHTT--GGGEEEEEEEEESSEEESSSS--TTB--SHHHH CS
  Adenylsucc_synt 192 erlkpyvvdtvallnealkegkkvLfEGaqgtllDidhGtYPfvTsSnttaggaltglglapkkidevlgvvKAyttrvGeGpfptelkdevge 285
                      + l++++vd+ +++n+a++ +++vL+EG qgt+l+++hGtYPfvTs  +ta+g+++  gl+pkk+dev+ v+K+y+trvG+Gp+  el   + e
       EPA06012.1 146 DSLSSLMVDVADEINSAISLNQNVLVEGTQGTFLSLWHGTYPFVTSKDVTASGICADVGLGPKKVDEVIVVFKSYVTRVGTGPLAKEL---TLE 236
                      678899*********************************************************************************9...334 PP

                      HHHHHTT.-B-TTT--B-EEE-EEHHHHHHHHHHHT-SEEEEE-GGGG CS
  Adenylsucc_synt 286 klrekGk.EfgtttgrpRrcGwlDlvllryavrvngvtelaltklDvl 332
                      + ++kG  Efgt+tgr+Rr   +D  l+r+a+++n++t++ +tklDv+
       EPA06012.1 237 EAENKGWsEFGTVTGRQRRAADFDFDLARRAIMLNSATQISITKLDVI 284
                      44566644**************************************97 PP

  == domain 3  score: 20.0 bits;  conditional E-value: 1.5e-08
                      T---GGGS-HHHHHHHHHHHHHHTS-EEEEE-SSSTT-EE CS
  Adenylsucc_synt 380 gvrsfedlpenakkyvefieellgvpvkiisvGpereqti 419
                      g +sf++l ++a+ +++ ie+ l++pv+ii++Gp  +++i
       EPA06012.1 290 GKTSFNELSKDAQLFIKNIENKLNTPVTIIGTGPAINEII 329
                      5689******************************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2251.02
//
Query:       EPA06013.1  [L=69]
Description: hypothetical protein BG20_I1207 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.017   15.1   1.4      0.023   14.7   1.4    1.2  1  zinc_ribbon_6   Zinc-ribbon
      0.023   14.0   0.8       0.15   11.4   1.8    1.8  2  zf-TFIIB        Transcription factor zinc-finger
      0.043   13.5   4.0      0.079   12.7   4.0    1.4  1  Ribosomal_S27e  Ribosomal protein S27
      0.081   13.0   0.4      0.092   12.8   0.4    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.18   11.6   2.7        1.3    8.8   2.8    2.0  2  YacG            DNA gyrase inhibitor YacG
       0.18   11.7   6.8        2.4    8.2   6.8    2.1  1  zinc_ribbon_4   zinc-ribbon domain
        5.3    7.2   8.3        8.6    6.5   2.7    2.3  2  zf-ACC          Acetyl-coA carboxylase zinc finger domain


Domain annotation for each model (and alignments):
>> zinc_ribbon_6  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   1.4   9.1e-06     0.023      29      54 ..       2      27 ..       1      32 [. 0.93

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 9.1e-06
  zinc_ribbon_6 29 kilCnDCekksevkfhvlglkCkeCg 54
                   ki C  C+k+ e ++ +  +kC++C+
     EPA06013.1  2 KIKCPKCKKTAELSMDFSFVKCETCD 27
                   79***********************6 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.8   5.9e-05      0.15       1      23 [.       4      27 ..       4      28 .. 0.90
   2 ?   -1.8   0.0      0.81   2.1e+03      32      40 ..      32      40 ..      31      41 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.9e-05
    zf-TFIIB  1 kCPkCqdele.eserggveidyCp 23
                kCPkC+ + e  ++++ v++++C+
  EPA06013.1  4 KCPKCKKTAElSMDFSFVKCETCD 27
                8*****988889999999999996 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.81
    zf-TFIIB 32 rgeleklle 40
                +ge++k ++
  EPA06013.1 32 YGEYVKFVA 40
                69**99876 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   4.0   3.1e-05     0.079       6      32 ..       1      26 [.       1      30 [. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.1e-05
                    EEEE-TTTS-EEEEESS-SS-EEESSS CS
  Ribosomal_S27e  6 ldvkCpdCenetvvFshaatvvkCisC 32
                    +++kCp+C+++    s   + vkC++C
      EPA06013.1  1 MKIKCPKCKKT-AELSMDFSFVKCETC 26
                    89******875.5679999******** PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.4   3.6e-05     0.092      70      94 ..       2      28 ..       1      41 [. 0.79

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.6e-05
                EEEETTTS-EEECHHH..HHS-TTTSS CS
        HypA 70 kvrCreCgkefeleek..alrCpkCgs 94
                k++C +C+k+ el+ +   ++C++C+ 
  EPA06013.1  2 KIKCPKCKKTAELSMDfsFVKCETCDL 28
                799*********887554568999964 PP

>> YacG  DNA gyrase inhibitor YacG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   2.8   0.00052       1.3       1      18 [.       3      20 ..       3      34 .. 0.77
   2 ?    1.8   0.1      0.08     2e+02       1      14 [.      21      34 ..      21      39 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00052
        YacG  1 vkCPtCkkevewseenpf 18
                +kCP+Ckk+ e s + +f
  EPA06013.1  3 IKCPKCKKTAELSMDFSF 20
                69********99986554 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.08
        YacG  1 vkCPtCkkevewse 14
                vkC tC+ ++++ e
  EPA06013.1 21 VKCETCDLDMSYGE 34
                78999988777765 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   6.8   0.00093       2.4       1      11 [.       1      11 [.       1      28 [. 0.83

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00093
  zinc_ribbon_4  1 MkitCpsCkak 11
                   Mki Cp+Ck++
     EPA06013.1  1 MKIKCPKCKKT 11
                   9*******997 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   2.7    0.0033       8.6       2       9 ..       3      10 ..       3      11 .. 0.86
   2 ?    3.9   0.3     0.023        58       1       7 [.      20      26 ..      20      27 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0033
      zf-ACC  2 tKCpsCge 9 
                +KCp+C+ 
  EPA06013.1  3 IKCPKCKK 10
                8*****96 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.023
      zf-ACC  1 WtKCpsC 7 
                ++KC+ C
  EPA06013.1 20 FVKCETC 26
                79****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 440.72
//
Query:       EPA06014.1  [L=140]
Description: putative translation initiation factor aIF-2, beta subunit [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-29  102.3   0.0    1.7e-29  102.0   0.0    1.1  1  eIF-5_eIF-2B     Domain found in IF2B/IF5
  ------ inclusion threshold ------
      0.068   13.2   0.2       0.13   12.3   0.2    1.6  1  Elf1             Transcription elongation factor Elf1 like
      0.096   13.1   0.3       0.15   12.5   0.3    1.3  1  Lar_restr_allev  Restriction alleviation protein Lar
       0.11   12.6   0.1       0.13   12.3   0.1    1.3  1  PDCD2_C          Programmed cell death protein 2, C-terminal 
       0.13   11.9   0.7        0.3   10.7   0.7    1.6  1  GATA             GATA zinc finger


Domain annotation for each model (and alignments):
>> eIF-5_eIF-2B  Domain found in IF2B/IF5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.0   0.0   4.8e-33   1.7e-29       4     117 .]      21     132 ..      18     132 .. 0.97

  Alignments for each domain:
  == domain 1  score: 102.0 bits;  conditional E-value: 4.8e-33
                   CCSSSS--SSTT--EEEETT.EEEETTHHHHHHHHTTSHHHHHHHHHHHHTSEEEESETTEEEESSSSSCCHHHHHHHHHHHHHTSTSSSTSTCEEE CS
  eIF-5_eIF-2B   4 kedkkerykmpklqvkvegkkktvivNfeeiakaLnrdpehvlkyllkelgtqgsidengrlilngkfeakkleklldkyieeyVlCkeCkspetel 100
                   k+ +++r+++p ++v+ eg+ kt ++Nf+e  k L+rdp++vl+yl+ke+++ ++  +++++++ g+   +++++l++ y+++y+ C++Cksp+t++
    EPA06014.1  21 KKASTTRFELPVVDVMWEGQ-KTFLRNFSEFPKVLRRDPDKVLQYLSKEFAVPAER-SGDKAMFVGRRAPDDFTRLFQIYVKDYLECHTCKSPDTKI 115
                   567889**************.**********************************9.9999************************************ PP

                   CCSSSCEEEEESSSTCE CS
  eIF-5_eIF-2B 101 ekeerllvlkCkaCgak 117
                    ke+r+++l C+aCgak
    EPA06014.1 116 LKENRISFLICEACGAK 132
                   ***************85 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   3.7e-05      0.13      19      58 ..     100     136 ..      85     140 .] 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.7e-05
        Elf1  19 ptkFdCpfCnheksvevkldkkekiaevsCkvCgesfetk 58 
                 + + +C  C++    + k+ k+++i  + C+ Cg++ ++k
  EPA06014.1 100 KDYLECHTCKSP---DTKILKENRISFLICEACGAKSTLK 136
                 667899999999...89*****************998765 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.3   4.1e-05      0.15       3      37 ..     102     133 ..     100     140 .] 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.1e-05
  Lar_restr_allev   3 LkpCPfCggravlersqrvvaeigqcvyCadCga.s 37 
                       + C  C+++++++  +++ +    + +C+ Cga s
       EPA06014.1 102 YLECHTCKSPDTKILKENRIS----FLICEACGAkS 133
                      678*************99999....9********43 PP

>> PDCD2_C  Programmed cell death protein 2, C-terminal putative domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   3.6e-05      0.13      44      96 ..      18     112 ..       1     136 [. 0.53

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.6e-05
     PDCD2_C  44 ekskeekes......eeeeleky......eksldktfekFkkriaaepeQvlRYelggkPLwls................................... 95 
                 ++sk+ +++             +      +k+  + f++F k ++++p+ vl Y  ++   ++                                    
  EPA06014.1  18 GDSKK-ASTtrfelpV------VdvmwegQKTFLRNFSEFPKVLRRDPDKVLQYLSKEFAVPAErsgdkamfvgrrapddftrlfqiyvkdylechtck 109
                 33322.2221332220......233342222337899*****************664444444444555555557777777776666666666666655 PP

     PDCD2_C  96 ..s 96 
                   +
  EPA06014.1 110 spD 112
                 542 PP

>> GATA  GATA zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.7   8.4e-05       0.3       1      34 [.     105     137 ..     105     138 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 8.4e-05
        GATA   1 CsnCgttkTplWRrgpdgnksLCnaCGlyykkkg 34 
                 C+ C++ +T+  ++++      C+aCG +  +kg
  EPA06014.1 105 CHTCKSPDTKILKENRISFL-ICEACGAKSTLKG 137
                 99*************77777.******9888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1070.48
//
Query:       EPA06015.1  [L=382]
Description: putative membrane protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-89  299.4  15.4    4.7e-89  299.1  15.4    1.0  1  DUF373    Domain of unknown function (DUF373)
  ------ inclusion threshold ------
          7    6.8   7.2        0.5   10.5   0.5    2.5  4  SPC12     Microsomal signal peptidase 12 kDa subunit (SPC12)


Domain annotation for each model (and alignments):
>> DUF373  Domain of unknown function (DUF373)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  299.1  15.4   5.2e-93   4.7e-89       1     320 [.      19     354 ..      19     368 .. 0.87

  Alignments for each domain:
  == domain 1  score: 299.1 bits;  conditional E-value: 5.2e-93
      DUF373   1 ktLvlcvDrDdDlgrkagvktPvvGreavleaavklaladPeDSDvNalfgaikvydeLkaegedvevavvtGdekvgveadrkiaeqldevlsklead 99 
                 k+Lv+cvDrD+D+g+kag++tPv+Gr+a+++aa++lal+dPeD+D+N++f+aik+y++L ++g +vev++v+G +k+gv+ad+ki  +++++ ++++a+
  EPA06015.1  19 KLLVICVDRDNDIGEKAGITTPVIGRNACIDAAQRLALEDPEDADSNSMFAAIKTYEDLISKGYQVEVVIVAGIKKRGVQADEKILMEIKKISESFSAN 117
                 68************************************************************************************************* PP

      DUF373 100 saivVsDGaeDesvlpiiqsrvkvdsvkrVvVkqsrniEstyyll....kkalkdpelrktiLvplGlllliyalllllglpelalaiillllGlylll 194
                 +a++VsDG++Desv+p+iq+ ++v+sv+rVv+k sr++E++y+++    k++ +d++++k++L+++G+llli ++ +++g+++ ++a+++ +lG+++l+
  EPA06015.1 118 GAVIVSDGEDDESVIPVIQNVLPVISVQRVVMKVSRSVEYSYAVFgkylKMLAYDSKYSKFFLGVPGILLLIGGIGTIFGYTAEIFAVLVSILGAAFLI 216
                 *********************************************999999************************************************ PP

      DUF373 195 rGfgldelleelleklkesleegritfvtyvvallllligiisgyislesvss...asvssglltlila..fiygavewlalailtaslgkiideylkr 288
                 r+f++d++     ++l + + +g i+++t+v+++l++l +i +g++s+++      ++  s ++++i++  f+ g++++l++++ ++++g ++++++ +
  EPA06015.1 217 RAFDVDRA----WSNLTKPTPMGFIRIFTMVAGILIILSSIPAGINSIDQKLIekdSELISIITDKIVIgqFVIGVLPTLWIGLGAIFAGVLLSNWIGG 311
                 ******95....569******************************99776544566666667777777688**************************54 PP

      DUF373 289 e...ekdiarllllpflvlaiglvlygasaylls............l 320
                      +di r+++l+ l+ ++ + ++ ++    s            l
  EPA06015.1 312 IprqITDILRIIVLVALYPITSQFIIIMM----SydvgsitlvpplL 354
                 44444444455544444444444444444....33444444444443 PP

>> SPC12  Microsomal signal peptidase 12 kDa subunit (SPC12)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.5   5.5e-05       0.5      16      50 ..     185     219 ..     182     231 .. 0.88
   2 ?   -2.3   0.1      0.54   4.9e+03      37      37 ..     291     291 ..     262     315 .. 0.54
   3 ?   -2.5   0.5      0.65   5.8e+03      27      27 ..     309     309 ..     282     344 .. 0.61
   4 ?   -1.8   0.1      0.37   3.3e+03      41      41 ..     353     353 ..     314     377 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 5.5e-05
       SPC12  16 ilvlsaviafivGyitqdlkltlyillagvvltll 50 
                 il+l++ i+ i+Gy ++ + +++ il+a++++ ++
  EPA06015.1 185 ILLLIGGIGTIFGYTAEIFAVLVSILGAAFLIRAF 219
                 89999************************998766 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.54
       SPC12  37 t 37 
                 t
  EPA06015.1 291 T 291
                 2 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 0.65
       SPC12  27 v 27 
                 +
  EPA06015.1 309 I 309
                 3 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 0.37
       SPC12  41 l 41 
                 l
  EPA06015.1 353 L 353
                 2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       811  (0.045234); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2381.41
//
Query:       EPA06016.1  [L=189]
Description: KH domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.1e-10   38.2  10.1    8.8e-05   22.3   1.2    2.7  3  KH_1      KH domain
     0.0082   15.9   0.1      0.026   14.2   0.0    1.8  2  GP57      Phage Tail fiber assembly helper gene product 57
  ------ inclusion threshold ------
       0.03   14.1   5.6        2.8    7.9   0.2    2.9  2  KH_2      KH domain
       0.16   11.8   0.0       0.23   11.3   0.0    1.2  1  DUF4335   Domain of unknown function (DUF4335)


Domain annotation for each model (and alignments):
>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   1.2     2e-08   8.8e-05       4      58 ..       7      57 ..       4      75 .. 0.82
   2 ?   -1.4   0.0      0.47   2.1e+03      16      26 ..      97     107 ..      95     108 .. 0.86
   3 !   20.7   1.4   5.8e-08   0.00026      11      65 ..     107     153 ..     104     154 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 2e-08
                EEEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEESSTT...T.-EEEEEESHHHHH CS
        KH_1  4 ilvPsslvgriIGkgGsnIkeIreetgakIkvpksedegsderevtisGspeave 58
                + +P++ +  +IGk Gs   +I+e + +  +++ +++   +e  +t  G+ e++e
  EPA06016.1  7 LRIPNDRIAVLIGKSGSIKSKIEELCRVTLDID-GQS---GEVFITSNGKVEDIE 57
                48**********************889999977.544...455666567666665 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.47
                 TGGGHHHHHHH CS
        KH_1  16 GkgGsnIkeIr 26 
                 Gk ++nI +I+
  EPA06016.1  97 GKSNANIERIK 107
                 99999999995 PP

  == domain 3  score: 20.7 bits;  conditional E-value: 5.8e-08
                 HHHHHTGGGHHHHHHHHHHT-EEEEESSTT...T.-EEEEEESHHHHHHHHHHHH CS
        KH_1  11 vgriIGkgGsnIkeIreetgakIkvpksedegsderevtisGspeavekAkelie 65 
                  griIG gG+  k++++ tg++I v  +       ++v i+G+  +    +++i+
  EPA06016.1 107 KGRIIGEGGKARKNMENLTGTHISVY-G-------KTVSIIGDTSKLRLVVDAIS 153
                 69**********************87.5.......58*****7777988888875 PP

>> GP57  Phage Tail fiber assembly helper gene product 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.67     3e+03      43      61 ..      12      31 ..       2      43 .. 0.54
   2 !   14.2   0.0   5.9e-06     0.026       9      70 ..      98     157 ..      94     161 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.67
        GP57 43 aeiaravGitGdt.ikveei 61
                  ia  +G +G    k+ee+
  EPA06016.1 12 DRIAVLIGKSGSIkSKIEEL 31
                44555555555421345544 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 5.9e-06
        GP57   9 klsaeivtlksrildtqdqaarlmeeskilqGtlaei.aravGitGdtikveeiveavknlta 70 
                 k  a+i  +k ri+    +a + me+   l Gt   +  ++v i Gdt k+  +v+a+  ++ 
  EPA06016.1  98 KSNANIERIKGRIIGEGGKARKNMEN---LTGTHISVyGKTVSIIGDTSKLRLVVDAISSISN 157
                 66799999****************97...88997665389*****************987765 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.2   0.00061       2.8      34      74 ..      12      54 ..       6      57 .. 0.76
   2 ?    7.5   0.9   0.00077       3.4      36      68 ..     107     138 ..     104     141 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00061
                SCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTC..EEEEEE.EET CS
        KH_2 34 sqpgivIGkgGsnikkigkelrkdieklegkk..Vklniv.kVk 74
                 + +++IGk Gs   ki++  r  ++ + g+   V++ +  kV+
  EPA06016.1 12 DRIAVLIGKSGSIKSKIEELCRVTLD-IDGQSgeVFITSNgKVE 54
                6889***************9998886.33333348877777775 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00077
                 HHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEE CS
        KH_2  36 pgivIGkgGsnikkigkelrkdieklegkkVkl 68 
                 +g++IG gG+  k+++   +  i  + gk V++
  EPA06016.1 107 KGRIIGEGGKARKNMENLTGTHIS-VYGKTVSI 138
                 89**************99999995.88888875 PP

>> DUF4335  Domain of unknown function (DUF4335)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   5.2e-05      0.23      26      87 ..     116     180 ..     108     188 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.2e-05
     DUF4335  26 elkdllfiLsfdeprlveeqvslkGgreqLeaLvkaVsaYvqefLsgvs..hpkessseea.elv 87 
                 + ++ +  L+   + + +++vs+ G+ ++L   v+a+s+  +  ++g    ++++++ +++ e  
  EPA06016.1 116 KARKNMENLTGTHISVYGKTVSIIGDTSKLRLVVDAISSISNGSIHGAVynKLEAANRKNKqEKM 180
                 56778899999999********************************6654545555444442233 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1198.01
//
Query:       EPA06017.1  [L=173]
Description: THUMP domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-13   50.3   1.7    3.2e-13   50.0   1.7    1.1  1  THUMP     THUMP domain


Domain annotation for each model (and alignments):
>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.0   1.7   1.8e-17   3.2e-13      10     143 ..      27     156 ..      18     157 .. 0.89

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 1.8e-17
                 TT.H-SEEEEETTEEEEECTEEEEEETHHHHHHHHHTST....TECEEEEEEEEEESSHHHHHHHHHHHHHHHHHHCT-EEEEEEEESSSTSSSHHHHH CS
       THUMP  10 gkvnverveagkgrivvelkgekpeedeellkealekar....giqrvipvcevceadledileaakeivkkkfeeeketFaVrvkrrgkhfeftsrei 104
                 g+ + + ++ +  +i+  +++ +p+   +++ke l   +    +  r+ip+  + e+++e+i++  + +++   e+e  ++++ +++r+++  ++s+ei
  EPA06017.1  27 GDSEPSIIITNMSGILTAETKLDPIQVVNKIKEMLLDEPwsirYCLRIIPIQKIMETNIESIENGLSDLINLISENE--SYRISIEKRNSN--ISSQEI 121
                 5566677777778888888999999999999999998888888****************************777766..***********5..****** PP

                 HHHHHHHHHCCTT-EE-SSS-SEEEEEEEETTEEEEEEE CS
       THUMP 105 nrevGkaivektglkVdlenPdivvrveiikdkayisid 143
                  + ++k i++    kV+le Pd+vv++ei+++k++i i+
  EPA06017.1 122 ISRIAKKIKN----KVSLEFPDKVVLIEILGNKTGIAIV 156
                 *********9....999*******************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       932  (0.0519828); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1124.70
//
Query:       EPA06018.1  [L=162]
Description: hypothetical protein BG20_I1198 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.98    9.2   7.3       0.86    9.4   2.6    2.1  2  MAT1      CDK-activating kinase assembly factor MAT1


Domain annotation for each model (and alignments):
>> MAT1  CDK-activating kinase assembly factor MAT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.2    0.0075   1.3e+02      41      64 ..      38      61 ..      34      64 .. 0.91
   2 ?    9.4   2.6   4.8e-05      0.86      38      85 ..     111     158 ..     103     161 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.0075
        MAT1 41 keYndYLeeveeivfnLtngidve 64
                 +Y++YL+ v +i   L ++id+e
  EPA06018.1 38 SDYENYLDGVKKIHQVLHESIDTE 61
                68************99**999986 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 4.8e-05
        MAT1  38 esLkeYndYLeeveeivfnLtngidveeTekkleqYekenkelIlknk 85 
                 e Lk++n+Y+ e   +   L++g +  +T +k+e+ + e +elI+k+ 
  EPA06018.1 111 EALKKFNEYIIETKVVANMLKEGQNSIDTIQKIESLKLESQELIKKSD 158
                 579**********999999*************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1338  (0.0746277); expected 358.6 (0.02)
Passed bias filter:                      752  (0.0419432); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1016.37
//
Query:       EPA06019.1  [L=246]
Description: orotidine 5'-phosphate decarboxylase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.3e-26   92.3   0.0    3.8e-26   92.1   0.0    1.0  1  OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS famil


Domain annotation for each model (and alignments):
>> OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.1   0.0   2.1e-30   3.8e-26       2     224 ..      17     238 ..      16     239 .. 0.88

  Alignments for each domain:
  == domain 1  score: 92.1 bits;  conditional E-value: 2.1e-30
                 EEEEEE-SSSH.....HHHHHHHHHHGGGSSEEEEEHHHHHHHTHH.HHTHHHHHHHHHTSEEEEEEEE-S-HHHHHHHHHSTCHHHHTTESEEEEEGT CS
   OMPdecase   2 nLclalDvata.....relleladkvgpsivvlKthydlvegwgfegtgaklaalarkhgflifeDrKfaDIGntvekqatagsarikewadivtvhav 95 
                 n++la D+++       + ++ ++k+ p+ + +K +  l+   gf+  + k+ + a++ g   ++D+K+ DIGnt +   +      +++ d+v++++ 
  EPA06019.1  17 NIILANDYDSSvsnleTKTIQNIKKLSPYLCGIKLNFHLLLPLGFK-EISKINKIAHECGLQTIADIKLNDIGNTNKVTTE---RLWDLGFDAVIANPI 111
                 6778888888777777889999**********************99.889******************************9...678************ PP

                 GHHHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHH...H.SHHHHHHHHHHHHHHHTTESEEECCCHTHHHHHHTTCSCEEEHHHTTEEEEECTTCC CS
   OMPdecase  96 aGkasvkalaeaaekwgnrgllilaqmsskgnlmlqe...k.gytqacveaarehkaedfvmGfvaqetlnateedaddfihltpgigleqggdgkgqq 190
                 +G +s+k l++ a k + +g++ l+ ms +++    +   k g +q++++   + + e++ +G+v+++t +   ++  +    + g +l+  + g g q
  EPA06019.1 112 MGLDSLKLLVKSAHKEN-KGVITLCHMSAPEAKLSYDmeiKmGKKQQLYQLFLDWAIESKADGIVVGATFP---KI-IQYCYNKAGTKLDIFSPGIGTQ 205
                 ****************6.9************9777777443888888888888888888889*******99...22.4666777788888888888888 PP

                 GGGHHHHHHHTTCSEEEESHHHHTSSSHHHHHHH CS
   OMPdecase 191 yntpekligiagadiiivGRgIlkagdpveeaer 224
                   +++++i+ ag+ ++ivGR I+++++pv  +++
  EPA06019.1 206 GGNTKEVIS-AGTRYLIVGRTIINSKNPVDVLKE 238
                 888889999.89*****************98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1826.01
//
Query:       EPA06020.1  [L=106]
Description: ribosomal S17 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-18   66.8   4.5    2.2e-18   66.3   4.5    1.3  1  Ribosomal_S17e  Ribosomal S17
  ------ inclusion threshold ------
      0.016   15.0   3.8      0.019   14.7   3.5    1.2  1  DUF4201         Domain of unknown function (DUF4201)
      0.018   14.8   1.6       0.15   11.8   0.2    2.0  2  NUDIX_5         NUDIX, or N-terminal NPxY motif-rich,  region


Domain annotation for each model (and alignments):
>> Ribosomal_S17e  Ribosomal S17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.3   4.5   3.6e-22   2.2e-18       9      82 ..       4      78 ..       1     102 [. 0.85

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 3.6e-22
                    HHHHHHHHHHS-TTT--S-HHHHHHHHHHHS----SHHHHHHHHHHHHHHHH.TTSS--SS---HHHHHHHHHHH CS
  Ribosomal_S17e  9 vKkaarviiekyyskltndFhtnkkvceevaiipskklrnkiaGyvthlmkr.iqkgpvrgislklqeeererrd 82
                    +K+ +++++ ++++k+++dF++nkkv++++aii+sk l+n+iaGy+t+++k+ i++++v+  +++ ++ e    +
      EPA06020.1  4 IKRLSYEVLVEHKPKFGEDFADNKKVLDQIAIIRSKGLKNEIAGYITKFIKKeIREEKVKQSQIESSKIENHTLK 78
                    9**************************************************99**********998876655444 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   3.5   3.2e-06     0.019      18      67 ..      41      90 ..      32      97 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.2e-06
     DUF4201 18 lkhqlakiqeklekkeelgegLtlidFeqlqienqalnkkIeernkeLkr 67
                lk+ +a   +k  kke   e+++ ++ e+ +ien++l++kI e ++++++
  EPA06020.1 41 LKNEIAGYITKFIKKEIREEKVKQSQIESSKIENHTLKEKISEGDDDVQE 90
                6888999999********************************98888876 PP

>> NUDIX_5  NUDIX, or N-terminal NPxY motif-rich,  region of KRIT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   2.5e-05      0.15      11      57 ..       8      55 ..       3      64 .. 0.88
   2 ?    2.7   0.1     0.015        92      27      57 ..      71     101 ..      57     106 .] 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.5e-05
     NUDIX_5 11 ayeilllevpleGk.kkkrkKvLlevklraseeksksildyvlettks 57
                +ye+l+  +p +G+   ++kKvL ++ +  s+   ++i  y+++ +k+
  EPA06020.1  8 SYEVLVEHKPKFGEdFADNKKVLDQIAIIRSKGLKNEIAGYITKFIKK 55
                7*************558999**********9999999****9999887 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.015
     NUDIX_5  27 krkKvLlevklraseeksksildyvlettks 57 
                 k +   l+ k+ ++++  +++++ v e t +
  EPA06020.1  71 KIENHTLKEKISEGDDDVQEVIEMVSEPTAN 101
                 55566788999999***********998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1383  (0.0771376); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 696.81
//
Query:       EPA06021.1  [L=63]
Description: hypothetical protein BG20_I1209 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 465.88
//
Query:       EPA06022.1  [L=153]
Description: hypothetical protein BG20_I1206 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0015   18.6   0.1     0.0028   17.7   0.1    1.4  1  Annexin       Annexin
     0.0062   16.7   0.1         30    4.9   0.0    3.2  3  Catalase-rel  Catalase-related immune-responsive


Domain annotation for each model (and alignments):
>> Annexin  Annexin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   3.2e-07    0.0028      18      60 ..      65     107 ..      62     111 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.2e-07
                 HHHHHHHHHSTHHHHHHHHHHHHHHHSS-HHHHHHHHS-HHHH CS
     Annexin  18 ktlieIlatRsnaqlqaifeeYkkkygkdLekdIksetsGdfe 60 
                 kt+ eIl+t s++q+ + f  Y+k+ +k+ +k I   ++G +e
  EPA06022.1  65 KTWLEILTTLSEEQRNELFSGYIKEISKSPQKLIIFNLDGILE 107
                 6899************************988888777777665 PP

>> Catalase-rel  Catalase-related immune-responsive
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0      0.01        91      17      30 ..      35      48 ..      29      55 .. 0.79
   2 !    4.9   0.0    0.0033        30      18      40 ..      74      96 ..      71     101 .. 0.86
   3 !    4.7   0.0    0.0039        35      14      47 ..     108     141 ..     107     151 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.01
                  HS-HHHHHHHHHHH CS
  Catalase-rel 17 smseeekerlvnni 30
                  sm e ek+ ++nn 
    EPA06022.1 35 SMGETEKKEIINNA 48
                  78888888888886 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0033
                  S-HHHHHHHHHHHHHHHTTSS-H CS
  Catalase-rel 18 mseeekerlvnniafelskvede 40
                  +see+++ l++ + +e+sk +++
    EPA06022.1 74 LSEEQRNELFSGYIKEISKSPQK 96
                  89***************998755 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.0039
                   HHHHS-HHHHHHHHHHHHHHHTTSS-HHHHHHHH CS
  Catalase-rel  14 lyrsmseeekerlvnniafelskvedeeiqerql 47 
                    + s+++eek+ l + i++ +s+ e ee ++ +l
    EPA06022.1 108 IFLSLKDEEKQILSQTIRKIISDLEVEEKRKVML 141
                   5789**************9999998777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       907  (0.0505884); expected 358.6 (0.02)
Passed bias filter:                      597  (0.033298); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1001.25
//
Query:       EPA06023.1  [L=613]
Description: DNA topoisomerase VI, B subunit [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.1e-55  184.8   0.0    1.4e-54  184.2   0.0    1.3  1  Topo-VIb_trans  Topoisomerase VI B subunit, transducer
    2.9e-06   27.7   0.0      6e-06   26.7   0.0    1.6  1  HATPase_c       Histidine kinase-, DNA gyrase B-, and HSP90-l
    0.00033   20.5   0.0    0.00071   19.4   0.0    1.5  1  HATPase_c_3     Histidine kinase-, DNA gyrase B-, and HSP90-l


Domain annotation for each model (and alignments):
>> Topo-VIb_trans  Topoisomerase VI B subunit, transducer
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.2   0.0   2.4e-58   1.4e-54       1     158 [.     415     570 ..     415     571 .. 0.97

  Alignments for each domain:
  == domain 1  score: 184.2 bits;  conditional E-value: 2.4e-58
  Topo-VIb_trans   1 PstdclspigeeliekglkkelkpefvaavtrkpkvyeghpfivEvgiayGGelekeekaeilRfaNrvPLlydegadvitkavksinwkrYkle 95 
                     P+ +cl+p+gee +ekg+kk +kp+f+a+++r++++y+g pf+vE+giayGGe++    ++++R+aNr+PLlydeg+dv++k+v++++w+rYk++
      EPA06023.1 415 PDPSCLAPLGEEPLEKGMKKFFKPDFCAVIQRPASAYSGFPFVVEMGIAYGGEIR-PGGPHVYRYANRIPLLYDEGSDVVLKVVHDTDWTRYKVK 508
                     899*************************************************995.5789*********************************** PP

  Topo-VIb_trans  96 qpedpvvvlvhvastkvPfksegKeaiadveeiekeiklalqevarkLkkylskkekekeeke 158
                      +  p+v++ h++st++P+k++gKe++ad +eie+e++l lq + rkL +y+sk+ +++ +k+
      EPA06023.1 509 GDP-PFVIVSHICSTRIPYKTVGKENVADRQEIERELRLGLQFLSRKLAAYMSKRGQAEMAKK 570
                     765.***************************************************99998886 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0     1e-09     6e-06       4      83 ..      30     122 ..      27     179 .. 0.69

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 1e-09
                 HHHHHHHHHHHHHHHHHHSTTT...EEEEEEEE...EE...TEEEEEEEESSSSSTTHHHTGTCS.TTCH...HCSTCHTSTSSSHHHHHHHH CS
   HATPase_c   4 krLrqiisnlvdNavkfatkag...eieveika...se...ddlvisveDnGiGipkedlkklfe.kfsq...ddstkrggggtGlGlsivkk 83 
                 + L+ +++++v+N++++  ++g   +++ +ika   ++   + + ++v+DnG+Gi  +++++ f+  ++      +++rg +g G  ++i   
  EPA06023.1  30 RSLYTAVREFVENSLDACDQKGifpDVHMSIKAvdpDKpdpKPYILTVKDNGPGIESKHVPLAFGtVLYGskfGLKQARGMFGLGATMAILYG 122
                 67999***********955555555566666666662255689******************88876444444433555555555555555544 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   1.2e-07   0.00071       3      82 ..      32     120 ..      30     168 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.2e-07
  HATPase_c_3   3 lekAlaelvdNsldAdaen.......vkievn...knrgktgeivieDdGkGmseeelknal.rlatsskeakrkstslGkkGiGlklAsl 82 
                  l++A+ e+v+NsldA  ++        +i++    k + k+  ++++D+G G++ + +  a+ ++   sk     ++ +G +G+G  +A+l
   EPA06023.1  32 LYTAVREFVENSLDACDQKgifpdvhMSIKAVdpdKPDPKPYILTVKDNGPGIESKHVPLAFgTVLYGSKFG--LKQARGMFGLGATMAIL 120
                  578************99999****66444444332333445789**************99774688888884..58899999999766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (613 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.44
# Mc/sec: 4149.79
//
Query:       EPA06024.1  [L=95]
Description: hypothetical protein BG20_I1210 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-11   43.7   0.2    2.5e-11   43.4   0.2    1.2  1  HTH_45          Winged helix-turn-helix
    2.9e-07   30.3   0.0    3.9e-07   29.9   0.0    1.2  1  MarR_2          MarR family
    5.7e-05   22.8   0.0    7.4e-05   22.5   0.0    1.2  1  HTH_IclR        IclR helix-turn-helix domain
    0.00028   20.6   0.1    0.00033   20.4   0.1    1.1  1  RP-C            Replication protein C N-terminal domain
    0.00033   20.4   0.0    0.00044   20.0   0.0    1.3  1  DUF4364         Domain of unknown function (DUF4364)
    0.00042   20.2   0.0     0.0006   19.7   0.0    1.2  1  MarR            MarR family
    0.00048   20.0   0.0    0.00066   19.5   0.0    1.2  1  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0007   19.1   0.4     0.0014   18.1   0.1    1.6  2  HTH_24          Winged helix-turn-helix DNA-binding
     0.0033   17.2   0.0     0.0045   16.8   0.0    1.2  1  RQC             RQC domain
     0.0036   17.7   0.0     0.0044   17.5   0.0    1.2  1  HTH_27          Winged helix DNA-binding domain
      0.004   17.1   0.0      0.005   16.8   0.0    1.2  1  Dimerisation2   Dimerisation domain
      0.006   16.9   0.1      0.014   15.7   0.1    1.7  1  Linker_histone  linker histone H1 and H5 family
     0.0089   15.8   0.1      0.011   15.5   0.1    1.2  1  FtsK_gamma      Ftsk gamma domain
     0.0094   16.6   0.0      0.013   16.1   0.0    1.2  1  RPA_C           Replication protein A C terminal
  ------ inclusion threshold ------
      0.013   15.6   0.0      0.018   15.1   0.0    1.4  1  Mrr_N           Mrr N-terminal domain
      0.015   15.6   0.1      0.019   15.3   0.1    1.2  1  Rrf2            Transcriptional regulator
      0.019   14.8   0.1      0.034   14.0   0.1    1.4  1  HTH_5           Bacterial regulatory protein, arsR family
      0.021   14.6   0.0      0.028   14.2   0.0    1.5  1  DUF1495         Winged helix DNA-binding domain (DUF1495)
      0.025   14.6   0.2       0.04   13.9   0.1    1.5  1  HTH_36          Helix-turn-helix domain
      0.025   14.7   0.1      0.031   14.5   0.1    1.2  1  Ribosomal_S25   S25 ribosomal protein
      0.028   13.8   0.1      0.032   13.6   0.1    1.0  1  RNA_pol_Rpc34   RNA polymerase Rpc34 subunit
       0.03   14.1   0.1      0.036   13.8   0.1    1.1  1  DUF4194         Domain of unknown function (DUF4194)
      0.036   14.0   0.0      0.046   13.7   0.0    1.3  1  PadR            Transcriptional regulator PadR-like family
      0.051   13.7   0.1      0.093   12.9   0.1    1.6  1  DUF2250         Uncharacterized protein conserved in archaea 
      0.055   13.5   0.1      0.083   12.9   0.1    1.3  1  Cdc6_C          CDC6, C terminal winged helix domain
      0.064   13.3   0.0      0.091   12.8   0.0    1.2  1  HTH_20          Helix-turn-helix domain
      0.084   13.0   0.3       0.12   12.6   0.3    1.1  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
       0.11   12.6   0.9       0.16   12.0   0.6    1.5  1  HTH_46          Winged helix-turn-helix DNA binding
       0.11   12.5   0.0       0.13   12.3   0.0    1.1  1  Replic_Relax    Replication-relaxation


Domain annotation for each model (and alignments):
>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.4   0.2   4.1e-14   2.5e-11       1      75 [.       4      87 ..       4      89 .. 0.89

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 4.1e-14
      HTH_45  1 rRskleIiadILeais.....egeakkTkimykanLsykllnkYLdmLvekgli....kkskekYvlTekGlelleklkeleel 75
                +R+ ++Ii +IL+ ++     e++a+ T ++ kan+s +++++ L++Lv++gl+    ++ ++kY++ + G+e+l+ + ++ ++
  EPA06024.1  4 YRTHMKIIGEILSTTRddlqdENGASVTYLIRKANISHSRISRILKTLVSQGLLeqvdSHGSNKYKISQSGREFLQAYYTFTSF 87
                69***********985333347899****************************977666799****************999876 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.0   6.3e-10   3.9e-07      15      56 ..      23      62 ..      12      65 .. 0.90

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 6.3e-10
                HCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
      MarR_2 15 grrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                 ++ g   +v+ l r+ ++s+s++srilk Lv++GL+e++++
  EPA06024.1 23 QDENG--ASVTYLIRKANISHSRISRILKTLVSQGLLEQVDS 62
                55666..8******************************9976 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   1.2e-07   7.4e-05      18      51 ..      27      60 ..      13      61 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.2e-07
                S-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
    HTH_IclR 18 eltlselArrtglpkStvhRlLqtLvelGyveqd 51
                + +++ l r++ ++ S  +R+L+tLv +G++eq 
  EPA06024.1 27 GASVTYLIRKANISHSRISRILKTLVSQGLLEQV 60
                359999**************************96 PP

>> RP-C  Replication protein C N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.1   5.3e-07   0.00033      61     125 ..      21      81 ..       4      82 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 5.3e-07
        RP-C  61 dlseearlivfpsNaqLsralglsestlrrhlaaLveaGliirrDspngkRyarrdreGeieeAf 125
                 dl++e++    +s + L r+ ++s+s+++r+l+ Lv  Gl+   Ds     y   +++ e  +A+
  EPA06024.1  21 DLQDENG----ASVTYLIRKANISHSRISRILKTLVSQGLLEQVDSHGSNKYKISQSGREFLQAY 81 
                 4555554....577899****************************************99999998 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   7.1e-07   0.00044      26      72 ..      34      80 ..      10      86 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 7.1e-07
     DUF4364 26 leneytnYfdlqqalseLvesglieeeekenktlykiTekGketlel 72
                + +  ++   ++ +l+ Lv++gl+e+ ++++++ yki+++G+e l+ 
  EPA06024.1 34 IRKANISHSRISRILKTLVSQGLLEQVDSHGSNKYKISQSGREFLQA 80
                5677788888999******************************9986 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   9.7e-07    0.0006      12      54 ..      22      64 ..      20      68 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 9.7e-07
                HHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETT CS
        MarR 12 lyeqgplsvseLakklgvskstvtrvldrLekkGlieRskspe 54
                l +++++sv+ L +k ++s s ++r+l++L+ +Gl+e   s++
  EPA06024.1 22 LQDENGASVTYLIRKANISHSRISRILKTLVSQGLLEQVDSHG 64
                6678899*****************************9877765 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   1.1e-06   0.00066      22      63 ..      27      69 ..      21      73 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.1e-06
                CCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.TTEEE CS
        TrmB 22 patadeiaeelgvprskvYevLrsLedkGlVerekgr.pklYr 63
                 a+++ + +++++++s++ ++L+ L++ Gl e +++   ++Y+
  EPA06024.1 27 GASVTYLIRKANISHSRISRILKTLVSQGLLEQVDSHgSNKYK 69
                677888999***********************99977666776 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0         4   2.5e+03       4      13 ..       6      15 ..       5      19 .. 0.71
   2 !   18.1   0.1   2.3e-06    0.0014      12      47 ..      22      57 ..      20      58 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 4
      HTH_24  4 tdrkILelLq 13
                t+ kI+ ++ 
  EPA06024.1  6 THMKIIGEIL 15
                7788887765 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 2.3e-06
      HTH_24 12 LqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                Lq++ + s + L ++ ++S s ++r lk L+++Gl+
  EPA06024.1 22 LQDENGASVTYLIRKANISHSRISRILKTLVSQGLL 57
                8999******************************97 PP

>> RQC  RQC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   7.2e-06    0.0045      58      98 ..      38      79 ..      29      85 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 7.2e-06
                TS-HHHHHHHHHHHHHTTSE.EEE..SSSBEEE-CCGHHHHT CS
         RQC 58 dlskkewrrlirqLiaegyL.eedveeygvlkltekarevlk 98
                ++s + + r+++ L+++g+L ++d ++ + +k+++++re+l+
  EPA06024.1 38 NISHSRISRILKTLVSQGLLeQVDSHGSNKYKISQSGREFLQ 79
                678999**************555555666***********98 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   7.1e-06    0.0044      15      54 ..      24      63 ..      13      74 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 7.1e-06
      HTH_27 15 rrrrkkladlcgrlnvedshisyslkkLtekGLvertgde 54
                 +++++ + l+++ n++ s is +lk L+ +GL+e+  + 
  EPA06024.1 24 DENGASVTYLIRKANISHSRISRILKTLVSQGLLEQVDSH 63
                566777799*************************887665 PP

>> Dimerisation2  Dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   8.1e-06     0.005      26      85 ..      21      79 ..      19      89 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 8.1e-06
  Dimerisation2 26 lLkeeeplsaeevaeelgasvkGterLldacvaLgLLerekkeekkalYsntelastyLv 85
                    L++e+  s+  + ++ ++s++ ++r+l+++v+ gLLe+  +++ ++ Y+ ++  +++L 
     EPA06024.1 21 DLQDENGASVTYLIRKANISHSRISRILKTLVSQGLLEQVDSHG-SNKYKISQSGREFLQ 79
                   577788899999999***********************776666.69*****99999996 PP

>> Linker_histone  linker histone H1 and H5 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   2.3e-05     0.014      40      73 ..      37      70 ..      11      71 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.3e-05
  Linker_histone 40 skf.ksllkkalkkgvekgelvqpkgkGasGsfKL 73
                    +++  s++++ lk++v++g l+q+ ++G s+++K+
      EPA06024.1 37 ANIsHSRISRILKTLVSQGLLEQVDSHG-SNKYKI 70
                    3334899*****************9999.678887 PP

>> FtsK_gamma  Ftsk gamma domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   1.8e-05     0.011      16      55 ..      24      63 ..      13      71 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.8e-05
  FtsK_gamma 16 eegkaStSllQRrlriGYnRAarlidqLeeeGiVgpaegs 55
                +e+ aS+ +l R+ +i ++R +r++  L ++G+ ++ ++ 
  EPA06024.1 24 DENGASVTYLIRKANISHSRISRILKTLVSQGLLEQVDSH 63
                6789****************************99987765 PP

>> RPA_C  Replication protein A C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   2.1e-05     0.013      53      97 ..      13      57 ..       3      60 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.1e-05
                HHHHHHHH.SXSTTTEEHHHHHHHSTSXHHHHHHHHHHHHHTTSE CS
       RPA_C 53 qvlnlikqspeseeGvhvdeiaqklrlsvndvkqavdeLsneGii 97
                ++l++ ++  ++e+G +v ++ +k ++s + + +++++L+++G++
  EPA06024.1 13 EILSTTRDDLQDENGASVTYLIRKANISHSRISRILKTLVSQGLL 57
                688899999**********************************85 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0     3e-05     0.018      47      86 ..      37      79 ..       4      80 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3e-05
       Mrr_N 47 qtrfknrvgWartyLkkagllespk...rgvwkiTekGrevlk 86
                 ++ ++r++  +++L+ +glle+ +     ++ki++ Gre+l+
  EPA06024.1 37 ANISHSRISRILKTLVSQGLLEQVDshgSNKYKISQSGREFLQ 79
                47788999999***********999866778*********996 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.1   3.1e-05     0.019      20      58 ..      23      60 ..       5      66 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.1e-05
                SSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
        Rrf2 20 eeeeepvsseeiaerqnispsylekilakLrkaglvksv 58
                ++e++ +s++ + ++ nis+s +++il++L  +gl++ v
  EPA06024.1 23 QDENG-ASVTYLIRKANISHSRISRILKTLVSQGLLEQV 60
                44444.999**************************9865 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   5.5e-05     0.034      16      46 ..      28      58 ..      22      59 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.5e-05
                EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
       HTH_5 16 lcvcelaeelglsqstvShHLkkLreaGLVe 46
                ++v+ l ++ ++s s +S+ Lk L  +GL+e
  EPA06024.1 28 ASVTYLIRKANISHSRISRILKTLVSQGLLE 58
                7888999**********************86 PP

>> DUF1495  Winged helix DNA-binding domain (DUF1495)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   4.5e-05     0.028      57      87 ..      49      78 ..       6      80 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.5e-05
     DUF1495 57 ssLielGLveeeeeseglklYklteeGieiv 87
                + L+++GL e + +s+g + Yk++++G+e+ 
  EPA06024.1 49 KTLVSQGLLE-QVDSHGSNKYKISQSGREFL 78
                57*******6.7999*************985 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   6.5e-05      0.04      19      55 .]      23      57 ..       5      57 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.5e-05
      HTH_36 19 nknggcfpsqetlakrlglsknTvsraikeLeqlGyi 55
                ++++g  +s+ +l ++ ++s + +sr++k L+  G++
  EPA06024.1 23 QDENG--ASVTYLIRKANISHSRISRILKTLVSQGLL 57
                55666..7***************************97 PP

>> Ribosomal_S25  S25 ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1     5e-05     0.031      57      94 ..      28      65 ..       6      70 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5e-05
  Ribosomal_S25 57 itpsvvserlkingslArraLreleekgliklvskhra 94
                    +++ ++ + +i+ s   r+L++l ++gl+++v +h +
     EPA06024.1 28 ASVTYLIRKANISHSRISRILKTLVSQGLLEQVDSHGS 65
                   56788999*************************88865 PP

>> RNA_pol_Rpc34  RNA polymerase Rpc34 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   5.2e-05     0.032      14      73 ..      13      71 ..       2      76 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.2e-05
                   HHHHHHHCS.SSSSHCCHHHHHHHSTTSHHHHHHHHHHHHHHCTSEECCC.STTSCECEE- CS
  RNA_pol_Rpc34 14 rlleelrka.seqklfsqqdLqddipslslklllsavqeLldkkllvllknsndeLvyrav 73
                   ++l+  r++ +++++ s + L ++  ++s++ + +++++L++++ll+++  s+++ +y++ 
     EPA06024.1 13 EILSTTRDDlQDENGASVTYLIRK-ANISHSRISRILKTLVSQGLLEQVD-SHGSNKYKIS 71
                   567777777777777788888887.7888888888888888888888888.4444477765 PP

>> DUF4194  Domain of unknown function (DUF4194)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   5.8e-05     0.036     100     156 ..      17      73 ..       8      80 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.8e-05
     DUF4194 100 vsveeivekles...flpldrdeakfkkrldaalrklkelgllrrldgd.eertryeIrpi 156
                 +++++++++  +   +l+++ + +    r+ ++l++l++ gll+++d++ +++  y+I+ +
  EPA06024.1  17 TTRDDLQDENGAsvtYLIRKAN-I-SHSRISRILKTLVSQGLLEQVDSHgSNK--YKISQS 73 
                 5677777776666444444444.4.489*******************986666..***976 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   7.5e-05     0.046      16      74 ..      31      79 ..      14      80 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.5e-05
                HHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHHH CS
        PadR 16 ikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrela 74
                +  +++      ++s++++ ++Lk+L  +gl+e+  +        + Y++ + Gr+ l+
  EPA06024.1 31 TYLIRKA-----NISHSRISRILKTLVSQGLLEQVDSH-----GSNKYKISQSGREFLQ 79
                5555555.....599*****************998664.....56779******99987 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   0.00015     0.093      29      58 ..      34      63 ..      21      91 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00015
     DUF2250 29 akeleipleevrellkkLeelGLlervegk 58
                 ++ +i+ ++++++lk L + GLle+v+++
  EPA06024.1 34 IRKANISHSRISRILKTLVSQGLLEQVDSH 63
                577899********************9875 PP

>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   0.00013     0.083      37      70 ..      39      68 ..      32      75 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00013
                --HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEE CS
      Cdc6_C 37 ltqrevsdllseLemlgileleksskGrregrtr 70
                ++++++s++l+ L ++g+le   s +G+   +++
  EPA06024.1 39 ISHSRISRILKTLVSQGLLEQVDS-HGS---NKY 68
                79*******************888.333...333 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00015     0.091      19      59 ..      22      62 ..       5      63 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00015
                HSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
      HTH_20 19 LaraegltaselaerldlskntlsyHLrvLeeagLvevvre 59
                L ++ g++++ l +   +s + +s+ L++L++ gL+e+v++
  EPA06024.1 22 LQDENGASVTYLIRKANISHSRISRILKTLVSQGLLEQVDS 62
                3788999999999999*********************9975 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.3   0.00019      0.12      17      73 ..      26      82 ..      23      83 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00019
  B-block_TFIIIC 17 sGitqsdLakeskqdprslfyrlksLekkgLIvkqsiidsatkksistsllvlkkyf 73
                    +G   + L++  +++ + +  +lk+L ++gL + +    s+++k+ ++   +l+ y+
      EPA06024.1 26 NGASVTYLIRKANISHSRISRILKTLVSQGLLEQVDSHGSNKYKISQSGREFLQAYY 82
                    788888999**************************999**********999999998 PP

>> HTH_46  Winged helix-turn-helix DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.6   0.00025      0.16      26      54 ..      30      58 ..      15      65 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00025
      HTH_46 26 lkyIqkrtnLSrSsimkvLseLkkggyIe 54
                + y  ++ n+S S+i ++L  L  +g +e
  EPA06024.1 30 VTYLIRKANISHSRISRILKTLVSQGLLE 58
                57999***************998777665 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0    0.0002      0.13      11      71 ..      29      80 ..      20      90 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0002
  Replic_Relax 11 TtrqiarllfashratarrrLarLrelgllsrlrkrvggarggsepyvYaLtpkGarllaa 71
                  +  ++ r  + sh++ ++r+L++L ++gll+ ++ +  g +       Y + + G+++l+a
    EPA06024.1 29 SVTYLIRKANISHSR-ISRILKTLVSQGLLEQVDSH--GSN------KYKISQSGREFLQA 80
                  566777888999999.****************9998..444......49999999999954 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        29  (0.00161749); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              29  [number of targets reported over threshold]
# CPU time: 0.58u 0.35s 00:00:00.93 Elapsed: 00:00:00.55
# Mc/sec: 522.77
//
Query:       EPA06025.1  [L=139]
Description: hydrolase, NUDIX family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.5e-21   74.2   0.4    1.1e-20   74.0   0.4    1.0  1  NUDIX         NUDIX domain
  ------ inclusion threshold ------
       0.04   13.8   0.2      0.055   13.4   0.2    1.1  1  PhosphMutase  2,3-bisphosphoglycerate-independent phosphoglyc


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.0   0.4   1.3e-24   1.1e-20       4     124 ..       5     125 ..       3     131 .. 0.77

  Alignments for each domain:
  == domain 1  score: 74.0 bits;  conditional E-value: 1.3e-24
                 EEEEEEEEETTSE...EEEEEESSSSTTTEESSEEECBTTSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEEEEEE..EEEEE.EEEEEEECSGC CS
       NUDIX   4 ravgvvllnekge...vLlvrrskkpfpgWelPgGkvepgEtpeeAArREleEEtGleaellellgrlhylapydgpygd..eheil.yvfleevegel 96 
                  ++g+vl+++++    +Ll+  + +p  +W++++Gk+e+gEt+  +A+RE++EEtG+   ++e+++ ++++  y++ y     h    +vf+ +++ + 
  EPA06025.1   5 TSAGIVLFRKENSkilFLLL--N-YPSGHWDFVKGKMEEGETIHHTAIRETREETGI--TDIEFIENFEEWIEYNFQYQGelVH--KkVVFFLAETKTK 96 
                 5799**99999888644444..3.56666****************************..889****************985422..2455555555555 PP

                 SSTSTTTEEEEEEEEHHHH.HHHHTHCTH CS
       NUDIX  97 epndenevsevrwvpleel.lkeklaaes 124
                 e + ++e+ ++ w++++ +  k+++++++
  EPA06025.1  97 EITISHEHLDYAWMDYQTAvEKTTFDNAK 125
                 55569**************5555544444 PP

>> PhosphMutase  2,3-bisphosphoglycerate-independent phosphoglycerate mutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   6.1e-06     0.055      66     166 ..      37     137 ..      30     138 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.1e-06
                   C..TTCEEETTGGG-.-TTHHH....HHHHT-EEE.TTEEEEEEE-STTEEEEEE.--S-B--S--..SSTTS------BS..SGGGHHHHHHHHHH CS
  PhosphMutase  66 deedgiiidrragristeeake....Likalneeleegvevkfypgveyrhllvl.lsdkitdtdpphdkegkeikellpl.kseeaketaellnel 156
                   + e+g  i+++a r ++ee+      +i+  +e +e  ++++++    ++ ++ +  + k  +++  h++ +  ++++    +    k t +  +++
    EPA06025.1  37 KMEEGETIHHTAIRETREETGItdieFIENFEEWIE--YNFQYQGELVHKKVVFFlAETKTKEITISHEHLDYAWMDYQTAvE----KTTFDNAKSI 127
                   556778889999999888876522224444444444..77777777888888888988888999999*************644....8999****** PP

                   HHHHHHHHHH CS
  PhosphMutase 157 ieksqeiLed 166
                   + ks+++L++
    EPA06025.1 128 LTKSKQLLDK 137
                   ******9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 941.47
//
Query:       EPA06026.1  [L=176]
Description: hypothetical protein BG20_I1218, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 1015.08
//
Query:       EPA06027.1  [L=251]
Description: hydrolase, TatD family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-45  155.6   0.0    1.7e-45  155.4   0.0    1.0  1  TatD_DNase     TatD related DNase
  ------ inclusion threshold ------
       0.05   13.4   0.1      0.079   12.8   0.1    1.3  1  BP28CT         BP28CT (NUC211) domain
       0.18   11.3   0.0       0.27   10.7   0.0    1.2  1  FAD_binding_7  FAD binding domain of DNA photolyase


Domain annotation for each model (and alignments):
>> TatD_DNase  TatD related DNase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.4   0.0   2.8e-49   1.7e-45       2     254 ..       6     249 ..       5     250 .. 0.93

  Alignments for each domain:
  == domain 1  score: 155.4 bits;  conditional E-value: 2.8e-49
                 EEEE-TTSCCCTTTHHHHHHHHHHTTEEEEEEE-SSGGGHHHHHHHHTT.TTTEEEEE---GGGGGCC.CCHHHHHHHHHHCCCTSEEEEEEEEEET.- CS
  TatD_DNase   2 DaHcHldskefeedreeileraeeagvaavvvvgtsskdskavlelakkypnkvyavlGiHPnevdeasedlleelkelanvkhskvvaiGeiGLDy.y 99 
                 D+H+Hl ++++++d + il+ +e+ +++a++ v++++++sk++le+ k+++  v + +GiHP + ++     le + e+ n +++ +++iGeiGLD  y
  EPA06027.1   6 DSHIHLSDSSYQSDLDYILNGMENMKIKACC-VSVDTETSKKTLEIGKRSKL-VLPFIGIHPENTND----NLELMTEMINENKTLISGIGEIGLDPtY 98 
                 ***************************9996.89999************886.*********77774....455555556779*************978 PP

                 CCCCCGHHHHHHHHHHHHHHHHHTTEEEEEEEES-HHHHHHHHHHCGGCCSEEEETT--S-HHHHHHHHHTTEEEEE-GGGGTTTTHHHHHHHHHS-GG CS
  TatD_DNase 100 sreestkeaqeevFeeqlrlAkelklplviHlrkaeedlleilkeaaeakakvvlHsfsgsaeeakkflklgyyislsglltfknakelrelvkavpld 198
                  + e++ ++q ++Fe +l+lA++l++p++iH+rk+ +d+ +i+++++ +k    lH+f gs+++++k++++++++s++ ++ +  a + + l+ +   +
  EPA06027.1  99 AKLEEDTKRQIHFFETFLSLAEKLQKPVSIHSRKSLDDIFSIMTSYD-TK-HALLHWFDGSKKQLQKAMDMDFFVSYGPVMIY--AGDKQTLLSKTTET 193
                 9999*****************************************95.56.58******************************..55678899****** PP

                 GEEE---TTSSEECCCTTSE--GGGHHHHHHHHHHHHTS-HHHHHHHHHHHHHHHH CS
  TatD_DNase 199 rlLiETDaPyltpkpyrgkrnepanvayvveklaelkaltleelaeitaeNakrlf 254
                 ++L+ETD P      ++ k+ +  +++ vv + +++ + +++e+a  +++N+k+++
  EPA06027.1 194 KILVETDGPVRFSRCFEMKSGQISFIPSVVFCASNILGKSYDEMALLLENNSKAFL 249
                 **********99999999**********************************9986 PP

>> BP28CT  BP28CT (NUC211) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   1.3e-05     0.079      76     121 ..     102     147 ..      94     193 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.3e-05
                 -----HHHHHHHHHHHHH--------TTHHHHHHHHHHHHH----- CS
      BP28CT  76 kdskeRlitfykllnklaekLkslftsYasyllenavelLkalnek 121
                 +++++R+i f++ + +laekL++ ++      l+++ ++++++++k
  EPA06027.1 102 EEDTKRQIHFFETFLSLAEKLQKPVSIHSRKSLDDIFSIMTSYDTK 147
                 45679***********************************888543 PP

>> FAD_binding_7  FAD binding domain of DNA photolyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   4.5e-05      0.27      76     126 ..     140     187 ..     137     220 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 4.5e-05
                    HHHHHHCTTT-B-HHHHHHHHHHH-TT--CCHHHHHHHHHCT-STTS-STT CS
  FAD_binding_7  76 ivasFltkdLlidWregeevFeellvDadlasnagnwqwlagtgadaapaf 126
                    i+ s+ tk+ l++W  g +   ++ +D+d+ + +g +++ ag   d+++++
     EPA06027.1 140 IMTSYDTKHALLHWFDGSKKQLQKAMDMDFFVSYGPVMIYAG---DKQTLL 187
                    678999************************************...665544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.36s 00:00:00.94 Elapsed: 00:00:00.54
# Mc/sec: 1396.70
//
Query:       EPA06028.1  [L=97]
Description: bacterial Fe(2+) trafficking [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-07   30.7   0.0    2.2e-07   30.5   0.0    1.3  1  Iron_traffic  Bacterial Fe(2+) trafficking
  ------ inclusion threshold ------
      0.067   13.2   2.1        8.2    6.6   0.1    2.2  2  XPA_N         XPA protein N-terminal
       0.91    9.2   4.1          3    7.5   0.2    2.4  2  zf_C2H2_13    Zinc finger domain


Domain annotation for each model (and alignments):
>> Iron_traffic  Bacterial Fe(2+) trafficking
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.0   3.6e-11   2.2e-07      34      73 ..      31      70 ..       6      85 .. 0.90

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 3.6e-11
  Iron_traffic 34 vskeawqeWlkkqtmLiNekrLnladpkarkfLeeqmekf 73
                  v+++ w eW +   m++Ne rL++  p++rk+L+++ + f
    EPA06028.1 31 VCNKCWGEWKEYRVMVMNEMRLDMSMPDHRKLLKKHEKIF 70
                  8899*****************************9876554 PP

>> XPA_N  XPA protein N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1    0.0014       8.2       3      14 ..       8      19 ..       6      24 .. 0.90
   2 ?    6.5   0.2    0.0015       8.8      21      28 ..      28      35 ..      27      36 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0014
       XPA_N  3 kCdeCgkefldS 14
                +C +C+ ++ dS
  EPA06028.1  8 TCTKCKNPIPDS 19
                8*********99 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0015
       XPA_N 21 dysVCDkC 28
                +y+VC+kC
  EPA06028.1 28 KYPVCNKC 35
                59****** PP

>> zf_C2H2_13  Zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.4     0.014        81      18      27 ..       7      16 ..       3      23 .. 0.87
   2 ?    7.5   0.2    0.0005         3      10      23 ..      21      35 ..      18      37 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.014
  zf_C2H2_13 18 RvCnkCGkPi 27
                R C kC  Pi
  EPA06028.1  7 RTCTKCKNPI 16
                99****9999 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0005
  zf_C2H2_13 10 pLdtn.lnYRvCnkC 23
                +Ld    +Y vCnkC
  EPA06028.1 21 TLDMVaEKYPVCNKC 35
                67766679******* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       725  (0.0404373); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.32s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 578.20
//
Query:       EPA06029.1  [L=153]
Description: hypothetical protein BG20_I1191 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.029   13.1   1.1      0.038   12.8   1.1    1.1  1  DUF2207          Predicted membrane protein (DUF2207)
      0.052   12.4   0.8      0.066   12.0   0.8    1.1  1  LptF_LptG        Lipopolysaccharide export system permease Lp
      0.059   13.5   1.7      0.085   13.0   1.7    1.2  1  DUF4870          Domain of unknown function (DUF4870)
       0.13   12.5   0.0       0.17   12.1   0.0    1.2  1  Shisa            Wnt and FGF inhibitory regulator
       0.17   11.4   2.3       0.35   10.4   2.3    1.5  1  VEGFR-2_TMD      VEGFR-2 Transmembrane domain
       0.19   11.6   0.3       0.28   11.1   0.3    1.2  1  RseC_MucC        Positive regulator of sigma(E), RseC/MucC
        3.7    6.6   8.9         11    5.0   8.6    1.7  2  ABC2_membrane_3  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.1   1.5e-05     0.038     386     442 ..      16      68 ..       3      73 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.5e-05
     DUF2207 386 lglgliilglilillallllvlllvfllilllillliaiivlllfsrllgrrteeGa 442
                 +++ ++++++++i++++ +     ++ +++++il+ +a+i +++  ++l++ t++ +
  EPA06029.1  16 FAIPIMVILFLGIIYIMTQ----RSGSGFVSFILIGAAAITMFYWVHVLKKMTKDQK 68 
                 4556666666666777666....99999999999999999*****9*****999865 PP

>> LptF_LptG  Lipopolysaccharide export system permease LptF/LptG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.8   2.6e-05     0.066     277     324 ..      15      62 ..       4      71 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.6e-05
   LptF_LptG 277 alplaclvfaliaaplglvkrrggrglr..lliaillfvlyyvllslgka 324
                  +++ ++v +++++   ++ r g++  +  l+ a +++++y+v +  +k+
  EPA06029.1  15 NFAIPIMVILFLGIIYIMTQRSGSGFVSfiLIGAAAITMFYWV-HV-LKK 62 
                 4455567777788877777755555555755555555566665.43.344 PP

>> DUF4870  Domain of unknown function (DUF4870)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.7   3.3e-05     0.085      45      97 ..      11      65 ..       7      74 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.3e-05
     DUF4870 45 kealNFqislliysiilivlsllvligf..lllllllllllnlvlviiaaikane 97
                 ++lNF i ++++++++i+  ++   g   ++++l+ ++++ +++ +    k+ +
  EPA06029.1 11 EQSLNFAIPIMVILFLGIIYIMTQRSGSgfVSFILIGAAAITMFYWVHVLKKMTK 65
                689********99888888766665554323333333333344443433444444 PP

>> Shisa  Wnt and FGF inhibitory regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   6.5e-05      0.17      89     121 ..      32      70 ..       2      93 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.5e-05
       Shisa  89 v....ktifivfvivgvvvivcc..cgclkkkqrekrpg 121
                      ++ f++f+++g+ +i++   +++lkk+ ++++p 
  EPA06029.1  32 MtqrsGSGFVSFILIGAAAITMFywVHVLKKMTKDQKPI 70 
                 14444899*********99998777*********99942 PP

>> VEGFR-2_TMD  VEGFR-2 Transmembrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   2.3   0.00014      0.35       9      22 ..      44      57 ..      43      60 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00014
  VEGFR-2_TMD  9 iligtgViAvFFWl 22
                 ilig++ i +F+W+
   EPA06029.1 44 ILIGAAAITMFYWV 57
                 9************8 PP

>> RseC_MucC  Positive regulator of sigma(E), RseC/MucC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.3   0.00011      0.28      69     122 ..      14      68 ..       5      73 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00011
   RseC_MucC  69 lvYllPllllilgallgsall.gssellaalgallglvlgflivrllskrlkkks 122
                 l +++P++++++  ++  +    +s ++++++  ++++  f++v++l+k +k+++
  EPA06029.1  14 LNFAIPIMVILFLGIIYIMTQrSGSGFVSFILIGAAAITMFYWVHVLKKMTKDQK 68 
                 6788998776666555555556889999999999999999*****9999877664 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   8.6    0.0042        11     215     262 ..      14      60 ..      12      70 .. 0.89
   2 ?   -0.4   0.0      0.19   4.9e+02      48      89 ..      82     120 ..      60     137 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0042
  ABC2_membrane_3 215 lvyllqlllilll.afglgipfgnlglllllfllfglayialgyllssl 262
                      l++++++++il+l ++   i+   +g+ ++ f+l g a+i+++y++ +l
       EPA06029.1  14 LNFAIPIMVILFLgIIY--IMTQRSGSGFVSFILIGAAAITMFYWVHVL 60 
                      78999**9999998888..9999*********************98665 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.19
  ABC2_membrane_3  48 lvealeaspsvelvyevdseeeakkalkngdidgilvipkgf 89 
                      +++ ++ ++++    +v+     ++++  + idgil+i   +
       EPA06029.1  82 VYDLIKGEDDFV---FVSEVPGPEDKIAVRLIDGILYIRGSM 120
                      455566677777...999999999999999999999995443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       959  (0.0534888); expected 358.6 (0.02)
Passed bias filter:                      625  (0.0348597); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1076.87
//
Query:       EPA06030.1  [L=224]
Description: hypothetical protein BG20_I1203 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       245  (0.013665); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1552.19
//
Query:       EPA06031.1  [L=74]
Description: hypothetical protein BG20_I1189 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0021   17.7   2.2     0.0021   17.6   2.2    1.0  1  BaxI_1    Bax inhibitor 1 like


Domain annotation for each model (and alignments):
>> BaxI_1  Bax inhibitor 1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   2.2   1.2e-07    0.0021      15      77 ..       3      65 ..       1      71 [. 0.71

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.2e-07
      BaxI_1 15 eaaaeamtvddvvvktaillgvlvvtavvtwflvlaaaaalllvgalvglvlalvas.fkkkvs 77
                ++++e++t++d+v k  i+ g++++  +++++++ +   + l+ +a++g v+ ++a+ f+ k+s
  EPA06031.1  3 NSKSEKLTMSDIVLKGSIIAGIVTIPSIASFLIAWTVLDN-LIQAAIIGAVMHFIAMgFSLKIS 65
                456677**********************999998755544.45566666665555442455544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 503.31
//
Query:       EPA06032.1  [L=263]
Description: ThiS family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      4e-07   30.6   0.1    1.1e-06   29.1   0.0    1.8  2  ThiS            ThiS family
     0.0004   20.5   3.9    0.00076   19.6   3.5    1.7  2  CGI-121         Kinase binding protein CGI-121
     0.0058   17.0   2.1      0.011   16.1   0.4    2.5  3  Urm1            Urm1 (Ubiquitin related modifier)
  ------ inclusion threshold ------
        1.5    8.8   8.6        1.6    8.7   1.8    3.0  3  Staphostatin_A  Staphostatin A


Domain annotation for each model (and alignments):
>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   2.6e-10   1.1e-06      14      77 .]      24      91 ..      10      91 .. 0.87
   2 ?   -2.8   0.0       2.3     1e+04      28      47 ..     121     141 ..     120     149 .. 0.63

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 2.6e-10
                EEEEESSTSBHHHHHHHHHHHTCHHG...TTTTEEEEETTEEEGC.CTTTSB--TTCEEEEEESTTC- CS
        ThiS 14 eelelaegstvaelleaLgerypela...lerrvavavNgeivpr.lwldtelkdgDevailppVaGG 77
                e   ++++ ++++ll+ L e  p  +     +++ +avNg + +  +++ t +k++D+v+i+p++ GG
  EPA06032.1 24 ELKIDKSDISIQQLLDLLLELKPSNTpdlDVENILIAVNGADSSAmEGKMTLIKNNDVVSIIPVIHGG 91
                5667889999*******98777777789977**************99********************9 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.3
                 HHHHHHHTCHHG.TTTTEEEE CS
        ThiS  28 leaLgerypela.lerrvava 47 
                 l+ L +++p+++      ++ 
  EPA06032.1 121 LDTLRKKFPKIKlQAVSANFI 141
                 678888999888633344444 PP

>> CGI-121  Kinase binding protein CGI-121
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.6     7e+03      33      53 ..      53      73 ..      52      81 .. 0.80
   2 !   19.6   3.5   1.7e-07   0.00076      18     156 ..     128     256 ..      99     261 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.6
                -HHHHHHHHHHHHHHHHHS-- CS
     CGI-121 33 skehllsAvlrallaaargkl 53
                + e +l+Av+ a ++a +gk+
  EPA06032.1 53 DVENILIAVNGADSSAMEGKM 73
                567899999999888888877 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 1.7e-07
                 CHCTT-EEE-GGG---HHHHHHHHHHHHHHHHHS---SSSHHHHHHHHHSSSS-HHHHHHHHB--TT-S-EEEEEEESSS--HHHHHHHHHHHS-SEEE CS
     CGI-121  18 raeldfafldaslilskehllsAvlrallaaargklktktlhsEilfsLspnnnIgealkrfgisdkttsllvvkvssseadeeevlkslkevvegelv 116
                  ++++   + a+ il++ hl   +  +l + +++ l +++l+ +il+++  +++I+ a++  gi++k++  +++ ++++     + l+ l +  ++ +v
  EPA06032.1 128 FPKIKLQAVSANFILNNYHLKKIIGLSLYSDKNNLLLSNKLEMDILMRFAISQQISTAINSAGIKPKQN-FILIAIGNR-----KALDLLYTELSKISV 220
                 4566677889999******************************************************99.999999887.....444444444444333 PP

                 --SHHHHHH--HHHHHHHTT--..TT---SSHHHHHHHHH CS
     CGI-121 117 pleeeleeltdwkkikkiYklneleeekeeevkeledlvv 156
                   +  +++  + + +kk++k+n+++ +   +++ led+ +
  EPA06032.1 221 --DM-FSK-DNSSFLKKHFKINDKQLSIVLSKTPLEDILI 256
                 ..22.222.4567899999999543333334444666665 PP

>> Urm1  Urm1 (Ubiquitin related modifier)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.4   2.5e-06     0.011      24      96 .]      25      91 ..       7      91 .. 0.74
   2 ?   -3.3   0.0       2.6   1.2e+04      78      93 ..     109     124 ..      99     127 .. 0.61
   3 ?   -1.9   0.1      0.98   4.4e+03      33      33 ..     142     142 ..     105     187 .. 0.60

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.5e-06
                E-SSSSS-BHHHHHHHHCCCC-SSGHHHCBSTTSB-TTEEEEETTCEHHHCTCCCSB--TTEEEEEEETTT-- CS
        Urm1 24 leieseevnleeliayikknlikerkevFlekdkvrPGilvLindaDwellgekdyelkdkDkivFistlhGG 96
                l+i+++++++++l++ + +   ++ +++ +e       il+ +n aD + ++ k + +k++D+++ i  +hGG
  EPA06032.1 25 LKIDKSDISIQQLLDLLLELKPSNTPDLDVE------NILIAVNGADSSAMEGKMTLIKNNDVVSIIPVIHGG 91
                4445666777777776666666666666555......499********************************9 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.6
                 CSB--TTEEEEEEETT CS
        Urm1  78 dyelkdkDkivFistl 93 
                 + + +++  i+F+ tl
  EPA06032.1 109 EIQGQNQIDIIFLDTL 124
                 4444555566777666 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.98
                 H CS
        Urm1  33 l 33 
                 l
  EPA06032.1 142 L 142
                 1 PP

>> Staphostatin_A  Staphostatin A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1       0.2     9e+02      62      89 ..      73     100 ..      67     105 .. 0.58
   2 ?    8.7   1.8   0.00036       1.6      10      82 ..     108     181 ..      99     199 .. 0.80
   3 ?    2.5   0.1     0.029   1.3e+02      63      87 ..     220     244 ..     201     253 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.2
  Staphostatin_A  62 klilsnkdnssivieiilindkklllti 89 
                       ++ n d  si+  i    +k+ll+++
      EPA06032.1  73 MTLIKNNDVVSIIPVIHGGSSKRLLFNM 100
                     3334555555655555556677777775 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00036
  Staphostatin_A  10 vkdd.skseekyylnileGiwhpveledsplkiilskeidsdyvcklineeskklilsnkdnssivieiilind 82 
                      + +  ++ ++++l++l  ++   +l+    ++il++    + +   +  ++++l+lsnk + +i++ + +  +
      EPA06032.1 108 IEIQgQNQIDIIFLDTLRKKFPKIKLQAVSANFILNNYHLKKIIGLSLYSDKNNLLLSNKLEMDILMRFAISQQ 181
                     444404556899****************************************************9998877543 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.029
  Staphostatin_A  63 lilsnkdnssivieiilindkklll 87 
                     + ++ kdnss + + + indk+l +
      EPA06032.1 220 VDMFSKDNSSFLKKHFKINDKQLSI 244
                     4468899************998754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       710  (0.0396006); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1592.82
//
Query:       EPA06033.1  [L=50]
Description: hypothetical protein BG20_I2673 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00022   21.1   0.2    0.00025   20.9   0.2    1.1  1  Cdc6_C    CDC6, C terminal winged helix domain
     0.0047   16.2   0.1     0.0052   16.1   0.1    1.0  1  DUF512    Protein of unknown function (DUF512)


Domain annotation for each model (and alignments):
>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.2   2.8e-08   0.00025      45      83 ..       1      38 [.       1      39 [. 0.94

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.8e-08
                HHHHHHHTTSEEEEEEE-CC.C-EEEEEEESSSCHHHHH CS
      Cdc6_C 45 llseLemlgileleksskGrregrtrkisLnvdpddvle 83
                +lse e  gi++ + +++G  +grt+k++L+++++ +++
  EPA06033.1  1 MLSEIELSGIISGRLVHQGI-HGRTKKYKLTISTEMIKK 38
                79*****************9.8************99986 PP

>> DUF512  Protein of unknown function (DUF512)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   5.8e-07    0.0052     138     186 ..       4      49 ..       3      50 .] 0.92

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.8e-07
      DUF512 138 titVaGLltgqDlieqlkekelgeelllpsvmlreeeevfLDdltleel 186
                 +i+ +G+++g+ + + +++++ + +l +++ m++   ++f Ddltl+++
  EPA06033.1   4 EIELSGIISGRLVHQGIHGRTKKYKLTISTEMIK---KTFKDDLTLQDI 49 
                 7999***************99999*********6...689*****9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.51
# Mc/sec: 294.01
//
Query:       EPA06034.1  [L=112]
Description: hypothetical protein BG20_I2674, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-05   24.6   0.0      2e-05   24.0   0.0    1.3  1  DNA_pol_E_B    DNA polymerase alpha/epsilon subunit B
    0.00095   19.4   0.0     0.0011   19.2   0.0    1.2  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d


Domain annotation for each model (and alignments):
>> DNA_pol_E_B  DNA polymerase alpha/epsilon subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   2.3e-09     2e-05     159     204 ..       4      49 ..       1      54 [. 0.91

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2.3e-09
                  HHHHHHHHHHHHTBS---SS--B-GGGGGGGB-GGG---SEEE--- CS
  DNA_pol_E_B 159 rlrklvktildqrhlaPlaptlrpvswdkddalvleplPdvlvlpd 204
                  +  +++k++l+ rhl+P++ +  p+  +  d +v++++Pd++ ++ 
   EPA06034.1   4 KPTNVMKHLLRARHLSPIYGSQTPIAPEIEDLMVIDEIPDIFHVGH 49 
                  56789*************************************9986 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.2e-07    0.0011     117     149 ..      40      72 ..       5      85 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.2e-07
  Metallophos_2 117 egsdvvvcGHtHvpevekeggvlvvnPGsvgep 149
                    e  d++ +GH H++e++  +g+l++n Gs + +
     EPA06034.1  40 EIPDIFHVGHVHRAELDMYKGILLINSGSWQKQ 72 
                    4456999**********************9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       250  (0.0139439); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 797.78
//
Query:       EPA06035.1  [L=112]
Description: hypothetical protein BG20_I2676, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-05   24.6   0.0      2e-05   24.0   0.0    1.3  1  DNA_pol_E_B    DNA polymerase alpha/epsilon subunit B
    0.00095   19.4   0.0     0.0011   19.2   0.0    1.2  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d


Domain annotation for each model (and alignments):
>> DNA_pol_E_B  DNA polymerase alpha/epsilon subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   2.3e-09     2e-05     159     204 ..       4      49 ..       1      54 [. 0.91

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2.3e-09
                  HHHHHHHHHHHHTBS---SS--B-GGGGGGGB-GGG---SEEE--- CS
  DNA_pol_E_B 159 rlrklvktildqrhlaPlaptlrpvswdkddalvleplPdvlvlpd 204
                  +  +++k++l+ rhl+P++ +  p+  +  d +v++++Pd++ ++ 
   EPA06035.1   4 KPTNVMKHLLRARHLSPIYGSQTPIAPEIEDLMVIDEIPDIFHVGH 49 
                  56789*************************************9986 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.2e-07    0.0011     117     149 ..      40      72 ..       5      85 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.2e-07
  Metallophos_2 117 egsdvvvcGHtHvpevekeggvlvvnPGsvgep 149
                    e  d++ +GH H++e++  +g+l++n Gs + +
     EPA06035.1  40 EIPDIFHVGHVHRAELDMYKGILLINSGSWQKQ 72 
                    4456999**********************9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       250  (0.0139439); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 805.47
//
Query:       EPA06036.1  [L=60]
Description: hypothetical protein BG20_I2675, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-08   32.9   0.5    5.5e-08   32.7   0.5    1.1  1  Cdc6_C    CDC6, C terminal winged helix domain
     0.0014   18.0   0.1     0.0016   17.8   0.1    1.0  1  DUF512    Protein of unknown function (DUF512)


Domain annotation for each model (and alignments):
>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.5   6.1e-12   5.5e-08      36      83 ..       2      48 ..       1      49 [. 0.94

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 6.1e-12
                ---HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESSSCHHHHH CS
      Cdc6_C 36 pltqrevsdllseLemlgileleksskGrregrtrkisLnvdpddvle 83
                 ltqr++ ++lse e  gi++ + +++G  +grt+k++L+++++ +++
  EPA06036.1  2 ELTQRRITQMLSEIELSGIITGRLVHQGI-HGRTKKYKLTISTEMIKK 48
                79**************************9.8************99986 PP

>> DUF512  Protein of unknown function (DUF512)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   1.8e-07    0.0016     138     186 ..      14      59 ..      12      60 .] 0.92

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.8e-07
      DUF512 138 titVaGLltgqDlieqlkekelgeelllpsvmlreeeevfLDdltleel 186
                 +i+ +G++tg+ + + +++++ + +l +++ m++   ++f Ddltl+++
  EPA06036.1  14 EIELSGIITGRLVHQGIHGRTKKYKLTISTEMIK---KTFKDDLTLQDI 59 
                 7999***************99999*********6...689*****9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.44
# Mc/sec: 411.06
//
Query:       EPA06037.1  [L=182]
Description: hypothetical protein BG20_I0605 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0059   17.0   3.0     0.0059   17.0   3.0    3.0  3  CPBP           CPBP intramembrane metalloprotease
  ------ inclusion threshold ------
       0.27   11.0   0.2       0.27   11.0   0.2    2.0  2  NADH_oxidored  MNLL subunit


Domain annotation for each model (and alignments):
>> CPBP  CPBP intramembrane metalloprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.2      0.11   9.4e+02      64      73 ..      50      59 ..       8      87 .. 0.66
   2 ?    1.8   0.2     0.035   3.1e+02       6      24 ..      98     116 ..      93     118 .. 0.80
   3 !   17.0   3.0   6.5e-07    0.0059      46      91 ..     123     170 ..     121     171 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.11
                HHHHHHHHHH CS
        CPBP 64 laGlvlgyly 73
                ++G++++y++
  EPA06037.1 50 AFGILFAYVI 59
                3444444443 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.035
                 HHHHHHHHHHHHHHHHHHT CS
        CPBP   6 lvfllalllapllEEllfR 24 
                  +++++++    +EEl+fR
  EPA06037.1  98 PLLVYMFIHINYVEELYFR 116
                 5667788888899*****9 PP

  == domain 3  score: 17.0 bits;  conditional E-value: 6.5e-07
                 HHHHHCSGGGHHHH...HHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
        CPBP  46 ilFglaHlpngpsv...llaalaGlvlgylylktgsllaaillHallnl 91 
                 ++++++H++ g++v   l ++ +G+++ y+y k+g l  a ++H+ +n+
  EPA06037.1 123 VVWAMIHIAMGIQVhmaLILLPIGFLFKYIYDKKG-LNDAYAMHFTTNI 170
                 89********9995344888899************.***********98 PP

>> NADH_oxidored  MNLL subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.7       1.1   9.4e+03      21      26 ..      11      16 ..      11      17 .. 0.87
   2 ?   11.0   0.2     3e-05      0.27       1      30 [.     127     156 ..     127     165 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.1
                   HHHHHH CS
  NADH_oxidored 21 FvvGwy 26
                   F++G+y
     EPA06037.1 11 FLIGYY 16
                   99***9 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 3e-05
                    XX-HHCCCCCHCCCCHHHHHHHHHHHHHHH CS
  NADH_oxidored   1 mvnllqlvrdhwvhvlvPlGFvvGwyLDkk 30 
                    m+ ++  ++ h + +l P+GF++ +  Dkk
     EPA06037.1 127 MIHIAMGIQVHMALILLPIGFLFKYIYDKK 156
                    7888888999***************99*98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       778  (0.0433934); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 1058.68
//
Query:       EPA06038.1  [L=269]
Description: DSBA-like thioredoxin domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-40  138.7   0.1      4e-40  137.7   0.0    1.5  2  Thioredoxin_4  Thioredoxin
      6e-20   71.8   0.4    6.1e-18   65.3   0.4    2.2  1  DSBA           DSBA-like thioredoxin domain
      2e-11   44.3   0.1    5.8e-11   42.8   0.1    1.8  1  Thioredoxin_2  Thioredoxin-like domain
  ------ inclusion threshold ------
      0.038   13.7   0.0      0.068   12.8   0.0    1.5  1  Thioredoxin_5  Thioredoxin


Domain annotation for each model (and alignments):
>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.74   3.3e+03     113     128 ..      58      71 ..       7      84 .. 0.53
   2 !  137.7   0.0   8.9e-44     4e-40       4     165 ..      90     264 ..      87     265 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.74
                    HTS-------HHHHHH CS
  Thioredoxin_4 113 feacleeekldalvea 128
                    +++  + ek++ ++ +
     EPA06038.1  58 LND--AIEKIESKILK 71 
                    222..22233333333 PP

  == domain 2  score: 137.7 bits;  conditional E-value: 8.9e-44
                    SSEEES-TT-SEEEEEEE-TT-HHHHHHHHHHH.HHHHHHHHTTSEEEEEEE-..---S.TTTHHHHHHHTT--TTHHHHHHHHHHHHTHHHHTTS CS
  Thioredoxin_4   4 tdiviGnpdApvtvieyedlrCphCakfeeeve.klleeyidtGkvkfiirdfpldkek.eslkaamaarcageespeaflaikallysqqeewae 97 
                    +d++iG+++Ap+t+ie++d++Cp Ca+f+++++  +le+y++tGkvkf++rdfp++  + +++ aa+aa+ca+e++  ++ + ++l+++q  + + 
     EPA06038.1  90 DDPIIGDQNAPITIIEFSDFQCPFCARFQTQTLpLILEQYVNTGKVKFVFRDFPIQSSHpNAMPAAVAAECANEQD-RYWQFHDELFENQGVWNKM 184
                    799*****************************967*********************9999***************9.6766667766666666666 PP

                    -....HHHHH.......H.HHHHTS-------HHHHHHHHHHHHHHT--SS-EEEETTEE.....E-TT--HHHHHHHHT CS
  Thioredoxin_4  98 s....lkela..aealdk.dekfeacleeekldalveaeskeakkagiestPtfiingek.....veepqtyeelkalid 165
                    s    ++ ++  a++l+  +e+f++cl+++k+  ++  ++++ +k gi++tP f+i+ ek     v+++q++e +k++id
     EPA06038.1 185 SivdaTDVFKgyAAKLKLnQEQFNSCLDSGKYIGEINSDLNDGRKYGITGTPGFFIGNEKtgfvkVNGAQPFEVFKSVID 264
                    6766433333443344444889**********************************99884544459**********998 PP

>> DSBA  DSBA-like thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.3   0.4   1.4e-21   6.1e-18       1     192 [.     102     263 ..     102     264 .. 0.93

  Alignments for each domain:
  == domain 1  score: 65.3 bits;  conditional E-value: 1.4e-21
                 EEEEEEBTTBHHHHHHH.HHHHHHHHHC...CTEEEEEEE-SSSCHHHHCT.S.GGGSHHHHHHHHHHHHHHHHHHT....GGSSHHHHHHHHHHHHHH CS
        DSBA   1 tvdeffDvlCPyCylgk.erleklaars...pdvkvvlrpfelagakkasgnvgpselpeklkylledlkrlaeaegiplrfpkdklknstraarllla 95 
                 t++ef+D++CP+C  ++ + l+ +++++    +vk+v+r+f+++ + +                                        n+  aa ++  
  EPA06038.1 102 TIIEFSDFQCPFCARFQtQTLPLILEQYvntGKVKFVFRDFPIQSSHP----------------------------------------NAMPAAVAAEC 160
                 79***********99973679999999999667*************66........................................8999******* PP

                 HHHHHGHHHHHHHHHH..HHHTSSS-TSSHHHHHHHHHHTTS.HHHHHHHHTSHHHHHHHHHHHHHHHHTT-SSSSEEEETTC....EEEESSSSHHHH CS
        DSBA  96 agaeglaekvvrelfe..alwsegqaitddqellevaekaGldaeeldealeseavkeavrentaaaqslgvtGvPtvvvdgk....rmvfGadrldtl 188
                 a++++++ ++  elfe   +w++   ++ +++++  a k+ l+ e++   l+s++++ +++ + + ++++g+tG+P ++++++    + v Ga++++ +
  EPA06038.1 161 ANEQDRYWQFHDELFEnqGVWNKMSIVDATDVFKGYAAKLKLNQEQFNSCLDSGKYIGEINSDLNDGRKYGITGTPGFFIGNEktgfVKVNGAQPFEVF 259
                 ***************73369************************************************************998899999********** PP

                 HHHH CS
        DSBA 189 adal 192
                 ++ +
  EPA06038.1 260 KSVI 263
                 9876 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.8   0.1   1.3e-14   5.8e-11       4     108 ..      98     262 ..      96     263 .. 0.94

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 1.3e-14
  Thioredoxin_2   4 ngkpvlvvftdpdCpyCkklkkelkel........ddvtvrvllfp...lkpsfepkavaiwcakekkkafkd....................... 65 
                    n   +++ f+d +Cp+C+++++++ +l         +v++  ++fp    +p+++p+ava  ca+e+ + ++                        
     EPA06038.1  98 NAPITIIEFSDFQCPFCARFQTQTLPLileqyvntGKVKFVFRDFPiqsSHPNAMPAAVAAECANEQDRYWQFhdelfenqgvwnkmsivdatdvf 193
                    66678999**************999999*****9889999999999**********************9999999********************* PP

  Thioredoxin_2  66 ..........................ieenvelarkygvrgtPtivfldgkeivarlpGyvpaeeleal 108
                                              i++    +rkyg++gtP +++ ++k+ + ++ G+ p+e ++ +
     EPA06038.1 194 kgyaaklklnqeqfnscldsgkyigeINSDLNDGRKYGITGTPGFFIGNEKTGFVKVNGAQPFEVFKSV 262
                    ***************************************************888899******999865 PP

>> Thioredoxin_5  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.5e-05     0.068     111     185 ..     188     260 ..     145     261 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.5e-05
  Thioredoxin_5 111 skeellleiaekaglDveefkeDlesklakkafqcDlklakemgvtevPtlvffneneeeeglkveglksyevye 185
                    + +++ +  a k +l+ e+f+  l s       ++Dl+  + +g+t +P +++ n  e+   +kv+g +++ev++
     EPA06038.1 188 DATDVFKGYAAKLKLNQEQFNSCLDSGKYIGEINSDLNDGRKYGITGTPGFFIGN--EKTGFVKVNGAQPFEVFK 260
                    456889999*********************************************9..6667799***99999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       762  (0.042501); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 1704.36
//
Query:       EPA06039.1  [L=321]
Description: response regulator receiver domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      6e-27   94.5  15.0      9e-27   94.0  15.0    1.2  1  TackOD1         Thaumarchaeal output domain 1
    5.4e-11   42.6   0.0    8.9e-11   41.9   0.0    1.4  1  Response_reg    Response regulator receiver domain
     0.0074   16.3  15.8       0.25   11.3   2.5    3.0  3  zinc-ribbons_6  zinc-ribbons
  ------ inclusion threshold ------
      0.014   14.9   7.6       0.34   10.5   0.2    3.6  3  Sgf11           Sgf11 (transcriptional regulation protein)
      0.041   13.7   3.8       0.31   10.9   0.1    3.0  3  zf-FPG_IleRS    Zinc finger found in FPG and IleRS
        0.1   12.6   0.6        0.1   12.6   0.6    3.3  3  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
       0.15   11.6  14.5       0.73    9.5   0.1    4.4  5  zf_UBZ          Ubiquitin-Binding Zinc Finger
       0.36   10.9  17.2        4.7    7.3   2.0    3.1  3  DZR             Double zinc ribbon
       0.62   10.2   6.6         29    4.8   0.2    3.3  3  Thioredoxin_4   Thioredoxin
        1.1    9.1  14.0        7.6    6.5   0.2    3.4  3  zf-C3HC4_3      Zinc finger, C3HC4 type (RING finger)
        1.4    8.7  12.3       0.63    9.8   0.4    3.7  3  Rubredoxin_2    Rubredoxin metal binding domain
        1.4    8.8  11.3       0.97    9.3   1.6    3.5  3  HNH_5           HNH endonuclease
        1.4    9.1  14.4       0.26   11.4   1.0    3.3  3  Spt4            Spt4/RpoE2 zinc finger
        1.5    8.9  18.9        2.8    8.0   1.2    3.4  2  HypA            Hydrogenase/urease nickel incorporation, meta
        2.5    8.1  13.5       0.84    9.6   1.4    3.3  3  C1_1            Phorbol esters/diacylglycerol binding domain 
        2.6    8.6   5.9        2.3    8.7   0.5    2.6  2  Evr1_Alr        Erv1 / Alr family


Domain annotation for each model (and alignments):
>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.0  15.0     8e-30     9e-27      30     174 ..     150     290 ..     120     298 .. 0.85

  Alignments for each domain:
  == domain 1  score: 94.0 bits;  conditional E-value: 8e-30
     TackOD1  30 dpkskelysypllealskekeeseelleelvkrglleeelvdrirlCpsCksghlnvrevCpkCkSidieeqelihhftCgnvgpeeeflkegkleCpk 128
                 +    +    +l++ ++ ++e+++++l+el k+g + e    + +lC++C+s + +++ +Cp+Ck  ++++++li+h++Cg++ p   f +++   Cp+
  EPA06039.1 150 KAVR-KTSMCRLMQNFNFSEEKMSQCLQELRKEGDVLEMKPIKEMLCNKCNSVNTSIIFACPNCKRYNFSQTKLIEHYDCGAIHPDYMFENDK---CPQ 244
                 3333.4455677888887888**********999777666667889*******************************************9998...*** PP

     TackOD1 129 CktkLrhiGvDYdrplevykCnsCkslfsepevkarClsCekeses 174
                 Ck+ ++++GvD + +++ ++C++C++ f +p + ++C++Ce++++ 
  EPA06039.1 245 CKKYIKALGVDHRTISNLFTCKECNEKFPNPTLDLNCIKCENKFSF 290
                 ******************************************9986 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   0.0     8e-14   8.9e-11       1     111 [.       8     123 ..       8     124 .. 0.93

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 8e-14
                   EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHH....ESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEESSTS.HHHHHHHHHC CS
  Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeek....vdlillDinmpgmdGlellkeireedpelpviiltahse.eedavealka 92 
                   vli++D++ +r  l+q++++ g+++++ea +gk  +e++ e +      l++l   +p+m+  e++  +  ++pe + ++ t+++  ee + + +++
    EPA06039.1   8 VLIIEDSESIRITLSQYIKKMGFTKIEEAVTGKRGIEKFIELTeigiTPLVFLGYHLPDMSAAEIVPIMLSKSPEAKLVLETSKDRnEESVRHLFSL 104
                   8*************************************98888888899**********************9********997776377888888** PP

                   TESEEEESSG-HHHHHHHH CS
  Response_reg  93 gaddflsKpfdpeeLlkal 111
                   g++ f++Kp++ e++++ +
    EPA06039.1 105 GVSHFIAKPLRFENMKDVI 123
                   ************9999877 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   2.5   0.00033      0.37       5      37 ..     173     214 ..     169     236 .. 0.78
   2 !   11.3   2.5   0.00022      0.25       2      41 ..     208     251 ..     207     254 .. 0.82
   3 !    7.6   1.5    0.0033       3.7       2      27 ..     264     289 ..     263     294 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00033
                     SS-S--EE-S........SEEE-TTT--.EEEEEEE-SSS-S CS
  zinc-ribbons_6   5 eCqqelekrg........eqyhCeaCqe.dlkkealCpeCeq 37 
                     +C qel+k+g        +++ C++C++ + +    Cp+C+ 
      EPA06039.1 173 QCLQELRKEGdvlemkpiKEMLCNKCNSvNTSIIFACPNCKR 214
                     7999999888899999999********978889999****74 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00022
                     --SSS-S--EE-S...SEEE-TTT--EEEEE.EE-SSS-S---E CS
  zinc-ribbons_6   2 kCpeCqqelekrg...eqyhCeaCqedlkke.alCpeCeqelev 41 
                      Cp+C++   +++   e+y C a + d+  e   Cp+C++ ++ 
      EPA06039.1 208 ACPNCKRYNFSQTkliEHYDCGAIHPDYMFEnDKCPQCKKYIKA 251
                     6****998876666899********998765168*****98876 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0033
                     --SSS-S--EE-SSEEE-TTT--EEE CS
  zinc-ribbons_6   2 kCpeCqqelekrgeqyhCeaCqedlk 27 
                     +C+eC+++  + +  ++C +C+++++
      EPA06039.1 264 TCKECNEKFPNPTLDLNCIKCENKFS 289
                     69999999999999999999998875 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.2    0.0003      0.34       2      13 ..     204     215 ..     203     215 .. 0.86
   2 ?    5.4   0.1     0.012        13       6      16 ..     241     251 ..     240     253 .. 0.92
   3 ?    1.0   0.5      0.28   3.1e+02       3      11 ..     261     269 ..     260     271 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0003
                 C-EEE-TTTSSE CS
       Sgf11   2 seyvtCpnCgRq 13 
                 s  + CpnC+R+
  EPA06039.1 204 SIIFACPNCKRY 215
                 6789*******5 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.012
                 E-TTTSSEEEG CS
       Sgf11   6 tCpnCgRqiaa 16 
                 +Cp C+++i+a
  EPA06039.1 241 KCPQCKKYIKA 251
                 6********97 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.28
                 -EEE-TTTS CS
       Sgf11   3 eyvtCpnCg 11 
                  ++tC+ C+
  EPA06039.1 261 NLFTCKECN 269
                 68******6 PP

>> zf-FPG_IleRS  Zinc finger found in FPG and IleRS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       6.9   7.7e+03      22      27 ..     193     198 ..     192     198 .. 0.82
   2 ?    2.8   0.0     0.095   1.1e+02       4      10 ..     209     215 ..     208     226 .. 0.88
   3 ?   10.9   0.1   0.00028      0.31       3      19 ..     241     257 ..     239     258 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 6.9
                   EE-TTT CS
  zf-FPG_IleRS  22 yfCprC 27 
                   ++C  C
    EPA06039.1 193 MLCNKC 198
                   789998 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.095
                   -TTT--B CS
  zf-FPG_IleRS   4 CpRCwry 10 
                   Cp C+ry
    EPA06039.1 209 CPNCKRY 215
                   9***998 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00028
                   B-TTT--BBEEEECTTE CS
  zf-FPG_IleRS   3 pCpRCwryiervgqagr 19 
                   +Cp+C+ yi+  g++ r
    EPA06039.1 241 KCPQCKKYIKALGVDHR 257
                   9*********9999876 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   3.0      0.11   1.2e+02      19      40 ..     207     228 ..     191     230 .. 0.70
   2 ?   12.6   0.6   9.1e-05       0.1      20      45 ..     241     270 ..     236     271 .. 0.88
   3 ?   -2.6   0.0       5.3   5.9e+03      20      27 ..     280     287 ..     273     292 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.11
  Zn_Tnp_IS1595  19 fvCPhCgsrkayrikt..rglfqC 40 
                    f CP+C+  ++ + +t   + + C
     EPA06039.1 207 FACPNCK--RYNFSQTklIEHYDC 228
                    78****9..666655533555555 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 9.1e-05
  Zn_Tnp_IS1595  20 vCPhCgsr.kayrikt...rglfqCkeCrk 45 
                     CP C++  ka  + +     lf CkeC++
     EPA06039.1 241 KCPQCKKYiKALGVDHrtiSNLFTCKECNE 270
                    5*****999999999988889*******85 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 5.3
  Zn_Tnp_IS1595  20 vCPhCgsr 27 
                     C +C+++
     EPA06039.1 280 NCIKCENK 287
                    58888876 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.2      0.98   1.1e+03       4      10 ..     194     200 ..     192     201 .. 0.84
   2 ?    3.8   0.0     0.038        42       3      22 ..     207     227 ..     206     227 .. 0.82
   3 ?    6.3   0.2    0.0063         7       3      13 ..     240     250 ..     238     253 .. 0.84
   4 ?    9.5   0.1   0.00065      0.73       2      15 ..     262     275 ..     261     278 .. 0.84
   5 ?   -3.5   0.2       7.6   8.5e+03       5      13 ..     281     289 ..     280     292 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.98
      zf_UBZ   4 lCerCgk 10 
                 lC +C++
  EPA06039.1 194 LCNKCNS 200
                 7****96 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.038
      zf_UBZ   3 ylCerCgke.ipeselqEHeD 22 
                 + C+ C+++ +++++l EH D
  EPA06039.1 207 FACPNCKRYnFSQTKLIEHYD 227
                 78*****95388889999976 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0063
      zf_UBZ   3 ylCerCgkeip 13 
                   C++C+k+i 
  EPA06039.1 240 DKCPQCKKYIK 250
                 68******996 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.00065
      zf_UBZ   2 tylCerCgkeipes 15 
                  ++C++C++++p +
  EPA06039.1 262 LFTCKECNEKFPNP 275
                 59*********976 PP

  == domain 5  score: -3.5 bits;  conditional E-value: 7.6
      zf_UBZ   5 CerCgkeip 13 
                 C +C  +++
  EPA06039.1 281 CIKCENKFS 289
                 888988776 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   2.0    0.0042       4.7      17      48 ..     173     212 ..     172     222 .. 0.77
   2 ?    5.5   8.5     0.015        17       1      37 [.     195     248 ..     195     253 .. 0.84
   3 ?    6.1   7.2    0.0099        11       1      37 [.     242     287 ..     242     293 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0042
         DZR  17 eCgtklkavaa........edrCpsCgekvdpearfCpeC 48 
                 +C ++l+++ +        e  C +C++ +++    Cp+C
  EPA06039.1 173 QCLQELRKEGDvlemkpikEMLCNKCNSVNTSIIFACPNC 212
                 6777777666677777777888888888888888888888 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.015
         DZR   1 CpqCgeelppdarfCseCgtklkavaa.................edrCpsCgek 37 
                 C +C++ +++    C++C+    ++++                 +d+Cp+C++ 
  EPA06039.1 195 CNKCNSVNTSIIFACPNCKRYNFSQTKliehydcgaihpdymfeNDKCPQCKKY 248
                 99****************988444444667788999***************975 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0099
         DZR   1 CpqCgee.........lppdarfCseCgtklkavaaedrCpsCgek 37 
                 CpqC++          + ++  +C+eC++k ++++   +C +C+ k
  EPA06039.1 242 CPQCKKYikalgvdhrTISNLFTCKECNEKFPNPTLDLNCIKCENK 287
                 99999998888866644455559*******99888899*****987 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1     0.058        65      78     129 ..     113     164 ..      79     194 .. 0.63
   2 ?    3.8   0.4     0.051        57      23      45 ..     207     228 ..     199     234 .. 0.87
   3 ?    4.8   0.2     0.026        29      19      34 ..     236     251 ..     232     257 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.058
                    HHHHHHHHHHHHTHHHHTTS-HHHHH......HHHHHTS-------HHHHHHH CS
  Thioredoxin_4  78 peaflaikallysqqeewaeslkelaae.aldkdekfeacleeekldalveae 129
                    p +f+++k+++++ +ee++ +  ++  e +l k ++  ++++++++ +l++++
     EPA06039.1 113 PLRFENMKDVINTIKEEFELQ-TNISVEtELVKIRDHLKAVRKTSMCRLMQNF 164
                    66899**************99.7766333444444444445444444444333 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.051
                    TT-HHHHHHHHHHHHHHHHHHHT CS
  Thioredoxin_4  23 lrCphCakfeeeveklleeyidt 45 
                    ++Cp+C++++ +  kl+e y d 
     EPA06039.1 207 FACPNCKRYNFSQTKLIEHY-DC 228
                    79********9999999998.55 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.026
                    EEE-TT-HHHHHHHHH CS
  Thioredoxin_4  19 eyedlrCphCakfeee 34 
                     +e+ +Cp C+k+ + 
     EPA06039.1 236 MFENDKCPQCKKYIKA 251
                    69*********98765 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   1.9      0.06        68      23      45 ..     193     214 ..     172     217 .. 0.80
   2 ?    6.5   0.2    0.0068       7.6      36      48 ..     238     250 ..     226     252 .. 0.74
   3 ?    6.3   0.6     0.008         9      24      46 ..     263     287 ..     257     290 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.06
                 EEE-HHHHHHHHHTT-B-TTT-- CS
  zf-C3HC4_3  23 lvlCeeCaekllkrkkkCpiCrr 45 
                 + lC++C +   +    Cp C+r
  EPA06039.1 193 M-LCNKCNSVNTSIIFACPNCKR 214
                 5.899999988889999999987 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0068
                 TT-B-TTT--B-- CS
  zf-C3HC4_3  36 rkkkCpiCrrpie 48 
                 +++kCp C++ i+
  EPA06039.1 238 ENDKCPQCKKYIK 250
                 899******9997 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.008
                 EE-HHHHHHHHH..TT-B-TTT--B CS
  zf-C3HC4_3  24 vlCeeCaekllk..rkkkCpiCrrp 46 
                 ++C+eC ek+ +   + +C  C  +
  EPA06039.1 263 FTCKECNEKFPNptLDLNCIKCENK 287
                 69********999999999999876 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.4   0.00056      0.63       3      24 ..     195     216 ..     194     216 .. 0.95
   2 ?    2.2   1.8      0.14   1.5e+02      16      22 ..     241     247 ..     227     248 .. 0.82
   3 ?    2.0   0.2      0.16   1.8e+02       1      10 [.     263     272 ..     263     274 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00056
  Rubredoxin_2   3 CsqCGfesakwfGrCpsCgsWn 24 
                   C++C+++  +    Cp+C+ +n
    EPA06039.1 195 CNKCNSVNTSIIFACPNCKRYN 216
                   *******************987 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.14
  Rubredoxin_2  16 rCpsCgs 22 
                   +Cp+C+ 
    EPA06039.1 241 KCPQCKK 247
                   7****96 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.16
  Rubredoxin_2   1 YvCsqCGfes 10 
                   + C++C+ ++
    EPA06039.1 263 FTCKECNEKF 272
                   7899998765 PP

>> HNH_5  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.2     0.029        32      31      42 ..     192     201 ..     185     206 .. 0.78
   2 ?    9.3   1.6   0.00087      0.97      27      43 ..     257     272 ..     242     280 .. 0.88
   3 ?   -1.3   0.2       1.8     2e+03      36      43 ..     281     288 ..     273     292 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.029
       HNH_5  31 nlvtlCkkCNqk 42 
                 ++  lC+kCN+ 
  EPA06039.1 192 EM--LCNKCNSV 201
                 45..9*****85 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00087
       HNH_5  27 ltisnlvtlCkkCNqkk 43 
                  tisnl  +Ck+CN+k+
  EPA06039.1 257 RTISNL-FTCKECNEKF 272
                 589999.9*******98 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.8
       HNH_5  36 CkkCNqkk 43 
                 C kC +k+
  EPA06039.1 281 CIKCENKF 288
                 67777665 PP

>> Spt4  Spt4/RpoE2 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.2       2.1   2.4e+03       6      27 ..     157     178 ..     152     187 .. 0.63
   2 ?    5.0   1.9     0.024        26       4      30 ..     195     218 ..     192     224 .. 0.80
   3 ?   11.4   1.0   0.00023      0.26       6      36 ..     227     259 ..     226     273 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.1
        Spt4   6 lCklvktedqFeeegCpnC.eil 27 
                  C+l+++ + F ee+   C + l
  EPA06039.1 157 MCRLMQNFN-FSEEKMSQClQEL 178
                 466666554.6777777774444 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.024
        Spt4   4 CllCklvktedqFeeegCpnCeilelk 30 
                 C +C+ v+t        CpnC+  ++ 
  EPA06039.1 195 CNKCNSVNTSII---FACPNCKRYNFS 218
                 999999999999...57****766655 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00023
        Spt4   6 lCklvktedqFeeegCpnC.eilelk.gdkekv 36 
                 +C++++++  Fe+++Cp C ++++    d++++
  EPA06039.1 227 DCGAIHPDYMFENDKCPQCkKYIKALgVDHRTI 259
                 6******************87776441455555 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5  10.4      0.13   1.5e+02      42      98 ..     169     218 ..     117     254 .. 0.64
   2 ?    8.0   1.2    0.0025       2.8      66      94 ..     258     286 ..     250     292 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.13
                 HHHHHHHHHHHCC.TTTT-EEEEEEE--EEEETTTS-EEECHHHHHS-TTTSSS-EE CS
        HypA  42 eaLefafellaegtvlegaeLeieevpvkvrCreCgkefeleekalrCpkCgsadve 98 
                 e ++++++ l+     eg +Le++ ++ ++ C++C++  ++    + Cp+C++ +++
  EPA06039.1 169 EKMSQCLQELR----KEGDVLEMKPIK-EMLCNKCNSVNTSI--IFACPNCKRYNFS 218
                 33333333333....335566666554.57799998444433..4689999887765 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0025
                 EE--EEEETTTS-EEECHHHHHS-TTTSS CS
        HypA  66 evpvkvrCreCgkefeleekalrCpkCgs 94 
                 +++  ++C+eC+++f   + +l+C kC++
  EPA06039.1 258 TISNLFTCKECNEKFPNPTLDLNCIKCEN 286
                 5566799*********886579*****97 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.9     0.021        24      11      36 ..     192     214 ..     187     216 .. 0.87
   2 ?    9.6   1.4   0.00075      0.84      10      38 ..     238     272 ..     230     275 .. 0.87
   3 ?    5.2   1.8     0.017        19       5      32 ..     256     285 ..     255     296 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.021
                 --B-TTT-SB--SSSS-EEEETTT-- CS
        C1_1  11 ptfCkhCgeflwgkekqglkCswCkl 36 
                 ++ C++C++      + +++C +Ck+
  EPA06039.1 192 EMLCNKCNSVN---TSIIFACPNCKR 214
                 67899999988...99********97 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00075
                 S--B-TTT-SB-.....-S.SSS-EEEETTT--EE CS
        C1_1  10 qptfCkhCgefl.....wg.kekqglkCswCkllv 38 
                 +  +C +C++ +      +   +  ++C++C++++
  EPA06039.1 238 ENDKCPQCKKYIkalgvDHrTISNLFTCKECNEKF 272
                 6789************9555***********9875 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.017
                 EE--SS--B-TTT-SB-..-SSSS-EEEET CS
        C1_1   5 hrnfkqptfCkhCgefl..wgkekqglkCs 32 
                 hr+ ++  +Ck+C+e +   ++ + ++kC+
  EPA06039.1 256 HRTISNLFTCKECNEKFpnPTLDLNCIKCE 285
                 677778889********5333666666665 PP

>> Evr1_Alr  Erv1 / Alr family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.7      0.28   3.1e+02      47      90 ..     172     209 ..     121     221 .. 0.59
   2 ?    8.7   0.5    0.0021       2.3      33      64 ..     256     286 ..     234     317 .. 0.66

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.28
                 HHHHHHHHHCH.CCCGSSHHHHHHHHHHHHHHHHHHTT...T-H CS
    Evr1_Alr  47 ehfekvlaenppekevesrdelvlWlweaHNeVnkrlakeefdc 90 
                 ++  + l++   e +v + + + + l++  N+Vn+++    f+c
  EPA06039.1 172 SQCLQELRK---EGDVLEMKPIKEMLCNKCNSVNTSII---FAC 209
                 222221222...23456667778889999999999887...444 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0021
                 HHHHHHHSSCHHHHHHHHH.HHHHCH.CCCGSS CS
    Evr1_Alr  33 lkliakfypCeeCaehfek.vlaenppekeves 64 
                  ++i++++ C+eC e+f + +l  n+ +   e+
  EPA06039.1 256 HRTISNLFTCKECNEKFPNpTLDLNCIK--CEN 286
                 6899*************98666666543..333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1384  (0.0771934); expected 358.6 (0.02)
Passed bias filter:                      654  (0.0364772); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); expected 17.9 (0.001)
Passed Fwd filter:                        38  (0.00211947); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.66u 0.26s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 1948.19
//
Query:       EPA06040.1  [L=48]
Description: hypothetical protein BG20_I0591 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 370.61
//
Query:       EPA06041.1  [L=65]
Description: hypothetical protein BG20_I0612 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      190  (0.0105974); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 462.37
//
Query:       EPA06042.1  [L=86]
Description: hypothetical protein BG20_I0611 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 613.58
//
Query:       EPA06043.1  [L=455]
Description: KamA family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.7e-05   23.6   0.1    0.00019   21.8   0.1    2.1  1  Radical_SAM  Radical SAM superfamily
    0.00093   19.5   0.1     0.0022   18.3   0.1    1.7  1  Fer4_12      4Fe-4S single cluster domain
     0.0011   19.1   0.0     0.0045   17.1   0.0    2.0  2  Fer4_14      4Fe-4S single cluster domain
  ------ inclusion threshold ------
       0.29   11.1   1.1       0.44   10.5   0.1    1.8  2  Flg_hook     Flagellar hook-length control protein FliK


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.1   4.3e-08   0.00019       5     158 ..     153     311 ..     150     318 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 4.3e-08
                  SEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC...CCTEEEEEEECSSCHG......... CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxx......... RF
  Radical_SAM   5 rgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla...vpgiritvetngtlpd......... 90 
                  + C+  CsfC r+     + ++    ++e +++v++l++++ +  v+++gg+p+  + +v+ +     l+    + ++i++ t ++            
   EPA06043.1 153 QTCHAYCSFCFRWPQ-FVGMDELKFAMREGEQLVQYLREHPEISDVLFTGGDPMIMKAKVFSTYINPLLEanlPNLRTIRIGTKALSYWpykfltddd 249
                  67***********96.44444445556666777777765555*************9777777666666666773444444444444433447778777 PP

                  .HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHH CS
                  .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM  91 .eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGende 158
                   ee+le +++     ++l +    +   l  +       +v+ea++k+r+ g   + +  ++l+  nd+
   EPA06043.1 250 aEEMLEIFKRVIDKGIHLAVMGHFNH--LVEL----KTNAVKEAIKKIRATGAQ-IRTQSPLLRHINDD 311
                  78999999998899999999999996..4444....357899999999999888.89999999999986 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1     5e-07    0.0022      12      80 ..     152     220 ..     137     282 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 5e-07
     Fer4_12  12 vsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkk.esiegltllGGEPllpenaeallelvkevk 80 
                  + C   C++Cf         + +f     e++++ l + ++i+++ ++GG+P+  ++a+++   ++ + 
  EPA06043.1 152 SQTCHAYCSFCFRWPQFVGMDELKFAMREGEQLVQYLREhPEISDVLFTGGDPMI-MKAKVFSTYINPLL 220
                 588*********6555555566677788999****99854999***********9.77777666655555 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0     1e-06    0.0045       7      92 ..     154     239 ..     150     264 .. 0.72
   2 ?   -0.9   0.0      0.39   1.7e+03      66      96 ..     252     289 ..     241     311 .. 0.51

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1e-06
     Fer4_14   7 gCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeey.pe.kkiwletngtle 92 
                  C+  C +C++  ++    + +++ ++ eq ++ l ++   i+ + +tGG+P++  + k++ + ++ l e   p+   i++ t ++  
  EPA06043.1 154 TCHAYCSFCFRWPQFVGMDELKFAMREGEQLVQYLREHPE-ISDVLFTGGDPMIM-KAKVFSTYINPLLEANlPNlRTIRIGTKALSY 239
                 6*********999888877777777777788876666655.677*********65.99999999998877664554667777766654 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.39
     Fer4_14  66 ellklvkrlkeeype........kkiwletngtleiele 96 
                 e+l++ kr+ +++ +        + + l+tn++ e  ++
  EPA06043.1 252 EMLEIFKRVIDKGIHlavmghfnHLVELKTNAVKE-AIK 289
                 45555555555553311111222334444444444.222 PP

>> Flg_hook  Flagellar hook-length control protein FliK
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   9.8e-05      0.44       3      38 ..      97     134 ..      95     137 .. 0.84
   2 ?   -3.2   0.1       1.8     8e+03      52      61 ..     219     228 ..     219     229 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 9.8e-05
                 HHHHHHCCTTSEEEEEECCCCCEEEEEEE.EEETT.EE CS
    Flg_hook   3 kvakaasngsqeatlrLdppeLGkvevkl.tlrgg.ql 38 
                  ++k+ +n  +e++l+L+p   G +e+++ tl++g +l
  EPA06043.1  97 GDKKEIQNTANEIRLQLNPHPAGQMELNVpTLKDGtKL 134
                 6788899*********************9777766455 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.8
                 HHHHTHHHHH CS
    Flg_hook  52 lLeqnlprLr 61 
                 lLe+nlp Lr
  EPA06043.1 219 LLEANLPNLR 228
                 69*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (455 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2973.45
//
Query:       EPA06044.1  [L=87]
Description: hypothetical protein BG20_I0618 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 554.70
//
Query:       EPA06045.1  [L=393]
Description: peptidase families S8 and S53 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-48  165.7  15.1    2.2e-48  165.1  15.1    1.3  1  Peptidase_S8  Subtilase family
    6.8e-08   33.1   0.0    1.6e-07   31.9   0.0    1.6  1  Inhibitor_I9  Peptidase inhibitor I9


Domain annotation for each model (and alignments):
>> Peptidase_S8  Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.1  15.1   2.4e-52   2.2e-48       4     278 ..     142     369 ..     139     381 .. 0.90

  Alignments for each domain:
  == domain 1  score: 165.1 bits;  conditional E-value: 2.4e-52
                   -EEEEECS-B-TT-TTTGGGEEE..EEEE---TTSG.GGEETT-SS-TT-SC-SSS....HHHHHHHHHH-B..SSSSSB-SSTTSEEEEEE-SSTT CS
                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Peptidase_S8   4 vlvavlDtGvdpshpdlsvttdgerklvdvideegagfngadsettstnwarddngnsieHGthvAGiaaanapeegekngvapgakilsvkvldts 100
                   v vav+DtG+dp+hpdl+                   ++++ + +  ++w++ +ng    HGthvAG++aa+ +++ +++gvap+a++ +v+vld++
    EPA06045.1 142 VDVAVIDTGIDPTHPDLN-------------------VVDGVNFAKGNSWSD-GNG----HGTHVAGTIAAK-NNDIGVVGVAPDARLHAVRVLDNR 213
                   669***************...................888888888877765.568....************.************************ PP

                   SB-HH..HHHHHHHHHHHHCT-S...EEEE-EESCETTCHHCHHHHHHHHHHHH.CCT-EEEEE--SS-T-HHEEE-TTCEECTTTSTTCEEEEEES CS
                   xxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Peptidase_S8 101 ggsmetgteliraieeaaedkvd...vinmslgestslpktgrsiealainravnkkgvlvviSaGNngktgsslqagspvgtpstsknvitvgayt 194
                   g+  +  +++i++++++a  ++d   v nmslg +++ +   +     a+++av + gv++v++aGN++       + +  ++p+++ n+itv+a +
    EPA06045.1 214 GSGFT--SDVIAGVNWVAA-NADiieVANMSLG-GSQSNALNT-----AVENAV-NAGVVFVVAAGNES-------TDACSKSPASAPNAITVSALD 293
                   *9997..8********999.5554459******.444444444.....899***.89************.......4555789**9*********** PP

                   ......TTSSB-TT--B-TT.......-EEEE-S-CCCCCCCCCHHHTTTHHEEEE-SHHHCHHHHHHHHHHHHHHHTT--HHHHHHHHH CS
                   ......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Peptidase_S8 195 ......tegkiapfSsrGpssdgklkpdivapGgnivstwsrqsnnsaglssyqsmsGTSmAsPnaagaaAlllsalpkltpetvraall 278
                         +++  a+fS++G+++      d+ apG+ i+stw+  +        y+++sGTSmA+P++agaaAl l  +p  tp++v +al 
    EPA06045.1 294 drdgvsNNDPFASFSNYGSCV------DVIAPGVLILSTWKDGG--------YNTISGTSMATPHVAGAAALYLVSHPTDTPAQVVDALQ 369
                   *****999999*********9......6****************........********************************998885 PP

>> Inhibitor_I9  Peptidase inhibitor I9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0   1.8e-11   1.6e-07      37      81 ..      58     102 ..      36     103 .. 0.84

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 1.8e-11
                   --EEEEEEESSSSSEEEEEE-GGGHHHHHTSTTEEEEEEEEEEEE CS
  Inhibitor_I9  37 akagilysYkilfnGfavklteeqaeklrkrpeVesVepDqsvrl 81 
                      gi + Y+++++Gf++++ + q++k+  +p V++Ve+D++v +
    EPA06045.1  58 RGLGISHVYETAIHGFSGVVPKGQLDKILSDPRVKYVEQDSIVTI 102
                   467999************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2708.79
//
Query:       EPA06046.1  [L=553]
Description: putative acetolactate synthase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-55  186.2   0.0    1.3e-53  181.1   0.0    2.2  2  TPP_enzyme_N     Thiamine pyrophosphate enzyme, N-terminal TP
    3.8e-39  133.9   0.0    1.1e-38  132.4   0.0    1.8  1  TPP_enzyme_C     Thiamine pyrophosphate enzyme, C-terminal TP
    1.4e-31  109.0   0.2    4.1e-31  107.5   0.0    1.9  2  TPP_enzyme_M     Thiamine pyrophosphate enzyme, central domai
  ------ inclusion threshold ------
      0.014   15.2   0.1      0.035   13.9   0.1    1.7  1  CO_dh            CO dehydrogenase beta subunit/acetyl-CoA syn
       0.18   11.2   1.7        3.7    6.9   0.5    2.2  2  AAA-ATPase_like  Predicted AAA-ATPase


Domain annotation for each model (and alignments):
>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.1   0.0   3.8e-57   1.3e-53       1     167 [.       1     165 [.       1     169 [. 0.98
   2 ?    2.8   0.0     0.022        80     114     163 ..     493     540 ..     436     545 .. 0.70

  Alignments for each domain:
  == domain 1  score: 181.1 bits;  conditional E-value: 3.8e-57
                   EEHHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHHHHHHHHHHT--EEEEE CS
  TPP_enzyme_N   1 mtvaealvraLkalgvehvfgvpGsrilplldalseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnaltalaeAkvdriPllvls 97 
                   m++++++v++L+++gve++fg+pG+++ +++++l ++ +i+++l+rhEq+aaf+Ad y r+t k+gv+l+t gpGatn++t++a+A+ d++ +l+++
    EPA06046.1   1 MKASDLFVKCLESEGVEYIFGLPGEENSDFCMSLLNS-KIKFILVRHEQSAAFMADVYGRITPKVGVCLATLGPGATNLTTGIASANMDSSRVLAIT 96 
                   789**********************************.5********************************************************** PP

                   EE--CCCHHS..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--EEEEEEEHHHCC-E CS
  TPP_enzyme_N  98 gdrptslrgqgvlqqeldqlalfrpvtkyaervtspeelpealrrAirtalsgrpgPvylelpkdvllee 167
                   g+++++l +++  q ++d+  lf+p+tk+++ +++ +++pe++rrA++++l++++g++++elp+dv + +
    EPA06046.1  97 GQTDSHLLHKESHQ-NMDAITLFKPITKWNWSIRNTDNIPEIVRRAFKISLEEKCGATHIELPQDVAKRQ 165
                   *********99888.***************************************************9876 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.022
                   T..-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--EEEEEEEHHH CS
  TPP_enzyme_N 114 l..dqlalfrpvtkyaervtspeelpealrrAirtalsgrpgPvylelpkdv 163
                      d ++l++++    ++++s ee+p++l++A    ++++  Pv +++  d 
    EPA06046.1 493 NnpDFVKLAQSFGAIGYHIKSTEEFPKILEEA----KKSKDKPVIIAIDVDY 540
                   14477777888888888888888888877776....4555889999988875 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.4   0.0   3.2e-42   1.1e-38       1     152 [.     389     535 ..     389     536 .. 0.96

  Alignments for each domain:
  == domain 1  score: 132.4 bits;  conditional E-value: 3.2e-42
                   ESSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHTGGGHHHHHHTT-SEEEEEEE-SBCCCHHHHHHHHTC CS
  TPP_enzyme_C   1 diGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmilqelatavrrnlpitvvvlnNegygmtggqqepfgg 97 
                   d+G +++w+a+ ++ ++p+++l ++g+ +mG+++p+Ai+ +l +p+++vva++GDG+flm++qe++ta r +lpi+++v+ ++gyg++  +++ ++g
    EPA06046.1 389 DVGAHKMWIAKTYNTYEPNTCLIPNGFCSMGFSVPGAIASQLVYPEKKVVAMCGDGSFLMNVQEIETASRLKLPIIIIVWVDGGYGLISLKEMDEYG 485
                   89**********************************************************************************************9 PP

                   CTTTTSBB.BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHH.CSSSEEEEE CS
  TPP_enzyme_C  98 krksgpagkdlkpvdfaklaealGakgarvekadveeleealkeal.ekkgpalie 152
                   k  +++    ++++df+kla+++Ga g+ ++++  ee+ ++l+ea  +k++p++i 
    EPA06046.1 486 KDAFTK----FNNPDFVKLAQSFGAIGYHIKST--EEFPKILEEAKkSKDKPVIIA 535
                   998874....7999***************9999..**********98999999986 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.5   0.0   1.1e-34   4.1e-31       1     136 [.     186     319 ..     186     324 .. 0.92
   2 ?   -3.1   0.0       1.6   5.8e+03     100     112 ..     526     539 ..     506     542 .. 0.55

  Alignments for each domain:
  == domain 1  score: 107.5 bits;  conditional E-value: 1.1e-34
                   HHHHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGGTTSS-TTSTTEEEESGGGSCHHHHHHHHH-SEEEEES-SSSTCCCTTTT CS
  TPP_enzyme_M   1 iekaaellkaakrpvilvGggvarsgaseelrelaeklgiPvvttlmgkgvipedhplylgmlglhgskaanealeeaDlvlalGarfddirttgse 97 
                   +++a++++ ++k+p+ilvG+g++r++ s ++r++aek+gi  ++t+m+kgvi+++++++l  +g+ ++++a  a+++aD+v+a+G ++ +     ++
    EPA06046.1 186 VKAAVKIILESKKPLILVGNGCIRENSSSHIRQFAEKTGICSMNTFMAKGVISDKSERHLQTIGIKQADHALIAMKNADVVIAIGYDLVE-----YS 277
                   689**********************************************************************************88866.....44 PP

                   T.TTTTT..-EEEEEESSCCCCTTCC--SEEEECTHHHHHHH CS
  TPP_enzyme_M  98 p.efape..akiihididpaeigknyqvdlaivgdvketlea 136
                   p +++++  +kiihid  +ae++  y++++++ +dv  t++a
    EPA06046.1 278 PkNWNSDltKKIIHIDFTSAEVDTYYPPTVEMSADVEYTIDA 319
                   44677664349*************************987776 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.6
                   TTTT-.EEEEEESS CS
  TPP_enzyme_M 100 fapea.kiihidid 112
                    ++++  ii id+d
    EPA06046.1 526 KSKDKpVIIAIDVD 539
                   23333347777776 PP

>> CO_dh  CO dehydrogenase beta subunit/acetyl-CoA synthase epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   9.7e-06     0.035      23     113 ..     184     270 ..     164     311 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9.7e-06
                 --SHHHHHHHHHSSSEEEEE-S--.-HH.HHHHHHHHHTSSSEEEEETHHHTT-G..GGSE-HHHHHHHHHSTT--TTTSS---SEEEEES CS
       CO_dh  23 ealkvvakmikkakrPllivGpqvlkaeneeakekkilekklkvvatalkeaglkdyekknklveltkllkdpepkgfdgegeydlvlfiG 113
                 e +k ++k+i   k+Pl++vG+   ++    ++ +  ++  +  + t + +  + d ++ +   +    +k+ +  ++    + d+v+ iG
  EPA06046.1 184 ELVKAAVKIILESKKPLILVGNGCIRENSSSHIRQFAEKTGICSMNTFMAKGVISDKSERHLQTIG---IKQADHALI-AMKNADVVIAIG 270
                 33457*******************998888999999999999999999888888888887744332...333333444.444567777777 PP

>> AAA-ATPase_like  Predicted AAA-ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.5     0.001       3.7      68     142 ..     275     353 ..     271     374 .. 0.79
   2 ?    2.9   0.0     0.017        60      91     146 ..     482     537 ..     475     548 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.001
  AAA-ATPase_like  68 ekletkwkeknkypvlkldfsavklese....eeleeslkeklkelekefgkkkeekslakrlkelieraaektgkkvv 142
                      e  +++w+++ +  ++++df +++++++     e+++ ++ +++ +++e++k+k+e+s  +  k+ + ++ ++ +++vv
       EPA06046.1 275 EYSPKNWNSDLTKKIIHIDFTSAEVDTYypptVEMSADVEYTIDAILEELEKEKQENSSIDYPKKEMPELFKQIKQQVV 353
                      567899***************9998775222267888888888888888888888777777777777777777777765 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.017
  AAA-ATPase_like  91 kleseeeleeslkeklkelekefgkkkeekslakrlkelieraaektgkkvvvLiD 146
                          ++++++  +  + +l+++fg+   + + ++++ +++e+a+++++k+v++ iD
       EPA06046.1 482 DEYGKDAFTKFNNPDFVKLAQSFGAIGYHIKSTEEFPKILEEAKKSKDKPVIIAID 537
                      54555555555566677788888888889999***********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (553 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       737  (0.0411066); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.48
# Mc/sec: 3446.62
//
Query:       EPA06047.1  [L=223]
Description: hypothetical protein BG20_I0595 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1574.28
//
Query:       EPA06048.1  [L=385]
Description: hypothetical protein BG20_I0608 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 2545.13
//
Query:       EPA06049.1  [L=183]
Description: arginine decarboxylase, pyruvoyl-dependent [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-56  191.2   0.0    1.2e-56  191.0   0.0    1.0  1  PvlArgDC  Pyruvoyl-dependent arginine decarboxylase (PvlArgDC


Domain annotation for each model (and alignments):
>> PvlArgDC  Pyruvoyl-dependent arginine decarboxylase (PvlArgDC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.0   0.0   6.5e-61   1.2e-56       1     161 [.       5     181 ..       5     182 .. 0.98

  Alignments for each domain:
  == domain 1  score: 191.0 bits;  conditional E-value: 6.5e-61
    PvlArgDC   1 vPkkvfltkGvgeskeelasFdlALldAgIenfNLvkvSSilPpeaeivsveeglkelppGsivevvmarassnepgrliaaavgvaipkdekkgGyia 99 
                 v kk+fltkG+g ++++l+sF+ AL+dAgI+ +NLv +SSi+Pp+a+++s++eglk+++pG+i++++++++++ne +rl +a+vg+a+pkd +++Gy++
  EPA06049.1   5 VAKKLFLTKGKGVHEDRLTSFEYALRDAGIAGTNLVLISSIFPPNAKLISRNEGLKQIKPGQILFTIYSKNQTNEAHRLCSASVGIARPKDTNRYGYLS 103
                 579************************************************************************************************ PP

    PvlArgDC 100 Eysgfgeseeeaeeeaeelaaemlattrgl................leekiietkeievaaveakvekygtvlaaavf 161
                 Ey+++g++e++++++ae+ aa+mla+ +g+                ++++i++t++++++++++k++k++tv+aaav+
  EPA06049.1 104 EYESYGQNEQQSGDYAEDIAAQMLASSLGIpfdidkswdekrqqwtISGQIYKTQNVTQSTKGDKDGKWTTVFAAAVL 181
                 **************************9999***************8888****************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1279.18
//
Query:       EPA06050.1  [L=115]
Description: hypothetical protein BG20_I0598 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.43   10.7   7.9       0.08   13.1   2.9    2.1  2  KIP1         KIP1-like protein
        1.3    9.3   8.4        3.1    8.0   8.6    1.5  1  DUF5514      Family of unknown function (DUF5514)
        2.2    8.2  14.1       0.24   11.3   6.4    2.8  2  Shugoshin_N  Shugoshin N-terminal coiled-coil region


Domain annotation for each model (and alignments):
>> KIP1  KIP1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.5      0.12     7e+02      19      28 ..      19      28 ..       3      48 .. 0.54
   2 ?   13.1   2.9   1.3e-05      0.08      26      67 ..      60     101 ..      31     109 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.12
        KIP1 19 tlseldekvk 28
                +++e+++k+k
  EPA06050.1 19 EIEEINHKIK 28
                2223333332 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 1.3e-05
        KIP1  26 kvkemlklieedadsfakraemyykkrpeLielveefyrsyr 67 
                 k  + +k+ie+d +++++++++  ++   Lie+v+e+ + ++
  EPA06050.1  60 KFSKHVKIIENDLEELKHQNKTLRENNSVLIEIVKEICKDHK 101
                 445568********************************9997 PP

>> DUF5514  Family of unknown function (DUF5514)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   8.6   0.00053       3.1      22     101 ..      11      91 ..       3     103 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00053
     DUF5514  22 rtiiednikkgenhflirnddygecfevdfekniteeenenwile.avidfakkyritefelwkkhegdstydkgfgivie 101
                   i ed+ +  e    i+n+dy +  ev  +k + e  +     +   i f+k+ +i e +l + +  + t  +   ++ie
  EPA06050.1  11 LEIQEDENEIEEINHKIKNNDYNQLKEVHHDKMVLETRKIALQNKiQSIKFSKHVKIIENDLEELKHQNKTLRENNSVLIE 91 
                 4577888888888889******************9988765544314799**********998866666676666666665 PP

>> Shugoshin_N  Shugoshin N-terminal coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.9     0.089   5.3e+02      21      31 ..      11      21 ..       1      29 [. 0.63
   2 ?   11.3   6.4   3.9e-05      0.24      10      45 .]      48      87 ..      42      87 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.089
  Shugoshin_N 21 lkirelekevs 31
                 l i+e e+e++
   EPA06050.1 11 LEIQEDENEIE 21
                 34555555555 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 3.9e-05
  Shugoshin_N 10 reLAKsNsalslk....irelekevseLlsENlnLRelil 45
                 r++A +N+++s+k    ++++e+ ++eL+ +N +LRe+++
   EPA06050.1 48 RKIALQNKIQSIKfskhVKIIENDLEELKHQNKTLRENNS 87
                 78999********999999******************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2692  (0.150148); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.34s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 651.54
//
Query:       EPA06051.1  [L=75]
Description: transcriptional regulator, AsnC family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-08   33.9   0.1    2.4e-08   33.8   0.1    1.0  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
      7e-05   22.7   0.1    7.7e-05   22.6   0.1    1.1  1  GYD             GYD domain
     0.0023   17.6   0.1     0.0028   17.3   0.1    1.1  1  RecO_N_2        RecO N terminal


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.1     4e-12   2.4e-08       9      73 ..      14      74 ..       6      75 .] 0.89

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 4e-12
                    GTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEE CS
  AsnC_trans_reg  9 hpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivl 73
                    +    e + e+l+ + +V+ +y + G yd +++v + d +++e+ + + +++l  v +t t+ v+
      EPA06051.1 14 A---EEYIVEELKHMNNVKNAYLTYGAYDVIAEVNTNDQHEFEKAVAD-IRKLSRVVSTMTLNVI 74
                    5...6678899*************************************.**********998776 PP

>> GYD  GYD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.1   1.3e-08   7.7e-05      35      81 ..      26      73 ..      13      75 .] 0.82

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.3e-08
         GYD 35 gkleslyatlGeyDvvvivEapDdetaaalslalaasGtvrt.etlra 81
                 ++++ y+t G yDv++ v+ +D+++++++   +++   v +  tl +
  EPA06051.1 26 NNVKNAYLTYGAYDVIAEVNTNDQHEFEKAVADIRKLSRVVStMTLNV 73
                4799********************************999877577765 PP

>> RecO_N_2  RecO N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   4.7e-07    0.0028       3      64 ..       4      66 ..       2      73 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.7e-07
    RecO_N_2  3 Gfilriqkvkdedlivtilt.keklktlyrfyGarhsliqlgtkidfeleengkfLprLravl 64
                Gfil   + + e+ iv+ l   +++k++y+ yGa   + ++ t    e+e+    + +L  v+
  EPA06051.1  4 GFILLNCDLGAEEYIVEELKhMNNVKNAYLTYGAYDVIAEVNTNDQHEFEKAVADIRKLSRVV 66
                9***************87751689************888888887788887777777776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       803  (0.0447878); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 542.51
//
Query:       EPA06052.1  [L=179]
Description: inorganic diphosphatase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.6e-56  188.3   0.1    8.9e-56  188.1   0.1    1.0  1  Pyrophosphatase  Inorganic pyrophosphatase


Domain annotation for each model (and alignments):
>> Pyrophosphatase  Inorganic pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.1   0.1     5e-60   8.9e-56       1     160 []      21     173 ..      21     173 .. 0.98

  Alignments for each domain:
  == domain 1  score: 188.1 bits;  conditional E-value: 5e-60
                      EEEEE-TTCSEEEEEETTTTEEEEEEE-SSSB-BSSEEEEETT--BTCCBEETSSSEEEEEESSS---TTEEEEEEEEEEEEEEETTEEEEEEE CS
  Pyrophosphatase   1 vvvEiprgsnaKyeidkeegklrldrvlftskgypanYGfipqTledtelkGDgDPlDvlvlgeeplspgevvevkvlGvlamiDegetDdKii 94 
                      v+vEip+gs +Kye+dk++++++ldrvlf+ ++yp +YG ipqTl++     DgDPlD+lvl++++++pg ++e++++G+l+m D+g+ DdKii
       EPA06052.1  21 VIVEIPKGSMNKYEYDKKHNMIKLDRVLFSPFHYPGDYGLIPQTLSE-----DGDPLDALVLVTNSTYPGILIEARPIGLLQMKDDGNPDDKII 109
                      79*********************************************.....****************************************** PP

                      EEETTSGGGTT-SSGGGSTHHHHHHHHHHHHHTTTTSCCT-SEEEEEEEEHHHHHHHHHHHHHHHH CS
  Pyrophosphatase  95 avpvkdprlkkindiedlpgllleeiehfFetykdlegkkknvkveewkdkeeAekvieeaheryk 160
                      +v+++dpr+ +  di+d++++ ++ei hfF+ ykdlegk  +v++ +wk+ ++A+++i e+++ryk
       EPA06052.1 110 CVSTNDPRYLHTADITDIEDHYRSEIGHFFQVYKDLEGK--KVEILGWKGSKDAKEIIVESIKRYK 173
                      *************************************65..79*********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1224.09
//
Query:       EPA06053.1  [L=132]
Description: response regulator receiver domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-12   47.9   0.0    1.5e-12   47.7   0.0    1.2  1  Response_reg  Response regulator receiver domain
      0.001   19.3   0.0      0.056   13.7   0.0    2.2  2  YnfE          Uncharacterized YnfE-like
  ------ inclusion threshold ------
       0.12   12.4   0.0       0.19   11.8   0.0    1.3  1  BRCT_3        BRCA1 C Terminus (BRCT) domain


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.7   0.0   2.5e-16   1.5e-12       1      91 [.       8     106 ..       8     127 .. 0.84

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 2.5e-16
                   EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHH.........ESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEESSTSHHHHHH CS
  Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeek.........vdlillDinmpgmdGlellkeireedpelpviiltahseeedave 88 
                   +liv+D++++++  +q+le++g  +v+++ dgk  le++++e          +dli+ D +m +m+G+++ k i++  pe +  ++t++++    v 
    EPA06053.1   8 ILIVEDSKALANWYKQILESNGH-KVTVTYDGKTELEIYEKELknglvsktpFDLIISDNSMKEMNGVDAGKIIHDFFPEQKFFFITGEKNRVLDVF 103
                   8**********************.***************6655577888888***********************************9988655544 PP

                   HHH CS
  Response_reg  89 alk 91 
                    ++
    EPA06053.1 104 DVD 106
                   444 PP

>> YnfE  Uncharacterized YnfE-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   9.4e-06     0.056      33      57 ..      39      63 ..      31      75 .. 0.88
   2 ?    3.5   0.0     0.015        89      13      44 ..      96     127 ..      87     130 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9.4e-06
        YnfE 33 keqlelYekqLkqesssdedfDevv 57
                k +le Yek+Lk++ +s+  fD ++
  EPA06053.1 39 KTELEIYEKELKNGLVSKTPFDLII 63
                789*******************886 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.015
        YnfE  13 nietinapDYeGkeeDlekqkeqlelYekqLk 44 
                 +  +++  D +Gk+ D+e++   l l++k++k
  EPA06053.1  96 KNRVLDVFDVDGKNIDVEEKPISLALFNKKVK 127
                 5566778899*********9999999888876 PP

>> BRCT_3  BRCA1 C Terminus (BRCT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.2e-05      0.19       6      58 ..       6      69 ..       3      77 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.2e-05
      BRCT_3  6 lkillvseqkefeelWseilklaGaavvkkekseaee...........islgkldvvvtdsscp 58
                lkil+v ++k +++ +++il+  G +v  +   ++e            +s   +d++++d+s+ 
  EPA06053.1  6 LKILIVEDSKALANWYKQILESNGHKVTVTYDGKTELeiyekelknglVSKTPFDLIISDNSMK 69
                79***********************996665555444578888999988888999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       798  (0.0445089); expected 358.6 (0.02)
Passed bias filter:                      595  (0.0331865); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 870.06
//
Query:       EPA06054.1  [L=281]
Description: hypothetical protein BG20_I0592 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.061   13.4   0.1       0.21   11.7   0.0    1.9  2  Coiled-coil_56  Coiled-coil domain-containing protein 56


Domain annotation for each model (and alignments):
>> Coiled-coil_56  Coiled-coil domain-containing protein 56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   1.2e-05      0.21      31      90 ..      63     124 ..      38     135 .. 0.73
   2 ?   -1.6   0.0      0.16   2.9e+03      63      76 ..     210     225 ..     207     227 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.2e-05
  Coiled-coil_56  31 efmrkvelaqlqkklqkrrrrnlltGlaiGglvlgiygytfysv..kqekfldeleeeakaa 90 
                     +++++  l++l +++  + +   l G++iG ++ gi+ y fy    k++ f  +le+  ++ 
      EPA06054.1  63 DYLKLDYLNDLVQNIAANSSIYDLIGFSIGMVIYGIFVYHFYRFlsKRDMFSFNLENRLSSK 124
                     6666666677777777777778899****************986224555666777666544 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.16
  Coiled-coil_56  63 vlgiygyt..fysvkq 76 
                     +lgi++y   fys+ q
      EPA06054.1 210 LLGIFLYNpeFYSLDQ 225
                     6999999555999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       921  (0.0513693); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1957.31
//
Query:       EPA06055.1  [L=281]
Description: CBS domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-36  123.3  10.8      2e-09   37.7   0.0    4.3  4  CBS       CBS domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.0   1.1e-13     2e-09       1      51 [.       4      53 ..       4      58 .. 0.89
   2 !   30.5   0.2     2e-11   3.7e-07       4      54 ..      73     121 ..      68     123 .. 0.90
   3 !   25.1   0.2     1e-09   1.8e-05       1      53 [.     132     184 ..     132     187 .. 0.93
   4 !   34.7   0.5     1e-12   1.8e-08       1      56 [.     224     278 ..     224     279 .. 0.90

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 1.1e-13
                HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEE.ETTTBEEEEEEHHHH CS
         CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVV.dedgklvGivtlrDl 51
                V++im +++ t+  ++++ +a+ lm ++++srl  + +e+g++vGi+t++D+
  EPA06055.1  4 VKQIMKKPI-TIENSASIFKAMTLMNNSKISRL-LTtNESGEIVGIITEKDI 53
                899996655.***************6666****.966**************9 PP

  == domain 2  score: 30.5 bits;  conditional E-value: 2e-11
                 HSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
         CBS   4 imtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54 
                 i  ++++ v+++t++e+++ +m+ k+++++ V  +++  +Givt++Dl+r+
  EPA06055.1  73 ILEKPLIQVNESTPVEDVAHIMITKNIGSIGVS-SSN-TIGIVTKTDLARY 121
                 567899*********************888775.777.***********98 PP

  == domain 3  score: 25.1 bits;  conditional E-value: 1e-09
                 HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEE.ETTTBEEEEEEHHHHHH CS
         CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVV.dedgklvGivtlrDllr 53 
                 Vgd+mt  + + + d++l +++ +m+e +vsrl ++ ++ ++ +G+v+ rDl+ 
  EPA06055.1 132 VGDVMTVSYSSMYSDDPLYKIVSKMIEDKVSRL-IIkNKKNEAIGVVSFRDLFG 184
                 89***99999****************999****.99888889*********986 PP

  == domain 4  score: 34.7 bits;  conditional E-value: 1e-12
                 HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEE.EETTTBEEEEEEHHHHHHHHH CS
         CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPV.VdedgklvGivtlrDllrall 56 
                 ++d+mt++vvt++ +++l  a  +m++ +++++ V +  d++l Giv+++D+++al 
  EPA06055.1 224 AKDVMTPNVVTIDYNDDLVMACTEMIDDKINGVGVlI--DNQLSGIVSKTDVIKALD 278
                 68***********************9999**996637..566*************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2016.71
//
Query:       EPA06056.1  [L=78]
Description: hypothetical protein BG20_I0585, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-12   47.8   0.0    2.3e-12   47.6   0.0    1.0  1  Usp       Universal stress protein family


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6   0.0   1.3e-16   2.3e-12      71     141 .]       8      78 .]       2      78 .] 0.93

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 1.3e-16
                 HHHHHHCTTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
         Usp  71 akaaaeaggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                 a++ a  + vk ++++  g+p+ ei+++ ++ + d iV+ ++g ++  + +lGSvs+yv++++++pV +++
  EPA06056.1   8 ATEHAGNKNVKFKTKTIRGSPSIEIVKLSQSGKFDDIVMSTTGAGSATGEMLGSVSNYVVHKSKVPVYLIK 78 
                 467788999**********************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.23s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 634.02
//
Query:       EPA06057.1  [L=252]
Description: amidohydrolase family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.2e-34  118.4   0.0    5.9e-34  118.2   0.0    1.0  1  Amidohydro_2  Amidohydrolase
  ------ inclusion threshold ------
      0.048   12.5   0.0       0.11   11.3   0.0    1.6  2  Trp_syntA     Tryptophan synthase alpha chain


Domain annotation for each model (and alignments):
>> Amidohydro_2  Amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.2   0.0   6.6e-38   5.9e-34      83     290 ..      55     250 ..      22     251 .. 0.89

  Alignments for each domain:
  == domain 1  score: 118.2 bits;  conditional E-value: 6.6e-38
                   TCBECEEECTSSHCHHHHHHHHHHHHTTECEEEEESSTTTCCTTTCGGHHHHHHHHHHHT-EEEEE....CHHHCHHHHHHHHHHHHHHHCCHHHHC CS
  Amidohydro_2  83 rfvggaavvpldpedaaaeleraveelgfkGvrlnphvggddllgdrldrpifealeelglpvdihtGpspewlfggpqettraiqplllsgvarkf 179
                   ++v+g ++ +++ ++ ++ ++ ++++  +kG+++++ +++ +++++r+  +++ +++e g+p ++htG         p  ++r+  pl l++va++ 
    EPA06057.1  55 GVVAG-FSIDNHTDEDLKNFRTWIKDGLVKGLKIYSGYEHYYPYDERYQ-KVYDICVEFGVPAMFHTG-----DTYSPKGKLRYARPLNLDEVAVDN 144
                   34444.4445566666899******************************.****************99.....7788999***************** PP

                   TTSEEEESGGGTTTTCHHHHHHHHHHHHHCCEEECCGHHHSSEEECCHHCHHHHHHHHHHH-G.GGEEEE--BTSTTSTSCTTHHHHCHHHHHSSHH CS
  Amidohydro_2 180 PnlkivlaHgGgpserlraalellarrpnvyvklsglytellyfdspladppalarlieavgp.drilfGsDyPhptleaepealalldlvallsde 275
                   P+lkivl+H+G+p  + ++a e +++ +nvy+++sgl+ ++++   ++ + + +a+li+ +g+ + +l+G+D+P++t + +++++a+l      ++e
    EPA06057.1 145 PELKIVLCHLGNP--WIQDAQEVIYKNKNVYADISGLVIGSFDHFFEKMIKEKVAELINYAGEpKYLLYGTDWPISTMDSYLSFVAKLNI----KKE 235
                   *************..*********************9877888888888888899999998862669**********************9....*** PP

                   HHHHHHTHHHHHHCT CS
  Amidohydro_2 276 erekilggNAarlyg 290
                    r+k+++ NA  l++
    EPA06057.1 236 FRDKFMYQNAKDLFK 250
                   *************97 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   1.3e-05      0.11     181     230 ..      36      88 ..       9     110 .. 0.84
   2 ?   -2.4   0.0      0.19   1.7e+03      90     121 ..     149     181 ..     137     204 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.3e-05
                 SB-TTHHHHHHHHHHCTSS-EEEESSS-..SHHHHHHHH.TT-SEEEE-HHHH CS
   Trp_syntA 181 avaaevdelverlkkltavPvavGFGis..tkeqvkqva.kvadGvivGSalv 230
                 +   + ++++ ++kk++++ v  GF i   t e+ k++  ++ dG + G ++ 
  EPA06057.1  36 SERPSAKQILDAIKKYDNLGVVAGFSIDnhTDEDLKNFRtWIKDGLVKGLKIY 88 
                 555677899******************7225689999999*******998875 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.19
                 EEEEE-CHHHCCC-HHHHCHHH.HHCTEEEEEE CS
   Trp_syntA  90 ivlltylnlvlsygeerflael.keagvdgliv 121
                 ivl    n+ ++  +e ++++    a++ gl++
  EPA06057.1 149 IVLCHLGNPWIQDAQEVIYKNKnVYADISGLVI 181
                 555555555555555554443203455555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       723  (0.0403257); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1871.07
//
Query:       EPA06058.1  [L=453]
Description: putative ATP-dependent RNA helicase DeaD [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-50  170.9   0.1    1.2e-49  168.5   0.1    2.0  2  DEAD           DEAD/DEAH box helicase
    7.5e-31  106.7   0.0    1.7e-29  102.4   0.1    2.5  3  Helicase_C     Helicase conserved C-terminal domain
    1.2e-05   24.7   0.2    1.8e-05   24.1   0.2    1.2  1  ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
    0.00046   20.2   0.0    0.00078   19.5   0.0    1.3  1  ResIII         Type III restriction enzyme, res subunit
     0.0012   18.6   0.1     0.0026   17.5   0.1    1.5  1  AAA_30         AAA domain
     0.0099   15.2   0.1      0.036   13.4   0.1    1.9  2  CMS1           U3-containing 90S pre-ribosomal complex subuni
  ------ inclusion threshold ------
       0.12   12.4   0.1       0.22   11.5   0.1    1.4  1  Flavi_DEAD     Flavivirus DEAD domain
       0.16   11.8   0.0       0.29   11.0   0.0    1.4  1  Helicase_RecD  Helicase


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.5   0.1   5.3e-53   1.2e-49       1     173 [.      33     195 ..      33     198 .. 0.96
   2 ?   -0.0   0.0      0.28   6.4e+02      63     104 ..     261     302 ..     233     311 .. 0.63

  Alignments for each domain:
  == domain 1  score: 168.5 bits;  conditional E-value: 5.3e-53
                 -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHHHHHHHTTCS CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        DEAD   1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaardqlskldngvd 99 
                 ++iQ+++ip +l+g+dv+++a+TGsGKT+af++++lq++   + k+g + l+++PtreLa q+ +++kkf+ky+++rv  ++gg+    ql++ld+gv+
  EPA06058.1  33 FPIQEAVIPVLLTGRDVIGQAHTGSGKTAAFALAMLQEI---QPKKGIQGLVMAPTRELAMQITTEIKKFGKYTGIRVATVYGGQGMGLQLDALDRGVE 128
                 58*************************************...68******************************************************* PP

                 EEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEEEEEESSBSHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        DEAD 100 ivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrqvivlSATlpkdv 173
                 ivv+tpgrl+d+l++g+++l +v+ +VlDEad++ld+gf d+i+ il          +++r + ++SAT+p+++
  EPA06058.1 129 IVVATPGRLIDHLKRGSIELGDVTHIVLDEADTMLDMGFVDDIQFILDLA-------PEERVMSLFSATMPTEI 195
                 *********************************************99999.......5667799******9765 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.28
                 HHHHHHHHTTTSTSEEEEE...ETTSSHHHHHHHHHTT.CSEEEEE CS
                 xxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxx.xxxxxxx RF
        DEAD  63 tlnnlkkfkkyidlrvlli...iggvaardqlskldng.vdivvgt 104
                 +++ l + k      +++i   ++++++++ + k+++g vdi+v+t
  EPA06058.1 261 VAKYLHQEKF----DAVAIegdMSQSRREQSMGKFRSGkVDILVAT 302
                 3333333333....2333311144666666677777667***9999 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.18   3.9e+02      12      51 ..      72     115 ..      62     134 .. 0.67
   2 ?   -2.5   0.0       2.9   6.5e+03      46      81 ..     187     222 ..     145     224 .. 0.57
   3 !  102.4   0.1   7.7e-33   1.7e-29       1     111 []     232     340 ..     232     340 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.18
                 HTTTTSEEEEEESSHH.HHHH....HHHHHHHTTSTEEEESTTST CS
  Helicase_C  12 leeeggkilifvntid.rlek....vklllekkgikvavlhgelp 51 
                 + ++g + l++++t++    +    +k + +  gi+va+++g   
  EPA06058.1  72 QPKKGIQGLVMAPTRElA-MQitteIKKFGKYTGIRVATVYGGQG 115
                 567777889999999952.333435566666669***99999755 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.9
                 ESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSST CS
  Helicase_C  46 lhgelpqnereeileqfnkgesdvLiatdvaerGid 81 
                 + +++p++  + + e  ++ ++ +L a d  ++Gid
  EPA06058.1 187 FSATMPTEILRLAEEYLKNPKQFLLDADDLSGEGID 222
                 333444444444445554545445556666667776 PP

  == domain 3  score: 102.4 bits;  conditional E-value: 7.7e-33
                 HHHHHHHHHHHHTTTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEESSSSSSHH CS
  Helicase_C   1 dkleallellkleeeggkilifvntidrlek.vklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVinfdlprnvt 98 
                 dk+++l++++  +  +g+i++f+ t+ r  + +k+l +++++ ++++ g+++q+ re+++ +f++g++d+L+atdva+rGid+p+v+lV+n+d+p +  
  EPA06058.1 232 DKMKYLIDFI--KPLKGQIIVFCSTKYRTRDvAKYL-HQEKFDAVAIEGDMSQSRREQSMGKFRSGKVDILVATDVASRGIDVPRVELVVNYDVPNQEM 327
                 6889999998..7899***********997766777.6778********************************************************** PP

                 HHHHHHTTSSSTT CS
  Helicase_C  99 syiqriGRtgRag 111
                  y +riGRt+Rag
  EPA06058.1 328 AYFHRIGRTARAG 340
                 ***********97 PP

>> ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.2   8.1e-09   1.8e-05      49     151 ..     234     339 ..     221     354 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 8.1e-09
  ERCC3_RAD25_C  49 cefLikyhekrgDkiivfsDnvfaLkeyakklkk.....pyiyGetseaerlkilqkfkknpkvntiflskvgDtsiDlPeanvliqisshfgsrr 139
                    +++Li++ +  + +iivf+   +  +++ak l++       i G++s++ r + + kf++  kv+ ++   v+   iD+P+ + ++  +       
     EPA06058.1 234 MKYLIDFIKPLKGQIIVFCSTKYRTRDVAKYLHQekfdaVAIEGDMSQSRREQSMGKFRSG-KVDILVATDVASRGIDVPRVELVVNYDVP----N 324
                    68***************************9876521111569****************976.89*****************9998865433....3 PP

  ERCC3_RAD25_C 140 qea...qrlGriLra 151
                    qe     r+Gr  ra
     EPA06058.1 325 QEMayfHRIGRTARA 339
                    333111455555555 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   3.5e-07   0.00078      30      88 ..      52     110 ..      36     192 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 3.5e-07
                 EESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEE CS
      ResIII  30 kmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseaykeigkk 88 
                 ++ TG+GKT   a ++ +  + +k  + l+++p+++l  q  +e+kkf + +  ++ ++
  EPA06058.1  52 QAHTGSGKTAAFALAMLQEIQPKKGIQGLVMAPTRELAMQITTEIKKFGKYTGIRVATV 110
                 678********9777777776666669******************99987654444444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   1.2e-06    0.0026       6      98 ..      36     160 ..      33     182 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.2e-06
      AAA_30   6 QaaavealltsgdrvavltGpAGtGKtta..lkalreaweaaggrviglAptgkaAkvLa....................eelgieastiakllkrlk. 81 
                 Q+a++  llt++d  ++ ++  G+GKt a  l+ l+e+  ++g + +++Apt + A +++                    +                + 
  EPA06058.1  36 QEAVIPVLLTGRD--VIGQAHTGSGKTAAfaLAMLQEIQPKKGIQGLVMAPTRELAMQITteikkfgkytgirvatvyggQ----------------Gm 116
                 8888888888888..99**********751166779999999****************99444444433333333333331................23 PP

      AAA_30  82 ...........................grarlepgtllivDEag 98 
                                            g  +l + t ++ DEa 
  EPA06058.1 117 glqldaldrgveivvatpgrlidhlkrGSIELGDVTHIVLDEAD 160
                 33333444444444455555555554755667777888888874 PP

>> CMS1  U3-containing 90S pre-ribosomal complex subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.1   1.6e-05     0.036     178     209 ..     127     158 ..     122     184 .. 0.90
   2 ?   -2.3   0.0      0.99   2.2e+03     128     148 ..     247     267 ..     242     274 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.6e-05
        CMS1 178 igiavGtpgRildLleeeslsvdeLkrivlDa 209
                 + i v tpgR++d l+ +s+++ ++++ivlD 
  EPA06058.1 127 VEIVVATPGRLIDHLKRGSIELGDVTHIVLDE 158
                 67899*************************96 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.99
        CMS1 128 elLvltlaalRaaDlaralkk 148
                 +++v +++  R  D+a+ l++
  EPA06058.1 247 QIIVFCSTKYRTRDVAKYLHQ 267
                 68999***********99875 PP

>> Flavi_DEAD  Flavivirus DEAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   9.9e-05      0.22      10      54 ..      52      97 ..      45     109 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.9e-05
                E--TTS-TTTTHHHHHHHHHH.HTT--EEEEESSHHHHHHHHHHTT CS
  Flavi_DEAD 10 dlhPGaGktrkvlpelvkeai.errlrtlvLaPtrvvlaemeealk 54
                ++h G+Gkt  +   +++e   ++ ++ lv+aPtr  +  ++  +k
  EPA06058.1 52 QAHTGSGKTAAFALAMLQEIQpKKGIQGLVMAPTRELAMQITTEIK 97
                68*********999999887626789*********98887766555 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00013      0.29       4      57 ..      53     107 ..      50     175 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00013
  Helicase_RecD   4 AdRGRGKSaalGlalaaliaegk.snilvtapskenvktlfeflakglealglke 57 
                    A+ G GK+aa +la+ + i+ +k  + lv ap++e + ++++ ++k  + +g++ 
     EPA06058.1  53 AHTGSGKTAAFALAMLQEIQPKKgIQGLVMAPTRELAMQITTEIKKFGKYTGIRV 107
                    889************9999999889***********9999999977666665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2956.57
//
Query:       EPA06059.1  [L=67]
Description: hypothetical protein BG20_I0606 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
        4.6    7.3   5.1       0.87    9.7   1.4    1.6  2  FSAP_sig_propep  Frog skin active peptide family signal and p


Domain annotation for each model (and alignments):
>> FSAP_sig_propep  Frog skin active peptide family signal and propeptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   1.4   4.8e-05      0.87       8      20 ..      28      40 ..      27      41 .. 0.94
   2 ?   -2.1   0.1      0.24   4.3e+03      24      24 ..      62      62 ..      55      67 .] 0.43

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 4.8e-05
  FSAP_sig_propep  8 LLvLFLGlVSlSl 20
                     LL+ FLG+++lSl
       EPA06059.1 28 LLITFLGVINLSL 40
                     89**********8 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.24
  FSAP_sig_propep 24 e 24
                     +
       EPA06059.1 62 K 62
                     1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 477.86
//
Query:       EPA06060.1  [L=104]
Description: hypothetical protein BG20_I0594 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.9e-08   31.8   4.3    1.8e-07   30.7   4.3    1.7  1  SHOCT     Short C-terminal domain


Domain annotation for each model (and alignments):
>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   4.3   9.8e-12   1.8e-07       3      28 .]      76     101 ..      74     101 .. 0.96

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 9.8e-12
       SHOCT   3 LekLkeLyarGeIteEEFeakKakLL 28 
                 +e+L +L+++G+Ite EF+akK++LL
  EPA06060.1  76 IERLGKLKESGLITEKEFQAKKKELL 101
                 89***********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1007  (0.056166); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 686.74
//
Query:       EPA06061.1  [L=41]
Description: hypothetical protein BG20_I0614 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.28s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 293.48
//
Query:       EPA06062.1  [L=590]
Description: oligoendopeptidase, PepF/M3 family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.5e-46  157.2   0.7    5.2e-45  154.5   0.7    2.1  1  Peptidase_M3    Peptidase family M3
    1.4e-05   25.2   5.5    2.9e-05   24.2   0.2    4.0  4  Peptidase_M3_N  Oligopeptidase F
     0.0031   17.4   0.1     0.0087   16.0   0.1    1.8  1  Peptidase_M78   IrrE N-terminal-like domain
  ------ inclusion threshold ------
      0.096   12.6   2.7       0.58   10.0   0.3    2.5  2  Colicin         Colicin pore forming domain
       0.14   12.4   0.0       0.28   11.5   0.0    1.4  1  FG-GAP_2        FG-GAP repeat
       0.29   11.0   4.2        7.8    6.5   0.4    3.2  2  DUF3198         Protein of unknown function (DUF3198)


Domain annotation for each model (and alignments):
>> Peptidase_M3  Peptidase family M3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.5   0.7   1.8e-48   5.2e-45       4     456 ..     199     576 ..     196     578 .. 0.85

  Alignments for each domain:
  == domain 1  score: 154.5 bits;  conditional E-value: 1.8e-48
                   C-S-HHHHHHHHHHHCTTTCCSS..THHHHHHHHHHHHHHHH.HHHTT-SSHHHHHHTTSTT-SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
  Peptidase_M3   4 espdrelRkeayeashskaaeqrntlensklleellklrael.Akllgyesyaelaledkmaknpetvldfleelvkklrpllekelkllkelkkke 99 
                   +s+++++R++ay+   +k++e++  l   +++++++ + + +  +++gy+s ++++     ++ +++  + l ++ +k++p+++k + ++++     
    EPA06062.1 199 RSTNPKTRETAYKTILTKYSENKGVL--GEIYQNIVLNWKDEgIEIRGYKSPISMRNIG--NDVDDKTIESLLTVCRKNSPVFQKFFVQKAK----I 287
                   6899****************988778..888888887766666****************..***************************9999....8 PP

                   CT-SSS--CCCHHHHHHHHHCCCCS--CCCCGG.G-BHHHHHHCHHHHHHHHHTEEEE...EETTS..--SSTT-EEEEEEET.TT-EEEEEEEEEE CS
  Peptidase_M3 100 lglegelqpwDvaYYsekqreekydldqeelke.yfpletvleGllelfeeLfGikfv...eekdakgevwhedVrkleVvdeilsegligeiylDl 192
                   l+ + +l+ +D+           y++++ ++ke ++++++ ++           + f+   +  + k e++++     +V++         e  +D 
    EPA06062.1 288 LKMK-KLRRYDL-----------YAPSAAKIKEkNYQYDKSVK-----------LVFEslgRFSP-KLEEFAK-----KVFN---------EKHVDS 346
                   8777.9******...........44444444331344455555...........33330002222.2455666.....4555.........5558** PP

                   C--TTS-SS-EEEEEE--BTTS-B--EEEEEEEEE---BTTS--B--HHHHHHHHHHHHHHHHHHC--BSSGGGSTT-S-CCCCCHHHHHHHHGGGS CS
  Peptidase_M3 193 yerkgKrggAasfglvksredgtrqlpviylllNftkpsskkPsLLtldevetLfHEfGHsmHsllsrteysnvsgtnvpidfvElpSqlmEnllte 289
                     r+gKr+gA++++l ++          +++llNft+         + ++v+tL+HE+GH++Hs  ++++   +   + p+ ++E +S++ E ll +
    EPA06062.1 347 SIRPGKRDGAFCSTLTPK--------ITPFVLLNFTG---------KTRDVFTLAHELGHAVHSQAAQNRS--ILVQEAPLPLAETASTFSELLLYD 424
                   *****************6........89*********.........**********************996..567799****************** PP

                   HHHHHCC-B-TTT--B--HHHHHHHHCCCCTTHHHHHHHHHHHHHHHHHCTT-TCCGHH....HHHHHHHHHHCTTSCTTBTTSSGGGC-CCCHTSS CS
  Peptidase_M3 290 pevlkslskhyetgeaipeelleklikaknvnaalellrqlvfaafdqelHeeaeeeqilkkdlletyaelrkkflglpvapdeasqasFghlfahg 386
                   +++ k +   ++++++++ e++++l         ++++rq++f+ f++  He++ ++ + + ++++ty +  k+ +g +va  e +    + +  h+
    EPA06062.1 425 NLSDKIT---DNEKKTMLSEKIDDLY--------ATIMRQAYFTIFEVAAHEQIGKGTTVD-EISKTYIQNLKEQFGSSVAISEDFAVEWSCI-PHF 508
                   9999888...57799999********........**********************99877.5888777777777888999999888887777.4** PP

                   -TTTTCHHHHHHHH..HHHHHHCCHHCCTT-..CCHHHHHHHHTTTTTTSS-HHHHHHCCCSS---SHHHHHHC CS
  Peptidase_M3 387 YaanYYsylyaevl..aldifekffeedpln..retGeryrkeiLsrGgskdplellkkflgrepsadallkal 456
                   Y+ ++Y+y y+ +   al++f+++++e+  +  +      + eiL++Ggs++p +ll++ + + +s++ +++ +
    EPA06062.1 509 YHTPFYCYAYSFGNllALSLFQRYKKEG--SsfV----PSYIEILAAGGSEKPEKLLARHGLDITSQKFWQEGF 576
                   **********987667**********99..4356....79******************************9976 PP

>> Peptidase_M3_N  Oligopeptidase F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1      0.61   1.8e+03      42      57 ..      60      75 ..       5      87 .. 0.59
   2 !   24.2   0.2   9.8e-09   2.9e-05       4      67 ..     115     175 ..     114     178 .. 0.92
   3 ?    0.2   0.0      0.31   9.2e+02       5      39 ..     258     289 ..     256     292 .. 0.79
   4 ?   -2.5   0.0       2.2   6.6e+03      39      50 ..     552     563 ..     552     568 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.61
  Peptidase_M3_N 42 eEklLaelsevggaaw 57
                     Ek+  +++++gg a+
      EPA06062.1 60 IEKISEKMNQIGGYAS 75
                    3555555555555555 PP

  == domain 2  score: 24.2 bits;  conditional E-value: 9.8e-09
  Peptidase_M3_N   4 aldeekleellkeepelaeyrfyleeilrqkphtLseeeEklLaelsevggaawnifsdltnad 67 
                     ++d+   ++l+ke+ el+ey   l+  + ++++ Lse eEk+++ l ++g +a  +++d  ++ 
      EPA06062.1 115 KVDDSNAKRLIKESGELSEY---LNHKRLFAKYALSEPEEKIINTLDVTGISALVKLYDKMTSA 175
                     6799999*****99999999...*******************************9999988875 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.31
  Peptidase_M3_N   5 ldeekleellkeepelaeyrfyleeilrqkphtLs 39 
                     +d++++e+ll+     ++  + +++++ qk+ +L 
      EPA06062.1 258 VDDKTIESLLTV---CRKNSPVFQKFFVQKAKILK 289
                     79999****996...77777778888888888875 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 2.2
  Peptidase_M3_N  39 seeeEklLaels 50 
                     se+ EklLa  +
      EPA06062.1 552 SEKPEKLLARHG 563
                     7899****9866 PP

>> Peptidase_M78  IrrE N-terminal-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   2.9e-06    0.0087      28      62 ..     366     399 ..     340     494 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.9e-06
  Peptidase_M78  28 tkvivlnsnhsptrqrftlaHElgHlllhherdkf 62 
                    t++++ln    +tr  ftlaHElgH+++ +  +++
     EPA06062.1 366 TPFVLLNFT-GKTRDVFTLAHELGHAVHSQAAQNR 399
                    555555555.789**************98887665 PP

>> Colicin  Colicin pore forming domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.3   0.00019      0.58      40      87 ..      20      67 ..      10      71 .. 0.86
   2 ?    1.8   0.1     0.065   1.9e+02      24      62 ..     179     219 ..     150     236 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00019
     Colicin 40 edarGkkirslsdalksfekikrnlnkkikakdrvaiakalesvdkki 87
                + a  k+i  l+   k fekik  ln k++ k+ + i + +e++ +k+
  EPA06062.1 20 SSAFQKQITELEGLAKKFEKIKSKLNPKMSSKEFMNILHQIEKISEKM 67
                445579999999999***************************999987 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.065
     Colicin  24 tkklGekakelare.laedarGkkirslsdalksf.ekikr 62 
                   k+G+k+k+++re + + +r  + ++ + a k++  k+ +
  EPA06062.1 179 KMKIGNKTKTMTREeITNFIRSTNPKTRETAYKTIlTKYSE 219
                 23678888888774266666766666666666653144444 PP

>> FG-GAP_2  FG-GAP repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   9.3e-05      0.28      16      30 ..     486     500 ..     483     500 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.3e-05
    FG-GAP_2  16 DyFGssVaisgdtlv 30 
                  +FGssVais+d++v
  EPA06062.1 486 EQFGSSVAISEDFAV 500
                 68**********998 PP

>> DUF3198  Protein of unknown function (DUF3198)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.4    0.0026       7.8      16      44 ..      21      48 ..      11      50 .. 0.80
   2 ?    4.5   0.5     0.011        32      14      32 ..      49      67 ..      47      70 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0026
                HHHHHHHHHHHHHHHHH-SHHHHHHHHHH CS
     DUF3198 16 stFvknlkeLekiarklGssYqqrLeeak 44
                s F k ++eLe +a+k+ +  +++L+ ++
  EPA06062.1 21 SAFQKQITELEGLAKKFEK-IKSKLNPKM 48
                5799*************64.566666665 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.011
                -HHHHHHHHHHHHHHHHHH CS
     DUF3198 14 SKstFvknlkeLekiarkl 32
                S ++F++ l + eki+ k+
  EPA06062.1 49 SSKEFMNILHQIEKISEKM 67
                5689************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (590 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1158  (0.0645881); expected 358.6 (0.02)
Passed bias filter:                      597  (0.033298); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.68u 0.31s 00:00:00.99 Elapsed: 00:00:00.47
# Mc/sec: 3746.62
//
Query:       EPA06063.1  [L=236]
Description: putative membrane protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.14   11.2  24.7       0.19   10.8  14.8    2.1  2  Acyl_transf_3  Acyltransferase family
        4.9    6.4   7.5        2.1    7.7   1.4    2.2  2  YhfC           YhfC intramembrane metalloprotease


Domain annotation for each model (and alignments):
>> Acyl_transf_3  Acyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8  14.8   2.1e-05      0.19     149     271 ..      24     158 ..       6     158 .. 0.57
   2 ?    3.5   6.9    0.0035        31     146     220 ..     153     227 ..     145     229 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 2.1e-05
                    xx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Acyl_transf_3 149 ll.....lrllrkvrkshlllllilllllslvfirhel........fgpatsvgllplpsvla..llfflfGalladaddrdrnlsrglkisllls 229
                    +      +    + + +h  ++l+++l+++l++    +             sv+ +++  ++   +++flfG+++ + +  + ++  + ++s+ ls
     EPA06063.1  24 IVcivnnF--KIGKGGKHGQSWLFFTLAIALWYTAERIwtipeltnS---DSVFSYADLFWFSgyVFYFLFGVMYLKPFSSQISR--KNILSTSLS 112
                    33455432..3333333333344444444444333333334443333...333333333333367*********97777666655..99******* PP

                    xxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxx RF
  Acyl_transf_3 230 llllalillalfgqtdg....gglvasvliqsaslllvslgimlll 271
                    +++++++++++ + + +    + +  +  + s+ l+  +lgi+l++
     EPA06063.1 113 VVVVLIFIFYIIMPSSNisenILNASYPVADSFMLIPSILGIFLFF 158
                    *************998877665555555566666666666666665 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.0035
                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Acyl_transf_3 146 llplllrllrkvrkshlllllilllllslvfirhelfgpatsvgllplpsvlallfflfGalladaddrdrnlsr 220
                     ++l+++  +k+ +s l++  ++++ + ++f++++ +g +    l  +p+  a++ f++G+++  + ++++n++ 
     EPA06063.1 153 GIFLFFKGRTKFSWSLLFFGMLVFVGSDFGFMYFNSTGDYYEGHLIDIPYLYAYSIFIAGLIANLNLWNKTNKNK 227
                    567788888888888888888888888888888888777777776666666669999999999999988888875 PP

>> YhfC  YhfC intramembrane metalloprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.5     0.014   1.2e+02      25      69 ..      80     124 ..      72     132 .. 0.77
   2 ?    7.7   1.4   0.00023       2.1       5      34 ..     148     179 ..     145     184 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.014
        YhfC  25 glGalvFalfalvlerplhlallkqneatakalsapllfavygaL 69 
                 + G ++++lf ++  +p++  ++++n   + ++ +++l  +++++
  EPA06063.1  80 FSGYVFYFLFGVMYLKPFSSQISRKNILSTSLSVVVVLIFIFYII 124
                 5699****************9999997666664444444455444 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00023
        YhfC   5 lpig..lvvwlrkklklslkvvglGalvFalf 34 
                 +p +  ++++++ + k+s+  ++ G+lvF+ +
  EPA06063.1 148 IPSIlgIFLFFKGRTKFSWSLLFFGMLVFVGS 179
                 554446999********************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       887  (0.0494729); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1516.89
//
Query:       EPA06064.1  [L=421]
Description: hypothetical protein BG20_I0587 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1248  (0.0696079); expected 358.6 (0.02)
Passed bias filter:                      735  (0.040995); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.63u 0.34s 00:00:00.97 Elapsed: 00:00:00.50
# Mc/sec: 2546.19
//
Query:       EPA06065.1  [L=56]
Description: hypothetical protein BG20_I0616 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.4e-07   30.4   0.1    3.8e-07   30.2   0.1    1.1  1  DUF1059    Protein of unknown function (DUF1059)
  ------ inclusion threshold ------
      0.056   14.0   0.1      0.061   13.9   0.1    1.1  1  FliG_N     FliG N-terminal domain
      0.076   12.9   0.1      0.087   12.8   0.1    1.1  1  AAA_lid_9  AAA lid domain


Domain annotation for each model (and alignments):
>> DUF1059  Protein of unknown function (DUF1059)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.1   6.3e-11   3.8e-07       1      49 [.       1      48 [.       1      54 [. 0.85

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 6.3e-11
     DUF1059  1 mkefkCgDvgpdCgfeitaeteeEvlrkvaeHakaaHglteippelvek 49
                m ++kC D g+dC+f  ++ + +E++++ a+H+ ++Hg+    ++l++ 
  EPA06065.1  1 MIKLKCEDYGYDCSFVSEG-EVNEIIEEFAKHTEEEHGIDYSKEALMQF 48
                5689***********9855.5667**************98888888765 PP

>> FliG_N  FliG N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1     1e-05     0.061      45      82 ..      16      53 ..      12      56 .] 0.87

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1e-05
                XXHHHHHHHHHHHHHHHHCCCCHHCHHHHHHHHHHHHH CS
      FliG_N 45 vskeeveaVleefleeleaqeylseggeeyarelLeka 82
                vs+ ev++++eef +++e++ ++  + e+ ++ +L+k+
  EPA06065.1 16 VSEGEVNEIIEEFAKHTEEEHGIDYSKEALMQFILRKT 53
                8899****************999999999888888876 PP

>> AAA_lid_9  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   1.5e-05     0.087       4      31 ..      20      47 ..      17      52 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.5e-05
   AAA_lid_9  4 etieiLrglkekyekhHgvkisdealea 31
                e  ei++  +++ e+ Hg+ +s+eal +
  EPA06065.1 20 EVNEIIEEFAKHTEEEHGIDYSKEALMQ 47
                6679*********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 357.35
//
Query:       EPA06066.1  [L=587]
Description: transporter, small conductance mechanosensitive ion channel MscS family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.3e-28   98.3   0.0    9.8e-28   97.1   0.0    1.6  1  MS_channel   Mechanosensitive ion channel
  ------ inclusion threshold ------
      0.028   14.7   0.6      0.087   13.1   0.6    1.8  1  DUF1774      Fungal protein of unknown function (DUF1774)
        0.1   11.7   0.6       0.16   11.1   0.6    1.2  1  LMF1         Lipase maturation factor
       0.24   11.3   1.7        1.8    8.6   1.8    2.1  2  Ninjurin     Ninjurin


Domain annotation for each model (and alignments):
>> MS_channel  Mechanosensitive ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.1   0.0   2.2e-31   9.8e-28       6     206 .]     312     541 ..     307     541 .. 0.94

  Alignments for each domain:
  == domain 1  score: 97.1 bits;  conditional E-value: 2.2e-31
                 HHHHHHHHHHHHHTTT--SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESS.SEEEEEEEE-SSEEEEEETTSE.EEEEEHHHHH CS
  MS_channel   6 iliivvgilivlsllgvnvsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveig.dieGtVediglrttkirtfdgr.ivtiPnsslv 102
                 ++ ++ ++l ++s++gv++  l ++ G +++++g+alk++++n++a +++  +k f  G+++ ++ + +G+V +i+ r+t +r + ++ + ++P+++lv
  EPA06066.1 312 LGFFLGAVLGIISWWGVDLFVLATASGGIAIGVGFALKETFENYFAYLMIRKDKIFVEGERIALAsGYKGIVYKITSRVTFVRHPLNEsVAIVPTRQLV 410
                 56677799********************************************************99******************977516689****** PP

                 TS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-T.............................TS-EEEEEEEE-SSSEEEEE CS
  MS_channel 103 tsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlk.............................dkellvvldefgdsslnfev 172
                 ts+i+N+++e   + ++v++gv y  d+k++  +l ++ + ++++  + k                              ++++v++++f dssl+f v
  EPA06066.1 411 TSEIINYTKEFAIVPATVEVGVSYLNDPKQVAAALMKVGTRALSEVVDSKgrhlavqakcpnldenkpscgcdkqfvldLEQPTVRFQKFNDSSLDFAV 509
                 ***************************99988888888888877776766999**************************9******************* PP

                 EEEEET...TTHHHHHHHHHHHHHHHHHHHT--- CS
  MS_channel 173 rvfvktvvpeeylsvqseinlrikkileeegiei 206
                 +v+v++  ++ +++++++ +  i +++++ gi+i
  EPA06066.1 510 WVYVRD--YGLQFKMETDMRMMIYEEFKRYGIRI 541
                 ******..************************97 PP

>> DUF1774  Fungal protein of unknown function (DUF1774)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.6     2e-05     0.087      43      79 ..      24      60 ..       4      72 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2e-05
     DUF1774 43 lltkvialQwifafviaavlfvlslvvavakllgree 79
                ll+  i+lQ  fa +++++++++++++ +++++++++
  EPA06066.1 24 LLSSSISLQIAFAILVVGLIVIATIYTKFRQWTRTKK 60
                67788***************************99884 PP

>> LMF1  Lipase maturation factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.6   3.5e-05      0.16     177     274 ..      27     144 ..       6     166 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.5e-05
        LMF1 177 erllsllvvallvllvvslfslkiseeekkvesklaftkeefaklltkvlvelllllllalllvvvkalvkt.....................akkliq 254
                 +++   +++a+lv++++ + ++ ++ ++++ + k++++k  fa++++++++ +l+l+l++++ ++++++                          kl++
  EPA06066.1  27 SSISLQIAFAILVVGLIVIATIYTKFRQWTRTKKFSYSKPIFAEIVRRAVLPILALALISSINIYIQTFE-LfddpaellkeklsaeltpgetFAKLLN 124
                 333344455999999999999999999999***************************9999999994444.359999***9999999999777666666 PP

        LMF1 255 svlllvllllavlvftlslv 274
                 s++++v+++++  ++t+ l 
  EPA06066.1 125 SMNIIVIAFTVGHIITILLE 144
                 66665555555444444444 PP

>> Ninjurin  Ninjurin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   1.8    0.0004       1.8      33      64 ..      11      42 ..       6      95 .. 0.57
   2 ?   -0.3   0.0      0.22   9.9e+02      43      73 ..     123     154 ..     102     179 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0004
    Ninjurin 33 sgekskfyiallvLislSllLqvvvgillili 64
                ++++     +l+ L+s S+ Lq++++il++ +
  EPA06066.1 11 EQAAVGQIGTLIELLSSSISLQIAFAILVVGL 42
                5554444467899*************998762 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.22
    Ninjurin  43 llvLislSllLqvvvgillili.asklnleke 73 
                 l  + ++ +++ v + i+++l  ++kl+leke
  EPA06066.1 123 LNSMNIIVIAFTVGHIITILLEkKEKLKLEKE 154
                 44444566666666666666643555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (587 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       778  (0.0433934); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.74u 0.36s 00:00:01.10 Elapsed: 00:00:00.53
# Mc/sec: 3319.61
//
Query:       EPA06067.1  [L=46]
Description: hypothetical protein BG20_I0593 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.022   15.0   3.0       0.03   14.5   3.0    1.2  1  LIM       LIM domain
      0.033   14.2   4.6       0.19   11.8   5.0    1.8  2  XPA_N     XPA protein N-terminal


Domain annotation for each model (and alignments):
>> LIM  LIM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   3.0   3.4e-06      0.03      29      56 ..      12      40 ..      10      42 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.4e-06
                -TTT-SB-CTT..CEEETTEEEEHHHHHH CS
         LIM 29 CsdCqkeLkegs.fyekdgklyCkkdylk 56
                C++C+ +  + + +y kd+ ++C+k+y +
  EPA06067.1 12 CFECGVKEHDAKlVYTKDKPVLCEKCYKN 40
                77887777777779*************76 PP

>> XPA_N  XPA protein N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   5.0   2.1e-05      0.19       2      28 ..      10      37 ..       9      37 .. 0.91
   2 ?    1.9   0.6     0.026   2.3e+02       4       9 ..      34      39 ..      31      41 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.1e-05
       XPA_N  2 pkCdeCgkefldSyLldnFdysV.CDkC 28
                ++C+eCg +++d +L  + d +V C kC
  EPA06067.1 10 EECFECGVKEHDAKLVYTKDKPVlCEKC 37
                68*************9999999888888 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.026
       XPA_N  4 CdeCgk 9 
                C++C k
  EPA06067.1 34 CEKCYK 39
                999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 306.42
//
Query:       EPA06068.1  [L=52]
Description: hypothetical protein BG20_I0603 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0056   16.7   1.9      0.015   15.3   2.0    1.7  2  zinc_ribbon_6   Zinc-ribbon
  ------ inclusion threshold ------
       0.27   11.2   3.1       0.35   10.8   3.1    1.2  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain


Domain annotation for each model (and alignments):
>> zinc_ribbon_6  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   2.0   1.6e-06     0.015      27      53 ..       8      37 ..       2      39 .. 0.75
   2 ?    1.0   0.2     0.049   4.4e+02      29      36 ..      31      38 ..      28      44 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.6e-06
  zinc_ribbon_6 27 kvkilCnDCekksevkfhvlglk...CkeC 53
                   +   +C DC+k+s+v+f  +  +   CkeC
     EPA06068.1  8 MYPCTCSDCGKESQVPFQPIEGRdvfCKEC 37
                   56679************9875432337666 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.049
  zinc_ribbon_6 29 kilCnDCe 36
                   +++C+ C 
     EPA06068.1 31 DVFCKECL 38
                   68899996 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   3.1     4e-05      0.35      30      55 ..      12      40 ..      10      43 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 4e-05
  OrfB_Zn_ribbon 30 tCseCgsknke...alsgrtfkCpnCgfe 55
                    tCs Cg++++    + +gr + C++C  +
      EPA06068.1 12 TCSDCGKESQVpfqPIEGRDVFCKECLPK 40
                    8*********99*99***********765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      195  (0.0108762); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 368.48
//
Query:       EPA06069.1  [L=216]
Description: hypothetical protein BG20_I0620, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.023   14.6   0.7      0.036   14.0   0.7    1.4  1  Glyco_hydro_44  Glycoside hydrolase family 44


Domain annotation for each model (and alignments):
>> Glyco_hydro_44  Glycoside hydrolase family 44
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.7     2e-06     0.036      18     133 ..      44     181 ..      15     186 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2e-06
                     .EEESHHHHHTT--GGEEEEE--SSEEES--.SE.....E--GG....G-SSSTTEEE................................EES-- CS
  Glyco_hydro_44  18 sssdefletnkkagaksllTvpligyvakdkasg.....sfseskygeqaapdsrwke......................dagngvasdgvkikk 85 
                      +++ +le++++++++++l ++l+gyv +++ +      ++  ++yg+ +++++ ++e                      +     + ++ ++++
      EPA06069.1  44 VKNQIMLENVRNHKTDEILEIQLVGYVIEKNPKLieraiNVLYKSYGNSEEFNNVFSEysienmgptqislnefesdhkiK-----SIKDLQFTD 133
                     45666889999*****************99977789999888899*********999877664444443333222111111.....111122222 PP

                     SS---SS--SSSSEEEHHH.............HHHHHHHHH--TSTTS--EEEESS CS
  Glyco_hydro_44  86 taelsltpdptdtsvyadeeftke........wvnhlvkklgsasatgvkfysLDN 133
                     ++   + p++++       + +ke         v+ l +k+++ s++++k+ ++DN
      EPA06069.1 134 KEISDKMPQIKE-------SNSKElkefsnpdKVKSLYSKIKE-SEKEFKIKKIDN 181
                     222222222222.......111112223333366666666655.445666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1283  (0.07156); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1500.42
//
Query:       EPA06070.1  [L=193]
Description: acetyltransferase, GNAT family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-07   31.7   0.0     0.0011   19.1   0.0    2.2  2  Acetyltransf_9  Acetyltransferase (GNAT) domain
    1.5e-07   31.7   0.0    2.1e-07   31.2   0.0    1.2  1  Acetyltransf_1  Acetyltransferase (GNAT) family
     0.0016   18.9   0.0     0.0051   17.2   0.0    1.8  1  Acetyltransf_7  Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.8e-07    0.0011       2      78 ..      12      91 ..      11     104 .. 0.79
   2 !   10.8   0.0   6.5e-05      0.39      77      96 ..     108     127 ..      98     131 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.8e-07
                    EEEE-GGGHHHHHHHHHHHTT----H..HHHHHHHHHHT......TSEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEE CS
  Acetyltransf_9  2 irelteedldevlellkyaFqdeespleeireyfrklle......esrvlgaedngelvgqlallplelnvpGktlkaagvtg 78
                    ir+lt+ed+++v+el+k+aF +   +     +++ + le      ++  ++ae++g+++g++  l ++l    ++ +  gv+g
      EPA06070.1 12 IRTLTKEDIPKVVELQKAAFPYMAAQG---VYWKPDQLEahlkifPEGQFVAEYHGKIIGSCSSLIVKLESEYAEHTWKGVCG 91
                    8************************98...345555555333344557789***********999999987777777777765 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 6.5e-05
                     EEEEE-CCGTTS-HHHHHHH CS
  Acetyltransf_9  77 tgVavapehrgrgvlskLla 96 
                     ++V+++p++r+ gv++kL +
      EPA06070.1 108 ADVSTHPDNRRLGVATKLYD 127
                     79***************976 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0   3.5e-11   2.1e-07       2      99 ..      21     143 ..      20     152 .. 0.84

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 3.5e-11
                     HHHHHHHHHHTH......HHHHHHHHHHHHHHHHSTTCEEEEEEETTEEEEEEEEEEEET......................TSTTEEEEEEEEE CS
  Acetyltransf_1   2 rdlvellvesff......ppnedaseeefeesfsleaegllvaeedgeliGfisllkipd......................ekggvayieslaV 68 
                     +++vel+++ f+        ++ +++e++ ++    +eg +vae+ g++iG +s l++                        +kg+  y  ++  
      EPA06070.1  21 PKVVELQKAAFPymaaqgVYWKPDQLEAHLKI---FPEGQFVAEYHGKIIGSCSSLIVKLeseyaehtwkgvcgdsflsghnPKGDSLYGADVST 112
                     56788888888877777766777778887777...899***************88888888888877777777777788888999999999**** PP

                     SGGGTTSSHHHHHHHHHHHHHHHTTESEEEE CS
  Acetyltransf_1  69 speyrgkGlGsaLlealeerareegikkivl 99 
                     +p+ r+ G++++L++a    a + ++++i +
      EPA06070.1 113 HPDNRRLGVATKLYDARKTLAIKLNLRRIIA 143
                     ****************999999999988765 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   8.5e-07    0.0051       6      49 ..      58     134 ..      52     168 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 8.5e-07
                     EEEEETTEEEEEEEEEEES............................TCTEE..EEE-GGGTTSSHHHHHHHH.....T CS
  Acetyltransf_7   6 fVaeddgkivGfialslld............................aeitr..laVdpeyrgkGiGraLlea.....a 49 
                     fVae  gki+G ++  +++                             +  +  + ++p+ r+ G++++L +a     +
      EPA06070.1  58 FVAEYHGKIIGSCSSLIVKleseyaehtwkgvcgdsflsghnpkgdsLY--GadVSTHPDNRRLGVATKLYDArktlaI 134
                     7899999999888777777888888777777777777666666654334..15599***************98333320 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.33s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1240.24
//
Query:       EPA06071.1  [L=278]
Description: hypothetical protein BG20_I1814, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-06   27.5   0.1    5.2e-06   26.5   0.1    1.4  1  Phage_integr_3  Archaeal phage integrase


Domain annotation for each model (and alignments):
>> Phage_integr_3  Archaeal phage integrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.1   2.9e-10   5.2e-06       8     152 ..     129     264 ..     122     271 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 2.9e-10
                     HHHHHHHHHHHH-HHHHHHHHHHHHH---HHHHHHHHHS..GGG-EEETTEEEEEEEE-SSS-EEEEEEESS---.....--B--HHHHHHHHHT CS
  Phage_integr_3   8 evrealeelkekseevelvykllvfsGiRLkevlklLreyDpekliveddiarYpialekgeKkafyiylptelakele.rlelseeavkefeak 101
                     ++ ++l+++++ ++ +   ++ ++ sG+R  e+ +++++   +k  ++d+    +i +++++K+a + +    l+ +++  l+ ++++ k+ e +
      EPA06071.1 129 SINHVLDNITKLEPLYSDFALFMLTSGLRTIEARTVFEN---HKKFCHDGTI--EIFWHRKTKNANATFCHPLLHDKMDkDLKFDYDHFKKLECE 218
                     57778888888877788888999**************99...8889988865..79*************99999988874688888887777666 PP

                     -T--GHHHHHHHHHHHHHTT--HHHHHHHTTSS-CCTTSCHHCHHHHHHHH CS
  Phage_integr_3 102 kkvkakyiRkwvatklaelgvpeevidFiqGrkpssvlekhYlnllvlAde 152
                          +++Rk ++t +a+ +++  +++F+qGr+    +++++l ++ +  +
      EPA06071.1 219 ----LRFLRKLNYTIVAT-KIDPLLANFMQGRTGDVSQRHYFLPMMSQHRK 264
                     ....99*******98775.68888********9875555555777766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1850.58
//
Query:       EPA06072.1  [L=196]
Description: hypothetical protein BG20_I1810 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.06   12.9   0.4        1.1    8.8   0.1    2.1  2  DUF1444   Protein of unknown function (DUF1444)
      0.076   12.9   0.5       0.13   12.2   0.5    1.5  1  DUF4488   Domain of unknown function (DUF4488)
       0.13   12.7   0.0       0.24   11.8   0.0    1.4  1  ZapA      Cell division protein ZapA


Domain annotation for each model (and alignments):
>> DUF1444  Protein of unknown function (DUF1444)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.017     1e+02     216     254 ..       8      46 ..       6      57 .. 0.88
   2 ?    8.8   0.1   0.00018       1.1     167     225 ..      70     124 ..      54     130 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.017
     DUF1444 216 irnetGyDvlaqlaleffaeGrvPitaLsflyedgkLeP 254
                 i+n+   ++l+   l f +   v it+ sf++++ +++P
  EPA06072.1   8 IKNNIVKNILKGYGLLFLGLIVVGITSASFTHDEVNIKP 46 
                 7888888999999999999999************99998 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00018
     DUF1444 167 gnkfyflntnDgydasriLnesllkelkekveGelavavPhqDvliiaDirnetGyDvl 225
                 gn +y  + ++ y       e+ll+++    +G+  v++  qD ++ia ++n+ G+Dv+
  EPA06072.1  70 GNGWYQTDEQEVYYD---HAEKLLEKYVLTYKGKDHVGLDMQDAMLIA-LTNKCGFDVM 124
                 566666655555432...2478899999999****************9.89*******8 PP

>> DUF4488  Domain of unknown function (DUF4488)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.5   2.1e-05      0.13      52     116 ..      69     137 ..      37     144 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.1e-05
     DUF4488  52 igyGeYelksdsvyvEsveksvhlpqle.gkknelkfelkddnllvlkyklkkd...dkwvtEyWkrve 116
                 +g+G Y+ ++++vy ++ ek +++  l+ + k ++  +++d  l+ l+ k   d   dk  tE+W  v 
  EPA06072.1  69 MGNGWYQTDEQEVYYDHAEKLLEKYVLTyKGKDHVGLDMQDAMLIALTNKCGFDvmlDKSNTETWVSVS 137
                 58999*****************77666515578999****999******99999999********9886 PP

>> ZapA  Cell division protein ZapA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   4.1e-05      0.24      16      53 ..      77     115 ..      74     132 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.1e-05
        ZapA  16 egeeeylreaaklvdekikeireaggn.lseerllvmaa 53 
                 +++e y+ +a+kl+++++  ++++ ++ l+ ++++++a 
  EPA06072.1  77 DEQEVYYDHAEKLLEKYVLTYKGKDHVgLDMQDAMLIAL 115
                 569***********************5599988887764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       762  (0.042501); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1323.37
//
Query:       EPA06073.1  [L=553]
Description: hypothetical protein BG20_I1812 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
        6.5    6.9   9.3         16    5.6   4.1    2.6  2  BSMAP       Brain specific membrane anchored protein


Domain annotation for each model (and alignments):
>> BSMAP  Brain specific membrane anchored protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   4.1    0.0009        16      99     157 ..     100     159 ..      87     189 .. 0.54
   2 ?    3.1   0.2    0.0054        97      76     155 ..     195     265 ..     187     291 .. 0.62

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0009
       BSMAP  99 lqaDdgkvvvfqsepeielflsea.....edtklgpkdkkakvkkkkeeekeklksskaeeeqp 157
                 +  D+gkv++ ++e e+ ++l+++     e  k  +k+ k++++k+++eek++  ++k+++++ 
  EPA06073.1 100 FKYDNGKVMI-EEEKEVFVPLDSKlklfeE--K-LEKELKEETEKESKEEKTENATDKQKDKDR 159
                 56799*9876.6666688887777554321..2.333333333333333333333222222211 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.0054
       BSMAP  76 vsslfedivssaqsfisstwtfylqaDdg.kvvvfqsepeielflseaedtklgpkdkkakvkkkkeeekeklksskaeee 155
                 +  +f+ i+s+  ++i++  t++    +  +  +f+ +p+i+++ ++ e ++ ++++ + + ++ +           ++++
  EPA06073.1 195 LWDFFKPILSQDTKLIRHNTTNKQSGSNRlQKTIFKGKPSISYASAKDEAKTDITNEIDSRFQTIS----------LRSNP 265
                 56799999********99999995544433779*********995444333322222222222222..........22222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (553 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2353  (0.13124); expected 358.6 (0.02)
Passed bias filter:                      622  (0.0346924); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.76u 0.32s 00:00:01.08 Elapsed: 00:00:00.49
# Mc/sec: 3360.16
//
Query:       EPA06074.1  [L=774]
Description: hypothetical protein BG20_I1813 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0011   18.5   4.2     0.0033   16.9   4.2    1.9  1  Rax2      Cortical protein marker for cell polarity
  ------ inclusion threshold ------
      0.085   12.8   0.1       0.18   11.8   0.1    1.5  1  MuF_C     Phage MuF-C-terminal domain
       0.18   11.7   1.4       0.25   11.2   0.4    1.8  2  DUF919    Nucleopolyhedrovirus protein of unknown function (D
        2.8    8.0   6.5         15    5.7   0.7    2.7  2  MotCF     Bacteriophage T4 MotA, C-terminal


Domain annotation for each model (and alignments):
>> Rax2  Cortical protein marker for cell polarity
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   4.2   7.4e-07    0.0033      15     109 ..     440     541 ..     427     593 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 7.4e-07
        Rax2  15 sganelpgpvtsftladsdisqlwvagkssngssfllkydgskWssiddinlgesttirglqvlslt...nshsssdlldknqvLlvtGql....nlpd 106
                  ++n+++ + +s ++ ++       +g +s+++s ++ ++gskW+ ++++ + +s ti++ ++l+++   + ++s+ ++ +n +L v G++     +++
  EPA06074.1 440 MHTNKVQFNTQSNIVSNETLGPHSGEGVISDEKSCITMIEGSKWNPTSNTCVVSSFTIHSGKILTISsdvTLSNSKGIITNNGILTVLGNIinfgAIEN 538
                 344677788888888888888888899999********************9****************88655666778***********9833333455 PP

        Rax2 107 fGn 109
                 fG+
  EPA06074.1 539 FGT 541
                 555 PP

>> MuF_C  Phage MuF-C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1     4e-05      0.18      23      93 ..     117     198 ..      94     208 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4e-05
       MuF_C  23 aLadPiavfkskteenslvvltelk......dkdgkpvivalhlngkekgraevneiaSaYgrdn....delkrwied.gkl 93 
                   +dP ++f+s++  n +  +te +      +++  + i++++ ++   +++ +++i++ +++++    +el +w ++ +++
  EPA06074.1 117 GFNDPKIIFQSENTINGIPGITEAQllrtytNGEMTQRILVVETEQPTGEQQFFKNIVNSFRKEQnnpnNELVSWNSNdKNC 198
                 569**********99999999999999999899999999999999776666668**********546778888888774444 PP

>> DUF919  Nucleopolyhedrovirus protein of unknown function (DUF919)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.4   5.7e-05      0.25      33      58 ..     411     436 ..     408     440 .. 0.91
   2 ?   -3.2   0.0       1.7   7.8e+03      38      53 ..     660     675 ..     658     677 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.7e-05
      DUF919  33 itKnpkElqdlekklnklRqeFLnfg 58 
                 itKn++  ++++ +l+k+R+++++ +
  EPA06074.1 411 ITKNTNNQEKMQIELQKCRMQYIEMA 436
                 9*********************9876 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.7
      DUF919  38 kElqdlekklnklRqe 53 
                 +El+ + ++l +lR +
  EPA06074.1 660 SELAPQVQQLRELRDN 675
                 6888889999999976 PP

>> MotCF  Bacteriophage T4 MotA, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.7    0.0034        15      20      85 ..     489     554 ..     485     565 .. 0.86
   2 ?    4.4   0.8    0.0086        39      52      84 ..     573     605 ..     557     616 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0034
                 T--EEEEEEETTEEEEEEEEEETTEEEEEEETTSEEEEEEES--HHHHHHHHCTT-EEEE-TTSEE CS
       MotCF  20 gfvlkkveiyrsnylailekrtngirnfeinnngnmrifgykmmehhiqkftdigmsckiakngnv 85 
                   v+    i+  + l+i    t    +  i nng + ++g  +    i++f  i +s k+ ++gn+
  EPA06074.1 489 TCVVSSFTIHSGKILTISSDVTLSNSKGIITNNGILTVLGNIINFGAIENFGTIHVSGKLGNQGNL 554
                 566667777777888888888888888889*************99*******************97 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0086
                 TSEEEEEEES--HHHHHHHHCTT-EEEE-TTSE CS
       MotCF  52 ngnmrifgykmmehhiqkftdigmsckiakngn 84 
                   n+  fg  + eh+i +f +i   c+ +  gn
  EPA06074.1 573 TSNVNNFGTILNEHRIINFGQINNHCNASISGN 605
                 478899********************9999888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (774 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       915  (0.0510346); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.43
# Mc/sec: 5455.22
//
Query:       EPA06075.1  [L=111]
Description: hypothetical protein BG20_I1811 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 756.05
//
Query:       EPA06076.1  [L=55]
Description: hypothetical protein BG20_I1809, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 405.19
//
Query:       EPA06077.1  [L=82]
Description: hypothetical protein BG20_I1985, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.081   12.8  11.8      0.089   12.6  11.8    1.1  1  TrbI        Bacterial conjugation TrbI-like protein
       0.63   11.1   7.3       0.77   10.9   7.3    1.1  1  SOXp        SOX transcription factor


Domain annotation for each model (and alignments):
>> TrbI  Bacterial conjugation TrbI-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6  11.8   9.9e-06     0.089     113     164 ..      23      81 ..       7      82 .] 0.65

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.9e-06
                 EEEES---EEEE------------.......HHHHHHHHT-TT-BHHHHHHHHHHHHTT CS
        TrbI 113 sllsgagellnaassssttsstgt.......qslaaavgegasqalsqvaqrilkraen 164
                 ++ + +++ +++ +s+ +++++++       +++++a+ ++a+qa++q+aq++ ++a +
  EPA06077.1  23 TVTTNVSNGQSNGQSNGQSNGQSNgqsdgqsNDIQQAAQQAAQQAAQQAAQQAAQQAAQ 81 
                 44445555454555554444444467778887888888888888888888888777765 PP

>> SOXp  SOX transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   7.3   8.6e-05      0.77      16      85 ..      13      78 ..      11      82 .] 0.60

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 8.6e-05
        SOXp 16 ysLpggllaaggggvqssvgvglsgvgqrldgyahmNGyangaYssmmqdaqlaysqhpglsaaaaaaaq 85
                y+Lpgg+ a++   v+++v++g s++    ++  + NG ++g  + + q aq a++q +   a ++aa+q
  EPA06077.1 13 YALPGGIPATT---VTTNVSNGQSNGQSNGQSNGQSNGQSDGQSNDIQQAAQQAAQQAAQQAA-QQAAQQ 78
                99****98774...4557888876444444566788888877776766666655554444444.333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2834  (0.158068); expected 358.6 (0.02)
Passed bias filter:                      734  (0.0409393); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 652.38
//
Query:       EPA06078.1  [L=405]
Description: response regulator receiver domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.5e-25   87.7   1.8    1.9e-24   86.0   1.8    2.0  1  Response_reg    Response regulator receiver domain
    5.1e-14   51.9   0.1    1.6e-13   50.3   0.0    1.9  2  TrmB            Sugar-specific transcriptional regulator TrmB
    1.5e-05   24.3   1.4      2e-05   23.9   0.6    1.6  2  Regulator_TrmB  Archaeal transcriptional regulator TrmB
  ------ inclusion threshold ------
        0.3   10.9   6.9        2.3    8.0   0.4    3.2  4  DisA-linker     DisA bacterial checkpoint controller linker r


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.0   1.8   4.2e-28   1.9e-24       1     109 [.     294     402 ..     294     405 .] 0.98

  Alignments for each domain:
  == domain 1  score: 86.0 bits;  conditional E-value: 4.2e-28
                   EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEESSTSHHHHHHHHHCTESEE CS
  Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviiltahseeedavealkagaddf 97 
                   +l+vdDdp+++++++++le +g+++v+ ++d+k+a+e++k+ ++  ++lDi+mp+mdG++ll+eir+ +p++++i++ta  +  ++++  ++   d+
    EPA06078.1 294 ILVVDDDPDAVNIFSEYLEIKGITTVERCTDSKKAMEIFKKIRPETVFLDIMMPEMDGFHLLEEIRKIEPKTKIIMVTADMSAVTKKKLQEVKPTDV 390
                   8************************************************************************************************ PP

                   EESSG-HHHHHH CS
  Response_reg  98 lsKpfdpeeLlk 109
                   + Kp+d+++++ 
    EPA06078.1 391 IYKPYDIKQIMR 402
                   ********9986 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.3   0.0   3.5e-17   1.6e-13       1      68 []      25      92 ..      25      92 .. 0.98
   2 ?   -3.3   0.0         2     9e+03       1      12 [.     120     131 ..     114     132 .. 0.69

  Alignments for each domain:
  == domain 1  score: 50.3 bits;  conditional E-value: 3.5e-17
                HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE--HH CS
        TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravdpe 68
                L+++GL e Ea++Y+ L +lg+a+a+ei+  ++++r + Y++L++L++ G+ +   ++p +++a dpe
  EPA06078.1 25 LRDFGLEEDEAQTYVGLARLGSAKASEISTFTKIERVRTYKILENLKNLGFATSTLSSPIKFSANDPE 92
                789*************************************************************9997 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2
                 HHHCHHHHHCCC CS
        TrmB   1 LqklGLseyEak 12 
                 L+kl L+e E++
  EPA06078.1 120 LSKLKLNESEIE 131
                 566667777765 PP

>> Regulator_TrmB  Archaeal transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.6   4.5e-09     2e-05       2     140 ..     135     282 ..     134     318 .. 0.83
   2 ?   -2.6   0.0      0.57   2.5e+03      66      91 ..     350     376 ..     345     390 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 4.5e-09
                     EEEESSHHHHHHHHHHHHHH-SSEEEEEE-GGGHHH.....HHHHHHHHHHTT-EEEEEESS..----GGGSSSSEEEEEE-S---S.EEEEETT CS
  Regulator_TrmB   2 vwvvksretvierieelIesAenelivslpselLee.....lreeliaaaergvtVllliyp..dedleeldleevatevrvrrsgapllvivDr 89 
                     + +v +r+++ ++i ++I++++ e+ + l ++ L +     +re +++a +r+v + l+  +  ++++e  + +++ +  ++  ++++  +i ++
      EPA06078.1 135 LTIVSNRDNIYDQIIKIIDETNDEIHIVLAPSDLIRmyytpMREIIKNALQRKVIIKLMTDDelASKREYIQRLGI-SYFKITTLPTSGRLICNK 228
                     6799*********************99988877744222336899999****999999999965444444455544.8888888888888***** PP

                     TEEEEE-SSS-..EEEE--HHHHHHHHHHHHHH........HHH-EEEEE.EES CS
  Regulator_TrmB  90 krgvvaprevl..rdkeeeyaiifkekelihvlshyFlttlWktsevikt.dep 140
                     ++++++ ++++  +++++e ++++++++ i   +++  + lW+t++ i+   ++
      EPA06078.1 229 SQVLMSGNTSSysDKNRNEESVMVTNSKDIVRNMQSLCKFLWETGKGIHIeNKQ 282
                     ********99999999**********99999999************99964222 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.57
                     SSSSEEEEEE-S---S..EEEEETTTE CS
  Regulator_TrmB  66 dleevatevrvrrsga.pllvivDrkr 91 
                     d      e+r+++ ++  ++v++D + 
      EPA06078.1 350 DGFHLLEEIRKIEPKTkIIMVTADMSA 376
                     556667789999999978888888764 PP

>> DisA-linker  DisA bacterial checkpoint controller linker region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.2    0.0039        17      82     136 ..      11      65 ..       3      70 .. 0.87
   2 ?    8.0   0.4   0.00051       2.3       5      38 ..      96     129 ..      94     159 .. 0.87
   3 ?   -2.1   0.0      0.64   2.9e+03     118     135 ..     193     210 ..     166     239 .. 0.63
   4 ?   -3.0   0.0       1.3   5.7e+03      35      61 ..     311     337 ..     307     339 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0039
                  HHHHTTHHHHHHHHHHHHSSS--HHHHHHHHHHH...HTTS---HHHHHHHTT-- CS
  DisA-linker  82 eeLlanveeeeellikDYlkeekeeeaeeileelkelsseelldlskiaklLGye 136
                  +e ++n e +e  +++D+  ee e+++   l++l + +++e+ + +ki ++  y+
   EPA06078.1  11 DEDYQNNELDEISILRDFGLEEDEAQTYVGLARLGSAKASEISTFTKIERVRTYK 65 
                  6667899999**********999999999*******************9987776 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00051
                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
  DisA-linker   5 evilakanqalqTLekYrsvldevlsnLsalEfe 38 
                  + i++k  q ++ Lek  s++ + ls+L+  E e
   EPA06078.1  96 KNIITKQKQKIENLEKNSSKFLKILSKLKLNESE 129
                  679***********************99888755 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.64
                  .HTTS---HHHHHHHTT- CS
  DisA-linker 118 lsseelldlskiaklLGy 135
                  ++++el ++++ ++ LG 
   EPA06078.1 193 MTDDELASKREYIQRLGI 210
                  455555555555555554 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 1.3
                  HHHTT-EBHHHHHHHHHHHHHHHHHHH CS
  DisA-linker  35 lEfedlVtlsdVaeviqrlemvlrike 61 
                  lE++ + t++  ++  + +e+ ++i  
   EPA06078.1 311 LEIKGITTVERCTDSKKAMEIFKKIRP 337
                  789999999988888888888888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1482  (0.0826594); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2548.05
//
Query:       EPA06079.1  [L=501]
Description: ATPase/histidine kinase/DNA gyrase B/HSP90 domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-19   70.2   0.0    4.3e-19   69.1   0.0    1.6  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    4.5e-10   39.3   0.1      1e-08   35.0   0.0    2.8  2  HATPase_c_5  GHKL domain
    3.4e-09   36.6   0.2    1.3e-08   34.7   0.2    2.1  1  HisKA        His Kinase A (phospho-acceptor) domain
    5.6e-09   36.2   0.0    1.6e-08   34.7   0.0    1.9  1  HAMP         HAMP domain
    5.4e-05   22.8   8.7    5.4e-05   22.8   8.7    3.4  2  4HB_MCP_1    Four helix bundle sensory module for signal tran
  ------ inclusion threshold ------
       0.15   12.3   0.2       0.15   12.3   0.2    2.4  2  Sigma_reg_N  Sigma factor regulator N-terminal


Domain annotation for each model (and alignments):
>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.1   0.0   1.4e-22   4.3e-19       2     110 ..     376     476 ..     375     478 .. 0.92

  Alignments for each domain:
  == domain 1  score: 69.1 bits;  conditional E-value: 1.4e-22
                 HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHHHHHHHHHTTTEEEEEEETTT CS
   HATPase_c   2 dekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsivkklvelmgGeiwvesepgr 100
                 d+ rL  +++nl+dNa  +  k+g i ++i   ++d+ i++eD+G+Gip ++ +k+f+++ +     +++ gtGlGls ++++++ ++G+i+++++p  
  EPA06079.1 376 DSCRLDVVFKNLIDNACYAVDKNGVIIIRIIDAQNDVLIEIEDSGPGIPDSISEKIFDPLFT-----TKQVGTGLGLSSCRSIIDAHDGKISIKNNP-- 467
                 5668999***********977**********7669***********************6666.....699***********************9999.. PP

                 EEEEEEEEES CS
   HATPase_c 101 Gttftftlpl 110
                  ttft++lp+
  EPA06079.1 468 -TTFTIRLPK 476
                 .******997 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1      0.12   3.5e+02      27      51 ..     126     150 ..      95     175 .. 0.78
   2 !   35.0   0.0   3.4e-12     1e-08       6      97 ..     380     473 ..     375     475 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.12
  HATPase_c_5  27 ekrfIrltvrekkksliisieNsye 51 
                  ++++I+l+ +  ++ +i++++N ++
   EPA06079.1 126 SNKMIQLKTSGASGIVILNLNNDFD 150
                  4889999999999999999999876 PP

  == domain 2  score: 35.0 bits;  conditional E-value: 3.4e-12
  HATPase_c_5   6 lcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg.....ekkkle..sskskkeehGiGlksireivkkykgnlsieaedglFtl 96 
                  l v++ nl+dNA  a++k      +I + +   +++++i+ie s  g     + +k++    ++k+   G+Gl+s r+i++ ++g++si+++ ++Ft 
   EPA06079.1 380 LDVVFKNLIDNACYAVDKN----GVIIIRIIDAQNDVLIEIEDSGPGipdsiS-EKIFdpLFTTKQVGTGLGLSSCRSIIDAHDGKISIKNNPTTFTI 472
                  6799********9999885....59*******************777554431.33333344667799****************************97 PP

  HATPase_c_5  97 s 97 
                   
   EPA06079.1 473 R 473
                  5 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.2   4.5e-12   1.3e-08       3      61 ..     272     332 ..     270     337 .. 0.88

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 4.5e-12
                 HHHHHHHHHHHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHH CS
       HisKA   3 grflagvaHELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedlLdl 61 
                 g ++  +aH++r+PLs+i+   e+++ +  ++   +l  ++++i++++ r++h+++d+L +
  EPA06079.1 272 GSLATRLAHDIRNPLSVIQNGFEIIRIKsqNNSGSNLDSNFDSIRRSILRITHQIDDVLNF 332
                 678889*******************66666666789999*******************987 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.0   5.5e-12   1.6e-08       2      52 ..     207     256 ..     206     257 .. 0.94

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 5.5e-12
                 HHHTTHHHHHHHHHHHHHHTTTBTSSTCCTTSSSHHHHHHHHHHHHHHHHH CS
        HAMP   2 larrilrPLrrLaraarriaaGdldtrlpvsgrDEiGeLarafNaMldrLr 52 
                 + ++i++PL++++++++ ia+G++    p++g+DEi eL++++N M+++L+
  EPA06079.1 207 ILKSISKPLQKIKSVTQDIAKGNFML-YPEKGNDEISELGKNINIMSTNLK 256
                 6789******************9999.999*******************97 PP

>> 4HB_MCP_1  Four helix bundle sensory module for signal transduction
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   8.7   1.8e-08   5.4e-05      16     166 ..       2     167 ..       1     173 [. 0.84
   2 ?   -1.0   0.5      0.36   1.1e+03      75     106 ..     235     266 ..     213     279 .. 0.71

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.8e-08
   4HB_MCP_1  16 allliivGvvGlyslkkinknletmYedrllpikdlgeikanlrelradlleliltkdkae.............kdellkdieeleaeidkllekyekt 101
                  +l++i++ + ++++k +++ ++++ ++ l  +++l++++   ++l +++ e+il +d+ +              ++   +ie+ +  +++  ++y ++
  EPA06079.1   2 FILIGIISTIAIINTKYVQETFSSINSETLPILNTLKNMRYASTQLSSLTNEIILIEDETRnasekefpeleeiLETNFYKIEKAKLLFNESFSEYSSI 100
                 799*****************************************************9999866666666643332222224666666788888888887 PP

   4HB_MCP_1 102 iltee..EkelleefkeqlnaYrevrkkvlelakegkkdeAyqlyetegrparekliealeelvdln 166
                  ++    + +++e++ +++n+   +++k+++l ++g     +  ++++ + a+++++ a+++ ++l 
  EPA06079.1 101 VTNNYpnDIDHIETVAKKWNEMLFISNKMIQLKTSGASGIVILNLNNDFDFAFDEMNLAIDKAIELT 167
                 76665325679**********************************************9999999876 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.36
   4HB_MCP_1  75 aekdellkdieeleaeidkllekyektiltee 106
                 ++ ++ ++++ ++ + + ++l++ +k +l++e
  EPA06079.1 235 EKGNDEISELGKNINIMSTNLKELNKKMLEKE 266
                 55556666677777777777777777766665 PP

>> Sigma_reg_N  Sigma factor regulator N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.4      0.69   2.1e+03      21      38 ..       3      24 ..       1      42 [. 0.54
   2 ?   12.3   0.2   5.2e-05      0.15      11      51 ..     180     224 ..     178     249 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.69
  Sigma_reg_N 21 ivlllifvilvvtllyl....a 38
                 i++ +i+ i +++++y+    +
   EPA06079.1  3 ILIGIISTIAIINTKYVqetfS 24
                 3333444444666666644331 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 5.2e-05
  Sigma_reg_N  11 silrivlislivlllifvilvvtllyl....aekegnklrevlel 51 
                  s+lr+v+ s+i++l +fv + ++++y+    ++k  +k+ +v+++
   EPA06079.1 180 SLLRNVTWSIILALNLFVATTLIIRYYilksISKPLQKIKSVTQD 224
                  78******************9999999655555555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (501 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1108  (0.0617993); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 3292.28
//
Query:       EPA06080.1  [L=373]
Description: hypothetical protein BG20_I1982 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1049  (0.0585086); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2568.64
//
Query:       EPA06081.1  [L=38]
Description: hypothetical protein BG20_I2505 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (38 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      155  (0.00864521); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.50
# Mc/sec: 229.53
//
Query:       EPA06082.1  [L=41]
Description: hypothetical protein BG20_I2506 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 284.42
//
Query:       EPA06083.1  [L=273]
Description: ATP phosphoribosyltransferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-44  150.6   0.0    4.3e-44  150.3   0.0    1.1  1  HisG      ATP phosphoribosyltransferase


Domain annotation for each model (and alignments):
>> HisG  ATP phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.3   0.0   2.4e-48   4.3e-44       1     159 [.      50     236 ..      50     237 .. 0.87

  Alignments for each domain:
  == domain 1  score: 150.3 bits;  conditional E-value: 2.4e-48
                 -GGGHHHHHHTTSSSEEEEEHHHHHHCT...TEEEEEEESESEEEEEEEEETTSS--SGCGG......TT.-.EEEEES-HHHHHHHHHHT........ CS
        HisG   1 raadiptyVeegavdlGitGkDvveEskeeeeveelldLgfgkcklvvavpeesevkslkdl.....ved.kgkriaTsypnlakkyfeek........ 85 
                 r+++ipt+V eg +d+GitGkD+v E++  ++ve +ldL++gk +lvva pe++++k+l+++     + + k +ri ++y  +a+k++++         
  EPA06083.1  50 RPQEIPTLVSEGLYDVGITGKDWVGETN--ADVEPILDLEYGKIRLVVAFPEKYHYKNLDEMiadyaK-KkKILRISSEYLITASKFLKQSksykkhyg 145
                 89************************74..47****************************99655532.256688*************99977777777 PP

                 ...............T-EEEEEE-SS-CTHHHHTTS-SEEEEEESSSHHHHHTTEEEEEEEEEEEEEEEEEHHHHHS...HHHHHHHHHHHH CS
        HisG  86 ...............glkveiiklsGsvEaapalglaDaIvDlvetGeTLrangLkaietilessavLiankkslkk...kekieellerlr 159
                                + +v+i+ + G++Ea+p+ + +DaI+D++etG+TL++n+Lk+++++++s+a+Li+nkksl++   +eki ++++ +r
  EPA06083.1 146 tkdplivtpwvrlgtNKNVQIHLSFGATEAKPPED-VDAIMDVTETGTTLKQNKLKIVDEVITSTAHLIVNKKSLRDpqkREKIFDIVTLMR 236
                 777777777766666559****************7.9**************************************97444448888877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1755.09
//
Query:       EPA06084.1  [L=295]
Description: histidinol dehydrogenase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   3.3e-113  378.8   0.1   3.7e-113  378.6   0.0    1.0  1  Histidinol_dh  Histidinol dehydrogenase
  ------ inclusion threshold ------
      0.023   14.8   0.0      0.038   14.1   0.0    1.4  1  ssDNA_DBD      Non-canonical single-stranded DNA-binding doma
       0.15   12.5   0.2       0.15   12.5   0.2    2.0  2  CelTOS         Cell-traversal protein for ookinetes and sporo


Domain annotation for each model (and alignments):
>> Histidinol_dh  Histidinol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  378.6   0.0  6.2e-117  3.7e-113     117     409 .]       2     295 .]       1     295 [] 0.99

  Alignments for each domain:
  == domain 1  score: 378.6 bits;  conditional E-value: 6.2e-117
                    T--CHHHHHHHHHHHHHT-SEEEEEE-SS.GG.--HHHHHHHHHCT-SEEEE--HHHHHHHHHH--SSS---SEEE---SHHHHHHHHHHCTTBEE CS
  Histidinol_dh 117 aaypStvlmnavpAkvAgvkeivvvtPpq.dgkvnpavlaaaklagvdeiykvGGaqAiaalAyGtesipkvdkivGPGniyVaaAKrlvsgevgi 211
                    a ypS+v+m+++pAk+Agvk+ivvv+Pp+ dgk++p +++aa+l+g++eiy+vGGaqAiaal++Gt sipkvdkivGPG  +V+ AK +++++++i
     EPA06084.1   2 ARYPSSVIMSVIPAKIAGVKRIVVVSPPNsDGKIDPLTIVAANLCGASEIYRVGGAQAIAALSFGTISIPKVDKIVGPGGPFVTLAKSMINDKTSI 97 
                    78********************************************************************************************** PP

                    S----S-EEEEEE-TTS-HHHHHHHHHHHHTT-TT-EEEEEES-HHHHHHHHHHHHHHHCC-TTHHHHHHHHCCH-EEEE-SSHHHHHHHHHHH-- CS
  Histidinol_dh 212 DmiaGPsEvlviaDetadpefvAaDLlsqaEHdedaqavlvttseelaeaveeevekqleelprkeiaekslekqsaiilvedleeaielaneyAp 307
                    Dm+aGP+E+ +iaD+ta+p++vA+DL+sq+EH +d+ ++l+t+se+la+ v++ v++ + +++r++++++sl +++ + ++++ +++i+lane+Ap
     EPA06084.1  98 DMLAGPTELGIIADSTANPQYVALDLISQSEHSNDTFCYLITNSEKLAKTVDKIVDDLVGKVKRNNFVKTSLIENGFLAICKNNSDIIKLANELAP 193
                    ************************************************************************************************ PP

                    SEEEEESTTHHHHGGG--S-SEEEESTT--HHHHHHTSSS------TTGGGT---S-GGGGEEEEEEEEE-HHHHHHHHHHHHHHHHHTT-HHHHH CS
  Histidinol_dh 308 EHlelqvedpeellekiknaGaiflGeyspeslgDYaaGtnhvLPTsgtArfssglsvedFlkkisvqelskealkelaeavetlAeaEgLeaHae 403
                    EHl++++++p+++++ki++ G i+lG+++p s+ DY+ G+nh+LPT+g+ ++ ++lsv dF+k  + ++ sk++l++++++++ ++e EgL++H e
     EPA06084.1 194 EHLQIMTKNPSAFASKITSSGLILLGDNTPSSASDYLLGSNHILPTNGFGKVRGSLSVLDFMKINTQITASKKSLSKISKSMQIFTESEGLPNHYE 289
                    ************************************************************************************************ PP

                    HHHHHH CS
  Histidinol_dh 404 avkvRl 409
                    av+ R+
     EPA06084.1 290 AVRGRM 295
                    **9985 PP

>> ssDNA_DBD  Non-canonical single-stranded DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   6.4e-06     0.038       4      75 ..     143     215 ..     140     237 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.4e-06
                 HHHHHHHHHHHHHHHHHT-GGGGGSTHHHHHHHHHHHHH.H-HHHHHHHGGGCHHHHH-------HHCCCHHH CS
   ssDNA_DBD   4 tllekaqqfveelaselqlpelsqtkLaeNLlLLllKyn.ESpkLseqfqleYqelleerkqeyallqekkee 75 
                 +l++ ++++v  l+ ++++++  +t+L+eN +L + K n +  kL++++  e+ ++++++   +a  + ++  
  EPA06084.1 143 KLAKTVDKIVDDLVGKVKRNNFVKTSLIENGFLAICKNNsDIIKLANELAPEHLQIMTKNPSAFASKITSSGL 215
                 79999********************************87245789*******999999988888875555444 PP

>> CelTOS  Cell-traversal protein for ookinetes and sporozoites
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.4      0.76   4.5e+03      71     100 ..       7      34 ..       6      41 .. 0.81
   2 ?   12.5   0.2   2.5e-05      0.15      10      60 ..     131     175 ..     123     196 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.76
      CelTOS  71 kvllevlksllpvvekivadavkPPvvdra 100
                 +v+++v+ + +  v +iv+  v PP+ d++
  EPA06084.1   7 SVIMSVIPAKIAGVKRIVV--VSPPNSDGK 34 
                 5788999999999999997..789988876 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 2.5e-05
      CelTOS  10 qkslssklseiiradldskgdelvdliandlekelqknslvaasfLqsgfd 60 
                 + ++   +++  +++l++     vd i++dl+ ++++n++v++s++++gf 
  EPA06084.1 131 NDTFCYLITN--SEKLAKT----VDKIVDDLVGKVKRNNFVKTSLIENGFL 175
                 4455555555..5555555....55666799999999999******99983 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1930.21
//
Query:       EPA06085.1  [L=267]
Description: hypothetical protein BG20_I1954, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.1e-05   24.0   0.0       0.33   11.2   0.0    2.1  2  Hydrolase  haloacid dehalogenase-like hydrolase
    0.00075   19.6   3.6       0.16   12.1   3.6    2.5  1  HAD_2      Haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   3.9e-05      0.35       2      53 ..      24      76 ..      23     150 .. 0.63
   2 !   11.2   0.0   3.6e-05      0.33     125     199 ..     190     266 ..     178     267 .] 0.76

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.9e-05
                SEEEEESBTTTBCHHHHHHHHHHHH.CHHHHHHHHHH..HHCHHHHHHHHHHHHH CS
                xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx..xxxxxxxxxxxxxxxx RF
   Hydrolase  2 ktvvfDkdGTLttgepsvedvivsa.alalaaaletg..sehpigkalvaaakar 53
                + ++fD+dG+L++ ++s   +i++  +   a        ++  i  +++  +k  
  EPA06085.1 24 DGIIFDCDGVLIDVTKSYDLAIQKTtQYIVANMA--NisNPITINSKIIDGFKST 76
                569*********9998888888888211111122..1235555555555555544 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 3.6e-05
                 HHHHHHHHT.TEEEEEEESSEHHHHH.HHHHHTT.GGGE.SEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESS CS
                 xxxxxxxxx.xxxxxxxxxxxxxxxx.xxxxxxx.xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
   Hydrolase 125 eavasLkaa.gievvlltgdnpetae.raanqlG.ddyf.daviasdietvakpspegkvaaireLqgkpeevamVGDg 199
                 +++++L ++   ++ +++g  +e ++ ++ + l+ +d   +a ++ +  + akp+pe + + i+ +      ++ VGD+
  EPA06085.1 190 KLIEKLAKKiTSKISIVSGRGKESVKySLKSLLDkFDLKnSAFLEDESRELAKPNPESLIRSIKGMVCTN--CVYVGDS 266
                 566777766455899***********666666886555534444444445****************6555..******8 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   3.6   1.8e-05      0.16       1     161 [.      26     266 ..      26     267 .] 0.59

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.8e-05
       HAD_2   1 iiFDlDgTlldteeliiqafnelleey........................................................................ 27 
                 iiFD Dg+l+d ++ +  a++++ +                                                                          
  EPA06085.1  26 IIFDCDGVLIDVTKSYDLAIQKTTQYIvanmanisnpitinskiidgfkstggfndevdltyaailsivaaeklridqqkfifdviantdssgilsveh 124
                 577777777776654433333333222333377777777777777777777777777777777777777777777777777777777666666666666 PP

       HAD_2  28 .........glselseeelrkliglslrellrklgeseeeeekieellrkyneekkkkevkpydgvkelLeeL.keagyklgivTsksreaveekleql 116
                          ++ + ++++  ++ + +l +++++++   e   k+ +  +++ e+    +  ++   ++l+e+L k+   k+ iv+ + +e+v+ +l+ l
  EPA06085.1 125 yiekladvnDI-KNKLSYPGTHHNNPLYQIFDQIFYGPELYLKFFKKPSQFSESGLI-NNDVVIVTNKLIEKLaKKITSKISIVSGRGKESVKYSLKSL 221
                 55544432111.333334444444444444444444433332333333444444444.444455567889999666788*****************998 PP

       HAD_2 117 giesyFdvivtsedvekk..KPdpeviekaleklklkkeeviyvGDs 161
                   +  ++     ed +++  KP+pe++ + ++ + ++  +++yvGDs
  EPA06085.1 222 LDKFDLKNSAFLEDESRElaKPNPESLIRSIKGMVCT--NCVYVGDS 266
                 64444444444555555455*********99988886..79*****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       869  (0.048469); expected 358.6 (0.02)
Passed bias filter:                      604  (0.0336884); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 1587.51
//
Query:       EPA06086.1  [L=100]
Description: hypothetical protein BG20_I1951 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      5e-10   38.9   0.9    5.7e-10   38.8   0.9    1.1  1  Histidinol_dh  Histidinol dehydrogenase


Domain annotation for each model (and alignments):
>> Histidinol_dh  Histidinol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.9   3.2e-14   5.7e-10      10      83 ..      23      95 ..      17     100 .] 0.88

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 3.2e-14
                   HHHHHHHHHHHHHHHHCHHHHHHHHHHCCSSSSGGCCEE-HHHHHHHHHCS-HHHHHHHHHHHHHHHHHHHCC- CS
  Histidinol_dh 10 eveetvkeiledvreeGdealleytekFDkvkkleslrvseeeieealekldeelkealeeaaenirkfheaqk 83
                   + +  v++il+dv+++Gd a+++++ekF +  k +slr+s++ei++a++k++++  +a++ ++++++k  ++ k
     EPA06086.1 23 KNKLVVDSILKDVQKNGDFAIKKFEEKFSGS-KITSLRLSQNEIKSAFSKVSQNEINAIKLSKQRLEKTESSVK 95
                   456689***********************54.5799******************************99877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1502  (0.0837749); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.33s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 594.91
//
Query:       EPA06087.1  [L=249]
Description: hypothetical protein BG20_I1949, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1808.86
//
Query:       EPA06088.1  [L=356]
Description: putative histidinol-phosphate transaminase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.3e-45  153.5   0.0    9.9e-45  153.3   0.0    1.0  1  Aminotran_1_2  Aminotransferase class I and II
     0.0016   17.4   0.0       0.15   11.0   0.0    2.1  2  Aminotran_5    Aminotransferase class-V
  ------ inclusion threshold ------
       0.05   12.9   0.0        0.1   11.8   0.0    1.5  1  LYTB           LytB protein
       0.12   12.5   0.1       0.51   10.5   0.1    2.1  2  HTH_22         HTH domain


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.3   0.0   2.2e-48   9.9e-45      45     360 ..      64     348 ..      27     351 .. 0.88

  Alignments for each domain:
  == domain 1  score: 153.3 bits;  conditional E-value: 2.2e-48
                    HHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHT CS
  Aminotran_1_2  45 glpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealk 140
                    g   l  +l kfl+      ++    + vg+G++++++++   + + ++++il ++pt++ +++ ++l+ ++v ++p++  +d++ld++++++ ++
     EPA06088.1  64 GVERLIAQLSKFLK------VDST-MIGVGNGSDQILDLILSNI-ATKQTKILTSNPTFGFFEERCKLYAIPVTTIPFS--NDMTLDVKEFLK-IS 148
                    46677777888888......6666.899****************.9*******************************77..************.66 PP

                    THHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEE CS
  Aminotran_1_2 141 eapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgn 236
                    +         ++++ sp+NPtG  + +++l+kl   +k    l+++DeaY++f   sl        v++  nl++v++lsK+fGlaG+R+Gy+++n
     EPA06088.1 149 K------NADILYLDSPNNPTGFQFQKDDLQKL---VKTFDGLIIIDEAYGEFGEFSL-----SGMVKTQENLVVVQTLSKSFGLAGLRLGYFIAN 230
                    5......447***********************...88889***********999854.....688889999************************ PP

                    HHHHHHHHHH.HHHHTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS.TEEEECCSCSSEEEEEETHHCHHHHHHHHHHTCTE CS
  Aminotran_1_2 237 aavvsqlrkl.srpflsssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLael.glkvlasqsgmflltdlsaetakelskkLleevgv 330
                    +++ ++ +++ + p+ +s+++ + +  al+ +     ++++++q ++++rk++ ++L++   ++v++s+++++l+     +  k ++++L+e+ g+
     EPA06088.1 231 KKFTDTFNQIlQYPYPVSTITIESAILALEQSA----QMKNAVQLIKEERKRIIENLRKYdAFEVFDSKANFVLFDAHGSY--KRVYDALAEQ-GI 319
                    ******998725578889999999999999999....89******************9999******************99..9*********.** PP

                    EEEEGGGGTS.TTEEEEECTTS-HHHHHHHH CS
  Aminotran_1_2 331 yvtpgtsftv.pgrlRitvAglteeeleelv 360
                     +++    ++  g+lR+tv  +t+e++ +++
     EPA06088.1 320 SIRKLGKIGKhDGCLRVTV--GTKEMNSKFL 348
                    ****999999*********..8888877665 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0   3.3e-05      0.15      54     177 ..      74     188 ..      62     192 .. 0.75
   2 !    4.3   0.0    0.0036        16     260     338 ..     251     325 ..     244     345 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.3e-05
                  HHHT-STGGGEEEESSHHH.HHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBET CS
  Aminotran_5  54 elinaeseeeiiftsGtte.ainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsn 150
                  ++++++s  ++i + ++++  + l++ ++     ++++ ++t++   + +   +e +k   + v+ ip+ ++ +ld++e+  +++++++++++   +n
   EPA06088.1  74 KFLKVDS--TMIGVGNGSDqILDLILSNI----ATKQTKILTSNPTFGFF---EERCKLYAIPVTTIPFSNDMTLDVKEFL-KISKNADILYLDSPNN 161
                  5555554..55555555552334444444....34444444555555655...67777888899****************5.79************** PP

                  TTTEB--HHHHHHHHHHTT-EEEEE-T CS
  Aminotran_5 151 vtGtiqpveeigklakkkgalvlvDaa 177
                   tG  ++ +++ kl+k  + l+++D a
   EPA06088.1 162 PTGFQFQKDDLQKLVKTFDGLIIIDEA 188
                  *****************9999999976 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0036
                  HHHHHHHHH.HCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CTCBSEEEEEETTCSHHHHHHHHHHTTEEEEE.E CS
  Aminotran_5 260 glgaaleyl.eeigleaiekhekelaeyllerlkslpgvrlygpdkaerrasivsfnfkgvhaedvatlLdeegIavrs.G 338
                   ++ a+  l ++ +++++ +  ke ++++ e l++++ +++++      +a+ v f  +g + + v  +L+e+gI +r  G
   EPA06088.1 251 TIESAILALeQSAQMKNAVQLIKEERKRIIENLRKYDAFEVFD-----SKANFVLFDAHG-SYKRVYDALAEQGISIRKlG 325
                  44445444449999***************************76.....467777777665.45789999*******99874 PP

>> LYTB  LytB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.3e-05       0.1      30      83 ..     269     321 ..     250     324 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.3e-05
                 EEECS-SSS-HHHHHHHHHCTEEEE.SSSSTEEEE-TT---HHHHHHHHHTTEEE CS
        LYTB  30 vyvlgeivHNeqvverLeekgvkfi.eeleevviirAhGvskeveeelkekglev 83 
                 v +++e    ++++e+L++ ++  + ++++++v++ AhG  k+v+++l+e+g+++
  EPA06088.1 269 VQLIKE--ERKRIIENLRKYDAFEVfDSKANFVLFDAHGSYKRVYDALAEQGISI 321
                 444333..346778899888887774666679******************99765 PP

>> HTH_22  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.3   5.8e+03      20      34 ..     201     215 ..     186     216 .. 0.81
   2 ?   10.5   0.1   0.00011      0.51      15      40 ..     266     291 ..     251     296 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.3
      HTH_22  20 ltkeekieivraLde 34 
                  +++e++ +v+ L +
  EPA06088.1 201 VKTQENLVVVQTLSK 215
                 477899999999865 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00011
      HTH_22  15 kpverltkeekieivraLdekGiFll 40 
                 k + +l kee+++i+++L +  +F++
  EPA06088.1 266 KNAVQLIKEERKRIIENLRKYDAFEV 291
                 3345799*****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 2288.03
//
Query:       EPA06089.1  [L=188]
Description: GTP diphosphokinase domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.8e-17   61.6   0.0    8.6e-17   61.3   0.0    1.1  1  HD_4         HD domain
  ------ inclusion threshold ------
      0.064   13.3   0.0       0.11   12.5   0.0    1.5  1  AalphaY_MDB  Mating type protein A alpha Y mating type depend


Domain annotation for each model (and alignments):
>> HD_4  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.3   0.0   9.6e-21   8.6e-17       1     137 [.      12     139 ..      12     151 .. 0.88

  Alignments for each domain:
  == domain 1  score: 61.3 bits;  conditional E-value: 9.6e-21
        HD_4   1 Alelaaelha.gqrkltgepllahalevAailaelg.ldaetviAalLhdvveda.lsleeirerfGeevarLvegvsklkrlqkvaaadeaeekaeqv 96 
                 A ++a+++h+ ++r +  +p++ h+ +v++ l++lg  d+e+++Aa Lhd++e +  + ++i+erfG eva +v  ++k +++ k+      +++ +++
  EPA06089.1  12 AKKFAQDKHKnQKRNDGVTPYVVHLEGVVTRLKNLGiSDKESLCAAWLHDILEATdVTFDQINERFGREVAVIVLSLTKDQKIPKK------DRETQYI 104
                 5689******777777779*****************99***************985566***************************......8999999 PP

        HD_4  97 enlRkmLlAmveDirvvliklAdrlqtlrslaaakeekrrd 137
                  +l+    ++    +  +ikl+d   +l+ l++a+  k ++
  EPA06089.1 105 NQLKN--ASF----QTKIIKLCDISANLKDLSNAPISKTQK 139
                 99999..666....99***************9996665533 PP

>> AalphaY_MDB  Mating type protein A alpha Y mating type dependent binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.3e-05      0.11      69      98 ..      48      77 ..      39     110 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.3e-05
  AalphaY_MDB 69 lsayesacarwkhdleeafdrtahsisphn 98
                 +s  es ca w hd+ ea d t   i    
   EPA06089.1 48 ISDKESLCAAWLHDILEATDVTFDQINERF 77
                 6889******************99987654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1314  (0.0732891); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1199.47
//
Query:       EPA06090.1  [L=80]
Description: hypothetical protein BG20_I2420 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 513.44
//
Query:       EPA06091.1  [L=90]
Description: hypothetical protein BG20_I2422 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.089   12.8   0.1       0.13   12.2   0.1    1.7  1  Y_Y_Y     Y_Y_Y domain


Domain annotation for each model (and alignments):
>> Y_Y_Y  Y_Y_Y domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   7.2e-06      0.13      30      47 ..      48      65 ..       5      84 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.2e-06
                EEEEES--SEEEEEEEEE CS
       Y_Y_Y 30 easytnlppGdYtlkVka 47
                  s+t  +pG Yt++V++
  EPA06091.1 48 AQSWTSTEPGMYTIEVFV 65
                569*************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 592.26
//
Query:       EPA06092.1  [L=38]
Description: hypothetical protein BG20_I2576 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.049   13.5   0.5      0.049   13.5   0.5    1.0  1  Spc29            Spindle Pole Component 29
      0.055   14.1   0.4      0.055   14.1   0.4    1.1  1  Vir_act_alpha_C  Virulence activator alpha C-term


Domain annotation for each model (and alignments):
>> Spc29  Spindle Pole Component 29
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.5   5.5e-06     0.049     110     141 ..       6      37 ..       2      38 .] 0.93

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.5e-06
       Spc29 110 dsiyssvkkivelekklddqkleIkeLkrele 141
                 ++i++ v   ++l k++++++  I+ L+++l+
  EPA06092.1   6 EQIRDTVAIRDNLAKQIEKHQKAIELLEKILQ 37 
                 78***************************985 PP

>> Vir_act_alpha_C  Virulence activator alpha C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.4   6.2e-06     0.055      16      43 ..      10      37 ..       1      38 [] 0.89

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.2e-06
  Vir_act_alpha_C 16 dpealieeLerrreeheekLaeyeeiee 43
                     d+ a+++ L+++ e+h++ ++ +e+i +
       EPA06092.1 10 DTVAIRDNLAKQIEKHQKAIELLEKILQ 37
                     7789********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (38 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1515  (0.0845); expected 358.6 (0.02)
Passed bias filter:                      744  (0.041497); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 259.35
//
Query:       EPA06093.1  [L=172]
Description: hypothetical protein BG20_I2577 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.8e-25   89.6   0.3    2.4e-25   89.2   0.3    1.2  1  MAF_flag10  Protein of unknown function DUF115


Domain annotation for each model (and alignments):
>> MAF_flag10  Protein of unknown function DUF115
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.2   0.3   1.4e-29   2.4e-25      44     168 ..       2     117 ..       1     120 [. 0.84

  Alignments for each domain:
  == domain 1  score: 89.2 bits;  conditional E-value: 1.4e-29
  MAF_flag10  44 lkelrdkaviiaadtalkaLlkegIkPDivvs.lDpqeasyevfkeaekkgdiplvfasgvnpellkkykgpkiflvtgstqalelleeekneilfgGg 141
                 lk+ +++ + i ad+a+k+L+++gI PDivv+ lD+   + e + ++ k  +i +v+a+g+n+  l+  ++ k ++ t+  + ++ +      ++fgG+
  EPA06093.1   2 LKNFKKE-LKIVADSAVKVLIENGINPDIVVTdLDG---DEESLIKVGKTDSIFVVHAHGDNIARLNLAENFKNYVGTTQSKPFKKI------QNFGGF 90 
                 5666544.44567***********************...6666566666569********************999777655445555......9***** PP

  MAF_flag10 142 svantaldlAvklgfkeIiliGqDlay 168
                 +++++a++lA ++++k+Iil+G+D+  
  EPA06093.1  91 TDGDRAVFLASHFEAKKIILFGMDFEE 117
                 ************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1205.60
//
Query:       EPA06094.1  [L=253]
Description: anticodon-binding domain protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.5e-18   64.6   0.2    1.6e-17   63.9   0.2    1.3  1  Anticodon_1  Anticodon-binding domain of tRNA


Domain annotation for each model (and alignments):
>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.9   0.2   8.8e-22   1.6e-17      10     150 ..       2     127 ..       1     131 [. 0.81

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 8.8e-22
  Anticodon_1  10 klvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkraaqevllevletllrllaPfmPfitEelwqreeeelgkkesimlaew 107
                  +lv++vt ++e++r+++a++++   f  dl +wy + v  +  ++       ++ +l+ + +  + +l+Pf+P+itEe+w    e+lg+ + ++ + w
   EPA06094.1   2 SLVSQVTGSIEKMRLREALHDILFSFESDL-SWYTKRVNAKSRTN-------ISGILHQINSVRVAMLSPFAPHITEEMW----EKLGNHTLVSTSLW 87 
                  799***************************.***99987655433.......66**************************....999***99*9999* PP

  Anticodon_1 108 pe.kaeelekeleeeevellkeivkairklrselkikpsselkv 150
                  pe +a+  ++ +  ++ el   +  +i ++ ++lk+ + +++k+
   EPA06094.1  88 PEySADSINASA-IQSEEL---LKLLIDDIANILKVTKITPKKI 127
                  *97776665555.566667...5556666666666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       818  (0.0456244); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1561.96
//
Query:       EPA06095.1  [L=168]
Description: riboflavin biosynthesis protein RibD C-terminal domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.6e-18   65.5   0.4    1.6e-15   57.4   0.4    2.1  1  RibD_C    RibD C-terminal domain
    7.3e-08   32.3   0.0    8.2e-08   32.1   0.0    1.1  1  DHFR_1    Dihydrofolate reductase


Domain annotation for each model (and alignments):
>> RibD_C  RibD C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.4   0.4   1.8e-19   1.6e-15       2     196 ..       3     158 ..       2     162 .. 0.83

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 1.8e-19
                 EEEEEEEEETTSBSSCTTSSGCTSS-HHHHHHHHHHHHTSSEEEEEHHHHHHHT--SS--SSCHSCHHHTT.GSS-EEEEEETTS-S-TTSH.HHHSSS CS
      RibD_C   2 yvilklavSlDGklaaaggeskwitgeearadvhelraeadailvGrgtvladnpsltvrwvkkreaeadaearqpvrvVvdstlrvpldak.vltdda 99 
                 ++++ +a SlDG++a+++g+ +w+ +++  +  ++  +  d++++G +t  +       +++           ++   +V+++t++ +++ + +++ d 
  EPA06095.1   3 KIQVYIASSLDGFIARESGDIDWLPESS-ESSYDAFYKSIDTVIMGKTTYDQVLT--FGEYPY----------KDKKSIVFSKTQQNDDENAeFVS-D- 86 
                 789999****************865555.4778999999********77655555..111222..........56678999988775554442665.4. PP

                 -EEEEESSCSCHHHHHHCCESE-HHHHHHHHHHTT--EEEEEETHHHHHHHHHTTT-SEEEEEEESCE--TTSBCSSSSST-SSEEEEEEEEEEETT CS
      RibD_C 100 ptlvatteeadkekveklkvrvdlkelleeLkergirsllveGGatLagsllraglvDelrlyiaPkllGgagktlfdgegfkalklklvksealge 196
                                         ++ ++    + ++++++ GG++L+gs+l+ g+vDe++ +  P++lG  g +lf++++ + +kl+lvk+e++g+
  EPA06095.1  87 -----------------------VEKFVKGGFPGAGENIWLVGGGKLIGSFLKLGVVDEIITTLIPIVLGR-GIPLFQDTEND-TKLELVKTERYGQ 158
                 .......................8999999999999***********************************.**********9.7*********997 PP

>> DHFR_1  Dihydrofolate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.0   9.1e-12   8.2e-08      38     118 ..      42     128 ..      12     157 .. 0.86

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 9.1e-12
                 CEEEEEHHHHHCC-....S--TTCEEEEE-S-TT---TTEEEESSHHHHCC.CCTTS.SEEEEEE-HHHHHHCGG..G-SEEEEEEE CS
      DHFR_1  38 kpvimGrkTfeslg...krpLpnrkniVltrnedlkvegvevvssleeala.lakeekeevfviGGaeiYkqalp..ladklylTei 118
                  +vimG+ T++ +    + p +++k+iV +++++ + e++e+vs++e++++     + e+++++GG+++   +l+  ++d+++ T i
  EPA06095.1  42 DTVIMGKTTYDQVLtfgEYPYKDKKSIVFSKTQQNDDENAEFVSDVEKFVKgGFPGAGENIWLVGGGKLIGSFLKlgVVDEIITTLI 128
                 589*******986444488*************999999************864455569**********999987335888888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.33s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 991.24
//
Query:       EPA06096.1  [L=293]
Description: SCP-like protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-19   69.7   1.9    6.7e-19   69.0   0.9    1.9  2  CAP              Cysteine-rich secretory protein family
  ------ inclusion threshold ------
       0.11   12.6   0.7       0.43   10.7   0.0    2.2  2  ArfGap           Putative GTPase activating protein for Arf
       0.12   12.2   0.9       0.23   11.3   0.9    1.5  1  Ephrin_rec_like  Putative ephrin-receptor like
       0.12   12.3   0.9       0.25   11.3   0.9    1.5  1  Chlorosome_CsmC  Chlorosome envelope protein C
       0.26    9.2   2.0       0.65    7.9   1.2    1.6  1  Prominin         Prominin


Domain annotation for each model (and alignments):
>> CAP  Cysteine-rich secretory protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       4.1   1.5e+04      63      71 ..      79      87 ..      59     106 .. 0.57
   2 !   69.0   0.9   1.9e-22   6.7e-19       2     126 .]     147     292 ..     146     292 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 4.1
                EES--CCCH CS
         CAP 63 aaseaaeda 71
                +as++a+d+
  EPA06096.1 79 DASKTAQDI 87
                333333333 PP

  == domain 2  score: 69.0 bits;  conditional E-value: 1.9e-22
                 HHHHHHHHHTT----EE-HHHHHHHHHHHHHHHHH.T---S-GGG--HHHHHHTT-T...................................E.EEEEE CS
         CAP   2 eahNeyRaaaglppLkwdatLekaAqdhardcaashsdsssspeggdllkyaenagk...................................e.niaaa 64 
                 +++N+yR+++gl+ L wd++L++ A++h+ d+aa++++++  p+g+d+ ++a +  +                                   + + +++
  EPA06096.1 147 QLTNQYRTQNGLAELDWDEKLAVIARNHSIDMAARNYFDHENPQGQDPTDRANSQRYschktignliydgiaenifqnnlydtvwrtngvisSyEWNSQ 245
                 689******************************************************************999999999999999998877664233444 PP

                 S--CCCHHHHHHTSHH.............HHHHHT-SS--EEEEEEEEBTTS-E..EEEEEE CS
         CAP  65 seaaedavdsWysepgtynkgketegsighftnllwpkstkvGcavatcgngsftfivvcny 126
                 +e a+ +v +W+++pg             h++n+l +++ + G+++a ++++    + ++++
  EPA06096.1 246 DELAQTTVSGWMDSPG-------------HRQNILTKTYDREGIGIAISSDDKV--YITQDF 292
                 44499***********.............**********************955..999987 PP

>> ArfGap  Putative GTPase activating protein for Arf
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00012      0.43      28      58 ..       9      39 ..       2     103 .. 0.85
   2 ?   -0.2   0.1      0.29     1e+03      61      99 ..     163     202 ..     143     211 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00012
                ETTTTEEE-HHHHHHHCCS.TTT--EEETTT CS
      ArfGap 28 slnlgvflCieCsgvHrslgvhiskvrsltl 58
                + + g f+C++C++ H   +++  +++ +t 
  EPA06096.1  9 VYTQGYFVCTKCKARHYGKSRKSRNIKKITT 39
                45779*************9999999998875 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.29
                 --HHHHHHHH.HTCHHHHHHHHTTTC-TTTSG-TTCGHHH CS
      ArfGap  61 wedeelellk.algNkkaneileaklpkeekrskssskek 99 
                 w+++   + + +  +  a++++ +++p+ +++++++++++
  EPA06096.1 163 WDEKLAVIARnHSIDMAARNYFDHENPQGQDPTDRANSQR 202
                 5555555555344566788899999999888855554444 PP

>> Ephrin_rec_like  Putative ephrin-receptor like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.9   6.3e-05      0.23      13      46 ..       2      35 ..       1      36 [. 0.95

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.3e-05
  Ephrin_rec_like 13 pCprgtYqneegqlsClaCPlgtttkkpgatses 46
                     +C+ + Y  ++g   C++C + ++ k++ +++++
       EPA06096.1  2 ACRSHNYVYTQGYFVCTKCKARHYGKSRKSRNIK 35
                     6******************************986 PP

>> Chlorosome_CsmC  Chlorosome envelope protein C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.9   6.9e-05      0.25      53     135 ..      42     128 ..      34     132 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.9e-05
  Chlorosome_CsmC  53 tvgslidatGiskl...lgstsgvvgetidrvaitvkdvsraaGelysdavknven.vtdnaakavGdvgvsasevvknvagsfqkt 135
                      t+ ++i   G+  +   ++  + ++ ++i+ +   + d+s++a ++ +++  ++ + v +++ +   d   ++ e++kn+   +q+t
       EPA06096.1  42 TISAIIGIVGVLFVtgtIEFDQKIIDDSIKNIPQNIEDASKTAQDIATETRTTITQkVNEQIENVPPDPVATTVETIKNIPKKIQET 128
                      5555555555543300034567899************************9999866155566666679999999********99987 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   1.2   0.00018      0.65     120     202 ..      17      97 ..      11     141 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00018
    Prominin 120 crrCggempqkqkksdacrRktlgvllllltlllliGviiaFvtNkaldegleesketvkrgledlrtflkdvpqhidhvlvq 202
                 c +C+ + + k +ks + +++t g+++  ++   ++Gv++   t ++ ++ +++s +++++++ed+ +  +d++ + +  + q
  EPA06096.1  17 CTKCKARHYGKSRKSRNIKKITTGITISAIIG--IVGVLFVTGTIEFDQKIIDDSIKNIPQNIEDASKTAQDIATETRTTITQ 97 
                 68999999999999988888888887766554..3466655556666677777777777777777777776666665544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1257  (0.0701099); expected 358.6 (0.02)
Passed bias filter:                      741  (0.0413297); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.52
# Mc/sec: 1705.24
//
Query:       EPA06097.1  [L=154]
Description: hypothetical protein BG20_I1776 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-36  126.5   5.3    1.5e-36  126.4   5.3    1.0  1  DUF45          Protein of unknown function DUF45
    1.2e-05   25.4   4.1    1.8e-05   24.9   3.5    1.5  1  WLM            WLM domain
     0.0048   16.7   0.7      0.008   16.0   0.6    1.5  1  SprT-like      SprT-like family
     0.0073   15.5   2.6     0.0081   15.4   2.6    1.1  1  WavE           WavE lipopolysaccharide synthesis
  ------ inclusion threshold ------
      0.014   14.9   0.0      0.017   14.7   0.0    1.2  1  Peptidase_M64  IgA Peptidase M64
      0.036   14.1   0.4       0.89    9.6   0.0    2.4  2  HTH_6          Helix-turn-helix domain, rpiR family
      0.091   12.0   0.0        0.1   11.8   0.0    1.2  1  Zincin_2       Zincin-like metallopeptidase
       0.11   12.9   3.6       0.12   12.8   1.8    2.1  2  DUF4208        Domain of unknown function (DUF4208)


Domain annotation for each model (and alignments):
>> DUF45  Protein of unknown function DUF45
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.4   5.3   6.8e-40   1.5e-36      62     205 ..       2     147 ..       1     149 [. 0.93

  Alignments for each domain:
  == domain 1  score: 126.4 bits;  conditional E-value: 6.8e-40
       DUF45  62 pllGkkyrlkvekgk..easvklkreelelavkkeeeeeklrkaleewlrkeakeeleerlaklaaklgvkprsvsikdmktrWGscsskgkirlnwrL 158
                 p+lGk+y lk+  ++  ++ + +++e + +++ k+ ++++++++ ++wl + a++ +++ ++kla+kl ++ +++ ik+ k++WGs ++++ ++ln +L
  EPA06097.1   2 PYLGKNYDLKIMLSDyqNSILFTNNEFQVTVTRKKPSKKAIEEIYQNWLLESARKLFQNKTKKLAKKLSISQPKIIIKNLKNKWGSITANNIVTLNQNL 100
                 89************9844444566666777778888999999********************************************************* PP

       DUF45 159 vkappevidYVvvHElaHlleknHskrFwalvekllPdwkeakkeLk 205
                 +kap++vidYV++HEl+H++ k+H  +Fw++v+k++P++ +  ++L+
  EPA06097.1 101 AKAPSDVIDYVILHELCHVKIKEHDHHFWNYVKKFMPNYHDKVRWLE 147
                 **********************************************8 PP

>> WLM  WLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   3.5   7.9e-09   1.8e-05      82     114 ..     107     139 ..      98     145 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 7.9e-09
         WLM  82 simgtllHELaHnvygpHdakFyallkeLekev 114
                  i  ++lHEL+H++  +Hd++F++++k+   ++
  EPA06097.1 107 VIDYVILHELCHVKIKEHDHHFWNYVKKFMPNY 139
                 57789*********************9986655 PP

>> SprT-like  SprT-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.6   3.6e-06     0.008      28      76 ..      80     120 ..      48     143 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.6e-06
   SprT-like  28 rlnttaGranlkratvrhhasIeLseklldsrsedrllntLaHElcHla 76 
                 +l+++ G  +        ++ ++L+++l +  ++d +  +++HElcH+ 
  EPA06097.1  80 NLKNKWGSIT-------ANNIVTLNQNLAKA-PSDVIDYVILHELCHVK 120
                 5555555544.......44699********9.***************85 PP

>> WavE  WavE lipopolysaccharide synthesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   2.6   3.6e-06    0.0081     174     283 ..      22     139 ..       3     154 .] 0.72

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.6e-06
        WavE 174 lfedeelks.....aklkkaqkegyteakvaseQvlllallrkldlelrlkklldvsasklklwdkvlanNlivaepe..elgldlperflekak.raa 264
                 lf+++e++      + +kka +e y++  ++s  +l+ +  +kl ++l+++++  + ++ +++w  + anN++ ++++  ++  d+++ ++ ++  +++
  EPA06097.1  22 LFTNNEFQVtvtrkKPSKKAIEEIYQNWLLESARKLFQNKTKKLAKKLSISQPKIIIKNLKNKWGSITANNIVTLNQNlaKAPSDVIDYVILHELcHVK 120
                 6777666656666688899999**************************************************999876225566777776655552333 PP

        WavE 265 elesleWlelyekeclkti 283
                   e+ +  + y k++++++
  EPA06097.1 121 IKEHDHHFWNYVKKFMPNY 139
                 3333334444555555544 PP

>> Peptidase_M64  IgA Peptidase M64
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   7.6e-06     0.017      75     156 ..      36     122 ..      16     142 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 7.6e-06
                    B----TT--BSSBTTBTTB-B---HHHHHHHHTTS--SEEEEEES-SS--EEEETTTE.....EEEESSSTTHHHHHHHHHHHHTT- CS
  Peptidase_M64  75 verrsalgstydafdseRyllvvenrakrdaasfapydlvivlvNtekYgGgGifnly.....atvaadnsyatyilvHElgHslag 156
                       + a++  y+ + +e     ++n++k+ a++ +  +  i++ N ++ +G+   n           a ++   y+++HEl H   +
     EPA06097.1  36 KPSKKAIEEIYQNWLLESARKLFQNKTKKLAKKLSISQPKIIIKNLKNKWGSITANNIvtlnqNLAKAPSDVIDYVILHELCHVKIK 122
                    4456789999*****999999************999999999***99999998877751222123344566889*********5544 PP

>> HTH_6  Helix-turn-helix domain, rpiR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0    0.0004      0.89      23      52 ..      48      77 ..      39      79 .. 0.93
   2 ?    1.9   0.1     0.099   2.2e+02       5      37 ..      91     121 ..      88     125 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0004
                HHHHH-S---TT--HHHHHHHTT--HHHHH CS
       HTH_6 23 eyilaspdkaielsikalAkaaavSeativ 52
                +++l+s  k+ +   k+lAk++++S++ i+
  EPA06097.1 48 NWLLESARKLFQNKTKKLAKKLSISQPKII 77
                699************************986 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.099
                 HHHHHH-----HHHHHHHHHHHH-S---TT--H CS
       HTH_6   5 ekiqskkekltksekkiaeyilaspdkaielsi 37 
                 + i    ++l+k+ + +++y+    ++++++ i
  EPA06097.1  91 NNIVTLNQNLAKAPSDVIDYVIL--HELCHVKI 121
                 667788999**********9875..45566555 PP

>> Zincin_2  Zincin-like metallopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   4.7e-05       0.1     124     167 ..      76     119 ..      55     143 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.7e-05
                 SH---.---EEEE-HHHHHHHHHHTT--HHHHHHHHHHHHHHHH CS
    Zincin_2 124 vglplapegrllLvapnvaaverelevdpedvrlwvalrEaaha 167
                 + ++  +++   + a+n+++++++l   p+dv  +v l+E  h 
  EPA06097.1  76 IIIKNLKNKWGSITANNIVTLNQNLAKAPSDVIDYVILHELCHV 119
                 555666666677889*************************9995 PP

>> DUF4208  Domain of unknown function (DUF4208)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.2   2.7e+03      81      95 ..      33      47 ..      26      48 .. 0.74
   2 ?   12.8   1.8   5.5e-05      0.12      61      86 ..     116     144 ..      50     151 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.2
     DUF4208 81 wpkkvsgkkLeemYk 95
                + kk s+k +ee+Y+
  EPA06097.1 33 TRKKPSKKAIEEIYQ 47
                566788999999997 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 5.5e-05
     DUF4208  61 kkeekkeklkkhlWefvskfwp...kkvs 86 
                   + k+++  +h+W++v kf+p   +kv 
  EPA06097.1 116 LCHVKIKEHDHHFWNYVKKFMPnyhDKVR 144
                 334789999*************4322244 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1328  (0.0740699); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 891.79
//
Query:       EPA06098.1  [L=376]
Description: hypothetical protein BG20_I1783 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00053   19.7   0.4     0.0013   18.4   0.4    1.6  1  Peptidase_M57  Dual-action HEIGH metallo-peptidase
     0.0088   16.2   0.4      0.019   15.1   0.4    1.5  1  Reprolysin_5   Metallo-peptidase family M12


Domain annotation for each model (and alignments):
>> Peptidase_M57  Dual-action HEIGH metallo-peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.4   1.4e-07    0.0013     130     164 ..     264     298 ..     230     317 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.4e-07
  Peptidase_M57 130 vdvnehvithelGhtvGlRhsDyynrsisCGsagn 164
                     ++ + vi helGh++ +Rh        sCG +++
     EPA06098.1 264 ANMQNRVIAHELGHAINIRHHGQGGTHNSCGPNTE 298
                    478899***************9999999**98875 PP

>> Reprolysin_5  Metallo-peptidase family M12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.4   2.2e-06     0.019     144     179 ..     269     301 ..     247     319 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.2e-06
  Reprolysin_5 144 qvvaHElGHnfGavHDcdsssesqsCslsnstepag 179
                    v+aHElGH+++ +H  ++  +  sC ++  te +g
    EPA06098.1 269 RVIAHELGHAINIRHHGQGG-THNSCGPN--TERNG 301
                   799***************98.77777775..44444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2586.70
//
Query:       EPA06099.1  [L=159]
Description: hypothetical protein BG20_I1782 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.26   11.9   4.6       0.37   11.4   4.6    1.2  1  Pex14_N      Peroxisomal membrane anchor protein (Pex14p) con
       0.56   10.2  13.7       0.86    9.6  13.7    1.3  1  Trypan_PARP  Procyclic acidic repetitive protein (PARP)


Domain annotation for each model (and alignments):
>> Pex14_N  Peroxisomal membrane anchor protein (Pex14p) conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   4.6   4.1e-05      0.37      73     150 ..      15      95 ..       5      97 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.1e-05
     Pex14_N  73 ssatpqpqaasqtsqsspspsppaqqqqqqy......rpPivtypefltkppkppppPlrtwrdllitatalaglgaglyglsk 150
                 s+  p+p++++ +  ++p+ ++ ++  ++ +       +P  t     t+ p+ppp+P ++w  + i + ++ g++ g+  +s+
  EPA06099.1  15 SELVPSPSPPTIPYPTPPTIPT-PGD-ST-SpfpipiPSPAPTPVPTPTPVPNPPPTPSIDWVWVGIGVAVAIGIAIGVEWVSR 95 
                 2222222222222222222221.111.11.134566644444444445789999***********************9977776 PP

>> Trypan_PARP  Procyclic acidic repetitive protein (PARP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6  13.7   9.5e-05      0.86      60     112 ..      18      70 ..       5      90 .. 0.35

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 9.5e-05
  Trypan_PARP  60 epepepepepepepepepepetepeeepepepepepepepepepepepepepg 112
                   p p p   p p p + p p  +  + p p p p p p p p p p+p p p 
   EPA06099.1  18 VPSPSPPTIPYPTPPTIPTPGDSTSPFPIPIPSPAPTPVPTPTPVPNPPPTPS 70 
                  22222222233333333333222222222233333333333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.35s 00:00:00.93 Elapsed: 00:00:00.56
# Mc/sec: 856.01
//
Query:       EPA06100.1  [L=54]
Description: hypothetical protein BG20_I1777 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.024   14.6   0.2      0.024   14.6   0.2    1.0  1  Phage_Gp15  Bacteriophage Gp15 protein


Domain annotation for each model (and alignments):
>> Phage_Gp15  Bacteriophage Gp15 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.2   1.3e-06     0.024      15      59 ..       3      46 ..       1      54 [] 0.77

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.3e-06
  Phage_Gp15 15 eykidldFrtvlrfedmledeelseeeKinlalellldeepedle 59
                e++i++  +++l+f ++ +++ l+ eeKi+ +++++l  ++ + +
  EPA06100.1  3 EITIKFKDKDYLDFNKISNESGLTPEEKIQEIVQYYLI-IERNRK 46
                5667777789************************9997.333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.34s 00:00:00.84 Elapsed: 00:00:00.55
# Mc/sec: 297.16
//
Query:       EPA06101.1  [L=262]
Description: hypothetical protein BG20_I1778 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-45  155.5   0.0    2.6e-45  155.2   0.0    1.0  1  DUF72     Protein of unknown function DUF72


Domain annotation for each model (and alignments):
>> DUF72  Protein of unknown function DUF72
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.2   0.0   1.4e-49   2.6e-45       1     215 [.      20     241 ..      20     243 .. 0.88

  Alignments for each domain:
  == domain 1  score: 155.2 bits;  conditional E-value: 1.4e-49
                 B.TT..CCCHHHHHCCT-SEEEE-HHCCSSS-HHHHHHHHCTS-TT-EEEEE--CCCCCS.G-.SCHHHHHHHHHH.CHHHCT-EEEEEEE--TT--S. CS
       DUF72   1 YpeglkkkerLeyYarhfntVEinstFYalpspetvakwaaqtpedFrFavKapraitherne.daeealerflesalepLgeklgpllfQlppsfkfd 98 
                 Yp+ l+k ++L+yY++ f++ Einst+Y++p+++  +kw+a tp++FrF+ K+p+ ith ++  ++++ + +fl+s l pL+ek+ +l++Qlpps++f 
  EPA06101.1  20 YPKRLEKTDWLKYYSSIFEITEINSTYYKIPDQSITKKWNADTPDSFRFTAKFPSIITHDHKLkNVQDHVFKFLAS-LIPLHEKILALVLQLPPSLTFA 117
                 9**********************************************************752348**********9.*******************665 PP

                 HHHHHHHHHHTTTS-..S.EEEE--BGGGH..HHHHHHHHTT-EEEEE--SSC--------SSTEEEEEE--SHHTTB----H......HHHHHHHHHH CS
       DUF72  99 eenlerLeaflaalp..l.lavEvRhrswf..ellellrehgvavvldepkkpklpledvttadfvyvRlhgreeryayrYse......eelaewaeri 186
                 e    rL ++++ lp    + +E Rh+swf  e ++ l++++  +v+   + + +      t+d vyvRl+g+++  ++++ +      + +++w ++i
  EPA06101.1 118 E-AKPRLLELFSVLPedFkYPIEGRHESWFtdEATDYLKANNHCLVWN--EIAGVNNPAPITSDYVYVRLIGDRSIPDKDFGKiiinrkDLIQKWSDKI 213
                 4.67888888888888855***********955*********778875..455666666666**********96667778885555566********** PP

                 HHHHTCSSEEEEEE-SBCCCHHHHHHHHH CS
       DUF72 187 kawaaegrevyvffnndaegqaplnaraL 215
                 k++++  +++ v+ nn++eg  p++++ L
  EPA06101.1 214 KNLRN-VNSALVLANNHFEGFGPATVNSL 241
                 **977.79****************99988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1629.68
//
Query:       EPA06102.1  [L=185]
Description: hypothetical protein BG20_I1781 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0012   18.8   0.2     0.0026   17.7   0.1    1.6  1  HSDR_N_2  Type I restriction enzyme R protein N terminus (HSD
  ------ inclusion threshold ------
      0.016   15.7   1.4      0.019   15.4   0.5    1.7  2  DUF234    Archaea bacterial proteins of unknown function
      0.016   15.5   2.8      0.026   14.8   2.8    1.2  1  DUF5625   Domain of unknown function (DUF5625)


Domain annotation for each model (and alignments):
>> HSDR_N_2  Type I restriction enzyme R protein N terminus (HSDR_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   4.4e-07    0.0026      17      75 ..      37      98 ..      28     117 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.4e-07
    HSDR_N_2 17 lgypkeliavekelqlg......skkkraDivvykkdkkpllivecKapsvkiseevleqlksYl 75
                 + pk++i++e +++++        kk +Div++++dk+   ++e+K p+        eq++s++
  EPA06102.1 37 NKLPKHKIQLERNVSYFgltknkFIKKEIDIVIFNQDKTEKSAIEIKFPTNGQYP---EQMFSFC 98
                5789***********87674332234557******************99876654...5555555 PP

>> DUF234  Archaea bacterial proteins of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.5   3.2e-06     0.019      43      91 ..      34      86 ..       1      94 [. 0.61
   2 ?   -3.3   0.0       2.1   1.2e+04      57      68 ..     161     172 ..     151     177 .. 0.55

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.2e-06
      DUF234 43 lllelnkagklpfrftkvGrwW......kkeeeiDivaldeeekkalfgEvKwkn 91
                +l+  nk  k ++++++  +++        ++eiDiv +++++ +  ++E+K+ +
  EPA06102.1 34 FLR--NKLPKHKIQLERNVSYFgltknkFIKKEIDIVIFNQDKTEKSAIEIKFPT 86
                333..444444555666667776654322578********************976 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.1
      DUF234  57 ftkvGrwWkkee 68 
                 f+ +G++ +k +
  EPA06102.1 161 FNIIGSYVAKWQ 172
                 444555544433 PP

>> DUF5625  Domain of unknown function (DUF5625)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   2.8   4.4e-06     0.026      13      98 ..      15     103 ..      12     109 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.4e-06
                 EEEEEEE-SSEEEEEEEEE----CCCCTTH....HHHHH-TT--T---EEEEEEEEE-TTS-EEEEEEEEEEE-S--SSTTE...EEEEE CS
     DUF5625  13 vetdveieekgsyqlaLlfavndqkeemer....vekllGstdkdgvivpvklkivknkkndkkvildkkinakglgsgaateyereIkt 98 
                 ++++vei ++ s+q +L ++ +++  + +        ++G t+++++   + + i   +++++k  ++ k  ++g+   +++ + ++Ik 
  EPA06102.1  15 IQKEVEIYNEASIQYELAIFLRNKLPKHKIqlerNVSYFGLTKNKFIKKEIDIVIFN-QDKTEKSAIEIKFPTNGQYPEQMFSFCKDIKF 103
                 6789***9997777777777666543332222448889**98888877777777776.999***********************9*9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       739  (0.0412181); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1218.23
//
Query:       EPA06103.1  [L=249]
Description: hypothetical protein BG20_I1784 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00089   19.3   0.1      0.018   15.2   0.1    2.4  2  TPR_8     Tetratricopeptide repeat
     0.0027   18.0   0.1      0.022   15.1   0.0    2.6  2  TPR_17    Tetratricopeptide repeat
     0.0097   16.5   0.1          6    7.7   0.0    2.6  2  TPR_6     Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.013   15.6   0.0      0.022   14.8   0.0    1.4  1  G8        G8 domain
      0.015   15.3   0.2        0.2   11.8   0.1    2.3  2  TPR_2     Tetratricopeptide repeat
      0.035   14.4   0.0      0.062   13.6   0.0    1.4  1  TPR_12    Tetratricopeptide repeat
      0.082   11.6   0.1       0.11   11.3   0.1    1.1  1  DUF3808   Protein of unknown function (DUF3808)


Domain annotation for each model (and alignments):
>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.19   4.7e+02       5      32 ..     154     181 ..     151     183 .. 0.85
   2 !   15.2   0.1     7e-06     0.018       2      29 ..     185     212 ..     184     216 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.19
                 HHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
       TPR_8   5 ynlgsiylklgdyeeAkeyyekaleldp 32 
                 ++++   l+ ++ e+A+  +++    +p
  EPA06103.1 154 LRIAEYFLDRNNVEKAQLILNQLFNSNP 181
                 6788889999********9999988888 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 7e-06
                 CHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
       TPR_8   2 eayynlgsiylklgdyeeAkeyyekale 29 
                  +++nlg++ + ++d+++A+eyy  al+
  EPA06103.1 185 NVLFNLGRLEEIKEDKNKAQEYYLSALS 212
                 589*********************9997 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.7   4.5e+03      17      33 ..     154     170 ..     147     170 .. 0.80
   2 !   15.1   0.0   8.4e-06     0.022       9      34 .]     180     205 ..     174     205 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.7
      TPR_17  17 nnLAelllknGdlmtAr 33 
                    Ae++l +++ ++A+
  EPA06103.1 154 LRIAEYFLDRNNVEKAQ 170
                 56788999999998886 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 8.4e-06
      TPR_17   9 dPnnadaynnLAelllknGdlmtArq 34 
                 +P+++++++nL++l + + d+ +A++
  EPA06103.1 180 NPTSVNVLFNLGRLEEIKEDKNKAQE 205
                 9*******************999986 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0023         6       3      33 .]     153     183 ..     152     183 .. 0.93
   2 !    6.3   0.0    0.0068        17       2      30 ..     186     214 ..     185     221 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0023
                 HHHHHHHHHHHHHHHHHHHHHHHHHHH-TT- CS
       TPR_6   3 lyklalsyrklgdtdkAlealerlikeYPdS 33 
                 ++++a+ ++  ++ +kA  +l++l ++ P+S
  EPA06103.1 153 MLRIAEYFLDRNNVEKAQLILNQLFNSNPTS 183
                 8999*9888888*****************98 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0068
                 HHHHHHHHHH.HHHHHHHHHHHHHHHHHH- CS
       TPR_6   2 Alyklalsyr.klgdtdkAlealerlikeY 30 
                 +l++l+++ + k  d+ kA e++ + ++e+
  EPA06103.1 186 VLFNLGRLEEiKE-DKNKAQEYYLSALSEF 214
                 699****999888.*******876666654 PP

>> G8  G8 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   8.8e-06     0.022      59      98 ..      43      82 ..      13     101 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 8.8e-06
          G8 59 qggGkleiGteeepfkgkatItLyGteewsstelpdlgaK 98
                +++G+l iGt+++p+ ++++  L+G++++   ++ ++  K
  EPA06103.1 43 NDAGNLVIGTSDNPWYKQIKFYLNGKPSNVNFNILSFTPK 82
                566**********************666666665555555 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.26   6.6e+02       6      33 ..     155     182 ..     153     183 .. 0.83
   2 ?   11.8   0.1   7.9e-05       0.2       3      30 ..     186     213 ..     184     216 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.26
       TPR_2   6 nlGlayyklgdyeeAleafekAleldPn 33 
                 ++++  + +++ e+A   +++    +P+
  EPA06103.1 155 RIAEYFLDRNNVEKAQLILNQLFNSNPT 182
                 678899999******9988888877776 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 7.9e-05
       TPR_2   3 alynlGlayyklgdyeeAleafekAlel 30 
                 +l+nlG++ + + d ++A e++  Al+ 
  EPA06103.1 186 VLFNLGRLEEIKEDKNKAQEYYLSALSE 213
                 89**********************9975 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.4e-05     0.062      26      72 ..     166     211 ..     153     212 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.4e-05
      TPR_12  26 lekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeal 72 
                  eka  i ++l++  +p  +++l+nLgrl +  ++  +A+e++  al
  EPA06103.1 166 VEKAQLILNQLFNS-NPTSVNVLFNLGRLEEIKEDKNKAQEYYLSAL 211
                 57888899999986.899*************************9998 PP

>> DUF3808  Protein of unknown function (DUF3808)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   4.1e-05      0.11     249     296 ..     164     211 ..     141     220 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.1e-05
     DUF3808 249 apleeleelLlksrkrfPksalwllfearieslkgnldeAlelleeii 296
                  + e+++ +L +  +  P s+ +l++ +r+e++k + ++A+e++ +++
  EPA06103.1 164 NNVEKAQLILNQLFNSNPTSVNVLFNLGRLEEIKEDKNKAQEYYLSAL 211
                 68899**************************************99877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       749  (0.0417759); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1605.25
//
Query:       EPA06104.1  [L=195]
Description: hypothetical protein BG20_I1780 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.3e-16   58.6   0.0    9.8e-16   58.0   0.0    1.3  1  2_5_RNA_ligase2  2'-5' RNA ligase superfamily
  ------ inclusion threshold ------
       0.06   13.9   0.2       0.12   12.9   0.2    1.5  1  Ribosomal_L35p   Ribosomal protein L35


Domain annotation for each model (and alignments):
>> 2_5_RNA_ligase2  2'-5' RNA ligase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.0   0.0   1.1e-19   9.8e-16      16     146 ..      20     166 ..       5     170 .. 0.86

  Alignments for each domain:
  == domain 1  score: 58.0 bits;  conditional E-value: 1.1e-19
  2_5_RNA_ligase2  16 lydkayprwp.pHitLlypfvededladlaellsrlaketepfevrldgfgvFeh...........kksvvylsvsdsealqalraallealpe 97 
                      +  +++ ++p pH++L++pf  +    ++ +++ ++ + ++ ++ +ldgf++Fe+           +k+v++l++++se+l+++r +l+++l +
       EPA06104.1  20 HVRGSVLHRPvPHVSLFGPFGCKSL-REVIHCIGEVGSKYSELRYSLDGFDYFESkkkflfittssRKNVIFLKIKPSEELKEFRYELAKKLLK 112
                      55566777788************96.*****************************88888888886666888888****************999 PP

  2_5_RNA_ligase2  98 agdkeds.....geftPHlTiaqsadstsaaelleklaqalpplefevdevall 146
                       +d +d      ++f +H T+a ++ ++ +++++e+l+++    +  + +++ll
       EPA06104.1 113 ITDTVDFdhdskDKFEFHTTLAMKDIDRKFENIWEYLKNYEIKSTGVCYRITLL 166
                      977776677779*************************88777766666676666 PP

>> Ribosomal_L35p  Ribosomal protein L35
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   1.4e-05      0.12       7      45 ..     157     195 .]     155     195 .] 0.93

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.4e-05
  Ribosomal_L35p   7 kgakKRfkvtgsGkikrkkagkrHlltkKstkrkrrlrk 45 
                      g+  R+ ++++Gki++      + l ++s++ krr r+
      EPA06104.1 157 TGVCYRITLLKTGKIMYEYELATKRLLNRSQAIKRRVRR 195
                     68899*******************9999********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       709  (0.0395449); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1236.72
//
Query:       EPA06105.1  [L=242]
Description: IMP dehydrogenase / GMP reductase domain protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      8e-97  324.3   9.7    8.9e-97  324.2   9.7    1.0  1  IMPDH         IMP dehydrogenase / GMP reductase domain
    2.5e-07   30.4   1.1     0.0036   16.8   0.1    2.3  2  His_biosynth  Histidine biosynthesis protein
    2.7e-07   29.9   4.0      3e-07   29.8   3.1    1.5  2  FMN_dh        FMN-dependent dehydrogenase
    4.6e-05   23.0   7.0    8.8e-05   22.0   7.0    1.4  1  NMO           Nitronate monooxygenase
    0.00016   21.0   5.1    0.00036   19.9   1.3    2.1  2  DHO_dh        Dihydroorotate dehydrogenase
    0.00032   20.0   1.8    0.00062   19.0   1.8    1.5  1  NanE          Putative N-acetylmannosamine-6-phosphate epimer
     0.0064   16.0   0.5       0.02   14.3   0.1    1.8  2  PEP_mutase    Phosphoenolpyruvate phosphomutase
     0.0067   15.4   0.0     0.0083   15.0   0.0    1.2  1  PK            Pyruvate kinase, barrel domain
  ------ inclusion threshold ------
      0.017   15.2   0.1        6.9    6.9   0.1    2.6  2  BATS          Biotin and Thiamin Synthesis associated domain
      0.022   14.2   0.9      0.054   12.9   0.4    1.8  2  Aldolase      KDPG and KHG aldolase
      0.022   14.1   2.1      0.027   13.8   0.5    1.8  2  ThiG          Thiazole biosynthesis protein ThiG
      0.029   13.5   3.5      0.042   13.0   3.5    1.3  1  Glu_synthase  Conserved region in glutamate synthase
      0.041   13.3   1.1        1.7    8.0   0.1    2.3  2  G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
      0.045   13.5   0.2       0.27   11.0   0.1    2.1  2  QRPTase_C     Quinolinate phosphoribosyl transferase, C-termi
      0.062   13.3   0.1       0.14   12.2   0.1    1.5  1  B12-binding   B12 binding domain
       0.18   12.2   0.0         16    5.8   0.0    2.3  2  Radical_SAM   Radical SAM superfamily


Domain annotation for each model (and alignments):
>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  324.2   9.7    8e-100   8.9e-97      97     333 ..       1     242 []       1     242 [] 0.94

  Alignments for each domain:
  == domain 1  score: 324.2 bits;  conditional E-value: 8e-100
                 EEE-SSTTHHHHHHHHHHTT-SEEEEE-STSSSHHHHHHHHHHHHHTTTSEEEEEEE-SHHHHHHHHHTT-SEEEE-SS-STTBHHHHHCSB---HHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       IMPDH  97 aavgvkedalervkalveagvdvlvvdsahghsekvleavkeikkkveeveviaGnvataegakaLieagadavkvGiGpGsiCttrvvagvGvpqltA 195
                 aavgvk d +er + l+eag+dvlvvd+ahghse+ l+++++ikk+++++e+iaGnvata+g+++Li+ag+davkvG+G+GsiC+trv++g GvpqltA
  EPA06105.1   1 AAVGVKGDFMERTESLLEAGADVLVVDIAHGHSENALNTIRNIKKAFPKCELIAGNVATAQGTEDLIKAGVDAVKVGVGSGSICITRVITGSGVPQLTA 99 
                 8************************************************************************************************** PP

                 HHHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-SEEEESCCCTTBTTSSSEEEEETTEEEEEEEETTSHHHH.HH-SS-TTS-.....-...-SS-S CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx...xxx...xxxxx RF
       IMPDH 196 vaevaeaakkagvpviaDGGikysgdivkAlaaGadavmlGsllagteEspgeviliegrkyKeyrGmgslgam.kkgskdryfq...kke...klvpe 287
                 v+++a++ k++g+p+i+DGG ++sgd +kAlaaGa++vm+Gs+l gt+Espg v++ +g+++K yrGm+slga   ++sk+   +   + e    +v+e
  EPA06105.1 100 VMDCAKIGKDYGIPIISDGGTRTSGDATKALAAGASSVMVGSMLGGTDESPGTVLTKNGKRFKIYRGMASLGASlGRKSKETG-SislD-EdlnDYVAE 196
                 **************************************************************************533333322.22232.23459**** PP

                 BEEEEEE--B-HHHHHHHHHHHHHHHHHHHT-SSHHHHHHH-EEEE CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       IMPDH 288 GvegrvpykgsvkevveqlvgglrsgmgylGaktieelkekakfvr 333
                 Gve++vpykg+v+++++ql+gg+rsg++y+Ga+ti +++ +a+f++
  EPA06105.1 197 GVEAMVPYKGTVTDILKQLTGGVRSGLSYCGAHTIPQMQANAEFIK 242
                 ********************************************85 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.1   5.9e-05     0.066      28     102 ..       6      77 ..       3      90 .. 0.84
   2 !   16.8   0.1   3.2e-06    0.0036      66     105 ..     104     143 ..      88     202 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.9e-05
                   TTSHHHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEES CS
  His_biosynth  28 agdpvelakryeeegadelhvvDldaakegreanldlveeiaeevfipvqvGGGIrsledveelleagadkviig 102
                   +gd +e  +++ e+gad l vvD+  a+ ++e+ l+ +++i +++     + G + + +  e+l++ag+d v +g
    EPA06105.1   6 KGDFMERTESLLEAGADVL-VVDI--AHGHSENALNTIRNIKKAFPKCELIAGNVATAQGTEDLIKAGVDAVKVG 77 
                   68899999999999*9987.68**..8999999***********6666667777***************976655 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 3.2e-06
                   HHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHH CS
  His_biosynth  66 eeiaeevfipvqvGGGIrsledveelleagadkviigtaa 105
                   ++i +   ip+  +GG r+  d++++l aga+ v++g++ 
    EPA06105.1 104 AKIGKDYGIPIISDGGTRTSGDATKALAAGASSVMVGSML 143
                   57888899*****************************985 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   3.1   2.7e-10     3e-07     205     301 ..      37     141 ..       9     146 .. 0.78
   2 ?   -3.5   0.0       3.6     4e+03     315     342 ..     208     235 ..     206     237 .. 0.74

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 2.7e-10
                 HHHHHHHHHHHS.SEEEEEEE-SHHHHHHHHHTTESEEEE--GGG.....TSSTT---HHHCHHHHHHHH......SS-EEEESS--SHHHHHHHHHTT CS
      FMN_dh 205 wddikwlreqtk.lplvvKGvltaedakraveaGvdgivvSNHGG.....RqldgapatidvLpeiveavg...g.rievlvDgGirrGsDvlkAlalG 293
                  ++i++++++ +  +l+   v ta+  + +++aGvd++ v    G     R + g  + +  L ++++ ++   +  i+++ DgG r+  D+ kAla G
  EPA06105.1  37 LNTIRNIKKAFPkCELIAGNVATAQGTEDLIKAGVDAVKVGVGSGsicitRVITG--SGVPQLTAVMDCAKigkDyGIPIISDGGTRTSGDATKALAAG 133
                 45677777776547888899********************999996666655544..44555555544444321456********************** PP

                 -SEEEESH CS
      FMN_dh 294 AdavllGR 301
                 A+ v++G 
  EPA06105.1 134 ASSVMVGS 141
                 ******95 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.6
                 HHHHHHHHHHHHHHHHHHHT-SBHHHHH CS
      FMN_dh 315 vervleilraelertmallGvksvaeld 342
                 v+++l+ l+  +++ +  +G++++ +++
  EPA06105.1 208 VTDILKQLTGGVRSGLSYCGAHTIPQMQ 235
                 6667777888888888888888887765 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   7.0   7.8e-08   8.8e-05     127     238 ..      41     156 ..       3     162 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 7.8e-08
         NMO 127 evvarlkeagvvliptissvkearkvearGaDalivqGpeaGGhqGtpevgdkglfaLvpqvldavd.....iPviAaGGiidrrgvaaaLalGAsgvq 220
                  ++++      ++ + +++++    ++++G Da+ v G  +G    t+ + + g  +L + +  a       iP+i  GG  +  +   aLa+GAs v 
  EPA06105.1  41 RNIKKAFPKCELIAGNVATAQGTEDLIKAGVDAVKV-GVGSGSICITRVITGSGVPQLTAVMDCAKIgkdygIPIISDGGTRTSGDATKALAAGASSVM 138
                 44444444444566789999999*********9766.78777776666666566666555443333366788*************************** PP

         NMO 221 igtrfLltkesdakdahk 238
                 +g+ + +t+es+  +++k
  EPA06105.1 139 VGSMLGGTDESPGTVLTK 156
                 ***********9999887 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.056        63     229     275 ..      35      79 ..      32      92 .. 0.86
   2 !   19.9   1.3   3.2e-07   0.00036     244     276 ..     111     143 ..      89     150 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.056
                 HHHHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHH CS
      DHO_dh 229 ialkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvyta 275
                  al++ir+++k +  +  +I+ G + +++   + i+aG  +v+v+ +
  EPA06105.1  35 NALNTIRNIKKAFP-KCELIA-GNVATAQGTEDLIKAGVDAVKVGVG 79 
                 58999***999998.899997.99**************999999865 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 3.2e-07
                 .S-EEEESS--SHHHHHHHHHHTECEEEESHHH CS
      DHO_dh 244 eipiIgvGGiesgeDalekieaGAslvqvytal 276
                  ipiI+ GG  ++ Da   + aGAs v v++ l
  EPA06105.1 111 GIPIISDGGTRTSGDATKALAAGASSVMVGSML 143
                 4*****************************988 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   1.8   5.5e-07   0.00062      53     176 ..       9     143 ..       5     149 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 5.5e-07
                 SHHHHHHHHTTT-SEEEEE--SS--T--HHHHHHHHHHH-...-EEEEE-SSHHHHHHHHHTT-SEE....E-TTTTSSTTS-..SS--HHHHHHH... CS
        NanE  53 tlkdideLaaagadiialDatdrerpvtieelikkikeky...qllmaDistleeglvakklGvdiv....GttlsGytkeeek.aepDfalvkal... 140
                 +++  + L +agad++ +D ++ + +  +++ i++ik+ +    l+  +++t + +    k+Gvd v    G+     t   +    p ++ v +    
  EPA06105.1   9 FMERTESLLEAGADVLVVDIAHGHSENALNT-IRNIKKAFpkcELIAGNVATAQGTEDLIKAGVDAVkvgvGSGSICITRVITGsGVPQLTAVMDCaki 106
                 89999***************99888877765.7999999887456667899999999999999998633226666667777766678888888776111 PP

                 .HHTT--EEEES---SHHHHHHHHTT--SEEEE-HHH CS
        NanE 141 .seaglkviaeGrintPekakkaieiGvdavvvGsai 176
                  ++ g+ +i +G   t   a ka+  G+ +v+vGs +
  EPA06105.1 107 gKDYGIPIISDGGTRTSGDATKALAAGASSVMVGSML 143
                 2456899***************************987 PP

>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.1   1.8e-05      0.02     158     224 ..       9      81 ..       4      91 .. 0.78
   2 ?   -0.8   0.0      0.77   8.6e+02     164     178 ..     128     142 ..     123     155 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.8e-05
  PEP_mutase 158 aieRaraYaeAGAdgvfvpgl.....qkdaeiaelvaav.dvplnvvplkgtlsvaelaelGvarislgnhll 224
                  +eR +  +eAGAd+++v  +     +  ++i+++ +a+ ++ l++    ++  +++l ++Gv  + +g    
  EPA06105.1   9 FMERTESLLEAGADVLVVDIAhghseNALNTIRNIKKAFpKCELIAGNVATAQGTEDLIKAGVDAVKVGVGSG 81 
                 589*************99666554534556699999999557776666555799************9997655 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.77
  PEP_mutase 164 aYaeAGAdgvfvpgl 178
                   ++AGA+ v+v ++
  EPA06105.1 128 KALAAGASSVMVGSM 142
                 567899999998765 PP

>> PK  Pyruvate kinase, barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   7.4e-06    0.0083      10      71 ..       3      64 ..       1     118 [. 0.77

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 7.4e-06
                ESCCCTSHHHHHHHHHHTEEEEEEETTSS-HHHHHHHHHHHHHHHHTTTTS-EEEEE---S- CS
          PK 10 lGPasesvekleklieaGlnvvrlnfshGsheehqerienvreaekklgkkvaillDtkGpe 71
                +G + + +e+ e l+eaG++v+ ++ +hG+ e+  ++i n+++a  k +   + +   +G e
  EPA06105.1  3 VGVKGDFMERTESLLEAGADVLVVDIAHGHSENALNTIRNIKKAFPKCELIAGNVATAQGTE 64
                67788889999******************************999877766655555555655 PP

>> BATS  Biotin and Thiamin Synthesis associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.015        17      14      56 ..      37      78 ..      20      87 .. 0.89
   2 ?    6.9   0.1    0.0061       6.9      32      65 ..     119     153 ..      96     177 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.015
                HHHHHHHHHHSTTSECCCTCHH-HHHHHHHHHCCT--EEE-C- CS
        BATS 14 lkiiaalRlllPkagillsgResaefrdqlllklGansisags 56
                l +i  ++ ++Pk +++++   +a+  + l+ k+G++++ +g+
  EPA06105.1 37 LNTIRNIKKAFPKCELIAGNVATAQGTEDLI-KAGVDAVKVGV 78
                6678888999*********************.******99987 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0061
                 TCHH-HHHHHHHHHCCT--EEE-C---TTTGGG.....S CS
        BATS  32 sgResaefrdqlllklGansisagsktevggya.....f 65 
                 ++R+s +  + l   +Ga+s+++gs    gg        
  EPA06105.1 119 GTRTSGDATKAL--AAGASSVMVGSM--LGGTDespgtV 153
                 566655555555..5**********4..66655555552 PP

>> Aldolase  KDPG and KHG aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.4   4.8e-05     0.054      21      84 ..       8      74 ..       2     115 .. 0.80
   2 ?   -1.7   0.0       1.4   1.6e+03     152     180 ..     115     144 ..      88     149 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.8e-05
                GHHHHHHHHHHTT--EEEEET...TSTTHHHHHHHHHHH-TTSEEEEES--SHHHHHHHHHCT-SEE CS
    Aldolase 21 dalplaeaLvagGlrvlevtl...rteaaldairvlrkerpdllvgaGtvlnaeqlaeakeaGaqfv 84
                d ++  e+L++ G  vl v +    +e al+ ir ++k  p+  + aG v +a+  ++  +aG + v
  EPA06105.1  8 DFMERTESLLEAGADVLVVDIahgHSENALNTIRNIKKAFPKCELIAGNVATAQGTEDLIKAGVDAV 74
                6778899*****9888777652246999***********************************9854 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.4
                 EEBSS--TT.THHHHHTSTTBS-EEESCCC CS
    Aldolase 152 iPtGGispa.nvrdylalpsvlvvgGswlv 180
                 i  GG   + ++ + la+++  v++Gs l+
  EPA06105.1 115 ISDGGTRTSgDATKALAAGASSVMVGSMLG 144
                 445555433256667777777777777765 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.4   1.6e+03     194     223 ..      17      46 ..      10      69 .. 0.66
   2 ?   13.8   0.5   2.4e-05     0.027     168     209 ..     104     145 ..      78     154 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.4
                 HHTT-SEEEESHHHHTSSSHHHHHHHHHHH CS
        ThiG 194 melGadavllntavaeakdpvamArafkla 223
                 +e Gad ++++ a  ++++  +  r +k+a
  EPA06105.1  17 LEAGADVLVVDIAHGHSENALNTIRNIKKA 46 
                 677777777777777777776666666655 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 2.4e-05
                 HHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHT CS
        ThiG 168 kiiieeakvPvivDAGigspsdaaqamelGadavllntavae 209
                   i ++  +P+i D G +++ da++a+  Ga++v++ + +  
  EPA06105.1 104 AKIGKDYGIPIISDGGTRTSGDATKALAAGASSVMVGSMLGG 145
                 55677889****************************987665 PP

>> Glu_synthase  Conserved region in glutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   3.5   3.8e-05     0.042     222     304 ..      65     141 ..      26     143 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.8e-05
                   HHHHTT-SEEEEE-TT---SSEEHHHHHHB---HHHHHHHHHHHHHHTT-GGG-EEEEESS--SHHHHHHHHHHT-SEEE-SH CS
  Glu_synthase 222 gvakanadiilidGleGGTGAspkssikhaGlPlelalaevdqtlkeeglrdrvsliadGglktgadvvkalalGAdavgigt 304
                    + ka++d++++  +  G     + +i  +G+P ++a+    +  k++g    + +i dGg +t+ d  kala GA +v +g+
    EPA06105.1  65 DLIKAGVDAVKVG-VGSGS-ICITRVITGSGVPQLTAVMDCAKIGKDYG----IPIISDGGTRTSGDATKALAAGASSVMVGS 141
                   2566677777663.22222.3456788999********99998877776....78*************************997 PP

>> G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1     0.027        31     129     167 ..      38      76 ..      21      79 .. 0.85
   2 ?    8.0   0.1    0.0016       1.7     132     168 ..     104     140 ..      94     142 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.027
                   HHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE CS
  G3P_antiterm 129 kvikeikkelkipiiaGGLietkedveealkaGaiavst 167
                   ++i++ikk++    + +G + t +  e+++kaG++av +
    EPA06105.1  38 NTIRNIKKAFPKCELIAGNVATAQGTEDLIKAGVDAVKV 76 
                   578999999855555567899***************975 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0016
                   CTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE- CS
  G3P_antiterm 132 keikkelkipiiaGGLietkedveealkaGaiavsts 168
                   ++i k+  ipii+ G  +t+ d ++al+aGa++v+++
    EPA06105.1 104 AKIGKDYGIPIISDGGTRTSGDATKALAAGASSVMVG 140
                   6788999**************************9875 PP

>> QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00024      0.27      84     156 ..       4      78 ..       1      83 [. 0.77
   2 ?    0.1   0.0      0.54     6e+02      88     110 ..     121     143 ..     119     208 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00024
                 EEEESSHHHHHHHHHHT-SEEEEES--H..HHHHHHHHHHHHHSTTSEEEEESS-.-TTTHHHHHCTT-SEEEECH CS
   QRPTase_C  84 evevesleeleevleaeadiimLDnfsv..eelkkaveelkeknkrvlievSGgv.tlenveeyaksgvdvisvga 156
                  v  +++e +e  lea+ad+  +D  +   e+  +++  +k++ ++ ++  +G+v t +  e++ k gvd++ vg+
  EPA06105.1   4 GVKGDFMERTESLLEAGADVLVVDIAHGhsENALNTIRNIKKAFPKCEL-IAGNVaTAQGTEDLIKAGVDAVKVGV 78 
                 5777899*****************8754226666666666677776777.5688835677999********99986 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.54
                 SSHHHHHHHHHHT-SEEEEES-- CS
   QRPTase_C  88 esleeleevleaeadiimLDnfs 110
                 ++  +++++l+a+a+ +m+  + 
  EPA06105.1 121 RTSGDATKALAAGASSVMVGSML 143
                 56677888888888888877663 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00013      0.14      47     114 ..      16      80 ..       8      84 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
  B12-binding  47 iraekpdvvglSalltsqleavkelvellkrirprvkvvvGGahpsldpeetleaklgiddvvvgege 114
                  + +  +dv+++ +    + e++ ++++ +k++ p+  +++G ++     e++++   g+d v vg g 
   EPA06105.1  16 LLEAGADVLVVDI-AHGHSENALNTIRNIKKAFPKCELIAGNVATAQGTEDLIK--AGVDAVKVGVGS 80 
                  567789******9.****************************998888999887..899999888775 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.051        57      91     116 ..      10      39 ..       2      54 .. 0.76
   2 ?    5.8   0.0     0.014        16      95     146 ..      64     116 ..      47     121 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.051
                  HHHHHHHHHTT-SEEEEEEBSSSHH....H CS
                  xxxxxxxxxxxxxxxxxxxxxxxxx....x RF
  Radical_SAM  91 eeklerllelgvdrvslgleaadde....k 116
                   e  e lle+g d++ +++ ++++e    +
   EPA06105.1  10 MERTESLLEAGADVLVVDIAHGHSEnalnT 39 
                  688899*****************9944431 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.014
                  HHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEE CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM  95 erllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvv 146
                  e l ++gvd v +g+ +++   ++ +++ + + + +v+++ ++ +++gi+ ++
   EPA06105.1  64 EDLIKAGVDAVKVGVGSGSICITRVITGsGVPQLTAVMDCAKIGKDYGIPIIS 116
                  67999***************85555555989999***************9554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 1564.03
//
Query:       EPA06106.1  [L=97]
Description: hypothetical protein BG20_I2525, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-26   93.2   0.0    1.7e-26   93.0   0.0    1.0  1  ATP-sulfurylase  ATP-sulfurylase


Domain annotation for each model (and alignments):
>> ATP-sulfurylase  ATP-sulfurylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.0   0.0   9.4e-31   1.7e-26     122     211 ..       1      90 [.       1      91 [. 0.98

  Alignments for each domain:
  == domain 1  score: 93.0 bits;  conditional E-value: 9.4e-31
                      TTTT-STCSS-TTHHHHHHHHCHHHCTSEEEE---EEEETTTTEEEECCCC.GCCGGEEE--HHHHHCCHHTT----TTTS-HHHHHHHHH CS
  ATP-sulfurylase 122 rdhagvgdfYgpydaqellakvagelgiepvkfeeavYckkegevasektc.hkkeevesisgtelrkllregeeipewfsrpevlkvLre 211
                      rdhagvg+fY+p++aq+++++++ el+i pv+f  ++Yc+k+ ++++ k c h+++  e+isgt+lr+++ eg+ + e + rpev+kv+ e
       EPA06106.1   1 RDHAGVGTFYDPFAAQKIFDDYP-ELEIIPVFFPAFFYCRKCLTYTNPKACpHGDDAKEQISGTKLRQMIDEGKSPSEFILRPEVSKVILE 90 
                      9********************99.6**************************9999*********************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 621.50
//
Query:       EPA06107.1  [L=140]
Description: hypothetical protein BG20_I2524 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 924.94
//
Query:       EPA06108.1  [L=46]
Description: hypothetical protein BG20_I2523, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       204  (0.0113782); expected 358.6 (0.02)
Passed bias filter:                      148  (0.00825478); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.42
# Mc/sec: 327.07
//
Query:       EPA06109.1  [L=94]
Description: hypothetical protein BG20_I0643 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.32s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 567.85
//
Query:       EPA06110.1  [L=49]
Description: hypothetical protein BG20_I0653 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.098   12.8   0.1       0.14   12.4   0.1    1.3  1  DUF3493   Low psii accumulation1 / Rep27


Domain annotation for each model (and alignments):
>> DUF3493  Low psii accumulation1 / Rep27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   7.6e-06      0.14      11      36 ..      13      38 ..      10      49 .] 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.6e-06
     DUF3493 11 akaPfRglRlflYlafaaSaliGali 36
                + aPfR++ +f  ++++++a+iG+  
  EPA06110.1 13 VHAPFRKVVKFDLICIGIGAVIGMGA 38
                689********************865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 327.32
//
Query:       EPA06111.1  [L=56]
Description: hypothetical protein BG20_I0652 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.041   13.9   9.0      0.097   12.7   9.0    1.5  1  DZR             Double zinc ribbon
       0.12   12.3  11.3       0.74    9.8   8.7    2.0  2  zinc-ribbons_6  zinc-ribbons
       0.59    7.9   8.4       0.63    7.8   8.4    1.0  1  PolC_DP2        DNA polymerase II large subunit DP2
        1.4    9.3  13.2        1.2    9.5   9.7    2.1  2  C1_2            C1 domain


Domain annotation for each model (and alignments):
>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   9.0   2.2e-05     0.097       1      39 [.       6      38 ..       6      48 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.2e-05
         DZR  1 CpqCgeelppdarfCseCgtklkavaaedrCpsCgekvd 39
                C +Cg+e p+ a++C+ C ++++       C  C++ +d
  EPA06111.1  6 CRKCGKE-PSIAKYCDVCHQAIQ-----FECKICQKLTD 38
                7888887.888888888888887.....77888877655 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   8.7   0.00017      0.74      18      45 ..       5      33 ..       2      34 .. 0.86
   2 ?    5.1   1.4    0.0051        23      16      30 ..      27      41 ..      26      55 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00017
                    E-TTT--EEEEEEE-SSS-S---E.EEET CS
  zinc-ribbons_6 18 hCeaCqedlkkealCpeCeqelev.lkaC 45
                    +C++C ++ +  ++C+ C+q +++ +k C
      EPA06111.1  5 NCRKCGKEPSIAKYCDVCHQAIQFeCKIC 33
                    7*********************9635555 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0051
                    EEE-TTT--EEEEEE CS
  zinc-ribbons_6 16 qyhCeaCqedlkkea 30
                    q++C+ Cq+  +++ 
      EPA06111.1 27 QFECKICQKLTDEQI 41
                    577888877443332 PP

>> PolC_DP2  DNA polymerase II large subunit DP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   8.4   0.00014      0.63     618     667 ..       3      51 ..       1      55 [. 0.78

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00014
    PolC_DP2 618 rrkCkkCgke.tlearCeeCgekteeklvCkkceeeveeekcekcekeaka 667
                 + +C+kCgke ++ + C+ C + ++   +Ck c++ ++e+  +kc ++ ++
  EPA06111.1   3 TDNCRKCGKEpSIAKYCDVCHQAIQF--ECKICQKLTDEQIHSKCIAKRSK 51 
                 678****987488999****998877..99999998877777777766554 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.5     0.038   1.7e+02      19      27 ..       4      12 ..       2      18 .. 0.75
   2 ?    9.5   9.7   0.00027       1.2      14      47 .]      12      46 ..       9      46 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.038
        C1_2 19 fnCsaCgrk 27
                 nC+ Cg++
  EPA06111.1  4 DNCRKCGKE 12
                69****998 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00027
        C1_2 14 dssesfnCsaCgrkidgffYsCseC....dfslhvrCa 47
                + s+ + C++C + i   +++C++C    d ++h++C+
  EPA06111.1 12 EPSIAKYCDVCHQAI---QFECKICqkltDEQIHSKCI 46
                5678899*******8...589999854445999*9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1006  (0.0561102); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 359.29
//
Query:       EPA06112.1  [L=133]
Description: methionine-R-sulfoxide reductase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.5e-55  185.3   0.3    3.9e-55  185.1   0.3    1.0  1  SelR          SelR domain
      0.005   17.0   3.0      0.015   15.5   2.2    2.0  2  Yippee-Mis18  Yippee zinc-binding/DNA-binding /Mis18, centrom
     0.0071   15.2   1.2        0.7    8.7   0.1    2.0  2  HECT_2        HECT-like Ubiquitin-conjugating enzyme (E2)-bin
  ------ inclusion threshold ------
       0.22   11.5   4.3        1.4    9.0   0.7    2.5  2  ADK_lid       Adenylate kinase, active site lid
       0.24   11.9   2.5          5    7.6   0.1    2.1  2  DUF983        Protein of unknown function (DUF983)


Domain annotation for each model (and alignments):
>> SelR  SelR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.1   0.3   1.1e-58   3.9e-55       1     119 [.      11     128 ..      11     130 .. 0.98

  Alignments for each domain:
  == domain 1  score: 185.1 bits;  conditional E-value: 1.1e-58
                 HHHCTSHCCHHHHHHHTT-SSTTSSSTSS--SSCEEEETTTS-EEEECCCCE-STTSSSEESS-STTTTEEEEEEECTTSEEEEEEETTCECEEEEEEC CS
        SelR   1 elkkkLtpeqyevlrekgterpftgeyekekekGvyecavcgepLfssetkfdsgcGwpsFaeaikeeavkekkdtslgmertevvcakcdahlGhvFe 99 
                 e+k+ Ltp+qyev+ +kgte+pf+g+y+++ke+G+y+c +cge+Lf+s+tk+dsg+GwpsF++++++e++++ +d s+gm rtev c+kc+ahlGhvF+
  EPA06112.1  11 EWKEVLTPDQYEVCINKGTEPPFSGKYYNTKETGTYKCSCCGEELFKSDTKYDSGSGWPSFWKPLADEKIEYITDDSYGMIRTEVNCKKCGAHLGHVFD 109
                 7************************************************************************************************** PP

                 TSSSSS.SEEEEE-CCCEEE CS
        SelR 100 dgpkpttgkrycinsvslkf 119
                 dgpkpt ++rycinsvsl++
  EPA06112.1 110 DGPKPT-NLRYCINSVSLEL 128
                 ****95.***********87 PP

>> Yippee-Mis18  Yippee zinc-binding/DNA-binding /Mis18, centromere assembly
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   1.3      0.37   1.3e+03      55      64 ..      45      54 ..       3      58 .. 0.70
   2 !   15.5   2.2   4.3e-06     0.015      45      88 ..      84     129 ..      44     132 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.37
                  EEEETTT--E CS
  Yippee-Mis18 55 tlsCkgCnsv 64
                  t +C+ C+++
    EPA06112.1 45 TYKCSCCGEE 54
                  4566666655 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 4.3e-06
                   ETTSTTEEEEEEEETTT--EEEEEEEECSCC..CCCCCTCEEEEGG CS
  Yippee-Mis18  45 tdeegkctystlsCkgCnsvlGwkYksteee..lkykrglfiletk 88 
                   td++   + ++++Ck+C+++lG ++ + ++   l+y+++   le +
    EPA06112.1  84 TDDSYGMIRTEVNCKKCGAHLGHVFDDGPKPtnLRYCINSVSLELD 129
                   33333377899***************99876569999999999877 PP

>> HECT_2  HECT-like Ubiquitin-conjugating enzyme (E2)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.1    0.0011       3.8     101     132 ..      30      64 ..       6      86 .. 0.68
   2 !    8.7   0.1   0.00019       0.7     210     242 ..      92     127 ..      78     133 .] 0.73

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0011
      HECT_2 101 evpWsakdlsa.e.tslrCrsCknvllks.rkikr 132
                 e p s k  ++ e  + +C++C+++l+ks +k+  
  EPA06112.1  30 EPPFSGKYYNTkEtGTYKCSCCGEELFKSdTKYDS 64 
                 457777877776458899**********9555555 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00019
      HECT_2 210 eeslsCkrCkatlGeeds...aaegvkLfkwnvslq 242
                 ++++ Ck+C+a+lG++     +   ++    +vsl+
  EPA06112.1  92 RTEVNCKKCGAHLGHVFDdgpKPTNLRYCINSVSLE 127
                 789***********9765555444477777777666 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.7   0.00038       1.4       7      32 ..      34      56 ..      31      59 .. 0.73
   2 ?    3.4   0.2     0.022        77       4      10 ..      97     103 ..      95     117 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00038
                T--EEETTTB--SSTTB-TTT--.-B CS
     ADK_lid  7 CGrsYhvvfnpPkveglCDkCGepLv 32
                +G+ Y+ +        +C +CGe+L+
  EPA06112.1 34 SGKYYNTKE---TGTYKCSCCGEELF 56
                677777332...45669*******97 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.022
                 -TTT--E CS
     ADK_lid   4 CpkCGrs 10 
                 C+kCG+ 
  EPA06112.1  97 CKKCGAH 103
                 8899874 PP

>> DUF983  Protein of unknown function (DUF983)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.4     0.015        52      10      24 ..      47      61 ..      43      66 .. 0.84
   2 ?    7.6   0.1    0.0014         5       5      27 ..      91     112 ..      88     123 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.015
      DUF983 10 aCeaCgldlsharad 24
                +C+ Cg++l + ++ 
  EPA06112.1 47 KCSCCGEELFKSDTK 61
                8********998876 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0014
      DUF983   5 LkvadaCeaCgldlsharaddgP 27 
                 ++++ +C++Cg++l+h   ddgP
  EPA06112.1  91 IRTEVNCKKCGAHLGHV-FDDGP 112
                 667889********986.45555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 914.50
//
Query:       EPA06113.1  [L=45]
Description: hypothetical protein BG20_I0631 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0036   17.0   3.0     0.0047   16.7   3.0    1.4  1  Ephrin_rec_like  Putative ephrin-receptor like


Domain annotation for each model (and alignments):
>> Ephrin_rec_like  Putative ephrin-receptor like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   3.0   2.6e-07    0.0047       8      38 ..       3      32 ..       1      41 [. 0.82

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.6e-07
  Ephrin_rec_like  8 letCipCprgtYqneegqlsClaCPlgtttk 38
                     + +C +C +g++ ++ g  +C++C  + +  
       EPA06113.1  3 NMKCVSCGIGFFSPT-GADKCSRCAGQASEG 32
                     679*********996.899*****9776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      169  (0.00942607); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 303.80
//
Query:       EPA06114.1  [L=37]
Description: hypothetical protein BG20_I0640 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.49
# Mc/sec: 227.42
//
Query:       EPA06115.1  [L=283]
Description: tRNA methyltransferase complex GCD14 subunit [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-35  123.0   0.1    3.7e-35  121.8   0.1    1.5  1  GCD14            tRNA methyltransferase complex GCD14 subunit
    2.8e-09   37.0   0.1    3.9e-09   36.6   0.1    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    1.3e-08   34.8   0.0    1.9e-08   34.2   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    1.1e-06   28.2   0.1    1.8e-06   27.5   0.1    1.4  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    3.3e-06   27.7   0.0    6.2e-06   26.8   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    7.9e-05   23.6   0.0    0.00019   22.4   0.0    1.6  1  Methyltransf_24  Methyltransferase domain
    0.00015   21.3   0.0    0.00019   20.9   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    0.00025   20.8   0.0    0.00045   20.0   0.0    1.4  1  Methyltransf_16  Lysine methyltransferase
     0.0003   21.5   0.0    0.00094   19.9   0.0    1.9  1  Methyltransf_12  Methyltransferase domain
    0.00039   19.6   0.0     0.0006   19.0   0.0    1.4  1  Fibrillarin      Fibrillarin
    0.00039   19.7   0.1    0.00058   19.1   0.1    1.2  1  Methyltransf_3   O-methyltransferase
     0.0004   21.0   0.0    0.00083   20.0   0.0    1.6  1  Methyltransf_11  Methyltransferase domain
    0.00046   19.3   0.0    0.00078   18.6   0.0    1.3  1  RrnaAD           Ribosomal RNA adenine dimethylase
     0.0005   19.8   0.0    0.00079   19.1   0.0    1.4  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
      0.002   17.7   0.0     0.0046   16.5   0.0    1.7  1  MTS              Methyltransferase small domain
     0.0074   16.1   0.7      0.021   14.7   0.0    2.0  2  GCD14_N          tRNA methyltransferase complex GCD14 subunit
  ------ inclusion threshold ------
      0.019   14.9   0.0      0.034   14.1   0.0    1.6  1  Methyltransf_18  Methyltransferase domain
      0.023   14.0   0.0      0.038   13.3   0.0    1.3  1  CMAS             Mycolic acid cyclopropane synthetase
      0.023   14.4   0.0      0.035   13.9   0.0    1.2  1  DUF938           Protein of unknown function (DUF938)
        0.1   12.3   0.0       0.18   11.4   0.0    1.4  1  UPF0020          Putative RNA methylase family UPF0020
       0.17   11.7   0.0       0.23   11.3   0.0    1.4  1  Methyltransf_23  Methyltransferase domain


Domain annotation for each model (and alignments):
>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.8   0.1   4.3e-38   3.7e-35       1     190 [.      57     243 ..      57     280 .. 0.90

  Alignments for each domain:
  == domain 1  score: 121.8 bits;  conditional E-value: 4.3e-38
       GCD14   1 gfvyvlaptPeLWtlaLphrtqilytaDisliimkLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvtvthr 99 
                 ++vy+++pt   + ++L+h tqi+y +Di  ii +  +  G +++e GtGsgsl++ +a  v+P+Gh++tf+  ++ ++ a ++ ++ ++s++vt ++ 
  EPA06115.1  57 KYVYLIEPTMYDYVMKLQHGTQIVYPKDIGYIIARAGIGSGQKILEIGTGSGSLTSFVASVVKPRGHVYTFDVDDNFMKIAEKNIKKAGMSKYVTQQKL 155
                 69************************************************************************************************* PP

       GCD14 100 DvckeGfdeevsgkvDavfLDlPaPweaiphaakalkkeggrlCsfsPCieqvqrtceaLrelgfteietlevllrtyevrkskleeidla 190
                 D+     +  + +++D  ++Dl  Pw  +p++ k+lk + g + +  P ++q+ + + aL e +ft+ie+ e  +rt e+r+ k +++  +
  EPA06115.1 156 DIKIAK-KMPI-EEADVALIDLGDPWTVLPQVRKMLKGS-GSVFAICPTMNQLEKLTIALVENEFTDIESTEHIIRTIEAREGKTRHSFQG 243
                 **8543.3466.889*********************655.5566899**********************************9998876555 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.1   4.6e-12   3.9e-09      43     125 ..      66     148 ..      21     161 .. 0.89

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 4.6e-12
                 TSSS-EEEETTEEE--HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCS CS
        PCMT  43 YedaplsigynatiSaphmvalalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlen 125
                   d +++++ ++ i  p+ +++++    +  g+++Le+G+GsG lt  +a +v+++g+v + +   ++++ a++n+kk ++++
  EPA06115.1  66 MYDYVMKLQHGTQIVYPKDIGYIIARAGIGSGQKILEIGTGSGSLTSFVASVVKPRGHVYTFDVDDNFMKIAEKNIKKAGMSK 148
                 4478999***********************************************************************99984 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.0   2.3e-11   1.9e-08       2     127 ..      95     218 ..      94     245 .. 0.77

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 2.3e-11
  Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieelekl.ledekfDlilsnevlnaladpdki 93 
                       +g ++l++G+G+G lt   a+ + p+++v+ +D + +  + A++n +k g +  v+ ++ di  ++k  +e    D+     +l +l dp  +
       EPA06115.1  95 GSGQKILEIGTGSGSLTSFVASVVKPRGHVYTFDVDDNFMKIAEKNIKKAGMSkYVTQQKLDIKIAKKMpIE--EADV-----ALIDLGDPWTV 181
                      57899***********************************************94555555899887765566..5999.....56689999999 PP

  Methyltransf_31  94 leeiervlkpggilliedprllaelp....akveeesk 127
                      l ++ + lk  g + +  p  + +l     a ve+e +
       EPA06115.1 182 LPQVRKMLKGSGSVFAICPT-MNQLEkltiALVENEFT 218
                      99999999977766655444.55555433444444444 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.1   2.1e-09   1.8e-06      39     153 ..      88     199 ..      55     217 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 2.1e-09
                      HHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES-GGG-S-H CS
  Ubie_methyltran  39 veklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtvsfGlrnvtDk 132
                      ++ + +  +g+k+l++ +G+g l+  +++ v+ +g+v   D+++n +k++ek +k+ g+++  +++ +  +++  +  + +      l ++ D 
       EPA06115.1  88 IIARAGIGSGQKILEIGTGSGSLTSFVASVVKPRGHVYTFDVDDNFMKIAEKNIKKAGMSK--YVTQQKLDIKIAK-KMPIEEADVALIDLGDP 178
                      5666777899************************************************983..5554444444333.22333333445566688 PP

                      HHHHHHHHHHEEEEEEEEEEE CS
  Ubie_methyltran 133 lkaLkeayrvlkpGGrlvvle 153
                       ++L +++++lk  G ++ + 
       EPA06115.1 179 WTVLPQVRKMLKGSGSVFAIC 199
                      888888888888888887764 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.0   7.3e-09   6.2e-06       1      68 [.     100     171 ..     100     196 .. 0.75

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 7.3e-09
                      EEEET-TTSHHHHHHHCTS.TSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBC...CGBSSSTTTEEEE CS
  Methyltransf_25   1 vLdlGcGtGrltlalakrl.gkakvtgvDiseemleaareraeeegl..nvefvqgda...edlpfedgsfDlv 68 
                      +L++G+G+G lt  +a  + ++++v+ +D++++++++a+++++++g+   v+ ++ d+   +++p e++   + 
       EPA06115.1 100 ILEIGTGSGSLTSFVASVVkPRGHVYTFDVDDNFMKIAEKNIKKAGMskYVTQQKLDIkiaKKMPIEEAD--VA 171
                      8****************99659**********************99976555566665444556665544..43 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   2.2e-07   0.00019       1      88 [.     101     185 ..     101     197 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 2.2e-07
  Methyltransf_24   1 vEiGvysGvstlwllralrrngagrlvavdhdpgaeeaaalare....aglddrvrlikadseealaslaagsiDllfiDgghaaeavledl 88 
                      +EiG+ sG  t ++++ ++ +g  +++++d d    +++++a++    ag++++v++ k d + a +++  ++ D+++iD g +  +vl+ +
       EPA06115.1 101 LEIGTGSGSLTSFVASVVKPRG--HVYTFDVDD---NFMKIAEKnikkAGMSKYVTQQKLDIKIA-KKMPIEEADVALIDLG-DPWTVLPQV 185
                      7********************9..59*****99...777777766666********999988777.6666699*******98.555555544 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   2.2e-07   0.00019     161     229 ..      96     170 ..      90     225 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.2e-07
        PrmA 161 egeevlDvGtGSGiLa..iaaakLgakkvvavDiDevAvkvakeNaelNkveaklev.....alseellkeekadv 229
                 +g+++l +GtGSG L+  +a++     +v+  D+D+  +k+a++N+++ ++++ ++      +++++++  e+adv
  EPA06115.1  96 SGQKILEIGTGSGSLTsfVASVVKPRGHVYTFDVDDNFMKIAEKNIKKAGMSKYVTQqkldiKIAKKMPI-EEADV 170
                 5789*********99766777777889*********************9888755321011023333333.55555 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   5.3e-07   0.00045      46     115 ..      96     163 ..      69     176 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 5.3e-07
  Methyltransf_16  46 sklsvlELGsGtGlvGlavaell.peakviltDlee.llellkknielnknalkskvkvevLdWgeeleedl 115
                      s++++lE+G G+G     va+ + p+ +v+  D+++  +++ +kni+   + +++ v+ ++Ld   ++ +++
       EPA06115.1  96 SGQKILEIGTGSGSLTSFVASVVkPRGHVYTFDVDDnFMKIAEKNIKK--AGMSKYVTQQKLDI--KIAKKM 163
                      6789*********99999999977**********98799*********..55********9987..444444 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   1.1e-06   0.00094       1      93 [.     101     189 ..     101     195 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.1e-06
  Methyltransf_12   1 LeiGcGtGsllrallekl.pdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlkdirevldnirklL 93 
                      LeiG+G+Gsl++ ++    p+ +++  D++ ++++ a++ ++k +  +    +  ++ ++++ + +  D+ ++      l d+  vl ++rk+L
       EPA06115.1 101 LEIGTGSGSLTSFVASVVkPRGHVYTFDVDDNFMKIAEKNIKKAGMSKYVTQQKLDIKIAKKMPIEEADVALI-----DLGDPWTVLPQVRKML 189
                      8**************9999***************999999998887665555555555555555577777654.....3455555555555555 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0     7e-07    0.0006      65     109 ..      91     135 ..      83     178 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 7e-07
                  --S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHHHH CS
  Fibrillarin  65 elpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprvlr 109
                  +  i +g+k+L +G++sG+  s v+ +v+++g vy+ ++ +  ++
   EPA06115.1  91 RAGIGSGQKILEIGTGSGSLTSFVASVVKPRGHVYTFDVDDNFMK 135
                  567889******************************998887765 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.1   6.8e-07   0.00058      48     104 ..      97     153 ..      73     175 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 6.8e-07
                     --EEEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHHHTT-GGGEEEE CS
  Methyltransf_3  48 akrvleiGvftGyslLatalalPeDGkilaididreayeialkfiqkagvaekieli 104
                      +++leiG+  G     +a  + + G++ + d+d + ++ia k i+kag+ + +  +
      EPA06115.1  97 GQKILEIGTGSGSLTSFVASVVKPRGHVYTFDVDDNFMKIAEKNIKKAGMSKYVTQQ 153
                     6789*******9988899*******************************98766544 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   9.7e-07   0.00083       1      64 [.     101     170 ..     101     197 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 9.7e-07
                      EEET-TTSHHHHHHHHTT...SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECC...CTSS-TT-EEE CS
  Methyltransf_11   1 LdvGcGtGrlaealakrg...arvvgvDlskemlklakekaseegl..kvefvvadae...klpfednsfDl 64 
                      L++G+G+G+l+  +a+ +   ++v+++D++++++k+a+++++++g+   v+ ++ d++   k+p+e+   D+
       EPA06115.1 101 LEIGTGSGSLTSFVASVVkprGHVYTFDVDDNFMKIAEKNIKKAGMskYVTQQKLDIKiakKMPIEE--ADV 170
                      89*************6656679***********************9774444555555332455544..444 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   9.2e-07   0.00078      19      93 ..      85     162 ..      76     174 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 9.2e-07
                 HHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-...SEEEEE-S-HHHHHHHHCHTTTCCCEEEE-S-CCGHHHHHH CS
      RrnaAD  19 ineIldklnleekltvleigpGkGilTeeLakra...kqvvvlElderLakllqkklskdeklkvvhqDflkfetpee 93 
                 i  I+  + +   +++leig+G G lT  +a  +    +v  +  d +++k+ +k+++k++ +k v q  l+ ++ ++
  EPA06115.1  85 IGYIIARAGIGSGQKILEIGTGSGSLTSFVASVVkprGHVYTFDVDDNFMKIAEKNIKKAGMSKYVTQQKLDIKIAKK 162
                 566899999999****************999999884566789******************99999999988887775 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   9.2e-07   0.00079       9      86 ..      97     174 ..      94     215 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 9.2e-07
                      T-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--S.EEEEES-CTCCHHHHCC..EEEEEEE CS
  Methyltr_RsmB-F   9 eetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtn.tivleaDarkidkvlggelfDriLlD 86 
                      +++il++ ++ G+ T+++a ++k++g+v+  d++++ +k  ++n+k+ g+ + ++  + D++  +k+  +   D +L+D
       EPA06115.1  97 GQKILEIGTGSGSLTSFVASVVKPRGHVYTFDVDDNFMKIAEKNIKKAGMSKyVTQQKLDIKIAKKMPIE-EADVALID 174
                      688***********************************************95144456788888777775.77888877 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   5.3e-06    0.0046      32      90 ..      97     156 ..      88     225 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.3e-06
                 CSEEEEET-TTSHHHHHHHHH.TTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STT CS
         MTS  32 sgkvlDlGcGaGvlgaalake.speaevtlvdvdarAlesakenleanklevevvasdvl 90 
                  +k+l +G+G G l+  +a+  +p+ +v  +dvd + +++a++n+++ +++  v+++ + 
  EPA06115.1  97 GQKILEIGTGSGSLTSFVASVvKPRGHVYTFDVDDNFMKIAEKNIKKAGMSKYVTQQKLD 156
                 578***********9998875278889*********************999776666555 PP

>> GCD14_N  tRNA methyltransferase complex GCD14 subunit N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   2.5e-05     0.021      21      49 ..      21      49 ..      15      50 .. 0.83
   2 ?   -2.2   0.1       4.4   3.7e+03      21      36 ..     229     244 ..     224     246 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.5e-05
     GCD14_N 21 titLepGgefhthrGaieHDdlIGrpeGs 49
                 +   +  + hth G+i+H d IG++ Gs
  EPA06115.1 21 LVKISKKDSLHTHIGVIKHADAIGKEYGS 49
                5666777899***************9886 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4.4
     GCD14_N  21 titLepGgefhthrGa 36 
                 ti  ++G++ h+ +G+
  EPA06115.1 229 TIEAREGKTRHSFQGI 244
                 7888899999999885 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0     4e-05     0.034      12      70 ..      94     153 ..      88     227 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4e-05
  Methyltransf_18  12 vekgsrvaDiGtDHgylpiylvke.gkakkviasDinegplekakeniekagledkievr 70 
                      + +g++++ iGt  g l+ ++++  +   +v+  D+ ++ ++ a++ni+kag+++ ++  
       EPA06115.1  94 IGSGQKILEIGTGSGSLTSFVASVvKPRGHVYTFDVDDNFMKIAEKNIKKAGMSKYVTQQ 153
                      567899***********9998875155679***********************9987654 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   4.5e-05     0.038      53     119 ..      87     155 ..      78     169 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.5e-05
                 HHHTTTT--TT-EEEEES-TTSHHHHHHHH..HH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES CS
        CMAS  53 lileklelkpGmtlLdiGcGWGslvrrave..rydvkvvglTlSkeqaklakkrvdeldlerkvevkll 119
                  i+ ++++  G+++L+iG+G Gsl+   ++  +   +v    + ++ +k a+k+++++++++ v+ + l
  EPA06115.1  87 YIIARAGIGSGQKILEIGTGSGSLTSFVASvvKPRGHVYTFDVDDNFMKIAEKNIKKAGMSKYVTQQKL 155
                 567788999**************98765541155788999999****************9988776655 PP

>> DUF938  Protein of unknown function (DUF938)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   4.1e-05     0.035      26      87 ..      97     159 ..      85     176 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.1e-05
      DUF938  26 tervLEiasGtGqHAvffApalpnlkwq.psdqdeelresiaawadelalsnlkpPleldvta 87 
                 ++++LEi++G+G    f A+ ++++ +  + d+d++ ++  ++ ++++++s   +  +ld++ 
  EPA06115.1  97 GQKILEIGTGSGSLTSFVASVVKPRGHVyTFDVDDNFMKIAEKNIKKAGMSKYVTQQKLDIKI 159
                 457*******************99876527799999987667788888888877776666653 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00022      0.18      75     113 ..     120     158 ..      94     177 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00022
                 HH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GG CS
     UPF0020  75 aelklygsDldrrvvqgareNaekagvgdliefsqadaa 113
                 ++ ++y +D d + ++ a++N +kag+++ ++++++d++
  EPA06115.1 120 PRGHVYTFDVDDNFMKIAEKNIKKAGMSKYVTQQKLDIK 158
                 455699*****************************9987 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00027      0.23      22      62 ..      96     145 ..      78     235 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00027
  Methyltransf_23  22 aggrvLdiGcGtGillevlrengf...svtgvDlspeaveiae......k 62 
                      +g+++L+iG+G+G+l++  +  ++   +v+ +D +++  +iae      +
       EPA06115.1  96 SGQKILEIGTGSGSLTSFVASVVKprgHVYTFDVDDNFMKIAEknikkaG 145
                      6789**********999887776667788888888887777776454442 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 1807.46
//
Query:       EPA06116.1  [L=262]
Description: hypothetical protein BG20_I0660, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.24   12.0   0.1       0.24   12.0   0.1    3.8  3  PQQ_3     PQQ-like domain


Domain annotation for each model (and alignments):
>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   2.9     0.046   8.3e+02      10      37 ..      46      75 ..      40     111 .. 0.80
   2 ?   -1.1   0.2      0.17     3e+03      20      25 ..     143     148 ..     126     162 .. 0.59
   3 ?   12.0   0.1   1.3e-05      0.24      14      40 .]     187     214 ..     178     214 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.046
       PQQ_3 10 pgpvnsspavdgglvyvgtg..dGtlyAlD 37
                p+ +++++a+dg ++  +++     ly  D
  EPA06116.1 46 PSSIGTGVAFDGTHLWYSCYasTPDLYKAD 75
                778889999999999888876655555444 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.17
       PQQ_3  20 dgglvy 25 
                 d+gl y
  EPA06116.1 143 DDGLAY 148
                 344433 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 1.3e-05
       PQQ_3  14 nsspavdgglvyvgtg.dGtlyAlDaet 40 
                 ns++a++g+l++ g+    ++y +D +t
  EPA06116.1 187 NSGLAIGGNLLFQGSNgCAHVYVVDKTT 214
                 6899*********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1731.29
//
Query:       EPA06117.1  [L=287]
Description: YjeF C-terminal domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-47  162.3   0.5    1.5e-47  162.1   0.5    1.0  1  Carb_kinase    Carbohydrate kinase
    1.3e-09   37.8   0.1    2.3e-09   37.0   0.1    1.3  1  HK             Hydroxyethylthiazole kinase family
    1.2e-05   24.9   0.1    1.6e-05   24.4   0.1    1.2  1  Phos_pyr_kin   Phosphomethylpyrimidine kinase
  ------ inclusion threshold ------
       0.17   12.0   0.0       0.26   11.4   0.0    1.4  1  Cation_ATPase  Cation transport ATPase (P-type)


Domain annotation for each model (and alignments):
>> Carb_kinase  Carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.1   0.5   3.4e-51   1.5e-47       1     242 [.      30     276 ..      30     278 .. 0.91

  Alignments for each domain:
  == domain 1  score: 162.1 bits;  conditional E-value: 3.4e-51
                  EEEEE-BTTCHHHHHHHHHHHHCTT-SEEEEEESSTTTCCCCTTTTTCEECCTT.....HTTTS...--S....SS-SEEEE-TT-SSSHCHHH..HC CS
  Carb_kinase   1 vlvigGsedytGAallaalaalrlgaglvsvateseaiavlksylpevivhpll.....edeqakilekl....erldavviGpGLgrdekikk..ll 87 
                  vlvigGs+ y GA++l+ +aalr g++lv   + + ++++  + +p++iv pl      ++    ++++l    ++ld   iG+GL  +e++    l+
   EPA06117.1  30 VLVIGGSYIYHGAPILSSIAALRCGVDLVYTSVPKVNVTPTRAVSPNLIVIPLVdqkltRG---AVNKLLgalpHKLDSATIGMGLAVQERGSLllLI 124
                  79***************************************************96544322...3344332223789**************9888899 PP

                  HHHCCCCS-EEEEGGGGGSGGGG...TTTTSSEEEE--HHHHHHHCTTTCH.HCCSHHHHHHHHHHHHTTEEEEESTTSEEEECTTEEEEE----GGG CS
  Carb_kinase  88 eevlekdeplviDAdgLnllaqknelserkaeviLTPhkkEfkrLlkaivk.keddrlelarelaqklnavvllkgekdvivspegevlinstgssal 184
                  +  l++d+ l +DA++L           ++++v+ TPh++EfkrL++ +   ++++r  l++++a+  + +vllkg+ dvi + +  +++n++ ++++
   EPA06117.1 125 KTLLDRDVRLSLDASALVPDVLP---LLPNKNVVVTPHAGEFKRLFGTAPPnSKKERIALVEKNAKDNGITVLLKGATDVISD-GTTTYLNEKKTPGM 218
                  99***************865554...899*****************98876599999**********************9988.999*********** PP

                  -STTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHHHHHHHHHCCCT-TS-HCHHHHHHH CS
  Carb_kinase 185 akGGsGDvLaGligalLaqneasyeaaiaaawlhgaasdeaaekkgvgmlatelskii 242
                  ++GG+GDvL+Gl++++L+ n++++e a+aa++++g a+++ ++k g+ m++ +l++++
   EPA06117.1 219 TVGGTGDVLSGLVAGMLSKNRNALECAAAATFINGMAGKATQKKFGLHMTSMDLLDEL 276
                  *****************************************************99987 PP

>> HK  Hydroxyethylthiazole kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.1     5e-13   2.3e-09     137     242 ..     175     278 ..     161     281 .. 0.92

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 5e-13
                 SHHHHHHHHHHHHHHTSEEEEESSSEEEEESSEEEEEE-S-GGGGGSTTHHHHHHHHHHHHHTTBSSHHHHHHHHHHHHHHHH.HHHHHHHTTHHHHHH CS
          HK 137 ataavaavqkvAqklrvvvvvtGevDvvsdgkkvyklknGtellgkitasGCllgsvvaaflavkkdkllaaveavllykvAgkeaaarsegsgsFqve 235
                 +++ +a v+k A+  +++v++ G++Dv+sdg+++y  +  t+ ++ + ++G +l+  va +l+ ++++l+ a++a+ +  +Ag +a++++ g     + 
  EPA06117.1 175 KKERIALVEKNAKDNGITVLLKGATDVISDGTTTYLNEKKTPGMT-VGGTGDVLSGLVAGMLSKNRNALECAAAATFINGMAG-KATQKKFGLHMTSMD 271
                 555799******************************999999997.9************************************.788888899889999 PP

                 HHHHHHH CS
          HK 236 lldalsq 242
                 lld+l++
  EPA06117.1 272 LLDELAN 278
                 9999975 PP

>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.1   3.7e-09   1.6e-05     118     230 ..     151     253 ..     135     268 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 3.7e-09
                   GG-SEEE-BHHHHHHHHT.---SSHHHHHHHHHHHHHTT-SEEEEEEGGS-SSSEEEEEEEETSSEEEEEEEE----S--BTHHHHHHHHHHHHHHC CS
  Phos_pyr_kin 118 platvitPNlpEaeaLlg.ekikteedmkeaakkllklgakaVlikGghlegeeavvtdvlydgeeveeleaerietknthGtGCtlssaiaaelak 213
                   ++  v+tP   E ++L g  + +++++  +  +k +k +  +Vl+kG           dv+ ++++++ l++++++  +  GtG++ls  +a+ l+k
    EPA06117.1 151 NKNVVVTPHAGEFKRLFGtAPPNSKKERIALVEKNAKDNGITVLLKGAT---------DVI-SDGTTTYLNEKKTPGMTVGGTGDVLSGLVAGMLSK 237
                   456789************878889999999999999999999*****86.........666.566678888899999******************** PP

                   TSSHHHHHHHHHHHHHH CS
  Phos_pyr_kin 214 gesleeAvkkAkeyvte 230
                   +++  e  +   ++++ 
    EPA06117.1 238 NRNALECAAA-ATFING 253
                   *999887654.456655 PP

>> Cation_ATPase  Cation transport ATPase (P-type)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   5.7e-05      0.26      45      89 ..     162     207 ..     120     209 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.7e-05
  Cation_ATPase  45 etkkv.qeipFnssrKrmsvvlklepekkvrlyvKGApeiilkrCt 89 
                    e+k++  + p ns++ r + v k+ ++++++++ KGA ++i +  t
     EPA06117.1 162 EFKRLfGTAPPNSKKERIALVEKNAKDNGITVLLKGATDVISDGTT 207
                    5566534678899999999999999****************87655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1848.84
//
Query:       EPA06118.1  [L=45]
Description: hypothetical protein BG20_I0623 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.30s 00:00:00.69 Elapsed: 00:00:00.46
# Mc/sec: 296.83
//
Query:       EPA06119.1  [L=639]
Description: acetate--CoA ligase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-95  320.6   0.0    1.5e-95  320.3   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    6.6e-25   87.9   0.3    2.4e-24   86.1   0.1    1.9  2  AMP-binding_C  AMP-binding enzyme C-terminal domain
    8.3e-15   54.4   6.4    2.4e-14   53.0   6.4    1.8  1  ACAS_N         Acetyl-coenzyme A synthetase N-terminus


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  320.3   0.0   2.5e-99   1.5e-95       5     422 ..      70     504 ..      66     505 .. 0.87

  Alignments for each domain:
  == domain 1  score: 320.3 bits;  conditional E-value: 2.5e-99
                  HHHSTTSEEEEE...CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-HHHHHHHHHHHTESEEE CS
  AMP-binding   5 aaktpdkvalvd...sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptltaeelayiledseakvli 99 
                   + + dk+a+ +   +ge + lTY++++ +v++lA++L+slGv+kgdrV i+lp+ pe+ +++la++++Ga++ ++ ++++a +++  ++ds++kv+i
   EPA06119.1  70 QKDKSDKPAILWegeNGESKILTYKDMWVQVQKLANVLKSLGVQKGDRVTIYLPMIPELPISMLACARIGATHTVIFSGFSASAIKDRIDDSKSKVVI 167
                  56678*****99***99********************************************************************************* PP

                  .......E.TCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS......-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEHH CS
  AMP-binding 100 .......a.tvdsel.leklleaaakleavklvivldadellkeeelkeeeeseekae......kpeeeeelkpddlayiiYTSGTTGkPKGVmlshr 182
                         +     +   e ++ea ++ ++vk viv+++ + + +  +k+   ++          + +++e+l++ ++++i+YTSGTTGkPKGV + ++
   EPA06119.1 168 tadggyrRgS--VISlKEIIDEAIKDSKSVKNVIVVERTKTKIKMSSKDLF-WN---AlldnasDICPPEKLDSTHPLFILYTSGTTGKPKGVLHGTG 259
                  9998875242..344445556666667889999999987765543333322.22...12345667889999**************************7 PP

                  HHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGC.CHHHHHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHHCHHH CS
  AMP-binding 183 nlvanvaslkletrfklkeddvvlsilplahifglilelllallsGatvvllpkdaa.ldpklllelieklkvtviagvPrvlealle.sgalkaakk 278
                   +++ ++s  ++  f++k++dv+++++++ +++g+++ ++++ll+Gat v++++ ++ +d+ ++++ ++k+kvt+++++P++l+++++  +++    +
   EPA06119.1 260 GYLTHLHST-FKWAFDIKDSDVYFCTADIGWVTGHSYVVYAPLLHGATQVMYEGAPDfPDASRMWNILHKYKVTIFYTTPTALRMFMRfGDDIP---N 353
                  777776775.444488899**************************************88899999***********************887777...3 PP

                  HCCGTT-SEEEEESS-EBHHHHHHHHHHHTC...EEEEEEEEGGGSSECEE..CHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEE CS
  AMP-binding 279 akdlsslrlvllggeplspellrffralfge...evlegYGlTEttgvvtv..lpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrg 371
                  + dlsslrl+ ++gep++pe+++++ ++ g+   ++++++++TEt+g+++   + le+   k+gs  +p+pg ++ +vD++ g+ v  +++G l+++ 
   EPA06119.1 354 SFDLSSLRLLGSVGEPINPEVWKWYFKIIGKekcPIIDTWWQTETGGMLISalPGLETIPLKPGSGTRPIPGLQISVVDDD-GKDVSANTKGYLVIKN 450
                  45***************************99******************555433333334567777*************9.9*************** PP

                  T..TS-SEBTT-HHHHHHHEEET.CCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
  AMP-binding 372 p..gvmkgYlkkpeataeafdse.grwlrTGDlgrldedGyleivgRkkdlikl 422
                  p  g+    ++++++ +++++s+ ++++  GD +  d dGyl+++gR++d++k+
   EPA06119.1 451 PwpGMLLTLWGDDKKYRDVYWSKyKDCYYPGDYALKDSDGYLWLLGRADDVLKV 504
                  9778*****************87888**************************98 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.74   4.4e+03       2      19 ..     185     202 ..     166     210 .. 0.72
   2 !   86.1   0.1     4e-28   2.4e-24       1      76 []     513     592 ..     513     592 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.74
                    HHHHHHSSTTEEEEEEE- CS
  AMP-binding_C   2 vEsalvshpaVaeaaVvG 19 
                    + +a+  ++ V+++ Vv 
     EPA06119.1 185 IDEAIKDSKSVKNVIVVE 202
                    456666677777777773 PP

  == domain 2  score: 86.1 bits;  conditional E-value: 4e-28
                    HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE------....HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
  AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgsea....leeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                    e+Es++vshp+Vae aV G+pd++kGe++++f vlk+++++    le+eL+ ++r  +g++a+pk+++fv +lpktrsGK
     EPA06119.1 513 ELESCIVSHPDVAESAVCGIPDQLKGEVIIVFAVLKQNTTLdvktLEKELITKIRNDIGAIATPKEIYFVTKLPKTRSGK 592
                    89*********************************9874233467**********************************9 PP

>> ACAS_N  Acetyl-coenzyme A synthetase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.0   6.4   4.1e-18   2.4e-14      13      55 .]      24      65 ..      18      65 .. 0.94

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 4.1e-18
                HHHHHHHHCCS--SB--S-SECSTTTCT-EESTT-EE-HHHHH CS
      ACAS_N 13 eaFWaeqakeldWekpfdkvldgskgpfikWFeGGklNicyNc 55
                 +FW++qak+l+W+  ++k+ld+ ++pf+kWF+GGk+N++yN+
  EPA06119.1 24 IGFWEKQAKNLSWFSSWEKTLDW-NPPFAKWFVGGKINASYNA 65
                58*********************.9*****************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (639 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.69u 0.30s 00:00:00.99 Elapsed: 00:00:00.51
# Mc/sec: 3800.97
//
Query:       EPA06120.1  [L=44]
Description: hypothetical protein BG20_I0627 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 304.52
//
Query:       EPA06121.1  [L=452]
Description: peptidase dimerization domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-32  112.3   0.0    3.3e-32  111.9   0.0    1.2  1  Peptidase_M20  Peptidase family M20/M25/M40
    1.7e-14   53.6   0.0    3.6e-14   52.6   0.0    1.6  1  M20_dimer      Peptidase dimerisation domain
  ------ inclusion threshold ------
      0.094   12.5   0.0        6.1    6.6   0.1    2.4  2  Ribosomal_S21  Ribosomal protein S21


Domain annotation for each model (and alignments):
>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.9   0.0   5.6e-36   3.3e-32       1     206 [.      82     447 ..      82     448 .. 0.90

  Alignments for each domain:
  == domain 1  score: 111.9 bits;  conditional E-value: 5.6e-36
                    EEEEES-BSSTTCGGGSSS.TTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTTHHHHHHHHHHTTTCESEEE CS
                    xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Peptidase_M20   1 llgsHlDvVpeeetdgwtt.pfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggrgGakallegleerekvdavf 95 
                    ++++H+Dv+p+e+ d w+  pfs++++ +k++GrG++d+kg +++ ++a++a  ++ ++ + +i+++++++EE    G++++ + l+ ++k +++ 
     EPA06121.1  82 MFYNHYDVQPAEPFDLWDDpPFSGKIKGNKIFGRGSSDDKGELITRIKAVEASLKTTGDVPCNIKFVIEGEEE---TGSAHIDQYLK-KYKKKFAC 173
                    79********77779************99********************************************...57766555444.77888877 PP

                    EEEEESSSBTCHSTETEEEE............................................................................ CS
                    xxxxxxxxxxxxxxxxxxxx............................................................................ RF
  Peptidase_M20  96 elhieepgileagklaigvv............................................................................ 115
                    + +i+e g+ ++++  + ++                                                                            
     EPA06121.1 174 DGVIWEFGYVDSQN-RPIIGlgmkgllyvelsvkesirdahsslavliknpawrlleavqtlrdshgrilikdwykeviplsktdlkiisqepfde 268
                    88899999999666.555557899************************************************************************ PP

                    ....................................................................................EEEEEEEEEESH CS
                    ....................................................................................xxxxxxxxxxxx RF
  Peptidase_M20 116 ....................................................................................kvevelleggap 127
                                                                                                        +v ++ ++g+a+
     EPA06121.1 269 qsfkkefgiksfvgdmhgldakkalvggatcniagllsgytgngaktvlpgealvkidfrlvpkmdpkkqtlrlrkhlkskgfeDVLIKVFHGEAA 364
                    ***********************************************************************************76999999***** PP

                    EEEC.CHHHHHHHHHHHHHHHTSC.EEEEEESSSBHTHHHH...TTTEEEEEEESSG..GCTTSTTTEEEHHHHHHHHHHHHHHHH CS
                    xxxx.xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx...xxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Peptidase_M20 128 vtln.dsplvkalaeaaeelfgek.velivsgpggtdarff...agiptvmifgpgs..glaHspnEyvdledlekgikvlarlle 206
                    +++n ++p+v  ++eaa++ fg++  +++    g+  +  f   ++ p++  +g     +++HspnE+ +++ l+k +k ++ ++e
     EPA06121.1 365 ARTNpSEPFVSQVKEAADQSFGKSiLNVSNA--GTGPMHSFvkfLNAPCI-SVGSTYmfARIHSPNEFARIDLLKKTTKCIYLIME 447
                    *******************99*774333333..45555555333677877.57855348********************9998876 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.6   0.0     6e-18   3.6e-14       2     108 ..     194     353 ..     193     354 .. 0.96

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 6e-18
                 EB-EEEEEEEE..EE-B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC.................................................... CS
   M20_dimer   2 ghkGlaggkit..vkgkagHsgapgagaNAieklarllaeledeegdia...............................................eer 51 
                 g kGl+ ++++    ++++Hs+      N+ + l ++++ l+d +g+i                                                ++ 
  EPA06121.1 194 GMKGLLYVELSvkESIRDAHSSLAVLIKNPAWRLLEAVQTLRDSHGRILikdwykeviplsktdlkiisqepfdeqsfkkefgiksfvgdmhgldaKKA 292
                 6799999999955678*********************************************************************************** PP

                 TCCTCCCCCEECCE-C....CCCEESSEEEEEEEEEHHHHHHHHHHHHHHHHHHTSCCSTT CS
   M20_dimer  52 slprttlnvtgiegGs....aknvipdeaeakidiRllpgedpeevleeieeilekeaped 108
                  +++ t+n++g+ +G+    ak+v+p+ea +kid+Rl+p++dp++   +++++l++++ ed
  EPA06121.1 293 LVGGATCNIAGLLSGYtgngAKTVLPGEALVKIDFRLVPKMDPKKQTLRLRKHLKSKGFED 353
                 *******************************************************988765 PP

>> Ribosomal_S21  Ribosomal protein S21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1     0.001       6.1       6      30 ..      33      57 ..      30      60 .. 0.90
   2 ?    3.2   0.0     0.012        74      10      29 ..     160     179 ..     156     180 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.001
  Ribosomal_S21  6 dgenierALkrfkrkveragvirev 30
                   ++e ie+  k  k+++e++g+++e+
     EPA06121.1 33 KNEGIEECAKLVKKILEKSGIKSEI 57
                   6899******************998 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.012
  Ribosomal_S21  10 ierALkrfkrkveragvire 29 
                    i++ Lk++k+k++ +gvi e
     EPA06121.1 160 IDQYLKKYKKKFACDGVIWE 179
                    8999************9955 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 2969.42
//
Query:       EPA06122.1  [L=61]
Description: hypothetical protein BG20_I0656 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.012   15.8   2.1      0.013   15.7   2.1    1.0  1  DUF5368      Family of unknown function (DUF5368)
      0.028   13.9   0.7       0.03   13.8   0.7    1.0  1  SfLAP        Sap, sulfolipid-1-addressing protein
      0.096   12.5   1.3       0.12   12.3   1.3    1.0  1  VIT1         VIT family
        0.7    9.6   5.9       0.82    9.3   5.9    1.0  1  Tetraspanin  Tetraspanin family
        9.7    6.5   6.7    2.2e+02    2.2   6.7    2.0  1  DUF3040      Protein of unknown function (DUF3040)


Domain annotation for each model (and alignments):
>> DUF5368  Family of unknown function (DUF5368)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   2.1   3.6e-06     0.013      51      97 ..       3      53 ..       1      56 [. 0.75

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.6e-06
     DUF5368 51 vraelvglvGgvlalllv..aavtqsglsDigg.pvDlllllli.aaaglv 97
                 +a ++ +vGg+ +l+l   a+ + s+++D +g  + +++++++ +++g++
  EPA06122.1  3 FWAGVSFIVGGITSLALTlgATASLSHIEDTSGySIGWIIVGVTlIVIGFI 53
                589999******76655511677789****98868*****98761466776 PP

>> SfLAP  Sap, sulfolipid-1-addressing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.7   8.4e-06      0.03      33      86 ..       2      54 ..       1      60 [. 0.68

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.4e-06
       SfLAP 33 aFlvgwlvvlvalglivlfvlrslls.gasaapssaikalqivlGvlllllaave 86
                +F++g+     +++ ++l++++ ++  +++++ + +i++  i++Gv l+++++ +
  EPA06122.1  2 VFWAGVSFIVGGITSLALTLGATASLsHIEDTSGYSIGW--IIVGVTLIVIGFIK 54
                8***98655555555555555544432777777777777..79999999999876 PP

>> VIT1  VIT family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.3   3.2e-05      0.12     141     185 ..       5      55 ..       2      57 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.2e-05
        VIT1 141 salsfliGgliPllpylfve......svglalvvsiavtllalllfGavka 185
                  ++sf++Gg+ +l+  l ++      + + +  + +++++++l+++G++k+
  EPA06122.1   5 AGVSFIVGGITSLALTLGATaslshiEDTSGYSIGWIIVGVTLIVIGFIKK 55 
                 689***********99987766776658999999999************97 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   5.9   0.00023      0.82       5      66 ..       2      53 ..       1      53 [. 0.75

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00023
                 XXXXXXXXXXXXXXXXXXXXXXXXXXX.....................XXXXXXXXXXXXXX CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Tetraspanin  5 lfffnllfwligivllavGvwlrlkhaeaalacllsesaedpailaillivvGvllfllgfl 66
                 +f+  + f++ gi  la+             a+++ ++ ed++ ++i+ i+vGv+l+++gf+
   EPA06122.1  2 VFWAGVSFIVGGITSLALT----------LGATASLSHIEDTSGYSIGWIIVGVTLIVIGFI 53
                 5556666666666666665..........34456678899999*****************95 PP

>> DUF3040  Protein of unknown function (DUF3040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   6.7     0.061   2.2e+02      52      68 ..       3      38 ..       1      58 [. 0.42

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.061
     DUF3040 52 fvaGllllvlG.vaaaa..................v 68
                f+aG+ ++v+G +++a                   +
  EPA06122.1  3 FWAGVSFIVGGiTSLALtlgataslshiedtsgysI 38
                455555555553333323333333355555555552 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 409.12
//
Query:       EPA06123.1  [L=89]
Description: hypothetical protein BG20_I0625 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.037   14.0   0.5      0.051   13.5   0.5    1.2  1  SWIRM-assoc_1  SWIRM-associated region 1
      0.093   12.7   1.4       0.11   12.5   1.4    1.1  1  FB_lectin      Fungal fruit body lectin
        0.1   12.8   0.8       0.16   12.2   0.1    1.6  2  DUF3008        Protein of unknwon function (DUF3008)
       0.13   12.7   2.8        2.1    8.7   0.4    2.2  2  SWIRM          SWIRM domain
       0.15   12.2   4.0       0.21   11.7   1.9    2.2  3  Mst1_SARAH     C terminal SARAH domain of Mst1
       0.34   10.8   3.8         11    5.9   1.1    2.6  2  DUF4817        Helix-turn-helix domain (DUF4817)


Domain annotation for each model (and alignments):
>> SWIRM-assoc_1  SWIRM-associated region 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.5   1.7e-05     0.051      29      62 ..      26      59 ..      21      76 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.7e-05
  SWIRM-assoc_1 29 lvetqlkKlelKLkqfeelEklleaerrelekqr 62
                    v+t+l+K ++K +qf+ + +  e++r+ + ++ 
     EPA06123.1 26 SVNTTLQKYDIKKTQFQIIKEYYENKREHMSEKE 59
                   69*************************9986554 PP

>> FB_lectin  Fungal fruit body lectin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.4   3.6e-05      0.11      74     133 ..      20      84 ..      13      88 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.6e-05
   FB_lectin  74 kpWcDivtk..lkd...eetavkllpeyYeekkerakaresqraeyevknvkgrklkikytvaeg 133
                 + Wc+  ++  l++   ++t  ++  eyYe+k+e+++++e  +   + ++++  ++ + y +  +
  EPA06123.1  20 DYWCNRSVNttLQKydiKKTQFQIIKEYYENKREHMSEKEISQLAKRYRQKEPEQFLAMYDSIRD 84 
                 557764444114433357899********888888877776666666666677777777776665 PP

>> DUF3008  Protein of unknwon function (DUF3008)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   5.2e-05      0.16      35      56 ..      53      74 ..      44      75 .. 0.91
   2 ?   -2.1   0.0       1.5   4.4e+03      33      40 ..      78      85 ..      77      87 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.2e-05
     DUF3008 35 esMsekeLeelAsTkrkgkPeh 56
                e Mseke+++lA+  r++ Pe+
  EPA06123.1 53 EHMSEKEISQLAKRYRQKEPEQ 74
                78******************85 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.5
     DUF3008 33 MyesMsek 40
                My+s  +k
  EPA06123.1 78 MYDSIRDK 85
                99998766 PP

>> SWIRM  SWIRM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.2     0.012        35      30      58 ..       8      37 ..       3      42 .. 0.78
   2 ?    8.7   0.4   0.00072       2.1      39      65 ..      42      68 ..      37      82 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.012
       SWIRM 30 peeYlkiRnkiialyr.enpkeyltvteaq 58
                ++ Yl++R  i++ +  ++++  l++ +++
  EPA06123.1  8 IAGYLTYRLVIFDYWCnRSVNTTLQKYDIK 37
                567************944558888888873 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00072
       SWIRM 39 kiialyrenpkeyltvteaqkalkrrr 65
                +ii++y en +e+++ +e+++++kr r
  EPA06123.1 42 QIIKEYYENKREHMSEKEISQLAKRYR 68
                7******************99998443 PP

>> Mst1_SARAH  C terminal SARAH domain of Mst1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       0.6   1.8e+03      15      38 ..      15      38 ..      11      39 .. 0.70
   2 ?   -1.7   0.1       1.1   3.2e+03      31      38 ..      45      52 ..      42      55 .. 0.79
   3 ?   11.7   1.9   6.9e-05      0.21      22      37 ..      55      70 ..      50      72 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.6
  Mst1_SARAH 15 rlasLDpeMEqEieelrkrYqaKR 38
                rl   D    + ++ + ++Y  K+
  EPA06123.1 15 RLVIFDYWCNRSVNTTLQKYDIKK 38
                666666666777788889998885 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.1
  Mst1_SARAH 31 rkrYqaKR 38
                ++ Y++KR
  EPA06123.1 45 KEYYENKR 52
                56799999 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 6.9e-05
  Mst1_SARAH 22 eMEqEieelrkrYqaK 37
                + E+Ei +l+krY++K
  EPA06123.1 55 MSEKEISQLAKRYRQK 70
                559************9 PP

>> DUF4817  Helix-turn-helix domain (DUF4817)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1    0.0075        22       9      27 ..      18      35 ..      14      37 .. 0.80
   2 ?    5.9   1.1    0.0038        11       4      16 ..      39      51 ..      37      70 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0075
     DUF4817  9 VkaYykngesvtatqrafr 27
                +  Y++n  sv++t++++ 
  EPA06123.1 18 IFDYWCNR-SVNTTLQKYD 35
                55688888.*******995 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0038
     DUF4817  4 qRifiVkaYykng 16
                ++++i+k+Yy+n+
  EPA06123.1 39 TQFQIIKEYYENK 51
                6789*******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1925  (0.107368); expected 358.6 (0.02)
Passed bias filter:                      658  (0.0367003); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 638.76
//
Query:       EPA06124.1  [L=231]
Description: SPP-like hydrolase, Archaeal [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-30  106.3   2.7    1.8e-21   77.1   0.2    2.0  2  Hydrolase_3      haloacid dehalogenase-like hydrolase
    1.3e-07   31.4   0.1    0.00051   19.6   0.0    2.1  2  S6PP             Sucrose-6F-phosphate phosphohydrolase
    2.3e-07   30.2   0.1    0.00011   21.5   0.1    2.3  1  Trehalose_PPase  Trehalose-phosphatase
    4.1e-05   24.0   0.6      0.019   15.3   0.0    2.6  3  Hydrolase        haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.015   15.7   0.3       0.17   12.3   0.0    2.3  2  HAD              haloacid dehalogenase-like hydrolase
      0.029   14.5   0.5        0.1   12.6   0.0    2.2  3  HAD_2            Haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.5   1.4e-10   4.3e-07       2      79 ..       7      86 ..       6     101 .. 0.80
   2 !   77.1   0.2     6e-25   1.8e-21     156     255 .]     123     221 ..      86     221 .. 0.83

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 1.4e-10
                 EEEIIIIIS-TTS-.--HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEEEEGGGTEE.ECTTTEEEEE--B CS
  Hydrolase_3  2 alDlDGTLlnsdkk.isektkeaikklkekgikvviATGRslravlpvleelgldlpvialNGali.ddekgkilyksti 79
                 a+D+DGT+  ++   i+  + +a++ l + g++v++ TGRs +++  +    g + ++++ NG+ i   +++ +l  +  
   EPA06124.1  7 AVDIDGTITENGAGrINLDALSALRHLTNIGHNVIFVTGRSSVEAYLLSVFGGTTKIAVGENGGCItLNTNEHVLLGDLQ 86
                 89******8765545***************************999888887788899*********65555555554444 PP

  == domain 2  score: 77.1 bits;  conditional E-value: 6e-25
                  HHHHHHHHHCTTTEEEEEESTTEEEEEETT-SHHHHHHHHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--GGGTHHHH CS
  Hydrolase_3 156 elekelksklnklltitssskgyleimpkgvsKgtalkklakelnisleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksnnedGVak 253
                  +l+k+l ++ n +    s s++ + i+++g++Kgt+ ++++ +++is+++via+GD+  Di+++++a++++A+gn+se vk++A+ +t  ++ dGV +
   EPA06124.1 123 DLAKNLLHEKNLD-VLLSDSQYAFHINSPGIDKGTGFQEIMRRMSISSDDVIAIGDSATDIPLFKVAKTSIALGNSSEFVKSHATITTSAKSGDGVIE 219
                  4455555555544.7888999*******************************************************************99999***99 PP

                  HH CS
  Hydrolase_3 254 al 255
                  al
   EPA06124.1 220 AL 221
                  87 PP

>> S6PP  Sucrose-6F-phosphate phosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0   0.00019      0.56       2      48 ..       3      50 ..       2      55 .. 0.78
   2 !   19.6   0.0   1.7e-07   0.00051     138     242 ..     127     221 ..     118     224 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00019
                SEEEEE-TBTTTB...S-HHHHHHHHHHHH.GGGGGEEEEEE-SS-HHH CS
        S6PP  2 klllvsdLDntlv..dgdnealarlnelleaeerkdvllvfaTGRslds 48
                ++ ++ d+D+t++     + +l++l +l++   +  + ++f+TGRs  +
  EPA06124.1  3 QKTFAVDIDGTITenGAGRINLDALSALRH-LTNIGHNVIFVTGRSSVE 50
                677899*******54344566777777777.8889999*******9765 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 1.7e-07
                 HHHHTTTS-EEEEEETTTEEEEEETT-SHHHHHHHHHHHHT--GGGEEEEE-SGGGHHHHTSSSEEEE-TT--HHHHHHHHHH--TTE..EE-SS-THH CS
        S6PP 138 qlLekreldvkviyssgkdlDvlPkraskgeAlryLakkleleleqilvcGdsgnDeellignvlgVvVgnaqeellqwllenakeneriylaeercaa 236
                 +lL++++ldv  +  s+ ++ +   + +kg   + +++++ + ++ ++  Gds  D+ l++    ++ +gn++e           + ++++  ++++ +
  EPA06124.1 127 NLLHEKNLDVL-LSDSQYAFHINSPGIDKGTGFQEIMRRMSISSDDVIAIGDSATDIPLFKVAKTSIALGNSSEF---------VKSHATITTSAKSGD 215
                 55666666663.345667788999999*********************************************998.........233335667788889 PP

                 HHHHHH CS
        S6PP 237 Gilegl 242
                 G++e+l
  EPA06124.1 216 GVIEAL 221
                 999987 PP

>> Trehalose_PPase  Trehalose-phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.1   3.5e-08   0.00011       2     217 ..       8     204 ..       7     219 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 3.5e-08
                      EETBTTTB---SSGGG--B-TTHHHHHHHHHTTS-..EEEE-SS-HHHHHHH..H---SSEEEEGGGTEEE-TT--EEE-HHHHTTHHHHHHHH CS
  Trehalose_PPase   2 lDydGTlspivedpdaavpssellslLkkLasdpknvvaivSGrslkeeell..vkvpelglaaeHGaeirspsgedwenqaevedlewlkevk 93 
                      +D+dGT+++        ++  ++ls+L++L++  +  v++v+Grs  e++ll  ++ +    ++e+G  i+ +++e+         l  l++ +
       EPA06124.1   8 VDIDGTITENGA----GRINLDALSALRHLTNIGH-NVIFVTGRSSVEAYLLsvFGGTTKIAVGENGGCITLNTNEH-------VLLGDLQQCQ 89 
                      6999*9999887....77777899*********99.567789999999555411344445578***********933.......3344455555 PP

                      HHHHHHHTTSTT-EEEEETTEEEEE-TT--TT..THHHHHHHHHHHHHHH.--EEEE-SSEEEEE-S---HHHHHHHHHHTS--------EEEE CS
  Trehalose_PPase  94 eileektertpGsyiEekkfalsvHyrnaddeelqakelaehlesvltdkpdlevtqgkkvvevrpqgvsKGkaverlleslgsadseddfvlc 187
                        ++   +++++++ E+  f     ++ + ++ +  + +++ l++   ++ d+ +++ +  + + + g  KG   +++++++  +    d v++
       EPA06124.1  90 SAFQIIKNEIDNVV-EKPVF--PRMTEVVLERTFDLDLAKNLLHE---KNLDVLLSDSQYAFHINSPGIDKGTGFQEIMRRMSIS---SDDVIA 174
                      55555555555553.43322..22333343444555555555555...6779999****************************99...88888* PP

                      EE-SSTTHHHHTTS-TT...-EEEEE--TT CS
  Trehalose_PPase 188 iGDdrtDedmFsvlrktkesgvsievsave 217
                      iGD  tD   F+v ++    g+s e+ ++ 
       EPA06124.1 175 IGDSATDIPLFKVAKTSIALGNSSEFVKSH 204
                      **************9997777777666553 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.3     0.004        12       2      15 ..       4      17 ..       3      40 .. 0.82
   2 ?   -1.3   0.0      0.73   2.2e+03     122     148 ..      25      51 ..      19      98 .. 0.79
   3 !   15.3   0.0   6.3e-06     0.019     168     209 ..     147     188 ..     109     189 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.004
                SEEEEESBTTTBCH CS
                xxxxxxxxxxxxxx RF
   Hydrolase  2 ktvvfDkdGTLttg 15
                kt++ D+dGT+t+ 
  EPA06124.1  4 KTFAVDIDGTITEN 17
                89**********53 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.73
                 THHHHHHHHHHTTEEEEEEESSEHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
   Hydrolase 122 eaaeavasLkaagievvlltgdnpeta 148
                 +a  a+++L   g +v+ +tg ++  a
  EPA06124.1  25 DALSALRHLTNIGHNVIFVTGRSSVEA 51 
                 566788888888888888888776544 PP

  == domain 3  score: 15.3 bits;  conditional E-value: 6.3e-06
                 CESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHT CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
   Hydrolase 168 ietvakpspegkvaaireLqgkpeevamVGDgvnDaaalaaA 209
                 i+  +  +  g+++++r++ ++  +v+++GD+++D++ ++ A
  EPA06124.1 147 INSPGIDKGTGFQEIMRRMSISSDDVIAIGDSATDIPLFKVA 188
                 44444557899**************************99877 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.18   5.3e+02       3      13 ..       8      18 ..       6      34 .. 0.80
   2 ?   12.3   0.0   5.5e-05      0.17     160     188 .]     160     186 ..     120     186 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.18
         HAD  3 fDfDgTLldgd 13
                 D+DgT++ + 
  EPA06124.1  8 VDIDGTITENG 18
                6******9875 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 5.5e-05
         HAD 160 ewlaaegegidleevvayGDspsDlpllr 188
                 e   ++   i+ ++v+a+GDs +D+pl++
  EPA06124.1 160 E--IMRRMSISSDDVIAIGDSATDIPLFK 186
                 5..56777889999************986 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.2   0.2       5.2   1.6e+04       4      10 ..       9      15 ..       9      17 .. 0.85
   2 ?   12.6   0.0   3.5e-05       0.1     140     166 ..     157     183 ..     150     194 .. 0.88
   3 ?   -2.4   0.0       1.5   4.4e+03      76      91 ..     209     224 ..     197     227 .. 0.69

  Alignments for each domain:
  == domain 1  score: -4.2 bits;  conditional E-value: 5.2
       HAD_2  4 DlDgTll 10
                D+DgT+ 
  EPA06124.1  9 DIDGTIT 15
                99***96 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 3.5e-05
       HAD_2 140 viekaleklklkkeeviyvGDsptDie 166
                  ++++++++ +++++vi +GDs tDi 
  EPA06124.1 157 GFQEIMRRMSISSDDVIAIGDSATDIP 183
                 6799*********************95 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.5
       HAD_2  76 kevkpydgvkelLeeL 91 
                 ++ k  dgv+e+L++L
  EPA06124.1 209 TSAKSGDGVIEALDKL 224
                 4566778999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1745.55
//
Query:       EPA06125.1  [L=56]
Description: hypothetical protein BG20_I0624 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 377.23
//
Query:       EPA06126.1  [L=75]
Description: hypothetical protein BG20_I0622 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00018   22.2   0.1    0.00024   21.8   0.1    1.1  1  MJ1316       MJ1316 RNA cyclic group end recognition domain
  ------ inclusion threshold ------
      0.049   13.8   0.0      0.057   13.6   0.0    1.3  1  HicB-like_2  HicB_like antitoxin of bacterial toxin-antitoxin


Domain annotation for each model (and alignments):
>> MJ1316  MJ1316 RNA cyclic group end recognition domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.1   2.7e-08   0.00024       4      76 .]       7      69 ..       5      69 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 2.7e-08
      MJ1316  4 aqdvlnRirWdkeldkskfvvgyldRfkgikevpleeiswiedflleeeegelaIPlHRiryikrkgevvWdR 76
                +++++++ ++ +++  + + v y d f++++e +l+e++++++   +      +IP+ Ri  ik+++++++++
  EPA06126.1  7 IEEIFSKAIFADDV--ESYQVTYRD-FEKLRETSLKEFVKESN---N----FQTIPITRIMNIKKNHRILFEK 69
                88999999999995..799999977.799*********99888...2....257****************997 PP

>> HicB-like_2  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   6.4e-06     0.057       8      27 ..      16      35 ..      11      59 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.4e-06
  HicB-like_2  8 vdeeseeyeityrdfdelna 27
                 + ++ e y++tyrdf++l+ 
   EPA06126.1 16 FADDVESYQVTYRDFEKLRE 35
                 667889**********9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       810  (0.0451782); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 525.81
//
Query:       EPA06127.1  [L=102]
Description: hypothetical protein BG20_I0647 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.022   15.1   0.2      0.053   13.8   0.2    1.8  1  YvbH_ext  YvbH-like oligomerisation region


Domain annotation for each model (and alignments):
>> YvbH_ext  YvbH-like oligomerisation region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2     3e-06     0.053      36      60 ..      26      55 ..       6      56 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3e-06
                HHHHHHHHHHHS-S-.....-HHHHHHHH- CS
    YvbH_ext 36 FnWLedarkkynkKD.....FgevFekYIn 60
                Fn  ++++++++ KD      g vFekYI+
  EPA06127.1 26 FNMVNSTKENWEIKDihefvLGMVFEKYIH 55
                88888999999999955533499******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1160  (0.0646996); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 668.62
//
Query:       EPA06128.1  [L=158]
Description: hypothetical protein BG20_I0638 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-16   59.4   0.6    3.6e-16   58.9   0.6    1.2  1  PUA       PUA domain
  ------ inclusion threshold ------
      0.031   14.5   0.1      0.052   13.8   0.1    1.4  1  UPF0113   UPF0113 PUA domain


Domain annotation for each model (and alignments):
>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.9   0.6     4e-20   3.6e-16       1      74 []      72     145 ..      72     145 .. 0.95

  Alignments for each domain:
  == domain 1  score: 58.9 bits;  conditional E-value: 4e-20
                 CEEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETT.SCEEEEEEESS-HHHHHHHCTSEEEEEEEEE CS
         PUA   1 grvvvddgAvkallsgasLlapGvvevegdfeegdvVaivded.gelvavGlanysseelakikggksveiervl 74 
                 ++v+vd gAvk+ ++ga+++ pG+ +  + fe+  +V i+ e   +++avG++  ss+el +i++g +v++ +++
  EPA06128.1  72 PHVTVDMGAVKFMCKGANVMRPGIKGHSE-FEKEKIVCIIEESqHKVLAVGKSIISSSELDSIEKGEVVKNMHYI 145
                 689*********************98776.************769***************************985 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   5.8e-06     0.052       9      67 ..      80     142 ..      73     147 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.8e-06
     UPF0113   9 eklFLY.GrdvlkesilkitesvkenqvvvVlnengeplGiGkirkdt..k.aspgkivvknl 67 
                 + +F++ G +v++ +i+ ++e  ke+ v+++   + ++l++Gk+++++    + +++ vvkn+
  EPA06128.1  80 AVKFMCkGANVMRPGIKGHSEFEKEKIVCIIEESQHKVLAVGKSIISSseLdSIEKGEVVKNM 142
                 445554489***********99999*********************99873466777788775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1098.42
//
Query:       EPA06129.1  [L=339]
Description: flap structure-specific endonuclease [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.2e-24   84.2   0.0    1.5e-23   83.0   0.0    1.7  1  XPG_I       XPG I-region
    2.1e-21   76.3   0.0    8.4e-21   74.4   0.0    1.9  2  XPG_N       XPG N-terminal domain
    0.00057   20.4   0.0     0.0019   18.7   0.0    1.9  1  5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
  ------ inclusion threshold ------
       0.31   11.3   2.4       0.27   11.5   0.4    1.9  2  DUF4878     Domain of unknown function (DUF4878)


Domain annotation for each model (and alignments):
>> XPG_I  XPG I-region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.0   0.0   3.3e-27   1.5e-23       2      94 .]     141     236 ..     140     236 .. 0.93

  Alignments for each domain:
  == domain 1  score: 83.0 bits;  conditional E-value: 3.3e-27
                 HHT--EEE-SS-HHHHHHHHHHTTSSSEEE-SSSHHHHTT-SEEEESTT.ECECTT.......EEECEEEEEEHHHHHHHHT--HHHHHHHHHHHCET CS
       XPG_I   2 lmgipyvvApgEAEAqcayLqkkglvdaviseDsDlllFGapkvlrnlskkkskkk.....kekekkkvevidlekvlkelgltreqlidlaillgcD 94 
                  +gipy++Ap+E+EA +a+L+++g+++a +s+D D++l Ga++++rn++  +s+ +     +++++ ++e+i+++k+l+ lg+treql+d+ il+g+D
  EPA06129.1 141 YFGIPYIDAPSEGEAMAAHLTNTGQAYASASQDFDSILCGAKRLIRNFT--NSGRRkipnrNTYVEIEPEIIETQKTLDALGVTREQLVDIGILIGTD 236
                 69**********************************************9..33333357999999*******************************99 PP

>> XPG_N  XPG N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.4   0.0   1.9e-24   8.4e-21      18     100 ..      13     100 ..       3     101 .. 0.94
   2 ?   -1.5   0.0      0.77   3.5e+03      46      73 ..     116     144 ..     103     147 .. 0.67

  Alignments for each domain:
  == domain 1  score: 74.4 bits;  conditional E-value: 1.9e-24
                 EEEGGGGTTEEEEEEHHHHHHHHHHHSE.ETTEE-BS.....-HHHHHHHHHHHHHHHTTEEEEEEE--S--GGGHHHHHHHHHHHHH CS
       XPG_N  18 svsiealegkklaiDaslwlyrfliavreqlgnalen.....tshlmglfsrllrlldfgikPifVFdgkapdlkkeelekrserrqe 100
                 +  +ea++ k++aiDa+  +y+fl ++r ++g +l+      tshl gl++r + +l +gikP++VFdgk+p+lk  e+e+r++++++
  EPA06129.1  13 KTTLEAFSSKVIAIDAYNAIYQFLASIRGPDGLQLSDsegriTSHLSGLLYRNINFLSLGIKPVYVFDGKPPSLKTAEIERRKQIKKD 100
                 6789*******************************9999*********************************************9986 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.77
                 .ETTEE-BS-HHHHHHHHHHHHHH.HTTE CS
       XPG_N  46 eqlgnalentshlmglfsrllrll.dfgi 73 
                 +  + a ++ts + g++++ +++l +fgi
  EPA06129.1 116 DARKFAQQTTSMKDGMVKESKQILtYFGI 144
                 44455666789999999988765515555 PP

>> 5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   4.3e-07    0.0019       2      53 ..     222     272 ..     221     291 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 4.3e-07
  5_3_exonuc   2 kPeqiidlkaLvGDssDnipGvpgiGektAakLlkeygsleeilenldelke 53 
                 + eq++d+  L+G    n  G   iG+ktA k++k++  le+i +  ++l+e
  EPA06129.1 222 TREQLVDIGILIGTDF-NPNGFDRIGPKTALKMIKQHSCLEDIPQIQEQLQE 272
                 6689999999999776.789*********************99884444443 PP

>> DUF4878  Domain of unknown function (DUF4878)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.4     6e-05      0.27      10      45 ..      99     134 ..      94     139 .. 0.89
   2 ?   -3.5   0.1       2.8   1.2e+04      25      48 ..     300     323 ..     298     335 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6e-05
     DUF4878  10 eeavknFleavkeGdvedaikyltestreedalaek 45 
                 ++a+  + +a++ G++eda+k++ + t  +d++ ++
  EPA06129.1  99 KDATVKYEKAIAAGNMEDARKFAQQTTSMKDGMVKE 134
                 78999**********************999998776 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.8
     DUF4878  25 vedaikyltestreedalaeklkg 48 
                 +e + +yl e + +ed + ++l+ 
  EPA06129.1 300 YEGMTNYLKERSFSEDRIQSSLNR 323
                 556666777777777666666433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1161  (0.0647554); expected 358.6 (0.02)
Passed bias filter:                      714  (0.0398237); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.65u 0.34s 00:00:00.99 Elapsed: 00:00:00.55
# Mc/sec: 1871.08
//
Query:       EPA06130.1  [L=138]
Description: DoxX protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-14   53.6   6.4    2.5e-14   53.6   6.4    1.7  2  DoxX      DoxX
    2.9e-06   27.3   6.7    6.8e-06   26.1   6.4    1.6  2  DoxD      TQO small subunit DoxD
    1.1e-05   25.5   7.5    1.9e-05   24.7   7.5    1.5  1  DoxX_2    DoxX-like family


Domain annotation for each model (and alignments):
>> DoxX  DoxX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.6   6.4   4.2e-18   2.5e-14       5      84 ..      19      92 ..      17      93 .. 0.96
   2 ?   -1.6   0.1      0.72   4.3e+03      53      60 ..     109     116 ..      94     125 .. 0.64

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 4.2e-18
        DoxX  5 lRlllgvlfiahGlqkltgfglegtaaslaalglpppellaylaalvElvgglllllGlltRlaAlalavtllvatltvh 84
                +R ++gv+fi+ G +k++    +g+a++l+++g+  p+ + + +al+E++gg+ll++G+l R++A +la+++l+a+++v 
  EPA06130.1 19 IRAAIGVIFIVQGSGKFN----SGFANMLGNMGI--PVEMQIPIALAEVIGGILLIVGVLSRISASLLAIIMLGAIFVVK 92
                79****************....8***********..9999999**********************************996 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.72
        DoxX  53 lvggllll 60 
                 +++g+l++
  EPA06130.1 109 ILAGVLMI 116
                 23333333 PP

>> DoxD  TQO small subunit DoxD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0     0.099   5.9e+02     123     138 ..      20      35 ..      13      47 .. 0.77
   2 !   26.1   6.4   1.1e-09   6.8e-06      55     146 ..      40     132 ..      23     136 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.099
        DoxD 123 lvaaelvliltgsgkl 138
                   a+++++i++gsgk+
  EPA06130.1  20 RAAIGVIFIVQGSGKF 35 
                 4578888889999888 PP

  == domain 2  score: 26.1 bits;  conditional E-value: 1.1e-09
        DoxD  55 eivvlnrsllvtalvlftlvEiivGlllliGlltRlsslvafalalg.ialsayWlgstcedEyqiglllvaaelvliltgsgklslDylllk 146
                   ++ n  + v++ + ++l E+i G+ll++G+l+R+s+  ++ + lg i++  +  + t    y i ll  a+ l++i  g g++s+  +++k
  EPA06130.1  40 ANMLGNMGIPVEMQIPIALAEVIGGILLIVGVLSRISASLLAIIMLGaIFVVKGASNLTGNGGYAIDLLILAGVLMIITAGPGRISIAHIVKK 132
                 55666777778888889999****************9866655555425556666677789**************************988765 PP

>> DoxX_2  DoxX-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   7.5   3.2e-09   1.9e-05       5      81 ..      22      91 ..      19     120 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 3.2e-09
      DoxX_2  5 llalffllsGvakllraeevvakfaqlgfpssfvrllGvvellgalgLllplvtaprltplAavglallmvgAiath 81
                 + ++f+++G+ k+   + ++ +++ +g+p  +   ++++e++g+++L+++     +l+ + a +la++m+gAi++ 
  EPA06130.1 22 AIGVIFIVQGSGKF--NSGFANMLGNMGIPVEMQIPIALAEVIGGILLIVG-----VLSRISASLLAIIMLGAIFVV 91
                67799999*****9..78999999***************************.....69****************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.52
# Mc/sec: 805.36
//
Query:       EPA06131.1  [L=286]
Description: SPFH/Band 7/PHB domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-23   83.9   6.5    2.2e-23   83.1   6.5    1.4  1  Band_7    SPFH domain / Band 7 family
  ------ inclusion threshold ------
      0.082   13.1   0.5       0.17   12.1   0.5    1.5  1  CdiA_C    Contact-dependent growth inhibition CdiA C-terminal


Domain annotation for each model (and alignments):
>> Band_7  SPFH domain / Band 7 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.1   6.5   2.5e-27   2.2e-23       2     169 ..      39     218 ..      38     240 .. 0.92

  Alignments for each domain:
  == domain 1  score: 83.1 bits;  conditional E-value: 2.5e-27
      Band_7   2 iieegevgvvvrfGklsr...vlepGlhfilPfgrsvtvvsvrvqtldvsvsltvptkDglpvtidvtviyrv.pddapklvaaveresanldnlirrv 96 
                 i+e+g++gv+    +++    +le Glhf++Pf ++v+++ vr+ ++      +  ++D + v ++vtv+yr  p+ + +l+++v  + ++  ++i+++
  EPA06131.1  39 IVEAGNRGVLLHWSAVDTtvpPLEEGLHFVVPFQDKVINMEVRTLKFVKAT--SGASRDLQTVSTEVTVNYRAsPNSVHVLYKEV--GLDYESRIIQPA 133
                 899*******98777777788*****************9999999998888..999*****************************..************ PP

      Band_7  97 lesalrevisemtleellsnreelaeelknelneqlrkyGvevldvritdidpppevaqalaakqaaeaea............qa 169
                 +e++++++++++++eel+ +r  +++++++e++++l  y++    ++itd++++p + qa+++k +ae++a            +a
  EPA06131.1 134 VEEVVKQITAKYNAEELITKRPLVKADIETEITARLTPYNISTDAISITDFQFSPLFSQAIESKVEAEQKAlkaendlrrievEA 218
                 ************************************************************************7777777764333 PP

>> CdiA_C  Contact-dependent growth inhibition CdiA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.5   1.9e-05      0.17       7      80 ..     194     268 ..     193     269 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.9e-05
      CdiA_C   7 inGev.fDvKsptsgngkniisnilkkakkQakni.vlnlrdsdlsieeikegieralkwpkkglkeliiikkdgk 80 
                 i+++v  + K++++ n    i+   +  ++Qak i   n+ ++   + e +++i+ al+++++ l++l+++  dgk
  EPA06131.1 194 IESKVeAEQKALKAENDLRRIEVEARQQEQQAKGIaAANVAEA-SGEAEAIRIINDALAQNPNYLEWLKVQAWDGK 268
                 788888999****44444555555555555*****78888854.456999999*****999999999999888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1048  (0.0584528); expected 358.6 (0.02)
Passed bias filter:                      564  (0.0314574); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 1726.32
//
Query:       EPA06132.1  [L=43]
Description: hypothetical protein BG20_I0632 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.022   14.9   2.1      0.026   14.6   2.1    1.1  1  Fer4_21   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   2.1   1.5e-06     0.026      14      45 ..       6      38 ..       3      41 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.5e-06
     Fer4_21 14 CliaCedtshqaieidakt..vlkvvedeCvGCn 45
                C+  C+d++ ++ie++a++   +kv++ +C  C 
  EPA06132.1  6 CH-LCKDGGKNCIEVNANQdyAMKVLHPKCQICG 38
                44.5*********9987763356889****9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (43 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.42
# Mc/sec: 305.57
//
Query:       EPA06133.1  [L=97]
Description: hypothetical protein BG20_I0628 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00043   20.1   0.0     0.0006   19.7   0.0    1.2  1  TrmB         Sugar-specific transcriptional regulator TrmB
     0.0017   18.2   0.0     0.0022   17.8   0.0    1.1  1  HxlR         HxlR-like helix-turn-helix
  ------ inclusion threshold ------
      0.015   15.2   0.1      0.019   14.8   0.1    1.1  1  TFIIE_alpha  TFIIE alpha subunit
      0.098   12.3   0.0       0.15   11.8   0.0    1.2  1  GntR         Bacterial regulatory proteins, gntR family


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   1.3e-07    0.0006      18      58 ..      36      76 ..      31      89 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.3e-07
                HHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
        TrmB 18 lklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                l++g ++ d + ++lgv+  k ++vL+ Le+k + ++++++
  EPA06133.1 36 LSHGTKNFDALQKKLGVDNEKLNSVLEDLENKKFMKVVQKQ 76
                689*******************************9999876 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   4.8e-07    0.0022       8      69 ..      30      91 ..      26      94 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4.8e-07
                HHHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEES.SSS-EEEEEE-TCG CS
        HxlR  8 llilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierevyp.evPpkveYsltekG 69
                +l+l el +g+k f  l+++l ++ ++ L + L  Le++++++ +  +   +pk+e + te+G
  EPA06133.1 30 MLVLGELSHGTKNFDALQKKL-GVDNEKLNSVLEDLENKKFMKVVQKQgLFGPKIELHPTEEG 91
                89*******************.999***************99876655146899999988888 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   4.1e-06     0.019      22      62 ..      36      75 ..      27      86 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.1e-06
                 HHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEE CS
  TFIIE_alpha 22 LlekgevteedlakelkidlnelrklLnrLyearlvkykrr 62
                 L  +g  + + l+k+l++d ++l ++L +L +++++k++++
   EPA06133.1 36 LS-HGTKNFDALQKKLGVDNEKLNSVLEDLENKKFMKVVQK 75
                 44.77777899*************************99876 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.2e-05      0.15      12      63 ..      30      79 ..      28      79 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.2e-05
                HHHTTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTCEEE CS
        GntR 12 dIlsgelrpGdkLPsereLaaefgVsrttvReALrrLeaeglverrqgrGtf 63
                +++ gel++G+k     +L++++gV+   ++ +L  Le ++   + q++G f
  EPA06133.1 30 MLVLGELSHGTKN--FDALQKKLGVDNEKLNSVLEDLENKKFMKVVQKQGLF 79
                6778888889885..899******************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       817  (0.0455686); expected 358.6 (0.02)
Passed bias filter:                      633  (0.0353059); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.32s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 618.54
//
Query:       EPA06134.1  [L=57]
Description: hypothetical protein BG20_I0654 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       680  (0.0379274); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 429.15
//
Query:       EPA06135.1  [L=336]
Description: homoserine dehydrogenase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-54  184.7   0.2    2.2e-54  184.0   0.2    1.3  1  Homoserine_dh  Homoserine dehydrogenase
      3e-07   31.1   0.0    6.5e-07   30.0   0.0    1.6  1  NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
    3.6e-07   30.1   0.2    9.7e-07   28.8   0.2    1.6  1  ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydro


Domain annotation for each model (and alignments):
>> Homoserine_dh  Homoserine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.0   0.2   3.7e-58   2.2e-54       1     173 []     156     327 ..     156     327 .. 0.98

  Alignments for each domain:
  == domain 1  score: 184.0 bits;  conditional E-value: 3.7e-58
                    --HHHHHHTCTTSEEEEEEEE--HHHHHHHHHHHCHTT-HHHHHHHHHHTTSS-SSTHHHHTTHHHHHHHHHHHHHHCTTT--GGGSEE--STTS- CS
  Homoserine_dh   1 PiiktlkeilsgdritrieGilngtlnyiltemeeegasfsevlkeaqelGyaeaDptdDveGlDaarKlailarlafgleveledvevegisklt 96 
                    Pi++  k++l+g+rit+++Gilngt+nyilt+m++ g +f+++lk+a+++Gy eaD + D++GlDaa+Kl+ila+ +++++v++ d++++gi+++t
     EPA06135.1 156 PILDYAKNSLRGERITSFSGILNGTTNYILTNMAK-GLTFETALKDAKDKGYVEADESLDLDGLDAAAKLVILANWVMDMKVTMPDINCKGIRNVT 250
                    99999*****************************6.*9********************************************************** PP

                    HHHHHHHHCTTEEEEEEEEE.CEEEEEEEEEETTSGGGHSSST-EEEEEEESSSEEEEEEES-SSHHHHHHHHHHHHH CS
  Homoserine_dh  97 aedikeakeegkvlklvasa.vearVkpelvpkshplasvkgsenavlvetdrlgelviqGpgaGaepTAsavlsDll 173
                     +dik+a ++++ +kl+as+  e+ V+p++v+ ++pl+ v+g+ na+++++++ g+ +i G+gaG+++TAs++l+Dll
     EPA06135.1 251 TDDIKKATKNNCAIKLIASCnKELIVEPKEVSVDDPLC-VNGTLNAIAFTSEHSGTQTIIGKGAGGMETASSILRDLL 327
                    *******************97699*************9.*************************************96 PP

>> NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.0   1.1e-10   6.5e-07       1     113 [.       7     144 ..       7     148 .. 0.84

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 1.1e-10
                    --SHHHHHHHHHHHH---S......SEEEEEEEEESS.EEE-TT...............HHHHHT--CB---HHHHHHHHS-EEEEE-S--HHHH. CS
  NAD_binding_3   1 GlGaiGsavleqlkrqqse......ielelvavadrd.sllskd...............rkallasealtldlddliahldpdvvVEcasseava. 73 
                    G+G++G+++++++++  ++      ++ ++ +v d++ s+++k+               + ++ a+++  ++  d+i++l++dv++E ++s++   
     EPA06135.1   7 GFGVVGQSLVKLFNSRSEDlyakygLKPRVIGVFDSKgSAVDKAgleldklievkkkfgTVKNYANTKNNMSGVDMIKNLEADVLIETTASNYKDa 102
                    99************999999***99999*************999*********988888444555555555555678889********99887642 PP

                    ....TTHHHHHHTTEEEE-S--CGGG-HHHHHHHTSSSTTS--. CS
  NAD_binding_3  74 ....elvlkaLkagkdvvtankgaladealyeeLreaaeangak 113
                         ++ +a+k+ ++v+ +nkg la    +  L+e+a  n++ 
     EPA06135.1 103 epgmTHIISAMKKRMHVISVNKGPLA--LAFPSLMELATYNQVI 144
                    222269******************99..8899999999888775 PP

>> ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.2   1.6e-10   9.7e-07      36     118 ..       4      92 ..       1      99 [. 0.72

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 1.6e-10
                    EEE--SHHHHHHHHHHHHCT-..........EEEEEEESSEEEEETTEE-HHHHHHHHHCSSSSTTHSHHSTSTSEEESHHSHHHHSS-SEEE CS
  ELFV_dehydrog  36 aisGsGnvgsyaallltelga..........kvvavsDssGviydpeGldieellelkeerksvkeykkssekkaeyieneeellelkvdilv 118
                    +  G+G vg+  ++l+ ++ +          +v++v Ds+G  +d+ Gl++++l+e+k++ ++vk+y++++    + +++ + + +l++d+l+
     EPA06135.1   4 ILCGFGVVGQSLVKLFNSRSEdlyakyglkpRVIGVFDSKGSAVDKAGLELDKLIEVKKKFGTVKNYANTK----NNMSGVDMIKNLEADVLI 92 
                    566777777777777765443222222222269***********************************543....345555567778888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2065.97
//
Query:       EPA06136.1  [L=177]
Description: PAS domain S-box [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.9e-10   39.1   0.0    1.1e-09   38.5   0.0    1.3  1  PAS_9       PAS domain
    6.4e-09   35.8   0.0    8.2e-09   35.5   0.0    1.2  1  PAS         PAS fold
    1.3e-05   25.4   0.0    2.1e-05   24.7   0.0    1.4  1  PAS_3       PAS fold
    0.00033   20.9   0.0    0.00041   20.6   0.0    1.1  1  PAS_4       PAS fold
  ------ inclusion threshold ------
       0.66   10.0   4.4       0.19   11.8   0.9    2.0  2  PheRS_DBD2  PheRS DNA binding domain 2


Domain annotation for each model (and alignments):
>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   0.0     3e-13   1.1e-09       9     104 .]      22     117 ..      13     117 .. 0.89

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 3e-13
       PAS_9   9 pdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetfwvlltaspvkdddgelvgiivilrDite 104
                 + g il++N + ++ lGy + e+lgksi++ +  ++ +  n+ l+a +e+g+  + ++ +++ + +g+tf+  l a+ ++d++++l g   ++ Di+e
  EPA06136.1  22 SIGIILDCNSTYANKLGYAKSEILGKSIFEHVpkDSWEVMNDSLKAWFETGK--VTDRKITFKKQDGNTFPGILQATSLYDEKKNLLGSNTVIFDISE 117
                 567455**************************77777777888888888888..**********************************9999999997 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.0   2.3e-12   8.2e-09       9     105 ..      12     107 ..       4     115 .. 0.86

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 2.3e-12
                 HSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEECTTSSEEEEEEEEEEEEETTEEEEE CS
         PAS   9 slpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfklrdgrpihlevraspvrdaggeilg 105
                 ++p +   ++  g+il +N++++  lG++ +e+lgks+++ ++ + + e+    +++  ++ + ++ +i+fk++dg +++  ++a++++d+++++lg
  EPA06136.1  12 DAPIMWRRINSIGIILDCNSTYANKLGYAKSEILGKSIFEHVPKD-SWEVMNDSLKAWFETGKVTDRKITFKKQDGNTFPGILQATSLYDEKKNLLG 107
                 555555557788******************************875.44899999999999999*****************************99887 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   5.9e-09   2.1e-05       2      81 ..      27     104 ..      26     112 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 5.9e-09
       PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirdengk 81 
                 + ++ ++ + lGy ++e+lgk  s+ ++v  +  e ++++l++++++g++ +  + ++++dG ++    +a+ ++de+ +
  EPA06136.1  27 LDCNSTYANKLGYAKSEILGK--SIFEHVPKDSWEVMNDSLKAWFETGKVTDRKITFKKQDGNTFPGILQATSLYDEKKN 104
                 689999***************..***************************************999888888888777766 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   1.2e-07   0.00041       4     109 ..      13     119 ..      10     120 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.2e-07
       PAS_4   4 lpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.pgeerhyelrllPlrdesGevigvlvi 101
                  p ++  +++ g +l++N ++a  +g++  e+lGk+ +e +p+++ +   + l+++ e++++ ++ ++ +  +g + +  l+++ l de+   +g   +
  EPA06136.1  13 APIMWRRINSIGIILDCNSTYANKLGYAKSEILGKSIFEHVPKDSWEVMNDSLKAWFETGKVTDRKITFKKqDGNTFPGILQATSLYDEKKNLLGSNTV 111
                 5778888899999******************************************************99999*******************9**99999 PP

       PAS_4 102 srDiTerr 109
                 + Di+e++
  EPA06136.1 112 IFDISELK 119
                 99999976 PP

>> PheRS_DBD2  PheRS DNA binding domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.9   5.2e-05      0.19       4      26 ..     134     156 ..     132     156 .. 0.96
   2 ?   -2.6   0.1       1.6   5.7e+03      24      28 ..     169     173 ..     169     173 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.2e-05
  PheRS_DBD2   4 qekLkliqeGkadelddkeknEL 26 
                 +ekL  i++++++ ld++ k E+
  EPA06136.1 134 KEKLDDIKNNEYSKLDENSKSEY 156
                 89********************8 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.6
  PheRS_DBD2  24 nELKK 28 
                 ++LKK
  EPA06136.1 169 TDLKK 173
                 69**9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1364  (0.0760779); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1202.09
//
Query:       EPA06137.1  [L=174]
Description: hypothetical protein BG20_I0646 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       970  (0.0541023); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1216.17
//
Query:       EPA06138.1  [L=324]
Description: integral membrane protein, TerC family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      1e-49  168.7  13.8      1e-49  168.7  13.8    2.4  3  TerC       Integral membrane protein TerC family


Domain annotation for each model (and alignments):
>> TerC  Integral membrane protein TerC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    2.3   0.1    0.0066   1.2e+02      58     113 ..      10      67 ..       3      72 .. 0.71
   2 !  168.7  13.8   5.6e-54     1e-49       1     180 [.      86     290 ..      86     291 .. 0.92
   3 ?   -3.9   1.0      0.52   9.3e+03     130     137 ..     304     311 ..     295     318 .. 0.37

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.0066
        TerC  58 lfdlilligglfLlytavkellekr..le.nklvkeekkkkkktkstllavviqielaD 113
                 l +l +l+++++ + +a+++ l ++   +  k  + e ++  ++k+ l ++++ i la 
  EPA06138.1  10 L-ELWILFFAILGITIAIDLGLIHKlkRKlRKSSQPETEHIMSSKEALGWTLTWISLAG 67 
                 3.455667777777777765443333466788889999999999999999999998875 PP

  == domain 2  score: 168.7 bits;  conditional E-value: 5.6e-54
        TerC   1 ltlvlleivLsiDNlvviallvkk..lpeeqqkkalllGilgAlvlRillillavallelfdlilligglfLlytavkellekrlenklvkeekkkkkk 97 
                 +t++ le++Ls+DN++v++l++++  +p+++q+++l lGil A+++Ri+lil+++ lle f+++++++g +L +t+++++++k+ e+k++ e++   + 
  EPA06138.1  86 VTGYALEKSLSVDNMFVFLLVFTTlgIPHKYQHRVLSLGILSAIAMRIALILVGASLLENFHWMIYVFGGLLWFTSIRMIMQKE-EKKIELEKNIAVRI 183
                 589*********************99*******************************************************977.33444444444444 PP

        TerC  98 tkst........................llavviqielaDlvfslDSvlaavaitsdlfivitavilsilvlrflakllakllerfptlkylalallll 172
                  k++                        ll+ + +iel+Dlvf++DS++a++ait+d+fivit+++++il+lr+l++l+  +lerf++lk ++++lll+
  EPA06138.1 184 LKKFmpvnlslvgnsfviringvlhatpLLVGLAIIELTDLVFAMDSIPAVLAITRDPFIVITSNVFAILGLRALYFLIGGMLERFHYLKPGLIVLLLF 282
                 44446666777**************************************************************************************** PP

        TerC 173 igvklvle 180
                 ig+k++++
  EPA06138.1 283 IGTKMIIS 290
                 *****986 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 0.52
        TerC 130 dlfivita 137
                  ++i+ t 
  EPA06138.1 304 VFVILATV 311
                 22222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1114  (0.062134); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2281.89
//
Query:       EPA06139.1  [L=369]
Description: small GTP-binding protein domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.9e-29  100.5   3.9    9.6e-29   99.5   3.9    1.5  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
    1.9e-22   79.5   0.3    4.8e-22   78.2   0.0    1.8  2  MMR_HSR1      50S ribosome-binding GTPase
    4.5e-21   74.7   0.1    1.3e-20   73.2   0.0    1.9  2  TGS           TGS domain
      7e-15   54.9   2.0    9.9e-13   47.9   0.0    2.4  2  FeoB_N        Ferrous iron transport protein B
    6.4e-06   26.2   1.5     0.0091   15.9   0.0    2.5  2  RsgA_GTPase   RsgA GTPase
    0.00041   20.4   1.5       0.54   10.3   0.1    2.9  3  Dynamin_N     Dynamin family
    0.00052   20.2   0.1    0.00067   19.9   0.1    1.1  1  MnmE_helical  MnmE helical domain
     0.0013   18.1   0.0     0.0025   17.2   0.0    1.4  1  AIG1          AIG1 family
     0.0019   17.8   1.0      0.096   12.3   0.1    2.5  2  cobW          CobW/HypB/UreG, nucleotide-binding domain
     0.0031   17.0   1.6      0.038   13.4   0.0    2.4  2  Arf           ADP-ribosylation factor family
     0.0057   16.1   0.9      0.008   15.6   0.1    1.7  2  SRPRB         Signal recognition particle receptor beta subun
  ------ inclusion threshold ------
      0.023   14.9   0.1       0.13   12.5   0.0    2.2  2  AAA_22        AAA domain
      0.025   14.8   0.1      0.051   13.8   0.1    1.5  1  AAA_28        AAA domain
      0.029   14.8   0.4       0.18   12.2   0.1    2.3  2  AAA_16        AAA ATPase domain
      0.068   12.8   1.2        4.8    6.8   0.0    2.3  2  Ras           Ras family
      0.097   12.8   0.1       0.22   11.7   0.1    1.6  1  AAA_33        AAA domain


Domain annotation for each model (and alignments):
>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.5   3.9   8.5e-32   9.6e-29       2     105 ..     185     290 ..     184     291 .. 0.97

  Alignments for each domain:
  == domain 1  score: 99.5 bits;  conditional E-value: 8.5e-32
  MMR_HSR1_Xtn   2 gGikitstvkltkldeetvkkilkeykihnaevliredvtvDdlidviegnrvYipclyvlNKiDlisleeldelare..pnsvviSaekelnldeL 96 
                   gGi i+++vkltk++e++ k+il+ y+i++a+v++red+t ++l d i+gn +Y ++l++lNKiDl++ e l++l+++  ++++ +Sa++++n++ L
    EPA06139.1 185 GGIAIAQQVKLTKISEQHLKDILHIYGIVSARVVVREDITSEQLADHIAGNISYSKSLTILNKIDLVDREFLEDLKTKikSEVIEVSANSDINIELL 281
                   9***************************************************************************965479999************ PP

  MMR_HSR1_Xtn  97 kekiweeLn 105
                   keki+e+Ln
    EPA06139.1 282 KEKIYEKLN 290
                   ********8 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.2   0.0   4.3e-25   4.8e-22       2      87 ..      66     155 ..      65     182 .. 0.88
   2 ?   -2.1   0.1       3.6     4e+03      93      93 ..     251     251 ..     191     290 .. 0.59

  Alignments for each domain:
  == domain 1  score: 78.2 bits;  conditional E-value: 4.3e-25
                 EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHC.TSEEEEEEETT...T CS
    MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkaflalee.adlillvvdas...e 87 
                 v+++G p vGKStL+n+lt++k+ v+++++tT++++ g ++++g +i+++D+pG+i+gas++kglgk++l++ + adl+llv+d+    +
  EPA06139.1  66 VVFIGLPSVGKSTLLNKLTDAKSAVGAYQFTTLTVVPGMMDYRGAKIQVLDLPGIIKGASSGKGLGKRILSVARsADLVLLVLDVFqpfH 155
                 89*********************************************************************99978********873331 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.6
                 H CS
    MMR_HSR1  93 l 93 
                 +
  EPA06139.1 251 V 251
                 2 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       6.4   7.2e+03      12      27 ..     218     233 ..     212     236 .. 0.78
   2 !   73.2   0.0   1.2e-23   1.3e-20       1      60 []     292     365 ..     292     365 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 6.4
                 EEETTB-HHHHHHHHS CS
         TGS  12 dlprgatveDfAykIh 27 
                  +++  t e++A +I 
  EPA06139.1 218 VVREDITSEQLADHIA 233
                 4788899999999985 PP

  == domain 2  score: 73.2 bits;  conditional E-value: 1.2e-23
                 EEEEE.TTSSEEE......EETTB-HHHHHHHHSTTHHHHEEEEEECS.......EEEETTSBB-SSEEEEEEE CS
         TGS   1 irvyt.PdGkvpd......lprgatveDfAykIhrslakkfiyAlVnG.......qrvgldhvLedgdvveIvt 60 
                 ir+y+ P+G + d       ++g tveD+++k+hr ++k+f+y+ ++G       qrvgldh ++d+dv++I++
  EPA06139.1 292 IRIYMrPKGGETDfkepliAREGDTVEDICNKLHRNMKKQFRYGMIWGksvkfggQRVGLDHIVQDEDVLTIIK 365
                 89**********************************************************************97 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.9   0.0   8.8e-16   9.9e-13       2      98 ..      65     160 ..      64     171 .. 0.87
   2 !    6.1   0.3    0.0064       7.2     109     156 .]     242     285 ..     235     285 .. 0.85

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 8.8e-16
                 EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHH.CTSSSEEEEEEEGGGHHHHHHHH CS
      FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardfll.eeepdvvvnvvdatnlernLyLt 98 
                 tv+++G p vGk+tl+n+lt+ak+ vg ++ +t     g ++++g +++++DlPGi  ++  s+ + + +++l   +++d+v+ v+d  +   + +L+
  EPA06139.1  65 TVVFIGLPSVGKSTLLNKLTDAKSAVGAYQFTTLTVVPGMMDYRGAKIQVLDLPGI--IKGASSGKGLGKRILSvARSADLVLLVLDVFQPFHEDVLV 160
                 799****************************************************9..6788999999999997477899999999987765555555 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0064
                 EEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBTHHHHHHHH CS
      FeoB_N 109 vlalnmideaekkgieidlkkLsekLgvpvvktsakkkegieellkai 156
                 + +ln+id ++++ +    + L++k++ +v+++sa++  +ie l+++i
  EPA06139.1 242 LTILNKIDLVDREFL----EDLKTKIKSEVIEVSANSDINIELLKEKI 285
                 567788888877764....689**********************9986 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   8.1e-06    0.0091      99     124 ..      63      87 ..      13      98 .. 0.86
   2 !    9.1   0.4     0.001       1.2      49     102 ..     241     290 ..     194     293 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 8.1e-06
                  TSEEEEECSTTSSHHHHHHHHCTT-- CS
  RsgA_GTPase  99 dktsvlvGqSGvGKStLinallpele 124
                  d t+v++G   vGKStL+n+l+   +
   EPA06139.1  63 DATVVFIGLPSVGKSTLLNKLTDA-K 87 
                  5899*****************986.3 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.001
                  EEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTTSEE CS
  RsgA_GTPase  49 pvivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelkellkdkts 102
                   + +lnKiDl+++e  le+lk   +++  ev+ vsa++  ++e lke++ +k+ 
   EPA06139.1 241 SLTILNKIDLVDREF-LEDLK---TKIKSEVIEVSANSDINIELLKEKIYEKLN 290
                  56689*******999.66555...566678****************99988876 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.2       6.3   7.1e+03      59      72 ..      28      41 ..       5      53 .. 0.43
   2 !   10.3   0.1   0.00048      0.54       1      22 [.      66      87 ..      66     102 .. 0.80
   3 !    8.3   0.0     0.002       2.2     101     142 ..     110     154 ..      99     161 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 6.3
                T-EB--CHHHHHHH CS
   Dynamin_N 59 ekkledfsevreei 72
                     ++ ++++e+
  EPA06139.1 28 GLLKAKIAKLKREQ 41
                33333444444444 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00048
                EEEEEBTTTTHHHHHHHHHTS- CS
   Dynamin_N  1 iavvGsqSsGKSSvlnaLlged 22
                ++++G  S GKS++ln+L+ ++
  EPA06139.1 66 VVFIGLPSVGKSTLLNKLTDAK 87
                7899**************9877 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.002
                 -SEEEEE---B-SSSGTTS...HHHHHHHSTTEEEEEEEETTS-C CS
   Dynamin_N 101 kgltlvDlPGldsvnkrdq...elvkeyikkadiilavtsanhdl 142
                  ++ ++DlPG+++ +   +   + + + +++ad++l+v++  + +
  EPA06139.1 110 AKIQVLDLPGIIKGASSGKglgKRILSVARSADLVLLVLDVFQPF 154
                 67899********9999999999999999*********9987766 PP

>> MnmE_helical  MnmE helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.1     6e-07   0.00067      63     133 ..      19     292 ..       4     341 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 6e-07
                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................................................... RF
  MnmE_helical  63 seeelaekleelkeelekllatakrgellreGik............................................................... 96 
                    +++ ++ +  lk+++ kl ++ ++ e+ ++G+k                                                               
    EPA06139.1  19 INKATNHHIGLLKAKIAKLKREQEDREIQKSGVKtdgfdvrrsgdatvvfiglpsvgkstllnkltdaksavgayqfttltvvpgmmdyrgakiqvl 115
                   334667778889************************************************************************************* PP

                   ................................................................................................. RF
  MnmE_helical  97 ................................................................................................. 96 
                                                                                                                    
    EPA06139.1 116 dlpgiikgassgkglgkrilsvarsadlvllvldvfqpfhedvlvnelgnigirlnrlppnitvekspmggiaiaqqvkltkiseqhlkdilhiygi 212
                   ************************************************************************************************* PP

                   ....................................xxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxx.xx.x RF
  MnmE_helical  97 ....................................Dllkeke.....ekeeeevlkiSaktgegieeLeeaike.le.l 133
                                                       Dl +++      +k ++ev+++Sa+++ +ie L+e+i e l+ +
    EPA06139.1 213 vsarvvvreditseqladhiagnisysksltilnkiDLVDREFledlkTKIKSEVIEVSANSDINIELLKEKIYEkLNfI 292
                   ****************************999999994444444555557778999******************9966633 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.2e-06    0.0025       2     100 ..      65     157 ..      64     165 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.2e-06
                 EEEEESSTTSSHHHHHHHHHTS--SS--TTTS---SS-EEEEEEETTEEEEEEE--SCCCTTCCHHCHHHHHHHHHHHCTT-ESEEEEEEETTB-SHHH CS
        AIG1   2 tivlvGktgnGkSaTgNsilgkkaFesklsaqsvtkkcqkksrtwdgkkinViDTPglfdlsvsadkiskeivrclllseegihalllvlslgrfteed 100
                 t+v +G   +GkS+  N + + k        q  t ++       +g ki+V D Pg++   +s + + k i       + + + +llvl++ +  +ed
  EPA06139.1  65 TVVFIGLPSVGKSTLLNKLTDAKSAVGA--YQFTTLTVVPGMMDYRGAKIQVLDLPGIIKGASSGKGLGKRILS----VARSADLVLLVLDVFQPFHED 157
                 7999**************9888765544..567777888888899********************999998874....455589******997544455 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1     0.034        38       3      24 ..      66      87 ..      64      94 .. 0.81
   2 !   12.3   0.1   8.6e-05     0.096      91     166 ..     185     263 ..     155     272 .. 0.67

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.034
                EEEEESTTCCHHHHHHHHHCT- CS
        cobW  3 tvltGflGsGKTtLlnhllenr 24
                +v+ G +  GK+tLln+l++ +
  EPA06139.1 66 VVFIGLPSVGKSTLLNKLTDAK 87
                677899999********99543 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 8.6e-05
                 CTTTTHHHHHTT...SHHHHHCCCECEEEEEEETTTH....CCHCCHHHHHHHHHHTS.SEEEEE-HHHHCHC..HHHHHHHH CS
        cobW  91 tGlaePapvaft...eeelksdltldavvavvDaknl...eaeeekieekaedqlaaa.dllvlnKtDlldeeallekleerl 166
                 +G+a +++v +t   e++lk+     ++  +v+a+ +   +  +e+ ++ +   + ++ +l +lnK+Dl+d e+l e l++++
  EPA06139.1 185 GGIAIAQQVKLTkisEQHLKDI---LHIYGIVSARVVvreDITSEQLADHIAGNISYSkSLTILNKIDLVDREFL-EDLKTKI 263
                 4688888884442334444443...3455666665555543455666666667777773678**********987.6666555 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   3.4e-05     0.038      14      67 ..      63     119 ..      56     123 .. 0.79
   2 ?    2.2   0.3     0.094   1.1e+02     113     148 ..     236     273 ..     190     292 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.4e-05
                 EEEEEEEESTTSSHHHHHHHHHHSSCEE...CSSSSSEEEEEEEETTEEEEEEEE-S CS
         Arf  14 elrilllGLDnaGKtTilkklkleelvt...tvPTigfnveeleiknlkftvwDvGG 67 
                 ++ ++++GL + GK+T+l+kl++ + +    +  T+      + +++ k++v D+ G
  EPA06139.1  63 DATVVFIGLPSVGKSTLLNKLTDAKSAVgayQFTTLTVVPGMMDYRGAKIQVLDLPG 119
                 5679*****************988766544455566666667788999999999876 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.094
                 CTTSEEEEEEE-TTSTTSS-HHHHHHHTTGGGSS..SS CS
         Arf 113 lkevallvlaNKqDlpealseeelrellgleelk..gk 148
                 ++  + l + NK+Dl +    e+l+++++ e ++  ++
  EPA06139.1 236 ISYSKSLTILNKIDLVDREFLEDLKTKIKSEVIEvsAN 273
                 44556677889999999999888888888777663333 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.1       6.4   7.2e+03     127     141 ..      32      46 ..      12      57 .. 0.46
   2 !   15.6   0.1   7.1e-06     0.008       4      59 ..      64     120 ..      61     141 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 6.4
                 ---HHHHHHHHHHHH CS
       SRPRB 127 akspklikdaLEkEl 141
                 ak +kl +++ ++E+
  EPA06139.1  32 AKIAKLKREQEDREI 46 
                 233333333333333 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 7.1e-06
                 -EEEEE-STTSSHHHHHHHHHHSS---B---S.S-EEETTG...GGTT-SEEEETT- CS
       SRPRB   4 pavllvGlsdsGKTslftrLttdsvkktvtSq.essaalkvksekgskltliDfPGh 59 
                  +v+++Gl   GK +l+++Lt  +           +++  + + +g k++++D+PG 
  EPA06139.1  64 ATVVFIGLPSVGKSTLLNKLTDAKSAVGAYQFtTLTVVPGMMDYRGAKIQVLDLPGI 120
                 689*****************9874443333332555666667889**********95 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00012      0.13       5     112 ..      63     163 ..      59     180 .. 0.68
   2 ?   -0.7   0.1       1.4   1.6e+03      96     113 ..     244     260 ..     199     333 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
      AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevv.fvtlpsstsskdllrellralglelkaer.lsseellealeqalraravielliiDEaq 101
                 +  +v +G + +GK+tll++l++ + +        ++ + f tl++  +  d + +  + l+l++  ++  s + l +++   +r+++  +ll++D +q
  EPA06139.1  63 DATVVFIGLPSVGKSTLLNKLTDAKSA--------VGAYqFTTLTVVPGMMDYRGAKIQVLDLPGIIKGaSSGKGLGKRILSVARSADL-VLLVLDVFQ 152
                 5567899****************9863........333344444444444444444444444444443305556666999999999999.999999999 PP

      AAA_22 102 hlrs.eealeeL 112
                  + + + +++eL
  EPA06139.1 153 PF-HeDVLVNEL 163
                 88.535555555 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.4
      AAA_22  96 iiDEaqhlrseealeeLr 113
                 i+  ++ +   e le+L+
  EPA06139.1 244 ILNKIDLV-DREFLEDLK 260
                 44444444.444444443 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   4.6e-05     0.051       2      22 ..      66      86 ..      65     101 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.6e-05
      AAA_28  2 ivitGgestGKTtlleaLaar 22
                +v++G +s GK+tll++L++ 
  EPA06139.1 66 VVFIGLPSVGKSTLLNKLTDA 86
                9*****************965 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00016      0.18      20      48 ..      60      86 ..      44     107 .. 0.80
   2 ?   -0.7   0.0       1.4   1.6e+03     123     149 ..     131     156 ..     110     160 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00016
      AAA_16 20 rsgrpelvllsGesGvGKsslvrellral 48
                rsg+   v+++G + vGKs+l+++l + +
  EPA06139.1 60 RSGD-ATVVFIGLPSVGKSTLLNKLTD-A 86
                4444.7999***************995.3 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.4
      AAA_16 123 lkrllallsrderplvlvlDdlqwade 149
                  kr+l+ +++ ++ ++lvlD +q + e
  EPA06139.1 131 GKRILSVARS-ADLVLLVLDVFQPFHE 156
                 5678888888.55599****9997665 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0    0.0043       4.8       2      23 ..      66      87 ..      65     119 .. 0.80
   2 ?    4.7   0.2     0.018        20      95     159 ..     226     288 ..     191     291 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0043
                EEEEESTTSSHHHHHHHHHHSS CS
         Ras  2 lvlvGdsavGKtslllrfvkdk 23
                +v++G  +vGK++ll++ ++ k
  EPA06139.1 66 VVFIGLPSVGKSTLLNKLTDAK 87
                799*************999865 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.018
                 HHHHHHST...TTSEEEEEEETTTGGGG-SS-HHHHHHHHHHHTSEEEEEBTTTTCTHHHHHHHHHHH CS
         Ras  95 eeikrvae...envpivLvGnKvDleekravsteegeelakelglkfletSAktnenveeafeellre 159
                 e++ ++     +  + + + nK+Dl +     +e  e+l  +++ + +e+SA+++ n+e + e++ ++
  EPA06139.1 226 EQLADHIAgniSYSKSLTILNKIDLVD-----REFLEDLKTKIKSEVIEVSANSDINIELLKEKIYEK 288
                 444444443332344555667777765.....5666788899999*************9888777766 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1    0.0002      0.22       2      24 ..      66      88 ..      65      99 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0002
      AAA_33  2 vllvGlpGsGKstlaerllkklg 24
                v+++Glp +GKstl+ +l  +  
  EPA06139.1 66 VVFIGLPSVGKSTLLNKLTDAKS 88
                79*************99986655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       826  (0.0460706); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 2305.70
//
Query:       EPA06140.1  [L=186]
Description: hypothetical protein BG20_I0644 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1332.39
//
Query:       EPA06141.1  [L=79]
Description: hypothetical protein BG20_I0657 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0083   16.3   0.0      0.059   13.6   0.1    2.1  2  SAC3      Leucine permease transcriptional regulator helical 
  ------ inclusion threshold ------
      0.024   15.5   0.8       0.03   15.2   0.8    1.1  1  YodL      YodL-like
       0.14   11.8   0.7        3.6    7.3   0.0    2.7  3  CENP-B_N  CENP-B N-terminal DNA-binding domain


Domain annotation for each model (and alignments):
>> SAC3  Leucine permease transcriptional regulator helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.11   6.7e+02      50      58 ..       7      15 ..       4      19 .. 0.79
   2 !   13.6   0.1   9.9e-06     0.059      17      47 ..      47      77 ..      32      78 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.11
                HHHHHHHHH CS
        SAC3 50 ihEklYliy 58
                ++Ek+Y+i 
  EPA06141.1  7 LKEKIYQIK 15
                8999**985 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 9.9e-06
                HHHHHHHHHHHHH...HHHHHHHHHHHHHHH CS
        SAC3 17 lekilknllkeenrknerkqiIdsLseeLyd 47
                +++i ++ ++e + ++ ++qiI+ +++eL++
  EPA06141.1 47 FHSIFSDQVTESEWNKSKAQIIKRFQDELFH 77
                6788899999999999**************7 PP

>> YodL  YodL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.8     5e-06      0.03       3      59 ..      10      72 ..       8      77 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5e-06
        YodL  3 riyqlkedleeerelrFesleelkkegleidaenYelvyegel........setetleeiyekfn 59
                +iyq+k+d  ++++++  s+  l  ++++i a++Y +v   ++        + +++  +i ++f+
  EPA06141.1 10 KIYQIKQD--PQNNFKLVSYFPLSDQEKQIIAKDYGVVKFHSIfsdqvtesEWNKSKAQIIKRFQ 72
                7*******..5999******999999999999999887555553322233222255555555555 PP

>> CENP-B_N  CENP-B N-terminal DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.1      0.12   6.9e+02       9      22 ..       7      20 ..       6      23 .. 0.74
   2 ?    1.0   0.0     0.056   3.3e+02      25      35 ..      35      45 ..      32      47 .. 0.82
   3 ?    7.3   0.0    0.0006       3.6      16      32 ..      55      71 ..      52      72 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.12
                HHHHHHHHHHHHCT CS
    CENP-B_N  9 lreKievIqrleeg 22
                l+eKi  I++  ++
  EPA06141.1  7 LKEKIYQIKQDPQN 20
                78999888876555 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.056
                HHHHHHHHT-- CS
    CENP-B_N 25 kaelarrfnvp 35
                k+ +a++++v 
  EPA06141.1 35 KQIIAKDYGVV 45
                6679*****96 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0006
                HHHHHCTT-HHHHHHHH CS
    CENP-B_N 16 IqrleegeSkaelarrf 32
                ++++e ++Ska + +rf
  EPA06141.1 55 VTESEWNKSKAQIIKRF 71
                6899************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       905  (0.0504769); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 570.28
//
Query:       EPA06142.1  [L=34]
Description: hypothetical protein BG20_I0619, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (34 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      138  (0.00769703); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.26s 00:00:00.59 Elapsed: 00:00:00.41
# Mc/sec: 248.89
//
Query:       EPA06143.1  [L=628]
Description: arginine--tRNA ligase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.8e-28   97.2   0.1    3.8e-27   94.8   0.0    2.3  3  DALR_1           DALR anticodon binding domain
      1e-25   90.4   6.2    5.2e-21   75.0   0.4    2.2  2  tRNA-synt_1d     tRNA synthetases class I (R)
    3.7e-16   59.5   0.1      1e-15   58.1   0.1    1.8  1  Arg_tRNA_synt_N  Arginyl tRNA synthetase N terminal domain
     0.0017   17.8   0.2     0.0017   17.8   0.2    2.0  2  tRNA-synt_1e     tRNA synthetases class I (C) catalytic domai
     0.0052   15.6   0.1      0.012   14.4   0.1    1.6  1  tRNA-synt_1g     tRNA synthetases class I (M)
  ------ inclusion threshold ------
      0.039   12.9   0.4       0.13   11.2   0.1    2.0  2  tRNA-synt_1f     tRNA synthetases class I (K)
        2.3    8.8   5.8         16    6.1   0.4    3.3  3  PNPase           Polyribonucleotide nucleotidyltransferase, R


Domain annotation for each model (and alignments):
>> DALR_1  DALR anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       4.2   1.1e+04      35      54 ..      45      64 ..      31      71 .. 0.75
   2 ?   -2.0   0.1       1.5   3.9e+03      28      65 ..     212     248 ..     202     251 .. 0.66
   3 !   94.8   0.0   1.5e-30   3.8e-27       1     119 []     512     628 .]     512     628 .] 0.96

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 4.2
                HHHHHHHHHTHHHHHHHHHH CS
      DALR_1 35 ekeLlkalaqfpevleeaae 54
                   L+k+l + p+ +++++ 
  EPA06143.1 45 SFLLAKQLKKNPKEIANMLA 64
                56788888888888877654 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.5
                 CCS-SHHHHHHHHHHHTHHHHHHHHHHHT-THHHHHHH CS
      DALR_1  28 alleeeeekeLlkalaqfpevleeaaeelephklaeyl 65 
                 ++  ee  k++lk+l +  +  ++ a++ +  +l ++l
  EPA06143.1 212 SS-LEEIRKNVLKELEDGDSQTAKFADKITRRVLENQL 248
                 33.57888888888888888888888877666655555 PP

  == domain 3  score: 94.8 bits;  conditional E-value: 1.5e-30
                 HHHHHHHHHHHHHHTTCTTCCCCHCCHCCS-SHHHHHHHHHHHTHHHHHHHHHHHT-THHHHHHHHHHHHHHHHHHHHCTSTTSCTHHH.HHHHHHHHH CS
      DALR_1   1 vqyahaRiksilrkaeeegekleeealalleeeeekeLlkalaqfpevleeaaeelephklaeylyeLaatfhkfYnkervlkeeeeelaaaRLaLvka 99 
                 +qy+haR++ i +k++ +  + + + ++l ++++e+ L++++  f+ v+ +aa++l+p+++a+y+++La +f++fY++++v++  +++l+++RL Lv++
  EPA06143.1 512 IQYTHARASRIIEKSGRSP-SIDVDFSLL-TDDSELGLVRTIGLFELVVLNAAQNLSPKVIARYCHDLAVSFNSFYEHVKVIDLGDQKLENSRLCLVNS 608
                 7*************99766.667777776.99******************************************************************* PP

                 HHHHHHHHHHHTT----S-- CS
      DALR_1 100 vrqvLangLdlLGieapekm 119
                  + +L++ L lLGieap+km
  EPA06143.1 609 FKMTLEKSLGLLGIEAPDKM 628
                 *******************9 PP

>> tRNA-synt_1d  tRNA synthetases class I (R)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.0   0.4     2e-24   5.2e-21      14     222 ..     111     328 ..      95     337 .. 0.82
   2 !   18.1   1.0   4.1e-07     0.001     213     339 ..     354     488 ..     347     497 .. 0.70

  Alignments for each domain:
  == domain 1  score: 75.0 bits;  conditional E-value: 2e-24
                   ---SST-EEEEE----BTTS--BHHHHHHHHHHHHHHHHHHHCT-EEEEEE--B-SSTCHHHHHHHHHHHTTTTT.TS-----SC..CCHHHHHHHH CS
  tRNA-synt_1d  14 kksrekkkvvvdfssPniakemhvGhLrstiiGdavsrlleflGydvirlnhvGDWGtqfGlLiaylekkqdekl.lqeqelqdL..eafykeakkd 107
                   + ++++  +vv+++s n  k +h+Gh+r  iiGd+++r+l    y+v  ln+v D G q   +i+++   + e+     ++ ++   +++y+++  +
    EPA06143.1 111 VDLGKNSSIVVEHTSVNPNKALHIGHIRNIIIGDTIARILKKSNYKVNVLNYVDDSGLQVADIIVGFTYFGFEQEpPAGKKFDHYcgDDVYVKTTEK 207
                   6778999**********************************************************999876554313345555553379******** PP

                   CCCSHCCCHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHCT---EC.--CC..CCCCCHHHHHHHHHCTT-EE.ECTTCEE..EEECCCT CS
  tRNA-synt_1d 108 ydeeeifaerarnyvvkLqsgdedirklwkllvditrtelqklydrldvtlie.rGes..lykeslneivkelkkkglvk.esdGalv..vfldefg 198
                   y+++  ++e  +n++++L++gd ++ k+  +++  + +++ ++  +l v       es  +      +i ++lk+ +l++ es+G+      +    
    EPA06143.1 208 YEHDSSLEEIRKNVLKELEDGDSQTAKFADKITRRVLENQLETCWNLGVYYDClNFESqiIRSGLWSKIFEKLKEMSLIEfESEGKNAncWVIRGEN 304
                   *******************************99988887888888999988556778884555566899********99757888764113333335 PP

                   SSCCEECC-TTS-B-HHHHHHHHH CS
  tRNA-synt_1d 199 krlgvvvqksDGgylytttDiaaa 222
                   ++   v+++s+G+ +y ++Di  a
    EPA06143.1 305 NEEDKVIVRSNGTATYIAKDIPYA 328
                   66678***************9655 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 4.1e-07
                   -HHHHHHHHHHHHHHTT--SEEEEEEECCCHHHHHHHHHHHHCTTSSTT........TSEEEEE.EE--EE-TTSS..BSBCSSSTC-BHHHHHHHH CS
  tRNA-synt_1d 213 lytttDiaaakerkeelkadkvlyvidsrqslhlqqiflilkkigyvpe........skdleha.nfGmvlgkdkk..kfktrkGetvkLadlLdea 298
                   l++tt +a   e++++  adkv+ vidsrq    + i  ++ k    p+        s++l       + l  d+k  +++ rkG  v+ + + d  
    EPA06143.1 354 LWQTT-LADSNEQRQHFTADKVITVIDSRQARLQKIITTLMSKFKSAPDayvhlgyeSVTLSADtAQTLGLETDGKqaQMSGRKGLYVNADSVYDIL 449
                   55555.566667778899************97666666666666555553000000044443321222334466663369***************** PP

                   HHHHHHHHCCCCCCTS-CCCCHCHHHHHHHHHHHHCCCCTS CS
  tRNA-synt_1d 299 leralqlikeknkdkvlqadelekvaeavgvgaikyaDlsk 339
                    +++++  k +  +  ++  e +k+a+ v+vg+++y+ +++
    EPA06143.1 450 KNKTIEETKKRHSE--MNDSEIQKIAHIVSVGTLRYEMIKQ 488
                   **999966666666..9999***************987765 PP

>> Arg_tRNA_synt_N  Arginyl tRNA synthetase N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.1   0.1   3.9e-19     1e-15       2      84 ..       9      89 ..       4      90 .. 0.86

  Alignments for each domain:
  == domain 1  score: 58.1 bits;  conditional E-value: 3.9e-19
                     HHHHHHHHHHHHHHSS-HHHHGGG-E-.SSGGG-SEEEEGGGG--TT-..-HHHHHHHHHHT---TTT..EEEEEEETT.EEEEE CS
  Arg_tRNA_synt_N  2 elkeaiaealkkaagadleeeeiviekpknpkfGDyatnvamqlakklkknPreiAeeiaekleksei..iekvevagpGFiNff 84
                     e+++ i + l+++     + + +++e p++p fGD ++nv + lak+lkknP+eiA+ +a+k+e+s++  + +ve    G++Nff
       EPA06143.1  9 EIENNIHKILDEM---SISGILFSVE-PSKPGFGDASSNVSFLLAKQLKKNPKEIANMLASKFETSQNilVLRVESHHSGYLNFF 89
                     4555555555555...6777888998.8**************************************998899************9 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.2   6.7e-07    0.0017      21      56 ..     130     165 ..     115     177 .. 0.88
   2 ?   -2.2   0.2      0.77     2e+03     249     291 ..     454     496 ..     446     500 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 6.7e-07
                   S--BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB- CS
  tRNA-synt_1e  21 dashlGhaRslvafDilrrilqalgYdvqfvqnvtD 56 
                    a h+Gh R++++ D ++ril++++Y+v+ ++ v D
    EPA06143.1 130 KALHIGHIRNIIIGDTIARILKKSNYKVNVLNYVDD 165
                   578*************************98776655 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.77
                   ETTBE--TTTT---BHHHHHTTS-HHHHHHHHHSS-TTS-EEE CS
  tRNA-synt_1e 249 iegekmsksLknfitikdvlkkfdprqlRllllsahyrsqldf 291
                   ie+ k   s  n   i+++ + ++  +lR+ +++++  + + f
    EPA06143.1 454 IEETKKRHSEMNDSEIQKIAHIVSVGTLRYEMIKQDLDKIITF 496
                   7888888899999999999999999999999999988877766 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   4.6e-06     0.012      10      52 ..     128     170 ..     119     172 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.6e-06
                   -SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHH CS
  tRNA-synt_1g  10 angklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpi 52 
                   +n +lH+Gh++++i++D +aR  ++++++v  +   D  G ++
    EPA06143.1 128 PNKALHIGHIRNIIIGDTIARILKKSNYKVNVLNYVDDSGLQV 170
                   6999*************************99998888888765 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   5.1e-05      0.13      28      70 ..     123     165 ..     108     168 .. 0.86
   2 ?   -1.9   0.0      0.45   1.2e+03     271     321 ..     446     498 ..     427     508 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.1e-05
  tRNA-synt_1f  28 esGispSGliHiGnlrevltadlvaralrkrgeevrlilisDd 70 
                    + + p   +HiG +r+++ +d +ar l+k   +v+++ ++Dd
    EPA06143.1 123 HTSVNPNKALHIGHIRNIIIGDTIARILKKSNYKVNVLNYVDD 165
                   4667788889********************************9 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.45
  tRNA-synt_1f 271 Yelillkgge..kmssSkGnvltledwlevaepevlrflilrrkPkkakkldl 321
                   Y+++  k  e  k   S+ n   ++++ ++++  +lr+ ++++   k +++dl
    EPA06143.1 446 YDILKNKTIEetKKRHSEMNDSEIQKIAHIVSVGTLRYEMIKQDLDKIITFDL 498
                   55555554443355567777777888888888888888888877777666665 PP

>> PNPase  Polyribonucleotide nucleotidyltransferase, RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.4    0.0061        16      19      49 ..     203     233 ..     198     248 .. 0.73
   2 ?   -1.3   0.0       1.3   3.2e+03      24      42 ..     379     397 ..     372     402 .. 0.80
   3 ?    3.5   0.2     0.039     1e+02      33      75 ..     449     488 ..     431     490 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0061
                 TSSSHHHHHHHHHHHHHHHHHHHH...HHST CS
      PNPase  19 titeKqeRyaaldeikekvveafaaeleeed 49 
                 + teK e ++ l+ei+++v+++++    ++ 
  EPA06143.1 203 KTTEKYEHDSSLEEIRKNVLKELEDGDSQTA 233
                 459*******************994443333 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.3
                 HHHHHHHHHHHHHHHHHHH CS
      PNPase  24 qeRyaaldeikekvveafa 42 
                 + R+a+l++i ++ + +f 
  EPA06143.1 379 DSRQARLQKIITTLMSKFK 397
                 7899999999999998886 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.039
                 HHHHHHHHHH...HHSTTS-HHHHHHHHHHHHHHHHHHHHHHT CS
      PNPase  33 ikekvveafaaeleeedeedekeikeifkalekkvvRsrilde 75 
                 +k+k++e+     + ++e + +ei++i + ++  ++R +++++
  EPA06143.1 449 LKNKTIEETK---KRHSEMNDSEIQKIAHIVSVGTLRYEMIKQ 488
                 4555555555...5567999*****************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (628 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       945  (0.0527079); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.67u 0.29s 00:00:00.96 Elapsed: 00:00:00.46
# Mc/sec: 4136.94
//
Query:       EPA06144.1  [L=277]
Description: hypothetical protein BG20_I0648 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.5e-35  119.3  10.3    1.4e-34  118.6  10.3    1.3  1  CdvA           CdvA-like coiled-coil domain
  ------ inclusion threshold ------
      0.014   16.2   3.5      0.021   15.7   0.6    2.3  2  Fes1           Nucleotide exchange factor Fes1
      0.029   13.0  10.6      0.039   12.6  10.6    1.1  1  AAA_13         AAA domain
      0.045   14.6   8.7        0.7   10.7   0.1    2.7  2  FliT           Flagellar protein FliT
      0.055   13.8   0.2       0.13   12.6   0.2    1.6  1  CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) a
      0.082   12.9   0.7       0.18   11.9   0.7    1.6  1  Baculo_PEP_C   Baculovirus polyhedron envelope protein, PEP, 
        1.1    9.5   4.6        1.7    8.8   4.6    1.3  1  MutS_III       MutS domain III
        1.8    7.8   6.1        3.4    6.9   6.1    1.5  1  DUF4407        Domain of unknown function (DUF4407)
        6.1    7.4   8.0         10    6.8   1.6    3.0  3  MerR-DNA-bind  MerR, DNA binding


Domain annotation for each model (and alignments):
>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.6  10.3   6.9e-38   1.4e-34       1     123 []      84     206 ..      84     206 .. 0.99

  Alignments for each domain:
  == domain 1  score: 118.6 bits;  conditional E-value: 6.9e-38
        CdvA   1 krkkALeeLvsegdipkstyeeikekleealkklkekakelkeklkkrlkeledqikslekalanlkisyasGEidEeaYksaieairellesaleeke 99 
                 +r+kAL ++vse+d +k+++e i+ek++++l+ l+e ++++k kl++r +el++q+ks++++l+++k++y+s+Ei+E+++++++++ +el+e++++e +
  EPA06144.1  84 RRLKALIDIVSENDDMKEDAEIIHEKYKSKLESLDELENQIKAKLDARHAELDEQLKSTKMLLFDAKVQYKSNEISENTFETVKSCATELIEHVTHESS 182
                 8************************************************************************************************** PP

        CdvA 100 eikklleklskleleeeeveetke 123
                 ei+++++++++l++e ++v+e+++
  EPA06144.1 183 EISNVKRRIADLDAEVTSVTEPPQ 206
                 *******************99986 PP

>> Fes1  Nucleotide exchange factor Fes1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   0.6     1e-05     0.021      35      85 ..      77     125 ..      64     131 .. 0.85
   2 ?    0.5   0.1      0.56   1.1e+03      34      67 ..     164     200 ..     147     230 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1e-05
        Fes1  35 k.ekldpeildallggpsdaelmkeamevledeevtlenkliAldnleqlie 85 
                 + ++l+   l+al+   s+ + mke  e++    ++   kl++ld+le+ i+
  EPA06144.1  77 ReKQLTLRRLKALIDIVSENDDMKEDAEII---HEKYKSKLESLDELENQIK 125
                 3389999***********************...566778*********9986 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.56
        Fes1  34 sk.ekldpeildallggpsdaelmkeamevlede..e 67 
                 ++ +   +e+++++    s+    k  ++ l+ e  +
  EPA06144.1 164 ETvKSCATELIEHVTHESSEISNVKRRIADLDAEvtS 200
                 3446667777777777778888888777777554331 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6  10.6     2e-05     0.039     294     441 ..      74     214 ..      67     234 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2e-05
      AAA_13 294 kveskkselleklkavsdeasensafeedkeelkaeaealeeqLkglqraleaKrkepfksvelesvkakiesikklvaeineliakhNekvanleeek 392
                 +++++k+  l +lka++d  sen  ++ed e ++++ +   e+L++l+++++aK +   +     +++++++s k l+ +++ +  k Ne+++n  e +
  EPA06144.1  74 RLLREKQLTLRRLKALIDIVSENDDMKEDAEIIHEKYKSKLESLDELENQIKAKLDARHA-----ELDEQLKSTKMLLFDAKVQ-YKSNEISENTFETV 166
                 566777778899*******9***********************************65444.....4555555555666665555.578*********** PP

      AAA_13 393 eeakkklelhlveeleseldeykkkykklekaieklekelkeeeaelkk 441
                 ++++++l  h+  e  se+++ k+ +++l+++++++++  ++e++e + 
  EPA06144.1 167 KSCATELIEHVTHES-SEISNVKRRIADLDAEVTSVTEPPQKETQESAV 214
                 *******99999987.9********************988888877665 PP

>> FliT  Flagellar protein FliT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   5.2      0.03        59      36      75 ..      95     142 ..      73     145 .. 0.67
   2 ?   10.7   0.1   0.00035       0.7      23      70 ..     173     211 ..     158     229 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.03
                 -HHHHHHHHHHHH........HHHHHHHHHHHHHHHHHHHHHHHHCHT CS
        FliT  36 spaereekrellr........rilandaeirallqprldelqkllgal 75 
                 ++++ +e +e+++         + +++++i+a l++r +el ++l+++
  EPA06144.1  95 ENDDMKEDAEIIHekykskleSLDELENQIKAKLDARHAELDEQLKST 142
                 3344445555555555555559999********************987 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00035
                 HHHHHHCS--ST--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
        FliT  23 lverlreldaaplspaereekrellrrilandaeirallqprldelqk 70 
                 l+e++++++          e+ +++rri ++dae+ + ++p + e q+
  EPA06144.1 173 LIEHVTHES---------SEISNVKRRIADLDAEVTSVTEPPQKETQE 211
                 555555555.........9*********************99998886 PP

>> CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) and archaeal histone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   6.4e-05      0.13      19      53 ..     156     190 ..     150     191 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.4e-05
                    S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHCCTTS CS
  CBFD_NFYB_HMF  19 rkiakdAkeliaecveefieelaseAaeickkekr 53 
                    + i++   e++  c++e ie+++ e++ei + ++r
     EPA06144.1 156 NEISENTFETVKSCATELIEHVTHESSEISNVKRR 190
                    45999999********************9987665 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.7   8.8e-05      0.18      24     123 ..     116     199 ..      97     228 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.8e-05
  Baculo_PEP_C  24 airlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq..dtlrneLtnlnsiltnLlssvtNinstLnnllqalnnl 118
                   ++  ++ qi a                  +l +  aeld++l+++   L da  + +  +  +n  ++++s  t+L   vt   s ++n+   ++ l
    EPA06144.1 116 SLDELENQIKA------------------KLDARHAELDEQLKSTKMLLFDAKVQYKsnEISENTFETVKSCATELIEHVTHESSEISNVKRRIADL 194
                   33344444444..................55555555555555555555554444444445555555555555555555555555555555555555 PP

  Baculo_PEP_C 119 dlgal 123
                   d + +
    EPA06144.1 195 DAEVT 199
                   44433 PP

>> MutS_III  MutS domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   4.6   0.00086       1.7      78     186 ..      66     196 ..      34     199 .. 0.54

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00086
                 -....-HHHHHHHHHTT---HHHHHHH.....................HHHHHHHHTTTTT---SSTHHHHHHHHHHHHH..HHB-SS--SSGGGS--B CS
                 x....xxxxxxxxxxxxxxxxxxxxxx.....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxx RF
    MutS_III  78 p....DleRllsrislgkakardlkal.....................lealkaleelvallekeklaeseeeslaelle..eaideeplalekegedl 149
                 p    D +Rll++ +l   + r lkal                      ++l++l+el ++ +++  a+   ++l e l+  + ++ ++  + k++e++
  EPA06144.1  66 PkwrlDSQRLLREKQL---TLRRLKALidivsenddmkedaeiihekyKSKLESLDELENQIKAKLDARH--AELDEQLKstKMLLFDAKVQYKSNEIS 159
                 1445577777753333...222233321111111111111111122223333333333333333322211..123322221133566666666666666 PP

                 -THHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    MutS_III 150 raiealeqelfqelleeveealerlrrlaealaeLDv 186
                 ++  +  +++  el+e+v+ +++++ ++ + +a LD+
  EPA06144.1 160 ENTFETVKSCATELIEHVTHESSEISNVKRRIADLDA 196
                 667777799999******9999**************6 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   6.1    0.0017       3.4     106     205 ..     103     204 ..      79     250 .. 0.62

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0017
     DUF4407 106 keIdaelaeeqqeeakelkeqlaaaltaelaeleaqia.....alqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqldaaqael 199
                  eI +e+ + + e+ +el++q++a+l+a+ ael++q++       +a+++ +++++++++ e  k +    ++ ++ v  +  +  + k+ +++++ae+
  EPA06144.1 103 AEIIHEKYKSKLESLDELENQIKAKLDARHAELDEQLKstkmlLFDAKVQYKSNEISENTFETVKSCA---TELIEHVTHESSEISNVKRRIADLDAEV 198
                 57888888888899999999999999999999999998555544444444444444444444444444...3444444444444444444444444444 PP

     DUF4407 200 aelkak 205
                 +++++ 
  EPA06144.1 199 TSVTEP 204
                 444333 PP

>> MerR-DNA-bind  MerR, DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   1.6     0.005        10       9      56 ..      75     125 ..      69     126 .. 0.89
   2 ?    4.2   0.6     0.033        65      37      54 ..     124     141 ..     120     146 .. 0.83
   3 ?   -0.8   0.0       1.2   2.4e+03      47      57 ..     186     196 ..     178     201 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.005
                    HHHHTT--HHHHHHHHHHHHSTTTBHHHHH...HHHHHHHHHHHHHHHHHH CS
  MerR-DNA-bind   9 rarrlGFsLdeIrelLalyddrappcqdvr...allarklaeleeriaeLq 56 
                     +r+  ++L   ++l+++  +++++++d++   +  + kl++l+e  ++++
     EPA06144.1  75 LLREKQLTLRRLKALIDIVSENDDMKEDAEiihEKYKSKLESLDELENQIK 125
                    5788889***********9999999999999999**********9998886 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.033
                    HHHHHHHHHHHHHHHHHH CS
  MerR-DNA-bind  37 vrallarklaeleeriae 54 
                     +a l+++ ael+e+++ 
     EPA06144.1 124 IKAKLDARHAELDEQLKS 141
                    6899***********875 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.2
                    HHHHHHHHHHH CS
  MerR-DNA-bind  47 eleeriaeLqa 57 
                     + +ria+L+a
     EPA06144.1 186 NVKRRIADLDA 196
                    56667777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1629  (0.0908584); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.52
# Mc/sec: 1615.56
//
Query:       EPA06145.1  [L=266]
Description: hypothetical protein BG20_I0651 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.7e-07   29.3   0.2    2.8e-06   27.3   0.0    1.9  2  HTH_20     Helix-turn-helix domain
    3.4e-06   26.8   0.0    0.00071   19.4   0.0    2.3  2  MarR_2     MarR family
    5.1e-05   23.0   0.2    0.00019   21.2   0.0    2.0  3  DUF4423    Domain of unknown function (DUF4423)
     0.0026   17.7   0.1      0.015   15.3   0.0    2.1  2  HTH_Crp_2  Crp-like helix-turn-helix domain
     0.0027   17.6   0.5        3.5    7.6   0.0    3.1  3  MarR       MarR family
     0.0042   16.9   0.1      0.015   15.2   0.0    2.0  2  HTH_5      Bacterial regulatory protein, arsR family
     0.0055   16.8   0.3       0.37   10.9   0.0    2.4  2  DUF2250    Uncharacterized protein conserved in archaea (DUF2
  ------ inclusion threshold ------
      0.014   15.3   1.0       0.12   12.4   0.0    2.5  3  HTH_45     Winged helix-turn-helix
      0.015   15.1   1.1      0.033   14.0   0.1    1.8  2  DUF3449    Domain of unknown function (DUF3449)
      0.016   13.6   0.0      0.019   13.4   0.0    1.3  1  DUF505     Protein of unknown function (DUF505)
      0.024   14.8   0.4       0.05   13.8   0.4    1.5  1  DUF1724    Domain of unknown function (DUF1724)
      0.029   13.9   0.2       0.29   10.7   0.0    2.4  2  HTH_24     Winged helix-turn-helix DNA-binding
      0.059   13.3   0.0        1.8    8.5   0.0    2.4  2  TrmB       Sugar-specific transcriptional regulator TrmB


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0     2e-09   2.8e-06       7      59 ..      15      66 ..       9      68 .. 0.93
   2 ?   -1.1   0.1       1.5   2.1e+03      46      56 ..     190     200 ..     181     201 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 2e-09
                HS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
      HTH_20  7 LahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvre 59
                La+P R+ il  L   + lt++++a+++d +k+++++++  Lee gL++  + 
  EPA06145.1 15 LASPQRLNILFRL-LSKNLTPTAFAKEIDATKQEVHRNFSRLEESGLIKKKTD 66
                89********999.9*********************************98765 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.5
                 HHHHHCTTEEE CS
      HTH_20  46 rvLeeagLvev 56 
                 ++L+e gL+e+
  EPA06145.1 190 DKLVEKGLIER 200
                 589******96 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   5.1e-07   0.00071       4      56 ..      17      66 ..      13      68 .. 0.90
   2 ?    5.2   0.0     0.015        20      43      55 ..     190     202 ..     189     205 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 5.1e-07
                -HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
      MarR_2  4 tpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                +p+ + +L+ L       lt+++ a++ + +k+ v+r   rL++ GL+ ++++
  EPA06145.1 17 SPQRLNILFRLLSKN---LTPTAFAKEIDATKQEVHRNFSRLEESGLIKKKTD 66
                577888999998888...9*****************************99986 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.015
                 HHHHHTTSEEEEE CS
      MarR_2  43 krLvaaGLverrp 55 
                 ++Lv++GL+er+ 
  EPA06145.1 190 DKLVEKGLIERKM 202
                 69********984 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   1.4e-07   0.00019      31      93 ..      26      86 ..      20      99 .. 0.82
   2 ?   -1.7   0.0       1.4     2e+03      38      73 ..     103     138 ..      92     143 .. 0.71
   3 ?   -3.0   0.0       3.6     5e+03      61      75 ..     191     205 ..     189     212 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.4e-07
     DUF4423 31 plkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyrqtekslttssevksea 93
                +l  ++ +p + ak +   ++++ev++  ++L+++gl+kk+ dg+y+ t+    +  +v+s++
  EPA06145.1 26 RLLSKNLTPTAFAKEID--ATKQEVHRNFSRLEESGLIKKKTDGTYELTTFGQIVCTQVPSLV 86
                566677899********..****************************9986666666666665 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.4
     DUF4423  38 dpeelakrlrpkisaeevekalefLlklgllkkded 73 
                  p++ + r+++ +  + +    ++L++++ + k+  
  EPA06145.1 103 VPHKFQMRCGQLAVSQHITGVSKTLEQWKSIYKNST 138
                 566777777777777777777788888888877765 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 3.6
     DUF4423  61 fLlklgllkkdedgk 75 
                  L++ gl++++  ++
  EPA06145.1 191 KLVEKGLIERKMTKN 205
                 689999999988733 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.1e-05     0.015       4      54 ..       9      64 ..       6      73 .. 0.77
   2 ?   -0.6   0.0      0.99   1.4e+03      44      54 ..     191     201 ..     189     216 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.1e-05
                HHHHHHHHCTTT.C.EEEE...EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEET CS
   HTH_Crp_2  4 ArfLlrlaerag.g.eiel...pltqeelAsmlGltretvsrilseLkreglisrg 54
                A + l+la  ++ +  ++l   +lt +  A  + +t + v r +s+L++ gli+++
  EPA06145.1  9 ADYVLELASPQRlNiLFRLlskNLTPTAFAKEIDATKQEVHRNFSRLEESGLIKKK 64
                778888877644335333345599*****************************953 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.99
                 HHHHTTSEEET CS
   HTH_Crp_2  44 eLkreglisrg 54 
                 +L ++gli+r+
  EPA06145.1 191 KLVEKGLIERK 201
                 7999****953 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0025       3.5      16      51 ..      30      65 ..      17      67 .. 0.87
   2 ?   -0.0   0.0      0.63   8.7e+02      32      43 ..     118     129 ..     116     133 .. 0.89
   3 !    6.0   0.0    0.0083        11      39      50 ..     190     201 ..     189     205 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0025
                TTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
        MarR 16 gplsvseLakklgvskstvtrvldrLekkGlieRsk 51
                 +l+ +  ak +  +k  v r   rLe+ Gli+++ 
  EPA06145.1 30 KNLTPTAFAKEIDATKQEVHRNFSRLEESGLIKKKT 65
                689999**************************9986 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.63
                 HHHHHHHHHHHH CS
        MarR  32 stvtrvldrLek 43 
                  ++t v+++Le+
  EPA06145.1 118 QHITGVSKTLEQ 129
                 579********8 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.0083
                 HHHHHTTSEEEE CS
        MarR  39 drLekkGlieRs 50 
                 d+L++kGlieR+
  EPA06145.1 190 DKLVEKGLIERK 201
                 8**********7 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.1e-05     0.015       1      47 []      17      63 ..      17      63 .. 0.98
   2 ?   -3.2   0.1         6   8.2e+03      38      46 ..     191     199 ..     190     199 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.1e-05
                SHHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
       HTH_5  1 dptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVek 47
                +p+Rl IL+ L +++l+ +  a+e++ ++  v + +++L+e+GL++k
  EPA06145.1 17 SPQRLNILFRLLSKNLTPTAFAKEIDATKQEVHRNFSRLEESGLIKK 63
                69*******************************************86 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 6
                 HHHHTTSEE CS
       HTH_5  38 kLreaGLVe 46 
                 kL e GL+e
  EPA06145.1 191 KLVEKGLIE 199
                 799999996 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00027      0.37      27      59 ..      36      68 ..      16      73 .. 0.87
   2 ?    3.7   0.1      0.05        69      43      61 ..     189     207 ..     170     216 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00027
     DUF2250 27 siakeleipleevrellkkLeelGLlervegkt 59
                  ake+++ ++ev++ + +Lee GL+++++  t
  EPA06145.1 36 AFAKEIDATKQEVHRNFSRLEESGLIKKKTDGT 68
                578999**********************99765 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.05
     DUF2250  43 lkkLeelGLlervegktik 61 
                 ++kL e GL+er+  k ++
  EPA06145.1 189 YDKLVEKGLIERKMTKNVQ 207
                 689*********9988776 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   8.6e-05      0.12      11      65 ..      23      78 ..      19      85 .. 0.82
   2 ?   -3.6   0.0       8.6   1.2e+04       4      14 ..     137     147 ..     134     148 .. 0.65
   3 ?    0.7   0.1      0.38   5.2e+02      41      56 ..     190     205 ..     184     211 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.6e-05
      HTH_45 11 ILeaisegeakkTkimykanLsykllnkYLdmLvekgli.kkskekYvlTekGlel 65
                IL  + +++ ++T+  ++ + + + +++  + L e gli kk++++Y+lT  G+ +
  EPA06145.1 23 ILFRLLSKNLTPTAFAKEIDATKQEVHRNFSRLEESGLIkKKTDGTYELTTFGQIV 78
                555555678899999999999999999999*********55599******999865 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 8.6
      HTH_45   4 kleIiadILea 14 
                 ++e i++IL+ 
  EPA06145.1 137 STEYIYEILSE 147
                 56667888865 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.38
      HTH_45  41 dmLvekglikkskekY 56 
                 d+Lvekgli+ + +k 
  EPA06145.1 190 DKLVEKGLIERKMTKN 205
                 689******8876665 PP

>> DUF3449  Domain of unknown function (DUF3449)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1         1   1.4e+03      11      31 ..      36      56 ..      29      70 .. 0.77
   2 ?   14.0   0.1   2.4e-05     0.033     102     150 ..      91     137 ..      84     148 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1
                HTHHHHHHHHHHHHHHHT--H CS
     DUF3449 11 llskeieetkenverkqalta 31
                +++kei++tk++v+r+ ++ +
  EPA06145.1 36 AFAKEIDATKQEVHRNFSRLE 56
                567899999999999877654 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 2.4e-05
                 XXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
     DUF3449 102 GrkaFek.HFseerHaeglkcLgientklfkeitkiedaleLweklkkek 150
                  rk Fek HF e  H+++++c ++  ++   +it +++ le w+++ k++
  EPA06145.1  91 NRKYFEKhHFGEVPHKFQMRCGQLAVSQ---HITGVSKTLEQWKSIYKNS 137
                 589999846************9888875...5777777788888876665 PP

>> DUF505  Protein of unknown function (DUF505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.4e-05     0.019       9      71 ..      22      89 ..      17     213 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.4e-05
      DUF505  9 eiLeklkeeeekkeeeeieveeleeeei...lleLelagLvrleepekielTyaGkklaelldel...i 71
                +iL +l++++   +++++e+ ++ ++e+   +  Le +gL++ +++ ++elT +G+++   +  l   +
  EPA06145.1 22 NILFRLLSKNLTPTAFAKEIDAT-KQEVhrnFSRLEESGLIKKKTDGTYELTTFGQIVCTQVPSLvflL 89
                67777777666666655555554.3333344999********999***********9998887774543 PP

>> DUF1724  Domain of unknown function (DUF1724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.4   3.6e-05      0.05       9      58 ..     205     254 ..     201     257 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.6e-05
     DUF1724   9 eikplsltvtDkflslslfdkdgkydhk.dlisfdesAlkWGeeLFeyYlk 58 
                 ++   ++++++k + +++ + dgk d + +  s+d+  ++W  + F+y++ 
  EPA06145.1 205 NV-QTMIVMNEKEVCIMFPTIDGKSDLSeMFYSDDPMFHEWSLDYFRYCWY 254
                 55.678999*******************9999*****************95 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00021      0.29      18      48 .]      32      62 ..      18      62 .. 0.82
   2 ?    0.5   0.1      0.33   4.5e+02      39      48 .]     190     199 ..     189     199 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00021
      HTH_24 18 isqreLAerlglSpstvnrrlkrLeeeGlIk 48
                ++ +  A++++ +++ v+r   rLee+GlIk
  EPA06145.1 32 LTPTAFAKEIDATKQEVHRNFSRLEESGLIK 62
                6666669999999*****************8 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.33
      HTH_24  39 krLeeeGlIk 48 
                 ++L+e+GlI+
  EPA06145.1 190 DKLVEKGLIE 199
                 59*******7 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0    0.0013       1.8      17      58 ..      27      67 ..      21      74 .. 0.86
   2 ?    2.1   0.0      0.13   1.7e+02      45      56 ..     191     202 ..     189     214 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0013
                HHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
        TrmB 17 LlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                Ll ++++t +  a+e++  ++ v +  ++Le+ Gl++++   
  EPA06145.1 27 LL-SKNLTPTAFAKEIDATKQEVHRNFSRLEESGLIKKKTDG 67
                44.78999999**************************98755 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.13
                 HHHHCTSEEEES CS
        TrmB  45 sLedkGlVerek 56 
                 +L++kGl+er+ 
  EPA06145.1 191 KLVEKGLIERKM 202
                 8********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       841  (0.0469072); expected 358.6 (0.02)
Passed bias filter:                      626  (0.0349155); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 1608.51
//
Query:       EPA06146.1  [L=542]
Description: thymidylate synthase ThyX [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-34  119.1   1.8    1.7e-18   67.1   2.3    2.3  2  Thy1         Thymidylate synthase complementing protein
  ------ inclusion threshold ------
      0.047   13.5   0.1       0.16   11.8   0.1    1.9  1  DUF4817      Helix-turn-helix domain (DUF4817)
        2.7    8.4   4.7         20    5.6   0.0    3.6  4  Uteroglobin  Uteroglobin family
        3.6    8.1  10.4         11    6.6   1.5    3.7  3  FadA         Adhesion protein FadA


Domain annotation for each model (and alignments):
>> Thy1  Thymidylate synthase complementing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.4   0.0     1e-16   4.6e-13      25     182 ..      51     267 ..      28     271 .. 0.80
   2 !   67.1   2.3   3.7e-22   1.7e-18      18     188 .]     341     509 ..     315     509 .. 0.80

  Alignments for each domain:
  == domain 1  score: 49.4 bits;  conditional E-value: 1e-16
                 SHHHH......S.GCCHHHHHHHHH.HTTGGGGGGG-EEEEEEEEEEHHHHHHHTT-TT.SEEEE--TTTSGCCCTC.....BS--GGGCC.HHHHHHH CS
        Thy1  25 eaeele.....e.eekkeklikkll.khghgsplehasftfeiegvSravlrqlvrHRi.asfsqqSqRYvesskea.....fvippeieqkeeleely 110
                 +++++      + e++ e++++++l ++g  s+ e  +++++ieg+S  +++++   Ri +s+ ++S RYv   k+      f+  p + + +++++ly
  EPA06146.1  51 SMRRIFldeflQnESRGEEFYNRVLlEYGDDSVAELGEAQIAIEGLSNIAVKKIEDRRIgLSYLEKSSRYVAWNKKTdgeyrFYKDPVLMK-SKFSDLY 148
                 33333355554345666799999999**********************************************9884469998877777665.789999* PP

                 HHHHHHHHHHHHHHHHT................................................TCHHHHHGGGSBTTBEEEEEEEEEHHHHHHHHHH CS
        Thy1 111 eeamekaleaykellea................................................gvarEdaryvLPlatktklvvtmNlrsLlhflel 161
                  +a++ +++ y +++e                                                  +a + +r +LP +t t++ vt+N r++   l+ 
  EPA06146.1 149 VDACNFSFDVYSKNIEPmikyvrekypiekytfkdskdgkeksfsklkeendiksanmiyngstkAKALDILRGLLPASTLTNVGVTGNGRAFEYLLTI 247
                 ***********877776666777777777777777777777777777777888888888877777679************************9988888 PP

                 HSSTTS-HHHHHHHHHHHHHH CS
        Thy1 162 racsrAqwEirelaeemleel 182
                    s    E r+la ++++el
  EPA06146.1 248 LGAS-ELDEERDLASKIKKEL 267
                 7544.5566689999988876 PP

  == domain 2  score: 67.1 bits;  conditional E-value: 3.7e-22
                 HHHTTC..SSHHHH.SGCCHH.....HHHHHHHHTTGGGGGGG-EEEEEEEEEEHHHHHHHTT-TTSEEEE--TTTSGCCCTCBS--GGGC..C.HHHH CS
        Thy1  18 vcygss..eeaeeleeeekke.....klikkllkhghgsplehasftfeiegvSravlrqlvrHRiasfsqqSqRYvesskeafvippeie..qkeele 107
                 ++y  +  +++++l ++ek++     ++++k  +h+ ++ +e +++tf +     +++r + rHR   ++ + q  +  +     +p ei+  +   +e
  EPA06146.1 341 TSYH-NimQQVKKLSKDEKIKtinsfTILRKNRRHRPSRAFENVYYTFDLL-NNFGMFRDFHRHRA--LTLERQLLTTDHGH--NTPNEIKvlG---IE 430
                 3332.1233333332223333566779999999******************.**************..77788888888773..48*9*99762...45 PP

                 HHHHHHHHHHHHHHHHHHHTTCHHHHHGGGSBTTBEEEEEEEEEHHHHHHHHHHHSSTTS-HHHHHHHHHHHHHHHHHSHH CS
        Thy1 108 elyeeamekaleaykelleagvarEdaryvLPlatktklvvtmNlrsLlhflelracsrAqwEirelaeemleelkkvaPe 188
                 ++y+e m+++ +++++++++   +E+a+yv+  a++  + +++Nlr+  h +elr+ ++ + ++r++a++m++e+ kv+P+
  EPA06146.1 431 KEYQECMKNTKQTFDKIRNK--HPEQAQYVVNFAYNYPYFMKFNLREACHLIELRTVPQGHIDYRRVAQQMFKEIDKVHPN 509
                 88***************875..6*********************************************************6 PP

>> DUF4817  Helix-turn-helix domain (DUF4817)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   3.6e-05      0.16      10      32 ..     431     453 ..     429     456 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.6e-05
     DUF4817  10 kaYykngesvtatqrafrrrFpn 32 
                 k+Y +++++ ++t+++ r+++p+
  EPA06146.1 431 KEYQECMKNTKQTFDKIRNKHPE 453
                 79********************6 PP

>> Uteroglobin  Uteroglobin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.088   3.9e+02      23      52 ..     263     292 ..     244     305 .. 0.79
   2 ?   -2.8   0.0       1.8   8.1e+03      27      48 ..     326     349 ..     324     360 .. 0.62
   3 ?    5.6   0.0    0.0045        20      52      87 ..     430     465 ..     421     468 .. 0.86
   4 ?    0.3   0.2       0.2     9e+02      38      64 ..     518     542 .]     504     542 .] 0.79

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.088
                  --HHHHHHHHHHHHS-HHHHHHHHHTT--- CS
  Uteroglobin  23 gCpaleevvekflegseeeYkeeLqkynpd 52 
                  + + l++ +++f+   +++Y +++q+y ++
   EPA06146.1 263 IKKELDTTIKAFVRRADDKYGKSFQEYLKQ 292
                  5566778888888999*********99665 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.8
                  HHHHHHHHH..HS-HHHHHHHHHT CS
  Uteroglobin  27 leevvekfl..egseeeYkeeLqk 48 
                  ++++++ ++  +++ ++Y++ +q+
   EPA06146.1 326 IDKIITSIIyeQSPSTSYHNIMQQ 349
                  566667777644466777776664 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.0045
                  -HHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHTS CS
  Uteroglobin  52 dpeaeealaelKqcvdklsnetkenvakllekilss 87 
                  ++e +e +++ Kq +dk+ n++ e+++ +++  ++ 
   EPA06146.1 430 EKEYQECMKNTKQTFDKIRNKHPEQAQYVVNFAYNY 465
                  6788999*****************999999888876 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 0.2
                  -HHHHHHHHHTT---HHHHHHHHHHHH CS
  Uteroglobin  38 seeeYkeeLqkynpdpeaeealaelKq 64 
                    +eY  +L+++++++ +ee  ++lK+
   EPA06146.1 518 DLKEY--DLERFESEKRTEEKRKNLKK 542
                  55555..699**************996 PP

>> FadA  Adhesion protein FadA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   1.5    0.0024        11      34      83 ..     253     305 ..     249     309 .. 0.66
   2 ?   -0.7   0.0      0.46   2.1e+03       3      55 ..     344     357 ..     337     369 .. 0.53
   3 ?    4.8   0.4    0.0091        41       6      92 ..     430     461 ..     425     464 .. 0.63

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0024
        FadA  34 lakkkelkakieeklak.lea..dsevrfykdeYkellkeyksllkelekeik 83 
                 l+++++l  ki+++l+  ++a   +    y + ++e lk++k   k++ k+ik
  EPA06146.1 253 LDEERDLASKIKKELDTtIKAfvRRADDKYGKSFQEYLKQVKITSKKIAKKIK 305
                 55555555555555554122222344456999999999999999999999998 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.46
        FadA   3 naLeaelqkLekkeeqrykkekakaeaaaaklakkkelkakieeklakleads 55 
                  ++ ++++kL k                                        +
  EPA06146.1 344 HNIMQQVKKLSKD---------------------------------------E 357
                 2333333333333.......................................3 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.0091
        FadA   6 eaelqkLekkeeqrykkekakaeaaaaklakkkelkakieeklakleadsevrfykdeYkellkeyksllkelekeikekekkianf 92 
                 e                                                       +eY+e +k+ k+  +++ ++  e+++ + nf
  EPA06146.1 430 E-------------------------------------------------------KEYQECMKNTKQTFDKIRNKHPEQAQYVVNF 461
                 4.......................................................5666666666666666666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (542 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1037  (0.0578393); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.50
# Mc/sec: 3263.86
//
Query:       EPA06147.1  [L=197]
Description: putative proteasome endopeptidase complex, beta subunit [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.6e-46  157.5   0.0    3.2e-46  157.2   0.0    1.0  1  Proteasome  Proteasome subunit


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.2   0.0   1.8e-50   3.2e-46       4     190 .]       7     185 ..       5     185 .. 0.98

  Alignments for each domain:
  == domain 1  score: 157.2 bits;  conditional E-value: 1.8e-50
                 S-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGTCHHHHHHHHHHHHHHHHHHCTTT CS
  Proteasome   4 GttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrpipverlvarvaaklqaytqrsgrr 102
                 G t+vGi+++dg+vla++kr+ +g+ l+sk+t +K f i++++g+++aGl+aD+++l+ ++ a a+ ++++ +r++p+      +a+++++++++++  
  EPA06147.1   7 GATAVGITFQDGIVLASEKRIAFGNFLVSKTT-KKTFPITPKVGATCAGLVADMQILTLQIAALAKIRKMELKRDVPPN----TIAKMMSNMMYERRYF 100
                 89*************************88886.**********************************************....**************** PP

                 TTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHHSTTBSHHHHHHHHHHHHHHHHHHBTTSCSSEEEEEE CS
  Proteasome 103 pfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekeykedltleeavelavkalkealerdklsgknievavi 190
                 p++ +++++g+   ++p L+++dp Gs++ ++ ++a+G+g+e+a ++l+ ++k+++t+eea++la++a+++a+ rd++sg++++v vi
  EPA06147.1 101 PLLTQVIVGGII--DKPILFTLDPLGSVLPDE-YAAVGTGAEMALGVLDPQFKPNMTQEEAIDLAKRAVRSAALRDSASGDGLDVLVI 185
                 ************..66***************6.****************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1246.68
//
Query:       EPA06148.1  [L=328]
Description: phosphate transporter family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.8e-91  304.6  39.9    3.6e-90  302.4  39.9    1.8  1  PHO4      Phosphate transporter family
  ------ inclusion threshold ------
      0.078   12.8   0.3       0.29   11.0   0.0    2.0  2  HTH_IclR  IclR helix-turn-helix domain
      0.097   12.7   0.1      0.097   12.7   0.1    4.1  5  DUF1656   Protein of unknown function (DUF1656)


Domain annotation for each model (and alignments):
>> PHO4  Phosphate transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  302.4  39.9     6e-94   3.6e-90       1     337 []      19     317 ..      19     317 .. 0.94

  Alignments for each domain:
  == domain 1  score: 302.4 bits;  conditional E-value: 6e-94
        PHO4   1 iGanDvanafatsvgskaltlrqAvilaaifeflGavllGaeVaetirkgivdvelfdpselm.lgmlaallgaavwlllatvlglPvStthslvGali 98 
                 +G++D+an++at+vg+++l++  Av laa+ +f+G +l+G +Va ti+kgi+d     p+ ++  +++aal+ga+vw+l++++lglP+S++h+lvG++i
  EPA06148.1  19 NGFHDAANSIATVVGTRVLKPLHAVSLAAMANFFGPFLFGVAVATTIGKGIID-----PDFVTiHIVIAALVGAIVWNLITWWLGLPSSSSHALVGGII 112
                 8***************************************************5.....555553699******************************** PP

        PHO4  99 GaalaaeggeavkwkklvkivlswvlsPllggiiaallfllvkrlilvkeklknalralpvlvlvtiailalsilfkgeskkddeeteklfkflqvvsa 197
                 Ga++a  g++++  ++l k+++++++sPl+g++ a+ll++l+ ++                                   +k+  +++++f +lq+vsa
  EPA06148.1 113 GAGIAGVGTHVILFGGLEKVFTGILVSPLVGLAGAFLLATLIVKAFA---------------------------------NKNPANVNSIFGKLQLVSA 178
                 *****777799999************************998888833.................................3678899************ PP

        PHO4 198 alvsfahGanDvanaiGpllaalisiyk.a.sk.evplwvlllgglaialGlllgGkrviktvGekitkkltpsrGfaaelaaaltvllasklglPvSt 293
                 +++s++hGanD+++++G+++++l  +++ + ++ evp+wv+l+ ++ai+lG+++gG+r++kt+G +it +l+p++Gfaae+++a++++++ ++g+P St
  EPA06148.1 179 TYFSLTHGANDGQKTMGIIVLIL--LTEgVlTTfEVPFWVILIAAIAISLGTFFGGWRIVKTMGARIT-QLKPYQGFAAETSGATILAILAHIGIPAST 274
                 *******************5555..445656999**********************************.5***************************** PP

        PHO4 294 ThvlvgavvGvGlakkresavnwklvrnivlaWvlTlpvsalls 337
                 Th+++g+++G+G+++ r sav+w++ ++iv+aW++T+p+sa+++
  EPA06148.1 275 THAISGSIMGAGAVR-RVSAVRWGIGKRIVWAWIITIPASAAVA 317
                 ***************.9************************986 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.39   2.3e+03      28      39 ..      97     108 ..      97     113 .. 0.88
   2 ?   11.0   0.0   4.9e-05      0.29      12      50 ..     252     290 ..     251     292 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.39
                 HTS-HHHHHHHH CS
    HTH_IclR  28 tglpkStvhRlL 39 
                 +glp S+ h l+
  EPA06148.1  97 LGLPSSSSHALV 108
                 69*****99886 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 4.9e-05
                 -CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
    HTH_IclR  12 laeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50 
                 +a+++ + t+  + +++g+p St+h +  + +  G v++
  EPA06148.1 252 FAAETSGATILAILAHIGIPASTTHAISGSIMGAGAVRR 290
                 78999999*****************99888888888876 PP

>> DUF1656  Protein of unknown function (DUF1656)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.3       2.1   1.3e+04      11      20 ..      54      63 ..      51      65 .. 0.54
   2 ?    0.2   1.4      0.13   7.8e+02      13      34 ..      80      98 ..      77     100 .. 0.53
   3 ?   12.7   0.1   1.6e-05     0.097       3      31 ..     132     160 ..     130     163 .. 0.90
   4 ?   -1.9   0.4      0.59   3.5e+03      11      25 ..     213     227 ..     212     234 .. 0.80
   5 ?   -3.2   0.2       1.4   8.6e+03      16      26 ..     314     324 ..     311     326 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 2.1
     DUF1656 11 pllvlallAl 20
                p+l+ + +A 
  EPA06148.1 54 PFLFGVAVAT 63
                6666555554 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.13
     DUF1656 13 lvlallAllltlllrrllarlg 34
                +++al++ +++ l++++   lg
  EPA06148.1 80 VIAALVGAIVWNLITWW---LG 98
                45555555555555554...44 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 1.6e-05
     DUF1656   3 dlgGvyvPpllvlallAllltlllrrlla 31 
                 ++ G++v+pl+ la + ll+tl++  + +
  EPA06148.1 132 VFTGILVSPLVGLAGAFLLATLIVKAFAN 160
                 578*********************98876 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 0.59
     DUF1656  11 pllvlallAllltll 25 
                 p+ v +++A++++l 
  EPA06148.1 213 PFWVILIAAIAISLG 227
                 677888999998876 PP

  == domain 5  score: -3.2 bits;  conditional E-value: 1.4
     DUF1656  16 allAllltlll 26 
                 a +A+l+++++
  EPA06148.1 314 AAVAFLIMIII 324
                 56788887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       892  (0.0497518); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2169.56
//
Query:       EPA06149.1  [L=251]
Description: hypothetical protein BG20_I2109 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.1e-10   39.5   0.0    4.5e-10   39.0   0.0    1.2  1  DUF726        Protein of unknown function (DUF726)
    7.3e-10   38.8   0.0    9.7e-10   38.3   0.0    1.1  1  DUF900        Alpha/beta hydrolase of unknown function (DUF90
    9.1e-05   22.1   0.2    0.00017   21.2   0.2    1.5  1  DUF676        Putative serine esterase (DUF676)
     0.0011   18.2   0.3     0.0019   17.4   0.0    1.5  2  LCAT          Lecithin:cholesterol acyltransferase
     0.0011   18.1   0.0     0.0016   17.6   0.0    1.3  1  DUF1749       Protein of unknown function (DUF1749)
     0.0015   17.9   0.0     0.0031   16.8   0.0    1.5  2  Hydrolase_4   Serine aminopeptidase, S33
     0.0016   18.4   0.0     0.0022   18.0   0.0    1.2  1  Cutinase      Cutinase
     0.0018   17.9   0.2     0.0058   16.2   0.2    1.7  1  LIDHydrolase  Lipid-droplet associated hydrolase
     0.0076   16.1   0.0      0.012   15.5   0.0    1.2  1  Lipase_3      Lipase (class 3)
  ------ inclusion threshold ------
      0.054   12.3   0.0       0.11   11.3   0.0    1.4  1  Say1_Mug180   Steryl acetyl hydrolase


Domain annotation for each model (and alignments):
>> DUF726  Protein of unknown function (DUF726)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   0.0   2.5e-13   4.5e-10     217     293 ..     126     207 ..      96     216 .. 0.79

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 2.5e-13
      DUF726 217 GeRpvtLiGfslGARviyvCLlelakk.kalglvenvillGaPvtte....akvwlkvrsvvsgRlvnvysenDylLgflyR 293
                  +  + L+G+slG  vi++ + +lakk k++++ve ++l+Ga +t++    +k    +  ++ +++vn ys +D +L++ ++
  EPA06149.1 126 PKTKIRLMGHSLGSQVILSTVEYLAKKsKNTDIVESAYLFGASITSDvpssKKYGHLLEKIIKNKIVNYYSPTDEVLHWAHK 207
                 456799*********************999************987652221555566789****************998765 PP

>> DUF900  Alpha/beta hydrolase of unknown function (DUF900)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3   0.0   5.4e-13   9.7e-10      18     170 ..      41     204 ..      32     230 .. 0.79

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 5.4e-13
      DUF900  18 akeilvfvhGynnsFedavlraaqiaddlk...nqgaivvfsWPsagk..lldynyDre......saeasrdalekllrylatkksakkihllaHSmGt 105
                  ke ++ +hG +n   +a+ +a  + + l    + + +v+fs  s+ +   l +++ r+       a     +l  +++y +  +++ ki l+ HS G+
  EPA06149.1  41 SKELVIVIHGLRNDNAGAIAKAVLVKKRLLhigYCFPVVGFSYDSNTTgaHLLKHAKRAlstgqkIAIKNGRNLGMFIEYFKSISPKTKIRLMGHSLGS 139
                 6899**************999988877654222666899******9875544455555532211133445678999*********************** PP

      DUF900 106 wlvlealrqlaieadepaveakikeviLaAPDidvdvfkkqleslgkes...keltvyvsrdDraLkl 170
                 +++l++++ la++ ++   + +++   L+ + i +dv +++      e+   +++  y+s+ D +L+ 
  EPA06149.1 140 QVILSTVEYLAKKSKN---TDIVESAYLFGASITSDVPSSKKYGHLLEKiikNKIVNYYSPTDEVLHW 204
                 ************9986...67999*************99887754444457688999*********84 PP

>> DUF676  Putative serine esterase (DUF676)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.2   9.4e-08   0.00017       6     106 ..      43     155 ..      40     168 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 9.4e-08
      DUF676   6 hLvVlvHGlqgn....saDlelikeqleki.........keklpeekieflmsennesktfkgidvlgerlaeevlevvkkkkdknkkiSfvghSlGgl 91 
                  Lv+++HGl        a   l+k+ l  i         + +++     +l   + +  t++ i +   r +   +e++k+ + k +ki ++ghSlG  
  EPA06149.1  43 ELVIVIHGLRNDnagaIAKAVLVKKRLLHIgycfpvvgfSYDSNTTGAHLLKHAKRALSTGQKIAIKNGRNLGMFIEYFKSISPK-TKIRLMGHSLGSQ 140
                 69*******98766665666888999988888888888777777778888899999999*******7777777777899999999.6************ PP

      DUF676  92 iaraaiaklkekemt 106
                 ++ + + +l +k + 
  EPA06149.1 141 VILSTVEYLAKKSKN 155
                 ********9988753 PP

>> LCAT  Lecithin:cholesterol acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0         2   3.6e+03      92     117 ..      14      40 ..      13      52 .. 0.72
   2 !   17.4   0.0   1.1e-06    0.0019     107     152 ..     113     158 ..     109     185 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2
        LCAT  92 YDWRls.leerdkYfskLkelieealk 117
                 YD R+    +++ Yf   k+ +++   
  EPA06149.1  14 YDLRYGkTIKNNSYFLYPKKSFDKLIG 40 
                 899998777889999988888887654 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 1.1e-06
        LCAT 107 kLkelieealk.lsgkkvvliaHSmGnllvlyflkwveaeaWvdqhi 152
                 +L ++ie++   + + k+ l++HS+G++++l + + + ++  ++  i
  EPA06149.1 113 NLGMFIEYFKSiSPKTKIRLMGHSLGSQVILSTVEYLAKKS-KNTDI 158
                 7899******9999*******************99998888.55444 PP

>> DUF1749  Protein of unknown function (DUF1749)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0     9e-07    0.0016      86     135 ..     113     160 ..     108     213 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 9e-07
     DUF1749  86 eieklveYlkktksGeekkekvvlmGHstGsqdvl...yYltssnerdrekvd 135
                 ++   +eY+k +      k+k+ lmGHs Gsq +l    Yl ++ ++ ++ v+
  EPA06149.1 113 NLGMFIEYFKSI----SPKTKIRLMGHSLGSQVILstvEYLAKKSKN-TDIVE 160
                 567789****99....4689************987333577766553.33333 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       2.3     4e+03       4      14 ..      42      52 ..      41      63 .. 0.73
   2 !   16.8   0.0   1.7e-06    0.0031      62     142 ..     114     195 ..     111     215 .. 0.63

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.3
  Hydrolase_4  4 kavvvlvHGla 14
                 k +v+++HGl 
   EPA06149.1 42 KELVIVIHGLR 52
                 6789999*974 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 1.7e-06
  Hydrolase_4  62 laafvekvkeehpelplfllGhSmGGliallyl..lrypdkvaglilsaPalkikaklkappllklllkllgkllpklqvsnn 142
                  l  f+e +k+ +p++++ l+GhS+G+ + l+ +  l +++k + ++ sa +++     ++p+ +k    ll k++++  v+  
   EPA06149.1 114 LGMFIEYFKSISPKTKIRLMGHSLGSQVILSTVeyLAKKSKNTDIVESAYLFGASITSDVPSSKK-YGHLLEKIIKNKIVNYY 195
                  66899************************999987444444556666666665554432333333.35555555555444333 PP

>> Cutinase  Cutinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.2e-06    0.0022      68     147 ..     117     199 ..      78     208 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.2e-06
                 HHHHHHHH-TT-EEEEEEETHHHHHHHHHHTT.....S-HHHHHHEEEEEEES-TTC.....CCCTT....S-TTS-GGGEEEE--TT- CS
    Cutinase  68 lvqslaskCPdtkivlgGYSqGaqvidnaieggatatlpaavadkvaavvlfGdpsn.....vaglp....evsklyaskikslCdagD 147
                  ++ ++s  P tki l+G S G+qvi  ++e     + +++ +d v ++ lfG   +         +     ++k+ ++ki ++  ++D
  EPA06149.1 117 FIEYFKSISPKTKIRLMGHSLGSQVILSTVEY---LAKKSKNTDIVESAYLFGASITsdvpsS---KkyghLLEKIIKNKIVNYYSPTD 199
                 456667778**********************9...5567788899********8765333221...13333455666666666666666 PP

>> LIDHydrolase  Lipid-droplet associated hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.2   3.2e-06    0.0058      74     120 ..     116     167 ..      63     204 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.2e-06
  LIDHydrolase  74 ellek.aksekdvklilvGHSvGaYialevlkrlsers....ikkvvlLfPt 120
                    ++e  ++ + ++k+ l+GHS G+ ++l +++ l ++s    i +   Lf+ 
    EPA06149.1 116 MFIEYfKSISPKTKIRLMGHSLGSQVILSTVEYLAKKSkntdIVESAYLFGA 167
                   444444456799********************88777777887777777764 PP

>> Lipase_3  Lipase (class 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   6.5e-06     0.012      62     122 ..     125     185 ..     105     205 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.5e-06
                 TT-EEEEEEEETHHHHHHHHHHH.HHHHTT-SS---EEEEEES----B-HHHHHHHHT-TTE CS
    Lipase_3  62 ypeysivvtGHSLGgalAlLaal.dlvengenekkkvtvvtfGqPrvgnkefaklvdsqlnk 122
                  p+++i + GHSLG+ + +L+++ +l+++ +n++   +++ fG+  + +   +k + + l+k
  EPA06149.1 125 SPKTKIRLMGHSLGSQV-ILSTVeYLAKKSKNTDIVESAYLFGASITSDVPSSKKYGHLLEK 185
                 5799*********9876.66666155555556699999*****9999888777777766665 PP

>> Say1_Mug180  Steryl acetyl hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   6.2e-05      0.11     181     222 ..     113     155 ..      97     158 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.2e-05
  Say1_Mug180 181 slavy.dylvkskgfknvvvlGdSaGGnlvLslllklsklnkv 222
                  +l ++ +y+      +++ ++G S G +++Ls + +l k  k 
   EPA06149.1 113 NLGMFiEYFKSISPKTKIRLMGHSLGSQVILSTVEYLAKKSKN 155
                  5555438898888899*********************998885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1543.80
//
Query:       EPA06150.1  [L=62]
Description: hypothetical protein BG20_I2104, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.52
# Mc/sec: 360.07
//
Query:       EPA06151.1  [L=206]
Description: TIGR00153 family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-23   82.4  10.8    3.2e-23   82.2  10.8    1.0  1  PhoU_div  Protein of unknown function DUF47
  ------ inclusion threshold ------
       0.15   12.1   4.1       0.29   11.1   2.5    2.1  2  ArAE_1_C  Putative aromatic acid exporter C-terminal domain
       0.37   10.4   3.0        0.5   10.0   1.3    1.9  2  Med4      Vitamin-D-receptor interacting Mediator subunit 4


Domain annotation for each model (and alignments):
>> PhoU_div  Protein of unknown function DUF47
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.2  10.8   5.4e-27   3.2e-23       7     213 ..       6     203 ..       1     204 [. 0.87

  Alignments for each domain:
  == domain 1  score: 82.2 bits;  conditional E-value: 5.4e-27
    PhoU_div   7 sspekslqdhlekvsetvlkliellkallegdyekveellkeiselEreADeikreirlklekglflPvdRedllelveslDeildvlediamlvtlrk 105
                 +s+ k+l + + ++ +   +++e+l  l++ d ++  +    i  lE+eAD ++r+i  +l+k +++P+dRed+ ++++++D+++d +  ia +   +k
  EPA06151.1   6 KSNDKQLLAIFDDLAKKAVETAEALVVLFS-DLSD-AKQHTIIKRLENEADILTRDIFAELNKTFITPFDREDMQRIASKIDDVIDFMDGIAARTHSYK 102
                 677888888888888888899999999999.7444.455567999****************************************************** PP

    PhoU_div 106 vefpeelkdeflallkktveaiealaevieeleklletalskkdiveeieslEdeiDqlqrklikklfsredasnplevlllveiieklenvsdraedv 204
                 +       +  l ++k +v+a ++++ ++ +l  + +   +  +   + + +E+ +D+l+rk i+klf+ +d    + ++ l++i+e +e  sdr  dv
  EPA06151.1 103 I---TTTPPYALDIAKELVNATKEVEYMVSKLRSIKN-TQDMIAHCRNTSTIEHTVDELYRKSIEKLFETND---AITIIKLKDIYETMETASDRCVDV 194
                 7...55667788999*****************97544.44444888999********************888...5667778999************** PP

    PhoU_div 205 adrisiill 213
                 ad i+ i+l
  EPA06151.1 195 ADVIEDIVL 203
                 ***998876 PP

>> ArAE_1_C  Putative aromatic acid exporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       1.2   7.1e+03      13      28 ..      10      25 ..       5      40 .. 0.57
   2 ?   11.1   2.5   4.8e-05      0.29       4     135 ..      46     186 ..      43     188 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.2
                HHHHHHHHHHHHHHHS CS
    ArAE_1_C 13 eelkkilsemaeylre 28
                ++l  i+ ++a+  +e
  EPA06151.1 10 KQLLAIFDDLAKKAVE 25
                4444455555444433 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 4.8e-05
                 HHHHHHHHHHHHHHHHHHHHHHHHSTS--SHHHHHH.HHHHHHHHHHHHHHHCCCCS-HHHH.............HHHHHHHHHHHHHHHHHHHHHHHH CS
    ArAE_1_C   4 lkelqeeieeelkkilsemaeylrekekeidekelleeleellkeakklayrnleNtllsne.............eyylkYfemRekQlevLkrmleel 89 
                 +k+l++e +   ++i+ e+ ++  +  +  d +++ +++++ ++ +  +a r +  +++  +             ++ ++Y+    + l+ +k+ ++ +
  EPA06151.1  46 IKRLENEADILTRDIFAELNKTFITPFDREDMQRIASKIDDVIDFMDGIAARTHSYKITTTPpyaldiakelvnaTKEVEYM---VSKLRSIKNTQDMI 141
                 78889999999999999999999999999999999999999**999999999999999999988888887776666666666...47788999999999 PP

                 TT-SS--HHHHHHHHHHHHHHH----TTHHHHHHHHHHHHHHHHHT CS
    ArAE_1_C  90 skieetveqakiiaelleelaesvheendaeelleeLeelkeefke 135
                 +++++t + ++ + el ++  e++ e+nda +++ +L++++e++++
  EPA06151.1 142 AHCRNTSTIEHTVDELYRKSIEKLFETNDAITII-KLKDIYETMET 186
                 999999999********************99766.68888888875 PP

>> Med4  Vitamin-D-receptor interacting Mediator subunit 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.13   7.6e+02      42      70 ..      39      67 ..      34     103 .. 0.66
   2 ?   10.0   1.3   8.4e-05       0.5       2      88 ..     112     197 ..     111     206 .] 0.74

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.13
        Med4 42 DekikeivksLkeyekeLkavpdqenskl 70
                D k+ +i+k L +   +L++ ++ e +k 
  EPA06151.1 39 DAKQHTIIKRLENEADILTRDIFAELNKT 67
                77777888888888888887776666664 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 8.4e-05
        Med4   2 klaekLlaaddelskslkeleehqknearilqLraev...eslDekikeivksLkeyekeLkavpdqenskldtasiklaekrevdseeL 88 
                 ++a++L++a +e + ++++l+  ++ ++ i  +r+        De  ++ +++L e   +++       +++  +++++a  r vd+ ++
  EPA06151.1 112 DIAKELVNATKEVEYMVSKLRSIKNTQDMIAHCRNTStieHTVDELYRKSIEKLFETNDAITIIK---LKDI-YETMETASDRCVDVADV 197
                 689*******************************9752224679999999999999999887665...3333.34455555555544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1452  (0.0809861); expected 358.6 (0.02)
Passed bias filter:                      707  (0.0394333); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.54
# Mc/sec: 1149.22
//
Query:       EPA06152.1  [L=47]
Description: hypothetical protein BG20_I2108 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 294.43
//
Query:       EPA06153.1  [L=213]
Description: hypothetical protein BG20_I2110, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.7e-14   52.7   0.2    4.2e-14   52.1   0.2    1.3  1  tRNA-synt_1g  tRNA synthetases class I (M)
    1.1e-07   31.9   0.0    1.4e-07   31.6   0.0    1.2  1  Anticodon_1   Anticodon-binding domain of tRNA


Domain annotation for each model (and alignments):
>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.1   0.2   4.6e-18   4.2e-14     339     390 ..       3      55 ..       1      56 [. 0.91

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 4.6e-18
                   HHHHHHH-HHHHHHHHHHHS-.TTS-EEE-HHHHHHHHHHHCCCHHHHHHHHH CS
  tRNA-synt_1g 339 kealerldadllRYylaaeap.ekkDldfswedfvervNseLadklgnlvnRv 390
                   k++le+++ad+lRYyl+a +p  ++Dl+f w++f++r+NseL+++lgn+vnR+
    EPA06153.1   3 KQFLEYYPADYLRYYLVAINPySQDDLNFDWDEFTNRINSELIGNLGNFVNRA 55 
                   789***************66516789**************************8 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0   1.6e-11   1.4e-07       3     111 ..      79     179 ..      77     209 .. 0.83

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 1.6e-11
  Anticodon_1   3 wilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkra.aqevllevletllrllaPfmPfitEelwqreeeelgkk 99 
                  ++ +++ +l+ e    +e+  +++a+++++ef +  + + y++  +p+ ++      +a +  +   +++++ + l Pf+P  ++++w    e+lg +
   EPA06153.1  79 EAENKIKNLAGELGLLMEQNHLDRALKKIMEF-SSYF-NQYFQHKEPWKKGPG----TAnCVFLSVNAARSMAIALFPFLPVSSQKIW----EQLGFS 166
                  5677888888888889***************8.6666.**********85533....35599**************************....999999 PP

  Anticodon_1 100 esimlaewpe.ka 111
                    +  ++w++ ++
   EPA06153.1 167 GKVNTSKWESlSE 179
                  9999999996333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1351.57
//
Query:       EPA06154.1  [L=49]
Description: hypothetical protein BG20_I1635 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.011   15.6   0.5       0.24   11.3   0.2    2.1  2  zinc_ribbon_4  zinc-ribbon domain


Domain annotation for each model (and alignments):
>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   1.4e-05      0.24       3      16 ..       5      18 ..       4      19 .. 0.89
   2 ?    2.7   0.0    0.0069   1.2e+02      17      29 ..      28      41 ..      24      42 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.4e-05
  zinc_ribbon_4  3 itCpsCkakyeidd 16
                    +C  Ck+k++i++
     EPA06154.1  5 ARCRICKTKFSIPE 18
                   69**********97 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.0069
  zinc_ribbon_4 17 ek.lpakgvkvrCs 29
                   ek l+++gv+ +C 
     EPA06154.1 28 EKyLQDSGVSCKCG 41
                   56589999999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 331.14
//
Query:       EPA06155.1  [L=71]
Description: hypothetical protein BG20_I1634 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      571  (0.0318478); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 499.69
//
Query:       EPA06156.1  [L=159]
Description: hypothetical protein BG20_I1628, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1049.54
//
Query:       EPA06157.1  [L=278]
Description: NurA domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-17   64.1   0.1    2.2e-17   63.6   0.1    1.3  1  NurA      NurA domain
  ------ inclusion threshold ------
      0.084   12.4   0.0       0.14   11.7   0.0    1.3  1  OpuAC     Substrate binding domain of ABC-type glycine betain


Domain annotation for each model (and alignments):
>> NurA  NurA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.6   0.1   2.5e-21   2.2e-17       3     242 .]      48     253 ..      46     253 .. 0.83

  Alignments for each domain:
  == domain 1  score: 63.6 bits;  conditional E-value: 2.5e-21
                 EEEEEEEEEEEEETTCEEEEEEEEEEECCEEECCCEEEECEBTCCHHEEEEEHHHHHHHHHHHHHHHHHHHCGGCCSCEEEEECSHHCCCHHHHHHHHH CS
        NurA   3 vaAvDGSngvvrlsggilyilsayavvgggkerleealslasvdsispsdelerrirllmetlElklgallleekgedllllDGsligslvefdelhee 101
                 +a++D+S++  r+ g+ l +  a+++ + g+  +  + s    d+         + +    ++E++  a  +  + +dl+l+DGsl+  ++        
  EPA06157.1  48 TAGIDSSFNNTRFQGIELWATTAVSIKSDGEVLVDLHDSGLGSDI---------DLSKIASKMEIE--ACEKTVDLVDLVLMDGSLHSQFM-------- 127
                 799**********************55555555555555555555.........445555555555..444668889**************........ PP

                 HHHHHHHHHHHHHTT-TTCEEEEESS-SCTCCHCCC......S--HHHHCCHHCCHCH---STTS-HHHHTT-HCCHHHHHH-.EEEEEEESSTTTTEE CS
        NurA 102 leyeeylyslsrlleaglnlvgvaKsfrskellnllletlligesisDiallgallrkpgytspllkilrekpllrealidke.iyfaYvrlegggsil 199
                   +  +  ++ ++++++ n++++aK++++k+ ++ l      g    Di + + +++ pg+++ +           ++++ ++ i +++vrl+ + +i 
  EPA06157.1 128 TRQSSLDAMVVKTMKKRDNVIFIAKTSNTKKQFEDL------GSLAGDIFYYNHITKGPGFSKIFV---------EKKYGADKvISSTFVRLSDSTPII 211
                 7777888888899999********************......**************9999985333.........466677776*************** PP

                 EEEHHHHHH.CCHHHHHHHHHH..TTB-SSSBCCHHHHHHHHCC CS
        NurA 200 rleipaevs.takdedvlsllasqrlsisGYprpLalAhelaki 242
                 +le+    + +++++++ ++l+    s  GYp++L+lAh++ ki
  EPA06157.1 212 KLEFLGGHRgDDEIMSIMNKLY--KSSVGGYPYALKLAHNNCKI 253
                 ***7666666799999******..****************9887 PP

>> OpuAC  Substrate binding domain of ABC-type glycine betaine transport system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   1.6e-05      0.14     126     197 ..      19      86 ..       7     114 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.6e-05
                 STTSHHCCHHHHHHHHHHT-TTCEEEGSCEEEEHHHHHHHHHTTCSSEEEEETTSTHHHHTTEEE-B-TTST CS
       OpuAC 126 rpdgwgcekvtegllkaYgldkvelvegseaamdaelyaaykrgepvvvyawtPdwaikkydlvvLedpkgl 197
                 +  g + e++ +++++ +    ve v+ +++ ++a +++++ + + + + +w++++   k d  vL d  ++
  EPA06157.1  19 ILKGPKFEQILKKAKENW----VEFVPTKQNVVTAGIDSSFNNTRFQGIELWATTAVSIKSDGEVLVDLHDS 86 
                 555666666666666666....6677****************************************986555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1835.90
//
Query:       EPA06158.1  [L=329]
Description: putative membrane protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       741  (0.0413297); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2040.27
//
Query:       EPA06159.1  [L=692]
Description: RecF/RecN/SMC N-terminal domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.5e-17   61.7  23.2    4.9e-10   39.2   1.3    2.6  2  SMC_N           RecF/RecN/SMC N terminal domain
      9e-16   59.0  34.8      9e-16   59.0  34.8    4.2  1  AAA_23          AAA domain
      9e-12   45.4  11.4    2.3e-06   27.6   0.4    3.2  2  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
    1.2e-10   41.7  55.4    1.3e-06   28.4  26.2    2.4  2  AAA_15          AAA ATPase domain
    8.4e-09   35.0   0.2    1.7e-08   34.0   0.2    1.5  1  AAA_29          P-loop containing region of AAA domain
    1.1e-06   28.4   0.4    1.1e-06   28.4   0.4    2.7  3  AAA_27          AAA domain
    1.1e-05   25.5   0.1    2.3e-05   24.6   0.1    1.5  1  SbcCD_C         Putative exonuclease SbcCD, C subunit
     0.0002   21.9  23.2      0.012   16.2   0.1    5.1  2  ABC_tran        ABC transporter
      0.009   15.9   0.1      0.009   15.9   0.1    3.7  4  RsgA_GTPase     RsgA GTPase
  ------ inclusion threshold ------
      0.076   13.1   0.0       0.16   12.0   0.0    1.5  1  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
       0.15   12.2   2.4        2.6    8.3   0.3    2.7  2  Pim             Pesticin immunity protein
       0.28   11.0   0.0       0.28   11.0   0.0    3.4  4  MukB            MukB N-terminal
       0.79    9.8   6.3       0.74    9.9   0.1    3.6  2  MMR_HSR1        50S ribosome-binding GTPase
        9.6    5.3   7.8        1.4    8.1   0.3    2.6  2  Radical_SAM_N   Radical SAM N-terminal


Domain annotation for each model (and alignments):
>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   1.3   3.8e-13   4.9e-10       1      87 [.       1      78 [.       1     113 [. 0.81
   2 !   27.1  14.7   1.9e-09   2.4e-06     135     216 ..     357     685 ..     215     688 .. 0.77

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 3.8e-13
                EEEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETT CS
                xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       SMC_N  1 vlkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdned 87
                +++ +e+ +F s   ++++l+f +++t+ vG+NG+GKs+++dAi F L  +++    +++ + li++   ++++ +a+ve  ++ ++
  EPA06159.1  1 MITAIELGDFLSH--SQTKLEFGNGVTVFVGQNGAGKSSIIDAITFALFGQHT----RKSNKGLIKR---GSNQGFAKVEFNINGKQ 78
                58899*******9..699****************************9986777....5667889987...66666777776654444 PP

  == domain 2  score: 27.1 bits;  conditional E-value: 1.9e-09
                 T.................................................................................................. CS
                 x.................................................................................................. RF
       SMC_N 135 e.................................................................................................. 135
                 +                                                                                                  
  EPA06159.1 357 Qeehlkqeiitikeqiisaekervaynqkriefskklqdvrdaeatlrahsikdqedirkiqgeiklkkenvqkiplsingnlleisqidsnakrifes 455
                 044444444444444444444444444444444444444444444444555555577777777777777788888888888888888888889999999 PP

                 ................................................................................................... CS
                 ................................................................................................... RF
       SMC_N 136 ................................................................................................... 135
                                                                                                                    
  EPA06159.1 456 itkleeetkgfneeeflnlkksinekqttlsqtdqrlgaiiekiskyeeqikstqkivsdlkvvkkyvekldiiqmnifsrdgpvamslrswalntisa 554
                 999999999999999999999999999999999999999999999999999999999999999999********************************* PP

                 .......................................CS-HHHHHHHHHHHHHH...HHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHC..... CS
                 .......................................xxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..... RF
       SMC_N 136 .......................................lLSgGektLvalaLlfA...iqkvkpaplyllDeidaaLDeknvkkvaellkeks..... 187
                                                        +LSgGe+  valaL++    +  ++   l++lDe   +LD+++ k+++ +l + s     
  EPA06159.1 555 ksseyltllntkiqrialsekardisitcysksevldleSLSGGEQVSVALALRLGmasLLGASNLNLMILDEPTTHLDAERKKALVGVLSQLSdiani 653
                 ******************************************************9844566778889*******************9999877633333 PP

                 .TTSEEEEE-SSHHHCCC-..SCEEEEEEEET CS
                 .xxxxxxxxxxxxxxxxxx..xxxxxxxxxxx RF
       SMC_N 188 .knaQfivislreemleka..dklvgvtkven 216
                  k +Qfi+i++++e++e++  +++++  ++e+
  EPA06159.1 654 gKPMQFIIITHDAEIFEDSnvERIYKFESAEQ 685
                 3679************9985567776666555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.0  34.8     7e-19     9e-16       2     199 ..       5     281 ..       4     282 .. 0.69

  Alignments for each domain:
  == domain 1  score: 59.0 bits;  conditional E-value: 7e-19
      AAA_23   2 LkienfrsfrdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrks......grgfeksdveiesegkvkay.veltfenkdgrytrsiere 93 
                 +++  f s++ ++++F++g+t+++G+NGaGK++i+dAi++aL+g+ +r s+k       ++gf k +++i    ++k+y + +++ nk+g      +++
  EPA06159.1   5 IELGDFLSHSQTKLEFGNGVTVFVGQNGAGKSSIIDAITFALFGQHTRKSNKGlikrgsNQGFAKVEFNI----NGKQYqAVRKIDNKGG---LAAKFS 96 
                 5667799*************************************99998887788544333444444443....4444434444555555...244445 PP

      AAA_23  94 relskkkgkttkkaklelleideleqfisellgskkiilnlilflgqerfeefelkdkke....................................... 153
                  +++++  +   + ++++++ +  +q++++ +g  ++ l++ ++ +q++ + + ++++ke                                       
  EPA06159.1  97 ENVNDEFLEIAAG-ERKQFG-ESMTQEVEKTIGLGFEKLKIASIVQQGELNAIIKAKPKEfkellnaiigidkldvaseamktitknfrekirdekgyd 193
                 5555444333222.233333.456899999999999999999999999977777766666777777888888888888888888888888888999999 PP

      AAA_23 154 .....................................rleelekeleeledekkllekleqekekek.....eleeleeeleeilkel 199
                                                      ++ +l+ +le ++ +++++++le +k++ +     +++++++e++e + ++
  EPA06159.1 194 dthidillrelqksiidleesrpqkeqlvikqielqkEVSSLRAKLEIETPKIDKINQLELRKKELQsyakeAIQAIQQEITEKEHKI 281
                 9999997777777777777777777777777777666666677777776666666666633333333344458888888888777665 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.4   1.8e-09   2.3e-06       1      53 [.      24      78 ..      24      85 .. 0.85
   2 !   22.0   2.5   9.7e-08   0.00012      94     302 ..     459     669 ..     412     670 .. 0.62

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 1.8e-09
      AAA_21  1 lnvliGpNgsGKSnLLdaldllarl..drdvegltdelsggggirkipslldlyd 53
                ++v++G Ng+GKS+++da+ ++ +    r ++ + +++++++g++k+++ +++++
  EPA06159.1 24 VTVFVGQNGAGKSSIIDAITFALFGqhTRKSNKGLIKRGSNQGFAKVEFNINGKQ 78
                79*******************9875888888888888888888888888888776 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 9.7e-08
      AAA_21  94 lesgllldkrsleeedvfnpeargirggvsvfslkelsvsepndlqfgkaltditsrawsllllldglrkerigllnifadyfgfakekrllqrlvrsl 192
                 le  +  +++ ++   +++ +++ +    ++ +l +++ +++  ++++k + +i+s++   ++  ++l        +i +++++  + +  ++  +rs+
  EPA06159.1 459 LEEETKGFNEEEFLNLKKSINEKQTTLSQTDQRLGAIIEKISKYEEQIKSTQKIVSDLKVVKKYVEKL--------DIIQMNIFSRDGPVAMS--LRSW 547
                 44444444444444444444444444455555555555555555555555555555555555533333........22222222222222222..2222 PP

      AAA_21 193 klveielsdlgegee...liasvderlrergvvflengdgqelparelSdGtkrllalltallralkkg....sllliDEpEngLHPkllrrllellke 284
                  l+ i +  +++      +i ++++ ++ r++ +  +++   l++ +lS G +   al++ l  a   g     l ++DEp ++L+ ++ + l+++l++
  EPA06159.1 548 ALNTISAKSSEYLTLlntKIQRIALSEKARDISITCYSKSEVLDLESLSGGEQVSVALALRLGMASLLGasnlNLMILDEPTTHLDAERKKALVGVLSQ 646
                 222222222222222000223333333333888888888899999999****999999999988888889999************************99 PP

      AAA_21 285 lsr.....ngaQviltTHSplll 302
                 ls+     +  Q+i+ TH+ ++ 
  EPA06159.1 647 LSDianigKPMQFIIITHDAEIF 669
                 999999*************9885 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4  26.2     1e-09   1.3e-06       1     256 [.       1     315 [.       1     341 [. 0.46
   2 ?    1.6  42.1      0.14   1.8e+02      75     368 ..     277     668 ..     197     669 .. 0.51

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 1e-09
      AAA_15   1 MkIkkikikNFRslkdveidlseeltvliGkNnsGKSsilealdl.Flnnkekkn...........................kkvikiekedleifeni 71 
                 M I+ i++  F s++++++++ + +tv++G N++GKSsi++a+ + ++ + ++k+                           +             ++i
  EPA06159.1   1 M-ITAIELGDFLSHSQTKLEFGNGVTVFVGQNGAGKSSIIDAITFaLFGQHTRKSnkglikrgsnqgfakvefningkqyqaV-------------RKI 85 
                 7.99999999*********************************8644444444446999999999998855555544444441.............333 PP

      AAA_15  72 seskdikIdvef...........................aek..ekakeyektlkskekkkadlllkkkesdlkktikdkklklkknelsdekisvekk 141
                 +++    ++ +f                           + k  +   e +k++   ++ + + ++k k++++k++++  +  +k  ++ +e  +   k
  EPA06159.1  86 DNKG--GLAAKFsenvndefleiaagerkqfgesmtqevE-KtiGLGFEKLKIASIVQQGELNAIIKAKPKEFKELLNAIIGIDK-LDVASEAMKTITK 180
                 3222..2333331122212222222334444444443321.12322223334444445555555666666666666555544443.2222222222222 PP

      AAA_15 142 kskkelpkekeeklekekeelkidkedlkklikkleeslkkee..............elknvlksaiiklllisakRnvsdedsekkssllgklkekil 226
                 + + ++     +++  ++++++i   +l+k i +lees +++e              +l  +l+ + +k++ i+     ++e+    ++++ +++++i 
  EPA06159.1 181 NFREKIR----DEKGYDDTHIDILLRELQKSIIDLEESRPQKEqlvikqielqkevsSLRAKLEIETPKIDKINQLELRKKELQSYAKEAIQAIQQEIT 275
                 2222222....2333444566666444444444466666666545555554444333222222222222222222222222222222222222222222 PP

      AAA_15 227 eealqekl..............eeelteklkeiqeklkeidkkl 256
                 e+   e                + +l++k ++i+ +++e +k +
  EPA06159.1 276 EK---E-HkirdcegcfehislKNDLEQKMERIELAVEENQKRI 315
                 21...1.1234444444444443344444444444444444444 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.14
      AAA_15  75 kdikIdvef..............................................aek..ekakeyektlkskekkkadlllkkkesdlkktikdkklk 125
                 k+ kI+ ++                                              aek   k++++ ++  + ek  + ++ +++++++          
  EPA06159.1 277 KEHKIRDCEgcfehislkndleqkmerielaveenqkriqeltgkvaslkeklllAEKiqLKDNKCPVCDSKVEKLNPLFQEEHLKQEII--------T 367
                 333333333444544444444444444444444466666666666666644444422222334444444444444444433333333333........3 PP

      AAA_15 126 lkknelsdekisvekkks....kkelpkekeeklekekeelkidkedlkklikkleeslkkee............................elknvlks 192
                 +k++ +s ek  v  +++    +k+l + ++ +++++  ++ +d+ed++k+  +++ +++  +                            +l++   +
  EPA06159.1 368 IKEQIISAEKERVAYNQKriefSKKLQDVRDAEATLRAHSI-KDQEDIRKIQGEIKLKKENVQkiplsingnlleisqidsnakrifesitKLEEET-K 464
                 33333333333333333322222222222222232222222.3555555555533333322224444333333322233333332222221111111.1 PP

      AAA_15 193 aiiklllisakRnvsd..edsekkssllgklkekileealqekl............eeelteklkeiqeklkeidkklaeelkkilkkkidkikkfnyk 277
                  + + ++ + k+++++  ++  +++  lg+++eki+++  q                ++  ekl+ iq                               
  EPA06159.1 465 GFNEEEFLNLKKSINEkqTTLSQTDQRLGAIIEKISKYEEQ--IkstqkivsdlkvVKKYVEKLDIIQM------------------------------ 531
                 11112222222222221111112222222222222222111..12223333333333333333333333.............................. PP

      AAA_15 278 gkkneeieik.....................................................ddeelplnknGsGvqrllllillileaekkdekeek 323
                          +                                                       e l+l+  + G q  + l+l + +a+      ++
  EPA06159.1 532 ---------NifsrdgpvamslrswalntisaksseyltllntkiqrialsekardisitcysKSEVLDLESLSGGEQVSVALALRLGMASLL--GASN 619
                 .........1444444445556666666666666666666666666678999999999*****99****************************..99** PP

      AAA_15 324 nvilliEEPEahLHpqaqkvlikllkelandnkt....QviitTHSphi 368
                  ++ +++EP +hL  + +k l+  l  l++  +     Q ii TH   i
  EPA06159.1 620 LNLMILDEPTTHLDAERKKALVGVLSQLSDIANIgkpmQFIIITHDAEI 668
                 **********************999998887766788********8766 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.2   1.4e-11   1.7e-08      13      56 ..      14      56 ..       2      57 .. 0.82

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 1.4e-11
      AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiqalLvpakkvrfNk 56
                +++++e+  +g+t+++G++G+GKS+++DAi++ L ++++++ Nk
  EPA06159.1 14 SQTKLEFG-NGVTVFVGQNGAGKSSIIDAITFALFGQHTRKSNK 56
                44556665.669**************************999997 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.4   8.8e-10   1.1e-06       6     112 ..       5     109 ..       1     198 [. 0.84
   2 ?   -1.5   0.6       1.2   1.5e+03     159     205 ..     366     411 ..     348     412 .. 0.71
   3 ?   -3.1   0.1       3.8   4.8e+03     167     203 ..     447     484 ..     442     498 .. 0.47

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 8.8e-10
      AAA_27   6 LdLeryGkftdrsldfsaeeadlhliyGpNEAGKstalrAisdllfGipertkdnflhdakkLrigavle.eadgeelefaRrkgrkktlldaddqalp 103
                 ++L  + + ++++l+f+   +++++ +G N AGKs++++Ai+  lfG ++r++++ l ++ + +  a +e + +g++ + +R+  +k  l+++ +++++
  EPA06159.1   5 IELGDFLSHSQTKLEFG---NGVTVFVGQNGAGKSSIIDAITFALFGQHTRKSNKGLIKRGSNQGFAKVEfNINGKQYQAVRKIDNKGGLAAKFSENVN 100
                 56666666778889997...89*****************************99999988888777777765899**********************999 PP

      AAA_27 104 eevlaallg 112
                 +e l+ + g
  EPA06159.1 101 DEFLEIAAG 109
                 999986544 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.2
      AAA_27 159 revleaLeaeadelfkprkskkrainealeeleeakkelreaqvrae 205
                  ++ e++ +  +e  + ++++  ++ ++l+++++a+++lr+++++++
  EPA06159.1 366 ITIKEQIISAEKERVAYNQKRI-EFSKKLQDVRDAEATLRAHSIKDQ 411
                 5555665555555555555555.799999999999999999998876 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 3.8
      AAA_27 167 aeadelfkprkskk.rainealeeleeakkelreaqvr 203
                 ++a+++f++ ++ + ++    +ee+ ++kk+++e+q++
  EPA06159.1 447 SNAKRIFESITKLEeETKGFNEEEFLNLKKSINEKQTT 484
                 45555555444444122222333444444444444433 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.1   1.8e-08   2.3e-05      30      89 ..     592     645 ..     583     646 .. 0.92

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.8e-08
     SbcCD_C  30 sgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                  ++lSGGe+ + ++lal +++a+l++ +     +l l++LDE    lD+e+ ++l+++l 
  EPA06159.1 592 LESLSGGEQ-VSVALALRLGMASLLGAS-----NLNLMILDEPTTHLDAERKKALVGVLS 645
                 5789*****.*****************5.....8*****************999998875 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   9.2e-06     0.012      13      32 ..      24      43 ..      13     148 .. 0.90
   2 ?   -2.0  19.0       3.6   4.7e+03      38     136 ..     417     629 ..     199     630 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 9.2e-06
                EEEEEESTTSSHHHHHHHHT CS
                xxxxxxxxxxxxxxxxxxxx RF
    ABC_tran 13 kvaivGenGaGKStLlklla 32
                ++++vG+nGaGKS+++ +++
  EPA06159.1 24 VTVFVGQNGAGKSSIIDAIT 43
                6789*************997 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.6
                 SEEEEEETTCEGGG.........B-HHHCCHCEEEE-SS.--S-TTSBHHHH............................................... CS
                 xxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxx.xxxxxxxxxxxx............................................... RF
    ABC_tran  38 teGeilldgkdlke.........qeleslrkeigvlpqe.pqlfpeltvren............................................... 79 
                  +Gei+l+++++++          e+++ +++ + +++  ++l +      +                                               
  EPA06159.1 417 IQGEIKLKKENVQKiplsingnlLEISQIDSNAKRIFESiTKLEE------Etkgfneeeflnlkksinekqttlsqtdqrlgaiiekiskyeeqikst 509
                 677777777777775555554442222222222222222222222......123333345555555566557788777777777777777666555444 PP

                 ...................HHHTCHHHHHHHSTTGG......................................................TTCBGESTT CS
                 ...................xxxxxxxxxxxxxxxxx......................................................xxxxxxxxx RF
    ABC_tran  80 ...................esdeeiekalsklglke......................................................lkdtvvkss 105
                                                    +                                                       k +v+  +
  EPA06159.1 510 qkivsdlkvvkkyvekldiI---------------QmnifsrdgpvamslrswalntisaksseyltllntkiqrialsekardisitcySKSEVL--D 591
                 55554444444444444440...............3444444444444444444444444445555555555555555556555555543333333..4 PP

                 SGGS-HHHHHHHHHHHHH.......HHTSSEEEEESTT CS
                 xxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxx RF
    ABC_tran 106 pssLSgGqkqrvalaral.......lkkpkllllDEpt 136
                  +sLSgG+++ vala  l       +++ +l++lDEpt
  EPA06159.1 592 LESLSGGEQVSVALALRLgmasllgASNLNLMILDEPT 629
                 4************996443333333567799******9 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1     7e-06     0.009      96     121 ..      19      44 ..       5      69 .. 0.82
   2 ?   -1.6   0.0       1.7   2.2e+03      47      70 ..     159     180 ..     153     208 .. 0.70
   3 ?   -2.0   1.4       2.2   2.8e+03      35      99 ..     204     276 ..     194     282 .. 0.57
   4 ?   -2.2   0.6       2.6   3.4e+03      57      97 ..     371     421 ..     347     426 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 7e-06
                  HCTTSEEEEECSTTSSHHHHHHHHCT CS
  RsgA_GTPase  96 llkdktsvlvGqSGvGKStLinallp 121
                  ++ + ++v+vGq G+GKS++i+a++ 
   EPA06159.1  19 EFGNGVTVFVGQNGAGKSSIIDAITF 44 
                  456789***************99875 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.7
                  -EEEEEEE-GGG--HHH..HHHHHHH CS
  RsgA_GTPase  47 iepvivlnKiDlleeee..eleelke 70 
                  ++ +i + K+D+++e+         +
   EPA06159.1 159 LNAIIGIDKLDVASEAMktI----TK 180
                  57899999***999988431....22 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 2.2
                  HHHHHHHHHHTT-.EEEEEEE-GGG--HHH......HHHH.HHHHHHHTTSEEEE--TTTHTTHHHHHHHCTT CS
  RsgA_GTPase  35 ldrfLvlaeekgi.epvivlnKiDlleeee......elee.lkeelealgyevllvsaktkegleelkellkd 99 
                  l++ ++ +ee++  +  +v+  i+l +e +      e+e+   +++++l+++   +++  ke+++++++++++
   EPA06159.1 204 LQKSIIDLEESRPqKEQLVIKQIELQKEVSslraklEIETpKIDKINQLELRKKELQSYAKEAIQAIQQEITE 276
                  5555665555554355666777777666665555443332133455566666666666666666666666655 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 2.6
                  GG--HHH..........HHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHC CS
  RsgA_GTPase  57 Dlleeee..........eleelkeelealgyevllvsaktkegleelkell 97 
                   +++ e+          e+++  +++++++ ++ + s k++e++++++ ++
   EPA06159.1 371 QIISAEKervaynqkriEFSKKLQDVRDAEATLRAHSIKDQEDIRKIQGEI 421
                  333333333333333566777778888888888888888888888887665 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00012      0.16       1      11 [.     341     351 ..     341     366 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
  DNA_ligase_ZBD   1 hCPvCGsavvR 11 
                     +CPvC+s+v++
      EPA06159.1 341 KCPVCDSKVEK 351
                     6********98 PP

>> Pim  Pesticin immunity protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1       0.1   1.3e+02      26      78 ..     222     273 ..     206     276 .. 0.73
   2 ?    8.3   0.3     0.002       2.6      42      90 ..     473     521 ..     441     529 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.1
         Pim  26 lakdilknlelntfrnslrpriygdqttlkqteyritekkagakktialvdke 78 
                 + k+i  + e+ ++r  l+    ++   ++q e r  e ++ ak+ i ++++e
  EPA06159.1 222 VIKQIELQKEVSSLRAKLEI-ETPKIDKINQLELRKKELQSYAKEAIQAIQQE 273
                 44444444455555555543.3689999*********************9987 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.002
         Pim  42 slrpriygdqttlkqteyritekkagakktialvdkeqswvislkvlei 90 
                  l++ i  +qttl qt+ r+  +     k    ++  q  v  lkv+++
  EPA06159.1 473 NLKKSINEKQTTLSQTDQRLGAIIEKISKYEEQIKSTQKIVSDLKVVKK 521
                 4899999************999999888888889999999988988865 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00022      0.28      23      70 ..      19      66 ..      10      81 .. 0.87
   2 ?   -1.2   1.3       1.2   1.5e+03      87     161 ..     207     286 ..     200     304 .. 0.68
   3 ?   -2.2   0.7       2.2   2.9e+03      94     171 ..     382     457 ..     369     463 .. 0.71
   4 ?   -1.5   0.2       1.4   1.8e+03     136     167 ..     503     534 ..     472     536 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00022
                -HHHHHHHHHS--SHHHHHHHHHHHHHHS--TTT-------------- CS
        MukB 23 dldelvttlsGgnGaGksttmaafvtaliPdlsllhfrntteaGatsg 70
                ++ + vt + G nGaGks ++ a+  al    ++   + +   G+++g
  EPA06159.1 19 EFGNGVTVFVGQNGAGKSSIIDAITFALFGQHTRKSNKGLIKRGSNQG 66
                566789***********************9999988888888887776 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.2
                 EEEEEE-T...TS-EEEEEEEEEE.-SSTTT-EEEEEEEEES--T.T--HHHHHEE--SSS--EE--HHHHHHHHHTSTT CS
        MukB  87 svlevvns...reqrllvgvrleq.vagrdkkvdikpfalqglee.dvkltdvlleklddkkarvrelnelkekleeleg 161
                 s+++  +s   +eq ++  ++l++ v++   k++i++  + ++++ +++ +++     +  +a  +e++e  +k+ + eg
  EPA06159.1 207 SIIDLEESrpqKEQLVIKQIELQKeVSSLRAKLEIETPKIDKINQlELRKKELQSYAKEAIQAIQQEITEKEHKIRDCEG 286
                 55655555111467788889997548888889999998888887635566666666666666666677776666666555 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 2.2
                 TTS-EEEEEEEEEE-SSTTT-EEEEEEEEES--TT--HHHHHEE--SSS--EE--HHHHHHHHHTSTT-EEEE-S-HH CS
        MukB  94 sreqrllvgvrleqvagrdkkvdikpfalqgleedvkltdvlleklddkkarvrelnelkekleelegvrlkkfnsvt 171
                  +++r+ ++ +l++v  rd    +++ ++++ e+  k++  +  k ++ ++  +++n    +++++++   ++f+s+t
  EPA06159.1 382 YNQKRIEFSKKLQDV--RDAEATLRAHSIKDQEDIRKIQGEIKLKKENVQKIPLSINGNLLEISQIDSNAKRIFESIT 457
                 567788888888877..7888888888888888888877777666666666666666666666666666666666665 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 1.4
                 EE--SSS--EE--HHHHHHHHHTSTT-EEEE- CS
        MukB 136 leklddkkarvrelnelkekleelegvrlkkf 167
                  e+++ +++ v +l+ +k+ +e+l+ +++++f
  EPA06159.1 503 EEQIKSTQKIVSDLKVVKKYVEKLDIIQMNIF 534
                 45667778888899999999999998888887 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00058      0.74       3      26 ..      26      53 ..      24     123 .. 0.74
   2 ?   -1.1   3.1       1.5   1.9e+03      23      58 ..     256     289 ..     157     435 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00058
                EEEESTTSSHHHHHHHHH....TSTEEE CS
    MMR_HSR1  3 aivGrpNvGKStLinalt....gekaiv 26
                ++vG+  +GKS++i a+t    g++ + 
  EPA06159.1 26 VFVGQNGAGKSSIIDAITfalfGQHTRK 53
                79***************93333233333 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.5
                 TEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSS CS
    MMR_HSR1  23 kaivsdkpgtTrdinegrvklkgkeielvDtpGlie 58 
                 k + ++++   ++ ++ +++  +ke ++ D+ G +e
  EPA06159.1 256 KKELQSYAKEAIQAIQQEIT--EKEHKIRDCEGCFE 289
                 33334444444444444444..33455555555443 PP

>> Radical_SAM_N  Radical SAM N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.3    0.0011       1.4     229     293 ..     205     271 ..     117     275 .. 0.74
   2 ?   -0.3   2.5      0.39   4.9e+02     180     249 ..     405     475 ..     299     521 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0011
  Radical_SAM_N 229 afrlle.eetnplnakalvqkhg.dravvlnppalplsteelDevyelpyarkahpsykkkkipale 293
                    + ++++ ee++p +++ ++++ + ++ v   +++l+++t ++D++ +l+  +k  +sy+k+ i+a++
     EPA06159.1 205 QKSIIDlEESRPQKEQLVIKQIElQKEVSSLRAKLEIETPKIDKINQLELRKKELQSYAKEAIQAIQ 271
                    334444044555555555555441469**************************************97 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.39
  Radical_SAM_N 180 lakgeeveelkdirgtavllkkeakake.kevielpsyeevkedkklyaeafrlleeetnplnakalvqkh 249
                     ++ ++ e++++i+g + l+k+++++ + +   +l + +++ ++ k+  e+++ leeet+ +n++++++ +
     EPA06159.1 405 AHSIKDQEDIRKIQGEIKLKKENVQKIPlSINGNLLEISQIDSNAKRIFESITKLEEETKGFNEEEFLNLK 475
                    33334456677777776655543333334566778888888888888888888888888888887776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (692 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2010  (0.112109); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        33  (0.00184059); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 1.13u 0.38s 00:00:01.50 Elapsed: 00:00:00.55
# Mc/sec: 3806.45
//
Query:       EPA06160.1  [L=345]
Description: hypothetical protein BG20_I1629 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 1944.53
//
Query:       EPA06161.1  [L=145]
Description: hypothetical protein BG20_I1637, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 908.83
//
Query:       EPA06162.1  [L=496]
Description: hypothetical protein BG20_I1631 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-37  129.0   3.3    2.8e-37  129.0   3.3    1.7  2  DUF87          Helicase HerA, central domain
    0.00014   20.6   0.1     0.0097   14.5   0.0    2.1  2  DUF853         Bacterial protein of unknown function (DUF853)
  ------ inclusion threshold ------
      0.023   13.6   0.2      0.068   12.1   0.0    1.9  2  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
      0.034   14.3   0.0        0.1   12.7   0.0    1.9  1  HAS-barrel     HAS barrel domain
       0.04   14.2   1.1       0.11   12.8   1.1    1.7  1  DUF4709        Domain of unknown function (DUF4709)
      0.082   13.3   0.0       0.33   11.3   0.0    2.0  2  AAA_16         AAA ATPase domain
      0.083   13.4   1.6       0.18   12.3   1.6    1.6  1  ABC_tran       ABC transporter


Domain annotation for each model (and alignments):
>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.0   3.3   1.1e-40   2.8e-37       1     226 [.     114     315 ..     114     316 .. 0.93
   2 ?   -2.4   0.0       1.6   4.2e+03     102     131 ..     403     438 ..     384     477 .. 0.66

  Alignments for each domain:
  == domain 1  score: 129.0 bits;  conditional E-value: 1.1e-40
       DUF87   1 ieiGrllsgsevpvyldlnklvtrHlAilgsTGsGKSntvavLleellekkgatililDpHGEYgkalekllsekvkvitpspsakdkelkinpwsldp 99 
                 ++iG+ll +++++++++l+k+v rHl+il++TG+GKSn+v+++ +++  k ++t++i+D H++Y +++     ++++vi++         kinp++ld 
  EPA06162.1 114 VKIGNLLREKSIEAKINLDKIVARHLGILAMTGMGKSNLVSLITKQIG-KLKGTVIIFDYHNDYTTLN----IPRINVIDA---------KINPRLLDA 198
                 68**********************************************.*******************....********9.........9******** PP

       DUF87 100 eelldlleeddkpaaavqrsvleealdqakakeekekl.ssdepveklleelkkekeelrklknqaiarlldkledllrkggsf.snsstdlialllek 196
                 ++l ++le+  ++ a+vq++vl+ a+++ ++ e+ke + + ++ ve++ ++      +  k+ + ++ r++d +e+ +r+ +++ + ++ d+i+ +   
  EPA06162.1 199 DQLSEVLEI--RDGANVQQRVLRMAFTKQVK-ESKEFWkKLETEVEFIVNSED----KKIKEIRTSAYRVQDIIEEAQRRFEDIlDPDMGDPISFI--- 287
                 *********..**************997774.7777762578899**999999....8999999999999999999999999999999********... PP

       DUF87 197 lekegkitiidlsgvdelaqqlvvsvilrr 226
                   keg+ +i+++s+++e+++++  +++l++
  EPA06162.1 288 --KEGRTNILNISELSEKQANVALAFYLQQ 315
                 ..********************88888876 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.6
       DUF87 102 lldllee.ddkpaaavqrsvleealdqaka.....k 131
                 +++++ e d+++ aa+ +s  +e+++q+++     +
  EPA06162.1 403 IMKIIQEdDQRQIAAATESTSRELIAQLTSlnvgdA 438
                 566666666666666677777777777766555553 PP

>> DUF853  Bacterial protein of unknown function (DUF853)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.9   0.0    0.0062        16       8      67 ..     124     182 ..     118     206 .. 0.75
   2 !   14.5   0.0   3.8e-06    0.0097     263     402 ..     347     485 ..     338     493 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.0062
      DUF853   8 eaeqelalalklanrhGliaGatGtGktvtLqvlaeslseaGvpvfladvkGdLsgiaka 67 
                 + e+++ l  k++ rh  i   tG Gk   + ++++++ +   +v++ d   d + +  +
  EPA06162.1 124 SIEAKINLD-KIVARHLGILAMTGMGKSNLVSLITKQIGKLKGTVIIFDYHNDYTTLNIP 182
                 445555544.577899888889*******************************9987654 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 3.8e-06
      DUF853 263 fdeahLLf.ndapkallekveqvvrLirskGvGvyfvtqnPldlPdtvLaqLGnrvqhalraftpkdqkavkaaadtfranpefdveeaiteLgvGeal 360
                  +eah++  +d   +      ++ r  r  G G+  v+q P  +  +vL+qLG+     ++    +dq+ + aa+++       ++   +t+L+vG+a+
  EPA06162.1 347 IEEAHVFIpKDHDTSAKYWAAKIAREGRKFGLGLGIVSQRPRSVDLNVLSQLGSFA--IMKIIQEDDQRQIAAATESTS----RELIAQLTSLNVGDAV 439
                 577776653455555555567788889999***********************853..577888999999988877654....468889********97 PP

      DUF853 361 v....svLdekGaPsiveralvvpPasrlgplseeeraalvqespv 402
                 +    + L    + + v+  ++ + +s +++ +++e+ + ++ ++ 
  EPA06162.1 440 LvgqwTNLPSLVHVEEVKEKIMGADQSAVNAWANAEKMNEIAVEST 485
                 5121122333333344455566677777777777776666655555 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.7e-05     0.068      14      56 ..     135     177 ..     127     260 .. 0.91
   2 ?   -2.5   0.1       0.7   1.8e+03      94     111 ..     350     367 ..     348     372 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.7e-05
  TrwB_AAD_bind  14 etqhilivGttGsGKtqalekllrairargdraivlDltGafv 56 
                     ++h+ i+  tG+GK++ ++ + ++i + + ++i++D + +++
     EPA06162.1 135 VARHLGILAMTGMGKSNLVSLITKQIGKLKGTVIIFDYHNDYT 177
                    579**********************************998887 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.7
  TrwB_AAD_bind  94 AaalipedggssdpfWae 111
                    A+ +ip+d+  s ++Wa 
     EPA06162.1 350 AHVFIPKDHDTSAKYWAA 367
                    889*************85 PP

>> HAS-barrel  HAS barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.1e-05       0.1      22      72 ..       8      53 ..       2      75 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.1e-05
  HAS-barrel 22 dvkvGeyVeielpdgeivlGmvtdirrgnselsndlalvlsleeleeangd 72
                +++vGey++i+ + ++++lG+v+  +      s ++a+v++++e+ e+ ++
  EPA06162.1  8 PLSVGEYIKIDSD-EGEILGLVEKSSV----SSAAFADVKNFDEASESTEI 53
                689********99.********97665....56888888888887776655 PP

>> DUF4709  Domain of unknown function (DUF4709)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.1   4.3e-05      0.11      42      99 ..     203     259 ..     196     267 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.3e-05
     DUF4709  42 evkslkrdfeflkqllqakyeeklkeealelytrlndklkeleklykekvevvRksfk 99 
                 ev ++++ +++++++l++ + +++k e+ e++++l+++++ + +   +k++ +R s+ 
  EPA06162.1 203 EVLEIRDGANVQQRVLRMAFTKQVK-ESKEFWKKLETEVEFIVNSEDKKIKEIRTSAY 259
                 56678899999************98.589*************************9975 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00013      0.33      29      99 ..     141     209 ..     132     368 .. 0.72
   2 ?   -1.5   0.0       1.1   2.9e+03      93     107 ..     361     388 ..     311     437 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00013
      AAA_16  29 lsGesGvGKsslvrellralekdggif.lrgkcdql.esaipysalaqalareellrqlldeaesaeleawre 99 
                 +  + G+GKs lv  + +++ k +g + +     ++ + +ip+   ++++++ ++   lld+++ +e+ + r+
  EPA06162.1 141 ILAMTGMGKSNLVSLITKQIGKLKGTViIFDYHNDYtTLNIPR---INVIDA-KINPRLLDADQLSEVLEIRD 209
                 66789*****************987775666666664555665...666655.77777777766666555555 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.1
      AAA_16  93 eleawrekleeala.............a 107
                 ++ +w++k+ ++ +              
  EPA06162.1 361 SAKYWAAKIAREGRkfglglgivsqrpR 388
                 4555555555544444444444433330 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.6     7e-05      0.18      13      80 ..     138     227 ..     126     313 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7e-05
                 EEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH......................H CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......................x RF
    ABC_tran  13 kvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren......................e 80 
                  ++i+  +G GKS L++l++++  + +G++ + + + ++++l++ r ++   + +p+l +  ++ e                       +
  EPA06162.1 138 HLGILAMTGMGKSNLVSLITKQIGKLKGTVIIFDYHNDYTTLNIPRINVIDAKINPRLLDADQLSEVleirdganvqqrvlrmaftkqvK 227
                 6789999***********************666555555445544444444444444433333333333333344444444444443330 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (496 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1022  (0.0570026); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.68u 0.32s 00:00:01.00 Elapsed: 00:00:00.50
# Mc/sec: 3010.91
//
Query:       EPA06163.1  [L=384]
Description: Ser/Thr phosphatase family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.6e-09   36.7   0.2      7e-09   36.1   0.2    1.3  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    8.4e-08   32.9   3.8    1.5e-07   32.1   3.8    1.4  1  Metallophos    Calcineurin-like phosphoesterase
  ------ inclusion threshold ------
      0.011   15.9   0.0      0.024   14.9   0.0    1.5  1  CENP-C_C       Mif2/CENP-C like
      0.072   13.0   0.1       0.25   11.3   0.1    1.9  1  RST            RCD1-SRO-TAF4 (RST) plant domain
       0.19   11.9   3.1         18    5.5   1.3    3.5  3  DUF211         Uncharacterized ArCR, COG1888


Domain annotation for each model (and alignments):
>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.2   1.9e-12     7e-09       1     149 [.       1     212 [.       1     232 [. 0.76

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 1.9e-12
  Metallophos_2   1 MklaiiSDlH.............snldaleavlealkevgvdaiihaGDl.eeeep......evleellela....pvlaVrGNnD.......... 62 
                    M + +iSD+H             + ++  ++++++  +  vd +i+aGD+    +p      ++ ++l++l+    +   + G +D          
     EPA06163.1   1 MLFSHISDTHlglvqygseereqDVYHVFNQAIDISIKDHVDFVIFAGDIfHVPNPngtaivQMANALKRLKnnniDSFFILGEHDisriratpip 96 
                    999**************999998777777777888777779********987777755555523333333336669999**************999 PP

  Metallophos_2  63 .......................eev.veedvlreaaelgtdlp..eeaelelagekvlliHgdplgvkdalaellkeaeegsd.vvvcGHtHvpe 131
                                            ++ +++ +  e  ++++++   +e   +  g k+l++H+   + ++   el ++   +++ ++++GH H + 
     EPA06163.1  97 yvyhnlefsryigqgnpinhkgvLIAgFDKIRKTEIPQFEDKFRtiDEIASKHTGHKILVLHQGVTEFNKFAGELQSTDLPKNFtYYAMGHLHDHD 192
                    999999999999999888876552225566666666666666642244444459999******9768888888888886666669**********9 PP

  Metallophos_2 132 vekeggv..lvvnPGsvgep 149
                    +++   +   v +PGs++  
     EPA06163.1 193 IKQFSHLngPVAYPGSIELT 212
                    999874444999****9976 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   3.8   4.2e-11   1.5e-07       5     202 ..       5     189 ..       1     191 [. 0.59

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 4.2e-11
                  EEESBTB........TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHH....TSEEEEEC-TTS......CHHHHHHHH CS
  Metallophos   5 vigDlHl........algggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvky....pipvylllGNHe......gfeeellnk 84 
                  +i+D+Hl        +++   ++ +++++d  +++  +d+v++aGD+++  +++   + ++a  +k+    +i  +++lG H+      +        
   EPA06163.1   5 HISDTHLglvqygseEREQDVYHVFNQAIDISIKD-HVDFVIFAGDIFHVPNPNGTAIVQMANALKRlknnNIDSFFILGEHDisriraT-------- 93 
                  9**********666666666666666666555666.**********77775333334444333333335337777********2222110........ PP

                  HHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESECEEE.THHHHHHHHHHHSCHHHHCC..HHHHHHHHHHTTCSEEEEEESSESSCSSSCSC CS
  Metallophos  85 ygylgifsepwrsdaevfnnlplaslgsgslkvlllhGgspel.lvsldklgslnleleapepg..dewlkdlekrekadwvivlgHsplyrgsgylf 179
                         + p+      + nl  + ++++     + h g     +  +dk+++ + ++ ++  +  de      + +++  +i++ H +++    +  
   EPA06163.1  94 -------PIPYV-----YHNLEFSRYIGQ--GNPINHKG---VlIAGFDKIRKTEIPQFEDKFRtiDE-----IASKHTGHKILVLHQGVT-EFNKFA 168
                  .......22222.....244444444444..34444444...22222366666666666555434433.....444588889999999999.666666 PP

                  CHHHHHHHHHHTTESEEEEESSS CS
  Metallophos 180 gdealedllkkygvdlvisGHtH 202
                  g+ +  d    ++  ++ +GH H
   EPA06163.1 169 GELQSTD--LPKNFTYYAMGHLH 189
                  6666664..46667788999988 PP

>> CENP-C_C  Mif2/CENP-C like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   6.6e-06     0.024      33      74 ..      22      64 ..      16      72 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 6.6e-06
                EEEEEEEEESEEEEEETT.EEEEEETT-EEEE-TT-EEEEEE- CS
    CENP-C_C 33 atlvFyViqGrvevtvsk.tsfvigkgsvFqvPagneysieNk 74
                ++ v++V++ ++ +++++   fvi  g++F vP  n ++i   
  EPA06163.1 22 EQDVYHVFNQAIDISIKDhVDFVIFAGDIFHVPNPNGTAIVQM 64
                56699***********97369***************9998655 PP

>> RST  RCD1-SRO-TAF4 (RST) plant domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1     7e-05      0.25       9      41 ..     348     380 ..     340     382 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7e-05
         RST   9 FpmLlaalskklpkskmdllqkhYedlkkkkIs 41 
                 ++ Ll+ ls+   k+ ++++ +++e++kk+k++
  EPA06163.1 348 IKELLPLLSSAQLKEATQIIVENFEKFKKEKVN 380
                 678****************************86 PP

>> DUF211  Uncharacterized ArCR, COG1888
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.14     5e+02       7      29 ..      51      73 ..      49      87 .. 0.85
   2 ?    2.4   0.2      0.05   1.8e+02      54      76 ..     249     271 ..     208     275 .. 0.61
   3 ?    5.5   1.3    0.0051        18      47      67 ..     276     296 ..     258     299 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.14
                EEEEEESSS-HHHHHHHHHTSTT CS
      DUF211  7 LDvlkphepsivelakklaeleg 29
                + v  p+++ iv++a++l++l++
  EPA06163.1 51 FHVPNPNGTAIVQMANALKRLKN 73
                668899************99875 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.05
                 SSE-HHHHHHHHHCTT-EEEEEE CS
      DUF211  54 enidyeeieeaieelggvihSiD 76 
                  + +y+e++++++e+++ i Si 
  EPA06163.1 249 FKTNYDELTKTVDEISSKIGSIE 271
                 357999*********99999996 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.0051
                 EEEEEEESSE-HHHHHHHHHC CS
      DUF211  47 lkitieGenidyeeieeaiee 67 
                 ++i i+Ge+i+ ++i+ +i  
  EPA06163.1 276 VEIKIQGEDIETDQIQAQISR 296
                 799*************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       788  (0.0439511); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.63u 0.35s 00:00:00.98 Elapsed: 00:00:00.55
# Mc/sec: 2117.59
//
Query:       EPA06164.1  [L=570]
Description: hypothetical protein BG20_I0825 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.093   13.1   0.0       0.98    9.8   0.0    2.4  2  AAA_16    AAA ATPase domain


Domain annotation for each model (and alignments):
>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   5.5e-05      0.98      21      52 ..      27      58 ..      24     113 .. 0.82
   2 ?    0.0   0.0     0.054   9.7e+02      80     139 ..     202     257 ..     166     259 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 5.5e-05
      AAA_16 21 sgrpelvllsGesGvGKsslvrellralekdg 52
                +++p+++l+ G++G GK   v++ +++l k+g
  EPA06164.1 27 TNEPQVILFQGMRGAGKGVAVDKTAEELYKEG 58
                67899***********************9994 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.054
      AAA_16  80 ellrqlldeaesaeleawrekleealaavpelagaeasrllellkrllallsrderplvl 139
                 +ll q + + + +++++ ++   ++++  p+  +  ++ +  +++++++++++ ++ +v+
  EPA06164.1 202 QLLVQQKLK-KPKQFAPIPKIVVKTIT--PPTNATRKEVFQKQFTEIVVQARE-QKRIVV 257
                 333333333.33355555555555544..55555555999999*****99999.664655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (570 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1104  (0.0615762); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.46
# Mc/sec: 3728.24
//
Query:       EPA06165.1  [L=78]
Description: hypothetical protein BG20_I0830 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       768  (0.0428356); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 501.71
//
Query:       EPA06166.1  [L=227]
Description: hypothetical protein BG20_I0829 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1600.22
//
Query:       EPA06167.1  [L=436]
Description: DNA (cytosine-5-)-methyltransferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-45  154.5   0.0    6.1e-45  153.7   0.0    1.4  1  N6_N4_Mtase      DNA methylase
    1.3e-07   31.6   0.2      0.012   15.3   0.3    2.9  2  UPF0020          Putative RNA methylase family UPF0020
    7.8e-07   29.0   0.0    2.3e-05   24.2   0.0    2.6  3  Methyltransf_31  Methyltransferase domain
    1.3e-05   25.8   0.0      0.051   14.2   0.0    3.2  3  Methyltransf_11  Methyltransferase domain
    4.7e-05   24.0   0.0    0.00055   20.6   0.0    2.4  2  Methyltransf_25  Methyltransferase domain
  ------ inclusion threshold ------
      0.058   13.0   0.0        1.3    8.5   0.0    2.3  2  Methyltransf_15  RNA cap guanine-N2 methyltransferase
       0.11   12.3   0.0       0.26   11.1   0.0    1.6  1  Methyltransf_23  Methyltransferase domain
       0.13   13.0   0.0          5    7.9   0.0    2.9  3  Methyltransf_12  Methyltransferase domain


Domain annotation for each model (and alignments):
>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.7   0.0   2.7e-48   6.1e-45       1     231 []      27     272 ..      27     272 .. 0.90

  Alignments for each domain:
  == domain 1  score: 153.7 bits;  conditional E-value: 2.7e-48
                  EEEEEE--SSSSSCS................GCCGCCHHHHHHHHHHHHHHHHHHHEEEEEEEEEEE-CCCHHT...........HHHHHHHHHTT-E CS
  N6_N4_Mtase   1 vdlivtdpPYntgkdy...........endeqyeeedsyeeyleflekvlkevrrvLkddgsifiniddseikk...........elkaladeifggf 76 
                  v+l vt+pPY++  +y            +++  +   + ++yl+ ++++++ev++v +++g+ +i i d+  +            +l+ l de+ g +
   EPA06167.1  27 VALTVTSPPYGNAINYsqhvknlksgkGKEFRGNVGGTLDDYLNEMQEIFSEVKKVTMPGGFCCIVIADELSEGtlvplpsllvsKLVDLKDEDEG-W 123
                  6899*************99999999876666666777899*******************************999**********************.* PP

                  EEEEEEEEEES..............SSTTTSTCCS-B--EEEEEEEESSTT-..---GGGSSBSS-HHHHHHHHHHCHHHCC-B--BSEEE-SCCCTT CS
  N6_N4_Mtase  77 fllnvivwkkp..............nsmpesnkdrltsthEyilvfsknkkyllkfnldaikvpyeekdklekrgaytskkkgkkiediWdlseiqsn 160
                   l+++i+w+k                ++p + ++r++ +hEyi+v++k+kk  + +++++ kvp ++  k++                +Wd++ +++n
   EPA06167.1 124 HLRDMIIWNKVtagrsgagnrfgqfVKIPVPTRYRANIMHEYIIVLQKGKKARFLLKETEPKVPLNRAMKRQVA------------LSVWDITPVPPN 209
                  ***********99999999999884488888899******************6666666666666666655555............59**77777766 PP

                  STTS-CHH----SS---HHHHHHHHHHHS-TT-EEEETT-TTTHHHHHHHHTT-EEEEEESSHHHHHHHHH CS
  N6_N4_Mtase 161 ekkskgdtkkkHpaqkPvallerlIklstkkgdivlDpFaGSGtTavaakelgrkfiGieieeeyvelaek 231
                  + k        Hpa++P++++ rlI+++tk+gd+vlDp +GSG T+++a++l+rk+iG++i +eyv la+k
   EPA06167.1 210 AVK--------HPAVFPEQIPWRLIQMYTKPGDVVLDPMCGSGQTVKVANSLKRKYIGVDIRKEYVSLAKK 272
                  666........********************************************************9986 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   3.3e-05     0.075     108     154 ..      11      59 ..       4      94 .. 0.83
   2 !   15.3   0.3   5.4e-06     0.012      26      72 ..     230     277 ..     211     288 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.3e-05
                 EE--GGG--..STTS---EEEE----------HHHHHHHHHHHHHHHHH CS
     UPF0020 108 sqadaakLr..lkegevdvivtnpPYGerlgskkalekLYseflrelkr 154
                 ++ad + L    k ++v + vt pPYG++++  + +++L s  ++e+  
  EPA06167.1  11 VCADSKTLSklIKLNSVALTVTSPPYGNAINYSQHVKNLKSGKGKEFRG 59 
                 4555555555424459***********************9988888765 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 5.4e-06
                 --TTS-EEETT-TTS.HHHHHHHHHHTT--TTTT----SS.HHHHHHHH CS
     UPF0020  26 wkpgepllDPmCGsG.tilIEaallganiapgllrefvle.lkaeaeee 72 
                  kpg++ lDPmCGsG t+ +   l  ++i    +r++ +  +k++a+e+
  EPA06167.1 230 TKPGDVVLDPMCGSGqTVKVANSLKRKYIG-VDIRKEYVSlAKKRAKEK 277
                 589************555554444444444.444444444356666655 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.076   1.7e+02      84     113 ..      65      95 ..       9     133 .. 0.86
   2 !   24.2   0.0     1e-08   2.3e-05       4      51 ..     233     277 ..     230     283 .. 0.89
   3 ?   -3.1   0.0       2.6   5.9e+03      73      97 ..     381     406 ..     371     425 .. 0.59

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.076
  Methyltransf_31  84 l.naladpdkileeiervlkpggilliedpr 113
                      l ++l+++++i+ e+++v  pgg ++i  ++
       EPA06167.1  65 LdDYLNEMQEIFSEVKKVTMPGGFCCIVIAD 95 
                      55778999***************99987666 PP

  == domain 2  score: 24.2 bits;  conditional E-value: 1e-08
  Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqkl 51 
                      g +vlD+ CG+G+ +++++++   k +++G+Di +e ++lA+++a+++
       EPA06167.1 233 GDVVLDPMCGSGQTVKVANSL---KRKYIGVDIRKEYVSLAKKRAKEK 277
                      678****************76...568*****************9976 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 2.6
  Methyltransf_31  73 ekfDlilsnevl.naladpdkileei 97 
                      ++fDl+  +++l + ++d +  l ++
       EPA06167.1 381 DTFDLLDVKSILpDGIPDDPYSLVSL 406
                      67777766666665555544444433 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.0    0.0044       9.8      73      96 .]      68      91 ..      63      91 .. 0.90
   2 !   14.2   0.0   2.3e-05     0.051       1      42 [.     237     278 ..     237     305 .. 0.87
   3 ?    0.4   0.0      0.48   1.1e+03      23      87 ..     352     426 ..     331     429 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0044
                     C-CCHHHHHHHHHHHEEEEEEEEE CS
  Methyltransf_11 73 hvedpekalkeiaRvLkpgGllvi 96
                     ++++++++++e+++v  pgG+++i
       EPA06167.1 68 YLNEMQEIFSEVKKVTMPGGFCCI 91
                     57999****************986 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 2.3e-05
                      EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT CS
  Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeg 42 
                      Ld  cG+G+ ++   +  ++++gvD+ ke + lak++a+e+ 
       EPA06167.1 237 LDPMCGSGQTVKVANSLKRKYIGVDIRKEYVSLAKKRAKEKM 278
                      6788**********9999*******************99875 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.48
                      EEES-HHHHHHHHHHCCHHT-.......EEEETTEECCCT.S..S-TT-EEEEEEES-CCC-CCHHHHHHHHHHH CS
  Methyltransf_11  23 gvDlskemlklakekaseegl.......kvefvvadaekl.p..fednsfDlvvssevlhhvedpekalkeiaRv 87 
                      g    ++m+kl + k+  ++l         +f   d++++ p  ++d+ + lv +  vl++ +++++  + + +v
       EPA06167.1 352 GASQEPYMMKLGNPKKASSPLkkilsklPDTFDLLDVKSIlPdgIPDDPYSLVSLVDVLEYEKNVKRKTRSLTKV 426
                      555555666555555555554555555544566677777446668999999999999999999888877777666 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.57   1.3e+03      81      97 .]      71      87 ..      63      87 .. 0.88
   2 !   20.6   0.0   2.5e-07   0.00055       1      46 [.     236     279 ..     236     296 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.57
                     HHHHHHHHHHHHEEEEE CS
  Methyltransf_25 81 dlekalkeiarvLkpgG 97
                     +++++++e+++v+ pgG
       EPA06167.1 71 EMQEIFSEVKKVTMPGG 87
                     6789************9 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 2.5e-07
                      EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT CS
  Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl 46 
                      vLd  cG+G++++ +a+ l k k++gvDi +e++  a++ra+e+ +
       EPA06167.1 236 VLDPMCGSGQTVK-VANSL-KRKYIGVDIRKEYVSLAKKRAKEKMM 279
                      89*******8765.55565.5********************98755 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.062   1.4e+02      53      87 ..      10      43 ..       6      58 .. 0.79
   2 ?    8.5   0.0   0.00059       1.3       3      43 ..     235     275 ..     233     308 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.062
  Methyltransf_15 53 lvlgdvfellaklklekikvdlvflSpPwGG.psYk 87
                     +v++d ++l + +kl+++   l ++SpP G  ++Y+
       EPA06167.1 10 VVCADSKTLSKLIKLNSV--ALTVTSPPYGNaINYS 43
                     688899999999999999..999*******624554 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00059
  Methyltransf_15   3 vilDlfsGaGGnviqfalv.fekviaieinleklacaqhNae 43 
                      v+lD+++G+ G++++ a++  +k i+++i +e + +a++ a+
       EPA06167.1 235 VVLDPMCGS-GQTVKVANSlKRKYIGVDIRKEYVSLAKKRAK 275
                      79******8.599999999445689*********99999886 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00012      0.26      20      88 ..     230     349 ..     214     425 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00012
  Methyltransf_23  20 lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae...................................................k 62 
                       ++g  vLd  cG+G + +v+     +++gvD++ e v++a+                                                   k
       EPA06167.1 230 TKPGDVVLDPMCGSGQTVKVANSLKRKYIGVDIRKEYVSLAKkrakekmmlsnfmiplyfpvkwvdgvqsgkksdahidvedhipkgfkiifqK 323
                      578889*************9977778**************999999999999999999999999999998887777777777777777666663 PP

  Methyltransf_23  63 akkaqkdqfdeqeaaepqgkfdlIvl 88 
                       +k     +d   + +++++ d+I++
       EPA06167.1 324 LSKDSENGTDTTHIYYKNKSGDYICC 349
                      33333333333334444443333333 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.52   1.2e+03      78      98 ..      68      88 ..      63      89 .. 0.91
   2 ?    7.9   0.0    0.0022         5       5      42 ..     241     276 ..     237     284 .. 0.88
   3 ?   -0.3   0.0      0.82   1.8e+03      64      92 ..     395     426 ..     367     429 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.52
  Methyltransf_12 78 hlkdirevldnirklLkpgGr 98
                     +l++++e++++++k+  pgG 
       EPA06167.1 68 YLNEMQEIFSEVKKVTMPGGF 88
                     7899****************7 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0022
  Methyltransf_12   5 cGtGsllralleklpdieytgvDispsaiedakeklak 42 
                      cG+G+++++        +y+gvDi ++ +  ak++ ++
       EPA06167.1 241 CGSGQTVKVANSL--KRKYIGVDIRKEYVSLAKKRAKE 276
                      **********999..**************888888776 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.82
  Methyltransf_12  64 g...ssfDlvvasnvlhhlkdirevldnirkl 92 
                      g   + + lv + +vl++ k++++  +++ k+
       EPA06167.1 395 GipdDPYSLVSLVDVLEYEKNVKRKTRSLTKV 426
                      135579999********998877766666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2743.21
//
Query:       EPA06168.1  [L=207]
Description: DNA-3-methyladenine glycosylase I [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-73  245.9   0.5    2.8e-73  245.4   0.5    1.1  1  Adenine_glyco  Methyladenine glycosylase


Domain annotation for each model (and alignments):
>> Adenine_glyco  Methyladenine glycosylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  245.4   0.5   1.6e-77   2.8e-73       6     177 .]      30     201 ..      26     201 .. 0.98

  Alignments for each domain:
  == domain 1  score: 245.4 bits;  conditional E-value: 1.6e-77
  Adenine_glyco   6 plyvaYhDeeWGvpvtddkklFelLvLegfqaglswetilkkreafreafdgFdlekvakydeekveelladegiirnrlKieavisnAravlalq 101
                     + ++YhD+eWGvp + d+klFe+L+L+g+qaglsw+tilk+r+a+r++fd+F++ek++ y++++++++l+d+gi+rnr+K+e+ ++nAr++l+++
     EPA06168.1  30 GIHQKYHDREWGVPLHRDRKLFEFLLLDGAQAGLSWITILKRRSAYRKVFDNFNPEKISMYKKRDINSILKDDGIVRNRKKVESFVNNARRFLEVK 125
                    56789******************************************************************************************* PP

  Adenine_glyco 102 eefgsfseylwsfvdgkpiveelksaeevpattelsealskdLkkrGfkfvGptivysflqavGlvndhleeCfrk 177
                    +ef++f+ey+w+fvd k+ v+++k+ +e+p  +++s+ +sk+L  rGf+fvGpti+y+f+q+vG+vndh+++Cfr+
     EPA06168.1 126 DEFKTFDEYIWQFVDYKTKVNKFKTWSEIPPASSESKMMSKNLMSRGFTFVGPTICYAFMQSVGMVNDHTVNCFRH 201
                    *************************************************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       859  (0.0479112); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 1175.73
//
Query:       EPA06169.1  [L=92]
Description: hypothetical protein BG20_I0834 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.4e-06   25.4   0.0    2.2e-05   24.1   0.0    1.7  1  DUF5615   Domain of unknown function (DUF5615)
    0.00051   20.2   0.0    0.00068   19.8   0.0    1.2  1  PIN_10    PIN like domain
     0.0062   16.6   0.0     0.0069   16.5   0.0    1.1  1  Mut7-C    Mut7-C RNAse domain


Domain annotation for each model (and alignments):
>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   3.7e-09   2.2e-05       3      55 ..       6      59 ..       4      64 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 3.7e-09
     DUF5615  3 lllDenlsprlvellreaghdvlhvrelg..legasDeeileyAkeedriivTkD 55
                +l+Den+   l ++l   +++   + + +  ++g +D+e+ ++A++++++++T+D
  EPA06169.1  6 FLIDENIL-GLDRFLDGYEIKYRKIGDPDcpKRGSKDPEVAKFAQKNKLVVLTND 59
                78888875.5666666666666666555532778********************9 PP

>> PIN_10  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   1.1e-07   0.00068       2      65 ..       5      65 ..       4      68 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.1e-07
      PIN_10  2 kfflDenlppalakaLrelleeeghevvhlrdkf..aagtkDeeWiaalaeggwvvltkDrrirkr 65
                +f++Den+   l + L+     ++++++ + d     +g+kD e  + +++++ vvlt+D++++k+
  EPA06169.1  5 EFLIDENILG-LDRFLD----GYEIKYRKIGDPDcpKRGSKDPEVAKFAQKNKLVVLTNDDKLTKQ 65
                69********.999999....999******999999*************************99885 PP

>> Mut7-C  Mut7-C RNAse domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.2e-06    0.0069       3      75 ..       6      87 ..       4      91 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.2e-06
      Mut7-C  3 fllDamlgklakyLRllGydalyasdv.........edeellalaakekrillTrdreLlkraklkkg..vlltsrdveeqlre 75
                fl+D ++  l ++L   Gy+ +y++           +d e+++ a+k+k ++lT d +L k+ +l +   ++++ rd++++++e
  EPA06169.1  6 FLIDENILGLDRFL--DGYEIKYRKIGdpdcpkrgsKDPEVAKFAQKNKLVVLTNDDKLTKQCDLLDVeyLFMDLRDFAKKVNE 87
                66666666666665..467766655224566666679*************************9987666566677888777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.31s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 605.85
//
Query:       EPA06170.1  [L=521]
Description: hypothetical protein BG20_I0835, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-07   30.6   0.1    1.3e-06   28.3   0.0    2.2  2  Phage_integrase  Phage integrase family
     0.0016   18.9   2.5       0.14   12.6   1.5    3.6  2  Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
  ------ inclusion threshold ------
        1.2    9.5   6.1        1.1    9.6   1.4    2.8  2  Tup_N            Tup N-terminal


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.64   3.8e+03      68     109 ..     216     253 ..     197     255 .. 0.70
   2 !   28.3   0.0   2.3e-10   1.3e-06      57     158 ..     328     443 ..     314     450 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.64
                      EEEECTHHHHHHHHHHHHHHCHCCTTTSBSSBETTSSB--HH CS
  Phage_integrase  68 ravplseealellkellskaleeaeksellfaskrgkplsrq 109
                      ra ++++e + ++k + +k+   +++ ++ f sk ++++++q
       EPA06170.1 216 RASTVTSEQC-AIKAYFEKN---DSPINFRFDSKSTHKVTDQ 253
                      4444444433.466666666...8888999999999888887 PP

  == domain 2  score: 28.3 bits;  conditional E-value: 2.3e-10
                      EEEEECSSSSEEEEECTHHHHHHHHHHHHHH...CHCCTTTSBSSBETTSSB--HHHHHHHHHHHHHHCT-S...........SC--TTHHHHH CS
  Phage_integrase  57 vheregKgskeravplseealellkellska...leeaeksellfaskrgkplsrqtvrkafkraveeagie...........kpltpHtlRhs 136
                      +  +++K++ ++   l + a+ ++++ l+ +     + ++ e lf++ +g+p+s q +r++f+r+++ agi+           ++  +H+lR  
       EPA06170.1 328 IRLTRIKTGFSHLGFLDRDAVTAIQNHLDIRinkTGKLQEGEPLFVNPKGEPVSIQGMRRTFQRMAKTAGIQrklqsyslrekYEKDSHELRDL 421
                      444899*************************87666678889***************************************999999******* PP

                      HHHHHHHHCTSHHHHHHHHT-S CS
  Phage_integrase 137 fataLleagvdlrvvqkllGHs 158
                      + + L+ +g  ++v  +  GH+
       EPA06170.1 422 LKSILIDSGCRIDVADHCIGHR 443
                      *********************7 PP

>> Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   1.5   2.4e-05      0.14      17      42 ..     136     161 ..     114     236 .. 0.83
   2 ?   -1.2   0.0      0.48   2.9e+03      35      63 ..     441     469 ..     412     480 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.4e-05
  Phage_int_SAM_4  17 rTiksYlsaikrflrflkkkapeelt 42 
                      +T+k+Y++a+ rf ++l++k++e ++
       EPA06170.1 136 STQKNYTYALWRFSNWLQGKEFEYSQ 161
                      8*******************776444 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.48
  Phage_int_SAM_4  35 kkapeeltkedieaYlnyLanerklsast 63 
                      + +p+++ ++++e++ +  ++e k + s 
       EPA06170.1 441 GHRPKDSYEKQVELFPENIREEFKKASSK 469
                      46899999999999998888666633333 PP

>> Tup_N  Tup N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.2     0.083   4.9e+02      56      74 ..     405     423 ..     385     425 .. 0.85
   2 ?    9.6   1.4   0.00019       1.1       7      53 ..     457     505 ..     450     510 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.083
       Tup_N  56 rkikqqYEeeiarLkaeLe 74 
                  +++++YE++  +L+  L+
  EPA06170.1 405 YSLREKYEKDSHELRDLLK 423
                 56899*******9998876 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00019
       Tup_N   7 davkqEfdalsqeasslkaqkdeyelkiqsqi..qElqqirqtlyeLee 53 
                 + +++Ef+++s++++++ +  +++ ++ + q+  +E+ ++r++++ L +
  EPA06170.1 457 ENIREEFKKASSKINVFSNISNNMKKSANVQVlqNEVMSLREEVKRLIQ 505
                 79**********************9996666544999999999988866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (521 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1288  (0.0718389); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.46
# Mc/sec: 3422.20
//
Query:       EPA06171.1  [L=82]
Description: hypothetical protein BG20_I0810 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      616  (0.0343577); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 489.45
//
Query:       EPA06172.1  [L=132]
Description: hypothetical protein BG20_I0814 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-08   35.1   0.2    1.5e-08   34.8   0.2    1.1  1  EVE              EVE domain
  ------ inclusion threshold ------
       0.09   12.9   0.0       0.18   11.9   0.0    1.5  1  Peptidase_S78_2  Putative phage serine protease XkdF


Domain annotation for each model (and alignments):
>> EVE  EVE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.2   1.6e-12   1.5e-08       1     143 [.       5     128 ..       5     130 .. 0.81

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 1.6e-12
                 -EEEEEEBHHTSHHHHH..CHHHCEEE-EE-GHHHHHHHCC--TT-EEEEEETSSSS-EEEEEEEEECEEEE-GGGG-TTSTT--TTTBTTS-.-EEEE CS
         EVE   1 ayWllksepdefsiddl..krkkeegWdgvrnyqarnllramkkGDlvlfYhsgeklqaivgiaeVvseaypdetqfdpkskyydpkskkekp.wlrvd 96 
                 ++W+++ +      dd   +r k++ W   + y++  + +++++GD+v+fY+ ge+++   g ae +s ++ +e  +d + +       ++   w   +
  EPA06172.1   5 NFWIFVIKNT----DDElnRRIKKKEW---PVYSYTVNRKKIQPGDKVIFYKAGEGNKVCLGTAETASAIKGEEGGIDYTVEL------GNVSiW--KK 88 
                 6899998888....444489999****...45778999999*******************************99999655222......223335..44 PP

                 EEEEEEEEEEEEHHHHTTHGTCTTSHHHHCCT-SEEEE-HHHHHHHH CS
         EVE  97 vkpvkklkrplslkelkaepelegmkllrkgrlsvrpvteedwelil 143
                   ++k+l  +l++  +k++   +g+++    + +v+ ++e+d+ +i 
  EPA06172.1  89 SVMIKPLISKLEFIGNKEQ---WGLSM----QGGVIHISEKDYGTIY 128
                 4566788999999999993...99999....99*********99986 PP

>> Peptidase_S78_2  Putative phage serine protease XkdF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0     2e-05      0.18      87     117 ..       7      37 ..       2      40 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2e-05
  Peptidase_S78_2  87 WvvlvkvaddevwekikkgeitgySiagtak 117
                      W+ ++k +dde+  +ikk e + yS + + k
       EPA06172.1   7 WIFVIKNTDDELNRRIKKKEWPVYSYTVNRK 37 
                      *************************876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 964.45
//
Query:       EPA06173.1  [L=49]
Description: transcriptional regulator, AbrB family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-06   28.5   0.1    1.7e-06   28.3   0.1    1.0  1  PrlF_antitoxin  prlF antitoxin for toxin YhaV_toxin
    2.6e-06   27.2   0.1    2.7e-06   27.2   0.1    1.1  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
    0.00072   19.4   0.1    0.00078   19.3   0.1    1.1  1  Thump_like      THUMP domain-like
  ------ inclusion threshold ------
      0.058   13.2   0.1      0.089   12.6   0.1    1.4  1  eIF-1a          Translation initiation factor 1A / IF-1
      0.063   13.2   0.2       0.14   12.1   0.1    1.7  2  RHH_5           CopG-like RHH_1 or ribbon-helix-helix domain,
       0.16   11.9   0.1        4.5    7.3   0.0    2.1  2  PD40            WD40-like Beta Propeller Repeat


Domain annotation for each model (and alignments):
>> PrlF_antitoxin  prlF antitoxin for toxin YhaV_toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.1   5.8e-10   1.7e-06       2      42 ..       8      46 ..       7      48 .. 0.87

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 5.8e-10
  PrlF_antitoxin  2 stltergqttiPasvRkaLklkkgrdkiaytilddgkvvis 42
                    s++t r+q t+P+ vRk +k+k   d +++ ++d+++++is
      EPA06173.1  8 SKVTVRFQVTVPEEVRKKMKVKD-GDTLVF-VEDGKRIYIS 46
                    89********************8.678887.6788888886 PP

>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.1   9.1e-10   2.7e-06       6      38 ..      13      45 ..       8      48 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 9.1e-10
                    EEEEEE-CCCHHHCCEECTCEEEEEECTTCCCC CS
  MazE_antitoxin  6 sgavriPkevrfelgireGdevelevdgdkiil 38
                      +v+ P evr+++ ++ Gd++++++dg +i +
      EPA06173.1 13 RFQVTVPEEVRKKMKVKDGDTLVFVEDGKRIYI 45
                    689*********************999987765 PP

>> Thump_like  THUMP domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   2.6e-07   0.00078      27      73 ..       6      44 ..       2      48 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 2.6e-07
  Thump_like 27 gkanikkRgfpldpeeLrkklklkdggraatLvlTrvgegkagkava 73
                g+  +++R     pee+rkk k kdg+   tLv+  +  g   k++ 
  EPA06173.1  6 GSSKVTVRFQVTVPEEVRKKMKVKDGD---TLVFVED--G---KRIY 44
                5667777777778***********999...9***999..3...3355 PP

>> eIF-1a  Translation initiation factor 1A / IF-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1     3e-05     0.089      13      47 ..       7      34 ..       2      41 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3e-05
                TTEEEEEE.SSSSBEEEEE-HHHHCT----TT-EE CS
      eIF-1a 13 nnlfrVelpdngkevlaeipgkfRnkiwikrGdyV 47
                +++++V++        +++p   R+k+++k Gd  
  EPA06173.1  7 SSKVTVRF-------QVTVPEEVRKKMKVKDGDTL 34
                55555554.......59999999**********75 PP

>> RHH_5  CopG-like RHH_1 or ribbon-helix-helix domain, RHH_5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   4.6e-05      0.14       2      17 ..      12      27 ..      11      29 .. 0.87
   2 ?   -1.7   0.0      0.92   2.7e+03       1       7 [.      40      46 ..      40      46 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.6e-05
       RHH_5  2 kRvnvtLPeelleeLe 17
                 R +vt+Pee++++ +
  EPA06173.1 12 VRFQVTVPEEVRKKMK 27
                588*********9987 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.92
       RHH_5  1 SkRvnvt 7 
                +kR++++
  EPA06173.1 40 GKRIYIS 46
                69**996 PP

>> PD40  WD40-like Beta Propeller Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.017        50      18      26 ..      29      37 ..      28      38 .. 0.91
   2 ?    7.3   0.0    0.0015       4.5      17      27 ..      37      47 ..      35      48 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.017
                TTSSEEEEE CS
        PD40 18 PDGkrlaFs 26
                +DG +l+F+
  EPA06173.1 29 KDGDTLVFV 37
                7*******7 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0015
                -TTSSEEEEEE CS
        PD40 17 SPDGkrlaFsS 27
                  DGkr+++s 
  EPA06173.1 37 VEDGKRIYIST 47
                56******985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       793  (0.04423); expected 358.6 (0.02)
Passed bias filter:                      595  (0.0331865); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 336.33
//
Query:       EPA06174.1  [L=454]
Description: hypothetical protein BG20_I0827 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0023   17.4   0.1     0.0055   16.2   0.1    1.6  1  HTH_24    Winged helix-turn-helix DNA-binding
     0.0034   17.3   0.5      0.021   14.7   0.2    2.3  2  MarR      MarR family
     0.0091   15.3   0.0      0.026   13.8   0.0    1.8  1  EAP30     EAP30/Vps36 family
     0.0098   15.8   0.0        0.2   11.6   0.0    2.2  2  MarR_2    MarR family
  ------ inclusion threshold ------
       0.06   13.2   0.0       0.14   12.1   0.0    1.6  1  TrmB      Sugar-specific transcriptional regulator TrmB
      0.085   13.5   0.3       0.22   12.2   0.3    1.7  1  RPA_C     Replication protein A C terminal
       0.15   12.3   0.0       0.46   10.8   0.0    1.8  1  Rio2_N    Rio2, N-terminal


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   2.2e-06    0.0055      14      47 ..     359     392 ..     358     393 .. 0.96

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.2e-06
      HTH_24  14 knprisqreLAerlglSpstvnrrlkrLeeeGlI 47 
                  + +i+++eL + ++lS++ +++ +++L ++G+I
  EPA06174.1 359 NDDGITIKELTKVTHLSQNRTRELINQLLSNGFI 392
                 589*****************************99 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.75   1.9e+03      21      40 ..     302     321 ..     297     325 .. 0.85
   2 !   14.7   0.2   8.2e-06     0.021      16      52 ..     361     397 ..     358     399 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.75
                 HHHHHHHTS-HHHHHHHHHH CS
        MarR  21 seLakklgvskstvtrvldr 40 
                 ++ ++++++  s++t ++ +
  EPA06174.1 302 ADFQEAIQIAGSAITQTINK 321
                 5789999********99987 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 8.2e-06
                 TTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE CS
        MarR  16 gplsvseLakklgvskstvtrvldrLekkGlieRsks 52 
                 ++++++eL k  ++s+  + +++ +L  +G+i+R+k 
  EPA06174.1 361 DGITIKELTKVTHLSQNRTRELINQLLSNGFISREKT 397
                 689*******************************985 PP

>> EAP30  EAP30/Vps36 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0     1e-05     0.026     140     235 ..     247     395 ..     202     396 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1e-05
       EAP30 140 Dllraiekllvlgsglsvlqvggkkvvr.................................................Svptelntdqvevlevakrlvs 189
                 +++r ++k l+l + +  ++v +++ +r                                                                       
  EPA06174.1 247 TIRRDLPKILNLTCVVAFMHVTNRMCIRnkkgeefvvdsfgkteklytytiiaepadfqeaiqiagsaitqtinkinK--------------------- 324
                 566666666666666666666666667667777777777777777776644444444444444444444333333330..................... PP

       EAP30 190 llaekssg...................................ggvtaselaeeeenlgwsvarakeaLeelereGllwvD 235
                        +                                    g+t +el   ++++++s +r++e +++l+++G++ ++
  EPA06174.1 325 -------SsmdiyekfialyrqkmsdnsisvqnttlddsktndDGITIKEL---TKVTHLSQNRTRELINQLLSNGFISRE 395
                 .......12333333333333333333444555555555555688******...778*******************99876 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.11   2.9e+02      25      45 ..     302     322 ..     299     325 .. 0.84
   2 !   11.6   0.0   7.7e-05       0.2      18      55 ..     361     396 ..     357     400 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.11
                 HHHHHHHTSSHHHHHHHHHHH CS
      MarR_2  25 gelarrlglsksavsrilkrL 45 
                 ++  ++ ++  sa+++++++ 
  EPA06174.1 302 ADFQEAIQIAGSAITQTINKI 322
                 56668899**********996 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 7.7e-05
                 TTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
      MarR_2  18 pgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55 
                 +g  +t++el++ ++ls+ ++  +++ L + G++ r++
  EPA06174.1 361 DG--ITIKELTKVTHLSQNRTRELINQLLSNGFISREK 396
                 66..9*****************************9985 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   5.5e-05      0.14      23      66 ..     363     406 ..     359     408 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.5e-05
                 CHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE-- CS
        TrmB  23 atadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravd 66 
                  t++e+ + + +++++  e +++L++ G++ rek + k +++ +
  EPA06174.1 363 ITIKELTKVTHLSQNRTRELINQLLSNGFISREKTKSKEFEYFP 406
                 6899******************************9988887655 PP

>> RPA_C  Replication protein A C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.3   8.6e-05      0.22      45      97 ..     339     392 ..     304     393 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.6e-05
                 .XSXHHHHHHHHHHHH..SXSTTTEEHHHHHHHSTSXHHHHHHHHHHHHHTTSE CS
       RPA_C  45 kgltalaqqvlnlikq.speseeGvhvdeiaqklrlsvndvkqavdeLsneGii 97 
                 + ++++   v n+  + s  +++G+ ++e+ + ++ls n  ++ +++L+++G i
  EPA06174.1 339 QKMSDNSISVQNTTLDdSKTNDDGITIKELTKVTHLSQNRTRELINQLLSNGFI 392
                 457777777777655448899*******************************98 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00018      0.46      22      61 ..     360     399 ..     351     408 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00018
      Rio2_N  22 hevVptelieeisrlkeeevkkrlsrllkaklisrktaky 61 
                  + +  ++++++++l+++ +++ +++ll +++isr+++k 
  EPA06174.1 360 DDGITIKELTKVTHLSQNRTRELINQLLSNGFISREKTKS 399
                 56678899***************************77664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1045  (0.0582855); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 3076.02
//
Query:       EPA06175.1  [L=129]
Description: hypothetical protein BG20_I0821 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 828.67
//
Query:       EPA06176.1  [L=468]
Description: hypothetical protein BG20_I0813 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-07   31.3   0.3    3.2e-07   30.3   0.3    1.6  1  HATPase_c_3   Histidine kinase-, DNA gyrase B-, and HSP90-lik
    0.00016   22.1   0.3    0.00016   22.1   0.3    2.1  3  HATPase_c     Histidine kinase-, DNA gyrase B-, and HSP90-lik
  ------ inclusion threshold ------
      0.071   13.1   0.1       0.41   10.6   0.0    2.3  2  Ribosomal_S8  Ribosomal protein S8
      0.075   12.7   1.8       0.28   10.8   0.6    2.3  2  ThaI          Restriction endonuclease ThaI


Domain annotation for each model (and alignments):
>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.3   7.1e-11   3.2e-07       4     108 ..      30     130 ..      25     152 .. 0.78

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 7.1e-11
  HATPase_c_3   4 ekAlaelvdNsldAdaenvkievnknrgktgeivieDdGkGmseeelknalrlatsskeakrkstslGkkGiGlklAslslgkkltvitkkegesstl 101
                  e +++e + N++d ++ +++i++ k    +g i++  +G  m++++++++  +a+ssk+   k   +G  GiG k  +   g+  +++t + + ++ +
   EPA06176.1  30 EMVVTEAIANAIDVRSSEIDIKLYKTSDGVGVISFHNNGPPMNKQQFDDYHVIARSSKS---KGSGIGFAGIGAKVYMAAWGE-TKITTETTDGTTSF 123
                  889**********************9999******************************...7899*******7776666665.46666555444433 PP

  HATPase_c_3 102 tldvdki 108
                    ++++ 
   EPA06176.1 124 ASEMHVK 130
                  3333332 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.3   3.6e-08   0.00016       9     103 ..      32     121 ..      26     132 .. 0.77
   2 ?   -3.1   0.0       2.5   1.1e+04      36      48 ..     200     212 ..     165     237 .. 0.59
   3 ?   -4.0   1.3         4   1.8e+04      57      77 ..     366     386 ..     337     389 .. 0.58

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 3.6e-08
                 HHHHHHHHHHHHHSTTTEEEEEEEE.EETEEEEEEEESSSSSTTHHHT..GTCSTTCHHCSTCHTSTSSSHHHHHHHHHHHHTT..TEEEEEEETTTEE CS
   HATPase_c   9 iisnlvdNavkfatkageieveika.seddlvisveDnGiGipkedlk..klfekfsqddstkrggggtGlGlsivkklvelmg..GeiwvesepgrGt 102
                 ++ +++ Na++    ++ei++++ + s++  vis  +nG+ ++k++ +  ++ ++ s+       ++g+G+G++   + v  m   Ge ++++e + Gt
  EPA06176.1  32 VVTEAIANAIDV--RSSEIDIKLYKtSDGVGVISFHNNGPPMNKQQFDdyHVIARSSK-------SKGSGIGFAGIGAKVY-MAawGETKITTETTDGT 120
                 899********5..899******97444899*************99995555555454.......7888888888877555.33347888888887888 PP

                 E CS
   HATPase_c 103 t 103
                 t
  EPA06176.1 121 T 121
                 8 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.5
                 TEEEEEEEESSSS CS
   HATPase_c  36 ddlvisveDnGiG 48 
                  + +i+v   G+ 
  EPA06176.1 200 LRMEITVNVKGKQ 212
                 3344444444444 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 4
                 TCS.TTCHHCSTCHTSTSSSHH CS
   HATPase_c  57 lfe.kfsqddstkrggggtGlG 77 
                 +++ k  + ++ + gggg+ lG
  EPA06176.1 366 SGTpKGGT-NEGNAGGGGFSLG 386
                 33333333.4444445555555 PP

>> Ribosomal_S8  Ribosomal protein S8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.81   3.6e+03       8      28 ..      35      55 ..      29      62 .. 0.77
   2 ?   10.6   0.0   9.2e-05      0.41       3      48 ..     268     314 ..     267     335 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.81
                  HHHHHHHHTT-SEEEEE--HH CS
  Ribosomal_S8  8 trirNaekakkeevevpaskl 28
                   +i Na  ++++e++++  k+
    EPA06176.1 35 EAIANAIDVRSSEIDIKLYKT 55
                  479999999999999876665 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 9.2e-05
                   HHHHHHHHHHHHHTT-SEEEE.E--HHHHHHHHHHHHCTSEEEEEEE CS
  Ribosomal_S8   3 iadmltrirNaekakkeevev.pasklkeeilkvLkeeGyikdfeve 48 
                   i+d l+  + + k+++ +v    + ++ ++i ++L+++Gyikd ++ 
    EPA06176.1 268 ISDQLNLNKTNFKQGSGTVVTpVMQEVDRRIFNILEKKGYIKDNKAP 314
                   56666655555566666666636778999*************98874 PP

>> ThaI  Restriction endonuclease ThaI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.14   6.2e+02      55      79 ..      35      59 ..      20      69 .. 0.79
   2 ?   10.8   0.6   6.3e-05      0.28      76     152 ..     234     312 ..     201     323 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.14
                GGEE----TT-SS--EEETTEEEEE CS
        ThaI 55 knvetnipiteaevdvklfgspisi 79
                + + + i +  +e+d+kl+ +   +
  EPA06176.1 35 EAIANAIDVRSSEIDIKLYKTSDGV 59
                4678889999999999999766555 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 6.3e-05
                 EEEEEEEESSS--S-EEE----HHHHHHHHHH----SEEEEEEE-T.TSEEEE.EEE-HHHHHHHHHHH-HHHHEE--- CS
        ThaI  76 pisiktitgkeangvkliwtvdatkakefletykpkfdlilvhinw.gskggl.yyipkevqskvfdklgrekyiklpk 152
                 ++s k it k+++ +  +  +  ++ + +++  + + +l l + n+  ++g++   + +ev++++f+ l +++yik  k
  EPA06176.1 234 HVSGKVITTKKPEWIYDVKPLYMKRFHVYVNAIEISDQLNLNKTNFkQGSGTVvTPVMQEVDRRIFNILEKKGYIKDNK 312
                 57889999999998888888888888999999999999*******9866666516799*****************9776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (468 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 3313.95
//
Query:       EPA06177.1  [L=79]
Description: hypothetical protein BG20_I0824 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.28   11.0   0.1       0.28   11.0   0.1    2.2  3  MciZ      Mother cell inhibitor of FtsZ


Domain annotation for each model (and alignments):
>> MciZ  Mother cell inhibitor of FtsZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.2      0.54   9.8e+03      22      25 ..      11      14 ..       8      16 .. 0.61
   2 ?   11.0   0.1   1.6e-05      0.28      17      28 ..      35      46 ..      34      47 .. 0.93
   3 ?   -1.7   0.1      0.15   2.6e+03      15      19 ..      67      71 ..      67      72 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 0.54
                HHHH CS
        MciZ 22 kLKe 25
                kLK+
  EPA06177.1 11 KLKK 14
                5654 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 1.6e-05
                HHHHHHHHHHHH CS
        MciZ 17 WEIRekLKeYgk 28
                W IR+kLK Y +
  EPA06177.1 35 WKIRNKLKGYHR 46
                **********87 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.15
                EHHHH CS
        MciZ 15 KAWEI 19
                KAW I
  EPA06177.1 67 KAWCI 71
                89977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       766  (0.0427241); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 547.70
//
Query:       EPA06178.1  [L=258]
Description: hypothetical protein BG20_I0833 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-10   41.3   6.5    1.8e-10   41.0   6.0    1.3  1  DUF1837   Domain of unknown function (DUF1837)


Domain annotation for each model (and alignments):
>> DUF1837  Domain of unknown function (DUF1837)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   6.0     1e-14   1.8e-10      43     207 ..      62     228 ..      31     251 .. 0.74

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 1e-14
     DUF1837  43 k.............dknlksGelGEllLylllehflkapkllsKmelktssnmevkgaDgvhikvdddgklqLwlGeSKl..ysdlksaideaveslkk 126
                 +             ++n+k+G +GE+l  ++le f+++  +++K+++  ss +    +D + +k +  ++ ++ + eSKl  +sd +++i ea ++l +
  EPA06178.1  62 NkilesiitprltrTSNMKKGKFGEMLESSVLETFFDYVIPIKKWRYAISSDQSLPRCDIIAVKLEGQKIIEMSFIESKLttTSD-SNKIIEAHSQLME 159
                 033333444555669*****************************************************************53333.4446666666666 PP

     DUF1837 127 flnedslnkelnlisnrlddedeelreaikklldpstslddknvrlnfviligydsditkklkeesdeykdeikeeikkkv 207
                   +++ + + l++i  rl de    ++ + + + ++t   + + + ++ i ++yd++       ++++y ++++ +++k+ 
  EPA06178.1 160 E-KKSGFSDILSFIILRLIDE----KHPLQEAFIEYTL-IKDKPNDSYRIAATYDNAK------WNENYLTKLNDIHTKST 228
                 5.9******************....5555566666665.7788899999999999766......56666666666655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       844  (0.0470746); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1741.01
//
Query:       EPA06179.1  [L=189]
Description: hypothetical protein BG20_I0812 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0066   16.6   1.6      0.013   15.7   0.1    1.9  2  CREPT     Cell-cycle alteration and expression-elevated prote
  ------ inclusion threshold ------
      0.033   14.0   1.3       0.16   11.8   0.1    2.2  2  HeLo      Prion-inhibition and propagation
      0.067   13.0   5.8      0.091   12.6   0.9    2.8  3  CdvA      CdvA-like coiled-coil domain


Domain annotation for each model (and alignments):
>> CREPT  Cell-cycle alteration and expression-elevated protein in tumour
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   2.2e-06     0.013       4      84 ..      24     108 ..      23     118 .. 0.76
   2 ?   -0.1   0.2      0.16   9.4e+02      67     108 ..     145     186 ..     132     188 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.2e-06
       CREPT   4 ikaLkeLensassdaavReriaklPpevsdvsllekikdkeeaekl....lkqveealellaeYnkrLeaeleeRkklakmledf 84 
                 i+++++Le+  ss +++Re+i  + ++ +d+   +k  +k++++kl    +kq  +a ++la++nk++e+e e  +  + + +df
  EPA06179.1  24 IEVIMNLEDFESSGTSIRESIRDFKKKYTDAINQAKTVEKSAKTKLkkisSKQRWKAGKILADFNKKIENEFEIKNYKEAYSRDF 108
                 6789999*****************999988765555555555555511123555689**************99877766666666 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.16
       CREPT  67 LeaeleeRkklakmledfleaqkellakaeekleelkeklek 108
                  ++el+ R+ l+   + +l+  ke    ++ +++e+ +k++k
  EPA06179.1 145 VANELKRRNILEIEKQRLLRWAKEGNLPNRDEYREHLRKISK 186
                 577888888888888888777777776666666666666554 PP

>> HeLo  Prion-inhibition and propagation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1     0.046   2.8e+02     112     150 ..      39      78 ..       3      96 .. 0.63
   2 ?   11.8   0.1   2.7e-05      0.16      40      61 ..     155     177 ..     144     188 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.046
                 G-B--GGGS-HHHHHHH....HHHHHHHHHS----S-----E CS
        HeLo 112 lssereksfraefellk.r..lmrkaakkrqkrtslpkrlrW 150
                   +e+ ++f++++     +  + +k+ak++ k+ s+  + rW
  EPA06179.1  39 SIRESIRDFKKKYTDAInQakTVEKSAKTKLKKISS--KQRW 78 
                 444555556555555442333344444444444444..4444 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 2.7e-05
                 HHHHHHHHHHHHHHHTTT....- CS
        HeLo  40 LdieqlRLlqWgeavgllspd.s 61 
                 L+ie++RLl+W+++ +l ++d +
  EPA06179.1 155 LEIEKQRLLRWAKEGNLPNRDeY 177
                 9*************999644442 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.9   1.5e-05     0.091       6      47 ..      30      71 ..      27      76 .. 0.92
   2 ?    0.0   0.0      0.12   7.1e+02      74      99 ..     133     158 ..     130     165 .. 0.78
   3 ?    0.9   0.0     0.064   3.8e+02      86     110 ..     162     186 ..     158     188 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.5e-05
        CdvA  6 LeeLvsegdipkstyeeikekleealkklkekakelkeklkk 47
                Le+  s+g   ++  +++k+k+++a+++ k  +k  k klkk
  EPA06179.1 30 LEDFESSGTSIRESIRDFKKKYTDAINQAKTVEKSAKTKLKK 71
                88888999999*****************************97 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.12
        CdvA  74 EidEeaYksaieairellesaleeke 99 
                 Ei+ ++Y + ++  +el++++  e+e
  EPA06179.1 133 EIPYSTYAELSSVANELKRRNILEIE 158
                 78888888888888888888888776 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.064
        CdvA  86 airellesaleekeeikklleklsk 110
                  +r ++e +l  ++e +++l+k+sk
  EPA06179.1 162 LLRWAKEGNLPNRDEYREHLRKISK 186
                 5788999999999999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1577  (0.0879581); expected 358.6 (0.02)
Passed bias filter:                      591  (0.0329634); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1218.88
//
Query:       EPA06180.1  [L=96]
Description: hypothetical protein BG20_I0826 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.016   15.1   0.1      0.016   15.1   0.1    1.1  1  Ribosomal_L13e  Ribosomal protein L13e
      0.043   13.9   0.4       0.13   12.4   0.2    1.8  2  DUF4351         Domain of unknown function (DUF4351)


Domain annotation for each model (and alignments):
>> Ribosomal_L13e  Ribosomal protein L13e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.1   1.8e-06     0.016      48      96 ..      33      78 ..       7      91 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.8e-06
  Ribosomal_L13e 48 rPvVrcptvrYntkvraGrGFtleElkaagiskklArtiGIavDhRrkn 96
                    rP Vr   +    k+r GrG++ +El  ag+     r+ G + D Rr+ 
      EPA06180.1 33 RPYVRKRNQ--IGKIRIGRGWSKKELISAGLAVGRKRKFG-QYDCRRTS 78
                    555555443..3699*****************99999999.78999875 PP

>> DUF4351  Domain of unknown function (DUF4351)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   1.4e-05      0.13      34      59 .]       1      26 [.       1      26 [. 0.96
   2 ?   -1.3   0.0      0.26   2.3e+03      17      25 ..      66      74 ..      66      90 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.4e-05
     DUF4351 34 LsleqLEdLgealLDFsslaDLenWL 59
                ++l+qL++  e+lL  +s++DL n+L
  EPA06180.1  1 MNLNQLDQTFEKLLRVNSISDLYNFL 26
                689*********************98 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.26
     DUF4351 17 trrfGelsp 25
                +r+fG+   
  EPA06180.1 66 KRKFGQYDC 74
                699998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 734.11
//
Query:       EPA06181.1  [L=42]
Description: hypothetical protein BG20_I0820 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.16   11.6   0.1       0.21   11.2   0.1    1.2  1  SH3_1     SH3 domain


Domain annotation for each model (and alignments):
>> SH3_1  SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   1.2e-05      0.21       4      28 ..      15      39 ..      12      41 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 1.2e-05
                SSBEXSSTTBXEBSTTEEEEEEEEC CS
       SH3_1  4 YDYeaeesdELsfkkGDviivleks 28
                +D++  ++ E+++ ++D+ ++lek 
  EPA06181.1 15 HDFQDIHEKEIQISRDDKKQLLEKP 39
                7*********************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 302.64
//
Query:       EPA06182.1  [L=67]
Description: hypothetical protein BG20_I0828 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1962  (0.109432); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 448.25
//
Query:       EPA06183.1  [L=168]
Description: hypothetical protein BG20_I0832 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       814  (0.0454013); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1160.43
//
Query:       EPA06184.1  [L=466]
Description: DNA (cytosine-5-)-methyltransferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-55  188.2   0.1    4.7e-55  187.3   0.1    1.4  1  DNA_methylase  C-5 cytosine-specific DNA methylase


Domain annotation for each model (and alignments):
>> DNA_methylase  C-5 cytosine-specific DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.3   0.1   2.6e-59   4.7e-55       1     330 [.       8     454 ..       8     458 .. 0.77

  Alignments for each domain:
  == domain 1  score: 187.3 bits;  conditional E-value: 2.6e-59
                    -EEEEES-TT-HHHHHHHHTT.-EEEEEEE--TTTHHHHHHH-.................-SEEEES-TTTS-GS--.-SEEEE---GGGTECTSE CS
  DNA_methylase   1 lkfidLfaGiGGfrlgleaag.fecvaaseidkkaaktYeanfk................kvsigDitkidkkklpediDlLvgGfPCqpfSvaGk 79 
                    +k+  Lf+G+GG++ g+ +++ fe  +a++i +  a+tY+ n++                  + gD+t++d ++l++ iD ++gG+PCq+fS+ + 
     EPA06184.1   8 YKIATLFSGAGGLDSGFTRTKkFENQIANDILPIPAETYSLNHNakiltveefnknpktpCYIVGDVTEVDFQSLKK-IDCVIGGPPCQDFSITRG 102
                    57889***************99*********************9998888877766633333457888888889995.**************9754 PP

                    ...E--TTSGGGHHHHHHHHHHHHH--SEEEEEEEGGGGGGCCSHHHHHHHHHHHHHTEEEE....................EEEEEGGGTT-SB- CS
  DNA_methylase  80 ...qkgfedtrgtLffeiiriikekkPkvfllENVkgLlkhdkgktlkvilekleelGYevs....................ykllnasdyGvpQn 152
                         g++  rg+L+  +ir +  ++Pkvf++ENV+gL +++ g + k+i e++e+l  + s                     ++++++++GvpQ+
     EPA06184.1 103 sreTLGIKMVRGKLYSHFIRALSRTQPKVFVFENVPGLRSSNGGAAYKTITEDFENLHVRWSeikhdinngpnnaesyslifNDVVDSANIGVPQK 198
                    2336699999***********************************************98888899****************99************* PP

                    -EEEEEEEEEGGG---....-------SS---GGG............................TSGGGTTS-EE.....BTTTB--GGGSSSTT-E CS
  DNA_methylase 153 ReRvfivgirkdleln....vlvkvkefrfpkkkd.......................leasktlrdlleekse.....ldeektalsdklvekee 216
                    R+R++i+g+rkdl  +    + +++k++   k k+                        + ++++++++          ++ee  ++++++++k  
     EPA06184.1 199 RRRLIIIGVRKDLFSKedgkI-FAEKSNAILKGKNsllskypltamevfegetlpnlaQKYRDVMKEYE----GveketKTEESKKWKKNVWDKLT 289
                    ************976677752.33333333222235777777788887777878444434444444444....34444788888888888888888 PP

                    E--.......S---H..........HHTS--B--TTS...-B----S-STT-....................-B-TTS---EEEETTEEE--T... CS
  DNA_methylase 217 kikkttkaseegypk..........elsrnridkveelkglsatrrksgrge....................klekelaeagklqknkerfkp... 279
                     + ++     +g+++          e++r   +  e+l+++ +  + +++ +                    + ++ l  +g+++k k    +   
     EPA06184.1 290 FKIEEDYMFANGIKPndrkeveeafEEHR---RVLEDLEYYGKPLKGKDFEDnsneipkegspviermlripPDMNHLIVSGTKWKVKGTMSNiyr 382
                    88877777777777555655443333333...3334444444444444433366667777777788777777666666667777776666555777 PP

                    .....................TTGGG--B.-BHHHHHHHHT--TT-----SBHHHHHHHHTS--HHHHHHHH CS
  DNA_methylase 280 ....................viekkriRr.LtprEaarlqGfPddfefgskksaaykqiGnsVpvpvieaia 330
                                        ++++++ R  Lt+rE+arlq+fPd++ f++++s+++ qiG++Vpv + +++ 
     EPA06184.1 383 rshplkpaytvmayggggtwSYHYEKGRSmLTNRERARLQTFPDNYMFKGNRSQVRAQIGEAVPVRLGTKLS 454
                    7888888999999999999999999999747**********************************9988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (466 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       679  (0.0378716); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 3213.61
//
Query:       EPA06185.1  [L=241]
Description: hypothetical protein BG20_I0822 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-14   53.8   0.0    3.8e-14   53.0   0.0    1.4  1  HhH-GPD        HhH-GPD superfamily base excision DNA repair p
    1.7e-10   40.2   0.0    3.5e-10   39.2   0.0    1.6  1  HHH            Helix-hairpin-helix motif
    1.3e-06   28.5   6.1    2.3e-06   27.8   6.1    1.4  1  EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III
  ------ inclusion threshold ------
      0.053   13.5   0.0        1.1    9.3   0.0    2.8  2  HRDC           HRDC domain
       0.12   11.5   0.0       0.23   10.6   0.0    1.6  1  DUF763         Protein of unknown function (DUF763)
       0.14   12.8   0.0       0.51   11.0   0.0    2.0  2  HHH_5          Helix-hairpin-helix domain
       0.41   10.6   2.9       0.59   10.1   0.1    2.2  2  WSN            Domain of unknown function


Domain annotation for each model (and alignments):
>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.0   0.0   1.5e-17   3.8e-14       2     107 ..      64     198 ..      63     199 .. 0.96

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 1.5e-17
                 HHHHHTTS-HHHHHHHHHHHHHHHSHCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH.................................S CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................................x RF
     HhH-GPD   2 sailsqqtsderanriierlferfgfptpedladadeekLrelirelGfyrrKakyikelArilv.................................g 67 
                 s+il  +t+ + +++ + ++ +r++  +++dl ++d  kL++ +++lG+ +++ k +k+l+++++                                 g
  EPA06185.1  64 SEILLKKTTRKQVASEWSNITSRCN--DFNDLQNIDLRKLKKVLKPLGLEHTRSKHLKDLSKKILadfngkvpgtkkellslpgvgpytanavlcfafG 160
                 89*********************97..*********************************************************************987 PP

                 -SSS--TTSHHHHHHHHHHTTSSSSTTHHHHHHHHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
     HhH-GPD  68 kpdvlivvDvhvrrilkrlrsikekktkkkvekkleelle 107
                 + d +++ Dv++ r++kr++s++ek++++ +  +l+e  e
  EPA06185.1 161 H-D-VSMLDVNILRVIKRVFSLDEKNSREAIDMHLWEFAE 198
                 5.5.8999************************99999765 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   0.0   1.4e-13   3.5e-10       2      30 .]     129     157 ..     128     157 .. 0.96

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 1.4e-13
                 HHHHHTSSHHHHHTSTT-SHHHHHHHHHH CS
         HHH   2 leglipasreeLlalPGVGpktAeaIlsy 30 
                 ++g +p + +eLl+lPGVGp+tA+a+l++
  EPA06185.1 129 FNGKVPGTKKELLSLPGVGPYTANAVLCF 157
                 899************************97 PP

>> EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   6.1   8.9e-10   2.3e-06       1      17 []     221     237 ..     221     237 .. 1.00

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 8.9e-10
  EndIII_4Fe-2S   1 CTARkPkCeaCPLaDlC 17 
                    CTA++PkC +CP++ +C
     EPA06185.1 221 CTAKNPKCSECPVNKIC 237
                    ***************** PP

>> HRDC  HRDC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00044       1.1      28      57 ..     122     151 ..     121     154 .. 0.86
   2 ?    0.4   0.0      0.25   6.4e+02      29      41 ..     190     202 ..     188     205 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00044
                 -HHHHHHHHHH---SHHHHHTSTTT-HHHH CS
        HRDC  28 pdktLleiAeklPttleeLlqiegvgkrkl 57 
                 ++k L +   k P t++eLl+++gvg++ +
  EPA06185.1 122 SKKILADFNGKVPGTKKELLSLPGVGPYTA 151
                 677788888899**************9876 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.25
                 HHHHHHHHHH--- CS
        HRDC  29 dktLleiAeklPt 41 
                 d +L+e AeklP+
  EPA06185.1 190 DMHLWEFAEKLPP 202
                 668*******996 PP

>> DUF763  Protein of unknown function (DUF763)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0     9e-05      0.23     237     279 ..      93     155 ..       2     163 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 9e-05
      DUF763 237 l....................klpakhevlekvlekayelqpedfeellllkgvGpktlraLa 279
                 l                    + ++ +++ +k+l++ + + p + +ell+l+gvGp t  a+ 
  EPA06185.1  93 LqnidlrklkkvlkplglehtRSKHLKDLSKKILADFNGKVPGTKKELLSLPGVGPYTANAVL 155
                 133333334555566665543334445669***************************999875 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       2.7   6.9e+03      27      50 ..      23      35 ..       9      41 .. 0.44
   2 ?   11.0   0.0    0.0002      0.51       2      19 ..     138     155 ..     133     177 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.7
                HHHHHS-HHHHHTSTTS-HHHHHH CS
       HHH_5 27 edlaaadveeLakipGiGkktAer 50
                  l ++            +k+  +
  EPA06185.1 23 KSLHSL-----------KQKKFSK 35
                223333...........3333333 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0002
                 HHHHTSTT--HHHHHHHH CS
       HHH_5   2 eeLlsvsGiGpktAlall 19 
                 +eLls++G+Gp tA a+l
  EPA06185.1 138 KELLSLPGVGPYTANAVL 155
                 578888888888777766 PP

>> WSN  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.5      0.27   6.9e+02      29      62 ..       6      37 ..       2      39 .. 0.68
   2 ?   10.1   0.1   0.00023      0.59      21      65 ..      62     108 ..      61     109 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.27
         WSN 29 sikvddvisELLnlgsvklseivkldvdklkell 62
                s+k +  ++E+++ +   l+++++l+++k+++ l
  EPA06185.1  6 SMKKKSKLAEMIKNN--YLKSLHSLKQKKFSKIL 37
                566666677777655..48888888888887765 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00023
         WSN  21 LqaglidgsikvddvisELLnlgs..vklseivkldvdklkellekl 65 
                 L ++++ ++++ ++v sE  n+ s  +++++++++d  klk+ l+ l
  EPA06185.1  62 LLSEILLKKTTRKQVASEWSNITSrcNDFNDLQNIDLRKLKKVLKPL 108
                 567777888889999*******999777**************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       985  (0.0549389); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1584.31
//
Query:       EPA06186.1  [L=249]
Description: hypothetical protein BG20_I0823 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1552.02
//
Query:       EPA06187.1  [L=1143]
Description: DEAD/DEAH box helicase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.3e-24   85.2   0.0    1.1e-23   83.9   0.0    1.7  1  DEAD        DEAD/DEAH box helicase
    1.7e-11   44.4   0.1    5.3e-10   39.6   0.1    2.8  2  Helicase_C  Helicase conserved C-terminal domain
    1.9e-11   44.3   0.0    6.7e-11   42.5   0.0    2.0  1  ResIII      Type III restriction enzyme, res subunit
    2.2e-10   40.3   0.0    5.3e-10   39.1   0.0    1.6  1  HIRAN       HIRAN domain


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.9   0.0   2.5e-27   1.1e-23       2     174 ..     282     450 ..     281     452 .. 0.91

  Alignments for each domain:
  == domain 1  score: 83.9 bits;  conditional E-value: 2.5e-27
                 HHHHHHHHHHH..TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHHHHHHHTTC CS
                 xxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        DEAD   2 diQaeaiplil..gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaardqlskldngv 98 
                 + Q++ai+  l  ++ + +++++T +GKT ++ ++++q ++   +++g+k+++v+P r+L+ +  +++ +++  ++ rv+ i+g  +++   +kl +++
  EPA06187.1 282 PSQKNAIDSGLfnSNSNKVIKMPTSAGKTRIAELAMVQMLA---KNPGKKCIYVAPYRALVSELEDTFLNLFGDLGFRVSTIVGTYEQDPFEKKLIEDA 377
                 679999999998788899**********************5...69999***********************************99999999999888* PP

                 SEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEEEEEESSBS.HHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
        DEAD  99 divvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrqvivlSATlp.kdvk 174
                 d++v tp++ld +l++++  l++v++++lDE + + d++++ +++ +l++l+++  +     ++i++SA l+ ++v+
  EPA06187.1 378 DVLVLTPEKLDLVLRSHSELLDDVKLFILDEGHIIDDDKRGIKLELLLTRLKRKLIN----TRFIFISAVLSeETVQ 450
                 ***********999555545*******************************765554....45********977776 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0     0.097   4.4e+02       6      53 ..     317     367 ..     313     377 .. 0.78
   2 !   39.6   0.1   1.2e-13   5.3e-10      33     111 .]     608     691 ..     573     691 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.097
                 HHHHHHHTTTTSEEEEEESSHHHHHH.HHHHHHHT...TSTEEEESTTSTHH CS
  Helicase_C   6 llellkleeeggkilifvntidrlek.vklllekk...gikvavlhgelpqn 53 
                 ++++l  ++ g+k++ +++++  +++  + +l+ +   g++v ++ g+ +q+
  EPA06187.1 317 MVQML-AKNPGKKCIYVAPYRALVSElEDTFLNLFgdlGFRVSTIVGTYEQD 367
                 55666.7899************66445467766677789**99999988876 PP

  == domain 2  score: 39.6 bits;  conditional E-value: 1.2e-13
                 HHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEESSSS....SSH......HHHHHHHTTSSSTT CS
  Helicase_C  33 klllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVinfdlp....rnv......tsyiqriGRtgRag 111
                 +ll  ++   +a++hg+lp   r+ i ++f++++++v+++t+ +++G+++p  + +i+          +      ++y+  +GR+gRag
  EPA06187.1 608 QLL--QN--GIAIHHGRLPDILRRSIESDFRDKKFRVIVSTNTLAQGVNLPIKTILIHSCRRrrmdN-TqemisvSDYWNVAGRAGRAG 691
                 444..44..5677**************************************5555555555455540.1444555************97 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.5   0.0   1.5e-14   6.7e-11       6     148 ..     282     416 ..     271     446 .. 0.82

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 1.5e-14
                 HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B--........ CS
      ResIII   6 eyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseaykeigkkvsgdkkka.kekdstn 103
                 + Q++ai++ l  +  + + + +ikm+T +GKT++a  ++ ++l k++ +k++ ++p ++l++ ++++f +++ +   +++++v   ++++ ++k +++
  EPA06187.1 282 PSQKNAIDSGL--F--NSNSNKVIKMPTSAGKTRIAELAMVQMLAKNPGKKCIYVAPYRALVSELEDTFLNLFGDLGFRVSTIVGTYEQDPfEKKLIED 376
                 44555555554..2..7888999*************77777777777889************************9988888888888888877899*** PP

                 -SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T CS
      ResIII 104 kkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk 148
                 +++lv t ++ld  +      s++ l d  +++i DE H + ++k
  EPA06187.1 377 ADVLVLTPEKLDLVL-----RSHSELLDDVKLFILDEGHIIDDDK 416
                 ***************.....899999999**********888764 PP

>> HIRAN  HIRAN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   0.0   1.2e-13   5.3e-10      15      73 ..    1058    1115 ..    1043    1133 .. 0.85

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 1.2e-13
                  CT..---TTEEEEEEE-TT-SS-TT-EEEEETTS-EEEEE-HHHHHHHHHHHHTTSSEE CS
       HIRAN   15 sgtgylkpgtevilerepnnpadanavrvlnergfeiGrlprevakwlspLldsgfitf 73  
                   + +++k  + v+l r+ +n++d+na++v   +  e+G+l+r va+ l+p+ld  +i+f
  EPA06187.1 1058 VVANKIKESETVVLSRDYDNAYDRNAIKVFSSNKSELGFLSRNVAQYLAPYLDC-GIEF 1115
                  33799************************************************8.5555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.76u 0.29s 00:00:01.05 Elapsed: 00:00:00.47
# Mc/sec: 7384.53
//
Query:       EPA06188.1  [L=471]
Description: hypothetical protein BG20_I0815 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-12   47.5   1.3    2.6e-12   46.7   0.1    1.9  2  Lactamase_B_2  Beta-lactamase superfamily domain
    7.8e-07   29.3   0.4    0.00093   19.3   0.2    2.3  2  Lactamase_B    Metallo-beta-lactamase superfamily
    0.00014   21.7   0.5     0.0039   17.1   0.0    2.5  2  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
    0.00016   21.6   0.0    0.00052   19.9   0.0    2.0  1  Lactamase_B_3  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.032   14.1   0.0        4.5    7.1   0.0    2.3  2  SIS            SIS domain


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   0.1   7.3e-16   2.6e-12      26     147 ..      87     210 ..      68     261 .. 0.70
   2 ?   -1.5   0.1      0.41   1.5e+03     176     200 ..     422     446 ..     405     447 .. 0.82

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 7.3e-16
                    --..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTT.................TTEEEEEE-TTSEEEECSTTEE CS
  Lactamase_B_2  26 delppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleee.................pavnvheldwgesfelgdggle 104
                    +e p+idaVllthaH+DH   + +l e    ++p++    ++ +l+a   +  +  e                  + +++e+ +g++f++g   le
     EPA06188.1  87 EE-PDIDAVLLTHAHADHADYISFLHE----DIPIHMGSACHLILKALAERSSRTIEreildykprpysvkdepIKRKINEFRTGDKFKVG--SLE 175
                    44.89**************66666666....3555533333333333333333333333445556666677777999*************9..699 PP

                    EEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S--- CS
  Lactamase_B_2 105 itatparhksgrrldrnagdtlGlriegggkrvyyigDtgyip 147
                    ++++ + h+ +         ++G++i +++  v+y+gD     
     EPA06188.1 176 VEPIHVDHSVPG--------AYGFIIWTSEGPVAYTGDIRLHG 210
                    ************........******************99544 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.41
                    HT---STSHHHHCTTSSSSEEEEES CS
  Lactamase_B_2 176 mgHltpeeaveaaadlgakrlvliH 200
                     gH+  ++ + a+ +++ak l+++H
     EPA06188.1 422 SGHARGGDLLTAVSEIDAKMLFPVH 446
                    57888899999*************9 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.2   2.6e-07   0.00093      41      58 ..      87     104 ..      74     106 .. 0.87
   2 !    8.0   0.0   0.00074       2.7     121     155 ..     176     210 ..     113     254 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 2.6e-07
                  GGGGEEEEE-SBSSHHHH CS
  Lactamase_B  41 kpkdvdavilTHlHlDHi 58 
                  +  d+dav+lTH+H+DH+
   EPA06188.1  87 EEPDIDAVLLTHAHADHA 104
                  5689*************7 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00074
                  EEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSH CS
  Lactamase_B 121 ralyvtggpghghghgvveygggkvlftGDallag 155
                  ++  ++ + ++g+ +++++  +g v++tGD  l g
   EPA06188.1 176 VEPIHVDHSVPGAYGFIIWTSEGPVAYTGDIRLHG 210
                  34445668899999****************98744 PP

>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1     0.057   2.1e+02      10      27 ..      93     111 ..      88     116 .. 0.81
   2 !   17.1   0.0   1.1e-06    0.0039       6      42 ..     414     450 ..     412     467 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.057
       RMMBL  10 eid.fSgHadknellelir 27 
                  +    +Had+++ + +++
  EPA06188.1  93 AVLlTHAHADHADYISFLH 111
                 566689******9998885 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 1.1e-06
       RMMBL   6 arieeidfSgHadknellelirklkprnvilvHGeee 42 
                 +++ + ++SgHa   +ll  ++ +  + +++vH e+ 
  EPA06188.1 414 MQMFQSHCSGHARGGDLLTAVSEIDAKMLFPVHTEHP 450
                 6777888***************************985 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   1.5e-07   0.00052      27     116 ..      81     208 ..      14     223 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.5e-07
  Lactamase_B_3  27 nlgyeppaeeaDlvlisqaledHahletlkql............................................aenvkvleegeslevgglei 78 
                     +g +p+++++D+vl+++a++dHa+                                                   +++++  ++g++++vg+le+
     EPA06188.1  81 MAGRKPEEPDIDAVLLTHAHADHADYISFLHEdipihmgsachlilkalaerssrtiereildykprpysvkdepiKRKINEFRTGDKFKVGSLEV 176
                    34555566***************9876554435688899999999999998888888888888877777777777766667777799********* PP

  Lactamase_B_3  79 ravatshdavggsergenngflleqdgltiyhlGhlah 116
                    + ++ +h      ++g  +gf++  ++  +++ G++  
     EPA06188.1 177 EPIHVDHS-----VPG-AYGFIIWTSEGPVAYTGDIRL 208
                    ******93.....333.577888778888888888764 PP

>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0    0.0082        29      51     108 ..      73     130 ..      61     138 .. 0.81
   2 ?    7.1   0.0    0.0013       4.5      17      63 ..     281     327 ..     279     335 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0082
                 -STTCEEEEEESSSHHHHHHHHHH.HHHHTTSEEEEEESSTTSHHHHHSSEEEEEEEEC CS
         SIS  51 ideddlvilisfsgetkdlvaaae.lakergakiiaITdskgsplareadlalyinaep 108
                 + +ddl+++  + +e++d +a++  +a++++a  i++  +++ p+   + ++l++ a +
  EPA06188.1  73 VYRDDLMVMAGRKPEEPDIDAVLLtHAHADHADYISFL-HEDIPIHMGSACHLILKALA 130
                 5689******************************9997.55556666666666666655 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0013
                 HHHHHHHHHHH.HHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESS CS
         SIS  17 yaiakelalkl.eeiggivvevedaselkhgvlalideddlvilisfs 63 
                 y iake  +k+  +i+   +  +++ + kh  +++id++d+vi +  +
  EPA06188.1 281 YKIAKETGRKFvVKINDAFFLKHLSQD-KHLSVPNIDDEDIVIYLPKR 327
                 6799999***99999**9******999.9999***********87655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (471 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 3105.40
//
Query:       EPA06189.1  [L=355]
Description: hypothetical protein BG20_I0819 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.049   13.7   0.1      0.083   12.9   0.1    1.3  1  Ephrin_lbd  Ephrin receptor ligand binding domain


Domain annotation for each model (and alignments):
>> Ephrin_lbd  Ephrin receptor ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   4.6e-06     0.083      16      78 ..     263     326 ..     255     338 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.6e-06
  Ephrin_lbd  16 ttypkee.gWeevsvldekgakirtyqvCnvsekeqdnWLrtpfieregasrvyvelkFtvrdC 78 
                 ++y++++  W++v ++++k++  +++  C+ +   +++WL   ++e ++ +r+ v  k + +d 
  EPA06189.1 263 QAYEETKnSWRKVDGVKTKTELKTIFIDCKSDVVVKNKWLGEYHLEGKKVHRIKVGAKVASKDR 326
                 455544425***********************9********************99888777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2428.02
//
Query:       EPA06190.1  [L=882]
Description: ribonucleoside-diphosphate reductase, adenosylcobalamin-dependent [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   3.6e-183  609.9   0.0   8.5e-183  608.6   0.0    1.6  2  Ribonuc_red_lgC  Ribonucleotide reductase, barrel domain
    2.4e-31  107.6   0.0    5.1e-31  106.5   0.0    1.6  1  Ribonuc_red_lgN  Ribonucleotide reductase, all-alpha domain
    2.1e-21   76.3   1.7    5.6e-21   74.9   0.9    2.2  2  ATP-cone         ATP cone domain
  ------ inclusion threshold ------
       0.13   12.5   0.3        9.8    6.4   0.0    3.4  3  HEPN_RES_NTD1    HEPN/RES N-terminal domain 1


Domain annotation for each model (and alignments):
>> Ribonuc_red_lgC  Ribonucleotide reductase, barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.36   1.6e+03     335     384 ..      12      66 ..      10      69 .. 0.72
   2 !  608.6   0.0  1.9e-186  8.5e-183       1     524 []     280     781 ..     280     781 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.36
                      XXXXXXXXXXXXXXXXXXXXXXXXXXXX...........XXXXXXXXXXXXXXXX CS
                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxx RF
  Ribonuc_red_lgC 335 elAkergpfplfekskyskgilpvdefeeke.....kedweeLreeikkyGlrna 384
                      e+ k+ g+ + f+++k+s+ i++   +++k+      +  +++++++ ++G+ n+
       EPA06190.1  12 EIRKRSGAVTAFNQNKISNAIFKALAATSKAdrvlaDHLANKVVQKLVEQGFTNS 66 
                      5668889999999999999997666663332455556677778888888888886 PP

  == domain 2  score: 608.6 bits;  conditional E-value: 1.9e-186
                      EEE.....BSS-EEEE-X..............XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Ribonuc_red_lgC   1 ssCfvlsvedslesIletvkeaallskaggGvGlnlsklRakgslvkgtegaasGpvsfmklidavadvvkqgGkRrGAamvylevwHpDiekf 94 
                      s+Cfvl + d++e+I++++++aal++k+ggGvG+n s+lR++g++v++t+g asGpvsfm++i++v++vvkqgGkRrGA+m+++e+wHpD+ekf
       EPA06190.1 280 SACFVLGMPDDMEQIMKSTSDAALIFKSGGGVGINYSDLREEGDIVASTSGVASGPVSFMNIINTVTEVVKQGGKRRGANMGIIEAWHPDVEKF 373
                      79******************************************************************************************** PP

                      XXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXX.........................XXXXXXXXXXXXXXXXXXX CS
                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Ribonuc_red_lgC  95 idaKekntgeeenrlsnlnisvgvpdlFmeavke..dkdwtLfsPrtvvkleklygeefeeeyeeleekakikkkevkakeLfeeiaesawetg 186
                      i+ K     +e  +l+n+n+svg++++F++a+ +  d+++ L sPr+                           ke++a +L++ ia saw+++
       EPA06190.1 374 ITNK-----TEPGVLENFNVSVGIWEDFWNALVNteDGKYMLRSPRDR-----------------------KPVKEINAHQLIDLIALSAWKSA 439
                      ****.....4688*******************9877999*******32.......................23569****************** PP

                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Ribonuc_red_lgC 187 ePgvlfkDtiNrrnvlekakggkIratNlCgEiplleyesvavCnLasinLakfvkkdeegkkefdwdelkkviqlvvraLdnvidvnkyplpe 280
                      ePg++f+D+iN+ nv+ ka + + ratN+CgE+ l++yes   CnL+sinL ++vk++++g+ efdw++++++i++++r+Ldn+idvn+yp++e
       EPA06190.1 440 EPGLIFFDQINKYNVFAKARQAPLRATNPCGEQSLYPYES---CNLGSINLVNLVKRQADGEYEFDWQRYEETIRKTTRFLDNIIDVNHYPVKE 530
                      ****************************************...*************************************************** PP

                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....X......XX CS
                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxx RF
  Ribonuc_red_lgC 281 iekntkktRriGlGvmgladalaklgipydseealkfarkitelltyyaykaSvelAkergpfplfekskyskgilpvdef....eekekedwe 370
                      i+ ++k++RriGlGvmg+ad+l kl+ipy+s+e+ ++ +k+ e+ltyy++++Sv lAk rg fpl +k++y +g+ p++++    +e++  +w+
       EPA06190.1 531 IDIASKDSRRIGLGVMGVADLLYKLKIPYNSKEGYDLQSKLSEALTYYSMEESVALAKSRGEFPLCSKTEYPEGKIPIAGYyekpKESHCYEWD 624
                      *********************************************************************************87754445899** PP

                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXX CS
                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxx RF
  Ribonuc_red_lgC 371 eLreeikkyGlrnamvtalaPTgsiSliagtssgiePifalvykksvtvgeflevnpvfeeeLkklglwseellkki...lesvqgleeipeei 461
                       L e+ikk+G+rn  +t++aPTg+ S+ia++s+g+eP falv++k+vtvg+f+++n+ +ee Lk+ gl+s+ell+ki   ++s +g++eip+ +
       EPA06190.1 625 ALIEKIKKHGIRNVLTTTVAPTGTLSMIADCSNGMEPAFALVFEKRVTVGRFFYTNKIVEEVLKEHGLYSDELLAKIadnYGSLKGIPEIPQWM 718
                      *****************************************************************************888888*********** PP

                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Ribonuc_red_lgC 462 krvfktaldidqedhikaqaaiqkwidqsiSktinlpneatvedvkelyllAwklGlKgvtyY 524
                      ++v++ta+di++ dh+ aq ++q wi ++i ktin+p ++t+edvk++yllA++lGlKg+t+Y
       EPA06190.1 719 QDVYVTAMDIHWADHLMAQGVWQDWIGNAIAKTINMPYDVTAEDVKSAYLLAHELGLKGITVY 781
                      **************************************************************9 PP

>> Ribonuc_red_lgN  Ribonucleotide reductase, all-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.5   0.0   1.1e-34   5.1e-31       1      83 []     122     277 ..     122     277 .. 0.99

  Alignments for each domain:
  == domain 1  score: 106.5 bits;  conditional E-value: 1.1e-34
  Ribonuc_red_lgN   1 kkltynalkvledrYllkdengeivEspqqmfmRvAlalaiaealyd............................................... 47 
                      k++++n+l+vl++rYl++++++ei Esp qmf+RvA+++ i ++lyd                                               
       EPA06190.1 122 KEFDLNCLRVLASRYLFRNNKNEITESPTQMFERVAILVGIGDILYDaqvfdksgnisqstdearsylekldnfdykfkigdyflnkwhfrsli 215
                      689******************************************************************************************* PP

  Ribonuc_red_lgN  48 ..........................kleedkdlaeefydlmssqkflpasPtlmnaGtelg 83 
                                                k+++++d+++e++dlm+ q+flp+sPt+mnaG +lg
       EPA06190.1 216 nhyvtlaskgqmkvsfkdlltliaakKFDSYADKITEYFDLMTAQDFLPNSPTMMNAGGRLG 277
                      **********************************************************9986 PP

>> ATP-cone  ATP cone domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.9   0.9   1.2e-24   5.6e-21       3      85 ..      13     102 ..      11     103 .. 0.91
   2 ?   -2.2   0.0       1.4   6.3e+03      59      71 ..     681     693 ..     680     694 .. 0.87

  Alignments for each domain:
  == domain 1  score: 74.9 bits;  conditional E-value: 1.2e-24
                 EE-TTS-EEE--HHHHHHHHHHHHHH....-HHHHHHHHHHHHHHHHHH.HIIT..-BHHHHHHHHHHHHHHSS-HHHHHHHHHHHHHHH CS
    ATP-cone   3 ViKRdGtvepfdvekIkraiekAceg....seeeideiaeeveaevrkr.lrdg..isteeIqdlvektliehpdyavaaayilyrnlrk 85 
                 ++KR G v  f+++kI +ai kA+ +    ++  +d +a++v++++ ++ + +   +s+e+Iqd+ve tli++++ ++a+ayi+yr++r+
  EPA06190.1  13 IRKRSGAVTAFNQNKISNAIFKALAAtskaDRVLADHLANKVVQKLVEQgFTNSraPSVEDIQDIVESTLIDSGNSDIAKAYIVYRHERR 102
                 99*********************99987777777*********9996663555599*******************************997 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.4
                 HHHHHHHHHSS-H CS
    ATP-cone  59 dlvektliehpdy 71 
                 ++ve++l+eh+ y
  EPA06190.1 681 KIVEEVLKEHGLY 693
                 79********987 PP

>> HEPN_RES_NTD1  HEPN/RES N-terminal domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0022       9.8      97     121 ..     493     517 ..     487     522 .. 0.87
   2 ?    1.3   0.0      0.08   3.6e+02      95     117 ..     611     633 ..     607     639 .. 0.90
   3 ?   -1.6   0.0      0.65   2.9e+03      54      84 ..     674     705 ..     668     732 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0022
  HEPN_RES_NTD1  97 lsedealkysWeaFkelvkhksRyv 121
                     + d +++++W+++ e++++ +R++
     EPA06190.1 493 RQADGEYEFDWQRYEETIRKTTRFL 517
                    56788999****************7 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.08
  HEPN_RES_NTD1  95 yglsedealkysWeaFkelvkhk 117
                    y+++++e+  y+W+a  e +k++
     EPA06190.1 611 YYEKPKESHCYEWDALIEKIKKH 633
                    88999***************975 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.65
  HEPN_RES_NTD1  54 getydtedlleevi.eleaendeLiediadal 84 
                    g+ + t+ ++eev+ e+   +deL+ +iad+ 
     EPA06190.1 674 GRFFYTNKIVEEVLkEHGLYSDELLAKIADNY 705
                    55667777788877777999999999999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (882 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.76u 0.32s 00:00:01.08 Elapsed: 00:00:00.52
# Mc/sec: 5097.94
//
Query:       EPA06191.1  [L=41]
Description: hypothetical protein BG20_I2023 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.50
# Mc/sec: 246.22
//
Query:       EPA06192.1  [L=305]
Description: hypothetical protein BG20_I2020 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1868.52
//
Query:       EPA06193.1  [L=706]
Description: peptidase families S8 and S53, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-21   77.5   7.2    5.5e-14   52.1   0.4    3.0  2  Peptidase_S8    Subtilase family
     0.0093   15.6   2.7        1.9    8.0   0.0    2.9  3  Peripla_BP_4    Periplasmic binding protein domain
  ------ inclusion threshold ------
       0.41   11.1   2.7       0.33   11.4   0.3    2.1  2  PrlF_antitoxin  prlF antitoxin for toxin YhaV_toxin
       0.83   10.1   7.7        0.1   13.0   2.7    2.0  2  CENP-H          Centromere protein H (CENP-H)


Domain annotation for each model (and alignments):
>> Peptidase_S8  Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   1.6   7.7e-10   3.5e-06       1     179 [.     318     457 ..     318     490 .. 0.74
   2 !   52.1   0.4   1.2e-17   5.5e-14     179     298 .]     587     695 ..     570     695 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 7.7e-10
                   -TT-EEEEECS-B-TT-TTTGGGEEE..EEEE---T.TSG.GGEETT-SS-TT-SC-SSS....HHHHHHHHHH-B..SSSSSB-SSTTSEEEEEE- CS
                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Peptidase_S8   1 gkgvlvavlDtGvdpshpdlsvttdgerklvdvide.egagfngadsettstnwarddngnsieHGthvAGiaaanapeegekngvapgakilsvkv 96 
                   gk+v+vavlD  +d+++p++s++         +id  ++++  ++++ + s+  ++     +i HGt vA i+            vap+ k++ +++
    EPA06193.1 318 GKDVKVAVLDVMFDTNNPKISDN---------IIDFkSFRNSPENSMLEQSVTPGE-----KISHGTAVAEIITD----------VAPNSKLYLYEM 390
                   89*******************44.........444403344444444444444444.....456******88865..........6*******5555 PP

                   SSTTSB-HH..HHHHHHHHHHHHCT-SEEEE-EE.SCETTCHHCHHHHHHHHHHHH.CCT-EEEEE--SS-T-HHEEE-TTCEE CS
                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Peptidase_S8  97 ldtsggsmetgteliraieeaaedkvdvinmslg.estslpktgrsiealainravnkkgvlvviSaGNngktgsslqagspvg 179
                    ++         e  rai+ea+ ++vdvi+m  g    s++ t+ +++   +++av ++g+ v++ +GN        q+ ++++
    EPA06193.1 391 STD--------VEFGRAIDEAISNNVDVIAMAAGwPNLSTDGTSHITK--KVEDAV-NHGISVIVPSGNFA------QKHWKGY 457
                   533........56779******************55556666666666..9*****.9***********99......4444444 PP

  == domain 2  score: 52.1 bits;  conditional E-value: 1.2e-17
                   ECTTTSTTCEEEEEES.TTSSB-TT--B-TT.......-EEEE-S-CCCCCCCCCHHHTTTHHEEEE-SHHHCHHHHHHHHHHHHHHHTT--HHHHH CS
                   xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Peptidase_S8 179 gtpstsknvitvgayt.tegkiapfSsrGpssdgklkpdivapGgnivstwsrqsnnsaglssyqsmsGTSmAsPnaagaaAlllsalpkltpetvr 274
                     ps +++vi vga++ ++g + +fSs+Gp+ +gk  p +v p g    t+  ++         ++++GTS+ +P +ag+aAl+l+a+p+l+p ++ 
    EPA06193.1 587 VVPSDANGVIVVGAVSnKDGVLESFSSQGPTNNGKTVPNVVGPNGV--TTIAYNG---------NLFYGTSATTPYVAGIAALMLDANPDLSPSQLL 672
                   459999*********955677889*****************99886..5555555.........689****************************** PP

                   HHHHCCS-EE......SSSSSSTT CS
                   xxxxxxxxxxxxxxxxxxxxxxxx RF
  Peptidase_S8 275 aallntAqdlgkadniesfaqGaG 298
                     +++ A++  +++n+e+ ++G+G
    EPA06193.1 673 NEIEQHAKPNHMQPNYEN-EYGFG 695
                   *********999988765.67776 PP

>> Peripla_BP_4  Periplasmic binding protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   0.4    0.0012       5.3     101     171 ..      57     137 ..      24     157 .. 0.78
   2 !    8.0   0.0   0.00041       1.9      45      85 ..     397     444 ..     380     474 .. 0.83
   3 ?   -2.4   0.0      0.64   2.9e+03     185     248 ..     593     659 ..     533     660 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0012
                   EC-HHHHHHHHHHHHHHHCTTH...............EEEEEETSCCCHHHHHHHHHHHHHHHHH-TTCEECCEEESTTTCHHHH CS
  Peripla_BP_4 101 gfdneaaGelqaeylaeklggk..............kgkvvilaGspgdpnaeeriegfrkvlkeypgikivaevaganwdaeka 171
                   ++ + + Gel a++l +  +++               +++ il+ ++  + ++  +++f++vlk  pg+++va++     ++++ 
    EPA06193.1  57 AQKESKKGELVAKVLFSVAKKNldkefnektfdpiyQKQLSILNKQLEENTQKVKMAYFDNVLKVNPGFTVVADNL----KQTEV 137
                   55566667777777766666666667888899999999***********************************643....33333 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00041
                   HHHHHHHHHTT-SEEEE--SSH.......HHHHHHHHHHHHTT-EEEE CS
  Peripla_BP_4  45 vaqiedaiakgvdgiivapvds.......talapalkkakaaGIpVva 85 
                     +i+ ai+++vd+i++a+  +       + +++ +++a + GI V++
    EPA06193.1 397 GRAIDEAISNNVDVIAMAAGWPnlstdgtSHITKKVEDAVNHGISVIV 444
                   568***************999877776667777888888889999886 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 0.64
                   CEEEESSCCHHH.CHHHHHHHTTTTSTEEEEEES-HHHHHHHH.HTTSSE.EEEE--HHHHHHHHHH CS
  Peripla_BP_4 185 dgilaandgmae.galealeaaglagkvvvtgqDatpealeai.kdGtid.atvaqdpyelgyaave 248
                   +g++ ++++    g+le+++++g ++  + + + + p  ++ i  +G++  +t a  py  g aa++
    EPA06193.1 593 NGVIVVGAVSNKdGVLESFSSQGPTNNGKTVPNVVGPNGVTTIaYNGNLFyGTSATTPYVAGIAALM 659
                   3444444333334666677776664444444444455555444333333337777777777777665 PP

>> PrlF_antitoxin  prlF antitoxin for toxin YhaV_toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.3   7.3e-05      0.33       8      79 ..      46     118 ..      39     134 .. 0.83
   2 ?   -2.5   0.1       1.7   7.4e+03      29      68 ..     188     227 ..     179     239 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.3e-05
  PrlF_antitoxin   8 gqttiPasvRkaLklkkgrdkiaytilddgkvvisraeeeae.DpvleqFLeFlakdllknperlrpvelerl 79 
                     g tt+ +++++a k +k+ + +a ++    k  + ++ +e+  Dp+ ++ L+ l+k+l++n+++++ + + ++
      EPA06193.1  46 GLTTVEKAIKNAQKESKKGELVAKVLFSVAKKNLDKEFNEKTfDPIYQKQLSILNKQLEENTQKVKMAYFDNV 118
                     569**********999989888888888889999999666555*********************998766554 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.7
  PrlF_antitoxin  29 iaytilddgkvvisraeeeaeDpvleqFLeFlakdllknp 68 
                     ++ ++ +    +i++ +++++  v +  L  +  d+++ p
      EPA06193.1 188 VVLELSNTSPETIEKIQSQSDVEVQDDNLIQITTDVKNIP 227
                     4444444444455666666666666666666666666555 PP

>> CENP-H  Centromere protein H (CENP-H)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   2.7   2.3e-05       0.1       8      84 ..      26     112 ..      20     114 .. 0.85
   2 ?   -1.7   0.2      0.84   3.8e+03      50      73 ..     137     166 ..     130     215 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.3e-05
      CENP-H   8 rdelssellklsqelrelqeeltevekenlrlkrknr..elaaell.elakekesek.......eklkeelekleaelkksrqrwrv 84 
                 +d +++++ k+  e++e+ + lt+vek +++++++++  el+a++l   ak++  ++       + ++++l+ l ++l++  q++++
  EPA06193.1  26 TDSIIQAVGKILDESEEKYDGLTTVEKAIKNAQKESKkgELVAKVLfSVAKKNLDKEfnektfdPIYQKQLSILNKQLEENTQKVKM 112
                 6889999********************9888877665449*****548888888888987776655*****************9997 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.84
      CENP-H  50 llelakekesek......eklkeeleklea 73 
                 ++e+  + e+ k      +k ++++ +l +
  EPA06193.1 137 VQEKHLQMEQSKnpgiviKKIDKQIRELMQ 166
                 344444444444444444444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (706 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       966  (0.0538792); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.45
# Mc/sec: 4669.82
//
Query:       EPA06194.1  [L=83]
Description: hypothetical protein BG20_I2022 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.024   14.6   0.9      0.031   14.3   0.9    1.1  1  DZR           Double zinc ribbon
      0.032   12.1   0.0      0.032   12.1   0.0    1.0  1  PolC_DP2      DNA polymerase II large subunit DP2
       0.06   13.2   1.1      0.083   12.8   1.1    1.2  1  zf-C3HC4_3    Zinc finger, C3HC4 type (RING finger)
      0.062   13.3   0.1      0.064   13.3   0.1    1.1  1  HypA          Hydrogenase/urease nickel incorporation, metall
      0.092   11.2   0.0      0.092   11.2   0.0    1.0  1  FHIPEP        FHIPEP family
       0.87    9.2   6.8        4.4    6.9   0.4    2.2  2  TF_Zn_Ribbon  TFIIB zinc-binding


Domain annotation for each model (and alignments):
>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.9     1e-05     0.031      13      37 ..      59      79 ..      51      82 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1e-05
         DZR 13 rfCseCgtklkavaaedrCpsCgek 37
                  C eCg+k+      ++Cp+C++ 
  EPA06194.1 59 GICLECGSKIY----DQKCPNCDSL 79
                58********9....8******976 PP

>> PolC_DP2  DNA polymerase II large subunit DP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   1.1e-05     0.032     609     641 ..      49      81 ..      24      83 .] 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.1e-05
    PolC_DP2 609 kgeieveiarrkCkkCgketlearCeeCgekte 641
                 k+++e e+++  C +Cg++ + ++C++C++  e
  EPA06194.1  49 KKSVEKELGEGICLECGSKIYDQKCPNCDSLNE 81 
                 67899***********************98765 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.1   2.8e-05     0.083      25      45 ..      60      78 ..      58      83 .] 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.8e-05
                E-HHHHHHHHHTT-B-TTT-- CS
  zf-C3HC4_3 25 lCeeCaekllkrkkkCpiCrr 45
                +C eC +k+   ++kCp C +
  EPA06194.1 60 ICLECGSKI--YDQKCPNCDS 78
                8********..89******86 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   2.1e-05     0.064      64      96 ..      52      80 ..      31      83 .] 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.1e-05
                EEEE--EEEETTTS-EEECHHHHHS-TTTSSS- CS
        HypA 64 ieevpvkvrCreCgkefeleekalrCpkCgsad 96
                +e++  +  C eCg+++  +    +Cp+C+s +
  EPA06194.1 52 VEKELGEGICLECGSKIYDQ----KCPNCDSLN 80
                788888999*****888744....7****9976 PP

>> FHIPEP  FHIPEP family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   3.1e-05     0.092     254     293 ..       4      43 ..       2      74 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.1e-05
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
      FHIPEP 254 anpkalliaagvllllalvpglpklvflllaallallayl 293
                 +++ ++li++++l++++l+p +  +  +l+a+++ +   +
  EPA06194.1   4 EKRDIILIVGLLLFMIGLIPFMAPIYAVLIAIAMYFGIKF 43 
                 678899****************999888888777654432 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.4    0.0015       4.4      17      31 ..      56      70 ..      51      72 .. 0.73
   2 ?    6.0   1.2    0.0029       8.6       2       8 ..      72      78 ..      71      82 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0015
                  TTCEEESSSSBEEEE CS
  TF_Zn_Ribbon 17 rgelvCtdCGlVled 31
                   ge +C +CG+ + d
    EPA06194.1 56 LGEGICLECGSKIYD 70
                  577888888887755 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0029
                  EETTTTC CS
  TF_Zn_Ribbon  2 kCPnCgs 8 
                  kCPnC s
    EPA06194.1 72 KCPNCDS 78
                  9****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1048  (0.0584528); expected 358.6 (0.02)
Passed bias filter:                      602  (0.0335769); expected 358.6 (0.02)
Passed Vit filter:                       113  (0.00630264); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 522.76
//
Query:       EPA06195.1  [L=222]
Description: hypothetical protein BG20_I2398 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0037   16.2  21.4     0.0037   16.2  21.4    3.0  3  Spc7          Spc7 kinetochore protein
  ------ inclusion threshold ------
       0.21   10.8  28.4        1.1    8.4   4.0    2.2  2  TMPIT         TMPIT-like protein
       0.58    8.5  41.6       0.17   10.2  27.9    2.0  2  MAD           Mitotic checkpoint protein
        2.6    7.7  31.9       0.44   10.2   7.7    2.4  2  DUF745        Protein of unknown function (DUF745)
          8    7.2  26.8        1.3    9.7   3.1    4.1  4  DUF4404       Domain of unknown function (DUF4404)


Domain annotation for each model (and alignments):
>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5  14.9   2.7e-05     0.096     170     272 ..      14     116 ..       6     117 .. 0.93
   2 !   16.2  21.4     1e-06    0.0037     138     257 ..      46     166 ..      45     172 .. 0.93
   3 ?   -5.6  22.5       4.5   1.6e+04     160     246 ..     133     218 ..     122     222 .] 0.38

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.7e-05
        Spc7 170 peleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesev 268
                 +  +++ a+l++++e++ ++++ le+  +  L+++ +++++ k+++   +  l+++++qle+++  +++++e+  + ++++ eae+ le  k+ +e+++
  EPA06195.1  14 KTKKQKAANLRKKAERQLQQVRTLEKRSSSGLNSIDRKIESEKEDVTDVSGVLTQKTSQLESIQRLVTAASERLIREKDALVEAEQELEFAKNPEEENI 112
                 45567888******************************************************************************************* PP

        Spc7 269 srlk 272
                  + k
  EPA06195.1 113 AKSK 116
                 9987 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1e-06
        Spc7 138 egLkegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesid.keeLeelreelaelkaeieekkkelaelqeqleeleek 235
                 +++  ++e++ e++++ + +L+++ ++l+++   +++  ++l +e + l ea++ele  + +ee + ++++la ++++i+e++ e++++++  ++++e+
  EPA06195.1  46 NSIDRKIESEKEDVTDVSGVLTQKTSQLESIQRLVTAASERLIREKDALVEAEQELEFAKnPEEENIAKSKLAIINEKIQELEFEIKNREKTAKKITEE 144
                 6788889999999999999**************************************87769999********************************** PP

        Spc7 236 ieelkeqkseleeeiaeaervl 257
                 +++++e ks++ ++i+++ + +
  EPA06195.1 145 VSKINEIKSKISTQIQKQTKAK 166
                 ****************998865 PP

  == domain 3  score: -5.6 bits;  conditional E-value: 4.5
        Spc7 160 kqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqksel 246
                 ++e+ ++++ +e++ + +e+++++ ++ +++++ +   +e + e +++ ++  +e+e+k +  ++ ++ le+++++++el ++k+++
  EPA06195.1 133 NREKTAKKITEEVS-KINEIKSKISTQIQKQTKAKPTLRETMSESHKAAQKFAKELEQKIRSEESAKKALEKVNSRLQELLAKKRKM 218
                 33333333333322.222333333333333333333334444444444444444444444444444444555555554444444444 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   4.0   0.00031       1.1      34      95 ..       8      72 ..       3     110 .. 0.58
   2 ?    8.4  16.5   0.00031       1.1       2      86 ..     122     205 ..     121     220 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00031
       TMPIT 34 kcskeikkqkkrlkelksslkklkksvk...eeeeeeveelkeelkerkkvlkevesllpkkngl 95
                k+s+++k++k+++ +l+++ ++  ++v+   +++++ +++++++++++k+ + +v+ +l++k + 
  EPA06195.1  8 KISNSTKTKKQKAANLRKKAERQLQQVRtleKRSSSGLNSIDRKIESEKEDVTDVSGVLTQKTSQ 72
                34444444555544444444443333222224455556666666666666666666666666433 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00031
       TMPIT   2 eeweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlkeve 86 
                 e+++ele e+k+ e+tak++++++ ++++ +sk+s++i+kq+k    l++++++ +k++++  +e  +++++e  ++kk l++v+
  EPA06195.1 122 EKIQELEFEIKNREKTAKKITEEVSKINEIKSKISTQIQKQTKAKPTLRETMSESHKAAQKFAKELEQKIRSEE-SAKKALEKVN 205
                 7899***********************************************99999887644444444443332.2222233222 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2  27.9   4.6e-05      0.17      35     189 ..      12     165 ..       6     173 .. 0.85
   2 ?    8.5  20.6   0.00016      0.56     108     199 ..     119     211 ..     113     222 .] 0.85

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 4.6e-05
         MAD  35 kasalkrqleeesdrnqelqkrikllekreeekeealreqiElarlkkknlealnkkekekesklaearevisalknelaelkrqiekqelels.ekes 132
                  ++++k++ ++ +++ +  +++++ lekr +   ++   +iE ++      + ++  + +k+s+l++++ + +a  ++l + k  + ++e+el+ +k+ 
  EPA06195.1  12 STKTKKQKAANLRKKAERQLQQVRTLEKRSSSGLNSIDRKIESEK---EDVTDVSGVLTQKTSQLESIQRLVTAASERLIREKDALVEAEQELEfAKNP 107
                 445777788888888899999*********************999...7788899999********************999999998888888733444 PP

         MAD 133 .eleelqerldllkkklseleqliqqlekkqkelaeaeqrikeLefeiqsqeddsliv 189
                  e +  + +l + ++k++ele  i++ ek  k+ +e+  +i e++ +i+ q +++   
  EPA06195.1 108 eEENIAKSKLAIINEKIQELEFEIKNREKTAKKITEEVSKINEIKSKISTQIQKQTKA 165
                 1445567899***************************************988876654 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00016
         MAD 108 alknelaelkrqiekqelelsekeseleelqerldllkkklseleqliqqlekkqkelaeaeqri.keLefeiqsqeddslivknskselari 199
                  ++++++el+ +i++ e   ++ ++e+ +++e +    +++++ ++ + +l +  +e+ +a q+  keLe++i s e+ +  +++++s+l+ +
  EPA06195.1 119 IINEKIQELEFEIKNREKTAKKITEEVSKINEIKSKISTQIQKQTKAKPTLRETMSESHKAAQKFaKELEQKIRSEESAKKALEKVNSRLQEL 211
                 6899999************9*99********9999999999999999999988888887777775499*****************99999654 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   7.7   0.00012      0.44      86     163 ..      25     102 ..       7     113 .. 0.61
   2 ?    3.1  16.2     0.019        66      68     166 ..     121     216 ..     114     222 .] 0.87

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00012
      DUF745  86 qsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektqlleaAkkRveeLkkqlkearkdle 163
                 +++e++++ +++  k   + l+++ + +++ ke ++++  v ++  ++l++ + l++aA +R+ + k  l ea ++le
  EPA06195.1  25 KKAERQLQQVRTLEKRSSSGLNSIDRKIESEKEDVTDVSGVLTQKTSQLESIQRLVTAASERLIREKDALVEAEQELE 102
                 455666666666666666666666666666666666666666666666666666666666666666666666666655 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.019
      DUF745  68 eqelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektqlleaAkkRveeLkkqlkearkdlektk 166
                 +++++e e  +++ +k  ++  + ++  +++++++ +q++  +++  + +e++++++++a++ ++el++k    e+Akk +e+++++l+e  +   k +
  EPA06195.1 121 NEKIQELEFEIKNREKTAKKITEEVSKINEIKSKISTQIQKQTKAKPTLRETMSESHKAAQKFAKELEQKIRSEESAKKALEKVNSRLQELLA---KKR 216
                 56788888899999999999999999999**********************************************************998754...444 PP

>> DUF4404  Domain of unknown function (DUF4404)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   1.2      0.01        37       9      36 ..      28      55 ..      20      80 .. 0.81
   2 ?    0.0   2.2      0.39   1.4e+03      22      54 ..      90     125 ..      57     132 .. 0.60
   3 ?    7.6   3.6    0.0017       5.9       1      61 [.     120     184 ..     120     186 .. 0.71
   4 ?    9.7   3.1   0.00037       1.3       6      45 ..     181     220 ..     177     222 .] 0.90

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.01
     DUF4404  9 heeLeqnesldeetralLeslaedieel 36
                + +L+q+ +l++ + + L+s++++ie  
  EPA06195.1 28 ERQLQQVRTLEKRSSSGLNSIDRKIESE 55
                579**********************954 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.39
     DUF4404  22 tralLeslaedieellaeedaaaeeee...laerln 54 
                 +++ L ++++++e + + e+++ ++++   ++e+++
  EPA06195.1  90 EKDALVEAEQELEFAKNPEEENIAKSKlaiINEKIQ 125
                 555666666666655555555554444444444444 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0017
     DUF4404   1 LkelLekLheeLeqneslde...etralLeslaedieellaeedaaaeeee.laerlneaverFe 61 
                 ++e++++L+ e+++ e++ +   e+ +++++++++i+ +++++++a+++    + + ++a+++F+
  EPA06195.1 120 INEKIQELEFEIKNREKTAKkitEEVSKINEIKSKISTQIQKQTKAKPTLReTMSESHKAAQKFA 184
                 5788999999999777666512256667889999*********9999994444445566677776 PP

  == domain 4  score: 9.7 bits;  conditional E-value: 0.00037
     DUF4404   6 ekLheeLeqnesldeetralLeslaedieellaeedaaae 45 
                 +k  +eLeq+ + +e+ ++ Le++++ ++ella++ + a+
  EPA06195.1 181 QKFAKELEQKIRSEESAKKALEKVNSRLQELLAKKRKMAK 220
                 67789****************************9988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      4070  (0.227007); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); expected 358.6 (0.02)
Passed Vit filter:                       119  (0.00663729); expected 17.9 (0.001)
Passed Fwd filter:                        53  (0.0029561); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 1.10u 0.38s 00:00:01.48 Elapsed: 00:00:00.60
# Mc/sec: 1118.87
//
Query:       EPA06196.1  [L=101]
Description: PAP2 family protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.3e-17   61.4   0.9    8.4e-17   61.2   0.9    1.0  1  PAP2      PAP2 superfamily
    9.5e-10   38.5   1.7    1.1e-09   38.2   1.7    1.1  1  PAP2_3    PAP2 superfamily
    4.9e-06   27.0   0.1    6.4e-06   26.6   0.1    1.1  1  PAP2_C    PAP2 superfamily C-terminal
  ------ inclusion threshold ------
      0.034   14.3   0.6       0.33   11.1   0.6    2.0  1  DUF212    Divergent PAP2 family


Domain annotation for each model (and alignments):
>> PAP2  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.2   0.9   1.9e-20   8.4e-17      52     128 ..      16      87 ..       3      94 .. 0.90

  Alignments for each domain:
  == domain 1  score: 61.2 bits;  conditional E-value: 1.9e-20
        PAP2  52 akesfPSgHsafafalalllalllrrkrkkiglvllalillllavlvalsRlylgvHflsDvlaGlliGialaalay 128
                 ++ s+PSgH+a++  +a+++ + l +++++      a +l+l+ +lv+lsR+y+  H+++Dv++G+l+G++la ++ 
  EPA06196.1  16 FNASYPSGHAARTIIFAIVIGYALSERFPR-----GAYLLFLYPILVSLSRVYVLQHYPMDVIGGALLGVMLAGVLA 87 
                 35689*************************.....89***********************************98764 PP

>> PAP2_3  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   1.7   2.5e-13   1.1e-09     125     188 ..      18      83 ..       8      85 .. 0.88

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 2.5e-13
      PAP2_3 125 aafPSlHvawallvalalwrlrrkr..llrvlalllnvlmivatvatgnHYlvDviaGvalalvai 188
                 a+ PS H+a ++++a+++ +  + r  +  +l+ l+++l+ ++ v+   HY +Dvi+G++l+++ +
  EPA06196.1  18 ASYPSGHAARTIIFAIVIGYALSERfpRGAYLLFLYPILVSLSRVYVLQHYPMDVIGGALLGVMLA 83 
                 569***********999999999985566789999**************************99876 PP

>> PAP2_C  PAP2 superfamily C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.1   1.4e-09   6.4e-06       8      69 ..      22      83 ..      20      88 .. 0.95

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 1.4e-09
      PAP2_C  8 SGHtvvltlavlfileyspkklailkvillllallglfliiasrkHYtvDVllglyittlvf 69
                SGH++ +++++++i +  ++++    ++l+l+ +l +++ ++  +HY +DV+ g+++ +++ 
  EPA06196.1 22 SGHAARTIIFAIVIGYALSERFPRGAYLLFLYPILVSLSRVYVLQHYPMDVIGGALLGVMLA 83
                9******************************************************9999875 PP

>> DUF212  Divergent PAP2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.6   7.4e-05      0.33      59     127 ..      16      81 ..       4      82 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 7.4e-05
      DUF212  59 leegldsslfalalvfalivmyDAlgvRraagkqakvlnelveieeeklkellGHtpleVlvGallGii 127
                 ++  + s   a +++fa+++ y Al  R   g     l  ++ ++ +++  +l H p++V++GallG++
  EPA06196.1  16 FNASYPSGHAARTIIFAIVIGY-ALSERFPRGAYLLFLYPIL-VSLSRVY-VLQHYPMDVIGGALLGVM 81 
                 5555556666666666655555.7777777777777777777.3444554.789*************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 625.10
//
Query:       EPA06197.1  [L=103]
Description: hypothetical protein BG20_I2400 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 598.31
//
Query:       EPA06198.1  [L=70]
Description: ribosomal protein S28e [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.8e-27   94.5   4.4      3e-27   94.4   4.4    1.0  1  Ribosomal_S28e  Ribosomal protein S28e


Domain annotation for each model (and alignments):
>> Ribosomal_S28e  Ribosomal protein S28e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.4   4.4   1.7e-31     3e-27       2      64 .]       7      69 ..       6      69 .. 0.97

  Alignments for each domain:
  == domain 1  score: 94.4 bits;  conditional E-value: 1.7e-31
                    --EEEEEEEEEE---SSSSEEEEEEEE-S-SS-S-EEEEEEES---TT-EEEES--S--TT-- CS
  Ribosomal_S28e  2 eaklAeVikvlgrtGsrGevtqVrvellegkdkgriiiRnVkGPvreGDiLtLlEterEArrL 64
                    ++++ e+i+++grtG++Gev+qVrv++l+gkdkgri++RnVkG+vr G iL+L+EterEA+++
      EPA06198.1  7 DVTQSEIIQIVGRTGIAGEVIQVRVKVLSGKDKGRILTRNVKGSVRIGEILMLRETEREAKKI 69
                    68899********************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      196  (0.010932); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.30s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 495.09
//
Query:       EPA06199.1  [L=166]
Description: tRNA synthetase class II core domain (G, H, P, S and T), partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-26   93.1   0.0    2.1e-26   93.0   0.0    1.0  1  tRNA-synt_His  Histidyl-tRNA synthetase
    2.9e-12   46.9   0.1    4.3e-12   46.4   0.1    1.2  1  tRNA-synt_2b   tRNA synthetase class II core domain (G, H, P,
    0.00045   19.8   0.0    0.00056   19.5   0.0    1.2  1  tRNA-synt_2d   tRNA synthetases class II core domain (F)


Domain annotation for each model (and alignments):
>> tRNA-synt_His  Histidyl-tRNA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.0   0.0   3.4e-30   2.1e-26       1     159 [.       6     164 ..       6     166 .] 0.97

  Alignments for each domain:
  == domain 1  score: 93.0 bits;  conditional E-value: 3.4e-30
                    T---EETCHHHHHHHHHHHHHHHHHHTT-EEEE--SEEEHHHHCTTSTCCHH.HS-EEE-TTSSEEEE-SSSHHHHHHHHHHHHHTSS-EEEEEEE CS
  tRNA-synt_His   1 glrdllpeeaekieelrrrlldlfeswGYelVspPllEyldslltgagedld.qtfklvDqsgrllglRaDiTpqvaRiaahrlnrerplRlcYaG 95 
                    g++d+  +e ++ie++r+++ +l + +G++ V p+ +E l +l+t++g + + +++ ++D+ +r ++lR D+T+   R+a+   + + p+++  +G
     EPA06199.1   6 GMKDFEEQENANIEHIREHFKKLSNLYGFSFVDPSPIELLSVLETKSGPAIKdEIYYFKDKGDREVALRFDFTVGLTRYATLQKSMRLPAKFSAFG 101
                    799***********************************************8758*****************************99*********** PP

                    EEEESS-SSTT--CCEEEEEEEEESS-SHHHHHHHHHHHHHHHHHHCTSSSEEEEEEETCHHHH CS
  tRNA-synt_His  96 svlrtrpdglgrsreplQvGaEliGaegleadlEvlslllealeaaagvkelrldlghvglvra 159
                     v+r  + + gr r + Q  +E++G+ gle+++E+++l   +++ ++ +k++++d++h +lv++
     EPA06199.1 102 GVFRYDEPQKGRYRYFHQWDVEIYGKPGLESEAEIIELTSRLFD-SLLLKDIVIDINHRNLVES 164
                    *******************************************7.****************986 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4   0.1   7.2e-16   4.3e-12       1     104 [.      61     156 ..      61     163 .. 0.92

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 7.2e-16
                   EEEEETTSEEEEE-SSSHHHHHHHHHHHEEEBGGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGGHHHHHHHHHHHHHHHHHHTT.S CS
                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  tRNA-synt_2b   1 YkledrndreyiLkPtneetfvelirdevlrskrLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfhaeaslddslrdlikaisriferlgle 97 
                   Y ++d+ dre +L+   + ++++    +  +s rLP k+++++ ++R+ ++ ++G  R+r Fhq d +++++++   +s +++i+++sr+f +l+l+
    EPA06199.1  61 YYFKDKGDREVALRFDFTVGLTRYATLQ--KSMRLPAKFSAFGGVFRYDEP-QKG--RYRYFHQWDVEIYGKPG--LESEAEIIELTSRLFDSLLLK 150
                   889*******************999966..99*******************.***..*****************..8999***************99 PP

                   CEEEEEE CS
                   xxxxxxx RF
  tRNA-synt_2b  98 fraiiel 104
                      +i +
    EPA06199.1 151 DI-VIDI 156
                   66.4444 PP

>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   9.3e-08   0.00056      14     130 ..      13     123 ..       2     145 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 9.3e-08
                   SB-SHHHHHHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-ECESEEE-SSTHHHHHHHH...TTS-SSEEEEEE CS
  tRNA-synt_2d  14 gklhpltkvleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpekaveekllLRthttavqirtl...ekkkppikiisi 107
                    +   +++++e++k++   +gf+ v+ + +       + L v + ++  +++d  y  k++   ++++ LR   t    r+    ++ ++p+k+ ++
    EPA06199.1  13 QENANIEHIREHFKKLSNLYGFSFVDPSPI-------ELLSVLETKSGPAIKDEIYYFKDKG--DREVALRFDFTVGLTRYAtlqKSMRLPAKFSAF 100
                   555666777777777777777777777777.......5566666666666677666667777..799**********999988788889******** PP

                   EEEEBSST-SSSB-SEEEEEEEE CS
  tRNA-synt_2d 108 grvfRrdavDathlaeFhqvegl 130
                   g vfR d+  + +   Fhq +  
    EPA06199.1 101 GGVFRYDEPQKGRYRYFHQWDVE 123
                   *******************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1326.24
//
Query:       EPA06200.1  [L=45]
Description: YHS domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-17   62.5   1.2    3.2e-17   62.4   1.2    1.0  1  YHS              YHS domain
    0.00065   20.0   0.7    0.00082   19.7   0.7    1.2  1  Arc_trans_TRASH  Archaeal TRASH domain
  ------ inclusion threshold ------
      0.012   15.5   1.1      0.014   15.3   1.1    1.1  1  zf-FCS           MYM-type Zinc finger with FCS sequence motif
      0.034   13.7   0.1      0.038   13.5   0.1    1.0  1  FAP206           Domain of unknown function


Domain annotation for each model (and alignments):
>> YHS  YHS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.4   1.2   7.1e-21   3.2e-17       1      45 [.       1      43 [.       1      45 [] 0.94

  Alignments for each domain:
  == domain 1  score: 62.4 bits;  conditional E-value: 7.1e-21
         YHS  1 vtdPvcgmkvdkekaeekseYkGkeYyFcSegCkdkFedePekYa 45
                ++dPvcgm+v  +++   +eYkGk+Y Fc+++C+++Fe++P+++ 
  EPA06200.1  1 MKDPVCGMDV--GEKGDPLEYKGKKYMFCCASCRWAFEQNPDQFI 43
                69********..779999*************************97 PP

>> Arc_trans_TRASH  Archaeal TRASH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.7   1.8e-07   0.00082       9      33 ..      13      35 ..       5      38 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.8e-07
  Arc_trans_TRASH  9 vgePivyklknkvYyvCCktCksel 33
                     +g+P  +++k k Y +CC +C+  +
       EPA06200.1 13 KGDP--LEYKGKKYMFCCASCRWAF 35
                     3455..5667788********9777 PP

>> zf-FCS  MYM-type Zinc finger with FCS sequence motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   1.1   3.1e-06     0.014       9      38 ..       6      32 ..       5      35 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.1e-06
      zf-FCS  9 CkkyikgkpeftyvlendgvvgqFCStsCl 38
                C+ +   k +   +le++g+ + FC+ sC+
  EPA06200.1  6 CGMDVGEKGD---PLEYKGKKYMFCCASCR 32
                6666666777...9***************8 PP

>> FAP206  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   8.5e-06     0.038     226     253 ..      17      44 ..      15      45 .] 0.95

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.5e-06
      FAP206 226 lkykdkyyaFsseeaareFaadpdrfie 253
                 l+yk+k y F  +++  +F+++pd+fie
  EPA06200.1  17 LEYKGKKYMFCCASCRWAFEQNPDQFIE 44 
                 68************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 312.29
//
Query:       EPA06201.1  [L=293]
Description: radical SAM domain family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.9e-15   56.6   0.1    8.3e-15   55.6   0.0    1.6  2  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.6   0.0   4.6e-19   8.3e-15       2     158 ..      22     180 ..      21     191 .. 0.78
   2 ?   -2.2   0.0      0.27   4.9e+03      70      70 ..     238     238 ..     212     280 .. 0.55

  Alignments for each domain:
  == domain 1  score: 55.6 bits;  conditional E-value: 4.6e-19
                  EEESEESS-.-TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHH.HHTTSEEEEEESSTGGGS.TTHHHHHHHHHHTC.CCTEEEEEEECSSCHG...HH CS
                  xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx...xx RF
  Radical_SAM   2 vvtrgCnlr.CsfCarpetvrregrgrslsveeileevkelk.aekgvkevilgggeplly.pdfvellerlakla.vpgiritvetngtlpd...ee 92 
                   vt gC+++ CsfC+ ++     + + +++++e++ e++ ++ + ++++ ++l  g+ l   +++++++ ++ +++  +  ri++ + ++ +     e
   EPA06201.1  22 QVTLGCSFNeCSFCDMYR----SKQYSERPWDEVKLEIDLMAkQLPDTRKIFLADGDALNLdSEYIVKIVKYLHEKfPNLERISCYAMPMNILkksSE 115
                  5899*************5....8*******************77777*******997765425555555555555454444444444444444799** PP

                  HHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHH CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM  93 klerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGende 158
                   l+++ ++g+d ++lg+e+++d  vlk++ +g   + +++++ k++eag   ++ +i+gl G + +
   EPA06201.1 116 ELKKMHDAGLDMLYLGIESGSDI-VLKKVTKGAIAKTIIKSVNKAKEAGYIMSCMIILGLGGRTYS 180
                  ***********************.66666699*****************99888888888877764 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.27
                  H CS
                  x RF
  Radical_SAM  70 l 70 
                  +
   EPA06201.1 238 I 238
                  1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1936.95
//
Query:       EPA06202.1  [L=38]
Description: hypothetical protein BG20_I0560 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (38 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.30s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 246.08
//
Query:       EPA06203.1  [L=119]
Description: hypothetical protein BG20_I0564 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-08   33.8   4.4    3.4e-08   32.9   4.4    1.4  1  zinc_ribbon_2   zinc-ribbon domain
    1.9e-06   27.0   2.1    3.1e-06   26.4   2.1    1.3  1  zf-ribbon_3     zinc-ribbon domain
    5.5e-06   26.3   1.6    9.7e-06   25.5   1.6    1.4  1  DZR             Double zinc ribbon
    8.3e-05   23.3   0.2    0.00011   22.9   0.2    1.2  1  zinc_ribbon_15  zinc-ribbon family
    0.00021   21.3   4.0    0.00052   20.0   3.9    1.7  1  UPF0547         Uncharacterised protein family UPF0547
     0.0056   16.6   8.8       0.11   12.4   0.3    2.6  2  Nudix_N_2       Nudix N-terminal
  ------ inclusion threshold ------
      0.035   14.0   3.6        2.9    7.9   0.5    2.4  2  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
      0.041   13.6   1.7        2.1    8.2   0.2    2.3  2  A2L_zn_ribbon   A2L zinc ribbon domain
      0.062   13.0   5.6         20    4.9   5.6    2.2  1  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
      0.065   13.2   0.7      0.091   12.8   0.7    1.3  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.082   12.8   2.0       0.13   12.2   2.0    1.3  1  Prok-RING_1     Prokaryotic RING finger family 1
      0.085   11.6   0.4        0.1   11.4   0.4    1.1  1  NRDD            Anaerobic ribonucleoside-triphosphate reducta
       0.13   11.9   3.7        1.5    8.5   0.1    2.3  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
       0.34   10.9   2.9         12    6.0   2.9    2.2  1  ADK_lid         Adenylate kinase, active site lid
       0.36   11.0   6.5        3.8    7.8   6.8    2.2  2  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like
       0.58   10.5   4.0         25    5.3   4.0    2.3  1  GFA             Glutathione-dependent formaldehyde-activating
       0.75    9.4   2.9         20    4.8   2.9    2.1  1  RecR            RecR protein
       0.77    9.8   4.9         11    6.0   0.3    2.3  2  YhfH            YhfH-like protein
        1.2    8.8   5.9        3.9    7.2   0.8    2.2  2  zf-tcix         Putative treble-clef, zinc-finger, Zn-binding
        3.4    6.8   8.1        5.3    6.2   0.7    2.9  3  LisH_2          LisH


Domain annotation for each model (and alignments):
>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   4.4   3.8e-11   3.4e-08       1      21 [.      96     116 ..      96     117 .. 0.98

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 3.8e-11
  zinc_ribbon_2   1 fCpnCGaelqdnakFCpyCGt 21 
                    fC++CG++l+++akFCp+CGt
     EPA06203.1  96 FCSECGTTLSKTAKFCPECGT 116
                    9*******************8 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   2.1   3.5e-09   3.1e-06       3      24 ..      95     116 ..      94     118 .. 0.91

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 3.5e-09
  zf-ribbon_3   3 vrCPnCGaplssddnvCpyCGt 24 
                  ++C++CG+ ls+ +++Cp CGt
   EPA06203.1  95 KFCSECGTTLSKTAKFCPECGT 116
                  79******55***********8 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   1.6   1.1e-08   9.7e-06      10      36 ..      92     116 ..      84     119 .] 0.62

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1.1e-08
         DZR  10 pdarfCseCgtklkavaaedrCpsCge 36 
                 pd +fCseCgt+l+  +++++Cp+Cg+
  EPA06203.1  92 PDGKFCSECGTTLS--KTAKFCPECGT 116
                 45566666666665..44566666665 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.2   1.2e-07   0.00011      64      86 .]      86     115 ..      55     115 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.2e-07
  zinc_ribbon_15  64 e.......kkeCknCgkeveeefkyCpkCg 86 
                              k C++Cg+++++  k+Cp+Cg
      EPA06203.1  86 AfaepspdGKFCSECGTTLSKTAKFCPECG 115
                     0444445599*******************9 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   3.9   5.8e-07   0.00052       1      22 [.      95     116 ..      95     117 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 5.8e-07
     UPF0547   1 KvCPeCeakvPvaaqfCphCGy 22 
                 K C eC ++++  a+fCp+CG+
  EPA06203.1  95 KFCSECGTTLSKTAKFCPECGT 116
                 5699*****************8 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.3   0.00013      0.11       1      11 [.      95     105 ..      95     108 .. 0.89
   2 !    9.3   0.8    0.0011         1       1       8 [.     109     116 ..     109     118 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                 -B-TTT--B-E CS
   Nudix_N_2   1 kFCsqCGtpve 11 
                 kFCs+CGt+++
  EPA06203.1  95 KFCSECGTTLS 105
                 9*******987 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0011
                 -B-TTT-- CS
   Nudix_N_2   1 kFCsqCGt 8  
                 kFC++CGt
  EPA06203.1 109 KFCPECGT 116
                 8******8 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1    0.0069       6.2       2       8 ..      95     101 ..      95     107 .. 0.85
   2 ?    7.9   0.5    0.0032       2.9       2       8 ..     109     115 ..     108     116 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0069
                     EBESTTT CS
  RNA_POL_M_15KD   2 kFCpkCg 8  
                     kFC++Cg
      EPA06203.1  95 KFCSECG 101
                     7*****9 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0032
                     EBESTTT CS
  RNA_POL_M_15KD   2 kFCpkCg 8  
                     kFCp+Cg
      EPA06203.1 109 KFCPECG 115
                     7*****9 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1      0.03        27      21      30 ..      94     103 ..      92     105 .. 0.81
   2 ?    8.2   0.2    0.0023       2.1      23      31 ..     110     118 ..     108     119 .] 0.91

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.03
  A2L_zn_ribbon  21 ylvCieCgas 30 
                    + +C eCg++
     EPA06203.1  94 GKFCSECGTT 103
                    5699999975 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0023
  A2L_zn_ribbon  23 vCieCgasf 31 
                    +C+eCg+++
     EPA06203.1 110 FCPECGTTQ 118
                    9*****998 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   5.6     0.022        20       2      11 ..     107     116 ..      95     118 .. 0.46

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.022
  zf-NADH-PPase   2 thrFCgrCGa 11 
                    t +FC+ CG+
     EPA06203.1 107 TAKFCPECGT 116
                    3444444444 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.7    0.0001     0.091      72      95 ..      96     117 ..      76     119 .] 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.0001
                 EETTTS-EEECHHHHHS-TTTSSS CS
        HypA  72 rCreCgkefeleekalrCpkCgsa 95 
                  C+eCg++ ++++k   Cp+Cg++
  EPA06203.1  96 FCSECGTTLSKTAK--FCPECGTT 117
                 7*******997744..6****986 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   2.0   0.00014      0.13       4      30 ..      94     118 ..      91     119 .] 0.90

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
  Prok-RING_1   4 gkkCpvCgkelkeedDiVvCpeCgtpy 30 
                  gk C+ Cg +l++   +  CpeCgt +
   EPA06203.1  94 GKFCSECGTTLSKT--AKFCPECGTTQ 118
                  788**********9..899******75 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.4   0.00011       0.1     496     528 ..      83     117 ..      67     119 .] 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
                 TT--EEEEE--EEEETT.--..EESSSB-TTT--B CS
        NRDD 496 tgigYfsinpkidvCnecgy..kgeiekCpkCgse 528
                 +g  +++ +p+ ++C ecg+  +++ + Cp+Cg +
  EPA06203.1  83 YGNAFAEPSPDGKFCSECGTtlSKTAKFCPECGTT 117
                 5666777889999*******87777799*****65 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.1    0.0016       1.5       2      15 ..      94     107 ..      93     110 .. 0.82
   2 ?    4.8   0.5     0.023        21       3      10 ..     109     116 ..     107     117 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0016
      zf_UBZ   2 tylCerCgkeipes 15 
                   +C++Cg++++ +
  EPA06203.1  94 GKFCSECGTTLSKT 107
                 679******99876 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.023
      zf_UBZ   3 ylCerCgk 10 
                  +C++Cg+
  EPA06203.1 109 KFCPECGT 116
                 58****97 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   2.9     0.014        12       9      31 ..      81     104 ..      77     117 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.014
                 -EEETTT.B--SSTTB-TTT--.- CS
     ADK_lid   9 rsYhvvf.npPkveglCDkCGepL 31 
                  +Y  +f  p     +C +CG +L
  EPA06203.1  81 NVYGNAFaEPSPDGKFCSECGTTL 104
                 566446644445555677777766 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.6     0.009       8.1      23      37 ..      94     107 ..      86     109 .. 0.78
   2 ?    7.8   6.8    0.0042       3.8      10      31 ..      96     116 ..      94     118 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.009
  NOB1_Zn_bind  23 kkFCpkCGnktLkrv 37 
                    kFC++CG  tL ++
    EPA06203.1  94 GKFCSECGT-TLSKT 107
                   58******5.67776 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0042
  NOB1_Zn_bind  10 rChaCfkvtkdmtkkFCpkCGn 31 
                    C  C ++ +++  kFCp+CG 
    EPA06203.1  96 FCSECGTTLSKTA-KFCPECGT 116
                   5999999888765.6******7 PP

>> GFA  Glutathione-dependent formaldehyde-activating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   4.0     0.028        25      51      63 ..      96     108 ..      64     118 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.028
         GFA  51 fCpeCgsplysee 63 
                 fC+eCg++l  + 
  EPA06203.1  96 FCSECGTTLSKTA 108
                 5555555554332 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   2.9     0.022        20      17      34 ..      95     114 ..      93     118 .. 0.58

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.022
                 EE-TTT--E..ESSSS-CCC CS
        RecR  17 rhCsrCgnl..teedlCaIC 34 
                 ++Cs+Cg+    +   C+ C
  EPA06203.1  95 KFCSECGTTlsKTAKFCPEC 114
                 57777777642222356666 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.3     0.013        11      14      23 ..      95     104 ..      92     108 .. 0.83
   2 ?    5.7   0.7     0.017        15      13      21 ..     108     116 ..     106     118 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.013
        YhfH  14 KkCteCGkei 23 
                 K C+eCG  +
  EPA06203.1  95 KFCSECGTTL 104
                 89*****876 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.017
        YhfH  13 kKkCteCGk 21 
                 +K C+eCG 
  EPA06203.1 108 AKFCPECGT 116
                 699*****6 PP

>> zf-tcix  Putative treble-clef, zinc-finger, Zn-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   1.5     0.012        11      11      27 ..      95     111 ..      95     111 .. 0.85
   2 ?    7.2   0.8    0.0043       3.9      11      18 ..     109     116 ..     103     118 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.012
     zf-tcix  11 rkCpkCGtyNGtRglsC 27 
                 + C++CGt   + +++C
  EPA06203.1  95 KFCSECGTTLSKTAKFC 111
                 56******988888888 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0043
     zf-tcix  11 rkCpkCGt 18 
                 + Cp+CGt
  EPA06203.1 109 KFCPECGT 116
                 67*****9 PP

>> LisH_2  LisH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.1     1e+03       6      16 ..      11      21 ..      11      23 .. 0.74
   2 ?    4.3   0.4     0.023        20      21      27 ..      96     102 ..      96     103 .. 0.90
   3 ?    6.2   0.7    0.0059       5.3      21      27 ..     110     116 ..     110     117 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.1
      LisH_2  6 aeYLqsqgYnY 16
                +eY+ ++ + +
  EPA06203.1 11 QEYMSKHTLAF 21
                59999987665 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.023
      LisH_2  21 FlPEsGl 27 
                 F++E+G+
  EPA06203.1  96 FCSECGT 102
                 9*****7 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.0059
      LisH_2  21 FlPEsGl 27 
                 F+PE+G+
  EPA06203.1 110 FCPECGT 116
                 9*****7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 736.10
//
Query:       EPA06204.1  [L=250]
Description: hypothetical protein BG20_I0567 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-06   27.3   9.5    0.00031   20.7   3.3    2.5  2  DZR              Double zinc ribbon
    5.5e-06   26.4   0.5      1e-05   25.5   0.5    1.4  1  PRC              PRC-barrel domain
    1.6e-05   24.4   7.0    1.6e-05   24.4   7.0    2.3  3  zinc_ribbon_2    zinc-ribbon domain
    5.7e-05   23.8   3.6      0.058   14.2   0.2    2.3  2  zinc_ribbon_15   zinc-ribbon family
    0.00018   21.8   1.0          6    7.3   0.0    3.4  3  GFA              Glutathione-dependent formaldehyde-activatin
  ------ inclusion threshold ------
      0.043   14.0  10.7        2.1    8.6   0.8    3.2  3  zf-B_box         B-box zinc finger
      0.094   12.7  12.0       0.99    9.4   1.8    3.1  3  zinc-ribbons_6   zinc-ribbons
       0.12   12.7   9.4         11    6.3   0.0    3.8  3  Prim_Zn_Ribbon   Zinc-binding domain of primase-helicase
       0.39   10.5   0.1       0.39   10.5   0.1    4.3  3  A2L_zn_ribbon    A2L zinc ribbon domain
       0.54   10.3   7.4          3    7.9   0.5    2.5  2  HypA             Hydrogenase/urease nickel incorporation, met
        1.3    8.8  10.2        3.5    7.4   0.1    4.1  4  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
        1.4    9.2   5.9        1.9    8.8   0.1    3.0  3  zf-AD            Zinc-finger associated domain (zf-AD)
        1.7    8.6   8.8         14    5.6   0.1    3.3  3  PHD              PHD-finger
        2.3    8.8  10.2        5.2    7.6   2.1    2.6  2  zf-CHY           CHY zinc finger
        2.8    8.8   0.0        2.8    8.8   0.0    3.4  3  Tnp_zf-ribbon_2  DDE_Tnp_1-like zinc-ribbon
        3.9    7.2  12.9         19    5.0   0.2    4.1  4  zf_UBZ           Ubiquitin-Binding Zinc Finger
        5.4    7.3   7.8         15    5.9   0.2    2.8  3  DUF2197          Uncharacterized protein conserved in bacteri


Domain annotation for each model (and alignments):
>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.4   0.00067       0.7      12      42 ..      51     101 ..      44     106 .. 0.88
   2 !   20.7   3.3   2.9e-07   0.00031       1      23 [.     228     250 .]     228     250 .] 0.97

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00067
         DZR  12 arfCseCgtklkavaa....................edrCpsCgekvdpea 42 
                 + fC++C ++ + +++                    ++ C  C++ + +  
  EPA06204.1  51 KYFCNTCEKEFEGPPKieyenpneevaenlilaekgQYICNTCSATIAEYR 101
                 56********9999999999***********************99876665 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 2.9e-07
         DZR   1 CpqCgeelppdarfCseCgtklk 23 
                 C++Cg  ++++++fC+eCg+kl+
  EPA06204.1 228 CAKCGFSNKEGSKFCEECGSKLQ 250
                 ********************996 PP

>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.5   9.6e-09     1e-05       6      72 ..     155     213 ..     152     220 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 9.6e-09
                 S---TT-EEEETTSSEEEEEEEEEEETTTTEEEEEEEEETTT.....-EEEEEGG.CEECCCTEEEE CS
         PRC   6 asdliGkeVytedGeklGkVkDvvidekegrvralvvsvggflgigekevliPfdlavkigkdriiv 72 
                 +s+++G++Vy+e+ +k+Gk k v id  ++ v+ l+++  g       e  +P+  +++ ++ +i++
  EPA06204.1 155 ISSIEGLSVYDENARKIGKAKQVGIDS-NQSVVLLIIKNDG------TEGSVPWS-NIRKVGEIILL 213
                 89************************8.6666666666654......6668****.99999888876 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   1.1       4.9   5.2e+03       1       7 [.      53      59 ..      53      60 .. 0.61
   2 ?   -3.0   0.1       6.5   6.9e+03       2       9 ..      90      97 ..      89     100 .. 0.68
   3 !   24.4   7.0   1.5e-08   1.6e-05       1      23 []     227     249 ..     227     249 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 4.9
  zinc_ribbon_2  1 fCpnCGa 7 
                   fC  C +
     EPA06204.1 53 FCNTCEK 59
                   6777755 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 6.5
  zinc_ribbon_2  2 CpnCGael 9 
                   C  C a++
     EPA06204.1 90 CNTCSATI 97
                   77787666 PP

  == domain 3  score: 24.4 bits;  conditional E-value: 1.5e-08
  zinc_ribbon_2   1 fCpnCGaelqdnakFCpyCGtpl 23 
                    +C +CG  +++++kFC++CG++l
     EPA06204.1 227 KCAKCGFSNKEGSKFCEECGSKL 249
                    8*******************997 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.3   0.00073      0.77      36      81 ..      50     103 ..      34     106 .. 0.74
   2 !   14.2   0.2   5.5e-05     0.058      61      86 .]     221     246 ..     194     246 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00073
  zinc_ribbon_15  36 pylacskCkslleaskelgkeiekkesse........kkeCknCgkeveeefky 81 
                     + + c++C++ +e   + + e  ++e +e        +++C+ C++++ e  ++
      EPA06204.1  50 TKYFCNTCEKEFEGPPKIEYENPNEEVAEnlilaekgQYICNTCSATIAEYREF 103
                     3457********9999666666665555599***************99876655 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 5.5e-05
  zinc_ribbon_15  61 essekkeCknCgkeveeefkyCpkCg 86 
                     ++s+  +C++Cg + +e +k+C +Cg
      EPA06204.1 221 QQSQPGKCAKCGFSNKEGSKFCEECG 246
                     4555789******************9 PP

>> GFA  Glutathione-dependent formaldehyde-activating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.014        15      44      58 ..      46      60 ..       8      72 .. 0.80
   2 !    7.3   0.0    0.0057         6      48      78 ..      86     116 ..      74     128 .. 0.85
   3 ?    5.5   0.3      0.02        22      44      59 ..     234     249 ..     211     250 .] 0.72

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.014
         GFA 44 gnkvtrsfCpeCgsp 58
                ++k+t++fC++C  +
  EPA06204.1 46 SQKITKYFCNTCEKE 60
                7899********875 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0057
         GFA  48 trsfCpeCgsplyseesaapevvivrvGtld 78 
                  +++C++C +++   ++ ++++ +v+vG+  
  EPA06204.1  86 GQYICNTCSATIAEYREFKKQNEMVEVGSAK 116
                 579**********99***********99865 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.02
         GFA  44 gnkvtrsfCpeCgspl 59 
                 +nk   +fC+eCgs+l
  EPA06204.1 234 SNKEGSKFCEECGSKL 249
                 4555568******987 PP

>> zf-B_box  B-box zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.6     0.006       6.3      12      23 ..      48      59 ..      45      61 .. 0.83
   2 ?    4.0   0.1     0.053        56      15      23 ..      87      95 ..      83      97 .. 0.56
   3 ?    8.6   0.8     0.002       2.1       2      24 ..     224     248 ..     223     249 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.006
    zf-B_box 12 kpatlfCedCqq 23
                k +++fC++C++
  EPA06204.1 48 KITKYFCNTCEK 59
                6689******96 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.053
    zf-B_box 15 tlfCedCqq 23
                ++ C++C++
  EPA06204.1 87 QYICNTCSA 95
                555555554 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.002
    zf-B_box   2 eetkCpeHk..nkpatlfCedCqqp 24 
                 +  kC +++  nk+ + fCe+C++ 
  EPA06204.1 224 QPGKCAKCGfsNKEGSKFCEECGSK 248
                 667999999988**********975 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   2.8     0.015        16      14      58 ..      49      96 ..      39     102 .. 0.54
   2 ?    3.7   0.2      0.06        63      13      26 ..      84      97 ..      73     112 .. 0.69
   3 ?    9.4   1.8   0.00094      0.99      12      40 ..     221     250 .]     215     250 .] 0.81

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.015
                    SSEEE-TTT--EEEEEEE-...SSS-S---EEEETTEEEE--TTTT-- CS
  zinc-ribbons_6 14 geqyhCeaCqedlkkealC...peCeqelevlkaCgavdyfCnkcneL 58
                     ++y+C++C+++++  +     +  e+  e l    + +y+Cn+c + 
      EPA06204.1 49 ITKYFCNTCEKEFEGPPKIeyeNPNEEVAENLILAEKGQYICNTCSAT 96
                    478888888886653222200022233333344444445777777655 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.06
                    -SSEEE-TTT--EE CS
  zinc-ribbons_6 13 rgeqyhCeaCqedl 26
                    ++ qy C++C++ +
      EPA06204.1 84 EKGQYICNTCSATI 97
                    45677777777644 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.00094
                     E-SSEEE-TTT--.EEEEEEE-SSS-S--- CS
  zinc-ribbons_6  12 krgeqyhCeaCqe.dlkkealCpeCeqele 40 
                     ++++  +C +C   + +  ++C+eC+++l+
      EPA06204.1 221 QQSQPGKCAKCGFsNKEGSKFCEECGSKLQ 250
                     5667889****964778899*******997 PP

>> Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1     0.013        14      25      33 ..      51      59 ..      42      64 .. 0.79
   2 ?    6.3   0.0     0.011        11      23      31 ..      85      93 ..      71      98 .. 0.85
   3 ?    0.7   4.2      0.65   6.8e+02      23      32 ..     237     246 ..     223     249 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.013
                    -EEETTTTB CS
  Prim_Zn_Ribbon 25 twfCrqCgg 33
                     +fC++C++
      EPA06204.1 51 KYFCNTCEK 59
                    69*****88 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.011
                    .S-EEETTT CS
  Prim_Zn_Ribbon 23 rGtwfCrqC 31
                    +G ++C++C
      EPA06204.1 85 KGQYICNTC 93
                    59******* PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.65
                     .S-EEETTTT CS
  Prim_Zn_Ribbon  23 rGtwfCrqCg 32 
                      G+ fC +Cg
      EPA06204.1 237 EGSKFCEECG 246
                     399******5 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.5      0.15   1.5e+02      22      31 ..      52      61 ..      50      62 .. 0.81
   2 ?   10.5   0.1   0.00037      0.39      12      30 ..      79      96 ..      77      98 .. 0.88
   3 ?   -2.1   5.7       3.3   3.5e+03      20      28 ..     238     246 ..     223     248 .. 0.64

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.15
  A2L_zn_ribbon 22 lvCieCgasf 31
                   ++C+ C+ +f
     EPA06204.1 52 YFCNTCEKEF 61
                   89****9665 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00037
  A2L_zn_ribbon 12 ngilnseqgylvCieCgas 30
                   n il +e+g ++C+ C+a+
     EPA06204.1 79 NLIL-AEKGQYICNTCSAT 96
                   6778.***********996 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 3.3
  A2L_zn_ribbon  20 gylvCieCg 28 
                    g  +C eCg
     EPA06204.1 238 GSKFCEECG 246
                    445777777 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   1.4     0.018        19      70      95 ..      51      96 ..      43     110 .. 0.77
   2 ?    7.9   0.5    0.0028         3      69      95 ..     224     248 ..     203     250 .] 0.75

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.018
                EEEETTTS-EEECHHH.HH...................S-TTTSSS CS
        HypA 70 kvrCreCgkefeleek.al...................rCpkCgsa 95
                k+ C++C+kefe   k ++                    C++C+++
  EPA06204.1 51 KYFCNTCEKEFEGPPKiEYenpneevaenlilaekgqyICNTCSAT 96
                678********95544334668889999999999999999999875 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0028
                 -EEEETTTS-EEECHHHHHS-TTTSSS CS
        HypA  69 vkvrCreCgkefeleekalrCpkCgsa 95 
                    +C +Cg + ++   +  C++Cgs+
  EPA06204.1 224 QPGKCAKCGFSNKEG--SKFCEECGSK 248
                 4579*****555544..345*****85 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.34   3.6e+02       1      11 [.      52      62 ..      52      66 .. 0.86
   2 ?    1.6   0.3      0.21   2.2e+02       1       8 [.      88      95 ..      88      99 .. 0.86
   3 ?    7.4   0.1    0.0034       3.5      10      25 ..     218     233 ..     215     234 .. 0.91
   4 ?    2.1   0.2      0.15   1.5e+02      20      26 ..     242     248 ..     241     249 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.34
                    -B-SSS--B-- CS
  DNA_RNApol_7kD  1 YiCgeCgaevs 11
                    Y C  C++e++
      EPA06204.1 52 YFCNTCEKEFE 62
                    99*****9976 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.21
                    -B-SSS-- CS
  DNA_RNApol_7kD  1 YiCgeCga 8 
                    YiC  C+a
      EPA06204.1 88 YICNTCSA 95
                    9*****87 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0034
                     ----SSS----SSS-- CS
  DNA_RNApol_7kD  10 vslkkgdpiRCkeCGh 25 
                     v+++++ p +C +CG+
      EPA06204.1 218 VEIQQSQPGKCAKCGF 233
                     89*************8 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.15
                     -SSS--- CS
  DNA_RNApol_7kD  20 CkeCGhR 26 
                     C eCG++
      EPA06204.1 242 CEECGSK 248
                     9999987 PP

>> zf-AD  Zinc-finger associated domain (zf-AD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.55   5.8e+02      41      56 ..      46      61 ..      36      63 .. 0.81
   2 ?    8.8   0.1    0.0018       1.9      45      65 ..      86     106 ..      82     111 .. 0.89
   3 ?   -0.0   0.8         1   1.1e+03      44      57 ..     237     250 .]     221     250 .] 0.79

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.55
       zf-AD 41 ddslpekiCesClekl 56
                ++++ ++ C++C +++
  EPA06204.1 46 SQKITKYFCNTCEKEF 61
                67788999****8876 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0018
       zf-AD  45 pekiCesCleklqefyeFrek 65 
                 +++iC++C + + e  eF+++
  EPA06204.1  86 GQYICNTCSATIAEYREFKKQ 106
                 579***************987 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 1
       zf-AD  44 lpekiCesCleklq 57 
                  + k Ce+C +klq
  EPA06204.1 237 EGSKFCEECGSKLQ 250
                 45578999999986 PP

>> PHD  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1     0.014        14      39      51 ..      47      59 ..      40      60 .. 0.71
   2 ?    4.8   0.0     0.024        25      40      50 ..      84      94 ..      67      96 .. 0.73
   3 ?    0.4   2.4      0.57     6e+02       2      23 ..     228     247 ..     226     249 .. 0.56

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.014
                HHSSTBSSTTTHT CS
         PHD 39 kpegewlCekCke 51
                ++ ++++C++C++
  EPA06204.1 47 QKITKYFCNTCEK 59
                23348******86 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.024
                HSSTBSSTTTH CS
         PHD 40 pegewlCekCk 50
                ++g+++C++C+
  EPA06204.1 84 EKGQYICNTCS 94
                3449******7 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.57
                 BTTTTSTTSTTSCEEEETTTSC CS
         PHD   2 CavCkkksdeeeelvqCdgCkr 23 
                 Ca C+    ++e   +C++C++
  EPA06204.1 228 CAKCGF--SNKEGSKFCEECGS 247
                 666666..33333446777764 PP

>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   2.1    0.0049       5.2      19      67 ..      51     100 ..      43     110 .. 0.76
   2 ?    5.2   1.2     0.029        31      50      73 ..     221     246 ..     214     250 .] 0.56

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0049
      zf-CHY  19 lyaCreCHeele.dhelerlevkevlcllCeteqekavlCkkCkkefaey 67 
                  y C++C +e e   ++e  + +e ++ +   +++ + +C++C+ ++aey
  EPA06204.1  51 KYFCNTCEKEFEgPPKIEYENPNEEVAENLILAEKGQYICNTCSATIAEY 100
                 47899999886635566666666666777777778899999999999999 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.029
      zf-CHY  50 eqekavlCkkCkk..efaeyfCpiCk 73 
                 +q++  +C kC+   + ++ fC+ C 
  EPA06204.1 221 QQSQPGKCAKCGFsnKEGSKFCEECG 246
                 44555567777553233333577775 PP

>> Tnp_zf-ribbon_2  DDE_Tnp_1-like zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0    0.0027       2.8      12      24 ..      47      59 ..      40      65 .. 0.85
   2 ?    2.2   0.1      0.32   3.4e+02      16      23 ..      87      94 ..      83     100 .. 0.80
   3 ?   -0.5   3.3       2.2   2.3e+03       3      23 ..     228     246 ..     226     249 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0027
  Tnp_zf-ribbon_2 12 kkeTriiCqeCdv 24
                     +k T+++C+ C +
       EPA06204.1 47 QKITKYFCNTCEK 59
                     566********75 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.32
  Tnp_zf-ribbon_2 16 riiCqeCd 23
                      +iC+ C 
       EPA06204.1 87 QYICNTCS 94
                     68999995 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 2.2
  Tnp_zf-ribbon_2   3 CkvClkkkikkeTriiCqeCd 23 
                      C  C   + +     +C eC+
       EPA06204.1 228 CAKCGFSNKEG--SKFCEECG 246
                      66665544443..45799996 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.3     0.031        33       2      13 ..      51      62 ..      50      68 .. 0.85
   2 ?    4.3   0.1     0.029        30       2      14 ..      87      99 ..      86     103 .. 0.86
   3 ?    0.1   0.3      0.61   6.4e+02       4      10 ..     227     233 ..     226     236 .. 0.85
   4 ?    5.0   0.2     0.018        19       2      11 ..     239     248 ..     238     250 .] 0.81

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.031
      zf_UBZ  2 tylCerCgkeip 13
                 y+C  C ke++
  EPA06204.1 51 KYFCNTCEKEFE 62
                69*******997 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.029
      zf_UBZ  2 tylCerCgkeipe 14
                +y+C  C ++i e
  EPA06204.1 87 QYICNTCSATIAE 99
                7*********987 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.61
      zf_UBZ   4 lCerCgk 10 
                  C++Cg 
  EPA06204.1 227 KCAKCGF 233
                 5****95 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.018
      zf_UBZ   2 tylCerCgke 11 
                 + +Ce+Cg++
  EPA06204.1 239 SKFCEECGSK 248
                 579*****87 PP

>> DUF2197  Uncharacterized protein conserved in bacteria (DUF2197)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.2     0.015        15      23      39 ..      43      59 ..      40      67 .. 0.87
   2 ?    5.5   0.3     0.019        20      31      43 ..      87      99 ..      66     107 .. 0.82
   3 ?   -2.3   0.1       5.4   5.7e+03      33      41 ..     241     249 ..     240     250 .] 0.79

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.015
     DUF2197 23 rLrNrpihtYmCkeCee 39
                rL  ++i  Y+C++Ce+
  EPA06204.1 43 RLDSQKITKYFCNTCEK 59
                7788999********97 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.019
     DUF2197 31 tYmCkeCeeRiae 43
                 Y+C++C+  iae
  EPA06204.1 87 QYICNTCSATIAE 99
                7*******99987 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 5.4
     DUF2197  33 mCkeCeeRi 41 
                 +C+eC +++
  EPA06204.1 241 FCEECGSKL 249
                 59***8765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       807  (0.0450109); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        29  (0.00161749); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1861.41
//
Query:       EPA06205.1  [L=133]
Description: thioredoxin [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.3e-29  100.2   0.1    7.6e-29   99.7   0.1    1.3  1  Thioredoxin    Thioredoxin
    4.2e-07   30.4   0.1    1.5e-06   28.6   0.1    1.8  1  Thioredoxin_2  Thioredoxin-like domain
    4.7e-07   29.6   0.4    7.4e-07   29.0   0.4    1.4  1  Thioredoxin_9  Thioredoxin
    1.3e-06   28.6   0.2    5.8e-06   26.5   0.1    2.1  1  Thioredoxin_8  Thioredoxin-like
    4.4e-06   26.3   0.7    8.4e-06   25.3   0.7    1.5  1  OST3_OST6      OST3 / OST6 family, transporter family
      6e-05   22.1   0.0    6.6e-05   22.0   0.0    1.1  1  Phosducin      Phosducin
    0.00096   18.9   0.0     0.0012   18.6   0.0    1.2  1  Redoxin        Redoxin
     0.0014   18.7   0.1     0.0025   17.9   0.1    1.5  1  Thioredoxin_7  Thioredoxin-like
      0.007   16.3   0.0        0.2   11.7   0.0    2.0  2  HyaE           Hydrogenase-1 expression protein HyaE
     0.0071   16.2   0.1     0.0094   15.8   0.1    1.2  1  TraF           F plasmid transfer operon protein
      0.008   16.1   0.0       0.01   15.8   0.0    1.2  1  AhpC-TSA       AhpC/TSA family
  ------ inclusion threshold ------
      0.079   13.2   0.1        0.2   11.9   0.0    1.7  2  Glutaredoxin   Glutaredoxin


Domain annotation for each model (and alignments):
>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.7   0.1   5.1e-32   7.6e-29       3      94 ..      32     121 ..      30     130 .. 0.94

  Alignments for each domain:
  == domain 1  score: 99.7 bits;  conditional E-value: 5.1e-32
                  EESSHHHHHHHHTTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTEEEEEEESS-HH CS
  Thioredoxin   3 lvltkenFeeevakekklvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkngkevkkyegarek 94 
                  + l+++nF+e +++  ++ lv+F+A+wCg+Ck++ P++e+l++++  k+k+a+v+vd+n+++a +++v++iP +++fk+g+ v+k+ ga  +
   EPA06205.1  32 VDLNNSNFNEIISS-VNPTLVDFWAEWCGPCKMMHPVFESLSSKYP-KIKFARVNVDQNQNIAMRFAVQSIPMFIMFKSGQIVDKMMGAVGA 121
                  6799*********9.9******************************.****************************************99765 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.1     1e-09   1.5e-06       6     101 ..      47     120 ..      42     125 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 1e-09
  Thioredoxin_2   6 kpvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPtiv.fldgkeivarlpGyv 100
                     p+lv+f++++C+ Ck ++ ++++l    ++       p+++++ v+++++++              a ++ v++ P ++ f  g+ iv+++ G+v
     EPA06205.1  47 NPTLVDFWAEWCGPCKMMHPVFESL--SSKY-------PKIKFARVNVDQNQNI-------------AMRFAVQSIPMFImFKSGQ-IVDKMMGAV 119
                    699**********************..3334.......7778888888888876.............5899*******88466666.*****9998 PP

  Thioredoxin_2 101 p 101
                     
     EPA06205.1 120 G 120
                    5 PP

>> Thioredoxin_9  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.4     5e-10   7.4e-07      48     107 ..      53     109 ..       9     118 .. 0.89

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 5e-10
                    E--TT-HHHHHHHHHHHHHHHH-TTEEEEEE-HHHHHHHTTTTTT-SS--SSEEEEE-TT CS
  Thioredoxin_9  48 ltedwCgDaavnvPvlakiaelnpnievkillrdenlelmdqyltngaraiPtliildee 107
                    + ++wCg + ++ Pv++ +++  p+i++  +  d+n+++  ++     ++iP++i+++++
     EPA06205.1  53 FWAEWCGPCKMMHPVFESLSSKYPKIKFARVNVDQNQNIAMRF---AVQSIPMFIMFKSG 109
                    5689***************************************...56********9865 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.1   3.9e-09   5.8e-06       3      67 ..      48     107 ..      46     126 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 3.9e-09
                    EEEEEE--SSSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-SS-HHHHHHHGGGS-TTSEE.EE- CS
  Thioredoxin_8   3 vvlLyfgaswcppckaftpklkelyeklkkkkkveivyvsldkkeeefekylkknkkpwlsvpfd 67 
                     +l+ f+a+wc pck ++p    l++k+    k+++  v++d++++   ++  +    ++++ f+
     EPA06205.1  48 PTLVDFWAEWCGPCKMMHPVFESLSSKYP---KIKFARVNVDQNQNIAMRFAVQS--IPMFIMFK 107
                    589*************************6...***********987665555444..45555555 PP

>> OST3_OST6  OST3 / OST6 family, transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.7   5.7e-09   8.4e-06      11     104 ..      29     108 ..      16     119 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 5.7e-09
   OST3_OST6  11 ngviklndenykellkgprdysvvvllTatspqfkCelCrefepefelvakswrkdekskskklfFakvdfdegkdvFqklglnsaPhlllfpp 104
                  g+++ln++n++e++++  +  ++v + a+     C +C+ ++p fe +++ + k          Fa+v++d+++++ +++ ++s+P +++f++
  EPA06205.1  29 PGIVDLNNSNFNEIISSVNP--TLVDFWAE----WCGPCKMMHPVFESLSSKYPKI--------KFARVNVDQNQNIAMRFAVQSIPMFIMFKS 108
                 58999999999999964443..55666665....6**************9998777........4***************************97 PP

>> Phosducin  Phosducin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   4.4e-08   6.6e-05     105     214 ..       9     115 ..       1     121 [. 0.72

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 4.4e-08
                 HHHHHHHHHHHHHH-------S.EEE--SHHHHHHHHHSS-TT-EEEEEEE-TTSTTHHHHHHHHHHHHHH-TTSEEEEEEHH.HH--TTSS-TTT-SE CS
   Phosducin 105 kyrkqrmdemrqklskgprfkf.vlelesgeqfldtidkeqkitlivvhiyedgvkgtealnssliclaaeyptvkfckvkas.vigasdrfsrdvlpa 201
                 k ++++++em ++    p+ k  +++l+   +f ++i     +   +v  + +    ++ +   +  l+++yp +kf +v+   +   + rf+ + +p 
  EPA06205.1   9 KIKQRKLEEMIRQQ-NQPQIKPgIVDLN-NSNFNEIISS---VNPTLVDFWAEWCGPCKMMHPVFESLSSKYPKIKFARVNVDqNQNIAMRFAVQSIPM 102
                 55556666665443.3455554144444.3456666654...3344677888888889999999****************975277899********** PP

                 EEEEETTEEEEEE CS
   Phosducin 202 llvykagellsnf 214
                 ++++k+g+++  +
  EPA06205.1 103 FIMFKSGQIVDKM 115
                 ********99876 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   7.7e-07    0.0012      29      97 ..      47     112 ..      25     130 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 7.7e-07
                 SEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHH.HHHHHHHTT-TSEEEE-TTSHH CS
     Redoxin  29 kkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndaf.vkefwgkeglkfpvlsDgsaaf 97 
                 ++++v f++  +c++C+  hp +e l+ ++ +   ++  v++d+++  +++f+ +   +++++   ++ +
  EPA06205.1  47 NPTLVDFWAE-WCGPCKMMHPVFESLSSKYPKI--KFARVNVDQNQNiAMRFAVQSI-PMFIMFKSGQIV 112
                 5689******.***************9997665..5555888888887888887766.444444444444 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.1   1.7e-06    0.0025      19      82 ..      48     107 ..      36     108 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.7e-06
                    -EEEEE--TT-HHHHHHHHHHHH-HHHHH.HHHT-EEEEESS--S-GGG.-TT---SSEEEEE- CS
  Thioredoxin_7  19 pvlvffgaswcftCqalerdflsdeevkaalaekfvllrvdvterdanileldeqgvPvvafld 82 
                    p lv+f a+wc++C+ +  +f+s  +  +  + kf+ ++vd  ++ a  +++  q +P++++++
     EPA06205.1  48 PTLVDFWAEWCGPCKMMHPVFESLSSKYP--KIKFARVNVDQNQNIA--MRFAVQSIPMFIMFK 107
                    88********************9955544..5666666666554444..588889999999986 PP

>> HyaE  Hydrogenase-1 expression protein HyaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.075   1.1e+02      63     103 ..       7      47 ..       2      56 .. 0.87
   2 !   11.7   0.0   0.00013       0.2      63      98 ..      81     114 ..      66     119 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.075
                 EEEEETHHHHHHHHHCCT-TSSSEEEEEETTEEEEEEESSS CS
        HyaE  63 aavvadreqeealaerfgvlktPsllflrdgeylgvlakir 103
                 +a +++r+ ee+++++ + +  P ++ l + ++  +++ ++
  EPA06205.1   7 IAKIKQRKLEEMIRQQNQPQIKPGIVDLNNSNFNEIISSVN 47 
                 5667889999****************999999999998876 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00013
                 EEEEETHHHHHHHHHCCT-TSSSEEEEEETTEEEEE CS
        HyaE  63 aavvadreqeealaerfgvlktPsllflrdgeylgv 98 
                 a v    +q++++a rf v+  P +++++ g+++  
  EPA06205.1  81 ARVN--VDQNQNIAMRFAVQSIPMFIMFKSGQIVDK 114
                 3333..58999********************98865 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   6.3e-06    0.0094     133     204 ..      50     113 ..      33     124 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6.3e-06
        TraF 133 LlfFyrgkcpyceaqapilqafadky.glevraVsvdgrplpelpnarvdkgqaarlgvkrtPalvlvdpks..q 204
                 L+ F ++ c+ c+++ p+ +++  ky +++   V+vd++++  ++          r+ v+++P ++++++ +  +
  EPA06205.1  50 LVDFWAEWCGPCKMMHPVFESLSSKYpKIKFARVNVDQNQN--IAM---------RFAVQSIPMFIMFKSGQivD 113
                 55688899******************9************88..777.........**********9999886543 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   6.7e-06      0.01      26     100 ..      47     118 ..      23     130 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6.7e-06
                 SEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHHH-H.SSEEEE-TTSHHHHHTT- CS
    AhpC-TSA  26 kpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfiekeslnfpllsDeegkvakaygv 100
                 +p+++ f+++ wc +C+   p ++ l  ++   +++   v+vd+ ++++   + +s+++ ++  + + v k  g+
  EPA06205.1  47 NPTLVDFWAE-WCGPCKMMHPVFESLSSKYP--KIKFARVNVDQNQNIAMRFAVQSIPMFIMFKSGQIVDKMMGA 118
                 799*******.**************999999..677888888888888777777777777666666666666655 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       3.6   5.3e+03      38      53 ..      12      27 ..       4      33 .. 0.71
   2 ?   11.9   0.0   0.00013       0.2       6      38 ..      55      92 ..      42     102 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.6
                  HHHHHHHHTSSSSSEE CS
  Glutaredoxin 38 reelkelsgvrtvPqv 53
                  + +l+e+  ++  Pq+
    EPA06205.1 12 QRKLEEMIRQQNQPQI 27
                  5666777677777776 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00013
                  STSSHHHHHHHHHHHHTT.....GGEEEEEGCCSHHHH CS
  Glutaredoxin  6 kptCpyCkkakrlLkelg.....vkfeeidvdkdeeir 38
                    +C+ Ck++  ++++l      +kf+ ++vd++++i 
    EPA06205.1 55 AEWCGPCKMMHPVFESLSskypkIKFARVNVDQNQNIA 92
                  589***********88877776799********99654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1040.32
//
Query:       EPA06206.1  [L=48]
Description: hypothetical protein BG20_I0546 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      0.006   16.1   0.9        1.8    8.1   0.1    2.2  2  TF_Zn_Ribbon  TFIIB zinc-binding
  ------ inclusion threshold ------
      0.012   15.5   0.2      0.022   14.6   0.2    1.5  1  zf-C3HC4_5    Zinc finger, C3HC4 type (RING finger)
      0.027   14.5   0.2       0.03   14.3   0.2    1.1  1  zf-C2HC5      Putative zinc finger motif, C2HC5-type
      0.033   13.8   2.6       0.06   12.9   2.6    1.5  1  RecR          RecR protein
      0.092   13.2   0.7          2    9.0   0.0    2.1  2  zf-C2H2       Zinc finger, C2H2 type
      0.099   13.5   0.7         20    6.3   0.0    2.2  2  zf-C2H2_4     C2H2-type zinc finger
       0.11   12.4   1.1       0.39   10.6   0.0    2.0  2  zf-C2H2_3     zinc-finger of acetyl-transferase ESCO


Domain annotation for each model (and alignments):
>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.1    0.0013       3.4      21      28 ..      10      17 ..       5      28 .. 0.81
   2 !    8.1   0.1   0.00072       1.8       3      10 ..      30      37 ..      29      47 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0013
                  EESSSSBE CS
  TF_Zn_Ribbon 21 vCtdCGlV 28
                  +C+dCG V
    EPA06206.1 10 ICGDCGIV 17
                  9*****88 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00072
                  ETTTTCEE CS
  TF_Zn_Ribbon  3 CPnCgstn 10
                  CP+C+s++
    EPA06206.1 30 CPICKSRR 37
                  ******86 PP

>> zf-C3HC4_5  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.2   8.6e-06     0.022       2      12 ..      28      38 ..      27      44 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8.6e-06
  zf-C3HC4_5  2 eiCPvCkssrY 12
                + CP+Cks+rY
  EPA06206.1 28 DECPICKSRRY 38
                68********* PP

>> zf-C2HC5  Putative zinc finger motif, C2HC5-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2   1.2e-05      0.03      13      43 ..       4      36 ..       2      45 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.2e-05
    zf-C2HC5 13 LleaapnClnCGkiiCakegls..kpCsfCgsp 43
                L+  + +C  CG +  +    +   +C+ C+s 
  EPA06206.1  4 LSRNIRICGDCGIVYTSVSMTKyiDECPICKSR 36
                7778899********999988888******986 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   2.6   2.4e-05      0.06      11      37 ..       3      36 ..       1      37 [. 0.76

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.4e-05
                HHHHH-EE-TTT--E.ESSS.......S-CCCCST CS
        RecR 11 eakekvrhCsrCgnl.teed.......lCaICsdp 37
                ++ +++r C  Cg + t +         C+IC++ 
  EPA06206.1  3 KLSRNIRICGDCGIVyT-SVsmtkyidECPICKSR 36
                6789**********953.4336667668****986 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00079         2       3      15 ..      11      23 ..      10      25 .. 0.85
   2 ?    3.1   0.1     0.061   1.6e+02       2       7 ..      29      34 ..      28      40 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00079
                ETTTTEEESSHHH CS
     zf-C2H2  3 CpdCgksFkrksn 15
                C+dCg ++++ s+
  EPA06206.1 11 CGDCGIVYTSVSM 23
                ********98665 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.061
                EETTTT CS
     zf-C2H2  2 kCpdCg 7 
                +Cp+C+
  EPA06206.1 29 ECPICK 34
                6****7 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.008        20       2      14 ..      10      22 ..       9      27 .. 0.82
   2 ?    5.9   0.1     0.011        28       2      10 ..      29      38 ..      29      41 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.008
   zf-C2H2_4  2 kCpiCgksFsskk 14
                +C  Cg +++s +
  EPA06206.1 10 ICGDCGIVYTSVS 22
                6********7754 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.011
   zf-C2H2_4  2 kCpiC.gksF 10
                +CpiC ++++
  EPA06206.1 29 ECPICkSRRY 38
                6****66665 PP

>> zf-C2H2_3  zinc-finger of acetyl-transferase ESCO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00015      0.39      14      26 ..       8      21 ..       1      24 [. 0.72
   2 ?    1.4   0.2      0.12     3e+02      14      20 ..      28      34 ..      20      35 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00015
   zf-C2H2_3 14 sq.CkeCgMvYnpg 26
                 + C  Cg+vY++ 
  EPA06206.1  8 IRiCGDCGIVYTSV 21
                335********976 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.12
   zf-C2H2_3 14 sqCkeCg 20
                 +C+ C+
  EPA06206.1 28 DECPICK 34
                35****6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.36u 0.29s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 334.01
//
Query:       EPA06207.1  [L=89]
Description: hypothetical protein BG20_I0578 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1041  (0.0580624); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 565.62
//
Query:       EPA06208.1  [L=78]
Description: LSM domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-23   82.5   0.6    1.4e-23   82.4   0.6    1.0  1  LSM       LSM domain


Domain annotation for each model (and alignments):
>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.4   0.6   7.6e-28   1.4e-23       2      67 .]       9      73 ..       8      73 .. 0.97

  Alignments for each domain:
  == domain 1  score: 82.4 bits;  conditional E-value: 7.6e-28
                HHHHTTTSEEEEEETTSEEEEEEEEEEETTSEEEEEEEEEEETTETEEEEEEEEEEEGGGEEEEEE CS
         LSM  2 flkklinkkvtvelkngrelrGtLkgfDqfmNlvLedveetlkdkkekrklglvliRGnnivlisl 67
                 l+++in++v+++lk+g+++rG+L gfDq+mNl L+  ee+  ++ ++++lg++++RG+n+v+is+
  EPA06208.1  9 VLDESINQIVLIKLKGGKTIRGNLLGFDQHMNLLLDSSEEIPVEG-NSKSLGTIVVRGDNVVMISP 73
                699******************************************.******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 534.87
//
Query:       EPA06209.1  [L=167]
Description: hypothetical protein BG20_I0561 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.7e-08   33.4   0.0    5.4e-08   32.9   0.0    1.3  1  Cupredoxin_1  Cupredoxin-like domain


Domain annotation for each model (and alignments):
>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.0     3e-12   5.4e-08      30     104 .]      85     166 ..      64     166 .. 0.85

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 3e-12
  Cupredoxin_1  30 ggfePskievkagekvklkiknkdkt....p..eefesedlgee.kvlapgktttitiaplkpGeYeftcdmhmdakGkliV 104
                   +g++  + ++++g  v++++ n+ +        ++f +++++++ k+l + +t++it+ ++k G+++++c  h+++kG li+
    EPA06209.1  85 NGMTSPTWTIPKGNLVTIHLINEITNkpseKslHNFNIDEFNVHsKNLGYFDTQSITFLADKSGQFTYHCTVHPEMKGLLII 166
                   455556789********9987765553333257********9877*********************************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       763  (0.0425568); expected 358.6 (0.02)
Passed bias filter:                      589  (0.0328518); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1000.86
//
Query:       EPA06210.1  [L=37]
Description: hypothetical protein BG20_I0583 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.32s 00:00:00.75 Elapsed: 00:00:00.50
# Mc/sec: 223.77
//
Query:       EPA06211.1  [L=270]
Description: hypothetical protein BG20_I0576 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-06   26.4  16.2    5.9e-06   25.8  16.2    1.2  1  NicO      High-affinity nickel-transport protein


Domain annotation for each model (and alignments):
>> NicO  High-affinity nickel-transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8  16.2   3.3e-10   5.9e-06       6     201 ..      40     228 ..      36     267 .. 0.59

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 3.3e-10
        NicO   6 glsflyGvrHAvdagHgkai....irklmqagktalkrGil..lslgsslvvvlvavllvvaavlvlrltslsetgaaigteiasFllvilllnllllr 98 
                 g   ++G+ HA++a+H++a+    + + +++ k++l ++ l   sl+ ++  ++ + +l+++  lv     ++        +   Fl+ i+l++l + r
  EPA06211.1  40 GFGLTLGIQHAFEADHIAAVctqiTNSNTIQSKKQLVKSSLtkSSLLGAVWGAGHTTALILVGLLVYG---FTFSIQKEVFSGFEFLVGIMLIFLAITR 135
                 55679***************888877777777777766533113566666666666666666666666...3322222333345577777777777888 PP

        NicO  99 klrklfrklerlgrapaaeleaalakrgllsrilgklfrlitkswhmypvgflfglGfdtateiallaidpsealkgdsfdsilalpalfavGlrlcdg 197
                    k+++k ++ ++ +     +   + ++  +++++  + +++++ +y +g+++gl     t i +l+  +  +l    +  i ++     +G++l+ g
  EPA06211.1 136 ITNKSILKIKH-RHPH----MHKDGSIHFDVHNHED--KNHSHNHKSYLIGMIHGLAG-SGTLIVMLSGAIH-SL-STTLMFIGIFGLGSIIGMSLVGG 224
                 88888877766.3333....3333334555555555..66666777777777777632.2334444444444.23.34455677888888899999999 PP

        NicO 198 adiv 201
                 ++++
  EPA06211.1 225 LIGI 228
                 9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       780  (0.0435049); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2055.31
//
Query:       EPA06212.1  [L=138]
Description: hypothetical protein BG20_I0544 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-30  105.1   1.4    3.7e-30  105.0   1.4    1.0  1  Archease  Archease protein family (MTH1598/TM1083)
  ------ inclusion threshold ------
       0.03   15.0   0.0      0.049   14.3   0.0    1.3  1  YbjQ_1    Putative heavy-metal-binding
      0.035   13.4   0.3      0.043   13.1   0.3    1.1  1  RdgC      Putative exonuclease, RdgC


Domain annotation for each model (and alignments):
>> Archease  Archease protein family (MTH1598/TM1083)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.0   1.4   6.2e-34   3.7e-30       1     137 [.       3     137 ..       3     138 .] 0.95

  Alignments for each domain:
  == domain 1  score: 105.0 bits;  conditional E-value: 6.2e-34
                 EEE---SSEEEEEEE-SSSHHHHHHHHHHHHHHHS--TT---S-EEEEEEEESSSHHHHHHHHHHHHHHHHHT--S----EEEE.E-SSSEEEEEEEE- CS
    Archease   1 yeyldhtADviieawGksleeafesaalalfeymtdlskvepkeekeieveaedledlLfdfLdellylfdteyfvfkevkvdeeeeeeeleleaearg 99 
                 y++l+h  D  ie+++k+l+eaf  +a a+++++ d +kve+ke+kei ++++dl  +Lf++L+e+ + + te f++k+++++  +e++++++ a+a+g
  EPA06212.1   3 YKFLEHATDAFIEVTAKDLKEAFLVTANAVINITLDQDKVEEKEQKEIVAHGKDLRYVLFSWLEEITFVLITEGFAIKRIELEI-QENKGYKIIAKAYG 100
                 99******************************************************************************5544.8899********** PP

                 ---.-TT--------B--S---EEEEETTEEEEEEEEE CS
    Archease 100 ekfdkekhevqtevKAvTyhelrieeeddgweayvvvD 137
                 e++d  kh+++ e+KA T+ e++ie+++ g+ +++++D
  EPA06212.1 101 EPLDFLKHNFKVEIKAPTFYEMKIEQNN-GVFMRFLLD 137
                 *************************987.777777777 PP

>> YbjQ_1  Putative heavy-metal-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   8.1e-06     0.049      67      99 ..      22      54 ..       4      57 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.1e-06
      YbjQ_1 67 eeAeelGAnAvvgvrldtseigekgmlevlayG 99
                +eA  + AnAv+++ ld+++++ek+  e++a G
  EPA06212.1 22 KEAFLVTANAVINITLDQDKVEEKEQKEIVAHG 54
                5788899**************999999**9998 PP

>> RdgC  Putative exonuclease, RdgC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.3   7.1e-06     0.043     204     253 ..      34      84 ..      19      98 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.1e-06
        RdgC 204 vvrckrqdlesdeirahleaGkvvtkLaLtwedrisfvL.tedlslkrlkf 253
                  + + + ++e+ e ++ +++Gk    +  +w ++i+fvL te +++kr+++
  EPA06212.1  34 NITLDQDKVEEKEQKEIVAHGKDLRYVLFSWLEEITFVLiTEGFAIKRIEL 84 
                 56677888999999***********************975899******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 869.90
//
Query:       EPA06213.1  [L=128]
Description: 50S ribosomal protein L7Ae [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.2e-26   89.8   0.1    8.8e-26   89.5   0.1    1.1  1  Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 famil
     0.0013   18.6   0.0     0.0018   18.1   0.0    1.3  1  PELOTA_1        PELOTA RNA binding domain


Domain annotation for each model (and alignments):
>> Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.5   0.1   9.8e-30   8.8e-26       3      93 ..      19     109 ..      17     111 .. 0.96

  Alignments for each domain:
  == domain 1  score: 89.5 bits;  conditional E-value: 9.8e-30
                     HHHHHHHHHHHTEEEESHHHHHHHHHTTTESEEEEETTSSSGGHHHHHHHHHHHTTEEEEEESCHHHHHHHTTSSSECSEEEEEESTTTHH CS
  Ribosomal_L7Ae   3 ieevlkkakkagklvlGlkevtkalergeaklvilAedvepeekkkllealckekevpyvkvkskkeLGelvgkkrpvsalaikdegdskd 93 
                     i e++++a+ +gk+++G++e+tka+erg+ kl+++Aedvep+e +++l++lc+e++  y +v+sk+eLG+ +g   +++a+ai d+gd++ 
      EPA06213.1  19 ILEAVRVASSSGKVKKGTNEATKAIERGTSKLIVIAEDVEPPEVVAHLPILCEEQGAAYAFVPSKQELGKSLGIDITSAAAAILDAGDAQH 109
                     56899**********************************************************************99***********986 PP

>> PELOTA_1  PELOTA RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   2.1e-07    0.0018       7      70 ..      16      82 ..      10      87 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.1e-07
    PELOTA_1  7 veriaeeygie.dinliKPgigEaTRvlLRRvPekvlvrdeee..pdlahlllLakekgvpveevpd 70
                v+ i e+ ++  +   +K g  EaT+++ R + + ++++++ e  + +ahl +L++e+g ++  vp+
  EPA06213.1 16 VNPILEAVRVAsSSGKVKKGTNEATKAIERGTSKLIVIAEDVEppEVVAHLPILCEEQGAAYAFVPS 82
                5666666666514579********************999987765679**********998877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 874.30
//
Query:       EPA06214.1  [L=244]
Description: creatininase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.8e-50  169.3   0.0    1.3e-49  168.8   0.0    1.0  1  Creatininase  Creatinine amidohydrolase
  ------ inclusion threshold ------
       0.17   11.9   0.1       0.65   10.1   0.0    2.0  2  HflK_N        Bacterial membrane protein N terminal


Domain annotation for each model (and alignments):
>> Creatininase  Creatinine amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.8   0.0   1.5e-53   1.3e-49      12     237 ..      17     227 ..      10     230 .. 0.90

  Alignments for each domain:
  == domain 1  score: 168.8 bits;  conditional E-value: 1.5e-53
  Creatininase  12 lkeddvailPvGstEqHGphlplgtDtliaealaervaeklgakalvlPtlpyGvseehlgfpGTislspetliavlrdileslarhGfrrivlvng 108
                   +k+++va++P+Gs+EqHGphlp++tD+ i++++a+r+ +k +   l+lPt++yGvs eh  f + +s++++tl++++ d+++sl  + ++ i+++ng
    EPA06214.1  17 KKKNQVAVIPIGSIEQHGPHLPISTDSDIVTEVAKRLSKKKD--FLLLPTITYGVSYEHAPFFN-LSIKESTLRSIVIDLCTSLFVNNIKTIFIING 110
                   7899*********************************99966..***************99876.******************************** PP

  Creatininase 109 HggnsaalkeaarelraehdaaavrvtaaekelaaalkleeaaeaaeeseeeegggHAgelEtSlmlalrpelVrmdraedpeeaklakeg...... 199
                   H gn ++lk++ r+l++   ++ +r       +++  +++ +         +++  HAg +EtSlmla+    V+m+ a+++  ++  k++      
    EPA06214.1 111 HHGNLKPLKNIDRKLQQIS-GNRLR-------VFSLSYWHFM---------KREFDHAGFVETSLMLAVS-NNVKMKLAKKGLVTDGMKQQqikklg 189
                   *****************99.55443.......3333344433.........33899*************6.68********9999998888999999 PP

  Creatininase 200 vstaedaeelspsGvlGdpskataekGealleaaveel 237
                   +  + ++ +++++G++Gdp+ka++++G+ +l++++++l
    EPA06214.1 190 QLAEISFPKVTKNGIWGDPRKASKKDGQIILDEIIRNL 227
                   99999****************************99876 PP

>> HflK_N  Bacterial membrane protein N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       0.3   2.7e+03      32      45 ..     118     131 ..     118     132 .. 0.79
   2 ?   10.1   0.0   7.2e-05      0.65      12      41 ..     205     233 ..     198     238 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.3
      HflK_N  32 lrdlqdkLgglfgg 45 
                 l+++ +kL+++ g+
  EPA06214.1 118 LKNIDRKLQQISGN 131
                 578899**999876 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 7.2e-05
      HflK_N  12 WGqgrnkggggqgPPDLDEllrdlqdkLgg 41 
                 WG  r k ++++g+  LDE++r+l +k + 
  EPA06214.1 205 WGDPR-KASKKDGQIILDEIIRNLEKKCQT 233
                 99444.67999*************999665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1720.32
//
Query:       EPA06215.1  [L=36]
Description: hypothetical protein BG20_I0584, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (36 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       218  (0.0121591); expected 358.6 (0.02)
Passed bias filter:                      155  (0.00864521); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 249.84
//
Query:       EPA06216.1  [L=224]
Description: signal peptidase I [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-07   30.2   0.5    3.2e-07   30.2   0.5    2.3  2  Peptidase_S24  Peptidase S24-like
  ------ inclusion threshold ------
      0.054   13.8   2.3        0.1   12.9   0.0    2.2  2  MscL           Large-conductance mechanosensitive channel, Ms
        1.2    9.4   5.2        4.8    7.5   1.1    2.2  2  TrbC           TrbC/VIRB2 family
        1.3    8.8   8.0       0.29   10.9   0.5    2.4  2  Vpu            Vpu protein


Domain annotation for each model (and alignments):
>> Peptidase_S24  Peptidase S24-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.5   7.2e-11   3.2e-07       2      47 ..      44      93 ..      43     115 .. 0.85
   2 ?   -0.0   0.2      0.19   8.6e+02      41      53 ..     160     172 ..     148     185 .. 0.80

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 7.2e-11
                   XXSSTTCCTXXTTXEEEEE...CTS---TTSEEEEEETTCE.-EEEEEEE CS
  Peptidase_S24  2 vpGdSMeptlldGdlilVd...kfsepkrGdivvfrlpgee.eayiKrvi 47
                   v ++SM p l+  d+++V    +f+++k Gdi+vf+ p    +++++rv 
     EPA06216.1 44 VASGSMIPVLEVYDVLIVQghvPFEDIKVGDIIVFNRPTTHdRVIVHRVA 93
                   89*****************888888**********9998888999*9997 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.19
                    EEEEEEEEETTEE CS
  Peptidase_S24  41 ayiKrviglpgdr 53 
                     ++K+v+++++++
     EPA06216.1 160 MIVKQVYKKKNEK 172
                    589***9998876 PP

>> MscL  Large-conductance mechanosensitive channel, MscL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.7      0.16   7.1e+02      34      71 ..      13      49 ..       4      76 .. 0.56
   2 ?   12.9   0.0   2.2e-05       0.1      69     102 ..     141     175 ..      85     214 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.16
        MscL 34 lvkdiimpliglllggvdfselkikl..kaeaavlkygaf 71
                + kdii   ig+++  +++   ++++  +++  v++ g++
  EPA06216.1 13 ILKDIIIVAIGVIVIWISL---QVVFgtQNPFYVVASGSM 49
                4445555555555422222...222222445555555555 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 2.2e-05
        MscL  69 gafiqavinFliiafvi.Flivkainkkkkeeeee 102
                  ++++  in++ii +v+  +ivk++ kkk+e+e +
  EPA06216.1 141 TQLLKPPINYIIIVIVVgIMIVKQVYKKKNEKEIA 175
                 5788889*****************99966554443 PP

>> TrbC  TrbC/VIRB2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   1.1    0.0011       4.8      45      75 ..       9      39 ..       6      52 .. 0.82
   2 ?    3.7   0.2     0.016        73      59      70 ..     151     162 ..     137     169 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0011
        TrbC 45 ivdfltgplakviatiaiivaGimlafgrls 75
                + + + +++++v++ +++i+++++++fg ++
  EPA06216.1  9 MSKGILKDIIIVAIGVIVIWISLQVVFGTQN 39
                56677888********************865 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.016
        TrbC  59 tiaiivaGimla 70 
                 +i++iv+Gim++
  EPA06216.1 151 IIIVIVVGIMIV 162
                 677888888875 PP

>> Vpu  Vpu protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   1.7      0.07   3.1e+02      12      24 ..      17      29 ..       7      36 .. 0.76
   2 ?   10.9   0.5   6.5e-05      0.29      16      73 ..     151     204 ..     142     211 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.07
         Vpu 12 livaliiaivvWt 24
                +i++ i +iv+W 
  EPA06216.1 17 IIIVAIGVIVIWI 29
                6777788999996 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 6.5e-05
         Vpu  16 liiaivvWtivyreykkikkqkeierlikrireraedSgnESdGeeeeelakLvhshg 73 
                 +ii+ivv  +++++  k+k++kei   i+ i ++ +dS+ ES  +  e l+kL ++++
  EPA06216.1 151 IIIVIVVGIMIVKQVYKKKNEKEIA--IQGIPDT-NDSQIESTVDIPE-LEKLEKDKE 204
                 6789999999*************96..7778775.6899999999999.999977655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1025  (0.0571699); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1470.72
//
Query:       EPA06217.1  [L=464]
Description: amidohydrolase family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.9e-21   75.7   0.3    1.4e-20   74.0   0.3    1.9  1  Amidohydro_1  Amidohydrolase family
    2.5e-14   53.6   0.1    1.3e-08   34.7   0.0    3.3  3  Amidohydro_3  Amidohydrolase family
    0.00068   19.1   0.1     0.0013   18.2   0.0    1.6  2  TatD_DNase    TatD related DNase
  ------ inclusion threshold ------
       0.16   12.1   0.0        3.2    8.0   0.0    2.4  2  Hom_end       Homing endonuclease


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.0   0.3   3.1e-24   1.4e-20       3     344 .]      53     443 ..      51     443 .. 0.72

  Alignments for each domain:
  == domain 1  score: 74.0 bits;  conditional E-value: 3.1e-24
                   EE-EEEEEEECETTECSSSGHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTH...HHHHHHHHHHT.SSSEEEEEEESSEGGSGCCCSHH CS
  Amidohydro_1   3 lPGlIDaHvHleqsllrgatledwlvppetaaealesgiktalksGtttvadmgattst...giealleaaee.lplglrilggkvsldrgsaetsk 95 
                   +PG ID+HvH+  +              + + +a+++   +a  +G+tt+  m         +++  leaa++   +++ i+++ + +  ++ +  +
    EPA06217.1  53 IPGPIDTHVHYGVY--------------SPIDQAAKTESHAAAIGGITTMMRMLRLGNSfkaSLPEQLEAASKnHYVDYAIHASIFTP--QQINEMP 133
                   8**********644..............3456778888889999**********9998899999999999999966899999997777..5666677 PP

                   HHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHH.........HHHHHHHHHHHHTTEEEEEE..TSSCHHHHHHHHHHTTTEEEETTTTSTCC CS
  Amidohydro_1  96 asreklkagaaetikgkadgvvkvalapheapafsde.........elkealkeakkrdlpvaiHa..letkgevedaeaafgetiehgthlevaes 181
                    ++e+ ++ +  +i  + +g v    ++ ++++ + +         +++e++k a+  + pv +Ha   e+ +    + ++ +++        + es
    EPA06217.1 134 YCIEQGITSF--KIYMNLGGDVGHVYMDMPPYSSTLSeatvdvndkLVEEIVKTAASLGCPVLVHAedYESCACGIKTAKEKKRDGL----PAWSES 224
                   7888888887..5555555555544444445555555567778888********************997777777444444443322....222222 PP

                   ...HHTTTHCCEE....EHCTCEEE....HH.....HHHHHHHHHHHHCEE..HHHHHHHH.................SEHHHHHHHHHHHHTSCEE CS
  Amidohydro_1 182 ...lglldeikli....lahgvhlt....pt.....eaellkerlkeagva..hcpfsnsi.................lrsgrealrkaldeGvkvg 243
                         ++ ik+i    +  g+++      +      +++ +  + ++      cp    i                  +++ +a+++al+++++ +
    EPA06217.1 225 rspDFEAKAIKTIskfgRDYGCTIYfvhiGSqkaleQIKIERNLGSKI--FveTCPHYLTIsyenqkgylakvmppirTAQDNAAVWNALSNNLIDT 319
                   333344444555555557777777754441145554444433333344..2454444444444566699999999999999999************* PP

                   EEEECT........TSSCCGGHHHH.....HHHHHHHHHHCCTT.TTHCHCHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECCCT..... CS
  Amidohydro_1 244 lgtDga........asgnslnllee.....lrlalklqrgllye.deegglslkealrmaTingAkalglddkvGsievGkdADlvvvdldi..... 321
                   +gtD++        +  ++ + l +     ++l l+l+     e + +  ++l++++r++++n+Ak++g++ ++G++++  dAD++++dl++     
    EPA06217.1 320 IGTDHVanqlklklGGTDVWSALAGfpgigTALPLLLS-----EgVNKNRITLEQLIRFTSTNAAKIFGMYPRKGTLDKDADADITMIDLKKeqkvs 411
                   ******88888887444444555556554344444223.....3444555****************************************4445678 PP

                   .........CGGGTTTCTSEEEEEEEETTEEE CS
  Amidohydro_1 322 .........laafvglkkdgnvkkvivkGklv 344
                            +  ++g++ +g+++k+iv+G++v
    EPA06217.1 412 selfgsfsdYIVYEGMSLKGWPVKTIVRGQIV 443
                   9999****999******************998 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.8   0.2    0.0036        16       6      49 ..      48      90 ..      44      92 .. 0.85
   2 !   10.3   0.0   7.5e-05      0.34     224     292 ..     133     206 ..      84     225 .. 0.71
   3 !   34.7   0.0     3e-12   1.3e-08     381     473 .]     342     444 ..     331     444 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0036
  Amidohydro_3  6 kGrlvlPGFvDsHtHlagggvnlrllrlpdarvtslegvltavr 49
                  +G++ +PG +D H H +g+ + +  +   ++++ ++ g++t++r
    EPA06217.1 48 NGLISIPGPIDTHVH-YGVYSPIDQAAKTESHAAAIGGITTMMR 90
                  78999**********.8888888888888889999999999876 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 7.5e-05
  Amidohydro_3 224 pgseeltigavklfadgvlgsrtalltepyf.....tgwpdfedealaelvaaadergldvaihaigdaavddv 292
                   p + e  i ++k+  ++ ++  +++++ p        ++ d+ d+ ++e+v+ a+  g++v +ha ++++ + +
    EPA06217.1 133 PYCIEQGITSFKIYMNLGGDVGHVYMDMPPYsstlsEATVDVNDKLVEEIVKTAASLGCPVLVHAEDYESCACG 206
                   55778889999*****999999999998633599555555555666*******************999876655 PP

  == domain 3  score: 34.7 bits;  conditional E-value: 3e-12
  Amidohydro_3 381 fdpwprigaavmrktrrggevlrpdeelsleealalyTrgpAkalgledrkGtLevGadADlvvldadpldvdppelaear..............vr 463
                   +  +p+ig+a+++   +g      +++++le++++ +++++Ak++g+  rkGtL + adAD++++d +  +   +el+                 ++
    EPA06217.1 342 LAGFPGIGTALPLLLSEGV----NKNRITLEQLIRFTSTNAAKIFGMYPRKGTLDKDADADITMIDLKKEQKVSSELFGSFsdyivyegmslkgwPV 434
                   5668889999988887665....788****************************************55555555655555589999999******** PP

  Amidohydro_3 464 ltvvdGrvvy 473
                   +t+v+G++v+
    EPA06217.1 435 KTIVRGQIVA 444
                   ********95 PP

>> TatD_DNase  TatD related DNase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   2.9e-07    0.0013       1     136 [.      57     202 ..      57     295 .. 0.78
   2 ?   -3.4   0.0       1.1     5e+03     236     254 ..     364     382 ..     356     383 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.9e-07
                 EEEEE-TTS.CCCTTTHHHHHHHHHHTTEEEEEEE-SSGGGHH.HHHHHHTT.TTTEEEEE---GGGGGCC..CCHHHHHHHH.HHCCCTSEEEEEEEE CS
  TatD_DNase   1 iDaHcHlds.kefeedreeileraeeagvaavvvvgtsskdsk.avlelakkypnkvyavlGiHPnevdea.sedlleelkel.anvkhskvvaiGeiG 95 
                 iD+H+H    + +++ ++ + ++a+ +g+++++ + +  +++k  + e  + ++++ y+   iH    + +  +++   +++   ++k + + + G +G
  EPA06217.1  57 IDTHVHYGVySPIDQAAKTESHAAAIGGITTMMRMLRLGNSFKaSLPEQLEAASKNHYVDYAIHASIFTPQqINEMPYCIEQGiTSFKIYMNLG-GDVG 154
                 8*******9999999999999***********98888887777433344444555588888888744443312233355555555557766655.5666 PP

                 EET.......-CCCCCGHHHHHHHHHHHHHHHHHTTEEEEEEEES-HH CS
  TatD_DNase  96 LDy.......ysreestkeaqeevFeeqlrlAkelklplviHlrkaee 136
                   y       +  +e+t ++  ++ ee ++ A+ l++p+ +H+++ e 
  EPA06217.1 155 HVYmdmppysSTLSEATVDVNDKLVEEIVKTAASLGCPVLVHAEDYES 202
                 544444886557788899*************************99443 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.1
                 TS-HHHHHHHHHHHHHHHH CS
  TatD_DNase 236 altleelaeitaeNakrlf 254
                  +tle+l++ t++Na ++f
  EPA06217.1 364 RITLEQLIRFTSTNAAKIF 382
                 5899999999****99998 PP

>> Hom_end  Homing endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0     0.099   4.4e+02      44      85 ..      80     122 ..      65     131 .. 0.84
   2 ?    8.0   0.0   0.00071       3.2      35      68 ..     169     201 ..     156     215 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.099
     Hom_end  44 svmegivklarsLGikasvkt.keekidakgvkhqfcyaitls 85 
                   + gi+ + r L +  s+k+   e+ +a +++h + yai+ s
  EPA06217.1  80 AAIGGITTMMRMLRLGNSFKAsLPEQLEAASKNHYVDYAIHAS 122
                 56789***************98788899999999999999765 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00071
     Hom_end  35 satvktedksvmegivklarsLGikasvktkeek 68 
                 +atv+ +d +++e+ivk a sLG  + v +++ +
  EPA06217.1 169 EATVDVND-KLVEEIVKTAASLGCPVLVHAEDYE 201
                 78888766.6889***********9999987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 3266.60
//
Query:       EPA06218.1  [L=328]
Description: cytochrome C biogenesis protein transmembrane region [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-15   57.6  16.9    1.6e-15   57.6  16.9    1.5  2  DsbD      Cytochrome C biogenesis protein transmembrane regio
    4.7e-05   23.4  25.7    5.5e-05   23.2   8.6    2.7  3  DsbD_2    Cytochrome C biogenesis protein transmembrane regio


Domain annotation for each model (and alignments):
>> DsbD  Cytochrome C biogenesis protein transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.5      0.84   7.5e+03      85      93 ..      15      23 ..       5      35 .. 0.51
   2 !   57.6  16.9   1.8e-19   1.6e-15       1     212 [.      51     253 ..      51     254 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 0.84
        DsbD 85 ivillGlhf 93
                + +l+ l f
  EPA06218.1 15 VFVLFSLVF 23
                222222222 PP

  == domain 2  score: 57.6 bits;  conditional E-value: 1.8e-19
        DsbD   1 aflaGllsflsPCilpliPaylsyisgvsvedvktekkkvkvllkallFvlGlslvfvslglsaaflgqllk..dvkevirrvaglivillGlhflgvf 97 
                 a+laGl   + PC lpl+ + +     +s++   +     k l  allF  Gl+++++  g+++++lgq +   +++ ++  +ag+ + l+Gl++l +f
  EPA06218.1  51 AYLAGLSMIILPCTLPLVFIIV----PLSMGKTAK-----KGLSMALLFGAGLTITISFYGFGIGALGQTADldQISIYMFLIAGIAAFLFGLSQLKLF 140
                 589*************986654....445554444.....46899**********999888888888888755488999999***************** PP

        DsbD  98 kievleklklllkikkkaelsvlgalllGltFalgwsPCigPvlasvlalaaskeslakgallllvyvlGlaipfllvglllellkkklkslkkyskav 196
                 ++++ +     ++i++    ++ +++ +Gl+ +     C  P++  +l++ a ++++  ga+l  v+ +G aip++l+++l+    + +k +   + ++
  EPA06218.1 141 ELKLPTYSGTPKFIQN--RGDYSKSFFMGLLLGNAGVGCPNPMFYWLLIYIAGTGNMEIGASLGAVHGVGRAIPLILLSVLAIIGINATKGITTKKITI 237
                 *877776666655544..44569************************************************************9999************ PP

        DsbD 197 eiaggvllvllGvlll 212
                 e+++g +l+++G +l+
  EPA06218.1 238 EKLTGWMLIVIGSFLI 253
                 ************9886 PP

>> DsbD_2  Cytochrome C biogenesis protein transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8  14.8   0.00033       2.9     117     197 ..      47     133 ..       4     135 .. 0.72
   2 !   23.2   8.6   6.2e-09   5.5e-05      50     197 ..     102     249 ..      99     251 .. 0.66
   3 ?   -2.3   0.0      0.39   3.5e+03      67      93 ..     298     324 ..     289     327 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00033
      DsbD_2 117 slasalllGllnGllpCglvysalllalasgsal.eGalvmlaFgLGTlpalllfglllgllskklr.....kkllrlagvllillg 197
                  l  a+l+Gl + +lpC l ++++++ l++g+ + +G  + l+Fg G  +++ ++g+ +g l++ +        ++ +ag++++l+g
  EPA06218.1  47 WLVIAYLAGLSMIILPCTLPLVFIIVPLSMGKTAkKGLSMALLFGAGLTITISFYGFGIGALGQTADldqisIYMFLIAGIAAFLFG 133
                 456699*************999999999887766167777789*******************9955432222566666677766666 PP

  == domain 2  score: 23.2 bits;  conditional E-value: 6.2e-09
      DsbD_2  50 GalvgllgsvlqlageleglrallgvllgllllllglklllkkkllklerlgkllsrllkklakklkslasalllGllnGllp..C..glvysalllal 144
                 G  +g+lg+ +    +l+++++++ +++g+++ l+gl+ l     lkl + + +  +++++      ++++++++Gll G +   C  +++y  l++++
  EPA06218.1 102 GFGIGALGQTA----DLDQISIYMFLIAGIAAFLFGLSQLKLF-ELKLPTYS-GTPKFIQNRG----DYSKSFFMGLLLGNAGvgCpnPMFYWLLIYIA 190
                 44445555554....6677999***********9999998433.33444443.2444444444....45556666666555422243399********* PP

      DsbD_2 145 asgsaleGalvmlaFgLGTlpalllfglllgll...skklr......kkllrlagvllillg 197
                  +g++  Ga + ++ g+G  ++l+l+++l+ +    +   +       ++ +l+g++li++g
  EPA06218.1 191 GTGNMEIGASLGAVHGVGRAIPLILLSVLAIIGinaT---KgittkkITIEKLTGWMLIVIG 249
                 *******************888888887765532221...2122322455679999999998 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 0.39
      DsbD_2  67 eglrallgvllgllllllglklllkkk 93 
                 +  ++++ +l+g l+l+ +++++ +kk
  EPA06218.1 298 QMPQEFAPILFGSLILFPIIWYFTRKK 324
                 556789999999999999999987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       821  (0.0457917); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2037.75
//
Query:       EPA06219.1  [L=282]
Description: putative formyltetrahydrofolate deformylase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.1e-45  152.8   0.1    1.1e-44  152.3   0.1    1.2  1  Formyl_trans_N  Formyl transferase
    9.8e-07   28.7   0.0    2.2e-06   27.6   0.0    1.6  1  ACT_6           ACT domain
      0.005   16.6   0.2      0.029   14.2   0.1    2.4  2  ACT             ACT domain
  ------ inclusion threshold ------
      0.025   15.2   0.2      0.093   13.3   0.1    2.1  2  ACT_4           ACT domain


Domain annotation for each model (and alignments):
>> Formyl_trans_N  Formyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.3   0.1   2.5e-48   1.1e-44       1     181 []      87     262 ..      87     262 .. 0.95

  Alignments for each domain:
  == domain 1  score: 152.3 bits;  conditional E-value: 2.5e-48
                     -EEEEEESESSHHHHHHHHHHHHTTSECEEEEEEESCTTEHCHHHHHHCCHCCCECHHCCSCCCCCCCHHHHHHHHCTT-SEEEEES--S---HH CS
  Formyl_trans_N   1 kkivvlisgtgsnlqalldalkkgsleadvvlvvsnkdkaaglekaeaasiptkvfeekkleprsqfeeelaeelkelkadlivlagymkllpke 95 
                     k+i++++++++ +l+++l+a kk++l++ +  +++ +++++    a++a+ip+ v+ee +    +++ee++++  k+++ dlivla ymk+l+++
      EPA06219.1  87 KNIAIMVTKEPLCLETILEASKKKTLNGIISIIIGTEKTLE--PIAKKAKIPFVVLEETNQ---EKAEEKIIAICKKYEIDLIVLARYMKILSPN 176
                     69*************************99999999999999..678889********9765...55699************************** PP

                     HHHSSTTSEEEEESSSTTTTBSS-HHHHHHHTTSSEEEEEEEE--SSSSTS-EEEEEEEE--TT--HHHHHHHHHHHHHHHHHHHH CS
  Formyl_trans_N  96 lvqavrlkilniHpSLLPrfkGaaaiqraleaGdketGvtihfvdeelDtGailaqkkveiiaedtkeeleqrvadaehkalveal 181
                     +v +++++i+niHpSLLP+f+Ga a+ +a+e+G k  Gvt h+v+e+lD+G+i++q++ +++++dt+ee++++ +++e   l++a+
      EPA06219.1 177 FVWRYPNRIINIHPSLLPAFPGALAYAQAYERGTKIVGVTSHYVTENLDQGPIIFQDSFKVDPNDTLEEIKAKGQKLEADTLLKAV 262
                     *******************************************************************************9998875 PP

>> ACT_6  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   4.9e-10   2.2e-06       5      47 ..       8      50 ..       4      80 .. 0.76

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 4.9e-10
       ACT_6  5 itvtGpdrpGltasLtsvlaefgvnilDieqavihgrlsLgll 47
                itv+G+dr G++a++t  + e+g ni  i+q vi g +   l 
  EPA06219.1  8 ITVVGKDREGIVAAFTNFVFENGGNIEKINQNVIKGLFGMYLE 50
                9*********************************996644444 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.1   6.4e-06     0.029       4      38 ..       9      43 ..       6      74 .. 0.86
   2 ?   -2.2   0.0      0.84   3.8e+03      41      61 ..     112     132 ..     105     134 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.4e-06
                EEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEEST CS
         ACT  4 rvgvpDrPGlLarvfgaladrgiNidsieqrssed 38
                 v  +Dr G+ a++++ + ++g Ni++i+q   + 
  EPA06219.1  9 TVVGKDREGIVAAFTNFVFENGGNIEKINQNVIKG 43
                57789*************************98876 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.84
                 CEEEEEEEEEEHHHHHHHHHH CS
         ACT  41 agivfvvivvdeedleevlea 61 
                  + ++++i++ e+ le + ++
  EPA06219.1 112 LNGIISIIIGTEKTLEPIAKK 132
                 566777788888888877765 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   2.1e-05     0.093       8      51 ..       7      48 ..       3      76 .. 0.85
   2 ?   -1.8   0.0       1.1   4.9e+03      36      56 ..      74      93 ..      69     118 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.1e-05
       ACT_4  8 rleveaedrkglLaditqviseekanivsvnaktrkkdglaeik 51
                 ++v+++dr g++a  t+ + e+++ni+++n    k  gl+ + 
  EPA06219.1  7 GITVVGKDREGIVAAFTNFVFENGGNIEKINQNVIK--GLFGMY 48
                699****************************99865..566655 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.1
       ACT_4 36 svnaktrkkdglaeikitveV 56
                ++ ++t++ +  ae +i + V
  EPA06219.1 74 KMDVSTHH-ETNAEKNIAIMV 93
                44444443.445555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       693  (0.0386525); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2015.40
//
Query:       EPA06220.1  [L=47]
Description: hypothetical protein BG20_I0574 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       194  (0.0108205); expected 358.6 (0.02)
Passed bias filter:                      161  (0.00897987); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.44
# Mc/sec: 324.34
//
Query:       EPA06221.1  [L=508]
Description: 4-hydroxyphenylacetate 3-hydroxylase family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-95  319.2   0.0    4.4e-95  318.5   0.0    1.3  1  HpaB_N         4-hydroxyphenylacetate 3-hydroxylase N termina
    3.2e-71  238.6   0.3    4.4e-71  238.1   0.3    1.2  1  HpaB           4-hydroxyphenylacetate 3-hydroxylase C termina
  ------ inclusion threshold ------
      0.092   13.0   0.0       0.42   10.8   0.0    2.1  2  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
      0.094   12.3   0.2         15    5.1   0.0    2.3  2  Bt_P21         Bacillus thuringiensis P21 molecular chaperone


Domain annotation for each model (and alignments):
>> HpaB_N  4-hydroxyphenylacetate 3-hydroxylase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  318.5   0.0   9.7e-99   4.4e-95       1     272 []      10     277 ..      10     277 .. 0.98

  Alignments for each domain:
  == domain 1  score: 318.5 bits;  conditional E-value: 9.7e-99
                 -HHHHHHHHHHS---EEETTEE-S-TTTSTTTHHHHHHHHHHHHHTTSTTTHHHHEEEE..TTEEEEGGG----SHHHHHHHHHHHHHHHHHTTT--S- CS
      HpaB_N   1 TgeeYlesLrdkgrevYvdGekVedvtthpafrpavrsvarlYdlahdpeykdlltatspetgekvnrffhiprskeDllkkrkairelarktggclgR 99 
                 Tg++Y+esLr ++ +vY+ Ge V++ ++hp++rp++++va++Ydla ++e  +l+ a+s++tg +vnrf+hi++s++Dl+ ++k++r+l ++tg+c++R
  EPA06221.1  10 TGNDYIESLRGRDLKVYLFGELVKEPVDHPMIRPSINAVAETYDLAVREE--ELASAHSSLTGLTVNRFLHIAESAQDLVLQNKMQRKLGQNTGTCFQR 106
                 89*********7777*********************************98..9********************************************** PP

                 -THHHHHHHHHHHHTG.GGGG.G....GHHHHHHHHHHHHHHT--EEEEES--SS-TTS-GGGSSSTTSB-EEEEE-SSEEEEEEEEEEEE-.--SSEE CS
      HpaB_N 100 cpdydalnalalvaaa.dvfekegtkeyaenfrkyleyvqendlvlthaitdpkgdRskrpseqedpdvyvrvveetddGivVrGakvlaTgaaladei 197
                 c+++dalnal  ++ + d  ek++t+ y+++f ++++++q+++lv+ +a+tdpkgdRsk p+eq+dpd++ rvv ++d+Gi+V+Gak+++Tg++++++i
  EPA06221.1 107 CVGMDALNALHSTTFEiD--EKYKTN-YHKRFLEFVKMMQKENLVIGGAMTDPKGDRSKGPAEQDDPDLFTRVVSKDDKGIYVSGAKAHQTGCINSHWI 202
                 ****************99..988988.************************************************************************ PP

                 EE---SS-..TTSGGG-EEEEEETT-TTEEEEE------.-.S..-TTT-TTTTT----EEEEEEEEEEEEGGGEEE CS
      HpaB_N 198 lvlptramlkeedkdyavafavpvdapGlklicresfed.k.leesefdyplssrfdendalvvfDdVfVPwerVfl 272
                 +++pt ++ +e+dkd+av+ a+p+da+G+++i++++++d + +ee ++d +++ +f++++al+++++Vf+Pw++Vf+
  EPA06221.1 203 ILMPTVRL-TENDKDWAVVGAIPADAKGVTYIYGRQSCDtRsMEEGDIDDGNA-KFGGQEALMILENVFIPWDKVFM 277
                 *****888.******************************855889********.**********************8 PP

>> HpaB  4-hydroxyphenylacetate 3-hydroxylase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  238.1   0.3   9.9e-75   4.4e-71       2     202 .]     285     482 ..     284     482 .. 0.99

  Alignments for each domain:
  == domain 1  score: 238.1 bits;  conditional E-value: 9.9e-75
                 HHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTGGGSHHHHHHHHHHHHHHHHHHHHHHHHHHT-EE-TTS-EE--HHHHHHHHHHHHHHHH CS
        HpaB   2 gklveefaalhrqsyqgvirkavkldfliGlaalaaeanGiekfshvqeklgelialrellyalliaaeaeaekdpsGvylPdlllanaarvlvtrlyp 100
                 ++l+e+f+++hr sy +  +k + +d+liG+aa++a++nG+ + sh+++k++e+++l+e++ a++ia++++++k +sGvyl + +la++++++vtr+++
  EPA06221.1 285 SMLIERFTCYHRRSY-V--CKTGLGDVLIGAAAAIADYNGVPNVSHIKDKIIEMTHLNETIFAAGIASSHQGHKMKSGVYLNEDMLAQVCKHNVTRFPY 380
                 7899***********.6..9******************************************************************************* PP

                 HHHHHHHHHHGGGGT----HHHHHST.THHHHHHHT-BTT.B-HHHHHHHHHHHHHHHTSHHHHHHHHHHHHTT--HHHHHHHHHHHS--HHHHHHHHH CS
        HpaB 101 riveilqdiaGGglitlPseadfknpeigpllekylrgsegvsaeeRvkllklawdltgsefggrhelyerhgaGspeaqriaiyrqydleekkelvkk 199
                 +i +++qdiaGG+++tlPse+df++p  gp+l+kyl+g++g+++e+R+++l+l++++t++  +++++++++hgaGsp+aqri+++rq+++  kk+l+k+
  EPA06221.1 381 EISRLAQDIAGGLVVTLPSEKDFRHPIAGPMLKKYLKGRKGADVENRMRILRLIENMTLGRNAVGYLTESMHGAGSPQAQRIQMQRQMQIGYKKNLAKN 479
                 *************************************************************************************************** PP

                 HCH CS
        HpaB 200 llg 202
                 l+g
  EPA06221.1 480 LAG 482
                 996 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.78   3.5e+03      48      85 ..      54      99 ..      46     104 .. 0.62
   2 ?   10.8   0.0   9.4e-05      0.42      18      75 ..     174     232 ..     150     246 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.78
                   EEEETS---.----EEEEEEE..GG......GEEE.-----BSS-T CS
  Acyl-CoA_dh_M 48 vlartekpd.rarglslflvprdap......gvsv.rrieeklGlr 85
                   + +r+e+ + ++ +l+ + v+r         ++ + +++++klG++
     EPA06221.1 54 LAVREEELAsAHSSLTGLTVNRFLHiaesaqDLVLqNKMQRKLGQN 99
                   5555333335778888888874444444444777778888888876 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 9.4e-05
                    -EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEE...TS-------EEEEEEE..GGGEEE CS
  Acyl-CoA_dh_M  18 ttaaerdggeyvlnGeKiwitnaaiatlalvlar...tekpdrarglslflvprdapgvsv 75 
                    t+++++d+++++++G+K   t+   +++++++     te+++ +  + + ++p+da+gv+ 
     EPA06221.1 174 TRVVSKDDKGIYVSGAKAHQTGCINSHWIILMPTvrlTENDK-DWAV-VGAIPADAKGVTY 232
                    778999999**************99***99987766444444.5544.77999****9985 PP

>> Bt_P21  Bacillus thuringiensis P21 molecular chaperone protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0    0.0039        17      81     110 ..      85     114 ..      75     149 .. 0.82
   2 ?    5.1   0.0    0.0034        15      44      85 ..     324     368 ..     314     384 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0039
      Bt_P21  81 qtvlnnkgnssleeqvsdifdrcvymevek 110
                 + vl+nk +  l ++    f+rcv m++ +
  EPA06221.1  85 DLVLQNKMQRKLGQNTGTCFQRCVGMDALN 114
                 569***********************9854 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0034
      Bt_P21  44 nlehekncvitst.mnqtisfenmnskemgnkays..flnqtvln 85 
                 n+ h k+ +i  t +n+ti+   + s   g+k  s  +ln+ +l 
  EPA06221.1 324 NVSHIKDKIIEMThLNETIFAAGIASSHQGHKMKSgvYLNEDMLA 368
                 889999999987648****************98775477777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (508 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 3284.03
//
Query:       EPA06222.1  [L=109]
Description: thioredoxin [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.2e-31  106.2   0.1    8.2e-31  106.1   0.1    1.0  1  Thioredoxin    Thioredoxin
    3.7e-11   43.2   0.2    1.1e-06   28.8   0.0    2.2  2  Thioredoxin_8  Thioredoxin-like
      2e-08   34.6   0.1    8.1e-08   32.7   0.1    1.8  1  Thioredoxin_2  Thioredoxin-like domain
    3.2e-06   27.2   0.1    5.1e-06   26.6   0.1    1.3  1  Thioredoxin_7  Thioredoxin-like
      4e-06   26.8   0.1    4.6e-06   26.6   0.1    1.2  1  Thioredoxin_3  Thioredoxin domain
    4.8e-06   26.4   0.1    5.7e-06   26.1   0.1    1.1  1  Thioredoxin_9  Thioredoxin
    5.3e-05   23.1   0.0    6.1e-05   22.9   0.0    1.1  1  AhpC-TSA       AhpC/TSA family
    0.00021   21.2   0.0    0.00025   21.0   0.0    1.1  1  TraF           F plasmid transfer operon protein
    0.00034   20.1   0.0    0.00034   20.1   0.0    1.0  1  OST3_OST6      OST3 / OST6 family, transporter family
    0.00036   20.2   0.2    0.00075   19.2   0.2    1.5  1  Redoxin        Redoxin
      0.001   19.0   0.0     0.0013   18.7   0.0    1.2  1  HyaE           Hydrogenase-1 expression protein HyaE
      0.004   16.8   0.2       0.01   15.4   0.2    1.8  1  DUF953         Eukaryotic protein of unknown function (DUF953
     0.0061   16.5   0.0      0.018   14.9   0.0    1.7  2  Thioredoxin_6  Thioredoxin-like domain
  ------ inclusion threshold ------
       0.01   16.0   0.1       0.64   10.2   0.0    2.1  2  Thioredoxin_4  Thioredoxin
      0.029   14.6   0.0       0.05   13.8   0.0    1.4  1  Glutaredoxin   Glutaredoxin
      0.092   12.5   0.1        1.1    9.0   0.0    2.0  2  DSBA           DSBA-like thioredoxin domain
       0.13   12.7   0.0       0.18   12.3   0.0    1.3  1  DUF836         Glutaredoxin-like domain (DUF836)


Domain annotation for each model (and alignments):
>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.1   0.1   7.7e-34   8.2e-31       4     102 ..       6     104 ..       3     105 .. 0.96

  Alignments for each domain:
  == domain 1  score: 106.1 bits;  conditional E-value: 7.7e-34
                  ESSHHHHHHHHTTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTEEEEEEESS-HHHHHHHHH CS
  Thioredoxin   4 vltkenFeeevakekklvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkngkevkkyegarekeklaafl 101
                  v  ++++e +v++++ +v+v+F+A+wCg+C+++ P++e+la+++++kvk++kv+vde ++la+ky+v +iPtl+++++g+ v++ +ga++ke+ ++++
   EPA06222.1   6 VSDAKSWEINVSNSDIPVFVDFWAQWCGPCRMVGPVVEELANDYQGKVKFVKVNVDEANELASKYNVFSIPTLIILNKGEVVSQQVGAASKESYKNMI 103
                  456788****************************************************************************************9998 PP

                  H CS
  Thioredoxin 102 k 102
                  +
   EPA06222.1 104 D 104
                  7 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0   1.1e-09   1.1e-06       4      47 ..      23      64 ..      20      65 .. 0.94
   2 !   14.5   0.0   3.1e-05     0.033      71      93 ..      63      85 ..      61      87 .. 0.87

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 1.1e-09
                   EEEEE--SSSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-SS-H CS
  Thioredoxin_8  4 vlLyfgaswcppckaftpklkelyeklkkkkkveivyvsldkke 47
                   v++ f+a wc pc+ + p + el ++++   kv++v v++d+ +
     EPA06222.1 23 VFVDFWAQWCGPCRMVGPVVEELANDYQ--GKVKFVKVNVDEAN 64
                   899************************9..***********864 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 3.1e-05
                   HHHHTT-S--TT-SEEEEE-TT- CS
  Thioredoxin_8 71 rnklkkkynvkaiPtlvvldkng 93
                    n+l++kynv +iPtl++l+k  
     EPA06222.1 63 ANELASKYNVFSIPTLIILNKGE 85
                   689*****************965 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.1   7.7e-11   8.1e-08       7     107 ..      22     101 ..      17     103 .. 0.87

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 7.7e-11
  Thioredoxin_2   7 pvlvvftdpdCpyCkklkkelkel.ddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPtivfldgkeivarlpGyvp 101
                    pv+v+f++ +C+ C+    +++el +d         ++ +++++ v+++ a+e              a ky+v++ Pt+++l++ e+v + +G+ +
     EPA06222.1  22 PVFVDFWAQWCGPCRMVGPVVEELaND---------YQGKVKFVKVNVDEANEL-------------ASKYNVFSIPTLIILNKGEVVSQQVGAAS 95 
                    89**********************444.........466699999999999875.............79*********99999998*********9 PP

  Thioredoxin_2 102 aeelea 107
                    +e ++ 
     EPA06222.1  96 KESYKN 101
                    998776 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.1   4.8e-09   5.1e-06      16      82 ..      19      82 ..      16      83 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 4.8e-09
                   HT--EEEEE--TT-HHHHHHHHHHHH-HHHHH.HHHT-EEEEESS--S-GGG.-TT-.--SSEEEEE- CS
  Thioredoxin_7 16 rgkpvlvffgaswcftCqalerdflsdeevkaalaekfvllrvdvterdanilelde.qgvPvvafld 82
                   + +pv+v+f a+wc++C+ +  ++++    ++ +++k+ +++v+v+e ++   + ++   +P++++l+
     EPA06222.1 19 SDIPVFVDFWAQWCGPCRMVGPVVEEL---ANDYQGKVKFVKVNVDEANELA-SKYNvFSIPTLIILN 82
                   578*******************99877...455****************955.3333344*****998 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.1   4.4e-09   4.6e-06      10      62 ..      32      89 ..      20     104 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 4.4e-09
                   STTCHHHHHHHHHHCHCCTCECEEECC..TTHHHH.HHCT-SSSSEE.ECT.TCEEEE CS
  Thioredoxin_3 10 CakCpklekavkeaaaekgikaevekv..tdfeei.ekygVmsvPal.vid.gkvvvs 62
                   C  C+ +  +v+e+a++ + k++++kv   + +e+ +ky+V s+P+l +++ g+vv++
     EPA06222.1 32 CGPCRMVGPVVEELANDYQGKVKFVKVnvDEANELaSKYNVFSIPTLiILNkGEVVSQ 89
                   999***************87776666655999***************77778888873 PP

>> Thioredoxin_9  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.1   5.4e-09   5.7e-06      36     115 ..      14      92 ..       3     106 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 5.4e-09
                    HHT--S-EEEEE.E--TT-HHHHHHHHHHHHHH.HH-TTEEEEEE-HHHHHHHTTTTTT-SS--SSEEEEE-TT--EEEEEE CS
  Thioredoxin_9  36 iksiekklkilv.ltedwCgDaavnvPvlakia.elnpnievkillrdenlelmdqyltngaraiPtliildeegeelgvwg 115
                    i+  + ++ ++v + ++wCg ++++ Pv++++a +++ ++++  +  de +el  +y      +iPtliil+++  + ++ g
     EPA06222.1  14 INVSNSDIPVFVdFWAQWCGPCRMVGPVVEELAnDYQGKVKFVKVNVDEANELASKYN---VFSIPTLIILNKGEVVSQQVG 92 
                    55555555555546789***************966888999999999**********5...59********99855555555 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   5.8e-08   6.1e-05      26     104 ..      21      97 ..       4     107 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 5.8e-08
                 SEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHHH-H.SSEEEE-TTSHHHHHTT-EETT CS
    AhpC-TSA  26 kpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfiekeslnfpllsDeegkvakaygvlkee 104
                  pv + f+++ wc +C+   p  ++l+++++  +v+ + v+vd+  ++++  +  s++  +++ + + v+++ g+  +e
  EPA06222.1  21 IPVFVDFWAQ-WCGPCRMVGPVVEELANDYQ-GKVKFVKVNVDEANELASKYNVFSIPTLIILNKGEVVSQQVGAASKE 97 
                 499*******.********************.68************9999999999**999999999999999988665 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   2.4e-07   0.00025     136     217 ..      27      97 ..      18     105 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.4e-07
        TraF 136 FyrgkcpyceaqapilqafadkyglevraVsvdgrplpelpnarvdkgqaarlgvkrtPalvlvdpksqkvvpvaaGllsld 217
                 F ++ c+ c++  p+++++a++y+ +v++V+v+    +el++         +++v ++P+l++ ++   +vv   +G+ s +
  EPA06222.1  27 FWAQWCGPCRMVGPVVEELANDYQGKVKFVKVNVDEANELAS---------KYNVFSIPTLIILNKG--EVVSQQVGAASKE 97 
                 77889****************************998888888.........*************998..5554445555555 PP

>> OST3_OST6  OST3 / OST6 family, transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   3.2e-07   0.00034      12     106 ..       2      85 ..       1     108 [. 0.77

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 3.2e-07
   OST3_OST6  12 gviklndenykellkgprdysvvvllTatspqfkCelCrefepefelvakswrkdekskskklfFakvdfdegkdvFqklglnsaPhlllfppkk 106
                 g+i+++d++  e+  ++ d  v+v + a+     C +Cr + p +e +a+ ++ +       + F+kv++de+ ++ +k+++ s+P l++ +  +
  EPA06222.1   2 GIIEVSDAKSWEINVSNSDIPVFVDFWAQ----WCGPCRMVGPVVEELANDYQGK-------VKFVKVNVDEANELASKYNVFSIPTLIILNKGE 85 
                 56777777777776666666666666665....6****************99988.......88*************************998833 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.2   7.1e-07   0.00075      30     105 ..      22      95 ..       7     106 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 7.1e-07
                 EEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHHHHHHHHHTT-TSEEEE-TTSHHHHHTT-TT CS
     Redoxin  30 kvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndafvkefwgkeglkfpvlsDgsaaftkalGlrl 105
                 +v+v f++  +c++C+   p +e+la+   ++ v++v v++d+ +   +  +  +++ ++++  +  ++++ G++ 
  EPA06222.1  22 PVFVDFWAQ-WCGPCRMVGPVVEELAND-YQGKVKFVKVNVDEANELASKYNVFSIPTLIILNKGEVVSQQVGAAS 95 
                 6899*****.***************999.5667*********9988777777788888888888888888888664 PP

>> HyaE  Hydrogenase-1 expression protein HyaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   1.2e-06    0.0013      49      98 ..      41      89 ..      34      99 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.2e-06
                HHHHHHCT-TTS-EEEEEETHHHHHHHHHCCT-TSSSEEEEEETTEEEEE CS
        HyaE 49 vlpEllkaFpnalraavvadreqeealaerfgvlktPsllflrdgeylgv 98
                v+ El + ++   + + v+  ++ ++la++++v+  P+l++l +ge+++ 
  EPA06222.1 41 VVEELANDYQGKVKFVKVN-VDEANELASKYNVFSIPTLIILNKGEVVSQ 89
                7899*******99999999.888899********************9975 PP

>> DUF953  Eukaryotic protein of unknown function (DUF953)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.2   9.9e-06      0.01      36      94 ..      30      79 ..       8     103 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 9.9e-06
                BSSHHHHHHHHHHHHHHHH-SS-EEEEEEE---HHHHT-TTSHHHH..TS---SSSEEE CS
      DUF953 36 sWCPdCvkaepvieealkeapedvklvrvdvGdrevWkdpanpfRkdpklkltgvPtLl 94
                 WC  C    pv+ee  ++    vk+v+v+v + +    +         +++  +PtL+
  EPA06222.1 30 QWCGPCRMVGPVVEELANDYQGKVKFVKVNVDEANELASK---------YNVFSIPTLI 79
                5*****************************9876655444.........4444455554 PP

>> Thioredoxin_6  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.5   1.5e+03     144     156 ..      13      25 ..      11      27 .. 0.86
   2 !   14.9   0.0   1.7e-05     0.018     117     160 ..      42      83 ..      38     101 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.5
                    HTT--GGG-SEEE CS
  Thioredoxin_6 144 ylglsssdlPviv 156
                    ++++s+sd+Pv+v
     EPA06222.1  13 EINVSNSDIPVFV 25 
                    589999****987 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1.7e-05
                    HHHHHHHTTTT-EEEEEETTGGHHHHHHTT--GGG-SEEEEEES CS
  Thioredoxin_6 117 iekvakefkdkinfaladaksfkrpleylglsssdlPvivivds 160
                    +e++a+++++k++f+ +++++ +++ + +++   ++P+++i+++
     EPA06222.1  42 VEELANDYQGKVKFVKVNVDEANELASKYNVF--SIPTLIILNK 83 
                    799*****************999999999777..9*****9993 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00061      0.64      15      55 ..      23      60 ..      14      70 .. 0.78
   2 ?    5.7   0.1     0.014        15     127     154 ..      61      90 ..      56     105 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00061
                   EEEEEEE-TT-HHHHHHHHHHHHHHHHHHHTTSEEEEEEE- CS
  Thioredoxin_4 15 vtvieyedlrCphCakfeeeveklleeyidtGkvkfiirdf 55
                   v  + +    C  C+     ve+l ++y  +Gkvkf+  ++
     EPA06222.1 23 V-FVDFWAQWCGPCRMVGPVVEELANDY--QGKVKFVKVNV 60
                   4.44455567******************..******97666 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.014
                    HHHHHHHHHHT--SS-EEEE..TTEEE-TT CS
  Thioredoxin_4 127 eaeskeakkagiestPtfii..ngekveep 154
                     ++ + a k ++ s Pt+ii  +ge+v+++
     EPA06222.1  61 DEANELASKYNVFSIPTLIIlnKGEVVSQQ 90 
                    55667779************9878888543 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.8e-05      0.05       5      55 ..      28      80 ..      23      87 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.8e-05
                  ESTSSHHHHHHHHHHHHTT......GGEEEEEGCCSHHHHHHHHHHHTSSSSSEEEE CS
  Glutaredoxin  5 tkptCpyCkkakrlLkelg......vkfeeidvdkdeeireelkelsgvrtvPqvfi 55
                    ++C+ C+++  + +el       vkf  ++vd+      el ++ +v ++P++ i
    EPA06222.1 28 WAQWCGPCRMVGPVVEELAndyqgkVKFVKVNVDEA----NELASKYNVFSIPTLII 80
                  4589******99999777777777999999999996....66666668888888887 PP

>> DSBA  DSBA-like thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.028        29       5      34 ..      24      57 ..      20      61 .. 0.72
   2 ?    9.0   0.0     0.001       1.1     149     188 ..      56      99 ..      35     104 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.028
                EEBT...TBHHHHHHHHHHHHHHHHCCT.EEEEE CS
        DSBA  5 ffDv...lCPyCylgkerleklaarspd.vkvvl 34
                f D+    C+ C ++ +++e+la+ +++ vk+v+
  EPA06222.1 24 FVDFwaqWCGPCRMVGPVVEELANDYQGkVKFVK 57
                555522259999**************54577765 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.001
                 HHHHHHHHHHHHHHTT-SSSSEEEE..TTC..EEEESSSSHHHH CS
        DSBA 149 vkeavrentaaaqslgvtGvPtvvv..dgk..rmvfGadrldtl 188
                 vk  v+e  ++a +++v+ +Pt ++   g+   + +Ga + + +
  EPA06222.1  56 VKVNVDEANELASKYNVFSIPTLIIlnKGEvvSQQVGAASKESY 99 
                 78899********************6433356666777766655 PP

>> DUF836  Glutaredoxin-like domain (DUF836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00017      0.18       9      62 ..      31      87 ..      27     108 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00017
                T-HHHHHHHHHHHHHCCCTT..EEEEEEETTT-CCCHCCCCT.TTTEEEECTTCGGB CS
      DUF836  9 gChlCeqakekLkelkleeg..leleviDIakdeeleakYgl.eipvlalegvkkts 62
                 C+ C  +  +++el+ + +  ++ +++++++ +el +kY++  ip l + ++ +  
  EPA06222.1 31 WCGPCRMVGPVVEELANDYQgkVKFVKVNVDEANELASKYNVfSIPTLIILNKGEVV 87
                599999998899986655545699****************97579999887754443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 687.86
//
Query:       EPA06223.1  [L=172]
Description: hypothetical protein BG20_I0565 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.7e-07   28.8   4.9    9.9e-07   28.3   4.9    1.3  1  zinc_ribbon_2   zinc-ribbon domain
    9.5e-05   22.3   1.4    0.00014   21.9   1.4    1.2  1  DZR             Double zinc ribbon
    0.00072   20.3   0.2     0.0017   19.0   0.2    1.6  2  zinc_ribbon_15  zinc-ribbon family
      0.003   16.9   4.0      0.005   16.2   4.0    1.4  1  zf-ribbon_3     zinc-ribbon domain
  ------ inclusion threshold ------
      0.078   13.1   1.4       0.12   12.5   1.4    1.2  1  UPF0547         Uncharacterised protein family UPF0547
       0.16   11.7   0.7        0.2   11.3   0.7    1.1  1  YkyA            Putative cell-wall binding lipoprotein
       0.19   11.7   2.1       0.31   11.0   2.1    1.3  1  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
        2.5    8.1   7.1        2.1    8.3   1.4    2.2  2  Nudix_N_2       Nudix N-terminal


Domain annotation for each model (and alignments):
>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   4.9   4.4e-10   9.9e-07       2      22 ..     151     171 ..     151     172 .] 0.97

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 4.4e-10
  zinc_ribbon_2   2 CpnCGaelqdnakFCpyCGtp 22 
                    C++CG  l +nakFC++CGt+
     EPA06223.1 151 CKSCGSALRPNAKFCTKCGTK 171
                    *******************97 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   1.4   6.1e-08   0.00014       1      21 [.     151     171 ..     139     172 .] 0.84

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 6.1e-08
         DZR   1 CpqCgeelppdarfCseCgtk 21 
                 C++Cg++l+p+a+fC +Cgtk
  EPA06223.1 151 CKSCGSALRPNAKFCTKCGTK 171
                 888888888888888888876 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       2.6   5.9e+03      13      31 ..      53      72 ..      50      77 .. 0.74
   2 !   19.0   0.2   7.8e-07    0.0017      63      86 .]     146     169 ..     122     169 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.6
  zinc_ribbon_15 13 elvkkkkvlklffip.vfkw 31
                    ++v  +++l+++ i+ +f++
      EPA06223.1 53 DYVVAYSALEFLAIKvLFEL 72
                    68889999999999933455 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 7.8e-07
  zinc_ribbon_15  63 sekkeCknCgkeveeefkyCpkCg 86 
                     s+ + Ck+Cg+++ ++ k+C+kCg
      EPA06223.1 146 SDGNGCKSCGSALRPNAKFCTKCG 169
                     45789******************9 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   4.0   2.2e-06     0.005       5      25 ..     151     171 ..     149     172 .] 0.90

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.2e-06
  zf-ribbon_3   5 CPnCGa.plssddnvCpyCGtk 25 
                  C +CG+ + ++ +++C++CGtk
   EPA06223.1 151 CKSCGSaL-RPNAKFCTKCGTK 171
                  889***55.***********98 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.4   5.2e-05      0.12       3      22 ..     151     170 ..     150     171 .. 0.96

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.2e-05
     UPF0547   3 CPeCeakvPvaaqfCphCGy 22 
                 C+ C + +  +a+fC  CG+
  EPA06223.1 151 CKSCGSALRPNAKFCTKCGT 170
                 *******************8 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.7     9e-05       0.2     102     147 ..      15      60 ..       5      66 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 9e-05
        YkyA 102 eaeelieameeryeaydklykaYkealeldkeLYemLkkeeltlee 147
                 ++++l +  +  ye++ + ++ Yk+ l +dke++++L++  + +  
  EPA06223.1  15 KLQSLFDDSQGYYESFLDTNNMYKKGLLSDKEFFQKLGDYVVAYSA 60 
                 566777777778999999999****************997666665 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   2.1   0.00014      0.31      14      33 ..     151     170 ..     150     172 .] 0.94

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00014
     DUF35_N  14 CpdCGtvqfPPravCphCgs 33 
                 C++CG+   P   +C++Cg 
  EPA06223.1 151 CKSCGSALRPNAKFCTKCGT 170
                 ******************96 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.4     0.049   1.1e+02       3      11 ..     151     159 ..     150     161 .. 0.84
   2 ?    8.3   1.4   0.00094       2.1       1       9 [.     163     171 ..     163     172 .] 0.90

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.049
                 -TTT--B-E CS
   Nudix_N_2   3 CsqCGtpve 11 
                 C++CG++++
  EPA06223.1 151 CKSCGSALR 159
                 999999876 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00094
                 -B-TTT--B CS
   Nudix_N_2   1 kFCsqCGtp 9  
                 kFC++CGt+
  EPA06223.1 163 KFCTKCGTK 171
                 8******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.53
# Mc/sec: 974.23
//
Query:       EPA06224.1  [L=54]
Description: hypothetical protein BG20_I0579 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-10   40.7   0.0    1.9e-10   40.7   0.0    1.0  1  Thioredoxin_3  Thioredoxin domain
    0.00092   19.4   0.0     0.0013   18.9   0.0    1.3  1  Glutaredoxin   Glutaredoxin
     0.0026   17.5   0.0     0.0034   17.1   0.0    1.1  1  KaiB           KaiB domain


Domain annotation for each model (and alignments):
>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   0.0   3.1e-14   1.9e-10      24      73 ..       2      51 ..       1      54 [] 0.93

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 3.1e-14
                   CHCCTCECEEECCTTHHHH.HHCT-SSSSEEECTTCEEEESS---CCHHHH CS
  Thioredoxin_3 24 aaekgikaevekvtdfeei.ekygVmsvPalvidgkvvvsGkvpseeeirk 73
                   ++++g+k++v++vt+ +e  eky + + P+lvidgk++++G +p++ +++k
     EPA06224.1  2 LEQLGVKYDVIDVTEKPEYlEKYPIFMAPGLVIDGKLEFTG-IPKKTDLEK 51
                   6889*********9999999*********************.*****9998 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   2.2e-07    0.0013      19      58 ..       2      37 ..       1      39 [. 0.82

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.2e-07
                  HHHTTGGEEEEEGCCSHHHHHHHHHHHTSSSSSEEEETTE CS
  Glutaredoxin 19 LkelgvkfeeidvdkdeeireelkelsgvrtvPqvfidgk 58
                  L++lgvk+++idv++ +e+ e+   +      P ++idgk
    EPA06224.1  2 LEQLGVKYDVIDVTEKPEYLEKYPIF----MAPGLVIDGK 37
                  99*************99998888544....5588888887 PP

>> KaiB  KaiB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   5.6e-07    0.0034      30      56 ..       7      33 ..       2      36 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.6e-07
                EEEEEEETTTSHCHHCCTCEESCCCCC CS
        KaiB 30 yeLqvvdvleqPelaeedrlvatPaLi 56
                ++  v+dv+e+Pe +e++ +   P L+
  EPA06224.1  7 VKYDVIDVTEKPEYLEKYPIFMAPGLV 33
                44579*******************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       197  (0.0109878); expected 358.6 (0.02)
Passed bias filter:                      178  (0.00992805); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.32s 00:00:00.77 Elapsed: 00:00:00.50
# Mc/sec: 324.40
//
Query:       EPA06225.1  [L=100]
Description: transcriptional regulator, ArsR family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-09   37.9   0.5    4.3e-09   36.1   0.1    1.8  2  HTH_5           Bacterial regulatory protein, arsR family
    2.8e-05   24.1   0.0    7.4e-05   22.7   0.0    1.6  2  HTH_20          Helix-turn-helix domain
    7.7e-05   22.2   0.4    0.00015   21.3   0.4    1.5  1  HTH_24          Winged helix-turn-helix DNA-binding
    0.00011   22.1   0.1    0.00024   20.9   0.0    1.5  2  TrmB            Sugar-specific transcriptional regulator TrmB
    0.00058   19.7   0.2      0.001   18.9   0.2    1.4  1  HTH_11          HTH domain
     0.0013   18.7   2.3     0.0019   18.1   2.3    1.4  1  HTH_45          Winged helix-turn-helix
     0.0021   18.0   0.2      0.004   17.0   0.2    1.5  1  MarR            MarR family
     0.0072   16.2   0.0      0.016   15.1   0.0    1.6  2  MarR_2          MarR family
  ------ inclusion threshold ------
       0.01   16.0   0.1      0.015   15.5   0.1    1.3  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
      0.014   15.7   1.8      0.016   15.4   1.8    1.1  1  MSV199          MSV199 domain
      0.023   14.7   0.0      0.034   14.2   0.0    1.3  1  HTH_29          Winged helix-turn helix
      0.025   15.1   0.1      0.035   14.7   0.1    1.2  1  Phage_rep_O     Bacteriophage replication protein O
       0.03   14.0   0.9       0.13   12.0   0.9    1.8  1  DUF4423         Domain of unknown function (DUF4423)
      0.035   14.2   0.0      0.053   13.6   0.0    1.3  1  DprA_WH         DprA winged helix domain
      0.053   13.5   0.1      0.093   12.7   0.1    1.4  1  HTH_12          Ribonuclease R winged-helix domain
      0.063   13.2   0.0        0.1   12.5   0.0    1.3  1  HTH_1           Bacterial regulatory helix-turn-helix protein
      0.073   13.0   1.4       0.09   12.7   1.3    1.3  1  DUF3781         Protein of unknown function (DUF3781)
      0.096   12.4   0.1       0.21   11.3   0.1    1.6  1  HTH_41          Helix-turn-helix domain
       0.11   12.4   0.1       0.32   10.8   0.0    1.7  2  HTH_10          HTH DNA binding domain


Domain annotation for each model (and alignments):
>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.1   4.5e-12   4.3e-09       3      47 .]      23      67 ..      23      67 .. 0.97
   2 ?   -0.3   0.0       1.1     1e+03      14      29 ..      85     100 .]      74     100 .] 0.75

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 4.5e-12
                HHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
       HTH_5  3 tRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVek 47
                +Rl+I+++L + +l + +la+e+gl   ++ hH k+L++ ++++k
  EPA06225.1 23 NRLRIISILKKTPLNINQLAKEMGLDYKAIQHHIKVLEKNNMITK 67
                5****************************************9986 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.1
                 SSEEHHHHHHHHTS-H CS
       HTH_5  14 gelcvcelaeelglsq 29 
                 +  +  e+ ++l++s+
  EPA06225.1  85 NMETLEEIERKLDKSK 100
                 5567789999999986 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   7.9e-08   7.4e-05      12      59 ..      24      70 ..      23      72 .. 0.94
   2 ?   -1.5   0.0       2.8   2.7e+03      26      37 ..      88      99 ..      85     100 .] 0.75

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 7.9e-08
                HHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
      HTH_20 12 RrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvre 59
                R+ri + L  + +l  ++la++++l+ + + +H++vLe+   ++  +e
  EPA06225.1 24 RLRIISIL-KKTPLNINQLAKEMGLDYKAIQHHIKVLEKNNMITKIGE 70
                9*******.*******************************99998877 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.8
                -HHHHHHHHTS- CS
      HTH_20 26 taselaerldls 37
                t++e+ + ld s
  EPA06225.1 88 TLEEIERKLDKS 99
                678888888765 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.4   1.6e-07   0.00015       4      48 .]      23      66 ..      22      66 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.6e-07
      HTH_24  4 tdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                ++++I+++L+k   +++++LA++ gl   ++  ++k Le++  I+
  EPA06225.1 23 NRLRIISILKK-TPLNINQLAKEMGLDYKAIQHHIKVLEKNNMIT 66
                57899999999.55***************************9996 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   2.5e-07   0.00024      16      65 ..      29      78 ..      28      81 .. 0.91
   2 ?   -1.1   0.0         2   1.8e+03      18      34 ..      82      98 ..      72     100 .] 0.75

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.5e-07
                HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE- CS
        TrmB 16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYrav 65
                 +lk+ p++++++a+e g+++  ++  ++ Le+  +++++ +++ ++  +
  EPA06225.1 29 SILKKTPLNINQLAKEMGLDYKAIQHHIKVLEKNNMITKIGEKYSIMYFI 78
                689*************************************9998876655 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2
                HHHCCCHHCHHCCCTTS CS
        TrmB 18 lklgpatadeiaeelgv 34
                l+l   t +ei ++l+ 
  EPA06225.1 82 LELNMETLEEIERKLDK 98
                66777788888888775 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.2   1.1e-06     0.001       2      43 ..      24      63 ..      23      72 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.1e-06
      HTH_11  2 llqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg 43
                +l i+ +L +++ p+++++LA+e+++  ++++ +Ik Le+  
  EPA06225.1 24 RLRIISIL-KKT-PLNINQLAKEMGLDYKAIQHHIKVLEKNN 63
                57899999.444.4************************9976 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   2.3     2e-06    0.0019      11      58 ..      27      74 ..      24      95 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2e-06
      HTH_45 11 ILeaisegeakkTkimykanLsykllnkYLdmLvekglikkskekYvl 58
                I +++++   +  ++ ++  L+yk ++  ++ L ++++i+k +ekY++
  EPA06225.1 27 IISILKKTPLNINQLAKEMGLDYKAIQHHIKVLEKNNMITKIGEKYSI 74
                566666889999****************************99999987 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.2   4.3e-06     0.004      11      49 ..      30      67 ..      22      69 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.3e-06
                HHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
        MarR 11 ilyeqgplsvseLakklgvskstvtrvldrLekkGlieR 49
                il  + pl++ +Lak +g++  ++   ++ Lek+++i++
  EPA06225.1 30 IL-KKTPLNINQLAKEMGLDYKAIQHHIKVLEKNNMITK 67
                33.4568******************************86 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.7e-05     0.016      12      53 ..      29      67 ..       9      71 .. 0.83
   2 ?   -1.6   0.0       2.7   2.5e+03      23      33 ..      88      98 ..      69     100 .] 0.61

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.7e-05
                HHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
      MarR_2 12 aaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                  L   p   l++++la+++gl+  a++ ++k L++  ++++
  EPA06225.1 29 SILKKTP---LNINQLAKEMGLDYKAIQHHIKVLEKNNMITK 67
                4444444...9*************************999976 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.7
                EHHHHHHHHTS CS
      MarR_2 23 tvgelarrlgl 33
                t  e++r+l+ 
  EPA06225.1 88 TLEEIERKLDK 98
                66677777765 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.1   1.6e-05     0.015      21      51 ..      38      68 ..      25      81 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.6e-05
  B-block_TFIIIC 21 qsdLakeskqdprslfyrlksLekkgLIvkq 51
                     ++Lake++ d + + +++k+Lek++ I+k+
      EPA06225.1 38 INQLAKEMGLDYKAIQHHIKVLEKNNMITKI 68
                    589**************************96 PP

>> MSV199  MSV199 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   1.8   1.7e-05     0.016      38     121 ..      10      92 ..       6      96 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.7e-05
      MSV199  38 LeflgyeG.eykkqkkkfkklLkrnnieykelkykdeeielypslkeeikllkknaiaqkkWlilevkdfKkailrlntknseki 121
                 L ++ + G +    + +++++Lk+  ++ ++l   +e   +y+ +++ ik l+kn++++k     ++  f ++ l+ln +  e+i
  EPA06225.1  10 LLWFIFAGsRGGLNRLRIISILKKTPLNINQLA--KEMGLDYKAIQHHIKVLEKNNMITKIGEKYSIMYFISTFLELNMETLEEI 92 
                 55677767344567889***************9..8999***************9999987777777777777777777666655 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   3.6e-05     0.034       1      34 [.      24      57 ..      24      63 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.6e-05
      HTH_29  1 RaqallllaeGvstvsqiAkllglsrrtvyrwlk 34
                R++++  l++   ++ q+Ak +gl+++ +++++k
  EPA06225.1 24 RLRIISILKKTPLNINQLAKEMGLDYKAIQHHIK 57
                56666666666559*****************998 PP

>> Phage_rep_O  Bacteriophage replication protein O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   3.7e-05     0.035      46      93 ..      32      79 ..      30      81 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.7e-05
  Phage_rep_O 46 ksdwisnsqlveltgisrtkvskalkeLirekviikegrkvgvnknis 93
                 k+ +++ +ql++ +g++ +++++ +k L + ++i+k g+k+++   is
   EPA06225.1 32 KKTPLNINQLAKEMGLDYKAIQHHIKVLEKNNMITKIGEKYSIMYFIS 79
                 56788899******************************9999876665 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.9   0.00014      0.13      32      77 ..      31      73 ..      23      99 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
     DUF4423 32 lkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyr 77
                lk+   ++++lak ++  ++ + +++ ++ L+k+++++k ++ ky 
  EPA06225.1 31 LKKTPLNINQLAKEMG--LDYKAIQHHIKVLEKNNMITKIGE-KYS 73
                455556999*******..*********************998.886 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   5.6e-05     0.053      14      50 ..      24      60 ..      21      68 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.6e-05
     DprA_WH 14 errvLaaLgpePvhvDqLvrrtglpaaevsaaLleLE 50
                + r+ + L  +P+ + qL+++ gl+  +++++   LE
  EPA06225.1 24 RLRIISILKKTPLNINQLAKEMGLDYKAIQHHIKVLE 60
                67999************************99988888 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   9.9e-05     0.093      12      52 ..      34      69 ..      25      75 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.9e-05
      HTH_12 12 kpigakeiaeeLkkrgydigeravRyrLrkleergltrrvg 52
                +p+  +++a+e    g d+  +a+  ++++le+++++ + g
  EPA06225.1 34 TPLNINQLAKE---MGLDY--KAIQHHIKVLEKNNMITKIG 69
                45555555544...48899..9**************99987 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00011       0.1       2      39 ..      23      61 ..      22      62 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                HHHHHHHHHHHHS.SHHHHHHHHTS-HHHHHHHHHHHHH CS
       HTH_1  2 rqlrlfvavaeeg.sftrAAeeLglsqpavsrqikrLEe 39
                ++lr+   + ++  ++++ A+e+gl ++a+ ++ik LE+
  EPA06225.1 23 NRLRIISILKKTPlNINQLAKEMGLDYKAIQHHIKVLEK 61
                6666666677776688999******************96 PP

>> DUF3781  Protein of unknown function (DUF3781)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.3   9.5e-05      0.09       2      51 ..      26      73 ..      25      92 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.5e-05
     DUF3781  2 enidkihttelgieRIkknLslseddvveyckeiildknakiekkGKnyY 51
                ++i+ ++ t l i+++ k ++l+++ +++ +k  +l+kn++i+k G +y 
  EPA06225.1 26 RIISILKKTPLNINQLAKEMGLDYKAIQHHIK--VLEKNNMITKIGEKYS 73
                578889***********************996..89999*******9995 PP

>> HTH_41  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00023      0.21       9      37 ..      38      66 ..      36      70 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00023
      HTH_41  9 IeelakeleLSvGlvQkALklLeddkais 37
                I++lake++L    +Q  +k Le++ +i+
  EPA06225.1 38 INQLAKEMGLDYKAIQHHIKVLEKNNMIT 66
                999************************97 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00034      0.32      25      49 ..      37      61 ..      35      64 .. 0.89
   2 ?   -1.8   0.0       2.9   2.8e+03      42      51 ..      87      96 ..      85      97 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00034
      HTH_10 25 tlkeLAkelGIskstlsehLrkaes 49
                ++++LAke+G+   +++ h++  e+
  EPA06225.1 37 NINQLAKEMGLDYKAIQHHIKVLEK 61
                6899****************97766 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.9
      HTH_10 42 ehLrkaeskl 51
                e L+++e+kl
  EPA06225.1 87 ETLEEIERKL 96
                7799999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1008  (0.0562218); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 756.32
//
Query:       EPA06226.1  [L=215]
Description: ribose 5-phosphate isomerase A [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-53  181.2   0.1    1.4e-53  181.0   0.1    1.0  1  Rib_5-P_isom_A  Ribose 5-phosphate isomerase A (phosphoribois
     0.0046   16.9   0.1       0.23   11.4   0.0    2.2  2  DeoRC           DeoR C terminal sensor domain


Domain annotation for each model (and alignments):
>> Rib_5-P_isom_A  Ribose 5-phosphate isomerase A (phosphoriboisomerase A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.0   0.1   1.6e-57   1.4e-53       2     171 ..      43     208 ..      42     210 .. 0.96

  Alignments for each domain:
  == domain 1  score: 181.0 bits;  conditional E-value: 1.6e-57
                     EEESSHHHHHHHHHTT--BE-GGCCSSEEEEEE--SEEETTS-EE--TTS-HHHHHHHHHTEEEEEEEEEGGGBESSTTSS-EEEEE-GGGHHHH CS
  Rib_5-P_isom_A   2 gvptSeqteelaeelgipllsldeveeidlaiDGaDevdedlnliKGgGgallrEKivaaaakkfiviadesKlveklgkfpvPveVlpfaleav 96 
                     +vptS q +  ae+ gipl++ d+ve id+++DGaD++d+++ +iKGgGgallrE i+ + +kk++v+ad+sK+v+++    vPveV p a+++v
      EPA06226.1  43 AVPTSLQIKLIAEKGGIPLVEADHVEYIDVVFDGADQIDSQKFVIKGGGGALLRENILFNLSKKVVVMADKSKFVKNFT-REVPVEVHPLARNSV 136
                     8****************************************************************************96.89************* PP

                     HHHHHHTTT-EEEE-TETTTTEE-B-TTS-EEEEEESSSBSSSHHHHHHHHHTSTTEEEESEE-S--SEEEEEET CS
  Rib_5-P_isom_A  97 arelekllggkpelReakgkdgpvvTdngnlilDvkfeekiedpeelekelksipGVvetGlFlgladkvlvgke 171
                     +++++kl gg+++lR+  +++ p++T+ngn+ilD++f ++i++p++l +++k+i+GV+e+G+Fl+  d ++ +k+
      EPA06226.1 137 IDAIRKL-GGNAQLRS-LDRGYPFFTENGNIILDCNF-GTIKNPKSLTQKIKQITGVMESGIFLRKPDVIYKAKT 208
                     *****75.*******8.7789****************.5788***************************998876 PP

>> DeoRC  DeoR C terminal sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.5   0.0    0.0068        61      12      41 ..       4      33 ..       1      50 [. 0.87
   2 !   11.4   0.0   2.6e-05      0.23      93     143 ..      70     120 ..      66     129 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.0068
       DeoRC 12 aAaeliedgdtifldaGtTtlelaraLaek 41
                 A+++++dg +i l++G  ++ +++ L++ 
  EPA06226.1  4 DALKFVKDGFVIGLGSGRAATSFVKSLSSF 33
                699****************99999999875 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 2.6e-05
       DeoRC  93 vdkaflgangidaegglttsdeeeaevkralieaarrvillaDssKfgkra 143
                 +d++f ga+ id+++ +++        ++ l + +++v+++aD+sKf k+ 
  EPA06226.1  70 IDVVFDGADQIDSQKFVIKGGGGALLRENILFNLSKKVVVMADKSKFVKNF 120
                 6888888888888877777777777778889999*************8875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1670.02
//
Query:       EPA06227.1  [L=67]
Description: ribosomal protein L24e [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-18   67.0   1.0    1.3e-18   67.0   1.0    1.0  1  Ribosomal_L24e  Ribosomal protein L24e
  ------ inclusion threshold ------
      0.014   14.9   0.2      0.023   14.2   0.2    1.4  1  zf-FLZ          zinc-finger of the FCS-type, C2-C2
      0.065   13.4   6.0        5.6    7.2   0.1    3.0  3  DUF2256         Uncharacterized protein conserved in bacteria


Domain annotation for each model (and alignments):
>> Ribosomal_L24e  Ribosomal protein L24e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.0   1.0   2.1e-22   1.3e-18       3      55 ..       5      58 ..       3      67 .] 0.92

  Alignments for each domain:
  == domain 1  score: 67.0 bits;  conditional E-value: 2.1e-22
                    X-B-TTT-SB--SS--EEEE-TTS-EEEESSHHH.HHHHHTT--GGGSTTSTTT CS
  Ribosomal_L24e  3 tekCsFsgykiyPGhGkrfvrnDgkvfrFlssKc.eklfkqkrnPrklkWTkay 55
                    ++ CsF+ +++ +G G++  +nDg+v+ F+s+Kc +++ + kr PrklkWTk+y
      EPA06227.1  5 VKPCSFCARPVAKGSGTMLAKNDGTVLWFCSAKCkKNALELKRDPRKLKWTKKY 58
                    578*******************************6677899***********99 PP

>> zf-FLZ  zinc-finger of the FCS-type, C2-C2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.2   3.9e-06     0.023      14      50 ..       6      45 ..       2      49 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.9e-06
      zf-FLZ 14 saCflCkkkLgegkDiymYrGdka...FCSeeCRqqqiel 50
                + C++C +  ++g  + + + d     FCS+ C ++ +el
  EPA06227.1  6 KPCSFCARPVAKGSGTMLAKNDGTvlwFCSAKCKKNALEL 45
                67******************9987777*******998765 PP

>> DUF2256  Uncharacterized protein conserved in bacteria (DUF2256)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1   0.00093       5.6       7      17 ..       5      15 ..       1      18 [. 0.84
   2 ?    6.5   0.1    0.0015       8.9      32      40 .]      33      41 ..      23      41 .. 0.87
   3 ?    2.0   0.4     0.039   2.3e+02      15      24 ..      50      59 ..      49      61 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00093
     DUF2256  7 sKiCavCgrpf 17
                 K+C  C rp 
  EPA06227.1  5 VKPCSFCARPV 15
                69*******97 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0015
     DUF2256 32 yCSerCrrn 40
                +CS +C++n
  EPA06227.1 33 FCSAKCKKN 41
                8*****986 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.039
     DUF2256 15 rpftwRkkWe 24
                r+++w kk+ 
  EPA06227.1 50 RKLKWTKKYV 59
                8899***985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.49
# Mc/sec: 414.89
//
Query:       EPA06228.1  [L=118]
Description: ribonuclease HI [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.3e-12   45.2   0.0    8.6e-12   44.9   0.0    1.1  1  RVT_3         Reverse transcriptase-like
    2.2e-11   44.1   0.0    2.5e-11   43.9   0.0    1.1  1  RNase_H       RNase H
  ------ inclusion threshold ------
       0.06   13.2   0.1      0.075   12.9   0.1    1.1  1  Dynactin_p22  Dynactin subunit p22
        0.1   13.1   0.1       0.12   12.9   0.1    1.1  1  YflT          Heat induced stress protein YflT


Domain annotation for each model (and alignments):
>> RVT_3  Reverse transcriptase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.9   0.0   1.9e-15   8.6e-12      33     115 ..      31     111 ..      14     117 .. 0.92

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 1.9e-15
       RVT_3  33 klqgkasveeAElqALlrGLqlalklgirrlvvegDsktvvqllngrekvksselanlldeirkllksfesvsvehipReqNr 115
                 k ++ +++ +AE++A++ +L++ ++     + + +Dsk  +++ln +  +++++l+ l +e+++l+ + +++++ ++pR++N 
  EPA06228.1  31 K-KPEITNNQAEYMAIIAALKKFVDS-TDDIAIFSDSKNTISQLNHEFAINNEKLRELAREAWSLIGKYSKITLLWVPRKENL 111
                 3.7899*****************996.599***************************************************96 PP

>> RNase_H  RNase H
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   0.0   5.6e-15   2.5e-11       4      90 ..       3      82 ..       1     112 [. 0.74

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 5.6e-15
                EEEEEEEEEECTTTCEEEEEEECTT..EEEEEEECCCCHHHHHHHHHHHHHHH.TT.SCSEEEEEES-HHHHHHHHCCCHHHHHTTSS CS
     RNase_H  4 vvvYtDGsclgnpgeggagavlykegarnisapleeaqtnnraELsAvieaLk.alksdekvniytDSkYvvkgitqwvhrwkknawk 90
                + vY+DGs      +gg g+++++   + ++++ + + tnn+aE +A+i+aLk  ++s  ++ i++DSk++++ +++   +   n++k
  EPA06228.1  3 ISVYVDGSGG---PNGGFGYFVKET-GESFYEKKP-EITNNQAEYMAIIAALKkFVDSTDDIAIFSDSKNTISQLNH---EFAINNEK 82
                689*****54...789****99644.578888888.89***************767999************996665...43333333 PP

>> Dynactin_p22  Dynactin subunit p22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   1.7e-05     0.075      90     156 ..      34     102 ..      28     104 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.7e-05
  Dynactin_p22  90 eLkk.taalleqlqeLkpvldse.eikdvpelkekLekLsqihlkqqeeveelseevkkllekYnklvl 156
                   e+++ +a+ +  +  Lk+ +ds+  i   ++ k+++++L++     +e++ el +e  +l+ kY+k++l
    EPA06228.1  34 EITNnQAEYMAIIAALKKFVDSTdDIAIFSDSKNTISQLNHEFAINNEKLRELAREAWSLIGKYSKITL 102
                   555404566778999******972577778999*********************************986 PP

>> YflT  Heat induced stress protein YflT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   2.7e-05      0.12       3      57 ..      35      91 ..      34     112 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.7e-05
        YflT  3 vyeneeellsaieelkaeGyneddiyvvakdkdrlerlaentdaetettse..eglw 57
                + +n++e ++ i  lk+   ++ddi +++  k+ +++l ++  +++e+  e  +  w
  EPA06228.1 35 ITNNQAEYMAIIAALKKFVDSTDDIAIFSDSKNTISQLNHEFAINNEKLRElaREAW 91
                56899999*********999**************************99887764444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       829  (0.0462379); expected 358.6 (0.02)
Passed bias filter:                      577  (0.0321825); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 921.03
//
Query:       EPA06229.1  [L=310]
Description: hypothetical protein BG20_I0558 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      0.006   16.7   0.1      0.012   15.6   0.1    1.5  1  MTS_N        Methyltransferase small domain N-terminal
  ------ inclusion threshold ------
      0.034   14.5   0.3       0.33   11.3   0.2    2.6  2  Flagellin_C  Bacterial flagellin C-terminal helical region


Domain annotation for each model (and alignments):
>> MTS_N  Methyltransferase small domain N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   1.4e-06     0.012      23      88 ..     121     185 ..     105     200 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.4e-06
                 -SSHHHHS--SEEEEEE..SBHHHHHHHHHHHGGG.EEE-SS--HHTT-SEEEEE--SSHHHHHHH CS
       MTS_N  23 eddlpkelkkasksvtvlsqdfnhaqalkkklkeekvefgleleaeskfdlvilylpKaKeeakyl 88 
                 +d+l  el+++ ++vtv  ++ ++ q+ k+++k++k  f+ e ++e+k d +++  pK+++ ++++
  EPA06229.1 121 DDRL-YELSSKIANVTVPESKKEETQEAKQEIKTNKKVFDFEKPKETKLDPIVIPQPKSRQSFELT 185
                 3444.488888899***99******************************************98875 PP

>> Flagellin_C  Bacterial flagellin C-terminal helical region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.19   1.7e+03      44      65 ..       9      30 ..       4      34 .. 0.85
   2 ?   11.3   0.2   3.7e-05      0.33      19      77 ..      34      92 ..      27      96 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.19
                 CHHCCHHHHHHHHHHHHHHHHH CS
  Flagellin_C 44 srledvDpaeestrvtklqili 65
                 s+l +v +a+++ ++ ++++++
   EPA06229.1  9 SSLAGVATAAAARKMPRNKTQL 30
                 6788899999999999999985 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 3.7e-05
                 HHHHHHHHHHHHHHHHHHCHHHHHHCHHCCHHHHHHHHHHHHH..HHHHHHHHHHHHHCTC CS
  Flagellin_C 19 GavqnRlesaitnlkaqsenlkaaesrledvDpaeestrvtkl..qiliqasyallaqanq 77
                 Ga ++ ++s+i++lk  +++l++ +srl + D    + + +kl  + + q+++ +la++ +
   EPA06229.1 34 GA-SSHIKSQINSLKIEKDILTKTISRLYQSDLEFPKIQRDKLllKYQHQLGI-VLARLEK 92
                 54.4789*************************988888888861134444443.5666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1585  (0.0884043); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2028.71
//
Query:       EPA06230.1  [L=463]
Description: phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-36  124.8   0.0    3.4e-36  124.0   0.0    1.5  1  PGM_PMM_I    Phosphoglucomutase/phosphomannomutase, alpha/bet
    5.9e-25   87.9   0.0    1.2e-24   86.8   0.0    1.6  1  PGM_PMM_II   Phosphoglucomutase/phosphomannomutase, alpha/bet
    2.6e-23   82.4   0.0    4.5e-23   81.6   0.0    1.4  1  PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/bet
    1.5e-08   34.7   0.0    3.4e-08   33.6   0.0    1.5  1  PGM_PMM_IV   Phosphoglucomutase/phosphomannomutase, C-termina


Domain annotation for each model (and alignments):
>> PGM_PMM_I  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.0   0.0   7.6e-40   3.4e-36       3     134 ..       4     130 ..       2     134 .. 0.96

  Alignments for each domain:
  == domain 1  score: 124.0 bits;  conditional E-value: 7.6e-40
                 GBBTTCEEEECCHCTBSCCHHHHHHHHHHHHCHHCSTS-EEEEEE-S-TTHHHHHHHHHHHHHCCT-CEEEEEEB-HHHHHHHHHHCCECEEEEE--TT CS
   PGM_PMM_I   3 kfgtsGlRgkvgegeltpelveklgqaiaeylkaeakkkkvvvGrDtRvssrelaealaaglaanGvevillgllptPavsfairklkadagimitaSH 101
                  fgt+G+Rg+++e+ +t e+v  ++ aia+y+k+    +++++G+D+R ss+ +++ +++ l  +G++  ++gl+ptP + +a+++l++++gimitaSH
  EPA06230.1   4 FFGTNGIRGVFSED-FTLEFVHDMTLAIATYFKR----GPILIGYDGRESSPIISKVVCSALNYAGLDCNVAGLVPTPCLEYAVKSLGYSGGIMITASH 97 
                 59**********65.9*****************9....9************************************************************ PP

                 S-TTCCCEEEEETTTCE--CHHHHHHHHHHCCT CS
   PGM_PMM_I 102 nppeyngiKvylsnGgpispeveekIeaiieke 134
                 npp+yngiK   ++G++is+e+e  Ie+i+ k+
  EPA06230.1  98 NPPQYNGIKPAAKDGVEISREDELIIEDIFLKK 130
                 ****************************99876 PP

>> PGM_PMM_II  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.8   0.0   2.8e-28   1.2e-24       2     103 .]     151     251 ..     150     251 .. 0.98

  Alignments for each domain:
  == domain 1  score: 86.8 bits;  conditional E-value: 2.8e-28
                 HHHHHGGGTS-HHHHHHHT-EEEEE-TT-TTHHHHHHHHHHTT-EEEES-----TT-TTSS----TT-TTTTHHHHGGGGG-SEEEEE-TTS-BEEEEE CS
  PGM_PMM_II   2 aYiealkekvdseaikksglkvvidplhGaggeilkellkelgvdvvelnaepdpdfptkapnpeekealkllielvkkegadlglafDgDaDRlgvvd 100
                  Yi+++ +++ds++ik+++lkvv+d ++Ga + +++  +k++g+++  +n++ d+ f+++ ++p++ ++l++l+++v +++adlg+afDgD+DR +++d
  EPA06230.1 151 VYINGIISQIDSKKIKSKNLKVVLDLGNGAQAVTAPLFCKSIGCEIFLINEKIDGLFSGRGSEPTP-QNLSELSKIVLQNKADLGIAFDGDGDRSIFCD 248
                 6*****************************************************************.*******************************9 PP

                 TTE CS
  PGM_PMM_II 101 erG 103
                 ++G
  EPA06230.1 249 DKG 251
                 987 PP

>> PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.6   0.0     1e-26   4.5e-23       2     112 ..     256     364 ..     255     366 .. 0.95

  Alignments for each domain:
  == domain 1  score: 81.6 bits;  conditional E-value: 1e-26
                  HHHHHHHHHHHHHCHCSTTTCEEEEETTS-THHHHHHHHTT-EEEEESSSCHHHHHHHHHTTECEEEETTCEEEETTTBSS--HHHHHHHHHHHHHHH CS
  PGM_PMM_III   2 gdqllallakylleeklkpgagvvktvmtslalervakklgiklvetkvGdkyvleemkeegavlGgEeSghiifldeattkDGilaallvleilaet 99 
                  gd+ +++l+k +l++  +p+  vv+ + + + +erva++++ k+++tkvG+  v ++m  ++a++G+Ee+g+++f+++++ +DG ++ +l+le+la++
   EPA06230.1 256 GDKSALVLTKFILKN--NPNSLVVTCLNSGSSIERVANEFNSKVIRTKVGSVEVSRKMVPTNALIGFEENGGFMFGKHNQVRDGCMTLALMLELLANS 351
                  9***********995..55666**************************************************************************** PP

                  TS-HHHHHHHHHH CS
  PGM_PMM_III 100 gkslselleellk 112
                  +kslse++ +l++
   EPA06230.1 352 EKSLSEIILDLPP 364
                  *******988876 PP

>> PGM_PMM_IV  Phosphoglucomutase/phosphomannomutase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.0   7.5e-12   3.4e-08      16      66 ..     386     436 ..     371     442 .. 0.79

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 7.5e-12
                 CCCCCTTHHCCCCCCCCGCCEEEE.EEEETTCCEEEEEEEESSHHHHHHHH CS
  PGM_PMM_IV  16 laallkvasikeglkilledGrrlavRpSGTepllrvyvEaksdeelarla 66 
                 l++ + + ++ +g+ki      ++ +RpSGTep +r+y Ea s+++l++l 
  EPA06230.1 386 LKDEFPNSDTTDGIKISSDSKNWVMIRPSGTEPIIRIYGEAESQQKLDTLM 436
                 44444444899*****999999999*******************9998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 2860.61
//
Query:       EPA06231.1  [L=698]
Description: acetyl coenzyme A synthetase (ADP forming), alpha domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-79  266.4   1.0      3e-79  265.6   1.0    1.4  1  ATP-grasp_5    ATP-grasp domain
      5e-52  175.4   2.3    5.3e-52  175.3   0.8    1.9  2  Succ_CoA_lig   Succinyl-CoA ligase like flavodoxin domain
      5e-21   75.4   0.7    1.8e-20   73.5   0.1    2.2  3  CoA_binding_2  CoA binding domain
    2.7e-07   31.2   1.0    2.7e-07   31.2   1.0    2.5  2  CoA_binding    CoA binding domain
    5.8e-05   22.7   2.0    0.00012   21.7   2.0    1.6  1  ATP-grasp_2    ATP-grasp domain
     0.0032   16.6   0.3     0.0086   15.2   0.3    1.7  1  Dak1_2         Dihydroxyacetone kinase family
     0.0055   16.2   0.2       0.01   15.3   0.2    1.4  1  CPSase_L_D2    Carbamoyl-phosphate synthase L chain, ATP bind
  ------ inclusion threshold ------
       0.11   12.0   0.2       0.41   10.2   0.2    1.9  1  ATP-grasp      ATP-grasp domain


Domain annotation for each model (and alignments):
>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  265.6   1.0   1.3e-82     3e-79       2     221 ..     477     697 ..     476     698 .] 0.98

  Alignments for each domain:
  == domain 1  score: 265.6 bits;  conditional E-value: 1.3e-82
  ATP-grasp_5   2 alaegrtlLteaeakelleaygipvvetrlassaeeaveaaeeigypvvlKivspdilhKtdvgGvrlnlkdaeevraaaeeilervkekspearieg 99 
                  +++e+r  L e+e +e+l+ayg+p++++ la+++++a++++++igypvv+Ki+sp+i+hK+d+gGv++nl++++e+++a+++i++++k+++++a+i+g
   EPA06231.1 477 VKKEKRPNLLEEEGQEVLKAYGLPLPKSALAKTEADAIKIVKQIGYPVVMKIASPQIIHKSDAGGVKVNLTNDSEIKEAFKTIVANAKKYNKNAEIKG 574
                  78999********************************************************************************************* PP

  ATP-grasp_5 100 vlVqemakrggrElivgvteDpvFGpvilfGlGGtavevlkdvavalpplnstlareliertkaskllkgvrgekkadlaaleellvrlsqLvvdlpe 197
                  vl++em+k gg Eli+g++ +p FGpvi++G+GG++vevlkdv+++l+p+++++a ++i ++k+ kll+gvrgek++d+a+l+e+++rlsqLv+d++e
   EPA06231.1 575 VLIVEMVK-GGKELIIGSKLEPGFGPVIMLGMGGIYVEVLKDVTFKLAPVTDKEADDMIASIKTQKLLQGVRGEKPSDIAKLSECIQRLSQLVTDFKE 671
                  ********.***************************************************************************************** PP

  ATP-grasp_5 198 IreldinPllveeeg..vvalDarir 221
                  I+eld+nP+lv e+g  + +lD+ri 
   EPA06231.1 672 IKELDMNPVLVMEKGkgCKILDVRIG 697
                  ***********995555*******96 PP

>> Succ_CoA_lig  Succinyl-CoA ligase like flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       4.8   1.1e+04      80      98 ..      88     107 ..      79     112 .. 0.68
   2 !  175.3   0.8   2.4e-55   5.3e-52       2     137 ..     154     291 ..     153     292 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 4.8
  Succ_CoA_lig  80 rk.kpvvvlksGrseagara 98 
                   +k k v+++ +G +e  ++ 
    EPA06231.1  88 KKvKGVIIITAGFKEVDEEG 107
                   33688999999987766555 PP

  == domain 2  score: 175.3 bits;  conditional E-value: 2.4e-55
  Succ_CoA_lig   2 GkialisqSGalalalldwaasrglgfskvvslGneadvdvadlleylaedpetkvillylEsirdgrkflsaarraark..kpvvvlksGrseaga 96 
                   Gkial+sqSGa+++al++ a+++g+gfs v+s+Gn+a +++ d+l+ la++++tkvi++ylE+++dg++fl++++++++k  kpv+vlksGrs++ga
    EPA06231.1 154 GKIALVSQSGAICAALVEDASAQGIGFSAVISMGNKAAMSEVDILKILANHNQTKVIVMYLEDMGDGQEFLKVCKNITKKlkKPVLVLKSGRSPEGA 250
                   9*****************************************************************************9999*************** PP

  Succ_CoA_lig  97 raaashtgalagsdavvdaafrqaGvlrvdsleelfdaael 137
                   +aa+shtgal+gsd+++da+++q+G++rvd++eelfd+a +
    EPA06231.1 251 KAAMSHTGALMGSDEIYDALLKQSGAIRVDTMEELFDYAVA 291
                   *************************************9976 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.5   0.1   8.2e-24   1.8e-20       1     114 [.      10     134 ..      10     135 .. 0.97
   2 ?   -2.7   0.0       3.7   8.4e+03      67      80 ..     165     178 ..     152     212 .. 0.62
   3 ?   -2.9   0.0       4.2   9.4e+03      53      78 ..     192     217 ..     179     221 .. 0.78

  Alignments for each domain:
  == domain 1  score: 73.5 bits;  conditional E-value: 8.2e-24
                    --EEEET--S-TTSHHHHHHHHHHH..HT--EEEESSS-SEETTEES----T....T--EEEE-S-HHHHGGGHHHHHHH--SEEEE-TT...... CS
  CoA_binding_2   1 rtiaVvGasdnpgkfgykvlrylle..hglpvvpVnpkeeeilgekvyaslaedpepvdlvdvftppeatpeivkealalgakavwlqpg...... 88 
                    ++ia++Gasd++g+ g  +++++ +  +g  v+pV p++++++ +++y+s+ + p+pvdl++++++   ++++++e++++++k+v++  +      
     EPA06231.1  10 KSIAIIGASDKRGSVGATITSNIMNgfKG-IVYPVSPTRPTVFYKTAYKSVMDIPKPVDLAVIVINNLLVADVLEECGKKKVKGVIIITAgfkevd 104
                    79************************999.9*********************868********************************9999***** PP

                    ....---HHHHHHHHHTT-EEE.ES-HHHH CS
  CoA_binding_2  89 ....sedeeaaelaeeagirvvgdrCilve 114
                         +++++ ++a++++i+++g++C++v+
     EPA06231.1 105 eegaKREQKIKDIAKKYKIQIIGPNCLGVM 134
                    ****************************97 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.7
                    HHGGGHHHHHHH-- CS
  CoA_binding_2  67 atpeivkealalga 80 
                    +++++v++a+a+g+
     EPA06231.1 165 ICAALVEDASAQGI 178
                    44555555555543 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 4.2
                    ..T--EEEE-S-HHHHGGGHHHHHHH CS
  CoA_binding_2  53 pepvdlvdvftppeatpeivkealal 78 
                     ++vd++ ++ + + t  iv +++++
     EPA06231.1 192 MSEVDILKILANHNQTKVIVMYLEDM 217
                    56899999999999999988887766 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   1.0   1.2e-10   2.7e-07       3      96 .]       9      99 ..       8      99 .. 0.93
   2 ?   -1.9   0.1       2.5   5.6e+03       4      51 ..     154     201 ..     152     211 .. 0.73

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 1.2e-10
                 TEEEEEETTTSHHHHHHHHHHHHHHECEE.EEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHHHHHHHHHTT-SEEEEESST CS
  CoA_binding  3 dtkviviGagglgiaglyhfkeklkygik.avfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesaqeavdelveagikgiviiteg 96
                 ++++++iGa+ + + ++ ++ +++  g+k +v++v+p+    +v   ++yksv ++++   vd avi++ +  ++++ +e+ ++++kg++iit+g
   EPA06231.1  9 PKSIAIIGASDKRGSVGATITSNIMNGFKgIVYPVSPT--RPTVFYKTAYKSVMDIPKP--VDLAVIVINNLLVADVLEECGKKKVKGVIIITAG 99
                 579*********999996777777779998********..99*****************..********************************86 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.5
                  EEEEEETTTSHHHHHHHHHHHHHHECEEEEEEC-TTTTTCEETTEEEE CS
  CoA_binding   4 tkviviGagglgiaglyhfkeklkygikavfgvnprkvgtevlglpvy 51 
                  +k++++  +g   a l+  ++  ++g++av+  + + + +ev+ l++ 
   EPA06231.1 154 GKIALVSQSGAICAALVEDASAQGIGFSAVISMGNKAAMSEVDILKIL 201
                  566677777776667777778888889999888888888888877776 PP

>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   2.0   5.4e-08   0.00012       1     135 [.     484     613 ..     484     682 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 5.4e-08
                  BE-HHHHHHHHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEE.E--SSSTCCCTTCEEEESSH.HHHHHHHHCCTTSEEE-TTS-TT-EEE--EE CS
  ATP-grasp_2   1 nlhEyqakeilakygvkvpegevaesaeeaeeaakklgekelvvK.aQvlaGGRGKagGvklvksk.eeakeaakellgkelvtkqtgkeGkkvekvl 96 
                  nl E +++e+l+ yg++ p++++a+++ +a +++k++g  + v+K a  ++  +  agGvk+  ++ +e+kea k+++ +  +     ++  +++ vl
   EPA06231.1 484 NLLEEEGQEVLKAYGLPLPKSALAKTEADAIKIVKQIGYPV-VMKiASPQIIHKSDAGGVKVNLTNdSEIKEAFKTIVANAKK----YNKNAEIKGVL 576
                  6788899*********************************9.55536667778999*****9765516777777777766555....5667899**** PP

                  EEE---ECEEEEEEEEEETTTTEEEEEEESSTTS-HHHH CS
  ATP-grasp_2  97 veealdikkElYlsivlDraskkvvviaSseGGvdiEev 135
                  + e+++  kEl ++  l+    ++v+++  +GG+ +E +
   EPA06231.1 577 IVEMVKGGKELIIGSKLEPGF-GPVIML-GMGGIYVEVL 613
                  **********99998887543.455554.4677777654 PP

>> Dak1_2  Dihydroxyacetone kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.3   3.8e-06    0.0086     113     212 ..     176     280 ..     105     285 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.8e-06
      Dak1_2 113 kslgvdevieggqtmnPstedllkaiekvnakevivLp.....nnkniilaaeqaaelaedknvvviptktivqGlaallvfdper.sleenveamaea 205
                 ++ g++ vi+ g+++  s  d+lk + + n+ +viv+      + ++++  ++ +++ + +k+v v+++   ++G  a++++  +    +e  +a+ ++
  EPA06231.1 176 QGIGFSAVISMGNKAAMSEVDILKILANHNQTKVIVMYledmgDGQEFLKVCKNITKKL-KKPVLVLKSGRSPEGAKAAMSHTGALmGSDEIYDALLKQ 273
                 56799*************88****************75211113344444444444444.345*****************9998886777777777777 PP

      Dak1_2 206 akavktg 212
                  +a++++
  EPA06231.1 274 SGAIRVD 280
                 7777665 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.2   4.6e-06      0.01       6      75 ..     491     564 ..     487     589 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.6e-06
                  HHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTC.......CTTTTEEEESSHHHHHHHHHHHHHHHH CS
  CPSase_L_D2   6 kealkkinvpvvpssaapvetleealaiakeigyPviikaafg.......lGGkGmrvarneeelaelvkkalaeak 75 
                  +e lk+ + p+ +s+ a  +t+ +a++i+k+igyPv++k a          GG    + +n++e++e++k+ +a+ak
   EPA06231.1 491 QEVLKAYGLPLPKSALA--KTEADAIKIVKQIGYPVVMKIASPqiihksdAGGVKVNL-TNDSEIKEAFKTIVANAK 564
                  67788999999999999..*******************98753111111134444443.455566666666666554 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.2   0.00018      0.41       2      61 ..     495     559 ..     494     588 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00018
                 HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEE....ESSS-CTTTTEEE.ECTCCGHHCHHHHC CS
   ATP-grasp   2 eklglpvprflaveskeeleeaaeelglpvvvK....arrlgydGkGqsv.vrseedleqaleal 61 
                 ++ glp+p+ +++++++++ ++++++g+pvv+K    + ++ +d  G +v + +++++++a++++
  EPA06231.1 495 KAYGLPLPKSALAKTEADAIKIVKQIGYPVVMKiaspQIIHKSDAGGVKVnLTNDSEIKEAFKTI 559
                 6789*****************************33333356666666555355666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (698 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       678  (0.0378158); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.71u 0.30s 00:00:01.01 Elapsed: 00:00:00.47
# Mc/sec: 4440.47
//
Query:       EPA06232.1  [L=48]
Description: hypothetical protein BG20_I0573 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       267  (0.0148921); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.25s 00:00:00.57 Elapsed: 00:00:00.40
# Mc/sec: 362.97
//
Query:       EPA06233.1  [L=143]
Description: hypothetical protein BG20_I0582 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.4e-13   48.3   0.1    9.4e-13   47.8   0.1    1.3  1  HTH_AsnC-type    AsnC-type helix-turn-helix domain
    8.1e-11   41.3   0.1    1.3e-10   40.7   0.1    1.3  1  HTH_24           Winged helix-turn-helix DNA-binding
    2.1e-05   24.7   4.3    3.9e-05   23.9   4.3    1.5  1  Arc_trans_TRASH  Archaeal TRASH domain
    8.9e-05   22.3   0.0    0.00017   21.4   0.0    1.4  1  TrmB             Sugar-specific transcriptional regulator Trm
    0.00041   19.7   0.0    0.00061   19.1   0.0    1.2  1  HTH_Tnp_ISL3     Helix-turn-helix domain of transposase famil
    0.00079   19.2   0.0     0.0014   18.4   0.0    1.5  1  HTH_5            Bacterial regulatory protein, arsR family
     0.0043   17.1   1.5       0.28   11.3   1.5    2.2  1  DUF2250          Uncharacterized protein conserved in archaea
     0.0058   16.7   0.0     0.0096   16.0   0.0    1.4  1  HTH_9            RNA polymerase III subunit RPC82 helix-turn-
     0.0059   16.3   0.0      0.012   15.4   0.0    1.4  1  HTH_38           Helix-turn-helix domain
  ------ inclusion threshold ------
      0.012   15.4   0.0      0.019   14.9   0.0    1.2  1  MarR_2           MarR family
      0.022   14.5   0.0      0.038   13.8   0.0    1.4  1  HTH_23           Homeodomain-like domain
       0.03   14.2   3.6      0.066   13.2   3.6    1.5  1  zf-FCS           MYM-type Zinc finger with FCS sequence motif
      0.049   14.4   0.7      0.049   14.4   0.7    1.8  1  ATPase-cat_bd    Putative metal-binding domain of cation tran
      0.051   13.3   0.0      0.084   12.6   0.0    1.5  1  DUF4423          Domain of unknown function (DUF4423)
      0.087   13.0   0.2       0.24   11.6   0.0    1.7  2  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
      0.088   12.5   0.0       0.16   11.6   0.0    1.5  1  Sigma70_r4_2     Sigma-70, region 4


Domain annotation for each model (and alignments):
>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8   0.1   8.4e-16   9.4e-13       2      41 ..       6      45 ..       6      46 .. 0.99

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 8.4e-16
  HTH_AsnC-type  2 DeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrL 41
                   DeiD++I+e L +d+R s++++++++ +S++tv++R++rL
     EPA06233.1  6 DEIDIAIIESLLKDGRKSFRQISREIKVSTPTVQARYERL 45
                   9**************************************9 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   0.1   1.1e-13   1.3e-10       2      48 .]       6      52 ..       5      52 .. 0.98

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 1.1e-13
      HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                de+d++I+e L k++r s r++++++ +S +tv +r +rL++ GlIk
  EPA06233.1  6 DEIDIAIIESLLKDGRKSFRQISREIKVSTPTVQARYERLVNVGLIK 52
                99*******************************************97 PP

>> Arc_trans_TRASH  Archaeal TRASH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   4.3   3.5e-08   3.9e-05       1      36 [.      96     131 ..      96     132 .. 0.97

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 3.5e-08
  Arc_trans_TRASH   1 CDYCGkeivgePivyklknkvYyvCCktCkselkkk 36 
                      CD C + i ++P+v+k+ n   ++CC +C+s  k+k
       EPA06233.1  96 CDLCKGPISDKPHVLKIANFERFFCCTSCRSLYKEK 131
                      *******************************99997 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   1.5e-07   0.00017      10      54 ..       9      53 ..       6      57 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.5e-07
                CCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEE CS
        TrmB 10 EakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVer 54
                ++ +   Llk g+++ ++i++e++v+ ++v+   ++L++ Gl++ 
  EPA06233.1  9 DIAIIESLLKDGRKSFRQISREIKVSTPTVQARYERLVNVGLIKS 53
                6666678***********************************986 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   5.4e-07   0.00061      20      52 .]      13      46 ..       9      46 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 5.4e-07
  HTH_Tnp_ISL3 20 ilellles.rsvkavArqlgvSwtTVwrildryv 52
                  i  ll+++ +s+++++r+  vS+ TV+ ++ r+v
    EPA06233.1 13 IESLLKDGrKSFRQISREIKVSTPTVQARYERLV 46
                  445677779*********************9986 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.3e-06    0.0014       6      47 .]      11      53 ..       6      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.3e-06
                HHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
       HTH_5  6 kILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVek 47
                 I+ +L + g +++ ++++e+++s +tv     +L + GL+++
  EPA06233.1 11 AIIESLLKdGRKSFRQISREIKVSTPTVQARYERLVNVGLIKS 53
                588888888********************99999999999975 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   1.5   0.00025      0.28       7      56 ..       6      55 ..       2      89 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00025
     DUF2250  7 delalkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlerve 56
                de ++++++ l k +    ++i++e++++   v+  +++L ++GL++ v+
  EPA06233.1  6 DEIDIAIIESLLKDGRKSFRQISREIKVSTPTVQARYERLVNVGLIKSVS 55
                566778888888888888899*************************9986 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   8.5e-06    0.0096      17      45 ..      11      39 ..       6      52 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 8.5e-06
                HHHHHHHHHSSBEHHHHHHHHSSTHHHHH CS
       HTH_9 17 kVvetLlrkgrltlrelvkktkLsldqVk 45
                +++e Ll+ gr++ r++++++k+s   V 
  EPA06233.1 11 AIIESLLKDGRKSFRQISREIKVSTPTVQ 39
                79*********************998885 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0     1e-05     0.012      12      37 ..      12      38 ..       9      39 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1e-05
      HTH_38 12 eIerllaeG.lslreIArrLgrspsTI 37
                 Ie ll+ G +s+r+I r++++s+ T+
  EPA06233.1 12 IIESLLKDGrKSFRQISREIKVSTPTV 38
                69*********************9998 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.7e-05     0.019      18      54 ..      19      54 ..      11      59 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.7e-05
                TTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
      MarR_2 18 pgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                +gr+ + +++ r+ ++s ++v+ + +rLv  GL+  +
  EPA06233.1 19 DGRK-SFRQISREIKVSTPTVQARYERLVNVGLIKSV 54
                5555.999**************************765 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.4e-05     0.038      13      38 ..      15      43 ..      10      51 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.4e-05
      HTH_23 13 llae..GlsvreIAreLgvsrrTvy.rwl 38
                 l++  ++s r+I+re  vs  Tv+ r+ 
  EPA06233.1 15 SLLKdgRKSFRQISREIKVSTPTVQaRYE 43
                4554599*****************95554 PP

>> zf-FCS  MYM-type Zinc finger with FCS sequence motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   3.6   5.8e-05     0.066       5      41 .]      95     128 ..      93     128 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.8e-05
      zf-FCS   5 rCwfCkkyikgkpeftyvlendgvvgqFCStsCldsY 41 
                 +C+ Ck  i++kp    vl + + +  FC+tsC++ Y
  EPA06233.1  95 KCDLCKGPISDKPH---VLKIANFERFFCCTSCRSLY 128
                 8************7...9****************998 PP

>> ATPase-cat_bd  Putative metal-binding domain of cation transport ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.7   4.4e-05     0.049       1      36 [.      95     129 ..      95     137 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.4e-05
  ATPase-cat_bd   1 aCyHCglpveesaklkaeiegeerefCCkGCqavaq 36 
                    +C  C+ p++++ ++  +i++ er fCC+ C+++++
     EPA06233.1  95 KCDLCKGPISDK-PHVLKIANFERFFCCTSCRSLYK 129
                    6999*****886.78899*************99886 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   7.5e-05     0.084      32      72 ..      17      55 ..      10      95 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.5e-05
     DUF4423 32 lkdfkadpeelakrlrpkisaeevekalefLlklgllkkde 72
                lkd++++ +++++ ++  +s+  v++  e+L+++gl+k   
  EPA06233.1 17 LKDGRKSFRQISREIK--VSTPTVQARYERLVNVGLIKSVS 55
                78999***********..*******************9865 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00021      0.24      26      53 ..      25      52 ..      18      55 .. 0.90
   2 ?   -1.7   0.0       3.2   3.5e+03       1      14 [.      62      75 ..      62      90 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00021
                    HHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
  Fe_dep_repress 26 kdlaerLnvspssVsemlkkLekdGyve 53
                     +++++++vs ++V+   ++L + G+++
      EPA06233.1 25 RQISREIKVSTPTVQARYERLVNVGLIK 52
                    69*******************9999986 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.2
                    X--HHHHHHHHHHH CS
  Fe_dep_repress  1 dLvestEdYLetIY 14
                    +L ++tE+ +e I 
      EPA06233.1 62 MLENKTEKHIEKIK 75
                    67788888888874 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00015      0.16      27      49 ..      22      44 ..      16      46 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00015
                  --HHHHHHHHT--HHHHHHHHHH CS
  Sigma70_r4_2 27 lsykEIAellgisegtVksrlsR 49
                  +s ++I++++++s  tV+ r+ R
    EPA06233.1 22 KSFRQISREIKVSTPTVQARYER 44
                  6999****************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1247  (0.0695521); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 972.20
//
Query:       EPA06234.1  [L=149]
Description: nucleoside diphosphate kinase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-49  167.6   0.0    1.5e-49  167.4   0.0    1.0  1  NDK       Nucleoside diphosphate kinase
  ------ inclusion threshold ------
       0.17   12.0   0.0        0.3   11.2   0.0    1.4  1  DsrH      DsrH like protein


Domain annotation for each model (and alignments):
>> NDK  Nucleoside diphosphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.4   0.0   1.7e-53   1.5e-49       1     131 [.      19     149 .]      19     149 .] 0.99

  Alignments for each domain:
  == domain 1  score: 167.4 bits;  conditional E-value: 1.7e-53
                 EEEEEEE-HHHHHTT-HHHHHHHHHHHT-EEEEEEEECE-HHHHHHHTGGGTTSTTHHHHHHHHTSSEEEEEEEESTTHHHHHHHHH--SSTTTSSTTS CS
         NDK   1 ertlvliKPdavkrgligeiisrleekglkivalkmlrlteeqaeehYaehkgkpffeelvefmtsgpvvalvlegedaiekvreliGatnpaeaapgt 99 
                 ++tl ++KPdav+r+l+ge+i+r+e+kg+k+++lkm+++t++qae++Y  hk+kpff el++f+tsgpvva ++eg++ai++ r +iGat++ eaapg+
  EPA06234.1  19 QQTLFIVKPDAVARKLTGEVIARFERKGFKLLKLKMFTFTQKQAENFYGVHKDKPFFGELTSFITSGPVVAAIIEGNNAIATTRIMIGATKSFEAAPGS 117
                 79************************************************************************************************* PP

                 HHHHH-SSSTT-SEEE-SSHHHHHHHHHHHST CS
         NDK 100 iRadfgvslgeNlvHgSdseesaereiklfFk 131
                 iR+dfg+  ++N++H+Sds+es ++e ++ F+
  EPA06234.1 118 IRGDFGLGFSDNIIHASDSQESFDHESRVAFE 149
                 ***************************99995 PP

>> DsrH  DsrH like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   3.4e-05       0.3      37      69 ..      10      42 ..       5      54 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.4e-05
                TTHHHHHTSSSEEEEEHHHHHHTT-TTSB-TTS CS
        DsrH 37 rllkalkeasvklyaLkeDleARGlteqlsegv 69
                + ++++k ++++l++ k+D +AR lt ++++++
  EPA06234.1 10 NSTQEIKLTQQTLFIVKPDAVARKLTGEVIARF 42
                55677888899***************7787766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 957.90
//
Query:       EPA06235.1  [L=520]
Description: hypothetical protein BG20_I0545 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.4e-09   35.9   0.3      2e-08   34.3   0.3    1.9  1  He_PIG        Putative Ig domain
  ------ inclusion threshold ------
      0.042   14.6   1.4         13    6.6   0.1    2.5  2  Occludin_ELL  Occludin homology domain
       0.16   12.0   6.0       0.34   10.9   6.0    1.5  1  Trypan_PARP   Procyclic acidic repetitive protein (PARP)


Domain annotation for each model (and alignments):
>> He_PIG  Putative Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.3   3.4e-12     2e-08      12      46 ..     178     212 ..     173     215 .. 0.90

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 3.4e-12
      He_PIG  12 LPsGLtLdsstGtitGtpdqtvapGsytftVtatd 46 
                  P+G +++s+tG +t+tp+ ++ pGsy f++ a  
  EPA06235.1 178 APTGASINSETGQFTWTPTESQSPGSYVFDIVAQK 212
                 5******************************9975 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.2    0.0025        15       9      31 ..     281     303 ..     274     309 .. 0.84
   2 ?    6.6   0.1    0.0021        13       9      31 ..     330     352 ..     323     365 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0025
  Occludin_ELL   9 qrerYkaeFnkeYkeYkelhael 31 
                   +  +Yk+ F+++++eY ++++ +
    EPA06235.1 281 NEPTYKKWFDTNFPEYTSIYQAV 303
                   5678**************99876 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0021
  Occludin_ELL   9 qrerYkaeFnkeYkeYkelhael 31 
                   +  +Yk+ F+++++eY ++++ +
    EPA06235.1 330 NEPTYKKWFDTNFPEYTSIYQAV 352
                   5678**************99876 PP

>> Trypan_PARP  Procyclic acidic repetitive protein (PARP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   6.0   5.7e-05      0.34      82     111 ..     227     256 ..     210     283 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.7e-05
  Trypan_PARP  82 epeeepepepepepepepepepepepepep 111
                  +p +  +++p p  epe  pe e+ep pep
   EPA06235.1 227 KPAPVIQQDPTPVKEPEVIPESETEPTPEP 256
                  333333444444444444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (520 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.38
# Mc/sec: 4097.04
//
Query:       EPA06236.1  [L=593]
Description: translation initiation factor aIF-2 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.9e-32  111.8   0.0    7.2e-32  110.5   0.0    1.6  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    3.2e-22   78.2   0.2    1.2e-21   76.4   0.2    2.0  1  GTP_EFTU_D4  Elongation factor Tu domain 4
      1e-21   77.0   0.6      3e-21   75.5   0.6    1.9  1  IF-2         Translation-initiation factor 2
    6.9e-09   35.8   0.6    1.8e-07   31.2   0.0    2.8  3  MMR_HSR1     50S ribosome-binding GTPase
    3.3e-05   24.1   0.0    0.00011   22.4   0.0    2.0  2  Roc          Ras of Complex, Roc, domain of DAPkinase
    9.2e-05   22.8   0.7    0.00059   20.2   0.0    2.7  3  GTP_EFTU_D2  Elongation factor Tu domain 2
    0.00011   22.0   0.0    0.00047   20.0   0.0    1.9  2  ATP_bind_1   Conserved hypothetical ATP binding protein
    0.00074   19.6   0.5      0.059   13.4   0.1    2.8  2  Dynamin_N    Dynamin family
     0.0018   17.9   0.1      0.033   13.8   0.0    2.7  2  Ras          Ras family
     0.0079   15.8   1.6       0.71    9.4   0.3    2.8  2  cobW         CobW/HypB/UreG, nucleotide-binding domain
  ------ inclusion threshold ------
      0.023   14.2   0.1        0.1   12.1   0.0    2.2  2  SRPRB        Signal recognition particle receptor beta subuni
       0.11   12.3   0.3        1.6    8.4   0.0    2.9  3  PduV-EutP    Ethanolamine utilisation - propanediol utilisati
       0.18   12.4   0.6         17    6.0   0.1    2.7  2  DUF4473      Domain of unknown function (DUF4473)


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.5   0.0   5.2e-35   7.2e-32       5     192 ..       7     217 ..       4     219 .. 0.73

  Alignments for each domain:
  == domain 1  score: 110.5 bits;  conditional E-value: 5.2e-35
                 EEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHT..SCSSCEEEEEETTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEE CS
    GTP_EFTU   5 nigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErerg..iTiksaaisleketkkylinliDtPGHvdFskevirglrvlDgavlvv 101
                  ++++ghvD+GKt+L+dr+   tg   +++   +++    +l++E  +        +  +   e +   i +iDtPGH+ F++   rg +++D+a+lvv
  EPA06236.1   7 IVVVLGHVDSGKTSLLDRIR-GTGVQGREAGGITQHIGASFLPTETIKEtcGPLYKKLQES--ENQVPGILVIDTPGHEVFTNLRARGGSAADIAILVV 102
                 589****************9.5555444333334466678888885443003333333333..69999******************************* PP

                 ETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGST...........HHHHHHHHHHHHHHHHHH.....................HHHHHHHHHTTT... CS
    GTP_EFTU 102 daveGvepqteevlrlalkegvpiivfiNKmDrl...........kaelkeiveevkqklsrk.....................eeklekygekge... 165
                 d+++G +pqt+e l+++++++vp++v++NK+D++                 ++ + ++ +                                   e   
  EPA06236.1 103 DVNRGFQPQTNESLKILQSRKVPFVVALNKCDQIsgwrksdtkfiT-----QAIKEQDAF--IqtdldqkiydvvgtlsilgyqS----------Eafy 184
                 **********************************888855333332.....222223333..13344445666666655555541..........1444 PP

                 ......TTEEEEEEBTTTTBTHHHHHHHHHHHS CS
    GTP_EFTU 166 ......kevpvvfgSalkgegvktllealvell 192
                       +e+ +v++Sa +g g+ +ll +lv l+
  EPA06236.1 185 rvkdfkSEIAIVPISARSGVGIPELLAVLVGLT 217
                 44455578******************9998765 PP

>> GTP_EFTU_D4  Elongation factor Tu domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.4   0.2   8.6e-25   1.2e-21       4      86 .]     468     550 ..     465     550 .. 0.97

  Alignments for each domain:
  == domain 1  score: 76.4 bits;  conditional E-value: 8.6e-25
                  EEEEEEEEEEETCCCEEEEEEEEEEEEETT-EEEETTE.EEEEEEEEEETTEEESEEETT-EEEEEEESS-TTTS--TT-EEE CS
  GTP_EFTU_D4   4 kikilpgvvfrrsdpaivGvevlgGvikpgvklikedGrevGeilqiqdkgkkleeakaGqevaisiegkivGrqikegdily 86 
                  k++ l+g+vfr++dpa+ G+++  G++k +v+ ++++G+++G i q+q  +k++  akaGqeva s++g ++Gr+i e++++y
   EPA06236.1 468 KFTFLKGYVFRNTDPAVFGIKIDVGTLKQKVPFMNKEGKKIGIIHQLQLDKKTVVSAKAGQEVACSVQGITIGRHIFEEEVFY 550
                  7899**************************************************************************99987 PP

>> IF-2  Translation-initiation factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.5   0.6   2.2e-24     3e-21       3     104 ..     342     444 ..     340     445 .. 0.90

  Alignments for each domain:
  == domain 1  score: 75.5 bits;  conditional E-value: 2.2e-24
                 CHHHCCCSCSSCCEEEEEESSHHHHHHHHHHHHCTT.SSTEEEECEEEESSB-HHHHHHHHH..ST....EEEEEESSSCTHHHHHCCCCCTSEEEEES CS
        IF-2   3 elfeeikeegkelnviikaDvqGsleAlkeaLekleseevkvkvihsgvGaitesDvelasa..sn....aiiigFnvkvskkakklaekegvkirlyn 95 
                 ++++++  ++++ +v++k+D+ GsleA+ e+L++      +v++ ++++G+++++Dv+  +a  +n    ++i++Fnvkv ++ak++a++ ++ki++ +
  EPA06236.1 342 SEMKSVFIDTETNGVVLKCDTIGSLEAIVEMLRRS-----QVPIAKADIGPVNRRDVMETRAikENdrhlGVILAFNVKVLPDAKEEADDGHIKIFEDK 435
                 56666776778999********************8.....6*******************9965226789***************************** PP

                 SHHHHHHHH CS
        IF-2  96 vIYkliddv 104
                 +IY lid++
  EPA06236.1 436 IIYSLIDNY 444
                 *******86 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0   1.3e-10   1.8e-07       2     114 .]       8     132 ..       7     132 .. 0.71
   2 ?    1.8   0.0      0.18   2.5e+02      27      85 ..     142     200 ..     136     266 .. 0.64
   3 ?   -2.6   0.0       4.2   5.8e+03      51      58 ..     360     367 ..     327     431 .. 0.54

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 1.3e-10
                 EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEE...................EEEEECGGCSSHHHHHHHHHHHHHH.HHCTSEEE CS
    MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgke...................ielvDtpGliegaseekglgkafla.leeadlil 80 
                 v+++G+  +GK++L+ ++ g+ ++  +  g T++i    + ++  +                   i ++DtpG  e       +++  ++    ad+++
  EPA06236.1   8 VVVLGHVDSGKTSLLDRIRGTGVQGREAGGITQHIGASFLPTETIKetcgplykklqesenqvpgILVIDTPG-HE------VFTNLRARgGSAADIAI 99 
                 899***************99766666666777776554443221112333344444455566667********.44......2333233213348**** PP

                 EEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
    MMR_HSR1  81 lvvdaseeklkpldeeleelleeakkplilvlnk 114
                 lvvd++ ++++p+ +e  ++l+++k p++++lnk
  EPA06236.1 100 LVVDVN-RGFQPQTNESLKILQSRKVPFVVALNK 132
                 ****88.77************99*********98 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.18
                 SSSTTSSSSEEEEEEE.ETTEEEEEEECGGCSS..HHHHHHHHHHHHHHHHC..TSEEEEEEET CS
    MMR_HSR1  27 sdkpgtTrdinegrvk.lkgkeielvDtpGlie..gaseekglgkaflalee..adlillvvda 85 
                 sd+++ T+ i+e       + + +++D++G ++  g       ++af ++++  ++++++ ++a
  EPA06236.1 142 SDTKFITQAIKEQDAFiQTDLDQKIYDVVGTLSilG-----YQSEAFYRVKDfkSEIAIVPISA 200
                 789999999977765413447789******754111.....23334444443223444444443 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 4.2
                 EECGGCSS CS
    MMR_HSR1  51 vDtpGlie 58 
                 +Dt G +e
  EPA06236.1 360 CDTIGSLE 367
                 45555322 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   8.1e-08   0.00011       2     120 .]       8     135 ..       7     135 .. 0.69
   2 ?   -3.4   0.0       7.6     1e+04      15      35 ..     216     236 ..     216     243 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 8.1e-08
                 EEEESSTTSSHHHHHHCHCT-CCC-EE....ETTTTEEEEEEECGGSG......GCTTBTTTTCEEEEEEEE-SGGCTTTT-HHHHCTSCEEEEEEE.G CS
         Roc   2 vvlvGdsgvGKtsllkrfvedkfseke....kstigvdfltkevtkik......gvendkkvkkvklniWDtaGqerfrslhplylreaalailvyd.s 89 
                 vv++G   +GKtsll+r+    ++ +e    ++ ig++fl +e+ k +      ++++ ++ +   + + Dt G+e f +l+    ++a++ailv+d +
  EPA06236.1   8 VVVLGHVDSGKTSLLDRIRGTGVQGREaggiTQHIGASFLPTETIKETcgplykKLQE-SENQVPGILVIDTPGHEVFTNLRARGGSAADIAILVVDvN 105
                 799***************8776665542222799*****9876543222222113332.23334567899***************************54 PP

                 HHHH.CHHHHHHHHHHHCSSS-EEEEEE-TTT CS
         Roc  90 rsse.nlkeWlkelkkvagkspvilvgnkiDl 120
                 r ++ + +e lk l++  +k p+++  nk+D+
  EPA06236.1 106 RGFQpQTNESLKILQS--RKVPFVVALNKCDQ 135
                 4455234444444443..46788899999995 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 7.6
                 HHHCHCT-CCC-EEETTTTEE CS
         Roc  15 llkrfvedkfsekekstigvd 35 
                 l +++++++ ++kek+  g+ 
  EPA06236.1 216 LTQQYLQKRLDQKEKESRGIV 236
                 678999999999999888875 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       3.8   5.2e+03      30      51 ..      50      72 ..       8      77 .. 0.49
   2 !   20.2   0.0   4.2e-07   0.00059       1      74 []     246     325 ..     246     325 .. 0.93
   3 ?   -1.0   0.2       1.7   2.4e+03      25      63 ..     502     539 ..     491     543 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.8
                 E.EEEEEEEEEEETEEESEEETT CS
  GTP_EFTU_D2 30 e.ivtrissletfhededeavag 51
                 e i+++ + l++  ++ + +v+g
   EPA06236.1 50 EtIKETCGPLYKKLQESENQVPG 72
                 13445555555555555555555 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 4.2e-07
                  EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEE...........ETTSEEEEEEEESSCCSGSSTTCEEE CS
  GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededea...........vaganaGvivaikgledaiivGdtlt 74 
                  G++a +++++G +kk d + + +     + i+t+ ++++ + +++de+            + a+aG+++a ++le  ++ G+tl+
   EPA06236.1 246 GHTANIILIDGSIKKTDSIIVAKR---DSVIITKPKAILLP-KPLDEMrdprdkfkpvqSVDAAAGLKIASPDLEG-VLPGSTLY 325
                  67888999*************553...458***********.88********************************.******97 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.7
                  CTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSC CS
  GTP_EFTU_D2  25 dtskkeivtrissletfhededeavaganaGvivaikgl 63 
                   +++k  ++ i +l+  ++ +  a ag+ +   v ++ +
   EPA06236.1 502 NKEGK-KIGIIHQLQLDKKTVVSAKAGQEVACSVQGITI 539
                  33333.578888888888888888888888888877765 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.4   1.9e+03       1      15 [.      10      24 ..      10      27 .. 0.87
   2 !   20.0   0.0   3.4e-07   0.00047      73     233 ..      50     211 ..      39     219 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.4
  ATP_bind_1  1 vvGpaGsGKttfvga 15
                v+G++ sGKt++  +
  EPA06236.1 10 VLGHVDSGKTSLLDR 24
                89********99865 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 3.4e-07
  ATP_bind_1  73 eflresldwldeeleke.ed..dyllfDtPGQielfthseslakiveeLesefalvvvyLvDsqrltdptkfisgllsalsamlrlelPhvvvlnkfDl 168
                 e+++e++  l ++l++  ++    l++DtPG   + ++++ +         + a +++ +vD++r  +p +       +l+++ + ++P+vv+lnk+D 
  EPA06236.1  50 ETIKETCGPLYKKLQESeNQvpGILVIDTPGHEVFTNLRARGG--------SAADIAILVVDVNRGFQPQTNE-----SLKILQSRKVPFVVALNKCDQ 135
                 6666667677777766633345699******888888888888........9999**********98877644.....569****************** PP

  ATP_bind_1 169 lkeklekeleffe....dvealslllekee............ekykklaeaiaelleefalvlrflplssekeesiedlls 233
                 ++  ++ + +f++    + +a+ ++    +            +   ++ ea    +++f+  + ++p+s++++ +i +ll+
  EPA06236.1 136 ISGWRKSDTKFITqaikEQDAFIQT----DldqkiydvvgtlSILGYQSEAF-YRVKDFKSEIAIVPISARSGVGIPELLA 211
                 9966666666665000044443333....13334677776653333333333.3355666666777777777777777766 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.1   4.3e-05     0.059       1      34 [.       8      41 ..       8      44 .. 0.94
   2 ?    3.4   0.1      0.05        69      93     150 ..      63     116 ..      47     158 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.3e-05
                EEEEEBTTTTHHHHHHHHHTS--S---SSS---S CS
   Dynamin_N  1 iavvGsqSsGKSSvlnaLlgedilprgpnptTrr 34
                ++v+G++ sGK+S+l+ + g  +  r+++ +T+ 
  EPA06236.1  8 VVVLGHVDSGKTSLLDRIRGTGVQGREAGGITQH 41
                79**************************999975 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.05
                 EEEEETTS-SEEEEE---B-SSSGTTSHHHHHHHSTTEEEEEEEETTS-CCC-CHHHH CS
   Dynamin_N  93 lkilsllvkgltlvDlPGldsvnkrdqelvkeyikkadiilavtsanhdlsnsealfl 150
                 l+  + +v+g+ ++D+PG     + +     +    adi ++v++ n  +  + ++ l
  EPA06236.1  63 LQESENQVPGILVIDTPGHEVFTNLR----ARGGSAADIAILVVDVNRGFQPQTNESL 116
                 556677899999******87743333....3334555666666666655554444443 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   2.4e-05     0.033      30     118 ..      54     137 ..       7     160 .. 0.65
   2 ?   -2.5   0.0       2.4   3.3e+03     114     132 ..     514     532 ..     475     537 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.4e-05
                 TTSSEEEEEEEEEETTEEEEEEEEEETTSGGGHHHHHHHHTTESEEEEEEETTBHHHHHTHHHHHHHHHHHSTTTSEEEEEEETTTGGG CS
         Ras  30 sTigvdfytkeievdgkevkleiwDTAGqeefkslrelyyrdaegillvyditsresfenvkkwveeikrvaeenvpivLvGnKvDlee 118
                 +T     y+k  e +++   + + DT G e f++lr    + a+ ++lv d+++   f+  ++   +i +    +vp+v+  nK+D  +
  EPA06236.1  54 ETC-GPLYKKLQESENQVPGILVIDTPGHEVFTNLRARGGSAADIAILVVDVNR--GFQPQTNESLKILQSR--KVPFVVALNKCDQIS 137
                 222.224555555557777899***************************99975..6887666555555554..49999999***9765 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.4
                 TTGGGG-SS-HHHHHHHHH CS
         Ras 114 vDleekravsteegeelak 132
                   l++k +vs++ g+e+a 
  EPA06236.1 514 LQLDKKTVVSAKAGQEVAC 532
                 2333367777777777765 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.3   0.00052      0.71      72     169 ..      62     151 ..       6     159 .. 0.61
   2 ?   -2.9   0.1       3.1   4.3e+03     138     153 ..     257     272 ..     235     276 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00052
                 HHHHHHHHHTT-SEEEEEECTTTTHHHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHHHCHC..HHHHHHHHHHH CS
        cobW  72 elealeereerldviliEttGlaePapvafteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtDlldeeallekleerlrql 169
                 +l++ e++   + +++i t G        ft+ + +    +d+ + vvD+++  + +++++ k+ +  ++  ++ lnK+D+++  ++ +  + +++++
  EPA06236.1  62 KLQESENQV--PGILVIDTPGHEV-----FTNLRARGGSAADIAILVVDVNRGFQPQTNESLKILQSRKVPFVVALNKCDQISGWRK-SDTKFITQAI 151
                 444444444..5566666666443.....3344678888899999999999988888888888888888888999999999987744.4555555555 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.1
                 HHHTSSEEEEE-HHHH CS
        cobW 138 qlaaadllvlnKtDll 153
                  ++++d +++ K D +
  EPA06236.1 257 SIKKTDSIIVAKRDSV 272
                 5778888888888865 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   7.3e-05       0.1       2      62 ..       4      84 ..       3     103 .. 0.70
   2 ?   -3.3   0.0       3.7     5e+03     109     125 ..     120     136 ..     113     153 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.3e-05
                ---EEEEE-STTSSHHHHHHHHHHS................S---B---SS-EEETTG.......GGTT-SEEEETT-GCC CS
       SRPRB  2 skpavllvGlsdsGKTslftrLttd................svkktvtSqessaalkv....ksekgskltliDfPGhekl 62
                ++p+v+++G  dsGKTsl+ r+                   s+ +t t  e++  l      ++++   + +iD PGhe +
  EPA06236.1  4 RQPIVVVLGHVDSGKTSLLDRIRGTgvqgreaggitqhigaSFLPTETIKETCGPLYKklqeSENQVPGILVIDTPGHEVF 84
                5899*****************975557778888877777766666666665553322223322333345667888888765 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.7
                 HTT---EEEEEE-TTST CS
       SRPRB 109 lkdavdiliACnKqelf 125
                 +  +v++++A nK +  
  EPA06236.1 120 QSRKVPFVVALNKCDQI 136
                 56789999999998854 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0    0.0012       1.6       4      26 ..       8      30 ..       5      45 .. 0.86
   2 ?    0.2   0.0      0.43   5.9e+02      40      85 ..      75     116 ..      50     161 .. 0.63
   3 ?   -3.4   0.0       5.4   7.5e+03      87     102 ..     348     363 ..     329     377 .. 0.58

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0012
   PduV-EutP  4 illiGkvgsGKttLtqalkgeel 26
                ++++G+v+sGKt+L  +++g  +
  EPA06236.1  8 VVVLGHVDSGKTSLLDRIRGTGV 30
                899***************99765 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.43
   PduV-EutP  40 viDtPGeylenrklysalivtsaeadvialvqdateeesvfppgfa 85 
                 viDtPG       + +  +     ad+  lv+d+++  +  +++  
  EPA06236.1  75 VIDTPGHE----VFTNLRARGGSAADIAILVVDVNRGFQPQTNESL 116
                 59999953....2333333344455666666666655555555555 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 5.4
   PduV-EutP  87 vfnkeviGiitkidla 102
                 ++  e+ G++ k d+ 
  EPA06236.1 348 FIDTETNGVVLKCDTI 363
                 3345566666666665 PP

>> DUF4473  Domain of unknown function (DUF4473)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.1     0.012        17      39      71 ..     137     167 ..     126     170 .. 0.83
   2 ?    3.7   0.0     0.067        92      57      76 ..     563     582 ..     556     584 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.012
     DUF4473  39 kgdkeaakkafeklkaevdafiktqseeDqaay 71 
                 +g +++  k++++ ++e+dafi+t    Dq++y
  EPA06236.1 137 SGWRKSDTKFITQAIKEQDAFIQT--DLDQKIY 167
                 56678899**************65..7888888 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.067
     DUF4473  57 dafiktqseeDqaaykafve 76 
                  +f+ ++s e+q++ +++ve
  EPA06236.1 563 AKFMYKLSSEEQQILNEIVE 582
                 68***************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (593 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.70u 0.34s 00:00:01.04 Elapsed: 00:00:00.52
# Mc/sec: 3412.28
//
Query:       EPA06237.1  [L=150]
Description: hypothetical protein BG20_I0572 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0037   17.1   4.5     0.0045   16.8   4.5    1.0  1  DUF475    Protein of unknown function (DUF475)
  ------ inclusion threshold ------
       0.18   11.6   0.1       0.34   10.7   0.1    1.4  1  E1-N      E1 N-terminal domain
          1    7.9   4.8        1.3    7.6   4.8    1.0  1  Ndc1_Nup  Nucleoporin protein Ndc1-Nup


Domain annotation for each model (and alignments):
>> DUF475  Protein of unknown function (DUF475)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   4.5   7.5e-07    0.0045      41     165 ..      15     143 ..       9     149 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 7.5e-07
      DUF475  41 vivavsakldpiealklalekkdsyeell....taahpsiaafGgmflllvfldfllddrdikWlkwiekplaklgkldavsvvivlvlllllaallak 135
                 +++a++a++ +  ++   l++++ y +       +     ++fGg + l    ++ll+  ++   k    +++ +  l++ +vv ++v  +l+  +l+ 
  EPA06237.1  15 ILIAFTASITVSAIVAQMLSDQADYLNTTytlaVDYIIYFSTFGGLYYLDNRKKYLLESGQTDKAKLKHDLIKIVASLGVAEVVYTIVRWILQYYFLML 113
                 6899*****************88886543100034445679******************999999988888888999999999999999999999***9 PP

      DUF475 136 kaeqrqkvllagllglltyllvdglerlfe 165
                 +++ + + +++ +++ ++y+++ +l+  ++
  EPA06237.1 114 NYDAYLASIVSQVISTIIYMIIINLSVKMT 143
                 *********************999887765 PP

>> E1-N  E1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   5.6e-05      0.34     111     145 ..      16      50 ..      11      53 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 5.6e-05
        E1-N 111 llaavaacavaavvlrallddadlpavalplrldy 145
                 l+a +a+ +v+a+v ++l d+ad  ++++ l +dy
  EPA06237.1  16 LIAFTASITVSAIVAQMLSDQADYLNTTYTLAVDY 50 
                 7888999***************************9 PP

>> Ndc1_Nup  Nucleoporin protein Ndc1-Nup
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   4.8   0.00022       1.3      63     187 ..      15     141 ..       8     145 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00022
    Ndc1_Nup  63 lhvgprttssrlstllaslfsl.qtletllvyllSallfaevyi..wslpedarlgwvtskssrerprlNerplflllsglvlalvysllhllfdrdrl 158
                 + +  + + +  + + ++l+++   l+t+ + ++ ++++ ++++  + l  + + ++++s  +++++ l    + +++s+ v  +vy+++  + ++  l
  EPA06237.1  15 ILIAFTASITVSAIVAQMLSDQaDYLNTTYTLAVDYIIYFSTFGglYYLD-NRKKYLLES-GQTDKAKLKHDLIKIVASLGVAEVVYTIVRWILQYYFL 111
                 445555555556667777777789999999999999*9999999644444.334455555.559*********************************** PP

    Ndc1_Nup 159 sfkssfpivqpskyllkr.lpsilkkslil 187
                   ++++   + ++++++  +++i+++  ++
  EPA06237.1 112 MLNYDAYLASIVSQVISTiIYMIIINLSVK 141
                 999999999999999999999999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1042  (0.0581181); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 910.84
//
Query:       EPA06238.1  [L=460]
Description: hypothetical protein BG20_I0543 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00016   22.1  15.8       0.62   10.6   0.0    6.1  5  DUF3106      Protein of unknown function (DUF3106)
  ------ inclusion threshold ------
       0.63   10.1   8.6        6.7    6.7   0.1    3.8  3  FGAR-AT_N    Formylglycinamide ribonucleotide amidotransferas


Domain annotation for each model (and alignments):
>> DUF3106  Protein of unknown function (DUF3106)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1     0.019   1.7e+02      48      66 ..      34      52 ..      24      78 .. 0.61
   2 !    5.5   0.0    0.0027        24      46     101 ..      60     117 ..      36     120 .. 0.75
   3 !   10.6   0.0   6.9e-05      0.62      17     102 ..      87     180 ..      69     183 .. 0.70
   4 ?    2.5   0.1     0.023     2e+02      49      69 ..     257     277 ..     249     297 .. 0.65
   5 !    6.3   3.8    0.0015        13      32     103 ..     323     392 ..     309     393 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.019
     DUF3106 48 lqermeewakLspeqreqa 66
                l++r++++ k+++e+++q+
  EPA06238.1 34 LEDRLDNFCKMTDEEKRQL 52
                4455555555555555554 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0027
     DUF3106  46 krlqermeewakLspeqreqarenyqklk..qLppeereelrekweeyqkLppeerkk 101
                 +++++r++++ +Ls+++re a +++ + +  +   +e   + +  ++y +++++e+k 
  EPA06238.1  60 AQFKDRLAKFCELSDDEREIAIDTFIDENfpEARDNESYDIDDMLDRYCEMSDAEKKD 117
                 5678999999999999999999998554422666666667888888999998888876 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 6.9e-05
     DUF3106  17 eewnelspeqreklleiaerykkltpeeqkrl..........qermeewakLspeqreqarenyqklkqLppeereelrekweeyqkLppeerkkl 102
                 e++ e+++++   + ++ +ry +++ +e+k +           +rm+++ +L++++r++  +++++  q+  ++   ++ + + y k+++e +k++
  EPA06238.1  87 ENFPEARDNESYDIDDMLDRYCEMSDAEKKDFismhdkssdhVARMNAYCELDEDKRDAYIAEHKDEYQMYSDQD--MQTHLDLYCKMSDEDKKAV 180
                 555666666666666666666666666665431221111111479*************************99998..9**************9975 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.023
     DUF3106  49 qermeewakLspeqreqaren 69 
                  +++++  +++p++re+ +++
  EPA06238.1 257 LDKISKLCAMTPQEREKYKNE 277
                 455555566666666665544 PP

  == domain 5  score: 6.3 bits;  conditional E-value: 0.0015
     DUF3106  32 eiaerykkltpeeqkrlqermeew.....akLspeqreqarenyqklkqLppeereelrekweeyqkLppeerkkla 103
                 +  e+  +lt e++ +l+ ++e++     +k+s+e+++++ +++ ++k++  e r   +++    +++++ee+++l+
  EPA06238.1 323 KYIEKHGDLTDEKRFELKMKFENYmssikSKMSDERKSAIHDRLTDMKAFKSELR---ERS----SEMTDEEKQQLR 392
                 5566777788888888888887774444457999999999999999999999988...333....468899999887 PP

>> FGAR-AT_N  Formylglycinamide ribonucleotide amidotransferase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.11     1e+03      86     110 ..     209     233 ..     195     237 .. 0.81
   2 ?    4.5   1.9    0.0037        33      46     105 ..     239     299 ..     218     305 .. 0.73
   3 ?    6.7   0.1   0.00074       6.7      59     105 ..     325     371 ..     321     380 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.11
   FGAR-AT_N  86 eeelaalaalLhDrmtesvleeled 110
                 +e++++++a + D+m + + +++++
  EPA06238.1 209 KEHRDEYKAQMKDKMSDKIKDKRPH 233
                 6778899999999999999888776 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0037
   FGAR-AT_N  46 lGtiSpWsSkAtdIahncglekvkRiErgiayvlel..kelseeelaalaalLhDrmtesvl 105
                 l t+S  s +A +I+    l+k++++   +    e   +e ++e ++++ + +hD+m+  ++
  EPA06238.1 239 LCTLSE-SDRALEIVDSQVLDKISKLCAMTPQEREKykNESHDEMKDKMMDKIHDKMMSDMS 299
                 555554.7788888888888888888777776666654467777888999999999997766 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.00074
   FGAR-AT_N  59 IahncglekvkRiErgiayvlelkelseeelaalaalLhDrmtesvl 105
                 I ++ +l++ kR E  +++   +++++++  ++ ++++hDr+t++  
  EPA06238.1 325 IEKHGDLTDEKRFELKMKFENYMSSIKSKMSDERKSAIHDRLTDMKA 371
                 667778888899*********9*********************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1673  (0.0933125); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 3359.25
//
Query:       EPA06239.1  [L=249]
Description: fibrillarin, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.7e-88  295.6   0.2      2e-88  295.3   0.2    1.0  1  Fibrillarin  Fibrillarin
    4.7e-05   23.2   0.0    6.8e-05   22.7   0.0    1.2  1  GCD14        tRNA methyltransferase complex GCD14 subunit
     0.0019   18.0   0.0     0.0032   17.2   0.0    1.5  1  PCMT         Protein-L-isoaspartate(D-aspartate) O-methyltran
  ------ inclusion threshold ------
      0.019   14.8   0.0      0.047   13.5   0.0    1.6  1  DUF4651      Domain of unknown function (DUF4651)


Domain annotation for each model (and alignments):
>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  295.3   0.2   4.6e-92     2e-88       8     224 ..      31     247 ..      25     249 .] 0.97

  Alignments for each domain:
  == domain 1  score: 295.3 bits;  conditional E-value: 4.6e-92
                  TTEEEEETTSSEEEEEE-SSTT--SSSSEEEEETTEEEEEE-TTTSHHHHHHHTT-S--S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSH CS
  Fibrillarin   8 egvyivkekgdarlatknlvpgekvYgEklikveeeEyRvWnpfrsKlaaailkglkelpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsp 105
                  +  ++++++g+++lat+nlv g++vY+Ekli+ +++EyR W+pfrsKlaaai++gl+ +p+k+ s vLYlG+++GttvsH+sDivg++g++++ve+++
   EPA06239.1  31 YEFFWINSDGEKKLATENLVIGNQVYNEKLITKKGTEYRLWDPFRSKLAAAIMNGLEIFPFKNKSTVLYLGVSTGTTVSHISDIVGPTGLIFGVEHAS 128
                  5679999******************************************************************************************* PP

                  HHHHHHH.HHHTTSTTEEEEES-TTSGGGGTTTS--EEEEEEESSSTTHHHHHHHHHHHHEEEEEEEEEEEEHHHHHSSSSHHHHHHHHHHHHHHTTE CS
  Fibrillarin 106 rvlreli.evakkRknivPileDArkPekYralvekvDvifaDvaqpdqarilaknaklflkeggyllisikarsidvtkepeevfkeeveklkeegl 202
                  rv r+++ +va++R ni+Pil+DAr+P++Y ++  kvDv+++D+aqpdq++i+++n+k++lk++gy++++ik+rsidvtk+p+++  ee+ek++   +
   EPA06239.1 129 RVARDFLdRVASHRANIIPILQDARRPKEYFSVFGKVDVVYVDIAQPDQTNIAIENCKMYLKKDGYFFLVIKTRSIDVTKSPKKIVDEEIEKMEMY-F 225
                  ******978************************************************************************************875.* PP

                  EEEEEEE-TTTSTTEEEEEEEE CS
  Fibrillarin 203 kvleqvklepyekdhalvvgky 224
                  ++l++++l py+kdha+v++k+
   EPA06239.1 226 EILQVIDLHPYDKDHAMVIAKF 247
                  *******************986 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   1.5e-08   6.8e-05      39     143 ..      92     197 ..      76     237 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.5e-08
       GCD14  39 kpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvtvthrDvc..keGfdeevsgkvDavfLDlPaPwe...aiphaa 132
                 k+ s v+  G  +g+  + i+  v+PtG +f +e+  + a+  ++   +h+ + +     +D+   ke f   v gkvD v++D+ +P++   ai++ +
  EPA06239.1  92 KNKSTVLYLGVSTGTTVSHISDIVGPTGLIFGVEHASRVARDFLDRVASHRANIIP--ILQDARrpKEYF--SVFGKVDVVYVDIAQPDQtniAIENCK 186
                 6778999999999999999***************5555455555666666544433..345555348888..99**************97666899999 PP

       GCD14 133 kalkkeggrlC 143
                   lkk+g  + 
  EPA06239.1 187 MYLKKDGYFFL 197
                 99988876655 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   7.2e-07    0.0032      61     153 ..      78     175 ..      74     224 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 7.2e-07
                 HHHHHHHHTT...--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTTGGG-SE...EEEEESSBBS CS
        PCMT  61 mvalalelle...lkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrkGyeekaPY...daihvgaaap 153
                 + a++++ le   +k+++ vL +G  +G     ++ +vg++g++ ++e+  +++++   ++  + ++n+i +  D r   e ++ +   d+++v +a p
  EPA06239.1  78 LAAAIMNGLEifpFKNKSTVLYLGVSTGTTVSHISDIVGPTGLIFGVEHASRVARDFLDRVASH-RANIIPILQDARRPKEYFSVFgkvDVVYVDIAQP 175
                 5566777677666899*************************************99999999765.5567777777766544444432225556665555 PP

>> DUF4651  Domain of unknown function (DUF4651)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.1e-05     0.047      11      35 ..     156     180 ..     148     182 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.1e-05
     DUF4651  11 ReffsqlGeIavlYvnetesdqeel 35 
                 +e+fs +G++ v+Yv+  ++dq+++
  EPA06239.1 156 KEYFSVFGKVDVVYVDIAQPDQTNI 180
                 489******************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1662.00
//
Query:       EPA06240.1  [L=197]
Description: ribosomal RNA large subunit methyltransferase J [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-48  165.7   0.0    1.2e-48  165.5   0.0    1.0  1  FtsJ             FtsJ-like methyltransferase
    6.6e-05   22.7   0.0    8.5e-05   22.4   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    7.1e-05   23.4   0.1    0.00025   21.7   0.1    1.9  2  Methyltransf_25  Methyltransferase domain
     0.0043   16.7   0.0     0.0072   16.0   0.0    1.4  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
     0.0083   15.9   0.0      0.014   15.2   0.0    1.4  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
     0.0095   15.8   0.0      0.015   15.2   0.0    1.5  1  Methyltransf_23  Methyltransferase domain


Domain annotation for each model (and alignments):
>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.5   0.0   4.1e-52   1.2e-48       1     177 []      20     195 ..      20     195 .. 0.99

  Alignments for each domain:
  == domain 1  score: 165.5 bits;  conditional E-value: 4.1e-52
                 CCCCHHHHHHHHHHHHT-S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSSHHHTTEEEECS-CCCSSHHHHHCHCHHHSSEEEEEE--S-SS CS
        FtsJ   1 yrsRsayKLleidekfklfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpmaplpgvttiqgditdpetiekikealserkvdlvvsDgapdv 99 
                 yrsR+ayKL ++++ ++++ pg  v+Dlg+aPGgw+q++++ +g+kgkvv+vD+  ++ +pg ++i+ +i ++   ++++ ++ erkv+ v++D++p+v
  EPA06240.1  20 YRSRAAYKLKQLNHSYRIIGPGFYVLDLGCAPGGWTQMAVKLVGNKGKVVGVDTSYVEEIPGAHIIRENIENEFLVDELLSYF-ERKVNAVICDLSPQV 117
                 9*******************************************************************************999.67************* PP

                 -CHHHHHHHHHCCCCHHHHCCHCCCCECCCEEEECCCHCCCHHHHHHHHHCCEEEEEEEE-SS--CCG-EEEEEEEEC CS
        FtsJ 100 sgvhdldeylqsqLllaalelalkllkpggtfvlkifrgeeteallkqlkkfFekvsvvkPkssrsesseeflvcrgf 177
                 +g++++d+++q++L  +  +++ k+l ++g+ ++k+f+ge + ++   +kk+F++++++kP++sr++sse ++vc+gf
  EPA06240.1 118 TGNWSVDHAIQISLNYSCSKIMDKVLMHKGNAIFKVFDGEYSMEFRDYIKKKFSRINLTKPEASRKQSSELYYVCLGF 195
                 ****************************************************************************98 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   2.9e-08   8.5e-05       4     105 ..      41     147 ..      38     190 .. 0.71

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 2.9e-08
  Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDis.eeaielArenaqklgldnveFeqgdiee.leklledekfDlilsn....evl....... 84 
                      g +vlDlGC+ G  t  + +++g k++vvG+D s  e i  A  ++++ +    eF + +  + +e     +k++ ++++              
       EPA06240.1  41 GFYVLDLGCAPGGWTQMAVKLVGNKGKVVGVDTSyVEEIPGAHIIRENIE---NEFLVDELLSyFE-----RKVNAVICDlspqV-Tgnwsvdh 125
                      668*****************************995678888888766433...3577777777666.....67777777744430.14333444 PP

  Methyltransf_31  85 .naladpdkileeiervlkpgg 105
                         ++ + ++ + + +vl  +g
       EPA06240.1 126 aIQISLNYSCSKIMDKVLMHKG 147
                      4555555555555555555555 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.1   8.3e-08   0.00025       1      30 [.      44      74 ..      44     114 .. 0.84
   2 ?   -1.4   0.0       1.3   3.9e+03      15      33 ..      98     117 ..      91     128 .. 0.70

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 8.3e-08
                     EEEET-TTSHHHHHHHCTST.SSEEEEEESS CS
  Methyltransf_25  1 vLdlGcGtGrltlalakrlg.kakvtgvDis 30
                     vLdlGc +G +t+++ k +g k+kv+gvD s
       EPA06240.1 44 VLDLGCAPGGWTQMAVKLVGnKGKVVGVDTS 74
                     9******************65********98 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.3
                      HHCTS.TSSEEEEEESSHHH CS
  Methyltransf_25  15 lakrl.gkakvtgvDiseem 33 
                      l+  +  k + + +D+s++ 
       EPA06240.1  98 LLSYFeRKVNAVICDLSPQV 117
                      45555335777888888865 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   2.4e-06    0.0072      12      42 ..      44      74 ..      39      94 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.4e-06
                     EEESS-TTSHHHHHHHHHTTTTSEEEEEESS CS
  Methyltr_RsmB-F 12 ilDlcaaPGgKTthiaelmknkgtvvAvdan 42
                     +lDl +aPGg T    +l+ nkg+vv vd++
       EPA06240.1 44 VLDLGCAPGGWTQMAVKLVGNKGKVVGVDTS 74
                     8***************************986 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   4.6e-06     0.014      70     107 ..      37      74 ..       7      95 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.6e-06
                 T--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESB CS
        PCMT  70 elkkgarvLevGsGsGyltavlarlvgekgrvvsieri 107
                  + +g  vL++G+  G  t +  +lvg+kg+vv+++ +
  EPA06240.1  37 IIGPGFYVLDLGCAPGGWTQMAVKLVGNKGKVVGVDTS 74 
                 4789999****************************964 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   4.9e-06     0.015      25      62 ..      43      97 ..       6     183 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.9e-06
  Methyltransf_23 25 rvLdiGcGtGillevl.rengf..svtgvDlspeaveiae................k 62
                      vLd+Gc+ G +++ + +  g   +v+gvD s +  e+++                +
       EPA06240.1 43 YVLDLGCAPGGWTQMAvKLVGNkgKVVGVDTSYV--EEIPgahiirenieneflvdE 97
                     8***********9988666665689*****9963..444344555555555555550 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1285.54
//
Query:       EPA06241.1  [L=166]
Description: hypothetical protein BG20_I2090, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00013   21.4   0.5    0.00023   20.6   0.3    1.6  1  RNA_pol_Rpc34   RNA polymerase Rpc34 subunit
  ------ inclusion threshold ------
      0.018   15.0   0.1      0.035   14.0   0.1    1.4  1  MarR            MarR family
      0.041   13.7   0.1      0.065   13.0   0.1    1.4  1  PI3_PI4_kinase  Phosphatidylinositol 3- and 4-kinase
      0.073   13.4   4.0       0.13   12.7   4.0    1.4  1  DUF3194         Protein of unknown function (DUF3194)
       0.12   12.4   0.1       0.12   12.4   0.1    2.1  3  z-alpha         Adenosine deaminase z-alpha domain
       0.14   12.8   0.0        0.2   12.4   0.0    1.2  1  RPA_C           Replication protein A C terminal
       0.31   10.7   0.6       0.45   10.2   0.6    1.2  1  DUF4956         Domain of unknown function (DUF4956)


Domain annotation for each model (and alignments):
>> RNA_pol_Rpc34  RNA polymerase Rpc34 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.3   9.1e-08   0.00023     299     335 ..     119     155 ..      27     156 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 9.1e-08
                    SSSSTTXXSSXSSSSSXXTSSSSSSSSSSTTSSSSXX CS
  RNA_pol_Rpc34 299 lasglveapcgecpvfdlceeggavspkncvYlkeWl 335
                    ++  + +apc  cpv ++c+ +g++sp++c ++++W+
     EPA06241.1 119 STLSIENAPCLVCPVEQKCSLEGEISPRTCQFIEDWV 155
                    44456689****************************6 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   1.4e-05     0.035      14      52 ..      63     101 ..      62     106 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.4e-05
                 HSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE CS
        MarR  14 eqgplsvseLakklgvskstvtrvldrLekkGlieRsks 52 
                 e++++ +seL+kkl++++   +r++ +Le+ G i+R+k 
  EPA06241.1  63 ESEGMFQSELWKKLKLTSRDGSRLALKLERMGTIYREKL 101
                 678899******************************985 PP

>> PI3_PI4_kinase  Phosphatidylinositol 3- and 4-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   2.5e-05     0.065     183     231 ..      37      84 ..       7      94 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.5e-05
                     SHCSSSS-.SSSSS.S-THHHHHHTSTTCCHHHHHHHHHHHHHHHHHTHH CS
  PI3_PI4_kinase 183 ewkllpfpqekvPf.rltrelvlaidpskdeglfresceealealrrdqn 231
                     e +++++  ekv + rlt ++ +++ + ++eg+f++++++ l++ +rd  
      EPA06241.1  37 EIENFQI--EKVDMeRLTNKICDVLAERESEGMFQSELWKKLKLTSRDGS 84 
                     4444554..7*********************************9999865 PP

>> DUF3194  Protein of unknown function (DUF3194)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   4.0     5e-05      0.13       2      39 ..       7      44 ..       7      63 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5e-05
                ---SHHHHHHHHHHHHHHHHHHHHTTS-TTTEEEEEEE CS
     DUF3194  2 kkLteedldeiseflaeviekkifkkvskkevldldit 39
                kkLt+++l+ei +  ++++e+++ +++   e+++++i+
  EPA06241.1  7 KKLTKKELEEIKKEEEKTLEEELEEQLTDEEIENFQIE 44
                8***********************************96 PP

>> z-alpha  Adenosine deaminase z-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.4       1.1   2.9e+03      13      32 ..      14      34 ..       6      41 .. 0.61
   2 ?   12.4   0.1   4.8e-05      0.12       5      54 ..      51      99 ..      47     101 .. 0.91
   3 ?   -4.0   0.0       6.3   1.6e+04      41      51 ..     155     165 ..     155     165 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.1
                HHHC-.TTCECCHHHHHHHHC CS
     z-alpha 13 Leelg.ekkaatalalergLs 32
                Lee+  e++ +++ +le +L+
  EPA06241.1 14 LEEIKkEEEKTLEEELEEQLT 34
                444431445666667777776 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 4.8e-05
                HHHHHHHHHHHC-TTCECCHHHHHHHHCC-HHHHHHHHHHHHHTTSEEEE CS
     z-alpha  5 qaekilelLeelgekkaatalalergLstpkreiNrvLydlerkgkvyre 54
                  +ki+++L e +  ++  + +l  +L+   r+  r   +ler g +yre
  EPA06241.1 51 LTNKICDVLAERE-SEGMFQSELWKKLKLTSRDGSRLALKLERMGTIYRE 99
                5789*******99.99***99999999999******************98 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 6.3
                 HHHHHHHTTSE CS
     z-alpha  41 vLydlerkgkv 51 
                 vL d+++ +kv
  EPA06241.1 155 VLADMKKPAKV 165
                 67888888876 PP

>> RPA_C  Replication protein A C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   7.7e-05       0.2      33      98 ..      36      97 ..       9      99 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.7e-05
                XXXXXXXXXXXX.XSXHHHHHHHHHHHH.SXSTTTEEHHHHHHHSTSXHHHHHHHHHHHHHTTSEE CS
       RPA_C 33 galsgnqaklankgltalaqqvlnlikqspeseeGvhvdeiaqklrlsvndvkqavdeLsneGiiY 98
                 ++++ q +++   +++l++ +++++ +  ++ eG+  +e+ +kl+l  +d  + + +L+  G iY
  EPA06241.1 36 EEIENFQIEKVD--MERLTNKICDVLAE--RESEGMFQSELWKKLKLTSRDGSRLALKLERMGTIY 97
                555555666666..99************..9*********************************** PP

>> DUF4956  Domain of unknown function (DUF4956)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.6   0.00017      0.45     126     163 ..      12      50 ..       3      56 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00017
     DUF4956 126 drieliapedeeeliadleerl.glkvteveveeidfvr 163
                  ++e i+ e+e++l ++lee+l + +++++++e++d+ r
  EPA06241.1  12 KELEEIKKEEEKTLEEELEEQLtDEEIENFQIEKVDMER 50 
                 45788*************98652789**********855 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2368  (0.132077); expected 358.6 (0.02)
Passed bias filter:                     1082  (0.0603492); expected 358.6 (0.02)
Passed Vit filter:                       107  (0.00596798); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 1014.15
//
Query:       EPA06242.1  [L=212]
Description: ribonuclease HII [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.8e-45  153.4   0.2    7.7e-45  153.2   0.2    1.0  1  RNase_HII  Ribonuclease HII


Domain annotation for each model (and alignments):
>> RNase_HII  Ribonuclease HII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.2   0.2   4.3e-49   7.7e-45       1     197 [.      11     205 ..      11     206 .. 0.91

  Alignments for each domain:
  == domain 1  score: 153.2 bits;  conditional E-value: 4.3e-49
                 EEEEEE-TT-SBS-EEEEEEEECGHHHHHHHCTTGTTGTTS-HHHHHHHHHHHHSEEEEEEE-HHHHH...HHTTTS-HHHHHHHHHHHHHHHHHHTCE CS
   RNase_HII   1 iGiDEaGrGpvlGplvvaavavekereeelkklgvkDSKkLskqkreeLaklikkkiekrklvaeeiky..aseneinlneikaaltlaviklleklgv 97 
                 +G+D aGrG++lGplv+a+v ++k + ++lk lgvkDSK+L+++ reeL k+i   + + ++++   k   as+++ +ln+++a+ +++vi +l+++  
  EPA06242.1  11 CGVDDAGRGSMLGPLVIAGVSLKKSDVSKLKLLGVKDSKQLTPKLREELYKKIISLVDNYYVAKISPKLidASVKKHDLNHLEAKYMAKVILKLNPDTS 109
                 7*****************************************************6666554444333334499**********************9999 PP

                 ECCECCCE--SSHHHHHHHHHHHHC.CEEEEETTGGGT-HHHHHHHHHHHHHHHHHHHHHHHHCSH.--TTSSTTSHHHHHHHHHHHHH..S--TTB-T CS
   RNase_HII  98 kvdeilvdgvttpeslkkkleqiik.ikvtvekkadekyllvaaASiiAkverdeelellkrkpgtldkgsGyasdektrallkkgats..klpdivrl 193
                 +vd+ +v+    p+++ k++ +  +  k+   + ad+++++v+aASiiAkv+rd e+ +l+++    d gsGy+sd kt  ++k + +    lp +vr 
  EPA06242.1 110 YVDSCDVN----PNRFGKEISKLSNnKKIRSYHHADSRFIVVSAASIIAKVTRDREIMKLRKNH---DLGSGYPSDSKTIDFVKLYYKTnqILPVFVRK 201
                 99999999....9999999999988889**************************9999998885...8****************998887899****** PP

                 TSHH CS
   RNase_HII 194 sfkt 197
                 s+k 
  EPA06242.1 202 SWKP 205
                 **96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       749  (0.0417759); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1569.73
//
Query:       EPA06243.1  [L=390]
Description: N2,N2-dimethylguanosine tRNA methyltransferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-83  280.3   0.0      3e-83  280.1   0.0    1.0  1  TRM              N2,N2-dimethylguanosine tRNA methyltransfera
  ------ inclusion threshold ------
      0.013   15.3   0.0       0.23   11.2   0.0    2.2  2  Methyltransf_31  Methyltransferase domain
      0.014   15.2   0.0      0.021   14.6   0.0    1.3  1  Met_10           Met-10+ like-protein
      0.023   15.0   0.0      0.048   14.0   0.0    1.5  1  Rrf2             Transcriptional regulator
       0.03   14.2   0.0      0.099   12.6   0.0    1.9  2  MarR             MarR family
      0.051   13.1   0.0       0.14   11.7   0.0    1.8  2  HTH_24           Winged helix-turn-helix DNA-binding
      0.096   12.7   0.0        6.7    6.8   0.0    2.5  2  HTH_Mga          M protein trans-acting positive regulator (M
       0.14   11.7   0.0       0.27   10.8   0.0    1.4  1  MTS              Methyltransferase small domain
       0.19   12.4   0.0       0.39   11.4   0.0    1.5  1  Methyltransf_25  Methyltransferase domain


Domain annotation for each model (and alignments):
>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  280.1   0.0   1.5e-86     3e-83       1     375 [.      14     378 ..      14     379 .. 0.93

  Alignments for each domain:
  == domain 1  score: 280.1 bits;  conditional E-value: 1.5e-86
                 TTEEEEE----SS..--TT--SS--GGGHHHHHHHHHH...HHHHHHHH-S-EEEEESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHHHHHHHHHT CS
         TRM   1 Geakikvedkevt..vskkeeVFYNPvqefnRDlsvlvirqlellkkklgekikvldaLsasGlRaiRfalEvpgvkevlaNDisekAvelikeNvkln 97 
                 G++k+ v++k++t  v+ ke+ F+NP  ++nRD sv++    + + kk++ +   l++L++ G+R++R a E  + ++v++ND+++ A+++ k  ++ln
  EPA06243.1  14 GKTKVLVPKKSITdkVPPKEPAFFNPKARVNRDYSVIA---YSSFLKKFVGPKIFLEGLTGVGIRGLRVANE-LQIEKVIINDLNPTALKMAKYSAQLN 108
                 88999****998899***********************...55555566677779*****************.56788999****************** PP

                 T--GGEEEE-S-HHHHHC...--SS-EEEEEE--SS--GGGHHHHHHHEEEEEEEEEEE--HHHHTTSSHHHHHHHHSSB---STTHHHHHHHHHHHHH CS
         TRM  98 eveeivvineddAnvlla...ekkkrfdviDlDPfGspapfldsavqsvkekglLlvTaTDtavLaGaspekclrkYgavalkselcHEvalRillkav 193
                 + ++ ++++e++   +l+   +k+kr  + D+DPfGspapf d  +++  ++g+L+ TaTD+ vL G ++++c rkYg+ +++ e+  E+a+R++l+ +
  EPA06243.1 109 KLKN-IEFSEMEVCRFLSkfsKKDKRGSITDIDPFGSPAPFFDCGIRATMHGGILSTTATDLQVLNGLYQNACKRKYGGIPIRVEYGNEMAIRLMLGCL 206
                 ****.99**********98988999999*********************************************************************** PP

                 HHHHHTTTEEEEEEEEEEETTEEEEEEEEEE-HHHHHHHHTTEEEEEEETTT--EEEE--GGG--SB-TTT-SBEEEEEEEE-S-S--HHHHHHHHHHH CS
         TRM 194 areaakYekavepllslsadfYvrvfvkvktgaakvkkvleklglvlhCsgClseekvkglakfkaecehcgaklhlaGPlwlgplkdkefveevleea 292
                  + a +    ++pl++ s+ +Y+r++v+v   + +     e++g++lhC +C +++ v + +    ece c++kl+++GPlw++++ dkefve+++ e+
  EPA06243.1 207 RMVAGRIGVEIVPLFAESNMHYYRIYVQVLIRQDQ----KENIGYILHCKNCGDRRIVLEQY---YECELCKSKLSIGGPLWIDKIFDKEFVENMILEI 298
                 ****************************9876654....5789*********9966665554...59****************************9988 PP

                 CT..-TTS-HHHHHHHHHHHHHHS--SS-EEHHHHHHHHT-SS---HHHHHHH....TT-EE-TTSTTEEE-SS-HHHHHHHH CS
         TRM 293 ekekeeelkkrvkklLklikeElldaplyydlsqlasvlklsvpplkkvvsalkelgfevsrtHakpkaikTnapleavvevl 375
                  +    ++ k  +k L+++ +E+ +  +y++l+++a ++k+s p+l++ +++l++ g+ +s t ++p++++Tna+++++++v+
  EPA06243.1 299 PE---VSVDKVCEKTLQKCLKESEMPGIYFTLDEIAAKMKSSPPKLEDAIKNLQKNGYIASPTSFCPTGFRTNANIKEIIDVF 378
                 88...6889999999*******999999****************************************************996 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00012      0.23      29      67 ..      86     125 ..      70     181 .. 0.81
   2 ?    1.8   0.0     0.094   1.9e+02      82     108 ..     329     355 ..     284     371 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00012
  Methyltransf_31  29 aevvGiDiseeaielArenaqklgldnveFeqgdiee.le 67 
                       +v+  D +++a++ A+  aq ++l+n+eF++ ++   l+
       EPA06243.1  86 EKVIINDLNPTALKMAKYSAQLNKLKNIEFSEMEVCRfLS 125
                      347777************************9988776444 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.094
  Methyltransf_31  82 evlnaladpdkileeiervlkpggill 108
                      e+ + +++++  le ++++l+++g+++
       EPA06243.1 329 EIAAKMKSSPPKLEDAIKNLQKNGYIA 355
                      555888888888889999999999886 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0     1e-05     0.021     107     153 ..      68     114 ..      53     181 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1e-05
                 TT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCE CS
      Met_10 107 vfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvv 153
                  + G+G   + +a   + ++v+ +dlnP++ k+ k   +lNk++++ 
  EPA06243.1  68 GLTGVGIRGLRVANELQIEKVIINDLNPTALKMAKYSAQLNKLKNIE 114
                 578999999999999999*************************9863 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   2.4e-05     0.048      26      57 ..     325     356 ..     314     358 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.4e-05
                 B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
        Rrf2  26 vsseeiaerqnispsylekilakLrkaglvks 57 
                 ++++eia++++ sp+ le  +++L+k+g++ s
  EPA06243.1 325 FTLDEIAAKMKSSPPKLEDAIKNLQKNGYIAS 356
                 799***************************98 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       5.5   1.1e+04      46      59 .]     247     260 ..     244     260 .. 0.72
   2 ?   12.6   0.0     5e-05     0.099      14      49 ..     319     356 ..     314     359 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 5.5
                 SEEEEEETTSTTSE CS
        MarR  46 lieRskspeDrRev 59 
                 +i   k+ +DrR+v
  EPA06243.1 247 YILHCKNCGDRRIV 260
                 55555777899987 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 5e-05
                 HSTTEEHH..HHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
        MarR  14 eqgplsvs..eLakklgvskstvtrvldrLekkGlieR 49 
                 e+++++ +  e+a k++ s++ +  +++ L k+G+i +
  EPA06243.1 319 EMPGIYFTldEIAAKMKSSPPKLEDAIKNLQKNGYIAS 356
                 5667766677**************************86 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       2.9   5.8e+03       3      15 ..     166     178 ..     165     179 .. 0.80
   2 ?   11.7   0.0   7.2e-05      0.14      20      47 ..     327     354 ..     326     355 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.9
      HTH_24   3 etdrkILelLqkn 15 
                  td+++L+ L++n
  EPA06243.1 166 ATDLQVLNGLYQN 178
                 599****977777 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 7.2e-05
      HTH_24  20 qreLAerlglSpstvnrrlkrLeeeGlI 47 
                   e+A +   Sp+ +   +k+L+++G+I
  EPA06243.1 327 LDEIAAKMKSSPPKLEDAIKNLQKNGYI 354
                 579************************9 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.049        97      33      43 ..     307     317 ..     295     322 .. 0.88
   2 ?    6.8   0.0    0.0034       6.7      20      45 ..     324     349 ..     323     354 .. 0.94

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.049
     HTH_Mga  33 seltlqsdise 43 
                 +e+tlq+++ e
  EPA06243.1 307 CEKTLQKCLKE 317
                 899*****987 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0034
     HTH_Mga  20 sltldelakeLglseltlqsdiseLn 45 
                 ++tlde+a ++  s  +l + i +L+
  EPA06243.1 324 YFTLDEIAAKMKSSPPKLEDAIKNLQ 349
                 69***********************9 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00014      0.27      40      90 ..      70     121 ..      66     130 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00014
                 -TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STT CS
         MTS  40 cGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvl 90 
                 +G+G+ g+ +a+e +  +v + d +  Al++ak  ++ nkl+ +e+ + +v 
  EPA06243.1  70 TGVGIRGLRVANELQIEKVIINDLNPTALKMAKYSAQLNKLKnIEFSEMEVC 121
                 599**************************************99888877765 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0    0.0002      0.39       6      57 ..      70     122 ..      65     134 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0002
                      -TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCG CS
  Methyltransf_25   6 cGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaed 57 
                      +G G   l++a++l+ +kv+  D+++++l+ a+  a+ ++l n+ef ++++ +
       EPA06243.1  70 TGVGIRGLRVANELQIEKVIINDLNPTALKMAKYSAQLNKLkNIEFSEMEVCR 122
                      6888889999999999********************999999****9998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      597  (0.033298); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.48
# Mc/sec: 2442.25
//
Query:       EPA06244.1  [L=175]
Description: hypothetical protein BG20_I2671, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1136.14
//
Query:       EPA06245.1  [L=169]
Description: hypothetical protein BG20_I2672, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.2e-05   22.7   1.2    8.2e-05   22.7   1.2    3.6  3  He_PIG       Putative Ig domain
    9.5e-05   22.4   7.9    0.00015   21.8   7.9    1.3  1  Trypan_PARP  Procyclic acidic repetitive protein (PARP)
     0.0035   17.9  12.1     0.0066   17.0  12.1    1.4  1  TonB_N       TonB polyproline region
  ------ inclusion threshold ------
      0.011   16.0   5.7       0.27   11.6   0.9    2.5  2  fn3          Fibronectin type III domain


Domain annotation for each model (and alignments):
>> He_PIG  Putative Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   2.9      0.32   1.4e+03      36      47 ..      54      66 ..       2      68 .. 0.49
   2 !   22.7   1.2   1.8e-08   8.2e-05      12      48 ..      79     115 ..      72     116 .. 0.87
   3 ?   -2.3   0.9       1.2   5.3e+03       5       5 ..     131     131 ..     119     146 .. 0.50

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.32
      He_PIG 36 G.sytftVtatdg 47
                G  ++f V +td+
  EPA06245.1 54 GkLLSFIVKVTDS 66
                4356666777766 PP

  == domain 2  score: 22.7 bits;  conditional E-value: 1.8e-08
      He_PIG  12 LPsGLtLdsstGtitGtpdqtvapGsytftVtatdgs 48 
                  P+G  +++ tG +++tp++ + + sytf++ + +gs
  EPA06245.1  79 PPTGAKINTNTGLFSWTPTNLQGTKSYTFDIVVKQGS 115
                 59*******************7777********9997 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 1.2
      He_PIG   5 t 5  
                  
  EPA06245.1 131 N 131
                 1 PP

>> Trypan_PARP  Procyclic acidic repetitive protein (PARP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   7.9   3.3e-08   0.00015      76     107 ..     132     163 ..     106     168 .. 0.66

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 3.3e-08
  Trypan_PARP  76 epepetepeeepepepepepepepepepepep 107
                   pep t p+++pep   pep pep pep pep
   EPA06245.1 132 TPEPTTTPKSTPEPTKSPEPSPEPSPEPSPEP 163
                  45555555555555555555555555554444 PP

>> TonB_N  TonB polyproline region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0  12.1   1.5e-06    0.0066       9      57 ..     117     164 ..     109     168 .. 0.52

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.5e-06
                 XXX.XXXXXXXXXXXXXXX....XXXXXXXXXXX..XXXXXXXXXXXXX CS
      TonB_N   9 aeqkpisvtmvapaelepPapaaaepePapePavepePePePEvvPePp 57 
                 +++++i++t+  + + ++P  ++++++P+p+   ep PeP PE+ PeP 
  EPA06245.1 117 TDRQSITITVNDVLNTPEP-TTTPKSTPEPTKSPEPSPEPSPEPSPEPT 164
                 3445666665555555555.33444444333333556677777777775 PP

>> fn3  Fibronectin type III domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.9   5.9e-05      0.27      57      84 ..       2      29 ..       1      30 [. 0.88
   2 ?    6.5   0.3    0.0024        11       9      45 ..      83     120 ..      77     139 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.9e-05
                EEEEESSSTTEEEEEEEEEEETSEEEEE CS
         fn3 57 svtltgLkpgteYevrVqavngggegpe 84
                ++  tgL+ gt Y+ +V ++n +g++  
  EPA06245.1  2 TYSHTGLTTGTVYTYKVSTINSVGTSSA 29
                68899******************98766 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0024
                 EEESSSEEEEEEE-CSSSSSTEEEEEEEEEETTSTS.T CS
         fn3   9 sevtstsltvsWeppkdgggpitgYeveyrekgsee.e 45 
                   +++++  +sW+p + +g +   + + +++ + ++ +
  EPA06245.1  83 AKINTNTGLFSWTPTNLQGTKSYTFDIVVKQGSATDrQ 120
                 5679999********95555666677777776666642 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.38
# Mc/sec: 1322.98
//
Query:       EPA06246.1  [L=255]
Description: hypothetical protein BG20_I2237 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.2   11.7   3.5       0.19   11.7   0.3    2.2  2  DUF1910   Domain of unknown function (DUF1910)


Domain annotation for each model (and alignments):
>> DUF1910  Domain of unknown function (DUF1910)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.2     0.044   7.8e+02      20      42 ..      33      55 ..      15      82 .. 0.65
   2 ?   11.7   0.3   1.1e-05      0.19      54      86 ..     161     198 ..     151     238 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.044
     DUF1910 20 riaklkekieelsedeeksiqae 42
                +++k+++ ++ +++d ++ i++ 
  EPA06246.1 33 QVEKRENILKYSKKDTAEKIASC 55
                34555555555555555555544 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 1.1e-05
     DUF1910  54 kleliiakYSlGesieeleadyeelikeleel.....w 86 
                 ++ +++a+Y++G ++++++++y+ ++ e++++      
  EPA06246.1 161 YYLELMANYTQGINVDTIKQKYKGTYLEYNDYrlskiI 198
                 556789******************99999888444440 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       788  (0.0439511); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1708.06
//
Query:       EPA06247.1  [L=179]
Description: hypothetical protein BG20_I2235 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-05   24.8  17.9    2.8e-05   24.2  17.9    1.2  1  SpoIIM    Stage II sporulation protein M


Domain annotation for each model (and alignments):
>> SpoIIM  Stage II sporulation protein M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2  17.9   1.5e-09   2.8e-05       4     151 ..      10     162 ..       7     165 .. 0.67

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1.5e-09
      SpoIIM   4 lflvgillgallaa.......snfaeqis......seskensalslflaifanNlrvalllfllGllllgiptilvl.linGfvlGav.aalvaefggl 87 
                 +f++  l+ a++         +      +      +e ++       + if++Nl++al +f+ G+   g++  l+  + +Gf   a+ +++ a  +  
  EPA06247.1  10 FFIFMGLFSAVYQIgaistvnE------EeaamflDEFSNLVDGIDGFGIFVHNLTIALPMFIPGF---GLVWGLFAgWSTGFAFAAIvTSIPALANFP 99 
                 3433333333333355544331......02333443334444456799*****************5...999998888*****9996625555555778 PP

      SpoIIM  88 llflllilPhgilelpaiiiagaaglrlgkalrsrrkalkeakrellklllllvp.llliAaliE 151
                  l++l++ P gi+el a+ ++++ ++ + +a+ ++r  + ++   ++++ ++  + lll+++ +E
  EPA06247.1 100 PLAILYLSPFGIMELVAYSLGISRSYMIIYAIIKHRSIKPQLLITSIEIGIV--VaLLLVGGYLE 162
                 99******************************64444444444444444333..25788888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 1109.78
//
Query:       EPA06248.1  [L=125]
Description: nitrite/sulfite reductase ferredoxin domain protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.1e-17   61.0   0.0    1.1e-16   60.4   0.0    1.3  1  NIR_SIR_ferr  Nitrite/Sulfite reductase ferredoxin-like half 


Domain annotation for each model (and alignments):
>> NIR_SIR_ferr  Nitrite/Sulfite reductase ferredoxin-like half domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.4   0.0   6.2e-21   1.1e-16       7      69 .]      62     124 ..      56     124 .. 0.95

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 6.2e-21
  NIR_SIR_ferr   7 kgyymvrlrvpnGritaeqlraladiaekygsgeirlTtrQnlqlhgvpeedleeileeLaea 69 
                     y+mvr+++p+G i + ql+++ +++e++++g ++++tr n+qlh+v  ed+ eil+ Lae+
    EPA06248.1  62 SDYAMVRIKLPAGEIYPNQLEKISQLSEQFSIGSAHFSTRENIQLHWVILEDVSEILRGLAEV 124
                   4689********************************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 771.79
//
Query:       EPA06249.1  [L=37]
Description: hypothetical protein BG20_I2234 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       185  (0.0103185); expected 358.6 (0.02)
Passed bias filter:                      143  (0.0079759); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.47
# Mc/sec: 238.23
//
Query:       EPA06250.1  [L=280]
Description: thiazole biosynthesis enzyme [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-64  218.0   0.1    1.3e-64  217.7   0.1    1.1  1  Thi4            Thi4 family
    1.6e-13   50.5   0.3      1e-06   28.1   0.0    3.0  3  FAD_binding_2   FAD binding domain
    1.3e-09   38.0   0.0    2.7e-09   36.9   0.0    1.5  1  FAD_oxidored    FAD dependent oxidoreductase
    3.9e-08   32.9   0.0    5.2e-08   32.5   0.0    1.2  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    1.9e-07   31.2   0.0    4.2e-07   30.1   0.0    1.6  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
      2e-06   27.3   0.0    3.3e-06   26.6   0.0    1.3  1  FAD_binding_3   FAD binding domain
    2.3e-06   27.5   0.2    0.00028   20.6   0.1    2.3  2  DAO             FAD dependent oxidoreductase
    2.9e-06   26.3   0.0    4.1e-06   25.7   0.0    1.2  1  HI0933_like     HI0933-like protein
     0.0001   21.7   0.0    0.00015   21.1   0.0    1.2  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    0.00015   20.9   0.4     0.0019   17.3   0.0    2.3  3  Lycopene_cycl   Lycopene cyclase protein
     0.0003   20.0   0.1     0.0005   19.3   0.1    1.3  1  GIDA            Glucose inhibited division protein A
     0.0062   15.4   0.0        1.3    7.8   0.0    2.1  2  Trp_halogenase  Tryptophan halogenase
       0.01   15.2   0.0      0.016   14.5   0.0    1.3  1  Amino_oxidase   Flavin containing amine oxidoreductase
  ------ inclusion threshold ------
       0.01   15.1   0.0      0.025   13.9   0.1    1.5  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
      0.017   15.7   0.1      0.064   13.8   0.0    2.1  1  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
      0.054   12.0   0.0        0.1   11.1   0.0    1.4  1  GDI             GDP dissociation inhibitor
      0.071   13.1   0.1       0.14   12.2   0.1    1.4  1  NAD_binding_9   FAD-NAD(P)-binding
       0.11   12.7   0.0       0.25   11.6   0.0    1.6  1  TrkA_N          TrkA-N domain


Domain annotation for each model (and alignments):
>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  217.7   0.1   1.3e-67   1.3e-64       1     235 []      31     257 ..      31     257 .. 0.98

  Alignments for each domain:
  == domain 1  score: 217.7 bits;  conditional E-value: 1.3e-67
                 HHHHHHHHHHHHHHHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTTBSEEEEETTTHHHHHHTT---EEESSEEEESEHHHH CS
        Thi4   1 sraiveryfedllkyaesDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGqlfsaivvrkpakelLdelgikyedegdyvvvkdaalf 99 
                 +rai ++    l++ a+sDv+i+GaG++GLta++ l++  ++kv+++e++  +GGG wlGG + + + vr+pa+++ delg++y++  d++++     +
  EPA06250.1  31 TRAIANEWHAVLIDRAQSDVIIIGAGPAGLTASRDLSNM-GFKVLVVEQNNYLGGGYWLGGYMMNPVTVREPAQKIWDELGVPYKKVSDGLYITPGPHA 128
                 699999999*****************************9.*********************************************************** PP

                 HHHHHHHHHTSTTEEEEESEEEEEEEEETBTEEEEEEEEEHHHHTCTTTSS.-B-EEEEEEEEEE--GSSSTTTTHHHHHHHHCTTTS-----ECB-HH CS
        Thi4 100 tstllskvlqlanvkllnavaveDlivregegvaGvvinwtlvelahdtqscvDPlvirakvvvdatGhdgeivavvvkkikleakiekvkgeksldae 198
                 +s+l++++++ a+vk ln +  +Dl++++  +vaG+v+nw+ v+    + +cvDP  ++ak+++da+Ghd+    v+vk++++     + kg+ +++++
  EPA06250.1 129 VSKLIAAACD-AGVKFLNLTKFDDLVLKN-GRVAGIVVNWMPVSALPRNITCVDPIALEAKMIIDASGHDS----VAVKRLVDRG-LAEWKGMNPMYVN 220
                 **********.******************.8***************999*********************6....7889999988.6789********* PP

                 HHHHHHHHHECEEETTEEE-THHHHHHHT-EB--SB- CS
        Thi4 199 kaedaivkktrevvpnlyvaGmevaevdganRmGpif 235
                 ++e+++v+kt ev+p+l++aGm v+e +g+ RmGp++
  EPA06250.1 221 EGEEHVVHKTGEVYPGLVAAGMSVTETHGLARMGPTY 257
                 ***********************************96 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0     1e-09     1e-06       1      36 [.      49      84 ..      49     105 .. 0.93
   2 !   17.5   0.0   1.8e-06    0.0018     136     203 ..     121     197 ..     111     225 .. 0.80
   3 ?    1.8   0.1       0.1     1e+02     383     413 ..     225     254 ..     219     256 .. 0.89

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 1e-09
                   SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
  FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36
                   Dvi+iG+G AGL+A+  +++ G kv+vve+ ++ gg
     EPA06250.1 49 DVIIIGAGPAGLTASRDLSNMGFKVLVVEQNNYLGG 84
                   9******************************99887 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 1.8e-06
                    ...HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEET.........TTTCEEEEEESEEEE-----G CS
  FAD_binding_2 136 tlvtghallarlvesarkagvdfqerteadeLivedgrvtGavvenp.........esgrevrirakavvlatgGfg 203
                     +++g++ +  l+++a +agv+f++ t+ d+L+ ++grv G+vv+ +         +     +++ak +++a+g  +
     EPA06250.1 121 YITPGPHAVSKLIAAACDAGVKFLNLTKFDDLVLKNGRVAGIVVNWMpvsalprniTCVDPIALEAKMIIDASGHDS 197
                    5789****************************************988888666444334444888888888888666 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.1
                    BESTTEEESSBTEEE-STCEESSSSTTS--T CS
  FAD_binding_2 383 rvldadgqpipGLYAaGevaaggvhganrlg 413
                    +v  ++g++ pGL AaG    +  hg  r+g
     EPA06250.1 225 HVVHKTGEVYPGLVAAGMSV-TETHGLARMG 254
                    567899***********999.9****99987 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.0   2.7e-12   2.7e-09       1     145 [.      49     195 ..      49     201 .. 0.71

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 2.7e-12
  FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsgl.vatdignkaeeqvvtgiareflerlrq.rggarlkkrskwntfepevakavlee 95 
                   Dv+++G+gpaG++A     ++G kvl+ve++++lGG    g+ ++++++ +   + +++i++e+    ++  +g          t  p+++ +++ +
    EPA06250.1  49 DVIIIGAGPAGLTASRDLSNMGFKVLVVEQNNYLGGGYWLGGyMMNPVTVR---EPAQKIWDELGVPYKKvSDGL----Y---ITPGPHAVSKLIAA 135
                   9*********************************99765444034444434...667778888777775532222....1...36899********* PP

  FAD_oxidored  96 mlaeagvtvllntrlvevekegkriesvtve.........ske.g.rktirAkvfiDATgd 145
                    ++  gv+ l  t++++ + +++r+ +++v+         + +    ++++Ak++iDA+g 
    EPA06250.1 136 ACDA-GVKFLNLTKFDDLVLKNGRVAGIVVNwmpvsalprNITcVdPIALEAKMIIDASGH 195
                   *987.**********9999988666666653111111111112113788999999999986 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.0   5.2e-11   5.2e-08       2      82 ..      49     126 ..      48     159 .. 0.83

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 5.2e-11
                  SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHHHHHHCHHHHCCCCHCCTCEEEEESC CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeiasevvkklnqgielllgeevvkidpgk 82 
                  dv++iG+GpAGl+a+++l++ g+kv++v ++++ l+gg +l   + +    +e a++  ++l+  ++++ +  ++ i pg 
   EPA06250.1  49 DVIIIGAGPAGLTASRDLSNMGFKVLVV-EQNNYLGGGYWLGGYMMNPVTVREPAQKIWDELGVPYKKVSD--GLYITPGP 126
                  8***************************.999999999999888888888888888777777777777666..66555554 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.0   4.2e-10   4.2e-07       1      33 [.      52      84 ..      52     108 .. 0.93

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 4.2e-10
                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSG CS
  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGG 33
                   I+GaG +Gl+a + L++ gf+vl++e++++lGG
     EPA06250.1 52 IIGAGPAGLTASRDLSNMGFKVLVVEQNNYLGG 84
                   9*******************************8 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   3.3e-09   3.3e-06       2      33 ..      48      79 ..      47      82 .. 0.94

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 3.3e-09
                   EEEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
  FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekr 33
                    dV+I+GaGpaGl++++ Ls+ G +v++ve+ 
     EPA06250.1 48 SDVIIIGAGPAGLTASRDLSNMGFKVLVVEQN 79
                   69****************************86 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.1   2.8e-07   0.00028       1      35 [.      49      84 ..      49     109 .. 0.90
   2 ?    5.3   0.0     0.012        12     147     207 ..     127     200 ..      99     280 .] 0.65

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.8e-07
                EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSS CS
         DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiagsg 35
                dv+iiG+G +Gl++ ++L+  g  V+++e+++ +g g
  EPA06250.1 49 DVIIIGAGPAGLTASRDLSNMGfkVLVVEQNNYLG-G 84
                9*****************9999*********9999.4 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.012
                 HHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEE..........EECTEEEE.......EEEE..EEE--GGGHHHH CS
         DAO 147 kltaalaraaealGveilegtevtgleeedgkvwgve..........rttpgend.......aada..vVnaaGawsdll 207
                 +++  l +aa ++Gv++l+ t+  +l  ++g+v+g+           r   ++ +       +  a  ++ a G+ s  +
  EPA06250.1 127 HAVSKLIAAACDAGVKFLNLTKFDDLVLKNGRVAGIVvnwmpvsalpR---NI-TcvdpialE--AkmIIDASGHDSVAV 200
                 56677888888999***********98999999999886666532221...33.133555333..244888888887555 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   4.1e-09   4.1e-06       2      36 ..      49      83 ..      48     106 .. 0.94

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 4.1e-09
                 SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
  HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36
                 dvi+iG+G+AGl a+  +++ g +Vl++e+++ lg
   EPA06250.1 49 DVIIIGAGPAGLTASRDLSNMGFKVLVVEQNNYLG 83
                 8******************************9887 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   1.5e-07   0.00015       1      31 [.      51      80 ..      51      83 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.5e-07
  Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgn 31
                 iIiGaGPaGl+a   l ++g+ ++l++E++n
   EPA06250.1 51 IIIGAGPAGLTASRDLSNMGF-KVLVVEQNN 80
                 8********************.7*****987 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.9e-06    0.0019       1      36 [.      49      82 ..      49     121 .. 0.84
   2 ?    1.1   0.0      0.16   1.6e+02     114     143 ..     168     197 ..     150     215 .. 0.76
   3 ?   -0.9   0.1      0.67   6.7e+02     220     292 ..     202     277 ..     195     280 .] 0.79

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.9e-06
  Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieaspsl 36
                   Dv++iGaGpAgl     l  +++g kv+++e  + l
     EPA06250.1 49 DVIIIGAGPAGLTASRDL--SNMGFKVLVVEQNNYL 82
                   9*****************..**********976655 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.16
  Lycopene_cycl 114 eeeageslvvleggrkirarlvvdarglas 143
                    +++a  + +++ +   ++a++++da+g  s
     EPA06250.1 168 PVSALPRNITCVDPIALEAKMIIDASGHDS 197
                    455556789999999************444 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.67
  Lycopene_cycl 220 rlaaylra..lglkvkevveeEqgviPvtlggslprleqkvlaiGaaaglvh..PaTGYsvarslaeapllasaiaa 292
                    rl+ +  a  +g++  +v e E+ v+    g   p l ++ + +  + gl +  P+ G ++    ++a++ a+ i +
     EPA06250.1 202 RLVDRGLAewKGMNPMYVNEGEEHVVHK-TGEVYPGLVAAGMSVTETHGLARmgPTYGSMLFSGRRAAEITAEKIKE 277
                    5555543336899999999999999887.788899999999999998888776699999999999999999998866 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1     5e-07    0.0005       1      31 [.      49      79 ..      49      85 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 5e-07
                CEEEE-SSHHHHHHHHHHHHTT--EEEEES- CS
        GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithk 31
                dvi+iG+G AG+ A+  ++++G+kvl + ++
  EPA06250.1 49 DVIIIGAGPAGLTASRDLSNMGFKVLVVEQN 79
                8************************998655 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0013       1.3       1      34 [.      49      79 ..      49      83 .. 0.92
   2 !    5.5   0.0    0.0066       6.6     197     227 ..     183     213 ..     172     219 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0013
                    EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-S CS
  Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlvese 34
                    +++i+G+G+aG +a   l++++   ++v++ve++
      EPA06250.1 49 DVIIIGAGPAGLTASRDLSNMG---FKVLVVEQN 79
                    699****************999...899999986 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0066
                     EEE-SEEEE-SGGG-IIIIIIT---EEE-TT CS
  Trp_halogenase 197 eveadlfiDcsGfrgllieqaLktgfedwsd 227
                      +ea ++iD+sG+ +  +++ ++ g  +w+ 
      EPA06250.1 183 ALEAKMIIDASGHDSVAVKRLVDRGLAEWKG 213
                     689****************999999999976 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   1.6e-05     0.016       2      28 ..      58      84 ..      57      87 .. 0.96

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.6e-05
                   HHHHHHHHHHHTTEEEEEEESSSSSBT CS
  Amino_oxidase  2 aGLaaArqLlsaGfdVtvlEardrvGG 28
                   aGL+a r L++ Gf+V+v+E ++ +GG
     EPA06250.1 58 AGLTASRDLSNMGFKVLVVEQNNYLGG 84
                   9*************************9 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   2.5e-05     0.025      28      60 ..      47      79 ..      40      82 .. 0.91
   2 ?   -3.6   0.0       5.6   5.6e+03     128     162 ..     136     168 ..     132     176 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.5e-05
                 --EEEEESTSHHHHHHHHHHHHTT-EEEEEESS CS
  AlaDh_PNT_C 28 pakvlviGgGvaGlqAiatakglgakVtvlDvr 60
                 ++ v++iG+G aGl A +  +++g kV v++ +
   EPA06250.1 47 QSDVIIIGAGPAGLTASRDLSNMGFKVLVVEQN 79
                 578*************************99987 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 5.6
                  TGGGT-SBTT--TBBTTSEEEEETTEEEEEBSTGG CS
  AlaDh_PNT_C 128 AidqGGnvetsrltthgepvveekgvvhygvanlp 162
                  A+d+G  +   +lt+ ++ v+++  v  + v+ +p
   EPA06250.1 136 ACDAGVKFL--NLTKFDDLVLKNGRVAGIVVNWMP 168
                  566666555..788888888887778777777777 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   6.5e-05     0.064       2      35 ..      50      83 ..      49      97 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.5e-05
                EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
   Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35
                v+++G+G  gl +   l+++g kV vve ++ l 
  EPA06250.1 50 VIIIGAGPAGLTASRDLSNMGFKVLVVEQNNYLG 83
                89**************************999886 PP

>> GDI  GDP dissociation inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0    0.0001       0.1       5      41 ..      48      84 ..      44      87 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0001
                ECEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSSCG CS
         GDI  5 ydvivlGtGlkecilsGllsvdgkkvlhldrndyyGg 41
                 dvi++G+G      s  ls  g kvl++++n+y Gg
  EPA06250.1 48 SDVIIIGAGPAGLTASRDLSNMGFKVLVVEQNNYLGG 84
                69*********************************98 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00014      0.14       2      42 ..      52      87 ..      51      97 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
  NAD_binding_9  2 ivGaGprGlavlerLlarakkkspleitlfdpsep.gagrvw 42
                   i+GaGp+Gl++ + L +       +++ +++++++ g g+ w
     EPA06250.1 52 IIGAGPAGLTASRDLSNM-----GFKVLVVEQNNYlG-GGYW 87
                   9**************999.....6********88856.9888 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00025      0.25       1      30 [.      50      79 ..      50      82 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00025
                EEEES-SHHHHHHHHHHHH.TTEEEEEEESS CS
      TrkA_N  1 iiiiGlGrvGrslaeeLse.ggkdvvvidkd 30
                +iiiG+G  G +  + Ls+ g  +v+v++++
  EPA06250.1 50 VIIIGAGPAGLTASRDLSNmGF-KVLVVEQN 79
                79*****************666.6*****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 1704.31
//
Query:       EPA06251.1  [L=139]
Description: universal stress family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-29  103.0   0.0    2.1e-29  102.8   0.0    1.0  1  Usp       Universal stress protein family


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.8   0.0   1.2e-33   2.1e-29       1     141 []       1     139 []       1     139 [] 0.94

  Alignments for each domain:
  == domain 1  score: 102.8 bits;  conditional E-value: 1.2e-33
                 S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTCEEEEEEEESSHHHHHHHHH CS
         Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggvkvevvveegdpaeeileva 99 
                 m k+IlV++Dgs++s + le+A+e+ak++++ ++llh+   ++    + ++++++++ ++ +++  + + + +  ++ +  ++  v + dp   i ++a
  EPA06251.1   1 M-KKILVPIDGSPNSVRGLEKAIEFAKNDNSSITLLHIATLPPVHVIGHSKDKVKKSLAKNAQKFIKDA-EDRCINQSIHFTTKLVYGSDPPYDIEQFA 97 
                 5.9************************************************************988765.57777777777777888889999****** PP

                 HHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
         Usp 100 eeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                 ++++ dliV+G++g+s+l+rl+lGSvs+y+++ ++ pV+v++
  EPA06251.1  98 KKYKHDLIVIGAKGKSTLKRLFLGSVSSYLVETTKTPVTVIK 139
                 ****************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 914.45
//
Query:       EPA06252.1  [L=126]
Description: HAD ATPase, P-type, family IC domain protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.5e-10   39.3   0.5    1.6e-09   38.4   0.2    1.5  2  Hydrolase    haloacid dehalogenase-like hydrolase
    0.00064   19.5   0.3    0.00079   19.2   0.3    1.2  1  Hydrolase_3  haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
        0.6    8.9   4.2       0.72    8.6   4.2    1.1  1  DUF5423      Family of unknown function (DUF5423)


Domain annotation for each model (and alignments):
>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.2   2.6e-13   1.6e-09     175     209 ..       1      35 [.       1      36 [. 0.96
   2 ?   -1.7   0.0       0.5     3e+03      43      62 ..      45      64 ..      41     112 .. 0.58

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 2.6e-13
                 SHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHT CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
   Hydrolase 175 spegkvaaireLqgkpeevamVGDgvnDaaalaaA 209
                 +pe+kv a+++L+++  +v+mVGDg+nDa+ala+A
  EPA06252.1   1 LPEQKVIAVKKLKEEYGQVVMVGDGINDAPALAMA 35 
                 59*******************************98 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.5
                HHHHHHHHHHHHHHHHHHHH CS
                xxxxxxxxxxxxxxxxxxxx RF
   Hydrolase 43 gkalvaaakarsgaltgfat 62
                g a+ a a ++ + ++++a+
  EPA06252.1 45 GTAISADAADVVFLVDDIAK 64
                55555555555444444444 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.3   1.3e-07   0.00079     191     237 ..       8      50 ..       4      82 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.3e-07
                  HHHHHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHH CS
  Hydrolase_3 191 alkklakelnisleeviafGDgeNDieMLeaaglgvAmgnaseevkk 237
                  a+kkl +e+     +v+ +GDg ND + L +a +g+Amg     + +
   EPA06252.1   8 AVKKLKEEY----GQVVMVGDGINDAPALAMATTGIAMGAHGTAISA 50 
                  555555444....59***********************965555444 PP

>> DUF5423  Family of unknown function (DUF5423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   4.2   0.00012      0.72      41     106 ..      35     100 ..      29     116 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00012
     DUF5423  41 qgsglalfaiapalaigalgvtllvsdlaesqkskeiadtvaavslpfiltgtaaglmfsaiavgg 106
                   +g+a+ a   a++  a  v +lv d+a++    ei++    ++   i+ g  a +++ aia  g
  EPA06252.1  35 ATTGIAMGAHGTAISADAADVVFLVDDIAKTSDIVEISQRTLQIAKQGIFIGLGASFVLMAIASVG 100
                 568999***************************************************999999655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 785.51
//
Query:       EPA06253.1  [L=48]
Description: hypothetical protein BG20_I2394, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.3e-06   26.0   0.1    8.3e-06   26.0   0.1    1.0  1  MOFRL     MOFRL family
  ------ inclusion threshold ------
      0.018   14.7   0.2      0.018   14.7   0.2    1.0  1  DUF4940   Domain of unknown function (DUF4940)


Domain annotation for each model (and alignments):
>> MOFRL  MOFRL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.1   9.3e-10   8.3e-06      75     109 .]       8      42 ..       1      42 [. 0.88

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 9.3e-10
                 T--HHHHHHTT-HHHHHHHTT-EE-----S----E CS
       MOFRL  75 gldakeaLanndsyeffeklgallktgpTgtNVnD 109
                 +  +ke+L+n+ds +ff+k +  +kt+ T+tN++D
  EPA06253.1   8 ESIIKEFLKNSDSGRFFQKQKCNIKTDFTHTNLMD 42 
                 45679**************9**************9 PP

>> DUF4940  Domain of unknown function (DUF4940)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.2     2e-06     0.018     155     193 ..       3      41 ..       1      48 [] 0.91

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2e-06
     DUF4940 155 niqldekliesklrssDleklsellskdveevynkllkl 193
                 ni++de +i+++l+ sD  ++ ++ + +++  + +++ +
  EPA06253.1   3 NIKIDESIIKEFLKNSDSGRFFQKQKCNIKTDFTHTNLM 41 
                 89*****************************99888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.31s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 322.95
//
Query:       EPA06254.1  [L=258]
Description: hypothetical protein BG20_I2590, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.1e-64  215.8   0.1    1.2e-63  215.3   0.1    1.2  1  DUF521    Protein of unknown function (DUF521)


Domain annotation for each model (and alignments):
>> DUF521  Protein of unknown function (DUF521)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  215.3   0.1   6.5e-68   1.2e-63     100     376 ..       2     258 .]       1     258 [] 0.95

  Alignments for each domain:
  == domain 1  score: 215.3 bits;  conditional E-value: 6.5e-68
      DUF521 100 kqeriieayeklGveltftCtpyllgnapkkGehlawsESsavvyaNSvlGarTnreggpsalaaAitGrtpeyGlhldenRkptvlveveaesedead 198
                 kq +i + ye++Gv+++f+C+py + ++pk+G+++a++ES+a+++aNS+   +Tn+e+++sala+AitG+ p+  +  +   + t+ ++v+  + +e  
  EPA06254.1   2 KQLSIKNSYEAMGVTPSFSCIPYEIFDIPKEGTQVAFAESNAAIHANSYDNLKTNKESAFSALASAITGKSPYSSIRKEDSPNLTIRMKVK--DPNELT 98 
                 8999**********************************************************************99888877767666665..569*** PP

      DUF521 199 ygalGylvGkkvgeriPvlkglekpsedelKalgAalaasgavalfhiegvTPeaetleealgekekaekititkedleevleelskakeekvdlvalG 297
                 yg+lG+++Gk  g+    ++gl k++++++Ka++  +++sg++a f + +                  ek++++++++++v +el  ++ ek dl++lG
  EPA06254.1  99 YGMLGFFAGKV-GDTSVNISGLGKMDNRQCKAMCGGMGTSGTCAKFLFGDGDSS-------------CEKVDFDQKEMQNVHDEL--NTAEKGDLITLG 181
                 *********86.6677779****************************9888777.............89****************..999999****** PP

      DUF521 298 cPhlsleElrelaellkgkkkkvkvelwvttsrevkeeaerlglveklekaGvkvlsdtCmvvsplikkkevkkvatnS 376
                 +P+l leE+ +l+  l  k+++ +++++++++r+vke+a+++g++++le+aG+++lsd+C++++pli+k++v++v tnS
  EPA06254.1 182 SPQLGLEEISDLVGKL--KGRSFQKRCMIFCPRTVKEQARKIGYTNELERAGCEILSDCCTCLTPLINKNDVDAVTTNS 258
                 ****************..88999*******************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1522.33
//
Query:       EPA06255.1  [L=75]
Description: hypothetical protein BG20_I2570, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.31s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 467.78
//
Query:       EPA06256.1  [L=181]
Description: hypothetical protein BG20_I2571, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1314.00
//
Query:       EPA06257.1  [L=497]
Description: ATPase/histidine kinase/DNA gyrase B/HSP90 domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.1e-22   79.2   0.1    6.5e-22   78.2   0.1    1.6  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    1.4e-09   37.8   0.0    5.9e-09   35.8   0.0    2.2  1  HisKA        His Kinase A (phospho-acceptor) domain
    1.6e-09   37.6   0.8    1.2e-08   34.8   0.0    2.6  3  HATPase_c_5  GHKL domain
    4.1e-09   36.7   0.0    1.8e-08   34.6   0.0    2.2  2  HAMP         HAMP domain
     0.0036   16.9   7.8     0.0036   16.9   7.8    2.8  3  4HB_MCP_1    Four helix bundle sensory module for signal tran
  ------ inclusion threshold ------
      0.043   13.6   0.1       0.13   12.1   0.0    1.9  2  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like


Domain annotation for each model (and alignments):
>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.2   0.1   2.2e-25   6.5e-22       2     110 ..     373     473 ..     372     475 .. 0.93

  Alignments for each domain:
  == domain 1  score: 78.2 bits;  conditional E-value: 2.2e-25
                 HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHHHHHHHHHTTTEEEEEEETTT CS
   HATPase_c   2 dekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsivkklvelmgGeiwvesepgr 100
                 d+++L  +++nl+dNa  + + +gei+++i  s+dd+ +++eD+G G+p ++l+k+fe++ +     +++ gtGlGls +k++ve +gG+i+v+++p  
  EPA06257.1 373 DSSKLNIVFKNLIDNACYAINGNGEIRIRIIESQDDVLVEIEDSGSGVPDSILEKIFEPLFT-----TKQVGTGLGLSSCKSIVEAHGGKISVRNNP-- 464
                 7889999***********977999*******888************************6666.....699***********************9999.. PP

                 EEEEEEEEES CS
   HATPase_c 101 Gttftftlpl 110
                  ttft++lp+
  EPA06257.1 465 -TTFTIRLPK 473
                 .******997 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.0     2e-12   5.9e-09       9      61 ..     275     329 ..     267     334 .. 0.90

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 2e-12
                 HHHHHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHH CS
       HisKA   9 vaHELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedlLdl 61 
                 +aH++r+PLs+i+   e++k +  ++ +++l  ++e+i +++ r++h+++d+L +
  EPA06257.1 275 LAHDIRNPLSVIQNGFEIIKLKtkNNSDPSLNSNFESISRSVARITHQIDDVLNF 329
                 8*****************96666778899***********************987 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1      0.61   1.8e+03      28      51 ..     124     147 ..     113     171 .. 0.77
   2 ?   -1.0   0.1      0.57   1.7e+03      10      39 ..     153     181 ..     143     197 .. 0.63
   3 !   34.8   0.0     4e-12   1.2e-08       4      97 ..     375     470 ..     372     472 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.61
  HATPase_c_5  28 krfIrltvrekkksliisieNsye 51 
                  +++I+l+ +  ++ +i++++N ++
   EPA06257.1 124 NKMIQLKTSGASGGTILNLNNDFD 147
                  788888888888888888888876 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.57
  HATPase_c_5  10 lgnlLdNAieacskieeekrfIrltvrekk 39 
                  +  ++d Aie  ++  + +r+I ++   ++
   EPA06257.1 153 MNMAIDKAIELTTANID-QREIYVESLLRN 181
                  45579999998776554.788777665544 PP

  == domain 3  score: 34.8 bits;  conditional E-value: 4e-12
  HATPase_c_5   4 ldlcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg...ek.kkle..sskskkeehGiGlksireivkkykgnlsieaedglFt 95 
                    l +++ nl+dNA  a +     + +Ir+ + e++++++++ie s +g   ++ +k++    ++k+   G+Gl+s ++iv+ ++g++s++++ ++Ft
   EPA06257.1 375 SKLNIVFKNLIDNACYAING----NGEIRIRIIESQDDVLVEIEDSGSGvpdSIlEKIFepLFTTKQVGTGLGLSSCKSIVEAHGGKISVRNNPTTFT 468
                  57899********9777666....568*******************99955411444443344677899****************************9 PP

  HATPase_c_5  96 ls 97 
                    
   EPA06257.1 469 IR 470
                  75 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.0   5.9e-12   1.8e-08       2      52 ..     204     253 ..     203     254 .. 0.95
   2 ?   -2.7   0.0       2.7   8.2e+03       5      19 ..     311     325 ..     311     326 .. 0.77

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 5.9e-12
                 HHHTTHHHHHHHHHHHHHHTTTBTSSTCCTTSSSHHHHHHHHHHHHHHHHH CS
        HAMP   2 larrilrPLrrLaraarriaaGdldtrlpvsgrDEiGeLarafNaMldrLr 52 
                 + r+i++PL+++++++r ia+G++    p++g+DEi eL++ +N M++ L+
  EPA06257.1 204 ILRSISKPLNKIKSVTRDIAKGNFVL-YPEKGNDEISELGKDINIMSKDLK 253
                 78********************9999.9*******************9986 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.7
                 TTHHHHHHHHHHHHH CS
        HAMP   5 rilrPLrrLaraarr 19 
                 +i+r++ r++ +++ 
  EPA06257.1 311 SISRSVARITHQIDD 325
                 688999999988765 PP

>> 4HB_MCP_1  Four helix bundle sensory module for signal transduction
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   7.8   1.2e-06    0.0036      19     166 ..       2     164 ..       1     170 [. 0.85
   2 ?   -3.1   0.2       1.6   4.7e+03      37      57 ..     238     258 ..     229     265 .. 0.44
   3 ?   -2.4   0.2         1   3.1e+03      24      62 ..     329     367 ..     326     371 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.2e-06
   4HB_MCP_1  19 liivGvvGlyslkkinknletmYedrllpikdlgeikanlrelradlleliltkdkae..........kdellkd...ieeleaeidkllekyektilt 104
                 ++ +++++++++k +++ ++++ ++ l  +++l++++   ++l a++ e+il +d+ +           ++l+++   iee +  +++  ++y ++   
  EPA06257.1   2 IGGISAISIINTKYVQETFSSINTETLPILNTLKNMRYASTHLSALTNEIILIEDETRnasenefaalEETLETNfykIEEAKLLFNESFSEYSDIVSK 100
                 67899*************************************************999988888887775555554222677777799999999999888 PP

   4HB_MCP_1 105 ee..EkelleefkeqlnaYrevrkkvlelakegkkdeAyqlyetegrparekliealeelvdln 166
                 +   + +++e + e++n+   +++k+++l ++g     +  ++++ + ++ +++ a+++ ++l 
  EPA06257.1 101 SYpqDVDQIELVAEKWNEMLFISNKMIQLKTSGASGGTILNLNNDFDFSYVEMNMAIDKAIELT 164
                 763367799999***************9999999999999999999999999999998888775 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.6
   4HB_MCP_1  37 letmYedrllpikdlgeikan 57 
                 ++++ +d  +  kdl+e++++
  EPA06257.1 238 ISELGKDINIMSKDLKELNKK 258
                 333333333333333333333 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1
   4HB_MCP_1  24 vvGlyslkkinknletmYedrllpikdlgeikanlrelr 62 
                 ++++ +l++ +++l+++ +  l++  + +++k+ l e+ 
  EPA06257.1 329 FINISELHNSKNSLSSILKSTLQSMLIPENVKIILSEND 367
                 678888999999999999988888777666666666655 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       3.6   1.1e+04      84     105 ..     241     262 ..     239     268 .. 0.71
   2 ?   12.1   0.0   4.4e-05      0.13       4      62 ..     378     437 ..     375     485 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 3.6
  HATPase_c_3  84 lgkkltvitkkegesstltldv 105
                  lgk++++++k   e ++  +d 
   EPA06257.1 241 LGKDINIMSKDLKELNKKMIDQ 262
                  6888888888877777666665 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 4.4e-05
  HATPase_c_3   4 ekAlaelvdNsldAdaen..vkievnknrgktgeivieDdGkGmseeelknalrlatsske 62 
                  +++   l+dN+  A   n  + i + + + ++  + ieD G+G++ + l++ +++  ++k+
   EPA06257.1 378 NIVFKNLIDNACYAINGNgeIRIRIIESQ-DDVLVEIEDSGSGVPDSILEKIFEPLFTTKQ 437
                  778899********998855666666654.678899**************99998877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (497 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1073  (0.0598472); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 3355.82
//
Query:       EPA06258.1  [L=68]
Description: hypothetical protein BG20_I2005, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.02   14.9   5.7      0.021   14.8   5.7    1.0  1  GRA6      Granule antigen protein (GRA6)


Domain annotation for each model (and alignments):
>> GRA6  Granule antigen protein (GRA6)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   5.7   1.2e-06     0.021     159     211 ..      14      63 ..       8      68 .] 0.66

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.2e-06
        GRA6 159 vlaasvalltafflrrsgrrapgePrgendgndagdnagnrenegrgeGgege 211
                 +++ sv llt  f    g   + + +g++ gn ag+ agn+  +g g+G+++ 
  EPA06258.1  14 IISFSVLLLTGSFT---GAGLAFANSGNGAGNGAGNGAGNGAGNGAGNGAGNG 63 
                 67778888887776...555555666777777777777777777777776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      159  (0.00886831); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.30s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 459.18
//
Query:       EPA06259.1  [L=406]
Description: response regulator receiver domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      7e-24   84.2   1.0    1.8e-23   82.9   1.0    1.7  1  Response_reg    Response regulator receiver domain
    6.8e-14   51.5   0.0    1.8e-13   50.1   0.0    1.8  1  TrmB            Sugar-specific transcriptional regulator TrmB
    3.9e-05   23.0   1.3    5.2e-05   22.5   0.4    1.6  2  Regulator_TrmB  Archaeal transcriptional regulator TrmB
  ------ inclusion threshold ------
       0.11   12.2   1.5         10    5.9   0.1    2.5  2  Adenine_glyco   Methyladenine glycosylase
        0.6    9.9   6.3          5    6.9   0.8    2.9  3  DisA-linker     DisA bacterial checkpoint controller linker r


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.9   1.0   4.9e-27   1.8e-23       1     110 [.     294     403 ..     294     405 .. 0.98

  Alignments for each domain:
  == domain 1  score: 82.9 bits;  conditional E-value: 4.9e-27
                   EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEESSTSHHHHHHHHHCTESEE CS
  Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviiltahseeedavealkagaddf 97 
                   +l+vdDdp+++++++++le +g+++v+ ++d+k+a++ +k+ ++  ++lDi+mp+ dG+ ll+eir+ dp+++vi++ta  + +++++  k++  d+
    EPA06259.1 294 ILVVDDDPDAVNIFSEYLEIKGISTVEGCTDAKKAIDVFKKIRPEAVFLDIMMPDFDGFYLLDEIRKIDPKTKVIMVTADMSAATKKKLQKVNPTDV 390
                   8************************************************************************************************ PP

                   EESSG-HHHHHHH CS
  Response_reg  98 lsKpfdpeeLlka 110
                   + Kp+d++++++ 
    EPA06259.1 391 IYKPYDIKQIMSC 403
                   ********99875 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.1   0.0   5.1e-17   1.8e-13       1      68 []      25      92 ..      25      92 .. 0.98

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 5.1e-17
                HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE--HH CS
        TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravdpe 68
                L+++GL e Ea++Y+ L +lg+++a+ei+  ++++r + Y++L++L++ G+ +   ++p +++a dpe
  EPA06259.1 25 LRDFGLEEDEAQTYVGLARLGSSKASEISTFTKIERVRTYKILENLKNLGFATSTLSSPIKFSANDPE 92
                789*************************************************************9997 PP

>> Regulator_TrmB  Archaeal transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.4   1.4e-08   5.2e-05       2     143 ..     135     285 ..     134     321 .. 0.76
   2 ?   -2.4   0.0      0.62   2.2e+03      66      92 ..     350     377 ..     345     390 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.4e-08
                     EEEESSHHHHHHHHHHHHHH-SSEEEEEE-GGGH.HH....HHHHHHHHHHTT-EEEEEESS----GGGSSSSEEEEEE-S---S..EE..EEET CS
  Regulator_TrmB   2 vwvvksretvierieelIesAenelivslpselL.ee....lreeliaaaergvtVllliypdedleeldleevatevrvrrsga.pll..vivD 88 
                     + +v +r+++ ++i +lI++++ el + l ++ L ++    +re +++a+ r+v + l+  +  +le ++ + +   +++ +  + p+   ++ +
      EPA06259.1 135 LTIVSNRNNIYDQIIKLIDETNDELHIVLAPSDLiRMyytpVREAIKNATLRKVIIKLMTDD--ELESKREYIQRLGIKYFKITTlPTSgrLVCN 227
                     67999********************9888777662432222578888887777777776666..5555555555566666666665555559*** PP

                     TTEEEEE-SSS-..EEEE--HHHHHHHHHHHHHH........HHH-EEEEE.EES-TT CS
  Regulator_TrmB  89 rkrgvvaprevl..rdkeeeyaiifkekelihvlshyFlttlWktsevikt.depvek 143
                     +++++++ ++++  ++++ e ++++++++ i   +++  + lW+t++ i+   ++++k
      EPA06259.1 228 KSQVLMSGNTSSysNKNKSEESVMVTNSKDIVRNMQSLCKFLWETGKGIHIeNKQNKK 285
                     *******9999899999999999999999999999*************9965444444 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.62
                     SSSSEEEEEE-S---S..EEEEETTTEE CS
  Regulator_TrmB  66 dleevatevrvrrsga.pllvivDrkrg 92 
                     d     +e+r+++ ++  ++v++D + +
      EPA06259.1 350 DGFYLLDEIRKIDPKTkVIMVTADMSAA 377
                     5555678899999999889999998765 PP

>> Adenine_glyco  Methyladenine glycosylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1    0.0028        10      64     103 ..      84     122 ..      68     159 .. 0.83
   2 ?    5.1   0.1    0.0047        17      93     133 ..     254     291 ..     228     319 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0028
  Adenine_glyco  64 akydeekveelladegiirnrlKieavisnAravlalqee 103
                    +k++ ++ e++l++  ii++++Kie   +n+  +l++ ++
     EPA06259.1  84 IKFSANDPETILKN-IIIKQKQKIENLEKNSSKFLNILSK 122
                    56777888888776.8******************999765 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0047
  Adenine_glyco  93 nAravlalqeefgsfseylwsfvdgkpiveelksaeevpat 133
                    n++   ++ ++++s++++lw+  +g +i+++ +++e+ +++
     EPA06259.1 254 NSK---DIVRNMQSLCKFLWETGKGIHIENKQNKKEHSQKQ 291
                    444...46668899********9988888776654443333 PP

>> DisA-linker  DisA bacterial checkpoint controller linker region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.2    0.0054        19      80     136 ..       9      65 ..       2      70 .. 0.87
   2 ?    6.9   0.8    0.0014         5       5      38 ..      96     129 ..      93     159 .. 0.78
   3 ?   -2.3   0.0      0.95   3.4e+03     118     135 ..     193     210 ..     166     238 .. 0.62

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0054
                  HHHHHHTTHHHHHHHHHHHHSSS--HHHHHHHHHHH...HTTS---HHHHHHHTT-- CS
  DisA-linker  80 qleeLlanveeeeellikDYlkeekeeeaeeileelkelsseelldlskiaklLGye 136
                    +e  +n e +e  +++D+  ee e+++   l++l + +++e+ + +ki ++  y+
   EPA06259.1   9 NGDEHNQNNELDEITILRDFGLEEDEAQTYVGLARLGSSKASEISTFTKIERVRTYK 65 
                  556778899999**********999999999*******************9987776 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0014
                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
  DisA-linker   5 evilakanqalqTLekYrsvldevlsnLsalEfe 38 
                  + i+ k  q ++ Lek  s++ + ls+L+ +E e
   EPA06259.1  96 KNIIIKQKQKIENLEKNSSKFLNILSKLKLHESE 129
                  67999************************99976 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 0.95
                  .HTTS---HHHHHHHTT- CS
  DisA-linker 118 lsseelldlskiaklLGy 135
                  ++++el ++++ ++ LG 
   EPA06259.1 193 MTDDELESKREYIQRLGI 210
                  555555555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1477  (0.0823805); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2891.03
//
Query:       EPA06260.1  [L=371]
Description: hypothetical protein BG20_I2001 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       766  (0.0427241); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 2160.42
//
Query:       EPA06261.1  [L=300]
Description: pirin family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-36  124.6   0.3    2.7e-36  123.8   0.3    1.4  1  Pirin           Pirin
    4.1e-32  110.6   0.1    1.6e-30  105.5   0.0    2.5  3  Pirin_C         Pirin C-terminal cupin domain
     0.0019   17.9   2.0       0.55   10.0   0.4    3.0  3  Cupin_2         Cupin domain
  ------ inclusion threshold ------
       0.15   11.8   0.0       0.34   10.7   0.0    1.6  1  Cas9_b_hairpin  CRISPR-associated endonuclease Cas9 beta-hair


Domain annotation for each model (and alignments):
>> Pirin  Pirin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.8   0.3     6e-40   2.7e-36       4     108 .]      36     139 ..      33     139 .. 0.96

  Alignments for each domain:
  == domain 1  score: 123.8 bits;  conditional E-value: 6e-40
                 ECCGTCC.TTCCEECTCEECCEEESS.S.ETTEEEET-EEEEEEEBSEEEEEEEECSEEEEEETTS-EEEEETT-EEEEE-TT-EEEEEEE-SS....S CS
       Pirin   4 vrralgkaaelqsvdpFlfldefdpaelevgeedvigagfpphphrgletvtylleGevehrDslGnkgvirpGdvqwmtAgsGivhsEmneee....e 98 
                 v+ra+++  +l+++dpFl+lde++p e+++g+    ++g p+hphrg+etvty+++G++eh+Ds+G++g+i++GdvqwmtAgsG++hsEm+e+e    +
  EPA06261.1  36 VHRAFPN-GSLREFDPFLLLDEMGPIEISPGN----AKGAPDHPHRGFETVTYMIDGTFEHKDSQGHSGKIKSGDVQWMTAGSGVIHSEMPEKEfvqkG 129
                 6777888.8999********************....8********************************************************999999 PP

                 S-EEEEEEEE CS
       Pirin  99 esleglqlWv 108
                 ++l+g+qlWv
  EPA06261.1 130 GTLHGFQLWV 139
                 *********8 PP

>> Pirin_C  Pirin C-terminal cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.042   1.9e+02      17      54 ..      75     115 ..      64     131 .. 0.79
   2 ?   -3.1   0.0       2.2   9.9e+03      61      74 ..     166     179 ..     155     184 .. 0.68
   3 !  105.5   0.0   3.5e-34   1.6e-30       1     104 []     192     296 ..     192     296 .. 0.98

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.042
                 -TT-EEEEEEEES-EEESSTT...EEE-TTEEEEE-SSSEE CS
     Pirin_C  17 pegleaavyvleGelevgger...seieeeqlavlgdgdsl 54 
                   g+e++ y+++G+ e ++++    +i+ +++ ++++g+ +
  EPA06261.1  75 HRGFETVTYMIDGTFEHKDSQghsGKIKSGDVQWMTAGSGV 115
                 67899**********99988888889999999999866655 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.2
                 S-EEEEEEEE---- CS
     Pirin_C  61 kgarvlLlaGePlg 74 
                 +g++v ++aGe +g
  EPA06261.1 166 DGVQVKVIAGESMG 179
                 56777778888776 PP

  == domain 3  score: 105.5 bits;  conditional E-value: 3.5e-34
                 EEEEEE-TT-EEEEE--TT-EEEEEEEES-EEESSTTEEE-TTEEEEE-.SSSEEEEE--SS-EEEEEEEE----S--EEETTEEESSHHHHHHHHHHH CS
     Pirin_C   1 yldltleagaelelplpegleaavyvleGelevggerseieeeqlavlg.dgdslvvkaeekgarvlLlaGePlgepvvqyGpfVmntkeeieqafedy 98 
                 yl++t++++a++++ +p++++a++yv++Ge+ +g+++ + ++eq+++++ +g+++ +ka+ +++ vlL+aG Plgepv  yGpfVmnt++ei+qa+ dy
  EPA06261.1 192 YLHFTIQPNAQVKQIIPQNYNAFAYVVNGEGLFGNKQISAHKEQIILFEqEGNEISIKASVSPLDVLLIAGIPLGEPVTRYGPFVMNTQDEINQAILDY 290
                 89***********************************************9************************************************* PP

                 HTT-TT CS
     Pirin_C  99 regrfg 104
                 ++g++g
  EPA06261.1 291 NTGKMG 296
                 ***975 PP

>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.4   0.00012      0.55       7      52 ..      64     112 ..      60     118 .. 0.82
   2 ?   -0.6   0.0      0.26   1.1e+03      32      51 ..     163     182 ..     162     185 .. 0.86
   3 !    5.6   0.0    0.0029        13       2      32 ..     194     224 ..     193     242 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00012
                 TTE..EEEEECSSSEEEEEEEEESEEEEE.ECTEEEEEETTEEEEE-TT CS
     Cupin_2   7 pGe..sapshrHpgedeffyVleGegelt.vdgeeveleaGdsvyfpag 52 
                 pG    ap h H+g + + y ++G++e +   g+  +++ Gd+    ag
  EPA06261.1  64 PGNakGAPDHPHRGFETVTYMIDGTFEHKdSQGHSGKIKSGDVQWMTAG 112
                 444357889*******************988899999999999888776 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.26
                 EEECTEEEEEETTEEEEE-T CS
     Cupin_2  32 ltvdgeeveleaGdsvyfpa 51 
                 ++ dg +v++ aG+s+ ++a
  EPA06261.1 163 VQRDGVQVKVIAGESMGVKA 182
                 67899*********998876 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.0029
                 EEEEETTEEEEEEC.SSSEEEEEEEEESEEEE CS
     Cupin_2   2 lvelppGesapshr.HpgedeffyVleGegel 32 
                 +++++p+++ ++ +   ++ +f yV+ Geg +
  EPA06261.1 194 HFTIQPNAQVKQIIpQNYN-AFAYVVNGEGLF 224
                 6899999977766647777.*********976 PP

>> Cas9_b_hairpin  CRISPR-associated endonuclease Cas9 beta-hairpin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   7.6e-05      0.34      13      82 ..     171     248 ..     167     255 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 7.6e-05
  Cas9_b_hairpin  13 kvklgdalsvkeidrAstpaLwcALtrlpdfdekeGLPenesR.eirvngtklsa.......edevelFeskaaqlav 82 
                     kv  g+++ vk i    tp +++  t +p+ + k+ +P+n +    +vng+ l +       ++++ lFe++   + +
      EPA06261.1 171 KVIAGESMGVKAIIETRTPIMYLHFTIQPNAQVKQIIPQNYNAfAYVVNGEGLFGnkqisahKEQIILFEQEGNEISI 248
                     5556899*********************************88625677886554400000024566666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 2113.91
//
Query:       EPA06262.1  [L=276]
Description: von Willebrand factor type A domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.2e-24   85.4   0.8    1.1e-23   84.4   0.8    1.5  1  VWA            von Willebrand factor type A domain
    2.1e-16   60.5   0.1    6.9e-16   58.8   0.0    1.8  2  VWA_2          von Willebrand factor type A domain
     0.0077   16.4   0.0      0.019   15.1   0.0    1.6  1  vWA-TerF-like  vWA found in TerF C terminus
  ------ inclusion threshold ------
      0.041   13.8   0.0       0.12   12.3   0.0    1.9  2  VWA_3          von Willebrand factor type A domain
      0.099   11.8   0.2        1.4    8.1   0.1    2.1  2  DUF1194        Protein of unknown function (DUF1194)


Domain annotation for each model (and alignments):
>> VWA  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.4   0.8   3.1e-27   1.1e-23       1     174 [.      72     237 ..      72     238 .. 0.91

  Alignments for each domain:
  == domain 1  score: 84.4 bits;  conditional E-value: 3.1e-27
                 EEEEEEE-STTSCHHHHHHHHHHHHHHHHHHTBTTTTEEEEEEEESSSEEEEEETTSHCHHHHHHHHHHTGSGGGGSSC-HHHHHHHHHHHHHHHHGTS CS
         VWA   1 DivfvlDgSgsmgeenfekvkefikklveklevgpegtrvglvqfssevktefslndysskeellsalnnlkysgggttntgkalkyaleklfkssaga 99 
                 ++v+ lD Sgs ++ +f + k+++k++v+ l+  + +++ g+v fss+ +t++++++  s   +++ ln +++ gg+t+   ++++  ++ lf++++  
  EPA06262.1  72 NVVLTLDESGSLSPTEFVQEKNAAKSFVNLLS--SSRDKAGVVAFSSSSRTIIPITS--SLPNVINVLNGMNQLGGSTN-FFAGIDRSIN-LFDAANP- 163
                 79******************************..99999******************..77*********888888887.*********9.8888888. PP

                 STTSEEEEEEEESS--CSS..HTHHHHHHHHGCTEEEEEEEESSSHHHHHHHHHSSSSCHHCEEEESSHHHHHHHHH CS
         VWA 100 RenakkviilltdGksndg..dpkeaaneakeqgikvfavGvgnadekelLnkiasepgeghvftvtdfeeleelfe 174
                  ++ +kvii++tdG +n +   ++ a+ ea +++i ++a+G+g  +++++L   a++++  +vf ++df++l+++++
  EPA06262.1 164 PAGEPKVIIFFTDGFNNIDvnLLSGALSEAASKNIIIYAIGIGPSVDQNQLIHVAGSSS--RVF-NADFNSLNTIVN 237
                 6799************886668899999999******************9****99999..555.567888888876 PP

>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   0.0   1.9e-19   6.9e-16       1     106 [.      73     177 ..      73     178 .. 0.95
   2 ?   -1.8   0.1       1.3   4.8e+03      21      45 ..     229     257 ..     210     263 .. 0.56

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 1.9e-19
       VWA_2   1 lvfvlDtSgSmrngdygptrleaakdaveallksl..pgdrvglvtfsdgpevlipltkdkakilnalrnleakgggtnlaaaLqlarkalkkrr..kg 95 
                 +v+ lD SgS +++     ++ + k+a++++++ l   +d+ g+v+fs++++++ip t++   + n l+++++ gg tn+ a+++   +++++ +  +g
  EPA06262.1  73 VVLTLDESGSLSPT-----EFVQEKNAAKSFVNLLssSRDKAGVVAFSSSSRTIIPITSSLPNVINVLNGMNQLGGSTNFFAGIDRSINLFDAANppAG 166
                 6899*********8.....8*************7754699***************************************************99999*** PP

       VWA_2  96 ekrvivlitDg 106
                 e++vi+++tDg
  EPA06262.1 167 EPKVIIFFTDG 177
                 **********9 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.3
       VWA_2  21 leaakdaveallksl..pgd..rvglvtf 45 
                 +  +  +v+++l +   +++  +v+lv  
  EPA06262.1 229 FNSLNTIVNQILTDVviNTSptQVNLVET 257
                 44455555555553344333337776655 PP

>> vWA-TerF-like  vWA found in TerF C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   5.3e-06     0.019       3     145 ..      72     209 ..      70     244 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.3e-06
  vWA-TerF-like   3 rVvlVlDasgSmsklykkgvvqavverllavaaqlDddgelevwlfaskakrlpdvtladleeyvkeeeegllelkklggvneeapvleevlekvr 98 
                    +Vvl lD+sgS+s +   +  +a+   +  ++++ D  g   v++f+s+ + + ++t   l++ ++     l  +++lgg+++  + +++ ++ + 
     EPA06262.1  72 NVVLTLDESGSLSPTEFVQEKNAAKSFVNLLSSSRDKAG---VVAFSSSSRTIIPITS-SLPNVINV----LNGMNQLGGSTNFFAGIDRSINLFD 159
                    578888888888764322222233333334555555555...5678888888777764.46666643....3456889999999999988877766 PP

  vWA-TerF-like  99 k..epaelptlvlFitDGgvkkk.keiekalreaskepiFwqFvglgkse 145
                    +   pa  p  ++F+tDG ++ + +  + al ea+++ i    +g+g s 
     EPA06262.1 160 AanPPAGEPKVIIFFTDGFNNIDvNLLSGALSEAASKNIIIYAIGIGPSV 209
                    55245779**********66554388899*****************9764 PP

>> VWA_3  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.1   3.9e+03      93     115 ..      34      56 ..      17      59 .. 0.73
   2 ?   12.3   0.0   3.3e-05      0.12      76     146 ..     143     218 ..      71     222 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.1
       VWA_3  93 kpgevrsvilltDgssaqgeerv 115
                 k +++  ++l+  gs++ ++  +
  EPA06262.1  34 KIANPTDIVLFGTGSPDTTTVTI 56 
                 55778889999999988877655 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 3.3e-05
       VWA_3  76 gasnlegaLkealrqp....akpgevrsvilltDgssaqgeervsdlisrar.ekirfhalglgsslsaamlqaLA 146
                 g +n  + +++ +  +    ++ ge++ +i +tDg      + +s ++s+a+ ++i + a+g+g+s+++  l ++A
  EPA06262.1 143 GSTNFFAGIDRSINLFdaanPPAGEPKVIIFFTDGFNNIDVNLLSGALSEAAsKNIIIYAIGIGPSVDQNQLIHVA 218
                 55566666666665444445899*************8888888999999877588*************99998888 PP

>> DUF1194  Protein of unknown function (DUF1194)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.038   1.4e+02       4      24 ..      71      90 ..      68     104 .. 0.81
   2 ?    8.1   0.1   0.00038       1.4      94     158 ..     144     209 ..     122     228 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.038
     DUF1194  4 leLvLavDvSgSvdeeElrlQ 24
                l+ vL +D SgS++ +E+  Q
  EPA06262.1 71 LNVVLTLDESGSLSPTEFV-Q 90
                6789************984.4 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00038
     DUF1194  94 rtaigeAlefaaallae.npveglrrviDvSGDGpnneglepvtaardaaeakgvtingLaietke 158
                 +t   ++++ + +l+++ np +g  +vi +  DG nn  ++  + a ++a +k+++i ++ i+ + 
  EPA06262.1 144 STNFFAGIDRSINLFDAaNPPAGEPKVIIFFTDGFNNIDVNLLSGALSEAASKNIIIYAIGIGPSV 209
                 566667888889999752678899***********************************9998665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1852.35
//
Query:       EPA06263.1  [L=58]
Description: hypothetical protein BG20_I2051 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       845  (0.0471303); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.31s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 375.13
//
Query:       EPA06264.1  [L=204]
Description: hypothetical protein BG20_I2046, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    7.6e-21   74.7  25.8    5.3e-18   65.5   8.2    3.1  3  Big_9       Bacterial Ig domain
    4.9e-18   65.5  17.5    1.1e-14   54.8   6.5    3.6  4  Cadherin_4  Bacterial cadherin-like domain
    9.4e-16   57.6   5.6    9.4e-16   57.6   5.6    2.0  3  Cadherin_5  Cadherin-like domain
  ------ inclusion threshold ------
       0.12   12.5   0.0       0.82    9.9   0.0    2.0  2  Mtf2_C      Polycomb-like MTF2 factor 2


Domain annotation for each model (and alignments):
>> Big_9  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.8      0.23     1e+03       9      49 ..      24      68 ..      14      84 .. 0.55
   2 !   65.5   8.2   1.2e-21   5.3e-18      10      88 ..      90     171 ..      86     172 .. 0.93
   3 !   19.4   2.4   3.1e-07    0.0014       2      28 ..     178     204 .]     177     204 .] 0.92

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.23
       Big_9  9 tpvndaPvavddsvtvtedsv....landtdpdgdaltvtsltvt 49
                t +n a  + +++  ++++++     +  +d+ g +l v++l  +
  EPA06264.1 24 TWENVAQYVGNNDSRLSAGETfivsFTAGSDVSGLNLPVNDLANS 68
                334555555554444444444444555666666666665555443 PP

  == domain 2  score: 65.5 bits;  conditional E-value: 1.2e-21
       Big_9  10 pvndaPvavddsvtvtedsv........landtdpdgdaltvtsltvtlvtapanGtvtinadgtltytpnagfsgtdsftYtvsDg 88 
                 +vn aPva dd ++++ed++        l+ dtd dgd l+     + l+ a+  Gt+t+n+dg++ ytpn++f+g+d ftY ++Dg
  EPA06264.1  90 NVNSAPVADDDGYSTPEDTTlfvpapgvLNGDTDTDGDLLS-----AILDVATLFGTLTLNSDGSFDYTPNQDFNGDDGFTYHANDG 171
                 59*************************999*********96.....44677999********************************8 PP

  == domain 3  score: 19.4 bits;  conditional E-value: 3.1e-07
       Big_9   2 atvtvtvtpvndaPvavddsvtvteds 28 
                 a+ t+ vtpvnd+Pva +ds+ + ed+
  EPA06264.1 178 ASTTIEVTPVNDPPVADNDSFVTLEDT 204
                 789*****************9998885 PP

>> Cadherin_4  Bacterial cadherin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.5      0.17   7.5e+02      26      57 ..      18      52 ..       9      82 .. 0.60
   2 !   54.8   6.5   2.4e-18   1.1e-14       9      72 .]      90     152 ..      87     152 .. 0.95
   3 ?   -2.8   0.7       2.3     1e+04      64      72 .]     158     166 ..     157     166 .. 0.89
   4 !   23.4   3.2   1.6e-08   7.1e-05       1      27 [.     178     204 .]     178     204 .] 0.95

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.17
  Cadherin_4 26 dtpltitagnvl....andtDvdgddltvtavtvag 57
                ++++tit  nv     +nd+    +++ ++++t ag
  EPA06264.1 18 GGQTTITWENVAqyvgNNDSRLSAGETFIVSFT-AG 52
                455555555665555567777766666666666.22 PP

  == domain 2  score: 54.8 bits;  conditional E-value: 2.4e-18
  Cadherin_4   9 gvndaPvavddsatvtedtpltitagnvlandtDvdgddltvtavtvagtyGtltlnadGsftY 72 
                  vn aPva dd ++++edt+l ++a +vl+ dtD dgd l++  ++va+  Gtltln+dGsf Y
  EPA06264.1  90 NVNSAPVADDDGYSTPEDTTLFVPAPGVLNGDTDTDGDLLSAI-LDVATLFGTLTLNSDGSFDY 152
                 59************************************99998.6789**************99 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 2.3
  Cadherin_4  64 lnadGsftY 72 
                 +n+d+ ftY
  EPA06264.1 158 FNGDDGFTY 166
                 799999*99 PP

  == domain 4  score: 23.4 bits;  conditional E-value: 1.6e-08
  Cadherin_4   1 atvtitvtgvndaPvavddsatvtedt 27 
                 a+ ti vt+vnd+Pva +ds+ + edt
  EPA06264.1 178 ASTTIEVTPVNDPPVADNDSFVTLEDT 204
                 678**********************97 PP

>> Cadherin_5  Cadherin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.3   5.7e+03      34      48 ..      53      67 ..      49      83 .. 0.57
   2 !   57.6   5.6   2.1e-19   9.4e-16       1      97 [.      91     184 ..      91     185 .. 0.90
   3 ?   -2.1   0.1      0.88     4e+03       1      13 [.     187     201 ..     187     204 .] 0.66

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.3
  Cadherin_5 34 sDvdgdtLsvsslta 48
                sDv g +L v++l+ 
  EPA06264.1 53 SDVSGLNLPVNDLAN 67
                677777777777732 PP

  == domain 2  score: 57.6 bits;  conditional E-value: 2.1e-19
  Cadherin_5   1 vndaPvvssevtlaagseDtaltitaaqLLanasDvdgdtLsvssltadaenGtvvdngdGtftftpeanynGevtlsYtvsDgeggtttatasltv 97 
                 vn aPv+ ++    ++ eDt+l + a  +L++++D+dgd Ls   l++++  Gt++ n+dG+f +tp++++nG+  ++Y+ +Dg   +  a+++++v
  EPA06264.1  91 VNSAPVADDD--GYSTPEDTTLFVPAPGVLNGDTDTDGDLLSAI-LDVATLFGTLTLNSDGSFDYTPNQDFNGDDGFTYHANDGIVDSNIASTTIEV 184
                 799**99975..779*************************9964.4446679********************************9888888888887 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.88
  Cadherin_5   1 vndaPvvsse..vtl 13 
                 vnd Pv+ ++  vtl
  EPA06264.1 187 VNDPPVADNDsfVTL 201
                 799999998744444 PP

>> Mtf2_C  Polycomb-like MTF2 factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00018      0.82       7      27 ..      26      47 ..      25      50 .. 0.92
   2 ?   -0.2   0.0      0.25   1.1e+03       3      13 ..      63      73 ..      61      77 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00018
      Mtf2_C  7 ssvnkYFGaa.nRiasGEkfav 27
                ++v++Y G    R+ +GE f v
  EPA06264.1 26 ENVAQYVGNNdSRLSAGETFIV 47
                589*****9989********88 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.25
      Mtf2_C  3 edLkssvnkYF 13
                +dL +sv +Y 
  EPA06264.1 63 NDLANSVVNYL 73
                89******996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1360.16
//
Query:       EPA06265.1  [L=197]
Description: flavin reductase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-39  135.1   0.0      2e-39  134.8   0.0    1.1  1  FMN_red       NADPH-dependent FMN reductase
    8.4e-09   35.4   0.0    1.1e-08   35.0   0.0    1.2  1  Flavodoxin_2  Flavodoxin-like fold
  ------ inclusion threshold ------
       0.11   13.1   0.0       0.28   11.8   0.0    1.6  1  Pyr_redox     Pyridine nucleotide-disulphide oxidoreductase


Domain annotation for each model (and alignments):
>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.8   0.0   3.3e-43     2e-39       1     154 [.       9     163 ..       9     164 .. 0.98

  Alignments for each domain:
  == domain 1  score: 134.8 bits;  conditional E-value: 3.3e-43
                 -EEEEEES--STT-HHHHHHHHHHCCT-T.T-CEEEEETTTS.--..---HCHGHTCGGSHHHHHHHHHHHH-SCEEEEEEECTTCE-HHHHHHHHCHT CS
     FMN_red   1 mkilvisGSlrkgsntrklaewaaealkeagaevelidladlilpcalcdkdlesegqtsddvaellekiaaadaliivtPeYngsysgllKnalDrls 99 
                 +kil+++GS+r +s+++kl++ a   + eaga+v++idl+d++ p  l+d+dle++++ +  +++l+e + ++++++i++PeYn s+sg+lKn +D++s
  EPA06265.1   9 PKILAFAGSTRTDSFNKKLIKIASTGASEAGADVTIIDLRDYPMP--LYDEDLEKKEGLPSSTRKLKELMSSHHGFLISSPEYNSSISGVLKNTIDWTS 105
                 59*******************************************..**************************************************** PP

                 -.....SSCHCCTT-EEEEEEE-SSTTTTHHHHHHHHHHHHHTT-EEEECSEEEETSHH CS
     FMN_red 100 r....trgkkelrgKpvalvavgggrrgglraeeqlrqvlaelgaivvpraavavgkae 154
                 r    + +   +++K+++++++++g  gglr   + r +l ++g+iv+p+ + a++ka+
  EPA06265.1 106 RqgddESPMSCFKDKVAGIMSASPGGLGGLRGLVHVRAILENIGVIVIPT-QIAISKAH 163
                 ***99999999***************************************.***99987 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.0   1.9e-12   1.1e-08       2     174 ..      10     157 ..       9     189 .. 0.76

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 1.9e-12
                   EEEEEE--TTGGCCHHHCHHHHHHHHHCCCTTTEEEEEEHHCCT-----CCCCHCCHHHHTT.CHHHHHHHHHHHHCSSEEEEEEE-BTTB--HHHH CS
  Flavodoxin_2   2 kiLiinahprpeksfssalaqafvealekagphevtvrdLyadflpvlttrdlaaklayeek.padveseqiekllaadaivlqfPlwwfgvPailK 97 
                   kiL   ++ r+ +sf+++l + + +++ +ag ++vt++dL + ++p  +++      + +e+ p  +++ + e + +++  ++++P ++ +++ +lK
    EPA06265.1  10 KILAFAGSTRT-DSFNKKLIKIASTGASEAG-ADVTIIDLRDYPMPLYDEDL-----EKKEGlPSSTRKLK-ELMSSHHGFLISSPEYNSSISGVLK 98 
                   8999999****.6******************.99***************843.....34555678889999.************************* PP

                   HHHHHHS-TTTSCEETTCSSCCCCTTTTSEEEEEEEESS-GGGSSTTSSS-S-HHHHHHHHHHHHHHTT-EEEEEEE CS
  Flavodoxin_2  98 gwiDrvltagfafyteeggegrgggLkgkkalvivttGgpeesyqerglegaamdellpplrgilgfiGikdvepvl 174
                   + iD   ++g     +e+  +    +k+k a +++++ g             +++ l+ ++r+il+ iG+ ++++ +
    EPA06265.1  99 NTIDWTSRQGD----DES--P-MSCFKDKVAGIMSASPGG-----LG-----GLRGLV-HVRAILENIGVIVIPTQI 157
                   ******99998....223..3.678888877777777444.....11.....233344.577777777777776655 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   4.7e-05      0.28      19      44 ..      36      61 ..      30      63 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.7e-05
                HHTTSEEEEEESSSSSSTTSSHHHHH CS
   Pyr_redox 19 aelgkkVtvversdkllrllDeeask 44
                +e g++Vt+++ +d +++l+De+++k
  EPA06265.1 36 SEAGADVTIIDLRDYPMPLYDEDLEK 61
                6789*******************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1369.80
//
Query:       EPA06266.1  [L=119]
Description: transcriptional regulator, HxlR family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-24   86.1   1.4    1.3e-24   85.9   1.4    1.1  1  HxlR      HxlR-like helix-turn-helix
     0.0046   17.1   0.1     0.0065   16.6   0.1    1.2  1  HTH_34    Winged helix DNA-binding domain


Domain annotation for each model (and alignments):
>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.9   1.4   1.4e-28   1.3e-24       1      89 [.      29     118 ..      29     119 .] 0.97

  Alignments for each domain:
  == domain 1  score: 85.9 bits;  conditional E-value: 1.4e-28
                 HHHSTTHHHHHHHHTT.S-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHHHHHHHHHHHHHHC CS
        HxlR   1 liggkWkllilvellk.gkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslepvlqelkkwgeeylee 89 
                 ++g+ W llil +l +  + Rf+e+k+a+p+is+ +L++rLr  e +gli +++y evP +veYs+t++ ++l ++l++l +w+ ++ ++
  EPA06266.1  29 VLGKTWALLILKKLSEnESTRFNEIKKAIPMISNTVLSERLRDFEVHGLITKKIYAEVPLRVEYSITKQTHELGKILKQLDNWVVQWRKK 118
                 699***********997899******************************************************************9876 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   7.3e-07    0.0065       3      64 ..      36      97 ..      35     111 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 7.3e-07
      HTH_34  3 lavlsyLasvdeadfvelkeal.eatdgnLsvhlkkLekagYievdkefkgkkprtllriTpe 64
                l +l  L+++++  f+e+k+a+  +++  Ls  l+ +e  g i+ ++  +    r  ++iT++
  EPA06266.1 36 LLILKKLSENESTRFNEIKKAIpMISNTVLSERLRDFEVHGLITKKIYAEVP-LRVEYSITKQ 97
                568999***************945799***************9987776666.6778899987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 858.57
//
Query:       EPA06267.1  [L=70]
Description: hypothetical protein BG20_I2623 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1709  (0.0953204); expected 358.6 (0.02)
Passed bias filter:                      626  (0.0349155); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 509.77
//
Query:       EPA06268.1  [L=71]
Description: hypothetical protein BG20_I2622 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.50
# Mc/sec: 427.68
//
Query:       EPA06269.1  [L=66]
Description: hypothetical protein BG20_I2502 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      0.006   16.6   0.1     0.0068   16.4   0.1    1.2  1  DUF5389   Family of unknown function (DUF5389)


Domain annotation for each model (and alignments):
>> DUF5389  Family of unknown function (DUF5389)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   3.8e-07    0.0068      54      97 ..      20      64 ..       5      66 .] 0.82

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.8e-07
     DUF5389 54 flwlyPlvlaiiarilyklnqrkakla.kklllisavifygvlly 97
                   + P++l+ +  +++ ++qrk++ a k  l++sa+ f +++++
  EPA06269.1 20 QTLIIPFALSATIEVVHSIKQRKENNAtKPGLIVSAIGFISLVIF 64
                44578*****************998773679********999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.31u 0.26s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 520.69
//
Query:       EPA06270.1  [L=30]
Description: hypothetical protein BG20_I2504, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (30 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       227  (0.0126611); expected 358.6 (0.02)
Passed bias filter:                      180  (0.0100396); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.28s 00:00:00.63 Elapsed: 00:00:00.44
# Mc/sec: 204.91
//
Query:       EPA06271.1  [L=139]
Description: hypothetical protein BG20_I2503 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.8e-05   22.3   0.2    0.00011   22.0   0.2    1.1  1  Inhibitor_I71  Falstatin, cysteine peptidase inhibitor


Domain annotation for each model (and alignments):
>> Inhibitor_I71  Falstatin, cysteine peptidase inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.2   6.4e-09   0.00011      31     123 ..      22     120 ..       8     132 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 6.4e-09
  Inhibitor_I71  31 ekslsvnevlcinlea......vaGnGylwallGvhkekPlinPeefPkkkvkksyfseeisvtqPkkvkknendsskdvdeekesggqnesdsnk 120
                    e+ l+  + +ci +++       a  G++w+l  v+k+  ++   ef +kk    y   eis+ + k+++++ + ++k   ++k + ++ +s+s+k
     EPA06271.1  22 ENFLNEVQAVCILVNTkvlsqdFAEPGFVWVLTHVKKNPEIMAYVEFAQKKNYGYYSWGEISMYESKPYRRKIEYNTKIGFQDKFQLKNVDSNSDK 117
                    44455555555544331111114678***********999999**********99999*********99999888888888888888888888887 PP

  Inhibitor_I71 121 fkk 123
                    +k 
     EPA06271.1 118 WKT 120
                    765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 985.52
//
Query:       EPA06272.1  [L=228]
Description: hypothetical protein BG20_I2629, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-36  125.2   0.6    1.5e-36  124.7   0.6    1.2  1  UvrA_inter       UvrA interaction domain
  ------ inclusion threshold ------
      0.085   12.1   0.1       0.12   11.7   0.1    1.2  1  Calmodulin_bind  Calmodulin binding protein-like
       0.13   11.8   0.1       0.13   11.8   0.1    2.1  2  zf-ribbon_3      zinc-ribbon domain
       0.22   11.3   4.4        6.3    6.6   0.4    2.3  2  zinc_ribbon_2    zinc-ribbon domain
       0.52    9.9   2.5        1.4    8.5   0.3    2.1  2  Sgf11            Sgf11 (transcriptional regulation protein)


Domain annotation for each model (and alignments):
>> UvrA_inter  UvrA interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.7   0.6   4.3e-40   1.5e-36       1     107 [.      92     199 ..      92     201 .. 0.97

  Alignments for each domain:
  == domain 1  score: 124.7 bits;  conditional E-value: 4.3e-40
  UvrA_inter   1 QsveqIvdqilkleegtkllilaPvvrerkgefkkllenlkkkGfvrvriDgeiydlde.dieldknkkhsievvvDrlvvkkeersrlaesvetAlkl 98 
                 Qsve+I d+ilk   g+k+lil+P+++++kg+++kl+e++kk+G++r+r+Dgei +ld   ++ldk+k h+ie+vvDr++ +k+ersrl+e+++tA+k 
  EPA06272.1  92 QSVETICDSILKDFVGQKILILSPIIQRKKGTYEKLFEQIKKDGYSRIRLDGEILSLDGeFPTLDKQKWHNIEIVVDRIQTEKSERSRLFEAIQTAIKA 190
                 9********************************************************964899************************************ PP

  UvrA_inter  99 geglvivse 107
                 ++g v++s+
  EPA06272.1 191 SKGDVMISS 199
                 ******987 PP

>> Calmodulin_bind  Calmodulin binding protein-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   3.3e-05      0.12      42      99 ..     133     194 ..     116     209 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.3e-05
  Calmodulin_bind  42 sgplsslkv..eivvLdgdFnsedeenwteeeFnknivkeregkrplLtgdltvtLk..nGv 99 
                      +   s +++  ei++Ldg+F++ d+++w + e     ++  + +r+ L + ++  +k  +G 
       EPA06272.1 133 KDGYSRIRLdgEILSLDGEFPTLDKQKWHNIEIVVDRIQTEKSERSRLFEAIQTAIKasKGD 194
                      555566666448******************99987777888888888887877666633454 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.7      0.85     3e+03      19      22 ..      82      85 ..      80      88 .. 0.74
   2 ?   11.8   0.1   3.5e-05      0.13      14      24 ..     207     217 ..     202     219 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.85
  zf-ribbon_3 19 CpyC 22
                 C++C
   EPA06272.1 82 CTNC 85
                 6666 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 3.5e-05
  zf-ribbon_3  14 sddnvCpyCGt 24 
                  s+ n+CpyCG 
   EPA06272.1 207 SQNNACPYCGL 217
                  6899******6 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.3    0.0027       9.8       1      11 [.      81      91 ..      81      98 .. 0.84
   2 ?    6.6   0.4    0.0018       6.3      13      20 ..     209     216 ..     207     217 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0027
  zinc_ribbon_2  1 fCpnCGaelqd 11
                   +C+nC ++++ 
     EPA06272.1 81 YCTNCSRKISS 91
                   8*****99975 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0018
  zinc_ribbon_2  13 akFCpyCG 20 
                    ++ CpyCG
     EPA06272.1 209 NNACPYCG 216
                    578****9 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.3   0.00039       1.4       7      16 ..      82      91 ..      80      93 .. 0.89
   2 ?    1.0   0.1     0.089   3.2e+02       6      14 ..     211     219 ..     207     221 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00039
                -TTTSSEEEG CS
       Sgf11  7 CpnCgRqiaa 16
                C nC+R+i++
  EPA06272.1 82 CTNCSRKISS 91
                ********86 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.089
                 E-TTTSSEE CS
       Sgf11   6 tCpnCgRqi 14 
                  Cp+Cg +i
  EPA06272.1 211 ACPYCGLTI 219
                 6****9666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       856  (0.0477439); expected 358.6 (0.02)
Passed bias filter:                      691  (0.0385409); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1584.97
//
Query:       EPA06273.1  [L=130]
Description: hypothetical protein BG20_I2630, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-05   25.2   0.1      2e-05   24.6   0.1    1.3  1  UvrA_inter       UvrA interaction domain
  ------ inclusion threshold ------
       0.12   12.2   0.0       0.17   11.8   0.0    1.2  1  BsuBI_PstI_RE_N  BsuBI/PstI restriction endonuclease HTH doma


Domain annotation for each model (and alignments):
>> UvrA_inter  UvrA interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.1   2.2e-09     2e-05       1      38 [.      92     129 ..      92     130 .] 0.95

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 2.2e-09
  UvrA_inter   1 QsveqIvdqilkleegtkllilaPvvrerkgefkklle 38 
                 Qsve+I d+ilk   g+k+lil+P+++++k+++k+ l+
  EPA06273.1  92 QSVETICDSILKDFVGQKILILSPIIQRKKEHMKNYLN 129
                 9*****************************99999876 PP

>> BsuBI_PstI_RE_N  BsuBI/PstI restriction endonuclease HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.9e-05      0.17      35      93 ..      47     115 ..      41     127 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.9e-05
  BsuBI_PstI_RE_N  35 ikpedswaeatdeqalriteimafvkesy...........gkeyaentrEtiRrqtlhqlvqaglvvens 93 
                      i+++++ +++  +++ ++tei ++++  +           ++++++ + Eti ++ l+++v  ++++ ++
       EPA06273.1  47 IQQKTTSKNPR-STVGTTTEIYDYMRLLFarigipyctncSRKISSQSVETICDSILKDFVGQKILILSP 115
                      56666666777.889999**********9********************************999987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       845  (0.0471303); expected 358.6 (0.02)
Passed bias filter:                      596  (0.0332422); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 949.82
//
Query:       EPA06274.1  [L=83]
Description: hypothetical protein BG20_I2631, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.3e-14   53.4   0.1    2.6e-14   53.2   0.1    1.1  1  UvrA_inter   UvrA interaction domain
  ------ inclusion threshold ------
      0.019   14.3   0.1      0.032   13.7   0.1    1.4  1  zf-ribbon_3  zinc-ribbon domain


Domain annotation for each model (and alignments):
>> UvrA_inter  UvrA interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.2   0.1   2.9e-18   2.6e-14      59     107 ..       6      54 ..       1      56 [. 0.92

  Alignments for each domain:
  == domain 1  score: 53.2 bits;  conditional E-value: 2.9e-18
  UvrA_inter  59 edieldknkkhsievvvDrlvvkkeersrlaesvetAlklgeglvivse 107
                 e ++ldk+k h+ie+vvDr++ +k+ersrl+e+++tA+k ++g v++s+
  EPA06274.1   6 EFPTLDKQKWHNIEIVVDRIQTEKSERSRLFEAIQTAIKASKGDVMISS 54 
                 5789******************************************987 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   3.5e-06     0.032      14      24 ..      62      72 ..      57      74 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.5e-06
  zf-ribbon_3 14 sddnvCpyCGt 24
                 s+ n+CpyCG 
   EPA06274.1 62 SQNNACPYCGL 72
                 6899******6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       853  (0.0475766); expected 358.6 (0.02)
Passed bias filter:                      650  (0.0362541); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 559.51
//
Query:       EPA06275.1  [L=328]
Description: excinuclease ABC subunit C family protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-45  155.3   0.3    1.9e-45  154.5   0.0    1.6  2  UvrC_HhH_N  UvrC Helix-hairpin-helix N-terminal
    1.2e-08   34.4   0.4    2.3e-08   33.5   0.4    1.5  1  UVR         UvrB/uvrC motif


Domain annotation for each model (and alignments):
>> UvrC_HhH_N  UvrC Helix-hairpin-helix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1      0.58   5.2e+03     125     147 ..      21      43 ..       6      48 .. 0.58
   2 !  154.5   0.0   2.1e-49   1.9e-45       1     150 [.     183     328 .]     183     328 .] 0.94

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.58
                 SSSEEEE--TT-HHHHHHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxx RF
  UvrC_HhH_N 125 reeevlelkkssealkllqrird 147
                 + +e ++l+ +s+ ++  + ird
  EPA06275.1  21 KLKEEMTLAAESQQFERAKDIRD 43 
                 22222778888888888777777 PP

  == domain 2  score: 154.5 bits;  conditional E-value: 2.1e-49
                 HHHTT-SS---EEEEEEEEEETTTEEEEEEEEEETTEE-GGG-EEEEEE.-SS--HHHHHHHHHHHHHTTS.....---SEEEESSSHHHHHHHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  UvrC_HhH_N   1 kellglkekpkriecyDiShiqgtntvgsmvvfedgkpkkseyRkfkiksvkegdDyaamrevlrRrfkrllkefsklPdLiliDGGkgqlnaakevle 99 
                 ke+l+l+  p+ iec+DiS+  ++++vgsm  f dgkp+ks yRkfkik+v++ dD+a+++e+++Rr+ rl++e+s+lPdLiliDGGkgqlnaa + l+
  EPA06275.1 183 KEVLNLSIVPNIIECFDISNHGDEFAVGSMARFVDGKPHKSGYRKFKIKTVSGRDDFAMISEIIKRRYLRLQEENSQLPDLILIDGGKGQLNAALKSLQ 281
                 5899*********************************************************************************************** PP

                 HTT----EEEEES............SSSEEEE--TT-HHHHHHHHHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  UvrC_HhH_N 100 elglkipvvglaKdkkrktrakaeereeevlelkkssealkllqrirdeaH 150
                 ++gl+++ ++laK++++    + +++    ++++k+++ lk+lq+ rde+H
  EPA06275.1 282 SMGLSLDCISLAKENEEVFVPN-QKDP---IIIPKDKPSLKILQHARDETH 328
                 *************766644444.4444...9*******************9 PP

>> UVR  UvrB/uvrC motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.4   2.6e-12   2.3e-08       4      33 ..      19      48 ..      16      51 .. 0.93

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 2.6e-12
         UVR  4 ikeLeeemeeAaenedFEkAAklRDqinal 33
                +k+L+eem+ Aae+++FE+A  +RD + +l
  EPA06275.1 19 VKKLKEEMTLAAESQQFERAKDIRDTLIRL 48
                79*************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2076.73
//
Query:       EPA06276.1  [L=162]
Description: putative geranylgeranylglyceryl phosphate synthase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-25   89.1   0.0    3.3e-25   88.9   0.0    1.1  1  PcrB      PcrB family


Domain annotation for each model (and alignments):
>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.9   0.0   1.9e-29   3.3e-25      21     140 ..      37     156 ..      14     161 .. 0.89

  Alignments for each domain:
  == domain 1  score: 88.9 bits;  conditional E-value: 1.9e-29
                 HHHHHHHCTT-SEEEEECST...CHHHHHHHHHHHHHCTSSS-EEEEESSGGG--TTSSEEEEEEETTBSSTTTTTHHHHHHHHHHHHHHHCTEEEEEE CS
        PcrB  21 EiveiviesgtDavmigGsq...svtldntvrllkkvsriklPivlepsnvegvvryaDalFvmsllnsanadWivgahalglkkvkklieseeilaeg 116
                   ++ v + g+ a+++gGs+   ++++ ++v+ +kk   ik+Pi+l+p+nv+gvv++aDa+ + sl+ns+n+++i+ a+alg+  v k+   +e+l+ +
  EPA06276.1  37 KLAKDVEKIGASAILVGGSSatdQIEMAEVVKGIKKG--IKIPIILFPGNVTGVVPDADAILFSSLMNSENPYFITQAQALGAPSVLKFG--LEPLPTA 131
                 456777788*********9876778899999999999..***************************************************..******* PP

                 EEEBTTTSHHHHHTTB-.B-TTHHH CS
        PcrB 117 YlvvePdskvaavteak.vdlnked 140
                 Ylv+  ++ +  v+ a+ ++ + ++
  EPA06276.1 132 YLVIGDGTSAWFVGSARgIPFENQK 156
                 *****9999999****999987766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.33s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 928.92
//
Query:       EPA06277.1  [L=381]
Description: putative glutamine synthetase, type I, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   3.3e-115  384.8   0.0   3.8e-115  384.6   0.0    1.0  1  Gln-synt_C  Glutamine synthetase, catalytic domain


Domain annotation for each model (and alignments):
>> Gln-synt_C  Glutamine synthetase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  384.6   0.0  2.1e-119  3.8e-115       2     345 .]      14     378 ..      13     378 .. 0.96

  Alignments for each domain:
  == domain 1  score: 384.6 bits;  conditional E-value: 2.1e-119
                 T-HHHHHHHHHHHHHHTTC.EEEEEEEEEEEEESEECCCE...SSEEEEEEE.T........B...B.TSS-TTBHCCCCCTCCHHHHHHHHH.HHTT- CS
  Gln-synt_C   2 rdPRsvlkralarlaeeGl.tvvvgpElEFflfdkeedke...asksllevdse........ekgrpaekggyfsvapvdeaedlrreiveal.ealgi 87 
                 rdPR + ++a+++++ +G+     gpE+EFf+fdk++++     ++++++++s+        +++    ++gy++ +p d+ +++r+e v++l +++gi
  EPA06277.1  14 RDPRGISQKAEEYVKTQGFdYSAWGPEVEFFVFDKVHWDVltpYKGQSYSIESKeapwnnegSGYPMGLQEGYYPSTPSDTLTPYRNECVNILnNDFGI 112
                 79*****************77789**************98876677788888779******999999**************************668*** PP

                 -EECCEEECCCT.EEEEEE--EECHHHHHHHHHHHHHHHHHHHHTT-EEE-SSSSSTTS---BEEEEEEEEECTTEESSB-TTSGGGB-HHHHHHHHHH CS
  Gln-synt_C  88 eveashhEvatg.QvEinlkfadalkaaDnvvtfKrvvkevArkhgltatFmpKplegdnGsgmHvhlSlwdkdgknlfadeddeyalselarhfigGl 185
                   +++hhEvat+ Q+Ei++k++ + +aaD ++ +K+v+k+vA+k+g+ at mpKp++ d+GsgmHv++Slw k ++n+f+d+dd+ +ls++a++f gG+
  EPA06277.1 113 LCDNHHHEVATAgQCEIDIKYDYLTNAADAAQSYKYVIKNVAQKYGKVATMMPKPVAMDAGSGMHVNVSLW-KGKENVFYDPDDKDELSQTAKYFCGGI 210
                 ***********99**********************************************************.999************************ PP

                 HHHHHHHHHHHS-SCCHHHHCSSSTTSSSBEEEESS-TTCSEEEE-.....TSGGCSTEEEECEBTTS-HHHHHHHHHHHHHHHHHTT--------S-S CS
  Gln-synt_C 186 lkhakaltaltaptvnSYkRlvpgyeaPvalawgarNRsallRipa.....skekakrvElRlpdasaNPYLalAallaAgldGienklepgepvekdl 279
                 ++hakal+a+++pt+nSY+RlvpgyeaP+++aw+a NRsa++R+p+     s ++ kr+E+R+pd+s+NPYL++Aa+ aAg+dG+++k++pge+v++d+
  EPA06277.1 211 INHAKALSAICNPTTNSYHRLVPGYEAPAYIAWSAGNRSAIVRVPHhltgkSYANLKRLEFRAPDPSSNPYLVFAAVTAAGMDGVKKKIDPGEQVRDDI 309
                 **********************************************9988777889******************************************* PP

                 SSS-TTTH..TSS-B--SSHHHHHHHHHCS.HHHCCSS-HHHHHHHHHHHHHCHHHHHCT--HHHHHHH CS
  Gln-synt_C 280 yelspeer..kgieelPasleeAlealeed.ellkevlgeevieaylalkraEleeleeevsdwelery 345
                 +++++++r  +gi  lP+sl eAl++le+d ++l+ + +++vi++ ++l r + +e++ ++++ e+  y
  EPA06277.1 310 FKMTKSDRakRGIGVLPKSLGEALDELESDrKFLNSIYTNDVIDTLIELGRRDQREISIRPHPHEFYLY 378
                 ******99999******************************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 2266.20
//
Query:       EPA06278.1  [L=92]
Description: hypothetical protein BG20_I1505 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.026   14.7  10.2      0.031   14.5  10.2    1.1  1  DUF3792   Protein of unknown function (DUF3792)


Domain annotation for each model (and alignments):
>> DUF3792  Protein of unknown function (DUF3792)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5  10.2   1.7e-06     0.031      11      86 ..      12      90 ..       5      92 .] 0.71

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.7e-06
     DUF3792 11 ialvitlilllilall....lyftslsekvlsililiililsvfigGflagkkakkkgllnGllvGllyflillllslli 86
                + ++ +++++++l+ +    ++ ts+++ vl ++il++ +++++   + a+ + k++ l+ G+ +Gl+ + +++++++++
  EPA06278.1 12 FKYIYLIVFFVLLSGFfhplITHTSIDSVVLGTMILFVGLAGAV-LLYKAAVSEKRRELFLGGGFGLITISLFYIFQIIG 90
                44555555555555552333777777777777777777666664.447889999*********************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       793  (0.04423); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 660.84
//
Query:       EPA06279.1  [L=440]
Description: glycine hydroxymethyltransferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-77  260.1   0.0    3.6e-77  259.6   0.0    1.2  1  SHMT             Serine hydroxymethyltransferase
    1.6e-07   30.9   0.0      1e-06   28.2   0.0    2.2  1  Aminotran_1_2    Aminotransferase class I and II
    2.9e-05   23.5   0.0      9e-05   21.9   0.0    1.8  1  Beta_elim_lyase  Beta-eliminating lyase
     0.0017   17.4   0.0     0.0033   16.4   0.0    1.3  1  Aminotran_5      Aminotransferase class-V
      0.006   15.6   0.0     0.0097   14.9   0.0    1.3  1  SelA             L-seryl-tRNA selenium transferase


Domain annotation for each model (and alignments):
>> SHMT  Serine hydroxymethyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  259.6   0.0     1e-80   3.6e-77       5     399 .]      10     396 ..       6     396 .. 0.92

  Alignments for each domain:
  == domain 1  score: 259.6 bits;  conditional E-value: 1e-80
                 THHHHHHHHHHHHHHHHSEE-STT-----HHHHHHHTSGGGG----EETTEESSST-HHHHHHHHHHHHHHHHHCT-STTTEEEE---SSHHHHHHHHH CS
        SHMT   5 dpevaeiikkekerqkeeieliasenftskavlealGsvltnkyaeGyPGkryyGGcefvdeveelaqdrakelfkldpakwgvnvqplsGsqanlavy 103
                  +++++ +k+ ++  +++i liasen+ s+av ea+ s + n+yaeG+PG+r y Gc ++d ve  +++ ak+lfk++    +++v+p sG  anlavy
  EPA06279.1  10 YNKIFSKLKEHHKWFENSIPLIASENIPSPAVREAIISDFGNRYAEGWPGERVYAGCVYIDDVEFECMKLAKKLFKAK----FADVRPISGVVANLAVY 104
                 568999999999999***************************************************************....***************** PP

                 HHHT-TT-EEEEESCTTTSTGGGT-BTSS-B-SHHHHHSEEEEE-B-TTTSSB-HHHHHHHHHHH-.....-SEEEEE-SST-S---HHHHHHHHHHTT CS
        SHMT 104 tallepgdrilgldladGGhlthGakveskkisassklfesveykvdketglidydelekkakefk.....PklivaGtsaysrlidyarlreiadevg 197
                 +a+ +pgd +l+ ++++GGh++hG k +s   +      e+  y  d e+ +id d+ ++k +e k     Pk+ + G s +      + l +  ++ +
  EPA06279.1 105 SAFTNPGDVMLAPSIPAGGHISHGKKEHS-GTAGLVHGLEIEFYPFDAEEMTIDVDKTKQKVEELKkanhlPKMAMFGGSLFLFPHPVKELADFLKSFD 202
                 *************************9999.4455556679999*************999887665444455************999999999999999* PP

                 -EEEEE-GGGHHHHHTTSS--GCCT.SSEEEEESSSTT-S-S-EEEEEC-SEEEEETTTEEEEHHHHHHHHHHHTTTT-SS--HHHHHHHHHHHHHCTS CS
        SHMT 198 ayllvdmahiaGlvaagvipsPfey.advvtttthktlrGprgglillrkgvksvdktgkevleelekkinsavfPglqGGPlnhviaakavalkeale 295
                  ++  d ah+aGl+a+g + +P++  ad +t  thktl Gp+ggl+l                e+ e+ i++a fPgl    + h +a+kav++ eale
  EPA06279.1 203 MHINYDAAHVAGLIAGGRFQDPLREgADTMTMSTHKTLFGPQGGLVLGF--------------EKHEEAIKKATFPGLTSSHHIHHMAGKAVTFTEALE 287
                 **********************96439*******************987..............567899****************************97 PP

                 HHHHHHHHHHHHHHHHHHHHHHHTT-EEGGGS...-SSSEEEEEGGGGTS-HHHHHHHHHHTTEE-EEE--TTS.STT....TT-SEEEEESHHHHHTT CS
        SHMT 296 pefkvyqkqvlknakalaealkekgyklvsgG...tdnhlvlvdlrekgldGkraekvlekvnitankntvPgd.ksa....lvtsGlrlGtpaltsrg 386
                    k y++qv+knak++ae l++ g+k++ +    t++h + v++ +   dG ++e+ lek+ni +n+  +Pgd k a    + ++G+rlG + +t+ g
  EPA06279.1 288 FG-KDYANQVIKNAKVFAESLNDLGFKVLGESrgfTESHQIAVNVLDYS-DGGKVEADLEKANIIVNRQLIPGDiK-AgrnyFHPGGIRLGVSEITRLG 383
                 54.9************************95422259*********9875.999*********************63.334449**************** PP

                 --HHHHHHHHHHH CS
        SHMT 387 fkeedlekvakfi 399
                 +k+++++++a+++
  EPA06279.1 384 MKQNEMKEIASYM 396
                 **********996 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   2.9e-10     1e-06      70     306 ..      90     321 ..      24     324 .. 0.75

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 2.9e-10
                    GEEEESHHHHHHHHHHHHHHHTTT-EEEEEES...S-THHHH.....HHH.HTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEES CS
  Aminotran_1_2  70 avvvgsGagaliealifllklnpgdeilvpdp...tyasykn.....ilr.lsggevvryplyseedfhldlealeealkeapegnkktkvilves 156
                     v  +sG  a++++  ++++  pgd+ l+p+     + s+ +      +   +g+e+  yp  ++e++++d+++ +++++e+++ n  +k+  +  
     EPA06279.1  90 DVRPISGVVANLAVYSAFTN--PGDVMLAPSIpagGHISHGKkehsgTAGlVHGLEIEFYP-FDAEEMTIDVDKTKQKVEELKKANHLPKMAMFG- 181
                    67777777777777777774..777777665422233333221111122212455666777.448999999999999999999999955555554. PP

                    S-TTT--B.--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHHHT CS
  Aminotran_1_2 157 phNPtGtv.atleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaavvsqlrklsrpfl 251
                         G++ + +  +++l+d+ k+  +++  D a+ ++     ++      + e+ +++++++  + fG  G   G +lg ++  ++++k+  p+l
     EPA06279.1 182 -----GSLfLFPHPVKELADFLKSFDMHINYDAAHVAGLIAGGRF---QDPLREGADTMTMSTHKTLFGPQG---GLVLGFEKHEEAIKKATFPGL 266
                    .....3330445569**********************99997777...7789999999**************...*****************9999 PP

                    S.SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSS CS
  Aminotran_1_2 252 s.ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgm 306
                      s +  +++ +a+  ++   ++ ++ + +++k++k++ ++L++lg+kvl++  g+
     EPA06279.1 267 TsSHHIHHMAGKAVTFTEAL-EFGKDYANQVIKNAKVFAESLNDLGFKVLGESRGF 321
                    98999999999999999976.6****************************998876 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   2.5e-08     9e-05      54     242 ..      94     368 ..      59     414 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 2.5e-08
                      S-HHHHHHHHHHHH--TTEEEEEETT......-HHHHSSTTHHHHCC--EEE..EE-EBTTTBE-HHHHHHHS--S-T..TS-EEEEEEEESSB CS
  Beta_elim_lyase  54 pqGtaAnsillkillqrgeevivtep......ahihfdetgaiaelagvklr..dlknkeaGkmdlekleaaikevga..heekiklisltvTn 137
                       +G  An   +++++++g+ +++ +       +h+     g +  + g +    +++ +e  ++d++k +++++e ++  h +k+++       
       EPA06279.1  94 ISGVVANLAVYSAFTNPGDVMLAPSIpagghiSHGKKEHSGTAGLVHGLEIEfyPFDAEE-MTIDVDKTKQKVEELKKanHLPKMAM------- 179
                      588888888888888888877775556777777777777777777766544411444555.78888888888888766555555443....... PP

                      TTTTTB-.--HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHHHTTSSEEEEESSSTT--SS-EEEEE-HH................. CS
  Beta_elim_lyase 138 ntagGqv.vsleelrevaaiakkygiplhlDgARfanaakslgeivkemfsyvDsvtmslkKdllanvGgvlafrddel............... 215
                         gG   + +  ++e+a++ k+ ++++ +D+A +a    + g     + +++D++tms  K l+ + Gg++++ ++++               
       EPA06279.1 180 --FGGSLfLFPHPVKELADFLKSFDMHINYDAAHVAGLI-AGGRFQDPLREGADTMTMSTHKTLFGPQGGLVLGFEKHEeaikkatfpgltssh 270
                      ..56765145677999*****************999766.77777778889********************9998887789************* PP

                      .....................HHHHHHHHHHHHT---SSTHHHHH................................................. CS
  Beta_elim_lyase 216 ...................edylaerveqrkylggglrqagvlaa................................................. 241
                                         +dy ++ ++ +k  ++ l++ g+++                                                  
       EPA06279.1 271 hihhmagkavtftealefgKDYANQVIKNAKVFAESLNDLGFKVLgesrgfteshqiavnvldysdggkveadlekaniivnrqlipgdikagr 364
                      *****************************************99987777777776666666666666666666655555555555555555555 PP

                      .... CS
  Beta_elim_lyase 242 ...l 242
                          
       EPA06279.1 365 nyfH 368
                      5554 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   9.2e-07    0.0033      87     229 ..     121     266 ..     112     282 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 9.2e-07
                  TTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETT.SCBEGGGHHHH--TTEEEEEEESBETTTTEB....--HHHHHHHHHHTT-EEEEE-TTT CS
  Aminotran_5  87 pgdeivvteaehhanlvpwqelakrtgakvkvipldee.geldldelekllnektklvaithvsnvtGti....qpveeigklakkkgalvlvDaaqa 179
                  +g +i  ++ eh ++          +g++++++p+d+e  ++d+d+ +++++e  k+ ++  +    G +    +pv+e+++ +k  ++ +  Daa  
   EPA06279.1 121 AGGHISHGKKEHSGTA------GLVHGLEIEFYPFDAEeMTIDVDKTKQKVEELKKANHLPKMAMFGGSLflfpHPVKELADFLKSFDMHINYDAAHV 212
                  5566666666666555......334799999999986516799999999999999999998888888875233369********************97 PP

                  TT....TS---HHHHTESEEEEETTT.TTSSTT-EEEEEEHHHHHTS..SS.STT CS
  Aminotran_5 180 vg....hipidvkklgvDflafsghK.llgPtGiGvlyvrkellekleplllgge 229
                  +g     +  d  + g+D +++s+hK l+gP+G G++ + +++ e+++++ ++g 
   EPA06279.1 213 AGliagGRFQDPLREGADTMTMSTHKtLFGPQG-GLVLGFEKHEEAIKKATFPGL 266
                  6511116678999********************.899999999999999999886 PP

>> SelA  L-seryl-tRNA selenium transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   2.7e-06    0.0097     190     236 ..     215     261 ..     206     316 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.7e-06
                 -----BHHHHHHTT-SEEEEETTSTT-SSS-EEEEE-HHHHHHHHHS CS
        SelA 190 lskePtvqealaeGvdlvsfsGDkllGgpqaGiivGkkelieklkkn 236
                 l    ++q+ l+eG+d ++ s  k l gpq G+++G  +  e +kk 
  EPA06279.1 215 LIAGGRFQDPLREGADTMTMSTHKTLFGPQGGLVLGFEKHEEAIKKA 261
                 556667999***************************99888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.72u 0.29s 00:00:01.01 Elapsed: 00:00:00.49
# Mc/sec: 2680.55
//
Query:       EPA06280.1  [L=120]
Description: hypothetical protein BG20_I1497 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.021   14.7   0.6      0.043   13.7   0.3    1.6  2  HetR_C    Heterocyst differentiation regulator C-terminal Hoo
      0.038   14.0   0.3      0.088   12.9   0.0    1.7  2  FliH      Flagellar assembly protein FliH


Domain annotation for each model (and alignments):
>> HetR_C  Heterocyst differentiation regulator C-terminal Hood domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.49   4.4e+03      50      60 ..       8      18 ..       3      35 .. 0.62
   2 ?   13.7   0.3   4.8e-06     0.043      27      57 ..      86     116 ..      80     119 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.49
      HetR_C 50 eldeiirewad 60
                ++++iir+   
  EPA06280.1  8 NFNNIIRQIIK 18
                55666666543 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 4.8e-06
      HetR_C  27 kpkvlrvleeldippekleqaleeldeiire 57 
                  ++ +rv++e di pe+ eq ++ +d +ir+
  EPA06280.1  86 LSEQIRVINESDIFPEREEQVIDVIDRLIRQ 116
                 56789*************************8 PP

>> FliH  Flagellar assembly protein FliH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   9.8e-06     0.088      48      79 ..       5      36 ..       1      44 [. 0.90
   2 ?   -2.2   0.0      0.44   3.9e+03      76      88 ..      77      89 ..      74     103 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.8e-06
                -HHHHHHHHHHHHTTSCHHHS-EEEEE-HHHH CS
        FliH 48 dpekilalvrealaklpvdekkitlrvnpdDl 79
                d++ + + +r++++k +++e++i +++n++Dl
  EPA06280.1  5 DQSNFNNIIRQIIKKSLFTERQIEIILNQKDL 36
                7788899************************8 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.44
                HHHHHHHHHHHHH CS
        FliH 76 pdDlelvrehlge 88
                pdD++++ +  ++
  EPA06280.1 77 PDDIDVISKLSEQ 89
                7888877766553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 819.79
//
Query:       EPA06281.1  [L=342]
Description: Orc1/cdc6 family replication initiation protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-11   45.2   0.0    2.1e-11   44.2   0.0    1.5  1  AAA_22           AAA domain
    1.3e-11   45.0   1.4    5.9e-11   42.9   0.5    2.4  2  AAA              ATPase family associated with various cellul
    2.6e-08   34.5   0.0    4.7e-07   30.3   0.0    2.3  1  AAA_16           AAA ATPase domain
    5.5e-07   29.2   0.1    8.7e-07   28.5   0.1    1.3  1  TniB             Bacterial TniB protein
    7.4e-07   29.2   0.0    1.1e-06   28.6   0.0    1.3  1  NACHT            NACHT domain
    7.7e-06   26.0   3.9    1.4e-05   25.1   2.2    2.2  2  ATPase_2         ATPase domain predominantly from Archaea
    5.2e-05   22.6   0.0    7.2e-05   22.2   0.0    1.3  1  DUF2075          Uncharacterized conserved protein (DUF2075)
     0.0002   20.6   0.1     0.0005   19.3   0.0    1.6  2  PIF1             PIF1-like helicase
    0.00021   20.7   0.2       0.36   10.0   0.0    2.4  2  KAP_NTPase       KAP family P-loop domain
    0.00029   20.9   0.1    0.00092   19.2   0.1    1.8  1  AAA_5            AAA domain (dynein-related subfamily)
    0.00048   19.4   0.0     0.0012   18.1   0.0    1.7  1  DUF815           Protein of unknown function (DUF815)
    0.00056   20.3   0.1     0.0014   18.9   0.1    1.7  1  AAA_19           AAA domain
     0.0008   19.0   0.0     0.0023   17.5   0.0    1.8  1  AAA_7            P-loop containing dynein motor region
    0.00096   18.1   0.4       0.16   10.7   0.0    2.2  2  AAA_32           AAA domain
     0.0016   17.9   0.5       0.36   10.1   0.0    2.5  2  ATPase           KaiC
     0.0029   18.0   0.0     0.0077   16.6   0.0    1.7  1  RNA_helicase     RNA helicase
     0.0035   16.6   0.0     0.0068   15.6   0.0    1.5  1  NB-ARC           NB-ARC domain
     0.0055   16.6   0.3       0.13   12.1   0.1    2.4  2  NTPase_1         NTPase
  ------ inclusion threshold ------
       0.01   15.6   0.0       0.01   15.6   0.0    1.9  2  AAA_11           AAA domain
      0.017   15.3   0.0      0.043   14.0   0.0    1.8  1  TIP49_C          TIP49 AAA-lid domain
      0.017   15.2   0.2       0.35   10.8   0.0    2.3  2  ResIII           Type III restriction enzyme, res subunit
      0.019   15.3   0.1      0.052   13.9   0.1    1.7  1  AAA_assoc_2      AAA C-terminal domain
      0.029   14.1   0.1        0.1   12.3   0.0    1.8  2  AAA_24           AAA domain
      0.031   13.7   0.0      0.066   12.6   0.0    1.5  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
       0.05   13.3   0.0       0.11   12.1   0.0    1.6  1  Sigma54_activat  Sigma-54 interaction domain
      0.052   12.5   0.0       0.12   11.2   0.0    1.6  2  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
      0.067   13.2   0.0       0.15   12.1   0.0    1.5  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.077   12.0   0.0       0.18   10.8   0.0    1.5  1  T2SSE            Type II/IV secretion system protein
      0.081   12.9   5.0          8    6.5   0.1    3.2  3  Tfb5             Transcription factor TFIIH complex subunit T
      0.084   12.6   0.2       0.44   10.2   0.0    2.1  2  AAA_30           AAA domain


Domain annotation for each model (and alignments):
>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.0   3.6e-14   2.1e-11       4     130 ..      58     192 ..      55     197 .. 0.87

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 3.6e-14
      AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka...erlsseellealeqalraravielliiDE 99 
                 + + l+v+G +GtGKT++++++l++ + + +  + + ++v+ + +++t++  ll  + r+lg   k+    +l  +e+++++ +++++ +  ++++iDE
  EPA06281.1  58 RPSNLLVYGKPGTGKTLVVKKVLNKIQDRVEKSKFPIKLVYSNSKEETTLYGLLVSFGRQLGMTDKElpgTGLAISEVFKRILNNIDESKINAIFVIDE 156
                 56789********************988877777999999**********************9999999999999**************99******** PP

      AAA_22 100 aqhlr...s...eealeeLrsllnlsrkgvqliLvGt 130
                 +++l    s   +++l +L +++n + k+ +l LvG 
  EPA06281.1 157 IDYLAqlvSktgKDILYQL-TRANERLKQGSLTLVGI 192
                 ****877735678888888.55555688888888875 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       2.2   1.3e+03      49      94 ..      10      55 ..       4      61 .. 0.67
   2 !   42.9   0.5     1e-13   5.9e-11       1     120 [.      62     207 ..      62     218 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 2.2
                HHHHHHHTS....TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHH CS
         AAA 49 lfkeakeka....kpsilfiDEidalaksrsgseseeeervvnqLlteld 94
                l+++a++ +    +  il +  i +++++r    ++e+e+v + Ll+ l+
  EPA06281.1 10 LLDAAESGKsiikNRDILHFTYIPNIIQHR----NSEQEQVTQSLLPILK 55
                555555555666444888888888999999....6666777777777665 PP

  == domain 2  score: 42.9 bits;  conditional E-value: 1e-13
                 EEEESSTTSSHHHHHHHHHHHHT.....HE....EEEEETTTCSSS............................STTHHHHHHHHHHHHHHHTSTSEEE CS
         AAA   1 vllyGppGtGKTllakavakelg.....ve....fleisgsellsk............................yvgesekkirelfkeakekakpsil 62 
                 +l+yG pGtGKTl++k v ++++     ++    ++  +      k                             ++e  k+i + ++e k +    i+
  EPA06281.1  62 LLVYGKPGTGKTLVVKKVLNKIQdrvekSKfpikLVYSNS-----KeettlygllvsfgrqlgmtdkelpgtglAISEVFKRILNNIDESKIN---AIF 152
                 69*******************9523222222222222222.....133557888888888888888887775555666666666666554444...6** PP

                 EEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS...GGGSTHHHH CS
         AAA  63 fiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnr...pdkldpall 120
                 +iDEid la+      s+ +++++ qL ++ +++k+  + ++++g++n+    +kldp ++
  EPA06281.1 153 VIDEIDYLAQLV----SKTGKDILYQLTRANERLKQ--GSLTLVGISNDltfKEKLDPRVI 207
                 ********9999....8999**************99..57********9888889998877 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.0   7.9e-10   4.7e-07       5     163 ..      39     180 ..      37     190 .. 0.55

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 7.9e-10
      AAA_16   5 ReeeleqL.lsalervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekle 102
                 R  e+eq+ +s+l  ++ +rp+++l++G +G+GK+ +v+++l+ ++++   + + k+      + ys   +  +  +ll   +++     l+  +++l+
  EPA06281.1  39 RNSEQEQVtQSLLPILKHSRPSNLLVYGKPGTGKTLVVKKVLNKIQDR---VEKSKFPIK---LVYSNSKEETTLYGLLVSFGRQ-----LGMTDKELP 126
                 778899997777778888899************************999...333333333...2232222222222333333333.....333333333 PP

      AAA_16 103 ealaavpelagaeasrllellkrllallsrderplvlvlDdlq....wadeaslqllaaLlrlle 163
                 ++             ++ e++kr+l+ + + +   ++v+D+++     +  +  ++l++L r+ e
  EPA06281.1 127 GTGL-----------AISEVFKRILNNIDESKINAIFVIDEIDylaqLVSKTGKDILYQLTRANE 180
                 3222...........45555555554444433335666665553333333355555555555544 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.1   1.5e-09   8.7e-07      20     162 ..      44     192 ..      27     203 .. 0.78

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1.5e-09
        TniB  20 lerLeeLleypkrkrmpnlllvGdsnnGKtmivekFarlhppekdedaekvpvlvvqappkpdekrlyaaiLealgaplkara....rvskleqqvlrl 114
                  +  ++Ll   k++r++nll++G++ +GKt +v+k  ++ +++ ++++  +++++ +  ++ +  +l  +  ++lg+  k+       +s+  +++l+ 
  EPA06281.1  44 EQVTQSLLPILKHSRPSNLLVYGKPGTGKTLVVKKVLNKIQDRVEKSKFPIKLVYSNSKEETTLYGLLVSFGRQLGMTDKELPgtglAISEVFKRILNN 142
                 4455789999999************************99999999999999999999999999999999999999988665543334566666677777 PP

        TniB 115 lrelkvr.vLiiDEihnllagsarkqreflnalksLgnelki.pivlvGt 162
                 ++e k+  + +iDEi+ l +  +++ + +l +l + +++lk  ++ lvG+
  EPA06281.1 143 IDESKINaIFVIDEIDYLAQLVSKTGKDILYQLTRANERLKQgSLTLVGI 192
                 7777765488******9999888888888888877777775325556665 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   1.9e-09   1.1e-06       3     114 ..      62     177 ..      60     215 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 1.9e-09
                 EEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-...-HCHHHCCCCTS--SSS-C...CHHHHCCSCCCEE...........EEE CS
       NACHT   3 vilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgnarsladllfsqlpepaapvse...vwavllelperlL...........lil 87 
                 +++ G++G GKT  ++k+  +++++  ++   k+++ l  +  ++++   +l  ll+s + +++++ +e       + e+++r+L           +++
  EPA06281.1  62 LLVYGKPGTGKTLVVKKVLNKIQDRVEKS---KFPIKLVYSNSKEET---TLYGLLVSFGRQLGMTDKElpgTGLAISEVFKRILnnideskinaiFVI 154
                 689*********************99666...788888888777764...7888888888888888888777667788999999999999999999*** PP

                 E-STT-SS-TCH.........HHHHHC CS
       NACHT  88 DglDelvtdlgqkekqpvrtlLselir 114
                 D +D+l++  ++      ++ L +l r
  EPA06281.1 155 DEIDYLAQLVSK----TGKDILYQLTR 177
                 *******97777....55555555554 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   2.2   2.4e-08   1.4e-05       9     172 ..      48     200 ..      42     260 .. 0.69
   2 ?   -1.1   0.1       2.4   1.4e+03      82      83 ..     242     264 ..     194     307 .. 0.49

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 2.4e-08
    ATPase_2   9 keleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekalgiavpkaeleeilkeksklvfkaie 107
                 ++l+ il+ ++ + +++YG  g GKt ++k+++++ +d  ++  + i+l  +++++ ++          l   +g +++ +     l  +   + + ++
  EPA06281.1  48 QSLLPILKHSRPSNLLVYGKPGTGKTLVVKKVLNKIQDRVEKSKFPIKLVYSNSKEETTL-------YGLLVSFGRQLGMTDK--ELPGTGLAISEVFK 137
                 56788999999999**********************999998999888877776666655.......2333333333333222..1223445789999* PP

    ATPase_2 108 lllekikkkgkkiiiiiDelqklidlglngaellvkeLlnliesltkekhlcvviclsSeglfie 172
                 ++l++i +++   i +iDe+ +l +l ++  ++ +++L ++ e+ +k+  l++v   s +  f e
  EPA06281.1 138 RILNNIDESKINAIFVIDEIDYLAQLVSKTGKDILYQLTRANER-LKQGSLTLV-GISNDLTFKE 200
                 ****************************************9998.555555554.3355555555 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.4
    ATPase_2  82 l.....................g 83 
                 +                     +
  EPA06281.1 242 VedpalnlcaalaggehgdarrA 264
                 23333333333333333333331 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   1.2e-07   7.2e-05       3      55 ..      61     115 ..      59     200 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.2e-07
     DUF2075   3 vvlVtGvaGtGKtvvllnllael..eddeeertavylsvNhplvlvlrealakke 55 
                  +lV G++GtGKt+v  ++l+++  + ++++   ++++ N ++  +l+  l +  
  EPA06281.1  61 NLLVYGKPGTGKTLVVKKVLNKIqdRVEKSKFPIKLVYSNSKEETTLYGLLVSFG 115
                 689********************43223344456788999999999998876655 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   8.4e-07    0.0005       3      50 ..      40      87 ..      38      92 .. 0.93
   2 ?   -3.1   0.0       5.5   3.3e+03       9      27 ..     135     153 ..     133     174 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 8.4e-07
                -HHHHHHHHHH......HCTS-EEEEESTTSSCHHHHHHHHHHCHCTC CS
        PIF1  3 neeQkkvfdaiieavlnekgklfFvtGsgGtgKtflwkallkklrseg 50
                n+eQ++v ++ +  ++++++ ++ v+G  GtgKt + k++l+k++ + 
  EPA06281.1 40 NSEQEQVTQSLLPILKHSRPSNLLVYGKPGTGKTLVVKKVLNKIQDRV 87
                79******************************************9865 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.5
                 HHHHH......HCTS-EEE CS
        PIF1   9 vfdaiieavlnekgklfFv 27 
                 vf++i++ + ++k + +Fv
  EPA06281.1 135 VFKRILNNIDESKINAIFV 153
                 7777777777777777776 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0    0.0006      0.36       8      53 ..      50      92 ..      43     105 .. 0.80
   2 !    8.3   0.1     0.002       1.2     155     185 ..     130     160 ..     120     167 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0006
  KAP_NTPase  8 ladilseptlatpivvgLygkWGsGKssllnkledelkefakpvrf 53
                l  il++   ++p+ + +ygk G+GK+ +++k+ ++++++ ++ +f
  EPA06281.1 50 LLPILKH---SRPSNLLVYGKPGTGKTLVVKKVLNKIQDRVEKSKF 92
                5555664...479999*********************999555555 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.002
  KAP_NTPase 155 teveelladmektLdalqkrlVvviDdLDrc 185
                   ++e+++++ +++d+++   ++viD++D +
  EPA06281.1 130 LAISEVFKRILNNIDESKINAIFVIDEIDYL 160
                 567899***********************65 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   1.5e-06   0.00092       1      90 [.      61     173 ..      61     211 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.5e-06
                 EEEEE--SSSSHHHHHHHGGGGB.....S--EEEEE--TT--HHHHH--B--..........--------.................G-SEEEEESGGG CS
       AAA_5   1 dvlLvGppGtgKselaerlaaal.....nreveyvqltrdtteedlkgrreik.ngttslvdsplvraar.................egeilvlDEver 76 
                 ++l+ G+pGtgK+ ++++++  +     ++++ +++ +++ +ee+ ++++ ++ +++  ++d++l   +                    +i+v+DE++ 
  EPA06281.1  61 NLLVYGKPGTGKTLVVKKVLNKIqdrveKSKFPIKLVYSNSKEETTLYGLLVSfGRQLGMTDKELPGTGLaisevfkrilnnideskINAIFVIDEIDY 159
                 6899*******************999988888899999*******9***99999888889999988666688889999999999988889999999997 PP

                 --HHHHHHHHHHHH CS
       AAA_5  77 aesevlnsLlslle 90 
                 + + v ++   +l+
  EPA06281.1 160 LAQLVSKTGKDILY 173
                 76666555444444 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0     2e-06    0.0012      32      81 ..      38      87 ..      17     111 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2e-06
      DUF815 32 gidkqkealventeqfleglpannvLLwGarGtGKSslvkallneyaeeg 81
                  ++++e++++     l++ + +n+L++G+ GtGK  +vk +ln+++++ 
  EPA06281.1 38 HRNSEQEQVTQSLLPILKHSRPSNLLVYGKPGTGKTLVVKKVLNKIQDRV 87
                557889999999*********************************99875 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   2.4e-06    0.0014       8      75 ..      57     125 ..      52     198 .. 0.66

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.4e-06
      AAA_19   8 lkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae.atTiHrl 75 
                 ++ ++llv + pGtGKT v+k++++ ++++ + +  +i lv  +++    l   l ++g++  +T  +l
  EPA06281.1  57 SRPSNLLVYGKPGTGKTLVVKKVLNKIQDRVEKSKFPIKLVYSNSKEETTLYGLLVSFGRQlGMTDKEL 125
                 567899***********************9999999999998888877777666655554444555555 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   3.8e-06    0.0023      31      65 ..      57      90 ..      39     109 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.8e-06
       AAA_7 31 knkkpvllvGptGtGKtviikdllkkldkekylsl 65
                ++  ++l++G+ GtGKt+++k++l+k++ +++   
  EPA06281.1 57 SRPSNLLVYGKPGTGKTLVVKKVLNKIQ-DRVEKS 90
                4456799******************999.554444 PP

>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   0.00027      0.16      32      60 ..      61      89 ..      41     107 .. 0.79
   2 ?    5.2   0.3     0.012       7.4     479     508 ..     263     292 ..     259     298 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00027
      AAA_32 32 NifvlGesgtGrttlvkrlleeiakkept 60
                N+ v G++gtG+t +vk++l++i+++ ++
  EPA06281.1 61 NLLVYGKPGTGKTLVVKKVLNKIQDRVEK 89
                9********************99765444 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.012
      AAA_32 479 eiadllrEAdywakkegaevveaehVekAl 508
                 + +dl+r A  +a++++++ v++ehV++A 
  EPA06281.1 263 RAIDLIRVAGEIAERQQSDKVTQEHVREAS 292
                 6789***********************995 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   0.00061      0.36      20      38 ..      60      78 ..      55      90 .. 0.84
   2 ?    5.1   0.2     0.021        12     103     158 ..     131     186 ..     118     201 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00061
      ATPase 20 rvvlitGepGtGKtifalq 38
                +  l++G+pGtGKt+++++
  EPA06281.1 60 SNLLVYGKPGTGKTLVVKK 78
                6789***********9887 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.021
      ATPase 103 dleelieelaeaikeika.krvviDsitglayeekeavaReilrqlvrvlkklgvTa 158
                 +++e+ +++ + i+e k+    viD i+ l  +  +++ ++il ql+r  + l++ +
  EPA06281.1 131 AISEVFKRILNNIDESKInAIFVIDEIDYL-AQLVSKTGKDILYQLTRANERLKQGS 186
                 57788899999999999945569*******.66666666777766665544444433 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.3e-05    0.0077       2      44 ..      63     107 ..      62     111 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.3e-05
  RNA_helicase   2 wlyGpsgeGKStlakeLakallkkl...klkkkdsvysrnpeddfw 44 
                   ++yG++g+GK++++k++ +++++++   k++  + vys+++e++ +
    EPA06281.1  63 LVYGKPGTGKTLVVKKVLNKIQDRVeksKFPI-KLVYSNSKEETTL 107
                   79********************8884333443.6677776666655 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.1e-05    0.0068      18     111 ..      59     156 ..      39     165 .. 0.58

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.1e-05
                 SCSEEEEEEESTTSSHHHHHHHHCCSHC.CCCC.CBTEEEEEEEESXX.HHHHHHHXXHHHHHCCCTTSSSS-STTS..HHHHHHHHCCCT.TEEEEEE CS
      NB-ARC  18 lqslvvalvGmgGvGKttlakqilnksd.eveg.rFdsvawvvvsktd.kseeiletilkeLslseddleekeeves..lkrklvrlLltk.rfllvlD 110
                 +    + ++G++G GKt ++k++lnk +  ve+ +F++    + sk+  + + +l +  ++L+ ++++l       s   kr l ++ ++k + ++v+D
  EPA06281.1  59 PS--NLLVYGKPGTGKTLVVKKVLNKIQdRVEKsKFPIKLVYSNSKEEtTLYGLLVSFGRQLGMTDKELPGTGLAISevFKRILNNIDESKiNAIFVID 155
                 33..6889*****************97515666677755444444433033445555666666664444333322224344444444455567777777 PP

                 E CS
      NB-ARC 111 D 111
                  
  EPA06281.1 156 E 156
                 5 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.1   0.00022      0.13       2      26 ..      62      86 ..      61     101 .. 0.89
   2 ?    2.1   0.0      0.26   1.6e+02      86     107 ..     137     160 ..     128     188 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00022
                EEEE--TTSSHHHHHHHHHHHH... CS
    NTPase_1  2 vfiTGppGvGKtTlvkkvlellkss 26
                +++ G+pG+GKt +vkkvl++++++
  EPA06281.1 62 LLVYGKPGTGKTLVVKKVLNKIQDR 86
                6788*****************9865 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.26
                 HHHHHHHH..HHH-EEEE---STT CS
    NTPase_1  86 lealrkal..seadviviDEiGkm 107
                  ++l++ +  + + ++viDEi  +
  EPA06281.1 137 KRILNNIDesKINAIFVIDEIDYL 160
                 223333222123337777777444 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.0   1.7e-05      0.01      17      44 ..      59      86 ..      38     121 .. 0.70
   2 ?   -0.7   0.7       1.7   9.9e+02      97      97 ..     274     274 ..     129     317 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.7e-05
      AAA_11 17 seitliqGPPGtgKTktivellsqllsr 44
                ++  l+ G+PGtgKT ++ ++l+++  r
  EPA06281.1 59 PSNLLVYGKPGTGKTLVVKKVLNKIQDR 86
                23579*******************9422 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.7
      AAA_11  97 e 97 
                  
  EPA06281.1 274 I 274
                 2 PP

>> TIP49_C  TIP49 AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   7.2e-05     0.043       2      61 ..     229     292 ..     228     293 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.2e-05
     TIP49_C   2 lkiRakeEgv..kldeeAldlLaki..gtetSLRYaiqLltpasilakkrkkkevevedveeve 61 
                 l+ R+ke  +   +++ Al+l a +  g++   R ai L+ +a  +a+++++++v+ e+v+e++
  EPA06281.1 229 LEERIKEAFIpnSVEDPALNLCAALagGEHGDARRAIDLIRVAGEIAERQQSDKVTQEHVREAS 292
                 56666666554346666777666543356666799**************************985 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00059      0.35       6      56 ..      41      91 ..      37     100 .. 0.88
   2 ?    1.6   0.2      0.41   2.4e+02      46      74 ..     137     167 ..     128     243 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00059
                HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....- CS
      ResIII  6 eyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeek 56
                + Qe++ ++ll  lk+ r  ++l+    GtGKTlv  k+  +++   +++k
  EPA06281.1 41 SEQEQVTQSLLPILKHSRPSNLLVYGKPGTGKTLVVKKVLNKIQDRVEKSK 91
                6899*******999999999****************999998887766655 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.41
                 HHH-S.......-EEEEESSHHHHHHHHHHG CS
      ResIII  46 erllkkgkee..kflflvprkslleqtleef 74 
                 +r+l++ +e+  +++f++++++ l q+ ++ 
  EPA06281.1 137 KRILNNIDESkiNAIFVIDEIDYLAQLVSKT 167
                 4555554444569999999999999888554 PP

>> AAA_assoc_2  AAA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   8.7e-05     0.052       8      54 ..     243     291 ..     239     301 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.7e-05
                  XXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXX CS
  AAA_assoc_2   8 eddalealaelad...GDaRkaLnlLElaaeaaeakegkieitledleea 54 
                  ed al++ a+la+   GDaR+a+ l+ +a e ae+ +++ ++t+e+++ea
   EPA06281.1 243 EDPALNLCAALAGgehGDARRAIDLIRVAGEIAER-QQSDKVTQEHVREA 291
                  55566665666542228**************9986.9999******9987 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00017       0.1       4      22 ..      61      79 ..      58      94 .. 0.86
   2 ?   -1.5   0.0       2.9   1.7e+03      67      80 ..     150     163 ..     121     178 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00017
      AAA_24  4 kiliyGpsgiGKTtlakel 22
                ++l+yG++g+GKT ++k+ 
  EPA06281.1 61 NLLVYGKPGTGKTLVVKKV 79
                789************9987 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.9
      AAA_24  67 ktlviDtideleel 80 
                  + viD id l +l
  EPA06281.1 150 AIFVIDEIDYLAQL 163
                 33455555555554 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00011     0.066      24      65 ..      61     102 ..      42     109 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00011
  Mg_chelatase  24 nlllvGppGsGKtmlakrlpsllpplseeealevakiasvag 65 
                   nll++G pG+GKt++ k++ + + +  e+  + ++ ++s ++
    EPA06281.1  61 NLLVYGKPGTGKTLVVKKVLNKIQDRVEKSKFPIKLVYSNSK 102
                   89**************99887777777777777777776655 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00019      0.11       9      48 ..      44      85 ..      35     111 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00019
                     HHHHHHHHHHCTSS..S-EEEECSTTSSHHHHHHHHHHHSTT CS
  Sigma54_activat  9 kelleqikkvaktd..lsvlitGesGtGKellaraiheaskr 48
                     +++++++  + k++  +++l+ G+ GtGK+l+ +++ ++ + 
       EPA06281.1 44 EQVTQSLLPILKHSrpSNLLVYGKPGTGKTLVVKKVLNKIQD 85
                     444444544544434499***************999875443 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0    0.0002      0.12       7      44 ..      51      88 ..      45      90 .. 0.89
   2 ?   -2.9   0.0         4   2.4e+03     236     258 ..     137     163 ..     129     167 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0002
  TrwB_AAD_bind  7 vplpkeretqhilivGttGsGKtqalekllrairargd 44
                   +p+ k++  + +l+ G  G+GKt +++k l++i+ r +
     EPA06281.1 51 LPILKHSRPSNLLVYGKPGTGKTLVVKKVLNKIQDRVE 88
                   7999999999************************9965 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4
  TrwB_AAD_bind 236 s..lpesrerr..lWfflDElpaLgrl 258
                    +  l++ +e +    f++DE++ L +l
     EPA06281.1 137 KriLNNIDESKinAIFVIDEIDYLAQL 163
                    444444444441146899999999876 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00024      0.15       7      64 ..      43     103 ..      38     112 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00024
                 HHHHHHHHHHCH....TEEEEEEESTTSSHHHHHHHHHHHTT------TTTTSEEEEEE..S CS
        TsaE   7 tealgkklakal....gdvilLeGdLGaGKTtlvrglakalgveevkSPTFtlveeYeleke 64 
                  e++ ++l   l     + +l +G+ G+GKT  v++++++++ ++v+   F +   Y+++ke
  EPA06281.1  43 QEQVTQSLLPILkhsrPSNLLVYGKPGTGKTLVVKKVLNKIQ-DRVEKSKFPIKLVYSNSKE 103
                 44444455444433235569*******************984.3888888888888876655 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0    0.0003      0.18     111     156 ..      43      86 ..      34      92 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0003
       T2SSE 111 eealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinks 156
                 +e++++ +  +l+++  +  ++lv G  g+GKt ++  +l++i+++
  EPA06281.1  43 QEQVTQSLLPILKHS--RPSNLLVYGKPGTGKTLVVKKVLNKIQDR 86 
                 567788999999999..899*********************99987 PP

>> Tfb5  Transcription factor TFIIH complex subunit Tfb5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       1.7     1e+03      43      58 ..      74      89 ..      71      94 .. 0.70
   2 ?    6.5   0.2     0.014       8.3      17      45 ..     137     165 ..     134     183 .. 0.83
   3 ?    6.5   0.1     0.013         8      31      63 ..     204     236 ..     194     241 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.7
        Tfb5 43 fvkeevveelkkelee 58
                +v ++v++++++++e+
  EPA06281.1 74 LVVKKVLNKIQDRVEK 89
                5566777777777775 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.014
        Tfb5  17 kqlilkldeqepsqkfiiedLDethlfvk 45 
                 k ++ ++de++ +  f+i ++D    +v+
  EPA06281.1 137 KRILNNIDESKINAIFVIDEIDYLAQLVS 165
                 899*******99**********7766665 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.013
        Tfb5  31 kfiiedLDethlfvkeevveelkkeleellekn 63 
                 + +i  L e+ ++ ++  ve++kk lee++++ 
  EPA06281.1 204 PRVISSLGEEEVVFTNYNVEQIKKILEERIKEA 236
                 5599************************99886 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00074      0.44      19      44 ..      60      85 ..      39     162 .. 0.79
   2 ?   -0.5   0.1       1.5   8.7e+02     157     185 ..     283     311 ..     261     315 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00074
      AAA_30 19 rvavltGpAGtGKttalkalreawea 44
                   ++ G +GtGKt ++k++ + +++
  EPA06281.1 60 SNLLVYGKPGTGKTLVVKKVLNKIQD 85
                456789***********999766655 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.5
      AAA_30 157 qkeseeraaalalregdaeealealadrg 185
                  ++++ r+a+l+++e+++e+ l+++  ++
  EPA06281.1 283 VTQEHVREASLKIEENKEETSLKSYPLHE 311
                 45678999999999999999998887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       767  (0.0427799); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 0.70u 0.35s 00:00:01.04 Elapsed: 00:00:00.54
# Mc/sec: 1918.76
//
Query:       EPA06282.1  [L=201]
Description: hypothetical protein BG20_I1496 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.7e-06   27.3   0.1    6.4e-06   26.6   0.1    1.4  1  HTH_27        Winged helix DNA-binding domain
    0.00018   21.4   0.1    0.00042   20.1   0.1    1.6  1  TrmB          Sugar-specific transcriptional regulator TrmB
     0.0025   17.6   1.8      0.005   16.6   0.1    2.1  2  DUF4364       Domain of unknown function (DUF4364)
     0.0038   17.4   1.3     0.0058   16.8   0.3    1.7  2  HTH_34        Winged helix DNA-binding domain
     0.0072   16.2   3.7      0.012   15.5   1.2    2.6  2  DUF3116       Protein of unknown function (DUF3116)
      0.009   16.1   0.1      0.015   15.3   0.1    1.3  1  Replic_Relax  Replication-relaxation
  ------ inclusion threshold ------
      0.011   15.7   0.1      0.026   14.5   0.1    1.6  1  MarR          MarR family
      0.022   14.7   3.0      0.041   13.9   0.8    2.4  3  HTH_45        Winged helix-turn-helix
      0.038   14.6   1.0      0.071   13.7   1.0    1.5  1  MBG           MBG domain
      0.055   13.8   2.7       0.59   10.5   0.4    2.3  2  DUF5376       Family of unknown function (DUF5376)
      0.084   12.9   0.0       0.21   11.6   0.0    1.7  1  HTH_Crp_2     Crp-like helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.1   3.9e-09   6.4e-06       8      68 .]     132     187 ..     127     187 .. 0.95

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 3.9e-09
      HTH_27   8 vLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68 
                 vLhli   +  ++ +d+  +l+++  h+s  +kkL   G+v+r+   ++ ++ ++++T+kG
  EPA06282.1 132 VLHLIT--DKAMTSRDIQITLKRSREHTSRLMKKLFDDGYVKRN---TNSKPYTYSITEKG 187
                 89****..*********************************666...888**********9 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.1   2.6e-07   0.00042      16      65 ..     134     184 ..     127     186 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.6e-07
                 HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.TTEEEE- CS
        TrmB  16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.pklYrav 65 
                  L++ + +t ++i   l+++r    + +++L d G+V+r+  + p+ Y+ +
  EPA06282.1 134 HLITDKAMTSRDIQITLKRSREHTSRLMKKLFDDGYVKRNTNSkPYTYSIT 184
                 5789999*********************************9555***9865 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.55     9e+02      35      52 ..      82      99 ..      80     135 .. 0.80
   2 !   16.6   0.1   3.1e-06     0.005      37      75 ..     158     196 ..     155     199 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.55
     DUF4364 35 dlqqalseLvesglieee 52
                +l+q+l++L++++ + e+
  EPA06282.1 82 ELKQFLEKLTKNQQVIEK 99
                678888888888888765 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 3.1e-06
     DUF4364  37 qqalseLvesglieeeekenktlykiTekGketlelfen 75 
                 +  +++L ++g+++ +++++  +y+iTekGke ++++++
  EPA06282.1 158 SRLMKKLFDDGYVKRNTNSKPYTYSITEKGKEKIKTLQT 196
                 567899**************************9999876 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       4.1   6.6e+03      20      44 ..      72      96 ..      63      99 .. 0.58
   2 !   16.8   0.3   3.6e-06    0.0058       9      70 ..     135     192 ..     130     196 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 4.1
      HTH_34 20 lkealeatdgnLsvhlkkLekagYi 44
                l +++e  + +L   l+kL k++++
  EPA06282.1 72 LEQKIEEPNLELKQFLEKLTKNQQV 96
                5555555555555666677766665 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 3.6e-06
      HTH_34   9 LasvdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafk 70 
                 L++++ ++ ++++ +l+ +  + s  +kkL + gY++++ +    kp  +++iT++G+e+ k
  EPA06282.1 135 LITDKAMTSRDIQITLKRSREHTSRLMKKLFDDGYVKRNTN---SKPY-TYSITEKGKEKIK 192
                 7888889999**************************88754...3454.79*******9876 PP

>> DUF3116  Protein of unknown function (DUF3116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.76   1.2e+03      16      34 ..      76      94 ..      68     108 .. 0.70
   2 !   15.5   1.2   7.2e-06     0.012      53      84 ..     166     195 ..     122     196 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.76
     DUF3116 16 vkdpnftiknlqleeldek 34
                +++pn ++k++ ++ ++++
  EPA06282.1 76 IEEPNLELKQFLEKLTKNQ 94
                6667777777665554444 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 7.2e-06
     DUF3116  53 lkgyilRkeekannkkrYelTekGellykelk 84 
                   gy++R+ +  ++  +Y++TekG+++ k l+
  EPA06282.1 166 DDGYVKRNTN--SKPYTYSITEKGKEKIKTLQ 195
                 579*******..799************99986 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   9.3e-06     0.015       8      70 ..     139     192 ..     133     199 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 9.3e-06
  Replic_Relax   8 rvlTtrqiarllfashratarrrLarLrelgllsrlrkrvggarggsepyvYaLtpkGarlla 70 
                   + +T+r i+  l  s++  ++r +++L + g+++r +         s+py Y +t+kG++ ++
    EPA06282.1 139 KAMTSRDIQITLKRSREH-TSRLMKKLFDDGYVKRNTN--------SKPYTYSITEKGKEKIK 192
                   679*****9999999999.****************222........46**********99884 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   1.6e-05     0.026      16      52 ..     139     175 ..     129     177 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.6e-05
                 TTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE CS
        MarR  16 gplsvseLakklgvskstvtrvldrLekkGlieRsks 52 
                  +++  +++  l+ s+ +++r+ ++L ++G+++R  +
  EPA06282.1 139 KAMTSRDIQITLKRSREHTSRLMKKLFDDGYVKRNTN 175
                 579999****************************876 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.5   2.4e+03      36      49 ..      83      96 ..      81     107 .. 0.75
   2 ?   -0.3   0.0      0.68   1.1e+03      30      50 ..     122     142 ..     119     151 .. 0.80
   3 ?   13.9   0.8   2.5e-05     0.041      33      70 ..     154     195 ..     129     200 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.5
      HTH_45 36 lnkYLdmLvekgli 49
                l+++L++L++++ +
  EPA06282.1 83 LKQFLEKLTKNQQV 96
                67899999988765 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.68
      HTH_45  30 nLsykllnkYLdmLvekglik 50 
                 nL+ +++  Y+ +L+  +  +
  EPA06282.1 122 NLDHNNAVDYVLHLITDKAMT 142
                 999999999999999877665 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 2.5e-05
      HTH_45  33 ykllnkYLdmLvekgli....kkskekYvlTekGlelleklk 70 
                  + +++ +++L + g++    + +  +Y++TekG+e +++l+
  EPA06282.1 154 REHTSRLMKKLFDDGYVkrntNSKPYTYSITEKGKEKIKTLQ 195
                 56788999*********6653345568*********999887 PP

>> MBG  MBG domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   1.0   4.4e-05     0.071      32      78 ..     137     198 ..     106     201 .] 0.75

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.4e-05
         MBG  32 ktytltagDfewktadgn...............ttaptnvGtYtvkLtaaglaklkaanpNy 78 
                 +++ +t+ D++++ + +                ++ +tn   Yt++ t++g++k+k++++N 
  EPA06282.1 137 TDKAMTSRDIQITLKRSRehtsrlmkklfddgyVKRNTNSKPYTYSITEKGKEKIKTLQTNS 198
                 5666788888885555556667777777777779999*********************9996 PP

>> DUF5376  Family of unknown function (DUF5376)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.4   0.00036      0.59      37      93 ..      42      97 ..      35     102 .. 0.81
   2 ?    2.9   0.1     0.079   1.3e+02      27      63 ..     110     147 ..      97     151 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00036
     DUF5376 37 lsdldlelakkvldklkdkeieeedigseawdaeieedkvkigfllddeedekevli 93
                ++  +le  ++   +l+d +i+ + i++++++ +iee +++++++l++  ++++v i
  EPA06282.1 42 IDSSQLERLEYYERQLIDMKIRLDSIEMQGLEQKIEEPNLELKQFLEKLTKNQQV-I 97
                555667778888899*****************************87665555554.5 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.079
     DUF5376  27 kedesylaeylsdld.lelakkvldklkdkeieeedig 63 
                  + es+ ++ + +ld  + + +vl+ ++dk ++++di+
  EPA06282.1 110 SKVESVSTNRMPNLDhNNAVDYVLHLITDKAMTSRDIQ 147
                 4566777777888886677899*************997 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00013      0.21      31      54 ..     150     173 ..     128     182 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00013
                 TTSSHHHHHHHHHHHHHTTSEEET CS
   HTH_Crp_2  31 lGltretvsrilseLkreglisrg 54 
                 l  +re++sr++++L ++g+++r+
  EPA06282.1 150 LKRSREHTSRLMKKLFDDGYVKRN 173
                 5669*****************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1560  (0.0870099); expected 358.6 (0.02)
Passed bias filter:                      699  (0.0389871); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1456.59
//
Query:       EPA06283.1  [L=404]
Description: putative DNA polymerase II large subunit DP2 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   2.3e-138  462.5   0.2   2.9e-138  462.2   0.2    1.0  1  PolC_DP2  DNA polymerase II large subunit DP2


Domain annotation for each model (and alignments):
>> PolC_DP2  DNA polymerase II large subunit DP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  462.2   0.2  1.6e-142  2.9e-138       1     384 [.      21     400 ..      21     403 .. 0.96

  Alignments for each domain:
  == domain 1  score: 462.2 bits;  conditional E-value: 1.6e-142
    PolC_DP2   1 eYfeklekeleeayeiaekarskgldpkeevEiplAkdladRvekllgikgvaerirelekelsreevalkiakeiaegkvg.eaeskeeavdkavrta 98 
                 +Y+++l+k++ +++e a+ a+s+ +d +  +E ++A dladRv+k+++i+ +a+ +rel + +++e  al i+keia gk+  + ++ ++++d avr++
  EPA06283.1  21 DYYSNLSKDTYTIFEHAAFAKSTLVDSSGIIEPKIAFDLADRVAKMHDID-IADPLRELLRIHGKELSALIISKEIALGKYLlADATLQQKLDLAVRVG 118
                 69***********************************************9.*************************99887515567899********* PP

    PolC_DP2  99 lalltegvvaAPleGiakvkikknddgteylkvyyaGPiRsaGGtaqalsvLvaDyvrkklgldrykpr..eeeieRyveEielYer.vaslqyspsde 194
                 la++tegv++APl+Gi++v+ikkn+dg++yl+v+ aGP+RsaGGt++a+++L+aD+vrk++gl++y+++  ++e+ R+veE+++Yer  +s+q++  de
  EPA06283.1 119 LAIVTEGVTIAPLQGISEVTIKKNKDGSDYLSVSIAGPMRSAGGTESAVTILIADHVRKAVGLSKYQANcfDDETGRFVEELRIYEReASSFQFHILDE 217
                 *******************************************************************9988****************999********* PP

    PolC_DP2 195 eirlivknipveidGeatedeevsgyrdlervetnrvRGGmllvlaeGialkakKikkkvkklklegWewleelikaekeekkeeeeekkevkpkekyl 293
                 +i+ ++ n+pve+dG +t+  ev +++ + r++t+rvRGG+l+vl++G++ ++kK++k+++ ++l+gWewl +l+ a    ++++++e+    +++k +
  EPA06283.1 218 DIERVIANLPVELDGVDTDPFEVVNHKGMTRIKTDRVRGGALRVLNDGLIGRSKKLLKRIELYQLDGWEWLGDLKGA---IQTGDNQED----AAAKRM 309
                 **************************************************************************999...555555555....689*** PP

    PolC_DP2 294 rdliaGRpvlshpsrkGGfRLrYGRsrntglatagihPatmelldeflavGtqlkverPgKaaavvpvdsiegPtvklknGdvvriddvee 384
                 r++i+GR+vls+p+r GGfRLrYGRs+ntg+a++gihP   e+ld+ +avGtq+k++ PgK+a+v+ vdsi++Ptv+l+nGdvv+i++v++
  EPA06283.1 310 REVITGRSVLSMPNRLGGFRLRYGRSCNTGFAAVGIHPVIAEILDHTIAVGTQIKIDIPGKGATVAFVDSIDTPTVRLNNGDVVKIKNVKH 400
                 ***************************************************************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2481.90
//
Query:       EPA06284.1  [L=726]
Description: putative DNA polymerase II, large subunit DP2 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   7.4e-170  566.7   0.0   9.5e-170  566.4   0.0    1.1  1  PolC_DP2         DNA polymerase II large subunit DP2
  ------ inclusion threshold ------
      0.031   14.5   0.1       0.12   12.6   0.1    2.0  2  Acetyltransf_19  Acetyltransferase (GNAT) domain
       0.19   11.7  16.2        9.4    6.3   0.1    2.9  2  zinc-ribbons_6   zinc-ribbons


Domain annotation for each model (and alignments):
>> PolC_DP2  DNA polymerase II large subunit DP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  566.4   0.0  1.6e-173  9.5e-170     386     863 ..       3     477 ..       1     478 [. 0.95

  Alignments for each domain:
  == domain 1  score: 566.4 bits;  conditional E-value: 1.6e-173
    PolC_DP2 386 leikkeveeildlGeiLvayGeflennhpLvpasyveewwiqelekaaakkeaee.........kpsaeealelseeldvpLhPkytylwhdisveele 475
                 l+ik+e+e+il+lG+iL+++G+flenn++Lvp++yvee+wi+el+++ +k++ ++          p+ +eal+ls ++++pLhP+y y+w++is+e+l 
  EPA06284.1   3 LKIKNEIEKILHLGDILISFGDFLENNAQLVPTGYVEEFWIEELKEKLEKYAPNDkyliqfltkIPTLDEALKLSLDFQIPLHPQYLYFWDQISTEDLL 101
                 689******************************************999999888799******999*******************************99 PP

    PolC_DP2 476 kLaeavaekkkleeeklvleleeevkeiLekllvehkvkeekivi..eealallkslgldleeeklekeeekdalelvnelsglevrekaptrigaRmG 572
                 ++ +  + ++        +e++ evk+iLekl+v+h++++ +i++  +ea+++++ l  ++   ++   +++++ +++++ sg+++++k +t+ig+R+G
  EPA06284.1 102 QIIQPTKINE------DSIEYSIEVKNILEKLGVPHRMNNTQIILeeTEAKIFFNLLFRNKP--QI---NDSSVPQIISKSSGIQIKNKFSTSIGVRIG 189
                 9887766555......35778889*********************64455556666654333..33...456899************************ PP

    PolC_DP2 573 RPeKskeRkmkpavhvLfpigeaggkrrsvkeaakkkgeieveiarrkCkkCgketlearCeeCgekteeklvCkkceeeveeekcekcekeakavkkk 671
                 RPeK++ R+mkp++hvLfpi+++gg +r++ +a++ +++  ++i +r+Ck+C++ ++ ++C++Cg+kt+  ++C++c+ + e++ cekc+++a++++++
  EPA06284.1 190 RPEKAAARQMKPPTHVLFPINDKGGPTRDLLKASR-QDNFFTNIFNRYCKECNEPSIGIKCSNCGTKTTIIYRCNNCRDKLETQYCEKCKRKASSHSHQ 287
                 **********************************9.9999*********************************************************** PP

    PolC_DP2 672 kidlkellekaleklgereekleelkgvkgltskekipEpleKgilRakhdvsvfkdgtvRyDmtdlplthfrpkeigvsveklrelGYteDieGkple 770
                  + lk++l +a+ek g+  +++e +kgvk+l+++++i+EpleKg++R++ +++vfkdgtvR+D+t+ plt+f+p++ig+svekl++lGY +Di+Gkpl+
  EPA06284.1 288 AFPLKAKLLQAQEKTGI--RAQEPFKGVKELINQDRIAEPLEKGLIRQNFGLTVFKDGTVRFDATNSPLTQFKPSWIGTSVEKLNSLGYMQDIDGKPLT 384
                 *****************..679***************************************************************************** PP

    PolC_DP2 771 sedqivelkvqDivlsedaaeyllkvakfvDdlLeklyglerfYnvekkedLiGklviglaPHtsagvlgRiiGftkasvgyahPyfHaakRR 863
                 ++dqivel++qDi++++++a+yl++++k++D +Lek+y+   fYnv+++++LiG+l+iglaPHts+g++gRiiG+t+++v++a+P +H+akRR
  EPA06284.1 385 NPDQIVELRMQDIIIPNESARYLVSTCKYIDTILEKFYEKSTFYNVKNTDELIGHLIIGLAPHTSVGIVGRIIGYTETHVCFATPNWHSAKRR 477
                 ********************************************************************************************9 PP

>> Acetyltransf_19  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   2.1e-05      0.12       9      48 ..     403     442 ..     398     445 .. 0.92
   2 ?   -3.4   0.0       1.9   1.1e+04      37      55 ..     565     583 ..     563     586 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.1e-05
                      HHHHHHC-SS---HHHHTCHHHSEEEEEEETTEEEEEEEE CS
  Acetyltransf_19   9 rkaYlkslsaplDgmweeiilkskfykieendkliGyfcv 48 
                       ++Yl s  + +D  +e++ +ks+fy++++ d+liG  ++
       EPA06284.1 403 SARYLVSTCKYIDTILEKFYEKSTFYNVKNTDELIGHLII 442
                      578*********************************9887 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.9
                      EETTEEEEEEEE-TTSEEE CS
  Acetyltransf_19  37 eendkliGyfcvndeglLl 55 
                      e + ++ Gy+  +++ +L+
       EPA06284.1 565 ETERQFYGYYFTHSTSSLT 583
                      5677889999999998887 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7  12.5    0.0025        15       2      45 ..     236     277 ..     235     287 .. 0.76
   2 ?    6.3   0.1    0.0016       9.4      14      35 ..     641     662 ..     626     681 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0025
                     --SSS-S--EE-SSEEE-TTT--EEEEEEE-SSS-S---E..EEET CS
  zinc-ribbons_6   2 kCpeCqqelekrgeqyhCeaCqedlkkealCpeCeqelev..lkaC 45 
                     +C+eC+++       ++C++C ++ +    C++C+++le+  +++C
      EPA06284.1 236 YCKECNEPSI----GIKCSNCGTKTTIIYRCNNCRDKLETqyCEKC 277
                     6888888765....56799999999999999999999874114555 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0016
                     SSEEE-TTT--EEEEEEE-SSS CS
  zinc-ribbons_6  14 geqyhCeaCqedlkkealCpeC 35 
                      ++++C aC +++++ +l ++C
      EPA06284.1 641 RQNFRCTACGKSYRRMPLIQTC 662
                     4799***********9999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (726 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       883  (0.0492498); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.75u 0.35s 00:00:01.10 Elapsed: 00:00:00.52
# Mc/sec: 4166.01
//
Query:       EPA06285.1  [L=49]
Description: hypothetical protein BG20_I1499 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.4e-05   23.1   0.0    4.7e-05   22.9   0.0    1.0  1  PcrB          PcrB family
     0.0015   18.0   0.0     0.0016   17.9   0.0    1.0  1  His_biosynth  Histidine biosynthesis protein


Domain annotation for each model (and alignments):
>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   5.3e-09   4.7e-05     159     200 ..       1      44 [.       1      47 [. 0.90

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 5.3e-09
                 EE-.TTSSS-H.HHHHHHHHHHSSSEEEEESS--SHHHHHHHHC CS
        PcrB 159 lEa.sGaledv.eevialkkklekarlivGGGirsaEkAkevve 200
                 +Ea sGa+  v  e++++++k  +  livGGGir+  +A   v+
  EPA06285.1   1 MEAgSGAKSSVtPEMVKTVRKAFNGFLIVGGGIRDVKTATSLVK 44 
                 6999*******989999999999999*************98876 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.8e-07    0.0016      55      93 ..       6      44 ..       3      48 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.8e-07
                  CTTHHHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHH CS
  His_biosynth 55 kegreanldlveeiaeevfipvqvGGGIrsledveelle 93
                   +++++  ++v++++++++  + vGGGIr+++++++l++
    EPA06285.1  6 GAKSSVTPEMVKTVRKAFNGFLIVGGGIRDVKTATSLVK 44
                  5567777899***********************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.31s 00:00:00.72 Elapsed: 00:00:00.50
# Mc/sec: 296.58
//
Query:       EPA06286.1  [L=128]
Description: hypothetical protein BG20_I1494 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0027   18.0   0.0     0.0042   17.4   0.0    1.3  1  Penicillinase_R  Penicillinase repressor


Domain annotation for each model (and alignments):
>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   2.3e-07    0.0042       2      63 ..      56     119 ..      55     126 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.3e-07
                      --S-SHHHHHHHHHS-EEHHHHHHT--GG..G---HHHHHHHHHHHHHTTS-EEEEETTEEEEE CS
  Penicillinase_R   2 gelEaevmeilwekgeatvkevveeleee..kelaysTVktllrrLvkKgllsrekegrafiYs 63 
                      g+  +++ + +   g+ t++++ e+ e+e    ++ s + t l+r   Kg ++r ++gr+  Y+
       EPA06286.1  56 GSKIWHIVDKFFPMGKFTSTNILEKYEDEynEPVKLSIISTYLSRFSTKGKIDRIRTGREWTYQ 119
                      55568899999999**************9634469999***********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 913.88
//
Query:       EPA06287.1  [L=53]
Description: transcriptional regulator, AbrB family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.9e-07   30.3   0.1    3.5e-07   30.0   0.1    1.1  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
     0.0056   16.6   0.1     0.0075   16.2   0.1    1.1  1  Rubredoxin_C    Rubredoxin NAD+ reductase C-terminal domain
  ------ inclusion threshold ------
      0.078   12.8   0.0       0.13   12.1   0.0    1.6  1  eIF-1a          Translation initiation factor 1A / IF-1


Domain annotation for each model (and alignments):
>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.1   5.8e-11   3.5e-07       1      41 [.      10      50 ..      10      52 .. 0.96

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 5.8e-11
                    EEETTEEEEEE-CCCHHHCCEECTCEEEEEECTTCCCCCCC CS
  MazE_antitoxin  1 fkvGnsgavriPkevrfelgireGdevelevdgdkiilrpl 41
                    +k+++ g ++iPk +r+ ++i++G  v l+  +d++i+r++
      EPA06287.1 10 VKITSAGTISIPKQFRKYMDIQKGEYVKLILGKDRLIVRKI 50
                    69999*********************************996 PP

>> Rubredoxin_C  Rubredoxin NAD+ reductase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   1.3e-06    0.0075      10      48 ..      10      46 ..       8      47 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.3e-06
                  EEEEEES--TT---SEEEEEE-SS-..EEEEEEETTEEE CS
  Rubredoxin_C 10 idlfSvGdieeeekaeelveedkekgkYkklfikngklv 48
                  ++++S+G i+ +++++++ +++k +  Y kl++ +++l+
    EPA06287.1 10 VKITSAGTISIPKQFRKYMDIQKGE--YVKLILGKDRLI 46
                  789**********888887777777..*******99986 PP

>> eIF-1a  Translation initiation factor 1A / IF-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.2e-05      0.13      29      49 ..      18      38 ..       3      48 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.2e-05
                EEE-HHHHCT----TT-EEEE CS
      eIF-1a 29 aeipgkfRnkiwikrGdyVlV 49
                 +ip+ fR+++ i +G yV  
  EPA06287.1 18 ISIPKQFRKYMDIQKGEYVKL 38
                68*****************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 389.13
//
Query:       EPA06288.1  [L=567]
Description: thermosome, subunit [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   2.7e-184  613.4  21.4   3.1e-184  613.2  21.4    1.0  1  Cpn60_TCP1       TCP-1/cpn60 chaperonin family
    0.00014   21.8   3.0     0.0033   17.3   2.0    2.4  2  Dak2             DAK2 domain
  ------ inclusion threshold ------
      0.045   13.8   0.9        1.8    8.7   0.2    2.5  2  ADK              Adenylate kinase
      0.048   13.2   0.0       0.11   12.0   0.0    1.5  1  Ustilago_mating  Ustilago B locus mating-type protein
       0.54   11.0   3.9       0.49   11.1   1.5    2.1  2  DUF2853          Protein of unknown function (DUF2853)


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  613.2  21.4  8.5e-188  3.1e-184       1     490 [.      39     529 ..      39     530 .. 0.99

  Alignments for each domain:
  == domain 1  score: 613.2 bits;  conditional E-value: 8.5e-188
                 HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHHHHHHHCTXXHHHHHHHHHHHHH CS
  Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleeaekliaagvhpttiiegyekale 99 
                 +a+iv t+lGP+GmdKmlv++ g+v++TnDGatilke++++hPaak+lve+++++d+evGDGTt++viLag+Lle+ae+l++++vhpt i++gy+ka++
  EPA06288.1  39 IAEIVHTSLGPRGMDKMLVDSLGDVTITNDGATILKEIDVQHPAAKMLVEISKTTDNEVGDGTTSAVILAGALLENAESLLDQDVHPTIIVDGYRKAAK 137
                 79************************************************************************************************* PP

                 HHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHHHCHCCCS...EECSCCCEECCCCEECECTTSEEESEEEESS--SSTTS CS
  Cpn60_TCP1 100 kaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAvklieene...keldlgrikvvkieggsledselveGlvldkgvlspdm 195
                 ka ++L+eia+++ss+  d+++L k+a+ts+++kl++k++++l++++v+Av+++ e+e   +++d++ ikv+k+ ggs++ds +++G+vldk++++  m
  EPA06288.1 138 KAKQFLQEIAETVSSN--DKTILNKIAKTSMQTKLVRKDSDQLADIIVKAVLAVAEKEgekYNVDIDDIKVEKKAGGSIKDSVIIQGIVLDKEIVHGGM 234
                 *********8888876..9********************************88888888999************************************* PP

                 SCEEECEEEEEESS-BS--HHCCHHHCCCCSCCHHHHHHHHHHHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT CS
  Cpn60_TCP1 196 pkklenakvllldvsLeiektetkttvvlsdaeeleklekaeekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatG 294
                 p+k++nak++l+++ Lei ktet++++++s++++l++++++e+++l+++++k+i sg+nvv+cqkgidd+a+h+la++gi+a+rr+k++dl +lakatG
  EPA06288.1 235 PRKISNAKIALINKALEISKTETDAKINISNPQQLKSFLDEENRMLKNMVDKVIGSGANVVLCQKGIDDMAQHYLAQAGIIAVRRIKESDLTKLAKATG 333
                 *************************************************************************************************** PP

                 --EBSCGGGGGCGC-EEEEEEEECCETTCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHHHHHHHHCCCCT CS
  Cpn60_TCP1 295 atavssledltpeelGtakkveeekigsekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatelelakklkeyaks 393
                 a++v++l+d+ +++lG a+ vee+ki+++k+++ie++k++k++t+llrg ++ v+de+er+++d+l vvk +ie++++v+GGGa e+++a+k++++aks
  EPA06288.1 334 ARIVNNLDDIFEKDLGDAELVEERKIEEDKWVFIEGCKHPKSVTLLLRGGSQRVVDEVERSVHDSLMVVKDVIEKPEIVAGGGAPETYAATKIRSWAKS 432
                 *************************************************************************************************** PP

                 SXCCHHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTCEEECCCCTXEEEHHHHHHHHHHHHHHHHHHHCEEEEEXXX CS
  Cpn60_TCP1 394 vsgeeqlaieafakALevipktLaeNaGldpievlaklraahnkgekelgidvesgeiidlveagvvDplkvkrqalksAteaastiLrideiikak 490
                 ++g+eqla+e+fa++Le+ip tL eNaG+dpi++l+ lr+++ kgek++gidv +g+i +++++ +++pl+vk q++++A+eaa++iLrid++i ++
  EPA06288.1 433 LEGREQLAAEKFADSLESIPLTLSENAGMDPIDTLTVLRSRQMKGEKWTGIDVMKGKIANMKSSDIIEPLAVKLQIVSAAAEAACMILRIDDVIATQ 529
                 **********************************************************************************************875 PP

>> Dak2  DAK2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   2.0   9.3e-07    0.0033      18     131 ..      72     190 ..      63     197 .. 0.79
   2 ?    2.9   0.0     0.025        90      14      96 ..     383     465 ..     379     481 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 9.3e-07
                 HHHHHHC---SSHHHHHHHHHHHHHHH--..STHHHHHHHHHHHHHHHC........TT---HHHHHHHHHHHHHHHH.---TTSSSTHHHHHHHHHHH CS
        Dak2  18 vlkaleeleeaslaevlkalakallsgag..GtsGvlysqflralakalkekee...ldaedlaaalkaaleaiqavg.karpgdkTmlDvlrpaveal 110
                 +lk+++   ++ +a++l +++k+  +++g   ts v+++ +l++ a++l +++    + ++   +a+k+a + +q+++      dkT+l  +++++ + 
  EPA06288.1  72 ILKEIDV--QHPAAKMLVEISKTTDNEVGdgTTSAVILAGALLENAESLLDQDVhptIIVDGYRKAAKKAKQFLQEIAeTVSSNDKTILNKIAKTSMQT 168
                 5555554..5889999*******9999954379****************88777777777778888888888888886236789************999 PP

                 HT............T---HHHH CS
        Dak2 111 ekakd.gedlkealekaakaae 131
                 +  ++ +++l++++ ka+ a  
  EPA06288.1 169 KLVRKdSDQLADIIVKAVLAVA 190
                 9955548888888888776653 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.025
                 HHHHHHHHHHC---SSHHHHHHHHHHHHHHH--STHHHHHHHHHHHHHHHC.....TT---HHHHHHHHHHHHHHHH---TTS CS
        Dak2  14 gaeavlkaleeleeaslaevlkalakallsgagGtsGvlysqflralakalkekeeldaedlaaalkaaleaiqavgkarpgd 96 
                 g++ v++++e+   +sl  v + + k  + + gG+  +  ++ +r+ ak+l+++e+l ae++a+ l++   ++++ ++++p d
  EPA06288.1 383 GSQRVVDEVERSVHDSLMVVKDVIEKPEIVAGGGAPETYAATKIRSWAKSLEGREQLAAEKFADSLESIPLTLSENAGMDPID 465
                 556666666666555555555555555555556666666678899*********************99988888888888776 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.2   0.00049       1.8      67     127 ..     117     177 ..     102     193 .. 0.84
   2 ?    2.2   0.0     0.047   1.7e+02      77     114 ..     229     268 ..     212     282 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00049
                 HHHCHGTTTEEEEESB-SSHHHHHHHHHHHHHHTSEESEEEEEE--HHHHHHHHHTGSHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
         ADK  67 elekedkkkgfllDGfPRtveqaealeelleeekvkldlvleldvpeevlveRltgDneet 127
                 +l ++d +   ++DG+ +  ++a+++ + ++e+  + d  +  ++ +  + ++l++  +++
  EPA06288.1 117 SLLDQDVHPTIIVDGYRKAAKKAKQFLQEIAETVSSNDKTILNKIAKTSMQTKLVRKDSDQ 177
                 56667788899**************999999999999999999*******99999844444 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.047
                 EEEESB-SSHHHHHH..HHHHHHHHTSEESEEEEEE--HH CS
                 xxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx RF
         ADK  77 fllDGfPRtveqaea..leelleeekvkldlvleldvpee 114
                  +  G PR++++a+   +++ le +k+++d+ ++++ p++
  EPA06288.1 229 IVHGGMPRKISNAKIalINKALEISKTETDAKINISNPQQ 268
                 55679*******98433799999999**999999987765 PP

>> Ustilago_mating  Ustilago B locus mating-type protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0     3e-05      0.11      20      65 ..     319     364 ..     306     373 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3e-05
  Ustilago_mating  20 kllasdqsaraiatsdslvgnlddllrenlGrltpvdkeefeddwa 65 
                      ++  sd +  a at   +v+nldd+++++lG    v+ +++e+d  
       EPA06288.1 319 RIKESDLTKLAKATGARIVNNLDDIFEKDLGDAELVEERKIEEDKW 364
                      56778999999*********************99999999987743 PP

>> DUF2853  Protein of unknown function (DUF2853)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.5   0.00014      0.49      35      87 ..     147     199 ..     132     204 .. 0.85
   2 ?   -2.4   0.0       2.2   7.7e+03      47      70 ..     239     261 ..     225     288 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00014
                 CCB--TT-HHHHHHHHHHIIIIIT---SSHHHHHHHHHHHHHH-TT-S--BHH CS
     DUF2853  35 aslVsasdksElervrenflkkkLglkdsdeldaaikevlekmgksnrnkyRa 87 
                 a++Vs+ dk+ l+++ +  ++ kL  kdsd+l + i +++ ++++++ +ky +
  EPA06288.1 147 AETVSSNDKTILNKIAKTSMQTKLVRKDSDQLADIIVKAVLAVAEKEGEKYNV 199
                 89*****************************7777777777777777799866 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.2
                 HHHHHHIIIIIT---SSHHHHHHH CS
     DUF2853  47 ervrenflkkkLglkdsdeldaai 70 
                    +   + k L++++++  da+i
  EPA06288.1 239 SNAKIALINKALEISKTE-TDAKI 261
                 444444444444443333.33333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (567 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       931  (0.051927); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.67u 0.28s 00:00:00.95 Elapsed: 00:00:00.44
# Mc/sec: 3871.90
//
Query:       EPA06289.1  [L=46]
Description: hypothetical protein BG20_I2529 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-11   43.7   0.4    1.7e-11   43.7   0.4    1.0  1  LSM       LSM domain


Domain annotation for each model (and alignments):
>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.7   0.4   9.3e-16   1.7e-11      27      66 ..       3      41 ..       1      42 [. 0.95

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 9.3e-16
                EEETTSEEEEEEEEEEETTETEEEEEEEEEEEGGGEEEEE CS
         LSM 27 gfDqfmNlvLedveetlkdkkekrklglvliRGnnivlis 66
                ++D +mNl+++d+ee  ++k +++++g+v++RGnn+++i 
  EPA06289.1  3 NVDSYMNLIMTDAEELHDGK-TIANYGRVIVRGNNVLFIK 41
                79***************999.*****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 302.14
//
Query:       EPA06290.1  [L=138]
Description: S-adenosylmethionine synthetase, N-terminal domain protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-41  140.5   0.2    2.8e-41  140.2   0.2    1.1  1  S-AdoMet_synt_N  S-adenosylmethionine synthetase, N-terminal 
    5.9e-09   36.2   1.5    4.3e-07   30.2   0.2    2.2  2  S-AdoMet_synt_M  S-adenosylmethionine synthetase, central dom
     0.0025   16.7   0.4      0.093   11.5   0.2    2.0  2  AdoMet_Synthase  S-adenosylmethionine synthetase (AdoMet synt


Domain annotation for each model (and alignments):
>> S-AdoMet_synt_N  S-adenosylmethionine synthetase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.2   0.2   4.7e-45   2.8e-41       2      99 .]       5     105 ..       4     105 .. 0.96

  Alignments for each domain:
  == domain 1  score: 140.2 bits;  conditional E-value: 4.7e-45
  S-AdoMet_synt_N   2 ylftsesVseGHPDkvadqisdaildailkedpkarvacetlvttglvvvageittkakv...diekivrevikeigYekeelgfdaktcevlv 92 
                      +lftsesV+eGHPDk++dqisda ld++l++dp++rva+et+vtt++v vage+t+ka++     e++vr+vi++igY++++l+fd+++c+v+ 
       EPA06290.1   5 FLFTSESVTEGHPDKICDQISDAFLDEFLRQDPDSRVAVETMVTTDFVAVAGEVTSKANFdkrAQEELVRKVIRDIGYDNKDLMFDTESCQVIL 98 
                      89*******************************************************9986656899*************************** PP

  S-AdoMet_synt_N  93 aleeqsp 99 
                      +l++qsp
       EPA06290.1  99 KLHSQSP 105
                      ******7 PP

>> S-AdoMet_synt_M  S-adenosylmethionine synthetase, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.4   0.1    0.0034        20      46      99 ..      31      80 ..      16     102 .. 0.57
   2 !   30.2   0.2   7.1e-11   4.3e-07       1      21 [.     118     138 .]     118     138 .] 0.94

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0034
  S-AdoMet_synt_M 46 eylrpDaKsqvtveYeeelkpvrvdtvvistqh.deevsqeklredlkekvikkv 99
                     e+lr+D  s+v ve   ++  v v   v s  + d+     + +e+l +kvi+ +
       EPA06290.1 31 EFLRQDPDSRVAVETMVTTDFVAVAGEVTSKANfDK-----RAQEELVRKVIRDI 80
                     589999999999998545556666655555544233.....33333334444333 PP

  == domain 2  score: 30.2 bits;  conditional E-value: 7.1e-11
  S-AdoMet_synt_M   1 eigAgDqGimfGYAtdeteel 21 
                      e+gAgDqG+mfGYA++et+el
       EPA06290.1 118 EQGAGDQGLMFGYASNETKEL 138
                      69****************985 PP

>> AdoMet_Synthase  S-adenosylmethionine synthetase (AdoMet synthetase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.2   1.6e-05     0.093      25      71 ..      13      59 ..       8      63 .. 0.73
   2 !    5.5   0.0    0.0011       6.3      83     168 ..      50     135 ..      38     138 .] 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1.6e-05
                     -TTSHHHHHHHHHHHHHHHHHHHHHHHHSS---EEEEEEEEE--EEE CS
  AdoMet_Synthase 25 GiGHPDsiaDgiaeavsralskeylekfgailhhniDkvllvaGese 71
                       GHPD+i+D+i++a   ++ ++  ++  a+    +     vaGe++
       EPA06290.1 13 TEGHPDKICDQISDAFLDEFLRQDPDSRVAVETMVTTDFVAVAGEVT 59
                     57************998888777766666666666666666666665 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0011
                      EEEEEEEEEEEEE.EEE--HHHHHHHHHHHHHHHH-SS--TTTSEEEEEEEEEEEEHHHHHHCH-SS..-BESSSEEEEEEES--H CS
  AdoMet_Synthase  83 ieillsgratkevegekipveeialeaakeylkenlraldlekdvivdvklgkgsadLkdvferkkkevplaNDtSfgvgyaplse 168
                        + ++g +t++++ +k + ee++ + +++   +n   +   ++ +v +kl++ s d+ + ++++k++ + a D  +  gya   +
       EPA06290.1  50 DFVAVAGEVTSKANFDKRAQEELVRKVIRDIGYDNKDLMFDTESCQVILKLHSQSPDISQGVTATKEKEQGAGDQGLMFGYASNET 135
                      55789999999999999999*********977666665544457888999********887777777779***********98655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.53
# Mc/sec: 789.49
//
Query:       EPA06291.1  [L=57]
Description: hypothetical protein BG20_I2528, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-10   41.2   0.2    1.1e-10   41.2   0.2    1.0  1  Rad51          Rad51
    1.4e-08   34.4   0.7    1.5e-08   34.3   0.7    1.0  1  ATPase         KaiC
    3.8e-06   26.6   0.1    3.8e-06   26.6   0.1    1.0  1  RecA           recA bacterial DNA recombination protein
    0.00064   20.3   0.1    0.00068   20.2   0.1    1.0  1  ABC_tran       ABC transporter
     0.0016   18.0   0.0     0.0017   17.9   0.0    1.0  1  AAA_25         AAA domain
     0.0035   17.3   0.0     0.0035   17.3   0.0    1.0  1  ATPase_2       ATPase domain predominantly from Archaea
     0.0047   16.7   0.0     0.0047   16.7   0.0    1.1  1  IstB_IS21      IstB-like ATP binding protein
  ------ inclusion threshold ------
      0.035   13.5   0.0      0.041   13.2   0.0    1.0  1  DnaB_C         DnaB-like helicase C terminal domain
      0.039   14.3   0.0      0.039   14.3   0.0    1.1  1  AAA_16         AAA ATPase domain
      0.071   12.8   0.1      0.075   12.7   0.1    1.1  1  AAA_24         AAA domain
      0.075   12.2   0.1      0.078   12.1   0.1    1.0  1  NB-ARC         NB-ARC domain
      0.075   12.5   0.0      0.081   12.4   0.0    1.1  1  UvrD-helicase  UvrD/REP helicase N-terminal domain
      0.082   12.4   0.0      0.084   12.3   0.0    1.1  1  PhoH           PhoH-like protein
       0.18   11.0   0.1        0.2   10.9   0.1    1.0  1  DUF2075        Uncharacterized conserved protein (DUF2075)


Domain annotation for each model (and alignments):
>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   0.2   8.6e-14   1.1e-10      19      61 ..       2      44 ..       1      56 [. 0.93

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 8.6e-14
                E--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHT CS
       Rad51 19 lttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtv 61
                + tG +klD+ L+ Gi+ g it+i+G +++Gktql  ++cv +
  EPA06291.1  2 IYTGLQKLDDFLSDGIPNGVITDIYGASGTGKTQLLFQICVNT 44
                78**************************************974 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.7   1.2e-11   1.5e-08       2      53 ..       3      53 ..       2      54 .. 0.94

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 1.2e-11
      ATPase  2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvf 53
                 tg + lD++l++Gip+g ++ i+G +GtGKt +  q  ++ +++ g  +++
  EPA06291.1  3 YTGLQKLDDFLSDGIPNGVITDIYGASGTGKTQLLFQICVNTIKN-GGTVLY 53
                69****************************************999.877776 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.1   2.9e-09   3.8e-06      35      88 ..       3      55 ..       1      57 [] 0.89

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 2.9e-09
                --S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEE CS
        RecA 35 ssGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkkggvaafid 88
                 +G   ld  l   G+p+G i++iyG+  +Gkt l +++ +++ k+gg++ + d
  EPA06291.1  3 YTGLQKLDDFLS-DGIPNGVITDIYGASGTGKTQLLFQICVNTIKNGGTVLYQD 55
                577778888886.89**********************************99887 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.1   5.3e-07   0.00068       7      46 ..      16      55 ..      11      57 .] 0.90

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 5.3e-07
                EEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETT CS
                xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  7 klkegekvaivGenGaGKStLlkllagllkpteGeilldg 46
                 + +g ++ i G +G+GK+ Ll  ++ ++ ++ G++l+++
  EPA06291.1 16 GIPNGVITDIYGASGTGKTQLLFQICVNTIKNGGTVLYQD 55
                6789999*****************************9875 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.3e-06    0.0017      24      58 ..      11      45 ..       4      55 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.3e-06
      AAA_25 24 wlvkgllpagelallaGapgtGKttlaldlalava 58
                + + + +p g ++ ++Ga+gtGKt l+ ++++ + 
  EPA06291.1 11 DFLSDGIPNGVITDIYGASGTGKTQLLFQICVNTI 45
                5566667************************9876 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   2.7e-06    0.0035      21      54 ..      21      54 ..       4      57 .] 0.79

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.7e-06
    ATPase_2 21 eiyfiYGpegsGKtaLlkeiienledkdkyviyy 54
                 i  iYG  g GKt+Ll +i  n  + +  v+y 
  EPA06291.1 21 VITDIYGASGTGKTQLLFQICVNTIKNGGTVLYQ 54
                4667*******************98888888886 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   3.7e-06    0.0047      52      83 ..      25      56 ..       9      57 .] 0.91

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.7e-06
   IstB_IS21 52 llGpsGvGKshlaialgveavraglsvlfvrv 83
                + G sG+GK+ l   + v+++++g  vl++ +
  EPA06291.1 25 IYGASGTGKTQLLFQICVNTIKNGGTVLYQDT 56
                78***************************865 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   3.2e-05     0.041       2      46 ..       2      47 ..       2      55 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.2e-05
                BXSSTHHHHHHCT.SBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHC CS
                xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
      DnaB_C  2 lstgfkdLDklts.GlqkgdliiiAarpsmGktalalniaenaavk 46
                + tg+++LD+++s G+ +g ++ i + +++Gkt l ++i+ n+ ++
  EPA06291.1  2 IYTGLQKLDDFLSdGIPNGVITDIYGASGTGKTQLLFQICVNTIKN 47
                569******876449************************9987753 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0     3e-05     0.039      12      57 ..       9      53 ..       5      57 .] 0.64

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3e-05
      AAA_16 12 LlsalervrsgrpelvllsGesGvGKsslvrellralekdggiflr 57
                L + l++   ++  ++ ++G+sG+GK+ l+ ++     k+gg +l+
  EPA06291.1  9 LDDFLSDGIPNG-VITDIYGASGTGKTQLLFQICVNTIKNGGTVLY 53
                555555333332.67779***********96666555555566665 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   5.9e-05     0.075       7      23 ..      25      48 ..      19      56 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.9e-05
      AAA_24  7 iyGpsgiGKTtlakel.......g 23
                iyG sg+GKT l+ ++       g
  EPA06291.1 25 IYGASGTGKTQLLFQIcvntiknG 48
                9***********999865555555 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   6.1e-05     0.078       6      43 ..       7      43 ..       3      51 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.1e-05
                HHHHHHHHCTTTSCSEEEEEEESTTSSHHHHHHHHCCS CS
      NB-ARC  6 ekviekLlekdelqslvvalvGmgGvGKttlakqilnk 43
                +k+ + L+  + ++ ++  ++G  G GKt l+ qi  +
  EPA06291.1  7 QKLDDFLS-DGIPNGVITDIYGASGTGKTQLLFQICVN 43
                67777888.6666668999************9999755 PP

>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   6.3e-05     0.081      18      42 ..      25      49 ..      18      55 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.3e-05
                   EEE-TTSSHHHHHHHHHHHHHHTSS CS
  UvrD-helicase 18 veAsAGsGKTfvlaerilrlikeee 42
                   ++ + G+GKT+ l +  ++ ik+++
     EPA06291.1 25 IYGASGTGKTQLLFQICVNTIKNGG 49
                   77899*****************986 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   6.6e-05     0.084      17      47 ..      18      48 ..       5      52 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.6e-05
                HH-SEEEEE--TTSSTTHHHHHHHHHHHHTT CS
        PhoH 17 kkndivfaiGpaGtGKtylavalavealkkk 47
                 +  i+ + G +GtGKt l  ++ v+ +k++
  EPA06291.1 18 PNGVITDIYGASGTGKTQLLFQICVNTIKNG 48
                556688899****************999885 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00016       0.2       6      28 ..      25      45 ..      21      55 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00016
     DUF2075  6 VtGvaGtGKtvvllnllaeledd 28
                + G++GtGKt +l+++ ++    
  EPA06291.1 25 IYGASGTGKTQLLFQICVNT--I 45
                89*************99876..3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.42u 0.31s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 369.42
//
Query:       EPA06292.1  [L=47]
Description: hypothetical protein BG20_I2601, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 301.83
//
Query:       EPA06293.1  [L=162]
Description: hypothetical protein BG20_I2603, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-10   40.9   0.5    1.6e-10   40.7   0.5    1.1  1  Rad51     Rad51


Domain annotation for each model (and alignments):
>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   0.5   8.8e-15   1.6e-10      81     188 ..       1     103 [.       1     131 [. 0.90

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 8.8e-15
                 S---GGGGHHHHHHTT--HHHHGGGEEEEE--STTHHHHHHHHTHHHHHHS-EEEEEEETTTGGGCH-------THHHHHHHHHHHHHHHHHHHHH--E CS
       Rad51  81 gtfrperlveiaerykldkeevlenvayaRaytiehqeellqqaaallaedkfallivDsvtalyRtdfsgrgelakRqqklgkllrtLrkladefeva 179
                 g+frper++ei ++ +l   ++le++++ R+ ++ +q + +      ++ ++f+l+++D +t l+  ++s  ++  +++  + +++++L+ +a + ++ 
  EPA06293.1   1 GSFRPERILEIQKKQNLT-FDILEKITISRITNTSDQIKSI----DIMNCSNFSLIVIDNITDLFSYEYSKADKTFEKNSLFIRYIHNLSLVAINKKIP 94 
                 78**********999996.58*************9998766....57999************************************************* PP

                 EEEEEE--- CS
       Rad51 180 vvitnqvva 188
                 ++itn + +
  EPA06293.1  95 IIITNMIRN 103
                 *****8754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       877  (0.0489152); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1201.83
//
Query:       EPA06294.1  [L=39]
Description: hypothetical protein BG20_I2602 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 302.02
//
Query:       EPA06295.1  [L=162]
Description: hypothetical protein BG20_I2606, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.4e-12   45.3   0.3    7.6e-12   45.0   0.3    1.1  1  Rad51     Rad51
  ------ inclusion threshold ------
       0.14   12.2   0.6       0.18   11.8   0.6    1.2  1  RepA_C    Plasmid encoded RepA protein


Domain annotation for each model (and alignments):
>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.0   0.3   8.4e-16   7.6e-12      81     188 ..       1     103 [.       1     124 [. 0.91

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 8.4e-16
                 S---GGGGHHHHHHTT--HHHHGGGEEEEE--STTHHHHHHHHTHHHHHHS-EEEEEEETTTGGGCH-------THHHHHHHHHHHHHHHHHHHHH--E CS
       Rad51  81 gtfrperlveiaerykldkeevlenvayaRaytiehqeellqqaaallaedkfallivDsvtalyRtdfsgrgelakRqqklgkllrtLrkladefeva 179
                 g+frper++ei ++ +l   ++le++++ R+ ++ +q + l    +++++++f+l+++D +t l+  ++s  ++  +++  + k+l++L+ +a + ++ 
  EPA06295.1   1 GSFRPERILEIQKKQNLT-FDILEKITISRITNTSDQIKSL----STMNSSNFSLIVIDNITDLFSYEYSKEDKTFEKNLLFIKYLHNLSLIAINKKIP 94 
                 78**********999996.58*************9998766....479*************************************************** PP

                 EEEEEE--- CS
       Rad51 180 vvitnqvva 188
                 ++itn + +
  EPA06295.1  95 IIITNMIRN 103
                 *****8754 PP

>> RepA_C  Plasmid encoded RepA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.6     2e-05      0.18      59     155 ..      27     132 ..      14     140 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2e-05
      RepA_C  59 vsriaaceltvrwedaeslgdektailedki.lfederdseqgslfeselvlseaffk.hl..aehpvPid.evalr.....elkktptslDiyiyLay 147
                 +sri  +  ++++  + +  +    ++++   lf++e + +++  fe++l++ + +++  l   ++ +Pi   +++r     el++  t++D+++++ +
  EPA06295.1  27 ISRITNTSDQIKSLSTMNSSNFSLIVIDNITdLFSYEYS-KEDKTFEKNLLFIKYLHNlSLiaINKKIPIIiTNMIRnidgtELENMRTAVDLFTHIKI 124
                 567777777777665555444444455555415555555.5556677777776655432221246789975268999222223455689********** PP

      RepA_C 148 rlyrldks 155
                 +l +++ +
  EPA06295.1 125 KLRKINSK 132
                 ***99754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       896  (0.0499749); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1026.16
//
Query:       EPA06296.1  [L=47]
Description: hypothetical protein BG20_I2604, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 349.11
//
Query:       EPA06297.1  [L=39]
Description: hypothetical protein BG20_I2605 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 291.99
//
Query:       EPA06298.1  [L=53]
Description: hypothetical protein BG20_I2372 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 420.02
//
Query:       EPA06299.1  [L=142]
Description: hypothetical protein BG20_I2374, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.2e-16   58.6   0.0    6.5e-16   58.3   0.0    1.0  1  SBP_bac_5  Bacterial extracellular solute-binding proteins, f


Domain annotation for each model (and alignments):
>> SBP_bac_5  Bacterial extracellular solute-binding proteins, family 5 Middle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.3   0.0   3.6e-20   6.5e-16     150     259 ..      27     139 ..      14     141 .. 0.88

  Alignments for each domain:
  == domain 1  score: 58.3 bits;  conditional E-value: 3.6e-20
                 SSSSEEEEEE-.SHHHHHHHHHTTSSSEE.ESTTCCTHCHHHHHTTEEEEEEEEEEEEEEEEETTT....STGGGSHHHHHHHHHHS-HHHHHHHCTTT CS
   SBP_bac_5 150 pkldriefkvipdsdaraaalqsGeiddv.aepppsdieqlkeakglkvlyespgggvtylafNtk....kppfddkrvRqAlsyAiDreeivkavleg 243
                   +d+++f  + d++++++++++G++d++   ++p+ + ++k  +glkv  ++  gg++ + +N +     +pf+ k+vR Al+y iDr+ iv+++++g
  EPA06299.1  27 TFFDSVKFIQYLDENTALEEVRNGNLDIYyDKISPDRLSEQKSREGLKV--FDSAGGSYSILVNPAesneFNPFSLKEVRFALNYLIDRKLIVNELMGG 123
                 569***********************999999*****************..555555556666666698877*************************** PP

                 SSEEESSSSTTTSTTC CS
   SBP_bac_5 244 yatpansllppsspga 259
                 y+ p+ s+ +ps p +
  EPA06299.1 124 YGAPTVSYYSPSDPEY 139
                 **********999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1038.14
//
Query:       EPA06300.1  [L=53]
Description: hypothetical protein BG20_I2375 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.039   14.2   0.7      0.039   14.2   0.7    1.0  1  DUF4355   Domain of unknown function (DUF4355)


Domain annotation for each model (and alignments):
>> DUF4355  Domain of unknown function (DUF4355)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.7   2.2e-06     0.039      81     119 ..       8      46 ..       2      52 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.2e-06
     DUF4355  81 ekkipiellnlvvgedaeetkknvetfkelfnkavekav 119
                 e k+ +++l++ + ++ e t++  ++f++lf k++e+++
  EPA06300.1   8 EMKLMMNMLKVAIHQEREFTSDESKNFNDLFVKIIENKI 46 
                 678899******************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 381.74
//
Query:       EPA06301.1  [L=142]
Description: hypothetical protein BG20_I2373, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.5e-16   58.5   0.0    6.7e-16   58.2   0.0    1.0  1  SBP_bac_5  Bacterial extracellular solute-binding proteins, f


Domain annotation for each model (and alignments):
>> SBP_bac_5  Bacterial extracellular solute-binding proteins, family 5 Middle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.2   0.0   3.8e-20   6.7e-16     150     259 ..      27     139 ..      14     141 .. 0.88

  Alignments for each domain:
  == domain 1  score: 58.2 bits;  conditional E-value: 3.8e-20
                 SSSSEEEEEE-.SHHHHHHHHHTTSSSEE.ESTTCCTHCHHHHHTTEEEEEEEEEEEEEEEEETTT....STGGGSHHHHHHHHHHS-HHHHHHHCTTT CS
   SBP_bac_5 150 pkldriefkvipdsdaraaalqsGeiddv.aepppsdieqlkeakglkvlyespgggvtylafNtk....kppfddkrvRqAlsyAiDreeivkavleg 243
                   +d+++f  + d++++++++++G++d++   ++p+ + ++k  +glkv  ++  gg++ + +N +     +pf+ k+vR Al+y iDr+ iv+++++g
  EPA06301.1  27 TFFDSVKFIQYLDENTALEEVRNGNLDIYyDKISPDRLSEQKSREGLKV--FDSAGGSYSILVNPAesndFNPFSLKEVRFALNYLIDRKLIVNELMGG 123
                 569***********************999999*****************..555555566666766698877*************************** PP

                 SSEEESSSSTTTSTTC CS
   SBP_bac_5 244 yatpansllppsspga 259
                 y+ p+ s+ +ps p +
  EPA06301.1 124 YGAPTVSYYSPSDPEY 139
                 **********999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1034.04
//
Query:       EPA06302.1  [L=39]
Description: hypothetical protein BG20_I2382, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.4e-05   23.7   0.0    4.4e-05   23.7   0.0    1.0  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
      7e-05   22.5   0.0    7.6e-05   22.4   0.0    1.0  1  ApbA            Ketopantoate reductase PanE/ApbA
     0.0019   17.6   0.0     0.0019   17.6   0.0    1.0  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
     0.0095   16.2   0.0       0.01   16.1   0.0    1.0  1  TrkA_N          TrkA-N domain
  ------ inclusion threshold ------
      0.014   14.9   0.0      0.014   14.9   0.0    1.0  1  Epimerase       NAD dependent epimerase/dehydratase family
      0.017   15.7   0.0      0.017   15.7   0.0    1.0  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
      0.023   13.9   0.0      0.023   13.9   0.0    1.0  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
      0.056   13.0   0.0      0.059   13.0   0.0    1.0  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
      0.095   12.6   0.0      0.095   12.6   0.0    1.0  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
       0.11   12.7   0.0       0.13   12.5   0.0    1.1  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
       0.12   12.4   0.0       0.12   12.3   0.0    1.0  1  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
       0.17   11.2   0.0       0.17   11.2   0.0    1.0  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain


Domain annotation for each model (and alignments):
>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   2.9e-08   4.4e-05       1      35 [.       2      36 ..       2      39 .] 0.93

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 2.9e-08
                   EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHH CS
  NAD_binding_2  1 kigfiGlGvMGsnmalnllkagykvavynrtkekv 35
                   ki+++G+Gv Gs ++ +l++++++v++y+r++++ 
     EPA06302.1  2 KIAVMGMGVAGSYLMARLKNSEHDVTGYERSPQER 36
                   79*****************************9865 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   5.1e-08   7.6e-05       1      31 [.       3      33 ..       3      38 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 5.1e-08
                EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH CS
        ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr 31
                ia++G+G  Gs+l a+L++  +dvt + rs+
  EPA06302.1  3 IAVMGMGVAGSYLMARLKNSEHDVTGYERSP 33
                89***************99*********998 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.3e-06    0.0019      38      73 ..       2      37 ..       1      39 [] 0.92

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.3e-06
                  EEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH CS
  2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgmkviaydrskkkee 73
                  +++++G+G  G+ ++ rlk  + +v++y+rs+++++
    EPA06302.1  2 KIAVMGMGVAGSYLMARLKNSEHDVTGYERSPQERH 37
                  799****************************99765 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   6.8e-06      0.01       1      32 [.       3      34 ..       3      38 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 6.8e-06
                EEEES-SHHHHHHHHHHHHTTEEEEEEESSHH CS
      TrkA_N  1 iiiiGlGrvGrslaeeLseggkdvvvidkdee 32
                i+++G+G  G+ l+ +L+++++dv++ +++++
  EPA06302.1  3 IAVMGMGVAGSYLMARLKNSEHDVTGYERSPQ 34
                79*****************5558**9999987 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   9.1e-06     0.014       2      35 ..       4      36 ..       3      39 .] 0.85

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 9.1e-06
                EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTT CS
   Epimerase  2 lVtGatGfiGsalvkallekgyevigldrlssas 35
                 V+G  G  Gs+l+ +l++  ++v+g  r ++++
  EPA06302.1  4 AVMGM-GVAGSYLMARLKNSEHDVTGYERSPQER 36
                57776.*********************9996654 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   0.0   1.1e-05     0.017       1      39 [.       2      36 ..       2      39 .] 0.94

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.1e-05
                   EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCH CS
  F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpeka 39
                   ki++ G+G  g+ l+ +l ++    h+++ + +r+p+++
     EPA06302.1  2 KIAVMGMGVAGSYLMARLKNSE---HDVT-GYERSPQER 36
                   7********************9...****.99***9875 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.5e-05     0.023       2      30 ..       2      30 ..       1      38 [. 0.87

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.5e-05
                 SEEEE--SHHHHHHHHHHHHHTS-EEEEE CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlve 30
                 +++v G G+AG  ++ +l++++++vt +e
   EPA06302.1  2 KIAVMGMGVAGSYLMARLKNSEHDVTGYE 30
                 89************************997 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.9e-05     0.059       1      31 [.       1      31 [.       1      36 [. 0.91

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.9e-05
                    SEEEEE--STTHHHHHHHHHHCTSEEEEE-S CS
  UDPG_MGDP_dh_N  1 mkisviGlGYvGlvtaavlaeighevigvDi 31
                    mki+v+G+G  G   +a l +  h+v+g   
      EPA06302.1  1 MKIAVMGMGVAGSYLMARLKNSEHDVTGYER 31
                    8**************************9765 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   6.4e-05     0.095       1      34 [.       2      35 ..       2      39 .] 0.92

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.4e-05
                EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHH CS
     3HCDH_N  1 kvaviGaGtmGagiaavfasagleVvlvdiseea 34
                k+av+G G+ G+ + a + +++++V+ +++s++ 
  EPA06302.1  2 KIAVMGMGVAGSYLMARLKNSEHDVTGYERSPQE 35
                79***************************99876 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   8.8e-05      0.13       3      29 ..       7      33 ..       5      34 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.8e-05
                   --SHHHHHHHHHHHCCTEEEEEE-SSS CS
  NAD_binding_8  3 GaGlsGlvaAylLakagfdvlllekrd 29
                   G G++G+++ ++L++  +dv+ +e+++
     EPA06302.1  7 GMGVAGSYLMARLKNSEHDVTGYERSP 33
                   77*********************9986 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   8.4e-05      0.12       1      34 [.       2      35 ..       2      38 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.4e-05
                    -EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHH CS
  NAD_Gly3P_dh_N  1 kiavlGaGswGtalAkvlaenghevrlwvreeel 34
                    kiav+G+G  G+ l + l++  h+v+ + r++++
      EPA06302.1  2 KIAVMGMGVAGSYLMARLKNSEHDVTGYERSPQE 35
                    7***************************999865 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00011      0.17      30      64 ..       2      36 ..       1      39 [] 0.91

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                 EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHH CS
  AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrparl 64
                 k+ v+G GvaG   +a  k+ + +Vt ++ +p+ +
   EPA06302.1  2 KIAVMGMGVAGSYLMARLKNSEHDVTGYERSPQER 36
                 899*************************9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 277.88
//
Query:       EPA06303.1  [L=199]
Description: nitroreductase family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      5e-33  114.5   0.0    6.5e-33  114.2   0.0    1.2  1  Nitroreductase  Nitroreductase family
    1.3e-10   41.2   0.3    6.4e-05   22.6   0.4    2.8  2  TM1586_NiRdase  Putative TM nitroreductase
  ------ inclusion threshold ------
      0.018   15.0   0.1      0.025   14.5   0.1    1.3  1  DUF1951         Domain of unknown function (DUF1951)
       0.16   11.2   0.0       0.23   10.7   0.0    1.3  1  Zeta_toxin      Zeta toxin


Domain annotation for each model (and alignments):
>> Nitroreductase  Nitroreductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.2   0.0   1.5e-36   6.5e-33       1     170 []       7     176 ..       7     176 .. 0.92

  Alignments for each domain:
  == domain 1  score: 114.2 bits;  conditional E-value: 1.5e-36
                     HHH--B---B-S----HHHHHHHHHHHHTS--GGG---EEEEEE.-CCCHHHHHHHHHHHHHHHHTT-SS-GGGGGG...HHHHHHHHHHHHSSE CS
  Nitroreductase   1 irkRrSiRkFddepvpkeelekileaarraPsagnlqpwrfvvvqdkelryklaeaalelllkaeaqaelaqryrke...elklkaqkalagapv 92 
                     i++RrSi+ F++  ++k+e+ k++e a  +P++ n+q+wrfv +++++l++kl  ++ ++ ++aea+++ +   + +   +  +++ k++ + p 
      EPA06303.1   7 IKSRRSIKSFQNHEMSKDEINKLMEYAILSPTSYNIQNWRFVTITKQDLKDKLCVLSYGQRQVAEASLVIVLCADLKsweKNPERYWKNIPEEPR 101
                     89*******************************************************************99998888999888888888888888 PP

                     EEEE---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGGGGHHHHHHHHT-S..SEEEEEEEEE- CS
  Nitroreductase  93 livivatldkserkaaerayryalldagaaaqnllLaAtalGlgscpiggfdeaaeevrkllglpdeeeivvliavGy 170
                      ++i +   ++ + +++ + + a+ ++g+aaq+++LaA+++G++scp++gfd+ +  v +++glp+++ ++++++vG+
      EPA06303.1 102 NFLI-KGIKQAYTGNSKLEHDQAIRSCGIAAQTIMLAAQSMGYDSCPMEGFDYGK--VGEFIGLPPDHIVTMMVVVGK 176
                     8888.44455556678888999*********************************..*********99999*****96 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.4   1.4e-08   6.4e-05     141     187 ..       9      53 ..       7      79 .. 0.79
   2 !   14.9   0.0   3.2e-06     0.014      77     148 ..     120     193 ..     105     198 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.4e-08
                     ----HHHHBSS-GGGS-HHHHHHHHHHHTS--GGG----EEE.E-SS CS
  TM1586_NiRdase 141 krkpleelcevkeeelpewfkeileaarlAPsAlNqqpwrfelkddd 187
                      r++++++ + +    ++++++++e a+l+P++ N q wrf   +++
      EPA06303.1   9 SRRSIKSFQNHEM--SKDEINKLMEYAILSPTSYNIQNWRFVTITKQ 53 
                     5677777775555..479***********************976655 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 3.2e-06
                     SHHHHHHHHHHHHHHHHHHHHTT-EEEEE.S--SST...........T-S-EEEEE-BS----..-----HHHH CS
  TM1586_NiRdase  77 kedleekaGYygeqlvLkltalGlgtcWv.ggtykkkkakvelkkgeklvivIalGyaktklv.eakrkpleel 148
                     ++++ + +G   + ++L +++ G  +c + g+ y k+ + + l+ ++ + +++++G+ +++      + pl+el
      EPA06303.1 120 HDQAIRSCGIAAQTIMLAAQSMGYDSCPMeGFDYGKVGEFIGLPPDHIVTMMVVVGKKAKEPApRGGQLPLSEL 193
                     5677789********************875889************************99987733345566655 PP

>> DUF1951  Domain of unknown function (DUF1951)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   5.7e-06     0.025      16      67 ..       2      52 ..       1      80 [. 0.81

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.7e-06
     DUF1951 16 ekldfiksvresdtvanvevPlaklkelielikneetkhyarnffintellk 67
                + +d iks r   ++ n e+ + ++++l+e ++  +t +  +n+   t ++k
  EPA06303.1  2 DTFDAIKSRRSIKSFQNHEMSKDEINKLMEYAILSPTSYNIQNWRFVT-ITK 52
                579***********************************7777765443.444 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   5.2e-05      0.23     124     166 ..      72     115 ..      63     142 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 5.2e-05
  Zeta_toxin 124 vevvvvavkkelSrlgvldRyeeevae.gRlvpkeehdeafegl 166
                   +v+v +    S+++  +Ry++++ e +R+  ++ +++a++g 
  EPA06303.1  72 ASLVIVLCADLKSWEKNPERYWKNIPEePRNFLIKGIKQAYTGN 115
                 6799********************77758***********9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1555.91
//
Query:       EPA06304.1  [L=61]
Description: hypothetical protein BG20_I2381 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.024   14.7   7.9      0.096   12.7   7.9    2.0  1  DZR             Double zinc ribbon
      0.065   13.2   3.6        1.7    8.6   0.3    2.3  2  zf-dskA_traR    Prokaryotic dksA/traR C4-type zinc finger
       0.23   11.7   0.0        0.3   11.3   0.0    1.2  1  GDH_N           Glutamate dehydrogenase N terminal
       0.32   11.4   3.5       0.74   10.3   0.4    2.2  2  DUF983          Protein of unknown function (DUF983)
       0.51   10.1   7.3        2.4    8.0   0.8    2.6  3  zinc_ribbon_2   zinc-ribbon domain
        1.2    9.1   5.2        1.3    9.0   0.4    2.1  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
        2.3    8.2   8.5       0.55   10.2   3.8    2.3  2  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit


Domain annotation for each model (and alignments):
>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   7.9   3.7e-05     0.096      13      39 ..      31      57 ..       2      61 .] 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.7e-05
         DZR 13 rfCseCgtklkavaaedrCpsCgekvd 39
                r+C+ Cg + +a+  +drC +Cgek +
  EPA06304.1 31 RYCESCGLTKPAEGVHDRCEKCGEKYP 57
                8******99988888********9865 PP

>> zf-dskA_traR  Prokaryotic dksA/traR C4-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.2    0.0064        16       3      10 ..      30      37 ..      27      39 .. 0.78
   2 ?    8.6   0.3   0.00067       1.7       5      12 ..      48      55 ..      41      58 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0064
  zf-dskA_traR  3 ygsCeeCG 10
                   ++Ce CG
    EPA06304.1 30 MRYCESCG 37
                  467****9 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00067
  zf-dskA_traR  5 sCeeCGEp 12
                  +Ce+CGE+
    EPA06304.1 48 RCEKCGEK 55
                  3******6 PP

>> GDH_N  Glutamate dehydrogenase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00012       0.3      68      92 ..       7      31 ..       2      34 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00012
       GDH_N 68 defprrtpeqWaalavdmlefarkr 92
                 e pr+t+eqWa    +++e+  +r
  EPA06304.1  7 KEQPRHTSEQWAVCSKKLIELGIMR 31
                689**********999999986555 PP

>> DUF983  Protein of unknown function (DUF983)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1     0.085   2.2e+02       8      16 ..      30      38 ..      26      45 .. 0.81
   2 ?   10.3   0.4   0.00029      0.74       7      21 ..      45      59 ..      42      61 .] 0.87

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.085
      DUF983  8 adaCeaCgl 16
                   Ce+Cgl
  EPA06304.1 30 MRYCESCGL 38
                578*****8 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00029
      DUF983  7 vadaCeaCgldlsha 21
                v+d+Ce+Cg+++ + 
  EPA06304.1 45 VHDRCEKCGEKYPFS 59
                79*********9775 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       4.4   1.1e+04       2       3 ..      20      21 ..      19      22 .. 0.49
   2 ?    5.5   0.1    0.0056        14      15      20 ..      32      37 ..      30      39 .. 0.70
   3 ?    8.0   0.8   0.00093       2.4       1       9 [.      48      56 ..      48      58 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 4.4
  zinc_ribbon_2  2 Cp 3 
                   C+
     EPA06304.1 20 CS 21
                   54 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0056
  zinc_ribbon_2 15 FCpyCG 20
                   +C+ CG
     EPA06304.1 32 YCESCG 37
                   666666 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.00093
  zinc_ribbon_2  1 fCpnCGael 9 
                   +C +CG++ 
     EPA06304.1 48 RCEKCGEKY 56
                   588888775 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.4   0.00049       1.3      23      55 ..       9      39 ..       2      45 .. 0.88
   2 ?    4.7   3.5     0.011        29      30      55 ..      32      55 ..      31      57 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00049
  OrfB_Zn_ribbon 23 npayTSktCseCgsknkealsgrtfkCpnCgfe 55
                    +p++TS + ++C +k+ e   g   +C++Cg++
      EPA06304.1  9 QPRHTSEQWAVCSKKLIE--LGIMRYCESCGLT 39
                    7999**************..999999*****87 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.011
  OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkCpnCgfe 55
                     C  Cg ++    +g   +C++Cg +
      EPA06304.1 32 YCESCGLTKPA--EGVHDRCEKCGEK 55
                    6999**99999..999999****987 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1         1   2.6e+03      24      32 ..       2      10 ..       2      14 .. 0.69
   2 ?   10.2   3.8   0.00021      0.55       1      34 [.      30      59 ..      30      61 .] 0.92

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1
                    ESSSS-EEE CS
  RNA_POL_M_15KD 24 CrqCgYeep 32
                    C  C+ e+p
      EPA06304.1  2 CLICSKEQP 10
                    556888887 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00021
                    EEBESTTTSBEEEEECSCCCEEEESSSS-EEESS CS
  RNA_POL_M_15KD  1 lkFCpkCgNlLlpkedkegknfeCrqCgYeepad 34
                    ++ C +Cg l  p+e++  +   C +Cg ++p++
      EPA06304.1 30 MRYCESCG-LTKPAEGVHDR---CEKCGEKYPFS 59
                    899****9.9999*****98...*********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 494.51
//
Query:       EPA06305.1  [L=146]
Description: methyltransferase domain protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-16   60.0   0.0    4.2e-16   59.4   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
    3.5e-15   56.1   0.2    4.7e-15   55.7   0.2    1.1  1  Methyltransf_31  Methyltransferase domain
    1.2e-14   54.7   0.0    1.5e-14   54.4   0.0    1.2  1  Methyltransf_11  Methyltransferase domain
    1.5e-13   50.7   0.0    1.5e-13   50.6   0.0    1.0  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    1.4e-11   45.0   0.1    2.2e-11   44.3   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
      6e-08   32.7   0.0    8.7e-08   32.2   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
      8e-08   32.0   0.0    2.2e-07   30.6   0.0    1.6  1  MTS              Methyltransferase small domain
    2.2e-07   30.6   0.1    2.9e-07   30.2   0.1    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    1.1e-06   28.2   0.1    1.3e-06   28.0   0.1    1.1  1  TehB             Tellurite resistance protein TehB
    2.6e-06   27.2   0.0    3.1e-06   26.9   0.0    1.1  1  NodS             Nodulation protein S (NodS)
    0.00024   20.1   0.0    0.00027   20.0   0.0    1.1  1  Methyltransf_9   Protein of unknown function (DUF1698)
     0.0017   17.7   0.0     0.0023   17.3   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
  ------ inclusion threshold ------
      0.015   16.3   0.0      0.021   15.8   0.0    1.2  1  Methyltransf_24  Methyltransferase domain
      0.017   14.6   0.0       0.03   13.8   0.0    1.4  2  Methyltransf_4   Putative methyltransferase
      0.026   13.9   0.0      0.036   13.4   0.0    1.2  1  GidB             rRNA small subunit methyltransferase G
       0.04   13.9   0.0      0.052   13.5   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
      0.056   12.5   0.0      0.066   12.3   0.0    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase
      0.081   12.9   0.0       0.24   11.4   0.0    1.9  2  ADH_zinc_N       Zinc-binding dehydrogenase
       0.14   11.7   0.0       0.19   11.3   0.0    1.1  1  MetW             Methionine biosynthesis protein MetW
       0.18   11.5   0.1       0.31   10.8   0.1    1.5  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.4   0.0   4.6e-19   4.2e-16       1      97 []      47     136 ..      47     136 .. 0.92

  Alignments for each domain:
  == domain 1  score: 59.4 bits;  conditional E-value: 4.6e-19
                      EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHHHHHHHHHHHHHE CS
  Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssgalhhlsdedlekalkeiarvL 93 
                      +Ldl+cGtG l++++ak  ++++v+gvD+++++l+ a+++    g+ n+++v  dae+l+++ ++fD++vss+   +++   ++ +++++  +L
       EPA06305.1  47 ILDLACGTGILSRMIAKI-PNSEVVGVDVTQNYLDVAKKKS---GFdNISYVLEDAEKLDLD-KKFDFIVSSYIPKYCD---AKLLIAKCVTHL 132
                      8***************99.79*******************9...778************976.5*******87777765...6789******** PP

                      EEEE CS
  Methyltransf_25  94 kpgG 97 
                      +pgG
       EPA06305.1 133 NPGG 136
                      ***9 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.7   0.2   5.2e-18   4.7e-15       6     112 ..      46     143 ..      42     145 .. 0.88

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 5.2e-18
  Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnevlnaladpdkileeier 99 
                       +lDl+CGtG l+  +a   +p++evvG+D +++ + +A++   k g+dn++   +d+e+l+  l d+kfD+i+s  +    +d +  + +   
       EPA06305.1  46 MILDLACGTGILSRMIA--KIPNSEVVGVDVTQNYLDVAKK---KSGFDNISYVLEDAEKLD--L-DKKFDFIVSSYIP-KYCDAKLLIAKCVT 130
                      69***************..689*******************...8*****************..4.49*******7665.66777777778888 PP

  Methyltransf_31 100 vlkpggilliedp 112
                       l+pgg +++ d+
       EPA06305.1 131 HLNPGGQIILHDF 143
                      8999999998876 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.4   0.0   1.7e-17   1.5e-14       1      95 [.      48     139 ..      48     140 .. 0.95

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 1.7e-17
                      EEET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHHHHHHHHHHEEEEEE CS
  Methyltransf_11   1 LdvGcGtGrlaealakrg.arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedpekalkeiaRvLkpgGl 93 
                      Ld++cGtG+l++ +ak   ++vvgvD++++ l++ak+k+  ++  +++v +daekl + d++fD++vss    ++ d + ++++++  L pgG 
       EPA06305.1  48 LDLACGTGILSRMIAKIPnSEVVGVDVTQNYLDVAKKKSGFDN--ISYVLEDAEKLDL-DKKFDFIVSSYIPKYC-DAKLLIAKCVTHLNPGGQ 137
                      8**************9989********************9998..99**********9.55**************.79***************9 PP

                      EE CS
  Methyltransf_11  94 lv 95 
                      ++
       EPA06305.1 138 II 139
                      98 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.6   0.0   1.7e-16   1.5e-13       8     153 ..       7     142 ..       1     146 [] 0.86

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 1.7e-16
                      XXXXXXX-HHHHHHHHHHHHHTTTHHHHHHHHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEE CS
  Ubie_methyltran   8 kvkevfesvaskyDlmndvlslgihrlWkkfveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinie 101
                       v+  f+   s+yD + +  ++g  + Wk+ +   v++ +g  +lD+a+Gtg l+  +++    + +vv++D+ +n L+v++kk   +g+ ni 
       EPA06305.1   7 LVAIFFDGTGSSYDRVVNCTTFGRDKFWKRQI---VSKISGGMILDLACGTGILSRMIAKI--PNSEVVGVDVTQNYLDVAKKK---SGFDNIS 92 
                      477789999********************954...45567889*********998877775..4568**************987...79***** PP

                      EEE--TTT-TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEEEE CS
  Ubie_methyltran 102 flqanaeeLpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvvle 153
                      ++  +ae+L+ + + fD++  s+ +    D +  + +    l pGG+++  +
       EPA06305.1  93 YVLEDAEKLDLD-KKFDFIVSSY-IPKYCDAKLLIAKCVTHLNPGGQIILHD 142
                      *********985.67**997777.89999**9999***********998765 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   0.0   2.5e-14   2.2e-11       1      99 []      48     138 ..      48     138 .. 0.85

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 2.5e-14
  Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlkdirevldnirklLk 94 
                      L++ cGtG l+r++++  p++e++gvD+ ++ + d ++k +  +n +    + e     +ld  ++fD +v+s    ++ d + +++++  +L+
       EPA06305.1  48 LDLACGTGILSRMIAKI-PNSEVVGVDVTQNYL-DVAKKKSGFDNISYVLEDAE-----KLDLDKKFDFIVSSYIPKYC-DAKLLIAKCVTHLN 133
                      89**********99666.***************.88888788775454444444.....444556*************8.************** PP

  Methyltransf_12  95 pgGrl 99 
                      pgG++
       EPA06305.1 134 PGGQI 138
                      ***96 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.0   9.7e-11   8.7e-08      22     120 ..      43     143 ..      29     145 .. 0.78

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 9.7e-11
  Methyltransf_23  22 aggrvLdiGcGtGillevlrengf.svtgvDlspeaveiaekakkaqkdqfdeqeaae..pqgkfdlIvlrevlehvpdppellrqiatllkpg 112
                      +gg +Ld++cGtGil++ +++ +  +v+gvD   +  + a+k++   + ++  ++a++   ++kfd+Iv+++     +    l+++  t+l+pg
       EPA06305.1  43 SGGMILDLACGTGILSRMIAKIPNsEVVGVDVTQNYLDVAKKKSGFDNISYVLEDAEKldLDKKFDFIVSSYIPKYCDA-KLLIAKCVTHLNPG 135
                      67889**************999766*******9888877764444444444444444444788********98888877.6788888999**** PP

  Methyltransf_23 113 Gylllsep 120
                      G ++l+++
       EPA06305.1 136 GQIILHDF 143
                      *****986 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.0   2.5e-10   2.2e-07      31     135 ..      43     138 ..      35     141 .. 0.78

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 2.5e-10
                 TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEEEE---STTTCHCHHHHHHHHHHHHHHHE CS
         MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdlivsNPPfhagkatelavaeeliaeAkeaL 129
                   g +lDl+cG+G+l+ ++ak  p+ ev+ vdv  + l++ak+     +  +++v +d+ +   +kkfd+ivs   +      ++  a+ lia+   +L
  EPA06305.1  43 SGGMILDLACGTGILSRMIAK-IPNSEVVGVDVTQNYLDVAKKKSGFDN--ISYVLEDAEKLDLDKKFDFIVSSY-I-----PKYCDAKLLIAKCVTHL 132
                 5678**************999.7888****************9887777..578888888777789******852.1.....12333556777777777 PP

                 EEEEEE CS
         MTS 130 kegGeL 135
                 ++gG++
  EPA06305.1 133 NPGGQI 138
                 777776 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.1   3.2e-10   2.9e-07     163     258 ..      45     140 ..      35     142 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 3.2e-10
        PrmA 163 eevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellkeekadvivaNILaevl..ielaedikklvkeggllil 258
                   +lD+ +G+GiL+   ak+  ++vv+vD+ +  ++vak+   + +++  le a + +l  ++k+d iv+  + +      l+ +   ++++gg++il
  EPA06305.1  45 GMILDLACGTGILSRMIAKIPNSEVVGVDVTQNYLDVAKKKSGFDNISYVLEDAEKLDL--DKKFDFIVSSYIPKYCdaKLLIAKCVTHLNPGGQIIL 140
                 5799******************************************9998864333333..579********99987225699999********9996 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.1   1.5e-09   1.3e-06      25     128 ..      38     136 ..      23     142 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1.5e-09
                 HCCCS-S-EEEEES-TTSHHHHHHHHT.T-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG----S-EEEEEEESSGGGS-GGGHHHHHHHHHH CS
        TehB  25 avkivkpgkvldlgcgqgrnslylsll.gydvtawdknensiafleeikekenlknistalydineaklderydfilstvvlmfleaeripsiienmqe 122
                  v  ++ g +ldl cg g  s  ++ +   +v  +d  +n   +l+  k+k  ++nis  l d ++++ld+++dfi+s+ +  + +a+    +i+   +
  EPA06305.1  38 IVSKISGGMILDLACGTGILSRMIAKIpNSEVVGVDVTQN---YLDVAKKKSGFDNISYVLEDAEKLDLDKKFDFIVSSYIPKYCDAKL---LIAKCVT 130
                 56778999***********998887552679999998876...6788899999**************************9999988875...5777777 PP

                 TEEEEE CS
        TehB 123 ctkvgg 128
                 + ++gg
  EPA06305.1 131 HLNPGG 136
                 777777 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   3.5e-09   3.1e-06      45     143 ..      45     139 ..      23     142 .. 0.80

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 3.5e-09
        NodS  45 adalevGcaaGalterlapyckrltv.vdvveeaiararervkesshiswivsdvqqfstdekfdlivvaevlyyiedvaelraavrnlvsllapdgql 142
                 + +l++ c +G l+ ++a + ++  v vdv ++ ++ a+++     +is++  d +++++d+kfd iv + +  y     + +  +   v+ l p+gq+
  EPA06305.1  45 GMILDLACGTGILSRMIAKIPNSEVVgVDVTQNYLDVAKKKSGF-DNISYVLEDAEKLDLDKKFDFIVSSYIPKYC----DAKLLIAKCVTHLNPGGQI 138
                 56899*************9988766559*999999999988765.99********************998555555....4555566667777777777 PP

        NodS 143 v 143
                 +
  EPA06305.1 139 I 139
                 6 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0     3e-07   0.00027     102     218 ..      32     141 ..      22     146 .] 0.78

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 3e-07
                     HHHHHHGGGS.--TT-EEEEET-TTSHHHHHHHHCT-S.EEEEE---HHHHHHHHHHHCCTTTTSSEEEE---GGGS-T---EEEEEEES-GGG- CS
  Methyltransf_9 102 wkWdrvlphlsdlkgrtildvGcgnGyhlwrmvgegak.lvvGidPselfliqfeavrkllgedqrahllplgieqlpeleafdtvfsmGvlyhr 195
                       W+r  + +s++ g +ild+ cg+G  l rm+++ ++  vvG+d ++ +l   +  +k +g d+ +++l    e+l+  + fd + s  +  + 
      EPA06305.1  32 KFWKR--QIVSKISGGMILDLACGTGI-LSRMIAKIPNsEVVGVDVTQNYL---DVAKKKSGFDNISYVL-EDAEKLDLDKKFDFIVSSYIPKYC 119
                     55666..4579999************7.78***99875269*******998...6678999****99999.6889999999***99998776666 PP

                     S-HHHHHHHHHCTEEEEEEEEEE CS
  Methyltransf_9 196 rsPldhllqlkdqlvkgGelvle 218
                      + l  + +   +l  gG+++l 
      EPA06305.1 120 DAKL-LIAKCVTHLNPGGQIILH 141
                     6665.345556677777777776 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   2.5e-06    0.0023      63     165 ..      44     141 ..      32     145 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.5e-06
                 T-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEE.EES-GGG-----SEEEEES-GGGTSGGGHHHHHHHHHHHS-TT- CS
        CMAS  63 GmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvev.klldyedldekvdrvvsvgafehvgkenydtffkklkkllkedG 160
                 G  +Ld+ cG G l r  ++  + +vvg+ + ++   +akk+    ++++   v + ++  dld+k+d +vs  +         +  ++k+ + l+++G
  EPA06305.1  44 GGMILDLACGTGILSRMIAKIPNSEVVGVDVTQNYLDVAKKK---SGFDNISYVlEDAEKLDLDKKFDFIVSSYIPKYCDA---KLLIAKCVTHLNPGG 136
                 7789********************************999986...45545444415567789999******9655444333...344566666666666 PP

                 EEEEE CS
        CMAS 161 llllh 165
                  ++lh
  EPA06305.1 137 QIILH 141
                 66666 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.8   0.0   2.4e-05     0.021       8     106 .]      55     143 ..      47     143 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.4e-05
  Methyltransf_24   8 GvstlwllralrrngagrlvavdhdpgaeeaaalareaglddrvrlikadseealaslaagsiDllfiDgghaaeavledleallprlapggvv 101
                      G  + +++    +  ++++v vd  +   ++  +a+++   d++  + +d+e++  +l+ +++D+++    +++ +++  +  +  +l+pgg +
       EPA06305.1  55 GILSRMIA----KIPNSEVVGVDVTQ---NYLDVAKKKSGFDNISYVLEDAEKL--DLD-KKFDFIVSSYIPKYCDAKLLIAKCVTHLNPGGQI 138
                      44444444....33335789999999...9999999988888888888888888..788.99******************************** PP

  Methyltransf_24 102 lfdDi 106
                      +++D+
       EPA06305.1 139 ILHDF 143
                      ****5 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.3e-05      0.03       4      63 ..      46     100 ..      43     113 .. 0.85
   2 ?   -3.3   0.0       5.9   5.3e+03      99     115 ..     124     140 ..     122     141 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.3e-05
                     EEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCCH CS
  Methyltransf_4   4 vvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgdalkv 63 
                     ++l++ cG G +l+++  k P+ +++G+++ ++ ++ + kk   +++ N+ ++  da + 
      EPA06305.1  46 MILDLACGTG-ILSRMIAKIPNSEVVGVDVTQNYLDVAKKK---SGFDNISYVLEDA-EK 100
                     689*****99.678888899************999887665...6899****99999.43 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 5.9
                     HHHHHHHHEEEEEEEEE CS
  Methyltransf_4  99 llkelarvLkkgGvlel 115
                     l+++  + L++gG++ l
      EPA06305.1 124 LIAKCVTHLNPGGQIIL 140
                     56677889999999865 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   4.1e-05     0.036      86     122 ..      77     113 ..      72     141 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.1e-05
                 HHHHHHHHHCT-SSEEEEES-CCCTTTTT-EEEEEEC CS
        GidB  86 aFLeevkeelklenveivearaeekqeeekydvvtsR 122
                 ++L  +k++ + +n+ +v ++ae+ +  +k+d+++s 
  EPA06305.1  77 NYLDVAKKKSGFDNISYVLEDAEKLDLDKKFDFIVSS 113
                 89********************************985 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   5.8e-05     0.052      28      69 ..      46      84 ..      34     102 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.8e-05
  Methyltransf_32 28 tvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaek 69
                      ++D+++G g Ls+++a      + +vvg+d+ ++  + a+k
       EPA06305.1 46 MILDLACGTGILSRMIAK---IPNSEVVGVDVTQNYLDVAKK 84
                     699***************...6699********999988876 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   7.4e-05     0.066      33     123 ..      46     129 ..      26     141 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.4e-05
                 EEEEES-TTTCCHHHHHCC-.SEEEEE-S-HHHHHHHHCHTTTCCCEEEE-S-CCGHHHHHHHCTTTCCCCEEEEEEE--TTT.HHHHHHHHH CS
      RrnaAD  33 tvleigpGkGilTeeLakra.kqvvvlElderLakllqkklskdeklkvvhqDflkfetpeevtekdsihqeflvvanlPyei.stqlvkqll 123
                  +l+++ G+Gil++ +ak+   +vv +   ++ + + +kk s   ++  v +D+ k ++ +        +  f+v + +P +   + l+ +++
  EPA06305.1  46 MILDLACGTGILSRMIAKIPnSEVVGVDVTQNYLDVAKKK-SGFDNISYVLEDAEKLDLDK--------KFDFIVSSYIPKYCdAKLLIAKCV 129
                 69******************889999******99999994.4689*************999........789999999998651455566665 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0         3   2.7e+03      60      80 ..       9      27 ..       3      31 .. 0.56
   2 ?   11.4   0.0   0.00026      0.24       1      41 [.      53      94 ..      53     140 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3
                EEEEESSCSHHHHHHHHHCEE CS
  ADH_zinc_N 60 dvvfecvGsgatleaalkllk 80
                 + f+ +G  +++++ +++++
  EPA06305.1  9 AIFFDGTG--SSYDRVVNCTT 27
                45555555..55555555554 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00026
                HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.TTESEEEET CS
  ADH_zinc_N  1 gvGlaavqlAkalGaeviavdsseeklelakk.lGadeviny 41
                g G++  ++Ak+ + ev++vd++++ l+ akk  G d +   
  EPA06305.1 53 GTGILSRMIAKIPNSEVVGVDVTQNYLDVAKKkSGFDNISYV 94
                6799999************************98999987655 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00021      0.19      14      82 ..      44     113 ..      34     121 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00021
        MetW  14 gsrvldlGcGdGellellkeekqvdgrGleldeegvaecvak.Glsviqgdldkdlenfedksfdyvvls 82 
                 g  +ldl cG G l +++++  + +  G+++ ++ +  + +k G   i   l++  +   dk+fd++v s
  EPA06305.1  44 GGMILDLACGTGILSRMIAKIPNSEVVGVDVTQNYLDVAKKKsGFDNISYVLEDAEKLDLDKKFDFIVSS 113
                 5679****************9999999**999999877766548998888888888888899***99865 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00034      0.31      74     132 ..      44      97 ..      35     140 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00034
                 T-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES- CS
        PCMT  74 garvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgD 132
                 g  +L++ +G+G+l+ ++a++ ++   vv+++ +++  + ak+   k++ +n++ v  D
  EPA06305.1  44 GGMILDLACGTGILSRMIAKIPNS--EVVGVDVTQNYLDVAKK---KSGFDNISYVLED 97 
                 5569***************99655..56******999999986...4566666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1060.87
//
Query:       EPA06306.1  [L=622]
Description: carbamoyl-phosphate synthetase large chain, oligomerisation domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-27   96.4   0.0    2.3e-27   95.9   0.0    1.2  1  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
    8.1e-23   81.1   0.0    1.9e-22   79.9   0.0    1.6  1  CPSase_L_D3      Carbamoyl-phosphate synthetase large chain, 
    1.3e-14   54.1   0.5    2.8e-13   49.9   0.0    2.7  2  MGS              MGS-like domain
    8.3e-10   38.5   0.0    1.4e-09   37.7   0.0    1.3  1  ATP-grasp        ATP-grasp domain
    5.4e-09   35.9   0.0    1.4e-08   34.6   0.0    1.7  1  ATPgrasp_Ter     ATP-grasp in the biosynthetic pathway with T
    9.7e-09   35.1   0.0    1.8e-08   34.1   0.0    1.4  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    3.1e-05   23.9   0.0    0.00011   22.1   0.0    1.9  1  GARS_A           Phosphoribosylglycinamide synthetase, ATP-gr
     0.0015   18.8   0.0     0.0058   16.9   0.0    2.0  2  TrkA_N           TrkA-N domain
     0.0032   17.1   0.1      0.013   15.1   0.2    2.0  2  ATP-grasp_4      ATP-grasp domain
     0.0055   16.8   0.0      0.011   15.8   0.0    1.5  1  ATP-grasp_3      ATP-grasp domain


Domain annotation for each model (and alignments):
>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.9   0.0   1.3e-30   2.3e-27       2     210 ..     214     415 ..     213     416 .. 0.92

  Alignments for each domain:
  == domain 1  score: 95.9 bits;  conditional E-value: 1.3e-30
                  HHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHHSTS-EEEEE--SSSEEEEEEE CS
  CPSase_L_D2   2 kesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaafgnkqvlvekslkgpkeiEvev 99 
                  ++++++ l+k++++  + +a    ++ ea ++a+++g+Pvi+++++ l G  m+v+++++el++ vk+a++ ++    ++ v + k++ +  e++v+ 
   EPA06306.1 214 RSKFSAELDKLHIQQPRWQAF--ANIVEAKSFAQDVGFPVIVRPSYVLSGAAMKVVWSQDELKKYVKEATDVSP----DHPVVISKFMLNSLEVDVDG 305
                  677788888887777777766..8999**********************************************6....9******************* PP

                  EEETTS-EE.EEEEEEECCECTCCCCEEEES-SS--HHHHHHHHHHHHHHHHHHT-EEEEEEEEEEETTTTEEEEEEEESS--CCHHHHHHHHS--HH CS
  CPSase_L_D2 100 lrDakgnvi.tvcerenslqlrtqkvievAPsqtLtdeerqalreaavkvvrevgvvgagtveflldpkskeyyviEvNtRlsvesalaekaTGldlv 196
                  +   ++ +i  + e   s  ++ ++ +   P   L++++ +++ e + k++++ +v+g  +++fl++  +++ yviE+N R s++ +  +k    +l+
   EPA06306.1 306 VCNGTDVIIgAIVEHIESAGVHSGDAMMCIPPWRLNNKTIETITEYSTKIAKTFNVKGPFNLQFLIH--DDHVYVIELNIRASRSMPFVSKLVKTNLI 401
                  **9999888434555556777**********************************************..599************************** PP

                  HHHHHHHTT--GCG CS
  CPSase_L_D2 197 keaakialgekLee 210
                  + aak  lg++L++
   EPA06306.1 402 ALAAKAVLGKPLPK 415
                  ***********986 PP

>> CPSase_L_D3  Carbamoyl-phosphate synthetase large chain, oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.9   0.0   1.1e-25   1.9e-22      39     122 .]       4      84 ..       3      84 .. 0.96

  Alignments for each domain:
  == domain 1  score: 79.9 bits;  conditional E-value: 1.1e-25
  CPSase_L_D3  39 ekleelvelekelkkkkkeldeellreakklGfsDkqiaelleeeeeeevrelrkklgilpvykrvDtcAaeFeaetpYlYstY 122
                  +k++++v++e++lk+++  ++++ll e kklGfsD+qia+  ++++ ee+re+rkk+g+lp++k++Dt+Aae++a t+YlY tY
   EPA06306.1   4 RKIKNIVDIESKLKSES--ISTSLLWESKKLGFSDRQIARA-KDKSPEEIREIRKKAGVLPSVKQIDTLAAEWPAVTNYLYLTY 84 
                  599***********997..9*********************.5688888**********************************9 PP

>> MGS  MGS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1      0.23   4.1e+02       5      21 ..     467     483 ..     465     487 .. 0.91
   2 !   49.9   0.0   1.5e-16   2.8e-13       2      95 .]     497     590 ..     496     590 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.23
                 HHHHHHHTTCEEEEEHH CS
         MGS   5 lakklkelgfellATgG 21 
                 lak l ++g++l +Tg+
  EPA06306.1 467 LAKGLTSAGYTLPSTGT 483
                 89*************86 PP

  == domain 2  score: 49.9 bits;  conditional E-value: 1.5e-16
                 HHHHHHHHHHTTCEEEEEHHHHHHHHHT..T--EEECCCCHSTGSGGTHCHHHHHHHHTTSCCEEEEE--THHHHHH....CHHHHHHHHHHHTTSHEE CS
         MGS   2 lvelakklkelgfellATgGTakllkea..gipvtevvektgegerlggrveildaikngeidlvintlypfkatva....kdgykirraaenidIplp 94 
                 l++ + +lk+lgf+++AT+ Ta++++e+  g   +evv+k++e++r     +i d++ + +id++in++++ +  +     +d+y+irr  ++ +Ip+ 
  EPA06306.1 497 LLQPIARLKSLGFKIVATEHTAEFFEEKigG---IEVVHKISEPQRKP---NIADLLYERKIDFIINIPSTSTLEKYvgmlEDEYQIRRKSLELGIPVL 589
                 678899********************87444...66********8877...8*****************99998877899*****************98 PP

                 S CS
         MGS  95 t 95 
                 t
  EPA06306.1 590 T 590
                 7 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.0   8.1e-13   1.4e-09       2     160 ..     222     385 ..     221     388 .. 0.91

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 8.1e-13
                 HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC....GTTCEEEEE----SEEEEEEEEEETTC-EEE--EE CS
   ATP-grasp   2 eklglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal....keekvivEefvpfekElsvlvvrsaeGetafypvv 96 
                 +kl+++ pr++a ++  e++++a+++g+pv+v+ +    +G   +vv s+++l++ ++++     +++v++ +f+  + E+ v +v +    + + ++v
  EPA06306.1 222 DKLHIQQPRWQAFANIVEAKSFAQDVGFPVIVR-PSYVLSGAAMKVVWSQDELKKYVKEAtdvsPDHPVVISKFMLNSLEVDVDGVCNGTD-VIIGAIV 318
                 7899*****************************.99999********************99998899*******************98776.8899999 PP

                 EEEEE....TTEEEEEEECEE-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEETTCTEEEEEEESS- CS
   ATP-grasp  97 etvqe....dgilrlsvapaevsekaqkkaeeiakkiveeLggvGvfavElFvledgellvnElapRp 160
                 e++++    +g+  +++ p ++++k  ++++e+  ki++++++ G f + + +  d++++v El  R 
  EPA06306.1 319 EHIESagvhSGDAMMCIPPWRLNNKTIETITEYSTKIAKTFNVKGPFNLQFLIH-DDHVYVIELNIRA 385
                 999971111456789**********************************97777.888*****99885 PP

>> ATPgrasp_Ter  ATP-grasp in the biosynthetic pathway with Ter operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.0   7.6e-12   1.4e-08      44     119 ..     343     419 ..     287     427 .. 0.77

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 7.6e-12
  ATPgrasp_Ter  44 ekdeelielaerlaeefgldglvnvQvrededgpkLLEiNpRasGGlg.ysalaGvnlpylalklllgleteeveep 119
                   ++ e ++e+++++a++f+++g +n+Q+  ++d+ +++E N Ras  +  +s l   nl+ la+k++lg++ ++ +e 
    EPA06306.1 343 KTIETITEYSTKIAKTFNVKGPFNLQFLIHDDHVYVIELNIRASRSMPfVSKLVKTNLIALAAKAVLGKPLPKLPEN 419
                   456789*****************************************8468999**************865555444 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.0     1e-11   1.8e-08      29     173 ..     241     382 ..     221     386 .. 0.86

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 1e-11
                      HHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHTT..-SCEEEEE--.ESEEEEE.EEEETSSCEEEEEEEEE-SSSSS-HHHHHC CS
  Dala_Dala_lig_C  29 ekveeelgypvfVKpareGSSvGvskveseeelkeaieeafky..dekvlvEeai.egreiev.avlgneklevsevgeivvkkgfydyeakys 118
                      ++  + +g+pv+V+p+   S   ++ v s++elk++++ea     d+ v++ +++ +  e++v +v +  ++ +  ++e++ + g+       s
       EPA06306.1 241 KSFAQDVGFPVIVRPSYVLSGAAMKVVWSQDELKKYVKEATDVspDHPVVISKFMlNSLEVDVdGVCNGTDVIIGAIVEHIESAGVH------S 328
                      456789**********************************76434999*****9989999999556666678899999999999885......5 PP

                      .TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEEEEE CS
  Dala_Dala_lig_C 119 ddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDfflteegeivlnEvN 173
                      +d++++  p +l++++ e+i+e++ k+ k+ +++G   + f+++ ++++++ E+N
       EPA06306.1 329 GDAMMCIPPWRLNNKTIETITEYSTKIAKTFNVKGPFNLQFLIH-DDHVYVIELN 382
                      788889999********************************998.8999999999 PP

>> GARS_A  Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   6.1e-08   0.00011      10     109 ..     221     316 ..     214     387 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 6.1e-08
                 HHHTT--B--EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEESSHHHHHHHHHHHCTS-TTCCCCSSEEEEE-.--SEEEEEEEEECTTEEEE CS
      GARS_A  10 lkkagiptaeyeaftdpeeakeyieeatakalVvKadglaagKgvivakseeealkavkeilekkkfGeagekvviEel.leGeEvsllalvdgktvkp 107
                 l+k +i+ ++++af +  eak++ +++++++ +v+++ + +g  ++v+ s++e  k+vke  +     +  + vvi ++ l+  Ev +  +++g++v+ 
  EPA06306.1 221 LDKLHIQQPRWQAFANIVEAKSFAQDVGFPV-IVRPSYVLSGAAMKVVWSQDELKKYVKEATD----VSPDHPVVISKFmLNSLEVDVDGVCNGTDVII 314
                 57899**************************.9***************************997....45689999988647999**********99976 PP

                 -- CS
      GARS_A 108 lp 109
                  +
  EPA06306.1 315 GA 316
                 54 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   3.3e-06    0.0058      16     105 ..     126     214 ..     120     223 .. 0.86
   2 ?   -3.3   0.0       5.7     1e+04      90     114 ..     528     556 ..     506     557 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.3e-06
                 HHHH.TTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHHHHHHHHHHHTSSSEEE.EEESSGGGHHHH CS
      TrkA_N  16 eLse.ggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgddeanilavllakelnpkkkii.araqdpehaell 105
                  L+e g+k+v+v+  ++e+v +  +   + +  + t e +L+ a+ e+ +++++++g  +an l++ lak+   + +ii + a+d ++ae+ 
  EPA06306.1 126 GLQEnGEKNVSVVNCNPETVSTDYDICSRLYFEELTLERILDIAEFENPKGIVTCVGGQTANNLTLGLAKN---GVNIIgTSANDVDRAENR 214
                 578856689************************************************************96...456665778887777765 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 5.7
                 SEEEEEESSGGG....HHHHHHHTTSEEE CS
      TrkA_N  90 kkiiaraqdpeh....aellkklgadvvi 114
                 ++++ ++++p++    a+ll++  +d +i
  EPA06306.1 528 IEVVHKISEPQRkpniADLLYERKIDFII 556
                 56666666666655557777777777776 PP

>> ATP-grasp_4  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       4.9   8.8e+03     119     153 ..      75     110 ..      65     113 .. 0.68
   2 !   15.1   0.2   7.5e-06     0.013       2     150 ..     248     383 ..     247     388 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 4.9
  ATP-grasp_4 119 evnallglknfpvHiElrvsedg.kiipiEvnplrf 153
                  +v + l l+++  H  ++++ +   +i++   p r+
   EPA06306.1  75 AVTNYLYLTYGGHHHDIKINPEDkGVIVLGAGPYRI 110
                  566778888999999999875542455556666665 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 7.5e-06
  ATP-grasp_4   2 slPvviKPsvgffSlGVykinneeewkaavaaieeeleqakeeykeevveeesflvEeyieGeEfavdayfdeeGepvil.nilkkefaseedvsdrl 98 
                   +Pv+++Ps   +   + ++ +++e+k+ v++       ++   +++ v  ++f++       E+ vd+    +G+ vi+ +i+++  +   +  d +
   EPA06306.1 248 GFPVIVRPSYVLSGAAMKVVWSQDELKKYVKEAT----DVS---PDHPVVISKFMLN----SLEVDVDGVC--NGTDVIIgAIVEHIESAGVHSGDAM 332
                  6899999999999999999999999998555444....233...3333435677655....56******99..8999887478899888888888888 PP

  ATP-grasp_4  99 yvt.sakvieetlealeellkevnallglknfpvHiElrvsedgkiipiEvnp 150
                   ++ + ++ ++t+e+++e+ +++++ +++k +p+   + +++d ++++iE+n 
   EPA06306.1 333 MCIpPWRLNNKTIETITEYSTKIAKTFNVK-GPFNLQFLIHDD-HVYVIELNI 383
                  6551679********************996.9*********98.8******96 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   5.9e-06     0.011       2     158 ..     212     385 ..     211     388 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.9e-06
                  TSHHHHHHHHTTT.S---..........-EESS--.SSSEEEEESS-------B--SS--TTE................EEEE---SEEEEEEEEE.S CS
  ATP-grasp_3   2 sdKlktykkLkeagvkvP......tkleaeeleee.ekklvvKprdGaggesvrvveekeeaeaaieeve.........lvqefieGkplSvsllsdg 83 
                  ++  k+  +L++  ++ P      + +ea+++++    +++v p++   g ++ vv  ++e+++ ++e +         + + ++++ ++ v+ +++g
   EPA06306.1 212 ENRSKFSAELDKLHIQQPrwqafaNIVEAKSFAQDvGFPVIVRPSYVLSGAAMKVVWSQDELKKYVKEATdvspdhpvvISKFMLNSLEVDVDGVCNG 309
                  567778888999999999777665445555444334889***********99999999999999999888999*****66677789************ PP

                  SSEEEEEEEEEEEET....TEEEEEEES-..---HHHHHHHHHHHHHTTST...T--EEEEEEEEESS.SEEEEEEESS- CS
  ATP-grasp_3  84 ekvlvlavnrqliekaekefvyaGnvtpi..etelkeevvelaeevvekle...glaGyvGvDlvlkdeepyviEvNPRl 158
                   +v + a+ + +        v +G  +    + +l+++++e++ e   k+    +++G +   ++++d+  yviE N R 
   EPA06306.1 310 TDVIIGAIVEHIESA----GVHSGDAMMCipPWRLNNKTIETITEYSTKIAktfNVKGPFNLQFLIHDDHVYVIELNIRA 385
                  888887777666555....666665443311233466666666555555554449999999****************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (622 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.47
# Mc/sec: 3950.75
//
Query:       EPA06307.1  [L=83]
Description: hypothetical protein BG20_I1265 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.038   14.0   1.8       0.04   13.9   1.8    1.1  1  DUF327    Protein of unknown function (DUF327)


Domain annotation for each model (and alignments):
>> DUF327  Protein of unknown function (DUF327)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   1.8   2.2e-06      0.04      34      86 ..       2      53 ..       1      68 [. 0.83

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.2e-06
                HHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHH CS
      DUF327 34 eeeeseeelkelleeidkqgerLaesrtiedlkkYkklvkeflkevvknslkl 86
                ee++++  ++++ + i++ g  L  +++++ l+kYk+ vk+  + + + s+++
  EPA06307.1  2 EENKYNSLIEKIATMIENDGVSLD-EQNVQKLQKYKEHVKSNSNLTDDDSMEI 53
                5677888899999*********96.579************9888888877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1154  (0.064365); expected 358.6 (0.02)
Passed bias filter:                      622  (0.0346924); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 585.75
//
Query:       EPA06308.1  [L=126]
Description: hypothetical protein BG20_I1281 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.056   13.6   0.0      0.082   13.1   0.0    1.2  1  DUF2407_C  DUF2407 C-terminal domain


Domain annotation for each model (and alignments):
>> DUF2407_C  DUF2407 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   4.6e-06     0.082      72     118 ..      24      68 ..       7      73 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.6e-06
   DUF2407_C  72 geaakeeensvdseeskanedlliGlliGfflglfalllllkeegll 118
                   ++k+e++++ +++ +  +   iGl iG+f+g++   +++k+e ++
  EPA06308.1  24 MIDQKREHAEIYLDKVSNIQSKYIGLHIGLFWGIGT--FIIKNEDVI 68 
                 22333333778899999999999***********88..888877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       792  (0.0441742); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 785.12
//
Query:       EPA06309.1  [L=150]
Description: endoribonuclease L-PSP [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      7e-33  113.9   0.0    7.6e-33  113.7   0.0    1.0  1  YjgF_endoribonc  YjgF/chorismate_mutase-like, putative endori
    1.8e-21   76.4   0.0    2.2e-21   76.1   0.0    1.0  1  Ribonuc_L-PSP    Endoribonuclease L-PSP
  ------ inclusion threshold ------
      0.063   13.6   0.6       0.58   10.5   0.1    2.5  2  BON              BON domain
       0.17   11.9   0.0        0.3   11.1   0.0    1.4  1  MOEP19           KH-like RNA-binding domain
       0.22   10.3   0.0        0.3    9.9   0.0    1.1  1  DUF5382          Family of unknown function (DUF5382)


Domain annotation for each model (and alignments):
>> YjgF_endoribonc  YjgF/chorismate_mutase-like, putative endoribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.7   0.0   2.1e-36   7.6e-33       2     145 ..       4     146 ..       3     149 .. 0.93

  Alignments for each domain:
  == domain 1  score: 113.7 bits;  conditional E-value: 2.1e-36
                      HHHHHTT---------SSSS-SEEEETTEEEE--B--EETTEE--BS-BTTTB-HHHHHHHHHHHHHHHHHHHHHHHSSGGG-SEEEEEEEEE- CS
  YjgF_endoribonc   2 srlvalGlelpkvaaalGayepyaivasflttsfqlpylqekllyvGllGddvsvseGiaaarlaalnalaqlkeaaGelarvkrlirleGvln 95 
                       ++ ++G+++p ++   G+y p  + ++ l  s+q+p +++k+ + G++ d   ++    aa ++a+n laq+k+  G+l ++ r+++l G +n
       EPA06309.1   4 EKIKSIGIKIPIPPNPAGSYIPVVKSGNLLFVSGQIPMEDGKVVFTGKVSDA-NIETAKKAAIVCAVNILAQIKKEIGDLEKISRIVKLSGFVN 96 
                      567789******************************************9865.6778888999******************************* PP

                      B-TT---HHHHHHHHHHHHHHHHGGGG--EEEEEE-SS-GGGBSEEEEEE CS
  YjgF_endoribonc  96 vtqdyiempkvldaasdlllevlGeaGrhartiltnhvmplnalvllylf 145
                         ++ ++pkv++aasdll e++Ge+G+har++l+   +pln++  +   
       EPA06309.1  97 AVPEFTQHPKVINAASDLLYEIFGEKGKHARVALGVSSLPLNSMTEIDAI 146
                      *******************************************9876655 PP

>> Ribonuc_L-PSP  Endoribonuclease L-PSP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.1   0.0   6.2e-25   2.2e-21       5     120 ..      17     148 ..      15     149 .. 0.96

  Alignments for each domain:
  == domain 1  score: 76.1 bits;  conditional E-value: 6.2e-25
                    TTTSSS-BSEEEETTEEEEEEE-SB-T....TTSCB.-SSHHHHHHHHHHHHHHHHHHTT--GGG......EEEEEEEESSGGGHHHHHHHHHHHS CS
  Ribonuc_L-PSP   5 paaaapYsqavkagnlvyvsGqlpldp....etgelvegdveeqtrqalenlkavLaaagaslsd......vVkvtvFladiedfaevnevyaeaf 90 
                    p++a++Y ++vk+gnl++vsGq+p+++     tg++ ++++e  +++a+ ++ ++La++  +++d      +Vk++ F++ +++f++  +v++ a+
     EPA06309.1  17 PNPAGSYIPVVKSGNLLFVSGQIPMEDgkvvFTGKVSDANIETAKKAAIVCAVNILAQIKKEIGDlekisrIVKLSGFVNAVPEFTQHPKVINAAS 112
                    789***********************999999******************************999999**************************** PP

                    SSS......TS--EEEEEE-SBSGGG-SEEEEEEEE CS
  Ribonuc_L-PSP  91 del......keaParsaveVaaLpkgakvEIeaiav 120
                    d l      k+ +ar+a +V++Lp +   EI+ai++
     EPA06309.1 113 DLLyeifgeKGKHARVALGVSSLPLNSMTEIDAIVE 148
                    **9999995489**********************98 PP

>> BON  BON domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00016      0.58      29      52 ..      42      64 ..      38      69 .. 0.93
   2 ?    0.5   0.0      0.21   7.7e+02      32      40 ..      88      96 ..      70     112 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00016
                ETTCEEEECEEECHHHHHHHHHHH CS
         BON 29 enGvVtLsGtVdseaekekAveia 52
                e+G+V+ +G V s+a +e+A ++a
  EPA06309.1 42 EDGKVVFTGKV-SDANIETAKKAA 64
                79*********.*********998 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.21
                CEEEECEEE CS
         BON 32 vVtLsGtVd 40
                 V LsG+V+
  EPA06309.1 88 IVKLSGFVN 96
                488888885 PP

>> MOEP19  KH-like RNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   8.3e-05       0.3       7      34 ..      98     125 ..      94     135 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 8.3e-05
      MOEP19   7 vveeLkdPlvfyleawlleaiFGpdger 34 
                 v+e+ ++P+v++  ++ll  iFG++g++
  EPA06309.1  98 VPEFTQHPKVINAASDLLYEIFGEKGKH 125
                 678889*******************998 PP

>> DUF5382  Family of unknown function (DUF5382)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   8.5e-05       0.3     369     412 ..      51      96 ..      45      99 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 8.5e-05
     DUF5382 369 vvievrvrnleeaefiyavtillsradeiqeqrrvd..vkfkgyke 412
                 +v++++++++++a +++av+il +  +ei + +++   vk++g+ +
  EPA06309.1  51 KVSDANIETAKKAAIVCAVNILAQIKKEIGDLEKISriVKLSGFVN 96 
                 7999*********************999998887755589999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1150.46
//
Query:       EPA06310.1  [L=389]
Description: sugar-specific transcriptional regulator TrmB [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.8e-17   61.3   0.3      1e-15   57.3   0.2    2.4  2  TrmB      Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.041   13.9   0.4      0.041   13.9   0.4    2.3  2  DUF327    Protein of unknown function (DUF327)
       0.18   11.6   0.0       0.56   10.1   0.0    1.8  1  HTH_IclR  IclR helix-turn-helix domain


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.3   0.2   1.7e-19     1e-15       1      68 []      14      81 ..      14      81 .. 0.97
   2 ?    1.3   0.0     0.055   3.3e+02      24      51 ..     251     278 ..     234     285 .. 0.83

  Alignments for each domain:
  == domain 1  score: 57.3 bits;  conditional E-value: 1.7e-19
                HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE--HH CS
        TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravdpe 68
                L+++GLs+yEa++Y+aL+++g  +a e+a  +++pr+kvY +L +Le+k lV ++k++p +  a+ pe
  EPA06310.1 14 LEEFGLSKYEAQAYVALISKGTISAGELAYYSDLPRTKVYPTLLKLENKKLVIISKSKPIMCTAIAPE 81
                789*********************************************************99999886 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.055
                 HHCHHCCCTTSSCHCHHHHHHHHHHCTS CS
        TrmB  24 tadeiaeelgvprskvYevLrsLedkGl 51 
                 +++ +a +++ + + +Y+++r   + Gl
  EPA06310.1 251 KTESLADMTKNEAQEIYKIIRIINEYGL 278
                 6788999999999******999888887 PP

>> DUF327  Protein of unknown function (DUF327)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.6     0.069   4.1e+02      77     129 ..      99     149 ..      90     152 .. 0.66
   2 ?   13.9   0.4   6.8e-06     0.041      78     133 ..     244     300 ..     239     303 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.069
                 HHHHHHHHHHHT..-----H.HHHHHHHHHHHHHHHHHHHHHHHTTSTTCHHHH CS
      DUF327  77 kevvknslklkkersldrkg.rsrvykivkeiDekldeLteellkeekealdil 129
                 + +++n  k ++e s + +g +++ y  v+  ++ l++L   +++  k++++i+
  EPA06310.1  99 NTLISNLKKASEE-SRKSRGsEEKRYFHVSA-NNVLEQLK-TMIEGSKQSINIT 149
                 5555555555554.45555558888988875.77788875.4567777777776 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 6.8e-06
                 HHHHHHHHHHT..-----HHHHHHHHHHHHHH.HHHHHHHHHHTTSTTCHHHHHHHH CS
      DUF327  78 evvknslklkkersldrkgrsrvykivkeiDe.kldeLteellkeekealdilakid 133
                 ++ kn++k ++   +++++ +++yki+++i+e  l  + +++++++k  ld+l+ ++
  EPA06310.1 244 DIWKNAIKTESLADMTKNEAQEIYKIIRIINEyGLTHILNSIIESKKPDLDMLKLLE 300
                 6789999999999999999************956*******************9765 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   9.3e-05      0.56      19      48 ..      36      65 ..      31      65 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 9.3e-05
                -BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
    HTH_IclR 19 ltlselArrtglpkStvhRlLqtLvelGyv 48
                 +  elA  ++lp+++v+  L  L++ ++v
  EPA06310.1 36 ISAGELAYYSDLPRTKVYPTLLKLENKKLV 65
                5789*********************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1148  (0.0640303); expected 358.6 (0.02)
Passed bias filter:                      606  (0.0338); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2783.09
//
Query:       EPA06311.1  [L=97]
Description: hypothetical protein BG20_I1263 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    8.2e-14   51.7   0.0    9.2e-14   51.5   0.0    1.0  1  ATP-synt_F  ATP synthase (F/14-kDa) subunit
    0.00046   19.1   0.0    0.00048   19.1   0.0    1.0  1  Trp_syntA   Tryptophan synthase alpha chain
  ------ inclusion threshold ------
      0.056   13.2   0.0      0.056   13.2   0.0    1.1  1  LUD_dom     LUD domain


Domain annotation for each model (and alignments):
>> ATP-synt_F  ATP synthase (F/14-kDa) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.5   0.0   1.5e-17   9.2e-14       1      80 [.       3      82 ..       3      93 .. 0.93

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 1.5e-17
                EEEEESHHHHHHHHHTTCEEEECSSHHHHHHHHHHHHHHTTEEEEEEEHHHHCCCHHHHHHCTCSSSSEEEEESCSCCGG CS
  ATP-synt_F  1 iavIGdedtvtgfrlaGvgevevtdeeeieealkelleredigiilitekiaeeirelideykeealPaileIPskegpy 80
                i  +G++ +vt f+laGv ++ +++++e+ + +k+l++++d+g++l+++++ e i +++ e++ e+  ++  +Ps +++ 
  EPA06311.1  3 IFTVGSKSFVTSFQLAGVPGIISDTPKEALDEIKKLTDDSDVGLVLVSDDMTESIGDELTELRAEKSTLVFALPSAGSEK 82
                6789***********************************************************************98844 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   8.1e-08   0.00048      99     175 ..       3      80 ..       1      95 [. 0.83

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 8.1e-08
                 HCCC-HHHHCHHHHHCTEEEEEETTSBCCCHHHHHHHHHHTT-EEEEEE-TTS-..HHHHHHHHHH--S-EEEESTTC- CS
   Trp_syntA  99 vlsygeerflaelkeagvdglivpDlPleeaeelveaakkkglelvflvaptts..derlkevveqaegfvYvvsraGv 175
                 ++++g  +f+ +++ agv g i+ D P+e+ +e++++ ++ ++ lv +    t+  ++ l+e+ ++ +  v+++ +aG 
  EPA06311.1   3 IFTVGSKSFVTSFQLAGVPG-IISDTPKEALDEIKKLTDDSDVGLVLVSDDMTEsiGDELTELRAEKSTLVFALPSAGS 80 
                 8999****************.68**********************9887765542257888888888888888888875 PP

>> LUD_dom  LUD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   9.4e-06     0.056       4      56 ..      11      63 ..       8      92 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.4e-06
     LUD_dom  4 fienleangaevyyaktaeealelilellkeksvvseggstdlgeiglapalh 56
                f+++++  g+  ++ +t +eal+ i++l ++ +v+++ +s d+ e + +++ +
  EPA06311.1 11 FVTSFQLAGVPGIISDTPKEALDEIKKLTDDSDVGLVLVSDDMTESIGDELTE 63
                788888999999999****************************8877644444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.34u 0.27s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 731.40
//
Query:       EPA06312.1  [L=102]
Description: hypothetical protein BG20_I1264 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.015   15.1   0.0      0.028   14.2   0.0    1.4  1  UBA_3       Fungal ubiquitin-associated domain
      0.038   12.8   0.0      0.039   12.8   0.0    1.0  1  Herpes_U55  Human herpesvirus U55 protein


Domain annotation for each model (and alignments):
>> UBA_3  Fungal ubiquitin-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   3.1e-06     0.028      10      30 ..      25      45 ..      19      48 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.1e-06
                HHHHHHHHHHT--HHHHHHHH CS
       UBA_3 10 rdlVdefvsqGFekdkvievL 30
                + + + +vs+GF kdk+i +L
  EPA06312.1 25 EKATNALVSKGFSKDKIIMAL 45
                5567789***********998 PP

>> Herpes_U55  Human herpesvirus U55 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   4.3e-06     0.039     265     344 ..       7      86 ..       1      98 [. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.3e-06
  Herpes_U55 265 cedkkklevffpedmllvenetkkitlrGtfenkkavglfiPkks.svlklfpflWspreslklkvsc.erevsvtehDiiG 344
                  + +k++ +f   +m l+e  t+ +  +G  ++k + +l  P k  +v + +++lW+p ++ ++k++   +   v  + ++G
  EPA06312.1   7 IDTQKNIYLFTHGRMDLQEKATNALVSKGFSKDKIIMAL--PSKVgNVGDYMAMLWMPPTPDHIKIQHiTKVEEVKPEGMVG 86 
                 345799***********************7777777765..766516667889***********997514444566666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 790.28
//
Query:       EPA06313.1  [L=65]
Description: hypothetical protein BG20_I1278 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 503.91
//
Query:       EPA06314.1  [L=328]
Description: carbamoyl-phosphate synthase L chain, ATP binding domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-72  241.5   0.2    7.9e-72  241.2   0.2    1.1  1  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
    2.1e-07   31.3   0.0    5.2e-07   30.0   0.0    1.7  1  CPSase_L_D3      Carbamoyl-phosphate synthetase large chain, 
      1e-06   28.4   0.2    1.5e-06   27.9   0.2    1.2  1  ATP-grasp        ATP-grasp domain
    3.7e-06   26.6   0.2    6.6e-06   25.8   0.2    1.4  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
     0.0042   16.8   0.0     0.0078   16.0   0.0    1.4  1  ATPgrasp_Ter     ATP-grasp in the biosynthetic pathway with T
     0.0084   15.9   0.1      0.014   15.1   0.1    1.4  1  GARS_A           Phosphoribosylglycinamide synthetase, ATP-gr
  ------ inclusion threshold ------
       0.03   13.9   0.4      0.083   12.4   0.1    1.9  3  ATP-grasp_2      ATP-grasp domain
        0.1   12.1   0.0       0.18   11.2   0.0    1.4  1  ATP-grasp_5      ATP-grasp domain


Domain annotation for each model (and alignments):
>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  241.2   0.2   3.5e-75   7.9e-72       9     210 ..       1     198 [.       1     199 [. 0.98

  Alignments for each domain:
  == domain 1  score: 241.2 bits;  conditional E-value: 3.5e-75
                  HHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHHSTS-EEEEE--SSSEEEEEEEEEETTS- CS
  CPSase_L_D2   9 lkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaafgnkqvlvekslkgpkeiEvevlrDakgn 106
                  +++ nvpv +s ++  ++  +a +ia+e+gyPvii+ a++lGGkG++va+ne el+e+v+++l+++       qvlve+++ ++k+iE+ev++D  gn
   EPA06314.1   1 MNQCNVPVLKSRTV--KNFSDAKEIAEELGYPVIIRVAYTLGGKGGGVAYNEIELHEIVERGLRASL----VGQVLVEEYIGHWKQIEYEVMQDYGGN 92 
                  7899*******999..**************************************************6....89************************* PP

                  EEEEEEEEECCEC..TCCCCEEEES-SS--HHHHHHHHHHHHHHHHHHT-EEEEEEEEEEETTTTEEEEEEEESS--CCHHHHHHHHS--HHHHHHHH CS
  CPSase_L_D2 107 vitvcerenslql..rtqkvievAPsqtLtdeerqalreaavkvvrevgvvgagtveflldpkskeyyviEvNtRlsvesalaekaTGldlvkeaaki 202
                   ++vc++en+l +  +t++ i+vAPsqt++++e+++lr+aa++++++vg+vg+++++++ld+ s++y+ iE+N+Rls++sala+kaTG++l++++aki
   EPA06314.1  93 NVIVCNMENVLSMkvHTGDNIVVAPSQTIDNHEYHMLRTAALRATKHVGIVGECNIQYALDSVSDRYVAIEINPRLSRSSALASKATGYPLAYMSAKI 190
                  **********99999*********************************************************************************** PP

                  HTT--GCG CS
  CPSase_L_D2 203 algekLee 210
                  +lg++L+e
   EPA06314.1 191 GLGYTLPE 198
                  ******97 PP

>> CPSase_L_D3  Carbamoyl-phosphate synthetase large chain, oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.0   2.3e-10   5.2e-07       3      40 ..     291     328 .]     289     328 .] 0.95

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 2.3e-10
  CPSase_L_D3   3 lkeptdeRifaiaealrrglsveeiheltkidpwFLek 40 
                  l++p+d  ++++a al+ g+sve+i++l+ idpwF+ek
   EPA06314.1 291 LSHPNDLILYYVAAALKMGISVEKIYKLSAIDPWFIEK 328
                  7899*******************************986 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.2   6.9e-10   1.5e-06       2     146 ..       2     153 ..       1     173 [. 0.78

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 6.9e-10
                 HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC....GTTCEEEEE----SEEEEEEEEEETTC-EEE--EE CS
   ATP-grasp   2 eklglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal....keekvivEefvpfekElsvlvvrsaeGetafypvv 96 
                 ++ ++pv +  +v++ ++++e+aeelg+pv+++       GkG  v  +e +l++++e        ++v+vEe++   k +   v+++  G+ +++  +
  EPA06314.1   2 NQCNVPVLKSRTVKNFSDAKEIAEELGYPVIIR-VAYTLGGKGGGVAYNEIELHEIVERGlrasLVGQVLVEEYIGHWKQIEYEVMQDYGGNNVIVCNM 99 
                 578999***************************.899999************999998877776789************************97777666 PP

                 EEEEETTEE...EEEEECEE-SCH.HHHHHHHHHHHHHHHHTSSEEEEEEEEEE CS
   ATP-grasp  97 etvqedgil...rlsvapaevsek.aqkkaeeiakkiveeLggvGvfavElFvl 146
                 e+v + ++    +++vap++  ++ + +  ++ a ++++++g+vG   +   + 
  EPA06314.1 100 ENVLSMKVHtgdNIVVAPSQTIDNhEYHMLRTAALRATKHVGIVGECNIQYALD 153
                 66655544422257788877666515555566666*********9777765554 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.2   2.9e-09   6.6e-06      21     174 ..      15     166 ..       1     177 [. 0.78

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 2.9e-09
                      CH-H-HHHHHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHTT-..SCEEEEE--.ESEEEEEEEEE..TSSCEEEEEEEEE-SSS CS
  Dala_Dala_lig_C  21 keekkellekveeelgypvfVKpareGSSvGvskveseeelkeaieeafkyd..ekvlvEeai.egreievavlg..neklevsevgeivvkkg 109
                      k+ +    +++ eelgypv+++ a +    G   + +e el+e +e+ ++     +vlvEe+i + ++ie  v++   +++ +    e v++  
       EPA06314.1  15 KNFS--DAKEIAEELGYPVIIRVAYTLGGKGGGVAYNEIELHEIVERGLRASlvGQVLVEEYIgHWKQIEYEVMQdyGGNNVIVCNMENVLSM- 105
                      3333..57899************9887777888899***********988763379*******999********9322333333333333333. PP

                      SS-HHHHH.C.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEET.TTEEEEEEEES CS
  Dala_Dala_lig_C 110 fydyeaky.sddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDfflte.egeivlnEvNt 174
                            k  ++d++ +    ++++++++ ++++al+a k +++ G + + + l++ +++ v  E+N+
       EPA06314.1 106 ------KVhTGDNIVVAPSQTIDNHEYHMLRTAALRATKHVGIVGECNIQYALDSvSDRYVAIEINP 166
                      ......331568899999999********************************65266777789985 PP

>> ATPgrasp_Ter  ATP-grasp in the biosynthetic pathway with Ter operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   3.5e-06    0.0078      49     120 ..     129     203 ..     116     212 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.5e-06
  ATPgrasp_Ter  49 lielaerlaeefgldglvnvQvrededg..pkLLEiNpRasGGlg.ysalaGvnlpylalklllgleteeveepe 120
                   l  +a r ++++g+ g  n+Q+  d     ++ +EiNpR s      s ++G  l+y+++k  lg   +e ++  
    EPA06314.1 129 LRTAALRATKHVGIVGECNIQYALDSVSdrYVAIEINPRLSRSSAlASKATGYPLAYMSAKIGLGYTLPELVNRI 203
                   456788999*************99975445999*******96555156777**********99998666655554 PP

>> GARS_A  Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   6.4e-06     0.014      10      89 ..       1      75 [.       1     103 [. 0.92

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 6.4e-06
                HHHTT--B--EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEESSHHHHHHHHHHHCTS-TTCCCCSSEEEEE-- CS
      GARS_A 10 lkkagiptaeyeaftdpeeakeyieeatakalVvKadglaagKgvivakseeealkavkeilekkkfGeagekvviEell 89
                ++++++p  + +++++ ++ake+ ee++ ++ +++ +   +gKg  va +e e  ++v+  l+    G    +v++Ee++
  EPA06314.1  1 MNQCNVPVLKSRTVKNFSDAKEIAEELGYPV-IIRVAYTLGGKGGGVAYNEIELHEIVERGLRASLVG----QVLVEEYI 75
                7899***************************.999999999*********************999999....99999987 PP

>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   3.7e-05     0.083      12      81 ..       2      66 ..       1      86 [. 0.78
   2 ?   -3.3   0.0       2.5   5.6e+03      98     115 ..     149     166 ..     115     181 .. 0.58
   3 ?   -2.2   0.0       1.1   2.5e+03      67     110 ..     249     292 ..     240     315 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.7e-05
                 HCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE--SSSTCCCTTCEEEESSHHHHHHHHHCCTTSEEE CS
  ATP-grasp_2 12 akygvkvpegevaesaeeaeeaakklgekelvvKaQvlaGGRGKagGvklvkskeeakeaakellgkelv 81
                 ++ +v+v +++ +++  +a+e+a++lg  + +++     G  GK+gGv +   + e++e++++ l ++lv
   EPA06314.1  2 NQCNVPVLKSRTVKNFSDAKEIAEELGYPV-IIRVAYTLG--GKGGGVAYN--EIELHEIVERGLRASLV 66
                 6789************************99.898888888..578999654..55666666665555555 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.5
                  EE---ECEEEEEEEEEET CS
  ATP-grasp_2  98 eealdikkElYlsivlDr 115
                  + ald   + Y++i +  
   EPA06314.1 149 QYALDSVSDRYVAIEINP 166
                  444444444444444444 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.1
                  HHHHHHHCCTTSEEE-TTS-TT-EEE--EEEEE---ECEEEEEE CS
  ATP-grasp_2  67 eakeaakellgkelvtkqtgkeGkkvekvlveealdikkElYls 110
                   + +  +e l k ++    g++G   ++v  e+ ++ + E +ls
   EPA06314.1 249 AVGRSFEESLQKAIRMLDIGNDGLVLNRVTHESYTEEQIEDFLS 292
                  55566677888888888888999999988887777766666665 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   8.2e-05      0.18      21      54 ..       3      36 ..       1      39 [. 0.92

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 8.2e-05
  ATP-grasp_5 21 aygipvvetrlassaeeaveaaeeigypvvlKiv 54
                 + ++pv+++r +++  +a e+aee+gypv ++++
   EPA06314.1  3 QCNVPVLKSRTVKNFSDAKEIAEELGYPVIIRVA 36
                 5789**************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2423.42
//
Query:       EPA06315.1  [L=206]
Description: GroES-like protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      6e-24   84.0   2.2    9.7e-24   83.4   1.9    1.5  2  ADH_N        Alcohol dehydrogenase GroES-like domain
  ------ inclusion threshold ------
       0.03   13.8   0.0      0.047   13.2   0.0    1.2  1  Glu_dehyd_C  Glucose dehydrogenase C-terminus


Domain annotation for each model (and alignments):
>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.4   1.9   1.1e-27   9.7e-24       2     101 ..      25     121 ..      24     133 .. 0.91
   2 ?   -1.9   0.0      0.33     3e+03      52      61 ..     154     168 ..     119     185 .. 0.64

  Alignments for each domain:
  == domain 1  score: 83.4 bits;  conditional E-value: 1.1e-27
                 TEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHTT-GGG-TTBEETTTSS-SSSBSEEE CS
       ADH_N   2 gevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCkegeenlCeeakllgvsldGgfaeyvv 100
                 ge+li+++a+giCgsDl+ + g      ++ + lGHE +G++++v ++v+++k+GdrV+ +++++c +C+ Ck+g+e++C+++  +++s  G   eyvv
  EPA06315.1  25 GEILIQMQACGICGSDLEKVFG---EYGQPSMRLGHEPAGIIVDVSSDVSSFKKGDRVFTHHHVPCYSCHLCKHGNETMCPKYYETNLSPCGLSEEYVV 120
                 79******************99...46777789*****************************************************9998888888876 PP

                 E CS
       ADH_N 101 v 101
                  
  EPA06315.1 121 P 121
                 4 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.33
                 S.....--TT-EEEE CS
       ADH_N  52 k.....lkvGdrVvv 61 
                       ++ Gd V++
  EPA06315.1 154 AwtkysYQEGDSVAI 168
                 333344666777666 PP

>> Glu_dehyd_C  Glucose dehydrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   5.2e-06     0.047       7      67 ..     145     197 ..     140     201 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.2e-06
  Glu_dehyd_C   7 vEPisiveKaielaeasrsafewepesalvlGaGslGLLalalleaeerglervyvlgrrd 67 
                  +EP++   +a+ +          e +s+ + G G+ G++  ++l+ ++++++++++++ +d
   EPA06315.1 145 IEPLACCVRAWTKYS------YQEGDSVAIFGVGPTGMMH-VMLA-QSKKFSKIFCFDVND 197
                  666666666664432......345789************9.5665.4799******99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1569.14
//
Query:       EPA06316.1  [L=360]
Description: carbamoyl-phosphate synthase, small subunit [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-43  146.9   0.0    1.2e-42  144.7   0.0    2.0  2  CPSase_sm_chain  Carbamoyl-phosphate synthase small chain, CP
      7e-43  146.6   0.1      1e-42  146.1   0.1    1.2  1  GATase           Glutamine amidotransferase class-I
    7.7e-08   32.3   0.3    5.4e-06   26.3   0.3    2.3  1  Peptidase_C26    Peptidase C26
  ------ inclusion threshold ------
       0.18   11.7   0.0       0.34   10.9   0.0    1.5  1  Thump_like       THUMP domain-like


Domain annotation for each model (and alignments):
>> CPSase_sm_chain  Carbamoyl-phosphate synthase small chain, CPSase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.7   0.0   2.8e-46   1.2e-42      17     127 ..       3     124 ..       1     125 [. 0.89
   2 ?   -1.4   0.0      0.43   1.9e+03      69     105 ..     206     242 ..     190     244 .. 0.82

  Alignments for each domain:
  == domain 1  score: 144.7 bits;  conditional E-value: 2.8e-46
  CPSase_sm_chain  17 fg.akeavGEvvfnTgmtGYqeiltDpsYagqilvltypliGnyGv..........needvesekikvaglvvrelseepsnwraeesLsewlk 99 
                      fg  ++++GE+vfnTgm+GY+e+ltDpsY+gqil++typl+GnyGv            + +es+ki+++glvv+els ++s+w+ +++L+ewl 
       EPA06316.1   3 FGyPTTVFGEIVFNTGMVGYTETLTDPSYSGQILTITYPLVGNYGVpdpsikdkdgIPKFFESDKIQLRGLVVHELSLTASHWNLSMTLDEWLY 96 
                      7745889***************************************66655544443344555******************************* PP

  CPSase_sm_chain 100 eekipgisgvDTRaLtkklrekgamkgv 127
                      +ekipgisg+DTR+Ltk+lr+ g+++++
       EPA06316.1  97 KEKIPGISGIDTRELTKNLRTGGVKMAA 124
                      ***********************99876 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.43
  CPSase_sm_chain  69 ekikvaglvvrelseepsnwraeesLsewlkeekipg 105
                       + + +g+v+++   +p++ + + + ++ l ++++p 
       EPA06316.1 206 MSYHPKGVVISNGPGDPQKCSETIETARKLIDKNVPT 242
                      4678899999999999999999999999999988886 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.1   0.1   2.3e-46     1e-42       2     188 ..     173     349 ..     172     351 .. 0.96

  Alignments for each domain:
  == domain 1  score: 146.1 bits;  conditional E-value: 2.3e-46
                 EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT.TTTHHHHHHHHCTSTS-EEEETHHHHHHHHHTTTEEEEEECEE CS
      GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg.vegkieaikearenkiPiLGICLGmQllaiefgrkvvkekeke 99 
                 +iD +   +++++++++elg+kv  +p+++++e+i+    +p+g+++s+Gpg+p+ + ++ie++++++++++P LGICLG Q+++++   +++k k ++
  EPA06316.1 173 VIDTG--TKNAILRNIRELGYKVIRLPWNTTFEKIM--SYHPKGVVISNGPGDPQkCSETIETARKLIDKNVPTLGICLGAQIIGLAGNTETYKLK-YG 266
                 78888..99**************************6..699*******************************************************.** PP

                 EEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEEEEEEETTTEEEESSBTTSTTSTTHHHHHHHHHH CS
      GATase 100 hhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeelmeiiekknpfvgvQFHPEststpegpellfnfli 188
                 h+g++  + +     l+++ +++ ++++H+y ++p++l  +++   ++++dd+++++i +kk++ ++vQFHPE+ ++p + +++f++l 
  EPA06316.1 267 HRGQNKSCVN-----LEND-QVYVTSQNHGYGITPESLKASEFNLWFTNADDKTVEGIKHKKQNCIAVQFHPEAAPGPYDCKFVFEELK 349
                 **********.....6666.***************9999999*******************************************9875 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.3   1.2e-09   5.4e-06      84     216 .]     218     333 ..     208     333 .. 0.73

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 1.2e-09
  Peptidase_C26  84 eeadpeRdalelaLiraalergvPilgiCrGlqllnvalGGtlyq.dieeqsgltdhreheqsaashavkvekgsllaellgseeievnslHhqai 178
                    ++ dp+  + ++   r+ ++++vP lgiC+G q++  a  G++ + +++       hr ++    +  v++e+++++    +         H  +i
     EPA06316.1 218 GPGDPQKCSETIETARKLIDKNVPTLGICLGAQIIGLA--GNTETyKLK-----YGHRGQN----KSCVNLENDQVYVTSQN---------HGYGI 293
                    55566666677888999******************444..443320233.....4565555....44599999887766555.........88888 PP

  Peptidase_C26 179 ke...laeelrveAvae.DgviEaieseeakafvlgvQwHPE 216
                    +     a+e++   + + D ++E i++++++   ++vQ+HPE
     EPA06316.1 294 TPeslKASEFNLWFTNAdDKTVEGIKHKKQN--CIAVQFHPE 333
                    7666567888876554449********9955..9*******9 PP

>> Thump_like  THUMP domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   7.7e-05      0.34      12      51 ..     106     145 ..      99     180 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 7.7e-05
  Thump_like  12 fskkklkkllrergigkanikkRgfpldpeeLrkklklkd 51 
                  ++++l k lr+ g++ a + + ++ +++ e++k+l l  
  EPA06316.1 106 IDTRELTKNLRTGGVKMAALAVSDTEINVNEIKKQLALAP 145
                 57899*******************************9974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2658.03
//
Query:       EPA06317.1  [L=76]
Description: hypothetical protein BG20_I1282, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 564.55
//
Query:       EPA06318.1  [L=353]
Description: DHHA1 domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-16   59.6   0.4    4.3e-16   59.6   0.4    2.2  3  DHHA1     DHHA1 domain
    0.00024   21.3   1.8    0.00048   20.3   1.4    1.7  2  DHH       DHH family
  ------ inclusion threshold ------
      0.074   13.0   0.0       0.15   12.0   0.0    1.4  1  HD_3      HD domain


Domain annotation for each model (and alignments):
>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.82   4.9e+03      34      50 ..      23      40 ..       3      55 .. 0.39
   2 ?   -2.3   0.0       0.9   5.4e+03      30      57 ..     103     125 ..      87     144 .. 0.55
   3 !   59.6   0.4   7.3e-20   4.3e-16      39     136 ..     252     349 ..     218     351 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.82
                CEEEC..TCEEEEEECHCC CS
       DHHA1 34 aeevk..gvkvlvaevgee 50
                 ++++  ++ v+++++ e+
  EPA06318.1 23 PTKTNprTKVVCISHK-ED 40
                2223332222222222.22 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.9
                 HHHTCEEECTCEEEEEECHCCHHHHHHH CS
       DHHA1  30 llekaeevkgvkvlvaevgeewdagalg 57 
                 +l+k     ++ +++  +++++d+++++
  EPA06318.1 103 ILKK-----NHVTVTYIDHHDIDPKIVK 125
                 2222.....4444444444666666655 PP

  == domain 3  score: 59.6 bits;  conditional E-value: 7.3e-20
                 TCEEEEEECHCCHHHHHHHHHHHHHHTHGBT.TCEEEEEEEECT..EEEEEEEESSH.SS-HHHHHHHHHHHTTCCEEEETCEEEEEEEHCHHHHHHHH CS
       DHHA1  39 gvkvlvaevgeewdagalgiaadklksklkk.pvivfvakeegd..kvkvsarskkd.gvdagelakeaaaklgggGGGHdlAaGagipaekleealea 133
                 ++   + ++ e +d     +a++ ++    + + + +++ke+ d   ++vs+r +k+ ++++g++++ +a++lgg+GGGHd A+Ga ip+ k++ +l++
  EPA06318.1 252 KTMKNIGYM-EIMDS-GASGAVNFVLG--LSgKDVGVAYKERVDhgIYAVSVRGSKScKIHLGKIVNLLATELGGSGGGHDKACGAVIPKPKIQTFLKE 346
                 444445555.44444.44567888899..888999******9999**********99****************************************** PP

                 HHH CS
       DHHA1 134 lee 136
                 +++
  EPA06318.1 347 FNK 349
                 997 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   1.4   8.1e-08   0.00048       5      93 ..      34     161 ..      31     173 .. 0.70
   2 ?   -3.0   0.0       1.5   9.1e+03      26      35 ..     290     299 ..     231     307 .. 0.67

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 8.1e-08
                 E-ECSSSHHHHHHHHHHHH..............................CECS--TCGGCGCCH......HCCCSEEEEEEE-S---S....S---SS- CS
                 xxxxxxxxxxxxxxxxxxx..............................xxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxx....xxxxxxx RF
         DHH   5 vghknpDtDsigSaialan..............................llvDhneksqavege......akeeaedviiiDHHrlge....efetlap 63 
                 +  ++ D+D+i Sa ++++                               ++D + +++ +++       +k++ ++v  iDHH +      ++e++ +
  EPA06318.1  34 CISHKEDADGISSAALIRQafggdsilvdypgqmeaiqkvstdeklkslYICDLGLSKKNQDEFvellriLKKNHVTVTYIDHHDIDPkivkDLEKI-K 131
                 335667*******99999978888866666666666666555555555558888877777777699***9****************87888766666.4 PP

                 -EEEE-SSS-HHHHHHHHHHHTT----HHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
         DHH  64 ilflnepvgstaeivaelleekkeeiskei 93 
                 + +++    +t   v++ ++ k ++  + i
  EPA06318.1 132 VKMIHDINECTTVQVYNAFKSKLSDHAPFI 161
                 555666666777777777766554444444 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.5
                 CS--TCGGCG CS
                 xxxxxxxxxx RF
         DHH  26 vDhneksqav 35 
                 vDh++ + +v
  EPA06318.1 290 VDHGIYAVSV 299
                 6666666555 PP

>> HD_3  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.5e-05      0.15      65     149 ..      56     154 ..      53     166 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.5e-05
        HD_3  65 gDiispd...elak.eekeeeekeaaerilkl.lpeelaeellalwe.........EFeeretkeakfakdlDklepllqalekegdslaafeaklsqv 149
                 gD i +d   +++  ++ + +ek    +i+ l l+++ ++e+ +l+           + + ++ + k++kdl+k+++++ + ++e+ + + ++a+ s+ 
  EPA06318.1  56 GDSILVDypgQMEAiQKVSTDEKLKSLYICDLgLSKKNQDEFVELLRilkknhvtvTYIDHHDIDPKIVKDLEKIKVKMIHDINECTTVQVYNAFKSKL 154
                 67777776654333034455666667788888999999*********999**************************************99998888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       785  (0.0437838); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2211.61
//
Query:       EPA06319.1  [L=92]
Description: putative fructose-bisphosphate aldolase, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-06   28.3   0.0    1.5e-06   28.0   0.0    1.1  1  DeoC      DeoC/LacD family aldolase
     0.0084   15.4   0.1     0.0097   15.2   0.1    1.0  1  ThiG      Thiazole biosynthesis protein ThiG
  ------ inclusion threshold ------
      0.054   12.7   0.0       0.06   12.5   0.0    1.1  1  DUF561    Protein of unknown function (DUF561)


Domain annotation for each model (and alignments):
>> DeoC  DeoC/LacD family aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   2.5e-10   1.5e-06     180     235 .]       3      58 ..       1      58 [. 0.89

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 2.5e-10
                 HHHHHHHHHHHHHCHSSTEEEEETTS..SHHHHHHHHHHHHHHHTHCEEEESHHHHTT CS
        DeoC 180 teedaevfkdvikaapvpgvvlsGGv..seedfletvedAvkeagasGvlsGRaifqk 235
                 +++ +++f++v++++pvp ++++GG    e+d l+    A+ + ga Gv +GR+i+q+
  EPA06319.1   3 RPTIVRTFEKVVQSCPVP-IIVAGGKkiPERDALQLTFNAI-KGGAVGVDMGRNIWQS 58 
                 577899************.******9887788887777888.**************95 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   1.6e-06    0.0097     167     229 ..      10      77 ..       4      89 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.6e-06
                 HHHHHHH-SS-BEEES---SHHHHH.....HHHHTT-SEEEESHHHHTSSSHHHHHHHHHHHHHHHHH CS
        ThiG 167 lkiiieeakvPvivDAGigspsdaa.....qamelGadavllntavaeakdpvamArafklaveaGrl 229
                 ++ +++++ vP+iv  G   p+  a     +a++ Ga +v +   + ++++pvam ra++  v+   +
  EPA06319.1  10 FEKVVQSCPVPIIVAGGKKIPERDAlqltfNAIKGGAVGVDMGRNIWQSDNPVAMIRAVRSIVHGNAT 77 
                 567889999********999975431222268999************************998876555 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     1e-05      0.06     173     234 ..       4      72 ..       1      81 [. 0.75

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1e-05
      DUF561 173 stlasty.eiskkvslPvicasGlsd...vtvpl...alslgasGiGigsavsklndeeemvallseik 234
                 +t+  t+ +++++  +P+i a G +     + +l   a++ ga G+ +g+++ + ++ ++m+ +++ i 
  EPA06319.1   4 PTIVRTFeKVVQSCPVPIIVAGGKKIperDALQLtfnAIKGGAVGVDMGRNIWQSDNPVAMIRAVRSIV 72 
                 566666525889999******997541112344422367789**********************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 711.45
//
Query:       EPA06320.1  [L=387]
Description: putative 2-methylcitrate synthase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   1.1e-130  435.9   0.0   1.3e-130  435.7   0.0    1.0  1  Citrate_synt  Citrate synthase, C-terminal domain
  ------ inclusion threshold ------
       0.11   12.6   0.0       0.55   10.3   0.0    2.2  2  DUF1940       Domain of unknown function (DUF1940)
       0.17   12.1   0.2       0.39   10.9   0.2    1.7  1  FrhB_FdhB_N   Coenzyme F420 hydrogenase/dehydrogenase, beta s


Domain annotation for each model (and alignments):
>> Citrate_synt  Citrate synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  435.7   0.0  2.1e-134  1.3e-130       1     361 []       7     365 ..       7     365 .. 0.95

  Alignments for each domain:
  == domain 1  score: 435.7 bits;  conditional E-value: 2.1e-134
                   GGTTEEEEEESSEEEETTTTEEEETTEEHHHHHHHHS-HHHHHHHHHHSS---HHHHHHHHHHHHCTTS--HHHHHHHHCSSTTS-HHHHHHHHHHH CS
  Citrate_synt   1 glrgvaaleteisevdgekgelrYRGydieeLaeekssfeevaylLltgelPtkeelkefkeelaearklpekvlealealpkdahpmavlraavsa 97 
                   glrg+ +++t+is++dgekg+l+YRGydi eL  +kss+ee+aylLl+ +lPtke+l++fk++l+ear +p++++ ++ +++kda+pm++l+a vsa
    EPA06320.1   7 GLRGIEVADTKISNIDGEKGKLIYRGYDIFELT-KKSSYEETAYLLLHDDLPTKEQLAQFKSKLNEARWIPKRMQINMGNWRKDADPMDMLQAFVSA 102
                   899******************************.8************************************************************** PP

                   HHHHSTTCTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS.-----TTSSHHHHHHHHHHSS---HHHHHHHHHHHHHHS--SSSHHHHHHHHH CS
  Citrate_synt  98 lsaddeeseakeeseeaalrdalkliAklptiaaaiyrarlgreplepddklsyaenflymlrgkkpdeeeaklldlalvlhaDHelnaSTfaarvv 194
                   l+ +++   ++  ++ea +++a++liAk+pti+a ++r+r g e ++pd++l++a+nflym++g+kpd+e +k++d++l+lhaDH +naSTf+ar v
    EPA06320.1 103 LAGYYD---EEFATKEASYDKAINLIAKIPTIIASWQRVRDGLEIIDPDPSLDHAANFLYMMFGEKPDKEIEKIFDTCLILHADHTFNASTFVARQV 196
                   ****96...444466678888888******************96669**99********************************************** PP

                   HTTT--HHHHHHHHHHHHTSTTTTTHHHHHHHHHHHHSSGG.GHHHHHHHHHHTTTS--TTBC-SSSSS--HHHHHHHHHHHHHHTCHTHHHHHHHH CS
  Citrate_synt 195 aStladlysaiaagigalkGplhgganeavlkmleeigsaeveveeylekvlakekerlpGfGHrvykksDpRakilkelaeelaeekgkdpllkla 291
                   aSt+a++ysa +a+igal+G+lhggan++v+kml eig+ + +v  +++++++k+ er++G+GH+vyk++DpRa+ilkel ++l + k+ +p++++ 
    EPA06320.1 197 ASTRAHMYSAASAAIGALSGELHGGANTEVMKMLLEIGTID-NVVPWIKERMEKG-ERIMGMGHAVYKTYDPRATILKELSRKLGA-KTGEPWYDIT 290
                   ****************************************9.***********96.***************************988.69999***** PP

                   HHHHHHHHHHHHCHHGCT-EB-THHHHHHHHHHTT--GGGHHHHHHHHHHHHHHHHHHHHH.HT--....----E CS
  Citrate_synt 292 eeleevapevlkekeeknlypNvDfysgvlyralgipeelftvlfaisRvaGwlAhileql.adnk....iiRPr 361
                   e++e  + e +k+++ k++ypNvD+ys+ +y++l+ip +l t++faisRvaGw Ahi+e++ a+      ++RP+
    EPA06320.1 291 EKVETTTIEEMKKQKGKDIYPNVDLYSASIYYMLKIPMDLNTPIFAISRVAGWAAHIIEEKfAEAApkpaLYRPK 365
                   *******999998889*******************************************9765533456688885 PP

>> DUF1940  Domain of unknown function (DUF1940)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.75   4.5e+03      18      46 ..     118     145 ..      93     159 .. 0.64
   2 ?   10.3   0.0   9.3e-05      0.55      42      87 ..     250     295 ..     243     303 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.75
                 HHHHHHHHHHHHHHHHHT-SSHHHHHHHH CS
     DUF1940  18 yrseiklaeaslGlaiseGikvqatrell 46 
                 y++ i+l +a++   i++  +v++  e++
  EPA06320.1 118 YDKAINL-IAKIPTIIASWQRVRDGLEII 145
                 4444444.345555555555555555555 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 9.3e-05
                 HHHHHHHHHHHHHTTT-------HHHHHHHHH-------HHHHHHH CS
     DUF1940  42 trelldilDtlyqslsDpeskLkDeqrkkLnhadevWlDikekmsn 87 
                    ++ +   +y++   + + Lk+  rk    + e W+Di+ek++ 
  EPA06320.1 250 GERIMGMGHAVYKTYDPRATILKELSRKLGAKTGEPWYDITEKVET 295
                 5567788888888877777889999999999************986 PP

>> FrhB_FdhB_N  Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.2   6.5e-05      0.39       1      39 [.     203     241 ..     203     312 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 6.5e-05
  FrhB_FdhB_N   1 vvaArstdkeirkkaqsGGivtallkylLeegiidgviv 39 
                  +++A s+    + +   GG+ t+++k lLe g id v+ 
   EPA06320.1 203 MYSAASAAIGALSGELHGGANTEVMKMLLEIGTIDNVVP 241
                  78888888888899999*******************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.35s 00:00:01.02 Elapsed: 00:00:00.57
# Mc/sec: 2062.54
//
Query:       EPA06321.1  [L=186]
Description: hypothetical protein BG20_I1274 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1297.89
//
Query:       EPA06322.1  [L=219]
Description: Ser/Thr phosphatase family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-08   35.6   0.2    5.7e-08   33.5   0.2    1.9  1  Metallophos    Calcineurin-like phosphoesterase
    1.3e-06   28.7   0.1      2e-06   28.1   0.1    1.3  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
  ------ inclusion threshold ------
      0.016   14.1   0.0      0.032   13.1   0.0    1.5  1  Epimerase_2    UDP-N-acetylglucosamine 2-epimerase
       0.03   13.6   0.1       0.71    9.1   0.1    2.1  1  Metallophos_3  Metallophosphoesterase, calcineurin superfamil
      0.054   12.8   0.1        0.3   10.4   0.0    2.2  2  DNA_pol_E_B    DNA polymerase alpha/epsilon subunit B


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.2   1.6e-11   5.7e-08       5     117 ..      23     184 ..      20     216 .. 0.62

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 1.6e-11
                  EEESBTB............TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSS......HHHHHHHHHHHHHHHHTSEEEEEC-TTS......... CS
  Metallophos   5 vigDlHl............algggqlddllkllddllreekpdlvllaGDlvdrg......dlekellellaalvkypipvylllGNHe......... 75 
                  + +DlH+               + +++++++ l+ ++++ekpd ++l+GD+          ++++  + l+  ++k++  v+l++GNH+         
   EPA06322.1  23 IATDLHIgfesslasneifIGKNSSINETIEELSSVIDQEKPDSLILLGDVKSSIksisksEWDE--VPLFFNKIKQKCDVVLIPGNHDaniqrlvpd 118
                  679***999999999999987778888888888888999***********888878887667777..44556666668999********665555555 PP

                  ...................CHHHHHHHHHHHHHHH....HHHHEHHHCEEETSEEEEEETTE.EEE CS
  Metallophos  76 ...................gfeeellnkygylgif....sepwrsdaevfnnlplaslgsgs.lkv 117
                                     g+++ ++n+    +i      +++ ++++v+n+  +++  ++  +++
   EPA06322.1 119 nitmisstgmveenillthGHTMPSENFSHVDKIImghvHPVYFQEDSVLNGQRVWVSLKTEkQNI 184
                  555555555555555444432222222222222223333333333344444444444444444444 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.1   5.7e-10     2e-06       2     134 ..      20     164 ..      20     176 .. 0.69

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 5.7e-10
  Metallophos_2   2 klaiiSDlH..................snldaleavlealkevgvdaiihaGD.....leeeep..........evleellelapvlaVrGNnDee 64 
                    k++i +DlH                  s  + +e++ + ++++++d +i++GD                      + +++++ ++v+ ++GN+D  
     EPA06322.1  20 KHIIATDLHigfesslasneifigknsSINETIEELSSVIDQEKPDSLILLGDvkssiK----SisksewdevpLFFNKIKQKCDVVLIPGNHD-- 109
                    678999999999999999999999876566677888999999***********444430....244444443223677777777**********.. PP

  Metallophos_2  65 vveedvlreaaelgtdlpeeaelel....agekvlliHgdplgvkdalaellkeaeegsdvvvcGHtHvpevek 134
                              a +++ +p+  ++       +e++ll+Hg+    + ++ +        +d +++GH H  + ++
     EPA06322.1 110 ----------ANIQRLVPDNITMISstgmVEENILLTHGH--TMPSENFS-------HVDKIIMGHVHPVYFQE 164
                    ..........67777777666665433323345******9..33333333.......34458999999665554 PP

>> Epimerase_2  UDP-N-acetylglucosamine 2-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   8.9e-06     0.032      47      81 ..      43      77 ..      15      89 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.9e-06
                 -HHHHHHHHHHHHHHHHHHH--SEEEEESSSHHHH CS
  Epimerase_2 47 slakstgrvligleevleeekpDlvlvlGDtnetl 81
                 + + s+ +++++l+ v+++ekpD +++lGD  + +
   EPA06322.1 43 GKNSSINETIEELSSVIDQEKPDSLILLGDVKSSI 77
                 5677899***********************99865 PP

>> Metallophos_3  Metallophosphoesterase, calcineurin superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1    0.0002      0.71      19      44 ..      50      75 ..      40     143 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0002
                   GGHHHHHHHHHHH--SEEEEES---- CS
  Metallophos_3 19 ellerlveviedkdpDllvlvGdlvk 44
                   e +e+l  vi++ +pD l+l+Gd+ +
     EPA06322.1 50 ETIEELSSVIDQEKPDSLILLGDVKS 75
                   78999999***************954 PP

>> DNA_pol_E_B  DNA polymerase alpha/epsilon subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   8.5e-05       0.3      69      94 ..      87     112 ..      35     123 .. 0.70
   2 ?   -2.7   0.0      0.85     3e+03      71      90 ..     182     201 ..     176     205 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 8.5e-05
                  HTHHHHTTS-TTSEEEEE--TTBTT- CS
  DNA_pol_E_B  69 lllsilesllekttvvlvPgpnDpan 94 
                  ++  +++++++k++vvl+Pg  D+  
   EPA06322.1  87 EVPLFFNKIKQKCDVVLIPGNHDANI 112
                  455589*****************865 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.85
                  HHHHTTS-TTSEEEEE--TT CS
  DNA_pol_E_B  71 lsilesllekttvvlvPgpn 90 
                  ++i+++ + +++v+++P+ n
   EPA06322.1 182 QNIFPNKSGEIEVTIIPSFN 201
                  56788888899999999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.35s 00:00:00.92 Elapsed: 00:00:00.54
# Mc/sec: 1227.96
//
Query:       EPA06323.1  [L=68]
Description: hypothetical protein BG20_I1280 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.23s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 559.55
//
Query:       EPA06324.1  [L=147]
Description: hypothetical protein BG20_I1261 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.6e-15   54.7   0.0    1.3e-14   54.3   0.0    1.1  1  ADH_zinc_N    Zinc-binding dehydrogenase
    1.5e-07   32.5   0.0    1.9e-07   32.2   0.0    1.1  1  ADH_zinc_N_2  Zinc-binding dehydrogenase
    2.2e-06   27.3   0.2    2.7e-06   27.0   0.2    1.1  1  Glu_dehyd_C   Glucose dehydrogenase C-terminus


Domain annotation for each model (and alignments):
>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.3   0.0   2.1e-18   1.3e-14      26     128 ..       4     107 ..       3     109 .. 0.92

  Alignments for each domain:
  == domain 1  score: 54.3 bits;  conditional E-value: 2.1e-18
                 HHHHHHHTTESEEEET.TTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHHCEEEEEEEEECSCTSSEEE..EEHHHHHHTT-EEEEE-SSCHHHHH CS
  ADH_zinc_N  26 klelakklGadeviny.keadlverikeltggegvdvvfecvGsgatleaalkllkpgGrlvvvGggkgeee..fdlrnlllkeksilGsllgslreef 121
                 +l +akk+  +  in+ +e + +++i e+tgg+gvdv++ ++ s ++le+a++++++gG ++++G+++++ +  ++++++  ke++++ s  +s   + 
  EPA06324.1   4 RLSFAKKFNITDSINSfDE-NRKQKILEHTGGNGVDVAIVATSSLKALEDAIDMVRKGGAVMMFGVPSKDAKiiLNMGKIYSKEITLVTSYAAS-DTDT 100
                 7899************544.9*********************************************88877779********************.8888 PP

                 HHHHHHH CS
  ADH_zinc_N 122 kealdll 128
                 ke l+l+
  EPA06324.1 101 KESLRLI 107
                 8888886 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.0   3.1e-11   1.9e-07      10     133 .]      24     145 ..      16     145 .. 0.72

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 3.1e-11
                   TSTTHHHHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE----.S-EEE-CHHHCTT.T-EEEE--GGG...-.-HHHHHHHHHHHHHHH..-- CS
  ADH_zinc_N_2  10 rtedfeaatggegvDvvldtvggealleaslkvlpggGrlvsiggpplsaallkpakkrk.grsvkyeflfsmkasaqadileelaalieeGk..lr 103
                   r++ + ++tgg+gvDv++ ++ + ++le++++++++gG + + g p   ++++k  ++ +   s  +++++s  as  +d  +e ++li++ +  ++
    EPA06324.1  24 RKQKILEHTGGNGVDVAIVATSSLKALEDAIDMVRKGGAVMMFGVP---SKDAKIILNMGkIYSKEITLVTSYAAS-DTD-TKESLRLIDSSQidVK 115
                   45666689************9977777*******885776666543...333333332220233333333333444.778.************6667 PP

                   --EEEEEEGGGHHHHHHHHHSS--SSEEEE CS
  ADH_zinc_N_2 104 pvvdrvfpleeaaeAhrylesgrarGKiVl 133
                     v++++p+ee ++A+++ +sg    Ki++
    EPA06324.1 116 KLVTHTYPIEESQKAFDHARSGDNAMKIII 145
                   7899******************99999986 PP

>> Glu_dehyd_C  Glucose dehydrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.2   4.5e-10   2.7e-06      97     209 ..      33     144 ..       8     146 .. 0.81

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 4.5e-10
  Glu_dehyd_C  97 aseemdlvvEaTGsakhafeaiealapnGvaaLlGvpeds.evevdggelhrelvleNkalvGsvNanrrhfeaavdtLaalpeslldelvtkvvdld 193
                    + +d+ + aT s k++ +ai+ ++  G +++ Gvp++  ++ +++g++ ++       lv s  a+ +  +++++ +++ + + +++lvt+ ++++
   EPA06324.1  33 GGNGVDVAIVATSSLKALEDAIDMVRKGGAVMMFGVPSKDaKIILNMGKIYSK----EITLVTSYAASDTDTKESLRLIDSSQID-VKKLVTHTYPIE 125
                  45789********************************7543999****99876....6789999999999999988877665544.79********** PP

  Glu_dehyd_C 194 eleeAfe...dddetiKtv 209
                  e ++Af+   ++d+ +K +
   EPA06324.1 126 ESQKAFDharSGDNAMKII 144
                  ******8444566777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.28s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1081.79
//
Query:       EPA06325.1  [L=162]
Description: hypothetical protein BG20_I1273 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
     0.0069   16.3   0.9     0.0069   16.3   0.9    1.6  2  DASH_Spc19  Spc19
  ------ inclusion threshold ------
        1.6    9.1   9.0       0.12   12.7   1.9    2.5  2  Syntaxin_2  Syntaxin-like protein


Domain annotation for each model (and alignments):
>> DASH_Spc19  Spc19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.28   2.5e+03      76      76 ..      26      26 ..       7      66 .. 0.60
   2 !   16.3   0.9   7.7e-07    0.0069      59     128 ..      85     154 ..      75     161 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.28
                H CS
  DASH_Spc19 76 l 76
                l
  EPA06325.1 26 L 26
                1 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 7.7e-07
                 HHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH......HHHHT-XXXXXXXXXXXX....X CS
  DASH_Spc19  59 eeiePqieellekaekeleklerreetLkaklelqegrlsnaesskkeeeeseeskeeeeeeenkeeeks 128
                 e i+ +i+el+  ae++++k ++ +++L a ++l+++ l + ++s++e  + + ++ ++  ++++ ++ks
  EPA06325.1  85 ECIDDEISELILSAENSINKVKTMHTKLSADSDLKKSYLTEFADSESEIGSINLTNFTRAVNTSEYQQKS 154
                 6799*************************************99999988887777766665555555443 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.14   1.3e+03       6      17 ..      13      24 ..       7      40 .. 0.52
   2 ?   12.7   1.9   1.4e-05      0.12       3      78 ..      41     115 ..      39     133 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.14
  Syntaxin_2  6 qkinsnvstlek 17
                 +++s+  ++ek
  EPA06325.1 13 NQLQSLSANIEK 24
                222222222222 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 1.4e-05
  Syntaxin_2   3 snlqkinsnvstleklvkqLgtkkdteelreklhelieeinelikktnellkklsqldnsssdsqqklqkekLkkd 78 
                 ++lq in+ v   + ++ + ++kk+t+ l e++ +li+e  + ++ + + +++l   +++s + + k+++ kL+ d
  EPA06325.1  41 EELQDINKIVGLANYMLIKYEDKKETRLLLEQFVSLITESAQSVECIDDEISELILSAENSIN-KVKTMHTKLSAD 115
                 799*************************************************99988887755.778899999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1335  (0.0744604); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1107.73
//
Query:       EPA06326.1  [L=100]
Description: hypothetical protein BG20_I1266 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.071   12.8   0.1       0.11   12.2   0.1    1.4  1  SWIM      SWIM zinc finger


Domain annotation for each model (and alignments):
>> SWIM  SWIM zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   5.9e-06      0.11      14      40 .]      45      75 ..      30      75 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.9e-06
        SWIM 14 katCsCpefqk....ngipCkHalAvllalk 40
                  +CsC  + +    ++  C H+  v+la+k
  EPA06326.1 45 AEYCSCLGYYFgrliKKTTCYHLESVMLAKK 75
                669******99****************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 744.15
//
Query:       EPA06327.1  [L=180]
Description: aldolase domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-11   43.3   0.0    3.9e-11   43.0   0.0    1.0  1  DeoC      DeoC/LacD family aldolase


Domain annotation for each model (and alignments):
>> DeoC  DeoC/LacD family aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.0   0.0   2.2e-15   3.9e-11       2     172 ..      21     176 ..      20     179 .. 0.89

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 2.2e-15
                 EEEEECCSHHHHHHHHCTSSHHHHHHHHHHHHHHGGGSSEEEEETTTHHHHHHCSCTTSEEEEETECSSCCTTSTTEEEETTCHHHHHHHTT-SEEEEE CS
        DeoC   2 vilavDqrvankddtasaqneqledlkalvkealtpgasavlldpgviasaskeyakdiallvkldkgtyllkskqrdvdevasveeakalGAdavkvv 100
                 ++lavD++  +++ +        e++k++++ +l+ ++++ +l+ gv +   +    +++++++++ g  ++ +   +     s++ a++l A a+ + 
  EPA06327.1  21 LMLAVDHGYFLGPTEKL------ENPKKVIAPLLK-YCDSLMLTRGVQRTS-VPTFTNVPMVLRVSGGSSIIGEDLSQEEITVSIKDAIRLNASALAMS 111
                 58999999999999999......8**999998885.9*******9986654.444459********999999988665557899*************** PP

                 EEEHTTTTCHHHHHHHHHHHHHHHHHHHTEEEEEE.EEE-CTTBSSTTCHHHHHHHHHHHHTCCT-SEEEE-- CS
        DeoC 101 vyyradgseeeqqklaeikrvkeacheeglplile.lylrdeaikdekvdpdlvaeAarvsaelGaDiiKvev 172
                 +++   gs++e q + ++++  ++++e+g+p+++  ++ ++       +d++    A r++ae Ga i+K+ +
  EPA06327.1 112 IFV---GSKYEHQTIVNLGKLVSEAEEYGIPVLAVtAVGKELG-----KDARYLSLACRIAAEQGAHIVKTYY 176
                 ***...***************************9988889888.....5888******************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1147.27
//
Query:       EPA06328.1  [L=72]
Description: hypothetical protein BG20_I1270 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       206  (0.0114898); expected 358.6 (0.02)
Passed bias filter:                      202  (0.0112667); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.34s 00:00:00.81 Elapsed: 00:00:00.52
# Mc/sec: 416.12
//
Query:       EPA06329.1  [L=397]
Description: ATPase, AAA family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-37  129.0   0.0    3.3e-37  127.9   0.0    1.6  1  AAA           ATPase family associated with various cellular 
    1.8e-07   31.1   0.1    3.5e-07   30.2   0.1    1.5  1  MIT           MIT (microtubule interacting and transport) dom
    2.4e-07   31.0   0.0    4.9e-07   30.0   0.0    1.4  1  AAA_2         AAA domain (Cdc48 subfamily)
    3.8e-07   30.0   0.1    7.8e-06   25.8   0.0    2.4  2  Vps4_C        Vps4 C terminal oligomerisation domain
    3.1e-05   23.7   0.0    9.2e-05   22.2   0.0    1.8  1  AAA_lid_3     AAA+ lid domain
    4.5e-05   23.9   0.0     0.0077   16.6   0.0    2.6  3  AAA_16        AAA ATPase domain
    4.9e-05   23.1   0.0    0.00012   21.8   0.0    1.8  1  RuvB_N        Holliday junction DNA helicase RuvB P-loop doma
    7.4e-05   23.0   0.0      0.004   17.4   0.0    2.6  1  AAA_22        AAA domain
    0.00076   19.3   0.0     0.0013   18.5   0.0    1.4  1  AAA_24        AAA domain
     0.0013   18.3   0.0     0.0025   17.4   0.0    1.4  1  AAA_7         P-loop containing dynein motor region
     0.0022   18.0   0.0      0.016   15.2   0.0    2.4  1  AAA_5         AAA domain (dynein-related subfamily)
     0.0041   17.2   0.0      0.067   13.2   0.0    2.3  2  AAA_14        AAA domain
      0.005   16.8   0.3        2.2    8.1   0.0    2.8  2  ATPase_2      ATPase domain predominantly from Archaea
     0.0052   16.2   0.1      0.012   15.1   0.1    1.5  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.008   16.3   0.0      0.034   14.3   0.0    2.1  2  AAA_33        AAA domain
     0.0084   15.4   0.0      0.015   14.6   0.0    1.4  1  TIP49         TIP49 P-loop domain
  ------ inclusion threshold ------
      0.012   15.2   0.0      0.033   13.7   0.0    1.7  2  AAA_25        AAA domain
      0.017   14.9   0.0      0.032   14.0   0.0    1.5  1  IstB_IS21     IstB-like ATP binding protein
      0.023   14.0   0.0      0.067   12.5   0.0    1.8  1  Zeta_toxin    Zeta toxin
      0.047   13.5   0.0       0.13   12.0   0.0    1.7  2  AAA_11        AAA domain
      0.047   13.0   0.1        1.8    7.8   0.1    2.3  2  ATPase        KaiC
      0.071   12.3   0.0        1.1    8.4   0.0    2.1  2  KAP_NTPase    KAP family P-loop domain
       0.11   11.6   0.0       0.26   10.4   0.0    1.7  2  Parvo_NS1     Parvovirus non-structural protein NS1
       0.12   12.8   0.0       0.41   11.1   0.0    2.0  1  RNA_helicase  RNA helicase
       0.17   11.4   0.6       0.36   10.2   0.3    1.7  1  PhoH          PhoH-like protein


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.9   0.0   4.6e-40   3.3e-37       1     131 [.     152     286 ..     152     287 .. 0.94

  Alignments for each domain:
  == domain 1  score: 127.9 bits;  conditional E-value: 4.6e-40
                 EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS....TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHH CS
         AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakeka....kpsilfiDEidalaksrsgseseeeervvnqLlteldg 95 
                 +llyGppGtGKT+la a a+e++ +f+++++s+++sk++ge+ek++++lf+ a++      kp+ilf+DE+d+l +sr +se + e r+ nq+lte+dg
  EPA06329.1 152 MLLYGPPGTGKTMLAAATANEMDGYFINVDASSMMSKWLGEAEKNVSKLFAMARKYTekegKPVILFVDEVDSLLGSR-NSEVGGEVRTKNQFLTEMDG 249
                 89***************************************************8888889999***************.8899999************* PP

                 TTTS..SSTEEEEEEESSGGGSTHHHHSTTSSEEEETT CS
         AAA  96 vkkk..eskvivigatnrpdkldpallrgRfdrkieie 131
                 v+ k  +  + vigatn+p++ld ++l +Rf+++i+++
  EPA06329.1 250 VNGKgkDLMLYVIGATNKPWSLDWPFL-RRFQKRIYVS 286
                 **9955334789***************.7******997 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.1   4.9e-10   3.5e-07       3      64 ..      11      73 ..       9      74 .. 0.94

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 4.9e-10
         MIT  3 kAlelvkkAveeDnagnyeeAlelYkealelLlqalk.ekneerrellrekieeYleRaeeLk 64
                +A +++++A++ D++g    A+ +Y+ a++ L+++++   +++    ++ ++++Y +R+  L+
  EPA06329.1 11 SASKYATEAIKFDSQGARGMAITNYQYAIDSLMKLVQlYPTSKLNPIYKDRCNSYHTRITALQ 73
                7999*********************************55998****************98887 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.0   6.8e-10   4.9e-07       6      88 ..     152     231 ..     150     241 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 6.8e-10
                 EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG---..----THHHHHHHHHTTT-HHHHTTS.EEEEETGGG--------- CS
       AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselle..eeevehlvsrligappgyvgaeegG.ivllDEidKihpkessga 88 
                 +ll gp g+Gkt+la a+a+ ++      +i +das+++     e+e+ vs+l   +  y+++e +  i+++DE+d      s ++
  EPA06329.1 152 MLLYGPPGTGKTMLAAATANEMDG----YFINVDASSMMSkwLGEAEKNVSKLFAMARKYTEKEGKPvILFVDEVDSLLG--SRNS 231
                 5789******************95....9***********777899**************999988867788****8766..4444 PP

>> Vps4_C  Vps4 C terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.44   3.2e+02      26      49 ..      96     119 ..      84     123 .. 0.81
   2 !   25.8   0.0   1.1e-08   7.8e-06      25      60 ..     358     394 ..     349     394 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.44
      Vps4_C  26 ePpvtlkDflkalkkarptVskeD 49 
                 +++ + +Df++ + k +p V+ ++
  EPA06329.1  96 QRQTDENDFEELVMKEKPNVTWDE 119
                 5566679***********998766 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 1.1e-08
      Vps4_C  25 leP.pvtlkDflkalkkarptVskeDLekheeFTkef 60 
                  +P p+t  Df++++++ +p+Vs e ++ + ++ +ef
  EPA06329.1 358 IQPrPITTADFKEIMARRKPSVSLEMIRAYHKWSEEF 394
                 4455*******************************99 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   1.3e-07   9.2e-05       6      35 ..     314     343 ..     309     370 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.3e-07
   AAA_lid_3   6 eLAerTeGySGADlaalcreAallAlrrgi 35 
                 eLA++ +GyS  D + +c++A + A+ + +
  EPA06329.1 314 ELAKLFDGYSASDVKDVCQAAQIKAVHEIF 343
                 8*************************9942 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.1e-05    0.0077      24      59 ..     149     181 ..     144     197 .. 0.80
   2 ?    4.2   0.0     0.073        52     125     146 ..     203     224 ..     190     235 .. 0.78
   3 ?   -2.7   0.0       9.3   6.7e+03      87     106 ..     289     309 ..     268     345 .. 0.53

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.1e-05
      AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflrgk 59 
                 p  +ll+G++G+GK+ l+ + ++++   +g+f++ +
  EPA06329.1 149 PKGMLLYGPPGTGKTMLAAATANEM---DGYFINVD 181
                 5789**************9888644...37777655 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.073
      AAA_16 125 rllallsrderplvlvlDdlqw 146
                  + ++++++++p++l++D+++ 
  EPA06329.1 203 MARKYTEKEGKPVILFVDEVDS 224
                 3348899999*********995 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 9.3
      AAA_16  87 de.aesaeleawrekleeala 106
                 ++ a+++++e++ + l++ l+
  EPA06329.1 289 TQeAREKLFEQYTAPLRKDLK 309
                 333444455555555555544 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   1.7e-07   0.00012      34      96 ..     150     225 ..     112     283 .. 0.64

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.7e-07
      RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvkl.kitsgPvlek........agdlaalltnleekd....vlfideihrl 96 
                   +llyGpPG Gkt la+  a+e++  + ++ ++ +++k         + l a+  + +ek+    +lf+de+  l
  EPA06329.1 150 KGMLLYGPPGTGKTMLAAATANEMDGYFiNVDASSMMSKwlgeaeknVSKLFAMARKYTEKEgkpvILFVDEVDSL 225
                 468*********************8654133333333321111111134555665555555444557777777665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   5.6e-06     0.004       8     104 ..     152     226 ..     149     266 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5.6e-06
      AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseellealeqalraravielliiDEaqhlr 104
                 ++++G++GtGKT+l++  +++          +  ++ v+++s +      ++ l + +    +   + + l+++ +++ ++ +++++l +DE++ l 
  EPA06329.1 152 MLLYGPPGTGKTMLAAATANEM---------DGYFINVDASSMM------SKWLGEAE----K---NVSKLFAMARKYTEKEGKPVILFVDEVDSLL 226
                 689****************997.........4444555555555......22223333....3...6777888888888888888888888888864 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.9e-06    0.0013       5      77 ..     152     225 ..     149     249 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.9e-06
      AAA_24   5 iliyGpsgiGKTtlakel..gpkplfidtekGlksldadkfpdieswedfldevvelaaeladyktlviDtidel 77 
                 +l+yGp+g+GKT+la+    + +  fi++++++  +  + ++  +++ ++   + +  +++ +  +l++D +d l
  EPA06329.1 152 MLLYGPPGTGKTMLAAATanEMDGYFINVDASS-MMSKWLGEAEKNVSKLFAMARKYTEKEGKPVILFVDEVDSL 225
                 89*************9998889999******77.78888777666777777777777777777778888888876 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   3.5e-06    0.0025      35     110 ..     151     223 ..     148     226 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.5e-06
       AAA_7  35 pvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdiiesklek..rrkgvygPpggkklvvFvDDln 110
                  +ll+Gp GtGKt+++  + +++d       +in+ a+   ++     e+++ k     + y  + gk +++FvD+++
  EPA06329.1 151 GMLLYGPPGTGKTMLAAATANEMD-----GYFINVDASSMMSKWLGEAEKNVSKlfAMARKYTEKEGKPVILFVDEVD 223
                 689****************99999.....66777777777777777778888873335588**************985 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   2.2e-05     0.016       2      23 ..     152     173 ..     151     279 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.2e-05
                 EEEE--SSSSHHHHHHHGGGGB CS
       AAA_5   2 vlLvGppGtgKselaerlaaal 23 
                 +lL GppGtgK++la   a  +
  EPA06329.1 152 MLLYGPPGTGKTMLAAATANEM 173
                 89*************9887766 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.45   3.2e+02      50      86 ..      98     133 ..      81     144 .. 0.68
   2 !   13.2   0.0   9.3e-05     0.067       5      77 ..     152     241 ..     149     272 .. 0.57

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.45
      AAA_14  50 ekllelileklkeekktylflDEiqevpewekalksl 86 
                 ++ ++ + e++++ +k  +  DE+  ++++++al++ 
  EPA06329.1  98 QTDENDFEELVMK-EKPNVTWDEVIGLDDAKNALRES 133
                 2234556665555.66679999999999999999875 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 9.3e-05
      AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderd..........kkladpekllelileklkeekktylflDEiqev...............p 77 
                 +++ G+  +GKT+l+   ++e         +in+d  +             ++ +  + + + ek  e k  +lf DE+  +               +
  EPA06329.1 152 MLLYGPPGTGKTMLAAATANEMD-----GYFINVDASSMmskwlgeaekNVSKLF-AMARKYTEK--EGKPVILFVDEVDSLlgsrnsevggevrtkN 241
                 6899***********99997776.....334444443332233221110222222.333444443..24677799****9875555555555555554 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.018        13      24      44 ..     153     173 ..     148     181 .. 0.85
   2 !    8.1   0.0    0.0031       2.2      93     136 ..     188     229 ..     176     234 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.018
    ATPase_2  24 fiYGpegsGKtaLlkeiienl 44 
                 ++YGp g GKt L    +++ 
  EPA06329.1 153 LLYGPPGTGKTMLAAATANEM 173
                 79***********99888876 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0031
    ATPase_2  93 eilkeksklvfkaielllekikkkgkkiiiiiDelqklidlgln 136
                 + l e  k+v k ++ + +  +k+gk +i+++De+  l   g++
  EPA06329.1 188 KWLGEAEKNVSKLFAMARKYTEKEGKPVILFVDEVDSLL--GSR 229
                 445588899999999999999999999********9987..555 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   1.6e-05     0.012      25      41 ..     152     168 ..     149     177 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.6e-05
  Mg_chelatase  25 lllvGppGsGKtmlakr 41 
                   +ll+GppG+GKtmla++
    EPA06329.1 152 MLLYGPPGTGKTMLAAA 168
                   89************986 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       4.3   3.1e+03     100     123 ..      80     103 ..      40     114 .. 0.73
   2 !   14.3   0.0   4.8e-05     0.034       3      33 ..     153     185 ..     152     231 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 4.3
      AAA_33 100 rivvvetdeetlkeRlakRaangd 123
                  +v+ ++++++ ke ++++ +++d
  EPA06329.1  80 PAVDPNASPKEQKESVQRQTDEND 103
                 567788888888888877777654 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 4.8e-05
      AAA_33   3 llvGlpGsGKstlaerllkklgavllssdt..l 33 
                 ll G+pG+GK+ la   +++ ++++++ d+  +
  EPA06329.1 153 LLYGPPGTGKTMLAAATANEMDGYFINVDAssM 185
                 688****************99999999997331 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0     2e-05     0.015      51      95 ..     150     192 ..     141     225 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2e-05
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
       TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkk 95 
                 +++Ll Gp+gtGkt la a ++e+     f+ + +s + s  +  
  EPA06329.1 150 KGMLLYGPPGTGKTMLAAATANEMD--GYFINVDASSMMSKWLGE 192
                 799********************97..689999999998875554 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   4.7e-05     0.033      19      54 ..     137     170 ..     125     175 .. 0.75
   2 ?   -2.6   0.0       4.6   3.3e+03     133     158 ..     203     230 ..     180     248 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.7e-05
      AAA_25  19 ppprrwlvk.gllpagelallaGapgtGKttlaldla 54 
                 p++r +l++ g+ p+g   ll+G+pgtGKt+la   a
  EPA06329.1 137 PTKRPDLFPlGW-PKG--MLLYGPPGTGKTMLAAATA 170
                 666666666555.655..68*************8876 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.6
      AAA_25 133 leaaieeveg.vrlvviDplsralgg.d 158
                 ++++ +e eg ++ + +D ++++lg  +
  EPA06329.1 203 MARKYTEKEGkPVILFVDEVDSLLGSrN 230
                 3444444344577777888877777643 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   4.5e-05     0.032      49      70 ..     151     172 ..     146     228 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.5e-05
   IstB_IS21  49 nivllGpsGvGKshlaialgve 70 
                 +++l Gp+G+GK+ la+a + e
  EPA06329.1 151 GMLLYGPPGTGKTMLAAATANE 172
                 6899*************98876 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   9.4e-05     0.067      16      53 ..     149     184 ..     144     217 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.4e-05
  Zeta_toxin  16 PklillgGqpGAGKselaellkdelerqgnvvrldpDd 53 
                 Pk +ll G pG GK+ la+++++e+  +g ++ +d+ +
  EPA06329.1 149 PKGMLLYGPPGTGKTMLAAATANEM--DGYFINVDASS 184
                 88999********************..89999998765 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       4.3   3.1e+03     107     116 ..      89      98 ..      37     135 .. 0.53
   2 ?   12.0   0.0   0.00018      0.13      20      43 ..     152     194 ..     126     222 .. 0.67

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 4.3
      AAA_11 107 vsleekvekr 116
                    +e+v+++
  EPA06329.1  89 KEQKESVQRQ 98 
                 2222222221 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00018
      AAA_11  20 tliqGPPGtgKTktivellsqll...................s 43 
                  l+ GPPGtgKT   ++  +++                    +
  EPA06329.1 152 MLLYGPPGTGKTMLAAATANEMDgyfinvdassmmskwlgeaE 194
                 699*********9999999999765655555544443333330 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.1    0.0026       1.8      22      37 ..     152     167 ..     141     172 .. 0.87
   2 ?    3.0   0.0     0.076        54      78     154 ..     172     247 ..     167     251 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0026
      ATPase  22 vlitGepGtGKtifal 37 
                 +l++G pGtGKt++a+
  EPA06329.1 152 MLLYGPPGTGKTMLAA 167
                 89***********986 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.076
      ATPase  78 eeegklaiidasesaeesaeekdkedleelieelaeaikeika.krvviDsitglayeekeavaReilrqlvrvlkkl 154
                 e  g ++ +das+++++    + ++++++l +  +++ ++ +    + +D +++l   ++++++  ++r+  ++l ++
  EPA06329.1 172 EMDGYFINVDASSMMSKWLG-EAEKNVSKLFAMARKYTEKEGKpVILFVDEVDSL-LGSRNSEVGGEVRTKNQFLTEM 247
                 56788899999999987444.8999******99999998776637778*******.7788888888888777777655 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0       0.2   1.5e+02      24      56 ..     153     180 ..     149     189 .. 0.81
   2 ?    8.4   0.0    0.0015       1.1     153     197 ..     193     237 ..     182     243 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.2
  KAP_NTPase  24 gLygkWGsGKssllnkledelkefakpvrflfa 56 
                  Lyg+ G+GK+ l +   +e++       f+ +
  EPA06329.1 153 LLYGPPGTGKTMLAAATANEMDGY-----FINV 180
                 699************999999866.....5555 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0015
  KAP_NTPase 153 lqteveelladmektLdalqkrlVvviDdLDrceteevlqlleav 197
                   + v++l+a++ k+ +++ k++++++D+ D++  ++  ++   v
  EPA06329.1 193 AEKNVSKLFAMARKYTEKEGKPVILFVDEVDSLLGSRNSEVGGEV 237
                 567888899999999999***************999988876655 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00036      0.26     118     141 ..     153     176 ..      92     182 .. 0.93
   2 ?   -3.0   0.0       4.2     3e+03     170     188 ..     309     327 ..     305     340 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00036
   Parvo_NS1 118 wfyGpantGktnlaeaIakavply 141
                 ++yGp+ tGkt+la+a a+ ++ y
  EPA06329.1 153 LLYGPPGTGKTMLAAATANEMDGY 176
                 689*************99988765 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.2
   Parvo_NS1 170 yvsvvelakailggtavrv 188
                 +v++velak + g++a  v
  EPA06329.1 309 KVNKVELAKLFDGYSASDV 327
                 6899999999999987665 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00057      0.41       2      25 ..     153     176 ..     152     218 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00057
  RNA_helicase   2 wlyGpsgeGKStlakeLakallkk 25 
                   +lyGp+g+GK++la   a+++ + 
    EPA06329.1 153 LLYGPPGTGKTMLAAATANEMDGY 176
                   79************9977777654 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.3    0.0005      0.36      24      42 ..     154     172 ..     150     175 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0005
                 EE--TTSSTTHHHHHHHHH CS
        PhoH  24 aiGpaGtGKtylavalave 42 
                   Gp GtGKt+la a+a e
  EPA06329.1 154 LYGPPGTGKTMLAAATANE 172
                 68*************9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      626  (0.0349155); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.43
# Mc/sec: 2747.72
//
Query:       EPA06330.1  [L=167]
Description: hypothetical protein BG20_I2677, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-45  154.7   0.1    3.6e-45  154.5   0.1    1.0  1  TruD      tRNA pseudouridine synthase D (TruD)


Domain annotation for each model (and alignments):
>> TruD  tRNA pseudouridine synthase D (TruD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.5   0.1     2e-49   3.6e-45     150     297 ..       6     152 ..       1     159 [. 0.94

  Alignments for each domain:
  == domain 1  score: 154.5 bits;  conditional E-value: 2e-49
        TruD 150 ileeleekggvPNyfGvQRFGsrrpvthlvGkaivkgdleeAvelyvgkpfeeesedtreareavaetgdleealeelpkslryErallkrLaekpkdy 248
                  l+e  + + + N++G+QRFGs+rpvthl+Gka++++d+++Avel+v+ +++ +s++ +e+re++ ++ ++++ l+++p ++++Er +l+++++ ++d 
  EPA06330.1   6 RLSEFVDYQKILNFYGYQRFGSKRPVTHLIGKALLRRDFKKAVELIVSFTSKYDSKENTEIREKLVDKSNYKKYLDQVPPQMDIERIVLQEMID-HDDA 103
                 444555555699**********************************************************************************.9*** PP

        TruD 249 kkAlealpknLqrlFvhAyqSylFNrvlseRlerglpldepveGDvvif 297
                 +kA++a+p nL+r++v+AyqSylFN+ ls+ + +g +l  + +GDv+++
  EPA06330.1 104 QKAIHAVPLNLRRFYVQAYQSYLFNQTLSAAFTDGEDLFAAQTGDVCYD 152
                 **********************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       870  (0.0485247); expected 358.6 (0.02)
Passed bias filter:                      584  (0.0325729); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1125.85
//
Query:       EPA06331.1  [L=156]
Description: response regulator receiver domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-16   60.7   0.0    2.5e-16   59.9   0.0    1.4  1  Response_reg   Response regulator receiver domain
  ------ inclusion threshold ------
      0.063   12.5   0.1       0.08   12.1   0.1    1.4  1  ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.9   0.0   2.8e-20   2.5e-16       2     111 ..       6     128 ..       5     129 .. 0.86

  Alignments for each domain:
  == domain 1  score: 59.9 bits;  conditional E-value: 2.8e-20
                   EEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHH.............HHHH..ESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEESSTSH CS
  Response_reg   2 livdDdplvrellrqlleeegyeevaeaedgkealell.............keek..vdlillDinmpgmdGlellkeireedpelpviiltahsee 83 
                   li++D++  ++  +++le++gy +v+ ++dg+++le++             k  +  ++++llD +mp+m+G e++++ir+  pe +v++l+a+++ 
    EPA06331.1   6 LIAEDNKFTATQYKKFLESKGY-KVTIFNDGAKCLEKFtnelryrrvvlkdK--SspYHCVLLDHDMPKMNGSEVYEKIRKICPEQKVVFLSAYGQT 99 
                   9*********************.***************65555555555433..167*************************************996 PP

                   HHH.HHHHHCTESEEEESSG-HHHHHHHH CS
  Response_reg  84 eda.vealkagaddflsKpfdpeeLlkal 111
                     + +e+ +    ++++Kpf+ + Llk++
    EPA06331.1 100 ILKsQEGSREASLQIIQKPFSLDFLLKKI 128
                   555166667777899*********99998 PP

>> ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   8.9e-06      0.08      38      85 ..       5      51 ..       1     101 [. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.9e-06
  ERCC3_RAD25_C 38 lyvmnpnkfracefLikyhekrgDkiivfsDnvfaLkeyakklkkpyi 85
                   l++   nkf+a ++  k+ e++g k+ +f D    L++++++l+++ +
     EPA06331.1  5 LLIAEDNKFTATQYK-KFLESKGYKVTIFNDGAKCLEKFTNELRYRRV 51
                   788899********6.99***********************9987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1006.23
//
Query:       EPA06332.1  [L=237]
Description: archaeal flagellin N-terminal-like domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.6e-23   81.9   5.4    7.8e-23   81.5   5.4    1.2  1  Arch_flagellin  Archaebacterial flagellin
  ------ inclusion threshold ------
       0.26   11.2   3.4       0.72    9.8   3.4    1.7  1  DUF5325         Family of unknown function (DUF5325)


Domain annotation for each model (and alignments):
>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.5   5.4   8.6e-27   7.8e-23       1     163 [.      12     223 ..      12     224 .. 0.85

  Alignments for each domain:
  == domain 1  score: 81.5 bits;  conditional E-value: 8.6e-27
                     X--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEE.........EEE-SSSSSEEEEEEE--TTS--EEGGG CS
  Arch_flagellin   1 GfvgigtlIvfIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvg.........dsatngtineitiyvklnaGsspidlnk 86 
                     G +g++ +Iv+IA+V+VAA++a v++n+++ ++qk+++   +s e++ss++ei+g v+         + +++++in   i +k +aG++ ++++ 
      EPA06332.1  12 GVIGVESAIVMIAFVIVAAALAFVVLNMGFSTTQKVKTITTSSLEEASSAMEISGTVYgigctssasGCDATQKINATIIPIKIAAGGNLVNFAP 106
                     6789******************************************************8888777666666666777************999998 PP

                     -EEE..EEESS.--EE--E.......................................................T-EE-TT-EEEEEEE--TTT- CS
  Arch_flagellin  87 ttis..vtddg.qetlltad.......................efgivvisdtdgsltng..............devlekgekvelevnvneddg 141
                     +++   +++++ + t+++a                         f+ ++  +  +++  +              + +le ge + l+v ++++d 
      EPA06332.1 107 DITAisFFTKDvEYTNIYAGtittdeykqpvlafrqaaleagsAFDAFNGANPINGTLPSettafvywpkrlntNSILEAGEHAVLAVGFADTDR 201
                     7755337777767777777799999999999999999999999555555555444444445666777789999999******************* PP

                     --TT-EEEEEEE-SSS--EEEE CS
  Arch_flagellin 142 itagdevsvevvpenGasttie 163
                     + a +++s+e+  ++G ++ti+
      EPA06332.1 202 PLAHQKISIEIMLSDGGTLTID 223
                     *******************997 PP

>> DUF5325  Family of unknown function (DUF5325)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   3.4   8.1e-05      0.72      22      55 ..      14      47 ..      12      49 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 8.1e-05
     DUF5325 22 iGiaigersilgiiiaivalivvmGlGFktKkkm 55
                iG+  +   i+ +i+a ++++vv+ +GF+t +k+
  EPA06332.1 14 IGVESAIVMIAFVIVAAALAFVVLNMGFSTTQKV 47
                555555555666666667889********99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       896  (0.0499749); expected 358.6 (0.02)
Passed bias filter:                      568  (0.0316805); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1537.11
//
Query:       EPA06333.1  [L=283]
Description: matrixin [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.9e-10   38.8   0.0    2.3e-09   37.3   0.0    1.2  1  Peptidase_M10  Matrixin
    9.1e-05   22.2   0.1    0.00015   21.5   0.1    1.3  1  Peptidase_M57  Dual-action HEIGH metallo-peptidase
  ------ inclusion threshold ------
      0.013   14.4   0.0      0.025   13.5   0.0    1.4  1  Peptidase_M66  Peptidase M66
      0.064   13.8   0.0      0.099   13.2   0.0    1.4  1  Reprolysin_3   Metallo-peptidase family M12B Reprolysin-like
       0.21   11.2   1.1       0.61    9.7   1.1    1.7  1  Reprolysin_4   Metallo-peptidase family M12B Reprolysin-like


Domain annotation for each model (and alignments):
>> Peptidase_M10  Matrixin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.0   6.3e-13   2.3e-09     106     157 ..     221     271 ..     212     272 .. 0.86

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 6.3e-13
                    SEEHHHHHHHHHHHHTTBESXSSTTSTTSSSCTXTTTXSSXHHHHHHHHHHH CS
                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Peptidase_M10 106 gvslflVaaHEiGHalGLeHssdkdalmyplykeekkvrlskdDvkgiqelY 157
                      +l+++a HE+GHa+GL Hss++++lm+p+++++    +s+  +++i  lY
     EPA06333.1 221 SNQLETIARHEFGHAIGLGHSSAPEDLMAPTIDMTYP-YISECNIQAIVDLY 271
                    56799***************************87555.58999999999998 PP

>> Peptidase_M57  Dual-action HEIGH metallo-peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.1   4.1e-08   0.00015      76     150 ..     167     241 ..     117     245 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 4.1e-08
  Peptidase_M57  76 tfrltrgtntqasdmvvaditaktasgaggsaGfPsgGl.PykviqigtglesysvdvnehvithelGhtvGlRhs 150
                    +f +t +++ ++ ++++  +  +  +++g++  +  g +    +i+i + +++ s +  e +  he+Gh++Gl hs
     EPA06333.1 167 NFVITNSDKANGDIIIILSNIKDRSGNTGYTKTVLEGDHiVKAFITI-YNVNALSSNQLETIARHEFGHAIGLGHS 241
                    78889999998888887777777778888877776655514567888.***************************9 PP

>> Peptidase_M66  Peptidase M66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   7.1e-06     0.025     190     214 ..     222     246 ..     217     263 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.1e-06
  Peptidase_M66 190 atltgefiHEqGHalGLpHylagea 214
                    ++l+ +  HE GHa+GL+H+ a e+
     EPA06333.1 222 NQLETIARHEFGHAIGLGHSSAPED 246
                    56777889***********888655 PP

>> Reprolysin_3  Metallo-peptidase family M12B Reprolysin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.8e-05     0.099      59     124 .]     173     241 ..     120     241 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.8e-05
  Reprolysin_3  59 rgqagyDlvhlftarde.sgvgGlAyvgsvcnsskk....agvnsgssvlgkvgadtvaHEiGHnfganHt 124
                    ++a+ D+  ++++ +  sg+ G+   ++v + ++       ++ ++  + +     + HE GH +g+ H+
    EPA06333.1 173 SDKANGDIIIILSNIKDrSGNTGY--TKTVLEGDHIvkafITIYNVNALSSNQLETIARHEFGHAIGLGHS 241
                   467888888888775555777777..444444433332323333333333333458889***********5 PP

>> Reprolysin_4  Metallo-peptidase family M12B Reprolysin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   1.1   0.00017      0.61     127     154 ..     215     243 ..     167     277 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00017
  Reprolysin_4 127 sgvaasrdeydifA.HEiGHtfGaaHdls 154
                   ++ a s ++ +++A HE GH +G+ H+ +
    EPA06333.1 215 NVNALSSNQLETIArHEFGHAIGLGHSSA 243
                   333333477788666***********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1926.43
//
Query:       EPA06334.1  [L=226]
Description: archaeal flagellin N-terminal-like domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-21   77.5   4.8    1.5e-21   77.3   4.8    1.1  1  Arch_flagellin  Archaebacterial flagellin
  ------ inclusion threshold ------
      0.098   12.6   2.2       0.23   11.3   2.2    1.6  1  DUF5325         Family of unknown function (DUF5325)


Domain annotation for each model (and alignments):
>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.3   4.8   1.7e-25   1.5e-21       1     164 []      14     213 ..      14     213 .. 0.89

  Alignments for each domain:
  == domain 1  score: 77.3 bits;  conditional E-value: 1.7e-25
                     X--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEEEEE-SSSSSE..EEEEEE--TTS--EEGGG-EEE..E CS
  Arch_flagellin   1 GfvgigtlIvfIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvgdsatngtine..itiyvklnaGsspidlnkttis..v 91 
                     G +g++ +Iv+IA+V+VAA++a v++n+++ ++qk ++   +st+++ss+lei g +++s++ ++++    ++ +k   G+ +i+ln       +
      EPA06334.1  14 GVIGVESAIVMIAFVIVAAALAFVVLNMGFSTTQKTKQAIVSSTDEASSALEIAGKIIGSGHITAGKLnaTAVPIKIVSGGASINLNPQNAAirY 108
                     6789******************************************************665554444444****************987765337 PP

                     EESS--EE--E..................................................T-EE-TT-EEEEEEE--TTT---TT-EEEEEEE- CS
  Arch_flagellin  92 tddgqetlltad...................efgivvisdtdgsltng.............devlekgekvelevnvneddgitagdevsvevvp 154
                     + +++e+   ++                   + g+++ +  +g+  n+             + +l++ge +  +++++ ++ +   d ++ e++ 
      EPA06334.1 109 LSNNVEHGNIYVgalptgvydtlsdamdgaiSAGYISANPVNGGGPNStsavfyfnvnrnnNFILDQGEHGMMAIAFEASERPQSLDVIRAEIIL 203
                     7777555444557******************99999999999999999999********988999****************************** PP

                     SSS--EEEEE CS
  Arch_flagellin 155 enGasttief 164
                     ++Ga++t+e+
      EPA06334.1 204 PTGAPLTVER 213
                     *******986 PP

>> DUF5325  Family of unknown function (DUF5325)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   2.2   2.6e-05      0.23      22      56 ..      16      50 ..      14      52 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.6e-05
     DUF5325 22 iGiaigersilgiiiaivalivvmGlGFktKkkmR 56
                iG+  +   i+ +i+a ++++vv+ +GF+t +k  
  EPA06334.1 16 IGVESAIVMIAFVIVAAALAFVVLNMGFSTTQKTK 50
                555555555666666667889********998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       842  (0.046963); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1467.94
//
Query:       EPA06335.1  [L=255]
Description: ATPase/histidine kinase/DNA gyrase B/HSP90 domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.4e-16   60.2   0.8    4.9e-16   59.2   0.1    1.9  2  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    5.4e-09   35.9   0.3    5.4e-09   35.9   0.3    1.8  2  HATPase_c_5  GHKL domain
    3.9e-08   33.2   0.7    8.6e-08   32.1   0.7    1.6  1  HisKA        His Kinase A (phospho-acceptor) domain
     0.0011   18.7   0.7     0.0025   17.6   0.0    1.9  3  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like
  ------ inclusion threshold ------
      0.021   14.8   0.0      0.035   14.0   0.0    1.3  1  HATPase_c_2  Histidine kinase-like ATPase domain


Domain annotation for each model (and alignments):
>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       1.6   5.7e+03       9      32 ..     114     137 ..     110     143 .. 0.67
   2 !   59.2   0.1   1.4e-19   4.9e-16       2     109 ..     146     245 ..     145     251 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.6
                 HHHHHHHHHHHHHSTTTEEEEEEE CS
   HATPase_c   9 iisnlvdNavkfatkageieveik 32 
                  ++n++ +++++    +++ v+i+
  EPA06335.1 114 TLKNILNASIENLDIPSSVNVKIE 137
                 467888888887446666677666 PP

  == domain 2  score: 59.2 bits;  conditional E-value: 1.4e-19
                 HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCS.TTCHHCSTCHTSTSSSHHHHHHHHHHHHTTTEEEEEEETT CS
   HATPase_c   2 dekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfe.kfsqddstkrggggtGlGlsivkklvelmgGeiwvesepg 99 
                 d ++L+ ++ n+++Na+++ +++g i+++i  ++ + +i  eD+G Gi++  + k+ e  f++      ++ g+GlGl+i+k +ve++gG++ +++ p 
  EPA06335.1 146 DNRKLEAVFVNILKNALEAIKNQGYITIKILNNDSNTEIYFEDSGEGISQVVQSKMYEpMFTT------KQHGSGLGLAICKMIVEQHGGKLIYKNHP- 237
                 778999************97799999999997668***********************66666......99*********************998777. PP

                 TEEEEEEEEE CS
   HATPase_c 100 rGttftftlp 109
                   + f + lp
  EPA06335.1 238 --SAFSVILP 245
                 ..56666555 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       1.8   6.4e+03      13      24 ..     114     125 ..     108     144 .. 0.53
   2 !   35.9   0.3   1.5e-12   5.4e-09       4      96 ..     148     242 ..     145     245 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.8
  HATPase_c_5  13 lLdNAieacski 24 
                   L N ++a+ + 
   EPA06335.1 114 TLKNILNASIEN 125
                  444444444333 PP

  == domain 2  score: 35.9 bits;  conditional E-value: 1.5e-12
  HATPase_c_5   4 ldlcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg.....ekkkle.sskskkeehGiGlksireivkkykgnlsieaedglFt 95 
                    l +++ n+L NA+ea +++     +I++++ ++++++ i +e s eg     ++k +e   ++k++  G+Gl   + iv++++g+l ++++   F+
   EPA06335.1 148 RKLEAVFVNILKNALEAIKNQG----YITIKILNNDSNTEIYFEDSGEGisqvvQSKMYEpMFTTKQHGSGLGLAICKMIVEQHGGKLIYKNHPSAFS 241
                  56889*************9977....9*******************99965544323333445788899************************99998 PP

  HATPase_c_5  96 l 96 
                  +
   EPA06335.1 242 V 242
                  6 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.7   2.4e-11   8.6e-08       2      65 ..      42     106 ..      41     108 .. 0.80

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 2.4e-11
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHH...HHHHHHHHHHHHHHHHHHHHHHCCHH CS
       HisKA   2 lgrflagvaHELrtPLsailgnaeaLkregklteelke...yletiesearrldhlvedlLdlsrie 65 
                  g+f++ +aH++r+PL+ ++   e+L+  ++l+ +  +     ++i + +  ++h++ed+L++ r+ 
  EPA06335.1  42 IGQFTSRLAHDIRNPLTKLKISHEILSQAQNLSVM--DkikHQQRITDAIINITHIIEDVLEFVRMS 106
                 599***********************773233333..23357777777777************9986 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       1.5   5.3e+03      84     107 ..      69      94 ..      65     123 .. 0.53
   2 ?   -3.7   0.0       2.7   9.6e+03      11      25 ..     115     129 ..     112     140 .. 0.67
   3 !   17.6   0.0     7e-07    0.0025       4      62 ..     151     210 ..     148     224 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.5
  HATPase_c_3  84 lgkkltvitkkegess..tltldvdk 107
                  ++++l+v+ k + ++    + ++++ 
   EPA06335.1  69 QAQNLSVMDKIKHQQRitDAIINITH 94 
                  55555555543333331133333333 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 2.7
  HATPase_c_3  11 vdNsldAdaenvkie 25 
                  ++N l A+ en +i 
   EPA06335.1 115 LKNILNASIENLDIP 129
                  578888888886554 PP

  == domain 3  score: 17.6 bits;  conditional E-value: 7e-07
  HATPase_c_3   4 ekAlaelvdNsldAdaen..vkievnknrgktgeivieDdGkGmseeelknalrlatsske 62 
                  e + + +++N+l+A  ++  ++i++ +n+ +++ei +eD G+G+s+    ++ +++ ++k+
   EPA06335.1 151 EAVFVNILKNALEAIKNQgyITIKILNND-SNTEIYFEDSGEGISQVVQSKMYEPMFTTKQ 210
                  667899********888866888888876.79************98655556667766666 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   9.9e-06     0.035      40     110 ..     154     225 ..     150     229 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 9.9e-06
  HATPase_c_2  40 ctNavehayleap.egpvevrlesdeealtvevaDsGpgfdpetlpdpteeepkeslkegGrGlalikglvD 110
                  ++N+ + a +  + +g +++++  ++   ++ ++DsG+g     + +  e+  ++++  +G+Gla+ k++v+
   EPA06335.1 154 FVNILKNALEAIKnQGYITIKILNNDSNTEIYFEDSGEGISQVVQSKMYEPMFTTKQHGSGLGLAICKMIVE 225
                  678888888888889************************555555666677789**************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1164  (0.0649228); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1993.88
//
Query:       EPA06336.1  [L=217]
Description: hypothetical protein BG20_I1239, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.014   14.8   0.2      0.014   14.8   0.2    2.6  3  GAS             Growth-arrest specific micro-tubule binding
      0.022   15.1   0.3      0.022   15.1   0.3    3.2  3  FlaC_arch       Flagella accessory protein C (FlaC)
      0.041   13.2   4.3       0.57    9.5   0.5    2.3  2  Tropomyosin     Tropomyosin
      0.063   13.3   0.0       0.14   12.2   0.0    1.7  1  DUF2388         Protein of unknown function (DUF2388)
        0.3   11.4   4.6       0.12   12.7   0.8    2.3  2  Tup_N           Tup N-terminal
       0.31   10.1  10.9       0.39    9.8  10.9    1.1  1  Tmemb_cc2       Predicted transmembrane and coiled-coil 2 pro
       0.32   10.9   2.1       0.48   10.3   0.4    2.1  2  DUF4322         Domain of unknown function (DUF4322)
       0.37   10.9   0.1       0.37   10.9   0.1    2.7  2  Prefoldin_3     Prefoldin subunit
        0.4   10.5   1.9        4.7    7.1   0.3    2.5  3  DivIC           Septum formation initiator
       0.42   11.2   0.2       0.42   11.2   0.2    2.9  3  HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interac


Domain annotation for each model (and alignments):
>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.6      0.32   5.8e+02     148     171 ..      26      49 ..      18      75 .. 0.49
   2 ?   14.8   0.2   7.7e-06     0.014      92     137 ..     111     156 ..      91     167 .. 0.90
   3 ?   -1.4   0.5      0.71   1.3e+03      18      33 ..     171     188 ..     168     192 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.32
         GAS 148 ekklkalqeelEkkeaqleevlaa 171
                 ekk+++ + e ++ e  +e++ ++
  EPA06336.1  26 EKKVQKESTENDSIENMVESYNES 49 
                 333333333333333333333333 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 7.7e-06
         GAS  92 arlkelekelkdlkwehevleqrfekvekerdelykkfeaaiqevq 137
                 ++++ le+ +++ k++ ++ +q ++ v++e d+l+++fe+++ e++
  EPA06336.1 111 EKIEPLENTMNTFKMDFDQFKQDLTMVKEEVDALSSSFESTMTEIK 156
                 5788899**********************************99987 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.71
         GAS  18 nditrnNLelIk..slKe 33 
                 nd+++nN+++I+  +lK+
  EPA06336.1 171 NDTIKNNIQTINidQLKQ 188
                 789999999875225665 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   2.1      0.45   8.1e+02       6      24 ..      26      44 ..      18      55 .. 0.51
   2 ?   15.1   0.3   1.2e-05     0.022       1      42 [.     112     153 ..     112     169 .. 0.82
   3 ?   -1.1   0.0       1.5   2.6e+03      23      34 ..     171     182 ..     166     190 .. 0.64

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.45
   FlaC_arch  6 Enklsklsteletvkkene 24
                E+k++k ste +++++  e
  EPA06336.1 26 EKKVQKESTENDSIENMVE 44
                4555555554444443333 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 1.2e-05
   FlaC_arch   1 ridelEnklsklsteletvkkeneelsksveelkenVkdlls 42 
                 +i+ lEn ++ +++ ++  k+++  ++++v+ l  +++  + 
  EPA06336.1 112 KIEPLENTMNTFKMDFDQFKQDLTMVKEEVDALSSSFESTMT 153
                 7999***************************99988876665 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.5
   FlaC_arch  23 neelsksveelk 34 
                 n+ +++++++++
  EPA06336.1 171 NDTIKNNIQTIN 182
                 445555555554 PP

>> Tropomyosin  Tropomyosin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.2    0.0061        11     195     225 ..      25      55 ..      19      60 .. 0.91
   2 ?    9.5   0.5   0.00032      0.57     192     236 ..     113     157 ..      72     158 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0061
  Tropomyosin 195 AErsvqkLekevdrledeleaekekykaise 225
                   E++vqk   e+d++e+ +e++ e  k i+ 
   EPA06336.1  25 KEKKVQKESTENDSIENMVESYNESDKTITS 55 
                  59**********************9999976 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00032
  Tropomyosin 192 aeeAErsvqkLekevdrledeleaekekykaiseeLdqtlaeLee 236
                   e  E ++++ +++ d+  ++l+  ke+ +a+s   ++t+ e+++
   EPA06336.1 113 IEPLENTMNTFKMDFDQFKQDLTMVKEEVDALSSSFESTMTEIKC 157
                  5667899999********************************986 PP

>> DUF2388  Protein of unknown function (DUF2388)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   7.8e-05      0.14      26      63 ..      47      84 ..      18      90 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.8e-05
     DUF2388 26 dDAasFVASdGairGarLEaaLqelRsenpelqasDle 63
                ++    + SdG+i  +++Ea+L +  se+p  + sD e
  EPA06336.1 47 NESDKTITSDGTIGNSEIEAMLAKTNSEKPTEETSDIE 84
                55556699****************************87 PP

>> Tup_N  Tup N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.2       1.4   2.5e+03      31      49 ..      26      44 ..      17      55 .. 0.69
   2 ?   12.7   0.8   6.6e-05      0.12       2      46 ..     116     160 ..     115     189 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.4
       Tup_N 31 elkiqsqiqElqqirqtly 49
                e+k+q+   E ++i +++ 
  EPA06336.1 26 EKKVQKESTENDSIENMVE 44
                6677777777777776664 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 6.6e-05
       Tup_N   2 lnelLdavkqEfdalsqeasslkaqkdeyelkiqsqiqElqqirq 46 
                 l++ ++  k +fd+++q+++++k++ d + ++++s + E++ i  
  EPA06336.1 116 LENTMNTFKMDFDQFKQDLTMVKEEVDALSSSFESTMTEIKCITT 160
                 56789999********************************99876 PP

>> Tmemb_cc2  Predicted transmembrane and coiled-coil 2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8  10.9   0.00022      0.39     143     271 ..      18     164 ..      10     193 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00022
   Tmemb_cc2 143 SADninslksseeeseeesgskslssst.allvskskytsddesssssvesssadsnsnseestasa............sksaesesqeklekileelq 228
                 S+ ni+  +++ ++   +++++s+ +   ++++s +  tsd+ + +s++e++ a++ns++ ++++s             s++++ ++  +  +ile+++
  EPA06336.1  18 SSKNISTKEKKVQKE--STENDSIENMVeSYNESDKTITSDGTIGNSEIEAMLAKTNSEKPTEETSDiesllagaeyntSDTSNDQNLDTHLMILEKIE 114
                 777887766444333..2222333332202333333377888888888777666666666666555567777777766544555555566677788888 PP

   Tmemb_cc2 229 eikeeqerleeelerlkeq...lkkel....kllkqaLqeeryryerLEe 271
                  ++++++ ++++++++k++   +k+e+    + +++++ e ++ +++  +
  EPA06336.1 115 PLENTMNTFKMDFDQFKQDltmVKEEVdalsSSFESTMTEIKCITTDFNN 164
                 88888888888888888651113555533335555566666665555444 PP

>> DUF4322  Domain of unknown function (DUF4322)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.4   0.00027      0.48      42      61 ..      35      54 ..       9      56 .. 0.89
   2 ?   -1.2   0.1       1.1   1.9e+03      43      55 ..     171     183 ..     168     191 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00027
     DUF4322 42 lndsienkskaynvspqtvr 61
                 ndsien  ++yn s++t+ 
  EPA06336.1 35 ENDSIENMVESYNESDKTIT 54
                59****************85 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.1
     DUF4322  43 ndsienkskaynv 55 
                 nd+i n  ++ n+
  EPA06336.1 171 NDTIKNNIQTINI 183
                 7777777777766 PP

>> Prefoldin_3  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   1.0      0.52   9.4e+02      22      22 ..      37      37 ..      18      87 .. 0.50
   2 ?   10.9   0.1   0.00021      0.37       8      46 ..     128     166 ..     121     194 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.52
  Prefoldin_3 22 s 22
                 +
   EPA06336.1 37 D 37
                 1 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00021
  Prefoldin_3   8 reweaeydglkeeisalkeeddateedllriardfegsl 46 
                   + +++++ +kee++al+++ ++t++++  i+ df+  l
   EPA06336.1 128 DQFKQDLTMVKEEVDALSSSFESTMTEIKCITTDFNNPL 166
                  567889999**************************9743 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.3    0.0026       4.7      24      57 ..      20      53 ..      17      55 .. 0.88
   2 ?    2.0   0.0     0.097   1.7e+02      17      48 ..     125     156 ..     118     162 .. 0.78
   3 ?   -3.5   0.1         5     9e+03      33      38 ..     183     188 ..     173     191 .. 0.49

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0026
                HHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXX CS
       DivIC 24 qeiaalqaelaklkaeneeLeaevkdLksdedyi 57
                ++i +++++++k + en++ e  v+ ++ ++  i
  EPA06336.1 20 KNISTKEKKVQKESTENDSIENMVESYNESDKTI 53
                67999*********************97777666 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.097
                 XHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
       DivIC  17 laykqlkqeiaalqaelaklkaeneeLeaevk 48 
                 +++ q kq+++  ++e+++l+   e+   e+k
  EPA06336.1 125 MDFDQFKQDLTMVKEEVDALSSSFESTMTEIK 156
                 56778889999999999999888777777766 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 5
                 HHHHHH CS
       DivIC  33 laklka 38 
                 +++lk+
  EPA06336.1 183 IDQLKQ 188
                 333333 PP

>> HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interacting protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.8      0.67   1.2e+03      67      84 ..      35      52 ..      18     112 .. 0.57
   2 ?   11.2   0.2   0.00023      0.42      44      81 ..     117     154 ..     101     164 .. 0.84
   3 ?   -0.6   0.1       1.1     2e+03      44      60 ..     173     189 ..     166     197 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.67
  HIP1_clath_bdg 67 elarlkssLesseqsgeq 84
                    e +++++ +es ++s+++
      EPA06336.1 35 ENDSIENMVESYNESDKT 52
                    222222222222222222 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00023
  HIP1_clath_bdg  44 erkleeqkeelekLkreleakraelarlkssLesseqs 81 
                     e+ ++  k+  +++k++l++ ++e++ l ss es+ ++
      EPA06336.1 117 ENTMNTFKMDFDQFKQDLTMVKEEVDALSSSFESTMTE 154
                     56677788999*********************998665 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.1
  HIP1_clath_bdg  44 erkleeqkeelekLkre 60 
                     + k + q+ ++++Lk++
      EPA06336.1 173 TIKNNIQTINIDQLKQQ 189
                     55677899999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1720  (0.095934); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 1364.84
//
Query:       EPA06337.1  [L=279]
Description: hypothetical protein BG20_I1244 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.7e-06   27.0   0.0      1e-05   25.6   0.0    1.8  1  Cupredoxin_1  Cupredoxin-like domain
    7.8e-06   26.3   0.0    1.9e-05   25.0   0.0    1.7  1  Copper-bind   Copper binding proteins, plastocyanin/azurin fa


Domain annotation for each model (and alignments):
>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   1.1e-09     1e-05       4     102 ..       3     113 ..       1     114 [. 0.80

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.1e-09
  Cupredoxin_1   4 alavllllsskaaaaaektveitvkdg.....gfePskievkagekvklkiknkdktpeefesed.........lgeekvlapgktttitiaplkpG 86 
                   a++++ +l s+a+a+++ tv +   dg      f+P ++ +k+g   +++++n+d+t ++++s           +     l+pg++ +++++  + G
    EPA06337.1   3 AITFVPILLSPAFAENTWTVFLSQYDGtshkeLFSPIELPIKSGD--TVTWENHDSTNHKITSGIpkfpessgkFFSTSILKPGQSESVKLEHTDYG 97 
                   555555666666666666655554444454549***********9..89********9999987666888998866679****************** PP

  Cupredoxin_1  87 eYeftcdmhmdakGkl 102
                    Y ++c++h+ + Gk+
    EPA06337.1  98 AYYYFCEIHPWFTGKI 113
                   **********779997 PP

>> Copper-bind  Copper binding proteins, plastocyanin/azurin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   2.1e-09   1.9e-05      12      89 ..      34     108 ..      25     116 .. 0.76

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 2.1e-09
                  SEEESSEEEEETTEEEEEEEESSSSBEEEEETTSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEE..SSEEEEEEETTTTT CS
  Copper-bind  12 lqFetkeitvkkgekvtfvnlavmgHNvvldkdgvpagvdkdkvkaedetkliggGekdsvtfd..eagtYkffCsPHaa 89 
                    F++ e+ +k+g++vt+ n ++  H +     + p+   k+      +t++  +G++ sv+++  + g+Y +fC+ H  
   EPA06337.1  34 ELFSPIELPIKSGDTVTWENHDSTNHKITSGIPKFPESSGKFF-----STSILKPGQSESVKLEhtDYGAYYYFCEIHPW 108
                  5699****************99999988776666555444333.....46699***********656666******8873 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1789.62
//
Query:       EPA06338.1  [L=82]
Description: hypothetical protein BG20_I1257 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.031   14.2   0.4      0.038   14.0   0.4    1.1  1  Borealin    Cell division cycle-associated protein 8
      0.045   12.6   4.9       0.05   12.4   4.9    1.0  1  Fmp27_WPPW  RNA pol II promoter Fmp27 protein domain
      0.046   13.6   4.5      0.074   12.9   1.6    2.1  2  GIT_CC      GIT coiled-coil Rho guanine nucleotide exchange f


Domain annotation for each model (and alignments):
>> Borealin  Cell division cycle-associated protein 8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.4   6.3e-06     0.038      56     118 ..       2      64 ..       1      68 [. 0.82

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.3e-06
    Borealin  56 lsGSPlaegvvteevanvniPvgdGevlslqakeldevdeel..lekLdeetlkqlkkLqsnLak 118
                 lsGSPl +  v ++ a++++   +   l+l +kel+e d  +  ++k+ +e ++++ k +++L++
  EPA06338.1   2 LSGSPLENDPVLRDLAEISVNALKD--LELAKKELKENDFRMqeMNKMANERVQEMTKVNHQLQE 64 
                 68*******8888899988887776..9999999977665444599999999******9999987 PP

>> Fmp27_WPPW  RNA pol II promoter Fmp27 protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   4.9   8.4e-06      0.05     186     239 ..      26      79 ..      14      81 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.4e-06
  Fmp27_WPPW 186 qiekleekleelelksekedeelkeeieelekeikelkeklefletlledlkes 239
                 ++e  +++l+e++ ++++ ++  +e+++e++k  ++l+ek++f+e++ +++k++
  EPA06338.1  26 DLELAKKELKENDFRMQEMNKMANERVQEMTKVNHQLQEKISFVENMTKSIKKK 79 
                 456678888888888888899999**************************9987 PP

>> GIT_CC  GIT coiled-coil Rho guanine nucleotide exchange factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.2     0.016        94      22      39 ..      31      48 ..      15      50 .. 0.81
   2 ?   12.9   1.6   1.2e-05     0.074      27      56 ..      47      76 ..      45      79 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.016
      GIT_CC 22 KkalaaseakiqqLlkvN 39
                Kk+l   + ++q++ k+ 
  EPA06338.1 31 KKELKENDFRMQEMNKMA 48
                899999999999998875 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 1.2e-05
      GIT_CC 27 aseakiqqLlkvNtslsdelrlLQskvqkL 56
                 ++ ++q++ kvN +l+++++   ++ +++
  EPA06338.1 47 MANERVQEMTKVNHQLQEKISFVENMTKSI 76
                5899****************9887777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3223  (0.179765); expected 358.6 (0.02)
Passed bias filter:                      945  (0.0527079); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 531.91
//
Query:       EPA06339.1  [L=238]
Description: hypothetical protein BG20_I1248 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1736.41
//
Query:       EPA06340.1  [L=236]
Description: archaeal flagellin N-terminal-like domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.1e-22   78.2  11.0    1.1e-21   77.8  11.0    1.2  1  Arch_flagellin  Archaebacterial flagellin
  ------ inclusion threshold ------
       0.11   12.5   0.5       0.19   11.7   0.5    1.3  1  DUF2393         Protein of unknown function (DUF2393)
       0.61   10.0   4.5       0.51   10.3   2.8    1.8  2  DUF5325         Family of unknown function (DUF5325)


Domain annotation for each model (and alignments):
>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.8  11.0   1.8e-25   1.1e-21       1     164 []      14     223 ..      14     223 .. 0.81

  Alignments for each domain:
  == domain 1  score: 77.8 bits;  conditional E-value: 1.8e-25
                     X--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEE........EEE-SSSSSE......EEEEEE--TTS-- CS
  Arch_flagellin   1 GfvgigtlIvfIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvg........dsatngtine......itiyvklnaGssp 81 
                     G +g++ +Iv+IA+V+VAA++a v++n+++ ++qka++t  ++ ++ ss+le++g +         + a      +       +i +k + G+++
      EPA06340.1  14 GVIGVESAIVMIAFVIVAAALAFVVLNMGFSTTQKAKTTILSGLAESSSSLEVSGKITgvgcttsgTCA------TtpvlnaTAIPIKITSGGDS 102
                     6789***************************************************99956444443333......2566666************* PP

                     EEGGG-EEEEEESS--EE--E..........................................................T-EE-TT-EEEEEEE- CS
  Arch_flagellin  82 idlnkttisvtddgqetlltad.......................................efgivvisdtdgsltng.devlekgekvelevnv 136
                     ++l+  t++v++    +++ ++                                        +   +     +s+t++ + +l++ge + l+v +
      EPA06340.1 103 VELSAATTTVSYVS--NSIQYTdiyagplaatteyrslsdafdgaasasltgftgrqpitgAVASQTSAFVYWSVTSNtNAILDQGEHAVLAVGF 195
                     ***98888755555..44444444555****8888888888888888888887777766554444444444455554478999************ PP

                     -TTT---TT-EEEEEEE-SSS--EEEEE CS
  Arch_flagellin 137 neddgitagdevsvevvpenGasttief 164
                     +  d + a d+++ e++ ++Gas+t+e+
      EPA06340.1 196 ASADRPAALDKIRAEIIVSTGASLTVER 223
                     *99**********************986 PP

>> DUF2393  Protein of unknown function (DUF2393)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.5   3.2e-05      0.19      19      81 ..      20      82 ..      10      98 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.2e-05
     DUF2393 19 lfliflsllilflapfvvhliid.kylkkaeltilsqkrllyteafvvdgtitNeGkftikeCk 81
                +++++++++i+++a ++v l +   +++ka++tils  +  +++++ v+g+it  G  t + C 
  EPA06340.1 20 SAIVMIAFVIVAAALAFVVLNMGfSTTQKAKTTILSGLA-ESSSSLEVSGKITGVGCTTSGTCA 82
                4566666666666644444444325669*******9876.56789********99998888885 PP

>> DUF5325  Family of unknown function (DUF5325)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   2.8   8.5e-05      0.51      22      55 ..      16      49 ..      14      52 .. 0.71
   2 ?   -3.7   0.0       1.9   1.1e+04      43      49 ..     189     195 ..     188     197 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 8.5e-05
     DUF5325 22 iGiaigersilgiiiaivalivvmGlGFktKkkm 55
                iG+  +   i+ +i+a ++++vv+ +GF+t +k 
  EPA06340.1 16 IGVESAIVMIAFVIVAAALAFVVLNMGFSTTQKA 49
                555555555666666667889********98875 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 1.9
     DUF5325  43 vvmGlGF 49 
                 +v+++GF
  EPA06340.1 189 AVLAVGF 195
                 5788888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       884  (0.0493056); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1518.69
//
Query:       EPA06341.1  [L=41]
Description: hypothetical protein BG20_I1253 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1568  (0.0874561); expected 358.6 (0.02)
Passed bias filter:                      752  (0.0419432); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 279.71
//
Query:       EPA06342.1  [L=40]
Description: hypothetical protein BG20_I1256 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      196  (0.010932); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 249.87
//
Query:       EPA06343.1  [L=269]
Description: sugar-specific transcriptional regulator TrmB [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.1e-15   55.1   0.0    1.3e-14   53.8   0.0    1.7  1  TrmB            Sugar-specific transcriptional regulator TrmB
      2e-06   27.2   0.2    2.8e-06   26.7   0.2    1.2  1  Regulator_TrmB  Archaeal transcriptional regulator TrmB
     0.0041   16.9   0.0     0.0094   15.8   0.0    1.6  1  HTH_5           Bacterial regulatory protein, arsR family
  ------ inclusion threshold ------
      0.018   15.0   0.0      0.061   13.3   0.0    1.9  1  HTH_11          HTH domain
       0.03   13.6   0.2      0.083   12.1   0.0    1.8  2  DUF1386         Protein of unknown function (DUF1386)
      0.038   13.8   0.3      0.076   12.8   0.3    1.5  1  Bacillus_HBL    Bacillus haemolytic enterotoxin (HBL)
       0.04   13.6   1.5      0.047   13.4   0.1    1.8  2  PNK3P           Polynucleotide kinase 3 phosphatase
      0.044   14.2   0.1       0.11   13.0   0.1    1.7  1  Cep57_MT_bd     Centrosome microtubule-binding domain of Cep5
       0.19   12.7   0.1       0.41   11.6   0.1    1.6  1  Pup             Pup-like protein


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.8   0.0   6.5e-18   1.3e-14       3      67 ..      13      77 ..      11      78 .. 0.97

  Alignments for each domain:
  == domain 1  score: 53.8 bits;  conditional E-value: 6.5e-18
                HCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE--H CS
        TrmB  3 klGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravdp 67
                ++GL e +ak+Y+ Ll+ g+ t+ + a++l+v+r k+Y++L++L ++G++ +  ++p++ +av+p
  EPA06343.1 13 HFGLEEIDAKIYVGLLQMGSVTVGTMAQKLDVDRGKAYRSLNKLRNMGVISTTFSNPTIVNAVQP 77
                79*************************************************************98 PP

>> Regulator_TrmB  Archaeal transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.2   1.4e-09   2.8e-06       2     134 ..     121     262 ..     120     267 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 1.4e-09
                     EEEESSHHHHHHHHHHHHHH-SSEEEEEE-GGGHHH.....HHHHHHHHHHTT-EEEEEESS.----GGGSSSSEEEEEE-S---S.EEEEETTT CS
  Regulator_TrmB   2 vwvvksretvierieelIesAenelivslpselLee.....lreeliaaaergvtVllliyp.dedleeldleevatevrvrrsgapllvivDrk 90 
                     +++v++r+++ +ri +lI++ +n + + ++se L +     + +++ a+++ g  + ++  + +++++e      atevr+ ++++   +iv +k
      EPA06343.1 121 FSIVQGRSNIYTRIGKLIQESTNKIFLVTTSEDLMRmyhtsIPDKIHARVNDGADIKIITNEcNAKTMEIINQLGATEVRIGKLPSKSRMIVESK 215
                     799*****************************997522333678999999*********99997777777788888**********999****** PP

                     EEEEE-SSS-...EEEE--HHHHHHHH.HHHHHH........HHH-EE CS
  Regulator_TrmB  91 rgvvaprevl...rdkeeeyaiifkek.elihvlshyFlttlWktsev 134
                     r ++++ +++   +  +e  +i+ +++ e++ ++  +  t +Wk+s+ 
      EPA06343.1 216 RQLIMSGAMKesmDLIDEVDSIMYTNSeEMVENM-FSLCTHMWKKSKP 262
                     ********99887666777777766550555555.5555555999986 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   4.7e-06    0.0094      10      46 ..      27      63 ..      25      64 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.7e-06
                HHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
       HTH_5 10 lLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                lL+ g+ +v+  a +l++ +++  + L+kLr++G+++
  EPA06343.1 27 LLQMGSVTVGTMAQKLDVDRGKAYRSLNKLRNMGVIS 63
                45568999***************************97 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     3e-05     0.061      13      44 ..      30      61 ..      21      66 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3e-05
      HTH_11 13 rgpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                 g ++  ++A++L+v r   +r + +L+ +gv
  EPA06343.1 30 MGSVTVGTMAQKLDVDRGKAYRSLNKLRNMGV 61
                4559**************************95 PP

>> DUF1386  Protein of unknown function (DUF1386)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   4.1e-05     0.083     121     159 ..     104     142 ..      72     163 .. 0.92
   2 ?   -1.3   0.1      0.52     1e+03      52      80 ..     211     239 ..     187     255 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.1e-05
     DUF1386 121 fslnnfereisqdmldclqiilgrfeyfmrngkllrlst 159
                  +lnn+ere +   l  + i+ gr + + r gkl++ st
  EPA06343.1 104 ENLNNYERETTPTDLSSFSIVQGRSNIYTRIGKLIQEST 142
                 579********************************9988 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.52
     DUF1386  52 vtamrrlksgsctfdeavkmidacdsiks 80 
                 +   +r    s ++ e++ +id +dsi  
  EPA06343.1 211 IVESKRQLIMSGAMKESMDLIDEVDSIMY 239
                 55555555667788999999999999864 PP

>> Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.3   3.8e-05     0.076      73     144 ..      55     123 ..      51     150 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.8e-05
  Bacillus_HBL  73 tiqdiigYstkFqsyyktlveavdkkdkaellellekLqeeiqqnqkevkqlikeLkklklkla.kdsknFkt 144
                    ++++   st+F++  +t+v+av  + ++ l+++++k ++ei+  qk +++l+++L++++ +++  d ++F+ 
    EPA06343.1  55 KLRNMGVISTTFSN--PTIVNAV--QPSEALTSVIQKKEDEIIMLQKLARTLVENLNNYERETTpTDLSSFSI 123
                   56677777888885..99*****..78999*****************************87765378888876 PP

>> PNK3P  Polynucleotide kinase 3 phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       1.9   3.8e+03      38      73 ..      53      88 ..      48     109 .. 0.63
   2 ?   13.4   0.1   2.3e-05     0.047      11      75 ..     137     203 ..     134     227 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.9
       PNK3P 38 LkklkeegykivifsNqggvvekktkkslekfkeki 73
                L+kl + g++   fsN   v +++ +++l+++++k 
  EPA06343.1 53 LNKLRNMGVISTTFSNPTIVNAVQPSEALTSVIQKK 88
                666666666666777777766665555555555543 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 2.3e-05
       PNK3P  11 liktksgkefak.dadd.wkllsesvlekLkklkeegykivifsNqggvvekktkkslekfkekiea 75 
                 li+++++k f    ++d  +++++s+++k+++  ++g+ i i++N+ + ++ +  ++l     +i +
  EPA06343.1 137 LIQESTNKIFLVtTSEDlMRMYHTSIPDKIHARVNDGADIKIITNECNAKTMEIINQLGATEVRIGK 203
                 6666666655543555514578888*********************999987666666666666655 PP

>> Cep57_MT_bd  Centrosome microtubule-binding domain of Cep57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   5.5e-05      0.11       2      42 ..      70     110 ..      69     117 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.5e-05
  Cep57_MT_bd   2 tlrpsqspkeaLaevlkeLedEfehlklelqelaaqynald 42 
                  t+  +++p eaL +v+++ edE+  l++   +l + +n+ +
   EPA06343.1  70 TIVNAVQPSEALTSVIQKKEDEIIMLQKLARTLVENLNNYE 110
                  5667899**************************99999765 PP

>> Pup  Pup-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1    0.0002      0.41      42      60 ..     229     247 ..     212     250 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0002
         Pup  42 dlLDeIDevLEeNAeeFVr 60 
                 dl+De+D+++ +N+ee V 
  EPA06343.1 229 DLIDEVDSIMYTNSEEMVE 247
                 79**************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       745  (0.0415528); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 1782.45
//
Query:       EPA06344.1  [L=54]
Description: hypothetical protein BG20_I1254 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-06   28.4   0.3    1.4e-06   28.4   0.3    1.1  1  DUF1059   Protein of unknown function (DUF1059)


Domain annotation for each model (and alignments):
>> DUF1059  Protein of unknown function (DUF1059)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.3   7.6e-11   1.4e-06       1      41 [.       1      40 [.       1      54 [] 0.87

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 7.6e-11
     DUF1059  1 mkefkCgDvgpdCgfeitaeteeEvlrkvaeHakaaHglte 41
                mk+++C   g+dC+fei ++++ E ++k ++H  ++Hg ++
  EPA06344.1  1 MKKIACSNYGYDCKFEI-TDNDLEFIEKYQKHCMDEHGVEH 40
                9****************.999999**************554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.52
# Mc/sec: 311.58
//
Query:       EPA06345.1  [L=358]
Description: PAS domain S-box [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.5e-18   66.2   2.0    5.4e-18   65.2   0.2    2.4  2  PAS_9        PAS domain
    1.3e-16   61.1   0.3      3e-16   59.9   0.3    1.7  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    4.8e-13   48.9   0.3    1.2e-12   47.6   0.3    1.7  1  HisKA        His Kinase A (phospho-acceptor) domain
    1.4e-12   47.7   0.2    3.2e-12   46.6   0.2    1.6  1  PAS_3        PAS fold
    5.5e-10   39.3   0.0      2e-09   37.4   0.0    1.9  2  PAS          PAS fold
    1.4e-08   34.5   0.5    4.2e-08   33.0   0.5    1.8  1  HATPase_c_5  GHKL domain
    2.2e-08   34.3   0.0    3.3e-08   33.7   0.0    1.3  1  PAS_4        PAS fold
    0.00012   22.0   0.2    0.00028   20.7   0.2    1.7  1  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like
     0.0031   17.3   0.3      0.018   14.9   0.1    2.2  2  MAPKK1_Int   Mitogen-activated protein kinase kinase 1 intera
  ------ inclusion threshold ------
      0.034   14.2   0.0      0.094   12.8   0.0    1.7  1  PAS_8        PAS domain
       0.13   12.2   0.0       0.25   11.3   0.0    1.4  1  HATPase_c_2  Histidine kinase-like ATPase domain
       0.15   12.4   0.0        0.4   11.1   0.0    1.7  1  DuffyBP_N    Duffy binding protein N terminal


Domain annotation for each model (and alignments):
>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.2   0.2   3.6e-21   5.4e-18       4     104 .]      35     135 ..      31     135 .. 0.86
   2 ?   -0.3   0.1      0.88   1.3e+03      60      82 ..     246     268 ..     173     289 .. 0.59

  Alignments for each domain:
  == domain 1  score: 65.2 bits;  conditional E-value: 3.6e-21
       PAS_9   4 ilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk.kerevevvlirkngetfwvlltaspvkdddgelvgiivilrD 101
                 + i++ +g+i+y+N++++++  ysp e++gk+ + l  +d + +++ +++++++++   +++e+ +  k+g+++w + t++p++d++++++ +i+i++D
  EPA06345.1  35 VSITDAEGNITYINNKFCQISKYSPHEIVGKNHRILK-SDFHPENFYENMWKTISSgCIWHGEIKNKAKDGTYYWKKTTIVPIFDSNENIQQYISISTD 132
                 44799***************************77777.55555555555555555555***************************************** PP

       PAS_9 102 ite 104
                 it+
  EPA06345.1 133 ITD 135
                 **6 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.88
       PAS_9  60 kerevevvlirkngetfwvllta 82 
                 + ++ ev + +k  + ++v++ +
  EPA06345.1 246 PKKDIEVMCDKKRISVVMVNIIL 268
                 23455555555555555555555 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.9   0.3     2e-19     3e-16       2     109 ..     255     354 ..     254     357 .. 0.88

  Alignments for each domain:
  == domain 1  score: 59.9 bits;  conditional E-value: 2e-19
                 HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCS.TTCHHCSTCHTSTSSSHHHHHHHHHHHHTTTEEEEEEETT CS
   HATPase_c   2 dekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfe.kfsqddstkrggggtGlGlsivkklvelmgGeiwvesepg 99 
                 d+kr+  ++ n++ N +++ +++g+i+++ k  ++   i++eD+G Gip  +++k+fe  f++      +++gtGlGls vk +++ + G+i+v+ +p 
  EPA06345.1 255 DKKRISVVMVNIILNGIQAINENGNIKIRFKDADEFAIIEIEDSGSGIPDHIIDKIFEpMFTT------KQQGTGLGLSSVKTIINAHAGKISVKCNP- 346
                 78899999**********9889*********64478999*******************66666......99************9999*******9888. PP

                 TEEEEEEEEE CS
   HATPase_c 100 rGttftftlp 109
                   t f + +p
  EPA06345.1 347 --TVFSIIIP 354
                 ..77766665 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6   0.3   8.3e-16   1.2e-12       3      65 ..     153     215 ..     151     216 .. 0.90

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 8.3e-16
                 HHHHHHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHH..HHHHHHHHHHHHHHHHHHHHHHCCHH CS
       HisKA   3 grflagvaHELrtPLsailgnaeaLkregklteelke..yletiesearrldhlvedlLdlsrie 65 
                 g++ + +aH++r+PLs+i++++e Lk    ++ + ++  + ++i ++++r++h++ed+Ld+ r +
  EPA06345.1 153 GELSSRIAHDIRNPLSVIRAAVENLKI--LYSIDDAKlkNMDKIDRSIDRITHQIEDVLDFVRSD 215
                 789999*******************98..5666666667**********************9987 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.6   0.2   2.1e-15   3.2e-12       2      88 ..      45     129 ..      44     130 .. 0.90

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 2.1e-15
       PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirdengkpvrvigv 88 
                 +y+++++++i  ysp+e+ gk  +++ l      e+++e++++ +++g+ ++ge++ + kdG+y+w ++++++i+d+n +++++i++
  EPA06345.1  45 TYINNKFCQISKYSPHEIVGK--NHRILKSDFHPENFYENMWKTISSGCIWHGEIKNKAKDGTYYWKKTTIVPIFDSNENIQQYISI 129
                 79*******************..5555544445778**********************************************99986 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.0   1.4e-12     2e-09      12     112 ..      33     132 ..      21     133 .. 0.86
   2 ?   -1.9   0.0       2.2   3.3e+03      59      81 ..     264     286 ..     255     301 .. 0.71

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 1.4e-12
                 SEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEECTTSSEEEEEEEEEEEEETTEEEEEEEEEE CS
         PAS  12 dpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfklrdgrpihlevraspvrdaggeilgflgvl 110
                 + + ++D+ g+i+y+N +++++  +s+ e++gk+  +l +  +++ ++e +++ +++g  ++++ ++  + dg++++  ++ +p++d  ++i +++ + 
  EPA06345.1  33 SIVSITDAEGNITYINNKFCQISKYSPHEIVGKNHRILKSDFHPENFYENMWKTISSGCIWHGEIKNKAK-DGTYYWKKTTIVPIFDSNENIQQYISIS 130
                 67899****************************9877766555557***************995555555.********************99988776 PP

                 EE CS
         PAS 111 rd 112
                  d
  EPA06345.1 131 TD 132
                 66 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.2
                 HHHHHHHHHHTT-ECCCCEEEEC CS
         PAS  59 aelleqlleqgeesrageisfkl 81 
                 + ++++ +++ +e+ + +i+fk 
  EPA06345.1 264 VNIILNGIQAINENGNIKIRFKD 286
                 55666777777777777777765 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.5   2.8e-11   4.2e-08       4      97 ..     257     352 ..     254     354 .. 0.85

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 2.8e-11
  HATPase_c_5   4 ldlcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg....ekkkle..sskskkeehGiGlksireivkkykgnlsieaedglFt 95 
                  + ++v++ n++ N i+a ++       I++ ++  +++ ii+ie s +g     ++k++    ++k++  G+Gl+s++ i++ + g++s++ + ++F+
   EPA06345.1 257 KRISVVMVNIILNGIQAINENG----NIKIRFKDADEFAIIEIEDSGSGipdhIIDKIFepMFTTKQQGTGLGLSSVKTIINAHAGKISVKCNPTVFS 350
                  66899************99866....7*******************99955542355554445788899***************************98 PP

  HATPase_c_5  96 ls 97 
                    
   EPA06345.1 351 II 352
                  65 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   0.0   2.2e-11   3.3e-08       8     109 ..      35     137 ..      29     138 .. 0.90

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 2.2e-11
       PAS_4   8 lavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.pgeerhyelrllPlrdesGevigvlvisrDi 105
                 + + d++g+++y+N+ ++++ +++p+e++Gk  + l ++ + +++ +++ + ++++  ++ ++  +  +g   +  ++++P++d++  ++ ++ is+Di
  EPA06345.1  35 VSITDAEGNITYINNKFCQISKYSPHEIVGKNHRILKSDFHPENFYENMWKTISSGCIWHGEIKNKAkDGTYYWKKTTIVPIFDSNENIQQYISISTDI 133
                 5567******************************555555999********************9999888888888999*****9999*********** PP

       PAS_4 106 Terr 109
                 T+++
  EPA06345.1 134 TDQK 137
                 *998 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.2   1.9e-07   0.00028       5      63 ..     261     320 ..     257     344 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.9e-07
  HATPase_c_3   5 kAlaelvdNsldAdaen..vkievnknrgktgeivieDdGkGmseeelknalrlatsskea 63 
                  ++++ ++ N+++A  en  +ki +++ + + + i ieD G+G++   +++ ++++ ++k++
   EPA06345.1 261 VVMVNIILNGIQAINENgnIKIRFKDAD-EFAIIEIEDSGSGIPDHIIDKIFEPMFTTKQQ 320
                  57899********999855777777664.57899*********************999985 PP

>> MAPKK1_Int  Mitogen-activated protein kinase kinase 1 interacting
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.67     1e+03       7      28 ..      22      43 ..      16      63 .. 0.75
   2 !   14.9   0.1   1.2e-05     0.018      18      88 ..     280     349 ..     264     356 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.67
  MAPKK1_Int  7 lkkllsevdgllaiivtDrDGv 28
                lk++ + +d++  + +tD  G 
  EPA06345.1 22 LKNIHHALDQSSIVSITDAEGN 43
                6777777888888888887775 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1.2e-05
  MAPKK1_Int  18 laiivtDrDGvvllkvgddss..adsalrpslistfvlatdQasKLdlgknksiislyedyqvvqfnklplil 88 
                   i   D D + ++++ d  s  +d+++++ + + f+ + +Q+  L+l++ k+ii  +  ++ v+ n    ++
  EPA06345.1 280 IKIRFKDADEFAIIEIEDSGSgiPDHIIDKIFEPMFT-TKQQGTGLGLSSVKTIINAHAGKISVKCNP--TVF 349
                 5677789***********998899********99997.579*****************9999998874..333 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   6.3e-05     0.094      16      55 ..      37      77 ..      28      87 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.3e-05
       PAS_8 16 vvd.lgdrivdvNqaalellGys.adlkgellgqllpvlrpl 55
                ++d +g+ i+++N++++++  ys  ++ g+  ++l  +++p+
  EPA06345.1 37 ITDaEGN-ITYINNKFCQISKYSpHEIVGKNHRILKSDFHPE 77
                6886666.***************9999998886666666655 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00016      0.25      40     107 ..     263     331 ..     241     345 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00016
  HATPase_c_2  40 ctNavehayleap.egpvevrlesdeealtvevaDsGpgfdpetlpdpteeepkeslkegGrGlalikg 107
                  ++N++  + +  + +g +++r+++++e   +e++DsG g + + +++  e+  +++++  G+Gl  +k+
   EPA06345.1 263 MVNIILNGIQAINeNGNIKIRFKDADEFAIIEIEDSGSGIPDHIIDKIFEPMFTTKQQGTGLGLSSVKT 331
                  55666666666665799**********************877777777777767788888888765555 PP

>> DuffyBP_N  Duffy binding protein N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00027       0.4      19      57 ..     286     326 ..     279     330 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00027
   DuffyBP_N  19 GarnlvmldyeisssGqPdGildnvle..lvtedeGnslkn 57 
                  a  + +++ e s+sG Pd i+d + e  ++t+++G  l  
  EPA06345.1 286 DADEFAIIEIEDSGSGIPDHIIDKIFEpmFTTKQQGTGLGL 326
                 5777889999****************987888888876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       805  (0.0448993); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.67u 0.28s 00:00:00.95 Elapsed: 00:00:00.51
# Mc/sec: 2095.73
//
Query:       EPA06346.1  [L=797]
Description: hypothetical protein BG20_I1249 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-05   25.3  12.3    5.8e-05   23.0   0.3    4.9  5  Big_1       Bacterial Ig-like domain (group 1)
    0.00015   22.0  14.8      0.084   13.2   1.4    4.8  5  Invasin_D3  Invasin, domain 3


Domain annotation for each model (and alignments):
>> Big_1  Bacterial Ig-like domain (group 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.7   0.3    0.0017        15       8      64 .]     144     207 ..     139     207 .. 0.83
   2 ?   -1.9   0.1      0.38   3.4e+03      22      44 ..     262     285 ..     260     286 .. 0.78
   3 ?   -1.2   0.1      0.23   2.1e+03      56      64 .]     311     319 ..     301     327 .. 0.59
   4 ?    1.0   0.0     0.048   4.3e+02       1      21 [.     354     374 ..     354     395 .. 0.88
   5 !   23.0   0.3   6.5e-09   5.8e-05       5      64 .]     651     709 ..     648     709 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0017
       Big_1   8 tltatvkDangnpva...gatVtfsvsg.gals.assgtTdanGkatvt..ltstkagtvtvtA 64 
                  +t++++++ng pv+   +  V++s s+ g +s + s +  ++G+++ +  +t+ k g vt+tA
  EPA06346.1 144 IVTVVLTNENGIPVKadkDYLVKISYSKsGIISlSDSNIIISKGEFSSKqiITGMKDGIVTITA 207
                 69************63336779999999777779999999999999987778999999999998 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.38
       Big_1  22 agatVtfsvsg.galsassgtTda 44 
                 +++t++f++s+ + l+++s  +da
  EPA06346.1 262 SDITIHFKISSdSELVNTSKESDA 285
                 7899******97777777777765 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.23
       Big_1  56 kagtvtvtA 64 
                    t+tvtA
  EPA06346.1 311 MENTYTVTA 319
                 444555554 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.048
       Big_1   1 AdGvdtntltatvkDangnpv 21 
                 A+G+++    + + Dang+pv
  EPA06346.1 354 ANGNEQLIGVIYLEDANGHPV 374
                 8999999999999*******8 PP

  == domain 5  score: 23.0 bits;  conditional E-value: 6.5e-09
       Big_1   5 dtntltatvkDangnpvagatVtfsvsggalsassgtTdanGkatvtltstkagtvtvtA 64 
                 d+  +++ +k +ng p+++a ++++  gg ++ s ++T+  G+a +++  t    v++ A
  EPA06346.1 651 DSFIVSIQAK-QNGMPLQNAHINWELEGGITTISDQKTGPTGEAIASVIATSKDAVKIIA 709
                 6777777777.8***************************************999999876 PP

>> Invasin_D3  Invasin, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.38   3.4e+03      61      82 ..      86     107 ..      55     112 .. 0.75
   2 !    9.6   0.3   0.00012       1.1      20      88 ..     141     215 ..     126     224 .. 0.74
   3 ?   -1.7   0.6      0.42   3.8e+03      43      43 ..     268     268 ..     229     327 .. 0.51
   4 !    5.4   0.0    0.0026        23       7      48 ..     345     389 ..     339     409 .. 0.74
   5 !   13.2   1.4   9.4e-06     0.084       4      93 ..     636     727 ..     633     730 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.38
  Invasin_D3  61 tytatLtattagtatitptvnG 82 
                   +++L a ++g++++ + v+G
  EPA06346.1  86 KTIVKLDARKEGETQLYVYVEG 107
                 4567888999999999999999 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00012
  Invasin_D3  20 ststltvtlkDangnpvsglt...vtfsttsag..tlsavt...dngdGtytatLtattagtatitptvnGvaiaat 88 
                 ++  +tv l+++ng pv+ ++   v++s +++g  +ls+     ++g+   + ++t+ + g +tit++ +    +++
  EPA06346.1 141 NQGIVTVVLTNENGIPVKADKdylVKISYSKSGiiSLSDSNiiiSKGEFSSKQIITGMKDGIVTITAKTDD--LETS 215
                 56679***********88866578999999999555554446456666667789*************9986..3333 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.42
  Invasin_D3  43 f 43 
                 f
  EPA06346.1 268 F 268
                 2 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.0026
  Invasin_D3   7 ftaspasivAdGkststltvtlkDangnp.vsglt..vtfsttsa 48 
                 ++  p s +A+G+++    + l+Dang p +++    + fst+++
  EPA06346.1 345 IKFYPLSSLANGNEQLIGVIYLEDANGHPvIANRDiiIPFSTSDK 389
                 556777889********************8777554567776644 PP

  == domain 5  score: 13.2 bits;  conditional E-value: 9.4e-06
  Invasin_D3   4 kStftaspasivAdGkststltvtlkDangnpvsgltvtfsttsag..tlsavtdngdGtytatLtattagtatitptvnG...vaiaatatvtl 93 
                 + ++++s ++iv  G s   +++++k +ng p++++ +++  +  g  t+s+ ++   G  +a + at++++++i +++++   +++ a++ v++
  EPA06346.1 636 TPSIQISSENIVNEGDSF-IVSIQAK-QNGMPLQNAHINWELE-GGitTISDQKTGPTGEAIASVIATSKDAVKIIASIDNgpiQSAFASKIVKV 727
                 567888888887776655.4899998.79************98.77889999999999*********************5536555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (797 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       765  (0.0426683); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.42
# Mc/sec: 5741.32
//
Query:       EPA06347.1  [L=127]
Description: hypothetical protein BG20_I1252 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.14   12.5   0.1        1.4    9.3   0.1    2.1  2  Synapsin  Synapsin, N-terminal domain


Domain annotation for each model (and alignments):
>> Synapsin  Synapsin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0     0.025   4.5e+02      37      60 ..      44      67 ..      22      77 .. 0.78
   2 ?    9.3   0.1   7.7e-05       1.4       8      43 ..      86     119 ..      82     126 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.025
    Synapsin 37 efselnlvaysdkglvvdlkvsrn 60
                +f e++l + sd++l+v    s+ 
  EPA06347.1 44 NFGEFELFSLSDDSLTVRKLISKA 67
                688999999999999887665555 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 7.7e-05
    Synapsin   8 viddqktdwskyfrgkklsGeydirVEqaefselnl 43 
                 +i ++k d++k+++g k+ G+  ++ E a f +l+ 
  EPA06347.1  86 IIRRRKSDYAKVLKGDKVIGH--LELESARFGKLKW 119
                 678999**************9..7789999988865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 913.99
//
Query:       EPA06348.1  [L=589]
Description: tetratricopeptide repeat protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.5e-48  158.5  28.6    5.9e-08   32.2   1.3   12.7 12  TPR_1        Tetratricopeptide repeat
      2e-47  155.5  11.2    7.4e-05   22.6   0.4   14.2 14  TPR_2        Tetratricopeptide repeat
    1.2e-37  128.3   0.7    4.5e-06   27.1   0.0    9.0 10  TPR_19       Tetratricopeptide repeat
    6.4e-33  110.2  36.8    0.00027   20.9   0.0   14.7 15  TPR_8        Tetratricopeptide repeat
    3.1e-31  107.7   0.0    4.9e-07   30.3   0.0    7.1  7  TPR_16       Tetratricopeptide repeat
      4e-30  101.9   0.0       0.12   13.2   0.0   12.1 13  TPR_14       Tetratricopeptide repeat
    4.1e-28   96.8  19.0    0.00027   20.6   0.0   11.1 11  TPR_11       TPR repeat
    8.7e-25   85.7   0.2       0.77   10.5   0.0   12.9 13  TPR_6        Tetratricopeptide repeat
    1.4e-24   86.1  20.9    3.5e-07   30.4   0.0    6.8 10  ANAPC3       Anaphase-promoting complex, cyclosome, subunit 3
    5.6e-23   79.2   5.0      0.056   13.5   0.0   10.3 10  TPR_7        Tetratricopeptide repeat
    6.5e-23   79.4  18.6     0.0076   16.6   0.6   11.0 10  TPR_17       Tetratricopeptide repeat
    1.7e-19   69.8  12.3    0.00085   19.6   0.0    9.8  9  TPR_12       Tetratricopeptide repeat
    1.4e-15   57.2   0.0      0.039   14.1   0.0    6.5  8  TPR_9        Tetratricopeptide repeat
    5.5e-11   42.0   0.1        1.2    9.1   0.0    8.7 10  TPR_10       Tetratricopeptide repeat
    1.4e-09   38.1   3.0       0.33   11.3   0.0    7.0  9  TPR_20       Tetratricopeptide repeat
    2.8e-07   29.9  20.7      0.013   14.5   1.3    6.8  6  NARP1        NMDA receptor-regulated protein 1
    1.3e-06   28.4  17.7       0.99    9.5   0.1    8.2  9  Fis1_TPR_C   Fis1 C-terminal tetratricopeptide repeat
    1.1e-05   25.0  13.1       0.18   11.2   1.7    4.5  4  Coatomer_E   Coatomer epsilon subunit
    1.9e-05   24.3   0.0        1.5    8.5   0.0    5.2  5  HrpB1_HrpK   Bacterial type III secretion protein (HrpB1_HrpK
    4.7e-05   23.4   0.0         18    5.5   0.0    5.8  6  Rapsyn_N     Rapsyn N-terminal myristoylation and linker regi
    9.3e-05   21.5   3.9      0.012   14.6   0.3    3.6  4  DUF5588      Family of unknown function (DUF5588)
    0.00057   19.7   2.4        2.1    8.1   0.1    4.3  4  TOM20_plant  Plant specific mitochondrial import receptor sub
     0.0024   18.3   0.0        1.8    9.0   0.0    4.2  7  BTAD         Bacterial transcriptional activator domain
     0.0029   16.7   9.9       0.11   11.4   0.6    3.8  4  ChAPs        ChAPs (Chs5p-Arf1p-binding proteins)
     0.0041   17.1   7.2       0.67    9.9   0.6    4.4  5  DUF4919      Domain of unknown function (DUF4919)
  ------ inclusion threshold ------
       0.16   10.7   0.0        5.8    5.5   0.0    3.0  3  PknG_TPR     Protein kinase G tetratricopeptide repeat
        1.1    9.3  14.9        2.6    8.2   0.1    6.6  7  MIT          MIT (microtubule interacting and transport) doma
        7.8    7.0  10.1          2    8.9   0.3    3.8  3  DUF5099      Domain of unknown function (DUF5099)


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.2   1.7e-05     0.011       6      33 ..      62      89 ..      61      90 .. 0.95
   2 !   32.2   1.3   9.2e-11   5.9e-08       2      32 ..      92     122 ..      91     124 .. 0.92
   3 !    9.9   0.0     0.001      0.66       2      34 .]     126     158 ..     125     158 .. 0.95
   4 ?    4.5   0.0     0.053        34       3      34 .]     194     225 ..     193     225 .. 0.93
   5 !   17.0   0.0     6e-06    0.0038       2      34 .]     227     259 ..     226     259 .. 0.89
   6 !   23.3   0.0     6e-08   3.8e-05       2      34 .]     261     293 ..     260     293 .. 0.94
   7 !   13.5   0.0   7.5e-05     0.048       4      26 ..     297     319 ..     295     319 .. 0.88
   8 !    7.8   0.0    0.0047         3       5      25 ..     332     352 ..     329     355 .. 0.89
   9 ?    6.7   0.1     0.011       6.8       3      34 .]     364     395 ..     363     395 .. 0.90
  10 !    9.1   0.0    0.0019       1.2      13      32 ..     408     427 ..     405     429 .. 0.86
  11 !   23.3   0.1   6.2e-08   3.9e-05       3      34 .]     466     497 ..     464     497 .. 0.94
  12 ?    4.1   0.1     0.072        46       9      26 ..     506     523 ..     500     526 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.7e-05
                HHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
       TPR_1  6 nlGnayfklgkydeAleyyekALelnPn 33
                nl+n ++  +k+ e l+yye AL  nP+
  EPA06348.1 62 NLANYFLACKKFTESLKYYESALVKNPQ 89
                9***********************9997 PP

  == domain 2  score: 32.2 bits;  conditional E-value: 9.2e-11
                 HHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
       TPR_1   2 kalynlGnayfklgkydeAleyyekALelnP 32 
                  al+n+G+++++l ++d+A+e+y++AL+ ++
  EPA06348.1  92 SALCNKGLCLYNLSQLDDAIECYDEALKTYH 122
                 59*************************9766 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.001
                 HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                 +a+  +G +++++++  eA+  +  +L l+P+n
  EPA06348.1 126 EAFLMKGKILLSKQNIPEAINQFYHVLDLEPEN 158
                 78999**************************97 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.053
                 HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                 +l  lG++  k+ +  + l y +k Le+ Pnn
  EPA06348.1 194 SLLLLGQIAIKNSNSHKGLSYLNKLLEVSPNN 225
                 57789**************************8 PP

  == domain 5  score: 17.0 bits;  conditional E-value: 6e-06
                 HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                 +a+   G + ++ +  +eAl+++ek+Le+ Pnn
  EPA06348.1 227 DAHLLVGKINMNAKIINEALAHFEKVLEISPNN 259
                 6777788899999999****************8 PP

  == domain 6  score: 23.3 bits;  conditional E-value: 6e-08
                 HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                 +++  lG++ +  ++ deAl+++ek+Le+ Pn+
  EPA06348.1 261 ETHLLLGQIKMDVNNTDEALAHFEKVLEISPNH 293
                 67899**************************97 PP

  == domain 7  score: 13.5 bits;  conditional E-value: 7.5e-05
                 HHHHHHHHHHTT-HHHHHHHHHH CS
       TPR_1   4 lynlGnayfklgkydeAleyyek 26 
                 l+ +  ++ klgk deA+ey+e+
  EPA06348.1 297 LNSKIILLEKLGKVDEAIEYCER 319
                 67778899*************97 PP

  == domain 8  score: 7.8 bits;  conditional E-value: 0.0047
                 HHHHHHHHHTT-HHHHHHHHH CS
       TPR_1   5 ynlGnayfklgkydeAleyye 25 
                   +G ++f++++  eAl +++
  EPA06348.1 332 LKKGILLFNNNRISEALVCFN 352
                 679*****************7 PP

  == domain 9  score: 6.7 bits;  conditional E-value: 0.011
                 HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                 al  ++ ++  +++++eAl + +  L+ + +n
  EPA06348.1 364 ALLYKAKIFTLKQEFQEALSCIDLILKYDQSN 395
                 78899****************99999988776 PP

  == domain 10  score: 9.1 bits;  conditional E-value: 0.0019
                 HTT-HHHHHHHHHHHHHHST CS
       TPR_1  13 klgkydeAleyyekALelnP 32 
                 k g+y+ Al yy++ L+  P
  EPA06348.1 408 KVGDYENALLYYDQILSKLP 427
                 78************998766 PP

  == domain 11  score: 23.3 bits;  conditional E-value: 6.2e-08
                 HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                 +l+ lG +++ l +y++A+e ++ AL+ nP n
  EPA06348.1 466 ILCELGKIHLILHNYEKAIEIFDNALKKNPFN 497
                 689***************************65 PP

  == domain 12  score: 4.1 bits;  conditional E-value: 0.072
                 HHHHHTT-HHHHHHHHHH CS
       TPR_1   9 nayfklgkydeAleyyek 26 
                 +a+f+l+kyd  + + ek
  EPA06348.1 506 LAFFSLQKYDASILCLEK 523
                 689************998 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.1   0.00022      0.14       6      33 ..      62      89 ..      61      90 .. 0.95
   2 !   22.6   0.4   1.2e-07   7.4e-05       3      31 ..      93     121 ..      91     124 .. 0.92
   3 ?    6.6   0.0     0.015       9.5       1      34 []     125     158 ..     125     158 .. 0.93
   4 ?    3.0   0.0      0.21   1.3e+02       2      25 ..     160     183 ..     159     190 .. 0.88
   5 !    7.2   0.0    0.0096       6.1       3      34 .]     194     225 ..     192     225 .. 0.94
   6 !   17.5   0.0     5e-06    0.0032       2      34 .]     227     259 ..     226     259 .. 0.93
   7 !   21.4   0.0   2.8e-07   0.00018       2      34 .]     261     293 ..     260     293 .. 0.94
   8 !    9.2   0.0    0.0023       1.5      10      29 ..     303     322 ..     302     327 .. 0.83
   9 ?    4.8   0.0     0.055        35       5      26 ..     332     353 ..     329     361 .. 0.86
  10 ?    4.9   0.1     0.054        34       3      33 ..     364     394 ..     362     395 .. 0.88
  11 !    8.6   0.0    0.0034       2.2      11      33 ..     406     428 ..     398     429 .. 0.86
  12 ?   -0.8   0.0       3.6   2.3e+03      10      34 .]     439     463 ..     433     463 .. 0.76
  13 !   22.3   0.0   1.4e-07   9.1e-05       4      33 ..     467     496 ..     465     497 .. 0.93
  14 ?    4.8   0.0     0.055        35       3      26 ..     500     523 ..     498     528 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00022
       TPR_2  6 nlGlayyklgdyeeAleafekAleldPn 33
                nl++  ++ +++ e l+++e Al  +P+
  EPA06348.1 62 NLANYFLACKKFTESLKYYESALVKNPQ 89
                89************************97 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 1.2e-07
       TPR_2   3 alynlGlayyklgdyeeAleafekAleld 31 
                 al+n Gl++y+l ++++A+e++++Al+ +
  EPA06348.1  93 ALCNKGLCLYNLSQLDDAIECYDEALKTY 121
                 899***********************965 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.015
       TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                 +ea  + G++++ +++  eA++ f  +l l+P+n
  EPA06348.1 125 PEAFLMKGKILLSKQNIPEAINQFYHVLDLEPEN 158
                 5888999*****************9999999987 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.21
       TPR_2   2 ealynlGlayyklgdyeeAleafe 25 
                 ea ++lG+++ ++++ e A++ +e
  EPA06348.1 160 EAKFYLGKSLVESNRTENAVKILE 183
                 7889***************98765 PP

  == domain 5  score: 7.2 bits;  conditional E-value: 0.0096
       TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                  l  lG++++k+ +  + l +++k le  Pnn
  EPA06348.1 194 SLLLLGQIAIKNSNSHKGLSYLNKLLEVSPNN 225
                 6789**************************98 PP

  == domain 6  score: 17.5 bits;  conditional E-value: 5e-06
       TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                 +a+   G++ ++++  +eAl++fek+le+ Pnn
  EPA06348.1 227 DAHLLVGKINMNAKIINEALAHFEKVLEISPNN 259
                 57888999************************8 PP

  == domain 7  score: 21.4 bits;  conditional E-value: 2.8e-07
       TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                 e +  lG++ +  ++ +eAl++fek+le+ Pn+
  EPA06348.1 261 ETHLLLGQIKMDVNNTDEALAHFEKVLEISPNH 293
                 67899**************************97 PP

  == domain 8  score: 9.2 bits;  conditional E-value: 0.0023
       TPR_2  10 ayyklgdyeeAleafekAle 29 
                 +++klg+ +eA+e++e+  +
  EPA06348.1 303 LLEKLGKVDEAIEYCERFAA 322
                 589*************9665 PP

  == domain 9  score: 4.8 bits;  conditional E-value: 0.055
       TPR_2   5 ynlGlayyklgdyeeAleafek 26 
                    G +++++++  eAl +f+ 
  EPA06348.1 332 LKKGILLFNNNRISEALVCFND 353
                 56899***************86 PP

  == domain 10  score: 4.9 bits;  conditional E-value: 0.054
       TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                 al + +++   +++++eAl + +  l++d  
  EPA06348.1 364 ALLYKAKIFTLKQEFQEALSCIDLILKYDQS 394
                 67889999999***********999999865 PP

  == domain 11  score: 8.6 bits;  conditional E-value: 0.0034
       TPR_2  11 yyklgdyeeAleafekAleldPn 33 
                  +k gdye Al ++++ l+  P+
  EPA06348.1 406 SLKVGDYENALLYYDQILSKLPH 428
                 5788**************99886 PP

  == domain 12  score: -0.8 bits;  conditional E-value: 3.6
       TPR_2  10 ayyklgdyeeAleafekAleldPnn 34 
                 ++  lg++ee  + + +   ld +n
  EPA06348.1 439 VLSILGRHEESGQIYSELFNLDKTN 463
                 5666889999888888888888776 PP

  == domain 13  score: 22.3 bits;  conditional E-value: 1.4e-07
       TPR_2   4 lynlGlayyklgdyeeAleafekAleldPn 33 
                 l++lG++++ l +ye+A+e f+ Al+ +P 
  EPA06348.1 467 LCELGKIHLILHNYEKAIEIFDNALKKNPF 496
                 889*************************96 PP

  == domain 14  score: 4.8 bits;  conditional E-value: 0.055
       TPR_2   3 alynlGlayyklgdyeeAleafek 26 
                 +ly   la + l++y+  + ++ek
  EPA06348.1 500 LLYKKSLAFFSLQKYDASILCLEK 523
                 79999*****************98 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   2.9e-06    0.0019       5      66 ..      71     132 ..      67     134 .. 0.88
   2 !   21.5   0.0   3.9e-07   0.00025       1      55 [.     135     189 ..     135     201 .. 0.91
   3 ?    5.5   0.0     0.038        24      22      68 .]     189     235 ..     185     235 .. 0.83
   4 !   27.1   0.0   7.1e-09   4.5e-06       8      57 ..     243     292 ..     242     292 .. 0.95
   5 !   23.4   0.0     1e-07   6.5e-05       6      58 ..     275     327 ..     271     336 .. 0.90
   6 !   12.1   0.0   0.00033      0.21       5      66 ..     308     369 ..     308     371 .. 0.88
   7 !    8.7   0.0    0.0038       2.5       5      57 ..     342     394 ..     338     399 .. 0.87
   8 ?    6.8   0.0     0.016        10       3      26 ..     408     431 ..     406     462 .. 0.82
   9 !   17.7   0.1     6e-06    0.0038       6      63 ..     479     538 ..     474     544 .. 0.92
  10 ?    0.2   0.0       1.7   1.1e+03      26      56 ..     533     563 ..     531     570 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.9e-06
      TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryasLlA 66 
                 ++++e l+++e+al ++p++  a+ +   +l++l qld+A+++ d++++ +++ +++   ++
  EPA06348.1  71 KKFTESLKYYESALVKNPQSYSALCNKGLCLYNLSQLDDAIECYDEALKTYHNIPEAFLMKG 132
                 578999*************9999999***********************9999776666555 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 3.9e-07
      TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeed 55 
                 ll  ++  eA++ +  +l+ +p+n ea+ +L + l+++++++ A ++L+ +   +
  EPA06348.1 135 LLSKQNIPEAINQFYHVLDLEPENIEAKFYLGKSLVESNRTENAVKILESIVSNN 189
                 56778999*****************************************997665 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.038
      TPR_19  22 pknaearllLAeallalgqldeAealLdalpeedpddaryasLlAkl 68 
                 ++++e +llL ++ +++ +  +    L++l+e  p++ +++ L +k+
  EPA06348.1 189 NDHLESLLLLGQIAIKNSNSHKGLSYLNKLLEVSPNNIDAHLLVGKI 235
                 67888889999999999999999999999999999988888888775 PP

  == domain 4  score: 27.1 bits;  conditional E-value: 7.1e-09
      TPR_19   8 aeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                  eAla++e++l+ +p+n e  llL ++ +  +++deA a  ++++e  p+
  EPA06348.1 243 NEALAHFEKVLEISPNNIETHLLLGQIKMDVNNTDEALAHFEKVLEISPN 292
                 59**************************************9999998876 PP

  == domain 5  score: 23.4 bits;  conditional E-value: 1e-07
      TPR_19   6 dyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd 58 
                 + +eAla++e++l+ +p++ + +   +++l +lg +deA++ +++  ++ pd 
  EPA06348.1 275 NTDEALAHFEKVLEISPNHMDGLNSKIILLEKLGKVDEAIEYCERFAASLPDP 327
                 789******************************************99999993 PP

  == domain 6  score: 12.1 bits;  conditional E-value: 0.00033
      TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryasL.lA 66 
                 g+ +eA+++ e+  +  p+  e +l   ++l++++++ eA  + ++++ +  +  ++a L +A
  EPA06348.1 308 GKVDEAIEYCERFAASLPDPTEQLLKKGILLFNNNRISEALVCFNDILGKSNN-NNVALLyKA 369
                 7899********888889988888889**********************9999.888877455 PP

  == domain 7  score: 8.7 bits;  conditional E-value: 0.0038
      TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                 ++  eAl  +  +l ++++n  a+l+ A++     +++eA  ++d +++ d+ 
  EPA06348.1 342 NRISEALVCFNDILGKSNNNNVALLYKAKIFTLKQEFQEALSCIDLILKYDQS 394
                 667789999999999999999999989**********************9997 PP

  == domain 8  score: 6.8 bits;  conditional E-value: 0.016
      TPR_19   3 aegdyaeAlalleqalqedpknae 26 
                 + gdy++Al ++ q+l++ p++  
  EPA06348.1 408 KVGDYENALLYYDQILSKLPHSKS 431
                 669*****************9765 PP

  == domain 9  score: 17.7 bits;  conditional E-value: 6e-06
      TPR_19   6 dyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd.d.aryas 63 
                 +y+ A++++ +al+++p n+++++    a ++l  +d+ + +L+++ e+d   d a+y++
  EPA06348.1 479 NYEKAIEIFDNALKKNPFNSNLLYKKSLAFFSLQKYDASILCLEKISESDSLyDyAQYQK 538
                 89************************************************9986688874 PP

  == domain 10  score: 0.2 bits;  conditional E-value: 1.7
      TPR_19  26 earllLAeallalgqldeAealLdalpeedp 56 
                 +a+++  ++++  g++++ +++L++l +++ 
  EPA06348.1 533 YAQYQKSKIQMIRGNTKQSMEILSKLIKSNN 563
                 56777777788889**********9998875 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.7      0.17   1.1e+02       6      28 ..      62      84 ..      61      84 .. 0.92
   2 !   14.8   1.0   3.8e-05     0.024       2      29 ..      92     119 ..      91     121 .. 0.94
   3 !    8.9   0.0     0.003       1.9       2      34 .]     126     158 ..     125     158 .. 0.95
   4 ?    3.1   0.0      0.22   1.4e+02       7      28 ..     165     186 ..     159     190 .. 0.83
   5 !   13.0   0.0   0.00015     0.093       2      34 .]     193     225 ..     192     225 .. 0.96
   6 !   10.8   0.0   0.00072      0.46       2      34 .]     227     259 ..     226     259 .. 0.89
   7 !   20.9   0.0   4.2e-07   0.00027       2      34 .]     261     293 ..     260     293 .. 0.94
   8 !    8.0   0.0    0.0059       3.8      10      26 ..     303     319 ..     302     321 .. 0.91
   9 ?   -0.2   0.0       2.4   1.6e+03       5      26 ..     332     353 ..     331     356 .. 0.85
  10 ?   -0.4   0.3       2.9   1.9e+03       8      33 ..     369     394 ..     364     395 .. 0.84
  11 ?    4.4   0.1      0.08        51      12      28 ..     407     423 ..     402     424 .. 0.83
  12 ?    5.7   0.0     0.032        20       6      33 ..     435     462 ..     431     463 .. 0.88
  13 !   13.8   0.0   7.9e-05      0.05       2      32 ..     465     495 ..     464     497 .. 0.89
  14 !   10.1   0.2    0.0012      0.79       3      31 ..     500     528 ..     498     529 .. 0.90
  15 ?    5.2   0.1     0.046        29       3      31 ..     534     562 ..     533     564 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.17
                HHHHHHHHTT-HHHHHHHHHHHH CS
       TPR_8  6 nlgsiylklgdyeeAkeyyekal 28
                nl++  l  +++ e+ +yye al
  EPA06348.1 62 NLANYFLACKKFTESLKYYESAL 84
                8999999*************987 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 3.8e-05
                 CHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
       TPR_8   2 eayynlgsiylklgdyeeAkeyyekale 29 
                 +a++n+g+++ +l +++ A+e+y +al+
  EPA06348.1  92 SALCNKGLCLYNLSQLDDAIECYDEALK 119
                 699***********************98 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.003
                 CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
       TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                 ea +++g+i+l+++++ eA+  + ++l+l+p+n
  EPA06348.1 126 EAFLMKGKILLSKQNIPEAINQFYHVLDLEPEN 158
                 7899***************************86 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.22
                 HHHHHHHTT-HHHHHHHHHHHH CS
       TPR_8   7 lgsiylklgdyeeAkeyyekal 28 
                 lg+ + + ++ e+A++ +e  +
  EPA06348.1 165 LGKSLVESNRTENAVKILESIV 186
                 899999***********99655 PP

  == domain 5  score: 13.0 bits;  conditional E-value: 0.00015
                 CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
       TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                 e++++lg+i +k  + ++  +y++k le +p+n
  EPA06348.1 193 ESLLLLGQIAIKNSNSHKGLSYLNKLLEVSPNN 225
                 7899***************************97 PP

  == domain 6  score: 10.8 bits;  conditional E-value: 0.00072
                 CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
       TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                 +a+++ g+i ++ + ++eA + +ek+le++p+n
  EPA06348.1 227 DAHLLVGKINMNAKIINEALAHFEKVLEISPNN 259
                 5778889999999999***************97 PP

  == domain 7  score: 20.9 bits;  conditional E-value: 4.2e-07
                 CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
       TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                 e +++lg+i ++ ++ +eA + +ek+le++p++
  EPA06348.1 261 ETHLLLGQIKMDVNNTDEALAHFEKVLEISPNH 293
                 67899**************************97 PP

  == domain 8  score: 8.0 bits;  conditional E-value: 0.0059
                 HHHHTT-HHHHHHHHHH CS
       TPR_8  10 iylklgdyeeAkeyyek 26 
                 +++klg+ +eA+ey+e+
  EPA06348.1 303 LLEKLGKVDEAIEYCER 319
                 579************97 PP

  == domain 9  score: -0.2 bits;  conditional E-value: 2.4
                 HHHHHHHHHTT-HHHHHHHHHH CS
       TPR_8   5 ynlgsiylklgdyeeAkeyyek 26 
                 +++g ++++ +++ eA  +++ 
  EPA06348.1 332 LKKGILLFNNNRISEALVCFND 353
                 578999**********999985 PP

  == domain 10  score: -0.4 bits;  conditional E-value: 2.9
                 HHHHHHTT-HHHHHHHHHHHHHHHHH CS
       TPR_8   8 gsiylklgdyeeAkeyyekaleldpd 33 
                 ++i   +++++eA +++   l++d++
  EPA06348.1 369 AKIFTLKQEFQEALSCIDLILKYDQS 394
                 77778889999*****9999999876 PP

  == domain 11  score: 4.4 bits;  conditional E-value: 0.08
                 HHTT-HHHHHHHHHHHH CS
       TPR_8  12 lklgdyeeAkeyyekal 28 
                 lk gdye+A  yy + l
  EPA06348.1 407 LKVGDYENALLYYDQIL 423
                 678**********9977 PP

  == domain 12  score: 5.7 bits;  conditional E-value: 0.032
                 HHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
       TPR_8   6 nlgsiylklgdyeeAkeyyekaleldpd 33 
                 +++++++ lg++ee+ + y +   ld++
  EPA06348.1 435 KKSRVLSILGRHEESGQIYSELFNLDKT 462
                 6789999*************99999986 PP

  == domain 13  score: 13.8 bits;  conditional E-value: 7.9e-05
                 CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
       TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldp 32 
                 ++++ lg+i+l l +ye+A+e +  al+ +p
  EPA06348.1 465 SILCELGKIHLILHNYEKAIEIFDNALKKNP 495
                 57899*********************98666 PP

  == domain 14  score: 10.1 bits;  conditional E-value: 0.0012
                 HHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
       TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleld 31 
                 ++y+++++ ++l++y++++ ++ek  e d
  EPA06348.1 500 LLYKKSLAFFSLQKYDASILCLEKISESD 528
                 78**********************88765 PP

  == domain 15  score: 5.2 bits;  conditional E-value: 0.046
                 HHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
       TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleld 31 
                 a y++++i +  g+ ++++e + k ++ +
  EPA06348.1 534 AQYQKSKIQMIRGNTKQSMEILSKLIKSN 562
                 6799*********************9976 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.0   7.6e-10   4.9e-07       1      64 [.      61     121 ..      61     123 .. 0.96
   2 !   10.5   0.0    0.0012      0.75       1      59 [.     129     184 ..     129     191 .. 0.92
   3 !   11.6   0.0   0.00053      0.34       1      67 [.     196     259 ..     196     260 .. 0.97
   4 !   18.9   0.0   2.8e-06    0.0018       1      66 [.     264     326 ..     264     327 .. 0.95
   5 ?    1.3   0.0      0.88   5.6e+02       1      54 [.     332     382 ..     332     390 .. 0.84
   6 !    8.6   0.0    0.0045       2.9       8      58 ..     407     454 ..     405     456 .. 0.92
   7 !   16.2   0.0   1.9e-05     0.012       3      54 ..     470     518 ..     468     525 .. 0.91

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 7.6e-10
      TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraa 64 
                 l+la+++l+ +++++ ++++e al ++   P+ + Al ++g++++ ++ l++A++ y++al+ +
  EPA06348.1  61 LNLANYFLACKKFTESLKYYESALVKN---PQSYSALCNKGLCLYNLSQLDDAIECYDEALKTY 121
                 689************************...******************************9865 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0012
      TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyra 59 
                 l++++++l  ++ ++A++++  +l++    P++ eA ++lg ++ + +r + A+  +++
  EPA06348.1 129 LMKGKILLSKQNIPEAINQFYHVLDLE---PENIEAKFYLGKSLVESNRTENAVKILES 184
                 6899***********************...***********************976665 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00053
      TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                 l l+++a+++ +  + + +l+ +l+     P + +A+ll g +   ++   eA+a +++ l+ +p++
  EPA06348.1 196 LLLGQIAIKNSNSHKGLSYLNKLLEVS---PNNIDAHLLVGKINMNAKIINEALAHFEKVLEISPNN 259
                 5799***********************...**********************************986 PP

  == domain 4  score: 18.9 bits;  conditional E-value: 2.8e-06
      TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                 l l+++ ++ ++ d+A+a +e +l+     P + + l+ +  ++ ++g ++eA++++++ ++  pd
  EPA06348.1 264 LLLGQIKMDVNNTDEALAHFEKVLEIS---PNHMDGLNSKIILLEKLGKVDEAIEYCERFAASLPD 326
                 578999*********************...*****************************8887775 PP

  == domain 5  score: 1.3 bits;  conditional E-value: 0.88
      TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAa 54 
                 l+++ +++++++  +A+  ++  l +      +  All+++ ++  +++++eA+
  EPA06348.1 332 LKKGILLFNNNRISEALVCFNDILGKS---NNNNVALLYKAKIFTLKQEFQEAL 382
                 578999999999999999999999998...666668888888888888888886 PP

  == domain 6  score: 8.6 bits;  conditional E-value: 0.0045
      TPR_16   8 lragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyr 58 
                 l+ gdy+ A+ ++++ l +    P    +l  + +++  +gr++e  + y 
  EPA06348.1 407 LKVGDYENALLYYDQILSKL---PHSKSFLEKKSRVLSILGRHEESGQIYS 454
                 578*****************...*********************9987775 PP

  == domain 7  score: 16.2 bits;  conditional E-value: 1.9e-05
      TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAa 54 
                 l++++l + +y++A++ ++ alk++   P++   l+ + +a++ ++ +++ +
  EPA06348.1 470 LGKIHLILHNYEKAIEIFDNALKKN---PFNSNLLYKKSLAFFSLQKYDASI 518
                 777788889****************...********************9987 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0    0.0011      0.69       7      38 ..      63      94 ..      61     100 .. 0.89
   2 !   11.3   0.0   0.00081      0.52      11      43 ..     101     133 ..      97     134 .. 0.90
   3 !   13.2   0.0   0.00019      0.12       1      43 [.     125     167 ..     125     169 .. 0.97
   4 ?    4.3   0.0      0.14        92       7      43 ..     165     200 ..     164     201 .. 0.88
   5 ?    7.3   0.0     0.015       9.9       2      42 ..     193     233 ..     192     235 .. 0.91
   6 !   10.8   0.0    0.0012      0.74      19      44 .]     244     269 ..     242     269 .. 0.95
   7 !   12.5   0.0   0.00032      0.21       2      34 ..     261     293 ..     260     298 .. 0.92
   8 ?    7.6   0.0     0.012       7.9      10      34 ..     303     327 ..     300     332 .. 0.85
   9 ?    5.3   0.0     0.069        44       3      43 ..     330     370 ..     328     371 .. 0.91
  10 ?    2.7   0.0      0.46   2.9e+02      12      36 ..     407     431 ..     397     439 .. 0.82
  11 ?    0.4   0.0       2.6   1.6e+03       9      43 ..     438     472 ..     432     473 .. 0.87
  12 !   11.4   0.0   0.00073      0.47       6      34 ..     469     497 ..     464     509 .. 0.85
  13 ?    0.3   0.0       2.6   1.7e+03       3      29 ..     534     560 ..     528     564 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0011
      TPR_14  7 laeallalGdpdeAiallrralalaPddaeaw 38
                la ++la  ++ e++++++ al ++P++  a+
  EPA06348.1 63 LANYFLACKKFTESLKYYESALVKNPQSYSAL 94
                899***********************997776 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00081
      TPR_14  11 llalGdpdeAiallrralalaPddaeawlllaq 43 
                 l++l ++d+Ai+++++al+++ + +ea l+ ++
  EPA06348.1 101 LYNLSQLDDAIECYDEALKTYHNIPEAFLMKGK 133
                 67899****************999999999886 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 0.00019
      TPR_14   1 peallalaeallalGdpdeAiallrralalaPddaeawlllaq 43 
                 pea l+ +++ll  ++  eAi+ +  +l+l P++ ea ++l++
  EPA06348.1 125 PEAFLMKGKILLSKQNIPEAINQFYHVLDLEPENIEAKFYLGK 167
                 799**************************************97 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.14
      TPR_14   7 laeallalGdpdeAiallrralalaPddaeawlllaq 43 
                 l++ l ++ +++ A+++l+ +++ + d++e +lll+q
  EPA06348.1 165 LGKSLVESNRTENAVKILESIVS-NNDHLESLLLLGQ 200
                 7888999**************99.7788898888887 PP

  == domain 5  score: 7.3 bits;  conditional E-value: 0.015
      TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawllla 42 
                 e ll+l+++   + +  + + +l+++l+  P++ +a+ll +
  EPA06348.1 193 ESLLLLGQIAIKNSNSHKGLSYLNKLLEVSPNNIDAHLLVG 233
                 56899*******************************99865 PP

  == domain 6  score: 10.8 bits;  conditional E-value: 0.0012
      TPR_14  19 eAiallrralalaPddaeawlllaql 44 
                 eA+a+++++l+  P++ e++lll+q+
  EPA06348.1 244 EALAHFEKVLEISPNNIETHLLLGQI 269
                 8***********************96 PP

  == domain 7  score: 12.5 bits;  conditional E-value: 0.00032
      TPR_14   2 eallalaeallalGdpdeAiallrralalaPdd 34 
                 e +l+l+++ +   ++deA+a+++++l+  P++
  EPA06348.1 261 ETHLLLGQIKMDVNNTDEALAHFEKVLEISPNH 293
                 67899**************************87 PP

  == domain 8  score: 7.6 bits;  conditional E-value: 0.012
      TPR_14  10 allalGdpdeAiallrralalaPdd 34 
                 +l+ lG+ deAi++++r  a  Pd+
  EPA06348.1 303 LLEKLGKVDEAIEYCERFAASLPDP 327
                 7899*************88877775 PP

  == domain 9  score: 5.3 bits;  conditional E-value: 0.069
      TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawlllaq 43 
                  ll+ + +l+++ +  eA+ +++++l +  ++ +a+l+ a+
  EPA06348.1 330 QLLKKGILLFNNNRISEALVCFNDILGKSNNNNVALLYKAK 370
                 57888999***********************9999999997 PP

  == domain 10  score: 2.7 bits;  conditional E-value: 0.46
      TPR_14  12 lalGdpdeAiallrralalaPddae 36 
                 l  Gd++ A+ +++++l++ P +  
  EPA06348.1 407 LKVGDYENALLYYDQILSKLPHSKS 431
                 5569***************998765 PP

  == domain 11  score: 0.4 bits;  conditional E-value: 2.6
      TPR_14   9 eallalGdpdeAiallrralalaPddaeawlllaq 43 
                 ++l  lG+++e+ +++ ++  l+ ++  ++ +l++
  EPA06348.1 438 RVLSILGRHEESGQIYSELFNLDKTNISILCELGK 472
                 78999***********9999999999888888876 PP

  == domain 12  score: 11.4 bits;  conditional E-value: 0.00073
      TPR_14   6 alaeallalGdpdeAiallrralalaPdd 34 
                 +l++++l l ++++Ai++++ al+++P +
  EPA06348.1 469 ELGKIHLILHNYEKAIEIFDNALKKNPFN 497
                 6899**********************944 PP

  == domain 13  score: 0.3 bits;  conditional E-value: 2.6
      TPR_14   3 allalaeallalGdpdeAiallrrala 29 
                 a+++  ++ + +G++++++++l ++++
  EPA06348.1 534 AQYQKSKIQMIRGNTKQSMEILSKLIK 560
                 456666778899*********999876 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.1   0.00014      0.09       4      41 ..      67     104 ..      64     105 .. 0.91
   2 !   12.9   0.3   0.00011     0.068       4      31 ..     101     128 ..      98     133 .. 0.82
   3 !   17.5   0.0   3.7e-06    0.0024       1      38 [.     132     169 ..     132     173 .. 0.94
   4 !    8.0   0.1    0.0035       2.3      18      38 ..     216     236 ..     214     239 .. 0.89
   5 !   20.6   0.0   4.1e-07   0.00027      11      37 ..     243     269 ..     242     273 .. 0.93
   6 !    9.9   0.0   0.00092      0.59       1      27 [.     267     293 ..     267     299 .. 0.87
   7 ?   -0.6   0.0       1.7   1.1e+03       6      15 ..     306     315 ..     304     315 .. 0.89
   8 ?   -1.5   0.2       3.2     2e+03       8      18 ..     410     420 ..     408     421 .. 0.77
   9 !   10.7   0.0   0.00052      0.33       7      38 ..     443     474 ..     438     477 .. 0.92
  10 !    9.4   0.2    0.0012       0.8       9      40 ..     479     510 ..     476     512 .. 0.91
  11 ?    3.2   0.0      0.11        73       3      19 ..     507     523 ..     505     537 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
      TPR_11   4 yyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykq 41 
                 + +  k++e+++ Y+ Al  +P++ +a++n Gl +y++
  EPA06348.1  67 FLACKKFTESLKYYESALVKNPQSYSALCNKGLCLYNL 104
                 678899**************************999975 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00011
      TPR_11   4 yyeqGkyeeAieaYkkAlkldPdnaeay 31 
                 +y + ++++Aie+Y +Alk   + +ea+
  EPA06348.1 101 LYNLSQLDDAIECYDEALKTYHNIPEAF 128
                 68889*************9877777776 PP

  == domain 3  score: 17.5 bits;  conditional E-value: 3.7e-06
      TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlay 38 
                 G+++ ++++++eAi+++   l+l P+n ea + LG+ +
  EPA06348.1 132 GKILLSKQNIPEAINQFYHVLDLEPENIEAKFYLGKSL 169
                 89*********************************976 PP

  == domain 4  score: 8.0 bits;  conditional E-value: 0.0035
      TPR_11  18 kkAlkldPdnaeayynLGlay 38 
                 +k l+ +P+n +a++  G++ 
  EPA06348.1 216 NKLLEVSPNNIDAHLLVGKIN 236
                 899*************99986 PP

  == domain 5  score: 20.6 bits;  conditional E-value: 4.1e-07
      TPR_11  11 eeAieaYkkAlkldPdnaeayynLGla 37 
                 +eA+++++k l+++P+n e ++ LG++
  EPA06348.1 243 NEALAHFEKVLEISPNNIETHLLLGQI 269
                 8************************97 PP

  == domain 6  score: 9.9 bits;  conditional E-value: 0.00092
      TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdn 27 
                 G++ ++ ++ +eA+++++k l+++P+ 
  EPA06348.1 267 GQIKMDVNNTDEALAHFEKVLEISPNH 293
                 6777888999***************95 PP

  == domain 7  score: -0.6 bits;  conditional E-value: 1.7
      TPR_11   6 eqGkyeeAie 15 
                 ++Gk +eAie
  EPA06348.1 306 KLGKVDEAIE 315
                 58******97 PP

  == domain 8  score: -1.5 bits;  conditional E-value: 3.2
      TPR_11   8 GkyeeAieaYk 18 
                 G+ye+A+  Y 
  EPA06348.1 410 GDYENALLYYD 420
                 89999987775 PP

  == domain 9  score: 10.7 bits;  conditional E-value: 0.00052
      TPR_11   7 qGkyeeAieaYkkAlkldPdnaeayynLGlay 38 
                 +G+ ee+ + Y++  +ld +n +++++LG+++
  EPA06348.1 443 LGRHEESGQIYSELFNLDKTNISILCELGKIH 474
                 79999999**********************98 PP

  == domain 10  score: 9.4 bits;  conditional E-value: 0.0012
      TPR_11   9 kyeeAieaYkkAlkldPdnaeayynLGlayyk 40 
                 +ye+Aie + +Alk +P n +++y+  la++ 
  EPA06348.1 479 NYEKAIEIFDNALKKNPFNSNLLYKKSLAFFS 510
                 7***********************99888876 PP

  == domain 11  score: 3.2 bits;  conditional E-value: 0.11
      TPR_11   3 ayyeqGkyeeAieaYkk 19 
                 a+++++ky+++i +++k
  EPA06348.1 507 AFFSLQKYDASILCLEK 523
                 89**********99887 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1      0.54   3.5e+02      14      33 .]      71      90 ..      61      90 .. 0.79
   2 !    9.5   0.1    0.0026       1.7       6      30 ..      97     121 ..      93     121 .. 0.92
   3 ?   -1.0   0.0       5.7   3.6e+03       1      28 [.     126     153 ..     126     158 .. 0.76
   4 !   10.5   0.0    0.0012      0.77       1      29 [.     160     188 ..     160     190 .. 0.91
   5 ?    4.8   0.0     0.082        52       1      32 [.     193     224 ..     193     225 .. 0.92
   6 ?    4.7   0.0     0.085        54       1      32 [.     227     258 ..     227     259 .. 0.89
   7 !    8.9   0.0     0.004       2.6       4      33 .]     264     293 ..     261     293 .. 0.82
   8 ?    6.2   0.0     0.029        19      10      32 ..     304     326 ..     302     327 .. 0.87
   9 ?    0.0   0.0       2.7   1.7e+03       3      27 ..     331     355 ..     331     357 .. 0.88
  10 ?    5.6   0.1     0.045        29      13      33 .]     407     429 ..     363     429 .. 0.85
  11 ?    5.6   0.0     0.046        29      15      31 ..     479     495 ..     470     497 .. 0.90
  12 ?    1.9   0.0      0.66   4.3e+02       3      26 ..     501     524 ..     500     527 .. 0.88
  13 ?    5.2   0.0     0.061        39       6      29 ..     533     561 ..     528     562 .. 0.69

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.54
                HHHHHHHHHHHHHHHH-TT- CS
       TPR_6 14 gdtdkAlealerlikeYPdS 33
                ++ +++l+++e+ + + P+S
  EPA06348.1 71 KKFTESLKYYESALVKNPQS 90
                48899*************98 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0026
                 HHHHHHHHHHHHHHHHHHHHHHHH- CS
       TPR_6   6 lalsyrklgdtdkAlealerlikeY 30 
                  +l++++l + d+A+e +++ +k Y
  EPA06348.1  97 KGLCLYNLSQLDDAIECYDEALKTY 121
                 69*****99*************998 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 5.7
                 HHHHHHHHHHHH.HHHHHHHHHHHHHHHH CS
       TPR_6   1 dAlyklalsyrk.lgdtdkAlealerlik 28 
                 +A+++ ++ +++ + +  +A+  +  +++
  EPA06348.1 126 EAFLMKGKILLSkQ-NIPEAINQFYHVLD 153
                 69999999999846.99999987766655 PP

  == domain 4  score: 10.5 bits;  conditional E-value: 0.0012
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
       TPR_6   1 dAlyklalsyrklgdtdkAlealerlike 29 
                 +A ++l++s+ + ++t++A+++le+++++
  EPA06348.1 160 EAKFYLGKSLVESNRTENAVKILESIVSN 188
                 688*********77***********9987 PP

  == domain 5  score: 4.8 bits;  conditional E-value: 0.082
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
       TPR_6   1 dAlyklalsyrklgdtdkAlealerlikeYPd 32 
                 ++l++l++  +k  ++ k l +l++l++  P+
  EPA06348.1 193 ESLLLLGQIAIKNSNSHKGLSYLNKLLEVSPN 224
                 689*********88*************99998 PP

  == domain 6  score: 4.7 bits;  conditional E-value: 0.085
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
       TPR_6   1 dAlyklalsyrklgdtdkAlealerlikeYPd 32 
                 dA ++ ++   +++   +Al+ +e++++  P+
  EPA06348.1 227 DAHLLVGKINMNAKIINEALAHFEKVLEISPN 258
                 68888899999988999***********9998 PP

  == domain 7  score: 8.9 bits;  conditional E-value: 0.004
                 HHHHHHHHHHHHHHHHHHHHHHHHHH-TT- CS
       TPR_6   4 yklalsyrklgdtdkAlealerlikeYPdS 33 
                 ++l++     ++td+Al+ +e++++  P++
  EPA06348.1 264 LLLGQIKMDVNNTDEALAHFEKVLEISPNH 293
                 56677777746***************9995 PP

  == domain 8  score: 6.2 bits;  conditional E-value: 0.029
                 HHHHHHHHHHHHHHHHHHHH-TT CS
       TPR_6  10 yrklgdtdkAlealerlikeYPd 32 
                 ++klg+ d+A+e+ er+  + Pd
  EPA06348.1 304 LEKLGKVDEAIEYCERFAASLPD 326
                 56799************998876 PP

  == domain 9  score: 0.0 bits;  conditional E-value: 2.7
                 HHHHHHHHHHHHHHHHHHHHHHHHH CS
       TPR_6   3 lyklalsyrklgdtdkAlealerli 27 
                 l+k + ++++ ++ ++Al  +++++
  EPA06348.1 331 LLKKGILLFNNNRISEALVCFNDIL 355
                 7899999**988******9999875 PP

  == domain 10  score: 5.6 bits;  conditional E-value: 0.045
                 H..HHHHHHHHHHHHHHHH-TT- CS
       TPR_6  13 l..gdtdkAlealerlikeYPdS 33 
                 l  gd+++Al ++++++++ P S
  EPA06348.1 407 LkvGDYENALLYYDQILSKLPHS 429
                 1447**************99987 PP

  == domain 11  score: 5.6 bits;  conditional E-value: 0.046
                 HHHHHHHHHHHHHHH-T CS
       TPR_6  15 dtdkAlealerlikeYP 31 
                 +++kA+e++++ +k+ P
  EPA06348.1 479 NYEKAIEIFDNALKKNP 495
                 89*************99 PP

  == domain 12  score: 1.9 bits;  conditional E-value: 0.66
                 HHHHHHHHHHHHHHHHHHHHHHHH CS
       TPR_6   3 lyklalsyrklgdtdkAlealerl 26 
                 lyk  l++++l+++d+++  le++
  EPA06348.1 501 LYKKSLAFFSLQKYDASILCLEKI 524
                 8999******77****99999986 PP

  == domain 13  score: 5.2 bits;  conditional E-value: 0.061
                 HHHHHHHH.....HHHHHHHHHHHHHHHH CS
       TPR_6   6 lalsyrkl.....gdtdkAlealerlike 29 
                  a+ +++      g+t +++e+l +lik+
  EPA06348.1 533 YAQYQKSKiqmirGNTKQSMEILSKLIKS 561
                 44433332455667*************96 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   1.2   5.7e-07   0.00036       6      78 ..      74     147 ..      69     151 .. 0.91
   2 !   25.5   0.0   1.8e-08   1.2e-05       2      81 ..     138     217 ..     137     218 .. 0.93
   3 !   30.4   0.0   5.5e-10   3.5e-07       2      82 .]     172     252 ..     171     252 .. 0.97
   4 !   19.1   0.0   1.8e-06    0.0012      12      82 .]     215     286 ..     213     286 .. 0.94
   5 !   13.7   0.2   8.4e-05     0.054       4      79 ..     309     385 ..     306     388 .. 0.85
   6 !   14.2   1.5   6.1e-05     0.039       1      76 [.     340     416 ..     340     422 .. 0.87
   7 !    8.8   0.4     0.003       1.9       3      74 ..     376     448 ..     374     456 .. 0.85
   8 !   14.8   0.2   3.8e-05     0.024       3      81 ..     410     489 ..     408     490 .. 0.95
   9 !   14.3   1.1   5.4e-05     0.035       3      63 ..     478     534 ..     476     558 .. 0.79
  10 ?    5.3   0.2     0.037        23       3      54 ..     512     562 ..     510     575 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 5.7e-07
                 HHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHH CS
      ANAPC3   6 knAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaa 78 
                  + + ++e +l ++++s++++  ++lcly+++q + A+e +++a k++++ +++ + +++ ll  +++ eAi+ 
  EPA06348.1  74 TESLKYYESALVKNPQSYSALCNKGLCLYNLSQLDDAIECYDEAlKTYHNIPEAFLMKGKILLSKQNIPEAINQ 147
                 56677888888899*************************************************999**999975 PP

  == domain 2  score: 25.5 bits;  conditional E-value: 1.8e-08
                 TT-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCTSHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
      ANAPC3   2 qnnyknAiflaerllaaetespedayllAlclylngqykrAyellrkaklnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                 ++n+ +Ai  +  +l  e+e+ e+ ++l+++l ++++ + A ++l++  +n+ +l++++l++q ++k ++ +++++ L k
  EPA06348.1 138 KQNIPEAINQFYHVLDLEPENIEAKFYLGKSLVESNRTENAVKILESIVSNNDHLESLLLLGQIAIKNSNSHKGLSYLNK 217
                 56788888888889999**********************************************************99987 PP

  == domain 3  score: 30.4 bits;  conditional E-value: 5.5e-10
                 TT-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-SS CS
      ANAPC3   2 qnnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLekl 82 
                  n+++nA+ ++e ++ ++++++e+++ll++   +n++ ++ + +l+k+ +  ++++ +++l ++     k ++eA+a++ek+
  EPA06348.1 172 SNRTENAVKILESIV-SNNDHLESLLLLGQIAIKNSNSHKGLSYLNKLlEVSPNNIDAHLLVGKINMNAKIINEALAHFEKV 252
                 5899***********.***************************************************************985 PP

  == domain 4  score: 19.1 bits;  conditional E-value: 1.8e-06
                 HHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-SS CS
      ANAPC3  12 aerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLekl 82 
                 +++ll+ ++++ ++ +l ++   +++  ++A+  ++k  ++ +++++ ++l++q   + ++ +eA+a++ek+
  EPA06348.1 215 LNKLLEVSPNNIDAHLLVGKINMNAKIINEALAHFEKVlEISPNNIETHLLLGQIKMDVNNTDEALAHFEKV 286
                 679998888888888888***************************************************985 PP

  == domain 5  score: 13.7 bits;  conditional E-value: 8.4e-05
                 -HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCTSHHHC-HHHHHHHHHHHHHT.T-HHHHHHHH CS
      ANAPC3   4 nyknAiflaerllaaetespedayllAlclylngqykrAyellrkaklnskslgcrylfAqcllkL.kkyeeAiaaL 79 
                 + ++Ai ++er  a+ ++  e ++ ++  l++n++  +A+  +++   +s++ ++++l+    + L ++++eA++++
  EPA06348.1 309 KVDEAIEYCERFAASLPDPTEQLLKKGILLFNNNRISEALVCFNDILGKSNNNNVALLYKAKIFTLkQEFQEALSCI 385
                 6799*********9999999999999********************66666667777777667788899****9987 PP

  == domain 6  score: 14.2 bits;  conditional E-value: 6.1e-05
                 HTT-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHH CS
      ANAPC3   1 dqnnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAi 76 
                 ++n++ +A+ +++ +l ++++++ +++++A+ + l +++++A+  ++   k + ++l +  ++ + +lk + ye A+
  EPA06348.1 340 NNNRISEALVCFNDILGKSNNNNVALLYKAKIFTLKQEFQEALSCIDLIlKYDQSNLDAIECASELSLKVGDYENAL 416
                 6899************5555555555556***************9999999999********************998 PP

  == domain 7  score: 8.8 bits;  conditional E-value: 0.003
                 T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHH CS
      ANAPC3   3 nnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyee 74 
                 + +++A+ +++++l++++ +++++   ++  ++ g+y+ A+ ++++   + ++s+  +  + ++l  L+++ee
  EPA06348.1 376 QEFQEALSCIDLILKYDQSNLDAIECASELSLKVGDYENALLYYDQIlSKLPHSKSFLEKKSRVLSILGRHEE 448
                 6799*****************************************9977777777777777777777777776 PP

  == domain 8  score: 14.8 bits;  conditional E-value: 3.8e-05
                 T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
      ANAPC3   3 nnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                 ++y+nA+++++ +l++ ++s + +  ++ +l  +g++++  ++++++ +l+++++ ++  +++  l L++ye+Ai ++++
  EPA06348.1 410 GDYENALLYYDQILSKLPHSKSFLEKKSRVLSILGRHEESGQIYSELfNLDKTNISILCELGKIHLILHNYEKAIEIFDN 489
                 68************8889999889999*************************************************9986 PP

  == domain 9  score: 14.3 bits;  conditional E-value: 5.4e-05
                 T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCTSHHHC-HHHHHHHH CS
      ANAPC3   3 nnyknAiflaerllaaetespedayllAlclylngqykrAyellrkaklnskslgcrylfA 63 
                 +ny++Ai +++ +l++++ +++ +y ++l+++++++y+  +  l+k     +   ++y +A
  EPA06348.1 478 HNYEKAIEIFDNALKKNPFNSNLLYKKSLAFFSLQKYDASILCLEKI----SESDSLYDYA 534
                 89************999999999999******************999....3334444444 PP

  == domain 10  score: 5.3 bits;  conditional E-value: 0.037
                 T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC CS
      ANAPC3   3 nnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnsk 54 
                 ++y+  i+++e++ ++++  +++ y +++    +g+ k+ +e+l+k+ k+  +
  EPA06348.1 512 QKYDASILCLEKISESDSLYDYAQYQKSKIQMIRGNTKQSMEILSKLiKS--N 562
                 579999********988888999999********************9333..3 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0084       5.4       3      32 ..      61      88 ..      61      91 .. 0.90
   2 !   10.2   0.1   0.00096      0.61       1      26 [.      93     118 ..      93     126 .. 0.88
   3 ?    2.8   0.0      0.23   1.5e+02       4      24 ..     164     184 ..     163     210 .. 0.83
   4 ?   -0.6   0.0       2.7   1.7e+03      17      32 ..     244     257 ..     243     261 .. 0.72
   5 !   13.5   0.0   8.7e-05     0.056       1      33 [.     262     292 ..     262     295 .. 0.84
   6 !   10.5   0.0    0.0008      0.51       9      33 ..     304     328 ..     302     331 .. 0.82
   7 ?    4.5   0.1     0.064        41       1      31 [.     364     392 ..     364     397 .. 0.83
   8 !    7.6   0.0    0.0066       4.2      11      26 ..     408     423 ..     404     432 .. 0.82
   9 !   10.3   0.0   0.00089      0.57       2      34 ..     467     497 ..     466     499 .. 0.91
  10 ?    1.1   0.0       0.8   5.1e+02       8      24 ..     507     523 ..     502     532 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0084
       TPR_7  3 lnLarlysrlGdyeeAielyeqsLaltkdp 32
                lnLa+ + ++ ++ e +++ye   al k p
  EPA06348.1 61 LNLANYFLACKKFTESLKYYES--ALVKNP 88
                69********************..888777 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00096
       TPR_7   1 aLlnLarlysrlGdyeeAielyeqsL 26 
                 aL+n + +  +l + ++Aie+y ++L
  EPA06348.1  93 ALCNKGLCLYNLSQLDDAIECYDEAL 118
                 799*********************77 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.23
       TPR_7   4 nLarlysrlGdyeeAielyeq 24 
                 +L+   ++ +++e+A++++e 
  EPA06348.1 164 YLGKSLVESNRTENAVKILES 184
                 799999***********9986 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 2.7
       TPR_7  17 eAielyeqsLaltkdp 32 
                 eA+ ++e+  +l+ +p
  EPA06348.1 244 EALAHFEK--VLEISP 257
                 799*****..555555 PP

  == domain 5  score: 13.5 bits;  conditional E-value: 8.7e-05
       TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdpe 33 
                 ++l L+++  ++++++eA+ ++e+  +l+ +p+
  EPA06348.1 262 THLLLGQIKMDVNNTDEALAHFEK--VLEISPN 292
                 5789********************..6665555 PP

  == domain 6  score: 10.5 bits;  conditional E-value: 0.0008
       TPR_7   9 ysrlGdyeeAielyeqsLaltkdpe 33 
                  ++lG+ +eAie++e+  a   dp+
  EPA06348.1 304 LEKLGKVDEAIEYCERFAASLPDPT 328
                 689*************777777765 PP

  == domain 7  score: 4.5 bits;  conditional E-value: 0.064
       TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkd 31 
                 aLl+ a ++   ++++eA+++      l +d
  EPA06348.1 364 ALLYKAKIFTLKQEFQEALSCIDL--ILKYD 392
                 79999***************9877..55555 PP

  == domain 8  score: 7.6 bits;  conditional E-value: 0.0066
       TPR_7  11 rlGdyeeAielyeqsL 26 
                 ++Gdye+A+ +y q L
  EPA06348.1 408 KVGDYENALLYYDQIL 423
                 79************66 PP

  == domain 9  score: 10.3 bits;  conditional E-value: 0.00089
       TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdped 34 
                 L+ L+ ++  l +ye+Aie++    al k p++
  EPA06348.1 467 LCELGKIHLILHNYEKAIEIFDN--ALKKNPFN 497
                 7999*******************..99999886 PP

  == domain 10  score: 1.1 bits;  conditional E-value: 0.8
       TPR_7   8 lysrlGdyeeAielyeq 24 
                 ++++l++y+  i ++e+
  EPA06348.1 507 AFFSLQKYDASILCLEK 523
                 6899**********998 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.6   1.2e-05    0.0076       1      34 []      79     112 ..      79     112 .. 0.96
   2 !    8.7   0.0    0.0038       2.4       1      32 [.     113     144 ..     113     146 .. 0.90
   3 ?    5.4   0.0     0.042        27       5      33 ..     151     179 ..     148     180 .. 0.90
   4 ?   -0.5   0.0       3.4   2.2e+03       4      29 ..     183     208 ..     181     211 .. 0.79
   5 ?    4.7   0.1     0.074        47       2      22 ..     215     235 ..     214     246 .. 0.83
   6 !   16.2   0.0   1.5e-05    0.0099       2      33 ..     249     280 ..     248     281 .. 0.95
   7 !   11.9   0.0   0.00037      0.23       2      34 .]     283     315 ..     282     315 .. 0.96
   8 !    7.6   0.0    0.0086       5.5       7      34 .]     458     485 ..     452     485 .. 0.89
   9 !    8.4   0.2    0.0046         3       2      30 ..     487     515 ..     486     519 .. 0.84
  10 ?    0.7   0.0       1.4     9e+02      13      30 ..     527     549 ..     520     555 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.2e-05
      TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                 +y+ al ++P +  a++n++ +l+++ +l++A++
  EPA06348.1  79 YYESALVKNPQSYSALCNKGLCLYNLSQLDDAIE 112
                 6999****************************86 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0038
      TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtA 32 
                 +y +al+ ++n ++a+ +++++ll++ +  +A
  EPA06348.1 113 CYDEALKTYHNIPEAFLMKGKILLSKQNIPEA 144
                 8**********************988776666 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.042
      TPR_17   5 aleldPnnadaynnLAelllknGdlmtAr 33 
                 +l+l+P n +a ++L++ l + ++++ A+
  EPA06348.1 151 VLDLEPENIEAKFYLGKSLVESNRTENAV 179
                 7999*****************99999886 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 3.4
      TPR_17   4 kaleldPnnadaynnLAelllknGdl 29 
                 +++  + ++ +++ +L+++  kn ++
  EPA06348.1 183 ESIVSNNDHLESLLLLGQIAIKNSNS 208
                 677778888999******99887665 PP

  == domain 5  score: 4.7 bits;  conditional E-value: 0.074
      TPR_17   2 ylkaleldPnnadaynnLAel 22 
                 + k le  Pnn da+ + +++
  EPA06348.1 215 LNKLLEVSPNNIDAHLLVGKI 235
                 5799**********9887766 PP

  == domain 6  score: 16.2 bits;  conditional E-value: 1.5e-05
      TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                 ++k+le+ Pnn + + +L+++    +++++A+
  EPA06348.1 249 FEKVLEISPNNIETHLLLGQIKMDVNNTDEAL 280
                 8****************************997 PP

  == domain 7  score: 11.9 bits;  conditional E-value: 0.00037
      TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                 ++k+le+ Pn+ d +n +  ll+k+G+ ++A++
  EPA06348.1 283 FEKVLEISPNHMDGLNSKIILLEKLGKVDEAIE 315
                 8******************************86 PP

  == domain 8  score: 7.6 bits;  conditional E-value: 0.0086
      TPR_17   7 eldPnnadaynnLAelllknGdlmtArq 34 
                  ld++n   +++L++++l ++++++A++
  EPA06348.1 458 NLDKTNISILCELGKIHLILHNYEKAIE 485
                 5799**********************86 PP

  == domain 9  score: 8.4 bits;  conditional E-value: 0.0046
      TPR_17   2 ylkaleldPnnadaynnLAelllknGdlm 30 
                 + +al+++P n+++++ +  ++ ++ +++
  EPA06348.1 487 FDNALKKNPFNSNLLYKKSLAFFSLQKYD 515
                 789*************9988877777665 PP

  == domain 10  score: 0.7 bits;  conditional E-value: 1.4
      TPR_17  13 adaynnLAelll.....knGdlm 30 
                 +d+++ +A++++      +G+++
  EPA06348.1 527 SDSLYDYAQYQKskiqmIRGNTK 549
                 78999999999877777444443 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1     0.025        16       8      30 ..      62      84 ..      60      85 .. 0.91
   2 !   16.0   0.1   1.7e-05     0.011       4      36 ..      92     124 ..      89     155 .. 0.83
   3 ?    0.4   0.0       1.3   8.3e+02      12      69 ..     134     183 ..     126     188 .. 0.63
   4 ?    2.5   0.0      0.29   1.8e+02       5      33 ..     194     222 ..     190     239 .. 0.81
   5 !   19.6   0.0   1.3e-06   0.00085      20      75 ..     243     290 ..     228     292 .. 0.88
   6 ?    3.5   0.0      0.14        89      12      28 ..     303     319 ..     293     322 .. 0.85
   7 ?    1.9   0.1      0.43   2.7e+02      15      30 ..     408     423 ..     398     425 .. 0.70
   8 !   14.7   0.0   4.3e-05     0.027      12      72 ..     439     491 ..     432     492 .. 0.75
   9 !   13.3   0.0   0.00012     0.075      12      70 ..     466     523 ..     462     528 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.025
      TPR_12  8 nlaavlrrlgrydeAlellekal 30
                nla+  ++ ++++e+l+++e al
  EPA06348.1 62 NLANYFLACKKFTESLKYYESAL 84
                89999***************997 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1.7e-05
      TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrl 36 
                 +al n +++l+ l ++d+A+e++++al  + ++
  EPA06348.1  92 SALCNKGLCLYNLSQLDDAIECYDEALKTYHNI 124
                 57889**********************999766 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 1.3
      TPR_12  12 vlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelle 69 
                 +l+  ++  eA+  + ++l++      p++   +++ + Lg  + +++r+e A+++le
  EPA06348.1 134 ILLSKQNIPEAINQFYHVLDLE-----PEN---IEAKFYLGKSLVESNRTENAVKILE 183
                 5566666666777776666665.....443...4555556666666666666666665 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.29
      TPR_12   5 alnnlaavlrrlgrydeAlellekaleia 33 
                 +l  l+++  +  + ++ l++l+k le+ 
  EPA06348.1 194 SLLLLGQIAIKNSNSHKGLSYLNKLLEVS 222
                 4558999999999999999***9999987 PP

  == domain 5  score: 19.6 bits;  conditional E-value: 1.3e-06
      TPR_12  20 deAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                  eAl+++ek+lei      p++   ++t   Lg++    ++++eAl+++e++l+i 
  EPA06348.1 243 NEALAHFEKVLEIS-----PNN---IETHLLLGQIKMDVNNTDEALAHFEKVLEIS 290
                 58999999999999.....876...99********9899***************96 PP

  == domain 6  score: 3.5 bits;  conditional E-value: 0.14
      TPR_12  12 vlrrlgrydeAlellek 28 
                 +l +lg+ deA+e++e+
  EPA06348.1 303 LLEKLGKVDEAIEYCER 319
                 67899*********997 PP

  == domain 7  score: 1.9 bits;  conditional E-value: 0.43
      TPR_12  15 rlgrydeAlellekal 30 
                 + g+y+ Al ++++ l
  EPA06348.1 408 KVGDYENALLYYDQIL 423
                 4567777777776665 PP

  == domain 8  score: 14.7 bits;  conditional E-value: 4.3e-05
      TPR_12  12 vlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeal 72 
                 vl  lgr++e+ +++ +  ++      ++    +++l+ Lg +++ l +ye+A+e++  al
  EPA06348.1 439 VLSILGRHEESGQIYSELFNLD-----KT---NISILCELGKIHLILHNYEKAIEIFDNAL 491
                 5566777777777777776666.....43...48999999999999999999999997776 PP

  == domain 9  score: 13.3 bits;  conditional E-value: 0.00012
      TPR_12  12 vlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlellee 70 
                 +l++lg+ +  l ++eka+ei+ ++l +++p  ++ l+  + +++ l +y++ +  le+
  EPA06348.1 466 ILCELGKIHLILHNYEKAIEIFDNAL-KKNPFNSNLLYKKSLAFFSLQKYDASILCLEK 523
                 56777777777777777777774444.66788888888888888888888888877776 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   0.00048      0.31      10      57 ..      72     119 ..      64     134 .. 0.87
   2 ?    3.7   0.0      0.11        70      10      65 ..     106     161 ..     105     165 .. 0.93
   3 ?    6.5   0.0     0.015       9.5       6      68 ..     170     231 ..     165     236 .. 0.83
   4 !   14.1   0.0   6.1e-05     0.039       2      71 ..     199     268 ..     198     270 .. 0.93
   5 !   10.7   0.0   0.00072      0.46      11      62 ..     242     293 ..     234     303 .. 0.91
   6 !   11.6   0.0   0.00037      0.24      10      57 ..     309     356 ..     300     371 .. 0.86
   7 !    7.1   0.0    0.0091       5.8       8      61 ..     375     428 ..     369     434 .. 0.89
   8 ?   -0.2   0.0       1.8   1.2e+03       4      54 ..     473     523 ..     468     532 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00048
       TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeayla 57 
                 ++ + l+++e+ l+ +P++ + +   Gl+l+ l +l  A+++ + +l 
  EPA06348.1  72 KFTESLKYYESALVKNPQSYSALCNKGLCLYNLSQLDDAIECYDEALK 119
                 566779************************************999885 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.11
       TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                 + + a+++++  l   ++ pe  +  G +l    ++ +A++ + + l+l+p++ +a
  EPA06348.1 106 QLDDAIECYDEALKTYHNIPEAFLMKGKILLSKQNIPEAINQFYHVLDLEPENIEA 161
                 56899**********************************************98766 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.015
       TPR_9   6 ireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapdaeai 68 
                  ++++ e a +++e+++  + d+ e ++  G++  +  + +++l  L+  l+++p++ da+++
  EPA06348.1 170 VESNRTENAVKILESIVS-NNDHLESLLLLGQIAIKNSNSHKGLSYLNKLLEVSPNNIDAHLL 231
                 567788888888888765.77889999999999999999999999999999999999999876 PP

  == domain 4  score: 14.1 bits;  conditional E-value: 6.1e-05
       TPR_9   2 kaiaireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapdaeairaq 71 
                  +iai + ++ + l +++ ll + P+ ++ ++  G +++    +++Ala +e  l+++p++ + +++  q
  EPA06348.1 199 GQIAIKNSNSHKGLSYLNKLLEVSPNNIDAHLLVGKINMNAKIINEALAHFEKVLEISPNNIETHLLLGQ 268
                 689********************************************************99888877655 PP

  == domain 5  score: 10.7 bits;  conditional E-value: 0.00072
       TPR_9  11 weralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapda 62 
                   +ala  e +l + P+ +e ++  G++ + ++++ +Ala +e  l+++p+ 
  EPA06348.1 242 INEALAHFEKVLEISPNNIETHLLLGQIKMDVNNTDEALAHFEKVLEISPNH 293
                 56899********************************************965 PP

  == domain 6  score: 11.6 bits;  conditional E-value: 0.00037
       TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeayla 57 
                 + ++a++++er  +  Pd+ e ++  G+ll+  +++s+Al +++  l 
  EPA06348.1 309 KVDEAIEYCERFAASLPDPTEQLLKKGILLFNNNRISEALVCFNDILG 356
                 6789************************************99987665 PP

  == domain 7  score: 7.1 bits;  conditional E-value: 0.0091
       TPR_9   8 eedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                 ++++++al +++++l  +    + +     l  ++G+++ Al   ++ l++ p+
  EPA06348.1 375 KQEFQEALSCIDLILKYDQSNLDAIECASELSLKVGDYENALLYYDQILSKLPH 428
                 5789*******************9999999999999999999999888888776 PP

  == domain 8  score: -0.2 bits;  conditional E-value: 1.8
       TPR_9   4 iaireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLea 54 
                 i++  +++e+a+++ +  l  +P    +++   l+ + l  + a + +Le 
  EPA06348.1 473 IHLILHNYEKAIEIFDNALKKNPFNSNLLYKKSLAFFSLQKYDASILCLEK 523
                 555566788888888888888888888888888888888888777777775 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0    0.0086       5.5       7      29 ..      62      84 ..      61      85 .. 0.96
   2 ?    6.4   0.0     0.013       8.5       5      33 ..      94     122 ..      92     125 .. 0.83
   3 ?   -0.2   0.0       1.6     1e+03       8      27 ..     165     184 ..     164     187 .. 0.83
   4 ?    1.8   0.0      0.38   2.5e+02      19      31 ..     243     255 ..     242     256 .. 0.91
   5 !    9.1   0.0    0.0019       1.2       8      31 ..     266     289 ..     265     290 .. 0.92
   6 ?    1.1   0.0       0.6   3.8e+02      12      27 ..     304     319 ..     302     319 .. 0.84
   7 ?   -2.2   0.0       6.9   4.4e+03       9      22 ..     335     348 ..     335     353 .. 0.87
   8 ?   -0.0   0.0       1.4   8.8e+02      15      30 ..     409     424 ..     405     425 .. 0.86
   9 ?   -1.7   0.0       4.6     3e+03      10      25 ..     438     453 ..     437     458 .. 0.80
  10 ?    1.0   0.0      0.66   4.2e+02       4      29 ..     466     491 ..     464     494 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0086
      TPR_10  7 NLanalrqrgrydeAealleeal 29
                NLan+  + ++++e+++++e al
  EPA06348.1 62 NLANYFLACKKFTESLKYYESAL 84
                9*******************997 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.013
      TPR_10   5 lnNLanalrqrgrydeAealleealairr 33 
                 l N +  l+++ ++d+A + ++eal ++ 
  EPA06348.1  94 LCNKGLCLYNLSQLDDAIECYDEALKTYH 122
                 556666789999*************9996 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 1.6
      TPR_10   8 LanalrqrgrydeAeallee 27 
                 L+  l + +r + A+++le 
  EPA06348.1 165 LGKSLVESNRTENAVKILES 184
                 77778899*********996 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.38
      TPR_10  19 deAealleealai 31 
                 +eA+a++e++l+i
  EPA06348.1 243 NEALAHFEKVLEI 255
                 79*********98 PP

  == domain 5  score: 9.1 bits;  conditional E-value: 0.0019
      TPR_10   8 LanalrqrgrydeAealleealai 31 
                 L+ +  ++++ deA+a++e++l+i
  EPA06348.1 266 LGQIKMDVNNTDEALAHFEKVLEI 289
                 7888899***************98 PP

  == domain 6  score: 1.1 bits;  conditional E-value: 0.6
      TPR_10  12 lrqrgrydeAeallee 27 
                 l ++g+ deA +++e+
  EPA06348.1 304 LEKLGKVDEAIEYCER 319
                 5679*********996 PP

  == domain 7  score: -2.2 bits;  conditional E-value: 6.9
      TPR_10   9 analrqrgrydeAe 22 
                 +++l++ +r  eA+
  EPA06348.1 335 GILLFNNNRISEAL 348
                 78999*******98 PP

  == domain 8  score: -0.0 bits;  conditional E-value: 1.4
      TPR_10  15 rgrydeAealleeala 30 
                 +g+y+ A+ ++++ l+
  EPA06348.1 409 VGDYENALLYYDQILS 424
                 79*********99875 PP

  == domain 9  score: -1.7 bits;  conditional E-value: 4.6
      TPR_10  10 nalrqrgrydeAeall 25 
                 ++l+ +gr++e+ +++
  EPA06348.1 438 RVLSILGRHEESGQIY 453
                 688999***9986665 PP

  == domain 10  score: 1.0 bits;  conditional E-value: 0.66
      TPR_10   4 slnNLanalrqrgrydeAealleeal 29 
                 +l  L+ ++  + +y++A ++++ al
  EPA06348.1 466 ILCELGKIHLILHNYEKAIEIFDNAL 491
                 66778888888999999999998887 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0         4   2.6e+03       7      43 ..      76     112 ..      43     124 .. 0.75
   2 !   11.3   0.0   0.00051      0.33      14      54 ..     151     191 ..     137     194 .. 0.87
   3 ?    5.0   0.0     0.048        31       8      49 ..     212     253 ..     205     255 .. 0.86
   4 !    9.9   0.1    0.0014      0.89       7      60 ..     245     298 ..     243     324 .. 0.84
   5 ?   -0.9   0.0       3.4   2.2e+03       9      54 ..     315     360 ..     308     368 .. 0.81
   6 ?   -0.1   0.0       1.9   1.2e+03      16      55 ..     390     432 ..     375     442 .. 0.75
   7 ?    0.5   0.0       1.2   7.5e+02      19      54 ..     461     496 ..     453     518 .. 0.60
   8 ?    0.4   0.0       1.3   8.4e+02       7      48 ..     483     524 ..     478     533 .. 0.80
   9 ?    5.5   0.0     0.034        22      24      65 ..     534     575 ..     516     579 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 4
      TPR_20   7 elaeleaalaanpddldarldlAlallaagryeeAle 43 
                 +l+  e+al +np+ + a ++  l l+  ++ ++A+e
  EPA06348.1  76 SLKYYESALVKNPQSYSALCNKGLCLYNLSQLDDAIE 112
                 4555667777777777777777777777777777776 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00051
      TPR_20  14 alaanpddldarldlAlallaagryeeAleqLleilkrdrk 54 
                  l  +p++++a++ l + l++ +r e A++ L +i++++ +
  EPA06348.1 151 VLDLEPENIEAKFYLGKSLVESNRTENAVKILESIVSNNDH 191
                 56679******************************998865 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.048
      TPR_20   8 laeleaalaanpddldarldlAlallaagryeeAleqLleil 49 
                 l+ l + l+ +p+++da+l + +  + a+   eAl+++ ++l
  EPA06348.1 212 LSYLNKLLEVSPNNIDAHLLVGKINMNAKIINEALAHFEKVL 253
                 6678888999*************************9987666 PP

  == domain 4  score: 9.9 bits;  conditional E-value: 0.0014
      TPR_20   7 elaeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrkweddaa 60 
                  la +e+ l+ +p++++++l l +  +  ++ +eAl+++ ++l+   +  d+  
  EPA06348.1 245 ALAHFEKVLEISPNNIETHLLLGQIKMDVNNTDEALAHFEKVLEISPNHMDGLN 298
                 67899999********************************99999888877654 PP

  == domain 5  score: -0.9 bits;  conditional E-value: 3.4
      TPR_20   9 aeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrk 54 
                 +  e+ +a+ pd  +  l+   +l+ ++r  eAl  + +il +  +
  EPA06348.1 315 EYCERFAASLPDPTEQLLKKGILLFNNNRISEALVCFNDILGKSNN 360
                 5556667888999999999999999999999999988888877665 PP

  == domain 6  score: -0.1 bits;  conditional E-value: 1.9
      TPR_20  16 aanpddldarldlAlallaagryeeAl...eqLleilkrdrkw 55 
                 + + ++lda    +++ l+ g+ye Al   +q+l+ l + +++
  EPA06348.1 390 KYDQSNLDAIECASELSLKVGDYENALlyyDQILSKLPHSKSF 432
                 5577888998899999999******984445666666665555 PP

  == domain 7  score: 0.5 bits;  conditional E-value: 1.2
      TPR_20  19 pddldarldlAlallaagryeeAleqLleilkrdrk 54 
                 ++++ + ++l +  l   +ye+A+e + + lk++  
  EPA06348.1 461 KTNISILCELGKIHLILHNYEKAIEIFDNALKKNPF 496
                 556666666666666777777777766666665543 PP

  == domain 8  score: 0.4 bits;  conditional E-value: 1.3
      TPR_20   7 elaeleaalaanpddldarldlAlallaagryeeAleqLlei 48 
                  ++ +++al++np + ++ ++ +la ++ ++y++++  L +i
  EPA06348.1 483 AIEIFDNALKKNPFNSNLLYKKSLAFFSLQKYDASILCLEKI 524
                 5667789999**********9999999999998887666555 PP

  == domain 9  score: 5.5 bits;  conditional E-value: 0.034
      TPR_20  24 arldlAlallaagryeeAleqLleilkrdrkweddaarkqll 65 
                 a+++ ++ ++ +g+ ++++e L +++k++  ++  aa + l+
  EPA06348.1 534 AQYQKSKIQMIRGNTKQSMEILSKLIKSNNVFKYMAANEILF 575
                 89***************************9998887777665 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.1    0.0025       1.6     205     248 ..     104     147 ..      17     155 .. 0.84
   2 ?    5.1   0.2     0.014       8.8       3      73 ..     158     227 ..     156     236 .. 0.88
   3 !    7.0   0.1    0.0036       2.3      13      72 ..     235     294 ..     227     299 .. 0.86
   4 ?    2.7   0.0     0.075        48      10      71 ..     300     361 ..     297     364 .. 0.91
   5 !   14.5   1.3     2e-05     0.013       6      99 ..     364     456 ..     359     465 .. 0.90
   6 ?    1.8   0.3      0.14        90      45     232 ..     471     504 ..     458     554 .. 0.60

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0025
                 HT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHH CS
       NARP1 205 lgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaev 248
                 l + + A+e+ d+a++   ++ e +l+K++il  + ++ +A++ 
  EPA06348.1 104 LSQLDDAIECYDEALKTYHNIPEAFLMKGKILLSKQNIPEAINQ 147
                 56778899999999999999999999999999888888888765 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.014
                 HHHHHHHHHHHHHHHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CH CS
       NARP1   3 esellLyknqiieeagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpensk 73 
                 + e+  y  + + e++++e+A++ Le+  ++  D+l+ +   +++ +k ++ ++  +++++Lle  p+n +
  EPA06348.1 158 NIEAKFYLGKSLVESNRTENAVKILESIVSN-NDHLESLLLLGQIAIKNSNSHKGLSYLNKLLEVSPNNID 227
                 568888999999999*******999998875.699999999999999999999999999999999999975 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0036
                 HHHHHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-C CS
       NARP1  13 iieeagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpens 72 
                 i  +a  ++eAl+h+e++ +   ++++ +   +++ + +++++eA a +e+ le  p+++
  EPA06348.1 235 INMNAKIINEALAHFEKVLEISPNNIETHLLLGQIKMDVNNTDEALAHFEKVLEISPNHM 294
                 556677789999999999999999999999999999999999999999999999998875 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.075
                 HHHHHHHHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT- CS
       NARP1  10 knqiieeagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpen 71 
                 k+ ++e+ gk++eA+e  e+ + ++ D  + + +k+ ll++ +r +eA   ++++l +  +n
  EPA06348.1 300 KIILLEKLGKVDEAIEYCERFAASLPDPTEQLLKKGILLFNNNRISEALVCFNDILGKSNNN 361
                 56789999*********************************************999876665 PP

  == domain 5  score: 14.5 bits;  conditional E-value: 2e-05
                 HHHHHHHHHHHHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CHHHHHHHHHT..SSS-HHHHHHHHHHT CS
       NARP1   6 llLyknqiieeagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpenskYyeglekakklskedeeallalydel 99 
                 +lLyk++i++ +++ +eAl  ++   k    +l   e  +el lk+g++e+A  +y ++l++ p ++++ e+  +++++    +e+  ++y+el
  EPA06348.1 364 ALLYKAKIFTLKQEFQEALSCIDLILKYDQSNLDAIECASELSLKVGDYENALLYYDQILSKLPHSKSFLEKKSRVLSILGR-HEESGQIYSEL 456
                 79******************999998888889999999*************************************9997666.88888888886 PP

  == domain 6  score: 1.8 bits;  conditional E-value: 0.14
                 HHHHHHTT-HHHHHHHHHHHHHH-TT-CHHHHHHHHHT..SSS-HHHHHHHHHHTTTS-TT-SHHHHTHHHH--HHHHHHHHHHHHHHHHHCT-TTHHH CS
       NARP1  45 aelllkLgrkeeAeatyeaLlernpenskYyeglekakklskedeeallalydelaekyprsdaprRlpLdfleGeeFkelvdkYlrkaLrkgvPslfa 143
                 +++ l L ++e+A +++ + l++np ns+                                                                      
  EPA06348.1 471 GKIHLILHNYEKAIEIFDNALKKNPFNSN---------------------------------------------------------------------- 499
                 55666666666666666666666665443...................................................................... PP

                 HHGGGGGGSCHHHHHHHHHHHHHTTTTTSSSSTTGG.GSS----SSHHHHHHHHHHHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHH CS
       NARP1 144 nlksLYedkeKvkileelvegyvkslktsgklsesdnedsekepesallwvlyflAqhydklgsrekAleyidkaiehtptlvelyltK 232
                                                                                                     l + K
  EPA06348.1 500 ------------------------------------------------------------------------------------LLYKK 504
                 ....................................................................................33332 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.69   4.4e+02      15      35 ..      71      91 ..      64      94 .. 0.86
   2 ?   -1.5   0.0       4.2   2.7e+03      27      38 ..     151     162 ..     143     163 .. 0.83
   3 !    7.9   0.0    0.0049       3.1      18      45 ..     209     236 ..     202     244 .. 0.84
   4 ?    2.1   0.0      0.32     2e+02      19      46 ..     244     271 ..     240     280 .. 0.84
   5 ?   -2.6   0.0       9.6   6.2e+03      18      34 ..     277     293 ..     267     296 .. 0.84
   6 ?   -1.4   0.0       4.1   2.6e+03      13      27 ..     306     320 ..     305     326 .. 0.86
   7 ?    4.2   0.0     0.072        46      15      37 ..     376     398 ..     375     401 .. 0.91
   8 !    9.5   0.1    0.0016      0.99      12      34 ..     407     429 ..     406     438 .. 0.87
   9 !    7.4   0.1     0.007       4.5      14      36 ..     477     499 ..     474     502 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.69
                T-HHHHHHHHHHHHHHTTS-H CS
  Fis1_TPR_C 15 geYseArryvdalLeiEPenr 35
                ++++e+++y +  L + P+  
  EPA06348.1 71 KKFTESLKYYESALVKNPQSY 91
                789***********9999865 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 4.2
                 HHHHTTS-HHHH CS
  Fis1_TPR_C  27 lLeiEPenrQaq 38 
                 +L +EPen  a+
  EPA06348.1 151 VLDLEPENIEAK 162
                 6999****8886 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0049
                 HHHHHHHHHHHHHTTS-HHHHHHHHHHH CS
  Fis1_TPR_C  18 seArryvdalLeiEPenrQaqsLkelie 45 
                  + + y++ lLe+ P+n  a  L   i+
  EPA06348.1 209 HKGLSYLNKLLEVSPNNIDAHLLVGKIN 236
                 57899***************99987775 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.32
                 HHHHHHHHHHHHTTS-HHHHHHHHHHHH CS
  Fis1_TPR_C  19 eArryvdalLeiEPenrQaqsLkelied 46 
                 eA+   + +Lei P+n     L   i+ 
  EPA06348.1 244 EALAHFEKVLEISPNNIETHLLLGQIKM 271
                 78889999********999888877765 PP

  == domain 5  score: -2.6 bits;  conditional E-value: 9.6
                 HHHHHHHHHHHHHTTS- CS
  Fis1_TPR_C  18 seArryvdalLeiEPen 34 
                 +eA+   + +Lei P+ 
  EPA06348.1 277 DEALAHFEKVLEISPNH 293
                 6888889999**99985 PP

  == domain 6  score: -1.4 bits;  conditional E-value: 4.1
                 HHT-HHHHHHHHHHH CS
  Fis1_TPR_C  13 klgeYseArryvdal 27 
                 klg+ +eA +y++++
  EPA06348.1 306 KLGKVDEAIEYCERF 320
                 889999******997 PP

  == domain 7  score: 4.2 bits;  conditional E-value: 0.072
                 T-HHHHHHHHHHHHHHTTS-HHH CS
  Fis1_TPR_C  15 geYseArryvdalLeiEPenrQa 37 
                 +e++eA+ ++d +L+ + +n  a
  EPA06348.1 376 QEFQEALSCIDLILKYDQSNLDA 398
                 699**************999987 PP

  == domain 8  score: 9.5 bits;  conditional E-value: 0.0016
                 HHHT-HHHHHHHHHHHHHHTTS- CS
  Fis1_TPR_C  12 yklgeYseArryvdalLeiEPen 34 
                 +k+g+Y++A+ y d++L++ P  
  EPA06348.1 407 LKVGDYENALLYYDQILSKLPHS 429
                 79***************998865 PP

  == domain 9  score: 7.4 bits;  conditional E-value: 0.007
                 HT-HHHHHHHHHHHHHHTTS-HH CS
  Fis1_TPR_C  14 lgeYseArryvdalLeiEPenrQ 36 
                 l++Y++A +  d  L++ P n++
  EPA06348.1 477 LHNYEKAIEIFDNALKKNPFNSN 499
                 89*****************9975 PP

>> Coatomer_E  Coatomer epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0      0.05        32     212     266 ..      68     122 ..      61     132 .. 0.87
   2 !   11.2   1.7   0.00028      0.18     114     256 ..     171     315 ..     156     334 .. 0.81
   3 !    7.7   0.3    0.0032         2     181     238 ..     342     399 ..     330     435 .. 0.83
   4 !    7.4   0.1    0.0041       2.6     188     239 ..     451     502 ..     439     542 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.05
                 HHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHHHHHHHHHHHH- CS
  Coatomer_E 212 lllgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevsernlsqlklsh 266
                 l+ +++ e  +  ++aL k+++ + +L N   +  +l + ++++e + + lk+ h
  EPA06348.1  68 LACKKFTESLKYYESALVKNPQSYSALCNKGLCLYNLSQLDDAIECYDEALKTYH 122
                 677899999999******************9999999999999999988888877 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00028
                 HTT-HHHHHHHHTT-....-SHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHH-TTHHHHHHHHHHHHHHHS---HHHHHHHH CS
  Coatomer_E 114 kegdfddalkllkks....enLeavAlkvqillklhrvdlAekelkkmqdidedatltQLAqawvklavggekiqdAyyifqelsekykstplllngkA 208
                 + +  ++a+k+l++     + Le+  l  qi +k   +      l k+ +++ +++   L    +++   ++ i++A+  f+ + e  +++  +     
  EPA06348.1 171 ESNRTENAVKILESIvsnnDHLESLLLLGQIAIKNSNSHKGLSYLNKLLEVSPNNIDAHLLVGKINM--NAKIINEALAHFEKVLEISPNNIETHLLLG 267
                 6667777877665422222889999999999999999999999999999999999988886665554..457899*******99998777655544445 PP

                 HHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHHH CS
  Coatomer_E 209 vvslllgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevse 256
                  +++ +++ +eA    ++ L+  +++ + L   +++ ++lgk +e++e
  EPA06348.1 268 QIKMDVNNTDEALAHFEKVLEISPNHMDGLNSKIILLEKLGKVDEAIE 315
                 5899999***********************************998875 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0032
                 THHHHHHHHHHHHHHHS---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHH CS
  Coatomer_E 181 ekiqdAyyifqelsekykstplllngkAvvslllgryeeAeslLkeaLdkdakdeetL 238
                 ++i +A+  f+++ +k +++ + l  kA +  l ++++eA s +   L+ d+ + +++
  EPA06348.1 342 NRISEALVCFNDILGKSNNNNVALLYKAKIFTLKQEFQEALSCIDLILKYDQSNLDAI 399
                 6789999999999999999999999999999999999999999999988888877776 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.0041
                 HHHHHHHHHS---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHH CS
  Coatomer_E 188 yifqelsekykstplllngkAvvslllgryeeAeslLkeaLdkdakdeetLi 239
                  i++el +  k++  +l     ++l l++ye+A ++  +aL+k++ + + L 
  EPA06348.1 451 QIYSELFNLDKTNISILCELGKIHLILHNYEKAIEIFDNALKKNPFNSNLLY 502
                 6999*9999899999999999**********************998877775 PP

>> HrpB1_HrpK  Bacterial type III secretion protein (HrpB1_HrpK)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0023       1.5      40      78 ..     154     192 ..     109     239 .. 0.82
   2 ?    3.6   0.0     0.074        47       8      74 ..     189     255 ..     185     259 .. 0.82
   3 ?    4.7   0.0     0.035        23      40      76 ..     255     291 ..     243     297 .. 0.88
   4 ?    2.6   0.0      0.15        97      42      81 ..     325     364 ..     289     376 .. 0.86
   5 ?   -0.7   0.0       1.7   1.1e+03      52      83 ..     539     570 ..     508     570 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0023
  HrpB1_HrpK  40 LrPevaeldllegvlliergrweeAlrlLreveaeasgt 78 
                 L Pe+ e++++ g  l+e +r e+A+++L+++  ++ + 
  EPA06348.1 154 LEPENIEAKFYLGKSLVESNRTENAVKILESIVSNNDHL 192
                 89*****************************98776665 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.074
  HrpB1_HrpK   8 kelvggLievlslalasedtedaellLdalrvLrPevaeldllegvlliergrweeAlrlLreveae 74 
                 ++ ++ L+ +   a+++ ++      L+ l   +P++ +++ll g + ++ + ++eAl  +++v + 
  EPA06348.1 189 NDHLESLLLLGQIAIKNSNSHKGLSYLNKLLEVSPNNIDAHLLVGKINMNAKIINEALAHFEKVLEI 255
                 5667777777777887777777788888899999***********************9999998765 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.035
  HrpB1_HrpK  40 LrPevaeldllegvlliergrweeAlrlLreveaeas 76 
                 ++P++ e +ll g++ +  ++ +eAl  +++v + ++
  EPA06348.1 255 ISPNNIETHLLLGQIKMDVNNTDEALAHFEKVLEISP 291
                 68***************************99987655 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.15
  HrpB1_HrpK  42 PevaeldllegvlliergrweeAlrlLreveaeasgtpya 81 
                 P  +e  l  g+ll +++r++eAl  ++++ +++++ ++a
  EPA06348.1 325 PDPTEQLLKKGILLFNNNRISEALVCFNDILGKSNNNNVA 364
                 56667778899*******************9888776655 PP

  == domain 5  score: -0.7 bits;  conditional E-value: 1.7
  HrpB1_HrpK  52 gvlliergrweeAlrlLreveaeasgtpyaka 83 
                   +++ rg+ +  + +L+++ ++++ ++y +a
  EPA06348.1 539 SKIQMIRGNTKQSMEILSKLIKSNNVFKYMAA 570
                 56788899999999999999999888888765 PP

>> Rapsyn_N  Rapsyn N-terminal myristoylation and linker region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.027        18      11      48 ..      96     133 ..      91     143 .. 0.85
   2 ?    3.5   0.0      0.12        79      13      47 ..     166     199 ..     157     227 .. 0.78
   3 ?    0.9   0.0      0.75   4.8e+02      18      40 ..     272     294 ..     245     319 .. 0.78
   4 ?    4.3   0.0      0.07        45       6      38 ..     328     360 ..     325     373 .. 0.88
   5 ?   -2.4   0.0         8   5.1e+03      40      75 ..     434     469 ..     410     472 .. 0.63
   6 ?   -0.7   0.0       2.5   1.6e+03      21      36 ..     479     494 ..     476     499 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.027
    Rapsyn_N  11 ekGLklyesndtekalrvWrkvLkktsdregkfrvLGc 48 
                 +kGL ly+  + + a++ + ++Lk   +  + f + G 
  EPA06348.1  96 NKGLCLYNLSQLDDAIECYDEALKTYHNIPEAFLMKGK 133
                 79*********************998887777776665 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.12
    Rapsyn_N  13 GLklyesndtekalrvWrkvLkktsdregkfrvLG 47 
                 G  l esn te+a+++  +++ +  d+ + + +LG
  EPA06348.1 166 GKSLVESNRTENAVKILESIVSNN-DHLESLLLLG 199
                 67799***********99987653.4444455555 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.75
    Rapsyn_N  18 esndtekalrvWrkvLkktsdre 40 
                 + n+t++al  + kvL+   ++ 
  EPA06348.1 272 DVNNTDEALAHFEKVLEISPNHM 294
                 569999********999766555 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.07
    Rapsyn_N   6 tkrkiekGLklyesndtekalrvWrkvLkktsd 38 
                 t + ++kG+ l+++n   +al  +  +L k  +
  EPA06348.1 328 TEQLLKKGILLFNNNRISEALVCFNDILGKSNN 360
                 78899********************99988765 PP

  == domain 5  score: -2.4 bits;  conditional E-value: 8
    Rapsyn_N  40 egkfrvLGcLitahsemGk.ykealefalaqldiare 75 
                 e k rvL +L   h e G+ y e++++  + + i  e
  EPA06348.1 434 EKKSRVLSIL-GRHEESGQiYSELFNLDKTNISILCE 469
                 5667888766.45888887577777777777776655 PP

  == domain 6  score: -0.7 bits;  conditional E-value: 2.5
    Rapsyn_N  21 dtekalrvWrkvLkkt 36 
                 + eka++++ ++Lkk 
  EPA06348.1 479 NYEKAIEIFDNALKKN 494
                 679**********985 PP

>> DUF5588  Family of unknown function (DUF5588)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.36   2.3e+02      49      87 ..      68     107 ..      55     135 .. 0.80
   2 ?    4.0   0.1     0.029        18     103     158 ..     174     225 ..     163     236 .. 0.79
   3 !   14.6   0.3   1.8e-05     0.012      56     166 ..     403     505 ..     367     526 .. 0.80
   4 ?    1.2   0.0      0.21   1.3e+02     126     152 ..     499     525 ..     471     542 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.36
     DUF5588  49 ltikkfkgdlayrrqeyqkalqeyssisek.lsstnfamk 87 
                 l+ kkf   l y      k  q ys++++k l   n++  
  EPA06348.1  68 LACKKFTESLKYYESALVKNPQSYSALCNKgLCLYNLSQL 107
                 789**********************999874666666655 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.029
     DUF5588 103 rhaealeiaadlenkatntdhlttvlyl.qlaicsslqnlektilclqklislhpfn 158
                 r ++a++i   le+  +n dhl ++l l q+ai  s  n +k +  l+kl+ + p n
  EPA06348.1 174 RTENAVKI---LESIVSNNDHLESLLLLgQIAIKNS--NSHKGLSYLNKLLEVSPNN 225
                 55555555...89999******99988857888766..6788999999999988866 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 1.8e-05
     DUF5588  56 gdlayrrqeyqkalqeyssiseklsstnfamkrdvqegqarclahlgrhaealeiaadlen.katntdhlttvlylqlaicsslqnlektilclqklis 153
                  +l+ +  +y+ al  y  i  kl+ ++        e ++r l+ lgrh+e+ +i ++l n   tn   l  +  ++l     l n ek+i  ++  + 
  EPA06348.1 403 SELSLKVGDYENALLYYDQILSKLPHSKS-----FLEKKSRVLSILGRHEESGQIYSELFNlDKTNISILCELGKIHL----ILHNYEKAIEIFDNALK 492
                 57888999*****************9854.....56889*******************97625677776666666555....46788888888888888 PP

     DUF5588 154 lhpfnpwswgkla 166
                   pfn     k +
  EPA06348.1 493 KNPFNSNLLYKKS 505
                 8888876555555 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.21
     DUF5588 126 tvlylqlaicsslqnlektilclqkli 152
                  +ly +   + slq+ + +ilcl+k+ 
  EPA06348.1 499 NLLYKKSLAFFSLQKYDASILCLEKIS 525
                 456666666789************985 PP

>> TOM20_plant  Plant specific mitochondrial import receptor subunit TOM20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.33   2.1e+02       9      49 ..      75     115 ..      71     133 .. 0.76
   2 ?    1.3   0.0      0.38   2.4e+02      46      78 ..     136     168 ..     131     177 .. 0.88
   3 ?    4.4   0.1     0.043        28      46     100 ..     237     287 ..     228     302 .. 0.83
   4 !    8.1   0.1    0.0033       2.1      94     121 ..     478     507 ..     474     514 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.33
                  HHHHHHHHHHHH-TT-HHHHHHHHHHHHHHHHHS-HHHHHH CS
  TOM20_plant   9 earkdaeatykknPldadnllrWggallelsqfqsvaeakq 49 
                  e  k  e+  +knP     l   g  l +lsq++  +e   
   EPA06348.1  75 ESLKYYESALVKNPQSYSALCNKGLCLYNLSQLDDAIECYD 115
                  5567778899999999999*************998777655 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.38
                  HHHHHHHHHHHHHHHHHHH-TT-HHHHHHHHHH CS
  TOM20_plant  46 eakqmiqdaiskleeallidPkkhdalWcigna 78 
                   +kq i +ai ++ + l ++P+  +a + +g +
   EPA06348.1 136 LSKQNIPEAINQFYHVLDLEPENIEAKFYLGKS 168
                  5899*********************99999875 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.043
                  HHHHHHHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHHHHH---HHHHHHHHHHHH CS
  TOM20_plant  46 eakqmiqdaiskleeallidPkkhdalWcignaytsfafltpdeeeakenfekat 100
                     ++i++a++ +e+ l i P+  ++  ++g   +     +++++ea  +fek  
   EPA06348.1 237 MNAKIINEALAHFEKVLEISPNNIETHLLLGQIKM----DVNNTDEALAHFEKVL 287
                  56789******************999999998654....4667778888888765 PP

  == domain 4  score: 8.1 bits;  conditional E-value: 0.0033
                  HHHHHHHHHHHHHHHH-T..T-HHHHHHHH CS
  TOM20_plant  94 enfekatqffqqavdedP..dndlyrksle 121
                  +n+eka ++f++a +++P  +n ly+ksl 
   EPA06348.1 478 HNYEKAIEIFDNALKKNPfnSNLLYKKSLA 507
                  79****************444568****97 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0       1.5   9.4e+02      79     124 ..      74     119 ..      62     124 .. 0.71
   2 ?    1.9   0.0      0.44   2.8e+02      24      98 ..     109     195 ..      89     207 .. 0.62
   3 ?   -0.0   0.0       1.7   1.1e+03      71     124 ..     235     288 ..     216     296 .. 0.78
   4 ?   -0.7   0.0       2.8   1.8e+03      62     126 ..     260     324 ..     248     327 .. 0.71
   5 ?   -2.1   0.0       7.6   4.9e+03      74     120 ..     306     352 ..     294     354 .. 0.68
   6 !    9.0   0.0    0.0029       1.8      57     124 ..     391     458 ..     377     472 .. 0.91
   7 ?   -1.4   0.0       4.4   2.8e+03      56      99 ..     458     501 ..     454     510 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.5
                 HHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
        BTAD  79 eealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrr 124
                  e l+++e+++ ++P    + +   ++l+ + +  +A+e Y+++ +
  EPA06348.1  74 TESLKYYESALVKNPQSYSALCNKGLCLYNLSQLDDAIECYDEALK 119
                 5666677777777777777777777888888888888888887654 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.44
                 HHHHHHHHHHTT--SSTTGGGTT..........STTHHH..HHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHH CS
        BTAD  24 eaaelleaAlalwrGpaladlea..........gewlea..ererleelrlealealaeaelrlGraeealaelealvaehPlrErl 98 
                  a+e++++Al+ ++  + a l +           e +++  ++  le + +ea   l + +++ +r e+a++ le++v+++++ E l
  EPA06348.1 109 DAIECYDEALKTYHNIPEAFLMKgkillskqniPEAINQfyHVLDLEPENIEAKFYLGKSLVESNRTENAVKILESIVSNNDHLESL 195
                 556666666666665555555553333333333111111012334555666666666667777778888888888888888777765 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 1.7
                 HHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
        BTAD  71 aelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrr 124
                  ++    ++eala  e+ ++  P + ++h +l +  + ++++ eAL+ +e++ +
  EPA06348.1 235 INMNAKIINEALAHFEKVLEISPNNIETHLLLGQIKMDVNNTDEALAHFEKVLE 288
                 455555567888889999999999999999999999999999999999998765 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 2.8
                 HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
        BTAD  62 lealealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrrlL 126
                 +e +  l + ++ ++  +eala  e+ ++  P + +     +  l ++G+  eA+e+ er+ ++L
  EPA06348.1 260 IETHLLLGQIKMDVNNTDEALAHFEKVLEISPNHMDGLNSKIILLEKLGKVDEAIEYCERFAASL 324
                 55556666677777777788888888888777777777777777777777777777777666655 PP

  == domain 5  score: -2.1 bits;  conditional E-value: 7.6
                 HTT-HHHHHHHHHHHHHHSTT.-HHHHHHHHHHHHHTT-HHHHHHHHH CS
        BTAD  74 rlGraeealaelealvaehPl.rErlhrqlmrAlarsGrqaeALevYe 120
                 +lG+ +ea+++ e+ +a  P   E+l ++ ++ l+  +r +eAL  ++
  EPA06348.1 306 KLGKVDEAIEYCERFAASLPDpTEQLLKKGIL-LFNNNRISEALVCFN 352
                 57777888888888777766424555555554.777777788877665 PP

  == domain 6  score: 9.0 bits;  conditional E-value: 0.0029
                 HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
        BTAD  57 leelrlealealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrr 124
                 ++++ l+a+e   e+ l++G++e+al ++++++++ P+   + ++  r l  +Gr +e  + Y +l +
  EPA06348.1 391 YDQSNLDAIECASELSLKVGDYENALLYYDQILSKLPHSKSFLEKKSRVLSILGRHEESGQIYSELFN 458
                 578899*****************************************************999998865 PP

  == domain 7  score: -1.4 bits;  conditional E-value: 4.4
                 HHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHH CS
        BTAD  56 rleelrlealealaeaelrlGraeealaelealvaehPlrErlh 99 
                  l++  +++l +l + +l l  +e+a++  +++++++P++ +l 
  EPA06348.1 458 NLDKTNISILCELGKIHLILHNYEKAIEIFDNALKKNPFNSNLL 501
                 57788888999999999999999999999999999999998775 PP

>> ChAPs  ChAPs (Chs5p-Arf1p-binding proteins)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.1   7.2e+02     206     263 ..      63     120 ..      34     152 .. 0.83
   2 !   11.4   0.6   0.00018      0.11     180     289 ..     170     281 ..     162     286 .. 0.81
   3 !    5.9   0.3    0.0085       5.5     180     290 ..     305     418 ..     285     431 .. 0.81
   4 ?    2.6   0.0     0.086        55     194     242 ..     458     506 ..     437     527 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.1
                 HHHHHHHTT-HHHHHHHHHHHH-SSS-HHHHHHHHHHHHHHSS--HHHHHHHHHHHHH CS
       ChAPs 206 larvllladeEvdavkllneeleeeekdaelLllqaefllskkkeelAlevakravks 263
                 la  +l++ +  +++k  +++l +++++++ L+ +   l + ++ + A+e+ ++a k+
  EPA06348.1  63 LANYFLACKKFTESLKYYESALVKNPQSYSALCNKGLCLYNLSQLDDAIECYDEALKT 120
                 6888999999999999999999999999999999999999888889999998888765 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00018
                 HHHT-HHHHHHHHHHHHTT-..GGGHHHHHHHHHHTT-HHHHHHHHHHHH-SSS-H..HHHHHHHHHHHHHSS--HHHHHHHHHHHHH-TT-HHHHHHH CS
       ChAPs 180 rltkrydralellekLkeee..pevvillarvllladeEvdavkllneeleeeekd..aelLllqaefllskkkeelAlevakravksaPsefktWalL 274
                   ++r ++a+++le + +++   e   ll ++ + + +  +++  ln+ le ++++  a+lL+ + +   + k  + Al+  ++  +++P++ +t  lL
  EPA06348.1 170 VESNRTENAVKILESIVSNNdhLESLLLLGQIAIKNSNSHKGLSYLNKLLEVSPNNidAHLLVGKINM--NAKIINEALAHFEKVLEISPNNIETHLLL 266
                 45788999*******998773367777889******************99665555227777776665..55555666677899*************** PP

                 HHHHHHTT-HHHHHH CS
       ChAPs 275 vkvYikledienALl 289
                  ++ ++++++++AL 
  EPA06348.1 267 GQIKMDVNNTDEALA 281
                 *************97 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.0085
                 HHHT-HHHHHHHHHHHHTT-GGGH.HHHHH.HHHHTT-HH.HHHHHHHHHH-SSS-HHHHHHHHHHHHHHSS--HHHHHHHHHHHHH-TT-HHHHHHHH CS
       ChAPs 180 rltkrydralellekLkeeepevv.illar.vllladeEv.davkllneeleeeekdaelLllqaefllskkkeelAlevakravksaPsefktWalLv 275
                 +   ++d+a+e  e+++++ p+ +  ll + +ll +++ + +a+   n+ l +++++   Ll +a+    k++ + Al++ +   k   s+     + +
  EPA06348.1 305 EKLGKVDEAIEYCERFAASLPDPTeQLLKKgILLFNNNRIsEALVCFNDILGKSNNNNVALLYKAKIFTLKQEFQEALSCIDLILKYDQSNLDAIECAS 403
                 5556789999999999999988541566554777778888468888899997777776666677777777888889*********************** PP

                 HHHHHTT-HHHHHHH CS
       ChAPs 276 kvYikledienALlt 290
                 +  +k++d+enALl 
  EPA06348.1 404 ELSLKVGDYENALLY 418
                 *************96 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.086
                 HHHTT-GGGHHHHHHHHHHTT-HHHHHHHHHHHH-SSS-HHHHHHHHHH CS
       ChAPs 194 kLkeeepevvillarvllladeEvdavkllneeleeeekdaelLllqae 242
                 +L +++  +   l ++ l+  +  +a+++  ++l++++ +++lL  ++ 
  EPA06348.1 458 NLDKTNISILCELGKIHLILHNYEKAIEIFDNALKKNPFNSNLLYKKSL 506
                 3444455555557899998888889****************99987654 PP

>> DUF4919  Domain of unknown function (DUF4919)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.49   3.1e+02      65     123 ..      65     127 ..      52     135 .. 0.66
   2 ?   -0.4   0.1       1.4   9.3e+02      65     110 ..     133     178 ..     114     187 .. 0.76
   3 ?    5.2   0.0     0.029        18      61     118 ..     265     321 ..     251     324 .. 0.86
   4 ?    0.3   0.0      0.91   5.8e+02      63     117 ..     402     456 ..     373     468 .. 0.77
   5 !    9.9   0.6     0.001      0.67      55     110 ..     461     517 ..     408     526 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.49
     DUF4919  65 kkelseeelkeiislaeealkknPfdlkqlnl...layaykalgkk.eeakiyskrlnkllka 123
                 +  l  +++ e +++ e+al knP +  +l +    +y +++l+++ e + +  k ++++ +a
  EPA06348.1  65 NYFLACKKFTESLKYYESALVKNPQSYSALCNkglCLYNLSQLDDAiECYDEALKTYHNIPEA 127
                 5556668899999**************999752114555555555533344455555555555 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.4
     DUF4919  65 kkelseeelkeiislaeealkknPfdlkqlnllayaykalgkkeea 110
                 k  ls++++ e+i++  ++l+ +P ++++ ++l  ++ + +++e+a
  EPA06348.1 133 KILLSKQNIPEAINQFYHVLDLEPENIEAKFYLGKSLVESNRTENA 178
                 55678999999**********9999999888888777777666554 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.029
     DUF4919  61 lkldkkelseeelkeiislaeealkknPfdlkqlnllayaykalgkkeeakiyskrln 118
                 l l + +++ ++ +e++   e++l+  P  +  ln  ++ +++lgk +ea +y +r++
  EPA06348.1 265 L-LGQIKMDVNNTDEALAHFEKVLEISPNHMDGLNSKIILLEKLGKVDEAIEYCERFA 321
                 3.67789999****************************************99999886 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 0.91
     DUF4919  63 ldkkelseeelkeiislaeealkknPfdlkqlnllayaykalgkkeeakiyskrl 117
                  ++ +l+  ++++++ +  ++l+k P +   l+  + +++ lg++ee+ ++++ l
  EPA06348.1 402 ASELSLKVGDYENALLYYDQILSKLPHSKSFLEKKSRVLSILGRHEESGQIYSEL 456
                 4455677889999999999999999999999999999999999887766665555 PP

  == domain 5  score: 9.9 bits;  conditional E-value: 0.001
     DUF4919  55 eekleel.kldkkelseeelkeiislaeealkknPfdlkqlnllayaykalgkkeea 110
                 +++++ l +l k +l  ++++++i++  +alkknPf+ + l+  + a+ +l+k +++
  EPA06348.1 461 KTNISILcELGKIHLILHNYEKAIEIFDNALKKNPFNSNLLYKKSLAFFSLQKYDAS 517
                 4444333567777778899***********************999999999987765 PP

>> PknG_TPR  Protein kinase G tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.15        93     183     224 ..     147     188 ..     133     194 .. 0.80
   2 ?    5.5   0.0     0.009       5.8      87     180 ..     185     278 ..     167     316 .. 0.67
   3 ?   -0.5   0.0       0.6   3.9e+02     139     161 ..     407     429 ..     402     494 .. 0.59

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.15
                 HHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHTS-TT CS
    PknG_TPR 183 yYrtVwrtdrgvvsAaFGlaRqlaaagdraaAvaaLdeVpat 224
                 ++  V   +   + A F l + l++++++++Av++L+++ ++
  EPA06348.1 147 QFYHVLDLEPENIEAKFYLGKSLVESNRTENAVKILESIVSN 188
                 34457788888999**********************998665 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.009
                 ---GCC-SHHHHHHHHHHHHCT-HHHHHHHHHHHHHHH---HHHHHHHHHHHHHHT-HHHHHHHHHHHHHHSTT-SHHHHHHHHHHHHHT---T CS
    PknG_TPR  87 gvdaseslevpLaevrahldlGdveearelLdeleeeveedWrldWyrglaeLlegdyeeAaaeFdevlaalpGEiaPklaLAataElagetde 180
                  v  ++ le  L + ++++   ++++  ++L++l e ++++   +   g  ++ ++  +eA a+F++vl++ p  i   l L      +++tde
  EPA06348.1 185 IVSNNDHLESLLLLGQIAIKNSNSHKGLSYLNKLLEVSPNNIDAHLLVGKINMNAKIINEALAHFEKVLEISPNNIETHLLLGQIKMDVNNTDE 278
                 4445556677777777777777777777777777777777777777777777777777778888888777777777666666655444444443 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.6
                 HHHT-HHHHHHHHHHHHHHSTT- CS
    PknG_TPR 139 LlegdyeeAaaeFdevlaalpGE 161
                 L  gdye+A   +d++l+ lp  
  EPA06348.1 407 LKVGDYENALLYYDQILSKLPHS 429
                 66677777777777777777754 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.3       0.5   3.2e+02      19      45 ..      65      90 ..      60     103 .. 0.71
   2 ?    3.1   0.1      0.15        98      19      32 ..     106     119 ..      92     124 .. 0.80
   3 ?   -2.6   0.0       9.5   6.1e+03      17      29 ..     138     150 ..     136     161 .. 0.70
   4 ?   -1.7   0.0       4.9   3.1e+03      14      25 ..     304     315 ..     277     318 .. 0.70
   5 ?    0.6   0.0      0.96   6.2e+02      16      29 ..     408     421 ..     398     439 .. 0.84
   6 ?    8.2   0.1    0.0041       2.6      24      52 ..     477     504 ..     471     508 .. 0.83
   7 ?   -2.6   0.1       9.6   6.1e+03      44      57 ..     539     552 ..     511     563 .. 0.57

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.5
         MIT 19 nyeeAlelYkealelLlqalkekneer 45
                ny  A+++++e+l++   al  kn+++
  EPA06348.1 65 NYFLACKKFTESLKYYESALV-KNPQS 90
                677778888888888777776.56555 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.15
         MIT  19 nyeeAlelYkeale 32 
                 + ++A+e+Y eal+
  EPA06348.1 106 QLDDAIECYDEALK 119
                 67889999999885 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 9.5
         MIT  17 agnyeeAlelYke 29 
                 ++n++eA++ + +
  EPA06348.1 138 KQNIPEAINQFYH 150
                 6777888776655 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 4.9
         MIT  14 eDnagnyeeAle 25 
                 +++ g+ +eA+e
  EPA06348.1 304 LEKLGKVDEAIE 315
                 566677777776 PP

  == domain 5  score: 0.6 bits;  conditional E-value: 0.96
         MIT  16 nagnyeeAlelYke 29 
                 + g+ye Al +Y +
  EPA06348.1 408 KVGDYENALLYYDQ 421
                 56899999999987 PP

  == domain 6  score: 8.2 bits;  conditional E-value: 0.0041
         MIT  24 lelYkealelLlqalkekneerrellrek 52 
                 l++Y++a+e++  alk kn+   +ll +k
  EPA06348.1 477 LHNYEKAIEIFDNALK-KNPFNSNLLYKK 504
                 689************9.777666666665 PP

  == domain 7  score: -2.6 bits;  conditional E-value: 9.6
         MIT  44 errellrekieeYl 57 
                 ++ +++r ++++ +
  EPA06348.1 539 SKIQMIRGNTKQSM 552
                 44555555555554 PP

>> DUF5099  Domain of unknown function (DUF5099)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0         9   5.8e+03      92     108 ..      71      87 ..      64      88 .. 0.84
   2 ?    2.6   0.1      0.27   1.7e+02      32     103 ..     185     251 ..     159     255 .. 0.70
   3 ?    8.9   0.3    0.0031         2      22      93 ..     306     382 ..     284     395 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 9
     DUF5099  92 dvlvkaLehYseCeirn 108
                 + ++++L++Y++  ++n
  EPA06348.1  71 KKFTESLKYYESALVKN 87 
                 669999****9998887 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.27
     DUF5099  32 vkligekkdkvlikeeidfenksvlpdlvilcndklvFklksplllykaEilfkrkdfsedvlvkaLehYse 103
                 + + +++ +++l   +i ++n +++  l  ++n+ l+    sp ++  a +l  + +++ +++ +aL h+++
  EPA06348.1 185 IVSNNDHLESLLLLGQIAIKNSNSHKGLS-YLNKLLEV---SPNNI-DAHLLVGKINMNAKIINEALAHFEK 251
                 44555566666666677777766666663.55665554...44444.789999999*************976 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0031
     DUF5099  22 klkk.kygik....ivkligekkdkvlikeeidfenksvlpdlvilcndklvFklksplllykaEilfkrkdfsedv 93 
                 kl+k  + i+    +  ++ + ++++l k ++ f+n+ +   lv + +   + + ++  llyka i+  +++f+e +
  EPA06348.1 306 KLGKvDEAIEycerFAASLPDPTEQLLKKGILLFNNNRISEALVCFNDILGKSNNNNVALLYKAKIFTLKQEFQEAL 382
                 444434445555556677788899999999999*99999999*9999999999********************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (589 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       818  (0.0456244); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        28  (0.00156172); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              28  [number of targets reported over threshold]
# CPU time: 0.86u 0.35s 00:00:01.21 Elapsed: 00:00:00.56
# Mc/sec: 3182.74
//
Query:       EPA06349.1  [L=230]
Description: archaebacterial flagellin [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      4e-24   85.6  11.8    6.6e-24   84.9  11.8    1.3  1  Arch_flagellin  Archaebacterial flagellin
  ------ inclusion threshold ------
      0.042   13.0   1.6      0.054   12.7   1.2    1.4  1  Glutaminase     Glutaminase
       0.32   11.2   2.9         19    5.6   1.0    2.4  2  DUF4148         Domain of unknown function (DUF4148)
        3.5    8.6  10.5        8.2    7.4   7.3    2.6  3  Pilin_N         Archaeal Type IV pilin, N-terminal


Domain annotation for each model (and alignments):
>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.9  11.8   1.5e-27   6.6e-24       1     164 []      14     217 ..      14     217 .. 0.87

  Alignments for each domain:
  == domain 1  score: 84.9 bits;  conditional E-value: 1.5e-27
                     X--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEE..EEE-SSSSSEEEEEEE--TTS--EEGGG-EEEEEE CS
  Arch_flagellin   1 GfvgigtlIvfIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvg..dsatngtineitiyvklnaGsspidlnkttisvtd 93 
                     G +g++ +Iv+IA+V+VAA++a v++n+++ ++qka++   +s e++ss++++ g v+  ++  n+ i ++ i +k + G++ ++l+++t+ v +
      EPA06349.1  14 GVIGVESAIVMIAFVIVAAALAFVVLNMGFSTTQKAKTSIISSLEEASSSMQVAGKVIagGDVGNAWIHTVGIPIKIASGGDIVNLSNSTMAVKY 108
                     6789******************************************************555556666677*********************9777 PP

                     SS--EE--E..........................................................T-EE-TT-EEEEEEE--TTT---TT-EE CS
  Arch_flagellin  94 dgqetlltad.....................................efgivvisdtdgsltng...devlekgekvelevnvneddgitagdev 148
                         + +++d                                     ++g+++ + +  ++ ++   +e+le+ge++ l+++++  d +   d++
      EPA06349.1 109 VS--NDINYDdiyvgamngeykslssaaaaaladssgdmvdidanpfSSGLSTNTRAYIYFAQEvnsNEILEQGETAVLAITFKSGDTPQVLDKI 201
                     66..77999999999**999999998888888888777777777776666666666655555558889****************9999******* PP

                     EEEEE-SSS--EEEEE CS
  Arch_flagellin 149 svevvpenGasttief 164
                     + e++ ++Ga++t+e+
      EPA06349.1 202 KAEIIIPTGAALTVER 217
                     *************986 PP

>> Glutaminase  Glutaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.2   1.2e-05     0.054     183     263 ..      31     115 ..      20     132 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.2e-05
                  HHHHHHHHHTTTEETTTTEE-S-HHHHHHHHHHHHHHTTG....GGHHHHHHHT-S-EEE-TTSEEEEEETTTCEEEEE-S-B-T CS
  Glutaminase 183 lavlaatlangGvnpltgervlskesvrrvlalmltcGmY....dasgefavkvGlPaKSGVsGgilavvpgklgiavfSPrLde 263
                   a la ++ n G++ +++ +    +s+++  + m  +G      d  + ++ +vG+P K   +G i+ +  + +++   S  ++ 
   EPA06349.1  31 AAALAFVVLNMGFSTTQKAKTSIISSLEEASSSMQVAGKViaggDVGNAWIHTVGIPIKIASGGDIVNLSNSTMAVKYVSNDINY 115
                  57788888999999999999999999***********986233366667***************************999988775 PP

>> DUF4148  Domain of unknown function (DUF4148)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   1.0    0.0041        19       7      29 ..      21      51 ..      19      64 .. 0.71
   2 ?    5.2   0.0    0.0056        25      13      31 ..     131     163 ..     123     165 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0041
     DUF4148  7 aaalaaavaaaaala........ahskspkT 29
                a++++a+v +aaala        + ++  kT
  EPA06349.1 21 AIVMIAFVIVAAALAfvvlnmgfSTTQKAKT 51
                4667777777777777788888844444444 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0056
     DUF4148  13 avaaaaala..............ahskspkTRA 31 
                 ++aaaaala              ++  s+ TRA
  EPA06349.1 131 SSAAAAALAdssgdmvdidanpfSSGLSTNTRA 163
                 457788888999999999999999999999998 PP

>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   7.3    0.0018       8.2       7      57 ..      19      75 ..      13     112 .. 0.60
   2 ?   -1.1   0.0      0.86   3.8e+03      78      78 ..     110     110 ..      90     151 .. 0.56
   3 ?    1.4   0.0      0.14   6.2e+02      56      70 ..     179     199 ..     146     209 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0018
     Pilin_N  7 iGviLmvaitvIlaAviaafvlglasneekapqasievkidssastgkna.......v 57
                  +i m+a  vI+aA +a +vl++   +++++++si  ++++ +s+ ++a        
  EPA06349.1 19 ESAIVMIAF-VIVAAALAFVVLNMGFSTTQKAKTSIISSLEEASSSMQVAgkviaggD 75
                345899997.5677889999****7777778888885555555555443344334440 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.86
     Pilin_N  78 s 78 
                 s
  EPA06349.1 110 S 110
                 0 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.14
     Pilin_N  56 a.....vslehkgGdsidt.k 70 
                 +     + ++ k+Gd+ +  +
  EPA06349.1 179 QgetavLAITFKSGDTPQVlD 199
                 122346999999**9876544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       950  (0.0529868); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1622.92
//
Query:       EPA06350.1  [L=282]
Description: hypothetical protein BG20_I1539 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.081   12.1   4.5       0.11   11.7   4.5    1.1  1  DUF4106     Protein of unknown function (DUF4106)
        1.1    9.0   8.8        1.5    8.6   8.8    1.1  1  CT47        Cancer/testis gene family 47
        1.3    7.8   3.7        1.7    7.4   3.7    1.1  1  Nucleo_P87  Nucleopolyhedrovirus capsid protein P87


Domain annotation for each model (and alignments):
>> DUF4106  Protein of unknown function (DUF4106)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   4.5   1.9e-05      0.11     201     258 ..     151     208 ..     141     214 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.9e-05
     DUF4106 201 pkptqqptvqnpaqqptqqptvqqpaq..vqqpaqqpppqpaqqptvqnpaqqqpqteqg 258
                   pt++pt + p++ pt++pt + p++  ++ p+ + p  p ++pt   p+ ++p+ e g
  EPA06350.1 151 ETPTEEPTTETPTETPTEEPTTETPTEtpTETPTAEKPTVPVEKPTT--PTSEKPKVECG 208
                 5799*****************99998622467888888888888874..67777877766 PP

>> CT47  Cancer/testis gene family 47
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   8.8   0.00025       1.5     190     251 ..     132     193 ..     106     206 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00025
        CT47 190 eeaasveEpaveadlaemaeEpaeeaaeeeaaeeaaeeaaaeElaaeaaEEPaleeaeapee 251
                 e  a  eE +   +    +e p+ee+  e + e  +ee+++e +++  +E P++e+++ p e
  EPA06350.1 132 ELPAGTEEVEIIGSVFGSTETPTEEPTTETPTETPTEEPTTETPTETPTETPTAEKPTVPVE 193
                 444445677777777777999*********************************99988743 PP

>> Nucleo_P87  Nucleopolyhedrovirus capsid protein P87
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   3.7   0.00028       1.7     277     341 ..     137     199 ..     110     211 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00028
  Nucleo_P87 277 vedvrefaktvwrakntpmaeqslqspaqtpaperslqsPeqtparrkstkmteeslqsPaqtpa 341
                  e+v  +  +v+  ++tp+ e + ++p++tp++e   ++P++tp+++ +++++   +++P +tp+
  EPA06350.1 137 TEEVEII-GSVFGSTETPTEEPTTETPTETPTEEPTTETPTETPTETPTAEKPTVPVEKP-TTPT 199
                 5555443.5688889999999999999999999999999999997776666666666666.4444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       808  (0.0450667); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 1801.41
//
Query:       EPA06351.1  [L=74]
Description: hypothetical protein BG20_I1542 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       701  (0.0390987); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 456.86
//
Query:       EPA06352.1  [L=464]
Description: putative nitrite reductase, copper-dependent [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.5e-11   42.3   2.2    1.7e-09   37.7   0.5    2.5  2  Cu-oxidase_3  Multicopper oxidase
  ------ inclusion threshold ------
       0.13   11.5   0.0       0.18   11.0   0.0    1.2  1  DUF4420       Putative  PD-(D/E)XK family member, (DUF4420)


Domain annotation for each model (and alignments):
>> Cu-oxidase_3  Multicopper oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.5   1.9e-13   1.7e-09       7     116 ..      84     191 ..      79     193 .. 0.82
   2 !    3.3   0.1    0.0085        76      27      55 ..     296     324 ..     290     336 .. 0.85

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 1.9e-13
                   EECTTEESEEEEEECTSSBS-EEEEETT-EEEEEEEE-SSS-B-EEEET--S-GG.....GSCSGGG-B-TT-EEEEEEE--S-SEEEEEEE--TT. CS
  Cu-oxidase_3   7 vsplggterevitvNgqfpgptievregdtvvvnvtNkldentsihwhGlqqrktswmDGvpgvtqcpiqpgesftyrftvkqqagtlwYhshlsl. 102
                     ++gg++ +++t+ gq+pgpt++v++gd v++++t  + e   ++ hG +++++++    + +    ++pg++ +y + ++  agt+ Yh +  + 
    EPA06352.1  84 LPIMGGKTYNAMTFSGQVPGPTLRVTQGDVVKMTLTIPAGE---VTGHGNDMHASQM----SAGNFESVNPGQTSQYCYIAQA-AGTFKYHCSGVHl 172
                   5567788899********************99999855544...5667777777743....445777************9999.*******765444 PP

                   ....HHH.TT-EEEEEEE- CS
  Cu-oxidase_3 103 ....qqa.aGlaGaiiied 116
                       q++ +G++G+ i+++
    EPA06352.1 173 igmdQHVlSGMYGIAIVDP 191
                   77998889********986 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.0085
                   -EEEEETT-EEEEEEEE-SSS-B-EEEET CS
  Cu-oxidase_3  27 ptievregdtvvvnvtNkldentsihwhG 55 
                     + v++++ v++ v+N+ +e++  h+ G
    EPA06352.1 296 QLLFVENNQHVRLFVENQGNEPVFFHIVG 324
                   5678999*******************988 PP

>> DUF4420  Putative  PD-(D/E)XK family member, (DUF4420)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0     2e-05      0.18      43     113 ..     268     339 ..     203     345 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 2e-05
     DUF4420  43 lllssvkkasksrsak....lslkqvklsesstenskslelslkdselreiFatlcedlvesledeedekellsa 113
                  ll++ ++++++  a+    l+lkq++ +    en +++ l ++++ ++ +F +++ ++++++ + ++ +   sa
  EPA06352.1 268 NLLVKGDANKNIFVAQpwngLELKQYQSQLLFVENNQHVRLFVENQGNEPVFFHIVGEILDRVTQGNRVQ---SA 339
                 33333344444444447999999******999********************************988755...44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 3363.90
//
Query:       EPA06353.1  [L=285]
Description: hypothetical protein BG20_I1544 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.14   12.0   0.0       0.38   10.5   0.0    1.7  2  DUF5612   Domain of unknown function (DUF5612)


Domain annotation for each model (and alignments):
>> DUF5612  Domain of unknown function (DUF5612)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   2.1e-05      0.38      84     117 ..      98     131 ..      84     141 .. 0.89
   2 ?   -3.2   0.0      0.37   6.6e+03      73      92 ..     159     178 ..     154     184 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 2.1e-05
                 HHHHHHHHT.T-EEEEES-BSSHHHHSSEEESSH CS
     DUF5612  84 eavkklkeekdiivislnmaGsvtevadlvvtdp 117
                 e  +k+k+++di  i+ln +Gs  ++ d+v t+ 
  EPA06353.1  98 EFSQKIKNNNDISFITLNFTGSGNSKIDIVATEY 131
                 55689*************************9975 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.37
                 EESSB--THHHHHHHHHHHT CS
     DUF5612  73 laGslmGGkiteavkklkee 92 
                 +a +  G +++ +v++l+e 
  EPA06353.1 159 IATATYGSELAPQVQQLREL 178
                 56677788888888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1761.71
//
Query:       EPA06354.1  [L=217]
Description: hypothetical protein BG20_I1541 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1604.48
//
Query:       EPA06355.1  [L=315]
Description: tubulin/FtsZ family, GTPase domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.8e-16   59.5   2.7    1.2e-14   54.9   0.1    2.6  3  Tubulin         Tubulin/FtsZ family, GTPase domain
  ------ inclusion threshold ------
      0.053   13.1   0.0      0.076   12.5   0.0    1.3  1  PS_Dcarbxylase  Phosphatidylserine decarboxylase
      0.054   12.7   0.2        2.5    7.2   0.0    2.2  2  Tubulin_2       Tubulin like


Domain annotation for each model (and alignments):
>> Tubulin  Tubulin/FtsZ family, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.4   0.1    0.0064        38       2      25 ..       9      32 ..       8      63 .. 0.79
   2 !   54.9   0.1   2.1e-18   1.2e-14     101     195 ..      71     158 ..      63     160 .. 0.95
   3 ?   -2.9   0.0       1.1   6.4e+03      32      42 ..     199     218 ..     170     228 .. 0.50

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0064
                EEEEEEHHHHHHHHHHHHH...HH CS
     Tubulin  2 iivigvGqcGnqignelwellake 25
                i+vig+G++G++++ ++ ++l ++
  EPA06355.1  9 ILVIGLGGAGSKLAIQAKDSLNSD 32
                89**********999988876665 PP

  == domain 2  score: 54.9 bits;  conditional E-value: 2.1e-18
                 HTHHHHHHHHTT-SE.SEEEEEEETTSSHHHHHHHHHHHHHHHTSTTSEEEEEEEE--GG.G-HHHHHHHHHHHHHHHHT-SEEEEEEHHHHHCC CS
     Tubulin 101 eileeirkevekcdslqgffitaslgGGTGSGlgpvilevlkeeypkalvvtvvvlPsefsevvvepynailalkelieesdavividNdaLlki 195
                 +++++i+++++k  +   +++++ l+G TGS+++pv+ e++ke   ++ ++++ ++P++   ++ ++ n+  +lk+++ +s ++iv+dNd+Ll+ 
  EPA06355.1  71 KVADQIKEKISKYST---IVLMTNLAGKTGSAISPVVSEICKEA--DKGLISFAIMPFKY--EKDRIFNSGVSLKRVKANSACTIVLDNDSLLES 158
                 678999******999...**************************..999*********99..89****************************985 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.1
                 ..........HHHT.....T CS
     Tubulin  32 g.........dslesfFses 42 
                 +         dsl+ +++++
  EPA06355.1 199 NgqsleeslrDSLKMLYENT 218
                 02222333444455555544 PP

>> PS_Dcarbxylase  Phosphatidylserine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.3e-05     0.076      15      63 ..      35      83 ..      27     165 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.3e-05
  PS_Dcarbxylase 15 pidddpgaivsPaDgrilqigeieegsviqvKgityslrdLlgeasess 63
                     i++d+++i s+aD++ ++   + + sv  + g+ty+++d ++e+ +++
      EPA06355.1 35 IISNDQKDIQSGADSIKVSTDSVINPSVQLIRGSTYKVADQIKEKISKY 83
                    56788999*******************************9888765543 PP

>> Tubulin_2  Tubulin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0   0.00042       2.5       1      24 [.      10      33 ..      10      47 .. 0.83
   2 ?    3.8   0.1    0.0044        26     141     247 ..      71     175 ..      40     275 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00042
   Tubulin_2  1 lviGLGGtGgkvlaelrrrlreel 24
                lviGLGG G+k   + +++l+++ 
  EPA06355.1 10 LVIGLGGAGSKLAIQAKDSLNSDC 33
                89*****************99887 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.0044
   Tubulin_2 141 daikrlrgsageeeglnvfVvgSLaGGTGSGiflDvayllrkilkeekqkvkiiglvllPdvf.....plnkeggervkaNayaaLkELna..lkdsde 232
                 ++ +++++  + ++  ++ +++ LaG TGS i      ++ +i ke+++    i ++++P  +     + +  + +rvkaN++ +++ L++  l  s+ 
  EPA06355.1  71 KVADQIKE--KISKYSTIVLMTNLAGKTGSAISP----VVSEICKEADK--GLISFAIMPFKYekdriFNSGVSLKRVKANSACTIV-LDNdsLLESNP 160
                 33334443..2356689999999******99876....55566666666..456677777666666668888888899999887776.55555666666 PP

   Tubulin_2 233 etelevkypngdvtv 247
                 + +++ +y+  + ++
  EPA06355.1 161 DLSPKTCYNIANDAI 175
                 666666666555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2172.61
//
Query:       EPA06356.1  [L=171]
Description: hypothetical protein BG20_I1540 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1180.33
//
Query:       EPA06357.1  [L=461]
Description: lyase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.5e-88  294.6   1.4    1.2e-87  294.3   1.4    1.1  1  Lyase_1      Lyase
    1.3e-13   51.2   0.0    3.3e-13   49.8   0.0    1.8  1  FumaraseC_C  Fumarase C C-terminus


Domain annotation for each model (and alignments):
>> Lyase_1  Lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  294.3   1.4   1.3e-91   1.2e-87       1     312 []      19     348 ..      19     348 .. 0.97

  Alignments for each domain:
  == domain 1  score: 294.3 bits;  conditional E-value: 1.3e-91
                 CEEEEETCHHHHHHHHHHHHHGGGHHHHHC.....HHHHHHHHHHHTTSST....HHHHHHHHHHHHHHHCHCHHCGGHHHBSSSSSHHHHHHHHHHHH CS
     Lyase_1   1 grftvkadklmgiftersrenfrlseedik.....alaalkkaaakanvdl....keeaaaiikaldevleegklddqfvlkviqegsgtavnmnlnev 90 
                 g+++ ++d+++g+ft r+++++++++ + +      ++++k++aa+an+++     +  +ai+ a+d++l+ gk+ dqfv++ i+ g+gta+nmn+nev
  EPA06357.1  19 GKIKIPSDAYYGAFTGRAIQQYHVTGIRAHenlikSFVMIKRSAAIANMKTkaidVKRGKAIVTACDKILS-GKYIDQFVIEMINSGAGTAFNMNTNEV 116
                 78999*******************98777788999****************99888999************.*************************** PP

                 HH....HHTT......HSSGIIIIITTT--HHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHTTT-EEEEEETTEEEEEEEHHHHHHHHHHHH CS
     Lyase_1  91 ig....ellg......ekvepndkvhtgqSsnDqvpTalrlalkkalsekLlpaleqLidalkekakefkdvvkiGrThlqdAtPvtlgqelsayaeal 179
                 i+    e+l       ++++pnd+v+++qSsnD++pTa+++a+  +l e+ +pa+++Li++l++k+kef +  kiGrThl dA Pv lg e++ay++ +
  EPA06357.1 117 IAnvalEILHkkkgqyQHLHPNDHVNMSQSSNDTYPTAMHVAILINL-EETIPAIDKLIKSLTKKSKEFSSFKKIGRTHLMDALPVSLGSEFAAYVTSI 214
                 **888866668999*********************************.669************************************************ PP

                 HHHHHHHHHHHHHHTCEETTTTTTTSSTTTSCCTHHHHHHHHHHHHHCST.EESSSHHHHHHC-HHHHHHHHHHHHHHHHHHHHHHHHHHHTSTT.TSS CS
     Lyase_1 180 erdrerlkellkrllvellgggtavgtglnadpefaelvakelakvtglp.vkapnsfeavsdrDavvellgalkllatsLskfaeDlrllssge.agl 276
                 ++ ++ +  ++ ++l+ ++ ggtavgtg+n+ + + +  ++elak+++l+ v++++   a++++ av++l+gal++la+++ k+++D+rl++sg+ agl
  EPA06357.1 215 TKAKNEIISSQ-KELQNVALGGTAVGTGANTPKGYRKIAISELAKISKLQlVPEKDMQYALQSKFAVANLSGALRNLALEIGKLSNDIRLMASGPiAGL 312
                 *********99.99999********************************************************************************** PP

                 EEEEGCCTSSC-TTSTTTEBTHHHHHHHHHHHHHHH CS
     Lyase_1 277 velslaesepGSSiMPgKvNPvqlElltgvagrvvG 312
                  el +++  +GSSiMPgKvNP  +E +++++++++G
  EPA06357.1 313 AELGIPAVHAGSSIMPGKVNPSLAECMNMICFNIIG 348
                 **********************************98 PP

>> FumaraseC_C  Fumarase C C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.8   0.0   3.7e-17   3.3e-13       1      47 [.     414     460 ..     414     461 .] 0.97

  Alignments for each domain:
  == domain 1  score: 49.8 bits;  conditional E-value: 3.7e-17
                  GGGGGHHHHHHHHHHHHHHHHHHHT--HHHHHHHTT-.-HHHHHHHT CS
  FumaraseC_C   1 LVTaLnphIGYekAakIAkeAlkegktlreavlelgllteeeldell 47 
                  +VT L+p+IGY k+a++ ke lk+gkt+re+v  ++l++++e+d+l+
   EPA06357.1 414 IVTLLTPKIGYLKSAELFKESLKTGKTIRELVTSKKLMSNKEIDALF 460
                  8*******************************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (461 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2989.22
//
Query:       EPA06358.1  [L=152]
Description: ribosomal L15 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-44  152.3   4.9    1.5e-44  152.0   4.9    1.0  1  Ribosomal_L15e  Ribosomal L15


Domain annotation for each model (and alignments):
>> Ribosomal_L15e  Ribosomal L15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.0   4.9   8.4e-49   1.5e-44      22     147 ..      20     143 ..       7     147 .. 0.97

  Alignments for each domain:
  == domain 1  score: 152.0 bits;  conditional E-value: 8.4e-49
                     HHHHHHHHTTS-SEEEESS-SSHHHHHHHT--SSTTEEEEEEEEE-SS---..---SS---GGGG-SSS---SS-HHHHHHHHHHHHSTTSEEEE CS
  Ribosomal_L15e  22 lrerlweyrqepavvrverptrldrArrLGYkakqGivvvrvrvrrGgrkkkvskgktgrkpkrqgvnklkpakslqaiaeervgrklpnlrvLn 116
                     +rer++++r+e+a++r++rp+rl+rArrLGYkakqGivvvr+rv  Gg++k  ++ ++gr+pk+ gv+++k    ++++a +r+ +++pnl++L+
      EPA06358.1  20 IRERVVQWRKENAITRIDRPSRLQRARRLGYKAKQGIVVVRMRVGTGGMRK--QRPVAGRRPKHLGVTRIKADDDMKTVATRRALERYPNLKLLG 112
                     69*************************************************..****************************************** PP

                     EEEEEEESSEEEEEEEEE-TTSHHHHT-TTT CS
  Ribosomal_L15e 117 SYwvgeDgtykyyEvilvDpshkairndkki 147
                     SY+v +Dg++ ++Evi+ Dp+hk i +dk++
      EPA06358.1 113 SYFVYKDGMHYWFEVIMADPQHKRIAQDKEL 143
                     ****************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1074.53
//
Query:       EPA06359.1  [L=422]
Description: MiaB-like tRNA modifying enzyme, archaeal-type [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.3e-20   73.1   0.1    4.7e-20   72.6   0.1    1.2  1  Radical_SAM  Radical SAM superfamily
      2e-15   56.6   0.1      2e-15   56.6   0.1    1.8  2  UPF0004      Uncharacterized protein family UPF0004
     0.0092   16.1   0.2       0.05   13.8   0.2    2.3  1  TRAM_2       TRAM domain
  ------ inclusion threshold ------
      0.032   15.1   0.3       0.12   13.2   0.3    2.0  1  zf-PARP      Poly(ADP-ribose) polymerase and DNA-Ligase Zn-fi
      0.053   13.5   0.1        0.2   11.6   0.1    2.1  1  TRAM         TRAM domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.6   0.1   1.3e-23   4.7e-20       1     167 []     139     311 ..     139     311 .. 0.86

  Alignments for each domain:
  == domain 1  score: 72.6 bits;  conditional E-value: 1.3e-23
                  EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS.....TTHHHHHHHHHHTC.CCTEEEEEEECSSCHG.. CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx.. RF
  Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly.....pdfvellerlakla.vpgiritvetngtlpd.. 90 
                  v++  gC   CsfC+++      g+ +s  + +i+++v+   +++g+ke++l++ +   y      d+  l+++ +++  +  ir+ +  + ++p+  
   EPA06359.1 139 VEIASGCMSECSFCQTKL---AKGDLQSYRIGDIVRQVETE-VSDGCKEIWLTSTDNGCYgfdinTDLPTLVKAVSEIPeDFMIRVGMMNPMYMPRik 232
                  57899************9...8*******************.9**********888888887777555555555555544367777777777777688 PP

                  HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET...EEEEEEEBTTTSHHHHHHHHHHH CS
                  xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM  91 eeklerllelg.vdrvslgleaaddekvlklmnrghtfeevlealeklreagikr...vvdrivglpGendeeleellell 167
                   e +e +        +++++++++d+ vl+ m+rght+  ++e+++k+re+   +   ++d+ivg+p e++e++e+++ell
   EPA06359.1 233 NELIESFSSDKvYKFLHIPVQSGSDK-VLNDMRRGHTVNTFKEVVKKARER-YTDftiSTDIIVGFPSETREDFEKTVELL 311
                  899998888779**************.************************.555599*******************9986 PP

>> UPF0004  Uncharacterized protein family UPF0004
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.6   0.1   5.7e-19     2e-15       1      93 [.       3      90 ..       3      94 .. 0.92
   2 ?   -3.8   0.2       3.7   1.3e+04      74      80 ..     142     148 ..     138     155 .. 0.80

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 5.7e-19
                XEEEE--S-CCCCHHHHHHHHHTTTSSS----SSS--SEEEEEE--SSSSHHHHTHHHHHHHHTTST.--EEEEEEHHHHS-HHHHHHH-TTS CS
     UPF0004  1 kvaietlGCqmNevdseelaslLkkegyelvedeeeAdvvlvnTCavrekaekkviqalrelkalkkpekkvvvlGCmaqrekeellkeepev 93
                k+++e +GC+   +dse++ +l+ + g+++++++ e+d+ +v TC+v++++ +k+i+++++lk++      +vv+GC++++e +++ k  +++
  EPA06359.1  3 KIFVEAYGCSASFADSEMISGLIVNGGHTIAKNSTESDLNIVVTCSVKDSTANKMIHRIKSLKSKP-----LVVAGCLPKAELSTVEKISKNA 90
                7899*******************************************************9999866.....9*********999988887764 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 3.7
                 EEEHHHH CS
     UPF0004  74 vlGCmaq 80 
                 + GCm++
  EPA06359.1 142 ASGCMSE 148
                 6799987 PP

>> TRAM_2  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.2   1.4e-05      0.05       1      63 [.     366     420 ..     366     421 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.4e-05
                 BTSEEEEEEEEEETTEEEEEETTS-TTTS--EEEES---T...T-EEEEEEEEEETTEEEEEE CS
      TRAM_2   1 iGktvevlvdgeeeglyvGRsyadAPEvDgevyvtgaeklskvGdfvkvkItdadeyDLiGev 63 
                 iG + +vl d++++++  GR+ a        v+v+++    k+G+  +vkItda+ +  iGe+
  EPA06359.1 366 IGWKGKVLFDEKTDQGIKGRNFAY-----KSVFVKDEI---KIGQTQTVKITDASIHSIIGEI 420
                 677788999999999999999988.....799**9643...37******************96 PP

>> zf-PARP  Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.3   3.4e-05      0.12       1      32 [.     140     174 ..     140     187 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.4e-05
                 EE-S-S--B-SSS--B--SSSE...EEEE-...-- CS
     zf-PARP   1 EyAksgrakCkkCkkkIakgel...Rlgkkveiee 32 
                 E+A+  +++C  C++k akg+l   R+g +v+  e
  EPA06359.1 140 EIASGCMSECSFCQTKLAKGDLqsyRIGDIVRQVE 174
                 89999*****************8888888876655 PP

>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   5.7e-05       0.2      23      60 ..     383     419 ..     358     421 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.7e-05
                 EEEET.TEEEEETT--T..TEEEEEEEEEE-SSEEEEE CS
        TRAM  23 iGrtdngkvvfvpgdlpgIGdfVeVkItkvkrqyLrGe 60 
                  Gr+ ++k vfv++  + IG++ +VkIt++  ++  Ge
  EPA06359.1 383 KGRNFAYKSVFVKDEIK-IGQTQTVKITDASIHSIIGE 419
                 4788889*******544.***********987776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       765  (0.0426683); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.51
# Mc/sec: 2478.04
//
Query:       EPA06360.1  [L=310]
Description: 4-phosphoerythronate dehydrogenase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-63  213.6   0.4    2.2e-63  212.8   0.0    1.6  2  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
    1.2e-29  102.7   0.2    1.3e-29  102.6   0.2    1.0  1  2-Hacid_dh     D-isomer specific 2-hydroxyacid dehydrogenase,
     0.0031   17.7   0.7       0.01   16.0   0.0    2.0  2  NAD_binding_2  NAD binding domain of 6-phosphogluconate dehyd
  ------ inclusion threshold ------
      0.024   14.4   0.0      0.042   13.5   0.0    1.4  1  LXG            LXG domain of WXG superfamily


Domain annotation for each model (and alignments):
>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1      0.81   3.6e+03     112     131 ..      82     101 ..      77     107 .. 0.75
   2 !  212.8   0.0   4.9e-67   2.2e-63       1     178 []     109     284 ..     109     284 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.81
                   HHHHCSTTTEEEEESS-GGG CS
  2-Hacid_dh_C 112 eelakmkkgailiNtaRGgl 131
                   ++ a+  k+  +iN+a G++
    EPA06360.1  82 DQVAAKEKNIRVINAAEGAM 101
                   56677778888999999875 PP

  == domain 2  score: 212.8 bits;  conditional E-value: 4.9e-67
                   HHHHHHHHTTHHHHHHHHHTTCCHTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE CS
  2-Hacid_dh_C   1 lalllallrrlaeadeevregewksekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelvsleellaesDivsl 97 
                   l+l+l+l+r++a++d+++r+g+w  +++l+g+el+gk +Gi+GlG+IG+++ ++++a++m++i+yd+ + +ee  +e+g+ +++l++ll++sD++s+
    EPA06360.1 109 LGLMLSLARQTARGDRAIRNGQW-LKNELKGTELRGKYLGIVGLGNIGKRLGRLARALNMNIIGYDVVPIDEEFSKEVGLMKADLDTLLQSSDYISI 204
                   589********************.99********************************************99999999999**************** PP

                   -S--STTTTTSBSHHHHHCSTTTEEEEESS-GGGB-HHHHHHHHHTTSCCEEEES--SSSSSGTCHHHHHSTTEEE-SS-T CS
  2-Hacid_dh_C  98 hlpltpetrhlinaeelakmkkgailiNtaRGglvdeeaLleaLksgkiagaalDvfeeeplpedspllelpnviltPHia 178
                   h+pl ++t+hlina++++ mkk+a +iNt+RGg+vde+aL++aLksg+++gaalDvfe+ep++  ++l+el+nviltPHi+
    EPA06360.1 205 HVPLLDSTYHLINAQKISTMKKTAKIINTSRGGVVDEDALYDALKSGNLGGAALDVFEKEPAT-GNKLAELDNVILTPHIG 284
                   ***************************************************************.55*************98 PP

>> 2-Hacid_dh  D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.6   0.2   2.9e-33   1.3e-29       1     126 [.       7     308 ..       7     310 .] 0.99

  Alignments for each domain:
  == domain 1  score: 102.6 bits;  conditional E-value: 2.9e-33
                 EEEEST.CHHHHHHHHHTTEEEEEESCSSHHHCHHHHTTESEEEE-TTS-BSHHHHHHHTT--EEEESSSSCTTB-HHHHHHTT-EEEE-TTTTHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  2-Hacid_dh   1 vlileplreeelellkeegvevevkdellteellekakdadalivrsntkvtaevlealpkLkviaragvGvDnvDldaakerGilVtnvpgystesvA 99 
                 vli++++++   ++l+++g++v+++ +++ e+++ek++++ ++ivrs+t +t+e++e+++k+k+iar+gvG DnvD  aake++i V n+ +   ++vA
  EPA06360.1   7 VLICDEVDPVLNKILQDNGLKVSYEPKITPEQIKEKISNFNIVIVRSRTTITREIIEKADKCKIIARVGVGLDNVDQVAAKEKNIRVINAAEGAMNAVA 105
                 799**************999******************************************************************************* PP

                 HHH................................................................................................ CS
                 xxx................................................................................................ RF
  2-Hacid_dh 100 Elt................................................................................................ 102
                 El+                                                                                                
  EPA06360.1 106 ELVlglmlslarqtargdrairngqwlknelkgtelrgkylgivglgnigkrlgrlaralnmniigydvvpideefskevglmkadldtllqssdyisi 204
                 *************************************************************************************************** PP

                 ................................................................................T-BHHHHHHHHHHHHHHHH CS
                 ................................................................................xxxxxxxxxxxxxxxxxxx RF
  2-Hacid_dh 103 ................................................................................aaTeeaqeniaeeaaenlv 121
                                                                                                 a T+eaq+ +a ++ e+++
  EPA06360.1 205 hvplldstyhlinaqkistmkktakiintsrggvvdedalydalksgnlggaaldvfekepatgnklaeldnviltphigAQTKEAQSLAANITGEKII 303
                 *******************************************************************************999***************** PP

                 HHHTT CS
                 xxxxx RF
  2-Hacid_dh 122 aflkg 126
                 ++l+g
  EPA06360.1 304 QILRG 308
                 *9987 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1      0.34   1.5e+03      47      75 ..      79     110 ..      45     131 .. 0.54
   2 !   16.0   0.0   2.2e-06      0.01       2     106 ..     146     250 ..     145     260 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.34
                    SSHHHHHHHC...SEEEE-SSSHHHHHHHHHS CS
  NAD_binding_2  47 esieelvasl...dvvitmvkagkavdevieg 75 
                    +++ +++a+    +v+     a +av e++ g
     EPA06360.1  79 DNVDQVAAKEkniRVINAAEGAMNAVAELVLG 110
                    33333333332224444444555555555555 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 2.2e-06
                    EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS.HCCC--TT-EEEE-S---HHH CS
  NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdevieg.llealkkgdilidgstssped 96 
                    +g++GlG++G+ + +   + ++++++y++ +   ee+ +e   + +++  l++s d + + v+  + + ++i+   ++++kk + +i++s   + d
     EPA06360.1 146 LGIVGLGNIGKRLGRLARALNMNIIGYDVVP-IDEEFSKEVGLMKADLDTLLQSSDYISIHVPLLDSTYHLINAqKISTMKKTAKIINTSRGGVVD 240
                    69**************************995.456777777778999999**********************998889999*999**999988888 PP

                    HHHHHHHHHH CS
  NAD_binding_2  97 trelakelke 106
                       l+++lk+
     EPA06360.1 241 EDALYDALKS 250
                    8888888776 PP

>> LXG  LXG domain of WXG superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   9.4e-06     0.042      57     107 ..     203     251 ..     199     289 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.4e-06
         LXG  57 dlhlplltslqdlieqyeefLkkikealesvepssngfidedfLeqeleng 107
                 ++h+pll+s+ +li+   ++ +++k+  + +++s  g++ded+L + l+ g
  EPA06360.1 203 SIHVPLLDSTYHLINA--QKISTMKKTAKIINTSRGGVVDEDALYDALKSG 251
                 57*************9..99999**********************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2055.11
//
Query:       EPA06361.1  [L=175]
Description: hypothetical protein BG20_I2646 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1265.71
//
Query:       EPA06362.1  [L=102]
Description: hypothetical protein BG20_I2584, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 755.38
//
Query:       EPA06363.1  [L=129]
Description: hypothetical protein BG20_I2585, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 862.00
//
Query:       EPA06364.1  [L=651]
Description: hypothetical protein BG20_I2311, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.6e-06   27.0   0.0    0.00013   22.3   0.0    2.6  2  MG2        MG2 domain
     0.0023   18.5   0.0        3.4    8.3   0.1    2.7  2  YtkA       YtkA-like
     0.0072   15.3   8.1      0.009   14.9   8.1    1.2  1  DUF812     Protein of unknown function (DUF812)
  ------ inclusion threshold ------
      0.013   16.3   1.5       0.25   12.2   0.0    2.6  2  Filamin    Filamin/ABP280 repeat
      0.034   13.5   5.8       0.06   12.6   5.8    1.4  1  DUF3450    Protein of unknown function (DUF3450)
      0.053   12.4  14.7       0.11   11.4  14.7    1.4  1  Spc7       Spc7 kinetochore protein
      0.059   13.3   0.4       0.16   11.9   0.4    1.8  1  DUF3437    Domain of unknown function (DUF3437)
      0.062   12.8   8.3       0.11   11.9   8.3    1.3  1  Golgin_A5  Golgin subfamily A member 5
       0.15   12.5  11.6       0.35   11.3  11.6    1.6  1  KELK       KELK-motif containing domain of MRCK Ser/Thr prote
       0.15   10.9   3.4       0.24   10.2   3.4    1.2  1  LMBR1      LMBR1-like membrane protein
       0.25   11.4  13.1      0.019   15.1   7.8    1.8  2  Mod_r      Modifier of rudimentary (Mod(r)) protein
       0.26   10.1   9.8       0.51    9.2   9.8    1.4  1  CALCOCO1   Calcium binding and coiled-coil domain (CALCOCO1) 
       0.67    9.0  11.2        1.1    8.3  11.2    1.2  1  Atg14      Vacuolar sorting 38 and autophagy-related subunit 
          4    7.9   6.4        0.4   11.2   1.2    2.1  1  DUF4140    N-terminal domain of unknown function (DUF4140)
        7.8    7.0  14.6         24    5.5  14.6    1.8  1  APG6_N     Apg6 coiled-coil region
        7.9    5.6  11.1         13    4.9  11.1    1.3  1  TMPIT      TMPIT-like protein
        9.3    6.1  13.9       0.54   10.1   5.4    2.5  2  DivIC      Septum formation initiator
        9.9    6.7  14.5         24    5.5   9.3    2.6  2  ZapB       Cell division protein ZapB


Domain annotation for each model (and alignments):
>> MG2  MG2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.37   3.7e+02      34      80 ..     273     319 ..     258     335 .. 0.69
   2 !   22.3   0.0   1.3e-07   0.00013       8      94 ..     345     431 ..     339     433 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.37
                 EEEEEEEE-TTSSEEEEEEE.EE-CTTEEEEEEE--TT--SEEEEEEE CS
         MG2  34 lplkltirdpdgkevkelpl.atdetggaesefalpeaaklGeysvel 80 
                   ++++i d+++++v+     +++ +g ++ +++ p +ak G y+++ 
  EPA06364.1 273 ETITAEIFDSKNNKVNLAVEfVKQREGKFNIKID-PLNAKPGIYKIKT 319
                 4788999999999888766436666666665555.7899******997 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 1.3e-07
                 -SEE-TT-EEEEEEEEESTTCSB---EEEEEEEE-TTSS..EEEEEEEEE-CTTEEEEEEE--TT--SEEEEEEEEECSTTT.-EEEEEE CS
         MG2   8 RglYrPgetVslkallrdetlqglaklplkltirdpdgk..evkelplatdetggaesefalpeaaklGeysvelsadsaee.slssgsf 94 
                 + +Y+P et +++++++++t++++  +++ ++i  p+ +  + ++ +++ d+ g++  ++++   + +G+y+++++ad+ ++ + ++++f
  EPA06364.1 345 KSIYKPTETAKFEIVILNATGNPVCPANVLMQIIAPNLQstTLSSNDIVEDSCGLYTADYPT---SVTGNYTINVQADTGNGiANFETYF 431
                 78**********************99999988888875521667777799999999999986...589*******777665514455555 PP

>> YtkA  YtkA-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.1    0.0034       3.4      13      80 ..     264     326 ..     254     330 .. 0.77
   2 !    7.2   0.0    0.0077       7.7      19      85 ..     351     416 ..     338     417 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0034
        YtkA  13 speepkagentivvt.vtqggkpVedadvkvefwmpameGmeemttkvelkesedGvYeaevnfsmeGt 80 
                 ++++ + +++ti+++  + ++++V+     vef ++  eG+   + k+   + ++G Y+++++++ +G 
  EPA06364.1 264 QKDNWNGNKETITAEiFDSKNNKVN---LAVEFVKQR-EGKF--NIKIDPLNAKPGIYKIKTILNVNGN 326
                 5555677777888887778888898...556888885.6666..688888888**********998885 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0077
        YtkA  19 agentivvt.vtqggkpVedadvkvefwmpameGmeemttkvelkesedGvYeaevnfsmeGtWqvql 85 
                 ++ ++++++  +++g+pV  a+v  ++  p  +   + +++  +++   G Y a +  s  G +++ +
  EPA06364.1 351 TETAKFEIViLNATGNPVCPANVLMQIIAPNLQ-STTLSSNDIVED-SCGLYTADYPTSVTGNYTINV 416
                 3334688889********************765.555788888888.9****************9976 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   8.1   9.1e-06     0.009     316     424 ..     186     298 ..      17     301 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 9.1e-06
      DUF812 316 kkaeteeelkkkreeeleelqeqieeleskieeleeeikklessikqveeeleeekeeneelekevklkkktlellpd.....aeeniekLqalveasa 409
                  +++  ++ k   ++++++l+++i++l+++    ++eik+l+s++k +  +l+e+k +n++l++e+ + +k+++  ++      ++n e   a++ +s+
  EPA06364.1 186 DTKDIAKDNKSSDKAKIKQLKNEIKQLKQDKTLSTDEIKDLKSKLKILALQLKETK-QNAKLNSEITKIEKLANEFKEtqkdnWNGNKETITAEIFDSK 283
                 56667789999999**********************************99999876.667777777777888888866333334568899999999*** PP

      DUF812 410 qrlvelakqWekhRv 424
                 ++ v+la ++ k+R+
  EPA06364.1 284 NNKVNLAVEFVKQRE 298
                 *********999986 PP

>> Filamin  Filamin/ABP280 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.4      0.32   3.2e+02      60      90 ..     265     305 ..     179     332 .. 0.62
   2 ?   12.2   0.0   0.00025      0.25      20      93 ..     351     419 ..     337     426 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.32
                 .........EEEEEEEE-SSSEEE..EEE--SSSCEEEEEE CS
     Filamin  60 s........svkievvdnedgtyt..vsYtpeepgtyrvsv 90 
                 +         +++e+ d+++++ +  v++  +++g++++++
  EPA06364.1 265 KdnwngnkeTITAEIFDSKNNKVNlaVEFVKQREGKFNIKI 305
                 02222333344444444444433323555555555555554 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00025
                 TS-EEEEEEESSSTSCCCSTTS..EEEEE..ESSTS.....EEEEEEEE-SSSEEEEEE--SSSCEEEEEEEET CS
     Filamin  20 gesltFtvytkdakgeksevggdelqvrivtgsphgaatkssvkievvdnedgtytvsYtpeepgtyrvsvkld 93 
                  e ++F++   +a g++++      +v +++  p+ ++t      ++v+   g yt+ Y  +  g+y+++v  d
  EPA06364.1 351 TETAKFEIVILNATGNPVCP----ANVLMQIIAPNLQSTTL-SSNDIVEDSCGLYTADYPTSVTGNYTINVQAD 419
                 4778**************97....44444446666653331.1234888889*******************875 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   5.8     6e-05      0.06       6      98 ..     168     260 ..     165     292 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6e-05
     DUF3450   6 alllasgal.aatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierel 98 
                 +ll+  +++ aa+++++++++  a +++++  +ki++l++e ++l+++ +  ++e+++l+ + + l+ ++++ +q+ a+l+ +i++ie++++e 
  EPA06364.1 168 ILLFKIPSVdAAKPENLKDTKDIAKDNKSSDKAKIKQLKNEIKQLKQDKTLSTDEIKDLKSKLKILALQLKETKQN-AKLNSEITKIEKLANEF 260
                 5555556666777777777777777777777777777777777777777777777777777777777777666655.56777777777766554 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4  14.7   0.00011      0.11     182     267 ..     183     267 ..     178     277 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
        Spc7 182 eleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsese 267
                 +l++ ++ a++ +s+dk+++++l++e+++lk++     +e+++l+++l+ l+ +++e+ +q ++l++ei + e++ +e k+ ++++
  EPA06364.1 183 NLKDTKDIAKDNKSSDKAKIKQLKNEIKQLKQDKTLSTDEIKDLKSKLKILALQLKET-KQNAKLNSEITKIEKLANEFKETQKDN 267
                 56777788899999*****************************************998.78899**************99988876 PP

>> DUF3437  Domain of unknown function (DUF3437)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.4   0.00016      0.16      44      72 ..     250     278 ..     224     287 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00016
     DUF3437  44 rktvkktlseFkrthqDtWeedkkkFtee 72 
                  ++++k  +eFk t +D+W+ +k+  t e
  EPA06364.1 250 ITKIEKLANEFKETQKDNWNGNKETITAE 278
                 3578999*************9*9999987 PP

>> Golgin_A5  Golgin subfamily A member 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   8.3   0.00011      0.11      47     141 ..     179     279 ..     171     299 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
   Golgin_A5  47 aeldelkqerdllreelqklnqqieqlrtelqdleaqqq...aeaeslreqlqeleeqleeerkakeeveael...erlkeelryleeel.vrskatlq 138
                 a+ ++lk+ +d+++++  + + +i+ql++e+++l++ ++    e++ l+ +l+ l  ql+e +k++ ++++e+   e+l +e++ +++++   +k+t+ 
  EPA06364.1 179 AKPENLKDTKDIAKDNKSSDKAKIKQLKNEIKQLKQDKTlstDEIKDLKSKLKILALQLKE-TKQNAKLNSEItkiEKLANEFKETQKDNwNGNKETIT 276
                 5668899999999999999999999999999999987761114555566666666666664.4444445555400055556666555443134555555 PP

   Golgin_A5 139 sri 141
                 ++i
  EPA06364.1 277 AEI 279
                 554 PP

>> KELK  KELK-motif containing domain of MRCK Ser/Thr protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3  11.6   0.00036      0.35       1      60 [.     201     259 ..     201     269 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00036
        KELK   1 klkeLekqlrllkqEkeelqkelaeaqErlksqkkeLkdaisqrklamqefsevneklse 60 
                 k+k+L++++++lkq+k   + e+++++ +lk  + +Lk++++  kl   e +++++  +e
  EPA06364.1 201 KIKQLKNEIKQLKQDKTLSTDEIKDLKSKLKILALQLKETKQNAKL-NSEITKIEKLANE 259
                 89*************************************9888776.4567776655555 PP

>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   3.4   0.00024      0.24     193     297 ..     193     304 ..     159     343 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00024
       LMBR1 193 eiksdldeelkklyfeaaklntekeeaereledllkevkklrksisesdplrkyleeilk..kvPeeiaeklks.....nenkteeslaklekqlikal 284
                 + ks+ + ++k+l+ e+++l+++k+ +++e++dl++++k l  +++e+++  k ++ei k  k  +e++e+ k      +e+ t+e   + ++++  a+
  EPA06364.1 193 DNKSSDKAKIKQLKNEIKQLKQDKTLSTDEIKDLKSKLKILALQLKETKQNAKLNSEITKieKLANEFKETQKDnwngnKETITAEIFDSKNNKVNLAV 291
                 55788889*************************************999988888888877667777777775556655333335555566666666666 PP

       LMBR1 285 qkrertekqwkrl 297
                 +  +++e +++  
  EPA06364.1 292 EFVKQREGKFNIK 304
                 6666666555555 PP

>> Mod_r  Modifier of rudimentary (Mod(r)) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.2       4.9   4.9e+03      36      65 ..      21      61 ..      14      83 .. 0.56
   2 ?   15.1   7.8   1.9e-05     0.019      28     117 ..     173     263 ..     161     296 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 4.9
       Mod_r 36 eellaenesla...........eknlslepeleelrselqe 65
                +e+l+e+e+ a           e++ls  ++l+   s+ q+
  EPA06364.1 21 DEILKEIEQEAglhaqnnilplEEQLSFSDTLTYSHSQAQD 61
                44444444444444443333446666666666666655555 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 1.9e-05
       Mod_r  28 vkqlkeekeellaeneslaeknlsl.epeleelrselqekleelkelekefeekeqeldellqkfspdallarLqtavaeaeeeSealaee 117
                 + +++++k e l+ ++++a++n s+ + ++++l++e+++  +  +   +e ++++++l+ l  ++ +    a+L+ +++++e+++++  e 
  EPA06364.1 173 IPSVDAAKPENLKDTKDIAKDNKSSdKAKIKQLKNEIKQLKQDKTLSTDEIKDLKSKLKILALQLKETKQNAKLNSEITKIEKLANEFKET 263
                 667888899999*************999*******************************************************99986665 PP

>> CALCOCO1  Calcium binding and coiled-coil domain (CALCOCO1) like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   9.8   0.00051      0.51     110     208 ..     181     276 ..     174     301 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00051
    CALCOCO1 110 seelaeeksalleakeesearirELEeDiktltqralekEteLeRlkerakkalaqrkeeeaerkqlqakleqseeelrslskelqelr..nslaerdt 206
                  e+l++ k++  ++k  ++a+i+ L ++ik l q +     e++ lk + k ++ q+ke +++     akl++  + +++l++e++e +  n+  +++t
  EPA06364.1 181 PENLKDTKDIAKDNKSSDKAKIKQLKNEIKQLKQDKTLSTDEIKDLKSKLKILALQLKETKQN-----AKLNSEITKIEKLANEFKETQkdNWNGNKET 274
                 5789999***************************************************98654.....4566667778899999998763356667766 PP

    CALCOCO1 207 qv 208
                  +
  EPA06364.1 275 IT 276
                 55 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3  11.2    0.0011       1.1      71     154 ..     183     264 ..     174     304 .. 0.55

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0011
       Atg14  71 elksliadlrerlqelkdklsqlkkeieekkkklaklsdklkkRrsdleslqneleerrkkqiaklqdaikrieqklsslsskt 154
                 +lk ++ + +++++  k+k++qlk ei++ k+      d++k+ +s+l+ l  +l+e ++   akl ++i +ie+  ++++ + 
  EPA06364.1 183 NLKDTKDIAKDNKSSDKAKIKQLKNEIKQLKQDKTLSTDEIKDLKSKLKILALQLKETKQ--NAKLNSEITKIEKLANEFKETQ 264
                 555555555555555555555555555555555555555555555555555555554433..3344444444444444443332 PP

>> DUF4140  N-terminal domain of unknown function (DUF4140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.2    0.0004       0.4      58      98 .]     193     233 ..     172     233 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0004
     DUF4140  58 pnreaeeeelkalraeleeledelaaledelaaaearlafl 98 
                  n++++++++k+l++e+++l+++++  +de++ ++++l++l
  EPA06364.1 193 DNKSSDKAKIKQLKNEIKQLKQDKTLSTDEIKDLKSKLKIL 233
                 334444447****************************9987 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5  14.6     0.024        24      14     115 ..     184     282 ..     181     298 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.024
      APG6_N  14 ldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreyne.lqle 111
                 l+   + a++ + + ++  k+lk+e k+ +   ++   + +e+++l+++ + l  +Lke+ k++++l++e+ ++e+ +++ +e ++  w+  +e    e
  EPA06364.1 184 LKDTKDIAKDNKSSDKAKIKQLKNEIKQLK---QDKTLSTDEIKDLKSKLKILALQLKET-KQNAKLNSEITKIEKLANEFKETQKDNWNGNKEtITAE 278
                 555566666666666777788888877755...688899999999999999999999997.57899999999999999999999999998766644444 PP

      APG6_N 112 llel 115
                   + 
  EPA06364.1 279 IFDS 282
                 4444 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9  11.1     0.013        13       3      80 ..     186     265 ..     182     304 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.013
       TMPIT   3 eweelekefkeleeta.keykqkleelsklqskcskeikkqkkrlkelksslkklkksvk.eeeeeeveelkeelkerkk 80 
                 + ++++k+ k+  +++ k++k+++++l++ ++  + eik  k +lk l  +lk++k+++k ++e +++e+l++e+ke++k
  EPA06364.1 186 DTKDIAKDNKSSDKAKiKQLKNEIKQLKQDKTLSTDEIKDLKSKLKILALQLKETKQNAKlNSEITKIEKLANEFKETQK 265
                 55666666666555443777778888888888888888888888888888888888776656666777777777776654 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   5.4   0.00054      0.54      20      53 ..     196     228 ..     193     236 .. 0.88
   2 ?   -0.2   2.0      0.88   8.8e+02      31      50 ..     241     260 ..     229     278 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00054
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXX CS
       DivIC  20 kqlkqeiaalqaelaklkaeneeLeaevkdLksd 53 
                 ++ k++i++l++e+++lk+++   ++e+kdLk +
  EPA06364.1 196 SSDKAKIKQLKNEIKQLKQDKTLSTDEIKDLK-S 228
                 56799**************************6.4 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.88
                 HHHHHHHHHHHHHHHHHCC- CS
       DivIC  31 aelaklkaeneeLeaevkdL 50 
                 +++akl+ e+ + e+  ++ 
  EPA06364.1 241 KQNAKLNSEITKIEKLANEF 260
                 34444444444444333333 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   9.3     0.024        24      19      68 ..     201     252 ..     196     255 .. 0.73
   2 ?    3.9   1.8     0.072        72      11      39 ..     244     272 ..     243     298 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.024
        ZapB  19 titlLqmeieeLkeeneelkeenreleeene..qlkeereawqerlkkLLgk 68 
                 +i++L++ei++Lk+++   ++e++ l+++++  +l+   ++++++l++ + k
  EPA06364.1 201 KIKQLKNEIKQLKQDKTLSTDEIKDLKSKLKilALQLKETKQNAKLNSEITK 252
                 799************************7766223344444555555555555 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.072
        ZapB  11 skiqkaidtitlLqmeieeLkeeneelke 39 
                 +k ++ i++i++L +e +e +++n + ++
  EPA06364.1 244 AKLNSEITKIEKLANEFKETQKDNWNGNK 272
                 688999****************9944433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (651 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2212  (0.123376); expected 358.6 (0.02)
Passed bias filter:                      714  (0.0398237); expected 358.6 (0.02)
Passed Vit filter:                       107  (0.00596798); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.82u 0.31s 00:00:01.12 Elapsed: 00:00:00.51
# Mc/sec: 3815.01
//
Query:       EPA06365.1  [L=697]
Description: hypothetical protein BG20_I2270 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-27   95.8   0.0    4.9e-20   71.8   0.0    2.3  2  NRDD      Anaerobic ribonucleoside-triphosphate reductase
    4.4e-10   39.5   0.0    1.2e-09   38.0   0.0    1.8  1  HTH_20    Helix-turn-helix domain
    1.4e-06   28.7   1.8    1.2e-05   25.8   0.0    3.4  5  ATP-cone  ATP cone domain
     0.0066   16.4   0.9       0.65   10.0   0.0    3.3  3  Lig_C     Ligase Pab1020 C-terminal region
  ------ inclusion threshold ------
      0.085   12.5   1.8      0.094   12.4   0.2    1.9  2  TackOD1   Thaumarchaeal output domain 1


Domain annotation for each model (and alignments):
>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   2.6e-08   9.4e-05       4     103 ..     212     314 ..     210     333 .. 0.92
   2 !   71.8   0.0   1.4e-23   4.9e-20     271     527 ..     442     693 ..     380     696 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2.6e-08
                 TTHHHHHHHHHHHHHHHHHHHH-H..HHHHHHHHHHHTTSEEETTGGGTTT.S--EEE--SHHHHHH-CTT-SSS.....-B---SHHHHHHHHHHHHH CS
        NRDD   4 nvdskslsglrlklasevskeyalkkllpkevaeaheegdiHiHDldylallttyClgidlkdlleeGlktgngv.....srppkhietalalavnilq 97 
                 nv ++ ++gl  +++++v++e  l+++lpk+va+ h +gd+Hi      ++ ++  + +++k+l+e+G   g+++     + + k+++ +++ + +i+ 
  EPA06365.1 212 NV-DNGAEGLLFNTGQKVFAEHLLTNVLPKDVADSHLSGDMHISNPGIWSM-IPDTIFVNVKELIEDGVILGGKYldvsrITSSKSLDEVTSSLSIIIS 308
                 56.6778999999*********************************99998.99***************8777779**999999********9999999 PP

                 HHHTSS CS
        NRDD  98 tlqneq 103
                  l++e+
  EPA06365.1 309 LLSKEA 314
                 998875 PP

  == domain 2  score: 71.8 bits;  conditional E-value: 1.4e-23
                 -..EEEEEEEEEEHHHHHH..HH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT.-HHH..HTTSS-GE.............EEEEEEE-HHHHHH CS
        NRDD 271 g..rgslgvvtiNlprlaleakgdeekffelLdellelakealeerrkilekllakg.lpflm.gkgylksrkkkdeveevlkngtltiGfiGlaEalk 365
                 g     l+ v+iNlprla e+++de+ f ++L  l++ a  ++  r+k +++l+ +g  p+l  + +y++            ++  l + ++Gl E + 
  EPA06365.1 442 GplAITLQSVSINLPRLAFESNKDETYFRARLALLMKPALSSMALRKKDISDLTRRGlNPILAkNTQYMQ-----------RSSVSLIVNLVGLKESVF 529
                 366778999************************************************99**983444554...........35679999********** PP

                 HTTEEEE..-HHHHHHHHHHHHHHHHHHHHHHHHHSS-EEEEE---TTHHHHHHHHH..HH............HHG-SSSS-TTSSB-HHHHHHHHHHH CS
        NRDD 366 altgkkigeseeakefalkvlkhmrekadelkeetglnfsleatPaEslsgrfakldkkkfgeipgv.dke.pyYtNsfhvpvdekislfekikleaef 462
                 ++ g   ++++e++++  kv+++  ++a +  +e g + ++  t  E+ s rfa+ld +k+g+     + + + Y+  + +  +e ++  +k ++ +e+
  EPA06365.1 530 NILG--FQDNKEGRDILNKVIETAVDVAAKKGKELGDTVAISMTETEG-SSRFANLDGEKYGKNSALnSMDgDSYSQGIVLRASEIDDYTSKTDIISEC 625
                 **88..778**************************************9.67**********998887544478************99999999998776 PP

                 TGG...GTT-S-EEEEBSS--SSHHHHHHHHH.HHHHTT--EEEEE--EEEETT.--EESS..SB-TTT-- CS
        NRDD 463 qkl...ttGGailyieldeekknpealeklvk.iakktgigYfsinpkidvCnecgykgei..ekCpkCgs 527
                 +kl   ++GG  + + +d++ +    ++k ++ +a+   ++ f   +k+  C ecg+k e   +kCpkC+s
  EPA06365.1 626 NKLsklLNGGLLVTLDIDQNATHA-DIKKSIEkAAEL--TPSFRPVKKVALCGECGFKDEPfvDKCPKCKS 693
                 5543339*****999998775555.555555526555..8889999***********77776899****95 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   0.0   3.5e-13   1.2e-09       2      61 .]      25      88 ..      24      88 .. 0.89

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 3.5e-13
                HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHT...S-HHH.HHHHHHHHHHCTTEEEECTEE CS
      HTH_20  2 qiaeALahPvRrrilraLaraegltaselaerld...lsknt.lsyHLrvLeeagLvevvregr 61
                +i++++a+P R +ilr L+++++lt sel+ + +    + +    yHLr+L +  Lv + +++r
  EPA06365.1 25 MIFSVMASPNRIDILRILNSKGPLTYSELKSLAGfksKKESGkFAYHLRKLLRQSLVALNKSER 88
                69*******************************5555666666**************9998765 PP

>> ATP-cone  ATP cone domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   3.4e-09   1.2e-05       1      73 [.     117     189 ..     117     194 .. 0.95
   2 ?   -1.9   0.0       1.4   5.1e+03      49      61 ..     195     207 ..     187     209 .. 0.72
   3 ?   -1.2   0.1      0.87   3.1e+03      17      36 ..     372     390 ..     369     405 .. 0.68
   4 ?   -2.0   0.0       1.6   5.7e+03      10      20 ..     396     406 ..     392     414 .. 0.81
   5 ?   -2.5   0.0       2.2   7.7e+03      17      27 ..     650     660 ..     646     668 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 3.4e-09
                 -EEE-TTS-EEE--HHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHIIT-BHHHHHHHHHHHHHHSS-HHH CS
    ATP-cone   1 ikViKRdGtvepfdvekIkraiekAcegseeeideiaeeveaevrkrlrdgisteeIqdlvektliehpdyav 73 
                 ++V+    ++e+f+  kI++++ +     +e +++i+eeve+++ k +    + + I+++v  +l eh++ ++
  EPA06365.1 117 MYVRTSHESIEEFNSHKIIQSLVREGSLPLELAQKITEEVENRIYKYQTTYLTGSLIREMVNSVLLEHGHEEY 189
                 78999999*****************6668*****************************************998 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.4
                 IIT-BHHHHHHHH CS
    ATP-cone  49 rdgisteeIqdlv 61 
                 r g+++ +Iq+++
  EPA06365.1 195 RLGMPVYDIQEML 207
                 34599******98 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.87
                 HHHHHHHHHHHH-HHHHHHH CS
    ATP-cone  17 kIkraiekAcegseeeidei 36 
                 kI +ai +A ++   +i +i
  EPA06365.1 372 KIVNAIINAYKN-YTKITPI 390
                 788888888776.4444444 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 1.6
                 EEE--HHHHHH CS
    ATP-cone  10 vepfdvekIkr 20 
                 +++fd++kI++
  EPA06365.1 396 IVDFDKGKITD 406
                 689******87 PP

  == domain 5  score: -2.5 bits;  conditional E-value: 2.2
                 HHHHHHHHHHH CS
    ATP-cone  17 kIkraiekAce 27 
                  Ik++iekA+e
  EPA06365.1 650 DIKKSIEKAAE 660
                 59999999986 PP

>> Lig_C  Ligase Pab1020 C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1     0.045   1.6e+02      71     117 ..      59     105 ..      52     139 .. 0.75
   2 !   10.0   0.0   0.00018      0.65       7      57 ..     161     213 ..     157     220 .. 0.81
   3 ?   -0.2   0.0      0.25   9.1e+02      43      81 ..     540     580 ..     535     582 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.045
                 -SSHHHHHHHHHHHHCTT--EEEEEEE..TTEEEEE..EE-HHHHHH CS
       Lig_C  71 fkdeenieellehLrrlgvkaeveekekedgelvvkfkkiaqsttdk 117
                 fk++++  ++  hLr+l  +  v  ++ e  + + ++ k++ s   +
  EPA06365.1  59 FKSKKESGKFAYHLRKLLRQSLVALNKSERRYTITNLGKLVLSLARQ 105
                 67777778888888888777777777777777777777776665444 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00018
                 CGS-STSCHHHHHHHHHHHHHH--SHHHHHHHHHHHHHHH..HHHHHHHHHHH CS
       Lig_C   7 felgrdFlfsRviReafqavefeeseeelrerakeLGesi..Lepmvetikkv 57 
                 + ++  +l+  +iRe  ++v +e+ +ee r++  +LG  +  ++ m+ ++ +v
  EPA06365.1 161 YKYQTTYLTGSLIREMVNSVLLEHGHEEYRNKLARLGMPVydIQEMLTNLDNV 213
                 5688999******************************9873334555555555 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.25
                 HHHHHHHHHHHHHHH..HTT---EEEEEEE-SSHHHHHHHH CS
       Lig_C  43 GesiLepmvetikkv..keeekvkeefrvrfkdeenieell 81 
                 G+ iL+ ++et  +v  k+++++++++ + + + e   ++ 
  EPA06365.1 540 GRDILNKVIETAVDVaaKKGKELGDTVAISMTETEGSSRFA 580
                 88999999999877622678899999999999988777775 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1      0.66   2.4e+03      16      73 ..      97     152 ..      84     154 .. 0.67
   2 ?   12.4   0.2   2.6e-05     0.094      60      96 ..     656     694 ..     615     697 .] 0.74

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.66
     TackOD1  16 yllsrdeeklepvldpkskelysypllealskekeeseelleelvkrglleeelvdri 73 
                  l+++  +++e++   +s ++y     e +++   +s +++++lv++g l  el+++i
  EPA06365.1  97 KLVLSLARQIEERSIIESGKMYVRTSHESIEE--FNSHKIIQSLVREGSLPLELAQKI 152
                 55566666777777777766666555555443..388899999999999987777776 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 2.6e-05
     TackOD1  60 vkrglle..eelvdrirlCpsCksghlnvrevCpkCkSi 96 
                 +k   l+   + v+++ lC +C  +   + + CpkCkS+
  EPA06365.1 656 EKAAELTpsFRPVKKVALCGECGFKDEPFVDKCPKCKSS 694
                 44444543346799************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (697 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.82u 0.32s 00:00:01.13 Elapsed: 00:00:00.55
# Mc/sec: 3837.43
//
Query:       EPA06366.1  [L=42]
Description: hypothetical protein BG20_I2061 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0026   16.8   0.0     0.0027   16.8   0.0    1.0  1  Histidinol_dh  Histidinol dehydrogenase


Domain annotation for each model (and alignments):
>> Histidinol_dh  Histidinol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.5e-07    0.0027     369     408 ..       1      40 [.       1      41 [. 0.93

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.5e-07
                    EEEEEEEEE-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHH CS
  Histidinol_dh 369 lkkisvqelskealkelaeavetlAeaEgLeaHaeavkvR 408
                    +k  + ++ sk +l++++++++ ++e EgL++H eav+ R
     EPA06366.1   1 MKINTQISASKISLSKISKHLQIFTESEGLPNHYEAVRGR 40 
                    577788999****************************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 254.00
//
Query:       EPA06367.1  [L=325]
Description: ATP phosphoribosyltransferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.1e-44  149.4   0.0    1.1e-43  149.0   0.0    1.2  1  HisG      ATP phosphoribosyltransferase
    6.6e-15   55.0   0.0    1.6e-14   53.7   0.0    1.7  1  HisG_C    HisG, C-terminal domain


Domain annotation for each model (and alignments):
>> HisG  ATP phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.0   0.0   1.2e-47   1.1e-43       1     159 [.      50     236 ..      50     237 .. 0.87

  Alignments for each domain:
  == domain 1  score: 149.0 bits;  conditional E-value: 1.2e-47
                 -GGGHHHHHHTTSSSEEEEEHHHHHHCT...TEEEEEEESESEEEEEEEEETTSS--SGCGG......TT.-.EEEEES-HHHHHHHHHHT........ CS
        HisG   1 raadiptyVeegavdlGitGkDvveEskeeeeveelldLgfgkcklvvavpeesevkslkdl.....ved.kgkriaTsypnlakkyfeek........ 85 
                 r+++ipt+V eg +d+GitGkD+v E++  ++ve +ldL++gk +lvva p+++++k+l+++     + + k +ri ++y  +a+k++++         
  EPA06367.1  50 RPQEIPTLVSEGLYDVGITGKDWVGETN--ADVEPILDLEYGKIRLVVAFPDKYHYKNLDEMiadyaK-KkKILRISSEYLITASKFLKQSksykkyyg 145
                 89************************74..47****************************99655532.256688*************99977777777 PP

                 ...............T-EEEEEE-SS-CTHHHHTTS-SEEEEEESSSHHHHHTTEEEEEEEEEEEEEEEEEHHHHHS...HHHHHHHHHHHH CS
        HisG  86 ...............glkveiiklsGsvEaapalglaDaIvDlvetGeTLrangLkaietilessavLiankkslkk...kekieellerlr 159
                                + +v+i+ + G++Ea+p+ + +DaI+D++etG+TL++n+Lk+++++l+s+a+Li+nkksl++   +eki ++++ +r
  EPA06367.1 146 tkdplivtpwlrlgvNKNVQIHLSFGATEAKPPED-VDAIMDVTETGTTLKQNKLKIVDEVLTSTAHLIVNKKSLRDpqkREKIFDIVTLMR 236
                 777777777777755558****************7.9**************************************97444448888877766 PP

>> HisG_C  HisG, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.7   0.0   1.8e-18   1.6e-14       2      68 ..     242     307 ..     241     309 .. 0.95

  Alignments for each domain:
  == domain 1  score: 53.7 bits;  conditional E-value: 1.8e-18
                 TTEEEEEEEEEGGGHHHHHHH---SSS-EEEE-.SS-EEEEEEEEECCCHHHHHHHHHCTT-EEEEE CS
      HisG_C   2 rkyvllmynvpkesleevlkilPGlrsPTvspladegwvaVsavveekevaevideLkaaGAsdIlv 68 
                 +ky  + +nv++++l+++l+ +P+l++PT+spl+++gw+ +++++++ ++ ++i++L+++ A++++v
  EPA06367.1 242 KKYLHIYLNVEEKNLKKLLQQIPSLKKPTISPLSEDGWYGINTIIQKADFHKLIPKLRKI-AQGLVV 307
                 5889999****************************************************9.888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       816  (0.0455129); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1950.23
//
Query:       EPA06368.1  [L=382]
Description: histidinol dehydrogenase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.3e-126  423.0   0.0   1.6e-126  422.6   0.0    1.0  1  Histidinol_dh  Histidinol dehydrogenase
  ------ inclusion threshold ------
      0.016   15.3   0.1      0.034   14.2   0.1    1.5  1  ssDNA_DBD      Non-canonical single-stranded DNA-binding doma
      0.078   13.2   0.0       0.23   11.6   0.0    1.8  1  Tubulin_C      Tubulin C-terminal domain
        4.3    8.0  10.6      0.082   13.5   1.1    2.4  2  DUF643         Protein of unknown function (DUF643)


Domain annotation for each model (and alignments):
>> Histidinol_dh  Histidinol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  422.6   0.0  3.7e-130  1.6e-126      10     359 ..      24     373 ..      17     375 .. 0.97

  Alignments for each domain:
  == domain 1  score: 422.6 bits;  conditional E-value: 3.7e-130
                    HHHHHHHHHHHHHHHHCHHHHHHHHHHCCSSSSGGCCEE-HHHHHHHHHCS-HHHHHHHHHHHHHHHHHHHCC--..--EEEEEECTTEEEEEEEE CS
  Histidinol_dh  10 eveetvkeiledvreeGdealleytekFDkvkkleslrvseeeieealekldeelkealeeaaenirkfheaqke..seeevketepgvvlgqkvr 103
                    + ++ v++il+dv+++Gd a+++y++kF +++  +sl +s+++i++a++k++++  +a++ ++ +++k   a k+  +++  + +++g+++++k++
     EPA06368.1  24 KNKSIVESILNDVKNNGDLAIRKYEKKFSGAN-ITSLLLSQNDIKNAFSKVSKNEINAIKLSKLRLEKTEYAVKSilKNK--TIDTDGIKISKKFV 116
                    56789************************664.689*********************************99999864434..4699********** PP

                    E-SEEEEE---STT--CHHHHHHHHHHHHHT-SEEEEEE-SS.GG.--HHHHHHHHHCT-SEEEE--HHHHHHHHHH--SSS---SEEE---SHHH CS
  Histidinol_dh 104 piervGlYvPgGkaaypStvlmnavpAkvAgvkeivvvtPpq.dgkvnpavlaaaklagvdeiykvGGaqAiaalAyGtesipkvdkivGPGniyV 198
                    pi++vG+Y+PgG a ypS+v+m+++pAk+Agvk+i+vv+Pp+ dgk++p +++aa+l+g++eiy++GGaqAiaal++Gt+sipkvdkivGPG  +V
     EPA06368.1 117 PIQSVGCYIPGGLARYPSSVIMSVIPAKIAGVKRIAVVSPPNsDGKIDPLTIVAANLCGANEIYRIGGAQAIAALSFGTSSIPKVDKIVGPGGTFV 212
                    ************************************************************************************************ PP

                    HHHHHHHCTTBEES----S-EEEEEE-TTS-HHHHHHHHHHHHTT-TT-EEEEEES-HHHHHHHHHHHHHHHCC-TTHHHHHHHHCCH-EEEE-SS CS
  Histidinol_dh 199 aaAKrlvsgevgiDmiaGPsEvlviaDetadpefvAaDLlsqaEHdedaqavlvttseelaeaveeevekqleelprkeiaekslekqsaiilved 294
                      AK ++s++++iDm+aGP+E+ +iaDeta+p++vA+DL+sq+EH +d+ ++l+t+se+la++v++ +++ +++++r++++++sl+k++ + ++++
     EPA06368.1 213 SIAKSMISDRTSIDMLAGPTELGIIADETANPNYVALDLISQSEHSNDTFCYLITNSEKLAKSVDKIIHDLIDKIKRNNFVKTSLKKNGFLAICKN 308
                    ************************************************************************************************ PP

                    HHHHHHHHHHH--SEEEEESTTHHHHGGG--S-SEEEESTT--HHHHHHTSSS------TTGGGT CS
  Histidinol_dh 295 leeaielaneyApEHlelqvedpeellekiknaGaiflGeyspeslgDYaaGtnhvLPTsgtArf 359
                     +++i+lane+ApEHl++++++p+++++ki++ G ++lG+++p s+ DY+ G+nh+LPT+g+ ++
     EPA06368.1 309 YSDMIKLANELAPEHLQIMTKNPNSFASKITSSGLVLLGNNTPSSASDYLLGSNHILPTNGFGKY 373
                    *************************************************************9987 PP

>> ssDNA_DBD  Non-canonical single-stranded DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   7.6e-06     0.034       3      73 ..     270     341 ..     268     365 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.6e-06
                 HHHHHHHHHHHHHHHHHHT-GGGGGSTHHHHHHHHHHH.HHH-HHHHHHHGGGCHHHHH-------HHCCCH CS
   ssDNA_DBD   3 ktllekaqqfveelaselqlpelsqtkLaeNLlLLllK.ynESpkLseqfqleYqelleerkqeyallqekk 73 
                 ++l+++++++++ l+++ ++++  +t+L++N +L + K y++  kL++++  e+ ++++++ +++a  + ++
  EPA06368.1 270 EKLAKSVDKIIHDLIDKIKRNNFVKTSLKKNGFLAICKnYSDMIKLANELAPEHLQIMTKNPNSFASKITSS 341
                 57999********************************98999******************999999855544 PP

>> Tubulin_C  Tubulin C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   5.2e-05      0.23      23     100 ..     273     353 ..     264     364 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.2e-05
                 -HHHHHHHHHTCSG..GGBSSSTSTTTSSEEEEEEEEEESSSH.HHHHHHHHHHHHTTTS-BSTTSTTTEEEEEEECECT- CS
   Tubulin_C  23 ktsvqdvtrallep..knimvkvdprkgkylaiallirGdvep.kevnkavqrikekkkaqfveWiptgikvalnkkspyv 100
                  +sv++++++l+++  +n +vk++ +k+ +lai+  +   ++  +e+  +  +i +k+ ++f + i ++  v l ++ p  
  EPA06368.1 273 AKSVDKIIHDLIDKikRNNFVKTSLKKNGFLAICKNYSDMIKLaNELAPEHLQIMTKNPNSFASKITSSGLVLLGNNTPSS 353
                 5799********954489********************9998526788888888888888888877777777777666665 PP

>> DUF643  Protein of unknown function (DUF643)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   2.4      0.76   3.4e+03      36      78 ..      66     104 ..      33     118 .. 0.64
   2 ?   13.5   1.1   1.8e-05     0.082      47      88 ..     269     312 ..     252     317 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.76
      DUF643  36 lysavkkiqeykiktGksveeiindiiepekefikdvlkdknl 78 
                 + +a+ k+ + +i + k      +  +e +   +k +lk+k +
  EPA06368.1  66 IKNAFSKVSKNEINAIKLS----KLRLEKTEYAVKSILKNKTI 104
                 4444444444444433332....23466777778888888876 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 1.8e-05
      DUF643  47 kiktGksveeiindiiepek..efikdvlkdknlikkyknsknl 88 
                 + k  ksv++ii d+i+  k  +f+k  lk+  ++   kn+ ++
  EPA06368.1 269 SEKLAKSVDKIIHDLIDKIKrnNFVKTSLKKNGFLAICKNYSDM 312
                 56899************977558********9998888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       823  (0.0459033); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.52
# Mc/sec: 2208.50
//
Query:       EPA06369.1  [L=62]
Description: hypothetical protein BG20_I2056, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       244  (0.0136092); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 411.55
//
Query:       EPA06370.1  [L=104]
Description: hypothetical protein BG20_I2058 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.093   12.6   0.0       0.15   11.9   0.0    1.3  1  CBM32     Carbohydrate binding module family 32


Domain annotation for each model (and alignments):
>> CBM32  Carbohydrate binding module family 32
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   8.5e-06      0.15      28      53 ..      39      64 ..      32      66 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.5e-06
                TTEEEEE--SS-EEE-SS-EEEEEEE CS
       CBM32 28 gkevsvSpsnEVikwqaggsltield 53
                ++e+++S   E ikw +g  + i +d
  EPA06370.1 39 QNEIQISSNTELIKWGSGSLFDIFVD 64
                699***************99888665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 686.03
//
Query:       EPA06371.1  [L=314]
Description: putative histidinol-phosphate transaminase, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-38  132.4   0.0    2.5e-38  132.2   0.0    1.1  1  Aminotran_1_2  Aminotransferase class I and II
    1.3e-05   24.3   0.0    1.6e-05   24.0   0.0    1.2  1  Alliinase_C    Allinase
  ------ inclusion threshold ------
      0.029   13.3   0.0      0.097   11.6   0.0    1.7  2  Aminotran_5    Aminotransferase class-V


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.2   0.0   4.2e-42   2.5e-38      37     313 ..      57     305 ..      26     314 .] 0.85

  Alignments for each domain:
  == domain 1  score: 132.2 bits;  conditional E-value: 4.2e-42
                    TTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-H CS
  Aminotran_1_2  37 lneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldl 132
                    + ey+   g   l ++l kfl+      ++ +  + vg+G++++++++   l + +++++l ++pt++ +++ ++l+ ++v  +p++   +++ld+
     EPA06371.1  57 VREYP-LGGTERLIKQLSKFLK------VDSS-MIGVGNGSDQILDLILSNL-ASKQTQVLTSNPTFGFFEERCKLYSIPVTAIPFS--RNMTLDI 141
                    55554.455889999*******......7788.99*****************.9*******************************77..******* PP

                    HHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG CS
  Aminotran_1_2 133 ealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGe 228
                    ++++++ k+         ++++ sp+NPtG  + +++l+kl   +++   l+++DeaY++f   sl        v+   nl++v++lsK+fGlaG+
     EPA06371.1 142 KEFLKLSKN-------ADILYLDSPNNPTGFQFQKDDLQKL---VRSFDGLIIIDEAYGEFGEFSL-----SGMVKSQENLVVVQTLSKSFGLAGL 222
                    *****5554.......469**********************...99999***********998854.....678888888**************** PP

                    -EEEEEEEHHHHHHHHHHHH.HHTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS.TEEEECCSCSSEEEEEET CS
  Aminotran_1_2 229 RvGyilgnaavvsqlrklsr.pflsssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLael.glkvlasqsgmflltdls 313
                    R+Gy+++n+++ ++ +++ + p+ +s+l+ + +  al+ +     ++e+++q ++++rk++ ++L++   ++v++s+++++l+    
     EPA06371.1 223 RLGYFIANKKFTDAFNQVLQyPYPISTLAIESAILALEQST----QMENAVQVIKDERKRIIENLRKYdAFEVFDSKANFVLFDAHG 305
                    ****************9875255557777777777777766....89******************9999************997665 PP

>> Alliinase_C  Allinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   2.7e-09   1.6e-05      63     210 ..      77     231 ..      50     286 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2.7e-09
                  --TTSEEEEECHHHHHHHHHHHHHHHH..SSSSSEEEEE-SS--THHHHHTTTT-B..TTEEE....EEESTT-.--S..S-EEEEEESS-TTT--.- CS
  Alliinase_C  63 atddryivvGtGstqLlqalvyalspeasseskpvkvvaavPyysvykeqtsllds..klykw....eGdaaayvkkknpeefielvtsPnnPdgl.l 153
                  ++d   i vG+Gs q+l+ ++  l+++      +++v+++ P +  ++e+ +l++   +   +      d +++ k + ++  i    sPnnP g+ +
   EPA06371.1  77 KVDSSMIGVGNGSDQILDLILSNLASK------QTQVLTSNPTFGFFEERCKLYSIpvTAIPFsrnmTLDIKEFLKLS-KNADILYLDSPNNPTGFqF 167
                  68889999**********998888877......889***************998751144444111145677886655.666778889******9733 PP

                  --....----TT-EEEEEE-TT-.STTTS..---S-B--SEEEEEHHHHHS-GGG-EEEEEES- CS
  Alliinase_C 154 re....avvkgseakviyDlayY.WPhyt..pitskadedimLftlskltGhaGsrlGWalvkd 210
                  ++    ++v++ ++ +i D ay  + +++   + + +++ +++ tlsk  G aG rlG+ +   
   EPA06371.1 168 QKddlqKLVRSFDGLIIIDEAYGeFGEFSlsGMVKSQENLVVVQTLSKSFGLAGLRLGYFIANK 231
                  332222578999*********95366665215666666778889**************966543 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   1.6e-05     0.097      52     177 ..      72     188 ..      63     191 .. 0.77
   2 ?   -1.4   0.0      0.15   8.9e+02     265     302 ..     257     294 ..     245     299 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.6e-05
                  HHHHHT-STGGGEEEESSHHH.HHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESB CS
  Aminotran_5  52 vaelinaeseeeiiftsGtte.ainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithv 148
                  + ++++++s   +i + ++++  + l++ +l      +++ v+t++   + +   +e +k   + v+ ip+ ++ +ld++e+  +l+++++++++   
   EPA06371.1  72 LSKFLKVDS--SMIGVGNGSDqILDLILSNL----ASKQTQVLTSNPTFGFF---EERCKLYSIPVTAIPFSRNMTLDIKEFL-KLSKNADILYLDSP 159
                  556666665..55555555552344555555....45555556666666666...7778888999*****************6.689*********** PP

                  ETTTTEB--HHHHHHHHHHTT-EEEEE-T CS
  Aminotran_5 149 snvtGtiqpveeigklakkkgalvlvDaa 177
                  +n tG  ++ +++ kl++  + l+++D a
   EPA06371.1 160 NNPTGFQFQKDDLQKLVRSFDGLIIIDEA 188
                  *******************9999999976 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.15
                  HHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES. CS
  Aminotran_5 265 leyleeigleaiekhekelaeyllerlkslpgvrlygp 302
                  l + +++++e++ +  k  ++++ e l++++ ++++++
   EPA06371.1 257 LALEQSTQMENAVQVIKDERKRIIENLRKYDAFEVFDS 294
                  33337777777777777777777777777777777653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       751  (0.0418874); expected 358.6 (0.02)
Passed bias filter:                      571  (0.0318478); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2065.48
//
Query:       EPA06372.1  [L=455]
Description: hypothetical protein BG20_I2377, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.1e-17   61.6   4.0    5.5e-16   58.9   0.7    2.8  3  LTD       Lamin Tail Domain
    6.3e-08   33.0   0.2     0.0014   19.0   0.0    4.4  5  MG2       MG2 domain
  ------ inclusion threshold ------
       0.26   11.4   4.7       0.55   10.4   0.1    3.1  3  Big_8     Bacterial Ig domain


Domain annotation for each model (and alignments):
>> LTD  Lamin Tail Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.9   0.7   9.1e-20   5.5e-16       3     107 ..      23     118 ..      21     121 .. 0.90
   2 ?    2.6   0.1     0.027   1.6e+02      52     106 ..     264     324 ..     231     329 .. 0.65
   3 ?   -3.1   0.0       1.7     1e+04      60      74 ..     373     387 ..     357     429 .. 0.60

  Alignments for each domain:
  == domain 1  score: 58.9 bits;  conditional E-value: 9.1e-20
         LTD   3 aaagdvvIsevmedgagnnan...efvelyNtsskavdLsgwkledasge...ytfpngtgtlaageyvvvwsgsgttsasngskasssavwnnggdav 95 
                 ++ + vvI+ev+ +++g++++   e+velyN++++ +d+sgwk++  sg      +p gt  +++g+ ++++ +s                w +++ +v
  EPA06372.1  23 QSVNHVVINEVDTNPPGDDSKsisEWVELYNPTNSKIDISGWKIASTSGMkktLSIPTGT-FIESGKFLTFTFDS---------------LWFTDNNEV 105
                 66789************9999***************************98*********9.***********994...............477766666 PP

         LTD  96 a.Lydasgevvds 107
                 + L+d++g  +d 
  EPA06372.1 106 VeLKDKNGVSIDK 118
                 66***99999985 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.027
         LTD  52 fpngt....gtlaageyvvvwsgsgtt.sasngskasssavwnn........ggdavaLydasgevvd 106
                 f  g      t++  +++ +++++++            ++++++        +g + +++d++g++++
  EPA06372.1 264 FSVGDklvvETIPEESTLSITTNKSQYlP-------GDTLSLTGitskvipfEGLKFTIKDPNGNIIS 324
                 33333667778999999999999533221.......22222222334566678889999999999886 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 1.7
         LTD  60 aageyvvvwsgsgtt 74 
                 +  + + +w+++++ 
  EPA06372.1 373 KEEKAISLWTDKDAY 387
                 555566666664433 PP

>> MG2  MG2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       2.1   1.2e+04      38      69 ..      49      80 ..      27      82 .. 0.77
   2 ?   -2.6   0.0       1.3   7.8e+03      38      56 ..     106     124 ..      99     132 .. 0.79
   3 ?    2.1   0.0     0.045   2.7e+02      70      96 .]     243     266 ..     202     266 .. 0.78
   4 !   19.0   0.0   2.3e-07    0.0014       3      82 ..     282     357 ..     280     370 .. 0.87
   5 !    5.9   0.0    0.0029        17       3      25 ..     379     401 ..     377     454 .. 0.55

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.1
                EEEE-TTSSEEEEEEEEE-CTTEEEEEEE--T CS
         MG2 38 ltirdpdgkevkelplatdetggaesefalpe 69
                +++++p + +++   ++  +t+g++ ++ +p+
  EPA06372.1 49 VELYNPTNSKIDISGWKIASTSGMKKTLSIPT 80
                67778888888888888888888888888876 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.3
                 EEEE-TTSSEEEEEEEEE- CS
         MG2  38 ltirdpdgkevkelplatd 56 
                 ++++d +g  ++++pl +d
  EPA06372.1 106 VELKDKNGVSIDKTPLISD 124
                 7899999999999999665 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.045
                 T--SEEEEEEEEECSTTT-EEEEEEEE CS
         MG2  70 aaklGeysvelsadsaeeslssgsfrV 96 
                 +   G+ysv +   s ++++s++sf+V
  EPA06372.1 243 GINKGTYSVLV---SYGGATSQTSFSV 266
                 5678*******...9999999999998 PP

  == domain 4  score: 19.0 bits;  conditional E-value: 2.3e-07
                 EEEES-SEE-TT-EEEEEEEEESTTCSB---EEEEEEEE-TTSSEEEEEEEEE-CTTEEEEEEE--TT--SEEEEEEEEE CS
         MG2   3 fvytDRglYrPgetVslkallrdetlqglaklplkltirdpdgkevkelplatdetggaesefalpeaaklGeysvelsa 82 
                  + t +  Y Pg+t+sl++++    ++ +++  lk+ti+dp+g+ +++ +l  ++  +  + f    ++  G+ysv++++
  EPA06372.1 282 SITTNKSQYLPGDTLSLTGIT----SKVIPFEGLKFTIKDPNGNIISTGSLYPTNGKFSTNIFLSTVNPIYGKYSVTAEY 357
                 57899999***********98....66677777******************99999999999999***********9943 PP

  == domain 5  score: 5.9 bits;  conditional E-value: 0.0029
                 EEEES-SEE-TT-EEEEEEEEES CS
         MG2   3 fvytDRglYrPgetVslkallrd 25 
                  ++tD++ Y  getV +++ l +
  EPA06372.1 379 SLWTDKDAYNLGETVTVTGRLNQ 401
                 589*************9998865 PP

>> Big_8  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1      0.53   3.1e+03      20      56 ..      84     116 ..      68     123 .. 0.64
   2 ?   10.4   0.1   9.1e-05      0.55      41      68 ..     308     335 ..     278     355 .. 0.77
   3 ?    1.4   0.2     0.057   3.4e+02      19      51 ..     419     452 ..     410     455 .] 0.76

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.53
       Big_8  20 vkeGDyftitlpdnlkfngistsektfdikdsngnvi 56 
                 + +G + t+t++ +l f    ++++  ++kd+ng  i
  EPA06372.1  84 IESGKFLTFTFD-SLWF---TDNNEVVELKDKNGVSI 116
                 556666666653.4444...35666778888888766 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 9.1e-05
       Big_8  41 tsektfdikdsngnviakakvdpgtgti 68 
                  +  +f+ikd+ngn+i +++  p++g++
  EPA06372.1 308 FEGLKFTIKDPNGNIISTGSLYPTNGKF 335
                 45679*******************9985 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.057
       Big_8  19 svkeGDyft.itlpdnlkfngistsektfdikds 51 
                 s+++GD +  ++++d+lk++g ++   +f+i d+
  EPA06372.1 419 STNTGDIIApLKISDTLKISGDGSFTYSFKIPDN 452
                 5667776644899999999999999999998874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (455 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2987.57
//
Query:       EPA06373.1  [L=38]
Description: hypothetical protein BG20_I2568, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (38 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 273.13
//
Query:       EPA06374.1  [L=239]
Description: putative hydroxymethylglutaryl-CoA reductase, degradative, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.2e-64  216.3   3.6    7.4e-64  216.0   3.6    1.1  1  HMG-CoA_red  Hydroxymethylglutaryl-coenzyme A reductase
  ------ inclusion threshold ------
      0.057   13.3   0.1       0.11   12.4   0.1    1.6  1  GatB_Yqey    GatB domain


Domain annotation for each model (and alignments):
>> HMG-CoA_red  Hydroxymethylglutaryl-coenzyme A reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  216.0   3.6   8.3e-68   7.4e-64     160     367 .]       1     199 [.       1     199 [. 0.98

  Alignments for each domain:
  == domain 1  score: 216.0 bits;  conditional E-value: 8.3e-68
                  TC--HHHHHHHHHHHHHHHHHHHTSEEEEEEE-S--GGGEEEEEEEEEHHHH..-SSTTHHHHHHHHHHHHHHHHHH-HHHH..HHHHHHH....... CS
  HMG-CoA_red 160 DAmGaNmvnkateaaaelieeefgeeellsilsNlctdkkasainaiegrgksvvaeatigeevvekilkasaealvdlnranigtankGiggfnaha 257
                  DAmGaN++n+++ea+++l+e+++g+++ll+ilsN++t+++++a + ++++++        ge+vv++i+ a+++a  d++ra  +t+nkGi       
   EPA06374.1   1 DAMGANVTNTMCEAVSPLLEKITGGKALLRILSNYSTRRIVKASAIFDKKEI-------GGEDVVDDIILAYQFADNDVYRA--VTHNKGI------- 82 
                  9************************************************999.......9**********************..*******....... PP

                  HHHHHHHHHHTT--HHHHHHHHHHHTT.......SEEE...TTTEEEEEEEEE.----SBSHHHHH-HHHHHH.HHTT---HH...HHHHHHHHHHHH CS
  HMG-CoA_red 258 aNgiaAvflAtGqDlaaveesshaiaa.......leev...edgdlygsvtlPsleVGtvGGgtklppqaell.kllgvkgaknakeLaeiiaavgLA 344
                  +Ngi Av+ AtGqD +a+e++++a+aa       l+++   +dg+l+gs++lP l VG++GG  +++p a+++ k+lgv++ak   eLa +i a+gLA
   EPA06374.1  83 MNGIIAVANATGQDSRAIEAAANAYAArsgqyrsLSTWtkdDDGNLVGSLELP-LSVGIIGGIANVHPLAKICmKILGVSSAK---ELACVITATGLA 176
                  **********************************99998767777********.*****************999*********...************ PP

                  HHHHHHHHHT-----HHHHHHHH CS
  HMG-CoA_red 345 qelsalrALaaeglqkgHmklhr 367
                  q+ sa+rAL++eg+qkgHm+lh+
   EPA06374.1 177 QNYSAIRALSTEGIQKGHMRLHA 199
                  *********************96 PP

>> GatB_Yqey  GatB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   1.2e-05      0.11      27      67 ..     196     236 ..     172     239 .] 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.2e-05
                 HHHHHTXXTTCSSTTHHHHHHHH.HHHHTTSSGHHHHHHHHH CS
   GatB_Yqey  27 elnkegleieelkltpeqlaell.kliaegkIskkiakevle 67 
                 +l+ ++l+ ++   +peq+ +++ k+i+++kIs ++ake+l+
  EPA06374.1 196 RLHARNLAAAA-GAKPEQIDKIVqKMIDSKKISLDQAKEILR 236
                 67778888777.899****9998569**************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1681.64
//
Query:       EPA06375.1  [L=82]
Description: hypothetical protein BG20_I1750 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       832  (0.0464053); expected 358.6 (0.02)
Passed bias filter:                      627  (0.0349713); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.21s 00:00:00.52 Elapsed: 00:00:00.35
# Mc/sec: 693.05
//
Query:       EPA06376.1  [L=76]
Description: transcriptional regulator, AsnC family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.4e-10   39.1   0.1    5.7e-10   39.0   0.1    1.0  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   0.1   3.2e-14   5.7e-10       2      72 ..       7      74 ..       6      76 .] 0.91

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 3.2e-14
                    EEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEE CS
  AsnC_trans_reg  2 lvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsiv 72
                    l+s++ g+    + +  +l+e+pe++ c  + G+yd+++k  +  l+++++ +  k+++l+ +++t t+ v
      EPA06376.1  7 LISCDVGE---EHYVYSKLQEIPEIKDCIITYGSYDIVAKFETNTLDEMNQAILSKIRRLEKIRSTITLRV 74
                    57777777...788999*************************************************98766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 515.92
//
Query:       EPA06377.1  [L=63]
Description: hypothetical protein BG20_I1755 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 412.70
//
Query:       EPA06378.1  [L=125]
Description: hypothetical protein BG20_I1744 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.5e-05   23.6   8.6      0.035   14.0   0.7    2.3  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain
     0.0019   18.1   6.9       0.23   11.5   0.5    2.3  2  Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
     0.0087   15.7  15.8       0.44   10.3   4.0    2.7  2  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
  ------ inclusion threshold ------
      0.031   14.3  10.8       0.45   10.6   1.7    2.9  3  zinc_ribbon_6   Zinc-ribbon
       0.18   11.7   0.8         11    5.9   0.1    2.2  2  DUF866          Eukaryotic protein of unknown function (DUF86
       0.76   10.1   4.5         15    5.9   0.4    2.2  2  DUF1059         Protein of unknown function (DUF1059)
          3    8.1  12.8        7.3    6.9   2.5    2.3  2  LIM             LIM domain
        4.2    7.4  10.8        7.6    6.6   0.3    3.3  4  SCIFF           Six-cysteine peptide SCIFF
        6.5    6.9  11.1        3.8    7.6   0.1    3.0  3  Elf1            Transcription elongation factor Elf1 like


Domain annotation for each model (and alignments):
>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.7   1.7e-05     0.035       3      35 ..      10      43 ..       9      45 .. 0.91
   2 !   13.6   1.7   2.3e-05     0.046       3      36 ..      90     124 ..      89     125 .] 0.93

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.7e-05
  Zn_ribbon_SprT  3 yvYrCtgCgreythhlsirrhn.YrCrrCkgtLr 35
                    ++++C++Cg+e   +++ +  +  +Cr C ++++
      EPA06378.1 10 FTATCGDCGNECQIPFKPKDDRpVYCRECFQNHK 43
                    89*****************999*******77665 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 2.3e-05
  Zn_ribbon_SprT   3 yvYrCtgCgreythhlsirrhn.YrCrrCkgtLrg 36 
                     ++++C++Cg+e   +++ +  +  +Cr C +++r+
      EPA06378.1  90 FTATCGDCGNECQIPFKPKDDRpVYCRECFQNHRQ 124
                     89*****************99********888775 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.5   0.00011      0.23       6      30 ..      12      36 ..       8      69 .. 0.87
   2 !   10.2   1.1    0.0003       0.6       6      30 ..      92     116 ..      88     124 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00011
                    EE-SSBTT--EEEEEEETTEEEEEE CS
  Molybdop_Fe4S4  6 taCpyCgvgCglevhvkdgkivkve 30
                     +C  Cg  C++  ++kd++ v+ +
      EPA06378.1 12 ATCGDCGNECQIPFKPKDDRPVYCR 36
                    68******************99776 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0003
                     EE-SSBTT--EEEEEEETTEEEEEE CS
  Molybdop_Fe4S4   6 taCpyCgvgCglevhvkdgkivkve 30 
                      +C  Cg  C++  ++kd++ v+ +
      EPA06378.1  92 ATCGDCGNECQIPFKPKDDRPVYCR 116
                     68******************99877 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   4.0   0.00022      0.44       3      23 ..      14      38 ..      13      39 .. 0.68
   2 !   10.3   4.0   0.00022      0.44       3      23 ..      94     118 ..      93     120 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00022
                    -SSS--B---....-SSS----SSS CS
  DNA_RNApol_7kD  3 CgeCgaevsl....kkgdpiRCkeC 23
                    Cg+Cg+e ++    k   p+ C+eC
      EPA06378.1 14 CGDCGNECQIpfkpKDDRPVYCREC 38
                    887777777533224556******* PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00022
                     -SSS--B---....-SSS----SSS CS
  DNA_RNApol_7kD   3 CgeCgaevsl....kkgdpiRCkeC 23 
                     Cg+Cg+e ++    k   p+ C+eC
      EPA06378.1  94 CGDCGNECQIpfkpKDDRPVYCREC 118
                     887777777533224556******* PP

>> zinc_ribbon_6  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.7   0.00023      0.45      19      45 ..       1      27 [.       1      39 [. 0.81
   2 ?   -1.5   0.1       1.3   2.6e+03      30      37 ..      33      40 ..      28      44 .. 0.74
   3 ?    7.9   1.9    0.0016       3.1      27      45 ..      89     107 ..      83     120 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00023
  zinc_ribbon_6 19 mpeeyknkkvkilCnDCekksevkfhv 45
                   mp + ++++ + +C DC+++++++f+ 
     EPA06378.1  1 MPFDREREMFTATCGDCGNECQIPFKP 27
                   788888999999************986 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.3
  zinc_ribbon_6 30 ilCnDCek 37
                   ++C+ C +
     EPA06378.1 33 VYCRECFQ 40
                   78888865 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0016
  zinc_ribbon_6  27 kvkilCnDCekksevkfhv 45 
                    + + +C DC+++++++f+ 
     EPA06378.1  89 MFTATCGDCGNECQIPFKP 107
                    56779***********986 PP

>> DUF866  Eukaryotic protein of unknown function (DUF866)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1    0.0056        11      55      84 ..       4      33 ..       1      47 [. 0.78
   2 ?    4.6   0.1     0.014        28      58      83 ..      87     112 ..      80     124 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0056
                SS-EESEEE--SSSS--EEEEEE-.-TTTT CS
      DUF866 55 srgeanfvvkcklckressisikketeksy 84
                 r+   f+  c  c +e++i +k++  +++
  EPA06378.1  4 DREREMFTATCGDCGNECQIPFKPKDDRPV 33
                57778899***************9755544 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.014
                 EESEEE--SSSS--EEEEEE-.-TTT CS
      DUF866  58 eanfvvkcklckressisikketeks 83 
                    f+  c  c +e++i +k++  ++
  EPA06378.1  87 REMFTATCGDCGNECQIPFKPKDDRP 112
                 5679999************9975544 PP

>> DUF1059  Protein of unknown function (DUF1059)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.4    0.0073        15       1      18 [.       9      26 ..       9      33 .. 0.79
   2 ?    5.9   0.4    0.0073        15       1      18 [.      89     106 ..      89     113 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0073
     DUF1059  1 mkefkCgDvgpdCgfeit 18
                m +  CgD g +C+  ++
  EPA06378.1  9 MFTATCGDCGNECQIPFK 26
                66778********98775 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0073
     DUF1059   1 mkefkCgDvgpdCgfeit 18 
                 m +  CgD g +C+  ++
  EPA06378.1  89 MFTATCGDCGNECQIPFK 106
                 66778********98775 PP

>> LIM  LIM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   2.9    0.0046       9.1      29      56 ..      14      41 ..       8      43 .. 0.64
   2 ?    6.9   2.5    0.0037       7.3      29      56 ..      94     121 ..      89     123 .. 0.63

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0046
                -TTT-SB-CTT.CEEETT.EEEEHHHHHH CS
         LIM 29 CsdCqkeLkegsfyekdg.klyCkkdylk 56
                C dC++e +   f  kd+  +yC++++++
  EPA06378.1 14 CGDCGNECQIP-FKPKDDrPVYCRECFQN 41
                55555544433.44445538*******87 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0037
                 -TTT-SB-CTT.CEEETT.EEEEHHHHHH CS
         LIM  29 CsdCqkeLkegsfyekdg.klyCkkdylk 56 
                 C dC++e +   f  kd+  +yC++++++
  EPA06378.1  94 CGDCGNECQIP-FKPKDDrPVYCRECFQN 121
                 55555544433.44445538*******87 PP

>> SCIFF  Six-cysteine peptide SCIFF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.3    0.0038       7.6      17      28 ..      11      22 ..       5      26 .. 0.83
   2 ?   -1.0   0.1      0.89   1.8e+03      19      23 ..      34      38 ..      28      42 .. 0.79
   3 ?    6.4   0.2    0.0042       8.4      17      28 ..      91     102 ..      86     106 .. 0.85
   4 ?   -1.1   0.1      0.94   1.9e+03      19      23 ..     114     118 ..     108     121 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0038
       SCIFF 17 kggCgeCqtSCq 28
                +  Cg+C + Cq
  EPA06378.1 11 TATCGDCGNECQ 22
                678********9 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.89
       SCIFF 19 gCgeC 23
                 C+eC
  EPA06378.1 34 YCREC 38
                59**9 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0042
       SCIFF  17 kggCgeCqtSCq 28 
                 +  Cg+C + Cq
  EPA06378.1  91 TATCGDCGNECQ 102
                 678********9 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 0.94
       SCIFF  19 gCgeC 23 
                  C+eC
  EPA06378.1 114 YCREC 118
                 59**9 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.1    0.0019       3.8      37      61 ..       3      27 ..       1      34 [. 0.84
   2 ?    2.1   2.0       0.1   2.1e+02      24      53 ..      14      40 ..      13      45 .. 0.60
   3 ?    5.1   0.7     0.011        23      42      61 ..      88     107 ..      82     115 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0019
        Elf1 37 ldkkekiaevsCkvCgesfetkvna 61
                +d+++++ +++C+ Cg ++++ +++
  EPA06378.1  3 FDREREMFTATCGDCGNECQIPFKP 27
                678889999***********98776 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.1
        Elf1 24 CpfCnheksvevkldkkekiaevsCkvCge 53
                C  C++e  +++ ++ k+++  v C+ C +
  EPA06378.1 14 CGDCGNE--CQIPFKPKDDR-PVYCRECFQ 40
                6666666..66666655443.466777755 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.011
        Elf1  42 kiaevsCkvCgesfetkvna 61 
                 ++ +++C+ Cg ++++ +++
  EPA06378.1  88 EMFTATCGDCGNECQIPFKP 107
                 56789*********998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      179  (0.00998383); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 830.49
//
Query:       EPA06379.1  [L=60]
Description: hypothetical protein BG20_I1749 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       803  (0.0447878); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 382.10
//
Query:       EPA06380.1  [L=81]
Description: hypothetical protein BG20_I1751 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.056   13.1   0.7        0.1   12.3   0.7    1.4  1  TRAM1     TRAM1-like protein


Domain annotation for each model (and alignments):
>> TRAM1  TRAM1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.7   5.7e-06       0.1      31      45 ..      26      40 ..      24      43 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.7e-06
       TRAM1 31 fvffyvivftflRaf 45
                fvff +++++f++a+
  EPA06380.1 26 FVFFTMLILSFVHAT 40
                9************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 556.86
//
Query:       EPA06381.1  [L=130]
Description: hypothetical protein BG20_I1742 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-05   25.4   0.1    1.4e-05   25.1   0.1    1.2  1  ADH_zinc_N    Zinc-binding dehydrogenase
    0.00052   21.1   0.0    0.00053   21.1   0.0    1.2  1  ADH_zinc_N_2  Zinc-binding dehydrogenase
     0.0026   18.4   1.5      0.045   14.4   0.1    2.1  2  CoA_binding   CoA binding domain
  ------ inclusion threshold ------
      0.012   15.8   0.1      0.014   15.6   0.1    1.2  1  DUF4443       Domain of unknown function (DUF4443)
      0.074   11.9   0.0        0.1   11.4   0.0    1.2  1  TssC          Type VI secretion system, TssC, VipB


Domain annotation for each model (and alignments):
>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.1   3.9e-09   1.4e-05      31     127 ..       3      92 ..       1      95 [. 0.86

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 3.9e-09
                 HHTTESEEEETTTC.HHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHHCEEEEEEEEECSCTSSEEEEEHHHHHHTT-EEEEE-SSCHHHHHHHHHHH CS
  ADH_zinc_N  31 kklGadevinykea.dlverikeltggegvdvvfecvGsgatleaalkllkpgGrlvvvGggkgeeefdlrnlllkeksilGsllgslreefkealdl 127
                 kklGa  + + + + ++ +++ +   g  +d+++ ++ +  + ++a+k++k+gG +v+  +gk+++      ++++ek+i+G++ gs ++++++++++
  EPA06381.1   3 KKLGAIDAMTFRGDqEFLDELNKKH-G-LLDAAIVFAPADIVTDMAIKSVKKGGLIVIATVGKNPT-----FFAFEEKTIRGTVIGS-TKDMEQVIKI 92 
                 7888777777756558888888888.3.99999999999********************9999988.....56689***********.9*****9987 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   1.5e-07   0.00053      39     126 ..      46     121 ..       5     128 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.5e-07
                   HHHHEEEEEEEEE----.S-EEE-CHHHCTTT-EEEE--GGG...-.-HHHHHHHHHHHHHHH----EEEEEEGGGHHHHHHHHHSS- CS
  ADH_zinc_N_2  39 slkvlpggGrlvsiggpplsaallkpakkrkgrsvkyeflfsmkasaqadileelaalieeGklrpvvdrvfpleeaaeAhrylesgr 126
                   ++k +++ G l++i+          p++++     k+   + +  s  +d +e++ + ++e+kl + ++++fple+a+e +++l+  +
    EPA06381.1  46 AIKSVKK-GGLIVIAT-----VGKNPTFFA--FEEKTIRGT-VIGS-TKD-MEQVIKICDENKLSV-ITETFPLEKANEVLKKLKDSK 121
                   3445555.77777775.....345555555..333333333.4456.889.*************65.556*************99766 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   1.2e-05     0.045      54      93 ..      20      59 ..      17      62 .. 0.86
   2 ?    3.6   0.1      0.03   1.1e+02      47      88 ..      77     123 ..      60     130 .] 0.70

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.2e-05
                 HHHHHHHCT.TTEEEEES-HHHHHHHHHHHHHTT-SEEEEE CS
  CoA_binding 54 vdeleekte.vdvavitvPaesaqeavdelveagikgivii 93
                 +del +k++  d+a++++Pa+ + + +++ v++g  +ivi 
   EPA06381.1 20 LDELNKKHGlLDAAIVFAPADIVTDMAIKSVKKG-GLIVIA 59
                 6899****88**********************87.456655 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.03
                  TEEEESCHHHHHHHC...T.TTEEEEES..-HHHHHHHHHHHHHTT-S CS
  CoA_binding  47 glpvyksvdeleekt...e.vdvavitv..Paesaqeavdelveagik 88 
                  g  +  s +++e+ +   +  + +vit   P e+a e+ ++l + +i+
   EPA06381.1  77 GTVIG-STKDMEQVIkicDeNKLSVITEtfPLEKANEVLKKLKDSKIQ 123
                  54444.555555555333358999997666*******99999998886 PP

>> DUF4443  Domain of unknown function (DUF4443)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.1   3.9e-06     0.014      31      89 ..      42     102 ..      24     122 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.9e-06
     DUF4443  31 lrdeairffakgamilivknge.p.vfpederplrdtmeelamnieevlnfsdgdlivvtw 89 
                 + d ai+ + kg +i+i   g+ p  f  +e+ +r t+   + ++e+v+++ d + + v  
  EPA06381.1  42 VTDMAIKSVKKGGLIVIATVGKnPtFFAFEEKTIRGTVIGSTKDMEQVIKICDENKLSVIT 102
                 5699*************9888535257889**********************987665543 PP

>> TssC  Type VI secretion system, TssC, VipB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   2.9e-05       0.1     169     212 ..      79     122 ..      72     127 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.9e-05
        TssC 169 ylGsnkvvekwakiahenkvllvtdfadldkpddvvelfesanl 212
                  +Gs k +e+  ki+ enk  ++t+   l+k+++v++ ++++++
  EPA06381.1  79 VIGSTKDMEQVIKICDENKLSVITETFPLEKANEVLKKLKDSKI 122
                 58*********************************998877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       866  (0.0483016); expected 358.6 (0.02)
Passed bias filter:                      669  (0.0373138); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 787.71
//
Query:       EPA06382.1  [L=69]
Description: hypothetical protein BG20_I1753 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 486.66
//
Query:       EPA06383.1  [L=521]
Description: hypothetical protein BG20_I1747 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (521 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.51
# Mc/sec: 3068.01
//
Query:       EPA06384.1  [L=93]
Description: hypothetical protein BG20_I1756, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.7e-15   54.8   0.0    7.1e-15   54.7   0.0    1.0  1  TruD      tRNA pseudouridine synthase D (TruD)


Domain annotation for each model (and alignments):
>> TruD  tRNA pseudouridine synthase D (TruD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.7   0.0     4e-19   7.1e-15     332     416 .]       3      82 ..       1      82 [. 0.88

  Alignments for each domain:
  == domain 1  score: 54.7 bits;  conditional E-value: 4e-19
        TruD 332 aplvGtetelaegevgeierevleeegleledFklpklpelsskGtrRaillrvedlelsaeedeltleFsLpkGsYATvvlrEi 416
                 +p vG++   ++ + +  ++++l+ e+++++dF +++++e+ss+G +R++ ++++d ++    ++ t+eFsL +Gs+AT++lrEi
  EPA06384.1   3 LPFVGYSY-YKKTRFDFQISKILQAEEITPKDFFIKEMQEISSEGGFRQAAIQCTDYSA----KNNTVEFSLSRGSFATIILREI 82 
                 67888854.45677788889************************************663....4579*****************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 579.62
//
Query:       EPA06385.1  [L=107]
Description: hypothetical protein BG20_I1752 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       137  (0.00764125); expected 358.6 (0.02)
Passed bias filter:                      130  (0.00725082); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.30s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 726.46
//
Query:       EPA06386.1  [L=160]
Description: hypothetical protein BG20_I1743 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      8e-15   55.3   0.0    9.5e-15   55.0   0.0    1.1  1  AAA_33          AAA domain
      9e-05   23.0   0.0    0.00014   22.5   0.0    1.3  1  AAA_18          AAA domain
    0.00034   20.6   0.3     0.0011   19.0   0.3    1.8  1  DUF3791         Protein of unknown function (DUF3791)
     0.0029   17.8   0.0       0.25   11.6   0.0    2.1  2  UDPG_MGDP_dh    UDP-glucose/GDP-mannose dehydrogenase family,
     0.0034   17.8   0.1     0.0056   17.1   0.1    1.4  1  AAA_17          AAA domain
  ------ inclusion threshold ------
      0.017   15.2   0.8       0.03   14.4   0.2    1.6  2  ARL2_Bind_BART  The ARF-like 2 binding protein BART
      0.055   13.4   0.6       0.14   12.0   0.6    1.8  1  DUF5621         Domain of unknown function (DUF5621)
       0.16   11.6   0.6        1.5    8.4   0.5    2.1  1  SRP54           SRP54-type protein, GTPase domain
        0.2   11.4   0.7        0.5   10.1   0.2    1.8  2  ATP_bind_1      Conserved hypothetical ATP binding protein


Domain annotation for each model (and alignments):
>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.0   0.0   4.7e-18   9.5e-15       4     143 .]       1     147 [.       1     147 [. 0.84

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 4.7e-18
      AAA_33   4 lvGlpGsGKstlaerllkklgavllssdtlrrrlfgtdqqskt...dytrvldrlyqilnel...arkalsagrnvildatnlsrrer....arflkla 92 
                 ++G++GsGK+t++ ++    +++  s+d+++++l++    s t   dy++ ++++ +i+ ++   ++++    +++++d t l+r+ r     +++++a
  EPA06386.1   1 MIGVSGSGKTTWVNSHK---QYIACSTDSVIEQLAELMGISYTeafDYIQKKKKFDYITTKFfekIHDCILNDKDFVIDRTHLKRHIRisliNELRSFA 96 
                 89************966...8**************9777777766666666666666655550005566788999*************99999****** PP

      AAA_33  93 rrlgvpvri..vvvetdeetlkeRlakRaangddrsevpeealdrqkarferp 143
                 +++g + ++  v +e + +t+ eRl+kR+++++++   p++++++q+++f+ p
  EPA06386.1  97 KEHGKNLELvgVSFELPKSTIFERLKKREKHSGKS--IPKQVIQEQIDSFDIP 147
                 ***9888775689******************9876..************9976 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   6.8e-08   0.00014       4     120 ..       2     131 ..       1     143 [. 0.76

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 6.8e-08
      AAA_18   4 tGtpGvGKttlakeLskrlgf..gvnlrdvakenglllevdpe...aldeskrldedkldklldaleenss...aleegknlvidghlaeleseaakdi 94 
                  G++G+GKtt  +  ++  ++    ++ ++a   g+++++  +   + ++++ + +++ +k++d++ +  +   ++++ k  +  ++++el+s a   +
  EPA06386.1   2 IGVSGSGKTTWVNSHKQYIACstDSVIEQLAELMGISYTEAFDyiqKKKKFDYITTKFFEKIHDCILNDKDfviDRTHLKRHIRISLINELRSFAKEHG 100
                 59********9988766556687999999999999888887778999999999999999******9998888884444444444444444444433333 PP

      AAA_18  95 kk.....vvLtaspeelleRlekRgyeeaki 120
                 k      v  ++++++ +eRl+kR++++ k 
  EPA06386.1 101 KNlelvgVSFELPKSTIFERLKKREKHSGKS 131
                 3366677*******************99885 PP

>> DUF3791  Protein of unknown function (DUF3791)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.3   5.3e-07    0.0011       6      38 ..      27      59 ..      19      64 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 5.3e-07
     DUF3791  6 cIeeyarklglsgkevykllkksgvldylidcY 38
                +Ie++a+ +g+s +e++++++k + +dy++ ++
  EPA06386.1 27 VIEQLAELMGISYTEAFDYIQKKKKFDYITTKF 59
                7****************************8664 PP

>> UDPG_MGDP_dh  UDP-glucose/GDP-mannose dehydrogenase family, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.023        46      24      48 ..      28      52 ..      15      76 .. 0.83
   2 !   11.6   0.0   0.00012      0.25      14      67 ..      82     135 ..      78     139 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.023
  UDPG_MGDP_dh 24 lanlcealgidveeVieavgldpri 48
                  +++l+e +gi ++e ++ +++++++
    EPA06386.1 28 IEQLAELMGISYTEAFDYIQKKKKF 52
                  7899*****************9984 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00012
  UDPG_MGDP_dh  14 latkIsfiNelanlcealgidveeVieavgldprigpkflkpglGvGGsclpkD 67 
                   ++++Is+iNel  +++++g ++e V   ++l +   ++ lk+     G+ +pk 
    EPA06386.1  82 RHIRISLINELRSFAKEHGKNLELVGVSFELPKSTIFERLKKREKHSGKSIPKQ 135
                   6799*******************9998888887766777777777777777776 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   2.8e-06    0.0056       1     127 [.       2     130 ..       2     138 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.8e-06
                 EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTS..HSSHHHHCTSHHHH..HHHHHHHHHHHHHHHHHSSEEEEE.....E-SEEEETTEEEE CS
      AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrggl..akardemrklplee..kkelqkeaaekiaeeakkkgvlvd.....ghprikeqagfld 90 
                 +G+ GsGK+t +     + ++   s+ +++ + a+  g    +a+d+++k ++ +  + ++ +++ + i +   +k++++d      h ri     +l 
  EPA06386.1   2 IGVSGSGKTTWV---NSHKQYIACSTDSVIEQLAELMGIsyTEAFDYIQKKKKFDyiTTKFFEKIHDCILN---DKDFVIDrthlkRHIRISL-INELR 93 
                 69*********9...55566778888888888888887544888899986654431244555666666665...5667766211114556544.34467 PP

                 SSHHHHHHHH..SEEEEEE--HHHHHHHHHHH.TTST- CS
      AAA_17  91 glpkevleelkpdaiilleadpeeilerrlkd.rtrgr 127
                  + ke  ++l   + + +e ++ +i+er++k+ +++g 
  EPA06386.1  94 SFAKEHGKNL-ELVGVSFELPKSTIFERLKKReKHSGK 130
                 7788878887.3345679**************445665 PP

>> ARL2_Bind_BART  The ARF-like 2 binding protein BART
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.2   1.5e-05      0.03      40      95 ..       9      64 ..       5      75 .. 0.77
   2 ?   -1.7   0.0       1.5   3.1e+03      71      76 ..     116     121 ..      90     145 .. 0.51

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.5e-05
                    STTHHHHHHHHHHH.HHHHHHHHHTT-SSS--THHHHH....SS-GGSSHHHHHHHH CS
  ARL2_Bind_BART 40 kleytdihkeYkkl.veklleslleeigismeeflealekslsekkevakkvfeqll 95
                    k  + + hk+Y     ++++e+l e +gis  e ++++ +++++ + +++k+fe + 
      EPA06386.1  9 KTTWVNSHKQYIACsTDSVIEQLAELMGISYTEAFDYI-QKKKKFDYITTKFFEKIH 64
                    6678999****9872677888899999***********.455555577888887664 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.5
                     THHHHH CS
  ARL2_Bind_BART  71 efleal 76 
                     +++e l
      EPA06386.1 116 TIFERL 121
                     333333 PP

>> DUF5621  Domain of unknown function (DUF5621)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.6   7.2e-05      0.14      41      88 ..      13      65 ..       3     140 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.2e-05
                TTTTGGGTSTTTTT-SSHHHHHHHHHH-HHHHHHHHBTT.......T......T CS
     DUF5621 41 lnehlefYvkdselFinqleRELfKilYPktFnylFEknqfDsrfpe......d 88
                +n+h+++    ++  i ql  EL+ i+Y ++F y+  k +fD    +      d
  EPA06386.1 13 VNSHKQYIACSTDSVIEQL-AELMGISYTEAFDYIQKKKKFDYITTKffekihD 65
                5666666666667778887.5*********************754443335552 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.5   0.00077       1.5       6     107 ..       1      94 [.       1     109 [. 0.52

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00077
                 EEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEE...SSTTSCHHHH.HHHHHHHHHHTTSSEEEEEE--SSTTHHH CS
       SRP54   6 lvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvik...kkeeadpaav.akeavekakeekidvvlvDTaGrlqndke 100
                 ++G+ G+GKTt +    +++         +++D      +eQL++l      + ++   kk++ d +++  +e+++    ++ d+v+  T  + ++  +
  EPA06386.1   1 MIGVSGSGKTTWVNSHKQYI--------ACSTDSV----IEQLAELMGISYTEAFDyiqKKKKFDYITTkFFEKIHDCILNDKDFVIDRTHLKRHIRIS 87 
                 79********9876544444........3444432....444444433333232222212222233222134555555556666666666666666666 PP

                 HHHHHHH CS
       SRP54 101 lmeelkk 107
                 l++el++
  EPA06386.1  88 LINELRS 94 
                 6666655 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.2   0.00025       0.5       2      21 ..       2      21 ..       1      29 [. 0.85
   2 ?   -0.1   0.0      0.34   6.7e+02     179     179 ..      66      66 ..      21     136 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00025
  ATP_bind_1  2 vGpaGsGKttfvgalseile 21
                +G+ GsGKtt v++  +++ 
  EPA06386.1  2 IGVSGSGKTTWVNSHKQYIA 21
                8*************999876 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.34
  ATP_bind_1 179 f 179
                  
  EPA06386.1  66 C 66 
                 1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1021  (0.0569468); expected 358.6 (0.02)
Passed bias filter:                      651  (0.0363099); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1036.27
//
Query:       EPA06387.1  [L=163]
Description: hypothetical protein BG20_I1748 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00019   21.7   3.2    0.00022   21.5   1.4    2.0  2  Lar_restr_allev  Restriction alleviation protein Lar
     0.0077   16.0   1.5      0.016   14.9   1.5    1.5  1  zinc_ribbon_5    zinc-ribbon domain
  ------ inclusion threshold ------
      0.026   13.6   5.2      0.026   13.6   4.5    1.3  1  Tmemb_55A        Transmembrane protein 55A
      0.048   13.7   1.7      0.048   13.7   1.7    1.8  2  Elf1             Transcription elongation factor Elf1 like
      0.056   13.4   2.2       0.14   12.1   2.2    1.7  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.069   13.3   2.3        3.6    7.8   0.1    2.4  2  zf-RING_7        C4-type zinc ribbon domain
      0.083   12.4   5.3        0.2   11.2   5.3    1.6  1  TF_Zn_Ribbon     TFIIB zinc-binding
       0.42   10.5   3.1        5.5    6.9   0.1    2.3  2  ADD_ATRX         Cysteine Rich ADD domain
       0.97    9.4   6.2       0.57   10.1   2.9    2.2  2  Prok-RING_1      Prokaryotic RING finger family 1
        1.2    8.8  10.1        1.4    8.7   7.0    2.5  3  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit


Domain annotation for each model (and alignments):
>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.5   2.6e+03      20      36 ..      36      48 ..      23      67 .. 0.63
   2 !   21.5   1.4   1.2e-07   0.00022       4      37 ..     128     157 ..     125     163 .] 0.88

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.5
  Lar_restr_allev 20 rvvaeigqcvyCadCga 36
                     +  +     +y  +C+ 
       EPA06387.1 36 DSFN----IIYAGECEK 48
                     3333....788888987 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 1.2e-07
  Lar_restr_allev   4 kpCPfCggravlersqrvvaeigqcvyCadCgas 37 
                       pCP Cg++ ++e++  ++      + C++Cg s
       EPA06387.1 128 IPCPCCGSEMKVEKELENTT----IIRCTECGIS 157
                      6******************9....********93 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   1.5   9.1e-06     0.016       2      32 ..     127     155 ..     127     156 .. 0.96

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 9.1e-06
  zinc_ribbon_5   2 iirCpdCdtkFklvdsklKksgkkVrCakCa 32 
                    ii Cp C++  k+  +   ++   +rC  C+
     EPA06387.1 127 IIPCPCCGSEMKVEKEL--ENTTIIRCTECG 155
                    899************99..***********7 PP

>> Tmemb_55A  Transmembrane protein 55A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   4.5   1.4e-05     0.026      37      85 ..     106     155 ..      70     160 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.4e-05
   Tmemb_55A  37 lldeePPpYsplaseesgsapvitCrvCqslidvegkleq.hvvkCevCn 85 
                    e  P Y+  ++++s ++ +i C  C+s ++ve+ le   +++C+ C 
  EPA06387.1 106 RKPEPKPEYKIRSKHDSETSSIIPCPCCGSEMKVEKELENtTIIRCTECG 155
                 34466699*9999999999****************998752699*****6 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.9   3.4e+03      43      56 ..      38      51 ..      24      70 .. 0.59
   2 ?   13.7   1.7   2.7e-05     0.048      11      54 ..     117     157 ..     104     161 .. 0.65

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.9
        Elf1 43 iaevsCkvCgesfe 56
                  ++  + C++++e
  EPA06387.1 38 FNIIYAGECEKTTE 51
                55555556665443 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 2.7e-05
        Elf1  11 kkkkkkklptkFdCpfCnheksvevkldkkekiaevsCkvCges 54 
                 + k+  + ++   Cp C++e  ve +l   e++ +++C+ Cg s
  EPA06387.1 117 RSKHDSETSSIIPCPCCGSEMKVEKEL---ENTTIIRCTECGIS 157
                 2333334888999*******5555444...45799******965 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   2.2   7.8e-05      0.14      27      56 ..     126     158 ..     111     160 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.8e-05
  OrfB_Zn_ribbon  27 TSktCseCgsknke...alsgrtfkCpnCgfea 56 
                     +   C++Cgs++k      ++   +C++Cg + 
      EPA06387.1 126 SIIPCPCCGSEMKVekeLENTTIIRCTECGISD 158
                     3346*******99988556667789*****876 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.3     0.016        29      22      30 ..     123     134 ..     113     135 .. 0.67
   2 ?    7.8   0.1     0.002       3.6      13      30 ..     139     155 ..     137     155 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.016
                 B...-EE-TTT- CS
   zf-RING_7  22 e...vvtCpeCG 30 
                 e   ++ Cp CG
  EPA06387.1 123 EtssIIPCPCCG 134
                 14449******9 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.002
                 HHHHHCCSTB-EE-TTT- CS
   zf-RING_7  13 vlselragdevvtCpeCG 30 
                 v++el ++  +++C eCG
  EPA06387.1 139 VEKELENT-TIIRCTECG 155
                 57788888.5*******9 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   5.3   0.00011       0.2       3      26 ..     130     155 ..     128     156 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                   ETTTTCEE.CHEETSTTCE.EESSSS CS
  TF_Zn_Ribbon   3 CPnCgstn.lveDpergel.vCtdCG 26 
                   CP Cgs++ ++ + e++++ +Ct+CG
    EPA06387.1 130 CPCCGSEMkVEKELENTTIiRCTECG 155
                   ********9****7777777*****9 PP

>> ADD_ATRX  Cysteine Rich ADD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1    0.0031       5.5       1      22 [.     117     138 ..     117     143 .. 0.86
   2 ?    4.1   0.6     0.024        43       7      18 ..     144     155 ..     138     159 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0031
    ADD_ATRX   1 kkrgdkeleeivsCtaCgqqvn 22 
                 +++ d+e ++i+ C  Cg +++
  EPA06387.1 117 RSKHDSETSSIIPCPCCGSEMK 138
                 678899************9875 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.024
    ADD_ATRX   7 eleeivsCtaCg 18 
                 e + i+ Ct Cg
  EPA06387.1 144 ENTTIIRCTECG 155
                 56689******9 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       1.1     2e+03      29      37 ..      98     106 ..      96     116 .. 0.80
   2 ?   10.1   2.9   0.00032      0.57       6      29 ..     129     157 ..     126     160 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.1
  Prok-RING_1  29 pyHraCyek 37 
                   yH +C e+
   EPA06387.1  98 RYHPKCNER 106
                  589999776 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00032
  Prok-RING_1   6 kCpvCgkelkee.....dDiVvCpeCgtp 29 
                   Cp+Cg e+k e       i+ C+eCg +
   EPA06387.1 129 PCPCCGSEMKVEkelenTTIIRCTECGIS 157
                  6********9887777788*******965 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       4.1   7.4e+03       4       9 ..      44      49 ..      44      51 .. 0.74
   2 ?    0.5   1.3      0.27   4.9e+02      14      25 ..     124     135 ..     117     138 .. 0.77
   3 ?    8.7   7.0   0.00077       1.4       7      24 ..     138     155 ..     130     157 .. 0.70

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 4.1
                    SSS--B CS
  DNA_RNApol_7kD  4 geCgae 9 
                    geC++ 
      EPA06387.1 44 GECEKT 49
                    799886 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.27
                     SSS----SSS-- CS
  DNA_RNApol_7kD  14 kgdpiRCkeCGh 25 
                      + +i C  CG+
      EPA06387.1 124 TSSIIPCPCCGS 135
                     567899999996 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.00077
                     --B----SSS----SSS- CS
  DNA_RNApol_7kD   7 gaevslkkgdpiRCkeCG 24 
                     + e +l+++ +iRC+eCG
      EPA06387.1 138 KVEKELENTTIIRCTECG 155
                     334569999********* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       807  (0.0450109); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1129.99
//
Query:       EPA06388.1  [L=50]
Description: hypothetical protein BG20_I1746 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.29s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 337.84
//
Query:       EPA06389.1  [L=64]
Description: hypothetical protein BG20_I1745 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.9e-29   99.3   1.3    9.4e-29   99.2   1.3    1.0  1  DUF2196   Uncharacterized conserved protein (DUF2196)


Domain annotation for each model (and alignments):
>> DUF2196  Uncharacterized conserved protein (DUF2196)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.2   1.3   5.3e-33   9.4e-29       3      60 ..       5      62 ..       3      63 .. 0.97

  Alignments for each domain:
  == domain 1  score: 99.2 bits;  conditional E-value: 5.3e-33
     DUF2196  3 ktrkdikpGleVeivlkkdqrtGklteGiVkdilTnssthphGIKVrLedGeVGRVqe 60
                + r++ik+G +V+iv+k+dqr+G+lt GiVk+ilT+ss+hphGIKV+L++G++GRVq+
  EPA06389.1  5 PSRNKIKIGSSVQIVQKQDQRSGNLTPGIVKRILTSSSSHPHGIKVELDNGKIGRVQS 62
                689*****************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 455.80
//
Query:       EPA06390.1  [L=166]
Description: GroES-like protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.5e-24   83.5   0.1    1.4e-23   82.8   0.1    1.3  1  ADH_N         Alcohol dehydrogenase GroES-like domain
    6.2e-07   29.4   0.2    1.2e-06   28.5   0.2    1.5  1  ADH_zinc_N    Zinc-binding dehydrogenase
    0.00024   20.5   0.3    0.00034   20.0   0.3    1.2  1  2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, 
  ------ inclusion threshold ------
      0.023   14.0   0.2       0.03   13.6   0.2    1.2  1  AlaDh_PNT_C   Alanine dehydrogenase/PNT, C-terminal domain
       0.14   12.2   0.0       0.18   11.8   0.0    1.3  1  MA3           MA3 domain


Domain annotation for each model (and alignments):
>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.8   0.1   3.9e-27   1.4e-23      29     108 ..       9      89 ..       4      90 .. 0.95

  Alignments for each domain:
  == domain 1  score: 82.8 bits;  conditional E-value: 3.9e-27
                 SSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE.-SSSHHHHTT-GGG-TTBEETTTSS-SSSBSEEEECGGGEEE CS
       ADH_N  29 vklplilGHEivGeveevgpevkklkvGdrVvveplis.cgeCaaCkegeenlCeeakllgvsldGgfaeyvvvpekklvk 108
                  +lp ++GHE+vG+v e+g++v+k+k+GdrV + pl + c+eC++Ckeg+e+lCe+  ++g sl+Gg+aey++v+e+++ k
  EPA06390.1   9 PSLPTVPGHELVGKVIEIGNKVTKFKIGDRVGITPLLEaCKECQYCKEGKEQLCESSIITGESLKGGYAEYITVSEDFATK 89 
                 679********************************9999************************************998776 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.2   3.3e-10   1.2e-06       1      32 [.     131     162 ..     131     165 .. 0.97

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 3.3e-10
                 HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH CS
  ADH_zinc_N   1 gvGlaavqlAkalGaeviavdsseeklelakk 32 
                 gvG++avq+Ak  Ga+via ++s+e le akk
  EPA06390.1 131 GVGHMAVQFAKVEGAQVIAFSRSKEHLEVAKK 162
                 9*****************************98 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.3   9.5e-08   0.00034      35      73 ..     120     158 ..     105     165 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 9.5e-08
                   TTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH CS
  2-Hacid_dh_C  35 sgktvGiiGlGrIGqavakrlkafgmkviaydrskkkee 73 
                   s+k++Gi+G+G +G+ + + +k  g++via++rsk++ e
    EPA06390.1 120 SHKKIGIFGIGGVGHMAVQFAKVEGAQVIAFSRSKEHLE 158
                   789*******************************87544 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   8.4e-06      0.03      28      69 ..     121     162 ..     102     166 .] 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.4e-06
                  --EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH CS
  AlaDh_PNT_C  28 pakvlviGgGvaGlqAiatakglgakVtvlDvrparleqles 69 
                  + k+ ++G G +G  A++ ak  ga+V ++  +++ le  ++
   EPA06390.1 121 HKKIGIFGIGGVGHMAVQFAKVEGAQVIAFSRSKEHLEVAKK 162
                  56899***************************9999987776 PP

>> MA3  MA3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   5.1e-05      0.18      45      96 ..      44      94 ..      17     105 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.1e-05
                HHHS.SS--HHHHHHHHHHHCC-HHHHHHHHHHHHHHHHGGGGS-HH...HH CS
         MA3 45 aleesktyneyygllleklceknlilkkqfekgfwdvlesledleldipeai 96
                +le   ++ +y+ +  e+lce+  i+ ++++ g+ ++++  ed ++ ipe +
  EPA06390.1 44 LLEA-CKECQYCKEGKEQLCESSIITGESLKGGYAEYITVSEDFATKIPESM 94
                5555.566667777779********************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1099.33
//
Query:       EPA06391.1  [L=71]
Description: hypothetical protein BG20_I2500, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-05   25.0   0.1    1.2e-05   24.9   0.1    1.0  1  Met_synt_B12  Vitamin B12 dependent methionine synthase, acti


Domain annotation for each model (and alignments):
>> Met_synt_B12  Vitamin B12 dependent methionine synthase, activation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.1     7e-10   1.2e-05     121     176 ..       2      57 ..       1      65 [. 0.89

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 7e-10
  Met_synt_B12 121 dyiGlFavtagigieelaekfeaekddYs.silvkaladrLaeAfaellhekvrkel 176
                   d +++ avt+g ++++++e++++e d+Y+ +  ++ la  +aeA+ae++++k++ el
    EPA06391.1   2 DIVAFQAVTVGNKVSDVIEQWNKE-DKYTdAYYLHGLAVEVAEALAEWINRKIKSEL 57 
                   788888****************99.7775267899******************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 471.64
//
Query:       EPA06392.1  [L=223]
Description: hypothetical protein BG20_I2501, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-07   30.5   0.1      0.005   16.2   0.0    2.1  2  MTHFR         Methylenetetrahydrofolate reductase
  ------ inclusion threshold ------
       0.14   11.6   0.0       0.18   11.2   0.0    1.2  1  Beta_protein  Beta protein


Domain annotation for each model (and alignments):
>> MTHFR  Methylenetetrahydrofolate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   5.6e-07     0.005      31     113 ..       5      87 ..       1     104 [. 0.85
   2 !   12.6   0.0     7e-06     0.062     163     220 ..     124     180 ..     118     222 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.6e-07
                 HHHHHHGGGG-SEEEE---CCCTTHHHHHHHHHHHHH.HH-S-EEEEEESTTS-HHHHHHHHHHHHHCT--EEEEE--S--TT- CS
       MTHFR  31 eridrleevkplfvdvTwgaggstaeltssiakviqq.elgleailhlTctdaskeeldkalekakelGirnilALrGDppkde 113
                 e+++ +++   +++ vT+   g+++ +++s+ k +++ + +l+  + +  +d+++ ++++ +++  +l +  +l L+GDp k++
  EPA06392.1   5 EKVSEINTF-CDGIHVTDSVLGTKRISALSAGKLLKEnYPNLQITISMRVRDKDMTMIKQSVQESIDLKLDGVLVLKGDPSKEN 87 
                 444444433.48899*******9999999999999861569**************************************98874 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 7e-06
                 HHHHHHHHCT--EEEEEE-S-HHHHHHHHHHHHHCT-SS-EEEEE-.--SSHHHHHHHH CS
       MTHFR 163 kylkeKvdaGAdfiitQlffdvdkflkfveqvreagidipiipgim.piksykslkrla 220
                  ++++K+da  + ++tQ++  +++  +  e++r +g    iip i+ p +  ++  ++ 
  EPA06392.1 124 DKIQKKIDAAPQGFMTQVIHSAEQVQRISEKLRPKGF--RIIPCILlPTEKNENSAKFL 180
                 5789********************************9..9***9972554444444443 PP

>> Beta_protein  Beta protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0     2e-05      0.18      52     113 ..     124     177 ..      90     191 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2e-05
  Beta_protein  52 drikeawkrrravflDllddadqltedgrevleellellseegldiiPviqldrddsarlra 113
                   d+i+++++  ++ f            + +e ++++ e l+++g+ iiP+i l ++++ +++a
    EPA06392.1 124 DKIQKKIDAAPQGFMTQ-------VIHSAEQVQRISEKLRPKGFRIIPCILLPTEKN-ENSA 177
                   44444554444444444.......566999**********************77766.4443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1341.62
//
Query:       EPA06393.1  [L=367]
Description: hypothetical protein BG20_I2041 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2756.91
//
Query:       EPA06394.1  [L=379]
Description: hypothetical protein BG20_I2042 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0098   15.9   0.2       0.67   10.0   0.0    3.0  3  WhiA_N    WhiA N-terminal LAGLIDADG-like domain


Domain annotation for each model (and alignments):
>> WhiA_N  WhiA N-terminal LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0   3.8e-05      0.67      22      75 ..      65     115 ..      58     126 .. 0.88
   2 ?   -2.9   0.0      0.42   7.5e+03      62      73 ..     157     168 ..     155     171 .. 0.78
   3 !    2.4   0.0    0.0091   1.6e+02      37      62 ..     194     219 ..     188     242 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 3.8e-05
      WhiA_N  22 ngklvlevqtenaaiARriykllkelYgieaellvrkknklkknnvYivrvkeg 75 
                 +  ++l + +e +aiAR + + ++++    +e+++   n l k ++++vrv+  
  EPA06394.1  65 SSAINLLFGIEKIAIARQVKNDFQKV---VSEITTIGGNLLLKGERFLVRVEGT 115
                 6678899999**************99...8********************9876 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.42
      WhiA_N  62 lkknnvYivrvk 73 
                 l knn Y+ + +
  EPA06394.1 157 LTKNNAYVCIFS 168
                 899****98765 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.0091
      WhiA_N  37 ARriykllkelYgieaellvrkknkl 62 
                 A   ++++k+ Y++++ + +r+k+ l
  EPA06394.1 194 AISCFETIKQGYDTKIIICYRQKSEL 219
                 56678888888888888888888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       701  (0.0390987); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2451.93
//
Query:       EPA06395.1  [L=100]
Description: hypothetical protein BG20_I2039, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0062   16.8   0.6       0.01   16.1   0.1    1.5  1  Rpr2             RNAse P Rpr2/Rpp21/SNM1 subunit domain
  ------ inclusion threshold ------
       0.01   15.3   0.1        0.3   10.6   0.0    2.3  2  TF_Zn_Ribbon     TFIIB zinc-binding
      0.017   15.5   0.1      0.023   15.1   0.1    1.3  1  Lar_restr_allev  Restriction alleviation protein Lar
      0.034   14.4   0.4       0.22   11.8   0.0    2.2  2  Ribosomal_L32p   Ribosomal L32p protein family
      0.084   12.3   0.2       0.28   10.6   0.0    1.8  2  Vps36-NZF-N      Vacuolar protein sorting 36 NZF-N zinc-finge
      0.086   12.8   0.5        3.3    7.7   0.0    2.2  2  OrfB_Zn_ribbon   Putative transposase DNA-binding domain


Domain annotation for each model (and alignments):
>> Rpr2  RNAse P Rpr2/Rpp21/SNM1 subunit domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   3.5e-06      0.01      37      77 ..      44      84 ..      30      95 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.5e-06
                ---SSTCCCTB-TTT--B--CTTTEEEEEE-SSS-E..... CS
        Rpr2 37 lrlppsvkrtvCkkCgsvlipgvtcsvrvenkskkkkkkkk 77
                ++l+ + k+ +Ck+Cg + + ++ ++++ + ++k++ ++ k
  EPA06395.1 44 MKLDAATKHFICKRCGLYATREQVSDIKYRLNQKERTREDK 84
                78999*****************9999999765555444333 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1     0.028        83       3       8 ..       4       9 ..       2      33 .. 0.87
   2 ?   10.6   0.0    0.0001       0.3      13      27 ..      46      60 ..      40      71 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.028
                 ETTTTC CS
  TF_Zn_Ribbon 3 CPnCgs 8
                 CP+C  
    EPA06395.1 4 CPECTA 9
                 899865 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0001
                  EETSTTCEEESSSSB CS
  TF_Zn_Ribbon 13 eDpergelvCtdCGl 27
                  +D+++  ++C++CGl
    EPA06395.1 46 LDAATKHFICKRCGL 60
                  699999********8 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.1   7.6e-06     0.023       5      37 ..       3      66 ..       1      93 [. 0.82

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 7.6e-06
  Lar_restr_allev  5 pCPfCggravlersqrvvaeigq..........................cvyCadCga.....s 37
                      CP C  r++++ + +  ae  +                           ++C+ Cg       
       EPA06395.1  3 NCPECTAREKKKIQAKYEAETPEenrgredlfklfdeveipmkldaatkHFICKRCGLyatreQ 66
                     7********999999999987779**********************************653331 PP

>> Ribosomal_L32p  Ribosomal L32p protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.31   9.3e+02      42      52 ..       4      13 ..       2      18 .. 0.59
   2 ?   11.8   0.0   7.3e-05      0.22      37      53 ..      50      66 ..      40      69 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.31
                    BTTTTBSSSBX CS
  Ribosomal_L32p 42 cpscGyYkgre 52
                    cp+c + + ++
      EPA06395.1  4 CPEC-TAREKK 13
                    6777.444444 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 7.3e-05
                    CTTC-BTTTTBSSSBXS CS
  Ribosomal_L32p 37 lpHrvcpscGyYkgrev 53
                      H +c+ cG Y  re 
      EPA06395.1 50 TKHFICKRCGLYATREQ 66
                    57********9999985 PP

>> Vps36-NZF-N  Vacuolar protein sorting 36 NZF-N zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1      0.33   9.9e+02      35      39 ..       3       7 ..       1      27 [. 0.63
   2 ?   10.6   0.0   9.5e-05      0.28      22      62 ..      43      80 ..      38      84 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.33
  Vps36-NZF-N 35 pClaC 39
                  C  C
   EPA06395.1  3 NCPEC 7 
                 44444 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 9.5e-05
  Vps36-NZF-N 22 psnfdpnastplPpClaCGvkpdlelikksikasasskkse 62
                 p ++d  a t+  +C  CG  +++e++ + ik++ ++k+ +
   EPA06395.1 43 PMKLD--AATKHFICKRCGLYATREQVSD-IKYRLNQKERT 80
                 44444..5777778************976.66666666554 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.2     0.025        73      30      43 ..       3      15 ..       2      27 .. 0.77
   2 ?    7.7   0.0    0.0011       3.3      43      61 ..      49      67 ..      40      70 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.025
  OrfB_Zn_ribbon 30 tCseCgsknkeals 43
                    +C+eC ++ k+ + 
      EPA06395.1  3 NCPECTAREKK-KI 15
                    6*****99999.33 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0011
  OrfB_Zn_ribbon 43 sgrtfkCpnCgfeadrDvn 61
                    +++ f C++Cg++a r  +
      EPA06395.1 49 ATKHFICKRCGLYATREQV 67
                    6789*********999766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1252  (0.069831); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 659.49
//
Query:       EPA06396.1  [L=57]
Description: hypothetical protein BG20_I2044 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-09   36.7   0.0      7e-09   35.5   0.0    1.5  1  PUA_2     PUA-like domain


Domain annotation for each model (and alignments):
>> PUA_2  PUA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.0   3.9e-13     7e-09       1      59 [.       5      55 ..       5      57 .] 0.89

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 3.9e-13
                SS-TTSS----B--CHHHHHHHHHHHTS-EEE--HHHHHHHHHHHTTTTTT-SCC--HH CS
       PUA_2  1 ikphggkLvelvvedeekeellkeakelpsielskrelqdlellaeGgfsPLegFmree 59
                ikphggkLv+++++ +         + l si++++  ++d+e +a G+fsPLegF++++
  EPA06396.1  5 IKPHGGKLVNRITKAD--------PSGLFSITITEDLANDVENIADGIFSPLEGFLGKK 55
                689*******997754........356889**************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       212  (0.0118244); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.43
# Mc/sec: 401.37
//
Query:       EPA06397.1  [L=237]
Description: adenylylsulfate reductase, thioredoxin dependent [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-43  148.8   0.0      2e-43  148.5   0.0    1.1  1  PAPS_reduct  Phosphoadenosine phosphosulfate reductase family


Domain annotation for each model (and alignments):
>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.5   0.0   1.1e-47     2e-43       5     174 .]      36     208 ..      32     208 .. 0.96

  Alignments for each domain:
  == domain 1  score: 148.5 bits;  conditional E-value: 1.1e-47
                  E--SSCTCHHHHHHHHHHCTTHEEEEEE-STB-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH-S-THHHC.....HHHHHHTHHHHHHHHHC CS
  PAPS_reduct   5 svsgGkdslVllhLalkafkpvpvvfvdtghefpetiefvdeleeryglrlkvyepeeevaekinaekhgsslyee.....aaeriaKveplkkaLek 97 
                  + s+G++++V+++++lk++++++++ +dtg+  +et++ +d ++++y+++++v  p+ ++ e +++ek    +ye+      +++i+Kv+p+++ L+ 
   EPA06397.1  36 ASSFGAEDAVIMDIMLKINPKFRFFTLDTGRLPQETYDIMDIVRKKYNITIEVLFPDTKEVEDMVREKGMNLFYESienrkLCCEIRKVHPINRMLST 133
                  78******************************************************************66666666****99**************** PP

                  TTECEEE----CCCTTTTTTSSSEEECTTT-SCEEE-CCCT--HHHHHHHHHHCT--B-CCCCTT-SS--BCTTB-S CS
  PAPS_reduct  98 ldedalltGaRrdesksraklpiveidedfekslrvfPllnWteedvwqyilrenipynpLydqgfrsiGcvpctga 174
                  ld   ++tG+Rrd+++ r+  +i++id      l+++P+++Wt+ ++++yi+++n+pyn+L d+g+ siGc pct+a
   EPA06397.1 134 LD--GWITGLRRDQTEVRKDVNIFQIDHGHGGILKINPIIDWTWDQIQDYIKKNNLPYNSLLDKGYPSIGCEPCTRA 208
                  *9..***********************************************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       743  (0.0414412); expected 358.6 (0.02)
Passed bias filter:                      636  (0.0354733); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 1337.38
//
Query:       EPA06398.1  [L=51]
Description: hypothetical protein BG20_I2040 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.012   16.2   0.5      0.012   16.1   0.5    1.1  1  YtxH      YtxH-like protein


Domain annotation for each model (and alignments):
>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.1   0.5     7e-07     0.012      27      66 ..      10      49 ..       3      51 .] 0.91

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 7e-07
        YtxH 27 Rkdlkekaddlkekakelleeakekakekaedlkekvkek 66
                  ++ke+++++ e++ ++ ++++ +++e++++++ +v e+
  EPA06398.1 10 ISKIKENYNKYEENLGDFSKNFNPNGAENTAKIAASVLEE 49
                579*******************************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       885  (0.0493614); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 333.02
//
Query:       EPA06399.1  [L=98]
Description: hypothetical protein BG20_I2045, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.5e-27   94.0   0.1    8.4e-27   93.8   0.1    1.0  1  PUA_2     PUA-like domain
  ------ inclusion threshold ------
       0.12   11.7   0.0       0.12   11.7   0.0    1.1  1  Npa1      Ribosome 60S biogenesis N-terminal


Domain annotation for each model (and alignments):
>> PUA_2  PUA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.8   0.1   9.3e-31   8.4e-27      75     159 .]       2      86 ..       1      86 [. 0.98

  Alignments for each domain:
  == domain 1  score: 93.8 bits;  conditional E-value: 9.3e-31
                 E-SS---EEEECCHCHHHTT-SEEEEEETTTEEEEEEEEEEEEE-HHHHHHHHHHS---TTSHHHHHHCTS-SEEEEEEEEE-S- CS
       PUA_2  75 lwsiPivLdvseedakklkegdrvaLkdkegellAileveeiyeldkeeeaekvfgttdeaHPgvkkvleqgevlvgGkvevlee 159
                  w+iPi+Ldv++ +a+++k++ +v+L++++g  +Ail+v+ei+++dke+ a+ v+gt d+ HPgv+k+++++++lvgGk++ +++
  EPA06399.1   2 AWTIPIILDVDKSTAEQMKKAGKVLLQNHQGVGIAILHVKEIFTFDKEKTAKGVYGTIDSTHPGVAKTMSMQDYLVGGKIDYIQR 86 
                 6********************************************************************************9985 PP

>> Npa1  Ribosome 60S biogenesis N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   1.4e-05      0.12      73     112 ..      36      74 ..      11      96 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.4e-05
        Npa1  73 ptLrLlteivsfdggalarevlrsfdfslkvlpklltprk 112
                 ++L + +ei +fd+++ a+ v+ ++d ++++++k ++++ 
  EPA06399.1  36 AILHV-KEIFTFDKEKTAKGVYGTIDSTHPGVAKTMSMQD 74 
                 55555.9*****************************8865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.31s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 699.70
//
Query:       EPA06400.1  [L=187]
Description: class I glutamine amidotransferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-19   70.0   0.0    2.6e-19   69.7   0.0    1.0  1  GATase         Glutamine amidotransferase class-I
    9.7e-09   35.3   0.0      3e-07   30.4   0.0    2.1  1  Peptidase_C26  Peptidase C26
     0.0064   16.4   0.0       0.39   10.5   0.0    2.2  2  SNO            SNO glutamine amidotransferase family


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.7   0.0   4.4e-23   2.6e-19       2     175 ..       4     168 ..       3     180 .. 0.85

  Alignments for each domain:
  == domain 1  score: 69.7 bits;  conditional E-value: 4.4e-23
                 EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT..TTTHHHHHHHHCTSTS-EEEETHHHHHHHHHTTTEEEEEECE CS
      GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg..vegkieaikearenkiPiLGICLGmQllaiefgrkvvkekek 98 
                 +iDn++ +t+nl++ l   +  ++ ++i+ + +  +  l+n++  ++sg   + +   e   ++i++a +n++ +LGIC+G  +l++ +g+++ k    
  EPA06400.1   4 VIDNGSVYTKNLIDFLSDKK--IHYKKITPELLDLK-SLDNYNSFILSGRRKNEKkvNEINSKIINFAVNNDKKLLGICYGAEILTLTLGGTIKKSV-I 98 
                 89**************9666..66666665566663.489**********999999999999********************************999.8 PP

                 EEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEEEEEEETTTEEEESSBTTSTT CS
      GATase  99 ehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeelmeiiekknpfvgvQFHPEsts 175
                  ++g +     +e+ l +g+   +++  +H++e+ +   +p+ l+ +a+s++ ++++ i+ +k+p++g+QFHPE++ 
  EPA06400.1  99 LQRGNEKVSILKENPLSSGN---LHVFESHGFEISK---LPDVLIGIAESKN-CKFEIIQYDKKPIFGTQFHPEMSD 168
                 88888888888777777777...9************...*****99999955.566666666668*********875 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.0   4.9e-11     3e-07      91     216 .]      58     165 ..      40     165 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 4.9e-11
  Peptidase_C26  91 dalelaLiraalergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkvekgsllaellgseeievnslHhqaikelaeelr 186
                    ++++ ++i+ a+++++ +lgiC G ++l  +lGGt+ +++              +  + +v++ k+  l++     + +v   H + i++l + l 
     EPA06400.1  58 NEINSKIINFAVNNDKKLLGICYGAEILTLTLGGTIKKSVIL------------QRGNEKVSILKENPLSS----GNLHVFESHGFEISKLPDVLI 137
                    5677889999****************************9994............22345677777777664....6779***************** PP

  Peptidase_C26 187 veAvaeDgviEaieseeakafvlgvQwHPE 216
                     +A ++    E i+  +  ++++g Q+HPE
     EPA06400.1 138 GIAESKNCKFEIIQYDK--KPIFGTQFHPE 165
                    **************999..47********9 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.0   0.0    0.0067        40      56      88 ..      60      92 ..      32     108 .. 0.81
   2 !   10.5   0.0   6.6e-05      0.39     149     177 ..     142     172 ..     128     180 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.0067
                -HHHHHHHHHTT.--EEEETHHHHHHCCEETTB CS
         SNO 56 lyedllefvknsekvvlGtCaGlillskelene 88
                +  ++ +f+ n++k +lG C G  +l+  l++ 
  EPA06400.1 60 INSKIINFAVNNDKKLLGICYGAEILTLTLGGT 92
                4567899999***********998888777655 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 6.6e-05
                 ECTT..EEEEEEETTEEEESS-GGGSTTHCH CS
         SNO 149 eldg..eivvakqkkilatsfhPelaeddir 177
                  ++   ei+   +k i++t fhPe+++d++ 
  EPA06400.1 142 SKNCkfEIIQYDKKPIFGTQFHPEMSDDGKN 172
                 44433489999999**************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 1232.26
//
Query:       EPA06401.1  [L=319]
Description: tetratricopeptide repeat protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.2e-15   53.9  17.0    2.4e-08   33.5   1.4    4.7  4  TPR_1            Tetratricopeptide repeat
      2e-12   46.2  11.6    1.7e-06   27.7   0.5    4.5  4  TPR_2            Tetratricopeptide repeat
    1.3e-11   44.0  13.6    0.00032   20.9   1.4    3.5  3  TPR_17           Tetratricopeptide repeat
    2.1e-08   33.7  20.3    2.4e-05   24.2   0.9    5.1  4  TPR_8            Tetratricopeptide repeat
      4e-07   29.6  13.6    0.00013   21.6   0.2    3.9  3  TPR_11           TPR repeat
    1.3e-06   28.6   0.9     0.0013   19.0   0.1    3.4  3  TPR_12           Tetratricopeptide repeat
    2.3e-06   27.9   0.0       0.45   11.5   0.0    4.0  4  TPR_14           Tetratricopeptide repeat
    2.4e-06   27.9   2.4      0.024   15.1   0.1    3.2  3  TPR_19           Tetratricopeptide repeat
    8.5e-05   23.1   0.0        3.2    8.5   0.0    3.1  4  TPR_16           Tetratricopeptide repeat
    0.00012   22.7   0.0    0.00036   21.1   0.0    1.8  1  Peptidase_C39_2  Peptidase_C39 like family
    0.00014   22.3   3.4       0.37   11.5   0.0    4.1  4  TPR_6            Tetratricopeptide repeat
    0.00031   20.5   0.0     0.0097   15.7   0.0    2.5  2  Peptidase_C39    Peptidase C39 family
     0.0066   16.6   0.0      0.024   14.8   0.0    2.0  2  TPR_9            Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.071   13.2   1.1         10    6.4   0.1    3.5  3  TPR_7            Tetratricopeptide repeat
       0.11   12.4   0.0        0.2   11.7   0.0    1.3  1  Peptidase_C70    Papain-like cysteine protease AvrRpt2


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0    0.0012       1.4      14      34 .]     184     204 ..     181     204 .. 0.93
   2 !    9.1   0.1     0.001       1.2      13      31 ..     216     234 ..     206     237 .. 0.84
   3 !   33.5   1.4     2e-11   2.4e-08       2      33 ..     239     270 ..     238     271 .. 0.96
   4 !   10.9   1.5   0.00027      0.32       1      33 [.     273     305 ..     273     305 .. 0.96

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0012
                 TT-HHHHHHHHHHHHHHSTTH CS
       TPR_1  14 lgkydeAleyyekALelnPnn 34 
                 +++  +Ale  +k + l+ nn
  EPA06401.1 184 QKNTTDALESLKKSIDLDQNN 204
                 89999**************98 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.001
                 HTT-HHHHHHHHHHHHHHS CS
       TPR_1  13 klgkydeAleyyekALeln 31 
                 + ++  +++ yyek++eln
  EPA06401.1 216 NEQNSTDCITYYEKCIELN 234
                 56677789**********9 PP

  == domain 3  score: 33.5 bits;  conditional E-value: 2e-11
                 HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
       TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPn 33 
                  a+++lGn y+k +++d+ + yy+kA+e+nP+
  EPA06401.1 239 LAYNGLGNYYLKSNQFDKSEFYYSKAIEINPK 270
                 59*****************************7 PP

  == domain 4  score: 10.9 bits;  conditional E-value: 0.00027
                 HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
       TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPn 33 
                 ak+++n++++  k+++  +A  + +  L+l P+
  EPA06401.1 273 AKIYKNRAYLREKQKNNSDAKNDLKSYLKLFPK 305
                 899**************************9995 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.017        21      14      34 .]     184     204 ..     183     204 .. 0.92
   2 !    7.7   0.1    0.0037       4.4      11      32 ..     214     235 ..     207     237 .. 0.87
   3 !   27.7   0.5   1.4e-09   1.7e-06       2      33 ..     239     270 ..     238     271 .. 0.95
   4 !   10.2   0.9   0.00057      0.68       1      33 [.     273     305 ..     273     306 .. 0.95

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.017
       TPR_2  14 lgdyeeAleafekAleldPnn 34 
                 +++  +Ale ++k++ ld nn
  EPA06401.1 184 QKNTTDALESLKKSIDLDQNN 204
                 68899*************997 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0037
       TPR_2  11 yyklgdyeeAleafekAleldP 32 
                 +++ ++  +++ ++ek++el+ 
  EPA06401.1 214 LLNEQNSTDCITYYEKCIELNN 235
                 677888899***********96 PP

  == domain 3  score: 27.7 bits;  conditional E-value: 1.4e-09
       TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPn 33 
                  a++ lG+ y+k++++++ + ++ kA+e++P+
  EPA06401.1 239 LAYNGLGNYYLKSNQFDKSEFYYSKAIEINPK 270
                 589****************************7 PP

  == domain 4  score: 10.2 bits;  conditional E-value: 0.00057
       TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                 a+++ n++++ +k+++  +A+++++  l+l P+
  EPA06401.1 273 AKIYKNRAYLREKQKNNSDAKNDLKSYLKLFPK 305
                 6899***************************97 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.3   2.3e-05     0.027       3      27 ..     195     219 ..     194     222 .. 0.90
   2 !   20.9   1.4   2.7e-07   0.00032       1      32 [.     226     257 ..     226     259 .. 0.94
   3 !   15.7   0.7   1.2e-05     0.015       1      32 [.     260     292 ..     260     294 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.3e-05
      TPR_17   3 lkaleldPnnadaynnLAelllknG 27 
                 +k+++ld nn+ a+++LA ll +++
  EPA06401.1 195 KKSIDLDQNNPTALYLLASLLNEQN 219
                 79*******************8877 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 2.7e-07
      TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtA 32 
                 +y+k++el+     ayn L++++lk +++++ 
  EPA06401.1 226 YYEKCIELNNRFYLAYNGLGNYYLKSNQFDKS 257
                 6***************************9986 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 1.2e-05
      TPR_17   1 lylkaleldPn.nadaynnLAelllknGdlmtA 32 
                 +y ka+e++P+ +a+ y n+A+l +k+++  +A
  EPA06401.1 260 YYSKAIEINPKrSAKIYKNRAYLREKQKNNSDA 292
                 699********99***********998877666 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0      0.03        36      15      34 .]     185     204 ..     182     204 .. 0.89
   2 !   11.5   0.3   0.00023      0.27       3      32 ..     207     235 ..     205     237 .. 0.75
   3 !   24.2   0.9     2e-08   2.4e-05       3      33 ..     240     270 ..     238     271 .. 0.96
   4 ?    4.6   1.0     0.039        46       1      33 [.     273     305 ..     273     305 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.03
                 T-HHHHHHHHHHHHHHHHH. CS
       TPR_8  15 gdyeeAkeyyekaleldpdn 34 
                 ++   A e+++k ++ld++n
  EPA06401.1 185 KNTTDALESLKKSIDLDQNN 204
                 78889************986 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00023
                 HHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
       TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldp 32 
                 a+y+l+s++   ++    + yyek++el+ 
  EPA06401.1 207 ALYLLASLLN-EQNSTDCITYYEKCIELNN 235
                 5666666654.556677***********96 PP

  == domain 3  score: 24.2 bits;  conditional E-value: 2e-08
                 HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
       TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                 ay+ lg+ ylk +++++++ yy ka+e++p+
  EPA06401.1 240 AYNGLGNYYLKSNQFDKSEFYYSKAIEINPK 270
                 89****************************8 PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.039
                 CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
       TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33 
                 a++y n +++ +k+++   Ak  ++ +l+l p+
  EPA06401.1 273 AKIYKNRAYLREKQKNNSDAKNDLKSYLKLFPK 305
                 5677799**********************9885 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.2   1.1e-07   0.00013       8      38 ..     185     215 ..     182     219 .. 0.87
   2 !    7.8   1.6    0.0022       2.6      14      40 ..     224     250 ..     221     252 .. 0.92
   3 !    9.8   1.0   0.00053      0.63       1      41 [.     245     286 ..     245     287 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.1e-07
      TPR_11   8 GkyeeAieaYkkAlkldPdnaeayynLGlay 38 
                  + ++A+e++kk ++ld++n++a+y L+ ++
  EPA06401.1 185 KNTTDALESLKKSIDLDQNNPTALYLLASLL 215
                 56789**********************9776 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0022
      TPR_11  14 ieaYkkAlkldPdnaeayynLGlayyk 40 
                 i+ Y+k ++l++ +  ay++LG+ y+k
  EPA06401.1 224 ITYYEKCIELNNRFYLAYNGLGNYYLK 250
                 677********************9987 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00053
      TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPd.naeayynLGlayykq 41 
                 G+ y + ++++++   Y+kA++++P+ +a +y n++++  kq
  EPA06401.1 245 GNYYLKSNQFDKSEFYYSKAIEINPKrSAKIYKNRAYLREKQ 286
                 7889999999999999*********75899999999887776 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1     0.011        13      16      50 ..     184     216 ..     180     233 .. 0.69
   2 !   19.0   0.1   1.1e-06    0.0013       4      75 ..     206     268 ..     203     270 .. 0.88
   3 !   15.8   0.1   1.1e-05     0.013       5      76 ..     240     304 ..     237     305 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.011
      TPR_12  16 lgrydeAlellekaleiarrllGpdhpltattlrn 50 
                 +++ ++Ale l+k++++ ++   p+ ++++++l n
  EPA06401.1 184 QKNTTDALESLKKSIDLDQNN--PTALYLLASLLN 216
                 677788888888888888766..666666665554 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 1.1e-06
      TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                 tal+ la++l+++   +++++++ek++e+ +r     +     ++++Lg +y++++++++ + ++ +a++i 
  EPA06401.1 206 TALYLLASLLNEQNS-TDCITYYEKCIELNNRF----Y----LAYNGLGNYYLKSNQFDKSEFYYSKAIEIN 268
                 577789999977777.**************777....4....289************************996 PP

  == domain 3  score: 15.8 bits;  conditional E-value: 1.1e-05
      TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                 a+n l++ +++  ++d+++ ++ ka+ei      p++   a ++ n + l +++++  +A + l+  l++++
  EPA06401.1 240 AYNGLGNYYLKSNQFDKSEFYYSKAIEIN-----PKR--SAKIYKNRAYLREKQKNNSDAKNDLKSYLKLFP 304
                 67779999999999999999999999999.....888..899999999999999999999998888888765 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0024       2.8      14      43 ..     184     213 ..     174     214 .. 0.90
   2 ?    3.1   0.0      0.18   2.2e+02       9      38 ..     212     241 ..     210     245 .. 0.80
   3 !   11.5   0.0   0.00037      0.45       6      35 ..     243     272 ..     239     282 .. 0.81
   4 ?    2.0   0.0      0.42     5e+02       7      34 ..     279     306 ..     273     314 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0024
      TPR_14  14 lGdpdeAiallrralalaPddaeawlllaq 43 
                 + ++ +A++ l++ ++l+ ++++a++lla 
  EPA06401.1 184 QKNTTDALESLKKSIDLDQNNPTALYLLAS 213
                 67999***********************97 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.18
      TPR_14   9 eallalGdpdeAiallrralalaPddaeaw 38 
                 + ll+ ++  + i++++++++l+  +  a+
  EPA06401.1 212 ASLLNEQNSTDCITYYEKCIELNNRFYLAY 241
                 56888999999**********998776665 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.00037
      TPR_14   6 alaeallalGdpdeAiallrralalaPdda 35 
                  l+ ++l + ++d+++ ++ +a++ +P+  
  EPA06401.1 243 GLGNYYLKSNQFDKSEFYYSKAIEINPKRS 272
                 6899***********************853 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.42
      TPR_14   7 laeallalGdpdeAiallrralalaPdd 34 
                 +a + + + +  +A + l+ +l+l+P+ 
  EPA06401.1 279 RAYLREKQKNNSDAKNDLKSYLKLFPKA 306
                 67777889999***************74 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1     2e-05     0.024       4      41 ..     184     221 ..     182     222 .. 0.92
   2 !   11.1   0.0   0.00036      0.43       3      57 ..     216     270 ..     214     276 .. 0.88
   3 ?    4.6   0.1     0.038        46      13      57 ..     260     305 ..     258     309 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2e-05
      TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgql 41 
                 +++ ++Al+ l++ ++ d +n+ a++lLA +l +++ +
  EPA06401.1 184 QKNTTDALESLKKSIDLDQNNPTALYLLASLLNEQNST 221
                 7899**************************99988865 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00036
      TPR_19   3 aegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                  e++ ++ + ++e+ ++ ++    a  +L + +l+++q+d+ e   +++ e +p+
  EPA06401.1 216 NEQNSTDCITYYEKCIELNNRFYLAYNGLGNYYLKSNQFDKSEFYYSKAIEINPK 270
                 56777777899*******************************9999999998888 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.038
      TPR_19  13 lleqalqedpk.naearllLAeallalgqldeAealLdalpeedpd 57 
                 ++++a++ +pk +a +  + A +  ++++  +A++ L+ +++ +p+
  EPA06401.1 260 YYSKAIEINPKrSAKIYKNRAYLREKQKNNSDAKNDLKSYLKLFPK 305
                 7999*******888888899***************99999999887 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0027       3.2      10      49 ..     184     220 ..     184     222 .. 0.92
   2 ?    3.3   0.0      0.11   1.3e+02      38      65 ..     242     269 ..     233     272 .. 0.57
   3 !    7.2   0.0    0.0067         8       3      50 ..     244     289 ..     242     292 .. 0.82
   4 !    7.1   0.1    0.0074       8.9       3      33 ..     279     306 ..     277     310 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0027
      TPR_16  10 agdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgr 49 
                 +++ +dA++ l+  +++d     ++ Al+ll+ ++ +q+ 
  EPA06401.1 184 QKNTTDALESLKKSIDLD---QNNPTALYLLASLLNEQNS 220
                 6899**************...************9998875 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.11
      TPR_16  38 lllgdaalrqgrlaeAaalyraalraap 65 
                 ++lg+ +l+ + +++ + +y +a++  p
  EPA06401.1 242 NGLGNYYLKSNQFDKSEFYYSKAIEINP 269
                 5555555555555555555555544444 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0067
      TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrl 50 
                 l++++l+++++d+ + ++  a++ +p   + a  + +++ ++ +q++ 
  EPA06401.1 244 LGNYYLKSNQFDKSEFYYSKAIEINP--KRSAKIYKNRAYLREKQKNN 289
                 89***********************4..44777777777777777765 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.0074
      TPR_16   3 laraalragdyddAaaaleaalkrdpssPda 33 
                 +a+++ ++++  dA + l+ +lk++   P a
  EPA06401.1 279 RAYLREKQKNNSDAKNDLKSYLKLF---PKA 306
                 789999*******************...654 PP

>> Peptidase_C39_2  Peptidase_C39 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0     3e-07   0.00036      12     137 ..      15     115 ..       5     119 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3e-07
  Peptidase_C39_2  12 lpngCeptslamvlsylgkkvtqnelakelktnssgdpntgfvgnitdksglgvynepivklaekyglkvsdtrgssieevkkeidagkPvvvs 105
                       +n C p  +  v +y++ +++ +e  +++k++s             +++g +++ e i++ ae+ gl  +++ +ssi+e+kk id g+P +v+
       EPA06401.1  15 EENKCLPLPINVVSKYWNVNLSMSEAIETAKQYS-------------NYNG-SIMIEGIES-AERHGL-TCKIISSSISELKKIIDMGIPPMVI 92 
                      6777888888888888888888888888888887.............2233.455566666.677777.68889******************** PP

  Peptidase_C39_2 106 vttfkplndgeikftssgHlvvitGYdekgkr 137
                      +    p+       + ++H+ vi+GYd+++++
       EPA06401.1  93 L----PG-----IPEITQHVSVISGYDDGENT 115
                      *....33.....345689**********8854 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       1.8   2.2e+03      13      25 ..     184     196 ..     178     200 .. 0.79
   2 !   11.5   0.0   0.00031      0.37       2      28 ..     207     232 ..     206     234 .. 0.95
   3 ?    0.5   0.0         1   1.2e+03       7      32 ..     245     270 ..     243     270 .. 0.81
   4 !    7.0   0.2    0.0084        10       6      32 ..     279     305 ..     278     306 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.8
                 HHHHHHHHHHHHH CS
       TPR_6  13 lgdtdkAlealer 25 
                 +++t++Ale l++
  EPA06401.1 184 QKNTTDALESLKK 196
                 68999***99987 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00031
                 HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
       TPR_6   2 AlyklalsyrklgdtdkAlealerlik 28 
                 Aly+la ++ ++ ++++ ++++e++i+
  EPA06401.1 207 ALYLLASLLNEQ-NSTDCITYYEKCIE 232
                 9***********.************97 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 1
                 HHHHHHHHHHHHHHHHHHHHHHH-TT CS
       TPR_6   7 alsyrklgdtdkAlealerlikeYPd 32 
                 +  y+k ++ dk+  ++ + i+  P+
  EPA06401.1 245 GNYYLKSNQFDKSEFYYSKAIEINPK 270
                 566778679999999*****999885 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.0084
                 HHHHHHHHHHHHHHHHHHHHHHHH-TT CS
       TPR_6   6 lalsyrklgdtdkAlealerlikeYPd 32 
                 +a++++k+++ ++A+  l++ +k +P+
  EPA06401.1 279 RAYLREKQKNNSDAKNDLKSYLKLFPK 305
                 68999999******************7 PP

>> Peptidase_C39  Peptidase C39 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   8.1e-06    0.0097       8     122 ..      14     144 ..      11     158 .. 0.73
   2 ?    2.3   0.0      0.11   1.4e+02      97     130 ..     234     269 ..     181     272 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 8.1e-06
  Peptidase_C39   8 veeedcGlaalamilkyygsevsleeLrelagt..deeGlslsgLkkaakklglkakaikadlkel...kelkl.paIah..wdgklkHfvvveki 95 
                    +ee+ c +  ++++ ky+++++s++e  e a+   + +G  + + ++ a+++gl++k i+ +++el    ++ + p+++     + ++H  v+ ++
     EPA06401.1  14 EEENKCLPLPINVVSKYWNVNLSMSEAIETAKQysNYNGSIMIEGIESAERHGLTCKIISSSISELkkiIDMGIpPMVILpgIPEITQHVSVISGY 109
                    58999*******************9987777641256799888889999*****************7553334458888889888899******** PP

  Peptidase_C39  96 kkkkvliadP.akgkik.......lskeefekewt 122
                    ++ + +i    +kg+ +       + ++ f+kew+
     EPA06401.1 110 DDGENTILHYiQKGNQEgeqqegaIPQKIFDKEWS 144
                    65554444433666554111122266667888887 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.11
  Peptidase_C39  97 kkkvliadPakgkiklskeefeke..wtgvvllvap 130
                    ++++++a+++ g+++l+ ++f+k+  +   ++ ++p
     EPA06401.1 234 NNRFYLAYNGLGNYYLKSNQFDKSefYYSKAIEINP 269
                    789999999999****99999874333456666655 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       3.2   3.8e+03      48      68 ..     190     210 ..     186     234 .. 0.67
   2 !   14.8   0.0     2e-05     0.024       5      72 ..     248     316 ..     244     317 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.2
       TPR_9  48 AladLeaylalapdapdaeai 68 
                 Al+ L   ++l+ ++p+a  +
  EPA06401.1 190 ALESLKKSIDLDQNNPTALYL 210
                 666666666666666655433 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 2e-05
       TPR_9   5 aireedweralavverllllaPd.dpeerrdRGlllaqlGclsaAladLeaylalapdapdaeairaqL 72 
                 ++ ++++++   ++   + ++P+ ++  +  R+ l++++ + s A +dL  yl l p+a d+  i++++
  EPA06401.1 248 YLKSNQFDKSEFYYSKAIEINPKrSAKIYKNRAYLREKQKNNSDAKNDLKSYLKLFPKAKDRGIIEQAI 316
                 6777777777777777777777515667789*********************************99987 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.74   8.8e+02      14      35 ..     186     205 ..     181     206 .. 0.81
   2 ?    2.5   0.2      0.15   1.8e+02       2      30 ..     208     235 ..     207     238 .. 0.70
   3 ?    6.4   0.1    0.0084        10       1      27 [.     240     266 ..     240     285 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.74
       TPR_7  14 dyeeAielyeqsLaltkdpeda 35 
                 ++ +A+e +++   ++ d++++
  EPA06401.1 186 NTTDALESLKK--SIDLDQNNP 205
                 6789*******..888887776 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.15
       TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltk 30 
                 L+ La+l  ++++  + i++ye++++l +
  EPA06401.1 208 LYLLASL-LNEQNSTDCITYYEKCIELNN 235
                 5666666.4457777779*****988865 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0084
       TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLa 27 
                 a++ L++ y + +++++ + +y ++++
  EPA06401.1 240 AYNGLGNYYLKSNQFDKSEFYYSKAIE 266
                 7999*************9999988444 PP

>> Peptidase_C70  Papain-like cysteine protease AvrRpt2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00016       0.2      15     125 ..      14     118 ..       2     131 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00016
  Peptidase_C70  15 qaatgCwaaslsmiasyleqksidpselaalvdkwslmdeglngeekialaeklGlveevpeppqsyeieklvklLraggPlivaiaspgdvvgHv 110
                    ++++ C +  ++ +  y++  +++ se+ +  +++s ++  +   e i+ ae++Gl+ ++       +i++l k+++ g+P +v      + + Hv
     EPA06401.1  14 EEENKCLPLPINVVSKYWN-VNLSMSEAIETAKQYSNYNGSIM-IEGIESAERHGLTCKIIS----SSISELKKIIDMGIPPMVILPGIPEITQHV 103
                    7788888888889999998.77777777777777666666654.777999******333333....358************99999777778**** PP

  Peptidase_C70 111 iVltGidedgavivh 125
                    +V+ G d + + i+h
     EPA06401.1 104 SVISGYDDGENTILH 118
                    ******998886665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1019  (0.0568353); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2059.68
//
Query:       EPA06402.1  [L=753]
Description: hypothetical protein BG20_I2065, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-36  124.9   6.4    3.8e-35  121.3   6.4    2.3  1  UPF0182   Uncharacterised protein family (UPF0182)
  ------ inclusion threshold ------
        1.4    8.9   2.9        3.2    7.7   2.9    1.6  1  DUF2897   Protein of unknown function (DUF2897)


Domain annotation for each model (and alignments):
>> UPF0182  Uncharacterised protein family (UPF0182)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.3   6.4   4.2e-39   3.8e-35     237     757 ..      72     568 ..      53     569 .. 0.79

  Alignments for each domain:
  == domain 1  score: 121.3 bits;  conditional E-value: 4.2e-39
     UPF0182 237 avialvvavlllvaivlkk.....lklplialallvllaillgvvlpalvqkfiVkPnelekEkpYiernIeaTreAygLdkveveefeaeael..... 325
                 ++  +++a+ l+ +i  +       + + + +++++++a+++g+++  +v++ i + +++e   pY +++I++ r   +L+++++++ e++ +      
  EPA06402.1  72 LIGFTLLAFSLVDKIRARVlthmfKRDVYVRILTVIVIAVIVGGLV--TVNNSIADAKKIEYLGPYTAQQISVNRYIGQLNEIKENTHEVKLQSvspnn 168
                 4444444444444443222222211222344444455555555554..58999**********************************987766654433 PP

     UPF0182 326 taedleenaetienirLlDprplletfrqlqqirnYYkFedldvdrYtidgeerqvviaaREldysalpeeaktwvnkhlvYTH.GyGvvaspvnkvte 423
                  ++ +++n+++++ +r++D+++  +  +    + +Y +Fed d+ r++          + + +  s++ + a+tw n+hlvYTH  +G+ + +++    
  EPA06402.1 169 IKNYVSQNNDVLSVVRVWDWEAAFAKLKPEIGLIPYVDFEDNDILRFNNTL---YWTASMKPILPSSV-SLANTWYNEHLVYTHvPNGFLTLEATG--- 260
                 4677788****************************************7654...46778999999999.578************447777665543... PP

     UPF0182 424 eGlpeflvkdipseeeeslkieepriYfGel...tndyvivgtkvkEfdypsgeenvyntYdGkgGvkigsllrrllfaiklkdlklllsseitseski 519
                  G++      i s        ++ +iY+Ge    +++++  +++      +        +Y+GkgG++i+ +l+ + f     ++++lls    ++  +
  EPA06402.1 261 -GQI------IDS----GKFFKQREIYYGEGglfKDTWSAYPNSRGTNSAE----LGGVSYHGKGGLDISPPLS-WTF-----EPNFLLSFPA-ESVHV 337
                 .332......222....2246789******977777777777754433333....34589*********66554.333.....8999999664.4569* PP

     UPF0182 520 lfrRnikeRvekvaPfLtl.....DsdpYlvvadgrlyWivDaYTtsdrY..PySepeeatsgeeevnYiRNSVKvvvDAydGtvklYvvdeeDPiika 611
                 + +++i++R++++ P++ +     + d  +v+   + yW++      d++  P+S             Y+R    +++D+ydG+++l  +  +D   + 
  EPA06402.1 338 MRYKDIQDRMKTLYPYFLYnifgkELDSIPVTDGTKSYWLMPLIIGLDTHdvPWSIG---------NPYLRLVGFALIDSYDGNIQLLKTG-DDFFTEI 426
                 ****************99933333469999*999*****998777655432299965.........37*******************9997.8****** PP

     UPF0182 612 wskiFpglfkplsempeeLrshlrYPedlFkvqsellakYHvtdpevFYnredlWevpkeeeeqpvePyYlilklpgeekeefillspftp..ssrenl 708
                 +++ +p+ fkp   +p+ L+++ rYP +lF+ ++++++ YHv d+++F + +++ e+p+       e yY+ +k pg +++efi l+ +    s+  nl
  EPA06402.1 427 FAEQYPDQFKP---VPAWLENQTRYPVELFNWKAQMYNIYHVGDVQTFIQANEFYEIPQG-----LETYYVQAKPPGFNQTEFIGLLSLELrgSQGRNL 517
                 ***********...8********************************************9.....******************96655544227889** PP

     UPF0182 709 iawlaarsdgenygklllyelpkq..elvyGpeqiearinqdpeisqqlsL 757
                 ++++++++d +n g++  ye+p +  +++ Gp+ + + +++dp+ ++  +L
  EPA06402.1 518 AGYMIVQNDLKNLGHIQFYEIPLNstTKLIGPTAVREALDKDPTFAELKTL 568
                 ********************9977225678*************98876665 PP

>> DUF2897  Protein of unknown function (DUF2897)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   2.9   0.00036       3.2       4      21 ..     100     117 ..      98     122 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00036
     DUF2897   4 evWlIiilVlgvIvGnla 21 
                 +v +++++V++vIvG+l 
  EPA06402.1 100 YVRILTVIVIAVIVGGLV 117
                 66799***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (753 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.68u 0.29s 00:00:00.97 Elapsed: 00:00:00.48
# Mc/sec: 4750.98
//
Query:       EPA06403.1  [L=67]
Description: hypothetical protein BG20_I2298 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-09   37.0   0.0    2.3e-09   37.0   0.0    1.0  1  GSDH      Glucose / Sorbosone dehydrogenase


Domain annotation for each model (and alignments):
>> GSDH  Glucose / Sorbosone dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.0   1.3e-13   2.3e-09     275     329 ..       1      52 [.       1      64 [. 0.91

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 1.3e-13
                 EEETTTTEEEEEEEEEEEEEEEEEEEEESS-.-EEEEEE-TTS-EEEEE-TTTTT CS
        GSDH 275 vggLksqsllrleldegekvveeerlleelgeriRdVeqgpdGalyvltdeedgk 329
                 +++L++++l++l+l +   +++++++l+  g riRdV+qg+dG+lyv+t+++dgk
  EPA06403.1   1 MASLRATNLYQLDLYD--GLSSQKTILSGAG-RIRDVAQGQDGSLYVITSNTDGK 52 
                 689***********84..599*********9.*********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       172  (0.0095934); expected 358.6 (0.02)
Passed bias filter:                      157  (0.00875676); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 525.63
//
Query:       EPA06404.1  [L=98]
Description: hypothetical protein BG20_I2297, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      1e-24   87.3   0.0    1.1e-24   87.1   0.0    1.0  1  HMG-CoA_red  Hydroxymethylglutaryl-coenzyme A reductase


Domain annotation for each model (and alignments):
>> HMG-CoA_red  Hydroxymethylglutaryl-coenzyme A reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.1   0.0   6.3e-29   1.1e-24       2      80 ..      14      97 ..      13      98 .] 0.89

  Alignments for each domain:
  == domain 1  score: 87.1 bits;  conditional E-value: 6.3e-29
                 HHHHHHHHHH...S-HHHHHHHTT..----HHHHHHHSSS---------EEEEEEEETTEEEEEEE---STTHHHHHHHHHHHH CS
  HMG-CoA_red  2 veeRrkllee...lteeeleelke..esldeevadkmiEnviGyvqlPlGvagpllingkeylvPmAteEgslvAsasrgakai 80
                  +eR++++++   l+ eel+ l++  ++++ e+a++m+En iG+++lPlGva+ ++ingk+ylvPm++eE+s++A+as+gak++
   EPA06404.1 14 RKERLDIVRDfanLSSEELKVLQSidGGISFEKANNMVENAIGTFSLPLGVATSFKINGKDYLVPMVIEEPSVIAAASKGAKIA 97
                 579999998866677777777754447888****************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 678.12
//
Query:       EPA06405.1  [L=256]
Description: hypothetical protein BG20_I2299 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      5e-53  180.5   0.0    6.1e-53  180.3   0.0    1.0  1  GSDH      Glucose / Sorbosone dehydrogenase


Domain annotation for each model (and alignments):
>> GSDH  Glucose / Sorbosone dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.3   0.0   3.4e-57   6.1e-53       1     215 [.      50     251 ..      50     253 .. 0.93

  Alignments for each domain:
  == domain 1  score: 180.3 bits;  conditional E-value: 3.4e-57
                 -S-EEEEEE-TTS-EEEEETTTEEEEEE.TTEE.EEEEE-.----STT-SEEEEEE-TTTTTS-EEEEEEEE-...TTSSEEEEEEEEE-SS..-EEEE CS
        GSDH   1 lehPwslaflpdgrlLvtersGrlrlvkadgklkepiagvpevvakgqgGlldvalhpdfaenrlvYltyaeaeeekggagtavararlsedeaaledl 99 
                 l++P s+a+  d+r++vte++G++r+++++  l+ep+a++   ++   gGll++alhpdf++n+l+Y+ ++   ee+g+ +++v ++  s++  +l+d 
  EPA06405.1  50 LDKPRSIAIS-DDRIFVTEKNGQIRVIQNNTLLSEPLATFR-PADVFGGGLLGIALHPDFSNNHLMYVFFTY--EENGKLWNKVLQIIESKN--KLKDA 142
                 5788899877.66***************77777******95.456667***********************5..599999******999999..***** PP

                 EEEEEEE---TT-------EEE-TTS-EEEE---TT-.GGGGG-TT-SSSEEEEE-TTSSB-TT-TTTT-TTS-TTEEEE--SCE---EE-TTT--EEE CS
        GSDH 100 evifrqepkvesgahfGsrlafgpdgtLfvtvGdrsk.reeaqdlsselGkilrlnkdGsvpadnpfvgkagakpeiwsyGhRnpqGlaldpdtgeLwe 197
                 ++if+++p   s   +G+ l fgpd++L+v++G  s+ ++ +q l+s  Gkilrln+dG++p+dnpf      ++ ++s+GhR+pqG+++d++ ++++ 
  EPA06405.1 143 KTIFDKIPG--SVFTNGGFLKFGPDKKLYVGTGTISDsSHLPQSLDSLSGKILRLNDDGTIPDDNPF-----PNSPVYSLGHRDPQGMTWDNK-DQMYL 233
                 *********..889**********************9888***************************.....5799***************99.***** PP

                 EEE--SSSEEEEEE-TT- CS
        GSDH 198 sEhGprggDelnlieaGk 215
                  E Gp+++De+nli++Gk
  EPA06405.1 234 AELGPEKNDEINLIKPGK 251
                 *****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1822.43
//
Query:       EPA06406.1  [L=104]
Description: hypothetical protein BG20_I2301, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.084   13.1   0.0       0.11   12.7   0.0    1.2  1  tRNA_anti_2  OB-fold nucleic acid binding domain


Domain annotation for each model (and alignments):
>> tRNA_anti_2  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   6.1e-06      0.11      24      78 ..      10      66 ..       3      75 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.1e-06
  tRNA_anti_2 24 vrGeisnlkr.kasghvYftLkDekakisavifrsra.aklkftledGmkVlvkgrl 78
                 ++G + ++ +  + ghv+f++  +  k+++++ + +  + +  +l +G+k+ + g +
   EPA06406.1 10 ITGIVYDFPKiVKGGHVFFSILSNGLKLQCAVYKPTGiTLIASSLMKGDKICIGGGI 66
                 556666665434588*******999*********5552666677*******999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 746.04
//
Query:       EPA06407.1  [L=229]
Description: universal archaeal metal-binding-domain/4Fe-4S-binding-domain containing ABC transporter [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-56  191.9   0.1    1.2e-56  191.7   0.1    1.0  1  Diphthami_syn_2  Diphthamide synthase
  ------ inclusion threshold ------
      0.021   14.3   0.0      0.071   12.6   0.0    1.9  2  QueC             Queuosine biosynthesis protein QueC
        0.1   11.4   0.0       0.25   10.1   0.0    1.6  2  tRNA_Me_trans    tRNA methyl transferase


Domain annotation for each model (and alignments):
>> Diphthami_syn_2  Diphthamide synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.7   0.1   1.9e-60   1.2e-56       1     217 [.       1     223 [.       1     225 [. 0.93

  Alignments for each domain:
  == domain 1  score: 191.7 bits;  conditional E-value: 1.9e-60
  Diphthami_syn_2   1 mkvavlysGGkDsilaLykalke.sevesLvsvisenkesymfhvvnvhlvellaesvGipliklet.aGeeekevedLkgtl.kkld...vea 88 
                      mk a l+sGGkDs+++++ a k+ +e++ L sv+++ +es+  h +n+  ++l++e++ ip i  +  + + e+e++ L+++l + +d   +e+
       EPA06407.1   1 MKLASLFSGGKDSMYSIFLAKKQnHEIKCLLSVFPKSDESHLLHHPNLSWTHLQSEAMHIPQITIKSeSADTENEINLLEKILiQAIDqyqIEG 94 
                      899*****************9988*************************************776554145899999999887523344555*** PP

  Diphthami_syn_2  89 vviGaieseyqksriervCrelGlksvaPLWkkdpeelleeiveekfevivvavkaegldeslLGrridkklidelkklsekygidkagegGea 182
                      vv G+i+s+ qk+++e++C +l lk +aP+W++ ++e++ e ++e+fe iv++v+  gld+s+LG++i+k+ i  l++ls+k+g +  +egGea
       EPA06407.1  95 VVHGGIQSQFQKEKFENLCIKLNLKIIAPIWNRTSLEYMTELISENFEFIVISVSSGGLDDSWLGKIITKNDIVILNDLSKKFGFNLNFEGGEA 188
                      ********************************************************************************************** PP

  Diphthami_syn_2 183 etlvlDaPlfkkrlevkelekkwderrgyldiera 217
                      et+v++ Plf   +++ + +k wd+ rg ++i  a
       EPA06407.1 189 ETFVVNCPLFSNDIKIIKGKKIWDGYRGRFEIVEA 223
                      ****************************9998766 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.2e-05     0.071       4      33 ..       5      34 ..       2      91 .. 0.78
   2 ?   -1.0   0.0      0.17     1e+03       3      15 ..     146     158 ..     144     201 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.2e-05
                EE--SSHHHHHHHHHHHHH-SEEEEEEEES CS
        QueC  4 vllSGGlDSttvlalakkegkevealtfdY 33
                 l+SGG DS   ++lakk+ +e+++l   +
  EPA06407.1  5 SLFSGGKDSMYSIFLAKKQNHEIKCLLSVF 34
                69*********************9886555 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.17
                 EEE--SSHHHHHH CS
        QueC   3 vvllSGGlDSttv 15 
                 + + SGGlD + +
  EPA06407.1 146 ISVSSGGLDDSWL 158
                 6678888875543 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   4.3e-05      0.25       2      87 ..       2      91 ..       1      95 [. 0.72
   2 ?   -1.8   0.0      0.17     1e+03     241     279 ..     175     215 ..     145     227 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 4.3e-05
  tRNA_Me_trans  2 kvvvalSgGVDSsvaaallkeqgyevigvflklweeedeeg....keccaeedlkdaervaeklgiplevvdfekeyk..ekvfeefleeye 87
                   k++ ++SgG DS ++ +l k+q +e++ + l +  ++de +     + ++++  ++a+++  ++ i+ e  d+e+e    ek++ + +++y+
     EPA06407.1  2 KLASLFSGGKDSMYSIFLAKKQNHEIK-CLLSVFPKSDESHllhhPNLSWTHLQSEAMHIP-QITIKSESADTENEINllEKILIQAIDQYQ 91
                   677889******************976.556666665665556545666766667777764.678999988888875333777777777775 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.17
  tRNA_Me_trans 241 qrkGlkiag..aeeplyVvekdakkntvlvgkgedeealas 279
                    ++ G++++    e  ++Vv+  + +n++ + kg++  + ++
     EPA06407.1 175 KKFGFNLNFegGEAETFVVNCPLFSNDIKIIKGKKIWDGYR 215
                    55565554322677888888888888888888776655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 1330.93
//
Query:       EPA06408.1  [L=68]
Description: hypothetical protein BG20_I2306, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.049   12.8   0.0      0.054   12.7   0.0    1.0  1  DAP3      Mitochondrial ribosomal death-associated protein 3


Domain annotation for each model (and alignments):
>> DAP3  Mitochondrial ribosomal death-associated protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0     3e-06     0.054     166     209 ..      12      55 ..      10      66 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3e-06
                 GGGGSS-BS---TTS--B-GGGBHHHHTTHHH..HS--SSS-EE CS
        DAP3 166 lnallkntkyksadkkpihahdLtlvkhfldllsgksklknggv 209
                 ++++l +tky+ +++  ++   + l++ fl l+s++++    ++
  EPA06408.1  12 MSQWLGKTKYTLSEYDKVKRFSFYLGDDFLLLVSAEKDVDTNKI 55 
                 799*******************************9999877666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.32s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 438.64
//
Query:       EPA06409.1  [L=198]
Description: SRP54-type protein, helical bundle domain protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-31  108.2   0.3    1.1e-30  106.8   0.0    1.7  2  SRP54            SRP54-type protein, GTPase domain
    1.2e-17   63.8   1.6      2e-17   63.2   1.6    1.3  1  SRP54_N          SRP54-type protein, helical bundle domain
    1.1e-05   25.5   0.1    2.4e-05   24.4   0.0    1.7  2  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
      3e-05   23.6   0.5    4.9e-05   22.9   0.3    1.5  1  ParA             NUBPL iron-transfer P-loop NTPase
    0.00017   21.5   0.3    0.00041   20.3   0.3    1.6  1  MobB             Molybdopterin guanine dinucleotide synthesis
    0.00035   20.5   0.7    0.00089   19.2   0.1    1.9  2  APS_kinase       Adenylylsulphate kinase
    0.00038   19.8   0.0    0.00072   18.9   0.0    1.4  1  6PF2K            6-phosphofructo-2-kinase
    0.00056   19.0   0.1     0.0021   17.1   0.0    1.9  3  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
    0.00057   19.4   0.4     0.0011   18.5   0.0    1.6  2  KTI12            Chromatin associated protein KTI12
     0.0018   17.7   0.1      0.004   16.6   0.1    1.5  1  Arf              ADP-ribosylation factor family
     0.0021   17.4   0.0     0.0031   16.8   0.0    1.3  1  Zeta_toxin       Zeta toxin
     0.0035   17.0   0.8     0.0082   15.8   0.4    1.7  2  Thymidylate_kin  Thymidylate kinase
     0.0037   17.4   0.0     0.0071   16.5   0.0    1.5  1  AAA_33           AAA domain
     0.0039   17.5   0.1      0.018   15.3   0.0    2.0  2  AAA_22           AAA domain
     0.0056   16.5   0.1      0.011   15.5   0.1    1.4  1  ATP_bind_1       Conserved hypothetical ATP binding protein
     0.0062   15.7   0.1     0.0094   15.1   0.1    1.3  1  LpxK             Tetraacyldisaccharide-1-P 4'-kinase
     0.0063   16.1   0.1     0.0098   15.4   0.1    1.2  1  AAA_7            P-loop containing dynein motor region
     0.0065   17.0   0.3      0.016   15.7   0.0    1.9  2  AAA_18           AAA domain
     0.0099   15.1   0.3      0.017   14.3   0.1    1.5  1  G-alpha          G-protein alpha subunit
  ------ inclusion threshold ------
      0.011   15.5   0.0      0.015   15.0   0.0    1.3  1  AAA_30           AAA domain
      0.011   15.7   0.3      0.011   15.7   0.3    2.0  2  NTPase_1         NTPase
      0.012   15.6   0.4      0.012   15.6   0.4    2.3  3  AAA_31           AAA domain
      0.012   15.0   0.6       0.68    9.2   0.2    2.2  2  MipZ             ATPase MipZ
      0.015   15.3   1.7      0.057   13.4   0.6    1.9  2  ResIII           Type III restriction enzyme, res subunit
      0.025   14.2   0.3      0.064   12.8   0.3    1.8  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
      0.031   14.8   0.2      0.058   13.9   0.0    1.6  1  ABC_tran         ABC transporter
      0.037   13.5   0.1      0.086   12.3   0.1    1.6  1  SRPRB            Signal recognition particle receptor beta su
      0.042   13.8   0.2      0.081   12.9   0.2    1.5  1  AAA_5            AAA domain (dynein-related subfamily)
      0.043   13.6   2.4       0.11   12.3   1.6    2.1  2  SpoVIF           Stage VI sporulation protein F
      0.054   13.7   0.2      0.092   13.0   0.2    1.4  1  AAA_28           AAA domain
      0.063   13.7   0.4       0.17   12.2   0.1    1.8  2  AAA_16           AAA ATPase domain
       0.09   12.5   0.0       0.22   11.2   0.0    1.6  1  IstB_IS21        IstB-like ATP binding protein
      0.092   11.9   1.5        0.1   11.8   0.4    1.6  2  DLP_helical      Dynamin-like helical domain
        0.1   12.3   0.5        0.2   11.4   0.5    1.6  1  AAA_24           AAA domain
       0.14   11.0   0.1       0.23   10.4   0.1    1.3  1  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
       0.15   12.4   3.5       0.16   12.4   0.6    2.2  2  AAA_17           AAA domain
       0.16   11.7   1.1        0.3   10.8   0.3    1.8  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
       0.19   10.8   2.1        0.6    9.2   0.5    2.3  3  ArsA_ATPase      Anion-transporting ATPase


Domain annotation for each model (and alignments):
>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       2.4   1.1e+03      97     126 ..      22      54 ..      18      62 .. 0.72
   2 !  106.8   0.0   2.3e-33   1.1e-30       2      99 ..     100     197 ..      99     198 .] 0.98

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.4
                 THHHHHHHHHH.HHHHH..SSSEEEEEEETTBH CS
       SRP54  97 ndkelmeelkk.ikkvv..kpdevllvldattg 126
                 +d+el++el+k +++++  ++ +v lvl+ t +
  EPA06409.1  22 IDEELIKELSKdVQRALlqSDVNVRLVLEITKQ 54 
                 689999999762555557777788888887665 PP

  == domain 2  score: 106.8 bits;  conditional E-value: 2.3e-33
                 EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHHHHHHTTSSEEEEEE--SSTTHH CS
       SRP54   2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvikkkeeadpaavakeavekakeekidvvlvDTaGrlqndk 99 
                 n i+++G+qG+GKTt +aKLa+ l+k+g++v ++ aDt+R++A+ QLkt+ ek +v+v+++ +++d+ +++k+++++ ++   d++++DTaGr++++k
  EPA06409.1 100 NKIIMLGIQGSGKTTVTAKLAKFLTKQGYSVGVIGADTYRPGALVQLKTMCEKSNVEVYGEPNNKDSPDIVKNGLKHYENLPLDIIIIDTAGRHKEEK 197
                 6799******************************************************************************************9987 PP

>> SRP54_N  SRP54-type protein, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.2   1.6   4.2e-20     2e-17       2      75 .]       6      82 ..       5      82 .. 0.95

  Alignments for each domain:
  == domain 1  score: 63.2 bits;  conditional E-value: 4.2e-20
                HHHHHHHHHHHCCSSCGHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHCTTS...S-HHHHHHHHHHHHH CS
     SRP54_N  2 gkklnsalkklsgkskideedleealkeleeaLleaDVgvkvvkklienvkkkavgekk...lkpkqqvkkivkdeL 75
                 ++l++a+kk+ ++s idee+++e+ k++++aLl++DV+v++v +++++++ + ++e     l++k++++ki++deL
  EPA06409.1  6 RNNLRDAIKKIVKSSGIDEELIKELSKDVQRALLQSDVNVRLVLEITKQLEARSLNETPppgLSRKDHIVKILYDEL 82
                5789**********************************************998898555*****************8 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       9.5   4.5e+03      92     115 ..       8      33 ..       3      49 .. 0.56
   2 !   24.4   0.0     5e-08   2.4e-05       9      41 ..     109     141 ..     102     192 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 9.5
                 TCHHHHHHHHHHC..TS-EEEEEE-- CS
                 xxxxxxxxxxxxx..xxxxxxxxxxx RF
        CbiA  92 llkealeelkqry..gvpvlgviprd 115
                 +l++a++++ +      ++++++++d
  EPA06409.1   8 NLRDAIKKIVKSSgiDEELIKELSKD 33 
                 45555555544434444444444444 PP

  == domain 2  score: 24.4 bits;  conditional E-value: 5e-08
                 TSSHHHHHHHHHHHHHHTT--EEEEEEEESSCC CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        CbiA   9 GvGKTtlaanLaralarrglrVllvDaDpqann 41 
                 G+GKTt++a+La+ l ++g+ V ++ aD+ ++ 
  EPA06409.1 109 GSGKTTVTAKLAKFLTKQGYSVGVIGADTYRPG 141
                 9************************99987765 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.3     1e-07   4.9e-05       8      46 ..     103     141 ..      98     176 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1e-07
        ParA   8 vlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGps 46 
                 ++ g  G GK+tv+++lA  L+k+g++vg++ aD y p 
  EPA06409.1 103 IMLGIQGSGKTTVTAKLAKFLTKQGYSVGVIGADTYRPG 141
                 55566799**************************99775 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.3   8.6e-07   0.00041       3      33 ..     103     133 ..     101     139 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 8.6e-07
        MobB   3 givgksgsGKTtLleklipelkarglrvgti 33 
                  + g +gsGKTt   kl + l+++g++vg+i
  EPA06409.1 103 IMLGIQGSGKTTVTAKLAKFLTKQGYSVGVI 133
                 57899************************99 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1       2.9   1.3e+03      43      71 ..      28      56 ..       5      60 .. 0.66
   2 !   19.2   0.1   1.9e-06   0.00089       5      45 ..     102     142 ..      98     157 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 2.9
                TTTTTT--SSHHHHHHHHHHHHHHHHHHH CS
  APS_kinase 43 hgLnkdLgfseedRkenirrvaevaklla 71
                ++L+kd+     + + n+r v e++k+l 
  EPA06409.1 28 KELSKDVQRALLQSDVNVRLVLEITKQLE 56
                45666666666666677777777777765 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 1.9e-06
                 EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTT CS
  APS_kinase   5 vwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgL 45 
                 + + G+ gsGK+t++ +l+k L+++g+sv ++  d+ R g 
  EPA06409.1 102 IIMLGIQGSGKTTVTAKLAKFLTKQGYSVGVIGADTYRPGA 142
                 6788****************************999999775 PP

>> 6PF2K  6-phosphofructo-2-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.5e-06   0.00072      12      76 ..      98     169 ..      90     176 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.5e-06
                 S-EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHHHHHHSS......---GGGG.STT-HHHHHH CS
       6PF2K  12 sklvivlvGLpargKtyiskkltrylkwlgvrtkvFnvgkyrreaska......lsdaeff.rpdneealkl 76 
                 ++  i+++G+   gKt+++ kl ++l   g++  v  +  yr  a  +      +s++e++ +p+n+++ ++
  EPA06409.1  98 KQNKIIMLGIQGSGKTTVTAKLAKFLTKQGYSVGVIGADTYRPGALVQlktmceKSNVEVYgEPNNKDSPDI 169
                 55679******************************9999999876655555665677766535666666655 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       3.4   1.6e+03     206     227 ..      15      36 ..       3      48 .. 0.66
   2 !   17.1   0.0   4.4e-06    0.0021      30      67 ..     100     137 ..      93     157 .. 0.86
   3 ?   -2.8   0.0       5.3   2.5e+03     118     132 ..     178     192 ..     171     197 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3.4
                 EEEEEBCCCTBSHHHHHHHHHH CS
        MeaB 206 kvlktsavegeGidelvdaiee 227
                 k++k s+   e i+el + +++
  EPA06409.1  15 KIVKSSGIDEELIKELSKDVQR 36 
                 5666666666666666666654 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 4.4e-06
                 EEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE-- CS
        MeaB  30 qvvGltGvPGaGkstlvealglelrrrGkrvavlavDP 67 
                 +++ + G+ G+Gk t++ +l+  l+++G+ v+v+  D 
  EPA06409.1 100 NKIIMLGIQGSGKTTVTAKLAKFLTKQGYSVGVIGADT 137
                 567788****************************9884 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 5.3
                 HHTT-SEEEEEEESS CS
        MeaB 118 eaaGfDvvlietvGv 132
                 e +  D+++i+t G 
  EPA06409.1 178 ENLPLDIIIIDTAGR 192
                 566789999999985 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       4.8   2.3e+03      52      71 ..      22      41 ..       4      58 .. 0.60
   2 !   18.5   0.0   2.3e-06    0.0011       4      41 ..     102     139 ..     101     163 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 4.8
                GHHHHHHHHHHHHHHHHTT. CS
       KTI12 52 kekalRsslrsavkrdLske 71
                  ++l ++l ++v+r+L ++
  EPA06409.1 22 IDEELIKELSKDVQRALLQS 41
                33444444555555555444 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 2.3e-06
                 EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH CS
       KTI12   4 vvltGlPssGKstrakeLakaleeekrsvvviddeslg 41 
                 +++ G+  sGK+t++++Lak l+++++sv vi  ++++
  EPA06409.1 102 IIMLGIQGSGKTTVTAKLAKFLTKQGYSVGVIGADTYR 139
                 7999*****************************99987 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   8.5e-06     0.004      10      35 ..      95     120 ..      86     130 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 8.5e-06
                 T.TTEEEEEEEESTTSSHHHHHHHHH CS
         Arf  10 lkkkelrilllGLDnaGKtTilkklk 35 
                 + +k+ +i++lG+ ++GKtT+  kl 
  EPA06409.1  95 KPNKQNKIIMLGIQGSGKTTVTAKLA 120
                 5589*****************99996 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   6.6e-06    0.0031      14      56 ..      98     140 ..      85     170 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 6.6e-06
  Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvv.rldpDdlRe 56 
                 ++   i++ G +G+GK+++ ++l++ l++qg  v ++ +D++R+
  EPA06409.1  98 KQ-NKIIMLGIQGSGKTTVTAKLAKFLTKQGYSVgVIGADTYRP 140
                 33.346677889****************8887774788999995 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       5.7   2.7e+03     100     115 ..      20      35 ..      18      59 .. 0.68
   2 !   15.8   0.4   1.7e-05    0.0082       3      27 ..     106     130 ..     105     134 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 5.7
                      TTTTCHHHHHHGGGTT CS
  Thymidylate_kin 100 egvdldlvlslnedvl 115
                      +g+d +l+++l++dv 
       EPA06409.1  20 SGIDEELIKELSKDVQ 35 
                      5677788888887764 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 1.7e-05
                      ESTTSSHHHHHHHHHHHHHHTTE.E CS
  Thymidylate_kin   3 GlDGaGKttqaellkerlkeegikv 27 
                      G+ G+GKtt++++l++ l+++g++v
       EPA06409.1 106 GIQGSGKTTVTAKLAKFLTKQGYSV 130
                      99********************984 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.5e-05    0.0071       2      35 ..     102     140 ..     102     187 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.5e-05
      AAA_33   2 vllvGlpGsGKstlaerllkklg.....avllssdtlrr 35 
                 +++ G +GsGK+t+  +l+k l+     + ++  dt+r 
  EPA06409.1 102 IIMLGIQGSGKTTVTAKLAKFLTkqgysVGVIGADTYRP 140
                 79****************988887776666688888554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1       2.4   1.1e+03      74     124 ..      26      46 ..       3      89 .. 0.60
   2 !   15.3   0.0   3.8e-05     0.018       8      98 ..     102     188 ..      95     194 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 2.4
      AAA_22  74 sseellealeqalraravielliiDEaqhlrseealeeLrsllnlsrkgvq 124
                   +el + +++al + +v                              +v+
  EPA06409.1  26 LIKELSKDVQRALLQSDV------------------------------NVR 46 
                 333444444444443333..............................222 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 3.8e-05
      AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevv...fvtlpsstsskdllrellralglelkaerlsseellealeqalraravielliiD 98 
                 ++  G  G+GKTt+ ++l++ l+++      +++v+   ++ + ++  +k+++++   ++  e ++  ++s ++++   ++ ++     ++iiD
  EPA06409.1 102 IIMLGIQGSGKTTVTAKLAKFLTKQG----YSVGVIgadTYRPGALVQLKTMCEKSNVEVYGEPNN--KDSPDIVKNGLKHYENLPL-DIIIID 188
                 677899****************7554....589999444444444446666666655555544444..5666666666666666666.999999 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   2.3e-05     0.011       2      33 ..     105     136 ..     104     140 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.3e-05
  ATP_bind_1   2 vGpaGsGKttfvgalseilelrgrsvavvNLD 33 
                 +G  GsGKtt + +l+++l+++g+sv v+  D
  EPA06409.1 105 LGIQGSGKTTVTAKLAKFLTKQGYSVGVIGAD 136
                 7999**********************999766 PP

>> LpxK  Tetraacyldisaccharide-1-P 4'-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1     2e-05    0.0094      45      71 ..     107     133 ..      76     148 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2e-05
                 SS-HSHHHHHHHHHHHTTTS..-EEEE CS
        LpxK  45 vGGtGKTPlvialvkllqarglkvgvl 71 
                 + G+GKT +++ l+k+l+++g+ vgv+
  EPA06409.1 107 IQGSGKTTVTAKLAKFLTKQGYSVGVI 133
                 569***********************8 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   2.1e-05    0.0098      32     100 ..      98     164 ..      92     167 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.1e-05
       AAA_7  32 nkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdiiesklekrrkgvygPpggk 100
                 +++++++ G +G+GKt+++ +l k l k+ y++ +i    +   + +q  ++   ek + +vyg p++k
  EPA06409.1  98 KQNKIIMLGIQGSGKTTVTAKLAKFLTKQGYSVGVIGADTYRPGALVQ--LKTMCEKSNVEVYGEPNNK 164
                 688999****************************99988888777777..8888999999999999988 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       6.9   3.2e+03      38      44 ..      23      29 ..       2      62 .. 0.52
   2 !   15.7   0.0   3.4e-05     0.016       1      25 [.     102     134 ..     102     195 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 6.9
      AAA_18 38 llevdpe 44
                 +e  +e
  EPA06409.1 23 DEELIKE 29
                2222222 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 3.4e-05
      AAA_18   1 IlltGtpGvGKttlakeLskrl.gf.......g 25 
                 I+  G++G+GKtt++  L+k l +        g
  EPA06409.1 102 IIMLGIQGSGKTTVTAKLAKFLtKQgysvgviG 134
                 8899**************886533344554440 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.1   3.6e-05     0.017      21      53 ..      97     130 ..      80     180 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.6e-05
                 ..EEEEEEEESTTSSHHHHHHHHH.HHCS----H CS
     G-alpha  21 krevkllllGqseSGKsTilkqlk.llykkgfse 53 
                 +++ k+++lG ++SGK+T+  +l  +l k+g+s 
  EPA06409.1  97 NKQNKIIMLGIQGSGKTTVTAKLAkFLTKQGYSV 130
                 33569*************9766652667777765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   3.2e-05     0.015      21      52 ..     102     133 ..      96     194 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.2e-05
      AAA_30  21 avltGpAGtGKttalkalreaweaaggrvigl 52 
                  ++ G  G+GKtt+ ++l++ ++++g++v ++
  EPA06409.1 102 IIMLGIQGSGKTTVTAKLAKFLTKQGYSVGVI 133
                 578899********************999654 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0         7   3.3e+03     110     123 ..      26      39 ..       6      60 .. 0.57
   2 ?   15.7   0.3   2.3e-05     0.011       2      36 ..     102     136 ..     101     159 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 7
                 G-HHHHHHHHHHHT CS
    NTPase_1 110 kskkfkeaveevLk 123
                  +k++++ v+++L 
  EPA06409.1  26 LIKELSKDVQRALL 39 
                 33444444444333 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 2.3e-05
                 EEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEE CS
    NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgGfyte 36 
                 +++ G +G+GKtT+  k+++ l ++g++vg + + 
  EPA06409.1 102 IIMLGIQGSGKTTVTAKLAKFLTKQGYSVGVIGAD 136
                 778899**********************9755554 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       4.1   1.9e+03      64      90 ..      17      45 ..       3      76 .. 0.63
   2 ?   15.6   0.4   2.5e-05     0.012      12      40 ..     109     137 ..     100     164 .. 0.87
   3 ?   -0.1   0.1       1.6   7.4e+02     104     125 ..     167     189 ..     149     192 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 4.1
      AAA_31 64 ieeknikeaiiktkvenl..dlipssidL 90
                ++++ i+e +ik+ ++++   l+ s++++
  EPA06409.1 17 VKSSGIDEELIKELSKDVqrALLQSDVNV 45
                45555665555554444444666666654 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 2.5e-05
      AAA_31  12 GvGKTTtsvnlaaalaklgkkvLlvDlDp 40 
                 G GKTT + +la++l+k+g+ v ++ +D+
  EPA06409.1 109 GSGKTTVTAKLAKFLTKQGYSVGVIGADT 137
                 99***********************9997 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 1.6
      AAA_31 104 eeilkellekvkde.YDyiiiDc 125
                  +i+k+ l++ ++   D+iiiD+
  EPA06409.1 167 PDIVKNGLKHYENLpLDIIIIDT 189
                 5567888888888668******8 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.2    0.0014      0.68      11      39 ..     109     137 ..     101     145 .. 0.90
   2 ?    4.2   0.0     0.047        22      97     113 ..     179     195 ..     140     197 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0014
                 TSSHHHHHHHHHHHHHTTT--EEEEE--T CS
        MipZ  11 GsGksttavhvavaLlkkGarvaaidldl 39 
                 GsGk+t++  +a  L+k+G +v++i  d+
  EPA06409.1 109 GSGKTTVTAKLAKFLTKQGYSVGVIGADT 137
                 9************************9886 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.047
                 HHH-SEEEEE--SS--H CS
        MipZ  97 eaeldfividtPGsdsa 113
                 +  ld+i+idt G++++
  EPA06409.1 179 NLPLDIIIIDTAGRHKE 195
                 3458**********985 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0         1   4.9e+02      68     140 ..       7      81 ..       2      88 .. 0.57
   2 ?   13.4   0.6   0.00012     0.057      19      53 ..      94     128 ..      73     137 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 1
                 HHHHHHGGGGTGG......GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEET CS
      ResIII  68 eqtleefkkflseayke..igkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDE 140
                 + +++++kk+ ++   +    k++s+d ++a  +++ n +++++ +++l a+s +e+      ++d++  i+ DE
  EPA06409.1   7 NNLRDAIKKIVKSSGIDeeLIKELSKDVQRALLQSDVNVRLVLEITKQLEARSLNETPPPGLSRKDHIVKILYDE 81 
                 444455555544443223455556666666678888888888888888888883332222333333333555555 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00012
                 ....TTSEEEEEESTTSTHHHHHHHHHHHH-S... CS
      ResIII  19 lkskrdkrglikmaTGtGKTlvaaklierllkkgk 53 
                 +k ++++++++    G+GKT v akl++ l+k+g+
  EPA06409.1  94 FKPNKQNKIIMLGIQGSGKTTVTAKLAKFLTKQGY 128
                 33388999999999**************9999887 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.3   0.00013     0.064       3      38 ..     102     139 ..     100     195 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00013
                 EEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SS CS
        cobW   3 tvltGflGsGKTtLlnhll..enraglklavivNefge 38 
                 +++ G  GsGKTt+  +l     ++g+++ vi  + + 
  EPA06409.1 102 IIMLGIQGSGKTTVTAKLAkfLTKQGYSVGVIGADTYR 139
                 5778999***********999899********999884 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   0.00012     0.058       4      42 ..      92     130 ..      89     176 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00012
                 EEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEE CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran   4 vslklkegekvaivGenGaGKStLlkllagllkpteGei 42 
                  ++k ++ +k+ ++G  G+GK+t+ + la+ l+++  ++
  EPA06409.1  92 FDFKPNKQNKIIMLGIQGSGKTTVTAKLAKFLTKQGYSV 130
                 678888999*******************99998766555 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00018     0.086       2      28 ..      98     124 ..      97     140 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00018
                 ---EEEEE-STTSSHHHHHHHHHHSS- CS
       SRPRB   2 skpavllvGlsdsGKTslftrLttdsv 28 
                 ++++++++G++ sGKT++  +L +  +
  EPA06409.1  98 KQNKIIMLGIQGSGKTTVTAKLAKFLT 124
                 799***************999987554 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   0.00017     0.081       2      32 ..     102     133 ..     101     149 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00017
                 EEEE--SSSSHHHHHHHGGGGB.S--EEEEE- CS
       AAA_5   2 vlLvGppGtgKselaerlaaal.nreveyvql 32 
                 ++++G +G+gK++++ +la++l ++ + +  +
  EPA06409.1 102 IIMLGIQGSGKTTVTAKLAKFLtKQGYSVGVI 133
                 79*******************97665555554 PP

>> SpoVIF  Stage VI sporulation protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.6   0.00023      0.11       2      41 ..      14      53 ..      13      81 .. 0.83
   2 ?   -0.9   0.0         3   1.4e+03      36      48 ..      78      90 ..      70     106 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00023
      SpoVIF  2 kkvekKtnvkkedilkLansvqkadlkdektlRqlikqvs 41
                kk+ k  ++++e i++L ++vq+a l+++ ++R + +   
  EPA06409.1 14 KKIVKSSGIDEELIKELSKDVQRALLQSDVNVRLVLEITK 53
                7899999**************************7765554 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 3
      SpoVIF 36 likqvsklankpv 48
                l ++++kl++k+ 
  EPA06409.1 78 LYDELAKLLGKET 90
                4456666666653 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2    0.0002     0.092       1      25 [.     101     129 ..     101     140 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.0002
      AAA_28   1 kivitGgestGKTtlleaLa....argyp 25 
                 ki+++G +++GKTt++++La    ++gy+
  EPA06409.1 101 KIIMLGIQGSGKTTVTAKLAkfltKQGYS 129
                 7999****************555444776 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       3.2   1.5e+03      99      99 ..      43      43 ..       6      95 .. 0.50
   2 ?   12.2   0.1   0.00036      0.17      27      53 ..     102     128 ..      79     160 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 3.2
      AAA_16 99 e 99
                 
  EPA06409.1 43 V 43
                1 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00036
      AAA_16  27 vllsGesGvGKsslvrellralekdgg 53 
                 ++  G +G+GK+++  +l++ l+k+g 
  EPA06409.1 102 IIMLGIQGSGKTTVTAKLAKFLTKQGY 128
                 667899*****************9942 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00046      0.22      46      78 ..      98     130 ..      81     139 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00046
   IstB_IS21  46 kkenivllGpsGvGKshlaialgveavraglsv 78 
                 k++ i++lG  G GK+ +++ l++   ++g+sv
  EPA06409.1  98 KQNKIIMLGIQGSGKTTVTAKLAKFLTKQGYSV 130
                 4566999************************99 PP

>> DLP_helical  Dynamin-like helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.4   0.00022       0.1      41      77 ..       8      44 ..       6      64 .. 0.84
   2 ?   -2.5   0.0       4.7   2.2e+03     227     241 ..      82      96 ..      69     101 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00022
  DLP_helical 41 eLqdateekikknggelalieetkksvirdvlerqlp 77
                 +L+da+++++k++g  ++li+e +k+v r++l+  ++
   EPA06409.1  8 NLRDAIKKIVKSSGIDEELIKELSKDVQRALLQSDVN 44
                 7*****************************9998765 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.7
  DLP_helical 227 aakilgldlglKFKP 241
                  +ak+lg+++ + FKP
   EPA06409.1  82 LAKLLGKETDFDFKP 96 
                  578899999999999 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.5   0.00042       0.2       2      27 ..      99     123 ..      98     196 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00042
      AAA_24   2 klkiliyGpsgiGKTtlakelgpkpl 27 
                 ++ki++ G +g+GKTt+ ++l  k+l
  EPA06409.1  99 QNKIIMLGIQGSGKTTVTAKL-AKFL 123
                 679*****************9.5555 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00048      0.23      14      44 ..      98     128 ..      94     139 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00048
  TrwB_AAD_bind  14 etqhilivGttGsGKtqalekllrairargd 44 
                     +++i+++G +GsGKt+++ kl + + ++g 
     EPA06409.1  98 KQNKIIMLGIQGSGKTTVTAKLAKFLTKQGY 128
                    57899*****************999888875 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1       2.7   1.3e+03      51      69 ..      20      38 ..       4      62 .. 0.56
   2 ?   12.4   0.6   0.00034      0.16       1      27 [.     105     131 ..     105     158 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 2.7
                HHHHHHHHHHHHHHHHHHH CS
      AAA_17 51 leekkelqkeaaekiaeea 69
                  +++el ke+ ++++++ 
  EPA06409.1 20 SGIDEELIKELSKDVQRAL 38
                2345555555555555443 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00034
                 EE-TTSSHHHHHHHHHHHHTEEEEEHH CS
      AAA_17   1 lGgPGsGKgtqceklvekygfthlsaG 27 
                 lG+ GsGK+t+ +kl++ +  + +s G
  EPA06409.1 105 LGIQGSGKTTVTAKLAKFLTKQGYSVG 131
                 79**************98766666655 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       8.1   3.8e+03     120     140 ..      13      33 ..       4      36 .. 0.73
   2 ?   10.8   0.3   0.00064       0.3       2      22 ..     100     120 ..      99     130 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 8.1
   PduV-EutP 120 aekifevsavekegieellky 140
                 ++ki + s +++e i+el k 
  EPA06409.1  13 IKKIVKSSGIDEELIKELSKD 33 
                 678888888888888888765 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00064
   PduV-EutP   2 kkilliGkvgsGKttLtqalk 22 
                 +ki+++G  gsGKtt+t +l 
  EPA06409.1 100 NKIIMLGIQGSGKTTVTAKLA 120
                 69***************9996 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       2.1   9.8e+02     146     172 ..       7      37 ..       2      60 .. 0.52
   2 ?    9.2   0.5    0.0013       0.6       4      38 ..     102     136 ..     100     139 .. 0.87
   3 ?   -0.8   0.0       1.5   6.9e+02     117     133 ..     174     190 ..     169     192 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.1
                  HHHHHHHHHHHHHHH....HHHHHHHHHCCC CS
  ArsA_ATPase 146 evleklleklvklke....klsplakqlvkl 172
                  ++l   ++k+vk  +     +++l+k +++ 
   EPA06409.1   7 NNLRDAIKKIVKSSGideeLIKELSKDVQRA 37 
                  5566667777776662222344444444333 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0013
                  EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
  ArsA_ATPase   4 ilvgGKGGVGKttvsaatavklsekgkkvllistD 38 
                  i++ G  G GKttv a +a  l+++g++v +i  D
   EPA06409.1 102 IIMLGIQGSGKTTVTAKLAKFLTKQGYSVGVIGAD 136
                  455677799********************999887 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.5
                  HHHHHCSSSSEEEEESB CS
  ArsA_ATPase 117 lkyvkeeeydvvvlDta 133
                  lk++++   d++++Dta
   EPA06409.1 174 LKHYENLPLDIIIIDTA 190
                  688999999*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1087  (0.060628); expected 358.6 (0.02)
Passed bias filter:                      880  (0.0490825); expected 358.6 (0.02)
Passed Vit filter:                       155  (0.00864521); expected 17.9 (0.001)
Passed Fwd filter:                        38  (0.00211947); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              38  [number of targets reported over threshold]
# CPU time: 0.60u 0.34s 00:00:00.94 Elapsed: 00:00:00.48
# Mc/sec: 1242.65
//
Query:       EPA06410.1  [L=241]
Description: hypothetical protein BG20_I2561, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.4e-14   52.5   5.1    6.4e-14   52.5   5.1    2.1  2  Big_9           Bacterial Ig domain
    3.9e-12   46.0   3.6    8.4e-12   44.9   3.6    1.5  1  Cadherin_5      Cadherin-like domain
    7.8e-07   29.6   2.2    7.8e-07   29.6   2.2    2.2  2  Cadherin_4      Bacterial cadherin-like domain
    0.00024   21.7   9.5     0.0004   20.9   9.5    1.4  1  DUF4398         Domain of unknown function (DUF4398)
  ------ inclusion threshold ------
      0.051   13.6   4.6       0.48   10.5   1.8    2.3  2  PilJ            Type IV pili methyl-accepting chemotaxis tran
      0.087   12.8   0.1        3.7    7.5   0.0    2.4  2  Big_11          Bacterial Ig-like domain
      0.096   12.8   5.2       0.36   11.0   1.0    2.9  2  KIP1            KIP1-like protein
       0.15   12.0   0.5        4.7    7.2   0.2    2.7  2  TPR_1           Tetratricopeptide repeat
       0.16   12.5   2.3       0.23   12.0   0.6    2.0  2  RPAP3_C         Potential Monad-binding region of RPAP3
       0.19   12.1   5.5       0.26   11.7   5.0    1.5  1  DUF1771         Domain of unknown function (DUF1771)
       0.55   10.0   9.0       0.77    9.5   9.0    1.2  1  DUF445          Protein of unknown function (DUF445)
       0.89    9.8   3.5         32    5.0   0.2    3.8  4  TPR_2           Tetratricopeptide repeat
        1.4    9.6  14.2        0.5   11.1   4.2    3.2  3  Cytochrom_B562  Cytochrome b562
        1.7    8.7   6.6        7.2    6.7   1.9    3.1  3  GvpG            Gas vesicle protein G
        3.2    8.1   7.6         25    5.3   3.3    3.4  3  DUF2524         Protein of unknown function (DUF2524)
        6.7    5.9   8.6         22    4.2   8.4    1.8  1  CorA            CorA-like Mg2+ transporter protein


Domain annotation for each model (and alignments):
>> Big_9  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.5   5.1   5.7e-17   6.4e-14      32      89 ..       6      58 ..       2      59 .. 0.93
   2 ?    0.1   0.0       1.3   1.4e+03       1      10 [.      63      72 ..      63      86 .. 0.84

  Alignments for each domain:
  == domain 1  score: 52.5 bits;  conditional E-value: 5.7e-17
       Big_9 32 ndtdpdgdaltvtsltvtlvtapanGtvtinadgtltytpnagfsgtdsftYtvsDgs 89
                + +d+dgdalt     ++ ++ panG vt+n+dgt+tytp+ gf gtd f++t++Dg+
  EPA06410.1  6 TGSDVDGDALT-----FAKASDPANGMVTVNPDGTFTYTPDFGFVGTDIFEFTANDGH 58
                5799*****95.....7789************************************97 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.3
       Big_9  1 tatvtvtvtp 10
                +atv vtvtp
  EPA06410.1 63 SATVAVTVTP 72
                6999999998 PP

>> Cadherin_5  Cadherin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.9   3.6   7.5e-15   8.4e-12      34      98 .]       8      71 ..       5      71 .. 0.95

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 7.5e-15
  Cadherin_5 34 sDvdgdtLsvssltadaenGtvvdngdGtftftpeanynGevtlsYtvsDgeggtttatasltva 98
                sDvdgd+L+ ++ + d +nG v+ n dGtft+tp+  + G+  +++t +Dg+ ++ +at+ +tv+
  EPA06410.1  8 SDVDGDALTFAKAS-DPANGMVTVNPDGTFTYTPDFGFVGTDIFEFTANDGHLNSDSATVAVTVT 71
                8************7.667******************************************99996 PP

>> Cadherin_4  Bacterial cadherin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   2.2   6.9e-10   7.8e-07      40      72 .]       7      38 ..       2      38 .. 0.94
   2 ?    0.2   0.1       1.1   1.2e+03       1       9 [.      64      72 ..      48      77 .. 0.74

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 6.9e-10
  Cadherin_4 40 dtDvdgddltvtavtvagtyGtltlnadGsftY 72
                 +Dvdgd+lt++ ++ ++++G +t+n+dG+ftY
  EPA06410.1  7 GSDVDGDALTFAKAS-DPANGMVTVNPDGTFTY 38
                59*************.***************** PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.1
  Cadherin_4  1 atvtitvtg 9 
                atv +tvt+
  EPA06410.1 64 ATVAVTVTP 72
                566666665 PP

>> DUF4398  Domain of unknown function (DUF4398)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   9.5   3.6e-07    0.0004       3      66 ..     175     238 ..     173     241 .] 0.93

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 3.6e-07
     DUF4398   3 ladAraaleaAraagaeeyApaeleeAreaLaqAeaamaekdyeeAdhlaylAerdaelAearA 66 
                 +a A  a+++A++  ++   ++el +Ar+ L++++ + ++++ ++A h ++ A  +a++A+ +A
  EPA06410.1 175 RALADGAIDQAEEFEDQDKVQKELDRARDELQKGDDKLTKDESDKAIHHYEKAWKHAQKAMKKA 238
                 567889**********9999999*************999**********************998 PP

>> PilJ  Type IV pili methyl-accepting chemotaxis transducer N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1     0.053        60      39      89 ..      95     148 ..      78     165 .. 0.76
   2 ?   10.5   1.8   0.00043      0.48      25      95 ..     169     238 ..     164     241 .] 0.74

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.053
        PilJ  39 daaearaqlretiaqfdrtlaalrlgdpapgllvpae...avraqleaveqlWq 89 
                  + + +++l++++++++++l+     d+ ++ l+ ++   a++++ ++v +l++
  EPA06410.1  95 IDKKTSKDLEKSLKDLEKSLDDKFWEDKLTSTLDSKKghhAIHEEEKSVKDLMK 148
                 4778999*************9988888777777777677777777777766665 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00043
        PilJ  25 RlakeallaaagaydaaearaqlretiaqfdrtlaalrlgdpapgllvpaeavraqleaveqlWqelkkpa 95 
                 R++k   ++a ga d+ae++++ ++  +++dr  ++l++gd++ +    + +  +++e+  ++ q+++k a
  EPA06410.1 169 RIVKADRALADGAIDQAEEFEDQDKVQKELDRARDELQKGDDKLTKDESD-KAIHHYEKAWKHAQKAMKKA 238
                 7776667777888****************************996554444.44455555555555555444 PP

>> Big_11  Bacterial Ig-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.11   1.2e+02      33      45 ..      25      37 ..      21      41 .. 0.86
   2 ?    7.5   0.0    0.0033       3.7       3      23 ..      62      82 ..      60     100 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.11
      Big_11 33 ekevtinedGsvt 45
                ++ vt+n+dG++t
  EPA06410.1 25 NGMVTVNPDGTFT 37
                6789*******97 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0033
      Big_11  3 dsnggdvtvtPkksdgrtYap 23
                ds + +vtvtP ++++++Y+ 
  EPA06410.1 62 DSATVAVTVTPLTPIEQKYKA 82
                677889*************85 PP

>> KIP1  KIP1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.2      0.13   1.4e+02       8      27 ..      95     114 ..      93     116 .. 0.86
   2 ?   11.0   1.0   0.00032      0.36       2      40 ..     118     156 ..     117     179 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.13
        KIP1   8 isskqskwLqetlseldekv 27 
                 i+ k sk L++ l++l++ +
  EPA06410.1  95 IDKKTSKDLEKSLKDLEKSL 114
                 57899***********9976 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00032
        KIP1   2 WWwdshisskqskwLqetlseldekvkemlklieedads 40 
                 +W d  +s+  sk  ++ ++e ++ vk ++k+i++++++
  EPA06410.1 118 FWEDKLTSTLDSKKGHHAIHEEEKSVKDLMKIIKDENED 156
                 5888888899999999*****************887765 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.17     2e+02      15      28 ..     101     114 ..      98     115 .. 0.88
   2 ?    7.2   0.2    0.0042       4.7      16      27 ..     216     227 ..     206     234 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.17
                 T-HHHHHHHHHHHH CS
       TPR_1  15 gkydeAleyyekAL 28 
                 +++++ l++ ek L
  EPA06410.1 101 KDLEKSLKDLEKSL 114
                 799********998 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0042
                 -HHHHHHHHHHH CS
       TPR_1  16 kydeAleyyekA 27 
                 + d+A+ +yekA
  EPA06410.1 216 ESDKAIHHYEKA 227
                 679********9 PP

>> RPAP3_C  Potential Monad-binding region of RPAP3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.6   0.00021      0.23       3      64 ..      98     176 ..      96     196 .. 0.80
   2 ?   -1.0   0.0       2.4   2.7e+03       6      20 ..     222     236 ..     219     239 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00021
     RPAP3_C   3 ktayeFeklwrklkredkdlka..vllq.inp..............kqlpkiFknsledeilsdildalnerlqeekae 64 
                 kt+ ++ek+++ l+++ +d+     l + +++              k+l ki+k++ ed+++ d+++ + +r+ + +++
  EPA06410.1  98 KTSKDLEKSLKDLEKSLDDKFWedKLTStLDSkkghhaiheeeksvKDLMKIIKDENEDQTFLDMIQQVIDRIVKADRA 176
                 799999999999966554444467888876669999*******************************887777776554 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.4
     RPAP3_C   6 yeFeklwrklkredk 20 
                 +++ek+w++ ++  k
  EPA06410.1 222 HHYEKAWKHAQKAMK 236
                 6899****9977655 PP

>> DUF1771  Domain of unknown function (DUF1771)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   5.0   0.00023      0.26      11      62 ..     190     241 .]     184     241 .] 0.91

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00023
     DUF1771  11 harkrnelfekAaeAyrrGdgaaAkelseqGkehgekmeeanreAaeaIfee 62 
                  ++k ++ +++A++  ++Gd +  k+ s+++ +h ek+++ +++A ++ +ee
  EPA06410.1 190 DQDKVQKELDRARDELQKGDDKLTKDESDKAIHHYEKAWKHAQKAMKKAVEE 241
                 567888999**************************************98875 PP

>> DUF445  Protein of unknown function (DUF445)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   9.0   0.00069      0.77     102     230 ..      96     237 ..      62     241 .] 0.62

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00069
      DUF445 102 desikellkknlkkkleevipepllgkllellleeerhkklld..dlldriknllkdeevkekikelidelieeesgklv...........lesivsmf 187
                 d++ ++ l+k lk+  ++++ + +++kl ++l +++ h+++ +  + ++ + +++kde ++++  ++i++ i + ++              +++  +++
  EPA06410.1  96 DKKTSKDLEKSLKDLEKSLDDKFWEDKLTSTLDSKKGHHAIHEeeKSVKDLMKIIKDENEDQTFLDMIQQVIDRIVKADRaladgaidqaeEFEDQDKV 194
                 33333334444444334444444444444444444444444321134455555555555555555555555555544444555677777667788899* PP

      DUF445 188 lreltsilekvksdpdhllreeedkkvreliadllndpelaak 230
                 ++el++  +++++  d+l+++e dk+++ + + +++ +++++k
  EPA06410.1 195 QKELDRARDELQKGDDKLTKDESDKAIHHYEKAWKHAQKAMKK 237
                 ******************************9999996655544 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.28   3.2e+02      15      28 ..     101     114 ..      99     115 .. 0.89
   2 ?   -1.0   0.0       2.3   2.6e+03      14      26 ..     195     207 ..     194     208 .. 0.87
   3 ?    5.0   0.2     0.029        32      16      27 ..     216     227 ..     206     230 .. 0.86
   4 ?    2.5   0.3      0.18     2e+02      12      29 ..     223     240 ..     221     241 .] 0.68

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.28
       TPR_2  15 gdyeeAleafekAl 28 
                 +d+e+ l+++ek+l
  EPA06410.1 101 KDLEKSLKDLEKSL 114
                 799*********98 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.3
       TPR_2  14 lgdyeeAleafek 26 
                 ++++++A++ ++k
  EPA06410.1 195 QKELDRARDELQK 207
                 7899****99987 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.029
       TPR_2  16 dyeeAleafekA 27 
                 + ++A++++ekA
  EPA06410.1 216 ESDKAIHHYEKA 227
                 669********9 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.18
       TPR_2  12 yklgdyeeAleafekAle 29 
                  + + ++ A +a++kA+e
  EPA06410.1 223 HYEKAWKHAQKAMKKAVE 240
                 556667778888888876 PP

>> Cytochrom_B562  Cytochrome b562
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.61   6.9e+02      47      69 ..      86     115 ..      60     124 .. 0.66
   2 ?   11.1   4.2   0.00045       0.5      45      85 ..     141     187 ..     101     191 .. 0.75
   3 ?    2.3   1.7      0.24   2.7e+02      53      83 ..     190     220 ..     186     236 .. 0.68

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.61
  Cytochrom_B562  47 lek.......dseeqkdYqeGldklidqld 69 
                     l++       d++  kd ++ l++l + ld
      EPA06410.1  86 LNEliatpgiDKKTSKDLEKSLKDLEKSLD 115
                     333555666677777888888877777766 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00045
  Cytochrom_B562  45 sklek......dseeqkdYqeGldklidqldkaealakagkleeaka 85 
                     +++++      d++e +++ + ++++id + ka+++++ g +++a++
      EPA06410.1 141 KSVKDlmkiikDENEDQTFLDMIQQVIDRIVKADRALADGAIDQAEE 187
                     22222333555*********************************986 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.24
  Cytochrom_B562  53 eqkdYqeGldklidqldkaealakagkleea 83 
                     +q++ q+ ld   d+l+k + ++++++ ++a
      EPA06410.1 190 DQDKVQKELDRARDELQKGDDKLTKDESDKA 220
                     5566666677777777777777777776666 PP

>> GvpG  Gas vesicle protein G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.21   2.3e+02      30      46 ..     100     116 ..      71     117 .. 0.82
   2 ?    4.5   0.3     0.031        34      28      57 ..     161     191 ..     141     192 .. 0.74
   3 ?    6.7   1.9    0.0064       7.2      25      48 ..     186     209 ..     182     220 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.21
        GvpG  30 qenlrkeLaaLqqeLda 46 
                  ++l+k L +L+++Ld+
  EPA06410.1 100 SKDLEKSLKDLEKSLDD 116
                 57899********9996 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.031
        GvpG  28 ddqenlrkeLaaLqqeLdaGeIde.eeFdrr 57 
                 d  +++  ++ + +++L +G+Id+ eeF+ +
  EPA06410.1 161 DMIQQVIDRIVKADRALADGAIDQaEEFEDQ 191
                 44567778888999*********85689876 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0064
        GvpG  25 eqlddqenlrkeLaaLqqeLdaGe 48 
                 e+++dq++++keL +   eL++G+
  EPA06410.1 186 EEFEDQDKVQKELDRARDELQKGD 209
                 79********************98 PP

>> DUF2524  Protein of unknown function (DUF2524)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       2.7     3e+03      43      58 ..      73      88 ..      69      93 .. 0.79
   2 ?    3.4   0.1     0.084        94      25      64 ..     118     157 ..      97     159 .. 0.77
   3 ?    5.3   3.3     0.022        25       5      56 ..     157     208 ..     155     235 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2.7
     DUF2524 43 qlkLEeavneLeklak 58
                ++ +E+ ++ L+kl +
  EPA06410.1 73 LTPIEQKYKALDKLNE 88
                5678999999999865 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.084
     DUF2524  25 feeakrqehyndeeYteAqlkLEeavneLeklaksandqQ 64 
                 f e k     + ++ ++A  + E+ v++L k++k  n++Q
  EPA06410.1 118 FWEDKLTSTLDSKKGHHAIHEEEKSVKDLMKIIKDENEDQ 157
                 5555555566667778899999***************999 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.022
     DUF2524   5 qsveellqkceqaieeaeeqfeeakrqehyndeeYteAqlkLEeavneLekl 56 
                 q + +++q++ + i +a   ++++   ++ + e+  + q++L+ a  eL+k 
  EPA06410.1 157 QTFLDMIQQVIDRIVKADRALADGAIDQAEEFEDQDKVQKELDRARDELQKG 208
                 677899*******************99999999999*************985 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   8.4      0.02        22     126     208 ..      99     177 ..      94     235 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.02
        CorA 126 llekleeeldeledeledstkkeilrelaqlrrrlvklrralapnrevlkrllakaddkllddedkeylrdlldelerlleml 208
                 + ++le+ l++le+ l+d+  ++ l ++++ ++    +++  +  ++++ ++++ +++++   ++   +++++d++ ++++ l
  EPA06410.1  99 TSKDLEKSLKDLEKSLDDKFWEDKLTSTLDSKKGHHAIHEEEKSVKDLM-KIIKDENEDQTFLDM---IQQVIDRIVKADRAL 177
                 56789999**********************9999999999999999999.999977777777777...999999999976654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2253  (0.125662); expected 358.6 (0.02)
Passed bias filter:                      689  (0.0384294); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.52
# Mc/sec: 1406.93
//
Query:       EPA06411.1  [L=39]
Description: hypothetical protein BG20_I2138 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-07   31.4   0.6    1.3e-07   31.2   0.6    1.1  1  SHOCT     Short C-terminal domain


Domain annotation for each model (and alignments):
>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.6     7e-12   1.3e-07       1      27 [.       5      31 ..       5      32 .. 0.95

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 7e-12
       SHOCT  1 daLekLkeLyarGeIteEEFeakKakL 27
                d+L kL++L+++G+I+e EF ++K+ L
  EPA06411.1  5 DELVKLAKLKEQGIISESEFLQMKQAL 31
                7899*********************88 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.49
# Mc/sec: 239.76
//
Query:       EPA06412.1  [L=38]
Description: hypothetical protein BG20_I2132 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (38 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       815  (0.0454571); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.30s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 251.78
//
Query:       EPA06413.1  [L=46]
Description: hypothetical protein BG20_I2133 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0014   18.7   0.4     0.0018   18.3   0.4    1.3  1  Zn-ribbon_8      Zinc ribbon domain
     0.0018   19.0   4.0     0.0022   18.7   4.0    1.2  1  Tnp_zf-ribbon_2  DDE_Tnp_1-like zinc-ribbon
     0.0072   16.3   1.0     0.0093   15.9   1.0    1.2  1  ADK_lid          Adenylate kinase, active site lid
  ------ inclusion threshold ------
      0.013   15.9   1.0      0.025   14.9   1.0    1.4  1  DUF4379          Probable Zinc-ribbon domain
      0.016   15.2   0.9      0.016   15.2   0.9    1.1  1  zf-C2HC5         Putative zinc finger motif, C2HC5-type
      0.019   15.1   0.4        4.1    7.7   0.0    2.2  2  zf-RING_7        C4-type zinc ribbon domain
      0.021   14.6   6.2        1.1    9.0   1.5    2.1  2  Rubredoxin_2     Rubredoxin metal binding domain
      0.021   13.9   0.7      0.023   13.8   0.7    1.0  1  Tmemb_55A        Transmembrane protein 55A
      0.032   14.2   1.0        3.8    7.5   0.1    2.2  2  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
      0.065   13.5   2.8        1.1    9.6   0.3    2.0  2  Ribosomal_L32p   Ribosomal L32p protein family
      0.077   12.6   3.9        2.9    7.5   4.5    2.0  2  RecR             RecR protein
      0.088   12.2   3.3        2.3    7.8   0.1    2.2  2  zf-ribbon_3      zinc-ribbon domain
       0.11   12.0   3.9       0.21   11.1   0.2    2.1  2  TF_Zn_Ribbon     TFIIB zinc-binding
       0.14   12.0   4.4       0.21   11.5   0.3    2.0  2  zf-trcl          Probable zinc-ribbon domain


Domain annotation for each model (and alignments):
>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.4   1.4e-06    0.0018       8      33 ..      10      33 ..       6      38 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.4e-06
  Zn-ribbon_8  8 CeeCghefevlqsisdapltaCPeCg 33
                 Ce+Cg++f +    +      CP+C+
   EPA06413.1 10 CENCGNVFSKKILTK--TISRCPACN 33
                 *********554333..4555****6 PP

>> Tnp_zf-ribbon_2  DDE_Tnp_1-like zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   4.0   1.7e-06    0.0022       1      24 [.       8      34 ..       8      39 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.7e-06
  Tnp_zf-ribbon_2  1 kRCkvClk...kkikkeTriiCqeCdv 24
                     k+C +C     kki ++T  +C +C+v
       EPA06413.1  8 KICENCGNvfsKKILTKTISRCPACNV 34
                     79***********************97 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   1.0   7.2e-06    0.0093       3      29 ..       9      34 ..       8      37 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 7.2e-06
                E-TTT--EEETTTB--SSTTB-TTT-- CS
     ADK_lid  3 vCpkCGrsYhvvfnpPkveglCDkCGe 29
                +C++CG +++ +++  k+   C  C++
  EPA06413.1  9 ICENCGNVFS-KKILTKTISRCPACNV 34
                8*********.999***********95 PP

>> DUF4379  Probable Zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   1.0     2e-05     0.025      31      56 .]       9      32 ..       9      32 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2e-05
     DUF4379 31 kCakCgheWeasvsnrtkgsskCpkC 56
                +C++Cg+ +++++ ++t   s+Cp C
  EPA06413.1  9 ICENCGNVFSKKILTKT--ISRCPAC 32
                6****************..556**** PP

>> zf-C2HC5  Putative zinc finger motif, C2HC5-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.9   1.3e-05     0.016      18      41 ..       8      33 ..       3      46 .] 0.79

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.3e-05
    zf-C2HC5 18 pnClnCGkiiCakegls..kpCsfCg 41
                 +C nCG++  +k   +  ++C+ C+
  EPA06413.1  8 KICENCGNVFSKKILTKtiSRCPACN 33
                68*********99988889******8 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1     0.012        15      23      30 ..       7      14 ..       3      14 .. 0.80
   2 ?    7.7   0.0    0.0032       4.1      21      31 ..      24      34 ..      17      35 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.012
                -EE-TTT- CS
   zf-RING_7 23 vvtCpeCG 30
                +  C++CG
  EPA06413.1  7 LKICENCG 14
                568****9 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0032
                TB-EE-TTT-- CS
   zf-RING_7 21 devvtCpeCGR 31
                + + +Cp C++
  EPA06413.1 24 KTISRCPACNV 34
                4699*****97 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.2    0.0016         2       2      12 ..       9      19 ..       9      20 .. 0.84
   2 ?    9.0   1.5   0.00089       1.1      16      23 ..      28      35 ..      28      36 .. 0.95

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0016
  Rubredoxin_2  2 vCsqCGfesak 12
                  +C++CG++++k
    EPA06413.1  9 ICENCGNVFSK 19
                  5*****98865 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00089
  Rubredoxin_2 16 rCpsCgsW 23
                  rCp+C+ W
    EPA06413.1 28 RCPACNVW 35
                  8******* PP

>> Tmemb_55A  Transmembrane protein 55A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.7   1.8e-05     0.023     150     174 ..       9      33 ..       4      40 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.8e-05
   Tmemb_55A 150 iCghCkntflftelsrtlarCPhCr 174
                 iC  C n f  + l++t++rCP C 
  EPA06413.1   9 ICENCGNVFSKKILTKTISRCPACN 33 
                 7***********************6 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.1     0.003       3.8      17      27 ..       5      15 ..       4      18 .. 0.82
   2 ?    5.7   0.1     0.011        15       1       9 [.      25      33 ..      25      34 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.003
  PhnA_Zn_Ribbon 17 gallvCpeCah 27
                    ++l +C++C++
      EPA06413.1  5 NDLKICENCGN 15
                    56779****86 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.011
  PhnA_Zn_Ribbon  1 tlpkCplCa 9 
                    t + Cp C+
      EPA06413.1 25 TISRCPACN 33
                    5699****8 PP

>> Ribosomal_L32p  Ribosomal L32p protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.2     0.018        23      24      35 ..       5      16 ..       2      24 .. 0.73
   2 ?    9.6   0.3   0.00083       1.1      20      40 ..      20      40 ..      18      44 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.018
                    --EEEETTTCCE CS
  Ribosomal_L32p 24 pnlvecpncgel 35
                    ++l  c ncg++
      EPA06413.1  5 NDLKICENCGNV 16
                    567889999986 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00083
                    ------EEEETTTCCEECTTC CS
  Ribosomal_L32p 20 klkapnlvecpncgelklpHr 40
                    k+ ++++++cp c+  k +H+
      EPA06413.1 20 KILTKTISRCPACNVWKKQHS 40
                    556789***********9995 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   4.5    0.0023       2.9      15      34 ..       6      32 ..       3      33 .. 0.68
   2 ?    5.5   0.2      0.01        13      14      24 ..      24      34 ..      20      40 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0023
                H-EE-TTT--EESSS.......S-CCC CS
        RecR 15 kvrhCsrCgnlteed.......lCaIC 34
                +++ C++Cgn+  +         C+ C
  EPA06413.1  6 DLKICENCGNVFSKKiltktisRCPAC 32
                6899******95555444444458888 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.01
                HH-EE-TTT-- CS
        RecR 14 ekvrhCsrCgn 24
                +++++C+ C+ 
  EPA06413.1 24 KTISRCPACNV 34
                7899*****96 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.1    0.0018       2.3      18      25 ..       9      16 ..       6      18 .. 0.72
   2 ?    5.3   0.5     0.011        14       4       9 ..      28      33 ..      27      36 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0018
  zf-ribbon_3 18 vCpyCGtk 25
                 +C +CG +
   EPA06413.1  9 ICENCGNV 16
                 68888876 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.011
  zf-ribbon_3  4 rCPnCG 9 
                 rCP+C+
   EPA06413.1 28 RCPACN 33
                 8****6 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   0.00016      0.21      19      33 ..       6      21 ..       3      28 .. 0.78
   2 ?    3.0   0.4     0.057        73       2       8 ..      28      34 ..      27      45 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00016
                  CE.EESSSSBEEEECC CS
  TF_Zn_Ribbon 19 el.vCtdCGlVledns 33
                  +l +C++CG+V    +
    EPA06413.1  6 DLkICENCGNVFSKKI 21
                  6669*******87665 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.057
                  EETTTTC CS
  TF_Zn_Ribbon  2 kCPnCgs 8 
                  +CP C+ 
    EPA06413.1 28 RCPACNV 34
                  5999985 PP

>> zf-trcl  Probable zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.4     0.047        60       6      14 ..       9      17 ..       5      18 .. 0.84
   2 ?   11.5   0.3   0.00017      0.21      24      47 ..      17      40 ..      15      41 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.047
     zf-trcl  6 tCkdCgaef 14
                +C++Cg+ f
  EPA06413.1  9 ICENCGNVF 17
                7*****976 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00017
     zf-trcl 24 yaekgfdnepkRCkaCRkarkqrr 47
                + +k ++ + +RC+aC   +kq++
  EPA06413.1 17 FSKKILTKTISRCPACNVWKKQHS 40
                5677799999******99999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       886  (0.0494171); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.49
# Mc/sec: 280.35
//
Query:       EPA06414.1  [L=64]
Description: zinc finger, C2H2 type [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-06   27.2   7.7    0.00061   20.1   0.5    2.2  2  zf-C2H2          Zinc finger, C2H2 type
    2.9e-05   23.7   3.3      0.075   12.8   0.5    2.2  2  zf-C2H2_11       zinc-finger C2H2-type
      3e-05   24.5  10.2      0.017   15.9   0.6    2.2  2  zf-C2H2_4        C2H2-type zinc finger
    0.00048   20.0   4.0       0.03   14.3   0.3    2.4  2  zinc_ribbon_4    zinc-ribbon domain
     0.0012   19.5   2.1       0.23   12.2   0.2    2.0  2  zf-C2H2_3rep     Zinc finger C2H2-type, 3 repeats
     0.0025   17.9   5.2     0.0025   17.9   5.2    1.7  2  Zn-ribbon_8      Zinc ribbon domain
     0.0031   17.3   3.0       0.27   11.2   0.3    2.3  2  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
     0.0063   16.4   4.2        0.9    9.5   0.1    2.4  2  zf-trcl          Probable zinc-ribbon domain
  ------ inclusion threshold ------
       0.01   15.5   4.9       0.11   12.2   0.7    2.5  2  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
      0.013   15.3   2.9      0.014   15.1   2.9    1.1  1  zf-DNA_Pol       DNA Polymerase alpha zinc finger
      0.015   15.4   2.1       0.94    9.7   0.1    2.2  2  DUF678           Protein of unknown function (DUF678)
      0.016   15.3   2.3       0.65   10.1   0.1    2.0  2  CpXC             CpXC protein
      0.016   15.3   5.2        1.8    8.7   0.3    2.4  2  XPA_N            XPA protein N-terminal
      0.016   15.1   3.2       0.42   10.6   0.3    2.4  2  Prok-RING_1      Prokaryotic RING finger family 1
      0.018   15.8   6.6      0.023   15.4   6.6    1.3  1  zinc_ribbon_15   zinc-ribbon family
       0.02   14.8   0.9        4.1    7.4   0.1    2.2  2  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
       0.03   14.1   4.1        1.5    8.6   0.1    2.1  2  Ephrin_rec_like  Putative ephrin-receptor like
      0.035   14.2  10.2       0.27   11.4   3.7    2.0  2  FYVE             FYVE zinc finger
      0.041   14.2   7.5        1.8    8.9   2.8    2.0  2  zf-C2H2_2        C2H2 type zinc-finger (2 copies)
      0.045   13.7   2.1        2.1    8.4   0.1    2.3  2  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
      0.053   13.5   3.2      0.054   13.5   1.4    1.8  2  ADK_lid          Adenylate kinase, active site lid
      0.059   13.2   3.7          5    7.0   0.1    2.4  2  zf-HYPF          HypF finger
      0.062   13.3   6.1      0.093   12.8   6.1    1.4  1  DZR              Double zinc ribbon
      0.072   13.1  14.8       0.14   12.1   4.6    2.3  2  zf-C2H2_6        C2H2-type zinc finger
      0.074   12.7   3.4       0.86    9.3   0.2    2.3  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
      0.082   12.8   3.3       0.73    9.7   0.2    2.4  2  TFIIS_C          Transcription factor S-II (TFIIS)
       0.12   12.8   2.3        2.6    8.5   0.3    2.1  2  DUF983           Protein of unknown function (DUF983)
       0.12   12.8  13.6       0.97   10.0   0.9    3.1  3  zf-H2C2_2        Zinc-finger double domain
       0.13   12.3   6.7       0.15   12.1   4.0    1.9  2  HypA             Hydrogenase/urease nickel incorporation, met
       0.19   11.9   1.6        6.8    6.9   0.2    2.3  2  Fibrillin_U_N    Fibrillin 1 unique N-terminal domain
       0.23   11.2   4.2        5.2    6.9   0.3    2.1  2  zf-CSL           CSL zinc finger
       0.25   10.9   5.3        1.5    8.4   0.1    2.5  3  TF_Zn_Ribbon     TFIIB zinc-binding
       0.35   10.6   5.0        3.7    7.3   0.6    2.3  2  Rubredoxin_2     Rubredoxin metal binding domain
       0.38   11.3   7.8        3.9    8.1   7.8    2.1  1  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
        1.2    9.1  16.8          3    7.8   7.2    2.6  2  zf-C2HC_2        zinc-finger of a C2HC-type
        1.4    8.7  10.6        1.8    8.4   7.6    2.2  3  zinc_ribbon_5    zinc-ribbon domain
        4.2    7.5  12.1        2.7    8.1   4.6    2.3  2  zf-BED           BED zinc finger
        6.7    7.0  11.8        3.6    7.9   3.2    2.0  2  ARS2             Arsenite-resistance protein 2


Domain annotation for each model (and alignments):
>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.5   1.3e-06   0.00061       2      23 .]      11      33 ..      10      33 .. 0.95
   2 !   11.0   1.5     0.001      0.49       2      21 ..      39      58 ..      39      59 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.3e-06
                EETTTTEEESSHHHHHHHHHC.C CS
     zf-C2H2  2 kCpdCgksFkrksnLkrHirt.H 23
                kC++Cg +Fk ++ L++H+ + H
  EPA06414.1 11 KCKKCGSRFKYPERLEKHQEIaH 33
                8******************9888 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.001
                EETTTTEEESSHHHHHHHHH CS
     zf-C2H2  2 kCpdCgksFkrksnLkrHir 21
                kC  Cg  F + +nL++H +
  EPA06414.1 39 KCRACGSEFHSTENLRKHKK 58
                799***************76 PP

>> zf-C2H2_11  zinc-finger C2H2-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.1   0.00031      0.15       6      28 ..      11      33 ..       9      36 .. 0.95
   2 !   12.8   0.5   0.00016     0.075       6      23 ..      39      56 ..      34      58 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00031
  zf-C2H2_11  6 qCleCGlcftSqlsLsRHlfIvH 28
                +C +CG  f     L +H  I H
  EPA06414.1 11 KCKKCGSRFKYPERLEKHQEIAH 33
                8*********************9 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00016
  zf-C2H2_11  6 qCleCGlcftSqlsLsRH 23
                +C+ CG  f S   L++H
  EPA06414.1 39 KCRACGSEFHSTENLRKH 56
                8***************** PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.6   3.6e-05     0.017       2      24 .]      11      33 ..      10      33 .. 0.91
   2 !   13.0   3.4   0.00031      0.15       2      22 ..      39      59 ..      39      61 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.6e-05
   zf-C2H2_4  2 kCpiCgksFsskkaLlrHlkthH 24
                kC+ Cg +F+ +++L +H +  H
  EPA06414.1 11 KCKKCGSRFKYPERLEKHQEIAH 33
                8*****************98766 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00031
   zf-C2H2_4  2 kCpiCgksFsskkaLlrHlkt 22
                kC+ Cg  F+s ++L++H k+
  EPA06414.1 39 KCRACGSEFHSTENLRKHKKN 59
                7*****************986 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.3   6.3e-05      0.03      21      36 .]       5      20 ..       3      20 .. 0.87
   2 ?    7.1   0.3     0.011       5.1      19      35 ..      31      47 ..      24      48 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.3e-05
  zinc_ribbon_4 21 akgvkvrCskCghvFr 36
                   ++ +k++C+kCg  F+
     EPA06414.1  5 DSVRKLKCKKCGSRFK 20
                   5789********9995 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.011
  zinc_ribbon_4 19 lpakgvkvrCskCghvF 35
                   ++ +++k +C +Cg  F
     EPA06414.1 31 IAHNKKKEKCRACGSEF 47
                   78889999*****9877 PP

>> zf-C2H2_3rep  Zinc finger C2H2-type, 3 repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.2   0.00048      0.23      97     125 ..       5      33 ..       1      34 [. 0.86
   2 ?    7.5   0.1     0.014       6.4      34      51 ..      39      56 ..      34      62 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00048
  zf-C2H2_3rep  97 sgvrkfvcrfcGlkfdllpdlGrhhqaah 125
                   ++vrk+ c+ cG +f+    l +h + ah
    EPA06414.1   5 DSVRKLKCKKCGSRFKYPERLEKHQEIAH 33 
                   67999999999999999889999998888 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.014
  zf-C2H2_3rep 34 qcipcgshfgnaeelwlh 51
                  +c  cgs f ++e+l +h
    EPA06414.1 39 KCRACGSEFHSTENLRKH 56
                  466666666666666666 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   5.2   5.3e-06    0.0025       7      35 ..      11      46 ..       9      50 .. 0.85
   2 !    8.9   0.8    0.0035       1.6       7      22 ..      39      54 ..      39      62 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 5.3e-06
  Zn-ribbon_8  7 rCeeCghefe......vlqsisdaplta.CPeCgse 35
                 +C++Cg++f       + q+i+ +++++ C +Cgse
   EPA06414.1 11 KCKKCGSRFKyperleKHQEIAHNKKKEkCRACGSE 46
                 8************9999999995555555*****96 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0035
  Zn-ribbon_8  7 rCeeCghefevlqsis 22
                 +C++Cg+ef       
   EPA06414.1 39 KCRACGSEFHSTENLR 54
                 7********9555433 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.2     0.012       5.9      16      31 ..       4      19 ..       1      22 [. 0.78
   2 !   11.2   0.3   0.00057      0.27      16      34 ..      35      50 ..      30      52 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.012
                    CSCCCEEEESSSS-EE CS
  RNA_POL_M_15KD 16 dkegknfeCrqCgYee 31
                    d++++ + C +Cg+ +
      EPA06414.1  4 DDSVRKLKCKKCGSRF 19
                    67776699****9865 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00057
                    CSCCCEEEESSSS-EEESS CS
  RNA_POL_M_15KD 16 dkegknfeCrqCgYeepad 34
                    +k+ k   Cr Cg+e+ ++
      EPA06414.1 35 KKKEK---CRACGSEFHST 50
                    34443...*******9766 PP

>> zf-trcl  Probable zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.1    0.0019       0.9       4      16 ..       9      21 ..       7      30 .. 0.87
   2 !    8.5   0.5    0.0037       1.8       3      15 ..      36      48 ..      34      56 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0019
     zf-trcl  4 tltCkdCgaefvF 16
                +l+Ck+Cg+ f +
  EPA06414.1  9 KLKCKKCGSRFKY 21
                79*******9966 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0037
     zf-trcl  3 ktltCkdCgaefv 15
                k+ +C+ Cg+ef 
  EPA06414.1 36 KKEKCRACGSEFH 48
                6789*******96 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.7   0.00023      0.11      18      32 .]      10      24 ..       4      24 .. 0.80
   2 ?    5.1   0.2      0.04        19      19      25 ..      39      45 ..      28      47 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00023
                    ---SSS-----B--- CS
  DNA_RNApol_7kD 18 iRCkeCGhRilYKkR 32
                    ++Ck+CG+R  Y +R
      EPA06414.1 10 LKCKKCGSRFKYPER 24
                    68*******877655 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.04
                    --SSS-- CS
  DNA_RNApol_7kD 19 RCkeCGh 25
                    +C+ CG+
      EPA06414.1 39 KCRACGS 45
                    7****96 PP

>> zf-DNA_Pol  DNA Polymerase alpha zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   2.9   3.1e-05     0.014      16      59 ..       9      50 ..       2      63 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.1e-05
                EEE-TTT--EEEE-SSS--S.SEEEETTEEEET..TT--B--HH CS
  zf-DNA_Pol 16 elrCpsCkeefefegvfesaeeekvtasglrCsnesCkaslsta 59
                +l+C++C+++f++++  e+++e +++++  +C+  +C +++++ 
  EPA06414.1  9 KLKCKKCGSRFKYPERLEKHQEIAHNKKKEKCR--ACGSEFHST 50
                79******************999*********9..799998654 PP

>> DUF678  Protein of unknown function (DUF678)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.1     0.028        13      58      69 ..       9      20 ..       4      26 .. 0.85
   2 ?    9.7   0.1     0.002      0.94      48      70 ..      27      49 ..      22      54 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.028
      DUF678 58 tlrCaACgSsLt 69
                 l+C+ CgS  +
  EPA06414.1  9 KLKCKKCGSRFK 20
                79*******875 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.002
      DUF678 48 klkvavgkgntlrCaACgSsLtl 70
                k +  + + +  +C ACgS+  +
  EPA06414.1 27 KHQEIAHNKKKEKCRACGSEFHS 49
                5555667777889******9876 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1    0.0014      0.65      32      57 ..       4      29 ..       2      38 .. 0.83
   2 ?    6.4   0.3     0.019       8.8      37      58 ..      37      58 ..      23      62 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0014
        CpXC 32 dgslfeatCpkCgatakleapllyhd 57
                d+s+++ +C kCg ++k++  l  h+
  EPA06414.1  4 DDSVRKLKCKKCGSRFKYPERLEKHQ 29
                689999**********9988876555 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.019
        CpXC 37 eatCpkCgatakleapllyhdp 58
                + +C +Cg +++ + +l+ h++
  EPA06414.1 37 KEKCRACGSEFHSTENLRKHKK 58
                4579999999999999988875 PP

>> XPA_N  XPA protein N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.3    0.0038       1.8       2      12 ..      10      20 ..       9      21 .. 0.88
   2 ?    8.7   0.6    0.0038       1.8       2      13 ..      38      49 ..      37      51 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0038
       XPA_N  2 pkCdeCgkefl 12
                 kC++Cg++f+
  EPA06414.1 10 LKCKKCGSRFK 20
                69*******95 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0038
       XPA_N  2 pkCdeCgkefld 13
                +kC  Cg+ef+ 
  EPA06414.1 38 EKCRACGSEFHS 49
                79********85 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.2     0.052        24       4      15 ..       9      20 ..       6      23 .. 0.83
   2 ?   10.6   0.3   0.00089      0.42       1      17 [.      34      50 ..      34      53 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.052
  Prok-RING_1  4 gkkCpvCgkelk 15
                 + kC+ Cg ++k
   EPA06414.1  9 KLKCKKCGSRFK 20
                 679****99997 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00089
  Prok-RING_1  1 nytgkkCpvCgkelkee 17
                 n++++kC +Cg e+++ 
   EPA06414.1 34 NKKKEKCRACGSEFHST 50
                 6899**********976 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   6.6   4.8e-05     0.023      37      78 ..       9      50 ..       2      62 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 4.8e-05
  zinc_ribbon_15 37 ylacskCkslleaskelgkeiekkessekkeCknCgkeveee 78
                     l+c+kC+s+++  ++l+k+ e +++++k++C+ Cg+e ++ 
      EPA06414.1  9 KLKCKKCGSRFKYPERLEKHQEIAHNKKKEKCRACGSEFHST 50
                    589***********99999999999999********998765 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1    0.0088       4.1      13      25 ..      11      23 ..       3      25 .. 0.82
   2 ?    6.3   0.1     0.019       8.9      13      22 ..      39      48 ..      38      52 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0088
     DUF35_N 13 rCpdCGtvqfPPr 25
                +C++CG+ + +P+
  EPA06414.1 11 KCKKCGSRFKYPE 23
                8*****9987775 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.019
     DUF35_N 13 rCpdCGtvqf 22
                +C++CG+ ++
  EPA06414.1 39 KCRACGSEFH 48
                7999998766 PP

>> Ephrin_rec_like  Putative ephrin-receptor like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.1    0.0033       1.5      19      35 ..       3      19 ..       2      30 .. 0.86
   2 ?    6.8   1.1     0.012       5.7      22      48 .]      34      60 ..      28      60 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0033
  Ephrin_rec_like 19 YqneegqlsClaCPlgt 35
                     Y +++++l+C++C++ +
       EPA06414.1  3 YDDSVRKLKCKKCGSRF 19
                     88999********9765 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.012
  Ephrin_rec_like 22 eegqlsClaCPlgtttkkpgatsesdC 48
                     +  + +C aC+++++ ++   + ++ C
       EPA06414.1 34 NKKKEKCRACGSEFHSTENLRKHKKNC 60
                     667889999998888776655555555 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.4    0.0082       3.9      23      35 ..       7      19 ..       1      32 [. 0.65
   2 ?   11.4   3.7   0.00056      0.27       5      31 ..      33      60 ..      29      64 .] 0.77

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0082
                S--EE-TTT--EE CS
        FYVE 23 rrrhhCrlCGkvv 35
                +r+  C+ CG+ +
  EPA06414.1  7 VRKLKCKKCGSRF 19
                4666666666544 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00056
                ...--SB-TTT--B-.-SSS--EE-TTT CS
        FYVE  5 ddsevkkCeiCakkF.sllrrrhhCrlC 31
                ++++ +kC++C ++F s+ + r+h ++C
  EPA06414.1 33 HNKKKEKCRACGSEFhSTENLRKHKKNC 60
                677889*********6666778887887 PP

>> zf-C2H2_2  C2H2 type zinc-finger (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.6    0.0045       2.1      48      71 ..       8      30 ..       2      38 .. 0.79
   2 ?    8.9   2.8    0.0039       1.8      49      71 ..      36      58 ..      29      62 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0045
   zf-C2H2_2 48 eekleClyCekefkslealreHmk 71
                  kl+C  C+++fk  e l++H +
  EPA06414.1  8 R-KLKCKKCGSRFKYPERLEKHQE 30
                4.59******************54 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0039
   zf-C2H2_2 49 ekleClyCekefkslealreHmk 71
                +k +C  C++ef+s+e+lr+H k
  EPA06414.1 36 KKEKCRACGSEFHSTENLRKHKK 58
                4679*****************65 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1    0.0044       2.1       4      16 ..      11      23 ..      10      36 .. 0.81
   2 ?    5.0   0.3      0.05        24       4      12 ..      39      47 ..      38      50 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0044
  PhnA_Zn_Ribbon  4 kCplCaSeytYed 16
                    kC +C+S + Y +
      EPA06414.1 11 KCKKCGSRFKYPE 23
                    8********9943 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.05
  PhnA_Zn_Ribbon  4 kCplCaSey 12
                    kC  C+Se+
      EPA06414.1 39 KCRACGSEF 47
                    899999996 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.4   0.00012     0.054       4      31 ..      12      47 ..      10      49 .. 0.85
   2 ?    7.5   0.3    0.0084       3.9       4      24 ..      40      60 ..      39      61 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00012
                -TTT--EE........ETTTB--SSTTB-TTT--.- CS
     ADK_lid  4 CpkCGrsY........hvvfnpPkveglCDkCGepL 31
                C+kCG  +        h + +  k++ +C  CG+++
  EPA06414.1 12 CKKCGSRFkyperlekHQEIAHNKKKEKCRACGSEF 47
                *******98899888875557789*********985 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0084
                -TTT--EEETTTB--SSTTB- CS
     ADK_lid  4 CpkCGrsYhvvfnpPkveglC 24
                C++CG  +h + n  k +  C
  EPA06414.1 40 CRACGSEFHSTENLRKHKKNC 60
                99*******555877766655 PP

>> zf-HYPF  HypF finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1     0.011         5      24      32 ..      12      20 ..       9      21 .. 0.88
   2 ?    6.8   1.0     0.012       5.9       2      18 ..      40      56 ..      39      61 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.011
                -TTTS--EE CS
     zf-HYPF 24 CtnCGPrls 32
                C++CG r++
  EPA06414.1 12 CKKCGSRFK 20
                *******96 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.012
                -HHHHHHHC-TTSTTTT CS
     zf-HYPF  2 CedClrEykdpldRRfh 18
                C +C  E++  ++ R h
  EPA06414.1 40 CRACGSEFHSTENLRKH 56
                9***********98877 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   6.1    0.0002     0.093      14      43 ..      11      52 ..       4      62 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.0002
         DZR 14 fCseCgtklkavaa.............edrCpsCgekvdpear 43
                 C++Cg++ k  ++             +++C +Cg++ +++++
  EPA06414.1 11 KCKKCGSRFKY-PErlekhqeiahnkkKEKCRACGSEFHSTEN 52
                6*******984.445999999***************9998887 PP

>> zf-C2H2_6  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   2.5     0.017       8.1       3      24 ..      11      33 ..      11      36 .. 0.80
   2 ?   12.1   4.6   0.00031      0.14       3      23 ..      39      59 ..      39      61 .. 0.94

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.017
   zf-C2H2_6  3 eCsvCsksFpslqaLggHk.ksH 24
                +C+ C+ +F++   L++H  + H
  EPA06414.1 11 KCKKCGSRFKYPERLEKHQeIAH 33
                7*********9888888866666 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00031
   zf-C2H2_6  3 eCsvCsksFpslqaLggHkks 23
                +C  C+ +F+s  +L++Hkk+
  EPA06414.1 39 KCRACGSEFHSTENLRKHKKN 59
                6999***************96 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.2    0.0018      0.86       4      19 ..      11      26 ..       8      34 .. 0.89
   2 ?    4.6   0.4     0.052        25       4      16 ..      39      51 ..      36      57 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0018
      zf_UBZ  4 lCerCgkeipeselqE 19
                 C++Cg+++  +e+ E
  EPA06414.1 11 KCKKCGSRFKYPERLE 26
                7********9998876 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.052
      zf_UBZ  4 lCerCgkeipese 16
                 C  Cg+e+ ++e
  EPA06414.1 39 KCRACGSEFHSTE 51
                7********9984 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.2    0.0015      0.73      28      39 .]       9      20 ..       4      20 .. 0.82
   2 ?    3.4   0.3      0.14        68      30      37 ..      39      46 ..      38      48 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0015
     TFIIS_C 28 fykCtkCghrWr 39
                  kC+kCg r++
  EPA06414.1  9 KLKCKKCGSRFK 20
                679999999996 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.14
     TFIIS_C 30 kCtkCghr 37
                kC +Cg +
  EPA06414.1 39 KCRACGSE 46
                56666655 PP

>> DUF983  Protein of unknown function (DUF983)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1      0.11        53      10      19 ..      11      20 ..       7      24 .. 0.85
   2 ?    8.5   0.3    0.0055       2.6       7      21 ..      36      50 ..      33      53 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.11
      DUF983 10 aCeaCgldls 19
                +C++Cg +++
  EPA06414.1 11 KCKKCGSRFK 20
                8*****9996 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0055
      DUF983  7 vadaCeaCgldlsha 21
                 +++C+aCg ++++ 
  EPA06414.1 36 KKEKCRACGSEFHST 50
                589*********976 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.9    0.0021      0.97      13      26 .]       8      21 ..       5      21 .. 0.86
   2 ?    7.6   2.3     0.011       5.3       2      24 ..      25      47 ..      24      49 .. 0.88
   3 ?    2.3   0.1      0.55   2.6e+02       1       7 [.      52      58 ..      52      63 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0021
   zf-H2C2_2 13 kpyeCplCdkaFkt 26
                ++++C++C+ +Fk+
  EPA06414.1  8 RKLKCKKCGSRFKY 21
                578*********96 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.011
   zf-H2C2_2  2 LrrHirk.HtgekpyeCplCdkaF 24
                L++H+   H ++k+ +C +C+  F
  EPA06414.1 25 LEKHQEIaHNKKKE-KCRACGSEF 47
                89999998999998.******998 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.55
   zf-H2C2_2  1 nLrrHir 7 
                nLr+H +
  EPA06414.1 52 NLRKHKK 58
                7999987 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   4.0   0.00033      0.15      69      96 ..       8      47 ..       1      52 [. 0.77
   2 ?    9.0   2.1    0.0029       1.4      63      93 ..      30      61 ..      22      63 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00033
                -EEEETTTS-EEECHHH.HH...........S-TTTSSS- CS
        HypA 69 vkvrCreCgkefeleek.al...........rCpkCgsad 96
                 k++C++Cg++f+  e+ +            +C +Cgs+ 
  EPA06414.1  8 RKLKCKKCGSRFKYPERlEKhqeiahnkkkeKCRACGSEF 47
                5789*********66543224678999**********974 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0029
                EEEEE--EEEETTTS-EEECHHH.HHS-TTTS CS
        HypA 63 eieevpvkvrCreCgkefeleek.alrCpkCg 93
                ei + + k +Cr Cg+ef+++e+ + + ++C+
  EPA06414.1 30 EIAHNKKKEKCRACGSEFHSTENlRKHKKNCK 61
                5778888999********97764444445555 PP

>> Fibrillin_U_N  Fibrillin 1 unique N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.1     0.097        46      14      19 ..      15      20 ..       7      21 .. 0.87
   2 ?    6.9   0.2     0.014       6.8      13      20 ..      42      49 ..      39      51 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.097
  Fibrillin_U_N 14 CGsRfh 19
                   CGsRf 
     EPA06414.1 15 CGSRFK 20
                   *****5 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.014
  Fibrillin_U_N 13 vCGsRfhs 20
                    CGs fhs
     EPA06414.1 42 ACGSEFHS 49
                   6******9 PP

>> zf-CSL  CSL zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.3     0.011       5.2      20      34 ..      11      26 ..       3      36 .. 0.79
   2 ?    6.4   0.4     0.015       7.1      20      33 ..      39      53 ..      29      63 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.011
                EE.TTSSEEEEEHHHH CS
      zf-CSL 20 pC.RCgdeFelteedl 34
                +C  Cg++F+ +e+  
  EPA06414.1 11 KCkKCGSRFKYPERLE 26
                799*******998744 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.015
                EE.TTSSEEEEEHHH CS
      zf-CSL 20 pC.RCgdeFelteed 33
                +C  Cg+eF+ te+ 
  EPA06414.1 39 KCrACGSEFHSTENL 53
                7967******99975 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1    0.0032       1.5       2      10 ..      11      19 ..      10      28 .. 0.82
   2 ?    5.2   0.1     0.031        15       2      10 ..      39      47 ..      38      55 .. 0.79
   3 ?   -2.8   0.1       9.8   4.6e+03       4       8 ..      58      62 ..      58      63 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0032
                  EETTTTCEE CS
  TF_Zn_Ribbon  2 kCPnCgstn 10
                  kC++Cgs++
    EPA06414.1 11 KCKKCGSRF 19
                  9******96 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.031
                  EETTTTCEE CS
  TF_Zn_Ribbon  2 kCPnCgstn 10
                  kC  Cgs++
    EPA06414.1 39 KCRACGSEF 47
                  899***987 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 9.8
                  TTTTC CS
  TF_Zn_Ribbon  4 PnCgs 8 
                  +nC++
    EPA06414.1 58 KNCKG 62
                  58886 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.3     0.038        18       3       9 ..      12      18 ..      11      20 .. 0.76
   2 ?    7.3   0.6    0.0079       3.7       3      12 ..      40      49 ..      39      50 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.038
  Rubredoxin_2  3 CsqCGfe 9 
                  C++CG++
    EPA06414.1 12 CKKCGSR 18
                  9999986 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0079
  Rubredoxin_2  3 CsqCGfesak 12
                  C++CG+e+++
    EPA06414.1 40 CRACGSEFHS 49
                  9999999886 PP

>> Zn_ribbon_recom  Recombinase zinc beta ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   7.8    0.0082       3.9       5      49 ..       9      53 ..       7      64 .] 0.53

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0082
  Zn_ribbon_recom  5 llrCgeCGspmtr...........rkrkgkrhyYrCstyrrkgkkCsnhsireekl 49
                     +l+C++CGs++++           +++           +++k++ C +   ++e+l
       EPA06414.1  9 KLKCKKCGSRFKYperlekhqeiaHNK-----------KKEKCRACGSEFHSTENL 53
                     79*********9976665433333233...........233332333333333333 PP

>> zf-C2HC_2  zinc-finger of a C2HC-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   7.2    0.0064         3       4      22 ..      11      30 ..       9      41 .. 0.82
   2 ?    3.6   5.5      0.14        64       3      25 .]      38      61 ..      36      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0064
   zf-C2HC_2  4 pCpkCgRsF.npdrlekHep 22
                +C+kCg +F  p+rlekH+ 
  EPA06414.1 11 KCKKCGSRFkYPERLEKHQE 30
                8********99*******54 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.14
   zf-C2HC_2  3 vpCpkCgRsF.npdrlekHepvCk 25
                ++C+ Cg  F  ++ l kH++ Ck
  EPA06414.1 38 EKCRACGSEFhSTENLRKHKKNCK 61
                578899999999999********8 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   1.4    0.0063         3       4      13 ..      11      20 ..       5      21 .. 0.64
   2 ?    8.4   7.6    0.0039       1.8       4      35 ..      11      47 ..       9      49 .. 0.79
   3 ?    5.4   1.7     0.033        15       4      13 ..      39      48 ..      37      64 .] 0.74

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0063
  zinc_ribbon_5  4 rCpdCdtkFk 13
                   +C +C++ Fk
     EPA06414.1 11 KCKKCGSRFK 20
                   5666666665 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0039
  zinc_ribbon_5  4 rCpdCdtkFkl.....vdsklKksgkkVrCakCaevF 35
                   +C +C++ Fk         ++  + kk +C  C++ F
     EPA06414.1 11 KCKKCGSRFKYperleKHQEIAHNKKKEKCRACGSEF 47
                   8********9622223357899***********9977 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.033
  zinc_ribbon_5  4 rCpdCdtkFk 13
                   +C +C++ F 
     EPA06414.1 39 KCRACGSEFH 48
                   7********7 PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   1.5     0.082        39      16      28 ..       9      21 ..       3      34 .. 0.81
   2 ?    8.1   4.6    0.0056       2.7      12      38 ..      33      56 ..      19      61 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.082
                --EETTTTEE--- CS
      zf-BED 16 kavCryCgkilsr 28
                k +C+ Cg  +++
  EPA06414.1  9 KLKCKKCGSRFKY 21
                679*****98876 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0056
                GGSS--EETTTTEE----SSTHHHHHH CS
      zf-BED 12 lkeqkavCryCgkilsrgggttnLkrH 38
                  ++k +Cr Cg ++ +   t nL++H
  EPA06414.1 33 HNKKKEKCRACGSEFHS---TENLRKH 56
                468999******99987...8*****9 PP

>> ARS2  Arsenite-resistance protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   6.1      0.14        68      66      96 ..       8      38 ..       3      41 .. 0.85
   2 ?    7.9   3.2    0.0077       3.6      64      89 ..      34      59 ..      29      63 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.14
        ARS2 66 dKwlCplsGKkFkgpEFvrKHilnKHaekve 96
                 K  C   G +Fk pE + KH    H+ k e
  EPA06414.1  8 RKLKCKKCGSRFKYPERLEKHQEIAHNKKKE 38
                5889*****************9988888765 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0077
        ARS2 64 akdKwlCplsGKkFkgpEFvrKHiln 89
                 k+K  C + G  F++ E +rKH +n
  EPA06414.1 34 NKKKEKCRACGSEFHSTENLRKHKKN 59
                577888*****************887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1390  (0.077528); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                        39  (0.00217525); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              38  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 406.88
//
Query:       EPA06415.1  [L=43]
Description: hypothetical protein BG20_I2131 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0012   18.7   1.2     0.0014   18.5   1.2    1.1  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
  ------ inclusion threshold ------
      0.033   14.7   0.1      0.033   14.7   0.1    1.1  1  SAUGI            S. aureus uracil DNA glycosylase inhibitor
      0.036   13.7   1.2        0.4   10.3   0.0    2.1  2  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
      0.053   14.4   2.6       0.06   14.2   2.6    1.1  1  Ima1_N           Ima1 N-terminal domain
        0.2   11.9   3.1        6.3    7.1   3.3    2.0  1  zf-LITAF-like    LITAF-like zinc ribbon domain
       0.34   11.0   5.0        2.5    8.2   0.9    2.1  2  zf-C2H2_6        C2H2-type zinc finger
       0.52    9.7   8.5       0.39   10.1   1.0    2.2  2  zf-RanBP         Zn-finger in Ran binding protein and others
        1.1    9.7   4.7        1.6    9.1   0.3    1.9  1  C1_2             C1 domain


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   1.2   6.4e-07    0.0014      28      61 ..       2      39 ..       1      41 [. 0.91

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 6.4e-07
  OrfB_Zn_ribbon 28 SktCseCgsknke....alsgrtfkCpnCgfeadrDvn 61
                    S++C +C +   +      s+++++C+ Cg  +d D n
      EPA06415.1  2 STKCKVCNASRITnvnqLMSDEKWECQTCGNFLDVDGN 39
                    899****9988888888899**************9987 PP

>> SAUGI  S. aureus uracil DNA glycosylase inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   1.5e-05     0.033      10      28 ..      12      30 ..       2      39 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.5e-05
                HHHHHHT--SS---EEEEE CS
       SAUGI 10 yitrlfqlsrdekweceal 28
                 it++ ql  dekwec++ 
  EPA06415.1 12 RITNVNQLMSDEKWECQTC 30
                69**************976 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.3     0.052   1.2e+02       8      12 ..       4       8 ..       3      16 .. 0.86
   2 ?   10.3   0.0   0.00018       0.4       5      18 ..      23      36 ..      20      39 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.052
                     E-TTT CS
  Desulfoferrod_N  8 kCevC 12
                     kC+vC
       EPA06415.1  4 KCKVC 8 
                     9**** PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00018
                     -EEE-TTT--EEEE CS
  Desulfoferrod_N  5 evYkCevCGniVeV 18
                     e++ C+ CGn   V
       EPA06415.1 23 EKWECQTCGNFLDV 36
                     7899******8766 PP

>> Ima1_N  Ima1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   2.6   2.7e-05      0.06       2      39 ..       4      42 ..       3      43 .] 0.83

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.7e-05
      Ima1_N  2 nCffCnkkskvkyeekns...feCpsCeayNgfdedGdind 39
                +C  Cn++  +++++ +s   +eC++C   N++d dG++n+
  EPA06415.1  4 KCKVCNASRITNVNQLMSdekWECQTCG--NFLDVDGNVNS 42
                688899998888887777778*****97..99******986 PP

>> zf-LITAF-like  LITAF-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   3.3    0.0028       6.3       6      30 ..       3      27 ..       1      34 [. 0.76

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0028
  zf-LITAF-like  6 vdCpaCqqrvvTsveyksgkltwll 30
                   ++C+ C++  +T+v++  +   w +
     EPA06415.1  3 TKCKVCNASRITNVNQLMSDEKWEC 27
                   78999**999999998877777755 PP

>> zf-C2H2_6  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.9    0.0011       2.5       2      10 ..       3      11 ..       2      11 .. 0.88
   2 ?    4.8   0.2     0.013        29       3       8 ..      26      31 ..      25      32 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0011
   zf-C2H2_6  2 heCsvCsks 10
                ++C+vC++s
  EPA06415.1  3 TKCKVCNAS 11
                69*****97 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.013
   zf-C2H2_6  3 eCsvCs 8 
                eC++C+
  EPA06415.1 26 ECQTCG 31
                8****8 PP

>> zf-RanBP  Zn-finger in Ran binding protein and others
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   1.3     0.016        37      19      27 ..       3      11 ..       2      12 .. 0.64
   2 ?   10.1   1.0   0.00017      0.39       2      12 ..      22      32 ..      21      33 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.016
                SB-TTT--B CS
    zf-RanBP 19 tkCvaCqap 27
                tkC  C a+
  EPA06415.1  3 TKCKVCNAS 11
                777777766 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00017
                SSSEE-SSS-- CS
    zf-RanBP  2 egdWdCskClv 12
                 ++W+C +C++
  EPA06415.1 22 DEKWECQTCGN 32
                579******97 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.3   0.00072       1.6      13      26 ..      19      32 ..      12      39 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00072
        C1_2 13 edssesfnCsaCgr 26
                  s+e+++C++Cg+
  EPA06415.1 19 LMSDEKWECQTCGN 32
                56889999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (43 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 287.82
//
Query:       EPA06416.1  [L=139]
Description: hypothetical protein BG20_I2129, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       255  (0.0142228); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 1050.34
//
Query:       EPA06417.1  [L=62]
Description: hypothetical protein BG20_I2136 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.017   15.1   8.6      0.022   14.8   8.6    1.3  1  zinc-ribbons_6   zinc-ribbons
       0.17   11.9  10.4       0.17   11.9   9.2    1.6  1  DZR              Double zinc ribbon
       0.19    9.5   5.0       0.18    9.6   5.0    1.0  1  PolC_DP2         DNA polymerase II large subunit DP2
        2.5    9.0  12.6    1.3e+02    3.5  12.6    2.9  1  Tnp_zf-ribbon_2  DDE_Tnp_1-like zinc-ribbon


Domain annotation for each model (and alignments):
>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   8.6   4.8e-06     0.022      16      47 ..       3      35 ..       1      45 [. 0.89

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.8e-06
                    EEE-TTT--EEEEEEE-SSS-S---.EEEETTE CS
  zinc-ribbons_6 16 qyhCeaCqedlkkealCpeCeqele.vlkaCga 47
                    + +C++C+++l++e  C  C+q+ + +++aCg 
      EPA06417.1  3 KQSCKTCSSKLEVESRCKVCDQPTKlFCHACGI 35
                    679********************9835899995 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   9.2   3.8e-05      0.17      12      49 .]       3      34 ..       1      35 [. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.8e-05
         DZR 12 arfCseCgtklkavaaedrCpsCgekvdpearfCpeCG 49
                ++ C++C +kl+    e rC  C+++++    fC++CG
  EPA06417.1  3 KQSCKTCSSKLEV---ESRCKVCDQPTK---LFCHACG 34
                688********86...99*****98765...5788887 PP

>> PolC_DP2  DNA polymerase II large subunit DP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   5.0     4e-05      0.18     617     660 ..       2      44 ..       1      60 [. 0.77

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 4e-05
    PolC_DP2 617 arrkCkkCgke.tlearCeeCgekteeklvCkkceeeveeekcek 660
                 ++++Ck+C ++  +e+rC+ C++ t+    C+ c+ ++e+   + 
  EPA06417.1   2 QKQSCKTCSSKlEVESRCKVCDQPTKL--FCHACGITHENIIHPA 44 
                 678999997653799999999999998..9999998776544444 PP

>> Tnp_zf-ribbon_2  DDE_Tnp_1-like zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5  12.6     0.029   1.3e+02       3      27 ..       6      45 ..       4      47 .. 0.65

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.029
  Tnp_zf-ribbon_2  3 CkvClk........kkikkeTriiCqeCd.......vplC 27
                     Ck C++        k   + T+ +C++C+        p C
       EPA06417.1  6 CKTCSSklevesrcKVCDQPTKLFCHACGitheniiHPAC 45
                     88888865555554444445********654455666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       963  (0.0537119); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.33s 00:00:00.80 Elapsed: 00:00:00.51
# Mc/sec: 363.31
//
Query:       EPA06418.1  [L=132]
Description: hypothetical protein BG20_I2130 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0055   16.1   0.8     0.0055   16.1   0.8    1.7  2  SLATT_5         SMODS and SLOG-associating 2TM effector domai


Domain annotation for each model (and alignments):
>> SLATT_5  SMODS and SLOG-associating 2TM effector domain family 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.8   3.1e-07    0.0055     116     142 ..      13      39 ..       2      59 .. 0.76
   2 ?   -2.5   1.6      0.15   2.7e+03     114     135 ..     102     123 ..      88     130 .. 0.46

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.1e-07
     SLATT_5 116 edlkekykeiskeYeeiLdkyeNHdei 142
                 e+ +e  ++ +keY+eiL+k  NH++ 
  EPA06418.1  13 EEYEEDEQKTEKEYKEILEKTSNHSPR 39 
                 333444445889************986 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.15
     SLATT_5 114 seedlkekykeiskeYeeiLdk 135
                 +e+  +e+ + ++++ e++L++
  EPA06418.1 102 KEKIIQEREEVLNERQESLLKQ 123
                 3333344444333333344444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2147  (0.11975); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 969.33
//
Query:       EPA06419.1  [L=141]
Description: hypothetical protein BG20_I2139, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-09   37.2   0.0    2.7e-09   36.9   0.0    1.1  1  Guanylate_cyc  Adenylate and Guanylate cyclase catalytic doma


Domain annotation for each model (and alignments):
>> Guanylate_cyc  Adenylate and Guanylate cyclase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.0   1.5e-13   2.7e-09      61     157 ..       6     109 ..       3     133 .. 0.85

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 1.5e-13
  Guanylate_cyc  61 ymvvsglpeekaahaaklaelaLdmleal.eevaves.keglkvrvGihtGpvvagviG..akkprydvwGntvnlAsrmestgkagkiqvseety 152
                    y v+ +l+ + a+ a ++ae  L++l+   + + +++  ++lk+++Gi++G+  +   G   +  + d+ G +v +A++++ ++++++i+v  + y
     EPA06419.1   6 YFVAENLSASVADRAVTCAESMLKILKIGiNPILKNNnLPELKIKIGIDYGENTIVRYGddLQESHVDILGPSVSMAAKIQNLAQPDQIMVGGDIY 101
                    899999999999**************99866655555589***********9888887766999******************************** PP

  Guanylate_cyc 153 ellk...e 157
                    + l+   +
     EPA06419.1 102 SKLHnsiQ 109
                    *9995443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1093.64
//
Query:       EPA06420.1  [L=42]
Description: hypothetical protein BG20_I2134 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       721  (0.0402142); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.43
# Mc/sec: 296.00
//
Query:       EPA06421.1  [L=40]
Description: hypothetical protein BG20_I2135 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       789  (0.0440069); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 284.20
//
Query:       EPA06422.1  [L=125]
Description: prephenate dehydratase, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-39  134.2   0.0    4.7e-39  134.1   0.0    1.0  1  PDT       Prephenate dehydratase


Domain annotation for each model (and alignments):
>> PDT  Prephenate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.1   0.0   2.6e-43   4.7e-39       1     126 [.       4     123 ..       4     125 .] 0.94

  Alignments for each domain:
  == domain 1  score: 134.1 bits;  conditional E-value: 2.6e-43
                 EEEES-TTSHHHHHHCCCS.....EEEEES-HHHHHHHHCTTS-SEEEEEEEESSS-B-HHHHHHHHH.SSEEEEEEEEEE---EEEE-TT--TTT--E CS
         PDT   1 vaylGpegtyshqAalkvfkaedvelipvasieevfeavekgeadyavvPiENsteGsVnetlDlLlkesdlkivgEvvlpiehcLlakpktkleeikk 99 
                 v+++G++g+ys+ Aa+++f ++d++++p +++ ev+e+   g+++y+v+P+ENs+eGsV e++DlL++ ++l+ +gE++ +iehcL+++  + l+ei +
  EPA06422.1   4 VSFQGERGAYSEAAARAFF-NSDIQTVPLPTFAEVLENTTVGKTEYSVLPVENSLEGSVGESYDLLYS-TPLNAIGEIYHRIEHCLIGNG-M-LDEIDT 98 
                 78*****************.************************************************.99***************8765.4.6***** PP

                 EEE-HHHHHHTHHHHHH-.TTSEEEE- CS
         PDT 100 vyShpqalgQcrkfLeehlpqvervav 126
                 vyShpqalgQcr+f+e+h  +++ v++
  EPA06422.1  99 VYSHPQALGQCRNFIEKH--NMKTVPT 123
                 ******************..7777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 841.77
//
Query:       EPA06423.1  [L=59]
Description: hypothetical protein BG20_I2655, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.013   15.6   0.3      0.016   15.3   0.3    1.1  1  Ribosomal_L37e  Ribosomal protein L37e
      0.014   15.3   0.5      0.017   15.1   0.5    1.1  1  Prok-RING_1     Prokaryotic RING finger family 1
       0.19   11.4   8.0        2.9    7.6   8.0    2.1  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
       0.31   11.1   4.7        4.6    7.4   0.5    2.2  2  zf-ACC          Acetyl-coA carboxylase zinc finger domain


Domain annotation for each model (and alignments):
>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.3   3.6e-06     0.016      16      48 ..      15      48 ..      10      53 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.6e-06
  Ribosomal_L37e 16 HilCrrCgkrsyhvqkk.tCascGypsaklrkyn 48
                    +++Cr+Cg +   ++   +C +c++ ++++ + n
      EPA06423.1 15 FTKCRKCGGKVVQMRDAiKCTECAWIDERKLSTN 48
                    799*****99999987648******888876655 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.5   3.7e-06     0.017       5      27 ..      16      38 ..      14      49 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.7e-06
  Prok-RING_1  5 kkCpvCgkelkeedDiVvCpeCg 27
                 +kC  Cg ++ +  D++ C+eC 
   EPA06423.1 16 TKCRKCGGKVVQMRDAIKCTECA 38
                 69********************6 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   8.0   0.00066       2.9       2      23 ..      17      37 ..      17      39 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00066
                    B-SSS--B----SSS----SSS CS
  DNA_RNApol_7kD  2 iCgeCgaevslkkgdpiRCkeC 23
                    +C +Cg +v  + +d+i+C+eC
      EPA06423.1 17 KCRKCGGKVV-QMRDAIKCTEC 37
                    6999**9995.7789******* PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.5     0.001       4.6       1       8 [.      15      22 ..      15      25 .. 0.90
   2 ?    5.7   0.3    0.0036        16       2       9 ..      32      39 ..      32      40 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.001
      zf-ACC  1 WtKCpsCg 8 
                +tKC +Cg
  EPA06423.1 15 FTKCRKCG 22
                89*****9 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0036
      zf-ACC  2 tKCpsCge 9 
                +KC++C +
  EPA06423.1 32 IKCTECAW 39
                8*****86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 386.78
//
Query:       EPA06424.1  [L=68]
Description: hypothetical protein BG20_I0500 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 479.53
//
Query:       EPA06425.1  [L=217]
Description: TIGR00153 family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-19   69.8  10.2    2.4e-19   69.5  10.2    1.0  1  PhoU_div      Protein of unknown function DUF47
    0.00063   20.2  11.6     0.0097   16.4   1.9    2.9  3  PhoU          PhoU domain
  ------ inclusion threshold ------
      0.066   13.1   0.7      0.066   13.1   0.7    2.1  2  HATPase_c_5   GHKL domain
        0.2   11.6   0.3        0.2   11.6   0.3    2.4  3  WD40_alt      Alternative WD40 repeat motif
       0.56   10.6   6.5       0.33   11.3   1.2    2.7  3  Lzipper-MIP1  Leucine-zipper of ternary complex factor MIP1
        0.6    9.9  11.2         12    5.6   9.3    3.1  2  MCPsignal     Methyl-accepting chemotaxis protein (MCP) signa
        2.4    8.9   6.7        5.9    7.6   1.1    2.3  2  DUF2203       Uncharacterized conserved protein (DUF2203)
        9.1    4.6   9.2       0.68    8.3   3.0    2.0  2  S6OS1         Six6 opposite strand transcript 1 family


Domain annotation for each model (and alignments):
>> PhoU_div  Protein of unknown function DUF47
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.5  10.2   1.1e-22   2.4e-19      11     211 ..      16     213 ..       8     216 .. 0.92

  Alignments for each domain:
  == domain 1  score: 69.5 bits;  conditional E-value: 1.1e-22
    PhoU_div  11 kslqdhlekvsetvlkliellkallegdyekveellkeiselEreADeikreirlklekglflPvdRedllelveslDeildvlediamlvtlrkvef. 108
                 + lqd ++ + ++  +l+ l   ++++d   + + l++is +E+e  +++r+i ++++    l + Re+ll+ +  +Dei+ ++  ia+ ++ +k+   
  EPA06425.1  16 AVLQDEINRILNAARELATLPDLMMKKDKTGIKNSLEQISTIEEEVENLRRKITREVADVGGLIMNRENLLNTAYTMDEIAGYITGIAFKLSNIKITTl 114
                 56778888888888888888888999**9*****************************9888889***************************9999862 PP

    PhoU_div 109 .peelkdeflallkktveaiealaevieeleklletalskkdiveeieslEdeiDqlqrklikklfsredasnplevlllveiieklenvsdraedvad 206
                   ++l+ ++ +l++ +v+ +++l+e+i++l++  ++a++   +++e +++E eiD  +r+   kl+s  ++ n++e ll+++ ie +e++sd+ ++v+d
  EPA06425.1 115 kSAKLDGDITKLIELVVDEVYKLNEIIRSLNTNTANAIE---LAQETQKIEREIDVKYRQATIKLLS--EVTNTKELLLIKDVIEGIEEMSDKCQRVSD 208
                 356799**************************9999999...9************************..889*************************** PP

    PhoU_div 207 risii 211
                  + ++
  EPA06425.1 209 SFILL 213
                 98765 PP

>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.77   1.7e+03      30      52 ..       8      29 ..       6      41 .. 0.60
   2 !    9.0   1.3   0.00086       1.9      25      86 ..      49     103 ..      22     109 .. 0.74
   3 !   16.4   1.9   4.3e-06    0.0097      12      87 ..     137     208 ..     124     210 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.77
                HHHHHHHHHHHHHHHHHHHHHHH CS
        PhoU 30 vierddeidrlekeierslleal 52
                v ++++ i  l++ei r  l+a+
  EPA06425.1  8 VQAKRKAIAVLQDEINRI-LNAA 29
                555666666666666444.4444 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00086
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHGG-SHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
        PhoU  25 elarevierddeidrlekeierslleal.akrqplaedlrellsllriardlERigDhavnia 86 
                 + ++++   ++e+++l+++i+r+ +  + +   + ++       ll+ a+ +  i+ +++ ia
  EPA06425.1  49 NSLEQISTIEEEVENLRRKITRE-VADVgGLIMNREN-------LLNTAYTMDEIAGYITGIA 103
                 456788888***********999.5555244333333.......7888888888888888887 PP

  == domain 3  score: 16.4 bits;  conditional E-value: 4.3e-06
                 HHHHHHHHHCT-H...HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
        PhoU  12 lddalealeekdt...elarevierddeidrlekeiersllealakrqplaedlrellsllriardlERigDhavniae 87 
                 l++ +++l ++     ela+e  + ++eid  +++ + +ll ++ + ++l         + +++  +E ++D + ++++
  EPA06425.1 137 LNEIIRSLNTNTAnaiELAQETQKIEREIDVKYRQATIKLLSEVTNTKELLL-------IKDVIEGIEEMSDKCQRVSD 208
                 5778888877764556*************************99977666544.......5569***********99876 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.46     1e+03      15      42 ..      48      75 ..      44     123 .. 0.67
   2 ?   13.1   0.7     3e-05     0.066       6      51 ..     140     185 ..     135     209 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.46
  HATPase_c_5 15 dNAieacskieeekrfIrltvrekkksl 42
                  N++e  s+ieee + +r +++++  ++
   EPA06425.1 48 KNSLEQISTIEEEVENLRRKITREVADV 75
                 6888888888876666666666555443 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 3e-05
  HATPase_c_5   6 lcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsye 51 
                  +++ l     NAie ++++++ +r+I+++ r+   +l+ +++N+ e
   EPA06425.1 140 IIRSLNTNTANAIELAQETQKIEREIDVKYRQATIKLLSEVTNTKE 185
                  5566666678********************************9965 PP

>> WD40_alt  Alternative WD40 repeat motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       1.1   2.6e+03      20      30 ..      15      25 ..       7      32 .. 0.71
   2 ?   11.6   0.3   8.8e-05       0.2      19      37 ..      53      72 ..      39      82 .. 0.77
   3 ?   -3.7   0.2       5.1   1.1e+04      25      35 ..     132     142 ..     128     144 .. 0.66

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.1
    WD40_alt 20 vseLeeEVrtL 30
                ++ L++E++ +
  EPA06425.1 15 IAVLQDEINRI 25
                67799999876 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 8.8e-05
    WD40_alt 19 rvseLeeEVrtLr.KInkdL 37
                ++s+ eeEV++Lr KI ++ 
  EPA06425.1 53 QISTIEEEVENLRrKITREV 72
                89**********54999986 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 5.1
    WD40_alt  25 eEVrtLrKInk 35 
                 +EV  L  I +
  EPA06425.1 132 DEVYKLNEIIR 142
                 67777766655 PP

>> Lzipper-MIP1  Leucine-zipper of ternary complex factor MIP1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.2   0.00015      0.33      28      74 ..      24      68 ..       6      70 .. 0.69
   2 ?    1.0   0.1      0.23   5.3e+02      48      80 ..     118     147 ..     105     151 .. 0.69
   3 ?    0.5   0.3      0.33   7.4e+02      65      80 ..     132     147 ..     115     187 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00015
  Lzipper-MIP1 28 raLekalssssdgsllslstllpk....kakellkeiallEeevvkLEqkl 74
                  r+L  a       +l +l+ l+ k     +k+ l+ i+++Eeev +L++k+
    EPA06425.1 24 RILNAAR------ELATLPDLMMKkdktGIKNSLEQISTIEEEVENLRRKI 68
                  4444444......334455544432445799*****************998 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.23
  Lzipper-MIP1  48 llpkkakellkeiallEeevvkLEqkllsLyrk 80 
                    l+  +++l++ ++    ev kL + + sL+ +
    EPA06425.1 118 KLDGDITKLIELVV---DEVYKLNEIIRSLNTN 147
                   45566666665555...9999999999999876 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.33
  Lzipper-MIP1  65 eevvkLEqkllsLyrk 80 
                    ev kL + + sL+ +
    EPA06425.1 132 DEVYKLNEIIRSLNTN 147
                   6666666666666654 PP

>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.6     0.058   1.3e+02     120     139 ..      44      63 ..       6      81 .. 0.42
   2 ?    5.6   9.3    0.0055        12      16     152 ..      45     185 ..      41     210 .. 0.68

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.058
                 HHHHHHHCCHHHHHHHHHHH CS
   MCPsignal 120 selveetgealkeiveavae 139
                  + ++++ e++++i e+v++
  EPA06425.1  44 KTGIKNSLEQISTIEEEVEN 63 
                 22222222222222222222 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0055
                 HHHHHHHHHHHHHHHH....HHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH.............. CS
   MCPsignal  16 kevanvvkqmeeieks....skeis.diieVideiadQTNlLALNAaiEAARAGeqGrGFaVVAdEVrkLAersaqaakeiealiieiqkeindsvesl 109
                 + ++n ++q+ +ie++     ++i+ ++ +V   i +  NlL  N a       ++  G a   + ++    +sa+   +i++li+ ++ e+ +  e++
  EPA06425.1  45 TGIKNSLEQISTIEEEvenlRRKITrEVADVGGLIMNRENLL--NTAYTMDEIAGYITGIAFKLSNIKITTLKSAKLDGDITKLIELVVDEVYKLNEII 141
                 556677777777777622222233313445555566777774..55555555555666777777788888889999999******************** PP

                 HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHH.HHHHHHHHHHH CS
   MCPsignal 110 eetrqrveegselveetgealkeiveavaeva.dlvqeiaaase 152
                  + +++++++ el++et++  +ei  +  + + +l++e++ + e
  EPA06425.1 142 RSLNTNTANAIELAQETQKIEREIDVKYRQATiKLLSEVTNTKE 185
                 *******************9999977766655256667666543 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   1.1    0.0026       5.9       8      72 ..      11      75 ..       7      94 .. 0.62
   2 ?    4.4   0.5     0.026        58       9      43 ..     138     172 ..     113     209 .. 0.49

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0026
     DUF2203  8 AnalLpllkelleelralrkeleeleeeleeakaeaekse...aaeleaeleeleaeieelveeieel 72
                 ++ + +l++ ++++ ++++el++l + + ++ ++  k++    ++ e+e+e+l+   +++++e+ ++
  EPA06425.1 11 KRKAIAVLQDEINRILNAARELATLPDLMMKKDKTGIKNSleqISTIEEEVENLR---RKITREVADV 75
                5788999999999999999999998766655555554443222223333333333...3333444444 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.026
     DUF2203   9 nalLpllkelleelralrkeleeleeeleeakaea 43 
                 n+++  l+  ++++++l++e +++e+e++ + ++a
  EPA06425.1 138 NEIIRSLNTNTANAIELAQETQKIEREIDVKYRQA 172
                 22333333333333333333333333333222222 PP

>> S6OS1  Six6 opposite strand transcript 1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1      0.18   4.1e+02      10      30 ..       7      27 ..       5      35 .. 0.84
   2 ?    8.3   3.0    0.0003      0.68     155     219 ..     130     195 ..     122     212 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.18
       S6OS1 10 kikEkkkeilklkeninksde 30
                +++ k+k i+ l+++in++ +
  EPA06425.1  7 EVQAKRKAIAVLQDEINRILN 27
                57889************9755 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0003
       S6OS1 155 ivnlRlktediLklAetltkkslelkkeadelEikin..ylkkqiarllesknlsevleeknkelek 219
                 +v+  +k ++i++  +t t +++el +e++ +E++i+  y + +i+ l+e  n+ e l  k+  +e 
  EPA06425.1 130 VVDEVYKLNEIIRSLNTNTANAIELAQETQKIEREIDvkYRQATIKLLSEVTNTKELLLIKD-VIEG 195
                 55666899************************998852155555555667777777665554.4444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1376  (0.0767472); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 1458.00
//
Query:       EPA06426.1  [L=428]
Description: aspartate--tRNA ligase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-88  295.9   0.0    3.6e-88  295.7   0.0    1.1  1  tRNA-synt_2      tRNA synthetases class II (D, K and N)
    1.4e-11   44.2   1.0    2.6e-11   43.3   1.0    1.5  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
  ------ inclusion threshold ------
      0.014   14.9   0.1       0.17   11.3   0.0    2.3  2  tRNA-synt_2d     tRNA synthetases class II core domain (F)
       0.16   11.8   0.0       0.29   11.0   0.0    1.3  1  bacHORMA_2       Bacterial HORMA domain 2


Domain annotation for each model (and alignments):
>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  295.7   0.0   8.1e-92   3.6e-88       3     313 ..     115     422 ..     113     423 .. 0.95

  Alignments for each domain:
  == domain 1  score: 295.7 bits;  conditional E-value: 8.1e-92
                  CHHHHTHHHHCCSHHHHHHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT.TEEE....-E-S-SHHHHHHHHHCTHSEEEE CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxx RF
  tRNA-synt_2   3 elrlknryldlrtekvskvlrlrstvtkavrkyleengfieietPiLsksdteegarlFkvksrekekeff....aLtqspqlylellivagidrvfq 96 
                  ++rl++r ld+r++k+ ++++lr++v++++rk l e++fiei+tP ++ s++e+ga+lF +       ++f    +L+qspqly+e + ++ ++rv++
   EPA06426.1 115 DTRLNHRALDMRNQKTASIFKLRHHVLEILRKTLAEKKFIEITTPKIIGSASEGGANLFSL-------DYFgktaYLAQSPQLYKEQMTIG-LERVYE 204
                  89***********************************************************.......66677778***************.****** PP

                  EEEEE--S--BTTB-S-CEEEEEEEEET-SCHHHHHHHHHHHHHHHHHHHHCSCCCCCHTTTTTSEE-SSS-EEEEHHHHHHHHHTS......-SS-- CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxx RF
  tRNA-synt_2  97 iaraFRaEdsrtdrhlaEFtqieaemsfieeedimqvleelikslvkevlessakdiefvirrnskdlkkpfkrltykeaieklnei......gkdld 188
                  i++ +RaE+s+t rhl+EFt+i++e +f++++d+m++le l+  + k v  +++k+ e +i ++ + +k+pf+r+ty++ ie+l++       g+dl 
   EPA06426.1 205 ISNFYRAENSHTGRHLSEFTSIDIEAAFMDYNDVMNILESLVMGVYKFVSVNCKKEQE-NIGHTIEIPKSPFERITYTQVIEELKKVgekvefGDDLL 301
                  *************************************************888866655.555556678888*************99999****9**** PP

                  HHHHHHHHHHS--SEEEEEEEBGGGSTTCBBBSTTSTTBBSEEEEEETTEEEEEEEEB--SHHHHHHHHHHCCHHSSSGGGGHHHHHHHHCT--SEEE CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  tRNA-synt_2 189 kaderalvkkeknepvfvtdfPaelkpFyarkeeddkkltesyDllingvElvgGslRiedpeeleeklkskgldeeaeekfswylealeyGapphgG 286
                    ++r+  k ++  ++f+td+P +lkpFy r++++d+kl++s+Dl +  +El +G +R+++pe l+ +lk++gld   +++f + l+ +++G+pph+G
   EPA06426.1 302 DSHLRIIGK-NHPGFYFLTDWPMKLKPFYIREKDEDSKLSRSFDLQYGYLELSSGGTRLHNPETLKSRLKEQGLD---PAQFADHLQTFDWGMPPHSG 395
                  ********9.999**********************************777*************************...******************** PP

                  EEEEHHHHHHHHCT-SSGGGCSSS-XX CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  tRNA-synt_2 287 lglGldRlvmlllgsesIrdviaFPkl 313
                  +g+GldRl+++l+g +++r+v+++P+ 
   EPA06426.1 396 WGMGLDRLMTTLIGIDNVREVVLYPRD 422
                  *************************95 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.3   1.0   5.8e-15   2.6e-11       1      76 []      21      95 ..      21      95 .. 0.96

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 5.8e-15
                     EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEEEEEEECTTS..SEEEEEEEEEEE CS
  tRNA_anti-codon  1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvtGrvkrrpgg..elelkveeiell 76
                     V++ G+v +   r+ gk+ fi+lrD +g+ q+++   e  + +e+l + +v+ v+G v++++ +  ++e+k+eei +l
       EPA06426.1 21 VVLGGWVEDL--RKLGKMTFITLRDVSGISQIIVKG-ELNDNLEELNRQSVISVRGIVQETKARdfDFEIKAEEIDVL 95
                     7889******..************************.************************999999*******9875 PP

>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0     0.065   2.9e+02     105     148 ..     203     245 ..     190     263 .. 0.67
   2 ?   11.3   0.0   3.8e-05      0.17     213     235 ..     395     417 ..     381     425 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.065
                   EEEEEEEBSST.-SSSB-SEEEEEEE..EEEETT--HHHHHHHHHHH CS
  tRNA-synt_2d 105 isigrvfRrda.vDathlaeFhqveg..lvvdenvsladlkgvleel 148
                     i + +R ++    +hl eF++++    ++d n    d++ +le+l
    EPA06426.1 203 YEISNFYRAENsHTGRHLSEFTSIDIeaAFMDYN----DVMNILESL 245
                   5677889999967789*****9976400444444....444444444 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 3.8e-05
                   EEEEEHHHHHHHHHT-SSGHHHH CS
  tRNA-synt_2d 213 afGlGveRlamlkygieDiRelv 235
                   ++G+G++Rl    +gi+++Re+v
    EPA06426.1 395 GWGMGLDRLMTTLIGIDNVREVV 417
                   7*******************986 PP

>> bacHORMA_2  Bacterial HORMA domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   6.4e-05      0.29      76     137 ..     342     402 ..     329     410 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.4e-05
  bacHORMA_2  76 rwdidivydy..sdsdGslwtdtdqlkyaikkaGlvpsqaeydlllknkpGrpdvaGwskgslr 137
                    +d++y+y   +s G+   +++ lk  +k +Gl p+q   +l      G p  +Gw+ g  r
  EPA06426.1 342 S--FDLQYGYleLSSGGTRLHNPETLKSRLKEQGLDPAQFADHLQT-FDWGMPPHSGWGMGLDR 402
                 3..455666653788999999******************9877765.46799******998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2757.44
//
Query:       EPA06427.1  [L=99]
Description: hypothetical protein BG20_I0492 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.027   13.6   0.5      0.042   13.0   0.2    1.4  1  Memo      Memo-like protein
      0.089   12.8   2.6       0.17   12.0   2.6    1.5  1  Prp18     Prp18 domain


Domain annotation for each model (and alignments):
>> Memo  Memo-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   4.7e-06     0.042     199     237 ..      43      81 ..      25      95 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.7e-06
        Memo 199 DrevikaleelneeelkeylektnnticGekpiavilka 237
                  +e  +++eel+e+++ke l k+ +ticG+ +   i+k+
  EPA06427.1  43 QQESYQRIEELKEKGVKEDLIKYAKTICGNSVEREIIKI 81 
                 5677799**********************9987777665 PP

>> Prp18  Prp18 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   2.6   1.9e-05      0.17      18      83 ..      22      87 ..       4      89 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.9e-05
       Prp18 18 rseeekksvegkkesatlkqtkedlkpLlkklkkkkleedileklveivkalqkreyvkAndaYlk 83
                ++ ++ k  e ++e     + +++  + +++lk+k ++ed+++   +i+ +  +re +k +d+Yl+
  EPA06427.1 22 KEYQVMKIEELSAELRDAMKFQQESYQRIEELKEKGVKEDLIKYAKTICGNSVEREIIKIQDVYLE 87
                22222233333444444555555555667899********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2514  (0.14022); expected 358.6 (0.02)
Passed bias filter:                      760  (0.0423894); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 670.59
//
Query:       EPA06428.1  [L=37]
Description: hypothetical protein BG20_I0475 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0007   19.3   1.1    0.00083   19.0   1.1    1.1  1  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal
     0.0018   18.3   0.0     0.0026   17.7   0.0    1.3  1  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
     0.0055   16.8   0.5     0.0069   16.5   0.5    1.2  1  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 
  ------ inclusion threshold ------
      0.025   14.8   1.0      0.027   14.7   1.0    1.0  1  IBR             IBR domain, a half RING-finger domain
       0.04   14.3   0.9       0.51   10.7   0.0    2.0  2  DUF4379         Probable Zinc-ribbon domain
      0.044   13.1   2.2       0.89    8.9   0.1    2.1  2  zf-TFIIB        Transcription factor zinc-finger
      0.055   13.9   2.3       0.53   10.8   0.1    2.1  2  zf-H2C2_2       Zinc-finger double domain
      0.072   12.8   4.0        3.5    7.5   0.2    2.1  2  Rubredoxin_2    Rubredoxin metal binding domain
      0.094   12.7   1.9        6.9    6.7   0.1    2.1  2  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
       0.13   12.6   3.0        2.2    8.6   0.1    2.0  2  zinc_ribbon_9   zinc-ribbon
       0.26   10.9   1.6        1.8    8.2   0.2    2.1  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
        0.3   10.6   3.6          2    8.0   0.3    2.1  2  zf_C2H2_10      C2H2 type zinc-finger
       0.51   10.9   3.5        3.5    8.3   0.5    2.1  2  zf-C2H2         Zinc finger, C2H2 type


Domain annotation for each model (and alignments):
>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   1.1     6e-07   0.00083      27      52 ..       7      32 ..       6      34 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 6e-07
  zinc_ribbon_10 27 kChshnGlapkeeleevkyrCpkCga 52
                    +C + +G+  +e+ e +++ Cp C+ 
      EPA06428.1  7 QCPKCFGMIFREQGESISWFCPTCNL 32
                    788889******************96 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.9e-06    0.0026       1      21 [.       7      28 ..       7      33 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.9e-06
  DNA_ligase_ZBD  1 hCPvCGsavvReegeai.yRCt 21
                    +CP C   + Re+ge+i ++C+
      EPA06428.1  7 QCPKCFGMIFREQGESIsWFCP 28
                    6********************8 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.5     5e-06    0.0069      18      39 ..       8      30 ..       5      31 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5e-06
  Auto_anti-p27 18 CpvCgvPLmrdr.kggkvyCvaC 39
                   Cp+C   ++r++ ++  ++C++C
     EPA06428.1  8 CPKCFGMIFREQgESISWFCPTC 30
                   ****99999998778899***** PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   1.0   1.9e-05     0.027      17      48 ..       4      34 ..       1      35 [. 0.81

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.9e-05
         IBR 17 nlkwCprpdCeaiiekseg.cksvtCskCgfef 48
                ++ +Cp  +C ++i  ++g + s  C++C+ +f
  EPA06428.1  4 EIGQCP--KCFGMIFREQGeSISWFCPTCNLKF 34
                5679**..******99999555577****9887 PP

>> DUF4379  Probable Zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.2       0.1   1.4e+02      51      56 .]       7      11 ..       1      11 [. 0.69
   2 ?   10.7   0.0   0.00037      0.51      22      41 ..      17      36 ..      13      37 .] 0.81

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.1
     DUF4379 51 skCpkC 56
                + CpkC
  EPA06428.1  7 Q-CPKC 11
                3.**99 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00037
     DUF4379 22 pgskkkvwWkCakCgheWea 41
                + ++++++W C++C+ ++++
  EPA06428.1 17 REQGESISWFCPTCNLKFKT 36
                5678899*******988775 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.1   0.00065      0.89      18      30 ..       4      16 ..       2      25 .. 0.76
   2 ?    4.6   0.2     0.015        20       2       7 ..      27      32 ..      26      36 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00065
    zf-TFIIB 18 eidyCpqCrGvWl 30
                ei +Cp+C G+ +
  EPA06428.1  4 EIGQCPKCFGMIF 16
                5778999999866 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.015
    zf-TFIIB  2 CPkCqd 7 
                CP+C+ 
  EPA06428.1 27 CPTCNL 32
                ****85 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.4     0.077   1.1e+02      16      20 ..       7      11 ..       6      13 .. 0.86
   2 ?   10.8   0.1   0.00038      0.53      11      26 .]      20      36 ..      14      36 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.077
   zf-H2C2_2 16 eCplC 20
                +Cp+C
  EPA06428.1  7 QCPKC 11
                79999 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00038
   zf-H2C2_2 11 gekp.yeCplCdkaFkt 26
                ge++ + Cp C+ +Fkt
  EPA06428.1 20 GESIsWFCPTCNLKFKT 36
                7777789********97 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.5    0.0036         5      15      20 ..       6      11 ..       4      13 .. 0.91
   2 ?    7.5   0.2    0.0025       3.5      12      21 ..      22      31 ..      18      32 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0036
  Rubredoxin_2 15 GrCpsC 20
                  G+Cp C
    EPA06428.1  6 GQCPKC 11
                  9***** PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0025
  Rubredoxin_2 12 kwfGrCpsCg 21
                  +  + Cp C+
    EPA06428.1 22 SISWFCPTCN 31
                  67899****7 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.2    0.0087        12       3       8 ..       6      11 ..       4      13 .. 0.82
   2 ?    6.7   0.1     0.005       6.9      18      25 ..      23      30 ..      20      32 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0087
  PhnA_Zn_Ribbon  3 pkCplC 8 
                    ++Cp+C
      EPA06428.1  6 GQCPKC 11
                    799999 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.005
  PhnA_Zn_Ribbon 18 allvCpeC 25
                      + Cp+C
      EPA06428.1 23 ISWFCPTC 30
                    57899999 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.4     0.016        23      21      29 ..       4      13 ..       1      18 [. 0.72
   2 ?    8.6   0.1    0.0016       2.2      17      31 ..      19      34 ..      14      34 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.016
  zinc_ribbon_9 21 dv.lCPhCgg 29
                   ++  CP C g
     EPA06428.1  4 EIgQCPKCFG 13
                   3346****87 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0016
  zinc_ribbon_9 17 dedsdv.lCPhCgggF 31
                     +s++ +CP C+  F
     EPA06428.1 19 QGESISwFCPTCNLKF 34
                   56677789****9877 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1     0.095   1.3e+02       4       8 ..       7      11 ..       6      16 .. 0.87
   2 ?    8.2   0.2    0.0013       1.8       2      13 ..      24      35 ..      24      37 .] 0.83

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.095
      zf_UBZ  4 lCerC 8 
                +C++C
  EPA06428.1  7 QCPKC 11
                6**** PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0013
      zf_UBZ  2 tylCerCgkeip 13
                +++C+ C+ ++ 
  EPA06428.1 24 SWFCPTCNLKFK 35
                59******8886 PP

>> zf_C2H2_10  C2H2 type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.3    0.0015         2       5       9 ..       8      12 ..       6      15 .. 0.86
   2 ?    4.1   0.3     0.025        34       4      10 ..      26      32 ..      24      34 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0015
  zf_C2H2_10  5 CPKCq 9 
                CPKC+
  EPA06428.1  8 CPKCF 12
                ****8 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.025
  zf_C2H2_10  4 sCPKCqe 10
                 CP C+ 
  EPA06428.1 26 FCPTCNL 32
                5****95 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.055        76       2       7 ..       7      12 ..       6      21 .. 0.66
   2 ?    8.3   0.5    0.0025       3.5       3      12 ..      27      36 ..      25      37 .] 0.90

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.055
                EETTTT CS
     zf-C2H2  2 kCpdCg 7 
                +Cp+C 
  EPA06428.1  7 QCPKCF 12
                466664 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0025
                ETTTTEEESS CS
     zf-C2H2  3 CpdCgksFkr 12
                Cp C+ +Fk+
  EPA06428.1 27 CPTCNLKFKT 36
                ********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.33u 0.28s 00:00:00.61 Elapsed: 00:00:00.42
# Mc/sec: 262.11
//
Query:       EPA06429.1  [L=125]
Description: hypothetical protein BG20_I0462 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 898.98
//
Query:       EPA06430.1  [L=310]
Description: putative oligopeptide ABC transporter, ATP-binding protein OppD [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.7e-26   91.9   0.0    6.5e-26   91.5   0.0    1.2  1  ABC_tran   ABC transporter
    1.4e-17   64.0   0.1    2.3e-17   63.2   0.1    1.4  1  oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal reg
    5.4e-06   26.4   0.5      3e-05   24.0   0.1    2.1  2  AAA_21     AAA domain, putative AbiEii toxin, Type IV TA syst
     0.0044   16.5   0.6     0.0084   15.6   0.6    1.6  1  SMC_N      RecF/RecN/SMC N terminal domain
  ------ inclusion threshold ------
      0.089   12.5   0.0       0.13   12.0   0.0    1.3  1  PRK        Phosphoribulokinase / Uridine kinase family
       0.18   11.6   0.1       0.37   10.5   0.1    1.5  1  AAA_29     P-loop containing region of AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.5   0.0   2.2e-29   6.5e-26       2     136 ..      23     175 ..      22     176 .. 0.92

  Alignments for each domain:
  == domain 1  score: 91.5 bits;  conditional E-value: 2.2e-29
                 EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--..SEEEEEETTCEGGG.....B-HHHCCHCEEEE-SS..--S-TTSBHHHH............ CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxx..xxxxxxxxxxxx............ RF
    ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkp..teGeilldgkdlke.....qeleslrkeigvlpqe..pqlfpeltvren............ 79 
                 ++v+++lk ge ++i Ge+ +GKStL   ++++l    ++G++ +dg+++ +      ++e+  k+i++++q   ++l+p  t++e+            
  EPA06430.1  23 DDVNFDLKSGESLGIAGESACGKSTLGLSIMRMLLGgkAKGDVIFDGDSILDlsesvFTEEFRWKKISMIFQGamNSLDPVFTIKEQfieilkqhgydk 121
                 89************************9999988876679*************999998999999*********999*******************9887 PP

                 HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  80 esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                 ++d+ i++a+++++l++    v+k+ p++LSgG+kqrv++a+all +pk++++DEpt
  EPA06430.1 122 NYDDVITDAMHSVSLDD---VVLKKYPHELSGGMKQRVVIAMALLLRPKFVIADEPT 175
                 77777888888888777...8888889*****************************9 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.2   0.1   7.8e-21   2.3e-17       1      65 []     226     288 ..     226     288 .. 0.98

  Alignments for each domain:
  == domain 1  score: 63.2 bits;  conditional E-value: 7.8e-21
   oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerldeGCpFapRCpfaleeC 65 
                 vE g+s ++ ++p+HPYT++Ll+s+prl       + ikg++psl + ++ C+F++RCp+a e+C
  EPA06430.1 226 VEFGSSYDIYKNPKHPYTQGLLESIPRLSGDAP--KYIKGTPPSLLDPPTQCRFIDRCPHAIEKC 288
                 8***************************88888..99**************************** PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1      0.16   4.8e+02       4      31 ..      37      58 ..      35      84 .. 0.62
   2 !   24.0   0.1     1e-08     3e-05     174     302 ..      82     210 ..      73     211 .. 0.66

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.16
      AAA_21  4 liGpNgsGKSnLLdaldllarldrdveg 31
                + G  ++GKS+L   +      +r++ g
  EPA06430.1 37 IAGESACGKSTLGLSI------MRMLLG 58
                88999******96555......333333 PP

  == domain 2  score: 24.0 bits;  conditional E-value: 1e-08
      AAA_21 174 dyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrer..........gvvflengdgqelparelSdGtkrllalltallralkkgslll 262
                 ++f ++k+  ++q+ ++sl++v+   +   e  +++   ++ ++            +vv+ ++       ++elS G+k+   ++ all ++   ++++
  EPA06430.1  82 EEFRWKKISMIFQGAMNSLDPVFTIKEQFIEILKQHGYDKNYDDVItdamhsvsldDVVLKKY-------PHELSGGMKQRVVIAMALLLRP---KFVI 170
                 555555555555555555555554444444444443333333333354333333333333333.......5678******966666666666...89** PP

      AAA_21 263 iDEpEngLHPkllrrllellkelsrngaQviltTHSplll 302
                  DEp + L+  +++ ++ llk+l++ g  ++l TH+  +l
  EPA06430.1 171 ADEPTTALDVLIQAQIINLLKKLKKDGMSIMLITHDLAVL 210
                 ************************************9887 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.6   2.8e-06    0.0084     135     213 ..     122     221 ..      19     227 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.8e-06
                 T........................CS-HHHHH..HHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-S CS
                 x........................xxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx RF
       SMC_N 135 e........................lLSgGekt..LvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemlekad 206
                 +                        +LSgG k+  ++a+aLl      +p  +++ De   aLD    +++ +llk+ +k+ + ++ i+++  +l++  
  EPA06430.1 122 NyddvitdamhsvslddvvlkkyphELSGGMKQrvVIAMALL-----LRP-KFVIADEPTTALDVLIQAQIINLLKKLKKDgMSIMLITHDLAVLSEIA 214
                 24444444444444444444455559****776115555555.....344.599**********************9999889999******9999998 PP

                 CEEEEEE CS
                 xxxxxxx RF
       SMC_N 207 klvgvtk 213
                   +g++ 
  EPA06430.1 215 DKIGIMY 221
                 8888865 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.3e-05      0.13       3      41 ..      36      75 ..      34     126 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.3e-05
         PRK  3 gvagsSGaGkttvarklekifgrekvkaaei.egdsflrl 41
                g+ag+S++Gk+t+   +  ++ + k k  +i +gds+l l
  EPA06430.1 36 GIAGESACGKSTLGLSIMRMLLGGKAKGDVIfDGDSILDL 75
                9************999887766555554433466666554 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00013      0.37      13      49 ..      23      59 ..      18      64 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00013
      AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiqalLvpa 49
                d+  ++++  ++  ++G+s  GKSTl  +i+ +L++ 
  EPA06430.1 23 DDVNFDLKSGESLGIAGESACGKSTLGLSIMRMLLGG 59
                55667777555889***********976777666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1884.65
//
Query:       EPA06431.1  [L=149]
Description: hypothetical protein BG20_I0466 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.036   14.3   0.4       0.14   12.4   0.4    1.9  1  RNA_pol_Rbc25  RNA polymerase III subunit Rpc25
      0.042   14.0   0.0       0.12   12.5   0.0    1.8  2  Gal4_dimer     Gal4-like dimerisation domain


Domain annotation for each model (and alignments):
>> RNA_pol_Rbc25  RNA polymerase III subunit Rpc25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.4   1.5e-05      0.14      18      73 ..       6      60 ..       2     140 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.5e-05
                   CEEEEBTTBSEEEEECCCCSTTEEEECCCTCEEEEESSSEEEEE-TTSEEEEEEEE CS
  RNA_pol_Rbc25 18 gikvslgffddifvpkelLfepsefdeeeqawvweveeeeelyldvgeeirfrvee 73
                    ikv  +ff++  + +++L e+ +f++ ++a++ ++ ++++  +  g +i  r+e 
     EPA06431.1  6 EIKVGDEFFSTCSISEKELEEYFKFSRVKNAFLEDM-QKTKQKIVSGRAILSRMEG 60
                   589999******************************.6666666666666666654 PP

>> Gal4_dimer  Gal4-like dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.4e-05      0.12       2      45 ..      52      97 ..      51     104 .. 0.90
   2 ?   -2.1   0.1      0.49   4.4e+03      25      32 ..     110     117 ..      98     121 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.4e-05
  Gal4_dimer  2 RAhLTeVEsRvtqLEqlL..rrllpeeDiDnlLknkhnnflkeilt 45
                RA L  +E   t+L q+   + +++  D D + +n++  fl ++ t
  EPA06431.1 52 RAILSRMEGEFTRLSQIYgnHIIFVGTDGDSEWENRSSRFLNPLYT 97
                999**************966779******************99986 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.49
  Gal4_dimer  25 eeDiDnlL 32 
                 +eDiD + 
  EPA06431.1 110 KEDIDDEF 117
                 48999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1038.48
//
Query:       EPA06432.1  [L=82]
Description: hypothetical protein BG20_I0496 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.33s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 489.28
//
Query:       EPA06433.1  [L=76]
Description: hypothetical protein BG20_I0476 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       278  (0.0155056); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.44
# Mc/sec: 518.43
//
Query:       EPA06434.1  [L=363]
Description: putative membrane protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   9.6e-101  337.1  21.9   1.1e-100  336.9  21.9    1.0  1  Sbt_1           Na+-dependent bicarbonate transporter superfa
  ------ inclusion threshold ------
      0.048   14.0   6.3       0.44   10.9   2.4    2.6  2  DUF1772         Domain of unknown function (DUF1772)
      0.061   12.3   0.4       0.24   10.3   0.0    2.2  2  SHR3_chaperone  ER membrane protein SH3


Domain annotation for each model (and alignments):
>> Sbt_1  Na+-dependent bicarbonate transporter superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  336.9  21.9  1.9e-104  1.1e-100       1     306 [.      14     341 ..      14     343 .. 0.98

  Alignments for each domain:
  == domain 1  score: 336.9 bits;  conditional E-value: 1.9e-104
       Sbt_1   1 PvvlffilGllaallksdLeiPealykllslyLLlaiGlkGGvelaeselsaelllallaavvlgllipllaflilrkltkldkvdaaaiAalYGsvSa 99 
                 Pvvlff+lG++aa +ksdL++P+a++++l +yLL aiGl+GG e++++++ a++l+++l+a+ l+l+++l ++ ilr+l k++ +d+ a+A++YG+v a
  EPA06434.1  14 PVVLFFLLGIVAARIKSDLKMPDAISEFLPIYLLAAIGLHGGLEMRNTGF-ANMLIPMLTAIGLSLIFTLNHYQILRRLGKFNIFDSYALASTYGAVGA 111
                 99************************************************.************************************************ PP

       Sbt_1 100 vtfaaalavlesqgiayegymvallalmeipaivvalllakllkkkkkkese.......................lkevlkeallnksvvlLlggliiG 175
                 vtf ++l++l++qg++ egy++a+la++e  + ++a++l++l+ +k+ k+++                       l+evl+e++++k++++Llg+++iG
  EPA06434.1 112 VTFSVGLSFLKNQGLTSEGYLTAVLAVLEPVSFILAIFLTNLAVSKQLKSKKqslpndydndekilgmmgqsktkLSEVLRESITGKAIIILLGSIVIG 210
                 *****************************************9999988777689********************************************* PP

       Sbt_1 176 lltgekgleklepffedlFkgvLalfLLemGlvaarrlkelrkvglflilfailaplvnallgillakllglsaGgavllavLaaSaSyIavPaalrla 274
                 +++g++g+++++ +f+dlF+g++a+fLLemG++a++rl++++kvg+fl++f+il+p +n+++g+++a++lgls Gg+v++  L+aSaS+Ia+Pa+lr+a
  EPA06434.1 211 YAIGDNGFNSISIVFDDLFTGAIAIFLLEMGIIAGQRLDDIKKVGVFLVIFSILIPTFNGIIGVFIATALGLSLGGSVMFGLLMASASFIAAPAVLRHA 309
                 *************************************************************************************************** PP

       Sbt_1 275 iPeAnpslyltaslgitfpfniligiPlYlal 306
                 iP+A+psly+t++lgitfp+ni+i +P+ +++
  EPA06434.1 310 IPQAKPSLYITSALGITFPYNIIILLPIMFSI 341
                 ***************************98876 PP

>> DUF1772  Domain of unknown function (DUF1772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1    0.0075        45      36      96 ..     103     163 ..      60     212 .. 0.57
   2 ?   10.9   2.4   7.4e-05      0.44      35      90 ..     285     339 ..     255     349 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0075
     DUF1772  36 kavfpplallsalafayla........araasrgarllylaaaallllsivpyTllvmvPtNnkLaalk 96 
                 ++++++++++        +        +++  ++   l++++a+l  +s ++  +l +  + ++L+++k
  EPA06434.1 103 ASTYGAVGAV--------TfsvglsflKNQGLTSEGYLTAVLAVLEPVSFILAIFLTNLAVSKQLKSKK 163
                 2223333333........133444433555555555555444444335566666666666667777763 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 7.4e-05
     DUF1772  35 g.kavfpplallsalafa.ylaaraasrgarllylaaaallllsivpyTllvmvPtNn 90 
                 g +++f++l++ ++  +a ++ ++a  ++++ ly++ +al +  ++py +++  P+ +
  EPA06434.1 285 GgSVMFGLLMASASFIAApAVLRHAIPQAKPSLYIT-SALGI--TFPYNIIILLPIMF 339
                 449999*99999999999777799999999999955.66656..6********99865 PP

>> SHR3_chaperone  ER membrane protein SH3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1      0.21   1.2e+03      10      30 ..      11      33 ..       3      34 .. 0.68
   2 ?   10.3   0.0   4.1e-05      0.24       7      68 ..     135     196 ..     131     237 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.21
  SHR3_chaperone 10 iigst..sFflGvlfanfpyDyn 30
                    i++++  +F+lG++ a +  D++
      EPA06434.1 11 ILTPVvlFFLLGIVAARIKSDLK 33
                    55554226899999998888865 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 4.1e-05
  SHR3_chaperone   7 taliigstsFflGvlfanfpyDynlLwssesteeafdaalehykflhaspplikrilhivig 68 
                        ++ ++sF+l+++ +n+++  +l  +++s ++ +d+ ++ + ++ +s   ++ +l   i+
      EPA06434.1 135 VLAVLEPVSFILAIFLTNLAVSKQLKSKKQSLPNDYDNDEKILGMMGQSKTKLSEVLRESIT 196
                     567999*********************************************99999976554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.54
# Mc/sec: 2033.01
//
Query:       EPA06435.1  [L=126]
Description: hypothetical protein BG20_I0491 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.022   14.9   0.1      0.032   14.4   0.1    1.3  1  EF1_GNE   EF-1 guanine nucleotide exchange domain
       0.14   11.6   0.0       0.17   11.3   0.0    1.1  1  DUF1454   Protein of unknown function (DUF1454)


Domain annotation for each model (and alignments):
>> EF1_GNE  EF-1 guanine nucleotide exchange domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   3.5e-06     0.032      29      61 ..      75     106 ..      58     121 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.5e-06
                 TSEE--.--EEE-SSS-EEEEEEEEESSS-GGG CS
     EF1_GNE  29 glvwgeasklepiafGlkkLqiscvieddkvst 61 
                 + vw+e  k++ i fG+kk+++ + i+ +kv  
  EPA06435.1  75 EFVWEERKKVQTISFGIKKVRVWISID-KKVIR 106
                 479*******************99995.44433 PP

>> DUF1454  Protein of unknown function (DUF1454)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   1.9e-05      0.17     132     188 ..      41      98 ..      36     100 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.9e-05
     DUF1454 132 fePtlskeqsqkkleellskgkkkryysqneGalRyvvadsge.kgltFAvEPikLaL 188
                 ++P l+++++q++ ++++ k + ++++ ++ G + +v  +  + +++ F +  +++++
  EPA06435.1  41 LKPLLNAKHTQHQFSHIAIKTDLEEFFDESLGEIEFVWEERKKvQTISFGIKKVRVWI 98 
                 79**********************************9987654378889998887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.29s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 902.57
//
Query:       EPA06436.1  [L=590]
Description: ATP-dependent DNA ligase domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.7e-61  206.3   0.5    8.1e-61  205.2   0.5    1.6  1  DNA_ligase_A_M  ATP dependent DNA ligase domain
    1.9e-36  126.0   3.0    2.1e-36  125.9   1.6    1.8  2  DNA_ligase_A_N  DNA ligase N terminus
    4.6e-22   78.5   0.0    1.2e-21   77.2   0.0    1.7  1  DNA_ligase_A_C  ATP dependent DNA ligase C terminal region
    2.2e-07   31.3   0.3    4.1e-07   30.5   0.3    1.5  1  RNA_ligase      RNA ligase


Domain annotation for each model (and alignments):
>> DNA_ligase_A_M  ATP dependent DNA ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.2   0.5   1.8e-64   8.1e-61       1     204 []     229     427 ..     229     427 .. 0.99

  Alignments for each domain:
  == domain 1  score: 205.2 bits;  conditional E-value: 1.8e-64
                     -EEEEEESCHHHHHHHTTTSEEEEEEEESSEEEEEEEETTEEEEEETTS-B-GGGCHHHHHHHHHHBSTTESEEEEEEEEEEEETTTTCBEHHHH CS
  DNA_ligase_A_M   1 pmLAeslksiekalkkleekafivEiKyDGeRaqvhkegdkvklfSRrlkditaakpelvkalkeafkkdeksvilDGElvavdketgeilpfqk 95 
                     pmLA ++ks e+a++kl +++f +E+K+DGeR+q+h egdkv lfSR+l++it+++p++v+++ +a++++  +vil++E+va+++++ge+lpfq+
      EPA06436.1 229 PMLADRVKSEEEAIEKL-GAQFAAEYKLDGERVQLHIEGDKVVLFSRSLENITSYYPDIVEKIPKAIQAN--KVILEAEAVAINENSGEFLPFQE 320
                     9***************9.999***********************************************98..8********************** PP

                     HCHHHHCHCCTHHHHHHSEEEEEEEEEEEETTEEHTTSCHHHHHHHHHHHB--BTTTEEE--EEEESSHHHHHHHHHHHHHTTECEEEEEETT-C CS
  DNA_ligase_A_M  96 lasrkkkkkkveeklkeaelclfvFDiLyldgesltdeplkeRrklLeeilkesedrvelaeslevkdveeleelleeaiseglEGlvvKnpdsk 190
                     l++r ++k+++e+++ ++++ + +FD+Ly+dg+s ++ p+keRr+lLe+i+ ++++  + + ++ +++ e++ee+le++i++g+EG+++K+ d +
      EPA06436.1 321 LMHR-RRKYQIEKAVLQYPITVNFFDVLYYDGKSCLEFPYKERRELLEKIV-KEDEYAKHVPMTIINNQEDIEEFLENSINSGCEGVMLKMLDKP 413
                     ****.99********************************************.999999************************************* PP

                     C-TTCEEEEEEEEE CS
  DNA_ligase_A_M 191 YepgkrsknwlKvK 204
                     Y++g+r++ wlK+K
      EPA06436.1 414 YQAGSRGSYWLKLK 427
                     ************99 PP

>> DNA_ligase_A_N  DNA ligase N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.9   1.6   4.6e-40   2.1e-36       1     173 []       2     178 ..       2     178 .. 0.94
   2 ?   -2.6   0.0       1.3   5.9e+03      77      98 ..     189     210 ..     184     221 .. 0.76

  Alignments for each domain:
  == domain 1  score: 125.9 bits;  conditional E-value: 4.6e-40
                     BCHHHHHHHHHHCC.---HHHHHHHHHHHHHTS-..SHHHHHHHHHH....SS-CCCS------HHHHHHHHHHHHT--..HHHHHHHHHHHS-H CS
  DNA_ligase_A_N   1 pFaelaelfekieestkkrlekrailanffrkvesagpedlypalrL....llPdydgreygigesllakalaealgls..kkkikdalakvgDl 89 
                     +F+ l+e+f+k+e+ t+krle +++l ++f+k+   +++ +  +++L    l Pd++g e+g+ e+l ++a+a+ +g +  +kki+d+++k gDl
      EPA06436.1   2 EFSILSEAFSKMES-TTKRLELTQHLVELFEKT---PQDVISRIVYLlqgkLRPDFEGVELGVAEKLAIRAIAKSAGSDnaEKKIEDEYRKSGDL 92 
                     5999**********.899************775...46679999999******************************7743559*********** PP

                     HHHHHHHHCCHHHH.------BHHHHHHHHHHHHH-.STTHHHHHHHHHHHHHHHS-HHHHHHHHHHHCT---SS--HHHHHHHHH CS
  DNA_ligase_A_N  90 gevaeevlskrstl.akkspltieevnelLdklaaa.gkgsedekkkilkkllkraspeEakyliriilkdlriglsektvldala 173
                     g +a+++l+++ ++ +  +++t+e v+e L  +a+  g++++d+k+k +++ll+ a+peE k++ +i+l+ lr+g++e+tv+dala
      EPA06436.1  93 GHAASKILEQKEQTtFMVQDITVERVYENLVTIAKLeGNKTQDRKMKYISGLLNDANPEESKFILKILLGTLRLGIAENTVMDALA 178
                     ********8777777*******************9999**********************************************97 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.3
                     HHHHHHHHHHS-HHHHHHHHHC CS
  DNA_ligase_A_N  77 kkikdalakvgDlgevaeevls 98 
                     k +++a++   Dlg+vae +  
      EPA06436.1 189 KALEHAYNVSSDLGKVAETIAI 210
                     4577778888999999998765 PP

>> DNA_ligase_A_C  ATP dependent DNA ligase C terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.2   0.0   2.6e-25   1.2e-21       1      96 [.     452     559 ..     452     562 .. 0.87

  Alignments for each domain:
  == domain 1  score: 77.2 bits;  conditional E-value: 2.6e-25
                     GGGSEEEEEEEEEE..TTEEEEEEEE-SS--HHHHHHHHHHHG.GGEECTTCESS---HHHHTTEEE-TT-EEEEEESEEECTSSSTT....... CS
  DNA_ligase_A_C   1 rgglvgslllgvyd..dgkleyvgkvgtGfsdaeleelrkklk.elerkkppfaekvpeeekrdvWvePelvveVkfaeitasgkyka....... 85 
                     r+g++g+lll+ yd  ++++++++kvgtGf+d++l++l++ l+ ++  kk+p     + e ++dvW+ePelv+e+ ++eit s+ +ka       
      EPA06436.1 452 RTGKYGTLLLASYDydRDMFTSICKVGTGFTDDDLDQLYQILSdKVTIKKNPR---IDSEMEADVWFEPELVIEIVASEITLSPIHKAarneirk 543
                     6899**********98888***********************87666666666...333333459****************************** PP

                     ....EECT-EEE.EE- CS
  DNA_ligase_A_C  86 ....slRfPrfk.rlR 96 
                         +lRfP f+ ++R
      EPA06436.1 544 dtglALRFPKFTgKIR 559
                     **********985666 PP

>> RNA_ligase  RNA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.3   9.1e-11   4.1e-07       3     161 .]     249     427 ..     247     427 .. 0.68

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 9.1e-11
                 EEEEEE-SSEEEEEEEE..TTEEEEETTCEB.CTTTHHHHHHTHHHHHHHHHHHHH..ECCEEEEEEEES................SS...TTSS.... CS
  RNA_ligase   3 vvvtEKlDGtnfriylv..kevgvasRsqil.pfgeekfkefkrwaaalrkklkeklaneelilyGElig...............hsi.kygglpk... 79 
                 + ++ KlDG++++++++  k v ++sRs +  +           ++ +  +k+++ ++ +++il  E +                h   ky+   +   
  EPA06436.1 249 FAAEYKLDGERVQLHIEgdK-VVLFSRSLENiT----------SYYPDIVEKIPKAIQANKVILEAEAVAinensgeflpfqelmHRRrKYQI--Ekav 334
                 77899***********9644.*******99953..........34444456778888866899999999866544433333333322144433..0346 PP

                 .....EEEEEEEEEEECTTBECE--HHHHHHHHHCCT.......B..EEEEE.SSHHHHHCCC.HHHHTC--EEEEEESSSSBE.TTE.BSEEEEE CS
  RNA_ligase  80 .....efyvFdifdirdkeeqrylspdevealakglg.......tvpvlyegkflaaeellelllskgnkrEGlVikpeselyk.nkg.raifKvk 161
                          Fd++  +  ++    +++e+++l++++        +vp+    + ++ ee+le   s ++ +EG+ +k  ++ y+  ++ ++++K+k
  EPA06436.1 335 lqypiTVNFFDVLYYD-GKSCLEFPYKERRELLEKIVkedeyakHVPMTIINNQEDIEEFLEN--SINSGCEGVMLKMLDKPYQaGSRgSYWLKLK 427
                 6665566669999887.4589999999996666645345667789999943333333344443..44669**************98889*****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (590 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 4339.32
//
Query:       EPA06437.1  [L=608]
Description: KH domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-12   45.9   0.0    6.6e-12   45.1   0.0    1.4  1  T2SSE            Type II/IV secretion system protein
    2.1e-07   30.7   2.6    3.1e-07   30.1   0.4    2.4  2  KH_2             KH domain
    2.6e-07   30.4   0.3      2e-06   27.5   0.1    2.5  2  KH_1             KH domain
      5e-05   23.7   0.0    0.00013   22.4   0.0    1.6  1  AAA_16           AAA ATPase domain
    6.9e-05   22.9   0.0    0.00061   19.8   0.0    2.5  3  AAA_14           AAA domain
    8.9e-05   22.1   0.0    0.00018   21.2   0.0    1.4  1  AAA_25           AAA domain
    9.1e-05   22.5   1.1    0.00069   19.6   0.2    2.8  2  KH_5             NusA-like KH domain
    0.00016   22.3   0.0      0.002   18.7   0.0    2.8  3  AAA_18           AAA domain
    0.00027   20.7   0.0    0.00055   19.7   0.0    1.4  1  IstB_IS21        IstB-like ATP binding protein
     0.0006   20.1   0.2      0.003   17.9   0.2    2.2  1  PIN_4            PIN domain
    0.00091   19.5   0.1      0.026   14.8   0.0    2.9  3  AAA_22           AAA domain
     0.0031   17.3   0.1       0.01   15.7   0.1    1.8  1  KH_4             KH domain
     0.0042   17.6   0.0      0.019   15.5   0.0    2.1  1  ABC_tran         ABC transporter
     0.0072   16.7   0.1      0.094   13.1   0.0    2.6  2  AAA              ATPase family associated with various cellul
     0.0074   15.3   0.0      0.025   13.6   0.0    1.8  2  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
  ------ inclusion threshold ------
      0.011   16.0   0.0      0.023   15.0   0.0    1.6  1  AAA_28           AAA domain
      0.013   15.4   0.0      0.062   13.2   0.0    2.2  1  NTPase_1         NTPase
      0.018   14.8   0.1      0.057   13.2   0.1    1.8  1  AAA_29           P-loop containing region of AAA domain
       0.02   14.9   0.0      0.049   13.6   0.0    1.7  1  AAA_5            AAA domain (dynein-related subfamily)
      0.024   14.8   0.0      0.076   13.2   0.0    1.8  1  AAA_33           AAA domain
      0.038   13.9   0.0       0.13   12.2   0.0    1.9  1  NACHT            NACHT domain
      0.042   13.6   0.0       0.13   12.0   0.0    1.7  2  AAA_30           AAA domain
      0.053   13.9   0.0       0.14   12.5   0.0    1.8  1  RNA_helicase     RNA helicase
      0.075   12.3   0.0       0.17   11.1   0.0    1.5  1  Zeta_toxin       Zeta toxin
      0.087   13.0   0.1       0.28   11.4   0.0    1.8  1  Flt3_lig         flt3 ligand
      0.098   13.0   0.3       0.63   10.4   0.3    2.5  1  PIN_9            PIN like domain
       0.11   12.2   0.1       0.23   11.2   0.1    1.5  1  ATP_bind_1       Conserved hypothetical ATP binding protein
       0.13   11.7   0.0       0.34   10.3   0.0    1.6  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
       0.15   11.8   0.0       0.33   10.6   0.0    1.6  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
       0.16   12.4   1.0       0.53   10.7   0.1    2.4  2  AAA_17           AAA domain


Domain annotation for each model (and alignments):
>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.1   0.0   1.1e-14   6.6e-12      74     243 ..     213     375 ..     148     394 .. 0.76

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 1.1e-14
       T2SSE  74 p....ekgvrlrvvllPvvagealviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderivtvEDpvE 168
                       + +r+ + ++P +++ +++i  +   +ltldd+ ++e+l ++   +  +a      i++sG+ gsGK+tl+ +l  +  ++ + + t E p+ 
  EPA06437.1 213 AsvvqYNDYRIAITHPPFSEAFEITIV-HPIVKLTLDDYDISEELMKR---FSDRA----EGIIISGPPGSGKSTLASSLADFYYHKGKIVKTFESPRD 303
                 03345799************9999997.566788*****999876555...55566....6799**************999999999777789****** PP

       T2SSE 169 iql.eganq.vqlnakkakvtfadllraaLRlrPDrimvGEiRdketlei.lkAvnTGHlgslsTlHansaagalerL 243
                 +q+  g+ q ++l     +  f +    +L  rPD  +  E+R +e ++       TG    ++ +Hans+ +a++r 
  EPA06437.1 304 LQVnPGITQyTKL-----DGSFDNSADILLLVRPDYTIFDEVRRREDFRTfADLRLTGVGM-VGVVHANSPLDAIQRF 375
                 **93333330333.....34577777778999****************9977788899777.9*************96 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.4   5.1e-10   3.1e-07       8      63 ..     474     525 ..     467     529 .. 0.84
   2 ?   -2.3   0.1       6.7     4e+03      40      65 ..     573     598 ..     570     606 .. 0.53

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 5.1e-10
                 HHTECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHT CS
        KH_2   8 veikkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdiekleg 63 
                 +   +  + kveI  ++nr+++++ ++ ++ +IGkgGsni++i+k l+  i+++e+
  EPA06437.1 474 K---FDPAVKVEI-LSENRARVMVNKNSMASIIGKGGSNINEIEKLLKIHIDVVEK 525
                 4...566778999.4589*****************************999988886 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 6.7
                 HTGGGHHHHHHHHHHHHHHHHHHTTC CS
        KH_2  40 IGkgGsnikkigkelrkdieklegkk 65 
                 +Gk+G+ +   ++e+ + i kl  ++
  EPA06437.1 573 VGKKGEIMIPKRSEASRSIVKLASSQ 598
                 68888744333444444444565555 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       2.4   1.4e+03      21      53 ..      64      93 ..      63     103 .. 0.74
   2 !   27.5   0.1   3.4e-09     2e-06       3      38 ..     490     526 ..     488     544 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 2.4
                HHHHHHHHHT-EEEEESSTT...T.-EEEEEES CS
        KH_1 21 nIkeIreetgakIkvpksedegsderevtisGs 53
                ++k++ ++ g  I +  ++ +  +++ +++ Gs
  EPA06437.1 64 KLKDLADKFGLVISIK-GSHP--TSEDIRMAGS 93
                6899999889999987.5554..7777777654 PP

  == domain 2  score: 27.5 bits;  conditional E-value: 3.4e-09
                 EEEEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEES.S CS
        KH_1   3 rilvPsslvgriIGkgGsnIkeIreetgakIkvpk.s 38 
                 r+ v+++ + +iIGkgGsnI+eI++  + +I+v++  
  EPA06437.1 490 RVMVNKNSMASIIGKGGSNINEIEKLLKIHIDVVEkT 526
                 899**********************66*****99423 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   2.1e-07   0.00013      20     129 ..     260     378 ..     251     387 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 2.1e-07
      AAA_16  20 rsgrpelvllsGesGvGKsslvrellralekdggif.lrgkcdqlesa...ipysalaqalareellrqllde.....aesaeleawrekleealaavp 109
                  s+r e +++sG++G+GKs+l+ +l++ +  +g i+ + +  ++l+ +   + y  l   ++++  +  l ++     +e + +e++r++ + +l+ v+
  EPA06437.1 260 FSDRAEGIIISGPPGSGKSTLASSLADFYYHKGKIVkTFESPRDLQVNpgiTQYTKLDGSFDNSADILLLVRPdytifDEVRRREDFRTFADLRLTGVG 358
                 4567799*******************8777665444455555555444444555445555555555555555566666666778888888888888888 PP

      AAA_16 110 elagaeasrllellkrllal 129
                  +   +a++ l++++r++ +
  EPA06437.1 359 MVGVVHANSPLDAIQRFIGK 378
                 88888889999999999854 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       5.8   3.5e+03      69     116 ..      40      95 ..      28     102 .. 0.66
   2 ?   -1.3   0.0       3.4     2e+03      31     109 ..     107     186 ..      90     197 .. 0.63
   3 !   19.8   0.0     1e-06   0.00061       5      82 ..     267     349 ..     263     357 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 5.8
      AAA_14  69 flDEiqev...........pewekalkslvdegknldvivtGSnskllskeiatslagr 116
                 +lDE q              e+ k lk+l d+   l + + GS+    s++i+   +gr
  EPA06437.1  40 VLDELQSQasqkkehgfigLEVIKKLKDLADKF-GLVISIKGSHPT--SEDIRMAGSGR 95 
                 566666665666666655556667777777777.777777888764..33555555555 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 3.4
      AAA_14  31 esilyinldderdkkladpekllelileklke..ekktylflDEiqevpewekalkslvdegknldvivtGSnskllskei 109
                 ++ + ++ d+ +   ++  e l++++ + l++  + + + f+D   ++ ++++ +  + ++gk + +++t  +  llske 
  EPA06437.1 107 NQAILYTSDNVQHLVAQ-AEGLESIFVKPLSKniDLEFLKFFDSETMSVHLKENMSPMAKKGKPGSFVLTKLSDELLSKEY 186
                 34444444444444333.233555555553333555677788888888888888888888888888888877777777765 PP

  == domain 3  score: 19.8 bits;  conditional E-value: 1e-06
      AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkla....dpekllelileklke.....ekktylflDEiqevpeweka 82 
                 ++i+G+  +GK+tl+  l++ ++  ++  +  +++++rd + +    +++kl+  + ++  +      +  y ++DE+ + ++++++
  EPA06437.1 267 IIISGPPGSGKSTLASSLADFYY--HKGKIVKTFESPRDLQVNpgitQYTKLDGSFDNS--AdilllVRPDYTIFDEVRRREDFRTF 349
                 79*****************9999..67777779******76553322333444444444..0345566789**********999987 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0     3e-07   0.00018      23     157 ..     254     397 ..     251     409 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 3e-07
      AAA_25  23 rwlvkgllpagelallaGapgtGKttlaldlalava.tGkpwlg......pvapeqgkVlyvsaEdsedelrrRlravgeal....rddarllvldlag 110
                 + l+k++  + e +++ G+pg+GK+tla++la  +  +Gk   +      ++++ +g + y  +++s d+ +  l  v+ ++    + ++r+++ +   
  EPA06437.1 254 EELMKRFSDRAEGIIISGPPGSGKSTLASSLADFYYhKGK-IVKtfesprDLQVNPGITQYTKLDGSFDNSADILLLVRPDYtifdEVRRREDFRTF-- 349
                 56899999999************************96555.44557788878889999999999999999999999999888877644555555554.. PP

      AAA_25 111 veslpLfakdrggtl.ltadvdaleaaieevegvrlv..viDplsralgg 157
                   +l+L+  +  g + +++ +da+++ i ++e ++ +  viD++ ++ +g
  EPA06437.1 350 -ADLRLTGVGMVGVVhANSPLDAIQRFIGKIE-LGIIpnVIDTVVFVKDG 397
                 .3578887777777777888888888888876.66666688888777665 PP

>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1       1.9   1.1e+03      29      58 ..      95     124 ..      86     124 .. 0.85
   2 !   19.6   0.2   1.2e-06   0.00069       2      49 ..     486     527 ..     485     534 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.9
        KH_5  29 rikavsseLkgekidvvewseDlaefiana 58 
                 ri a++++ ++ +  +   s++++ ++a+a
  EPA06437.1  95 RIDAIIKDVAKQNQAILYTSDNVQHLVAQA 124
                 999******999999999999999999876 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 1.2e-06
        KH_5   2 GertkvaVkshnpnvdpvGaivgkkGsrikavsseLkgekidvvewse 49 
                 ++r+ v+V ++      +++i+gk+Gs+i+++++ L +  idvve+++
  EPA06437.1 486 ENRARVMVNKNS-----MASIIGKGGSNINEIEKLL-KIHIDVVEKTS 527
                 68999*******.....*******************.9******9875 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       4.1   2.4e+03      18      88 ..     103     183 ..      60     198 .. 0.59
   2 ?   -1.6   0.0       6.4   3.8e+03     104     114 ..     254     264 ..     225     266 .. 0.83
   3 !   18.7   0.0   3.3e-06     0.002       1      20 [.     267     286 ..     267     350 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 4.1
      AAA_18  18 Lskrl.gf...gvnlrdvakenglllevdpealdeskrldedkldklldaleenss........aleegknlvidghlaeles 88 
                 ++k + ++   ++n+++++++ + l++ + +  + sk +d ++l+   ++ +            + +++++ v+  +  el+s
  EPA06437.1 103 VAKQNqAIlytSDNVQHLVAQAEGLESIFVK--PLSKNIDLEFLKFFDSETMSVHLkenmspmaKKGKPGSFVLTKLSDELLS 183
                 4444433355555666666555555555555..34444433333332222222222233334445566666666666555555 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 6.4
      AAA_18 104 eelleRlekRg 114
                 eel++R+++R 
  EPA06437.1 254 EELMKRFSDRA 264
                 89*****9997 PP

  == domain 3  score: 18.7 bits;  conditional E-value: 3.3e-06
      AAA_18   1 IlltGtpGvGKttlakeLsk 20 
                 I+++G+pG+GK+tla  L++
  EPA06437.1 267 IIISGPPGSGKSTLASSLAD 286
                 9****************976 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   9.2e-07   0.00055      39      86 ..     256     304 ..     243     343 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 9.2e-07
   IstB_IS21  39 atlsfiekkenivllGpsGvGKshlaialgveavraglsvl.fvrvedL 86 
                     f +++e+i++ Gp+G GKs la +l+    ++g+ v  f + +dL
  EPA06437.1 256 LMKRFSDRAEGIIISGPPGSGKSTLASSLADFYYHKGKIVKtFESPRDL 304
                 556899************************9988888877524444555 PP

>> PIN_4  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.2     5e-06     0.003       1     126 [.       8     128 ..       8     131 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 5e-06
       PIN_4   1 fVlDTnvlLhdpealksf....keehdvviPitVleELdklKkgsserelarlarqanrlldellekesgrlkvqtsaeelpeeeseseknDnrIlava 95 
                 +V DT+++++   ++ ++     ++ +++iP+ Vl+EL+++ ++++  e +    ++++ l++l  k    + ++ s+   ++          rI a+ 
  EPA06437.1   8 IVSDTSIIINGQ-LVAQIesgnIKNSEIIIPQAVLDELQSQASQKK--EHGFIGLEVIKKLKDLADKFGLVISIKGSHPTSEDIR---MAGSGRIDAII 100
                 6899**999887.66666677778999************9999999..6666666788888888888888888888877666632...24555666666 PP

       PIN_4  96 lelkeekpdrkvvLvskDinlrikAkalgie 126
                   +++++   + +L + D    + A+a+g+e
  EPA06437.1 101 KDVAKQN---QAILYTSDNVQHLVAQAEGLE 128
                 6666655...678999999999999988886 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0       1.2     7e+02      95     126 ..      39      77 ..      11      87 .. 0.71
   2 ?   -1.1   0.0       3.6   2.1e+03      87     112 ..     104     130 ..      93     147 .. 0.68
   3 !   14.8   0.0   4.3e-05     0.026       6      29 ..     265     288 ..     259     327 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1.2
      AAA_22  95 liiDEaqh.lr.s.......eealeeLrsllnlsrkgvqli 126
                  ++DE q   + +        e++++L++l++  ++g+ + 
  EPA06437.1  39 AVLDELQSqASqKkehgfigLEVIKKLKDLAD--KFGLVIS 77 
                 57888888443514567777899999999998..7777665 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 3.6
      AAA_22  87 raravielliiDEaqhlr.seealeeL 112
                  ++    l   D++qhl  ++e le +
  EPA06437.1 104 AKQNQAILYTSDNVQHLVaQAEGLESI 130
                 333334788889999996666666655 PP

  == domain 3  score: 14.8 bits;  conditional E-value: 4.3e-05
      AAA_22   6 gilvvtGesGtGKTtllrrlleql 29 
                   +++ G++G+GK+tl+  l++ +
  EPA06437.1 265 EGIIISGPPGSGKSTLASSLADFY 288
                 5689****************9987 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   1.7e-05      0.01       2      60 ..     466     518 ..     463     527 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.7e-05
        KH_4   2 elvedilkalvddpeevevteeeeeeeveielnvegedlGrvIGkrGrtldAlqylvsa 60 
                 + ++d++k++  dp +v+v++    +e++ ++ v+++ ++ +IGk G +++ +  l+++
  EPA06437.1 466 DKIRDYFKKF--DP-AVKVEIL---SENRARVMVNKNSMASIIGKGGSNINEIEKLLKI 518
                 6788888886..34.7888886...5678999999***************988877765 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   3.2e-05     0.019      12      42 ..     265     294 ..     261     340 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.2e-05
                 SEEEEEESTTSSHHHHHHHHTTSS--SEEEE CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  12 ekvaivGenGaGKStLlkllagllkpteGei 42 
                 e + i G+ G+GKStL++ la  +   +G+i
  EPA06437.1 265 EGIIISGPPGSGKSTLASSLADFYY-HKGKI 294
                 567899****************997.68888 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1       1.5     9e+02      26      62 ..      75     111 ..      38     149 .. 0.75
   2 !   13.1   0.0   0.00016     0.094       1      20 [.     267     286 ..     267     302 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.5
                 EEEEETTTCS.SSSTTHHHHHHHHHHHHHHHTSTSEEE CS
         AAA  26 fleisgsell.skyvgesekkirelfkeakekakpsil 62 
                 +++i+gs  + +++  +++ +i +++k++ +++ + il
  EPA06437.1  75 VISIKGSHPTsEDIRMAGSGRIDAIIKDVAKQN-QAIL 111
                 688888888866688899999999999966665.4555 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00016
                 EEEESSTTSSHHHHHHHHHH CS
         AAA   1 vllyGppGtGKTllakavak 20 
                 ++++GppG GK++la+++a 
  EPA06437.1 267 IIISGPPGSGKSTLASSLAD 286
                 5799*************996 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   4.1e-05     0.025      15      60 ..     253     295 ..     240     299 .. 0.82
   2 ?   -2.0   0.0       2.3   1.4e+03     213     252 ..     455     495 ..     390     508 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.1e-05
                 HHHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--E CS
        MeaB  15 akellerllakaGraqvvGltGvPGaGkstlvealglelrrrGkrv 60 
                 ++el++r    + ra+ + + G PG+Gkstl + l+  + ++Gk v
  EPA06437.1 253 SEELMKRF---SDRAEGIIISGPPGSGKSTLASSLADFYYHKGKIV 295
                 45555554...468999********************999999876 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.3
                 CCTBSHHHHH.HHHHHHHHHHHHTTHHHHHHHHHHHHHHHH CS
        MeaB 213 vegeGidelv.daieehrevlkktGllekrrrerakeelre 252
                 +++ Gi++l+ d+i+++++  + + ++e   ++ra  ++ +
  EPA06437.1 455 TQKVGIEKLAeDKIRDYFKKFDPAVKVEILSENRARVMVNK 495
                 34568888873578888888887777666666666555555 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   3.8e-05     0.023       2      21 ..     267     286 ..     266     304 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.8e-05
      AAA_28   2 ivitGgestGKTtlleaLaa 21 
                 i+i+G++++GK+tl++ La+
  EPA06437.1 267 IIISGPPGSGKSTLASSLAD 286
                 89****************96 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0    0.0001     0.062       2      33 ..     267     298 ..     266     306 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.0001
                 EEEE--TTSSHHHHHHHHHHHH...GGGEEEE CS
    NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgGf 33 
                 ++i+GppG+GK+Tl + +++   ++g  v+ f
  EPA06437.1 267 IIISGPPGSGKSTLASSLADFYYHKGKIVKTF 298
                 89****************99999998888766 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   9.5e-05     0.057      22      38 ..     265     280 ..     255     286 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.5e-05
      AAA_29  22 kgatlltGpsGsGKSTl 38 
                 +  ++++Gp GsGKSTl
  EPA06437.1 265 E-GIIISGPPGSGKSTL 280
                 3.499***********9 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   8.3e-05     0.049       2      24 ..     267     291 ..     266     342 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.3e-05
                 EEEE--SSSSHHHHHHHGGGGB..S CS
       AAA_5   2 vlLvGppGtgKselaerlaaal..n 24 
                 +++ GppG+gKs+la +la ++  +
  EPA06437.1 267 IIISGPPGSGKSTLASSLADFYyhK 291
                 7999***************988541 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00013     0.076       2      20 ..     267     285 ..     267     291 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00013
      AAA_33   2 vllvGlpGsGKstlaerll 20 
                 +++ G+pGsGKstla +l+
  EPA06437.1 267 IIISGPPGSGKSTLASSLA 285
                 6789***********9987 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00021      0.13       3      22 ..     267     286 ..     265     296 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00021
                 EEEEC-TTTCHHHHHHHHHH CS
       NACHT   3 vilqGeaGsGKTtLlqklal 22 
                 +i+ G++GsGK+tL+ +la+
  EPA06437.1 267 IIISGPPGSGKSTLASSLAD 286
                 79***************986 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       5.4   3.2e+03      99     128 ..      90     119 ..      88     131 .. 0.84
   2 ?   12.0   0.0   0.00022      0.13      20      49 ..     266     295 ..     254     301 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 5.4
      AAA_30  99 mvdtkqlaallkaaekagakvilvGDerQl 128
                 m+++  ++a++k ++k++  ++   D+ Q+
  EPA06437.1  90 MAGSGRIDAIIKDVAKQNQAILYTSDNVQH 119
                 888889999999999999999999998886 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00022
      AAA_30  20 vavltGpAGtGKttalkalreaweaaggrv 49 
                   ++ Gp+G+GK+t+ ++l++ + ++g+ v
  EPA06437.1 266 GIIISGPPGSGKSTLASSLADFYYHKGKIV 295
                 5799*****************999998655 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00024      0.14       1      20 [.     267     286 ..     267     304 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00024
  RNA_helicase   1 iwlyGpsgeGKStlakeLak 20 
                   i+++Gp+g GKStla +La+
    EPA06437.1 267 IIISGPPGSGKSTLASSLAD 286
                   789**************886 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00029      0.17      15      47 ..     263     295 ..     249     297 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00029
  Zeta_toxin  15 rPklillgGqpGAGKselaellkdelerqgnvv 47 
                 r   i+++G pG+GKs+la+ l+d   ++g++v
  EPA06437.1 263 RAEGIIISGPPGSGKSTLASSLADFYYHKGKIV 295
                 555699**************9998766666665 PP

>> Flt3_lig  flt3 ligand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00047      0.28       8     113 ..     450     557 ..     446     571 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00047
    Flt3_lig   8 Piss.tfaskikelsdyllkdyPvtvasnlqddelCkalWhlvlakrtlerlktvaGsklqellekvnteidfvekCafqplpsClrfvqtn.iselle 104
                 P+s  t ++ i++l++  ++dy  +    ++ + l ++  ++++ k+ +  +    Gs+++e  + ++++id vek +   + s l f+  +  + ll 
  EPA06437.1 450 PVSKrTQKVGIEKLAEDKIRDYFKKFDPAVKVEILSENRARVMVNKNSMASIIGKGGSNINEIEKLLKIHIDVVEKTSHSDPSSPLSFTFSEsKTALLL 548
                 665414567799**************************************************9999************999999999975441455666 PP

    Flt3_lig 105 dvssqleal 113
                 +v ++ +++
  EPA06437.1 549 NVGREYSSM 557
                 666666655 PP

>> PIN_9  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.3    0.0011      0.63      25      62 ..      29      65 ..       8     132 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0011
       PIN_9 25 llgsvelvvpkavleELerlakagkgkertaakvalsL 62
                + ++ e+++p+avl+EL++ a+++k++     +v ++L
  EPA06437.1 29 I-KNSEIIIPQAVLDELQSQASQKKEHGFIGLEVIKKL 65
                4.789*************99888877766666665554 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00039      0.23       1      26 [.     269     294 ..     269     298 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00039
  ATP_bind_1   1 vvGpaGsGKttfvgalseilelrgrs 26 
                 + Gp+GsGK+t+ ++l++++  +g+ 
  EPA06437.1 269 ISGPPGSGKSTLASSLADFYYHKGKI 294
                 67****************99888765 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00056      0.34      25      43 ..     267     285 ..     264     291 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00056
  Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                   +++ GppGsGK+ la+ l+
    EPA06437.1 267 IIISGPPGSGKSTLASSLA 285
                   7899***********9986 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00056      0.33       1      23 [.     267     290 ..     267     342 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00056
  Viral_helicase1   1 ivvhGvpGcGKStlirkllrts.l 23 
                      i+++G pG+GKStl  +l++   +
       EPA06437.1 267 IIISGPPGSGKSTLASSLADFYyH 290
                      699************999988543 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00088      0.53       2      19 ..     271     288 ..     270     297 .. 0.87
   2 ?   -2.4   0.1       9.6   5.7e+03      40      73 ..     466     499 ..     456     522 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00088
                 E-TTSSHHHHHHHHHHHH CS
      AAA_17   2 GgPGsGKgtqceklveky 19 
                 G+PGsGK+t+++ l++ y
  EPA06437.1 271 GPPGSGKSTLASSLADFY 288
                 9***********999866 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 9.6
                 HSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSE CS
      AAA_17  40 akardemrklpleekkelqkeaaekiaeeakkkg 73 
                 +k rd+++k +  +k e++ e  ++++ +++++ 
  EPA06437.1 466 DKIRDYFKKFDPAVKVEILSENRARVMVNKNSMA 499
                 4567888888888888887777777776655444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (608 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                       109  (0.00607954); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 0.71u 0.32s 00:00:01.03 Elapsed: 00:00:00.48
# Mc/sec: 3833.11
//
Query:       EPA06438.1  [L=85]
Description: hypothetical protein BG20_I0467 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.13   11.5   0.1       0.14   11.4   0.1    1.1  1  M157      MHC class I-like protein M157


Domain annotation for each model (and alignments):
>> M157  MHC class I-like protein M157
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1     8e-06      0.14     112     157 ..      22      67 ..      10      76 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8e-06
                 -HHHHT-S-THHHHHSHHHHHHHHHHHHHHTGGGSSGGGEEE---- CS
        M157 112 llddanarglrellerveeirerWretvlklkklaklsrvevefwy 157
                   ++ +a++lr  + + +ei+er ++t+++ +++a  s ve+e++ 
  EPA06438.1  22 VKNQREAFALRDQIFHDQEIKERIHSTIKQSQQIAANSPVEMEVII 67 
                 55666778888888889*************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       837  (0.0466841); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 626.12
//
Query:       EPA06439.1  [L=43]
Description: hypothetical protein BG20_I0497 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (43 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      198  (0.0110436); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.48
# Mc/sec: 269.36
//
Query:       EPA06440.1  [L=46]
Description: hypothetical protein BG20_I0458, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.44
# Mc/sec: 314.01
//
Query:       EPA06441.1  [L=186]
Description: putative 3-methyladenine DNA glycosylase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-62  210.4   0.0    1.4e-62  210.2   0.0    1.0  1  Pur_DNA_glyco  Methylpurine-DNA glycosylase (MPG)


Domain annotation for each model (and alignments):
>> Pur_DNA_glyco  Methylpurine-DNA glycosylase (MPG)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.2   0.0   7.9e-67   1.4e-62       2     171 ..       8     183 ..       7     186 .] 0.97

  Alignments for each domain:
  == domain 1  score: 210.2 bits;  conditional E-value: 7.9e-67
  Pur_DNA_glyco   2 ffdrdalevAkeLLGkvlvreleegkvagrivEtEAYlgeeDpAshayrgrternavmFgppgtlYvYliygihhclnvvteeeg.easaVLiRal 96 
                    f+++d+++vAk++LGk lvr++++++++g+i+EtEAY  ++DpAsha+r+ tern+vmFg+ g++YvY++yg+h+c+nvv+++++  a+aVLiRa+
     EPA06441.1   8 FYSQDTVTVAKSILGKKLVRKIDNKEISGIIIETEAYRHKDDPASHAFRKITERNKVMFGEVGRAYVYFTYGMHYCFNVVARNSKfAAGAVLIRAI 103
                    9********************************************************************************876625789****** PP

  Pur_DNA_glyco  97 evveglelmrarrg......lanGPgkLcqaLgidkelngadlleseelvlekeeaeeeeivagpRiGiskaaelpwRfyi 171
                    ++ +g+++m+++rg      l++GP+kL+qa+gi+ke++g dl+++++l+++ +  ++ +i+a+pR+Gi++a++++w f i
     EPA06441.1 104 QPEKGIDIMEKNRGvndkkrLTDGPAKLTQAFGITKEQYGIDLTQDSKLFIT-DGIKTGKIIASPRVGIKEATDKLWNFKI 183
                    ****************************************************.79************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1336.49
//
Query:       EPA06442.1  [L=594]
Description: oxidoreductase, short chain dehydrogenase/reductase family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-39  136.0   0.1    2.9e-32  111.7   0.0    2.8  2  adh_short        short chain dehydrogenase
    1.3e-32  113.2   0.0    8.7e-24   84.4   0.0    3.5  4  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    5.1e-13   49.3   0.0    1.1e-09   38.5   0.0    2.4  2  KR               KR domain
      1e-06   28.4   0.1    3.9e-06   26.5   0.0    2.0  2  Epimerase        NAD dependent epimerase/dehydratase family
  ------ inclusion threshold ------
      0.011   14.9   0.1      0.023   13.9   0.1    1.5  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
      0.015   15.4   2.6       0.36   10.9   0.5    2.5  2  ApoLp-III        Apolipophorin-III precursor (apoLp-III)
      0.037   14.6   0.3       0.18   12.4   0.1    2.4  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.7   0.0   1.1e-35   2.9e-32       1     185 [.       7     203 ..       7     210 .. 0.88
   2 !   21.1   0.0   6.8e-08   0.00017      16     182 ..     377     556 ..     375     569 .. 0.75

  Alignments for each domain:
  == domain 1  score: 111.7 bits;  conditional E-value: 1.1e-35
                 SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT.......TSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEEE---S.S--S CS
   adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkee.......gakalaiqvDvtdreevealvekavkklgkldvLvnNAGi.tgsg 91 
                 kv+lvtG + GIG+aiak+++++Ga+v++++r++e+lee+   lke        +   ++  vDv+d++ +++++++ +k+  ++d ++nNAG+   ++
  EPA06442.1   7 KVALVTGSGTGIGQAIAKKFIENGASVIILGRRKEPLEETSVILKEIiakvnsgAFVRIFSGVDVSDEDGMNQMFDTLKKENITVDYVINNAGVsGPVT 105
                 89************************************9876666655435432233578899*******************************76778 PP

                 SGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGG......TSB-TTBHHHHHHHHHHHHHHHHHHHHHGGGTEEEEEEEESSBSS CS
   adh_short  92 pfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvag......kvpvagvaaYsAsKaavagltrslakelaptgirvnavaPGlvdT 184
                  fs+   ee++++i++ ltg+f+ + ++l+ m+  ++G+Iv++s   +      + p+   ++Y+A+ +a + l+++++ el +++i  ++ +PG+v +
  EPA06442.1 106 CFSNAALEEFKSTIDIHLTGTFWGSVQALRVMK--ENGKIVTISTFFTeerpleQRPYRFRSPYTAAQGAKNRLVEAMSWELTDKKIISIGTNPGPVHS 202
                 89*****************************98..9********98762222225688999***********************************998 PP

                 H CS
   adh_short 185 d 185
                 d
  EPA06442.1 203 D 203
                 6 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 6.8e-08
                 HHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT.TSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEEE---S.S--SSGGGCSHHHHHHHHHHHTHHH CS
   adh_short  16 iakelakeGakvvvvdrseekleevakelkee.gakalaiqvDvtdreevealvekavkklgkldvLvnNAGi.tgsgpfselseeewervievNltgv 112
                 +a++++k+G kv++  +se++     kel+e  ++k++   v++++ eev++ +++a  +lg++ ++++ +G   + ++  el  ++w++++e  +t +
  EPA06442.1 377 LAQHVIKNGGKVAC-FISESTP----KELQEYiSSKFHSHVVNIKNPEEVKKWLNTANTNLGNILAVIHITGKlPNISKLVELPRAKWQELVEKFITTP 470
                 79999999999966.5555555....6777777789************************************988889999****************** PP

                 HHHHHHHHHHHH..........HCTTEEEEEEEE...GGGTSB-TTBHHHHHHHHHHHHHHHHHHHHHGG...GTEEEEEEEESSB CS
   adh_short 113 flltravlpaml..........kqssGrIvnvsS...vagkvpvagvaaYsAsKaavagltrslakelap...tgirvnavaPGlv 182
                   +++ vl +++          k  +G+I  v+    v +kv   + a      +a++ +t ++ +el++   ++ir ++v PG v
  EPA06442.1 471 ATVAQGVLGQFVpggdkdprlyKDAKGAIMIVGPdlpVGAKVTGLQRAQVEVFRGALRPFTTTVNQELSDvlnSKIRLITVFPGSV 556
                 ********999877777777777777777777642213345555555555555666666666666665541113466666666655 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.4   0.0   3.4e-27   8.7e-24       4     176 ..      16     202 ..      12     220 .. 0.83
   2 !    5.1   0.0    0.0057        15     176     228 ..     276     330 ..     249     333 .. 0.82
   3 !   19.4   0.0   2.5e-07   0.00064       9     114 ..     376     478 ..     375     486 .. 0.83
   4 ?   -3.4   0.0       2.2   5.6e+03     204     218 ..     563     577 ..     555     579 .. 0.82

  Alignments for each domain:
  == domain 1  score: 84.4 bits;  conditional E-value: 3.4e-27
                   TSHHHHHHHHHHHTT-EEEEEESSGGHHHH....HHHHHHHTTSEE.....EE--TTSHHHHHHHHHHHHHHHSSEEEEEE-----EGCSS-GGGH- CS
  adh_short_C2   4 sgIGraiAkalaeeGaevvltdlneeakkr....veelaeelgaev.....lecDVtdeeqvealveevvekfgklDilvnnagiapklkgpflets 91 
                    gIG+aiAk++ e+Ga+v++  +++e  ++    ++e+ +++++ +       +DV+de+ +++++++++++  ++D+++nnag++ +  + f ++ 
    EPA06442.1  16 TGIGQAIAKKFIENGASVIILGRRKEPLEEtsviLKEIIAKVNSGAfvrifSGVDVSDEDGMNQMFDTLKKENITVDYVINNAGVSGP-VTCFSNAA 111
                   7**********************9999554022245555565544234667889**********************************.999***** PP

                   HHHHHHHHHHHTHHHHHHHHHHHHHCTSCCEEEEEEEG.GGTSBSTTTT.....HHHHHHHHHHHHHHHHHHHHGGGTEEEEEEEE--BHC CS
  adh_short_C2  92 reefdraldvnlyslfllakaalplmkeggsivnlssv.gaervvpnyn.....aygaaKaalealtrylAvelgpkgiRvNavspgpikT 176
                    eef+ ++d+ l+++f  + +al++mke+g+iv++s +   er +++        y+aa +a + l+ ++  el +k+i      pgp++ 
    EPA06442.1 112 LEEFKSTIDIHLTGTFWGSVQALRVMKENGKIVTISTFfTEERPLEQRPyrfrsPYTAAQGAKNRLVEAMSWELTDKKIISIGTNPGPVHS 202
                   ***********************************87625555555543335559*********************999877777777765 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0057
                   CTGGGGSTT.HHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGG.GTT--SEEEE CS
  adh_short_C2 176 Tlaasgikg.fdelleelearaplgrlgtpeevaeaalfLasde.asyitGqtlv 228
                   T++ ++i+  +++++++  +++  +++ ++ +vae +l L+ de a+  +G+++ 
    EPA06442.1 276 TNLLNKIQTiAEKVQKNTSHMIADQQFLSQGQVAESVLNLCDDEiARILNGKVIP 330
                   566667777678899999999999******************9835667887775 PP

  == domain 3  score: 19.4 bits;  conditional E-value: 2.5e-07
                   HHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEE..EE--TTSHHHHHHHHHHHHHHHSSEEEEEE-----EGCSS-GGGH-HHHHHHHHHHHT CS
  adh_short_C2   9 aiAkalaeeGaevvltdlneeakkrveelaeelgaev..lecDVtdeeqvealveevvekfgklDilvnnagiapklkgpfletsreefdraldvnl 103
                   ++A+++ ++G +v++   +       +el+e +++++    ++++++e+v+++ +++  ++g++  +++  g  p+  ++++e++r+++++ ++  +
    EPA06442.1 376 HLAQHVIKNGGKVACFISESTP----KELQEYISSKFhsHVVNIKNPEEVKKWLNTANTNLGNILAVIHITGKLPN-ISKLVELPRAKWQELVEKFI 467
                   6799999999999987555554....5555555566445889**********************************.99************999888 PP

                   HHHHHHHHHHH CS
  adh_short_C2 104 yslfllakaal 114
                   +  + +a+ +l
    EPA06442.1 468 TTPATVAQGVL 478
                   88888887766 PP

  == domain 4  score: -3.4 bits;  conditional E-value: 2.2
                   HHHHHHHHHHHCSGG CS
  adh_short_C2 204 peevaeaalfLasde 218
                    e +a+a  fL+sd 
    EPA06442.1 563 NERIAQALNFLVSDI 577
                   6889********995 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   0.0   4.2e-13   1.1e-09       3     115 ..       9     125 ..       8     129 .. 0.80
   2 !    8.3   0.0   0.00077         2      44     107 ..     396     461 ..     372     468 .. 0.74

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 4.2e-13
                 EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHT...T-EEEE--.--TT-HHHHHHHHHHHHHHSS---EEEE------.--- CS
          KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaeleal...gaevevva.aDvsdkdavealleeikaeeppikGvihaAgvlr.dkl 96 
                  l+tG   g+G+++a+  +e+ga+ ++l +R++++ e+ +  ++e+ a+   ga v++++ +Dvsd+d ++++++++k+e+ ++  vi+ Agv+   + 
  EPA06442.1   9 ALVTGSGTGIGQAIAKKFIENGASVIIL-GRRKEPLEETSVILKEIIAKvnsGAFVRIFSgVDVSDEDGMNQMFDTLKKENITVDYVINNAGVSGpVTC 106
                 59********************987665.666566666665666665543448999987648*******************************984567 PP

                 TTT--HHHHHHHHTTTTHH CS
          KR  97 leemtaedleqvlapKvkG 115
                 +++   e++++ +   ++G
  EPA06442.1 107 FSNAALEEFKSTIDIHLTG 125
                 7888888888776655555 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00077
                 HHHHHHHT.T-EEEE----TT-HHHHHHHHHHHHHHSS---EEEE------.---TTT--HHHHHH CS
          KR  44 liaeleal.gaevevvaaDvsdkdavealleeikaeeppikGvihaAgvlr.dklleemtaedleq 107
                 + +el+++   + +   + + ++++v+++l++++++ ++i  vih  g l   ++l e+  +++++
  EPA06442.1 396 TPKELQEYiSSKFHSHVVNIKNPEEVKKWLNTANTNLGNILAVIHITGKLPnISKLVELPRAKWQE 461
                 4566777657789999999***************************99875235566666666655 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   1.5e-09   3.9e-06       1     194 [.       9     218 ..       9     244 .. 0.73
   2 ?   -2.2   0.0      0.89   2.3e+03      13      62 ..     376     427 ..     375     442 .. 0.72

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 1.5e-09
                 EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC...............EEEE--TT-HHHHHHHHH....HH.T-SEEEE--S---HHH CS
   Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl...............elveldltdrsalerlfk....ee.qpdavihlAavggvaa 79 
                 +lVtG    iG+a++k++ e+g  vi l r+  +++ ++   +                +  +d+ d++ ++++f+    e+  +d+vi+ A+v+g+ +
  EPA06442.1   9 ALVTGSGTGIGQAIAKKFIENGASVIILGRR--KEPLEETSVIlkeiiakvnsgafvrIFSGVDVSDEDGMNQMFDtlkkENiTVDYVINNAGVSGPVT 105
                 59*****************************..33333333337899**********999*********6666664222144789********999988 PP

                 HHHSHH.....HHHHHHTHHH....HHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHHHHHHHT-EEEEEEE CS
   Epimerase  80 ssedpa.....dfieknlqgt....lnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklveayaaqyglnaiilrl 169
                  ++++a      +i+++l gt    ++ l +++++g  +++ +s+   +       +e  +++ p++ +spY aa  a  +lvea+  +  ++  i+ +
  EPA06442.1 106 CFSNAAleefkSTIDIHLTGTfwgsVQALRVMKENG--KIVTIST--FFT------EERPLEQRPYRFRSPYTAAQGAKNRLVEAMSWEL-TDKKIISI 193
                 777664222225666666654222245555555555..5999999..555......345577779*******************998887.45555555 PP

                 SEEESTTS-TTSTTSHHHHHHHHHH CS
   Epimerase 170 fnlyGprngegevsrvipalirkil 194
                  ++ Gp + ++  + v+p++++ +l
  EPA06442.1 194 GTNPGPVHSDRIYKTVYPKAAAEFL 218
                 5555777566667777777776665 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.89
                 HHHHHHHHCTSEEEEEES-STTTTCHHCHHC....EEEE--TT-HHHHHHHHHH CS
   Epimerase  13 alvkallekgyevigldrlssasntarledl....elveldltdrsalerlfke 62 
                 +l++++ ++g +v ++ ++s+ ++ ++   +    + + +++++++++++ +++
  EPA06442.1 376 HLAQHVIKNGGKVACFISESTPKELQEY--IsskfHSHVVNIKNPEEVKKWLNT 427
                 7888888999888888888555554433..244677888888888888887765 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   8.9e-06     0.023       2      80 ..      10      88 ..       9     109 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.9e-06
                     EEETTTSHHHHHHHHHHHHHB-SEEEEEES-HH..HHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-SE CS
  Polysacc_synt_2  2 lvtGagGsiGselvrqilkkkpkkiillerdEl..klyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvdv 80
                     lvtG+g  iG+++ ++++++ ++ iil  r+E   +   i ke+ +++++  + v+ +    dv d++ +++++++lk + 
       EPA06442.1 10 LVTGSGTGIGQAIAKKFIENGASVIILGRRKEPleETSVILKEIIAKVNSGAF-VR-IFSGVDVSDEDGMNQMFDTLKKEN 88
                     8********************99999999998522445566776666665433.33.445679********9998766443 PP

>> ApoLp-III  Apolipophorin-III precursor (apoLp-III)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.5   0.00014      0.36      32      82 ..     247     297 ..     232     318 .. 0.78
   2 ?    3.8   0.1     0.022        56      45     107 ..     408     474 ..     374     480 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00014
   ApoLp-III  32 enlvdqlkqvikslqeelkkksdeleealkevkkkieetadklseenPevk 82 
                 +++ d + + +++l +++ k  ++l+ +++++ +ki+ +a+k++++ + + 
  EPA06442.1 247 KTVKDGITKASQKLAPSIGKDAGKLATTITNLLNKIQTIAEKVQKNTSHMI 297
                 55667788899999999999999*******************999777664 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.022
   ApoLp-III  45 lqeelkk..ksdeleealkevkkkieetadklse..enPevkkkaqelqekvQsgvqslvkesqkla 107
                 + + + +  + +e+++ l+ +++++ ++ + +    + P++ k ++  ++k Q+ v++ ++  +++a
  EPA06442.1 408 FHSHVVNikNPEEVKKWLNTANTNLGNILAVIHItgKLPNISKLVELPRAKWQELVEKFITTPATVA 474
                 444444441334799999*********99998888899*******************9998776666 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1     7e-05      0.18       2      47 ..       8      51 ..       7      94 .. 0.76
   2 ?   -2.2   0.0       2.5   6.4e+03      33      42 ..     394     403 ..     374     433 .. 0.47

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7e-05
                   EEEE.TTSH.HHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC CS
  F420_oxidored  2 igii.GaGn.mgealasgllaagaqpheivvansrnpekaeelaeelg 47
                   ++++ G+G  +g+a+a++++++g    ++++   r +e +ee+   l+
     EPA06442.1  8 VALVtGSGTgIGQAIAKKFIENG---ASVIIL-GRRKEPLEETSVILK 51
                   67777777559************...999966.888888888776665 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.5
                    ESSCCCHHHH CS
  F420_oxidored  33 srnpekaeel 42 
                    +++p++++e 
     EPA06442.1 394 ESTPKELQEY 403
                    4444444332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (594 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       868  (0.0484132); expected 358.6 (0.02)
Passed bias filter:                      737  (0.0411066); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.71u 0.36s 00:00:01.06 Elapsed: 00:00:00.50
# Mc/sec: 3557.71
//
Query:       EPA06443.1  [L=210]
Description: SNARE-like domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-16   60.6   0.8      2e-16   60.6   0.8    1.9  2  SNARE_assoc    SNARE associated Golgi protein
     0.0014   18.5   2.3      0.042   13.7   0.4    2.1  2  DUF1418        Protein of unknown function (DUF1418)
  ------ inclusion threshold ------
      0.055   13.2   0.0       0.16   11.7   0.0    1.8  2  DUF697         Domain of unknown function (DUF697)
      0.055   13.7   0.6        7.9    6.8   0.0    2.3  2  Glycophorin_A  Glycophorin A


Domain annotation for each model (and alignments):
>> SNARE_assoc  SNARE associated Golgi protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.6   0.8   4.4e-20     2e-16       2     117 ..      34     147 ..      31     150 .. 0.85
   2 ?   -3.0   0.8       2.2   9.8e+03      18      30 ..     171     183 ..     166     189 .. 0.49

  Alignments for each domain:
  == domain 1  score: 60.6 bits;  conditional E-value: 4.4e-20
  SNARE_assoc   2 Psevll..vaaGvlfglllgtlvtslgallGaslayllgrylgrkalrrkllsekrvkalerlverygflallllrllpivPrdlvnyvaGltrvsfk 97 
                  P+ +ll  + +G  f+l + +l++++ a++++ + +++++  gr+++++k+  +kr++ +erlv+ryg+ a++++  +pi P+dl+ +++Gl+++++k
   EPA06443.1  34 PGFLLLasMSVGDEFNLHVLVLISAVTATVAKQIIFYASY-QGRRIMNEKT--RKRMRPFERLVKRYGAAAAFVAAATPI-PDDLIYVPLGLSKYNPK 127
                  555555568888889***********************84.4436666654..444555********************7.8**************** PP

  SNARE_assoc  98 rFflatfiGsipwalvyayl 117
                  rFf+at+ G+i+ + v++++
   EPA06443.1 128 RFFIATLSGKIVLSYVIVLI 147
                  ************99999886 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.2
  SNARE_assoc  18 lgtlvtslgallG 30 
                  +g++v ++ ++++
   EPA06443.1 171 IGIVVFAVMMTAA 183
                  4444444444443 PP

>> DUF1418  Protein of unknown function (DUF1418)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.5   0.1     0.007        32      16      86 ..      15      85 ..      12      91 .. 0.77
   2 !   13.7   0.4   9.3e-06     0.042       8      67 ..     126     190 ..     121     209 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.007
     DUF1418 16 vlGliLLvlayLsvndylsLPgplsskeaaivmif.lGvllllPaavalvwrvaqalapllrkrsPdkksrs 86
                +lGl LL   + s+  ++ LPg+l   +  +   f l vl+l+ a+ a v + +   a+   +r  ++k+r+
  EPA06443.1 15 YLGLALLNF-FGSLIPFIPLPGFLLLASMSVGDEFnLHVLVLISAVTATVAKQIIFYASYQGRRIMNEKTRK 85
                567776654.679999*******9999999998886789999999999998888777777766666666665 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 9.3e-06
     DUF1418   8 PrsvlilevlGliLLvlayLsvndy..lsLPgplsskeaaivmiflGvl...lllPaavalvwrv 67 
                 P+  +i+ + G i+L  +++ ++++  lsL +p  ++   +  i++G++   +++ aa++lv+r+
  EPA06443.1 126 PKRFFIATLSGKIVLSYVIVLISHSlgLSLIEPYLKDVHDMSTIYIGIVvfaVMMTAAIVLVLRL 190
                 8888899999988886555555554127899****************9733369********985 PP

>> DUF697  Domain of unknown function (DUF697)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   3.6e-05      0.16       8      43 ..      76     111 ..      69     117 .. 0.88
   2 ?   -2.2   0.0      0.66   2.9e+03     108     133 ..     132     157 ..     130     166 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.6e-05
      DUF697   8 elaeqelleqrdqeakkliekyawekAlvvavsPla 43 
                 +++ +e+ ++r +  ++l+++y +++A v+a++P++
  EPA06443.1  76 RRIMNEKTRKRMRPFERLVKRYGAAAAFVAAATPIP 111
                 67778899999999********************98 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.66
      DUF697 108 tklsaraaQGvvagllTarvGlsaie 133
                 + ls++++ + v  l++  +Gls+ie
  EPA06443.1 132 ATLSGKIVLSYVIVLISHSLGLSLIE 157
                 66888888888888899999999887 PP

>> Glycophorin_A  Glycophorin A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0    0.0018       7.9      54      91 ..      47      85 ..      40      92 .. 0.67
   2 ?    5.1   0.1    0.0059        26      52      71 ..     163     184 ..     158     194 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0018
                   SSS-TTHHHHHHHHHHHHHH.HHHHHHHHHHTHS.XXXXX CS
  Glycophorin_A 54 dFselvitliifgvmAgvig.tillisYlirRli.KKssv 91
                   +F   v+  +i +v A v   +i++ sY  rR++  K+  
     EPA06443.1 47 EFNLHVL-VLISAVTATVAKqIIFYASYQGRRIMnEKTRK 85
                   5655555.5578999999872567789**99965155555 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0059
                    SSSSS-TTHHHHHHHHH..HHH CS
  Glycophorin_A  52 vhdFselvitliifgvm..Agv 71 
                    vhd s   i  ++f+vm  A++
     EPA06443.1 163 VHDMSTIYIGIVVFAVMmtAAI 184
                    79**************933333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       967  (0.053935); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1515.29
//
Query:       EPA06444.1  [L=258]
Description: putative membrane protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-52  179.1  33.9    1.3e-52  178.8  33.9    1.0  1  TauE           Sulfite exporter TauE/SafE
  ------ inclusion threshold ------
       0.35   10.7   5.2      0.086   12.7   1.4    2.0  2  PMP22_Claudin  PMP-22/EMP/MP20/Claudin family


Domain annotation for each model (and alignments):
>> TauE  Sulfite exporter TauE/SafE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.8  33.9   1.4e-56   1.3e-52       2     236 .]       9     244 ..       8     244 .. 0.94

  Alignments for each domain:
  == domain 1  score: 178.8 bits;  conditional E-value: 1.4e-56
        TauE   2 llagllaGfvagllGiGggliavPlLlll.lppavavatsllavvatslsgalahrrrgnvdwrlllllllgsliGallGallllllpsellkllfgvl 99 
                 + +g++aG++++++G+Ggg+++vP+L+++ +pp +a+  sl+a++ +++++++++ r+++++++l+l l+l s++G++lGall++ + + ++k+lfg++
  EPA06444.1   9 IPLGFAAGVLGSMIGLGGGIVVVPVLTFFgFPPTLAASNSLFAAFSNAVGSTFSYSRQKRIEYSLGLKLGLLSIPGTILGALLSSDVTPGIFKILFGLV 107
                 789*************************769********************************************************9*********** PP

        TauE 100 llllallmllrkkrsrakgrerrptaillvligglvGllsGllGiGgGfllvpllllllglplkkavatslllilvislagalgyalagavdwplllll 198
                 l+ +a++++lrkk+++ +++ +++  i+++ + +++G++s+++GiGgG++ vpl+++  g+++kka+ ts ++ l+ sl+g++++ ++g+ d+  ++ll
  EPA06444.1 108 LISSAIYIFLRKKIETREKKLTKQMIIFAIGASFFAGIVSSFFGIGGGTIFVPLMVVGIGMTMKKAAPTSQFILLFASLSGIITHSILGHPDFIQAGLL 206
                 **********9998776655555555555555577**************************************************99************ PP

        TauE 199 lpgallGallGarlarrlsertlrrlfallllvlgvkl 236
                 ++ga++G+l+Garl+  ++er+l++l+ ++++++++kl
  EPA06444.1 207 AAGAFVGGLVGARLSLDIKERYLQILVSAIIIIAAIKL 244
                 ***********************************986 PP

>> PMP22_Claudin  PMP-22/EMP/MP20/Claudin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.4   9.6e-06     0.086     101     165 ..      91     157 ..      52     158 .. 0.81
   2 ?   -2.5   0.1      0.47   4.2e+03       3      20 ..     229     246 ..     227     253 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.6e-06
                    GTTTSSHHHHHHHHHHHHHH.HHHHHHHHHHH----SS-S.SSS-EE-TTHHHHHHHHHHHHHHHHH CS
  PMP22_Claudin 101 gerfklaGiiflvsgLcvlv.gasiYtsriaedlskslsk.kqkysfGysfilgwvafllallsGvl 165
                    ++++++ Gi+ ++ gL  +  ++ i+  ++ e  +k+l+k    +  G+sf+ g v+ ++ + +G +
     EPA06444.1  91 LSSDVTPGIFKILFGLVLISsAIYIFLRKKIETREKKLTKqMIIFAIGASFFAGIVSSFFGIGGGTI 157
                    5788999********98764255677777777777777666778899*************9999887 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.47
                    HHHHHHHHHHHHHHHHHH CS
  PMP22_Claudin   3 vlllgiivlaiaavillv 20 
                    +++l+  +++iaa+ l +
     EPA06444.1 229 LQILVSAIIIIAAIKLFF 246
                    555555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       948  (0.0528752); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 1740.16
//
Query:       EPA06445.1  [L=78]
Description: hypothetical protein BG20_I0464 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.29s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 530.10
//
Query:       EPA06446.1  [L=431]
Description: transporter, major facilitator family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    8.4e-34  117.0  35.3    8.4e-34  117.0  35.3    2.0  2  MFS_1       Major Facilitator Superfamily
    8.6e-31  107.3  32.5    4.2e-23   81.9  10.1    2.3  2  Sugar_tr    Sugar (and other) transporter
    0.00045   18.9  10.6    0.00045   18.9  10.6    2.3  2  MFS_2       MFS/sugar transport protein


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.0  35.3   1.4e-37   8.4e-34      22     349 ..      40     382 ..      16     386 .. 0.76
   2 ?    1.8   0.4     0.016        94     310     349 ..     377     416 ..     373     420 .. 0.85

  Alignments for each domain:
  == domain 1  score: 117.0 bits;  conditional E-value: 1.4e-37
       MFS_1  22 alaedlgispse.igllltl..yalga...avaslplGrlsdrfGrrrvlllglllfalg.lllllf...a.....sslwlllvlrvlqGlgagalfpa 105
                  +++ +  s++  +++l+t+  y+++     ++s+++G  +d+fGr++ +++++l+f+++ ++++l+   a     ++++ l+ +r++qG++ag+ + +
  EPA06446.1  40 SISQLFFPSEDHiFSILATFasYTVTLimrPLGSVIFGIYGDKFGRKKSMIITILGFSIAtFAVGLLptyAvvgvlAPIF-LISVRLIQGIFAGGEWGS 137
                 55555444444334554444333332244589999*************************55555544332445555555.****************** PP

       MFS_1 106 gaaliadwfpkeergraigllsagfslGailgpllggllasslg........Wravfyilaivsllafvlfllllpeepperkrkspkeeekgtgpapl 196
                 ga+l+ +  pk++rg+  g+l++gfs+G++l+++   +++ ++         Wr +f+   i +++a+    + l  ++++ + k+ ke   + +++pl
  EPA06446.1 138 GAVLTIESIPKQKRGLLSGFLQSGFSFGFLLAAISFQIITILFPgnlfeeigWRMLFFTGIIPGFVALF---VRLSMDESPLWVKKNKES--KLEKTPL 231
                 *****************************99998888777555558888888**************944...444444444444444444..4477777 PP

       MFS_1 197 vp.awkallkdpvlwillialllfffgfsg..lltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalgla 292
                 ++ ++++++++ +   ll+a++++++++++    + lp+yl +   +    +++l++  + + + i+++++g+ls+++gr++ +l+++++ +l+++ la
  EPA06446.1 232 RSiVLGKIHRKEF---LLCAAIMTGLVYMYhgSISVLPTYLGQFGSFE-KKEIALIMIYATASSWIGMIVTGWLSQKIGRKKSMLIFVSASILVSIPLA 326
                 7776788888883...6677777766666688********88888899.6777777777777777889******************************* PP

       MFS_1 293 llavtssavllllvlvl.iGfglgfvfpsllalasdlappeeagtasglfntagslgg 349
                  + +   +v +l+++v+ + f ++++++++ a+ s+ +p++ + +a+g+   ag + g
  EPA06446.1 327 TMILD--NVYGLIFYVIvFAFVVSTASGPIPAYFSERFPTQIRNSAAGFSYNAGLIFG 382
                 *****..55555544443899***************************9887766655 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.016
       MFS_1 310 iGfglgfvfpsllalasdlappeeagtasglfntagslgg 349
                 +G+ +g  +p+++ ++++ +p+ +   a+g++ ++gs+  
  EPA06446.1 377 AGLIFGSWSPLIALYLMSGVPKPMIPVALGINIIIGSIIL 416
                 5788999999999999999999999999999999998765 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.9  10.1     7e-27   4.2e-23       7     205 ..      21     225 ..      16     234 .. 0.84
   2 !   34.6  12.3   1.6e-12   9.8e-09     238     433 ..     227     415 ..     219     427 .. 0.81

  Alignments for each domain:
  == domain 1  score: 81.9 bits;  conditional E-value: 7e-27
                 HHH.HHHHHHHHCGGGTHHHHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTT..... CS
    Sugar_tr   7 lgg.llfgYdtgvigafltllkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgk..... 99 
                 + g  l gYd+ ++  ++ +++++++   ++  s        + ++  ++l+ + +Gs+++g+ gd+fGRkks++i+++ f+i+++  ++ + +     
  EPA06446.1  21 FLGwSLDGYDIVLMLLVIPSISQLFFPSEDHIFSIL-----ATFASYTVTLIMRPLGSVIFGIYGDKFGRKKSMIITILGFSIATFAVGLLPTYavvgv 114
                 445578889999988888888844444444433333.....357788889999***************************************8877766 PP

                 SS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-.....TTHHHHHHHCCHHHHHHHHHHGGGS-- CS
    Sugar_tr 100 nsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsn.....adgwrillglqlvpallllilllflPE 193
                  +   li  R++ Gi++G++ +   +++ E  pk++Rg l ++ q++ +fG+l+aai+  ++          + gwr+l++  ++p  + l+++l ++E
  EPA06446.1 115 LAPIFLISVRLIQGIFAGGEWGSGAVLTIESIPKQKRGLLSGFLQSGFSFGFLLAAISFQIITILFPgnlfeEIGWRMLFFTGIIPGFVALFVRLSMDE 213
                 666667777************************************************999995554448999*************************** PP

                 -HHHHHHTT-HH CS
    Sugar_tr 194 SPrylvekgkee 205
                 SP +  ++++ +
  EPA06446.1 214 SPLWVKKNKESK 225
                 ****87666544 PP

  == domain 2  score: 34.6 bits;  conditional E-value: 1.6e-12
                 ....HTTHHHHSH...HHHHHHHHHHHHHHTTHHHHHHHTTTHHHHSS-THH..HHHHHHHHHHHHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHH CS
    Sugar_tr 238 ekaswkellssktvrqrlligvvlqifqqltGinaimyysptifenlglsks..llvtiivgvvnfvatfvaiflvdrfGRRtllllGaagmaicfvil 334
                 ek+ +++++  k +r+ +l++++++ +  + ++ +i  +++++ +   ++k+  +l+ i   +  ++  +v  +l+ ++GR++ +l+ ++  +++ + l
  EPA06446.1 227 EKTPLRSIVLGKIHRKEFLLCAAIMTGLVYMYHGSISVLPTYLGQFGSFEKKeiALIMIYATASSWIGMIVTGWLSQKIGRKKSMLIFVSASILVSIPL 325
                 3667777777766899999999999999999999999999999888888888667777777788888888888*********99888777777777777 PP

                 H..HHHHTTSS...CHHHHHHHHHHHHHHHTTTTHHHHHHHHHHSHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHT-HHHHHHHHHHHHHHHHH CS
    Sugar_tr 335 givalllvakskaasivaivfialfialfalgwgpvpwvlvsElfpqsvRskalaiavavnwlanflisllfpiiteaigggyvflvfaglavlfiifv 433
                 +    ++ ++     +++i+ +++f+++ ++  gp+p  + sE fp+++R++a+ +++++  ++     l+  ++++ +   ++  v  g++++   ++
  EPA06446.1 326 A---TMILDN----VYGLIFYVIVFAFVVSTASGPIP-AYFSERFPTQIRNSAAGFSYNAGLIFGSWSPLIALYLMSGVP-KPMIPVALGINIIIGSII 415
                 5...777777....6999999999*99**********.6679**********************9999999999999999.555556666666554444 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   5.9     0.032   1.9e+02     265     327 ..      62     124 ..      49     135 .. 0.64
   2 !   18.9  10.6   7.6e-08   0.00045     131     330 ..     150     349 ..     136     359 .. 0.60

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.032
       MFS_2 265 llvvtisallgiplwqplakrlgkkntyllgalltivllvlvlllqpsnlllflvllviagfg 327
                 ++v+ i+  lg++++     ++g+k+++++ +l   + ++ v ll+++ ++ +l+  +++++ 
  EPA06446.1  62 YTVTLIMRPLGSVIFGIYGDKFGRKKSMIITILGFSIATFAVGLLPTYAVVGVLAPIFLISVR 124
                 344566666999999999999998876666555444444444444477777777776666654 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 7.6e-08
       MFS_2 131 eRtsltsvrsflsvlggvlaailafllvlilgglkserkgylifaliialLmll.gviivvlgtkervem.rkkekteqkeklslleqlkevfrnrafl 227
                  R  l+++ +    +g +laai   ++ + + g   e+ g++++  +++ ++ + ++++v l   e+     kk+k+ + ek++l+  +      + fl
  EPA06446.1 150 KRGLLSGFLQSGFSFGFLLAAISFQIITILFPGNLFEEIGWRML--FFTGIIPGfVALFVRLSMDES-PLwVKKNKESKLEKTPLRSIVLGKIHRKEFL 245
                 55555555555555555555555555555555545566666644..444444440344444555555.4457899999999999998776666666776 PP

       MFS_2 228 illllfllaalalgvlnglllYyltyvlg.ngsaasvfllvvtisallgiplwqplakrlgkkntyllg..alltivllvlvlllqpsnlllflvllvi 323
                 + +++    + ++    + l  yl  +   ++++++++++ +t+s+ +g+++  +l +++g+k+++l++  a++++++ + +++l   n++ +++ +++
  EPA06446.1 246 LCAAIMTGLVYMYHGSISVLPTYLGQFGSfEKKEIALIMIYATASSWIGMIVTGWLSQKIGRKKSMLIFvsASILVSIPLATMIL--DNVYGLIFYVIV 342
                 666665555555555555555566666666*******************************886655550044455555555555..444444444444 PP

       MFS_2 324 agfgvgv 330
                 + f v +
  EPA06446.1 343 FAFVVST 349
                 4433333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 3027.61
//
Query:       EPA06447.1  [L=115]
Description: hypothetical protein BG20_I0480 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 704.27
//
Query:       EPA06448.1  [L=358]
Description: hypothetical protein BG20_I0468 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0004   20.2   1.8     0.0075   16.1   1.8    2.6  1  Peptidase_M10  Matrixin
    0.00093   18.2   0.0     0.0018   17.3   0.0    1.4  1  Peptidase_M66  Peptidase M66
     0.0012   18.8   0.0     0.0024   17.8   0.0    1.5  1  Peptidase_M43  Pregnancy-associated plasma protein-A
     0.0012   18.5   0.3     0.0019   17.9   0.3    1.4  1  Reprolysin_4   Metallo-peptidase family M12B Reprolysin-like
     0.0016   19.0   0.4      0.005   17.4   0.0    2.1  2  Reprolysin_3   Metallo-peptidase family M12B Reprolysin-like
     0.0018   17.6   0.1     0.0031   16.8   0.1    1.3  1  DUF4953        Met-zincin
     0.0057   16.8   0.1      0.011   15.9   0.1    1.5  1  Reprolysin_5   Metallo-peptidase family M12
  ------ inclusion threshold ------
      0.014   15.4   0.0      0.023   14.7   0.0    1.4  1  Peptidase_M54  Peptidase family M54
      0.033   14.1   0.0      0.058   13.3   0.0    1.5  1  Reprolysin_2   Metallo-peptidase family M12B Reprolysin-like
      0.043   13.4   0.8      0.086   12.5   0.8    1.6  1  Astacin        Astacin (Peptidase family M12A)
      0.058   13.3   1.4       0.19   11.6   0.3    2.4  3  RuvB_C         RuvB C-terminal winged helix domain
       0.11   12.2   3.8       0.36   10.4   0.9    2.1  2  Peptidase_M57  Dual-action HEIGH metallo-peptidase
       0.17   12.0   0.0       0.41   10.8   0.0    1.6  1  Zincin_1       Zincin-like metallopeptidase


Domain annotation for each model (and alignments):
>> Peptidase_M10  Matrixin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   1.8   5.4e-06    0.0075     108     130 ..     173     195 ..      69     239 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.4e-06
                    EHHHHHHHHHHHHTTBESXSSTT CS
                    xxxxxxxxxxxxxxxxxxxxxxx RF
  Peptidase_M10 108 slflVaaHEiGHalGLeHssdkd 130
                    +l +  +HEiGHalGL H ++ d
     EPA06448.1 173 KLRTTITHEIGHALGLGHYQADD 195
                    5778899***********77544 PP

>> Peptidase_M66  Peptidase M66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.3e-06    0.0018     191     217 ..     173     199 ..     162     212 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.3e-06
  Peptidase_M66 191 tltgefiHEqGHalGLpHylageaask 217
                    +l  +  HE GHalGL+Hy a + + +
     EPA06448.1 173 KLRTTITHEIGHALGLGHYQADDVKVN 199
                    6778899***********999865554 PP

>> Peptidase_M43  Pregnancy-associated plasma protein-A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.7e-06    0.0024      49      91 ..     155     197 ..     142     233 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.7e-06
  Peptidase_M43  49 varvvfnGaylaadststnksstLthelGhfLgLihtfeggCe 91 
                       + +n  y  +   s++ ++t+the+Gh LgL h    + +
     EPA06448.1 155 AQYIYYNLCYGEDMLISEKLRTTITHEIGHALGLGHYQADDVK 197
                    4457899999999999********************8766654 PP

>> Reprolysin_4  Metallo-peptidase family M12B Reprolysin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.3   1.4e-06    0.0019     137     189 ..     176     231 ..      97     241 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.4e-06
  Reprolysin_4 137 difAHEiGHtfGaaHdlsdegeglsskt..eegsgqtIMsyaseasq..eafapisi 189
                    ++ HEiGH +G+ H  +d+ + ++ +     ++ ++IM+  s+ +     + pi i
    EPA06448.1 176 TTITHEIGHALGLGHYQADDVK-VNAAWakGGAEADSIMAVFSHENSklMKIKPIDI 231
                   459***************9999.55444226678899**976554431444455555 PP

>> Reprolysin_3  Metallo-peptidase family M12B Reprolysin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   3.6e-06     0.005      85     123 ..     147     190 ..      59     191 .. 0.71
   2 ?   -1.8   0.0       3.1   4.3e+03      21      54 ..     297     331 ..     276     338 .. 0.61

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.6e-06
  Reprolysin_3  85 gsvcnsskkagvnsgssvlgkvga.....dtvaHEiGHnfganH 123
                   + +c+ ++++ ++++  +  ++ +      t++HEiGH +g+ H
    EPA06448.1 147 VKICQTNDAQYIYYNLCYGEDMLIseklrTTITHEIGHALGLGH 190
                   67888888855555553333333366677*************** PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.1
  Reprolysin_3  21 irlqlv.aiiitdkasdpytkkdatealdelaevt 54 
                   i++ ++ +ii +++ s+ + +    ++++++a+++
    EPA06448.1 297 IEFLVKsEIIKVSSVSQTDDSDTIPTWVKNNAKWW 331
                   55555555555555554444444455566666655 PP

>> DUF4953  Met-zincin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   2.3e-06    0.0031       6      29 ..     167     190 ..     165     215 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.3e-06
     DUF4953   6 delmgallrfvvaHEvGhtLGLrh 29 
                 d l+ + lr  ++HE+Gh+LGL h
  EPA06448.1 167 DMLISEKLRTTITHEIGHALGLGH 190
                 67899*****************99 PP

>> Reprolysin_5  Metallo-peptidase family M12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   7.7e-06     0.011     117     191 ..     150     220 ..      60     224 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 7.7e-06
  Reprolysin_5 117 cnsgsagsvstrveks........nsvvvstatevqvvaHElGHnfGavHDcdsssesqsCslsnstepaggryiMapssspn 191
                   c+ ++a+                 +  ++ + +   +++HE+GH++G  H  +++  + + +   +  +a   +iMa  s  n
    EPA06448.1 150 CQTNDAQ--------YiyynlcygEDMLI-SEKLRTTITHEIGHALGLGHYQADDV-KVNAAW--AKGGAEADSIMAVFSHEN 220
                   3333333........24444444244444.7778899*************888764.222222..345677777887666655 PP

>> Peptidase_M54  Peptidase family M54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.6e-05     0.023     139     167 ..     168     196 ..     124     220 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.6e-05
                    HHHHHHHHHHHHHHHHHHTT----S-TST CS
  Peptidase_M54 139 eLflervvkevlhelGhlyGLshCkedCv 167
                     L  e+    ++he+Gh +GL+h + d v
     EPA06448.1 168 MLISEKLRTTITHEIGHALGLGHYQADDV 196
                    4556777889*************998544 PP

>> Reprolysin_2  Metallo-peptidase family M12B Reprolysin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   4.2e-05     0.058     115     177 ..     163     221 ..      92     252 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.2e-05
  Reprolysin_2 115 nsgsaveetkeidv.vaHEvGHaFGatHdndgssasegveenaatsvedaggkfiMapasksnn 177
                    +g+ +  +++    + HE+GHa G  H ++ +     v+ naa +   a+  +iMa  s+ n 
    EPA06448.1 163 CYGEDMLISEKLRTtITHEIGHALGLGHYQADD-----VKVNAAWAKGGAEADSIMAVFSHENS 221
                   377777665555444*************98844.....33333333345555555554433222 PP

>> Astacin  Astacin (Peptidase family M12A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.8   6.2e-05     0.086      81      98 ..     176     193 ..     119     260 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.2e-05
                 HHHHHHHHHHHTB--GGG CS
     Astacin  81 giivHElmHalGffHeqs 98 
                  +i+HE++HalG+ H q+
  EPA06448.1 176 TTITHEIGHALGLGHYQA 193
                 689************986 PP

>> RuvB_C  RuvB C-terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       5.5   7.5e+03      36      48 ..      34      46 ..      15      52 .. 0.75
   2 ?   11.6   0.3   0.00014      0.19       7      52 ..     229     269 ..     226     274 .. 0.84
   3 ?   -2.1   0.0       2.6   3.6e+03      36      56 ..     289     308 ..     287     310 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 5.5
                -HHHHHHTTHHHH CS
      RuvB_C 36 eketiedviEPyL 48
                +k+ ++  +EP+L
  EPA06448.1 34 SKNPLICTYEPVL 46
                4556666778776 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00014
                 HHHHHHHHHHHT.TT--B-HHHHHHHTT--HHHHHHTTHHHHHHTT CS
      RuvB_C   7 ldikyLkllkekfkggpvglktlaailgeeketiedviEPyLlkeg 52 
                 +di+ +k+++     +p g k++  +l+e+ ++ie++ EP ++++ 
  EPA06448.1 229 IDIEKIKSIY-----TPNGFKSIQDTLKEQPTEIETIPEPQIVQKT 269
                 6777777776.....699***********************99874 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 2.6
                 -HHHHHHTTHHHHHHTTSEEE CS
      RuvB_C  36 eketiedviEPyLlkeglIer 56 
                 + +t+ + iE +L+k++ I+ 
  EPA06448.1 289 DDQTFVNAIE-FLVKSEIIKV 308
                 6788999999.8999999975 PP

>> Peptidase_M57  Dual-action HEIGH metallo-peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.065        90      12      75 ..      78     139 ..      69     166 .. 0.69
   2 ?   10.4   0.9   0.00026      0.36     135     150 ..     176     191 ..     152     213 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.065
  Peptidase_M57  12 easremlqteeetkeqyrttnlvsssvkvikiivntgsafsstsklrtgLdlaianynalglsl 75 
                    ++ re+ ++ + + +   t   +  s+k+ ++ ++  s  + +s+  + L +   nyn+ +++l
     EPA06448.1  78 NEKRELRDNWRIDYRVL-TDKNI-DSKKECNVLIQFESMPQEKSEWYSVLGVTYSNYNNTDVKL 139
                    55566654444433333.44445.46788888888888889999***************98875 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00026
  Peptidase_M57 135 hvithelGhtvGlRhs 150
                      ithe+Gh++Gl h 
     EPA06448.1 176 TTITHEIGHALGLGHY 191
                    579**********995 PP

>> Zincin_1  Zincin-like metallopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00029      0.41      65      86 ..     166     188 ..     156     203 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00029
                 T--.HHHHHHHHHHHHHHHHHTT CS
    Zincin_1  65 ree.leeevretllHEighhfGl 86 
                 ++  + e+ r+t++HEigh +Gl
  EPA06448.1 166 EDMlISEKLRTTITHEIGHALGL 188
                 455478999************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2221.54
//
Query:       EPA06449.1  [L=68]
Description: hypothetical protein BG20_I0474 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-43  146.0   3.3    2.6e-43  145.8   3.3    1.0  1  NitrOD1   Nitrosopumilus output domain 1
  ------ inclusion threshold ------
      0.099   12.7   1.8        4.5    7.4   0.2    2.1  2  YolD      YolD-like protein


Domain annotation for each model (and alignments):
>> NitrOD1  Nitrosopumilus output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.8   3.3   2.8e-47   2.6e-43       1      66 [.       2      67 ..       2      68 .] 0.99

  Alignments for each domain:
  == domain 1  score: 145.8 bits;  conditional E-value: 2.8e-47
     NitrOD1  1 snavkiryklkGdkqyttcvvtriqyenfkilPvvkvceiverdvsisGdeieqinqklveaikke 66
                +navkiryklkGd+++ttc+vtriqyenf+ilP+++vcei+erdvsisGdeieqinqkl +aikk+
  EPA06449.1  2 NNAVKIRYKLKGDVRFTTCIVTRIQYENFRILPIIEVCEIMERDVSISGDEIEQINQKLIDAIKKD 67
                8****************************************************************9 PP

>> YolD  YolD-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.002        18      43      73 ..       2      32 ..       1      39 [. 0.90
   2 ?    7.4   0.2    0.0005       4.5      23      42 ..      47      66 ..      35      68 .] 0.87

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.002
        YolD 43 eqpvtityyedgeleevtgyiekidelnkel 73
                + +v+i+y  +g+++ +t+ +++i+  n ++
  EPA06449.1  2 NNAVKIRYKLKGDVRFTTCIVTRIQYENFRI 32
                6789********************9998776 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0005
        YolD 23 eLDeqqleeineklqealee 42
                +++ +++e+in+kl +a+++
  EPA06449.1 47 SISGDEIEQINQKLIDAIKK 66
                6899*************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 429.09
//
Query:       EPA06450.1  [L=163]
Description: hypothetical protein BG20_I0473 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-29  101.0   0.0    3.9e-29  100.7   0.0    1.1  1  DUF192    Uncharacterized ACR, COG1430


Domain annotation for each model (and alignments):
>> DUF192  Uncharacterized ACR, COG1430
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.7   0.0   2.2e-33   3.9e-29       2      95 ..      50     159 ..      49     160 .. 0.91

  Alignments for each domain:
  == domain 1  score: 100.7 bits;  conditional E-value: 2.2e-33
                 EEEEE-SHHHHHHTTTT-----TTEEEEEEECCEEEEEE--TT--S-EEEEEE-TTSBEEEEEEEE-TT-................ECEEEEEETTHHH CS
      DUF192   2 tvevAdteeerarGLmgreslpedegmlfvfdkerehsfwMkntripLdiifldadgriveieealkpqs................vryvLElpaGaak 84 
                 +v++Adte  r rGLm++e+lp d+gm+fvfdk++ +s+wM n++++Ld+i++d+dg++v+ie++++p++                + y+LE+ +G+++
  EPA06450.1  50 QVQIADTEPRRVRGLMFQEQLPYDQGMIFVFDKPDLYSLWMLNMQFSLDMIWFDQDGNVVHIEKDVQPCKtaletmtcqsltpgteALYILEVTSGFVD 148
                 89*******************************************************************44455566666777777899********** PP

                 HHT--TT-EEE CS
      DUF192  85 klgikpGdrle 95 
                 k++i++ ++l+
  EPA06450.1 149 KYNITKSSKLS 159
                 *****999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1044.33
//
Query:       EPA06451.1  [L=154]
Description: iron dependent repressor, N-terminal DNA binding domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.6e-18   65.5   2.3    5.6e-18   64.9   2.3    1.3  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
    4.2e-17   62.0   0.1    8.4e-17   61.0   0.1    1.5  1  Fe_dep_repr_C   Iron dependent repressor, metal binding and d
    2.4e-07   30.6   0.4    5.6e-06   26.2   0.2    2.0  2  DUF4423         Domain of unknown function (DUF4423)
    0.00017   21.4   0.0    0.00027   20.7   0.0    1.3  1  MarR_2          MarR family
    0.00046   20.1   0.1     0.0014   18.5   0.0    1.8  2  MarR            MarR family
    0.00048   20.1   0.0     0.0011   18.9   0.0    1.6  1  HTH_Crp_2       Crp-like helix-turn-helix domain
     0.0011   19.0   1.1     0.0031   17.4   0.9    1.8  2  HTH_45          Winged helix-turn-helix
     0.0012   18.9   1.2     0.0019   18.3   0.5    1.7  2  DUF2250         Uncharacterized protein conserved in archaea 
     0.0014   18.5   0.2     0.0028   17.5   0.2    1.5  1  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0026   17.4   0.1     0.0049   16.5   0.0    1.4  1  RexA            Intracellular sensor of Lambda phage, Abi com
     0.0031   17.4   0.1     0.0066   16.4   0.1    1.6  1  HTH_12          Ribonuclease R winged-helix domain
     0.0053   16.4   0.1      0.011   15.4   0.1    1.5  1  HipN            Hsp70-interacting protein N N-terminal domain
     0.0072   16.8   0.1      0.033   14.7   0.1    2.1  2  HTH_27          Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.011   15.3   0.1      0.019   14.5   0.1    1.4  1  HTH_24          Winged helix-turn-helix DNA-binding
      0.012   16.0   0.2      0.074   13.4   0.1    2.1  2  WYL_3           WYL domain
      0.014   15.2   0.0      0.036   13.8   0.0    1.7  2  LexA_DNA_bind   LexA DNA binding domain
      0.033   14.0   0.0      0.055   13.3   0.0    1.4  1  HTH_IclR        IclR helix-turn-helix domain
      0.038   14.2   0.0         11    6.4   0.0    3.3  3  NUMOD1          NUMOD1 domain
      0.043   13.7   0.4        0.2   11.5   0.1    2.0  2  TFIIE_alpha     TFIIE alpha subunit
      0.051   13.3   0.0       0.11   12.2   0.0    1.5  1  Ribosomal_S19e  Ribosomal protein S19e
      0.056   13.7   0.1       0.12   12.6   0.1    1.6  1  Rio2_N          Rio2, N-terminal
      0.057   13.4   0.0       0.16   12.0   0.0    1.8  1  HTH_1           Bacterial regulatory helix-turn-helix protein
      0.066   13.6   0.1       0.13   12.6   0.1    1.5  1  Rrf2            Transcriptional regulator
      0.077   12.7   0.0       0.18   11.5   0.0    1.6  1  GntR            Bacterial regulatory proteins, gntR family
      0.098   13.6   0.4       0.32   11.9   0.4    1.9  1  DUF2624         Protein of unknown function (DUF2624)


Domain annotation for each model (and alignments):
>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.9   2.3   7.8e-21   5.6e-18       3      59 ..      24      80 ..      22      81 .. 0.97

  Alignments for each domain:
  == domain 1  score: 64.9 bits;  conditional E-value: 7.8e-21
                    -HHHHHHHHHHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTTE CS
  Fe_dep_repress  3 vestEdYLetIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyveyekykg 59
                    ++++EdYLe+I +l e k++++t d+++ +nvs++sV++ml++Le++ ++eyeky g
      EPA06451.1 24 STRMEDYLEVISELVELKGYATTLDISRYMNVSAPSVTKMLQRLEENKLLEYEKYHG 80
                    789****************************************************99 PP

>> Fe_dep_repr_C  Iron dependent repressor, metal binding and dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.0   0.1   1.2e-19   8.4e-17       1      64 [.      84     146 ..      84     150 .. 0.98

  Alignments for each domain:
  == domain 1  score: 61.0 bits;  conditional E-value: 1.2e-19
                    -HHHHHHHHHHHHHHHHHHHHHHHHCT--CCCHHHHCCCCGGGS-HHHHHHHHHHCT-.SB-TT CS
  Fe_dep_repr_C   1 TekGrelAkrlvrrhrllerfLvdvlgvdweeaheeAerlEhalseelierldellgfpeecPh 64 
                    TekG ++A ++ ++h +l +f+ ++lgv+ e a ++Ae +Eh+l++++i++l++++ f++++P+
     EPA06451.1  84 TEKGTRIAIEIRQNHGILLEFF-EILGVNHETANKDAEGIEHHLNPKTIKQLRKFITFLKSNPK 146
                    9*********************.***************************************96 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.2   7.9e-09   5.6e-06      11      90 ..      19      95 ..      11      98 .. 0.90
   2 ?    2.6   0.0      0.14        98      31      64 ..     111     143 ..     104     149 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 7.9e-09
     DUF4423 11 deeefeyfssWyypvirellplkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyrqtekslttssevk 90
                ++++++   + y  vi el++lk + a++  +++ ++  +sa  v k l++L++++ll+ ++   ++ tek + +  e++
  EPA06451.1 19 EKSSYSTRMEDYLEVISELVELKGY-ATTLDISRYMN--VSAPSVTKMLQRLEENKLLEYEKYHGINLTEKGTRIAIEIR 95
                66777778889999***********.***********..***********************999999999998888876 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.14
     DUF4423  31 plkdfkadpeelakrlrpkisaeevekalefLlk 64 
                 + +++++d e ++++l+pk + ++ +k + fL++
  EPA06451.1 111 NHETANKDAEGIEHHLNPK-TIKQLRKFITFLKS 143
                 4556789**********55.88999999999986 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   3.8e-07   0.00027      18      55 ..      41      77 ..      30      80 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 3.8e-07
                TTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
      MarR_2 18 pgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                 g+  t  ++ r++++s ++v+++l+rL++  L+e+++
  EPA06451.1 41 KGY-ATTLDISRYMNVSAPSVTKMLQRLEENKLLEYEK 77
                555.47779*************************9985 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.9e-06    0.0014      19      48 ..      45      74 ..      31      78 .. 0.84
   2 ?   -1.9   0.0       4.6   3.3e+03      14      28 ..     125     139 ..     124     144 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.9e-06
                EHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
        MarR 19 svseLakklgvskstvtrvldrLekkGlie 48
                +  ++ + ++vs ++vt++l rLe++ l+e
  EPA06451.1 45 TTLDISRYMNVSAPSVTKMLQRLEENKLLE 74
                44499********************98876 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.6
                 HSTTEEHHHHHHHHT CS
        MarR  14 eqgplsvseLakklg 28 
                 + +p ++++L k++ 
  EPA06451.1 125 HLNPKTIKQLRKFIT 139
                 667888899988876 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.5e-06    0.0011      22      57 ..      44      81 ..      25      87 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.5e-06
                HHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ETEE.E CS
   HTH_Crp_2 22 ltqeelAsmlGltretvsrilseLkreglis.rgrr.i 57
                 t  +++++++++  +v+++l++L++ +l++  +++ i
  EPA06451.1 44 ATTLDISRYMNVSAPSVTKMLQRLEENKLLEyEKYHgI 81
                5788***************************5443336 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.9   4.4e-06    0.0031       5      71 ..      31      96 ..      27     101 .. 0.85
   2 ?   -1.2   0.0       2.9   2.1e+03      34      46 ..     132     144 ..     105     151 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.4e-06
      HTH_45  5 leIiadILeaisegeakkTkimykanLsykllnkYLdmLvekglikk.skekYvlTekGlelleklke 71
                le+i+++ e + +g a+   i    n s   + k+L+ L e++l++  + +   lTekG ++  ++++
  EPA06451.1 31 LEVISELVE-L-KGYATTLDISRYMNVSAPSVTKMLQRLEENKLLEYeKYHGINLTEKGTRIAIEIRQ 96
                577777777.3.788888899999*********************884667899*******9988876 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.9
      HTH_45  34 kllnkYLdmLvek 46 
                 k+l+k++ +L ++
  EPA06451.1 132 KQLRKFITFLKSN 144
                 6677788877765 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.5   2.6e-06    0.0019       8      77 ..      28      98 ..      20     100 .. 0.86
   2 ?   -2.5   0.0         8   5.7e+03      19      38 ..     107     126 ..     101     137 .. 0.46

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.6e-06
     DUF2250  8 elalkvlkhlkkanvdYa..ksiakeleipleevrellkkLeelGLlervegktikrteaklKkksevhkhH 77
                e++l+v+  l +++  Ya  + i+++++++   v+++l++Lee  Lle+ + + i+ te+  + + e +++H
  EPA06451.1 28 EDYLEVISELVELKG-YAttLDISRYMNVSAPSVTKMLQRLEENKLLEYEKYHGINLTEKGTRIAIEIRQNH 98
                667788888777765.551146899*********************************************** PP

  == domain 2  score: -2.5 bits;  conditional E-value: 8
     DUF2250  19 kanvdYaksiakeleiplee 38 
                  ++v++     +   i+ + 
  EPA06451.1 107 ILGVNHETANKDAEGIEHHL 126
                 55555544444444444433 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.2   3.8e-06    0.0028      17      55 ..      37      76 ..      30      85 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.8e-06
                HH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
        TrmB 17 Ll.klgpatadeiaeelgvprskvYevLrsLedkGlVere 55
                L+  +g at+ +i++  +v+ ++v ++L++Le+  l e e
  EPA06451.1 37 LVeLKGYATTLDISRYMNVSAPSVTKMLQRLEENKLLEYE 76
                77567899************************99887766 PP

>> RexA  Intracellular sensor of Lambda phage, Abi component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   6.9e-06    0.0049     160     208 ..      88     137 ..      75     147 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.9e-06
        RexA 160 grtaievnkssellkelvevLlgnsvda.ellesleitlKPklkknikka 208
                 +r+aie+ +++ +l e+ e+L+ n   a ++ e++e +l Pk+ k+++k 
  EPA06451.1  88 TRIAIEIRQNHGILLEFFEILGVNHETAnKDAEGIEHHLNPKTIKQLRKF 137
                 59*********************9877769************99999985 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   9.1e-06    0.0066      29      63 ..      54      88 ..      31      90 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 9.1e-06
      HTH_12 29 digeravRyrLrkleergltrrvgyagreltEkGl 63
                ++++ +v   L+ lee++l +   y g +ltEkG 
  EPA06451.1 54 NVSAPSVTKMLQRLEENKLLEYEKYHGINLTEKGT 88
                7788899999***********************96 PP

>> HipN  Hsp70-interacting protein N N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   1.6e-05     0.011       1      23 [.     127     149 ..     127     151 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.6e-05
        HipN   1 DpaklseLkqFVklckanPeiLh 23 
                 +p+++++L++F+ ++k+nP+++ 
  EPA06451.1 127 NPKTIKQLRKFITFLKSNPKVIE 149
                 5889****************986 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   4.6e-05     0.033      20      68 .]      45      87 ..      30      87 .. 0.81
   2 ?   -1.4   0.0         5   3.6e+03      12      27 ..     122     137 ..     120     144 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.6e-05
      HTH_27 20 kladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                +  d+++++nv++ ++ ++l +L+e+ L+e   +e   ++  + lT+kG
  EPA06451.1 45 TTLDISRYMNVSAPSVTKMLQRLEENKLLE---YE---KYHGINLTEKG 87
                5669*************************3...33...55677788877 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 5
      HTH_27  12 irhrrrrkkladlcgr 27 
                 i+h +++k++++l+++
  EPA06451.1 122 IEHHLNPKTIKQLRKF 137
                 6788899999999876 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   2.7e-05     0.019       9      46 ..      34      72 ..      31      74 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.7e-05
      HTH_24  9 LelLqk.nprisqreLAerlglSpstvnrrlkrLeeeGl 46
                +++L + ++  +  ++++  ++S + v++ l+rLee+ l
  EPA06451.1 34 ISELVElKGYATTLDISRYMNVSAPSVTKMLQRLEENKL 72
                5555556999**************************876 PP

>> WYL_3  WYL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1    0.0001     0.074      12      54 ..      34      79 ..      26      80 .. 0.84
   2 ?   -0.2   0.0       1.8   1.3e+03      34      62 ..     115     143 ..     107     144 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.0001
       WYL_3 12 mkdgvtkedyAkkLgIadkiak.aessagaleklmqTs..eYkKye 54
                + ++v  + yA++L I+  ++  a s ++ l++l + +  eY+Ky 
  EPA06451.1 34 ISELVELKGYATTLDISRYMNVsAPSVTKMLQRLEENKllEYEKYH 79
                568889999************9999999999999876444888885 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.8
       WYL_3  34 aessagaleklmqTseYkKyeaYlnfLnd 62 
                 a++ a+++e   + +  k +++++ fL++
  EPA06451.1 115 ANKDAEGIEHHLNPKTIKQLRKFITFLKS 143
                 67788888888888888888888888865 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   5.1e-05     0.036       6      53 ..      25      70 ..      20      78 .. 0.84
   2 ?   -2.9   0.0       8.4     6e+03      40      48 ..     119     127 ..     117     133 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.1e-05
                   HHHHHHHHHHHHHHHHHSS---HHHHHHHHTS-.HHHHHHHHHHHHHT CS
  LexA_DNA_bind  6 erQrevldlikasieetgypPsireiaralglkSpsaveehLkaLerK 53
                    r ++ l++i + +e +gy+ +  +i+r ++++ + +v + L++Le  
     EPA06451.1 25 TRMEDYLEVISELVELKGYATT-LDISRYMNVS-APSVTKMLQRLEEN 70
                   677888**************66.59******97.7789*******975 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 8.4
                    HHHHHHHHH CS
  LexA_DNA_bind  40 psaveehLk 48 
                    ++++e+hL+
     EPA06451.1 119 AEGIEHHLN 127
                    578999985 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   7.6e-05     0.055      23      51 ..      48      76 ..      34      77 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.6e-05
                HHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
    HTH_IclR 23 elArrtglpkStvhRlLqtLvelGyveqd 51
                +++r   ++ ++v  +Lq L+e +++e++
  EPA06451.1 48 DISRYMNVSAPSVTKMLQRLEENKLLEYE 76
                899***********************975 PP

>> NUMOD1  NUMOD1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.015        11      20      36 ..      47      63 ..      39      64 .. 0.86
   2 ?   -1.7   0.0       5.3   3.8e+03      12      20 ..      74      82 ..      68      86 .. 0.71
   3 ?    3.8   0.0       0.1        73      24      35 ..     106     117 ..     101     117 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.015
      NUMOD1 20 reAakyLgishntInky 36
                 + ++y+++s ++++k 
  EPA06451.1 47 LDISRYMNVSAPSVTKM 63
                689***********996 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 5.3
      NUMOD1 12 tigkFsSir 20
                ++ k++ i+
  EPA06451.1 74 EYEKYHGIN 82
                478999886 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.1
      NUMOD1  24 kyLgishntInk 35 
                 ++Lg++h t nk
  EPA06451.1 106 EILGVNHETANK 117
                 68********97 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00028       0.2      17      63 ..      32      79 ..      24      91 .. 0.82
   2 ?   -0.0   0.0       1.1   7.8e+02      29      53 ..     118     143 ..      90     150 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00028
                 HHHHHHHC.TTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEE CS
  TFIIE_alpha 17 lvldvLle.kgevteedlakelkidlnelrklLnrLyearlvkykrrr 63
                 +v+  L+e kg  t  d+++ +++  + + k+L rL e +l +y +  
   EPA06451.1 32 EVISELVElKGYATTLDISRYMNVSAPSVTKMLQRLEENKLLEYEKYH 79
                 5555554338888999****************************9865 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.1
                  BHHHHHHHHTS-.HHHHHHHHHHHHH CS
  TFIIE_alpha  29 teedlakelkid.lnelrklLnrLye 53 
                    e ++++l+ + +++lrk +  L++
   EPA06451.1 118 DAEGIEHHLNPKtIKQLRKFITFLKS 143
                  34556666665425788888877775 PP

>> Ribosomal_S19e  Ribosomal protein S19e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00015      0.11      89     128 ..      53      92 ..      42      98 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00015
                     HHHHHHTTSSS--SSS---SS-HHHHHTHHHHH--SS--S CS
  Ribosomal_S19e  89 vkasgsvirkilqqLeklglvkkekkkgrrltkkGqrlld 128
                      + s   + k+lq Le+ +l++ ek +g  lt+kG r+  
      EPA06451.1  53 MNVSAPSVTKMLQRLEENKLLEYEKYHGINLTEKGTRIAI 92 
                     5666777889***********99999*********99765 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00017      0.12      29      70 ..      48      87 ..      31      91 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00017
      Rio2_N 29 lieeisrlkeeevkkrlsrllkaklisrktakydGYkLtyeG 70
                 i+++ ++++ +v+k l+rl ++kl++++  ky+G +Lt +G
  EPA06451.1 48 DISRYMNVSAPSVTKMLQRLEENKLLEYE--KYHGINLTEKG 87
                57788889999*****************9..7******9988 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00022      0.16      22      59 ..      52      87 ..      50      88 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00022
                HHTS-HHHHHHHHHHHHHHHTS-SEEESS.SEEEE-HHH CS
       HTH_1 22 eLglsqpavsrqikrLEeelgvpLfeRtg.rglrLTeaG 59
                 +++s p+v+++++rLEe    +L+e  + +g+ LTe G
  EPA06451.1 52 YMNVSAPSVTKMLQRLEEN---KLLEYEKyHGINLTEKG 87
                589**************85...88886442578888887 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00019      0.13       3      59 ..      23      77 ..      22      93 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00019
                --HHHHHHHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
        Rrf2  3 lsskteyalhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvr 59
                +s+++e  l ++ +L + ++   +++ +i++ +n+s++ + k+l++L++++l++ ++
  EPA06451.1 23 YSTRMEDYLEVISELVELKGY--ATTLDISRYMNVSAPSVTKMLQRLEENKLLEYEK 77
                578888888888999888885..6999*************************99776 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00025      0.18      33      61 ..      52      80 ..      47      83 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00025
                HHTS-HHHHHHHHHHHHHTTSEEEETTCE CS
        GntR 33 efgVsrttvReALrrLeaeglverrqgrG 61
                 ++Vs+++v + L+rLe+ +l+e ++  G
  EPA06451.1 52 YMNVSAPSVTKMLQRLEENKLLEYEKYHG 80
                689*******************9887666 PP

>> DUF2624  Protein of unknown function (DUF2624)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.4   0.00045      0.32       1      45 [.      53      97 ..      53     142 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00045
     DUF2624  1 MniiqqlVnqklnsiTaeellkyakqygveltksqAekivkilre 45
                Mn+    V + l+ + ++ ll+y k +g++lt++ ++  ++i ++
  EPA06451.1 53 MNVSAPSVTKMLQRLEENKLLEYEKYHGINLTEKGTRIAIEIRQN 97
                8888888999***********************998877666444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       952  (0.0530983); expected 358.6 (0.02)
Passed bias filter:                      647  (0.0360868); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 938.06
//
Query:       EPA06452.1  [L=101]
Description: hypothetical protein BG20_I0498 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00076   19.8   0.1     0.0012   19.1   0.1    1.4  1  DUF190         Uncharacterized ACR, COG1993
    0.00083   19.9   0.0     0.0012   19.4   0.0    1.3  1  P-II           Nitrogen regulatory protein P-II
  ------ inclusion threshold ------
      0.025   14.6   0.5      0.079   13.0   0.5    1.8  1  Nit_Regul_Hom  Uncharacterized protein, homolog of nitrogen r
       0.09   13.0   0.0       0.11   12.7   0.0    1.1  1  MetallophosC   C terminal of Calcineurin-like phosphoesterase
       0.11   12.7   0.0        0.3   11.3   0.0    1.7  1  DUF3240        Protein of unknown function (DUF3240)


Domain annotation for each model (and alignments):
>> DUF190  Uncharacterized ACR, COG1993
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.1   3.5e-07    0.0012      19      89 ..      18      86 ..      14      94 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 3.5e-07
                HHHHHHHHHHTT-S--EEEE-S---------------------EEEEEEEE-HHHHHHHHHHHHT----...SE CS
      DUF190 19 yeaivelareeglagatvlrGieGfgassrihtakllelsedlPvvieivdteekieaflpelkelvke...gl 89
                 +a++e++ ++g++g t+++ + G g+++ i+ +    l+++  + ieiv teek++++ +el + + +    +
  EPA06452.1 18 QKAVLEILYKHGITGYTIYE-VDGNGSKG-IRGK---GLKNEKNIKIEIVSTEEKLKDISEELARSLFSdfaII 86
                589****************9.89*99777.5554...5677889******************998776534334 PP

>> P-II  Nitrogen regulatory protein P-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   3.5e-07    0.0012      11      76 ..      19      77 ..      13      83 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 3.5e-07
                HHHHHHHHHTTGGCEEEEEEEEEESTCCEEEECTTEEEEEEEEEEEEEEEEEEGGGHHHHHHHHHH CS
        P-II 11 eevkeaLekagvkgltvtevkGrGkqkghtelyrgaeyevellpkvkleivvsdedvekvveaiik 76
                ++v e L k g++g+t+ ev G G++      +rg+  ++e  + +k+eiv ++e+++++ e + +
  EPA06452.1 19 KAVLEILYKHGITGYTIYEVDGNGSKG-----IRGKGLKNE--KNIKIEIVSTEEKLKDISEELAR 77
                57999*****************99988.....899988888..89************999887765 PP

>> Nit_Regul_Hom  Uncharacterized protein, homolog of nitrogen regulatory protein PII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.5   2.2e-05     0.079      14      60 ..      18      64 ..       6      96 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.2e-05
  Nit_Regul_Hom 14 lgkvinalseagitGfylieYkGlsPqewkgflleedpesaikiikd 60
                      v+ +l ++gitG+ ++e  G   +  +g  l+++ +  i+i++ 
     EPA06452.1 18 QKAVLEILYKHGITGYTIYEVDGNGSKGIRGKGLKNEKNIKIEIVST 64
                   456899*************************9999999999999975 PP

>> MetallophosC  C terminal of Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.1e-05      0.11      25      62 ..      31      69 ..      29      85 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.1e-05
  MetallophosC 25 nGYsvyevdgndik.wrykaagededyqmrlyapgevkk 62
                   GY +yevdgn  k +r k+ +++++ +++++  +e  k
    EPA06452.1 31 TGYTIYEVDGNGSKgIRGKGLKNEKNIKIEIVSTEEKLK 69
                  59*********9999****************98777654 PP

>> DUF3240  Protein of unknown function (DUF3240)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   8.3e-05       0.3      12      85 ..      14      81 ..       5      93 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.3e-05
     DUF3240 12 prelkddlvDlLlelpdllsGFtlldakghsrevslatiaEkvrGradkvvveivleeaalerllaeLrkavak 85
                +   +++++ +L +    ++G+t+++++g +++  +     k   +++++++eiv +e++l+ + +eL++++++
  EPA06452.1 14 EILAQKAVLEILYKH--GITGYTIYEVDGNGSKGIR----GKGLKNEKNIKIEIVSTEEKLKDISEELARSLFS 81
                555567778888877..6889999999999876443....33333578999*****************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       777  (0.0433376); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 715.14
//
Query:       EPA06453.1  [L=99]
Description: hypothetical protein BG20_I0477 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0012   18.6   2.8     0.0014   18.4   2.8    1.1  1  Claudin_2  PMP-22/EMP/MP20/Claudin tight junction
     0.0041   17.4   6.5     0.0041   17.4   6.5    2.1  2  DUF4064    Protein of unknown function (DUF4064)
  ------ inclusion threshold ------
       0.04   14.3   0.3       0.04   14.3   0.3    1.8  2  PEMT       Phospholipid methyltransferase
        0.2   11.6   6.4       0.31   10.9   6.4    1.4  1  DUF2721    Protein of unknown function (DUF2721)
       0.22   11.5   4.0       0.29   11.1   4.0    1.2  1  DUF2678    Protein of unknown function (DUF2678)


Domain annotation for each model (and alignments):
>> Claudin_2  PMP-22/EMP/MP20/Claudin tight junction
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   2.8   3.9e-07    0.0014      89     150 ..      30      92 ..      23      99 .] 0.83

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 3.9e-07
   Claudin_2  89 arfvqvlliLslvli.vlavvlgllallkqsvlllkaagilfllagvlgllavvvfiesvkkv 150
                 a+ +++l i+s +l+ ++++v++++ ++k+   +l ++++ +l+++vl+ ++ vvfi  + k+
  EPA06453.1  30 AGLFIALGIISSTLSiFTVIVTFVIKNPKKVGKILFFMAFAILASSVLIGVVGVVFILISSKN 92 
                 566778888887776499999999***************************999999888655 PP

>> DUF4064  Protein of unknown function (DUF4064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   6.5   1.1e-06    0.0041      52      98 ..      24      69 ..      16      74 .. 0.78
   2 ?    2.3   4.0     0.056     2e+02      63      85 ..      69      92 ..      65      96 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.1e-06
     DUF4064 52 avleflstllivlgvialiaivlgivgalllkknkkvsGilfiiaai 98
                  l+ + +l+i+lg+i+  +++++++ ++++k+ kkv+ ilf+  a 
  EPA06453.1 24 RDLSEIAGLFIALGIISSTLSIFTVIVTFVIKNPKKVGKILFFM-AF 69
                5689999*************************555555555544.33 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.056
     DUF4064 63 vlgvi.aliaivlgivgalllkkn 85
                +++++ +++++v+g+v++l+ +kn
  EPA06453.1 69 FAILAsSVLIGVVGVVFILISSKN 92
                333334788888888888888777 PP

>> PEMT  Phospholipid methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.2      0.22   7.9e+02      63      79 ..      33      49 ..      27      55 .. 0.39
   2 ?   14.3   0.3   1.1e-05      0.04      51      85 ..      54      88 ..      52      94 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.22
        PEMT 63 flGlaLitgsaagllla 79
                f++l +i++++ +++++
  EPA06453.1 33 FIALGIISSTLSIFTVI 49
                33333333333322222 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 1.1e-05
        PEMT 51 lnnPeyvgstlgflGlaLitgsaaglllallvllv 85
                ++nP+ vg +l f++ a++ +s+++ ++ ++++l+
  EPA06453.1 54 IKNPKKVGKILFFMAFAILASSVLIGVVGVVFILI 88
                78**********************98888777665 PP

>> DUF2721  Protein of unknown function (DUF2721)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   6.4   8.8e-05      0.31      66     116 ..      33      79 ..      25      91 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 8.8e-05
     DUF2721  66 ailllvlsallvvlvvlllflsallsldlsllaailfvlalllllvslllf 116
                  i+l+++s +l++++v++ f+      + + + +ilf++a ++l+ s+l+ 
  EPA06453.1  33 FIALGIISSTLSIFTVIVTFV----IKNPKKVGKILFFMAFAILASSVLIG 79 
                 466777777777777777777....7899*****************99875 PP

>> DUF2678  Protein of unknown function (DUF2678)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   4.0   8.1e-05      0.29      32      77 ..      34      78 ..      22      92 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 8.1e-05
     DUF2678 32 lvvggltsllvlvtvvssfvfpslppkplniffavcillisssviv 77
                +++g ++s l + tv+ +fv+ +++  +  +ff +   + +ssv++
  EPA06453.1 34 IALGIISSTLSIFTVIVTFVIKNPKKVGKILFF-MAFAILASSVLI 78
                7899****************9876655554555.555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1136  (0.063361); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 726.14
//
Query:       EPA06454.1  [L=37]
Description: hypothetical protein BG20_I0469 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.24s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 290.54
//
Query:       EPA06455.1  [L=131]
Description: hypothetical protein BG20_I0481 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   12.0   0.0       0.16   11.6   0.0    1.1  1  DUF4747   Domain of unknown function (DUF4747)


Domain annotation for each model (and alignments):
>> DUF4747  Domain of unknown function (DUF4747)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   8.7e-06      0.16     107     171 ..      40     106 ..      34     123 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.7e-06
     DUF4747 107 kdkknlslspkqikalleeifnraeiltkygsve...vdvlteresieriLalpklkklkieitfsNp 171
                 k++ nl l+ +q+ ++ +e+ +r+e+ +ky ++e   v   t+r     i++ p+++k  + +  +N 
  EPA06455.1  40 KENINLRLNDAQMDEVCKELASRVEKRKKY-DFElgrVKYSTSRREHVVIMSFPVYEKVVMIVAEPNV 106
                 667789999********************9.665334888899888889*****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       788  (0.0439511); expected 358.6 (0.02)
Passed bias filter:                      661  (0.0368676); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 889.95
//
Query:       EPA06456.1  [L=45]
Description: hypothetical protein BG20_I0470 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1641  (0.0915277); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 297.52
//
Query:       EPA06457.1  [L=197]
Description: uracil-DNA glycosylase, family 4 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.7e-39  133.6   0.0    7.3e-39  133.2   0.0    1.1  1  UDG          Uracil DNA glycosylase superfamily
  ------ inclusion threshold ------
       0.05   12.5   0.0      0.059   12.2   0.0    1.3  1  Epimerase_2  UDP-N-acetylglucosamine 2-epimerase


Domain annotation for each model (and alignments):
>> UDG  Uracil DNA glycosylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.2   0.0   8.1e-43   7.3e-39       1     138 [.      29     162 ..      29     183 .. 0.94

  Alignments for each domain:
  == domain 1  score: 133.2 bits;  conditional E-value: 8.1e-43
                 HHC-CTT-SEEEEESSTCHHHHHHSSSS.-STT--HHHHHHHCCCCCCCHHGCTEEEEESSS....SECGCTTCCCCTCCHHHHHHHHHHHHSSEEEEE CS
         UDG   1 pgegppdakvvivGeaPgaeedatglpFsgragnllrkllneaglkrdleseqgvyitnvvkcrppgnrdtptsaeikacaplleeeiellkprlivll 99 
                 pg g+ +++v++vGeaPg++ed++g+pF+g ag++l ++l++ag++r     + +yitnvvkcrpp nr  pt  e + c ++l++ei+++kp++i++l
  EPA06457.1  29 PGKGNFQSDVIFVGEAPGRNEDKKGEPFVGIAGQRLSAALESAGVSR-----ESIYITNVVKCRPPNNR-VPTVMERDMCHDYLQKEISIIKPKIICIL 121
                 688999*****************************************.....*****************.***************************** PP

                 SHHHHHH...HHHHSCESCCCSCT..SEEEEES-SSTTTTT CS
         UDG 100 Gktaakall.geklgklrgklleak.irvlplphPsplnrn 138
                 G+ta++++l g +++k rgk+++++   ++ + hP++  +n
  EPA06457.1 122 GNTAFNSILgGSEITKYRGKIVKKDkEFYFLTVHPAATIYN 162
                 *******99777************9899**********999 PP

>> Epimerase_2  UDP-N-acetylglucosamine 2-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   6.5e-06     0.059     142     199 ..     113     165 ..      70     189 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.5e-06
                  --GGGEEE---HHHHHHHHHHHHHH...T-HHHHHH--SS-EEEEE---HHHHTSHHH CS
  Epimerase_2 142 eeeerifvvGntviDalllskeeieeklkaseilkelkekkyvlvtlHrrenedeper 199
                  ++++ i + Gnt++ ++l  +e  +  + + +i k  k+k+++ +t+H++++  ++e 
   EPA06457.1 113 IKPKIICILGNTAFNSILGGSEITK--Y-RGKIVK--KDKEFYFLTVHPAATIYNQEL 165
                  4788999**********99988886..4.447755..69************9996533 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1273.40
//
Query:       EPA06458.1  [L=206]
Description: hypothetical protein BG20_I0472 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.31s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1368.12
//
Query:       EPA06459.1  [L=98]
Description: hypothetical protein BG20_I0479 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1156  (0.0644765); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 629.83
//
Query:       EPA06460.1  [L=627]
Description: ATPase/histidine kinase/DNA gyrase B/HSP90 domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-26   93.1   0.1    3.9e-26   91.8   0.1    1.8  1  HATPase_c       Histidine kinase-, DNA gyrase B-, and HSP90-l
    2.8e-15   56.1   1.5      7e-15   54.8   0.2    2.4  2  HisKA           His Kinase A (phospho-acceptor) domain
    7.9e-08   32.6   0.0      3e-07   30.7   0.0    2.1  2  HAMP            HAMP domain
      5e-05   23.1   0.1    0.00021   21.1   0.0    2.1  2  HATPase_c_3     Histidine kinase-, DNA gyrase B-, and HSP90-l
    0.00033   20.7   0.0      0.038   14.0   0.0    2.8  2  PilJ            Type IV pili methyl-accepting chemotaxis tran
  ------ inclusion threshold ------
      0.045   13.7   0.0       0.11   12.5   0.0    1.6  1  HATPase_c_2     Histidine kinase-like ATPase domain
      0.045   12.5   0.2      0.076   11.7   0.2    1.2  1  AtuA            Acyclic terpene utilisation family protein At
        1.5    9.9   4.8        7.1    7.7   0.5    3.2  3  Myb_DNA-bind_3  Myb/SANT-like DNA-binding domain


Domain annotation for each model (and alignments):
>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.8   0.1   1.7e-29   3.9e-26       2     111 ..     505     616 ..     504     617 .. 0.94

  Alignments for each domain:
  == domain 1  score: 91.8 bits;  conditional E-value: 1.7e-29
                 HHHHHHHHHHHHHHHHHHH.HSTTTEEEEEEEEEE..TEEEEEEEESSSSSTTHHHTGTCSTTCH.HCSTCHTSTSSSHHHHHHHHHHHHTTTEEEEEE CS
   HATPase_c   2 dekrLrqiisnlvdNavkf.atkageieveikase..ddlvisveDnGiGipkedlkklfekfsq.ddstkrggggtGlGlsivkklvelmgGeiwves 96 
                 de+r++q++snl++N++ + ++++g i++++   +  +++++sv+DnGiGip +++++lf+kf+q d + +r+++g+GlGl+i+k +++++gG i ++s
  EPA06460.1 505 DEDRIKQVLSNLIKNSMIAvEPEKGVIDITMI--DypQTVQVSVKDNGIGIPADKQENLFKKFYQvDTTLTREKSGSGLGLAICKGIIDTHGGGIFCKS 601
                 89****************9777**********..3347***************************999999999************************* PP

                 ETTTEEEEEEEEESS CS
   HATPase_c  97 epgrGttftftlple 111
                  pg+ t ftftlp++
  EPA06460.1 602 IPGQETVFTFTLPKK 616
                 ************975 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       1.4   3.1e+03      29      53 ..     163     184 ..     144     186 .. 0.62
   2 !   54.8   0.2   3.1e-18     7e-15       1      66 [.     392     459 ..     392     460 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.4
                 C..T-HSSCHHHHHHHHHHHHHHHH CS
       HisKA  29 regklteelkeyletiesearrldh 53 
                 r      + ke  +++e++a+ + +
  EPA06460.1 163 R---DYNRHKEIANDLENSAKEIGQ 184
                 2...446677777777777777666 PP

  == domain 2  score: 54.8 bits;  conditional E-value: 3.1e-18
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHH CS
       HisKA   1 slgrflagvaHELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedlLdlsriea 66 
                 ++ +fla++ HEL+tPL  i+g++++L  e  gklt+++ke +++i+s+++ l++l++dlLd  ++e 
  EPA06460.1 392 AKDEFLAMITHELKTPLVPIQGYSDILLSEhlGKLTDKQKERINIIKSSSETLLALISDLLDAQKLEL 459
                 589***********************97777********************************99985 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       3.8   8.6e+03      32      40 ..     177     185 ..     156     186 .. 0.75
   2 !   30.7   0.0   1.3e-10     3e-07       1      51 [.     329     379 ..     329     381 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.8
                 TSSSHHHHH CS
        HAMP  32 sgrDEiGeL 40 
                 ++  EiG+L
  EPA06460.1 177 NSAKEIGQL 185
                 456799998 PP

  == domain 2  score: 30.7 bits;  conditional E-value: 1.3e-10
                 HHHHTTHHHHHHHHHHHHHHTTTBTSSTCCTTSSSHHHHHHHHHHHHHHHH CS
        HAMP   1 llarrilrPLrrLaraarriaaGdldtrlpvsgrDEiGeLarafNaMldrL 51 
                 +++r+ l PL  ++ a  +i +G +   ++ +  DEiG L+++fN+M++ +
  EPA06460.1 329 FVIRQSLLPLGLITNALTEIKEGAYGRKIEYEKSDEIGNLVQTFNVMSNTI 379
                 6899*******************************************9876 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       4.7   1.1e+04      99     119 ..     219     238 ..     216     246 .. 0.71
   2 !   21.1   0.0   9.4e-08   0.00021       4      82 ..     510     586 ..     507     589 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 4.7
  HATPase_c_3  99 stltldvdkidkenekvleel 119
                  st+ ld++ i+++ne  +e +
   EPA06460.1 219 STNDLDLKSIEQKNEDLIE-I 238
                  5678899999988877665.3 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 9.4e-08
  HATPase_c_3   4 ekAlaelvdNsldAdaen...vkievnknrgktgeivieDdGkGmseeelknal.rlatsskeakrkstslGkkGiGlklAsl 82 
                  +++l  l++Ns+ A   +   ++i++ + + +t +++++D+G G++ ++ +n + ++ + +++     + ++  G+G  lA++
   EPA06460.1 510 KQVLSNLIKNSMIAVEPEkgvIDITMIDYP-QTVQVSVKDNGIGIPADKQENLFkKFYQVDTTL---TREKSGSGLG--LAIC 586
                  67899*********9888899*******98.699******************883577777774...3334444555..6655 PP

>> PilJ  Type IV pili methyl-accepting chemotaxis transducer N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   1.7e-05     0.038      13     106 ..      39     128 ..      31     136 .. 0.83
   2 ?    3.3   0.0     0.035        79      76     106 ..     241     275 ..     213     281 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.7e-05
        PilJ  13 INvAGslRMqsqRlakeallaaagaydaaearaqlretiaqfdrtlaalrlgdpapgllvpae...avraqleaveqlWqelkkpaeaalaqqddaa 106
                 I  +G l +q+  +  +a+ +a g+     + +++ + i+  d t+a  ++g+     ++ ++   +++++++++   W+ +k+ a   l+++++ +
  EPA06460.1  39 IIKTGDLKVQTEAISGLAVSIANGN---VDDEEKIYKDIEHVDVTIAGIKNGGMIN-NKPIQKippSITTEYNKLVISWNDYKEKA---LNAKKTSV 128
                 6679*********************...8899********************8664.333334566*******************9...55555554 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.035
        PilJ  76 avraqleaveqlWqelkkpa....eaalaqqddaa 106
                 + +++l ++++lW+ l+  +    e+al ++d + 
  EPA06460.1 241 ENSDALRKLDPLWESLRPKIeileERALLSPDFNS 275
                 77899***************777777777777655 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   4.7e-05      0.11      49     111 ..     526     592 ..     498     610 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.7e-05
  HATPase_c_2  49 leapegpvevrlesdeealtvevaDsGpgfdpetlpdpteeep......keslkegGrGlalikglvDe 111
                  +  ++g + +++ + +++++v+v+D+G g ++ ++++  ++ +      + ++  +G+Gla+ kg+ D+
   EPA06460.1 526 P--EKGVIDITMIDYPQTVQVSVKDNGIGIPADKQENLFKKFYqvdttlTREKSGSGLGLAICKGIIDT 592
                  3..25788999999***************8888766655544489999999999************996 PP

>> AtuA  Acyclic terpene utilisation family protein AtuA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   3.4e-05     0.076       7      98 ..     425     517 ..     421     534 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.4e-05
        AtuA   7 fagDrveaalelae..kgeldvlvgdylaEltialaakrkkkdpekgyeptllealekllpelaekgikvvtnaGalnpkalaekvaelakelg 98 
                   +D+ ++ +++++  ++ l +l+ d l   ++ l + r+k  +++  ++t+ e +e++ p++++++ik ++n   ++++   +++++++++l 
  EPA06460.1 425 KLTDKQKERINIIKssSETLLALISDLLDAQKLELGQLRMKM-ETNNIKKTITEVIESFTPQAQKNNIKFISNLKDVHTEYDEDRIKQVLSNLI 517
                 566777777777774455788899999999999999999988.5569*********************************99999999988765 PP

>> Myb_DNA-bind_3  Myb/SANT-like DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.5    0.0032       7.1      20      73 ..     121     173 ..     103     178 .. 0.85
   2 ?    2.2   0.0      0.17   3.8e+02      16      68 ..     346     399 ..     339     404 .. 0.75
   3 ?   -1.2   0.1       1.9   4.4e+03      31      65 ..     472     504 ..     446     518 .. 0.56

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0032
  Myb_DNA-bind_3  20 kgnriekktfkkeawkeileefnaktgakytkkqlknrlkklrkeyklvkelle 73 
                      + + + + f kea + +   ++++ ++    + l + l++l ++y+  ke+ +
      EPA06460.1 121 LNAK-KTSVFDKEATSAMNYVLQKNGELILLTNSLSSELSNLDRDYNRHKEIAN 173
                     3444.6899****************************************99976 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.17
  Myb_DNA-bind_3  16 eqvkkgnriekktf.kkeawkeileefnaktgakytkkqlknrlkklrkeyklv 68 
                     +++k+g + +k ++ k++   +++++fn   ++  +k++l ++++ +++e+ ++
      EPA06460.1 346 TEIKEGAYGRKIEYeKSDEIGNLVQTFNVMSNTILEKEELAKKTDIAKDEFLAM 399
                     555666653344440446678999*****999***************9999665 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.9
  Myb_DNA-bind_3  31 keawkeileefnaktgakytkkqlknrlkklrkey 65 
                     k++ +e++e+f+   +a++++ +  + lk + +ey
      EPA06460.1 472 KKTITEVIESFTP--QAQKNNIKFISNLKDVHTEY 504
                     3334444444443..33445555556666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (627 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1444  (0.0805399); expected 358.6 (0.02)
Passed bias filter:                      646  (0.036031); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.68u 0.30s 00:00:00.98 Elapsed: 00:00:00.46
# Mc/sec: 4117.19
//
Query:       EPA06461.1  [L=46]
Description: hypothetical protein BG20_I0487 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 352.44
//
Query:       EPA06462.1  [L=171]
Description: hypothetical protein BG20_I0494 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.029   14.4   0.1      0.064   13.4   0.1    1.8  1  KH_5      NusA-like KH domain


Domain annotation for each model (and alignments):
>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   3.6e-06     0.064      36      68 ..      89     120 ..      32     121 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.6e-06
        KH_5  36 eLkgekidvvewseDlaefianalsPaevlsVk 68 
                 ++   ki +ve +++ ++fi+++++P ++ls++
  EPA06462.1  89 QF-HGKIWLVEDDKNDKKFIEDLFFPTKILSIN 120
                 44.458*************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1255.75
//
Query:       EPA06463.1  [L=119]
Description: hypothetical protein BG20_I0485 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.7e-05   23.3   0.0    7.3e-05   22.9   0.0    1.3  1  Hpt             Hpt domain
  ------ inclusion threshold ------
      0.014   15.1   0.1      0.022   14.5   0.1    1.3  1  KRAP_IP3R_bind  Ki-ras-induced actin-interacting protein-IP3R
      0.019   15.2   1.1       0.96    9.8   0.2    2.6  2  KxDL            Uncharacterized conserved protein
      0.022   15.3   0.5      0.096   13.2   0.3    2.0  2  Syntaxin-6_N    Syntaxin 6, N-terminal
      0.023   14.9   1.9       0.03   14.6   0.3    1.8  2  Seryl_tRNA_N    Seryl-tRNA synthetase N-terminal domain
      0.031   13.0   0.6      0.034   12.8   0.6    1.1  1  Tweety          Tweety
      0.037   14.1   1.8      0.098   12.8   0.3    2.3  2  Vps51           Vps51/Vps67
       0.04   14.1   0.7       0.12   12.6   0.6    1.7  1  SesA            N-terminal domain on NACHT_NTPase and P-loop 
      0.045   14.3   0.1      0.077   13.5   0.1    1.5  1  RPAP3_C         Potential Monad-binding region of RPAP3
      0.053   13.2   1.4      0.059   13.0   1.4    1.0  1  DUF4559         Domain of unknown function (DUF4559)
        0.1   12.7   1.7       0.22   11.5   1.7    1.7  1  Baculo_PEP_C    Baculovirus polyhedron envelope protein, PEP,
       0.17   12.3   3.1        3.5    8.2   0.4    2.7  2  NPV_P10         Nucleopolyhedrovirus P10 protein
        0.2   11.7   3.2       0.34   11.0   0.8    2.1  2  DUF1664         Protein of unknown function (DUF1664)
       0.22   11.8   1.5          2    8.7   1.5    2.4  1  DUF948          Bacterial protein of unknown function (DUF948
       0.77    9.6   5.7        8.1    6.2   5.7    2.1  1  MCPsignal       Methyl-accepting chemotaxis protein (MCP) sig
        1.1    9.7   7.2        3.7    8.0   2.0    3.2  2  FlaC_arch       Flagella accessory protein C (FlaC)


Domain annotation for each model (and alignments):
>> Hpt  Hpt domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   6.5e-08   7.3e-05       3      82 ..       6      93 ..       4     116 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 6.5e-08
                HHHHHHHHHHHHHHHHHHH........SCCHHHHHHHHHHHHHHHHHHTTBHHHHHHHHHHHHHHHHCTSCHHHHHHHHHHHHHHHHH CS
         Hpt  3 lelfleeaeelleqleqal........dqedlqelaraaHtLKGsagmlGltelaelahelEdlldragelelepellealkalleal 82
                l +  +e+ e++ q+ + +          ++  e++   H++KG a m+G +el+ l + l +++++ +++++++e++  l  +++++
  EPA06463.1  6 LKIATDEINEEISQIITIVdtchngteLCQNAGEIQKSTHKIKGLAPMMGKEELGSLSALLDSIFKKIQSVSITDEMFSSLVSAVNEM 93
                5666778888888888888887764433347778******************************************999444444443 PP

>> KRAP_IP3R_bind  Ki-ras-induced actin-interacting protein-IP3R-interacting domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1     2e-05     0.022      85     130 ..      66     111 ..      54     118 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2e-05
  KRAP_IP3R_bind  85 lasrFrqlevldavanafssLlsdvsklpvqaeekaeeeeaqstsv 130
                     l s F++++ +  + + fssL+s v+++++++++++ + +  +++v
      EPA06463.1  66 LDSIFKKIQSVSITDEMFSSLVSAVNEMKNSMTQTDYDLDEIKQKV 111
                     7899**************************9888776655544444 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.047        53      54      73 ..      56      75 ..      31      79 .. 0.85
   2 ?    9.8   0.2   0.00086      0.96      40      78 ..      80     118 ..      76     119 .] 0.78

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.047
        KxDL 54 tkllkevkkdLesifkkirs 73
                ++ l ++ + L+sifkki+s
  EPA06463.1 56 KEELGSLSALLDSIFKKIQS 75
                5667778888********98 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00086
        KxDL  40 qerlaklrarfkqgtkllkevkkdLesifkkirslkakl 78 
                 +e +++l + +++ ++ + ++  dL+ i++k++++ + l
  EPA06463.1  80 DEMFSSLVSAVNEMKNSMTQTDYDLDEIKQKVSKISSSL 118
                 556677777788888889999999999999999998765 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0       0.7   7.8e+02       7      13 ..      37      43 ..       3      63 .. 0.58
   2 ?   13.2   0.3   8.6e-05     0.096      13      68 ..      58     115 ..      33     118 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.7
  Syntaxin-6_N  7 keeVqks 13
                  + e+qks
    EPA06463.1 37 AGEIQKS 43
                  2333444 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 8.6e-05
  Syntaxin-6_N  13 slnkaeslyrrw.erlledtss.stseeldetrteLrkalrsiewdledLeetvrive 68 
                   +l ++ +l+++  +++++++++ +  ++l ++ +e+++++ + ++dl+++++ v+ ++
    EPA06463.1  58 ELGSLSALLDSIfKKIQSVSITdEMFSSLVSAVNEMKNSMTQTDYDLDEIKQKVSKIS 115
                   5666777777776788888888778999************************997655 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1       1.2   1.4e+03      60      62 ..      18      20 ..       4      51 .. 0.52
   2 ?   14.6   0.3   2.6e-05      0.03      45     104 ..      59     118 ..      55     119 .] 0.89

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.2
                  CCC CS
  Seryl_tRNA_N 60 gka 62
                  +++
    EPA06463.1 18 SQI 20
                  222 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 2.6e-05
                   HHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCTS CS
  Seryl_tRNA_N  45 leelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaeleklllai 104
                   l +l a   ++ k+I++ +  +e  ++l+  v+e+k+ + +++ +l+e+++++ k+ +++
    EPA06463.1  59 LGSLSALLDSIFKKIQSVSITDEMFSSLVSAVNEMKNSMTQTDYDLDEIKQKVSKISSSL 118
                   5566777778889999999999********************************998776 PP

>> Tweety  Tweety
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.6     3e-05     0.034     106     181 ..      38     114 ..      10     117 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3e-05
      Tweety 106 agikklvseteesleekleeeLtkleeifakrtdlletlrlvqeqveevvqqlselp.flkkkdvsltelaeqvelv 181
                   i+k +++++    +  +eeL +l+ ++++  + ++++ ++ e+ +++v++++e++  + ++d +l+e+ ++v+ +
  EPA06463.1  38 GEIQKSTHKIKGLAPMMGKEELGSLSALLDSIFKKIQSVSITDEMFSSLVSAVNEMKnSMTQTDYDLDEIKQKVSKI 114
                 56888888888888888899************************************988999*********999866 PP

>> Vps51  Vps51/Vps67
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.81   9.1e+02      69      69 ..      32      32 ..       4      58 .. 0.56
   2 ?   12.8   0.3   8.7e-05     0.098      58      86 ..      88     116 ..      83     117 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.81
       Vps51 69 k 69
                +
  EPA06463.1 32 E 32
                2 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 8.7e-05
       Vps51  58 dtIrkmksemdkldqklselkqaiskiae 86 
                 +++++mk++m++ d  l+e+kq +ski++
  EPA06463.1  88 SAVNEMKNSMTQTDYDLDEIKQKVSKISS 116
                 5789**********************986 PP

>> SesA  N-terminal domain on NACHT_NTPase and P-loop NTPases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.6    0.0001      0.12       6      86 ..      32     110 ..      17     118 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0001
        SesA   6 aiveaaiklydaikdikglpeaFrevgkrLplvqetLedaksqlesskldedtesaikpvlesckekatkleeifekvapa 86 
                  +++ a ++ ++ ++ikgl +     +++L  +++ L+++ ++++s ++ +++ s++ +++++ k+ +t+ ++ +++++++
  EPA06463.1  32 ELCQNAGEIQKSTHKIKGLAPMMG--KEELGSLSALLDSIFKKIQSVSITDEMFSSLVSAVNEMKNSMTQTDYDLDEIKQK 110
                 234444444444444444444443..58999**************************************999988888554 PP

>> RPAP3_C  Potential Monad-binding region of RPAP3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   6.9e-05     0.077      29      65 ..      65     101 ..      26     118 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.9e-05
     RPAP3_C  29 inpkqlpkiFknsledeilsdildalnerlqeekaed 65 
                 +  + ++ki + s++de++s+++ a+ne +++ ++ d
  EPA06463.1  65 LLDSIFKKIQSVSITDEMFSSLVSAVNEMKNSMTQTD 101
                 444667788889*****************99976554 PP

>> DUF4559  Domain of unknown function (DUF4559)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.4   5.3e-05     0.059     188     301 ..      12     118 ..       2     119 .] 0.76

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.3e-05
     DUF4559 188 eaeeaieellkilkqefeislkeddevrvltdvllslqklkeleeellkedatkldelvlraeeqkiskeellkelqvlkeflnknkdLkenlkedvkk 286
                 e++e+i ++  i++   + +++    ++   ++ +s++k+k l   + ke+   l++l l    +ki++ ++  ++++++ ++  ++++k+ +++   +
  EPA06463.1  12 EINEEISQIITIVD-TCHNGTEL---CQNAGEIQKSTHKIKGLAPMMGKEELGSLSAL-LDSIFKKIQSVSI--TDEMFSSLVSAVNEMKNSMTQTDYD 103
                 34445555433332.33334444...778888999999************99999999.6666788899998..99************9998888889* PP

     DUF4559 287 lqeieekldkldedv 301
                 l+ei++k+ k+ + +
  EPA06463.1 104 LDEIKQKVSKISSSL 118
                 ********9998776 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.7    0.0002      0.22      47     118 ..      40     114 ..       6     119 .] 0.49

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0002
  Baculo_PEP_C  47 Lnalsedlksllaeldt.rldtlltnLtdalnalq.dtlrneL.tnlnsiltnLlssvtNinstLnnllqalnnl 118
                   +++ ++++k l + + + +l +l++ L++  +++q  +++ e+  +l s ++++ +s+t +   L  + q +  +
    EPA06463.1  40 IQKSTHKIKGLAPMMGKeELGSLSALLDSIFKKIQsVSITDEMfSSLVSAVNEMKNSMTQTDYDLDEIKQKVSKI 114
                   334444444444433324455555555555555554223333215555555555555555555555554444443 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1     0.064        72      41      61 ..      56      76 ..       1      85 [. 0.67
   2 ?    8.2   0.4    0.0031       3.5      35      66 ..      88     119 .]      79     119 .] 0.82

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.064
     NPV_P10 41 nekLdaqsaqLaeletkvenI 61
                +e+L ++sa L+++ +k++++
  EPA06463.1 56 KEELGSLSALLDSIFKKIQSV 76
                567778888888887777764 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0031
     NPV_P10  35 pdvtelnekLdaqsaqLaeletkvenIqdiLn 66 
                   v+e+++ + +    L+e+++kv++I++ L+
  EPA06463.1  88 SAVNEMKNSMTQTDYDLDEIKQKVSKISSSLT 119
                 56788888888888899999999999999886 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1      0.22   2.4e+02      81      81 ..      30      30 ..       4      77 .. 0.42
   2 ?   11.0   0.8    0.0003      0.34      78     116 ..      79     117 ..      54     119 .] 0.63

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.22
     DUF1664 81 i 81
                 
  EPA06463.1 30 G 30
                1 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0003
     DUF1664  78 qkeiskeikeevtevredlseigedvesvkeaveglesk 116
                 + e+ +++ + v+e+++ +++++ d++++k+ v+++ s+
  EPA06463.1  79 TDEMFSSLVSAVNEMKNSMTQTDYDLDEIKQKVSKISSS 117
                 335555666777777777777777777777777777665 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   1.5    0.0018         2      43      84 ..      76     118 ..       5     119 .] 0.80

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0018
      DUF948  43 dpilkev.edllakvnelledvneklekvdplteavadlgesv 84 
                  +i++e+   l++ vne+ + +++   ++d++ ++v +++ s+
  EPA06463.1  76 VSITDEMfSSLVSAVNEMKNSMTQTDYDLDEIKQKVSKISSSL 118
                 4566665367888899999999999999999999999988875 PP

>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   5.7    0.0072       8.1     106     164 ..      59     117 ..       3     119 .] 0.57

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0072
                 ....HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
   MCPsignal 106 vesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasieevnqa 164
                 + sl+     + +  + v+ t e ++++v+av+e+++++++     +e+ + +++++++
  EPA06463.1  59 LGSLSALLDSIFKKIQSVSITDEMFSSLVSAVNEMKNSMTQTDYDLDEIKQKVSKISSS 117
                 33444444444444455555555555555555555555555555555555555555544 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.2      0.31   3.5e+02       3      19 ..      11      27 ..       7      50 .. 0.64
   2 ?    8.0   2.0    0.0033       3.7       2      29 ..      90     117 ..      56     119 .] 0.79

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.31
   FlaC_arch  3 delEnklsklsteletv 19
                de+ +++s++ t ++t 
  EPA06463.1 11 DEINEEISQIITIVDTC 27
                56666666666655554 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0033
   FlaC_arch   2 idelEnklsklsteletvkkeneelsks 29 
                 ++e+ n + +++  l+ +k++ +++s+s
  EPA06463.1  90 VNEMKNSMTQTDYDLDEIKQKVSKISSS 117
                 5666666666666666666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1450  (0.0808746); expected 358.6 (0.02)
Passed bias filter:                      743  (0.0414412); expected 358.6 (0.02)
Passed Vit filter:                       114  (0.00635841); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 800.16
//
Query:       EPA06464.1  [L=110]
Description: hypothetical protein BG20_I0459 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.022   14.4   0.0      0.034   13.8   0.0    1.3  1  MASE3     Membrane-associated sensor domain
      0.026   15.0   0.0      0.036   14.5   0.0    1.3  1  DUF5447   Family of unknown function (DUF5447)


Domain annotation for each model (and alignments):
>> MASE3  Membrane-associated sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.8e-06     0.034     133     176 ..       9      53 ..       2      57 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.8e-06
       MASE3 133 iegsGlTpfkiisEylii.lllllalllllrrrkkfekkvlrlll 176
                 i+g  l+ fki+ E++i  +++l+al+ ll+ r ++++k +++++
  EPA06464.1   9 IPGGFLSFFKIAGEVIILgAVFLFALAWLLKARPHNRPKKYSVVV 53 
                 8888899********986267899**************9998876 PP

>> DUF5447  Family of unknown function (DUF5447)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0     4e-06     0.036      58      89 ..      39      71 ..      23      74 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4e-06
     DUF5447 58 khtpserpakywsvvyds.gkptpfvpvrepfe 89
                k  p +rp ky  vv+d  gk +  v +r  f+
  EPA06464.1 39 KARPHNRPKKYSVVVFDVyGKKSEIVDIRTEFK 71
                789**************669*********9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 736.15
//
Query:       EPA06465.1  [L=178]
Description: tRNA intron endonuclease [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.6e-27   92.9   0.0    1.6e-26   92.2   0.0    1.3  1  tRNA_int_endo    tRNA intron endonuclease, catalytic C-termin
    1.9e-17   62.7   0.0    3.6e-17   61.8   0.0    1.5  1  tRNA_int_endo_N  tRNA intron endonuclease, N-terminal domain


Domain annotation for each model (and alignments):
>> tRNA_int_endo  tRNA intron endonuclease, catalytic C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.2   0.0   1.8e-30   1.6e-26       1      84 [.      86     169 ..      86     170 .. 0.96

  Alignments for each domain:
  == domain 1  score: 92.2 bits;  conditional E-value: 1.8e-30
                    HHHHHHHHHHHHHTT-EEEECGGGTSSEEEETSCTTTSSCSEEEEEEETTSEEEHHHHHHHHHHHHHTTSEEEEEEETTTSCEE CS
  tRNA_int_endo   1 falkyavyrdLrekGyvvrsGlkFGadFrvYqrrpslehseylVvvvsedeeldwpdlsaavrlahsvkKklilaivdaegdvt 84 
                    f++ky vy+++r+kGy++++G+kFG+dF+vY+++p+ +h+ +l++v++ +++++ + ++ a+rla+ v+K++ilai + +++v+
     EPA06465.1  86 FDKKYLVYKNFRDKGYIINPGIKFGCDFAVYEKGPGIDHAPFLIQVYNRSDPITSTGIVLAGRLATTVRKQFILAIPKGKEQVD 169
                    899*************************************************************************98877775 PP

>> tRNA_int_endo_N  tRNA intron endonuclease, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.8   0.0     4e-21   3.6e-17       1      66 [.       1      75 [.       1      76 [. 0.97

  Alignments for each domain:
  == domain 1  score: 61.8 bits;  conditional E-value: 4e-21
                     EEEEEETTEEEESSHHHHHHHHHTTT-SEE.........CCTSSEEEEHHHHHHHHHTTSEEEETTSEEE-HHHH CS
  tRNA_int_endo_N  1 vegeLsgdrvlvedeeaakrlyekgfYGkp.........lidepLqLslvEAlYLlekGklevvkggeplsfeel 66
                     +++eL ++r++v+++e++++l+ +g+YGkp         +i+ pL L+l+E+lYLle++k+++ k ++++++ e+
       EPA06465.1  1 MKAELIENRIIVWNIEDSRKLFTHGYYGKPigipkpkpdEINVPLILDLIEGLYLLENKKISISKLNQKITVSEM 75
                     89***************************************************************9999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1122.67
//
Query:       EPA06466.1  [L=120]
Description: putative chemotaxis protein Chey [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-27   94.7   0.8    4.2e-27   94.5   0.8    1.0  1  Response_reg     Response regulator receiver domain
  ------ inclusion threshold ------
      0.077   12.8   0.0      0.086   12.7   0.0    1.1  1  Sulfotransfer_4  Sulfotransferase domain


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.5   0.8   4.7e-31   4.2e-27       1     111 [.       4     114 ..       4     115 .. 0.96

  Alignments for each domain:
  == domain 1  score: 94.5 bits;  conditional E-value: 4.7e-31
                   EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEESSTSHHHHHHHHHCTESEE CS
  Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviiltahseeedavealkagaddf 97 
                   ++i+dD+ ++r +l+++l  ++ + v+ea+dg+ea+el+ + ++dl+llD+ mp+ dGl+++kei ++ p+ ++i++ta ++++ ++++l++ga+ +
    EPA06466.1   4 IMIADDSDAIRLVLTDILLIDEHTIVGEARDGAEAVELFSQLTPDLLLLDLAMPKKDGLTVVKEIIAKYPTAKIILITASDDQKIIQNVLSCGASSY 100
                   89*****************66666************************************************************************* PP

                   EESSG-HHHHHHHH CS
  Response_reg  98 lsKpfdpeeLlkal 111
                   +sKpfd +++lk +
    EPA06466.1 101 ISKPFDFTNVLKTI 114
                   ******99998876 PP

>> Sulfotransfer_4  Sulfotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   9.6e-06     0.086      79     114 ..      63      99 ..      58     120 .] 0.74

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.6e-06
  Sulfotransfer_4  79 lfaeelleayPdakvIlteR.dpekWlksmkktllal 114
                       +++e+++ yP ak+Il++  d +k  +++ ++ ++ 
       EPA06466.1  63 TVVKEIIAKYPTAKIILITAsDDQKIIQNVLSCGASS 99 
                      5799**************9977777777666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 759.37
//
Query:       EPA06467.1  [L=311]
Description: hypothetical protein BG20_I1905 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0022   17.9   0.9      0.049   13.5   0.9    2.4  1  PLDc_2           PLD-like domain
     0.0025   17.0   0.7      0.016   14.4   0.7    1.9  1  Regulator_TrmB   Archaeal transcriptional regulator TrmB
     0.0037   17.6   0.0        3.3    8.2   0.0    2.2  2  RAMA             Restriction Enzyme Adenine Methylase Associa
  ------ inclusion threshold ------
       0.09   12.6   0.0        0.2   11.5   0.0    1.5  1  PhdYeFM_antitox  Antitoxin Phd_YefM, type II toxin-antitoxin 


Domain annotation for each model (and alignments):
>> PLDc_2  PLD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.9   1.1e-05     0.049       2     133 .]     162     295 ..     161     295 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.1e-05
      PLDc_2   2 iqliksAkksidiatyyfvsdreildallkaakrgvkvrilldskkddagavdeaslkelkellleagvevrvfet.llgslHaKlylidgktvivGSs 99 
                 +++i+ Ak++i ++t +   ++ i++++lk+++ g  v+il d++ ++++++d++     + +  ++  +v   ++   + + + ++ +  +++iv S 
  EPA06467.1 162 LEMIEFAKHEIILCTRFA--NDLIINSILKKSTMGISVKILADNSLAESYLNDDTAGVSKSDKNSNERKNVVS-NPyYPSKIDRRYIDVPFSMLIVDSL 257
                 578999**********77..9999*******************988744444433333333332222222111.1111133334444444445555555 PP

      PLDc_2 100 Nltkrgl....dlnlElnvviedkelakeleeeFerlw 133
                 N   + +     + +   v++++++la++++++F+++w
  EPA06467.1 258 NVGIELVnnydGSKFKGVVFVTGETLASQMKQNFNSMW 295
                 54444433333444455566666666666666666666 PP

>> Regulator_TrmB  Archaeal transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.7   3.5e-06     0.016       4     134 ..     150     300 ..     148     309 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.5e-06
                     EESSHHHHHHHHHHHHHH-SSEEEEEE-GGGHHHHHHHHHHHHHTT-EEEEEESS.......................----GGGSSSSEEEEEE CS
  Regulator_TrmB   4 vvksretvierieelIesAenelivslpselLeelreeliaaaergvtVllliyp.......................dedleeldleevatevr 75 
                     ++ ++e +++++ e+Ie A++e+i+++   +   +   + ++   g++V +l  +                       +++   + ++    + r
      EPA06467.1 150 YTSNFEDMVSKVLEMIEFAKHEIILCTRFAN-DLIINSILKKSTMGISVKILADNslaesylnddtagvsksdknsneRKNVVSNPYYPSKIDRR 243
                     67899**********************9998.6677777788888*********99988888766666664433322222222222333333333 PP

                     -S---S.EEEEETTTEEEEE-SSS-EEEE--HHHHH.HHHHHHHHH........HHH-EE CS
  Regulator_TrmB  76 vrrsgapllvivDrkrgvvaprevlrdkeeeyaiif.kekelihvlshyFlttlWktsev 134
                     +++ + + ++ivD+ ++ +   +   d +++++++f + ++l+ ++ + F+++ W +s++
      EPA06467.1 244 YIDVP-FSMLIVDSLNVGIELVNN-YDGSKFKGVVFvTGETLASQMKQNFNSM-WAKSST 300
                     33332.456888886666553322.5666666666525678888888888888.888876 PP

>> RAMA  Restriction Enzyme Adenine Methylase Associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0   0.00074       3.3      22      49 ..      62      91 ..      43     104 .. 0.71
   2 !    7.2   0.0    0.0014       6.4      12      69 ..     228     294 ..     215     304 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00074
        RAMA 22 rar..vtlkdLleagllepGekll.ieykgr 49
                + +  ++lk+L++ g+le  e ++   ++g+
  EPA06467.1 62 K-QyyTRLKQLVDLGILEKNESVYhHTTLGK 91
                2.23589*****************7777775 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0014
        RAMA  12 eealk..tapsr..rar...vtlkdLleagllepGekllieykgrthkAdlladGkIk....gqefgsp 69 
                 +++++   +ps+  r r   v +++L+ +  l+ G +l+ +y g ++k+++   G+       q+f+s+
  EPA06467.1 228 KNVVSnpYYPSKidR-RyidVPFSMLIVDS-LNVGIELVNNYDGSKFKGVVFVTGETLasqmKQNFNSM 294
                 444445434444333.2456******9876.688888888***********999988876655557775 PP

>> PhdYeFM_antitox  Antitoxin Phd_YefM, type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   4.4e-05       0.2       6      33 ..     284     310 ..     281     310 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.4e-05
                      HHHHHHTHHHHHHHHHHHT-EEEEEETT CS
  PhdYeFM_antitox   6 iseakanlselldeveegeepviItrrG 33 
                      +s+ k+n++++  +  ++++ +iItr++
       EPA06467.1 284 ASQMKQNFNSMWAKSSTTPP-QIITRNN 310
                      6899***************7.******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       911  (0.0508115); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2229.37
//
Query:       EPA06468.1  [L=286]
Description: hydrolase, alpha/beta domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-38  131.0   0.0    5.5e-38  130.6   0.0    1.0  1  Hydrolase_4      Serine aminopeptidase, S33
    7.1e-19   68.5   0.1    9.5e-15   54.9   0.0    2.1  2  Abhydrolase_1    alpha/beta hydrolase fold
    1.8e-12   48.3   0.0    2.4e-12   47.9   0.0    1.1  1  Abhydrolase_6    Alpha/beta hydrolase family
    0.00024   20.8   0.1    0.00066   19.3   0.1    1.8  1  LIDHydrolase     Lipid-droplet associated hydrolase
     0.0005   19.2   0.0     0.0009   18.4   0.0    1.4  2  DUF1749          Protein of unknown function (DUF1749)
    0.00054   19.5   0.0      0.004   16.6   0.0    2.0  2  Peptidase_S9     Prolyl oligopeptidase family
    0.00074   19.4   0.0     0.0017   18.3   0.0    1.6  1  Ser_hydrolase    Serine hydrolase
     0.0016   17.5   0.0      0.024   13.6   0.1    2.0  2  Tannase          Tannase and feruloyl esterase
      0.002   17.8   0.1      0.036   13.7   0.0    2.3  2  FSH1             Serine hydrolase (FSH1)
     0.0023   17.6   0.0       0.99    8.9   0.0    2.1  2  Peptidase_S15    X-Pro dipeptidyl-peptidase (S15 family)
  ------ inclusion threshold ------
       0.01   15.4   0.0       0.63    9.6   0.1    2.1  2  DLH              Dienelactone hydrolase family
      0.024   13.6   0.0       0.12   11.2   0.0    2.1  2  Chlorophyllase2  Chlorophyllase enzyme
      0.031   13.3   0.0      0.048   12.7   0.0    1.4  1  DUF1057          Alpha/beta hydrolase of unknown function (DU
      0.066   13.0   0.0        1.5    8.6   0.0    2.6  3  Abhydrolase_5    Alpha/beta hydrolase family
      0.067   12.5   0.0       0.12   11.7   0.0    1.4  1  DUF1350          Protein of unknown function (DUF1350)


Domain annotation for each model (and alignments):
>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.6   0.0   4.6e-41   5.5e-38       5     228 ..      26     250 ..      22     253 .. 0.89

  Alignments for each domain:
  == domain 1  score: 130.6 bits;  conditional E-value: 4.6e-41
  Hydrolase_4   5 avvvlvHGlaehsgryaelaeaLaaqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpelplfllGhSmGGliallyllrypdkva 102
                  +++v +HGl+  ++ ++ la++L+ +Gf+v+ +D  GhG s+gk+g  p+fdd++d l +++ k+k   + ++++ll hS G + +l yl+ry++ ++
   EPA06468.1  26 KTIVCIHGLCCDARIFQYLAQDLTSRGFSVISIDLFGHGTSDGKKG-DPNFDDCLDSLYEIIFKIK---QYSKVYLLSHSIGCTYSLWYLQRYENTLD 119
                  79********************************************.79*********99998888...6679************************* PP

  Hydrolase_4 103 glilsaPalkikakl..k.appllklllkllgk.llpklqv.snnlkadslsrdpevvaayeadplvhgkitvrlllelldamkrleeraakitlPll 195
                  glil aP ++++ k   +  p ++++l  ll + + p l v  +n+++++      +++++ +d+l+ +k ++r l++++ + ++  ++ +ki++P+l
   EPA06468.1 120 GLILLAPYVRVNIKKrsDvEPNIAQFLYLLLRRiISPGLLVdVRNTLPNYTKVGGYQIESMIKDKLLNFKYSLRYLVDVVALKNQNATNLSKIDIPVL 217
                  **********998776533333333333333331346666687899**************************************************** PP

  Hydrolase_4 196 llhGeaDkvvdpeasrelyerlgskdktlklyp 228
                  +lhG++D+ v p+ s+++++ ++s++k+++l++
   EPA06468.1 218 ILHGKKDRQVYPQVSEAFFKMIKSEKKSIQLFD 250
                  *****************************9986 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.9   0.0     8e-18   9.5e-15       2     125 ..      27     146 ..      26     156 .. 0.87
   2 !   11.8   0.0   0.00012      0.14     199     254 ..     189     257 ..     159     258 .. 0.79

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 8e-18
                    EEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHH.HHHHHCTTSSEEEEEETHHHHHHHHHHHHHGG CS
  Abhydrolase_1   2 vlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddld.rildalgddkltlvGhSmGGmialayaaeype 96 
                    ++v++hGl+  + ++    la++L  +gf vi +Dl G+g S+  +    +++ +    d+l+  i       k++l+ hS G++ +l+y+++y +
     EPA06468.1  27 TIVCIHGLCCDARIFQY--LAQDLTSRGFSVISIDLFGHGTSDGKKGD--PNFDD--CLDSLYeIIFKIKQYSKVYLLSHSIGCTYSLWYLQRYEN 116
                    79***************..***************************98..44555..566666366****************************** PP

                    GEEEEEEESE.CSSCCHHHHHHHHHHHHHH CS
  Abhydrolase_1  97 rVkalvllga.idpaaslieaqrqqaksfp 125
                      ++l+ll++ +  +++ +++ +  +++f 
     EPA06468.1 117 TLDGLILLAPyVRVNIKKRSDVEPNIAQFL 146
                    **********98777777777666666665 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00012
                    HHHHHHHC............THHHHSEEEEEEETTCSSSCHHHHHHHHHCHTS.EEEEEEETCSSSHHH CS
  Abhydrolase_1 199 klllrlre............lknvlaptlvisgtsDplvppkaledlaqllpk.krlvvisdagHlafl 254
                    k+ lr+              l+++ +p+l+++g +D+ v p+++e + + +++ k+ ++++d+ H+ f 
     EPA06468.1 189 KYSLRYLVdvvalknqnatnLSKIDIPVLILHGKKDRQVYPQVSEAFFKMIKSeKKSIQLFDCDHWFFD 257
                    33344444566655566777888888***************99999999977779***********985 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.9   0.0     2e-15   2.4e-12       1     211 [.      28     257 ..      28     263 .. 0.67

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 2e-15
                    EEEE--GC.....GCHHHHHHHHCCT.CEEEEE--TTSTS-GGCS--HHHCHHHHHHHCCTT.....TTSEEEEEETCHHHHHHHHHHCC...... CS
  Abhydrolase_6   1 vlllHGagssassWlvapLaallaag.vhvlapDlpGhGrsdpppldledladlaalldelaa...gggpvvlvGHSlGGalalaaapla.....l 87 
                    ++++HG+ ++a++++   La  l+++ + v+++Dl GhG+sd++  d +  +d+++ l e++    ++ +v+l+ HS G++++l    ++      
     EPA06468.1  28 IVCIHGLCCDARIFQ--YLAQDLTSRgFSVISIDLFGHGTSDGKKGDPNF-DDCLDSLYEIIFkikQYSKVYLLSHSIGCTYSLW---YLqryenT 117
                    89************8..8855555555999*********99999999988.8885544444444779999***********9999...66555796 PP

                    .EE.EEES-........----TTTS----TTHHHHHH.TT-C....CCCHCCH.......S-HSCCCCHHHCCCCHCHCCCGHHHHCCHHCHTTCC CS
  Abhydrolase_6  88 vvg.vlldppp......talpagllaaalelllalla.llrl....lawlsre.......plprlfladedadaawrarlarlaallaglgllpaa 164
                    + g +ll+p++       ++  +++a +l lll+++  +  l     ++           +  +++++d      + + l+ l +  a   ++ a+
     EPA06468.1 118 LDGlILLAPYVrvnikkRSDVEPNIAQFLYLLLRRIIsPGLLvdvrNTL---PnytkvggYQIESMIKDKL--LNFKYSLRYLVDVVALKNQN-AT 207
                    6778*****7777665545555553333333333333222222233222...0223445567778888555..55555555555555544444.88 PP

                    HHTT-TTGCEEE.CTT-C.HHHHCHHCCCH..STTEEETCE...SSS-HHH CS
  Abhydrolase_6 165 awadlpvpllvl.ggeDp.lvprllerlla..qagarlpvvlpgaGHlphl 211
                    ++  +  p+l+l g++D+ ++p+  e++    +  ++  + l +++H++++
     EPA06468.1 208 NLSKIDIPVLILhGKKDRqVYPQVSEAFFKmiKSEKKS-IQLFDCDHWFFD 257
                    *********99967999975555555555566466666.7799****9885 PP

>> LIDHydrolase  Lipid-droplet associated hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   5.5e-07   0.00066      81     162 ..      89     171 ..      43     256 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 5.5e-07
  LIDHydrolase  81 sekdvklilvGHSvGaYialevlkrlsersikkvvlLfPtiedi..akSpngkkltkllaylpflalvvglllrvlkllPesvk 162
                    ++ +k++l++HS+G+  +l  l+r+++   ++++lL P +  +  ++S  +  ++++l+ l    +  gll++v ++lP++ k
    EPA06468.1  89 IKQYSKVYLLSHSIGCTYSLWYLQRYENT-LDGLILLAPYVRVNikKRSDVEPNIAQFLYLLLRRIISPGLLVDVRNTLPNYTK 171
                   45778***********************8.**********98751245666667777766666666677788877788888766 PP

>> DUF1749  Protein of unknown function (DUF1749)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   7.6e-07    0.0009      49     142 ..      41     126 ..       6     144 .. 0.83
   2 ?   -3.8   0.0       4.5   5.4e+03     226     246 ..     211     231 ..     205     241 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 7.6e-07
     DUF1749  49 vkelanaldeagwsvvelqlsssyggwGtgsLkrDaeeieklveYlkktksGeekkekvvlmGHstGsqdvlyYltssnerdrekvdgailqap 142
                  + la+ l   g+sv+++ l     g+Gt+  k+ + + + +++ l ++    ++ +kv l+ Hs G+   l Yl++ ++    ++dg il ap
  EPA06468.1  41 FQYLAQDLTSRGFSVISIDL----FGHGTSDGKKGDPNFDDCLDSLYEIIFKIKQYSKVYLLSHSIGCTYSLWYLQRYEN----TLDGLILLAP 126
                 46689999999999999987....69********************9997668899*******************99955....8999999887 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 4.5
     DUF1749 226 kvkepllillsekDefvpesv 246
                 k+  p+lil   kD  v ++v
  EPA06468.1 211 KIDIPVLILHGKKDRQVYPQV 231
                 677789999999998877665 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.33   3.9e+02      10      93 ..      48     122 ..      40     137 .. 0.63
   2 !   16.6   0.0   3.4e-06     0.004     133     178 ..     205     248 ..     196     284 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.33
                   HHCCT-EEEEE--TTSSTTHCHHHHTTSGGGGHHHHHHHHHHHHHHHHTTS--GGGEEEEEETHHHHHHHHHHHH-GGG-SEEE CS
  Peptidase_S9  10 ladrGyvvvvanirGsggyGeafhdagkrklgqnefdDfiaaaealakegyvdserlaitGgSyGGyltgaalnqrpdlFkaav 93 
                   l++rG+ v+ +++ G g          ++k+g+  fdD+++ + +++ + + + +++++  +S G + +++ l +  ++ ++++
    EPA06468.1  48 LTSRGFSVISIDLFGHG--------TSDGKKGDPNFDDCLDSLYEIIFK-IKQYSKVYLLSHSIGCTYSLWYLQRYENTLDGLI 122
                   56788888888877766........446677777777777766666433.3334666666666666666666666555555555 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 3.4e-06
                   HH-CGGG-----EEEEEEETT-SSS-THHHHHHHHHHH--S-SEEE CS
  Peptidase_S9 133 pyspldnvkaypplLlihGlaDdrvppaealklvaaLqkkgknvll 178
                   ++++l +  ++ p+L++hG +D +v p+ ++ +++  ++++k ++l
    EPA06468.1 205 NATNLSK--IDIPVLILHGKKDRQVYPQVSEAFFKMIKSEKKSIQL 248
                   4444444..99**************************988887665 PP

>> Ser_hydrolase  Serine hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.4e-06    0.0017      36      92 ..      72     129 ..      65     164 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.4e-06
                    S--HHHHHHHHHHHHHC-ST..TEEEEEETCHHHHHHHHHHHTTSSSEEEEEEET--SG CS
  Ser_hydrolase  36 kPdledWvaaleaaveaaee..kvvlvAHSlgclavlhaaelqlakkvagalLVapadv 92 
                    +P+++d +++l + + ++++  kv+l++HS+gc  +l ++ ++ ++ ++g +L ap   
     EPA06468.1  72 DPNFDDCLDSLYEIIFKIKQysKVYLLSHSIGCTYSLWYL-QRYENTLDGLILLAPYVR 129
                    577778888888777666542279**********999999.9**************643 PP

>> Tannase  Tannase and feruloyl esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.065        78     111     151 ..      90     130 ..      85     166 .. 0.87
   2 !   13.6   0.1     2e-05     0.024     322     421 ..     188     286 .]     159     286 .] 0.84

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.065
     Tannase 111 kspersYfeGcSdGGRegltaaqRypddydGiiagapalnf 151
                 k++ ++Y    S G   +l   qRy +  dG i  ap ++ 
  EPA06468.1  90 KQYSKVYLLSHSIGCTYSLWYLQRYENTLDGLILLAPYVRV 130
                 67889999999**********************99998776 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 2e-05
     Tannase 322 kttslvelsslidatepdlskfrsrgGklilyhgtaDpvvspadsikyyesveaklgad.leeleeFarlylvpGvaHcgggsgtsaidlLealvdWVE 419
                  ++sl+ l +++   + + +++++    ++++hg++D  v p+ s ++++ ++++  +  l + +++  ++ v   + + ++s +s  d L+ l dW E
  EPA06468.1 188 FKYSLRYLVDVVALKNQNATNLSKIDIPVLILHGKKDRQVYPQVSEAFFKMIKSEKKSIqLFDCDHW--FFDVIFYEQTQNNSQESRNDFLKHLSDWLE 284
                 36788888999999999999999999999***********************998855446666666..9****************************9 PP

     Tannase 420 ng 421
                  +
  EPA06468.1 285 RN 286
                 75 PP

>> FSH1  Serine hydrolase (FSH1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.17     2e+02       5      26 ..      26      47 ..      21      53 .. 0.84
   2 !   13.7   0.0     3e-05     0.036     153     200 ..     205     253 ..     176     255 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.17
        FSH1  5 kkiLcLhGytqsgeiFraktsa 26
                k+i c+hG   +++iF++  ++
  EPA06468.1 26 KTIVCIHGLCCDARIFQYLAQD 47
                789*************986665 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 3e-05
        FSH1 153 eyyeedkiqtptLhvlGelDtvvdeerseaLaeafkns.skvlkHpggH 200
                 ++ + +ki +p+L ++G++D  v ++ sea+ +++k++ + +  ++ +H
  EPA06468.1 205 NATNLSKIDIPVLILHGKKDRQVYPQVSEAFFKMIKSEkKSIQLFDCDH 253
                 44467899****************************9965555565555 PP

>> Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.0    0.0043       5.1      53      75 ..      48      70 ..       8      86 .. 0.76
   2 !    8.9   0.0   0.00083      0.99     218     258 ..     204     244 ..     193     254 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0043
                   HHHTT-EEEEEE-TTSTTS-S-- CS
  Peptidase_S15 53 fvarGYavVvqdvrGtggSeGef 75
                   + +rG+ v+  d  G+g S+G+ 
     EPA06468.1 48 LTSRGFSVISIDLFGHGTSDGKK 70
                   789******************74 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00083
                    T-HHHHHCT--S-EEEEEECCSSTTCCHHHHHH.HHHCCTT- CS
  Peptidase_S15 218 rnlsedadkvkapvllvgGwnDwnvkngaikly.ealkapgv 258
                    +n+ ++++k+++pvl+++G  D +v  ++++++ + +k++++
     EPA06468.1 204 QNA-TNLSKIDIPVLILHGKKDRQVYPQVSEAFfKMIKSEKK 244
                    444.479***************99996666655055555544 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.027        33       2      53 ..      14      65 ..      13      95 .. 0.82
   2 ?    9.6   0.1   0.00053      0.63     135     213 ..     204     283 ..     198     286 .] 0.73

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.027
         DLH  2 daylatpknakkpvvvviqeifGvndnikdiserlaeeGYvalaPdlYarqa 53
                +++ +tp+++  +++v i+ +      ++  ++ l + G+ ++  dl+  + 
  EPA06468.1 14 NTINFTPQKPSGKTIVCIHGLCCDARIFQYLAQDLTSRGFSVISIDLFGHGT 65
                56778999999********999999999999*************99998776 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00053
         DLH 135 keleeaakikapilalfgeeDefipadevekleealkaanvdlelkvYpgagHaFan....dsresyneeaaedawervlelf 213
                 ++ ++  ki  p+l+l+g++D  +  +  e + + +k +++ ++l  ++  +H F+     ++ ++ ++e+ +d  +++ +++
  EPA06468.1 204 QNATNLSKIDIPVLILHGKKDRQVYPQVSEAFFKMIKSEKKSIQL--FD-CDHWFFDvifyEQTQNNSQESRNDFLKHLSDWL 283
                 66778899****************999999999999877777665..55.778886522224444666666666666666666 PP

>> Chlorophyllase2  Chlorophyllase enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0    0.0001      0.12      19     142 ..      27     144 ..      12     148 .. 0.74
   2 ?   -2.0   0.0       1.1   1.4e+03      23      54 ..     172     205 ..     165     219 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0001
  Chlorophyllase2  19 vllflhGylllnslYsqlLkhiashgfivvapqlykvaeadakeiksaakvlnWlakgLesvlpeevepdlsklalsgHSrGgktafalalgka 112
                       ++ +hG+++   +++ l + ++s gf v++  l    ++   + k+     +   + L +++ + +  + sk+ l  HS G+  ++     ++
       EPA06468.1  27 TIVCIHGLCCDARIFQYLAQDLTSRGFSVISIDLFGHGTS---DGKKGDPNFDDCLDSLYEIIFK-I-KQYSKVYLLSHSIGCTYSLWYLQRYE 115
                      46789****************************9887444...5555555555555666655543.3.46899999999999999887766666 PP

  Chlorophyllase2 113 ktslkfsaligvdPvag..askskqtepkiLt 142
                      +   ++  li + P      +k + +ep+i +
       EPA06468.1 116 N---TLDGLILLAPYVRvnIKKRSDVEPNIAQ 144
                      6...8899999999776456667777888765 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.1
  Chlorophyllase2  23 lhGylllnslYsqlLkhiashgfiv..vapqlyk 54 
                      ++Gy++ + +  +lL+   s +++v  va + ++
       EPA06468.1 172 VGGYQIESMIKDKLLNFKYSLRYLVdvVALKNQN 205
                      5789999999999999888888886224444333 PP

>> DUF1057  Alpha/beta hydrolase of unknown function (DUF1057)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0     4e-05     0.048      36     137 ..      26     128 ..      16     237 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4e-05
     DUF1057  36 GtvvalhGsPGshnDfkYirskleelkiRligvnyPGfefvtgylgqkytnaeRnsyskalleelelkgklillghsRGcenaLqlavtl..eahGlvl 132
                  t+v +hG     + f+Y+ + l +    +i+++  G    +g +g+   +   +s  + ++ +++   k+ ll+hs Gc  +L     +   + Gl+l
  EPA06468.1  26 KTIVCIHGLCCDARIFQYLAQDLTSRGFSVISIDLFGHGTSDGKKGDPNFDDCLDSLYEIIF-KIKQYSKVYLLSHSIGCTYSLWYLQRYenTLDGLIL 123
                 49*************************************99999999877777777766555.455569*************99876665447889999 PP

     DUF1057 133 inptG 137
                 + p  
  EPA06468.1 124 LAPYV 128
                 98864 PP

>> Abhydrolase_5  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.47   5.6e+02       5      32 ..      31      58 ..      27      61 .. 0.82
   2 ?    8.6   0.0    0.0013       1.5      48      92 ..      84     129 ..      78     143 .. 0.82
   3 ?   -0.1   0.0      0.57   6.8e+02      93     124 ..     206     237 ..     159     272 .. 0.65

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.47
  Abhydrolase_5  5 YpGakveaesYaelaeklaksGyevvlv 32
                     G   +a+ + +la++l++ G++v+ +
     EPA06468.1 31 IHGLCCDARIFQYLAQDLTSRGFSVISI 58
                   567788999999***********99755 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0013
  Abhydrolase_5  48 eiikeapklekfvvgGhslGGvvasrfaaeee.kiegvvflasYPe 92 
                    eii + ++  k ++  hs+G   +  + ++ e +++g+++la Y  
     EPA06468.1  84 EIIFKIKQYSKVYLLSHSIGCTYSLWYLQRYEnTLDGLILLAPYVR 129
                    6777788888999***********9999976549*********975 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.57
  Abhydrolase_5  93 kdelselskkvlsivgteDgvlnvkslekakk 124
                      +ls+  ++vl + g++D  +  +  e   k
     EPA06468.1 206 ATNLSKIDIPVLILHGKKDRQVYPQVSEAFFK 237
                    35688999999999999998776655555555 PP

>> DUF1350  Protein of unknown function (DUF1350)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   9.7e-05      0.12      36     122 ..      41     125 ..      19     148 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.7e-05
     DUF1350  36 yrwlleelgeagyvviatpfvntldhqai.arsvlnkleiilerlqkrgeltkallpvyglghslgcklhlligslyeveragnilva 122
                 +++l ++l+ +g++vi+    + + h++   ++   +++  l+ l +     k++  vy l hs+gc   l     ye    g il+a
  EPA06468.1  41 FQYLAQDLTSRGFSVISI---DLFGHGTSdGKKGDPNFDDCLDSLYEIIFKIKQYSKVYLLSHSIGCTYSLWYLQRYENTLDGLILLA 125
                 667788888888888874...5577765414666789**********9999999*****************99999999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 1886.14
//
Query:       EPA06469.1  [L=110]
Description: hypothetical protein BG20_I1906 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       846  (0.0471861); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.33s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 649.39
//
Query:       EPA06470.1  [L=268]
Description: methyltransferase domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-16   60.9   0.0    1.7e-16   60.4   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    1.3e-13   51.5   0.0    2.3e-13   50.6   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    1.8e-13   50.7   0.0    2.7e-13   50.1   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    5.3e-12   46.2   0.0    8.2e-12   45.6   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    3.8e-08   32.9   0.0    5.5e-08   32.4   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
    1.3e-07   32.3   0.0    3.5e-07   30.9   0.0    1.7  2  Methyltransf_12  Methyltransferase domain
    5.8e-07   29.5   0.0      1e-06   28.7   0.0    1.4  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    4.3e-05   23.1   0.2      9e-05   22.1   0.1    1.7  2  MTS              Methyltransferase small domain
    4.7e-05   22.8   0.2    8.3e-05   22.0   0.1    1.5  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    0.00024   21.2   0.1     0.0014   18.8   0.1    2.0  2  FtsJ             FtsJ-like methyltransferase
    0.00062   19.2   0.3    0.00094   18.6   0.3    1.2  1  TehB             Tellurite resistance protein TehB
      0.002   17.6   0.9       0.02   14.4   0.4    2.2  2  CheR             CheR methyltransferase, SAM binding domain
     0.0093   15.4   0.1      0.014   14.8   0.1    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
       0.01   15.6   0.1        0.2   11.4   0.0    2.2  2  N6_N4_Mtase      DNA methylase
  ------ inclusion threshold ------
       0.01   15.8   0.0      0.017   15.1   0.0    1.3  1  Methyltransf_32  Methyltransferase domain
      0.031   13.9   0.1      0.068   12.7   0.1    1.6  2  MetW             Methionine biosynthesis protein MetW
      0.039   12.9   0.0      0.068   12.1   0.0    1.3  1  Methyltransf_9   Protein of unknown function (DUF1698)
      0.043   12.9   0.1      0.082   12.0   0.1    1.4  1  DREV             DREV methyltransferase
       0.12   11.9   0.0       0.22   11.0   0.0    1.4  1  Methyltransf_4   Putative methyltransferase


Domain annotation for each model (and alignments):
>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.4   0.0   1.8e-19   1.7e-16       2     118 ..      38     145 ..      37     190 .. 0.86

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 1.8e-19
  Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnevlnaladpdkile 95 
                      + g+r +D+GCG G+ ++ + e +g+ + v+G Di+++ + ++++n ++l   n++F+q di + +  ++  kfD++ s+  + +l+++ k+++
       EPA06470.1  38 KPGMRCIDIGCGIGNVSKLMKEMVGKSGSVIGTDIEKKYVDYCNNNWKSL---NISFSQDDILNSN--IS-GKFDIVYSRLMFVHLKNKLKAIK 125
                      6799*****************************************97744...778********77..77.9********************** PP

  Methyltransf_31  96 eiervlkpggilliedprllael 118
                       +++ +k++g ++i++ +     
       EPA06470.1 126 LMKEIVKKNGMIIIQELD---HA 145
                      ****************99...33 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.6   0.0   2.5e-16   2.3e-13       2      97 .]      44     135 ..      43     135 .. 0.90

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 2.5e-16
                      EEET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHHHHHHHHHHHHHEE CS
  Methyltransf_25   2 LdlGcGtGrltlalakrlg.kakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsdedlekalkeiarvLk 94 
                      +d+GcG G++++ + + +g +++v+g+Di ++++++++++   ++ln++f q d+ + +   g+fD+v+s+ ++ hl+  +  ka+k +++++k
       EPA06470.1  44 IDIGCGIGNVSKLMKEMVGkSGSVIGTDIEKKYVDYCNNNW--KSLNISFSQDDILNSNIS-GKFDIVYSRLMFVHLK--NKLKAIKLMKEIVK 132
                      59***************9669********************..568*********999865.7*******87777776..66799******999 PP

                      EEE CS
  Methyltransf_25  95 pgG 97 
                      ++G
       EPA06470.1 133 KNG 135
                      998 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.1   0.0   2.9e-16   2.7e-13      15     161 ..      31     192 ..      18     195 .. 0.76

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 2.9e-16
  Methyltransf_23  15 rllpk.lraggrvLdiGcGtGillevlren.gf..svtgvDlspeaveiae..kakkaqkdqfdeqeaaepqgkfdlIvlrevlehvpdppell 102
                       l +  l++g+r++diGcG G+++++++e  g+  sv+g D+  + v+      ++ +++ + d +  ++ +gkfd++++r ++ h+++  +++
       EPA06470.1  31 ALIKAgLKPGMRCIDIGCGIGNVSKLMKEMvGKsgSVIGTDIEKKYVDYCNnnWKSLNISFSQDDILNSNISGKFDIVYSRLMFVHLKNKLKAI 124
                      333333899******************88647788999*9*97655554447745555555555556777888********************* PP

  Methyltransf_23 103 rqiatllkpgGylllseplasl...........kedrllldwlylvpagrhisffsarslkelleeaGle 161
                      + +++++k +G ++++e +  +           ++ + l+++    ++ + +  fs r + +l+ + Gl+
       EPA06470.1 125 KLMKEIVKKNGMIIIQELD--HapgswlshpdkPSVEVLRKIYVKLIKKTGGDPFSGRKIYDLFLDEGLQ 192
                      *****************85..3235556666654666666677777777888888888888888887776 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.0   8.7e-15   8.2e-12       2      96 .]      45     139 ..      44     139 .. 0.93

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 8.7e-15
                      EET-TTSHHHHHHHHTT...SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHHHHHHHHHHEEEEE CS
  Methyltransf_11   2 dvGcGtGrlaealakrg...arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedpekalkeiaRvLkpgG 92 
                      d+GcG G +++ +++ +   ++v+g+D+ k+ +++++++ +  +  ++f + d+ + ++ +++fD+v+s+ ++ h+++  ka+k ++ ++k++G
       EPA06470.1  45 DIGCGIGNVSKLMKEMVgksGSVIGTDIEKKYVDYCNNNWKSLN--ISFSQDDILNSNI-SGKFDIVYSRLMFVHLKNKLKAIKLMKEIVKKNG 135
                      9*************7777889***************99999987..99*******9766.56******************************** PP

                      EEEE CS
  Methyltransf_11  93 llvi 96 
                      +++i
       EPA06470.1 136 MIII 139
                      *986 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.0   5.9e-11   5.5e-08      53     168 ..      30     143 ..      12     173 .. 0.84

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 5.9e-11
                 HHHTTTT--TT-EEEEES-TTSHH...HHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG-----SEEEEES-GGGTSGGGHHHH CS
        CMAS  53 lileklelkpGmtlLdiGcGWGsl...vrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedldekvdrvvsvgafehvgkenydtf 148
                  +l k++lkpGm+ +diGcG G++   ++++v +   +v+g  + k+   +++++ ++l+++ +++  l    ++++k+d v s  +f h++++   + 
  EPA06470.1  30 EALIKAGLKPGMRCIDIGCGIGNVsklMKEMVGK-SGSVIGTDIEKKYVDYCNNNWKSLNISFSQDDILN--SNISGKFDIVYSRLMFVHLKNK--LKA 123
                 67889*****************862226677777.779*********************98876654433..689*************999755..566 PP

                 HHHHHHHS-TT-EEEEEEEE CS
        CMAS 149 fkklkkllkedGllllhtit 168
                 +k +k+++k++G+++++ + 
  EPA06470.1 124 IKLMKEIVKKNGMIIIQELD 143
                 8*************999765 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.0   3.7e-10   3.5e-07       2      99 .]      45     137 ..      44     137 .. 0.84
   2 ?   -2.4   0.0       8.8   8.3e+03      76      97 ..     150     173 ..     148     174 .. 0.73

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 3.7e-10
  Methyltransf_12   2 eiGcGtGsllrallekl.pdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg..ssfDlvvasnvlhhlkdirevldnirkl 92 
                      +iGcG G++++ + e   +  +++g+Di ++ +        +++nnn++ +++   +++ l ++  ++fD+v++   + hlk++ ++++ +++ 
       EPA06470.1  45 DIGCGIGNVSKLMKEMVgKSGSVIGTDIEKKYV--------DYCNNNWKSLNISFSQDDILNSNisGKFDIVYSRLMFVHLKNKLKAIKLMKEI 130
                      9*************9998888888*********........77777777666555554444444559*************************** PP

  Methyltransf_12  93 LkpgGrl 99 
                      +k++G++
       EPA06470.1 131 VKKNGMI 137
                      *****86 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 8.8
  Methyltransf_12  76 lhhlkdir.evldnir.klLkpgG 97 
                      l+h +++  evl++i+ kl+k+ G
       EPA06470.1 150 LSHPDKPSvEVLRKIYvKLIKKTG 173
                      667755555999999988888765 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0   1.1e-09     1e-06      69     124 ..      32      90 ..       8     104 .. 0.84

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 1.1e-09
                 TT...--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTC CS
        PCMT  69 le...lkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldle 124
                 l    lk+g+r +++G+G G  + ++ ++vg++g v++ +  k+ v+  ++n k l+++
  EPA06470.1  32 LIkagLKPGMRCIDIGCGIGNVSKLMKEMVGKSGSVIGTDIEKKYVDYCNNNWKSLNIS 90 
                 33367*****************************************9999999888765 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.1   9.5e-08     9e-05      32     103 ..      40     110 ..      27     141 .. 0.87
   2 ?   -3.5   0.0       7.1   6.7e+03     144     164 ..     230     250 ..     224     254 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 9.5e-08
                 CSEEEEET-TTSHHHHHHHHHTTC.E.EEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEEEE CS
         MTS  32 sgkvlDlGcGaGvlgaalakespeae.vtlvdvdarAlesakenleanklevevvasdvleeveekkfdlivs 103
                   + +D+GcG+G ++  ++++  +   v  +d++++ ++ +++n+++ +  +++ + d+l+    +kfd++ s
  EPA06470.1  40 GMRCIDIGCGIGNVSKLMKEMVGKSGsVIGTDIEKKYVDYCNNNWKSLN--ISFSQDDILNSNISGKFDIVYS 110
                 4578****************99887669*****************9876..7999****999888****9865 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 7.1
                 CHHHHHHHHHS--EEEEEESS CS
         MTS 144 gyeslleelfgnvevvaktkk 164
                   es  e+lf +++++ k+k+
  EPA06470.1 230 MTESQFEQLFDDLKEISKDKR 250
                 456778999999999888876 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.1   8.8e-08   8.3e-05      44     157 ..      36     145 ..      14     169 .. 0.85
   2 ?   -3.7   0.0       6.2   5.8e+03     176     187 ..     211     222 ..     201     241 .. 0.67

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 8.8e-08
                      -S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES-GGG-S-HHHHHH CS
  Ubie_methyltran  44 avkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtvsfGlrnvtDklkaLk 137
                      + k+g + +D+ +G g+++  + ++vg++g v++ Di+++ ++  ++  k     ni f q +  +     + fD+v     +  + +klka+k
       EPA06470.1  36 GLKPGMRCIDIGCGIGNVSKLMKEMVGKSGSVIGTDIEKKYVDYCNNNWKS---LNISFSQDDILNS-NISGKFDIVYSRLMFVHLKNKLKAIK 125
                      668999************************************999887664...5777766554443.35699****999999999******** PP

                      HHHHHEEEEEEEEEEEE--- CS
  Ubie_methyltran 138 eayrvlkpGGrlvvlefskv 157
                       +  ++k  G +++ e+ + 
       EPA06470.1 126 LMKEIVKKNGMIIIQELDHA 145
                      **********9999988765 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 6.2
                      HHHHHHHS-HHH CS
  Ubie_methyltran 176 vlGkllakdlds 187
                       lG ++a++l+s
       EPA06470.1 211 ELGWMFADSLKS 222
                      578888888775 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   1.5e-06    0.0014      16      77 ..      35     103 ..      23     144 .. 0.74
   2 ?    0.4   0.0      0.63   5.9e+02       9      36 ..     121     150 ..     116     159 .. 0.62

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.5e-06
                 HT-S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS......HHH...TTEEEECS-CCCSSHHH CS
        FtsJ  16 fklfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm......apl...pgvttiqgditdpetie 77 
                  + +kpg++++D+g++ G+ s+ + + +g++g v++ D+ +       +      ++++ q di++ +   
  EPA06470.1  35 AG-LKPGMRCIDIGCGIGNVSKLMKEMVGKSGSVIGTDIEKKyvdycnN-NwksLNISFSQDDILNSNISG 103
                 45.789***********************9*********7665765432.123346666688888766554 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.63
                 HHHHHHHHT-S-.TT-E.EEECT-TTSHHH CS
        FtsJ   9 Lleidekfklfk.pgkt.vvDlgaaPGgws 36 
                 L  i+   +++k +g+  + +l  aPG+w 
  EPA06470.1 121 LKAIKLMKEIVKkNGMIiIQELDHAPGSWL 150
                 444444444444233333456777888885 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.3     1e-06   0.00094      29     132 ..      37     139 ..      28     146 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1e-06
                 S-S-.EEEEES-TTSHHHHHH.HHTT-E..EEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG----S-EEEEEEESSGGGS-GGGHHHHHHHHHHT CS
        TehB  29 vkpg.kvldlgcgqgrnslyl.sllgyd..vtawdknensiafleeikekenlknistalydineaklderydfilstvvlmfleaeripsiienmqec 123
                 +kpg +++d+gcg g  s  + +++g    v   d +++ + + ++    ++l+ is +  di + +++ ++d++ s ++++ l+++   + i+ m+e 
  EPA06470.1  37 LKPGmRCIDIGCGIGNVSKLMkEMVGKSgsVIGTDIEKKYVDYCNNN--WKSLN-ISFSQDDILNSNISGKFDIVYSRLMFVHLKNK--LKAIKLMKEI 130
                 56763689*******99866515666531155556666666655543..44565.99********************9777777666..5779999999 PP

                 EEEEEEEEE CS
        TehB 124 tkvggynli 132
                  k  g  +i
  EPA06470.1 131 VKKNGMIII 139
                 998886544 PP

>> CheR  CheR methyltransferase, SAM binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0       0.2   1.9e+02      32      80 ..      40      80 ..      16      85 .. 0.64
   2 !   14.4   0.4   2.1e-05      0.02     119     173 ..      88     139 ..      79     147 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.2
                SEEEEEES-TTTHHHHHHHHHHHCHSTTTSSS-EEEEEEESSCHHHHHH CS
        CheR 32 rvriwsagcssGeEpYslAmllketlpkaaklkvkilAtDidlkvlekA 80
                 +r   +gc+ G+    ++ l+ke++ k      ++++tDi++k ++ +
  EPA06470.1 40 GMRCIDIGCGIGN----VSKLMKEMVGKSG----SVIGTDIEKKYVDYC 80
                4666666776665....4455566444444....599****99998766 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 2.1e-05
                 TEEEEE--TTT-SGGG--EEEEEE-SSGGGC-CHHHHHHHHHHHCCEEEEEEEEE CS
        CheR 119 lvkFeklnllekksvlgklDvifcrnvliYfdeetqekvlerfaeklkpgglLll 173
                 ++ F + ++l+ ++++gk+D++ +r   ++ + +++ k ++ + e +k++g++++
  EPA06470.1  88 NISFSQDDILN-SNISGKFDIVYSRL--MFVHLKNKLKAIKLMKEIVKKNGMIII 139
                 699********.*************5..55566778889999*********9987 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   1.4e-05     0.014     159     258 ..      37     139 ..      27     141 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.4e-05
        PrmA 159 vkegeevlDvGtGSGiLa.iaaakLgak.kvvavDiDevAvkvakeNaelNkvea.klevalseellkeekadvivaNILaevlie...laedikklvk 251
                 +k+g + +D+G+G G  + +   ++g + +v+++Di++  v+  ++N +  +++  + ++ l++++ + +k+d++ +  +   l +    ++ +k++vk
  EPA06470.1  37 LKPGMRCIDIGCGIGNVSkLMKEMVGKSgSVIGTDIEKKYVDYCNNNWKSLNISFsQDDI-LNSNI-S-GKFDIVYSRLMFVHLKNklkAIKLMKEIVK 132
                 688899********97773666677754389****************9987777734443.54555.4.79*****99998877651113556789999 PP

        PrmA 252 eggllil 258
                 ++g++i+
  EPA06470.1 133 KNGMIII 139
                 9999985 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   0.00021       0.2     183     229 ..      31      80 ..      28      82 .. 0.93
   2 ?    2.4   0.0      0.12   1.1e+02      35      59 ..     120     144 ..     115     250 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00021
                  HHHHHHS-TT-EEEETT-TTTHHHHHHHHTT-E...EEEEESSHHHHHHH CS
  N6_N4_Mtase 183 rlIklstkkgdivlDpFaGSGtTavaakelgrk...fiGieieeeyvela 229
                   lIk+ +k+g  ++D  +G G   +  ke+  k    iG++ie++yv+  
   EPA06470.1  31 ALIKAGLKPGMRCIDIGCGIGNVSKLMKEMVGKsgsVIGTDIEKKYVDYC 80 
                  69****************************9998999*********9865 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.12
                  HHHHHHHHHHHEEEEEEEEEEE-CC CS
  N6_N4_Mtase  35 lekvlkevrrvLkddgsifinidds 59 
                    k +k+++++ k++g i+i+  d+
   EPA06470.1 120 KLKAIKLMKEIVKKNGMIIIQELDH 144
                  568899*************996655 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   1.8e-05     0.017      24      78 ..      38      91 ..      15     111 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.8e-05
  Methyltransf_32 24 sgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkf 78
                     ++ ++ +D+G+G g  s  ++   + ++ +v+g d++++ v+ +++  + l+  f
       EPA06470.1 38 KPGMRCIDIGCGIGNVSKLMKE-MVGKSGSVIGTDIEKKYVDYCNNNWKSLNISF 91
                     556789**************99.67799*****************9998888554 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   7.2e-05     0.068       6      79 ..      32     108 ..      28     140 .. 0.65
   2 ?   -2.6   0.0       3.8   3.6e+03      75     112 ..     219     258 ..     207     259 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.2e-05
        MetW   6 liaelikpgsrvldlGcGdGellellkeekqvdgr..Gleldeegvaecva..kGlsviqgdldkdlenfedksfdyv 79 
                 li+  +kpg r +d+GcG G++ +l+ke  + +g   G +++++ v  c +  k l++     d+ l+   + +fd+v
  EPA06470.1  32 LIKAGLKPGMRCIDIGCGIGNVSKLMKEMVGKSGSviGTDIEKKYVDYCNNnwKSLNIS-FSQDDILNSNISGKFDIV 108
                 5667789********************98766664225566677777776522455543.334445666666666665 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.8
        MetW  75 sfdyvvlsqtlqatrnpkevldellrig..rraivsfPnf 112
                 s+   +ls  + +  + ++++d+l  i+  +r+ v++  f
  EPA06470.1 219 SLKSSILSNNFMTESQFEQLFDDLKEISkdKRCFVTYARF 258
                 5566777777777777888888887776224777777655 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   7.2e-05     0.068     118     219 ..      42     141 ..      34     149 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.2e-05
                     EEEEET-TTSH...HHHHHHHCT-SEEEEE---HHHHHHHHHHHCCTTTTSSEEEE---GGGS-T...---EEEEEEES-GGG-S-HHHHHHHHH CS
  Methyltransf_9 118 tildvGcgnGy...hlwrmvgegaklvvGidPselfliqfeavrkllgedqrahllplgieqlpe...leafdtvfsmGvlyhrrsPldhllqlk 206
                     + +d+Gcg G     +  mvg+   +v+G d ++ ++          +++ ++ ++ ++ +++ +      fd+v+s  ++ h +  l  +  +k
      EPA06470.1  42 RCIDIGCGIGNvskLMKEMVGKS-GSVIGTDIEKKYVDY-------CNNNWKSLNISFSQDDILNsniSGKFDIVYSRLMFVHLKNKLKAIKLMK 128
                     678****9986222467788865.5799*9999988743.......3344444444444444433122568************************ PP

                     CTEEEEEEEEEEE CS
  Methyltransf_9 207 dqlvkgGelvlet 219
                     + ++k+G ++++ 
      EPA06470.1 129 EIVKKNGMIIIQE 141
                     ********99875 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   8.7e-05     0.082      96     186 ..      41     139 ..      24     143 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.7e-05
        DREV  96 kklldlGaGdGeitkrvaptfee...vyatelsetmrdrl..kkkkynv.lsalelqetdv..kldlilclnlldrcfdplklledirsalepngrviv 186
                  + +d+G G G+++k +++++ +   v  t++ ++  d    ++k  n+ +s+ ++ ++++  k+d++ +  ++    + lk ++ ++++ + ng +i+
  EPA06470.1  41 MRCIDIGCGIGNVSKLMKEMVGKsgsVIGTDIEKKYVDYCnnNWKSLNIsFSQDDILNSNIsgKFDIVYSRLMFVHLKNKLKAIKLMKEIVKKNGMIII 139
                 6889*****************98899*********99865227999998345555655554339***98866666666666666666666777777765 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00024      0.22       4      49 ..      42      88 ..      39     106 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00024
                    EEEEET-TTSHHHHHHHHHSTTS.EEEEEES-HHHHHHHHHHHHHCT CS
  Methyltransf_4  4 vvleiGcGkGeflvalAkknPdk.nflGiEirvkvvakvlkkieale 49
                     +++iGcG G++   + ++  +  +++G +i++k v++++++ + l+
      EPA06470.1 42 RCIDIGCGIGNVSKLMKEMVGKSgSVIGTDIEKKYVDYCNNNWKSLN 88
                    589*******9887777776654389**************9988774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       909  (0.0507); expected 358.6 (0.02)
Passed bias filter:                      631  (0.0351944); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 1635.58
//
Query:       EPA06471.1  [L=112]
Description: hypothetical protein BG20_I1901, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.028   14.3   0.0      0.043   13.7   0.0    1.3  1  TrmB      Sugar-specific transcriptional regulator TrmB


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.4e-06     0.043      23      58 ..      33      68 ..      25      80 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.4e-06
                CHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
        TrmB 23 atadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                +++  i e+ ++p++++Y+ +++L++ G+  + k +
  EPA06471.1 33 KNVAIIMEKNDLPQTTCYRKINELIKEGFFIITKYT 68
                6788899*********************98887755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       747  (0.0416643); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 773.26
//
Query:       EPA06472.1  [L=88]
Description: hypothetical protein BG20_I1907, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00022   20.8   0.0    0.00022   20.8   0.0    1.0  1  DUF1129   Protein of unknown function (DUF1129)
  ------ inclusion threshold ------
      0.017   15.8   0.3       0.02   15.6   0.3    1.1  1  PrgI      PrgI family protein
      0.023   14.8   0.0      0.029   14.5   0.0    1.2  1  DUF2178   Predicted membrane protein (DUF2178)
      0.091   11.5   0.0      0.098   11.4   0.0    1.0  1  DUF2207   Predicted membrane protein (DUF2207)
       0.13   10.9   1.8       0.14   10.8   1.8    1.0  1  EMP70     Endomembrane protein 70


Domain annotation for each model (and alignments):
>> DUF1129  Protein of unknown function (DUF1129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   6.2e-08   0.00022      69     143 ..       6      84 ..       1      88 [] 0.76

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 6.2e-08
     DUF1129  69 akkeskenpwlmalDnsLlllalfallfgilalfskkkqtas.iGlitlllva..lvgGlamvlvyrlltre..kkkkkr 143
                 +++e+ +n +   +D + l++ l+++++g+la  +  + ++s  G+++l ++a  ++ G++++ +++ ++ e  ++kk+r
  EPA06472.1   6 EQDEP-DNSKESSVDFAILFFTLLCVFMGLLAGYGAFTIHSSlLGVMVLCFLAatVLCGFIFTAINKNVSDEklDHKKSR 84 
                 22333.478999********************99998888888898888777622578***********98754444444 PP

>> PrgI  PrgI family protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.3   5.6e-06      0.02      22      66 ..      27      69 ..      12      85 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.6e-06
        PrgI 22 liflvlallvaiglylllrafleelasvlvillavPvaalgfykk 66
                l++++++ll+++g++ + +++l    +vl++l+a  ++ + f + 
  EPA06472.1 27 LLCVFMGLLAGYGAFTIHSSLL--GVMVLCFLAATVLCGFIFTAI 69
                89***************99999..888888887666555444332 PP

>> DUF2178  Predicted membrane protein (DUF2178)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0     8e-06     0.029       2      53 ..      27      79 ..      22      84 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 8e-06
     DUF2178  2 liivavialvglgi.waaignvllaviavaaGvllaillkkkveevveDERla 53
                l+ v+++ l g+g+  + ++ ++++v+ ++a ++l  ++   +++ v DE+l 
  EPA06472.1 27 LLCVFMGLLAGYGAfTIHSSLLGVMVLCFLAATVLCGFIFTAINKNVSDEKLD 79
                67899********9666999999***************************975 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   2.7e-05     0.098     378     440 ..      14      76 ..       5      83 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.7e-05
     DUF2207 378 kklkklsalglgliilglilillallllvlllvfllilllillliaiivlllfsrllgrrtee 440
                 k+     a++++ ++++++++l++ +++++++++l++++l +l + +++ ++f+++ +  ++e
  EPA06472.1  14 KESSVDFAILFFTLLCVFMGLLAGYGAFTIHSSLLGVMVLCFLAATVLCGFIFTAINKNVSDE 76 
                 333333444444444444455555555555588888888888888888888877766666655 PP

>> EMP70  Endomembrane protein 70
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.8   3.8e-05      0.14     274     328 ..      23      77 ..      17      88 .] 0.72

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.8e-05
       EMP70 274 lllmalvtlllallgflspsnrgslltvalllyvllgliaGYvsarlyktfggek 328
                 l++++l++++  l g   ++ ++sll v++l+++ + ++ G++ + ++k +++ek
  EPA06472.1  23 LFFTLLCVFMGLLAGYGAFTIHSSLLGVMVLCFLAATVLCGFIFTAINKNVSDEK 77 
                 4555555555555666669999999999999999999999999999999986543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       930  (0.0518713); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 564.06
//
Query:       EPA06473.1  [L=301]
Description: prenyltransferase, UbiA family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.4e-28   97.5  14.7      1e-27   97.0  14.7    1.2  1  UbiA           UbiA prenyltransferase family


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.0  14.7   5.8e-32     1e-27       8     231 ..      38     262 ..      29     277 .. 0.86

  Alignments for each domain:
  == domain 1  score: 97.0 bits;  conditional E-value: 5.8e-32
        UbiA   8 g.lalaag.gspdlllllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllilgllllalllnpltallgllalllyv 104
                 g +++a g ++pd +++l +++ t+l+a+a++++Nd+ D + D+ + +t      s +   k  l + ++++++g++l+ + +np + l +l+ + l++
  EPA06473.1  38 GtYFIANGfQVPDVFIILKITASTYLLALATYLYNDLTDLKVDSVN-NTDTS-YSSKKAEYKRILYATTMFFVIGVILA-FSINPMVGLASLAFCGLAI 133
                 3466664414566688899999999********************4.55544.89************************.******************* PP

        UbiA 105 vYt.g.lrlKrrtllgtvvggiafglppllgwaavtgslsllalllalavflltwaialandlrdregDrkagiktlpvvlGrkaaril.lalllavll 200
                 +Y+ +   lK + +++tvv ++ + ++ ++g++a+ +  s l+l+ +++vfl+ +     nd+rd++gD+ +g++t+p+v+G +++++l  a++  v++
  EPA06473.1 134 AYShPfTHLKNIFVIKTVVTALGGFIASMMGAFAAENI-SSLVLASSVIVFLFYFVNGPLNDIRDVKGDKSGGRRTIPIVIGVQNSFYLvNAIIFSVMS 231
                 ***9999***************************9885.9************************************************98555555556 PP

        UbiA 201 lallllllalllllylllalllaalallraa 231
                 ++++ +ll+++  l l ++ll+ +++l++  
  EPA06473.1 232 ILVISFLLFNVHALGLTAGLLITGYLLVKIK 262
                 6678899999999999999999999888733 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1061  (0.0591779); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.34s 00:00:00.96 Elapsed: 00:00:00.52
# Mc/sec: 1739.66
//
Query:       EPA06474.1  [L=319]
Description: NAD dependent epimerase/dehydratase family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.7e-15   55.3   0.0    1.2e-14   54.6   0.0    1.5  1  NAD_binding_10   NAD(P)H-binding
    2.2e-11   43.7   0.1    1.1e-10   41.4   0.1    1.9  2  Epimerase        NAD dependent epimerase/dehydratase family
    2.6e-11   43.5   0.0    3.7e-11   43.0   0.0    1.3  1  NmrA             NmrA-like family
    1.3e-10   40.7   0.0      2e-10   40.1   0.0    1.2  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    4.7e-06   26.2   0.1    7.7e-06   25.5   0.1    1.3  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    0.00065   19.2   0.1     0.0037   16.8   0.1    2.2  2  adh_short        short chain dehydrogenase
      0.002   17.4   0.1     0.0054   15.9   0.0    1.8  3  NAD_binding_4    Male sterility protein
     0.0025   16.9   0.0     0.0042   16.2   0.0    1.3  1  RmlD_sub_bind    RmlD substrate binding domain
     0.0056   15.9   1.2        0.1   11.7   1.2    2.2  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
  ------ inclusion threshold ------
      0.016   15.1   0.4       0.09   12.7   0.4    2.0  1  KR               KR domain
       0.15   12.2   0.0       0.26   11.4   0.0    1.4  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh


Domain annotation for each model (and alignments):
>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.6   0.0   7.6e-18   1.2e-14       1     104 [.      21     128 ..      21     210 .. 0.77

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 7.6e-18
                     TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCCHHHH...........HHHHHHH CS
  NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggkdeeg...........aknivda 84 
                     GAtG +G++l++ l+++ g++v+ + R  +kl+   ++ +++ +++dv dve+l++a++g+++ +  l + ++d+e            a+n ++a
      EPA06474.1  21 GATGFIGSRLIRNLVSN-GFTVKGMSR--SKLT---DKTNVKYIQADVFDVEQLESAMNGIEVAYYLLHSMEGDKEHwrefasrekiqAQNFLKA 109
                     9****************.5******87..5666...568***********************99999966655555555566666778******* PP

                     HHHCT--EEEEEEETTTTSG CS
  NAD_binding_10  85 akeagvkRfvlvsaigvgde 104
                     a +a+vkR+++++++  +d+
      EPA06474.1 110 ATNANVKRIIYLGGLV-NDS 128
                     ***********99874.443 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   0.1   6.5e-14   1.1e-10       1     114 [.      17     122 ..      17     125 .. 0.90
   2 ?   -0.2   0.0      0.33   5.5e+02     213     241 .]     194     220 ..     144     220 .. 0.83

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 6.5e-14
                 EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHHHSHHHHHHHHTHHHHHHH CS
   Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggvaassedpadfieknlqgtlnll 99 
                 ilVtGatGfiGs l+++l ++g +v g++r + +++t+    ++ +++d+ d ++le +++  ++++ + l    + +   e+  +f+ +  + ++n l
  EPA06474.1  17 ILVTGATGFIGSRLIRNLVSNGFTVKGMSRSKLTDKTN----VKYIQADVFDVEQLESAMN--GIEVAYYL--LHSMEGDKEHWREFASREKIQAQNFL 107
                 8******************************5555554....488****************..99999999..6777777778888999999******* PP

                 HHHHHHTCTEEEEEE CS
   Epimerase 100 eaarkagvkrllfls 114
                 +aa  a+vkr+++l+
  EPA06474.1 108 KAATNANVKRIIYLG 122
                 *************98 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.33
                 EEHHHHHHHHHHHHHHHTT-STTEEEEES CS
   Epimerase 213 lyveDvaeaillvlehvdagdkgeiyniG 241
                 + v+Dv+  ++  l+h+++   g+i+ iG
  EPA06474.1 194 IAVDDVIAYLVGCLNHPETS--GKIFEIG 220
                 67999******9****8884..7799998 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.0   0.0   2.3e-14   3.7e-11       1     228 [.      17     241 ..      17     283 .. 0.85

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 2.3e-14
                 EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEEEE---GG...........S-HHHHHHHHHHH CS
        NmrA   1 IlviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdlddkeslvealkgvdvvfsvtgfy...........skeiedgkklvdA 88 
                 Ilv+GaTG +G+ ++r l+++g++v+ + R   +++        v+ +++d+ d e l++a++g +v++  + ++           s e  + ++  +A
  EPA06474.1  17 ILVTGATGFIGSRLIRNLVSNGFTVKGMSRSKLTDK------TNVKYIQADVFDVEQLESAMNGIEVAYYLLHSMegdkehwrefaSREKIQAQNFLKA 109
                 9***************************99876664......45999************************99989999*****9955555566889** PP

                 HHHHS-SEEEEEE---GG.GT.SSS---TTTHHHHHHHHHHHHCTS-EEEEEE-EEGGG-BSSS-SS-BEEE-TTS.-EEEEESS-TTS-EE.-HHHHH CS
        NmrA  89 akeaGvkhfiySslgddndrsnaeepavphfdsKaeieeyvralgipytfvyagffmenflsllaqlkvgdtappedkvtllgpgnpkavll.daeeDi 186
                 a +a vk++iy +   ++ +        ph  s  e+ e + +  ip t ++a +  +   +++a l+   ++      ++ +p+ +k     +a++D+
  EPA06474.1 110 ATNANVKRIIYLGGLVNDSIE-----LSPHMRSRKEVGEILASGNIPVTQLRASLIIGAQGGSYAMLRYLVERLR----VMVTPSWVKSLAQpIAVDDV 199
                 ***********7766655344.....689*****************************99999999554444443....344555544444345***** PP

                 HHHHHHHHHHHHHH.TTEEEEE-SEEE-HHHHHHHHHHHHTS- CS
        NmrA 187 Gafvikilkdprkl.kgkriklagntlsgneivelfekkigkt 228
                  a+ +  l++p++  k+  i  + ++++++e++++++  ++k+
  EPA06474.1 200 IAYLVGCLNHPETSgKIFEIGGP-DIMTYEELMRVYSAYLNKN 241
                 ************99777777766.899**********999987 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   0.0   1.2e-13     2e-10       1     114 [.      18     121 ..      18     125 .. 0.80

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 1.2e-13
   3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslvdvagkltedeimkvnvkGTrnv 99 
                 +vtG++GF+G++l+++Lv+ +   +v+ +      + ++ + k+nvk +i++Dv d ++le a++g++v  +l   ++  ++  ++   +  ++  +n 
  EPA06474.1  18 LVTGATGFIGSRLIRNLVSNGF--TVKGM------SRSKLTDKTNVK-YIQADVFDVEQLESAMNGIEVAYYLLHSMEGDKEHWREFASREKIQ-AQNF 106
                 69*****************994..55543......222356788999.************************9444444445555555555555.8*** PP

   3Beta_HSD 100 leacvkagvrvlvYt 114
                 l+a+++a+v++++Y 
  EPA06474.1 107 LKAATNANVKRIIYL 121
                 **************6 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.1   4.7e-09   7.7e-06       1      43 [.      18      59 ..      18      78 .. 0.78

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 4.7e-09
                   EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCT CS
  GDP_Man_Dehyd  1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehla 43
                   L+TG +GfiGs l++ L+++g++v g+ r s++++ ++++ ++
     EPA06474.1 18 LVTGATGFIGSRLIRNLVSNGFTVKGMSR-SKLTDKTNVKYIQ 59
                   9*************************865.4555555555444 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   2.2e-06    0.0037       3      76 ..      17      80 ..      15     146 .. 0.82
   2 ?   -0.6   0.0      0.47   7.6e+02      96     125 ..     283     312 ..     274     315 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.2e-06
                EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHS CS
   adh_short  3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklg 76
                +lvtGa++ IG  + ++l+++G++v  ++rs+       ++     +++ +iq+Dv d e++e +++ ++  + 
  EPA06474.1 17 ILVTGATGFIGSRLIRNLVSNGFTVKGMSRSKL-----TDK-----TNVKYIQADVFDVEQLESAMNGIEVAYY 80
                89***********************99888833.....334.....3489999999999999999999987775 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.47
                 CSHHHHHHHHHHHTHHHHHHHHHHHHHHHH CS
   adh_short  96 lseeewervievNltgvflltravlpamlk 125
                 ++++ + ++i +Nl++v + +  ++++m +
  EPA06474.1 283 VNDNSITKIIPLNLKSVRESIDIATKEMRE 312
                 56778999*********9999999999875 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   3.3e-06    0.0054       1      20 [.      19      38 ..      19      89 .. 0.81
   2 ?   -2.8   0.0       1.7   2.8e+03     194     211 ..     148     164 ..     141     199 .. 0.66
   3 ?   -3.9   0.0       3.7     6e+03     103     124 ..     287     308 ..     282     312 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.3e-06
                   EE-TTSHHHHHHHHHHHHHS CS
  NAD_binding_4  1 lTGaTGFLGkvLlekLLrtt 20
                   +TGaTGF+G++L+++L+++ 
     EPA06474.1 19 VTGATGFIGSRLIRNLVSNG 38
                   7***************9875 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.7
                    H---EEEEEE-EEE--SS CS
  NAD_binding_4 194 sglpvvivRpsiitgesk 211
                    +++pv+ +R s i+g  +
     EPA06474.1 148 GNIPVTQLRASLIIGA-Q 164
                    6889999999999882.3 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 3.7
                    TSSEEHHHHHHHHHHHHHHHTS CS
  NAD_binding_4 103 pykellrvNveGtrevlelakk 124
                    ++ +++  N++++re +++a+k
     EPA06474.1 287 SITKIIPLNLKSVRESIDIATK 308
                    5677888999999999999875 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   2.6e-06    0.0042       3      49 ..      17      74 ..      15      84 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.6e-06
                   EEEESTTSHHHHHHHHHCTTTSEEEEEE-TT...........T--TTSHHHHHHHHHH CS
  RmlD_sub_bind  3 ilvtGanGqlGseLakqlaeeglevlaltre...........eldltdaeavaellke 49
                   ilvtGa+G +Gs L+++l ++g+ v +++r+           ++d+ d e+++++++ 
     EPA06474.1 17 ILVTGATGFIGSRLIRNLVSNGFTVKGMSRSkltdktnvkyiQADVFDVEQLESAMNG 74
                   9***************************999888888888888888888888877765 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   1.2   6.3e-05       0.1       1      74 [.      17      73 ..      17     123 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.3e-05
                     EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT CS
  Polysacc_synt_2  1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekale 74
                     +lvtGa+G iGs+l+r+++++  +       + ++  ++++++       ++      + +dv d e+le+a++
       EPA06474.1 17 ILVTGATGFIGSRLIRNLVSNGFT------VKGMSRSKLTDKT-------NV----KYIQADVFDVEQLESAMN 73
                     89***************9987532......1222222222221.......11....123456666666666666 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.4   5.5e-05      0.09       3      76 ..      17      76 ..      16      85 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.5e-05
                EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHH CS
          KR  3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeik 76
                 l+tG++G +G  l+r l+++g  ++  +sRs+            l++  ++v++++aDv d +++e++++ i+
  EPA06474.1 17 ILVTGATGFIGSRLIRNLVSNGF-TVKGMSRSK------------LTD-KTNVKYIQADVFDVEQLESAMNGIE 76
                69********************6.578899992............222.3567777777777777777776665 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00016      0.26       7      66 ..      23      85 ..      17     120 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00016
                   -SHHHHHHHHHHHHTT-EEEEE-SSH...HHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSH CS
  NAD_binding_2  7 lGvMGsnmalnllkagykvavynrtk...ekveelvaegakaaesieelvasldvvitmvkag 66
                   +G +Gs +++nl+++g++v ++ r+k   +   + +++ +  +e++e+++++++v   ++++ 
     EPA06474.1 23 TGFIGSRLIRNLVSNGFTVKGMSRSKltdKTNVKYIQADVFDVEQLESAMNGIEVAYYLLHSM 85
                   5889*******************9973323333455556778888888888888877777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.68u 0.39s 00:00:01.07 Elapsed: 00:00:00.57
# Mc/sec: 1696.57
//
Query:       EPA06475.1  [L=83]
Description: hypothetical protein BG20_I2326 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 556.65
//
Query:       EPA06476.1  [L=32]
Description: hypothetical protein BG20_I2328, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.097   12.9   1.5       0.14   12.3   1.5    1.4  1  ATPase_gene1  Putative F0F1-ATPase subunit Ca2+/Mg2+ transpor


Domain annotation for each model (and alignments):
>> ATPase_gene1  Putative F0F1-ATPase subunit Ca2+/Mg2+ transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.5     8e-06      0.14      12      37 ..       2      31 ..       1      32 [] 0.67

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8e-06
  ATPase_gene1 12 vapillggllG...ywLDkkfgt.spwfli 37
                  +++ ++++l+G   ywLD ++   +p++ +
    EPA06476.1  2 LISLIVMALIGttyYWLDDRLDVyDPIWIF 31
                  444455555544449*******99999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (32 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 234.18
//
Query:       EPA06477.1  [L=158]
Description: hypothetical protein BG20_I2543, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.7e-34  117.9   0.0    6.3e-34  117.8   0.0    1.0  1  Diphthamide_syn  Putative diphthamide synthesis protein


Domain annotation for each model (and alignments):
>> Diphthamide_syn  Putative diphthamide synthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.8   0.0   3.5e-38   6.3e-34     151     295 ..       1     143 [.       1     152 [. 0.95

  Alignments for each domain:
  == domain 1  score: 117.8 bits;  conditional E-value: 3.5e-38
  Diphthamide_syn 151 ailyigdgrfhllslmlsnpklpvyrydpyskklteesydakkllrrRyaaiekakdakkvGiivgtlgvqgrlelverlkkllkeagkksylv 244
                      a++++g+ +fh+ +++ls++ +p+y +dpy ++++e ++ a kl ++   ai ka++a+++Gii+g +++q +   + + k++l+++gk++ l+
       EPA06477.1   1 AYVFLGQSNFHAAGIALSTN-MPTYVLDPYFNEVREVTEFAGKLKKKATLAIYKAAEAQTFGIIIGLKEGQLSKVFALKFKNELEKEGKTVQLF 93 
                      589****************5.5************************************************************************ PP

  Diphthamide_syn 245 lvgelnpakLanfaeidafVlvaCprlsiddgkeFekPvltpyElevalg.e 295
                      +++ ++ ++L+n++ idaf++vaCpr+s+d+  +F+kPvl+   ++ +l+  
       EPA06477.1  94 ALTDITNERLKNLKGIDAFIQVACPRISTDN--QFDKPVLSTPQANALLKiL 143
                      ******************************7..7********9999999863 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1020.51
//
Query:       EPA06478.1  [L=129]
Description: hypothetical protein BG20_I2544, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-10   39.8   2.2     0.0001   22.0   0.0    4.1  4  TPR_1         Tetratricopeptide repeat
    7.1e-08   32.0   0.1      0.054   13.6   0.0    4.1  4  TPR_2         Tetratricopeptide repeat
      6e-06   26.7   0.0    0.00022   21.6   0.0    2.5  3  TPR_19        Tetratricopeptide repeat
    0.00042   20.3   0.2      0.051   13.7   0.1    2.9  3  Fis1_TPR_C    Fis1 C-terminal tetratricopeptide repeat
    0.00056   19.9   0.1      0.013   15.5   0.1    2.0  1  SRP_TPR_like  Putative TPR-like repeat
      0.002   18.8   0.0        5.1    8.2   0.0    3.5  4  TPR_14        Tetratricopeptide repeat
     0.0032   17.5   2.2        7.1    7.1   0.0    4.0  4  TPR_8         Tetratricopeptide repeat
     0.0082   16.4   0.0        3.8    7.9   0.0    2.4  3  TPR_12        Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.015   15.5   0.7       0.54   10.5   0.3    2.1  3  ANAPC3        Anaphase-promoting complex, cyclosome, subunit 
      0.018   14.7   0.1         17    5.2   0.1    3.5  3  TPR_11        TPR repeat
      0.029   15.0   0.0          6    7.7   0.0    3.5  4  TPR_6         Tetratricopeptide repeat
      0.066   13.6   0.5         65    4.2   0.0    3.3  3  TPR_17        Tetratricopeptide repeat
      0.089   12.7   0.0        1.3    8.9   0.0    2.1  2  ATP13         Mitochondrial ATPase expression
       0.14   12.8   0.0       0.31   11.7   0.0    1.5  2  TPR_16        Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.2    0.0013       1.7      20      33 ..       1      14 [.       1      15 [. 0.95
   2 !   22.0   0.0   7.9e-08    0.0001       4      34 .]      19      49 ..      17      49 .. 0.90
   3 ?    5.0   0.0     0.018        22      10      24 ..      59      73 ..      58      74 .. 0.91
   4 ?    0.9   0.0      0.35   4.5e+02      16      29 ..      99     112 ..      93     113 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0013
                HHHHHHHHHHHSTT CS
       TPR_1 20 AleyyekALelnPn 33
                A+++y+ +L+l P+
  EPA06478.1  1 AIQCYDAVLKLAPQ 14
                9***********96 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 7.9e-08
                HHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1  4 lynlGnayfklgkydeAleyyekALelnPnn 34
                l n+   ++k+gk+ eAl+y++  Le nP++
  EPA06478.1 19 LVNKISSLRKKGKFSEALQYCDNILENNPKY 49
                56778899*********************97 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.018
                HHHHTT-HHHHHHHH CS
       TPR_1 10 ayfklgkydeAleyy 24
                ++f++++++e l ++
  EPA06478.1 59 ILFSMNQFEESLLCC 73
                689*********999 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 0.35
                 -HHHHHHHHHHHHH CS
       TPR_1  16 kydeAleyyekALe 29 
                 k d+Al   ekA++
  EPA06478.1  99 KIDDALFILEKAIS 112
                 78999999999995 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.1     0.005       6.5      20      33 ..       1      14 [.       1      15 [. 0.94
   2 !   13.6   0.0   4.2e-05     0.054      10      34 .]      25      49 ..      24      49 .. 0.93
   3 ?    2.6   0.0      0.14   1.8e+02      10      29 ..      59      78 ..      58      83 .. 0.78
   4 ?    3.7   0.0     0.064        82       3      29 ..      86     112 ..      84     113 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.005
       TPR_2 20 AleafekAleldPn 33
                A+++++++l+l+P+
  EPA06478.1  1 AIQCYDAVLKLAPQ 14
                99***********7 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 4.2e-05
       TPR_2 10 ayyklgdyeeAleafekAleldPnn 34
                +++k+g++ eAl++++  le +P++
  EPA06478.1 25 SLRKKGKFSEALQYCDNILENNPKY 49
                5899*******************85 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.14
       TPR_2 10 ayyklgdyeeAleafekAle 29
                +++ ++++ee l +++  l 
  EPA06478.1 59 ILFSMNQFEESLLCCDVILD 78
                7899*******999876665 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.064
       TPR_2   3 alynlGlayyklgdyeeAleafekAle 29 
                 +l+   ++++   + ++Al  +ekA++
  EPA06478.1  86 VLFDKSCSLAMISKIDDALFILEKAIS 112
                 688888899999999**********96 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       3.7   4.8e+03      44      57 ..       1      14 [.       1      22 [. 0.51
   2 !   21.6   0.0   1.7e-07   0.00022       2      57 ..      27      82 ..      26      87 .. 0.94
   3 ?    2.1   0.0      0.22   2.8e+02       7      19 ..     100     112 ..      97     121 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3.7
      TPR_19 44 AealLdalpeedpd 57
                A+++ da+++ +p+
  EPA06478.1  1 AIQCYDAVLKLAPQ 14
                44444444444444 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 1.7e-07
      TPR_19  2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57
                 + g++ eAl++  ++l+ +pk+  +++   ++l++++q++e   ++d +++++p 
  EPA06478.1 27 RKKGKFSEALQYCDNILENNPKYNIVLYHKERILFSMNQFEESLLCCDVILDDYPL 82
                6789************************************************9986 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.22
      TPR_19   7 yaeAlalleqalq 19 
                  ++Al +le+a++
  EPA06478.1 100 IDDALFILEKAIS 112
                 6899999999975 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       1.1   1.5e+03      20      35 ..       1      16 [.       1      20 [. 0.79
   2 !   13.7   0.1     4e-05     0.051      13      34 ..      28      49 ..      26      53 .. 0.90
   3 ?    2.8   0.0     0.096   1.2e+02      14      35 ..      63      84 ..      61      91 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.1
                HHHHHHHHHHHTTS-H CS
  Fis1_TPR_C 20 ArryvdalLeiEPenr 35
                A ++ da+L++ P+  
  EPA06478.1  1 AIQCYDAVLKLAPQEL 16
                568899****999865 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 4e-05
                HHT-HHHHHHHHHHHHHHTTS- CS
  Fis1_TPR_C 13 klgeYseArryvdalLeiEPen 34
                k g++seA++y+d +Le  P+ 
  EPA06478.1 28 KKGKFSEALQYCDNILENNPKY 49
                6799**************9985 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.096
                HT-HHHHHHHHHHHHHHTTS-H CS
  Fis1_TPR_C 14 lgeYseArryvdalLeiEPenr 35
                + +++e++ ++d +L   P n 
  EPA06478.1 63 MNQFEESLLCCDVILDDYPLNG 84
                6899***********9888775 PP

>> SRP_TPR_like  Putative TPR-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1     1e-05     0.013       3      73 ..       3     112 ..       1     128 [. 0.74

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1e-05
  SRP_TPR_like   3 eeyekilrlegkelkkf..kvvaliklekyeeaLkllkkgs.....................................alsedvrfEkaYvlYklkk 60 
                   ++y+ +l+l+ +el+    k+ +l k +k++eaL+++++                                        l++dv f+k+  l  + k
    EPA06478.1   3 QCYDAVLKLAPQELSVLvnKISSLRKKGKFSEALQYCDNILennpkynivlyhkerilfsmnqfeesllccdvilddyPLNGDVLFDKSCSLAMISK 99 
                   78999*****999998788999999***********9987656666666666666666666666666666666666666667777777766666677 PP

  SRP_TPR_like  61 ykkalkilkkvea 73 
                     +al il+k+ +
    EPA06478.1 100 IDDALFILEKAIS 112
                   7766666666655 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.039        49      20      38 ..       1      19 [.       1      25 [. 0.88
   2 !    8.2   0.0     0.004       5.1      11      34 ..      26      49 ..      22      57 .. 0.85
   3 ?   -1.2   0.0         4   5.1e+03       9      34 ..      58      83 ..      51      89 .. 0.73
   4 ?    0.9   0.0      0.84   1.1e+03      17      30 ..     100     113 ..      97     115 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.039
      TPR_14 20 AiallrralalaPddaeaw 38
                Ai++++++l+laP+++ ++
  EPA06478.1  1 AIQCYDAVLKLAPQELSVL 19
                89***********998776 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.004
      TPR_14 11 llalGdpdeAiallrralalaPdd 34
                l+  G++ eA+++++ +l+ +P+ 
  EPA06478.1 26 LRKKGKFSEALQYCDNILENNPKY 49
                7788******************85 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 4
      TPR_14  9 eallalGdpdeAiallrralalaPdd 34
                ++l+   +++e++ +++ +l+++P +
  EPA06478.1 58 RILFSMNQFEESLLCCDVILDDYPLN 83
                56777888888887777777777765 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 0.84
      TPR_14  17 pdeAiallrralal 30 
                  d+A+ +l++a+++
  EPA06478.1 100 IDDALFILEKAISQ 113
                 699********997 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1     0.021        27      20      33 ..       1      14 [.       1      15 [. 0.94
   2 !    7.1   0.0    0.0055       7.1      10      33 ..      25      48 ..      18      49 .. 0.90
   3 ?    0.6   0.0      0.68   8.7e+02       9      21 ..      58      70 ..      53      74 .. 0.84
   4 ?    1.2   0.0      0.45   5.8e+02      16      29 ..      99     112 ..      85     113 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.021
                HHHHHHHHHHHHHH CS
       TPR_8 20 Akeyyekaleldpd 33
                A+++y  +l+l+p+
  EPA06478.1  1 AIQCYDAVLKLAPQ 14
                9***********97 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0055
                HHHHTT-HHHHHHHHHHHHHHHHH CS
       TPR_8 10 iylklgdyeeAkeyyekaleldpd 33
                 ++k+g++ eA +y+   le +p+
  EPA06478.1 25 SLRKKGKFSEALQYCDNILENNPK 48
                5789***************99998 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.68
                HHHHHTT-HHHHH CS
       TPR_8  9 siylklgdyeeAk 21
                +i+++++++ee+ 
  EPA06478.1 58 RILFSMNQFEESL 70
                58999*****985 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.45
                 -HHHHHHHHHHHHH CS
       TPR_8  16 dyeeAkeyyekale 29 
                 +++ A   +eka++
  EPA06478.1  99 KIDDALFILEKAIS 112
                 57889999999996 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       2.9   3.7e+03      22      34 ..       1      14 [.       1      17 [. 0.73
   2 !    7.9   0.0     0.003       3.8       3      31 ..      16      44 ..      14      46 .. 0.89
   3 ?    6.1   0.0     0.011        14      13      72 ..      53     111 ..      51     113 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2.9
      TPR_12 22 Alellekaleia.r 34
                A+++++++l +a +
  EPA06478.1  1 AIQCYDAVLKLApQ 14
                78888888888755 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.003
      TPR_12  3 atalnnlaavlrrlgrydeAlellekale 31
                +++l+n  + lr+ g++ eAl++++  le
  EPA06478.1 16 LSVLVNKISSLRKKGKFSEALQYCDNILE 44
                678899999***************99997 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.011
      TPR_12  13 lrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeal 72 
                 l++ +r   +   +e++l  +  +l +d+pl   +l++ +  + +  + ++Al +le+a+
  EPA06478.1  53 LYHKERILFSMNQFEESLLCCDVIL-DDYPLNGDVLFDKSCSLAMISKIDDALFILEKAI 111
                 5666666666677999999998776.79******************************97 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.2   0.00064      0.83       8      76 ..       1      70 [.       1      76 [. 0.83
   2 ?   10.5   0.3   0.00042      0.54       3      82 .]      30     110 ..      29     110 .. 0.83
   3 ?    2.4   0.0      0.14   1.8e+02       4      16 ..      99     111 ..      96     116 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00064
                HHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHH CS
      ANAPC3  8 AiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAi 76
                Ai +++ +l+  ++ ++ +  +  +l + g++ +A++++++  + n+k   ++y + + l+ ++++ee +
  EPA06478.1  1 AIQCYDAVLKLAPQELSVLVNKISSLRKKGKFSEALQYCDNIlENNPKYNIVLYHKERILFSMNQFEESL 70
                56677777777777777777778899****************888888889999999***9999999965 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00042
                 T-HHHHHHHHHHHH.HHH--HHHHHHH..HHHHHHTT-HHHHHHHHHCTSHHHC-HHHHHHHHHHH.HHT.T-HHHHHHHH-SS CS
      ANAPC3   3 nnyknAiflaerllaaetespedayll..AlclylngqykrAyellrkaklnskslgcrylfAqcl.lkL.kkyeeAiaaLekl 82 
                 +++ +A+ +++ +l  e++  +++ l+     l++++q+++ +  ++   l++  l+  +lf +++ l++ +k+++A+ +Lek+
  EPA06478.1  30 GKFSEALQYCDNIL--ENNPKYNIVLYhkERILFSMNQFEESLLCCDVI-LDDYPLNGDVLFDKSCsLAMiSKIDDALFILEKA 110
                 56789999999999..666666666655699***********9999999.888888889999987768888**********985 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.14
                 -HHHHHHHHHHHH CS
      ANAPC3   4 nyknAiflaerll 16 
                 ++++A+f++e++ 
  EPA06478.1  99 KIDDALFILEKAI 111
                 5788999999886 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1     0.013        17      13      26 ..       1      14 [.       1      21 [. 0.91
   2 ?    3.6   0.0     0.043        55       4      15 ..      26      37 ..      24      38 .. 0.89
   3 ?    1.8   0.0      0.16     2e+02       3      14 ..      59      70 ..      58      72 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.013
      TPR_11 13 AieaYkkAlkldPd 26
                Ai++Y + lkl P+
  EPA06478.1  1 AIQCYDAVLKLAPQ 14
                9**********997 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.043
      TPR_11  4 yyeqGkyeeAie 15
                ++++Gk+ eA++
  EPA06478.1 26 LRKKGKFSEALQ 37
                799*******96 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.16
      TPR_11  3 ayyeqGkyeeAi 14
                ++++ +++ee++
  EPA06478.1 59 ILFSMNQFEESL 70
                89********97 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0       1.1   1.4e+03      19      32 ..       1      14 [.       1      15 [. 0.87
   2 ?    7.7   0.0    0.0047         6       9      32 ..      25      48 ..      18      49 .. 0.88
   3 ?    1.3   0.0      0.51   6.5e+02      10      31 ..      60      81 ..      58      83 .. 0.85
   4 ?   -0.1   0.0       1.5   1.9e+03      15      28 ..      99     112 ..      85     113 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.1
                HHHHHHHHHHH-TT CS
       TPR_6 19 AlealerlikeYPd 32
                A++ ++ ++k  P+
  EPA06478.1  1 AIQCYDAVLKLAPQ 14
                89999999999886 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0047
                HHHHHHHHHHHHHHHHHHHHH-TT CS
       TPR_6  9 syrklgdtdkAlealerlikeYPd 32
                s+rk g+ ++Al++ ++++++ P+
  EPA06478.1 25 SLRKKGKFSEALQYCDNILENNPK 48
                677777****************97 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.51
                HHHHHHHHHHHHHHHHHHHH-T CS
       TPR_6 10 yrklgdtdkAlealerlikeYP 31
                ++++++ +++l   + ++++YP
  EPA06478.1 60 LFSMNQFEESLLCCDVILDDYP 81
                6788899999999999*****9 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 1.5
                 HHHHHHHHHHHHHH CS
       TPR_6  15 dtdkAlealerlik 28 
                 + d+Al +le+ i+
  EPA06478.1  99 KIDDALFILEKAIS 112
                 67889999999886 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.051        65       1      34 []       4      37 ..       4      37 .. 0.94
   2 ?    1.9   0.4      0.28   3.6e+02       2      17 ..      39      55 ..      38      56 .. 0.74
   3 ?    3.9   0.0     0.067        85       6      32 ..      77     103 ..      66     105 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.051
      TPR_17  1 lylkaleldPnnadaynnLAelllknGdlmtArq 34
                +y  +l+l P    ++ n+   l+k+G++ +A+q
  EPA06478.1  4 CYDAVLKLAPQELSVLVNKISSLRKKGKFSEALQ 37
                8999************************999987 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.28
      TPR_17  2 ylkaleldPn.nadayn 17
                + + le++P+ n ++y+
  EPA06478.1 39 CDNILENNPKyNIVLYH 55
                6789*****95566665 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.067
      TPR_17   6 leldPnnadaynnLAelllknGdlmtA 32 
                 l+ +P n d+++ +   l+++ + ++A
  EPA06478.1  77 LDDYPLNGDVLFDKSCSLAMISKIDDA 103
                 5668*********99999988888877 PP

>> ATP13  Mitochondrial ATPase expression
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0     0.001       1.3      54      86 ..      16      48 ..      10      57 .. 0.82
   2 ?    1.5   0.0      0.21   2.6e+02      64      89 ..      60      84 ..      51      99 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.001
       ATP13 54 selLkaivssfsynneiesAlklvdkfskkYpe 86
                  +L++ +ss+ +++++++Al++ d++ +  p+
  EPA06478.1 16 LSVLVNKISSLRKKGKFSEALQYCDNILENNPK 48
                56888889*******************987654 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.21
       ATP13 64 fsynneiesAlklvdkfskkYpeiel 89
                ++++n++e+ l   d +   Yp ++ 
  EPA06478.1 60 LFSMNQFEESLLCCDVILDDYP-LNG 84
                77899****************9.554 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00024      0.31      16      66 ..       1      48 [.       1      50 [. 0.95
   2 ?   -1.9   0.0       4.3   5.5e+03      24      41 ..      77      91 ..      58     111 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00024
      TPR_16 16 AaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66
                A+  ++a+lk++   P+    l ++  ++ ++g + eA+++++  l++ p+
  EPA06478.1  1 AIQCYDAVLKLA---PQELSVLVNKISSLRKKGKFSEALQYCDNILENNPK 48
                7889********...****************************99999986 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.3
      TPR_16 24 lkrdpssPdaaeAllllg 41
                l+++   P++ + l+ + 
  EPA06478.1 77 LDDY---PLNGDVLFDKS 91
                5555...66555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1035.76
//
Query:       EPA06479.1  [L=158]
Description: hypothetical protein BG20_I2541, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-34  119.4   0.0    2.2e-34  119.3   0.0    1.0  1  Diphthamide_syn  Putative diphthamide synthesis protein


Domain annotation for each model (and alignments):
>> Diphthamide_syn  Putative diphthamide synthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.3   0.0   1.2e-38   2.2e-34     151     295 ..       1     143 [.       1     152 [. 0.95

  Alignments for each domain:
  == domain 1  score: 119.3 bits;  conditional E-value: 1.2e-38
  Diphthamide_syn 151 ailyigdgrfhllslmlsnpklpvyrydpyskklteesydakkllrrRyaaiekakdakkvGiivgtlgvqgrlelverlkkllkeagkksylv 244
                      a++++g+ +fh+ +++ls++ +p+y +dpy ++++e ++ a+kl ++   ai ka++a+++Gii+g +++q +   + + k++l+++gk++ l+
       EPA06479.1   1 AYVFLGQSNFHAAGIALSTN-MPTYVLDPYFNEVREVTEFAQKLKKKATLAIYKAAEAQTFGIIIGLKEGQLSKVFALKFKNELEKEGKTVQLF 93 
                      589****************5.5************************************************************************ PP

  Diphthamide_syn 245 lvgelnpakLanfaeidafVlvaCprlsiddgkeFekPvltpyElevalg.e 295
                      +++ ++ ++L+n++ idaf++vaCpr+s+d+  +F+kPvl+   ++ +l+  
       EPA06479.1  94 ALTDITNERLKNLKGIDAFIQVACPRISTDN--QFDKPVLSTPQANALLKiL 143
                      ******************************7..7********9999999863 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1011.08
//
Query:       EPA06480.1  [L=141]
Description: hypothetical protein BG20_I2542, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.4e-10   39.8   3.1    9.9e-05   22.0   0.0    4.3  4  TPR_1       Tetratricopeptide repeat
      2e-08   33.7   0.4      0.028   14.5   0.0    4.2  4  TPR_2       Tetratricopeptide repeat
    1.7e-05   25.2   0.0    0.00014   22.3   0.0    2.3  3  TPR_19      Tetratricopeptide repeat
    8.7e-05   22.5   0.2      0.052   13.6   0.1    3.2  3  Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
    0.00048   19.8   0.3        3.3    7.5   0.0    4.2  4  TPR_11      TPR repeat
    0.00073   20.2   0.0        5.1    8.2   0.0    3.6  4  TPR_14      Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.015   15.6   0.0        2.6    8.4   0.0    2.3  2  TPR_12      Tetratricopeptide repeat
      0.022   14.9   4.2        5.9    7.4   0.1    4.0  4  TPR_8       Tetratricopeptide repeat
      0.028   15.0   0.0        8.2    7.3   0.0    3.8  4  TPR_6       Tetratricopeptide repeat
      0.037   14.2   1.4       0.42   10.9   1.1    2.0  2  ANAPC3      Anaphase-promoting complex, cyclosome, subunit 3
      0.041   13.7   0.0        1.1    9.2   0.0    2.3  2  ATP13       Mitochondrial ATPase expression
      0.059   13.4   0.1       0.21   11.6   0.1    1.9  2  DMP12       DNA-mimic protein
       0.16   12.4   1.8         64    4.3   0.0    3.3  3  TPR_17      Tetratricopeptide repeat
        0.2   12.3   0.0          2    9.1   0.0    2.1  2  TPR_16      Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.1    0.0022       2.8      20      33 ..       1      14 [.       1      15 [. 0.94
   2 !   22.0   0.0   7.7e-08   9.9e-05       4      34 .]      19      49 ..      17      49 .. 0.90
   3 !    6.1   0.0     0.008        10      10      26 ..      59      75 ..      58      78 .. 0.87
   4 ?    1.3   0.1      0.28   3.5e+02      16      29 ..      99     112 ..      99     113 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0022
                HHHHHHHHHHHSTT CS
       TPR_1 20 AleyyekALelnPn 33
                A+++y+ +L+l P+
  EPA06480.1  1 AIQCYDAVLKLSPQ 14
                9**********996 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 7.7e-08
                HHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1  4 lynlGnayfklgkydeAleyyekALelnPnn 34
                l n+   ++k+gk+ eAl+y++  Le nP++
  EPA06480.1 19 LVNKISSLRKKGKFSEALKYCDNILENNPKY 49
                56777899*********************97 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.008
                HHHHTT-HHHHHHHHHH CS
       TPR_1 10 ayfklgkydeAleyyek 26
                ++f++++++e l +++ 
  EPA06480.1 59 ILFSMNQFEESLLCCDA 75
                689***********986 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.28
                 -HHHHHHHHHHHHH CS
       TPR_1  16 kydeAleyyekALe 29 
                 k d+Al   ekA++
  EPA06480.1  99 KIDDALYTLEKAIS 112
                 5799********96 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.0    0.0089        11      20      33 ..       1      14 [.       1      15 [. 0.94
   2 !   14.5   0.0   2.2e-05     0.028      10      34 .]      25      49 ..      24      49 .. 0.93
   3 ?    4.7   0.0      0.03        38      10      32 ..      59      81 ..      58      83 .. 0.87
   4 ?    3.4   0.0     0.081     1e+02       3      29 ..      86     112 ..      84     113 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0089
       TPR_2 20 AleafekAleldPn 33
                A+++++++l+l P+
  EPA06480.1  1 AIQCYDAVLKLSPQ 14
                99**********96 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 2.2e-05
       TPR_2 10 ayyklgdyeeAleafekAleldPnn 34
                +++k+g++ eAl++++  le +P++
  EPA06480.1 25 SLRKKGKFSEALKYCDNILENNPKY 49
                5899*******************85 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.03
       TPR_2 10 ayyklgdyeeAleafekAleldP 32
                +++ ++++ee l ++++ l  +P
  EPA06480.1 59 ILFSMNQFEESLLCCDAILDDYP 81
                7899***********99998877 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.081
       TPR_2   3 alynlGlayyklgdyeeAleafekAle 29 
                 +l+   ++++   + ++Al  +ekA++
  EPA06480.1  86 VLFDKSCSLAMIYKIDDALYTLEKAIS 112
                 678888888888899**********96 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       3.4   4.3e+03      10      24 ..       1      15 [.       1      22 [. 0.65
   2 !   22.3   0.0   1.1e-07   0.00014       2      57 ..      27      82 ..      26      87 .. 0.94
   3 ?   -0.7   0.0       1.6   2.1e+03       7      19 ..     100     112 ..      98     117 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3.4
      TPR_19 10 Alalleqalqedpkn 24
                A++ + ++l+ +p+ 
  EPA06480.1  1 AIQCYDAVLKLSPQE 15
                566667777777765 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 1.1e-07
      TPR_19  2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57
                 + g++ eAl++  ++l+ +pk+  +++   ++l++++q++e   ++da+++++p 
  EPA06480.1 27 RKKGKFSEALKYCDNILENNPKYNIVLYHKERILFSMNQFEESLLCCDAILDDYPL 82
                6789************************************************9986 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.6
      TPR_19   7 yaeAlalleqalq 19 
                  ++Al  le+a++
  EPA06480.1 100 IDDALYTLEKAIS 112
                 6899999999865 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.98   1.3e+03      20      35 ..       1      16 [.       1      20 [. 0.80
   2 !   13.6   0.1     4e-05     0.052      13      34 ..      28      49 ..      26      53 .. 0.90
   3 ?    4.7   0.0     0.025        33      14      35 ..      63      84 ..      61      88 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.98
                HHHHHHHHHHHTTS-H CS
  Fis1_TPR_C 20 ArryvdalLeiEPenr 35
                A ++ da+L++ P+  
  EPA06480.1  1 AIQCYDAVLKLSPQEL 16
                568899*****99865 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 4e-05
                HHT-HHHHHHHHHHHHHHTTS- CS
  Fis1_TPR_C 13 klgeYseArryvdalLeiEPen 34
                k g++seA++y+d +Le  P+ 
  EPA06480.1 28 KKGKFSEALKYCDNILENNPKY 49
                6799**************9985 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.025
                HT-HHHHHHHHHHHHHHTTS-H CS
  Fis1_TPR_C 14 lgeYseArryvdalLeiEPenr 35
                + +++e++ ++da+L   P n 
  EPA06480.1 63 MNQFEESLLCCDAILDDYPLNG 84
                6899***********9888775 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.0    0.0026       3.3      13      26 ..       1      14 [.       1      21 [. 0.92
   2 ?    3.3   0.0     0.053        68       4      15 ..      26      37 ..      24      38 .. 0.89
   3 ?    1.6   0.0      0.18   2.3e+02       3      14 ..      59      70 ..      58      72 .. 0.87
   4 ?    2.0   0.1      0.13   1.7e+02       9      22 ..      99     112 ..      99     113 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0026
      TPR_11 13 AieaYkkAlkldPd 26
                Ai++Y + lkl+P+
  EPA06480.1  1 AIQCYDAVLKLSPQ 14
                9************7 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.053
      TPR_11  4 yyeqGkyeeAie 15
                ++++Gk+ eA++
  EPA06480.1 26 LRKKGKFSEALK 37
                799*******96 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.18
      TPR_11  3 ayyeqGkyeeAi 14
                ++++ +++ee++
  EPA06480.1 59 ILFSMNQFEESL 70
                89********97 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.13
      TPR_11   9 kyeeAieaYkkAlk 22 
                 k+++A+  ++kA+ 
  EPA06480.1  99 KIDDALYTLEKAIS 112
                 6899********95 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.079     1e+02      20      38 ..       1      19 [.       1      24 [. 0.87
   2 !    8.2   0.0     0.004       5.1      11      34 ..      26      49 ..      22      56 .. 0.85
   3 ?    3.5   0.0      0.13   1.6e+02       9      37 ..      58      86 ..      52      90 .. 0.85
   4 ?   -1.3   0.0       4.6   5.9e+03      18      30 ..     101     113 ..      99     114 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.079
      TPR_14 20 AiallrralalaPddaeaw 38
                Ai++++++l+l P+++ ++
  EPA06480.1  1 AIQCYDAVLKLSPQELSVL 19
                89***********998776 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.004
      TPR_14 11 llalGdpdeAiallrralalaPdd 34
                l+  G++ eA+++++ +l+ +P+ 
  EPA06480.1 26 LRKKGKFSEALKYCDNILENNPKY 49
                7788******************85 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.13
      TPR_14  9 eallalGdpdeAiallrralalaPddaea 37
                ++l+   +++e++ +++++l+++P + ++
  EPA06480.1 58 RILFSMNQFEESLLCCDAILDDYPLNGDV 86
                6788999*****************87665 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 4.6
      TPR_14  18 deAiallrralal 30 
                 d+A+  l++a+++
  EPA06480.1 101 DDALYTLEKAISQ 113
                 7888899999987 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0    0.0021       2.6       3      31 ..      16      44 ..      14      47 .. 0.90
   2 ?    5.0   0.0     0.024        31      13      72 ..      53     111 ..      51     113 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0021
      TPR_12  3 atalnnlaavlrrlgrydeAlellekale 31
                +++l+n  + lr+ g++ eAl++++  le
  EPA06480.1 16 LSVLVNKISSLRKKGKFSEALKYCDNILE 44
                678899999****************9997 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.024
      TPR_12  13 lrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeal 72 
                 l++ +r   +   +e++l  + ++l +d+pl   +l++ +  + +  + ++Al+ le+a+
  EPA06480.1  53 LYHKERILFSMNQFEESLLCCDAIL-DDYPLNGDVLFDKSCSLAMIYKIDDALYTLEKAI 111
                 5566666666667999999999887.6899999999999999999999999999999997 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.023        29      20      33 ..       1      14 [.       1      15 [. 0.94
   2 ?    7.4   0.1    0.0046       5.9      10      33 ..      25      48 ..      18      49 .. 0.90
   3 ?    1.0   0.0      0.49   6.3e+02       9      24 ..      58      73 ..      53      78 .. 0.83
   4 ?   -1.2   0.1       2.6   3.3e+03      10      12 ..      97      99 ..      92     112 .. 0.53

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.023
                HHHHHHHHHHHHHH CS
       TPR_8 20 Akeyyekaleldpd 33
                A+++y  +l+l+p+
  EPA06480.1  1 AIQCYDAVLKLSPQ 14
                99**********97 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0046
                HHHHTT-HHHHHHHHHHHHHHHHH CS
       TPR_8 10 iylklgdyeeAkeyyekaleldpd 33
                 ++k+g++ eA +y+   le +p+
  EPA06480.1 25 SLRKKGKFSEALKYCDNILENNPK 48
                5789***************99998 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.49
                HHHHHTT-HHHHHHHH CS
       TPR_8  9 siylklgdyeeAkeyy 24
                +i+++++++ee+  ++
  EPA06480.1 58 RILFSMNQFEESLLCC 73
                58999*****997665 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 2.6
                HHH CS
       TPR_8 10 iyl 12
                iy+
  EPA06480.1 97 IYK 99
                553 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       2.2   2.8e+03      19      31 ..       1      13 [.       1      14 [. 0.85
   2 ?    7.3   0.0    0.0064       8.2       9      32 ..      25      48 ..      18      49 .. 0.88
   3 ?    1.4   0.0       0.5   6.4e+02      10      31 ..      60      81 ..      58      83 .. 0.86
   4 ?    0.6   0.0      0.91   1.2e+03      15      28 ..      99     112 ..      85     113 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 2.2
                HHHHHHHHHHH-T CS
       TPR_6 19 AlealerlikeYP 31
                A++ ++ ++k  P
  EPA06480.1  1 AIQCYDAVLKLSP 13
                8999999999887 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0064
                HHHHHHHHHHHHHHHHHHHHH-TT CS
       TPR_6  9 syrklgdtdkAlealerlikeYPd 32
                s+rk g+ ++Al++ ++++++ P+
  EPA06480.1 25 SLRKKGKFSEALKYCDNILENNPK 48
                677777****************97 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.5
                HHHHHHHHHHHHHHHHHHHH-T CS
       TPR_6 10 yrklgdtdkAlealerlikeYP 31
                ++++++ +++l   + ++++YP
  EPA06480.1 60 LFSMNQFEESLLCCDAILDDYP 81
                6788899999999999*****9 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 0.91
                 HHHHHHHHHHHHHH CS
       TPR_6  15 dtdkAlealerlik 28 
                 + d+Al +le+ i+
  EPA06480.1  99 KIDDALYTLEKAIS 112
                 67899999999886 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.2   0.00041      0.52       8      76 ..       1      70 [.       1      76 [. 0.87
   2 ?   10.9   1.1   0.00033      0.42       2      82 .]      29     110 ..      28     110 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00041
                HHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHH CS
      ANAPC3  8 AiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAi 76
                Ai +++ +l+ +++ ++ +  +  +l + g++ +A++++++  + n+k   ++y + + l+ ++++ee +
  EPA06480.1  1 AIQCYDAVLKLSPQELSVLVNKISSLRKKGKFSEALKYCDNIlENNPKYNIVLYHKERILFSMNQFEESL 70
                6778888888888888888889999*****************8888888899999999999999999965 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00033
                 TT-HHHHHHHHHHHH.HHH--HHHHHHH..HHHHHHTT-HHHHHHHHHCTSHHHC-HHHHHHHHHHH.HHT.T-HHHHHHHH-SS CS
      ANAPC3   2 qnnyknAiflaerllaaetespedayll..AlclylngqykrAyellrkaklnskslgcrylfAqcl.lkL.kkyeeAiaaLekl 82 
                 ++++ +A+ +++ +l  e++  +++ l+     l++++q+++ +  ++   l++  l+  +lf +++ l++  k+++A+ +Lek+
  EPA06480.1  29 KGKFSEALKYCDNIL--ENNPKYNIVLYhkERILFSMNQFEESLLCCDAI-LDDYPLNGDVLFDKSCsLAMiYKIDDALYTLEKA 110
                 678899*********..66666666666569******************9.888888899999987768888**********985 PP

>> ATP13  Mitochondrial ATPase expression
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00083       1.1      54      86 ..      16      48 ..       7      60 .. 0.83
   2 ?    2.2   0.0      0.12   1.6e+02      64      89 ..      60      84 ..      52      92 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00083
       ATP13 54 selLkaivssfsynneiesAlklvdkfskkYpe 86
                  +L++ +ss+ +++++++Alk+ d++ +  p+
  EPA06480.1 16 LSVLVNKISSLRKKGKFSEALKYCDNILENNPK 48
                56888999*******************987654 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.12
       ATP13 64 fsynneiesAlklvdkfskkYpeiel 89
                ++++n++e+ l   d++   Yp ++ 
  EPA06480.1 60 LFSMNQFEESLLCCDAILDDYP-LNG 84
                78899****************9.654 PP

>> DMP12  DNA-mimic protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.35   4.4e+02      38      86 ..      20      69 ..       7      80 .. 0.61
   2 ?   11.6   0.1   0.00016      0.21      64     113 ..      81     127 ..      23     129 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.35
                HHHHHHHHHHTHHHHHHHHHS--TTS.--SEEEEE-HHHHHHHHHHHHTS CS
       DMP12 38 enqiieyqnrglwrlvseitdnwlfg.psegdwlidkesilavkeklqns 86
                 n+i   +++g ++   +  dn l   p     l  ke il   +++++s
  EPA06480.1 20 VNKISSLRKKGKFSEALKYCDNILENnPKYNIVLYHKERILFSMNQFEES 69
                45666666666666666666776643144455566677777666666555 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00016
                 --SEEEEE-HHHHHHHHHHHHTSTTTTSHHHHHHHHHHHHHHHCT--EEE CS
       DMP12  64 psegdwlidkesilavkeklqnsdfsteplvkniihvleyaiknektvif 113
                 p +gd l dk   la+  k++++ ++   l k i + ++y ik +kt  f
  EPA06480.1  81 PLNGDVLFDKSCSLAMIYKIDDALYT---LEKAISQGIQYKIKAKKTKSF 127
                 889****************9998876...5588889999*******9776 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0      0.05        64       1      33 [.       4      36 ..       4      37 .. 0.93
   2 ?    1.7   0.4      0.32   4.1e+02       2      17 ..      39      55 ..      38      56 .. 0.74
   3 ?    3.8   0.0     0.068        87       1      32 [.      72     103 ..      72     105 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.05
      TPR_17  1 lylkaleldPnnadaynnLAelllknGdlmtAr 33
                +y  +l+l P    ++ n+   l+k+G++ +A+
  EPA06480.1  4 CYDAVLKLSPQELSVLVNKISSLRKKGKFSEAL 36
                899************************999987 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.32
      TPR_17  2 ylkaleldPn.nadayn 17
                + + le++P+ n ++y+
  EPA06480.1 39 CDNILENNPKyNIVLYH 55
                6789*****95566665 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.068
      TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtA 32 
                 ++   l+ +P n d+++ +   l+++ + ++A
  EPA06480.1  72 CCDAILDDYPLNGDVLFDKSCSLAMIYKIDDA 103
                 567778889********999888877666666 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0    0.0016         2      16      66 ..       1      48 [.       1      56 [. 0.87
   2 ?    1.1   0.0      0.51   6.5e+02       6      39 ..      59      89 ..      57     114 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0016
      TPR_16 16 AaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66
                A+  ++a+lk+    P+    l ++  ++ ++g + eA+ +++  l++ p+
  EPA06480.1  1 AIQCYDAVLKLS---PQELSVLVNKISSLRKKGKFSEALKYCDNILENNPK 48
                778899999999...999999999999999999999999999988888886 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.51
      TPR_16  6 aalragdyddAaaaleaalkrdpssPdaaeAlll 39
                +++  +++++ +   +a l+++   P++ + l+ 
  EPA06480.1 59 ILFSMNQFEESLLCCDAILDDY---PLNGDVLFD 89
                6788899999999999999999...998888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       802  (0.044732); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 849.89
//
Query:       EPA06481.1  [L=239]
Description: hypothetical protein BG20_I1428 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1488.10
//
Query:       EPA06482.1  [L=119]
Description: putative large conductance mechanosensitive channel protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.3e-21   75.2   7.5    5.8e-21   75.0   7.5    1.0  1  MscL             Large-conductance mechanosensitive channel, 
     0.0015   18.5   0.6     0.0018   18.2   0.6    1.1  1  Reticulon        Reticulon
  ------ inclusion threshold ------
      0.023   15.1   5.9      0.035   14.6   5.9    1.3  1  FtsX             FtsX-like permease family
      0.042   13.5   0.6      0.042   13.5   0.6    1.4  1  DUF1449          Protein of unknown function (DUF1449)
        5.9    7.2   9.7        1.9    8.7   0.9    2.4  2  DUF3951          Protein of unknown function (DUF3951)


Domain annotation for each model (and alignments):
>> MscL  Large-conductance mechanosensitive channel, MscL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.0   7.5   1.6e-24   5.8e-21       1      95 [.      11     113 ..      11     119 .] 0.86

  Alignments for each domain:
  == domain 1  score: 75.0 bits;  conditional E-value: 1.6e-24
        MscL   1 llkeFkefilrGnvidLAvgviiGaaftkiVtslvkdiimpliglllggvdfselkikl....kaeaavlkygafiqavinFliiafviFlivkaink. 94 
                 +++eF  f+    +i LA++ +iGaa +k+Vt++v+dii+p++gl l + d++ l+ ++    + + + +kyg fi+++i+Fliia+++F++ k++++ 
  EPA06482.1  11 FVQEFMGFLKTFGIIGLAIAFVIGAAASKLVTAFVNDIINPIVGLALPSGDLKGLQSSIvnsaTGAISEFKYGDFIANIIDFLIIALIVFIMYKVLSRf 109
                 689******************************************9977788888777766665566889*************************9996 PP

        MscL  95 ...k 95 
                    +
  EPA06482.1 110 klvE 113
                 4431 PP

>> Reticulon  Reticulon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.6   5.1e-07    0.0018      38     126 ..      19     112 ..      11     113 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 5.1e-07
   Reticulon  38 vsklllllllvlflwaeyagllnks.kp....pepelelseesvreladsllellnkalselrrlalgedlklflkvalllyilsilgslfsll 126
                 +  ++++ l++ f+++ +a++l +   +    p+  l l+  +++ l +s++++++ a+se++   ++ ++ +fl +al+++i++++ s f+l+
  EPA06482.1  19 LKTFGIIGLAIAFVIGAAASKLVTAfVNdiinPIVGLALPSGDLKGLQSSIVNSATGAISEFKYGDFIANIIDFLIIALIVFIMYKVLSRFKLV 112
                 5567788999999999888888886555577688*******************************************************99875 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   5.9   9.7e-06     0.035      28      80 ..      22     103 ..      11     112 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9.7e-06
        FtsX  28 itlvalviGlglgllaaqllsdvllssvf.........................s....selkisidlitvliiivllllla 80 
                 +++++l+i++++g++a++l+ ++++ + +                         +       ++  ++i++lii++++++++
  EPA06482.1  22 FGIIGLAIAFVIGAAASKLVTAFVNDIINpivglalpsgdlkglqssivnsatgAisefKYGDFIANIIDFLIIALIVFIMY 103
                 6788999999999999999888888885555567777777777777766665551556799999999999999999999876 PP

>> DUF1449  Protein of unknown function (DUF1449)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.6   1.2e-05     0.042      74     142 ..      16      84 ..      12      91 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.2e-05
     DUF1449  74 vlfLtlFglvGlvlqslvasllgallpallaaaialllalplvrvlaallakilpkdetsavseeslvG 142
                 + fL +Fg++Gl++  ++ +    l++a++  +i  +++l+l     ++l+  +++  t a+se ++  
  EPA06482.1  16 MGFLKTFGIIGLAIAFVIGAAASKLVTAFVNDIINPIVGLALPSGDLKGLQSSIVNSATGAISEFKYGD 84 
                 679**********************************99999999999999999999999999876655 PP

>> DUF3951  Protein of unknown function (DUF3951)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.9   0.00054       1.9       3      26 ..      19      40 ..      18      47 .. 0.85
   2 ?    2.6   2.3     0.043   1.5e+02      12      25 ..      91     104 ..      83     109 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00054
     DUF3951  3 LltiGillltlvilviIgfvaykl 26
                L t+G  +++l+i ++Ig  a kl
  EPA06482.1 19 LKTFG--IIGLAIAFVIGAAASKL 40
                89***..899*******9877766 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.043
     DUF3951  12 tlvilviIgfvayk 25 
                   +i+ +I+f+ yk
  EPA06482.1  91 DFLIIALIVFIMYK 104
                 45667777777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       860  (0.047967); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 752.49
//
Query:       EPA06483.1  [L=125]
Description: hypothetical protein BG20_I1419 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.34s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 723.26
//
Query:       EPA06484.1  [L=153]
Description: hypothetical protein BG20_I1416 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.5e-14   52.6   0.0    6.2e-14   52.5   0.0    1.0  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra
  ------ inclusion threshold ------
      0.028   14.6   0.0      0.032   14.4   0.0    1.1  1  Polyketide_cyc   Polyketide cyclase / dehydrase and lipid tra


Domain annotation for each model (and alignments):
>> Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.5   0.0   6.9e-18   6.2e-14       3     141 ..      13     150 ..      11     152 .. 0.81

  Alignments for each domain:
  == domain 1  score: 52.5 bits;  conditional E-value: 6.9e-18
                      EEEEEEEESS-HHHHHHHHTTTTGGGGT-TTEEEEECSESTSSSTTTEEEEE.CCCSSEEEEEEEEEETTTTEEEEEEE.SSS-TSEEEEEEEE CS
  Polyketide_cyc2   3 kvtvsvviaappekVwalvsdfenwprWhpevarveleggggpargvegtvr.vggrgtvreelvevdpegrllsyrivkpvpvanyvatwtvt 95 
                      +v++++ i+a+ +kVw  +s+ +++p W   v+++++ +++ + +g+ ++++   g +t++e +v++   +  ++y +++ +p++ yvat++++
       EPA06484.1  13 SVKKTISINASKQKVWQKISNIAGLPLWVVDVKKTTYLSKKKKNVGAIRKITfDDG-NTIEEHIVAWKN-EEYFTYIATEGLPLRAYVATISIK 104
                      799********************************988734443445578885666.99********96.88889888789************* PP

                      ECCET.EEEEEEEEEEE.E--TT--HHHHHHHHHHHHHHHHHHHHHHH CS
  Polyketide_cyc2  96 pdggg.trvtwtgefda.gplggpfekpaaakavkgdleagLerLkar 141
                      +     t++tw+  +      ++ f ++ + +++++++e++L +Lk  
       EPA06484.1 105 AKNKKtTQLTWQSYLNSkKMSKKQF-TD-FVEFMGRFYETSLGNLKNI 150
                      *9966488*****555422233444.44.457*************975 PP

>> Polyketide_cyc  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   3.6e-06     0.032       1      65 [.      20      99 ..      20     140 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.6e-06
                    ESS-HHHHHHHHTTTGGCCSCCCCEEEEEE.SSSEE...E............EEECSTTSSCEEEEEEEEEEETTT...E CS
  Polyketide_cyc  1 vpapadqvyalvadvesypeflphcssvevleeaesglsa............dlevgfggltesftarvtldppee...i 65
                    ++a+ ++v++ ++++  +p ++  +++ + l+++ +++ a            + +++ +   e+ft  +t++ p +    
      EPA06484.1 20 INASKQKVWQKISNIAGLPLWVVDVKKTTYLSKKKKNVGAirkitfddgntiEEHIVAWKNEEYFTYIATEGLPLRayvA 99
                    78999******************************977777889999999999999999999999998888888776662 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1132  (0.0631379); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1128.75
//
Query:       EPA06485.1  [L=424]
Description: hypothetical protein BG20_I1415 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00042   19.7  29.7     0.0039   16.6   5.5    2.9  2  GAS              Growth-arrest specific micro-tubule binding
    0.00046   19.2  31.2      0.014   14.3   6.9    3.1  2  Spc7             Spc7 kinetochore protein
    0.00085   18.1  35.3     0.0026   16.5  14.0    2.2  2  AAA_13           AAA domain
    0.00096   19.2   1.7    0.00096   19.2   1.7    5.1  5  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
     0.0022   18.2  23.1        0.4   11.0   1.0    5.6  5  DUF948           Bacterial protein of unknown function (DUF94
     0.0024   17.9   5.6     0.0024   17.9   5.6    3.8  4  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
     0.0025   18.3  27.5      0.016   15.7   4.4    2.9  3  APG6_N           Apg6 coiled-coil region
     0.0045   17.4   4.9     0.0045   17.4   4.9    4.9  5  Snapin_Pallidin  Snapin/Pallidin
  ------ inclusion threshold ------
       0.02   15.1   1.8      0.053   13.8   0.2    2.6  2  BEN              BEN domain
      0.026   14.6   0.4      0.026   14.6   0.4    3.3  2  Imm30            Immunity protein 30
      0.033   14.4   2.4      0.033   14.4   2.4    5.1  4  XhlA             Haemolysin XhlA
       0.04   12.1  33.8        0.3    9.2  17.0    2.3  2  HOOK             HOOK protein
       0.04   13.2  16.1       0.29   10.4   6.5    2.9  2  HemX             HemX, putative uroporphyrinogen-III C-methyl
       0.13   12.7   3.2        0.5   10.9   0.3    2.9  2  Pullulanase_Ins  Pullulanase Ins domain
        0.2   11.1   6.8        3.2    7.1   0.2    2.7  2  DUF4349          Domain of unknown function (DUF4349)
       0.21   11.7  10.8         10    6.2   0.1    4.3  4  DUF4351          Domain of unknown function (DUF4351)
       0.23   11.6   5.9       0.72   10.0   0.1    2.9  2  Cep57_CLD_2      Centrosome localisation domain of PPC89
        0.3   11.2  27.1       0.26   11.4   8.7    3.5  2  DHR10            Designed helical repeat protein 10 domain
        0.3   10.7   4.7         12    5.6   0.1    3.7  3  Vac_Fusion       Chordopoxvirus multifunctional envelope prot
       0.31   11.2  22.8       0.22   11.7   8.0    3.1  2  Tropomyosin_1    Tropomyosin like
       0.39   11.1  22.3       0.27   11.6   2.9    4.9  5  CLZ              C-terminal leucine zipper domain of cyclic n
       0.47   10.8  34.5      0.069   13.5   7.3    5.2  5  BLOC1_2          Biogenesis of lysosome-related organelles co
       0.54    9.8  16.6       0.53    9.8   5.7    2.6  2  Phage_GPO        Phage capsid scaffolding protein (GPO) serin
       0.57    9.4  25.9          2    7.6   3.0    3.7  3  DUF3450          Protein of unknown function (DUF3450)
       0.65   10.3  16.6       0.06   13.6   1.2    3.9  3  Rx_N             Rx N-terminal domain
        1.3    7.5  35.6       0.11   11.1  11.9    3.1  3  FapA             Flagellar Assembly Protein A
        1.3    8.7   8.2        7.8    6.2   1.8    2.9  2  Alpha-E          A predicted alpha-helical domain with a cons
        2.6    7.3  13.1       0.35   10.2   5.8    2.2  2  DUF4407          Domain of unknown function (DUF4407)
        3.1    8.3  39.3       0.13   12.7   1.9    6.6  6  NPV_P10          Nucleopolyhedrovirus P10 protein
        7.8    6.6  26.4          6    6.9   6.1    4.0  4  TPR_MLP1_2       TPR/MLP1/MLP2-like protein


Domain annotation for each model (and alignments):
>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7  15.4    0.0017         1      56     167 ..     142     257 ..     121     275 .. 0.76
   2 !   16.6   5.5   6.6e-06    0.0039      62     140 ..     329     412 ..     306     420 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0017
         GAS  56 nkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekvekerdelykkfeaaiqevqqktglknll....Lekk 150
                  k++ e+Lk+   +++  + ++++    + + + + +++ ++ ke+kd+++e   +eqr+++++ ++d l kk  ++ + +++  g ++++    L k 
  EPA06485.1 142 AKKYAEKLKEILLQMQSNHSKIQQMLTNFDETQTTSTEILDSLKEIKDIEEEVSKKEQRISELQTHIDSLDKKIISSEDSIKKIKGSEEYVklleLTKI 240
                 6788899999999999999999999999999*****************************************986665555544444444400025555 PP

         GAS 151 lkalqeelEkkeaqlee 167
                 l+al+e+ ++ + q+++
  EPA06485.1 241 LDALTESKNQIKDQITS 257
                 55666655555555554 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 6.6e-06
         GAS  62 pLkkaeeeveeLrkqlknyekdkqslknlk.....arlkelekelkdlkwehevleqrfekvekerdelykkfeaaiqevqqkt 140
                 +L++ ee ++ L +q+++y  ++++++n+       +l++l+k+lk+l  ++e  e ++++ ++e++e++++ ++ i ++  k 
  EPA06485.1 329 QLTEIEEALDGLIHQVNDYADKQEKIQNQIkslepHELQDLTKNLKNLMTDKEDSELKIKTFQSEINEIHSNSTKLIVDIETKL 412
                 455666666666666666655555544432011125799****************************************99886 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7  15.4   0.00058      0.35     160     247 ..     144     226 ..     134     276 .. 0.75
   2 !   14.3   6.9   2.3e-05     0.014     154     239 ..     319     404 ..     303     419 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00058
        Spc7 160 kqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqksele 247
                 k  e+l+e+l +++++++++++ l++  e ++      ++e+    +e++++++e+++k+++++elq+ +++l++ki + ++++++++
  EPA06485.1 144 KYAEKLKEILLQMQSNHSKIQQMLTNFDETQTT-----STEILDSLKEIKDIEEEVSKKEQRISELQTHIDSLDKKIISSEDSIKKIK 226
                 778999999*************99999994443.....44444444468888888888888888888888888888877777776654 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 2.3e-05
        Spc7 154 dkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieel 239
                   + ++k+ ++l+e+ ++l+    ++++ ++k+++ +++++s+++ eL+ l ++l++l+++ e  + ++++ q++++e+ ++ ++l
  EPA06485.1 319 SVKDVDKSFSQLTEIEEALDGLIHQVNDYADKQEKIQNQIKSLEPHELQDLTKNLKNLMTDKEDSELKIKTFQSEINEIHSNSTKL 404
                 5677889999********************************************************************99988776 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1  13.7     0.003       1.8     317     474 ..      69     230 ..      34     240 .. 0.66
   2 !   16.5  14.0   4.3e-06    0.0026     280     452 ..     243     411 ..     235     423 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.003
      AAA_13 317 safeedkeelkaeaealeeqLkglqraleaKrkepfk..sve.lesvkakiesikklvaeineliakhNekvanleeekeeakkklelhlv...eeles 409
                 ++ + ++++++++++ +    +g q++++  +k+  +  +v+ ++++++  + +++ +++i ++  +  + ++ ++++ +e  k++ l++    +++++
  EPA06485.1  69 EKDNLQVDDIDKHLRIIV--VRGKQQVIDMIKKDAISlpDVKsYTDAENINVILNQMLKKIGDVLGRQTRVIHIFAKKYAEKLKEILLQMQsnhSKIQQ 165
                 345555666666665554..3455556655555555512222144444444677888888888888999999999999888888877766433377888 PP

      AAA_13 410 eldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeLkaf.Glge 474
                 +l+++++  + ++++i +  ke+k++e+e+ k+e++i+eL++ + +  + +   ++ +k++ G +e
  EPA06485.1 166 MLTNFDE-TQTTSTEILDSLKEIKDIEEEVSKKEQRISELQTHIDSLDKKIISSEDSIKKIkGSEE 230
                 8877775.5555667878888************************999999999999999988554 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 4.3e-06
      AAA_13 280 efeekqerLekliekveskkselleklkavsdeasensafeedkeelkaeaealeeq.LkglqraleaKrkepfk.svelesvkakiesikklvaeine 376
                 + +e+++++++ i++  +k+s+ l +++ +s+ ++e  + +     +++ +e+l  +  +++   le+ rk +++ s+++++v++  ++++++ +++  
  EPA06485.1 243 ALTESKNQIKDQITSQFTKISRPLSRYEHISAMEKE--QKNLLSGLIEDPFEVLMPKnKDSIILILENVRKAISSdSISVKDVDKSFSQLTEIEEALDG 339
                 355666666666666666666666666666665554..33555666666776655441666888999999**999899********************* PP

      AAA_13 377 liakhNekvanleeekeeakkklelhlveeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekq 452
                 li + N + ++ e+ ++++ k+le h++++l+++l+++++++++ e +i+  + e++e+ ++  kl     ++e++
  EPA06485.1 340 LIHQVNDYADKQEKIQNQI-KSLEPHELQDLTKNLKNLMTDKEDSELKIKTFQSEINEIHSNSTKLIV---DIETK 411
                 *******998887777765.68***********************************99988777644...44444 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   2.5      0.69   4.1e+02      17     115 ..      27     127 ..      17     139 .. 0.64
   2 ?    6.7  13.2     0.012       6.9       3      95 ..     162     267 ..     110     286 .. 0.85
   3 !   19.2   1.7   1.6e-06   0.00096      15     118 ..     234     347 ..     221     351 .. 0.79
   4 !    9.2   2.3     0.002       1.2      61     104 ..     320     376 ..     294     382 .. 0.53
   5 ?    3.8   1.3      0.09        54      39      72 ..     386     419 ..     367     422 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.69
  Baculo_PEP_C  17 dLtnvLnai.rlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnlnsiltnLls..svtNinstLnn 110
                   +++ ++  i  l ++qil+++++  d+ +  +++l+  + s+l++ + ++d+  ++L   + + ++++   ++     l +  s  +  Nin  Ln 
    EPA06485.1  27 EVSGIVRKIlELRTSQILSDIKSVRDTTQPLIKDLTV-IGSALEKDNLQVDDIDKHLRIIVVRGKQQVIDMIKKDAISLPDVKSytDAENINVILNQ 122
                   5555555552456678888888888888887777654.77777766677777777777777776666666665555555555542244566666666 PP

  Baculo_PEP_C 111 llqal 115
                   +l+ +
    EPA06485.1 123 MLKKI 127
                   66655 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.012
  Baculo_PEP_C   3 dvqqL..ngggg.nqfldLtnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldt...........rldtlltnLtdalnalqdtlrn 85 
                   ++qq+  n  ++ +   ++ + L+ i+  + ++ ++ ++ + +++t +++l++++ s+  ++++           +l++ l++Lt++ n+++d++++
    EPA06485.1 162 KIQQMltNFDETqTTSTEILDSLKEIKDIEEEV-SKKEQRISELQTHIDSLDKKIISSEDSIKKikgseeyvkllELTKILDALTESKNQIKDQITS 257
                   567776644433123468888888888888888.777888888888888888888888888888999999*************************** PP

  Baculo_PEP_C  86 eLtnlnsilt 95 
                   + t +   l+
    EPA06485.1 258 QFTKISRPLS 267
                   ***9988776 PP

  == domain 3  score: 19.2 bits;  conditional E-value: 1.6e-06
  Baculo_PEP_C  15 fldLtnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldt........rldtlltnLtdalnalqdtlrneLtnln...siltnLlss 100
                    l+Lt++L+a+   + qi  q+++++++i + L+   e+++++ +e+++         ++ l+ + +d++  + +++r+++ +     +++    s+
    EPA06485.1 234 LLELTKILDALTESKNQIKDQITSQFTKISRPLSR-YEHISAMEKEQKNllsgliedPFEVLMPKNKDSIILILENVRKAISSDSisvKDVDKSFSQ 329
                   69****************************98887.344666555555555555556888888889999999999***9998765112345556899 PP

  Baculo_PEP_C 101 vtNinstLnnllqalnnl 118
                   +t i+++L +l++ +n +
    EPA06485.1 330 LTEIEEALDGLIHQVNDY 347
                   ***************976 PP

  == domain 4  score: 9.2 bits;  conditional E-value: 0.002
  Baculo_PEP_C  61 ldt......rldtlltnLtdalnalq......dtlrneLtnln.siltnLlssvtNi 104
                   +++      +l++  ++L+  + +++      ++++n++++l+  +l +L+ ++ N+
    EPA06485.1 320 VKDvdksfsQLTEIEEALDGLIHQVNdyadkqEKIQNQIKSLEpHELQDLTKNLKNL 376
                   222223444555555555555555555555556666666666634566666666665 PP

  == domain 5  score: 3.8 bits;  conditional E-value: 0.09
  Baculo_PEP_C  39 lldaietqLnalsedlksllaeldtrldtlltnL 72 
                    +++ ++++n++ ++ ++l+ +++t+l ++++++
    EPA06485.1 386 KIKTFQSEINEIHSNSTKLIVDIETKLRKFSNTI 419
                   5677888999999999999999999999988765 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1       1.4   8.4e+02      59      83 ..      43      67 ..      17      85 .. 0.57
   2 !    7.3   3.8    0.0097       5.8      17      83 ..     142     214 ..     115     218 .. 0.80
   3 ?    5.4   0.1     0.036        22      21      50 ..     234     263 ..     231     282 .. 0.83
   4 !   11.0   1.0   0.00068       0.4      28      80 ..     323     376 ..     302     382 .. 0.74
   5 ?    5.6   0.4     0.032        19      24      75 ..     369     420 ..     364     423 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.4
      DUF948 59 lledvneklekvdplteavadlges 83
                +l+d+++  ++ +pl++ +  +g +
  EPA06485.1 43 ILSDIKSVRDTTQPLIKDLTVIGSA 67
                4444444444444444444444433 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0097
      DUF948  17 livvllklkktldeaaatieele......kqvdpilkevedllakvnelledvneklekvdplteavadlges 83 
                   +   klk++l ++++   +++      ++++ +++e+ d l++++++ e+v++k +++ +l +++  l ++
  EPA06485.1 142 AKKYAEKLKEILLQMQSNHSKIQqmltnfDETQTTSTEILDSLKEIKDIEEEVSKKEQRISELQTHIDSLDKK 214
                 44555566666666666666666777888999999999999999****************9999999877665 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.036
      DUF948  21 llklkktldeaaatieelekqvdpilkeve 50 
                 ll+l+k+ld+++++ +++++q+++  +++ 
  EPA06485.1 234 LLELTKILDALTESKNQIKDQITSQFTKIS 263
                 8999****************9988776665 PP

  == domain 4  score: 11.0 bits;  conditional E-value: 0.00068
      DUF948  28 ldeaaatieelekqvdpilkevedllakvnelledvne.klekvdplteavadl 80 
                 +d+  ++++e+e+ +d+++++v+d  +k +++++++++ +  +++ lt+++++l
  EPA06485.1 323 VDKSFSQLTEIEEALDGLIHQVNDYADKQEKIQNQIKSlEPHELQDLTKNLKNL 376
                 566667889999*****************9966665554455555555555444 PP

  == domain 5  score: 5.6 bits;  conditional E-value: 0.032
      DUF948  24 lkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplte 75 
                 l+k l+++ +  e+ e +++    e++++ +++ +l  d++ kl k  + ++
  EPA06485.1 369 LTKNLKNLMTDKEDSELKIKTFQSEINEIHSNSTKLIVDIETKLRKFSNTIY 420
                 45555555555556667888999999999999999******99999877765 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.2       3.5   2.1e+03      50      89 ..      24      61 ..       8      81 .. 0.59
   2 !    9.2  13.9    0.0019       1.2      51     130 ..     143     236 ..     141     246 .. 0.77
   3 ?    3.3   0.1      0.13        79      38     100 ..     297     362 ..     294     363 .. 0.68
   4 !   17.9   5.6     4e-06    0.0024      17      77 ..     349     410 ..     340     417 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 3.5
  CENP-F_leu_zip 50 skaevetlkeeieelaeelreleldLvalrsekeeLekel 89
                    +  ev+++  +i el++  +++ +d++++r   + L k+l
      EPA06485.1 24 QLSEVSGIVRKILELRT--SQILSDIKSVRDTTQPLIKDL 61
                    55566666666666554..455556666665555544444 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0019
  CENP-F_leu_zip  51 kaevetlkeeieelaeelreleldLvalr.............sekeeLekelqkkqervseLeslnsslenlleekEqekvqmkeesk.aavee 130
                     k+ +e+lke + +++++ +++++ L+++              +e +++e+e+ kk +r+seL++   sl + +  +E+  +++k + +  ++ e
      EPA06485.1 143 KKYAEKLKEILLQMQSNHSKIQQMLTNFDetqttsteildslKEIKDIEEEVSKKEQRISELQTHIDSLDKKIISSEDSIKKIKGSEEyVKLLE 236
                     6777777777777777777777777777777777778888889***********************************9777775433134444 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.13
  CENP-F_leu_zip  38 enqekvileaEtskaevetlkeeieela...eelreleldLvalrsekeeLekelqkkqervseLe 100
                     +n++++il  E+ ++++++    ++      ++l+e+e  L+ l  + ++ + + +k q+++++Le
      EPA06485.1 297 KNKDSIILILENVRKAISSDSISVKDVDksfSQLTEIEEALDGLIHQVNDYADKQEKIQNQIKSLE 362
                     677888888888888888844444444300045666777888888888888888888888888887 PP

  == domain 4  score: 17.9 bits;  conditional E-value: 4e-06
  CENP-F_leu_zip  17 rkadsLkdkvenLe.relemseenqekvileaEtskaevetlkeeieelaeelreleldLva 77 
                      k++++++++++Le  el+++ +n+ ++++++E+s  +++t+++ei+e+ ++ ++l +d+++
      EPA06485.1 349 DKQEKIQNQIKSLEpHELQDLTKNLKNLMTDKEDSELKIKTFQSEINEIHSNSTKLIVDIET 410
                     578899********77****************************************999975 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1  13.2    0.0029       1.7      12     125 ..     147     258 ..     142     266 .. 0.77
   2 ?   -0.7   0.3       3.3     2e+03      25      67 ..     241     283 ..     233     288 .. 0.46
   3 !   15.7   4.4   2.7e-05     0.016      24     123 ..     298     398 ..     294     404 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0029
      APG6_N  12 eeldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeee.rfwreyne.l 108
                 e+l++ l q+++ + + ++ l ++++++++++    e+ ++ +e++++e+e +++++ + el+++ ++l++++ + e   ++++  ee  ++ e  + l
  EPA06485.1 147 EKLKEILLQMQSNHSKIQQMLTNFDETQTTST----EILDSLKEIKDIEEEVSKKEQRISELQTHIDSLDKKIISSEDSIKKIKGSEEyVKLLELTKiL 241
                 67888888899999999999999999977755....9*****************************************999998766514455555533 PP

      APG6_N 109 qlelleleeeldsleaq 125
                 +   +++++ +d++++q
  EPA06485.1 242 DALTESKNQIKDQITSQ 258
                 43344444445555555 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 3.3
      APG6_N  25 rdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeell 67 
                  da++e  +++k++ +++ ++ +   +  e ++++eke+++ll
  EPA06485.1 241 LDALTESKNQIKDQITSQFTKISRPLSRYEHISAMEKEQKNLL 283
                 4444444555555544444322222222333555555555555 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 2.7e-05
      APG6_N  24 erdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaale.eelealeeeeerfwreynelqlelleleeelds 121
                  +d+    l++++k  ++++ + ++++++  +l ++e++ + l+ + ++  +++e++++++++le  el++l ++ ++ +++  + +l+ + ++ e + 
  EPA06485.1 298 NKDSIILILENVRKAISSDSISVKDVDKSFSQLTEIEEALDGLIHQVNDYADKQEKIQNQIKSLEpHELQDLTKNLKNLMTDKEDSELKIKTFQSEINE 396
                 6777778889999998887766677777777788888888999*********************96799**************************9988 PP

      APG6_N 122 le 123
                 + 
  EPA06485.1 397 IH 398
                 76 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1       3.7   2.2e+03      28      65 ..      90     127 ..      66     140 .. 0.64
   2 ?    6.3   2.0     0.021        12      52      82 ..     136     166 ..     114     172 .. 0.79
   3 ?    1.2   6.4      0.85   5.1e+02      14      85 ..     186     254 ..     174     257 .. 0.70
   4 ?    0.9   0.6       1.1   6.3e+02      17      45 ..     236     264 ..     232     282 .. 0.73
   5 !   17.4   4.9   7.5e-06    0.0045       9      82 ..     331     404 ..     326     409 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 3.7
  Snapin_Pallidin  28 sQeeLleqldrlnekLkeleeaqe.aevlpdlkeyakKL 65 
                      + +++ +++++ + +L +++ +++ +++ + l++ +kK+
       EPA06485.1  90 K-QQVIDMIKKDAISLPDVKSYTDaENINVILNQMLKKI 127
                      3.3456677777777777777777666666666666665 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.021
  Snapin_Pallidin  52 aevlpdlkeyakKLvnikkrmsslnerlqkl 82 
                        +  ++k+ya+KL++i  +m+s ++++q++
       EPA06485.1 136 RVIHIFAKKYAEKLKEILLQMQSNHSKIQQM 166
                      3456889*********************997 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.85
  Snapin_Pallidin  14 kldeldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqklkkR 85 
                      ++++++e++++ +q  +eL+ ++d+l +k+ + e+  +     +  e   KL ++ k + +l e+ +++k+ 
       EPA06485.1 186 EIKDIEEEVSKKEQRISELQTHIDSLDKKIISSEDSIK--K-IKGSEEYVKLLELTKILDALTESKNQIKDQ 254
                      57888888888888888999999999999865555555..3.333334457777777777777777777765 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 1.1
  Snapin_Pallidin  17 eldeklkelrqsQeeLleqldrlnekLke 45 
                      el++ l +l++s ++ ++q++++ +k+ +
       EPA06485.1 236 ELTKILDALTESKNQIKDQITSQFTKISR 264
                      67777889999999999999998888765 PP

  == domain 5  score: 17.4 bits;  conditional E-value: 7.5e-06
  Snapin_Pallidin   9 ellepkldeldeklkelrqsQeeLleqldrln.ekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqkl 82 
                      + +e +ld l +++++  ++Qe+ ++q+++l  ++L++l ++ + ++++d +    K+++++ +++++++ ++kl
       EPA06485.1 331 TEIEEALDGLIHQVNDYADKQEKIQNQIKSLEpHELQDLTKNLK-NLMTDKEDSELKIKTFQSEINEIHSNSTKL 404
                      568899************************87589*****9999.99***********************99986 PP

>> BEN  BEN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       6.8   4.1e+03      42      73 ..      28      50 ..       6      60 .. 0.52
   2 ?   13.8   0.2   8.8e-05     0.053      33      77 ..     357     401 ..     344     402 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 6.8
                HHHHHHHHHHHH--..........-HHHHHHH CS
         BEN 42 lsaIrnyveerypsekededwwrecldqInki 73
                +s I +++ e  +s         ++l++I++ 
  EPA06485.1 28 VSGIVRKILELRTS---------QILSDIKSV 50
                54444444444444.........344444443 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 8.8e-05
                 --EE--HHHHHHHHHHHHHHH--..........-HHHHHHHHHHH CS
         BEN  33 pkkaLDpnklsaIrnyveerypsekededwwrecldqInkilrrk 77 
                   k L+p++l+++ + +++ +++++++e ++++++++In+i++++
  EPA06485.1 357 QIKSLEPHELQDLTKNLKNLMTDKEDSELKIKTFQSEINEIHSNS 401
                 5689*************************************9985 PP

>> Imm30  Immunity protein 30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   1.9      0.78   4.7e+02      21      76 ..     154     214 ..     141     235 .. 0.68
   2 ?   14.6   0.4   4.4e-05     0.026      18      71 ..     306     362 ..     297     380 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.78
       Imm30  21 llkeqnkdnledlckafdD.dtedeevmFgl..vHlled..leveeylkklvealpkllkn 76 
                 l+++ n+ +++++ + fd+ +t   e++ +l  +  +e+   + e+ +++l + ++ l+k+
  EPA06485.1 154 LQMQSNHSKIQQMLTNFDEtQTTSTEILDSLkeIKDIEEevSKKEQRISELQTHIDSLDKK 214
                 5677888999999999987357888998887556667665555566666666666555544 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 4.4e-05
       Imm30  18 lekllkeqnkdn..ledlckafdDdtedeevmFglvHlledle.veeylkklvealp 71 
                 le++ k ++ d   ++d+ k f   te ee + gl+H ++d++  +e++++ +++l+
  EPA06485.1 306 LENVRKAISSDSisVKDVDKSFSQLTEIEEALDGLIHQVNDYAdKQEKIQNQIKSLE 362
                 56666666666512689************************9626789999999886 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   1.5      0.98   5.9e+02       2      46 ..     149     192 ..     147     193 .. 0.75
   2 ?   10.8   7.0   0.00075      0.45       4      46 ..     185     227 ..     179     230 .. 0.94
   3 ?   14.4   2.4   5.6e-05     0.033       5      49 ..     329     374 ..     328     378 .. 0.94
   4 ?    4.2   3.0     0.084        50       6      47 ..     366     400 ..     364     408 .. 0.66

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.98
        XhlA   2 ikerlerietkldnleervdkleekaaeaeekiknleedlkkles 46 
                 +ke l ++++++ ++++ ++  +e +++  e +++l  ++k++e+
  EPA06485.1 149 LKEILLQMQSNHSKIQQMLTNFDETQTTSTEILDSLK-EIKDIEE 192
                 5777888888888888888888888888888888875.4777765 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00075
        XhlA   4 erlerietkldnleervdkleekaaeaeekiknleedlkkles 46 
                 ++++ ie+++ + e+r+++l+ + +  ++ki++ e+ +kk++ 
  EPA06485.1 185 KEIKDIEEEVSKKEQRISELQTHIDSLDKKIISSEDSIKKIKG 227
                 78999************************************96 PP

  == domain 3  score: 14.4 bits;  conditional E-value: 5.6e-05
        XhlA   5 rlerietkldnleervdkleekaaeaeekiknle.edlkklesnqk 49 
                  l++ie+ ld l  +v++  +k+++ +++ik+le ++l +l++n+k
  EPA06485.1 329 QLTEIEEALDGLIHQVNDYADKQEKIQNQIKSLEpHELQDLTKNLK 374
                 599******************************989********99 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.084
        XhlA   6 lerietkldnleervdkleekaaeaeekiknleedlkklesn 47 
                 l+ + ++l+nl++       +++  e kik  + +++++ sn
  EPA06485.1 366 LQDLTKNLKNLMT-------DKEDSELKIKTFQSEINEIHSN 400
                 4555566666666.......5666777777777777777776 PP

>> HOOK  HOOK protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2  17.0    0.0005       0.3     450     575 ..     145     263 ..     115     285 .. 0.70
   2 ?    8.0   9.0    0.0011      0.67     476     563 ..     326     411 ..     292     422 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0005
        HOOK 450 lpaevreklirLqhENKmLklkqegseeekltelqelledanrrkneLetenrlanqrileLeaqveelqkalqeqgskaedssllkkkleehleklke 548
                  + +++e l+++q+    +  +q  ++ ++ +++++++ d+ ++++++e+e  +++qri+eL+++++ l k+  +    +ed s +k k +e   kl e
  EPA06485.1 145 YAEKLKEILLQMQSNHSKI--QQMLTNFDETQTTSTEILDSLKEIKDIEEEVSKKEQRISELQTHIDSLDKKIIS----SED-SIKKIKGSEEYVKLLE 236
                 4556777777777766555..66655555555555555559999**********************999998876....677.4455666666777888 PP

        HOOK 549 vqeelqkkkeqleelepklssnkqkie 575
                 + + l   +e  ++++ +++s+ +ki+
  EPA06485.1 237 LTKILDALTESKNQIKDQITSQFTKIS 263
                 888888877777777778888877775 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0011
        HOOK 476 eeekltelqelledanrrkneLetenrlanqrileLe.aqveelqkalqeqgskaedssllkkkleehleklkevqeelqkkkeqleel 563
                 +  +lte++e l+   +++n+  +++ + +++i++Le +++++l+k+l++  + +ed   ++ k+++ + +++e++++ +k    +e  
  EPA06485.1 326 SFSQLTEIEEALDGLIHQVNDYADKQEKIQNQIKSLEpHELQDLTKNLKNLMTDKED---SELKIKTFQSEINEIHSNSTKLIVDIETK 411
                 4578999*****************************945799**************9...45567788888999999988877777664 PP

>> HemX  HemX, putative uroporphyrinogen-III C-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   6.5   0.00048      0.29      29     109 ..     155     235 ..     141     259 .. 0.79
   2 ?    7.5   1.5    0.0036       2.1      38     104 ..     335     402 ..     292     413 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00048
        HemX  29 qvqeltaevaelqqqlaaleqqlaq...veaekeqkqeleerlqqlaeklealekeleqlqkqleelqqqlskvsgaerkdWlL 109
                 q+q+++   +++qq l++ ++++++   +  + ++ +++ee++ ++++++++l++++++l+k++ + ++ ++k++g+e+   lL
  EPA06485.1 155 QMQSNH---SKIQQMLTNFDETQTTsteILDSLKEIKDIEEEVSKKEQRISELQTHIDSLDKKIISSEDSIKKIKGSEEYVKLL 235
                 333333...556666666555555544477888899999************************************998776666 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0036
        HemX  38 aelqqqlaaleqqlaqveaekeqkqele.erlqqlaeklealekeleqlqkqleelqqqlskvsgaer 104
                 ++l+  ++++++ +++ e+ ++q + le ++lq+l+++l++l + +e+ + ++++ q+++++++++++
  EPA06485.1 335 EALDGLIHQVNDYADKQEKIQNQIKSLEpHELQDLTKNLKNLMTDKEDSELKIKTFQSEINEIHSNST 402
                 33333333333333333334444444443678888888888888889999999999999998888765 PP

>> Pullulanase_Ins  Pullulanase Ins domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.2       1.1   6.3e+02      34      72 ..     171     212 ..     151     213 .. 0.63
   2 ?   10.9   0.3   0.00083       0.5       4      53 ..     313     364 ..     311     382 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 1.1
  Pullulanase_Ins  34 aeyCsssktiaevleelk...kdDskenpqVqeLnrlvaetD 72 
                       e  + s+ i + l+e+k   ++ sk+++ + eL++++ + D
       EPA06485.1 171 DETQTTSTEILDSLKEIKdieEEVSKKEQRISELQTHIDSLD 212
                      444455555666666555111445667777777777777666 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00083
  Pullulanase_Ins   4 inEdpdkvadidqpFskLCevnpavkn..seFaeyCsssktiaevleelkkd 53 
                      i+ d+  v d+d++Fs+L e+++a+     +  +y ++++ i++ +++l+ +
       EPA06485.1 313 ISSDSISVKDVDKSFSQLTEIEEALDGliHQVNDYADKQEKIQNQIKSLEPH 364
                      7889999*****************9987789999999999999888877655 PP

>> DUF4349  Domain of unknown function (DUF4349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   2.1     0.014       8.5     113     146 ..     182     215 ..     156     261 .. 0.69
   2 ?    7.1   0.2    0.0053       3.2      10      71 ..     317     376 ..     313     418 .. 0.63

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.014
     DUF4349 113 ksvedlleiereLsevqaeieslegqlryLdnqv 146
                 +s++++  ie+e+s+ +++i +l++ + +Ld+++
  EPA06485.1 182 DSLKEIKDIEEEVSKKEQRISELQTHIDSLDKKI 215
                 3445555555555555555555555555555544 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0053
     DUF4349  10 tlevedvdaavaairelveeagGyvesssersgtegdersasltlRvPaarldafldelael 71 
                 ++ v+dvd+++++++e+ e+++G +++ + ++++++++ + +++  + + +l+++ ++l++l
  EPA06485.1 317 SISVKDVDKSFSQLTEIEEALDGLIHQVN-DYADKQEKIQNQIKS-LEPHELQDLTKNLKNL 376
                 689**************************.444444444444432.3334555555555544 PP

>> DUF4351  Domain of unknown function (DUF4351)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1     0.017        10       7      51 ..     114     158 ..      88     167 .. 0.83
   2 ?   -2.0   0.1       6.6     4e+03      28      36 ..     198     206 ..     190     215 .. 0.56
   3 ?    3.9   0.2     0.094        56       7      38 ..     246     279 ..     226     289 .. 0.87
   4 ?    6.2   0.2     0.018        11      25      46 ..     352     373 ..     333     377 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.017
     DUF4351   7 geqsLilrlLtrrfGelspeleeqIksLsleqLEdLgealLDFss 51 
                 + +++il ++ +++G++    +  I     +  E+L e lL ++s
  EPA06485.1 114 ENINVILNQMLKKIGDVLGRQTRVIHIFAKKYAEKLKEILLQMQS 158
                 7899****************6688999999999999999999876 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 6.6
     DUF4351  28 eeqIksLsl 36 
                 e++I++L++
  EPA06485.1 198 EQRISELQT 206
                 455555543 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.094
     DUF4351   7 geqsLilrlLtrrfGelspele..eqIksLsleq 38 
                 + ++ i  ++t  f ++s  l   e+I++++ eq
  EPA06485.1 246 ESKNQIKDQITSQFTKISRPLSryEHISAMEKEQ 279
                 77899**************99999****999998 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.018
     DUF4351  25 peleeqIksLsleqLEdLgeal 46 
                 +++++qIksL+  +L dL ++l
  EPA06485.1 352 EKIQNQIKSLEPHELQDLTKNL 373
                 4567**************9876 PP

>> Cep57_CLD_2  Centrosome localisation domain of PPC89
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1    0.0012      0.72       2      28 ..     198     224 ..     198     227 .. 0.91
   2 ?    1.4   2.6      0.56   3.3e+02       9      57 ..     355     404 ..     350     414 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0012
  Cep57_CLD_2   2 eaevktLqnrLdsltrklqvheeelkr 28 
                  e+ +++Lq++ dsl+ k+ + e+ +k+
   EPA06485.1 198 EQRISELQTHIDSLDKKIISSEDSIKK 224
                  7899***************99999886 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.56
  Cep57_CLD_2   9 qnrLdslt.rklqvheeelkrLnkERdsalrqLgvAyeelneLkaeveal 57 
                  qn+ +sl+ ++lq     lk+L+++ + ++ ++    +e+ne ++    l
   EPA06485.1 355 QNQIKSLEpHELQDLTKNLKNLMTDKEDSELKIKTFQSEINEIHSNSTKL 404
                  7777888745678888999***********************99876665 PP

>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   8.7   0.00043      0.26      20      98 ..     148     226 ..     142     231 .. 0.81
   2 ?    7.5   5.9     0.007       4.2       5     107 ..     307     414 ..     305     422 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00043
       DHR10  20 elqakidalqvvekdlrsciklleeieaelakleeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerlr 98 
                 +l++ +  +q     +++ ++  +e ++   +  ++ k++k+ ++++++ke++ +el+++++ l +++ + e+ + + +
  EPA06485.1 148 KLKEILLQMQSNHSKIQQMLTNFDETQTTSTEILDSLKEIKDIEEEVSKKEQRISELQTHIDSLDKKIISSEDSIKKIK 226
                 5566666677788888888999999999999999999999999999999999999999999999999999988887765 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.007
       DHR10   5 aeekeelaelErkarelqakidalqvvekdlrsciklleeieaelakleeakk.....klkelrdaleekeielrelerkeerlqrqlenaeeklerlr 98 
                 ++ ++++++     +++ ++   l+++e+ l  +i ++++ +++++k + + k     +l++l ++l+++ +++++ e k++  q  ++  +   ++l 
  EPA06485.1 307 ENVRKAISSDSISVKDVDKSFSQLTEIEEALDGLIHQVNDYADKQEKIQNQIKslephELQDLTKNLKNLMTDKEDSELKIKTFQSEINEIHSNSTKLI 405
                 66677777777778899999999999**************99999999986541111167788888888888888888888888888888888888888 PP

       DHR10  99 eqaeekrea 107
                  + e+k ++
  EPA06485.1 406 VDIETKLRK 414
                 888887665 PP

>> Vac_Fusion  Chordopoxvirus multifunctional envelope protein A27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.2     0.031        18      14      46 ..     185     217 ..     177     227 .. 0.86
   2 ?   -2.7   0.0       7.7   4.6e+03      11      24 ..     236     249 ..     231     270 .. 0.56
   3 ?    5.6   0.1      0.02        12       2      36 ..     330     364 ..     329     380 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.031
                 HHHHHHHHHHHHHHHHHHHHH-XXXXXXXXXXX CS
  Vac_Fusion  14 kdfqlvikcckrvnealkRlEnHleTlRkamla 46 
                 k+ ++++++ ++++++++ l  H + l k +++
  EPA06485.1 185 KEIKDIEEEVSKKEQRISELQTHIDSLDKKIIS 217
                 7789999*******************9999885 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 7.7
                 HHHHHHHHHHHHHH CS
  Vac_Fusion  11 vlekdfqlvikcck 24 
                  l+k+   ++++  
  EPA06485.1 236 ELTKILDALTESKN 249
                 44444444333333 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.02
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-X CS
  Vac_Fusion   2 lkdleerllvlekdfqlvikcckrvnealkRlEnH 36 
                 l+++ee l  l +++++ ++++ + ++++k lE H
  EPA06485.1 330 LTEIEEALDGLIHQVNDYADKQEKIQNQIKSLEPH 364
                 6899999999***********************99 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   8.0   0.00037      0.22       2      66 ..     163     230 ..     162     251 .. 0.80
   2 ?    5.8   4.9     0.024        15      13      72 ..     348     401 ..     318     415 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00037
  Tropomyosin_1   2 lnsLkleaeeaqekaeele...ekvKeleqenlekeqeiksLtkknqqleeevekleeklkeakekae 66 
                    ++++ ++ +e q+   e+    +++K+ e+e  +keq i++L++ ++ l++++   e+++k+ k + e
     EPA06485.1 163 IQQMLTNFDETQTTSTEILdslKEIKDIEEEVSKKEQRISELQTHIDSLDKKIISSEDSIKKIKGSEE 230
                    5666666666666655554111568899********************************99987665 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.024
  Tropomyosin_1  13 qekaeeleekvKeleqenlekeqeiksLtkknqqleeevekleeklkeakekaeesekkk 72 
                     +k      + K ++q +  + +e+++Ltk +++l  + e  e k+k+ +++ +e ++++
     EPA06485.1 348 ADK------QEKIQNQIKSLEPHELQDLTKNLKNLMTDKEDSELKIKTFQSEINEIHSNS 401
                    222......222233333333355555555555555555555555555555555555444 PP

>> CLZ  C-terminal leucine zipper domain of cyclic nucleotide-gated channels
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.4      0.58   3.5e+02      45      68 ..     147     170 ..     143     173 .. 0.81
   2 ?    7.3   0.7    0.0098       5.8      25      62 ..     186     223 ..     178     226 .. 0.71
   3 ?    0.7   0.2       1.2   6.9e+02      34      63 ..     235     264 ..     217     271 .. 0.62
   4 ?   11.6   2.9   0.00045      0.27      12      63 ..     338     389 ..     336     397 .. 0.89
   5 ?    7.5   0.6    0.0089       5.3      19      62 ..     373     416 ..     369     422 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.58
         CLZ  45 trlarLlaeyessqrkLkqRitkL 68 
                  +l+ +l +++s ++k++q +t+ 
  EPA06485.1 147 EKLKEILLQMQSNHSKIQQMLTNF 170
                 588899999999999999988875 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0098
         CLZ  25 eqkeleekverLessLeaLqtrlarLlaeyessqrkLk 62 
                 e k++ee v++ e+++  Lqt++  L ++  ss+  +k
  EPA06485.1 186 EIKDIEEEVSKKEQRISELQTHIDSLDKKIISSEDSIK 223
                 55777788888888888888877777777776666665 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 1.2
         CLZ  34 erLessLeaLqtrlarLlaeyessqrkLkq 63 
                  +L + L+aL+   +++ ++ +s  +k+ +
  EPA06485.1 235 LELTKILDALTESKNQIKDQITSQFTKISR 264
                 344555777777777766666666666655 PP

  == domain 4  score: 11.6 bits;  conditional E-value: 0.00045
         CLZ  12 dglLDeeaakagaeqkeleekverLe.ssLeaLqtrlarLlaeyessqrkLkq 63 
                 dgl+ +  ++  ++q+++++++++Le  +L+ L++ l+ L+++ e s+ k+k 
  EPA06485.1 338 DGLIHQV-NDYADKQEKIQNQIKSLEpHELQDLTKNLKNLMTDKEDSELKIKT 389
                 7888887.566689***********9668*********************995 PP

  == domain 5  score: 7.5 bits;  conditional E-value: 0.0089
         CLZ  19 aakagaeqkeleekverLessLeaLqtrlarLlaeyessqrkLk 62 
                  ++  +++++ e k++ ++s+++ ++    +L+ + e+  rk  
  EPA06485.1 373 LKNLMTDKEDSELKIKTFQSEINEIHSNSTKLIVDIETKLRKFS 416
                 6677899****************************999888865 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       4.3   2.6e+03      50      73 ..      58      81 ..      32      85 .. 0.53
   2 ?   13.5   7.3   0.00012     0.069       2      95 ..     122     215 ..     121     216 .. 0.92
   3 ?    2.3   0.2      0.34     2e+02      33      68 ..     228     263 ..     225     277 .. 0.89
   4 ?    5.7   0.8      0.03        18      37      78 ..     321     362 ..     305     364 .. 0.56
   5 ?    5.7   4.5     0.029        18      29      77 ..     356     404 ..     353     422 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 4.3
     BLOC1_2 50 leklnekyeelqpylqqidqiekq 73
                +++l     +l++   q+d+i+k+
  EPA06485.1 58 IKDLTVIGSALEKDNLQVDDIDKH 81
                333333333555555566666665 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00012
     BLOC1_2   2 rmfekvskyleaeleatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLEakf 95 
                 +m++k+ ++l  ++ +     k   +  ++   + ++  ++++++ +++++++ ++ e+   l++i++ie++v++ e+ +seL + + +L +k+
  EPA06485.1 122 QMLKKIGDVLGRQTRVIHIFAKKYAEKLKEILLQMQSNHSKIQQMLTNFDETQTTSTEILDSLKEIKDIEEEVSKKEQRISELQTHIDSLDKKI 215
                 68888888888888888888888888889999999999****************************************************9986 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.34
     BLOC1_2  33 sekykklkdvaaslekkleklnekyeelqpylqqid 68 
                 se+y kl + ++ l +  e  n+ ++++ +++++i 
  EPA06485.1 228 SEEYVKLLELTKILDALTESKNQIKDQITSQFTKIS 263
                 688999999999999999999999999999999986 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.03
     BLOC1_2  37 kklkdvaaslekkleklnekyeelqpylqqidqiekqvteLe 78 
                 k+++++ ++l++  e+l+ + ++++ y ++ ++i++q+++Le
  EPA06485.1 321 KDVDKSFSQLTEIEEALDGLIHQVNDYADKQEKIQNQIKSLE 362
                 444445555555555555555555555555555555555555 PP

  == domain 5  score: 5.7 bits;  conditional E-value: 0.029
     BLOC1_2  29 NeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteL 77 
                 N+  s + ++l+d +++l++ + + +  + +++ + ++i++i+ + t+L
  EPA06485.1 356 NQIKSLEPHELQDLTKNLKNLMTDKEDSELKIKTFQSEINEIHSNSTKL 404
                 788888899**********************************999998 PP

>> Phage_GPO  Phage capsid scaffolding protein (GPO) serine peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   5.7    0.0009      0.53     180     254 ..     136     214 ..     106     233 .. 0.54
   2 ?    5.9   2.3     0.014       8.5     146     246 ..     274     378 ..     265     404 .. 0.55

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0009
   Phage_GPO 180 rikallskkkksd....darfadveeavelvAeevkelsekveallaleaelaalkkeveklkaeleaLkekLsktdak 254
                 r+ ++++kk +++      ++++ ++ ++++ +++ e++++ ++ l++ +e++++++ev+k+++++++L++++++ d+k
  EPA06485.1 136 RVIHIFAKKYAEKlkeiLLQMQSNHSKIQQMLTNFDETQTTSTEILDSLKEIKDIEEEVSKKEQRISELQTHIDSLDKK 214
                 4555555555544322223344444455555555555555555555555555555555555555555555555554442 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.014
   Phage_GPO 146 krkqspenlftaavetalefeeeeeeeegeslferikallskkkksd...darfa...dveeavelvAeevkelsekveallaleaelaalk.kevekl 237
                 + +++++nl++  +e  +e+   +++++   ++e++++ +s+++ s    d+ f+   ++eea++ + ++v+++++k+e   + ++++++l+ +e+++l
  EPA06485.1 274 AMEKEQKNLLSGLIEDPFEVLMPKNKDSIILILENVRKAISSDSISVkdvDKSFSqltEIEEALDGLIHQVNDYADKQE---KIQNQIKSLEpHELQDL 369
                 5667778888888888888777777777777778887777776654433455555111444444444444444444444...44444444441233334 PP

   Phage_GPO 238 kaeleaLke 246
                 +++l++L +
  EPA06485.1 370 TKNLKNLMT 378
                 444433332 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   8.7     0.018        10      17      91 ..     145     218 ..     135     236 .. 0.55
   2 ?    5.8   0.7     0.012       7.5      55     107 ..     236     288 ..     228     292 .. 0.91
   3 ?    7.6   3.0    0.0034         2      30      93 ..     335     399 ..     302     418 .. 0.57

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.018
     DUF3450  17 tldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieei 91 
                  ++++++   + +++ +++q+  ++  de+q+ + e+ +  +e++++e + ++ e+ ++++++ i+sl+++i + 
  EPA06485.1 145 YAEKLKEILLQMQSNHSKIQQMLTNF-DETQTTSTEILDSLKEIKDIEEEVSKKEQRISELQTHIDSLDKKIISS 218
                 45555555566666666666665554.345555555555555566666666666666666666666655555333 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.012
     DUF3450  55 alkeeleslevyneqlerlvasqeqeiasleeqieeieeierelvpllekmid 107
                 +l++ l++l+  ++q +++++sq ++i++   + e i+++e+e + ll  +i+
  EPA06485.1 236 ELTKILDALTESKNQIKDQITSQFTKISRPLSRYEHISAMEKEQKNLLSGLIE 288
                 6788899************************************9999987776 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0034
     DUF3450  30 aaaaqsqkkidklddekqellaeyralk.eeleslevyneqlerlvasqeqeiasleeqieeiee 93 
                 +a      ++++++d+++++++++++l+  el++l++  ++l    ++ e +i+  + +i+ei  
  EPA06485.1 335 EALDGLIHQVNDYADKQEKIQNQIKSLEpHELQDLTKNLKNLMTDKEDSELKIKTFQSEINEIHS 399
                 22233334556666666666666666653455555555555555555555555555555555543 PP

>> Rx_N  Rx N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1      0.38   2.3e+02       2      43 ..      28      70 ..      28      95 .. 0.88
   2 ?   13.6   1.2    0.0001      0.06       2      64 ..     120     190 ..     119     209 .. 0.94
   3 ?    1.7   2.9      0.53   3.1e+02      16      70 ..     316     382 ..     304     403 .. 0.61

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.38
        Rx_N  2 vsallqkLadllaeea.kllkgvkeeleklkdeLesiqavLed 43
                vs +++k+ +l ++++ + +k+v++  + l + L  i + Le+
  EPA06485.1 28 VSGIVRKILELRTSQIlSDIKSVRDTTQPLIKDLTVIGSALEK 70
                67789999999999999*******************9999985 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 0.0001
        Rx_N   2 vsallqkLadllaeea........kllkgvkeeleklkdeLesiqavLedaeerqikdeavkeWlkelrdl 64 
                 ++ +l+k++d+l  +         k  +++ke l +++++ ++iq++L   +e q+++ ++   lke++d+
  EPA06485.1 120 LNQMLKKIGDVLGRQTrvihifakKYAEKLKEILLQMQSNHSKIQQMLTNFDETQTTSTEILDSLKEIKDI 190
                 67789*****************9999*******************************************96 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.53
        Rx_N  16 eakllkgvkeeleklkdeLesiqavLedaee.........rqikd......eavkeWlkelrdlaydaeD 70 
                    ++k+v++ + +l +  e+++++++++ +                    ++++   k+l++l+ d eD
  EPA06485.1 316 DSISVKDVDKSFSQLTEIEEALDGLIHQVNDyadkqekiqN---QikslepHELQDLTKNLKNLMTDKED 382
                 55555666665555555555555555544443332333332...03335557788888999999988888 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1  11.9   0.00019      0.11     305     418 ..     116     226 ..     111     233 .. 0.83
   2 ?    1.1   3.5       0.2   1.2e+02     336     407 ..     212     286 ..     209     303 .. 0.65
   3 ?    7.0   7.5    0.0033         2     328     419 ..     315     406 ..     305     413 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00019
        FapA 305 ikalkevkakklGselgtkteievgldepelkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelke 403
                 i++  +  +kk+G  lg +t++   +     k+  ++l+e l +++++  k++++++ +++++ ++    + ++++k ++e+  k +++++el++++++
  EPA06485.1 116 INVILNQMLKKIGDVLGRQTRVIHIFA----KKYAEKLKEILLQMQSNHSKIQQMLTNFDETQTTSTEILDSLKEIKDIEEEVSKKEQRISELQTHIDS 210
                 556666677899*********999777....444567999999999999999999999999888999999999************************** PP

        FapA 404 lkeeleskkeea.kik 418
                 l++++ s+++++ kik
  EPA06485.1 211 LDKKIISSEDSIkKIK 226
                 *****99955554444 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.2
        FapA 336 keklkeleeeleel.....eeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkee 407
                 ++k+   e+ ++++       +l +l+k ++ l +   ++q++ ++ +q+ k+ + + +++ + +  +e+++ l+  
  EPA06485.1 212 DKKIISSEDSIKKIkgseeYVKLLELTKILDALTE--SKNQIKDQITSQFTKISRPLSRYEHISAMEKEQKNLLSGL 286
                 45554555555555443222233333333555555..3678999999999999999999988888888888777655 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0033
        FapA 328 v.gldepelkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeeleskkeea.kikv 419
                   +++ +++++++++l e  e+l   ++++++  +k +k  +++q++s    +l+ l++++++l+++ e+ e ++k+ ++e+++ ++++ k++v
  EPA06485.1 315 SdSISVKDVDKSFSQLTEIEEALDGLIHQVNDYADKQEK--IQNQIKSLEPHELQDLTKNLKNLMTDKEDSELKIKTFQSEINEIHSNStKLIV 406
                 556677788888888888888888888888888777776..67788999999******************************999777667665 PP

>> Alpha-E  A predicted alpha-helical domain with a conserved ER motif.
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   1.8     0.013       7.8     226     292 ..     179     259 ..     173     260 .. 0.75
   2 ?    5.4   0.3     0.022        13     222     280 ..     328     393 ..     326     420 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.013
     Alpha-E 226 eleealaalspaeseegrsseaerllgellaelrladieell.e................glhelldelqeelaelsdaiserY 292
                 e+ ++l++++     e++ s+ e+++ el+++++  d + +  e                +l ++ld+l+e+ ++++d+i+ ++
  EPA06485.1 179 EILDSLKEIKD---IEEEVSKKEQRISELQTHIDSLDKKIISsEdsikkikgseeyvkllELTKILDALTESKNQIKDQITSQF 259
                 55666777744...4456778888999999999955554333424555666778999999*********************998 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.022
     Alpha-E 222 fqleeleealaalspaeseegrsseaerllgellaelrladieelleglhel..........ldelqee 280
                  ql e+eeal+ l  ++   ++ ++ ++++++  ++l+ +++++l+++l++l          ++++q+e
  EPA06485.1 328 SQLTEIEEALDGL-IHQ--VNDYADKQEKIQNQIKSLEPHELQDLTKNLKNLmtdkedselkIKTFQSE 393
                 5899999999999.534..34667778889999999999999999988888833333333334444444 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   5.8   0.00058      0.35     101     222 ..     138     282 ..     131     289 .. 0.57
   2 ?    1.4   0.7      0.28   1.7e+02     192     229 ..     351     386 ..     310     418 .. 0.51

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00058
     DUF4407 101 LkiFekeIdaelaeeqqeeakelkeqlaaa.........ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk...gtgttgvaGkgpaake 187
                 + iF k  +++l+e+  ++++ + +++++           ++e+ +  ++i+++++e++++e+r+++l+++ +  ld +     + +++++G +++ k 
  EPA06485.1 138 IHIFAKKYAEKLKEILLQMQSNH-SKIQQMltnfdetqtTSTEILDSLKEIKDIEEEVSKKEQRISELQTHID-SLDKKIissEDSIKKIKGSEEYVKL 234
                 66777777777777766666555.4444445667777776666666677777777777777777777777777.4454446555556667777666666 PP

     DUF4407 188 .............kkaqldaaqaelaelkakldatarlaalraelael 222
                              k++  d+++ + +++++ l++ + ++a ++e++ l
  EPA06485.1 235 leltkildaltesKNQIKDQITSQFTKISRPLSRYEHISAMEKEQKNL 282
                 444444444444444444444444444444444555555555554444 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.28
     DUF4407 192 ldaaqaelaelkakldatarlaalraelaeleaerake 229
                  +++q+++++l+    + ++l+++ ++l + +++ + +
  EPA06485.1 351 QEKIQNQIKSLEPH--ELQDLTKNLKNLMTDKEDSELK 386
                 22222222222222..2222222222222222222222 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   4.3       2.5   1.5e+03       8      52 ..      42      83 ..      40     137 .. 0.57
   2 ?    4.3   2.3     0.097        58      24      64 ..     150     190 ..     143     194 .. 0.87
   3 ?    5.3   2.9     0.047        28      13      58 ..     201     255 ..     192     267 .. 0.51
   4 ?   12.7   1.9   0.00022      0.13      20      65 ..     313     358 ..     301     367 .. 0.82
   5 ?    2.9   1.3      0.25   1.5e+02      17      63 ..     355     399 ..     352     408 .. 0.70
   6 ?    4.1   0.2      0.11        63      17      53 ..     384     421 ..     372     423 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 2.5
     NPV_P10  8 vIradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLa 52
                +I++dik v d  + l + ++ + + l++ +  n ++d++ + L 
  EPA06485.1 42 QILSDIKSVRDTTQPLIKDLTVIGSALEK-D--NLQVDDIDKHLR 83
                56666666666665555555444444433.2..233333333333 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.097
     NPV_P10  24 qqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdi 64 
                 ++ + ++q+n+ +++++ +++d+ +++ +e+ +++++I+di
  EPA06485.1 150 KEILLQMQSNHSKIQQMLTNFDETQTTSTEILDSLKEIKDI 190
                 5556789999************9999999999999999998 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.047
     NPV_P10  13 ikavddkVdalqqqv.......ddvqenlpdvt..elnekLdaqsaqLaeletkv 58 
                 i+++++ +d+l++++       ++++   + v+  el++ Lda++++ +++++++
  EPA06485.1 201 ISELQTHIDSLDKKIissedsiKKIKGSEEYVKllELTKILDALTESKNQIKDQI 255
                 4555555555555552221111554433333322245555555555555555544 PP

  == domain 4  score: 12.7 bits;  conditional E-value: 0.00022
     NPV_P10  20 VdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiL 65 
                 +++ + +v+dv++ + ++te++e Ld++  q+++  +k e+Iq+  
  EPA06485.1 313 ISSDSISVKDVDKSFSQLTEIEEALDGLIHQVNDYADKQEKIQNQI 358
                 44445589**********************************9855 PP

  == domain 5  score: 2.9 bits;  conditional E-value: 0.25
     NPV_P10  17 ddkVdalq.qqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqd 63 
                 ++++++l+ ++++d+++nl++   l +  ++   +++++++++++I++
  EPA06485.1 355 QNQIKSLEpHELQDLTKNLKN---LMTDKEDSELKIKTFQSEINEIHS 399
                 556666653467888888888...444446667788888888888876 PP

  == domain 6  score: 4.1 bits;  conditional E-value: 0.11
     NPV_P10  17 ddkVdalqqqvddvqenlpd.vtelnekLdaqsaqLae 53 
                 + k++  q++++++++n+ + + ++++kL + s+++ +
  EPA06485.1 384 ELKIKTFQSEINEIHSNSTKlIVDIETKLRKFSNTIYS 421
                 569999*********99876367899999998888765 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2  12.1     0.069        41      17      99 ..     142     227 ..     133     258 .. 0.77
   2 ?    6.9   6.1      0.01         6       1     101 [.     185     283 ..     185     289 .. 0.79
   3 ?    2.8   5.5      0.19   1.1e+02       2      74 ..     329     402 ..     328     404 .. 0.79
   4 ?    6.9   0.4      0.01       6.3       2      56 ..     365     419 ..     364     423 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.069
  TPR_MLP1_2  17 keeaeaklqklqedlekqaeiakeaqqkYerelvkhae...dvkelqalreelnelkaeiaelkaeaesakaeleeseesweeqke 99 
                 ++++++kl+++  ++++ ++  +++  ++ +  +   e    +ke++++ ee+++ +++i+el++  +s+ +++  se s+++ k 
  EPA06485.1 142 AKKYAEKLKEILLQMQSNHSKIQQMLTNFDETQTTSTEildSLKEIKDIEEEVSKKEQRISELQTHIDSLDKKIISSEDSIKKIKG 227
                 57888888899999999999999999998877766665222456667777999999999999999999999999999999987664 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.01
  TPR_MLP1_2   1 kelksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesakaeleeseesweeqke 99 
                 ke+k  eee+++++++++e+++++ +l +++ + +++ k+ +   ++e vk  e +k l al e  n++k++i++  ++  +  +  e   +  +eqk+
  EPA06485.1 185 KEIKDIEEEVSKKEQRISELQTHIDSLDKKIISSEDSIKKIKG--SEEYVKLLELTKILDALTESKNQIKDQITSQFTKISRPLSRYEHISAMEKEQKN 281
                 5788889999999999999999999999999999999999988..899999999999999999999999999888777777766666666666666666 PP

  TPR_MLP1_2 100 el 101
                  l
  EPA06485.1 282 LL 283
                 65 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.19
  TPR_MLP1_2   2 elksleeeikslkeekeeaeaklqklqedlekqa.eiakeaqqkYerelvkhaedvkelqalreelnelkaeia 74 
                 +l++ ee ++ l  + +++++k++k+q+++++ +  ++++  ++ ++ ++ +++   +++++ +e+ne+ +  +
  EPA06485.1 329 QLTEIEEALDGLIHQVNDYADKQEKIQNQIKSLEpHELQDLTKNLKNLMTDKEDSELKIKTFQSEINEIHSNST 402
                 67888999999999999999999999999998763688888888888888888888888888888888776655 PP

  == domain 4  score: 6.9 bits;  conditional E-value: 0.01
  TPR_MLP1_2   2 elksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedv 56 
                 el+ l++++k+l ++ke++e k+++ q+++++ ++  ++   + e+ l k ++++
  EPA06485.1 365 ELQDLTKNLKNLMTDKEDSELKIKTFQSEINEIHSNSTKLIVDIETKLRKFSNTI 419
                 78999***************************99999998888888887776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (424 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3217  (0.17943); expected 358.6 (0.02)
Passed bias filter:                      724  (0.0403815); expected 358.6 (0.02)
Passed Vit filter:                       129  (0.00719505); expected 17.9 (0.001)
Passed Fwd filter:                        74  (0.00412739); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 1.11u 0.34s 00:00:01.45 Elapsed: 00:00:00.52
# Mc/sec: 2449.58
//
Query:       EPA06486.1  [L=66]
Description: transcriptional regulator, AsnC family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-09   37.7   0.1    1.8e-09   37.4   0.1    1.0  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
  ------ inclusion threshold ------
      0.022   14.4   1.0      0.023   14.3   1.0    1.0  1  DUF4795         Domain of unknown function (DUF4795)
      0.032   14.4   0.2        2.8    8.2   0.0    2.0  2  Flu_M1_C        Influenza Matrix protein (M1) C-terminal doma
      0.059   13.6   0.3      0.078   13.2   0.2    1.3  1  NEXCaM_BD       Regulatory region of Na+/H+ exchanger NHE bin
      0.061   13.6   0.3      0.066   13.5   0.3    1.0  1  GLTP            Glycolipid transfer protein (GLTP)


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.1     5e-13   1.8e-09      14      71 ..       5      62 ..       2      63 .. 0.96

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 5e-13
                    HHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEE CS
  AsnC_trans_reg 14 eefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsi 71
                    e++ e+l+++++Vv ++ + G +d+++k  +++ e +++++++ +++++ ++ ++t+i
      EPA06486.1  5 ENIMEQLRQIEQVVDVFGTIGTHDMMVKLEAENFEKIRELVSRNIQKIEKIRTISTLI 62
                    77899***************************************************97 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   1.0   6.4e-06     0.023     114     147 ..       7      54 ..       2      66 .] 0.72

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.4e-06
     DUF4795 114 aldtLq..............eelkekldrlelepLkeqleerlkelqk 147
                 ++++L+               ++  kl++ ++e+++e + +++++++k
  EPA06486.1   7 IMEQLRqieqvvdvfgtigtHDMMVKLEAENFEKIRELVSRNIQKIEK 54 
                 34444444455555556666********************99999984 PP

>> Flu_M1_C  Influenza Matrix protein (M1) C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0   0.00077       2.8      43      66 ..       5      28 ..       1      32 [. 0.87
   2 ?    5.1   0.0    0.0071        25      39      66 ..      35      62 ..      28      66 .] 0.81

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00077
                XXXXXXXXXXXXXXXXXXXXXXXX CS
    Flu_M1_C 43 eevqklaeelrqnvqvlrslGasq 66
                e++++   +++q v+v+ ++G+++
  EPA06486.1  5 ENIMEQLRQIEQVVDVFGTIGTHD 28
                678999999*************97 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0071
                XXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
    Flu_M1_C 39 sekaeevqklaeelrqnvqvlrslGasq 66
                +e+ e++++l ++  q+++ +r++ +  
  EPA06486.1 35 AENFEKIRELVSRNIQKIEKIRTISTLI 62
                67788999999999999******99865 PP

>> NEXCaM_BD  Regulatory region of Na+/H+ exchanger NHE binds to calmodulin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   2.2e-05     0.078      18      47 ..      28      58 ..      15      60 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.2e-05
   NEXCaM_BD 18 rllPklskeeveeirdiLskNlykiRq.Rtl 47
                 ++ kl +e+ e+ir++ s+N++ki + Rt 
  EPA06486.1 28 DMMVKLEAENFEKIRELVSRNIQKIEKiRTI 58
                5566899*****************9653665 PP

>> GLTP  Glycolipid transfer protein (GLTP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.3   1.8e-05     0.066       7      59 ..      11      65 ..       6      66 .] 0.70

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.8e-05
                HHHHHHHHHHHHHT-GGGGGHHHHTHHHHHHHHHHTT.......T-SBHHHHHHHH CS
        GLTP  7 leacrelvklfdllGsafsfvksDvegniekleeaykkn.pe..eystleslveaE 59
                l  ++++v +f ++G+   +vk + e n ek++e + +n ++  +++t+ +l++++
  EPA06486.1 11 LRQIEQVVDVFGTIGTHDMMVKLEAE-NFEKIRELVSRNiQKieKIRTISTLIKKD 65
                667899**********6666666654.66666666666633244888999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       966  (0.0538792); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.36u 0.28s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 461.69
//
Query:       EPA06487.1  [L=471]
Description: hypothetical protein BG20_I1425 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (471 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 2875.50
//
Query:       EPA06488.1  [L=50]
Description: hypothetical protein BG20_I1433 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.46
# Mc/sec: 326.94
//
Query:       EPA06489.1  [L=53]
Description: hypothetical protein BG20_I1423 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1002  (0.0558871); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.29s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 367.76
//
Query:       EPA06490.1  [L=58]
Description: hypothetical protein BG20_I1420 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       747  (0.0416643); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 425.91
//
Query:       EPA06491.1  [L=129]
Description: hypothetical protein BG20_I1439, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.031   13.9   0.1      0.048   13.3   0.1    1.3  1  Guanylate_cyc  Adenylate and Guanylate cyclase catalytic doma


Domain annotation for each model (and alignments):
>> Guanylate_cyc  Adenylate and Guanylate cyclase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   2.7e-06     0.048       7      58 ..      78     129 .]      73     129 .] 0.91

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.7e-06
  Guanylate_cyc   7 devtilFadIvgftalssahspievvklLnelyarfdelldekkvykvktiG 58 
                     ++++lF d+vg+t +  +   +++ ++  +  +++  +++++++   k++G
     EPA06491.1  78 MNMAVLFVDLVGSTPMILNLPKEKLATVFTTFAQEMAYVIKRHQGFILKFMG 129
                    689*****************88889999999999**********99999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 856.41
//
Query:       EPA06492.1  [L=106]
Description: hypothetical protein BG20_I1430 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1593  (0.0888505); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 772.55
//
Query:       EPA06493.1  [L=137]
Description: hypothetical protein BG20_I1414 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-12   46.3   0.0    4.6e-12   45.8   0.0    1.3  1  Prok-JAB  Prokaryotic homologs of the JAB domain


Domain annotation for each model (and alignments):
>> Prok-JAB  Prokaryotic homologs of the JAB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   0.0   2.6e-16   4.6e-12       2     103 ..      21     112 ..      20     128 .. 0.77

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 2.6e-16
    Prok-JAB   2 esvlsalvaharrahpeEtcGlllgkeseseevivvplvnewsnrfeipdpedslarlkf....earerglevvgiwHSHpggsarPSetDrrdaaala 96 
                 ++vl+ ++   +  hpeE++ +l gk+  ++  i+v+ +        i +p d   +       +    ++++vgi+HSHp+g+a+PS tD++++++l+
  EPA06493.1  21 KKVLDSILSYCQIKHPEECVLILKGKS--KHGNILVDGLV-------I-PPFDYVGHTFAgfpsSFLPFDMSYVGIVHSHPTGPAEPSLTDLQNFFGLV 109
                 57889999999999************9..77778888776.......4.55555554433556699******************************964 PP

    Prok-JAB  97 rvkalli 103
                     +  
  EPA06493.1 110 ----SVT 112
                 ....333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.32s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 856.20
//
Query:       EPA06494.1  [L=142]
Description: hypothetical protein BG20_I1437 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.4e-21   74.9   0.3    7.2e-21   74.7   0.3    1.0  1  AHSA1            Activator of Hsp90 ATPase homolog 1-like pro
  ------ inclusion threshold ------
      0.033   14.4   0.1      0.042   14.1   0.1    1.5  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra
       0.04   14.5   0.1      0.061   14.0   0.1    1.4  1  DUF960           Staphylococcal protein of unknown function (
      0.042   14.4   0.3      0.068   13.7   0.3    1.3  1  S_locus_glycop   S-locus glycoprotein domain


Domain annotation for each model (and alignments):
>> AHSA1  Activator of Hsp90 ATPase homolog 1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.7   0.3   1.6e-24   7.2e-21       2     125 .]      15     141 ..      14     141 .. 0.95

  Alignments for each domain:
  == domain 1  score: 74.7 bits;  conditional E-value: 1.6e-24
                 S-HHHHHHHHH-HHHHHHHEEEEEEEE--STTEEEEEEETTTSEEEEEEEEEEEEETTTEEEEE.EEEETSET...EEEEEEEEEEEEETTEEEEEEEE CS
       AHSA1   2 apperVfraltdpellkrWftlteaemdlrpGgkfrlrdspdgkefgnegeylevvpperlvyt.wrledepe...eeestvtieleeegggTrltlth 96 
                 a +++V++a+t+p+ +k+++ +t++ + +++G+++ ++ +++gk+f  +g++++++ ++ + yt w+ ++ +e   e++s vt+el   ++ T+lt+++
  EPA06494.1  15 ANASKVWDAITNPKVIKKYLFGTKVISTWEVGSEIIFEGNWEGKKFRDKGIIEKIEIQKLFQYTyWSIFSGMEdkkENYSLVTFELSGDDKTTKLTVSQ 113
                 6789***************9*****************999*****************************666666799********************* PP

                 EEEEHCHHHHHHHHHHHHHHHHHHHHHHH CS
       AHSA1  97 tglprkqkeeegveeGweqsldqLkalle 125
                 +g+++k+ +e+   +Gw+++l+++k lle
  EPA06494.1 114 KGFADKALQEH-SDKGWRTVLQKIKVLLE 141
                 **********9.*************9986 PP

>> Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   9.5e-06     0.042       3      44 ..       6      47 ..       4     141 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 9.5e-06
                     EEEEEEEESS-HHHHHHHHTTTTGGGGT-TTEEEE.ECSESTS CS
  Polyketide_cyc2  3 kvtvsvviaappekVwalvsdfenwprWhpevarv.elegggg 44
                     +v+++v i a + kVw+++++++ + ++  + +   ++e  g+
       EPA06494.1  6 TVRKTVKISANASKVWDAITNPKVIKKYLFGTKVIsTWEV-GS 47
                     899******************9999998665554434554.33 PP

>> DUF960  Staphylococcal protein of unknown function (DUF960)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   1.4e-05     0.061       5      57 ..      62     115 ..      58     139 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.4e-05
                 EHHHHTTS-..HHHHHHHHHHHHHHTTTTS---SEEEEEEEEETTEEEEEEEETT CS
      DUF960   5 tkgvveelp..lelqlllWeiidellkgvvpldylqiFeLkenkgkltiehsqee 57 
                  kg+ e++   + +q + W+i   + +++++  +l +FeL+ ++++++++ sq+ 
  EPA06494.1  62 DKGIIEKIEiqKLFQYTYWSIFSGM-EDKKENYSLVTFELSGDDKTTKLTVSQKG 115
                 567777655115699**********.66699999************999999875 PP

>> S_locus_glycop  S-locus glycoprotein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.3   1.5e-05     0.068       4      76 ..      53     135 ..      51     139 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.5e-05
  S_locus_glycop   4 GpwaktrF..tgip.emkelelvkssft.......denegevslsysverssklsrlvltseGslkrftWeenekeWklllsa 76 
                     G w++++F  +gi  +++  +l+++++        d++e+ + ++++++ ++k+++l+++++G + +   e+++k W+++l++
      EPA06494.1  53 GNWEGKKFrdKGIIeKIEIQKLFQYTYWsifsgmeDKKENYSLVTFELSGDDKTTKLTVSQKGFADKALQEHSDKGWRTVLQK 135
                     88999988444665233333445555444456886777777889*********************999999*******99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1041.64
//
Query:       EPA06495.1  [L=109]
Description: hypothetical protein BG20_I1417 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0019   18.5   1.2     0.0026   18.0   1.2    1.1  1  DUF4064   Protein of unknown function (DUF4064)
  ------ inclusion threshold ------
      0.077   11.7   0.1      0.095   11.4   0.1    1.0  1  DUF2207   Predicted membrane protein (DUF2207)
       0.27   11.3   5.9        2.1    8.4   0.5    2.2  2  DUF3185   Protein of unknown function (DUF3185)


Domain annotation for each model (and alignments):
>> DUF4064  Protein of unknown function (DUF4064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   1.2   4.4e-07    0.0026      10      81 ..       8      82 ..       3      87 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4.4e-07
     DUF4064 10 lIGgilgillglllllflfllssgefsqelteeqalsgedasavleflstlli...vlgvialiaivlgivgall 81
                +IG++l + ++l+l++f  + ++ + + e   e  +  ed + v+   stl+i   +++++++++i++giv++++
  EPA06495.1  8 IIGVALVFAGFLILGVFGHQYQIASIQSEEFRECYQYYEDRDPVAVNCSTLMIeqiLFFTFVIVLIAVGIVSLIK 82
                788888888888888887777666655555555777778888888888888875435566688888888888876 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   1.6e-05     0.095     390     439 ..       6      90 ..       2      95 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.6e-05
     DUF2207 390 liilglilillallllvll...................................lvfllilllillliaiivlllfsrllgrrte 439
                 +ii+g++l+++++l l+++                                   +  +l+++++++lia++++ l+++  g++  
  EPA06495.1   6 YIIIGVALVFAGFLILGVFghqyqiasiqseefrecyqyyedrdpvavncstlmIEQILFFTFVIVLIAVGIVSLIKGARGKWDN 90 
                 3333333333333333333445566699**************************8888888888888888888888888888855 PP

>> DUF3185  Protein of unknown function (DUF3185)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.5   0.00036       2.1       2      20 ..       8      27 ..       7      40 .. 0.79
   2 ?    5.7   0.7    0.0025        15       5      18 ..      70      83 ..      67      87 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00036
     DUF3185  2 iiGiiLlvaG.ivLlvfGyn 20
                iiG++L++aG ++L+vfG +
  EPA06495.1  8 IIGVALVFAGfLILGVFGHQ 27
                8*********4478899976 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0025
     DUF3185  5 iiLlvaGivLlvfG 18
                i+L+++Giv l+ G
  EPA06495.1 70 IVLIAVGIVSLIKG 83
                99*******99888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       837  (0.0466841); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 724.47
//
Query:       EPA06496.1  [L=128]
Description: hypothetical protein BG20_I1438 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.58   10.6   6.3        5.9    7.3   0.7    2.2  2  DUF2628        Protein of unknown function (DUF2628)
       0.63    9.8   4.6        8.4    6.2   0.7    2.4  2  Sensor_TM1     Sensor N-terminal transmembrane domain
       0.95   10.0   7.8       0.19   12.3   1.0    2.5  3  Phage_holin_1  Bacteriophage holin


Domain annotation for each model (and alignments):
>> DUF2628  Protein of unknown function (DUF2628)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.6     0.002        12      42      87 ..       7      66 ..       2      74 .. 0.76
   2 ?    7.3   0.7   0.00098       5.9      37      68 ..      79     112 ..      77     124 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.002
     DUF2628 42 wlkalvllviavavsvvlavl..............gfsdavrlllalliaillgleansl 87
                ++k l+++  ++ ++ +  ++              ++ d++ +++ ++++ ++gl a +l
  EPA06496.1  7 FKKILSFVNFSLIIVFIFGLIniehsslgipepliEITDQTMIFFDIIFWTIVGLLALEL 66
                566666666666666666666888888888888889999999************998774 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00098
     DUF2628  37 lyrklwlkalvllv..iavavsvvlavlgfsdav 68 
                 +++k+wl+ ++l++  i v +++  + l++ +++
  EPA06496.1  79 FVKKYWLEIIMLVLmpIFVGFKILKISLKIIKQI 112
                 89********999955555555555555555555 PP

>> Sensor_TM1  Sensor N-terminal transmembrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.7    0.0014       8.4       8      28 ..       2      22 ..       1      34 [. 0.74
   2 ?    5.1   0.2    0.0031        19      16      35 ..      53      72 ..      51      81 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0014
  Sensor_TM1  8 nfSsLtrkIillnLlaLvvLv 28
                 fS+L +kI+++  ++L++ +
  EPA06496.1  2 IFSPLFKKILSFVNFSLIIVF 22
                69********99666666543 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0031
  Sensor_TM1 16 IillnLlaLvvLvaGiLYln 35
                Ii++ +++L++L   i Yl 
  EPA06496.1 53 IIFWTIVGLLALELVIAYLK 72
                9***************9994 PP

>> Phage_holin_1  Bacteriophage holin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.9      0.11   6.8e+02      19      37 ..      18      33 ..       6      68 .. 0.49
   2 ?    0.2   0.1      0.19   1.1e+03      11      33 ..      54      76 ..      45      81 .. 0.77
   3 ?   12.3   1.0   3.3e-05      0.19       9      46 ..      80     113 ..      70     125 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.11
  Phage_holin_1 19 avlllilavlglfgldltv 37
                   +++++i+   gl++++ ++
     EPA06496.1 18 LIIVFIF---GLINIEHSS 33
                   3333333...333333333 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.19
  Phage_holin_1 11 afwvalisavlllilavlglfgl 33
                    fw+ + ++ l l+ a+l++  +
     EPA06496.1 54 IFWTIVGLLALELVIAYLKIRDT 76
                   68888888888888888887665 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 3.3e-05
  Phage_holin_1   9 nkafwvalisavlllilavlglfgldltvaklaeqllq 46 
                     k++w+++i +vl++i++ +++ ++ l++     + ++
     EPA06496.1  80 VKKYWLEIIMLVLMPIFVGFKILKISLKII----KQIK 113
                    589*******************99999887....3333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       911  (0.0508115); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 913.63
//
Query:       EPA06497.1  [L=68]
Description: hypothetical protein BG20_I1435 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 483.40
//
Query:       EPA06498.1  [L=45]
Description: hypothetical protein BG20_I1431 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       803  (0.0447878); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.23s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 357.24
//
Query:       EPA06499.1  [L=57]
Description: hypothetical protein BG20_I1413, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       202  (0.0112667); expected 358.6 (0.02)
Passed bias filter:                      176  (0.0098165); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.28s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 397.00
//
Query:       EPA06500.1  [L=52]
Description: hypothetical protein BG20_I1424 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       230  (0.0128284); expected 358.6 (0.02)
Passed bias filter:                      192  (0.0107089); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.43
# Mc/sec: 364.56
//
Query:       EPA06501.1  [L=41]
Description: hypothetical protein BG20_I1436 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.33s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 249.16
//
Query:       EPA06502.1  [L=43]
Description: hypothetical protein BG20_I1434 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (43 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1160  (0.0646996); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.29s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 309.52
//
Query:       EPA06503.1  [L=47]
Description: hypothetical protein BG20_I1429 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.28u 0.21s 00:00:00.49 Elapsed: 00:00:00.33
# Mc/sec: 424.44
//
Query:       EPA06504.1  [L=378]
Description: malic enzyme, NAD binding domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.8e-26   90.8   7.2    3.1e-23   82.5   0.4    3.6  2  malic            Malic enzyme, N-terminal domain
    1.7e-25   89.8   5.2    1.1e-24   87.1   5.2    2.2  1  Malic_M          Malic enzyme, NAD binding domain
    0.00012   22.2   2.3     0.0015   18.6   1.3    2.9  2  AdoHcyase_NAD    S-adenosyl-L-homocysteine hydrolase, NAD bin
    0.00093   19.3   0.1     0.0021   18.1   0.1    1.6  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
      0.003   16.9   0.8     0.0058   16.0   0.8    1.4  1  ThiF             ThiF family
     0.0064   15.8   0.0     0.0094   15.2   0.0    1.2  1  FAD_binding_3    FAD binding domain
  ------ inclusion threshold ------
      0.021   14.6   0.8      0.049   13.3   0.3    1.8  2  ELFV_dehydrog    Glutamate/Leucine/Phenylalanine/Valine dehyd
       0.19   11.0   2.8        2.8    7.2   0.2    3.6  4  THF_DHG_CYH_C    Tetrahydrofolate dehydrogenase/cyclohydrolas
        2.9    8.2   9.6        7.2    7.0   0.1    4.2  5  Phage_int_SAM_3  Phage integrase, N-terminal SAM-like domain


Domain annotation for each model (and alignments):
>> malic  Malic enzyme, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.5   0.4   1.5e-26   3.1e-23      13     178 ..      23     142 ..      13     146 .. 0.92
   2 ?    3.8   1.0     0.022        44      62     100 ..     178     220 ..     169     223 .. 0.79

  Alignments for each domain:
  == domain 1  score: 82.5 bits;  conditional E-value: 1.5e-26
                 CCCHHHHHHHHSTTCHHHHHHHHHHHGGCHHSCCCEGGGETCHHHHHTTSS.SS..EEEEE-SSSBTTTBS-G.HHHHHHHHHHHHHHHHHHS-EGGGE CS
       malic  13 kekleellpivYtPtvgeacqeyseeyrkarglylsikdkekikeilknlpeedvkvivvtdgeriLGlGdlG.vagvgimvGKlaLytalagidPekv 110
                  +  e+ l ++YtP+v+++c+e+ ++ ++ + ++++++++                v+++tdg+riLGlGd+G  a++++m+GK +Ly + ++i+   +
  EPA06504.1  23 DKITEKNLQLIYTPGVATVCNEIFKNRKTRY-QLTAKGNN----------------VAIITDGTRILGLGDIGpDAALPVMEGKSVLYRKYGNIS---A 101
                 4556789******************999999.99999999................9****************99********************...* PP

                 EEEEECS-BS.HHHHC.TT..S.SSB...SHHHHHHHHHHHHHHHHHHGCTSEEEE-S--CCHHHHHH CS
       malic 111 lpvvldvgtnneelledplYlGlrkkRvkgeeydefvdefveavkelfppkaliqfEDfkaknafeil 178
                 +p++ld++                           + d+++e+vk++ p ++ i++ED+++++ ++i 
  EPA06504.1 102 FPICLDTK---------------------------DKDKIIETVKAISPVFGAINLEDIESPKVLDIS 142
                 ********...........................88************************9998876 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.022
                 SS.SS..EEEEE-SSSBTTTBS-....GHHHHHHHHHHHHHHH CS
       malic  62 lpeedvkvivvtdgeriLGlGdl....GvagvgimvGKlaLyt 100
                  +  +vk+++v  g++  G+G+l    G++ + +   K a+y+
  EPA06504.1 178 KKMAEVKIVIVGAGSAGYGIGNLlyfaGCKNIIVLDSKGAIYK 220
                 45678*****************855556677777778888886 PP

>> Malic_M  Malic enzyme, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.1   5.2   5.5e-28   1.1e-24       3     241 ..     160     366 ..     159     377 .. 0.90

  Alignments for each domain:
  == domain 1  score: 87.1 bits;  conditional E-value: 5.5e-28
                 HHHHHHHHHHHHHHHHH-S-GGG--EEEEC-SHHHHHHHHHHHHHHHTTTS-HHHHHTTEEEEETTEE-BTT-S---TTTGGGSBS--SS--S....SH CS
     Malic_M   3 gTaavalagllaalkitgkklseqkivvlGaGsagiGiaeqivealvkeGlseeeakkkiylvDrkGLltedrekleeekkpfakkkeelkeakdkltL 101
                 gT++v+la+ll++l + +kk++e kiv++GaGsag Gi +++  a    G       k+i ++D+kG + ++r   ee  +++  + +e+++++ k ++
  EPA06504.1 160 GTSVVVLAALLNSLVLVKKKMAEVKIVIVGAGSAGYGIGNLLYFA----G------CKNIIVLDSKGAIYKGR---EESMNKYKDEIAEFTNREAKGHI 245
                 9**************************************998754....4......689**************...4567788888888888888899* PP

                 HHHHHHH--SEEEE-SSSSS-S-HHHHHHHHHHSSS-EEEE--SSGGGSSS-HHHHHHHTTT-SEEEESS----EEETSEEE--EE--GGGTHHHHHHH CS
     Malic_M 102 eevvkkvkptvliGlsgvagafteeivremaksterPiilplSNPtskaEataedvlkwtdgkalvasGsPfkpvelngktyeigQaNNayifPglglg 200
                 ++v++   ++v iG+sg++++++ e++++m++   +Pi+++l NP+ ++    + vl+   g+ +va+Gs     ++       +  NNa++fP l  +
  EPA06504.1 246 DDVIAG--ADVFIGVSGIKNLLKSEMIKKMSQ---NPIVFALTNPDPEI----NPVLAKKAGAKIVATGSF----SY------ENKVNNALVFPYLMRA 325
                 ****75..79*******************986...6*********9865....45777889********94....34......3567************ PP

                 HHHTT-SS--HHHHHHHHHHHHTT--HHHHHTT-SS--GGG CS
     Malic_M 201 vivarakritdemllaaaealaelvseeelkegsllPelse 241
                 ++  ++++it + l+a++ a+a+++ +++lke+++ Pe+ +
  EPA06504.1 326 ILDLKIQKITLDTLYAVSVAIAKTIPKNKLKEDNIIPEIGN 366
                 *************************************9964 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.63   1.3e+03      25      49 ..      68      91 ..      44     135 .. 0.59
   2 !   18.6   1.3   7.7e-07    0.0015      71     122 ..     244     295 ..     168     305 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.63
                   EEEEE--SHHHHHHHHHHHHCT-EE CS
  AdoHcyase_NAD 25 vavvaGyGdvGkGcaaslkglGarv 49
                    + + G Gd+G  +a  +   G  v
     EPA06504.1 68 GTRILGLGDIGPDAALPVM-EGKSV 91
                   3345555555554444332.23334 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 7.7e-07
                    -HHHCTTT-SEEEE-SSSSSSB-HHHHCCS-TTEEEEE-SSTTTTBTHHHHH CS
  AdoHcyase_NAD  71 tleevvkkadivvtttGnkdiitlehlkkmkddaivcniGhfdseidvaale 122
                    ++++v++ ad+++ ++G k+++++e++kkm ++ iv  +   d ei+    +
     EPA06504.1 244 HIDDVIAGADVFIGVSGIKNLLKSEMIKKMSQNPIVFALTNPDPEINPVLAK 295
                    589*************************************999999865544 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   1.1e-06    0.0021       9     114 ..     179     285 ..     173     303 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.1e-06
                   ..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCG......HHHHHHT-SEEEE-SSSSS-SB-HHHHHCCH CS
  Shikimate_DH   9 slkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealklee......lkellaeadvvisataseepilekeeveeal 99 
                   +++e k++++GaG  +  + + L+ +g+k+++v+    +  k   e++++++ e+ ++++      +++++a adv  + ++  +++l++e++++++
    EPA06504.1 179 KMAEVKIVIVGAGSAGYGIGNLLYFAGCKNIIVLDSKGAIYKGREESMNKYKDEIAEFTNreakghIDDVIAGADVF-IGVSGIKNLLKSEMIKKMS 274
                   57899*****************************9875544444444444444444444311222277888889975.56777888999****9998 PP

                   HH.S..EEEEE--SS CS
  Shikimate_DH 100 kkrkkplllvDiavP 114
                   ++     +++ +++P
    EPA06504.1 275 QN----PIVFALTNP 285
                   66....577888888 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.8   2.9e-06    0.0058      12      49 ..     176     213 ..     161     215 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.9e-06
                 HHHHHHTSEEEEE--SHHHHHHHHHHHHHTTTEEEEEE CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        ThiF  12 gqekLrdskvllvGaGglGsellknLalsGvgkltlvD 49 
                   +k++++k+++vGaG  G  +  +L  +G++++ + D
  EPA06504.1 176 VKKKMAEVKIVIVGAGSAGYGIGNLLYFAGCKNIIVLD 213
                 56899*******************************99 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   4.7e-06    0.0094       1      43 [.     182     224 ..     182     235 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.7e-06
                    EEEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS-- CS
  FAD_binding_3   1 etdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlprad 43 
                    e++++IVGaG aG   ++lL  aG ++++v   + +++++r +
     EPA06504.1 182 EVKIVIVGAGSAGYGIGNLLYFAGCKNIIVLDSKGAIYKGREE 224
                    5789*************************98888888888755 PP

>> ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.98     2e+03      13      53 ..      37      87 ..      35      92 .. 0.56
   2 ?   13.3   0.3   2.5e-05     0.049      11      86 ..     162     240 ..     154     278 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.98
                   HHHHHHHHHHHHTTTS...-STTEEEEE.......E--SHHHHHHHHHHHH CS
  ELFV_dehydrog 13 Gvvyyveemlkklkld...slegkrvai.......sGsGnvgsyaalllte 53
                   Gv+++++e++k+ k++   + +g++vai        G G++g  aal ++e
     EPA06504.1 37 GVATVCNEIFKNRKTRyqlTAKGNNVAIitdgtriLGLGDIGPDAALPVME 87
                   666666677666555555656666665411111115777777777776655 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 2.5e-05
                    HHHHHHHHHHHHHHTTTS-STTEEEEEE--SHHHHHHHHHHHHCT-EEEEEEESSEEEEETTEE....-HHHHHHHHHCS CS
  ELFV_dehydrog  11 glGvvyyveemlkklkldslegkrvaisGsGnvgsyaallltelgakvvavsDssGviydpeGl....dieellelkeer 86 
                    ++ v++++ + l  +k  ++++ +++i G G  g    +ll  +g k + v Ds+G+iy+         ++e++e+ +++
     EPA06504.1 162 SVVVLAALLNSLVLVKK-KMAEVKIVIVGAGSAGYGIGNLLYFAGCKNIIVLDSKGAIYKGREEsmnkYKDEIAEFTNRE 240
                    44444444444444344.59999************************************644332355556666664444 PP

>> THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       2.2   4.3e+03      29      44 ..      52      67 ..      31      71 .. 0.71
   2 ?   -0.5   0.0      0.33   6.5e+02     123     140 ..     111     128 ..     105     130 .. 0.86
   3 ?    7.2   0.2    0.0014       2.8      71     100 ..     243     272 ..     176     279 .. 0.85
   4 ?    0.5   0.0      0.17   3.3e+02      85     115 ..     342     371 ..     331     376 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.2
                   HCT---TT-EEEEE-- CS
  THF_DHG_CYH_C 29 etgielegkkvvvvGr 44
                   +++ + +g++v+++  
     EPA06504.1 52 RYQLTAKGNNVAIITD 67
                   4677788889988865 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.33
                    HHHHCTTSSEE--TTTSC CS
  THF_DHG_CYH_C 123 feevkevasaitPvpgGV 140
                     +++ e+++ai+Pv g++
     EPA06504.1 111 KDKIIETVKAISPVFGAI 128
                    5789999*******9987 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0014
                    CCHHHHHCCSSEEEE-SS-TT-B-GGGS-T CS
  THF_DHG_CYH_C  71 kdlaeitreadivvvavGkpelikaemvke 100
                     ++++++  ad+ +   G ++l+k+em+k+
     EPA06504.1 243 GHIDDVIAGADVFIGVSGIKNLLKSEMIKK 272
                    47889999********************97 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.17
                    E-SS-TT-B-GGGS-TT-EEEE---EEC-TT CS
  THF_DHG_CYH_C  85 vavGkpelikaemvkegavviDvGinrvekg 115
                    v+v  ++ i ++ +ke++++ ++G +++ ++
     EPA06504.1 342 VSVAIAKTIPKNKLKEDNIIPEIGNKSL-QK 371
                    67888999****************9988.33 PP

>> Phage_int_SAM_3  Phage integrase, N-terminal SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1      0.32   6.4e+02      40      54 ..      20      34 ..      15      36 .. 0.81
   2 ?    7.0   0.1    0.0036       7.2      32      49 ..     120     137 ..     110     145 .. 0.82
   3 ?   -3.5   0.0       6.6   1.3e+04      19      29 ..     223     233 ..     222     247 .. 0.66
   4 ?    0.0   0.0      0.54   1.1e+03      35      46 ..     320     335 ..     308     341 .. 0.70
   5 ?    2.9   0.2     0.069   1.4e+02      30      44 ..     357     371 ..     347     376 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.32
                     SBGGG--HHHHHHHH CS
  Phage_int_SAM_3 40 iklkkItpadiqkfq 54
                      k++kIt + +q  +
       EPA06504.1 20 SKIDKITEKNLQLIY 34
                     69********99765 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0036
                      THHHHTTSSBGGG--HHH CS
  Phage_int_SAM_3  32 hIlPyFgniklkkItpad 49 
                       I P+Fg i l++I++  
       EPA06504.1 120 AISPVFGAINLEDIESPK 137
                      59************9654 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 6.6
                      HHHHHHHHHHH CS
  Phage_int_SAM_3  19 esTyatyksii 29 
                      e ++++yk  i
       EPA06504.1 223 EESMNKYKDEI 233
                      56666666554 PP

  == domain 4  score: 0.0 bits;  conditional E-value: 0.54
                      HHT....TSSBGGG-- CS
  Phage_int_SAM_3  35 PyF....gniklkkIt 46 
                      Py+     ++k++kIt
       EPA06504.1 320 PYLmraiLDLKIQKIT 335
                      5555555899*****9 PP

  == domain 5  score: 2.9 bits;  conditional E-value: 0.069
                      TTTHHHHTTSSBGGG CS
  Phage_int_SAM_3  30 knhIlPyFgniklkk 44 
                      ++ I+P +gn+ l+k
       EPA06504.1 357 EDNIIPEIGNKSLQK 371
                      567********9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.47
# Mc/sec: 2395.27
//
Query:       EPA06505.1  [L=48]
Description: hypothetical protein BG20_I1418 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 333.00
//
Query:       EPA06506.1  [L=197]
Description: hypothetical protein BG20_I1432 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.056   14.1   0.5      0.096   13.3   0.1    1.7  2  DUF3892       Protein of unknown function (DUF3892)
      0.056   14.1   1.6      0.075   13.7   0.6    1.8  2  SlyX          SlyX
       0.28   11.1   7.9        1.4    8.9   4.9    2.3  2  Prefoldin_2   Prefoldin subunit
       0.42   10.7   2.8        1.7    8.7   3.0    1.9  2  DUF2680       Protein of unknown function (DUF2680)
        1.5    9.1   6.9        0.6   10.4   2.4    2.1  2  Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain


Domain annotation for each model (and alignments):
>> DUF3892  Protein of unknown function (DUF3892)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   2.7e-05     0.096      21      76 .]      29      97 ..       9      97 .. 0.85
   2 ?   -3.2   0.0       3.8   1.4e+04      10      20 ..     109     119 ..     103     132 .. 0.53

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.7e-05
     DUF3892 21 gsntlstgekyskeeaislikngkkagVevvrsk..............dGekYlrtkadgtetdNLlsLp 76
                 ++  ++ge++++ ++ s+ik g   ++++ ++k              dGe+Ylr + ++ + d L+++p
  EPA06506.1 29 TEKGITNGEQVDRITLTSDIKHGLS-YITIYSGKdswkkgyklkifsiDGEYYLRIDGNKAKLDYLGDIP 97
                556678999****************.888888889999999999****************9999998877 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.8
     DUF3892  10 gnsherItevk 20 
                 ++s++ I +++
  EPA06506.1 109 ETSSKQIKALE 119
                 44555555555 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.8   6.5e+03      46      53 ..     114     121 ..     107     133 .. 0.55
   2 ?   13.7   0.6   2.1e-05     0.075      23      57 ..     160     194 ..     143     197 .] 0.86

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.8
                 T-XXXXXX CS
        SlyX  46 rlkelees 53 
                 ++k+le++
  EPA06506.1 114 QIKALESK 121
                 33333333 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 2.1e-05
                 HHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXX CS
        SlyX  23 ndvvaeqqqqidrlqrqlrllaerlkeleessgas 57 
                 +d+  eq q++++l++q+++l +++k+ ++ss++s
  EPA06506.1 160 DDATPEQLQRLEQLEKQIKQLSRKVKSKKPSSKKS 194
                 67777999*******************99998755 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.029     1e+02      69      84 ..     106     121 ..     101     125 .. 0.85
   2 ?    8.9   4.9    0.0004       1.4      59      97 ..     158     196 ..     156     197 .] 0.90

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.029
                  HHHHHHHHHHHHHHHH CS
  Prefoldin_2  69 erketlekeiktlekq 84 
                   +ket +k+ik+le++
   EPA06506.1 106 SDKETSSKQIKALESK 121
                  679**********987 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0004
                  -HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
  Prefoldin_2  59 dkeevkeeLeerketlekeiktlekqleklekeleelke 97 
                  + +++++e  +r+e+lek+ik+l+++ ++++   ++ k+
   EPA06506.1 158 ESDDATPEQLQRLEQLEKQIKQLSRKVKSKKPSSKKSKK 196
                  5689999999*******************9999888887 PP

>> DUF2680  Protein of unknown function (DUF2680)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0         3   1.1e+04      31      46 ..     135     150 ..     134     152 .. 0.73
   2 ?    8.7   3.0   0.00046       1.7       2      23 ..     163     184 ..     162     188 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 3
     DUF2680  31 GllTkeqgekikkniD 46 
                 G+l+k+  ++  + +D
  EPA06506.1 135 GVLPKQSSDELPQELD 150
                 8888888887766665 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00046
     DUF2680   2 TdeQkkeleaLyqqiaelrKqi 23 
                 T+eQ + le+L++qi +l +++
  EPA06506.1 163 TPEQLQRLEQLEKQIKQLSRKV 184
                 99**************998876 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.2      0.16   5.6e+02      45      66 ..     101     122 ..      98     147 .. 0.77
   2 ?   10.4   2.4   0.00017       0.6      29      68 ..     154     193 ..     147     197 .] 0.86

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.16
                   HHHHHHHHHHHHHHCCCCCCTT CS
  Seryl_tRNA_N  45 leelqaerNelskeIgkakkkk 66 
                   l++ ++ + + sk+I+ +  k 
    EPA06506.1 101 LDKYNSDKETSSKQIKALESKP 122
                   6778888889999998887665 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00017
                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS- CS
  Seryl_tRNA_N  29 delleldekrrelqveleelqaerNelskeIgkakkkked 68 
                   + + e d++  e  ++le+l ++ ++ls++++++k + ++
    EPA06506.1 154 EPITESDDATPEQLQRLEQLEKQIKQLSRKVKSKKPSSKK 193
                   5688999999999**********************98744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1716  (0.0957109); expected 358.6 (0.02)
Passed bias filter:                      859  (0.0479112); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1204.40
//
Query:       EPA06507.1  [L=180]
Description: hypothetical protein BG20_I1426 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.18   11.9   0.1        1.9    8.6   0.0    2.1  2  Glyc_hyd_38C_2  Glycosyl hydrolases family 38 C-terminal sub-


Domain annotation for each model (and alignments):
>> Glyc_hyd_38C_2  Glycosyl hydrolases family 38 C-terminal sub-domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1     0.023   4.2e+02      60      86 ..       8      35 ..       5      38 .. 0.71
   2 ?    8.6   0.0   0.00011       1.9      29      79 ..      55     104 ..      41     113 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.023
  Glyc_hyd_38C_2 60 tflqtleqlesk.vaPelcpmeteayvi 86
                     flq l ++e+  +a  + ++ ++ +vi
      EPA06507.1  8 VFLQSLTKIETPtLAVLISSITATIFVI 35
                    59*******9651555666666677776 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00011
  Glyc_hyd_38C_2  29 llqcgeeeeqaeklnvcnvlqatarcerttltflqtleqleskvaPelcpm 79 
                     ll+   +e+ +++l+   +l++t+ c+r +  +l+t++q+   +  +  p+
      EPA06507.1  55 LLRGF-HEDLTNRLDKNSILKTTEDCHRYANDYLNTIDQIAFLAIQKKIPI 104
                     55544.788999***************************976666555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       764  (0.0426125); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 1024.63
//
Query:       EPA06508.1  [L=349]
Description: leucyl-tRNA synthetase domain protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.7e-16   57.5   0.2      3e-15   55.5   0.2    1.7  1  tRNA-synt_1   tRNA synthetases class I (I, L, M and V)
    1.6e-10   40.3   0.0    2.6e-10   39.6   0.0    1.2  1  tRNA-synt_1g  tRNA synthetases class I (M)
      9e-07   28.5   0.0    1.3e-06   28.0   0.0    1.2  1  tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
  ------ inclusion threshold ------
       0.15   12.1   0.0       0.28   11.2   0.0    1.5  1  CHB_HEX_C     Chitobiase/beta-hexosaminidase C-terminal domai


Domain annotation for each model (and alignments):
>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.5   0.2   6.8e-19     3e-15     321     601 ..      25     301 ..      22     302 .. 0.82

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 6.8e-19
  tRNA-synt_1 321 gtlteeaaefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkpiiyrateqWfvrvke..ladaalkavekvqfvpkskekryaswleni 416
                  g+l+ ++++f+g+kv  a++++ e l ++       + + +   c  + + ++  + +qWf +  +   ++ a k  +++++ p+  +++++  +   
   EPA06508.1  25 GKLKANTEQFSGIKVAYAKDTIKEWLIKNKHADILLELTNTPVRCRCGAECVVKVLNNQWFLNYGDkdWKELATKCFDEMSILPQEIRSEFNYVIGWL 122
                  88999*******************99877655555555555555667778899999******9855459999999999******************** PP

  tRNA-synt_1 417 qdWciSRqrwWGhripl...fvsketeevvvreelkelvagreeeeaekkalekeakdklkkekgelekdedvlDvWFsSgswpfstlgypeedteel 511
                  ++ +  Rq   G+++p    ++ ++  + v+      + +  ++ + ++++l+ e+ d +  +kg+ + ++ +         +  s+     + ++e+
   EPA06508.1 123 RERACARQHGLGTKLPWdkdWIVESLSDSVIYMAYYTISKFVNNGTLHAEKLSGEFFDYIFVGKGDANNVSTI---------TGLSVDTIN-QIKKEF 210
                  ****************755587777777777666666666667777777777788888886667666665544.........444443333.3489** PP

  tRNA-synt_1 512 kkffpadmlleGlDiirgWvarlillslaltgsePf.kevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltli.lsdvgrdinl 601
                  + f+p d   +G D +   ++  +l  +a++ ++ + ke++v+g v+  +G KmSKs+gN+i   + i+ ygad +Rl++i +++ ++d ++
   EPA06508.1 211 DYFYPVDSRHSGRDLVPNHLTFFVLNHVAIFPESNWpKEIVVNGSVL-MNGSKMSKSMGNIIPLRKAIQDYGADPIRLAIIiSAELLQDADF 301
                  *****************************99877554999****998.57******************************988899988765 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   0.0   5.7e-14   2.6e-10     289     377 ..     222     312 ..     193     323 .. 0.89

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 5.7e-14
                   EGGGHHHHHTHHHHHHHH..TT----S-EEEE--EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HHHHHHHHHH CS
  tRNA-synt_1g 289 gkdiikFHtifwPaillg..aelklpkkvvaheyltvegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfswedfvervNs 377
                   g+d ++ H  f+     +   e + pk++v+++ + ++g+K+SkS g+++  ++a++ + ad +R  ++ +a+  +D+df++e++    N+
    EPA06508.1 222 GRDLVPNHLTFFVLNHVAifPESNWPKEIVVNGSVLMNGSKMSKSMGNIIPLRKAIQDYGADPIRLAIIISAELLQDADFNMESVSGIQNK 312
                   99**********999999888999***********************************************************99888875 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0     3e-10   1.3e-06     211     295 ..     219     305 ..     204     311 .. 0.84

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 3e-10
                   EEEEGGGTTTHHHHHHHHHHHHSS.S--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHH.HSS-TTS-EEE-HHH CS
  tRNA-synt_1e 211 hsGGiDLafPhhenelaqseaafd.kqlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRlll.lsahyrsqldfkeel 295
                      G DL+  h    +  + a f  +++ k  + ng + ++g kmsks++n+i ++++++ + +  +Rl++ +sa+  +  df+ e 
    EPA06508.1 219 RHSGRDLVPNHLTFFVLNHVAIFPeSNWPKEIVVNGSVLMNGSKMSKSMGNIIPLRKAIQDYGADPIRLAIiISAELLQDADFNMES 305
                   556889998888888889999998799*****************************************9861566777777777665 PP

>> CHB_HEX_C  Chitobiase/beta-hexosaminidase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   6.3e-05      0.28      18      52 ..      19      54 ..      16      71 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.3e-05
   CHB_HEX_C 18 GAkvengkLeanv.alPGltieYsldggetwqkyta 52
                G ++  gkL+an+ ++ G+++ Y  d  ++w   ++
  EPA06508.1 19 GKEFYGGKLKANTeQFSGIKVAYAKDTIKEWLIKNK 54
                566778******956****************87664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2195.12
//
Query:       EPA06509.1  [L=185]
Description: hypothetical protein BG20_I2364 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1363.54
//
Query:       EPA06510.1  [L=181]
Description: hypothetical protein BG20_I2363, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 1168.56
//
Query:       EPA06511.1  [L=70]
Description: hypothetical protein BG20_I2365, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.33s 00:00:00.77 Elapsed: 00:00:00.51
# Mc/sec: 415.47
//
Query:       EPA06512.1  [L=46]
Description: hypothetical protein BG20_I1686 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       234  (0.0130515); expected 358.6 (0.02)
Passed bias filter:                      158  (0.00881254); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 287.97
//
Query:       EPA06513.1  [L=172]
Description: hypothetical protein BG20_I1696, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
        0.1   13.1   2.7        4.2    7.9   0.0    2.5  2  Calci_bind_CcbP  Calcium binding


Domain annotation for each model (and alignments):
>> Calci_bind_CcbP  Calcium binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   1.6    0.0043        77      93     105 .]      25      37 ..       4      37 .. 0.71
   2 ?    7.9   0.0   0.00024       4.2      49      99 ..      66     116 ..      46     119 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.0043
                      HHHHHHHHHHHHH CS
  Calci_bind_CcbP  93 etkeaiadweyWv 105
                        +  i+dweyW+
       EPA06513.1  25 GKSMKIDDWEYWL 37 
                      445679******6 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00024
                      EEEEEEEEE--HHHCTTS-EEEEEESSCEEEEEGGGEEEES--HHHHHHHH CS
  Calci_bind_CcbP  49 gkevevlglasedecekemfveveaeedklavpLeeleaieadeetkeaia 99 
                      gke++v++++ +    + ++ ev+++++ +   +e++e+ie++++++++i+
       EPA06513.1  66 GKELSVVAMSRHPIWGTYVINEVAWTRKWFIDFIESIEIIETQKNGRQIID 116
                      7899******99999999999***************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1140.70
//
Query:       EPA06514.1  [L=619]
Description: hypothetical protein BG20_I1694 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-17   63.7   0.9      2e-16   60.8   0.4    2.4  2  DUF87          Helicase HerA, central domain
    0.00032   20.1   0.0      0.006   16.0   0.0    2.2  2  FtsK_SpoIIIE   FtsK/SpoIIIE family
     0.0039   17.3   0.6      0.011   15.8   0.2    1.9  2  FliH           Flagellar assembly protein FliH
     0.0078   15.2   0.0      0.022   13.7   0.0    1.7  2  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
  ------ inclusion threshold ------
      0.053   13.6   0.1       0.16   12.1   0.1    1.8  1  MMR_HSR1       50S ribosome-binding GTPase
      0.074   13.5   1.3          7    7.1   0.0    3.5  3  AAA            ATPase family associated with various cellular


Domain annotation for each model (and alignments):
>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.8   0.4   6.6e-20     2e-16       1     152 [.     178     367 ..     178     453 .. 0.56
   2 ?    0.4   0.0      0.19   5.6e+02     100     175 ..     443     520 ..     429     544 .. 0.59

  Alignments for each domain:
  == domain 1  score: 60.8 bits;  conditional E-value: 6.6e-20
       DUF87   1 ieiGrllsgsevpvyldlnklvtrHlAilgsTGsGKSntvavLleelle..kkgatililDpHGEYgkal..................ekllsekvkvi 79 
                 + iG+l+++++v + ++ + +++ H++i+g TG+GKSn+v+ L++++l   + + + +++D+  EY  +l                  + l ++ +++i
  EPA06514.1 178 VTIGKLIKNDNVNIFVNSEDFIKVHFGIFGYTGAGKSNLVSTLISSVLTqaRTNNKFVLFDIMDEYTGLLidqllnpningmlvslgqRYLPQSVIDYI 276
                 579*********************************************9777777***************97777777777777776633334444444 PP

       DUF87  80 tpspsakdkelkinpwsldpeelldllee.ddkpaaavqrsvleealdqakakeekeklssdepveklleelk........................k 152
                 t+++   ++el i  ++ + + l+ +l+  + kp  ++ r +++++l q k   ++ +l++++ ve+  +e +                        +
  EPA06514.1 277 TAPQ--RNEELLI--AATN-DLLAGMLFPkKLKPFKEQYRPFVNQLLIQNK--IKVIDLTFNRTVEEYSQEFWetifdeyvtgptevdlrvilnrifR 367
                 4431..2222222..1111.1223333333444444444555555555555..555555555555555555555544444444444444444444431 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.19
       DUF87 100 eelldllee..ddkpaaav.qrsvleealdqaka...keekeklssdepveklleelkkekeelrklknqaiarlldkledl 175
                 +e   l++   dd+++  +  +++ +++++q  +   ++ + ++ +de +e++ ++ +    +++k+++++ ++l+++ +++
  EPA06514.1 443 DEGKALIILtsDDPNNMREhAKKIGQSIYNQRSRratTTPIVSFIFDEADEFIPQKPE----GSKKHSRDIVETLSRRGRKF 520
                 5555555554222222222344444444444333444455555555666666665555....88888888888888777666 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0     2e-06     0.006      19      70 ..     177     231 ..     168     241 .. 0.79
   2 ?    1.5   0.0     0.051   1.5e+02     147     241 ..     447     531 ..     408     533 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2e-06
                   EEEEEEETTS-EEEEEGGGS-....SEEEE--TTSSHHHHHHHHHHHHHTT--TT CS
  FtsK_SpoIIIE  19 pvalgkeisgnplvldlkkma...shllvaGatgsGKStalntLilSlatthtPe 70 
                   +v +gk i ++++ ++ ++      h  + G tg GKS+ + tLi S++t +  +
    EPA06514.1 177 TVTIGKLIKNDNVNIFVNSEDfikVHFGIFGYTGAGKSNLVSTLISSVLTQARTN 231
                   6667777777777777776667778999*********************977654 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.051
                   --B-TT-......................-----------B-----EEEEEEC-HHHHHHHHHHH....HHHHHHHHHHHCGGGTEEEEEEES-- CS
  FtsK_SpoIIIE 147 gdvflvlDnyddlaaeneritsLsnqgpsygvhvlvtagrelekrpslvvivderieLrlaapkdssvlvedaivRlarkgraaglHlllatqrl 241
                   +++ l +D+ +++++  +          + g+ +   + r+++  p +  i+de  e + ++p+ s++  +d++  l r+gr+ gl   + tqr+
    EPA06514.1 447 ALIILTSDDPNNMREHAK----------KIGQSIYNQRSRRATTTPIVSFIFDEADEFIPQKPEGSKKHSRDIVETLSRRGRKFGLGVGISTQRI 531
                   555555555555555444..........3456666666677777777777788888888888888888888888888888887777776666665 PP

>> FliH  Flagellar assembly protein FliH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.8   5.4e+03      64      79 ..     183     198 ..     179     202 .. 0.85
   2 !   15.8   0.2   3.7e-06     0.011      11      89 ..     380     466 ..     373     473 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.8
                 CHHHS-EEEEE-HHHH CS
        FliH  64 pvdekkitlrvnpdDl 79 
                 +++++++ ++vn +D+
  EPA06514.1 183 LIKNDNVNIFVNSEDF 198
                 68899********997 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 3.7e-06
                 HHHHHHHHHHH........HHHHHHHHHHHHHHHHHHHHHHS--S-HHHHHHHHHHHHTTSCHHHS-EEEEE-HHHHHHHHHHHHHH CS
        FliH  11 leelenslael........deeledqlvqlaldiarkvikkelsvdpekilalvrealaklpvdekkitlrvnpdDlelvrehlgee 89 
                 + el+++++++        d+++ d+l ++   +   +i   l+  p++++ +v++++++l +de+k+ +++  dD + +reh+++ 
  EPA06514.1 380 ARELRQEVEQAkrpsnvgrDKTINDRLTSIQQLLDMDIINPSLNPLPQEVAYNVNQLITELNSDEGKALIILTSDDPNNMREHAKKI 466
                 566777777777777788899999999999999999***********************************************9965 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   7.4e-06     0.022      15      60 ..     200     248 ..     187     256 .. 0.80
   2 ?   -2.8   0.0      0.74   2.2e+03     261     286 ..     510     535 ..     508     549 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.4e-06
  TrwB_AAD_bind  15 tqhilivGttGsGKtqalekllrairarg...draivlDltGafvsrfy 60 
                    + h+ i+G tG+GK++ ++ l+ ++  ++   ++ + +D + +++    
     EPA06514.1 200 KVHFGIFGYTGAGKSNLVSTLISSVLTQArtnNKFVLFDIMDEYTGLLI 248
                    67*********************99887766689999998777765544 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.74
  TrwB_AAD_bind 261 lksllaegRkfGgavvlglqsiaqlr 286
                    +++l  +gRkfG  v +  q i  l 
     EPA06514.1 510 VETLSRRGRKFGLGVGISTQRITYLD 535
                    5677789*********9999998775 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   5.3e-05      0.16       2      27 ..     203     231 ..     202     238 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.3e-05
                 EEEEESTTSSHHHHHHHHHTS...TEEES CS
    MMR_HSR1   2 vaivGrpNvGKStLinaltge...kaivs 27 
                 ++i+G++ +GKS L+++l+ +   +a+++
  EPA06514.1 203 FGIFGYTGAGKSNLVSTLISSvltQARTN 231
                 68*****************9855345554 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.32   9.5e+02       4      22 ..     206     224 ..     203     250 .. 0.62
   2 ?    2.8   0.0      0.05   1.5e+02      84     119 ..     431     463 ..     414     474 .. 0.81
   3 ?    7.1   0.0    0.0023         7      44      90 ..     464     514 ..     458     539 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.32
                 ESSTTSSHHHHHHHHHHHH CS
         AAA   4 yGppGtGKTllakavakel 22 
                 +G  G GK+ l++ +++++
  EPA06514.1 206 FGYTGAGKSNLVSTLISSV 224
                 6777777777777776663 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.05
                 HHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHH CS
         AAA  84 rvvnqLlteldgvkkkeskvivigatnrpdkldpal 119
                   vnqL+tel+  +    k ++i+++ +p+++ +  
  EPA06514.1 431 YNVNQLITELNSDEG---KALIILTSDDPNNMREHA 463
                 5699********999...589*****9999988765 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0023
                 HHHHHHHHHHHHTS...TS.EEEEEETGGGHHHHHTTCCCHHHHHHHHHHH CS
         AAA  44 kkirelfkeakeka...kp.silfiDEidalaksrsgseseeeervvnqLl 90 
                 kki + + + ++ +   +p + +++DE+d++++++ ++++++++++v++L 
  EPA06514.1 464 KKIGQSIYNQRSRRattTPiVSFIFDEADEFIPQKPEGSKKHSRDIVETLS 514
                 4554444443333346667566789**********8899999999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (619 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.42
# Mc/sec: 4387.43
//
Query:       EPA06515.1  [L=518]
Description: hypothetical protein BG20_I1693 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.036   14.0   0.1        0.5   10.3   0.0    2.6  2  HisK_N    Histidine kinase N terminal


Domain annotation for each model (and alignments):
>> HisK_N  Histidine kinase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   2.8e-05       0.5      73     101 ..     171     199 ..     156     208 .. 0.83
   2 ?   -0.1   0.0     0.046   8.3e+02      41      70 ..     485     514 ..     480     517 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 2.8e-05
                 HT--THHHHHHHHHHHHHHHHHHHCC--- CS
      HisK_N  73 anvnigdfvyNvnvgrsivlkallklnvs 101
                  +vni+df   +n+ ++iv++++ k  ++
  EPA06515.1 171 KKVNIADFAKENNLEKQIVFNKIKKYLLT 199
                 589*******************9987655 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.046
                 HHHHHHHHHHTTSS-GGGGHHHHHHHHHHH CS
      HisK_N  41 alfelviellkeeiseedlkelaekiakeR 70 
                 ++ + v +++k++ +  +++ la+ + +eR
  EPA06515.1 485 SMNKKVANMIKSSGKFLKIRPLAKTLRQER 514
                 67788999******************9999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (518 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.68u 0.37s 00:00:01.05 Elapsed: 00:00:00.58
# Mc/sec: 2703.66
//
Query:       EPA06516.1  [L=475]
Description: hypothetical protein BG20_I1691 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.2e-05   22.9   0.9    0.00012   21.7   0.9    1.6  1  H2O2_YaaD  Peroxide stress protein YaaA
     0.0089   15.9   0.9        6.7    6.5   0.0    3.1  4  DUF5591    Domain of unknown function (DUF5591)
  ------ inclusion threshold ------
      0.061   12.5   0.0       0.36    9.9   0.0    2.1  2  TGT        Queuine tRNA-ribosyltransferase


Domain annotation for each model (and alignments):
>> H2O2_YaaD  Peroxide stress protein YaaA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.9     2e-08   0.00012      29     130 ..     307     404 ..     250     436 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2e-08
   H2O2_YaaD  29 eea.eellealkklseeelkkllkisdklaelnveryqefeealkkkpAilaynGvvYkaldaeslseedleyaqehlrIlSglYGlLrpldliqpY.. 124
                 +e  ee  e+++++  +++ +l++ ++ l   + er +    + ++ pAi++y+G +++ ++    +++ + y    l+I+S+ YGl++p+ +i +Y  
  EPA06516.1 307 DELrEERFEEINRFLHKKIYSLMHPKKLLVVSCSERKKI---EVNRMPAIEMYDGPMFRMIR----KHKPFFYNGVDLLIVSAKYGLMKPTLQIANYdk 398
                 222356666666777777777777777777666666555...67789*************99....678999*************************55 PP

   H2O2_YaaD 125 RLemgt 130
                 RL+ ++
  EPA06516.1 399 RLSPEQ 404
                 555444 PP

>> DUF5591  Domain of unknown function (DUF5591)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.58   3.5e+03      88     110 ..     105     127 ..      76     149 .. 0.64
   2 !    6.4   0.0    0.0012       7.4       3      43 ..     175     215 ..     174     229 .. 0.91
   3 ?   -2.5   0.0       0.7   4.2e+03      97     134 ..     263     301 ..     256     321 .. 0.58
   4 !    6.5   0.0    0.0011       6.7      51     139 ..     374     458 ..     317     468 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.58
                 HHHHHHHHHHHHHHHHHT-SEEE CS
     DUF5591  88 eeiefvaellakylektkyekvi 110
                 ++i+ +++++++y +k++  k i
  EPA06516.1 105 KTIQSAKNAIKEYKKKKRSFKLI 127
                 44555555555555555554444 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0012
                 HHHHHHHHH---S..SSEEEEEE--SSSSGGGSHHHHHHHH CS
     DUF5591   3 rfrervlerYeppeekkvlvLlPcsakkPyseskshrkfae 43 
                 +f e v++  +++  k+ l Ll c+ +k y   k++r f  
  EPA06516.1 175 KFLENVVSELRSRYAKDWLFLLGCFHTKRYPLLKKYRIFGA 215
                 799999999999999*********************99965 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 0.7
                 HHHHHHHHT-SEEEE---THHHHHHHHHH.TT-SSEEEE CS
     DUF5591  97 lakylektkyekviahleeeyreiveeva.eelgleiiy 134
                 l++ +e  +yek++a  ++  ++i +++  e+l++ + +
  EPA06516.1 263 LNEQFEIDEYEKILALKKKISKKIKNQEYyEKLNQLLSL 301
                 555666667777777766666666555443555544444 PP

  == domain 4  score: 6.5 bits;  conditional E-value: 0.0011
                 .SEEEEE-SS-.EEEGGGTT----------------HHHHHHHHHHHHHHHHHHT-SEEEE---THHHHHHHHHHTT-SSEEEE--.SS CS
     DUF5591  51 kvheviltsPlGvvPreleevYPaaqYdiavtgewseeeiefvaellakylektkyekviahleeeyreiveevaeelgleiiytvved 139
                  v+ +i+++ +G++   l+     a+Yd  +++e   +  + + + l+k++++++y++++  + ++y ++ + v + l  +++++ +++
  EPA06516.1 374 GVDLLIVSAKYGLMKPTLQI----ANYDKRLSPEQIPKLQKQTLSRLEKFVSNENYKEIMFSMGKDYLSLFDGVDNVLPPKCTVKIAKG 458
                 56666666667666555554....5999999999999999999999***********************99999888887777776555 PP

>> TGT  Queuine tRNA-ribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0     6e-05      0.36     147     211 ..     102     172 ..      97     193 .. 0.78
   2 ?   -0.9   0.0      0.12     7e+02     108     156 ..     417     472 ..     390     474 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 6e-05
                 HHHHHHHHHHHHHHHH.....SE.EEEEE--TT-HHHHHHHHHHHHHH--SEEEE-S.SSSSSHHHHHHHHH CS
         TGT 147 sverTlrwldrcleah.....qa.lfgivqGglyedlreesaeelakrdfdgyaigG.lsvgeekeellevv 211
                   + T++ ++ +++++     +  l+g+ qG +  ++  e+ + l++++++ +a+gG l+ +e+++ ++ v 
  EPA06516.1 102 NKNKTIQSAKNAIKEYkkkkrSFkLIGVTQGKTV-KEYLECYKILKRIGYKHIAVGGlLAKKENTARFVTVR 172
                 557899999999977778888557*******655.6789******************667777777776654 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.12
                 EEEE-HHHHHHHHHHHT-SEEE-----...--S....S--HHHHHHHHHHHHHHHH CS
         TGT 108 kvlltpeesieiqeklgsDiimalddv...vps....paskkrveksverTlrwld 156
                 ++++++e++ ei+ ++g D    +d v    p+    +  k ++ ++++ T +wl+
  EPA06516.1 417 EKFVSNENYKEIMFSMGKDYLSLFDGVdnvLPPkctvKIAKGKIGQKLHKTKNWLN 472
                 57999999999999999999999887533333333333345566677777777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1572  (0.0876792); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.68u 0.34s 00:00:01.02 Elapsed: 00:00:00.52
# Mc/sec: 2747.65
//
Query:       EPA06517.1  [L=221]
Description: protein ExsB [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.4e-66  221.6   0.0    8.3e-66  221.5   0.0    1.0  1  QueC             Queuosine biosynthesis protein QueC
     0.0066   16.2   0.0      0.013   15.2   0.0    1.5  1  ATP_bind_3       PP-loop family
  ------ inclusion threshold ------
      0.011   15.2   0.0      0.015   14.8   0.0    1.2  1  Diphthami_syn_2  Diphthamide synthase
      0.019   14.1   0.0       0.11   11.6   0.0    1.9  2  NAD_synthase     NAD synthase
      0.048   12.4   0.0      0.073   11.8   0.0    1.3  1  tRNA_Me_trans    tRNA methyl transferase
      0.057   13.1   0.0      0.082   12.6   0.0    1.1  1  Asn_synthase     Asparagine synthase
       0.07   12.7   0.0       0.12   12.0   0.0    1.4  1  ThiI             Thiamine biosynthesis protein (ThiI)


Domain annotation for each model (and alignments):
>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  221.5   0.0   3.2e-69   8.3e-66       1     209 [.       2     211 ..       2     212 .. 0.95

  Alignments for each domain:
  == domain 1  score: 221.5 bits;  conditional E-value: 3.2e-69
                 EEEEE--SSHHHHHHHHHHHHH-SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-GGGGGGSCGGG---------...--......------- CS
        QueC   1 kavvllSGGlDSttvlalakkegkevealtfdYgqrhkkeleaakkiakelgveehkildldllkelggsaLtdeeievpk...eelee...eelpntf 93 
                 k+v+++SGGlDStt+l+   +eg+ev+ ltf Ygq+h ke e+ak+i++ l++ +hki+d++ l+++ +saLt+ +i++p+       +   e+l++t 
  EPA06517.1   2 KSVLIFSGGLDSTTLLYKLINEGHEVYPLTFLYGQKHCKESESAKEITNILKI-NHKIIDITALQSVLDSALTNPSISIPTvpsG---SqfyETLKTTV 96 
                 6799*************************************************.************************9995433...2355******* PP

                 -TTHHHHHHHHHHHHHHHHT-SEEEE---S-STT--GGGSHHHHHHHHHHHHHH.HTS--EEE-TTTT--HHHHHHHHHHTTHHHHH-B-STTS.-BTT CS
        QueC  94 VpaRNliflslaasyaealgaeaiiiGvneedfsgYPDcrdefvkalnkalnlg.edkkieieaPlidlsKaeivklgkelgvpleetlsCYegeeegk 191
                 Vp+RN+ifl++aa+ya++++a++i+++++ +d   YPDcr+ef++a++k+ +l+  +++ ++  P+ +++K+ +vk+g++l+vp+++t+sCYeg++  +
  EPA06517.1  97 VPNRNAIFLAIAAGYAQSIKADNIFFAAHYSDRGMYPDCRSEFISAFEKMTKLSlDNSNASVSSPFAKINKSGVVKIGDSLNVPFQLTWSCYEGKD--R 193
                 ******************************************************877899**********************************54..5 PP

                 TTSSSHHHHHHHHHHHHH CS
        QueC 192 aCgeCdaCalRkkgfeea 209
                 +Cg+C aC+ Rk++f ea
  EPA06517.1 194 HCGRCSACRERKNAFVEA 211
                 ***************986 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   5.2e-06     0.013       3      57 ..       4      58 ..       2      75 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.2e-06
                EEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHT CS
  ATP_bind_3  3 lvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckkl 57
                ++ +SgGlDS++Ll+ l ++ ++ +   ++    h + +es++e + + ++++k+
  EPA06517.1  4 VLIFSGGLDSTTLLYKLINEGHEVYPLTFLYGQKHCKESESAKEITNILKINHKI 58
                5679***************988777677777777777777777777777666654 PP

>> Diphthami_syn_2  Diphthamide synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   5.8e-06     0.015       1      41 [.       1      44 [.       1      67 [. 0.76

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.8e-06
  Diphthami_syn_2  1 mkvavlysGGkDsilaLykalke.sevesLvsvi..senkesym 41
                     mk++ ++sGG Ds+  Lyk ++e +ev  L  +   ++ kes  
       EPA06517.1  1 MKSVLIFSGGLDSTTLLYKLINEgHEVYPLTFLYgqKHCKESES 44
                     89*********************9***98876642245555554 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   4.4e-05      0.11      21      93 ..       3      73 ..       1      82 [. 0.85
   2 ?    0.1   0.0      0.14   3.7e+02     149     171 ..     160     182 ..     155     185 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.4e-05
                  EEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE---HHHHHHHHHHHH CS
  NAD_synthase 21 vvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievktidikpivrafeqelk 93
                   vl  SGG+DS++   l + + + ++v  l +   +++ ++ e a+++ + l+i+ k idi+   ++++++l+
    EPA06517.1  3 SVLIFSGGLDSTTL--LYKLINEGHEVYPLTFLYGQKHCKESESAKEITNILKINHKIIDITALQSVLDSALT 73
                  58889******974..555566778999999999999999**********************99998887665 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.14
                   ETTTTS-HHHHHHHHHHTT--HH CS
  NAD_synthase 149 apiaellKtevkeLakelnvPer 171
                    p a+++K+ v ++   lnvP +
    EPA06517.1 160 SPFAKINKSGVVKIGDSLNVPFQ 182
                   5899*****************76 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.8e-05     0.073       4      70 ..       4      61 ..       1      72 [. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.8e-05
  tRNA_Me_trans  4 vvalSgGVDSsvaaallkeqgyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdf 70
                   v  +SgG DS+  ++ l ++g+ev  +++   ++      +c+   + + a+++ + l i+++++d+
     EPA06517.1  4 VLIFSGGLDSTTLLYKLINEGHEVYPLTFLYGQK------HCK---ESESAKEITNILKINHKIIDI 61
                   5678********************9998876555......343...345677777777777777775 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   3.2e-05     0.082      23      81 ..       6      63 ..       3      73 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.2e-05
  Asn_synthase 23 lLSGGlDSSliaalaarqsksplktFsigfeekgsdeakyakevaehlgtehtelvlte 81
                   +SGGlDS+++ + +  + + ++   +  + +k+ +e++ ake+ + l+++h  + +t+
    EPA06517.1  6 IFSGGLDSTTLLYKLINEGH-EVYPLTFLYGQKHCKESESAKEITNILKINHKIIDITA 63
                  58*******99998887776.66666666667********************9998886 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.6e-05      0.12       5      59 ..       2      55 ..       1      74 [. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.6e-05
        ThiI  5 kvlaLlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeaiekveklaellaey 59
                k +++ SgG+DS    y l++ G +v  +++  +  +  ++ e  ++++++l  +
  EPA06517.1  2 KSVLIFSGGLDSTTLLYKLINEGHEVYPLTFL-YGQKHCKESESAKEITNILKIN 55
                578899**********************9996.4445555566666676666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1650.39
//
Query:       EPA06518.1  [L=258]
Description: hypothetical protein BG20_I1685, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.8e-11   42.3   0.7    6.3e-09   35.8   0.7    2.2  1  Q_salvage  Potential Queuosine, Q, salvage protein family
  ------ inclusion threshold ------
      0.066   12.8   0.5       0.18   11.4   0.5    1.8  1  EF-hand_1  EF hand
          3    8.0   4.6       0.68   10.0   0.5    2.1  2  EF-hand_6  EF-hand domain


Domain annotation for each model (and alignments):
>> Q_salvage  Potential Queuosine, Q, salvage protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.7   1.1e-12   6.3e-09      58     271 ..      38     225 ..       2     244 .. 0.77

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 1.1e-12
   Q_salvage  58 eegipitdpeflsketeeelkkvfrsa.teeeiplleeRlellreagkvllekfdgsfvnlikkanksaakLvnlvveefpsFrDeavyegkkvrlyKR 155
                 ++  +i+d + lsk+t ee++++f+ +  +  +p le+R++   ++++ l + f+g+++n+ik++n+s  k+ n   + f+ F+D  +         K 
  EPA06518.1  38 KKTFDILDTKKLSKITLEEFRTIFQDDsGNDVLPELEKRHKNWLDLATKLNDLFEGKTLNIIKSCNNSLIKFTNSFRQ-FKAFDDPLS---------K- 125
                 34789**********************445779***********************************9999988655.999998754.........2. PP

   Q_salvage 156 AqilvaDlwaafegeglgefedidkltmfADyrvpqvLrqlgvLeyseeLekklkekellesgseeeveiRacsiwavelireeiekkkeeakekvnai 254
                   i+v  +  +++g+gl +fe+   +    Dy++ + L   gv+    ++e+k+k+ ell++++   +e+R + + a  +i ++++         +   
  EPA06518.1 126 -MIMVNAI--MHQGRGLIKFEQ--PIIPGMDYQLLKQLLRQGVIVAPADIEEKIKNYELLDNNE--AMELRKAGLFALHEIMNQTS---------IPGD 208
                 .4788866..568999999995..566777***99999999*****************998765..56799999999999887765.........3334 PP

   Q_salvage 255 liDffLwdlakelekee 271
                  iD+++w  + + e+ee
  EPA06518.1 209 YIDNMIWGNRTKCEDEE 225
                 57777777777766664 PP

>> EF-hand_1  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.5   3.1e-05      0.18       3      27 ..      38      62 ..      38      64 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.1e-05
                HHHHHHHTTTSSSEEEHHHHHHHHH CS
   EF-hand_1  3 keiFrefDkDgdGkIdfeEfkellk 27
                k+ F+++D+ +  kI++eEf+++++
  EPA06518.1 38 KKTFDILDTKKLSKITLEEFRTIFQ 62
                689******************9986 PP

>> EF-hand_6  EF-hand domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.5   0.00011      0.68       4      28 ..      39      63 ..      37      70 .. 0.90
   2 ?   -2.9   0.3       1.6   9.5e+03       6      10 ..     116     120 ..     114     121 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00011
   EF-hand_6  4 eaFklfDkdgdGkidaeElrkalrk 28
                + F+++D+ +  ki+ eE+r ++++
  EPA06518.1 39 KTFDILDTKKLSKITLEEFRTIFQD 63
                68*******************9985 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.6
   EF-hand_6   6 FklfD 10 
                 Fk+fD
  EPA06518.1 116 FKAFD 120
                 99999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       725  (0.0404373); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 2108.56
//
Query:       EPA06519.1  [L=54]
Description: hypothetical protein BG20_I1687 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       231  (0.0128842); expected 358.6 (0.02)
Passed bias filter:                      170  (0.00948185); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 393.82
//
Query:       EPA06520.1  [L=54]
Description: hypothetical protein BG20_I1692 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.01   16.0   1.3      0.013   15.8   1.3    1.0  1  Cor1            Cor1/Xlr/Xmr conserved region
      0.016   14.0   0.0      0.017   14.0   0.0    1.0  1  SAPS            SIT4 phosphatase-associated protein
       0.05   13.6   0.6       0.91    9.6   0.0    2.0  2  Lip_prot_lig_C  Bacterial lipoate protein ligase C-terminus


Domain annotation for each model (and alignments):
>> Cor1  Cor1/Xlr/Xmr conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.8   1.3   2.1e-06     0.013      31      78 ..       4      50 ..       2      52 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.1e-06
        Cor1 31 tqqeerqklkeeysqqfltlfqqwetdvqkvkeqeeklsnlfqqqqkl 78
                ++qe+ qk+++++ ++++ +++++++dv k+++ +++l ++f q q +
  EPA06520.1  4 KRQENAQKFYSDFFKNLIRIYSDFDEDV-KIRQLQNSLKRVFWQNQDF 50
                57899**********************9.689999*******999976 PP

>> SAPS  SIT4 phosphatase-associated protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   2.8e-06     0.017      74     113 ..       4      43 ..       1      50 [. 0.89

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.8e-06
        SAPS  74 eesediqssasdfLkaiItisanatanlqssigpneLtre 113
                 + +e+ q+  sdf+k++I+i+++  ++++  + +n+L r 
  EPA06520.1   4 KRQENAQKFYSDFFKNLIRIYSDFDEDVKIRQLQNSLKRV 43 
                 56788899*****************************986 PP

>> Lip_prot_lig_C  Bacterial lipoate protein ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.2     0.018   1.1e+02      32      39 ..      11      18 ..       8      20 .. 0.84
   2 ?    9.6   0.0   0.00015      0.91      31      57 ..      21      47 ..      19      51 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.018
                    EEEESBSS CS
  Lip_prot_lig_C 32 kiyGDffg 39
                    k+y+Dff+
      EPA06520.1 11 KFYSDFFK 18
                    9******7 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00015
                    EEEEESBSSSSHCHHHHHHHTTSBSSH CS
  Lip_prot_lig_C 31 ikiyGDffgpkdieeleekLigvkyek 57
                    i+iy+Df ++  i +l++ L+ v ++ 
      EPA06520.1 21 IRIYSDFDEDVKIRQLQNSLKRVFWQN 47
                    89******************9876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       765  (0.0426683); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 367.16
//
Query:       EPA06521.1  [L=106]
Description: hypothetical protein BG20_I1688 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.033   14.0   0.1      0.033   14.0   0.1    1.7  2  DUF4187       Domain of unknown function (DUF4187)
      0.067   13.6   9.1       0.11   12.9   9.1    1.3  1  Transp_Tc5_C  Tc5 transposase C-terminal domain
       0.19   11.7   1.4       0.46   10.5   1.4    1.7  1  RHH_3         Ribbon-helix-helix domain


Domain annotation for each model (and alignments):
>> DUF4187  Domain of unknown function (DUF4187)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   5.5e-06     0.033      11      46 ..      31      67 ..      20      68 .. 0.78
   2 ?   -2.0   0.1      0.54   3.2e+03      12      16 ..      83      87 ..      75      98 .. 0.47

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.5e-06
     DUF4187 11 aeerLeklleyLReeylYCfwCgtkY.edeedLeenC 46
                 +  +e  l+y  + +lYCf Cg k+  ++ d  ++C
  EPA06521.1 31 RSRIIESFLSYVSDPHLYCFSCGEKFlVSKADVCSKC 67
                4555788999***************966777777777 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.54
     DUF4187 12 eerLe 16
                +e+ +
  EPA06521.1 83 TEQTS 87
                33334 PP

>> Transp_Tc5_C  Tc5 transposase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   9.1   1.8e-05      0.11      15      51 ..      43      80 ..      34      82 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.8e-05
  Transp_Tc5_C 15 ktPaeycfg.ektsedCkiegCselafikCarCkellC 51
                    P  ycf   ++    k + Cs+++f+kC+ Ck++ C
    EPA06521.1 43 SDPHLYCFScGEKFLVSKADVCSKCSFVKCVKCKNCSC 80
                  568889998544555566677***************99 PP

>> RHH_3  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.4   7.8e-05      0.46       2      33 ..       5      36 ..       4      40 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 7.8e-05
       RHH_3  2 ktrttvsidpelaekL.kaLSekTrIprSklld 33
                k+++t++id+e ++k  k+LSek  IprS++++
  EPA06521.1  5 KVKVTIAIDEEVLKKSeKNLSEK-NIPRSRIIE 36
                99*********99985389***9.8******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1074  (0.059903); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 768.76
//
Query:       EPA06522.1  [L=117]
Description: 6-pyruvoyl tetrahydropterin synthase/QueD family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-25   88.5   0.0    3.6e-25   88.3   0.0    1.0  1  PTPS      6-pyruvoyl tetrahydropterin synthase
  ------ inclusion threshold ------
      0.065   13.0   0.3      0.094   12.5   0.3    1.4  1  DUF2326   Uncharacterised protein conserved in bacteria (DUF2


Domain annotation for each model (and alignments):
>> PTPS  6-pyruvoyl tetrahydropterin synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.3   0.0     4e-29   3.6e-25       3     121 ..       6     116 ..       4     117 .] 0.94

  Alignments for each domain:
  == domain 1  score: 88.3 bits;  conditional E-value: 4e-29
                 EEEEEEEEEE--TTTTGGGGSTEEEEEEEEEEEEEC-....STCTTBSS-HHHHHHHHHHHHHCTTTEECCCC-CCHHCCS.--HHHHHHHHHHHHHHH CS
        PTPS   3 skefeFdaaHrlrkhegkcrnlHGHnykvevtvegee....ldetgmvvdfgelkealkeileelDhkflnaddpeleellspTaEnlaklifeelker 97 
                  +efe+d +H+l++h+ kc+++HGH+ k++v+++g+     + +++m++df+++k+   +++++lDh++ln   +++e    pT+En+ ++i+e+l+++
  EPA06522.1   6 GVEFEIDFSHVLKGHP-KCGQMHGHTSKIQVEIQGDIskgsTYQDNMIMDFADMKKQCWQVISQLDHNHLN---NMFEY---PTSENITSWIYENLESK 97 
                 579************9.*******************8888889999************************9...78886...***************** PP

                 HGCCCGCEEEEEEEEETTEEEEEE CS
        PTPS  98 lqekevklskvrvwEtpnswaeyr 121
                 +      +s+v+++E  ++w+ ++
  EPA06522.1  98 I-----PISSVKFYEGNGKWCIIE 116
                 *.....9*************9876 PP

>> DUF2326  Uncharacterised protein conserved in bacteria (DUF2326)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.3     1e-05     0.094      22      52 ..      30      60 ..       8      90 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1e-05
     DUF2326 22 rlefeveiqtdestGikymkilcfDlallkl 52
                  +++veiq+d s+G +y   +++D+a +k 
  EPA06522.1 30 TSKIQVEIQGDISKGSTYQDNMIMDFADMKK 60
                679***********************98886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 786.59
//
Query:       EPA06523.1  [L=215]
Description: IMP dehydrogenase / GMP reductase domain protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.2e-79  266.1   8.9    4.9e-79  265.8   8.9    1.0  1  IMPDH         IMP dehydrogenase / GMP reductase domain
    1.7e-06   27.3   4.5    1.8e-06   27.2   3.5    1.5  2  FMN_dh        FMN-dependent dehydrogenase
    3.5e-06   26.6   4.0    5.3e-06   26.0   4.0    1.2  1  NMO           Nitronate monooxygenase
     0.0003   20.1   1.3     0.0003   20.1   1.3    1.8  2  DHO_dh        Dihydroorotate dehydrogenase
      0.001   18.5   0.6     0.0029   17.1   0.1    1.9  2  His_biosynth  Histidine biosynthesis protein
  ------ inclusion threshold ------
      0.013   14.9   0.9      0.024   13.9   0.4    1.5  1  ThiG          Thiazole biosynthesis protein ThiG
      0.028   13.6   3.4      0.041   13.0   3.4    1.2  1  Glu_synthase  Conserved region in glutamate synthase
      0.062   12.5   2.5       0.53    9.4   0.1    2.1  2  NanE          Putative N-acetylmannosamine-6-phosphate epimer


Domain annotation for each model (and alignments):
>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  265.8   8.9   2.2e-82   4.9e-79     140     333 ..      17     215 .]       5     215 .] 0.91

  Alignments for each domain:
  == domain 1  score: 265.8 bits;  conditional E-value: 2.2e-82
                 HHHTTTSEEEEEEE-SHHHHHHHHHTT-SEEEE-SS-STTBHHHHHCSB---HHHHHHHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-SEEEESCC CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       IMPDH 140 kkkveeveviaGnvataegakaLieagadavkvGiGpGsiCttrvvagvGvpqltAvaevaeaakkagvpviaDGGikysgdivkAlaaGadavmlGsl 238
                 kk+++++e+iaGnvata+g+++Li+ag+davkvG+G+GsiC+trv++g GvpqltAv+++a++ k++g+p+i+DGG ++sgd +kAlaaGa++vm+Gs+
  EPA06523.1  17 KKAFPNCELIAGNVATAQGTEDLIKAGVDAVKVGVGSGSICITRVITGSGVPQLTAVMDCAKIGKDYGIPIISDGGTRTSGDATKALAAGASSVMVGSM 115
                 789999********************************************************************************************* PP

                 CTTBTTSSSEEEEETTEEEEEEEETTSHHHH.HH-SS-TTS-.....-...-SS-SBEEEEEE--B-HHHHHHHHHHHHHHHHHHHT-SSHHHHHHH-E CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx...xxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       IMPDH 239 lagteEspgeviliegrkyKeyrGmgslgam.kkgskdryfq...kke...klvpeGvegrvpykgsvkevveqlvgglrsgmgylGaktieelkekak 330
                 l gt+Espg v++ +g+++K yrGm+slga   ++sk+   +   + e    +v+eGve++vpykg+v+++++ql+gg+rsg++y+Ga+ti +++++a+
  EPA06523.1 116 LGGTDESPGTVLTKNGKRFKIYRGMASLGASlGRKSKETG-SislD-EdlnDYVAEGVEAMVPYKGTVTDILKQLTGGVRSGLSYCGAHTIPQMQTNAE 212
                 *******************************533333322.22232.23459*********************************************** PP

                 EEE CS
                 xxx RF
       IMPDH 331 fvr 333
                 f++
  EPA06523.1 213 FIK 215
                 *85 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   3.5     8e-10   1.8e-06     221     301 ..      27     114 ..       5     119 .. 0.78
   2 ?   -2.7   0.0         1   2.3e+03     315     343 ..     181     209 ..     178     211 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 8e-10
                 EEEE-SHHHHHHHHHTTESEEEE--GGG.....TSSTT---HHHCHHHHHHHH......SS-EEEESS--SHHHHHHHHHTT-SEEEESH CS
      FMN_dh 221 vKGvltaedakraveaGvdgivvSNHGG.....RqldgapatidvLpeiveavg..g..rievlvDgGirrGsDvlkAlalGAdavllGR 301
                    v ta+  + +++aGvd++ v    G     R + g  + +  L ++++ ++  +   i+++ DgG r+  D+ kAla GA+ v++G 
  EPA06523.1  27 AGNVATAQGTEDLIKAGVDAVKVGVGSGsicitRVITG--SGVPQLTAVMDCAKigKdyGIPIISDGGTRTSGDATKALAAGASSVMVGS 114
                 55688999999************999996666655544..44555555544444322346****************************95 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1
                 HHHHHHHHHHHHHHHHHHHT-SBHHHHHC CS
      FMN_dh 315 vervleilraelertmallGvksvaeldr 343
                 v+++l+ l+  +++ +  +G++++ +++ 
  EPA06523.1 181 VTDILKQLTGGVRSGLSYCGAHTIPQMQT 209
                 67788888888888899999998888765 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   4.0   2.4e-09   5.3e-06     126     238 ..      12     129 ..       2     135 .. 0.78

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 2.4e-09
         NMO 126 eevvarlkeagvvli.ptissvkearkvearGaDalivqGpeaGGhqGtpevgdkglfaLvpqvldavd.....iPviAaGGiidrrgvaaaLalGAsg 218
                 ++v+ ++ + ++ li + +++++    ++++G Da+ v G  +G    t+ + + g  +L + +  a       iP+i  GG  +  +   aLa+GAs 
  EPA06523.1  12 QFVISKKAFPNCELIaGNVATAQGTEDLIKAGVDAVKV-GVGSGSICITRVITGSGVPQLTAVMDCAKIgkdygIPIISDGGTRTSGDATKALAAGASS 109
                 55666666666655525799**************9866.88887776666666566666555444333366788************************* PP

         NMO 219 vqigtrfLltkesdakdahk 238
                 v +g+ + +t+es+  +++k
  EPA06523.1 110 VMVGSMLGGTDESPGTVLTK 129
                 *************9999887 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.2       0.3   6.6e+02     247     275 ..      25      52 ..       5      74 .. 0.73
   2 !   20.1   1.3   1.3e-07    0.0003     244     276 ..      84     116 ..      62     123 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.3
                 EEEESS--SHHHHHHHHHHTECEEEESHH CS
      DHO_dh 247 iIgvGGiesgeDalekieaGAslvqvyta 275
                 +I+ G + +++   + i+aG  +v+v+ +
  EPA06523.1  25 LIA-GNVATAQGTEDLIKAGVDAVKVGVG 52 
                 453.7888888888889999888887755 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 1.3e-07
                 .S-EEEESS--SHHHHHHHHHHTECEEEESHHH CS
      DHO_dh 244 eipiIgvGGiesgeDalekieaGAslvqvytal 276
                  ipiI+ GG  ++ Da   + aGAs v v++ l
  EPA06523.1  84 GIPIISDGGTRTSGDATKALAAGASSVMVGSML 116
                 4*****************************988 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.39   8.8e+02      80     102 ..      28      50 ..      14      60 .. 0.72
   2 !   17.1   0.1   1.3e-06    0.0029      66     105 ..      77     116 ..      60     174 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.39
                   SSSSSHHHHHHHHHCT-SEEEES CS
  His_biosynth  80 GGIrsledveelleagadkviig 102
                   G + + +  e+l++ag+d v +g
    EPA06523.1  28 GNVATAQGTEDLIKAGVDAVKVG 50 
                   44667777788888888865554 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 1.3e-06
                   HHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHH CS
  His_biosynth  66 eeiaeevfipvqvGGGIrsledveelleagadkviigtaa 105
                   ++i +   ip+  +GG r+  d++++l aga+ v++g++ 
    EPA06523.1  77 AKIGKDYGIPIISDGGTRTSGDATKALAAGASSVMVGSML 116
                   57888899*****************************985 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.4   1.1e-05     0.024     168     209 ..      77     118 ..      56     126 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.1e-05
                 HHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHT CS
        ThiG 168 kiiieeakvPvivDAGigspsdaaqamelGadavllntavae 209
                   i ++  +P+i D G +++ da++a+  Ga++v++ + +  
  EPA06523.1  77 AKIGKDYGIPIISDGGTRTSGDATKALAAGASSVMVGSMLGG 118
                 45677889****************************987655 PP

>> Glu_synthase  Conserved region in glutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   3.4   1.8e-05     0.041     223     304 ..      39     114 ..       6     116 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.8e-05
                   HHHTT-SEEEEE-TT---SS...EEHHHHHHB---HHHHHHHHHHHHHHTT-GGG-EEEEESS--SHHHHHHHHHHT-SEEE-SH CS
  Glu_synthase 223 vakanadiilidGleGGTGA...spkssikhaGlPlelalaevdqtlkeeglrdrvsliadGglktgadvvkalalGAdavgigt 304
                   + ka++d++++     G G      + +i  +G+P ++a+    +  k++g    + +i dGg +t+ d  kala GA +v +g+
    EPA06523.1  39 LIKAGVDAVKV-----GVGSgsiCITRVITGSGVPQLTAVMDCAKIGKDYG----IPIISDGGTRTSGDATKALAAGASSVMVGS 114
                   44555555555.....4443001345678899********99998877776....78*************************997 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.3     0.021        47     144     174 ..      22      51 ..       8      65 .. 0.76
   2 ?    9.4   0.1   0.00024      0.53     142     176 ..      82     116 ..      58     122 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.021
                 T--EEEES---SHHHHHHHHTT--SEEEE-H CS
        NanE 144 glkviaeGrintPekakkaieiGvdavvvGs 174
                 ++++ia G + t +  ++ i+ Gvdav vG 
  EPA06523.1  22 NCELIA-GNVATAQGTEDLIKAGVDAVKVGV 51 
                 455554.899999999999999999999874 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00024
                 HTT--EEEES---SHHHHHHHHTT--SEEEE-HHH CS
        NanE 142 eaglkviaeGrintPekakkaieiGvdavvvGsai 176
                 + g+ +i +G   t   a ka+  G+ +v+vGs +
  EPA06523.1  82 DYGIPIISDGGTRTSGDATKALAAGASSVMVGSML 116
                 67899***************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1399.49
//
Query:       EPA06524.1  [L=238]
Description: hypothetical protein BG20_I2309, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1509.82
//
Query:       EPA06525.1  [L=400]
Description: hypothetical protein BG20_I2310, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.011   16.2   5.9      0.011   16.2   5.9    3.1  3  Fil_haemagg  Haemagluttinin repeat


Domain annotation for each model (and alignments):
>> Fil_haemagg  Haemagluttinin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   3.9    0.0029        53      26      76 ..      64     121 ..      62     122 .. 0.77
   2 ?   16.2   5.9   6.3e-07     0.011       6      77 .]     118     196 ..     115     235 .. 0.83
   3 ?   -2.0   0.0      0.31   5.5e+03      22      39 ..     236     253 ..     199     273 .. 0.60

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0029
  Fil_haemagg  26 nlsaqggltlaaagllnqggilqsggalvlraaqlidng.......lkisaaGdLdnq 76 
                  n+ ++  lt++++ +l++g i+    + v++    i ++       ++i++ G+++++
   EPA06525.1  64 NIESGDSLTINSGITLSTGDIININTDGVVTNMGTIRSDdgeialyGTINNYGTIQLN 121
                  6778899999999999977777666666666666666666999999999999999886 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 6.3e-07
  Fil_haemagg   6 ltvnaaswfalgslfdnrggnlsaqggltlaaagllnqggilqsggalvlraaqlidng........lkisaaGdLdnqG 77 
                   ++na+ +f   +  +n  g   ++ gltl+++g ln+ g+l ++g+++++ ++ i+n+           + aG+++n+G
   EPA06525.1 118 IQLNAG-SFDMQGILNNEVGGEITNTGLTLTVSGELNNFGTLNNKGGVNVSDNSSITNDglietfddHEFAVAGTFTNRG 196
                  566666.6666677777777778999*********************************999999994444444444444 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.31
  Fil_haemagg  22 nrggnlsaqggltlaaag 39 
                    +   +++ +++l  +g
   EPA06525.1 236 LESSEFLNESEIDLGQTG 253
                  333333344444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2776.30
//
Query:       EPA06526.1  [L=131]
Description: hypothetical protein BG20_I2619 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1199  (0.0668749); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 769.29
//
Query:       EPA06527.1  [L=102]
Description: hypothetical protein BG20_I2618, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 620.31
//
Query:       EPA06528.1  [L=44]
Description: hypothetical protein BG20_I2654, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       203  (0.0113224); expected 358.6 (0.02)
Passed bias filter:                      177  (0.00987227); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.49
# Mc/sec: 267.94
//
Query:       EPA06529.1  [L=89]
Description: hypothetical protein BG20_I2652 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-09   38.0   0.0    1.4e-09   37.8   0.0    1.1  1  Diphthamide_syn  Putative diphthamide synthesis protein


Domain annotation for each model (and alignments):
>> Diphthamide_syn  Putative diphthamide synthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.0     8e-14   1.4e-09       2      58 ..      26      83 ..      25      88 .. 0.95

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 8e-14
  Diphthamide_syn  2 Pegllpdsaeiadil.eefgaevvilgDttYGaCcvdevaaehlgadllvHyGhscls 58
                     P+g+lp+ +e a ++ ++fg+  ++l+Dtt+G C+++   a+ lga++   +Gh+  +
       EPA06529.1 26 PDGILPQVQETAMNItKRFGIPAYVLADTTWGTCDLNSNGAKVLGAEIQFNIGHTINT 83
                     9*****************************************************9755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       220  (0.0122706); expected 358.6 (0.02)
Passed bias filter:                      199  (0.0110993); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 615.64
//
Query:       EPA06530.1  [L=171]
Description: TFIIE alpha subunit [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-15   56.6   0.8    1.9e-15   56.6   0.8    1.5  2  TFIIE_alpha      TFIIE alpha subunit
     0.0049   16.4   0.8      0.011   15.3   0.8    1.5  1  TF_Zn_Ribbon     TFIIB zinc-binding
  ------ inclusion threshold ------
      0.051   13.8   0.8      0.081   13.2   0.8    1.4  1  IBR              IBR domain, a half RING-finger domain
      0.071   13.0   0.0       0.14   12.1   0.0    1.5  1  TrmB             Sugar-specific transcriptional regulator Trm
      0.075   13.1   0.4        0.2   11.7   0.0    1.9  2  Sigma70_r3       Sigma-70 region 3
      0.076   13.1   0.7       0.29   11.2   0.2    2.2  2  zf-ACC           Acetyl-coA carboxylase zinc finger domain
       0.08   12.2   0.1       0.13   11.5   0.1    1.3  1  DUF3834          Protein of unknown function (DUF3834)
       0.16   11.4   0.1       0.16   11.4   0.1    1.9  2  zf-ribbon_3      zinc-ribbon domain
       0.18   12.3   0.1       0.18   12.3   0.1    2.3  2  Zn_ribbon_recom  Recombinase zinc beta ribbon domain


Domain annotation for each model (and alignments):
>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.6   0.8   9.6e-19   1.9e-15       9     103 ..      15     109 ..      10     111 .. 0.94
   2 ?   -2.9   0.4       3.1   6.2e+03      83      97 ..     154     168 ..     146     170 .. 0.57

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 9.6e-19
                  HCS-HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEEEECCCHCCCHHHHHHHHHHHHHHHHCCC CS
  TFIIE_alpha   9 kfygeeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywrinyeklvdvvkrkleevvkkLeekleke 103
                   + g+e  +v  +Ll+    t+e++a  +++ +n +rk+L++L+++ l+   r +de k+w  y wr   e++ + +  +++++  +L++  + e
   EPA06530.1  15 MIGGDEYLKVARSLLKAEDATDEEIASSTGLRINMVRKVLYDLFGKSLITGIRVKDERKGWFVYRWRTRREEVEHFIESQKKKITERLQQRFDYE 109
                  45579************************************************************************************998876 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.1
                  CCHHHHHHHHHHHHH CS
  TFIIE_alpha  83 dvvkrkleevvkkLe 97 
                  ++ ++k++e+ k+++
   EPA06530.1 154 KAYSKKIDEIKKDMQ 168
                  455566666666554 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.8   5.3e-06     0.011       6      38 ..     122     153 ..     116     155 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.3e-06
                   TTCEECHEETSTTCEEESSSSBEEEECCCCCCC CS
  TF_Zn_Ribbon   6 CgstnlveDpergelvCtdCGlVlednsidegp 38 
                   C+  +  eD+ +g + C++CG+Vl    +d+ +
    EPA06530.1 122 CNRVT-FEDALEGMFKCPSCGSVLNLKKNDKSK 153
                   66553.89****************877777765 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.8   4.1e-05     0.081      11      47 ..     107     143 ..      90     155 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.1e-05
         IBR  11 slesdpnlkwCprpdCeaiieksegcksvtCskCgfe 47 
                  +e+ +++ +C + dC+++  +++ +++ +C++Cg  
  EPA06530.1 107 DYENYSDFYHCGNEDCNRVTFEDALEGMFKCPSCGSV 143
                 367778899*************************975 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   7.1e-05      0.14      16      57 ..      27      68 ..      22      81 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.1e-05
                HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESS CS
        TrmB 16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekg 57
                 Llk + at +eia+ +g+  + v +vL  L  k l++ ++ 
  EPA06530.1 27 SLLKAEDATDEEIASSTGLRINMVRKVLYDLFGKSLITGIRV 68
                69*****************************99999886665 PP

>> Sigma70_r3  Sigma-70 region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0    0.0001       0.2      20      42 ..      33      55 ..      19      71 .. 0.86
   2 ?   -1.9   0.2       1.8   3.6e+03       7      19 ..      96     108 ..      94     109 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0001
                XXXHHHHHHHHTXXHHHHHHHHH CS
  Sigma70_r3 20 ePtpeEiAeeLglseekVrevle 42
                ++t+eEiA ++gl ++ Vr+vl 
  EPA06530.1 33 DATDEEIASSTGLRINMVRKVLY 55
                89*******************96 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.8
                 HHHHHHHHHHHSS CS
  Sigma70_r3   7 kraqreLeqelgr 19 
                 k+++++L+q++++
  EPA06530.1  96 KKITERLQQRFDY 108
                 789999**99886 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       1.2   2.5e+03       5      17 ..     120     132 ..     120     133 .. 0.83
   2 ?   11.2   0.2   0.00015      0.29       2      11 ..     135     144 ..     135     148 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.2
      zf-ACC   5 psCgemlykkeLe 17 
                 + C+ +++   Le
  EPA06530.1 120 EDCNRVTFEDALE 132
                 5799999998887 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00015
      zf-ACC   2 tKCpsCgeml 11 
                 +KCpsCg++l
  EPA06530.1 135 FKCPSCGSVL 144
                 5*******98 PP

>> DUF3834  Protein of unknown function (DUF3834)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   6.4e-05      0.13     128     174 ..     125     170 ..     112     171 .] 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.4e-05
     DUF3834 128 eafedllkklgvyvpGsCgaavken.eeefidaYeeGIelikedpeea 174
                  +fed l+  g++   sCg   + + +++  +aY++ I+ ik+d +++
  EPA06530.1 125 VTFEDALE--GMFKCPSCGSVLNLKkNDKSKKAYSKKIDEIKKDMQQT 170
                 68999999..666655****99987699999*************9875 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.2      0.96   1.9e+03      21      24 ..     116     119 ..     115     120 .. 0.69
   2 ?   11.4   0.1   7.9e-05      0.16       2      11 ..     134     144 ..     133     151 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.96
  zf-ribbon_3  21 yCGt 24 
                  +CG 
   EPA06530.1 116 HCGN 119
                  7885 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 7.9e-05
  zf-ribbon_3   2 tvrCPnCGa.p 11 
                  + +CP+CG+ +
   EPA06530.1 134 MFKCPSCGSvL 144
                  67899999844 PP

>> Zn_ribbon_recom  Recombinase zinc beta ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   1.4       1.1   2.1e+03      22      32 ..     110     120 ..      73     126 .. 0.72
   2 ?   12.3   0.1   9.2e-05      0.18       2      27 ..     131     156 ..     130     160 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.1
  Zn_ribbon_recom  22 gkrhyYrCsty 32 
                      ++ + Y+C++ 
       EPA06530.1 110 NYSDFYHCGNE 120
                      33367888875 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 9.2e-05
  Zn_ribbon_recom   2 LsGllrCgeCGspmtrrkrkgkrhyY 27 
                      L G+ +C  CGs +  +k+ +++ +Y
       EPA06530.1 131 LEGMFKCPSCGSVLNLKKNDKSKKAY 156
                      88**************9988777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1388  (0.0774165); expected 358.6 (0.02)
Passed bias filter:                      655  (0.036533); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1151.12
//
Query:       EPA06531.1  [L=115]
Description: hypothetical protein BG20_I2253, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.6e-08   32.7   0.0    1.2e-07   32.2   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    1.8e-06   28.6   0.0    2.9e-06   27.9   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    5.5e-06   26.2   0.0    6.1e-06   26.0   0.0    1.0  1  TPMT             Thiopurine S-methyltransferase (TPMT)
    5.7e-06   27.0   0.0    1.4e-05   25.8   0.0    1.6  2  Methyltransf_12  Methyltransferase domain
    3.1e-05   23.8   0.1    3.4e-05   23.7   0.1    1.2  1  Methyltransf_31  Methyltransferase domain
     0.0016   18.3   0.0     0.0019   18.1   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
     0.0023   17.3   0.1     0.0029   17.0   0.1    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
  ------ inclusion threshold ------
      0.059   12.7   0.0      0.069   12.5   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.0   5.5e-11   1.2e-07      51      95 ..       5      51 ..       1      52 [. 0.92

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 5.5e-11
                     ECCCTSS-TT-EEEEEEES-CCC-..CCHHHHHHHHHHHEEEEEEEE CS
  Methyltransf_11 51 daeklpfednsfDlvvssevlhhv..edpekalkeiaRvLkpgGllv 95
                     d+ + +fe++sfD ++ + ++h +  +d+e +l++i+R+Lk++G+++
       EPA06531.1  5 DILNSKFESESFDYILDRGCFHVLsiDDRETYLNQIKRILKKNGIIF 51
                     666779*******************9*******************98 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   1.3e-09   2.9e-06      50      97 .]       1      48 [.       1      48 [. 0.95

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 1.3e-09
                     EEESBCCGBSSSTTTEEEEEEESTGGGSSHHHHHHHHHHHHHHEEEEE CS
  Methyltransf_25 50 fvqgdaedlpfedgsfDlvvssgalhhlsdedlekalkeiarvLkpgG 97
                     f+  d+ + +fe++sfD+++ +g++h+ls +d+e++l++i+r+Lk++G
       EPA06531.1  1 FEIDDILNSKFESESFDYILDRGCFHVLSIDDRETYLNQIKRILKKNG 48
                     567899999*************99**********************99 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   2.7e-09   6.1e-06     116     190 ..      15      91 ..       5     110 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 2.7e-09
                 .EEEEEEESSTTTS-GGGHHHHHHHHHHHEEEEEE..EEEEE---S---..-SS----HHHHHHHHGGTEEEEEEEE CS
        TPMT 116 kfdliydraalvAlppelreryakslaelLkpdgeglLvtldypqaehe..GPPfsvpeaeleallsagfkvaelee 190
                 +fd i dr+ +  l  ++re y ++++++Lk++g ++L  ++ ++ +     +P +  ++e+ +++ + f ++++++
  EPA06531.1  15 SFDYILDRGCFHVLSIDDRETYLNQIKRILKKNGIIFLKCMSKDEKNLPddKGPHKFFKNEIIHYFQNDFDIKKSKD 91 
                 69***************************************99988764444599999************9999876 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   6.2e-09   1.4e-05      60      99 .]       8      50 ..       1      50 [. 0.83
   2 ?   -1.4   0.0       1.9   4.2e+03      75      83 ..      76      87 ..      57     100 .. 0.53

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 6.2e-09
  Methyltransf_12 60 dldgg.ssfDlvvasnvlhhl..kdirevldnirklLkpgGrl 99
                     +++ + +sfD+++  +++h+l  +d++ +l++i++ Lk++G++
       EPA06531.1  8 NSKFEsESFDYILDRGCFHVLsiDDRETYLNQIKRILKKNGII 50
                     3333358**********************************85 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.9
  Methyltransf_12 75 vlhhl...kdir 83
                      +h++    di+
       EPA06531.1 76 IIHYFqndFDIK 87
                     233333333333 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.1   1.5e-08   3.4e-05      58     113 ..       1      56 [.       1     100 [. 0.82

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.5e-08
  Methyltransf_31  58 FeqgdieeleklledekfDlilsnevl..naladpdkileeiervlkpggilliedpr 113
                      Fe+ di + +  +e e+fD+il+++ +    + d + +l++i+r lk++gi+ +  ++
       EPA06531.1   1 FEIDDILNSK--FESESFDYILDRGCFhvLSIDDRETYLNQIKRILKKNGIIFLKCMS 56 
                      5666666655..999*********99988999*******************9987666 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   8.4e-07    0.0019      79     147 ..      12      81 ..       2      88 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 8.4e-07
  Methyltransf_23  79 pqgkfdlIvlrevle..hvpdppellrqiatllkpgGylllseplaslkedrllldwlylvpagrhisffs 147
                      ++++fd+I  r +++  +++d + +l+qi+++lk +G ++l    ++ k++   ++ +  + +++ i++f+
       EPA06531.1  12 ESESFDYILDRGCFHvlSIDDRETYLNQIKRILKKNGIIFLKCMSKDEKNLP-DDKGPHKFFKNEIIHYFQ 81 
                      5679****9999998556779*********************9966532222.233344455556666665 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   1.3e-06    0.0029     125     189 ..      13      76 ..       3      80 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.3e-06
                 ----SEEEEES-GGGTSGGGHHHHHHHHHHHS-TT-EEEEEEEEE--HHHHHCTTCCCHHHHHHT CS
        CMAS 125 dekvdrvvsvgafehvgkenydtffkklkkllkedGllllhtitslhkkelaerglklkfidkei 189
                 +e +d +   g f  +  +  +t+ +++k++lk++G++ l+++ + +k+   ++g + kf ++ei
  EPA06531.1  13 SESFDYILDRGCFHVLSIDDRETYLNQIKRILKKNGIIFLKCMSKDEKNLPDDKG-PHKFFKNEI 76 
                 4699**************************************9877777666555.559998887 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.1e-05     0.069     111     160 ..      10      61 ..       5      87 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.1e-05
                      TTS-T-EEEEE..EES-GGG-S-HHHHHHHHHHHEEEEEEEEEEEE----SH CS
  Ubie_methyltran 111 pfeddsfDvvt..vsfGlrnvtDklkaLkeayrvlkpGGrlvvlefskvelp 160
                      +fe +sfD++     f +  + D+++ L+++ r+lk  G+++   +sk e +
       EPA06531.1  10 KFESESFDYILdrGCFHVLSIDDRETYLNQIKRILKKNGIIFLKCMSKDEKN 61 
                      6889999998522579999********************9987777766544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       692  (0.0385967); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 727.94
//
Query:       EPA06532.1  [L=176]
Description: tRNA 2'-O-methylase domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.8e-49  165.2   0.6    6.4e-49  164.8   0.3    1.3  2  Trm56            tRNA ribose 2'-O-methyltransferase, aTrm56
    0.00056   19.3   0.0    0.00074   18.9   0.0    1.3  1  SPOUT_MTase_2    AF2226-like SPOUT RNA Methylase fused to THU
  ------ inclusion threshold ------
      0.039   14.0   0.2       0.46   10.6   0.1    2.2  2  SSB              Single-strand binding protein family
      0.046   14.3   0.2      0.098   13.3   0.2    1.5  1  HMG_box_2        HMG-box domain
        0.1   12.4   0.0       0.16   11.8   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
       0.13   12.1   0.1        4.5    7.1   0.0    2.2  2  Methyltrn_RNA_4  SAM-dependent RNA methyltransferase
       0.15   12.4   0.0       0.25   11.6   0.0    1.4  1  DUF3085          Protein of unknown function (DUF3085)


Domain annotation for each model (and alignments):
>> Trm56  tRNA ribose 2'-O-methyltransferase, aTrm56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       4.1   1.1e+04      30      44 ..      36      50 ..      27      52 .. 0.51
   2 !  164.8   0.3   2.5e-52   6.4e-49       1     118 [.      54     169 ..      54     170 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 4.1
                E-TTSEEHHHHHHHH CS
       Trm56 30 ltmyGenieevieei 44
                +t    +i++++e+i
  EPA06532.1 36 MTEVNPEIKDTVEKI 50
                333334444444444 PP

  == domain 2  score: 164.8 bits;  conditional E-value: 2.5e-52
                 H-S--EEE.E--HHHHHHC-S...SEEEEE-TTSEEHHHHHHHHHC-SE.EEEEE------TCHHHHSSEEEESSSS---HHHHHHHHHHHHC.--TTT CS
       Trm56   1 wGgefkvevakslkklikefkkeggivvhltmyGenieevieeikkkekdllvvvGaekvprevyeladynvsvgnqPhsevaalaifldrllegkele 99 
                 wGg+f ve+ +++k+++k+ k e+ ++vhltmyGe+i++v e+++k+ k+ll+vvGaekvpre+yeladyn+s+gnqPhse++alai+ldr+++gk+++
  EPA06532.1  54 WGGDFVVEFIDNWKSIVKKKK-EEYKIVHLTMYGESIDDVDEQLRKE-KNLLIVVGAEKVPREIYELADYNISIGNQPHSEISALAITLDRIQKGKQFK 150
                 ******************987.789*******************986.66************************************************* PP

                 ---TT-SSEEE--SSS-EE CS
       Trm56 100 kefedaklkviPsergkkv 118
                 ++f++ak k+iP+++gk+v
  EPA06532.1 151 NNFSGAKRKIIPTKKGKNV 169
                 *****************99 PP

>> SPOUT_MTase_2  AF2226-like SPOUT RNA Methylase fused to THUMP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   2.9e-07   0.00074      86     148 ..      68     125 ..      35     141 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.9e-07
  SPOUT_MTase_2  86 qlvrkrrkkellivtdPeGeeisevkeelaealrkakevvvlvGsReGiPkGlfrfadfvvDl 148
                     +v+k++++  ++ +   Ge+i++v e    +lrk+k++ ++vG+   +P+ ++++ad+ + +
     EPA06532.1  68 SIVKKKKEEYKIVHLTMYGESIDDVDE----QLRKEKNLLIVVGAE-KVPREIYELADYNISI 125
                    456677777788899999999987765....678999*******95.5***********9877 PP

>> SSB  Single-strand binding protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00018      0.46      25      74 ..      55     104 ..      39     115 .. 0.83
   2 ?    1.2   0.0      0.14   3.7e+02      66      76 ..     163     173 ..     152     175 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00018
                 EEEEEEEEEEEEEETTCCEEEEEEEEEEEEEHHHHHHHHHH--TT-EEEE CS
         SSB  25 varftlatnrrfkdqegekdeetewhrvvvfgklaevvaeylkkGslvyv 74 
                   +f++++ +++k+  ++k+ee + +  +++g+  + v e+l+k +++++
  EPA06532.1  55 GGDFVVEFIDNWKSIVKKKKEEYKIVHLTMYGESIDDVDEQLRKEKNLLI 104
                 56899*********99****************************996554 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.14
                 --TT-EEEEEE CS
         SSB  66 lkkGslvyveG 76 
                 +kkG++v+v+G
  EPA06532.1 163 TKKGKNVFVSG 173
                 59********9 PP

>> HMG_box_2  HMG-box domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   3.8e-05     0.098      13      55 ..      34      78 ..      31      79 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.8e-05
                HHHHTTHHHHHHHT--...-SSHHHHTGGGHHHHHHS-HHHHHHHH CS
   HMG_box_2 13 lfvqemipelkrkGnp...viglaevsklcsekWkalseeeKekYe 55
                +f++e  pe+k    +       ++++ +  ++Wk++ ++ Ke+Y+
  EPA06532.1 34 IFMTEVNPEIKDT-VEkinKTWGGDFVVEFIDNWKSIVKKKKEEYK 78
                69**********9.6634455589*********************6 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   6.1e-05      0.16      36     107 ..      22     101 ..      19     104 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.1e-05
  Methyltransf_23  36 llevlrengf.svtgvDlspeaveiaekakkaqkdqfdeqeaae.......pqgkfdlIvlrevlehvpdppellrqiat 107
                      ++ v+r++g+ ++ + + +pe  + +ek+ k     f  +++++       +++ +++++l+++ e+++d+ e lr+ ++
       EPA06532.1  22 VALVARAFGCtKIFMTEVNPEIKDTVEKINKTWGGDFVVEFIDNwksivkkKKEEYKIVHLTMYGESIDDVDEQLRKEKN 101
                      5678899999899999**999999999555555555555544444455555778*****************999987665 PP

>> Methyltrn_RNA_4  SAM-dependent RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0    0.0018       4.5      31     111 ..      22     109 ..      19     116 .. 0.65
   2 ?    4.2   0.0     0.014        35     120     180 ..      90     143 ..      86     145 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0018
                      HHHHHHHTT-SEEEEE---HHHHHHHHHHHHHHHTSGGGGT-S.......SSHHHHTTEEEESSHHHHHHHHHHHHSS--EEEE--SS CS
  Methyltrn_RNA_4  31 iaRsartygvkkyyvvtpleaqrelverilehWtegagaeynp.......dRkealslvkvvesleealeeiekeegkkplvvatsAr 111
                      +a +ar++g +k ++ +   + ++ ve+i + W  ++  e+         ++ke  ++v+++   e++ +  e+ +++k l+++  A+
       EPA06532.1  22 VALVARAFGCTKIFMTEVNPEIKDTVEKINKTWGGDFVVEFIDnwksivkKKKEEYKIVHLTMYGESIDDVDEQLRKEKNLLIVVGAE 109
                      67799****************************9988877765233333345555555555433333322223334445555555555 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.014
                      HHHHHHHHH--S-EEEEE--TT---HHHHTT-SEEB--TTTTSS-----HHHHHHHHHHHH CS
  Methyltrn_RNA_4 120 eelrelleeeekpvlllfGtgwGlaeevlekadyiLepirgaseynHLsvrsAvaiilDRl 180
                      +++ e+l ++ek++l++ G+   + +e+ e ady ++ i   +   H s  sA ai+lDR+
       EPA06532.1  90 DDVDEQL-RKEKNLLIVVGAE-KVPREIYELADYNIS-IGN-Q--PH-SEISALAITLDRI 143
                      5666777.6777777777754.478888888888764.222.2..23.67799******98 PP

>> DUF3085  Protein of unknown function (DUF3085)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   9.9e-05      0.25      29      70 ..      34      74 ..      11      90 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9.9e-05
     DUF3085 29 aYaeecdPktnpedwwevkrqelGgDdgveflda.evlarlls 70
                ++ +e++P++   d  e  +++ GgD +vef+d  +++ +  +
  EPA06532.1 34 IFMTEVNPEIK--DTVEKINKTWGGDFVVEFIDNwKSIVKKKK 74
                56677888887..599*****************9855544433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       721  (0.0402142); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 1041.29
//
Query:       EPA06533.1  [L=373]
Description: GTP-binding protein HflX [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.4e-19   68.2   0.5      3e-18   66.3   0.1    2.3  2  GTP-bdg_N     GTP-binding GTPase N-terminal
    6.7e-18   64.8   0.3    3.9e-17   62.4   0.1    2.2  2  MMR_HSR1      50S ribosome-binding GTPase
    9.8e-16   58.1   3.2    2.3e-15   57.0   3.2    1.7  1  GTP-bdg_M     GTP-binding GTPase Middle Region
    2.1e-09   37.1   0.2    4.2e-09   36.1   0.2    1.5  1  FeoB_N        Ferrous iron transport protein B
    3.8e-06   26.9   5.2     0.0034   17.3   0.2    2.5  2  RsgA_GTPase   RsgA GTPase
    0.00013   21.6   2.7      0.012   15.1   0.4    2.5  2  GTP_EFTU      Elongation factor Tu GTP binding domain
     0.0041   16.6   2.0     0.0083   15.6   2.0    1.6  1  SRPRB         Signal recognition particle receptor beta subun
     0.0087   15.7   4.3        0.8    9.3   0.2    2.4  2  cobW          CobW/HypB/UreG, nucleotide-binding domain
  ------ inclusion threshold ------
       0.01   15.3   4.7      0.056   12.9   4.0    2.4  1  Arf           ADP-ribosylation factor family
      0.012   15.6   1.0       0.04   13.9   0.3    2.2  2  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
      0.017   14.2   0.1      0.034   13.2   0.1    1.5  1  T2SSE         Type II/IV secretion system protein
      0.019   15.2   0.3       0.91    9.8   0.1    3.0  3  Roc           Ras of Complex, Roc, domain of DAPkinase
      0.024   15.2   0.2      0.076   13.5   0.2    2.0  1  ABC_tran      ABC transporter
      0.031   14.0   6.2       0.49   10.1   4.9    3.1  2  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
      0.033   14.2   1.8       0.58   10.2   0.4    2.9  3  Dynamin_N     Dynamin family
      0.066   13.3   1.9        1.1    9.4   0.3    2.8  2  DUF1192       Protein of unknown function (DUF1192)
       0.12   12.3   1.0        0.4   10.6   0.1    2.3  3  MobB          Molybdopterin guanine dinucleotide synthesis pr
       0.14   12.0   0.1       0.14   12.0   0.1    2.6  3  Remorin_C     Remorin, C-terminal region


Domain annotation for each model (and alignments):
>> GTP-bdg_N  GTP-binding GTPase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.3   0.1     3e-21     3e-18       2      88 ..      13      98 ..      12      99 .. 0.96
   2 ?   -2.6   0.0         9     9e+03       4      13 ..     340     349 ..     329     355 .. 0.78

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 3e-21
   GTP-bdg_N  2 esleEleeLaktaglevvgevvqkrekpdpatyiGkGkveeikelveeeeadlvifddeLspsqqrnLekelevkViDRtqLILdIF 88
                + ++E+  L+++ag++v++++ q+    +p++ iG G +e+++e+ e+ + d+++fd+ L+psq  nL + l+ +++DR +LIL+IF
  EPA06533.1 13 DAVNEAIGLCDAAGIQVIHTIKQNF-LKRPKYGIGGGVLEKLEEISEKLKPDIIVFDEILKPSQNYNLASVLHREILDREALILEIF 98
                6789********************8.568********************************************************** PP

  == domain 2  score: -2.6 bits;  conditional E-value: 9
   GTP-bdg_N   4 leEleeLakt 13 
                 + El+eLak+
  EPA06533.1 340 IGELKELAKN 349
                 5688888875 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       1.1   1.1e+03      46      70 ..      17      37 ..       6     113 .. 0.67
   2 !   62.4   0.1   3.9e-20   3.9e-17       2     114 .]     186     305 ..     185     305 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.1
                EEEEEEECGGC.....SSHHHHHHHHHHHH CS
    MMR_HSR1 46 keielvDtpGl.....iegaseekglgkaf 70
                + i l+D +G+     i         +++f
  EPA06533.1 17 EAIGLCDAAGIqvihtI---------KQNF 37
                46789999995332221.........2222 PP

  == domain 2  score: 62.4 bits;  conditional E-value: 3.9e-20
                 EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHC....TSEEEEEEETTTTCSHHHHHH CS
    MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkaflalee....adlillvvdaseeklkpldee 96 
                 + ++G++ +GK+tL+n++tge+ + s+  +tT+ ++++r++++++++ ++Dt+G+i+  +    + +af++  e    +d+i++vvd+s ++l +l+++
  EPA06533.1 186 ISLAGYTSSGKTTLFNKITGETKEQSKSLFTTLSTTTRRFSIDHEPYLIADTVGFIS--KLPAYMIDAFKSTLEelvhTDVIIVVVDIS-DTLFELKKK 281
                 789***************************************************887..44556666666633334449*********9.546667777 PP

                 HHHHHHH......TTSEEEEEEES CS
    MMR_HSR1  97 leellee......akkplilvlnk 114
                 ++++++       +++++i++lnk
  EPA06533.1 282 FASCMRTlselgvEMDKIIFALNK 305
                 777766566677788888999987 PP

>> GTP-bdg_M  GTP-binding GTPase Middle Region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.0   3.2   2.3e-18   2.3e-15       1      79 []     101     178 ..     101     178 .. 0.90

  Alignments for each domain:
  == domain 1  score: 57.0 bits;  conditional E-value: 2.3e-18
                 H--SHHHHHHHHHHHHHHHHHHHCXXXXXXXXX..X..XXXXXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHH.....T CS
   GTP-bdg_M   1 rArtkeaklQVelAqlkyllprLeglgkelsrqgGgigtrGpGetkleldrrlireriaklkkeLekvkkkrelqrkkR 79 
                 rA+++e+klQV+lAql+y++ r  + + +ls +g + g++G G+ +++++ + i++r++++k++Le+  k+rel+r+ R
  EPA06533.1 101 RASSAESKLQVKLAQLRYEMVRA-KEKIRLSSMGEQPGFMGIGKFEIDVYHNDIKHRMQTVKEKLERAGKQRELHRQGR 178
                 9**********************.55555666644456**************************************988 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.2   4.3e-12   4.2e-09       2     154 ..     185     345 ..     184     347 .. 0.78

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 4.3e-12
                 EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SS.SSSSSHHH.HHHHHHHH.CTSSSEEEEEEEGG.GHHHHHH CS
      FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYs.lsayseee.kvardfll.eeepdvvvnvvdat.nlernLy 96 
                 t+ l+G   +Gkttlfn++tg +++ +    +t   ++ +++++++ + i D  G  s l ay ++  k + + l+ ++ + vvv++ d+  +l++++ 
  EPA06533.1 185 TISLAGYTSSGKTTLFNKITGETKEQSKSLFTTLSTTTRRFSIDHEPYLIADTVGFISkLPAYMIDAfKSTLEELVhTDVIIVVVDISDTLfELKKKFA 283
                 799****************************************************85526666666422233333302333356666665347899987 PP

                 HHH.HHHHTTS...SEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBTHHHHHH CS
      FeoB_N  97 Ltl.qllelgv...pvvlalnmideaekkgieidlkkLsekLgvpvvktsakkkegieellk 154
                   +  l elgv   +++ aln++d ++ ++ie  ++ L+ k   + +++sak++++i el++
  EPA06533.1 284 SCMrTLSELGVemdKIIFALNKSDLLSVDEIEEKIELLNLKDYKKRIAVSAKTGSNIGELKE 345
                 65515778986222569**************999999999989999***********99986 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.2   3.5e-06    0.0034      87     161 ..     171     240 ..     141     244 .. 0.78
   2 !   11.2   0.9   0.00026      0.26      17      99 ..     263     349 ..     253     353 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.5e-06
                  HTTHHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT-----S--------------SEEEEEETTTEEEESS-SS CS
  RsgA_GTPase  87 kegleelkellkdktsvlvGqSGvGKStLinallpelelktgevseklgrGkhTTtavellelaegglliDtPGf 161
                  +e +++ +++l  kt+ l+G +  GK+tL n++++e    t+e s++l +   TTt++  ++ +   l++Dt Gf
   EPA06533.1 171 RELHRQGRKRLGFKTISLAGYTSSGKTTLFNKITGE----TKEQSKSLFTTLSTTTRRFSIDHE-PYLIADTVGF 240
                  45555667788889*********************9....777788888888888888777777.78999**998 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00026
                  -EEEEEEESTTTT--HH....HHHHHHHHHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSE.EEE--TTTHTTHHHHHHHCTT CS
  RsgA_GTPase  17 dqllivvslkepelsln....lldrfLvlaeekgiepvivlnKiDlleeeeeleelkeelealgye.vllvsaktkegleelkellkd 99 
                  d +++vv +++  ++l+       r L ++  +  +++ +lnK Dll+ +e +ee  e l+  +y+  ++vsakt++++ elkel k+
   EPA06533.1 263 DVIIVVVDISDTLFELKkkfaSCMRTLSELGVEMDKIIFALNKSDLLSVDE-IEEKIELLNLKDYKkRIAVSAKTGSNIGELKELAKN 349
                  55666666665555443111145677888888888999*************.9999999999999725799***********998765 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.2    0.0068       6.8       6      33 ..     186     213 ..     182     231 .. 0.81
   2 !   15.1   0.4   1.2e-05     0.012      88     188 ..     256     347 ..     215     353 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0068
                 EEEEESTTSSHHHHHHHHHHHTTSSCHH CS
    GTP_EFTU   6 igiighvDhGKtTLtdrLlyktgaiskk 33 
                 i+++g + +GKtTL  +++ +t++ sk+
  EPA06533.1 186 ISLAGYTSSGKTTLFNKITGETKEQSKS 213
                 77888899***********999998874 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 1.2e-05
                 HHHHHT-SEEEEEEETTTB...STHHHHHHHHHHHHTTTE...EEEEEESCGST.HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTB CS
    GTP_EFTU  88 irglrvlDgavlvvdaveG...vepqteevlrlalkegvp...iivfiNKmDrl.kaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkge 179
                  + l  +D+ ++vvd+++     + +    +r ++++gv+   ii+++NK D l     +ei e+++  l       + + +k+      + +Sa++g 
  EPA06533.1 256 LEELVHTDVIIVVVDISDTlfeLKKKFASCMRTLSELGVEmdkIIFALNKSDLLsV---DEIEEKIE-LL-------NLKDYKK-----RIAVSAKTGS 338
                 4457889**********9877789999999*********9999*********9843...44444444.22.......2233333.....3667777777 PP

                 THHHHHHHH CS
    GTP_EFTU 180 gvktlleal 188
                 ++ +l e  
  EPA06533.1 339 NIGELKELA 347
                 666665555 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   2.0   8.3e-06    0.0083       5      92 ..     185     278 ..     183     360 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 8.3e-06
                 EEEEE-STTSSHHHHHHHHHHSS---B---S..S-EEETTG...GGTT-SEEEETT-.GCCSHHHHHHHHHHGG....EEEEEEEEETTS-HHHH CS
       SRPRB   5 avllvGlsdsGKTslftrLttdsvkktvtSq..essaalkvksekgskltliDfPGh.eklrqklleklkakss....lkglvfvvDStidpkev 92 
                 ++ l+G + sGKT+lf+++t ++++++       s+++ ++ s +++   ++D  G   kl   +++ +k   +       ++ vvD +    e+
  EPA06533.1 185 TISLAGYTSSGKTTLFNKITGETKEQSKSLFttLSTTTRRF-SIDHEPYLIADTVGFiSKLPAYMIDAFKSTLEelvhTDVIIVVVDISDTLFEL 278
                 6789***************9886655544332145555555.77777788888888635777777776443322221134466666654444444 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.2    0.0008       0.8       3      25 ..     186     210 ..     184     230 .. 0.80
   2 !    7.7   0.7    0.0024       2.4      85     160 ..     232     316 ..     212     332 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0008
                 EEEEESTTCCHHHHHHHHH..CT-- CS
        cobW   3 tvltGflGsGKTtLlnhll..enra 25 
                 + l+G+  sGKTtL n+++  ++++
  EPA06533.1 186 ISLAGYTSSGKTTLFNKITgeTKEQ 210
                 6799**************9743333 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0024
                 EEEEEECTTTTHHHH.HTT..SHHHHHCCCECEEEEEEETTTH......CCHCCHHHHHHHHHHTSSEEE.EE-HHHHCHC..HH CS
        cobW  85 viliEttGlaePapv.aft..eeelksdltldavvavvDaknl.....eaeeekieekaedqlaaadllv.lnKtDlldeealle 160
                 +++  t+G  +  p  ++   +++l++ +  d++++vvD + +     ++  +  +++ e ++++  ++  lnK Dll+ ++  e
  EPA06533.1 232 YLIADTVGFISKLPAyMIDafKSTLEELVHTDVIIVVVDISDTlfelkKKFASCMRTLSELGVEMDKIIFaLNKSDLLSVDEIEE 316
                 6788889944444443333469999***************998888754444445555555666655543589999999875533 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   4.0   5.6e-05     0.056      19     166 ..     188     342 ..     171     353 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.6e-05
                 EEESTTSSHHHHHHHHHHSSCEE...CSSSSSEEEEEEEETTEEEEEEE.E-SSGGGGGGGGGGCT.......TESEEEEEEETT-CTTHHHHHHHHHH CS
         Arf  19 llGLDnaGKtTilkklkleelvt...tvPTigfnveeleiknlkftvwD.vGGqeklRplWknYfe.......ktdavifvvDsadreRleeakeeLka 106
                 l G  ++GKtT+ +k++ e  ++      T+  ++++ +i +  + + D vG  +kl  +  + f+       +td++i vvD +d+  l e k+++++
  EPA06533.1 188 LAGYTSSGKTTLFNKITGETKEQsksLFTTLSTTTRRFSIDHEPYLIADtVGFISKLPAYMIDAFKstleelvHTDVIIVVVDISDT--LFELKKKFAS 284
                 457888999999999976554442336788999999999988888888845556667666555554111122258*********997..4455555555 PP

                 HCT...SGCCTTSEEEEEEE-TTSTTSS-HHHHHHHTTGGGSS.SSSSEEEEEEBTTTTBTHHH CS
         Arf 107 lle...eeelkevallvlaNKqDlpealseeelrellgleelk.gkrkleiqkcsavkgeglke 166
                  ++   e  ++  +++   NK Dl   ls +e++e+++l +lk  k+++ +   sa +g+++ e
  EPA06533.1 285 CMRtlsELGVEMDKIIFALNKSDL---LSVDEIEEKIELLNLKdYKKRIAV---SAKTGSNIGE 342
                 4440003344455566667****9...577888888888888832344444...4444444443 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       3.7   3.7e+03      22      53 ..      69     101 ..      52     104 .. 0.71
   2 ?   13.9   0.3     4e-05      0.04      57      98 ..     298     345 ..     293     351 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 3.7
  MMR_HSR1_Xtn  22 kilk.eykihnaevliredvtvDdlidviegnr 53 
                   +ilk + +++ a+vl re ++ + li  i ++r
    EPA06533.1  69 EILKpSQNYNLASVLHREILDREALILEIFESR 101
                   555533456668888888888888887776655 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 4e-05
  MMR_HSR1_Xtn  57 pclyvlNKiDlisleeldelare......pnsvviSaekelnldeLke 98 
                   + +++lNK Dl+s +e++e  +       ++ + +Sa+++ n+ eLke
    EPA06533.1 298 KIIFALNKSDLLSVDEIEEKIELlnlkdyKKRIAVSAKTGSNIGELKE 345
                   57899******999999886664566776899**************98 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   3.4e-05     0.034     130     162 ..     184     216 ..     103     222 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.4e-05
       T2SSE 130 glilvsGgTgsGKttllyallkeinksderivt 162
                 ++i ++G T+sGKttl + +  e +++++ + t
  EPA06533.1 184 KTISLAGYTSSGKTTLFNKITGETKEQSKSLFT 216
                 47889******************9999777765 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       1.4   1.4e+03      57      79 ..      18      40 ..       4      46 .. 0.77
   2 ?    9.8   0.1   0.00091      0.91       2      41 ..     186     225 ..     185     237 .. 0.83
   3 ?    1.2   0.0      0.41   4.1e+02      80     119 ..     262     307 ..     250     308 .. 0.65

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.4
                EEEEEEE-SGGCTTTT-HHHHCT CS
         Roc 57 klniWDtaGqerfrslhplylre 79
                 + + D aG + ++++++ +l++
  EPA06533.1 18 AIGLCDAAGIQVIHTIKQNFLKR 40
                4567799***********99976 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00091
                 EEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEEC CS
         Roc   2 vvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkev 41 
                 + l G +++GKt+l+++++ ++ +++++  + ++++t+++
  EPA06533.1 186 ISLAGYTSSGKTTLFNKITGETKEQSKSLFTTLSTTTRRF 225
                 568899*************999999988877777777665 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.41
                 SCEEEEEEE.GHHH....HCHHHHHHHHHHHCS.SS-EEEEEE-TT CS
         Roc  80 aalailvyd.srss....enlkeWlkelkkvag.kspvilvgnkiD 119
                  +++i+v+d s++     +++ + ++ l++ +   +++i+  nk D
  EPA06533.1 262 TDVIIVVVDiSDTLfelkKKFASCMRTLSELGVeMDKIIFALNKSD 307
                 5678888885444312224455677777777551568889999999 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   7.7e-05     0.076      12      42 ..     184     214 ..     182     347 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.7e-05
                 SEEEEEESTTSSHHHHHHHHTTSS--SEEEE CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  12 ekvaivGenGaGKStLlkllagllkpteGei 42 
                 +++ + G + +GK+tL++ ++g++k ++ ++
  EPA06533.1 184 KTISLAGYTSSGKTTLFNKITGETKEQSKSL 214
                 578999*******************998776 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.2   1.2e+03     105     126 ..     154     175 ..     145     187 .. 0.72
   2 ?   10.1   4.9   0.00049      0.49       2     140 ..     184     346 ..     183     349 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.2
   PduV-EutP 105 eenieaveelLksaGaekifev 126
                 ++++++v+e+L+ aG ++  + 
  EPA06533.1 154 KHRMQTVKEKLERAGKQRELHR 175
                 5789999********9876655 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00049
   PduV-EutP   2 kkilliGkvgsGKttLtqalkg..........eelkY.kktqaiefsdevi.DtPGeylenrkly.salivt...saeadvialvqdateeesvfppgf 84 
                 k i l G + sGKttL ++++g           +l+  ++  +i++++ +i Dt G   +   ++  a+++t    + +dvi +v+d++++   + ++f
  EPA06533.1 184 KTISLAGYTSSGKTTLFNKITGetkeqskslfTTLSTtTRRFSIDHEPYLIaDTVGFISKLPAYMiDAFKSTleeLVHTDVIIVVVDISDTLFELKKKF 282
                 678899***************9665555433322222022235777777654888855554444323333331113568******************** PP

   PduV-EutP  85 asvfnk.........eviGiitkidlaedeenieaveelLksaGaekifevsavekegieellky 140
                 as+++          ++i  + k dl  + ++ie   elL+    +k + vsa + ++i el++ 
  EPA06533.1 283 ASCMRTlselgvemdKIIFALNKSDLL-SVDEIEEKIELLNLKDYKKRIAVSAKTGSNIGELKEL 346
                 *99974322222222566667888888.88999999999999999999********999999875 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       6.9   6.9e+03      91     122 ..       7      38 ..       3      67 .. 0.73
   2 ?   10.2   0.4   0.00058      0.58       1      34 [.     186     219 ..     186     227 .. 0.82
   3 ?    2.7   0.2      0.12   1.2e+02      91     150 ..     220     283 ..     207     306 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 6.9
                 EEEEEEETTS-SEEEEE---B-SSSGTTSHHH CS
   Dynamin_N  91 illkilsllvkgltlvDlPGldsvnkrdqelv 122
                 i++ + +  ++ + l D  G++ +++ +q+ +
  EPA06533.1   7 ITYDKEDAVNEAIGLCDAAGIQVIHTIKQNFL 38 
                 66777777777888888888888777776544 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00058
                 EEEEEBTTTTHHHHHHHHHTS--S---SSS---S CS
   Dynamin_N   1 iavvGsqSsGKSSvlnaLlgedilprgpnptTrr 34 
                 i + G +SsGK+++ n+++ge    +++  tT  
  EPA06533.1 186 ISLAGYTSSGKTTLFNKITGETKEQSKSLFTTLS 219
                 567899***************9777777777755 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.12
                 EEEEEEETTS-SEEEEE---B-SSSGTTS....HHHHHHHSTTEEEEEEEETTS-CCC-CHHHH CS
   Dynamin_N  91 illkilsllvkgltlvDlPGldsvnkrdq....elvkeyikkadiilavtsanhdlsnsealfl 150
                 ++++ +s++ + + + D+ G++s     +    + + e + + d+i++v++ +  l + +++f 
  EPA06533.1 220 TTTRRFSIDHEPYLIADTVGFISKLPAYMidafKSTLEELVHTDVIIVVVDISDTLFELKKKFA 283
                 5567778888888899999999998888888888888888899*******99998877766665 PP

>> DUF1192  Protein of unknown function (DUF1192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1      0.24   2.4e+02      25      44 ..     109     128 ..     104     133 .. 0.88
   2 ?    9.4   0.3    0.0011       1.1      18      33 ..     307     322 ..     304     323 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.24
     DUF1192  25 LeerIalLeaEIaRleaaia 44 
                 L+   a+L+ E  R++++i+
  EPA06533.1 109 LQVKLAQLRYEMVRAKEKIR 128
                 77889************986 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0011
     DUF1192  18 slLSveELeerIalLe 33 
                 +lLSv+E+ee I+lL 
  EPA06533.1 307 DLLSVDEIEEKIELLN 322
                 68***********995 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1    0.0004       0.4       2      43 ..     186     228 ..     185     231 .. 0.75
   2 ?   -2.5   0.0       4.4   4.4e+03      71      96 ..     286     311 ..     273     340 .. 0.64
   3 ?   -1.5   0.0       2.2   2.1e+03      19      51 ..     329     365 ..     323     369 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0004
        MobB   2 lgivgksgsGKTtLleklipelkarglrv.gtiKhahhgfdvd 43 
                 ++++g+  sGKTtL +k+  e k++  ++  t+  ++  f++d
  EPA06533.1 186 ISLAGYTSSGKTTLFNKITGETKEQSKSLfTTLSTTTRRFSID 228
                 7899***************999987655425556666666666 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.4
        MobB  71 ikeleeaelsleellarlsevDlvlv 96 
                 ++ l+e  +++++++  l++ Dl+ v
  EPA06533.1 286 MRTLSELGVEMDKIIFALNKSDLLSV 311
                 33346667777777777777777655 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 2.2
        MobB  19 lipelkarglrvgtiKhahhgfd....vdkpgkDsyr 51 
                  i++ ++ g ++g +K  ++++       +  kDs++
  EPA06533.1 329 RIAVSAKTGSNIGELKELAKNIIqsqkSPEYKKDSWK 365
                 5677778888888888877665411113334688887 PP

>> Remorin_C  Remorin, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.2       1.9   1.9e+03      55      77 ..     102     124 ..      94     134 .. 0.52
   2 ?   -1.0   0.3       1.6   1.6e+03      41      54 ..     154     167 ..     149     179 .. 0.59
   3 ?   12.0   0.1   0.00014      0.14      43     105 ..     295     357 ..     280     359 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.9
   Remorin_C  55 rakaleklknklariekkAeekR 77 
                  ++a+ kl+ kla+ + +   ++
  EPA06533.1 102 ASSAESKLQVKLAQLRYEMVRAK 124
                 44444445545444444433333 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.6
   Remorin_C  41 eaelrkleeklEkk 54 
                 +++++ ++eklE+ 
  EPA06533.1 154 KHRMQTVKEKLERA 167
                 55555566666553 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 0.00014
   Remorin_C  43 elrkleeklEkkrakaleklknklariekkAeekRasaeakrreeelktkekankirstgklp 105
                 e++k+   l k    + +++++k++  + k  +kR+++ ak ++++ + ke a++i +++k+p
  EPA06533.1 295 EMDKIIFALNKSDLLSVDEIEEKIELLNLKDYKKRIAVSAKTGSNIGELKELAKNIIQSQKSP 357
                 56666677788888899****************************************999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       978  (0.0545485); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.47
# Mc/sec: 2374.20
//
Query:       EPA06534.1  [L=357]
Description: site-specific recombinase, phage integrase family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-06   27.5   0.1     0.0074   16.1   0.1    2.5  2  Phage_integrase  Phage integrase family


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0   7.4e-05       1.3       4      51 ..     107     152 ..     104     161 .. 0.88
   2 !   16.1   0.1   4.1e-07    0.0074     104     158 ..     216     280 ..     192     294 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 7.4e-05
                      HHHHHHHHHHCCGCHHHHHHHHHHHHHHHHT--HHHHTT-BGGG.EECT CS
  Phage_integrase   4 tedeverllaaleeslkirdklllellyetGlRisEllsLrvkd.ldle 51 
                      t +e++r+l+ +++   i+dk ++ l  + G+R       ++kd + ++
       EPA06534.1 107 TTKEIQRMLDVSND---ITDKVIILLFSSAGFRLESWDYFTWKDvIFFQ 152
                      679***********...**************************944444 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 4.1e-07
                      SB--HHHHHHHHHHHHHHCT-S..........SC--TTHHHHHHHHHHHHHCTSHHHHHHHHT-S CS
  Phage_integrase 104 kplsrqtvrkafkraveeagie..........kpltpHtlRhsfataLleagvdlrvvqkllGHs 158
                      k+l+++ vrk++ ++v   g+           +    H +R+sf t+L +a v+    ++++GH+
       EPA06534.1 216 KRLNHKGVRKRIDKVVHDIGLRptlppgqrrhEVQLDHGFRKSFHTNLRRAKVNYADMEDMMGHR 280
                      6788888888888888888888888888777555567***************************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       791  (0.0441185); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 2199.68
//
Query:       EPA06535.1  [L=105]
Description: hypothetical protein BG20_I2294 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 752.68
//
Query:       EPA06536.1  [L=56]
Description: hypothetical protein BG20_I2295 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      193  (0.0107647); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.50
# Mc/sec: 335.27
//
Query:       EPA06537.1  [L=294]
Description: aspartyl/glutamyl-tRNA amidotransferase subunit B family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-70  238.0   0.0    1.5e-70  237.7   0.0    1.0  1  GatB_N    GatB/GatE catalytic domain


Domain annotation for each model (and alignments):
>> GatB_N  GatB/GatE catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  237.7   0.0   8.3e-75   1.5e-70      48     270 ..       1     231 [.       1     234 [. 0.93

  Alignments for each domain:
  == domain 1  score: 237.7 bits;  conditional E-value: 8.3e-75
                 EEHHHHHHHHHHHHHTTEEE-SEE-EEEEE-TCTTCTTSEEEEESS....S.SEEEEEEEE.TEEEEEEEEEEEE---EEEE....EETTEEEEETTST CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxx RF
      GatB_N  48 lnkeavelaikaalalnceiaeeskfdRKnyfypdlpkgyQitqke....eplakeGslel.ekkvrierihlEeDaaksvh....eekeeslvdlnRa 137
                 +n++ave+a  +a+alnc+  e++ f RKnyfypdlpk++Qitq +    +++   G l + +kk+ri+ri+lEeD ++ ++    e++  +lvd+nRa
  EPA06537.1   1 MNQKAVEKATLIAMALNCSTPEKIVFFRKNYFYPDLPKNFQITQLNiygdTSVGGAGVLMVgDKKIRITRIQLEEDPGRLIYegssEKNLITLVDYNRA 99 
                 69******************************************65333356667777777999*****************97765566689******* PP

                 T-EEEEEEE-STB-SHHHHHHHHHHHHHHHHHHTSB--SGGGTTEEEEEEEEECTSETTSSS.--EEEEEE-SHHHHHHHHHHHHHHHHHHH....... CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....... RF
      GatB_N 138 GvpLiEivtepdlrspeearavveklrellralgvsdgnmeeGslRcDvNvSvreeekgeeegtrvEiKnlnslksiekaieyeierqiell....... 229
                 G+pL+Eivtepd+++p+e+r++++ l +ll+ l+vs+ ++ eG++R+D+NvS++        g++vEiKn+ s++ +eka+++ei+rq +l        
  EPA06537.1 100 GTPLVEIVTEPDFENPKEVREFLNILSNLLENLDVSEPSL-EGAMRADANVSIEG-------GNKVEIKNIGSFHDLEKAVHFEITRQQSLHsrdipiv 190
                 ****************************************.7************4.......49*********************************** PP

                 -EEEEEETTTTEEEEECC----...-EEE-TTS--EE--HH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
      GatB_N 230 qeTrkfdedkgetvslRskeeaedYryfpepdlppleisee 270
                 qeTr++d++++ t+s Rskee  dYryf e d+p + i+ +
  EPA06537.1 191 QETRHWDDKRKITISSRSKEEDLDYRYFLEGDIPAIIIEYK 231
                 ************************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2096.09
//
Query:       EPA06538.1  [L=69]
Description: hypothetical protein BG20_I1144 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
        0.1   12.6   0.0       0.13   12.3   0.0    1.2  1  Sulfolobus_pRN  Sulfolobus plasmid regulatory protein


Domain annotation for each model (and alignments):
>> Sulfolobus_pRN  Sulfolobus plasmid regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   7.3e-06      0.13       4      35 ..       3      34 ..       1      41 [. 0.92

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.3e-06
  Sulfolobus_pRN  4 ltlsekillilsrrcatleeleektGiekeel 35
                    lt+ eki+ i+s++ a     +e+  ++k++ 
      EPA06538.1  3 LTNKEKIIAIISNGIAVYSLYQERGTLPKNTS 34
                    89***************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 451.17
//
Query:       EPA06539.1  [L=83]
Description: hypothetical protein BG20_I1147 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.6e-22   79.3   0.0    2.8e-22   79.2   0.0    1.0  1  tRNA-synt_2   tRNA synthetases class II (D, K and N)
     0.0089   15.5   0.0     0.0089   15.5   0.0    1.2  1  tRNA-synt_2d  tRNA synthetases class II core domain (F)
  ------ inclusion threshold ------
      0.061   12.6   0.0      0.071   12.4   0.0    1.1  1  tRNA-synt_2e  Glycyl-tRNA synthetase alpha subunit


Domain annotation for each model (and alignments):
>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.2   0.0   4.7e-26   2.8e-22     237     313 ..       4      77 ..       1      78 [. 0.96

  Alignments for each domain:
  == domain 1  score: 79.2 bits;  conditional E-value: 4.7e-26
                  TEEEEEEEEB--SHHHHHHHHHHCCHHSSSGGGGHHHHHHHHCT--SEEEEEEEHHHHHHHHCT-SSGGGCSSS-XX CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  tRNA-synt_2 237 gvElvgGslRiedpeeleeklkskgldeeaeekfswylealeyGapphgGlglGldRlvmlllgsesIrdviaFPkl 313
                  ++El +Gs+Rie+++elee++k+kg++    + f+  l a++yG+pph+G+g+Gl+Rl+m l+g+e+Irdv+++P+ 
   EPA06539.1   4 DLELSSGSTRIEKRHELEERMKNKGMK---IDAFEYHLGAFDYGVPPHAGCGIGLERLIMALTGTENIRDVTFYPRD 77 
                  56*************************...*********************************************95 PP

>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.5e-06    0.0089     212     239 ..      49      78 ..      18      82 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.5e-06
                   EEEEEEHHHHHHHHHT-SSGHH..HHTT.H CS
  tRNA-synt_2d 212 fafGlGveRlamlkygieDiRe..lvendl 239
                   ++ G+G+eRl m  +g e+iR+  ++ +d+
    EPA06539.1  49 AGCGIGLERLIMALTGTENIRDvtFYPRDV 78 
                   568******************822444455 PP

>> tRNA-synt_2e  Glycyl-tRNA synthetase alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.2e-05     0.071     130     178 ..      27      74 ..      20      80 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.2e-05
                   TTCEEEEEEEEEEETTEE-SS--EEEEEEHHHHHHHHCT-SSGGG-ECC CS
  tRNA-synt_2e 130 dGmeitqftYfqqvgglelkpvsveityGleRlamylqevdnvydlewn 178
                    Gm i  f Y   +  + +    +    GleRl m l +++n+ d+++ 
    EPA06539.1  27 KGMKIDAFEYHLGAFDYGVP-PHAGCGIGLERLIMALTGTENIRDVTFY 74 
                   68999999996544444444.4566899******************984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 628.89
//
Query:       EPA06540.1  [L=47]
Description: hypothetical protein BG20_I1140 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.29s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 313.00
//
Query:       EPA06541.1  [L=107]
Description: hypothetical protein BG20_I1160 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.051   13.4   0.1      0.083   12.7   0.1    1.3  1  IF2_N     Translation initiation factor IF-2, N-terminal regi


Domain annotation for each model (and alignments):
>> IF2_N  Translation initiation factor IF-2, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   4.7e-06     0.083      28      52 ..      69      92 ..      62      94 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.7e-06
       IF2_N 28 lGievkshsssLDeetaeliaeefg 52
                 Gi+ k++ +++++e++e+++++f+
  EPA06541.1 69 NGIS-KTIVQGVTKEQKEILVKAFQ 92
                6***.*****************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 714.39
//
Query:       EPA06542.1  [L=64]
Description: hypothetical protein BG20_I1143 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-22   79.1   0.0    2.8e-22   78.9   0.0    1.0  1  DUF1246   Protein of unknown function (DUF1246)


Domain annotation for each model (and alignments):
>> DUF1246  Protein of unknown function (DUF1246)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.9   0.0   1.6e-26   2.8e-22       1      58 [.       4      61 ..       4      63 .. 0.97

  Alignments for each domain:
  == domain 1  score: 78.9 bits;  conditional E-value: 1.6e-26
                EEEESSTTHHHHHHHHHHTT--EEEEC-CCCHHHHHTTTT-SEEEE.S.S..TTSS-- CS
     DUF1246  1 iatlaSHsalqilkgAkkegfrtlavcekgreklYekfkvidevivldkfkdilkeev 58
                iatl+SH+alq+lkgAk+eg++t++vcek+rek+Y++f++ide+i++++f+++l++++
  EPA06542.1  4 IATLGSHCALQVLKGAKDEGLKTILVCEKKREKIYRRFPFIDELILVNSFSEVLEKNI 61
                89****************************************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 413.20
//
Query:       EPA06543.1  [L=407]
Description: hypothetical protein TIGR00300 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.1e-35  119.6   0.2    1.5e-34  118.4   0.2    1.7  1  Saccharop_dh_N  LOR/SDH bifunctional enzyme conserved region
    0.00055   19.7   1.0      0.019   14.7   0.1    2.3  2  TPP_enzyme_M    Thiamine pyrophosphate enzyme, central domain
  ------ inclusion threshold ------
      0.014   14.7   1.3       0.18   11.0   0.2    2.6  3  DS              Deoxyhypusine synthase
      0.067   12.7   0.2       0.27   10.7   0.0    2.0  3  Citrate_bind    ATP citrate lyase citrate-binding


Domain annotation for each model (and alignments):
>> Saccharop_dh_N  LOR/SDH bifunctional enzyme conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.4   0.2   3.3e-38   1.5e-34       1      99 [.       5     103 ..       5     104 .. 0.98

  Alignments for each domain:
  == domain 1  score: 118.4 bits;  conditional E-value: 3.3e-38
                     EEEEEEEEXXTTSSHHHHHHHHHHHTTXEEEEEEEEXXSSTTSXEEEEEEEEESSHHHHHHHHHHHHHHHHHSCCCCEEEECESSCTTB--TTB- CS
  Saccharop_dh_N   1 sreveleGhliDsgilnkvldlileaggsfevlefevGkkkkdtSyaelevsaedeevLeeileeltelgaelveeedvklekaekdgvlpedFY 95 
                     s+e+e++GhliDs il+k++d+i++++g+f+v+e+++Gkkkkd+Sya+l+++++++++L+eile++ + ga ++ ++ ++l+ka+kd+v+p+dFY
      EPA06543.1   5 SQEIEVSGHLIDSSILTKIFDKIMDLHGEFQVEEINIGKKKKDPSYARLSITGKNQKHLDEILETVYREGAVSKIQKGISLKKAPKDMVMPDDFY 99 
                     589***********************************************************************99******************* PP

                     ---S CS
  Saccharop_dh_N  96 sttn 99 
                     sttn
      EPA06543.1 100 STTN 103
                     ***9 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1     0.011        50       3      37 ..     188     226 ..     186     263 .. 0.76
   2 !   14.7   0.1   4.3e-06     0.019      68     134 ..     329     396 ..     309     399 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.011
                   HHHHHHHH-S....SEEEEE-CHHCHTTGHHHHHHHHHH CS
  TPP_enzyme_M   3 kaaellkaak....rpvilvGggvarsgaseelrelaek 37 
                   k+ae + + k    ++vi+ G  +   ga+++++el++ 
    EPA06543.1 188 KVAEDIYKTKksggKIVIVGGPAIVHTGAADAVAELIKL 226
                   566666666644447799999999999********9975 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 4.3e-06
                   CHHHHHHHHH-SEEEEES-SSSTCCCTTTTTTTTTT-.EEEEEESSCCCCTTCC....--SEEEECTHHHHH CS
  TPP_enzyme_M  68 skaanealeeaDlvlalGarfddirttgsepefapea.kiihididpaeigkny....qvdlaivgdvketl 134
                   +k+ +++l++a  v+++ + ++ i t++      p + k+i idi++ ++ k      + +l+iv dv+++l
    EPA06543.1 329 QKEYKKILKDANMVIMISTMLHSIATGNML----PANvKVIVIDINQPTVTKLMdrgtWQALGIVTDVGAFL 396
                   6778899****************8776543....44559********99888874444588*******9998 PP

>> DS  Deoxyhypusine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.2   4.1e-05      0.18      28      99 ..     197     266 ..     165     276 .. 0.80
   2 ?    1.1   0.0     0.042   1.9e+02     149     167 ..     292     310 ..     278     346 .. 0.73
   3 ?   -1.2   0.0      0.21   9.3e+02      15      53 ..     324     368 ..     321     374 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.1e-05
          DS  28 kdekctiflgltsnlissGlreiiadlvkeklvdvivtTaggieeDlikalgkktylgdfelddeeLrekgi 99 
                 k++  +i++    +++ +G  + +a+l+k +++d + +  +   +D+  a+   t lg ++++d++L  +g 
  EPA06543.1 197 KKSGGKIVIVGGPAIVHTGAADAVAELIKLGYIDGVLAGNALAVHDIEYATLG-TSLG-MNVHDATLAYRGH 266
                 445556666667789********************************999988.8998.7899999987775 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.042
          DS 149 eeSilywAykndipvfcpa 167
                 +++i+y++ kn+ip    +
  EPA06543.1 292 TRGIMYQCVKNKIPFVLAG 310
                 589***********65554 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.21
          DS  15 slgeaidilnkmrkdekctiflgl......tsnlissGlreiiad 53 
                 +++ a ++++k+ kd ++ i+++       t+n+ ++ ++ i+ d
  EPA06543.1 324 DVAVAQKEYKKILKDANMVIMISTmlhsiaTGNMLPANVKVIVID 368
                 567778888888888888887764333333788888877777665 PP

>> Citrate_bind  ATP citrate lyase citrate-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   5.9e-05      0.27      66     116 ..     175     225 ..     161     228 .. 0.84
   2 ?   -3.2   0.0       1.1   4.9e+03      94     118 ..     275     299 ..     264     310 .. 0.74
   3 ?   -2.4   0.0      0.63   2.8e+03     109     136 ..     320     347 ..     300     364 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 5.9e-05
  Citrate_bind  66 GapseeqtyeyaktildlmtrekrpdgkvliiGggianftnvaatfkgiir 116
                    + se+ t + ak++ + + ++k+  gk++i+Gg  +  t  a++++ +i+
    EPA06543.1 175 SSSSERPTQHIAKKVAEDIYKTKKSGGKIVIVGGPAIVHTGAADAVAELIK 225
                   34567889****************************999999998887775 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.1
  Citrate_bind  94 vliiGggianftnvaatfkgiiral 118
                   +++  g+i+n+ + ++  +gi+ ++
    EPA06543.1 275 AVFRAGSIVNMVKSKKLTRGIMYQC 299
                   5566788888888888888888765 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 0.63
  Citrate_bind 109 atfkgiiraleelksklkehkvkiyvrr 136
                   + ++ +  a +e+k+ lk++++ i + +
    EPA06543.1 320 DVITDVAVAQKEYKKILKDANMVIMIST 347
                   5566677788899999999888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       739  (0.0412181); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 2583.03
//
Query:       EPA06544.1  [L=161]
Description: hypothetical protein BG20_I1142 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       824  (0.0459591); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1019.43
//
Query:       EPA06545.1  [L=87]
Description: hypothetical protein BG20_I1152 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.022   15.3   0.1      0.025   15.1   0.1    1.2  1  Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase


Domain annotation for each model (and alignments):
>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.1   1.4e-06     0.025      12      60 ..       9      57 ..       5      79 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.4e-06
                HHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECS CS
   Pyr_redox 12 lElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievlln 60
                +E+ ++la+  + V    +++   r+lDe++++il+e+ ++n ++v ++
  EPA06545.1  9 IEFIKILANSDSTVLQAGMNEATKRKLDEQIGSILREYYKENTMNVKTG 57
                688888888888888888888889******************6666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 545.22
//
Query:       EPA06546.1  [L=271]
Description: putative 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-74  249.6   0.1    1.9e-74  249.3   0.1    1.1  1  DUF1297   Domain of unknown function (DUF1297)
      5e-14   52.3   0.0    9.8e-14   51.4   0.0    1.5  1  DUF1246   Protein of unknown function (DUF1246)


Domain annotation for each model (and alignments):
>> DUF1297  Domain of unknown function (DUF1297)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  249.3   0.1   2.1e-78   1.9e-74       1     188 []      86     271 .]      86     271 .] 0.98

  Alignments for each domain:
  == domain 1  score: 249.3 bits;  conditional E-value: 2.1e-78
                 HHHHHHHHHHCTTSSSHHHHCCEEEEE---SEEEEEEEEEETTTTEEEEEEEEEEEEEECCCHCCS-HHHHHCCT----EEEEEEEEEEE-GGGHHHHH CS
     DUF1297   1 efeekleellekglieeedlkkasieeyvvGanfnlnyfysplkeevellgidrRyesnldglvrlpakeqlelevepeyvvvGnipvvlREsllekvf 99 
                 ++++k e+l+ +g+++  + ++ +i+ey +G+ ++l++fysplkee+e++g d+R+es+++g+ r+p+++ql+ ++ p+++v+Gn p++lREsll++v+
  EPA06546.1  86 DYNKKREQLITQGILS--KDESLYIQEYAAGVLAYLQFFYSPLKEELEFFGADQRHESDIEGMARIPSEQQLKSNKVPSFNVIGNSPIILRESLLDEVY 182
                 89*************4..45679**************************************************************************** PP

                 HHHHHHHHHHHHHSTT---EEEEEEEEE-TTS-EEEEEEESSB-GGGGGGTT--CCHHHTTSS---HHHHHHHHHHHHHHCT-GGGCEE CS
     DUF1297 100 elgekfveaakklvppGiiGpFcLqsvvtkdlelvvfdvsaRivggtnvymegspyskllfgeplsmGrrialEikeaiekdrleeivt 188
                 ++ge+fveaak++v+pG++GpFc+++v++++++++ f++saRiv+gtn+ym+gspy  llf+ep+smG+ria+Eik+a e+++l++i+t
  EPA06546.1 183 TMGENFVEAAKRIVSPGMNGPFCIEGVYDENAKFTSFEFSARIVAGTNIYMDGSPYYSLLFNEPMSMGKRIAREIKTAKETNQLDKITT 271
                 ***************************************************************************************98 PP

>> DUF1246  Protein of unknown function (DUF1246)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.4   0.0   1.1e-17   9.8e-14      69     120 ..       2      53 ..       1      55 [. 0.97

  Alignments for each domain:
  == domain 1  score: 51.4 bits;  conditional E-value: 1.1e-17
                 E--BTTHHHHC-HHHHHC-SS-EES-TTHHHHHCSHHHHHHHHHHTT-BB-- CS
     DUF1246  69 lvPhgsfveYvgiekieelkvpifGnrkllrwEerrekkrkyLekAgiriPk 120
                 l+Phg++++ ++ e+ie++k+pifGn+ +lrwE++r +k+k++++A++++Pk
  EPA06546.1   2 LIPHGTLIAQMSSEQIESIKTPIFGNKWILRWESDRIMKEKLMREAKLPVPK 53 
                 8**************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1677.07
//
Query:       EPA06547.1  [L=216]
Description: hypothetical protein BG20_I1156 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-09   38.0   0.2    1.8e-09   38.0   0.2    2.3  2  Arc_PepC_II    Archaeal Peptidase A24 C-terminus Type II
    7.1e-06   26.4   7.9    1.3e-05   25.5   7.9    1.5  1  Peptidase_A24  Type IV leader peptidase family


Domain annotation for each model (and alignments):
>> Arc_PepC_II  Archaeal Peptidase A24 C-terminus Type II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   1.1       1.8   1.6e+04      74      78 ..      56      60 ..      42      62 .. 0.52
   2 !   38.0   0.2     2e-13   1.8e-09      47      92 .]     150     209 ..     100     209 .. 0.71

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.8
  Arc_PepC_II 74 Pflip 78
                 Pf+i+
   EPA06547.1 56 PFVIF 60
                 45544 PP

  == domain 2  score: 38.0 bits;  conditional E-value: 2e-13
  Arc_PepC_II  47 d.............eelrkelkkykkkglieet.vWvtygvPflipitaGfiialvlGDl 92 
                                ++++ ++++ ++++  ++   W+t+g+P+l++it Gfii l++GD+
   EPA06547.1 150 PkfcfsiektvkgkKKINLKIQHAENQNYCSKPnTWITPGIPYLLLITGGFIIQLMYGDI 209
                  2444444444446588889999999999888766*************************7 PP

>> Peptidase_A24  Type IV leader peptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   7.9   1.4e-09   1.3e-05       3      92 ..       2      95 ..       1     118 [. 0.72

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1.4e-09
  Peptidase_A24  3 lltillvlsviDldtrtlpdeltlpllllgvlfaqllllglpnlaqavlgalvgalvlllislvdeqamGgGDvklaavlgaflgwerl.......l 92
                   +lt+l+++s++D+ +r++ d+ ++ +   g+l+   + l    +   v  ++++ +  ++i++++++ +Gg+D+  +++l+++ ++ +        +
     EPA06547.1  2 ALTMLIIGSIVDIWKREIHDYYWIGFGGAGFLLI--F-LDSDIIPHLVNIGIALIIAPFVIFIWRLGLFGGADAFALIALAVIAPMTTFsenpstpF 95
                   589**********************888888876..2.3333344444333444444444477*********************9988777777752 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 1235.08
//
Query:       EPA06548.1  [L=113]
Description: hypothetical protein BG20_I1136, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.5e-05   23.3   0.1    7.5e-05   22.5   0.1    1.4  1  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0001   22.1   0.2    0.00018   21.4   0.2    1.5  1  HTH_11          HTH domain
    0.00032   20.7   0.0    0.00047   20.2   0.0    1.2  1  HTH_20          Helix-turn-helix domain
    0.00043   20.1   0.1    0.00083   19.2   0.1    1.5  1  HTH_5           Bacterial regulatory protein, arsR family
     0.0008   19.4   0.1     0.0017   18.4   0.1    1.6  1  HTH_7           Helix-turn-helix domain of resolvase
     0.0011   18.7   0.0     0.0016   18.2   0.0    1.3  1  HTH_IclR        IclR helix-turn-helix domain
     0.0012   18.5   0.0     0.0023   17.7   0.0    1.4  1  HTH_23          Homeodomain-like domain
     0.0018   18.7   0.1     0.0026   18.2   0.1    1.3  1  HTH_40          Helix-turn-helix domain
     0.0025   18.4   1.8     0.0072   16.9   0.4    2.0  2  Mga             Mga helix-turn-helix domain
     0.0042   17.2   0.0     0.0049   17.0   0.0    1.4  1  FUR             Ferric uptake regulator family
     0.0042   16.8   0.1     0.0049   16.6   0.1    1.2  1  DUF4423         Domain of unknown function (DUF4423)
     0.0077   16.1   0.0      0.013   15.4   0.0    1.4  1  MarR_2          MarR family
  ------ inclusion threshold ------
      0.013   15.7   0.2      0.018   15.2   0.2    1.2  1  DUF1492         Protein of unknown function (DUF1492)
      0.019   15.1   0.1      0.031   14.5   0.1    1.4  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.019   14.5   0.0      0.039   13.5   0.0    1.6  1  HTH_24          Winged helix-turn-helix DNA-binding
      0.022   14.8   0.0      0.041   14.0   0.0    1.5  1  HTH_22          HTH domain
      0.027   14.2   0.1      0.048   13.3   0.1    1.5  1  Sigma70_r4_2    Sigma-70, region 4
      0.047   13.7   0.1        0.1   12.6   0.1    1.5  1  HTH_Crp_2       Crp-like helix-turn-helix domain
      0.058   12.4   0.2      0.062   12.3   0.2    1.2  1  TnsD            Tn7-like transposition protein D


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.1     8e-08   7.5e-05      19      54 ..      32      67 ..      26      83 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 8e-08
                HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEE CS
        TrmB 19 klgpatadeiaeelgvprskvYevLrsLedkGlVer 54
                k+++++a++ia el+++ s+vY++L+ Le+  l e+
  EPA06548.1 32 KNESKDATQIADELKISISTVYKTLSTLEELALAEV 67
                8999*************************9888776 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.2   1.9e-07   0.00018      18      43 ..      38      63 ..      25      80 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.9e-07
      HTH_11 18 geeLAeeLnvSrrtvrrdIkaLeelg 43
                + ++A+eL++S +tv++ + +Leel 
  EPA06548.1 38 ATQIADELKISISTVYKTLSTLEELA 63
                789*******************9985 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   4.9e-07   0.00047       3      58 ..      15      69 ..      13      70 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 4.9e-07
                HHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
      HTH_20  3 iaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvr 58
                i+e L++   r++l  +  +e   a+++a++l +s +t+++ L +Lee  L ev r
  EPA06548.1 15 IIESLSSVCTRAVLFSI-KNESKDATQIADELKISISTVYKTLSTLEELALAEVDR 69
                66777774455555555.688999************************98888876 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   8.7e-07   0.00083       7      44 ..      27      64 ..      25      67 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 8.7e-07
                HHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTS CS
       HTH_5  7 ILklLaegelcvcelaeelglsqstvShHLkkLreaGL 44
                +L++  ++++ ++++a+el++s stv   L+ L+e+ L
  EPA06548.1 27 VLFSIKNESKDATQIADELKISISTVYKTLSTLEELAL 64
                688889999*************************9865 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   1.8e-06    0.0017      24      43 ..      38      57 ..      33      59 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.8e-06
                STTTSSSS---SSSS--SS- CS
       HTH_7 24 iskIAkevnisRsTvYRyla 43
                +++IA+e++is sTvY+ l+
  EPA06548.1 38 ATQIADELKISISTVYKTLS 57
                69***************887 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.7e-06    0.0016      21      51 ..      38      68 ..      26      69 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.7e-06
                HHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
    HTH_IclR 21 lselArrtglpkStvhRlLqtLvelGyveqd 51
                 +++A+++ ++ Stv+  L+tL+el + e d
  EPA06548.1 38 ATQIADELKISISTVYKTLSTLEELALAEVD 68
                69**********************9988866 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   2.4e-06    0.0023      21      43 ..      39      61 ..      36      68 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.4e-06
      HTH_23 21 reIAreLgvsrrTvyrwlkryre 43
                ++IA+eL +s +Tvy+ l++ +e
  EPA06548.1 39 TQIADELKISISTVYKTLSTLEE 61
                69***************999755 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   2.8e-06    0.0026      10      68 ..      33      90 ..      24     105 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.8e-06
      HTH_40 10 eeglsieeIAkerglkesTIegHLaelieegeeidlerlvseeeekeIeeaiekvgsek 68
                +e+++  +IA+e +++ sT+++ L  l e     +++r+v ++e k+I+++  ++g+ +
  EPA06548.1 33 NESKDATQIADELKISISTVYKTLSTLEELAL-AEVDRFVISREGKKIKQYRSRIGKVE 90
                78999*********************999976.999*****999999999988777554 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.4   7.6e-06    0.0072      16      57 ..      21      62 ..       5      68 .. 0.79
   2 ?    0.9   0.0      0.72   6.8e+02      49      66 ..      77      94 ..      66     101 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 7.6e-06
                SHHHHHHHHHHHHSEEEHHHHHHHCT--HHHHHHHHHHHHHH CS
         Mga 16 slkyqllkflfeeeevsieelaqelyiSestlkrkikelnkl 57
                s+  + + f +++e+++ +++a+el iS st+++ +  l++l
  EPA06548.1 21 SVCTRAVLFSIKNESKDATQIADELKISISTVYKTLSTLEEL 62
                55556666778*************************999875 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.72
                HHHHHHHHHCHCCT-EEE CS
         Mga 49 rkikelnklLkefdlelt 66
                +kik+ + ++ +++++lt
  EPA06548.1 77 KKIKQYRSRIGKVEITLT 94
                789999999999999983 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   5.2e-06    0.0049      36      57 ..      43      64 ..      10      88 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5.2e-06
                TTTT--HHHHHHHHHHHHHTTS CS
         FUR 36 edpeislaTVYrtLklleeagl 57
                ++ +is++TVY+tL +lee+ l
  EPA06548.1 43 DELKISISTVYKTLSTLEELAL 64
                5679**************9876 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   5.2e-06    0.0049      28      72 ..      26      69 ..       4      89 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.2e-06
     DUF4423 28 e.llplkdfkadpeelakrlrpkisaeevekalefLlklgllkkde 72
                + l ++k++++d  ++a+ l+  is + v k+l++L++l l++ d+
  EPA06548.1 26 AvLFSIKNESKDATQIADELK--ISISTVYKTLSTLEELALAEVDR 69
                43799****************..*****************998775 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.4e-05     0.013       8      52 ..      25      66 ..      23      78 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.4e-05
                HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
      MarR_2  8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                + vL+ + ++      ++++a++l++s s+v ++l  L++  L e
  EPA06548.1 25 RAVLFSIKNESK---DATQIADELKISISTVYKTLSTLEELALAE 66
                579999999998...9************************99987 PP

>> DUF1492  Protein of unknown function (DUF1492)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.2   1.9e-05     0.018      49      93 ..      13      57 ..       3      64 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.9e-05
     DUF1492 49 qrlidklensdsrsvLrmvyidkltvwqvidklnisrstyyrllr 93
                q++i++l+   +r+vL  +  +   + q+ d+l+is st y++l 
  EPA06548.1 13 QKIIESLSSVCTRAVLFSIKNESKDATQIADELKISISTVYKTLS 57
                789**************************************9876 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   3.3e-05     0.031      25      49 ..      38      62 ..      28      69 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.3e-05
                    HHHHHHHHTS-HHHHHHHHHHHHHT CS
  Fe_dep_repress 25 tkdlaerLnvspssVsemlkkLekd 49
                     +++a +L++s s+V ++l+ Le+ 
      EPA06548.1 38 ATQIADELKISISTVYKTLSTLEEL 62
                    589*******************985 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   4.1e-05     0.039      21      43 ..      39      61 ..      31      62 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.1e-05
      HTH_24 21 reLAerlglSpstvnrrlkrLee 43
                +++A++l +S+stv + l  Lee
  EPA06548.1 39 TQIADELKISISTVYKTLSTLEE 61
                79*****************9998 PP

>> HTH_22  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   4.3e-05     0.041      45      62 ..      39      56 ..      28      57 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.3e-05
      HTH_22 45 ekvAekLgiSraTvYryL 62
                 ++A++L+iS  TvY+ L
  EPA06548.1 39 TQIADELKISISTVYKTL 56
                589************987 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   5.1e-05     0.048      16      48 ..      25      57 ..      12      58 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.1e-05
                  HHHHHHHHTS---HHHHHHHHT--HHHHHHHHH CS
  Sigma70_r4_2 16 reifllryleglsykEIAellgisegtVksrls 48
                  r+++  +  e ++  +IA +l+is +tV++ ls
    EPA06548.1 25 RAVLFSIKNESKDATQIADELKISISTVYKTLS 57
                  666666777788889**************9886 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00011       0.1      25      59 ..      39      72 ..      37      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00011
                HHHHHHTTSSHHHHHHHHHHHHHTTSEEETEEEEE CS
   HTH_Crp_2 25 eelAsmlGltretvsrilseLkreglisrgrriri 59
                +++A+ l ++ +tv ++ls L++  l +  r ++i
  EPA06548.1 39 TQIADELKISISTVYKTLSTLEELALAEVDR-FVI 72
                59*********************99998775.665 PP

>> TnsD  Tn7-like transposition protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   6.5e-05     0.062     195     227 ..      32      63 ..       9      94 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.5e-05
        TnsD 195 veeeglslkeiAkelgvdiktVlryakklgllk 227
                 ++ e+++  +iA el+++i+tV++ +++l++l+
  EPA06548.1  32 KN-ESKDATQIADELKISISTVYKTLSTLEELA 63 
                 33.899999******************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       853  (0.0475766); expected 358.6 (0.02)
Passed bias filter:                      576  (0.0321267); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 692.88
//
Query:       EPA06549.1  [L=245]
Description: KaiC protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-59  200.7   0.2    2.5e-59  200.4   0.2    1.0  1  ATPase           KaiC
    4.7e-12   45.3   0.0    6.2e-12   44.9   0.0    1.1  1  GvpD             GvpD gas vesicle protein
    1.6e-05   24.4   0.1    7.5e-05   22.2   0.0    2.1  3  DnaB_C           DnaB-like helicase C terminal domain
    2.7e-05   23.9   0.0      8e-05   22.3   0.0    1.9  1  AAA_25           AAA domain
    0.00076   19.3   0.3      0.002   17.9   0.2    1.8  1  AAA_24           AAA domain
     0.0024   18.4   0.7      0.019   15.5   0.4    2.4  2  AAA_18           AAA domain
     0.0032   17.9   0.0     0.0045   17.4   0.0    1.4  1  AAA_16           AAA ATPase domain
     0.0042   16.6   0.0     0.0087   15.5   0.0    1.5  1  RecA             recA bacterial DNA recombination protein
     0.0045   16.1   0.0     0.0084   15.2   0.0    1.4  1  T2SSE            Type II/IV secretion system protein
     0.0065   16.3   0.0      0.019   14.7   0.0    1.8  2  AAA_11           AAA domain
     0.0069   16.7   0.1      0.017   15.4   0.0    1.9  2  AAA_22           AAA domain
     0.0079   16.1   0.0      0.016   15.2   0.0    1.4  1  ATPase_2         ATPase domain predominantly from Archaea
  ------ inclusion threshold ------
      0.011   15.7   0.0      0.056   13.5   0.0    2.1  3  AAA_14           AAA domain
      0.019   14.7   0.0       0.15   11.8   0.0    2.2  3  IstB_IS21        IstB-like ATP binding protein
      0.021   14.7   0.0      0.038   13.9   0.0    1.4  1  NACHT            NACHT domain
      0.022   14.5   0.0       0.49   10.1   0.0    2.2  2  AAA_30           AAA domain
      0.045   14.1   0.0       0.37   11.1   0.0    2.1  2  AAA_19           AAA domain
      0.051   12.8   0.0       0.08   12.2   0.0    1.3  1  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.052   12.7   0.0       0.13   11.4   0.0    1.6  2  DAP3             Mitochondrial ribosomal death-associated pro
      0.052   13.2   0.0       0.12   12.0   0.0    1.9  2  Terminase_6      Terminase-like family
       0.06   12.2   0.1        5.5    5.7   0.0    2.2  2  PPV_E1_C         Papillomavirus helicase
      0.061   13.5   0.1       0.15   12.2   0.1    1.9  1  AAA_33           AAA domain
      0.097   12.2   0.0       0.28   10.7   0.0    1.6  2  AAA_7            P-loop containing dynein motor region
        0.1   12.5   0.0       0.17   11.8   0.0    1.4  1  Rad17            Rad17 P-loop domain
        0.1   12.6   0.0       0.21   11.6   0.0    1.5  1  AAA_5            AAA domain (dynein-related subfamily)
       0.11   12.1   0.0       0.24   10.9   0.0    1.7  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
       0.13   12.0   0.0       0.37   10.5   0.0    1.8  3  Viral_helicase1  Viral (Superfamily 1) RNA helicase
       0.15   12.3   0.0       0.35   11.1   0.0    1.6  1  Roc              Ras of Complex, Roc, domain of DAPkinase
       0.21   11.8   0.0       0.39   10.9   0.0    1.5  1  AAA_28           AAA domain


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.4   0.2     4e-62   2.5e-59       1     228 [.       8     240 ..       8     242 .. 0.94

  Alignments for each domain:
  == domain 1  score: 200.4 bits;  conditional E-value: 4e-62
      ATPase   1 vktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleeegklaiidasesaeesaee. 98 
                 vktgI+glD i++gG+ ++r+v i+G pG+GKt+f+lqFl +ga++++ep+v+v++ ++ +++++++ks+ wdl++l +++k+ ++da   +++++   
  EPA06549.1   8 VKTGIPGLDSIISGGLRKNRSVVISGPPGSGKTTFGLQFLHSGAKDFEEPCVYVSMSQNISEIKNDCKSFSWDLDDLINKDKILMVDARPFKIQDELIg 106
                 79**************************************************************************************98877644336 PP

      ATPase  99 .......kdkedleelieelaeaikeikakrvviDsitgl.ayeekeavaReilrqlvrvlkklgvTailvsekssseeaaggygveefivdgvivLdl 189
                         ++   e+l++ l + ik+i+akrvviDsit l ++++++  +R+ l+ +++ l+++gvT+i++se     +++ +  +e f+++g+i+L++
  EPA06549.1 107 kddslyrGEEIPFEHLTKLLLSSIKRIEAKRVVIDSITILaMQYADKFYMRQGLQGMIQALENYGVTSIIISEF----TENLEIPIEWFAASGIIQLRH 201
                 68999966677789**************************9999999**************************4....5668899************** PP

      ATPase 190 keieeelvRtleivkmRgtkhskkehpfeIteegikvle 228
                 ++++++++R+l++ kmRg khs+++hp+ I+e+g  +++
  EPA06549.1 202 TRKDDTMERSLQVTKMRGIKHSQQIHPIIIDENGMHIQH 240
                 ***********************************9986 PP

>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.9   0.0     1e-14   6.2e-12      10     203 ..      26     229 ..      15     238 .. 0.75

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 1e-14
        GvpD  10 GktllikGaPGtGktlftlrgldvlrr..esdvlyvstrvddetvseay....fsgeaeldktall...........dllkdpleldldvdvPiekldl 91 
                  ++++i G PG+Gkt+f l++l +  +  e++ +yvs   + + +++       + +  ++k ++l           +l+     l    ++P+e+l  
  EPA06549.1  26 NRSVVISGPPGSGKTTFGLQFLHSGAKdfEEPCVYVSMSQNISEIKNDCksfsWDLDDLINKDKILmvdarpfkiqdELIGKDDSLYRGEEIPFEHLT- 123
                 5799******************9965522689*****9988888887765533333444557888878888766665455444456677789998885. PP

        GvpD  92 esllefvdeiaaiatkliialdswelvyeylaerydsPediktvkndlvvlaresgvrlvlvletaans..rleyiv.dGvvtl.nvkeddrgrlrrdl 186
                 + ll+ ++ i+a  +   + +ds    +  la +y +   ++     ++   ++ gv  ++++e  +n   ++e+++  G++ l + ++d    + r+l
  EPA06549.1 124 KLLLSSIKRIEA--K--RVVIDS----ITILAMQYADKFYMRQGLQGMIQALENYGVTSIIISEFTENLeiPIEWFAaSGIIQLrHTRKD--DTMERSL 212
                 667787775543..3..3567**....788888888877777766777777789**********887642268998537*****766555..4789*** PP

        GvpD 187 rleklrGvrignrlqPf 203
                 ++ k+rG++  ++++P 
  EPA06549.1 213 QVTKMRGIKHSQQIHPI 229
                 *********99999996 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   1.2e-07   7.5e-05       2      61 ..       8      68 ..       7      87 .. 0.89
   2 ?   -1.8   0.0       2.6   1.6e+03      71     107 ..     130     141 ..     111     186 .. 0.59
   3 ?   -1.7   0.0       2.3   1.5e+03     119     136 ..     215     232 ..     190     237 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.2e-07
                BXSSTHHHHHHCT.SBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHH CS
                xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
      DnaB_C  2 lstgfkdLDklts.GlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsae 61
                ++tg   LD+++s Gl+k+  ++i + p+ Gkt++ l++ ++ a++ + p++++s+  + +
  EPA06549.1  8 VKTGIPGLDSIISgGLRKNRSVVISGPPGSGKTTFGLQFLHSGAKDFEEPCVYVSMSQNIS 68
                789999***988637*****************************99999999999976655 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.6
                 HHTXXHHHHHHTTSXHHHHHHHHHHHHHHHHSEEEEE CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
      DnaB_C  71 eaeidskklrtgklkeedweklteaieelseaklfid 107
                  ++i++k++                         +id
  EPA06549.1 130 IKRIEAKRV-------------------------VID 141
                 333333333.........................222 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 2.3
                 HHHHHHHHHTTEEEEEEE CS
                 xxxxxxxxxxxxxxxxxx RF
      DnaB_C 119 skarrlkkekglgliviD 136
                 +k+r +k++++++ i+iD
  EPA06549.1 215 TKMRGIKHSQQIHPIIID 232
                 567778888888888888 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   1.3e-07     8e-05      13      59 ..       6      52 ..       1     180 [. 0.81

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.3e-07
      AAA_25 13 adlaapppprrwlvkgllpagelallaGapgtGKttlaldlalavat 59
                +++++ +p ++ ++ g l+++  +++ G+pg+GKtt+ l+  ++ a+
  EPA06549.1  6 SKVKTGIPGLDSIISGGLRKNRSVVISGPPGSGKTTFGLQFLHSGAK 52
                6678899*********99***********************999885 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.2   3.2e-06     0.002       2      79 ..      26     148 ..      25     171 .. 0.64

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3.2e-06
      AAA_24   2 klkiliyGpsgiGKTtlakelgpkplfidtek.Glksldadkfpdie......swedfldevvel.................................. 59 
                 +++++i Gp+g+GKTt+ +++  +    d+e+  +      ++ +i+      sw d+ d    l                                  
  EPA06549.1  26 NRSVVISGPPGSGKTTFGLQF-LHSGAKDFEEpCVYVSMSQNISEIKndcksfSW-DLDD----Linkdkilmvdarpfkiqdeligkddslyrgeeip 118
                 7899*****************.555555555522222222222222233333322.1222....13333556777777777777777778888888888 PP

      AAA_24  60 ..........aaeladyktlviDtidelee 79 
                           + +  + k +viD+i+ l  
  EPA06549.1 119 fehltklllsSIKRIEAKRVVIDSITILAM 148
                 888888888866666668888888887754 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.4   3.1e-05     0.019       1      94 [.      29     155 ..      29     177 .. 0.58
   2 ?   -0.3   0.0       2.3   1.4e+03      24      80 ..     170     232 ..     160     238 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.1e-05
      AAA_18   1 IlltGtpGvGKttlakeL.skrl.gf.........gvnlrdvakenglllevdpe...aldeskrldedkldklldaleenss................ 69 
                 ++++G+pG+GKtt++     +    f         ++n++++  +   ++++d +     d+ + +++ +  k++d+l + ++                
  EPA06549.1  29 VVISGPPGSGKTTFGLQFlHSGAkDFeepcvyvsmSQNISEIKND-CKSFSWDLDdliNKDKIL-MVDARPFKIQDELIGKDDslyrgeeipfehltkl 125
                 78************8665333322336666777754444333333.222222222222122222.2222234444455544445555666666666666 PP

      AAA_18  70 .....aleegknlvidghlaeleseaakdi 94 
                      ++ e+k +vid++     ++a+k++
  EPA06549.1 126 llssiKRIEAKRVVIDSITILAMQYADKFY 155
                 666667777888888888877777777765 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 2.3
      AAA_18  24 f...gvnlrdvakenglllevdpe....aldeskrldedkldklldaleenssaleegknlvid 80 
                 +   ++++++   + ++ +e++++    +l+ +++ d++ +   +++++++   +++ ++++id
  EPA06549.1 170 YgvtSIIISEFTENLEIPIEWFAAsgiiQLRHTRKDDTMERSLQVTKMRGIKH-SQQIHPIIID 232
                 34456667777777777777777777774444444444444444444444443.5667777777 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   7.2e-06    0.0045      22      66 ..      21      64 ..      15     175 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 7.2e-06
      AAA_16 22 grp...elvllsGesGvGKsslvrellralekdggiflrgkcdqlesa 66
                g+    ++v++sG++G+GK++   ++l++  kd    +++ c+  +++
  EPA06549.1 21 GGLrknRSVVISGPPGSGKTTFGLQFLHSGAKD----FEEPCVYVSMS 64
                44455699**************99999887777....55555555333 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.4e-05    0.0087      33      88 ..       7      62 ..       2      88 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.4e-05
                EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHT.T--EEEEE CS
        RecA 33 tissGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkk.ggvaafid 88
                 + +G  +ld+ +  GGl k r + i Gp  sGktt+ l+ + +  k     ++++ 
  EPA06549.1  7 KVKTGIPGLDSIIS-GGLRKNRSVVISGPPGSGKTTFGLQFLHSGAKDfEEPCVYVS 62
                57788899998886.************************998765554145566665 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.4e-05    0.0084     117     150 ..      14      47 ..       3      67 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.4e-05
       T2SSE 117 kiaevlrkavrerglilvsGgTgsGKttllyall 150
                  ++++++  +r++ ++++sG+ gsGKtt+    l
  EPA06549.1  14 GLDSIISGGLRKNRSVVISGPPGSGKTTFGLQFL 47 
                 577899999999****************966555 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   3.1e-05     0.019      13      42 ..      22      51 ..      15      92 .. 0.78
   2 ?   -1.6   0.0         3   1.9e+03     213     228 ..     222     236 ..     210     240 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.1e-05
      AAA_11 13 alseseitliqGPPGtgKTktivellsqll 42
                 l+++  ++i+GPPG+gKT++ +++l++ +
  EPA06549.1 22 GLRKNRSVVISGPPGSGKTTFGLQFLHSGA 51
                56777789*************999999874 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3
      AAA_11 213 klakkfdvviIDEAaq 228
                 +  +++  +iIDE ++
  EPA06549.1 222 HS-QQIHPIIIDENGM 236
                 33.389999***9876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   2.7e-05     0.017       4      30 ..      25      51 ..      23     180 .. 0.75
   2 ?   -1.1   0.0       3.4   2.1e+03      80      99 ..     214     233 ..     144     234 .. 0.57

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.7e-05
      AAA_22  4 tagilvvtGesGtGKTtllrrlleqld 30
                + +++v+ G++G+GKTt   ++l++  
  EPA06549.1 25 KNRSVVISGPPGSGKTTFGLQFLHSGA 51
                56899************9999998852 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 3.4
      AAA_22  80 ealeqalraravielliiDE 99 
                  +  + +++ + i+ +iiDE
  EPA06549.1 214 VTKMRGIKHSQQIHPIIIDE 233
                 22233333333356677776 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   2.5e-05     0.016      19     161 ..      25     175 ..      12     179 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.5e-05
    ATPase_2  19 pneiyfiYGpegsGKtaLlkeiienl.edkdkyviyyialreesiskldefie...eeeekkklekal............giavpkaeleeilkekskl 101
                 +n+ ++i Gp gsGKt++  +++    +d ++  +y++  +++s+ k d +     + ++  + +  +             + ++k+     l +  + 
  EPA06549.1  25 KNRSVVISGPPGSGKTTFGLQFLHSGaKDFEEPCVYVSMSQNISEIKNDCK-SfswDLDDLINKD--KilmvdarpfkiqDELIGKDDS---LYRGEEI 117
                 46779******************9987999999999999988887666655.2334222222222..2335555544444333333333...3366666 PP

    ATPase_2 102 vfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeLlnliesltkekhlcvv 161
                  f+ +++ll +  k+     ++iD +  l  ++   +++++ + l+ + + ++++ ++ +
  EPA06549.1 118 PFEHLTKLLLSSIKRIEAKRVVIDSITILA-MQYA-DKFYMRQGLQGMIQALENYGVTSI 175
                 777776655444333333344556666666.3333.466665555555555555555555 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   9.1e-05     0.056       2      48 ..      26      73 ..      25     105 .. 0.71
   2 ?   -2.0   0.0       5.5   3.4e+03      51      73 ..     121     143 ..      78     155 .. 0.62
   3 ?   -1.0   0.0       2.8   1.7e+03      33      72 ..     196     233 ..     171     238 .. 0.53

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.1e-05
      AAA_14  2 rkilvitGaRrvGKTtllkqlikell.vkkesilyinldderdkklad 48
                ++ +vi+G+  +GKTt+  q++++     +e ++y+++ ++  + ++d
  EPA06549.1 26 NRSVVISGPPGSGKTTFGLQFLHSGAkDFEEPCVYVSMSQNISEIKND 73
                6789*****************987777557999999998865543333 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 5.5
      AAA_14  51 kllelileklkeekktylflDEi 73 
                 +l +l+l+++k+ + + +++D i
  EPA06549.1 121 HLTKLLLSSIKRIEAKRVVIDSI 143
                 44445555544434444666655 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 2.8
      AAA_14  33 ilyinldderdkkladpe.kllelileklkeekktylflDE 72 
                 i+ +   +++d++++  + + ++ i+ +   ++ + +++DE
  EPA06549.1 196 IIQLRHTRKDDTMERSLQvTKMRGIKHS---QQIHPIIIDE 233
                 4444444444444443321222333332...3445588888 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00024      0.15      45      93 ..      24      73 ..      15     103 .. 0.74
   2 ?   -2.1   0.0       4.3   2.7e+03     111     145 ..     137     177 ..     121     186 .. 0.55
   3 ?   -0.3   0.0       1.2   7.7e+02      89     119 ..     198     236 ..     174     240 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00024
   IstB_IS21 45 ekkenivllGpsGvGKshlaialgveavr.aglsvlfvrvedLveelkra 93
                +k+ ++v+ Gp+G GK+ +   + +++++  +   ++v++++ ++e+k +
  EPA06549.1 24 RKNRSVVISGPPGSGKTTFGLQFLHSGAKdFEEPCVYVSMSQNISEIKND 73
                78899**************9999998887346667888887777666554 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.3
   IstB_IS21 111 llilDdlgllpldqaeaellfe....vie..kryerrsiii 145
                  +++D + +l ++ a++ ++ +    +i+  + y+ +siii
  EPA06549.1 137 RVVIDSITILAMQYADKFYMRQglqgMIQalENYGVTSIII 177
                 45667776666666655444331111332123466666666 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1.2
   IstB_IS21  89 elkrarrdgklaralkrl........lkvdllilDdlgl 119
                 +l+  r+d+ ++r l+          ++++ +i+D+ g+
  EPA06549.1 198 QLRHTRKDDTMERSLQVTkmrgikhsQQIHPIIIDENGM 236
                 567777777777766543001100003445567777665 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   6.1e-05     0.038       1      58 [.      27      85 ..      27      97 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.1e-05
                SCEEEEC-TTTCHHHH.HHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-.....-HCHHH CS
       NACHT  1 rlvilqGeaGsGKTtL.lqklalawaegklpqgafklvFflslrelsrsgna..rsladll 58
                r v++ G++GsGKTt+ lq l++ +++ + p+  + ++   + +e++ ++++    l+dl+
  EPA06549.1 27 RSVVISGPPGSGKTTFgLQFLHSGAKDFEEPC--VYVSMSQNISEIKNDCKSfsWDLDDLI 85
                5699************6777777777777666..467777777777777777666666666 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0    0.0008      0.49      18      34 ..      26      42 ..      19      69 .. 0.87
   2 ?    2.2   0.0       0.2   1.3e+02      71      99 ..     206     236 ..     161     241 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0008
      AAA_30 18 drvavltGpAGtGKtta 34
                +r +v+ Gp+G+GKtt 
  EPA06549.1 26 NRSVVISGPPGSGKTTF 42
                5689***********96 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.2
      AAA_30  71 stiakllkrlk..grarlepg.tllivDEagm 99 
                 +t+++ l+ +k  g  + +++ + +i+DE gm
  EPA06549.1 206 DTMERSLQVTKmrG-IKHSQQiHPIIIDENGM 236
                 45555555555754.333444589*******9 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0    0.0006      0.37       9      26 ..      25      42 ..      17     104 .. 0.86
   2 ?    0.9   0.0      0.83   5.1e+02      68     113 ..     187     236 ..     122     240 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0006
      AAA_19  9 kekvllvtaGpGtGKTrv 26
                k++ +++ ++pG+GKT+ 
  EPA06549.1 25 KNRSVVISGPPGSGKTTF 42
                678899**********96 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.83
      AAA_19  68 e.....atTiHrlalldfddlltealelleeaeeekklqeeellivDEfqd 113
                 +     a+ i +l     dd+++  l++ +  +  k+ q+   +i+DE  +
  EPA06549.1 187 PiewfaASGIIQLRHTRKDDTMERSLQVTK-MRGIKHSQQIHPIIIDENGM 236
                 233333333333333455555544444422.22222222334789999765 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00013      0.08       3      40 ..      28      64 ..      26      88 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
     DUF2075  3 vvlVtGvaGtGKtvvllnllaeleddeeertavylsvN 40
                 v+++G +G+GKt  +l++l+    ++ e+  vy+s +
  EPA06549.1 28 SVVISGPPGSGKTTFGLQFLHSG-AKDFEEPCVYVSMS 64
                589****************9987.44444444444444 PP

>> DAP3  Mitochondrial ribosomal death-associated protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00022      0.13      21      60 ..      24      64 ..      20      82 .. 0.78
   2 ?   -2.1   0.0       2.7   1.7e+03     271     291 ..     183     205 ..     142     219 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00022
                S---EEEEE-SSSSSTTTTHHHHHHHGGGS.--EEEEES-G CS
        DAP3 21 kkvkrlvltGekgsGKSvlLlqalayAlek.gwvvlhvpea 60
                +k+  +v++G +gsGK++  lq l+ ++++ +   + v+  
  EPA06549.1 24 RKNRSVVISGPPGSGKTTFGLQFLHSGAKDfEEPCVYVSMS 64
                688899*******************9987754444555554 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.7
                 GTHHHHHHHHHTT---ST..TSS CS
        DAP3 271 Earslleyyadsgvlqek..vne 291
                  ++  +e++a sg++q +  +++
  EPA06549.1 183 NLEIPIEWFAASGIIQLRhtRKD 205
                 35555788888888876643344 PP

>> Terminase_6  Terminase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0    0.0002      0.12       2      57 ..      31      87 ..      30     204 .. 0.89
   2 ?   -0.4   0.0       1.2   7.3e+02      88      89 ..     156     157 ..     100     233 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0002
                 EEE-SSS-HHHHHHHHHHHHHHSSSS.-EEEEE..ESSHHHHHHHHHHHHHHHHTS-T CS
  Terminase_6  2 ilggrqsGKTfagarellrhalgrgprnqvfls..asktqareeggqfekgigelake 57
                 i g+++sGKT+ g+ +l + a + +  + v++s  +++++++++   f++++  l+ +
   EPA06549.1 31 ISGPPGSGKTTFGLQFLHSGAKDFEE-PCVYVSmsQNISEIKNDCKSFSWDLDDLINK 87
                 789**********************5.*****98899999999988877777666554 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.2
                  SH CS
  Terminase_6  88 ta 89 
                   +
   EPA06549.1 156 MR 157
                  33 PP

>> PPV_E1_C  Papillomavirus helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0    0.0089       5.5     260     283 ..      24      47 ..      14      51 .. 0.83
   2 ?    4.1   0.0     0.027        17     307     336 ..     134     164 ..     125     171 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0089
    PPV_E1_C 260 PkknclvllGppntGkslfamsli 283
                  k  ++v+ Gpp +Gk++f+  ++
  EPA06549.1  24 RKNRSVVISGPPGSGKTTFGLQFL 47 
                 567799*************98776 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.027
    PPV_E1_C 307 eakvallDDatkacwkyiDt.ylrnalDGne 336
                 eak +++D  t   ++y+D+ y+r+ l G  
  EPA06549.1 134 EAKRVVIDSITILAMQYADKfYMRQGLQGMI 164
                 8999***************868*****9975 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00024      0.15       2      20 ..      29      47 ..      29     181 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00024
      AAA_33  2 vllvGlpGsGKstlaerll 20
                v++ G+pGsGK+t+  + l
  EPA06549.1 29 VVISGPPGSGKTTFGLQFL 47
                6789*********976654 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00045      0.28      29      59 ..      22      52 ..      15      73 .. 0.73
   2 ?   -1.8   0.0       3.2     2e+03       9      57 ..     135     184 ..     130     208 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00045
       AAA_7 29 llknkkpvllvGptGtGKtviikdllkkldk 59
                 l+++++v++ Gp G+GKt+   ++l++  k
  EPA06549.1 22 GLRKNRSVVISGPPGSGKTTFGLQFLHSGAK 52
                57899****************9998776653 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.2
       AAA_7   9 fseilVptvdtvrysyllelllknkkpvllvGptGtGKtviikd.llkkl 57 
                  +++++  +  + ++y  + +++++ + ++   +  G t+ii + ++++l
  EPA06549.1 135 AKRVVIDSITILAMQYADKFYMRQGLQGMIQALENYGVTSIIISeFTENL 184
                 56667777777777777777777777777777777777666655566665 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00027      0.17      43     131 ..      24     106 ..      17     151 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00027
       Rad17  43 rkkriLLisGPsGCgkstv.vkvLskelgiklrewlnpvslkepdnqksdfkgltekesrflsqiesfkeleLkdakylklqklGddlrt 131
                 rk+r ++isGP+G gk+t  ++ L        +++  p  + + + + s++k +++ +s  l  +     +++ da+  k+q   d+l +
  EPA06549.1  24 RKNRSVVISGPPGSGKTTFgLQFLH----SGAKDFEEPCVYVSMSQNISEIKNDCKSFSWDLDDLINKDKILMVDARPFKIQ---DELIG 106
                 5678899**********96366553....45567788888888999999999999999976777777777778888888888...44443 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00033      0.21       2      38 ..      29      69 ..      28      74 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00033
                EEEE--SSSSHHHHHHHGGGGB....S--EEEEE--TT--H CS
       AAA_5  2 vlLvGppGtgKselaerlaaal....nreveyvqltrdtte 38
                v++ GppG+gK+++  ++++      + + +yv ++++++e
  EPA06549.1 29 VVISGPPGSGKTTFGLQFLHSGakdfEEPCVYVSMSQNISE 69
                8999*************999887788899999999988775 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0    0.0004      0.24       3      21 ..      29      47 ..      27      97 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0004
                EEEEESTTCCHHHHHHHHH CS
        cobW  3 tvltGflGsGKTtLlnhll 21
                +v++G++GsGKTt+  + l
  EPA06549.1 29 VVISGPPGSGKTTFGLQFL 47
                79***********866555 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00059      0.37       2      29 ..      30      55 ..      29      94 .. 0.65
   2 ?   -3.2   0.0         9   5.6e+03      53      75 ..     125     147 ..     120     154 .. 0.71
   3 ?   -2.6   0.0       6.2   3.8e+03      48      70 ..     210     233 ..     168     237 .. 0.52

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00059
  Viral_helicase1  2 vvhGvpGcGKStlirkllrts.liltvnr 29
                     v++G pG+GK+t   ++l++   +     
       EPA06549.1 30 VISGPPGSGKTTFGLQFLHSGaKD---FE 55
                     89***********99999994433...33 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 9
  Viral_helicase1  53 flmalvkstkgkililDEylllh 75 
                      +l + +k+ ++k++++D ++ l 
       EPA06549.1 125 LLLSSIKRIEAKRVVIDSITILA 147
                      55566666789999999887665 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 6.2
  Viral_helicase1  48 rtvdsflmalvks.tkgkililDE 70 
                      r ++   m  +k+ ++ + +i+DE
       EPA06549.1 210 RSLQVTKMRGIKHsQQIHPIIIDE 233
                      333333344444434455566666 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00056      0.35       2      50 ..      29      73 ..      28      83 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00056
                EEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTB CS
         Roc  2 vvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvend 50
                vv+ G  g+GKt++  +f+++  ++ e++ + v++++ ++++ik   nd
  EPA06549.1 29 VVISGPPGSGKTTFGLQFLHSGAKDFEEPCVYVSMSQ-NISEIK---ND 73
                7899***************************999965.454444...33 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00063      0.39       2      16 ..      29      43 ..      28      77 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00063
      AAA_28  2 ivitGgestGKTtll 16
                +vi+G++++GKTt  
  EPA06549.1 29 VVISGPPGSGKTTFG 43
                8************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                        29  (0.00161749); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              29  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 1598.63
//
Query:       EPA06550.1  [L=135]
Description: hypothetical protein BG20_I1153 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.1e-11   43.0   1.9      6e-11   42.1   1.9    1.5  1  ACAS_N       Acetyl-coenzyme A synthetase N-terminus
  ------ inclusion threshold ------
      0.076   11.6   0.0       0.11   11.1   0.0    1.1  1  AMP-binding  AMP-binding enzyme


Domain annotation for each model (and alignments):
>> ACAS_N  Acetyl-coenzyme A synthetase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   1.9   6.7e-15     6e-11       7      51 ..      36      83 ..      29      86 .. 0.89

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 6.7e-15
                HHHH-HHHHHHHHHCC..S--SB--S-SECSTTTC.T-EESTT-EE-H CS
      ACAS_N  7 eSiedpeaFWaeqake..ldWekpfdkvldgskgp.fikWFeGGklNi 51
                ++ e+ e+FW+e+ +   + W++p++kvld+skg  + kW+++Gk+Ni
  EPA06550.1 36 KANENLEWFWQEVENYfgIIWDTPYTKVLDTSKGIpWSKWYVDGKTNI 83
                567899*********87899*************966***********8 PP

>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   1.2e-05      0.11       2      34 ..      89     124 ..      88     127 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 1.2e-05
                  HHHHHHSTTSEEEEE...CCSTEEEEHHHHHHHHHH CS
  AMP-binding   2 eeqaaktpdkvalvd...sgegqtlTYreldervnr 34 
                  e+ a+k+pdk+a+v+   +++  ++TY+eld ++++
   EPA06550.1  89 EKFAKKNPDKTAYVFvseDDKVSKITYSELDIKSQQ 124
                  6789*************99999********987766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       804  (0.0448435); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 863.33
//
Query:       EPA06551.1  [L=110]
Description: sugar-specific transcriptional regulator TrmB [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.4e-13   48.4   0.3    9.2e-13   47.9   0.3    1.2  1  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0016   18.7   0.2     0.0062   16.9   0.1    1.8  2  Rrf2            Transcriptional regulator
     0.0031   17.0   2.2       0.05   13.2   2.2    2.2  1  HTH_24          Winged helix-turn-helix DNA-binding
     0.0062   16.6   0.0     0.0089   16.1   0.0    1.2  1  HTH_20          Helix-turn-helix domain
     0.0065   16.5   0.1      0.014   15.5   0.1    1.6  1  HTH_9           RNA polymerase III subunit RPC82 helix-turn-h
  ------ inclusion threshold ------
      0.032   14.2   1.8       0.11   12.6   0.2    2.1  2  HTH_46          Winged helix-turn-helix DNA binding
      0.053   13.4   0.2       0.15   12.0   0.1    1.7  2  RNA_pol_Rpb5_C  RNA polymerase Rpb5, C-terminal domain
      0.075   13.0   0.1       0.15   12.0   0.1    1.5  1  PadR            Transcriptional regulator PadR-like family
       0.13   12.8   0.0       0.19   12.3   0.0    1.2  1  HTH_27          Winged helix DNA-binding domain


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.9   0.3   4.6e-16   9.2e-13       6      67 ..      30      91 ..      27      92 .. 0.96

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 4.6e-16
                HHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE--H CS
        TrmB  6 LseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravdp 67
                L+ + ++vYl L k+g +ta+ i+e+l ++r+  Ye+L++L +k +V+ + g+p++++a+++
  EPA06551.1 30 LKPNQVEVYLHLNKNGVKTATSISEALRLSRTETYEILSELQKKEIVTSIYGKPTKFNAIEI 91
                78999******************************************************985 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.85   1.7e+03      30      47 ..      14      31 ..       2      32 .. 0.80
   2 !   16.9   0.1   3.1e-06    0.0062      16      61 ..      38      82 ..      34      87 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.85
                HHHHHHTS-HHHHHHHHH CS
        Rrf2 30 eiaerqnispsylekila 47
                 i e  +i++s+le il+
  EPA06551.1 14 RINEINEINRSILEYILK 31
                577888999999998886 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 3.1e-06
                HHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT CS
        Rrf2 16 yLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrGk 61
                yL +++++   ++++i+e   +s++    il++L+k+++v+s+ Gk
  EPA06551.1 38 YLHLNKNGV-KTATSISEALRLSRTETYEILSELQKKEIVTSIYGK 82
                667777765.899******************************997 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   2.2   2.5e-05      0.05       5      48 .]      34      77 ..      18      77 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.5e-05
      HTH_24  5 drkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                + +++  L kn+  + + ++e+l lS++ + + l +L+++++++
  EPA06551.1 34 QVEVYLHLNKNGVKTATSISEALRLSRTETYEILSELQKKEIVT 77
                5566778889********************************96 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   4.5e-06    0.0089       3      55 ..      25      77 ..      23      79 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.5e-06
                HHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
      HTH_20  3 iaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55
                i+e ++ P + +++ +L+ ++  ta+ + e+l+ls+++ +  L +L++ ++v+
  EPA06551.1 25 ILEYILKPNQVEVYLHLNKNGVKTATSISEALRLSRTETYEILSELQKKEIVT 77
                7778889***************************************9999887 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   7.1e-06     0.014      16      58 ..      35      77 ..      22      80 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7.1e-06
                HHHHHHHHHHSSBEHHHHHHHHSSTHHHHHHHHHHHHHTTSEE CS
       HTH_9 16 akVvetLlrkgrltlrelvkktkLsldqVkksLvvLiqhrlVq 58
                  V+ +L ++g +t++ ++++++Ls+++   +L+ L++  +V+
  EPA06551.1 35 VEVYLHLNKNGVKTATSISEALRLSRTETYEILSELQKKEIVT 77
                5799********************************9999886 PP

>> HTH_46  Winged helix-turn-helix DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.2      0.14   2.7e+02      25      57 ..      11      43 ..       2      53 .. 0.72
   2 ?   12.6   0.2   5.3e-05      0.11      26      59 ..      49      82 ..      42      90 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.14
      HTH_46 25 vlkyIqkrtnLSrSsimkvLseLkkggyIeier 57
                  + I++  ++ rS    +L   + + y+++++
  EPA06551.1 11 FDNRINEINEINRSILEYILKPNQVEVYLHLNK 43
                555577777788888888888877777777766 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 5.3e-05
      HTH_46 26 lkyIqkrtnLSrSsimkvLseLkkggyIeierGk 59
                +  I++  +LSr    ++LseL+k + ++   Gk
  EPA06551.1 49 ATSISEALRLSRTETYEILSELQKKEIVTSIYGK 82
                556888899****************999888777 PP

>> RNA_pol_Rpb5_C  RNA polymerase Rpb5, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.69   1.4e+03       3      43 ..      25      35 ..       7      55 .. 0.58
   2 ?   12.0   0.1   7.4e-05      0.15      11      52 ..      63     104 ..      56     108 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.69
                    -TSSSS--EEEEE-HHHHHHHHHHTT--TTCSS-EETTSHH CS
  RNA_pol_Rpb5_C  3 itkHelvPkhevlseeekkellkklkikeeqLPkisksDpv 43
                    i+++ l P                                v
      EPA06551.1 25 ILEYILKP------------------------------NQV 35
                    33333333..............................333 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 7.4e-05
                     EEEEE-HHHHHHHHHHTT--TTCSS-EETTSHHHHCCT--TT CS
  RNA_pol_Rpb5_C  11 khevlseeekkellkklkikeeqLPkisksDpvarylglkkG 52 
                      +e+lse +kke+++++  k++++  i+ +D+v   ++++ +
      EPA06551.1  63 TYEILSELQKKEIVTSIYGKPTKFNAIEIDDAVTTLIDAEIN 104
                     589*******************************99999876 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   7.6e-05      0.15      22      49 ..      51      78 ..      41      86 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.6e-05
                CSTT-CCTTHHHHHHHHHHHHHTTSEEE CS
        PadR 22 lsegllelseGslYpaLkrLekeglves 49
                +++++l+ls ++ Y +L++L+k+++v+s
  EPA06551.1 51 SISEALRLSRTETYEILSELQKKEIVTS 78
                4456699*******************97 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   9.5e-05      0.19       1      48 [.      30      76 ..      30      84 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.5e-05
      HTH_27  1 ltrqqalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLv 48
                l+++q+ v  +++  ++ k+++ ++++l ++ + + ++l++L +k+ v
  EPA06551.1 30 LKPNQVEVYLHLN-KNGVKTATSISEALRLSRTETYEILSELQKKEIV 76
                6899999966677.6999999***********************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       840  (0.0468515); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 715.04
//
Query:       EPA06552.1  [L=122]
Description: GatB/Yqey domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.2e-29  103.1   4.1    1.4e-29  102.9   4.1    1.0  1  GatB_Yqey  GatB domain
  ------ inclusion threshold ------
      0.085   13.1   0.0       0.11   12.6   0.0    1.3  1  ApbA_C     Ketopantoate reductase PanE/ApbA C terminal


Domain annotation for each model (and alignments):
>> GatB_Yqey  GatB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.9   4.1   1.5e-33   1.4e-29      36     148 .]      11     122 .]       2     122 .] 0.95

  Alignments for each domain:
  == domain 1  score: 102.9 bits;  conditional E-value: 1.5e-33
                 TCSSTTHHHHHHHHHHHHTTSSGHHHHHHHHHHHHHHTXXHHHHHHHCTXXXXXXSSXHHHHHHHHHHTXHHHHHHHTTXXTTSTHHHHHHHHHTTSSX CS
   GatB_Yqey  36 eelkltpeqlaellkliaegkIskkiakevleelleegkspeeiieekgLkqisdeeeleklveeviaenpkavedyksgkekalkflvGqvMkktkGk 134
                 e++kl++++l+++ + i++gkI+ ++ak+ l e++++gk+ +++i+e +L  +sde+el +++  vi+e+ +ave+ ks + + +++lvG+vM+kt+Gk
  EPA06552.1  11 ESSKLKASHLKDIADSIQSGKIARNSAKNALYEIIKNGKDLSTVISELDLGNVSDESELSNIISSVISEETQAVEQAKSNP-QTINYLVGKVMQKTRGK 108
                 5678****************************************************************************9.69*************** PP

                 SXHHHHHHHHHHHS CS
   GatB_Yqey 135 adpklvnellkekL 148
                 adpkl+ +llk+++
  EPA06552.1 109 ADPKLTLDLLKKMI 122
                 ***********976 PP

>> ApbA_C  Ketopantoate reductase PanE/ApbA C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.3e-05      0.11      20      87 ..      53     119 ..      25     121 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.3e-05
      ApbA_C  20 talldckngellespelralvrallkEalavaeaegvelseerleeaveavlektaan.rsSMlqDvea 87 
                 t++ +++ g++ ++ el +++ +++ E  +  e+++   +++ ++  v +v++kt+ + ++++  D+++
  EPA06552.1  53 TVISELDLGNVSDESELSNIISSVISEETQAVEQAK--SNPQTINYLVGKVMQKTRGKaDPKLTLDLLK 119
                 8999*******************9988777776666..69999***********999889999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1030  (0.0574488); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 865.45
//
Query:       EPA06553.1  [L=124]
Description: hypothetical protein BG20_I1161, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.051   13.4   0.6        2.2    8.2   0.1    2.2  2  Hen1_Lam_C  Hen1 La-motif C-terminal domain
      0.099   12.9   0.0       0.23   11.8   0.0    1.5  1  Phi-29_GP4  Phi-29-like late genes activator (early protein G


Domain annotation for each model (and alignments):
>> Hen1_Lam_C  Hen1 La-motif C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.1   0.00024       2.2      75     107 ..      11      43 ..       3      57 .. 0.83
   2 ?    3.7   0.0    0.0059        53      17      34 ..      77      94 ..      64     105 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00024
                 --------------B-HHHHHHHTS--BSSEEE CS
  Hen1_Lam_C  75 elaekkeeselekslNarAsylsgqdiyGdail 107
                 +++++++e+  ++ +N++ s  s q++ Gd +l
  EPA06553.1  11 STNNDSNEIYSQSVINEKLSLSSVQQVNGDVLL 43 
                 445667888899******************988 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.0059
                EEEEEEEBTTC-HHHHHH CS
  Hen1_Lam_C 17 eavtlnisseeyYldvia 34
                ++ + ++s + yY+dvi 
  EPA06553.1 77 KTAINDVSGTPYYMDVII 94
                566668999*******96 PP

>> Phi-29_GP4  Phi-29-like late genes activator (early protein GP4)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.5e-05      0.23      44      81 ..      72     109 ..      62     122 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.5e-05
                 HHHHHHHHHHTT---S---HHHHHHHHHHHH-TS---E CS
  Phi-29_GP4  44 yrkkfnkkiervavtpwnmdmladitfysevekrgfha 81 
                 y  +f+  i+ v+ tp+ md++ d  +y  v+   f +
  EPA06553.1  72 YTSNFKTAINDVSGTPYYMDVIIDHKIYGIVKSSIFNS 109
                 88899***********************9998877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 758.02
//
Query:       EPA06554.1  [L=428]
Description: hydantoinase/oxoprolinase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-36  126.3   1.3    2.4e-36  125.5   1.3    1.4  1  Hydantoinase_A  Hydantoinase/oxoprolinase


Domain annotation for each model (and alignments):
>> Hydantoinase_A  Hydantoinase/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.5   1.3   1.3e-40   2.4e-36      86     290 ..       1     226 [.       1     227 [. 0.98

  Alignments for each domain:
  == domain 1  score: 125.5 bits;  conditional E-value: 1.3e-40
  Hydantoinase_A  86 mGGTstDvslikdgevevsleteiagvkvrlpaldirtvgagGgsilvvdeggklrvgpesagadpgp........................... 153
                     mGGTst ++ ik+g++e+++ t  +++++ ++++d+r +g++Ggs++  d+++   vgp+sa++++                             
      EPA06554.1   1 MGGTSTNICIIKNGKPEIRYVTV-KDHPTCIRSMDVRILGVAGGSMVGLDKNRISHVGPRSAHISGLKyscyaepddlktgkiilikpkqndkse 94 
                     9******************9998.******************************************999************************** PP

  Hydantoinase_A 154 ...acyrkGgteltvTDanlvLGrlqpedflsgpdgdqkldvelarrafeelakelnlkveevAegilsvavenmanavrklsvergldpkeltl 245
                        +  +kG  ++t T+a++ LG ++++d++       ++++e a+ a+++la+ ++++  e+A+ i+++a+ ++ + + k+++e +++p+ +tl
      EPA06554.1  95 yvaIKCEKGTYAITNTCAANALGMIEKDDYA-------YANQESAKIAIKTLAEFVGVSYHEIAMSIIQTASFDITKTISKILKEFKMNPSATTL 182
                     **988999999********************.......9******************************************************** PP

  Hydantoinase_A 246 vvfGGaGaqhaaalaeelgvkkvivppyagvlsalGmalAdvree 290
                     ++ GG++ ++++ +a++lg+k   ++++ +v+s +G+a ++++ee
      EPA06554.1 183 IGGGGGASVLVPFVAKQLGIKYEKAEHA-EVISSIGVASSMLQEE 226
                     *********************9999998.*********9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       933  (0.0520386); expected 358.6 (0.02)
Passed bias filter:                      645  (0.0359752); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2957.32
//
Query:       EPA06555.1  [L=312]
Description: nucleic acid-binding domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-43  149.0   0.2      2e-43  148.7   0.2    1.1  1  tRNA-synt_2      tRNA synthetases class II (D, K and N)
    1.2e-11   44.5   0.0    2.1e-11   43.6   0.0    1.4  1  tRNA_anti-codon  OB-fold nucleic acid binding domain


Domain annotation for each model (and alignments):
>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.7   0.2   2.2e-47     2e-43       3     183 ..     105     279 ..     103     300 .. 0.88

  Alignments for each domain:
  == domain 1  score: 148.7 bits;  conditional E-value: 2.2e-47
                  CHHHHTHHHHCCSHHHHHHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT.TEEE-E-S-SHHHHHHHHHCTHSEEEEEEEE CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  tRNA-synt_2   3 elrlknryldlrtekvskvlrlrstvtkavrkyleengfieietPiLsksdteegarlFkvksrekekeffaLtqspqlylellivagidrvfqiara 100
                  ++rl+ r +dlr++ +++++++rs v+k++r+y+ +++f+ei+tP ++ ++te+ga lF +   +k  e f L+qspqly+e l ++ +++vf+i++ 
   EPA06555.1 105 DTRLEVRPIDLRRKTLQHIFNVRSDVLKSIRDYFYKEEFTEINTPKMIATATEGGAALFAIFYYNK--EAF-LAQSPQLYKEQLTMS-FEKVFEIGPI 198
                  799**********************************************************44433..555.***************.********** PP

                  E--S--BTTB-S-CEEEEEEEEET-SCHHHHHHHHHHHHHHHHHHHHCSCCCCCHTTTTTSEE-SSS-EEEEHHHHHHHHHTS CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  tRNA-synt_2 101 FRaEdsrtdrhlaEFtqieaemsfieeedimqvleelikslvkevlessakdiefvirrnskdlkkpfkrltykeaieklnei 183
                  FRaE srt+rhlaE ++i++e +f++++d+m+ +e++ik  ++ v++  +++   + +    +++++++r++y++ +ek+++ 
   EPA06555.1 199 FRAEPSRTNRHLAEAISIDLEEAFVDYNDVMNRIENIIKISLNSVIDYAKNN--PDAEFVIPQIPDSIPRYSYDDLVEKMQKA 279
                  ***************************************9999996555333..3333334678899***********98876 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   0.0   2.3e-15   2.1e-11       1      75 [.       6      84 ..       6      85 .. 0.96

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 2.3e-15
                     EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET....HHHHHHHTTS-TTSEEEEEEEEEEC...TTSSEEEEEEEEEE CS
  tRNA_anti-codon  1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfr....eeatklaenlkeGdvvrvtGrvkrr...pggelelkveeiel 75
                     Vtv G++ ++  r++g+++f++lrD+ g i +v+ +    +e ++ ++ lk  + + v G+vk++   p+g +e++ +++++
       EPA06555.1  6 VTVMGWILTV--RGHGNISFVTLRDKNGDIPIVAKKgdcpDELREKLSVLKAHSSIAVVGKVKSSekaPTG-FEIIPTDLRV 84
                     8*********..*****************************************************999999.***9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1877.72
//
Query:       EPA06556.1  [L=282]
Description: sugar-specific transcriptional regulator TrmB [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.4e-11   43.3   0.0    4.8e-11   42.4   0.0    1.5  1  TrmB       Sugar-specific transcriptional regulator TrmB
     0.0058   16.4   0.0     0.0099   15.7   0.0    1.4  1  HTH_IclR   IclR helix-turn-helix domain
  ------ inclusion threshold ------
      0.021   14.9   0.0      0.045   13.8   0.0    1.6  1  HTH_9      RNA polymerase III subunit RPC82 helix-turn-helix 
      0.048   13.6   0.6      0.079   12.9   0.1    1.6  2  BOP1NT     BOP1NT (NUC169) domain
      0.078   12.9   0.2         21    5.1   0.0    2.9  4  TnpB_IS66  IS66 Orf2 like protein
       0.72    9.7   3.5       0.72    9.7   1.0    2.2  2  HSBP1      Heat shock factor binding protein 1


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   0.0   1.6e-14   4.8e-11       1      67 [.      33      99 ..      33     100 .. 0.96

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 1.6e-14
                HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE--H CS
        TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravdp 67
                L+ +GL+++ +kv+++L k+g +ta e+ ++l++pr+  Y  L+ L +kG+V    + p  + a+++
  EPA06556.1 33 LSQYGLTSNQSKVFIYLGKYGAKTAPEVCKALKLPRTETYHLLSALQNKGIVSATFQHPIQFTALPL 99
                789***************************************************9999999999886 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   3.3e-06    0.0099      20      49 ..      56      85 ..      44      87 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.3e-06
                BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
    HTH_IclR 20 tlselArrtglpkStvhRlLqtLvelGyve 49
                t  e+++++ lp++ +++lL+ L++ G+v 
  EPA06556.1 56 TAPEVCKALKLPRTETYHLLSALQNKGIVS 85
                6789***********************995 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.5e-05     0.045      16      58 ..      43      85 ..      34      88 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.5e-05
                HHHHHHHHHHSSBEHHHHHHHHSSTHHHHHHHHHHHHHTTSEE CS
       HTH_9 16 akVvetLlrkgrltlrelvkktkLsldqVkksLvvLiqhrlVq 58
                +kV  +L ++g++t+ e  k++kL++++  + L++L++ ++V+
  EPA06556.1 43 SKVFIYLGKYGAKTAPEVCKALKLPRTETYHLLSALQNKGIVS 85
                78999*********************************99997 PP

>> BOP1NT  BOP1NT (NUC169) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       1.3   3.7e+03     135     144 ..     122     135 ..      89     168 .. 0.55
   2 ?   12.9   0.1   2.7e-05     0.079      78     146 ..     185     261 ..     173     270 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.3
      BOP1NT 135 ekvydlWed....e 144
                 +   +lW++    +
  EPA06556.1 122 KGLSELWDNiptfD 135
                 33334444432221 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 2.7e-05
      BOP1NT  78 dvvelftseeeihplseapepkrrfipskweakkvaklvrairkgrikl........ekkekeee......ekvydlWedeee 146
                 +++e f +++++  l ++ ++k  +i ++ e+k+++kl ++i+++   +                      ++ y +W+++++
  EPA06556.1 185 EFLESFVKSKQKFRLLSSCSEKTTYIFDNLERKNIKKLNNEIQNNLCFIlkdnsellF------FtknansSEPYAMWTNSKS 261
                 56788999999999999*************************9998887555555551......0344444999****99765 PP

>> TnpB_IS66  IS66 Orf2 like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       3.4     1e+04      30      43 ..      39      52 ..      34      55 .. 0.70
   2 ?    5.1   0.0    0.0069        21      27      57 ..      94     124 ..      81     132 .. 0.88
   3 ?   -2.0   0.0       1.1   3.3e+03      18      51 ..     153     183 ..     141     194 .. 0.62
   4 ?    4.4   0.1     0.012        34      32      62 ..     204     235 ..     187     266 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 3.4
   TnpB_IS66 30 dpfsgalFvFrnrr 43
                   ++++F+++++ 
  EPA06556.1 39 TSNQSKVFIYLGKY 52
                55567899999886 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0069
   TnpB_IS66  27 lkldpfsgalFvFrnrrrdrlKiLlwdgnGf 57 
                 + + p+++a+++ +n +++rlK L + ++G+
  EPA06556.1  94 FTALPLNKAIWILVNSEKERLKSLEHMEKGL 124
                 6677999******************999997 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.1
   TnpB_IS66  18 gLaalVqeelkldpfsgalFvFrnrrrdrlKiLl 51 
                 ++   ++e    d   ++ F+ ++ ++d +K+ +
  EPA06556.1 153 QIQSKITEM--TDN-FKDEFLILGSEKDYIKLYH 183
                 444444333..222.2356777888888888765 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.012
   TnpB_IS66  32 fsgalFvFrnrrrdrlKiLlwd.gnGfvllyk 62 
                  +++ ++F n +r+++K L  + +n ++ + k
  EPA06556.1 204 SEKTTYIFDNLERKNIKKLNNEiQNNLCFILK 235
                 45569************998773445555555 PP

>> HSBP1  Heat shock factor binding protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   1.0   0.00024      0.72      13      33 ..     140     162 ..     139     165 .. 0.91
   2 ?   -2.3   0.1       1.4   4.1e+03      37      48 ..     212     224 ..     211     227 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00024
       HSBP1  13 qlqdkFqtm..sdqilsriDdMs 33 
                 ++++kFq +  s+qi s+i +M+
  EPA06556.1 140 EVEEKFQMLqgSNQIQSKITEMT 162
                 789****99*************7 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.4
       HSBP1  37 DdLE.ksiadlmt 48 
                 D+LE k+i++l +
  EPA06556.1 212 DNLErKNIKKLNN 224
                 8888557887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       953  (0.0531541); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1767.31
//
Query:       EPA06557.1  [L=495]
Description: AMP-binding enzyme [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.8e-60  203.1   0.0    6.9e-60  202.8   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    9.8e-17   61.7   0.0    1.7e-16   61.0   0.0    1.4  1  AMP-binding_C  AMP-binding enzyme C-terminal domain
  ------ inclusion threshold ------
       0.53   10.6   2.1       0.58   10.4   0.1    2.1  2  AFP_2          Bacterial antifreeze protein repeat


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.8   0.0   1.2e-63   6.9e-60      59     422 ..       4     377 ..       1     378 [. 0.82

  Alignments for each domain:
  == domain 1  score: 202.8 bits;  conditional E-value: 1.2e-63
                  HHHHHHHHHHHTT-EEEEEETTS-HHHHHHHHHHHTESEEE.........ETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTT CS
  AMP-binding  59 ewvvallailkaGavvvplnptltaeelayiledseakvli.........atvdselleklleaaakleavklvivldadellkeeelkeeeeseeka 147
                  e ++a+la++k+Ga+  ++ +++++e l+  l+d++ak+l+         + +++++   + ++a k+ + +++iv + +++++++e++     + + 
   EPA06557.1   4 EAFLAILACAKIGAIQTVIFSGYSSESLQIRLQDCKAKILFvcdgfqrngKPISQKQ---IINTAIKDTKIEKIIVASYAQIDNYDESDLVV-YY-S- 95 
                  8899*************************************9988865431333333...33333333344455555555555443333222.22.2. PP

                  S......-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHH.HHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCG CS
  AMP-binding 148 e......kpeeeeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslk.letrfklkeddvvlsilplahifglilelllallsGatvvllpkda 238
                  +        + +e++ ++d+++i+YTSGTTGkPKGV+++h+ ++ ++  ++ +    +++e+d +l+ +++ +i+gl++++++ l+ Ga+ +++++  
   EPA06557.1  96 KlistqdSVCSTESTASEDPLFILYTSGTTGKPKGVIHTHGGFSVFAGYQSgF--LIDMNENDILLWPADIGWITGLVWNVYGLLILGACAIIYDGAL 191
                  0234455677888999************************9998886665432..255889************************************9 PP

                  C.CHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTC...EEEEEEEEGGGSSEC.EECHCTT CS
  AMP-binding 239 a.ldpklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrffralfge...evlegYGlTEttgvv.tvlplee 331
                    +d +++++++++++vt++   P++++ + +++ +    k +++ +++ + + gepl ++ + ++ +++g+   +++++ G TE +g++ +v+p ++
   EPA06557.1 192 NyPDFNRIWDMLHHYNVTIFGISPTAVRLFKKNNIEPL--KLHSFEKIKNIPTTGEPLDEDSWWWLFEKVGNkkiPIMNLSGGTEIGGAMlSVFPGMK 287
                  988899999******************99966544443..3458889999999****************9999*****************53266555 PP

                  TCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEET..TS-SEBTT-HHHHHHHEEET.CC.EEEEEEEEEEETTSEEEEEEECCCEEEE CS
  AMP-binding 332 dkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgp..gvmkgYlkkpeataeafdse.gr.wlrTGDlgrldedGyleivgRkkdlikl 422
                     k+++vG p pg+ + ++De+ g+ v  ++ G l+v++p   ++kg l++ e+  ++++s  ++ w++ GD +++d++G  +  gR++d+i++
   EPA06557.1 288 L--KPSTVGIPCPGMNLDVIDEH-GKSV-IEKDGYLVVKSPwpAMTKGLLNNNERYIQTYWSRfENiWFH-GDYVFVDKEGLWYMKGRADDVINV 377
                  5..789****************9.7777.7889********667*****************835565999.**********************98 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.0   0.0   2.8e-20   1.7e-16       1      76 []     386     462 ..     386     462 .. 0.95

  Alignments for each domain:
  == domain 1  score: 61.0 bits;  conditional E-value: 2.8e-20
                    HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE------.HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
  AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgsea.leeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                    e+E +++sh+++++aa v++pd+++Gea+++f v k+ +e+ l  e+  ++++++g++a+pk v+ +++lpktr+GK
     EPA06557.1 386 EIEHVVISHDKISDAASVAIPDQITGEAIIVFFVSKNKNELiLGTEISNYIAEKIGKIARPKIVYQISDLPKTRTGK 462
                    8*********************************9854456899********************************9 PP

>> AFP_2  Bacterial antifreeze protein repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.4      0.95   5.7e+03      31      39 ..     230     238 ..     222     239 .. 0.74
   2 ?   10.4   0.1   9.7e-05      0.58      20      40 ..     332     352 ..     327     360 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.95
       AFP_2  31 kvsnFENIK 39 
                 k+  FE IK
  EPA06557.1 230 KLHSFEKIK 238
                 8999***99 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 9.7e-05
       AFP_2  20 dyyanvdniQnkvsnFENIKv 40 
                   ++n  +iQ + s FENI +
  EPA06557.1 332 LLNNNERYIQTYWSRFENIWF 352
                 5689***************77 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (495 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 3123.63
//
Query:       EPA06558.1  [L=733]
Description: FTR1 family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-20   73.9  20.3    3.3e-14   52.8   4.8    2.5  2  FTR1      Iron permease FTR1 family
  ------ inclusion threshold ------
      0.034   13.9   0.9      0.073   12.8   0.0    2.0  2  DUF2228   Uncharacterised conserved protein (DUF2228)
        9.1    6.5   0.0        9.1    6.5   0.0    5.2  6  HemY_N    HemY protein N-terminus


Domain annotation for each model (and alignments):
>> FTR1  Iron permease FTR1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.8   4.8   5.5e-18   3.3e-14     135     232 ..     454     554 ..     409     568 .. 0.84
   2 !   25.8   8.5     9e-10   5.4e-06     135     188 ..     572     623 ..     555     651 .. 0.87

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 5.5e-18
        FTR1 135 lfilsFlivlREGlEavLfvaaivaytvk....rvsalilgvvlGaliavvlglliyrglvklslqsffilegflLllvaagLfsvgtlellekaeacn 229
                 +f +sF +++REGlE vL+++ai++y+      +  ++i   ++ al+a+++++l+  + + +s++s++++e +  l ++a+Lf+v+ +++l k e ++
  EPA06558.1 454 AFTSSFAVIFREGLESVLILGAILTYLEAsrntKFKPYIYYGIVLALVATIITWLVTSYIIDISGASRELVEAIAALSATAVLFYVS-FWILNKIEHKK 551
                 47789**********************999888445555555555789***************************************.*********99 PP

        FTR1 230 gkd 232
                 + +
  EPA06558.1 552 WME 554
                 976 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 9e-10
        FTR1 135 lfilsFlivlREGlEavLfvaaivaytvkrvsalilgvvlGaliavvlglliyr 188
                 +++lsF++v REG+E+vLf  a++a ++     l++g   ++ ia++lgl++++
  EPA06558.1 572 FVMLSFFTVYREGFETVLFYQAMFAFAK--YMELYVGLGFVLGIASLLGLFFVM 623
                 789*************************..8********************986 PP

>> DUF2228  Uncharacterised conserved protein (DUF2228)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.2      0.92   5.5e+03      76     128 ..     144     197 ..     135     203 .. 0.59
   2 ?   12.8   0.0   1.2e-05     0.073     179     234 ..     216     271 ..     204     279 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.92
     DUF2228  76 eitvvgdnlfaa.vkkflekklkkkdkkkkkelkklkkklekfakekeisleqk 128
                 ++ +  +nl++  +++ l +++k++ k++ ++ ++l+++l  f k+ + s+++k
  EPA06558.1 144 QLAIQQNNLESYfFTQSLVEHSKNTVKQNPSNNDRLNQELDSFFKDLDESISKK 197
                 555555555553134455555566666777777777777777777766555544 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 1.2e-05
     DUF2228 179 eeakneeerekaleklqelvtavqianDecdfGmgLElGldLFcsgskslhkvakq 234
                 ++ + ++++++ ++k+++l+++ +     +d+ ++ ElG++ ++++ ++l++ +++
  EPA06558.1 216 QTETIDSNKKNTYDKIRTLYSELSASLKSGDYSTAEELGIEAYLDNFEYLESDIEK 271
                 455578999****************************************9998876 PP

>> HemY_N  HemY protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1      0.35   2.1e+03      30      47 ..       5      22 ..       1      42 [. 0.52
   2 ?   -3.5   0.0         2   1.2e+04      69      81 ..     241     253 ..     223     257 .. 0.82
   3 ?    6.5   0.0    0.0015       9.1      60      85 ..     357     382 ..     346     393 .. 0.88
   4 ?   -0.2   0.3      0.19   1.2e+03      23      48 ..     496     521 ..     491     525 .. 0.66
   5 ?    1.5   0.9     0.055   3.3e+02      16      40 ..     523     547 ..     520     551 .. 0.90
   6 ?    1.4   0.4     0.062   3.7e+02      11      33 ..     689     711 ..     687     714 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.35
      HemY_N 30 lylllrllrlllrlparv 47
                +yl l ++ +++++ a +
  EPA06558.1  5 FYLYLIIVVFVFGIFAFT 22
                333444444444444444 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2
      HemY_N  69 alaeGdfarAeka 81 
                 +l +Gd+++Ae++
  EPA06558.1 241 SLKSGDYSTAEEL 253
                 67899**999976 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.0015
      HemY_N  60 realseGlialaeGdfarAekaaaka 85 
                 re+l++ l+++a Gdf+ A  +a++a
  EPA06558.1 357 RERLEDTLVHYARGDFQSAHTSARSA 382
                 789*****************999987 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 0.19
      HemY_N  23 lvllfvllylllrllrlllrlparvr 48 
                 +vl++v+ ++ + + + ++ +++++r
  EPA06558.1 496 IVLALVATIITWLVTSYIIDISGASR 521
                 56667777777777777777666655 PP

  == domain 5  score: 1.5 bits;  conditional E-value: 0.055
      HemY_N  16 lvvavlllvllfvllylllrllrll 40 
                 lv a+++l +++vl+y+ +++l+++
  EPA06558.1 523 LVEAIAALSATAVLFYVSFWILNKI 547
                 678999***************9876 PP

  == domain 6  score: 1.4 bits;  conditional E-value: 0.062
      HemY_N  11 rietslvvavlllvllfvllyll 33 
                 ++et++ + +ll+v lf++ y+l
  EPA06558.1 689 TLETTIGQIILLAVYLFAASYVL 711
                 589****************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (733 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1452  (0.0809861); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.84u 0.33s 00:00:01.17 Elapsed: 00:00:00.54
# Mc/sec: 4121.06
//
Query:       EPA06559.1  [L=481]
Description: putative aspartyl/glutamyl-tRNA amidotransferase subunit A [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   4.2e-136  454.5   0.0   4.8e-136  454.3   0.0    1.0  1  Amidase   Amidase


Domain annotation for each model (and alignments):
>> Amidase  Amidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  454.3   0.0  2.7e-140  4.8e-136       6     451 .]      28     464 ..      23     464 .. 0.98

  Alignments for each domain:
  == domain 1  score: 454.3 bits;  conditional E-value: 2.7e-140
                 HHHHHHHHHHHH--EEEEEHCCCCHHHHT---TTT......TTTT-EEEEETTB--TTSB--TTSGGGTT-B-SS--HHHHHHHHTT-EEEEEE--SGG CS
     Amidase   6 flkrieavneklnalvtvfieealaqAakldkkrargkekgpLhGvPisvKDnidvkgvpttaGskalenypaekDatvverLkkaGavilgkTnmdef 104
                  ++ i++++ +l+ ++ +++e+a+ qA+ +dkk+++g++ g  +G+Pis+KDni++k+ +tt++sk+len++a++Datv+++Lk+++a+++gk n+def
  EPA06559.1  28 TMEHIQRIDGNLH-AFLSLNEKAIDQARVIDKKIKSGEKIGQCFGMPISIKDNICIKDSKTTCASKMLENFIAPYDATVITKLKQQDAIFVGKVNLDEF 125
                 6778999999***.88999******************************************************************************** PP

                 G-SSSSTT-TT---BBTTCTCCB--SSSHHHHHHHHTTSSSCEEEEESSSTTHHHHHHCTSEEEE--TTSC--TTB--SSTTT-EEEEEESSHHHHHHH CS
     Amidase 105 amgsstensvfgptrNPwdksrtpGGSSGGsAAavAaglvplaiGtDtGGSiRiPAsfcglvGlKPtygrvSragvvalessldvvGplarsvedlall 203
                 amg++te s++gp +NPw+++++pGGSSGGsA+ v+a  +++++G+DtGGS+R PAsfc++vG+KPtyg++Sr+g++++++s++++Gpl+r+ved+a++
  EPA06559.1 126 AMGLTTEFSAYGPSKNPWNTDYVPGGSSGGSAVSVSAFECVASLGSDTGGSVRNPASFCSTVGFKPTYGLISRYGLISYANSIEQIGPLTRTVEDTAFM 224
                 *************************************************************************************************** PP

                 HHHHBS--TT-TTS----HHHHHHHHCTT---TT-EEEEEGGGCSS---CCHHHHHHHHHHHHHCTT-EEEEEE-CCGGGHHHHHHHHHHHHHHHHTTT CS
     Amidase 204 lrvilgedpkdstssvipeesedlaeelkkslkglriGvvkedgvasldpevqravekalkaLeeaGhevvevelpsleealslyylilvaeassnlar 302
                 l  i+g dp+d t+ +  + +ed+ +   +  +g++iG++ke+  + +d +v  a+++a+ +L ++G+  +ev+l  +++ +++yy+i + ea+snlar
  EPA06559.1 225 LNLISGIDPNDNTTVD--NHNEDYLKDIDSGIEGKKIGIIKEMIGEGIDSNVLSATKNAISKLDNMGAICEEVSLDMVKYSVAAYYTITATEAGSNLAR 321
                 ****************..8899***************************************************************************** PP

                 -SSSSS.---SS-SCCCCCCCHHHHCCS-HHHHHHHHHHHHHCSCCCCCCCHHHHHHHHHHHHHHHHHHCCCBSEEEEESSSSS--BCCCCCHHHCSHH CS
     Amidase 303 ylgvry.erlsetkvlsellpksraellgeevkrrielgnyalsaeasskyylkaqkvrrllrrefakafeelDvllsPtaptpaprlgekdktidsyt 400
                 y++ ry + +s   +  + + ++ +++lg+ev+rr++lg+++ sa+  +ky+lka kv+  l+r++++af+++D+l++Pt+p  ++++gek    d++ 
  EPA06559.1 322 YDNLRYgYDFSVEGYEFNSYIEKARKKLGPEVTRRMILGGFVPSAGHAGKYFLKALKVKNKLTRQINEAFKKFDLLIAPTVPVLPFKIGEKI---DDPV 417
                 *******8888887778888889999****************************************************************96...99** PP

                 HHHGCCTTT...HHHHHTT--EEEEECCCCT.TECEEEEEEESTT-HHHHH CS
     Amidase 401 vlynlldftavvvpvnlaglpalsvpagksedglPvGvqvigkafqeetlL 451
                 +l++++  t   v +nl+g+pa+s+p+  s  glP+G+q+ig+ ++++ +L
  EPA06559.1 418 ALFLIDINT---VTANLTGKPAISIPYDISH-GLPIGIQLIGNSMNDKLVL 464
                 *********...****************996.****************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (481 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 2949.55
//
Query:       EPA06560.1  [L=261]
Description: hydantoinase/oxoprolinase N-terminal domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-20   73.1   6.9    5.1e-20   71.9   6.9    1.6  1  Hydant_A_N      Hydantoinase/oxoprolinase N-terminal region
    1.8e-10   40.6   0.8    2.6e-09   36.8   0.0    2.4  2  Hydantoinase_A  Hydantoinase/oxoprolinase
      1e-05   24.4   0.7    1.3e-05   24.0   0.7    1.2  1  MutL            MutL protein
    2.3e-05   24.1   1.3    7.8e-05   22.4   1.2    1.9  1  FGGY_N          FGGY family of carbohydrate kinases, N-termin
    3.8e-05   23.3   2.4    3.9e-05   23.3   1.3    1.4  1  BcrAD_BadFG     BadF/BadG/BcrA/BcrD ATPase family
     0.0066   16.4   0.1      0.013   15.4   0.1    1.5  1  ACT_6           ACT domain
  ------ inclusion threshold ------
      0.032   14.4   0.0      0.077   13.1   0.0    1.6  1  HisG_C          HisG, C-terminal domain
       0.04   13.8   0.6       0.16   11.8   0.1    2.0  2  DEDD_Tnp_IS110  Transposase


Domain annotation for each model (and alignments):
>> Hydant_A_N  Hydantoinase/oxoprolinase N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.9   6.9   2.3e-23   5.1e-20       1     176 [.       8     177 ..       8     179 .. 0.85

  Alignments for each domain:
  == domain 1  score: 71.9 bits;  conditional E-value: 2.3e-23
  Hydant_A_N   1 rigIDvGGTfTDavaldeke.eevavlKllst...pdavaegirealeevleesiprtskidvvrmGTTvatNallerkgervaLittkgfrdlleigr 95 
                 r+gIDvGGTfT ava+d k+   +a+  +++t   ++ v+egi++al + ++e+++  ++i+ + ++TT+a+Nalle + ++v++i +   +    +  
  EPA06560.1   8 RVGIDVGGTFTKAVAIDVKTgSLLAKSTVPTThsaDKGVSEGIVSALTKIIDETGIGVNDIELISHSTTQAINALLESDTSKVGIIAMGVGPTKKDVI- 105
                 79***************88877889999999999999*************************************************998665544333. PP

  Hydant_A_N  96 qnrpdlfelrikkplvlyeevvevderveadgevlkpldeeevrealkalkaagvesiavvllhSylnpehElrvaeiare 176
                  +r +l     ++ ++  +++  ++  +e+  +    + e+ev  ++++lk++g+e i+ + ++ +  p++El v ++a++
  EPA06560.1 106 -KRTNL-----QDASI--NTNQDIKTTHEF-LDTSHLISESEVADTINRLKKNGAEVIIATEAFGVDDPSNELFVMNVASK 177
                 .33444.....22333..444455666666.56778889************************************999876 PP

>> Hydantoinase_A  Hydantoinase/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.3     0.056   1.2e+02      82      97 ..       9      24 ..       2      65 .. 0.86
   2 !   36.8   0.0   1.2e-12   2.6e-09       1      54 [.     197     250 ..     197     253 .. 0.97

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.056
  Hydantoinase_A 82 ItfDmGGTstDvslik 97
                    +++D+GGT t++ +i+
      EPA06560.1  9 VGIDVGGTFTKAVAID 24
                    789********99987 PP

  == domain 2  score: 36.8 bits;  conditional E-value: 1.2e-12
  Hydantoinase_A   1 rtetavvnAylspilreylesvekslekrgakarlmvmqsdGglvsadearkkp 54 
                     rt t++vnA + p+  + ++ ve++++k g++a+lm+m++dGg++s+d++r kp
      EPA06560.1 197 RTLTSAVNASVLPKTFQVANYVEEAIHKTGVTAPLMIMKGDGGVTSMDTFRTKP 250
                     899************************************************997 PP

>> MutL  MutL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.7   5.9e-09   1.3e-05       4      56 ..      11      62 ..       8      99 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 5.9e-09
        MutL  4 iDiGSttTkvtlvdlekvderllgqaeapTtvee.edvleGleealeeleeklg 56
                iD+G t+Tk++++d+++  ++ll+++  pTt ++ + v eG+ +al+++ +++g
  EPA06560.1 11 IDVGGTFTKAVAIDVKT--GSLLAKSTVPTTHSAdKGVSEGIVSALTKIIDETG 62
                8**************87..*************99999***********988865 PP

>> FGGY_N  FGGY family of carbohydrate kinases, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   1.2   3.5e-08   7.8e-05       3      93 ..       9      91 ..       7     105 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 3.5e-08
                EEEEEESSEEEEEEEE.TTS-EEEEEEEE--EB-SSTT--EE-HHHHHHHHHHHHHHHHHHCT.-GCCEEEEEEEE-SS-EEEEETTTEESS CS
      FGGY_N  3 lglDcGttstkaivld.ekgkvvasaqaelelsspkegwaeqdpeeiwqalaeairkvleqagisekqikaIgisgqreglvllDkndkpLy 93
                +g+D+G+t+tka+++d ++g ++a+++++ + s + +g +e         + +a++k++++ gi  ++i+ I+ s+ +   +ll+ +++ ++
  EPA06560.1  9 VGIDVGGTFTKAVAIDvKTGSLLAKSTVPTTHSAD-KGVSE--------GIVSALTKIIDETGIGVNDIELISHSTTQAINALLESDTSKVG 91
                89************************999876665.55554........67889999999999**************999999999997765 PP

>> BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   1.3   1.7e-08   3.9e-05       1      65 [.       9      71 ..       9      98 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 1.7e-08
                 EEEEE-SSEEEEEEEETTTEEEEEEEE--TTS-HHH.........HHHHHHHHHHT--GGGECEE CS
  BcrAD_BadFG  1 vGiDgGsTttkavlmdekgevlgrgitnsanlesvrfeaaekvleealtealerageeeadieet 65
                 vGiD+G+T tkav +d k   l    t+++  + ++ +++ + ++ alt++++++g   +die +
   EPA06560.1  9 VGIDVGGTFTKAVAIDVKTGSLLAKSTVPTTHS-AD-KGVSEGIVSALTKIIDETGIGVNDIELI 71
                 8***************99775655566665555.44.799*********************9966 PP

>> ACT_6  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1     6e-06     0.013      13      58 ..      48      93 ..      46     103 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 6e-06
       ACT_6 13 pGltasLtsvlaefgvnilDieqavihgrlsLgllvsgpedalarl 58
                 G++++Lt+++ e g+ + Die+  + ++ ++ +l++ + ++++ +
  EPA06560.1 48 EGIVSALTKIIDETGIGVNDIELISHSTTQAINALLESDTSKVGII 93
                69*************************************9988766 PP

>> HisG_C  HisG, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   3.4e-05     0.077      43      69 ..     131     157 ..     115     159 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.4e-05
                 EEEEECCCHHHHHHHHHCTT-EEEEEE CS
      HisG_C  43 savveekevaevideLkaaGAsdIlvl 69 
                 s +++e+eva++i++Lk+ GA+ I+ +
  EPA06560.1 131 SHLISESEVADTINRLKKNGAEVIIAT 157
                 56799*****************99987 PP

>> DEDD_Tnp_IS110  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   7.3e-05      0.16       1      68 [.       9      84 ..       9     108 .. 0.72
   2 ?    0.1   0.0       0.3   6.7e+02      30      57 ..     135     162 ..     103     181 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.3e-05
  DEDD_Tnp_IS110  1 vGiDvakdkhdacvida.egkvllservpnde...eglea.lleklaakagevlvvv...eatghygallvaflle 68
                    vGiDv+ +  +a++id  +g+ l++ +vp+++   +g+++ ++++l++  +e+ ++v   e  +h     +++lle
      EPA06560.1  9 VGIDVGGTFTKAVAIDVkTGSLLAKSTVPTTHsadKGVSEgIVSALTKIIDETGIGVndiELISHSTTQAINALLE 84
                    8**************9758888899999999733346655355557777777777753336666666666665555 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.3
  DEDD_Tnp_IS110  30 deeglealleklaakagevlvvveatgh 57 
                     +e+++++ +++l+++  ev ++ ea g 
      EPA06560.1 135 SESEVADTINRLKKNGAEVIIATEAFGV 162
                     5778889999999999999999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       762  (0.042501); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.57u 0.36s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 1495.84
//
Query:       EPA06561.1  [L=59]
Description: hypothetical protein BG20_I1145 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 383.10
//
Query:       EPA06562.1  [L=87]
Description: hypothetical protein BG20_I1148 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.065   13.2   0.0      0.081   12.9   0.0    1.2  1  PUB       PUB domain


Domain annotation for each model (and alignments):
>> PUB  PUB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   4.5e-06     0.081      25      72 ..      11      68 ..       7      78 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.5e-06
         PUB 25 ekyrrIrleNkafkekvlplegavelLealGFeekne..........eeeeflvleee 72
                +k  rI l+++ + ++v++  g +++L+++G e ++            e+e++ ++e+
  EPA06562.1 11 AKLMRIELDDPSIYKRVDKMIGYFDILDSAGVESEEIffteislanlREDEYIPFNEK 68
                68889**************************976544666666666555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.33s 00:00:00.78 Elapsed: 00:00:00.50
# Mc/sec: 518.96
//
Query:       EPA06563.1  [L=84]
Description: hypothetical protein BG20_I0753 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 590.28
//
Query:       EPA06564.1  [L=188]
Description: hypothetical protein BG20_I0747 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.9e-50  169.5   0.1    7.7e-50  169.3   0.1    1.0  1  DUF655    Protein of unknown function (DUF655)
    5.9e-05   23.3   0.0    0.00011   22.4   0.0    1.6  1  HHH_6     Helix-hairpin-helix motif
     0.0047   17.2   0.0      0.012   15.9   0.0    1.7  1  HHH_3     Helix-hairpin-helix motif


Domain annotation for each model (and alignments):
>> DUF655  Protein of unknown function (DUF655)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.3   0.1   1.3e-53   7.7e-50       2     181 .]      12     187 ..      11     187 .. 0.97

  Alignments for each domain:
  == domain 1  score: 169.3 bits;  conditional E-value: 1.3e-53
                 --EEEEEEEETT--TT--S-GGG---EEEEEETTT--EEEEEE-TT----TT-EEE-SSS--SSEEEEEEE--GGGS-HHHHHHHHHHHHHHHHTTHHH CS
      DUF655   2 eeeaivLDylpeGypddkhrehrdkpvvqalgereltLlelvplkevdilkldevaigkgksdkivkikreisyedLtdvaraeLpdvvekivkekEdr 100
                 ee+a+vLD+ p G+++  +   r+  ++ a+ge++lt+le+   ++  + + ++++igk+ ++ki ++  +++ye+++++a++eLp vve+iv+++E r
  EPA06564.1  12 EEYAYVLDFNPRGKSSTVR--GREGIIITAIGEDRLTILEVLGVPNSTFDVGERIYIGKEGRTKILSVLGKLEYEQISSSAQSELPGVVENIVTNNETR 108
                 89************99986..7999************************************************************************** PP

                 HHHHH-----B-SSSBGGGGSTT--HHHHHHHHHHHHHS---SHHHHHHHSTT---HHHHHHHHHHHHHH-TTSS--SS-- CS
      DUF655 101 fveffneaepitiRlHaLelLpgvgkklarkileeRerrrFesFedvkkrvkglkdpaeilverileEiedktekYylFve 181
                 fve+ n+a+p+t R+HaLel+pg+gk ++++++eeRe+++F+s++d+++rv g k+p + + eri++Ei ++ ++ +lFv+
  EPA06564.1 109 FVEYLNNAQPLTPRIHALELIPGIGKTYMKTMIEEREKKKFQSYADLQERV-GFKEPIRHISERIMHEITGE-SRMNLFVK 187
                 ***************************************************.5*****************99.88899985 PP

>> HHH_6  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   1.8e-08   0.00011      28      65 ..     125     161 ..      98     180 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.8e-08
       HHH_6  28 GLaaikglgeaaaerivaeRekegpfksledlarrvds 65 
                 +L+ i g+g++ ++++++eRe +++f+s +dl +rv+ 
  EPA06564.1 125 ALELIPGIGKTYMKTMIEERE-KKKFQSYADLQERVGF 161
                 7999****************9.8*************93 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0     2e-06     0.012      15      52 ..     125     161 ..     120     164 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2e-06
       HHH_3  15 eLqklpGlgpklAknIvayReknGpfksreeLlkvkgl 52 
                  L+ +pG+g+++ k +++ Rek+ +f+s  +L++  g+
  EPA06564.1 125 ALELIPGIGKTYMKTMIEEREKK-KFQSYADLQERVGF 161
                 6999****************666.********997666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1275.53
//
Query:       EPA06565.1  [L=38]
Description: hypothetical protein BG20_I0774, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-06   27.6   0.0    1.7e-06   27.4   0.0    1.0  1  HTH_24         Winged helix-turn-helix DNA-binding
    7.5e-06   25.7   0.0    8.6e-06   25.5   0.0    1.0  1  HTH_AsnC-type  AsnC-type helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0     2e-10   1.7e-06       2      32 ..       5      35 ..       4      37 .. 0.95

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 2e-10
      HTH_24  2 detdrkILelLqknprisqreLAerlglSps 32
                de+d k+L +L k+++is   L+++lg+  s
  EPA06565.1  5 DELDMKLLFELTKDGSISVPVLSKKLGINAS 35
                99**************************987 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   9.6e-10   8.6e-06       2      32 ..       5      35 ..       4      36 .. 0.95

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 9.6e-10
  HTH_AsnC-type  2 DeiDrkILeaLqedaRisyaeLAervGlSes 32
                   De+D k+L +L +d++is+  L++++G+ +s
     EPA06565.1  5 DELDMKLLFELTKDGSISVPVLSKKLGINAS 35
                   ***************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (38 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       252  (0.0140554); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.46
# Mc/sec: 250.07
//
Query:       EPA06566.1  [L=98]
Description: 50S ribosomal protein L12P [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.4e-12   45.9  15.2    7.4e-12   45.7  15.2    1.1  1  Ribosomal_60s  60s Acidic ribosomal protein
  ------ inclusion threshold ------
      0.066   13.2   6.2       0.24   11.4   3.1    2.1  2  PepSY_2        Peptidase propeptide and YPEB domain


Domain annotation for each model (and alignments):
>> Ribosomal_60s  60s Acidic ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.7  15.2   8.3e-16   7.4e-12       1      88 []      16      97 ..      16      97 .. 0.69

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 8.3e-16
                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XX--SS--.STTT CS
  Ribosomal_60s  1 eptaenikkvlkaagveveaarvkllvkalegkdieellangaaklaaaaaaaaaaaaaaaaaaaaeekkkeeeeeEeedddmG.fgLF 88
                   e++++ni +v+ka+g++v++a+vk+lv+al++++iee+++++  ++      aaaa++aaaa++a++e++ +  +  ee  ++G  +LF
     EPA06566.1 16 EVNEANISSVVKASGATVNDAQVKALVAALADVNIEEAIKAAPVAV------AAAAGPAAAAPEAKKEAPVDHSKT-EEAAMEGlSSLF 97
                   689**************************************96553......333333333333333333333332.333455555555 PP

>> PepSY_2  Peptidase propeptide and YPEB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1     0.011        97      27      51 ..      14      38 ..      11      46 .. 0.88
   2 ?   11.4   3.1   2.7e-05      0.24       4      40 ..      57      94 ..      54      98 .] 0.75

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.011
     PepSY_2 27 adwlpreklvakleaqGykvkkiev 51
                ++++++++++  ++a G +v +++v
  EPA06566.1 14 QKEVNEANISSVVKASGATVNDAQV 38
                6788999*************99998 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 2.7e-05
     PepSY_2  4 lalalallaaaAlA.grrdtdspkadwlpreklvakle 40
                + +a+a++a++A A  + ++++p++   ++e++++ l 
  EPA06566.1 57 APVAVAAAAGPAAAaPEAKKEAPVDHSKTEEAAMEGLS 94
                4456667776666637788999***********99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1097  (0.0611858); expected 358.6 (0.02)
Passed bias filter:                      600  (0.0334653); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 697.16
//
Query:       EPA06567.1  [L=190]
Description: hypothetical protein BG20_I0761 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.077   12.8   0.1       0.17   11.7   0.1    1.3  1  Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit
        2.5    8.0   4.3        5.4    7.0   4.3    1.4  1  DUF2897      Protein of unknown function (DUF2897)


Domain annotation for each model (and alignments):
>> Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   1.9e-05      0.17      71      98 ..     115     149 ..     100     168 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.9e-05
                  GGSSEEEEESHHHHH-TGGGSTT-TEE.......- CS
  Oxidored_q6  71 ekakaviavGtCAafGGipaaannpsv.......g 98 
                     + via G+C+ +G +++a++  +        g
   EPA06567.1 115 LGVNSVIAKGKCSFYGAVMKANDGKTLgatmllkG 149
                  55678**************9988663322233331 PP

>> DUF2897  Protein of unknown function (DUF2897)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   4.3   0.00061       5.4       8      21 ..      28      41 ..      28      43 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00061
     DUF2897  8 IiilVlgvIvGnla 21
                Ii+l+l+vIvG+l 
  EPA06567.1 28 IIFLALSVIVGSLI 41
                9***********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 1097.66
//
Query:       EPA06568.1  [L=277]
Description: Ser/Thr phosphatase family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.1e-19   69.9   0.4      6e-19   69.4   0.4    1.2  1  Metallophos    Calcineurin-like phosphoesterase
      2e-15   57.4   0.0    2.8e-15   56.9   0.0    1.2  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
      7e-07   28.8   0.1    0.00055   19.3   0.1    2.2  2  Metallophos_3  Metallophosphoesterase, calcineurin superfamil
      0.005   16.7   0.0     0.0081   16.1   0.0    1.3  1  DUF2124        Uncharacterized protein conserved in archaea (


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.4   0.4   1.3e-22     6e-19       2     204 .]      31     211 ..      30     211 .. 0.70

  Alignments for each domain:
  == domain 1  score: 69.4 bits;  conditional E-value: 1.3e-22
                  EEEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSS...HHHHHHHHHHHHHHHHTSEEEEEC-TTSCHHH.HHHHHHHHHHHHHHHH CS
  Metallophos   2 rilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrg...dlekellellaalvkypipvylllGNHegfee.ellnkygylgifsepw 95 
                   i++i+DlH        d++++l+d++++  +p++++++GDl+++g   ++e  ++ell+++ +  ++++++ GNH+ +++ ++l +           
   EPA06568.1  31 LIVQISDLH-VGSQFLQDKFDQLVDEVNQL-NPNVIVVTGDLTNEGlmhEYER-CQELLTKFKS--KKIITISGNHD-YRNtGYLLF----------- 111
                  599******.44445555555555555555.*****************66666.9999777777..69*********.555555555........... PP

                  EHHHCEEETSEEEEEETTEEEEEEEESECEEETHHHHHHHHHHHSCHHHHCC...HHHHHHHHHHTTCSEEEEEESSESSCSSSCSCCHHHHH..... CS
  Metallophos  96 rsdaevfnnlplaslgsgslkvlllhGgspellvsldklgslnleleapepg...dewlkdlekrekadwvivlgHsplyrgsgylfgdeale..... 185
                     +++f +  +++l ++   vl+  G  ++             ++++ e g   ++wl++++k+ k++++i+  H+ l   + +  g+++l      
   EPA06568.1 112 ---KKFFPFEAINELSDD--VVLVTLGT-ARP------------DRNEGEVGyrqNLWLERTMKKYKDKVKILAMHHHLI--AIPDTGSDQLTvvdag 189
                  ...677788888886666..55555555.222............334444446658888889999999999999999999..3333333333336666 PP

                  ...HHHHHTTESEEEEESSSSE CS
  Metallophos 186 ...dllkkygvdlvisGHtHvy 204
                     +   + gvdlv++GH H++
   EPA06568.1 190 dvlRTILDTGVDLVLCGHKHRP 211
                  6665667888**********85 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.9   0.0   6.2e-19   2.8e-15       1     164 [.      30     247 ..      30     248 .. 0.74

  Alignments for each domain:
  == domain 1  score: 56.9 bits;  conditional E-value: 6.2e-19
  Metallophos_2   1 MklaiiSDlH....snldaleavlealkevgvdaiihaGDl.eeeepevleellela......pvlaVrGNnD....................... 62 
                    M ++ iSDlH       d  +++++++++ +++ i+++GDl +e+  +  e+++el+      +++++ GN+D                       
     EPA06568.1  30 MLIVQISDLHvgsqFLQDKFDQLVDEVNQLNPNVIVVTGDLtNEGLMHEYERCQELLtkfkskKIITISGNHDyrntgyllfkkffpfeainelsd 125
                    999*******9755445667788*****************97666666666666666777888*******************99999999999985 PP

  Metallophos_2  63 .....eev..veedvlreaaelgtdlpeeaelel..agekvlliHgdpl............gvkdalaellkeaeegsdvvvcGHtHvpevekegg 137
                              ++ d+ + + +++++l  e++++   +++k+l +H++               ++ ++ +++ +   g+d+v+cGH H+p   + g+
     EPA06568.1 126 dvvlvT-LgtARPDRNEGEVGYRQNLWLERTMKKykDKVKILAMHHHLIaipdtgsdqltvVDAGDVLRTILD--TGVDLVLCGHKHRPWEWNFGK 218
                    333321.1233444444444444444444444435677779999999559***99998755444444444444..8999**********99999** PP

  Metallophos_2 138 vlvvnPGsvgeprdgdpe..tyaildtde 164
                    ++vvn+G ++  r +     ty i+++++
     EPA06568.1 219 LMVVNAGTATSERVRGLFenTYNIITISN 247
                    **********9977665566888887765 PP

>> Metallophos_3  Metallophosphoesterase, calcineurin superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   1.2e-07   0.00055       8      74 ..      32     102 ..      25     131 .. 0.72
   2 !    7.6   0.0   0.00046       2.1     166     252 ..     154     250 ..     142     254 .. 0.64

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.2e-07
                    EEEEE--TT-....GGGHHHHHHHHHHH--SEEEEES-----HHHHHHHHHHHHTT---.-THHHHHHHHHH CS
  Metallophos_3   8 vlaisdlkge....vellerlveviedkdpDllvlvGdlvkaeakadeyesaqeerrep.dkkeileeknei 74 
                    ++ isdl+       + +++lv+ +++ +p+++v++Gdl  +e+  +eye++qe   +   kk i    n++
     EPA06568.1  32 IVQISDLHVGsqflQDKFDQLVDEVNQLNPNVIVVTGDL-TNEGLMHEYERCQELLTKFkSKKIITISGNHD 102
                    55666666431112477899*******************.9***********98766653666665444444 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00046
                    GGGGGS---EEEEEESS--S-SST..BTTBS---S-HHHHHHHHHH--SEEEE-SS--EEEE.ETTEEEEE--B........GGGTEEEEEETTTT CS
  Metallophos_3 166 kvlkelkdrrkvlllatpPigelv..adkglkekgsevvaelvktlnPevvvvghavkehee.lgktlvvnPGa........leeGdfavvdleek 250
                    + +k+ kd+ k+l ++   i   +   d+     + +v+ +++ +   ++v++gh ++  e+  gk +vvn G         l e  + ++ +++k
     EPA06568.1 154 RTMKKYKDKVKILAMHHHLIAIPDtgSDQLTVVDAGDVLRTIL-DTGVDLVLCGHKHRPWEWnFGKLMVVNAGTatservrgLFENTYNIITISNK 248
                    5677777888887777766555552133333334556666655.56789*********998758********972222222233455666666666 PP

                    EE CS
  Metallophos_3 251 kv 252
                     +
     EPA06568.1 249 SI 250
                    65 PP

>> DUF2124  Uncharacterized protein conserved in archaea (DUF2124)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.8e-06    0.0081      68     125 ..      50     107 ..      25     120 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.8e-06
                 EEEEEE-.-S-EEEEEEEGGGGSTTTS--HHHHHHHHHHHEEEEEEEEEETTHHHHTT CS
     DUF2124  68 mqleeeaeeekadvvvllGGlampkikveaedvkeliekiekkkviGvcfmsifekag 125
                  ql +e+++ +++v+v+ G l+ + +  e e  +el++k+++kk+i ++  + ++++g
  EPA06568.1  50 DQLVDEVNQLNPNVIVVTGDLTNEGLMHEYERCQELLTKFKSKKIITISGNHDYRNTG 107
                 58999*****************************************998776666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 1765.50
//
Query:       EPA06569.1  [L=286]
Description: hypothetical protein BG20_I0758 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2005.43
//
Query:       EPA06570.1  [L=318]
Description: hypothetical protein BG20_I0755 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.017   15.3   1.1      0.041   14.0   1.1    1.7  1  DUF1102          Protein of unknown function (DUF1102)
       0.14   12.0   0.1       0.24   11.3   0.1    1.3  1  Glyco_hydro2_C5  Glycoside hydrolase family 2 C-terminal doma


Domain annotation for each model (and alignments):
>> DUF1102  Protein of unknown function (DUF1102)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   1.1   4.6e-06     0.041      47      87 ..      18      67 ..      14     124 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.6e-06
     DUF1102 47 seYvFdevfevsndlweneespivveiksenssv..klyage.......v 87
                  Yv d+v+++s ++  + +s+iv++i+s+ + v  k ++ +       +
  EPA06570.1 18 NSYVIDDVIKISGKVVFDANSSIVIQIRSTSDIVaiKQFSPSksgtfstS 67
                57**************************9888651156777744443332 PP

>> Glyco_hydro2_C5  Glycoside hydrolase family 2 C-terminal domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   2.7e-05      0.24      19      98 ..      20     104 ..      15     108 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.7e-05
  Glyco_hydro2_C5  19 fvtvevvDknGnlvpnadnevtfeveGpGelvgvdngdptslesfksn.....erkafnGkalaivrstkeaGkitltasaeglk 98 
                      +v  +v+   G++v +a+  + ++++   ++v++++ +p++   f+++        + +G+ ++iv  t+e+ + t ++sa +++
       EPA06570.1  20 YVIDDVIKISGKVVFDANSSIVIQIRSTSDIVAIKQFSPSKSGTFSTSfdaagPKWTQSGTYTVIVSYTGEKSEKTFNFSAVNIS 104
                      5666677778*****************************99998888877777677889*************9999999987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       897  (0.0500307); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2132.30
//
Query:       EPA06571.1  [L=107]
Description: RNA polymerase Rpb4 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.9e-08   32.7   0.9    1.5e-07   31.8   0.9    1.5  1  RNA_pol_Rpb4  RNA polymerase Rpb4
     0.0077   16.2   0.0        2.9    7.9   0.0    2.4  2  Integrase_Zn  Integrase Zinc binding domain
  ------ inclusion threshold ------
      0.027   15.0   0.3      0.049   14.2   0.2    1.5  1  DUF4844       Domain of unknown function (DUF4844)


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb4  RNA polymerase Rpb4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.9   2.4e-11   1.5e-07      39     120 ..      25     105 ..       2     107 .] 0.85

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 2.4e-11
                   CHHCHHHHHHHHHHHCTHHTTSSHHHHHHHHHHHTTSTSTHHHHHHHHHCSTSSHHHHHHHSTTGTTTSTSHHHHHHHHHHH CS
  RNA_pol_Rpb4  39 gnlnkilkktleyltnkfsrlkneekfnelvellksfeLtkaEklqlvnlkPesavelktlieeleerfedeqleeiLdelk 120
                   +++++i++ t++y+++ f + + +++ +   +l+k  +Lt+ E++ +vn++P+s++el++     ++ +  e+le++L+++k
    EPA06571.1  25 EEMDQIQRWTYDYVSK-FVKIDPKDAKEMKKQLMKDCDLTEEEAVEIVNIRPTSLAELRSFTFGWKKLILAETLEKMLKIIK 105
                   6899***********9.****95555555556666888*****************************************998 PP

>> Integrase_Zn  Integrase Zinc binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0   0.0     0.002        12      14      30 ..       3      19 ..       1      21 [. 0.89
   2 !    7.9   0.0   0.00048       2.9      14      31 ..      55      72 ..      53      73 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.002
  Integrase_Zn 14 aLrkkFgitrkqAreIV 30
                   ++kk++i++++ +eI+
    EPA06571.1  3 EIKKKQSISLSEVKEIL 19
                  5799************6 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00048
  Integrase_Zn 14 aLrkkFgitrkqAreIVq 31
                   L k++ +t ++A eIV+
    EPA06571.1 55 QLMKDCDLTEEEAVEIVN 72
                  6899*************6 PP

>> DUF4844  Domain of unknown function (DUF4844)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.2   8.2e-06     0.049      61     105 ..       3      48 ..       1      54 [. 0.87

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 8.2e-06
     DUF4844  61 klqkklkltlerldkqylelDtEdrerildYmee.lmdivklessd 105
                  ++kk  ++l+++++ ++++D E++++i ++ ++ +++ vk++ +d
  EPA06571.1   3 EIKKKQSISLSEVKEILGKVDVEEMDQIQRWTYDyVSKFVKIDPKD 48 
                 5688999***********************9775378999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       957  (0.0533772); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 704.41
//
Query:       EPA06572.1  [L=327]
Description: NOSIC domain protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-65  220.2   0.1    3.5e-65  219.7   0.1    1.2  1  Nop       snoRNA binding domain, fibrillarin


Domain annotation for each model (and alignments):
>> Nop  snoRNA binding domain, fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  219.7   0.1     2e-69   3.5e-65       2     218 ..      76     288 ..      75     304 .. 0.90

  Alignments for each domain:
  == domain 1  score: 219.7 bits;  conditional E-value: 2e-69
                 HHHHHHHHHHHHHHHHHHHTTTSTCHHHHS-SHHHHHHHHHHCCCCHCCT.HH.TT.HHHHHHHHHHHHCHHHH-SSS-S-HHHHHHHHHHHHHHHHHH CS
         Nop   2 ldeidkeintlhkrvrewYswhFpELeslvkdnleYakvvkligneredlekk.eedeelakevimaakvtastsmgaelseedlknikelcdrvlele 99 
                 ldeidk  n l++r+rewY+ hFpEL++++++   Ya++v + +  r+ l+kk  ed   ++++ ++++  as+s g ++se +l+ ++++++++l+++
  EPA06572.1  76 LDEIDKIANGLSSRLREWYGLHFPELDNIIDSINGYAQIVLAGK--RDALTKKvYEDAGFPESKADMISLLASKSRGGDISEVNLTIVQSIAKQILDFH 172
                 799*************************************9988..45665553445559*************************************** PP

                 HHHHHHHHHHHHHHHHHSHHHHHHCHHHHHHHHHHHHSSHHHHHCS-HHHHTTTT-HHHHCCCHH.T---SSSCHHHCSHHHHHTS-CCCHHHHHHHHH CS
         Nop 100 elrkelleYlesrmsaiAPNlsaLvGeevaarLishaGgLtnLakmPastiqilGaekalfralk.kkntpkyGliyhselvqkatppklkkkiaRlla 197
                 +lrk+l++++es+m+++APNlsa++G+ v+ar+++ aG+L++La mPastiqi+Gaekalfr+lk + + pk+Gl++++ +v+ a+p+++++kiaR++a
  EPA06572.1 173 DLRKKLESHVESEMQTVAPNLSAILGAAVGARILGRAGSLKKLAAMPASTIQIIGAEKALFRSLKtGAQPPKHGLLFQHAMVH-AAPRWQRGKIARAIA 270
                 *****************************************************************777***************.66************* PP

                 HHHHHHHHHHHTT----SHHH CS
         Nop 198 aKvalaaRiDafsekdgslGk 218
                 aK+++aaR+D ++e    + k
  EPA06572.1 271 AKAVIAARVDVYGEG---INK 288
                 **********77533...333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2187.17
//
Query:       EPA06573.1  [L=396]
Description: DNA repair and recombination protein RadA [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-89  299.9   0.0    1.9e-89  299.3   0.0    1.3  1  Rad51            Rad51
    4.7e-11   42.7   0.1    7.8e-11   41.9   0.1    1.3  1  RecA             recA bacterial DNA recombination protein
    8.5e-10   39.1   0.1    3.4e-09   37.2   0.1    2.1  1  HHH_5            Helix-hairpin-helix domain
    7.7e-09   35.4   0.0    1.3e-08   34.7   0.0    1.3  1  AAA_25           AAA domain
    2.3e-07   30.4   0.1    2.3e-07   30.4   0.1    1.9  2  ATPase           KaiC
     0.0005   19.8   0.1     0.0015   18.3   0.0    1.8  2  AAA_24           AAA domain
  ------ inclusion threshold ------
      0.051   13.4   0.0        1.2    9.0   0.0    2.7  2  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
       0.15   12.0   0.0       0.37   10.7   0.0    1.6  2  NACHT            NACHT domain
        1.8    7.4   8.6        2.8    6.8   8.6    1.2  1  NARP1            NMDA receptor-regulated protein 1


Domain annotation for each model (and alignments):
>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  299.3   0.0   9.5e-93   1.9e-89       2     254 ..      71     318 ..      70     319 .. 0.99

  Alignments for each domain:
  == domain 1  score: 299.3 bits;  conditional E-value: 9.5e-93
                 S-EBHHHHHHHHHSS-EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEESSS---GGGGHHHHHHTT--HH CS
       Rad51   2 gfvsavellekrsellqlttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyidtegtfrperlveiaerykldke 100
                 +fvsa+e++++r+++ ++ttG++ lD+l +GG+et+++te++Gef+sGktq++htl+v+vq p+  gG +g ++yidte tfrper+v+ia+ +++d+e
  EPA06573.1  71 DFVSATEVYKRRQDIGKITTGTNCLDTLFDGGVETQALTEVYGEFGSGKTQFAHTLSVMVQKPKTEGGLDGGVLYIDTENTFRPERIVSIAQAHEMDPE 169
                 69************************************************************************************************* PP

                 HHGGGEEEEE--STTHHHHHHHHTHHHHHHS-EEEEEEETTTGGGCH-------THHHHHHHHHHHHHHHHHHHHH--EEEEEEE-------.------ CS
       Rad51 101 evlenvayaRaytiehqeellqqaaallaedkfallivDsvtalyRtdfsgrgelakRqqklgkllrtLrkladefevavvitnqvvaqvdgqaalfsa 199
                 +vl+++ +aRay++ hq+ +l++a   + e++++l++vDs++ l+R+++ grg l++Rqqkl++++++L+++a+ ++ a + tnqv+a++d     f +
  EPA06573.1 170 KVLDRIIVARAYNSAHQTLILEEAGPVIEENNIKLIVVDSAVGLFRAEYLGRGTLSNRQQKLNHFVHMLSRIAETYNCAAIATNQVMASPDV----FFG 264
                 *******************************************************************************************9....99* PP

                 ------HHHHHHHH-SEEEEEEE-STTEEEEEEES-SSS-S-EEEEEEETTEEE- CS
       Rad51 200 dpkkPigGlvlahasttRlalrkgkgeeRivkvvdsPnlpeleavfaigeeGied 254
                 dp++PigG+v+ah+st R++++k  g++Ri+++vdsP+ pe+e+ fa+ge G++d
  EPA06573.1 265 DPTRPIGGNVVAHTSTYRIYFKK-SGKKRIARMVDSPHHPEEEVLFALGEAGVMD 318
                 ********************966.79***************************98 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   0.1   3.9e-14   7.8e-11      27     224 ..      81     290 ..      70     299 .. 0.76

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 3.9e-14
                 .-----EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHH..HHHHHHHHHT.T...--EEEEESS----HH....HHHHTT--....GGG-EEE CS
        RecA  27 eklkvetissGslaldialGiGGlpkGriieiyGpessGkttla..lhaiaeaqkk.g...gvaafidaehaldpk....yakklGvd....idellvs 111
                 +++++  i++G+  ld+ +  GG+    ++e+yG   sGkt +a  l+++++  k+ g   g + +id+e ++ p+     a++  +d    +d ++v+
  EPA06573.1  81 RRQDIGKITTGTNCLDTLFD-GGVETQALTEVYGEFGSGKTQFAhtLSVMVQKPKTeGgldGGVLYIDTENTFRPErivsIAQAHEMDpekvLDRIIVA 178
                 46899***********9776.********************986226666665554241224589********99633224666667733445667898 PP

                 --.SSHHHH..HHHHHHHHTTT--SEEEEE-TTT---STT-----------HHHHHHHHHHHHHHHHHTTT--EEEEEEE-----------------HH CS
        RecA 112 qp.dtGeqa..leiadalvrsgaidlivvdsvaalvpkaeieGemgdskvglqarlmsqalrkltgaisksntvvifinqirekiGvmfgnpetttGGr 207
                 +  ++  q+  le a  +++ + i livvds   l  +ae  G     +++ + + + + +  l+   +  n+++i  nq+     v fg+p    GG+
  EPA06573.1 179 RAyNSAHQTliLEEAGPVIEENNIKLIVVDSAVGLF-RAEYLGR---GTLSNRQQKLNHFVHMLSRIAETYNCAAIATNQVMASPDVFFGDPTRPIGGN 273
                 87245567622456667**************99986.6776554...333444444567788888888999**************************** PP

                 HHHHH-SEEEEEEEES- CS
        RecA 208 alkfyasvrldvrriee 224
                  +   ++ r+  +++++
  EPA06573.1 274 VVAHTSTYRIYFKKSGK 290
                 ****9999999888765 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   0.1   1.7e-12   3.4e-09       3      56 ..       6      59 ..       4      60 .. 0.95

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 1.7e-12
                HHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHHH CS
       HHH_5  3 eLlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriilelk 56
                 L s++G+Gp+t ++l +aG+  v dl+   + e+a+i+G+ k+tAe+i+  ++
  EPA06573.1  6 RLDSLEGVGPVTTRKLSDAGVHNVMDLIVRGPVEIAEITGMEKDTAEKIVNKAR 59
                699**********************************************98887 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.0   6.4e-12   1.3e-08      10     188 ..      83     254 ..      74     258 .. 0.76

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 6.4e-12
      AAA_25  10 vsvadlaapppprrwlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravg..ealrddarllvl 106
                 ++++++ +   +++ l++g +  ++l+ ++G  g+GKt +a  l++ v + k   g      g Vly+++E++    ++R+  +   +++++ + l+ +
  EPA06573.1  83 QDIGKITTGTNCLDTLFDGGVETQALTEVYGEFGSGKTQFAHTLSVMVQKPKTEGG----LDGGVLYIDTENTF--RPERIVSIAqaHEMDPEKVLDRI 175
                 467778888899999***999*************************9997665544....58***********9..34444444411555555555555 PP

      AAA_25 107 dlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralgg.......densnsdvgalvealeriarrtgaavllvhH 188
                  +a+       ++ +++tl+ ++      +iee ++++l+v+D+   ++++        +n++ + +++v +l ria+ +++a +++ +
  EPA06573.1 176 IVARA------YNSAHQTLILEE---AGPVIEE-NNIKLIVVDSAVGLFRAeylgrgtLSNRQQKLNHFVHMLSRIAETYNCAAIATNQ 254
                 45443......566677775554...4668899.88********9999888777674445555557*****************998765 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.1   1.2e-10   2.3e-07       2     167 ..      89     266 ..      88     298 .. 0.74
   2 ?   -3.4   0.4       2.5   4.9e+03      84     104 ..     318     338 ..     310     363 .. 0.50

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 1.2e-10
      ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaeky.....gepgvfvtveepa..edlrenakslGwdlekleeegklaiidasesae 93 
                  tg++ lD++++gG+  ++ + ++Ge G+GKt fa +  +   + +     +  ++++ +e +   e +   a++  +d ek+ ++  +++  a++sa+
  EPA06573.1  89 TTGTNCLDTLFDGGVETQALTEVYGEFGSGKTQFAHTLSVMVQKPKtegglDGGVLYIDTENTFrpERIVSIAQAHEMDPEKVLDR--IIVARAYNSAH 185
                 79*********************************987664433330111134679*****98666********************..77777776655 PP

      ATPase  94 esaeekdkedleelieelaeaikeikakrvviDsitgl..a.......yeekeavaReilrqlvrvlkklgvTailvsekss........s 167
                 +            ++ee   +i+e ++k +v+Ds  gl  a        +++++++ + ++ l r+ + +++ ai ++++           
  EPA06573.1 186 Q----------TLILEEAGPVIEENNIKLIVVDSAVGLfrAeylgrgtLSNRQQKLNHFVHMLSRIAETYNCAAIATNQVMAspdvffgdP 266
                 4..........5678889999*************988853222211112456667777777777777899999999999776455555444 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.5
      ATPase  84 aiidasesaeesaeekdkedl 104
                  + da +++++++++k++++ 
  EPA06573.1 318 DLEDAEKKTTKKTSKKTTKKE 338
                 444444444444443222222 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   7.5e-07    0.0015       7      77 ..     111     213 ..     108     234 .. 0.80
   2 ?   -2.6   0.1         2   3.9e+03     134     134 ..     327     327 ..     287     360 .. 0.62

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 7.5e-07
      AAA_24   7 iyGpsgiGKTtlakel.............gpkplfidtekGlksldadkfpdie.....swedfldevvel.................aaeladyktlv 70 
                 +yG+ g+GKT +a +l                +l+idte+      + ++++i        e++ld +                      e++++k +v
  EPA06573.1 111 VYGEFGSGKTQFAHTLsvmvqkpktegglDGGVLYIDTEN---TFRPERIVSIAqahemDPEKVLDRIIVAraynsahqtlileeagpVIEENNIKLIV 206
                 8*******************99999999989999999999...55888888888555664444444444447777888888998999977888899999 PP

      AAA_24  71 iDtidel 77 
                 +D++  l
  EPA06573.1 207 VDSAVGL 213
                 9998666 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2
      AAA_24 134 r 134
                  
  EPA06573.1 327 T 327
                 1 PP

>> DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0    0.0006       1.2       8      29 ..      12      33 ..       9      46 .. 0.91
   2 ?    0.9   0.0      0.21   4.1e+02      20      32 ..     314     326 ..     311     336 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0006
  DNA_pol_lambd_f  8 GVGpktAkkwyakGirtledlr 29
                     GVGp+t +k+ ++G+ ++ dl 
       EPA06573.1 12 GVGPVTTRKLSDAGVHNVMDLI 33
                     9*****************9996 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.21
  DNA_pol_lambd_f  20 kGirtledlrakr 32 
                      +G+++led+ +k+
       EPA06573.1 314 AGVMDLEDAEKKT 326
                      79********944 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       4.1   8.1e+03     143     161 ..      39      57 ..      21      58 .. 0.77
   2 ?   10.7   0.0   0.00018      0.37       5      47 ..     111     153 ..     108     190 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 4.1
                 ..EEEE--TCCHHHHHHHH CS
       NACHT 143 ivlevegfsesrrkqlvrk 161
                 +++e+ g++++ ++++v+k
  EPA06573.1  39 EIAEITGMEKDTAEKIVNK 57 
                 4679999999999999876 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00018
                 EEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTT CS
       NACHT   5 lqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsr 47 
                 + Ge GsGKT +++ l +  +++k ++g    v+++    + r
  EPA06573.1 111 VYGEFGSGKTQFAHTLSVMVQKPKTEGGLDGGVLYIDTENTFR 153
                 78********************999988766666666555555 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   8.6    0.0014       2.8     385     469 ..     295     384 ..     280     392 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0014
                 HHHH-TTGGG---H....HHHHT-S-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH--........-------------S-SSSTTTT-S- CS
       NARP1 385 kledkpkakeeeke....eaksaelseaerkklrkkakkaekkaekeeaekaekekekk.aaekkakkedeeakkededplgekLvktee 469
                 ++ d+p++ eee      ea   +l++ae+k  +k  kk  kk+++ e e a +++e + +++k++kke+e++ + + +    +Lv+t+e
  EPA06573.1 295 RMVDSPHHPEEEVLfalgEAGVMDLEDAEKKTTKKTSKKTTKKEKESEPEIAVESSELElETKKTTKKEKESEPEIAVESSNLELVQTTE 384
                 567777776666554333444458889999988888899988888888887776666443666666666666666777788888888764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2058  (0.114786); expected 358.6 (0.02)
Passed bias filter:                      907  (0.0505884); expected 358.6 (0.02)
Passed Vit filter:                       118  (0.00658152); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.47
# Mc/sec: 2515.06
//
Query:       EPA06574.1  [L=280]
Description: hypothetical protein BG20_I0766 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.085   13.4   0.1       0.16   12.4   0.1    1.4  1  IZUMO     Izumo sperm-egg fusion, Ig domain-associated


Domain annotation for each model (and alignments):
>> IZUMO  Izumo sperm-egg fusion, Ig domain-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   9.1e-06      0.16      18     108 ..      27     124 ..      16     132 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.1e-06
                 HTHHHHHSGGHHHHHHHHHHHHHTTT.....---SG.GGGGGSEEEHHHHHHHHHHHHHHHHHHHHS---HHHHHH.HHHHHHHHHHHHHHHHHHHHH CS
       IZUMO  18 edllpselehreklleraealledls.....ekela.enkflgvvdeetlekvasslkkelkrltdsdlkgelllk.eLlwllqkqkkklkealkefq 108
                  d+l s +  ++ +l+r  +++++ +     ++ ++ ++ ++g+v+ + le+   s +++l++l+ +  +   l++ eL +++ k+ +++ + l+e+ 
  EPA06574.1  27 GDYLDSVMYLNKFVLSRYPQIILHKQgepyeSRFSNvNSGYIGAVKMTVLEEQIHSTQETLQKLNRDAATKVNLINeELATIILKLDNQIVNELSEYL 124
                 55555555555556666666666555445443333313479****************************99999999*********999999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       889  (0.0495845); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1947.85
//
Query:       EPA06575.1  [L=60]
Description: hypothetical protein BG20_I0742 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.6e-11   41.7   3.2    1.5e-10   41.1   3.2    1.4  1  Ribosomal_S30  Ribosomal protein S30


Domain annotation for each model (and alignments):
>> Ribosomal_S30  Ribosomal protein S30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   3.2   8.5e-15   1.5e-10       2      54 ..       3      54 ..       2      59 .. 0.80

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 8.5e-15
                   TBX-STTTTHHHHHS-------------THHHHHHHHHHHTTSSS--SSSSS- CS
  Ribosomal_S30  2 vhGsLarAGKVrnqTPKveKqekkKkptGRakkRlqYnrRfvnvvvggkkkkg 54
                    hGsL++AGKVr+qTPKve   k        + +  +++Rf+   + g+ k g
     EPA06575.1  3 THGSLTKAGKVRGQTPKVEGR-KIVGTNSSLRNKSNFKKRFELGRFPGQNKPG 54
                   6******************99.55555666777789******97777776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       265  (0.0147805); expected 358.6 (0.02)
Passed bias filter:                      169  (0.00942607); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.40
# Mc/sec: 453.67
//
Query:       EPA06576.1  [L=270]
Description: oxidoreductase NAD-binding domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-09   37.7   0.1    6.5e-09   36.4   0.0    1.7  2  NAD_binding_1    Oxidoreductase NAD-binding domain
    1.7e-07   30.9   8.8    3.8e-07   29.8   8.8    1.6  1  DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydr
      0.002   18.4   0.0     0.0048   17.2   0.0    1.6  2  FAD_binding_6    Oxidoreductase FAD-binding domain
  ------ inclusion threshold ------
        0.6   10.2   2.9         19    5.3   0.0    2.8  3  NAD_binding_6    Ferric reductase NAD binding domain


Domain annotation for each model (and alignments):
>> NAD_binding_1  Oxidoreductase NAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.4   1.1e+04      70     103 ..       5      43 ..       2      47 .. 0.55
   2 !   36.4   0.0   1.4e-12   6.5e-09       1     106 [.     107     201 ..     107     204 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.4
                    SSSEESSHHHHHHHHHHH.....HSSTTEEEEEECSHHH CS
  NAD_binding_1  70 weggkgrvqdalleells.....lkkeethvyvCGppgM 103
                     ++ k  v +++++e+        +++ +  ++ G  +M
     EPA06576.1   5 HNHTKICVIEKVIDETPTvrtliFSDDVMSSVMPGQFAM 43 
                    455566666666666555555544455555555555555 PP

  == domain 2  score: 36.4 bits;  conditional E-value: 1.4e-12
                    EEEEGGGGHHHHHHHHHHHHHCTTCSEEEEEEEESSGCGSTTHHHHHHHHHHCTTEEEEEEEESSCTTTSSSEESSHHHHHHHHHHHHSSTTEEEE CS
  NAD_binding_1   1 miagGtGiaPvrsvlraileeakdktkvvlvyGnrteedllyreeleelakklpgrlkvvavvsreeagweggkgrvqdalleellslkkeethvy 96 
                    +++gGtG+ P++ +l  +  e +    v+++ G++++e++++++  ++l k++ ++  +v+    +++g+ g+kg+v+d + + +++  +  + vy
     EPA06576.1 107 LVGGGTGLVPMMRLLTYVRPE-D---DVTVLIGAKSKEEVFFENLANNLLKNNTHK-VIVT----TDDGSYGEKGFVTDMVEKLVAG--SHFDGVY 191
                    79*************999887.4...59*********************7777775.3333....57888899******99777777..99***** PP

                    EECSHHHHHH CS
  NAD_binding_1  97 vCGppgMika 106
                     CGp++M+  
     EPA06576.1 192 TCGPEKMMYK 201
                    *******965 PP

>> DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   8.8   8.5e-11   3.8e-07       1      40 [.     218     249 ..     218     251 .. 0.92

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 8.5e-11
                      ----SSSSSSS-TTEEEETTCTT.CEEETTTT-CEEECCC CS
  DHODB_Fe-S_bind   1 eerMaCGvGaClgCvvktkggdggeykrvCkdGPvFdade 40 
                      e++M+CGvG+C++C++            vC+dG vFd+  
       EPA06576.1 218 ERMMKCGVGICGSCCMGE--------DLVCRDGTVFDGAH 249
                      89**************99........48*********975 PP

>> FAD_binding_6  Oxidoreductase FAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.1e-06    0.0048      16      97 ..      25      97 ..      10      98 .. 0.70
   2 ?   -3.8   0.0       3.9   1.8e+04      71      87 ..     170     186 ..     155     188 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.1e-06
                   EEEEEESTTTS-----TT-EEEEEEC.ETTCCEEEEEE.BSSTTECCEEEEEEE--TT-HHHHHHHCS-TT-EEEEEEEE-SE CS
  FAD_binding_6 16 ifrfklpsekqklglpvGqhvflrlk.ikgeaviRsYtpissenekGelellvkvypgGkmsqaLdelkigdtleikGPlGkf 97
                   ++ f+ + +++    ++Gq+ ++ ++ i++     + +++  ++e+G+  + v+  ++G  s  L ++k+g+++ ++GP+G++
     EPA06576.1 25 TLIFSDDVMSS---VMPGQFAMVWIPgINEL----PMSVM-ISQESGKAAFTVR--KHGTASTGLFNVKVGQQIGVRGPYGNA 97
                   44444444433...67788888888833332....44533.3467899999999..58***********************86 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 3.9
                    TT-HHHHHHHCS-TT-E CS
  FAD_binding_6  71 pgGkmsqaLdelkigdt 87 
                    ++G ++ + ++l  g++
     EPA06576.1 170 EKGFVTDMVEKLVAGSH 186
                    56667777777666655 PP

>> NAD_binding_6  Ferric reductase NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0    0.0043        19       3      21 ..     104     122 ..     102     168 .. 0.82
   2 ?    4.7   0.0    0.0065        29     138     153 ..     189     204 ..     174     207 .. 0.84
   3 ?   -2.5   0.8       1.1   4.9e+03     135     150 ..     221     236 ..     211     238 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0043
                    xxxxxxxxxxxxxxxxxxx RF
  NAD_binding_6   3 nvllvagGiGitpfisilk 21 
                     +llv+gG+G+ p++ +l 
     EPA06576.1 104 KLLLVGGGTGLVPMMRLLT 122
                    599**********998876 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0065
                    xxxxxxxxxxxxxxxx RF
  NAD_binding_6 138 gvfvCGppklvkevkk 153
                    gv++CGp+k+++++ +
     EPA06576.1 189 GVYTCGPEKMMYKTVQ 204
                    8*********998765 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 1.1
                    xxxxxxxxxxxxxxxx RF
  NAD_binding_6 135 ssvgvfvCGppklvke 150
                     + gv +CG+ ++ ++
     EPA06576.1 221 MKCGVGICGSCCMGED 236
                    5779999**9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1916.50
//
Query:       EPA06577.1  [L=624]
Description: ATPase/histidine kinase/DNA gyrase B/HSP90 domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-17   63.3   0.2    6.1e-17   62.1   0.2    1.6  1  HATPase_c       Histidine kinase-, DNA gyrase B-, and HSP90-l
    1.4e-14   54.5  11.9    1.4e-14   54.5  11.9    2.2  2  dCache_1        Cache domain
    7.1e-11   42.0   0.0    1.6e-10   40.8   0.0    1.6  1  HisKA           His Kinase A (phospho-acceptor) domain
    1.3e-06   28.2   1.9    2.6e-06   27.3   0.1    2.6  2  HATPase_c_5     GHKL domain
    0.00086   19.6   0.0     0.0025   18.2   0.0    1.9  1  HAMP            HAMP domain
  ------ inclusion threshold ------
       0.02   14.9   2.0        7.1    6.7   0.1    2.9  2  Lip_prot_lig_C  Bacterial lipoate protein ligase C-terminus
       0.09   12.3   0.0       0.26   10.8   0.0    1.8  1  LMSTEN          LMSTEN motif


Domain annotation for each model (and alignments):
>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.1   0.2   2.4e-20   6.1e-17       2     111 ..     519     621 ..     518     622 .. 0.88

  Alignments for each domain:
  == domain 1  score: 62.1 bits;  conditional E-value: 2.4e-20
                 HHHHHHHHHHHHHHHHHHH.HSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHHHHHHHHHTTTEEEEEEETT CS
   HATPase_c   2 dekrLrqiisnlvdNavkf.atkageieveikaseddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsivkklvelmgGeiwvesepg 99 
                 d+k+++ ++ n++ Na+++   ++g+i ++ k+ +d+++i+++D+G+ + + +l+k+fe++ +     ++ +gtGlGls +k+++e++gG+i+ +++p 
  EPA06577.1 519 DSKKMETVFANIILNAIQAiGESGGKILIKSKRINDKIEIKISDSGPEVAEGILEKIFEPLFT-----TKEKGTGLGLSSCKNIIEQHGGTISASNNP- 611
                 7888999***********944477788887775448***********************6666.....5899**********************8888. PP

                 TEEEEEEEEESS CS
   HATPase_c 100 rGttftftlple 111
                   ttft+ lp++
  EPA06577.1 612 --TTFTIILPEK 621
                 ..*****99986 PP

>> dCache_1  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.5  11.9   5.4e-18   1.4e-14      18     248 ..      48     305 ..      38     306 .. 0.73
   2 ?    0.3   0.3       0.2   5.1e+02      17      81 ..     421     509 ..     414     537 .. 0.62

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 5.4e-18
    dCache_1  18 lanniedvldslenlaetlasnpslqdlleepnra.............................neasreslqallksilksnpdi..sgvylvdadGq 85 
                 + +++++++d++    +++++ p++q++l+e n                               + +  ++l++ ++ + + +++   s++y+ +a G 
  EPA06577.1  48 MMQDLDEYIDKRIGDFKQITQIPTVQNSLKESNLKfsqiknieqiiklqdtinkeknqpfigsnDMKLTSELTDVINFYKSEYDYDviSELYITNAYGA 146
                 6799***************************999788777777777777666666666665555444445555555545444444456799******** PP

    dCache_1  86 viassdpssppnlegtddpadrdwykealaggggkpvisdpyvdqtggkpvitiavpiyddsgkfiGvlaadldldnlqd.llsni...klgetgyvfi 180
                 +ia  +  s       +   d+ w++e +++g   ++i+d+  d++  ++++ti   i dd g+fiG+l ++l+l+++ + +++++   +  ++  +++
  EPA06577.1 147 NIAIGSGTS------EYRHDDETWWQESKSKG---VYIGDVIYDKEHKNYTTTIGLRINDDEGNFIGILSVSLTLNDVIHeFINDAeilSTIQNRTILL 236
                 *99654443......4577899********99...99****87788789**************************875555***995553344577*** PP

    dCache_1 181 vdsdGniiahpd.kdl.lgknlrdelkaqealekalakiesgvssvklngeeylvayapip.....tglgWylvv 248
                 v+++G+ii++   +d+ + k + d        +  + k  + ++    n++ +l+ +a++      +g+gW+ +v
  EPA06577.1 237 VNEKGQIIYSDGiQDFkDSKPI-DYF-----DKINSLKDVGTINISNNNDDPRLISFAKSTgykqfEGFGWITIV 305
                 **********876555322222.221.....22222244555555555557777778877778888669998775 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.2
    dCache_1  17 qlanniedvldslenlaetl.....asnpslqdlleepnra...................neasreslqallksilksnpdisgvylvd 81 
                 ++a+++++ l+++++++  +     +s+p++ ++ +  nra                   +++s+++++++++   +s +  +++ + +
  EPA06577.1 421 SMAHDLKNPLATIKTSSAIIqkqgnNSDPEVEKAIQRMNRAifrmshqiddvlnfvrmtpMNLSEKKVAEIINYAIDSLEIPNNIKIET 509
                 55666666666666666666666555556666666666666666666666666666666666677777777776666665335555555 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   0.0   6.3e-14   1.6e-10       3      64 ..     416     478 ..     414     480 .. 0.94

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 6.3e-14
                 HHHHHHHHHHHHHHHHHHHHHHHHHHC...T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCH CS
       HisKA   3 grflagvaHELrtPLsailgnaeaLkre.gklteelkeyletiesearrldhlvedlLdlsri 64 
                 g++ a++aH+L++PL++i+  + +++++ ++ ++e++++++++ + + r++h+++d+L + r+
  EPA06577.1 416 GQLSASMAHDLKNPLATIKTSSAIIQKQgNNSDPEVEKAIQRMNRAIFRMSHQIDDVLNFVRM 478
                 89***********************99998889***************************998 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.2       1.6   4.1e+03      42      61 ..      68      87 ..      45     113 .. 0.59
   2 !   27.3   0.1     1e-09   2.6e-06       4      96 ..     521     616 ..     518     619 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.6
  HATPase_c_5 42 liisieNsyegekkklessk 61
                  i +++Ns ++++ k+ + k
   EPA06577.1 68 QIPTVQNSLKESNLKFSQIK 87
                 44466777666554444333 PP

  == domain 2  score: 27.3 bits;  conditional E-value: 1e-09
  HATPase_c_5   4 ldlcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyegek....kkle..sskskkeehGiGlksireivkkykgnlsieaedglFt 95 
                  + + +++ n++ NAi+a  +      +I ++ ++ ++++ i+i+ s  +      +k++    ++k++  G+Gl+s ++i+++++g++s +++ ++Ft
   EPA06577.1 521 KKMETVFANIILNAIQAIGESG---GKILIKSKRINDKIEIKISDSGPEVAegilEKIFepLFTTKEKGTGLGLSSCKNIIEQHGGTISASNNPTTFT 615
                  56789************99977...5899999999999******9966633223355443434677899***************************98 PP

  HATPase_c_5  96 l 96 
                   
   EPA06577.1 616 I 616
                  5 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   9.8e-07    0.0025       3      52 ..     342     391 ..     340     392 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 9.8e-07
                 HHTTHHHHHHHHHHHHHHTTTBTSSTCCTTSSSHHHHHHHHHHHHHHHHH CS
        HAMP   3 arrilrPLrrLaraarriaaGdldtrlpvsgrDEiGeLarafNaMldrLr 52 
                 +  i+rPLr L++ a++ + G +d     s   Ei +++++fN M  +L+
  EPA06577.1 342 SYFISRPLRFLSQMAKQFSVGKFDLKFRGSKISEINMIGKSFNSMGLSLE 391
                 5679*****************9999999*****************87776 PP

>> Lip_prot_lig_C  Bacterial lipoate protein ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.3    0.0033       8.6      34      82 ..      60     108 ..      58     109 .. 0.93
   2 ?    6.7   0.1    0.0028       7.1       6      43 ..     353     388 ..     349     407 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0033
                     EESBSSSSHCHHHHHHHTTSBSSHHHHHHHHHTSCHHHHCCTHHHHHHH CS
  Lip_prot_lig_C  34 yGDffgpkdieeleekLigvkyekeaieealekidlseyfggieleell 82 
                      GDf +  +i  +++ L+   ++ ++i+++ + i+l++ +++ +++ ++
      EPA06577.1  60 IGDFKQITQIPTVQNSLKESNLKFSQIKNIEQIIKLQDTINKEKNQPFI 108
                     59**************************************998888775 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0028
                     EEEEEEETTEEEEEEEEEETTEEEEEEEEESBSSSSHC CS
  Lip_prot_lig_C   6 vkkkkrfdwGtvevrldvekgiIkdikiyGDffgpkdi 43 
                      +++k+f++G++++++  + ++I++i++ G +f++  +
      EPA06577.1 353 SQMAKQFSVGKFDLKF--RGSKISEINMIGKSFNSMGL 388
                     5789*******99887..6889*********9987654 PP

>> LMSTEN  LMSTEN motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0    0.0001      0.26       4      30 ..     430     456 ..     427     459 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0001
      LMSTEN   4 leviqsssafiQrpfvddDPdKEkriK 30 
                 l +i+ ssa+iQ+  ++ DP+ Ek i 
  EPA06577.1 430 LATIKTSSAIIQKQGNNSDPEVEKAIQ 456
                 667899******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (624 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1134  (0.0632495); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.68u 0.27s 00:00:00.95 Elapsed: 00:00:00.45
# Mc/sec: 4171.10
//
Query:       EPA06578.1  [L=212]
Description: membrane family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-38  128.8  24.9    1.4e-20   72.9   5.5    2.4  3  UPF0126   UPF0126 domain


Domain annotation for each model (and alignments):
>> UPF0126  UPF0126 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.9   5.5   7.8e-25   1.4e-20       2      77 ..      14      87 ..      13      88 .. 0.93
   2 !   65.0   7.8   2.3e-22   4.2e-18       3      76 ..     100     172 ..      98     174 .. 0.95
   3 ?   -3.4   0.1      0.52   9.3e+03      66      74 ..     183     191 ..     178     194 .. 0.47

  Alignments for each domain:
  == domain 1  score: 72.9 bits;  conditional E-value: 7.8e-25
                HHHHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHHHHHTTSSSSGHHHSSTCHHHHHHHHHHHHHHHH CS
     UPF0126  2 ildaiGlaafavsGalvAlkkgldllgvvvlGvvTAvgGGvlRDvllgrevPvvllreelyataallgalvvvlla 77
                ild++G++afav+Ga +A+++++d++g+++l+++T+v+GG++RD++lg+  P  l +++ y++++++ ++ +++l+
  EPA06578.1 14 ILDLFGTMAFAVTGAFKAIEHKFDIVGIMLLATITGVAGGTIRDIVLGQ-FPNSL-SDPAYVAITVISGVGIFFLY 87
                89**********************************************6.**999.679**999999999888876 PP

  == domain 2  score: 65.0 bits;  conditional E-value: 2.3e-22
                 HHHHHHHHHHHHHHHHHHHT.TS-HHHHHHHHHHHHHHHHHHHHHHTTSSSSGHHHSSTCHHHHHHHHHHHHHHH CS
     UPF0126   3 ldaiGlaafavsGalvAlkk.gldllgvvvlGvvTAvgGGvlRDvllgrevPvvllreelyataallgalvvvll 76 
                 +daiGl++f+++Ga  A +  gl+ll +++ G++TAvgGG+lRDv++ + +P+v+++e +y++a+++g+ v++l+
  EPA06578.1 100 FDAIGLGVFSIIGATFAYHLvGLNLLAIMLAGILTAVGGGILRDVIVSH-TPIVFIKE-FYISASFIGISVFYLM 172
                 8******************99***************************6.******98.**********999986 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 0.52
                 HHHHHHHHH CS
     UPF0126  66 allgalvvv 74 
                 +++g+++++
  EPA06578.1 183 TVIGIVLTT 191
                 333444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       849  (0.0473534); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 1312.20
//
Query:       EPA06579.1  [L=99]
Description: ribosomal protein L21e [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.3e-19   67.7   1.8    7.9e-19   67.4   1.8    1.1  1  Ribosomal_L21e  Ribosomal protein L21e


Domain annotation for each model (and alignments):
>> Ribosomal_L21e  Ribosomal protein L21e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.4   1.8   4.4e-23   7.9e-19       3      99 ..       9      97 ..       3      98 .. 0.83

  Alignments for each domain:
  == domain 1  score: 67.4 bits;  conditional E-value: 4.4e-23
                    -S-STTTT-TTTTS--GGG-SS--SHHHH----TT-EEEE---TT--SS---GGGTT-EEEE..EEEETTEEEEEEEETTE..EEEEEE-GGGEEE- CS
  Ribosomal_L21e  3 nskglrrgtrklfskkfrkkgvpplstylreykkGdkVdikidpsvqkgmphkryhGktgrvynvtkravgvivnkkvggkileKriivriehlkks 99
                    +s+g++++ r +++    k     +s +lrey++G++  + idp  +kg ph+ryhGk+g++ nv++ra    + +k+g+k  +K++i+r +h+k++
      EPA06579.1  9 RSHGFKHKARAVMT----KTAPRGVSFLLREYHEGEQALVIIDPRQHKGLPHRRYHGKVGKITNVGRRAI--TLDVKLGDK--TKTLITRLDHIKPF 97
                    45555555555555....5556678999**************************************9976..577799999..9***********85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 685.46
//
Query:       EPA06580.1  [L=574]
Description: radical SAM domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-08   35.5   0.0    2.9e-08   34.2   0.0    1.7  1  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.0   1.6e-12   2.9e-08       1     157 [.     272     449 ..     272     462 .. 0.63

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 1.6e-12
                  EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGS.............TTHHHHHHHHHHTCCCTEEEEEEE CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggeplly.............pdfvellerlaklavpgiritvet 84 
                  v+v+rgC ++C+fC+++      +  r+ s+e++++e++ +  +kg +k  ++++++ ++y             ++  e+l+ ++             
   EPA06580.1 272 VEVMRGCGRGCKFCDVT-----LRSLRYYSPEKVKREIEVN-IKKGgAKSAWIHSDDIFVYgmdprtakgmepnREALEELFTAIMS----------- 352
                  689**************.....69*****************.67777************9977766665554333333333333333........... PP

                  CSSCHG.............HHHHHHHHHTT..-SEEEEEEBSSSHH...........HHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTS CS
                  xxxxxx.............xxxxxxxxxxx..xxxxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM  85 ngtlpd.............eeklerllelg..vdrvslgleaadde...........kvlklmnrghtfeevlealeklreagikrvvdrivglpGen 156
                   g+ ++             e+ +  l +         +g++a+ +            + l +  + +    v+e++++l++  + + ++ i+gl   n
   EPA06580.1 353 TGVGHTnpthgtlagaiadEKLIPNLSRIIksSPDNMIGIQAGFETgslrligkyadRKLAPYDPSEWHWVVKEGVKTLNKDYWIPAFTLIMGLD--N 448
                  33333333333366677774444444444444344455555555553333555555544444434444489999999999998888888888876..3 PP

                  H CS
                  x RF
  Radical_SAM 157 d 157
                  d
   EPA06580.1 449 D 449
                  3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (574 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.69u 0.34s 00:00:01.03 Elapsed: 00:00:00.56
# Mc/sec: 3091.43
//
Query:       EPA06581.1  [L=288]
Description: ribosomal protein L10 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-20   72.6   0.1    4.6e-20   71.4   0.1    1.7  1  RL10P_insert   Insertion domain in 60S ribosomal protein L10P
    9.1e-19   67.5   0.6    9.1e-19   67.5   0.6    2.1  2  Ribosomal_L10  Ribosomal protein L10
  ------ inclusion threshold ------
        0.1   11.2   0.7       0.17   10.5   0.7    1.3  1  HPHLAWLY       Domain of unknown function


Domain annotation for each model (and alignments):
>> RL10P_insert  Insertion domain in 60S ribosomal protein L10P
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.4   0.1   7.7e-24   4.6e-20       1      71 []     111     181 ..     111     181 .. 0.99

  Alignments for each domain:
  == domain 1  score: 71.4 bits;  conditional E-value: 7.7e-24
  RL10P_insert   1 AraGtiAtedviipagplelaPgsiepeLrklglptklkkGkivleedylvckkGetltseqaqlLklLgi 71 
                   Ar G+iA+ d+ +pa++++ aPg++ +e++++g+ptk+++G+i++++d++ +kkG +++ + a+lL +L+i
    EPA06581.1 111 ARGGDIASVDILVPAKNTGIAPGPMLTEFKEAGIPTKIDQGTIWIQKDTTPVKKGGVINEKLAALLGKLDI 181
                   9********************************************************************98 PP

>> Ribosomal_L10  Ribosomal protein L10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.5   0.6   1.5e-22   9.1e-19       3      98 ..       9     105 ..       7     107 .. 0.95
   2 ?   -1.2   0.0      0.37   2.2e+03      11      38 ..     192     219 ..     188     255 .. 0.70

  Alignments for each domain:
  == domain 1  score: 67.5 bits;  conditional E-value: 1.5e-22
                    CCCHCCCCCCCCCCCTTSSEEEEEE-TTS-HHHHHHCCCHHHHHGCEEEEESCCCCCCCCHCCTSS.S...SCGCCSSSEEEEEESS-TCHHHHCC CS
  Ribosomal_L10   3 kekKeelvkelkellkkyksvvvvdyegltvaqlqelRkklrengaelkvvKntlmrrAleetgeeek...lkellkgpvalvftnedpvalakvl 95 
                    +++K+ ++++l e  kkyk+v++v+ e+++++ql  lRk+l+++ +e++ vK +++++Ale++++      +++ l+g+++++ftn++p++l  +l
     EPA06581.1   9 PKRKTVMYQQLIEMPKKYKVVALVKTEKVRASQLLPLRKALKGQ-VEFVCVKDRVAQKALEKSDIP-GikgISDELVGQCLFIFTNMSPFKLNVLL 102
                    789****************************************9.********************7.3469**********************999 PP

                    CCC CS
  Ribosomal_L10  96 eef 98 
                    +++
     EPA06581.1 103 AKN 105
                    987 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.37
                    CCCCCCCTTSSEEEEEE-TTS-HHHHHH CS
  Ribosomal_L10  11 kelkellkkyksvvvvdyegltvaqlqe 38 
                      l+e lk +++ +v+d+e +++a  q 
     EPA06581.1 192 TALEEGLKYTSAELVIDVEAVRNAFAQY 219
                    5677777777777888888887765554 PP

>> HPHLAWLY  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.7   2.9e-05      0.17     248     309 ..       1      63 [.       1      76 [. 0.81

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 2.9e-05
    HPHLAWLY 248 vhekreqyrkmqaqmlgaklripss.kvkvlsfaeqsqkphqLpkdkylesdasfaensdtsk 309
                 +he r qy k+++ m ++ + +p + kv  l  +e+ + ++ Lp  k l+ ++ f    d   
  EPA06581.1   1 MHENRTQYPKRKTVMYQQLIEMPKKyKVVALVKTEKVRASQLLPLRKALKGQVEFVCVKDRVA 63 
                 6***************999998853255556679999************99999876666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       710  (0.0396006); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2239.40
//
Query:       EPA06582.1  [L=307]
Description: putative dihydroorotate dehydrogenase 1B [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      7e-55  186.3   1.0      8e-55  186.1   1.0    1.0  1  DHO_dh           Dihydroorotate dehydrogenase
    3.9e-07   29.5   0.5    0.00026   20.2   0.2    2.0  2  Dus              Dihydrouridine synthase (Dus)
    1.9e-05   24.3   0.2      0.047   13.1   0.0    2.6  3  His_biosynth     Histidine biosynthesis protein
    0.00015   21.3   0.4     0.0012   18.3   0.4    2.0  1  NMO              Nitronate monooxygenase
    0.00017   20.8   8.4    0.00046   19.4   0.1    3.6  4  DUF561           Protein of unknown function (DUF561)
     0.0011   18.4   2.5       0.82    9.1   0.2    2.7  4  G3P_antiterm     Glycerol-3-phosphate responsive antiterminat
     0.0013   18.1   2.4        0.2   10.9   0.7    2.7  3  ThiG             Thiazole biosynthesis protein ThiG
     0.0028   16.7   0.5      0.012   14.7   0.0    1.9  2  IMPDH            IMP dehydrogenase / GMP reductase domain
  ------ inclusion threshold ------
      0.082   13.1   0.0       0.27   11.4   0.0    2.0  1  Antimicrobial_8  Uperin family


Domain annotation for each model (and alignments):
>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.1   1.0     4e-58     8e-55       2     295 .]       9     289 ..       8     289 .. 0.90

  Alignments for each domain:
  == domain 1  score: 186.1 bits;  conditional E-value: 4e-58
                 G-EEETTEEESSSEEE-TTSSTTSSS.HHHHHCTTSSEEEEEEE-SS-B--S-S--EEEETTCTEEEE---S-BS-HHHHHHHHHHHHHHHHCC.CEEE CS
      DHO_dh   2 latkvlglkfknpiglAaGfdkegee.ilkllklgfgaieigsvtpkpqeGnpkPrvfrlkedrsvlNslGlnneGldavlekllkrrkeqeekkelgi 99 
                 l t++ +++++ p++lA+G+ + +   +++l+  g+ga+ ++s  ++p  G p+P++f+++ +   +N++Gl n+G+ + ++ ++ +        +++i
  EPA06582.1   9 LVTSIGKIQLERPVMLASGILGISLDvFNRLYRSGAGAVVTKSLSTEPWDGYPNPTIFSVNGG-GWINAVGLSNPGAPNFAKMIESNT-------TVPI 99 
                 67889999*************98865156777888**************************99.9************99887776554.......69** PP

                 EEEE-TTSS.HHHHHHHHHHHHG.GGESEEEEES-SCTCC.TSCCCGCHHHHHHHHHHHHHHHHSSEEEEEE-SSSSHHHHHHHHHHHHHHTECEEEE. CS
      DHO_dh 100 nlskakktenavddyvevvrkig.pfadilelNvSsPntp.glrdlqekeelkaillkvvkevskvpvlvKlaPdltdeekkdiadvllelkldgiivt 196
                 ++s  ++    ++d+  +v +++   + + elN+S+P+++  + +++ ++el +++++ vk+ ++vpv++K+      ++  + ++ +   ++d+i ++
  EPA06582.1 100 IVSLVGSI---AEDFEMMVSQFKnCKVTAYELNLSCPHVAkVGLEVGDDPELVKKIVSTVKNSTTVPVIAKVGL--GTTHYLNTVKTAIDSGIDAITAI 193
                 *******7...************5568999*********98899****************************86..55555566666668888888888 PP

                 ..BSEE--CTTCCGCCCCTTSSEEEEEGGGHHHHHHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHHHHHHHHHHHHH CS
      DHO_dh 197 NttvqrlaidlkseknvkanktGGlsGkalkdialkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegpkiakkikkeleelL 295
                 Nt v+ +aid+++++++  nk+GGlsG ++k+ial+ ++e++++ +  ipiIg+GGi++ eDa+e i  GAs++q+++a+  +   ++++i +++ + +
  EPA06582.1 194 NT-VRAMAIDVETQRPILSNKFGGLSGTPIKPIALRCVYEISSKYD--IPIIGCGGISTWEDAIEFILGGASAIQLGSAIGDRWLNVFNDINDGIIRYM 289
                 86.67777************************************99..********************************999999******9998765 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.2   1.3e-07   0.00026      44     156 ..      87     191 ..      74     200 .. 0.89
   2 !    7.6   0.0   0.00091       1.8     170     202 ..     225     257 ..     218     273 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.3e-07
                 HHH-GGGGGTSCEEEEEE-S-HHHHHHHHHHHHHTT-SCEEEEESSTTEEETTEEEGGGGGGSHHHHHHHHHHHHCCSSS-EEEEEESESSTTTC.HHH CS
         Dus  44 irmlseeeeetplavQlggsdpallaeaAklvadlgadeIdlNvGCPskkvtrggaGaaLlrkpdlvaqivkavvkaveiPvtvkirigiddeeenale 142
                 + ++ e+++  p++v l+gs ++     +   ++ ++ + +lN+ CP     + ++G     +p+lv++iv++v++ + +Pv +k+ +g      + l+
  EPA06582.1  87 FAKMIESNTTVPIIVSLVGSIAEDFEMMVSQFKNCKVTAYELNLSCPHVAKVGLEVG----DDPELVKKIVSTVKNSTTVPVIAKVGLGTT----HYLN 177
                 55666777778************************************9887777777....8**************************998....4789 PP

                 HHHHHHHCT-SEEE CS
         Dus 143 lakiveaaGaqalt 156
                  +k++ ++G++a+t
  EPA06582.1 178 TVKTAIDSGIDAIT 191
                 9999******9998 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00091
                 --CHHHHHHHHH-SS-EEEESS--SHHHHHHHH CS
         Dus 170 adweaIkevkqavsipviaNGdIkdaedaqail 202
                 + ++ ++e+  +  ip+i+ G+I ++eda + +
  EPA06582.1 225 IALRCVYEISSKYDIPIIGCGGISTWEDAIEFI 257
                 567789**********************98765 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.3   2.6e+03      73     103 ..      19      51 ..       7      56 .. 0.68
   2 !    8.3   0.0   0.00072       1.4     167     217 ..     133     190 ..     108     196 .. 0.78
   3 !   13.1   0.0   2.4e-05     0.047      61     105 ..     226     270 ..     217     282 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.3
                   SSEEEEESSSS..SHHHHHHHHHCT-SEEEESH CS
  His_biosynth  73 fipvqvGGGIr..sledveelleagadkviigt 103
                   + pv++ +GI   sl+ +++l ++ga  v+  +
    EPA06582.1  19 ERPVMLASGILgiSLDVFNRLYRSGAGAVVTKS 51 
                   467777888743367778888888888777655 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00072
                   EETTTTTTSS---HHHHHHHHHHH....SSEEEEESS--SHHHHHHHH...HTTCSEE CS
  His_biosynth 167 tdidrdGtlsGpdleltkelaeav....kipviasGGvgsledlkelk...segvdav 217
                     ++++G + G d el+k++ ++v    ++pvia  G g+   l ++k   ++g+da+
    EPA06582.1 133 PHVAKVGLEVGDDPELVKKIVSTVknstTVPVIAKVGLGTTHYLNTVKtaiDSGIDAI 190
                   57999********99988876554222289*********9998888884445566554 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 2.4e-05
                   HHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHH CS
  His_biosynth  61 nldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaa 105
                    l +v ei ++ +ip+   GGI++ ed+ e +  ga+ + +g+a 
    EPA06582.1 226 ALRCVYEISSKYDIPIIGCGGISTWEDAIEFILGGASAIQLGSAI 270
                   566677777777777777777777777777777777777777765 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.4   6.1e-07    0.0012      98     224 ..     142     269 ..      91     270 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 6.1e-07
         NMO  98 egvr..fyrkvevvldekvev.vsfgfglpteevvarlkeagvvliptissvkearkvearGaDalivqGpeaGGhqGtpevgdkglfaLvpqvldavd 193
                 +g+    ++k+    ++ + v v+  +gl t + ++  k+a+   i  i++++ +r+++        +   + GG  Gtp +     ++ v ++ +  d
  EPA06582.1 142 VGDDpeLVKKIVSTVKNSTTVpVIAKVGLGTTHYLNTVKTAIDSGIDAITAINTVRAMAIDVETQRPILSNKFGGLSGTPIK--PIALRCVYEISSKYD 238
                 4443666667766666644433667777777777777777777777777777777776655544444445788999994333..4689999******** PP

         NMO 194 iPviAaGGiidrrgvaaaLalGAsgvqigtr 224
                 iP+i  GGi + ++    +  GAs++q+g++
  EPA06582.1 239 IPIIGCGGISTWEDAIEFILGGASAIQLGSA 269
                 **************9999999********98 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.11   2.1e+02     185     212 ..      18      45 ..       8      54 .. 0.81
   2 ?   -0.4   0.0      0.26   5.2e+02      50      69 ..      85     104 ..      82     116 .. 0.82
   3 ?    2.3   0.4     0.038        77     180     222 ..     155     195 ..     149     215 .. 0.59
   4 !   19.4   0.1   2.3e-07   0.00046     174     218 ..     226     271 ..     216     291 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.11
      DUF561 185 vslPvicasGlsdvtvplalslgasGiG 212
                 ++ Pv+ asG+  ++ ++   l  sG G
  EPA06582.1  18 LERPVMLASGILGISLDVFNRLYRSGAG 45 
                 456*************999888888877 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.26
      DUF561  50 pklvkkvksvsniPiCvsav 69 
                 p++ k ++s++ +Pi vs v
  EPA06582.1  85 PNFAKMIESNTTVPIIVSLV 104
                 66778999999999999977 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.038
      DUF561 180 eiskkvslPvicasGlsdvtvplalslgasGiGigsavsklnd 222
                 ++ +++++Pvi+  Gl +    l     a   Gi +a++ +n 
  EPA06582.1 155 TVKNSTTVPVIAKVGLGTT-HYLNTVKTAIDSGI-DAITAINT 195
                 6778899999999999754.33333333333333.23333333 PP

  == domain 4  score: 19.4 bits;  conditional E-value: 2.3e-07
      DUF561 174 tlastyeiskkvslPvicasGlsdvtvplalsl.gasGiGigsavs 218
                 +l ++yeis+k ++P+i   G+s+    + + l gas i +gsa+ 
  EPA06582.1 226 ALRCVYEISSKYDIPIIGCGGISTWEDAIEFILgGASAIQLGSAIG 271
                 799**************************9987369*******995 PP

>> G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       2.7   5.3e+03     141     167 ..      22      49 ..       7      51 .. 0.62
   2 ?   -3.4   0.0       2.7   5.4e+03     128     145 ..      85     102 ..      83     116 .. 0.71
   3 !    9.1   0.2   0.00041      0.82     124     167 ..     146     192 ..     141     196 .. 0.86
   4 !    8.4   0.0   0.00064       1.3     128     166 ..     227     265 ..     222     269 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.7
                   EEEEESS--SHHHH.HHHCTT.SSEEEE CS
  G3P_antiterm 141 piiaGGLietkedv.eealkaGaiavst 167
                    ++a+G++  + dv ++++++Ga av t
    EPA06582.1  22 VMLASGILGISLDVfNRLYRSGAGAVVT 49 
                   4567777766666624456777777766 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.7
                   HHHHCTSTTS...EEEEE CS
  G3P_antiterm 128 pkvikeikkelkipiiaG 145
                   p+++k i++++++pii +
    EPA06582.1  85 PNFAKMIESNTTVPIIVS 102
                   567777788888888765 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.00041
                   SGGGHHHHCTSTTS...EEEE.ESS--SH..HHHHHHCTT.SSEEEE CS
  G3P_antiterm 124 Pglvpkvikeikkelkipiia.GGLietk..edveealkaGaiavst 167
                   P lv+k+++ +k+++++p+ia  GL +t+  ++v++a+++G++a+++
    EPA06582.1 146 PELVKKIVSTVKNSTTVPVIAkVGLGTTHylNTVKTAIDSGIDAITA 192
                   8899****************9547766653389************96 PP

  == domain 4  score: 8.4 bits;  conditional E-value: 0.00064
                   HHHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEE CS
  G3P_antiterm 128 pkvikeikkelkipiiaGGLietkedveealkaGaiavs 166
                    +++ ei+++ +ipii  G i+t ed  e +  Ga+a+ 
    EPA06582.1 227 LRCVYEISSKYDIPIIGCGGISTWEDAIEFILGGASAIQ 265
                   5678899******************************97 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.48   9.6e+02     164     181 ..      85     102 ..      75     114 .. 0.74
   2 !   10.9   0.7    0.0001       0.2     161     212 ..     148     202 ..     103     206 .. 0.71
   3 !    5.5   0.0    0.0044       8.8     167     208 ..     230     271 ..     214     274 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.48
                 HHHHHHHHHH-SS-BEEE CS
        ThiG 164 kealkiiieeakvPvivD 181
                 +++ k+i ++++vP+iv 
  EPA06582.1  85 PNFAKMIESNTTVPIIVS 102
                 44567788888*****95 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0001
                 -S-HHHHHHHHHH-SS-BEEES---SHH...HHHHHHHTT-SEEE.ESHHHHTSSS CS
        ThiG 161 llnkealkiiieeakvPvivDAGigsps...daaqamelGadavl.lntavaeakd 212
                 l  k+ ++++ ++++vPvi   G+g++     + +a++ G+da+  +nt  a+a d
  EPA06582.1 148 L-VKKIVSTVKNSTTVPVIAKVGLGTTHylnTVKTAIDSGIDAITaINTVRAMAID 202
                 3.356778888999***********98622267899*******9636887777766 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.0044
                 HHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHH CS
        ThiG 167 lkiiieeakvPvivDAGigspsdaaqamelGadavllntava 208
                 +  i ++ ++P+i   Gi + +da++ +  Ga+a+ l +a+ 
  EPA06582.1 230 VYEISSKYDIPIIGCGGISTWEDAIEFILGGASAIQLGSAIG 271
                 45577889*******************************995 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1       0.2   3.9e+02      97     120 ..     166     190 ..     115     211 .. 0.63
   2 !   14.7   0.0     6e-06     0.012     195     239 ..     226     270 ..     218     273 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.2
                 EEE-SST.THHHHHHHHHHTT-SEE CS
                 xxxxxxx.xxxxxxxxxxxxxxxxx RF
       IMPDH  97 aavgvke.dalervkalveagvdvl 120
                 a vg  + ++l+ vk+ +++g+d++
  EPA06582.1 166 AKVGLGTtHYLNTVKTAIDSGIDAI 190
                 2222221123333333333333333 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 6e-06
                 HHHHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-SEEEESCCC CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       IMPDH 195 AvaevaeaakkagvpviaDGGikysgdivkAlaaGadavmlGsll 239
                 A+  v+e+ +k+++p+i  GGi++ +d +  +  Ga+a+ lGs +
  EPA06582.1 226 ALRCVYEISSKYDIPIIGCGGISTWEDAIEFILGGASAIQLGSAI 270
                 667789999*********************************986 PP

>> Antimicrobial_8  Uperin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00014      0.27       5      15 ..     148     158 ..     142     159 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00014
  Antimicrobial_8   5 liRKiVsaIKN 15 
                      l +KiVs++KN
       EPA06582.1 148 LVKKIVSTVKN 158
                      789******** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2131.39
//
Query:       EPA06583.1  [L=174]
Description: putative methylase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.5e-09   36.0   0.3      2e-08   34.2   0.3    1.8  1  Methyltransf_31  Methyltransferase domain
    3.1e-07   30.9   0.0      6e-07   30.0   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
    3.9e-06   26.5   0.0    1.1e-05   25.1   0.0    1.7  1  MTS              Methyltransferase small domain
    8.9e-06   25.6   0.0    3.9e-05   23.6   0.0    1.8  1  Methyltransf_23  Methyltransferase domain
    4.7e-05   24.0   0.2    0.00012   22.7   0.2    1.8  1  Methyltransf_12  Methyltransferase domain
    5.2e-05   23.9   0.1    0.00013   22.6   0.1    1.7  1  Methyltransf_25  Methyltransferase domain
    0.00038   20.3   0.0      0.001   18.8   0.0    1.7  2  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
      0.002   17.5   0.1     0.0028   17.0   0.1    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
     0.0033   17.4   0.0     0.0051   16.8   0.0    1.3  1  Methyltransf_32  Methyltransferase domain
  ------ inclusion threshold ------
      0.036   13.1   0.0       0.21   10.6   0.0    1.9  1  RrnaAD           Ribosomal RNA adenine dimethylase
      0.086   12.2   0.1       0.19   11.1   0.1    1.5  2  PrmA             Ribosomal protein L11 methyltransferase (Prm
       0.15   12.0   0.0       0.33   10.9   0.0    1.6  1  Methyltransf_18  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.3   1.3e-11     2e-08       2     123 ..      22     143 ..      21     165 .. 0.80

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 1.3e-11
  Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeq.gdieeleklledekfDlilsn.......evl... 84 
                      ++gl+ lD+G+G+G+lt+ la++ ++   vvG Di+  +++  +  +     +n+  +  +d+ +         fDl+++n       +vl   
       EPA06583.1  22 ENGLTALDVGSGSGYLTKLLAKNFIF---VVGTDINFIVLKNQTYST-----KNLVCCNgSDALKS-------EFDLVVCNlpylatdQVLdat 100
                      578999***************98876...*******99999888864.....46666662444443.......4*******7777777444777 PP

  Methyltransf_31  85 .....naladpdkileeiervlkpggilliedprllaelpakve 123
                           + +  p+ki+ +i +++k gg +l  + + l+++ + + 
       EPA06583.1 101 tdggiDGFEIPKKIFDSIYKNIKVGGKFLFVTSS-LSDYQKLMD 143
                      88888************************99999.666554444 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.0     4e-10     6e-07       1      96 []      28     130 ..      28     130 .. 0.77

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 4e-10
                      EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES.......-CCC-C........CHHH CS
  Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvsse.......vlhhve........dpek 79 
                      LdvG+G+G+l++ lak++  vvg+D++  +l   ++ +s+++    +v+++ ++  + ++ fDlvv++        vl+            p+k
       EPA06583.1  28 LDVGSGSGYLTKLLAKNFIFVVGTDINFIVL--KNQTYSTKN----LVCCNGSD-AL-KSEFDLVVCNLpylatdqVLDATTdggidgfeIPKK 113
                      8*************************99999..344455544....49999998.44.559*******98775555333331444444449999 PP

                      HHHHHHHHEEEEEEEEE CS
  Methyltransf_11  80 alkeiaRvLkpgGllvi 96 
                      +++ i++  k gG++++
       EPA06583.1 114 IFDSIYKNIKVGGKFLF 130
                      99999999999999876 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   7.2e-09   1.1e-05      22     150 ..      14     143 ..      10     162 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 7.2e-09
                 HHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEEEE---STTTCHCHH..... CS
         MTS  22 lLletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdlivsNPPfhagkatel..... 115
                 +++++++ke   ++lD+G+G G+l+  lak+     v+ +d+++  l   ++++++++    +v +++ ++++  +fdl+v+N P+ a  ++ +     
  EPA06583.1  14 FIADYIEKENGLTALDVGSGSGYLTKLLAKNFIF--VVGTDINFIVL--KNQTYSTKN----LVCCNGSDALK-SEFDLVVCNLPYLATDQVLDattdg 103
                 6778899998889***************996654..78888887655..567777766....48899999999.9**********98877654411111 PP

                 .....HHHHHHHHHHHHHEEEEEEEEEEEETTSCHHHHHH CS
         MTS 116 .....avaeeliaeAkeaLkegGeLliVanrklgyeslle 150
                      ++ ++++ +  +  k gG++l+V+++  +y++l++
  EPA06583.1 104 gidgfEIPKKIFDSIYKNIKVGGKFLFVTSSLSDYQKLMD 143
                 1212246678899999999999999999999999998875 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   2.6e-08   3.9e-05      20     125 ..      21     138 ..       2     157 .. 0.68

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 2.6e-08
  Methyltransf_23  20 lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiaekakkaqkdqfdeqeaaepqgkfdlIvlrevlehvpdpp.............. 99 
                      ++ g   Ld+G G+G+l+++l++n+  v+g D++++  +   +   + k  +  +  +  +  fdl+v++      + +               
       EPA06583.1  21 KENGLTALDVGSGSGYLTKLLAKNFIFVVGTDINFIVLK---NQTYSTKNLVCCNGSDALKSEFDLVVCNLPYLATDQVLdattdggidgfeip 111
                      4555589***************************98333...2222222222223444455599999998644444443345577888888888 PP

  Methyltransf_23 100 .ellrqiatllkpgGylllseplaslk 125
                       + +++i++++k gG +l+ ++  s++
       EPA06583.1 112 kKIFDSIYKNIKVGGKFLFVTSSLSDY 138
                      888888888888888888888766654 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.2   8.3e-08   0.00012       1      98 [.      28     127 ..      28     128 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 8.3e-08
  Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvv......as.nvlhhl........ 79 
                      L++G+G+G l++ l+++  +i ++g+Di+  ++     k + ++ +n  +++  +         s fDlvv      a  +vl ++        
       EPA06583.1  28 LDVGSGSGYLTKLLAKN--FIFVVGTDINFIVL-----KNQTYSTKNLVCCNGSDALK------SEFDLVVcnlpylATdQVLDATtdggidgf 108
                      8****************..*********99999.....77777777777777776554......39*****44444422345555588887876 PP

  Methyltransf_12  80 kdirevldnirklLkpgGr 98 
                      + +++++d+i+k +k gG+
       EPA06583.1 109 EIPKKIFDSIYKNIKVGGK 127
                      6666888888888888776 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.1   8.4e-08   0.00013       2      80 ..      28      94 ..      27     103 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 8.4e-08
                     EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHH CS
  Methyltransf_25  2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsde 80
                     Ld+G G+G lt+ lak++    v+g+Di+   l++            ++v+++ +d    +++fDlvv++  l +l  +
       EPA06583.1 28 LDVGSGSGYLTKLLAKNF--IFVVGTDINFIVLKNQTYST------KNLVCCNGSDAL--KSEFDLVVCN--LPYLATD 94
                     9****************9..*********99988654444......368899988765..356******6..5665544 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   6.9e-07     0.001      65      93 ..      15      43 ..       5      68 .. 0.85
   2 ?   -1.7   0.0       1.3     2e+03     159     186 ..     118     146 ..     105     160 .. 0.58

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 6.9e-07
                HHHHTT--TT-EEEEES-TTSHHHHHHHH CS
        PCMT 65 alellelkkgarvLevGsGsGyltavlar 93
                + +++e ++g  +L+vGsGsGylt +la+
  EPA06583.1 15 IADYIEKENGLTALDVGSGSGYLTKLLAK 43
                6799999*****************99987 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.3
                 HHHTEEEEEEEEEEESB.SSSEEEEEEEE CS
        PCMT 159 lidQLkeGGrlvvPvge.eeeQvlklvdk 186
                 + + +k GG+++    + +  Q+l+ + +
  EPA06583.1 118 IYKNIKVGGKFLFVTSSlSDYQKLMDYAQ 146
                 34456667776655554555565555544 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   1.9e-06    0.0028      38     158 ..      14     137 ..      10     154 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.9e-06
                      HHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS........TEEEEE--TTT-TTS-T-EEEEEEE CS
  Ubie_methyltran  38 fveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki........nieflqanaeeLpfeddsfDvvtvs 123
                      f+ +   + +g ++lDv +G+g l+  l+++      vv+ Din  +Lk      k+            + ++++ n   L  +d+  D  t  
       EPA06583.1  14 FIADYIEKENGLTALDVGSGSGYLTKLLAKN---FIFVVGTDINFIVLKNQTYSTKNLVCCngsdalksEFDLVVCNLPYLA-TDQVLDATT-D 102
                      7888899999************999877665...457999********9987777765444334455568888888877775.578899877.5 PP

                      S-GGG-S-HHHHHHHHHHHEEEEEEEEEEEE---- CS
  Ubie_methyltran 124 fGlrnvtDklkaLkeayrvlkpGGrlvvlefskve 158
                       G+  +   +k + ++y+ +k+GG+++ +  s   
       EPA06583.1 103 GGIDGFEIPKKIFDSIYKNIKVGGKFLFVTSSLSD 137
                      5*************************998777554 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   3.4e-06    0.0051      13      61 ..      15      55 ..      11      73 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.4e-06
  Methyltransf_32 13 vakllkelakesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidake 61
                     +a+    + ++++ lt +DvG+G gYL+  la     + + vvg d++ 
       EPA06583.1 15 IAD----YIEKENGLTALDVGSGSGYLTKLLAK----NFIFVVGTDINF 55
                     444....44558899*****************9....467788888775 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00014      0.21      22     119 ..      15      97 ..      13     115 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00014
                 HHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTTTCCCEEEE-S-CCGHHHHHHHCTTTCCCCEEEEEEE--TTTHHHHH CS
      RrnaAD  22 IldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkklskdeklkvvhqDflkfetpeevtekdsihqeflvvanlPyeistqlv 119
                 I d ++ e+ lt l++g+G G lT+ Lak +  vv    d +++ l +++ s ++ +     D+lk e+               vv nlPy ++ q  
  EPA06583.1  15 IADYIEKENGLTALDVGSGSGYLTKLLAKNFIFVV--GTDINFIVLKNQTYSTKNLVCCNGSDALKSEFDL-------------VVCNLPYLATDQVL 97 
                 556667778999****************9885544..4566666666665554444444566777777766.............66666666666555 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00013      0.19     161     234 ..      23      88 ..      13     100 .. 0.69
   2 ?   -3.1   0.0       2.7   4.1e+03     104     119 ..     118     133 ..     113     149 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00013
        PrmA 161 egeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellkeekadvivaNI 234
                 +g + lDvG GSG L+   ak +   vv++Di+ + +k  +   ++N v       + +++lk +++d++v+N 
  EPA06583.1  23 NGLTALDVGSGSGYLTKLLAK-NFIFVVGTDINFIVLKN-QTYSTKNLVCC-----NGSDALK-SEFDLVVCNL 88 
                 33499**********743333.45568999998776653.44444444443.....3467888.899****995 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.7
        PrmA 104 yykPvrigerltivps 119
                  yk +++g ++++v s
  EPA06583.1 118 IYKNIKVGGKFLFVTS 133
                 4666666666655544 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00022      0.33       8      56 ..      15      63 ..      13      87 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00022
  Methyltransf_18  8 iaslvekgs..rvaDiGtDHgylpiylvkegkakkviasDinegplekake 56
                     ia+++ek++  + +D+G+  gyl+  l+k+ +   v+ +Din   l++   
       EPA06583.1 15 IADYIEKENglTALDVGSGSGYLTKLLAKNFIF--VVGTDINFIVLKNQTY 63
                     78999987766999***********99987665..9999999888776544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1262.85
//
Query:       EPA06584.1  [L=84]
Description: hypothetical protein BG20_I0767 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.50
# Mc/sec: 510.33
//
Query:       EPA06585.1  [L=44]
Description: hypothetical protein BG20_I0760 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 338.75
//
Query:       EPA06586.1  [L=138]
Description: hypothetical protein BG20_I0762 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.019   15.1   2.1      0.023   14.9   1.4    1.5  1  FMP23        Found in mitochondrial proteome
       0.04   14.0   1.2      0.063   13.4   0.7    1.6  2  EIF_2_alpha  Eukaryotic translation initiation factor 2 alpha


Domain annotation for each model (and alignments):
>> FMP23  Found in mitochondrial proteome
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   1.4   2.5e-06     0.023      17      60 ..      59     102 ..      48     118 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.5e-06
       FMP23  17 ksakiakdeykqlPedsnyiekfydeleafsneflekqlkksya 60 
                 ++ +i ++  kql ++s+yi + y e  ++s  fl +q+k + +
  EPA06586.1  59 DKLNIDHRFLKQLKDNSEYIKNRYLENIELSTRFLDEQIKMQTS 102
                 4456777778*************************999986654 PP

>> EIF_2_alpha  Eukaryotic translation initiation factor 2 alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.7     7e-06     0.063       8      46 ..      34      74 ..      30     105 .. 0.88
   2 ?   -1.8   0.0      0.36   3.3e+03       8      25 ..      98     116 ..      94     126 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7e-06
                 HHTTTTS-HHHHH..HHHHSTTHHHHHTTS-TTTHHHHHHC CS
  EIF_2_alpha  8 klyekyghaydaF..klaitdeevldkleipeeveeaLvei 46
                 +ly+++ h++d     + i+++e++dkl+i+  + ++L+++
   EPA06586.1 34 NLYAEFLHVFDNIygTCYINEKEFFDKLNIDHRFLKQLKDN 74
                 6999******99999***********************975 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.36
                  HHTTTTS-HHHHH.HHHHS CS
  EIF_2_alpha   8 klyekyghaydaF.klait 25 
                  k++    h ++ F +++++
   EPA06586.1  98 KMQTSAMHSFENFaNIMMD 116
                  5555666777777555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       807  (0.0450109); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.35s 00:00:00.86 Elapsed: 00:00:00.53
# Mc/sec: 789.14
//
Query:       EPA06587.1  [L=56]
Description: hypothetical protein BG20_I0765 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0033   17.2   1.6     0.0046   16.7   1.6    1.4  1  DivIC     Septum formation initiator
  ------ inclusion threshold ------
      0.035   12.4   0.1      0.035   12.4   0.1    1.0  1  CCD48     Coiled-coil domain-containing protein 48
      0.046   14.2   0.5      0.051   14.1   0.5    1.0  1  NUDE_C    NUDE protein, C-terminal conserved region
       0.08   13.0   2.9       0.13   12.3   2.6    1.7  1  DUF1192   Protein of unknown function (DUF1192)


Domain annotation for each model (and alignments):
>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   1.6     1e-06    0.0046      25      71 ..       4      48 ..       1      56 [] 0.82

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1e-06
                HHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXXXXXXXXXXXXXXX CS
       DivIC 25 eiaalqaelaklkaeneeLeaevkdLksdedyieerARselglvkpg 71
                e +++ + +akl +e++ L +ev+ Lk  ++   ++AR e  ++k+g
  EPA06587.1  4 EAETIYERVAKLEDEIALLRSEVDILK--RALRNKIARHEISMIKKG 48
                667777888888888888888888886..88889***********99 PP

>> CCD48  Coiled-coil domain-containing protein 48
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   7.9e-06     0.035     176     210 ..       5      39 ..       1      52 [. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.9e-06
       CCD48 176 ggpdeervarleeensslrelvedlraalqssdar 210
                 + +  erva+le+e + lr  v+ l+ al+   ar
  EPA06587.1   5 AETIYERVAKLEDEIALLRSEVDILKRALRNKIAR 39 
                 555679***********************998887 PP

>> NUDE_C  NUDE protein, C-terminal conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.5   1.1e-05     0.051      29      72 ..       4      43 ..       2      54 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.1e-05
      NUDE_C 29 ErEsLrievQRLrDelsDLkveleiiqeklrkaeeklrrrkpls 72
                E E++ + v +L De++ L+ e++i ++ lr++     +r+++s
  EPA06587.1  4 EAETIYERVAKLEDEIALLRSEVDILKRALRNK----IARHEIS 43
                889999*************************93....2344444 PP

>> DUF1192  Protein of unknown function (DUF1192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   2.6     3e-05      0.13      22      48 ..      12      38 ..       5      43 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3e-05
     DUF1192 22 veELeerIalLeaEIaRleaaiakkka 48
                v+ Le+ IalL++E++ l++a+++k a
  EPA06587.1 12 VAKLEDEIALLRSEVDILKRALRNKIA 38
                667899999999999999999999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       869  (0.048469); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 350.97
//
Query:       EPA06588.1  [L=351]
Description: radical SAM enzyme, Cfr family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-19   70.6   0.0    3.1e-19   69.9   0.0    1.4  1  Radical_SAM  Radical SAM superfamily
    0.00032   20.8   0.0    0.00058   20.0   0.0    1.4  1  Fer4_14      4Fe-4S single cluster domain
  ------ inclusion threshold ------
        0.1   12.8   0.0       0.21   11.8   0.0    1.5  1  Fer4_12      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.9   0.0   5.2e-23   3.1e-19       1     159 [.     113     277 ..     113     286 .. 0.89

  Alignments for each domain:
  == domain 1  score: 69.9 bits;  conditional E-value: 5.2e-23
                  EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHH.......HTTSEEEEEESSTGGGSTTHHHHHHHHHHTC....CCTEEEEEEECSS CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxx RF
  Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelka.......ekgvkevilgggepllypdfvellerlakla....vpgiritvetngt 87 
                  v+++ gC+++C+fCa+++     g +r++  eei+++v  +++       +  ++ v++g+gepl+++d++  + rl           ++it++t g+
   EPA06588.1 113 VSTQVGCAMGCTFCATGQ----MGFERNIKAEEIVAQVIHFAEllekrgqHV-TNLVFMGMGEPLVNYDETIRAVRLLTHPrgfgIGQRNITISTIGI 205
                  57899************6....8***************66642344432244.8889999*******************99***************** PP

                  CHGHHHHHHHHHTT.-SEEEEEEBSSSHH..HHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHH CS
                  xxxxxxxxxxxxxx.xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM  88 lpdeeklerllelg.vdrvslgleaadde..kvlklmnrghtfeevlealeklreagikrvvdrivglpGendee 159
                        +++l+e      ++++l+a++d+  + l ++ ++h+++++++a +++ ++ ++rv++ + +++G+nd+ 
   EPA06588.1 206 IS---GIDKLAEEDlQIGLAISLHAPNDKlrQKLVPTAGPHSVDDLIAAGKRYFKKTGRRVTFEYALIEGVNDSP 277
                  *8...9******99***************77777777799****************9999*************84 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   9.7e-08   0.00058       7      91 ..     118     206 ..     113     225 .. 0.65

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 9.7e-08
     Fer4_14   7 gCnlsCkgCdnke.twkselgkpqteelleqilk...dlkkseikiqglvltG.GePLhyenkkellklvkrlkeey....pekkiwletngtl 91 
                 gC + C++C + +  ++ +   +++ee++ q+++    l+k+  +  +lv++G GePL   n +e ++ v+ l +       + +i++ t g +
  EPA06588.1 118 GCAMGCTFCATGQmGFERN---IKAEEIVAQVIHfaeLLEKRGQHVTNLVFMGmGEPL--VNYDETIRAVRLLTHPRgfgiGQRNITISTIGII 206
                 9********9655044444...44555555555555467777778889**********..5555555555544332212244467777776665 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.6e-05      0.21      13      77 ..     117     183 ..     104     225 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.6e-05
     Fer4_12  13 sgCnlsCkgCfnketwsfksgkeftkelleei...iedlkk..esiegltllG.GEPllpenaeallelvk 77 
                  gC + C +C   ++  f+++ +  +e+ +++    e l+k  ++++ l+++G GEPl+  n+++ ++ v+
  EPA06588.1 117 VGCAMGCTFCATGQMG-FERNIKA-EEIVAQVihfAELLEKrgQHVTNLVFMGmGEPLV--NYDETIRAVR 183
                 69*******9855543.3333333.3333444010455555556679************..6655544333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 2206.39
//
Query:       EPA06589.1  [L=51]
Description: hypothetical protein BG20_I0756 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      188  (0.0104858); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.45
# Mc/sec: 342.52
//
Query:       EPA06590.1  [L=343]
Description: dehydrogenase, isocitrate/isopropylmalate family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-83  280.8   0.6    1.8e-83  280.6   0.6    1.0  1  Iso_dh    Isocitrate/isopropylmalate dehydrogenase


Domain annotation for each model (and alignments):
>> Iso_dh  Isocitrate/isopropylmalate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  280.6   0.6     1e-87   1.8e-83       3     348 .]       6     333 ..       4     333 .. 0.95

  Alignments for each domain:
  == domain 1  score: 280.6 bits;  conditional E-value: 1e-87
                 EEEEESTTHHHHHHHHHHHHHHHHHHHT-EEEEEE---THHHHHHHS....SSS-HHHHHHHHHSSEEEEEE---.CSSSSSSHHHHHHHHHHHTTEEE CS
      Iso_dh   3 allegdgiGpevveaalkvlkaakekaglelefeevdvGgaaidetg....eplpeetleaikeadvvllgavgt.pkekevrpengLlaLrkeldlfa 96 
                 a++ gdgiGpevv+++lkvlk+ +++++    +  +d+G ++ d+ g    + +p++t+++++e+d+  +g+++t p++   r+    ++Lr++++l++
  EPA06590.1   6 AVMRGDGIGPEVVDSMLKVLKECNSQSE----IILCDAGSEQWDKNGrkdkSYIPDATMKILEESDACFKGPTTTiPVPDAPRSVA--VTLRQKFELYS 98 
                 799*********************6655....88999****999998766678*******************99956688889988..99********* PP

                 EEEEEE-BCCTTCCSSBTHHHHCT-EEEEEEE-SSCGGCSSEEEEETTG.GGGEEEEEEEEEHHHHHHHHHHHHHHHHHTTTSEEEEEESTTTTHHHH. CS
      Iso_dh  97 nlrpvkvfeklkvksplkrevveevdlvivReltggiYfgeekekkgsifteevavdtklyseeeieriaraafelAlkrgkkkvtlvdKanvlksse. 194
                 n+rp k f      +p k+     +d v++Re+t+g+Y g+e ++++       a+ + ++++++++r+++ a++ A+k + kk+++++K+n+lk+++ 
  EPA06590.1  99 NIRPTKTF---DRLTPNKK-----LDCVCFREATEGLYTGIEVKITDD-----AAIAIRKITRQGSRRFMNSAVNWAKKYNMKKMVAITKRNILKQTDg 184
                 ********...67788886.....9********************997.....8********************************************* PP

                 HHHHHHHHHHCCTTTTSEEEEEEHHHHHHHHHHSGGGGS..EEEE-HHHHHHHHHHHHHHTTSGCC-EEEEEETSS-EEEEESS---CCCTTSS-S-TH CS
      Iso_dh 195 lwrkiveevaeeeypdielehqlvDsaamqlvkspkqfd..VivtkNlfGDilSDeaaalvGslGllpSaslgekkvaifEavHGsapdiagkdkaNpi 291
                  + ++v++ ++    di l++ ++D++a+q+v  p+qf+  V+v +Nlf Di+S +a+ lvGs+Gl+ Sa++g +++a+fEa+HGsap++ag++k+Np+
  EPA06590.1 185 IFWEEVQNAIK--GTDIALSEIYIDNMAQQMVVAPEQFNgaVLVSTNLFMDIISELASGLVGSIGLIYSANMG-DNFAMFEAAHGSAPQFAGQNKVNPT 280
                 78888888888..89***********************999********************************.78*********************** PP

                 HHHHHHHHHHHHTTT-HHHHHHHHHHHHHHHHH.TSCCHHHCTTSTCCCHHHHHHHHH CS
      Iso_dh 292 avilSaalmLryslgleeaAdkiekAvekvlea.givTkDlageaakevstsefgdav 348
                 a++lS a m +y lg++e  d+i +A e+v+++ ++vT D++g+a    st++++da+
  EPA06590.1 281 ATVLSGAWMAEY-LGESEIRDAIFAATEQVINEgKTVTWDIGGNA----STTQMTDAI 333
                 ************.********************899*********....9*****997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2273.58
//
Query:       EPA06591.1  [L=121]
Description: putative chemotaxis protein Chey [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.4e-24   84.8   1.2      5e-24   84.6   1.2    1.0  1  Response_reg  Response regulator receiver domain


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.6   1.2   2.8e-28     5e-24       1     111 [.       7     117 ..       7     118 .. 0.96

  Alignments for each domain:
  == domain 1  score: 84.6 bits;  conditional E-value: 2.8e-28
                   EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEESSTS.HHHHHHHHHCTESE CS
  Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviiltahse.eedavealkagadd 96 
                   +livdDd +++e+++ l++++gy +v  a++g++a++++ke +++l+l+D++mp +dG++++ +i++ d + +vi++ta++  e+  ++a +++  d
    EPA06591.1   7 ILIVDDDVDLLENTAFLIKSAGY-DVIMAQNGADAVHKYKETRPNLVLMDVRMPILDGYDAFFKIKQFDTNAKVILITAYAHdEKKHIKAKSLNLID 102
                   8**********************.9999**************************************************8776478889********* PP

                   EEESSG-HHHHHHHH CS
  Response_reg  97 flsKpfdpeeLlkal 111
                    +sKp+++e+L + +
    EPA06591.1 103 TISKPYTIEHLEEVI 117
                   ***********9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.50
# Mc/sec: 732.21
//
Query:       EPA06592.1  [L=235]
Description: ribosomal RNA adenine dimethylase family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.2e-40  136.9   1.1    8.4e-40  136.5   1.1    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase
    7.7e-05   22.5   0.0    0.00015   21.6   0.0    1.5  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
     0.0011   19.6   0.0     0.0028   18.3   0.0    1.7  1  Methyltransf_25  Methyltransferase domain
  ------ inclusion threshold ------
      0.019   15.7   0.0      0.067   13.9   0.0    1.9  2  Methyltransf_12  Methyltransferase domain
      0.053   13.3   0.2        7.7    6.4   0.1    2.7  2  SAM_3            SAM domain (Sterile alpha motif)
      0.059   13.4   0.0       0.09   12.8   0.0    1.4  1  Methyltransf_32  Methyltransferase domain
      0.099   12.5   0.0       0.17   11.7   0.0    1.6  1  Methyltransf_23  Methyltransferase domain
       0.12   13.0   0.0       0.25   12.0   0.0    1.5  1  Methyltransf_11  Methyltransferase domain


Domain annotation for each model (and alignments):
>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.5   1.1   3.7e-43   8.4e-40       4     232 ..       3     211 ..       2     232 .. 0.88

  Alignments for each domain:
  == domain 1  score: 136.5 bits;  conditional E-value: 3.7e-43
                 CXXGCG--EE--HHHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTTTCCCEEEE-S-CCGHHHHHHHCTTTCCCC CS
      RrnaAD   4 lrksygqnflknkkvineIldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkklskdeklkvvhqDflkfetpeevtekdsihq 102
                 +rk++gq+fl++++++++I++++n++ ++ v e+g+G GilT  L + ak+v ++  d++L++  + ++s   +l+v   D+             ++++
  EPA06592.1   3 KRKRLGQHFLTSNSIAQSIVSEANISGNDIVFELGTGLGILTPLLCEKAKKVISIDADRELYENAKSRFSHIDNLTVEFGDGF------------QKQD 89 
                 699******************************************************************96666666444443............3444 PP

                 EE.EEEEE--TTTHHHHHHHHHHGGGGCEEEEEEEEEHHHHHHHH--TTSTT-SHHHHHHHHHEEEEEEEEC-GGCECS--SSSEEEEEEEE-SS-S-- CS
      RrnaAD 103 ef.lvvanlPyeistqlvkqlleesrfglvkmllwlqkefarrllarpgskkrsrlsvlreaftdvklvakveksifsPppkvdsalvelerkdedlpq 200
                 +f ++v+nlPy +s++ + +l    + +++  ++++qkefa++ll   + k+r+++s++++++++++  ++v+k++fsPppkvds+++++++k+  +  
  EPA06592.1  90 KFsIFVSNLPYSKSKEAIEWLA---ITPFSHGVIMVQKEFAEKLLT-KSTKNRRSVSIITNYVFEIEKFLNVGKNNFSPPPKVDSVVLKITKKKS-I-- 181
                 442689***********99987...45579****************.599*****************************************9999.5.. PP

                 S-HHHHHHHHHHHHCTTTSBCCCHCCCTSTCH CS
      RrnaAD 201 kdlkkyesvvrkllnrkrktlstslksllpgg 232
                    k +  v++k++  +rkt+++ +k+ +++ 
  EPA06592.1 182 --EKDLINVLNKMFSYRRKTIQNIFKQFGKET 211
                 ..67778899**************99766654 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   6.8e-08   0.00015      73     136 ..      29      87 ..       9     100 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 6.8e-08
                 TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGT CS
        PCMT  73 kgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrkG 136
                   + v e+G+G G+lt +l +   +  +v+si+  +el+e+ak +   ++++n++v +gDG + 
  EPA06592.1  29 GNDIVFELGTGLGILTPLLCE---KAKKVISIDADRELYENAKSRF--SHIDNLTVEFGDGFQK 87 
                 566799**********99876...555789*************987..6789*********875 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.3e-06    0.0028       1      50 [.      33      81 ..      33     109 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.3e-06
                     EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHH.TTTTEEE CS
  Methyltransf_25  1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraee.eglnvef 50
                     v +lG+G G lt  l ++   +kv+ +D + e+ e+a++r+++ ++l vef
       EPA06592.1 33 VFELGTGLGILTPLLCEKA--KKVISIDADRELYENAKSRFSHiDNLTVEF 81
                     789*************996..9*******************8755556655 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0     3e-05     0.067       2      58 ..      35      89 ..      34     103 .. 0.92
   2 ?   -1.3   0.0       1.6   3.7e+03      75      89 ..     188     203 ..     151     227 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3e-05
  Methyltransf_12  2 eiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdl 58
                     e+G+G G l+  l+ek   ++++ +D +++  e+ak ++++++n+ +++ + +++++
       EPA06592.1 35 ELGTGLGILTPLLCEK--AKKVISIDADRELYENAKSRFSHIDNLTVEFGDGFQKQD 89
                     9***************..**************************9999988888775 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.6
  Methyltransf_12  75 vlhhl.kdirevldni 89 
                      vl+ +   +r++++ni
       EPA06592.1 188 VLNKMfSYRRKTIQNI 203
                      3322222233333333 PP

>> SAM_3  SAM domain (Sterile alpha motif)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.015        35       9      29 ..     100     120 ..      97     132 .. 0.85
   2 ?    6.4   0.1    0.0035       7.7      23      49 ..     206     234 ..     191     235 .] 0.85

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.015
       SAM_3   9 kStpeeVkaWLtakgFskktv 29 
                  S+ +e  +WL+   Fs+ ++
  EPA06592.1 100 YSKSKEAIEWLAITPFSHGVI 120
                 58999************9865 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0035
       SAM_3  23 gFskktv..esLgklsGaqLfsLskeeLe 49 
                 +F k+t+  ++L++lsG ++  L ke Le
  EPA06592.1 206 QFGKETLmdKRLDDLSGDEIIDLAKEILE 234
                 56666554479***************987 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     4e-05      0.09      13      84 ..      17      81 ..       7     145 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4e-05
  Methyltransf_32 13 vakllkelakesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrlsf 84
                     +a+ + + a+ sg+  v ++G G g L+  l      +  kv++ida +el e+a+ r +++    n  ++f
       EPA06592.1 17 IAQSIVSEANISGNDIVFELGTGLGILTPLLCE----KAKKVISIDADRELYENAKSRFSHID---NLTVEF 81
                     444343336778888999*************99....4789***************9988887...334455 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   7.8e-05      0.17      25      62 ..      32      88 ..       9     210 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.8e-05
  Methyltransf_23 25 rvLdiGcGtGillevlrengfsvtgvDlspeaveiae...................k 62
                      v ++G+G Gil+++l e+ ++v+ +D+++e+ e a+                   +
       EPA06592.1 32 IVFELGTGLGILTPLLCEKAKKVISIDADRELYENAKsrfshidnltvefgdgfqkQ 88
                     688**************************9988888777777775555544433331 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00011      0.25       2      45 ..      35      79 ..      34     101 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                     EET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-.EE CS
  Methyltransf_11  2 dvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl.kv 45
                     ++G+G G+l+  l +++++v+ +D + e+ + ak++ s  ++ +v
       EPA06592.1 35 ELGTGLGILTPLLCEKAKKVISIDADRELYENAKSRFSHIDNlTV 79
                     79********************************99987765444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       898  (0.0500865); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 1596.40
//
Query:       EPA06593.1  [L=272]
Description: hypothetical protein BG20_I0764 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-40  138.6   0.0    1.6e-40  138.2   0.0    1.1  1  Transglut_core2  Transglutaminase-like superfamily
    3.8e-15   55.8   0.0    5.8e-15   55.2   0.0    1.3  1  TPR_9            Tetratricopeptide repeat
    0.00022   21.2   0.1       0.58   10.3   0.0    2.8  2  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
     0.0006   19.5   0.1        1.4    8.9   0.1    2.5  2  TPR_1            Tetratricopeptide repeat
  ------ inclusion threshold ------
       0.13   12.4   0.0         26    5.3   0.0    2.5  2  TPR_2            Tetratricopeptide repeat
       0.14   13.1   0.0        3.6    8.7   0.0    2.3  2  TPR_14           Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> Transglut_core2  Transglutaminase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.2   0.0   5.3e-44   1.6e-40       2     154 ..      43     191 ..      42     192 .. 0.96

  Alignments for each domain:
  == domain 1  score: 138.2 bits;  conditional E-value: 5.3e-44
  Transglut_core2   2 avlaeLdalaaevraelsseraaaekleaLnellyeelgFagneddyydprnslldqVLerrrGiPislsvvylevArrlglplegvgfPghfl 95 
                      ++ ++++ + + +++++s+ +++   + +Lne l+++lgF+g+ ddyy+p+n +l++V++++ G+Pi++s++y+e+A+ +gl+l+ +gfP h+l
       EPA06593.1  43 EYIQKINVIGKSLKETISDVKNPTYLISILNEHLFQNLGFSGDGDDYYNPKNNFLNEVIDKKSGLPITISILYVEIAKFIGLDLKIIGFPSHIL 136
                      6788999999999999999999999********************************************************************* PP

  Transglut_core2  96 vrvgespegevliDPfnaGrllskedleellraalgaeaeltreflapasnrdvltRll 154
                      v+++    +e+++DPfn+G ll+++dl+e+l++++g e+e+++efl+++ ++++l Rl 
       EPA06593.1 137 VKYN----EEMILDPFNDGMLLDVDDLQEILDENFGGELEFKPEFLDSIGHEQILVRLA 191
                      **98....68***********************************************97 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.2   0.0   1.9e-18   5.8e-15       1      72 [.     194     265 ..     194     266 .. 0.98

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 1.9e-18
       TPR_9   1 lkaiaireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapdaeairaqL 72 
                 lk+ + ++  +++al++ +++l++ P++p+++rd G+l+++l +  +Al+ L+ yl+++p+a+d++ i +++
  EPA06593.1 194 LKNSYVQSFVYDKALRCTNMVLAIEPNSPDDIRDKGILEERLLNSDTALKYLNMYLEINPNAEDVDFILELI 265
                 89******************************************************************9987 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   0.00019      0.58      17      33 ..     204     220 ..     198     222 .. 0.92
   2 !    7.9   0.0    0.0011       3.3      17      44 ..     238     265 ..     233     271 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00019
                 HHHHHHHHHHHHHHTTS CS
  Fis1_TPR_C  17 YseArryvdalLeiEPe 33 
                 Y++A+r+++++L+iEP+
  EPA06593.1 204 YDKALRCTNMVLAIEPN 220
                 ****************7 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0011
                 HHHHHHHHHHHHHHTTS-HHHHHHHHHH CS
  Fis1_TPR_C  17 YseArryvdalLeiEPenrQaqsLkeli 44 
                  ++A++y+++ Lei P+ + +    eli
  EPA06593.1 238 SDTALKYLNMYLEINPNAEDVDFILELI 265
                 589*************998887666666 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0   0.00074       2.2      17      33 ..     204     220 ..     204     221 .. 0.96
   2 !    8.9   0.1   0.00047       1.4       8      33 ..     229     254 ..     227     255 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00074
                 HHHHHHHHHHHHHHSTT CS
       TPR_1  17 ydeAleyyekALelnPn 33 
                 yd+Al + + +L ++Pn
  EPA06593.1 204 YDKALRCTNMVLAIEPN 220
                 9***************9 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00047
                 HHHHHHTT-HHHHHHHHHHHHHHSTT CS
       TPR_1   8 GnayfklgkydeAleyyekALelnPn 33 
                 G +  +l + d Al+y +  Le+nPn
  EPA06593.1 229 GILEERLLNSDTALKYLNMYLEINPN 254
                 566667778899*************8 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0    0.0086        26      17      33 ..     204     220 ..     196     221 .. 0.92
   2 ?    4.6   0.1     0.014        42       8      33 ..     229     254 ..     226     255 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0086
       TPR_2  17 yeeAleafekAleldPn 33 
                 y++Al++ + +l+++Pn
  EPA06593.1 204 YDKALRCTNMVLAIEPN 220
                 9***************9 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.014
       TPR_2   8 GlayyklgdyeeAleafekAleldPn 33 
                 G + ++l + + Al++++  le++Pn
  EPA06593.1 229 GILEERLLNSDTALKYLNMYLEINPN 254
                 556667778899*************9 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.12   3.5e+02      17      35 ..     204     222 ..     185     231 .. 0.82
   2 ?    8.7   0.0    0.0012       3.6       8      36 ..     229     257 ..     222     266 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.12
      TPR_14  17 pdeAiallrralalaPdda 35 
                 +d+A+++ + +la  P+++
  EPA06593.1 204 YDKALRCTNMVLAIEPNSP 222
                 79************99987 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0012
      TPR_14   8 aeallalGdpdeAiallrralalaPddae 36 
                 + ++++l + d+A+++l+ +l+ +P+ ++
  EPA06593.1 229 GILEERLLNSDTALKYLNMYLEINPNAED 257
                 6677788899***************8765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1754.67
//
Query:       EPA06594.1  [L=290]
Description: methyltransferase domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.8e-09   36.5   0.0    9.6e-09   35.8   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    1.4e-08   34.7   0.0    2.6e-08   33.8   0.0    1.4  1  Methyltransf_31  Methyltransferase domain
    1.6e-08   35.0   0.0    2.9e-08   34.2   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    3.6e-08   33.4   0.0    4.9e-08   33.0   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    7.5e-08   33.0   0.0    1.8e-07   31.8   0.0    1.7  1  Methyltransf_12  Methyltransferase domain
    9.3e-07   28.2   1.2    1.4e-06   27.6   0.4    1.4  2  DREV             DREV methyltransferase
    0.00033   21.1   0.8      0.003   18.1   0.5    2.7  3  Trm112p          Trm112p-like protein
     0.0015   18.0   0.2     0.0023   17.3   0.2    1.3  1  TehB             Tellurite resistance protein TehB
     0.0015   18.2   0.0     0.0042   16.7   0.0    1.6  2  NodS             Nodulation protein S (NodS)
      0.002   17.7   0.0     0.0058   16.2   0.0    1.7  2  MTS              Methyltransferase small domain
     0.0074   16.0   0.9      0.017   14.9   0.9    1.6  1  zf-CSL           CSL zinc finger


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.0   5.9e-12   9.6e-09       1      89 [.     133     213 ..     133     220 .. 0.88

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 5.9e-12
                      EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHHHHHHHHHH CS
  Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsdedlekalkei 89 
                      vL+ Gc  G+++++la++     v g+D s +++  a++  +e   n+++ ++d+ +  f + +fDl+++ ++l+++++++l   l++i
       EPA06594.1 133 VLEYGCSIGTISKYLANHN--NLVFGIDRSFSAISVAKKSQKE---NLDYFVADLMSDVFGKIKFDLILALNVLELIEPQEL---LEHI 213
                      8***************994..9*****************9954...8***********************988***997765...4433 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.0   1.6e-11   2.6e-08       6     114 ..     132     237 ..     128     272 .. 0.77

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 1.6e-11
  Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdiee.leklledekfDlilsnevlnaladpdkileei 97 
                       vl++GC  G++++ la   + +  v+GiD+s  ai++A++ +qk +ld  v    +d++  +       kfDlil+ +vl  l +p++ le i
       EPA06594.1 132 LVLEYGCSIGTISKYLA---NHNNLVFGIDRSFSAISVAKK-SQKENLDyFVADLMSDVFGkI-------KFDLILALNVL-ELIEPQELLEHI 213
                      59***************...55667****************.688888834444446666633.......5******9999.7789******** PP

  Methyltransf_31  98 ervlkpggilliedpr........l 114
                      ++ ++ +g ++i+dp         +
       EPA06594.1 214 SKQIE-HGTFVISDPYdfdrgkssI 237
                      ****9.8888888887455444432 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.0   1.8e-11   2.9e-08       1      91 [.     134     220 ..     134     224 .. 0.90

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 1.8e-11
                      EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHHHHHHHHHHEEEE CS
  Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedpekalkeiaRvLkpg 91 
                      L+ Gc  G ++++la++   v+g+D s  ++ +ak+ ++e+   +++ vad+ +  f + +fDl+++ +vl+ + +p+++l+ i +  + g
       EPA06594.1 134 LEYGCSIGTISKYLANHNNLVFGIDRSFSAISVAKKSQKEN---LDYFVADLMSDVFGKIKFDLILALNVLELI-EPQELLEHISKQIEHG 220
                      789************999*************9998777765...89*******989******************.6999999998776655 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.0     3e-11   4.9e-08      22     120 ..     129     227 ..     101     267 .. 0.81

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 3e-11
  Methyltransf_23  22 aggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae..kakkaqkdqfdeqeaaepqgkfdlIvlrevlehvpdppellrqiatllkpgG 113
                      +++ vL++Gc  G+ +++l+ +   v g+D s+ a++ a+  ++ +     +d +++ + + kfdlI + +vle +++  ell +i + ++  G
       EPA06594.1 129 KSKLVLEYGCSIGTISKYLANHNNLVFGIDRSFSAISVAKksQKENLDYFVADLMSDVFGKIKFDLILALNVLELIEP-QELLEHISKQIE-HG 220
                      5667***************99999999**********9875545555555555556666777************9986.99*******999.56 PP

  Methyltransf_23 114 ylllsep 120
                       +++s+p
       EPA06594.1 221 TFVISDP 227
                      6666665 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.0   1.1e-10   1.8e-07       1      94 [.     134     218 ..     134     223 .. 0.77

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 1.1e-10
  Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlkdirevldnirklLk 94 
                      Le Gc  G+++++l+++  +  + g+D s sai  ak+  +++ +++++ +       +d +g+ +fDl++a+nvl+ + +++e+l++i k + 
       EPA06594.1 134 LEYGCSIGTISKYLANH--NNLVFGIDRSFSAISVAKKSQKENLDYFVADL------MSDVFGKIKFDLILALNVLELI-EPQELLEHISKQIE 218
                      899**************..99999*********555555555444333333......34444456*************9.999****9998665 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.1   1.8e+03      68      84 ..      68      85 ..      60     102 .. 0.64
   2 !   27.6   0.4   8.7e-10   1.4e-06      72     179 ..     107     218 ..      86     226 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.1
        DREV 68 Gsmfvlseeq.frkllai 84
                G++f +s +q ++k+++ 
  EPA06594.1 68 GKLFHFSSNQkMKKFIKD 85
                789999998835566653 PP

  == domain 2  score: 27.6 bits;  conditional E-value: 8.7e-10
        DREV  72 vlseeqfrkllaiekespasdqedkklldlGaGdGeitkrvaptfeevyatelsetmr.....drlkkkkynvlsalelqetdvkldlilclnlldrcf 165
                 ++   q  k+  i k++ +s  ++k +l+ G   G i+k +a++ + v+  + s   +      + + ++y v   +     ++k+dlil+ln+l+   
  EPA06594.1 107 IYQSSQKSKFYSIVKNELNSFVKSKLVLEYGCSIGTISKYLANHNNLVFGIDRSFSAIsvakkSQKENLDYFVADLMSDVFGKIKFDLILALNVLE-LI 204
                 56778999*****************************************9988765541110034444567777766655579************8.57 PP

        DREV 166 dplklledirsale 179
                 +p +lle i +  e
  EPA06594.1 205 EPQELLEHISKQIE 218
                 899****9987655 PP

>> Trm112p  Trm112p-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.5   1.9e-06     0.003       5      66 ..       6      46 ..       2      47 .. 0.85
   2 ?   -0.8   0.0       1.4   2.3e+03      17      40 ..     100     127 ..      75     154 .. 0.72
   3 ?   -2.3   0.0       4.3     7e+03      13      31 ..     237     256 ..     234     276 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.9e-06
                CCC-B-TTTHHC--HHHHHHHHHTT---S-SS----SCHHTTEECCCCEEEETTTTEEEEEE CS
     Trm112p  5 lniLaCpackgpLdwealvevaalglnelpkekpedyellleldieegeLvCpncgraYpIk 66
                l++L C  c ++L+++++ +                     e++i+eg L+C  c + +pI 
  EPA06594.1  6 LDFLRCVRCGSKLELDVFKQ---------------------ETEIDEGLLQCIQCSLYFPII 46
                89*********996666655.....................478*****************6 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.4
                 -..-HHHHHHHHH.TT---.S-SS---- CS
     Trm112p  17 L..dwealvevaa.lglne.lpkekped 40 
                 L  +w+ +++ ++  ++++ ++ e+ ++
  EPA06594.1 100 LeeRWSRIYQSSQkSKFYSiVKNELNSF 127
                 3556888888888888888555555554 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 4.3
                 THHC--HHHHHHHHH.TT-- CS
     Trm112p  13 ckgpLdwealvevaa.lgln 31 
                 +k+pLd  al      lg++
  EPA06594.1 237 IKKPLDDMALRSSLSdLGFQ 256
                 78899877777666666655 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.2   1.4e-06    0.0023      27     120 ..     126     216 ..     103     225 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.4e-06
                 CCS-S-EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG---.-S-EEEEEEESSGGGS-GGGHHHHHHHH CS
        TehB  27 kivkpgkvldlgcgqgrnslylsllgydvtawdknensiafleeikekenlknistalydineakl.derydfilstvvlmfleaeripsiienm 120
                   vk   vl+ gc  g  s yl+     v  +d+  ++i+ + +  +kenl+   +   d+ +  + + ++d+il+  vl ++e++ + + i+  
  EPA06594.1 126 SFVKSKLVLEYGCSIGTISKYLANHNNLVFGIDRSFSAIS-VAKKSQKENLDYFVA---DLMSDVFgKIKFDLILALNVLELIEPQELLEHISKQ 216
                 46778889**************************998887.5666899****6555...54444441559**************98876555443 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.2     2e+03      79     120 ..      88     129 ..      77     132 .. 0.74
   2 !   16.7   0.0   2.6e-06    0.0042      47     123 ..     133     208 ..     112     218 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.2
        NodS  79 ararervkesshiswivsdvqqfstdekfdlivvaevlyyie 120
                   +++++ + + +    s + q s++ kf  iv  e+  +++
  EPA06594.1  88 INSKRQTSDRTSLEERWSRIYQSSQKSKFYSIVKNELNSFVK 129
                 556666666677777778899999999999999988776665 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 2.6e-06
        NodS  47 alevGcaaGalterlapyckrltvvdvveeaiararervkesshiswivsdvq.qfstdekfdlivvaevlyyiedva 123
                 +le Gc+ G++++ la + + +  +d   +ai+ a++  ke  ++ + v+d+   +  + kfdli+  +vl  ie  +
  EPA06594.1 133 VLEYGCSIGTISKYLANHNNLVFGIDRSFSAISVAKKSQKE--NLDYFVADLMsDVFGKIKFDLILALNVLELIEPQE 208
                 89**********************************99998..89999999762577899***********9887655 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.99   1.6e+03      77     104 ..      97     122 ..      77     124 .. 0.73
   2 !   16.2   0.0   3.5e-06    0.0058      31     102 ..     129     196 ..     116     198 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.99
                 HTTGCEEEEE-STTTTSTTS-EEEEEE- CS
         MTS  77 anklevevvasdvleeveekkfdlivsN 104
                 +   ++e ++s +++  ++ kf  iv N
  EPA06594.1  97 R--TSLEERWSRIYQSSQKSKFYSIVKN 122
                 2..3367788889999998999888887 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 3.5e-06
                 TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTST.TS-EEEEE CS
         MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeve.ekkfdliv 102
                 +s+ vl  Gc +G ++  la++++   v  +d ++ A+ +ak+  ++n    +++  d++++v  + kfdli+
  EPA06594.1 129 KSKLVLEYGCSIGTISKYLANHNNL--VFGIDRSFSAISVAKKSQKENL---DYFVADLMSDVFgKIKFDLIL 196
                 566799**************98777..99**************999886...566666666665345699886 PP

>> zf-CSL  CSL zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.9     1e-05     0.017      20      54 ..      10      43 ..       7      48 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1e-05
                EE.TTSSE..EEEEHHHHHTT....--EEEETTSSEEE CS
      zf-CSL 20 pC.RCgde..FelteedleegaegaevvvqCssCSLwi 54
                 C RCg++   ++ +++ e      e ++qC +CSL  
  EPA06594.1 10 RCvRCGSKleLDVFKQETEID----EGLLQCIQCSLYF 43
                6*******5555556666555....9**********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       873  (0.0486921); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 1730.46
//
Query:       EPA06595.1  [L=169]
Description: hypothetical protein BG20_I0769 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1055.72
//
Query:       EPA06596.1  [L=220]
Description: L1P family of ribosomal protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.2e-38  131.1   1.8    5.4e-38  130.8   1.8    1.1  1  Ribosomal_L1  Ribosomal protein L1p/L10e family


Domain annotation for each model (and alignments):
>> Ribosomal_L1  Ribosomal protein L1p/L10e family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.8   1.8     3e-42   5.4e-38       5     203 ..      19     206 ..       9     207 .. 0.93

  Alignments for each domain:
  == domain 1  score: 130.8 bits;  conditional E-value: 3e-42
                   S-SSS--EEEEEEEESSS-TTSGGG--EEEEE-STSTSSCS-EEEEE-HHHHH...HHHHTT..-SEEETCHHHHHHT-HHHHHHTCCH-SEEEEEG CS
  Ribosomal_L1   5 akkkfdesveialnlttkkpkkadqrkpgkipLphplgkevkiclitkdpqaeyakeakeagriakviglkklkkkyksfeakrkllkefdlfladd 101
                   +++kf++sve+++ ++++++kk     ++ ++Lp+   +++++c+ + ++  +   +akea+  + v+g  +l k   +++ +rk+++++d+flad 
    EPA06596.1  19 KQRKFKQSVELIMVFKDIDVKK-GFALNEVVQLPKT-SSPATVCIMATGDMGQ---KAKEAK-ADAVVGSAELDKFAADKRTSRKFINKYDFFLADT 109
                   4789***********9999777.6679*******85.589************9...777777.778******************************* PP

                   GGHHHHHHHCHHHHGGGT-S-ECC..CT.BTS-HHHHHHHHCTTEEEEE-TTTSEEEEEEEETTSSHHHHHHHHHHHHHHHHHTSTTTSGSEEEEEE CS
  Ribosomal_L1 102 rimpllpklLGkvfgkrkkmPipvltkgtvkedvkkevekalkstvvvrldkgtclsvkvGklsftaeelaeNieavvkalvekvpkkwkniksiyl 198
                   +imp ++k+LG+ +g+r+kmP+pv      ++++++ + ++ + +++vr++ +  +s+k+G  s+++++la N++av++a+++k+p++ kn+k i +
    EPA06596.1 110 QIMPVVGKVLGQLLGPRGKMPTPV--P--FNASIEAFLTRFRS-SIKVRARATLAMSCKIGDESMDNADLAINAHAVISAVEKKLPNGEKNLKRIII 201
                   ************************..6..4678*******999.9****99999******************************************* PP

                   EETTS CS
  Ribosomal_L1 199 kttms 203
                   kttm+
    EPA06596.1 202 KTTMG 206
                   ****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1340.86
//
Query:       EPA06597.1  [L=37]
Description: hypothetical protein BG20_I0738 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.49
# Mc/sec: 228.92
//
Query:       EPA06598.1  [L=57]
Description: hypothetical protein BG20_I0754 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.25s 00:00:00.57 Elapsed: 00:00:00.40
# Mc/sec: 428.34
//
Query:       EPA06599.1  [L=53]
Description: hypothetical protein BG20_I0763 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.039   13.9   1.1        1.9    8.5   0.1    2.1  2  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
       0.04   13.8   0.3      0.043   13.8   0.3    1.1  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
      0.067   13.0   3.4        3.8    7.4   0.1    2.1  2  zf-RING_4       RING/Ubox like zinc-binding domain
       0.14   12.4   0.8        0.3   11.3   0.9    1.7  1  DUF4451         Domain of unknown function (DUF4451)


Domain annotation for each model (and alignments):
>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1    0.0067        30       3       9 ..      20      26 ..      18      28 .. 0.78
   2 ?    8.5   0.1   0.00042       1.9       3      14 ..      42      53 .]      34      53 .] 0.81

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0067
  PhnA_Zn_Ribbon  3 pkCplCa 9 
                    + CplC+
      EPA06599.1 20 GMCPLCK 26
                    67****6 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00042
  PhnA_Zn_Ribbon  3 pkCplCaSeytY 14
                    +kC++C  e+++
      EPA06599.1 42 GKCEKCRQEFEL 53
                    699999877765 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.3   9.5e-06     0.043      18      55 ..       8      50 ..       2      52 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9.5e-06
  OrfB_Zn_ribbon 18 kveevnpay.TSktCseCgsknke....alsgrtfkCpnCgfe 55
                    k++   p + T   C+ C  ++k     ++ +++ kC++C  e
      EPA06599.1  8 KIIRTGPKNaTTGMCPLCKTIGKVfllgPPGQERGKCEKCRQE 50
                    5666677777999***************9***********876 PP

>> zf-RING_4  RING/Ubox like zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1   0.00086       3.8      34      45 ..      16      27 ..       7      28 .. 0.81
   2 ?    6.7   0.6    0.0014       6.1      36      48 .]      40      52 ..      35      52 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00086
   zf-RING_4 34 eeeegrCPaCre 45
                ++++g+CP C++
  EPA06599.1 16 NATTGMCPLCKT 27
                46799*****96 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0014
   zf-RING_4 36 eegrCPaCreeYk 48
                e g+C +Cr+e++
  EPA06599.1 40 ERGKCEKCRQEFE 52
                689*******995 PP

>> DUF4451  Domain of unknown function (DUF4451)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.9   6.8e-05       0.3      10      31 ..       8      27 ..       3      52 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.8e-05
     DUF4451 10 rvvrgekdknekkeglCpiCee 31
                +++r+    ++ + g+Cp+C++
  EPA06599.1  8 KIIRT--GPKNATTGMCPLCKT 27
                55555..467899*******93 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 360.42
//
Query:       EPA06600.1  [L=79]
Description: ammecr1, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.6e-20   71.2   0.0    8.3e-20   71.1   0.0    1.0  1  AMMECR1   AMMECR1


Domain annotation for each model (and alignments):
>> AMMECR1  AMMECR1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.1   0.0   4.6e-24   8.3e-20     103     165 ..       2      64 ..       1      65 [. 0.96

  Alignments for each domain:
  == domain 1  score: 71.1 bits;  conditional E-value: 4.6e-24
                 --TTT-EEEEEETTEEEEE-THHHHHTT--HHHHHHHHHHHHTS-TTCCCSTTSEEEEE-EEE CS
     AMMECR1 103 levgkhGliiekgsrsatlLPqvaveqgwdkeeflasllrKaglrpdewkdseikltryevek 165
                 ++vg++Gli+++g +s++lLPqv+ e+gwd+eefl+++++Kag+++d+wk+ +++++++e+ +
  EPA06600.1   2 IKVGRDGLIVKHGFYSGLLLPQVPIEYGWDEEEFLEHTCEKAGIPKDYWKNAKTEIQKFEGIV 64 
                 89*********************************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 543.16
//
Query:       EPA06601.1  [L=50]
Description: hypothetical protein BG20_I2628 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0038   17.0   0.1     0.0054   16.5   0.1    1.3  1  DUF126    Aconitase X swivel domain


Domain annotation for each model (and alignments):
>> DUF126  Aconitase X swivel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1     3e-07    0.0054      59      79 ..       1      21 [.       1      22 [. 0.96

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3e-07
                EEESS--HHHHHHHHHHT--E CS
      DUF126 59 lilreadpilalGaivadiPl 79
                +i+++ad  +a+G+++a+iPl
  EPA06601.1  1 MICQKADLTVATGCALANIPL 21
                8*******************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 342.66
//
Query:       EPA06602.1  [L=55]
Description: hypothetical protein BG20_I2626 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.8e-06   25.4   0.0    1.5e-05   24.7   0.0    1.4  2  DUF126    Aconitase X swivel domain


Domain annotation for each model (and alignments):
>> DUF126  Aconitase X swivel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.23   4.2e+03      11      11 ..      10      10 ..       2      19 .. 0.50
   2 !   24.7   0.0   8.1e-10   1.5e-05       1      27 [.      20      46 ..      20      53 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.23
                T CS
      DUF126 11 t 11
                +
  EPA06602.1 10 Q 10
                2 PP

  == domain 2  score: 24.7 bits;  conditional E-value: 8.1e-10
                --TTS-B-TTT-BB-S.-SSSTT-B-T CS
      DUF126  1 lSflggvdpetGkvidkghplegqsia 27
                ++flg vd++tG+++dk+h+l+++s++
  EPA06602.1 20 INFLGTVDKKTGIISDKNHELYDKSLK 46
                78***********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       228  (0.0127168); expected 358.6 (0.02)
Passed bias filter:                      180  (0.0100396); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 410.92
//
Query:       EPA06603.1  [L=274]
Description: E1-E2 ATPase, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-48  164.1   0.8      3e-48  163.7   0.8    1.2  1  E1-E2_ATPase  E1-E2 ATPase
    3.1e-06   27.6   0.0    6.5e-06   26.6   0.0    1.5  1  Hydrolase     haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
       0.03   14.0   0.6      0.049   13.3   0.6    1.3  1  ABC_membrane  ABC transporter transmembrane region
      0.084   11.9   0.0       0.12   11.4   0.0    1.1  1  DUF1402       Protein of unknown function (DUF1402)


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.7   0.8   6.7e-52     3e-48       3     181 .]      23     193 ..      21     193 .. 0.97

  Alignments for each domain:
  == domain 1  score: 163.7 bits;  conditional E-value: 6.7e-52
                   S--EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-G-TTEE-TT-EEEE-EEEEEEEE-TTTSTTTTTST CS
  E1-E2_ATPase   3 lpptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvekekgdmvfsGtvvvsgeakavVtatgedtelgkiar 99 
                   +p+ a++ +dg +++i++++++++D++l+++gd +p+Dg+i+eg+ae+desaLTGE lp  k+ g+ vfsGtv+v + +k+   +t  +++++ki++
    EPA06603.1  23 SPRIANLQKDGDIKQIKVEDVQIDDVLLVRSGDLIPVDGIILEGTAEIDESALTGEPLPKIKTSGNAVFSGTVNVGDAFKITCSKTSVNSQYSKIVQ 119
                   68899999***************************************************************************************** PP

                   TS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHHHHS-TTHHHHHHHHHHHHHHHHHHT CS
  E1-E2_ATPase 100 lveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeallralallvaaiPcaLplavplalalgarrlakk 181
                   lv++a+++k+p+q+ +dk++ +++p+v++i++l ++i+        +    +la+lv+a+Pc L+ a+p+a++ g++r+ak+
    EPA06603.1 120 LVRKAQQEKAPIQRLADKYAVWFTPIVIVISVLGWFIT--------KNPETVLAVLVVATPCPLIFATPTAIISGISRAAKR 193
                   *********************************99998........4446799***************************96 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   1.5e-09   6.5e-06       2      53 ..     210     267 ..     209     272 .. 0.90

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 1.5e-09
                 SEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHH......HHCHHHHHHHHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxx RF
   Hydrolase   2 ktvvfDkdGTLttgepsvedvivsaalalaaaletg......sehpigkalvaaakar 53 
                 k+ vfDk+GT+t g+p + ++i  + +   + l+ +      s hp + alv   k+ 
  EPA06603.1 210 KVAVFDKTGTITLGTPTIDEIITLNGVNYDVLLRNVasieqmSSHPAAIALVQMGKEK 267
                 789**********************888888888889999***********9998876 PP

>> ABC_membrane  ABC transporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.6   1.1e-05     0.049     115     172 ..     134     191 ..     132     206 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.1e-05
                   HCHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
  ABC_membrane 115 lgeklglffqslltfvgglivmfylgwkltlvllailpliilvsaviakilkklkkke 172
                   l++k  ++f+++++++++l++ ++ ++   l++l+++  + l++a  + i++ +++  
    EPA06603.1 134 LADKYAVWFTPIVIVISVLGWFITKNPETVLAVLVVATPCPLIFATPTAIISGISRAA 191
                   678999*******************************999999998888888887765 PP

>> DUF1402  Protein of unknown function (DUF1402)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   2.7e-05      0.12      28      79 ..     100     153 ..      86     163 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.7e-05
     DUF1402  28 arrtkaakttyekkyqkvlellkkdksliakikkvaaayki..dPihivGaivG 79 
                 a +   +kt+ +++y k+++l++k ++  a i++ a +y +   Pi iv +++G
  EPA06603.1 100 AFKITCSKTSVNSQYSKIVQLVRKAQQEKAPIQRLADKYAVwfTPIVIVISVLG 153
                 55667889*******************************975579999988877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 2043.47
//
Query:       EPA06604.1  [L=274]
Description: E1-E2 ATPase, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-48  164.1   0.8      3e-48  163.7   0.8    1.2  1  E1-E2_ATPase  E1-E2 ATPase
    2.2e-06   28.1   0.0    4.7e-06   27.0   0.0    1.5  1  Hydrolase     haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
       0.03   14.0   0.6      0.049   13.3   0.6    1.3  1  ABC_membrane  ABC transporter transmembrane region
      0.084   11.9   0.0       0.12   11.4   0.0    1.1  1  DUF1402       Protein of unknown function (DUF1402)


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.7   0.8   6.7e-52     3e-48       3     181 .]      23     193 ..      21     193 .. 0.97

  Alignments for each domain:
  == domain 1  score: 163.7 bits;  conditional E-value: 6.7e-52
                   S--EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-G-TTEE-TT-EEEE-EEEEEEEE-TTTSTTTTTST CS
  E1-E2_ATPase   3 lpptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvekekgdmvfsGtvvvsgeakavVtatgedtelgkiar 99 
                   +p+ a++ +dg +++i++++++++D++l+++gd +p+Dg+i+eg+ae+desaLTGE lp  k+ g+ vfsGtv+v + +k+   +t  +++++ki++
    EPA06604.1  23 SPRIANLQKDGDIKQIKVEDVQIDDVLLVRSGDLIPVDGIILEGTAEIDESALTGEPLPKIKTSGNAVFSGTVNVGDAFKITCSKTSVNSQYSKIVQ 119
                   68899999***************************************************************************************** PP

                   TS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHHHHS-TTHHHHHHHHHHHHHHHHHHT CS
  E1-E2_ATPase 100 lveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeallralallvaaiPcaLplavplalalgarrlakk 181
                   lv++a+++k+p+q+ +dk++ +++p+v++i++l ++i+        +    +la+lv+a+Pc L+ a+p+a++ g++r+ak+
    EPA06604.1 120 LVRKAQQEKAPIQRLADKYAVWFTPIVIVISVLGWFIT--------KNPETVLAVLVVATPCPLIFATPTAIISGISRAAKR 193
                   *********************************99998........4446799***************************96 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0     1e-09   4.7e-06       2      53 ..     210     267 ..     209     272 .. 0.91

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 1e-09
                 SEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHH......HHCHHHHHHHHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxx RF
   Hydrolase   2 ktvvfDkdGTLttgepsvedvivsaalalaaaletg......sehpigkalvaaakar 53 
                 k+ vfDk+GT+t g+p + ++i  + ++  + l+ +      s hp + alv   k+ 
  EPA06604.1 210 KVAVFDKTGTITLGTPTIDEIITLNGVDYDVLLRNVasieqmSSHPAAIALVQMGKEK 267
                 789**********************999999999999999***********9998876 PP

>> ABC_membrane  ABC transporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.6   1.1e-05     0.049     115     172 ..     134     191 ..     132     206 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.1e-05
                   HCHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
  ABC_membrane 115 lgeklglffqslltfvgglivmfylgwkltlvllailpliilvsaviakilkklkkke 172
                   l++k  ++f+++++++++l++ ++ ++   l++l+++  + l++a  + i++ +++  
    EPA06604.1 134 LADKYAVWFTPIVIVISVLGWFITKNPETVLAVLVVATPCPLIFATPTAIISGISRAA 191
                   678999*******************************999999998888888887765 PP

>> DUF1402  Protein of unknown function (DUF1402)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   2.7e-05      0.12      28      79 ..     100     153 ..      86     163 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.7e-05
     DUF1402  28 arrtkaakttyekkyqkvlellkkdksliakikkvaaayki..dPihivGaivG 79 
                 a +   +kt+ +++y k+++l++k ++  a i++ a +y +   Pi iv +++G
  EPA06604.1 100 AFKITCSKTSVNSQYSKIVQLVRKAQQEKAPIQRLADKYAVwfTPIVIVISVLG 153
                 55667889*******************************975579999988877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 2015.96
//
Query:       EPA06605.1  [L=490]
Description: hypothetical protein BG20_I1791 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-10   39.5   2.3      0.059   12.9   0.0    3.8  4  C5-epim_C        D-glucuronyl C5-epimerase C-terminus
    8.6e-08   31.6   0.1       0.29   10.2   0.0    3.8  4  Glyco_hydro_88   Glycosyl Hydrolase Family 88
    3.3e-05   22.6   0.4       0.15   10.6   0.0    3.2  3  Glyco_hydro_127  Beta-L-arabinofuranosidase, GH127
    8.9e-05   22.2   0.0       0.43   10.0   0.0    3.3  3  Glyco_hydro_76   Glycosyl hydrolase family 76
    0.00037   19.9   0.1        3.7    6.7   0.0    3.7  4  GlcNAc_2-epim    N-acylglucosamine 2-epimerase (GlcNAc 2-epim
     0.0079   14.8   0.4        5.6    5.4   0.1    3.6  4  LANC_like        Lanthionine synthetase C-like protein
  ------ inclusion threshold ------
      0.027   13.8   0.3        7.8    5.7   0.1    2.7  3  Pec_lyase        Pectic acid lyase


Domain annotation for each model (and alignments):
>> C5-epim_C  D-glucuronyl C5-epimerase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.1   3.3e-05     0.085      33      75 ..      88     132 ..      81     147 .. 0.80
   2 !   12.9   0.0   2.3e-05     0.059      32      63 ..     232     263 ..     229     278 .. 0.91
   3 ?   -1.7   0.1       0.7   1.8e+03      36      59 ..     294     317 ..     288     321 .. 0.80
   4 !   11.2   0.0   7.5e-05      0.19      35      61 ..     361     387 ..     355     403 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.3e-05
   C5-epim_C  33 qaisvllrAYeltgdekYlkaakkalksfk..ipvekGGvlktle 75 
                  + + +++AY+ t+d  Yl++ +k l++++  +++++GG+ +  +
  EPA06605.1  88 LIPVNYVEAYQITKDPFYLEVLNKTLDFVLreMTAKNGGFYSAYD 132
                 566789*********************986225678899877655 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 2.3e-05
   C5-epim_C  32 gqaisvllrAYeltgdekYlkaakkalksfki 63 
                 + +i ++++ Y +tgd kYl+aak+ ++++++
  EPA06605.1 232 ALMITAFAKGYGVTGDTKYLDAAKNCVHFIET 263
                 56899*******************99988765 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.7
   C5-epim_C  36 svllrAYeltgdekYlkaakkalk 59 
                  +ll  +e+  ++kYl++a k+ +
  EPA06605.1 294 NALLDVFEVEPESKYLDLALKLGN 317
                 567778999999******999766 PP

  == domain 4  score: 11.2 bits;  conditional E-value: 7.5e-05
   C5-epim_C  35 isvllrAYeltgdekYlkaakkalksf 61 
                  sv+lr Y+lt+dek+lk+a + ++s 
  EPA06605.1 361 CSVMLRLYHLTHDEKFLKIATQIMESQ 387
                 6899*****************998875 PP

>> Glyco_hydro_88  Glycosyl Hydrolase Family 88
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.051   1.3e+02     134     175 ..      25      67 ..      23      74 .. 0.86
   2 !   10.2   0.0   0.00011      0.29      72     118 ..      84     129 ..      60     165 .. 0.75
   3 !    9.0   0.0   0.00026      0.67      31     124 ..     231     339 ..     222     350 .. 0.79
   4 !    6.5   0.0    0.0015       3.8      30      63 ..     356     389 ..     324     415 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.051
                     HHHHHHHHHHHHCGTHHHHHHHHHHHHHHHH.HBETTTSEB-S CS
  Glyco_hydro_88 134 aipllaklskvtgepkyldeaikqflltarh.lfdpetGlyyh 175
                     +i +l++++k+tg  k+ ++a+k + ++ar  +fd+  G +++
      EPA06605.1  25 NISFLFRYAKLTGLSKFNEFALKTLNKMARGgIFDQIGGGFHR 67 
                     689*************************997788887776665 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00011
                     GGGTGHHHHHHHHHHHH-THHHHHHHHHHHHHHHHCS-B.TTS.B.S CS
  Glyco_hydro_88  72 lDdidigllllllyeltkderykeaaeeladyvlakpprtseGgfwh 118
                      D++ i   ++  y++tkd+ y e +++  d+vl+++   ++Ggf  
      EPA06605.1  84 YDNALIPVNYVEAYQITKDPFYLEVLNKTLDFVLREMTA-KNGGFYS 129
                     455566666777777777777777777777777777776.6677765 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.00026
                     HHHHHHHHHHHHHHH--HHHHHHHHH..........HHHHCCCTTS-.....CTTSGGGTGHHHHHHHHHHHH-THHHHHHHHHHHHHHHHCS-B CS
  Glyco_hydro_88  31 nGvflsglleayeatgdkeyldyaka..........wadslideggk.....telelDdidigllllllyeltkderykeaaeeladyvlakppr 110
                     n+++++++++ y  tgd +yld+ak+          + d+l+ + ++       +  D+   +  ll+ +e +++++y  +a +l +y++++  +
      EPA06605.1 231 NALMITAFAKGYGVTGDTKYLDAAKNcvhfiettllINDKLLRTSKNgitkiDGYLEDYSYFANALLDVFEVEPESKYLDLALKLGNYLVDHFWD 325
                     789999********************777777666644444444444777766667788888889999*****************9999998877 PP

                     .TTS.B.SBTTSTT CS
  Glyco_hydro_88 111 tseGgfwhkkkepe 124
                      +   f+  + ++e
      EPA06605.1 326 SESSSFFMTSDNHE 339
                     77777776555555 PP

  == domain 4  score: 6.5 bits;  conditional E-value: 0.0015
                     HHHHHHHHHHHHHHHH--HHHHHHHHHHHHHCCC CS
  Glyco_hydro_88  30 tnGvflsglleayeatgdkeyldyakawadslid 63 
                      n v  s +l++y  t d+++l++a+++++s+ +
      EPA06605.1 356 GNSVSCSVMLRLYHLTHDEKFLKIATQIMESQAQ 389
                     4678888899******************999876 PP

>> Glyco_hydro_127  Beta-L-arabinofuranosidase, GH127
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0     0.057   1.5e+02     134     157 ..      93     116 ..      64     145 .. 0.66
   2 !   10.6   0.0   5.7e-05      0.15     180     267 ..     234     320 ..     186     324 .. 0.64
   3 !    7.1   0.0   0.00064       1.6     177     208 ..     357     388 ..     292     395 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.057
                      HHHHHHHH--HHHHHHHHHHHHHH CS
  Glyco_hydro_127 134 avayyqatgkeklldvatrladyl 157
                       v++yq t++   l+v+ +  d++
       EPA06605.1  93 YVEAYQITKDPFYLEVLNKTLDFV 116
                      445555555555555555555555 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 5.7e-05
                      HHHHHHHHHHHHT-CHHHHHHHHCCHHCCHCC.T-HCTTT-SSTCGCHHCHHCCHHHHHHHHHHHHHHHHHCTTHCCHHHHHHHHHHHH CS
  Glyco_hydro_127 180 ieealvklyelTgdkrYldlAkrfidergldp.eklaykqdelpvrhqntaigkavRatylysgladvyeetgddkllkaaerlwdnvv 267
                      +  a++k y +Tgd++Yld Ak+ ++   ++   +++  ++++++    ++ g +    y++  l dv+e+  ++k+l+ a +l + +v
       EPA06605.1 234 MITAFAKGYGVTGDTKYLDAAKNCVHFIETTLlINDKLLRTSKNGIT--KIDGYLEDYSYFANALLDVFEVEPESKYLDLALKLGNYLV 320
                      44788899999999999999998666443333111333333333333..4445555555666666666666666666666666555555 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.00064
                      HCTHHHHHHHHHHHHT-CHHHHHHHHCCHHCC CS
  Glyco_hydro_127 177 hggieealvklyelTgdkrYldlAkrfiderg 208
                       +  + ++++ly lT d+++l++A+++++ ++
       EPA06605.1 357 NSVSCSVMLRLYHLTHDEKFLKIATQIMESQA 388
                      44556789999999999999999999988765 PP

>> Glyco_hydro_76  Glycosyl hydrolase family 76
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.26   6.7e+02      92     128 ..      89     120 ..      19     139 .. 0.53
   2 !   10.0   0.0   0.00017      0.43     163     195 ..     238     270 ..     224     326 .. 0.69
   3 !    7.9   0.0   0.00077         2     108     184 ..     303     385 ..     280     395 .. 0.58

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.26
                     HHHHHHHHHHH.....H--HHHHHHHHHHHHHHHHCB CS
  Glyco_hydro_76  92 wglaamtaaernfpeptdepswLalAqavfntqasrw 128
                     + +  ++a+++     t++p +L++ +++ +++ ++ 
      EPA06605.1  89 IPVNYVEAYQI-----TKDPFYLEVLNKTLDFVLREM 120
                     33334444443.....444444444444444444444 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00017
                     HHHHHHHH--CHHHHHHHHHHHHHHHHSCSBTT CS
  Glyco_hydro_76 163 aarLarytgnetYlewAekvwdWvedvglidde 195
                      a+ + +tg+ +Yl+ A+++++++e++ li+d+
      EPA06605.1 238 FAKGYGVTGDTKYLDAAKNCVHFIETTLLINDK 270
                     455567788888999999999999888887444 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.00077
                     H--HHHHHHHHHHHHHHHHC.B-SCSCCS-BBSE.....C..ESS--SEEEHHHHHHHHHHHHHHHHHH--CHHHHHHHHHHH CS
  Glyco_hydro_76 108 tdepswLalAqavfntqasr.wdeetcgGGlrWq.....iftwnsgydyknsisngplfqlaarLarytgnetYlewAekvwd 184
                     + e ++L+lA ++ n+++++ wd+e+    +        i + +s+yd+     n+ +  + +rL+  t +e++l+ A+++++
      EPA06605.1 303 EPESKYLDLALKLGNYLVDHfWDSESSSFFMTSDnheklIIRPKSNYDLSLPSGNSVSCSVMLRLYHLTHDEKFLKIATQIME 385
                     34566666666666666666666666444443330000123334555555555666666666777777777777777776654 PP

>> GlcNAc_2-epim  N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.036        91      41     124 ..      41     128 ..      23     147 .. 0.51
   2 ?    2.8   0.0     0.023        58     275     310 ..     230     264 ..     215     274 .. 0.80
   3 !    6.4   0.0    0.0017       4.5      88     180 ..     236     328 ..     231     338 .. 0.71
   4 !    6.7   0.0    0.0014       3.7     131     172 ..     350     388 ..     305     398 .. 0.61

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.036
                    HHHHHHHHHHHTTTTTB.-TTTSSB-SEEETTEEEE-..-EEHHHHHHHHHHHHHHHT.TT-TTHHHHHHHHHHHHHHHTEETTTTEE CS
  GlcNAc_2-epim  41 wldlvehGlkflekvlr.daehggyfsalrdggvlda..skdaYdhaFvllalasala.ageeeakdlldetlavlekhlweekaglv 124
                    + + + + l+ +++ +  d+  gg+ +  +d + l +  +k +Yd a +   + +a++ + ++ + ++l++tl+++ +++  ++ g++
     EPA06605.1  41 FNEFALKTLNKMARGGIfDQIGGGFHRYSTDAKWLVPhfEKMLYDNALIPVNYVEAYQiTKDPFYLEVLNKTLDFVLREMTAKNGGFY 128
                    4444444444444443334444455555555554433113445666666666666554133344566666666666655555544443 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.023
                    HHHHHHHHHHHHHHHHH--CHHHHHHHHHHHHHHHH CS
  GlcNAc_2-epim 275 WpqtEalkaaaalaeltgearylewyarvaeylerh 310
                    W  +  + a a+++++tg+ +yl+ ++++++++e+ 
     EPA06605.1 230 WNAL-MITAFAKGYGVTGDTKYLDAAKNCVHFIETT 264
                    5544.3788899999999999999999999888765 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0017
                    HHHHH.HHTTT-TTHHHHHHHHHHHHHHHTEETTTTEE--EE-TTSS-BEEHHHH.HHHHHHHHHHHHTT-BTHHHHHHHHHHHHHTTTTGGGGT CS
  GlcNAc_2-epim  88 lalas.alaageeeakdlldetlavlekhlweekaglvkeesdkefsklrgsnpn.MhlleAmLalaeatgdkeyleraeeiaelvisefadaes 180
                     a+a+    +g++++ d++++ ++++e+ l  +++ l +  s++  +k+ g   +     +A+L ++e++ +++yl++a ++ +  +++f d es
     EPA06605.1 236 TAFAKgYGVTGDTKYLDAAKNCVHFIETTLLINDKLL-RT-SKNGITKIDGYLEDySYFANALLDVFEVEPESKYLDLALKLGNYLVDHFWDSES 328
                    4666644567888888888888888887776664433.33.34446666444333156678999999***********99999999999998776 PP

  == domain 4  score: 6.7 bits;  conditional E-value: 0.0014
                    TSS-BEEHHHHHHHHHHHHHHHHTT-BTHHHHHHHHHHHHHT CS
  GlcNAc_2-epim 131 efsklrgsnpnMhlleAmLalaeatgdkeyleraeeiaelvi 172
                    + s +   n     + +mL l+ +t+d+++l+ a +i+e   
     EPA06605.1 350 DLSLP-SGN--SVSCSVMLRLYHLTHDEKFLKIATQIMESQA 388
                    22222.333..47899*********************99766 PP

>> LANC_like  Lanthionine synthetase C-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.39     1e+03      15      41 ..      26      52 ..      22      56 .. 0.49
   2 !    4.5   0.0    0.0043        11     177     214 ..      95     132 ..      89     145 .. 0.78
   3 ?   -0.2   0.0      0.11   2.8e+02      17     198 ..     237     261 ..     232     279 .. 0.61
   4 !    5.4   0.1    0.0022       5.6     113     196 ..     294     385 ..     247     404 .. 0.67

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.39
                HHHHHHHHHHHTHHHHHHHHHHHHHHH CS
   LANC_like 15 allllelykvtknekylklahkyleki 41
                + +l++++k t+ +k+ + a+k l+k+
  EPA06605.1 26 ISFLFRYAKLTGLSKFNEFALKTLNKM 52
                344555555555555555555555544 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0043
                 CCCHT.-HHHHHHHHHHHHHHHHHTS-TGTST--SBCT CS
   LANC_like 177 alykgtksekllelikkllkylkslkfksegnWpdsis 214
                 ++y++tk++ +le ++k+l+++++  + ++g++ + ++
  EPA06605.1  95 EAYQITKDPFYLEVLNKTLDFVLREMTAKNGGFYSAYD 132
                 67888999999999999999999999888888777664 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.11
                 HHHHHHHHHTHHHHHHHHHHHHHHHHHHHCCH.-S--STTTSHHHHHHHHHHHHHHCTHHHHHHHHHHHHHCCHHHCTCHT..GHSSTTTSHHHHHHHH CS
   LANC_like  17 lllelykvtknekylklahkylekikkelselglesisffsGaagiafalavaskklgnyqellkaldsllelieeekledekkdyDvisGlaGilsyl 115
                 ++++ y vt++ kyl+ a++++                                                                             
  EPA06605.1 237 AFAKGYGVTGDTKYLDAAKNCVH---------------------------------------------------------------------------- 259
                 44555555555555555555554............................................................................ PP

                 HHHHHHH-SGHHHHHHHHHHHHHHHCHHCCTTTCHSCHH-BTTBEB-STTTSHHHHHHHHHCCCHT.-HHHHHHHHHHHHHHH CS
   LANC_like 116 lllneetkieedllkqilkylvelgiksenqvswsplmyepegesnlGlAHGlsGialallalykgtksekllelikkllkyl 198
                                                                                                  ++
  EPA06605.1 260 ---------------------------------------------------------------------------------FI 261
                 .................................................................................33 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.0022
                 HHHHHHHHHH-SGHHHHHHHHHHHHHHH.....CHHCCTTTCHSCHH....-BTTBEB-STTTSHHHHHHHHHCCCHT.-HHHHHHHHHHHHH CS
   LANC_like 113 syllllneetkieedllkqilkylvelg.....iksenqvswsplmy....epegesnlGlAHGlsGialallalykgtksekllelikkllk 196
                 ++ll + e    e+++l+++lk+ ++l      ++s + +  s+ ++    +p++++ l+l  G+s  + + l+ly+ t++ek+l++++++++
  EPA06605.1 294 NALLDVFEVE-PESKYLDLALKLGNYLVdhfwdSESSSFFMTSDNHEkliiRPKSNYDLSLPSGNSVSCSVMLRLYHLTHDEKFLKIATQIME 385
                 5555555555.6677777777777777777776333333333222221111355788888888888888888888888888888888887765 PP

>> Pec_lyase  Pectic acid lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1     0.003       7.8      50      87 ..      95     133 ..      85     144 .. 0.86
   2 ?    5.1   0.0    0.0048        12      45      71 ..     235     261 ..     200     268 .. 0.87
   3 ?   -2.6   0.0         1   2.7e+03      47      74 ..     295     322 ..     290     329 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.003
   Pec_lyase  50 evykatkdekykdavrkglefll.kaqYsnGgwpqfyPl 87 
                 e+y+ tkd  y + + k+l+f+l ++  +nGg+   y +
  EPA06605.1  95 EAYQITKDPFYLEVLNKTLDFVLrEMTAKNGGFYSAYDA 133
                 79*******************98458899***9888865 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0048
   Pec_lyase  45 llflaevykatkdekykdavrkglefl 71 
                 ++ +a+ y  t+d+ky da+++ + f+
  EPA06605.1 235 ITAFAKGYGVTGDTKYLDAAKNCVHFI 261
                 67899********************98 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1
   Pec_lyase  47 flaevykatkdekykdavrkglefllka 74 
                  l +v++ + ++ky d ++k  ++l++ 
  EPA06605.1 295 ALLDVFEVEPESKYLDLALKLGNYLVDH 322
                 57789999************99999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (490 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.70u 0.37s 00:00:01.06 Elapsed: 00:00:00.54
# Mc/sec: 2740.52
//
Query:       EPA06606.1  [L=151]
Description: hypothetical protein BG20_I1789 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.14   11.9   0.0       0.16   11.7   0.0    1.2  1  Pox_RNA_Pol_22  Poxvirus RNA polymerase 22 kDa subunit


Domain annotation for each model (and alignments):
>> Pox_RNA_Pol_22  Poxvirus RNA polymerase 22 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   9.2e-06      0.16      53     116 ..       3      72 ..       1     122 [. 0.77

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.2e-06
  Pox_RNA_Pol_22  53 kvdssktvfqvfnessvkyspleddyGe......piiitsylqkehnkfpisllyidvvasdlfpkfarl 116
                     k+d +   f++f+  ++     + dyGe         i + ++k+h+k+p  ll i +v+  lf +   +
      EPA06606.1   3 KLDLDDEYFRIFDSNKLIAGYFDPDYGEifpkanSTEIIAQMLKNHDKIPGGLLMIPLVKFGLFDTDLDI 72 
                     67888889999999999999999****8442222245889999*****************9999875554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.33s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 883.45
//
Query:       EPA06607.1  [L=534]
Description: CBS domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      7e-51  173.2  54.8    8.7e-51  172.9  54.8    1.1  1  Na_H_Exchanger  Sodium/hydrogen exchanger family
    1.1e-12   48.2   1.0    5.7e-06   26.7   0.1    2.7  2  CBS             CBS domain


Domain annotation for each model (and alignments):
>> Na_H_Exchanger  Sodium/hydrogen exchanger family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.9  54.8   9.7e-55   8.7e-51       3     375 ..      11     378 ..       6     384 .. 0.88

  Alignments for each domain:
  == domain 1  score: 172.9 bits;  conditional E-value: 9.7e-55
                     HHHHHHHHHHHHHHHTTSXHHHHHHHHHHHHTTTTTS.....HHHCHCCHHHHCHHCCHHHHCT.CGCCT.GCCTHHHHHHHHHHHHHHHHHHHH CS
  Na_H_Exchanger   3 llillallvgllarrlklpeivgliiaGlllGpsglgliepseedlevlselglilllFlaGle.ldlre.lrknlksilllallgvlitvvliG 95 
                     +li++a l+g l++r+ +p i+g ++aG+++Gp ++ l++p  + +e++  +g+++l Fl+Gle +dl+  +r +++ i++++++ +li++ + G
      EPA06607.1  11 VLIVAAKLFGELMHRIHQPTIIGNVLAGVIVGPALFALVQPI-DEIEIFTSIGVFFLFFLIGLEeIDLSGlFRVMRGRIFAGSIAAFLIPFTVAG 104
                     445556666669******************************.********************55****956667889***************77 PP

                     HHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC.CCCTSTCCCCCCHHHHHHHHHHHCCCCCHHHHHHTXXXXXTSSSTSXH.HHHHHHHHHH CS
  Na_H_Exchanger  96 lllylllilgiplleallfgailsatdpvvvlailkeegrvperlgtlllgesvlnDavavvllavllalakeeaggetsllll.lliflvvavg 189
                     l+     +l+++++ a+++g++++a++++v++++l+++g++++ +g  ++ +  + + +a++l++vl++++++ + ++++ ++l ++ +++++v+
      EPA06607.1 105 LFGL---LLDMDFVKAFAIGSVIAASSLGVTAKVLSDLGKLRSAIGLEIFTVTAIVEFIAIILTSVLIQVHSSVDPQVSDFFWLfAKMIVFFVVA 196
                     7666...49*************************************************************9866666666666514566666777 PP

                     HHHHHHHHHHHHHHHHHHSCTHHHHHHHHHHHHHHHHHHHHHTSXXXHHHHHHHHHHHHH...HHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHS CS
  Na_H_Exchanger 190 glllglvigwllrlitrftdddrelevllvlllallaallaellgvsgilgaflaGlvls...eyefsnklseklesfreglfnplfFvlvGlsl 281
                     gll  +v++ ++r+i++++ + +++++ +v+ ++ll+a++ae+ g++g++ga+l+G+++s   ++e+s+ +s++++ ++ g+f+p+fF+ +Gl++
      EPA06607.1 197 GLLSVFVLPRVFRVIRKHL-YAEQIYFSIVIGIILLVAYFAEISGIHGAIGALLLGIAVSrmnKVEYSE-ISKSINVIGHGIFIPIFFAGIGLHF 289
                     7777778888888888886.****************************************995566666.************************* PP

                     XHHHHHXXHHHHHHHHHHHHHHHTHHHHHHHHHTTTXSSXHHHHHHCCCCSS.BHHHHHHHHHHHHHHXHHHHTTSSTTTCSTSXHHHHHHHHH CS
  Na_H_Exchanger 282 dlkvlnnhlsvlilvllilvaillgrilavflllrllglslrealiigfgglqrgavalalaalgpalgllarelyallivvvlftvlvqGlsl 375
                      +++ln  l+++i+ ++ l +++ +++++ ++++r  + ++r a ++++g   +gav lal +++ +   l+ el++ll++ +l+ +++  + l
      EPA06607.1 290 SFSFLN--LDLWII-AGFLGIMIGVKFIGSYIAVR--IANMRPATTVAYGVMAKGAVDLALMLSLLQVAMLSDELFSLLVLGTLIIMIISSVEL 378
                     *****5..665555.555555558***********..56************************************9999999999999776655 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1     1e-07    0.0009       5      54 ..     415     463 ..     406     466 .. 0.79
   2 !   26.7   0.1   6.4e-10   5.7e-06       2      56 ..     474     529 ..     473     530 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1e-07
                 SBSSCEEEETTSBHHHHHHHHH.HHTSSEEEEEETTTBEEEEEEHHHHHHH CS
         CBS   5 mtrdvvtvppdttleealelmr.ekgvsrlPVVdedgklvGivtlrDllra 54 
                   +d++  + + t++e l++ +  k++ +l V+de++klvGi+++r + r+
  EPA06607.1 415 IVTDYLKTTQNVTIKEFLDKTElGKKI-CL-VMDENNKLVGIISKREINRF 463
                 456777888889999999888545668.99.***************99665 PP

  == domain 2  score: 26.7 bits;  conditional E-value: 6.4e-10
                 HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEE.ETTTBEEEEEEHHHHHHHHH CS
         CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVV.dedgklvGivtlrDllrall 56 
                 +d m ++++t++pd+ l  ++++m ++ ++ +PV+ ++ + +vGivt   ++++l+
  EPA06607.1 474 SDAMYTKFHTASPDEYLYSVIQKMNSHPFDIIPVIdPKTDSVVGIVTNQSIMNLLV 529
                 788*********************6666*999***766668******999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (534 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1213  (0.0676558); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.71u 0.35s 00:00:01.06 Elapsed: 00:00:00.53
# Mc/sec: 3039.47
//
Query:       EPA06608.1  [L=95]
Description: hypothetical protein BG20_I1787 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 596.91
//
Query:       EPA06609.1  [L=78]
Description: hypothetical protein BG20_I1794 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      0.001   19.4   0.5     0.0011   19.3   0.5    1.0  1  PP_kinase_N  Polyphosphate kinase N-terminal domain
  ------ inclusion threshold ------
      0.028   15.0   0.3      0.031   14.8   0.3    1.1  1  LPD25        Large polyvalent protein associated domain 25


Domain annotation for each model (and alignments):
>> PP_kinase_N  Polyphosphate kinase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.5   1.2e-07    0.0011      27      85 ..      10      72 ..       2      78 .] 0.73

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.2e-07
                 HHHHHHHHHHHHHHHHHHHHCCHHHHH....HTT-...-----------HHHHHHHHHHHHHH CS
  PP_kinase_N 27 leRlkFlaIfssNlDEFfmvRvaslkr...qleak.vekksedgltpeeqlkaiseeveelve 85
                  eR+k l I+ss  +EF +  + +lkr    +e+k +++ +++++++ + l++i+ ++ el e
   EPA06609.1 10 RERVKLLQIISSSKNEFKKLTLVQLKRlqeLVEKKdYSHDKKAQKSKVKLLNKINVRIYELEE 72
                 59****************999998888443444442223334477777889999888887765 PP

>> LPD25  Large polyvalent protein associated domain 25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.3   3.4e-06     0.031       9      64 ..      17      73 ..      10      78 .] 0.79

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.4e-06
       LPD25  9 liewsespefeegellsfaeanellekldekqykernepgy..lydktkFtitfdegg 64
                +i  s+++ef++ +l++++++ el+ek d   +++++++    l +k++++i+  e+g
  EPA06609.1 17 QIISSSKNEFKKLTLVQLKRLQELVEKKDY-SHDKKAQKSKvkLLNKINVRIYELEEG 73
                57789************************9.445555555444499999999855555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1861  (0.103798); expected 358.6 (0.02)
Passed bias filter:                      598  (0.0333538); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.32s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 492.67
//
Query:       EPA06610.1  [L=64]
Description: hypothetical protein BG20_I1790 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 431.39
//
Query:       EPA06611.1  [L=163]
Description: hypothetical protein BG20_I1788 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00015   21.1   0.8    0.00018   20.8   0.8    1.1  1  Phage_HK97_TLTM  Tail length tape measure protein
     0.0011   19.2   0.7      0.002   18.3   0.7    1.4  1  WXG100           Proteins of 100 residues with WXG
  ------ inclusion threshold ------
      0.019   15.1   0.1      0.035   14.2   0.1    1.4  1  MAS20            MAS20 protein import receptor
      0.027   13.2   2.9      0.034   12.8   2.9    1.0  1  WEMBL            Weak chloroplast movement under blue light
       0.04   13.5   0.6      0.049   13.2   0.6    1.2  1  SLATT_6          SMODS and SLOG-associating 2TM effector doma
      0.091   12.8   0.9      0.091   12.8   0.9    1.8  2  ETRAMP           Malarial early transcribed membrane protein 
       0.48   11.4   4.1       0.92   10.4   3.8    1.8  2  PRKG1_interact   cGMP-dependent protein kinase interacting do


Domain annotation for each model (and alignments):
>> Phage_HK97_TLTM  Tail length tape measure protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.8     7e-08   0.00018      43     150 ..      29     145 ..      15     162 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 7e-08
  Phage_HK97_TLTM  43 qkqAresAreyAkeieevkeklkklsleevadekdklkeslkeqnklvkeaeqkveelkkeldkyq.........vsingylvnkldskeeaik 127
                       +q r++ +++ +e+ ++++++k+l++ e   + ++ ke    q+ l k  ++ +e++++ + ky          +s+ ++ +      +++  
       EPA06611.1  29 YDQTRQKGLKFGNELSQIQDEVKQLQV-EFDSNVKQWKEGDMSQQELEKFSKEHIEKMQDVILKYDgltppesfaPSVKLFKISTQAQLDSDKE 121
                      4799*********************97.678888888887777799999*****************9999999999999998876655555555 PP

  Phage_HK97_TLTM 128 .laeatdklsesqsaleavtkksk 150
                       +  ++++    + + + ++++s 
       EPA06611.1 122 fIEWIKTNDEAHNIRSDSLLQESF 145
                      454555555555555555555444 PP

>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.7   7.7e-07     0.002       2      69 ..      25      94 ..      24      96 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 7.7e-07
                HCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCGCGCT.HHHCHHHHHHHH.HHHHHHHHHHHHHHH CS
      WXG100  2 ikvdpeelrqaaarfqkqaeeledelqrlkaevdalqsgWs.Gaaadafqaefe.ewkqaaqklvdaLee 69
                +++++++ rq+  +f+++ ++++de+++l+ e d+   +W+ G+ +++  + f  e  +++q+++ ++++
  EPA06611.1 25 YNYSYDQTRQKGLKFGNELSQIQDEVKQLQVEFDSNVKQWKeGDMSQQELEKFSkEHIEKMQDVILKYDG 94
                6899*************************************98888887777777999999999988876 PP

>> MAS20  MAS20 protein import receptor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   1.4e-05     0.035       3      76 ..      17      90 ..      14      92 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.4e-05
       MAS20  3 vaaaaflgYcvYFDrkRrsdpefkkklrerrkkqakaakeeeeaekaekkkkealeeakeelptda.eevekfFl 76
                ++ ++++gY   +D+ R++  +f ++l + + + + + + e  ++ +++k+ ++ +++ e++ +++ e+++ + l
  EPA06611.1 17 TILLGIVGYNYSYDQTRQKGLKFGNELSQIQDEVK-QLQVEFDSNVKQWKEGDMSQQELEKFSKEHiEKMQDVIL 90
                556899****99***************99999888.445677777777777668888888877555499998766 PP

>> WEMBL  Weak chloroplast movement under blue light
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   2.9   1.3e-05     0.034     218     339 ..      33     154 ..      29     160 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.3e-05
       WEMBL 218 eqdklnwekeLkqaeeelqrLneellsakdlkskletasallldLkaeLaayvesklkeeaeeeeeekksetsikealasarkELeevkanie..kakd 314
                 +q  l++ +eL q+++e+++L+ e  s+    ++ +++++ l +  +e    +++ + +     +  ++   s+k    s++  L+  k+ ie  k++d
  EPA06611.1  33 RQKGLKFGNELSQIQDEVKQLQVEFDSNVKQWKEGDMSQQELEKFSKEHIEKMQDVILKYDGL-TPPESFAPSVKLFKISTQAQLDSDKEFIEwiKTND 130
                 57778999*********************************************9877766543.44467777777777888888888888888444445 PP

       WEMBL 315 evklLkvaaas.LrseLekekaeLas 339
                 e++ ++  + s L+   e e ++La+
  EPA06611.1 131 EAHNIR--SDSlLQESFEYEMSALAE 154
                 555554..444156667888887776 PP

>> SLATT_6  SMODS and SLOG-associating 2TM effector domain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.6   1.9e-05     0.049      62     130 ..      15      84 ..       3     128 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.9e-05
     SLATT_6  62 alliiigiialyisayekdkekYekagkeltklfneLkelysevks..seeedlskleaelkeieaefkev 130
                 a+ i++gi++     y+++++k  k g+el ++ +e+k+l  e +s  ++ ++ + +++el++  +e+ e 
  EPA06611.1  15 AITILLGIVGYN-YSYDQTRQKGLKFGNELSQIQDEVKQLQVEFDSnvKQWKEGDMSQQELEKFSKEHIEK 84 
                 355778999955.5689999999*****************9988774334444555555666666665544 PP

>> ETRAMP  Malarial early transcribed membrane protein (ETRAMP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.9   3.6e-05     0.091      49      77 ..       2      27 ..       1      35 [. 0.76
   2 ?   -2.0   0.1       1.5   3.9e+03      33      47 ..      68      82 ..      41      90 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.6e-05
      ETRAMP 49 kkkkkKliiistiatalallvasalGlgi 77
                kk+kk++iii++ia++++l    ++G+ +
  EPA06611.1  2 KKSKKQNIIIASIAITILLG---IVGYNY 27
                6699999*****99999554...577765 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.5
      ETRAMP 33 ekakkaikkiddkie 47
                + ++++++k+ ++  
  EPA06611.1 68 DMSQQELEKFSKEHI 82
                555666666666544 PP

>> PRKG1_interact  cGMP-dependent protein kinase interacting domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   3.8   0.00036      0.92       3      63 ..      26      86 ..      24     143 .. 0.83
   2 ?   -1.3   0.0       1.6   4.1e+03      71      80 ..     127     136 ..     104     158 .. 0.46

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00036
  PRKG1_interact  3 kkLYeeekeenerLkreLeelekelselkseleklkqqrqesvskrssllelekrerrsle 63
                       Y + +++  +  +eL++++ e+++l+ e+++  +q +e   ++++l +++k++ ++++
      EPA06611.1 26 NYSYDQTRQKGLKFGNELSQIQDEVKQLQVEFDSNVKQWKEGDMSQQELEKFSKEHIEKMQ 86
                    556888889988999*******************887765555555555555555555544 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.6
  PRKG1_interact  71 eelkeleeLr 80 
                     + + e +++r
      EPA06611.1 127 KTNDEAHNIR 136
                     2222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1857  (0.103575); expected 358.6 (0.02)
Passed bias filter:                      950  (0.0529868); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 1258.75
//
Query:       EPA06612.1  [L=36]
Description: hypothetical protein BG20_I1795, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00086   19.5   0.9    0.00086   19.5   0.9    1.0  1  EamA      EamA-like transporter family


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.9   4.8e-08   0.00086       2      34 ..       1      33 [.       1      36 [] 0.93

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 4.8e-08
        EamA  2 lgillallaalfwaiyfvlskillrkvspltlt 34
                +g+++a+++a+++++  vl+k l+++v+p+ l+
  EPA06612.1  1 MGYVFAIVSAITFGSVSVLAKPLVSTVDPILLA 33
                599**************************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (36 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      195  (0.0108762); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.30u 0.26s 00:00:00.56 Elapsed: 00:00:00.39
# Mc/sec: 276.49
//
Query:       EPA06613.1  [L=106]
Description: hypothetical protein BG20_I1792 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      0.003   17.6   0.9     0.0039   17.2   0.9    1.2  1  Arcadin_1  Arcadin 1


Domain annotation for each model (and alignments):
>> Arcadin_1  Arcadin 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.9   2.2e-07    0.0039      25     102 ..      25     104 ..       8     105 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.2e-07
                 EEEEEE---------...---------------------------.--EEEEEEEEEE-HHHHHHH-.---TT-EEEEEEE CS
   Arcadin_1  25 elvEerelpgpvlva...sdeedaeiaRevapivqqivrslpllslnkvkvpritLvlteeEleklevklevgdvyeieis 102
                 e v    +++ +++    s   da+ + +v+p+++ i++  p +++n+++  ++ + + +  +e+++ +++vg v+ ++++
  EPA06613.1  25 ENVSTEPISQKQMIIdnvSKTLDADTKEQVMPLLEAILQAQPTININSYQQAQMSITMPRSRYESMG-RPQVGSVMAVNLK 104
                 44444555555544311133457888999**************************************.*********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 812.12
//
Query:       EPA06614.1  [L=61]
Description: hypothetical protein BG20_I1785, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-08   33.6   0.0      5e-08   33.6   0.0    1.1  1  Usp       Universal stress protein family
  ------ inclusion threshold ------
      0.039   14.2   0.0      0.044   14.1   0.0    1.1  1  DUF1400   Alpha/beta hydrolase of unknown function (DUF1400)


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.0   5.5e-12     5e-08       3      46 ..       5      48 ..       3      59 .. 0.90

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 5.5e-12
                SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCC CS
         Usp  3 krIlVavDgseeskkAlewAlelakargaelillhvidprasga 46
                ++IlV++Dgs+ s +Al++Al la  +++e+++l+vi++  ++ 
  EPA06614.1  5 HKILVPIDGSKKSFEALDRALTLASFTQGEVTCLNVIPHVIKEG 48
                79***********************************9977665 PP

>> DUF1400  Alpha/beta hydrolase of unknown function (DUF1400)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   4.9e-06     0.044      81     116 ..       5      41 ..       1      44 [. 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.9e-06
     DUF1400  81 geviq.tesdqngkealrsAlilaaadpeglsllnfL 116
                  +++   + +++++eal  Al+la+  +++++ ln++
  EPA06614.1   5 HKILVpIDGSKKSFEALDRALTLASFTQGEVTCLNVI 41 
                 55544044566999*********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       211  (0.0117686); expected 358.6 (0.02)
Passed bias filter:                      202  (0.0112667); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.31u 0.26s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 482.27
//
Query:       EPA06615.1  [L=182]
Description: hypothetical protein BG20_I1793 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-77  258.1   0.1    3.6e-77  257.9   0.1    1.0  1  Thioredox_DsbH  Protein of unknown function, DUF255
    2.5e-11   43.6   0.3    4.5e-11   42.8   0.1    1.6  2  Thioredoxin_7   Thioredoxin-like
     0.0064   16.9   0.2      0.012   16.1   0.0    1.5  2  Thioredoxin_2   Thioredoxin-like domain
  ------ inclusion threshold ------
       0.11   10.9   0.0       0.18   10.3   0.0    1.2  1  DUF2193         Uncharacterized protein conserved in archaea 


Domain annotation for each model (and alignments):
>> Thioredox_DsbH  Protein of unknown function, DUF255
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  257.9   0.1   8.1e-81   3.6e-77       1     162 [.       3     164 ..       3     165 .. 0.99

  Alignments for each domain:
  == domain 1  score: 257.9 bits;  conditional E-value: 8.1e-81
  Thioredox_DsbH   1 knrlaeekspYllqhaknpvdWypwgeealekakeedkpillsiGysachWChvmekesfedeevaallnesfvsvkvDreerPdldkiymeavq 95 
                     +nrl++e+spYllqha+npvdWy+w+ee+l+kak+e+kpi+ls+GysachWChvm++esfe+e+va+++ne+fv++kvDreerPdld+iy++++q
      EPA06615.1   3 ENRLKNETSPYLLQHAHNPVDWYAWNEESLKKAKDENKPIFLSVGYSACHWCHVMAHESFENEDVAKFMNENFVNIKVDREERPDLDDIYQKVCQ 97 
                     59********************************************************************************************* PP

  Thioredox_DsbH  96 altgsggWPlnvfltpdlkpffggtYfpkeeregrpgflevlekiaelweeereeleeeaeelleal 162
                     + tg+ggWPl+vfltp +kpf+ gtYfp  +++grpgf ++++++a++w+e+ +++e++a+++l al
      EPA06615.1  98 IATGQGGWPLSVFLTPYQKPFYVGTYFPVLDSYGRPGFGSICRQLAQAWKEKPKDIEKSADNFLVAL 164
                     *************************************************************998877 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.8   0.1     1e-14   4.5e-11       1      83 []      23     113 ..      23     113 .. 0.84
   2 ?   -2.2   0.0       1.1   4.9e+03      40      57 ..     148     163 ..     139     180 .. 0.52

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 1e-14
                    ---SSHHHHHHHHHHHT--EEEEE--TT-HHHHHHHHHHHH-HHHHH.HHHT-EEEEESS--S-GGG..........-TT---SSEEEEE-T CS
  Thioredoxin_7   1 ewlsdldealakaaergkpvlvffgaswcftCqalerdflsdeevkaalaekfvllrvdvterdani.........leldeqgvPvvafldp 83 
                    +w+++ +e l ka+ ++kp+++ +g s c+ C++++ +  ++e+v++ ++e+fv  +vd +er + +         +++ + g P  +fl+p
     EPA06615.1  23 DWYAWNEESLKKAKDENKPIFLSVGYSACHWCHVMAHESFENEDVAKFMNENFVNIKVDREERPD-LddiyqkvcqIATGQGGWPLSVFLTP 113
                    7**********************************9999999999999************99987.33445555433333355888888877 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.1
                    HH-HHHHH.HHHT-EEEE CS
  Thioredoxin_7  40 lsdeevkaalaekfvllr 57 
                    ++++++ +  a++f l+ 
     EPA06615.1 148 EKPKDIEK-SADNF-LVA 163
                    44555555.44444.233 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   2.6e-06     0.012       1      60 [.      35      85 ..      35     126 .. 0.80
   2 ?   -2.6   0.0       1.7   7.7e+03      24      33 ..     143     153 ..     137     175 .. 0.51

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.6e-06
  Thioredoxin_2  1 akgngkpvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekk 60
                   ak ++kp+++ +  + C  C+ +  e +e++dv ++     ++++    +v+i+ ++e+ 
     EPA06615.1 35 AKDENKPIFLSVGYSACHWCHVMAHESFENEDVAKF-----MNEN----FVNIKVDREER 85
                   6789********************************.....7777....55555555544 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.7
  Thioredoxin_2  24 kkelkel.ddv 33 
                     +  ke  +d+
     EPA06615.1 143 AQAWKEKpKDI 153
                    33333332222 PP

>> DUF2193  Uncharacterized protein conserved in archaea (DUF2193)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   3.9e-05      0.18     307     363 ..      30      86 ..      26      96 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 3.9e-05
     DUF2193 307 kaleklkseydvlslatgasaaavekileldgfnaemvvdlltkrfhnyvqlyptrg 363
                 ++l+k k+e + + l+ g sa+   +++  ++f+ e v +++ + f n     ++r 
  EPA06615.1  30 ESLKKAKDENKPIFLSVGYSACHWCHVMAHESFENEDVAKFMNENFVNIKVDREERP 86 
                 6788999************************************99988766666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       687  (0.0383178); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1192.10
//
Query:       EPA06616.1  [L=166]
Description: hypothetical protein BG20_I2678, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.3e-45  153.5   0.1    8.3e-45  153.3   0.1    1.0  1  TruD      tRNA pseudouridine synthase D (TruD)


Domain annotation for each model (and alignments):
>> TruD  tRNA pseudouridine synthase D (TruD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.3   0.1   4.6e-49   8.3e-45     150     297 ..       6     152 ..       1     159 [. 0.94

  Alignments for each domain:
  == domain 1  score: 153.3 bits;  conditional E-value: 4.6e-49
        TruD 150 ileeleekggvPNyfGvQRFGsrrpvthlvGkaivkgdleeAvelyvgkpfeeesedtreareavaetgdleealeelpkslryErallkrLaekpkdy 248
                  l+e  + + + N++G+QRFGs+rpvthl+Gka++++d+++Avel+v+ ++  +s++ +e+re++ ++ ++++ l+++p ++++Er +l+++++ ++d 
  EPA06616.1   6 RLSEFVDYQKILNFYGYQRFGSKRPVTHLIGKALLRRDFKKAVELIVSFTSRYDSKENTEIREKLVDKSNYKKYLNQVPPQMDIERIVLQEMID-HDDA 103
                 444555555699**********************************************************************************.9*** PP

        TruD 249 kkAlealpknLqrlFvhAyqSylFNrvlseRlerglpldepveGDvvif 297
                 +kA++a+p nL+r++v+AyqSylFN+ ls+ + +g +l  + +GDv+++
  EPA06616.1 104 QKAIHAVPLNLRRFYVQAYQSYLFNQTLSAAFTDGEDLFAAQTGDVCYD 152
                 **********************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       853  (0.0475766); expected 358.6 (0.02)
Passed bias filter:                      600  (0.0334653); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1023.94
//
Query:       EPA06617.1  [L=42]
Description: hypothetical protein BG20_I2166 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.014   15.7   2.3      0.017   15.5   2.3    1.2  1  DnaJ_CXXCXGXG  DnaJ central domain
      0.014   15.1   0.4      0.014   15.1   0.4    1.8  2  PADR1          PADR1 (NUC008) domain
       0.66   10.2   5.0        3.9    7.7   5.0    1.9  1  DUF5351        Family of unknown function (DUF5351)


Domain annotation for each model (and alignments):
>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   2.3   2.9e-06     0.017      16      50 ..       2      28 ..       1      39 [. 0.46

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.9e-06
  DnaJ_CXXCXGXG 16 tCktCkGsGvvreeqktlgpfvqqsqstCpeCeGt 50
                   tC +C+G+G+ ++e   +g       ++C++C+ +
     EPA06617.1  2 TCFRCDGKGKFKNE---FGI-----MEKCESCQKK 28
                   35555555532211...222.....1244444444 PP

>> PADR1  PADR1 (NUC008) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.2     0.072   4.3e+02      16      27 ..       3      13 ..       1      15 [. 0.63
   2 ?   15.1   0.4   2.4e-06     0.014       9      28 ..      15      34 ..      13      37 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.072
       PADR1 16 CpeCkegqlvfd 27
                C  C  g+ +f+
  EPA06617.1  3 CFRCD-GKGKFK 13
                77777.666655 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 2.4e-06
       PADR1  9 lfGalekCpeCkegqlvfds 28
                 fG +ekC++C++ ++ f+s
  EPA06617.1 15 EFGIMEKCESCQKKEMTFES 34
                59**********99999876 PP

>> DUF5351  Family of unknown function (DUF5351)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   5.0   0.00066       3.9       1      24 [.       3      26 ..       3      30 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00066
     DUF5351  1 CpYCeGkGYfqLlLGGSETCesCe 24
                C  C GkG f+   G  E CesC+
  EPA06617.1  3 CFRCDGKGKFKNEFGIMEKCESCQ 26
                666********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       760  (0.0423894); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.29s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 286.34
//
Query:       EPA06618.1  [L=40]
Description: hypothetical protein BG20_I2165 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       751  (0.0418874); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 298.91
//
Query:       EPA06619.1  [L=66]
Description: hypothetical protein BG20_I2164 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 481.64
//
Query:       EPA06620.1  [L=517]
Description: hypothetical protein BG20_I2163 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.1e-20   71.9   0.1    2.4e-19   70.2   0.0    1.9  2  Helicase_C_2  Helicase C-terminal domain
    7.2e-06   25.7   0.5    2.1e-05   24.2   0.2    1.9  2  DEAD_2        DEAD_2


Domain annotation for each model (and alignments):
>> Helicase_C_2  Helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1      0.44   3.9e+03      34      51 ..     146     162 ..     107     228 .. 0.60
   2 !   70.2   0.0   2.6e-23   2.4e-19      10     157 ..     361     495 ..     352     508 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.44
  Helicase_C_2  34 eskkieifveekeesrek 51 
                    ++k++if+e  ++ +++
    EPA06620.1 146 LNRKVSIFDE-AHKIEDQ 162
                   4444555554.3332222 PP

  == domain 2  score: 70.2 bits;  conditional E-value: 2.6e-23
  Helicase_C_2  10 ggvlvffpSyklleevverlkeeleskkieifvee..keesrekvleeykekkkkgaillavcrGklsEGidfsddllraviivglPfpnpkdpeve 104
                   ++ l++++S    +++ ++l+ +  +++i+i ++   + +++++++ e+ +    + +ll++    l+EG+d++ddl r  ii ++P+pn+k+ +++
    EPA06620.1 361 ERGLILTSSIPRCQKILRYLSPKN-TRRIRICHSYnkDGKTQDEIILEHAS--DPTGVLLSSS---LWEGVDLKDDLSRFQIIAKVPYPNYKEKRTR 451
                   67799999***********99986.46787777555555566667777776..6888999885...9************************999998 PP

  Helicase_C_2 105 akreyldekgkknsgkewylpealravnQaiGRliRhkdDygaivllDeRfak 157
                   ak++         ++  wy+ ++l+++ Q++GR iR++dD++  ++lD+  ++
    EPA06620.1 452 AKMD---------KFPLWYTSQTLTKLLQGFGRSIRSEDDWARTYVLDTAANN 495
                   8864.........6889*******************************97766 PP

>> DEAD_2  DEAD_2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.2   2.3e-09   2.1e-05      59     171 ..      48     171 ..      37     176 .. 0.72
   2 ?   -2.9   0.0      0.51   4.6e+03      26      47 ..     237     258 ..     205     265 .. 0.59

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 2.3e-09
                 HHHHHCCHHCCH.......TTTTTT-SCCCCHHHH...HHHHHHC---CHHHHHHHHHCT--HHHHHHHHHCCTSEEEEEHHHHTS..CCCHHHHHT.. CS
      DEAD_2  59 Ckelkkkkaeek.......eekCsffenleelkkl...kkllleevvdiedlvelgeklklCPYylsrelledadiiilpYqyLld..ekireslkgis 145
                 C ++ ++++  +         +C+  + +e+++k      ++ +   +i ++ e  ++ + C Yyl +  +   +  +  Y+ +++  +  r+ ++   
  EPA06620.1  48 CLKMMESEKVDNprramrwGLTCDKGQCQERINKNgkeIIEVCKFKPTIKQVDEHTQEANSCHYYLQKYDALVSKHSLWNYHAFFQimKFNRKLFE-DY 145
                 5555555544445555666444555555555555421123344556799999********************************983233455555.78 PP

                 GCGCEEEECTCCCHHHHHHHCC-EEE CS
      DEAD_2 146 lknsivilDEAhNiedvceeaasvei 171
                 l+ ++ i+DEAh ied + +   ++i
  EPA06620.1 146 LNRKVSIFDEAHKIEDQIMQFIGFDI 171
                 99*****************9999887 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.51
                 HS---EEEE--CCCC-SCHHCC CS
      DEAD_2  26 kekvkvviLgSRknlCineevk 47 
                  ++ k+ iL+ ++n+ +n+ v+
  EPA06620.1 237 AAQAKIDILTNKNNFVVNDPVQ 258
                 4455666666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (517 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       849  (0.0473534); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.39
# Mc/sec: 3927.19
//
Query:       EPA06621.1  [L=31]
Description: hypothetical protein BG20_I2161, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (31 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       160  (0.00892409); expected 358.6 (0.02)
Passed bias filter:                      103  (0.00574488); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 230.47
//
Query:       EPA06622.1  [L=105]
Description: hypothetical protein BG20_I2162 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.9e-06   26.1   0.2      1e-05   25.7   0.2    1.3  1  GIY-YIG         GIY-YIG catalytic domain
  ------ inclusion threshold ------
      0.027   13.9   0.0      0.031   13.8   0.0    1.1  1  PP_kinase_C     Polyphosphate kinase C-terminal domain 2
      0.054   12.8   0.1      0.061   12.6   0.1    1.0  1  Endonuc-HincII  Restriction endonuclease HincII


Domain annotation for each model (and alignments):
>> GIY-YIG  GIY-YIG catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.2   1.7e-09     1e-05       3      56 ..      23      87 ..      21     105 .] 0.66

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.7e-09
                EEEEEEETTT--EEEEEESSHHHHHHHH....HHHHHHT--S-H.........S.STEEEEEEEE-- CS
     GIY-YIG  3 gvYiirskenkliYvGstknlekRlkqH....nagkkakytrkk.........gkkpfeliileifp 56
                gvY+++++++++iY+G++ nlek + ++    ++  ++ +++k+         + k+ ++  +e+f+
  EPA06622.1 23 GVYVLYNRNKDVIYIGESDNLEKTFTKYvdtgFE--GNECKQKTssyqreftdKPKERQMQLIEEFK 87
                9**********************99999664422..2222222233555556644444444444444 PP

>> PP_kinase_C  Polyphosphate kinase C-terminal domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   5.2e-06     0.031      93     160 ..      24      88 ..       7      97 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.2e-06
  PP_kinase_C  93 iyifenggeeevyisSaDlmtRnldrRvevlvpvedeklkkelkeilelqlkDnvkareldedgeykk 160
                  +y+ +n++++ +yi+ +D +++ +++ v++ ++   +++k++  + ++  ++D+ k r+++  +e+kk
   EPA06622.1  24 VYVLYNRNKDVIYIGESDNLEKTFTKYVDTGFEG--NECKQKT-SSYQREFTDKPKERQMQLIEEFKK 88 
                  89****************************9964..5565554.567889999999999998777766 PP

>> Endonuc-HincII  Restriction endonuclease HincII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1     1e-05     0.061     169     242 ..      16      89 ..       7      93 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1e-05
  Endonuc-HincII 169 klvcvdthfaelfksnpeelyinwaaamqiqfhvsdldqlfegnk.eewakrylkhfvtqakkraedmiekfvkp 242
                     k+v     +  l++ n + +yi  +  ++  f  + +d +fegn+ ++ + +y + f  + k+r  ++ie+f k 
      EPA06622.1  16 KFVKAIPGVYVLYNRNKDVIYIGESDNLEKTFT-KYVDTGFEGNEcKQKTSSYQREFTDKPKERQMQLIEEFKKE 89 
                     555555556678999999999999999999885.789******97578899*********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 670.19
//
Query:       EPA06623.1  [L=163]
Description: hypothetical protein BG20_I1600, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-09   38.5   0.0    1.6e-09   38.3   0.0    1.1  1  Tubulin   Tubulin/FtsZ family, GTPase domain
  ------ inclusion threshold ------
      0.091   12.6   0.0       0.15   11.8   0.0    1.3  1  Whirly    Whirly transcription factor


Domain annotation for each model (and alignments):
>> Tubulin  Tubulin/FtsZ family, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3   0.0   1.7e-13   1.6e-09       2     131 ..      12     162 ..      11     163 .] 0.79

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 1.7e-13
                 EEEEEEHHHHHHHHHHHHH...HHHCH....................HHHT..............TTEEEEE....EEESBHHHHHTS-GS........ CS
     Tubulin   2 iivigvGqcGnqignelwellakehgiqsdg................dslesfFse.........sgkveyiprsvaidtdpqvlneikags.elfn.. 72 
                 +++i +G cG+ +g e ++ l+ + g+++ +                +       +          ++  +ipr++++d+dp++ n i ++  +lf   
  EPA06623.1  12 VLMICFGHCGIGLGAESYRRLLLDVGADPLKptlnakdesrvlkrygS-------TilrfapsygGNDIPLIPRALLVDLDPRAANLILQSYpDLFAlr 103
                 6899*******************9999755579999877655555542.......15555555665559999*******************99777521 PP

                 .EEEE--CCCCTTC--TT-HHHHHHHHHHTHHHHHHHHTT-SE...SEEEEEEETTSSHHH CS
     Tubulin  73 pnklllgkegagnngaggypevgkeaaeeileeirkevekcds..lqgffitaslgGGTGS 131
                  + ++ g  ga+ n+a g+    +e+    +  i+k+++      ++g ++   +gGGTGS
  EPA06623.1 104 DQHVIHGAGGAARNWAEGKTRFLEEMKT--KVDIKKQLSAISPepVRGYVVPFAMGGGTGS 162
                 5667778888***********9776655..5567788776654459**************9 PP

>> Whirly  Whirly transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.7e-05      0.15      11      43 ..      39      70 ..      35      73 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.7e-05
                EEE--EEEEEGGGTEEEEE--EEEEEEEEEEET CS
      Whirly 11 elvkptfeklesgklkvkreGvvlLefapavge 43
                +++kpt++++++ ++ +kr G+ +L fap+ g 
  EPA06623.1 39 DPLKPTLNAKDESRV-LKRYGSTILRFAPSYGG 70
                689*********999.**************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 995.37
//
Query:       EPA06624.1  [L=95]
Description: hypothetical protein BG20_I1594 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-08   32.9   3.3    5.7e-08   32.7   3.3    1.1  1  MtN3_slv         Sugar efflux transporter for intercellular e
    0.00012   21.8   4.1    0.00012   21.8   4.1    1.5  2  PQ-loop          PQ loop repeat
     0.0084   16.0   3.1       0.88    9.5   0.9    2.0  2  DUF4389          Domain of unknown function (DUF4389)
  ------ inclusion threshold ------
      0.012   15.8  13.9       0.15   12.3  13.9    2.0  1  DUF3784          Domain of unknown function (DUF3784)
      0.075   13.1   2.9        0.1   12.7   2.9    1.3  1  LAB_N            Lipid A Biosynthesis N-terminal domain
       0.56   10.0   9.4          1    9.2   9.4    1.6  1  Imp-YgjV         Bacterial inner membrane protein


Domain annotation for each model (and alignments):
>> MtN3_slv  Sugar efflux transporter for intercellular exchange
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   3.3   1.9e-11   5.7e-08       4      79 ..       9      84 ..       6      92 .. 0.83

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 1.9e-11
    MtN3_slv  4 gllcvvftvavFlsPlsilrkiikkksveelsfllflagllsallWllYGllkkdaliiivNlvgvlleliylllf 79
                 +l++   v+  +  + ++ k +k+ks +++s  l+l+   +++lWl+YG+ ++d +ii  N+  ++l++i l++ 
  EPA06624.1  9 TILGIAAGVLILSGWVDQIIKGYKTKSLKDVSKYLMLFISGGSILWLIYGIIVSDVFIIGTNIAAIVLMMIVLFMK 84
                55555566666566677888889*********************************************99988765 PP

>> PQ-loop  PQ loop repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   4.1     4e-08   0.00012       2      58 ..       8      64 ..       7      67 .. 0.92
   2 ?   -3.0   0.1       2.2   6.5e+03       9      15 ..      73      79 ..      68      83 .. 0.50

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 4e-08
     PQ-loop  2 seilgyislvlwlvsyiPQiikNykrkSteGlSilflllwllGdilsllylilngfp 58
                 +ilg+++ vl l   + Qiik yk+kS + +S + +l+   G+il+l+y i+ ++ 
  EPA06624.1  8 LTILGIAAGVLILSGWVDQIIKGYKTKSLKDVSKYLMLFISGGSILWLIYGIIVSDV 64
                579999999999999999*********************************998765 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.2
     PQ-loop  9 slvlwlv 15
                ++vl ++
  EPA06624.1 73 AIVLMMI 79
                3344333 PP

>> DUF4389  Domain of unknown function (DUF4389)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.1     0.002         6      17      57 ..       7      47 ..       5      49 .. 0.90
   2 !    9.5   0.9    0.0003      0.88       8      44 ..      52      88 ..      51      93 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.002
     DUF4389 17 vlslaslvlwvvvvvqflivLvtgrpnepLrdfgksllrYi 57
                +l +++++++v+++  ++  ++ g + ++L d++k l  +i
  EPA06624.1  7 LLTILGIAAGVLILSGWVDQIIKGYKTKSLKDVSKYLMLFI 47
                67899***************************999887665 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0003
     DUF4389  8 lllmllfaivlslaslvlwvvvvvqflivLvtgrpne 44
                +l+++  +iv  +  +++ ++++v ++ivL+++r+ e
  EPA06624.1 52 ILWLIYGIIVSDVFIIGTNIAAIVLMMIVLFMKRRYE 88
                57888889999999******************99865 PP

>> DUF3784  Domain of unknown function (DUF3784)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3  13.9     5e-05      0.15       3      90 ..       8      84 ..       6      88 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5e-05
     DUF3784  3 lallflilGilflkgkganLiaGYntmskeekekydekklsrfmgivlllig...ilflllgllsaiesealliialiviiiiviylivya 90
                l +l +++G+l+l+g  ++ i+GY+t           k l   + +++l+i+   il+l+ g++    s++++i++ i+ i+++++++++ 
  EPA06624.1  8 LTILGIAAGVLILSGWVDQIIKGYKT-----------KSLKDVSKYLMLFISggsILWLIYGII---VSDVFIIGTNIAAIVLMMIVLFMK 84
                67788999****************97...........888899999999999788888888888...999999999888887777776654 PP

>> LAB_N  Lipid A Biosynthesis N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   2.9   3.4e-05       0.1       1      65 [.      11      76 ..      11      82 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.4e-05
       LAB_N  1 lGflgqllFtlRfvvQwiasekkkksvlpvlFWvlSl.lGslllliYailrkDpvlilgqslglvi 65
                lG+++ +l  + +v Q i   k+k+    + + +l +  Gs+l liY+i+ +D+ +i  +++ +v 
  EPA06624.1 11 LGIAAGVLILSGWVDQIIKGYKTKSLKDVSKYLMLFIsGGSILWLIYGIIVSDVFIIGTNIAAIVL 76
                68888888888888898888888876655555555441689999*********9888877776654 PP

>> Imp-YgjV  Bacterial inner membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   9.4   0.00034         1     115     153 ..      44      82 ..       5      88 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00034
    Imp-YgjV 115 RllflvssllWlvynilvgsigglllevlflisnlitiy 153
                  l++  +s+lWl+y i+v  ++ + +++  ++ ++i ++
  EPA06624.1  44 MLFISGGSILWLIYGIIVSDVFIIGTNIAAIVLMMIVLF 82 
                 4567789*************************9999775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1074  (0.059903); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 689.62
//
Query:       EPA06625.1  [L=199]
Description: cytidine and deoxycytidylate deaminase zinc-binding region [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-26   91.3   1.3    3.9e-26   90.9   1.3    1.2  1  dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-
    3.1e-14   52.9   0.2    4.2e-14   52.5   0.2    1.1  1  MafB19-deam      MafB19-like deaminase


Domain annotation for each model (and alignments):
>> dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.9   1.3   4.4e-30   3.9e-26       2     100 ..      33     158 ..      32     159 .. 0.98

  Alignments for each domain:
  == domain 1  score: 90.9 bits;  conditional E-value: 4.4e-30
                      HHHHHHHHHHHHHHHHHHTTTSCSEEEEEEETTEEEEEEESBHHCCTG...........................TTB-HHHHHHHHHHHHT.S CS
  dCMP_cyt_deam_1   2 ekdekllelalkaakeaqkcsnfkVGavivkngeiistgyngepaggs...........................ktiHAEvnAilkaakng.g 67 
                      ++de+++ +a +a+ ++ +c+  +VGaviv+++++++tgyng+p+g +                            ++HAE nAi+++a  g +
       EPA06625.1  33 NWDEYFMLQAELAKLRS-NCMTRQVGAVIVRKNRQLATGYNGTPPGIKncfeggcrrcqlrmegkiesgasldrcLCNHAEANAIMHCAILGiE 125
                      79***************.*************99********************************************************99999 PP

                      SCETTEEEEEEE--BHHHHHHHHHHT-SEEEEE CS
  dCMP_cyt_deam_1  68 sklegatlyvtlePCsmCakaiiqsgikkvvvg 100
                        + ga+ly+t+ PC +C+k+ i++gikk+v++
       EPA06625.1 126 AGIAGAILYTTFVPCLECTKMAITIGIKKFVCL 158
                      9*****************************985 PP

>> MafB19-deam  MafB19-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.5   0.2   4.7e-18   4.2e-14       2     112 ..      33     179 ..      32     197 .. 0.90

  Alignments for each domain:
  == domain 1  score: 52.5 bits;  conditional E-value: 4.7e-18
  MafB19-deam   2 dkekafrkalaevekatkikedkigavivkdkkviargsn...........................ekelnakataHaEiaalqqAakklkskrldd 72 
                  +++++f+ ++++++ ++++  +++gaviv +++ +a+g+n                             +l+    +HaE++a++  a  +++    +
   EPA06625.1  33 NWDEYFMLQAELAKLRSNCMTRQVGAVIVRKNRQLATGYNgtppgikncfeggcrrcqlrmegkiesGASLDRCLCNHAEANAIMHCAILGIEAGIAG 130
                  799************************************************************999988999999*********************** PP

  MafB19-deam  73 atlyvtlepCdmCagaivqaglkklvygagnpks.........lnkLkv 112
                  a+ly+t  pC  C ++ +  g+kk v   ++p++         ++++++
   EPA06625.1 131 AILYTTFVPCLECTKMAITIGIKKFVCLDSYPETdfellkeagVEVVQM 179
                  *************************999999888777766666444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       801  (0.0446762); expected 358.6 (0.02)
Passed bias filter:                      580  (0.0323498); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1319.53
//
Query:       EPA06626.1  [L=897]
Description: pyruvate, phosphate dikinase, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-84  283.5   0.6    2.7e-84  282.8   0.6    1.4  1  PEP-utilizers_C  PEP-utilising enzyme, TIM barrel domain
    9.1e-58  196.1   0.1      1e-42  146.6   0.0    3.7  3  PPDK_N           Pyruvate phosphate dikinase, PEP/pyruvate bi
    2.4e-26   91.3   0.2    5.6e-26   90.1   0.2    1.7  1  PEP-utilizers    PEP-utilising enzyme, mobile domain


Domain annotation for each model (and alignments):
>> PEP-utilizers_C  PEP-utilising enzyme, TIM barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  282.8   0.6   4.5e-88   2.7e-84       5     292 ..     519     876 ..     515     878 .. 0.96

  Alignments for each domain:
  == domain 1  score: 282.8 bits;  conditional E-value: 4.5e-88
                      TSCCCCCCCHCCCXBCEEEEEESSCHHHHHHHHCTXSSEEEEEHHHHCTTSCCHHHHHH....................HHHHHHHHHHHTTTS CS
  PEP-utilizers_C   5 gklktllavtkdgkkikvlaNidtpedaekalengaeGiGLlRtEflfmareelpteee....................qaeaykkvleamngr 78 
                      +++kt+l +++++k+i + aN+dtpe a+ a+e+g +GiGL+RtE++f+ ++++  + e                    q++++ ++l+am+g 
       EPA06626.1 519 EDFKTILEWAQKVKQIGIRANADTPEGARLAREFGGQGIGLCRTERMFNGSDRIGLFVEmimaenieerkkvltklgelQKSDFIEILKAMEGY 612
                      7899*************************************************9999999********************************** PP

                      EEEEEXXXSSCCGGSGGC............................HHHH.XSXGGGSSXTHHHHCCSHHHHHHHHHHHHHHCCCC.......E CS
  PEP-utilizers_C  79 pvvvRtlDiggdkelpel............................keepeevNPmlGfRgirlglsepelfetqlrAllrasaag.......k 137
                      +v++R+lD++ +++lp+                              + ++e NPm+G+Rg+r+g+++pe++e+q+rA+++a+a+        +
       EPA06626.1 613 AVTIRLLDPPLHEFLPNPeelaekihkleqkndtselekakillkrARDLAEINPMMGHRGVRVGITYPEIYEMQIRAVFEAAAELaknkvdaH 706
                      ****************98899***********************9989999*********************************666788999* PP

                      EEEEESSXXSHHHHHHHHHHHHHHHHHHHHCTCTXXTTXEEEEEEXSHHHHHTHHHHCTTSSEEEEXHHHHHHHHHTXXCCCHC....HHHH.. CS
  PEP-utilizers_C 138 leimlPmvasveeleeakkiieevkeelekegvkkkkkvkvGiMiEvpsaalladklakevdFfSiGtNDLtQytlavdRdnee....vakl.. 225
                       +im+P ++s+ el++ kki   +k+e+e +  ++k k+++G+MiEv++aal+a++la+ ++FfS+GtNDLtQ t++ +R++ e    + ++  
       EPA06626.1 707 PQIMIPQISSIAELNHIKKIYDAIKKEMELK-HNMKLKINFGTMIEVVRAALTANELANTAEFFSFGTNDLTQGTFSFSREDVEgkflPEYMdk 799
                      *****************************99.999*************************************************7887666688 PP

                      ....SXTTTCHHCCCHHHHHHHHHHCC......XEEEEESCCCCSCCCHHHHHHCTXSEEEEXGGGHHHHHHHHHCT CS
  PEP-utilizers_C 226 ....ydplepavlrlikevikaaeekg......lkvgiCGelagdpsavellvglGldelSmsaasvpaaraalaqv 292
                           +p++  + +++++++k+  ++g      +++giCGe++gdps+++++++  l ++S+s++++p+a +a+aq+
       EPA06626.1 800 eileKNPFQSIDVNGVGSLMKIGITAGrsikpnMEIGICGEHGGDPSSIKFCHKTNLSYVSASPHRIPIAIIAAAQA 876
                      99999*********************9999999*************************************9999987 PP

>> PPDK_N  Pyruvate phosphate dikinase, PEP/pyruvate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.6   0.0   1.7e-46     1e-42       2     216 ..      16     287 ..      15     299 .. 0.95
   2 !   40.8   0.3   2.6e-14   1.5e-10     270     327 ..     302     357 ..     291     358 .. 0.92
   3 ?   -2.1   0.1       0.3   1.8e+03      42      66 ..     633     654 ..     593     743 .. 0.53

  Alignments for each domain:
  == domain 1  score: 146.6 bits;  conditional E-value: 1.7e-46
      PPDK_N   2 elvGGKganLaellneagipvPpgfaitadafrefleengleekideelkeldvddvdelrkaskeirelilsaelPeeleeaikeayeelgkkfgde. 99 
                 +l+GGKga+L e+ +++++pvPpgf+it+++++e++++n   +k+ + l                             e++++i+++++++gkk +++ 
  EPA06626.1  16 KLLGGKGAGLCEM-TRLKLPVPPGFTITTEVCKEYYQNN---KKLPKTLMP---------------------------EVKKNIAKIEKRTGKKWNSKe 83 
                 69***********.77***********************...555555554...........................8****************9998 PP

      PPDK_N 100 .elpvaVRSSataEDlpkasfaGqqdtyLnvggeeevle............................................................ 137
                  +l+v+VRS+      +  s++G++dt+Ln+g ++e++e                                                            
  EPA06626.1  84 nPLLVSVRSG------AAISMPGMMDTILNLGLNDETVEglakksnnsrfawdsyrrfvqlfgkvvfgvedkkfdmvlenaklnqavqadsalnekslk 176
                 89********......99********************************************************************************* PP

      PPDK_N 138 ............................aikavfaSlfnerAilYrkekgldhe.evalavvvqkmvnsdlg...asGVafsldpetG...fkdevlin 201
                                             aikavf S++ erA++Yr++++++++   ++av+v +m ++++g   a+GV+f+++p +G     +e+l+n
  EPA06626.1 177 avvseykkicekhtgvafpsdpfeqlelAIKAVFGSWMGERAVVYRERNNITKDiADGTAVNVVSMAFGNMGndsATGVVFTRNPGDGtrhLFGEYLVN 275
                 ***************************************************9652458******************************7776799**** PP

      PPDK_N 202 asyGlGeaVVaGrvt 216
                 a   +Ge+VVaG +t
  EPA06626.1 276 A---QGEDVVAGVRT 287
                 *...********987 PP

  == domain 2  score: 40.8 bits;  conditional E-value: 2.6e-14
      PPDK_N 270 veeLaeiakkiekhygtpmdiEfaideeegklyllQaRpetrtsekkekkaaetleee 327
                  ++L+e  +++e+hy++p+diEf+i+  +gk+yllQ+R+ + +   ++k+  ++ +e+
  EPA06626.1 302 YKQLEETCERLERHYKEPQDIEFTIE--QGKFYLLQTRNAKMNAVGMVKTSVDMVNEK 357
                 589***********************..*******************99999998875 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.3
      PPDK_N  42 leekideelkeldvddvdelrkask 66 
                 l+eki+++ ++   +d++el+ka+ 
  EPA06626.1 633 LAEKIHKLEQK---NDTSELEKAKI 654
                 66666555555...44333333322 PP

>> PEP-utilizers  PEP-utilising enzyme, mobile domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.1   0.2   9.4e-30   5.6e-26       5      73 .]     423     503 ..     419     503 .. 0.97

  Alignments for each domain:
  == domain 1  score: 90.1 bits;  conditional E-value: 9.4e-30
                    -EEEEES---HHHHTTS-GEEEEEES--TTHHHHHHHHHHTT--EEE--SSHH.............HH--TEEEEEETTTT CS
  PEP-utilizers   5 gvILvaeetspsdiagldkaaGivterGGmtSHaAivArelgiPaVvgvgeati............elkegdlitvDgstG 73 
                    +vIL++eet+p+d++++    Gi+t+rGG+tSHaA+vAr++g+P++vg+++++i            +++egd it+DgstG
     EPA06626.1 423 KVILIREETKPEDVPAFFESVGILTSRGGKTSHAAVVARGMGKPCIVGCSDLRIdydnkqcsvdgrVVHEGDAITIDGSTG 503
                    59***************************************************************999999*********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (897 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       862  (0.0480785); expected 358.6 (0.02)
Passed bias filter:                      579  (0.032294); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.44
# Mc/sec: 6188.25
//
Query:       EPA06627.1  [L=206]
Description: SNF7 family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-06   27.7   0.0    2.4e-06   27.2   0.0    1.1  1  Snf7             Snf7
    7.2e-05   21.5   1.2     0.0001   21.0   1.2    1.2  1  Proteasom_PSMB   Proteasome non-ATPase 26S subunit
     0.0021   17.8   1.8        7.9    6.4   0.2    3.9  4  DASH_Dam1        DASH complex subunit Dam1
  ------ inclusion threshold ------
      0.096   13.4   1.1        1.1   10.0   0.4    2.3  2  Phage_int_SAM_2  Phage integrase, N-terminal


Domain annotation for each model (and alignments):
>> Snf7  Snf7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.0   5.4e-10   2.4e-06       4     170 ..      34     195 ..      31     197 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 5.4e-10
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTC CS
        Snf7   4 rsLrkaerkldkkqeslekkikkleaelkklakkgnkdralllLKqkkryekqldqldnqlanleqvslaienlksnkevlnamkqgakamkamnkkvd 102
                 ++L+++  +ld k + l +k +kl + +   +k+ +  + ++l++++ +++k ++ l +++ +leqv+l + + ++  + + +++    +m +mn  ++
  EPA06627.1  34 VQLNRTVSSLDYKVKTLNEKDAKLFNRIVMAKKSHDITTGKVLANELAELRKNKKILTTMKVSLEQVNLRLSTVSDLGDAMSSLGP---IMATMNA-LK 128
                 689*******************************************************************9988876655555555...5555543.34 PP

                 CHHHHHHHHHHHHHHHH.HTCHHHHHHHHHTT-...GGTTHHHHHHHHHHHHHHHHHCSH.HHHHHHHTXXX CS
        Snf7 103 idkidklmdeiedqmek.aeeisEalsrsldda...deedEeeleaeLdaLeqelgdeelldesvklpevPs 170
                  + + k+m e++++ e   +++++ +s+s++     d ++ ee+e++L + ++  g       + k p++P+
  EPA06627.1 129 -PALGKIMPEVSREFESlFGILNDSVSSSFEGSfgsDTVSNEETENILKEAAAVAGTRV----GDKFPSIPT 195
                 .6788**********97358999999999987677899999999999987666655544....777777776 PP

>> Proteasom_PSMB  Proteasome non-ATPase 26S subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   1.2   2.3e-08    0.0001      95     173 ..      26     105 ..      13     109 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.3e-08
  Proteasom_PSMB  95 npnvkalvLaeleRiveekegalellknee..lllliikalreedlsvaeeairllskllkqeagleelkskLkallkrnd 173
                     +p+++   L +l+R+v + +  +++l++++  l   i+ a +++d+  ++   + l++l k++++l  +k +L++++ r +
      EPA06627.1  26 KPRIQSS-LVQLNRTVSSLDYKVKTLNEKDakLFNRIVMAKKSHDITTGKVLANELAELRKNKKILTTMKVSLEQVNLRLS 105
                     5788888.******************976433999****************************************987755 PP

>> DASH_Dam1  DASH complex subunit Dam1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.4   0.0    0.0037        16       7      41 ..      11      45 ..       5      57 .. 0.78
   2 !    6.4   0.2    0.0018       7.9       7      34 ..      75     102 ..      74     107 .. 0.90
   3 ?    2.5   0.0     0.028   1.2e+02       5      30 ..     107     132 ..     103     137 .. 0.86
   4 ?   -0.0   0.1      0.18     8e+02      24      38 ..     148     163 ..     130     163 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0037
   DASH_Dam1  7 eLaDsletLdknledLqqihesLsdfNeSFasfLY 41
                 ++D l+ L+k      +i+ sL+++N+ ++s+ Y
  EPA06627.1 11 GISDHLRGLKKEAPLKPRIQSSLVQLNRTVSSLDY 45
                56777777777777777899999999999999855 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0018
   DASH_Dam1   7 eLaDsletLdknledLqqihesLsdfNe 34 
                  La +l++L+kn + L  ++ sL+++N 
  EPA06627.1  75 VLANELAELRKNKKILTTMKVSLEQVNL 102
                 6999*********************995 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.028
   DASH_Dam1   5 faeLaDsletLdknledLqqihesLs 30 
                  ++L D+++ L   +  ++ ++ +L 
  EPA06627.1 107 VSDLGDAMSSLGPIMATMNALKPALG 132
                 68999***********9999998875 PP

  == domain 4  score: -0.0 bits;  conditional E-value: 0.18
   DASH_Dam1  24 qihesLsd.fNeSFas 38 
                  +++s+s+ f  SF+s
  EPA06627.1 148 ILNDSVSSsFEGSFGS 163
                 4567777778778876 PP

>> Phage_int_SAM_2  Phage integrase, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.4   0.00025       1.1      29      80 ..      33      85 ..      26      89 .. 0.88
   2 ?    2.2   0.0     0.068   3.1e+02      26      49 ..      87     110 ..      85     113 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00025
  Phage_int_SAM_2 29 lqrlareLlalniqvrdvkslKarHieayieerlaeeiskr.tlqNemaalRs 80
                     l +l r +  l+++v++ ++  a+  +  +  +++++i+++  l Ne+a lR 
       EPA06627.1 33 LVQLNRTVSSLDYKVKTLNEKDAKLFNRIVMAKKSHDITTGkVLANELAELRK 85
                     55789999******************************985279*******97 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.068
  Phage_int_SAM_2  26 erilqrlareLlalniqvrdvksl 49 
                      ++il  +  +L + n+++ +v++l
       EPA06627.1  87 KKILTTMKVSLEQVNLRLSTVSDL 110
                      6999****************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       950  (0.0529868); expected 358.6 (0.02)
Passed bias filter:                      632  (0.0352502); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1615.86
//
Query:       EPA06628.1  [L=83]
Description: hypothetical protein BG20_I1597 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.18   11.9   0.0       0.23   11.6   0.0    1.2  1  Abhydrolase_4  TAP-like protein


Domain annotation for each model (and alignments):
>> Abhydrolase_4  TAP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   1.3e-05      0.23      28      76 ..       7      55 ..       1      64 [. 0.68

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.3e-05
  Abhydrolase_4 28 esta.kgaapvLllqnerDpaTPyegakklakalggavlvtvege.GHgal 76
                   e+++ ++ +p +l+++++D++T ++  k + + + + +l+ +++e GH+ +
     EPA06628.1  7 ETEKiTSMPPSMLVSATYDNITRTAVLK-FYEPISQ-KLILWNDEtGHKPY 55
                   334314469*************998755.4444543.66666666588765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       268  (0.0149478); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 576.57
//
Query:       EPA06629.1  [L=48]
Description: zinc finger CDGSH type [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-11   43.2   1.2    4.3e-11   42.9   1.2    1.2  1  zf-CDGSH  Iron-binding zinc finger CDGSH type


Domain annotation for each model (and alignments):
>> zf-CDGSH  Iron-binding zinc finger CDGSH type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   1.2   2.4e-15   4.3e-11      16      47 ..       3      34 ..       1      35 [. 0.85

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 2.4e-15
    zf-CDGSH 16 dgesvelregrevvaLCrCgrSknkPfCDgsH 47
                dg ++ + +g+++ aLCrCg S++kP CDgsH
  EPA06629.1  3 DGPCIVNVDGTKIAALCRCGVSNKKPHCDGSH 34
                5666667778889******************* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.46
# Mc/sec: 312.60
//
Query:       EPA06630.1  [L=672]
Description: DNA-directed DNA polymerase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.7e-45  153.4   1.8    1.5e-44  152.5   1.8    1.4  1  DNA_pol_B       DNA polymerase family B
    2.1e-37  129.0   3.0    3.4e-37  128.3   3.0    1.4  1  DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain
    1.3e-06   28.5   4.0    1.7e-06   28.2   2.0    2.1  2  RNase_H_2       RNase_H superfamily
    1.7e-05   24.6   1.7    0.00011   22.0   1.7    2.2  1  DNA_pol_B_exo2  Predicted 3'-5' exonuclease related to the ex
  ------ inclusion threshold ------
      0.033   14.0   0.5       0.15   11.8   0.0    2.3  2  SpoVIF          Stage VI sporulation protein F
       0.11   12.5   0.3       0.28   11.1   0.0    1.8  2  CNP1            CNP1-like family


Domain annotation for each model (and alignments):
>> DNA_pol_B  DNA polymerase family B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.5   1.8     5e-48   1.5e-44      10     346 ..     343     648 ..     335     667 .. 0.84

  Alignments for each domain:
  == domain 1  score: 152.5 bits;  conditional E-value: 5e-48
                 -HHHHHHHHHHHHHHHTTBE-B-----.--SS............-S----BE----EEESS-EEEEEETTHHHHHHHHTT-STTTCE-HCCHCCT--BT CS
   DNA_pol_B  10 gqqirveslLlrlakeegfilpdrtekkgkeee...........gYqGatVlePkkglydkpvlvlDFaSLYPsiiqahNlcyttlvaseeeakeleae 97 
                 g ++ + slL+ ++++++  +p+r+e  +k++e           +Y G++V++Pk+g++ + v+v+DFaSLYPsii   N++y+t+ +s+ee k+ +  
  EPA06630.1 343 GVSQWIRSLLYYEHRQRNALIPKREEL-EKRSEgvtsdavikdkKYRGGLVIDPKEGIHFD-VVVMDFASLYPSIIKVRNISYETVRCSHEECKKNTIP 439
                 66778999**************75555.55555588889999867*************986.789***************************9965543 PP

                 T...TEEE-TCC-EEE-TTS---HHHHHHHHHHHHHHHHHHHHH..CS--HHHHHHHHHHHHHHHHHHHHHHHHHTSTTSTT--HHHHHHHHHHHHHHH CS
   DNA_pol_B  98 deyleveveprlvefvkksvregllpklLkdllakRkaikkelk..eekdefekalldkqQlalKvtaNsvYGftGvansrlpclalAasvTtiGRemL 194
                 +       +    + +   +r+g+ ++++ +l + R ++ k l   e+ +e +++++    +alKv+ N+ YG++G++  +l+ l+ A+  T+iGR ++
  EPA06630.1 440 Q-------T----NHWACTKRNGITAIIIGSLRDLRVNYYKSLSkkETLTEDQRQQYTVVSQALKVILNASYGVMGAEIFPLYFLPAAEATTAIGRFTI 527
                 3.......3....45788899******************99998445556789********************************************** PP

                 HHHHHHHHHT...SSGGGT-SS.....T-EEEEEBSSEEEEE-S-SSHHHHHHHHHHHHHHHHT.TSTTT--EEEEEEEEEEEEEE.TTEEEEEEEEES CS
   DNA_pol_B 195 ektkelvekkaellskllalpeeaeeeklkviYGDTDSvfielkvkdveellkigkelaeevseklfkkplklefekvykkllLis.KKkYaglkvekt 292
                 ++t +  e+                  +++v YGDTDS+fi+  +++         +++ ++++++  + + le++kvy   +L + KK Y g++ +  
  EPA06630.1 528 LETIKKCEAI-----------------GIEVLYGDTDSLFIKKPTDQ---------QIHTVIEQAKKDHGVDLEIDKVYRYCVLSNrKKNYLGVTKS-- 598
                 ***9999987.................9**************98853.........3444556666677789*******98888752778***9999.. PP

                 STTSEEEEESSGGGSTTS-HHHHHHHHHHHHHHSSS.......S-HHHHHHHHHHHH CS
   DNA_pol_B 293 skanklliKGvdlvRrdncklvkevikkvlelllkdet...eersleeglealksil 346
                    + +++KG+   +    ++++++  ++l+ l k +t   +    e++ +++ + +
  EPA06630.1 599 ---GTVDVKGLTGKKSHTPPFIRNLFYELLDVLSKVQTvadF----ENAKKEITDKI 648
                 ...999*************************99999655543....33333333333 PP

>> DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.3   3.0   1.1e-40   3.4e-37      66     327 ..       4     257 ..       1     275 [. 0.87

  Alignments for each domain:
  == domain 1  score: 128.3 bits;  conditional E-value: 1.1e-40
                     CCHHCEEEEEESSTCHHHHHHHHHHHCCCCCCCCSSS--HHHHHHHHCTS-TTCEEEEE.......TEEEEGCC--C-.SEEEEEETTTSCEETT CS
  DNA_pol_B_exo1  66 kkpvpylkvsvsnpnelkkirkelspleeivdvyeydvdylerflidnkivgfgwysvk.......kylvraegkisncdveidcdvddliakpk 153
                     +++v++ k++v++p  +  +   +s +++i++++e+d++y+e++l+d+++ ++++y++        + ++++e k++++++ +d+ +++++ +pk
      EPA06630.1   4 DEEVNLSKITVADPLTIGGTTGDKS-IRNIIETWESDIKYYENYLYDRSLIVGKYYEIIdgkikphDLEISDEVKLALKSLLWDKVDSENMVDPK 97 
                     4455699****************97.********************************99999999999************************** PP

                     T............CC..S-EEEEEEEEEETEETTSEETTTT..--EEEEEEEE.CCTC.SS.SEEEEEEECCCTSS----EE--SSTCSTTEEEE CS
  DNA_pol_B_exo1 154 e............se..pplrvlsFDIeckskkgkfpdaensedpiiqIscvl.dglgekepearklftlrecaseeeedfeltpkpeypgvkvl 233
                     e            ++  p+++ ls DIe+ ++ g++pd++  e+++++I +    + +       ++f+l++    ++e  +       ++ k++
      EPA06630.1  98 EfkelisdwadllNQpiPRIKRLSVDIEVEAEIGRIPDPKVAEKKVTAIGLKGtNDFD-------QIFVLKTEG--TDEGTNELG----KNIKIV 179
                     *99999888777644899***********************************88888.......899999888..223222233....355777 PP

                     EE..SSHHHHHHHHHHHHHHH--SEEEESSTTTTHHHHHHHHHHHCCTCCHCG.SCCSCTCEECCCCESEEEEEECEEEETTSEEEEHHHHHHHH CS
  DNA_pol_B_exo1 234 ef..dsEkelLqaflefikqydPdvitgYNidnFDlpYilnRakelykvklsklgrlnkggrskvseigfskqarekvkisgrihlDlyrvvkrk 326
                     ++  d+Eke++ + +++i +    ++++YN+d+FDlpY+ nRa+              + g++k +++ ++  ++++ ++++ +hlDlyr+ +++
      EPA06630.1 180 FYdqDKEKEMILDAFKIIEEF--PFVVTYNGDEFDLPYLYNRAE--------------RLGIKKEENPLYM--MKDSATLKQGVHLDLYRTLSNR 256
                     662268*************77..*********************..............99***********..******************9998 PP

                     S CS
  DNA_pol_B_exo1 327 l 327
                     +
      EPA06630.1 257 S 257
                     3 PP

>> RNase_H_2  RNase_H superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   2.0   5.6e-10   1.7e-06      36     115 ..     179     280 ..     165     319 .. 0.77
   2 ?   -2.5   0.0       1.5   4.5e+03      72     120 ..     615     661 ..     610     668 .. 0.53

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 5.6e-10
   RNase_H_2  36 llaeepeeekailelflellekkkalvtfngksFDvpflkrlfkkyklde..............eefrhiDLlkelrkkkl.........esysLksve 111
                 ++ ++ +e++ il++f +++e+++ +vt+ng +FD+p+l +++++  +++              ++  h+DL++ l++  +         + +sL sv 
  EPA06630.1 179 VFYDQDKEKEMILDAF-KIIEEFPFVVTYNGDEFDLPYLYNRAERLGIKKeenplymmkdsatlKQGVHLDLYRTLSNRSFqiyafsqkyTDFSLNSVS 276
                 456778899999**99.**************************9999999888888888887766669*****99977766455555555666677766 PP

   RNase_H_2 112 kelg 115
                 k+l 
  EPA06630.1 277 KALL 280
                 6655 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.5
   RNase_H_2  72 pflkrlf.kkykldeeefrhiDLlkelrkkklesysLksvekelgierre 120
                 pf+++lf +  ++ + +++++  ++++ kk+++  ++++++k+ gi+r++
  EPA06630.1 615 PFIRNLFyELLDVLS-KVQTVADFENA-KKEITD-KIATCAKKSGIKRDT 661
                 555555522222222.33333222222.233366.688888888888875 PP

>> DNA_pol_B_exo2  Predicted 3'-5' exonuclease related to the exonuclease domain of PolB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   1.7   3.7e-08   0.00011      33      81 ..     182     229 ..     167     316 .. 0.64

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 3.7e-08
  DNA_pol_B_exo2  33 eessekelikkffegvekkkpqlVsfngrgfDlpvleyralkhgvsapk 81 
                     ++++eke+i   f+++e+  p +V++ng +fDlp l+ ra + g++ ++
      EPA06630.1 182 DQDKEKEMILDAFKIIEEF-PFVVTYNGDEFDLPYLYNRAERLGIKKEE 229
                     6789***********9986.8*******************999998653 PP

>> SpoVIF  Stage VI sporulation protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   5.2e-05      0.15      18      51 ..      84     117 ..      76     120 .. 0.90
   2 ?   -1.8   0.2      0.93   2.8e+03      48      70 ..     640     662 ..     625     663 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.2e-05
      SpoVIF  18 LansvqkadlkdektlRqlikqvsklankpvske 51 
                 L ++v  +++ d k+ ++li++ ++l+n+p++  
  EPA06630.1  84 LWDKVDSENMVDPKEFKELISDWADLLNQPIPRI 117
                 5689**************************9865 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.93
      SpoVIF  48 vskekedkivkaivndkvpkdle 70 
                   ke +dki    ++++++ d++
  EPA06630.1 640 AKKEITDKIATCAKKSGIKRDTA 662
                 35788888888888888888876 PP

>> CNP1  CNP1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   9.3e-05      0.28      62     124 ..     418     477 ..     392     491 .. 0.79
   2 ?   -2.8   0.0         2   5.8e+03      42      61 ..     572     591 ..     555     599 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.3e-05
        CNP1  62 arnvsyeGirCataerklYatgrkdnkrWikaraaeWqrieeseanrlraaLardyfCeekav 124
                  rn+sye +rC+ +e k     ++  ++W+ ++++  + i  ++  +lr + +++ + ++++ 
  EPA06630.1 418 VRNISYETVRCSHEECKKNTIPQT--NHWACTKRNGITAIIIGSLRDLRVNYYKS-LSKKETL 477
                 79***************9877666..79**9999999998888888888877777.4444444 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2
        CNP1  42 isvgkdgvvRYtlvitsksG 61 
                 + ++ d+v RY ++ + k+ 
  EPA06630.1 572 VDLEIDKVYRYCVLSNRKKN 591
                 66778999999998877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (672 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       825  (0.0460148); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.76u 0.34s 00:00:01.10 Elapsed: 00:00:00.52
# Mc/sec: 3917.41
//
Query:       EPA06631.1  [L=45]
Description: hypothetical protein BG20_I1590 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00021   21.8   0.3    0.00041   21.0   0.3    1.5  1  zf-C2H2_4    C2H2-type zinc finger
     0.0022   17.4   0.1     0.0025   17.2   0.1    1.1  1  DUF2688      Protein of unknown function (DUF2688)
     0.0025   18.2   0.5     0.0043   17.4   0.5    1.4  1  zf-C2H2      Zinc finger, C2H2 type
     0.0048   16.6   0.2     0.0097   15.6   0.2    1.5  1  zf-C2H2_11   zinc-finger C2H2-type
     0.0091   16.0   0.1      0.012   15.6   0.1    1.3  1  zf-BED       BED zinc finger
  ------ inclusion threshold ------
       0.01   15.6   0.5      0.014   15.2   0.0    1.5  2  zf-C2H2_3    zinc-finger of acetyl-transferase ESCO
      0.017   15.5   1.8      0.018   15.4   1.8    1.1  1  zf-C2H2_2    C2H2 type zinc-finger (2 copies)
      0.029   14.8   4.8       0.36   11.3   0.7    2.2  2  zf-H2C2_2    Zinc-finger double domain
      0.041   12.4   1.1      0.038   12.5   1.1    1.0  1  DUF629       Protein of unknown function (DUF629)
      0.082   12.1   2.4      0.078   12.1   2.4    1.0  1  Actin_micro  Putative actin-like family


Domain annotation for each model (and alignments):
>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.3   2.3e-07   0.00041       2      24 .]      14      36 ..      13      36 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.3e-07
   zf-C2H2_4  2 kCpiCgksFsskkaLlrHlkthH 24
                kC+ Cg  Fs  +++lrH+ + H
  EPA06631.1 14 KCRECGMEFSETERMLRHMIKAH 36
                8********99999*****9988 PP

>> DUF2688  Protein of unknown function (DUF2688)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   1.4e-06    0.0025       4      24 ..       9      29 ..       6      38 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.4e-06
     DUF2688  4 eiVtTqCrRCGkslstlsrSL 24
                 iV T+Cr CG   s ++r L
  EPA06631.1  9 IIVETKCRECGMEFSETERML 29
                59***************9987 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.5   2.4e-06    0.0043       2      23 .]      14      36 ..      13      36 .. 0.96

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.4e-06
                EETTTTEEESSHHHHHHHHHC.C CS
     zf-C2H2  2 kCpdCgksFkrksnLkrHirt.H 23
                kC +Cg+ F+  + + rH+ + H
  EPA06631.1 14 KCRECGMEFSETERMLRHMIKaH 36
                8*******************999 PP

>> zf-C2H2_11  zinc-finger C2H2-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.2   5.4e-06    0.0097       6      28 ..      14      36 ..      13      37 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.4e-06
  zf-C2H2_11  6 qCleCGlcftSqlsLsRHlfIvH 28
                +C+eCG+ f+      RH++  H
  EPA06631.1 14 KCRECGMEFSETERMLRHMIKAH 36
                8*********9999999*98666 PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   6.9e-06     0.012      17      43 ..      13      36 ..       3      37 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 6.9e-06
                -EETTTTEE----SSTHHHHHHHHHS- CS
      zf-BED 17 avCryCgkilsrgggttnLkrHLrrkH 43
                ++Cr Cg ++s    t ++ rH+ ++H
  EPA06631.1 13 TKCRECGMEFSE---TERMLRHMIKAH 36
                68********98...8*********** PP

>> zf-C2H2_3  zinc-finger of acetyl-transferase ESCO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   8.1e-06     0.014      13      26 ..      12      25 ..       2      27 .. 0.74
   2 ?   -2.2   0.1       2.2   3.9e+03      35      36 ..      37      38 ..      33      44 .. 0.48

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 8.1e-06
   zf-C2H2_3 13 asqCkeCgMvYnpg 26
                +++C eCgM+++++
  EPA06631.1 12 ETKCRECGMEFSET 25
                356*******9976 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.2
   zf-C2H2_3 35 kk 36
                 k
  EPA06631.1 37 TK 38
                32 PP

>> zf-C2H2_2  C2H2 type zinc-finger (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   1.8   9.8e-06     0.018      44      77 ..       6      38 ..       2      44 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 9.8e-06
   zf-C2H2_2 44 rekieekleClyCekefkslealreHmkkkgHck 77
                +eki  + +C  C+ ef+++e +  Hm k+ H+k
  EPA06631.1  6 KEKIIVETKCRECGMEFSETERMLRHMIKA-HTK 38
                678888899999999999999999999864.554 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.2     0.012        21      10      25 ..       5      23 ..       1      24 [. 0.73
   2 ?   11.3   0.7    0.0002      0.36       4      14 ..      30      41 ..      28      45 .] 0.88

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.012
   zf-H2C2_2 10 tgekpy...eCplCdkaFk 25
                 +ek+    +C +C+  F+
  EPA06631.1  5 NKEKIIvetKCRECGMEFS 23
                5677656779*****9985 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.0002
   zf-H2C2_2  4 rHirk.Htgekp 14
                rH+ k Ht++kp
  EPA06631.1 30 RHMIKaHTKKKP 41
                9**********9 PP

>> DUF629  Protein of unknown function (DUF629)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.1   2.1e-05     0.038      57      83 ..      13      39 ..       1      44 [. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.1e-05
      DUF629 57 WvCrtCsekfsdaeeckqHlvqeHvak 83
                 +Cr+C  +fs+ e ++ H+ + H +k
  EPA06631.1 13 TKCRECGMEFSETERMLRHMIKAHTKK 39
                58**********************986 PP

>> Actin_micro  Putative actin-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   2.4   4.3e-05     0.078     223     252 ..      10      40 ..       1      44 [. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.3e-05
  Actin_micro 223 kkefsCkvCdvkfev.ekiseHllkkHiike 252
                    e +C  C+++f+  e++  H++k H++k+
   EPA06631.1  10 IVETKCRECGMEFSEtERMLRHMIKAHTKKK 40 
                  34678********999***********9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       961  (0.0536003); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 286.54
//
Query:       EPA06632.1  [L=142]
Description: hypothetical protein BG20_I1592 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.049   13.7   3.6        5.9    7.0   1.0    2.5  2  YolD      YolD-like protein


Domain annotation for each model (and alignments):
>> YolD  YolD-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   1.0   0.00033       5.9      33      57 ..      27      51 ..       3      56 .. 0.85
   2 ?    6.8   0.1   0.00039       6.9      23      79 ..      75     130 ..      63     141 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00033
        YolD 33 neklqealeeeqpvtityyedgele 57
                  k+ +++e++ p+ +++y+++++e
  EPA06632.1 27 TVKIIRKYETQTPIYVQMYSNYYDE 51
                56899****************9987 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.00039
        YolD  23 eLDeqqleeineklqealeeeqpvtityyedgeleevtgyiekidelnkelkledee 79 
                  LDe++l + + k +  ++e+    i +y +++ +++++ ++ +++ln  +++ ++ 
  EPA06632.1  75 GLDEKTLIAAD-KFWNDFTETTISNIDIYTNFRKTQFDMMVTGMKTLNDFVQMGMDY 130
                 56677666654.4567788899999**********************9998887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       791  (0.0441185); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 940.56
//
Query:       EPA06633.1  [L=155]
Description: glyoxalase family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-07   31.4   0.0    2.9e-07   30.7   0.0    1.4  1  Glyoxalase    Glyoxalase/Bleomycin resistance protein/Dioxyge
    2.1e-05   25.3   0.0    3.3e-05   24.6   0.0    1.3  1  Glyoxalase_6  Glyoxalase-like domain


Domain annotation for each model (and alignments):
>> Glyoxalase  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.0   3.2e-11   2.9e-07       9     127 ..      18     130 ..       8     131 .. 0.93

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 3.2e-11
                 ESHHHHHHHHHHHHHTSEEEEEEEEEEST.EEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSCTSEEEEEEEEEHCHHHHHHHHHHHTTGEEEEEEE CS
  Glyoxalase   9 vgdleksldFYtkvLGfklvkktdnteet.eglriaffhaggghielvlneapsgaakhvkkieetvhhvafialdvedvgkaldrlkeagvkvvaepg 106
                    ++++++FY+k++++k v +++  +++ ++ ++a +++g+  ++l ++ ++ g +++     +t+   + i+l v+d +  ++++ + g k  ++  
  EPA06633.1  18 IHGASEAIEFYKKAFDAKEVYRFP--GPDgKSIMHAEIRIGDSALMLCDEMPEMGCLSPT----STGGPSGAIYLYVNDADSVFNKAISSGAKSLMPMM 110
                 556899******************..6666*****************************9....889999***************************** PP

                 CHHCTEEEEEEEEETTSEEEE CS
  Glyoxalase 107 rhyfgalysfyfrDpdGille 127
                 + ++g+++++   Dp+G+++ 
  EPA06633.1 111 DGFWGDRFGI-LSDPFGHRWT 130
                 *********9.*******995 PP

>> Glyoxalase_6  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   3.7e-09   3.3e-05       9     107 .]      21     132 ..      15     132 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 3.7e-09
  Glyoxalase_6   9 paalaaFwaaalgweveree.....aaledpegvgpaaedaatllfqrvpe........paknrvHldlavedldaevarlvalGArvlreprdgth 92 
                   + ++++F+++a++ + + +       ++ ++e      +d+a +l  + pe        ++     + l v+d+d   +++++ GA+ l +  dg +
    EPA06633.1  21 ASEAIEFYKKAFDAKEVYRFpgpdgKSIMHAEI---RIGDSALMLCDEMPEmgclsptsTGGPSGAIYLYVNDADSVFNKAISSGAKSLMPMMDGFW 114
                   678999******888777775755533333333...345889999999999****98763333688999**************************** PP

  Glyoxalase_6  93 gr...vlaDPeGneFcvv 107
                   g+   +l DP G++++v+
    EPA06633.1 115 GDrfgILSDPFGHRWTVA 132
                   99*************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.54
# Mc/sec: 866.43
//
Query:       EPA06634.1  [L=99]
Description: hypothetical protein BG20_I1595 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       789  (0.0440069); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 686.04
//
Query:       EPA06635.1  [L=218]
Description: triose-phosphate isomerase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.1e-10   39.1   4.6    1.4e-09   37.7   0.4    2.0  2  TIM           Triosephosphate isomerase
    2.2e-05   23.9   0.1    3.5e-05   23.2   0.1    1.4  1  ThiG          Thiazole biosynthesis protein ThiG
    0.00014   21.0   0.0    0.00025   20.2   0.0    1.3  1  FMN_dh        FMN-dependent dehydrogenase
     0.0072   15.5   0.1      0.016   14.3   0.1    1.6  1  IGPS          Indole-3-glycerol phosphate synthase
  ------ inclusion threshold ------
      0.029   13.8   0.0      0.043   13.2   0.0    1.2  1  NMO           Nitronate monooxygenase
      0.034   13.1   0.2      0.082   11.9   0.1    1.6  1  POC1          POC1 chaperone
      0.064   12.4   2.2       0.47    9.5   2.2    2.1  1  Glu_synthase  Conserved region in glutamate synthase


Domain annotation for each model (and alignments):
>> TIM  Triosephosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.4   5.4e-13   1.4e-09       4     134 ..       3     127 ..       1     131 [. 0.85
   2 ?    3.9   0.3     0.012        30     159     243 .]     132     210 ..     125     210 .. 0.76

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 5.4e-13
                 EEE-TBTS..-HHHHHHHHHHHHHHCHGCTSEEEEE--GGGHHHHHHHHTTSSECEEES--BSSSSBS-TT--BHHHHHHTT-SEEEES-HHHHHHST- CS
         TIM   4 agNwKmnk..tleeakellkklkaklkeekvevviappflylekvkklleesklklgaqnvsaeksGafTGevsaemlkdlgvkyviiGHsErrqlfkE 100
                 + N K +     +++ e++k +++  k+ k++++iapp   +     l+++s++ + aq ++ +k G+ TG +  e lk+ +++  +i HsE r    E
  EPA06635.1   3 IINCKNYEeiAGSKIIEFVKIVEKISKKYKIKIAIAPPQHLIG----LVANSTIPILAQHIDNSKVGSTTGFIVPELLKKSKISGSLINHSEHRISSDE 97 
                 66778777223457889999988888889*********87766....678899*****************************************97766 PP

                 -HHHHHHHHHHHHHTT-EEEEEE---HHHHHTT. CS
         TIM 101 tdelvakKvkaalksglkpilCvGEtleereagk 134
                       k v+++ + ++  i+Cv +  e+++ +k
  EPA06635.1  98 I----SKLVSKLRELKMISIVCVKDVAEAKKYSK 127
                 5....5556778999**********999988765 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.012
                 EEEE--GGGSSSS----HHHHHHHHHHHHHHHHHHSTHHHHTTSEEEEE.SS--TTTHHHHHTSTT--EEEESGGGCSHHHHHHHH CS
         TIM 159 viAYePvWAiGtgktatpeqaqevhaairkelaekvskevaekirilYG.GsvnkenakellkqkdidGlLvGgaslkaesFlkii 243
                 +iA eP   iG gk +++e+ + +++a  + +     k+ ++k+++l G G v+ +++ + l+  + +G+Lv +  +ka++++kii
  EPA06635.1 132 YIAIEPPELIGSGKAVSNEKPEIIVKA-SNAV-----KSSKNKTKLLCGaGIVSGQDVVKALELGS-NGILVASGIIKAKNWTKII 210
                 799999999*****9999987655554.3343.....44567777888768888999988887765.9999999999999999887 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.1   1.4e-08   3.5e-05     155     224 ..     141     217 ..     114     218 .] 0.76

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.4e-08
                 TTS----S-HHHH......HHHH.HH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHHHHHHHHHH CS
        ThiG 155 iGsglGllnkeal......kiii.eeakvPvivDAGigspsdaaqamelGadavllntavaeakdpvamArafklav 224
                 iGsg+ ++n++        + +  ++ k  ++  AGi s +d+++a+elG +++l+++ + +ak+  ++ + f++a+
  EPA06635.1 141 IGSGKAVSNEKPEiivkasNAVKsSKNKTKLLCGAGIVSGQDVVKALELGSNGILVASGIIKAKNWTKIIEEFTKAM 217
                 677766666542200111112220233778999**********************************9999998885 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   9.7e-08   0.00025     264     303 ..     161     200 ..     145     206 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 9.7e-08
                 HHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHH CS
      FMN_dh 264 iveavggrievlvDgGirrGsDvlkAlalGAdavllGRpf 303
                  v+  ++++++l+  Gi +G+Dv+kAl lG +++l++  +
  EPA06635.1 161 AVKSSKNKTKLLCGAGIVSGQDVVKALELGSNGILVASGI 200
                 35555679*************************9998665 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.1   6.4e-06     0.016     146     253 ..      97     212 ..      90     213 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.4e-06
                 HHHHHHHHHCCTT-EEEEEESSHHHHHHHHHTT-SEEEEESEET.........TTTEE-CHHHHHHCHCC-TTSEEEEESSS-SHHHHHHHCCTT-SEE CS
        IGPS 146 eleelaeaakslglevLvEvhdeeeleralklgakiiGvNnRnL.........ktlevdlntteeLaklvpkdvllvaeSGiktredveklkeegvnaf 235
                 e+++l++  ++l +  +v v+d +e ++  kl+ + i +   +L         ++ e+ ++ ++ +++  ++++ l +  Gi + +dv k  e g n++
  EPA06635.1  97 EISKLVSKLRELKMISIVCVKDVAEAKKYSKLNPDYIAIEPPELigsgkavsnEKPEIIVKASNAVKS-SKNKTKLLCGAGIVSGQDVVKALELGSNGI 194
                 55666666666666666666666666666666666666666666332222221223444444444444.3346888999******************** PP

                 EESHHHHC-TTHHHHHHH CS
        IGPS 236 LvGeslmrqedvekaire 253
                 Lv + ++++++ +k i+e
  EPA06635.1 195 LVASGIIKAKNWTKIIEE 212
                 ***********9999987 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.7e-05     0.043     126     229 ..      99     204 ..      86     213 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.7e-05
         NMO 126 eevvarlkeagvvliptissvkearkvearGaDalivqGpeaGGhqGtpevgdkglfaLvpqvldavd.....iPviAaGGiidrrgvaaaLalGAsgv 219
                  ++v +l e+ ++ i+ +  v ea+k  ++ +D + ++ pe  G     +v  ++  +++ ++ +av+       ++   Gi+ +++v  aL lG +g+
  EPA06635.1  99 SKLVSKLRELKMISIVCVKDVAEAKKYSKLNPDYIAIEPPELIGSGK--AV-SNEKPEIIVKASNAVKssknkTKLLCGAGIVSGQDVVKALELGSNGI 194
                 57899************************************888644..33.35677777788888877888999************************ PP

         NMO 220 qigtrfLltk 229
                  +++  + +k
  EPA06635.1 195 LVASGIIKAK 204
                 ***9988777 PP

>> POC1  POC1 chaperone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   3.2e-05     0.082     147     193 ..      93     142 ..      74     157 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.2e-05
                 HHHHHHHHHHTT--EE..EEEEEETT-SS-EEEES...S-----TT--B- CS
        POC1 147 iarsvisqlaqlspdikdivigtsdkiaelkklte...decslePPefit 193
                 i+ + is+l+  ++++k i i+    +ae kk ++   d  ++ePPe+i 
  EPA06635.1  93 ISSDEISKLVSKLRELKMISIVCVKDVAEAKKYSKlnpDYIAIEPPELIG 142
                 677779***********************9976543338899*****994 PP

>> Glu_synthase  Conserved region in glutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   2.2   0.00018      0.47     186     306 ..      94     200 ..      76     209 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00018
                   SHHHHHHHHHHHHHH-TTSEEEEEEE-STTHHHHHHHHHHTT-SEEEEE-TT---SSEEHHHHHHB---HHHHHHHHHHHHHHTT-GGG-EEEEESS CS
  Glu_synthase 186 siedlaqliedLkevnkeakvsvKlvaeagvetiaagvakanadiilidGleGGTGAspkssikhaGlPlelalaevdqtlkeeglrdrvsliadGg 282
                   s +++++l+++L+e++     ++ +v+ + v   +   +k n+d i+i+  e   G  + +s ++   P +  ++++ +++k++  +++ +l    g
    EPA06635.1  94 SSDEISKLVSKLRELK-----MISIVCVKDVAEAKK-YSKLNPDYIAIEPPEL-IGSGKAVSNEK---PEI--IVKASNAVKSS--KNKTKLLCGAG 176
                   5567888888888888.....444555555555555.6788888888887663.44445555554...332..67788888766..5777899999* PP

                   --SHHHHHHHHHHT-SEEE-SHHH CS
  Glu_synthase 283 lktgadvvkalalGAdavgigtaa 306
                   + +g+dvvkal lG + + ++++ 
    EPA06635.1 177 IVSGQDVVKALELGSNGILVASGI 200
                   **************9998888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 1714.75
//
Query:       EPA06636.1  [L=420]
Description: phosphoribosylamine--glycine ligase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      8e-79  263.9   0.2    1.1e-78  263.5   0.2    1.2  1  GARS_A           Phosphoribosylglycinamide synthetase, ATP-gr
    5.8e-33  113.5   0.0    1.4e-32  112.3   0.0    1.7  1  GARS_N           Phosphoribosylglycinamide synthetase, N doma
    3.8e-28   97.6   0.0    7.9e-28   96.6   0.0    1.6  1  GARS_C           Phosphoribosylglycinamide synthetase, C doma
    1.1e-07   31.5   0.0    1.9e-07   30.8   0.0    1.3  1  ATP-grasp        ATP-grasp domain
    5.7e-07   29.3   0.1    9.7e-07   28.5   0.1    1.3  1  ATP-grasp_2      ATP-grasp domain
    5.3e-06   26.6   0.0    1.1e-05   25.5   0.0    1.6  1  ATP-grasp_3      ATP-grasp domain
    6.2e-05   22.6   0.1    0.00027   20.5   0.1    2.1  2  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
    0.00031   20.3   0.0    0.00046   19.8   0.0    1.3  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    0.00036   20.2   0.0     0.0011   18.5   0.0    1.8  2  RimK             RimK-like ATP-grasp domain
     0.0016   17.7   0.1      0.022   14.0   0.1    2.3  2  ATPgrasp_ST      Sugar-transfer associated ATP-grasp
     0.0058   16.2   0.0       0.01   15.4   0.0    1.4  1  ATP-grasp_4      ATP-grasp domain
  ------ inclusion threshold ------
      0.028   14.5   0.2      0.068   13.3   0.1    1.7  1  Phage_TAC_9      Phage tail assemb.y chaperone protein, TAC
      0.031   13.7   0.0      0.061   12.8   0.0    1.5  1  ATP-grasp_5      ATP-grasp domain
      0.078   13.1   0.1       0.19   11.9   0.1    1.7  1  SR1P             SR1 protein


Domain annotation for each model (and alignments):
>> GARS_A  Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  263.5   0.2   8.3e-82   1.1e-78       1     194 []      98     290 ..      98     290 .. 0.99

  Alignments for each domain:
  == domain 1  score: 263.5 bits;  conditional E-value: 8.3e-82
                 HBHHHHHHHHHHTT--B--EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEESSHHHHHHHHHHHCTS-TTCCCCSSEEEEE---SEEEEEEEE CS
      GARS_A   1 asKsfakdllkkagiptaeyeaftdpeeakeyieeatakalVvKadglaagKgvivakseeealkavkeilekkkfGeagekvviEelleGeEvsllal 99 
                 +sK +ak+++k+ gi+ta++e f+dp++akey+++++ ++ VvKadgla+gKgviv+++++ea++a++ il+kk+fG+ag+++++Ee+++G+E s +al
  EPA06636.1  98 SSKIWAKNFMKRNGIQTARFEIFDDPKKAKEYVKSLDYNV-VVKADGLASGKGVIVCNTADEAIEAIDTILVKKTFGDAGNRIIVEERIDGIEASYIAL 195
                 59**************************************.********************************************************** PP

                 ECTTEEEE---BEEEEEEECCCEEEEECECEEEES-TTS-HHHHHHHHHHTHHHHHHHHHCTT---EEEEEEEEEEETTEEEEEEEESS--TTCH CS
      GARS_A 100 vdgktvkplplaqdhkrvlegDkgpnTGGmGayspapvvteellekikeeileptveglkkegipfkGvLyaglmlvedgpkvlefnvRfgDpet 194
                 +dg+t +p++++qdhkr+++gDkgpnTGGmGaysp+p++ + l +ki+++i+++t++ +k+egi fkG+Lyag+m+ ++ p+vle+n+R gDpe+
  EPA06636.1 196 CDGNTAIPMASSQDHKRIFDGDKGPNTGGMGAYSPTPIIDDILAKKIQDKIIDKTIQSMKSEGIIFKGFLYAGVMIRDNEPYVLEYNARMGDPEC 290
                 **********************************************************************************************8 PP

>> GARS_N  Phosphoribosylglycinamide synthetase, N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.3   0.0   1.1e-35   1.4e-32       2      90 .]       3      97 ..       2      97 .. 0.95

  Alignments for each domain:
  == domain 1  score: 112.3 bits;  conditional E-value: 1.1e-35
                EEEEEESSHHHHHHHHHHTTSTTESEEEEEE--CGG........TTHHHHHHHHHHCTESEEEE-SHHHHHTTHHHHHHHHHT-EEES--CCCCHHH CS
      GARS_N  2 kvLvvGsGGRehalawklaqspkvekvyvapgNagt........edlealvefakeekidlvvvGpeapLvaGvadaleeekgikvfGpskeaAqlE 90
                +vLv+GsGGRehal wkl+qs+kv+kv++apgN+gt        +dl+ l+efa+++++ ++vvGpe pL+aG++d++++  ++k+fGp+k+aAqlE
  EPA06636.1  3 NVLVIGSGGREHALSWKLSQSSKVDKVFTAPGNGGTennislnvDDLDGLAEFAQKNNC-FTVVGPEVPLAAGIVDKFNQM-NLKIFGPTKNAAQLE 97
                8***********************************9999988878889*******995.99****************666.**************9 PP

>> GARS_C  Phosphoribosylglycinamide synthetase, C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.6   0.0   6.2e-31   7.9e-28       1      80 []     326     415 ..     326     415 .. 0.98

  Alignments for each domain:
  == domain 1  score: 96.6 bits;  conditional E-value: 6.2e-31
                 EEEEEEEETTTTSS--ST-EEBS.....TTEEEEESSEE.....EEE-SSEEEEEEEEESSHHHHHHHHHHHHTTCB-TTEE--STTTHH CS
      GARS_C   1 avgvvlaskGYPgsyekgkeitg.....egvkvfhagtk.....lvtsGGRvlavvavgetleeArakayeavkkikfeglfyRkDIGar 80 
                 +v++vlas+GYP+s++k++eitg     +++++fhagtk     ++++GGRvl+v+a+g+tl+ A+++ay+a++ki+++ +++RkDIG++
  EPA06636.1 326 SVCIVLASDGYPESFPKDEEITGfdlvpKNTMIFHAGTKkkdgkILSNGGRVLGVTALGDTLSSAISNAYAAAEKISWPHKYCRKDIGKK 415
                 69**************************9999******999***********************************************85 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.0   1.5e-10   1.9e-07       2      73 ..     108     186 ..     107     215 .. 0.87

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 1.5e-10
                 HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC........GTTCEEEEE--- CS
   ATP-grasp   2 eklglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal........keekvivEefvp 73 
                 +++g++++rf + ++ ++++e +++l++ vvvK + +  +GkG  v++ ++++ +a++++        +++++ivEe+++
  EPA06636.1 108 KRNGIQTARFEIFDDPKKAKEYVKSLDYNVVVK-ADGLASGKGVIVCNTADEAIEAIDTIlvkktfgdAGNRIIVEERID 186
                 6789*****************************.566678*************99999999999**99999*******98 PP

>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.1   7.6e-10   9.7e-07       7     111 ..     103     195 ..     100     208 .. 0.90

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 7.6e-10
                  HHHHHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE--SSSTCCCTTCEEEESSHHHHHHHHHCCTTSEEE-TTS-TT-EEE--EEEEE---EC CS
  ATP-grasp_2   7 akeilakygvkvpegevaesaeeaeeaakklgekelvvKaQvlaGGRGKagGvklvkskeeakeaakellgkelvtkqtgkeGkkvekvlveealdik 104
                  ak+ ++++g++++++e+ +++++a+e +k+l+ ++ vvKa  la G+    Gv ++++++ea ea++++l k+         G   ++++vee++d  
   EPA06636.1 103 AKNFMKRNGIQTARFEIFDDPKKAKEYVKSLDYNV-VVKADGLASGK----GVIVCNTADEAIEAIDTILVKKTF-------GDAGNRIIVEERIDGI 188
                  899******************************99.****9999876....6******************99999.......99999********988 PP

                  EEEEEEE CS
  ATP-grasp_2 105 kElYlsi 111
                  +  Y+++
   EPA06636.1 189 EASYIAL 195
                  8888875 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   8.9e-09   1.1e-05      14     158 ..     110     285 ..      98     288 .. 0.72

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 8.9e-09
                  T.S---...........-EESS--SSSEEEEESS-------B--SS--TTE...................EEEE---SEEEEEEEEE.SSSEEEEEEE CS
  ATP-grasp_3  14 agvkvP.......tkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve............lvqefieGkplSvsllsdgekvlvlavn 92 
                  +g+++         k  +e +++ ++++vvK    a g++v v +  +ea +ai+++             +v e i+G ++S  +l+dg+++ ++a +
   EPA06636.1 110 NGIQTArfeifddPKKAKEYVKSLDYNVVVKADGLASGKGVIVCNTADEAIEAIDTILvkktfgdagnriIVEERIDGIEASYIALCDGNTAIPMASS 207
                  55555544444422444555666699999*999999999******9999999999887899**********************************998 PP

                  EEEEE.T.......TEEEEEEES----H...HHHHH.HHHHHHHTTST....T--EEEEEEEEESS.SEEEEEEESS- CS
  ATP-grasp_3  93 rqlie.kaeke...fvyaGnvtpietel...keevv.elaeevvekle....glaGyvGvDlvlkdeepyviEvNPRl 158
                  + +   + +++       G  +p +  +   +++++ +++ +++++++      +G++   ++++d+epyv+E N+R+
   EPA06636.1 208 QDHKRiFDGDKgpnTGGMGAYSPTPIIDdilAKKIQdKIIDKTIQSMKsegiIFKGFLYAGVMIRDNEPYVLEYNARM 285
                  876541334444554455555554443334555554145667777776653345788888999**************8 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1   2.1e-07   0.00027       3     179 ..     101     284 ..      99     290 .. 0.67
   2 ?   -2.3   0.0         2   2.6e+03     188     199 ..     344     355 ..     339     361 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.1e-07
                  HHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHHST..S-EEEEE--SSSEEEEEE CS
  CPSase_L_D2   3 esakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaafgn..kqvlvekslkgpkeiEve 98 
                    ak+ +k+ ++++++ ++   ++ ++a + +k++ y v++ka     GkG  v+++ +e +e++ + l + +  fg+  +++ ve+ ++g  e  + 
   EPA06636.1 101 IWAKNFMKRNGIQTARFEIF--DDPKKAKEYVKSLDYNVVVKADGLASGKGVIVCNTADEAIEAIDTILVKKT--FGDagNRIIVEERIDGI-EASYI 193
                  6689999*******999998..9******************************************99988885..65422899***999985.33444 PP

                  EEEETTS-EEEEEEEEECCEC......TCCCCEEEES-SS--HHHHHHHHHHHH.HHHHHHT-EEEEEEEEE...EETTTTEEEEEEEESS CS
  CPSase_L_D2  99 vlrDakgnvitvcerenslql......rtqkvievAPsqtLtdeerqalreaav.kvvrevgvvgagtvefl...ldpkskeyyviEvNtR 179
                   l D +  + +  + +            t+ +    P++ ++d   ++++ + + k++++++ +g     fl   +  +++e yv+E N+R
   EPA06636.1 194 ALCDGNTAIPMASSQDHKRIFdgdkgpNTGGMGAYSPTPIIDDILAKKIQDKIIdKTIQSMKSEGIIFKGFLyagVMIRDNEPYVLEYNAR 284
                  4555554444444444332224445556666666666666666655555554442344444444333333330013335666666666666 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2
                  HHHHS--HHHHH CS
  CPSase_L_D2 188 ekaTGldlvkea 199
                  e++TG+dlv ++
   EPA06636.1 344 EEITGFDLVPKN 355
                  89******9765 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   3.6e-07   0.00046       2     113 ..     107     216 ..     106     286 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 3.6e-07
                      HHHTT--B--EEEEETTHHCH-H-HHHHHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHTT-......SCEEEEE--ESEEEEEE CS
  Dala_Dala_lig_C   2 lkaaGlpvvpyvvlekeeakeekkellekveeelgypvfVKpareGSSvGvskveseeelkeaieeafkyd......ekvlvEeaiegreieva 89 
                      +k++G++++ +++++  ++ +e        +++l y v+VK+  + S  Gv  +++++e  eai++ + +       ++++vEe i+g e    
       EPA06636.1 107 MKRNGIQTARFEIFDDPKKAKEY-------VKSLDYNVVVKADGLASGKGVIVCNTADEAIEAIDTILVKKtfgdagNRIIVEERIDGIEASYI 193
                      89999999999999988777766.......99*******************************988654321222338********99987755 PP

                      EEETSSCEEEEEEEEE-SSSSS-H CS
  Dala_Dala_lig_C  90 vlgneklevsevgeivvkkgfydy 113
                       l ++ +++ ++   + +k ++d 
       EPA06636.1 194 ALCDG-NTAIPMASSQDHKRIFDG 216
                      55434.444455555555556665 PP

>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0     9e-07    0.0011       4      72 ..     100     175 ..      97     195 .. 0.81
   2 ?   -2.2   0.0       2.1   2.7e+03     147     168 ..     267     286 ..     262     302 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 9e-07
                 HHHHHHHHHHTT-----EEEESS-S-HHHHHHTT-.-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHH.........G CS
        RimK   4 KlkslklLakakikvpntalardeedaekliekiklrfPvvvKsvegsqGikvvlakkeqklkqvlea.........l 72 
                 K+ + + + +++i++ ++++  d+++a+++++ +     vvvK      G +v+++++ +++ + +++          
  EPA06636.1 100 KIWAKNFMKRNGIQTARFEIFDDPKKAKEYVKSL--DYNVVVKADGLASGKGVIVCNTADEAIEAIDTilvkktfgdA 175
                 6667788999*********************999..589**********************99998876544433333 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.1
                 EEEEEEEETTEEEEEEEESS-- CS
        RimK 147 aGvDllrakrgllvlEvnsspg 168
                 aGv  +  +++++vlE n+  g
  EPA06636.1 267 AGV--MIRDNEPYVLEYNARMG 286
                 555..33577899*****9876 PP

>> ATPgrasp_ST  Sugar-transfer associated ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.1   1.7e-05     0.022      20      85 ..      98     159 ..      82     187 .. 0.83
   2 ?    1.1   0.0      0.15   1.9e+02     249     267 ..     269     286 ..     243     293 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.7e-05
  ATPgrasp_ST  20 ddKlkfkelalraglkvpkllgvikeqaeiseleafvkeleegvviKpakgsgGkGilviteredq 85 
                   +K+  k++++r+g+++ +    ++  ++ ++++++vk+l+ +vv+K+    +GkG++v++  +++
   EPA06636.1  98 SSKIWAKNFMKRNGIQTAR----FEIFDDPKKAKEYVKSLDYNVVVKADGLASGKGVIVCNTADEA 159
                  5688889999999999999....6667889999*******999*****************875543 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.15
  ATPgrasp_ST 249 ivldeekgplllElNarpg 267
                  + + +++ p++lE Nar g
   EPA06636.1 269 VMIRDNE-PYVLEYNARMG 286
                  5677777.********977 PP

>> ATP-grasp_4  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0     8e-06      0.01       2      77 ..     134     199 ..     133     216 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 8e-06
  ATP-grasp_4   2 slPvviKPsvgffSlGVykinneeewkaavaaieeeleqakeeykeevveeesflvEeyieGeEfavdayfdeeGe 77 
                  +++vv+K    ++  GV+++n+++e  +a+++i      +k+++ ++   +++++vEe i+G E +  a+ d   +
   EPA06636.1 134 DYNVVVKADGLASGKGVIVCNTADEAIEAIDTIL-----VKKTFGDA---GNRIIVEERIDGIEASYIALCDG--N 199
                  699*****9999*************999999998.....56777764...889***********998888754..3 PP

>> Phage_TAC_9  Phage tail assemb.y chaperone protein, TAC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   5.3e-05     0.068      21      72 ..     122     172 ..     111     188 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.3e-05
  Phage_TAC_9  21 alkkavkLlkgvDidalakekgvaavalgailsnlGdpevkeiedlvlkyta 72 
                    kka + +k +D + + k+ g a+   g i+ n  d+++++i+ +++k+t 
   EPA06636.1 122 DPKKAKEYVKSLDYNVVVKADGLASGK-GVIVCNTADEAIEAIDTILVKKTF 172
                  568999****************99875.9*******************9985 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   4.7e-05     0.061      14      54 ..     102     142 ..      92     170 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.7e-05
  ATP-grasp_5  14 eakelleaygipvvetrlassaeeaveaaeeigypvvlKiv 54 
                   ak+ ++  gi+++++ + +++++a e++++++y vv+K +
   EPA06636.1 102 WAKNFMKRNGIQTARFEIFDDPKKAKEYVKSLDYNVVVKAD 142
                  578899999******************************75 PP

>> SR1P  SR1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00015      0.19       2      25 ..     149     172 ..     148     177 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00015
        SR1P   2 GtIvCqtCnatIdhfedekVttLY 25 
                 G+IvC t +++I+ +++  V++ +
  EPA06636.1 149 GVIVCNTADEAIEAIDTILVKKTF 172
                 9***************98887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 2763.97
//
Query:       EPA06637.1  [L=368]
Description: succinate-CoA ligase, beta subunit [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.9e-46  156.2   1.0    1.4e-45  155.3   1.0    1.4  1  ATP-grasp_2  ATP-grasp domain
      2e-15   56.9   1.5    2.5e-15   56.6   0.3    1.8  2  Ligase_CoA   CoA-ligase
    1.3e-13   50.9   0.1    4.4e-13   49.2   0.1    1.8  1  ATP-grasp_5  ATP-grasp domain
    1.6e-05   24.5   0.0    2.8e-05   23.7   0.0    1.4  1  CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP bindin
  ------ inclusion threshold ------
       0.03   13.9   0.0      0.054   13.1   0.0    1.4  1  ATP-grasp    ATP-grasp domain
      0.087   12.2   1.2       0.94    8.9   0.1    2.3  2  DUF4152      Protein of unknown function (DUF4152)


Domain annotation for each model (and alignments):
>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.3   1.0   4.8e-49   1.4e-45       2     201 ..       3     188 ..       2     189 .. 0.96

  Alignments for each domain:
  == domain 1  score: 155.3 bits;  conditional E-value: 4.8e-49
                  E-HHHHHHHHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE--SSSTCCCTTCEEEESSHHHHHHHHHCCTTSEEE-TTS-TT-EEE--EEEEE CS
  ATP-grasp_2   2 lhEyqakeilakygvkvpegevaesaeeaeeaakklgekelvvKaQvlaGGRGKagGvklvkskeeakeaakellgkelvtkqtgkeGkkvekvlvee 99 
                  l E+qake++++yg++   ++  ++ ee ++ ak+lg    v+K Qv +GGRGKagG++ +++ +e+  +  ++lg +++       G+k  ++l+e+
   EPA06637.1   3 LLEFQAKELFRQYGINLLPSKASTNIEEGRRHAKELGYPF-VIKIQVPVGGRGKAGGIQKCQNDDEFDLKYPQVLGLTIK-------GEKARAILLEK 92 
                  89***********************************998.***************************************.......*********** PP

                  ---ECEEEEEEEEEETTTTEEEEEEESSTTS-HHHHHHH-GGGEEEEEEBTTTB--HHHHHHHHHHCT--CHHHHHHHHHHHHHHHHHHHTTEEEEEE CS
  ATP-grasp_2 100 aldikkElYlsivlDraskkvvviaSseGGvdiEevaakkPekiikvaidpakglkeeqareiakklglekelvkkaakiikklyklfveldatlvEi 197
                  + dikkElYls+ l r+++++++iaS eGGv+iE v +    +ii+ +     +++e+ a+e+ak+++le+++++++++i++kl kl +e++a+l+Ei
   EPA06637.1  93 MADIKKELYLSMFLNRSKRCYTIIASPEGGVEIESVKN----QIIREV--GLGNVSEQVAKEVAKEMKLEGKAADDFVDILQKLSKLTIEKEAELAEI 184
                  ***********************************975....466654..4567899***************************************** PP

                  EEEE CS
  ATP-grasp_2 198 NPLv 201
                  NPL+
   EPA06637.1 185 NPLA 188
                  ***8 PP

>> Ligase_CoA  CoA-ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       1.1   3.4e+03      78     100 ..     133     154 ..     126     164 .. 0.70
   2 !   56.6   0.3   8.3e-19   2.5e-15       3     150 ..     247     362 ..     245     364 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.1
                 EEEEEESSSEHHHHHHHHHHHHH CS
  Ligase_CoA  78 lldivlGygahedpaaellkaik 100
                 + ++ lG   +e++a+e++k++k
  EPA06637.1 133 IREVGLG-NVSEQVAKEVAKEMK 154
                 4455566.567788888888876 PP

  == domain 2  score: 56.6 bits;  conditional E-value: 8.3e-19
                 SSHHHHHHHHHHHHHT..............T--BSEEEE-TSS--..........HHHHHHHHHHHHS-TT-SEEEEEEEESSSEHHHHHHHHHHHHHH CS
  Ligase_CoA   3 nGGtLayeamdlikealgdvasnkklknvlgseqheiidlGddaftkGrpHPmiDptkriealkklaadpevkvilldivlGygahedpaaellkaike 101
                 nG++L + ++d+++++              g++++ ++d+G++a+t          ++++eal+ + ++++vk+il+++ +G+++++ +a+++lka+ +
  EPA06637.1 247 NGAGLVMSTLDMLSDN--------------GGKPACFLDVGGGATT----------ESVYEALTLISKMSRVKGILVNLYGGIVKTTVVAEAFLKAYDD 321
                 8***************..............***************6..........******************************************* PP

                 TT...--S-EEEEEECTTHH.....HHHHHHHTTTSSEEE-SSHHHHHH CS
  Ligase_CoA 102 akaegrelpvvarvaGteadpqelseqakaleeagveiasskaqalraa 150
                       +lpv ar+ Gte +     +++k+l+ +  +i +s + a  aa
  EPA06637.1 322 KL---IDLPVYARLKGTESE-----KAKKMLKGSRTKIFDSVEDAINAA 362
                 99...***************.....99***********99999888776 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2   0.1   1.5e-16   4.4e-13      10     219 ..       3     201 ..       1     203 [. 0.85

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 1.5e-16
  ATP-grasp_5  10 LteaeakelleaygipvvetrlassaeeaveaaeeigypvvlKivspdilhKtdvgGvrlnlkdaeevraaaeeilervkekspeariegvlVqemak 107
                  L e++akel+++ygi++++++  ++ ee  + a+e+gyp v+Ki++p +  + ++gG++   ++++e   ++ ++l    +   +++ + +l+++ma+
   EPA06637.1   3 LLEFQAKELFRQYGINLLPSKASTNIEEGRRHAKELGYPFVIKIQVP-VGGRGKAGGIQK-CQNDDEFDLKYPQVLGLTIK---GEKARAILLEKMAD 95 
                  789*******************************************9.899********9.99***********9998755...78999********9 PP

  ATP-grasp_5 108 rggrElivgvt..eDpvFGpvilfGlGGtavevlkdv...avalpplnstlareliertkaskllkgvrgekkadlaaleellvrlsqLvvdlpeIre 200
                    + El ++++  + +    +i+  +GG+++e +k+     v+l  ++++ a+e         ++k+++ e  +  + ++++l++ls+L ++ +e + 
   EPA06637.1  96 -IKKELYLSMFlnRSKRCYTIIASPEGGVEIESVKNQiirEVGLGNVSEQVAKE---------VAKEMKLE-GKAADDFVDILQKLSKLTIE-KEAEL 181
                  .7777777775226777889****************933334444444444444.........44444555.567889**************.999** PP

  ATP-grasp_5 201 ldinPllveeeg.vvalDar 219
                   +inPl + ++g ++alD++
   EPA06637.1 182 AEINPLAIMQDGsLMALDGK 201
                  **********999*****87 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   9.3e-09   2.8e-05       4      95 ..       7     100 ..       5     118 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 9.3e-09
                  HHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTE....EEESSHHHHHHHHHHHHHHHHHHHSTS-EEEEE--SSSEEE CS
  CPSase_L_D2   4 sakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGm....rvarneeelaelvkkalaeakaafgnkqvlvekslkgpkei 95 
                  +ake+ ++ ++++ ps+a   +++ee  + ake+gyP +ik  + +GG+G     + ++n++e+   + + l  +      + +l+ek+ +  ke+
   EPA06637.1   7 QAKELFRQYGINLLPSKAS--TNIEEGRRHAKELGYPFVIKIQVPVGGRGKaggiQKCQNDDEFDLKYPQVLGLTIKGEKARAILLEKMADIKKEL 100
                  578899999*********9..***************************985322245899999998888888888877788888888887777765 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.8e-05     0.054       4     128 ..      15     152 ..      12     162 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.8e-05
                 TT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC............GTTCEEEEE----SEEE..EEEEEEETTC CS
   ATP-grasp   4 lglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal............keekvivEefvpfekEl..svlvvrsaeG 88 
                  g+++ +  a ++ ee ++ a+elg+p+v+K  ++   G+G+    ++ + ++ ++              k++ +++E++++ +kEl  s+   rs++ 
  EPA06637.1  15 YGINLLPSKASTNIEEGRRHAKELGYPFVIK-IQVPVGGRGKAGGIQKCQNDDEFDLKypqvlgltikgeKARAILLEKMADIKKELylSMFLNRSKRC 112
                 56667777777888999999***********.777788888764333333333333222466899999999999************6447888888888 PP

                 -EEE--EEEEEEETTEEEEEEECEE-SCHHHHHHHHHHHH CS
   ATP-grasp  89 etafypvvetvqedgilrlsvapaevsekaqkkaeeiakk 128
                  t +  + + v+ + + ++ +    + +  ++ a+e+ak+
  EPA06637.1 113 YTIIASPEGGVEIESVKNQIIREVGLGNVSEQVAKEVAKE 152
                 8888888777777777777777776666666666666654 PP

>> DUF4152  Protein of unknown function (DUF4152)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.1   0.00031      0.94      57     117 ..      95     154 ..      84     173 .. 0.88
   2 ?    1.8   0.1     0.044   1.3e+02     134     202 ..     288     358 ..     273     366 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00031
                 HHHHHHHHHHHHHHHH--SEEEESS-SSS-BGGG--HHHHHTSSS-HHHHHHHHHHHHHHH CS
     DUF4152  57 airdevllavelarkvkpdvvhldstlggielrkldeptiealgisdkgkevwkelskdlq 117
                  i+ e +l++ l r  +   + + s  gg+e+  + +  i  +g+ +   +v ke++k+++
  EPA06637.1  95 DIKKELYLSMFLNRSKRCYTI-IASPEGGVEIESVKNQIIREVGLGNVSEQVAKEVAKEMK 154
                 5899********998777666.78999******************************9986 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.044
                 -GGG-.HHHHHHHHHHHHHHHHHHHCTT.TTSSEEEEEESTTEEEEEETTEEEEEES-GGGTS-EEEEE-- CS
     DUF4152 134 igkss.vpvriaeiyagiysakwaieyv.ekegkllvglprymevdikdgkiigesldpregglygkievs 202
                 i k+s v   + ++y gi  +    e   +     l+ lp y +++  + +   + l      ++ ++e +
  EPA06637.1 288 ISKMSrVKGILVNLYGGIVKTTVVAEAFlKAYDDKLIDLPVYARLKGTESEKAKKMLKGSRTKIFDSVEDA 358
                 45544245556789999988877777651555788999****99999999999999999888888888854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 2086.53
//
Query:       EPA06638.1  [L=115]
Description: hypothetical protein BG20_I1530 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-06   27.8   0.0    2.9e-06   27.3   0.0    1.2  1  ABM       Antibiotic biosynthesis monooxygenase
  ------ inclusion threshold ------
      0.021   15.2   0.0       0.03   14.7   0.0    1.3  1  DUF1330   Domain of unknown function (DUF1330)


Domain annotation for each model (and alignments):
>> ABM  Antibiotic biosynthesis monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   3.2e-10   2.9e-06       1      76 [.      22      94 ..      22      96 .. 0.93

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 3.2e-10
                CEEEEEEEEESTTGHHHHHHHHHHHHHHHHHTSTTEEEEEEEEEETSTTEEEEEEEESSHHHHHHHHTSHHHHHHH CS
         ABM  1 mviviaeirvkpgqaeafldafaeavesllaeepGclgyellrstedpdevvvieeWeseaaleahlksphfkaah 76
                m++vi  i++k+++ ++f + f e ++ ++++ +G+   +ll+ +++++   v+ e+e+ + + + +ksp++++ h
  EPA06638.1 22 MFVVISDIKIKSDSVDDFKKWFSESNK-IVSKFDGFVNRRLLETSDGKH--RVLVEFENLDKFSQMHKSPEHEKLH 94
                9**************************.559************888888..66779*****************988 PP

>> DUF1330  Domain of unknown function (DUF1330)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   3.3e-06      0.03      42      81 ..      60      98 ..      25     103 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.3e-06
     DUF1330 42 evlEGdeeptrlvvieFpsveaarawyeSpeYqaakalRq 81
                + lE  ++ ++ v++eF++++++ ++++Spe +++ +  +
  EPA06638.1 60 RLLET-SDGKHRVLVEFENLDKFSQMHKSPEHEKLHSTAA 98
                46777.788999********************99887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       739  (0.0412181); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.34s 00:00:00.94 Elapsed: 00:00:00.55
# Mc/sec: 627.33
//
Query:       EPA06639.1  [L=53]
Description: hypothetical protein BG20_I1533, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.33s 00:00:00.82 Elapsed: 00:00:00.52
# Mc/sec: 309.23
//
Query:       EPA06640.1  [L=287]
Description: tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-58  197.1   1.0    1.7e-58  196.5   1.0    1.3  1  THF_DHG_CYH_C    Tetrahydrofolate dehydrogenase/cyclohydrolas
    8.9e-39  132.4   0.7    8.9e-39  132.4   0.7    1.6  2  THF_DHG_CYH      Tetrahydrofolate dehydrogenase/cyclohydrolas
     0.0016   17.8   1.1     0.0018   17.6   0.1    1.6  2  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
     0.0059   16.9   0.1      0.011   16.0   0.1    1.5  1  Hydrolase        haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.084   13.1   0.1       0.28   11.4   0.0    1.9  2  DUF1884          Domain of unknown function (DUF1884)
       0.13   12.7   0.0       0.25   11.8   0.0    1.7  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
       0.18   12.1   2.0       0.32   11.2   0.1    2.3  3  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma


Domain annotation for each model (and alignments):
>> THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.5   1.0   6.5e-62   1.7e-58       2     157 ..     124     280 ..     123     283 .. 0.97

  Alignments for each domain:
  == domain 1  score: 196.5 bits;  conditional E-value: 6.5e-62
                    HHHHHHHHTT--SS--HHHHHHHHHHHHCT---TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTSCCHHHHHCCSSEEEE-SS-TT..-B-G CS
  THF_DHG_CYH_C   2 plnlgrlvkgeeallpctpkgvvellketgielegkkvvvvGrsnivgkplallLleknatVtvchsktkdlaeitreadivvvavGkpe..lika 95 
                    p n+g l++++ al++ctp gv+e+ + ++i legk+vv ++rsn+vgkpl  lLl+++atV +chsktk+++e+++ adi+++avG  +   +++
     EPA06640.1 124 PHNAGLLAMKKAALVACTPSGVMEMFDYHNIALEGKTVVLINRSNLVGKPLYHLLLARDATVITCHSKTKNIKEMCQMADIIITAVGDRNkfTLTQ 219
                    78*************************************************************************************87744689* PP

                    GGS-TT-EEEE---EEC-TTEEE-SB-HHHHCTTSSEE--TTTSCHHHHHHHHHHHHHHHHH CS
  THF_DHG_CYH_C  96 emvkegavviDvGinrvekgklvGDvdfeevkevasaitPvpgGVGpmTvamllkntleaak 157
                    +m+k++a+viDv i+r  ++kl+GD d+e++ ++as+ tPvpgGVGpmTvamllknt++aa+
     EPA06640.1 220 DMIKKDAIVIDVAISRY-EEKLSGDSDYEQIIQKASYATPVPGGVGPMTVAMLLKNTITAAS 280
                    *****************.****************************************9986 PP

>> THF_DHG_CYH  Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.4   0.7   3.5e-42   8.9e-39       2     116 .]       6     120 ..       5     120 .. 0.99
   2 ?   -2.3   0.1       2.1   5.4e+03      31      63 ..     204     236 ..     186     259 .. 0.54

  Alignments for each domain:
  == domain 1  score: 132.4 bits;  conditional E-value: 3.5e-42
                  --HHHHHHHHHHHHHHHHHHHHHHT---EEEEEEES--HHHHHHHHHHHHHHHHTT-EEEEEEE-TT--HHHHHHHHHHHHH-TT--EEEE-SS-STT CS
  THF_DHG_CYH   2 ldGkalakeireelkeeveklkekgvkpkLavilvgddpasevYvrnkkkaceevGieseliklpedvseeellklieelneddsvdGilvqlPlpkh 99 
                  +dG ++ak++++++++ v++lk++g++p+La+ilvgd++as++Yvrnk+kaceevGi ++ +kl +++++ el k+i +ln+d+sv+GilvqlPlp++
   EPA06640.1   6 IDGIEIAKNVKDRVRKAVDELKKQGINPCLATILVGDNQASATYVRNKHKACEEVGIATKDFKLAANTTQLELNKIITDLNNDKSVHGILVQLPLPSQ 103
                  89************************************************************************************************ PP

                  S-HHHHHCCS-GGGBTT CS
  THF_DHG_CYH 100 idekaileaispeKDVD 116
                  +de a +++isp KDVD
   EPA06640.1 104 LDEFATTSRISPLKDVD 120
                  ****************9 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.1
                  EEEEEES--HHHHHHHHHHHHHHHHTT-EEEEE CS
  THF_DHG_CYH  31 LavilvgddpasevYvrnkkkaceevGieseli 63 
                  + +  vgd+++ ++  ++ kk +  +++ ++ +
   EPA06640.1 204 IIITAVGDRNKFTLTQDMIKKDAIVIDVAISRY 236
                  444445555555555555555555555554444 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       1.5   3.9e+03     168     195 ..      44      71 ..      42      83 .. 0.67
   2 !   17.6   0.1   6.9e-07    0.0018      75     130 ..     185     234 ..     134     241 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.5
                  HHHHHHHHHHHHHHHHHC.HHHTCCHHHC CS
  AlaDh_PNT_C 168 tasalltnntlpyleell.adkglkkalk 195
                  +asa + +n  +  ee+  a k++ k+  
   EPA06640.1  44 QASATYVRNKHKACEEVGiATKDF-KLAA 71 
                  788888888888888887666666.3333 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 6.9e-07
                  CEEHCHHHHHHHHHHHH-SEEEE---BTTSS---SC-HHHHHTS-TTEEEEETTGG CS
  AlaDh_PNT_C  75 vevlksqeellaeavkeadvvigtvlipGkkaPkLvteemvksMkpgsVivDvAid 130
                  v + +s+ ++++e ++ ad++i++v   G +    +t++m+   k+ ++++DvAi+
   EPA06640.1 185 VITCHSKTKNIKEMCQMADIIITAV---GDRNKFTLTQDMI---KKDAIVIDVAIS 234
                  4558999*****************6...99999999***98...68********96 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   4.4e-06     0.011     111     156 ..       9      55 ..       5     103 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.4e-06
                 HHHHHTHHBHTTHHHHHHHHHHTTEEEEEEE...SSEHHHHHHHHHHTT CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxx RF
   Hydrolase 111 ftiadplkvkpeaaeavasLkaagievvllt...gdnpetaeraanqlG 156
                 ++ia +  vk+ +++av +Lk++gi+ +l+t   gdn++ a  + n+  
  EPA06640.1   9 IEIAKN--VKDRVRKAVDELKKQGINPCLATilvGDNQASATYVRNKHK 55 
                 678889..******************99999999****88887777655 PP

>> DUF1884  Domain of unknown function (DUF1884)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00011      0.28       6      43 ..      14      55 ..       9      86 .. 0.76
   2 ?   -2.1   0.0       1.9   4.9e+03      68      75 ..     224     231 ..     216     240 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
                HHHHHHHHHHHHHHHTT----E..EEE-HHH..HHHHHHHHH CS
     DUF1884  6 rilevieekineLkleGfePdi..iLvGkea..ieflkealk 43
                ++++ + ++++eLk++G++P +  iLvG +     +++++ k
  EPA06640.1 14 NVKDRVRKAVDELKKQGINPCLatILVGDNQasATYVRNKHK 55
                78999***************6433999975411567777665 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.9
                 TEEEEE-T CS
     DUF1884  68 gDavvvDs 75 
                 +Da+v+D 
  EPA06640.1 224 KDAIVIDV 231
                 69999996 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   9.6e-05      0.25      28      97 ..     161     232 ..     137     274 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.6e-05
                     EEEEESTTTTTSBHHHHSG.GGTTTECEBEEEGGGGGC.TT-SEEEE-SCHHHHHHHHHHHHHTTSEEEESS CS
  Semialdhyde_dh  28 vvllsssrsaGkklaeavk.aleegkdlkvedvdeeel.kevdivflalpagvskelapklaeagvkviDls 97 
                     vvl+ +s+  Gk+l  +     +++ +   ++ +++e+ + +di+++a++      l++++++++++viD +
      EPA06640.1 161 VVLINRSNLVGKPLYHLLLaRDATVITCHSKTKNIKEMcQMADIIITAVGDRNKFTLTQDMIKKDAIVIDVA 232
                     56666677777777777663222222233333445555599*****************************87 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       4.4   1.1e+04      29      47 ..      11      29 ..       8      37 .. 0.57
   2 ?   -1.3   0.1      0.95   2.4e+03      27      61 ..      60      90 ..      43      97 .. 0.51
   3 ?   11.2   0.1   0.00013      0.32       9      81 ..     170     236 ..     167     249 .. 0.60

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 4.4
                     EEESSHHHHHHHHCHHTTT CS
  Sacchrp_dh_NADP 29 vadrskeklealaakalgv 47
                     +a   k+++++++++++++
       EPA06640.1 11 IAKNVKDRVRKAVDELKKQ 29
                     5555555555555555444 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.95
                     EEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHH CS
  Sacchrp_dh_NADP 27 itvadrskeklealaakalgvrfeaialdaenyea 61
                     + +a+++ +    laa++++ ++++i  d +n+++
       EPA06640.1 60 VGIATKDFK----LAANTTQLELNKIITDLNNDKS 90
                     333333332....3333355555666666665555 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.00013
                      HHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-SSGGG CS
  Sacchrp_dh_NADP   9 vGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnlsppis 81 
                      vG+++ +ll++++      ++ + sk+k  ++++  +  +++++a+   n+  +++ ++k+  +v++++ + +
       EPA06640.1 170 VGKPLYHLLLARDAT----VITCHSKTK--NIKEMCQMADIIITAVGDRNKFTLTQDMIKKDAIVIDVAISRY 236
                      667777777666654....444444444..3333335566666666666666667777777777777766544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       740  (0.0412739); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 1857.45
//
Query:       EPA06641.1  [L=109]
Description: hypothetical protein BG20_I1524 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0018   18.2   0.5     0.0064   16.5   0.5    1.8  1  PH_18      Pleckstrin homology domain
  ------ inclusion threshold ------
      0.035   13.7   0.0       0.04   13.5   0.0    1.0  1  DeoC       DeoC/LacD family aldolase
       0.05   13.7   0.0      0.063   13.4   0.0    1.2  1  tRNA_bind  Putative tRNA binding domain


Domain annotation for each model (and alignments):
>> PH_18  Pleckstrin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.5   1.1e-06    0.0064      78     131 ..      33     108 ..      24     109 .] 0.80

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.1e-06
       PH_18  78 livy.dekeedskkkdpiliqlNkdlvkkqlkkkg..lleaeaedf...................ekiidylrrQa 131
                 +i y ++ ee++++ + i+++l kd v +ql+++g  l+++  ++f                     +id+l+ Q+
  EPA06641.1  33 IILYrQTLEEEEESYEEIVCTLTKDYVIEQLVTSGgvLVPSFHQQFvftieefpqellrksrdrfLMVIDFLEEQL 108
                 456634558899999****************999843445555688999999999999999999877999999986 PP

>> DeoC  DeoC/LacD family aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   6.6e-06      0.04     147     208 ..       6      72 ..       1      85 [. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.6e-06
                 TCHHHHHHHHHHHHTCCT-SEE.EE--S.....SCC.B.HHHHHHHHHHHHHCHSSTEEEEETTSSHH CS
        DeoC 147 kvdpdlvaeAarvsaelGaDii.Kvevp.....kevvnateedaevfkdvikaapvpgvvlsGGvsee 208
                 ++d++ +++ + +  + G+Di+ K++ p     ++  +++e  +e+ ++++k+  ++ +v sGGv   
  EPA06641.1   6 SLDAWQIQHLMDLL-KKGSDIVaKTNKPiilyrQTLEEEEESYEEIVCTLTKDYVIEQLVTSGGVLVP 72 
                 47999999999986.559**988*******9987777788888999******************9333 PP

>> tRNA_bind  Putative tRNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0     1e-05     0.063      18      59 ..      35      76 ..      25      92 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1e-05
                EEEEEEEESSSSEEEEEESCTTTSTHHHHTTEEEEEETTSES CS
   tRNA_bind 18 LlvlkvdvGeeeprqivsgaknvyepeelvakkvvvvanlkp 59
                L++ +++  ee++ +iv+ +++ y  e+lv   +v+v+++  
  EPA06641.1 35 LYRQTLEEEEESYEEIVCTLTKDYVIEQLVTSGGVLVPSFHQ 76
                777788888999*************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.34u 0.21s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 902.35
//
Query:       EPA06642.1  [L=82]
Description: hypothetical protein BG20_I1521 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       957  (0.0533772); expected 358.6 (0.02)
Passed bias filter:                      622  (0.0346924); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 531.64
//
Query:       EPA06643.1  [L=189]
Description: 5-formyltetrahydrofolate cyclo-ligase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-39  135.5   0.0    2.1e-39  135.3   0.0    1.0  1  5-FTHF_cyc-lig  5-formyltetrahydrofolate cyclo-ligase family


Domain annotation for each model (and alignments):
>> 5-FTHF_cyc-lig  5-formyltetrahydrofolate cyclo-ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.3   0.0   1.2e-43   2.1e-39       1     187 []       7     179 ..       7     179 .. 0.97

  Alignments for each domain:
  == domain 1  score: 135.3 bits;  conditional E-value: 1.2e-43
                     HHHHHHHHHHHHHTS-HHHHHHHHHHHHHHHHTSHHHHH-SEEEE----TTS---HHHHHHHHHTTEEEEEEEECSSCTEECEEEEEECCCCCCC CS
  5-FTHF_cyc-lig   1 KqelRkqllaalralseeevaaesealsqrieslkesqeakrvalyvsvkgeidtkelikklleegkevllPrvrlesgslkvvrlttlkeedsl 95 
                     K++lRk ll++++a s + ++  ++++++++++++ +++a+++ +y++++ e+ t+ +i+++l+egk+v+lP+v  ++      ++ + ++ ++l
      EPA06643.1   7 KASLRKLLLEKRDATSFDLMNILAKSIQKKLKKIESYRQAQKIGAYYPIGSEVHTQDIIQEVLSEGKQVFLPKVIGKN-----IEFRKIESFSNL 96 
                     789************************************************************************999.....89999******* PP

                     CCHCTSSCE--TTECCBCGGGG-SEEEE--SEEETTS-EE-SSTTHHHHHHHHHTST-SS--EEEEE--GGGEES-----ST----SEEE-S CS
  5-FTHF_cyc-lig  96 esgkyglkePeeeeerelalekldlvlvPgvAfdkeGaRlGkGkGyyDrflarlkggagdkpltvglaldeqlverlPleehDvpvdevvte 187
                     e+g++ ++eP+ee ++ +   kld++lvP v+++ +G+RlG+G G+yDrfla+ k        t++l++++q+++++P+++hDv +d +v e
      EPA06643.1  97 ENGSFDIMEPKEECPKDN---KLDILLVPTVGISPKGVRLGYGHGFYDRFLAENKI------ETISLIFEKQIIKNIPRSDHDVTIDWIVSE 179
                     ***************866...8*******************************999......9**************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1158.71
//
Query:       EPA06644.1  [L=195]
Description: ferritin-like protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-21   76.0   0.0    3.8e-21   75.5   0.0    1.2  1  Ferritin  Ferritin-like domain


Domain annotation for each model (and alignments):
>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.5   0.0   2.1e-25   3.8e-21       3     135 ..      28     165 ..      24     168 .. 0.91

  Alignments for each domain:
  == domain 1  score: 75.5 bits;  conditional E-value: 2.1e-25
                 HHHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHH......C-SSSSCSSHHHHHHHHHHHHHHH CS
    Ferritin   3 aLneqladeltaayqylamawyvkgpgleglaeffdeqaeeerehadklaerilalGgtpvltraelee......ieapkefgsveevleaalehekkv 95 
                  L +  + e+ta+y++ ++ +++ g + egl+  +++   e + h++ ++eri +lGg  + +  e+ +      ++ p + ++ +++le++l++e+ +
  EPA06644.1  28 ELIKNASVEFTAYYYFTNLRAHCTGLEGEGLKGIIEDARLEDLSHFESCLERIYQLGGALPNDATEFIKmsgcefLQLPANPTDHKAILEKCLKAEQGA 126
                 566677889*************************************************99999999999999997444555569*************** PP

                 HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHH CS
    Ferritin  96 teslrelielaeeegDpatadfledfleeqeeheweleal 135
                 + + +++++++  + Dpat+d+++d+l+e+ ehe ++ +l
  EPA06644.1 127 IVNWNKICQMTLGK-DPATYDIAKDILAEEIEHESWFLEL 165
                 ************96.*********************9776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1239.00
//
Query:       EPA06645.1  [L=77]
Description: cupin domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.7e-09   35.8   0.0      5e-09   35.7   0.0    1.0  1  Cupin_2        Cupin domain
    9.6e-06   25.7   0.0      1e-05   25.6   0.0    1.0  1  CENP-C_C       Mif2/CENP-C like
      0.001   19.0   0.0     0.0011   18.9   0.0    1.1  1  AraC_binding   AraC-like ligand binding domain
  ------ inclusion threshold ------
      0.014   15.1   0.1      0.019   14.6   0.1    1.3  1  3-HAO          3-hydroxyanthranilic acid dioxygenase
      0.026   14.7   0.0       0.03   14.5   0.0    1.1  1  Ectoine_synth  Ectoine synthase
      0.037   14.4   0.0      0.045   14.1   0.0    1.0  1  Pirin_C        Pirin C-terminal cupin domain
      0.094   12.4   0.0      0.098   12.3   0.0    1.2  1  Auxin_BP       Auxin binding protein


Domain annotation for each model (and alignments):
>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.0     2e-12     5e-09       2      66 ..       5      68 ..       4      73 .. 0.90

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 2e-12
                EEEEETTEEEEEECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS-EE CS
     Cupin_2  2 lvelppGesapshrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgdepar 66
                + +l+pGe+  ++ H+   e++y+++G g l++ + ++++++  ++++ +++pH f+ +++e  +
  EPA06645.1  5 VLVLQPGEKDTQEPHDSD-EVYYIIKGDGFLKIKDTDYPISENKMYFVGSKVPHFFHGNSKELIV 68
                6789*************8.*************************************988876444 PP

>> CENP-C_C  Mif2/CENP-C like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   4.1e-09     1e-05      12      83 ..       1      71 [.       1      73 [. 0.92

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 4.1e-09
                -EEEEEEE-TCCCEEEEE--SEEEEEEEEESEEEEEETTEEEEEETT-EEEE-TT-EEEEEE-SSS-EEEEE CS
    CENP-C_C 12 lasGilkLppgaeKkkknskkatlvFyViqGrvevtvsktsfvigkgsvFqvPagneysieNklnkeaklfF 83
                +a+G+l L+pg eK +++ ++   v+y+i+G+   ++++t + i++ +++ v +     ++ ++++  +l+F
  EPA06645.1  1 MAAGVLVLQPG-EKDTQEPHDSDEVYYIIKGDGFLKIKDTDYPISENKMYFVGSKVPHFFHGNSKELIVLYF 71
                89*******97.6999************************************99988888888888888887 PP

>> AraC_binding  AraC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   4.2e-07    0.0011      18      64 ..      16      62 ..       9      75 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 4.2e-07
                  EETT-SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS-EEEEE- CS
  AraC_binding 18 phvhdeyvihyvteGtgrlrlngrtydlgpGdlfLlppgepHdyesd 64
                  +  hd  ++ y+++G g l++++  y ++++ + ++   +pH+++  
    EPA06645.1 16 QEPHDSDEVYYIIKGDGFLKIKDTDYPISENKMYFVGSKVPHFFHGN 62
                  6789999************************************9965 PP

>> 3-HAO  3-hydroxyanthranilic acid dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   7.3e-06     0.019      42      94 ..      10      58 ..       4      70 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 7.3e-06
                SB--S-EEE-SS-EEEEEEES-EEEEEEETTCCCEEEE-TTEEEEE-TT--EE CS
       3-HAO 42 PnerkdyhleegeeffyqkkGdmvlkvldegkardivireGeifllParvphs 94
                P e+     ++++e++y  kGd  lk+ d     d +i e +++++ ++vph 
  EPA06645.1 10 PGEKDTQEPHDSDEVYYIIKGDGFLKIKD----TDYPISENKMYFVGSKVPHF 58
                5555566667899*************987....599****************5 PP

>> Ectoine_synth  Ectoine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.2e-05      0.03      56     107 ..      22      72 ..       5      76 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.2e-05
                    EEEEEEEE--EEEEETTT--EEEE-TTEEEEETTT-EEEEEESS.-EEEEEEE CS
  Ectoine_synth  56 leavycieGegeveeledgevyeikpgtlYlldkhdkHllrakk.elrlvcvF 107
                     e  y+i+G+g ++ +  ++ y+i+++++Y + ++  H  ++++ el ++  F
     EPA06645.1  22 DEVYYIIKGDGFLKIK--DTDYPISENKMYFVGSKVPHFFHGNSkELIVLYFF 72 
                    57889******99987..578*******************9988688887777 PP

>> Pirin_C  Pirin C-terminal cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.8e-05     0.045       6      72 ..       8      75 ..       5      76 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.8e-05
                E-TT-EEEEE--TT-EEEEEEEES-E..EESSTTEEE-TTEEEEE-SSSEEEEE--SS-EEEEEEEE-- CS
     Pirin_C  6 leagaelelplpegleaavyvleGel..evggerseieeeqlavlgdgdslvvkaeekgarvlLlaGeP 72
                l++g++ +++ p++ + + y+++G++  ++++++ +i+e+++  +g++   +++ ++k++ vl + G P
  EPA06645.1  8 LQPGEKDTQE-PHDSDEVYYIIKGDGflKIKDTDYPISENKMYFVGSKVPHFFHGNSKELIVLYFFGGP 75
                8999999999.9**********999655999999************99999999999999999888866 PP

>> Auxin_BP  Auxin binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   3.8e-05     0.098      51      89 ..       8      44 ..       3      68 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.8e-05
                E-TT-B--EEEESS-EEEEEEE--EEEEE--SSSSS--S CS
    Auxin_BP 51 lapgsrtpihrhsceevfvvlkgkgtlylasssskypgk 89
                l pg++     h  +ev+ ++kg+g l + ++  +yp  
  EPA06645.1  8 LQPGEKDTQEPHDSDEVYYIIKGDGFLKIKDT--DYPIS 44
                789**********************9998776..45544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.45
# Mc/sec: 519.40
//
Query:       EPA06646.1  [L=1065]
Description: isoleucine--tRNA ligase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   1.6e-137  459.3   0.2   2.4e-137  458.8   0.2    1.2  1  tRNA-synt_1   tRNA synthetases class I (I, L, M and V)
      8e-32  110.3   1.0    2.1e-31  109.0   1.0    1.7  1  Anticodon_1   Anticodon-binding domain of tRNA
    8.9e-25   87.3   0.1    1.4e-10   40.5   0.0    3.7  4  tRNA-synt_1g  tRNA synthetases class I (M)
    4.4e-06   26.3   0.0    0.00013   21.4   0.0    2.5  2  tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
    0.00087   18.3   0.4     0.0044   16.0   0.0    2.4  3  tRNA-synt_1f  tRNA synthetases class I (K)
  ------ inclusion threshold ------
      0.068   13.8   1.1       0.91   10.1   0.1    3.0  2  POTRA         Surface antigen variable number repeat
       0.21   10.5   0.0        0.4    9.6   0.0    1.4  1  DUF4438       Domain of unknown function (DUF4438)
        2.6    8.0   4.6        1.1    9.2   1.1    2.3  2  UL11          Membrane-associated tegument protein


Domain annotation for each model (and alignments):
>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  458.8   0.2  1.1e-140  2.4e-137      20     596 ..      33     633 ..      23     639 .. 0.93

  Alignments for each domain:
  == domain 1  score: 458.8 bits;  conditional E-value: 1.1e-140
  tRNA-synt_1  20 kekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieakvekklgakekke..rkklgreefrekvrewkaeyaeei 115
                  ++ ++ +++ gPP  +G +H Gh   +++kd+  r+++++Gk+ ++  GwD+ Gl++e + ek+lg +++k+   +k+g e+ +e+++ +++++  ++
   EPA06646.1  33 DKPEKIMFIEGPPTMNGIPHAGHLRGRVIKDLWYRFNTLQGKKITFNGGWDTQGLPVELQAEKELGVTGGKSevIEKVGIEKLVEECKRIVKKFNTKW 130
                  445678999**********************************************************998762258********************** PP

  tRNA-synt_1 116 rkqvkrlGvsvDfdreylTldkeleeavkevfvrladkgliyrgkklvnwstklktalselEv..eykdkkdalihvafpladkeevklviaTTtPeT 211
                   +  + lG+s+ +++ y T  +e+ e  ++v+++ +++ ++ +   ++ ++++++t+ls +Ev   y+++kd++++ + +l d+++ +l+++TT P T
   EPA06646.1 131 VEVDELLGMSFNHNKAYWTYRDEFIEREWQVLKKAHENKILEEDFTVIAYCPSCQTSLSHAEVnqGYEEVKDPSLYYKVKLRDEDA-YLIVWTTMPFT 227
                  ***************************************************************7669**************99999.*********** PP

  tRNA-synt_1 212 llgdtavavnpeldyv...itkeklilaeallkslvkke.sek.kiledergkeLegkevelpl............vnrkipiiaddyvdkeaGtGvV 292
                  l++d  v +np++dy+   +++e++++ +++l++l+k+  +e  +i ++++g+e+egk++++pl            +n+  + +++++v+  +G+G+V
   EPA06646.1 228 LVTDAMVGLNPDEDYAyvkVENETWVVGKTRLEELFKEInVEGyEIIKTVKGSEFEGKKYIHPLlnlipgldecakENNFHVAVSEEFVEITTGSGLV 325
                  ***************999999****************9974445*******************************76666677999************ PP

  tRNA-synt_1 293 kiaPahdedDyevgkkynlevinildedgtlteeaaefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkpiiyrateqWfvrvkelada 390
                  +++Pa +e+D ++++k +++v ++++++ ++t  a+++eg+ v da++++ve+lke + l+k+ ki+h++p+c+rs++pi+  a + Wf ++++l+++
   EPA06646.1 326 HLSPANGEEDIKIANKRKVKVFSPINDQVKFTSLAGKYEGMFVRDADRIIVEDLKECNGLVKIGKIKHKYPLCWRSHHPIVWLARKGWFYKLDRLEEK 423
                  ************************************************************************************************** PP

  tRNA-synt_1 391 alkavekvqfvpkskekryaswleniqdWciSRqrwWGhriplfvsketeevv.vreelkelvagreeeeaekkalekeakdkl.....kkekgelek 482
                  a++a e+v++  ++ ++r+  ++++++ WciSR+r+WG ++p+++  +  +   + + ++ ++ + +  ++ + +l++  +d++     +++  + ++
   EPA06646.1 424 AINAAENVEYFFEQPKNRFLGIIKERHPWCISRERIWGCPLPVWICGDCRKQNwFFTRKEIIASAAKLPDGPNFELHRPWIDNItikckHCNSTNTKR 521
                  ********************************************987755443033344444555678899999999999999999887788899999 PP

  tRNA-synt_1 483 dedvlDvWFsSgswpfstlgypeedteelkkffpadmlleGlDiirgWvarlillslaltgse..PfkevlvhglvrdeeGrKmSKslgNvidpldvi 578
                  +e vlD+W +Sgs p+s+l       ee++k  pa +++eG+D++rgW ++l++  + l++    Pf++ l +g v+de+G KmSKslgNvid  +++
   EPA06646.1 522 EEYVLDTWHNSGSAPYSSLT-----DEEYSKSIPAPFFTEGIDQTRGWAYTLLIENVILNNGPvaPFRSFLFQGHVLDEKGGKMSKSLGNVIDGAELL 614
                  *******************9.....679999**************************99986556********************************* PP

  tRNA-synt_1 579 kkygadalRltli.lsdvg 596
                  +ky +d +R++ i +++  
   EPA06646.1 615 EKYPVDLIRFYFIwKASPI 633
                  ***********99776655 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.0   1.0   9.2e-35   2.1e-31       1     149 [.     689     837 ..     689     840 .. 0.91

  Alignments for each domain:
  == domain 1  score: 109.0 bits;  conditional E-value: 9.2e-35
  Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedk..ra.aqevllevletllrllaPfmPfitEelwqreeee 95 
                  d w+ls+l+kl+k++te  e ++f++aa+a+ +f++n+l++ y+ +++ +l++e++++k  r  +++vl +vl+tl +l++P +Pf++E+l+q   + 
   EPA06646.1 689 DIWLLSKLQKLIKKITERNEACKFHEAAKAVDDFVINNLSQIYIPITRGELWDEDESKKnrRLaIYAVLSDVLKTLDILIHPLCPFTSEYLYQ---TI 783
                  67****************************************************998889555566**************************5...55 PP

  Anticodon_1  96 lgkkesimlaewpe.kaeel..ekeleeeevellkeivkairklrselkikpsselk 149
                  +++k+si+l +wp+ ++  +  ++e+ ee+++++k+iv++  ++r + k+k++++l+
   EPA06646.1 784 FNGKKSILLDKWPQyQE--NlvNEEI-EESFDIMKDIVSISAAARMKGKLKRRWPLN 837
                  5999*********6554..4447777.99**********************999976 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.5   0.0   6.3e-14   1.4e-10      10     146 ..      47     188 ..      43     205 .. 0.80
   2 !    9.2   0.1    0.0002      0.46     176     238 ..     405     465 ..     380     479 .. 0.82
   3 !   32.9   0.0   1.3e-11   2.8e-08     320     383 ..     592     654 ..     573     659 .. 0.85
   4 ?   -4.0   0.1         2   4.5e+03     187     227 ..     692     732 ..     666     737 .. 0.75

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 6.3e-14
                   -SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHT.TS-HHHHHHHHHHHHHHHHHHTT---SEEEETTSHHHHHHHHHHHH CS
  tRNA-synt_1g  10 angklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAeke.gvtpeelvekvheeikelfkklnisfdkygrttseehkelvqeifk 105
                   +ng +H Ghl+  ++ D ++R++ l+g++++f +g D+ G p+el+Aeke gvt  +     +  i++l ++++    k+++   e ++ l  ++ +
    EPA06646.1  47 MNGIPHAGHLRGRVIKDLWYRFNTLQGKKITFNGGWDTQGLPVELQAEKElGVTGGKSEVIEKVGIEKLVEECKRIVKKFNTKWVEVDELLGMSFNH 143
                   79*********************************************98758887665555555677888888888888887777777666666543 PP

                   ...HHHHTT-EEEEEEEEEEETTTTEEE-GGG.-EE........- CS
  tRNA-synt_1g 106 ...klkekgliyekeieqlycpkderflpdry.vegtCPkcksee 146
                       ++ ++++ e+e+++l   ++++ l + + v   CP c+++ 
    EPA06646.1 144 nkaYWTYRDEFIEREWQVLKKAHENKILEEDFtVIAYCPSCQTSL 188
                   111577899999999999999999999988776889999999764 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0002
                   .EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS-SSS-EET CS
  tRNA-synt_1g 176 pevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlaisrdldwGipvP 238
                    ++  ++ +f+kl+++e+k  +   e+ +   e+ k+  + ++ke  ++++isr+  wG p+P
    EPA06646.1 405 IVWLARKGWFYKLDRLEEKAINAA-ENVEYFFEQPKNRFLGIIKE-RHPWCISRERIWGCPLP 465
                   45556899***********99988.777678999999999***99.8**************99 PP

  == domain 3  score: 32.9 bits;  conditional E-value: 1.3e-11
                   -EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HHHHHHHHHHHCCCHH CS
  tRNA-synt_1g 320 yltvegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfswedfvervNseLadkl 383
                    l  +g+K+SkS g+v++  e+le++++dl+R+y++ +a+  + l+fs+e+++ r  + + ++l
    EPA06646.1 592 VLDEKGGKMSKSLGNVIDGAELLEKYPVDLIRFYFIWKASPIEPLSFSTEELMSRPYQ-VLNTL 654
                   456789**********************************************998644.34455 PP

  == domain 4  score: -4.0 bits;  conditional E-value: 2
                   -GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE- CS
  tRNA-synt_1g 187 klskfekklkewieeeekeleenvkkivkewlkegLkdlai 227
                    lsk++k +k+ +e++e+ + +++ k v +++ ++L+++ i
    EPA06646.1 692 LLSKLQKLIKKITERNEACKFHEAAKAVDDFVINNLSQIYI 732
                   48899999999998888778888888888888888887665 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.055   1.2e+02      11      50 ..      39      78 ..      29      80 .. 0.80
   2 !   21.4   0.0   5.9e-08   0.00013     239     296 ..     584     643 ..     576     647 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.055
                  EEEEEEEBTTS--BHHHHHHHHHHHHHHHHHHHTT-EEEE CS
  tRNA-synt_1e 11 tlYvCGptvydashlGhaRslvafDilrrilqalgYdvqf 50
                   +    pt+    h Gh R  v+ D+  r+   +g +++f
    EPA06646.1 39 MFIEGPPTMNGIPHAGHLRGRVIKDLWYRFNTLQGKKITF 78
                  333344799999*****************99999988887 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 5.9e-08
                   EEEEEE--EE.ETTBE--TTTT---BHHHHHTTS-HHHHHHHHH.SS-TTS-EEE-HHHH CS
  tRNA-synt_1e 239 kyflhnghlk.iegekmsksLknfitikdvlkkfdprqlRllll.sahyrsqldfkeell 296
                   + fl +gh+   +g kmsksL+n+i   ++l+k+    +R++++ +a   ++l f+ e+l
    EPA06646.1 584 RSFLFQGHVLdEKGGKMSKSLGNVIDGAELLEKYPVDLIRFYFIwKASPIEPLSFSTEEL 643
                   678999997515678*************************99871445567888877665 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1      0.99   2.2e+03     156     182 ..     160     186 ..     145     201 .. 0.79
   2 !   16.0   0.0   1.9e-06    0.0044     274     322 ..     592     641 ..     581     676 .. 0.84
   3 ?   -2.6   0.0      0.86   1.9e+03     134     174 ..     797     837 ..     792     850 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.99
  tRNA-synt_1f 156 eilekyrgeereetyspylpvcekcgr 182
                   ++l+k  ++++ e+ + + ++c++c+ 
    EPA06646.1 160 QVLKKAHENKILEEDFTVIAYCPSCQT 186
                   689999999998999999999**9987 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1.9e-06
  tRNA-synt_1f 274 illkggekmssSkGnvltledwlevaepevlrflil.rrkPkkakkldld 322
                   +l+++g+kms+S Gnv+  +++le ++ +++rf+++ ++ P + ++++ +
    EPA06646.1 592 VLDEKGGKMSKSLGNVIDGAELLEKYPVDLIRFYFIwKASPIEPLSFSTE 641
                   7899999*************************876526778777777776 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 0.86
  tRNA-synt_1f 134 lYksglydeaikealenrekikeilekyrgeereetyspyl 174
                   +Y+++l +e+i+e  +  ++i +i +  r + + ++ +p++
    EPA06646.1 797 QYQENLVNEEIEESFDIMKDIVSISAAARMKGKLKRRWPLN 837
                   79*******************99999999888888777775 PP

>> POTRA  Surface antigen variable number repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00041      0.91      32      80 .]     914     960 ..     871     960 .. 0.83
   2 ?    0.7   0.1      0.35   7.8e+02       1      20 [.    1036    1056 ..     987    1065 .] 0.59

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00041
                 CHHHHHHHHHHHHHHHHCTT-EE.EEEEEEHSSTTSEEEEEEEEEEEE- CS
       POTRA  32 npekleadkealksryanlGyfdasVqvelpeddedknrvdltinvdEg 80 
                   e le+dke++ s+++++G +d +++ e   ++ dk +++++++ +Eg
  EPA06646.1 914 VNEFLETDKEKIISALEKQGKYDYKIDGEV--ISLDKEDFIVDFDAKEG 960
                 44789*********************4444..58899999999999998 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.35
                  EEEEEEEEES..SSS-HHHHH CS
       POTRA    1 vkikkinfeG.nkktkdeelr 20  
                  v++kk+nfe   k++kd++++
  EPA06646.1 1036 VRVKKVNFEQsCKEYKDDDID 1056
                  355555555543355555554 PP

>> DUF4438  Domain of unknown function (DUF4438)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00018       0.4     133     187 ..     294     348 ..     285     388 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00018
                 HHTTS--EEETTEEEEEESEEE-GGGB-TTTT-S-TTS--EEB--SSG...GGGT CS
     DUF4438 133 LleklkieeedgklevpvtalvpaalmGsGigsasaakgdydimtsdkeavkeyg 187
                 L+  l+  +++++ +v+v ++     +GsG+ + s a+g+ di+ ++k++vk + 
  EPA06646.1 294 LIPGLDECAKENNFHVAVSEEFVEITTGSGLVHLSPANGEEDIKIANKRKVKVFS 348
                 566677788999************************************9999774 PP

>> UL11  Membrane-associated tegument protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1       4.8   1.1e+04      11      20 ..     469     480 ..     468     482 .. 0.79
   2 ?    9.2   1.1    0.0005       1.1      22      39 .]     940     956 ..     939     956 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 4.8
        UL11  11 C..CcrkNeLvT 20 
                 C  C ++N   T
  EPA06646.1 469 CgdCRKQNWFFT 480
                 77799*998777 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0005
        UL11  22 dGEvveLdseffdtvDld 39 
                 dGEv++Ld e+f  vD+d
  EPA06646.1 940 DGEVISLDKEDF-IVDFD 956
                 8***********.68887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1065 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       978  (0.0545485); expected 358.6 (0.02)
Passed bias filter:                      651  (0.0363099); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.92u 0.33s 00:00:01.25 Elapsed: 00:00:00.53
# Mc/sec: 6002.44
//
Query:       EPA06647.1  [L=305]
Description: succinyl-CoA synthetase, alpha subunit [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.8e-22   79.2   2.4    5.1e-22   78.4   1.3    2.0  2  CoA_binding     CoA binding domain
    1.2e-08   34.9   0.2    2.1e-08   34.1   0.2    1.4  1  Ligase_CoA      CoA-ligase
    1.2e-05   25.7   0.0    2.1e-05   25.0   0.0    1.4  1  CoA_binding_2   CoA binding domain
    7.3e-05   22.6   0.0    0.00012   21.8   0.0    1.4  1  Succ_CoA_lig    Succinyl-CoA ligase like flavodoxin domain
  ------ inclusion threshold ------
      0.013   16.3   0.1      0.023   15.5   0.1    1.4  1  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
      0.045   13.1   0.1      0.075   12.4   0.1    1.3  1  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family


Domain annotation for each model (and alignments):
>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.4   1.3   1.7e-25   5.1e-22       2      95 ..      18     110 ..      17     111 .. 0.96
   2 ?   -2.7   0.0       3.2   9.7e+03       9      19 ..     188     198 ..     172     214 .. 0.61

  Alignments for each domain:
  == domain 1  score: 78.4 bits;  conditional E-value: 1.7e-25
                  TTEEEEEETTTSHHHHHHHHHHHHHHECEEEEEEC-TTTTTCEET.TEEEESCHHHHHHHCTTTEEEEES-HHHHHHHHHHHHHTT-SEEEEESS CS
  CoA_binding   2 kdtkviviGagglgiaglyhfkeklkygikavfgvnprkvgtevl.glpvyksvdeleektevdvavitvPaesaqeavdelveagikgiviite 95 
                  k++ viv+G++g    g +h k+++ yg+++v+gv+p+k+g++ +  +p+y++v+e+++ t++++++++vPa++   a+ e++eagik+ v+i e
   EPA06647.1  18 KKKGVIVQGITGA--YGSLHAKNMITYGTNIVAGVTPGKGGQKFEdKVPIYNTVKEAVDATGAKISIVFVPAKFFLGAAREALEAGIKLLVAIPE 110
                  6789*********..999***********************999868********************************************9977 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.2
                  ETTTSHHHHHH CS
  CoA_binding   9 iGagglgiagl 19 
                  iG+gg  i g+
   EPA06647.1 188 IGIGGDPINGT 198
                  44444444333 PP

>> Ligase_CoA  CoA-ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.2   7.1e-12   2.1e-08       1     145 [.     163     277 ..     163     284 .. 0.90

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 7.1e-12
                 EESSHHHHHHHHHHHHHT..............T--BSEEEE-TSS--..........HHHHHHHHHHHHS-TT-SEEEEEEEESSSEHHHHHHHHHHHH CS
  Ligase_CoA   1 lvnGGtLayeamdlikealgdvasnkklknvlgseqheiidlGddaftkGrpHPmiDptkriealkklaadpevkvilldivlGygahedpaaellkai 99 
                 l+++GtL ye  d++++a              g +q+  i++G+d  +         +t++i+a++ +   p  +++++ +++G g +e++ a+ +  i
  EPA06647.1 163 LSKSGTLLYEISDALTNA--------------GFGQSITIGIGGDPIN---------GTRMIDAFEMVKDIPDLEGLVVVGEIG-GDSEEILAQRIIDI 237
                 689***************..............***************8.........***************************.99988877666666 PP

                 HHTT...--S-EEEEEECTTHH.....HHHHHHHTTTSSEEE-SSH CS
  Ligase_CoA 100 keakaegrelpvvarvaGteadpqelseqakaleeagveiasskaq 145
                          +p va++aG  a++ +++++a+a+  +    a+sk  
  EPA06647.1 238 GFK------KPTVAYIAGRAAPKEKRMGHAGAIVMGTYGSAESKVS 277
                 555......5***********************9999888888765 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   6.9e-09   2.1e-05      20     114 ..      36     140 ..      25     142 .. 0.79

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 6.9e-09
                    HHHHHHHT--EEE.ESSS-..SEETT.EES----T......T--EEEE-S-HHHHGGGHHHHHHH--SEEEE-TT....---HHHHHHHHHTT-EE CS
  CoA_binding_2  20 lryllehglpvvp.Vnpke..eeilg.ekvyaslae.d.pepvdlvdvftppeatpeivkealalgakavwlqpg....sedeeaaelaeeagirv 105
                    ++++   g ++v+ V+p +  ++ +  ++ y +++e    +  ++  vf+p++  +  ++eal++g+k ++  p+        e+++la+++g  +
     EPA06647.1  36 AKNMITYGTNIVAgVTPGKggQKFEDkVPIYNTVKEaVdATGAKISIVFVPAKFFLGAAREALEAGIKLLVAIPEhvpvRDTMEVLDLANKKGAVI 131
                    56666666555543777776544444378899999632466666*********************************988889************* PP

                    E.ES-HHHH CS
  CoA_binding_2 106 vgdrCilve 114
                    +g++ ++++
     EPA06647.1 132 IGPNTPGIM 140
                    *****9997 PP

>> Succ_CoA_lig  Succinyl-CoA ligase like flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   4.1e-08   0.00012       1     107 [.     157     265 ..     157     293 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 4.1e-08
  Succ_CoA_lig   1 pGkialisqSGalalalldwaasrglgfskvvslGn..eadvdvadlleylaedpetkvillylEsirdgrk.flsaarraarkkpvvvlksGrsea 94 
                   +Gkia++s+SG+l+ ++ d++++ g+g s  + +G      + + d +e++++ p+ + ++++ E  +d ++ +++ +  +  kkp v++ +Gr + 
    EPA06647.1 157 AGKIAVLSKSGTLLYEISDALTNAGFGQSITIGIGGdpINGTRMIDAFEMVKDIPDLEGLVVVGEIGGDSEEiLAQRIIDIGFKKPTVAYIAGRAAP 253
                   59*******************************998333567889999999**************999965516789999*************9555 PP

  Succ_CoA_lig  95 garaaashtgala 107
                   + +  + h ga++
    EPA06647.1 254 K-EKRMGHAGAIV 265
                   4.44567777764 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.1   7.8e-06     0.023       7     116 ..      26     131 ..      20     133 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7.8e-06
                   TT.SHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-GGGHHHHHHHHHHTT-EEEEESSS-SSHHHH CS
  GFO_IDH_MocA   7 Ga.GkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladpeidavivatpngtheelakaaleagkhvllEKPlattveea 102
                   G+ G +gs h++++     ++++va + p++  ++ +  + +v+ y+ ++e ++ + +++ iv +p++     a++aleag+++l+  P   +v++ 
    EPA06647.1  26 GItGAYGSLHAKNMITY--GTNIVAGVTPGKGGQK-F--EDKVPIYNTVKEAVDATGAKISIVFVPAKFFLGAAREALEAGIKLLVAIPEHVPVRDT 117
                   65566788888666666..7777777888875555.4..68999************9999999****999999************************ PP

                   HHHHHHHHHHTS-E CS
  GFO_IDH_MocA 103 kelvelaekkgklv 116
                    e+++la+kkg ++
    EPA06647.1 118 MEVLDLANKKGAVI 131
                   **********9865 PP

>> Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   2.5e-05     0.075     132     193 ..      46     107 ..      36     110 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.5e-05
                     EEESS-TT-SS----CCHHHHHHHHHHHHHHHT---E.EEEESS--TTTCHHHHHHT--EEEE CS
  Ribul_P_3_epim 132 llmsvePgfgGQkFipevlekikkvrklidekeldlk.ievDGGvkldnieqiaeagadvlVa 193
                     ++  v Pg+gGQkF ++v +  ++v++++d+++ ++  ++v     l +++++ eag+++lVa
      EPA06647.1  46 IVAGVTPGKGGQKFEDKV-PIYNTVKEAVDATGAKISiVFVPAKFFLGAAREALEAGIKLLVA 107
                     57789*********8875.77899999999999877625799999999999999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1916.07
//
Query:       EPA06648.1  [L=205]
Description: phosphoribosylglycinamide formyltransferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.8e-53  178.6   0.0    1.1e-52  178.4   0.0    1.0  1  Formyl_trans_N  Formyl transferase


Domain annotation for each model (and alignments):
>> Formyl_trans_N  Formyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.4   0.0   6.2e-57   1.1e-52       4     181 .]       5     187 ..       2     187 .. 0.95

  Alignments for each domain:
  == domain 1  score: 178.4 bits;  conditional E-value: 6.2e-57
                     EEEESESSHHHHHHHHHHHHTTSECEEEEEEESCTTEHCHHHHHHCCHCCCECHHCCSCCC.CCCCHHHHHHHHCTT-....SEEEEES--S--- CS
  Formyl_trans_N   4 vvlisgtgsnlqalldalkkgsleadvvlvvsnkdkaaglekaeaasiptkvfeekklepr.sqfeeelaeelkelka....dlivlagymkllp 93 
                      +lisg gsn++ +l++ k +++  + + v+snk++a+gle a++ +i t+v+e k+++ +  +++++++++l+++++     l++lag+m++++
      EPA06648.1   5 GILISGRGSNMESILKSIKRKKIPINPAIVISNKQDARGLEIARKLGIKTEVIESKDFKGSrWEYDKKIISVLEKHGVtpknGLVCLAGFMRIIS 99 
                     589******************************************************9876479***********987444359*********** PP

                     HHHHHSSTTSEEEEESSSTTTTBSS-HHHHHHHTTSSEEEEEEEE--SSSSTS-EEEEEEEE--TT--HHHHHHHHHHHHHHHHHHHH CS
  Formyl_trans_N  94 kelvqavrlkilniHpSLLPrfkGaaaiqraleaGdketGvtihfvdeelDtGailaqkkveiiaedtkeeleqrvadaehkalveal 181
                     +e+v++++++i+niHp+LLP+f+G++a+++a+e G k++G+t+hfvd ++DtG+i++q+ v+i + dt+++l++r+  +eh+a++ea+
      EPA06648.1 100 PEFVKKYKNRIINIHPALLPAFPGLDAQKQAIEYGSKYSGCTVHFVDSGVDTGPIILQSVVKIKKGDTEKTLSKRILAKEHQAYPEAI 187
                     *************************************************************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1301.43
//
Query:       EPA06649.1  [L=259]
Description: hypothetical protein BG20_I2589, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-65  220.3   0.0    3.9e-65  220.1   0.0    1.0  1  DUF521    Protein of unknown function (DUF521)


Domain annotation for each model (and alignments):
>> DUF521  Protein of unknown function (DUF521)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  220.1   0.0   2.2e-69   3.9e-65     100     376 ..       2     258 ..       1     259 [] 0.95

  Alignments for each domain:
  == domain 1  score: 220.1 bits;  conditional E-value: 2.2e-69
      DUF521 100 kqeriieayeklGveltftCtpyllgnapkkGehlawsESsavvyaNSvlGarTnreggpsalaaAitGrtpeyGlhldenRkptvlveveaesedead 198
                 kq +i + ye++Gv+++f+C+py + ++pk+G+++a++ES+a+++aNS+   +Tn+e+++sala+AitG+ p+  +  +   + t+ ++v+  + +e  
  EPA06649.1   2 KQLSIKNSYEAMGVSPSFSCIPYEIFDIPKEGTQVAFAESNAAIHANSYDNLKTNKESAFSALASAITGKSPYSSIRKEDSPNLTIRMKVK--DPNELT 98 
                 78999*********************************************************************99888877767666665..569*** PP

      DUF521 199 ygalGylvGkkvgeriPvlkglekpsedelKalgAalaasgavalfhiegvTPeaetleealgekekaekititkedleevleelskakeekvdlvalG 297
                 yg+lG+++Gk  g+    ++gl k++++++Ka++  +++sg++a f + +  P               eki+++++++++v +el  ++ ek dl++lG
  EPA06649.1  99 YGMLGFFAGKV-GDTSVNVSGLGKMDNRQCKAMCGGMGTSGTCAKFLFGDGDPS-------------CEKIDFDQKEMQNVHDEL--NTAEKGDLITLG 181
                 *********86.55666799**********************************.............89****************..999999****** PP

      DUF521 298 cPhlsleElrelaellkgkkkkvkvelwvttsrevkeeaerlglveklekaGvkvlsdtCmvvsplikkkevkkvatnS 376
                 +P+l leE+ +l+  l  k+++ +++++++++r+vke+a+++g++++le+aG+++lsd+C++++pli+k++v++v+tnS
  EPA06649.1 182 SPQLGLEEMSDLVGKL--KGRSFQKRCMIFCPRTVKEQARKIGYTNELERAGCEILSDCCTCLTPLINKNDVDAVITNS 258
                 ****************..88999*******************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1743.73
//
Query:       EPA06650.1  [L=65]
Description: hypothetical protein BG20_I2218 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0024   17.5   2.2     0.0057   16.3   2.2    1.6  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit


Domain annotation for each model (and alignments):
>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   2.2   3.2e-07    0.0057       1      32 []      22      55 ..      22      55 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.2e-07
                    -B-SSS--B--...--SSS----SSS-----B--- CS
  DNA_RNApol_7kD  1 YiCgeCgaevs...lkkgdpiRCkeCGhRilYKkR 32
                    Y C +Cg++vs   l +   i+C  CG+R++ K R
      EPA06650.1 22 YSCLRCGTNVSnteLFRLPEIKCI-CGFRVFTKVR 55
                    99*****9987656889999***9.******9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.47
# Mc/sec: 418.42
//
Query:       EPA06651.1  [L=432]
Description: translation elongation factor EF-1, subunit alpha [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.6e-46  156.1   0.1    9.8e-46  155.7   0.1    1.1  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    2.6e-37  127.5   0.2    6.2e-37  126.3   0.2    1.7  1  GTP_EFTU_D3  Elongation factor Tu C-terminal domain
    8.6e-16   58.1   1.2      3e-15   56.3   1.2    2.0  1  GTP_EFTU_D2  Elongation factor Tu domain 2
      1e-05   25.4   1.1    2.3e-05   24.2   1.1    1.6  1  GTP_EFTU_D4  Elongation factor Tu domain 4
  ------ inclusion threshold ------
      0.084   12.5   0.0       0.14   11.8   0.0    1.4  1  NIF3         NIF3 (NGG1p interacting factor 3)


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.7   0.1   2.7e-49   9.8e-46       1     182 [.       4     200 ..       4     262 .. 0.88

  Alignments for each domain:
  == domain 1  score: 155.7 bits;  conditional E-value: 2.7e-49
                 TCEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHH...HHHST..............HCHSHHHHHHTSCSSCEEEEEETTCSSEEEEEEEESSSGG CS
    GTP_EFTU   1 krirnigiighvDhGKtTLtdrLlyktgaiskkgeka...eeerv..............lDtlkeErergiTiksaaisleketkkylinliDtPGHvd 82 
                 k+++n+++ gh+D GK+T++++ l+++g +++++  a   e                  +D+ k+ErergiTi+ a  ++e  t ky ++liD+PGH+d
  EPA06651.1   4 KPHLNLIVTGHIDNGKSTTMGHFLMDLGVVDDRTIAAhaaE---SektgkgdtfkyawvMDNIKDERERGITIDLAFQKFE--TPKYFFTLIDAPGHRD 97 
                 579*****************************999985542...2345899999***************************..**************** PP

                 GHHHHHHHHHT-SEEEEEEETTTB.......STHHHHHHHHHHHHTTTE.EEEEEESCGST...HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEE CS
    GTP_EFTU  83 FskevirglrvlDgavlvvdaveG.......vepqteevlrlalkegvp.iivfiNKmDrl...kaelkeiveevkqklsrkeeklekygekgekevpv 170
                 F+k++i+g++ +D a+lv++a+eG          q +e++ l++++gv  +iv+iNKmD +   +a +k  +e+  +kl      ++++g+k e +vp+
  EPA06651.1  98 FIKNMITGASEADAAILVLSAKEGetdtaiaAGGQAREHAFLLKTLGVGqLIVAINKMDAVeykEAAFKAAKEKG-EKL------VRSVGYKLE-NVPF 188
                 *****************************9999***************99***********99555555555555.588......899999996.**** PP

                 EEEBTTTTBTHH CS
    GTP_EFTU 171 vfgSalkgegvk 182
                 +++S++kg+++ 
  EPA06651.1 189 IPVSGWKGDNLV 200
                 *********876 PP

>> GTP_EFTU_D3  Elongation factor Tu C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.3   0.2   1.7e-40   6.2e-37       2     111 ..     319     426 ..     318     427 .. 0.98

  Alignments for each domain:
  == domain 1  score: 126.3 bits;  conditional E-value: 1.7e-40
                  -EEECCEEEEEEESSS..SS-BSTT-EEEEESSS-EEEEEEEEEEECCSSTTSB-BSS-SSCCSTT-CEEEEEEECCEEEE--TTTHCCCCEEEEECT CS
  GTP_EFTU_D3   2 ikphtkfeAqvyilekerhtpitagYrpvlyirtadvtgkvveLlskldkktekvsekkpefvkpGdnvivevelikpialekgseypqlGrFaiReg 99 
                   k +++f+Aq++++++  +t+i  gY+pv++++t++v+++v+e+l+++++ t+ v+e++p+f+k Gd++iv++++ +p ++e+++e+p++GrFa+R++
   EPA06651.1 319 PKVAKEFKAQIIVIHH--PTAIAPGYTPVMHCHTSQVAATVTEFLQRINPATGAVEEENPKFLKVGDAAIVKIRPVRPTCIETFQEFPEMGRFALRDM 414
                  6889************..******************************************************************************** PP

                  TCEEEEEEEEEE CS
  GTP_EFTU_D3 100 grTvaaGvvtei 111
                  g T+aaG+v+ei
   EPA06651.1 415 GATIAAGIVKEI 426
                  **********99 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.3   1.2   8.5e-19     3e-15       1      73 [.     246     312 ..     246     313 .. 0.94

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 8.5e-19
                  EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEE CS
  GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtl 73 
                  Gtv  grv++G++k G+++ +  +++   + +++i+s+et+h ++ +a+ag+n+G+++++++ +d i++Gd+l
   EPA06651.1 246 GTVPVGRVETGIMKAGQKIIV--MPS---GALGEIKSIETHHTEMPTAEAGDNIGFNLRGIEKKD-IKRGDVL 312
                  99*******************..555...457*********************************.******9 PP

>> GTP_EFTU_D4  Elongation factor Tu domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   1.1   6.5e-09   2.3e-05      20      85 ..     249     312 ..     231     313 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 6.5e-09
                  EEEEEEEEEEEETT-EEEETTE.EEEEEEEEEETTEEESEEETT-EEEEEEESS-TTTS--TT-EE CS
  GTP_EFTU_D4  20 ivGvevlgGvikpgvklikedGrevGeilqiqdkgkkleeakaGqevaisiegkivGrqikegdil 85 
                   vG +v +G++k+g k+i      +Gei++i++++ ++ +a+aG++++  ++g    ++ik gd+l
   EPA06651.1 249 PVG-RVETGIMKAGQKIIVMPSGALGEIKSIETHHTEMPTAEAGDNIGFNLRGIE-KKDIKRGDVL 312
                  588.9***********98766669****************************965.899**99998 PP

>> NIF3  NIF3 (NGG1p interacting factor 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.9e-05      0.14      10      65 ..     283     338 ..     274     360 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.9e-05
        NIF3  10 aplelaeswDnvGlqvg.dpek..evkkvllaldlteevleeAiekgadliithHPlif 65 
                  +   ae  Dn+G+ +    +k  +   vl + d+ ++v++e ++   + i+ hHP+ +
  EPA06651.1 283 TEMPTAEAGDNIGFNLRgIEKKdiKRGDVLGTPDAPPKVAKEFKA---QIIVIHHPTAI 338
                 567789********99854444235556***********887765...********976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2853.61
//
Query:       EPA06652.1  [L=332]
Description: fructose-1,6-bisphosphatase, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.2e-144  482.0   0.1   1.3e-144  481.8   0.1    1.0  1  FBPase_3  Fructose-1,6-bisphosphatase


Domain annotation for each model (and alignments):
>> FBPase_3  Fructose-1,6-bisphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  481.8   0.1  7.4e-149  1.3e-144       1     334 [.       2     331 ..       2     332 .] 0.99

  Alignments for each domain:
  == domain 1  score: 481.8 bits;  conditional E-value: 7.4e-149
    FBPase_3   1 kvtlsvikaDvGslaGhtkvheellekveevleeakkkgllidfyvtkvGDDielimthtkgvdneevhklawdafkeatevakelklygaGqDlLkda 99 
                 k+t+svikaDvG+++Ght++++ l+e+v++++++++  +llid+y+ ++GDD++++m+ht+g+dn+++hklawdaf+++t+vak+ +lygaGqDlLkd+
  EPA06652.1   2 KITVSVIKADVGGIGGHTRPSDGLIEAVRKTVKSSS--DLLIDYYIGYCGDDVHIVMSHTHGTDNDKIHKLAWDAFMAGTQVAKQEGLYGAGQDLLKDS 98 
                 89******************************9865..58*********************************************************** PP

    FBPase_3 100 fsGnvkGlGPgvaelefeeRksepvvvfaaDktepgafnlplykifadpfntaGlvidpklheGfkfevlDvieekkillsapeelydllallgakery 198
                 fsGnvkG+GPgvae+efeeR++e++ vfaaDktepgafn+p+y++f+d ++++Gl+++++l++G+ ++v+Dv+e k  +ls +e+  ++ a l+ ++ry
  EPA06652.1  99 FSGNVKGMGPGVAEMEFEERPNEAFTVFAADKTEPGAFNYPIYRMFVDSLSNTGLIVNKSLASGVIINVMDVEEGKIAKLSLWEDKPTIEAALMYPGRY 197
                 *************************************************************************************************** PP

    FBPase_3 199 vikrvyskkdeeiaavvsterlsliaGkYvGkDDPvaivRaqsglPavgevlepfalphlvaGwmrGshngplmPvslkdakptrfdgpprvvalgfql 297
                 v+++v++k ++e++ ++st+rl++iaG+YvGkDDP++++R+q+++Pa++ev ++f++ph+vaG++rGshn+plmPv+l++++ +  ++ p+v al f++
  EPA06652.1 198 VVSTVTTK-QGEPILAASTDRLHNIAGTYVGKDDPICLIRTQKNFPATEEVGSVFNNPHYVAGNTRGSHNMPLMPVKLNSPA-SINFCIPIVQALVFSM 294
                 *******9.99**********************************************************************9.9999************ PP

    FBPase_3 298 kegklvgpvDlfddpafdeaRekaaeiadelRrqGpf 334
                 ++gk++gp D f++p +d++Re a+++a  +R+qG++
  EPA06652.1 295 HNGKFTGPFDGFSTPDWDYIREIATKKALAMRSQGFI 331
                 ***********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2073.33
//
Query:       EPA06653.1  [L=102]
Description: ribosomal protein S10 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.1e-23   80.9   0.0    6.8e-23   80.7   0.0    1.0  1  Ribosomal_S10  Ribosomal protein S10p/S20e
  ------ inclusion threshold ------
      0.032   14.4   0.0      0.045   14.0   0.0    1.2  1  CTX_RstB       CTX phage RstB protein


Domain annotation for each model (and alignments):
>> Ribosomal_S10  Ribosomal protein S10p/S20e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.7   0.0   7.6e-27   6.8e-23       1      97 [.       6      99 ..       6     100 .. 0.98

  Alignments for each domain:
  == domain 1  score: 80.7 bits;  conditional E-value: 7.6e-27
                   EEEEEESSHHHHHHHHHHHHHHTTSSS-EE---EEEEEEEEEEEEE--SS--.S--EEEEEEEEEEEEEEEE.E-HHHHHHHS-...S---SS-EEEE CS
  Ribosomal_S10  1 rirlkSydsklLekavkkivraakelgikvkgpvplPtkrkrvtvlksphvd.kksreqfeirthkRlidisdatketidtllkllqlnlpegVsvev 97
                   r++l+S +   L+ ++++i+ + k++g+kvkgp plP k++ v ++ksp+++ +++ e++e+++h+R+i is a+++ i++l++   l++p+ V +e+
     EPA06653.1  6 RVKLTSISLPKLDGVCNEIMGIGKKTGVKVKGPTPLPVKKLHVATRKSPCGNgTETYEKWEMKMHRRIINIS-ADDKAIRQLMR---LKIPDDVYIEL 99
                   799********************************************************************6.***********...*******9986 PP

>> CTX_RstB  CTX phage RstB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0     5e-06     0.045       4      77 ..      24     101 ..      22     102 .] 0.81

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5e-06
    CTX_RstB   4 vigvelseGvskkspkPYdiaklfylvparswkkdkgniea..vGldkkeiamqsnpellrklkglelp..vlveLel 77 
                 ++g+ +  Gv  k p P  ++kl ++   +   ++    e+  + + ++ i+++ +++ +r+l  l++p  v +eL+l
  EPA06653.1  24 IMGIGKKTGVKVKGPTPLPVKKLHVATRKSPCGNGTETYEKweMKMHRRIINISADDKAIRQLMRLKIPddVYIELSL 101
                 68999999*****************9987766666555554115678999*******************667777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 646.62
//
Query:       EPA06654.1  [L=178]
Description: hypothetical protein BG20_I2575 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.5e-25   88.3   0.4    6.1e-25   87.9   0.4    1.2  1  MAF_flag10     Protein of unknown function DUF115
  ------ inclusion threshold ------
      0.057   13.5   0.1        0.1   12.7   0.1    1.6  1  TPK_catalytic  Thiamin pyrophosphokinase, catalytic domain


Domain annotation for each model (and alignments):
>> MAF_flag10  Protein of unknown function DUF115
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.9   0.4   6.8e-29   6.1e-25      44     169 ..       2     118 ..       1     120 [. 0.85

  Alignments for each domain:
  == domain 1  score: 87.9 bits;  conditional E-value: 6.8e-29
  MAF_flag10  44 lkelrdkaviiaadtalkaLlkegIkPDivvs.lDpqeasyevfkeaekkgdiplvfasgvnpellkkykgpkiflvtgstqalelleeekneilfgGg 141
                 lk+ +++ + i ad+a+k+L+++gI PDi+v+ lD+   + e + ++ k  +i +v+a+g+n+  l+   + k ++ t+  + ++ +      ++fgG+
  EPA06654.1   2 LKNFKKE-LKIVADSAVKVLVENGINPDIIVTdLDG---DKESLIKVGKTDSIFVVHAHGDNIVRLNLAANFKNYVGTTQSKPFKKI------QNFGGF 90 
                 5666544.44567***********************...6666666666669**********************9777655445555......9***** PP

  MAF_flag10 142 svantaldlAvklgfkeIiliGqDlayt 169
                 +++++a++lA ++++k+Iil+G+D++ +
  EPA06654.1  91 TDGDRAVFLASHFEAKKIILFGMDFGEK 118
                 *************************976 PP

>> TPK_catalytic  Thiamin pyrophosphokinase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   1.1e-05       0.1       8      62 ..       7      56 ..       3     113 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.1e-05
  TPK_catalytic  8 aslrvcaDgGanrlyeeekerlellpdvivGDlDSirpevkefyeskgteivkkp 62
                   ++l+++aD +++ l+     ++++ pd+iv DlD  +++  +  ++  + +v+ +
     EPA06654.1  7 KELKIVADSAVKVLV-----ENGINPDIIVTDLDGDKESLIKVGKTDSIFVVHAH 56
                   6799***********.....**************999998888777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1218.48
//
Query:       EPA06655.1  [L=66]
Description: hypothetical protein BG20_I2574 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1071  (0.0597356); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 410.09
//
Query:       EPA06656.1  [L=384]
Description: ATPase/histidine kinase/DNA gyrase B/HSP90 domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-19   70.3   0.4    1.9e-19   70.3   0.4    2.4  3  HATPase_c     Histidine kinase-, DNA gyrase B-, and HSP90-lik
    8.6e-08   32.1   0.0    2.9e-07   30.4   0.0    1.9  1  HisKA         His Kinase A (phospho-acceptor) domain
    2.7e-05   24.0   0.2    2.7e-05   24.0   0.2    2.7  2  HATPase_c_5   GHKL domain
    2.8e-05   23.9   0.9    8.3e-05   22.4   0.0    2.3  2  HATPase_c_3   Histidine kinase-, DNA gyrase B-, and HSP90-lik
  ------ inclusion threshold ------
      0.035   13.1   3.3      0.057   12.4   3.3    1.3  1  Ribosomal_L3  Ribosomal protein L3
      0.045   13.8   0.3       0.16   12.0   0.3    2.1  1  BSD           BSD domain
      0.083   13.2   0.7       0.38   11.1   0.6    2.2  1  Uteroglobin   Uteroglobin family
       0.09   12.7   0.0       0.19   11.7   0.0    1.5  1  HATPase_c_2   Histidine kinase-like ATPase domain
       0.13   12.0   1.6       0.66    9.8   0.1    2.7  2  Scm3          Centromere protein Scm3
       0.18   10.9  15.2       0.26   10.3  15.2    1.3  1  Atg14         Vacuolar sorting 38 and autophagy-related subun
       0.84    8.6   4.4        1.9    7.4   4.4    1.6  1  DUF2252       Uncharacterized protein conserved in bacteria (


Domain annotation for each model (and alignments):
>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.88   1.4e+03       7      32 ..      73     116 ..      67     155 .. 0.53
   2 ?   -2.9   0.1       5.9   9.6e+03      11      32 ..     248     269 ..     247     276 .. 0.68
   3 !   70.3   0.4   1.1e-22   1.9e-19       4     109 ..     280     377 ..     277     379 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.88
                 HHHHHHHHHHHHHH.................HS.TTTEEEEEEE CS
   HATPase_c   7 rqiisnlvdNavkf.................at.kageieveik 32 
                  +++++++d a+ +                 ++ k++e+ ++++
  EPA06656.1  73 SKALNEIIDKALANtpkkprksfskylekyiEPeKSKEVLITLQ 116
                 44455555555554222244433333333331113334444443 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.9
                 HHHHHHHHHHHSTTTEEEEEEE CS
   HATPase_c  11 snlvdNavkfatkageieveik 32 
                 + +v N+++  +  ++++++ +
  EPA06656.1 248 KDIVNNSIEQLQIPDKVTITQS 269
                 5688999997666676766654 PP

  == domain 3  score: 70.3 bits;  conditional E-value: 1.1e-22
                 HHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCS.TTCHHCSTCHTSTSSSHHHHHHHHHHHHTTTEEEEEEETTTE CS
   HATPase_c   4 krLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfe.kfsqddstkrggggtGlGlsivkklvelmgGeiwvesepgrG 101
                 ++++ ii n++ Na+++ + +gei++ ++ +e+++ i+++D+G+Gip+++++k+fe  f++      +  gtGlGl+ + ++ e++gG+i+v+++p   
  EPA06656.1 280 TKIKGIITNILHNAIQAINGKGEISIVVEENEKTIDIKITDSGPGIPENIMDKIFEpMFTT------KALGTGLGLASCVQFLEMHGGTIKVKNNP--- 369
                 567789**********977999999999977789999*******************66666......889**************9*******9999... PP

                 EEEEEEEE CS
   HATPase_c 102 ttftftlp 109
                 ttft+tlp
  EPA06656.1 370 TTFTITLP 377
                 ******98 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.0   1.8e-10   2.9e-07       3      61 ..     174     234 ..     172     238 .. 0.79

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 1.8e-10
                 HHHHHHHHHHHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHH CS
       HisKA   3 grflagvaHELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedlLdl 61 
                 g++ + +aH++r+PLs++++ ++++k +  ++ +e     + ++ + +  ++++++d+L++
  EPA06656.1 174 GKMSSKMAHDIRNPLSVLKMQVDLMKLKqkKQEDEIMSSSITRMDKAISDITNQINDVLTF 234
                 678899*******************664444555666668888888888888888888876 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   2.0       1.5   2.4e+03      29      60 ..      97     129 ..      69     214 .. 0.64
   2 !   24.0   0.2   1.7e-08   2.7e-05       5      97 ..     281     375 ..     277     377 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.5
  HATPase_c_5  29 rfIrltvr.ekkksliisieNsyegekkkless 60 
                  ++++  ++ ek+k ++i+++ ++e ek+   + 
   EPA06656.1  97 KYLEKYIEpEKSKEVLITLQKEIEIEKQIQAEI 129
                  555555552333456666666555544222211 PP

  == domain 2  score: 24.0 bits;  conditional E-value: 1.7e-08
  HATPase_c_5   5 dlcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg...ek.kkle..sskskkeehGiGlksireivkkykgnlsieaedglFtl 96 
                   +  i+ n+L NAi+a +       +I++ v+e++k++ i+i+ s  g   ++ +k++    ++k    G+Gl s  + ++ ++g+++++++ ++Ft 
   EPA06656.1 281 KIKGIITNILHNAIQAINGKG----EISIVVEENEKTIDIKITDSGPGipeNImDKIFepMFTTKALGTGLGLASCVQFLEMHGGTIKVKNNPTTFTI 374
                  566799**********98855....7******************977744322555544444778899****************************97 PP

  HATPase_c_5  97 s 97 
                  +
   EPA06656.1 375 T 375
                  5 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.2       3.2   5.3e+03     102     123 ..     126     147 ..     108     160 .. 0.51
   2 !   22.4   0.0   5.1e-08   8.3e-05       4      92 ..     283     362 ..     279     382 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.2
  HATPase_c_3 102 tldvdkidkenekvleeltvee 123
                  + +++ + + ++k+l++  +e 
   EPA06656.1 126 QAEIKHSIDTKSKSLKKARTEL 147
                  3333333334444444444443 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 5.1e-08
  HATPase_c_3   4 ekAlaelvdNsldAdaen..vkievnknrgktgeivieDdGkGmseeelknalrlatsskeakrkstslGkkGiGlklAslslgkkltvit 92 
                  ++ ++ ++ N+++A   +  ++i+v++n+ kt +i+i+D G G++e+ +++ ++++ ++k            G Gl lAs+++  ++   t
   EPA06656.1 283 KGIITNILHNAIQAINGKgeISIVVEENE-KTIDIKITDSGPGIPENIMDKIFEPMFTTKAL----------GTGLGLASCVQFLEMHGGT 362
                  5668899******9877666999999997.79*************************99983..........4444467766666666555 PP

>> Ribosomal_L3  Ribosomal protein L3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   3.3   3.5e-05     0.057      98     202 ..      56     170 ..      20     183 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.5e-05
                   EEEEEEEEESSS.SHHHHCCCS.......TSTTTSSSSSSHCCCCHCSSCCCCCCHHHH.HHHHHHSCSCEEEEEEEECCCSS-SCCSSHHEEEEEC CS
  Ribosomal_L3  98 Glrslktvwaehlseevkrrly.......knwykskkkaftkyskkyeskdvkkliead.leeikkeasvvrviahtvirktkslaqKkahllEiqv 186
                   G +s +t+  e+++ ++ + l         n  k  +k+f+ky +ky + +++k +     +ei+ e ++   i h+   k ksl++ +++l+E q 
    EPA06656.1  56 GSKSNETKENEQVESNISKALNeiidkalANTPKKPRKSFSKYLEKYIEPEKSKEVLITlQKEIEIEKQIQAEIKHSIDTKSKSLKKARTELVENQK 152
                   55555555555555555444431111000566677799********9777766666665156677777888889*********************99 PP

                   HCSCHH..HHHHHHHHCC CS
  Ribosomal_L3 187 ngGtia..ekldfareal 202
                   ++  +   e+ +f +++l
    EPA06656.1 153 KLDLVIetEIKNFENNRL 170
                   887554114455655555 PP

>> BSD  BSD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.3    0.0001      0.16       6      34 ..     120     150 ..     116     182 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0001
         BSD   6 kld..kteeiaqsllkedpeLrklynelVPs 34 
                 +++  +++ei +s+ ++ ++L+k+++elV +
  EPA06656.1 120 EIEkqIQAEIKHSIDTKSKSLKKARTELVEN 150
                 5566689*********************965 PP

>> Uteroglobin  Uteroglobin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.6   0.00024      0.38      22      67 ..      71     120 ..      66     143 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00024
                  ---HHHHHHHHHHH....HS-HHHHHHHHHTT---HHHHHHHHHHHHHHT CS
  Uteroglobin  22 egCpaleevvekfl....egseeeYkeeLqkynpdpeaeealaelKqcvd 67 
                  ++ +al e+++k l    +++ +++ ++L+ky+++++ +e l +l++ + 
   EPA06656.1  71 NISKALNEIIDKALantpKKPRKSFSKYLEKYIEPEKSKEVLITLQKEIE 120
                  47788888888888777788999******************999988664 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00012      0.19      40     103 ..     286     350 ..     272     357 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00012
  HATPase_c_2  40 ctNavehayleap.egpvevrlesdeealtvevaDsGpgfdpetlpdpteeepkeslkegGrGla 103
                  +tN+ + a +  + +g++++ +e +e+++ ++++DsGpg +    ++  e+  ++++   G+Gla
   EPA06656.1 286 ITNILHNAIQAINgKGEISIVVEENEKTIDIKITDSGPGIPENIMDKIFEPMFTTKALGTGLGLA 350
                  566666666666667999999******************77665555555555667777777765 PP

>> Scm3  Centromere protein Scm3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1    0.0004      0.66      12      36 ..      11      34 ..       3      48 .. 0.83
   2 ?    0.1   0.2      0.44   7.1e+02      13      26 ..      92     105 ..      64     116 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0004
                H.HHHHHHHHHHHHSG..GGSS--B- CS
        Scm3 12 l.kkrwesifeKYeridfedqgDEID 36
                l k++ esi+ KY +   ++ g E+D
  EPA06656.1 11 LkKSVVESIMRKYMH-KESE-GKELD 34
                55899**********.7766.***99 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.44
                 HHHHHHHHHHHHSG CS
        Scm3  13 kkrwesifeKYeri 26 
                 +k++++ +eKY ++
  EPA06656.1  92 RKSFSKYLEKYIEP 105
                 68899999999774 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3  15.2   0.00016      0.26      36     182 ..      63     209 ..       6     241 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00016
       Atg14  36 sekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklkkRrsdleslqneleerrkkqia 134
                 +e+e++++ i+kal++       ++++ n+ +k ++  s+  ++  + ++ k+ l +l+keie+ k+  a+ ++++ ++ ++l+++++el e++kk+  
  EPA06656.1  63 KENEQVESNISKALNEII-----DKALANTPKKPRKSFSKYLEKYIEPEKSKEVLITLQKEIEIEKQIQAEIKHSIDTKSKSLKKARTELVENQKKLDL 156
                 678888888888888887.....89999*********************************************************************** PP

       Atg14 135 klqdaikrieqk....lsslssktles...rsslcselaklyglrrtsyergkwv 182
                  + ++ik+ e++    + ++ssk+++     +s +++ + l++l++ + e +  +
  EPA06656.1 157 VIETEIKNFENNrlelIGKMSSKMAHDirnPLSVLKMQVDLMKLKQKKQEDE--I 209
                 *******7777655556677777777787799**************555554..2 PP

>> DUF2252  Uncharacterized protein conserved in bacteria (DUF2252)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   4.4    0.0012       1.9     137     227 ..      62     158 ..       1     161 [. 0.55

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0012
     DUF2252 137 elleeatseeakgvvrkalekarkrtr.......eklldklteleegkrrikddppkllrlseaereaieaalesyaetlpadrrelldrfrlkDvar 227
                 +  +e+ +++ ++ ++++++ka  +t         k+l+k+ e e++k+ +++  +k ++++++ +++i++ +++ +++l+++r+el+++ +  D+++
  EPA06656.1  62 TKENEQVESNISKALNEIIDKALANTPkkprksfSKYLEKYIEPEKSKEVLITL-QKEIEIEKQIQAEIKHSIDTKSKSLKKARTELVENQKKLDLVI 158
                 122222222333333333333333322000011145666777777555555544.4556777*************************99988888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2285  (0.127447); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.74u 0.35s 00:00:01.08 Elapsed: 00:00:00.54
# Mc/sec: 2151.71
//
Query:       EPA06657.1  [L=52]
Description: hypothetical protein BG20_I1972 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00041   20.1   1.3    0.00044   20.0   1.3    1.0  1  Iron_permease  Low affinity iron permease
  ------ inclusion threshold ------
      0.021   13.7   1.1      0.022   13.7   1.1    1.0  1  Spc7           Spc7 kinetochore protein
      0.026   14.5   0.4      0.029   14.3   0.4    1.1  1  DASH_Dad4      DASH complex subunit Dad4
      0.036   14.1   0.5      0.054   13.6   0.4    1.4  1  PspB           Phage shock protein B
      0.039   14.3   0.9      0.043   14.1   0.9    1.1  1  OmpH           Outer membrane protein (OmpH-like)
        0.1   12.7   0.2       0.35   11.0   0.2    1.8  1  HHH_2          Helix-hairpin-helix motif
        0.1   12.7   0.5       0.13   12.4   0.1    1.4  2  DUF3378        Domain of unknown function (DUF3378)


Domain annotation for each model (and alignments):
>> Iron_permease  Low affinity iron permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   1.3   1.7e-07   0.00044      73     120 ..       1      48 [.       1      51 [. 0.93

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.7e-07
  Iron_permease  73 lkLdeLirasksaknrlidleelteeeleelakeyerlaeaakeeeev 120
                    +k++e++++ k++  r+ +le+l+e++l+e+++ +++ a+++++++ +
     EPA06657.1   1 MKIQEIMQTAKQLGRRINNLEDLDEDTLQEMHHAIKEYAKNKNNSHVI 48 
                    79**************************************99998865 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   1.1   8.5e-06     0.022     176     213 ..       3      40 ..       1      47 [. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.5e-06
        Spc7 176 kaeleeeleklqeaaeelesidkeeLeelreelaelka 213
                  +e+++++++l ++ ++le++d++ L+e++++++e  +
  EPA06657.1   3 IQEIMQTAKQLGRRINNLEDLDEDTLQEMHHAIKEYAK 40 
                 689******************************98765 PP

>> DASH_Dad4  DASH complex subunit Dad4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.4   1.1e-05     0.029      11      51 ..      11      52 .]       4      52 .] 0.86

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.1e-05
   DASH_Dad4 11 alLsRIiknvekLne.svvelnkeleeinkkNknvelvsqlw 51
                + L R i+n+e L e +++e+ ++++e+ k+ +n +++  +w
  EPA06657.1 11 KQLGRRINNLEDLDEdTLQEMHHAIKEYAKNKNNSHVIDYMW 52
                558899*******983589*********99999999999888 PP

>> PspB  Phage shock protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.4   2.1e-05     0.054      42      63 ..       2      23 ..       1      33 [. 0.89

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.1e-05
        PspB 42 rLeellekAekleeRietLEri 63
                +++e++++A++l +Ri+ LE++
  EPA06657.1  2 KIQEIMQTAKQLGRRINNLEDL 23
                6899****************95 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.9   1.7e-05     0.043      69     116 ..       3      49 ..       1      51 [. 0.69

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.7e-05
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEEEE CS
        OmpH  69 eqelqqkqqqkaqelqkkqqellkpildkinkaikevakekgydlvld 116
                  qe++q ++q  + +++ + +l +  l++++ aike+ak k+ + v+d
  EPA06657.1   3 IQEIMQTAKQLGRRINNLE-DLDEDTLQEMHHAIKEYAKNKNNSHVID 49 
                 4555553333334444444.566678999*************999998 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.2   0.00014      0.35      14      39 ..       8      33 ..       7      48 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00014
       HHH_2 14 ktAklLakrFksldaLkkasleeLle 39
                +tAk+L +r ++l+ L + +l+e+ +
  EPA06657.1  8 QTAKQLGRRINNLEDLDEDTLQEMHH 33
                79********************9964 PP

>> DUF3378  Domain of unknown function (DUF3378)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       3.1   7.9e+03      12      18 ..       4      10 ..       2      16 .. 0.52
   2 ?   12.4   0.1     5e-05      0.13       6      31 ..      23      48 ..      18      50 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3.1
     DUF3378 12 kkmkeyy 18
                ++++++ 
  EPA06657.1  4 QEIMQTA 10
                4444433 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 5e-05
     DUF3378  6 vskktikkmkeyyksklrskkppyav 31
                ++++t+++m +  k+++++k++ +++
  EPA06657.1 23 LDEDTLQEMHHAIKEYAKNKNNSHVI 48
                799*******************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1833  (0.102237); expected 358.6 (0.02)
Passed bias filter:                      938  (0.0523175); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.54u 0.34s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 299.82
//
Query:       EPA06658.1  [L=319]
Description: ATPase/histidine kinase/DNA gyrase B/HSP90 domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.3e-21   76.4   0.3    4.9e-21   75.3   0.3    1.6  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    1.6e-11   44.1   0.0    3.7e-11   42.9   0.0    1.6  1  HisKA        His Kinase A (phospho-acceptor) domain
    8.8e-07   28.8   1.8    1.4e-06   28.1   0.3    2.1  2  HATPase_c_5  GHKL domain
    0.00027   20.8   0.0    0.00095   19.0   0.0    1.9  1  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like
  ------ inclusion threshold ------
      0.021   14.8   0.0      0.044   13.7   0.0    1.5  1  HATPase_c_2  Histidine kinase-like ATPase domain
      0.041   13.8   0.1      0.068   13.1   0.1    1.3  1  CHASE3       CHASE3 domain
      0.046   13.8   0.4        1.3    9.1   0.1    2.7  2  bPH_5        Bacterial PH domain
       0.33   11.3   4.7        1.1    9.6   4.7    1.9  1  DUF4064      Protein of unknown function (DUF4064)


Domain annotation for each model (and alignments):
>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.3   0.3   2.2e-24   4.9e-21       2     110 ..     210     313 ..     209     315 .. 0.93

  Alignments for each domain:
  == domain 1  score: 75.3 bits;  conditional E-value: 2.2e-24
                 HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHHHHHHHHHTTTEEEEEEETTT CS
   HATPase_c   2 dekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsivkklvelmgGeiwvesepgr 100
                 de++++ ++ n++ Na++   ++g+i+++ k++++++++++eDnGiGi +e+lk++fe++++     ++++gtGlGls +k++++ +gG i+ +++ ++
  EPA06658.1 210 DEEKITIVFVNMMLNAIQSLESGGTITISAKSNKKEVMVKIEDNGIGIKPEILKRVFEPLVT-----TKQSGTGLGLSSCKSIIDSHGGFIEASNKFEK 303
                 78889999**********86689999999997668***************************.....99************************9999** PP

                 EEEEEEEEES CS
   HATPase_c 101 Gttftftlpl 110
                 G  f ++lp 
  EPA06658.1 304 GAIFCIHLPN 313
                 *******996 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   0.0   1.6e-14   3.7e-11       3      63 ..     108     168 ..     106     171 .. 0.92

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 1.6e-14
                 HHHHHHHHHHHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCC CS
       HisKA   3 grflagvaHELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedlLdlsr 63 
                 g++++ + H++r+PLs+i++ +e Lkr+  ++  e++++++++i++ + r++h+ +d++d+ +
  EPA06658.1 108 GEMASRIGHDIRNPLSVIQMSIENLKRTyeIN--EQQQKQFDKIQRAIFRISHQMDDVMDFVK 168
                 7899999********************96555..**************************987 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       1.3     3e+03      20      46 ..      48      75 ..      42     107 .. 0.58
   2 !   28.1   0.3   6.3e-10   1.4e-06       3      90 ..     211     300 ..     209     311 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.3
  HATPase_c_5 20 acskiee.ekrfIrltvrekkksliisi 46
                   s+ e+ +++f +l+v   +++++i+i
   EPA06658.1 48 NISQDEKfDSKFNKLSVFGYDGNFFIII 75
                 4455444556666666666555554444 PP

  == domain 2  score: 28.1 bits;  conditional E-value: 6.3e-10
  HATPase_c_5   3 dldlcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg...ek..kkle.sskskkeehGiGlksireivkkykgnlsieae 90 
                  +  +++++ n++ NAi++ +        I+++++++kk ++++ie +  g   e+  + +e   ++k++  G+Gl+s ++i+++++g+++ +++
   EPA06658.1 211 EEKITIVFVNMMLNAIQSLESGG----TITISAKSNKKEVMVKIEDNGIGikpEIlkRVFEpLVTTKQSGTGLGLSSCKSIIDSHGGFIEASNK 300
                  67899************999877....7****************9875552333363334355578899******************9987654 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   4.2e-07   0.00095      11      62 ..     222     274 ..     212     290 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 4.2e-07
  HATPase_c_3  11 vdNsldAda..envkievnknrgktgeivieDdGkGmseeelknalrlatsske 62 
                    N++++     +++i+++ n+ k+ +++ieD+G G+++e lk+++++  ++k+
   EPA06658.1 222 MLNAIQSLEsgGTITISAKSNK-KEVMVKIEDNGIGIKPEILKRVFEPLVTTKQ 274
                  5566665430045899999886.799********************98777766 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0     2e-05     0.044      32     104 ..     214     283 ..     179     297 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2e-05
  HATPase_c_2  32 irlaveEactNavehayleapegpvevrlesdeealtvevaDsGpgfdpetlpdpteeepkeslkegGrGlal 104
                  i ++   ++ Na++        g+++++++s+++++ v+++D+G g +pe l++  e+  ++++   G+Gl  
   EPA06658.1 214 ITIVFVNMMLNAIQSLES---GGTITISAKSNKKEVMVKIEDNGIGIKPEILKRVFEPLVTTKQSGTGLGLSS 283
                  556666677777766665...688*************************999888887766666666666655 PP

>> CHASE3  CHASE3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1     3e-05     0.068      50      95 ..     124     169 ..     117     180 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3e-05
      CHASE3  50 eiqealeelreltadnpeqqerldrlealieqklaeleetialrre 95 
                  iq ++e+l+++++ n++qq+++d+++++i +   +++ +++ +++
  EPA06658.1 124 VIQMSIENLKRTYEINEQQQKQFDKIQRAIFRISHQMDDVMDFVKA 169
                 68999*************************9988888888887765 PP

>> bPH_5  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.087   1.9e+02      21      51 ..      41      74 ..      25     101 .. 0.83
   2 ?    9.1   0.1   0.00058       1.3      56      92 ..     229     265 ..     187     271 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.087
       bPH_5 21 IplseIeavrvsegvi...kgvrlfgtskpgyal 51
                I+  +Ie+++++e++    +++ +fg+ ++++++
  EPA06658.1 41 INQVSIENISQDEKFDskfNKLSVFGYDGNFFII 74
                5666777888877777666889999999999876 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00058
       bPH_5  56 ikdigkarmyatrlkrvlllktkdkiygisPedleeF 92 
                 ++ +g++++ a+++k+ +++k +d+ +gi Pe l+++
  EPA06658.1 229 LESGGTITISAKSNKKEVMVKIEDNGIGIKPEILKRV 265
                 5679***************************977665 PP

>> DUF4064  Protein of unknown function (DUF4064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   4.7   0.00047       1.1      42      88 ..      37      99 ..       4     108 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00047
     DUF4064 42 e...............qalsgedas.avleflstllivlgvialiaivlgivgalllkknkkv 88
                e               ++++ ++++ +v ++ ++++i++ v++ +a +lg+v +l+++++kk+
  EPA06658.1 37 ElqginqvsienisqdEKFDSKFNKlSVFGYDGNFFIIINVASSFAMILGVVTLLKIETKKKI 99
                14555444444433333333333321345999999*************************993 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1384  (0.0771934); expected 358.6 (0.02)
Passed bias filter:                      672  (0.0374812); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2020.90
//
Query:       EPA06659.1  [L=475]
Description: hypothetical protein BG20_I1973 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0091   16.2   0.5     0.0091   16.2   0.5    2.0  2  Kinesin_assoc  Kinesin-associated
  ------ inclusion threshold ------
      0.031   14.4   0.3      0.065   13.4   0.3    1.6  1  DUF4070        Domain of unknown function (DUF4070)


Domain annotation for each model (and alignments):
>> Kinesin_assoc  Kinesin-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.5     1e-06    0.0091      73     162 ..      22     112 ..       8     122 .. 0.81
   2 ?   -1.6   0.2      0.29   2.6e+03      64      94 ..     366     396 ..     315     435 .. 0.49

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1e-06
  Kinesin_assoc  73 lsalssraesvssleerivfspaseeaierlketekiiaelnetWeeklrkteairlereallaelGvairedGGtlGvfsPkkt.Phlvn 162
                    +s  +s++++ ++l+  ++  p  ++ ++++++t k i el e   ekl    ++  +r++ l++l   ++e       +sPk+    +vn
     EPA06659.1  22 YSFSQSDSSEQVTLSGDLTNNPVAQDILKKIEQTKKWIKELEEKNYEKLEAKKELETKRSQALEKLNQDLKEWEALWEYYSPKNSfSRFVN 112
                    333444555666777888899999************************************************9999999999975245555 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.29
  Kinesin_assoc  64 vaglspssslsalssraesvssleerivfsp 94 
                    +  +s +  +  + ++a + s+++e+++  +
     EPA06659.1 366 IKQASLKKEYDKKYANALEESKSDEKLAIKN 396
                    2222222222222222333344444443333 PP

>> DUF4070  Domain of unknown function (DUF4070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.3   7.3e-06     0.065      41     104 ..      95     162 ..      69     218 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.3e-06
     DUF4070  41 evleqlYspeayleRvdklllklkpar.kkkksk...alslkelrallrllwrqgvlrktRlqfWkql 104
                 e+l++ Ysp++ + R+ + +++ + +     + +   +   ++ +al +++ ++g l++ R+++ + +
  EPA06659.1  95 EALWEYYSPKNSFSRFVNTVENSQIQDvFWDQFEfhqMKVNAGKEALKKVIANGGSLSEARQAYLNAA 162
                 589****************99998776444433366677778889*******************9843 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2207  (0.123097); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 3060.51
//
Query:       EPA06660.1  [L=107]
Description: hypothetical protein BG20_I1976, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.6e-13   49.9   0.2    3.1e-13   49.7   0.2    1.0  1  F420_ligase  F420-0:Gamma-glutamyl ligase
  ------ inclusion threshold ------
      0.036   14.1   0.3      0.098   12.8   0.1    1.8  2  DUF3906      Protein of unknown function (DUF3906)
       0.16   12.2   0.1       0.27   11.5   0.1    1.3  1  SelB-wing_2  Elongation factor SelB, winged helix
       0.18   12.1   0.0       0.21   11.8   0.0    1.2  1  Cyclase      Putative cyclase


Domain annotation for each model (and alignments):
>> F420_ligase  F420-0:Gamma-glutamyl ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.7   0.2   6.9e-17   3.1e-13      11     133 ..       9     107 .]       5     107 .] 0.90

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 6.9e-17
                  --HHHHHHCCS-.....--TT-EEEEEHHHHHHHTT-EEEGGGS---HHHHHHHHHH.TS-H..................HHHHHHHHTEEEEEE-.. CS
  F420_ligase  11 ddlaeivvesvkkagleledgDivvvtekvvakaegnyvsledikpsekAeeiaeklkvidpilSrnrfsliLkalakatrkvevvlsepsdevgn.. 106
                   d+ e ++++++k++  l++gDivv++ k +++++g++++l+++k+s++ ee+++k+ +i p                  +  ev+l+e+++++g   
   EPA06660.1   9 FDVFEALLDTLEKNNQILQEGDIVVISTKYISNSQGRLIDLSNVKTSKEGEEVSKKF-QIRP------------------EIAEVILRESDKIFGGit 87 
                  589999***************************************************.****..................9**************988 PP

                  .S-EEEE.......TTS-EEEGGG-B-T CS
  F420_ligase 107 .qlidekytdevlvklGllgsnagides 133
                   ++i+    d       +++ nagid+s
   EPA06660.1  88 gFVITSA--D------NIMAPNAGIDKS 107
                  8888877..3......455667777765 PP

>> DUF3906  Protein of unknown function (DUF3906)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       0.5   2.2e+03      22      37 ..       6      21 ..       5      42 .. 0.69
   2 ?   12.8   0.1   2.2e-05     0.098      33      64 .]      59      91 ..      55      91 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.5
     DUF3906 22 endeqAFrqleielek 37
                en+   F++l  +lek
  EPA06660.1  6 ENEFDVFEALLDTLEK 21
                5666667777667776 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 2.2e-05
     DUF3906 33 ielekhylklPevkevallEkKrirkg.aayvi 64
                +e+ k +   Pe+ ev l+E  +i  g +++vi
  EPA06660.1 59 EEVSKKFQIRPEIAEVILRESDKIFGGiTGFVI 91
                6899****************9999887688987 PP

>> SelB-wing_2  Elongation factor SelB, winged helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1     6e-05      0.27      34      55 ..      11      32 ..       6      33 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6e-05
                 CHHHHHHHHHHTTSEEE-SSEE CS
  SelB-wing_2 34 lfqallealvargilavegdwv 55
                 +f+all+ l++++++ +egd+v
   EPA06660.1 11 VFEALLDTLEKNNQILQEGDIV 32
                 79******************87 PP

>> Cyclase  Putative cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   4.8e-05      0.21      71     122 ..      13      78 ..       1      85 [. 0.68

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.8e-05
     Cyclase  71 edleaalakqgveikpgdivlirTgwskrl..............edkeky.rnpglseeaaewlaek 122
                 e l ++l+k++  +++gdiv+i T + ++               e  e+  ++  + +e+ae ++++
  EPA06660.1  13 EALLDTLEKNNQILQEGDIVVISTKYISNSqgrlidlsnvktskE-GEEVsKKFQIRPEIAEVILRE 78 
                 55677888888899**********987776777777777665421.233345566777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 707.42
//
Query:       EPA06661.1  [L=39]
Description: hypothetical protein BG20_I2305, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.01   16.4   0.1      0.011   16.3   0.1    1.0  1  AAA_23    AAA domain
       0.01   16.3   0.1      0.012   16.1   0.1    1.1  1  ABC_tran  ABC transporter


Domain annotation for each model (and alignments):
>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.3   0.1   1.2e-06     0.011       1      32 [.       5      39 .]       5      39 .] 0.88

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.2e-06
      AAA_23  1 kLkienfrsfrdqeidF...skgltlItGpNGaGK 32
                kLki++ r ++ ++id    +++l++I+G  G+GK
  EPA06661.1  5 KLKIRGARHHNLKNIDVdipKNKLVVISGLSGSGK 39
                79********666666666999************9 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.1   0.1   1.4e-06     0.012       1      24 [.      16      39 .]      16      39 .] 0.98

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.4e-06
                EEEEEEEEETTSEEEEEESTTSSH CS
                xxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  1 lknvslklkegekvaivGenGaGK 24
                lkn+++++ ++++v+i G +G+GK
  EPA06661.1 16 LKNIDVDIPKNKLVVISGLSGSGK 39
                79*********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 271.66
//
Query:       EPA06662.1  [L=647]
Description: excinuclease ABC, B subunit, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-28   98.7   1.2    7.3e-28   96.6   0.6    2.4  2  UvrB_inter     UvrB interaction domain
    9.8e-23   79.7   4.1    2.8e-22   78.3   4.1    1.9  1  UvrB           Ultra-violet resistance protein B
      8e-19   68.0   1.1    2.3e-18   66.6   0.2    2.3  3  Helicase_C     Helicase conserved C-terminal domain
    1.1e-09   37.8   4.5    1.1e-09   37.8   4.5    2.7  2  UVR            UvrB/uvrC motif
    1.6e-07   31.5   0.0    1.6e-07   31.5   0.0    3.0  4  ResIII         Type III restriction enzyme, res subunit
    3.5e-07   30.2   0.2    0.00029   20.7   0.1    3.4  3  DEAD           DEAD/DEAH box helicase
    0.00067   19.4   0.0      0.037   13.8   0.0    2.8  3  AAA_30         AAA domain
  ------ inclusion threshold ------
      0.025   14.1   0.3       0.11   12.0   0.2    2.0  2  Met_synt_B12   Vitamin B12 dependent methionine synthase, act
      0.036   14.2   0.0        8.5    6.6   0.0    2.6  2  Rhomboid_N     Cytoplasmic N-terminal domain of rhomboid seri
      0.045   14.0   0.9       0.95    9.7   0.0    3.1  3  AAA_22         AAA domain
       0.19   11.6   0.6        1.2    9.0   0.1    2.5  2  MEDS           MEDS: MEthanogen/methylotroph, DcmR Sensory do
       0.56   10.5   5.1         14    6.0   0.3    2.9  2  AAA_19         AAA domain
       0.63   10.4  11.3        3.4    8.0   0.0    4.0  3  Tup_N          Tup N-terminal
       0.87   10.1   3.8        5.1    7.6   0.0    2.8  2  ABC_tran       ABC transporter


Domain annotation for each model (and alignments):
>> UvrB_inter  UvrB interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.6   0.6   5.7e-31   7.3e-28       1      91 []     157     246 ..     157     246 .. 0.98
   2 ?   -1.1   0.0       1.7   2.2e+03      51      79 ..     460     488 ..     453     493 .. 0.77

  Alignments for each domain:
  == domain 1  score: 96.6 bits;  conditional E-value: 5.7e-31
  UvrB_inter   1 lelkvgqkidreellrkLvelqYerndvelkrGtFrvrGdtveifpasaeevairieffgdeiesireidpltgkslekleeitifPakhf 91 
                 ++++ g+ i+r++l++k +++ Yernd+e+ +G+Frv+Gdt++i+pa+ +e ++ri++fgd +e+i  +d ++ k ++k+++i+ifPakh+
  EPA06662.1 157 ITINSGDVIKRSDLIKKFIDARYERNDTEIAPGNFRVKGDTIDIIPAY-SEDIVRISMFGDDVEKIMLLDNISLKEKRKINQIKIFPAKHY 246
                 67999*******************************************.5****************************************9 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.7
  UvrB_inter  51 evairieffgdeiesireidpltgkslek 79 
                 ++ +r+     eie +++ + + +  l +
  EPA06662.1 460 KKHVRVRYMHSEIEGLQRTELIRQLRLGE 488
                 67789999999999999988887766655 PP

>> UvrB  Ultra-violet resistance protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.3   4.1   2.2e-25   2.8e-22       1      42 [.     544     585 ..     544     586 .. 0.98

  Alignments for each domain:
  == domain 1  score: 78.3 bits;  conditional E-value: 2.2e-25
                 EE-SS--HHHHHHHHHHHHHHHHHHHHHHHHT------XXXX CS
        UvrB   1 lYADkiTdSMkkAideTerRReiQeaYNeehgItPktikKki 42 
                 +YAD+iT+SM  AideT+rR+e+Q++YN+eh+ItP+ti+K++
  EPA06662.1 544 MYADNITKSMSSAIDETNRRKEKQIQYNKEHNITPQTIIKSV 585
                 9***************************************97 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       8.1     1e+04      14      32 ..      53      76 ..      42      96 .. 0.56
   2 ?   -3.0   0.0       7.2   9.2e+03      49      75 ..     228     252 ..     210     258 .. 0.67
   3 !   66.6   0.2   1.8e-21   2.3e-18       4     109 ..     425     536 ..     422     538 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 8.1
                TTTSEEEEEESSHH...HHHH..H CS
  Helicase_C 14 eeggkilifvntid...rlek..v 32
                + g+++l+++++++   +l++   
  EPA06662.1 53 RTGKNTLVISHNKTlaaQLYSelK 76
                456666666666664332222322 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 7.2
                 TSTHHHHHHHHHHHHTTSSSEEEESGG CS
  Helicase_C  49 elpqnereeileqfnkgesdvLiatdv 75 
                 +l+ + ++  ++ f +   ++Lia dv
  EPA06662.1 228 SLKEKRKINQIKIFPA--KHYLIAKDV 252
                 5666666666667755..347777776 PP

  == domain 3  score: 66.6 bits;  conditional E-value: 1.8e-21
                 HHHHHHH.HHTTTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEESSSS.....S CS
  Helicase_C   4 eallell.kleeeggkilifvntidrlek.vklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVinfdlp.....r 95 
                 + l++++ k+ ++++++l+ + t++++e+ +++l +kk+++v ++h+e++  +r e ++q + ge+dvL+  + + +G+dip+v+lV ++d++     r
  EPA06662.1 425 DDLIQEIaKRAAKNERVLVTTLTKRMAEDlAEYL-SKKHVRVRYMHSEIEGLQRTELIRQLRLGEFDVLVGINLLREGLDIPEVSLVAILDADkegflR 522
                 55666666999**************999977888.6677******************************************************999999 PP

                 SHHHHHHHHTTSSS CS
  Helicase_C  96 nvtsyiqriGRtgR 109
                 n ts+iq  GR++R
  EPA06662.1 523 NFTSLIQTFGRAAR 536
                 99***********9 PP

>> UVR  UvrB/uvrC motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       4.2   5.4e+03       3      16 ..     416     429 ..     415     430 .. 0.81
   2 !   37.8   4.5   8.3e-13   1.1e-09       4      36 .]     607     639 ..     606     639 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 4.2
         UVR   3 likeLeeemeeAae 16 
                 +i++ +++m+ +++
  EPA06662.1 416 EIRSTKDQMDDLIQ 429
                 68999999998876 PP

  == domain 2  score: 37.8 bits;  conditional E-value: 8.3e-13
         UVR   4 ikeLeeemeeAaenedFEkAAklRDqinalkkq 36 
                 i eLe++m++++e++dFE+A ++RD+i++l+k+
  EPA06662.1 607 IIELESQMKKYSEELDFERAIECRDRIKRLEKE 639
                 789****************************85 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.0   1.2e-10   1.6e-07       2      89 ..      10      88 ..       9     151 .. 0.75
   2 ?    0.9   0.2      0.31     4e+02      59     143 ..     222     335 ..     206     391 .. 0.56
   3 ?   -1.5   0.0       1.7   2.2e+03      96     117 ..     429     452 ..     376     491 .. 0.67
   4 ?   -3.5   0.2       6.8   8.7e+03     101     112 ..     568     579 ..     541     618 .. 0.52

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 1.2e-10
                -EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEEE CS
      ResIII  2 lelreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseaykeigkkv 89
                +e+   Q +ai+ l+e +k kr+ + l+   TG+GKT+ +a++i+r  k     ++l++ ++k+l  q+++e+k+f+++++  +g +v
  EPA06662.1 10 FEPTGDQPQAIDLLVEGVK-KRQIQTLL-GVTGSGKTFSIANVIARTGK-----NTLVISHNKTLAAQLYSELKQFFPKNN--VGYFV 88
                677778************8.55555555.68***************999.....8**********************9986..33333 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.31
                 EEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B--.......................-SEEEEEHHHHHHTH.........HHHTTT-S...... CS
      ResIII  59 flvprkslleqtleefkkflseaykeigkkvsgdkkka................kekdstnkkilvttiqsldadseee.eeeseellrdrfd...... 134
                 +l +++sl e+ + +  k+++ ++  i k+v+++  ++                k++ +  +k+ ++ i++l   s  + e++s ++     d      
  EPA06662.1 222 MLLDNISLKEKRKINQIKIFPAKHYLIAKDVREKAVRSikdelekrlpelneleKQRLEMRTKYDLEMIEELGYCS--GiENYSRHF-----Dgrnpge 313
                 5666666666666444444444444444443333333322223333443333323333333333333344433333..122222222.....1112234 PP

                 .............EEEEETGGG CS
      ResIII 135 .............viiiDEaHr 143
                              +++iDE+H 
  EPA06662.1 314 kafclmdffgddyLLVIDESHV 335
                 5555666666777899999995 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.7
                 -.........-SEEEEEHHHHHHT CS
      ResIII  96 a..kekdstnkkilvttiqsldad 117
                 +   +++++n ++lvtt  +  a+
  EPA06662.1 429 QeiAKRAAKNERVLVTTLTKRMAE 452
                 144555667777777776554444 PP

  == domain 4  score: -3.5 bits;  conditional E-value: 6.8
                 ...-SEEEEEHH CS
      ResIII 101 stnkkilvttiq 112
                 ++ +k + +t q
  EPA06662.1 568 IQYNKEHNITPQ 579
                 222222222333 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.1   2.2e-07   0.00029       3      75 ..      15      83 ..      13     145 .. 0.75
   2 ?    2.6   0.0     0.079     1e+02     124     174 ..     327     394 ..     322     396 .. 0.65
   3 ?    2.5   0.1     0.084   1.1e+02      36     103 ..     428     494 ..     422     516 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.2e-07
                HHHHHHHHHHTT....CEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST CS
                xxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        DEAD  3 iQaeaiplilgg....gdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyid 75
                 Q +ai+l+++g    +   + + TGsGKT   +  +         +tg+ +l+++  + La q +++lk+f+ + +
  EPA06662.1 15 DQPQAIDLLVEGvkkrQIQTLLGVTGSGKTFSIANVIA--------RTGKNTLVISHNKTLAAQLYSELKQFFPKNN 83
                588889998866543233458899******88444444........789999********************98543 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.079
                 EEEEETHHHHHHT...TTHHHHHHHHHHSHHHCTTSTTT.................SEEEEEESSBSHHHH CS
                 xxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxx.................xxxxxxxxxxxxxxx RF
        DEAD 124 flVlDEadrlldq...gfsdfinrilnqlpqitcdgklq.................rqvivlSATlpkdvk 174
                 +lV+DE +  l q    ++ +++r  + + +   +                     +++i++SAT+++  k
  EPA06662.1 327 LLVIDESHVTLPQlhgMYKGDYSRKKELV-TYGFRL--PsaydnrplkfeefegylKNTIFVSATPSDYEK 394
                 68999999998887765666666633333.222222..124566666688888888889999999985444 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.084
                 HHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEE.EEETTSSHHHHHHHHHTT.CSEEEE CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx.xxxxxx RF
        DEAD  36 lqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvl.liiggvaardqlskldng.vdivvg 103
                 +q++++ +  ++ ++l+ + t+ +ae+ ++ l+k     ++r++ + i+g ++++ +++l+ g  d++vg
  EPA06662.1 428 IQEIAK-RAAKNERVLVTTLTKRMAEDLAEYLSKKHV--RVRYMhSEIEGLQRTELIRQLRLGeFDVLVG 494
                 666666.566666888888888888888888866555..4666658899999999999999666999998 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   2.9e-05     0.037       5      67 ..      15      76 ..      12     113 .. 0.80
   2 ?    2.2   0.0       0.1   1.3e+02      41      69 ..     431     461 ..     421     498 .. 0.69
   3 ?   -2.1   0.0       2.1   2.7e+03      56     105 ..     532     603 ..     526     611 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.9e-05
      AAA_30  5 eQaaaveallt..sgdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelg 67
                +Q +a++ l++  +++++++l G+ G+GKt++++   +++++ g++ ++++++++ A++L  el 
  EPA06662.1 15 DQPQAIDLLVEgvKKRQIQTLLGVTGSGKTFSIA---NVIARTGKNTLVISHNKTLAAQLYSELK 76
                67777777765224678**************976...5677888999999999999999987765 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.1
      AAA_30  41 aweaa..ggrviglAptgkaAkvLaeelgie 69 
                 ++++a  ++rv++ + t+++A++Lae l  +
  EPA06662.1 431 IAKRAakNERVLVTTLTKRMAEDLAEYLSKK 461
                 4443323589**************9976643 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 2.1
      AAA_30  56 gkaAkvLaeelgieastiakllkrlk......................grarlepgtllivDEagmvdtkql 105
                 g+aA++++ ++ + a++i k +++                           +  p+++   DE+ + +++++
  EPA06662.1 532 GRAARNVNGSVIMYADNITKSMSSAIdetnrrkekqiqynkehnitpqTIIKSVPEQVTTLDESKLKSIHDM 603
                 567777777777777777666644335555555555566656666655333445566666777666666665 PP

>> Met_synt_B12  Vitamin B12 dependent methionine synthase, activation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.3   1.7e+03      25      50 ..     105     130 ..      90     178 .. 0.72
   2 ?   12.0   0.2   8.3e-05      0.11     132     192 ..     422     482 ..     413     486 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.3
  Met_synt_B12  25 pkiledeevgeeakklfkdaqallkr 50 
                     i +d++ +e+ +kl  +a+a+l +
    EPA06662.1 105 TYIEKDTQINEKIEKLRLEATAMLLS 130
                   5688899999999*******999965 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 8.3e-05
  Met_synt_B12 132 igieelaekfeaekddYssilvkaladrLaeAfaellhekvrkelWgyakdeklsneelik 192
                    ++++l+++  ++  + +++lv +l+ r+ae +ae+l +k  +  + +++ e l+ +eli+
    EPA06662.1 422 DQMDDLIQEIAKRAAKNERVLVTTLTKRMAEDLAEYLSKKHVRVRYMHSEIEGLQRTELIR 482
                   56888899999999999********************876555567788889999999887 PP

>> Rhomboid_N  Cytoplasmic N-terminal domain of rhomboid serine protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.026        34      29      57 ..      51      79 ..      15      83 .. 0.72
   2 ?    6.6   0.0    0.0066       8.5       4      33 ..     442     471 ..     440     481 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.026
  Rhomboid_N 29 lrseeegvq..lwledeeqlaqveaeleeFl 57
                + ++  g+   +++++++ +aq+ +el++F 
  EPA06662.1 51 IART--GKNtlVISHNKTLAAQLYSELKQFF 79
                4444..444425666***************6 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0066
  Rhomboid_N   4 LlslenpraaqafidYlrsqgiklelrsee 33 
                 L++    r+a  + +Yl+++++ ++++++e
  EPA06662.1 442 LVTTLTKRMAEDLAEYLSKKHVRVRYMHSE 471
                 5566678******************99986 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00074      0.95       4      29 ..      29      54 ..      25     101 .. 0.81
   2 ?    0.9   0.1      0.39     5e+02      42      95 ..     382     442 ..     365     484 .. 0.73
   3 ?   -3.5   0.1         9   1.2e+04      38      78 ..     563     603 ..     550     613 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00074
      AAA_22  4 tagilvvtGesGtGKTtllrrlleql 29
                +++i ++ G +G+GKT++++++  + 
  EPA06662.1 29 KRQIQTLLGVTGSGKTFSIANVIART 54
                6888999**************99886 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.39
      AAA_22  42 vvfvtlpsstsskdllrellralglelka......erlsseellealeqalrarav.iell 95 
                 ++fv ++ s   k++  +++++l +++         r +++++ +++++ ++++a+  ++l
  EPA06662.1 382 TIFVSATPSDYEKKISAQIAEQLVRPTGLldpaveIRSTKDQMDDLIQEIAKRAAKnERVL 442
                 6677777777666666667766666555577778666666666677777777766664444 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 9
      AAA_22  38 erpevvfvtlpsstsskdllrellralglelkaerlsseel 78 
                 ++ +++ ++  +  +++++ + + ++++   +++ +s +++
  EPA06662.1 563 RKEKQIQYNKEHNITPQTIIKSVPEQVTTLDESKLKSIHDM 603
                 45566666666666777777777777775555544444444 PP

>> MEDS  MEDS: MEthanogen/methylotroph, DcmR Sensory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.97   1.2e+03      68      95 ..     243     268 ..     216     292 .. 0.55
   2 ?    9.0   0.1   0.00091       1.2       8      80 ..     418     491 ..     414     503 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.97
        MEDS  68 aeetylrgggfdpermlealrralakal 95 
                 a ++++++ +++   +++ ++++l+k l
  EPA06662.1 243 AKHYLIAKDVREK--AVRSIKDELEKRL 268
                 5555544444444..4444444444433 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00091
        MEDS   8 edeeellealvpfikaglargekvlyvas.astldelrealrkagldvdaalesgqleildaeety..lrgggfdp 80 
                 ++ +++++ l++ i++  a++e+vl+ +  ++  ++l e+l+k+++ v   + s+ +e l+ +e+   lr g+fd 
  EPA06662.1 418 RSTKDQMDDLIQEIAKRAAKNERVLVTTLtKRMAEDLAEYLSKKHVRVRY-MHSE-IEGLQRTELIrqLRLGEFDV 491
                 688999*******************97767999999*****998885554.4443.55555555555566666665 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1     0.014        18       9      38 ..      29      58 ..      22      73 .. 0.80
   2 ?    6.0   0.3     0.011        14      34      75 ..     431     471 ..     422     587 .. 0.62

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.014
      AAA_19  9 kekvllvtaGpGtGKTrvlkhivallvelg 38
                k+++  +++  G+GKT  +  ++a   +++
  EPA06662.1 29 KRQIQTLLGVTGSGKTFSIANVIARTGKNT 58
                56778899*************999877655 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.011
      AAA_19  34 lvelggvkpeeillvaftgrAakelrerlaalgaeatTiHrl 75 
                 + ++   k e++l+ ++t+r a+ l+e l++  ++ + +H+ 
  EPA06662.1 431 IAKRA-AKNERVLVTTLTKRMAEDLAEYLSKKHVRVRYMHSE 471
                 44444.45599****************998777776666633 PP

>> Tup_N  Tup N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   1.7     0.052        66      31      66 ..     254     289 ..     243     293 .. 0.77
   2 ?    8.0   0.0    0.0027       3.4      11      40 ..     373     402 ..     372     434 .. 0.87
   3 ?    2.2   0.9      0.17   2.2e+02      35      63 ..     594     622 ..     550     642 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.052
       Tup_N  31 elkiqsqiqElqqirqtlyeLeeahrkikqqYEeei 66 
                 e+ ++s  +El++   +l eLe++  +++++Y+ e+
  EPA06662.1 254 EKAVRSIKDELEKRLPELNELEKQRLEMRTKYDLEM 289
                 445777777888888889999999999999999775 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0027
       Tup_N  11 qEfdalsqeasslkaqkdeyelkiqsqiqE 40 
                 +Ef+   +++  + a   +ye+ki++qi+E
  EPA06662.1 373 EEFEGYLKNTIFVSATPSDYEKKISAQIAE 402
                 5999999999999***************99 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.17
       Tup_N  35 qsqiqElqqirqtlyeLeeahrkikqqYE 63 
                 +s+++ ++ +   + eLe++ +k  ++ +
  EPA06662.1 594 ESKLKSIHDMTTDIIELESQMKKYSEELD 622
                 577888999999********999888765 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0     0.004       5.1       8      37 ..      27      57 ..      23     139 .. 0.62
   2 ?    2.2   0.7      0.18   2.3e+02      25      87 ..     525     616 ..     525     641 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.004
                EETTSEEEEEESTTSSHH.HHHHHHTTSS-- CS
                xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
    ABC_tran  8 lkegekvaivGenGaGKS.tLlkllagllkp 37
                +k+ ++  ++G +G+GK+ ++++++a+  k+
  EPA06662.1 27 VKKRQIQTLLGVTGSGKTfSIANVIARTGKN 57
                78889999**********5566677665543 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.18
                 HHHHHHHTTSS--SEEEEEETTCEGGG.......B-HHHCCHCEEEE-SS--S-TTSBHHHH.......................HHHTCHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxx.......................xxxxxxxx RF
    ABC_tran  25 StLlkllagllkpteGeilldgkdlke.......qeleslrkeigvlpqepqlfpeltvren.......................esdeeiek 87 
                 ++L++++ +  ++ +G++ +  +++++       ++ ++ +k+i++ +++ ++ p++ +++                        e +++++k
  EPA06662.1 525 TSLIQTFGRAARNVNGSVIMYADNITKsmssaidETNRRKEKQIQYNKEH-NITPQTIIKSVpeqvttldesklksihdmttdiiELESQMKK 616
                 57888888888888999977777777777778766777777788887777.666666566556566666655666555555555544444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (647 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1516  (0.0845557); expected 358.6 (0.02)
Passed bias filter:                      711  (0.0396564); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.83u 0.36s 00:00:01.19 Elapsed: 00:00:00.55
# Mc/sec: 3548.69
//
Query:       EPA06663.1  [L=57]
Description: hypothetical protein BG20_I2667, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.4e-06   25.2   1.2     0.0037   17.0   0.1    2.1  2  TPR_1     Tetratricopeptide repeat
    1.1e-05   25.0   0.2    1.5e-05   24.6   0.2    1.1  1  TPR_11    TPR repeat
    7.8e-05   22.5   0.1     0.0019   18.1   0.0    2.1  2  TPR_2     Tetratricopeptide repeat
    0.00021   21.9   0.0    0.00026   21.6   0.0    1.1  1  TPR_14    Tetratricopeptide repeat
    0.00074   20.0   0.0      0.001   19.5   0.0    1.3  1  TPR_19    Tetratricopeptide repeat
    0.00075   19.7   1.9     0.0023   18.2   0.2    2.3  2  TPR_17    Tetratricopeptide repeat
     0.0026   18.3   0.1      0.044   14.4   0.0    2.0  2  TPR_6     Tetratricopeptide repeat
     0.0035   18.0   0.0     0.0041   17.7   0.0    1.1  1  TPR_16    Tetratricopeptide repeat
     0.0053   16.9   0.0     0.0056   16.9   0.0    1.0  1  ANAPC3    Anaphase-promoting complex, cyclosome, subunit 3
     0.0056   16.8   0.4       0.35   11.2   0.0    2.1  2  TPR_8     Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   2.1e-06    0.0037       8      34 .]      16      42 ..      12      42 .. 0.93
   2 !    7.7   0.1    0.0018       3.3       2      13 ..      44      55 ..      43      57 .] 0.85

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.1e-06
                HHHHHHTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1  8 GnayfklgkydeAleyyekALelnPnn 34
                ++ ++++++++ A++ ++k L+ nP+n
  EPA06663.1 16 AMSLMEKNQPKGAIALFNKILKQNPKN 42
                78899********************98 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0018
                HHHHHHHHHHHH CS
       TPR_1  2 kalynlGnayfk 13
                +alyn+G+a+ +
  EPA06663.1 44 EALYNKGLALNQ 55
                89******9976 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.2   8.1e-09   1.5e-05       4      38 ..      19      53 ..      18      56 .. 0.94

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 8.1e-09
      TPR_11  4 yyeqGkyeeAieaYkkAlkldPdnaeayynLGlay 38
                ++e+++ ++Ai+ ++k lk +P+n ea+yn Gla+
  EPA06663.1 19 LMEKNQPKGAIALFNKILKQNPKNIEALYNKGLAL 53
                6899999**************************97 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.1e-06    0.0019       8      34 .]      16      42 ..      16      42 .. 0.96
   2 ?    2.7   0.1     0.095   1.7e+02       2      11 ..      44      53 ..      43      55 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.1e-06
       TPR_2  8 GlayyklgdyeeAleafekAleldPnn 34
                +++++++++++ A+++f+k l+ +P+n
  EPA06663.1 16 AMSLMEKNQPKGAIALFNKILKQNPKN 42
                689**********************97 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.095
       TPR_2  2 ealynlGlay 11
                ealyn Gla+
  EPA06663.1 44 EALYNKGLAL 53
                6777777765 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   1.4e-07   0.00026       9      41 ..      17      49 ..      11      52 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.4e-07
      TPR_14  9 eallalGdpdeAiallrralalaPddaeawlll 41
                  l++  +p++Aial++++l+++P++ ea++  
  EPA06663.1 17 MSLMEKNQPKGAIALFNKILKQNPKNIEALYNK 49
                5688999*********************99765 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   5.7e-07     0.001       1      30 [.      19      50 ..      19      57 .] 0.86

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 5.7e-07
      TPR_19  1 llaegdyaeAlalleqalqedpknaearl..l 30
                l++ +++  A+al+ ++l+++pkn ea++  +
  EPA06663.1 19 LMEKNQPKGAIALFNKILKQNPKNIEALYnkG 50
                78999***********************9444 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.47   8.4e+02      12      17 ..       9      14 ..       6      30 .. 0.57
   2 !   18.2   0.2   1.3e-06    0.0023       1      23 [.      31      53 ..      31      57 .] 0.91

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.47
      TPR_17 12 nadayn 17
                n+d+++
  EPA06663.1  9 NSDLMY 14
                555555 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 1.3e-06
      TPR_17  1 lylkaleldPnnadaynnLAell 23
                l+ k l+++P+n +a++n++ +l
  EPA06663.1 31 LFNKILKQNPKNIEALYNKGLAL 53
                799*****************998 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   2.4e-05     0.044       7      32 ..      16      41 ..      11      42 .. 0.82
   2 ?    2.3   0.0      0.18   3.3e+02       1      10 [.      44      53 ..      44      57 .] 0.85

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.4e-05
                HHHHHHHHHHHHHHHHHHHHHHH-TT CS
       TPR_6  7 alsyrklgdtdkAlealerlikeYPd 32
                a+s+ + +++  A++++++++k+ P+
  EPA06663.1 16 AMSLMEKNQPKGAIALFNKILKQNPK 41
                56666656*****************8 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.18
                HHHHHHHHHH CS
       TPR_6  1 dAlyklalsy 10
                +Aly+ +l++
  EPA06663.1 44 EALYNKGLAL 53
                79*****997 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   2.3e-06    0.0041       4      45 ..      16      54 ..      16      57 .] 0.94

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.3e-06
      TPR_16  4 araalragdyddAaaaleaalkrdpssPdaaeAllllgdaal 45
                a+++++ +++  A+a+++  lk++   P + eAl+++g+a+ 
  EPA06663.1 16 AMSLMEKNQPKGAIALFNKILKQN---PKNIEALYNKGLALN 54
                78999*******************...************985 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   3.1e-06    0.0056      20      67 ..       6      54 ..       3      57 .] 0.88

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.1e-06
                H--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHH CS
      ANAPC3 20 tespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcll 67
                + +++d+++ A +l + +q k A+ l++k  k+n+k+++++y ++ +l 
  EPA06663.1  6 STNNSDLMYDAMSLMEKNQPKGAIALFNKIlKQNPKNIEALYNKGLALN 54
                5688899999********************************8887765 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   0.00019      0.35       8      34 .]      16      42 ..      16      42 .. 0.93
   2 ?    4.2   0.1     0.034        61       2      13 ..      44      55 ..      43      57 .] 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00019
                HHHHHHTT-HHHHHHHHHHHHHHHHH. CS
       TPR_8  8 gsiylklgdyeeAkeyyekaleldpdn 34
                ++ ++++++ + A++ ++k l+ +p+n
  EPA06663.1 16 AMSLMEKNQPKGAIALFNKILKQNPKN 42
                578999*******************97 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.034
                CHHHHHHHHHHH CS
       TPR_8  2 eayynlgsiylk 13
                ea+yn+g+++ +
  EPA06663.1 44 EALYNKGLALNQ 55
                89*****99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.48
# Mc/sec: 358.49
//
Query:       EPA06664.1  [L=108]
Description: hypothetical protein BG20_I2669, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 824.82
//
Query:       EPA06665.1  [L=416]
Description: ATPase/histidine kinase/DNA gyrase B/HSP90 domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.1e-18   65.0   0.0    1.7e-17   64.0   0.0    1.5  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    7.2e-08   33.1   0.0    1.2e-07   32.4   0.0    1.4  1  GAF          GAF domain
    1.3e-06   28.3   1.4    2.5e-06   27.4   0.1    2.0  2  HisKA        His Kinase A (phospho-acceptor) domain
    4.6e-05   23.7   0.0    8.9e-05   22.8   0.0    1.4  1  GAF_2        GAF domain
    0.00044   20.1   0.2     0.0031   17.4   0.0    2.2  2  HATPase_c_5  GHKL domain
     0.0045   17.3   0.0     0.0098   16.2   0.0    1.6  1  GAF_3        GAF domain
  ------ inclusion threshold ------
       0.11   12.3   0.0       0.25   11.2   0.0    1.6  1  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like
       0.15   11.4  14.0       0.16   11.3   0.1    2.2  2  GAS          Growth-arrest specific micro-tubule binding
       0.79    9.9   2.9        1.3    9.2   1.5    2.0  2  DUF2703      Domain of unknown function (DUF2703)


Domain annotation for each model (and alignments):
>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.0   0.0   8.4e-21   1.7e-17       2     110 ..     311     411 ..     310     413 .. 0.91

  Alignments for each domain:
  == domain 1  score: 64.0 bits;  conditional E-value: 8.4e-21
                 HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHHHHHHHHHTTTEEEEEEETTT CS
   HATPase_c   2 dekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsivkklvelmgGeiwvesepgr 100
                 d k+++ ++snl  N++++ +++gei++ +  s+++++i  eD+G+Gip++ l+++fe++ +     ++++gtGlGl i+ +++++++G+++v+++p  
  EPA06665.1 311 DAKKMEAVFSNLFLNSIQAIGYSGEIKIILVDSSEKVSIIFEDSGPGIPENVLPRIFEPLFT-----TKSSGTGLGLGICLAIIKQHHGTLNVKNNP-- 402
                 66778899**********988*********97668***********************6666.....5899***********9998*******9999.. PP

                 EEEEEEEEES CS
   HATPase_c 101 Gttftftlpl 110
                  t+f+++lp+
  EPA06665.1 403 -TRFIIELPK 411
                 .999999986 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.0   6.2e-11   1.2e-07       2     131 ..      26     155 ..      25     157 .. 0.85

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 6.2e-11
                 HHHHHHHHHHHHHHHHTESEEEEEEEEETTEEE.CEEEEECCEEEETTSHHHHHHHHHSSSEEESTGGTSTTHHTTHHHHHHHHTTESEEEEEEEEE.T CS
         GAF   2 leelldtvveelrellgadrvalylpdydGlhy.dipqasrwlfmkngrgicgqvlatgqplvipdstpdprfaqynrrdllenmgirsslvvPlvn.d 98 
                 +ee +d++++ ++ ++++  +++ l d++   + +  ++++  +++   ++c +++ +++ ++i+d+t+d rf++  ++ + + + ir +++ P+++ +
  EPA06665.1  26 PEERFDRITKIAQIIFDVPIALVSLVDSNRQ-WfKSCAGLSAKETPRSMSFCSHAIYEQELMTINDATKDIRFLD--NPLVTGVPYIRFYAGKPIRApN 121
                 58899999999*******9999988434442.1235555555666666669************************..99999999***********99* PP

                 TEEEEEEEEEESSS.CSHHHHHHHHHHHHHHHHH CS
         GAF  99 gelwGllvlhnpsp.pftreelellqvladqvav 131
                 ++++G+l++++++p  f++++  +l  la  v+ 
  EPA06665.1 122 NQMLGTLCIIDTKPrDFSKADKSILSDLAKWVES 155
                 ***********77777*************99875 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       1.3   2.5e+03      42      59 ..     164     181 ..     153     193 .. 0.63
   2 !   27.4   0.1   1.2e-09   2.5e-06       2      63 ..     206     269 ..     205     272 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.3
                 HHHHHHHHHHHHHHHHHH CS
       HisKA  42 etiesearrldhlvedlL 59 
                 +++++ a+rl++  +dlL
  EPA06665.1 164 NSLQETAKRLENAQQDLL 181
                 445555555555555554 PP

  == domain 2  score: 27.4 bits;  conditional E-value: 1.2e-09
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCC CS
       HisKA   2 lgrflagvaHELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedlLdlsr 63 
                 +g +++ +aH+L++PL +++ +++ L+ +  +  +++ +    t+++++  +++l++d+L + +
  EPA06665.1 206 MGTMASRIAHDLKNPLQVLQITSDFLRQDleKHMDDKMRLRCSTLQNSIVKMNRLIDDVLNFVK 269
                 5789999*******************7766755557777799******************9987 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   4.5e-08   8.9e-05       4     130 ..      26     150 ..      23     152 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 4.5e-08
                 HHHHHHHHHHHHHHS.S..EEEEEEE-TTS-EEEEEEEES-TTSTT-S-B---TT.HHHHHHHHTS-EEES-GGG-S-HHHHH.HHHHTT--E.EEEEE CS
       GAF_2   4 leelldlvldelvel.gaalgyillvdddgglrlaawgeaeeefgaaldrplgeg.lvgealrtgrpvilndleedpdkkglp.aghaglrsf.lavPl 98 
                 +ee +d++++ ++ + ++ ++ + lvd +++     w    ++++a+    +++   + +a+ +++ + +nd   d +    p   ++++ +f ++ P+
  EPA06665.1  26 PEERFDRITKIAQIIfDVPIALVSLVDSNRQ-----WFKSCAGLSAKE--TPRSMsFCSHAIYEQELMTINDATKDIRFLDNPlVTGVPYIRFyAGKPI 117
                 6777888888887756999999999996665.....888888888888..6645548***************5555555555559999999999***** PP

                 -T.TS---EEEEES......--HHHHHHHHHHH CS
       GAF_2  99 is.egrvvGvlnlyankppafdeedlelLeela 130
                 ++ +++ +G l++  +kp++f+ +d ++L+ la
  EPA06665.1 118 RApNNQMLGTLCIIDTKPRDFSKADKSILSDLA 150
                 *****************************9987 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.2      0.45   9.1e+02      14      42 ..     173     202 ..     160     228 .. 0.80
   2 !   17.4   0.0   1.6e-06    0.0031       5      97 ..     314     408 ..     310     410 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.45
  HATPase_c_5  14 LdNAieacskiee.ekrfIrltvrekkksl 42 
                  L+NA +   k+++  ++++++++++ k+  
   EPA06665.1 173 LENAQQDLLKQNQnLEQEVKVKAEQLKNER 202
                  899999999988878888888888877654 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 1.6e-06
  HATPase_c_5   5 dlcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg..ek..kkle..sskskkeehGiGlksireivkkykgnlsieaedglFtl 96 
                   + ++++nl+ N+i+a         +I++ +  +++++ i++e s  g  e+   +++    ++k++  G+Gl     i+k+++g+l+++++ ++F  
   EPA06665.1 314 KMEAVFSNLFLNSIQAIGYSG----EIKIILVDSSEKVSIIFEDSGPGipENvlPRIFepLFTTKSSGTGLGLGICLAIIKQHHGTLNVKNNPTRFII 407
                  56789***********99877....69999999999999999999777442234333334335667899************************99976 PP

  HATPase_c_5  97 s 97 
                  +
   EPA06665.1 408 E 408
                  5 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   4.9e-06    0.0098      84     123 ..     112     153 ..      26     156 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.9e-06
       GAF_3  84 la.vPLvagr.qviGvlalastkprafdaedlelleslArqi 123
                 +a  P++a++ q++G+l++  tkpr+f+ +d++ l++lA ++
  EPA06665.1 112 YAgKPIRAPNnQMLGTLCIIDTKPRDFSKADKSILSDLAKWV 153
                 5556***********************************996 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00013      0.25       8      62 ..     320     375 ..     313     391 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00013
  HATPase_c_3   8 aelvdNsldA..daenvkievnknrgktgeivieDdGkGmseeelknalrlatsske 62 
                    l  Ns++A   + ++ki + +   ++ +i +eD G G++e+ l + +++  ++k+
   EPA06665.1 320 SNLFLNSIQAigYSGEIKIILVDSS-EKVSIIFEDSGPGIPENVLPRIFEPLFTTKS 375
                  5677899997224667****99985.799****************999998888877 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   9.4     0.044        87      23      68 ..     158     203 ..     154     207 .. 0.91
   2 ?   11.3   0.1     8e-05      0.16      57      96 ..     215     254 ..     206     264 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.044
         GAS  23 nNLelIkslKeeieelkkkeernekelseisqenkrlkepLkkaee 68 
                 +NL+l +sl e  ++l++ ++   k+ ++++qe k   e+Lk+ + 
  EPA06665.1 158 KNLSLTNSLQETAKRLENAQQDLLKQNQNLEQEVKVKAEQLKNERI 203
                 79***********************************999998765 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 8e-05
         GAS  57 krlkepLkkaeeeveeLrkqlknyekdkqslknlkarlke 96 
                  +lk pL+ ++   + Lr++l+++  dk++l+ +  +++ 
  EPA06665.1 215 HDLKNPLQVLQITSDFLRQDLEKHMDDKMRLRCSTLQNSI 254
                 579****************************998877665 PP

>> DUF2703  Domain of unknown function (DUF2703)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   1.5   0.00064       1.3      16      58 ..     164     206 ..     154     229 .. 0.84
   2 ?   -1.8   0.0       1.7   3.4e+03       7      41 ..     238     273 ..     235     281 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00064
     DUF2703  16 ercgeTgktleeavkelkeaLealgievelekvelseeelare 58 
                 +  +eT k le+a ++l ++ ++l+ ev+++ ++l++e+++  
  EPA06665.1 164 NSLQETAKRLENAQQDLLKQNQNLEQEVKVKAEQLKNERISVM 206
                 6789**********************************99966 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.7
     DUF2703   7 hldle.getCercgeTgktleeavkelkeaLealgi 41 
                 h+d++ + +C+  ++ + +++++++++ +  ++  +
  EPA06665.1 238 HMDDKmRLRCSTLQNSIVKMNRLIDDVLNFVKTSSL 273
                 667776777777777777777777766665555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1825  (0.10179); expected 358.6 (0.02)
Passed bias filter:                      846  (0.0471861); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.74u 0.37s 00:00:01.10 Elapsed: 00:00:00.53
# Mc/sec: 2348.70
//
Query:       EPA06666.1  [L=138]
Description: transcription factor TFIIB repeat protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-12   47.2   0.0    5.3e-12   45.6   0.0    1.7  2  TFIIB     Transcription factor TFIIB repeat
  ------ inclusion threshold ------
      0.038   14.0   0.1      0.051   13.6   0.1    1.2  1  RB_B      Retinoblastoma-associated protein B domain


Domain annotation for each model (and alignments):
>> TFIIB  Transcription factor TFIIB repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.0   5.9e-16   5.3e-12       6      68 ..      28      90 ..      24      93 .. 0.95
   2 ?   -1.1   0.0      0.23     2e+03       1      13 [.     117     129 ..     117     134 .. 0.83

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 5.9e-16
                HHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--S CS
       TFIIB  6 daleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVse 68
                ++l+Lpe V ++  +++++ +++k+l+Grs   i+ A  yi cr+ ++ rt  +i++  +V+ 
  EPA06666.1 28 AKLGLPESVVEQTAYWFRKISAKKMLAGRSTVVILCATTYIVCRLTNTPRTIHDIAEAGNVKI 90
                79*******************************************************999975 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.23
                 HHHHHHHTT--HH CS
       TFIIB   1 ikrfadaleLpek 13 
                 ++r+a a++++ek
  EPA06666.1 117 VTRLARAINISEK 129
                 6899999999985 PP

>> RB_B  Retinoblastoma-associated protein B domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   5.7e-06     0.051      15      94 ..      21      98 ..      12     106 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.7e-06
        RB_B 15 vrlrdLcerLklsselrekiwtlfehvlveetellkdRhlDqillcavYvvakvtkeelsFkeiikaYrkqpqasskvyr 94
                + l  L ++L l +++ e+    f+++  +++++l  R    il ++ Y+v+++t++ ++ ++i +a + + ++ +++yr
  EPA06666.1 21 TLLDGLRAKLGLPESVVEQTAYWFRKI--SAKKMLAGRSTVVILCATTYIVCRLTNTPRTIHDIAEAGNVKIKHLQRIYR 98
                556666677777776666655556554..5678999999877777779****************9998888877777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 861.86
//
Query:       EPA06667.1  [L=53]
Description: hypothetical protein BG20_I2482 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      7e-05   22.3   0.5    8.6e-05   22.0   0.5    1.1  1  TF_Zn_Ribbon    TFIIB zinc-binding
  ------ inclusion threshold ------
      0.017   14.8   0.1       0.02   14.6   0.1    1.1  1  Ribosomal_S27e  Ribosomal protein S27
      0.087   13.5   0.0       0.14   12.9   0.0    1.3  1  zf-ISL3         zinc-finger of transposase IS204/IS1001/IS109


Domain annotation for each model (and alignments):
>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.5   1.4e-08   8.6e-05       6      32 ..      11      37 ..      10      41 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.4e-08
                  TTCEECHEETSTTCEEESSSSBEEEEC CS
  TF_Zn_Ribbon  6 CgstnlveDpergelvCtdCGlVledn 32
                  C+ + +++D  +ge++C++CG+Vl + 
    EPA06667.1 11 CKKSIVITDDITGEITCSNCGVVLAEK 37
                  66444799999************9876 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   3.3e-06      0.02      12      40 ..      10      38 ..       5      49 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.3e-06
                    TTS-EEEEESS-SS-EEESSSTCEEEEEC CS
  Ribosomal_S27e 12 dCenetvvFshaatvvkCisCgkvLvePt 40
                    +C++  v+ +     ++C  Cg vL+e  
      EPA06667.1 10 GCKKSIVITDDITGEITCSNCGVVLAEKY 38
                    8************************9955 PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.3e-05      0.14       3      30 ..      25      52 ..      23      52 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.3e-05
     zf-ISL3  3 hrCPnCgsktvvkhgkkerrvrhlpigg 30
                ++C nCg + + k g+   ++++l+++g
  EPA06667.1 25 ITCSNCGVVLAEKYGRLDMKIQDLQMMG 52
                79*******99999999*******9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 360.26
//
Query:       EPA06668.1  [L=38]
Description: hypothetical protein BG20_I2481 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (38 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 284.35
//
Query:       EPA06669.1  [L=74]
Description: hypothetical protein BG20_I2533, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0062   16.8   1.5       0.04   14.2   1.5    2.1  1  MAP       MAP domain
     0.0081   15.8   0.0     0.0092   15.7   0.0    1.2  1  Auxin_BP  Auxin binding protein
  ------ inclusion threshold ------
      0.022   14.4   0.1      0.035   13.8   0.1    1.3  1  Cupin_2   Cupin domain


Domain annotation for each model (and alignments):
>> MAP  MAP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   1.5   6.6e-06      0.04      48      76 ..      31      59 ..      15      68 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.6e-06
         MAP 48 edlklakkAvYtvyfknGskkvvdlksei 76
                +++k  ++  Y vyf+nG k  + l++ +
  EPA06669.1 31 SKIKSKEQDIYHVYFENGAKTKMHLHNGN 59
                589999***************99998766 PP

>> Auxin_BP  Auxin binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.5e-06    0.0092      41      78 ..      35      72 ..      21      74 .] 0.89

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.5e-06
                -SSEEEEEEEE-TT-B--EEEESS-EEEEEEE--EEEE CS
    Auxin_BP 41 mkevevwlqtlapgsrtpihrhsceevfvvlkgkgtly 78
                 ke +++   +  g +t +h h  ++v++v kg g+l 
  EPA06669.1 35 SKEQDIYHVYFENGAKTKMHLHNGNQVLIVTKGIGSLE 72
                589999*****************************985 PP

>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   5.8e-06     0.035       3      33 ..      43      72 ..      41      73 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.8e-06
                EEEETTEEEEEECSSSEEEEEEEEESEEEEE CS
     Cupin_2  3 velppGesapshrHpgedeffyVleGegelt 33
                v ++ G+++++h H g+ ++++V +G g l+
  EPA06669.1 43 VYFENGAKTKMHLHNGN-QVLIVTKGIGSLE 72
                6788999**********.********99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       820  (0.045736); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 525.75
//
Query:       EPA06670.1  [L=214]
Description: tetratricopeptide repeat protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-27   93.8   7.8    0.00016   21.5   0.0    6.1  6  TPR_2        Tetratricopeptide repeat
    7.9e-26   88.8  15.1    2.5e-06   27.0   0.0    6.1  6  TPR_1        Tetratricopeptide repeat
    3.1e-20   71.6   4.3     0.0013   18.4   0.0    5.8  6  TPR_11       TPR repeat
    1.5e-18   65.8   7.5    5.8e-05   23.2   0.2    5.9  6  TPR_17       Tetratricopeptide repeat
    2.8e-16   59.6   0.5    9.1e-06   25.9   0.0    3.9  3  TPR_12       Tetratricopeptide repeat
      3e-16   58.2  11.8    3.7e-05   23.6   0.0    6.1  6  TPR_8        Tetratricopeptide repeat
    2.9e-15   55.8   0.1      0.064   13.9   0.0    6.2  6  TPR_6        Tetratricopeptide repeat
    3.7e-15   56.2   0.3    0.00047   20.6   0.0    3.5  4  TPR_19       Tetratricopeptide repeat
    2.2e-14   53.8   0.0      5e-05   23.9   0.0    3.7  4  TPR_16       Tetratricopeptide repeat
    8.2e-14   51.1   0.0       0.25   12.3   0.0    6.1  6  TPR_14       Tetratricopeptide repeat
    1.1e-11   44.7   3.7    1.5e-06   28.3   0.8    2.6  3  ANAPC3       Anaphase-promoting complex, cyclosome, subunit 3
    1.1e-10   41.0   3.1       0.06   13.2   0.8    5.1  5  TPR_10       Tetratricopeptide repeat
    1.9e-08   34.3   0.0     0.0033   17.5   0.0    3.1  3  TPR_9        Tetratricopeptide repeat
    9.3e-08   31.6   0.0       0.11   12.6   0.0    5.2  6  TPR_7        Tetratricopeptide repeat
    1.9e-05   24.7   6.7        1.1    9.4   0.1    4.9  6  MIT          MIT (microtubule interacting and transport) doma
    1.9e-05   24.7   5.8       0.19   11.9   0.0    5.2  6  Fis1_TPR_C   Fis1 C-terminal tetratricopeptide repeat
    0.00088   18.3   3.2       0.62    8.9   0.9    2.8  2  NARP1        NMDA receptor-regulated protein 1
     0.0018   17.3   0.1     0.0031   16.6   0.1    1.3  1  ChAPs        ChAPs (Chs5p-Arf1p-binding proteins)
     0.0028   17.4   1.2        4.1    7.1   0.0    3.7  3  TOM20_plant  Plant specific mitochondrial import receptor sub
     0.0084   16.4   1.6       0.15   12.4   0.2    3.2  4  TPR_20       Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.055   13.6   0.1       0.11   12.6   0.1    1.6  1  MerR_1       MerR HTH family regulatory protein
      0.057   13.7   1.5         25    5.4   0.0    4.0  3  PPR          PPR repeat
      0.082   12.5   0.0        0.2   11.3   0.0    1.6  1  HrpB1_HrpK   Bacterial type III secretion protein (HrpB1_HrpK
       0.13   12.8   1.8       0.65   10.6   1.8    2.3  1  s48_45       Sexual stage antigen s48/45 domain
       0.19   10.5   0.0       0.58    8.8   0.0    1.6  2  PknG_TPR     Protein kinase G tetratricopeptide repeat
       0.86    9.6   4.4        6.5    6.8   0.4    3.4  5  DUF627       Protein of unknown function (DUF627)


Domain annotation for each model (and alignments):
>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.016        11      17      34 .]       1      18 [.       1      18 [. 0.94
   2 !   20.5   0.1   5.1e-07   0.00035       1      34 []      19      52 ..      19      52 .. 0.95
   3 !   20.4   0.0   5.5e-07   0.00038       3      33 ..      55      85 ..      53      86 .. 0.94
   4 !   21.5   0.0   2.3e-07   0.00016       2      34 .]      88     120 ..      87     120 .. 0.95
   5 !   12.7   0.1   0.00016      0.11       2      32 ..     122     152 ..     121     154 .. 0.90
   6 !   12.4   0.0   0.00019      0.13      12      33 ..     166     187 ..     156     188 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.016
       TPR_2 17 yeeAleafekAleldPnn 34
                y +A+ +f+  ++++P++
  EPA06670.1  1 YSDAATCFDLLIKINPKD 18
                789*************86 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 5.1e-07
       TPR_2  1 aealynlGlayyklgdyeeAleafekAleldPnn 34
                a a +n+G a +++++ + A e+++ A++ dP++
  EPA06670.1 19 AAAMNNMGIAMAEMKNIQGASECYDNAIKADPKY 52
                6799****************************85 PP

  == domain 3  score: 20.4 bits;  conditional E-value: 5.5e-07
       TPR_2  3 alynlGlayyklgdyeeAleafekAleldPn 33
                 ++n G ++ kl+++eeAl++++kA+ ++P+
  EPA06670.1 55 SYFNKGVLLDKLQEHEEALNFLDKAITIEPR 85
                69**************************996 PP

  == domain 4  score: 21.5 bits;  conditional E-value: 2.3e-07
       TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                  al++ G ++ kl+++eeAl++fe + +  P++
  EPA06670.1  88 NALFYKGIVLGKLKRHEEALNCFENVYKKHPTH 120
                 79**************************99986 PP

  == domain 5  score: 12.7 bits;  conditional E-value: 0.00016
       TPR_2   2 ealynlGlayyklgdyeeAleafekAleldP 32 
                 +al+ +G  +++++++++A+e f+k l+   
  EPA06670.1 122 DALFHIGIELAENNQHKKAIEIFDKILANHK 152
                 699**********************998665 PP

  == domain 6  score: 12.4 bits;  conditional E-value: 0.00019
       TPR_2  12 yklgdyeeAleafekAleldPn 33 
                  +l +y e le+++kA+ l+P+
  EPA06670.1 166 SALEEYPESLELLKKAINLNPK 187
                 5789*****************7 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1      0.13        90      17      34 .]       1      18 [.       1      18 [. 0.92
   2 !   19.3   0.4   1.1e-06   0.00072       1      34 []      19      52 ..      19      52 .. 0.96
   3 !   27.0   0.0   3.6e-09   2.5e-06       3      33 ..      55      85 ..      53      86 .. 0.95
   4 !   21.1   0.0   2.8e-07   0.00019       2      33 ..      88     119 ..      87     120 .. 0.90
   5 !   13.7   0.1   5.9e-05      0.04       2      30 ..     122     150 ..     121     154 .. 0.90
   6 !   11.3   0.1   0.00033      0.23      13      33 ..     167     187 ..     165     188 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.13
                HHHHHHHHHHHHHHSTTH CS
       TPR_1 17 ydeAleyyekALelnPnn 34
                y +A  +++  +++nP++
  EPA06670.1  1 YSDAATCFDLLIKINPKD 18
                889*************86 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 1.1e-06
                HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1  1 akalynlGnayfklgkydeAleyyekALelnPnn 34
                a a +n+G a  ++++ + A e+y+ A++ +P++
  EPA06670.1 19 AAAMNNMGIAMAEMKNIQGASECYDNAIKADPKY 52
                6799****************************97 PP

  == domain 3  score: 27.0 bits;  conditional E-value: 3.6e-09
                HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
       TPR_1  3 alynlGnayfklgkydeAleyyekALelnPn 33
                +++n+G+++ kl++++eAl + +kA++++P 
  EPA06670.1 55 SYFNKGVLLDKLQEHEEALNFLDKAITIEPR 85
                79***************************95 PP

  == domain 4  score: 21.1 bits;  conditional E-value: 2.8e-07
                 HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
       TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPn 33 
                 +al+ +G ++ kl++++eAl ++e + +  P+
  EPA06670.1  88 NALFYKGIVLGKLKRHEEALNCFENVYKKHPT 119
                 79**********************98877776 PP

  == domain 5  score: 13.7 bits;  conditional E-value: 5.9e-05
                 HHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
       TPR_1   2 kalynlGnayfklgkydeAleyyekALel 30 
                 +al+ +G  + +++++++A+e ++k L  
  EPA06670.1 122 DALFHIGIELAENNQHKKAIEIFDKILAN 150
                 79***********************9975 PP

  == domain 6  score: 11.3 bits;  conditional E-value: 0.00033
                 HTT-HHHHHHHHHHHHHHSTT CS
       TPR_1  13 klgkydeAleyyekALelnPn 33 
                  l++y e le  +kA+ lnP+
  EPA06670.1 167 ALEEYPESLELLKKAINLNPK 187
                 589*****************7 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   8.1e-05     0.056      10      41 ..       1      32 [.       1      33 [. 0.91
   2 !   17.7   0.2     3e-06    0.0021       9      38 ..      34      63 ..      31      67 .. 0.88
   3 !   18.4   0.0   1.9e-06    0.0013       7      41 ..      66     100 ..      64     101 .. 0.93
   4 ?    5.4   0.0     0.022        15       8      35 ..     101     128 ..      99     135 .. 0.89
   5 ?    0.2   0.0      0.92   6.3e+02       4      19 ..     131     146 ..     128     160 .. 0.67
   6 !   14.6   0.0   2.8e-05     0.019       7      29 ..     168     190 ..     166     194 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.1e-05
      TPR_11 10 yeeAieaYkkAlkldPdnaeayynLGlayykq 41
                y +A +++   +k++P++a a +n+G a++++
  EPA06670.1  1 YSDAATCFDLLIKINPKDAAAMNNMGIAMAEM 32
                77899999999*****************9876 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 3e-06
      TPR_11  9 kyeeAieaYkkAlkldPdnaeayynLGlay 38
                ++ +A e+Y +A+k dP++   y+n G+++
  EPA06670.1 34 NIQGASECYDNAIKADPKYGASYFNKGVLL 63
                6789***********************987 PP

  == domain 3  score: 18.4 bits;  conditional E-value: 1.9e-06
      TPR_11   7 qGkyeeAieaYkkAlkldPdnaeayynLGlayykq 41 
                 +++ eeA++ + kA+ + P  ++a++  G ++ k+
  EPA06670.1  66 LQEHEEALNFLDKAITIEPRKPNALFYKGIVLGKL 100
                 6899*************************999886 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.022
      TPR_11   8 GkyeeAieaYkkAlkldPdnaeayynLG 35 
                  + eeA++++++  k  P+  +a++++G
  EPA06670.1 101 KRHEEALNCFENVYKKHPTHLDALFHIG 128
                 689***************9999999998 PP

  == domain 5  score: 0.2 bits;  conditional E-value: 0.92
      TPR_11   4 yyeqGkyeeAieaYkk 19 
                 + e ++ ++Aie + k
  EPA06670.1 131 LAENNQHKKAIEIFDK 146
                 6688999999986655 PP

  == domain 6  score: 14.6 bits;  conditional E-value: 2.8e-05
      TPR_11   7 qGkyeeAieaYkkAlkldPdnae 29 
                 + +y+e++e +kkA++l+P+  +
  EPA06670.1 168 LEEYPESLELLKKAINLNPKTIR 190
                 679****************9876 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   4.3e-05      0.03       3      32 ..       9      38 ..       7      40 .. 0.84
   2 !   23.2   0.2   8.4e-08   5.8e-05       1      33 [.      41      73 ..      41      74 .. 0.96
   3 !   12.9   0.0   0.00016      0.11       2      33 ..      76     107 ..      75     108 .. 0.94
   4 !   12.1   0.0    0.0003       0.2       1      34 []     109     142 ..     109     142 .. 0.95
   5 ?    1.3   0.0       0.8   5.5e+02       2      18 ..     144     160 ..     143     174 .. 0.85
   6 ?    0.3   0.0       1.7   1.2e+03       1      11 [.     177     187 ..     177     188 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.3e-05
      TPR_17  3 lkaleldPnnadaynnLAelllknGdlmtA 32
                   ++++P++a a+nn++ ++++ ++ + A
  EPA06670.1  9 DLLIKINPKDAAAMNNMGIAMAEMKNIQGA 38
                5579****************9988876655 PP

  == domain 2  score: 23.2 bits;  conditional E-value: 8.4e-08
      TPR_17  1 lylkaleldPnnadaynnLAelllknGdlmtAr 33
                +y +a++ dP++  +y+n+++ll k+ ++++A+
  EPA06670.1 41 CYDNAIKADPKYGASYFNKGVLLDKLQEHEEAL 73
                8***************************99995 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 0.00016
      TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                 + ka+ ++P  ++a+++++ +l k++++++A+
  EPA06670.1  76 LDKAITIEPRKPNALFYKGIVLGKLKRHEEAL 107
                 579*************************9995 PP

  == domain 4  score: 12.1 bits;  conditional E-value: 0.0003
      TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                 +++++ +++P++ da++  +  l++n+++++A++
  EPA06670.1 109 CFENVYKKHPTHLDALFHIGIELAENNQHKKAIE 142
                 799999**************************86 PP

  == domain 5  score: 1.3 bits;  conditional E-value: 0.8
      TPR_17   2 ylkaleldPnnadaynn 18 
                 + k l+++++n++  + 
  EPA06670.1 144 FDKILANHKDNVNIIYA 160
                 78999******998776 PP

  == domain 6  score: 0.3 bits;  conditional E-value: 1.7
      TPR_17   1 lylkaleldPn 11 
                 l++ka+ l+P+
  EPA06670.1 177 LLKKAINLNPK 187
                 679*******6 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.1   8.3e-08   5.7e-05       3      74 ..      19      82 ..      17      84 .. 0.90
   2 !   25.9   0.0   1.3e-08   9.1e-06       9      75 ..      93     151 ..      87     153 .. 0.85
   3 ?    5.6   0.0     0.028        19      14      31 ..     166     183 ..     154     187 .. 0.61

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 8.3e-08
      TPR_12  3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74
                a+a+nn++ + +++++ + A e+++ a+ +      p+   + ++++n g l+++l ++eeAl++l +a+ i
  EPA06670.1 19 AAAMNNMGIAMAEMKNIQGASECYDNAIKAD-----PK---YGASYFNKGVLLDKLQEHEEALNFLDKAITI 82
                56777**********************6666.....54...799*************************976 PP

  == domain 2  score: 25.9 bits;  conditional E-value: 1.3e-08
      TPR_12   9 laavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                  + vl +l+r++eAl ++e +   +     ++hp  + +l+ +g+ + + +++++A+e++ + la  
  EPA06670.1  93 KGIVLGKLKRHEEALNCFENV---Y-----KKHPTHLDALFHIGIELAENNQHKKAIEIFDKILANH 151
                 677888888888888888888...5.....77888899************************99876 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.028
      TPR_12  14 rrlgrydeAlellekale 31 
                  +l++y e+lell+ka++
  EPA06670.1 166 SALEEYPESLELLKKAIN 183
                 455566666666666554 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.56   3.9e+02      19      34 .]       3      18 ..       1      18 [. 0.85
   2 !   10.3   0.4   0.00098      0.68       3      33 ..      21      51 ..      19      52 .. 0.88
   3 !   23.6   0.0   5.3e-08   3.7e-05       3      32 ..      55      84 ..      53      86 .. 0.95
   4 !    8.4   0.0     0.004       2.8       7      27 ..      93     113 ..      87     115 .. 0.83
   5 !    8.9   0.0    0.0028       1.9       2      28 ..     122     148 ..     121     150 .. 0.92
   6 !    8.7   0.1    0.0033       2.3       4      33 ..     158     187 ..     155     188 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.56
                HHHHHHHHHHHHHHH. CS
       TPR_8 19 eAkeyyekaleldpdn 34
                 A  ++   ++++p++
  EPA06670.1  3 DAATCFDLLIKINPKD 18
                58899*********96 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00098
                HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
       TPR_8  3 ayynlgsiylklgdyeeAkeyyekaleldpd 33
                a++n+g +  ++++++ A e+y  a+++dp+
  EPA06670.1 21 AMNNMGIAMAEMKNIQGASECYDNAIKADPK 51
                77888888899*******************8 PP

  == domain 3  score: 23.6 bits;  conditional E-value: 5.3e-08
                HHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
       TPR_8  3 ayynlgsiylklgdyeeAkeyyekaleldp 32
                +y+n+g +++kl+++eeA  ++ ka++++p
  EPA06670.1 55 SYFNKGVLLDKLQEHEEALNFLDKAITIEP 84
                8***************************99 PP

  == domain 4  score: 8.4 bits;  conditional E-value: 0.004
                 HHHHHHHTT-HHHHHHHHHHH CS
       TPR_8   7 lgsiylklgdyeeAkeyyeka 27 
                 +g ++ kl+++eeA  ++e +
  EPA06670.1  93 KGIVLGKLKRHEEALNCFENV 113
                 677899************976 PP

  == domain 5  score: 8.9 bits;  conditional E-value: 0.0028
                 CHHHHHHHHHHHTT-HHHHHHHHHHHH CS
       TPR_8   2 eayynlgsiylklgdyeeAkeyyekal 28 
                 +a++++g  + + +++++A+e + k l
  EPA06670.1 122 DALFHIGIELAENNQHKKAIEIFDKIL 148
                 7999*******************9976 PP

  == domain 6  score: 8.7 bits;  conditional E-value: 0.0033
                 HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
       TPR_8   4 yynlgsiylklgdyeeAkeyyekaleldpd 33 
                  y +++  + l++y e+ e ++ka+ l+p+
  EPA06670.1 158 IYAKSRSKSALEEYPESLELLKKAINLNPK 187
                 588889999999*****************8 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0       1.6   1.1e+03      16      32 ..       1      17 [.       1      18 [. 0.88
   2 !    7.7   0.0    0.0092       6.3       5      32 ..      24      51 ..      20      52 .. 0.92
   3 !    7.8   0.0    0.0083       5.7       2      31 ..      55      84 ..      54      85 .. 0.89
   4 !   13.9   0.0   9.6e-05     0.066       2      32 ..      89     119 ..      88     120 .. 0.95
   5 !   13.9   0.0   9.3e-05     0.064       1      32 [.     122     153 ..     122     154 .. 0.88
   6 ?    3.4   0.1       0.2   1.4e+02      13      32 ..     168     187 ..     159     188 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 1.6
                HHHHHHHHHHHHHH-TT CS
       TPR_6 16 tdkAlealerlikeYPd 32
                +++A + ++ lik  P+
  EPA06670.1  1 YSDAATCFDLLIKINPK 17
                5789*********9997 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0092
                HHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
       TPR_6  5 klalsyrklgdtdkAlealerlikeYPd 32
                +++ ++ ++++ + A e +++ ik  P+
  EPA06670.1 24 NMGIAMAEMKNIQGASECYDNAIKADPK 51
                799*********************9996 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0083
                HHHHHHHHHHHHHHHHHHHHHHHHHHHH-T CS
       TPR_6  2 AlyklalsyrklgdtdkAlealerlikeYP 31
                ++++ + ++ kl+++++Al  l++ i+  P
  EPA06670.1 55 SYFNKGVLLDKLQEHEEALNFLDKAITIEP 84
                68999******77***********998776 PP

  == domain 4  score: 13.9 bits;  conditional E-value: 9.6e-05
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
       TPR_6   2 AlyklalsyrklgdtdkAlealerlikeYPd 32 
                 Al++ +  + kl+++++Al  +e++ k++P+
  EPA06670.1  89 ALFYKGIVLGKLKRHEEALNCFENVYKKHPT 119
                 9**********9******************7 PP

  == domain 5  score: 13.9 bits;  conditional E-value: 9.3e-05
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
       TPR_6   1 dAlyklalsyrklgdtdkAlealerlikeYPd 32 
                 dAl++++  + + +++ kA+e++++++ ++ d
  EPA06670.1 122 DALFHIGIELAENNQHKKAIEIFDKILANHKD 153
                 8******8888877*************99865 PP

  == domain 6  score: 3.4 bits;  conditional E-value: 0.2
                 HHHHHHHHHHHHHHHHH-TT CS
       TPR_6  13 lgdtdkAlealerlikeYPd 32 
                 l ++ ++le+l++ i+  P+
  EPA06670.1 168 LEEYPESLELLKKAINLNPK 187
                 45788899999999998887 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   2.4e-05     0.016      15      60 ..       9      55 ..       1      59 [. 0.84
   2 !   15.5   0.0   2.6e-05     0.018       5      55 ..      67     117 ..      65     126 .. 0.89
   3 !   20.6   0.0   6.8e-07   0.00047       5      57 ..     101     153 ..      91     156 .. 0.95
   4 !   19.2   0.0   1.9e-06    0.0013       1      58 [.     131     188 ..     131     198 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.4e-05
      TPR_19 15 eqalqedpknaearllLAeallalgqldeAealLdalpeedpdd.ar 60
                  +++ +pk+a+a  ++ +a+ ++++++ A ++ d + ++dp+  a 
  EPA06670.1  9 DLLIKINPKDAAAMNNMGIAMAEMKNIQGASECYDNAIKADPKYgAS 55
                556678************************************95454 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 2.6e-05
      TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeed 55 
                 + ++eAl++l +a++ +p  ++a+ +  ++l +l++ +eA ++ + + ++ 
  EPA06670.1  67 QEHEEALNFLDKAITIEPRKPNALFYKGIVLGKLKRHEEALNCFENVYKKH 117
                 6799*************************************9987666555 PP

  == domain 3  score: 20.6 bits;  conditional E-value: 6.8e-07
      TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                 ++++eAl+ +e+++++ p +++a+    + l +++q ++A+++ d++++  +d
  EPA06670.1 101 KRHEEALNCFENVYKKHPTHLDALFHIGIELAENNQHKKAIEIFDKILANHKD 153
                 5899********************************************99988 PP

  == domain 4  score: 19.2 bits;  conditional E-value: 1.9e-06
      TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd 58 
                 l +++++  A++++ ++l+   +n ++ ++  +   al ++ e  +lL+++ + +p++
  EPA06670.1 131 LAENNQHKKAIEIFDKILANHKDNVNIIYAKSRSKSALEEYPESLELLKKAINLNPKT 188
                 56899*************************************************9996 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.42   2.9e+02      13      41 ..       1      26 [.       1      31 [. 0.86
   2 !   23.9   0.0   7.3e-08     5e-05       8      64 ..      30      83 ..      23      89 .. 0.88
   3 !   23.4   0.0     1e-07   7.1e-05       6      64 ..      96     151 ..      93     155 .. 0.91
   4 ?   -0.6   0.0       3.2   2.2e+03       8      27 ..     166     185 ..     159     188 .. 0.60

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.42
      TPR_16 13 yddAaaaleaalkrdpssPdaaeAllllg 41
                y dAa  ++ ++k +   P +a+A+++ g
  EPA06670.1  1 YSDAATCFDLLIKIN---PKDAAAMNNMG 26
                789************...99999998755 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 7.3e-08
      TPR_16  8 lragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraa 64
                ++ ++ + A + ++ a+k+d   P   ++++++g+++ ++++++eA+ ++++a++  
  EPA06670.1 30 AEMKNIQGASECYDNAIKAD---PKYGASYFNKGVLLDKLQEHEEALNFLDKAITIE 83
                678999**************...***************************9998544 PP

  == domain 3  score: 23.4 bits;  conditional E-value: 1e-07
      TPR_16   6 aalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraa 64 
                  + ++++ ++A++ +e + k++   P + +Al++ g  +++++ +++A++ +++ l++ 
  EPA06670.1  96 VLGKLKRHEEALNCFENVYKKH---PTHLDALFHIGIELAENNQHKKAIEIFDKILANH 151
                 677899****************...99999***********************999875 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 3.2
      TPR_16   8 lragdyddAaaaleaalkrd 27 
                  ++ +y++ +++l+ a+ ++
  EPA06670.1 166 SALEEYPESLELLKKAINLN 185
                 55666777777777666555 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0      0.14     1e+02      18      39 ..       2      23 ..       1      28 [. 0.85
   2 ?    6.0   0.0     0.038        26       8      36 ..      26      54 ..      24      62 .. 0.85
   3 ?    7.3   0.0     0.014       9.9      11      40 ..      63      92 ..      59      97 .. 0.83
   4 !   12.3   0.0   0.00036      0.25       1      40 [.      87     126 ..      87     129 .. 0.88
   5 !   11.2   0.0   0.00079      0.54       3      37 ..     123     157 ..     121     164 .. 0.84
   6 ?    7.0   0.0     0.018        12       9      38 ..     163     192 ..     155     195 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.14
      TPR_14 18 deAiallrralalaPddaeawl 39
                 +A+++++ +++ +P+da+a  
  EPA06670.1  2 SDAATCFDLLIKINPKDAAAMN 23
                6899**************9965 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.038
      TPR_14  8 aeallalGdpdeAiallrralalaPddae 36
                + a+++  + ++A ++++ a++++P+  +
  EPA06670.1 26 GIAMAEMKNIQGASECYDNAIKADPKYGA 54
                78899999*****************9755 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.014
      TPR_14 11 llalGdpdeAiallrralalaPddaeawll 40
                l  l++++eA++ l++a+   P  + a+++
  EPA06670.1 63 LDKLQEHEEALNFLDKAITIEPRKPNALFY 92
                55789***************9987777766 PP

  == domain 4  score: 12.3 bits;  conditional E-value: 0.00036
      TPR_14   1 peallalaeallalGdpdeAiallrralalaPddaeawll 40 
                 p+al   + +l  l +++eA+++++ + +++P++++a+++
  EPA06670.1  87 PNALFYKGIVLGKLKRHEEALNCFENVYKKHPTHLDALFH 126
                 56777788899999*********************99987 PP

  == domain 5  score: 11.2 bits;  conditional E-value: 0.00079
      TPR_14   3 allalaeallalGdpdeAiallrralalaPddaea 37 
                 al  ++  l+++ ++++Ai++++++la + d+  +
  EPA06670.1 123 ALFHIGIELAENNQHKKAIEIFDKILANHKDNVNI 157
                 66677888999******************999765 PP

  == domain 6  score: 7.0 bits;  conditional E-value: 0.018
      TPR_14   9 eallalGdpdeAiallrralalaPddaeaw 38 
                 +   al+++ e+++ll++a+ l+P+  ++w
  EPA06670.1 163 RSKSALEEYPESLELLKKAINLNPKTIRTW 192
                 556789999****************99988 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       7.6   5.3e+03       5      22 ..       1      18 [.       1      24 [. 0.68
   2 !   24.0   0.1   4.8e-08   3.3e-05       2      81 ..      32     112 ..      31     113 .. 0.95
   3 !   28.3   0.8   2.1e-09   1.5e-06       4      81 ..     102     180 ..     101     181 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 7.6
                HHHHHHHHHHHH.HHH-- CS
      ANAPC3  5 yknAiflaerllaaetes 22
                y +A  ++++l + ++++
  EPA06670.1  1 YSDAATCFDLLIKINPKD 18
                677888888888655555 PP

  == domain 2  score: 24.0 bits;  conditional E-value: 4.8e-08
                 TT-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
      ANAPC3   2 qnnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                 ++n++ A  +++ + +a+++   + + ++  l +++++++A+++l+ka  ++++ +++++ ++ +l kLk++eeA++++e+
  EPA06670.1  32 MKNIQGASECYDNAIKADPKYGASYFNKGVLLDKLQEHEEALNFLDKAiTIEPRKPNALFYKGIVLGKLKRHEEALNCFEN 112
                 689999*********999999999999***************************************************997 PP

  == domain 3  score: 28.3 bits;  conditional E-value: 2.1e-09
                 -HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
      ANAPC3   4 nyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                 ++++A+ ++e ++++++ ++++++  +  l +n+q+k+A+e+++k     + + ++ y + ++  +L++y e + +L+k
  EPA06670.1 102 RHEEALNCFENVYKKHPTHLDALFHIGIELAENNQHKKAIEIFDKIlANHKDNVNIIYAKSRSKSALEEYPESLELLKK 180
                 799*******************************************555566667777777999************998 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.8   8.6e-05      0.06       2      30 ..      19      47 ..      19      48 .. 0.94
   2 !    9.4   0.0    0.0014      0.95       7      31 ..      58      82 ..      54      83 .. 0.89
   3 !    7.8   0.0    0.0046       3.1       9      29 ..      94     114 ..      93     117 .. 0.89
   4 ?    2.3   0.0      0.24   1.7e+02       8      30 ..     127     149 ..     121     152 .. 0.88
   5 ?    3.9   0.0     0.078        54      13      31 ..     166     184 ..     162     185 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.6e-05
      TPR_10  2 AsslnNLanalrqrgrydeAealleeala 30
                A+++nN+++a  ++++ ++A + ++ a+ 
  EPA06670.1 19 AAAMNNMGIAMAEMKNIQGASECYDNAIK 47
                89*********************999985 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0014
      TPR_10  7 NLanalrqrgrydeAealleealai 31
                N +++l ++++++eA+++l++a+ i
  EPA06670.1 58 NKGVLLDKLQEHEEALNFLDKAITI 82
                56889999**************986 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0046
      TPR_10   9 analrqrgrydeAealleeal 29 
                 +++l +++r++eA++ +e ++
  EPA06670.1  94 GIVLGKLKRHEEALNCFENVY 114
                 7999************99876 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.24
      TPR_10   8 LanalrqrgrydeAealleeala 30 
                 +++ l + +++++A +++++ la
  EPA06670.1 127 IGIELAENNQHKKAIEIFDKILA 149
                 78889999**********99886 PP

  == domain 5  score: 3.9 bits;  conditional E-value: 0.078
      TPR_10  13 rqrgrydeAealleealai 31 
                 +++ +y e+++ll++a+++
  EPA06670.1 166 SALEEYPESLELLKKAINL 184
                 5678999*********985 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   4.8e-06    0.0033      13      61 ..       3      51 ..       1      57 [. 0.93
   2 !   10.7   0.0   0.00064      0.44       9      61 ..      67     119 ..      59     125 .. 0.90
   3 ?    2.6   0.0      0.22   1.5e+02       6      60 ..     132     186 ..     127     196 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.8e-06
       TPR_9 13 ralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61
                 a  + ++l+ ++P+d+      G++ a++ ++++A ++ + ++  +p+
  EPA06670.1  3 DAATCFDLLIKINPKDAAAMNNMGIAMAEMKNIQGASECYDNAIKADPK 51
                6899****************************************99996 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00064
       TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                 +++e+al  ++  + + P+ p  ++  G++l +l + ++Al+++e    + p 
  EPA06670.1  67 QEHEEALNFLDKAITIEPRKPNALFYKGIVLGKLKRHEEALNCFENVYKKHPT 119
                 6899*****************************************88777775 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.22
       TPR_9   6 ireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalap 60 
                 ++++++ +a+++ + +l+ + d +  ++   +    l+ + + l+ L  ++ l+p
  EPA06670.1 132 AENNQHKKAIEIFDKILANHKDNVNIIYAKSRSKSALEEYPESLELLKKAINLNP 186
                 68999************99999999999888888888888888888888888877 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       8.1   5.6e+03      15      23 ..       1       9 [.       1      15 [. 0.82
   2 ?   -0.1   0.0       1.8   1.2e+03       2      32 ..      22      50 ..      21      51 .. 0.76
   3 !   12.6   0.0   0.00016      0.11       1      34 [.      55      86 ..      55      88 .. 0.87
   4 ?    4.1   0.0     0.081        56       1      24 [.      89     112 ..      89     124 .. 0.79
   5 ?    5.1   0.0     0.039        27      12      31 ..     134     153 ..     123     154 .. 0.84
   6 ?    2.0   0.0      0.38   2.6e+02      11      29 ..     167     183 ..     160     190 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 8.1
       TPR_7 15 yeeAielye 23
                y++A++++ 
  EPA06670.1  1 YSDAATCFD 9 
                789999986 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.8
       TPR_7  2 LlnLarlysrlGdyeeAielyeqsLaltkdp 32
                 +n++ +  ++ + + A e+y    a+  dp
  EPA06670.1 22 MNNMGIAMAEMKNIQGASECYDN--AIKADP 50
                57888888888888899999998..776665 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 0.00016
       TPR_7  1 aLlnLarlysrlGdyeeAielyeqsLaltkdped 34
                +++n ++l  +l+++eeA+ ++ +  a+t +p +
  EPA06670.1 55 SYFNKGVLLDKLQEHEEALNFLDK--AITIEPRK 86
                699*********************..88766655 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.081
       TPR_7   1 aLlnLarlysrlGdyeeAielyeq 24 
                 aL++ + +  +l ++eeA+ ++e 
  EPA06670.1  89 ALFYKGIVLGKLKRHEEALNCFEN 112
                 56777778888999********98 PP

  == domain 5  score: 5.1 bits;  conditional E-value: 0.039
       TPR_7  12 lGdyeeAielyeqsLaltkd 31 
                  +++++Aie++ + La +kd
  EPA06670.1 134 NNQHKKAIEIFDKILANHKD 153
                 5899*********9998887 PP

  == domain 6  score: 2.0 bits;  conditional E-value: 0.38
       TPR_7  11 rlGdyeeAielyeqsLalt 29 
                 +l +y e +el+++  a+ 
  EPA06670.1 167 ALEEYPESLELLKK--AIN 183
                 5889*********9..665 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       5.5   3.8e+03      27      42 ..       1      18 [.       1      25 [. 0.76
   2 ?    6.7   0.2     0.011       7.5       4      32 ..      19      47 ..      16      48 .. 0.87
   3 ?    6.6   0.0     0.012       8.2       5      31 ..      54      80 ..      51      82 .. 0.86
   4 ?   -1.7   0.0       4.7   3.3e+03      18      35 ..     101     111 ..      93     120 .. 0.64
   5 ?    1.7   0.0      0.39   2.7e+02      27      42 ..     137     153 ..     134     164 .. 0.72
   6 !    9.4   0.1    0.0016       1.1      21      45 ..     165     188 ..     160     204 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 5.5
         MIT 27 YkealelLlqalk.e.kn 42
                Y++a   + +++k + k+
  EPA06670.1  1 YSDAATCFDLLIKiNpKD 18
                899999999999955544 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.011
         MIT  4 AlelvkkAveeDnagnyeeAlelYkeale 32
                A ++ ++ + + + +n++ A e+Y +a++
  EPA06670.1 19 AAAMNNMGIAMAEMKNIQGASECYDNAIK 47
                77777888999999*************96 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.012
         MIT  5 lelvkkAveeDnagnyeeAlelYkeal 31
                 ++++k v +D+ ++ eeAl+   +a+
  EPA06670.1 54 ASYFNKGVLLDKLQEHEEALNFLDKAI 80
                57899***************9877776 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 4.7
         MIT  18 gnyeeAlelYkealelLl 35 
                 +  eeAl+++        
  EPA06670.1 101 KRHEEALNCF-------E 111
                 4455555554.......4 PP

  == domain 5  score: 1.7 bits;  conditional E-value: 0.39
         MIT  27 YkealelLlqalke.kn 42 
                  k+a+e++ ++l++ k+
  EPA06670.1 137 HKKAIEIFDKILANhKD 153
                 689*********94333 PP

  == domain 6  score: 9.4 bits;  conditional E-value: 0.0016
         MIT  21 eeAlelYkealelLlqalkekneer 45 
                 + Ale Y e+lelL++a++  n+++
  EPA06670.1 165 KSALEEYPESLELLKKAINL-NPKT 188
                 78****************93.3333 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.25   1.7e+02      17      35 ..       1      19 [.       1      23 [. 0.89
   2 ?   -2.3   0.0       6.9   4.8e+03       9      33 ..      27      51 ..      25      52 .. 0.75
   3 !   11.9   0.0   0.00027      0.19      13      38 ..      65      90 ..      64      96 .. 0.91
   4 !    7.4   0.1    0.0065       4.5       3      37 ..      89     123 ..      87     125 .. 0.88
   5 ?    1.5   0.0      0.46   3.2e+02       2      34 ..     122     154 ..     121     158 .. 0.86
   6 ?    1.4   0.1       0.5   3.4e+02      14      33 ..     168     187 ..     156     189 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.25
                HHHHHHHHHHHHHHTTS-H CS
  Fis1_TPR_C 17 YseArryvdalLeiEPenr 35
                Ys+A  + d l++i P+  
  EPA06670.1  1 YSDAATCFDLLIKINPKDA 19
                99**************875 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 6.9
                HHHHHHT-HHHHHHHHHHHHHHTTS CS
  Fis1_TPR_C  9 lGhyklgeYseArryvdalLeiEPe 33
                ++ + +++ + A ++ d  ++ +P+
  EPA06670.1 27 IAMAEMKNIQGASECYDNAIKADPK 51
                6667778888888888888888885 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.00027
                HHT-HHHHHHHHHHHHHHTTS-HHHH CS
  Fis1_TPR_C 13 klgeYseArryvdalLeiEPenrQaq 38
                kl+e++eA++++d  + iEP+  +a+
  EPA06670.1 65 KLQEHEEALNFLDKAITIEPRKPNAL 90
                99******************987775 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.0065
                 HHHHHHHHHHHHT-HHHHHHHHHHHHHHTTS-HHH CS
  Fis1_TPR_C   3 clYylAlGhyklgeYseArryvdalLeiEPenrQa 37 
                  l+y  +   kl++++eA+++ + + +++P    a
  EPA06670.1  89 ALFYKGIVLGKLKRHEEALNCFENVYKKHPTHLDA 123
                 6888888899********************87766 PP

  == domain 5  score: 1.5 bits;  conditional E-value: 0.46
                 HHHHHHHHHHHHHT-HHHHHHHHHHHHHHTTS- CS
  Fis1_TPR_C   2 eclYylAlGhyklgeYseArryvdalLeiEPen 34 
                 + l+++ +  +   ++++A +  d +L+ + +n
  EPA06670.1 122 DALFHIGIELAENNQHKKAIEIFDKILANHKDN 154
                 678888888888999************999888 PP

  == domain 6  score: 1.4 bits;  conditional E-value: 0.5
                 HT-HHHHHHHHHHHHHHTTS CS
  Fis1_TPR_C  14 lgeYseArryvdalLeiEPe 33 
                 l eY e++++++  +++ P+
  EPA06670.1 168 LEEYPESLELLKKAINLNPK 187
                 789*******9999998885 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0014      0.98     203     253 ..      30      80 ..      13      86 .. 0.90
   2 !    8.9   0.9    0.0009      0.62       6      98 ..      89     180 ..      84     212 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0014
                 HHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
       NARP1 203 dklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeear 253
                  ++++ + A e+ d+ai+ +p+    y +K+ +l +  + ++A + +++a 
  EPA06670.1  30 AEMKNIQGASECYDNAIKADPKYGASYFNKGVLLDKLQEHEEALNFLDKAI 80 
                 5678888999*************************************9985 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0009
                 HHHHHHHHHHHHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CHHHHHHHHHT..SSS-HHHHHHHHHH CS
       NARP1   6 llLyknqiieeagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpenskYyeglekakklskedeeallalyde 98 
                 +l yk  ++ +  ++eeAl+ +e++ k+   +l  +   +  l + +++++A +++ ++l   ++n +   +  ++k+  +e   + l+l+++
  EPA06670.1  89 ALFYKGIVLGKLKRHEEALNCFENVYKKHPTHLDALFHIGIELAENNQHKKAIEIFDKILANHKDNVNIIYAKSRSKSALEE-YPESLELLKK 180
                 6778888888888888888888888888888888888888888888888888888888888888887655554554442222.3333333333 PP

>> ChAPs  ChAPs (Chs5p-Arf1p-binding proteins)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   4.5e-06    0.0031     182     285 ..     100     206 ..      90     209 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.5e-06
                 HT-HHHHHHHHHHHHTT-GGGHHHHHHHHH..H.TT-HHHHHHHHHHHH-SSS-HHHHHHHHHHHHHHSS--HHHHHHHHHHHHH-TT-HHHHHHHHHH CS
       ChAPs 182 tkrydralellekLkeeepevvillarvll..l.adeEvdavkllneeleeeekdaelLllqaefllskkkeelAlevakravksaPsefktWalLvkv 277
                  kr+++al+ +e++ +++p     l ++ +  + +++  +a+++  + l++++++++++ +++      +++   le+ k+a+++ P   +tWa+  k+
  EPA06670.1 100 LKRHEEALNCFENVYKKHPTHLDALFHIGIelAeNNQHKKAIEIFDKILANHKDNVNIIYAKSRSKSALEEYPESLELLKKAINLNPKTIRTWAKEEKI 198
                 57999*************9988777766441142567789************************999999**9*************************9 PP

                 HHHTT-HH CS
       ChAPs 278 Yikledie 285
                 + kl+  e
  EPA06670.1 199 FEKLHTNE 206
                 99987766 PP

>> TOM20_plant  Plant specific mitochondrial import receptor subunit TOM20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0       0.4   2.7e+02      21      46 ..      15      40 ..       2      57 .. 0.61
   2 !    7.1   0.0    0.0059       4.1      46      74 ..      64      92 ..      54      96 .. 0.85
   3 ?    4.9   0.0     0.028        19       3      46 ..      99     142 ..      97     155 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.4
                 -TT-HHHHHHHHHHHHHHHHHS-HHH CS
  TOM20_plant 21 nPldadnllrWggallelsqfqsvae 46
                 nP da  +   g a+ e+   q  +e
   EPA06670.1 15 NPKDAAAMNNMGIAMAEMKNIQGASE 40
                 56666666666666655555554444 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0059
                 HHHHHHHHHHHHHHHHHHH-TT-HHHHHH CS
  TOM20_plant 46 eakqmiqdaiskleeallidPkkhdalWc 74
                 +  q  ++a+  l++a++i+P+k +al+ 
   EPA06670.1 64 DKLQEHEEALNFLDKAITIEPRKPNALFY 92
                 556677899*****************975 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.028
                  HHHHHHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHHHHHS-HHH CS
  TOM20_plant   3 rlllfeearkdaeatykknPldadnllrWggallelsqfqsvae 46 
                  +l   eea +  e+ ykk P   d l + g  l e  q ++ +e
   EPA06670.1  99 KLKRHEEALNCFENVYKKHPTHLDALFHIGIELAENNQHKKAIE 142
                  566678888999******************99999999988766 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1       1.1   7.5e+02      16      55 ..      13      52 ..       8      71 .. 0.80
   2 ?   -0.3   0.0         2   1.4e+03      13      45 ..      44      76 ..      37      87 .. 0.81
   3 ?    0.6   0.0       1.1   7.5e+02       4      45 ..      69     110 ..      66     117 .. 0.79
   4 !   12.4   0.2   0.00022      0.15       5      55 ..     104     154 ..     100     208 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 1.1
      TPR_20 16 aanpddldarldlAlallaagryeeAleqLleilkrdrkw 55
                + np+d +a+ ++  a ++ ++ + A e   + +k+d k+
  EPA06670.1 13 KINPKDAAAMNNMGIAMAEMKNIQGASECYDNAIKADPKY 52
                6699999999999999999999998887666666666655 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 2
      TPR_20 13 aalaanpddldarldlAlallaagryeeAleqL 45
                +a++a+p+  +  ++   +l + +++eeAl+ L
  EPA06670.1 44 NAIKADPKYGASYFNKGVLLDKLQEHEEALNFL 76
                678888888888888888888999999999876 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 1.1
      TPR_20   4 dapelaeleaalaanpddldarldlAlallaagryeeAleqL 45 
                 +++ l  l++a++ +p   +a +    +l + +r+eeAl+ +
  EPA06670.1  69 HEEALNFLDKAITIEPRKPNALFYKGIVLGKLKRHEEALNCF 110
                 556677788899999999999999999999999999999865 PP

  == domain 4  score: 12.4 bits;  conditional E-value: 0.00022
      TPR_20   5 apelaeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrkw 55 
                 ++ l  +e+ ++++p+ lda +     l++++++++A+e + +il+++++ 
  EPA06670.1 104 EEALNCFENVYKKHPTHLDALFHIGIELAENNQHKKAIEIFDKILANHKDN 154
                 566677888999*****************************9999999875 PP

>> MerR_1  MerR HTH family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00016      0.11       6      31 ..     178     203 ..     174     210 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00016
                 HHHHHTS-HHHHHHHHHHTT-S-EE- CS
      MerR_1   6 vakilgvtthtlrywekegllkpkrt 31 
                 + k+++++++t+r w ke ++  k +
  EPA06670.1 178 LKKAINLNPKTIRTWAKEEKIFEKLH 203
                 67899***************988763 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       5.4   3.7e+03      15      25 ..      68      78 ..      65      80 .. 0.80
   2 ?    4.4   0.1     0.077        53      10      24 ..      97     111 ..      95     116 .. 0.89
   3 ?    5.4   0.0     0.036        25      11      27 ..     132     148 ..     131     151 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 5.4
         PPR 15 kleeAlelfke 25
                ++eeAl ++++
  EPA06670.1 68 EHEEALNFLDK 78
                57999999886 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.077
         PPR  10 ycknGkleeAlelfk 24 
                 ++k  ++eeAl +f+
  EPA06670.1  97 LGKLKRHEEALNCFE 111
                 799**********98 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.036
         PPR  11 cknGkleeAlelfkeMk 27 
                 + n+++++A+e+f++++
  EPA06670.1 132 AENNQHKKAIEIFDKIL 148
                 67999*********986 PP

>> HrpB1_HrpK  Bacterial type III secretion protein (HrpB1_HrpK)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00029       0.2      20      77 ..      59     119 ..      53     142 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00029
  HrpB1_HrpK  20 lal...asedtedaellLdalrvLrPevaeldllegvlliergrweeAlrlLreveaeasg 77 
                 +++   + +++e+a + Ld    + P+ +++ ++ g++l + +r eeAl  +++v ++++ 
  EPA06670.1  59 KGVlldKLQEHEEALNFLDKAITIEPRKPNALFYKGIVLGKLKRHEEALNCFENVYKKHPT 119
                 55556678999********************************************988775 PP

>> s48_45  Sexual stage antigen s48/45 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.8   0.00094      0.65      48      90 ..     105     144 ..       3     168 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00094
                 ESTTCTTEEEEEETTEEEEGCCCCC-T-EEE--SCTTTTEEEE CS
      s48_45  48 ePenCFenvlekkeeekvkleellkkkielekdsnkknttsyl 90 
                 e  nCFenv+   +++ ++l+ l++  iel +++++k+ ++++
  EPA06670.1 105 EALNCFENVY---KKHPTHLDALFHIGIELAENNQHKKAIEIF 144
                 5679******...788888888888555555555544444443 PP

>> PknG_TPR  Protein kinase G tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.11        75     144     220 ..       1      78 [.       1      86 [. 0.85
   2 ?    8.8   0.0   0.00085      0.58     108     219 ..      67     179 ..      61     188 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.11
                 HHHHHHHHHHHHHHSTT-SHHHHHHH.HHHHHHT---TT-HHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHT CS
    PknG_TPR 144 yeeAaaeFdevlaalpGEiaPklaLA.ataElagetdeekyYrtVwrtdrgvvsAaFGlaRqlaaagdraaAvaaLde 220
                 y+ Aa++Fd ++++ p ++a    +  a aE+ + + +++ Y+   + d  + +  F     l +  + ++A++ Ld+
  EPA06670.1   1 YSDAATCFDLLIKINPKDAAAMNNMGiAMAEMKNIQGASECYDNAIKADPKYGASYFNKGVLLDKLQEHEEALNFLDK 78 
                 6789999999999999999986555523589999999999**********9999999999999999999999999996 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00085
                 T-HHHHHHHHHHHHHHH---HHHHHHHHHHHHHHT-HHHHHHHHHHHHHHSTT-SHHHHHHHHH.HHHHT---TT-HHHHHHHH-TT-HHHHHHHHHHH CS
    PknG_TPR 108 GdveearelLdeleeeveedWrldWyrglaeLlegdyeeAaaeFdevlaalpGEiaPklaLAat.aElagetdeekyYrtVwrtdrgvvsAaFGlaRql 205
                  ++eea + Ld+  +  +++    +y+g+     ++ eeA ++F++v++  p  +   + + +  aE ++++++ + ++ +  + +  v   +  +R +
  EPA06670.1  67 QEHEEALNFLDKAITIEPRKPNALFYKGIVLGKLKRHEEALNCFENVYKKHPTHLDALFHIGIElAENNQHKKAIEIFDKILANHKDNVNIIYAKSRSK 165
                 5788999999999999999999999****999999*****************99998888776324444555556899999999999999999999999 PP

                 HHTT-HHHHHHHHH CS
    PknG_TPR 206 aaagdraaAvaaLd 219
                 +a ++  + ++ L 
  EPA06670.1 166 SALEEYPESLELLK 179
                 98888887777765 PP

>> DUF627  Protein of unknown function (DUF627)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.96   6.6e+02      55      99 ..      31      75 ..      20      84 .. 0.72
   2 ?   -0.8   0.0       2.2   1.5e+03       9      30 ..      67      88 ..      63      94 .. 0.80
   3 ?    0.6   0.0       0.8   5.5e+02      11      31 ..     103     123 ..      97     128 .. 0.79
   4 ?    6.8   0.4    0.0094       6.5       5      29 ..     131     155 ..     127     165 .. 0.85
   5 ?   -1.1   0.0       2.7   1.9e+03      10      29 ..     170     189 ..     160     206 .. 0.69

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.96
      DUF627 55 kfayllasvecfseavelsrfyArsLfelasqlgsklyYkkavkk 99
                +++ ++++ ec+ +a +    y  s f+ +  l++ ++ ++a++ 
  EPA06670.1 31 EMKNIQGASECYDNAIKADPKYGASYFNKGVLLDKLQEHEEALNF 75
                556677888888888888888888888888777777777777654 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.2
      DUF627  9 gnhikALeiiedlisrhgedek 30
                ++h +AL  ++++i  + ++ +
  EPA06670.1 67 QEHEEALNFLDKAITIEPRKPN 88
                57999*****999988877655 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.8
      DUF627  11 hikALeiiedlisrhgedeks 31 
                 h +AL  +e+++++h  + ++
  EPA06670.1 103 HEEALNCFENVYKKHPTHLDA 123
                 889***********9997544 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.0094
      DUF627   5 llargnhikALeiiedlisrhgede 29 
                 l ++  h kA+ei+++++++h+++ 
  EPA06670.1 131 LAENNQHKKAIEIFDKILANHKDNV 155
                 678899***************9864 PP

  == domain 5  score: -1.1 bits;  conditional E-value: 2.7
      DUF627  10 nhikALeiiedlisrhgede 29 
                 ++ + Le+++++i  + +  
  EPA06670.1 170 EYPESLELLKKAINLNPKTI 189
                 56777888888887776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       830  (0.0462937); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 1302.33
//
Query:       EPA06671.1  [L=93]
Description: hypothetical protein BG20_I1648 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-26   94.0   0.0    1.1e-26   94.0   0.0    1.0  1  Arginase  Arginase family


Domain annotation for each model (and alignments):
>> Arginase  Arginase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.0   0.0   6.1e-31   1.1e-26     202     277 ..      10      82 ..       1      85 [. 0.91

  Alignments for each domain:
  == domain 1  score: 94.0 bits;  conditional E-value: 6.1e-31
                 SEEEEEEEGGGBBTTTSTSSSS-BSS-B-HHHHHHHHHHHHCHSEEEEEEEE-B-GGGSSTTTHHHHHHHHHHHHH CS
    Arginase 202 dpvylSfDiDvlDpavaPGtGtpepgGltlrellallrelaeklnlvgaDvvEvnPaldteaeqtarlaarlvrel 277
                 + +y SfD+DvlDpa+aPG+G pe+ G+t+rel++l+  l++ +n++g+D+vE+nP++d+ +  ta++aa+++ +l
  EPA06671.1  10 NSMYTSFDLDVLDPAYAPGVGNPEAAGMTSRELFDLIYSLEN-KNVTGVDIVELNPQYDN-G-ATASIAAKIMSTL 82 
                 579*************************************99.9***************9.5.8*********995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 630.47
//
Query:       EPA06672.1  [L=115]
Description: hypothetical protein BG20_I1643 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       231  (0.0128842); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 774.84
//
Query:       EPA06673.1  [L=114]
Description: rhodanese-like protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.8e-09   37.5   0.2    5.7e-09   36.5   0.2    1.4  1  Rhodanese  Rhodanese-like domain


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.2   3.2e-13   5.7e-09       2     105 ..      12      98 ..      11      99 .. 0.87

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 3.2e-13
   Rhodanese   2 akelkell.ekgkvallDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycdgggraaaaaallkklGyknvsvldG 99 
                  kel++l+ ++++  + D R +eeY+kghI+ ++ +             +++e++   +++     ++vv++ ++ ++++ +a  l+  +  + ++l G
  EPA06673.1  12 EKELYDLIcNNDELLIYDLRKKEEYAKGHIKKSILI-------------QFDEKNLINASK----SSKVVLVSKDEEQSKKVALSLRNQN-IDAFYLIG 92 
                 589999998888888*********************.............665555555554....899**********9********888.79****** PP

   Rhodanese 100 Gfkawk 105
                 G+k+w 
  EPA06673.1  93 GIKNWT 98 
                 *****7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       800  (0.0446204); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.31s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 742.57
//
Query:       EPA06674.1  [L=102]
Description: hypothetical protein BG20_I1638, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.054   13.4   1.0      0.073   13.0   0.2    1.6  2  DUF4389   Domain of unknown function (DUF4389)


Domain annotation for each model (and alignments):
>> DUF4389  Domain of unknown function (DUF4389)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.23   4.1e+03      17      18 ..      22      23 ..       8      39 .. 0.56
   2 ?   13.0   0.2   4.1e-06     0.073      19      58 ..      44      84 ..      43      88 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.23
     DUF4389 17 vl 18
                ++
  EPA06674.1 22 AI 23
                22 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 4.1e-06
     DUF4389 19 slaslvlwvvvvvqflivLvtg.rpnepLrdfgksllrYia 58
                +++ +vl+ vv+v   i Lvtg ++ ++L+++ k+++ Y+ 
  EPA06674.1 44 GFMLIVLITVVLVTSGIWLVTGlQQFRSLSSWNKRYSNYLK 84
                678899***************6488899*********9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1178  (0.0657036); expected 358.6 (0.02)
Passed bias filter:                      681  (0.0379832); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 702.20
//
Query:       EPA06675.1  [L=95]
Description: ribosomal protein S26e [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.1e-23   81.1   0.7    8.6e-23   80.8   0.7    1.1  1  Ribosomal_S26e  Ribosomal protein S26e
     0.0059   16.7   0.5     0.0071   16.4   0.5    1.1  1  CxC5            CxC5 like cysteine cluster associated with KD
  ------ inclusion threshold ------
      0.018   15.1   3.3        1.8    8.6   0.1    2.1  2  zinc_ribbon_11  Probable zinc-ribbon
      0.047   13.6   1.0        1.1    9.3   0.1    2.3  2  zf-dskA_traR    Prokaryotic dksA/traR C4-type zinc finger


Domain annotation for each model (and alignments):
>> Ribosomal_S26e  Ribosomal protein S26e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.8   0.7   1.9e-26   8.6e-23       1      96 [.       1      92 [.       1      95 [] 0.92

  Alignments for each domain:
  == domain 1  score: 80.8 bits;  conditional E-value: 1.9e-26
                    X--S-SSTT----S-S---EEE-TTT--EEES----EEEEEEESS-SSSHHHHTTSBSSSS----EEEEEEE--HHHHHHTTSS----TTTTS--S CS
  Ribosomal_S26e  1 mtkKRrnngrnkkgrghvkivrCsncarlvpkdKaikrfvvrniveaaavrdlseasvyeeyalPklYiklaycvscaihskvvrvRsredrknre 96
                    m+ KR ++gr k g+g+  +v+C nc+ +vpkdKa k +   n+ve++ +++l+ + +y   a P +   + yc+scaih k+++ Rs+++r++r 
      EPA06675.1  1 MPLKRASRGRTKGGKGSSGTVQCVNCGCTVPKDKAKKVTGRINLVEHTLAKELRAQGAYI--ASPTV--LKWYCISCAIHFKILKIRSEDSRRQRG 92
                    99******************************************************8874..45654..4689********************996 PP

>> CxC5  CxC5 like cysteine cluster associated with KDZ transposases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.5   1.6e-06    0.0071      10      60 ..      20      79 ..      17      91 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.6e-06
        CxC5 10 tkkClnceckrrs..llqkesqrdvvlftldkg..vlpvw.....vlslyCpkCktrYyp 60
                t +C+nc c+ ++  + + + +++ v +tl k+  ++ ++     vl +yC +C +++  
  EPA06675.1 20 TVQCVNCGCTVPKdkAKKVTGRINLVEHTLAKElrAQGAYiasptVLKWYCISCAIHFKI 79
                679*******999999999************996633355666779**********9975 PP

>> zinc_ribbon_11  Probable zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.8   0.00067         3      22      43 ..      14      35 ..       6      52 .. 0.78
   2 ?    8.6   0.1    0.0004       1.8      88     108 ..      58      78 ..      32      85 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00067
  zinc_ribbon_11 22 aklnrqdvlcvscgctltlqrg 43
                     k + + v cv cgct+  ++ 
      EPA06675.1 14 GKGSSGTVQCVNCGCTVPKDKA 35
                    56678899********976665 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0004
  zinc_ribbon_11  88 adyalpkvrkwycvlcdedye 108
                     a  a p v kwyc+ c  +++
      EPA06675.1  58 AYIASPTVLKWYCISCAIHFK 78 
                     33467899********87765 PP

>> zf-dskA_traR  Prokaryotic dksA/traR C4-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1   0.00024       1.1       2      21 ..      17      38 ..      16      42 .. 0.80
   2 ?    3.0   0.1     0.022     1e+02      26      31 ..      69      74 ..      67      77 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00024
  zf-dskA_traR  2 iygs..CeeCGEpIpeaRlral 21
                  + g+  C  CG ++p  + + +
    EPA06675.1 17 SSGTvqCVNCGCTVPKDKAKKV 38
                  667789*********9988765 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.022
  zf-dskA_traR 26 lCveCq 31
                  +C++C+
    EPA06675.1 69 YCISCA 74
                  8****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 587.09
//
Query:       EPA06676.1  [L=600]
Description: CBS domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.1e-25   87.2  28.4    8.9e-17   60.7  15.7    2.7  2  TrkH      Cation transport protein
    1.1e-15   57.8   4.9    2.1e-07   31.3   0.4    2.6  2  CBS       CBS domain


Domain annotation for each model (and alignments):
>> TrkH  Cation transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   8.1   4.5e-11     4e-07      38     244 ..     216     403 ..     186     431 .. 0.73
   2 !   60.7  15.7   9.9e-21   8.9e-17     309     491 ..     429     595 ..     401     599 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 4.5e-11
        TrkH  38 ivkaaeialsvdgtlklll......esaslafldalfeavsgltttglsvivveeslprsgltlraqlqqiGglgvvvlaylslptlgrgsaflylsea 130
                  v a++++l   g +++l+      +++   f+da fe+  g+tt g s++ + e+lprs +++r  +q++Ggl+++   yl++  +      + ++++
  EPA06676.1 216 LVFASFMILVLFGMIPQLFvihfdtNDPVKLFADAFFESSAGFTTGGYSLVEHPEELPRSFTFYRGYAQFVGGLSFI---YLIVTVF------YPEKRV 305
                 444555555555555555445544344555579****************************************6555...5554444......333333 PP

        TrkH 131 qkeelggk..elrslselikilvvyyvgleilafvllvvliytakaysevvdstgvsplwwaffhsmSafnnlGfsltpnSlasfnknivillvaiifi 227
                  k ++g +  +++ l+el +i++++++++ ++ +++l   +y+    +e++         + f  ++Sa++++G s  +  +  f +    ++v++i +
  EPA06676.1 306 -KTMKGFIsgNVPHLKELFSIITIIFSIYAVIIALAL---FYLGG--GEIL---------DDFALAFSALSTGGTSPDSKIFDGFTT--PEYIVMMIAM 387
                 .4444433115899*************9999999999...55544..5665.........99*************************..45789***** PP

        TrkH 228 ilGnigFpillrviiai 244
                 ilG   F  ++ +   +
  EPA06676.1 388 ILGSLPFGFHYAFVR-T 403
                 ********9997654.3 PP

  == domain 2  score: 60.7 bits;  conditional E-value: 9.9e-21
        TrkH 309 sipkgsrvlkalFqsvstrta.GFsvvdlsnlhpaikvllvlmmyigglpgStaggIrrtnvyeefslgkyeieqekepkavskksidgkhlerqllvd 406
                  ++     lk +F ++s++t+ GF+++ ++nl+p    +++++m igg++ StaggI++ +++ + +l +y +++++ +        d+k +   l++ 
  EPA06676.1 429 TLSMDGNSLKNTFNMISASTTtGFATMNMDNLSPVAYTIMIIAMIIGGCGFSTAGGIKIFRFMQLAKL-RYIFDKNSVKI----SESDKKDIVVGLIIL 522
                 45555777999*********99****************************************998765.66666555433....555777777777777 PP

        TrkH 407 lwslflvlliilileglklsdvqepdfsffdiLfevvSaygtvGLSlGaknaslsaqlttisklvlialmirGrlrglpvlldra 491
                   s+++ ll++  +        +   ++f d++f  vSa++t G   G     +sa l+++  +v+++lmi+Gr +++ ++  ++
  EPA06676.1 523 GVSIIIPLLVAAYMH-----TLG---YDFQDAFFDGVSAITTTGHVAG----TVSAALNPFITMVFGFLMILGRIEIILLVYMFV 595
                 777776666666666.....455...9*********************....9************************98877776 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.4   2.3e-11   2.1e-07       1      56 [.      15      70 ..      15      71 .. 0.90
   2 !   28.1   0.4   2.3e-10   2.1e-06       2      55 ..      82     135 ..      81     137 .. 0.90

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 2.3e-11
                HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
         CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56
                V+++ +++v+++++   + ea  ++++k+v+ + VVd++ +++Givt++D+l +l+
  EPA06676.1 15 VSQYYRTNVLMLSEHVKITEACTILKKKDVDEIIVVDDSYNPIGIVTDEDILTKLS 70
                778889*******************8888****99965557***********9986 PP

  == domain 2  score: 28.1 bits;  conditional E-value: 2.3e-10
                 HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
         CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                 gdim  +v+t+ +d  l+eale+mrek+++ + V+ +++ +vGi+ l  +++++
  EPA06676.1  82 GDIMVFPVITIGEDHFLSEALEIMREKKIRKIAVLSKSNLVVGILYLDTIVNLV 135
                 89*********************************8888566*****9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (600 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1101  (0.0614089); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.26s 00:00:00.90 Elapsed: 00:00:00.46
# Mc/sec: 3943.03
//
Query:       EPA06677.1  [L=185]
Description: hypothetical protein BG20_I1651, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.94    9.5   6.7        3.2    7.8   0.1    3.0  3  DUF4083   Domain of unknown function (DUF4083)


Domain annotation for each model (and alignments):
>> DUF4083  Domain of unknown function (DUF4083)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.6     0.002        36       2      26 ..       6      30 ..       5      35 .. 0.90
   2 ?   -2.5   0.1      0.29   5.1e+03      18      24 ..      48      54 ..      45      71 .. 0.58
   3 ?    7.8   0.1   0.00018       3.2       7      34 ..     100     127 ..      95     141 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.002
     DUF4083  2 lgdliyliivivLilllvfsftlfi 26
                ++  ++ ++ i ++++ v s ++f+
  EPA06677.1  6 IFGFLFICVAIAVTIASVASEIIFL 30
                7999****************99987 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.29
     DUF4083 18 lvfsftl 24
                +vf++++
  EPA06677.1 48 IVFGLYF 54
                4444443 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.00018
     DUF4083   7 yliivivLilllvfsftlfiRrvvsrsa 34 
                 ++ ++++ i+l+ fs ++f+  ++s++ 
  EPA06677.1 100 FQYLILLGIGLGNFSTYIFMKNLSSQNN 127
                 677888889***************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       758  (0.0422779); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1178.93
//
Query:       EPA06678.1  [L=44]
Description: hypothetical protein BG20_I1640 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0007   19.9   0.5     0.0011   19.3   0.5    1.4  1  zf-C2H2      Zinc finger, C2H2 type
     0.0027   18.4   0.3     0.0044   17.7   0.3    1.4  1  zf-C2H2_4    C2H2-type zinc finger
     0.0036   17.6   1.3     0.0037   17.6   1.3    1.1  1  zf-C2H2_2    C2H2 type zinc-finger (2 copies)
      0.004   17.0   0.9     0.0045   16.8   0.9    1.1  1  zf-C2H2_9    C2H2 type zinc-finger (1 copy)
      0.006   15.8   2.5      0.006   15.8   2.5    1.0  1  Actin_micro  Putative actin-like family
  ------ inclusion threshold ------
      0.024   14.9   0.2      0.024   14.9   0.2    1.0  1  CTU2         Cytoplasmic tRNA 2-thiolation protein 2
      0.031   12.8   0.9      0.029   12.9   0.9    1.0  1  DUF629       Protein of unknown function (DUF629)


Domain annotation for each model (and alignments):
>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.5   4.4e-07    0.0011       2      23 .]      11      33 ..      10      33 .. 0.97

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 4.4e-07
                EETTTTEEESSHHHHHHHHHC.C CS
     zf-C2H2  2 kCpdCgksFkrksnLkrHirt.H 23
                kC++C + F++++  k+H+ + H
  EPA06678.1 11 KCKICEMEFTDPERTKKHMIKaH 33
                8*******************999 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.3   1.7e-06    0.0044       2      24 .]      11      33 ..      10      33 .. 0.95

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.7e-06
   zf-C2H2_4  2 kCpiCgksFsskkaLlrHlkthH 24
                kC+iC   F+++++ ++H+ + H
  EPA06678.1 11 KCKICEMEFTDPERTKKHMIKAH 33
                8*************999**9988 PP

>> zf-C2H2_2  C2H2 type zinc-finger (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   1.3   1.4e-06    0.0037      50      78 ..       9      36 ..       2      44 .] 0.77

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.4e-06
   zf-C2H2_2 50 kleClyCekefkslealreHmkkkgHcki 78
                +++C +Ce ef++ e +++Hm k  H k 
  EPA06678.1  9 SNKCKICEMEFTDPERTKKHMIK-AHSKP 36
                589******************85.56664 PP

>> zf-C2H2_9  C2H2 type zinc-finger (1 copy)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.9   1.8e-06    0.0045       2      34 ..      10      44 .]       9      44 .] 0.82

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.8e-06
                -B-TTT--B-SSHHHHHHHHHHHTS..SS--HHHH CS
   zf-C2H2_9  2 plCPvCevkfnswkdlseHilsaas..ksdaeHvm 34
                + C +Ce++f + ++  +H+++a s  k d+eH m
  EPA06678.1 10 NKCKICEMEFTDPERTKKHMIKAHSkpKRDKEHPM 44
                57******************888762257888855 PP

>> Actin_micro  Putative actin-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   2.5   2.3e-06     0.006     220     257 ..       2      42 ..       1      44 [] 0.87

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.3e-06
  Actin_micro 220 lkekkefs..CkvCdvkfev.ekiseHllkkHiikehvkeh 257
                  +k ++efs  Ck+C+++f+  e+ ++H++k H + +  keh
   EPA06678.1   2 FKRDNEFSnkCKICEMEFTDpERTKKHMIKAHSKPKRDKEH 42 
                  7888888555**********9************98888887 PP

>> CTU2  Cytoplasmic tRNA 2-thiolation protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.2   9.4e-06     0.024      44      74 ..       8      38 ..       2      44 .] 0.69

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 9.4e-06
        CTU2 44 tsekCalCglplddkakewkrtitiselset 74
                 s+kC++C++++ d ++++k+ i++ +  ++
  EPA06678.1  8 FSNKCKICEMEFTDPERTKKHMIKAHSKPKR 38
                579*********7777777777766655443 PP

>> DUF629  Protein of unknown function (DUF629)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.9   1.1e-05     0.029      58      82 ..      11      35 ..       5      44 .] 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.1e-05
      DUF629 58 vCrtCsekfsdaeeckqHlvqeHva 82
                +C++C+ +f+d+e  k+H+ + H +
  EPA06678.1 11 KCKICEMEFTDPERTKKHMIKAHSK 35
                7**********************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.32u 0.21s 00:00:00.53 Elapsed: 00:00:00.37
# Mc/sec: 353.30
//
Query:       EPA06679.1  [L=194]
Description: arginase family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-36  126.2   0.0    2.3e-36  125.8   0.0    1.0  1  Arginase  Arginase family


Domain annotation for each model (and alignments):
>> Arginase  Arginase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.8   0.0   1.3e-40   2.3e-36       4     183 ..      19     188 ..      17     192 .. 0.91

  Alignments for each domain:
  == domain 1  score: 125.8 bits;  conditional E-value: 1.3e-40
                 EEEEEE--TTTSSSGGGGGHHHHHHHHHHTSBTHCHEETTTTE.SCCSEEEEEEEEE--SSCHHHHHHHHHHHHHHHHHTTCEEEEEESSGGGHHHHHH CS
    Arginase   4 allGvPfdaagsgrpGarfGPraireasarleealeynlelgv.leelkivdlgdvavtpvdneevleqieeavaeilkagklpivlGGDHsialgilr 101
                 +++G+Pfd++ s++pG+rfGP+ ir+a +++e    ++++ g+ le+++i+dlg+ + t+   +e+++ + + ++e+++++++  +lGG+Hs+++g++ 
  EPA06679.1  19 TVFGIPFDSTHSYKPGCRFGPDVIRDAFNNIEI---FHPQFGMdLESVNIEDLGNTTHTV-VASEMIDMVGKITKELVAKKRQLFILGGEHSLTFGTYM 113
                 69******************************8...5555555578**********9997.6667*******************************999 PP

                 HHHHHHSTTEEEEEESSS----SSCTTTBSSSTTSHHHHHHHHTSECGCEEEEEEE-STCSHHHHHHHHTTSEEEEHHHHHH CS
    Arginase 102 alaekygkplgvihfDAHaDlrtpetegsgnshGtpfrraaeegllkpkklvqiGirsvdneeyelakelgirvitmreide 183
                 ++ ++     g + fDAH+Dlr++   ++++sh+ ++rr++e++    ++++++G r++ +ee e++ke++i++it+r+++e
  EPA06679.1 114 SFPKE----TGYVVFDAHYDLRDEF-ANTKLSHAAYLRRIVEQRGS--DNILHVGARAFVKEELEFLKEHNIKTITDRQVRE 188
                 88764....789***********98.99*************66655..6******************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 1091.47
//
Query:       EPA06680.1  [L=133]
Description: hypothetical protein BG20_I1644 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 847.08
//
Query:       EPA06681.1  [L=193]
Description: CDP-alcohol phosphatidyltransferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-11   43.5   0.5    3.9e-11   43.5   0.5    2.4  2  CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase


Domain annotation for each model (and alignments):
>> CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.5   0.5   2.2e-15   3.9e-11       2      66 .]      26      92 ..      25      92 .. 0.87
   2 ?    0.1   1.1     0.077   1.4e+03      27      27 ..     151     151 ..      94     182 .. 0.53

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 2.2e-15
                     -HHHHHHHHHHHHHHHHHGGGS-H........HHHHHHHHHHHHHTTHHHHHHHHTT---HHHHHHHHHHH CS
  CDP-OH_P_transf  2 lPnaiTllrlllsvlailllltyyp......lvlailllliasltDalDGklARrlnqvstlGkllDslaD 66
                      Pn  T ++l++++++++ +   y+      l+++ +lll+++++D++DG++AR ++++s+ G +lDs+ D
       EPA06681.1 26 SPNFWTAVGLAFALASAF-V---YGlsiefgLIIGGVLLLVSGFFDMVDGQVARVTGKTSQKGSYLDSMFD 92
                     69**********777774.4...23346899999999999******************999*******988 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.077
                      . CS
  CDP-OH_P_transf  27 l 27 
                      l
       EPA06681.1 151 L 151
                      2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       762  (0.042501); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1209.47
//
Query:       EPA06682.1  [L=143]
Description: threonyl-tRNA synthetase domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.8e-45  154.4   0.2      2e-45  154.2   0.2    1.0  1  tRNA-Thr_ED  Archaea-specific editing domain of threonyl-tRNA


Domain annotation for each model (and alignments):
>> tRNA-Thr_ED  Archaea-specific editing domain of threonyl-tRNA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.2   0.2   1.1e-49     2e-45       1     136 [.       1     131 [.       1     132 [. 0.98

  Alignments for each domain:
  == domain 1  score: 154.2 bits;  conditional E-value: 1.1e-49
                  -EEEEEEEEEEEEEEEEESSSS-.SS---EEEESSEEEEEEE-BTT--H...HHHHHHHHHHHHHHHHHT-SEEEEEE-STS-SSB--HHHHHHHHHH CS
  tRNA-Thr_ED   1 mrlLlihadeleyeakkkalkeaeeeeekegrleealvvFiavEkeDeeekekvvekavkeikkvakkvkakkvvlypyaHLssslaspevakeilkk 98 
                  mr+L++h+d++ey+++kk++k+aee  ++++rlee++v+F+a+E++D++   +v+++a+++ik+ ++k+++kk++lypyaHLss+lasp++a ++lk+
   EPA06682.1   1 MRILQLHCDSIEYTPTKKEIKSAEEIVPETKRLEEVVVAFVAIENGDDS---SVAQNAISQIKNSMTKIGCKKLLLYPYAHLSSNLASPSTALSLLKE 95 
                  9***********************************************9...9********************************************* PP

                  HHHHHHTT.-EEEE--SSEEEEEEEEE--STTSEEEEE CS
  tRNA-Thr_ED  99 leeklkekglevkraPFGwykefeisckGhpLaelsre 136
                  +e++ +e  lev+++PFGw k+++i++kGhpLae s++
   EPA06682.1  96 MESSASE--LEVSHSPFGWTKSYKIQVKGHPLAESSKS 131
                  **99887..7*************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.35s 00:00:00.90 Elapsed: 00:00:00.56
# Mc/sec: 773.15
//
Query:       EPA06683.1  [L=477]
Description: threonine--tRNA ligase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      9e-24   83.5   0.3    1.7e-23   82.5   0.3    1.5  1  HGTP_anticodon  Anticodon binding domain
    1.3e-15   57.9   0.2    2.5e-15   56.9   0.2    1.5  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P


Domain annotation for each model (and alignments):
>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.5   0.3   1.9e-27   1.7e-23       1      93 [.     364     453 ..     364     454 .. 0.98

  Alignments for each domain:
  == domain 1  score: 82.5 bits;  conditional E-value: 1.9e-27
                     SEEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTCEEEEEETTHHHHHHHH CS
  HGTP_anticodon   1 qvvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtreqervsldelveklke 93 
                     qv vipl+e   e+   ++ l ++L+  +irv++dd+nesigk+ir+a++ +i++++v+Geke++++ +++rdr+t+  +++++d++++++ e
      EPA06683.1 364 QVRVIPLKE---EFSSICDTLVDKLSSFNIRVDIDDRNESIGKRIRDAEKDWIRYTLVIGEKEANSENLSIRDRQTGNVRELTFDNFINEINE 453
                     89*******...9***************************************************99************************987 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.9   0.2   2.8e-19   2.5e-15       5     178 ..     137     343 ..     134     344 .. 0.81

  Alignments for each domain:
  == domain 1  score: 56.9 bits;  conditional E-value: 2.8e-19
                   ETTSEEEEE-SSSHHHHHHHHHHHEEEB.GGSSEEEEEEEEE.EBTTTS.TBCTTTB-SEEEEEEEEEEES.GGGHHHHHHHHHHHHHHHHHHTT.S CS
                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx.xxxxxx.xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
  tRNA-synt_2b   5 drndreyiLkPtneetfvelirdevlrs.krLPlklyqiqtk.yRdEks.dsrGLlRvreFhqkdgyvfha.easlddslrdlikaisriferlgle 97 
                   d +++++ L+  ++ +   + ++    s k+LP +ly++++  +R+E+s ++ GL R+r F++ d++ f++  +++  +++  + +  +++++lg+ 
    EPA06683.1 137 DSEGKKLFLRFAACFGQFLMANEY-QMSyKNLPYRLYELTRYsFRREQSgELVGLRRLRAFTMPDCHAFCKdIEQSIKEIKVRFDLSRNVLKELGIV 232
                   344688999999999999999887.555499*******99855*****98999******************76999*******************96 PP

                   C....EEEEEEGTTSC...........................BTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHTTEEEECTTSSEEEEEEEE CS
                   x....xxxxxxxxxxx...........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  tRNA-synt_2b  98 f....raiielmsaks...........................adykdkkefeavsesltkgieigtiqklgtrlserlgatvldennreksvimic 163
                         ai+   ++                             +    k ef+ v+  ++k+  ++t q +  +  +r g++++de+n +k++i+++
    EPA06683.1 233 DsdyeMAIRFTEDF-YnenkpsieelvkkhgrpvlvemwkekfFYFVLKWEFNFVDS-MGKASALSTDQID-VENGNRYGIEFVDEHNVRKHPIILH 326
                   64554333333222.235567778888888888888888877433456778888888.9999999998888.8999********************* PP

                   EE.EE.HHHHHHHHHHH CS
                   xx.xx.xxxxxxxxxxx RF
  tRNA-synt_2b 164 aa.ig.veRllsaileq 178
                    +  g +eR++ ++le+
    EPA06683.1 327 NSpSGaIERIVYVLLEK 343
                   **9999*******9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (477 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3188.43
//
Query:       EPA06684.1  [L=120]
Description: hypothetical protein BG20_I1639 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-06   27.2   0.5    4.9e-06   26.4   0.5    1.3  1  HTH_45    Winged helix-turn-helix
    2.1e-05   24.4   0.0    3.3e-05   23.7   0.0    1.3  1  MarR      MarR family
  ------ inclusion threshold ------
      0.024   14.8   0.0      0.036   14.3   0.0    1.4  1  HTH_34    Winged helix DNA-binding domain
      0.067   13.2   0.0       0.14   12.1   0.0    1.5  1  PadR      Transcriptional regulator PadR-like family
      0.078   12.6   0.1       0.15   11.6   0.1    1.5  1  HTH_24    Winged helix-turn-helix DNA-binding


Domain annotation for each model (and alignments):
>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.5   1.4e-09   4.9e-06       1      69 [.      27     104 ..      27     111 .. 0.91

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 1.4e-09
      HTH_45   1 rRskleIiadILeais.egeakkTkimykanLsykllnkYLdmLvekgli........kkskekYvlTekGlellekl 69 
                 +R+++ I+ dI   +s  g+ ++T++     L+ +  ++ Ld L ++++i        k + + +++T+kG+++ +++
  EPA06684.1  27 YRDRIYIVKDIILTLSeYGQLNQTSLFSFCGLNISKHKEILDSLEKNEIIqrtevadgKRTVTIFKVTNKGMNFCHEI 104
                 69********97777758999*****************************99999998888899*********99886 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   9.2e-09   3.3e-05       8      58 ..      37      87 ..      36      88 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 9.2e-09
                HHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTSTTS CS
        MarR  8 iLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRskspeDrRe 58
                i+ +l+e g+l+++ L ++ g+++s   ++ld Lek++ i+R+   + +R 
  EPA06684.1 37 IILTLSEYGQLNQTSLFSFCGLNISKHKEILDSLEKNEIIQRTEVADGKRT 87
                7899**************************************998877776 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0     1e-05     0.036      30      67 ..      59      99 ..      37     111 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1e-05
      HTH_34 30 nLsvh...lkkLekagYievdkefkgkkprtllriTpeGre 67
                n+s+h   l+ Lek++ i+++   +gk+  t++++T++G +
  EPA06684.1 59 NISKHkeiLDSLEKNEIIQRTEVADGKRTVTIFKVTNKGMN 99
                555553337789***************************87 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.9e-05      0.14      37      72 ..      66     100 ..      65     103 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.9e-05
                 HHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHH CS
        PadR  37 aLkrLekeglveseweesgegpprkyYrlTdaGrre 72 
                 +L++Lek+++++++++  + +++  ++++T++G + 
  EPA06684.1  66 ILDSLEKNEIIQRTEVA-DGKRTVTIFKVTNKGMNF 100
                 8*************998.589999*********876 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   4.2e-05      0.15       5      48 .]      34      77 ..      32      82 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.2e-05
      HTH_24  5 drkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                 ++I+ +L + + ++q+ L   +gl +s  ++ l+ Le++++I+
  EPA06684.1 34 VKDIILTLSEYGQLNQTSLFSFCGLNISKHKEILDSLEKNEIIQ 77
                589***************************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       731  (0.0407719); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 840.01
//
Query:       EPA06685.1  [L=185]
Description: CBS domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.1e-15   55.4   0.2    2.9e-10   40.5   0.0    2.2  2  CBS             CBS domain
    1.6e-13   50.5   0.3    2.9e-13   49.6   0.3    1.4  1  HTH_3           Helix-turn-helix
    1.9e-08   34.2   0.1    3.5e-08   33.4   0.1    1.5  1  HTH_19          Helix-turn-helix domain
    2.1e-06   28.0   0.0    3.2e-06   27.4   0.0    1.2  1  HTH_31          Helix-turn-helix domain
     0.0086   15.9   0.0      0.015   15.2   0.0    1.4  1  HTH_25          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.022   14.9   0.0      0.044   13.9   0.0    1.4  1  MqsA_antitoxin  Antitoxin component of bacterial toxin-antito
      0.087   12.8   0.0       0.21   11.6   0.0    1.7  1  HTH_Crp_2       Crp-like helix-turn-helix domain
       0.13   11.8   0.1       0.26   10.9   0.1    1.5  1  Sigma70_r4      Sigma-70, region 4
       0.13   12.2   0.0       0.27   11.1   0.0    1.5  1  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.5   0.0   1.4e-13   2.9e-10       1      56 [.      67     121 ..      67     122 .. 0.89
   2 !   13.1   0.1   4.9e-05     0.098       5      53 ..     137     182 ..     131     185 .] 0.81

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 1.4e-13
                 HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
         CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                 +gd++++dvv ++p+ tl++a+++m e+ +s++P+ ++  +lvG++++  +++ l+
  EPA06685.1  67 AGDFCSKDVVKLKPNNTLHDAIKKMHESSISQIPIFNGT-ELVGMISEDGIVKHLA 121
                 68***********************5555*******655.5**********99987 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 4.9e-05
                 SBSSCEEEETTSBHHHHHHHHHHHTSS.EEEEEETTTBEEEEEEHHHHHH CS
         CBS   5 mtrdvvtvppdttleealelmrekgvs.rlPVVdedgklvGivtlrDllr 53 
                 m + ++ v+ dt+   ++ l+ +  +s ++  V +  k++Gi+t +D l+
  EPA06685.1 137 MEPVPPIVDYDTPANVLVPLI-R--YSkCI-LVSKKSKIIGIITASDTLK 182
                 6666789**************.7..66366.5657778*********876 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6   0.3   1.5e-16   2.9e-13       1      45 [.       8      52 ..       8      56 .. 0.96

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 1.5e-16
                HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHH CS
       HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkkla 45
                +k++R++ g++q++LA ++Gvs s i++iE+G+++Ps et+k++ 
  EPA06685.1  8 IKQMRLKIGITQKKLASMTGVSTSMINQIESGRSQPSYETAKRIF 52
                8*****************************************996 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.1   1.7e-11   3.5e-08       4      48 ..       8      51 ..       5      68 .. 0.95

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 1.7e-11
      HTH_19  4 LkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllki 48
                +k++R + g+tq++la+++g+s s+i++iE+g++  ps+e+ ++i
  EPA06685.1  8 IKQMRLKIGITQKKLASMTGVSTSMINQIESGRS-QPSYETAKRI 51
                89*******************************9.******9987 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   1.6e-09   3.2e-06       7      52 ..       9      53 ..       6      59 .. 0.91

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 1.6e-09
      HTH_31  7 ralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealar 52
                +++R + G++q+ +A  +gvs s ++++E+Gr + ps ++  ++ +
  EPA06685.1  9 KQMRLKIGITQKKLASMTGVSTSMINQIESGRSQ-PSYETAKRIFD 53
                7899999**************************6.****9999876 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   7.3e-06     0.015       3      36 ..       9      42 ..       7      48 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 7.3e-06
                HHHHHTTT--HHHHHHHSS--HHHHHHHHCT--T CS
      HTH_25  3 raaRearglsleevaketkIrkdylealEeddfd 36
                ++ R++ g++ +++a  t ++++++ ++E+++++
  EPA06685.1  9 KQMRLKIGITQKKLASMTGVSTSMINQIESGRSQ 42
                789***************************9875 PP

>> MqsA_antitoxin  Antitoxin component of bacterial toxin-antitoxin system, MqsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.2e-05     0.044      73     114 ..       7      48 ..       3      56 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.2e-05
  MqsA_antitoxin  73 fiarvrkkleldqreaaeifGgGvnafsryekGkvrpplalv 114
                      i+++r k++++q+++a++ G+ +   ++ e+G+++p+  + 
      EPA06685.1   7 SIKQMRLKIGITQKKLASMTGVSTSMINQIESGRSQPSYETA 48 
                     699**********************************97665 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00011      0.21      17      41 ..      12      36 ..       2      38 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                EEEEEHHHHHHHHHTTSSHHHHHHH CS
   HTH_Crp_2 17 eielpltqeelAsmlGltretvsri 41
                ++++ +tq+ lAsm G++ + +++i
  EPA06685.1 12 RLKIGITQKKLASMTGVSTSMINQI 36
                67899*************9999976 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00013      0.26      20      42 ..      16      38 ..       9      39 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00013
                T--HHHHHHHHTS-HHHHHHHHH CS
  Sigma70_r4 20 glTleEIgerlgiSrerVrqiek 42
                g T++ ++ + g+S + + qie+
  EPA06685.1 16 GITQKKLASMTGVSTSMINQIES 38
                78*******************96 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00014      0.27       7      43 ..      15      51 ..      10      55 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00014
  YdaS_antitoxin  7 ivGgqkaLAealgvsqqaVsqWlkgkkqvpaervpeI 43
                    i  +qk+LA   gvs + ++q  +g++q + e    I
      EPA06685.1 15 IGITQKKLASMTGVSTSMINQIESGRSQPSYETAKRI 51
                    5578******************999999777776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1223.97
//
Query:       EPA06686.1  [L=182]
Description: hypothetical protein BG20_I1517 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.1e-12   45.9   0.4    1.2e-11   45.3   0.1    1.5  2  Hemerythrin  Hemerythrin HHE cation binding domain
  ------ inclusion threshold ------
      0.026   14.6   0.3       0.34   11.0   0.0    2.0  2  Nuf2         Nuf2 family
      0.064   13.2   0.0      0.072   13.0   0.0    1.2  1  APC1_C       Anaphase-promoting complex sub unit 1 C-terminal


Domain annotation for each model (and alignments):
>> Hemerythrin  Hemerythrin HHE cation binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   0.1   2.1e-15   1.2e-11       3     125 ..       4     130 ..       2     135 .. 0.89
   2 ?   -2.6   0.0       1.4   8.2e+03      59      79 ..     148     162 ..     137     171 .. 0.49

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 2.1e-15
                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC....HCCHHHHHHHHHHHHHHHHHHHHHHCHHHHH.CCC.HHHHHHHHHHHHHHHHHHHHHHHHCHT CS
  Hemerythrin   3 vealdeeHralrallerlraladaaaevhga....lrklaelldelvdeleaHhaaEEellfPlledrpggravldvlereHdeirelleelrellkg 96 
                  ++ l+e+H  +r+l + ++++++++ + ++     l+k+  ++ e+vd   +Hh +EE+ +fP ++  ++ +++++    eH+  r +++++ e+lk+
   EPA06686.1   4 TNQLREDHVQVRRLEKIVSKCSQEIYKGADIpfsdLEKITVIISEFVDT--IHHSREEDSYFPCVASYDNLKEEIRKFMIEHEFGRNIARKISEYLKK 99 
                  5789************99******555554459***************8..*********************************************** PP

                  CG..GSTCHHHHHHHHHHHHHHHHHHHHHHH CS
  Hemerythrin  97 le..epsaaafaelleeladllreHiakEes 125
                  +   e s + +a+ l+++a  l++H+ kE++
   EPA06686.1 100 WRegEDSREPVARYLRTYAIFLDDHLNKENK 130
                  **54555555555****************95 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.4
                  CHHHHH.CCC.HHHHHHHHHH CS
  Hemerythrin  59 lfPlledrpggravldvlere 79 
                  ++  ++      +v++ ++++
   EPA06686.1 148 MYEQYR------SVIAIMKKV 162
                  444444......444444443 PP

>> Nuf2  Nuf2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.035   2.1e+02      83     127 ..      15      59 ..       6      80 .. 0.76
   2 ?   11.0   0.0   5.7e-05      0.34      24      92 ..     102     169 ..      82     175 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.035
        Nuf2  83 rslkrflkacgvedFslsDllkPdpkRtrriLSaliNFirFreer 127
                 r+l++++++c+ e  +  D+   d +++ +i+S +++ i++  e+
  EPA06686.1  15 RRLEKIVSKCSQEIYKGADIPFSDLEKITVIISEFVDTIHHSREE 59 
                 677777777777777777777777788888888777777766554 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 5.7e-05
        Nuf2  24 teedlakPtpefvqklyeqfleilmgiseedieqaaraaleeleepelyedslpllillrslkrflkac 92 
                 + ed ++P + ++++ y  fl+  ++ +++ ++ a+ ++l+++ee e+ye+  +++++++++++++ ++
  EPA06686.1 102 EGEDSREPVARYLRT-YAIFLDDHLNKENKFFDDAEANVLSKEEEIEMYEQYRSVIAIMKKVEQMIAEI 169
                 567777787777765.999********9999*********************************98776 PP

>> APC1_C  Anaphase-promoting complex sub unit 1 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.2e-05     0.072      82     145 ..      46     133 ..       4     163 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.2e-05
                 HHHHHSSSGGGTTTTS............SS-SSSSS-STTHHHHHHHHHHHHHHHHHH.TTHHHHHHHHS-................. CS
      APC1_C  82 vlefyssearlsalgaa..........eeksresLlrpsllesleqrvdalldswgke.gsakllsrylrsgav.............d 145
                 ++ef +  +++++  +           +e+ r+ ++++++   ++++++++l++w++   s++ + rylr+ a+             d
  EPA06686.1  46 ISEFVDTIHHSREEDSYfpcvasydnlKEEIRKFMIEHEFGRNIARKISEYLKKWREGeDSREPVARYLRTYAIflddhlnkenkffD 133
                 445555555555544447777888888899999**********************9994444889*****977676665555555551 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       988  (0.0551063); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 1106.94
//
Query:       EPA06687.1  [L=57]
Description: hypothetical protein BG20_I1515 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0072   15.8   0.9     0.0072   15.8   0.9    1.0  1  TryThrA_C      Tryptophan-Threonine-rich plasmodium antigen C
  ------ inclusion threshold ------
      0.047   13.4   0.1      0.047   13.4   0.1    1.0  1  Fibin          Fin bud initiation factor homologue
       0.23   11.4   0.0       0.24   11.4   0.0    1.0  1  NAD_binding_9  FAD-NAD(P)-binding


Domain annotation for each model (and alignments):
>> TryThrA_C  Tryptophan-Threonine-rich plasmodium antigen C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.9   1.2e-06    0.0072       6      58 ..       1      53 [.       1      57 [] 0.88

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.2e-06
   TryThrA_C  6 lkkleeeWekFneslenekkkwlekkekeweewlkeienKWlhynekldeeyk 58
                + +le+e +++  +  +ek +++ + +k ++++lk+i++K ++  e  d+  k
  EPA06687.1  1 MLRLENELKDLILNNMSEKIELMLESDKTFSKYLKQIQSKKMDPFEAADKITK 53
                6789************************************9988776666555 PP

>> Fibin  Fin bud initiation factor homologue
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   7.9e-06     0.047      74     117 ..       9      52 ..       1      57 [] 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.9e-06
       Fibin  74 aarvleglgksisydldGeesygkylrressqiseafsnsdksl 117
                  + +l+ ++  i+  l+ +++++kyl++ +s+  + f ++dk  
  EPA06687.1   9 KDLILNNMSEKIELMLESDKTFSKYLKQIQSKKMDPFEAADKIT 52 
                 56799********************************9999865 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   3.9e-05      0.24      48      95 ..       9      55 ..       3      57 .] 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.9e-05
  NAD_binding_9 48 eelllNvpasemslftddpptfaeWlrergaleeaeeldpddfvpRal 95
                   + l+lN  +++++l+ + ++tf ++l++ +  ++++ ++  d ++++l
     EPA06687.1  9 KDLILNNMSEKIELMLESDKTFSKYLKQIQS-KKMDPFEAADKITKSL 55
                   6799************************995.4467777777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1157  (0.0645323); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 373.99
//
Query:       EPA06688.1  [L=132]
Description: methylmalonyl-CoA epimerase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-22   80.1   0.0    1.5e-22   79.9   0.0    1.0  1  Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxyge
    9.8e-12   45.2   0.0      1e-11   45.1   0.0    1.1  1  Glyoxalase    Glyoxalase/Bleomycin resistance protein/Dioxyge
    1.6e-10   41.4   0.0    1.8e-10   41.2   0.0    1.0  1  Glyoxalase_3  Glyoxalase-like domain
      0.004   17.9   0.0      0.005   17.6   0.0    1.1  1  Glyoxalase_6  Glyoxalase-like domain
  ------ inclusion threshold ------
      0.025   14.5   0.1      0.042   13.7   0.1    1.4  1  TPR_10        Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.9   0.0   4.1e-26   1.5e-22       1     109 []       5     114 ..       5     114 .. 0.96

  Alignments for each domain:
  == domain 1  score: 79.9 bits;  conditional E-value: 4.1e-26
                   EEEEEE-S-HHHHHHHHHH.TT-EESS--E.EETTTTEEEEEEEETTEEEEEEEESSTT....-THHHTS-EEEEEEEEES-HHHHHHHHCTTTEEE CS
  Glyoxalase_4   1 dQigivVeDleaavarfsallGvgpwqryrdepqevdlafallgsgsvqieLieplegp....eflaehgeglhhlaywvddldaavarleeqGfev 93 
                   d+i+i+V+D+e+ ++ ++++lG++  +  ++e+++v++a+ +l +g  +ieL++p +++    +fl+++g+glhh a+++++++  v r+e  G+++
    EPA06688.1   5 DHIAIAVNDVEESAKVYQQALGIDHVEFETVESEGVKVAIIHLENG--RIELMQPTNDAspikKFLDKKGPGLHHMALETNNIEGEVTRMEGCGVQF 99 
                   6********************************************9..9********99777788888****************************9 PP

                   EEEEE-GGGTT-EEEE CS
  Glyoxalase_4  94 vqkgvragaagrrfay 109
                   + k +r+g ag+++++
    EPA06688.1 100 LGK-IRPGSAGTKVTF 114
                   996.7*********98 PP

>> Glyoxalase  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.1   0.0   2.9e-15     1e-11       1     116 [.       3     114 ..       3     127 .. 0.91

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 2.9e-15
                 EEEEEEEEESHHHHHHHHHHHHHTSEEEEEEEEEESTEEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSCTSEEEEEEEEEHCHHHHHHHHHHHTTG CS
  Glyoxalase   1 gidhvallvgdleksldFYtkvLGfklvkktdnteeteglriaffhaggghielvlneapsgaakhvkkieetvhhvafialdvedvgkaldrlkeagv 99 
                 +idh+a++v+d+e+s++ Y+++LG + v+ +    e eg++ a +h ++g+iel+   ++ ++ k++  + +++ +++++al++++++  + r++  gv
  EPA06688.1   3 KIDHIAIAVNDVEESAKVYQQALGIDHVEFET--VESEGVKVAIIHLENGRIELMQPTNDASPIKKF--LDKKGPGLHHMALETNNIEGEVTRMEGCGV 97 
                 69***************************999..999************************999999..55579************************* PP

                 EEEEEEECHHCTEEEEE CS
  Glyoxalase 100 kvvaepgrhyfgalysf 116
                 ++ +++     g  ++f
  EPA06688.1  98 QFLGKIRPGSAGTKVTF 114
                 ***99987766666655 PP

>> Glyoxalase_3  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   0.0   5.1e-14   1.8e-10       1     109 [.       4     105 ..       4     131 .. 0.83

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 5.1e-14
  Glyoxalase_3   1 lDHvvlavpdleeaaarfarrlGftvtpggehpglgtaNalvmfgdgYlEllavdpeapaperprlfgldrlakgeglhtlalrtddidataarlra 97 
                   +DH+ +av+d ee a+ ++++lG+  ++    ++ g + a++++ +g +El+++ ++a +   ++ f ld+  kg+glh++al+t++i+ ++ r++ 
    EPA06688.1   4 IDHIAIAVNDVEESAKVYQQALGIDHVEFETVESEGVKVAIIHLENGRIELMQPTNDASP--IKK-F-LDK--KGPGLHHMALETNNIEGEVTRMEG 94 
                   7**************************99999999*****************98777776..344.4.454..8**********************9 PP

  Glyoxalase_3  98 aGvdeagrrvrp 109
                    Gv+ +++ +rp
    EPA06688.1  95 CGVQ-FLGKIRP 105
                   9997.6666665 PP

>> Glyoxalase_6  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.4e-06     0.005       2      93 ..       7     109 ..       6     119 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.4e-06
  Glyoxalase_6   2 vvldaadpaalaaFwaaalgweveree.aaledpegvgpaaedaatllfqrvpe..........paknrvHldlavedldaevarlvalGArvlrep 87 
                   ++++++d+++ a+ +++alg + ++ e ++ e  +++  + e++   l+q++ +          ++    H+ l++++++ ev r++ +G + l++ 
    EPA06688.1   7 IAIAVNDVEESAKVYQQALGIDHVEFEtVESEGVKVAIIHLENGRIELMQPTNDaspikkfldkKGPGLHHMALETNNIEGEVTRMEGCGVQFLGKI 103
                   8999******************999995444444455555666666677777779999999865333458********************8888777 PP

  Glyoxalase_6  88 rdgthg 93 
                   r g +g
    EPA06688.1 104 RPGSAG 109
                   776665 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   1.2e-05     0.042      21      41 ..      10      30 ..       6      31 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.2e-05
      TPR_10 21 AealleealairrrllGpdHP 41
                A+++ ee+  +++++lG dH 
  EPA06688.1 10 AVNDVEESAKVYQQALGIDHV 30
                99******************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 944.56
//
Query:       EPA06689.1  [L=134]
Description: hypothetical protein BG20_I1513 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.33s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 784.22
//
Query:       EPA06690.1  [L=176]
Description: putative nicotinamide-nucleotide adenylyltransferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.9e-15   55.3   0.0    1.4e-14   54.5   0.0    1.6  1  CTP_transf_like  Cytidylyltransferase-like
      5e-05   22.7   0.1     0.0016   17.7   0.0    2.1  2  HIGH_NTase1      HIGH Nucleotidyl Transferase
     0.0072   16.0   0.0      0.075   12.7   0.0    2.1  2  Citrate_ly_lig   Citrate lyase ligase C-terminal domain
  ------ inclusion threshold ------
      0.064   13.4   0.0       0.15   12.3   0.0    1.6  1  MazG             MazG nucleotide pyrophosphohydrolase domain
      0.087   12.0   0.0       0.14   11.3   0.0    1.4  1  Pantoate_ligase  Pantoate-beta-alanine ligase


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.5   0.0   3.9e-18   1.4e-14       2      75 ..       5      86 ..       4     172 .. 0.76

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 3.9e-18
                     EEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHH...........H CS
  CTP_transf_like  2 agGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkkkplasaeeRlemlelakevdevisvdpweltr...........e 75
                     + G+F+p+H+GHl+l++q++++ +e +i++++s++ +  + k+++++ eR+em++   ++++ +  + + ++            +
       EPA06690.1  5 MMGRFQPFHNGHLNLAKQILEECDE-VIIAITSSQFNYLE-KDPFTSGERIEMIHNSLKESK-FDLSRCFIVAienqfniatwgS 86
                     78***********************.***********998.***************988777.7777766665444444444441 PP

>> HIGH_NTase1  HIGH Nucleotidyl Transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   4.5e-07    0.0016      10      41 ..       9      39 ..       6      41 .. 0.92
   2 ?    3.0   0.0     0.013        48     204     240 ..     127     160 ..     107     174 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.5e-07
  HIGH_NTase1 10 YNPfHnGHlyhlekakeltgadvviavmSGnF 41
                 + PfHnGHl + +++ e+  ++v+ia+ S++F
   EPA06690.1  9 FQPFHNGHLNLAKQILEE-CDEVIIAITSSQF 39
                 67***************8.5789*******99 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.013
  HIGH_NTase1 204 aSAtaiRkalkeekkleelkklvPestleilkeelkk 240
                    At iR+++      ++ k+lvP++++++l++  +k
   EPA06690.1 127 YNATHIRSLIVVG---DDWKTLVPHAVVKFLEKINAK 160
                  579*******555...689*********999876433 PP

>> Citrate_ly_lig  Citrate lyase ligase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   2.1e-05     0.075       9      55 ..      10      61 ..       3      88 .. 0.81
   2 ?    1.4   0.0     0.064   2.3e+02     126     181 ..     102     153 ..      69     154 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.1e-05
  Citrate_ly_lig  9 nPftlGhryLvekaakendvvhlfvvke.....dkslfsyeerlklvkkGik 55
                     Pf +Gh  L ++  +e+d v++ + +      +k  f+  er++++++ +k
      EPA06690.1 10 QPFHNGHLNLAKQILEECDEVIIAITSSqfnylEKDPFTSGERIEMIHNSLK 61
                    7************************997333334667788899999988766 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.064
  Citrate_ly_lig 126 nqalkevlekaeievveierkekeeelisaskvrkllkeknleklaelvPkttley 181
                     n+ +k  l +++i+v+    k  + +   a+++r+l+  ++  + ++lvP++  ++
      EPA06690.1 102 NDYVKMLLADSSIDVIS--PKFLDRTQYNATHIRSLIVVGD--DWKTLVPHAVVKF 153
                     77788888888776654..4444555667888888887664..4566777777766 PP

>> MazG  MazG nucleotide pyrophosphohydrolase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0     4e-05      0.15       2      31 ..      15      44 ..      14      45 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4e-05
                -HHHHHHHHHHHHHHHHHHHHTT-HHHHHH CS
        MazG  2 tpetllaylleEvgEvaeaIkkedrdelee 31
                ++++l++ +leE++Ev+ aI + +++ le+
  EPA06690.1 15 GHLNLAKQILEECDEVIIAITSSQFNYLEK 44
                58899*****************99999986 PP

>> Pantoate_ligase  Pantoate-beta-alanine ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0     4e-05      0.14      32      55 ..      12      35 ..       5      55 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4e-05
                     -GHHHHHHHHHHHHHSSEEEEEEE CS
  Pantoate_ligase 32 LHeGHlsLvkaakeendvvvvSiF 55
                     +H+GHl+L k+  ee+d v+++i 
       EPA06690.1 12 FHNGHLNLAKQILEECDEVIIAIT 35
                     6*******************9984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1114.25
//
Query:       EPA06691.1  [L=832]
Description: peptidase family M1 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.7e-89  297.7   1.4    9.2e-89  296.7   1.4    1.5  1  Peptidase_M1    Peptidase family M1 domain
    2.5e-63  214.5   0.4    9.2e-63  212.7   0.1    1.9  2  ERAP1_C         ERAP1-like C-terminal domain
    1.1e-54  185.5   4.1    2.3e-54  184.4   4.1    1.6  1  Peptidase_M1_N  Peptidase M1 N-terminal domain
     0.0049   16.3   0.1      0.016   14.6   0.1    1.8  1  Aminopep        Putative aminopeptidase
  ------ inclusion threshold ------
      0.055   13.3   0.9       0.29   11.0   0.0    2.6  3  DUF3013         Protein of unknown function (DUF3013)


Domain annotation for each model (and alignments):
>> Peptidase_M1  Peptidase family M1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  296.7   1.4   2.6e-92   9.2e-89       1     218 []     217     434 ..     217     434 .. 1.00

  Alignments for each domain:
  == domain 1  score: 296.7 bits;  conditional E-value: 2.6e-92
                   HHHHHHHHHHHHHHHHHTS--SSSEEEEEEESSTTSSEEEETTEEEEEGGGC-SSTTTS-HHHHHHHHHHHHHHHHHHHBTTTEEESSGGGGHHHHH CS
  Peptidase_M1   1 yalevtkkllefleeyfkvpYplpkldlvalpdfsagAMEnwglityreelllvdpenssesdkrsvaeviaHElaHqWfGnlVtmkwWddlwLnEG 97 
                   y+le +kkll+ +e+yf+++Yplpkldl+a+pdf+agAMEnwg+it+re+ ll+dp++ss+++k+ +aevi HE+aHqWfGnlVtmkwW+dlwLnE+
    EPA06691.1 217 YSLELGKKLLSSYEKYFGIKYPLPKLDLIAIPDFAAGAMENWGAITFRETILLYDPKTSSTRTKQYIAEVISHEIAHQWFGNLVTMKWWNDLWLNES 313
                   799********************************************************************************************** PP

                   HHHHHHHHHHHHHSCCCHCHHHHHHHCHHHHHHHHTSTTHHHSSGG-GSHHHHHHTSSHHHHHHHHHHHHHHHHHCTHHHHHHHHHHHHHHCTTEEE CS
  Peptidase_M1  98 fatyleylildklepewevseqllleeveealsedaldeshpitqevekpseidevFdsiaYeKGasllrmlekllgeevFqkglksYlkefkykna 194
                   fat+++ +++dk++pew++++q++ +++++a+  d+l+++hpi ++v++ sei e+Fd+i+Y+KG ++lrmle+++ge++Fqkglk+Yl++fky+na
    EPA06691.1 314 FATFMATKFVDKFYPEWDLWNQFIEDAMNTAMGLDSLKNTHPIDVKVNSTSEIREIFDAISYDKGGCVLRMLENYVGESNFQKGLKQYLADFKYDNA 410
                   ************************************************************************************************* PP

                   -HHHHHHHHHHCCCSCHHTHHHHH CS
  Peptidase_M1 195 etedlwdaleealnkdisevmdtw 218
                   e +dlwda+ + ++  ++++++tw
    EPA06691.1 411 EGKDLWDAIGKISKMPVRTMVSTW 434
                   ***********************9 PP

>> ERAP1_C  ERAP1-like C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.24   8.7e+02       4      23 ..      94     113 ..      94     133 .. 0.77
   2 !  212.7   0.1   2.6e-66   9.2e-63       3     314 ..     506     817 ..     505     818 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.24
                 ESGGG-SSSEEEE-HHHHHH CS
     ERAP1_C   4 lNdddtGyyrVnYdeeslaa 23 
                 lNd  +G+yr +Y +    +
  EPA06691.1  94 LNDRLLGFYRSQYKQNGKTK 113
                 79***********8876555 PP

  == domain 2  score: 212.7 bits;  conditional E-value: 2.6e-66
                 EESGGG-SSSEEEE-HHHHHHHHHHHH.GGGS-HHHHHHHHHHHHHHHHTTSS-HHHHHHGGG.GGGG--SHHHHHHHHHHHHHHHHHHTTSTTHHHHH CS
     ERAP1_C   3 llNdddtGyyrVnYdeeslaalleqll.skklspldRaglisdafalaragelsaadlldlllgylanEtdylvwsqalsqlatlksllsadplyaalk 100
                 + N++ +G+yrV+Yd++ l  l+  l   kk+ ++dR  + +d+f+l+ +g+ +++++ld+  +y  +E++yl    +  +la+l+ +   +++++++k
  EPA06691.1 506 VANYGRKGFYRVKYDASTLLDLKM-LVdQKKIASIDRWAIQNDLFSLCISGDDTVRNYLDFSDAY-YDEDSYLATVNVAHNLASLYFRAFGEDFAQEIK 602
                 58*****************99988.455999********************************99.6*****************866554888999*** PP

                 HHHHHHHHHHHHHHHH.T.T.TS-HHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHCSTT-S-HHHHHHHHHHHHHH.S-HHHHHHHHHHHHC-SSHH CS
     ERAP1_C 101 aflrklleplaeklgw.epg.eshldaqlrslllsaacaagdpevveearklfkawlegddlippdlrwavycalaan.ggeaewdallerykdtsaps 196
                 +++ + l++++  lgw +++ ++h+da++r  ++s++++++d+ev+ e++ +++++++++++i+pdl  ++ c+++a+ g+ +  d+l  +y+++++ +
  EPA06691.1 603 SYTVNYLKKILYDLGWtPKKtDKHTDAMMRGFVISTLGKLDDDEVILECKTRYRQFMKNQKTISPDLVEPI-CSVMAWiGTSKTHDELTRLYRNAKTME 700
                 ****************54336************************************98768********7.5555777*************999877* PP

                 HHHHHHHHHCC-S-HHHHHHHHHHCTTT..S-GGGHHHHHHHH.HSTTHHHHHHHHHHHCHCCHHHHTSSTS.CHHHHHHHHHTT--SHHHHHHHHHHH CS
     ERAP1_C 197 ekeaalralaatpdpellerllnfvlesdevrnqdlrallaglannpegrellwefvkenwdalakrwsgge.ildrivkgllpgftseeelaeieaff 294
                 ek + l+al++++d++ll + lnf+ +++evr+q+++ ++  +a np g ++lw+++k+nw +l+k+ + g+ +++riv ++ +  ++++  +ei++ff
  EPA06691.1 701 EKLRFLGALCSFKDEKLLLKSLNFS-QTSEVRSQNMQLPIMKVAANPYGKKILWPWLKKNWPKLSKKVGRGNpLFNRIVASISS-IADDSMEKEIRQFF 797
                 *************************.599**************999**********************9778799999977666.777999******** PP

                 CHTT--GGGHHHHHHHHHHH CS
     ERAP1_C 295 adkdtpglrrtlkqaletvr 314
                 ++++tpg +rt +q+le++r
  EPA06691.1 798 KKNPTPGTERTQEQTLERIR 817
                 *******************9 PP

>> Peptidase_M1_N  Peptidase M1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.4   4.1   6.5e-58   2.3e-54       2     186 .]       5     183 ..       4     183 .. 0.90

  Alignments for each domain:
  == domain 1  score: 184.4 bits;  conditional E-value: 6.5e-58
                     EEEEEEEEEEETTTTEEEEEEEEEEEESS-ECEEEEEESSEEEECEEEEECTTCTCEEEEEEEECTTTTCEEEEECCEEETTCEEEEEEEEEEE- CS
  Peptidase_M1_N   2 pehYdldlkidlkektfkGsvtitlqlkeatseivldakdlkiksvslsaevksesvkidfkieqkdeelltiklkeslqqtskytLeieyegel 96 
                     p +Y l++++ +k++tf+G+  it+++ke++++i++++ ++kiks s+++++  ++  + +k ++k+ee l+i +k++   ++++ +eie++gel
      EPA06691.1   5 PVNYMLEFEPIFKNFTFNGKEIITVDCKESVNTITMHCAEIKIKSCSVIHNNVVQK--AVTKTDEKKEE-LSIIIKNKI--KGRAFIEIEFTGEL 94 
                     789****************************************9999996666655..44455666666.555555533..699*********** PP

                     BSSSSEEEEEEEEETSCEEEEEEEE-TTTTGGGTS-B--STTSEBEEEEEEEEETTSEEEESSECCCEEEETTCEEEEEEEEEESBEGGG CS
  Peptidase_M1_N  97 ndklaGlykstYtdkgekkvvvvTqfeatdARsafPCfDePsvKAtftisikapkeetalSnmpeeeseklengqkiteFeqtpkmstYL 186
                     nd l G+y+s+Y+++g++k++++Tqfea+dAR+afPC+DeP+ KAtf+isi+a++++ta+Snmp++++++ + +++ ++F++tp mstYL
      EPA06691.1  95 NDRLLGFYRSQYKQNGKTKYLATTQFEAADARRAFPCWDEPESKATFEISIIAENKFTAISNMPIISKKRMK-NKTLYKFAKTPIMSTYL 183
                     ******************************************************************766665.688*************9 PP

>> Aminopep  Putative aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   4.4e-06     0.016     144     189 ..     277     328 ..     268     346 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.4e-06
    Aminopep 144 elseeelarlifHElaHq......vlYvkgdtafnEsfAtaVeregverwla 189
                 +  ++ +a++i HE+aHq      ++   +d   nEsfAt+++++ v +++ 
  EPA06691.1 277 TRTKQYIAEVISHEIAHQwfgnlvTMKWWNDLWLNESFATFMATKFVDKFYP 328
                 4567889**********9444332334569***************9999984 PP

>> DUF3013  Protein of unknown function (DUF3013)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.5   5.4e+03      67      92 ..      96     122 ..      92     124 .. 0.77
   2 ?   11.0   0.0   8.2e-05      0.29      54      87 ..     252     285 ..     243     296 .. 0.86
   3 ?   -1.8   0.3      0.67   2.4e+03      73     111 ..     571     612 ..     555     615 .. 0.50

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.5
                 EEEE.EE-TTT---BGGGSSEEEE-BG CS
     DUF3013  67 davl.lydpekskfdeddyLavipyeg 92 
                 d +l +y  + ++  +  yLa+  +e+
  EPA06691.1  96 DRLLgFYRSQYKQNGKTKYLATTQFEA 122
                 555547888889999999***999986 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 8.2e-05
                 --------EEEEEEEEEEE-TTT---BGGGSSEE CS
     DUF3013  54 eGevseediiefedavllydpekskfdeddyLav 87 
                  G + +   i+f +++llydp+ s++  ++y+a 
  EPA06691.1 252 AGAMENWGAITFRETILLYDPKTSSTRTKQYIAE 285
                 677777889**********************985 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.67
                 -TTT..---BGGGSSEEEE-BG.GGBEEHHHHHHHHHHHHHH CS
     DUF3013  73 dpek..skfdeddyLavipyeg.kkGlskevlkalveyLqdv 111
                 d++   ++++    La + + +  + +++e+ ++ v+yL+++
  EPA06691.1 571 DEDSylATVNVAHNLASLYFRAfGEDFAQEIKSYTVNYLKKI 612
                 333333333333334444443312445566666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (832 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       935  (0.0521501); expected 358.6 (0.02)
Passed bias filter:                      589  (0.0328518); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.72u 0.30s 00:00:01.02 Elapsed: 00:00:00.44
# Mc/sec: 5681.15
//
Query:       EPA06692.1  [L=285]
Description: hypothetical protein BG20_I1519 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1937  (0.108037); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 1690.33
//
Query:       EPA06693.1  [L=248]
Description: putative LAO/AO transport system ATPase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-66  223.8   2.8    2.5e-66  223.4   2.8    1.1  1  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
    2.4e-06   27.3   0.1    5.3e-06   26.1   0.1    1.6  1  cobW          CobW/HypB/UreG, nucleotide-binding domain
    1.2e-05   25.2   0.3     0.0051   16.6   0.1    2.2  2  ATP_bind_1    Conserved hypothetical ATP binding protein
    3.6e-05   23.7   0.9     0.0098   15.8   0.1    2.5  2  RsgA_GTPase   RsgA GTPase
    0.00071   18.9   0.3    0.00072   18.9   0.3    1.3  1  KAP_NTPase    KAP family P-loop domain
     0.0043   17.4   0.1     0.0057   17.0   0.1    1.5  1  AAA_16        AAA ATPase domain
     0.0045   17.1   1.0      0.014   15.4   1.0    2.1  1  MMR_HSR1      50S ribosome-binding GTPase
  ------ inclusion threshold ------
      0.012   16.2   0.1      0.023   15.2   0.1    1.7  1  ABC_tran      ABC transporter
      0.012   15.8   0.0      0.035   14.4   0.1    1.7  2  AAA_22        AAA domain
      0.014   15.4   0.2      0.035   14.0   0.0    1.7  2  ATPase_2      ATPase domain predominantly from Archaea
      0.017   14.8   0.4      0.026   14.2   0.4    1.4  1  AAA_30        AAA domain
      0.018   14.8   0.2      0.039   13.7   0.2    1.6  1  PRK           Phosphoribulokinase / Uridine kinase family
      0.033   14.1   0.2       0.09   12.7   0.2    1.7  1  NTPase_1      NTPase
      0.046   12.6   0.2      0.094   11.6   0.1    1.5  2  AAA_10        AAA-like domain
      0.056   13.2   0.3       0.12   12.1   0.3    1.5  1  AAA_29        P-loop containing region of AAA domain
       0.06   12.5   0.1        0.1   11.8   0.1    1.3  1  NB-ARC        NB-ARC domain
      0.074   13.2   0.0       0.08   13.1   0.0    1.4  1  MnmE_helical  MnmE helical domain
      0.093   11.5   0.1       0.14   10.9   0.1    1.3  1  AAA_35        AAA-like domain
       0.11   13.0   5.7        1.7    9.1   5.6    2.1  1  AAA_23        AAA domain
       0.13   12.6   0.4       0.16   12.3   0.4    1.5  1  AAA_19        AAA domain


Domain annotation for each model (and alignments):
>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  223.4   2.8   2.8e-69   2.5e-66       1     234 [.      14     241 ..      14     246 .. 0.93

  Alignments for each domain:
  == domain 1  score: 223.4 bits;  conditional E-value: 2.8e-69
                 HHHHHHHHH--SHHHHHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE------------------HCCCTSTTEEEEEE-- CS
        MeaB   1 LaraitlveserpeakellerllakaGraqvvGltGvPGaGkstlvealglelrrrGkrvavlavDPsspftGGsilGDklRleelavdegvfiRslps 99 
                 +a+ai +ve++  ea++ll+++ +++G+a  +G+tG  GaGks l+++  + l++  ++ avla+DP+s +tGG+ilGD++R++e ++d g +iRs++s
  EPA06693.1  14 IAKAISIVENDPIEARKLLKKIYKETGNASIIGITGPAGAGKSSLINKTSVALKKLRTKPAVLAIDPTSHVTGGAILGDRVRMTE-STDSGTYIRSIAS 111
                 59*********************************************************************************98.689********** PP

                 ---HHHHHHHHHHHHHHHHHTT-SEEEEEEESSTTHHHHHHTT-SEEEEEEESSTTTTTTT--CCCHHH-SEEEEE---HHHHHHHHHHHHHHHHHCST CS
        MeaB 100 rGalGGlaaktrevvllleaaGfDvvlietvGvGqsevdvaevvdtfvvlllpeaGDelqgikkGileiaDiivvnkaDkkeaekaarelraaleleee 198
                 rGa G +++  r+ +++le aGf+ ++ie vG+Gq ev++ +++d++vv+  p++GD +q+ik+G+ ei+Di+ vnk+D+ +a++    +r  +  +e 
  EPA06693.1 112 RGATGAVSRSLRNSIRILEYAGFNPIIIESVGAGQTEVEISNIADITVVVFNPNTGDSIQTIKAGLTEIGDIYLVNKSDLDGANQLFDAVREYVGSTE- 209
                 ***********************************************************************************998777776655443. PP

                 TBTTB--EEEEEBCCCTBSHHHHHHHHHHHHHHHHH CS
        MeaB 199 kekeWrpkvlktsavegeGidelvdaieehrevlkk 234
                      +   lkts +++ Gi e+++++++ +++ +k
  EPA06693.1 210 ----KNIIFLKTSVKKNTGISEFAKTLKDMMSIKNK 241
                 ....45678999999999999999999988776555 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.1   5.9e-09   5.3e-06       2     172 ..      44     211 ..      43     216 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 5.9e-09
                 EEEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCHCCCCCCHCCCT..........EEEETTTTECCHCTT-HHHHHHHHHHHHTT-SEEEEE CS
        cobW   2 vtvltGflGsGKTtLlnhll..enraglklavivNefgevsiDaellretgve.........ivelenGciCctlredllkelealeereerldviliE 89 
                 ++++tG+ G+GK++L+n++    ++   k av+  +  +    +++l ++  +         i +++  +   +++  l ++++ le     ++ i+iE
  EPA06693.1  44 IIGITGPAGAGKSSLINKTSvaLKKLRTKPAVLAIDPTSHVTGGAILGDRVRMtestdsgtyIRSIASRGATGAVSRSLRNSIRILEYAG--FNPIIIE 140
                 689***************99888889999*******997777777774443331222334446666655555555666666665555555..9****** PP

                 ECTTTTHHHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHHHCHC..HHHHHHHHHHHHTT CS
        cobW  90 ttGlaePapvafteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtDlldeeallekleerlrqlnpe 172
                 ++G  +             +  +d++v+v +     + +++i++      +  d+ ++nK Dl  +++l ++++e++ + +++
  EPA06693.1 141 SVGAGQTEVE--------ISNIADITVVVFNP----NTGDSIQTIKAGLTEIGDIYLVNKSDLDGANQLFDAVREYVGSTEKN 211
                 ***7765443........36678999999999....889999999999999*****************99****999887765 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   5.7e-06    0.0051       1      36 [.      47      82 ..      47      86 .. 0.94
   2 !    6.8   0.0    0.0058       5.2     179     238 ..     176     235 ..     154     238 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.7e-06
  ATP_bind_1  1 vvGpaGsGKttfvgalseilelrgrsvavvNLDPAa 36
                ++GpaG+GK++++++ s  l++  +++av+ +DP +
  EPA06693.1 47 ITGPAGAGKSSLINKTSVALKKLRTKPAVLAIDPTS 82
                68********************************86 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0058
  ATP_bind_1 179 ffedvealslllekeeekykklaeaiaelleefalvlrflplssekeesiedllslidea 238
                  ++++ ++ l+++++ +  ++l+ a++e++  ++ ++ fl  s++k+++i+++ ++++++
  EPA06693.1 176 GLTEIGDIYLVNKSDLDGANQLFDAVREYVGSTEKNIIFLKTSVKKNTGISEFAKTLKDM 235
                 45677777777777778899********************************99988766 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   1.1e-05    0.0098      88     121 ..      30      64 ..       7      86 .. 0.77
   2 ?    6.2   0.1      0.01       9.1      45     102 ..     178     237 ..     146     239 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.1e-05
                  TTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
  RsgA_GTPase  88 egleelkellkd.ktsvlvGqSGvGKStLinallp 121
                  + l+++ ++  + +++ + G+ G+GKS+Lin+   
   EPA06693.1  30 KLLKKIYKETGNaSIIGITGPAGAGKSSLINKTSV 64 
                  455666666666578889*************9765 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.01
                  TT-EEEEEEE-GGG--HHHHHHHHHHHHHHTT..SEEEE--TTTHTTHHHHHHHCTTSEE CS
  RsgA_GTPase  45 kgiepvivlnKiDlleeeeeleelkeelealg..yevllvsaktkegleelkellkdkts 102
                  ++i  + ++nK Dl   ++ +++++e + +++  + +l++s+k+++g++e ++ lkd +s
   EPA06693.1 178 TEIGDIYLVNKSDLDGANQLFDAVREYVGSTEknIIFLKTSVKKNTGISEFAKTLKDMMS 237
                  556667789******999956666665555540055667899999**********99776 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.3   8.1e-07   0.00072       6      62 ..      29      82 ..      26     244 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 8.1e-07
  KAP_NTPase  6 saladilseptlatpivvgLygkWGsGKssllnkledelkefakpvrflfaefnaws 62
                 +l + + + t ++ +++g++g+ G+GKssl+nk   +lk+    ++ ++  +++ s
  EPA06693.1 29 RKLLKKIYKET-GNASIIGITGPAGAGKSSLINKTSVALKKL--RTKPAVLAIDPTS 82
                67888888777.9***********************999998..5565555555544 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   6.4e-06    0.0057      17      51 ..      37      68 ..      27     215 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.4e-06
      AAA_16 17 ervrsgrpelvllsGesGvGKsslvrellralekd 51
                +   +g  +++ ++G++G GKssl+++   al+ +
  EPA06693.1 37 K--ETGNASIIGITGPAGAGKSSLINKTSVALK-K 68
                4..4566799***************98874443.3 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   1.0   1.6e-05     0.014       2      86 ..      45     165 ..      44     245 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.6e-05
                 EEEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEE.....ETTEE................................EEEEECGGC....SS CS
    MMR_HSR1   2 vaivGrpNvGKStLinaltge.kaivsdkpgtTrdinegrvk.....lkgke................................ielvDtpGl....ie 58 
                 ++i G   +GKS+Lin+ + + k   ++ +   +d++ +            +                                i+++  +G+    ie
  EPA06693.1  45 IGITGPAGAGKSSLINKTSVAlKKLRTKPAVLAIDPTSHVTGgailgD---RvrmtestdsgtyirsiasrgatgavsrslrnsIRILEYAGFnpiiIE 140
                 89***************9864222222222333333333221111110...112222233334444444444444444555555899999994332133 PP

                 HHHHHHHHHHHHHHHHC.TSEEEEEEETT CS
    MMR_HSR1  59 gaseekglgkaflalee.adlillvvdas 86 
                     + g g++  ++ + ad+ ++v++ +
  EPA06693.1 141 ----SVGAGQTEVEISNiADITVVVFNPN 165
                 ....4577777777777678888888744 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.1   2.6e-05     0.023      11      30 ..      42      61 ..      32     130 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.6e-05
                TSEEEEEESTTSSHHHHHHH CS
                xxxxxxxxxxxxxxxxxxxx RF
    ABC_tran 11 gekvaivGenGaGKStLlkl 30
                 ++++i+G+ GaGKS+L++ 
  EPA06693.1 42 ASIIGITGPAGAGKSSLINK 61
                6799*************985 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   3.9e-05     0.035       4      60 ..      41      93 ..      37     129 .. 0.72
   2 ?   -2.1   0.0       4.6   4.2e+03      41      89 ..     158     208 ..     142     215 .. 0.56

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.9e-05
      AAA_22  4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrel 60
                +a+i+ +tG++G+GK+ l+++    l++       +p v+ ++++s  +   +l + 
  EPA06693.1 41 NASIIGITGPAGAGKSSLINKTSVALKKLR----TKPAVLAIDPTSHVTGGAILGDR 93
                789999*************99877774222....36666677777666665555554 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.6
      AAA_22  41 evvfvtlpsst...sskdllrellralglelkaerlsseellealeqalrar 89 
                 +vv ++++ +    + k  l+e+  ++ +++++  +   +l++a+++++ ++
  EPA06693.1 158 TVVVFNPNTGDsiqTIKAGLTEIGDIYLVNKSD-LDGANQLFDAVREYVGST 208
                 455555555552333333345555555555555.666677777777776665 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   3.9e-05     0.035      15      47 ..      37      69 ..      27      84 .. 0.78
   2 ?   -1.8   0.0       2.7   2.4e+03     156     165 ..     208     217 ..     159     246 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.9e-05
    ATPase_2 15 lerepneiyfiYGpegsGKtaLlkeiienledk 47
                 e+++++i+ i+Gp g GK++L+++    l+++
  EPA06693.1 37 KETGNASIIGITGPAGAGKSSLINKTSVALKKL 69
                3678899****************9977666554 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.7
    ATPase_2 156 khlcvvicls 165
                 +++ ++++ +
  EPA06693.1 208 TEKNIIFLKT 217
                 2222222222 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.4     3e-05     0.026      17      52 ..      41      78 ..      29     122 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3e-05
      AAA_30 17 gdrvavltGpAGtGKttalkalreaweaag..grvigl 52
                ++ +  +tGpAG+GK+ ++++   a+++      v+++
  EPA06693.1 41 NASIIGITGPAGAGKSSLINKTSVALKKLRtkPAVLAI 78
                4557789**************99888887512444444 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   4.3e-05     0.039       1      35 [.      44      78 ..      44     105 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.3e-05
         PRK  1 vIgvagsSGaGkttvarklekifgrekvkaaeieg 35
                +Ig++g+ GaGk+++ +k   ++++   k+a+   
  EPA06693.1 44 IIGITGPAGAGKSSLINKTSVALKKLRTKPAVLAI 78
                8******************9999999888887644 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2    0.0001      0.09       2      25 ..      45      68 ..      44      75 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0001
                EEEE--TTSSHHHHHHHHHHHH.. CS
    NTPase_1  2 vfiTGppGvGKtTlvkkvlellks 25
                + iTGp G GK+ l++k + +lk+
  EPA06693.1 45 IGITGPAGAGKSSLINKTSVALKK 68
                67****************999986 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1    0.0001     0.094      14      59 ..      35      82 ..      24      92 .. 0.76
   2 ?   -2.9   0.0       2.6   2.4e+03     114     142 ..     184     212 ..     160     236 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0001
      AAA_10 14 vkgsktnasasliiGdlGnGKSvl.akllvlyisllg.gkaliiDpkk 59
                +  +  nas   i+G+ G+GKS l +k+ v    l+    +l iDp+ 
  EPA06693.1 35 IYKETGNASIIGITGPAGAGKSSLiNKTSVALKKLRTkPAVLAIDPTS 82
                555566888889*********8651677777777776246789***86 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.6
      AAA_10 114 lgvkkkesekkaalseaveavlegkqrgl 142
                 + v+k++ ++ + l +av++ + + ++++
  EPA06693.1 184 YLVNKSDLDGANQLFDAVREYVGSTEKNI 212
                 44445555666666666666666665554 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.3   0.00014      0.12      25      40 ..      45      60 ..      35      68 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00014
      AAA_29 25 tlltGpsGsGKSTllD 40
                + +tGp G+GKS+l+ 
  EPA06693.1 45 IGITGPAGAGKSSLIN 60
                459***********95 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00011       0.1       6      41 ..      29      63 ..      26      73 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
                HHHHHHHHCTTTSCSEEEEEEESTTSSHHHHHHHHC CS
      NB-ARC  6 ekviekLlekdelqslvvalvGmgGvGKttlakqil 41
                +k+ +k  ++ +    ++++ G +G GK+ l+++  
  EPA06693.1 29 RKLLKKIYKETGNA-SIIGITGPAGAGKSSLINKTS 63
                57888888644444.6***************98765 PP

>> MnmE_helical  MnmE helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   8.9e-05      0.08      96     135 ..     152     241 ..       6     248 .] 0.70

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.9e-05
                   x.....................................xxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx.xx RF
  MnmE_helical  96 k.....................................Dllkeke...........ekeeeevlkiSaktgegieeLeeaike.lel.ee 135
                   +                                     Dl  +++           ++++   lk+S+k+++gi+e+ +++k+ +++ ++
    EPA06693.1 152 SniaditvvvfnpntgdsiqtikaglteigdiylvnksDLDGANQlfdavreyvgsTEKNIIFLKTSVKKNTGISEFAKTLKDmMSIkNK 241
                   0555555555555555555555555558888888888855555556666667778777888888******************95545233 PP

>> AAA_35  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00016      0.14      23      68 ..      31      79 ..      15      85 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00016
      AAA_35 23 cyeeiekp...GalirikapkkmGKtSLlarilakakqqgyktvsldlq 68
                ++++i k+    ++i i +p   GK+SL++++    k+ ++k ++l ++
  EPA06693.1 31 LLKKIYKEtgnASIIGITGPAGAGKSSLINKTSVALKKLRTKPAVLAID 79
                44555443111469*****************999999988888877765 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   5.6    0.0019       1.7      21     142 ..      44     222 ..      32     247 .. 0.46

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0019
      AAA_23  21 ltlItGpNGaGKTTildAiklaLygetprlsrks..........grgfeksdveiesegkvkayvelt.fenkdgry...................... 86 
                 +  ItGp GaGK+++++    aL     r+++            g+ +  + v+ + +++  +y++    +  +g                        
  EPA06693.1  44 IIGITGPAGAGKSSLINKTSVALKKL--RTKPAVlaidptshvtGGAILGDRVRMTESTDSGTYIRSIaSRGATGAVsrslrnsirileyagfnpiiie 140
                 788*************9988888763..22222244556666663333333333333333333322220111111113333333333344444444444 PP

      AAA_23  87 ...............trsiererelskkkgkttkkaklellei............deleqfisellgskkiilnlilflgqer 142
                                + +    ++ + +++ +t ka l ++++            ++l + ++e++gs+++++ ++    +++
  EPA06693.1 141 svgagqteveisniaD-ITVVVFNPNTGDSIQTIKAGLTEIGDiylvnksdldgaNQLFDAVREYVGSTEKNIIFLKTSVKKN 222
                 4444444444443321.122334444444444444444444444555555555567777777777777666333333333333 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.4   0.00017      0.16       7      53 ..      39      83 ..      33     245 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00017
      AAA_19  7 alkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgr 53
                + +++++ +t+++G GK+ ++++    l++l++     +l++ +t++
  EPA06693.1 39 TGNASIIGITGPAGAGKSSLINKTSVALKKLRTK--PAVLAIDPTSH 83
                55788999***************99999999977..47888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       789  (0.0440069); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 1537.65
//
Query:       EPA06694.1  [L=332]
Description: ketol-acid reductoisomerase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-66  223.4   0.5    1.6e-66  222.9   0.5    1.2  1  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind
    1.9e-57  193.6   1.9    2.8e-57  193.1   1.9    1.2  1  IlvC           Acetohydroxy acid isomeroreductase, catalytic 
    6.7e-06   25.6   0.1    1.2e-05   24.7   0.1    1.4  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
    1.3e-05   25.5   0.3    0.00013   22.2   0.1    2.5  2  NAD_binding_2  NAD binding domain of 6-phosphogluconate dehyd
    0.00019   22.0   0.1    0.00062   20.3   0.1    1.9  2  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
      0.016   15.3   0.2      0.038   14.0   0.2    1.6  1  AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD bindi


Domain annotation for each model (and alignments):
>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  222.9   0.5   5.5e-70   1.6e-66       2     165 .]      15     178 ..      14     178 .. 0.99

  Alignments for each domain:
  == domain 1  score: 222.9 bits;  conditional E-value: 5.5e-70
                 HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHHHHHHHHHTGGG--TT-EEEESSSHHHH CS
        IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDelqkevyeeeiepnlkegkalafahGfnih 100
                 +k ++iaviGyG qG aqa+n++dsgl+v+vgl++g++s+kkA+++g+ v++v++a+kkad++++l+PD++q++vy++ei pnl+egkal+f+h+  ih
  EPA06694.1  15 IKAQTIAVIGYGIQGDAQANNMKDSGLKVIVGLKKGGNSWKKAESDGHIVMSVSDACKKADIIHVLLPDMIQSQVYKDEIGPNLSEGKALSFSHAAAIH 113
                 7899*********************************************************************************************** PP

                 TTSS---TTSEEEEEEESS-SHHHHHHHHTT----EEEEEEE-SSS-HHHHHHHHHHHTTHHHH- CS
        IlvN 101 fglikppkdvdvvlvAPkgpGhlvreeyeegkGvpaliaveqdasgkakelalayakgiGatraG 165
                 ++ i++pk+vd+++vAPkgpG+ vre+y +++G+p+++av+qd +gka++ +l +ak+iG++raG
  EPA06694.1 114 WKWIDAPKNVDIIMVAPKGPGSKVRETYLDNFGTPSIVAVHQDFTGKAWDRTLGIAKAIGSARAG 178
                 ****************************************************************9 PP

>> IlvC  Acetohydroxy acid isomeroreductase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.1   1.9   9.3e-61   2.8e-57       1     142 [.     184     326 ..     184     327 .. 0.99

  Alignments for each domain:
  == domain 1  score: 193.1 bits;  conditional E-value: 9.3e-61
                 HHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHTT--HHHHHHHHTHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHS-HHHHHHHHHHHHHH CS
        IlvC   1 FkeEtetDlfgEqavLcGgvselveagFetlveaGyspelAyfeclhelklivdliyegGiakmresiSdtaeygdltagprviteevkeemkeileei 99 
                 F+eE+etD fgEqa LcGg +++v+a+FetlveaGy+pe+Ayfe+lhelklivd+i++ Gi++m++++S+ta+yg+lt+gp vit+++k++mk++l+ i
  EPA06694.1 184 FQEEVETDWFGEQADLCGGSASMVKAAFETLVEAGYQPEIAYFEVLHELKLIVDMIQRYGINGMWRRVSETARYGGLTRGPMVITDDAKANMKKVLTMI 282
                 99************************************************************************************************* PP

                 HTTHHHHHHHHHHHT.TSHHHHHHHHHHHTSHHHHHHHHHHHCH CS
        IlvC 100 qsGefakevieenka.grpelkklrkeeaeheiekvgkklralm 142
                 q+G+f ke+i e+++ g+ +++k++ke++ h+iekvgk++r++m
  EPA06694.1 283 QDGTFNKEWISEYQKnGKDSFDKYMKETEAHQIEKVGKQMRKMM 326
                 ************8887***************************9 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.1   4.1e-09   1.2e-05      21     100 ..       3      82 ..       1      89 [. 0.87

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 4.1e-09
                   TCCHTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH.CHHHHTCEECSHHHHHHH-SEEEE-S- CS
  2-Hacid_dh_C  21 gewksekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkee.eeeelgvelvsleellaesDivslhlp 100
                   ++w ++++++   ++ +t+++iG+G  G a a+ +k  g+kvi+  ++  ++  ++e+ g  ++s+ ++++++Di+ + lp
    EPA06694.1   3 KTW-KDNDISLDPIKAQTIAVIGYGIQGDAQANNMKDSGLKVIVGLKKGGNSWkKAESDGHIVMSVSDACKKADIIHVLLP 82 
                   678.99999********************************99876666544447888888899*************9998 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.1   4.3e-08   0.00013       1      85 [.      19     103 ..      19     111 .. 0.91
   2 ?   -0.4   0.0      0.39   1.2e+03      51      75 ..     270     294 ..     250     303 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 4.3e-08
                    EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHCCC--TT-E CS
  NAD_binding_2   1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdeviegllealkkgdi 85 
                    +i++iG G+ G   a+n++++g kv+v   +  +  + +++  +++ s++++++++d++ +++++  + +   +++ ++l++g+ 
     EPA06694.1  19 TIAVIGYGIQGDAQANNMKDSGLKVIVGLKKGGNSWKKAESDGHIVMSVSDACKKADIIHVLLPDMIQSQVYKDEIGPNLSEGKA 103
                    59*************************99999999999999999*********************88877777779999999986 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.39
                    HHHHHCSEEEE-SSSHHHHHHHHHS CS
  NAD_binding_2  51 elvasldvvitmvkagkavdevieg 75 
                    ++ a++++v+tm+++g+  +e i++
     EPA06694.1 270 DAKANMKKVLTMIQDGTFNKEWISE 294
                    5567779999999999877776655 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   2.1e-07   0.00062       1      75 [.      19      87 ..      19     104 .. 0.78
   2 ?   -2.6   0.0       2.8   8.4e+03       8      26 ..     204     222 ..     202     248 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.1e-07
                   EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHH CS
  F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedve 75
                   +i++iG+G +g a a+++  +g    +++v+ ++  ++ ++++++   + + ++ ++a+++ad++ + ++    +
     EPA06694.1 19 TIAVIGYGIQGDAQANNMKDSG---LKVIVGLKKGGNSWKKAESD---GHIVMSVSDACKKADIIHVLLPDMIQS 87
                   59********************...****9977777777666555...4566689*********98877755555 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.8
                    SHHHHHHHHHHHHTTS-GG CS
  F420_oxidored   8 Gnmgealasgllaagaqph 26 
                     +m +a  + l++ag+qp+
     EPA06694.1 204 ASMVKAAFETLVEAGYQPE 222
                    5677888888888886554 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2   1.3e-05     0.038      23      82 ..      17      77 ..      10      89 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.3e-05
                   TSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHH.HHHCTT-EE--HHHCTTT-SEE CS
  AdoHcyase_NAD 23 GkvavvaGyGdvGkGcaaslkglGarvivtevdPical.qaameGfevvtleevvkkadiv 82
                    +++ v+GyG  G   a+ +k  G +viv      ++  +a  +G+ v+ + ++ kkadi+
     EPA06694.1 17 AQTIAVIGYGIQGDAQANNMKDSGLKVIVGLKKGGNSWkKAESDGHIVMSVSDACKKADII 77
                   567899***********************99888887626889****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       789  (0.0440069); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2346.60
//
Query:       EPA06695.1  [L=533]
Description: methylmalonyl-CoA mutase N-terminal domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   3.9e-212  705.3   0.2   4.5e-212  705.2   0.2    1.0  1  MM_CoA_mutase  Methylmalonyl-CoA mutase
  ------ inclusion threshold ------
      0.049   13.9   0.0       0.12   12.6   0.0    1.7  1  HigB_toxin     HigB_toxin, RelE-like toxic component of a tox


Domain annotation for each model (and alignments):
>> MM_CoA_mutase  Methylmalonyl-CoA mutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  705.2   0.2    5e-216  4.5e-212       2     513 .]      17     525 ..      16     525 .. 0.99

  Alignments for each domain:
  == domain 1  score: 705.2 bits;  conditional E-value: 5e-216
  MM_CoA_mutase   2 TaegievkplYtaedleekklgeslPGefPftRGvkatmyrgrpWtirqyagfstaeetnerykklLeaGqtglsvafdlptlrgyDsdhpraege 97 
                    T ++++vk++Y ++     k+ ++  G +P+tRG++++m r+r Wt+rqy gf++a+ tner+k  Le+Gqtgls+afdlpt++g+D+d++ aege
     EPA06695.1  17 TDSNFPVKRIYHKSSK---KYVKEDSGVYPYTRGIHPSMFRERFWTMRQYSGFGDAKLTNERFKFMLEKGQTGLSMAFDLPTQIGHDPDSAPAEGE 109
                    899*********9995...478899*********************************************************************** PP

  MM_CoA_mutase  98 vGkaGvaidsledmetlldgidldkvsvsmtinaaalpllamylaaaeeqgvdleklsgtiqnDiLkellargtyiyppepslrliadiieyaake 193
                    vGk+Gv+i+sl+dm +++dgi+l kvs smtin++a +lla y+ + e+qg + ++l+gt qnDiLke++ar+tyiypp+ps+rli+d+i y+a++
     EPA06695.1 110 VGKVGVSIASLKDMMIAFDGIPLGKVSSSMTINSTASTLLAYYIIVGESQGFKSTELRGTTQNDILKEYIARNTYIYPPQPSMRLIGDMIGYCAEK 205
                    ************************************************************************************************ PP

  MM_CoA_mutase 194 vpkfntisvsgyhireaGatavqElAftladGveYvralleaGldvdefaprlsFffaigsdffeeiAklRAaRrlWarivkekfgakeekslklr 289
                    vp+++++s+sgyh+reaG ta+qE+Aft+a++++Y++++l++Gl++d+faprlsFff ++ +ffee+Ak+R+aR+++a+i+kekf+ak+++sl+l+
     EPA06695.1 206 VPQWYPVSISGYHMREAGCTATQEVAFTIANAIAYIQTCLDRGLKIDDFAPRLSFFFCCTIEFFEEVAKFRVARKVYAKILKEKFHAKDPRSLQLK 301
                    ************************************************************************************************ PP

  MM_CoA_mutase 290 vhaqTsgvsltaqdpyvNilRttlealaAvlggtqslhtnsfDealalPtefsariArntqlilaeEsgvakvvDPlgGSyyvEaLTdelaekawk 385
                    +h+qTsg sltaq+p +Ni+R++++++aAvlggtqslhtns DealalPt++sa+iA++tq+i+a+Esgv+k++DP++GSyy+E+L ++++e++wk
     EPA06695.1 302 FHTQTSGESLTAQQPDNNIVRVAIQTMAAVLGGTQSLHTNSRDEALALPTQESAKIALRTQQIVAHESGVTKTADPMAGSYYLEELCAQIEENVWK 397
                    ************************************************************************************************ PP

  MM_CoA_mutase 386 lfqeieeaGGmlkaiesGlvqeeiaesaarrqkaiesrkevivGvNkfrpneeekelevlkideeveerqaerlealraerdeaavkaaLaalgea 481
                    ++++ie++GG +kaie+G++q+ei+++a+r +k+ + +++vivGvNk+ ++ e k  e+l+id+++e +q ++l++lra+rd+++ ++aL+a+++a
     EPA06695.1 398 YLKQIEKMGGSIKAIEKGFFQSEIRQNAYRLKKETDAGERVIVGVNKY-SEVEGKSPELLRIDDRIEIQQRKALKELRATRDNTKLEKALSAMKSA 492
                    ************************************************.788889***************************************** PP

  MM_CoA_mutase 482 arse.nllaraveaaralatlGeisdaleevfg 513
                    a+++ nl+++++ aa+a+at Geis++++evfg
     EPA06695.1 493 ADTDeNLMPYIISAAKAYATTGEISNTFREVFG 525
                    **889**************************98 PP

>> HigB_toxin  HigB_toxin, RelE-like toxic component of a toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.4e-05      0.12       5      49 ..     384     428 ..     381     433 .. 0.96

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.4e-05
                 HHHHHHHHHHS--SSHHHHHHH-TT-EE-SSTEEEEEETTTTEEE CS
  HigB_toxin   5 leawykevkkaewksladvkqtfpsadavgnnrvvFnIkgNkyRL 49 
                 le+++++++++ wk l+++ ++  s++a+++ ++  +I++N yRL
  EPA06695.1 384 LEELCAQIEENVWKYLKQIEKMGGSIKAIEKGFFQSEIRQNAYRL 428
                 8999****************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (533 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       876  (0.0488594); expected 358.6 (0.02)
Passed bias filter:                      607  (0.0338558); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.46
# Mc/sec: 3461.00
//
Query:       EPA06696.1  [L=156]
Description: elongation factor Tu domain 2, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.1e-10   40.8   0.2    4.6e-10   39.7   0.2    1.6  1  GTP_EFTU_D2  Elongation factor Tu domain 2
  ------ inclusion threshold ------
      0.077   12.9   0.5       0.15   11.9   0.5    1.5  1  GTP_EFTU_D4  Elongation factor Tu domain 4


Domain annotation for each model (and alignments):
>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   0.2   5.1e-14   4.6e-10       1      73 [.       4      70 ..       4      71 .. 0.94

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 5.1e-14
                 EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEE CS
  GTP_EFTU_D2  1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtl 73
                 Gtv+lg+v+sG++k  d++++   +    +i + i+s++++  +++e v+ a++G+ v++ + ++ + +Gd++
   EPA06696.1  4 GTVILGKVVSGKIKQYDNLKL--YPA---GIDVMIKSIQMHDDPVEESVCPARVGLAVKGAKPDE-VGRGDVI 70
                 9********************..555...466*********************************.******9 PP

>> GTP_EFTU_D4  Elongation factor Tu domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.5   1.7e-05      0.15      19      81 ..       6      66 ..       3      71 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.7e-05
                 EEEEEEEEEEEEETT-EEE.ETTE.EEEEEEEEEETTEEESEEETT-EEEEEEESS-TTTS--T CS
  GTP_EFTU_D4 19 aivGvevlgGvikpgvkli.kedGrevGeilqiqdkgkkleeakaGqevaisiegkivGrqike 81
                 +i G +v++G+ik   +l   + G +v  i++iq +++ +ee    ++v+++++g+    ++  
   EPA06696.1  6 VILG-KVVSGKIKQYDNLKlYPAGIDV-MIKSIQMHDDPVEESVCPARVGLAVKGAK-PDEVGR 66
                 8999.********98887525789888.8*************************986.444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1036.66
//
Query:       EPA06697.1  [L=39]
Description: hypothetical protein BG20_I1509 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00058   18.4   0.6    0.00059   18.4   0.6    1.0  1  DUF4503         Domain of unknown function (DUF4503)
     0.0015   18.4   4.5      0.013   15.4   4.5    2.0  1  zinc_ribbon_4   zinc-ribbon domain
  ------ inclusion threshold ------
      0.033   14.3   3.4       0.11   12.7   1.0    2.2  2  Zn-ribbon_8     Zinc ribbon domain
      0.043   13.5   1.2      0.076   12.7   1.2    1.5  1  zf-RRN7         Zinc-finger of RNA-polymerase I-specific TFII
      0.061   13.2   3.7       0.22   11.4   1.0    2.2  2  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
      0.086   12.8   5.5       0.13   12.3   5.5    1.4  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
       0.28   11.2   2.6       0.28   11.2   0.5    1.8  2  DUF1451         Zinc-ribbon containing domain
       0.32   10.6   5.4       0.86    9.2   5.3    1.9  1  TF_Zn_Ribbon    TFIIB zinc-binding
        1.2    8.8   7.0        1.9    8.1   0.2    2.3  2  Sgf11           Sgf11 (transcriptional regulation protein)
        1.6    9.0   7.8        3.7    7.9   7.8    1.7  1  Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase


Domain annotation for each model (and alignments):
>> DUF4503  Domain of unknown function (DUF4503)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.6   3.3e-07   0.00059     280     311 ..       7      38 ..       3      39 .] 0.94

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 3.3e-07
     DUF4503 280 WPvCdrCgsekleqspedrgafsCgsCssvvt 311
                  P+C +Cgs+++e+ p d  +++C+ C+++++
  EPA06697.1   7 CPICPNCGSKRFERLPGDIVTVKCRGCKKIIQ 38 
                 59**************************9985 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   4.5   7.1e-06     0.013       5      35 ..      10      37 ..       9      38 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 7.1e-06
  zinc_ribbon_4  5 CpsCkakyeiddeklpakgvkvrCskCghvF 35
                   Cp+C++k+    e+lp+++v v+C  C++++
     EPA06697.1 10 CPNCGSKR---FERLPGDIVTVKCRGCKKII 37
                   *****996...589*************9986 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.0     6e-05      0.11      27      39 ..       8      21 ..       1      22 [. 0.81
   2 ?    2.2   0.1      0.11     2e+02       7      13 ..      29      35 ..      24      38 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6e-05
  Zn-ribbon_8 27 taCPeCgs.evrrv 39
                 + CP+Cgs + +r+
   EPA06697.1  8 PICPNCGSkRFERL 21
                 56******999996 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.11
  Zn-ribbon_8  7 rCeeCgh 13
                 +C+ C++
   EPA06697.1 29 KCRGCKK 35
                 5666654 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.2   4.3e-05     0.076       5      16 ..       8      19 ..       4      20 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.3e-05
     zf-RRN7  5 ppCgvCgcrsft 16
                p+C+ Cg+++f 
  EPA06697.1  8 PICPNCGSKRFE 19
                79********96 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.0   0.00012      0.22      26      37 .]       8      19 ..       3      19 .. 0.86
   2 ?    2.8   0.1      0.06   1.1e+02      11      18 ..      27      34 ..      22      37 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
     DUF35_N 26 avCphCgsddle 37
                ++Cp+Cgs+ +e
  EPA06697.1  8 PICPNCGSKRFE 19
                79******9886 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.06
     DUF35_N 11 gqrCpdCG 18
                  +C+ C 
  EPA06697.1 27 TVKCRGCK 34
                55899996 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   5.5   7.2e-05      0.13      19      45 ..       8      35 ..       3      36 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.2e-05
  Zn_Tnp_IS1595 19 fvCPhCgsrkayrikt.rglfqCkeCrk 45
                   ++CP+Cgs+++ r+ +     +C+ C+k
     EPA06697.1  8 PICPNCGSKRFERLPGdIVTVKCRGCKK 35
                   89*******9999999877899999986 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.5   0.00015      0.28     131     146 ..       6      21 ..       1      22 [. 0.83
   2 ?    0.6   0.1       0.3   5.4e+02     114     125 ..      27      38 ..      23      39 .] 0.72

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00015
     DUF1451 131 eippCpkCgateFrRe 146
                   p Cp+Cg+++F+R 
  EPA06697.1   6 ACPICPNCGSKRFERL 21 
                 5688***********6 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.3
     DUF1451 114 tlvCekCgkela 125
                 t+ C+ C+k ++
  EPA06697.1  27 TVKCRGCKKIIQ 38 
                 678888887665 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   5.3   0.00048      0.86       2      13 ..       9      20 ..       8      34 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00048
                  EETTTTCEECHE CS
  TF_Zn_Ribbon  2 kCPnCgstnlve 13
                  +CPnCgs+++++
    EPA06697.1  9 ICPNCGSKRFER 20
                  6******98865 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   1.9     0.023        41       7      11 ..      10      14 ..       5      16 .. 0.86
   2 ?    8.1   0.2     0.001       1.9       3      15 ..      26      38 ..      24      39 .] 0.86

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.023
                -TTTS CS
       Sgf11  7 CpnCg 11
                CpnCg
  EPA06697.1 10 CPNCG 14
                99997 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.001
                -EEE-TTTSSEEE CS
       Sgf11  3 eyvtCpnCgRqia 15
                ++v+C  C++ i+
  EPA06697.1 26 VTVKCRGCKKIIQ 38
                689*******997 PP

>> Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   7.8     0.002       3.7       6      32 ..      10      34 ..       4      37 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.002
                    -TTTT-TTTEEETT.....S-EEETTTT CS
  Prim_Zn_Ribbon  6 CPvCGGrDrFrfddkdgr.GtwfCrqCg 32
                    CP+CG++   rf++ +g   t  Cr C+
      EPA06697.1 10 CPNCGSK---RFERLPGDiVTVKCRGCK 34
                    ******9...999999998999999994 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 270.11
//
Query:       EPA06698.1  [L=140]
Description: B12 binding domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-21   76.2   0.1    2.3e-21   76.1   0.1    1.0  1  B12-binding      B12 binding domain
  ------ inclusion threshold ------
      0.017   14.2   0.0      0.021   13.8   0.0    1.1  1  IMPDH            IMP dehydrogenase / GMP reductase domain
      0.043   14.0   0.1         25    5.0   0.1    2.9  3  Isochorismatase  Isochorismatase family
       0.15   11.7   0.0       0.17   11.5   0.0    1.1  1  Peptidase_M22    Glycoprotease family


Domain annotation for each model (and alignments):
>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.1   0.1   5.2e-25   2.3e-21       2     114 ..      11     121 ..      10     127 .. 0.94

  Alignments for each domain:
  == domain 1  score: 76.1 bits;  conditional E-value: 5.2e-25
  B12-binding   2 kvllatvggdlhplGlavlaaalrdagfeVqllganvenedivaairaekpdvvglSalltsqleavkelvel..lkrirprvkvvvGGahpsldpee 97 
                  k+l+a++g d h++G+ vl +a+rdag+eV++ g+ +++++i++ +++e++d++++S+l +++ + + ++v++  +k+i ++v vv GG++p+ d ++
   EPA06698.1  11 KILVAKLGLDGHDRGALVLCRAFRDAGMEVIYSGLFATPDRIAQIAEDEDVDAIAMSLLNGAHGTLFPRVVQAlnKKGI-KDVLVVGGGVIPEEDKKD 107
                  799***********************************************************************88888.88**************** PP

  B12-binding  98 tleaklgiddvvvgege 114
                   l++  g +d v+g g+
   EPA06698.1 108 -LKK-SG-VDEVFGPGT 121
                  .544.**.777****97 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.6e-06     0.021     107     170 ..      50     116 ..      36     122 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.6e-06
                 HHHHHHH.HTT-SEEEEE-STSSSH.HHHHHHHHHHHH.TTTSEEEEEEE-SHHHHHHHHHTT-SEE CS
                 xxxxxxx.xxxxxxxxxxxxxxxxx.xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       IMPDH 107 ervkalv.eagvdvlvvdsahghse.kvleavkeikkk.veeveviaGnvataegakaLieagadav 170
                 +r+++++ +++vd++++   +g       ++v+++ kk +++v v++G v  +e  k+L + g+d v
  EPA06698.1  50 DRIAQIAeDEDVDAIAMSLLNGAHGtLFPRVVQALNKKgIKDVLVVGGGVIPEEDKKDLKKSGVDEV 116
                 56666551578*****99998865505567778886661566***********************88 PP

>> Isochorismatase  Isochorismatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0     0.078   3.5e+02      33      47 ..      29      43 ..      26      62 .. 0.87
   2 ?    5.0   0.1    0.0056        25     103     120 ..      79      96 ..      72      99 .. 0.90
   3 ?    4.1   0.0     0.011        48      55      83 ..     103     131 ..      98     136 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.078
  Isochorismatase 33 llkaarkagipvift 47
                     l +a+r+ag+ vi++
       EPA06698.1 29 LCRAFRDAGMEVIYS 43
                     6799*********97 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0056
  Isochorismatase 103 dldeiLkelgiktivlaG 120
                      +++++L+++gik+++++G
       EPA06698.1  79 RVVQALNKKGIKDVLVVG 96 
                      6789************99 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.011
  Isochorismatase  55 evkgdlderkaaphfkpgttgaelvpela 83 
                      e+k+dl++   +++f+pgt+ +++++ ++
       EPA06698.1 103 EDKKDLKKSGVDEVFGPGTPLNDIIDHIT 131
                      678999*******************9887 PP

>> Peptidase_M22  Glycoprotease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   3.9e-05      0.17     176     233 ..      35      98 ..      10     117 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.9e-05
                    T..TEEE.CHHHHHHHHHHST.T...HHHHHHHHHHHHHHHHHHHHHHHHHHCTBSEEEEESGG CS
  Peptidase_M22 176 g..ldfsfsGlktavlkelek.e...vedlaasfqeavvdhlvekteralklpkakelvilGGv 233
                    +  +++++sGl +   + ++  e   v+ +a+s+ + +  +l  ++ +al+++++k+++++GG 
     EPA06698.1  35 DagMEVIYSGLFATPDRIAQIaEdedVDAIAMSLLNGAHGTLFPRVVQALNKKGIKDVLVVGGG 98 
                    35589999999877777774443568********************************999883 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1122.37
//
Query:       EPA06699.1  [L=148]
Description: CBS domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-20   71.8   0.8    2.8e-10   40.5   0.0    2.2  2  CBS       CBS domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.2   2.7e-11   4.9e-07       1      55 [.      27      79 ..      27      81 .. 0.88
   2 !   40.5   0.0   1.6e-14   2.8e-10       7      56 ..      96     144 ..      87     145 .. 0.88

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 2.7e-11
                HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEE.ETTTBEEEEEEHHHHHHHH CS
         CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVV.dedgklvGivtlrDllral 55
                V+dim+++++t++ +tt +++ ++m e g++++  V ++++   Gi+t+rD + ++
  EPA06699.1 27 VKDIMSKKLITASSSTTAHQISKMM-EQGIGSV-LVkNGSD-DMGIITDRDFAIKI 79
                89***********************.999****.7745555.78*******97665 PP

  == domain 2  score: 40.5 bits;  conditional E-value: 1.6e-14
                 SSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
         CBS   7 rdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                  ++ t+  ++++ +a+++m++k+++ l V+ e++k+vGivt +Dl+r l+
  EPA06699.1  96 FPLQTIGSNESVLDAAKQMASKKIRKLAVI-ENDKVVGIVTSSDLIRQLS 144
                 477799*************9999*******.8999***********9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       757  (0.0422221); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 998.70
//
Query:       EPA06700.1  [L=443]
Description: ATPase, AAA family, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-64  215.2   0.0    1.2e-47  161.6   0.0    2.4  2  AAA              ATPase family associated with various cellul
    6.2e-24   83.5   0.8    2.8e-12   46.2   0.0    2.6  2  AAA_lid_3        AAA+ lid domain
    1.1e-07   32.3   0.1    6.7e-06   26.6   0.1    2.6  1  AAA_16           AAA ATPase domain
    3.5e-06   27.2   0.0    9.3e-06   25.9   0.0    1.7  1  AAA_2            AAA domain (Cdc48 subfamily)
    5.6e-05   22.5   0.2    0.00038   19.8   0.0    2.1  2  TIP49            TIP49 P-loop domain
    0.00019   21.7   0.1     0.0015   18.8   0.1    2.3  1  AAA_22           AAA domain
    0.00021   21.3   0.2     0.0052   16.8   0.1    3.1  2  AAA_5            AAA domain (dynein-related subfamily)
    0.00038   20.6   0.0    0.00083   19.5   0.0    1.6  1  AAA_33           AAA domain
     0.0018   18.0   0.0     0.0059   16.4   0.0    1.9  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
     0.0041   16.8   0.0       0.02   14.6   0.0    2.0  2  Sigma54_activat  Sigma-54 interaction domain
  ------ inclusion threshold ------
       0.01   15.9   0.0      0.027   14.5   0.0    1.7  1  AAA_14           AAA domain
      0.011   15.5   0.0       0.02   14.6   0.0    1.3  1  IstB_IS21        IstB-like ATP binding protein
      0.016   15.2   0.2      0.044   13.8   0.1    1.7  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.034   14.2   1.0        8.3    6.5   0.1    2.5  2  Vps4_C           Vps4 C terminal oligomerisation domain
      0.038   13.9   0.1       0.39   10.6   0.1    2.2  2  NACHT            NACHT domain
      0.046   13.6   0.1        1.7    8.4   0.0    2.7  3  Bac_DnaA         Bacterial dnaA  protein
      0.061   12.8   0.0       0.13   11.7   0.0    1.5  1  PhoH             PhoH-like protein
      0.065   12.7   0.0       0.19   11.3   0.0    1.7  1  AAA_7            P-loop containing dynein motor region
      0.068   13.6   0.0       0.14   12.5   0.0    1.6  1  RNA_helicase     RNA helicase
        0.1   12.0   0.3       0.62    9.4   0.0    2.4  3  ATPase           KaiC
        0.1   11.9   0.5       0.24   10.7   0.1    1.7  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
       0.11   13.0   0.2       0.72   10.4   0.0    2.4  3  AAA_18           AAA domain
       0.15   12.5   0.0       0.44   11.1   0.0    1.8  1  ABC_tran         ABC transporter
       0.17   12.1   0.0       0.35   11.1   0.0    1.6  1  AAA_28           AAA domain


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.2   0.0   2.1e-16   1.6e-13      77     131 ..       4      58 ..       1      59 [. 0.92
   2 !  161.6   0.0   1.6e-50   1.2e-47       1     132 []     202     333 ..     202     333 .. 0.97

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 2.1e-16
                 CCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
         AAA  77 seseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                  + e+e+rvv+q+l+ +dg++ + +kvivi+atnrp+ +dpal+r gRfdr+iei+
  EPA06700.1   4 VTGEVERRVVSQMLSLMDGLEAR-GKVIVIAATNRPNAIDPALRRpGRFDREIEIK 58 
                 56789*****************6.77***************************986 PP

  == domain 2  score: 161.6 bits;  conditional E-value: 1.6e-50
                 EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH.TTCCCHHHHHHHHHHHHHHHHTTT CS
         AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr.sgseseeeervvnqLlteldgvkk 98 
                 +ll+Gp GtGKTllakava++++++f+++ g+ellsk+vgese+ ire+f++a++ + p+++f+DEid++a+ r  g+e+ ++ervv+qLlteldg+++
  EPA06700.1 202 ILLHGPSGTGKTLLAKAVATQSEANFVSVRGPELLSKWVGESERGIREIFRRARQAS-PCVVFFDEIDSIAPIRgAGGETAVTERVVSQLLTELDGMEN 299
                 69******************************************************9.****************9999********************* PP

                 SSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETTS CS
         AAA  99 keskvivigatnrpdkldpallr.gRfdrkieiel 132
                   + v+v++atnrpd++dpallr gRfd++i+i+l
  EPA06700.1 300 M-HGVVVLAATNRPDMIDPALLRpGRFDKIIQIPL 333
                 7.55****************************985 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   0.0   3.8e-15   2.8e-12       1      42 [.      81     122 ..      81     125 .. 0.96
   2 !   35.1   0.3   1.1e-11   8.5e-09       2      45 .]     362     420 ..     361     420 .. 0.87

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 3.8e-15
   AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeitmed 42 
                 dv+++++ + ++Gy+GADl+ lc+eAa+ +lrr ++e++me+
  EPA06700.1  81 DVNVEKISSVSHGYVGADLEYLCKEAAMKCLRRLLPELNMEE 122
                 9************************************99997 PP

  == domain 2  score: 35.1 bits;  conditional E-value: 1.1e-11
   AAA_lid_3   2 vdlkeLAerTeGySGADlaalcreAallAlrr..............gike.itmedfee 45 
                 vd++++Ae+T+G SGAD aa+ + A+ l + +              ++++ +tm++fe+
  EPA06700.1 362 VDIDKIAELTDGLSGADTAAIANTAVSLVIHEfldahpdvkdieksSTDAkVTMKHFEA 420
                 9*****************************998888888887776556645******95 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.1     9e-09   6.7e-06      16     132 ..     191     299 ..     189     306 .. 0.64

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 9e-09
      AAA_16  16 lervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekleealaavpelaga 114
                 ++++    p+ +ll+G+sG+GK+ l+++++++ e++   f++ +  +l     +s ++    ++++ +   ++ +++    + +++++ +  ++ + g+
  EPA06700.1 191 YDKLGHKMPRGILLHGPSGTGKTLLAKAVATQSEAN---FVSVRGPEL-----LSKWVGES-ERGIREIFRRARQASPCVVFFDEIDSIAP-IRGAGGE 279
                 667777889*********************998888...877777777.....44466666.32555555555555555555555544333.5555555 PP

      AAA_16 115 ea..srllellkrllallsr 132
                  a  +r+  +l   l+ +++
  EPA06700.1 280 TAvtERVVSQLLTELDGMEN 299
                 55666666666666655555 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   1.2e-08   9.3e-06       6     105 ..     202     296 ..     199     302 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 1.2e-08
                 EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG----.---------HHHHHHHHH CS
       AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpk.essgadvSregVqrdLLq 101
                 ill gp+g+Gkt+laka+a   ++    +++ +   ell     + + +++ g ++   +a +    +v++DEid i+p  +  g+    e V+  LL 
  EPA06700.1 202 ILLHGPSGTGKTLLAKAVATQSEA----NFVSVRGPELLS----KWVGESERGIREIFRRARQASpcVVFFDEIDSIAPIrGAGGETAVTERVVSQLLT 292
                 7999***************99985....************....99999999******999999999************97777777888899999988 PP

                 HHH- CS
       AAA_2 102 ileg 105
                  l+g
  EPA06700.1 293 ELDG 296
                 7776 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   5.1e-07   0.00038      47     106 ..     197     254 ..     193     257 .. 0.87
   2 ?    0.0   0.1      0.51   3.8e+02     133     165 ..     408     440 ..     390     443 .] 0.77

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 5.1e-07
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXX CS
       TIP49  47 klaGravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkktev.ltqalrks 106
                 k+  r++Ll GpsgtGkt la a++ +  ++  fv++ g e+ s  v  +e  + + +r++
  EPA06700.1 197 KMP-RGILLHGPSGTGKTLLAKAVATQ--SEANFVSVRGPELLSKWVGESERgIREIFRRA 254
                 454.9*******************986..5789*************999996477888887 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.51
                 SS-..TTS--EEEEEE-SS-EEEEEE-HHHHHH CS
       TIP49 133 plskekkikevkitlktakeekklklgskiaee 165
                 +++ + ++k+ + ++k + e+k+lk+g+k++ +
  EPA06700.1 408 STDAKVTMKHFEAAVKKVREQKNLKIGEKLVAS 440
                 3335667899999999***********999865 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1     2e-06    0.0015       8      43 ..     202     228 ..     197     310 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2e-06
      AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevv 43 
                 ++++G+sGtGKT+l++ ++ q          ++ +v
  EPA06700.1 202 ILLHGPSGTGKTLLAKAVATQS---------EANFV 228
                 79******************98.........34444 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.99   7.4e+02     113     136 ..      25      47 ..       4      48 .. 0.72
   2 !   16.8   0.1     7e-06    0.0052       2     124 ..     202     313 ..     201     322 .. 0.68

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.99
                 ....-EEEEEESS--.-TT-TTHHHHT CS
       AAA_5 113 r...frviatanpldrslnelspalrs 136
                 +   + via++n+++     ++palr+
  EPA06700.1  25 ArgkVIVIAATNRPN----AIDPALRR 47 
                 134589999999999....89999986 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 7e-06
                 EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..- CS
       AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEveraesevlnsLlslleerrlllee 98 
                 +lL Gp+GtgK+ la+ +a   +++++ v +++      l+ ++    g+ ++   ++ r ar  +++++++DE++ + +   +   +   er ++   
  EPA06700.1 202 ILLHGPSGTGKTLLAKAVATQSEANFVSVRGPE------LLSKWV---GESERGIREIFRRARqaSPCVVFFDEIDSIAPIRGAGGETAVTERVVS-QL 290
                 89*****************99999999999987......666776...455555567777777799999999999988765555555555555555.33 PP

                 SSSEEE---......-EEEEEESS-- CS
       AAA_5  99 ggelvkaknddllerfrviatanpld 124
                 ++el + +n   +  + v+a++n++d
  EPA06700.1 291 LTELDGMEN---MHGVVVLAATNRPD 313
                 344444443...34456666666555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   1.1e-06   0.00083       2      46 ..     202     248 ..     202     312 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.1e-06
      AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt 46 
                 +ll+G++G+GK+ la+ ++ +    +v ++ ++l+++ +g+ ++ ++
  EPA06700.1 202 ILLHGPSGTGKTLLAKAVATQSEanFVSVRGPELLSKWVGESERGIR 248
                 689****************9999889999999999988886655554 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   7.8e-06    0.0059      35      70 ..     201     236 ..     166     274 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 7.8e-06
      RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgPvle 70 
                  +ll+Gp G Gkt lak +a++ ++++ +  gP l 
  EPA06700.1 201 GILLHGPSGTGKTLLAKAVATQSEANFVSVRGPELL 236
                 58******************************9873 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   2.7e-05      0.02      22      52 ..     199     226 ..     192     238 .. 0.83
   2 ?   -1.6   0.0       2.5   1.9e+03      90     106 ..     255     271 ..     252     312 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.7e-05
                      SS-EEEECSTTSSHHHHHHHHHHHSTTTTS- CS
  Sigma54_activat  22 dlsvlitGesGtGKellaraiheaskrkekp 52 
                      +  +l++G sGtGK+lla+a+ ++s+   ++
       EPA06700.1 199 PRGILLHGPSGTGKTLLAKAVATQSE---AN 226
                      5679****************998876...44 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.5
                      HHTTTSEEEEETGGGS- CS
  Sigma54_activat  90 ekadgGtlfLDeigelp 106
                      ++a+  ++f+Dei ++ 
       EPA06700.1 255 RQASPCVVFFDEIDSIA 271
                      57888899999998875 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   3.6e-05     0.027       5      77 ..     202     271 ..     199     305 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.6e-05
      AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqevp 77 
                 +++ G+  +GKT l+k ++ ++     +++ +   +   k   ++e+ +++i++++++    ++f+DEi  + 
  EPA06700.1 202 ILLHGPSGTGKTLLAKAVATQSE---ANFVSVRGPELLSKWVGESERGIREIFRRARQASPCVVFFDEIDSIA 271
                 6899**************97777...6777777666666666666544555555444458899******9874 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   2.7e-05      0.02      49      74 ..     201     226 ..     197     240 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.7e-05
   IstB_IS21  49 nivllGpsGvGKshlaialgveavra 74 
                 +i+l GpsG+GK+ la a++++  ++
  EPA06700.1 201 GILLHGPSGTGKTLLAKAVATQSEAN 226
                 689****************9987655 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       5.1   3.8e+03      85     103 ..     169     187 ..     161     194 .. 0.64
   2 ?   13.8   0.1     6e-05     0.044      13      49 ..     193     231 ..     185     236 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 5.1
                 TCCCCSTSCEEEEETGGGG CS
        TsaE  85 leeyleeeavvlvEWpekl 103
                   e +++e   +vEWp k+
  EPA06700.1 169 GLEDVKRELQEAVEWPMKY 187
                 4444444456789**9885 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 6e-05
                 HHHHCHTEEEEEEESTTSSHHHHHHHHHHHTT--..--- CS
        TsaE  13 klakalgdvilLeGdLGaGKTtlvrglakalgve..evk 49 
                 kl++++ + ilL+G+ G+GKT l++++a + + +  +v+
  EPA06700.1 193 KLGHKMPRGILLHGPSGTGKTLLAKAVATQSEANfvSVR 231
                 555555557*******************99887655565 PP

>> Vps4_C  Vps4 C terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1     0.021        16      14      44 ..     120     150 ..     116     152 .. 0.85
   2 ?    6.5   0.1     0.011       8.3      25      42 ..     409     426 ..     399     430 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.021
      Vps4_C  14 mtwmdipsdkllePpvtlkDflkalkkarpt 44 
                 m  +++p++ l +  v+ +Df+kal ++ p+
  EPA06700.1 120 MEEEKLPPETLDKLIVNNEDFQKALIEVTPS 150
                 5556699999999************999887 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.011
      Vps4_C  25 lePpvtlkDflkalkkar 42 
                 +  +vt+k+f++a+kk+r
  EPA06700.1 409 TDAKVTMKHFEAAVKKVR 426
                 5669************98 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00053      0.39       3      23 ..     202     222 ..     200     231 .. 0.89
   2 ?    0.8   0.0      0.56   4.2e+02      57     111 ..     235     293 ..     221     316 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00053
                 EEEEC-TTTCHHHHHHHHHHH CS
       NACHT   3 vilqGeaGsGKTtLlqklala 23 
                 ++l+G++G GKT L++ +a++
  EPA06700.1 202 ILLHGPSGTGKTLLAKAVATQ 222
                 89**************99975 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.56
                 HHCCCCTS--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH..............HHH CS
       NACHT  57 llfsqlpepaapvsevwavllelperlLlilDglDelvtdlgq.....kekqpvrtlLse 111
                 ll +   e+++ ++e +  +++++   +  +D +D ++ + g+      +++ v +lL+e
  EPA06700.1 235 LLSKWVGESERGIRE-IFRRARQASPCVVFFDEIDSIAPIRGAggetaVTERVVSQLLTE 293
                 555555666666777.66678888888999999999999999975444444444444444 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0       0.3   2.3e+02     118     177 ..      15      71 ..       8      95 .. 0.73
   2 ?    8.4   0.0    0.0023       1.7      37      65 ..     202     230 ..     194     255 .. 0.90
   3 ?   -1.4   0.0       2.3   1.7e+03     129     181 ..     300     349 ..     280     358 .. 0.61

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.3
                 HHHHHHHHHHTTT-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHHHHH CS
    Bac_DnaA 118 elfhtfnalleegkqvvlssDrsPkeleeledrlrsrfeaGlvvdieppdletrlailkk 177
                 +++ +++ l   gk +v+++   P++++    r   rf++   ++i+ pd++ r +il  
  EPA06700.1  15 QMLSLMDGLEARGKVIVIAATNRPNAIDPAL-RRPGRFDRE--IEIKVPDKKGRKDILAI 71 
                 5667788889999***********9987654.335788775..66777899999888864 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0023
                 EEEE-SSSSSHHHHHHHHHHHHHHHSSSS CS
    Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapel 65 
                 ++++g++G Gkt L ka++ + ++n+ + 
  EPA06700.1 202 ILLHGPSGTGKTLLAKAVATQSEANFVSV 230
                 79*****************9998887665 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 2.3
                 TT-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHHHHHHHHH CS
    Bac_DnaA 129 egkqvvlssDrsPkeleeledrlrsrfeaGlvvdieppdletrlailkkkiea 181
                  +  vvl++   P  ++    r   rf+   +++i  pd+e r  ilk ++e+
  EPA06700.1 300 MHGVVVLAATNRPDMIDPALLR-PGRFDK--IIQIPLPDKESRKMILKINAEK 349
                 5555556666666555432222.234544..6778889999999999866654 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00017      0.13      24      42 ..     204     222 ..     196     230 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00017
                 EE--TTSSTTHHHHHHHHH CS
        PhoH  24 aiGpaGtGKtylavalave 42 
                   Gp+GtGKt+la a+a +
  EPA06700.1 204 LHGPSGTGKTLLAKAVATQ 222
                 68*************9987 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00025      0.19      34      58 ..     200     224 ..     190     232 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00025
       AAA_7  34 kpvllvGptGtGKtviikdllkkld 58 
                 + +ll Gp+GtGKt+++k + ++ +
  EPA06700.1 200 RGILLHGPSGTGKTLLAKAVATQSE 224
                 679**************99877766 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00019      0.14       1      26 [.     202     227 ..     202     268 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00019
  RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl 26 
                   i+l+Gpsg+GK++lak +a++ + ++
    EPA06700.1 202 ILLHGPSGTGKTLLAKAVATQSEANF 227
                   689**************888766554 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00083      0.62      15      42 ..     195     222 ..     185     230 .. 0.80
   2 ?   -2.2   0.0       2.8   2.1e+03     125     154 ..     267     297 ..     264     309 .. 0.81
   3 ?   -2.2   0.0       2.9   2.2e+03      57     120 ..     405     427 ..     376     435 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00083
      ATPase  15 GipegrvvlitGepGtGKtifalqFlik 42 
                 G  + r +l+ G +GtGKt++a+  + +
  EPA06700.1 195 GHKMPRGILLHGPSGTGKTLLAKAVATQ 222
                 55566779*************9876655 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.8
      ATPase 125 iDsitgl.ayeekeavaReilrqlvrvlkkl 154
                 iDsi+++     ++av+ + + ql+++l ++
  EPA06700.1 267 IDSIAPIrGAGGETAVTERVVSQLLTELDGM 297
                 9999999777778888889999999988665 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 2.9
      ATPase  57 eepaedlrenakslGwdlekleeegklaiidasesaeesaeekdkedleelieelaeaikeika 120
                 e                                         k+++d++  +++++ a+k++++
  EPA06700.1 405 E-----------------------------------------KSSTDAKVTMKHFEAAVKKVRE 427
                 3.........................................4455555555555555555444 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       6.7     5e+03      39      53 ..     108     122 ..     104     143 .. 0.82
   2 ?   10.7   0.1   0.00032      0.24      25      43 ..     202     220 ..     196     224 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 6.7
  Mg_chelatase  39 akrlpsllpplseee 53 
                    k+l  llp+l++ee
    EPA06700.1 108 MKCLRRLLPELNMEE 122
                   588999999999877 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00032
  Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                   +ll Gp+G+GKt+lak+++
    EPA06700.1 202 ILLHGPSGTGKTLLAKAVA 220
                   89*************9976 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       9.8   7.3e+03      15      58 ..     103     141 ..     101     149 .. 0.67
   2 ?   10.4   0.0   0.00096      0.72       1      21 [.     202     222 ..     202     258 .. 0.80
   3 ?   -2.0   0.0       6.5   4.8e+03      43      70 ..     356     382 ..     347     408 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 9.8
      AAA_18  15 akeLskrlgfgvnlrdvakenglllevdpealdeskrldedkld 58 
                 +ke + ++     lr +++e ++++e  p+++ ++++++ +  +
  EPA06700.1 103 CKEAAMKC-----LRRLLPELNMEEEKLPPETLDKLIVNNEDFQ 141
                 56665565.....7888888888888888866666666655544 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00096
      AAA_18   1 IlltGtpGvGKttlakeLskr 21 
                 Ill G++G+GKt lak+++  
  EPA06700.1 202 ILLHGPSGTGKTLLAKAVATQ 222
                 89***************9654 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 6.5
      AAA_18  43 pealdeskrldedkldklldaleenss..a 70 
                 p+   + +r+d+dk ++l d+l +++    
  EPA06700.1 356 PN---DPQRVDIDKIAELTDGLSGADTaaI 382
                 33...6679999999999999998776542 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00059      0.44      14      37 ..     202     225 ..     194     304 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00059
                 EEEEESTTSSHHHHHHHHTTSS-- CS
                 xxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  14 vaivGenGaGKStLlkllagllkp 37 
                 + + G++G+GK+ L+k++a +++ 
  EPA06700.1 202 ILLHGPSGTGKTLLAKAVATQSEA 225
                 5689**************998764 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00047      0.35       2      32 ..     202     237 ..     201     266 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00047
      AAA_28   2 ivitGgestGKTtlleaLaar...gypvv..pEaar 32 
                 i + G+++tGKT l++a a +   +++ v  pE   
  EPA06700.1 202 ILLHGPSGTGKTLLAKAVATQseaNFVSVrgPELLS 237
                 7899***************66545554444566554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.48
# Mc/sec: 2780.21
//
Query:       EPA06701.1  [L=66]
Description: hypothetical protein BG20_I2370, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-17   61.8   0.4    3.8e-17   61.3   0.4    1.2  1  GatD_N    GatD N-terminal domain


Domain annotation for each model (and alignments):
>> GatD_N  GatD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.3   0.4   2.1e-21   3.8e-17       3      47 ..      22      65 ..      20      66 .] 0.93

  Alignments for each domain:
  == domain 1  score: 61.3 bits;  conditional E-value: 2.1e-21
                TT-EEEEE-SS-EEEEEE----TTS-SSEEEEEETTS-EEEEE-T CS
      GatD_N  3 vGDlikvekkgreyeGilmPrselsdddiivlKLdnGYNiGikie 47
                vGD +k+   + +y Gi+mPr+e sdd+++vlKL++GYNiG++ie
  EPA06701.1 22 VGDTVKIL-SDLTYFGIIMPRYEHSDDKHLVLKLKSGYNIGLEIE 65
                89****95.689*******************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       196  (0.010932); expected 358.6 (0.02)
Passed bias filter:                      177  (0.00987227); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 440.54
//
Query:       EPA06702.1  [L=270]
Description: hypothetical protein BG20_I1467 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0044   17.4   0.1     0.0082   16.6   0.1    1.5  1  MG2       MG2 domain
  ------ inclusion threshold ------
       0.13   12.5   0.5       0.28   11.4   0.5    1.6  1  DUF4458   Domain of unknown function (DUF4458)
       0.17   11.9   1.5        1.1    9.3   0.1    2.7  3  DUF2187   Uncharacterized protein conserved in bacteria (DUF2


Domain annotation for each model (and alignments):
>> MG2  MG2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   1.4e-06    0.0082       4      81 ..      41     115 ..      38     139 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.4e-06
                 EEES-SEE-TT-EEEEEEEEESTTCSB---EEEEEEEE-TTSSEEEEEEEEE-CTTEEEEEEE--TT..--SEEEEEEEE CS
         MG2   4 vytDRglYrPgetVslkallrdetlqglaklplkltirdpdgkevkelplatdetggaesefalpea..aklGeysvels 81 
                 v+tD++ Y  ++++ +       +  ++ k+p++lt+++p++  v   +l+ +++g++e+++ +  +   + G+y+++++
  EPA06702.1  41 VWTDKTTYDHNDKIMVH-----GNVATVSKMPVTLTVTSPNNSIVTIAQLDVNSDGSFETTLMTGGElwKQKGTYTIKVN 115
                 56666666666665554.....45688999**********************************99855699*****992 PP

>> DUF4458  Domain of unknown function (DUF4458)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.5   4.7e-05      0.28      29      92 ..      63     128 ..      46     139 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.7e-05
                 --EEEEEEEE.CTTS-EEEEEEEEEE----SSEEEEEEEEEEEESEEEEE.EEEEEEECCTEEEEE CS
     DUF4458  29 ikkvdvtvkn.qftqetvtftllkvkykeknaeyglrdsklqLeaGtYkv.isYtlydkkgeelet 92 
                 ++k+ vt++  + +++ vt+ +l v+ +   + ++++   l+ + GtY++ ++Y +++k++++l  
  EPA06702.1  63 VSKMPVTLTVtSPNNSIVTIAQLDVNSDGSFETTLMTGGELWKQKGTYTIkVNYGTFEKNNKVLVE 128
                 5666666654145777889999999998898999999*************669********88765 PP

>> DUF2187  Uncharacterized protein conserved in bacteria (DUF2187)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1      0.67     4e+03      35      35 ..      73      73 ..      50      97 .. 0.52
   2 ?    0.1   0.0      0.14   8.2e+02      26      35 ..     121     130 ..     105     138 .. 0.73
   3 ?    9.3   0.1   0.00018       1.1      17      50 ..     161     194 ..     153     196 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.67
     DUF2187 35 t 35
                t
  EPA06702.1 73 T 73
                2 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.14
     DUF2187  26 nenSViVdlt 35 
                 ++n V+V+lt
  EPA06702.1 121 KNNKVLVELT 130
                 4899****99 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.00018
     DUF2187  17 kltGiVekvnenSViVdltimdnfdelele.ekTV 50 
                 k+tG  +++n++S+iV ++  d+   l+l+ +k V
  EPA06702.1 161 KVTGASINSNDKSIIVKIS-ADEDGTLTLNpDKSV 194
                 7899999************.777778888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2107.58
//
Query:       EPA06703.1  [L=1115]
Description: DNA-directed RNA polymerase subunit B [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   5.1e-125  417.6   0.0   7.6e-125  417.0   0.0    1.3  1  RNA_pol_Rpb2_6  RNA polymerase Rpb2, domain 6
    2.5e-48  164.3   0.0    3.8e-48  163.7   0.0    1.3  1  RNA_pol_Rpb2_1  RNA polymerase beta subunit
    3.5e-32  110.6   0.1    7.5e-32  109.6   0.1    1.6  1  RNA_pol_Rpb2_7  RNA polymerase Rpb2, domain 7
    1.2e-27   95.8   0.1    2.9e-27   94.6   0.1    1.7  1  RNA_pol_Rpb2_3  RNA polymerase Rpb2, domain 3
    1.5e-23   83.5   0.0    3.4e-23   82.3   0.0    1.6  1  RNA_pol_Rpb2_2  RNA polymerase Rpb2, domain 2
    4.9e-19   68.4   0.1    1.1e-18   67.2   0.1    1.7  1  RNA_pol_Rpb2_4  RNA polymerase Rpb2, domain 4
    7.5e-09   36.0   0.0    1.9e-08   34.7   0.0    1.7  1  RNA_pol_Rpb2_5  RNA polymerase Rpb2, domain 5
  ------ inclusion threshold ------
        0.1   12.8   0.1       0.19   12.0   0.1    1.4  1  FYVE_2          FYVE-type zinc finger
       0.27   11.2   2.3       0.59   10.1   1.5    2.0  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
       0.37   11.0   0.9       0.83    9.9   0.9    1.5  1  Ribosomal_L37e  Ribosomal protein L37e
       0.56    9.8   2.1        1.9    8.1   0.6    2.3  2  RecR            RecR protein


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb2_6  RNA polymerase Rpb2, domain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  417.0   0.0  4.7e-128  7.6e-125       2     390 .]     645    1018 ..     644    1018 .. 0.96

  Alignments for each domain:
  == domain 1  score: 417.0 bits;  conditional E-value: 4.7e-128
                      HHT-SS-TTB-HHHHHHHHHHGGGB-S---TTTTT---SSEEEESS----SSB-S.TTTTTS........GGGS-SEEEEEBBBS--TTTTTT CS
  RNA_pol_Rpb2_6    2 aklapvvehvqspriiiqaamekqalgiyslnkfkrsnqktyllcinqkPlvktgdkveagqvldgpatekgelalGqnavVAvmsyeGYniE 94  
                      a+++p++eh+qspr+++++am+kq+lg+ +  + + +  + +l+ ++q+P+v+t+ ++++++         ++ ++Gqn+vVAv++++GYniE
      EPA06703.1  645 ASIIPYPEHNQSPRNTYESAMAKQSLGFSTPMMNTSTYVRQHLMLYPQTPIVNTK-AMKLLG--------LEDRPAGQNCVVAVLPFDGYNIE 728 
                      889************************9888888888888999************.******........9********************** PP

                      T-EEEBCHHHHTTTT-EEEEEE..EEE--SSSS---.-S--..-.......-SS-GGGS-TTSB--SS-EEETT-EEE---..B-----...- CS
  RNA_pol_Rpb2_6   95 Daiilnerlvdrdvftsihikeyeveardtklgeeeitrdipnv.......seealkkLdedGivrvgaevkegdilvgkvtkgeteltpeek 180 
                      Dai+l++++vdr++ ++++++ y+ ea+++++g +++++ ++ +       +e+a++ L+edG+v  ++ v+ gdil+gk+  ++ ++++e +
      EPA06703.1  729 DAIVLSRASVDRGLGRTFFFRIYDAEAKQYPGGMRDTFEIPNAEdnirgykGEKAYRLLEEDGVVASESPVHGGDILIGKT--SPPRFMEEYR 819 
                      **********************************9966655555999***9*****************************8..8888886555 PP

                      ----------..-B---EE--TT-EEEEEEEEE.......EE-TT--EEEEEEEEEEE---TT-BEEETTS---BBEEEB-TTTSEEETTS-- CS
  RNA_pol_Rpb2_6  181 llraifgekarevkdtslrvksgeegvVdkvkvfsrekgdelkagvnklvkvyvaqkRklqvGDKfasrhGqKGvvslilpqeDmPfledGiv 273 
                      +    f++++   +dts+ v+++e+gvVd+v +       ++++++ k++k++v++ R +++GDKfasrhGqKGv++++++ eD+P+++dGi 
      EPA06703.1  820 E----FESSGPYRRDTSIGVRPSETGVVDTVVM-------TQSNEGGKMYKIRVRDMRIPEIGDKFASRHGQKGVLGILAKAEDLPYTADGIS 901 
                      4....566666799*******************.......89999************************************************ PP

                      -SEEE-GGGCHHH-BTTHHHHHHHHHCCCSSSS--B--TT-...-HHHHHHHHHTTS-TT-EE-EEETTTS-B-SS-EEB-EEEEEEBS--CC CS
  RNA_pol_Rpb2_6  274 vDivlNPlgvPSRmtigqllEtllgkaaalegkkvdatvFdgakeeeikelLeeagleasGkevlydGrtGekleaeifvGviYylkLkhlve 366 
                      +D+++NP+++PSRmt+g+ +E+++gkaaal+g+++d+++F g+k ee+k  ++ ag+++sGke++ydGrtG+ +  e+f+Gv+Yy+kL+h+v+
      EPA06703.1  902 PDVLINPHAFPSRMTVGMFMESICGKAAALRGSQFDGSAFVGEKMEEVKPVMDAAGFKYSGKETMYDGRTGKSFPVEVFIGVVYYQKLHHMVA 994 
                      ********************************************************************************************* PP

                      CS----SS--B-TTT--B-SCGGG CS
  RNA_pol_Rpb2_6  367 dKihaRstGpyslltqQPlgGkaq 390 
                      dKihaR++G++++lt+QP++G+a+
      EPA06703.1  995 DKIHARARGQVQMLTKQPTEGRAR 1018
                      **********************96 PP

>> RNA_pol_Rpb2_1  RNA polymerase beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.7   0.0   2.3e-51   3.8e-48       2     198 ..      21     387 ..      20     392 .. 0.96

  Alignments for each domain:
  == domain 1  score: 163.7 bits;  conditional E-value: 2.3e-51
                     TTHHHHHHHHHHHHTHHHHHCTTSSECCHCSSSHCSSSCEEEEEEEEEEESCSSECTTSCEEES.HHHHHHCTSBXEEEEEEEEEEEECCCCTCC CS
                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  RNA_pol_Rpb2_1   2 LvsqqldSFnkfveqdlekiikeeaaieseeeiqssgeelelkfvsirlgkPvvdesdasereiyPkearlrnltYsaplyvklklvvyekdnke 96 
                     +++q+l+SF++f+e  l+ ii+e  +ie+e+ +    + +++++++++l++P + e d+s ++i+P earlrn++Ysap++++   v     +++
      EPA06703.1  21 IARQHLNSFDEFLERGLQSIINEVGQIEIENAE----YPYKIQLGKVKLQQPRMMELDGSITHITPAEARLRNVSYSAPVMMEASVVE----DGK 107
                     679*************************99985....68****************************************998887777....899 PP

                     EEEEEEEEEEEEEXBTTSTTSSSTTS.HHHHHHTTS.TTS..SSEEETTCEEEEXEEEE.................................... CS
                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................................... RF
  RNA_pol_Rpb2_1  97 eikeeevyiGelPlMlrskacvlseaseeelvelkEcpldqGGyFiinGtekvivaqek.................................... 155
                       +++ v iG++P+M +s+ac+l++ s ++l+e++E+p+d+GGyFiinG+e+viv +e+                                    
      EPA06703.1 108 ILESRFVHIGDVPVMAKSNACILHNFSTQKLIEHGEDPNDPGGYFIINGSERVIVGLEDlsynkiivdresvggntvfkakvyssivgyraklel 202
                     9999******************************************************************************************* PP

                     ............................................................................................... CS
                     ............................................................................................... RF
  RNA_pol_Rpb2_1 156 ............................................................................................... 155
                                                                                                                    
      EPA06703.1 203 vmkndglivaripgspvdipvvtltralglesdreiaaavslvdeiqnelegsfekagdvptakdaivyiskriapgmleefqikraetlldwgl 297
                     *********************************************************************************************** PP

                     ...............................................XHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSSSSSHHHHSCS CS
                     ...............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  RNA_pol_Rpb2_1 156 ...............................................laGeLlaslfrvllkklerdvkerlqksleklddlmlqllvna 198
                                                                     aG++la+lfr+++++l+rd+k +l++s +k    +++++++ 
      EPA06703.1 298 lphlgkhpenrkekaqflgeaackllelklgwispddkdhygnkvikFAGQMLADLFRTAFRNLVRDMKYQLERSGQKRGINAVAAAIRP 387
                     ************************************************************************999777665556666655 PP

>> RNA_pol_Rpb2_7  RNA polymerase Rpb2, domain 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.6   0.1   4.6e-35   7.5e-32       1      85 [.    1020    1110 ..    1020    1112 .. 0.98

  Alignments for each domain:
  == domain 1  score: 109.6 bits;  conditional E-value: 4.6e-35
                      BBEEEEHHHHHHHHHHTBHHHHHHHHTTTTTEEEEEEESSSSSCCCEE......EBTTTTCSSSEEEEEEEHHHHHHHHHHHHTTBEEEEE CS
  RNA_pol_Rpb2_7    1 GGlrfGEMErdaliayGaaalLkerltikSDavevdvcgrckllaaan......eCkivkseekiekveipeafklLlqeLqslgialkll 85  
                      GGlrfGEMErd+liayGa+++Lk+rl+++SD++++ vc+rc+l+a+ +       C+++ +++k+++v++ +afklLlqe+qsl++a++ll
      EPA06703.1 1020 GGLRFGEMERDCLIAYGASMILKDRLLDESDKSDIFVCERCGLVAYHDvkqrkyVCRVCGDKAKVSSVSVAYAFKLLLQEMQSLNVAPRLL 1110
                      9*********************************************99*****9**********************************986 PP

>> RNA_pol_Rpb2_3  RNA polymerase Rpb2, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.6   0.1   1.8e-30   2.9e-27       1      65 [.     412     473 ..     412     476 .. 0.97

  Alignments for each domain:
  == domain 1  score: 94.6 bits;  conditional E-value: 1.8e-30
  RNA_pol_Rpb2_3   1 qvldrlnplselshlrrvsslrgglskerkttevRdlhpshwGriCpveTPEGencGlvksLall 65 
                     q+ldr+n+ls++shlrr++s+   ls+++ ++e+Rdlh++h+GriCp+eTPEG+ncGlvk+Lal+
      EPA06703.1 412 QLLDRTNYLSTISHLRRIQSP---LSRTQPNFEARDLHATHFGRICPSETPEGSNCGLVKNLALS 473
                     89*******************...***************************************86 PP

>> RNA_pol_Rpb2_2  RNA polymerase Rpb2, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.3   0.0   2.1e-26   3.4e-23       3     189 ..     170     343 ..     168     344 .. 0.92

  Alignments for each domain:
  == domain 1  score: 82.3 bits;  conditional E-value: 2.1e-26
                     SCEEEEE-SSSSSE..SSSCCEECCCEEEEECCCCSTSCEEEEECTTSSSEEEHHHHHHHTT--STTHHHHHHTSSSTTHHHHHHHHHHHHHHCT CS
  RNA_pol_Rpb2_2   3 ngiyvekekdknki..satvtsslisqrgsvlklekdgktliwtriskkrkipivivlkAlglvsdreIlericydsedsqlleelleeleekee 95 
                     n+i+v +e+   ++  +a+v ss+  +r+++  + k+++ +++  +    +ip+v + +Algl sdreI  +++     +++++el  + e++ +
      EPA06703.1 170 NKIIVDRESVGGNTvfKAKVYSSIVGYRAKLELVMKNDGLIVARIPGSPVDIPVVTLTRALGLESDREIAAAVS---LVDEIQNELEGSFEKAGD 261
                     788888888888888888999999999999999999999999********************************...699*************** PP

                     SSSCHHHHHHHHHCSSTTSSSCCCCCHHHHHHHCHHHHHHHTTTTSSTTTTTSSSTCHH..HHHHHHHHHHHHHHHHTTSSSS--TTSGGGEEE CS
  RNA_pol_Rpb2_2  96 iqtqeealdyigkvvalrrgeearlqsareilqkrydlgeigreklnkhlglseslenkrlkaqdilymidrLlslklgrrevDDiDhlgnkRv 189
                     ++t+++a+ yi k++a +  ee ++++a+ +l         +   l+ hlg++ +  +   kaq++++++ +Ll+lklg +++DD+Dh+gnk +
      EPA06703.1 262 VPTAKDAIVYISKRIAPGMLEEFQIKRAETLL---------DWGLLP-HLGKHPENRK--EKAQFLGEAACKLLELKLGWISPDDKDHYGNKVI 343
                     *****************************999.........566777.******9444..6*******************************66 PP

>> RNA_pol_Rpb2_4  RNA polymerase Rpb2, domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.2   0.1     7e-22   1.1e-18       1      62 []     511     577 ..     511     577 .. 0.97

  Alignments for each domain:
  == domain 1  score: 67.2 bits;  conditional E-value: 7e-22
                     EECTT-BEEE-S-HCCHHHHHHHHCCTTSS-TT-EEEE-TT.....T--EEEE-SSEEB-EEEEE-S CS
  RNA_pol_Rpb2_4   1 VfvNGrllGvtrdpkklvetlRelRRkgkiseevsivlnek.....qkevkiatDgGRvcRPliiVe 62 
                     +fv+Grl+G+++d+++l+e+lR+lRR+ ki+++v i+++++     +k++++++++GRv+RPlii++
      EPA06703.1 511 IFVDGRLIGYYKDGAQLAESLRDLRRNSKIHPHVGISFHKSeiegsTKRLYVNCNAGRVLRPLIIIK 577
                     7**************************************9999999999****************96 PP

>> RNA_pol_Rpb2_5  RNA polymerase Rpb2, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.0   1.2e-11   1.9e-08       1      33 [.     598     630 ..     598     662 .. 0.90

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 1.2e-11
                     HHHHHHTTSEEEEEHHHHTT--EESSTTTCSST CS
  RNA_pol_Rpb2_5   1 wddLlregvvEylDaeEEetamIamtpedleks 33 
                     w+dLlr gv E++Da+EEe+++I ++++d++k+
      EPA06703.1 598 WTDLLRMGVLEMIDANEEENCYITLDEKDTKKH 630
                     ******************************998 PP

>> FYVE_2  FYVE-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00011      0.19      75     116 ..    1050    1094 ..    1020    1096 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
      FYVE_2   75 ldCklnvCkkCsve...nkkekvwlCkiCseaRevkkksleWfyk 116 
                  ++  ++vC++C+     + k++ ++C++C  + +v   s+++ +k
  EPA06703.1 1050 DKSDIFVCERCGLVayhDVKQRKYVCRVCGDKAKVSSVSVAYAFK 1094
                  556789*****9877778999**********99999999888776 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       6.6   1.1e+04      52      66 ..     230     244 ..     228     246 .. 0.84
   2 ?   10.1   1.5   0.00036      0.59      31      55 ..    1057    1081 ..    1055    1085 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 6.6
  OrfB_Zn_ribbon  52 CgfeadrDvnAaiNi 66 
                      g+e dr + Aa+ +
      EPA06703.1 230 LGLESDREIAAAVSL 244
                     68899*******987 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00036
  OrfB_Zn_ribbon   31 CseCgsknkealsgrtfkCpnCgfe 55  
                      C +Cg + ++++++r+++C+ Cg +
      EPA06703.1 1057 CERCGLVAYHDVKQRKYVCRVCGDK 1081
                      **********************976 PP

>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.9   0.00051      0.83      17      38 ..    1055    1079 ..    1048    1085 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00051
  Ribosomal_L37e   17 ilCrrCgkrsyhvqkkt...CascG 38  
                       +C+rCg  +yh  k++   C  cG
      EPA06703.1 1055 FVCERCGLVAYHDVKQRkyvCRVCG 1079
                      58**********7655422388888 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.35   5.7e+02       2      15 ..     524     537 ..     523     540 .. 0.86
   2 ?    8.1   0.6    0.0012       1.9      13      37 ..    1051    1081 ..    1049    1082 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.35
                 HHHHHHHHHHHHHH CS
        RecR   2 aeeLaeaLqeakek 15 
                 + +Lae+L++++++
  EPA06703.1 524 GAQLAESLRDLRRN 537
                 679********998 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0012
                  HHH-EE-TTT--EESSS......S-CCCCST CS
        RecR   13 kekvrhCsrCgnlteed......lCaICsdp 37  
                  k+++  C+rCg ++ +d      +C++C d+
  EPA06703.1 1051 KSDIFVCERCGLVAYHDvkqrkyVCRVCGDK 1081
                  567889**********98899889****996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.77u 0.32s 00:00:01.09 Elapsed: 00:00:00.50
# Mc/sec: 6760.37
//
Query:       EPA06704.1  [L=275]
Description: hypothetical protein BG20_I1468 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.3e-05   23.6   0.2     0.0098   16.3   0.1    2.5  2  MG2           MG2 domain
     0.0066   16.4   0.0      0.049   13.6   0.0    2.2  2  P_proprotein  Proprotein convertase P-domain
  ------ inclusion threshold ------
        1.2    9.4   4.3        3.7    7.8   0.3    2.8  3  Trp_ring      Trimeric autotransporter adhesin Trp ring domai


Domain annotation for each model (and alignments):
>> MG2  MG2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   1.6e-06    0.0098      33      96 .]      49     114 ..      25     114 .. 0.86
   2 !    4.9   0.0     0.006        36      34      96 .]     170     234 ..     155     234 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.6e-06
                 -.EEEEEEEE-TTSSEEEEEEEEE-CTTEEEEEEE--TT.--SEEEEEEEEECSTTT-EEEEEEEE CS
         MG2  33 k.lplkltirdpdgkevkelplatdetggaesefalpea.aklGeysvelsadsaeeslssgsfrV 96 
                 + + +++t+ +p+++ v+  +++ d++g +++ef++++   + G y++++++++++++l++ s+rV
  EPA06704.1  49 QiTDITFTVISPSQNIVSVDQIKPDAKGNFSTEFKTNSMwKENGFYTIKVEQSPKGSALYKLSLRV 114
                 24669********************************982558**************999999998 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.006
                 EEEEEEEE-TTSSEEEEEEE..EE-CTTEEEEEEE-..-TT--SEEEEEEEEECSTTT-EEEEEEEE CS
         MG2  34 lplkltirdpdgkevkelpl..atdetggaesefal..peaaklGeysvelsadsaeeslssgsfrV 96 
                  ++++++  p+g++v   ++    +e+g +  ++++  p   + G+y++++  ++ e++ +++s++V
  EPA06704.1 170 NSITMKVIAPNGNVVVVDQFvpILNEQGHFFKDIKTggPLWKQDGQYQIVA--QQGEDPRYKHSIEV 234
                 46889999999998888888778999999888887733566899*******..77777777777776 PP

>> P_proprotein  Proprotein convertase P-domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   8.3e-06     0.049      11      71 ..      46     101 ..      37     114 .. 0.84
   2 ?    0.2   0.0      0.13     8e+02      16      34 ..     170     188 ..     160     225 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.3e-06
                   EESSGGGEEEEEE-TTS-EEEEE---TT---SS-EEEEEEEESTTTTS---EEEEEEEEES CS
  P_proprotein  11 thtrrgdlritLvsPsGtrsvLlnrrgkdksrsgfldwtfmsthlwgeraeGeWkLevkds 71 
                   t++ + d++ t +sPs + + + + +++    +g++  +f ++ +w+e+  G ++++v+ s
    EPA06704.1  46 TMSQITDITFTVISPSQNIVSVDQIKPD---AKGNFSTEFKTNSMWKEN--GFYTIKVEQS 101
                   457789****************999999...9**************996..8999999873 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.13
                   GGEEEEEE-TTS-EEEEE- CS
  P_proprotein  16 gdlritLvsPsGtrsvLln 34 
                     ++ + ++P+G+++v+ +
    EPA06704.1 170 NSITMKVIAPNGNVVVVDQ 188
                   678889999***9998755 PP

>> Trp_ring  Trimeric autotransporter adhesin Trp ring domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.3   0.00062       3.7      26      48 ..      36      57 ..      21      58 .. 0.93
   2 ?   -3.5   0.0       2.1   1.3e+04      38      46 ..      90      98 ..      89      99 .. 0.74
   3 ?    2.3   0.1     0.032   1.9e+02      25      48 ..     155     176 ..     153     177 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00062
    Trp_ring 26 GeggakVsGktdedgvrtiTVkV 48
                G+++++VsG t   ++  iT++V
  EPA06704.1 36 GSNTISVSGHT-MSQITDITFTV 57
                99*********.99999999987 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.1
    Trp_ring 38 edgvrtiTV 46
                e+g +ti V
  EPA06704.1 90 ENGFYTIKV 98
                788888877 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.032
    Trp_ring  25 vGeggakVsGktdedgvrtiTVkV 48 
                 +G++ +++ G+t  d    iT kV
  EPA06704.1 155 AGSNIISIVGTT--DSANSITMKV 176
                 6999********..6777888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1726.65
//
Query:       EPA06705.1  [L=390]
Description: hypothetical protein BG20_I1475, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
        0.2   11.6   0.9        1.5    8.8   0.2    2.3  2  DUF1425       Protein of unknown function (DUF1425)
        1.5    8.8   5.9        5.3    7.1   0.1    4.4  4  HCBP_related  Haemolysin-type calcium binding protein related


Domain annotation for each model (and alignments):
>> DUF1425  Protein of unknown function (DUF1425)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0     0.055   4.9e+02       7      36 ..     205     234 ..     199     240 .. 0.78
   2 ?    8.8   0.2   0.00017       1.5      20      76 ..     304     357 ..     298     367 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.055
                 EEEEEEEEEEEEEECCCEEEEEEEEEE-SS CS
     DUF1425   7 laagisveelklresngllraqvtlsnksk 36 
                   +gi+v+++++++++g   ++ t++ +++
  EPA06705.1 205 DLSGIEVSAIETTADSGIFVGTITFAQNQS 234
                 4579************99999999875554 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00017
                 ECCCEEEEEEEEEE-SSS-EEEEEEEEEE-TTS-EE--TT---EEEEE-TT-EEEEE CS
     DUF1425  20 esngllraqvtlsnkskkdltlqYrFyWyDkqGlevepeespWksltlhgketvtvs 76 
                 ++n++ ++   +sn+++ ++++ Y F+  D++   v+    +W +  ++++++  vs
  EPA06705.1 304 STNDQIQIVGAVSNEQNFKQKFVYLFQVKDSSNSVVSV---SWVQGEISPNQKLDVS 357
                 68999**********************99999888854...5999999999988886 PP

>> HCBP_related  Haemolysin-type calcium binding protein related domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.1    0.0006       5.3      29      38 ..     142     151 ..      99     155 .. 0.75
   2 ?    0.2   0.0      0.08   7.2e+02      25      36 ..     159     170 ..     152     176 .. 0.75
   3 ?   -0.6   0.1      0.15   1.3e+03       9      23 ..     305     318 ..     304     324 .. 0.81
   4 ?   -1.2   0.0      0.23   2.1e+03      22      31 ..     365     374 ..     357     376 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0006
  HCBP_related  29 qieFaDGtvW 38 
                    ++FaDG+v+
    EPA06705.1 142 SFTFADGVVL 151
                   79******98 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.08
  HCBP_related  25 yrieqieFaDGt 36 
                     i qi+F+ G 
    EPA06705.1 159 WNIAQIQFSEGN 170
                   4599****9885 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.15
  HCBP_related   9 tgDsitiknwfsssg 23 
                   t+D+i i +  s+ +
    EPA06705.1 305 TNDQIQIVGAVSN-E 318
                   79*****999885.3 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 0.23
  HCBP_related  22 sgsyrieqie 31 
                   sg y ie+++
    EPA06705.1 365 SGEYTIETFV 374
                   79999***97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2604.66
//
Query:       EPA06706.1  [L=76]
Description: LSM domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.7e-17   61.2   2.3    6.4e-17   61.0   2.3    1.0  1  LSM       LSM domain


Domain annotation for each model (and alignments):
>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.0   2.3   3.6e-21   6.4e-17       2      66 ..       8      70 ..       7      71 .. 0.94

  Alignments for each domain:
  == domain 1  score: 61.0 bits;  conditional E-value: 3.6e-21
                HHHHTTTSEEEEEETTSEEEEEEEEEEETTSEEEEEEEEEEETTETEEEEEEEEEEEGGGEEEEE CS
         LSM  2 flkklinkkvtvelkngrelrGtLkgfDqfmNlvLedveetlkdkkekrklglvliRGnnivlis 66
                ++ + +nk ++++l+n++ +rG L+ fD +mNl L+++e ++++  ++  lg++l+RG+ni+ +s
  EPA06706.1  8 LMTNNKNKVILLRLRNNKSVRGSLQDFDIHMNLTLDNAEDISDN--KVVPLGRILLRGDNILAVS 70
                678999**********************************9977..7**************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.34s 00:00:00.83 Elapsed: 00:00:00.52
# Mc/sec: 438.97
//
Query:       EPA06707.1  [L=137]
Description: hypothetical protein BG20_I1465, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0032   17.6   1.0     0.0054   16.9   1.0    1.5  1  Big_3_5   Bacterial Ig-like domain (group 3)


Domain annotation for each model (and alignments):
>> Big_3_5  Bacterial Ig-like domain (group 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   1.0     3e-07    0.0054       4      68 ..      33     102 ..      28     123 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3e-07
                 EETTSEEEEEEE--CCCCTTS--EEEEEETTEE-.SS-EE--TTSEEEEEEE-.....SS-EEEEEEEEEE CS
     Big_3_5   4 vtagqtvtltatVtaasggtptGtVtftdggttl.gtavllsanGtAtltvsa.....laaGthsitAtYs 68 
                  + g+t+ ++ tV+++  gtp  t +++++g+ +  ++++++a+G+ + t+ a     ++aG+++i A+Y 
  EPA06707.1  33 YKEGETIVISGTVSTVLPGTPI-TMQIFSEGNLVdIAQITVAADGSYSHTIIAqgplwTKAGEYTIRASYG 102
                 5668999999999999444443.66666666655346778889*******9665666677**********5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 885.60
//
Query:       EPA06708.1  [L=271]
Description: hypothetical protein BG20_I1469 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0024   18.3   0.1     0.0051   17.2   0.1    1.6  1  MG2       MG2 domain
  ------ inclusion threshold ------
      0.065   13.7   0.2       0.31   11.5   0.0    2.1  2  CBM60     Ca-dependent carbohydrate-binding module xylan-bind


Domain annotation for each model (and alignments):
>> MG2  MG2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   5.7e-07    0.0051       4      95 ..      33     121 ..      30     122 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5.7e-07
                 EEES-SEE-TT-EEEEEEEEESTTCSB---EEEEEEEE-TTSSEEEEEEEEE-CTTEEEEEEE--TT..--SEEEEEEEEECSTTT-EEEEEEE CS
         MG2   4 vytDRglYrPgetVslkallrdetlqglaklplkltirdpdgkevkelplatdetggaesefalpea..aklGeysvelsadsaeeslssgsfr 95 
                 v tD++ Y  g+t+ +++ ++d     l++ p++l+++ p+g+ v   +++ +++ +++se+    a   + G+y++++   ++e+++++++f+
  EPA06708.1  33 VTTDKTSYEDGDTILVTGAVKD----RLTGVPVSLRVVAPNGNLVTVAQIDVNADKTFSSELIAGGAlmKSSGTYKITA-FYGTEHRVAETTFE 121
                 789**************99976....4778899*****************9999999****98877633568******9.88899999999886 PP

>> CBM60  Ca-dependent carbohydrate-binding module xylan-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.22     2e+03      12      39 ..      57      85 ..      45     130 .. 0.67
   2 ?   11.5   0.0   3.5e-05      0.31      11      55 ..     190     232 ..     185     233 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.22
       CBM60 12 gdeppefrl.lvdGqkvgeadvasteakt 39
                 ++p+++r+   +G+ v+ a+++    kt
  EPA06708.1 57 TGVPVSLRVvAPNGNLVTVAQIDVNADKT 85
                55666666645577777655544333333 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 3.5e-05
       CBM60  11 agdeppefrllvdGqkvgeadvasteaktytftadltagahklqi 55 
                  gd+  +f +lvdG++v   +  ++++++ t t++++aga++++i
  EPA06708.1 190 MGDQDDTFFVLVDGEEVDFEE--TATSTDRTLTIQFPAGAEEIEI 232
                 4778889**********9888..5688899999999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2006.76
//
Query:       EPA06709.1  [L=1263]
Description: DNA-directed RNA polymerase subunit A' [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-93  312.5   0.0    1.5e-92  310.3   0.0    2.0  2  RNA_pol_Rpb1_1  RNA polymerase Rpb1, domain 1
    7.5e-84  281.3   1.7    1.7e-83  280.1   1.7    1.6  1  RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
    3.5e-73  245.3   0.0    5.8e-73  244.6   0.0    1.4  1  RNA_pol_Rpb1_2  RNA polymerase Rpb1, domain 2
    6.8e-35  120.3   0.0      2e-34  118.8   0.0    1.9  1  RNA_pol_Rpb1_3  RNA polymerase Rpb1, domain 3
      8e-24   83.7   0.2    1.4e-22   79.6   0.1    2.8  2  RNA_pol_Rpb1_4  RNA polymerase Rpb1, domain 4
  ------ inclusion threshold ------
      0.075   13.3   0.0         13    6.1   0.0    2.8  2  Peptidase_C34   Putative closterovirus papain-like endopeptid


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb1_1  RNA polymerase Rpb1, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  310.3   0.0   4.9e-96   1.5e-92       2     312 .]       7     316 ..       6     316 .. 0.93
   2 ?   -1.4   0.1      0.39   1.2e+03     252     281 ..    1000    1029 ..     995    1037 .. 0.76

  Alignments for each domain:
  == domain 1  score: 310.3 bits;  conditional E-value: 4.9e-96
                     E---EEEEEE--HHHHHHH-SBB--STTSTCSTSSSSBBSSSSSSSSS-SSSSSTSTTTSSTTTT-----EEEEEECEEE-HHHHHHHHHHCTTC CS
                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  RNA_pol_Rpb1_1   2 kkikeiqfgiaspeeirkwSvvevtkaetieekslkPeegGllDerlgtidkdleCetCgkkkkeCeghfGhieLakPvfhigffklilkilecv 96 
                     k+i++i+f++ sp eirk+Sv+e+t +et++e+   P +gGl+D rlgt +   +C tCg++ ++C+ghfGhieLa+P++hi f++ i+k+l+++
      EPA06709.1   7 KSIDAIRFSVWSPTEIRKYSVAEITAPETYDEDG-MPVQGGLMDGRLGTLEPGQKCLTCGNTAARCPGHFGHIELAEPILHIAFIDNIYKLLQST 100
                     789*****************************95.************************************************************ PP

                     ETTTTEBSS-TTSH....HHHHHH...CSSSCCCCHHHHHHHHCCS-BE-SSSSB-EEEEEETTEEEEEESSSSTSCEEEE-HHHHHHHHHCSTH CS
                     xxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  RNA_pol_Rpb1_1  97 ckecskllldeekkkllsklkkre...kleelkkrlkaieelckkinlcekCgavqpkleeegeklkaalkkskeeekeklsaekvkkllkried 188
                     c+ c +l + +e+ + + k+k+++   ++ + k+  ++i e+ kk + c +Cg  + ++e  + k +  ++k++   ++ l + ++++ +++i d
      EPA06709.1 101 CRSCARLKVPQEDLDEFRKIKEKHaayTVISEKRIPEQIIEKAKKAKECPHCG--KTQYELIFTKPTIFVEKTEI-GEHRLLPITIRERFSQIID 192
                     ************7766766664441014445557899****************..56687788888777777766.789999************* PP

                     HHHHHTTSBTTTB-GGGCCECCEEE--GGGS-BEESSSSSEEBECCCCHHHHHHHHHHHHHHHHHSSSSSTCHHHHHHHHHHHHHHCC-TTSSSS CS
                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  RNA_pol_Rpb1_1 189 edvevlgfkssgsrPewliltvlPVpPpeiRPsvqldggrrsedDlteklrdiikrNnrLkkaeeegapeliieeekelLQehvatlfdneisgl 283
                     +d+ +l  ++  +rPew+il+ lPVpP+++RPs+ l++g rsedDlt+k++dii+ N+rLk+ +e+g+p li+++ ++lLQ+h +t+fdne+sg+
      EPA06709.1 193 DDLHLLAYDPVTARPEWFILQALPVPPVTVRPSIILETGIRSEDDLTHKMVDIIRVNQRLKESKEAGTPPLIVQDLVDLLQYHATTYFDNEVSGI 287
                     *********************************************************************************************** PP

                     SEEBSTTSSS--THHHHHTSSSSCCCCCT CS
                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  RNA_pol_Rpb1_1 284 kpatqkskrplkslsqrLkGKeGrfRgnL 312
                     ++a+++s+rplk+l+qrLkGKeGrfRg+L
      EPA06709.1 288 PQAHHRSGRPLKTLTQRLKGKEGRFRGSL 316
                     ***************************98 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.39
                      HHSSSSSTCHHHHHHHHHHHHHHCC-TTSS CS
                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  RNA_pol_Rpb1_1  252 eeegapeliieeekelLQehvatlfdneis 281 
                      e+++  e++i+  +++LQ +v +l+  + +
      EPA06709.1 1000 ESKKSREKAIDVARNILQTKVSALISDSET 1029
                      5667789999999**********9955443 PP

>> RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  280.1   1.7   5.8e-87   1.7e-83       1     265 [.     786    1207 ..     786    1209 .. 0.97

  Alignments for each domain:
  == domain 1  score: 280.1 bits;  conditional E-value: 5.8e-87
                      B--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTEEEETTSEEEETTS-EEESSGGGTS........................... CS
                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................... RF
  RNA_pol_Rpb1_5    1 GLkvkefffhtmggReGLiDtAvkTaesGYlqRrlvkaledvvvkyddtvrnsggeivqflygedg........................... 66  
                      GL++ efffh+mggReGL+DtAv+T +sGY+qRrl++ale +  +yd+tvr+ +g+i+qflygedg                           
      EPA06709.1  786 GLSALEFFFHAMGGREGLVDTAVRTQQSGYMQRRLINALEHIRLEYDGTVRDPHGHIIQFLYGEDGidvaksdhgeafninrliesqtivdsg 878 
                      9******************************************************************************************** PP

                      .......................................................B--TT-BHHHHHHHHHHHHHHCCCSSTTSSTCSSTSSS CS
                      .......................................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  RNA_pol_Rpb1_5   67 .......................................................lvepGeavGiiaaQSiGePgTQltlnTFHfaGvasknv 104 
                                                                              vepG+avGii aQSiGePgTQ+tl+TFHfaG+a++nv
      EPA06709.1  879 kkatkeeitdlakkytktfnprlkqlvtdglldsklskegaeivckkglslynkaKVEPGQAVGIITAQSIGEPGTQMTLRTFHFAGIAERNV 971 
                      ********************************************************************************************* PP

                      SSSHHHHHHHHTT-SS-SS-EEEEEB-SSSSSCHHHCHHHHHHHSE............................................... CS
                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................................... RF
  RNA_pol_Rpb1_5  105 tlGvprlkeilnvskniksksltvllvdeeakelekakkvkkaiek............................................... 150 
                      tlG+prl e++++ k+  ++++ ++l +e +k++eka  v+++i +                                               
      EPA06709.1  972 TLGLPRLIELVDARKKPVTPTMDIYLDNESKKSREKAIDVARNILQtkvsalisdsetdyttqiklilspnrlkergctvgeveaalqsnkkf 1064
                      ******************************99999999999999889999******************************************* PP

                      ...................................CBTTEEEEEEEEEEEEEEETEEEEEEECS--HHHHTTSTTTBETTTEEESSHHHHHHH CS
                      ...................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  RNA_pol_Rpb1_5  151 ...................................gikkikrilvkeaekgkeeekelvletegvnlsevlkveevvdageilsndiaeilei 208 
                                                         g+++i+r+ ++     +++ +e+v++t g n+ +vl+v++ +d++++ +n++ ei+ +
      EPA06709.1 1065 kmettgelitlklveesdaptviairnkvlnttvkGVPDIERVTLV-----QKD-DEWVIQTTGSNIAKVLEVSG-IDKKNVRTNNVFEIAGT 1150
                      ********************99999999999988888888888888.....333.68******************.***************** PP

                      HCHHHHHHHHHHHHHHHHHHTTS---HHHHHHHHHHHTTTSS---SSTTCHCCSSSH CS
                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  RNA_pol_Rpb1_5  209 lgieaarkallkeiqevykvqgvsvndrHlelivdqmtkkgeivavnrsGinkaels 265 
                      lgiea+r+al++e++++++ qg++v+dr ++l+ d+m+ +g++ +++r+Gi  ++ s
      EPA06709.1 1151 LGIEASRNALINELNNTLEDQGLEVDDRYIMLVSDLMCSRGYMQQIGRHGIAGTKDS 1207
                      ***************************************************987765 PP

>> RNA_pol_Rpb1_2  RNA polymerase Rpb1, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  244.6   0.0   1.9e-76   5.8e-73       1     166 []     318     485 ..     318     485 .. 0.98

  Alignments for each domain:
  == domain 1  score: 244.6 bits;  conditional E-value: 1.9e-76
                     SEEESSEEEEEEEEESSS-TTEEEEEHHHHTTSEEEEE-STTTHHHHHHHHHHTTTSSSSEEEEESTTSSEEETTTT-S..CHHCCTTTTSEEEE CS
  RNA_pol_Rpb1_2   1 GkrvdysaRsvispdpnlkldevgvPisvakkltvpeivtelnikklrklvengpevyPgasyvkredgsekklkakkr..klakelekgdiver 93 
                     Gkrvd+s+R+vispdpnl+l evgvP ++a+klt+peivte+ni+++rklv+ngp++ Pg +y+ r dg + +l   ++  ++a++le+g+ ver
      EPA06709.1 318 GKRVDFSSRTVISPDPNLDLSEVGVPEQIAMKLTIPEIVTEWNIERMRKLVINGPNTFPGVNYIVRPDGVKIRLDFVEDrsTIAETLEIGYLVER 412
                     9*************************************************************************998874459************ PP

                     E--TTSEEEEE-SSTTSGGGEEEEEEEEESSSSEEEEGGGHCCCT--SSS-EEEEE--SSHHHHHHHHHCSBT CS
  RNA_pol_Rpb1_2  94 hvkdgdvvllNRqPsLhklsimahrvkvlekktlrlnlsvttayNaDFDGDemnlhlpqseearaEaeelllv 166
                     h+ +gd+vl+NRqPsLh++simah+v+vl++kt+rl+ sv+ +yNaDFDGDemnlh+pqseearaEa  l+ v
      EPA06709.1 413 HLANGDIVLFNRQPSLHQMSIMAHYVRVLPGKTFRLHPSVCPPYNADFDGDEMNLHVPQSEEARAEAILLMRV 485
                     *********************************************************************9975 PP

>> RNA_pol_Rpb1_3  RNA polymerase Rpb1, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.8   0.0   6.6e-38     2e-34       1     157 []     488     648 ..     488     648 .. 0.93

  Alignments for each domain:
  == domain 1  score: 118.8 bits;  conditional E-value: 6.6e-38
                     CSEETTTTEESSS--THHHHHHHHHSSTTEEEEHHHHHHHHHHSSSCCSSSSSSSSSBESS.SEBEEHHHHHHCCCHCCCCEEEE...SSSS... CS
  RNA_pol_Rpb1_3   1 nilspqsgkPvigivQDsllGvyllTkedvfidreeaqqllykgvgsdsktvtlrpailkp.kelwtgkqtfsrilpneinyerk...neek... 88 
                     +++sp+ g P+ig  +D+++G+yllTk+d++++++e+ ++ + g  +   ++ ++p  + +  + +tgkq+fs++lp+++ny  +   +  k   
      EPA06709.1 488 QLISPRYGGPIIGALRDFVTGAYLLTKDDTLLTPQEFYNYAMLGGYN---EKFPKPGSKNKdGPMYTGKQLFSLFLPKDFNYVITskwS--Kgtk 577
                     689*****************************************777...56788888888889**************99999875441..2557 PP

                     ..STSEEECSSEEEES--SHHHHSSSSTTSHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHCEB-TGGGG CS
  RNA_pol_Rpb1_3  89 ..dgkvlikngelikGvidkkvvgkksqgslihvlakeygiketvrfldslqrlgfkyllqsgftigigDt 157
                       +++v+ikngeli+Gvidk+ +g+++ +s++h +ak+yg +++++fl+s+  ++ +y++++gf+ g++D+
      EPA06709.1 578 gaQKDVVIKNGELISGVIDKSSIGAEEPESVLHRIAKDYGNTKAKNFLNSILIMVKQYITHYGFSYGYADL 648
                     889*****************************************************************995 PP

>> RNA_pol_Rpb1_4  RNA polymerase Rpb1, domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.17   5.2e+02      29      56 ..     608     633 ..     590     634 .. 0.71
   2 !   79.6   0.1   4.8e-26   1.4e-22       3     108 .]     675     779 ..     672     779 .. 0.96

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.17
                     HHHHHHHHHHHHHHHCSTTTSHHHHHHH CS
  RNA_pol_Rpb1_4  29 ilnkardkagkiaskslaasNsiliMvk 56 
                     +l ++ ++ g++  k+    NsiliMvk
      EPA06709.1 608 VLHRIAKDYGNTKAKNF--LNSILIMVK 633
                     44444555566666665..4******96 PP

  == domain 2  score: 79.6 bits;  conditional E-value: 4.8e-26
                     HHCTHTCCHHHTTHCHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTTSHHHHHHHCTSSS-HHHHHHHHTB-EEEEBTTBSS--SSTSCSSTTSSS CS
  RNA_pol_Rpb1_4   3 eaerygkledlpgksleelfeakinkilnkardkagkiaskslaasNsiliMvksGaKGsiinisqiagclGqqnvegkripkgfsgrtlphfkk 97 
                     ++e+ g l+ + g++ ee +ea i + l kardkag +a +sl+ sN   iM+ +Ga+Gs +ni q+ag lGqq+ +g+r   g+++r+lph+++
      EPA06709.1 675 QYEK-GTLKLTRGMKPEEALEAYIVNELGKARDKAGMTADQSLDQSNAGRIMATTGARGSSLNIGQMAGALGQQSRRGSRLHAGYNNRALPHYQE 768
                     4566.99999**********************************88************************************************* PP

                     SESSTTTSSEE CS
  RNA_pol_Rpb1_4  98 idespesrGFv 108
                     +d+ p ++GFv
      EPA06709.1 769 HDNNPDAHGFV 779
                     **********8 PP

>> Peptidase_C34  Putative closterovirus papain-like endopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0    0.0044        13      34      89 ..     909     964 ..     889     967 .. 0.91
   2 ?    4.0   0.0      0.02        60      10      66 ..    1014    1072 ..    1005    1084 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0044
  Peptidase_C34  34 vldrcisnkgcslddlkaiceayeikvevegdcglvevgsiglslgrlllrgnhfs 89 
                    +ld  +s  g ++   k +    + kve     g++   sig +  +++lr  hf+
     EPA06709.1 909 LLDSKLSKEGAEIVCKKGLSLYNKAKVEPGQAVGIITAQSIGEPGTQMTLRTFHFA 964
                    688889999999999999999999******************************96 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.02
  Peptidase_C34   10 dclfsslaeliskkpeevmlkvpnvld.rcisnkgcslddlka.iceayeikvevegdc 66  
                     + l + +++lis  + +   ++  +l    + ++gc + ++ a + ++ ++k+e+ g+ 
     EPA06709.1 1014 NILQTKVSALISDSETDYTTQIKLILSpNRLKERGCTVGEVEAaLQSNKKFKMETTGEL 1072
                     567788999************99999735689*******99862667889999999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       769  (0.0428914); expected 358.6 (0.02)
Passed bias filter:                      675  (0.0376485); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.90u 0.34s 00:00:01.24 Elapsed: 00:00:00.52
# Mc/sec: 7314.41
//
Query:       EPA06710.1  [L=83]
Description: RNA polymerase Rpb5, C-terminal domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.7e-27   93.2   0.1    7.9e-27   92.9   0.1    1.1  1  RNA_pol_Rpb5_C  RNA polymerase Rpb5, C-terminal domain


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb5_C  RNA polymerase Rpb5, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.9   0.1   4.4e-31   7.9e-27       3      73 .]      10      80 ..       8      80 .. 0.98

  Alignments for each domain:
  == domain 1  score: 92.9 bits;  conditional E-value: 4.4e-31
                    -TSSSS--EEEEE-HHHHHHHHHHTT--TTCSS-EETTSHHHHCCT--TTSEEEEEEEETTTEEEEEEEEE CS
  RNA_pol_Rpb5_C  3 itkHelvPkhevlseeekkellkklkikeeqLPkisksDpvarylglkkGdvvkItrksetageavtYRlV 73
                    + +H +vPkhe++s++e++e+lkk+++k+++LP i  +Dp++  lg+k+Gd++kItrks+tage+ +YR+V
      EPA06710.1 10 VPDHIYVPKHEIISKQEAEEVLKKYNCKPTELPLIFVNDPAILGLGVKPGDMIKITRKSPTAGESLYYRYV 80
                    678******************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.38
# Mc/sec: 650.88
//
Query:       EPA06711.1  [L=198]
Description: WD40-like protein, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-19   67.7  16.3    4.4e-05   23.3   0.5    5.4  5  PD40             WD40-like Beta Propeller Repeat
    8.3e-06   24.8   0.5      0.045   12.5   0.2    3.2  2  DPPIV_N          Dipeptidyl peptidase IV (DPP IV) N-terminal 
    2.2e-05   23.9   0.2    0.00075   18.8   0.2    2.8  2  DUF5050          Domain of unknown function (DUF5050)
     0.0052   15.5   0.1       0.28    9.8   0.0    2.2  2  Pectate_lyase22  Oligogalacturonate lyase
  ------ inclusion threshold ------
      0.019   14.5   0.5      0.033   13.7   0.5    1.4  1  Tachylectin      Tachylectin
       0.42   10.6   2.5        7.6    6.5   0.2    3.0  3  Big_11           Bacterial Ig-like domain


Domain annotation for each model (and alignments):
>> PD40  WD40-like Beta Propeller Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.3   6.5e-08   0.00019      14      30 ..       2      18 ..       1      29 [. 0.87
   2 !   23.3   0.5   1.5e-08   4.4e-05      10      37 ..      39      67 ..      31      68 .. 0.80
   3 !   15.7   0.1   3.6e-06     0.011      13      26 ..      88     101 ..      87     104 .. 0.90
   4 !   15.0   0.2   5.9e-06     0.018       8      35 ..     127     152 ..     127     154 .. 0.89
   5 ?   -0.3   0.0      0.38   1.1e+03       2      14 ..     173     185 ..     173     185 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 6.5e-08
                EEE-TTSSEEEEEEECT CS
        PD40 14 PsfSPDGkrlaFsSdRg 30
                P +SPDG++++FsS+++
  EPA06711.1  2 PNWSPDGTKIVFSSSGD 18
                88************976 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 1.5e-08
                .EEEEEE-TTSSEEEEEEECT.TCEE..EE CS
        PD40 10 negaPsfSPDGkrlaFsSdRgsGkpd..Iy 37
                +  +Ps+SPDG+++a++ ++   ++d  Iy
  EPA06711.1 39 DQSSPSWSPDGTKIAYTHQGY-TGTDngIY 67
                6679*************8876.66666777 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 3.6e-06
                 EEEE-TTSSEEEEE CS
        PD40  13 aPsfSPDGkrlaFs 26 
                 +Ps+S DG++++F 
  EPA06711.1  88 SPSWSADGTKIVFQ 101
                 7************6 PP

  == domain 4  score: 15.0 bits;  conditional E-value: 5.9e-06
                 SS.EEEEEE-TTSSEEEEEEECT.TCEE CS
        PD40   8 pgnegaPsfSPDGkrlaFsSdRgsGkpd 35 
                 +gn  +P fS DG++++F+ d + G+++
  EPA06711.1 127 SGNARGPVFSTDGTKIIFAVD-D-GNWN 152
                 58999*************999.6.8775 PP

  == domain 5  score: -0.3 bits;  conditional E-value: 0.38
                 EE--SSSS.EEEE CS
        PD40   2 krltntpgnegaP 14 
                 +rltn+  +e++P
  EPA06711.1 173 TRLTNGVYDEFNP 185
                 699****999998 PP

>> DPPIV_N  Dipeptidyl peptidase IV (DPP IV) N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.2   1.5e-05     0.045      48     118 ..       2      55 ..       1      64 [. 0.76
   2 !    4.8   0.0    0.0033       9.7     179     241 ..      79     141 ..      59     182 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.5e-05
                 EEEESSTTEEEEEETTEEEEESTTTSEEEECES-STTTEEESB--HHHHHHTSSSSBEEEE-TTSSEEEEE CS
     DPPIV_N  48 akwSPagdklafvrnnnLyvrelatgkeiqlTsdgsagifnGvadWvyeEEvlgsnsavwWspdgsrlayl 118
                 ++wSP+g+k++f  + ++y  +    +   l+sd                   +++s+  Wspdg+++ay+
  EPA06711.1   2 PNWSPDGTKIVFSSSGDIYSINADGTNLANLSSDQ-----------------AYDQSSPSWSPDGTKIAYT 55 
                 68999999999999999999988777888888777.................2445677777777777776 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0033
                 HCTTCEEEEEEEECTTSCCEEEEEEETTSTEEEEEEEETTTCCEEEEEEEESSS-SSS-S-EE CS
     DPPIV_N 179 lsekdeyitrvkWtsdeksllvqwlnRsqnrlkvvlvdaetgravvkleetsdgWvelhdevh 241
                 ls++ +++++ +W+ d++++++q++n +  +  +++++a+ +  v  l+ +++g v  +d ++
  EPA06711.1  79 LSNDIYIWASPSWSADGTKIVFQYFNWDTFENGISIMNADGSGRVQLLSGNARGPVFSTDGTK 141
                 456677888888988888899999888887777777766543333333555666665555555 PP

>> DUF5050  Domain of unknown function (DUF5050)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.0    0.0015       4.6      26      48 ..      15      37 ..       6      40 .. 0.79
   2 !   18.8   0.2   2.5e-07   0.00075     119     259 ..      17     182 ..      14     187 .. 0.55

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0015
                GTTEEEEEETTS-S-EEEEEEEE CS
     DUF5050 26 denkLYkmnsdgsnlkklsddsv 48
                 ++ +Y++n dg+nl +ls+d++
  EPA06711.1 15 SSGDIYSINADGTNLANLSSDQA 37
                56679999999999999999987 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 2.5e-07
                 EEEEEEETTS---EEEESS---.....-SEEETTEEEEE-T....TT--EEEEETTTTEEEEEE-S-EEE....EEEEETTE...EEEEG.GGTT-EEE CS
     DUF5050 119 lklykikidgkektklsdeaie.....plsvkdgwiYytge...sedhslykldtdgksiskvseenlyl....lvvegdyi...Yyidl.sknyaLyr 201
                 +++y+i+ dg++  +ls++++      + s ++ +i yt +    +d+ +y+++ dg+ + ++s++ +       +++g +i   Y+    + ++ +  
  EPA06711.1  17 GDIYSINADGTNLANLSSDQAYdqsspSWSPDGTKIAYTHQgytGTDNGIYTMNPDGSGKIRLSNDIYIWaspsWSADGTKIvfqYFN-WdTFENGISI 114
                 5677777777777777544333011113345666777776544456667777777776666666654332232245566666443332.2333333444 PP

                 E-SSS---..EE-S-S-EEEEEEETTEEEEEE-SSS-E.........EEEEETTS---EEEEES-EEE CS
     DUF5050 202 vklsgsek..evltedkvdnyNvtgnwiYyqkesdeeka........lyrikldGsekeklaegnvsn 259
                 ++ +gs     +  + +  ++ ++g++i +++++++ +         +  ++ dG++ + l++g +++
  EPA06711.1 115 MNADGSGRvqLLSGNARGPVFSTDGTKIIFAVDDGNWNPvpgyqtfnIHIMNVDGTGDTRLTNGVYDE 182
                 44444444103344555566777777777777766655556677777777777777777777777765 PP

>> Pectate_lyase22  Oligogalacturonate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0   9.4e-05      0.28     218     273 ..      19      73 ..       6      89 .. 0.86
   2 !    4.1   0.0    0.0052        16      42      63 ..     134     154 ..      90     183 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 9.4e-05
  Pectate_lyase22 218 mwlinedgsnlrkvkehaegescthevwvpdgsalayvsylkgsterviysadpvt 273
                      ++ in dg+nl ++ +    +  +   w pdg+ +ay       t+  iy+++p+ 
       EPA06711.1  19 IYSINADGTNLANLSSDQAYDQ-SSPSWSPDGTKIAYTHQGYTGTDNGIYTMNPDG 73 
                      6789*********998765554.4568***********999999999******985 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0052
  Pectate_lyase22  42 cftrdgskllfggafdgprnyy 63 
                      +f+ dg+k++f+ + dg++n  
       EPA06711.1 134 VFSTDGTKIIFAVD-DGNWNPV 154
                      79*********987.9999954 PP

>> Tachylectin  Tachylectin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.5   1.1e-05     0.033      83     179 ..       9     109 ..       3     131 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.1e-05
                  SEEEE-TTS-EEEEETT.E.EE...EE---SSTTS-HHHH-EEEESSSGGG-SEEEE-TT--EEEEE.TT........EEEEES--SSTT--HHHH-E CS
  Tachylectin  83 kkivvdpkGvlYavtadGe.Ly...kgppPsdeetsWeavatkvidtgwkdfdslfadpdGvlYavtstG........rlvkrakPaevgddwlssst 168
                   kiv+  +G++Y ++adG+ L      ++ ++ + sW   +tk+  t       ++ +++G +Y ++++G        +++ +a P+       +++ 
   EPA06711.1   9 TKIVFSSSGDIYSINADGTnLAnlsSDQAYDQSSPSWSPDGTKIAYTHQ----GYTGTDNG-IYTMNPDGsgkirlsnDIYIWASPSWSA---DGTKI 98 
                  589***************534455477788888999******9975543....45666666.5888888877776666667777776544...23344 PP

                  E-S-S-GGG-S CS
  Tachylectin 169 lvstedWrdlk 179
                  +++  +W+ ++
   EPA06711.1  99 VFQYFNWDTFE 109
                  44455666665 PP

>> Big_11  Bacterial Ig-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.047   1.4e+02      22      43 ..       6      27 ..       4      42 .. 0.89
   2 ?    6.5   0.2    0.0025       7.6      29      49 ..      59      80 ..      39      81 .. 0.73
   3 ?   -1.1   0.0      0.59   1.8e+03      35      47 ..     112     124 ..      93     143 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.047
      Big_11 22 apGttvklpGiekevtinedGs 43
                ++Gt++ +    + + in dG+
  EPA06711.1  6 PDGTKIVFSSSGDIYSINADGT 27
                68*******************8 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0025
      Big_11 29 lpGiek.evtinedGsvtipns 49
                + G ++  +t+n+dGs++i  s
  EPA06711.1 59 YTGTDNgIYTMNPDGSGKIRLS 80
                45776668**********9866 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.59
      Big_11  35 evtinedGsvtip 47 
                   ++n dGs+ ++
  EPA06711.1 112 ISIMNADGSGRVQ 124
                 4577888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1391.57
//
Query:       EPA06712.1  [L=401]
Description: 40-residue YVTN family beta-propeller repeat protein (3 repeats), partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.1e-10   38.9   3.6     0.0022   17.3   0.0    3.8  4  Lactonase     Lactonase, 7-bladed beta-propeller
    1.5e-07   31.1   7.7      0.055   13.5   0.1    4.6  4  NHL           NHL repeat
    1.7e-06   27.8   0.5    5.6e-06   26.2   0.5    2.0  1  PD40          WD40-like Beta Propeller Repeat
      4e-06   25.6   0.6     0.0096   14.5   0.1    2.6  3  Cytochrom_D1  Cytochrome D1 heme domain
    1.4e-05   25.2  14.6        1.1    9.5   0.1    6.1  6  Arylesterase  Arylesterase
     0.0028   17.3   3.1       0.13   11.8   0.1    3.2  3  SGL           SMP-30/Gluconolactonase/LRE-like region
  ------ inclusion threshold ------
      0.015   14.9   3.1       0.43   10.1   0.1    3.2  3  DUF4221       Domain of unknown function (DUF4221)
      0.015   15.6   0.0         12    6.3   0.0    2.8  3  ANAPC4_WD40   Anaphase-promoting complex subunit 4 WD40 domai
        1.8    8.8   5.8        2.1    8.6   0.2    3.2  4  FlaG          FlaG protein


Domain annotation for each model (and alignments):
>> Lactonase  Lactonase, 7-bladed beta-propeller
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.1e-06    0.0022     182     223 ..      26      67 ..      12      75 .. 0.80
   2 !   11.6   0.0   6.2e-05      0.12     283     318 ..      70     104 ..      63     111 .. 0.76
   3 !    7.2   0.1    0.0013       2.6      61     116 ..     227     277 ..     207     290 .. 0.75
   4 !    8.9   0.2   0.00039      0.78     252     317 ..     255     315 ..     252     317 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.1e-06
                 EEEEE-STT--EEEEEE-TTSSEEEEEETTTTEEEEEEEE-T CS
   Lactonase 182 pasvklppgsGPRHlaFhpdgkiaYvvnELsstvsvfsydea 223
                  a++++  g+GPR +aF ++++++Yv+n  +++vsv++  ++
  EPA06712.1  26 YATTTIGVGAGPRGMAFDTNNNYIYVANSNANSVSVIDSTTN 67 
                 556667779999999999999999999999999999976644 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 6.2e-05
                 EEEEE-SSS.--EEEE-TTSSEEEEEETTTTEEEEE CS
   Lactonase 283 veevstegkfPRdfaldpsgklllvanqksdnvtvf 318
                 ++++s  g+fP d +++p++ +l+van  s+nv+v+
  EPA06712.1  70 ITTIS-VGAFPVDVTFNPTNGYLYVANHFSGNVSVI 104
                 44444.489999999999999999999999999887 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0013
                 TEEEEEEEETTTTEEEEEEEEE.SSS-EEEEEE-TTSSEEEEEETTTTEEEEEEB. CS
   Lactonase  61 ggvsafaidkdsgeltllnkvssegaspchlsvdedgkllavAnYsggsvsvfpld 116
                 gg+ af+ ++   +l++ ++    g ++   ++++d+++l+++nY ++s+s++++ 
  EPA06712.1 227 GGIKAFDTST---NLSVGGTL--LGPNVFGATYNPDNQYLYASNYDSASISIIDVI 277
                 5555655553...35544444..477777888999999********9999998875 PP

  == domain 4  score: 8.9 bits;  conditional E-value: 0.00039
                 -TTSSEEEEEETSSTEEEEEEE-TTT--EEEEEEEE-SSS.--EEEE-TTSSEEEEEETTTTEEEE CS
   Lactonase 252 spdgkflyvSnRgadsiavfavdeadgtltlveevstegkfPRdfaldpsgklllvanqksdnvtv 317
                  pd+++ly+Sn  + si++ +v     t t v+++s+ g++P  +  +p ++ ++v+n ++++++v
  EPA06712.1 255 NPDNQYLYASNYDSASISIIDVI----TNTIVDTISV-GNNPFAILYNPVNHSIYVSNLSDGTISV 315
                 68999999999999999999993....3378888888.8889999999999999999999999887 PP

>> NHL  NHL repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.1   2.7e-05     0.055       3      27 ..      36      61 ..      35      62 .. 0.93
   2 !    6.6   0.1    0.0043       8.6       3      22 ..      78     100 ..      77     103 .. 0.88
   3 !   12.3   0.4   6.9e-05      0.14       3      22 ..     120     141 ..     119     143 .. 0.91
   4 ?   -2.2   0.0       2.7   5.3e+03       3      10 ..     165     172 ..     164     175 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.7e-05
                SEEEEEEE.TTTEEEEEECCCTEEEE CS
         NHL  3 yPhGvavd.snGdiyVaDsenhrvqv 27
                 P+G a d +n+ iyVa+s+ ++v v
  EPA06712.1 36 GPRGMAFDtNNNYIYVANSNANSVSV 61
                6*********************9987 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0043
                 SEEEEEEE.TTTEEEEEE..CCC CS
         NHL   3 yPhGvavd.snGdiyVaD..sen 22 
                 +P +v+ + +nG +yVa+  s+n
  EPA06712.1  78 FPVDVTFNpTNGYLYVANhfSGN 100
                 7****************977666 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 6.9e-05
                 SEEEEEEE.TTTEEEEEE.CCC CS
         NHL   3 yPhGvavd.snGdiyVaD.sen 22 
                 +P+G++++  nG+iyVa+ ++n
  EPA06712.1 120 FPNGITYNsINGNIYVANdYNN 141
                 7*****************8888 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 2.7
                 SEEEEEEE CS
         NHL   3 yPhGvavd 10 
                  P+G++ +
  EPA06712.1 165 GPSGITFN 172
                 7****997 PP

>> PD40  WD40-like Beta Propeller Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.5   2.8e-09   5.6e-06       3      38 .]     346     383 ..     344     383 .. 0.95

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 2.8e-09
                 E--SSSS..EEEEEE-TTSSEEEEEEECT..TCEEEEE CS
        PD40   3 rltntpg.negaPsfSPDGkrlaFsSdRg.sGkpdIyv 38 
                  +t+tp+ +e +P++SPDG+++a+  + + +G+ dI+v
  EPA06712.1 346 NITHTPSvDENDPAISPDGTKIAYWKYSPsYGSADIWV 383
                 6899***********************99********8 PP

>> Cytochrom_D1  Cytochrome D1 heme domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   4.8e-06    0.0096       5     118 ..      47     163 ..      42     168 .. 0.81
   2 ?    0.1   0.0      0.11   2.3e+02      12      36 ..     141     165 ..     130     192 .. 0.83
   3 !    8.7   0.0   0.00028      0.56      18     117 ..     189     287 ..     178     310 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.8e-06
                   GEEEEEEGGGTEEEEEETTT-SEEEEEE-STTEEEEEE-TT.SSEEEEEET.TSEEEEEESSSSSEEEEEE-SSEEEEEEE.--TTSEEEEEEEETT CS
  Cytochrom_D1   5 nlfvvverdagkvalldgdskeilavletgyalHisrvfasdgRyvyvigR.DgkvtliDLwakeivaevkiGlnarsvav.SqddryvivgnYlPg 99 
                   n   v  ++a +v ++d+++++ + ++ + +a  + + f + + y+yv+    g+v++i   +++++a++ iG+   ++   S ++   ++  Y  g
    EPA06712.1  47 NYIYVANSNANSVSVIDSTTNTVITTI-SVGAFPVDVTFNPTNGYLYVANHfSGNVSVINGATNTVIATISIGGFPNGITYnSINGNIYVANDYNNG 142
                   556688899999999999999999988.567888999999999999999864799999999999999999999988887752688999999999865 PP

                   ..EEEEEETTT--EEEEEE-- CS
  Cytochrom_D1 100 ..qlvildaetLelvkvisar 118
                      + ++ + t   +++i++ 
    EPA06712.1 143 agSIPVISGSTNTVIATIPTS 163
                   115778899999999888885 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.11
                   GGGTEEEEEETTT-SEEEEEE-STT CS
  Cytochrom_D1  12 rdagkvalldgdskeilavletgya 36 
                    +ag++ ++ g++++ +a++ t y 
    EPA06712.1 141 NGAGSIPVISGSTNTVIATIPTSYG 165
                   57999**************999985 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.00028
                   EEEETTT-SEEEEEE-STTEEEEEE-TT.SSEEEEEETTSEEEEEESSSSSEEEEEE-SSEEEEEEE--TTSEEEEEEEETTEEEEEETTT--EEEE CS
  Cytochrom_D1  18 alldgdskeilavletgyalHisrvfasdgRyvyvigRDgkvtliDLwakeivaevkiGlnarsvavSqddryvivgnYlPgqlvildaetLelvkv 114
                    ++dg++++ +    + +   ++ +  + + y y++g  g+++ +D  ++  v    +G n  +     d++y+ ++nY    ++i+d  t   v +
    EPA06712.1 189 YVIDGTTNTFVPGSLSVGFTQAGSILNPTNGYQYIFG-NGGIKAFDTSTNLSVGGTLLGPNVFGATYNPDNQYLYASNYDSASISIIDVITNTIVDT 284
                   5777777777655444444445555555577888888.47788888888888888888888888888888888888888888888888888777777 PP

                   EE- CS
  Cytochrom_D1 115 isa 117
                   is 
    EPA06712.1 285 ISV 287
                   765 PP

>> Arylesterase  Arylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.1   0.00056       1.1      56      83 ..      37      64 ..      20      67 .. 0.86
   2 ?    3.4   0.1     0.046        91      44      82 ..      67     105 ..      61     109 .. 0.84
   3 !    8.1   0.3    0.0015       2.9      45      72 ..     110     137 ..     102     143 .. 0.81
   4 !    6.7   0.1    0.0042       8.3      43      82 ..     153     192 ..     145     196 .. 0.85
   5 ?    1.5   0.1      0.17   3.4e+02      58      83 ..     251     276 ..     229     279 .. 0.79
   6 ?    2.1   0.1      0.12   2.3e+02      55      78 ..     290     313 ..     277     316 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00056
  Arylesterase 56 anGInidadkkyiyvadilresihvmkk 83
                  + G+ +d+++ yiyva++ ++s+ v++ 
    EPA06712.1 37 PRGMAFDTNNNYIYVANSNANSVSVIDS 64
                  89********************988765 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.046
  Arylesterase  44 sevkvvasglssanGInidadkkyiyvadilresihvmk 82 
                   + v++ +s   ++  +++++ + y+yva+    ++ v++
    EPA06712.1  67 NTVITTISVGAFPVDVTFNPTNGYLYVANHFSGNVSVIN 105
                   56788888889999**************99988887765 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0015
  Arylesterase  45 evkvvasglssanGInidadkkyiyvad 72 
                    v+  +s   ++nGI++++ +  iyva+
    EPA06712.1 110 TVIATISIGGFPNGITYNSINGNIYVAN 137
                   55666666779***************97 PP

  == domain 4  score: 6.7 bits;  conditional E-value: 0.0042
  Arylesterase  43 psevkvvasglssanGInidadkkyiyvadilresihvmk 82 
                   ++ v+  +   + + GI++++ + y+y ++  ++s +v++
    EPA06712.1 153 TNTVIATIPTSYGPSGITFNPINGYLYSTSFNQNSAYVID 192
                   5566777778889************************986 PP

  == domain 5  score: 1.5 bits;  conditional E-value: 0.17
  Arylesterase  58 GInidadkkyiyvadilresihvmkk 83 
                   G ++++d++y+y ++    si ++++
    EPA06712.1 251 GATYNPDNQYLYASNYDSASISIIDV 276
                   889*********99988888877766 PP

  == domain 6  score: 2.1 bits;  conditional E-value: 0.12
  Arylesterase  55 sanGInidadkkyiyvadilresi 78 
                    +  I +++++++iyv+++ +  i
    EPA06712.1 290 NPFAILYNPVNHSIYVSNLSDGTI 313
                   566799**********99877666 PP

>> SGL  SMP-30/Gluconolactonase/LRE-like region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.1   6.7e-05      0.13     181     243 ..      33      94 ..      15      97 .. 0.81
   2 ?    3.9   0.1     0.018        35     115     205 ..      99     186 ..      93     199 .. 0.66
   3 ?   -0.0   0.0      0.27   5.3e+02      40      97 ..     309     364 ..     247     378 .. 0.45

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.7e-05
         SGL 181 kgegepDGlavDa.eGnvwvAvwgggkvvrfdpd.GklieeiklpakrvtscaFgGpdlrtLyit 243
                  g g p G+a D  +++++vA  +++ v+++d    ++i++i++  + +  ++F  p    Ly++
  EPA06712.1  33 VGAG-PRGMAFDTnNNYIYVANSNANSVSVIDSTtNTVITTISVG-AFPVDVTF-NPTNGYLYVA 94 
                 3444.88******8999***************999********99.89999999.5667888875 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.018
         SGL 115 galyrldpd.gklervlddltipNGlawspdgktlYlaDsltrkiwaydvdaeggklsnrrvfadlkkgegepDGlavDa.eGnvwvAvwggg 205
                 g++ ++++  +++  +++  ++pNG+  ++ +  +Y+a+  ++   +++v + +      +v+a++++  g p G++    +G+++++ ++++
  EPA06712.1  99 GNVSVINGAtNTVIATISIGGFPNGITYNSINGNIYVANDYNNGAGSIPVISGS----TNTVIATIPTSYG-PSGITFNPiNGYLYSTSFNQN 186
                 556666666566666666667788888888888888877777777777773222....3666677777765.777777777777777776655 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.27
         SGL  40 pe.svGaiaprkd..grlvvask.sglalldlasgeletladeeedekpllrfNDgvvdpdG 97 
                 ++  +++i+p ++   ++++    ++++++ ++  +++ +++      p++  ND +++pdG
  EPA06712.1 309 SDgTISVIIP-PAvgPNVIAYDDfHDIYIMYTDGASVTNITHT-----PSVDENDPAISPDG 364
                 2235555555.33323333333312333333344445555544.....44445555555555 PP

>> DUF4221  Domain of unknown function (DUF4221)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.27   5.4e+02      52      85 ..      43      74 ..      35      83 .. 0.67
   2 ?    2.9   0.1     0.033        66      56     152 ..      88     181 ..      81     197 .. 0.67
   3 ?   10.1   0.1   0.00022      0.43      44      88 ..     246     289 ..     228     316 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.27
                EETTEEEEEEEE-ST--EEEEEETTTTEEEEEEE CS
     DUF4221 52 ssdgkeyLaflnkqesaeieiyDleelklvkrip 85
                +++ ++ ++ +++++  +++++D  + + + +i+
  EPA06712.1 43 DTNNNYIYVANSNAN--SVSVIDSTTNTVITTIS 74
                555555554444444..68888877777777775 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.033
                 EEEEEEEE-ST--EEEEEETTTTEEEEEEE-BSSSTTB-TT---EEESSSTTSEEEEGGGTEEEEE....-TT--EEEEEE---TTS-------BTTTT CS
     DUF4221  56 keyLaflnkqesaeieiyDleelklvkripfekeGPngigkpvgfkqvldsiflllgnafnelflf....nesgekvkkinlesnelegeenefgsfvn 150
                 + yL+  n+ +  ++++++  + + + +i++   +Pngi     +  ++++i++ ++ ++n+ +++    +++++  ++i+++  + ++  n ++ +++
  EPA06712.1  88 NGYLYVANHFS-GNVSVINGATNTVIATISIGG-FPNGIT----YNSINGNIYVAND-YNNGAGSIpvisGSTNTVIATIPTSYGPSGITFNPINGYLY 179
                 67999999997.79*****************99.9**995....5567778888877.33333332112234444445555555445555566666655 PP

                 B- CS
     DUF4221 151 sp 152
                 s+
  EPA06712.1 180 ST 181
                 55 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.00022
                 -SSEEEE.EETTEEEEEEEE-ST--EEEEEETTTTEEEEEEE-BS CS
     DUF4221  44 skglqsfdssdgkeyLaflnkqesaeieiyDleelklvkripfek 88 
                 +++++ ++ +++++yL+  n ++sa+i+i+D  + ++v++i+   
  EPA06712.1 246 GPNVFGATYNPDNQYLYASN-YDSASISIIDVITNTIVDTISVGN 289
                 55666666789*****6555.6679***************98765 PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0    0.0076        15      42      79 ..      38      76 ..      22      85 .. 0.87
   2 ?   -2.2   0.0       2.6   5.1e+03      49      77 ..      88     116 ..      81     119 .. 0.71
   3 ?    6.3   0.0     0.006        12      42      81 ..     250     290 ..     239     313 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0076
  ANAPC4_WD40 42 rsLaWkpdgklLavaysdg.evrlldaesgkvvhslsvk 79
                 r++a+  +++ + va s+  +v+++d+ + +v+ ++sv+
   EPA06712.1 38 RGMAFDTNNNYIYVANSNAnSVSVIDSTTNTVITTISVG 76
                 78999**********998549*************99986 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.6
  ANAPC4_WD40  49 dgklLavaysdgevrlldaesgkvvhsls 77 
                  +g l +  +  g+v++++  + +v+ ++s
   EPA06712.1  88 NGYLYVANHFSGNVSVINGATNTVIATIS 116
                  44444555778999999999999988876 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.006
  ANAPC4_WD40  42 rsLaWkpdgklLava.ysdgevrlldaesgkvvhslsvkse 81 
                   +  ++pd++ L  + y+  +++++d+ + ++v ++sv+++
   EPA06712.1 250 FGATYNPDNQYLYASnYDSASISIIDVITNTIVDTISVGNN 290
                  556789999998655166669***************99887 PP

>> FlaG  FlaG protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.2    0.0011       2.1      48      79 ..      42      73 ..      40      74 .. 0.88
   2 ?   -2.3   0.1       2.6   5.1e+03      65      79 ..     101     115 ..     100     115 .. 0.88
   3 ?    1.2   0.0      0.21   4.2e+02      64      81 ..     145     162 ..     128     164 .. 0.86
   4 ?   -1.6   0.1       1.6   3.1e+03      54      79 ..     260     285 ..     252     285 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0011
                SS--EEEEEEEETTEEEEEEEETTT-SEEEEE CS
        FlaG 48 lnteleFsvdedtkrvvVkviDketgevIrqi 79
                ++t+ ++ +  +++ + V+viD++t+ vI  i
  EPA06712.1 42 FDTNNNYIYVANSNANSVSVIDSTTNTVITTI 73
                6777788888999****************877 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.6
                 EEEEETTT-SEEEEE CS
        FlaG  65 VkviDketgevIrqi 79 
                 V+vi+  t+ vI  i
  EPA06712.1 101 VSVINGATNTVIATI 115
                 89*********9776 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.21
                 EEEEEETTT-SEEEEE-H CS
        FlaG  64 vVkviDketgevIrqiPs 81 
                  + vi  +t+ vI  iP+
  EPA06712.1 145 SIPVISGSTNTVIATIPT 162
                 5789999**********7 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 1.6
                 EEEEEETTEEEEEEEETTT-SEEEEE CS
        FlaG  54 FsvdedtkrvvVkviDketgevIrqi 79 
                 + +  + ++  +++iD  t+ ++  i
  EPA06712.1 260 YLYASNYDSASISIIDVITNTIVDTI 285
                 556667788899****9999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.46
# Mc/sec: 2623.34
//
Query:       EPA06713.1  [L=169]
Description: hypothetical protein BG20_I0079 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0034   17.7   0.3     0.0085   16.4   0.1    1.6  2  DUF4878   Domain of unknown function (DUF4878)


Domain annotation for each model (and alignments):
>> DUF4878  Domain of unknown function (DUF4878)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   4.7e-07    0.0085      63     103 ..      42      82 ..      34      85 .. 0.91
   2 ?   -1.9   0.0      0.23   4.1e+03      82      82 ..     134     134 ..     104     161 .. 0.56

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4.7e-07
     DUF4878  63 kqgnlkeveikdeeesgdtAvvtVkvtlkdGkekkeeieli 103
                  + +l +vei+d++++++tA+ +V+   k+ +ek+++++li
  EPA06713.1  42 VEIKLSNVEILDVNKIENTAKLQVTFLVKNPSEKTFTVPLI 82 
                 5678999*******************************998 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.23
     DUF4878  82 A 82 
                 +
  EPA06713.1 134 T 134
                 1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 1113.93
//
Query:       EPA06714.1  [L=213]
Description: hypothetical protein BG20_I0041 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.6e-05   22.7   0.3    0.00013   22.1   0.2    1.5  1  Cas_Cas4     Domain of unknown function DUF83
  ------ inclusion threshold ------
      0.038   14.2   0.3      0.075   13.3   0.3    1.4  1  DDE_Tnp_1_6  Transposase DDE domain
       0.19   11.6   1.8        3.5    7.5   1.8    2.0  1  PDDEXK_1     PD-(D/E)XK nuclease superfamily


Domain annotation for each model (and alignments):
>> Cas_Cas4  Domain of unknown function DUF83
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.2   2.3e-08   0.00013      45     161 ..      76     193 ..      31     194 .. 0.62

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 2.3e-08
    Cas_Cas4  45 ekkevelse...sikiDvvekekeklvvvEvKkskkkeeaaklQllyYlllLe..kkgveikeGvleypkekkreevelteelreelekaikei...ee 135
                 + ke++++e   +++ D++     +  +v ++ sk   ea    +   ll+L+  +   +++ G++ y++  ++e +    ++++  e++i+++   ++
  EPA06714.1  76 DPKEFSIDEiklRGQADMIV----DDSIVLFRPSKTVIEAP---VANDLLYLNacMWIYDKTDGIIVYITGDREEIMFSLTRDKKMFEEIIRRVrvlND 167
                 44444443344455555555....22233344444444444...4444444444334456677999998766555433334455556666666511168 PP

    Cas_Cas4 136 iissekppkvkkkkiCkkCayaelCl 161
                 +++++k+p  + ++ C +C y++ C+
  EPA06714.1 168 LLKEQKTPILEPSNDCAECQYYQRCF 193
                 999**********************8 PP

>> DDE_Tnp_1_6  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.3   1.3e-05     0.075      29      53 ..     179     204 ..     165     209 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.3e-05
  DDE_Tnp_1_6  29 rlkdCrgCplreqCtkkkk.grqlti 53 
                    +dC +C++ ++C+++kk ++q+++
   EPA06714.1 179 PSNDCAECQYYQRCFTTKKnTKQVSL 204
                  569***********999774666665 PP

>> PDDEXK_1  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   1.8   0.00058       3.5     128     254 ..      85     192 ..       2     193 .. 0.56

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00058
    PDDEXK_1 128 vrLkGriDrvddkegelriiDyKtgsappkskelaelkeglQlllYllalaegeelkeegepagalylrleepkvkdeevvkkmalteeeleallqele 226
                 ++L+G+ D++ d++  +     Kt  + p   +          llYl a++    + +   ++ ++y+       + ee++ + + +++ +e++ ++++
  EPA06714.1  85 IKLRGQADMIVDDSI-VLFRPSKTVIEAPVAND----------LLYLNACMWI--YDKT--DGIIVYITG-----DREEIMFSLTRDKKMFEEIIRRVR 163
                 555555555554444.44444444443333333..........4444444433..2211..333333333.....133333444666777799999999 PP

    PDDEXK_1 227 elaeeilagefparpskk.CeyCpyksvC 254
                  l + +++++ p+ +  + C+ C+y ++C
  EPA06714.1 164 VLNDLLKEQKTPILEPSNdCAECQYYQRC 192
                 88666666688876555559999999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1575.27
//
Query:       EPA06715.1  [L=208]
Description: hypothetical protein BG20_I0016 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       835  (0.0465726); expected 358.6 (0.02)
Passed bias filter:                      692  (0.0385967); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1372.52
//
Query:       EPA06716.1  [L=276]
Description: ACT domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.3e-26   93.7   0.2    4.3e-26   92.0   0.0    1.8  2  AA_kinase   Amino acid kinase family
    3.9e-21   74.5   0.8    2.7e-09   36.6   0.1    2.3  2  ACT         ACT domain
    5.2e-19   67.8   4.5      4e-12   45.7   0.3    2.4  2  ACT_7       ACT domain
     0.0084   16.1   1.7       0.51   10.4   0.1    3.0  3  ACT_6       ACT domain
  ------ inclusion threshold ------
      0.032   14.3   0.6       0.05   13.7   0.6    1.3  1  Mfa_like_1  Fimbrillin-like


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.0   0.0   1.2e-29   4.3e-26     144     241 .]       2      98 ..       1      98 [. 0.98
   2 ?   -0.4   0.1       0.2   7.2e+02      47      53 ..     151     157 ..     104     259 .. 0.58

  Alignments for each domain:
  == domain 1  score: 92.0 bits;  conditional E-value: 1.2e-29
                 ESEEEEETTTE...EEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHHCSSS.TTTHHHHCHHHHHHHHHCTT-EEEE CS
   AA_kinase 144 tgfigldeege...lgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaeesaselatgGmkvkhpaalaaarrggipvvI 239
                 +gf g+d++g+   +grg+sD++a++++ +++Ad++++++d+dG+++adpk+v++a+ll+e+s+ ea e    +a +G+k +hp++++++  ++ip+ I
  EPA06716.1   2 GGFTGADQHGHittFGRGGSDYTATIIGSCIKADEIWLMSDIDGLMTADPKIVKNAKLLKEVSYIEAIE----MALFGAKQIHPRTFEPLLTKKIPMKI 96 
                 79*******************************************************************....************************** PP

                 EE CS
   AA_kinase 240 tn 241
                 +n
  EPA06716.1  97 RN 98 
                 98 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.2
                 HHHHHHH CS
   AA_kinase  47 tdgllal 53 
                  + l+++
  EPA06716.1 151 FATLAKA 157
                 2222222 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.1   1.1e-12   3.9e-09       7      62 ..     140     189 ..     139     191 .. 0.77
   2 !   36.6   0.1   7.6e-13   2.7e-09       3      59 ..     213     266 ..     211     272 .. 0.89

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 1.1e-12
                 EESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHH CS
         ACT   7 vpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevleal 62 
                 + + PG++a++f++la++ iN+ +i+q +se      + ++ivv   dl+++++al
  EPA06716.1 140 MVGTPGTAAKIFATLAKASINVMMISQNPSE------SSITIVVKNTDLDKAVNAL 189
                 6789**************************5......5555555555555555554 PP

  == domain 2  score: 36.6 bits;  conditional E-value: 7.6e-13
                 EEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHH CS
         ACT   3 lrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevl 59 
                 + +g+++ +G++++vfga+ ++ +N+++i+q+sse    +++fvv  +d + + ++l
  EPA06716.1 213 IGLGMRGTVGVASKVFGAIEKNKVNVAMITQGSSEL---NLAFVVKDADSNIAVQAL 266
                 7789******************************98...899999999887776665 PP

>> ACT_7  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.7   0.3   1.1e-15     4e-12       9      64 ..     133     190 ..     131     191 .. 0.94
   2 !   23.5   0.5     1e-08   3.6e-05       3      65 .]     204     268 ..     202     268 .. 0.95

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 1.1e-15
                 EEE-S-.---SS--HHHHHHHHHHTTT---EEEE...-SS-EEEEEEGGGHHHHHHHHH CS
       ACT_7   9 lsvvgsglpfdvtGivaklaspLaeagIsifqiS...tyrtdyiLVpeedlekAveaLh 64 
                 + + g+++ + ++G +ak+++ La+a I++ +iS   ++ ++ i+V+  dl+kAv+aL+
  EPA06716.1 133 IDIRGGSMVG-TPGTAAKIFATLAKASINVMMISqnpSESSITIVVKNTDLDKAVNALE 190
                 5678888977.***********************************************7 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 1e-08
                 EEEEEEEEE-S-.---SS--HHHHHHHHHHTTT---EEEE...-SS-EEEEEEGGGHHHHHHHHHH CS
       ACT_7   3 edgwiklsvvgsglpfdvtGivaklaspLaeagIsifqiS...tyrtdyiLVpeedlekAveaLhe 65 
                   +++ + ++g g+++ ++G+++k++++  ++++++ +i+   ++    ++V+++d   Av+aLhe
  EPA06716.1 204 TTDVAIIALIGLGMRG-TVGVASKVFGAIEKNKVNVAMITqgsSELNLAFVVKDADSNIAVQALHE 268
                 56789999********.**********************9999**********************6 PP

>> ACT_6  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.27   9.5e+02       7      31 ..       4      28 ..       3      30 .. 0.84
   2 !   10.4   0.1   0.00014      0.51      13      66 ..     144     197 ..     141     208 .. 0.80
   3 ?    3.0   0.0     0.029     1e+02      14      46 ..     222     254 ..     218     272 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.27
       ACT_6  7 vtGpdrpGltasLtsvlaefgvnil 31
                +tG+d+ G++  + +  +++ ++i+
  EPA06716.1  4 FTGADQHGHITTFGRGGSDYTATII 28
                79*******9998888888888776 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00014
       ACT_6  13 pGltasLtsvlaefgvnilDieqavihgrlsLgllvsgpedalarlekaLlfla 66 
                 pG  a+++++la+  +n++ i q   +++ ++++  +  ++a+++le +Ll + 
  EPA06716.1 144 PGTAAKIFATLAKASINVMMISQNPSESSITIVVKNTDLDKAVNALEMELLGKI 197
                 9***********************988877777665555999999999998764 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.029
       ACT_6  14 GltasLtsvlaefgvnilDieqavihgrlsLgl 46 
                 G+ +++++++ +++vn++ i q   + +l++++
  EPA06716.1 222 GVASKVFGAIEKNKVNVAMITQGSSELNLAFVV 254
                 8999**************999988777776654 PP

>> Mfa_like_1  Fimbrillin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.6   1.4e-05      0.05     127     212 ..     100     180 ..      95     204 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.4e-05
                 .EE.EEE--SSEEEEEEEE....EE-TSEEEEEEETTTTEEEE-SSS-EE--EE-TTTS--B--EES-EEE--STSSTTSSEEEEEEE CS
  Mfa_like_1 127 fkl.kagdgftvkvskltiltv.kltglktkatfdlttgtltattstaasataeaatitantatatataillPqtttagkltltltvd 212
                 f+l  +g+ +t + sk t+ tv +++++++++ +d+  g++ +t +      + aa+i a+ a a+++++++ q+ ++ ++t+ +++ 
  EPA06716.1 100 FNLkNEGTLVTDSPSKSTKNTVkCVSNIRHNGLIDIRGGSMVGTPG------T-AAKIFATLAKASINVMMISQNPSESSITIVVKNT 180
                 8885556777777789999999999******************999......4.888888889999*********8888888888544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.55
# Mc/sec: 1504.76
//
Query:       EPA06717.1  [L=384]
Description: thiolase, C-terminal domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-21   76.3   0.0      1e-20   74.2   0.0    2.0  2  Thiolase_N       Thiolase, N-terminal domain
      4e-12   45.9   0.5    4.2e-10   39.4   0.0    3.0  3  Thiolase_C       Thiolase, C-terminal domain
      9e-05   22.2   0.2       0.04   13.5   0.1    2.8  3  ketoacyl-synt    Beta-ketoacyl synthase, N-terminal domain
  ------ inclusion threshold ------
      0.041   13.9   0.8        3.5    7.7   0.0    3.2  3  Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain


Domain annotation for each model (and alignments):
>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.2   0.0   2.2e-24     1e-20       2     259 ..       5     221 ..       4     222 .. 0.87
   2 ?   -1.5   0.0      0.29   1.3e+03     110     144 ..     247     280 ..     244     290 .. 0.71

  Alignments for each domain:
  == domain 1  score: 74.2 bits;  conditional E-value: 2.2e-24
                 EEEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSC.HHHHHHHHTTS-TTSEEEEEEHGGGHHHHHHHHHHHHH CS
  Thiolase_N   2 vivsaartpigkfggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqagegqn.iarqaalkagipeevpavtvnkvcsSglkavalaaqsi 99 
                  + +a  t+ gk      + s+ ++ ++a   ++e+ag+dp+e++  +++nv   ++ q  +   ++ ++gip++ p+ t++ +c+Sg  +  +a  ++
  EPA06717.1   5 CVLGAGSTKYGK-----LSESIADITTQASVLAIENAGIDPKEIKASYISNVFGVADKQVhLGPVLMSRLGIPDK-PSLTIESACGSGSVSFREAYANV 97 
                 566677777777.....556788999999999***********************9999979999999****876.99********************* PP

                 HTTSHSEEEEEEEEESTTS-EEETCTTTTGGSSSSEEEEEHHHHHHTEETTTTSEHHHHHHHHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE CS
  Thiolase_N 100 aageadvvvagGvEsmsnaptaestdvrsglklgdekakdllipdgladafneehmGltaenlakkykisReeqdefAvkshqkaaaaqkagkFkdeiv 198
                 aag +d++v+ GvE+ +++ t  +t+         ++ +d+  ++g a a+     +  a+ ++ +++++ e+ +++Avk+h ++  ++ka+  +++i 
  EPA06717.1  98 AAGFYDCLVVTGVEKVTHTGTEWTTTY-------FAYCSDFF-YEGQAGASFPGLFASMARAYLTEFGATEEDFARVAVKNHDNGFLNPKAH-MQKKI- 186
                 ******************999998544.......44445544.33344444445677889********************************.88888. PP

                 -EEEEESSSEEEE-S-TTS-TT--HHHHHTS-BSSSTTSS-BTTSB--BEEEEEEEEEEEH CS
  Thiolase_N 199 PvkvkgkkgkktvdkdeairsevtaekLaklkpaFkkeGtvtAgnasqisDGaaavllmse 259
                              + d+ ++s+v+a +L+ +             ++++ sDGa+ v+l+se
  EPA06717.1 187 -------------TIDDVMNSPVVASPLKLY-------------DCCPFSDGASSVILCSE 221
                 .............89****************.............***************98 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.29
                 EEEEESTTS-EEETCTTTTGGSSSSEEEEEHHHHH CS
  Thiolase_N 110 gGvEsmsnaptaestdvrsglklgdekakdllipd 144
                  G E+m++ p  +  ++ + +k+   +akd+   +
  EPA06717.1 247 QGREHMTTIPSTKI-AAADAYKMAGITAKDIDFAE 280
                 58899999998886.66777777777777765555 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.33   1.5e+03      31      47 ..      32      48 ..      24      96 .. 0.68
   2 !   39.4   0.0   9.3e-14   4.2e-10      18     106 ..     250     358 ..     241     364 .. 0.87
   3 ?    3.6   0.1     0.011        49      75      95 ..     362     382 ..     357     384 .] 0.85

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.33
                HHHHHT--GGGESEEEE CS
  Thiolase_C 31 vlkkagltvedidlfEi 47
                ++++ag++ ++i +  i
  EPA06717.1 32 AIENAGIDPKEIKASYI 48
                44444444444444333 PP

  == domain 2  score: 39.4 bits;  conditional E-value: 9.3e-14
                 GGGGGHHH..HHHHHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--G..................GGBSTT--HHHH-B-TTTHHHHHHHHHHHH CS
  Thiolase_C  18 eilglgPa..yaikkvlkkagltvedidlfEinEAFaaqaLavakaldldl..................ekvNvnGGaialGHPlGasGaRivvtllse 96 
                 e++++ P    a+  + k ag+t +did+ E+++ F+   ++ +++l++ +                    +N  GG  + GHP+Ga+G+ +vv +  +
  EPA06717.1 250 EHMTTIPStkIAAADAYKMAGITAKDIDFAEVHDCFTIAEIVDTEDLGFFEkgqgvqavregrtklnsdISINPSGGLKSKGHPIGATGVGQVVEVFDQ 348
                 56666665115777899********************************999**************998889**************************9 PP

                 HHHCTTSEEE CS
  Thiolase_C  97 lkkeggklgv 106
                 l+ + g  +v
  EPA06717.1 349 LTGKAGARTV 358
                 9987766555 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.011
                 HHHH-B-TTTHHHHHHHHHHH CS
  Thiolase_C  75 aialGHPlGasGaRivvtlls 95 
                  i l H +Ga+Ga  +v++ +
  EPA06717.1 362 KIGLTHNFGATGASCAVHIFQ 382
                 58899*********9999875 PP

>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.3   0.0    0.0028        13      93     123 ..      26      56 ..      19      67 .. 0.87
   2 !   13.5   0.1     9e-06      0.04     167     208 ..      75     116 ..      73     121 .. 0.94
   3 ?   -2.0   0.0      0.47   2.1e+03      27      58 ..     246     277 ..     245     286 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0028
                    HHHHHHHHHHHTS-HHTCTTGGEEEEEEESS CS
  ketoacyl-synt  93 leaawealedagltpeeldgsrvgvfiGvga 123
                     +a+  a+e+ag++p+e++ s + ++ Gv+ 
     EPA06717.1  26 TQASVLAIENAGIDPKEIKASYISNVFGVAD 56 
                    578888**************99999999875 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 9e-06
                    SEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SH CS
  ketoacyl-synt 167 psvtvdtACsSslvavhaavqslrsgeadvalaGGvellltp 208
                    ps+t+++AC S+ v    a+ ++ +g  d+ ++ Gve  ++ 
     EPA06717.1  75 PSLTIESACGSGSVSFREAYANVAAGFYDCLVVTGVEKVTHT 116
                    89***********************************88775 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.47
                    HTT---EEES-TTSSCGTTSBTSSTTEEE-BS CS
  ketoacyl-synt  27 legrdaiselpadrwdadklydpparaagkik 58 
                    l+gr++++++p+++  a + y+ +  +a++i+
     EPA06717.1 246 LQGREHMTTIPSTKIAAADAYKMAGITAKDID 277
                    57888888899888666666666666666554 PP

>> Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.13   5.8e+02      27      45 ..      26      44 ..       5      50 .. 0.75
   2 ?    7.7   0.0   0.00079       3.5      27      52 ..     259     284 ..     241     292 .. 0.80
   3 ?    1.8   0.0      0.05   2.2e+02      87     108 ..     330     351 ..     319     359 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.13
                     HHHHHHHHHHHT--GGGEE CS
  Ketoacyl-synt_C 27 araiekalaeagvdpedvd 45
                      +a   a+++ag+dp++++
       EPA06717.1 26 TQASVLAIENAGIDPKEIK 44
                     455667999******9996 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00079
                      HHHHHHHHHHHT--GGGEEEEE-SS- CS
  Ketoacyl-synt_C  27 araiekalaeagvdpedvdyveahgt 52 
                      + a ++a+++ag++++d+d  e h+ 
       EPA06717.1 259 KIAAADAYKMAGITAKDIDFAEVHDC 284
                      446789******************86 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.05
                      H-B-GGGHHHHHHHHHHHHHHH CS
  Ketoacyl-synt_C  87 iGHleaAaGvaelikvvlalkh 108
                       GH  +A Gv +++ v+ +l  
       EPA06717.1 330 KGHPIGATGVGQVVEVFDQLTG 351
                      4***************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.67u 0.33s 00:00:01.00 Elapsed: 00:00:00.55
# Mc/sec: 2106.20
//
Query:       EPA06718.1  [L=122]
Description: hypothetical protein BG20_I0064 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-13   50.3   0.0    3.8e-13   49.9   0.0    1.1  1  Methyltransf_25  Methyltransferase domain
    2.1e-12   47.1   0.3    2.5e-12   46.9   0.3    1.1  1  Methyltransf_31  Methyltransferase domain
    2.1e-11   43.6   0.0    2.2e-11   43.5   0.0    1.0  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    1.4e-09   38.5   0.0    1.8e-09   38.1   0.0    1.2  1  Methyltransf_11  Methyltransferase domain
    1.9e-06   27.5   0.0    2.3e-06   27.3   0.0    1.1  1  MTS              Methyltransferase small domain
    4.5e-06   27.3   0.0      6e-06   26.9   0.0    1.1  1  Methyltransf_12  Methyltransferase domain
    6.2e-06   26.1   0.0    7.4e-06   25.9   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    0.00012   21.9   0.0    0.00014   21.7   0.0    1.1  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    0.00018   20.7   0.0    0.00021   20.4   0.0    1.0  1  RrnaAD           Ribosomal RNA adenine dimethylase
    0.00046   19.7   0.2    0.00058   19.3   0.2    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
     0.0016   18.1   0.0     0.0019   17.9   0.0    1.1  1  NodS             Nodulation protein S (NodS)
     0.0041   16.8   0.0      0.005   16.5   0.0    1.1  1  MetW             Methionine biosynthesis protein MetW
     0.0059   16.7   0.0     0.0065   16.6   0.0    1.1  1  FtsJ             FtsJ-like methyltransferase
  ------ inclusion threshold ------
      0.038   13.3   0.0      0.038   13.3   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
      0.041   13.5   0.0       0.05   13.2   0.0    1.1  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
      0.096   11.8   0.0       0.11   11.6   0.0    1.1  1  Fibrillarin      Fibrillarin
       0.76    9.2   3.7        1.4    8.3   1.0    2.1  2  CheR             CheR methyltransferase, SAM binding domain


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.9   0.0   3.6e-16   3.8e-13       1      76 [.      41     116 ..      41     122 .] 0.89

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 3.6e-16
                      EEEET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEEST.GGG CS
  Methyltransf_25   1 vLdlGcGtGrltlalakrlg.kakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvssga.lhh 76 
                      vLdl+cGtG +t+++ +++g k+ v+g D s +++++a++ +   g+  n++f++ dae+++f + +fD++++++a + +
       EPA06718.1  41 VLDLACGTGVVTKKIRDKVGaKGYVVGADASITAIKIAKKWN---GVksNLNFINIDAEKFNFYH-EFDIITCQYAlFFF 116
                      9******************779*******************9...4555**************87.9******9995544 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.9   0.3   2.3e-15   2.5e-12       3      84 ..      37     113 ..      35     122 .] 0.91

  Alignments for each domain:
  == domain 1  score: 46.9 bits;  conditional E-value: 2.3e-15
  Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDlilsnevl 84 
                      +g +vlDl+CGtG  t+++ +++g k+ vvG D s +ai+ A++    +g++ n++F   d+e+++  +    fD+i+++ +l
       EPA06718.1  37 NGDSVLDLACGTGVVTKKIRDKVGAKGYVVGADASITAIKIAKK---WNGVKsNLNFINIDAEKFN--FY-HEFDIITCQYAL 113
                      5789****************************************...589999***********99..77.79******9988 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.5   0.0   2.1e-14   2.2e-11      38     126 ..      28     113 ..       2     121 .. 0.88

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 2.1e-14
                      HHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES-G CS
  Ubie_methyltran  38 fveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtvsfGl 126
                      ++ +lv+v +g +vlD+a+Gtg ++ k+ d+vg+kg vv++D + + +k+++k   +  k+n++f++ +ae+++f    fD++t  + l
       EPA06718.1  28 KLVELVNVNNGDSVLDLACGTGVVTKKIRDKVGAKGYVVGADASITAIKIAKK--WNGVKSNLNFINIDAEKFNFYH-EFDIITCQYAL 113
                      678899********************************************987..467788**************86.5*****99987 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.0   1.7e-12   1.8e-09       1      74 [.      42     116 ..      42     122 .] 0.90

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 1.7e-12
                      EEET-TTSHHHHHHHHTT...SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC- CS
  Methyltransf_11   1 LdvGcGtGrlaealakrg...arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhv 74 
                      Ld++cGtG +++++ +++   + vvg D s +++k+ak+ +  + + ++f+  daek++f    fD+++++ +l+++
       EPA06718.1  42 LDLACGTGVVTKKIRDKVgakGYVVGADASITAIKIAKKWNGVKSN-LNFINIDAEKFNFYH-EFDIITCQYALFFF 116
                      8**************6666999***************999888885.99**********988.9********99987 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   2.2e-09   2.3e-06      20     101 ..      26     107 ..      20     110 .. 0.76

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 2.2e-09
                 HHHHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.E.EEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEE CS
         MTS  20 sklLletlpkelsgkvlDlGcGaGvlgaalakespeae.vtlvdvdarAlesakenleanklevevvasdvleeveekkfdli 101
                 ++ L+e ++ +  ++vlDl+cG+Gv++ ++ ++      v+  d++  A+++ak+  +  k ++++++ d+ +    ++fd+i
  EPA06718.1  26 TSKLVELVNVNNGDSVLDLACGTGVVTKKIRDKVGAKGyVVGADASITAIKIAKKW-NGVKSNLNFINIDAEKFNFYHEFDII 107
                 667899999999999***************99988877799***********9973.33333355555555554445566666 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   5.7e-09     6e-06       1      76 [.      42     113 ..      42     120 .. 0.80

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 5.7e-09
  Methyltransf_12   1 LeiGcGtGsllralleklpdieyt.gvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvl 76 
                      L++ cGtG +++ +++k   + y+ g D s  ai     k+ak+ n   +n+++ ++d+++    + fD++++  +l
       EPA06718.1  42 LDLACGTGVVTKKIRDKVGAKGYVvGADASITAI-----KIAKKWNGVKSNLNFINIDAEKFNFYHEFDIITCQYAL 113
                      89****************6666666*********.....555555555567888888876666669******97665 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0     7e-09   7.4e-06      12      90 ..      28     111 ..      11     115 .. 0.73

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 7e-09
  Methyltransf_23  12 klerllpklraggrvLdiGcGtGillevlren.gf..svtgvDlspeaveiae.........kakkaqkdqfdeqeaaepqgkfdlIvlre 90 
                      kl +l+ + + g +vLd++cGtG +++ +r++ g+   v+g D+s  a++ia+         ++++   ++f      +    fd+I++ +
       EPA06718.1  28 KLVELV-NVNNGDSVLDLACGTGVVTKKIRDKvGAkgYVVGADASITAIKIAKkwngvksnlNFINIDAEKF------NFYHEFDIITCQY 111
                      444455.258888****************88757767799***********987666666554444444444......3334788887766 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   1.3e-07   0.00014      63     115 ..      27      79 ..      17      98 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.3e-07
                 HHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHH CS
        PCMT  63 alalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeak 115
                 ++++el+++++g++vL++ +G+G  t  +   vg+kg vv+ + +   ++ ak
  EPA06718.1  27 SKLVELVNVNNGDSVLDLACGTGVVTKKIRDKVGAKGYVVGADASITAIKIAK 79 
                 5789*************************************998766666655 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0     2e-07   0.00021      22      93 ..      29     103 ..      24     119 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2e-07
                 HHHHH-GGTTSEEEEES-TTTCCHHHHHCC-..SEEEEE-S-HHHHHH.HHCHTT.TCCCEEEE-S-CCGHHHHHH CS
      RrnaAD  22 IldklnleekltvleigpGkGilTeeLakra..kqvvvlElderLakl.lqkkls.kdeklkvvhqDflkfetpee 93 
                  ++ +n+++ + vl+++ G+G+ T+++ + +  k + v+  d ++ ++   kk +  +++l+ ++ D+ kf+++ e
  EPA06718.1  29 LVELVNVNNGDSVLDLACGTGVVTKKIRDKVgaKGY-VVGADASITAIkIAKKWNgVKSNLNFINIDAEKFNFYHE 103
                 677899*********************999985555.55666666554156667789*****************95 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.2   5.5e-07   0.00058     159     232 ..      35     109 ..      23     111 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 5.5e-07
        PrmA 159 vkegeevlDvGtGSGiLaiaa.akLgak.kvvavDiDevAvkvakeNaelNkveaklev.alseellk.eekadviva 232
                 v++g++vlD+ +G+G+ +     k+gak  vv+ D    A+k+ak   + N+v+++l+  ++ +e ++  +++d+i +
  EPA06718.1  35 VNNGDSVLDLACGTGVVTKKIrDKVGAKgYVVGADASITAIKIAK---KWNGVKSNLNFiNIDAEKFNfYHEFDIITC 109
                 68899***********996542689998579*************9...588998877652344555545788999976 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.8e-06    0.0019      45     118 ..      39     115 ..      16     121 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.8e-06
        NodS  45 adalevGcaaGalterlapyc.krltvv..dvveeaiararervkesshiswivsdvqqfstdekfdlivvaevlyy 118
                  ++l++ c +G +t+++      +  vv  d    ai+ a++    +s++++i  d ++f+  ++fd+i +   l++
  EPA06718.1  39 DSVLDLACGTGVVTKKIRDKVgAKGYVVgaDASITAIKIAKKWNGVKSNLNFINIDAEKFNFYHEFDIITCQYALFF 115
                 579*************9765413444443488899*******99999************************999887 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   4.7e-06     0.005      11      78 ..      35     106 ..      26     115 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.7e-06
        MetW  11 ikpgsrvldlGcGdGellellkeekqvdgrGleldeegvaecvakGlsviqgdl...dkdlenfe.dksfdy 78 
                 +++g  vldl cG G + + ++++ + +g+ +  d++  a  +ak  + ++ +l   + d e+f+  ++fd+
  EPA06718.1  35 VNNGDSVLDLACGTGVVTKKIRDKVGAKGYVVGADASITAIKIAKKWNGVKSNLnfiNIDAEKFNfYHEFDI 106
                 678999************************999999998888888776666664111445555542345665 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   6.2e-06    0.0065       8      97 ..      28     113 ..      23     122 .] 0.67

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6.2e-06
                 HHHHHHHHHT-S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS..HHHTTEEEECS-CCCSSHHHHHCHCHHHSSEEEEEE--S- CS
        FtsJ   8 KLleidekfklfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm..aplpgvttiqgditdpetiekikealserkvdlvvsDgap 97 
                 KL e+   ++ +++g+ v+Dl++++G  ++ +  ++gakg vv+ D      +  ++ + ++ + +  +   +  ++   +++d++++  a 
  EPA06718.1  28 KLVEL---VN-VNNGDSVLDLACGTGVVTKKIRDKVGAKGYVVGADASITaiKIAKKWNGVKSNLNFINIDAEKFNFY--HEFDIITCQYAL 113
                 44444...33.56899******************************95553233366666655554444333333333..347777776665 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.6e-05     0.038      49     102 ..      24      79 ..       9     109 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.6e-05
                 HHHHHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--E..EEEEES-HHHHHHHH CS
        CMAS  49 aKldlileklelkpGmtlLdiGcGWGslvrraverydvk..vvglTlSkeqaklak 102
                 + +  ++e +++++G+ +Ld+ cG G ++++  ++ ++k  vvg   S    k ak
  EPA06718.1  24 QSTSKLVELVNVNNGDSVLDLACGTGVVTKKIRDKVGAKgyVVGADASITAIKIAK 79 
                 5566788999*******************999999888655677666666666555 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.8e-05      0.05       3      73 ..      32     100 ..      30     109 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.8e-05
                      HH---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHH CS
  Methyltr_RsmB-F   3 lLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidk 73 
                      l + ++++ +lDl+++ G  T  i + +  kg vv  da+ + +k +a+  +++  + +  ++ Da k++ 
       EPA06718.1  32 LVNVNNGDSVLDLACGTGVVTKKIRDKVGAKGYVVGADASITAIK-IAKKWNGVKSN-LNFINIDAEKFNF 100
                      568899********************************9987664.67777776655.8888888888854 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0    0.0001      0.11      62     135 ..      29     102 ..      12     113 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0001
                  T-S--S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHTTSTTEEEEES-TTSGGGGT CS
  Fibrillarin  62 glkelpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprvlrelievakkRknivPileDArkPekYr 135
                   ++ + +++g++vL l  ++G     + D vg +g v + + s ++++   +    ++n+  i  DA+k + Y+
   EPA06718.1  29 LVELVNVNNGDSVLDLACGTGVVTKKIRDKVGAKGYVVGADASITAIKIAKKWNGVKSNLNFINIDAEKFNFYH 102
                  5677899***********************************99999988888888888888888888776665 PP

>> CheR  CheR methyltransferase, SAM binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1      0.14   1.5e+02      53      82 ..      51      80 ..      22      88 .. 0.79
   2 ?    8.3   1.0    0.0014       1.4     116     154 ..      84     121 ..      81     122 .] 0.86

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.14
                HHCHSTTTSSS-EEEEEEESSCHHHHHHHH CS
        CheR 53 lketlpkaaklkvkilAtDidlkvlekAka 82
                + +++++++++k  +++ D +  +++ Ak+
  EPA06718.1 51 VTKKIRDKVGAKGYVVGADASITAIKIAKK 80
                555677777888899999999999999986 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0014
                 HHTTEEEEE--TTT-SGGG--EEEEEE-SSGGGC-CHHH CS
        CheR 116 ikelvkFeklnllekksvlgklDvifcrnvliYfdeetq 154
                 +k++ +F + ++ +  ++ +++D+i+c+  l +f  +++
  EPA06718.1  84 VKSNLNFINIDAEK-FNFYHEFDIITCQYALFFFLMHKK 121
                 68888999999888.****************99976655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.53u 0.33s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 706.36
//
Query:       EPA06719.1  [L=153]
Description: topoisomerase DNA-binding C4 zinc finger domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-07   31.1   7.9      3e-06   26.9   1.0    2.7  2  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
      0.008   16.1   9.7       0.58   10.2   1.6    3.2  2  Ogr_Delta        Ogr/Delta-like zinc finger
  ------ inclusion threshold ------
      0.098   11.8   0.2       0.18   10.9   0.1    1.4  2  Phage_HK97_TLTM  Tail length tape measure protein
       0.53   10.9   7.9        1.3    9.6   0.8    2.4  2  Zn_ribbon_recom  Recombinase zinc beta ribbon domain


Domain annotation for each model (and alignments):
>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   1.0   6.6e-10     3e-06       2      27 ..      66      94 ..      65     107 .. 0.69
   2 !    7.4   1.0   0.00082       3.7       4      33 ..     117     147 ..     114     152 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 6.6e-10
                    EE-SSS-.-EEEEEE-SSS..EEEEESST CS
  zf-C4_Topoisom  2 ekCPkCg.gdLvlkrgkkG..kFvGCsnY 27
                    ++CP+C+ g+L++ r++    +F+GCsn+
      EPA06719.1 66 VECPECRlGQLMVIRSRSTrkRFMGCSNF 94
                    58****996654444443335*******7 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00082
                     -SSS-.-EEEEEE-SSSEEE.EESST.T---- CS
  zf-C4_Topoisom   4 CPkCg.gdLvlkrgkkGkFv.GCsnYPeCkft 33 
                     C+ C+   ++ ++++k k    Csn+ +C+  
      EPA06719.1 117 CEVCKwPMIIFRYSRKQKWTrQCSNF-NCDSR 147
                     9****666778*****988647****.**976 PP

>> Ogr_Delta  Ogr/Delta-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   1.4   0.00045         2       2      39 ..      68     104 ..      67     109 .. 0.76
   2 !   10.2   1.6   0.00013      0.58       2      33 ..     117     144 ..     116     148 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00045
   Ogr_Delta   2 CPhC..gapaaartsrnlskdvreryyqCsnfe..Cgatfva 39 
                 CP+C  g+ +++r+     + +r+r+  Csnf   C a++  
  EPA06719.1  68 CPECrlGQLMVIRS-----RSTRKRFMGCSNFYggCKASSPL 104
                 88886667788875.....5799*********5579998865 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00013
   Ogr_Delta   2 CPhCgapaaartsrnlskdvreryyqCsnfeC 33 
                 C  C+ p+ + +  ++ k++r    qCsnf+C
  EPA06719.1 117 CEVCKWPMIIFRYSRKQKWTR----QCSNFNC 144
                 888999999999999999887....9****** PP

>> Phage_HK97_TLTM  Tail length tape measure protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   4.1e-05      0.18      83     137 ..      13      66 ..       3      77 .. 0.82
   2 ?   -1.9   0.0      0.34   1.5e+03     208     225 ..     104     123 ..      72     150 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.1e-05
  Phage_HK97_TLTM  83 lkeqnklvkeaeqkveelkkeldkyqvsingylvnkldskeeaiklaeatdklse 137
                      +k+  + vk  + k+  +kke+ +y   ingyl   ++ ++  i  +++ +++++
       EPA06719.1  13 VKKTRHVVKSTKSKIAIFKKEIVQYL-DINGYLSWSSKDRKYMILGTNSPKNGLV 66 
                      56777889*****************8.******9988888877776776666665 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.34
  Phage_HK97_TLTM 208 Lleeikk..veiPvrvkeae 225
                      Ll++ k   ++iP +v +++
       EPA06719.1 104 LLQKAKLraMKIPCEVCKWP 123
                      44443323478888888884 PP

>> Zn_ribbon_recom  Recombinase zinc beta ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.8   0.00028       1.3       4      40 ..      64      99 ..      63     113 .. 0.76
   2 ?    5.1   1.2    0.0074        33       6      33 ..     115     143 ..     110     152 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00028
  Zn_ribbon_recom  4 GllrCgeC..GspmtrrkrkgkrhyYrCstyrrkgkkCs 40
                     Gl+ C eC  G+ m+ r+r+ +++   Cs+   ++   +
       EPA06719.1 64 GLVECPECrlGQLMVIRSRSTRKRFMGCSNFYGGC---K 99
                     99******555669999999999******974444...3 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0074
  Zn_ribbon_recom   6 lrCgeCGspmtr.rkrkgkrhyYrCstyr 33 
                      + C  C  pm+  r++++++   +Cs+ +
       EPA06719.1 115 IPCEVCKWPMIIfRYSRKQKWTRQCSNFN 143
                      66********9987777666444555532 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       852  (0.0475208); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 1118.73
//
Query:       EPA06720.1  [L=133]
Description: hypothetical protein BG20_I0051 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.073   12.6   0.0      0.076   12.5   0.0    1.1  1  DUF1129   Protein of unknown function (DUF1129)


Domain annotation for each model (and alignments):
>> DUF1129  Protein of unknown function (DUF1129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   4.3e-06     0.076      41     136 ..      31     130 ..      12     133 .] 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.3e-06
     DUF1129  41 aQkkGktArqLyg..tptekaeellekkkkakkeskenpwlmalDnsLlllalfallfg...ilalfskkkqtasiGlitlllvalvgGlamvlvyrll 134
                 +Qk+G   +  yg    +e+ +++l +  k+  +++ ++  ++ D   +l++l +l+ g   i ++f++  +++++ + t +l+++v+G++ +++ + +
  EPA06720.1  31 GQKNGAKKQFRYGnlHIREYDDKFLVHTDKVDPRKD-PIGHLVYDAPEVLVGLTCLILGgskISKIFQNYGKSNKSTIATTVLSSIVAGYVGYVTTKKI 128
                 666666666666654556666666666665555555.67777778878888888888876778999**99999999***************99999888 PP

     DUF1129 135 tr 136
                 ++
  EPA06720.1 129 KK 130
                 75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 944.05
//
Query:       EPA06721.1  [L=53]
Description: hypothetical protein BG20_I0001 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.7e-05   22.6   0.4    9.9e-05   22.3   0.4    1.1  1  DZR             Double zinc ribbon
    0.00013   21.3   3.2       0.08   12.4   0.4    2.2  2  zf-ribbon_3     zinc-ribbon domain
    0.00052   19.6   3.6       0.13   12.1   0.3    2.2  2  zinc_ribbon_2   zinc-ribbon domain
     0.0011   18.5   0.7        1.2    8.8   0.1    2.2  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
     0.0025   17.3   0.8       0.48   10.0   0.1    2.2  2  TF_Zn_Ribbon    TFIIB zinc-binding
     0.0026   18.0   0.4       0.77   10.1   0.0    2.2  2  zf-LITAF-like   LITAF-like zinc ribbon domain
     0.0061   16.3   2.9       0.25   11.2   0.3    2.2  2  zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
     0.0069   16.6   0.4      0.044   14.0   0.4    2.1  1  Chordopox_RPO7  Chordopoxvirus DNA-directed RNA polymerase 7 
     0.0079   15.5   1.0       0.03   13.6   0.2    2.0  2  zf-TFIIB        Transcription factor zinc-finger
  ------ inclusion threshold ------
       0.01   15.9   2.9       0.24   11.5   0.2    2.2  2  zf-ACC          Acetyl-coA carboxylase zinc finger domain
      0.011   15.9   1.3      0.041   14.1   1.2    1.8  1  FANCL_C         FANCL C-terminal domain
      0.012   15.7   0.2      0.013   15.5   0.2    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.015   14.8   0.6        2.1    8.0   0.1    2.1  2  Sgf11           Sgf11 (transcriptional regulation protein)
      0.016   15.2   4.3          2    8.4   0.1    2.2  2  YhfH            YhfH-like protein
      0.028   14.3   3.8        2.2    8.3   0.1    2.1  2  DUF4428         Domain of unknown function (DUF4428)
      0.029   14.3   0.3        2.5    8.1   0.0    2.1  2  zf-dskA_traR    Prokaryotic dksA/traR C4-type zinc finger
      0.034   14.3   0.6       0.11   12.6   0.6    1.7  1  DiS_P_DiS       Bacterial Peptidase A24 N-terminal domain
      0.036   14.0   2.0        2.6    8.1   0.1    2.2  2  zinc_ribbon_4   zinc-ribbon domain
      0.036   14.3   0.2      0.083   13.1   0.2    1.6  1  LIM             LIM domain
      0.044   14.4   0.4        6.2    7.6   0.1    2.1  2  zf-ISL3         zinc-finger of transposase IS204/IS1001/IS109
      0.045   13.9   2.4       0.21   11.8   2.4    1.9  1  Zn-ribbon_8     Zinc ribbon domain
      0.053   13.6   1.5       0.31   11.1   0.1    2.1  2  UPF0547         Uncharacterised protein family UPF0547
      0.054   13.5   1.0       0.67   10.0   1.0    2.0  1  zinc-ribbons_6  zinc-ribbons
      0.054   13.5   2.4       0.14   12.1   2.4    1.7  1  zf-C2HC5        Putative zinc finger motif, C2HC5-type
      0.056   13.8   0.2       0.22   11.8   0.2    1.8  1  zf-Di19         Drought induced 19 protein (Di19), zinc-bindi
      0.081   12.8   1.8        6.9    6.6   0.1    2.1  2  TFIIS_C         Transcription factor S-II (TFIIS)
      0.082   12.8   1.5        1.6    8.7   0.1    2.1  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain
      0.084   12.9   0.3        3.2    7.8   0.1    2.1  2  Ogr_Delta       Ogr/Delta-like zinc finger
       0.09   12.7   1.5       0.46   10.4   1.5    1.8  1  zf-C3HC4_3      Zinc finger, C3HC4 type (RING finger)
       0.12   12.8   1.5         11    6.7   0.0    2.2  2  zf-C2H2         Zinc finger, C2H2 type
       0.15   12.5   0.2        5.9    7.4   0.0    2.1  2  DUF983          Protein of unknown function (DUF983)
       0.16   12.6   3.8       0.44   11.1   3.8    1.6  1  Cript           Microtubule-associated protein CRIPT
       0.32   10.7   4.4          5    6.9   0.3    2.1  2  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
       0.41   11.0   3.4         10    6.6   0.6    2.2  2  Fer2_BFD        BFD-like [2Fe-2S] binding domain
       0.41   10.2   2.2        6.4    6.4   0.1    2.2  2  zf_C2H2_10      C2H2 type zinc-finger
       0.45   10.6   2.9         23    5.0   3.0    2.1  1  CpXC            CpXC protein
       0.47   10.2   5.5       0.45   10.3   0.9    2.1  2  Rubredoxin_2    Rubredoxin metal binding domain
       0.65   10.0   3.2        4.1    7.4   0.3    2.0  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
        1.4    9.0   5.5        8.4    6.5   5.4    2.0  1  ADK_lid         Adenylate kinase, active site lid


Domain annotation for each model (and alignments):
>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.4   2.2e-07   9.9e-05      12      40 ..       4      43 ..       2      47 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 2.2e-07
         DZR 12 arfCseCgtklkavaa...........edrCpsCgekvdp 40
                +++C++Cg+k+ +++            + +CpsCg+k++ 
  EPA06721.1  4 DITCGKCGEKIANMKMlkslkdvmnpyNGKCPSCGQKLST 43
                579*******988777999*****************9876 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.1    0.0011       0.5      16      26 .]       4      14 ..       2      14 .. 0.90
   2 !   12.4   0.4   0.00018      0.08       4      14 ..      33      43 ..      32      45 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0011
  zf-ribbon_3 16 dnvCpyCGtkl 26
                 d++C +CG+k+
   EPA06721.1  4 DITCGKCGEKI 14
                 899*****997 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00018
  zf-ribbon_3  4 rCPnCGaplss 14
                 +CP+CG++ls+
   EPA06721.1 33 KCPSCGQKLST 43
                 58888876565 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.3     0.003       1.4       2       9 ..       7      14 ..       4      16 .. 0.64
   2 !   12.1   0.3   0.00028      0.13       1      10 [.      33      42 ..      33      45 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.003
  zinc_ribbon_2  2 CpnCGael 9 
                   C +CG+++
     EPA06721.1  7 CGKCGEKI 14
                   66666665 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00028
  zinc_ribbon_2  1 fCpnCGaelq 10
                   +Cp+CG +l+
     EPA06721.1 33 KCPSCGQKLS 42
                   8*****9997 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.1    0.0029       1.3       3      13 ..       5      15 ..       3      20 .. 0.85
   2 !    8.8   0.1    0.0026       1.2       4      17 ..      33      46 ..      31      47 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0029
      zf_UBZ  3 ylCerCgkeip 13
                ++C +Cg++i 
  EPA06721.1  5 ITCGKCGEKIA 15
                79*******97 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0026
      zf_UBZ  4 lCerCgkeipesel 17
                 C+ Cg+++++se+
  EPA06721.1 33 KCPSCGQKLSTSEF 46
                6*********9986 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.1     0.001      0.48      17      30 ..       2      15 ..       1      19 [. 0.82
   2 ?    6.3   0.1     0.015         7       2       9 ..      33      40 ..      32      51 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.001
                  TTCEEESSSSBEEE CS
  TF_Zn_Ribbon 17 rgelvCtdCGlVle 30
                  + +++C++CG+ + 
    EPA06721.1  2 SVDITCGKCGEKIA 15
                  5689******9986 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.015
                  EETTTTCE CS
  TF_Zn_Ribbon  2 kCPnCgst 9 
                  kCP Cg +
    EPA06721.1 33 KCPSCGQK 40
                  67777654 PP

>> zf-LITAF-like  LITAF-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1      0.02       9.2      55      68 ..       3      16 ..       1      18 [. 0.80
   2 !   10.1   0.0    0.0017      0.77       3      17 ..      29      43 ..      19      45 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.02
  zf-LITAF-like 55 vehyCpnCgallgt 68
                   v+ +C++Cg++++ 
     EPA06721.1  3 VDITCGKCGEKIAN 16
                   78899999999986 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0017
  zf-LITAF-like  3 ptqvdCpaCqqrvvT 17
                   p++ +Cp+C+q+  T
     EPA06721.1 29 PYNGKCPSCGQKLST 43
                   555566666665555 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1     0.024        11       2      11 ..       5      14 ..       4      20 .. 0.85
   2 !   11.2   0.3   0.00054      0.25       2      11 ..      32      41 ..      31      44 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.024
                    EE-SSS--EE CS
  zf-C4_Topoisom  2 ekCPkCggdL 11
                    ++C kCg+++
      EPA06721.1  5 ITCGKCGEKI 14
                    69*****998 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00054
                    EE-SSS--EE CS
  zf-C4_Topoisom  2 ekCPkCggdL 11
                    +kCP+Cg++L
      EPA06721.1 32 GKCPSCGQKL 41
                    79*****998 PP

>> Chordopox_RPO7  Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide (RPO7)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.4   9.5e-05     0.044       1      46 [.       1      43 [.       1      51 [. 0.86

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 9.5e-05
  Chordopox_RPO7  1 mvfplvCstCGrDlseeryrLlvkkkkLkdvlatvkrkC..CrlkLst 46
                    m  ++ C  CG+ +++ + +     k+Lkdv++ ++ kC  C  kLst
      EPA06721.1  1 MSVDITCGKCGEKIANMKML-----KSLKDVMNPYNGKCpsCGQKLST 43
                    566799******99998754.....89********999988999**99 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.76   3.5e+02       2       6 ..       7      11 ..       6      25 .. 0.69
   2 !   13.6   0.2   6.6e-05      0.03       1      15 [.      33      47 ..      33      51 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.76
    zf-TFIIB  2 CPkCq 6 
                C kC+
  EPA06721.1  7 CGKCG 11
                44554 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 6.6e-05
    zf-TFIIB  1 kCPkCqdeleeserg 15
                kCP+C++ l +se++
  EPA06721.1 33 KCPSCGQKLSTSEFS 47
                8************96 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.3     0.053        24       2      11 ..       5      14 ..       5      24 .. 0.79
   2 ?   11.5   0.2   0.00053      0.24       3      15 ..      33      45 ..      33      47 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.053
      zf-ACC  2 tKCpsCgeml 11
                + C +Cge +
  EPA06721.1  5 ITCGKCGEKI 14
                67*****966 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00053
      zf-ACC  3 KCpsCgemlykke 15
                KCpsCg+ l + e
  EPA06721.1 33 KCPSCGQKLSTSE 45
                9*****9887766 PP

>> FANCL_C  FANCL C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   1.2   8.9e-05     0.041      41      68 ..      17      44 ..       4      46 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.9e-05
                HHHHHSSS-TTT--EEE-TTT-SEEEGG CS
     FANCL_C 41 lrslkesrqsfdvlfGeCPyCkkkisvk 68
                ++ lk+ + +++   G+CP C +k+s++
  EPA06721.1 17 MKMLKSLKDVMNPYNGKCPSCGQKLSTS 44
                567788899999999**********987 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.2   2.8e-05     0.013      69      95 ..       3      40 ..       1      51 [. 0.78

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.8e-05
                -EEEETTTS-EEECHHHHH............S-TTTSSS CS
        HypA 69 vkvrCreCgkefeleekal............rCpkCgsa 95
                v ++C +Cg+++   +  l            +Cp+Cg++
  EPA06721.1  3 VDITCGKCGEKIANMKM-LkslkdvmnpyngKCPSCGQK 40
                7899******9996653.12358899***********96 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.027        12       2      15 ..       2      15 ..       1      16 [. 0.87
   2 ?    8.0   0.1    0.0045       2.1       6      19 ..      33      46 ..      31      47 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.027
                C-EEE-TTTSSEEE CS
       Sgf11  2 seyvtCpnCgRqia 15
                s+++tC  Cg +ia
  EPA06721.1  2 SVDITCGKCGEKIA 15
                6789******9998 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0045
                E-TTTSSEEEGGGH CS
       Sgf11  6 tCpnCgRqiaasRF 19
                +Cp Cg++ ++s F
  EPA06721.1 33 KCPSCGQKLSTSEF 46
                6*******999866 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.9    0.0053       2.4      15      26 ..       6      17 ..       5      19 .. 0.88
   2 ?    8.4   0.1    0.0044         2      15      24 ..      33      42 ..      31      47 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0053
        YhfH 15 kCteCGkeieEq 26
                +C +CG++i  +
  EPA06721.1  6 TCGKCGEKIANM 17
                7********876 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0044
        YhfH 15 kCteCGkeie 24
                kC++CG+++ 
  EPA06721.1 33 KCPSCGQKLS 42
                7******975 PP

>> DUF4428  Domain of unknown function (DUF4428)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.6    0.0078       3.6      23      36 ..       7      19 ..       4      28 .. 0.57
   2 ?    8.3   0.1    0.0047       2.2      23      37 ..      34      50 ..      33      53 .] 0.78

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0078
     DUF4428 23 CkdClkKlseflsd 36
                C +C +K+ +++ +
  EPA06721.1  7 CGKCGEKIANMK-M 19
                777777773331.2 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0047
     DUF4428 23 CkdClkKl..seflsdv 37
                C++C +Kl  sef+ dv
  EPA06721.1 34 CPSCGQKLstSEFSLDV 50
                99999999777777665 PP

>> zf-dskA_traR  Prokaryotic dksA/traR C4-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0054       2.5       6      17 ..       7      18 ..       2      23 .. 0.79
   2 ?    4.8   0.1     0.061        28       5      11 ..      32      39 ..      28      41 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0054
  zf-dskA_traR  6 CeeCGEpIpeaR 17
                  C +CGE+I+  +
    EPA06721.1  7 CGKCGEKIANMK 18
                  889*****9766 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.061
  zf-dskA_traR  5 s.CeeCGE 11
                    C  CG+
    EPA06721.1 32 GkCPSCGQ 39
                  45*****8 PP

>> DiS_P_DiS  Bacterial Peptidase A24 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.6   0.00024      0.11      29      67 ..       6      46 ..       1      51 [. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00024
   DiS_P_DiS 29 rCpkCghklkwleliPvlSyll..lrgrCraCkakislryp 67
                +C kCg+k++ ++++  l  ++    g+C +C++k+s   +
  EPA06721.1  6 TCGKCGEKIANMKMLKSLKDVMnpYNGKCPSCGQKLSTSEF 46
                69999999999999998888874568999999999998765 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.1    0.0056       2.6      24      35 ..       3      14 ..       1      15 [. 0.81
   2 ?    5.6   0.3     0.032        15      27      33 ..      33      39 ..      32      42 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0056
  zinc_ribbon_4 24 vkvrCskCghvF 35
                   v ++C kCg+++
     EPA06721.1  3 VDITCGKCGEKI 14
                   678999999875 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.032
  zinc_ribbon_4 27 rCskCgh 33
                   +C+ Cg+
     EPA06721.1 33 KCPSCGQ 39
                   4555554 PP

>> LIM  LIM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.2   0.00018     0.083       1      41 [.       7      46 ..       7      52 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00018
                -TTT--BE-TTTEEEEETTEEEETTTSB-TTT-SB-CTT.C CS
         LIM  1 CagCnkkiadrelvlkaldkvwHeeCFtCsdCqkeLkegsf 41
                C +C++kia+ +++ k l +v  +   +C +C+++L++ +f
  EPA06721.1  7 CGKCGEKIANMKML-KSLKDVMNPYNGKCPSCGQKLSTSEF 46
                9********99998.899999999999*********99974 PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.063        29       3      11 ..       5      13 ..       4      25 .. 0.82
   2 ?    7.6   0.1     0.013       6.2       4      11 ..      33      40 ..      31      46 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.063
     zf-ISL3  3 hrCPnCgsk 11
                ++C +Cg+k
  EPA06721.1  5 ITCGKCGEK 13
                69*****98 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.013
     zf-ISL3  4 rCPnCgsk 11
                +CP Cg+k
  EPA06721.1 33 KCPSCGQK 40
                7*****98 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   2.4   0.00045      0.21       7      36 ..       6      41 ..       4      43 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00045
  Zn-ribbon_8  7 rCeeCghefe......vlqsisdapltaCPeCgsev 36
                  C +Cg++         l  ++ + + +CP+Cg+++
   EPA06721.1  6 TCGKCGEKIAnmkmlkSLKDVMNPYNGKCPSCGQKL 41
                 5999998888665444444444444788*****976 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1      0.71   3.3e+02       3      11 ..       7      15 ..       6      16 .. 0.73
   2 ?   11.1   0.1   0.00068      0.31       2      12 ..      33      43 ..      33      44 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.71
     UPF0547  3 CPeCeakvP 11
                C  C +k++
  EPA06721.1  7 CGKCGEKIA 15
                777888886 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00068
     UPF0547  2 vCPeCeakvPv 12
                +CP C +k+++
  EPA06721.1 33 KCPSCGQKLST 43
                7*******997 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   1.0    0.0015      0.67       2      40 ..       6      42 ..       1      47 [. 0.51

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0015
                    --SSS-S--EE-S...........SEEE-TTT--EEEEEEE-SSS-S--- CS
  zinc-ribbons_6  2 kCpeCqqelekrg...........eqyhCeaCqedlkkealCpeCeqele 40
                    +C +C +++ + +                         +  Cp C+q+l+
      EPA06721.1  6 TCGKCGEKIANMKmlkslkdvmnpY-------------NGKCPSCGQKLS 42
                    4555555555444233333333333.............445666666665 PP

>> zf-C2HC5  Putative zinc finger motif, C2HC5-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   2.4   0.00031      0.14      19      48 ..       6      45 ..       1      50 [. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00031
    zf-C2HC5 19 nClnCGkiiCakegls..........kpCsfCgspllsse 48
                 C +CG  i +++ l+          ++C++Cg++l +se
  EPA06721.1  6 TCGKCGEKIANMKMLKslkdvmnpynGKCPSCGQKLSTSE 45
                699999988888888788888889999********98775 PP

>> zf-Di19  Drought induced 19 protein (Di19), zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   0.00048      0.22       3      43 ..       5      43 ..       3      51 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00048
     zf-Di19  3 ftCPyCgkeltvkeLveHvedeHrveskevvCPvCaekvtk 43
                +tC  Cg++++  ++++ ++d   ++  ++ CP C +k++ 
  EPA06721.1  5 ITCGKCGEKIANMKMLKSLKD--VMNPYNGKCPSCGQKLST 43
                688889999999999998888..888899999999877653 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1     0.015       6.9       1       9 [.       5      13 ..       1      20 [. 0.73
   2 ?    6.0   0.3     0.023        11       2       9 ..      33      40 ..      32      44 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.015
     TFIIS_C  1 akCpkCgsr 9 
                ++C kCg++
  EPA06721.1  5 ITCGKCGEK 13
                468888776 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.023
     TFIIS_C  2 kCpkCgsr 9 
                kCp+Cg++
  EPA06721.1 33 KCPSCGQK 40
                79999986 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1      0.14        65      27      33 ..       7      13 ..       5      15 .. 0.55
   2 ?    8.7   0.1    0.0036       1.6       3      13 ..      30      40 ..      29      45 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.14
  Zn_ribbon_SprT 27 CrrCkgt 33
                    C++C+++
      EPA06721.1  7 CGKCGEK 13
                    5555544 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0036
  Zn_ribbon_SprT  3 yvYrCtgCgre 13
                    y  +C++Cg++
      EPA06721.1 30 YNGKCPSCGQK 40
                    66799999953 PP

>> Ogr_Delta  Ogr/Delta-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0      0.14        65       1      21 [.       6      26 ..       6      31 .. 0.72
   2 ?    7.8   0.1    0.0071       3.2       1      12 [.      33      44 ..      33      46 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.14
   Ogr_Delta  1 rCPhCgapaaartsrnlskdv 21
                +C +Cg+++a  +    +kdv
  EPA06721.1  6 TCGKCGEKIANMKMLKSLKDV 26
                699****99877666666665 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0071
   Ogr_Delta  1 rCPhCgapaaar 12
                +CP Cg++  ++
  EPA06721.1 33 KCPSCGQKLSTS 44
                6******98876 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.5   0.00099      0.46      25      48 ..       6      42 ..       4      44 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00099
                E-HHHHHHHHH.............TT-B-TTT--B-- CS
  zf-C3HC4_3 25 lCeeCaekllk.............rkkkCpiCrrpie 48
                +C +C ek+ +              + kCp C ++ +
  EPA06721.1  6 TCGKCGEKIANmkmlkslkdvmnpYNGKCPSCGQKLS 42
                79999999987889999999999999******99976 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0     0.024        11       2      17 ..       6      21 ..       5      22 .. 0.82
   2 ?    5.3   0.4     0.065        30       2      13 ..      33      44 ..      33      46 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.024
                EETTTTEEESSHHHHH CS
     zf-C2H2  2 kCpdCgksFkrksnLk 17
                +C++Cg++  +  +Lk
  EPA06721.1  6 TCGKCGEKIANMKMLK 21
                8*****9988888876 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.065
                EETTTTEEESSH CS
     zf-C2H2  2 kCpdCgksFkrk 13
                kCp Cg++ +++
  EPA06721.1 33 KCPSCGQKLSTS 44
                7*****998886 PP

>> DUF983  Protein of unknown function (DUF983)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0      0.17        79       7      19 ..       3      15 ..       1      20 [. 0.79
   2 ?    7.4   0.0     0.013       5.9       8      21 ..      31      44 ..      28      50 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.17
      DUF983  7 vadaCeaCgldls 19
                v  +C +Cg++++
  EPA06721.1  3 VDITCGKCGEKIA 15
                6668******986 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.013
      DUF983  8 adaCeaCgldlsha 21
                + +C++Cg++ls  
  EPA06721.1 31 NGKCPSCGQKLSTS 44
                569*******9876 PP

>> Cript  Microtubule-associated protein CRIPT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   3.8   0.00096      0.44      19      56 ..       9      43 ..       3      48 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00096
       Cript 19 etggrkigenkllskkk.rfnpyaaysskCkiCktkveq 56
                +  g ki++ k+l++ k  +npy+    kC +C +k++ 
  EPA06721.1  9 KC-GEKIANMKMLKSLKdVMNPYNG---KCPSCGQKLST 43
                44.489*******776658899988...9****999876 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.4     0.024        11       6      12 ..       7      13 ..       7      15 .. 0.87
   2 ?    6.9   0.3     0.011         5       6      13 ..      34      41 ..      33      45 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.024
  zf-NADH-PPase  6 CgrCGap 12
                   Cg+CG +
     EPA06721.1  7 CGKCGEK 13
                   *****86 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.011
  zf-NADH-PPase  6 CgrCGapt 13
                   C+ CG++ 
     EPA06721.1 34 CPSCGQKL 41
                   77888775 PP

>> Fer2_BFD  BFD-like [2Fe-2S] binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.6     0.022        10      37      47 ..       6      16 ..       2      17 .. 0.85
   2 ?    6.4   0.1     0.024        11      22      45 ..      17      41 ..      14      43 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.022
    Fer2_BFD 37 gCggCrpaiee 47
                 Cg+C ++i++
  EPA06721.1  6 TCGKCGEKIAN 16
                5*******986 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.024
    Fer2_BFD 22 lttveevkrrtkagtg.CggCrpai 45
                ++ ++++k+ ++  +g C +C +++
  EPA06721.1 17 MKMLKSLKDVMNPYNGkCPSCGQKL 41
                45556666666667777****9986 PP

>> zf_C2H2_10  C2H2 type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1     0.014       6.4       4      15 ..       6      17 ..       4      21 .. 0.79
   2 ?    3.6   0.4      0.11        50       5      12 ..      34      41 ..      32      42 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.014
  zf_C2H2_10  4 sCPKCqeklPDi 15
                 C KC+ek+  +
  EPA06721.1  6 TCGKCGEKIANM 17
                6******97655 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.11
  zf_C2H2_10  5 CPKCqekl 12
                CP C+ kl
  EPA06721.1 34 CPSCGQKL 41
                ****9986 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   3.0     0.051        23      39      48 ..      33      42 ..       5      52 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.051
        CpXC 39 tCpkCgatak 48
                +Cp+Cg++ +
  EPA06721.1 33 KCPSCGQKLS 42
                6888887765 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.3      0.28   1.3e+02       3       8 ..       7      12 ..       6      16 .. 0.74
   2 ?   10.3   0.9   0.00097      0.45      15      22 ..      32      39 ..      28      39 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.28
  Rubredoxin_2  3 CsqCGf 8 
                  C +CG 
    EPA06721.1  7 CGKCGE 12
                  777875 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00097
  Rubredoxin_2 15 GrCpsCgs 22
                  G+CpsCg+
    EPA06721.1 32 GKCPSCGQ 39
                  9*****96 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   3.1     0.018       8.4      30      55 ..       6      40 ..       4      41 .. 0.82
   2 ?    7.4   0.3     0.009       4.1      30      40 ..      33      43 ..      21      52 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.018
  OrfB_Zn_ribbon 30 tCseCgsknke.........alsgrtfkCpnCgfe 55
                    tC +Cg+k  +           ++ + kCp+Cg +
      EPA06721.1  6 TCGKCGEKIANmkmlkslkdVMNPYNGKCPSCGQK 40
                    89999999998889987776677888999999975 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.009
  OrfB_Zn_ribbon 30 tCseCgsknke 40
                    +C+ Cg+k+++
      EPA06721.1 33 KCPSCGQKLST 43
                    69999999887 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   5.4     0.018       8.4       3      31 ..       6      41 ..       5      43 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.018
                E-TTT--.EEETTT.B--S.....STTB-TTT--.- CS
     ADK_lid  3 vCpkCGr.sYhvvf.npPk.....veglCDkCGepL 31
                +C kCG+ + ++++ +  k      +g+C  CG +L
  EPA06721.1  6 TCGKCGEkIANMKMlKSLKdvmnpYNGKCPSCGQKL 41
                79999987778774333345555579********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                       101  (0.00563333); expected 17.9 (0.001)
Passed Fwd filter:                        39  (0.00217525); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              39  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.48
# Mc/sec: 335.25
//
Query:       EPA06722.1  [L=123]
Description: hypothetical protein BG20_I0060 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      4e-20   72.1   0.2    5.8e-20   71.6   0.2    1.2  1  PPS_PS        Phosphopantothenate/pantothenate synthetase
  ------ inclusion threshold ------
      0.048   13.9   0.1      0.063   13.6   0.1    1.1  1  DUF3035       Protein of unknown function (DUF3035)
      0.054   13.2   0.6      0.082   12.6   0.6    1.3  1  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain


Domain annotation for each model (and alignments):
>> PPS_PS  Phosphopantothenate/pantothenate synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.6   0.2   9.7e-24   5.8e-20       1      55 [.      66     120 ..      66     122 .. 0.97

  Alignments for each domain:
  == domain 1  score: 71.6 bits;  conditional E-value: 9.7e-24
      PPS_PS   1 lllakkpvisvNGNtaaLvaeeiveLaealgaklevNlfyrteeRvekiaellke 55 
                 +llak pvisvNGN+aaL+++eiv+La++++ak+evNlfy +e+R ++i ++lk+
  EPA06722.1  66 ILLAKLPVISVNGNIAALCPKEIVKLAKTTKAKIEVNLFYANEKRKRNIIKTLKK 120
                 689**************************************************97 PP

>> DUF3035  Protein of unknown function (DUF3035)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   1.1e-05     0.063      48     122 ..      40     114 ..      36     121 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.1e-05
     DUF3035  48 aeavaaLgGnpsaalkaksglsagekaLlkqagrdgvdpniRetlaaedaelrkadssfvdellfwqeeeaeaea 122
                  ea   L G++++++++k+   a+ + Ll++ +  +v++ni +   +e  +l+k+ +  ++  lf  +e+ +++ 
  EPA06722.1  40 GEAFDYLLGEKTRNAAKKAIKAAAAQILLAKLPVISVNGNIAALCPKEIVKLAKTTKAKIEVNLFYANEKRKRNI 114
                 678888999999998878888889999***************************************999986554 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.6   1.4e-05     0.082       1      42 [.      59      99 ..      59     107 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.4e-05
                  HHHHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EE CS
  TPP_enzyme_M  1 iekaaellkaakrpvilvGggvarsgaseelrelaeklgiPv 42
                  i++aa+ +  ak pvi v g +a + + +e+++la+++++ +
    EPA06722.1 59 IKAAAAQILLAKLPVISVNGNIA-ALCPKEIVKLAKTTKAKI 99
                  789*******************9.99************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       807  (0.0450109); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 826.15
//
Query:       EPA06723.1  [L=381]
Description: aminotransferase, class V [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-37  128.4   0.0    4.1e-37  128.0   0.0    1.1  1  Aminotran_5      Aminotransferase class-V
    9.4e-05   21.1   0.9    0.00014   20.5   0.9    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
  ------ inclusion threshold ------
      0.057   12.5   0.0      0.093   11.8   0.0    1.2  1  Lipoprotein_9    NLPA lipoprotein


Domain annotation for each model (and alignments):
>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.0   0.0   6.8e-41   4.1e-37       5     338 ..       7     325 ..       3     348 .. 0.90

  Alignments for each domain:
  == domain 1  score: 128.0 bits;  conditional E-value: 6.8e-41
                  TTTS----HHHHHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHH.HHHHHHHHCCCC-TTTSEEEEETTSHGGG CS
  Aminotran_5   5 saAttqkpqeVldalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtte.ainlvalslarslkpgdeivvteaehhan 101
                   +++t++p++V++a+              + h++ ++ + ++++ +k ++++++++  +i+ +s +++ a+++ ++++   +k+gd+i++ +++  + 
   EPA06723.1   7 LPGPTNVPNRVMRAMLAP----------IINHRSDDFVELYTDVVDKTQQVFQTKN--DIVALSASGTgAVEASVINI---VKKGDKIIIPVNGEFSG 89 
                  579999999999999888..........689************************7..77777766666*********...***************** PP

                  THHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH-..-TTEEEEEEESBETTTTE.B--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEE CS
  Aminotran_5 102 lvpwqelakrtgakvkvipldeegeldldelekll..nektklvaithvsnvtGt.iqpveeigklakkkgalvlvDaaqavghipidvkklgvDfla 196
                  +   +el +++ga+v++++  ++++ + d+++++   n+++k+ ++ h++++tGt ++ +++i +l  +++ +++vD+++ +g  ++ v+k+++D+ +
   EPA06723.1  90 R--LAELIEAQGAHVVKLQTPPGQNATFDQVKEAFdnNKDVKAFYVVHNETSTGTmVNYLDRISDLTSRNDSMYIVDSVSILGGVNLPVDKWNIDVCM 185
                  *..77777899************************65699********************************************************** PP

                  EETTT.TTSSTT-EEEEEEHHHHHTS..SS.STTSEEEEET.TEEE.EHCTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHH CS
  Aminotran_5 197 fsghK.llgPtGiGvlyvrkellekleplllggemveevsl.eett.faeapskfeaGTpnvagiiglgaaleyleeigleaiekhekelaeyllerl 291
                   +++K + +P+Gi+ ++v++++++ +    +++ +++  ++ +++   + +p+     Tp  + +++ ++al ++ e gle++ k++k  +++l++ l
   EPA06723.1 186 TGAQKaIAAPPGISPISVSPKAKKYMIANPPPTMYFNLARYfKYYEeSKHTPF-----TPALPLLYAYREALSIMLEEGLEHVFKRHKVCSDALYSSL 278
                  **************************666666776776666555541455666.....9*************************************** PP

                  CTSTTEEEES.-B-CTCBSEEEEEE.TTCSHHHHHHHHHHT.TEEEEEE CS
  Aminotran_5 292 kslpgvrlygpdkaerrasivsfnf.kgvhaedvatlLdee.gIavrsG 338
                  ++++ + +  +++++r+ si+++n+ +g++ + ++  L+++ ++ v +G
   EPA06723.1 279 SAIGLTPF--AKQEDRSISIIALNYlDGLEDKIFRDTLADKfKVLVAGG 325
                  ********..568999*******99899999999999999889988887 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.9   2.4e-08   0.00014      70     199 ..      55     191 ..      36     194 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.4e-08
                      EEEESSHHHHHHHHHHTTS-TTEEEEEE..STSSHHHHHHHHHTHHH.TTCEEEEESTTSHHHHHHHCCT..TEEEEEE...ESS-TTTT---- CS
  Cys_Met_Meta_PP  70 alavssGmaAiaaailallkaGdeivvs..ddlYggtqrllkkvlkk.lgievkfvdtsdleelekaike..ntklvyl...EtptnpllkvvD 155
                      + + +sG++A++a++++++k+Gd+i++    +  g   +l++    + +++++   + + ++++++a+++   +k++y+   Et t  +++ +D
       EPA06723.1  55 VALSASGTGAVEASVINIVKKGDKIIIPvnGEFSGRLAELIEAQGAHvVKLQTPPGQNATFDQVKEAFDNnkDVKAFYVvhnETSTGTMVNYLD 148
                      45679*******************9975113444445556655544435566666667899*******98445788887655888888887776 PP

                      HHHHHHHHHHTT-EEEEEGTTTHTTTS-GG.GGT-SEEEEETTTT CS
  Cys_Met_Meta_PP 156 iekiaklakkagvlvvvDntfaspllqrpl.klgaDivvhSaTKy 199
                        +i++l+  ++ + +vD + + + +  p+ k+++D+ +  a K 
       EPA06723.1 149 --RISDLTSRNDSMYIVDSVSILGGVNLPVdKWNIDVCMTGAQKA 191
                      ..9***************9876665555552799***99999885 PP

>> Lipoprotein_9  NLPA lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.6e-05     0.093      91     140 ..      70     121 ..      57     133 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.6e-05
                    GGG--TT-EEEEESSHHHHHHHHHHHHHTT..SSEE-TT-CTT--GGGEEE- CS
  Lipoprotein_9  91 lselkeGatiavpndpsnegRaLllLekag..LikLkdgkgllatvkdIteN 140
                    ++ +k+G++i++p +   +gR+  l+e++g  ++kL+++ g++at ++++e 
     EPA06723.1  70 INIVKKGDKIIIPVNGEFSGRLAELIEAQGahVVKLQTPPGQNATFDQVKEA 121
                    6668**********************99775589*************99973 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.51
# Mc/sec: 2243.33
//
Query:       EPA06724.1  [L=411]
Description: putative dGTPase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-17   63.5   0.2    4.5e-17   62.4   0.2    1.6  1  HD        HD domain
  ------ inclusion threshold ------
      0.023   14.2   0.0      0.043   13.3   0.0    1.4  1  HDOD      HDOD domain


Domain annotation for each model (and alignments):
>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.4   0.2     5e-21   4.5e-17       1     121 [.      54     173 ..      54     174 .. 0.84

  Alignments for each domain:
  == domain 1  score: 62.4 bits;  conditional E-value: 5e-21
                 HHHHHHHHHHHHHHHHHHHHH.....HHHHHHHHHHHHHTTTTHHHHTS..HHH.HHHCTCCHHHHHHHHHHHHHHHHHHHHH.....HHHHHHHHHTT CS
          HD   1 rleHsleVaklarrlaedlge.....eedrellllaaLlHDiGkgpfgdafekk.eeefekflaHekvgaeilrevekrlgld.....ledvaklireh 88 
                 r+eHsl+V+++a + ++ l+e      +d e+l+la+LlHDiG+gpf++ fe+  ++   k  +He++g ei+ ++e+ + l+      +++ k++   
  EPA06724.1  54 RFEHSLGVMHIASQAGQALNEkgiikSDDIEILRLAGLLHDIGHGPFSHLFEEViQQ---KKFSHEDFGKEIILKSEIGDSLSksgydKKLITKIAFGD 149
                 79**************************************************99644...4556************99997778877666666666666 PP

                 CCHHHHHHHHHHHHCCTSCHHHHHHHHHHHHHH CS
          HD  89 heswegkkrprglaerqlslearivklaDrlaa 121
                 ++           ++ ++++ a+ ++ +D+l +
  EPA06724.1 150 SKLQ---------YMNEIISGALSADMMDYLLR 173
                 6665.........45588888888888888876 PP

>> HDOD  HDOD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   4.8e-06     0.043      91     145 ..      50     110 ..      36     133 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.8e-06
                 -HHHHHHHHHHHHHHHHHHHHHT......T-S-HHHHHHHHHTTTHHHHHHHHHSHHHHHH CS
        HDOD  91 dlkklwehslavAlvarelaeel......gledpeeaflaGLLhdiGklvllsllpeelee 145
                   ++  ehsl v  +a +  ++l      +++d e + laGLLhdiG   + +l++e +++
  EPA06724.1  50 AQHTRFEHSLGVMHIASQAGQALnekgiiKSDDIEILRLAGLLHDIGHGPFSHLFEEVIQQ 110
                 55566688888888888877777666666777779****************9999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.51
# Mc/sec: 2419.53
//
Query:       EPA06725.1  [L=118]
Description: hypothetical protein BG20_I0044 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.049   14.0   0.0      0.077   13.4   0.0    1.4  1  Glyco_trans_1_2  Glycosyl transferases group 1
       0.18   11.7   0.0         15    5.5   0.0    2.3  2  DUF3081          Protein of unknown function (DUF3081)


Domain annotation for each model (and alignments):
>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   8.6e-06     0.077       8      48 ..      14      65 ..       9      93 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.6e-06
  Glyco_trans_1_2  8 sespnlrlfEaaacGafaltddaegleelftpgk............evilfed 48
                     + + ++++fE+a++G + lt++    +++f  g+             v + +d
       EPA06725.1 14 AGKSQMKMFEVAGFGMLTLTTKK-IDGKFFPVGEedfvavinspdgYVAILAD 65
                     56678****************54.44667766664444444444444444445 PP

>> DUF3081  Protein of unknown function (DUF3081)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0    0.0017        15      30      46 ..      51      67 ..      46      70 .. 0.86
   2 ?    3.9   0.0    0.0052        47       1      19 [.      77      95 ..      77     106 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0017
     DUF3081 30 eatedfDGYtvfLadkd 46
                 + +++DGY  +Ladkd
  EPA06725.1 51 AVINSPDGYVAILADKD 67
                56789*********986 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.0052
     DUF3081  1 ldvkklLsvfekvktkGek 19
                l+++++Ls++ k++++G +
  EPA06725.1 77 LEKNEALSIYKKLRESGIP 95
                578899**********965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.35s 00:00:00.94 Elapsed: 00:00:00.57
# Mc/sec: 624.80
//
Query:       EPA06726.1  [L=43]
Description: hypothetical protein BG20_I0027 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (43 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1771  (0.0987785); expected 358.6 (0.02)
Passed bias filter:                      720  (0.0401584); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 270.36
//
Query:       EPA06727.1  [L=122]
Description: hypothetical protein BG20_I0002 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.4e-09   35.3   0.2    1.1e-08   34.9   0.2    1.2  1  OB_aCoA_assoc   DUF35 OB-fold domain, acyl-CoA-associated
    1.2e-06   28.2   0.3    1.8e-06   27.7   0.3    1.2  1  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
    0.00014   21.5   3.2    0.00023   20.8   3.2    1.4  1  zinc_ribbon_2   zinc-ribbon domain
     0.0018   18.0   0.3     0.0022   17.7   0.3    1.1  1  TackOD1         Thaumarchaeal output domain 1
     0.0048   17.1   0.2     0.0073   16.5   0.2    1.3  1  PHF5            PHF5-like protein
     0.0089   16.0   0.3      0.014   15.4   0.3    1.3  1  DZR             Double zinc ribbon
  ------ inclusion threshold ------
       0.08   12.7   0.7         10    5.9   0.1    2.3  2  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal
       0.17   11.8   2.3        4.2    7.3   0.1    2.2  2  TFIIS_C         Transcription factor S-II (TFIIS)


Domain annotation for each model (and alignments):
>> OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.2   5.1e-12   1.1e-08       2      62 ..      46     108 ..      45     111 .. 0.86

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 5.1e-12
                    EEE-GG-EEEEEEEEEE-TTS-EEEEEEEEEEEE-TT....-EE-EEEEE.EES..TT-B-EE CS
  OB_aCoA_assoc   2 velsgrGtvysftvvhrappgfaeeaPyvvgvVeLde.gvrimarlvgvd.pdevriGmrVra 62 
                    v l g G + ++t++  ap gf++++Py+ +v +Ld+   ri + + g++ p+++ +G+r ++
     EPA06727.1  46 VVLDGVGSIATYTIITVAPAGFEKYTPYAFVVLQLDNtHLRISGFMAGIAtPADLPVGTRAKI 108
                    6789*********************************77788888888774556889999875 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.3   7.9e-10   1.8e-06       4      37 .]      11      44 ..       9      44 .. 0.95

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 7.9e-10
     DUF35_N  4 aaegrLvgqrCpdCGtvqfPPravCphCgsddle 37
                a++g+L+  +C++CG+++     +C +Cgs+ +e
  EPA06727.1 11 AKQGKLLTHKCTKCGHLHLSTAYYCLKCGSKGFE 44
                89****************************9987 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   3.2     1e-07   0.00023       1      22 [.      20      41 ..      20      42 .. 0.95

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1e-07
  zinc_ribbon_2  1 fCpnCGaelqdnakFCpyCGtp 22
                   +C++CG+ +  +a +C +CG++
     EPA06727.1 20 KCTKCGHLHLSTAYYCLKCGSK 41
                   8*******************87 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.3   9.9e-07    0.0022      72      99 ..      17      44 ..       2      48 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 9.9e-07
     TackOD1 72 rirlCpsCksghlnvrevCpkCkSidie 99
                 ++ C++C + hl+  ++C kC+S  +e
  EPA06727.1 17 LTHKCTKCGHLHLSTAYYCLKCGSKGFE 44
                5799********************8665 PP

>> PHF5  PHF5-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.2   3.3e-06    0.0073      51      77 ..      13      40 ..       3      55 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.3e-06
        PHF5 51 fgkl.eekciicgskgvsdayyclecvr 77
                +gkl ++kc  cg+   s+ayycl+c  
  EPA06727.1 13 QGKLlTHKCTKCGHLHLSTAYYCLKCGS 40
                4554479*******************75 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.3   6.2e-06     0.014       1      21 [.      21      41 ..       9      50 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 6.2e-06
         DZR  1 CpqCgeelppdarfCseCgtk 21
                C +Cg+ + + a +C +Cg+k
  EPA06727.1 21 CTKCGHLHLSTAYYCLKCGSK 41
                999999999999999999986 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0    0.0077        17      38      53 ..      12      27 ..       7      28 .. 0.81
   2 ?    5.9   0.1    0.0046        10      43      53 ..      31      41 ..      29      42 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0077
  zinc_ribbon_10 38 eeleevkyrCpkCgal 53
                    ++ + ++ +C kCg+l
      EPA06727.1 12 KQGKLLTHKCTKCGHL 27
                    56677899******97 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0046
  zinc_ribbon_10 43 vkyrCpkCgal 53
                    + y+C kCg++
      EPA06727.1 31 TAYYCLKCGSK 41
                    68*******86 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.1    0.0019       4.2      27      36 ..      17      26 ..      11      28 .. 0.79
   2 ?    4.2   0.2     0.018        39      27      36 ..      31      40 ..      29      41 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0019
     TFIIS_C 27 vfykCtkCgh 36
                + +kCtkCgh
  EPA06727.1 17 LTHKCTKCGH 26
                6689999998 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.018
     TFIIS_C 27 vfykCtkCgh 36
                + y C+kCg 
  EPA06727.1 31 TAYYCLKCGS 40
                6799****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.51
# Mc/sec: 720.99
//
Query:       EPA06728.1  [L=293]
Description: kinase, PfkB family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-24   86.6   0.1    3.1e-24   85.8   0.1    1.3  1  PfkB          pfkB family carbohydrate kinase
    3.6e-05   23.3   0.0    6.7e-05   22.4   0.0    1.4  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase
     0.0021   17.6   0.4       0.81    9.1   0.1    2.5  3  Carb_kinase   Carbohydrate kinase
  ------ inclusion threshold ------
      0.081   12.5   0.0       0.16   11.6   0.0    1.4  1  OstA_2        OstA-like protein


Domain annotation for each model (and alignments):
>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.8   0.1     7e-28   3.1e-24       5     295 ..       3     273 ..       1     279 [. 0.85

  Alignments for each domain:
  == domain 1  score: 85.8 bits;  conditional E-value: 7e-28
                 EEEEEEEEEEEEECSSHTTSEEEESEEEEEEESHHHHHHHHHHHTT-EEEEEEEEESSHHHHHHHHHHHHTTEEETTEEEESSSEEEEEEEEETTT..S CS
        PfkB   5 vviGealidliavseklegelvevktveksaGGagaNvAvalarlgadvafigavGdDnfGeflleelkkegvdtdyvkidedtrtglalivvded..g 101
                  v+G++  d i++ +k         t++   GGa+   A + a+  +d+ +i +vG+D+  +++ + l+k  +d +++ i+e+ +t  +    d++   
  EPA06728.1   3 TVFGSTALDTIRTPKK---------TLKDVLGGAA-TFAAISASNFVDTGLIAVVGKDF-PKEYHQILSKY-LDLKGLTIKEG-KTFRYDGSYDKTlsT 88 
                 5677777777777655.........7777788887.888888888899***********.77777666554.88899998888.666666666666555 PP

                 EEEEEEEEGGGGGHHHHHHHHHHHHHGCTSEEEEESEECTTSHHHHHHHHHHHHHHTTEEEEEECESSSHHHHHHHHHHHCTESEEEEEHHHHHHHHTS CS
        PfkB 102 ertivfnrgaaadltkeeleededlleeadllyisgllsselpeavleelaeaaknggtfdpnlldplgaqfkeallellaladllkpneeElealtge 200
                 + t+ + ++  ad++++    + ++ ++++++y++   +++ ++a+ +e  +++ ++   +  + +++     e + +++  +d++  n+eE++ lt+e
  EPA06728.1  89 RETLKTELNVLADFKPT----VPEEYKKSQFVYLAN-NDPDQNSALIKEFDKVKFSMCDTIEFWISTKR----ESVIKMIKAVDAVVINDEEAKLLTKE 178
                 67788888888888885....78999*********9.88888999999999999999976666666666....78999999****************** PP

                 CTHSHHHHHHHHHHHHHTTSSEEEEEEGGGEEEEEETTEEEEEEE.SSSS-SBGTTHHHHHHHHHHHHHHT.....THHHHHHHHHHHHHHHHHHTSSS CS
        PfkB 201 kledieealaalhklkakgaktvvvtlGkeGalvvekdgelkvpavpkvkvvDttGAGDsfvggflaalle.....gksleealrfanavAalvvqkkg 294
                       +++++++k+ + gak v++++G+ G+l +  d  +++  +  ++vvD+tGAGDsf+g+++  l++     ++++++a+ ++n +++++v+k+g
  EPA06728.1 179 F-----NLIKCAKKIMEWGAKYVIIKKGEHGSLMFFDDVIFPCVGFSLEDVVDPTGAGDSFAGAMIGYLASknsinSAEIKKAVVYGNVLGSFAVEKYG 272
                 *.....788888888889*******************************************************************************99 PP

                 S CS
        PfkB 295 a 295
                  
  EPA06728.1 273 L 273
                 6 PP

>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   1.5e-08   6.7e-05     113     225 ..     156     257 ..     146     269 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.5e-08
                   HHHTGGG-SEEE-BHHHHHHHHT---SSHHHHHHHHHHHHHTT-SEEEEEEGGS-SSSEEEEEEEETSSEEEEEEEE----S--BTHHHHHHHHHHH CS
  Phos_pyr_kin 113 keeLlplatvitPNlpEaeaLlgekikteedmkeaakkllklgakaVlikGghlegeeavvtdvlydgeeveeleaerietknthGtGCtlssaiaa 209
                     ++++ ++ ++ N +Ea+ L++     e ++ ++akk+++ gak+V+ik g++ g+   + dv++   +   ++ e +   +  G+G++++ a+ +
    EPA06728.1 156 I-KMIKAVDAVVINDEEAKLLTK-----EFNLIKCAKKIMEWGAKYVIIKKGEH-GSLMFFDDVIFPCVG---FSLEDVV--DPTGAGDSFAGAMIG 240
                   3.4899999999*******9998.....7799*****************77653.455666677775443...4444444..678************ PP

                   HHHCTSSHHHH.HHHHH CS
  Phos_pyr_kin 210 elakgesleeA.vkkAk 225
                   +la ++s++ A +kkA 
    EPA06728.1 241 YLASKNSINSAeIKKAV 257
                   *******9998566665 PP

>> Carb_kinase  Carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0   0.0    0.0016         7      11      33 ..      25      48 ..      21      74 .. 0.84
   2 ?   -2.2   0.0      0.51   2.3e+03      42      73 ..     137     167 ..     129     170 .. 0.69
   3 !    9.1   0.1   0.00018      0.81     145     221 ..     183     262 ..     157     284 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0016
                 HHHHHHHHHHHHCTT.-SEEEEEE CS
  Carb_kinase 11 tGAallaalaalrlg.aglvsvat 33
                  GAa +aa++a++++  gl+ v+ 
   EPA06728.1 25 GGAATFAAISASNFVdTGLIAVVG 48
                 69************999***9986 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.51
                  CTTTTTCEECCTTHTTTS...--SSS-SEEEE CS
  Carb_kinase  42 ksylpevivhplledeqakileklerldavvi 73 
                  k+ + + i  +++ +++ ++++  +++davvi
   EPA06728.1 137 KFSMCDTIEFWIS-TKRESVIKMIKAVDAVVI 167
                  5555556666666.455578899999999998 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.00018
                  HHHHHHHH.HHTTEEEEESTTSEEEECTTEEEEE----GGG-S...TTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHHHHH CS
  Carb_kinase 145 elarelaq.klnavvllkgekdvivspegevlinstgssalak...GGsGDvLaGligalLaqneasyeaaiaaawlhgaa 221
                  ++a+++ +   + v++ kge+  ++   ++v+    g s+  +    G GD  aG++ + La++++   a i  a++ g+ 
   EPA06728.1 183 KCAKKIMEwGAKYVIIKKGEHGSLMFF-DDVIFPCVGFSLEDVvdpTGAGDSFAGAMIGYLASKNSINSAEIKKAVVYGNV 262
                  555555541345566666666666553.33333334444332212279*****************9999999998887764 PP

>> OstA_2  OstA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   3.5e-05      0.16      47     103 ..     125     180 ..     112     194 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.5e-05
      OstA_2  47 eeeNsleAFgnVrleQgDTlsltgdrleYdGntklaelrknvrledrektLtTdsld 103
                 +++  ++ F++V++   DT+     +   +  +k++++ + v+++d+e+ L T++ +
  EPA06728.1 125 QNSALIKEFDKVKFSMCDTIEFWISTK-RESVIKMIKAVDAVVINDEEAKLLTKEFN 180
                 567789**************9887664.5789*********************9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1793.61
//
Query:       EPA06729.1  [L=395]
Description: efflux ABC transporter, permease protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.8e-19   68.6   2.0    1.5e-18   67.9   2.0    1.3  1  MacB_PCD  MacB-like periplasmic core domain
    3.2e-14   53.2   1.8    3.2e-14   53.2   1.8    2.2  2  FtsX      FtsX-like permease family


Domain annotation for each model (and alignments):
>> MacB_PCD  MacB-like periplasmic core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.9   2.0   1.7e-22   1.5e-18       4     189 ..      22     231 ..      18     234 .. 0.72

  Alignments for each domain:
  == domain 1  score: 67.9 bits;  conditional E-value: 1.7e-22
    MacB_PCD   4 tvLGiaiGvaaviaivslgeglqasvlsqisdlgnlvtvtpgk.gsgeslsdpdveal.rrevp.veavapvv.......tvrgggsg....eeevtvv 88 
                 +vL+++iG+ ++ + +++ +gl +++ ++isd  n +++ +++ ++ +  ++++v+ + + ++p vea++p++        +++   g     + + +v
  EPA06729.1  22 AVLAVTIGILVIHVNFVIFQGLFDAIVRDISDYRNGNVLVTDEeNFITKSDQSLVK-WfE-RIPyVEAATPRLssstsinMTKF---GtlheKTRIPIV 115
                 89*****************************9965333333323444443334442.223.58********9865533321133...133332347799 PP

    MacB_PCD  89 gvdpdyfkvfglklaeGrffteadlrggpnvvvigeelaerlf..pvGdtirl...........kpftVvGvledppgsgsalgddavylplttl.... 170
                 gvdp + +++  ++    + t+ +   ++n++v+g+++a++l    vGd+++l           ++f V+G++++p g+g    d +v++ + tl    
  EPA06729.1 116 GVDP-LRDIRTSTV--SETVTDGQYVYARNSIVLGSNVARDLGgaQVGDSLKLkivdrygqdqiRRFVVTGIAKSPGGQG---FDYSVVVHIDTLrdmm 208
                 9995.444433322..334777777789*************99*99**************999999******97663444...3788***977764445 PP

    MacB_PCD 171 ....qrrsitvrlkdgadleaaa 189
                     +++si+v+lkd++ +++++
  EPA06729.1 209 nrhgESSSIMVKLKDPTKATDVK 231
                 55444555**********99987 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1      0.22     2e+03      31      45 ..      20      34 ..      16      64 .. 0.59
   2 !   53.2   1.8   3.5e-18   3.2e-14       2      94 ..     294     386 ..     293     388 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.22
        FtsX 31 valviGlglgllaaq 45
                +++v+++ +g+l++ 
  EPA06729.1 20 IGAVLAVTIGILVIH 34
                333333333333333 PP

  == domain 2  score: 53.2 bits;  conditional E-value: 3.5e-18
        FtsX   2 reigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfsselkisidlitvliiivlllllallagllsiskilkk 94 
                 reigi+r++G+++k++l +++ ++++i+++++ +G+++gl ++ +      s+ +s  l +s +++ ++ ++vl+++la++a+l+++++++k 
  EPA06729.1 294 REIGIMRSIGATRKDILVIFIFQGMIIGAIGAGVGTAAGLGYTFYAKETKMSFNNSLPLEVSYNWEKIVQTAVLSFILAIIASLYPSYRATKL 386
                 9**********************************88888887776666666666799********************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       741  (0.0413297); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 2311.46
//
Query:       EPA06730.1  [L=127]
Description: ribbon-helix-helix protein, CopG family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-11   44.2   2.3    2.5e-11   43.5   2.3    1.4  1  NikR_C          NikR C terminal nickel binding domain
    1.6e-06   27.8   0.1    2.7e-06   27.1   0.1    1.3  1  RHH_1           Ribbon-helix-helix protein, copG family
     0.0039   17.1   0.0     0.0067   16.3   0.0    1.3  1  VapB_antitoxin  Bacterial antitoxin of type II TA system, Vap
  ------ inclusion threshold ------
      0.056   13.5   0.1      0.077   13.0   0.1    1.2  1  DUF1327         Protein of unknown function (DUF1327)


Domain annotation for each model (and alignments):
>> NikR_C  NikR C terminal nickel binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.5   2.3   5.7e-15   2.5e-11      11      76 ..      61     126 ..      54     127 .] 0.92

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 5.7e-15
                 TSTTHHHHHHHHHHHHSSEEEEEEEEEESSSEEEEEEEEEE-HHHHHHHHHHHHTSTTEEEEEEEE CS
      NikR_C  11 hqrelserltdiqheyhdliisslhvhldhdncLevivlkGeaeeikelaeklralkgVkhvkltl 76 
                 h  e ++ ++ i+h+++dli++ lh  ++ ++c+e++v++G+ae+++++++ +   k + +vkl++
  EPA06730.1  61 HNDEFDHVVSGIKHNFEDLITTHLHSKIEGEKCMELFVIDGDAERVSTITKDFQVNKNMDTVKLVT 126
                 4458888999******************************************************97 PP

>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.1     6e-10   2.7e-06       2      37 ..       4      40 ..       4      42 .. 0.95

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 6e-10
                EEEEEEHHHHHHHHHHHHHHT.SSHHHHHHHHHHHHH CS
       RHH_1  2 vsirldeellerLdelarrrg.rSrSelIReAlreyl 37
                vsi+l +e+l +Ld+l + +g + rSe+IR+ +r ++
  EPA06730.1  4 VSISLNQEILSELDKLQKSMGfSGRSEAIRAGIRTFV 40
                8******************************999775 PP

>> VapB_antitoxin  Bacterial antitoxin of type II TA system, VapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.5e-06    0.0067      16      44 ..      20      49 ..      14      51 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.5e-06
                    XXXXXXXXXXXXXXXXXXX-------H.H. CS
  VapB_antitoxin 16 irltglktKrEaVnlALreLiqrrkre.el 44
                    ++ +g ++++Ea++ ++r+++ ++k++ el
      EPA06730.1 20 QKSMGFSGRSEAIRAGIRTFVSEEKQKsEL 49
                    678999*******************99555 PP

>> DUF1327  Protein of unknown function (DUF1327)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   1.7e-05     0.077       4      58 ..      64     119 ..      61     127 .] 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.7e-05
     DUF1327   4 kyelvvkGvr.nyedkvtvtvaleikerfdlllfdvavaldrveGaalefyeaeak 58 
                 +++ vv G++ n+ed +t  +  +i++   ++lf ++   +rv   + +f   +  
  EPA06730.1  64 EFDHVVSGIKhNFEDLITTHLHSKIEGEKCMELFVIDGDAERVSTITKDFQVNKNM 119
                 7899*****669*******************************9999998766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 888.38
//
Query:       EPA06731.1  [L=116]
Description: hypothetical protein BG20_I0098 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0056   16.7   0.0     0.0085   16.1   0.0    1.3  1  FeoC      FeoC like transcriptional regulator
     0.0079   16.0   0.5     0.0096   15.8   0.5    1.0  1  IPPT      IPP transferase
  ------ inclusion threshold ------
      0.039   13.9   3.6       0.12   12.3   3.5    2.0  1  HTH_45    Winged helix-turn-helix
      0.088   13.0   0.8       0.65   10.3   0.1    2.0  2  Rio2_N    Rio2, N-terminal
        0.1   12.5   0.0       0.21   11.5   0.0    1.6  1  MarR      MarR family


Domain annotation for each model (and alignments):
>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   2.4e-06    0.0085       3      57 ..      15      69 ..      13      79 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.4e-06
        FeoC  3 telkeyleergrvslkeLsrhfkaspealeamLeqwvrkGrvekvaataccsgsC 57
                t ++++   ++ +s+ +Ls++ k++ + l   ++++++kG +++   ++ ++  C
  EPA06731.1 15 TIIQKFTTYKNWISFMQLSIEAKIEHQNLTNYIDVLIKKGIINEYRGKNKSRLFC 69
                667888888999****************************999888777766666 PP

>> IPPT  IPP transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.5   2.7e-06    0.0096     122     206 ..      11     101 ..       3     107 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.7e-06
                 HHHHHHHHHHHHHSS-HH...ECEEEEEECSHHHHHHHHHHHHHHHHHTTHHHHHHHHHH......C.CCCSTTSHHHHHHHTTS..S-HHHHHHHH CS
        IPPT 122 qRiiRalevyeetgkpls...ellviglesdreelyeridkRvdemleaGlleEveklla......k.alqaigykelleylege..lsleeaiekl 206
                 +Rii  ++ +    ++++   +++++ +  + ++ ++++++++d ++++G+++E +   +      + +   i+y+e +++l+++  ls eea ++l
  EPA06731.1  11 KRIITIIQKF----TTYKnwiSFMQLSI--EAKIEHQNLTNYIDVLIKKGIINEYRGKNKsrlfcmNgYHDDIEYNEKFRMLTQKnlLSKEEAYNEL 101
                 4444444443....33441113344444..99999********************997766666554458899999999999864224677776655 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   3.5   3.4e-05      0.12      24      52 ..      31      64 ..       7     103 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.4e-05
      HTH_45 24 kimykanLsykllnkYLdmLvekgli.....kks 52
                ++  +a ++ ++l +Y+d L++kg+i     k++
  EPA06731.1 31 QLSIEAKIEHQNLTNYIDVLIKKGIIneyrgKNK 64
                677899********************65554444 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00018      0.65      10      56 ..      12      58 ..       5      75 .. 0.85
   2 ?    1.8   0.1     0.079   2.8e+02      41      60 ..      79      98 ..      66     113 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00018
      Rio2_N 10 rvLtavEmgmrnhevVptelieeisrlkeeevkkrlsrllkaklisr 56
                r++t +       +++++ +++  ++++++++++ ++ l+k+++i+ 
  EPA06731.1 12 RIITIIQKFTTYKNWISFMQLSIEAKIEHQNLTNYIDVLIKKGIINE 58
                78888888888899******************************987 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.079
      Rio2_N 41 vkkrlsrllkaklisrktak 60
                 +++ + l +++l+s+++a 
  EPA06731.1 79 YNEKFRMLTQKNLLSKEEAY 98
                55666777777777776543 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   5.9e-05      0.21      19      52 ..      28      61 ..      11      66 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.9e-05
                EHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE CS
        MarR 19 svseLakklgvskstvtrvldrLekkGlieRsks 52
                s  +L    +++  ++t+ +d L+kkG i+ ++ 
  EPA06731.1 28 SFMQLSIEAKIEHQNLTNYIDVLIKKGIINEYRG 61
                5558889999*******************98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       875  (0.0488036); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 955.17
//
Query:       EPA06732.1  [L=160]
Description: hypothetical protein BG20_I0066 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       984  (0.0548832); expected 358.6 (0.02)
Passed bias filter:                      596  (0.0332422); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1219.16
//
Query:       EPA06733.1  [L=281]
Description: hypothetical protein BG20_I0012 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1891.42
//
Query:       EPA06734.1  [L=51]
Description: hypothetical protein BG20_I0088 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      190  (0.0105974); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.31s 00:00:00.73 Elapsed: 00:00:00.48
# Mc/sec: 320.17
//
Query:       EPA06735.1  [L=266]
Description: hydrolase, carbon-nitrogen family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.6e-50  171.2   0.0    3.2e-50  170.9   0.0    1.0  1  CN_hydrolase  Carbon-nitrogen hydrolase


Domain annotation for each model (and alignments):
>> CN_hydrolase  Carbon-nitrogen hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.9   0.0   1.8e-54   3.2e-50      19     260 ..      17     247 ..       8     248 .. 0.95

  Alignments for each domain:
  == domain 1  score: 170.9 bits;  conditional E-value: 1.8e-54
                   HHHHHHHHHHHHTTESEEEEETTTTTBS...SSHHHHHHHHBHSSSHHHHHHHHHHHHHTEEEEEEEEEEECCTTEEEEEEEEEEEETTSEEEEEEE CS
  CN_hydrolase  19 qklleliaeAarkgadLivlPElfitgy...keeahfleaAeaglgetlallaalarkngiavvigliereltngklqayntavlldldgklvgkyr 112
                   +k+ ++i++Aa+ +a L+++PE+  +     + +++   +Ae+++g+++  + + a++n i vv+ + e+  +++++  y t +++d++gk+++ yr
    EPA06735.1  17 KKIINYITKAAEGKATLVAFPEFMMFYTnssQTSNQLANLAETIQGNFVSTIGNTAKENHIQVVGSFYEKSPKKNRV--YDTSFVIDKSGKVISTYR 111
                   68999*******************985588877888888888****************************8888888..****************** PP

                   -SS--EECTTSCECCGHHTSCS-SS.S-EEEETTEEEEEEEGGGGGSHHHHHHHHHTT-SEEEEBH.GCCCTCHHHHHHHHHHHHHHHHHHTSEEEE CS
  CN_hydrolase 113 KlhLfpgeprpptaverelfepgdg.ipvfdtpvgkiGaaiCyeigfpellralalkgaeilvnlserapvpksmgppqwellgraralengcfvia 208
                   K+hL    ++  ++ e+  + +g +  ++++t++gkiG++iCy+ +fpe +r la  g eil++   +a+v +++ +++w ++ ++ra+engc+via
    EPA06735.1 112 KIHL----YDALGFKESNKMVKGSKiAKPVKTSLGKIGMMICYDLRFPEMSRSLAVAGSEILIA--PSAWVKGNLKEEHWITINKTRAIENGCYVIA 202
                   ***8....789***************9999**********************************..77***************************** PP

                   EEBEEEHCETTEEEE--EEEE-TTS-EEEECCSSSTEEEEEEEEHHHHHHHH CS
  CN_hydrolase 209 anqvggyeqlilwpvghSaiidpdGrilaglgeeeegvliaeidladvratr 260
                     qvg+       ++g S ++dp Gril +  +++ g+ ++ idl+ ++++r
    EPA06735.1 203 PDQVGN------IYCGRSIVVDPYGRILLDMKKKQ-GIGYVNIDLENIKKIR 247
                   ******......****************9999999.9**********99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       791  (0.0441185); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 1532.95
//
Query:       EPA06736.1  [L=61]
Description: zinc finger, C2H2 type [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-06   28.7   4.1     0.0056   17.1   0.4    2.2  2  zf-C2H2          Zinc finger, C2H2 type
      4e-06   27.2   6.2      0.031   15.1   0.3    2.1  2  zf-C2H2_4        C2H2-type zinc finger
     0.0004   19.8   0.5       0.12   11.9   0.0    2.2  2  TF_Zn_Ribbon     TFIIB zinc-binding
     0.0033   16.8   0.9       0.35   10.3   0.1    2.3  2  zf-ribbon_3      zinc-ribbon domain
     0.0072   17.0   5.0     0.0079   16.9   5.0    1.1  1  zinc_ribbon_15   zinc-ribbon family
  ------ inclusion threshold ------
      0.017   14.9   2.1          1    9.2   0.1    2.3  2  zf-C2H2_11       zinc-finger C2H2-type
       0.03   14.3   4.1        1.2    9.1   0.3    2.3  2  zinc_ribbon_4    zinc-ribbon domain
      0.032   14.2   5.4      0.048   13.7   5.4    1.4  1  DZR              Double zinc ribbon
      0.037   14.1   4.4      0.037   14.1   4.4    2.1  2  Zn-ribbon_8      Zinc ribbon domain
      0.037   13.5   3.0       0.29   10.6   0.3    2.2  2  DUF2688          Protein of unknown function (DUF2688)
      0.055   13.5   4.9       0.38   10.8   0.6    2.3  2  XPA_N            XPA protein N-terminal
      0.059   13.3   2.8        1.5    8.7   0.2    2.2  2  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
      0.061   13.2   5.5        1.9    8.4   5.5    2.2  2  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
       0.11   12.5   3.2        0.7    9.9   3.1    2.1  1  ADK_lid          Adenylate kinase, active site lid
       0.11   12.6   6.4       0.39   10.9   1.7    2.1  2  FYVE             FYVE zinc finger
       0.15   12.5   1.9        4.3    7.8   0.3    2.1  2  DUF983           Protein of unknown function (DUF983)
       0.17   11.5   4.4        4.2    7.0   0.3    2.3  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
       0.26   11.1   7.1       0.41   10.4   1.4    2.1  2  Ephrin_rec_like  Putative ephrin-receptor like
       0.54   10.4   0.4       0.54   10.4   0.4    3.1  4  zf-ACC           Acetyl-coA carboxylase zinc finger domain
       0.96    9.4   4.7         12    5.9   0.4    2.3  2  Fer4             4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.4   6.3e-06    0.0056       2      23 .]      11      33 ..      10      33 .. 0.95
   2 !   13.3   0.3   9.5e-05     0.085       2      21 ..      39      58 ..      39      59 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6.3e-06
                EETTTTEEESSHHHHHHHHHC.C CS
     zf-C2H2  2 kCpdCgksFkrksnLkrHirt.H 23
                kC++Cg + ++++ +k+H+ + H
  EPA06736.1 11 KCKKCGTVLTDPERMKKHQEVaH 33
                8******************9888 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 9.5e-05
                EETTTTEEESSHHHHHHHHH CS
     zf-C2H2  2 kCpdCgksFkrksnLkrHir 21
                kC  Cg  F ++++L++H +
  EPA06736.1 39 KCRACGSEFDTSEELRKHKK 58
                799***************75 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.3   3.5e-05     0.031       2      24 .]      11      33 ..      10      33 .. 0.91
   2 !   15.1   1.2   3.5e-05     0.031       2      21 ..      39      58 ..      39      61 .] 0.93

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.5e-05
   zf-C2H2_4  2 kCpiCgksFsskkaLlrHlkthH 24
                kC+ Cg++ ++++++++H +  H
  EPA06736.1 11 KCKKCGTVLTDPERMKKHQEVAH 33
                8*****************98766 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 3.5e-05
   zf-C2H2_4  2 kCpiCgksFsskkaLlrHlk 21
                kC+ Cg  F ++++L++H k
  EPA06736.1 39 KCRACGSEFDTSEELRKHKK 58
                7*****************87 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   0.00013      0.12      20      33 ..      10      23 ..       6      32 .. 0.75
   2 !    6.7   0.1    0.0056         5       2      12 ..      39      49 ..      38      54 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00013
                  EEESSSSBEEEECC CS
  TF_Zn_Ribbon 20 lvCtdCGlVledns 33
                  + C++CG+Vl d  
    EPA06736.1 10 TKCKKCGTVLTDPE 23
                  56999999988764 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0056
                  EETTTTCEECH CS
  TF_Zn_Ribbon  2 kCPnCgstnlv 12
                  kC  Cgs++++
    EPA06736.1 39 KCRACGSEFDT 49
                  8******8743 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.1   0.00039      0.35      17      26 .]      10      19 ..       6      19 .. 0.87
   2 ?    5.1   0.1     0.018        16      18      25 ..      39      46 ..      36      50 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00039
  zf-ribbon_3 17 nvCpyCGtkl 26
                 ++C++CGt+l
   EPA06736.1 10 TKCKKCGTVL 19
                 89*****997 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.018
  zf-ribbon_3 18 vCpyCGtk 25
                 +C  CG++
   EPA06736.1 39 KCRACGSE 46
                 68888875 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   5.0   8.8e-06    0.0079      37      78 ..       9      50 ..       3      60 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 8.8e-06
  zinc_ribbon_15 37 ylacskCkslleaskelgkeiekkessekkeCknCgkeveee 78
                      +c+kC+++l++ ++++k+ e +++++k++C+ Cg+e + +
      EPA06736.1  9 ETKCKKCGTVLTDPERMKKHQEVAHNKKKEKCRACGSEFDTS 50
                    579************9999999999999********998765 PP

>> zf-C2H2_11  zinc-finger C2H2-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.2     0.015        13       6      28 ..      11      33 ..       9      34 .. 0.79
   2 ?    9.2   0.1    0.0011         1       6      23 ..      39      56 ..      34      58 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.015
  zf-C2H2_11  6 qCleCGlcftSqlsLsRHlfIvH 28
                +C +CG   t     ++H  + H
  EPA06736.1 11 KCKKCGTVLTDPERMKKHQEVAH 33
                8*****98888877788877766 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0011
  zf-C2H2_11  6 qCleCGlcftSqlsLsRH 23
                +C+ CG  f  +  L++H
  EPA06736.1 39 KCRACGSEFDTSEELRKH 56
                8********999999999 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.3    0.0014       1.2      25      34 ..       9      18 ..       4      20 .. 0.80
   2 ?    6.9   0.4    0.0066       5.9      19      35 ..      31      47 ..      26      58 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0014
  zinc_ribbon_4 25 kvrCskCghv 34
                   + +C+kCg+v
     EPA06736.1  9 ETKCKKCGTV 18
                   569*****98 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0066
  zinc_ribbon_4 19 lpakgvkvrCskCghvF 35
                   ++ +++k +C +Cg  F
     EPA06736.1 31 VAHNKKKEKCRACGSEF 47
                   56677788899998766 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   5.4   5.4e-05     0.048      14      42 ..      11      51 ..       6      61 .] 0.88

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.4e-05
         DZR 14 fCseCgtklkavaa............edrCpsCgekvdpea 42
                 C++Cgt l  +++            +++C +Cg++ d  +
  EPA06736.1 11 KCKKCGTVLTDPERmkkhqevahnkkKEKCRACGSEFDTSE 51
                6********9888899******************9988765 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   4.4   4.1e-05     0.037       7      35 ..      11      46 ..       8      50 .. 0.82
   2 ?    9.7   2.1     0.001       0.9       7      20 ..      39      55 ..      37      61 .] 0.66

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.1e-05
  Zn-ribbon_8  7 rCeeCghefe......vlqsisdaplta.CPeCgse 35
                 +C++Cg++ +      + q+++ +++++ C +Cgse
   EPA06736.1 11 KCKKCGTVLTdpermkKHQEVAHNKKKEkCRACGSE 46
                 8*********9998888888884455555*****96 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.001
  Zn-ribbon_8  7 rCeeCghefe...vlqs 20
                 +C++Cg+ef+   +l++
   EPA06736.1 39 KCRACGSEFDtseELRK 55
                 7*********4443333 PP

>> DUF2688  Protein of unknown function (DUF2688)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.3   0.00032      0.29       6      19 ..       8      21 ..       6      27 .. 0.83
   2 ?    3.5   0.2     0.055        49       9      19 ..      39      49 ..      36      55 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00032
     DUF2688  6 VtTqCrRCGkslst 19
                + T+C++CG+ l  
  EPA06736.1  8 IETKCKKCGTVLTD 21
                579*******9875 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.055
     DUF2688  9 qCrRCGkslst 19
                +Cr CG    t
  EPA06736.1 39 KCRACGSEFDT 49
                7*****87765 PP

>> XPA_N  XPA protein N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.3     0.036        32       2      12 ..      10      20 ..       9      21 .. 0.77
   2 ?   10.8   0.6   0.00042      0.38       2      14 ..      38      50 ..      37      55 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.036
       XPA_N  2 pkCdeCgkefl 12
                +kC++Cg  + 
  EPA06736.1 10 TKCKKCGTVLT 20
                69****97665 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00042
       XPA_N  2 pkCdeCgkefldS 14
                +kC  Cg+ef++S
  EPA06736.1 38 EKCRACGSEFDTS 50
                79*********98 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.2    0.0017       1.5      12      20 ..      10      18 ..      10      24 .. 0.88
   2 ?    5.0   0.2     0.025        23      13      19 ..      39      45 ..      37      47 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0017
     DUF35_N 12 qrCpdCGtv 20
                ++C++CGtv
  EPA06736.1 10 TKCKKCGTV 18
                69******9 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.025
     DUF35_N 13 rCpdCGt 19
                +C++CG+
  EPA06736.1 39 KCRACGS 45
                7999986 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.2      0.11        94       4       8 ..      12      16 ..       6      22 .. 0.68
   2 ?    8.4   5.5    0.0022       1.9      16      35 ..      36      51 ..      11      52 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.11
                    ESTTT CS
  RNA_POL_M_15KD  4 CpkCg 8 
                    C kCg
      EPA06736.1 12 CKKCG 16
                    55555 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0022
                    CSCCCEEEESSSS-EEESSC CS
  RNA_POL_M_15KD 16 dkegknfeCrqCgYeepadq 35
                    +ke+    Cr Cg+e+ +++
      EPA06736.1 36 KKEK----CRACGSEFDTSE 51
                    3333....********9987 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   3.1   0.00079       0.7       4      30 ..      12      46 ..      10      49 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00079
                -TTT--EE........ETTTB--SSTTB-TTT--. CS
     ADK_lid  4 CpkCGrsY........hvvfnpPkveglCDkCGep 30
                C+kCG++         h + +  k++ +C  CG++
  EPA06736.1 12 CKKCGTVLtdpermkkHQEVAHNKKKEKCRACGSE 46
                ********9999999885568889*********98 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   4.3     0.013        11      27      59 ..      11      43 ..       7      43 .. 0.70
   2 ?   10.9   1.7   0.00044      0.39       5      26 ..      33      56 ..      29      61 .] 0.66

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.013
                E-TTT--EE-STTS-EEE.EEGGGTEEEEEEE- CS
        FYVE 27 hCrlCGkvvCekCssklvallekeaeeksvrvC 59
                 C+ CG v+ +    k+ + + ++++++++r C
  EPA06736.1 11 KCKKCGTVLTDPERMKKHQEVAHNKKKEKCRAC 43
                588999998877666666666666777777766 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00044
                ...--SB-TTT--B--SS..S--E CS
        FYVE  5 ddsevkkCeiCakkFsll..rrrh 26
                ++++ +kC++C ++F ++   r+h
  EPA06736.1 33 HNKKKEKCRACGSEFDTSeeLRKH 56
                567889999999999655434444 PP

>> DUF983  Protein of unknown function (DUF983)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1     0.053        47       7      19 ..       8      20 ..       6      25 .. 0.82
   2 ?    7.8   0.3    0.0048       4.3       7      21 ..      36      50 ..      32      53 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.053
      DUF983  7 vadaCeaCgldls 19
                ++ +C++Cg+ l+
  EPA06736.1  8 IETKCKKCGTVLT 20
                6789*****8765 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0048
      DUF983  7 vadaCeaCgldlsha 21
                 +++C+aCg +++  
  EPA06736.1 36 KKEKCRACGSEFDTS 50
                689********9875 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.3    0.0047       4.2       4      17 ..      11      24 ..       9      29 .. 0.82
   2 ?    6.3   0.5    0.0081       7.3       4      20 ..      39      56 ..      36      57 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0047
      zf_UBZ  4 lCerCgkeipesel 17
                 C++Cg+ + ++e+
  EPA06736.1 11 KCKKCGTVLTDPER 24
                6******9999965 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0081
      zf_UBZ  4 lCerCgkeipes.elqEH 20
                 C  Cg+e+ +s el  H
  EPA06736.1 39 KCRACGSEFDTSeELRKH 56
                7**********9777666 PP

>> Ephrin_rec_like  Putative ephrin-receptor like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.4     0.033        29      26      39 ..      10      23 ..       5      31 .. 0.75
   2 ?   10.4   1.4   0.00046      0.41      22      48 .]      34      60 ..      27      60 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.033
  Ephrin_rec_like 26 lsClaCPlgtttkk 39
                     ++C++C++  t+ +
       EPA06736.1 10 TKCKKCGTVLTDPE 23
                     79****97766655 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00046
  Ephrin_rec_like 22 eegqlsClaCPlgtttkkpgatsesdC 48
                     +  + +C aC++++ t+++  + ++dC
       EPA06736.1 34 NKKKEKCRACGSEFDTSEELRKHKKDC 60
                     67889**************99999999 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.4    0.0006      0.54       2      11 ..      10      19 ..      10      22 .. 0.93
   2 ?   -2.4   0.0       6.1   5.5e+03      14      20 ..      29      35 ..      25      36 .. 0.67
   3 ?    2.0   1.2      0.25   2.2e+02       3       9 ..      39      45 ..      39      46 .. 0.90
   4 ?   -1.1   0.1       2.4   2.1e+03      14      21 ..      51      58 ..      50      61 .] 0.72

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0006
      zf-ACC  2 tKCpsCgeml 11
                tKC +Cg++l
  EPA06736.1 10 TKCKKCGTVL 19
                8******997 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 6.1
      zf-ACC 14 keLernl 20
                +e+++n+
  EPA06736.1 29 QEVAHNK 35
                5777775 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.25
      zf-ACC  3 KCpsCge 9 
                KC +Cg+
  EPA06736.1 39 KCRACGS 45
                9****96 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 2.4
      zf-ACC 14 keLernly 21
                +eL+++++
  EPA06736.1 51 EELRKHKK 58
                68888875 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.4     0.013        12       5      12 ..       9      16 ..       6      17 .. 0.85
   2 ?    5.4   0.4     0.019        17       5      12 ..      37      44 ..      34      45 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.013
                TTTSSS-T CS
        Fer4  5 eekCigCG 12
                e kC +CG
  EPA06736.1  9 ETKCKKCG 16
                88*****9 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.019
                TTTSSS-T CS
        Fer4  5 eekCigCG 12
                +ekC +CG
  EPA06736.1 37 KEKCRACG 44
                69*****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1521  (0.0848346); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 379.99
//
Query:       EPA06737.1  [L=47]
Description: hypothetical protein BG20_I0037 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 339.10
//
Query:       EPA06738.1  [L=51]
Description: tautomerase enzyme [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-12   46.2   0.0    3.3e-12   46.1   0.0    1.0  1  Tautomerase    Tautomerase enzyme
    3.5e-05   23.8   0.0    3.5e-05   23.8   0.0    1.0  1  Tautomerase_2  Tautomerase enzyme
  ------ inclusion threshold ------
      0.095   12.9   0.0       0.11   12.8   0.0    1.0  1  Tautomerase_3  Putative oxalocrotonate tautomerase enzyme


Domain annotation for each model (and alignments):
>> Tautomerase  Tautomerase enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.1   0.0   5.6e-16   3.3e-12       9      55 ..       3      49 ..       1      51 [] 0.95

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 5.6e-16
                 TCS-HHHHHHHHHHHHHHHHHHHTS-GGG-EEEEEEE-TTSEEETTE CS
  Tautomerase  9 egrsaeqKaeLaervTealvealgaprsaivVvieEvpaenwgvgge 55
                  gr+++qK+e a+++T+++ve+l+ ++s + Vv+e+ p+enw+++g+
   EPA06738.1  3 PGRTQQQKDEYAKAITKSAVEILKTKESHVIVVFEDNPKENWFLAGN 49
                 69*******************************************97 PP

>> Tautomerase_2  Tautomerase enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   5.9e-09   3.5e-05      39      79 ..       4      44 ..       1      47 [. 0.96

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 5.9e-09
                   ---HHHHHHHHHHHHHHHHHHH---GGGEEEEEEEE-GGGE CS
  Tautomerase_2 39 gRseeqKkaLyralaerlaaklgirpeDvfivlvenpkedW 79
                   gR+++qK +  +a+++   + l  ++++v++v+  npke+W
     EPA06738.1  4 GRTQQQKDEYAKAITKSAVEILKTKESHVIVVFEDNPKENW 44
                   9**************************************** PP

>> Tautomerase_3  Putative oxalocrotonate tautomerase enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.8e-05      0.11      14      57 ..       6      50 ..       3      51 .] 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.8e-05
                   -HHHHHHHHHHHHHHHHHT.T--GGG-EEEEEE--TTSEEETTEE CS
  Tautomerase_3 14 tkeekealakkiteiYtsv.glPaFyvnvlFieieaedffvGges 57
                   t+++k++ ak+it+  +++ +     v v+F + ++e+ f +g++
     EPA06738.1  6 TQQQKDEYAKAITKSAVEIlKTKESHVIVVFEDNPKENWFLAGNQ 50
                   689999999999999998879999999999999999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       765  (0.0426683); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 333.73
//
Query:       EPA06739.1  [L=144]
Description: hypothetical protein BG20_I0082 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 1161.41
//
Query:       EPA06740.1  [L=304]
Description: GHMP kinase, N-terminal domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.6e-11   41.8   0.1      2e-10   40.8   0.1    1.5  1  GHMP_kinases_N   GHMP kinases N terminal domain
  ------ inclusion threshold ------
      0.018   14.6   0.2      0.086   12.5   0.1    2.1  2  Telomere_Sde2_2  Telomere stability C-terminal
      0.052   12.9   0.0       0.11   11.9   0.0    1.5  1  AnfO_nitrog      Iron only nitrogenase protein AnfO (AnfO_nit


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   0.1   3.3e-14     2e-10       7      66 .]      99     158 ..      93     158 .. 0.88

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 3.3e-14
                     SSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
  GHMP_kinases_N   7 eiPvgaGLGSSAAlavalvaAllallglsleeaklaleaerlaqggngsggDvaasvyGg 66 
                     +iPvg GLGSS+A+a++l +Al + l  +l+   ++  a+++    +++ gDv as++Gg
      EPA06740.1  99 TIPVGYGLGSSSAVALSLSYALDHVLKTKLDQTIIGKIAHNAEINCKTGLGDVLASYHGG 158
                     79************************888977777777777777899************8 PP

>> Telomere_Sde2_2  Telomere stability C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.28   1.6e+03      40      55 ..     199     214 ..     198     219 .. 0.77
   2 ?   12.5   0.1   1.4e-05     0.086       6      32 ..     231     257 ..     228     260 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.28
  Telomere_Sde2_2  40 aRLfsvKglsleeldk 55 
                      +RLf + gl  + +d+
       EPA06740.1 199 ERLFQINGLGGKMVDR 214
                      79**999988777776 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 1.4e-05
  Telomere_Sde2_2   6 fssaeeLealglerLKeaLqalGLKcG 32 
                      f++  + ++l +e+L ++L++ G+KcG
       EPA06740.1 231 FAKYVQVMTLRMEKLIKELSSNGIKCG 257
                      667778899*****************9 PP

>> AnfO_nitrog  Iron only nitrogenase protein AnfO (AnfO_nitrog)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.8e-05      0.11     101     168 ..      22      96 ..       3      97 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.8e-05
  AnfO_nitrog 101 vlekeeeeaeeakk..............keesiplpeelkeGnYridlkeiqkknpeltSkqvLlpfLkktefeeLevicdH 168
                    +k+ e      +              +++  + p+++++ n++i  +  q++++++ S  vL +fLk ++fe+L   ++H
   EPA06740.1  22 NNQKKSE------ElgsmgagfsikegvTTHVNIFPKDNQNSNFKITTTGYQSDKTDV-SEYVLNEFLKLGNFENLFFDIQH 96 
                  3333333......1334455888888888889999********************998.789*************9766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2014.52
//
Query:       EPA06741.1  [L=193]
Description: dTMP kinase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-38  131.9   0.2    2.4e-38  131.7   0.2    1.0  1  Thymidylate_kin  Thymidylate kinase
     0.0024   18.2   0.0     0.0031   17.8   0.0    1.2  1  AAA_28           AAA domain
     0.0025   17.7   2.5      0.034   14.0   2.5    2.1  1  dNK              Deoxynucleoside kinase
  ------ inclusion threshold ------
       0.69   11.0   3.5        6.5    7.9   1.1    2.4  2  RNase_J_C        Ribonuclease J C-terminal domain


Domain annotation for each model (and alignments):
>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.7   0.2   5.3e-42   2.4e-38       1     185 []       5     183 ..       5     183 .. 0.94

  Alignments for each domain:
  == domain 1  score: 131.7 bits;  conditional E-value: 5.3e-42
                      EEESTTSSHHHHHHHHHHHHHHTTE..EEEESSSTTSHHHHHHHHHHHTCS---HHHHHHHHHHHHHHTTHHHHHHHHHTT-EEEEES-HHHHH CS
  Thymidylate_kin   1 iEGlDGaGKttqaellkerlkeegik.vvltrepggteiGekirelllkeeeleeqteallfaadriehleekikpalkqgktvivdRylfSsl 93 
                      iEG D aGK tq++ll+++lk+++ik + +++++ +t+iG+ i ++l+ ++++ +q ++ l+aa+r ++  + i  a +++ ++i+ Ry+ S+l
       EPA06741.1   5 IEGGDQAGKKTQTALLAKALKQRKIKtTTFSFPDYKTPIGKEISKYLNGKRKFPPQVIHCLLAANR-WEKLNDILNAQSKNSVLIMNRYYQSNL 97 
                      8*****************************************************************.88788888889999************* PP

                      HHHHTTTTTTCHHHHHHGGGTTSE-SEEEEEESSHHHHHTSCCTTSSTTTSHHHHHHHHHHHHHHHHHHHHTTSTEEEEETTS-HHHHHHHH CS
  Thymidylate_kin  94 aYqgakegvdldlvlslnedvllkPdltflldvdpevalkRlakrdeldeeeeeqldflrkvrerylelakederiliidasksieevheeI 185
                      +Y  a + +  +++ +l   ++ k dl++lldv+  ++ +R ++++    + e++++flr++ + y ++ak +e+++iidask+++evh++I
       EPA06741.1  98 IYGLANG-MNRKWLENLDSGLP-KADLVILLDVSQTESFRRKKTNRD---KFEKNEEFLRNISKIYRKIAK-KENWKIIDASKPKQEVHKNI 183
                      **88655.77788888888777.*******************99999...7899****************7.*****************988 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   6.8e-07    0.0031       2     148 ..       3     161 ..       2     175 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 6.8e-07
      AAA_28   2 ivitGgestGKTtlleaLa....ar..gypvv..pEaareileekl...akgedalpwvedllafaervleeqleeeaaaaankvlfcDrglldtlaYa 89 
                 ivi Gg  +GK t ++ La    +r  +++++  p++ + i +e +     +++  p+v   + +a+ + e+    + a+++n vl++ r +  +l+Y 
  EPA06741.1   3 IVIEGGDQAGKKTQTALLAkalkQRkiKTTTFsfPDYKTPIGKEISkylNGKRKFPPQV-IHCLLAANRWEKLNDILNAQSKNSVLIMNRYYQSNLIYG 100
                 89*********998877774443456755555668888877777663333334445555.4444455555544444455589***************** PP

      AAA_28  90 rayggeaeaelea.aarekrydlvfllppap.ei.dddgeRredleereaiderlrealrel 148
                  a g +  + le+      + dlv+ll+++  e  ++ ++ r+++e+ e++ + + +++r++
  EPA06741.1 101 LANGMN-RKWLENlDSGLPKADLVILLDVSQtESfRRKKTNRDKFEKNEEFLRNISKIYRKI 161
                 **9999.7788875556999********9666555777777777999999999888888874 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   2.5   7.7e-06     0.034       1     198 [.       3     186 ..       3     192 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.7e-06
                 EEEEESTTSSHHHHHHHHHCCSTCEEEE-...HHHHCCSSSSHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHCHHSSS-EEEEES-HHHHHHTHHHHHH CS
         dNK   1 ivveGnIgaGKstlvklLskklgvkvfeE...pvdkwtnvqknlLekfYkdpsrwsfalqtyvllsrlkqqlealatkqvvvleRsiysdryiFakala 96 
                 iv+eG   aGK t + lL+k+l+   ++    +  +++   ++ ++k+ + + ++  ++    +l   ++      +k +++l+    +++ + ++  +
  EPA06741.1   3 IVIEGGDQAGKKTQTALLAKALKQRKIKTttfSFPDYKTPIGKEISKYLNGKRKFPPQV--IHCLLAANRW-----EKLNDILNAQSKNSV-LIMNRYY 93 
                 67777777777777777777776444444111333443333366666555555544332..2222222222.....222333333333333.3444455 PP

                 HTTSS-HHHHHHHHHHHHHHHHHCCH-SEEEEEE--HHHHHHHHHHCTTCCCTTS-HHHHHHHHHHHHHHHTSGGCS-EEEEETSS.-TTTHCCHHHHH CS
         dNK  97 ekgtlseeelkiykelldnlleelakpdlliYLkasletclerikkRgreeekkieldYlekLhekyeewlkklnevpvlvidveeldlvaeeekredv 195
                 +++ +   +  +  ++l+nl + l+k dl+i L++s  + ++r k   +++ek  ++++l+++ + y +  kk n+    +id+++     ++e ++++
  EPA06741.1  94 QSNLIYGLANGMNRKWLENLDSGLPKADLVILLDVSQTESFRRKKTNRDKFEK--NEEFLRNISKIYRKIAKKENW---KIIDASK----PKQEVHKNI 183
                 555555566666789***************************98888888877..589***********9999666...4666666....455555555 PP

                 HHH CS
         dNK 196 vee 198
                 +++
  EPA06741.1 184 LQA 186
                 555 PP

>> RNase_J_C  Ribonuclease J C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.059   2.6e+02      28      67 ..      22      62 ..      13      66 .. 0.75
   2 ?    7.9   1.1    0.0015       6.5      13      60 ..     145     191 ..     143     192 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.059
   RNase_J_C 28 etie.ealeekesdwnelkrkirealkkflykktkrrPmIl 67
                ++++ ++++++++   + k+ i ++++k+l+ k k  P ++
  EPA06741.1 22 KALKqRKIKTTTFSFPDYKTPIGKEISKYLNGKRKFPPQVI 62
                4444155556888999999***********99988887765 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0015
   RNase_J_C  13 keseeLieeakkvvretieealeekesdwnelkrkirealkkflykkt 60 
                 +++ee++++++k+ r++ ++ +  k++d ++ k+++++++ + + kk+
  EPA06741.1 145 EKNEEFLRNISKIYRKIAKKENW-KIIDASKPKQEVHKNILQAFTKKI 191
                 57899******999999888666.5**************999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1258  (0.0701657); expected 358.6 (0.02)
Passed bias filter:                      564  (0.0314574); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 1365.52
//
Query:       EPA06742.1  [L=199]
Description: hypothetical protein BG20_I0031 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.4e-19   68.4   5.0    5.4e-19   68.4   5.0    1.8  2  vATP-synt_E  ATP synthase (E/31 kDa) subunit
     0.0074   16.3   0.8      0.025   14.7   0.8    2.0  1  FliH         Flagellar assembly protein FliH
  ------ inclusion threshold ------
      0.021   14.2   0.6      0.032   13.6   0.6    1.3  1  DUF4407      Domain of unknown function (DUF4407)
      0.083   11.5   0.6      0.088   11.5   0.6    1.0  1  Hamartin     Hamartin protein
       0.18   11.9   0.7         11    6.2   0.1    2.6  2  Imm30        Immunity protein 30
       0.38   10.4   5.9        1.5    8.5   4.9    2.0  2  YkyA         Putative cell-wall binding lipoprotein


Domain annotation for each model (and alignments):
>> vATP-synt_E  ATP synthase (E/31 kDa) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.51   1.5e+03     176     194 ..       8      26 ..       4      30 .. 0.60
   2 !   68.4   5.0   1.8e-22   5.4e-19      20     197 ..      32     194 ..      27     195 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.51
                  CCCHHHCHHHHHHHHHHCC CS
  vATP-synt_E 176 nnTlearLelvleqllpei 194
                  + T++ +L++  + +l++ 
   EPA06742.1   8 EQTIDKILTQTEKTILSNL 26 
                  5566666666666666655 PP

  == domain 2  score: 68.4 bits;  conditional E-value: 1.8e-22
                  HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSHHCCCCHHHHHHCCCCCCC-SSCEEE CS
  vATP-synt_E  20 efeiekaklveeeeekieeayekkeKqaelqkkiaiSnalnkarlkvLkareevleevfeeaekkLaeveedkdeYkellkkLivqalvkleepeviv 117
                  e ++ ++    + e++ +++  + +K+a+   k+ + +    ar + L + e+ +++vf +a ++++++e+    Y++l+k+L+++    l+  +v++
   EPA06742.1  32 ESNQVLDDSIPKLEQEYDKIISDGKKEADKIEKQLVGSSDIGARNSALLVLEKAVDDVFTKAIEQISNMERSG-DYSKLIKTLLDESTKILGTTKVVI 128
                  56666666666778888999999***********************************************999.9*********************** PP

                  EECCCCHHCCCCTHCCCCCCHHCCSSSS--SEEEEESSEBTTSSSEEEECCSSSCEEECCCHHHCHHHHHHHHHHCCCCC CS
  vATP-synt_E 118 rarkeDaelveealdkaaeeykaktkkktvevagdeedfledvlGGvvleaadgkikvnnTlearLelvleqllpeirka 197
                  + + +D+++v+++      ++ ++      e++ ++    ++++GGvv+++++g +k +nTl+ar+++++  +++ei+++
   EPA06742.1 129 YTNSKDKDVVQSV----LSQFSGA------ELSSET----ITCIGGVVVKSKAGAMKFDNTLDARIQRLKPLIRKEIATK 194
                  ************5....7888884......788899....9***********************************9875 PP

>> FliH  Flagellar assembly protein FliH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.8   8.3e-06     0.025      29     128 .]      86     183 ..       4     183 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 8.3e-06
                 HHHHHHHHHHHHHHHS--S-HHHHHHHHHHHHTTSCHHHS-EEEEE-HHHHHHHHHHHHHHHHHCT-EEEE-TTS-TT-EEEEESSCEE..EHHHHHHH CS
        FliH  29 lvqlaldiarkvikkelsvdpekilalvrealaklpvdekkitlrvnpdDlelvrehlgeelsargwrlvaDsslsrGgcrieseegei..DatietRl 125
                 + ++ +++ +++   e+s d +k+++++     +++  ++k++++ n +D ++v++ l+++    g +l +++    Gg+ ++s+ g    D t+++R+
  EPA06742.1  86 VDDVFTKAIEQISNMERSGDYSKLIKTLLDES-TKILGTTKVVIYTNSKDKDVVQSVLSQF---SGAELSSETITCIGGVVVKSKAGAMkfDNTLDARI 180
                 55666777789999999999999999999998.9*************************44...467899999999********999753389999999 PP

                 HHH CS
        FliH 126 kkl 128
                 ++l
  EPA06742.1 181 QRL 183
                 985 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.6   1.1e-05     0.032     186     257 ..      17      86 ..       4     103 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.1e-05
     DUF4407 186 kekkaqldaaqaelaelkakldatarlaalraelaeleaerakeraasqaaaaaddGllarlealdrltked 257
                 ++ k+ l  +  +l+e ++    ++ +++l++e++++ ++ +ke+++ +++  ++++++ar+ al  l k+ 
  EPA06742.1  17 QTEKTILSNLHSALTESNQV--LDDSIPKLEQEYDKIISDGKKEADKIEKQLVGSSDIGARNSALLVLEKAV 86 
                 45566666666777777777..*******************************************9998765 PP

>> Hamartin  Hamartin protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.6     3e-05     0.088     430     561 ..      16     146 ..       3     193 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3e-05
    Hamartin 430 venekeleeslkskssvtlseLsdvikelleaesedsvekeeeeaaisqel...seiteekketlvsrggldspfsrtleslaksqrrkrlasalsses 525
                 +++ek++ ++l+s  + + + L d+i +l +++ ++++ +++e ++i+++l   s+i  +++  lv ++++d  f + +e++++ + r   +s+l ++ 
  EPA06742.1  16 TQTEKTILSNLHSALTESNQVLDDSIPKLEQEYDKIISDGKKEADKIEKQLvgsSDIGARNSALLVLEKAVDDVFTKAIEQISNME-RSGDYSKLIKTL 113
                 36778888888777777777899999999888899999************987455666666669*******************99.577777777775 PP

    Hamartin 526 isdaegaatkkeaksskeaesslekekscsakqsft 561
                 + +++++  +++      +++s +k+  +s+ ++f+
  EPA06742.1 114 LDESTKILGTTK---VVIYTNSKDKDVVQSVLSQFS 146
                 555666555555...344444555555555555554 PP

>> Imm30  Immunity protein 30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1    0.0035        11      13      40 ..       6      33 ..       3      52 .. 0.89
   2 ?    3.6   0.1     0.023        68      12      41 ..      88     117 ..      76     121 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0035
       Imm30 13 lFesalekllkeqnkdnledlckafdDd 40
                + e++++k+l++++k +l++l++a+ ++
  EPA06742.1  6 ALEQTIDKILTQTEKTILSNLHSALTES 33
                679********************99765 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.023
       Imm30  12 elFesalekllkeqnkdnledlckafdDdt 41 
                 ++F +a+e++ + ++  + ++l+k++ D++
  EPA06742.1  88 DVFTKAIEQISNMERSGDYSKLIKTLLDES 117
                 5899999*9999999999999998887764 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   4.9   0.00049       1.5       3      67 ..      11      76 ..       9     116 .. 0.69
   2 ?    2.5   0.1     0.035     1e+02      23      92 ..      75     143 ..      68     157 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00049
        YkyA  3 eekiyealeeav..elEkefeeqqekLtelekkeqelyeeiielgmdefdkikklsdealenveeRe 67
                ++ki ++ e+++  +l+++++e ++ L +   k ++ y++ii+ g++e dki+k+     + + +R+
  EPA06742.1 11 IDKILTQTEKTIlsNLHSALTESNQVLDDSIPKLEQEYDKIISDGKKEADKIEKQLVGSSD-IGARN 76
                56788888887522667999********************************998765444.33444 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.035
        YkyA  23 qqekLtelekkeqelyeeiielgmdefdkikklsdealenveeReellekekesieeakeefekikeeie 92 
                  ++ L  lek   +++++ ie +++++++  + s+   ++++e +++l + k +i    +  + +++ ++
  EPA06742.1  75 RNSALLVLEKAVDDVFTKAIE-QISNMERSGDYSKLIKTLLDESTKILGTTKVVIYTNSKDKDVVQSVLS 143
                 566777788888888888887.778888888888888888888888888888777666666655555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1343  (0.0749066); expected 358.6 (0.02)
Passed bias filter:                      731  (0.0407719); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1298.52
//
Query:       EPA06743.1  [L=234]
Description: hypothetical protein BG20_I0034 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1479.83
//
Query:       EPA06744.1  [L=170]
Description: hydrolase, NUDIX family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.3e-17   64.0   0.0    1.7e-17   63.7   0.0    1.1  1  NUDIX      NUDIX domain
  ------ inclusion threshold ------
      0.092   13.0   0.1       0.16   12.3   0.1    1.3  1  TetR_C_10  Tetracyclin repressor-like, C-terminal domain


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.7   0.0   1.9e-21   1.7e-17       2     116 ..      32     145 ..      31     159 .. 0.78

  Alignments for each domain:
  == domain 1  score: 63.7 bits;  conditional E-value: 1.9e-21
                 EEEEEEEEEEETTSEEEEEEESSSSTTT..EESSEEECBTTSHHHHHHHHHHHHHHSEEE.EEEEEEEEEEEEEEEEEEEEE...EEEEEEEEE.EEEC CS
       NUDIX   2 lrravgvvllnekgevLlvrrskkpfpg..WelPgGkvepgEtpeeAArREleEEtGlea.ellellgrlhylapydgpygd...eheilyvfl.eeve 93 
                 +r a++++ ++e+++v+lv+++ ++++g   e+P+G++e+ E+p  +A REleEEtG++a +++ l++          +y++   ++ei+++f    ++
  EPA06744.1  32 HRGAAAMLAFDENNKVILVKQH-RYPHGyvIEIPAGTLEKKEDPIKCAFRELEEETGYSAkKMTPLIS----------YYPSigyNTEIIHCFIaSGLK 119
                 56678888**************.999996448****************************77777777..........555566688999999984444 PP

                 SGCSST.STTTEEEEEEEEHHHH..H CS
       NUDIX  94 gelepn.denevsevrwvpleel..l 116
                    +++ de+e+ +v  ++l+++  +
  EPA06744.1 120 KIANLKlDEDEILSVVKMDLKKVisM 145
                 44444457999999977888888543 PP

>> TetR_C_10  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   1.8e-05      0.16      69     119 ..     108     158 ..     101     167 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.8e-05
   TetR_C_10  69 dfltdliekGkekGvirslpskaliaivygallklyklletgkieatkdlv 119
                 ++++ +i  G +k    +l+ + ++++v   l k++ ++++gki+ +k + 
  EPA06744.1 108 EIIHCFIASGLKKIANLKLDEDEILSVVKMDLKKVISMIKNGKIQDSKTIC 158
                 67888999999999999****************************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 1166.57
//
Query:       EPA06745.1  [L=258]
Description: rhodanese-like protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.8e-42  143.6   0.2      2e-21   76.5   0.0    2.1  2  Rhodanese  Rhodanese-like domain


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.5   0.0   1.1e-25     2e-21       3     106 ..       6     114 ..       4     115 .. 0.93
   2 !   65.4   0.1   3.2e-22   5.7e-18       6     106 ..     147     250 ..     143     251 .. 0.82

  Alignments for each domain:
  == domain 1  score: 76.5 bits;  conditional E-value: 1.1e-25
   Rhodanese   3 kelkellekgkvallDvRppeeYekghIpgAvnv...skdtlsrakkseapllelpeellel.gidnkktvvvycdgggr.aaaaaallkklGyknvsv 96 
                 +el  +l+++++++ D+R++ eY++ghIpgAvn+   ++ ++ ++k+  ++++++ + ll+  g++++k+v++y++ +g  aa+  ++l +  ++nvs 
  EPA06745.1   6 TELNSILNDPNIIIADTRSFKEYSEGHIPGAVNLdlfAFHWIDTTKQGIENFNNQSKNLLSFlGVTPEKKVIFYDSVSGMlAARGVWMLHYFSHQNVSM 104
                 79999********************************99999999999999999999999999*****************8999999***999888*** PP

   Rhodanese  97 ldGGfkawke 106
                 ldGGf++wk+
  EPA06745.1 105 LDGGFTKWKK 114
                 ********97 PP

  == domain 2  score: 65.4 bits;  conditional E-value: 3.2e-22
   Rhodanese   6 kellekgkvallDvRppeeY.......ek.ghIpgAvnvskdtlsrakkseapllelpeellel.gidnkktvvvycdgggraaaaaallkklGyknvs 95 
                 +e+l++   +++DvR++ eY       ++ ghIp+++n+      +++  e+   ++++el+++ ++ +++++v+yc+g+ raa++  +lkklG+knv+
  EPA06745.1 147 RENLDNV--KIIDVRSSGEYdgsviraAQsGHIPNSINI----DWNQNIKEDGTFKNNDELSKMyDFPKDSEIVTYCQGAYRAANTFLALKKLGFKNVR 239
                 5666554..5**********99999995559********....4445555555566666666666999**************999999999******** PP

   Rhodanese  96 vldGGfkawke 106
                 v+ G++ +w +
  EPA06745.1 240 VYLGSWGEWGN 250
                 *********76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1587.58
//
Query:       EPA06746.1  [L=222]
Description: hypothetical protein BG20_I0038 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0097   15.5   2.2      0.014   14.9   2.2    1.2  1  DUF334    Domain of unknown function (DUF334)
  ------ inclusion threshold ------
      0.071   13.2   0.1       0.16   12.1   0.1    1.6  1  SAM_2     SAM domain (Sterile alpha motif)


Domain annotation for each model (and alignments):
>> DUF334  Domain of unknown function (DUF334)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   2.2   1.6e-06     0.014      48     144 ..     108     204 ..      95     215 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.6e-06
      DUF334  48 lkkqnklvvkylaeikeqqdlrekelkeikselkkatkdfrdkskkvrndfvdllqkklkrvdaeelkiilrkdvykvreeidrmlrevkrshehyq 144
                 l k+  lv   ++e+k++++l ek   e  s+ k+  k +r+ s  + n    ++qk +k    +++k+ l  d+ k+++  d+ l   k+  e + 
  EPA06746.1 108 LTKKGILVALSISEVKNKEQLLEKFFSEADSKEKEYEKTIRNLSENIPNFTYSIFQKYVKAFCDNKIKNLLPFDLSKLKDISDESLVIQKEILEAFL 204
                 77888899999***************************************************************99999988887766666655555 PP

>> SAM_2  SAM domain (Sterile alpha motif)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   1.8e-05      0.16      18      65 ..     162     206 ..     161     207 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.8e-05
                 TGGGHHHHHHTTCSHHHHHTTSCHHHHHHTTHHHHHHHHHHHHHHHHH CS
       SAM_2  18 lkqytdnFrdagitgaelllrlteedLkrlGitsvghrkkilkkiqel 65 
                 +++y+++F d++i     ll +++++Lk++  +s+  +k+il ++ +l
  EPA06746.1 162 FQKYVKAFCDNKIKN---LLPFDLSKLKDISDESLVIQKEILEAFLKL 206
                 689************...888***********************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1130  (0.0630264); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1578.22
//
Query:       EPA06747.1  [L=240]
Description: ABC transporter, ATP-binding protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.8e-36  125.7   0.1    1.6e-35  122.6   0.0    1.9  2  ABC_tran     ABC transporter
    1.1e-13   51.7   0.8    5.5e-07   29.7   0.3    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    6.4e-06   25.8   2.0    0.00027   20.4   2.0    2.1  1  SMC_N        RecF/RecN/SMC N terminal domain
    7.9e-05   23.2   3.2    0.00019   22.0   3.2    1.7  1  AAA_23       AAA domain
    0.00021   21.0   0.1    0.00038   20.1   0.1    1.4  1  AAA_29       P-loop containing region of AAA domain
    0.00076   19.3   0.2       0.89    9.3   0.0    2.7  3  IstB_IS21    IstB-like ATP binding protein
     0.0011   18.6   0.0     0.0022   17.6   0.0    1.4  1  AAA_27       AAA domain
     0.0077   16.1   0.1      0.043   13.7   0.0    2.1  3  RsgA_GTPase  RsgA GTPase
     0.0091   16.1   0.0      0.018   15.1   0.0    1.6  1  MMR_HSR1     50S ribosome-binding GTPase
  ------ inclusion threshold ------
      0.018   15.5   1.3       0.13   12.7   1.3    2.2  1  AAA          ATPase family associated with various cellular a
       0.02   14.1   0.0      0.046   12.9   0.0    1.6  1  NB-ARC       NB-ARC domain
       0.02   15.2   0.1      0.068   13.4   0.1    1.9  1  AAA_22       AAA domain
      0.022   15.0   0.0        1.1    9.6   0.0    2.4  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
      0.033   14.2   0.6        1.9    8.5   0.0    2.4  2  AAA_14       AAA domain
       0.08   13.3   0.0       0.25   11.7   0.0    1.8  1  AAA_16       AAA ATPase domain
        0.1   12.3   6.4       0.24   11.1   6.4    1.8  1  AAA_15       AAA ATPase domain
        0.2   11.8   0.1       0.88    9.7   0.1    2.1  1  AAA_33       AAA domain
        2.6    8.1   5.8         18    5.3   1.5    2.3  2  DUF87        Helicase HerA, central domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.6   0.0   1.6e-38   1.6e-35       2     136 ..      21     159 ..      20     160 .. 0.94
   2 ?    1.2   0.0       0.5     5e+02      30      86 ..     173     234 ..     169     240 .] 0.69

  Alignments for each domain:
  == domain 1  score: 122.6 bits;  conditional E-value: 1.6e-38
                 EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH..........HHHTCHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxx RF
    ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren..........esdeeiekals 90 
                 ++vs+++++g  ++i+G+nGaGKStL+++++gl ++ +G+i++ ++d+k+   + + keig++pq+p + ++  +  n           ++++i+k+l+
  EPA06747.1  21 DDVSFNVEQGDFLGIIGPNGAGKSTLFAAMLGLNSKYKGTIKFFNTDIKK--SKNYLKEIGYVPQKPIFERNFPATVNdvvkmglhkeSDENKIDKILQ 117
                 89************************************************..**************777777765555669****99777778****** PP

                 HSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  91 klglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                 +l ++el ++++     +LSgGq+qrv +a+al+++pk+l+lDEp 
  EPA06747.1 118 QLWIHELSERRI----GELSGGQQQRVFIAKALVNNPKVLILDEPV 159
                 ************....*****************************6 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.5
                 HHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSB.HHHH......HHHTCHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx......xxxxxxx RF
    ABC_tran  30 llagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpelt.vren......esdeeie 86 
                 +l +l ++++ +i + ++dl+    ++l +++++l  + ++  e+    en      +s++ ++
  EPA06747.1 173 ILKELNSKQNITIIWSSHDLDA--VKQLANHVACLNRTLFFHGESDdFFENnelvkqYSEASMQ 234
                 4555666677788888999988..9999999999999977777766677776666654444444 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.3   5.5e-10   5.5e-07       2      91 ..      33     109 ..      32     128 .. 0.81
   2 !   21.0   0.0   2.5e-07   0.00024     231     299 ..     126     192 ..     106     195 .. 0.87

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 5.5e-10
      AAA_21   2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrlersqv...eeklssve 91 
                  ++iGpNg+GKS+L+ a+ +l +                ++++ +++++++ ++++  +  +  + q++ ++ ++    ++v   + ++ s e
  EPA06747.1  33 LGIIGPNGAGKSTLFAAMLGLNS----------------KYKGTIKFFNTDIKKSKNYLKEIGYVPQKPIFERNFPATVNDVvkmGLHKESDE 109
                 68*******************66................******************************************975433333332 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 2.5e-07
      AAA_21 231 elparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSp 299
                 e+ + elS G+++  +++ al   +   ++l++DEp +g++ + +  ++ +lkel++  ++ +i ++H+ 
  EPA06747.1 126 ERRIGELSGGQQQRVFIAKALVNNP---KVLILDEPVTGIDQQSIDLFYSILKELNSkQNITIIWSSHDL 192
                 567899******9999999999988...9********************99966666699********95 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   2.0   2.7e-07   0.00027      24     198 ..      30     188 ..       7     207 .. 0.59

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.7e-07
                 SSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEETTSEEEEEETTEEE-HHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       SMC_N  24 ksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrvkrkgeseykingkevtkke 122
                   f  i+GpNG+GKs l+ A+   LG +s+ k   + ++  i+k +++   + ++v      e + ++ +     + +   +k++ e ki++  + ++ 
  EPA06747.1  30 GDFLGIIGPNGAGKSTLFAAM---LGLNSKYKGTIKFFNTDIKK-SKNYLKEIGYVPQKPIFERN-FPAT--VNDVVKMGLHKESDENKIDK--ILQQL 119
                 35999****************...99877655555566666665.55555555555443111111.1211..12222222223333446654..33444 PP

                 HHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SS CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       SMC_N 123 vsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislr 198
                   + l++ +i   +LSgG+++ v +a       v+   + +lDe    +D++ +  + ++lke ++  Q i i  +
  EPA06747.1 120 WIHELSERRIG--ELSGGQQQRVFIA----KALVNNPKVLILDEPVTGIDQQSIDLFYSILKELNS-KQNITIIWS 188
                 56667777776..6999998755443....344555557789999999999999999999998763.344443333 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   3.2   1.9e-07   0.00019      12     125 ..      22     133 ..      16     235 .. 0.54

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.9e-07
      AAA_23  12 dqeidFsk.gltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkay..veltfenkdgrytrsiererelskkkgkttkka 107
                 d++++ ++  +  I+GpNGaGK+T++ A+  +L  + +++ +  +++++ks+  ++  g v++   +e++f  + ++    +  +   +++++++++k 
  EPA06747.1  22 DVSFNVEQgDFLGIIGPNGAGKSTLFAAML-GLNSKYKGTIKFFNTDIKKSKNYLKEIGYVPQKpiFERNFPATVND----VVKMGLHKESDENKIDKI 115
                 5556665524667***************85.5555444444444455555555555443333333355555444332....222222222222333333 PP

      AAA_23 108 klelleideleqfisell 125
                   +l+ ++ +e++i el 
  EPA06747.1 116 LQQLWIHELSERRIGELS 133
                 333333222223333333 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.1   3.9e-07   0.00038      13      43 ..      21      51 ..      16      65 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 3.9e-07
      AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiq 43
                d+ ++++++ ++  ++Gp+G+GKSTl+ A+ 
  EPA06747.1 21 DDVSFNVEQGDFLGIIGPNGAGKSTLFAAML 51
                55667777555888*************8875 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0   0.00089      0.89      44      73 ..      27      57 ..      11      73 .. 0.72
   2 ?   -1.6   0.0       1.9   1.9e+03      26      45 ..     103     122 ..      92     134 .. 0.71
   3 !    7.0   0.1    0.0043       4.3     105     145 ..     146     185 ..     131     209 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00089
   IstB_IS21 44 iekkenivllGpsGvGKshlaia.lgveavr 73
                +e+ + + ++Gp G+GKs l +a lg +   
  EPA06747.1 27 VEQGDFLGIIGPNGAGKSTLFAAmLGLNSKY 57
                67778889*********98765515665544 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.9
   IstB_IS21  26 aarsldkrkvkeLatlsfie 45 
                  ++++d++k++++ +  +i+
  EPA06747.1 103 LHKESDENKIDKILQQLWIH 122
                 45667777777777777775 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0043
   IstB_IS21 105 rllkvdllilDdlgllpldqaeaellfeviekryerrsiii 145
                  + ++++lilD+  ++ +dq++  l++ ++++   ++ i i
  EPA06747.1 146 LVNNPKVLILDEP-VTGIDQQSIDLFYSILKELNSKQNITI 185
                 455679******6.678***************999887644 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   2.2e-06    0.0022      19      49 ..      23      53 ..      17      58 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.2e-06
      AAA_27 19 ldfsaeeadlhliyGpNEAGKstalrAisdl 49
                ++f+ e+ d+  i+GpN AGKst+++A+  l
  EPA06747.1 23 VSFNVEQGDFLGIIGPNGAGKSTLFAAMLGL 53
                67888999*******************9765 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   4.4e-05     0.043      77     122 ..       7      53 ..       2      72 .. 0.83
   2 ?   -3.6   0.0       9.2   9.1e+03      26      42 ..     104     119 ..      95     125 .. 0.59
   3 ?   -0.5   0.0         1     1e+03      70     108 ..     175     215 ..     140     216 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.4e-05
                  SEEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
  RsgA_GTPase  77 yevllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallpe 122
                  +e l+++  + +++++++ ++++ ++  ++G+ G+GKStL  a+l+ 
   EPA06747.1   7 IEHLTIEYPDLKAIDDVSFNVEQgDFLGIIGPNGAGKSTLFAAMLGL 53 
                  56677777788999999999999899**************9998874 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 9.2
                  TTTT--HHHHHHHHHHH CS
  RsgA_GTPase  26 kepelslnlldrfLvla 42 
                  + +e ++n +d++L ++
   EPA06747.1 104 H-KESDENKIDKILQQL 119
                  4.555666666666555 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 1
                  HHHHHTTSEEEE--TTTHTTHHHHHHHCTT..SEEEEECST CS
  RsgA_GTPase  70 eelealgyevllvsaktkegleelkellkd..ktsvlvGqS 108
                  +el++ +  ++++s+++ +++++l+++++   +t ++ G+S
   EPA06747.1 175 KELNSKQNITIIWSSHDLDAVKQLANHVAClnRTLFFHGES 215
                  34444444456667777888888888776444777777776 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.8e-05     0.018       2      26 ..      33      57 ..      32     123 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.8e-05
                EEEEESTTSSHHHHHHHHHTSTEEE CS
    MMR_HSR1  2 vaivGrpNvGKStLinaltgekaiv 26
                 +i+G   +GKStL+ a++g +++ 
  EPA06747.1 33 LGIIGPNGAGKSTLFAAMLGLNSKY 57
                589***************9964433 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.3   0.00013      0.13       3     120 ..      35     200 ..      33     212 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00013
                 EESSTTSSHHHHHHHHHHHHT.....HEEEEEETTTCSSS.....................................................STTHHH CS
         AAA   3 lyGppGtGKTllakavakelg.....vefleisgsellsk.....................................................yvgese 43 
                 ++Gp G GK++l  a+    +     ++f++++ ++  +                                                       +ge +
  EPA06747.1  35 IIGPNGAGKSTLFAAMLGLNSkykgtIKFFNTDIKKSKNYlkeigyvpqkpifernfpatvndvvkmglhkesdenkidkilqqlwihelserRIGELS 133
                 68*******999999888742233345566666555554455666666666666666666666999999999999999999999988888888555555 PP

                 HHHHHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHH CS
         AAA  44 kkirelfkeakeka.kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpall 120
                    ++ +  ak+   +p++l++DE    + ++           ++ +++ l+++++k++ +++i  +++ d +++   
  EPA06747.1 134 GGQQQRVFIAKALVnNPKVLILDEPVTGIDQQ----------SIDLFYSILKELNSKQN-ITIIWSSHDLDAVKQLAN 200
                 44444443444444569*******66555555..........58888888888888655.999999999998877655 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   4.7e-05     0.046      19     117 ..      30     163 ..      17     239 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.7e-05
                 CSEEEEEEESTTSSHHHHHHHHCCSHCCCCCCBTEEEEE.........................................EEESXXHHHHHHHXXH.HH CS
      NB-ARC  19 qslvvalvGmgGvGKttlakqilnksdevegrFdsvawv.........................................vvsktdkseeiletil.ke 75 
                 + +++++ G  G GK+tl++ +l      ++++ + +                                             s++ k+ +il++++ +e
  EPA06747.1  30 G-DFLGIIGPNGAGKSTLFAAMLGL----NSKYKGTIKFfntdikksknylkeigyvpqkpifernfpatvndvvkmglhKESDENKIDKILQQLWiHE 123
                 3.79***************987654....3344433333334445578888888888888888888888888888776665666666666666654244 PP

                 HHCCCTTSSSS-STTSHHHHHHHHCCCTTEEEEEEEE-SHHH CS
      NB-ARC  76 LslseddleekeeveslkrklvrlLltkrfllvlDDVweeed 117
                 Ls++   + e + +++    + ++L +   +l+lD  ++  d
  EPA06747.1 124 LSER--RIGELSGGQQQRVFIAKALVNNPKVLILDEPVTGID 163
                 5444..444444444457778888888888888887666555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   6.9e-05     0.068       5      99 ..      30     157 ..      27     209 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.9e-05
      AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee...............................erpevvfvtlpsstsskdllrellralglelkaer 72 
                   +l ++G+ G+GK+tl + +l  + +++   +                                  +vv++ l ++++  ++ + l + + +el++  
  EPA06747.1  30 GDFLGIIGPNGAGKSTLFAAMLGLNSKYKGTIKffntdikksknylkeigyvpqkpifernfpaTVNDVVKMGLHKESDENKIDKILQQLWIHELSE-- 126
                 66888**************999998777666667777777666666666666666666655555555555555555555555544444444444444.. PP

      AAA_22  73 lsseell.ealeqalrarav...ielliiDE 99 
                  +  el   + ++ + a+a    +++li+DE
  EPA06747.1 127 RRIGELSgGQQQRVFIAKALvnnPKVLILDE 157
                 4444444444444444444455555666666 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0    0.0011       1.1      27      88 ..     126     174 ..     109     176 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0011
     SbcCD_C  27 srssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllell 88 
                 +r++g+lSGG++q ++   +a al           +++++++LDE   ++D++si+   ++l
  EPA06747.1 126 ERRIGELSGGQQQRVF---IAKAL----------VNNPKVLILDEPVTGIDQQSIDLFYSIL 174
                 6888999999996554...33222..........2357888999999999988887766665 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0    0.0019       1.9       4      47 ..      32      75 ..      29      94 .. 0.74
   2 ?    4.1   0.1     0.045        45      54     111 ..     139     200 ..      86     208 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0019
      AAA_14  4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkla 47
                 l i G+  +GK+tl   ++  +   k  i ++n d ++ k++ 
  EPA06747.1 32 FLGIIGPNGAGKSTLFAAMLGLNSKYKGTIKFFNTDIKKSKNYL 75
                6789***********99887555545667777777766665544 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.045
      AAA_14  54 elilek.lkeekktylflDE......iqevpewekalkslvdegknldvivtGSnskllskeiat 111
                 +++ +k l  ++ ++l+lDE       q ++ ++++lk+l  ++ n+ + +  S+ ++  k++a+
  EPA06747.1 139 RVFIAKaLV-NNPKVLILDEpvtgidQQSIDLFYSILKELNSKQ-NITI-IWSSHDLDAVKQLAN 200
                 334444233.4889999999544433367788888888888877.7555.455676666666665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00025      0.25      26     170 .]      32     186 ..      16     186 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00025
      AAA_16  26 lvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipy.........salaqalareellrqllde..aesaeleawrekleeala....... 106
                  + ++G+ G GKs+l  + l  l+ ++  +++  +++ +++  y          ++ +  +    ++++  +  +     e +  k+++ l+       
  EPA06747.1  32 FLGIIGPNGAGKSTLFAAML-GLNSKYKGTIKFFNTDIKKSKNYlkeigyvpqKPIFERNFP-ATVNDVVKMglH----KESDENKIDKILQqlwihel 124
                 46689***********9999.67777544455555555444344333222332222222212.233333333221....22233333444445556666 PP

      AAA_16 107 ...avpelagaeasrllellkrllallsrderplvlvlDd.lqwadeaslqllaaLlrllesk.pllvv 170
                     ++el+g + +r++ + k+l+        p vl+lD+ +  +d++s +l++++l++l+sk +++++
  EPA06747.1 125 serRIGELSGGQQQRVFIA-KALV------NNPKVLILDEpVTGIDQQSIDLFYSILKELNSKqNITII 186
                 7778888888888888777.4444......345577777438899999999999999999998788876 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   6.4   0.00024      0.24      14      74 ..      20      77 ..      16     222 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00024
      AAA_15 14 lkdveidlsee.ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifenises 74
                ++dv+ +++   +  +iG+N++GKS++  a+  + ++     k +ik+ + d+++++n+ ++
  EPA06747.1 20 IDDVSFNVEQGdFLGIIGPNGAGKSTLFAAMLGLNSKY----KGTIKFFNTDIKKSKNYLKE 77
                555444444445888****************7777744....45666666666666665544 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1   0.00088      0.88       4      20 ..      35      51 ..      33     212 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00088
      AAA_33  4 lvGlpGsGKstlaerll 20
                ++G++G+GKstl   +l
  EPA06747.1 35 IIGPNGAGKSTLFAAML 51
                58**********98876 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.3     0.021        21      26      47 ..      33      54 ..      22      64 .. 0.84
   2 ?    5.3   1.5     0.018        18     130     216 ..      96     200 ..      56     209 .. 0.61

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.021
       DUF87 26 lAilgsTGsGKSntvavLleel 47
                l+i+g  G+GKS++ a +l   
  EPA06747.1 33 LGIIGPNGAGKSTLFAAMLGLN 54
                689***********99998655 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.018
       DUF87 130 a...keekeklssdepveklleelk........kekeelrklknqaiarlldkledllrkggsf........snsstdliallleklekegkitii... 206
                 +   k   +k s +  + k+l++l+        +      +l+  +++r+  ++  + + + ++        +++s dl  ++l++l+++++itii   
  EPA06747.1  96 NdvvKMGLHKESDENKIDKILQQLWihelserrI-----GELSGGQQQRVFIAKALVNNPKVLIldepvtgiDQQSIDLFYSILKELNSKQNITIIwss 189
                 3344466666667777888999999776444442.....33344444444443333333333335555557899999******************9777 PP

       DUF87 207 .dlsgvdelaq 216
                  dl  v++la 
  EPA06747.1 190 hDLDAVKQLAN 200
                 77777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       753  (0.041999); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 1722.49
//
Query:       EPA06748.1  [L=362]
Description: putative pleiotropic regulatory protein DegT [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   7.2e-114  380.8   0.0   8.8e-114  380.6   0.0    1.0  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    7.8e-09   35.0   0.1    1.2e-08   34.3   0.1    1.2  1  Aminotran_5      Aminotransferase class-V
    8.2e-09   35.1   0.1    1.2e-08   34.5   0.1    1.2  1  Aminotran_1_2    Aminotransferase class I and II
    3.3e-08   32.5   0.2    5.5e-08   31.8   0.2    1.3  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    1.6e-05   24.4   0.0    4.9e-05   22.8   0.0    1.7  1  Beta_elim_lyase  Beta-eliminating lyase
    0.00034   20.3   0.0    0.00081   19.1   0.0    1.5  1  ComK             ComK protein


Domain annotation for each model (and alignments):
>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  380.6   0.0  2.9e-117  8.8e-114       3     360 ..      11     356 ..      10     357 .. 0.96

  Alignments for each domain:
  == domain 1  score: 380.6 bits;  conditional E-value: 2.9e-117
                      HHHHHHHHHHHHTSS-SSS.....SHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE- CS
  DegT_DnrJ_EryC1   3 keeeleaveevlksgwlts.....gpeveeFEkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvD 91 
                      ++ee+ av+ +lk+g+lts     g++v+ FEk  + ++++k+++av+sGtaAl+ aL al++++gdeV+vps+tFvatan+v+ +gakpvfvD
       EPA06748.1  11 GKEEISAVTSILKNGTLTSaaskgGKHVQLFEKSASFFIKSKYVVAVNSGTAALQAALYALDIKQGDEVLVPSFTFVATANSVVSTGAKPVFVD 104
                      6899**************999************************************************************************* PP

                      B-TTTSSB-GGGCGGG--TTEEEEEEB-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT-EETTEECCCSSSEEEEE-BTTSSS-SSS-EEEEE CS
  DegT_DnrJ_EryC1  92 vdpdtynidpaaieaaitertkaIlpVhlyGqvadmdalkaiaakhglkvieDaAhAlGatykgkkvGalgdaavfSFyptKnlttGeGGavvt 185
                      v ++ y++dp++++++it++tkaI+pVhlyG+va +d++ +ia+kh+l++ieDaA++lG+tykgk++G+++++++ S+yp+K++t GeGG v t
       EPA06748.1 105 VLKENYTMDPDDLQKKITKKTKAIIPVHLYGNVAFIDRISEIAKKHNLPIIEDAAQSLGSTYKGKHAGTFSELGCWSMYPAKVMTSGEGGFVAT 198
                      ********************************************************************************************** PP

                      STHHHHHHHHHHHBTTCECCTCSSCECCSS---B-B-BHHHHHHHHHHHCTHHHHHHHHHHHHHHHHHHHHTCCCCEESCGGTTSSSEEESCEE CS
  DegT_DnrJ_EryC1 186 ndeelaekarvlrnhGlkrkaekryvgevelGynyrlteiqAAiglaqLerldelvarRreiaelykeeLaelegtaelttpketkkhawhlya 279
                      n+++l +k+ ++rnhG++    + y +++ +G n+rl ei+AAig  q+++l ++++ R+++a+++++++++l+ +  l+ + +++k +w+ly+
       EPA06748.1 199 NNKKLYDKLLMIRNHGMV----HGYDTKI-FGLNLRLPEISAAIGTIQMKKLPDFLKIREKNAKHLSQLISDLDII--LPQQRKNEKVNWYLYT 285
                      ******************....79*****.********************************************75..4444444448****** PP

                      EEEHCCHHHCHHHHHHHHHHCCEE-B-SGSCHGGGSCCHHHHHHCCCHC-HHHHHHHHHEEEEEGGTTGSHHHHHHHHHHH CS
  DegT_DnrJ_EryC1 280 vlveeeaevkrdelvealkeegigtrvhypnplhrqpvyaerkeeasgdlpnaerlaervlsLplypelteedvdrVveal 360
                      +        kr++++++l+++g+g+  +yp+p+h++p+y+++      +lp +e++++ vlsLp++p++t+++++ ++++l
       EPA06748.1 286 IAAS-----KRNNILKKLNSKGVGAASYYPIPVHKTPFYQQKI-----KLPITEWASAHVLSLPIHPKVTSKNIELIAKTL 356
                      **99.....799****************************995.....58*************************999987 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.1   4.2e-12   1.2e-08      60     182 ..      51     164 ..      24     167 .. 0.85

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 4.2e-12
                  TGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEE.EBETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB- CS
  Aminotran_5  60 seeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvi.pldeegeldldelekllnektklvaithvsnvtGtiq 156
                  s + ++ + ++t a+++++++l   +k+gde++v +    a+ +  +      gak +++  l+e+ ++d+d+l+k++++ktk+++  h     G++ 
   EPA06748.1  51 S-KYVVAVNSGTAALQAALYAL--DIKQGDEVLVPSFTFVATANSVVST----GAKPVFVdVLKENYTMDPDDLQKKITKKTKAIIPVHL---YGNVA 138
                  3.56999999999*********..6************999998555555....44433331467799*******************9995...8**** PP

                  -HHHHHHHHHHTT-EEEEE-TTTTTT CS
  Aminotran_5 157 pveeigklakkkgalvlvDaaqavgh 182
                   +++i ++akk++  ++ Daaq++g+
   EPA06748.1 139 FIDRISEIAKKHNLPIIEDAAQSLGS 164
                  ***********************986 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.1   4.1e-12   1.2e-08      46     189 ..      37     159 ..       5     172 .. 0.79

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 4.1e-12
                    HHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTT CS
  Aminotran_1_2  46 lpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealke 141
                    + +l e+ a+f+        k +  vv  +  +a+++a+  +l++  gde+lvp+ t+    n +   g++ v + +  +e++++d ++l++++++
     EPA06748.1  37 HVQLFEKSASFFI-------KSK-YVVAVNSGTAALQAALYALDIKQGDEVLVPSFTFVATANSVVSTGAKPVFVDVL-KENYTMDPDDLQKKITK 123
                    6677777788877.......344.66666555566666666666********************************77.8999************* PP

                    HHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEET CS
  Aminotran_1_2 142 apegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDea 189
                          ktk i+   p +  G va  + + ++   akk+nl ++ D a
     EPA06748.1 124 ------KTKAII---PVHLYGNVAFIDRISEI---AKKHNLPIIEDAA 159
                    ......99**99...88888999999999999...9999999988866 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.2   1.8e-11   5.5e-08      55     175 ..      39     159 ..      33     168 .. 0.85

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 1.8e-11
                      HHHHHHHHHHHT-SEEEEESSHHHHHHHHHHTT.S-TTEEEEEESTSSHHHHHHHHHTHHH.TTCEEEEES.TTSHHHHHHHCCTTEEEEEEES CS
  Cys_Met_Meta_PP  55 svleeriaaLeggeaalavssGmaAiaaailal.lkaGdeivvsddlYggtqrllkkvlkk.lgievkfvd.tsdleelekaikentklvylEt 145
                      + +e++ +   +++ ++av+sG+aA++aa+ al +k+Gde++v +  +  t + + ++  k + ++v   + t d+++l+k+i+++tk++    
       EPA06748.1  39 QLFEKSASFFIKSKYVVAVNSGTAALQAALYALdIKQGDEVLVPSFTFVATANSVVSTGAKpVFVDVLKENyTMDPDDLQKKITKKTKAII--- 129
                      66788888888999******************9899*************99887666555537777766552589**************96... PP

                      S-TTTT----HHHHHHHHHHTT-EEEEEGT CS
  Cys_Met_Meta_PP 146 ptnpllkvvDiekiaklakkagvlvvvDnt 175
                      p     +v+ i +i+++akk++++++ D++
       EPA06748.1 130 PVHLYGNVAFIDRISEIAKKHNLPIIEDAA 159
                      8888999999**************998875 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   1.6e-08   4.9e-05      38     276 ..      42     269 ..      28     288 .. 0.65

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.6e-08
                      HHHHHHHTT-SEEEEES-HHHHHHHHHHHH-.-TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-.EBTTTBE-HHHHHHHS--S-TTS-EEE CS
  Beta_elim_lyase  38 edavaelfgkeaalfvpqGtaAnsillkill.qrgeevivtepahihfdetgaiaelagvklrdlk.nkeaGkmdlekleaaikevgaheekik 129
                      e+ +   +  ++++ v +GtaA + +l +l  ++g+ev+v   + ++   t + ++  g+k++ ++  ke+ +md+++l+++i+++ +     +
       EPA06748.1  42 EKSASFFIKSKYVVAVNSGTAALQAALYALDiKQGDEVLVP--SFTFV-ATANSVVSTGAKPVFVDvLKENYTMDPDDLQKKITKKTK-----A 127
                      333333344556666*********999777559****9985..55554.55555566777777776334449*************444.....5 PP

                      EEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHHHTTSSEEEEESSSTT--SS-EEEEE-HH.......... CS
  Beta_elim_lyase 130 lisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaakslgeivkemfsyvDsvtmslkKdllanvGgvlafrddel........ 215
                      +i +    n        ++ ++++++iakk+++p++ D+A  +      + + +  fs     +m   K ++   Gg++a+++++l        
       EPA06748.1 128 IIPVHLYGN--------VAFIDRISEIAKKHNLPIIEDAAQSLGST--YKGKHAGTFSELGCWSMYPAKVMTSGEGGFVATNNKKLydkllmir 211
                      555555444........589999*****************988776..5566677788888888888888888888888888887755544444 PP

                      ...........HHHHHHHHHHHHT---SSTHHHHH..HHHHHHHHSSTTHHHHHHHHHHHHHHHHHCT-- CS
  Beta_elim_lyase 216 .........edylaerveqrkylggglrqagvlaaleagiraleeglaslerdhktaeqlaeklelvrla 276
                                          k  g +lr  ++ aa   g + +++    l+   k+a++l + +++++++
       EPA06748.1 212 nhgmvhgydT----------KIFGLNLRLPEISAA--IGTIQMKKLPDFLKIREKNAKHLSQLISDLDII 269
                      4444444440..........444444444444444..444444444444444444444444444444444 PP

>> ComK  ComK protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   2.7e-07   0.00081       6      76 ..     121     187 ..     118     194 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 2.7e-07
        ComK   6 ineeTmailpkydekkklvskvieeedeflvkqkplqiiekScryygssyegrkegtkevlgikskvPivi 76 
                 i+++T ai+p+ + ++++    + +  + + k++ l iie++ + +gs+y+g+ +gt + lg  s+ P  +
  EPA06748.1 121 ITKKTKAIIPV-HLYGNV---AFIDRISEIAKKHNLPIIEDAAQSLGSTYKGKHAGTFSELGCWSMYPAKV 187
                 99*********.777664...44455556789999**************************9999999766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2349.90
//
Query:       EPA06749.1  [L=335]
Description: thiamine biosynthesis protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-22   78.7   0.1    5.9e-22   77.8   0.1    1.5  1  NFACT-R_2      NFACT protein RNA binding domain
    1.4e-12   47.6   0.0    2.4e-12   46.8   0.0    1.3  1  ThiI           Thiamine biosynthesis protein (ThiI)
    1.9e-08   33.5   0.1    3.6e-08   32.6   0.0    1.4  2  tRNA_Me_trans  tRNA methyl transferase
     0.0034   16.9   0.2      0.011   15.3   0.1    1.8  2  QueC           Queuosine biosynthesis protein QueC
  ------ inclusion threshold ------
      0.027   15.1   0.0      0.076   13.7   0.0    1.8  1  NFACT-R_1      NFACT protein RNA binding domain
      0.089   12.4   0.0       0.13   11.9   0.0    1.3  1  Asn_synthase   Asparagine synthase


Domain annotation for each model (and alignments):
>> NFACT-R_2  NFACT protein RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.8   0.1     2e-25   5.9e-22       1     102 [.     233     332 ..     233     334 .. 0.93

  Alignments for each domain:
  == domain 1  score: 77.8 bits;  conditional E-value: 2e-25
   NFACT-R_2   1 GRhfrlsekaklIvgReeeEnkflkgll.kkdfvslrakshkGplvlidgelseedlelaarivarYskgkeeeevevkvkkkegeeekeievkplsee 98 
                 GRhfrl+e++k +vgR+++En+++k+++  +d++ ++a++h Gp+ +++g+ +ee  +l +++++rYs++ + e+ +v ++k++ +ee  i ++ ++ee
  EPA06749.1 233 GRHFRLDEQTKFVVGRNKDENEMIKAIAlPGDVL-FQARDHMGPVSILRGKDTEEYEKLVSAVTLRYSDAPKGEQASVIINKNNVKEE--IITQSVEEE 328
                 9*********************************.*********************************************99888774..777777777 PP

   NFACT-R_2  99 eiek 102
                  + k
  EPA06749.1 329 SYIK 332
                 6655 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   0.0   8.2e-16   2.4e-12       4     144 ..       6     150 ..       3     154 .. 0.89

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 8.2e-16
        ThiI   4 gkvlaLlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlkeilekvkeklt.ivllkrkmlriAe 101
                  kv+aLlSgG+DS  a  ++ + G++v +v +k      +  ++   ++ e+  + + +l++ +   ++ e+lk+ ++ + ++   +v ++ +m+ +A+
  EPA06749.1   6 KKVVALLSGGLDSQLAVRMMQEQGFEVSAVAIKTPFCDFDCGRGCGFEIREKADDLNVNLKTVYLGDEYIEMLKHPKHGIGAGFNpCVDCRTMMFNAAK 104
                 69******************************977777778889999999*99999998999999999999999999999888644999********** PP

        ThiI 102 kvaeeegakalvtGesLgqV.aSqtleNlrvisavvnl..lilrPL 144
                 k  ee ga+ ++ Ge Lgq   Sq  + lr i++ + l   i+rPL
  EPA06749.1 105 KHMEEIGAEFIISGEVLGQRpMSQHAPSLRTIEKDSGLvgKIVRPL 150
                 *******************737**********99886522699998 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.0   1.2e-11   3.6e-08       1     123 [.       6     118 ..       6     133 .. 0.88
   2 ?   -3.2   0.0      0.89   2.6e+03     251     267 ..     240     256 ..     231     318 .. 0.61

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 1.2e-11
  tRNA_Me_trans   1 kkvvvalSgGVDSsvaaallkeqgyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfekeykekvfeefleeyeeGrTPnPdv 96 
                    kkvv++lSgG DS +a+ +++eqg+ev +v +k+   + + g++c       ++++ a+ l+++l++v + +ey e + ++   ++  G   nP+v
     EPA06749.1   6 KKVVALLSGGLDSQLAVRMMQEQGFEVSAVAIKTPFCDFDCGRGCGF-----EIREKADDLNVNLKTVYLGDEYIEMLKHP---KHGIGAGFNPCV 93 
                    69********************************9997777777776.....688889****************9876655...56678889**** PP

  tRNA_Me_trans  97 lCNkeiKfgallekakeelgadalatG 123
                     C +++ f+a  ++++e  ga+ + +G
     EPA06749.1  94 DC-RTMMFNAAKKHMEE-IGAEFIISG 118
                    **.5677**99999998.999999998 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.89
  tRNA_Me_trans 251 eeplyVvekdakkntvl 267
                    e++ +Vv  + ++n+++
     EPA06749.1 240 EQTKFVVGRNKDENEMI 256
                    56677777777777665 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   3.6e-06     0.011       1      31 [.       7      37 ..       7      39 .. 0.93
   2 ?   -3.1   0.0       1.5   4.6e+03      96     120 ..      95     118 ..      89     120 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.6e-06
                EEEEE--SSHHHHHHHHHHHHH-SEEEEEEE CS
        QueC  1 kavvllSGGlDSttvlalakkegkevealtf 31
                k+v llSGGlDS  ++ +++++g ev a+ +
  EPA06749.1  7 KVVALLSGGLDSQLAVRMMQEQGFEVSAVAI 37
                6899***********************9976 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.5
                 THHHHHHHHHHHHHHHHT-SEEEE- CS
        QueC  96 aRNliflslaasyaealgaeaiiiG 120
                  R  +++  a    e++gae ii G
  EPA06749.1  95 CRT-MMFNAAKKHMEEIGAEFIISG 118
                 443.344556666677777766665 PP

>> NFACT-R_1  NFACT protein RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.6e-05     0.076       5      77 ..     236     301 ..     234     328 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.6e-05
   NFACT-R_1   5 FkssdgylvimGkDkqeneelikkyleesdvwfhvdkessahvylrlsegeleeipeelleeaaqlakanSia 77 
                 F+  +++  ++G++k ene++   +l+  dv f +  + ++  +lr +++e      e  + + +++  +S a
  EPA06749.1 236 FRLDEQTKFVVGRNKDENEMIKAIALPG-DVLFQARDHMGPVSILRGKDTE------EYEKLVSAVTLRYSDA 301
                 66677788899***************99.*****************44444......2233334444455554 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   4.4e-05      0.13      17      51 ..       5      38 ..       1      69 [. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.4e-05
  Asn_synthase 17 dvpvGalLSGGlDSSliaalaarqsksplktFsig 51
                    +v alLSGGlDS l + ++++q   ++ +++i+
    EPA06749.1  5 KKKVVALLSGGLDSQLAVRMMQEQGF-EVSAVAIK 38
                  56899*****************9975.66666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2341.72
//
Query:       EPA06750.1  [L=603]
Description: V-type ATPase subunit family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-25   89.9   9.8    3.2e-19   68.4   0.0    3.1  3  V_ATPase_I       V-type ATPase 116kDa subunit family
  ------ inclusion threshold ------
       0.37   10.8   1.6         13    5.9   0.1    2.9  3  Molybdopterin_N  Molybdopterin oxidoreductase N-terminal doma


Domain annotation for each model (and alignments):
>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.4   0.0   3.6e-23   3.2e-19     203     415 ..      89     294 ..      18     301 .. 0.76
   2 !   10.4   1.9   1.2e-05      0.11     513     566 ..     369     422 ..     355     445 .. 0.88
   3 !   14.5   0.7   6.9e-07    0.0062     716     809 ..     504     587 ..     498     590 .. 0.79

  Alignments for each domain:
  == domain 1  score: 68.4 bits;  conditional E-value: 3.6e-23
  V_ATPase_I 203 ekveksvfiiffqgeqlkekikkicesfgaklyelpeseeereekl.keveeriedlekvleqteealkevleeiakeleewklkvkkekaiyhtLnlf 300
                 e+ eks+ +i+ + e+ ++k+ ki  sf+ +++++pe   +  +++ +  e++i++l+    + ++++  + ++i +++  ++ k    k + ++L + 
  EPA06750.1  89 ENKEKSALLIISNVEE-SDKVLKILRSFNSNTFKIPEGFPQIPSEAyALAESKIKELTAKQVSISKEIAGLKKKIRQDILVIHEKALVAKDVLEMLRKP 186
                 4455888888777665.689****************998877555405556788887766666666666666666666666666666666666666555 PP

  V_ATPase_I 301 nldvtkkvliaegWvpkeeleeiqkalkeateessssvpsilneietketpPTyfrtnkfteafQeivdaYGiarYrEvNpalftiitFPFlFavMFGD 399
                     tk++ + +g++pk+ +e+ +++ k+ +    s v+ + ++ +  ++ PT f   kf ++f  i  + Gi++  E  p+++   ++P  +++MF D
  EPA06750.1 187 --GGTKNFAVIQGYIPKKMEEKFKDSTKQWM----SVVEDV-SDPKLIDESPTLFDNKKFVRTFEVITKSQGIPKKGEPDPTPMIALMWPIFYGLMFAD 278
                 ..678999*************9999999877....333333.333445789************************************************ PP

  V_ATPase_I 400 iGHGlllllfalllvl 415
                 +GHGlll+ ++ll+ +
  EPA06750.1 279 MGHGLLLMGLGLLFKV 294
                 *******999988755 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 1.2e-05
  V_ATPase_I 513 mKlsvilGviqMlfgvllslvNalyfkkkldiilefiPqllfllsifgYlvlli 566
                 +K+s  +Gvi+++++++l +    ++ +kl +++e iP++ +   i++ ++++i
  EPA06750.1 369 LKVSLFIGVIHLVWAMVLRVRRLAQEGHKLVMFTEAIPNITLYGGIVVIMMCAI 422
                 69**************************************99999999998887 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 6.9e-07
  V_ATPase_I 716 ciSnTASYLRLWALSLAHaqLseVlwemvlkkallksksvlgvillvilfavfavltvavLllmeglsafLHaLRLhWVEfqsKFykgdGykFe 809
                 ++ +T SY RL  + L Ha L      m++++a+ +    lg ++   ++a+ +   ++++ ++egl  ++ +LRLh  Ef +K+y g   +F+
  EPA06750.1 504 SLAHTISYARLGIMLLVHAALL-----MTVNNAFVS----LGGAASGGAMAMIIGGNLGIM-MIEGLIVYIQSLRLHLYEFFTKWYVGGSQPFR 587
                 67899*************9984.....777776655....333444455666667777775.67************************999997 PP

>> Molybdopterin_N  Molybdopterin oxidoreductase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1     0.014   1.3e+02      24      34 ..     255     265 ..     244     269 .. 0.75
   2 ?   -1.7   0.0      0.35   3.2e+03       3       9 ..     301     307 ..     300     309 .. 0.79
   3 ?    5.9   0.1    0.0015        13       1      16 [.     328     343 ..     328     350 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.014
  Molybdopterin_N  24 egDpdPsplle 34 
                      +g pdP+p+++
       EPA06750.1 255 KGEPDPTPMIA 265
                      458******96 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.35
  Molybdopterin_N   3 sHWGafr 9  
                      s+WG++ 
       EPA06750.1 301 SRWGMLI 307
                      99**985 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.0015
  Molybdopterin_N   1 tasHWGafraevkdGk 16 
                      + sH+G+f++  ++G 
       EPA06750.1 328 HISHMGPFEGILEEGG 343
                      77********999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (603 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1010  (0.0563333); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.72u 0.36s 00:00:01.08 Elapsed: 00:00:00.55
# Mc/sec: 3285.47
//
Query:       EPA06751.1  [L=125]
Description: hypothetical protein BG20_I0096 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.32s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 763.36
//
Query:       EPA06752.1  [L=103]
Description: ATP synthase subunit C [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.3e-16   58.5  16.9    6.3e-16   58.5  16.9    2.0  2  ATP-synt_C  ATP synthase subunit C


Domain annotation for each model (and alignments):
>> ATP-synt_C  ATP synthase subunit C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.6     0.018   3.2e+02      39      57 ..       7      25 ..       2      26 .. 0.76
   2 !   58.5  16.9   3.5e-20   6.3e-16       1      60 []      41     100 ..      41     100 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.018
                HHHHHHHHHHHHHHHHHHH CS
  ATP-synt_C 39 sliilafaeaialygLiva 57
                +l+ ++ + a++l gL  a
  EPA06752.1  7 LLLAVIAISATGLTGLAYA 25
                5778888888898888765 PP

  == domain 2  score: 58.5 bits;  conditional E-value: 3.5e-20
                 HHHHHHH.GGGHHHHHHHHHHHHHHHHHHHHSGHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
  ATP-synt_C   1 lgaglavGlsalgsGigiGkagsagiravarnpklftksliilafaeaialygLivalil 60 
                 lgagla Gl+a g+Gig G +g+ag+  +++np l++k++i+++++e+ia+yg+++++i+
  EPA06752.1  41 LGAGLAFGLAAAGAGIGLGQVGAAGLAVISENPALQSKVFIFVGMVESIAIYGIVMMFII 100
                 7**********************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       892  (0.0497518); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 668.34
//
Query:       EPA06753.1  [L=170]
Description: flavoprotein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-33  116.1   0.7    1.5e-33  115.8   0.7    1.0  1  Flavoprotein   Flavoprotein
  ------ inclusion threshold ------
      0.051   14.0   0.0      0.096   13.1   0.0    1.5  1  BRCT           BRCA1 C Terminus (BRCT) domain
       0.07   13.6   0.0       0.11   13.0   0.0    1.4  1  NAD_binding_7  Putative NAD(P)-binding
       0.08   12.8   0.0        0.1   12.5   0.0    1.2  1  YjeF_N         YjeF-related protein N-terminus


Domain annotation for each model (and alignments):
>> Flavoprotein  Flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.8   0.7   3.4e-37   1.5e-33       1     125 [.      29     164 ..      29     169 .. 0.95

  Alignments for each domain:
  == domain 1  score: 115.8 bits;  conditional E-value: 3.4e-37
                   EEEEEEE-SSCGGGCHHHHHHHHHHTTEEEEEEESCHHHHCCHHGGS...........TCSSHHHHHH..CTTESEEEEEEEEHHHHHHHHTT--SS CS
  Flavoprotein   1 kkillgiTGsvaaikalellekLkkegievqvvltkaAkkfiskeklklaa.......redpilhiel..rrwadllviaPasantlakianGiadn 88 
                   kki+l+i Gsvaa+ka+el + L ++g++v++v ++a++k+++++++k+a+        +++++hi l   ++ dl++++Pa+antl+k+anGi d+
    EPA06753.1  29 KKIVLCIAGSVAAYKAIELARLLMRHGADVTCVTSNAVTKLVQPDYFKWATgnkvitkLTGDLEHIRLadYNKSDLIIVYPATANTLGKLANGIDDT 125
                   79*******************************************999999999999999********5556************************* PP

                   HHHHHHHT..HCCTTEEEEE.--HHCCTCSTCHHHHHHH CS
  Flavoprotein  89 lltlilra..takkpiliaPamnpamyenpqtlknlekl 125
                   ++++il +  ++k pil++Pam+ +my+n +++kn++ l
    EPA06753.1 126 PISTILTVgfGSKIPILMCPAMHASMYDNAAVKKNINFL 164
                   ******8888**************************988 PP

>> BRCT  BRCA1 C Terminus (BRCT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.1e-05     0.096       8      71 ..      30     108 ..      24     110 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.1e-05
                 TEEEEEEESTSSHHHHHHHHHHHHTTCEEESSCSTTSSEEEESSS...............HSHHHHHHHHHHTTSEEEE CS
        BRCT   8 gckfvitgvldnftrdeleelikehGGkvttevskktthlvvgep...............esrslkylealklnipivh 71 
                 +++ +i g+   ++  el +l+  hG+ vt   s+ +t lv  ++               +++  ++  ++k+   iv 
  EPA06753.1  30 KIVLCIAGSVAAYKAIELARLLMRHGADVTCVTSNAVTKLVQPDYfkwatgnkvitkltgDLEHIRLADYNKSDLIIVY 108
                 5677779999*******************99999999999987778877776676666666666667777777777776 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.4e-05      0.11       4      67 ..      25     107 ..      23     132 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.4e-05
  NAD_binding_7   4 dlkgkkvlvvGgGevAarkv....rklleagakvtvvapev.keele.elvklaeee............le.kdlegadlvia 67 
                    +l++kk+++  +G+vAa k+    r l++ ga+vt v+ +  ++ ++ + +k+a  +            ++ +d ++ dl+i+
     EPA06753.1  25 ELTEKKIVLCIAGSVAAYKAielaRLLMRHGADVTCVTSNAvTKLVQpDYFKWATGNkvitkltgdlehIRlADYNKSDLIIV 107
                    7899***************822224456799****998883233333433334422222222222222122233445555554 PP

>> YjeF_N  YjeF-related protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.3e-05       0.1      25      70 ..      27      69 ..      15     106 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.3e-05
      YjeF_N 25 aekkvlvlvGsgnnGgdglaaArhLaqegakVtvllleeeeklded 70
                 ekk+++++ +    ++++ +Ar L ++ga+Vt+++ +     ++ 
  EPA06753.1 27 TEKKIVLCIAGSVAAYKAIELARLLMRHGADVTCVTSN---AVTKL 69
                6889999999999*********************6543...33444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1131.69
//
Query:       EPA06754.1  [L=928]
Description: copper resistance protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.5e-14   51.9   0.1     0.0024   17.5   0.0    5.2  5  SGL            SMP-30/Gluconolactonase/LRE-like region
    1.3e-13   51.2   2.6    1.3e-13   51.2   2.6    2.9  3  CopD           Copper resistance protein D
    1.5e-09   38.8   0.1    3.4e-09   37.6   0.1    1.7  1  CopC           CopC domain
    6.4e-08   31.9  10.5        9.1    6.9   0.3    8.2  8  Reg_prop       Two component regulator propeller
     0.0039   17.8   0.2      0.015   15.9   0.0    2.1  2  YtkA           YtkA-like
  ------ inclusion threshold ------
       0.17   13.0   0.6       0.88   10.7   0.6    2.2  1  PPC            Bacterial pre-peptidase C-terminal domain
        6.7    7.1  12.4        0.6   10.5   2.2    3.0  3  DUF4149        Domain of unknown function (DUF4149)


Domain annotation for each model (and alignments):
>> SGL  SMP-30/Gluconolactonase/LRE-like region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.4   0.0    0.0092        24      11      75 ..     593     660 ..     588     673 .. 0.71
   2 !   12.8   0.0   2.6e-05     0.067     142     225 ..     630     713 ..     626     719 .. 0.72
   3 !    5.9   0.0    0.0032       8.1     189     219 ..     720     750 ..     713     760 .. 0.88
   4 !    7.8   0.0   0.00088       2.3     186     224 ..     760     798 ..     753     802 .. 0.89
   5 !   17.5   0.0   9.4e-07    0.0024     186     230 ..     803     846 ..     797     862 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0092
         SGL  11 egaLlwvDilgqrihrldpatgketvldtpesvGaiaprkd.grlvvas..ksglalldlasgeletl 75 
                 +++++ +D  + +++++++++++ t++++++  ++i  +++ g++ ++   ++++ ++++++++++t 
  EPA06754.1 593 KDSIWVSDPSAPKLWKFSLDSKNFTSYSFDGLTSIILTKDNqGKIWFTDtpRNQIGYFEPSTQKITTK 660
                 67788888888899999999999999999988888888444788888762234555667777777665 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 2.6e-05
         SGL 142 spdgktlYl.aDsltrkiwaydvdaeggklsnrrvf.adlkkgegepDGlavDaeGnvwvAvwgggkvvrfdpdGklieeiklpak 225
                 ++d++  ++ +D+++++i  ++ ++++   + +++  +d   +++    +  D +Gn+w+ v +++++ +++p+ +  ee+klp++
  EPA06754.1 630 TKDNQGKIWfTDTPRNQIGYFEPSTQKI--TTKTLPkIDPVINDNIATFIQADFDGNIWISVTNKDTILKYQPKFDSFEEVKLPTR 713
                 5566554444999999999999865554..444433345444443444466788********************999*******65 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.0032
         SGL 189 lavDaeGnvwvAvwgggkvvrfdpdGkliee 219
                 l++D eG++w +  ++gk+  ++p+ + i e
  EPA06754.1 720 LTIDGEGKIWFTESQAGKIGFINPQNNKISE 750
                 79***********************887776 PP

  == domain 4  score: 7.8 bits;  conditional E-value: 0.00088
         SGL 186 pDGlavDaeGnvwvAvwgggkvvrfdpdGklieeiklpa 224
                 p  l+ D +Gn+w+A   g  +++fdp  +  e+i++p 
  EPA06754.1 760 PEALMFDDKGNLWIAEHTGLAITKFDPILETFEKITVPD 798
                 556789**********************999******94 PP

  == domain 5  score: 17.5 bits;  conditional E-value: 9.4e-07
         SGL 186 pDGlavDaeGnvwvAvwgggkvvrfdpdGklieeiklpakrvtsc 230
                 p G+  D+ Gn+w+A+   +k++ +dpd k + e+ +p + ++  
  EPA06754.1 803 PYGMSFDKYGNIWIAQHTVDKIAAYDPDNKNLIEVPIP-TTTSFA 846
                 679*************************9988889998.444444 PP

>> CopD  Copper resistance protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   1.0     0.056   1.4e+02       6      57 ..     187     243 ..     183     251 .. 0.77
   2 ?   -2.0   0.1       1.8   4.7e+03      48      69 ..     292     315 ..     261     326 .. 0.67
   3 !   51.2   2.6   5.2e-17   1.3e-13       4     105 .]     331     433 ..     328     433 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.056
        CopD   6 rFsrlalaavavvlvtGvvnallrvg.....lagllttayGrlllaKlalllvllal 57 
                 +F ++  + + +++++ +++ ++++      + + ++t+ G ++l+ ++  +vllal
  EPA06754.1 187 KFMKITGIGLLLIFASNILMLAIQAIrletsVINVIQTNFGNIWLIRMVITIVLLAL 243
                 67788888888888999988766633333435777789********99999999998 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.8
        CopD  48 lalllvllalaalnrf..rlvprl 69 
                 +  +++++ ++++++f   l+p+l
  EPA06754.1 292 IHNFVAAVWIGGIIYFvfTLLPTL 315
                 555788888888888766666766 PP

  == domain 3  score: 51.2 bits;  conditional E-value: 5.2e-17
        CopD   4 lrrFsrlalaavavvlvtGvvnallrvg.lagllttayGrlllaKlalllvllalaalnrfrlvprleaatgaggqalrhrlrrsaalelvlalvvlll 101
                 ++rFs ++++av++v++tG ++++l+ + ++ ++++ yG+l+ aK+a  +++++++++ +f + + +e++ ++g+ a  ++l+rs+   ++l++  l++
  EPA06754.1 331 IPRFSIMVVIAVGIVIITGPTLMWLLESnVNLITESIYGKLIFAKIAIAAIMIGFGGYFQFKIQKNAERDLQKGTIAIYKKLKRSLKFDVALGITLLVV 429
                 78********************9998777788888********************************9996666666666******************* PP

        CopD 102 aaal 105
                 +a+l
  EPA06754.1 430 VALL 433
                 9987 PP

>> CopC  CopC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   0.1   1.3e-12   3.4e-09       1      92 []      22     117 ..      22     117 .. 0.88

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 1.3e-12
        CopC   1 HaalvsstPaagatvaaapeevtLtFsepvel..skvkvtdpdgke.evetvdaktveaelkvplpelaaGtYtVewrvvsa.DGHpvsGsfsFtv 92 
                 H+   +stP   +      +++ ++Fsepvel  s +kv+d++g+e + ++ +  + + +l v+ p+l++G YtV+ +++s+ DGH v  +f+F+v
  EPA06754.1  22 HPFTIDSTPNSSTNAPVGTTKIIVHFSEPVELdfSFLKVIDSNGEEiDNKDSKYFDGDSSLIVTTPPLDEGVYTVTTKALSKiDGHLVPSAFVFAV 117
                 778899**************************************6663333344447778889999999************88***********97 PP

>> Reg_prop  Two component regulator propeller
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1      0.15   3.9e+02       6      20 ..     217     231 ..     214     232 .. 0.84
   2 ?   -4.2   0.1         7   1.8e+04      13      21 ..     591     599 ..     590     599 .. 0.71
   3 ?    4.5   0.0     0.021        54      10      20 ..     629     639 ..     620     642 .. 0.79
   4 !    6.9   0.3    0.0035       9.1       4      21 ..     671     688 ..     668     691 .. 0.72
   5 ?    3.5   0.0     0.047   1.2e+02       7      20 ..     716     730 ..     710     731 .. 0.82
   6 ?    5.4   0.0     0.011        28       9      21 ..     762     774 ..     758     775 .. 0.89
   7 !    5.8   0.0    0.0078        20       9      21 ..     805     817 ..     799     819 .. 0.87
   8 ?    1.2   0.0      0.25   6.5e+02      13      20 ..     852     859 ..     840     860 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.15
                 CEEEEEE-TTSCEEE CS
    Reg_prop   6 nvtaileDsdGrlWv 20 
                 +v+ + +++ G++W+
  EPA06754.1 217 SVINVIQTNFGNIWL 231
                 67788999******7 PP

  == domain 2  score: -4.2 bits;  conditional E-value: 7
                 -TTSCEEEE CS
    Reg_prop  13 DsdGrlWvG 21 
                 D +  +Wv+
  EPA06754.1 591 DGKDSIWVS 599
                 556679*95 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.021
                 EEE-TTSCEEE CS
    Reg_prop  10 ileDsdGrlWv 20 
                 + +D++G++W+
  EPA06754.1 629 LTKDNQGKIWF 639
                 677*******9 PP

  == domain 4  score: 6.9 bits;  conditional E-value: 0.0035
                 SSCEEEEEE-TTSCEEEE CS
    Reg_prop   4 snnvtaileDsdGrlWvG 21 
                 +n  t i+ D dG++W++
  EPA06754.1 671 DNIATFIQADFDGNIWIS 688
                 455556777********8 PP

  == domain 5  score: 3.5 bits;  conditional E-value: 0.047
                 EE.EEEE-TTSCEEE CS
    Reg_prop   7 vt.aileDsdGrlWv 20 
                 v  a+  D +G++W+
  EPA06754.1 716 VPfALTIDGEGKIWF 730
                 4459999*******8 PP

  == domain 6  score: 5.4 bits;  conditional E-value: 0.011
                 EEEE-TTSCEEEE CS
    Reg_prop   9 aileDsdGrlWvG 21 
                 a++ D +G+lW++
  EPA06754.1 762 ALMFDDKGNLWIA 774
                 6889*******97 PP

  == domain 7  score: 5.8 bits;  conditional E-value: 0.0078
                 EEEE-TTSCEEEE CS
    Reg_prop   9 aileDsdGrlWvG 21 
                  +  D+ G++W++
  EPA06754.1 805 GMSFDKYGNIWIA 817
                 6788*******97 PP

  == domain 8  score: 1.2 bits;  conditional E-value: 0.25
                 -TTSCEEE CS
    Reg_prop  13 DsdGrlWv 20 
                 D +G++W+
  EPA06754.1 852 DDKGNVWF 859
                 99*****8 PP

>> YtkA  YtkA-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       2.4     6e+03      57      73 ..      82      98 ..      45     103 .. 0.56
   2 !   15.9   0.0   5.7e-06     0.015       9      85 ..     466     545 ..     459     546 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.4
        YtkA 57 tkvelkesedGvYeaev 73
                  v++ +   GvY +++
  EPA06754.1 82 LIVTTPPLDEGVYTVTT 98
                33444445667776665 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 5.7e-06
        YtkA   9 velvspeepkagentivvt.vtqggkpVedad.vkvefwmpameGmeemttkv...elkesedGvYeaevnfsmeGtWqvql 85 
                 ++++ + +++ g nti ++  + ++kp+ d + +kv+++ p+  + ++ + +      +es++ ++++e++f+ +G+Wqv++
  EPA06754.1 466 FDVEIT-PFSSGTNTIFIKmSDFEDKPLIDSNqIKVKISNPQ-RNIAPIEIPMkiiNQEESKPIEFQGEITFGFSGQWQVEI 545
                 444443.5799*******999999***999988********9.5666665555222344499******************87 PP

>> PPC  Bacterial pre-peptidase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.6   0.00034      0.88       8      66 ..      35      96 ..      25      99 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00034
                EE-TT-E.EEEEES-TT..SE...EEEE-TT..-SS-EE-STT-TTS-TTS-EE-.SSSEEEEE CS
         PPC  8 evpagds.ltididggtidld...Lylldsngtsvaaydansapsgsdeyiefta.pqaGtYyv 66
                ++p+g++ +++  +     ld   L + dsng ++++  ++ + +g++++i  t+ ++ G+Y v
  EPA06754.1 35 NAPVGTTkIIVHFSEPV-ELDfsfLKVIDSNGEEIDN-KDSKYFDGDSSLIVTTPpLDEGVYTV 96
                67888888888888888.55555********888888.7777888888888866679*****98 PP

>> DUF4149  Domain of unknown function (DUF4149)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.7     0.065   1.7e+02      45      82 ..     234     271 ..     191     274 .. 0.68
   2 ?   10.5   2.2   0.00023       0.6       2      61 ..     296     358 ..     295     399 .. 0.81
   3 ?   -3.8   0.0       6.6   1.7e+04      46      54 ..     425     433 ..     411     442 .. 0.60

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.065
     DUF4149  45 glalsvlllltevavg..seklaseellqlllllvvlllt 82 
                 ++++ vll+l ++  +  ++kl+ +++  +l++++vl+ t
  EPA06754.1 234 MVITIVLLALWFG--MdrKKKLSIKNKIPMLAVTLVLIGT 271
                 3334444444444..446999***********99999865 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00023
     DUF4149   2 slglllGsqlwvtfvvapvlfrsLprhqfgelqsklFplyfglglalsvlllltevavg....s 61 
                 ++++++G++++++f   p+l  +L++   +++   l p++  + ++  +++++t +  +    s
  EPA06754.1 296 VAAVWIGGIIYFVFTLLPTLS-QLEETKREKMTLVLIPRFSIMVVIAVGIVIITGPTLMwlleS 358
                 689****************95.5788889**************************999854440 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 6.6
     DUF4149  46 lalsvllll 54 
                 ++l v++ll
  EPA06754.1 425 TLLVVVALL 433
                 233333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (928 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       775  (0.0432261); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.74u 0.31s 00:00:01.05 Elapsed: 00:00:00.47
# Mc/sec: 5941.93
//
Query:       EPA06755.1  [L=114]
Description: dUTP diphosphatase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.1e-18   67.1   5.1    2.8e-13   50.4   0.2    2.0  2  dUTPase_2  dUTPase
    0.00057   20.3   0.0    0.00072   20.0   0.0    1.2  1  PRA-PH     Phosphoribosyl-ATP pyrophosphohydrolase


Domain annotation for each model (and alignments):
>> dUTPase_2  dUTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.4   0.2   3.1e-17   2.8e-13       2      88 ..       9      90 ..       8      92 .. 0.88
   2 !   21.6   0.9   2.2e-08    0.0002     139     166 .]      87     114 .]      83     114 .] 0.93

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 3.1e-17
                HHHHHHHHHHHHHHHSTTH.....HH-HHHHH....HHHHHHHHHHHTTS.---SSSSTT---HHHHHHHHHHHHHHHHHHHHCHHC CS
   dUTPase_2  2 lksllelQkeLderiekkwnlkkkrkklsdwleekllAllvElaElanetrsfKyWknkkksdlekvleElvDilHFllslalelkd 88
                l ++++lQk+L e+++ +   k+++ ++s ++    +A++ E+ El   t  +K+Wk+  + + ++ +eEl+Di+HF++   lel+ 
  EPA06755.1  9 LDEIFKLQKGLSEMMKLDRYPKDSEGRISALS----TAIMHEAVELQRTT-NWKWWKTPVPFNVSEAREELIDIWHFVVQASLELNL 90
                789*************9994444444666666....**********9999.****************************99999875 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 2.2e-08
                 HHTS-...HHHHHHHHHHHHHHHHHTTT CS
   dUTPase_2 139 llgfneeelvkaYvaKnelNlkRqengY 166
                  l+++ +++ ++Y++Kne+N +Rq ngY
  EPA06755.1  87 ELNLTPDDILEEYKKKNEINRERQRNGY 114
                 589999*********************9 PP

>> PRA-PH  Phosphoribosyl-ATP pyrophosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0     8e-08   0.00072      24      83 .]      36     103 ..      19     103 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 8e-08
                 HHHHHHHHHHHHHHHHHHT-SC........HHHHHHHHHHHHHHHHHHHHHHCT--CHHHHHHHHHHH CS
      PRA-PH  24 aslraaligEEavElleaaseg........dlaeladelaDllYvtygllvllGidldavfeevhran 83 
                  s ++++i+ EavEl+ +++ +        +  e  +el+D++ ++  +  +l++++d+++ee +++n
  EPA06755.1  36 ISALSTAIMHEAVELQRTTNWKwwktpvpfNVSEAREELIDIWHFVVQASLELNLTPDDILEEYKKKN 103
                 455789999**********97788889999*********************************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 741.05
//
Query:       EPA06756.1  [L=161]
Description: hypothetical protein BG20_I0084 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00098   19.0   3.6     0.0011   18.9   3.6    1.1  1  Yuri_gagarin  Yuri gagarin
     0.0043   17.1   1.9     0.0043   17.1   1.9    2.2  2  DUF2730       Protein of unknown function (DUF2730)
     0.0074   16.2   0.3     0.0087   16.0   0.3    1.2  1  Kei1          Inositolphosphorylceramide synthase subunit Kei
  ------ inclusion threshold ------
      0.036   14.3   0.3      0.063   13.6   0.0    1.5  2  MLANA         Protein melan-A
       0.11   11.4   7.9       0.13   11.2   7.9    1.1  1  Vps53_N       Vps53-like, N-terminal
        0.2   11.2   7.1       0.23   10.9   7.1    1.0  1  Allexi_40kDa  Allexivirus 40kDa protein
       0.24   11.6   7.9       0.16   12.2   5.9    1.5  2  Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
        0.3   10.4   8.4       0.43    9.9   8.4    1.2  1  FAM76         FAM76 protein
       0.33   11.1   3.4        4.6    7.4   0.2    2.8  3  CheY-binding  CheY binding
       0.36   10.1  10.1      0.098   11.9   4.1    2.0  2  DUF4763       Domain of unknown function (DUF4763)
        2.1    8.8  10.5        1.7    9.1   0.3    2.6  3  FlaC_arch     Flagella accessory protein C (FlaC)


Domain annotation for each model (and alignments):
>> Yuri_gagarin  Yuri gagarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   3.6   6.6e-07    0.0011      38     112 ..      84     157 ..      52     161 .] 0.80

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 6.6e-07
  Yuri_gagarin  38 difeekseqeqkekeflvanerlaceidalketlkdrdeqikqlqsmitsysdlsennrlkeeiydlkqknceqa 112
                   +i++  ++q   ++e+ +a ++l+ e+++lke++k +d  i++l++ i++ + l + + lk e+ +lk+  +e+ 
    EPA06756.1  84 QIYASGENQV-SLTEIKAAQNELSGELSKLKESVKLKDSEIERLNQEISNLQTLVQIESLKTELANLKMLASERK 157
                   4444444443.44556788889***********************************************988765 PP

>> DUF2730  Protein of unknown function (DUF2730)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.2      0.29   4.7e+02       7      38 ..      36      70 ..      34     108 .. 0.59
   2 !   17.1   1.9   2.6e-06    0.0043      34      76 ..     108     150 ..     104     159 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.29
     DUF2730  7 wglilavisvvvavilllldsk...Yakredlekl 38
                + +++av  + +  +  ++++k   Y+ +++ +  
  EPA06756.1 36 FVFLMAVPITWFLTFTCWISQKstdYMHKHETHMS 70
                56666666666666776666543336666666544 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 2.6e-06
     DUF2730  34 dleklaekveendkrlteletkvenLPtakdlekLkllladlr 76 
                 +l+kl+e+v+ +d+ +++l+++++nL t +++e+Lk++la+l+
  EPA06756.1 108 ELSKLKESVKLKDSEIERLNQEISNLQTLVQIESLKTELANLK 150
                 899**************************************98 PP

>> Kei1  Inositolphosphorylceramide synthase subunit Kei1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.3   5.3e-06    0.0087      73     147 ..      19      94 ..       7     144 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 5.3e-06
        Kei1  73 llla.vlYllDt..vistaytvlFavdWflvleehdaaaaastagsasaeatagatapaavssaasatsasvsaatss 147
                 +l+  + Y++D   ++++++ ++  ++Wfl+ +   ++++++   ++ ++++++ ++++  s+a++++  ++ +++ s
  EPA06756.1  19 VLTGlWPYFVDFapILNFVFLMAVPITWFLTFTCWISQKSTD-YMHKHETHMSHNEKKS-LSNAQTTQIYASGENQVS 94 
                 444449999996559***************966666555543.2233333333332222.222222222222222222 PP

>> MLANA  Protein melan-A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.9e-05     0.063      30      93 ..      39     102 ..      34     108 .. 0.79
   2 ?   -2.7   0.1       4.2   6.8e+03      68      68 ..     133     133 ..     110     158 .. 0.52

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.9e-05
       MLANA  30 llvvvLaillllgCwyykrrsGYkslrskslkvstlktlvgegeleelakadsklalqefknfe 93 
                 l++v ++  l ++Cw  ++   Y + ++ +++ +  k+l + ++++  a+ +++++l+e k  +
  EPA06756.1  39 LMAVPITWFLTFTCWISQKSTDYMHKHETHMSHNEKKSLSNAQTTQIYASGENQVSLTEIKAAQ 102
                 566778899**************998888776666666666666666699********997665 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.2
       MLANA  68 l 68 
                 l
  EPA06756.1 133 L 133
                 2 PP

>> Vps53_N  Vps53-like, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   7.9   7.8e-05      0.13      39     120 ..      75     155 ..      55     161 .] 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.8e-05
     Vps53_N  39 deiksvvraqanvgekgkealeeaqkaieelfqkikeikdkaekseemvkeitrdIkqLDiAKknlttsiTtlkrLkmLvta 120
                 +++ +++ +q   + + + +l+e+++a +el+ +++++k+  +  ++ ++ + ++I++L    + +    T l +LkmL++ 
  EPA06756.1  75 KSLSNAQTTQIYASGENQVSLTEIKAAQNELSGELSKLKESVKLKDSEIERLNQEISNLQTLVQ-IESLKTELANLKMLASE 155
                 33344444555556667999***************************************98754.77777999*****9875 PP

>> Allexi_40kDa  Allexivirus 40kDa protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   7.1   0.00014      0.23      55     132 ..      67     151 ..      59     161 .] 0.74

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00014
  Allexi_40kDa  55 thishdvdsiinklnpvslls...qttlLselrdalrtltklldklksvekklels....aetasdskllkklesietsleelha 132
                   th+sh+  + +++ +++++ +   ++ +L+e+++a ++l+ +l klk+  k +  +    ++++s+ ++l ++es++t+l +l++
    EPA06756.1  67 THMSHNEKKSLSNAQTTQIYAsgeNQVSLTEIKAAQNELSGELSKLKESVKLKDSEierlNQEISNLQTLVQIESLKTELANLKM 151
                   9**********99999998875656679**********99999999887654444400114556666777788888887777654 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   5.9   9.5e-05      0.16      44     107 ..      70     133 ..      60     134 .. 0.89
   2 ?   10.3   5.0   0.00038      0.61      42      94 ..      92     143 ..      89     159 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.5e-05
                   HHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCTS--- CS
  Seryl_tRNA_N  44 eleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaeleklllaiPNi 107
                     +e ++ +N+ + +I    +++   +e++a  +el+ el++l++ +k  ++e+e l ++i N+
    EPA06756.1  70 SHNEKKSLSNAQTTQIYASGENQVSLTEIKAAQNELSGELSKLKESVKLKDSEIERLNQEISNL 133
                   55678999999999999999999999***********************************997 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00038
                   HHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHH..HHHHHH CS
  Seryl_tRNA_N  42 qveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkalea..elkele 94 
                   qv l e++a +Nels e +k+k++    +    e++ l++e+++l++  + + l+
    EPA06756.1  92 QVSLTEIKAAQNELSGELSKLKESV---KLKDSEIERLNQEISNLQTlvQIESLK 143
                   7888999999999999999999765...334445555555555555433333333 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   8.4   0.00026      0.43     130     237 ..      55     155 ..      47     161 .] 0.35

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00026
       FAM76 130 sykralakakeeeeekrskskkkkskskkskkskekskekkaskkkskkhkkrssrlevskleeeklaeekesnetskksldsnssdhlvavtqLkeei 228
                 s k +    k+e++ +++++k+ + ++++++   + +   ++ + ++ k ++++ + e skl+e+ + + +e ++    + + ++ + lv+++ Lk+e+
  EPA06756.1  55 SQKSTDYMHKHETHMSHNEKKSLS-NAQTTQIYASGE---NQVSLTEIKAAQNELSGELSKLKESVKLKDSEIERL---NQEISNLQTLVQIESLKTEL 146
                 444444444444333222111111.111111111111...111111111222222233344442222222222222...33344445677777777777 PP

       FAM76 229 aslkkqleq 237
                 a+lk   ++
  EPA06756.1 147 ANLKMLASE 155
                 777655444 PP

>> CheY-binding  CheY binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       1.1   1.8e+03       2      22 ..      93     112 ..      92     117 .. 0.65
   2 ?    7.4   0.2    0.0028       4.6       6      27 ..     117     138 ..     111     141 .. 0.89
   3 ?    4.3   0.1     0.027        44      12      33 ..     139     160 ..     137     161 .] 0.84

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.1
  CheY-binding   2 veLsgvkekDvelLleELgnL 22 
                   v+L+++k+  ++ L+ EL +L
    EPA06756.1  93 VSLTEIKAA-QNELSGELSKL 112
                   667777665.45577777766 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0028
  CheY-binding   6 gvkekDvelLleELgnLGevse 27 
                   ++k++++e L +E+ nL ++++
    EPA06756.1 117 KLKDSEIERLNQEISNLQTLVQ 138
                   89***************98876 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.027
  CheY-binding  12 velLleELgnLGevseqekagd 33 
                   +e L++EL+nL  +++++k+++
    EPA06756.1 139 IESLKTELANLKMLASERKSKN 160
                   789********99888888765 PP

>> DUF4763  Domain of unknown function (DUF4763)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.5     0.046        74     185     211 ..      58      84 ..      51      88 .. 0.83
   2 ?   11.9   4.1     6e-05     0.098      92     154 ..      85     149 ..      78     157 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.046
     DUF4763 185 fsnlirslrtkmeeslkklvplreykq 211
                   ++++++ t+m++  kk + +++ +q
  EPA06756.1  58 STDYMHKHETHMSHNEKKSLSNAQTTQ 84 
                 568************999999888776 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 6e-05
     DUF4763  92 lelltseqpeileLqrnnhkLrqqlaelqqhlkasrkslkelreslcqekkrlr..klqkrlnel 154
                 + ++ ++q+ + e++ ++  L  +l++l+++ k  ++++++l++++++++  ++  +l+++l  l
  EPA06756.1  85 IYASGENQVSLTEIKAAQNELSGELSKLKESVKLKDSEIERLNQEISNLQTLVQieSLKTELANL 149
                 5567789***************************************9988754411676666655 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       5.4   8.8e+03       6      17 ..      66      78 ..      62      84 .. 0.45
   2 ?    9.1   0.3    0.0011       1.7      13      38 ..      92     117 ..      88     120 .. 0.91
   3 ?    5.8   1.3     0.011        18       2      27 ..     123     150 ..     122     155 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 5.4
   FlaC_arch  6 Enklsklst.ele 17
                E+ +s  +  +l+
  EPA06756.1 66 ETHMSHNEKkSLS 78
                3344444333444 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0011
   FlaC_arch  13 steletvkkeneelsksveelkenVk 38 
                 +++l+ +k+ ++els ++ +lke+Vk
  EPA06756.1  92 QVSLTEIKAAQNELSGELSKLKESVK 117
                 67999********************7 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.011
   FlaC_arch   2 idelEnklsklst..eletvkkeneels 27 
                 i+ l +++s+l+t  ++e++k+e+ +l+
  EPA06756.1 123 IERLNQEISNLQTlvQIESLKTELANLK 150
                 78899*******99999****9998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2520  (0.140554); expected 358.6 (0.02)
Passed bias filter:                      841  (0.0469072); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 1096.29
//
Query:       EPA06757.1  [L=84]
Description: hypothetical protein BG20_I0032 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.01   15.9   0.1      0.013   15.6   0.1    1.2  1  DUF1931   Domain of unknown function (DUF1931)
       0.11   12.4   0.0       0.14   12.1   0.0    1.2  1  Ub-Mut7C  Mut7-C ubiquitin


Domain annotation for each model (and alignments):
>> DUF1931  Domain of unknown function (DUF1931)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.1   1.4e-06     0.013      17      62 ..      21      65 ..      19      81 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.4e-06
                HHHHHHHHHHHHHHHCCCCHHHHHHHTT-SEE-GGGS---HHHHHH CS
     DUF1931 17 dlkrisdfVekklydLllvaeenAkangrdviepaDLPiTkglqes 62
                +++  +d+V+ +++dLll a+++ +    dvi+   +P+T g+ e 
  EPA06757.1 21 KIDSANDLVTPEIDDLLLEAQKTFQ-SIDDVIKGMGIPLTVGIMEI 65
                678899**************98866.578*************9886 PP

>> Ub-Mut7C  Mut7-C ubiquitin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   1.5e-05      0.14      25      47 ..      37      59 ..      19      75 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.5e-05
    Ub-Mut7C 25 lavafdeaatvkhviEalGVPht 47
                l  a + ++++ +vi  +G+P+t
  EPA06757.1 37 LLEAQKTFQSIDDVIKGMGIPLT 59
                55677899**************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 568.50
//
Query:       EPA06758.1  [L=165]
Description: hypothetical protein BG20_I0077 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-15   56.4   1.9    3.6e-15   56.2   0.2    1.7  2  CopD           Copper resistance protein D
     0.0035   16.9   3.1     0.0035   16.9   3.1    2.2  2  SieB           Super-infection exclusion protein B
     0.0043   17.3   8.5      0.013   15.7   8.5    1.6  1  UPF0093        Uncharacterised protein family (UPF0093)
     0.0075   15.7   1.9      0.011   15.1   1.9    1.2  1  7TM_GPCR_Srv   Serpentine type 7TM GPCR chemoreceptor Srv
  ------ inclusion threshold ------
      0.063   13.7   0.2      0.063   13.7   0.2    2.2  3  PEMT           Phospholipid methyltransferase
      0.082   13.2   6.3       0.38   11.1   6.3    2.1  1  DUF4149        Domain of unknown function (DUF4149)
      0.096   12.5   2.9       0.48   10.2   0.2    2.5  2  Flavi_M        Flavivirus envelope glycoprotein M
        1.3    9.1  10.5       0.21   11.7   6.4    1.8  2  DUF3278        Protein of unknown function (DUF3278)
        1.9    8.6   5.1       0.85    9.7   0.9    2.0  2  DHHC           DHHC palmitoyltransferase
        3.2    7.5   7.3       0.18   11.6   1.7    1.8  2  Brr6_like_C_C  Di-sulfide bridge nucleocytoplasmic transport 


Domain annotation for each model (and alignments):
>> CopD  Copper resistance protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1       1.2   2.1e+03      11      41 ..      12      40 ..       5      45 .. 0.56
   2 !   56.2   0.2     2e-18   3.6e-15       3     105 .]      52     161 ..      50     161 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.2
        CopD 11 alaavavvlvtGvvnallrvglagllttayG 41
                ++++ a++ v G + + +   ++ ll++ yG
  EPA06758.1 12 IHLLAAAIWVGGSLFIGIV--FSPLLKSMYG 40
                3444444445555544444..5666666666 PP

  == domain 2  score: 56.2 bits;  conditional E-value: 2e-18
        CopD   3 alrrFsrlalaavavvlvtGvvnallrvg.lagllttayGrlllaKlalllvllalaalnrfrlvprleaa......tgaggqalrhrlrrsaalelvl 94 
                 + +rF ++a++++++++ tG++n++l+++ ++ l +t+yG  l++K++l+++l++  +++ + +++ +e++       +++ q+lr+++  + ++ +vl
  EPA06758.1  52 VGKRFNKIAVPSLIILIGTGLYNSHLLLSkPDLLMATSYGHFLVIKIILVIALIITYVIHVRIIRKDVEEKimskqmSPQQIQKLRKKIIILGEITVVL 150
                 679**************************99*************************************88899999999******************** PP

        CopD  95 alvvlllaaal 105
                 ++++l+ a++l
  EPA06758.1 151 SVAILFFASLL 161
                 ******99876 PP

>> SieB  Super-infection exclusion protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1     0.059   1.1e+02      35      65 ..      10      45 ..       2      58 .. 0.62
   2 !   16.9   3.1   1.9e-06    0.0035       4      75 ..      64     136 ..      61     143 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.059
        SieB 35 iglvflis.....iayllaqvvskllaeikekikkk 65
                +++ +l +      ++++ +v+s ll+ ++  i+++
  EPA06758.1 10 LWIHLLAAaiwvgGSLFIGIVFSPLLKSMYGTIEER 45
                333333333344488889888888888887777643 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 1.9e-06
        SieB   4 LiiasglllllPdslleklnlgkfleeyglwiglvflisiayllaqvvskll..aeikekikkkreqkkvekkl 75 
                 Lii++g+ l  +  ll k  l  ++++yg+++++ ++++ia+++++v++  +  + + eki +k+   ++++kl
  EPA06758.1  64 LIILIGTGLYNSHLLLSKPDLL-MATSYGHFLVIKIILVIALIITYVIHVRIirKDVEEKIMSKQMSPQQIQKL 136
                 8999*********99*999988.9***********************987661144444444444444444444 PP

>> UPF0093  Uncharacterised protein family (UPF0093)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   8.5   7.3e-06     0.013       8     140 ..       9     157 ..       5     161 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 7.3e-06
     UPF0093   8 ikalHiiavisWmAglfyLpRlfVyhaeakeks.eekevlkimerrLlkiimtpamiltlvlGlll...lalae..glvalssgWlhvKlllvllllay 100
                 i ++H++a  +W+ g +++  +f    ++  ++ ee+  + i+  + ++ i  p++i+ + +Gl     l  ++   +++   ++l +K++lv++l++ 
  EPA06758.1   9 ILWIHLLAAAIWVGGSLFIGIVFSPLLKSMYGTiEERLQIMIKVGKRFNKIAVPSLIILIGTGLYNshlLLSKPdlLMATSYGHFLVIKIILVIALIIT 107
                 6789****************9999999999888666555556666777888******9999997534415555544333444589999*****999887 PP

     UPF0093 101 hlvlak.lrkklaag.........entksekfyrilNEvptlllivivll 140
                 +++ ++ +rk+++++         + +k  k   il E+ ++l ++i+++
  EPA06758.1 108 YVIHVRiIRKDVEEKimskqmspqQIQKLRKKIIILGEITVVLSVAILFF 157
                 76665514455544311100000044444455557788888888888776 PP

>> 7TM_GPCR_Srv  Serpentine type 7TM GPCR chemoreceptor Srv
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   1.9   6.3e-06     0.011     167     231 ..      92     160 ..      75     163 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 6.3e-06
  7TM_GPCR_Srv 167 ialivvvvtciiliiayvllfvvlrkkkk....kksqtkskslkrevrLaiqvlilvlaeliilifvil 231
                     l++ ++++i+lii+yv+ + ++rk  +    +k+ + ++ +k   +  i   i+v++ ++il+f +l
    EPA06758.1  92 HFLVIKIILVIALIITYVIHVRIIRKDVEekimSKQMSPQQIQKLRKKIIILGEITVVLSVAILFFASL 160
                   56788999*****************88854666444455555555566666677888888888888765 PP

>> PEMT  Phospholipid methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1       1.4   2.6e+03      77     103 ..      14      40 ..       7      43 .. 0.52
   2 ?   13.7   0.2   3.5e-05     0.063      59     101 ..      85     127 ..      66     132 .. 0.85
   3 ?   -3.2   0.2       6.3   1.1e+04      74      78 ..     147     151 ..     140     160 .. 0.38

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.4
        PEMT  77 llallvllvylialkfvEephlakiYg 103
                 lla+ +++   +++ +v  p l+ +Yg
  EPA06758.1  14 LLAAAIWVGGSLFIGIVFSPLLKSMYG 40 
                 444444444444444455566666655 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 3.5e-05
        PEMT  59 stlgflGlaLitgsaaglllallvllvylialkfvEephlaki 101
                  +++ +G+ L+ + +++++l+++ ++ + i++k vEe+ ++k+
  EPA06758.1  85 LMATSYGHFLVIKIILVIALIITYVIHVRIIRKDVEEKIMSKQ 127
                 467789**********************************997 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 6.3
        PEMT  74 aglll 78 
                 +++l 
  EPA06758.1 147 TVVLS 151
                 22111 PP

>> DUF4149  Domain of unknown function (DUF4149)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   6.3   0.00021      0.38       1      91 [.      15     112 ..      15     162 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00021
     DUF4149   1 lslglllGsqlwvtfvvapvlfrsL.prhqfgelqsklFplyfglglalsvlllltevavg......seklaseellqlllllvvllltllnafylep 91 
                 l++++++G+ l++++v +p l +   + ++  +++ k+  +++ + + ++++l+ t ++++         l +    ++l++ ++l+++l+ ++++  
  EPA06758.1  15 LAAAIWVGGSLFIGIVFSPLLKSMYgTIEERLQIMIKVGKRFNKIAVPSLIILIGTGLYNShlllskPDLLMATSYGHFLVIKIILVIALIITYVIHV 112
                 6789****************999976666678999999999999988888888888888888888876667777777888888888888877777655 PP

>> Flavi_M  Flavivirus envelope glycoprotein M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.4     0.049        88      42      60 ..     100     118 ..      92     120 .. 0.83
   2 ?   10.2   0.2   0.00027      0.48      13      44 ..     118     149 ..     110     165 .] 0.73

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.049
     Flavi_M  42 avialtlaylvGssitqkv 60 
                  vial+++y++   i +k 
  EPA06758.1 100 LVIALIITYVIHVRIIRKD 118
                 69********998888775 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00027
     Flavi_M  13 trtekWmssegaekqlqkverWalrnPffavi 44 
                   +ek ms +++ +q+qk+ + ++     +v+
  EPA06758.1 118 DVEEKIMSKQMSPQQIQKLRKKIIILGEITVV 149
                 5689***************9887766666554 PP

>> DUF3278  Protein of unknown function (DUF3278)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       1.4   2.5e+03      51      51 ..      20      20 ..       6      54 .. 0.57
   2 ?   11.7   6.4   0.00012      0.21      53     126 ..      84     157 ..      54     160 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.4
     DUF3278 51 v 51
                 
  EPA06758.1 20 W 20
                1 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00012
     DUF3278  53 lllakktpeselilglvltnlllvvlvsglYiliaskklglatkeveakdyekavkkivlks.ikfglyfaivly 126
                 ll+a ++ +  l+++++l++ l+ + v  + i+++  + ++++k+ + ++++k  kki++ + i + l+ ai+ +
  EPA06758.1  84 LLMATSYGH-FLVIKIILVIALIITYVIHVRIIRKDVEEKIMSKQMSPQQIQKLRKKIIILGeITVVLSVAILFF 157
                 455544444.67779***99999999****************************999987552556555555554 PP

>> DHHC  DHHC palmitoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.2      0.27   4.9e+02      95     115 ..      16      36 ..       4      79 .. 0.70
   2 ?    9.7   0.9   0.00047      0.85      48     117 ..      90     159 ..      87     163 .. 0.69

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.27
        DHHC  95 lsilllvlsllfllllgllll 115
                  + +++  sl+++++++ ll+
  EPA06758.1  16 AAAIWVGGSLFIGIVFSPLLK 36 
                 345666666666666666555 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00047
        DHHC  48 ykyFllfllylllllilalvlllialvklveeekkseflavtllkkllsilllvlsllfllllgllllfh 117
                 y +Fl++ ++l+++li++ v+++ +++k vee+  s+    ++++kl + ++++  + ++l +++l++ +
  EPA06758.1  90 YGHFLVIKIILVIALIITYVIHVRIIRKDVEEKIMSKQMSPQQIQKLRKKIIILGEITVVLSVAILFFAS 159
                 6678888888888888888888888888888877777766666666566666666666666666666544 PP

>> Brr6_like_C_C  Di-sulfide bridge nucleocytoplasmic transport domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1         4   7.2e+03       3      23 ..      11      31 ..      10      38 .. 0.63
   2 ?   11.6   1.7   9.9e-05      0.18       6      41 ..      94     129 ..      89     140 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 4
  Brr6_like_C_C  3 ylqllfnlllvllllylvisf 23
                   +++ll+ ++ v   l++ i f
     EPA06758.1 11 WIHLLAAAIWVGGSLFIGIVF 31
                   566666666666666666555 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 9.9e-05
  Brr6_like_C_C   6 llfnlllvllllylvisfvltikkDiekkleekkae 41 
                    l+++++lv+ l+++ +  v++i+kD+e+k+ +k++ 
     EPA06758.1  94 LVIKIILVIALIITYVIHVRIIRKDVEEKIMSKQMS 129
                    67889999999999999************9988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1578  (0.0880138); expected 358.6 (0.02)
Passed bias filter:                      791  (0.0441185); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 1058.35
//
Query:       EPA06759.1  [L=186]
Description: hypothetical protein BG20_I0043 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0037   17.5   0.7     0.0043   17.3   0.7    1.2  1  Arch_flagellin  Archaebacterial flagellin


Domain annotation for each model (and alignments):
>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.7   2.4e-07    0.0043      10     107 ..       7     122 ..       4     182 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.4e-07
                     HHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHT--EEEEEEE.EEE-SSSSSEEEEEEE--TTS--EEGGG-EEEEEESS--EE CS
  Arch_flagellin  10 vfIAmVlVAAvaagvlintagflqqkaqs....tgeesteqvssgleitgdvg.dsatngtineitiyvklnaGsspidlnkttisvtddgqetl 99 
                     v++A +  AA++ g+l+  + f+++  ++    t +es + +  ++e+  + + d++++++i e ++ +  n+  s+i ++ ++++++  g+++ 
      EPA06759.1   7 VIVAIIALAAALGGILLSGSSFISSTQKNdnqiTSHESQKILPISIELNDVSIlDITKRSAIIETSFKIS-NPNPSSIIIQVMDYQLFETGFSND 100
                     899********************9887653333666666777777777777779999999999*******.*****************9996666 PP

                     --E................... CS
  Arch_flagellin 100 ltad..............efgi 107
                        +               +++
      EPA06759.1 101 SQISggqigsrpegmvefGSNY 122
                     6555666666666666553333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 1152.61
//
Query:       EPA06760.1  [L=171]
Description: putative nicotinamide-nucleotide adenylyltransferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.6e-12   46.3   0.0    1.2e-11   45.0   0.0    1.7  1  CTP_transf_like  Cytidylyltransferase-like
  ------ inclusion threshold ------
       0.11   12.4   0.0       0.23   11.4   0.0    1.4  1  Homeobox_KN      Homeobox KN domain


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.0   0.0   1.3e-15   1.2e-11       2     118 ..      12     125 ..      11     151 .. 0.68

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 1.3e-15
                      EEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHH...HHHHHTTTTEEEEEEEHH CS
  CTP_transf_like   2 agGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkkkplasaeeRlemlelakevdevisvdpweltr...evlkklkpdklylvigad 92 
                      + G+F+p+HlGHl  l+ a+ ++++ l++g+ s+++p +k  +++saeeR em+ + ++ +   ++  + +     +++    +d   lv   d
       EPA06760.1  12 LIGRFQPFHLGHLSALRFALTKVDK-LWIGLGSSNKPLQK-NNPFSAEERKEMILASIDQSMKQRIQIYFIPDlenHIKWIDLID--TLVPKFD 101
                      78***********************.*********99987.9***********98886666544444433332222222222224..4444444 PP

                      HHHHHHCHHHHHHHHHHHHHEEEEEE CS
  CTP_transf_like  93 vledfsewkeleeilgnvklvvvsrp 118
                      v+ +   +   +++++++++ v+s+p
       EPA06760.1 102 VVFTN--DDLTKHLYSKRNVTVMSIP 125
                      44442..5555566666666666555 PP

>> Homeobox_KN  Homeobox KN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   2.6e-05      0.23       7      35 ..      51      80 ..      49      81 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.6e-05
  Homeobox_KN  7 hnPYPseedKeeLlkeTglsvkq.itnWFI 35
                 +nP+ +ee Ke++l+   +s+kq i+ +FI
   EPA06760.1 51 NNPFSAEERKEMILASIDQSMKQrIQIYFI 80
                 69********************99*****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 998.58
//
Query:       EPA06761.1  [L=50]
Description: hypothetical protein BG20_I0104, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       221  (0.0123264); expected 358.6 (0.02)
Passed bias filter:                      190  (0.0105974); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.47
# Mc/sec: 319.55
//
Query:       EPA06762.1  [L=189]
Description: hypothetical protein BG20_I0095 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 1075.66
//
Query:       EPA06763.1  [L=300]
Description: periplasmic solute binding family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      6e-69  232.3   0.3    6.9e-69  232.1   0.3    1.0  1  ZnuA      Zinc-uptake complex component A periplasmic


Domain annotation for each model (and alignments):
>> ZnuA  Zinc-uptake complex component A periplasmic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  232.1   0.3   3.9e-73   6.9e-69       1     256 []      37     298 ..      37     298 .. 0.88

  Alignments for each domain:
  == domain 1  score: 232.1 bits;  conditional E-value: 3.9e-73
                 EEESSHHHHHHHHHHHGGGCEEEECS-TTSTTTT----HHHHHHHHHSSEEEESSTTTSGTHHHHHHHHTTCCCEEEEETTTTCCSEBCSS........ CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........ RF
        ZnuA   1 VvattsplgdlvrqvaGdrvevtvLvppgadpHsyeptprdvrklaeAdllvynglelEtwldkllasssqatrvevidlsegveeeeeee........ 91 
                 V+ +++pl+++ ++v+ ++v+ ++Lvp g++pH++ept +d+++++++dl++ ng ++E+wldkl  +++  +   v+d+s gv   ++++        
  EPA06763.1  37 VISSFYPLQEFSQRVGQEKVDTKLLVPIGIEPHDWEPTIKDIQQMQKSDLIIINGIGFESWLDKLS-EINY-NG-IVVDTSLGVL--KNSHgssmslnh 130
                 789**************************************************************5.4432.22.4555554431..222222444444 PP

                 .....ESTGGGSHHHHHHHHHHHHHHHHHHTGGGHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSGTEGEEEESSSTTHHHHHHTT-EEEEEE.SSSSS. CS
                 .....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx. RF
        ZnuA  92 .....DpHiWlspknaiamveniadaLveadpanadtyeanaaayiekLeeldaeireelaeipeekrklvtthdafgylarayglevagia.giste. 183
                      DpHiWl+p  a+++v+nia+a+++ dp+n+++y++naa+yi++L+ ld++i++el+ ++    +++ +hd+f+y+a++y+l++ +i+ +  +  
  EPA06763.1 131 ngksnDPHIWLNPVFAKTQVQNIANAFSNSDPQNQQYYQENAANYIYELDLLDSKIHTELSGCN---HNFIAFHDSFSYFADEYDLTQHTIIsSYAPHv 226
                 55567********************************************************887...35********************9996555559 PP

                 ...HHHHHHHHHHHHHTT-SEEEEETTS-THHHHHHHHHHT-EEEEE-STSSSTSTTSTTSHHHHHHHHHHHHHHH CS
                 ...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        ZnuA 184 ...aaqiaalieeikeagvkaifveplaspklaetlaeeagvkvatlysldslgdegsaetYidmmranleslkea 256
                    a++++++i++++++++k+if+e++a+pk+ e +a+e+g k+++l +  ++g+++   tYi+ m++nl++lkea
  EPA06763.1 227 eptAKTLENVINKARDLDLKIIFTEETADPKTSEVIANEIGGKILVLSP-IEIGNNE---TYISKMTENLNNLKEA 298
                 999**********************************************.5567776...**************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       772  (0.0430587); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 1754.00
//
Query:       EPA06764.1  [L=493]
Description: hypothetical protein BG20_I0011 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.2e-07   29.2   1.5    0.00018   21.6   0.2    2.4  2  Wzt_C     Wzt C-terminal domain
  ------ inclusion threshold ------
      0.013   15.2   0.0      0.023   14.4   0.0    1.3  1  ApoM      ApoM domain
      0.023   15.7   0.0      0.051   14.6   0.0    1.5  1  DUF4927   Domain of unknown function (DUF4927)


Domain annotation for each model (and alignments):
>> Wzt_C  Wzt C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.1    0.0015         9      36     129 ..      96     182 ..      69     197 .. 0.77
   2 !   21.6   0.2     3e-08   0.00018      26     130 ..     346     445 ..     337     455 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0015
       Wzt_C  36 lrikvkahedvedpvfgfaik..drngqevfgtntelekksfeleelkagervevefefklpLapGeYlltvaledrdgeeneiydwlddalsfeV 129
                 l ++  +h +  d+++++  k  d n++ v+g+n       f  ++++ +++++v+  ++  L +G Y + + + + d ++  ++ ++ da +f+ 
  EPA06764.1  96 LLMRNLFHTHSGDLTLTIDSKdmDVNDVIVYGDNEP-----FLGGWTSVNDKITVKAPIL--LDAGLYHFEIEIFGIDFDK--NIFTVSDAPKFDS 182
                 555666777777777777776334566677887553.....667899************7..****************998..9999999999975 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 3e-08
       Wzt_C  26 stfesgeevtlrikv..kahedvedpvfgfaikdrngqevfgt.ntelekksfeleelkagervevefefklpLapGeYlltvaledrdgeeneiydwl 121
                 s ++sg ++ ++i++  k ++ ++ ++ g+ i d+ g  v+ + nt+   +s  +++l + ++ +  f+f+    +G+Y +t+al +++ +   ++ +l
  EPA06764.1 346 SKLVSGAKIPFEITFfdKDNKLLKWVTYGYRIEDSSGKVVYESqNTN--PNS--PGVLLTEGIDKHQFDFQ---STGKYKITLALFSHGID---NLQTL 434
                 5689999********855555569******************98994..334..99999999999999997...79**********99998...66666 PP

       Wzt_C 122 d..dalsfeVv 130
                    + +sf+++
  EPA06764.1 435 SgiSNASFDIT 445
                 63334556665 PP

>> ApoM  ApoM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   3.9e-06     0.023      28      89 ..     398     459 ..     383     467 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.9e-06
        ApoM  28 rlstsgvdkkefpeqylgqwyfvaaaatptkeeletfdavdnivfsvaagrveqkldlraai 89 
                  l t g+dk++f  q  g++ +  a  + + ++l+t++ + n+ f++++g+     ++ + i
  EPA06764.1 398 VLLTEGIDKHQFDFQSTGKYKITLALFSHGIDNLQTLSGISNASFDITQGTATGSNQIPSWI 459
                 5889****************99999999*********************9987766666555 PP

>> DUF4927  Domain of unknown function (DUF4927)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   8.6e-06     0.051      11      54 ..     285     327 ..     280     342 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8.6e-06
     DUF4927  11 kenALLrYLLdkddskdsllkdikPKlEeldskveqgsssklat 54 
                 ++  +L+YLL k++  d  +k  kP + +++ k +++s s+++ 
  EPA06764.1 285 ENTLILHYLLSKENILDI-AKSNKPGVKTMEFKLSPSSGSTTQK 327
                 56678***********96.9999*************98877654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (493 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 2946.28
//
Query:       EPA06765.1  [L=212]
Description: putative Xaa-Pro dipeptidase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-55  188.2   0.0    1.6e-55  188.1   0.0    1.0  1  Peptidase_M24  Metallopeptidase family M24


Domain annotation for each model (and alignments):
>> Peptidase_M24  Metallopeptidase family M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.1   0.0   8.7e-60   1.6e-55      19     208 ..       7     196 ..       1     197 [. 0.93

  Alignments for each domain:
  == domain 1  score: 188.1 bits;  conditional E-value: 8.7e-60
                    HHHHTTCBHHHHHHHHHHHHHHHTTTCEESS.....SSEEEEGGGGGSTTTBCSSSB--TTEEEEEEEEEEETTEEEEEEEEEECSSGSHHHHHHH CS
  Peptidase_M24  19 eaikpgvterelaaeieattlkrhgarglaf.....ppivasgenaavlhytpndrvlkegdlvlidagaeydgyasDitrTvlvGkftpeqrely 109
                    +++  g +e el+ ++  +  + +g  + ++     p i+a g+n++++h++ ++r++k+gdlv++d++ +y+gy+sD trT+++G+ + eq+++y
     EPA06765.1   7 KKMNIGQKESELQTILMSF-AIGQGMFDTGYkstlnPLIIAGGPNGSLPHAQVTNRKFKKGDLVVVDLTLRYKGYVSDATRTFAIGQISVEQKQVY 101
                    55677999*********88.6777877777777777***************999********************************9999****** PP

                    HHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHTTBCCGBSSCSEEEESSSSSEEEEEESSSTTCSSB--TTBEEEEEEEEEEETTTEEEEEBEEE CS
  Peptidase_M24 110 eavleaqeaaikavkpGvtlseidaaarevlesaglakffphglGHgvGlevhdegpsvsresndgrkleeGmvftiEpgiyfapgeggvriedtv 205
                    ++v++ q+ +++ vkp v+++++d a+r+++e+++++k+f h++GHg+Glevh+  p+vs  +++++kl+e+m +t+Epgiy +p+++gvried +
     EPA06765.1 102 QIVKDSQKLGLESVKPNVDCKDVDTACRKYIEENNFGKYFIHSTGHGIGLEVHEL-PTVS--YRSDTKLKENMAITVEPGIY-IPNKFGVRIEDSL 193
                    *****************************************************98.***9..6889****************.99*********** PP

                    EEE CS
  Peptidase_M24 206 lvt 208
                    +v+
     EPA06765.1 194 IVK 196
                    997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1286.51
//
Query:       EPA06766.1  [L=78]
Description: hypothetical protein BG20_I0040 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.53
# Mc/sec: 444.08
//
Query:       EPA06767.1  [L=248]
Description: peptidyl-prolyl cis-trans isomerase, FKBP-type [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-12   46.9   0.9    6.5e-12   45.4   0.9    1.8  1  FKBP26_C  FKBP26_C-terminal
    3.6e-11   43.2   0.2      2e-10   40.8   0.1    2.2  2  FKBP_C    FKBP-type peptidyl-prolyl cis-trans isomerase
     0.0023   17.9   0.0     0.0043   17.1   0.0    1.4  1  CAP_GLY   CAP-Gly domain
  ------ inclusion threshold ------
       0.18   11.6   0.2       0.18   11.6   0.2    1.7  2  DUF5399   Family of unknown function (DUF5399)


Domain annotation for each model (and alignments):
>> FKBP26_C  FKBP26_C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   0.9   1.5e-15   6.5e-12       2      70 ..     158     225 ..     157     226 .. 0.96

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 1.5e-15
                 HHHHHHHHHHH-TT--..--EEEEETTEEEEE--TTGGGSTTHHHHHHHHHHHHHHH-TTEEEEEEEEE CS
    FKBP26_C   2 kekikelIkryiPnidlekfkieiedktvtIelpeeakFieniqlaklrIAkdilkrieevekVkFvde 70 
                  +k+ ++ k ++P  d  k+ +e++dk+v I++pee + ++++q++k  I  di+k+++  ekV+F+++
  EPA06767.1 158 NDKVDGILKNRLPLED-SKITFELKDKEVNITIPEEILRADGLQIMKHFIQLDIFKFVPSLEKVNFIET 225
                 79***********766.9*************************************************98 PP

>> FKBP_C  FKBP-type peptidyl-prolyl cis-trans isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   0.1   4.5e-14     2e-10       6      82 ..       4      97 ..       1     151 [. 0.74
   2 ?    0.9   0.0      0.13   5.7e+02      10      27 ..     130     147 ..     123     193 .. 0.68

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 4.5e-14
                -TTCEEEEEEEEEET.TSSEEEEH............CC.HTSEEEEETTSSS..SCHHHHHHHTTSBTT-EEEEEEEGGGTTTTTTBCTTT..B. CS
      FKBP_C  6 kegdtVtvhykgkle.dgkvfdss............rs.rakplefkvGsgq..vikGfeealegmkvGekrtltippelaYgekglaggv..ip 82
                ++g+ + ++y++k++  ++vfd++             + +++p  + +G+    v+kG++eal++  vG+k t++++p+ ++ge+++ g+v  ip
  EPA06767.1  4 NKGSLILIDYTAKVKdTSEVFDTTieedakkhsiheSNvKYQPKLVSIGEVSypVLKGLDEALSKTAVGDKLTIEVTPDKGFGERDA-GKVrmIP 97
                799************77*******888888877654227**********96667******************************888.5445544 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.13
                 EEEEEEEEEETTSSEEEE CS
      FKBP_C  10 tVtvhykgkledgkvfds 27 
                 +V+++y+ ++++++++ +
  EPA06767.1 130 RVQIDYNHRYAGKTILYD 147
                 788999988875554443 PP

>> CAP_GLY  CAP-Gly domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   9.5e-07    0.0043       1      46 [.     110     167 ..     110     183 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 9.5e-07
     CAP_GLY   1 vgdrvklkegrrGvvryvGp..vp.fakgewvG.........ve.ldepnGkndGsvkg 46 
                 vgd++++ +++rG++r++G+  v+ + ++ ++G         v+ ld+pn k dG  k+
  EPA06767.1 110 VGDTIEV-DNKRGIIRFIGSgrVQiDYNHRYAGktilydvnvVKsLDSPNDKVDGILKN 167
                 7999985.999********633434445567777777777766689*********9886 PP

>> DUF5399  Family of unknown function (DUF5399)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1       1.8     8e+03     101     122 ..      17      38 ..      12      43 .. 0.60
   2 ?   11.6   0.2   4.1e-05      0.18      77     116 ..     206     242 ..     201     247 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.8
     DUF5399 101 eekiselkvltkeeekekkaik 122
                 ++ +se+ ++t ee  +k+ i+
  EPA06767.1  17 VKDTSEVFDTTIEEDAKKHSIH 38 
                 5556666666666666665554 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 4.1e-05
     DUF5399  77 qrfspfaffrvvPsLGslekqdedeekiselkvltkeeek 116
                 +++ +f   + vPsL  +++++ + +k+++ k++tkee+k
  EPA06767.1 206 IQLDIF---KFVPSLEKVNFIETHLNKTQAKKTETKEEKK 242
                 555666...55*************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       749  (0.0417759); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1600.93
//
Query:       EPA06768.1  [L=434]
Description: hypothetical protein BG20_I0053 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00052   20.2   1.3       0.63   10.3   0.0    3.8  4  NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosi
      0.002   18.4   3.7       0.78   10.1   1.8    2.4  2  DUF11        Domain of unknown function DUF11
  ------ inclusion threshold ------
       0.03   13.9   1.2      0.046   13.3   1.2    1.3  1  DUF5385      Family of unknown function (DUF5385)
      0.066   13.1   0.3       0.11   12.3   0.3    1.3  1  DUF4832      Domain of unknown function (DUF4832)


Domain annotation for each model (and alignments):
>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   0.00014      0.63       4      35 ..      64      95 ..      60     144 .. 0.74
   2 !    5.2   0.0    0.0055        24       6      28 ..     182     204 ..     181     206 .. 0.88
   3 ?    0.5   0.4      0.17   7.5e+02       7      43 ..     207     240 ..     204     254 .. 0.64
   4 ?   -2.5   0.0       1.4   6.3e+03      66      78 ..     363     375 ..     341     376 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00014
  NPCBM_assoc  4 GetvtltltvtndgtaaatnvslslslPeGWt 35
                 ++ v +t++++n gt+ +t+++ +lslP G +
   EPA06768.1 64 DSNVPFTVVFANVGTQDITGIKGQLSLPLGFS 95
                 45789***********************9987 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0055
  NPCBM_assoc   6 tvtltltvtndgtaaatnvslsl 28 
                  t+++ ++++ndgta++++v + +
   EPA06768.1 182 TNNIVIEISNDGTAPLSSVDIVA 204
                  78999**************9865 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.17
  NPCBM_assoc   7 vtltltvtndgtaaatnvslslslPeGWtvvevspas 43 
                  ++++l+ t++ t+ ++nv +   l ++W v ++ p+s
   EPA06768.1 207 TQTELASTSTSTTNVENVVI---LESNWDVGNINPKS 240
                  55666667777777777655...44566666555555 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 1.4
  NPCBM_assoc  66 aaGdyevtakarl 78 
                  ++G++++++++r+
   EPA06768.1 363 QYGEHNIQLTVRY 375
                  6899999999997 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0   0.00095       4.2       9      51 ..      59     102 ..      45     137 .. 0.73
   2 !   10.1   1.8   0.00017      0.78      20      83 ..     187     255 ..     181     261 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00095
       DUF11   9 evrpGd.tvtytltvtNtgpasangvvvtDtlPaglayvsvsas 51 
                 ev+pGd +v +t+++ N g+++ +g++ +  lP g++   +s s
  EPA06768.1  59 EVDPGDsNVPFTVVFANVGTQDITGIKGQLSLPLGFSSADGSGS 102
                 899***99**************9999887777777776665555 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00017
       DUF11  20 ltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsv........gsLeagesatlsftvrvtrtaa 83 
                 +  +N g+a+++     D++ +++++  +s+s++t +++  v        g++++ +s++l++tv v+   +
  EPA06768.1 187 IEISNDGTAPLSS---VDIVASNTQTELASTSTSTTNVENVVilesnwdvGNINPKSSKYLTATVYVPENLQ 255
                 6678999999954...4888888888888888778888877788888888***************9987665 PP

>> DUF5385  Family of unknown function (DUF5385)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   1.2     1e-05     0.046       2      31 ..     403     431 ..     402     434 .] 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1e-05
     DUF5385   2 ngnfliiliiiiiiilvivfllrkkkkqke 31 
                 n++ l+i+ iii++  ++++++ ++kk+k 
  EPA06768.1 403 NNSQLMIIPIIIVV-AIVMYVILRRKKSKV 431
                 89999999999988.899999999999875 PP

>> DUF4832  Domain of unknown function (DUF4832)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.3   2.5e-05      0.11     122     199 ..     181     267 ..     173     278 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.5e-05
     DUF4832 122 gtlsleltlkNeGfAaly......nerkvelvlrdeegee...kyklkldadprkwlpgttttitiklklpselakGkykvyLnlpd 199
                 +t ++ +++ N+G A+l       +++++el  ++++++     + l+++ d+ ++ p++++ +t+++ +p++l++ + ++ L ++ 
  EPA06768.1 181 KTNNIVIEISNDGTAPLSsvdivaSNTQTELASTSTSTTNvenVVILESNWDVGNINPKSSKYLTATVYVPENLQQDTLRIPLTIKY 267
                 678999**********86111111567777777777776644333345************999*****************9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 2761.92
//
Query:       EPA06769.1  [L=347]
Description: putative NAD(P)-dependent glycerol-1-phosphate dehydrogenase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-72  244.1   1.2    1.8e-72  244.1   1.2    1.3  2  Fe-ADH_2      Iron-containing alcohol dehydrogenase
    1.4e-22   80.1   0.5    8.3e-22   77.5   0.5    1.8  1  Fe-ADH        Iron-containing alcohol dehydrogenase
    3.7e-05   23.0   0.4     0.0021   17.3   0.4    2.7  1  DHQ_synthase  3-dehydroquinate synthase
     0.0018   17.9   3.7      0.003   17.1   0.8    2.3  2  AIRC          AIR carboxylase


Domain annotation for each model (and alignments):
>> Fe-ADH_2  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  244.1   1.2     4e-76   1.8e-72       2     250 .]      14     269 ..      13     269 .. 0.93
   2 ?   -3.4   0.0       1.4   6.5e+03     170     198 ..     283     311 ..     274     325 .. 0.55

  Alignments for each domain:
  == domain 1  score: 244.1 bits;  conditional E-value: 4e-76
    Fe-ADH_2   2 igegaleklgellkele.lkkvllvadentkkaagekveeslkeagikvevveeveeeadleeveklvealreketdlvvavGgGtiiDiakyvsakln 99 
                 ige  + + g+++++l+  k v l+++ n+ k++ +k+e+slk++ ik   ++ +++++++++++++++++++++  l+v++GgG+ +D+ak+++++l+
  EPA06769.1  14 IGERNIGDFGKFVNSLNkSKSVSLISGVNVTKIVKKKIENSLKSNRIKFV-WH-MSGDNTISAINQIQKNVKKDGSHLIVGIGGGRSVDTAKMIAYNLG 110
                 88899999*******972579************************99995.65.99******************************************* PP

    Fe-ADH_2 100 vpyvsvpTaaSvDGfaspgaslvvdgkkrtvakaaaPlaviaDldvlaeAPrrllasGvGDllgkytaladwklan........evseplaklsaamvq 190
                 +p+vsvpTaaS+DG asp++s+v d+   ++  a aPl+v++D+d++++AP++llasG+GDl+++++a++dw+l++        ++s+ la++sa++v+
  EPA06769.1 111 KPFVSVPTAASHDGMASPFVSVVSDK-PHSI-VASAPLGVFVDIDIIRKAPAKLLASGCGDLIANIIAVKDWQLGHektgeyygRYSADLALMSAKIVM 207
                 *************************7.6677.799*****************************************9999999999************* PP

    Fe-ADH_2 191 eaaeklvedkketeal.eelleal.alsgigisrpaSGsEHliSHaldmlalkqalHGeqVG 250
                 e+ ++ ++++ +++++ e+l++a  a +++g+srp+SG+EHl+SHald++a+ + lHGe++G
  EPA06769.1 208 ENSSQYAKNGLDVRIIvEALISAGvASCIAGSSRPCSGAEHLFSHALDKIAPGRGLHGEKCG 269
                 ********9999776526677775377778889****************************8 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.4
    Fe-ADH_2 170 dwklanevseplaklsaamvqeaaeklve 198
                 + k+a+ +++  a ++a++v  + +++v+
  EPA06769.1 283 WKKIAKTLKDVGAPTTAKQVNLKSDEIVN 311
                 44455555555555555555555555543 PP

>> Fe-ADH  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.5   0.5   1.8e-25   8.3e-22       2     303 ..      10     293 ..       9     337 .. 0.75

  Alignments for each domain:
  == domain 1  score: 77.5 bits;  conditional E-value: 1.8e-25
                 SEEEEETTGGGGHHHHHTTT-...EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEEE.EEE-S---HHHHHHHHTTS-TT.--EEEEEESHHHHHHHHH CS
      Fe-ADH   2 trivfgkgaleelgellkklg.akralivtdkgslkksglldkvlesleeagievtvfdgvepnptleeveeaaalareegadvviavGGGsviDtAKa 99 
                 + i +g+  + + g+ + +l+  k++ ++ + ++  k  + +k+++sl+++ i+++    ++++ t++ ++++ + +++ g  +++++GGG ++DtAK+
  EPA06769.1  10 RLIEIGERNIGDFGKFVNSLNkSKSVSLISGVNVT-KI-VKKKIENSLKSNRIKFVW--HMSGDNTISAINQIQKNVKKDGSHLIVGIGGGRSVDTAKM 104
                 567789999999********856799999999966.55.8899*****999999995..579************************************* PP

                 HHHHTT..................--EEEEESS-S-S-TT-SEEEEE.-TTSEEEEE-..SS--SEEEEEHHHHHHS-HHHHHHHHHHHHHHHHHHHHH CS
      Fe-ADH 100 ialllanpevedylgegkakkkkalpliaiPTtaGtGsevtplavitdeeegeklsifdpellPdlaivDpeltltlPkrvtaatglDalahalEayvs 198
                 ia+ l+                   p++ +PT a+ +  ++p+  +  +++ +  si+     P  ++vD +++ ++P++++a++ +D +a  +     
  EPA06769.1 105 IAYNLG------------------KPFVSVPTAASHDGMASPFVSVV-SDKPH--SIV--ASAPLGVFVDIDIIRKAPAKLLASGCGDLIANIIAVKDW 180
                 ******..................79****************98888.55544..444..45899*****************************98433 PP

                 H........T---TTSSB--HHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHSS---.HHHHHHHHHHC.CGGG....GGS-HHHHHHHHH. CS
      Fe-ADH 199 k........kanplsdalaleairliaknleravadgedl.eareqmllastlaglafsnaglg.avHalahalgalfgip....hglanaillpavlr 283
                 +            +s  lal +++++++n  +  ++g d     e+++ a + + +a s+  ++ a H ++hal ++   p    hg+ ++i      +
  EPA06769.1 181 QlghektgeYYGRYSADLALMSAKIVMENSSQYAKNGLDVrIIVEALISAGVASCIAGSSRPCSgAEHLFSHALDKIA--PgrglHGEKCGIGSIMMAK 277
                 34455555588889999*******************9766544445555555555555555554599*******9943..2334677777773333222 PP

                 .........HHHHHHT.... CS
      Fe-ADH 284 fnaeaaperlaqlaralgge 303
                  +     ++ +++a++l+++
  EPA06769.1 278 LQG----QDWKKIAKTLKDV 293
                 222....3444444444333 PP

>> DHQ_synthase  3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.4   4.6e-07    0.0021      23     256 ..      79     314 ..      67     319 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.6e-07
                   HHHTT--TT-EEEEEESHHHHHHHHHHHHHBTT--EEEEEE-SHHHHHTTTSSSEEEEEETTEEEEEEEE---SEEEEEGGGGGGS-HHHHHHHHHH CS
  DHQ_synthase  23 lleakleRksllialGGGvvgDlaGfvAatylRGvrfvqvPttllaqvDssvGgKtainlplgKNliGafaqPkavlidlevLktLperelraGlaE 119
                     + k + ++l++ +GGG   D a  +A  y  G  fv vPt+  a  D      +++  ++   ++ +   P  v++d+++++  p++ l++G+++
    EPA06769.1  79 QKNVKKDGSHLIVGIGGGRSVDTAKMIA--YNLGKPFVSVPTA--ASHDGMASPFVSVVSDKPHSIVAS--APLGVFVDIDIIRKAPAKLLASGCGD 169
                   4444556678999999999999999998..8889999999997..788988888889988888888865..8999********************99 PP

                   HHHHH.HHT-HHHHHHHHHHHHHHHC...............TTTHHHHHHHHHHHHHHHH..HHHHHCCTTTTGGGGGGTTHHHHHHHHHHHTTTTS CS
  DHQ_synthase 120 viKya.likdeelfelleenaeallk...............eeeeealeeliarsievka..evveeDekekglralLnlGHtigHaiEallgyekl 198
                   +i    ++kd +l +  + +                     e++++ +++ +   i v a  +   +     + r +    H ++Ha+++++   + 
    EPA06769.1 170 LIANIiAVKDWQLGHEKTGEYY---GrysadlalmsakivmENSSQYAKNGLDVRIIVEAliSAGVASCIAGSSRPCSGAEHLFSHALDKIAPG-RG 262
                   9854404455555433333332...23446777788876662233333333333333333112222334557888889999**********987.9* PP

                   -HHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHTT---STTTT..-HHHHHHHHT CS
  DHQ_synthase 199 lHGeaVaiGmvlaaelseklgllkkeeverllkllkklglpvslkel.leveellealk 256
                   lHGe   iG ++ a+l         ++ +++ k+lk++g p++ k+  l+ +e+++al+
    EPA06769.1 263 LHGEKCGIGSIMMAKLQ-------GQDWKKIAKTLKDVGAPTTAKQVnLKSDEIVNALM 314
                   ************99998.......456899***********999987677888877765 PP

>> AIRC  AIR carboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.8   6.7e-07     0.003       3     100 ..      36     133 ..      34     164 .. 0.84
   2 ?    0.9   0.1     0.066   2.9e+02      43      75 ..     206     239 ..     196     243 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6.7e-07
                 EEEESSGGGHHHHHHHHHHHHHTT-EEEEEE--TTTSHHHHHHHHHHCHTTTEEEEEEEEES.S--HHHHHHHHSSS-EEEEEE--STTCCHHHHHHHH CS
        AIRC   3 giimGSdsDlevmkkaaeilkelgveyevrvvSahrtpeelleyaeeaeerglkviIagAGg.aahLpgvvaslttlPVigvPvkskalkgldsllSiv 100
                  +i G +    v kk+ + lk+ ++++  + +S   t + + ++ ++++++g + i+ + Gg + + + ++a +   P ++vP+ +++    +  +S+v
  EPA06769.1  36 SLISGVNVTKIVKKKIENSLKSNRIKFVWH-MSGDNTISAINQIQKNVKKDGSHLIVGIGGGrSVDTAKMIAYNLGKPFVSVPTAASHDGMASPFVSVV 133
                 566666666667788999999999999776.688999********************99888799*********************6655555567776 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.066
                 HHHHHHHCHTTTEEE.EEEEEESS--HHHHHHHH CS
        AIRC  43 lleyaeeaeerglkv.iIagAGgaahLpgvvasl 75 
                 ++e  ++++++gl+v iI+ A  +a +++ +a+ 
  EPA06769.1 206 VMENSSQYAKNGLDVrIIVEALISAGVASCIAGS 239
                 6677788999999995666677799999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 2027.72
//
Query:       EPA06770.1  [L=150]
Description: hypothetical protein BG20_I0092 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.1e-23   81.1   0.2    8.4e-23   80.9   0.2    1.0  1  MtrA      Tetrahydromethanopterin S-methyltransferase, subuni


Domain annotation for each model (and alignments):
>> MtrA  Tetrahydromethanopterin S-methyltransferase, subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.9   0.2   4.7e-27   8.4e-23      16     145 ..      17     149 ..      10     150 .] 0.90

  Alignments for each domain:
  == domain 1  score: 80.9 bits;  conditional E-value: 4.7e-27
                 EE--TT-SEEEE-TT-SS-HHHHHHCT....-SEEE----TTHHHHHHHHHHHT-TT--EEEEEE---TTT-HHHHHHHHHHH-B-TTSBBTT--SSS- CS
        MtrA  16 evGdaespvavvtlgshleeeavleaG....aaiaGplktenlGiekvvanvisnpnirflivtGaevkGhitGqalkalhenGvdkekkivgakGaiP 110
                   G+a+s++av+tl+s    +++ ++     + iaG l +en Gi+ ++  +  n  i+ ++v+G ev Gh +G++l  lh+nG+d+ ++i++++   P
  EPA06770.1  17 YLGNADSSIAVCTLSSINLLKQISNSDllnhVGIAGRLFSENKGIDSLIRYINQNKKIKTILVCGKEVWGHKAGHSLFELHKNGIDNRGRIINSTSPDP 115
                 57*************987666665554444489****************************************************************** PP

                 B-SSS-HHHHHHHHHH-EEEEEET---HHHHHHHH CS
        MtrA 111 fienlteeaverfqeqvelvdlidtedvgaikaki 145
                 f+  +t+  +  fq+ + lv+li+  + ++ik+ i
  EPA06770.1 116 FLT-VTKSEIIYFQNEITLVNLINEINFETIKKSI 149
                 **7.66677779******************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1004.38
//
Query:       EPA06771.1  [L=459]
Description: hypothetical protein BG20_I0022 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 2686.75
//
Query:       EPA06772.1  [L=227]
Description: putative UMP kinase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.2e-29  103.7   1.0    1.7e-29  103.1   1.0    1.2  1  AA_kinase  Amino acid kinase family


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.1   1.0   9.6e-34   1.7e-29       1     241 []       3     203 ..       3     203 .. 0.92

  Alignments for each domain:
  == domain 1  score: 103.1 bits;  conditional E-value: 9.6e-34
                 TEEEEEE-TTCCC.CTCCHHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHH..TCCCCCHHHC....E..HHHHHHHHHHHHHHHHHHHHHHHHHT CS
   AA_kinase   1 krvVvKlGGsslt.dkeeaslrrlaeqiaalkesgnklvvVhGggsftdgllal..ksglssgelaaglrstleeagevatrdalaslgerlvaallaa 96 
                 kr+V+Kl G +++ d+  ++l+++a  + ++ ++  +++v+ Ggg+++++++++   sg +++ l                 d+l++  +rl+a+ll +
  EPA06772.1   3 KRIVIKLSGRIFGmDNT-KMLKDYASFLVKI-SKICQPIVIAGGGNIARHYINHarSSGADESTL-----------------DELGIEISRLNAKLLIY 82 
                 79***********6555.5************.888999****************54444444444.................99*************** PP

                 THGEEEE-GGGTCEECCCE..HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEETTTEEEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCT CS
   AA_kinase  97 glpavglsaaaldateagrdegsdgnvesvdaeaieelleagvvpvltgfigldeegelgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpd 195
                 +l+++ +s  +++                   +++++ +++g ++v +g+     +g+    s+  +aal+Ae+++A++ +++tdVdGVyd dp+k ++
  EPA06772.1  83 ALKNKAYSHPPTT------------------LQEVRHAVDDGLIVVAGGLH----PGQ----STNGTAALIAEKINAEQFLNATDVDGVYDMDPNKFKN 155
                 ****999999888..................689********999999988....999....9999********************************* PP

                 TCECCEEEHHHCHH..CSSS.TTTHHHHCHHHHHHHHHCTT-EEEEEE CS
   AA_kinase 196 arllpeisvdeaee..saselatgGmkvkhpaalaaarrggipvvItn 241
                 a+++++i+ + +++  +++  + gG   ++  al++++r++i+++I++
  EPA06772.1 156 AKKFKRIELKNLKNmlVHEDSIAGGYDLMDIVALKIIERSKIKTRIIK 203
                 **********************************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1499.53
//
Query:       EPA06773.1  [L=242]
Description: DNA / pantothenate metabolism flavoprotein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-57  194.0   1.8    2.5e-57  193.7   1.8    1.1  1  DFP       DNA / pantothenate metabolism flavoprotein


Domain annotation for each model (and alignments):
>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.7   1.8   1.4e-61   2.5e-57       1     186 []      28     215 ..      28     215 .. 0.92

  Alignments for each domain:
  == domain 1  score: 193.7 bits;  conditional E-value: 1.4e-61
                 TTT-EEEEEES-EEEECCTTEEEEE----HHHHHHHHHHHHTT-EEEEEE-S-SS---TT-EEEE--SHHHHHHHHHHHHTT-.SEEEE---S--EEES CS
         DFP   1 legkkvlvtaGpTrEaiDpVRfisNrSSGkmGyalAeaaaarGaeVtlvsgpvsletpegvevvkvesaeemleaveealkea.divimaAAvaDyrpk 98 
                 l++kkvl+taGpT+E+iDp+R+i+N+SSGk+G+ lA+++++ Ga+Vtlv gp   + p+g++++k++++eem + v+++++++ divimaAA++Dy+p+
  EPA06773.1  28 LKNKKVLITAGPTIEYIDPIRVITNQSSGKTGVLLASELISSGAKVTLVYGPGIEKPPKGAKIIKISTSEEMFNVVKKEMNKKfDIVIMAAAISDYTPE 126
                 689*************************************************65566889*****************9997777*************** PP

                 -------------..----EEE---HHHHHHHC-S.S-EEEEEEE-SS....-HHHHHHHHHHHTT-SEEEEEEGGGTTGGG-SS-EEEEE. CS
         DFP  99 eaaeeKikkeeeeeeltleleknpdilaelaekkkkkqllvGFaaete....ellenareklerkgldlivaNdvskeeagfgsdenevtll 186
                 + +++Kik   ++++++++l+k p+ + ++ +k +k+ +lvGF+ae +    +l++ a++k+ + ++d+i+aNd+++ + + + d+ne++++
  EPA06773.1 127 KPSKNKIKS--SRNKIKISLKKVPKTIDQI-KKYQKDVFLVGFKAEANisknNLIKLAKKKIIESNADMIIANDIGSIKYKKNPDNNEILII 215
                 ********6..5668***************.55566779*******766677************************9977788888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1248  (0.0696079); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1584.78
//
Query:       EPA06774.1  [L=197]
Description: ABC transporter, ATP-binding protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-29  102.8   0.1      3e-29  102.3   0.1    1.2  1  ABC_tran      ABC transporter
    5.1e-06   26.1   4.3    5.5e-05   22.7   4.3    2.0  1  SMC_N         RecF/RecN/SMC N terminal domain
    0.00012   22.1   2.2      0.069   13.0   1.0    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
     0.0011   18.7   0.5     0.0064   16.2   0.4    2.2  2  AAA_29        P-loop containing region of AAA domain
     0.0026   17.7   1.1      0.011   15.6   0.2    2.1  2  RsgA_GTPase   RsgA GTPase
     0.0047   15.7   2.0      0.034   12.8   0.2    2.0  2  AAA_13        AAA domain
  ------ inclusion threshold ------
      0.012   14.8   0.0      0.013   14.7   0.0    1.1  1  G-alpha       G-protein alpha subunit
      0.013   15.2   1.4       0.16   11.6   0.2    2.1  2  AAA_15        AAA ATPase domain
      0.019   15.4   0.0       0.03   14.7   0.0    1.3  1  AAA_16        AAA ATPase domain
      0.021   15.3   0.4       0.07   13.6   0.4    1.7  1  NYN           NYN domain
      0.031   14.6   0.3      0.065   13.5   0.3    1.9  1  AAA_22        AAA domain
      0.056   13.5   1.0       0.56   10.2   0.1    2.2  2  Dynamin_N     Dynamin family
       0.07   13.6   1.5       0.13   12.7   1.6    1.6  1  AAA_23        AAA domain
       0.11   12.1   1.2       0.44   10.1   0.2    2.2  2  cobW          CobW/HypB/UreG, nucleotide-binding domain
       0.12   12.0   1.3       0.15   11.7   0.2    1.7  2  AAA_24        AAA domain
       0.17   11.2   1.7       0.39   10.0   0.6    2.1  3  FtsK_SpoIIIE  FtsK/SpoIIIE family
       0.19   11.8   2.4       0.32   11.1   2.4    1.9  1  MMR_HSR1      50S ribosome-binding GTPase
       0.33   11.1   1.2       0.45   10.7   1.2    1.7  1  AAA_33        AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.3   0.1     3e-32     3e-29      16     136 ..       2     134 ..       1     135 [. 0.96

  Alignments for each domain:
  == domain 1  score: 102.3 bits;  conditional E-value: 3e-32
                 EEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS--S-TTSBHHHH............HHHTCHHHHHHHSTTGGTT CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxx............xxxxxxxxxxxxxxxxxxx RF
    ABC_tran  16 ivGenGaGKStLlkllagllkpteGeilldgkdlke....qeleslrkeigvlpqepqlfpeltvren............esdeeiekalsklglkelk 98 
                 ivG++G+GKStLl+++  l +pt G++ +dg+d+++    +  ++ +k++g+++q ++l  +ltv en             +++++ ++l+ +g+++  
  EPA06774.1   2 IVGSSGSGKSTLLNMIGLLDHPTTGKVFIDGTDTTNltddKISTFRNKKLGFIFQFSNLLTDLTVLENillprqiagtnhSAEKDARELLKAVGIEDQM 100
                 9*********************************9999988899999*******************************9777788************99 PP

                 CBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  99 dtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                 ++++    +++SgGq qrva+ar l+++p+++l+DEpt
  EPA06774.1 101 NKRA----NKISGGQAQRVAIARGLINHPSIVLADEPT 134
                 9999....*****************************9 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   4.3   5.6e-08   5.5e-05      28     213 ..       1     181 [.       1     186 [. 0.85

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 5.6e-08
                 EEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEETTSEEEEEETTEEE-H.HHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
       SMC_N  28 aivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrvkrkgeseykingkevtk.kevse 125
                 +ivG+ GSGKs ll+ i    G  +      ++ +  i    +  +++  +++  f+n++  +  + +++ +  +v ++     +i g++ +  k+ +e
  EPA06774.1   1 MIVGSSGSGKSTLLNMI----GLLDH----PTTGKVFIDG-TDTTNLTDDKIST-FRNKKLGFIFQFSNLLTDLTVLENILLPRQIAGTNHSAeKDARE 89 
                 59************999....64333....4556666776.8888899999987.8999999999999999999999999999999999988779**** PP

                 HHHCTT-STT......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC-SCEEEEEE CS
                 xxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxx RF
       SMC_N 126 llesagiske......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivislreemlekadklvgvtk 213
                 ll+ +gi+ +       +SgG+ + va+a       ++  +++l De   +LD    + +++l+k+  kn    fi+++++++++ ++d+++ ++ 
  EPA06774.1  90 LLKAVGIEDQmnkranKISGGQAQRVAIAR----GLINHPSIVLADEPTGNLDSVTSATIVDLMKSMAKNlnQTFIIVTHDRQHFGDVDRVITIKD 181
                 *******9987888889*****99888764....456778899**********************999986355999*************999875 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   1.0   6.9e-05     0.069       4      62 ..       2      43 ..       1     111 [. 0.67
   2 !    8.5   0.0    0.0016       1.6     257     298 ..     125     166 ..     113     168 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.9e-05
      AAA_21  4 liGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefei 62
                ++G  gsGKS+LL  + ll                  +++    ++d++d++  +   i
  EPA06774.1  2 IVGSSGSGKSTLLNMIGLLD-----------------HPTTGKVFIDGTDTTNLTDDKI 43
                9***************9883.................2222222222222222222222 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0016
      AAA_21 257 kgsllliDEpEngLHPkllrrllellkelsrngaQv.iltTHS 298
                 + s++l DEp  +L+    +++++l+k+ ++n+ Q  i++TH+
  EPA06774.1 125 P-SIVLADEPTGNLDSVTSATIVDLMKSMAKNLNQTfIIVTHD 166
                 3.89999*******************99999999998*****8 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.4   6.5e-06    0.0064      26      41 ..       1      16 [.       1      29 [. 0.79
   2 ?   -0.3   0.0      0.93   9.3e+02      43      60 ..      68      85 ..      65      86 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 6.5e-06
      AAA_29 26 lltGpsGsGKSTllDA 41
                +++G sGsGKSTll  
  EPA06774.1  1 MIVGSSGSGKSTLLNM 16
                699**********954 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.93
      AAA_29 43 qalLvpakkvrfNkaane 60
                  +L+p++ +  N +a++
  EPA06774.1 68 ENILLPRQIAGTNHSAEK 85
                57999***999***9986 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.2   1.1e-05     0.011     104     130 ..       2      28 ..       1      44 [. 0.80
   2 ?    0.4   0.0      0.54   5.4e+02       8      30 ..     148     170 ..     139     183 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.1e-05
                  EECSTTSSHHHHHHHHCTT-----S-- CS
  RsgA_GTPase 104 lvGqSGvGKStLinallpelelktgev 130
                  +vG+SG GKStL+n++   ++  tg+v
   EPA06774.1   2 IVGSSGSGKSTLLNMIGLLDHPTTGKV 28 
                  89************9977666666665 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.54
                  ETTTTEES--EEEEEEESTTTT- CS
  RsgA_GTPase   8 lvrpkvaNvdqllivvslkepel 30 
                  l+++ + N++q +i+v+ +++++
   EPA06774.1 148 LMKSMAKNLNQTFIIVTHDRQHF 170
                  66777899999999999996665 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.041        41      20      49 ..       1      30 [.       1      56 [. 0.78
   2 !   12.8   0.2   3.4e-05     0.034     524     583 ..     122     179 ..     115     191 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.041
      AAA_13 20 liYGwNGaGKTtLSrllrslelgetepkfa 49
                +i G+ G+GK+tL +++  l +  t + f 
  EPA06774.1  1 MIVGSSGSGKSTLLNMIGLLDHPTTGKVFI 30
                578999********9999887666666555 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 3.4e-05
      AAA_13 524 igkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQ.lfiLTHnleffkevkkntkr 583
                 i+   iv  D P   LDs  +  ++ l+ks +   k+ +Q ++i TH  + f  v++ +  
  EPA06774.1 122 INHPSIVLADEPTGNLDSVTSATIVDLMKSMA---KNLNQtFIIVTHDRQHFGDVDRVITI 179
                 56789**************************9...7777725578****999999886664 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.3e-05     0.013      28     113 ..       2     105 ..       1     177 [. 0.63

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.3e-05
                 EEESTTSSHHHHHHHHHHHCS--.............--HHHHHCCHH......HHHHHHHHHHHHHHHHHHHTT.............HHHC-SS-SCCC CS
     G-alpha  28 llGqseSGKsTilkqlkllykkg.............fseeelatwra......viqlnivrsiktilealesleselsesf......elqelkerldpl 101
                 ++G+s+SGKsT+l+ + ll  ++              +++++ t+r+      + ++n+++++  + ++l                 + ++  ++l + 
  EPA06774.1   2 IVGSSGSGKSTLLNMIGLLDHPTtgkvfidgtdttnLTDDKISTFRNkklgfiFQFSNLLTDLTVLENILLPR-------QiagtnhSAEKDARELLKA 93 
                 79*****************999988998888888776666677777744444334445555444444444443.......1233333556666666666 PP

                 S-HCHHHH.... CS
     G-alpha 102 kkveasliakls 113
                   +e++++++ +
  EPA06774.1  94 VGIEDQMNKRAN 105
                 666776655443 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   0.00016      0.16      28      72 ..       2      50 ..       1     108 [. 0.74
   2 ?    2.9   0.1     0.075        75     324     365 ..     125     166 ..     113     168 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00016
      AAA_15 28 liGkNnsGKSsilealdlFlnnkekkn.....kkvikiekedleifenis 72
                ++G  +sGKS++l+++ l+   ++  +      +++++ ++++++f+n++
  EPA06774.1  2 IVGSSGSGKSTLLNMIGLLDHPTTG-KvfidgTDTTNLTDDKISTFRNKK 50
                8***************888776622.245677667777777777776554 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.075
      AAA_15 324 nvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                 + i+l +EP  +L       +++l+k++a++ ++  ii TH 
  EPA06774.1 125 PSIVLADEPTGNLDSVTSATIVDLMKSMAKNLNQTFIIVTHD 166
                 5677777777777777778899**********9778999*96 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0     3e-05      0.03      29     141 ..       2     164 ..       1     180 [. 0.60

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3e-05
      AAA_16  29 lsGesGvGKsslvrellralekd..ggiflrgkcdql..esa...ipy........salaqalareellrqllde....aesaeleawrekleeala.. 106
                 ++G sG+GKs+l++++   l     g +f+ g+ + +  + +   + +         ++ ++l+  ++l+ +l +     ++ ++e ++++l++a++  
  EPA06774.1   2 IVGSSGSGKSTLLNMIG-LLDHPttGKVFIDGTDTTNltD-DkisT-FrnkklgfiFQFSNLLTDLTVLENILLPrqiaGTNHSAEKDARELLKAVGie 97 
                 89***********9887.3333333567788888888642.24430.2444434444455555555666666666555533334444444455555578 PP

      AAA_16 107 ...................................avpelagaeasrllellkrllallsrderplvlvl 141
                                                    ++++l++  +  + +l+k++++ l +   ++++v 
  EPA06774.1  98 dqmnkrankisggqaqrvaiarglinhpsivladePTGNLDSVTSATIVDLMKSMAKNLNQ---TFIIVT 164
                 8888877777777777777777777777777666666666666667777777777744443...355555 PP

>> NYN  NYN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.4     7e-05      0.07       4     106 ..      28     167 ..      27     183 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7e-05
         NYN   4 vfiDgenlpvpak.........gke...vdyrklleeirskge..lvraraygnwedeeqnkfqdalsstgi.kvkhkplkkrg............... 72 
                 vfiDg +    ++         +     +++++ll  ++   +  l r  a +n  +++ +++++ l++ gi + + k+++k++               
  EPA06774.1  28 VFIDGTDTTNLTDdkistfrnkK-LgfiFQFSNLLTDLTVLENilLPRQIAGTN--HSAEKDARELLKAVGIeDQMNKRANKISggqaqrvaiarglin 123
                 89999999888888999998743.25779**********998854444444444..6667999999999999999999999988999999999999999 PP

         NYN  73 ..........gsgkkavDvelavdalelaydnkydtivLvsgDg 106
                           +++ ++v  + +vd+++ +++n   t+++v+ D+
  EPA06774.1 124 hpsivladepTGNLDSVTSATIVDLMKSMAKNLNQTFIIVTHDR 167
                 9999999**77777***************99955********95 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.3   6.6e-05     0.065       9      55 ..       1      40 [.       1     168 [. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.6e-05
      AAA_22  9 vvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskd 55
                +++G sG+GK+tll+++   ++       +  + vf++ +  t+++d
  EPA06774.1  1 MIVGSSGSGKSTLLNMIGLLDH-------PTTGKVFIDGTDTTNLTD 40
                599*************999885.......255555666666665554 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00057      0.56       3      18 ..       2      17 ..       1      30 [. 0.90
   2 ?    2.1   0.1      0.18   1.7e+02      85     137 ..     109     165 ..      64     183 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00057
                EEEBTTTTHHHHHHHH CS
   Dynamin_N  3 vvGsqSsGKSSvlnaL 18
                +vGs  sGKS++ln +
  EPA06774.1  2 IVGSSGSGKSTLLNMI 17
                89************87 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.18
                 S--SS-EEEEEEETTS-SEEEEE--.-B-SSSGTTS..HHHHHHH.STTEEEEEEEE CS
   Dynamin_N  85 giskkvillkilsllvkgltlvDlP.Gldsvnkrdq..elvkeyi.kkadiilavts 137
                 g + + + +    ++ + ++l D P G  ++ +  +  +l+k+++ + ++ ++ vt+
  EPA06774.1 109 GGQAQRVAIARGLINHPSIVLADEPtGNLDSVTSATivDLMKSMAkNLNQTFIIVTH 165
                 333333444444444444455554432222222222444444444444444444444 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.6   0.00013      0.13      24      41 ..       2      19 ..       1     114 [. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00013
      AAA_23 24 ItGpNGaGKTTildAikl 41
                I+G  G+GK+T+l+ i l
  EPA06774.1  2 IVGSSGSGKSTLLNMIGL 19
                9*************9976 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.2   0.00044      0.44       5      20 ..       2      17 ..       1      52 [. 0.85
   2 ?    0.9   0.1       0.3     3e+02     103     124 ..     164     185 ..      85     195 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00044
                EEESTTCCHHHHHHHH CS
        cobW  5 ltGflGsGKTtLlnhl 20
                ++G+ GsGK+tLln +
  EPA06774.1  2 IVGSSGSGKSTLLNMI 17
                89***********987 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.3
                 SHHHHHCCCECEEEEEEETTTH CS
        cobW 103 eeelksdltldavvavvDaknl 124
                 +++ ++   +d v+++ D+k++
  EPA06774.1 164 THDRQHFGDVDRVITIKDGKAF 185
                 2222333344555555555444 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   0.00015      0.15       6      47 ..       1      47 [.       1      91 [. 0.75
   2 ?   -2.0   0.0       2.4   2.4e+03     118     134 ..     153     169 ..     141     187 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00015
      AAA_24  6 liyGpsgiGKTtlakel......gpkplfidtekGlksldadkfpdie 47
                +i+G+sg+GK+tl++++      +   +fid  + + +l +dk+ + +
  EPA06774.1  1 MIVGSSGSGKSTLLNMIglldhpTTGKVFIDGTD-TTNLTDDKISTFR 47
                699*************999887755667777666.4577777776655 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.4
      AAA_24 118 lqelrknvifiahektr 134
                  ++l++++i++ h ++ 
  EPA06774.1 153 AKNLNQTFIIVTHDRQH 169
                 56666677777776654 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.6   0.00039      0.39      43      58 ..       1      16 [.       1      20 [. 0.91
   2 ?   -3.4   0.0       4.8   4.8e+03     151     173 ..      28      50 ..      22      55 .. 0.73
   3 ?   -0.6   0.0      0.69   6.9e+02     104     138 ..      86     122 ..      71     163 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00039
                  EEE--TTSSHHHHHHH CS
  FtsK_SpoIIIE 43 lvaGatgsGKStalnt 58
                  +++G++gsGKSt ln 
    EPA06774.1  1 MIVGSSGSGKSTLLNM 16
                  79***********995 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 4.8
                   TT-.................... CS
  FtsK_SpoIIIE 151 lvlDnyddlaaeneritsLsnqg 173
                   +++D++d+ +  + +i    n+ 
    EPA06774.1  28 VFIDGTDTTNLTDDKISTFRNKK 50 
                   78888888888888777666655 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.69
                   HHHHHHHHH..HHHHHHHHHHHHHTT-SSHHHHHHHH CS
  FtsK_SpoIIIE 104 ralraleeL..vkemeeryalfreagvrsiaaydgei 138
                   +a+++l+++  +++m++r+++++  +++ +a ++g i
    EPA06774.1  86 DARELLKAVgiEDQMNKRANKISGGQAQRVAIARGLI 122
                   5555555533267888888888877777776655555 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   2.4   0.00033      0.32       3      19 ..       1      17 [.       1     190 [. 0.90

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00033
                EEEESTTSSHHHHHHHH CS
    MMR_HSR1  3 aivGrpNvGKStLinal 19
                +ivG + +GKStL+n +
  EPA06774.1  1 MIVGSSGSGKSTLLNMI 17
                69*************87 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.2   0.00045      0.45       3      17 ..       1      15 [.       1     163 [. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00045
      AAA_33  3 llvGlpGsGKstlae 17
                ++vG +GsGKstl+ 
  EPA06774.1  1 MIVGSSGSGKSTLLN 15
                78**********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); expected 358.6 (0.02)
Passed Vit filter:                       102  (0.00568911); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 1309.52
//
Query:       EPA06775.1  [L=645]
Description: KH/beta-lactamase domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      3e-23   82.2   0.0    5.7e-23   81.3   0.0    1.5  1  Beta-Casp      Beta-Casp domain
    2.3e-21   75.5   1.6      1e-20   73.4   0.8    2.5  3  KH_7           KH domain
    6.7e-16   58.0   0.0    1.4e-15   56.9   0.0    1.6  1  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
    5.1e-14   52.2   0.0    9.5e-14   51.3   0.0    1.4  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
    4.5e-12   46.4   0.7    5.1e-11   42.9   0.2    2.5  2  Lactamase_B    Metallo-beta-lactamase superfamily
    8.3e-09   35.2   0.0    2.3e-08   33.8   0.0    1.7  2  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.011   15.6   0.0      0.035   14.0   0.0    1.9  1  Lactamase_B_3  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Beta-Casp  Beta-Casp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.3   0.0   2.2e-26   5.7e-23       1     109 [.     429     553 ..     429     554 .. 0.84

  Alignments for each domain:
  == domain 1  score: 81.3 bits;  conditional E-value: 2.2e-26
                 HHHHHHHH..HCTT..TTS-S-EEEEE-HHHHHHHHHGGGGGG.......................E-SHH....HHH.H...HHHS-SSEEEEES-TT CS
   Beta-Casp   1 aqellylLeelwkekkledlklpiyldsplaskatevYkeyae.......................veakslewmesk.ke.elnsskgpkvilassgm 74 
                 aqe+++++++++k+++   +++p++  + ++s+a +++++y+e                       +       +e+  ++ e  ++++p++ila+sgm
  EPA06775.1 429 AQEIMMVIDHYMKSGE--MVEAPVFTEG-MISEASAIHEAYPEylarelkqkiletddnpfdseyfT------NIEHAdAReEPMRDNSPCIILATSGM 518
                 7***********9955..6789****99.**************999998888888888876554431......2333332225557889********** PP

                 SSSSHHHHHHHHHTTSTTSEEEESS---TTSHHHH CS
   Beta-Casp  75 legGrsrellkklledprntvilvgyqaegTlgrk 109
                 legG++ e++k++++d++n v++v+yq++gT+gr+
  EPA06775.1 519 LEGGPVLEYFKNIAPDKKNKVLFVSYQVNGTMGRR 553
                 *********************************97 PP

>> KH_7  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.4   0.8     4e-24     1e-20       5      68 .]      14      77 ..      12      77 .. 0.97
   2 ?   -3.1   0.0       3.1   7.9e+03       5      21 ..      81      97 ..      78     101 .. 0.81
   3 ?   -1.9   0.0       1.4   3.5e+03      46      59 ..     465     478 ..     458     482 .. 0.79

  Alignments for each domain:
  == domain 1  score: 73.4 bits;  conditional E-value: 4e-24
        KH_7  5 eelkekieeklPkevkitdveFEGPelViYtknpklfaengdlirklAkelrkRiviRpDpsvl 68
                ++++++i +++Pke+k+t++e+EGP +++Yt+ p++++en++ i++l++ ++kRiv+R+D+s++
  EPA06775.1 14 QNMMATILQSIPKEAKVTKIEYEGPRIALYTNSPRYLMENNETISNLVNIIKKRIVVRTDESIR 77
                68999********************************************************986 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.1
        KH_7  5 eelkekieeklPkevki 21
                e+ ++ + e +Pke++ 
  EPA06775.1 81 EDARKILAECIPKEANF 97
                67889999999*99875 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.4
        KH_7  46 dlirklAkelrkRi 59 
                  + + lA+el+++i
  EPA06775.1 465 AYPEYLARELKQKI 478
                 56677999999998 PP

>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.9   0.0   5.6e-19   1.4e-15       2      62 .]     573     636 ..     572     636 .. 0.96

  Alignments for each domain:
  == domain 1  score: 56.9 bits;  conditional E-value: 5.6e-19
       RMMBL   2 ipvkarieeid.fSgHadknellelirklkprn..vilvHGeeeatsalarllkeeegidvfiP 62 
                 + +++++e++d fSgH+d+n+l+ ++++l+p+   v ++HGe+++ + la  +++ + + +++P
  EPA06775.1 573 VTINCSVEKLDgFSGHSDYNQLMSFVQRLRPKLrrVLVNHGERRKSENLAMNIRRMFRVPAHYP 636
                 679*******************************99999**************99999*99998 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.3   0.0   3.7e-17   9.5e-14       1     175 [.     205     374 ..     205     386 .. 0.83

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 3.7e-17
  Lactamase_B_6   1 lLeldnvkiLlDvGwdes.k..vslesalkelekviptvdliLLshatlehlGayallyakfksklllnipvyatlpvvkLGrvslldlyaskgll 93 
                    lL+  + kiL+D+G +   k  +++   l++l+ +++++d++++ ha l+h G ++ l+     k++ + p+y+t p+  + ++  ld+++ ++++
     EPA06775.1 205 LLSTPESKILVDCGINPGaKhpMDSFPRLDFLDITLDELDAVVIGHAHLDHTGFLPALC-----KFGYKGPIYCTEPTLPMMNLIQLDAIKVASAQ 295
                    5677789********95413113344478999999******************888777.....468899***********999999*99999888 PP

  Lactamase_B_6  94 gpedseeleledideafdkiktlkYsQklelkskldgltitaynaGhtlGGti..WkiskesekivYavdwnhakeshLngaal 175
                    g + +      d+++++++ +tl Ys  ++++    ++ ++  naGh lG ++  ++i ++ ++ vY  d+   k  + ++a++
     EPA06775.1 296 GRTPM--YAERDVKQIMKQAITLPYSTVTDISP---DIKLVFANAGHILGSALchFHIGNGDHNFVYSGDIKFGKSILFEAASW 374
                    77765..4779****************999996...7888899*******9764488999999****99998777777777666 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   0.2     2e-14   5.1e-11       5     158 ..     200     368 ..     197     389 .. 0.87
   2 ?   -2.9   0.0       2.3   5.8e+03      55      97 ..     436     478 ..     436     501 .. 0.71

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 2e-14
                  SSEEEEEEETTCEEEES--SCHHHHHHHH...HHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHHHHCCHH.. CS
  Lactamase_B   5 pvnsyliegdggviLiDtGtsteaaraal...elaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmeeaddaasrkgll.. 97 
                  + +++l+ ++++ iL+D+G+ + a+  ++   +l  l++ ++++dav++ H+HlDH+G l+ l++     ++++ e +  + +    da    ++   
   EPA06775.1 200 GRSCMLLSTPESKILVDCGINPGAKHPMDsfpRLDFLDITLDELDAVVIGHAHLDHTGFLPALCKFGYKGPIYCTEPTLPMMNLIQLDAIKVASAQgr 297
                  679***********************************************************************************9999999888** PP

                  ..........TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCC CS
  Lactamase_B  98 ..........lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetg 158
                             +   a+     +  + + +   ++  + ++ g+  +h+++++g+ +++++GD  +  +++
   EPA06775.1 298 tpmyaerdvkQIMKQAITLPYSTVTDISPDIKLVFANAGHILGSALCHFHIGNGDHNFVYSGDIKFGKSIL 368
                  *****888775555555555555555555666667777899999999****************98876655 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.3
                  HHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHHHHCCHH CS
  Lactamase_B  55 lDHiGglgglveatdvpvgavaeeapalfmeeaddaasrkgll 97 
                  +DH+   g+ vea  +  g+ +e+ + ++   ++ a++ k+ +
   EPA06775.1 436 IDHYMKSGEMVEAPVFTEGMISEASAIHEAYPEYLARELKQKI 478
                  5999999999999999999999888888888777777666543 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.0   8.8e-12   2.3e-08       2     148 ..     212     370 ..     211     414 .. 0.66
   2 ?   -3.3   0.0       2.1   5.4e+03     176     194 ..     586     604 ..     566     611 .. 0.73

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 8.8e-12
                    EEEES--TTHHHHHTCGG.S--S..SS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHH.....HCCTTCGHHHCHTT...TTEE CS
  Lactamase_B_2   2 riLiDagpdlrqqalral.qPve..lrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvla.....vleanfvylaleee...pavn 86 
                     iL+D+g +  +  ++    P+   l  +l+++daV++ haH DH+  l+ l ++ +k  p+y+++ +l      +l+a  v+ a+++    ++ +
     EPA06775.1 212 KILVDCGINPGAK-HPMDsFPRLdfLDITLDELDAVVIGHAHLDHTGFLPALCKFGYK-GPIYCTEPTLPmmnliQLDAIKVASAQGRTpmyAERD 305
                    59*****996555.44444444448999******************999*****7775.7*****9999966666444444444444445443333 PP

                    EEEE-TTSEEEE.......CSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---....H CS
  Lactamase_B_2  87 vheldwgesfel.......gdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyip....e 148
                    v+++  ++ ++l        +++  i+++ a+ ++        +  + + i++g+++++y+gD ++ +    e
     EPA06775.1 306 VKQIM-KQAITLpystvtdISPD--IKLVFANAGHIL-----GSALCHFHIGNGDHNFVYSGDIKFGKsilfE 370
                    33333.33333344445332345..555555555555.....348999****************976633332 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.1
                    HT---STSHHHHCTTSSSS CS
  Lactamase_B_2 176 mgHltpeeaveaaadlgak 194
                     gH++ ++ + ++++l++k
     EPA06775.1 586 SGHSDYNQLMSFVQRLRPK 604
                    5999999999999999876 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.4e-05     0.035       5      50 ..     199     256 ..     196     298 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.4e-05
  Lactamase_B_3   5 lghnsflletagarilvDPf......kanlgyeppa.............eeaDlvlisqaledHa 50 
                    +g +++ll+t++ +ilvD +      +       p              +e D+v+i +a+ dH 
     EPA06775.1 199 VGRSCMLLSTPESKILVDCGinpgakH-------PMdsfprldflditlDELDAVVIGHAHLDHT 256
                    689***************884443330.......334455677777778***************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (645 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.69u 0.30s 00:00:00.99 Elapsed: 00:00:00.47
# Mc/sec: 4125.24
//
Query:       EPA06776.1  [L=291]
Description: copper binding protein, plastocyanin/azurin family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.014   15.8   0.7      0.097   13.1   0.0    2.4  2  Copper-bind   Copper binding proteins, plastocyanin/azurin fa
       0.04   14.0   0.0       0.14   12.3   0.0    2.0  1  Cupredoxin_1  Cupredoxin-like domain
      0.043   13.8   0.0       0.96    9.5   0.1    2.5  3  IF3_C         Translation initiation factor IF-3, C-terminal 


Domain annotation for each model (and alignments):
>> Copper-bind  Copper binding proteins, plastocyanin/azurin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.6e-05     0.097      14      99 .]      54     130 ..      45     130 .. 0.78
   2 ?    0.3   0.2      0.16   9.7e+02      56      76 ..     166     186 ..     141     228 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.6e-05
                  EESSEEEEETTEEEEEEEESSSSBEEEEET..TSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEESSEEEEEEETTTTTTTSEEEEEEE CS
  Copper-bind  14 FetkeitvkkgekvtfvnlavmgHNvvldk..dgvpagvdkdkvkaedetkliggGekdsvtfdeagtYkffCsPHaaagMkgkvtve 99 
                  + +ke tv+ g  v f n+++ +H     +  dg p+g+ ++        +l  +G +++ + +e g++ ++C  H    M+g ++v+
   EPA06776.1  54 YIPKEATVDVGGVVIFSNTDSAAHTFTAGTaaDG-PSGAFDS--------SLAIAGSSYEWKPTEVGSFPYYCMVHP--WMEGLIVVQ 130
                  78999999**********9999997554332122.3333333........35668**********************..68**99986 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.16
                  CTTCEEEEBSTTEEEEEEEES CS
  Copper-bind  56 kaedetkliggGekdsvtfde 76 
                  k + +t+  ++Gek++v+++ 
   EPA06776.1 166 KVSVSTSAPTTGEKMKVNVEF 186
                  333344444444444444442 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.3e-05      0.14      28     104 .]      50     129 ..      10     129 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.3e-05
  Cupredoxin_1  28 kdggfePskievkagekvklkiknkdktpeefesed......lgeekvlapgktttitiaplkpGeYeftcdmhmdakGkliV 104
                   ++g + P++ +v  g    + + n+d+ +++f++          ++  la   ++  + +p + G+++++c  h+ ++G ++V
    EPA06776.1  50 AEGCYIPKEATVDVGG--VVIFSNTDSAAHTFTAGTaadgpsGAFDSSLAIAGSSY-EWKPTEVGSFPYYCMVHPWMEGLIVV 129
                   235999*********8..679************99999999988888888655554.3479**************99**9998 PP

>> IF3_C  Translation initiation factor IF-3, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0     0.097   5.8e+02      15      37 ..     148     170 ..     141     173 .. 0.87
   2 ?    9.5   0.1   0.00016      0.96      30      65 ..     176     216 ..     175     227 .. 0.72
   3 ?   -1.0   0.0       0.3   1.8e+03      28      48 ..     225     245 ..     212     255 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.097
                 HHHHHHHHHHHHHHHHT-EEEEE CS
       IF3_C  15 hDlevKlknarkFLeegdkvKvt 37 
                 +D  +K  +a+  L++g kv v+
  EPA06776.1 148 GDTMMKDVSATGMLSDGTKVSVS 170
                 788999999999********987 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00016
                 HT-EEEEEEE--S-TTSH.....HHHHHHHHHHHHHHTTTT CS
       IF3_C  30 egdkvKvtlrfrGReiah.....kelgkevleriaeeleev 65 
                  g+k+Kv++ f G e  +     ++ g++vl+++a++ ++ 
  EPA06776.1 176 TGEKMKVNVEFAGKEHVNhdimvTQNGEDVLNDMAAHHHDG 216
                 699***********966511111567999999999877764 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.3
                 HHHT-EEEEEEE--S-TTSHH CS
       IF3_C  28 LeegdkvKvtlrfrGReiahk 48 
                 L++ d v +t+ f+G  +  +
  EPA06776.1 225 LKSSDPVEITITFQGYGVDDP 245
                 78889999*****99666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1909.39
//
Query:       EPA06777.1  [L=137]
Description: creatinase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.4e-14   52.2   0.0    1.1e-13   52.0   0.0    1.0  1  Creatinase_N  Creatinase/Prolidase N-terminal domain
  ------ inclusion threshold ------
      0.013   15.2   0.0      0.016   14.9   0.0    1.3  1  PGBA_N        Plasminogen-binding protein pgbA N-terminal


Domain annotation for each model (and alignments):
>> Creatinase_N  Creatinase/Prolidase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.0   0.0   1.2e-17   1.1e-13       1     131 [.       4     123 ..       4     124 .. 0.90

  Alignments for each domain:
  == domain 1  score: 52.0 bits;  conditional E-value: 1.2e-17
                   HHHHHHHHHHHTT-SEEEEECCHHHHHHHSS...-SSSEEEEEEESSCE.EEEEECTTHHHHHHHH.TTSEEEEESTHSSHHHHHHHHHHHHT-EEE CS
  Creatinase_N   1 RlerlralmeekgldallvtspenlrYltGfatetgsrglalvvtadga.lllvdalryteaaeesatveevveyddpvealadllkellesekrvg 96 
                   R+++l ++ +e ++d l+ ++penl+Y+tGf    g++  +l  ++ g+ +++ ++l++++++ees +  +vv+ ++    l++ l ++++ +k+v 
    EPA06777.1   4 RRKNLLKFAQEFNCDTLVTFEPENLFYMTGF---WGEAIGIL--EKGGNtTIIAPELEVGRVKEES-ENCDVVTAER-GIGLISSLTSKIK-NKKVC 92 
                   999****************************...********..666666****************.********98.8999999999966.5**** PP

                   E-TTSSBHHHHHHHHHHCTTSEEEETHHHHHHHHS CS
  Creatinase_N  97 veldaltvafyealkealpdaelvdaselieelRv 131
                    + ++  ++ + +lk+ +p  ++++++e +   R+
    EPA06777.1  93 TDCQN--YSIMTSLKKSIP--SIKSSTEPFYNSRI 123
                   ***96..99999******9..78888877777766 PP

>> PGBA_N  Plasminogen-binding protein pgbA N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.8e-06     0.016     154     194 ..      86     128 ..      46     136 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.8e-06
      PGBA_N 154 lknkvnvlDcqsfaiLekkkl.kskieetklPFy.srveeidt 194
                 +knk +++Dcq+++i+++ k   ++i++ + PFy sr+ + ++
  EPA06777.1  86 IKNKKVCTDCQNYSIMTSLKKsIPSIKSSTEPFYnSRIVKDEK 128
                 58999************9887789**********778876555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1050.28
//
Query:       EPA06778.1  [L=151]
Description: peptidyl-prolyl cis-trans isomerase, cyclophilin-type [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-51  174.3   0.1    2.5e-51  174.1   0.1    1.0  1  Pro_isomerase  Cyclophilin type peptidyl-prolyl cis-trans iso


Domain annotation for each model (and alignments):
>> Pro_isomerase  Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.1   0.1   1.4e-55   2.5e-51       3     144 ..       5     142 ..       3     150 .. 0.91

  Alignments for each domain:
  == domain 1  score: 174.1 bits;  conditional E-value: 1.4e-55
  Pro_isomerase   3 dietsskGrivieLfadkaPktvenFlklvkegfYdgttFhRvikgfmvqgGdptgktsageqekkggesiraipdEitsklkhkrGalamartgk 98 
                     iet+ +G+iv++L +d aP+tv+nF kl+k+gfY+gt FhRvi+gfm+qgGdp++kt+++++   gg    +i++E+ s+ +h+rG+++mar+ +
     EPA06778.1   5 IIETN-LGTIVFKLLPDLAPETVRNFEKLAKDGFYNGTLFHRVIPGFMIQGGDPNTKTANKSTWGMGG-PGHTIKAEF-SSRSHHRGIVSMARA-Q 96 
                    689*7.***************************************************88555445555.579******.7889**********9.7 PP

  Pro_isomerase  99 epnsagsqFfItlkeaphldgkytvFGkVveGmdvvekiekvetde 144
                    +pnsagsqFfI++++ ++ld++ytvFG+V+eGmdv +ki ++++d+
     EPA06778.1  97 DPNSAGSQFFIVTTDSTFLDRQYTVFGEVTEGMDVADKIVNLPRDR 142
                    9****************************************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1021.35
//
Query:       EPA06779.1  [L=332]
Description: hypothetical protein BG20_I0087 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00086   19.3   0.0     0.0021   18.1   0.0    1.5  1  Allantoicase     Allantoicase repeat
     0.0039   16.6   0.9     0.0084   15.5   0.2    1.9  2  DUF5305          Family of unknown function (DUF5305)
     0.0062   16.7   1.0     0.0096   16.0   0.2    1.7  2  Podoplanin       Podoplanin
  ------ inclusion threshold ------
      0.014   14.8   0.4      0.049   13.0   0.0    1.8  2  Glucos_trans_II  Glucosyl transferase GtrII
      0.014   15.6   1.9      0.053   13.8   0.2    2.2  2  DUF4064          Protein of unknown function (DUF4064)


Domain annotation for each model (and alignments):
>> Allantoicase  Allantoicase repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   5.8e-07    0.0021      53     134 ..     168     255 ..     162     259 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 5.8e-07
  Allantoicase  53 sgviegvevdtahFkgnappevsvealeleaseeeaeeeaelkseewkellpktklkpdkrhlf....kvea.ee...klthvrlniyPD 134
                   + ++++v+vd + F  +    ++++ ++ ++++++ + +    ++++ +l+  ++l ++  ++f    k+ a +e   + thv ln+ PD
    EPA06779.1 168 PKILKNVQVDNKKFVIEIGTFAEINKFNFDQNTKRINFQV-SGDKQIVTLVIPQELLSGPYNVFlgdkKI-AfSEyinNGTHVWLNMRPD 255
                   67899************************87777666555.78899*************99999886522.222223367*********9 PP

>> DUF5305  Family of unknown function (DUF5305)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.75   2.7e+03     171     189 ..     176     195 ..     162     215 .. 0.67
   2 !   15.5   0.2   2.3e-06    0.0084      87     148 ..     260     327 ..     249     332 .] 0.64

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.75
     DUF5305 171 lgdek.vievdsledLvdva 189
                 ++++k vie+ +++++ ++ 
  EPA06779.1 176 VDNKKfVIEIGTFAEINKFN 195
                 33444478888888776554 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 2.3e-06
     DUF5305  87 yeikkdetd..eengeitetvtvkespslae..gilliilgllaliglvvlirriiftssk..aekye 148
                 ++i++++    ++++++  +++v++++++      +++i+g++++ig++++i  + +++s+  +e  +
  EPA06779.1 260 ISITSTTDIgmQKPTTQDDSSNVNQNNNTGFqnTSVYVIIGIIIAIGFAAAIIIMKKKKSAssTELND 327
                 55555555445666777777777777777777777788888888888888888755555553344444 PP

>> Podoplanin  Podoplanin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       2.1   7.4e+03      71      87 ..      39      55 ..      15      65 .. 0.53
   2 !   16.0   0.2   2.7e-06    0.0096     100     155 ..     264     318 ..     253     321 .. 0.66

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.1
                XXXX-----GGG-XXXX CS
  Podoplanin 71 stesvtdlrledlptae 87
                 ++s  +++++ + t+ 
  EPA06779.1 39 VINSSNEIHVKHVITSS 55
                23333344444444433 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 2.7e-06
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
  Podoplanin 100 ttlnvvtshstekvgeetettvekdGLatvtLvgiivGvllaigfiggiiivvvrk 155
                 +t+++   ++t + + ++    ++ G +  t v +i+G+++aigf + iii+  +k
  EPA06779.1 264 STTDIGMQKPTTQDDSSNVNQNNNTGFQ-NTSVYVIIGIIIAIGFAAAIIIMKKKK 318
                 4445544555444444444444455555.57799***************9976555 PP

>> Glucos_trans_II  Glucosyl transferase GtrII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.15   5.5e+02     226     256 ..       4      34 ..       1      41 [. 0.73
   2 ?   13.0   0.0   1.4e-05     0.049     209     256 ..     240     321 ..     195     325 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.15
  Glucos_trans_II 226 kpkklllililliliilllalllkkkkkkkk 256
                      k + +++il+++i i +++a +   +k  +k
       EPA06779.1   4 KHIAFFMILLFIIGIPTVYAQISMGEKAEQK 34 
                      5567899999999999988877766666555 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 1.4e-05
  Glucos_trans_II 209 ellqnlkryys..................................isnygvkpkklllililliliilllalllkkkkkkkk 256
                      e+++n ++++                                   ++n g++++++++i+ ++i+i + +a+++ kkkk+ +
       EPA06779.1 240 EYINNGTHVWLnmrpdnsgdisitsttdigmqkpttqddssnvnqNNNTGFQNTSVYVIIGIIIAIGFAAAIIIMKKKKSAS 321
                      55555555555555555555555555566666666666666676778999***************************99876 PP

>> DUF4064  Protein of unknown function (DUF4064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.16   5.7e+02      11      38 ..       6      33 ..       1      58 [. 0.57
   2 ?   13.8   0.2   1.5e-05     0.053      42      88 ..     267     319 ..     244     323 .. 0.52

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.16
     DUF4064 11 IGgilgillglllllflfllssgefsqe 38
                I++ + +l+++++  ++ ++s ge++++
  EPA06779.1  6 IAFFMILLFIIGIPTVYAQISMGEKAEQ 33
                5554444444555455555555554444 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1.5e-05
     DUF4064  42 e....qalsgedasavleflstllivlgvialia..ivlgivgalllkknkkv 88 
                 +    ++++++d+s+v    +t +  + v+++i   i++g+++a+++ k+kk 
  EPA06779.1 267 DigmqKPTTQDDSSNVNQNNNTGFQNTSVYVIIGiiIAIGFAAAIIIMKKKKS 319
                 25555445555555555444444444444444330034566666666666663 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1280  (0.0713927); expected 358.6 (0.02)
Passed bias filter:                      681  (0.0379832); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2300.35
//
Query:       EPA06780.1  [L=510]
Description: hypothetical protein BG20_I0009 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (510 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 3240.53
//
Query:       EPA06781.1  [L=129]
Description: Hsp20/alpha crystallin family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.7e-13   49.9   0.2    3.4e-13   49.6   0.2    1.1  1  HSP20       Hsp20/alpha crystallin family
    1.8e-08   33.8   0.1    1.4e-07   30.9   0.1    2.4  3  ArsA_HSP20  HSP20-like domain found in ArsA
  ------ inclusion threshold ------
      0.015   15.3   0.2      0.051   13.6   0.0    1.8  2  TubC_N      TubC N-terminal docking domain


Domain annotation for each model (and alignments):
>> HSP20  Hsp20/alpha crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6   0.2   5.6e-17   3.4e-13       2      93 ..      32     125 ..      31     129 .] 0.88

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 5.6e-17
                 --SSEEEEEEEEE-TT--CCCEEEEEETTEEEEEEE--..---TT----SS---EEEEEE--STTB-T.TT-EEEE.ETTEEEEEEEBSS--.. CS
       HSP20   2 ikeeeeefevkldvpglkkeelkvkvednrvlvkgeheeeeedekglikerssrkFsrkftLPenvda.dkvkasl.kdGvLtvtvpkkepekk 93 
                 i+ e+++  v +d+pg+ k+++k+++++n +++++ +e  +e+++ +i +++ +  ++k++LP ++d+  +v+++   dGvLtvt+p k++ k+
  EPA06781.1  32 IHLENDKLIVLIDIPGFTKKDIKLSLDGNILSIQACKEISDEKNHNMICNQRPNIIDKKMKLPVEIDDgGEVSSAKyVDGVLTVTIPVKKHGKD 125
                 6678899999****************************9999999999999999************87358987666***********988743 PP

>> ArsA_HSP20  HSP20-like domain found in ArsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.23   1.4e+03      24      41 ..       8      28 ..       3      30 .. 0.71
   2 !   30.9   0.1   2.4e-11   1.4e-07       1      62 [.      36     116 ..      36     117 .. 0.89
   3 ?   -2.2   0.0      0.54   3.2e+03      18      30 ..     117     129 .]     116     129 .] 0.79

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.23
  ArsA_HSP20 24 gdeLtIkignfrRq...itLP 41
                ++e++ +ign +R+   ++LP
  EPA06781.1  8 AKEMIKEIGNKSREfyeFVLP 28
                677788899999985555566 PP

  == domain 2  score: 30.9 bits;  conditional E-value: 2.4e-11
  ArsA_HSP20   1 ddeyvlkldLPfvdkeeidlsrsgdeLtIkig..................nfrRqitLPsvla.rkevtsAkfedgvLeIr 62 
                 +d+ ++ +d+P+++k++i+ls +g+ L+I++                      +++ LP  ++ + ev+sAk+ dgvL+++
  EPA06781.1  36 NDKLIVLIDIPGFTKKDIKLSLDGNILSIQACkeisdeknhnmicnqrpnIIDKKMKLPVEIDdGGEVSSAKYVDGVLTVT 116
                 578999**************************************9666555556699*****73579************97 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.54
  ArsA_HSP20  18 idlsrsgdeLtIk 30 
                 i + ++g++++I+
  EPA06781.1 117 IPVKKHGKDISIE 129
                 5688999999985 PP

>> TubC_N  TubC N-terminal docking domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.42   2.5e+03      14      22 ..      31      39 ..      30      41 .. 0.80
   2 ?   13.6   0.0   8.6e-06     0.051      10      47 ..      50      87 ..      46      88 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.42
      TubC_N 14 kLwleggrL 22
                 + le+++L
  EPA06781.1 31 DIHLENDKL 39
                5689***99 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 8.6e-06
      TubC_N 10 algIkLwleggrLrfrApkgaltpelraklkerKaeIi 47
                +++IkL+l+g+ L ++A k+       + + + ++ Ii
  EPA06781.1 50 KKDIKLSLDGNILSIQACKEISDEKNHNMICNQRPNII 87
                79*****************9999998888888888888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 942.95
//
Query:       EPA06782.1  [L=72]
Description: hypothetical protein BG20_I0099 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.014   14.6   0.1      0.017   14.3   0.1    1.0  1  DHQ_synthase  3-dehydroquinate synthase


Domain annotation for each model (and alignments):
>> DHQ_synthase  3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   9.6e-07     0.017     103     145 ..      19      60 ..      17      69 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 9.6e-07
                   GGGGGS-HHHHHHHHHHHHHHHHHT-HHHHHHHHHHHHHHHCT CS
  DHQ_synthase 103 evLktLperelraGlaEviKyalikdeelfelleenaeallke 145
                   ++L+tLpe++++ G +E+iK+  i+ ++ ++ le+ ++al ++
    EPA06782.1  19 KFLDTLPEQSVQLG-SEMIKTLTISSKNEIANLEAIEKALKRQ 60 
                   79**********99.7*******************99988664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       845  (0.0471303); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.49
# Mc/sec: 442.45
//
Query:       EPA06783.1  [L=341]
Description: RNA 3'-phosphate cyclase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.2e-76  255.0   0.1    4.9e-76  254.8   0.1    1.0  1  RTC             RNA 3'-terminal phosphate cyclase
  ------ inclusion threshold ------
      0.062   13.5   0.1       0.19   11.9   0.1    1.8  1  B-block_TFIIIC  B-block binding subunit of TFIIIC


Domain annotation for each model (and alignments):
>> RTC  RNA 3'-terminal phosphate cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  254.8   0.1   5.4e-80   4.9e-76       2     221 ..      11     320 ..      10     321 .. 0.98

  Alignments for each domain:
  == domain 1  score: 254.8 bits;  conditional E-value: 5.4e-80
                 TTTSTHHHHHHHHHHHHH---EEEESTTTTSSS-S--HHHHHHHHHHHHHHT-EEE--STT-SEEEEE------SEEEEEEESSEBHHHHHHHHHHHHT CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
         RTC   2 gegGgqiLRtalaLsaltgkpvrIenIRanRkkPGLraqhltavrllakitnaevegaeigsteleFkPgeikageyevdigtAGsitlllqtllplll 100
                 gegGgqi+Rta++Ls++t+kp+ IenIR+nRk PGL+aqhlta+++l+ki+naevega+igst+l+F+Pg++k+ ++  d+gtAGsi+l+ q+l+p++ 
  EPA06783.1  11 GEGGGQIIRTAITLSCITKKPIMIENIRKNRKIPGLKAQHLTAIKILQKICNAEVEGAKIGSTSLKFTPGNVKSCNLIEDVGTAGSISLISQVLIPAVG 109
                 8************************************************************************************************** PP

                 TSSS-EEEEEEEBSBBTTS--HHHHHHTHHHHHHHHT.-EEEEEEEE--BTTTB-EEEEEEEE-.-S---EB........................... CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................... RF
         RTC 101 fakkpseltlkGgTnvsaapsvdylktvllpllkrfgvlelelelkkrGfypkGgGevelevepskklkpie........................... 172
                 ++k++++lt+kGgT++ ++p++dy+++vl+++++r+g ++++++l krG+ypkGgG++el+veps ++++i+                           
  EPA06783.1 110 ICKEKLNLTIKGGTDALWSPTIDYTQYVLREAYSRMG-INFSIKLIKRGYYPKGGGQIELSVEPS-NVNAISlierktknvnlicsfsnlpselikkni 206
                 *************************************.7************************96.677777777************************ PP

                 .................................................................BSS-HHHHHHHHHHHHHHT.-EEEEESS--HHHH CS
                 .................................................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
         RTC 173 .................................................................acvDehlqdqlilfmaLakgksrirvaeltlhte 206
                                                                                    vDe l+d+l+l++ La++ + +rv+++++h+e
  EPA06783.1 207 egivkqltekkfivksqineentidsgatllifsadqesiigidsifdkkterfnlelqsfmennLGVDERLADMLVLPASLANKITIFRVGNISKHLE 305
                 *****************************************************************99******************************** PP

                 HHHHHHHHHSS-EEE CS
                 xxxxxxxxxxxxxxx RF
         RTC 207 tairvieqflgvkfk 221
                 t++ v+++++g+k+ 
  EPA06783.1 306 TNLFVTSKITGCKYG 320
                 ***********9975 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   2.1e-05      0.19      32      67 ..     203     238 ..     199     242 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.1e-05
  B-block_TFIIIC  32 prslfyrlksLekkgLIvkqsiidsatkksistsll 67 
                     ++++ +++k L++k++Ivk +i++ +t+ s  t l+
      EPA06783.1 203 KKNIEGIVKQLTEKKFIVKSQINEENTIDSGATLLI 238
                     578999****************98888777666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2123.91
//
Query:       EPA06784.1  [L=73]
Description: hypothetical protein BG20_I0085 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0063   16.3   0.0       0.01   15.6   0.0    1.5  1  HTH_23    Homeodomain-like domain
  ------ inclusion threshold ------
      0.046   13.5   0.0        0.2   11.5   0.0    1.8  2  HTH_IclR  IclR helix-turn-helix domain
      0.055   13.7   0.1      0.092   13.0   0.1    1.3  1  DUF5388   Family of unknown function (DUF5388)
      0.061   13.4   0.1       0.07   13.2   0.1    1.0  1  CC190     Coiled-coil domain-containing protein 190
      0.084   12.5   0.1       0.14   11.8   0.1    1.5  1  GntR      Bacterial regulatory proteins, gntR family


Domain annotation for each model (and alignments):
>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   2.8e-06      0.01      18      41 ..      27      50 ..      11      57 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.8e-06
      HTH_23 18 lsvreIAreLgvsrrTvyrwlkry 41
                + ++++ +eLgv+r Tv+r+ +  
  EPA06784.1 27 DIYTKVVDELGVPRPTVRRVARDL 50
                5688999************97765 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   5.5e-05       0.2      23      42 ..      31      50 ..      29      53 .. 0.86
   2 ?   -0.7   0.0      0.37   1.3e+03      27      35 ..      62      70 ..      61      71 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.5e-05
                HHHHHHTS-HHHHHHHHHHH CS
    HTH_IclR 23 elArrtglpkStvhRlLqtL 42
                 + +++g+p++tv+R  + L
  EPA06784.1 31 KVVDELGVPRPTVRRVARDL 50
                57899**********98877 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.37
                HHTS-HHHH CS
    HTH_IclR 27 rtglpkStv 35
                ++++pk+++
  EPA06784.1 62 QSDMPKTST 70
                789***997 PP

>> DUF5388  Family of unknown function (DUF5388)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   2.6e-05     0.092      32      63 ..       4      35 ..       2      37 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.6e-05
     DUF5388 32 ksqkeavkklveslidsLsesdkkrfkkqlei 63
                 +q++++k++++s++d+  ++++ +++k+++ 
  EPA06784.1  4 TNQSTIIKEAINSYLDKGVTDKQDIYTKVVDE 35
                69*************************99985 PP

>> CC190  Coiled-coil domain-containing protein 190
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1     2e-05      0.07      51     118 ..       2      68 ..       1      72 [. 0.77

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2e-05
       CC190  51 qrLqqadiiKKklsSylgngiqkrpedvltlspq.egqkhrvaeankvralatnltqeikktksqvppl 118
                 +r  q+ iiK  + Syl++g+  + +  + +  + +  + +v      r l+t+l+q+i+  +s +p+ 
  EPA06784.1   2 NRTNQSTIIKEAINSYLDKGVTDKQDIYTKVVDElGVPRPTVRRV--ARDLRTELLQKIQILQSDMPKT 68 
                 6889***************99888774444444404456666665..899**********999999986 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   3.9e-05      0.14      29      51 ..      31      53 ..       9      59 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.9e-05
                HHHHHHTS-HHHHHHHHHHHHHT CS
        GntR 29 eLaaefgVsrttvReALrrLeae 51
                ++++e+gV r+tvR++ r L +e
  EPA06784.1 31 KVVDELGVPRPTVRRVARDLRTE 53
                5789***************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 540.40
//
Query:       EPA06785.1  [L=41]
Description: hypothetical protein BG20_I0042 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.033   13.4   0.7      0.033   13.4   0.7    1.0  1  LGT       Prolipoprotein diacylglyceryl transferase


Domain annotation for each model (and alignments):
>> LGT  Prolipoprotein diacylglyceryl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.7   1.8e-06     0.033      78     101 ..       5      28 ..       1      37 [. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.8e-06
                 xxxxxxxxxxxxxxxxxxxxxxxx RF
         LGT  78 kiwegGlaihGgligvllalllya 101
                 ++ e Gla +G ++gv++al++++
  EPA06785.1   5 QMAEAGLAAFGSAVGVAIALAVVC 28 
                 67899****************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.28s 00:00:00.64 Elapsed: 00:00:00.44
# Mc/sec: 279.99
//
Query:       EPA06786.1  [L=85]
Description: hypothetical protein BG20_I0048 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      0.002   18.5   7.8     0.0038   17.6   7.8    1.6  1  DnaJ_CXXCXGXG  DnaJ central domain
  ------ inclusion threshold ------
      0.039   13.9   6.4       0.26   11.3   1.5    3.0  3  Anti-TRAP      Tryptophan RNA-binding attenuator protein inhi
        0.4   10.9   9.2       0.76   10.0   4.1    2.9  2  DUF5351        Family of unknown function (DUF5351)
        1.1    9.5  11.1        3.7    7.9   7.3    2.7  2  zf-nanos       Nanos RNA binding domain


Domain annotation for each model (and alignments):
>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   7.8   8.4e-07    0.0038       1      49 [.       6      57 ..       6      69 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 8.4e-07
  DnaJ_CXXCXGXG  1 CkkCkGsgakkgkkktCktCkGsGvvree.qkt....lgpfvqqsqstCpeCeG 49
                   C+ CkG g+   ++++C  C+G+G+ ++  q      + +++   ++ Cp C+ 
     EPA06786.1  6 CDFCKGVGS--ISSNSCVYCNGTGEWNQAaQAYvknhICQCIVLDRKFCPVCNK 57
                   9*******7..56789********643331322123344444455778888875 PP

>> Anti-TRAP  Tryptophan RNA-binding attenuator protein inhibitory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.5   5.7e-05      0.26      10      40 ..       3      27 ..       2      35 .. 0.87
   2 ?    7.3   0.5     0.001       4.5      12      25 ..      19      32 ..      17      44 .. 0.81
   3 ?    2.7   0.1     0.027   1.2e+02      13      26 ..      52      66 ..      47      84 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.7e-05
                EEE-TTTTTTSEETTE......E-TTTTTSS CS
   Anti-TRAP 10 EtkCdaCngsGkiepeeprasleCPkCsGkg 40
                E  Cd C+g G i ++       C  C+G g
  EPA06786.1  3 EDVCDFCKGVGSISSN------SCVYCNGTG 27
                778************9......999999987 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.001
                E-TTTTTTSEETTE CS
   Anti-TRAP 12 kCdaCngsGkiepe 25
                 C  Cng+G+ + +
  EPA06786.1 19 SCVYCNGTGEWNQA 32
                7********98776 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.027
                -TTTTTTSEETTE.. CS
   Anti-TRAP 13 CdaCngsGkiepe.e 26
                C+ Cn++ + ++  +
  EPA06786.1 52 CPVCNKACHHDTSlN 66
                999999887766543 PP

>> DUF5351  Family of unknown function (DUF5351)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   4.1   0.00017      0.76       1      28 [.       6      28 ..       6      29 .. 0.91
   2 ?   -1.3   0.2       0.6   2.7e+03      20      24 ..      52      56 ..      51      58 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00017
     DUF5351  1 CpYCeGkGYfqLlLGGSETCesCeGtgk 28
                C++C+G G +      S  C +C+Gtg+
  EPA06786.1  6 CDFCKGVGSIS-----SNSCVYCNGTGE 28
                99****99996.....9*********95 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.6
     DUF5351 20 CesCe 24
                C+ C+
  EPA06786.1 52 CPVCN 56
                66664 PP

>> zf-nanos  Nanos RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1     0.041   1.8e+02       1       8 [.       6      13 ..       2      19 .. 0.79
   2 ?    7.9   7.3   0.00082       3.7       1      42 [.      20      58 ..      20      68 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.041
    zf-nanos  1 CvFCknng 8 
                C FCk+ g
  EPA06786.1  6 CDFCKGVG 13
                88888876 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00082
    zf-nanos  1 CvFCknngeseevyssHslkdedgrvtCPvLrkyvCpiCgat 42
                Cv+C ++ge ++  +  +        +C vL +  Cp+C++ 
  EPA06786.1 20 CVYCNGTGEWNQAAQAYVKN---HICQCIVLDRKFCPVCNKA 58
                ********777776665433...477899**********764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       767  (0.0427799); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 543.70
//
Query:       EPA06787.1  [L=150]
Description: hypothetical protein BG20_I0090 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.14   12.7   0.1       0.42   11.2   0.1    1.8  1  LEA_2     Late embryogenesis abundant protein


Domain annotation for each model (and alignments):
>> LEA_2  Late embryogenesis abundant protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   2.3e-05      0.42       2      50 ..      53     100 ..      52     135 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.3e-05
                 EEEEESSSS-EEEEEEEEEEEESSSEEEEEEECE-EEESSSCEEEEEEE CS
       LEA_2   2 lrvrNPNsfgvrydgleldlsyngqrlasgtspqgfsqpargtttlevp 50 
                 ++  NP    ++  + e+ + +n++ ++ ++  ++f +pa gttt++++
  EPA06787.1  53 VKFSNPSLLVLTAGKTEFFVTANNEMIG-KGDLDSFVLPALGTTTVNGT 100
                 5667999999999999999*********.*****************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1080.08
//
Query:       EPA06788.1  [L=68]
Description: hypothetical protein BG20_I0010 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 512.13
//
Query:       EPA06789.1  [L=326]
Description: SpoVT/AbrB-like protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.1e-09   36.0   4.1    3.9e-06   27.2   1.7    2.8  2  PhoU            PhoU domain
     0.0018   18.2   0.0     0.0041   17.0   0.0    1.7  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an


Domain annotation for each model (and alignments):
>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   1.7   4.3e-10   3.9e-06       1      88 [.     138     228 ..     138     229 .. 0.87
   2 !    8.2   0.0   0.00037       3.3      13      85 ..     254     316 ..     247     320 .. 0.65

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 4.3e-10
                 HHHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SH..HHHHH..HHHHHHHHHHHHHHHHHHHHHHH CS
        PhoU   1 lrrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplae..dlrel..lsllriardlERigDhavniaer 88 
                 l+rm++i++ m dd+   l + d+  ++ + +rd e++r ++++ r +   l  ++ la+  +l+ +  l+++ +a+ lE  gD +v++a+ 
  EPA06789.1 138 LKRMSSIALGMYDDVSNGLISIDKSNLQTLSKRDVEVNRQYFLLVRLIRSTL-VDKRLANvfNLENIdiLDYRVAANLLENAGDTIVELANF 228
                 78******************************************99865555.356666677566644499*****************9975 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00037
                 HHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHHHHHHHH CS
        PhoU  13 ddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERigDhavni 85 
                 ++++ a+ ++d+ la e i    ++ + ++e+  +l + ++++++      + ++ll++++  ERi+   +++
  EPA06789.1 254 EKSINAFTKPDRRLAIEAI----SLHKKYQENLSKLRNTIGNKKQ------IPIDLLDLVYMFERIAKSWADV 316
                 5789999999999995554....3334444444443444433332......2367999********9876665 PP

>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   4.6e-07    0.0041       1      42 [.       9      50 ..       9      54 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.6e-07
                    EEETTEEEEEE-CCCHHHCCEECTCEEEEEECTTCCCCCCCH CS
  MazE_antitoxin  1 fkvGnsgavriPkevrfelgireGdevelevdgdkiilrplk 42
                    +++G+s  v++Pke++ ++++++ + vel +  d i ++  k
      EPA06789.1  9 QRIGSSILVSLPKEWVVANNLDKSSQVELDTGQDTISISANK 50
                    589**************************9999966665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       745  (0.0415528); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 1957.93
//
Query:       EPA06790.1  [L=264]
Description: precorrin-3B C(17)-methyltransferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.6e-39  134.9   0.0    4.3e-39  134.7   0.0    1.1  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.7   0.0   2.4e-43   4.3e-39       1     212 [.       4     215 ..       4     216 .. 0.85

  Alignments for each domain:
  == domain 1  score: 134.7 bits;  conditional E-value: 2.4e-43
  TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealragkdVvllvsGDPlvygtgs 97 
                   kly+VGvGpG+ +++T rA ++++++d ++g++  +  +++dl++ ++++++ m++e         e a + ++++++gk V l++sGDP +yg+++
    EPA06790.1   4 KLYIVGVGPGHHDHMTFRAKEVIEESDTIVGYE-TYVNLVQDLIEGKTVHRYAMTQE--------VERAHQCIDLAKSGKIVSLVSSGDPGIYGMAG 91 
                   79*******************************.9999**99996532333333333........3444555********9**************** PP

  TP_methylase  98 elvealrar....eagieveviPGvsslqaaaarlgiplteggevlsvl..lpglakeeereleallangdtlvllkapr.k.....laelaelLke 182
                    ++e l+a     + g++ve++PGvs+l+++a+ +g pl  ++ v+s +  l +++    +++ +++a+gd+++++++p  k     l++++++L++
    EPA06790.1  92 LIYETLAATnwnpKDGLQVEIVPGVSALNSCASIIGSPLMTDFAVVSMSdlLVPWE--IITQRVEAAAQGDFVIVIYNPAsKkrihqLEDTRKILLK 186
                   ****88874222257888*******************************9988888..444445556668******99997468999********99 PP

  TP_methylase 183 alyddttpvavveragtedervvrgtleel 212
                   + +++ttpva+++ a +e +++v + le l
    EPA06790.1 187 Y-RKPTTPVAIIKGAFRESQTIVMTDLENL 215
                   9.77799*******************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1682.02
//
Query:       EPA06791.1  [L=160]
Description: hypothetical protein BG20_I0065 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       862  (0.0480785); expected 358.6 (0.02)
Passed bias filter:                      648  (0.0361426); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1006.01
//
Query:       EPA06792.1  [L=210]
Description: proteasome endopeptidase complex, beta subunit [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.4e-52  176.7   0.1    3.9e-52  176.5   0.1    1.0  1  Proteasome  Proteasome subunit


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.5   0.1   2.2e-56   3.9e-52       3     190 .]      11     191 ..       9     191 .. 0.94

  Alignments for each domain:
  == domain 1  score: 176.5 bits;  conditional E-value: 2.2e-56
                 HS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGTCHHHHHHHHHHHHHHHHHHCTT CS
  Proteasome   3 kGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrpipverlvarvaaklqaytqrsgr 101
                 +Gtt+vGik+kdgvvl+ad+ra+ag  +++++   Ki kid+h g+++aG +aDa+++v+++r++ +l+r++ + pi+++    ++a++ +    +++ 
  EPA06792.1  11 HGTTTVGIKAKDGVVLCADMRASAGYFIANNN-TMKIQKIDEHAGLTLAGGVADAQNIVDILRYHSNLHRVEKQGPISIH----SLARLCSLIFHQNRG 104
                 9***************************7777.5**********************************************....666666666666667 PP

                 TTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHHSTTBSHHHHHHHHHHHHHHHHHHBTTSCSSEEEEEE CS
  Proteasome 102 rpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekeykedltleeavelavkalkealerdklsgknievavi 190
                  pf++ +l++g+d +g p L++id+ Gs+ +  ++v++Gsgs +a+++le+ey++dlt+eea+++a++a+k+a+ r   +g++i++av+
  EPA06792.1 105 YPFMADILVGGYDANG-PALFNIDMFGSVEKK-SYVTTGSGSPVAYGLLEEEYRPDLTVEEAKKIALRAVKAAIVRNIGTGDGINIAVM 191
                 8************888.**************9.6****************************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1670.82
//
Query:       EPA06793.1  [L=159]
Description: hypothetical protein BG20_I0089 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       978  (0.0545485); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1052.07
//
Query:       EPA06794.1  [L=486]
Description: hypothetical protein BG20_I0102 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.077   12.6   0.6         15    5.2   0.1    2.6  2  Lipoprotein_15  Secreted repeat of unknown function


Domain annotation for each model (and alignments):
>> Lipoprotein_15  Secreted repeat of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1    0.0011        20       7      20 ..      95     108 ..      91     109 .. 0.89
   2 ?    5.2   0.1   0.00082        15      12      30 ..     356     374 ..     353     376 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0011
  Lipoprotein_15   7 dGtkqvaykGmPLY 20 
                     +G+  ++ +G+++Y
      EPA06794.1  95 KGQSTWTIDGKTVY 108
                     899*********** PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.00082
  Lipoprotein_15  12 vaykGmPLYtFakDkkpgd 30 
                     +  +G+++Y+   D+ p++
      EPA06794.1 356 WGPDGKTIYYIITDTTPSG 374
                     889************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (486 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       784  (0.043728); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 3391.69
//
Query:       EPA06795.1  [L=210]
Description: V-type ATPase, D subunit [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.6e-48  164.5   7.6    2.9e-48  164.3   7.6    1.0  1  ATP-synt_D   ATP synthase subunit D
  ------ inclusion threshold ------
      0.053   13.3   0.0      0.081   12.8   0.0    1.3  1  CLU          Clustered mitochondria
      0.097   13.0   6.2        1.8    8.8   0.9    2.2  2  RNA_binding  RNA binding


Domain annotation for each model (and alignments):
>> ATP-synt_D  ATP synthase subunit D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.3   7.6   4.9e-52   2.9e-48       1     196 []      13     204 ..      13     204 .. 0.97

  Alignments for each domain:
  == domain 1  score: 164.3 bits;  conditional E-value: 4.9e-52
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSTSTTSTSHHHHHHHSSS.SS-..TSS-SEEEEEEBTTSEEEEEE CS
  ATP-synt_D   1 eLirlkkrlklaqrghslLkkKrdaLilefreilkelkelreeleeelkeayfslaeafaaggeediesavlesvklakvvkvelktenvaGVkvpvfe 99 
                 eL++ kk  ++a+ ++++L++Kr++L++ + e+++e+ ++r  + e l+++y+s+ ea++a g ++++s+++++++   v++v+++t+ v+ Vk+p+++
  EPA06795.1  13 ELLKYKKSSQVAKMVQKILDDKRKVLLKNIEEMIEEASKARGGIWEPLQDIYKSVNEAYLALGTSTVDSVAESTPP---VMEVDVHTRRVVDVKIPALT 108
                 799*****************************************************************99997776...7******************9 PP

                 E-..S.SSTSSSSSSSSTCHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
  ATP-synt_D 100 leeeksdstelygllrtgaqldeavealrellellvelasletslelLdeeikktnrRvNaLekvvIPrleetikyIkseLdEqereeffrlkkvkk 196
                 ++e k++++ +yg+++t++++d+a+++++ell+++ ++a++e+s+ +L+++++kt++  NaLe+v+IP+++++i++I   L+E+ereef+ lkkvk+
  EPA06795.1 109 VRE-KDTKSMPYGFADTNSSIDRAAKQIKELLPKICKAAEYENSIFSLAKALEKTQKLLNALENVIIPQYQQKIRFILATLEEREREEFAKLKKVKA 204
                 977.77889**************************************************************************************95 PP

>> CLU  Clustered mitochondria
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.3e-05     0.081     114     194 ..      86     169 ..      73     187 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.3e-05
         CLU 114 tlltaivDYrGkRliaqsllPgilk.kekeitivYGssdggktvhs.deefhellkkvakalnlkehk..vkdeegkevklylsa 194
                 t+  + vD + +R++    +P +   +++++++ YG+ d+++++    ++++ell k++ka + ++      ++ +k++kl  + 
  EPA06795.1  86 TPPVMEVDVHTRRVV-DVKIPALTVrEKDTKSMPYGFADTNSSIDRaAKQIKELLPKICKAAEYENSIfsLAKALEKTQKLLNAL 169
                 555666788877875.556665555155556*************9999************9999888744222333555665555 PP

>> RNA_binding  RNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.4    0.0012       7.1      41      88 ..       3      50 ..       2      52 .. 0.72
   2 ?    8.8   0.9   0.00031       1.8      16      93 ..     130     198 ..     121     209 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0012
                 CC-EEEEEEEEESSHHHHHHHHHHHHHHCCCCHHHHHHCCHCCB-TTS CS
  RNA_binding 41 ygnpitileaelekkkakkvlkkllellreeeikeLlkeleervdekg 88
                 +g+++   ++el k k+   + k+++++ ++++k+Llk++ee+++e +
   EPA06795.1  3 FGQNVAATKIELLKYKKSSQVAKMVQKILDDKRKVLLKNIEEMIEEAS 50
                 6677777788888878855555555666666679********999876 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00031
                  HHHHHHHTTSTTS.E---EEEEEE-CCC-EEEEEEEEESSHHH.HHHHHHHHHHHCCCCHHHHHHCCHCCB-TTSEEEEE CS
  RNA_binding  16 kVlealsnllpee.eveieeeeaeGhygnpitileaelekkka.kkvlkkllellreeeikeLlkeleervdekgklylr 93 
                  + ++ +++llp++ +           y+n+i  l   lek ++ +++l++++    +++i+ +l +leer   + + + +
   EPA06795.1 130 RAAKQIKELLPKIcK--------AAEYENSIFSLAKALEKTQKlLNALENVIIPQYQQKIRFILATLEER---EREEFAK 198
                  556666777776642........45688999999999999888888998888888888888888888884...3444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1859  (0.103687); expected 358.6 (0.02)
Passed bias filter:                      699  (0.0389871); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1452.24
//
Query:       EPA06796.1  [L=246]
Description: cob(II)yrinic acid a,c-diamide reductase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.1e-24   85.5   0.0    7.2e-24   84.7   0.0    1.4  1  Nitroreductase  Nitroreductase family
  ------ inclusion threshold ------
      0.015   14.9   1.0       0.27   10.7   0.1    2.6  3  TM1586_NiRdase  Putative TM nitroreductase


Domain annotation for each model (and alignments):
>> Nitroreductase  Nitroreductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.7   0.0   8.1e-28   7.2e-24       1     170 []      27     194 ..      27     194 .. 0.88

  Alignments for each domain:
  == domain 1  score: 84.7 bits;  conditional E-value: 8.1e-28
                     HHH--B--.-B-S----HHHHHHHHHHHHTS--GGG---EEEEEE.-CCCHHHHHHHHHHHHHHHHTT-SS-GGGGGGHHHHHHHHHHHHSSEEE CS
  Nitroreductase   1 irkRrSiR.kFddepvpkeelekileaarraPsagnlqpwrfvvvqdkelryklaeaalelllkaeaqaelaqryrkeelklkaqkalagapvli 94 
                     i +Rr +R +F+++ ++++++++il+aa++aPs g +qpw+f+++++  +++k+++++ e+  +  +  e+  r +   +   + + + ++pv +
      EPA06796.1  27 IYSRRDVRsHFTSRIIKDDVIARILNAAHHAPSVGFSQPWNFILIKNITTKKKIKDSFEEEKNRSSKLVEEPKRSK---YLSFKLEGILESPVNL 118
                     569*******************************************************999988877777777765...88888999999***** PP

                     EE---TTS-..--HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGGGGHHHHHHHHT-S..SEEEEEEEEE- CS
  Nitroreductase  95 vivatldks..erkaaerayryalldagaaaqnllLaAtalGlgscpiggfdeaaeevrkllglpdeeeivvliavGy 170
                     +++++++k        ++  +  l ++++a+qnl+LaA+ +G+g  +++ + ++   ++++l+lp++  +++ +++Gy
      EPA06796.1 119 CVTYDPSKFgpFVIGRSSIPEAGLYSVCCAIQNLWLAARTEGVGLGWVSILSNDI--LKEVLELPEHVVPIAYLCLGY 194
                     **66666652145667777888899******************************..********6666668899998 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0     0.028   2.6e+02       2      27 ..      23      49 ..      22      51 .. 0.82
   2 ?   10.7   0.1   3.1e-05      0.27     158     198 ..      45      83 ..      39      89 .. 0.80
   3 ?    1.4   0.0     0.022     2e+02      89     135 ..     150     197 ..     142     238 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.028
                    HHHHHHH--B---.B--S---HHHHHH CS
  TM1586_NiRdase  2 lyeaiekRhsvRk.Ykdealeeellee 27
                     y+ai  R+ vR+ ++++ ++++++ +
      EPA06796.1 23 FYKAIYSRRDVRShFTSRIIKDDVIAR 49
                    599*********758888888888766 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 3.1e-05
                     HHHHHHHHHHHTS--GGG----EEE.E-SSEE.....EEE- CS
  TM1586_NiRdase 158 ewfkeileaarlAPsAlNqqpwrfelkdddeikikasvlgk 198
                     + + +il+aa  APs   +qpw f l ++  i++k+++  +
      EPA06796.1  45 DVIARILNAAHHAPSVGFSQPWNFILIKN--ITTKKKIKDS 83 
                     56889********************8775..6666555544 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.022
                     HHHHHHHHHTT-EEEEES--SST............T-S-EEEEE-BS- CS
  TM1586_NiRdase  89 eqlvLkltalGlgtcWvggtykk.kkakvelkkgeklvivIalGyakt 135
                     ++l L + ++G+g  Wv++  +   k+ +el++    ++ + lGy+++
      EPA06796.1 150 QNLWLAARTEGVGLGWVSILSNDiLKEVLELPEHVVPIAYLCLGYVDE 197
                     78999*************988886555588888888888899999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       830  (0.0462937); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1629.86
//
Query:       EPA06797.1  [L=419]
Description: hypothetical protein BG20_I0008 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 2643.11
//
Query:       EPA06798.1  [L=273]
Description: ABC 3 transport family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.3e-65  218.7  37.5      1e-64  218.5  37.5    1.0  1  ABC-3     ABC 3 transport family
    8.8e-07   28.2  39.3    3.8e-06   26.1  39.2    1.8  1  FecCD     FecCD transport family


Domain annotation for each model (and alignments):
>> ABC-3  ABC 3 transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.5  37.5   1.2e-68     1e-64       2     255 ..       8     261 ..       7     264 .. 0.98

  Alignments for each domain:
  == domain 1  score: 218.5 bits;  conditional E-value: 1.2e-68
       ABC-3   2 yeflqrallasilvslacallgsfvvlrrqsllgdalsHaalpGvalayllgvnlllgailvgliaavalellkrktklkedtaigivlsvflalglvl 100
                 + f+ ra++ +i++++ c+++g f+vlrr sl+gda++H++++G+al+++ g+ +l+ a  v+++ a++++ +k +  ++ d++i+++ls+++a+glv+
  EPA06798.1   8 FSFMHRAIISGIAIAILCSIIGLFLVLRRYSLFGDAIAHSSFGGIALGLMAGIYPLWTAYGVSIVSALIMTRIKDRFNISGDASIAVLLSSGIAVGLVI 106
                 689************************************************************************************************ PP

       ABC-3 101 vslikkskvdldsyLfGniltisqedliliaiieavvllllllfwkelllitfdeelAkveglsvkllkllllalialavvvalqavGviLvialliiP 199
                 + l+ +   d++s+LfG+il +s +d ili+ ++ ++l+++ll++++ll  tf+ee+Akv+g++v+ +++l++ + +++vv+++q+vGv+L++al++iP
  EPA06798.1 107 IGLSGGFTLDIFSFLFGSILLVSVNDTILILSLTGIILIVILLLYRQLLYSTFNEEQAKVSGVPVEKINYLIVFMAGITVVTSIQLVGVLLISALFVIP 205
                 *************************************************************************************************** PP

       ABC-3 200 aatArrltrslesllivAillglvsvvaGlllSyyldlatGavivlvatllfllal 255
                  +tA++++r +++ +i+++ ++++svv+G+l+Sy++d+ + ++ivl a+++f + +
  EPA06798.1 206 NVTAIMYGRGFKQTAILSMSFSIFSVVSGILISYVFDITPAGTIVLFAIAIFACTM 261
                 *************************************99999*******9997766 PP

>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1  39.2   4.3e-10   3.8e-06      95     305 ..      58     257 ..      15     264 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 4.3e-10
       FecCD  95 lgslslfalplaaflgallalllvlllarkrkgasplkliLaGiavsallsaltsllllllneealesilfwllGslsgaswskvllllvlllllllll 193
                 +g  +l++   +++++al+++ +   +   ++ as + l+ +Giav++++ +l+  ++l        +i   l+Gs+  +s ++++l+l l+ ++l+++
  EPA06798.1  58 AGIYPLWTAYGVSIVSALIMTRIKDRFN-ISGDASIAVLLSSGIAVGLVIIGLSGGFTL--------DIFSFLFGSILLVSVNDTILILSLTGIILIVI 147
                 3455555555555555555555555555.7888888888889************99994........499***************************** PP

       FecCD 194 lllarkldllalgdetAkslGvnvervrllllllvalltavavalvGpigFvGL.ivPhiarllvgadhrkllplsallGallllladllarlllspte 291
                 lll+r+l   ++++e+Ak  Gv+ve++++l+++++ + + +++ lvG++   +L ++P++  ++ g+ ++++ +ls+ ++++ ++   l++ ++  +++
  EPA06798.1 148 LLLYRQLLYSTFNEEQAKVSGVPVEKINYLIVFMAGITVVTSIQLVGVLLISALfVIPNVTAIMYGRGFKQTAILSMSFSIFSVVSGILISYVF--DIT 244
                 *************************************************99998578**********************988887777776665..455 PP

       FecCD 292 lpvgivtaliGapf 305
                  p+g ++ + +a+f
  EPA06798.1 245 -PAGTIVLFAIAIF 257
                 .9999988888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       972  (0.0542138); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.66u 0.34s 00:00:01.00 Elapsed: 00:00:00.55
# Mc/sec: 1500.32
//
Query:       EPA06799.1  [L=508]
Description: ammonium transporter [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   3.5e-108  361.9  33.8   9.7e-108  360.4  33.8    1.7  1  Ammonium_transp  Ammonium Transporter Family
  ------ inclusion threshold ------
      0.032   14.6   1.0        0.1   13.0   1.0    1.9  1  IncF             Inclusion membrane protein F


Domain annotation for each model (and alignments):
>> Ammonium_transp  Ammonium Transporter Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  360.4  33.8  1.1e-111  9.7e-108       1     399 []      62     505 ..      62     505 .. 0.93

  Alignments for each domain:
  == domain 1  score: 360.4 bits;  conditional E-value: 1.1e-111
                      HHHHHHHHHHHHHHHHHHHHHHHHSSGGGHHHHHHHHHHHHHHHHHHHHHTHHHHHHSSCB.SSSSSCE-........................ CS
  Ammonium_transp   1 aflllsaalvifmqagfalleaglvrsknvlnilvknlldlavvvllyvlfGyslafgksk.gvsgfign........................ 69 
                      a++l ++ lv+fm +g++++++gl rsknv+n+l + l+ ++++++++vl+Gyslafg    + + ++g+                        
       EPA06799.1  62 AWMLTATSLVLFMSPGVGFFYGGLARSKNVVNVLGMTLIVMGLMSVQWVLWGYSLAFGPIDsDANMYMGSlqyvgfndvshfaplgepgpcadt 155
                      7*********************************************************987799999999999999999999999998888777 PP

                      ............TTTTSCCGCCTTCCHHHHHHHHHHHHHHHHHHHHHHCTTTB-HHHHHHHHHHHHHHTHHHHHHHHHS.SSHHHHTT--.... CS
  Ammonium_transp  70 ............lglsaagvqdetlldglfflfqlafaataitivsgavaerikfsayllfsallgtlvyppvahwvwgeggwlaklgvl.... 147
                                   ++  +g+++ t++++lf++fq++fa+++  ++ g++ +rikfsa+++f++l++t+vy pvahwvwg gg +    +     
       EPA06799.1 156 wsaayqmnamveGDVCGQGWPN-TVPHQLFAMFQATFAIITPILIIGGLIDRIKFSALIIFILLWATFVYDPVAHWVWG-GGYIGGGAIDlnpd 247
                      7777776666444444444444.566666**************************************************.88888777768999 PP

                      .......-SSSTTTTHHHHHHHHHHHHHHHS-STTTTGTTTSS--GSBHHHHHHHHHHHHHHHHHHHHGGGSSSSHHHHH.HHHHHHHHHHHHH CS
  Ammonium_transp 148 ......iDfAgstvVHlvggvagLaaalvlgkregrfegkeeaikghnlpfavlGtllLwfgWfgFNaGsaltankrararaavtTllAaaaga 235
                             DfAg+tvVH+++g+++La+al+lg+r g +   +  +++hn+p++vlG+ +LwfgWfgFNaGs   ++++  + a  +T++A+ ++a
       EPA06799.1 248 lspsfaLDFAGGTVVHITSGFSALAGALILGRRLGYG---KVPMEPHNIPMVVLGAGILWFGWFGFNAGSEVMVDGITVS-AWTVTNTATGMAA 337
                      9****99****************************99...9***************************************.************* PP

                      HHHHHHHHHHCSS-BHHHHHHHHHHHHHHHTTTTTTS-HHHHHHHHHHHHHHHHHHHHHHHHHHTC-CTTHHHHHHHHHHHHHHHHHHHHTSHH CS
  Ammonium_transp 236 ltallisrlkegkinvlglanGilAGlVAiTaacavvepwgAliiGlvAgvlsvlgvkklkeklkidDsldvvavHgvgGiwGllavgifaaek 329
                      +t++l+s+ ++gk++++g+a+G++AGlVAiT+a ++v p++++iiG+ Ag ++++ v+ +k+  k dD+ldv++vHg+gG+ G++++g +a + 
       EPA06799.1 338 ITWVLMSWAHTGKPSIVGAASGAVAGLVAITPASGWVGPMASIIIGIAAGTICYACVS-FKNARKWDDALDVWGVHGMGGLTGAILTGTLASPH 430
                      *********************************************************8.**********************************9 PP

                      HC.SSHSSTTGGGT-C..HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT..SB--HHHHHHSHHHHHHSSSSB CS
  Ammonium_transp 330 vv.askisggllsgeg..kqlvvqligilvilayafvvtlilllllklllg..LrvseeeeevglDvaehgetay 399
                         + +  g +++     +q  + +ig+++ ++yaf+vt+++l++++++    +rv+++eee+glD+a+hge ay
       EPA06799.1 431 IWdTGDGIGAWTGTPEgmEQQAISIIGAAISVGYAFGVTIVILKIMDAVWPggIRVTPKEEEIGLDLAQHGERAY 505
                      8788888888887655579999999**********************986558*******************998 PP

>> IncF  Inclusion membrane protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.0   1.1e-05       0.1      51      93 ..     358     400 ..     320     405 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.1e-05
        IncF  51 alcvlslvalcvgatpvgplavlvattlasflcaacvlfiaak 93 
                 + +v  lva+   +  vgp+a ++    a  +c acv f  a+
  EPA06799.1 358 SGAVAGLVAITPASGWVGPMASIIIGIAAGTICYACVSFKNAR 400
                 4568899********************************8875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (508 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.68u 0.32s 00:00:01.00 Elapsed: 00:00:00.50
# Mc/sec: 3035.37
//
Query:       EPA06800.1  [L=76]
Description: hypothetical protein BG20_I0013 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 453.36
//
Query:       EPA06801.1  [L=309]
Description: aspartate carbamoyltransferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.2e-41  139.3   0.0    1.4e-40  138.7   0.0    1.3  1  OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl
    4.2e-30  104.9   0.0      6e-30  104.4   0.0    1.2  1  OTCace    Aspartate/ornithine carbamoyltransferase, Asp/Orn b


Domain annotation for each model (and alignments):
>> OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.7   0.0   1.6e-44   1.4e-40       1     147 [.       7     147 ..       7     148 .. 0.93

  Alignments for each domain:
  == domain 1  score: 138.7 bits;  conditional E-value: 1.6e-44
                 S-BSSGGGS-HHHHHHHHHHHHHHHHHHHTTT-STTTTT-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEESTTTSCTTTGGSTTSSCHHHHHHHHHH CS
    OTCace_N   1 rhllsledlskeeieelldlaaelkekvkkekkekllkgktlallFeepStRTrvSfevAakrlGgkvlslseaediqlssvskgrkEsleDtarvlsr 99 
                 ++++s++d++k+++e+++   +++ +     ++++++kg tl+ lF+epStRTr+Sf++A++  Gg+ l +s   di +ss++kg  Esl+Dt+r++s+
  EPA06801.1   7 KDIISIKDFNKAQLEQIFASTDKIMKLG-PIDRREICKGNTLGYLFYEPSTRTRLSFDAAMASVGGNSLGIS---DISSSSTKKG--ESLADTVRIMSN 99 
                 689*****************99998654.58999*************************************9...5788889999..************ PP

                 HTSEEEEEES..SHHHHHHHHHHHSSEEEEEEETSSB-HHHHHHHHHHHH CS
    OTCace_N 100 yvdaiviRhp..gaeeleelakyasvpviNagdgdgeHPtQaLaDlltir 147
                 y+d++v+Rhp  g+   +  a+ +s pviNag+g++eHPtQa+ Dl+tir
  EPA06801.1 100 YSDVLVLRHPldGS--SRFAAEISSKPVINAGSGTEEHPTQAIQDLFTIR 147
                 **********8766..56668899*************************8 PP

>> OTCace  Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.4   0.0   6.7e-34     6e-30       1     155 [.     154     301 ..     154     303 .. 0.93

  Alignments for each domain:
  == domain 1  score: 104.4 bits;  conditional E-value: 6.7e-34
                 CC.EEEEESS.TTSHHHHHHHHHHHHCT-EEEEES-TTSSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEEEE--SSETTCCGGHH...HHHHH CS
      OTCace   1 kglkiafvGd.kknnvanslikllarlgmdvvlvaPkglepdkevleeakknakksggsititedleeavkgaDvvytdvwvsmgeekere...erlkk 95 
                 +glki ++Gd k+++++ sl+++l  +++dv+l++P++l+   + + e+kk       s+t ++++ee +++ Dv+y ++++     ker+   e++ k
  EPA06801.1 154 DGLKIGIIGDlKYGRTVYSLLYGLGNYDVDVHLISPESLRIRSDSVYEIKKR-----LSFTESTNIEEHIDDLDVLYVTRIQ-----KERFpdeEEYLK 242
                 699***********************************99998988888775.....79***********************.....666666688888 PP

                 HCC.CSB-HHHHHHS-TT-EEEE-S---BTTTB-HHHHTSTTBHHHHHHHHHHHHHHHHHH CS
      OTCace  96 lkd.yqvteellklakkdaivlHcLPakrgeEvtdeVfdsprsvvfeqaeNrlhtikAllv 155
                 +k+ y v  +ll+++++d i+lH+LP  r +E++++V++ +++ +feqae++ ht++All 
  EPA06801.1 243 VKGsYVVGLDLLQKMRDDSIILHPLP--RLDEISTDVDKTKNAKYFEQAEYGKHTRAALLG 301
                 8888**********************..*******************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 2134.59
//
Query:       EPA06802.1  [L=180]
Description: flavin reductase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-24   86.8   0.0    1.5e-24   86.5   0.0    1.1  1  FMN_red       NADPH-dependent FMN reductase
    8.6e-09   35.4   0.0    1.1e-08   35.1   0.0    1.2  1  Flavodoxin_2  Flavodoxin-like fold


Domain annotation for each model (and alignments):
>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.5   0.0   1.7e-28   1.5e-24       2     150 ..       6     145 ..       5     149 .. 0.92

  Alignments for each domain:
  == domain 1  score: 86.5 bits;  conditional E-value: 1.7e-28
                 EEEEEES--STT-HHHHHHHHHHCCT-T.T-CEEEEETTTS.--..---HCHGHTCGGSHHHHHHHHHHHH-SCEEEEEEECTTCE-HHHHHHHHCHT- CS
     FMN_red   2 kilvisGSlrkgsntrklaewaaealkeagaevelidladlilpcalcdkdlesegqtsddvaellekiaaadaliivtPeYngsysgllKnalDrlsr 100
                 k+++is+S+rk++nt+ l++++ e +k ++ +++li+lad       + + +e   + ++ ++++ + i++ad+++i++P+Yn  +s++lKn++++++ 
  EPA06802.1   6 KVVIISASPRKNGNTQILMKYVFEYAKSKNTDTKLINLADGKIE--CYRGPEE---EYNEYTKAAANDIMDADVWLIGSPIYNSFFSSALKNLFEYVN- 98 
                 9***************************************8666..4454443...48999************************************8. PP

                 .SSCHCCTT-EEEEEEE-SSTTTTHHHHHHHHHHHHHTT-EEEECSEEEE CS
     FMN_red 101 trgkkelrgKpvalvavgggrrgglraeeqlrqvlaelgaivvpraavav 150
                    +k  +gK++++v  ++g+ g   ++    q+l+++++i+ p+a+++ 
  EPA06802.1  99 ---YKKTEGKVAGMVILASGNMGFIDVQTLITQLLSYFRVITNPKAVFLT 145
                 ...************999999**********************9988765 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.0   1.2e-12   1.1e-08       2     105 ..       6      98 ..       5     138 .. 0.81

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 1.2e-12
                   EEEEEE--TTGGCCHHHCHHHHHHHHHCCCTTTEEEEEEHHCCT-----CCCCHCCHHHHTTCHHHHHHH.HHHHHCSSEEEEEEE-BTTB--HHHH CS
  Flavodoxin_2   2 kiLiinahprpeksfssalaqafvealekagphevtvrdLyadflpvlttrdlaaklayeekpadveseq.iekllaadaivlqfPlwwfgvPailK 97 
                   k++ii a+pr+ + ++  l + + e +++++  + + ++L+++ +           + +ee ++++++++   ++ +ad+ ++++P+++  ++++lK
    EPA06802.1   6 KVVIISASPRK-NGNTQILMKYVFEYAKSKN-TDTKLINLADGKIECY--------RGPEE-EYNEYTKAaANDIMDADVWLIGSPIYNSFFSSALK 91 
                   89*********.5998999999999999999.89********722222........34555.46666666669************************ PP

                   HHHHHHS- CS
  Flavodoxin_2  98 gwiDrvlt 105
                   + +++v +
    EPA06802.1  92 NLFEYV-N 98 
                   ****99.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1165.61
//
Query:       EPA06803.1  [L=258]
Description: peptidase, S54 family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.4e-32  110.2  17.1    8.4e-32  110.2  17.1    1.5  2  Rhomboid  Rhomboid family


Domain annotation for each model (and alignments):
>> Rhomboid  Rhomboid family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1      0.45   8.1e+03     113     118 ..      25      30 ..      13      48 .. 0.52
   2 !  110.2  17.1   4.7e-36   8.4e-32       7     147 ..      86     240 ..      82     243 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.45
                 CCCCHH CS
    Rhomboid 113 lnlvlg 118
                 +n+++ 
  EPA06803.1  25 VNVIVF 30 
                 222211 PP

  == domain 2  score: 110.2 bits;  conditional E-value: 4.7e-36
                 TTHHHHGGG--SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-S...-EESSHHHHHHHHHHHHHHHHCCCCGS----HC.. CS
    Rhomboid   7 lwrlltsmflHagwlHllfNmlallvfGsplerrlGslrflllyllsglagsllsllfsaesesplvGaSGaifgllgallvlvprnrkllrkliia.. 103
                 ++ ll+s+flH+g++Hl++Nml+l++fG ++e ++G+ ++l +yl  g+ ++l+++l +  s  p+vGaSGai+g+lga+lv +p+++++   ++++  
  EPA06803.1  86 YFSLLSSTFLHGGLMHLGGNMLFLWIFGDNIELKFGKIKYLGIYLFWGISAGLIHILGDTSSAIPAVGASGAISGVLGAYLVIFPKAKIQTVMIMGFfm 184
                 56799************************************************************************************9888777778 PP

                 ..........CCCCCCCCCCHHHCTSS.....STTTHHHHHHHHHHHHHHHHHHCC CS
    Rhomboid 104 .......llllllfillnlvlgllpra.....ggvsnlAHlgGllaGlllgllllr 147
                          +l ++++++ +l ++ +      +gv++lAH+gG+++Gl +g+l ++
  EPA06803.1 185 rmmhiqaKWFLPFWLIFQNLLPFFIGGfgiagDGVAYLAHIGGFIVGLGTGYLYRK 240
                 888888855555555554444333333588899******************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1682.92
//
Query:       EPA06804.1  [L=153]
Description: aspartate carbamoyltransferase, regulatory subunit [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-31  108.7   2.9      2e-31  108.1   2.9    1.3  1  PyrI      Aspartate carbamoyltransferase regulatory chain, al
    1.6e-14   53.5   1.5    3.2e-14   52.6   1.5    1.5  1  PyrI_C    Aspartate carbamoyltransferase regulatory chain, me
  ------ inclusion threshold ------
      0.018   14.4   0.2      0.023   14.0   0.2    1.2  1  SUa-2TM   SMODS- and Ubiquitin system-associated 2TM effector
      0.048   13.6   0.4        0.1   12.5   0.4    1.5  1  DUF1936   Domain of unknown function (DUF1936)


Domain annotation for each model (and alignments):
>> PyrI  Aspartate carbamoyltransferase regulatory chain, allosteric domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.1   2.9   4.4e-35     2e-31       1      93 [.       6      97 ..       6      98 .. 0.96

  Alignments for each domain:
  == domain 1  score: 108.1 bits;  conditional E-value: 4.4e-35
                X-----SCEEEEEEEETT-HHHHHHHCT--T...TS-EEEEEEEEETTTEEEEEEEEET----HHHHHHHCCC-TT-EEEEEETTEEEEEE-- CS
        PyrI  1 lkvkkienGiViDHIkagkalkvlklLkldklkseekvaiiknvkskklgkKdiikiegkelseeeldklaliapnatiniIkdgevveKkkv 93
                l v++i++G+V+DHI +gk+l+vl+ L++d+ k ++ ++i+ nv+s k +kKdiik+e+k+l+++++++l++iap+atiniIkd+++veK++v
  EPA06804.1  6 LMVRRIKEGTVLDHIDEGKGLQVLNALRIDG-KDGSLITIALNVPSGKFKKKDIIKVENKFLKDDDTNMLSVIAPKATINIIKDYKLVEKRRV 97
                5799**************************9.55559******************************************************98 PP

>> PyrI_C  Aspartate carbamoyltransferase regulatory chain, metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.6   1.5   7.1e-18   3.2e-14       1      44 [.     102     146 ..     102     150 .. 0.94

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 7.1e-18
                 EEESSS--S-TTBGGGT.TS-.-EEEEEETTTTEEEETTT--EEE CS
      PyrI_C   1 eiegvlkCpNpnCItnn.epveskFkvedkekvklkCkYCekeis 44 
                 ei+ +++C+Np CItn+ e++es + v+dke  +lkC+YC ++++
  EPA06804.1 102 EIDRIFRCSNPDCITNStEHIESVMDVIDKEGRVLKCRYCSRVLD 146
                 6999*************99*********************99876 PP

>> SUa-2TM  SMODS- and Ubiquitin system-associated 2TM effector domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2     5e-06     0.023     214     248 ..      56      89 ..      51     121 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5e-06
     SUa-2TM 214 keikklvrklpedistiNifattnPkntveiikkv 248
                 k+i+k+ +k+++d    N+++ + Pk t++iik+ 
  EPA06804.1  56 KDIIKVENKFLKD-DDTNMLSVIAPKATINIIKDY 89 
                 689**********.9*****************985 PP

>> DUF1936  Domain of unknown function (DUF1936)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.4   2.3e-05       0.1      21      30 ..     105     114 ..     101     116 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.3e-05
                 EEEEES-TT- CS
     DUF1936  21 KvFRCdredC 30 
                 ++FRC+++dC
  EPA06804.1 105 RIFRCSNPDC 114
                 69******** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1017.12
//
Query:       EPA06805.1  [L=92]
Description: hypothetical protein BG20_I0071 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.1e-11   43.4   0.5    3.5e-11   43.2   0.5    1.0  1  SepF         Cell division protein SepF
  ------ inclusion threshold ------
      0.023   15.0   0.7      0.034   14.5   0.7    1.2  1  SporV_AA     Stage V sporulation protein AA
      0.024   14.2   0.0      0.027   14.1   0.0    1.1  1  Herpes_IE68  Herpesvirus immediate early protein
      0.036   14.0   0.0      0.055   13.4   0.0    1.2  1  H_kinase_N   Signal transduction histidine kinase


Domain annotation for each model (and alignments):
>> SepF  Cell division protein SepF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   0.5   7.9e-15   3.5e-11       2      72 .]      11      84 ..      10      84 .. 0.97

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 7.9e-15
                EEEE-SSGGGHHHHHHHHHTT-EEEEE-CCCTC...HHHHHHHHHHHHHHHHCT-EEEEECTTEEEEE-TT-EE CS
        SepF  2 vvveprsfedaqeiadalkegkiVilnledldk...eeakrivdflsgvvyaldGdiqkvgkkvflitPknvdi 72
                +++++r+++d+  i++++k+  i+il ++ l +   e+++++v++l  +++a ++di+++g++ ++++P++++i
  EPA06805.1 11 KAITIRDISDVHSIKEDIKKEMILILRVTPLAQkdvEQLRKVVEELYSIAKAEGADIARLGEERIIVAPPSIKI 84
                5799*****************************9**************************************98 PP

>> SporV_AA  Stage V sporulation protein AA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.7   7.6e-06     0.034      16      84 ..      10      77 ..       2      79 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7.6e-06
    SporV_AA 16 kkeVtlgdvaevycsdkkvekklkaikvykikekkkkrvvisvlkvieaI..kkeypnvevenlGetdfiv 84
                 k +t++d+ +v++ +++++k++  i +++++    ++ v +  kv+e +   ++ +++++  lGe+ +iv
  EPA06805.1 10 LKAITIRDISDVHSIKEDIKKEM--ILILRVT-PLAQKDVEQLRKVVEELysIAKAEGADIARLGEERIIV 77
                5789*********9777666653..4444554.445567888888888885557899*************9 PP

>> Herpes_IE68  Herpesvirus immediate early protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   6.1e-06     0.027      30      72 ..      19      61 ..       6      78 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.1e-06
  Herpes_IE68 30 ldlarlvedinklFrcilraalnstgsanrLRrlvlDiylmGr 72
                  d++ + edi k    ilr+++ ++++ ++LR++v ++y + +
   EPA06805.1 19 SDVHSIKEDIKKEMILILRVTPLAQKDVEQLRKVVEELYSIAK 61
                 599*********9999**********************98865 PP

>> H_kinase_N  Signal transduction histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.2e-05     0.055       4      37 ..      34      67 ..      33      75 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.2e-05
                HHHHH----HHHHHHHHHHHHHTHHHHHHHTSEE CS
  H_kinase_N  4 llaehtdlseadiewLhalvgdwqllAdlsfaDl 37
                l+ + t l ++d+e+L+++v+++  +A+   aD+
  EPA06805.1 34 LILRVTPLAQKDVEQLRKVVEELYSIAKAEGADI 67
                5778899*************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       867  (0.0483574); expected 358.6 (0.02)
Passed bias filter:                      625  (0.0348597); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.31s 00:00:00.73 Elapsed: 00:00:01.47
# Mc/sec: 189.03
//
Query:       EPA06806.1  [L=88]
Description: hypothetical protein BG20_I0014 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.46
# Mc/sec: 580.45
//
Query:       EPA06807.1  [L=461]
Description: ATP synthase ab C-terminal domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-70  237.3   0.0    1.9e-70  236.8   0.0    1.2  1  ATP-synt_ab    ATP synthase alpha/beta family, nucleotide-bin
    6.5e-12   45.8   2.5    1.5e-11   44.6   2.5    1.7  1  ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel do
    0.00031   20.8   0.5     0.0016   18.5   0.4    2.3  2  HAS-barrel     HAS barrel domain


Domain annotation for each model (and alignments):
>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  236.8   0.0   3.2e-74   1.9e-70       1     213 []     135     353 ..     135     353 .. 0.98

  Alignments for each domain:
  == domain 1  score: 236.8 bits;  conditional E-value: 3.2e-74
                  SSHHHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTS....S.EEEEEEESEEHHHHHHHHHHCHHSSGGGGEEEEEEETTS-HHHHHHHHHHH CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  ATP-synt_ab   1 GirvlDalfpivqGqrtlipgafgvGktvisqslskqsnsd....d.aiiyvgiGergnevaevleefpegtimkrtvlvantsnepvaareasiytg 93 
                  G++v+D ++++v+Gq++ i++++g+ ++ +++++++q++      d a+++++iG + +e++ + ++++e++++kr+vl++nt+++p+++r+++++++
   EPA06807.1 135 GVSVIDGMITLVRGQKLPIFSGSGMSHNILAAQIARQASVVgtkdDfAVVFAAIGVQYSEAEYFRRSLEESGALKRSVLFLNTADDPAIERIITPRVA 232
                  899**********************************8655888679*************************************************** PP

                  HHHHHHHHH.TTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTHHHHHHHHHTTSEEETSSEEEEEEEEEEE-GGCSTTSHHHHHHHHHSSEE CS
                  xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  ATP-synt_ab  94 itlAEyfrd.qgknvlliadslsrwaeAlreislrlgempadqgypaylgaklaslyERagkapdrtGsvtivaavspaggDfsdpvttatlgitdgf 190
                  +t+AEy++   g++vl+i+++++++aeAlreis++ +e+p+++gyp+yl+++l+++yERagk++ r+Gsvt+v+++s++++D+++p+++ t +it+g+
   EPA06807.1 233 LTVAEYLAFdLGMHVLVILTDMTNYAEALREISAAREEVPGRKGYPGYLYTDLSTIYERAGKLNGRKGSVTQVPILSMPSDDITHPIPDLTGYITEGQ 330
                  *******9879*************************************************************************************** PP

                  EEB-HHHHHTTBSSSBCTTTEEE CS
                  xxxxxxxxxxxxxxxxxxxxxxx RF
  ATP-synt_ab 191 ivLdkklaqrkhfPainvlvSvS 213
                  +vL ++l++++++P+in+l+S+S
   EPA06807.1 331 VVLGRDLFRQGVYPPINILMSLS 353
                  *********************98 PP

>> ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.6   2.5   2.5e-15   1.5e-11       1      69 []      12      78 ..      12      78 .. 0.88

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 2.5e-15
                   EEEEETTEEEEESSTSCETCTTEEEEECCETCSTEEEEEEEEEETTEEEEEESS-STTBBT.TSEEEEES CS
  ATP-synt_ab_N  1 ivqviGpvvdvefgigrlpgiynalevelvefgtlllgvalnlgedkVrvivmgstdGlsr.GteVkrTG 69
                   i ++ Gp+v v++++    + ++++eve ++ g+ +lg +l++g++k++v+v+++t+Gls  Gt  k+ G
     EPA06807.1 12 IAEIKGPLVVVDDVEN--AAFDELVEVETTD-GERRLGKVLEVGNGKAIVQVFEGTTGLSIsGTSAKFVG 78
                   6789************..5566666666559.****************************9999999876 PP

>> HAS-barrel  HAS barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.4   2.7e-07    0.0016      11      83 ..      16      66 ..       9      95 .. 0.79
   2 ?   -1.8   0.0      0.59   3.5e+03      35      48 ..     135     148 ..     104     164 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.7e-07
  HAS-barrel 11 sslifrvegskdvkvGeyVeielpdgeivlGmvtdirrgnselsndlalvlsleeleeangddevalatedt.g 83
                 +++++v+ +++  + e+Ve+e++dge++lG+v+ + +                       + ++++++e+t g
  EPA06807.1 16 KGPLVVVDDVENAAFDELVEVETTDGERRLGKVLEVGN-----------------------GKAIVQVFEGTtG 66
                68999*********************************.......................6666666666551 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.59
  HAS-barrel  35 dgeivlGmvtdirr 48 
                 + +++ Gm+t +r 
  EPA06807.1 135 GVSVIDGMITLVRG 148
                 57788899988877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (461 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.68u 0.30s 00:00:00.98 Elapsed: 00:00:00.52
# Mc/sec: 2653.59
//
Query:       EPA06808.1  [L=300]
Description: hypothetical protein BG20_I0056 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-18   65.8   9.6    1.2e-10   40.7   1.6    2.6  2  HTH_24         Winged helix-turn-helix DNA-binding
    5.2e-18   64.6   0.5    7.1e-12   45.0   0.1    2.4  2  HTH_AsnC-type  AsnC-type helix-turn-helix domain
    1.2e-06   28.3   2.0    0.00082   19.2   0.4    2.5  2  MarR           MarR family
    1.9e-06   27.7   0.1       0.05   13.5   0.0    2.3  2  TrmB           Sugar-specific transcriptional regulator TrmB
    9.9e-05   22.2   3.0      0.062   13.3   0.3    2.8  2  HTH_11         HTH domain
    0.00041   20.2   0.0       0.43   10.5   0.0    2.3  2  MarR_2         MarR family
     0.0011   19.5   0.2       0.16   12.6   0.1    2.7  2  Mga            Mga helix-turn-helix domain
     0.0062   16.6   1.3      0.066   13.3   0.1    2.7  3  Trp_repressor  Trp repressor protein
     0.0073   16.1   1.1      0.039   13.8   0.2    2.4  2  HTH_5          Bacterial regulatory protein, arsR family
  ------ inclusion threshold ------
      0.012   15.3   0.0       0.99    9.3   0.0    2.6  2  HTH_23         Homeodomain-like domain
       0.02   14.9   3.7       0.02   14.9   3.7    3.4  3  HTH_Mga        M protein trans-acting positive regulator (MGA
       0.04   13.6   0.4       0.04   13.6   0.4    1.7  1  DUF1366        Protein of unknown function (DUF1366)
      0.042   13.5   0.3        8.4    6.1   0.0    2.6  2  DUF4423        Domain of unknown function (DUF4423)
      0.045   13.9   0.0         14    6.0   0.0    2.4  2  HTH_34         Winged helix DNA-binding domain
      0.061   13.2   1.7        3.1    7.7   0.2    2.5  2  TFIIE_alpha    TFIIE alpha subunit
      0.063   12.8   4.3        5.5    6.6   0.3    3.3  3  GerE           Bacterial regulatory proteins, luxR family
       0.19   12.0   1.5        4.2    7.6   0.2    2.4  2  GAIN_A         GPCR-Autoproteolysis-INducing (GAIN) subdomain


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   1.6   1.2e-13   1.2e-10       1      48 []       1      48 [.       1      48 [. 0.97
   2 !   29.1   1.3   5.1e-10   5.3e-07       1      44 [.     138     181 ..     138     184 .. 0.95

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 1.2e-13
      HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                +d++d+kIL+ L  n r s r++ ++lg+S ++vn+r++++e+  +I+
  EPA06808.1  1 MDKLDIKILSRLLNNCRESDRQIGKELGISGGAVNARIQKMEKIKIIE 48
                89*****************************************99986 PP

  == domain 2  score: 29.1 bits;  conditional E-value: 5.1e-10
      HTH_24   1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeee 44 
                 l +td++ILe L k+pr  +  +++ + lS  t++r++++L e+
  EPA06808.1 138 LTKTDLEILEQLIKEPRQKIEKISKDTKLSTKTITRCIDKLHEN 181
                 579**************************************886 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.0   0.1   6.7e-15   7.1e-12       1      42 []       1      42 [.       1      42 [. 0.99
   2 !   17.9   0.0   1.9e-06     0.002       1      42 []     138     179 ..     138     179 .. 0.95

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 6.7e-15
  HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                   +D++D+kIL+ L  ++R s +++++++G+S  +v +R++++e
     EPA06808.1  1 MDKLDIKILSRLLNNCRESDRQIGKELGISGGAVNARIQKME 42
                   9****************************************8 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 1.9e-06
  HTH_AsnC-type   1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42 
                    L ++D+ ILe L + +R   +++++ + lS+ t+ r +++L+
     EPA06808.1 138 LTKTDLEILEQLIKEPRQKIEKISKDTKLSTKTITRCIDKLH 179
                    678********************************9999985 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.1    0.0023       2.4      17      50 ..      15      50 ..       5      53 .. 0.82
   2 !   19.2   0.4   7.8e-07   0.00082       1      47 [.     138     184 ..     138     187 .. 0.94

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0023
                TEEHH..HHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
        MarR 17 plsvs..eLakklgvskstvtrvldrLekkGlieRs 50
                +++ s  +++k lg+s ++v   + ++ek   ie++
  EPA06808.1 15 NCRESdrQIGKELGISGGAVNARIQKMEKIKIIEKY 50
                45555559*********************9999987 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 7.8e-07
                 --HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
        MarR   1 ltltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGli 47 
                 lt t ++iL++l  ++ +++ ++ k  ++s+ t+tr +d+L +++ i
  EPA06808.1 138 LTKTDLEILEQLIKEPRQKIEKISKDTKLSTKTITRCIDKLHENEGI 184
                 899**************************************998866 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   0.00014      0.15       8      55 ..       3      50 ..       1      59 [. 0.90
   2 !   13.5   0.0   4.7e-05      0.05       5      50 ..     137     182 ..     135     196 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
                HHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
        TrmB  8 eyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVere 55
                + ++k+   Ll++++ + ++i +elg++   v+  ++++e+  ++e+ 
  EPA06808.1  3 KLDIKILSRLLNNCRESDRQIGKELGISGGAVNARIQKMEKIKIIEKY 50
                6799************************************99888875 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 4.7e-05
                 HHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCT CS
        TrmB   5 GLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkG 50 
                 +L++++ ++   L+k+ + ++++i+++++++  ++ + + +L +  
  EPA06808.1 137 NLTKTDLEILEQLIKEPRQKIEKISKDTKLSTKTITRCIDKLHENE 182
                 79****************************************9875 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.1    0.0022       2.3       5      42 ..       8      44 ..       5      55 .. 0.80
   2 !   13.3   0.3   5.9e-05     0.062       4      42 ..     144     182 ..     142     190 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0022
      HTH_11  5 ilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeel 42
                il +Ll++    s  ++ +eL++S  +v  +I+++e++
  EPA06808.1  8 ILSRLLNNCR-ESDRQIGKELGISGGAVNARIQKMEKI 44
                6666655555.37789******************9986 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 5.9e-05
      HTH_11   4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaL.eel 42 
                  ile+L+++     +e++++ +++S++t+ r I++L e  
  EPA06808.1 144 EILEQLIKEPR-QKIEKISKDTKLSTKTITRCIDKLhENE 182
                 79****77666.6***********************4444 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0   0.00041      0.43      25      53 ..      21      49 ..      10      53 .. 0.82
   2 !    7.4   0.0    0.0039       4.1       2      47 ..     137     180 ..     136     185 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00041
                HHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
      MarR_2 25 gelarrlglsksavsrilkrLvaaGLver 53
                +++ ++lg+s +av+ +++++++   +e+
  EPA06808.1 21 RQIGKELGISGGAVNARIQKMEKIKIIEK 49
                589*******************9777775 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0039
                 T--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHH CS
      MarR_2   2 gltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLva 47 
                  lt +++ +L  L  +p+    +  + + ++ls  +++r +++L +
  EPA06808.1 137 NLTKTDLEILEQLIKEPR--QKIEKISKDTKLSTKTITRCIDKLHE 180
                 57889999*********8..89*********************987 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.076        81      17      56 ..       4      43 ..       2      57 .. 0.85
   2 !   12.6   0.1   0.00015      0.16      16      56 ..     140     180 ..     107     185 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.076
                HHHHHHHHHHHHSEEEHHHHHHHCT--HHHHHHHHHHHHH CS
         Mga 17 lkyqllkflfeeeevsieelaqelyiSestlkrkikelnk 56
                l++++l  l+++ + s  ++ +el iS   ++  i++++k
  EPA06808.1  4 LDIKILSRLLNNCRESDRQIGKELGISGGAVNARIQKMEK 43
                6889999999999999*****************9999986 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00015
                 SHHHHHHHHHHHHSEEEHHHHHHHCT--HHHHHHHHHHHHH CS
         Mga  16 slkyqllkflfeeeevsieelaqelyiSestlkrkikelnk 56 
                  +++++l++l++e +++ie++++   +S  t+ r i++l +
  EPA06808.1 140 KTDLEILEQLIKEPRQKIEKISKDTKLSTKTITRCIDKLHE 180
                 57899*******************************99875 PP

>> Trp_repressor  Trp repressor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.52   5.5e+02      40      62 ..       7      30 ..       5      43 .. 0.81
   2 !   13.3   0.1   6.3e-05     0.066      39      76 ..     143     181 ..     139     189 .. 0.82
   3 ?   -2.8   0.0       6.9   7.3e+03      31      40 ..     248     257 ..     244     260 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.52
  Trp_repressor 40 qvvkeLLke.elsqreIaeelgvS 62
                   +++++LL++   s r+I +elg+S
     EPA06808.1  7 KILSRLLNNcRESDRQIGKELGIS 30
                   68888887636799********99 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 6.3e-05
  Trp_repressor  39 lqvvkeLLkeelsq.reIaeelgvSiAtItRvsrsLktg 76 
                    l+++++L+ke +   ++I++ ++ S+ tItR+  +L+  
     EPA06808.1 143 LEILEQLIKEPRQKiEKISKDTKLSTKTITRCIDKLHEN 181
                    68999999987654278***************9999854 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 6.9
  Trp_repressor  31 ErealaqRlq 40 
                    E++ l+qR++
     EPA06808.1 248 EMDELTQRVR 257
                    8899999986 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.83   8.8e+02      19      40 ..      21      42 ..       6      49 .. 0.66
   2 !   13.8   0.2   3.7e-05     0.039       3      41 ..     141     180 ..     139     182 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.83
                HHHHHHHTS-HHHHHHHHHHHH CS
       HTH_5 19 celaeelglsqstvShHLkkLr 40
                 ++ +elg+s ++v     k++
  EPA06808.1 21 RQIGKELGISGGAVNARIQKME 42
                6888999999999976666655 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 3.7e-05
                 HHHHHHHHHTTSS.EEHHHHHHHHTS-HHHHHHHHHHHHH CS
       HTH_5   3 tRlkILklLaege.lcvcelaeelglsqstvShHLkkLre 41 
                 t l+IL +L +++ +++  ++++++ls  t+ +   kL+e
  EPA06808.1 141 TDLEILEQLIKEPrQKIEKISKDTKLSTKTITRCIDKLHE 180
                 559**********9*****************988888776 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00094      0.99       9      35 ..       7      35 ..       6      45 .. 0.80
   2 ?    3.5   0.0     0.063        66      13      46 ..     148     184 ..     143     188 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00094
      HTH_23  9 rillllae..GlsvreIAreLgvsrrTvy 35
                +il  l++  + s r+I +eLg+s   v 
  EPA06808.1  7 KILSRLLNncRESDRQIGKELGISGGAVN 35
                577777777899************77776 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.063
      HTH_23  13 llae..GlsvreIAreLgvsrrTvyrwlkryre.eGl 46 
                  l +  ++ +++I++    s  T+ r + +  e eG+
  EPA06808.1 148 QLIKepRQKIEKISKDTKLSTKTITRCIDKLHEnEGI 184
                 44444899****************9987777554665 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1      0.71   7.4e+02       7      45 ..       5      42 ..       2      54 .. 0.68
   2 ?   14.9   3.7   1.9e-05      0.02       5      45 ..     140     179 ..     139     181 .. 0.95
   3 ?    0.2   0.0      0.73   7.7e+02      37      54 ..     211     228 ..     210     229 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.71
     HTH_Mga  7 klkLlelLteneksltldelakeLglseltlqsdiseLn 45
                ++k+l+ L+  + + +   + keLg+s  +++ +i+++ 
  EPA06808.1  5 DIKILSRLLN-NCRESDRQIGKELGISGGAVNARIQKME 42
                5666666666.4444444677889999888888888875 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1.9e-05
     HTH_Mga   5 krklkLlelLteneksltldelakeLglseltlqsdiseLn 45 
                 k++l++le L++ e++ ++ +++k + ls +t+  +i++L 
  EPA06808.1 140 KTDLEILEQLIK-EPRQKIEKISKDTKLSTKTITRCIDKLH 179
                 689*********.*************************996 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.73
     HTH_Mga  37 lqsdiseLnelFpeelsi 54 
                 +++ + ++n +F++++ +
  EPA06808.1 211 IRETLKKMNREFSDSFMQ 228
                 89999*********9876 PP

>> DUF1366  Protein of unknown function (DUF1366)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.4   3.8e-05      0.04      74     111 ..     146     183 ..     126     186 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.8e-05
     DUF1366  74 ldeliekakatiektEemlkaatetLneiidklkeeea 111
                 l++li+  +++iek+ + +k+ t+t+   idkl+e+e+
  EPA06808.1 146 LEQLIKEPRQKIEKISKDTKLSTKTITRCIDKLHENEG 183
                 55999******************************997 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.008       8.4      37      71 ..      18      50 ..       8      56 .. 0.87
   2 ?    4.8   0.0      0.02        21      33      66 ..     151     182 ..     133     196 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.008
     DUF4423 37 adpeelakrlrpkisaeevekalefLlklgllkkd 71
                ++ +++ k l+  is   v++ ++ ++k+++++k 
  EPA06808.1 18 ESDRQIGKELG--ISGGAVNARIQKMEKIKIIEKY 50
                56789******..*******************985 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.02
     DUF4423  33 kdfkadpeelakrlrpkisaeevekalefLlklg 66 
                 k+ ++++e+++k ++  +s++ + ++++ L +++
  EPA06808.1 151 KEPRQKIEKISKDTK--LSTKTITRCIDKLHENE 182
                 344567777777777..77777777777777665 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.013        14       3      45 ..       6      48 ..       4      57 .. 0.89
   2 ?    5.6   0.0     0.017        18       3      49 ..     143     189 ..     141     197 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.013
      HTH_34  3 lavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYie 45
                +++ls L+ + + + +++ ++l+++ g+  + ++k+ek + ie
  EPA06808.1  6 IKILSRLLNNCRESDRQIGKELGISGGAVNARIQKMEKIKIIE 48
                579999999999999***********************98776 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.017
      HTH_34   3 lavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdke 49 
                 l++l  L+++ + + +++++ +++++  +   ++kL +++ i+ ++ 
  EPA06808.1 143 LEILEQLIKEPRQKIEKISKDTKLSTKTITRCIDKLHENEGIQFTLV 189
                 899**********************************9998887665 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.031        32      16      58 ..       6      48 ..       2      79 .. 0.86
   2 ?    7.7   0.2    0.0029       3.1      16      60 ..     143     187 ..     136     224 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.031
                 HHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEE CS
  TFIIE_alpha 16 vlvldvLlekgevteedlakelkidlnelrklLnrLyearlvk 58
                 +++l  Ll +   ++ ++ kel+i    +   + ++ ++++++
   EPA06808.1  6 IKILSRLLNNCRESDRQIGKELGISGGAVNARIQKMEKIKIIE 48
                 68999********************999999999999999985 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0029
                  HHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEE CS
  TFIIE_alpha  16 vlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkyk 60 
                   ++l+ L+++   + e ++k++k+  + + + + +L e   +++ 
   EPA06808.1 143 LEILEQLIKEPRQKIEKISKDTKLSTKTITRCIDKLHENEGIQFT 187
                  6899********************************998777665 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0      0.01        11      20      41 ..      20      41 ..      18      50 .. 0.83
   2 ?   -0.5   0.1      0.88   9.3e+02      10      26 ..      63      79 ..      61      82 .. 0.82
   3 ?    6.6   0.3    0.0052       5.5       2      35 ..     137     172 ..     136     178 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.01
                HHHHHHHHTS-HHHHHHHHHHH CS
        GerE 20 nkeIAeelniSekTVkvhksni 41
                  +I++el+iS   V++ ++ +
  EPA06808.1 20 DRQIGKELGISGGAVNARIQKM 41
                579*************999875 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.88
                HHHHHCTTS-HHHHHHH CS
        GerE 10 vLrllaeGksnkeIAee 26
                vL  +++G+  keI e+
  EPA06808.1 63 VLYIVVSGQNIKEILEQ 79
                89999********9665 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.0052
                 SS-HHHHHHHHHHCTT..S-HHHHHHHHTS-HHHHH CS
        GerE   2 sLskRErevLrllaeG..ksnkeIAeelniSekTVk 35 
                 +L+k  +e+L+ l++   ++ ++I+++  +S+kT++
  EPA06808.1 137 NLTKTDLEILEQLIKEprQKIEKISKDTKLSTKTIT 172
                 79***********9985577889***********96 PP

>> GAIN_A  GPCR-Autoproteolysis-INducing (GAIN) subdomain A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1      0.13   1.4e+02       8      27 ..       3      22 ..       3      27 .. 0.84
   2 ?    7.6   0.2     0.004       4.2       8      27 ..     140     159 ..     138     168 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.13
      GAIN_A  8 KrdLqlLSqLLkhPqkasRr 27
                K d++ LS+LL + + + R+
  EPA06808.1  3 KLDIKILSRLLNNCRESDRQ 22
                66999*******99888775 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.004
      GAIN_A   8 KrdLqlLSqLLkhPqkasRr 27 
                 K dL+ L qL+k+P+++  +
  EPA06808.1 140 KTDLEILEQLIKEPRQKIEK 159
                 88************987555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1049  (0.0585086); expected 358.6 (0.02)
Passed bias filter:                      646  (0.036031); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 1922.38
//
Query:       EPA06809.1  [L=236]
Description: ATP-dependent protease La (LON) domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.3e-20   72.5   0.1      5e-20   72.3   0.1    1.1  1  LON_substr_bdg  ATP-dependent protease La (LON) substrate-bin


Domain annotation for each model (and alignments):
>> LON_substr_bdg  ATP-dependent protease La (LON) substrate-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.3   0.1   2.8e-24     5e-20       2     207 ..       7     234 ..       6     235 .. 0.88

  Alignments for each domain:
  == domain 1  score: 72.3 bits;  conditional E-value: 2.8e-24
  LON_substr_bdg   2 lpllpldnkvlfPgitlpltvsrpksiaaierlldkdkpyigvflvkesqkdaideesiselysvGtvarIvqil..rlddgrikvvlegleRvk 94 
                     lp++pl + vlfP++ lpl++++p++ +++++++  d + +gv+l+    +++i   ++ +l  +Gt+a+I+++   +ld  ++ + + g  ++k
      EPA06809.1   7 LPIFPL-DLVLFPRQELPLRIFEPRYKQLVDDCMLGDGQ-FGVCLI--DANNSISGWTAPKL--IGTIAKITKCKdvELDGMQLHIETVGRNKFK 95 
                     8*****.799**************************999.******..55555555445555..8*********98888888899999999**** PP

  LON_substr_bdg  95 ikkleke............................keegylvaeveiieddsepedsdslqkelkalvqeiiekikkslarellkllleielllk 161
                     i+k+ ++                            +e+ y++aeve i    ++ d++   ++ + lvq   +ki k+++ + + +   +  l+k
      EPA06809.1  96 IHKIIPPslaqpanydpytvkghqniselheklgtEEKMYIRAEVELI----PEIDENVSLDQWEILVQMWKNKIIKQALPQVVESHALDHVLEK 186
                     ****4446*******99999999999999999999999999*******....777888888***************9877777777777888899 PP

  LON_substr_bdg 162 yedlenpyr..LadlvaailpfsneekqelLeeldvedRlkkvlelLk 207
                     y+ +++++   +++++ a+ + +++e+q +Le+++ +d l +v elL+
      EPA06809.1 187 YYLITDTPTidFVYSLSALGAKDPNELQPILEANNMDDLLHNVKELLT 234
                     99999988879********************************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1582.45
//
Query:       EPA06810.1  [L=275]
Description: 3-methyl-2-oxobutanoate hydroxymethyltransferase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   3.8e-108  360.8   2.2   4.3e-108  360.6   2.2    1.0  1  Pantoate_transf  Ketopantoate hydroxymethyltransferase
      0.008   15.7   0.3      0.026   14.0   0.2    1.9  2  PEP_mutase       Phosphoenolpyruvate phosphomutase


Domain annotation for each model (and alignments):
>> Pantoate_transf  Ketopantoate hydroxymethyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  360.6   2.2  4.8e-112  4.3e-108       4     258 ..       5     258 ..       2     259 .. 0.99

  Alignments for each domain:
  == domain 1  score: 360.6 bits;  conditional E-value: 4.8e-112
  Pantoate_transf   4 vkdlrkmkeegekiamlTaydattAklvdeagvdviLVGDslgmvvlgyestlpvtleemiyhtkaVargakralvvadlPfgsyeaskeqale 97 
                      v d+ k+k++g+ki+++T+yd+t ++l+d+ag+d++LVGDs+gmv+lgye+t+pvt+e+m+++t+aV+r+ ++al+vadlPf+sy+as e+a++
       EPA06810.1   5 VYDIIKKKKDGQKISAITSYDYTLGSLCDKAGIDILLVGDSAGMVMLGYENTIPVTMEQMCMFTEAVSRARNNALLVADLPFMSYQASIEDAIK 98 
                      67899***************************************************************************************** PP

  Pantoate_transf  98 nAarllkeggadavKleggaevaetvkalveagipVmgHiGltPqsvnalggykvqgkteeeaeklledakaleeaGafalvlEavpaelakei 191
                      n++ l+k+ gadavKlegg+++++t++a+v+ gipVmgHiGl+Pq++    gykvqgkt+++a kl++dak++eeaGaf++vlE+v +e+a+ i
       EPA06810.1  99 NSGMLIKS-GADAVKLEGGNSMVKTISAIVDIGIPVMGHIGLQPQTTMLSQGYKVQGKTKDSAIKLIQDAKEIEEAGAFSIVLEMVSHEVAQMI 191
                      *******9.************************************************************************************* PP

  Pantoate_transf 192 teklsiptIGIGAGaacdGqvlvlhDllgltekfkpkfvkkyaelaesieeavkaYaeevkegsFPa 258
                      +e++siptIGIG+G +cdGq+lv++Dllg++ek kpkf+k+y++l+++i +a+++Y+++v++g FPa
       EPA06810.1 192 SETVSIPTIGIGSGVGCDGQILVVQDLLGMFEKIKPKFAKRYLNLNDDILKALENYKKDVESGVFPA 258
                      ******************************************************************8 PP

>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.2   2.9e-06     0.026       6     107 ..      13     116 ..       9     174 .. 0.89
   2 ?   -1.4   0.0      0.14   1.3e+03      89     105 ..     165     181 ..     146     198 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.9e-06
  PEP_mutase   6 akgeplvlpnawDalsakiveeagfkalatsSlavaaslGvpDgeelpleellaavraiaevvs.lPlivDle.dGygespeevaetvrrliaaGvvgv 102
                 + g+ + ++  +D    +++ +ag++ l ++  a   +lG++ +  +++e+++  ++a+ ++ +   l +Dl    y++s e+  ++   li+ G+ +v
  EPA06810.1  13 KDGQKISAITSYDYTLGSLCDKAGIDILLVGDSAGMVMLGYENTIPVTMEQMCMFTEAVSRARNnALLVADLPfMSYQASIEDAIKNSGMLIKSGADAV 111
                 566889999****************************************************99625668899746899999999999999********* PP

  PEP_mutase 103 niEDk 107
                  +E  
  EPA06810.1 112 KLEGG 116
                 *9977 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.14
  PEP_mutase  89 etvrrliaaGvvgvniE 105
                 +  +++++aG+  +++E
  EPA06810.1 165 QDAKEIEEAGAFSIVLE 181
                 44455555666555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1748.67
//
Query:       EPA06811.1  [L=345]
Description: ATP synthase, subunit C [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-52  178.0   6.4    4.4e-52  177.7   6.4    1.0  1  vATP-synt_AC39  ATP synthase (C/AC39) subunit
  ------ inclusion threshold ------
      0.035   14.2   0.1       0.17   12.0   0.0    2.1  2  Fibritin_C      Fibritin C-terminal region


Domain annotation for each model (and alignments):
>> vATP-synt_AC39  ATP synthase (C/AC39) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.7   6.4   4.9e-56   4.4e-52       7     331 ..      15     334 ..      10     338 .. 0.95

  Alignments for each domain:
  == domain 1  score: 177.7 bits;  conditional E-value: 4.9e-56
                     HHGGGS--HHHHHHHTTS.-HHHHHHHHHTSGGGGG--.....SSSHHHHHHHHHHHHHHHTTTGGGGS-H.HHHHHHHHHHHHHHHHHHHHHHH CS
  vATP-synt_AC39   7 amrsglLteedyenLlqcesledvkryLketdYgnfladelseplsrsdiekalreklarefnklreqapgpsrefldyllyrydidNvklllrg 101
                      +r++lL+++d++ L+++++l+++++ +k+t Yg+ +a++ ++p++ + ie alr +la++  ++ + +  +   +ld++ +++ + N+k +l+g
      EPA06811.1  15 SKRGKLLKKADFQTLAESRDLDELMTRIKNTVYGDSVAEV-EKPYTSQGIESALRSHLADTHYSIAKTSGNS--GVLDAYYMKFIVSNLKSILKG 106
                     579********************************86555.56*****************************..9******************** PP

                     HHH.T--GGGS-..--.S..SSS-HHHH.HHHHHSSSHHHHHHHHHT-HHHHHHHHHHCC...--SHHHHHHHHHHHHHHHHHHHHHTSS-HH.. CS
  vATP-synt_AC39 102 klsgdldleeleeklhpl..gelsaldl.dklieaksveelyeallgtpyakyleealdeleetgdleiienaLdkayledllkfckklggetae 193
                     k   ++++ee+e + +      ++++d+  k++ ak++ee +++l    +++ +++a + ++e+++++i+++  dk  +++l  + k+  +++  
      EPA06811.1 107 KAL-GKSQEEIETHVNLHaeELIKQRDIvIKALVAKDLEEAVASLNSVHFGDEIAKAAALYNEKKNIQIFDTYFDKILIQHLAGAMKNYTDKD-- 198
                     ***.5777999998865584599999*99**********************************************************999999.. PP

                     .HHHHHHHHHHHHHHHHHHHTTTSS......T...--SS-S--HHHHHHHHTT-G.....GG.GGSSTSSTTGGGTT--S.HHHHHHHHHHHHHH CS
  vATP-synt_AC39 194 ilreilgfeiDlrniniilrskkygelskedrkkllipggslypeglealaeaedveellaalkyteygelleealeeagslksledaldealvk 288
                       ++ +g+ iD+ ni  ++r k++g l++e++++l+++     +e l ++++a++  ++ + l++t+y++l+ ++++e +++ ++e+a+++a+++
      EPA06811.1 199 -ATKVVGMDIDFYNILSVIRGKFWG-LQEEQIQDLIVSQTPTAKELLGRMISAATTRDAFNELSNTKYKSLVPQTEKELDAIAEFERAFEKAIYQ 291
                     .**********************99.78888*99******9999*****************************99999666************** PP

                     HHHTTTSSSTSTHHHHHHHHHHHHHHHHHHHHHHHHHHT--SH CS
  vATP-synt_AC39 289 llkkafrqqfsvgvfyaYlklkeqEirnlrwIaegiaqglpke 331
                      + ++f++ fs++++++  kl   E+rnl +Ia  ++q++p e
      EPA06811.1 292 TALRSFTKMFSFATIVGITKLTTFEVRNLAAIAFAVEQKIPTE 334
                     ***************************************9987 PP

>> Fibritin_C  Fibritin C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.9e-05      0.17      18      68 ..      31      83 ..      19     102 .. 0.83
   2 ?   -1.6   0.0      0.34     3e+03       6      30 ..     226     250 ..     224     255 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.9e-05
  Fibritin_C 18 nssglkgaviklskdiyGtnpsgd..piekrGikktvkeleteiqlqalsesg 68
                +s+ l + ++ +++ +yG+ + +   p + +Gi ++ +++ +      ++ sg
  EPA06811.1 31 ESRDLDELMTRIKNTVYGDSVAEVekPYTSQGIESALRSHLADTHYSIAKTSG 83
                78999**************9876446************998887766666666 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.34
  Fibritin_C   6 ksvqdvevevGnnssglkgavikls 30 
                 +++qd+ v  +++ + l g +i++ 
  EPA06811.1 226 EQIQDLIVSQTPTAKELLGRMISAA 250
                 6899999999999999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2234.15
//
Query:       EPA06812.1  [L=592]
Description: ATP synthase ab C-terminal domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.1e-93  309.9   0.0    1.1e-92  309.5   0.0    1.2  1  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
    1.9e-38  131.0   0.0    3.3e-38  130.3   0.0    1.4  1  ATP-synt_ab_Xtn  ATPsynthase alpha/beta subunit N-term extens
    5.9e-14   52.3   0.6    1.4e-13   51.1   0.6    1.7  1  ATP-synt_ab_N    ATP synthase alpha/beta family, beta-barrel 
  ------ inclusion threshold ------
      0.048   13.9   0.3       0.12   12.6   0.0    1.7  2  AAA_22           AAA domain
       0.11   11.0   0.2       0.18   10.4   0.2    1.2  1  DUF853           Bacterial protein of unknown function (DUF85


Domain annotation for each model (and alignments):
>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  309.5   0.0   3.2e-96   1.1e-92       1     213 []     214     437 ..     214     437 .. 0.98

  Alignments for each domain:
  == domain 1  score: 309.5 bits;  conditional E-value: 3.2e-96
                  SSHHHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEEEEEESEEHHHHHHHHHHCHH......SS.GGGGEEEEEEETTS-HHHHHHHHH CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xx.xxxxxxxxxxxxxxxxxxxxxxxx RF
  ATP-synt_ab   1 GirvlDalfpivqGqrtlipgafgvGktvisqslskqsnsddaiiyvgiGergnevaevleefpe......gt.imkrtvlvantsnepvaareasiy 91 
                  G+rv+D++fpi++G++  ipgafg+Gktv +++++k+++s+ +++y+g+Gergne++evl efp+      g+ +m+rtvlvantsn+pvaareasiy
   EPA06812.1 214 GQRVIDTFFPIAKGGTGSIPGAFGTGKTVTLHQIAKWADSQ-VVVYIGCGERGNEMTEVLVEFPHlkdprsGKpLMDRTVLVANTSNMPVAAREASIY 310
                  9************************************9999.***********************988886337************************ PP

                  HHHHHHHHHHHTTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTHHHHHHHHHTTSEEE.....TSSEEEEEEEEEEE-GGCSTTSHHHHHHH CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  ATP-synt_ab  92 tgitlAEyfrdqgknvlliadslsrwaeAlreislrlgempadqgypaylgaklaslyERagka.....pdrtGsvtivaavspaggDfsdpvttatl 184
                  tg+t+AEy+rd+g++v+l+ads+srwae+lre+s+rl+empa++gyp+yl+++la++yERag++     pdr Gsvt v avsp+ggDf++pvtt+t+
   EPA06812.1 311 TGVTIAEYYRDMGYDVVLVADSTSRWAESLREMSGRLEEMPAEEGYPSYLASRLAEFYERAGRVkaigsPDRDGSVTLVGAVSPSGGDFTEPVTTHTM 408
                  ************************************************************************************************** PP

                  HHSSEEEEB-HHHHHTTBSSSBCTTTEEE CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  ATP-synt_ab 185 gitdgfivLdkklaqrkhfPainvlvSvS 213
                  +++++f+ Ld kla ++h+P+in+++S+S
   EPA06812.1 409 RFIKTFWALDAKLAYSRHYPSINWMNSYS 437
                  ****************************9 PP

>> ATP-synt_ab_Xtn  ATPsynthase alpha/beta subunit N-term extension
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.3   0.0   9.1e-42   3.3e-38       1     120 [.      85     204 ..      85     205 .. 0.96

  Alignments for each domain:
  == domain 1  score: 130.3 bits;  conditional E-value: 9.1e-42
                      EETTS-BHHHHHHHHTSBE-TT----SS-SSS-EEEEESS-TT-EEETT-EEEEEECTTCEEEEEE--TT-.EEEEEEE--EEEE-TTSECEEE CS
  ATP-synt_ab_Xtn   1 yDGiqrpLekiaeksgsfierGvkvpaldrekkwefkpkvkvgdkvsggdilGtvqeteliehkimvppkv.egkvkeiaeegeytvedtiaev 93 
                      yDGiqrpL++++++sgsfi rG++++++d  kk++f+p+v++gd + +g++lGtvqet+li+  i+vpp+   gk++++++eg+y++e+++++ 
       EPA06812.1  85 YDGIQRPLKELSKVSGSFIGRGITTTPVDMVKKYHFVPSVSNGDVIAAGNVLGTVQETDLITNSILVPPDHpGGKISNVVSEGDYDLETVLCTS 178
                      9********************************************************************775889*************999999 PP

                      CETT.ECEEEESSEEEETTS---ESEE CS
  ATP-synt_ab_Xtn  94 eteegkekeltllqkwPvrkprpvkek 120
                      e+++ ++  l+++++wPvrkprp++++
       EPA06812.1 179 EKDG-QKIPLKMYHRWPVRKPRPYHTR 204
                      9666.8******************987 PP

>> ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.1   0.6     4e-17   1.4e-13       1      69 []       7      69 ..       7      69 .. 0.97

  Alignments for each domain:
  == domain 1  score: 51.1 bits;  conditional E-value: 4e-17
                   EEEEETTEEEEESSTSCETCTTEEEEECCETCSTEEEEEEEEEETTEEEEEESS-STTBBTTSEEEEES CS
  ATP-synt_ab_N  1 ivqviGpvvdvefgigrlpgiynalevelvefgtlllgvalnlgedkVrvivmgstdGlsrGteVkrTG 69
                   iv v+Gp v+++++++   ++y+ + v+  +  ++l+g++++l +d++ ++v++st+Gl++G++V+ TG
     EPA06812.1  7 IVWVSGPAVKADGMSD--AKMYETVVVG--N--SKLVGEVIRLTGDVAFIQVYESTSGLKPGEPVVGTG 69
                   5679************..**********..9..***********************************8 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   3.5e-05      0.12       6      51 ..     228     265 ..     225     295 .. 0.78
   2 ?   -2.5   0.1       1.6   5.8e+03      55     118 ..     470     530 ..     465     539 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.5e-05
      AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevv.fvtlpsst 51 
                 g + + G  GtGKT++l ++++++d         ++vv ++ + + +
  EPA06812.1 228 GTGSIPGAFGTGKTVTLHQIAKWAD---------SQVVvYIGCGERG 265
                 678899*****************95.........4444377666555 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.6
      AAA_22  55 dllrellralglelkaerlsseellealeqalraravielliiDEaqhlrs.eealeeLrsllnl 118
                 d l+e++r lg e+     ++e l+  +++ ++  +  +    D+++   s +++++ L+ l+++
  EPA06812.1 470 DTLKEIVRLLGPEALP---DEEKLILEVARMVKIGHL-QQNSFDDVDTYCSpQKQYKLLKLLVEF 530
                 5567778888876666...777777777777777777.777777777743347777777777665 PP

>> DUF853  Bacterial protein of unknown function (DUF853)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.2   4.9e-05      0.18      24      50 ..     230     255 ..     223     262 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 4.9e-05
      DUF853  24 GliaGatGtGktvtLqvlaeslseaGv 50 
                 G i Ga GtGktvtL+++a+  ++  v
  EPA06812.1 230 GSIPGAFGTGKTVTLHQIAKW-ADSQV 255
                 7899**************974.44444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (592 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 4201.88
//
Query:       EPA06813.1  [L=348]
Description: tyrosine--tRNA ligase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-42  145.5   0.1    2.6e-42  145.2   0.1    1.1  1  tRNA-synt_1b  tRNA synthetases class I (W and Y)
  ------ inclusion threshold ------
      0.062   12.7   0.9      0.086   12.3   0.9    1.2  1  Not3          Not1 N-terminal domain, CCR4-Not complex compon
       0.12   12.3   0.0       0.19   11.6   0.0    1.2  1  DUF4092       Domain of unknown function (DUF4092)


Domain annotation for each model (and alignments):
>> tRNA-synt_1b  tRNA synthetases class I (W and Y)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.2   0.1   4.3e-46   2.6e-42       3     291 ..      31     326 ..      29     328 .. 0.86

  Alignments for each domain:
  == domain 1  score: 145.2 bits;  conditional E-value: 4.3e-46
                   HS--EEEEEEETSSS-BGGGHHHH.HHHHHHHHTTSEEEEEEEHHHHHTTTTT-SSHHHHHHHHHHHHHHHHHHHHHTCHTTTEEEEETHHHHTTH. CS
  tRNA-synt_1b   3 erplrvysGidPTgklHlGylvpl.kklvelqkaghevffliaDlhAiigdpskaeerklrkreevlenaikaqlakgldpekaevvlqsewlehl. 97 
                   ++  + y G + +g lHlG l+++  k+ ++ kag+++++++aD+h++i+d+   +++++   +++++ a       ++ p +a++vl+s+ ++++ 
    EPA06813.1  31 NSSPKHYIGLEISGFLHLGSLISTgFKINDFVKAGVKCTIFLADWHTLINDKLGGDWEMISRVSKYYKDA-----FNLVCP-EANIVLGSDLYKEKs 121
                   567789*************777773799*************************99************999.....444555.699999999876555 PP

                   HHHHHHHHHHTTCBHHHHHHHHHCCHHCSSSC--BHHHHHHHHHHHHHHHHTCHSEEEEEGGGHHHHHHHHHHHHHHHHHSTTSS-EEEEET..... CS
  tRNA-synt_1b  98 elaellrdlgklgslnrmlqfksvkkrleegegislgeftYplLqaaDilllkadlvpgGsDQkqnielgrdlarrfnkkevfkkpegltvp..... 189
                   e++  l +++k++sl+r ++  +++ r e++e+i l+ ++Yp +qa Di +l++d+   G+DQ+++  l r++ ++++ k     p+++ ++     
    EPA06813.1 122 EYWSELVKFTKHVSLARTMRTLTIMGRSENEEKIDLAKLLYPPMQAVDIHFLDVDIAHAGMDQRKIHMLVREVFPKMKWK----VPVAVHHKllpgl 214
                   ******************************99*********************************************999....8888888844444 PP

                   ....-BBSTTSSSBTTCETTCGC-BTTCCHHHHHHHHHHCHCSTTC..SHHHHHHHHHTHHH....CHHHHHHHHCCSEEESSHHHHHHHHHCCCCH CS
  tRNA-synt_1b 190 ....lltgldGekKmSKSagnsaIfLddekesvkkkiqkavtdsde..evekllklktelsn....elierleavsgkkpkreaeellaeevtklvh 276
                          +++   KmSKS++ns If+  + ++++ ki+ka ++  +  ++  l+  k++++     + +er e+++g++ ++e+++l+ ++++k++h
    EPA06813.1 215 skpaTTNDSQILGKMSKSDPNSGIFIHNSDDEIRTKIKKAWCEEANiqNNPLLEISKHVIFHefseFKVERPEKFGGNMSYTEYSKLESDFAEKKLH 311
                   4444444444456********************************99544444333333333444499***************************** PP

                   HHHHHHHHHHHHHHH CS
  tRNA-synt_1b 277 ggdlkkalaealnel 291
                   ++dlk+ + e + ++
    EPA06813.1 312 PTDLKQTVGEYIVKI 326
                   *******99988776 PP

>> Not3  Not1 N-terminal domain, CCR4-Not complex component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.9   1.4e-05     0.086      57     150 ..     248     345 ..     245     348 .] 0.77

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.4e-05
        Not3  57 Rdqi.ktwlssneikdkkkLlenrkliEeamerFkavEkesKtK......afSkeglakaaaekldpkekekeearewlkdaideLneqvekleaeiek 148
                 R +i k+w+++ +i+++  L+ +++ i ++  +Fk vE+ +K        ++Sk  l++ +aek+ + ++ k+ + e++ ++i+ ++e+++  e+  e 
  EPA06813.1 248 RTKIkKAWCEEANIQNNPLLEISKHVIFHEFSEFK-VERPEKFGgnmsytEYSK--LESDFAEKKLHPTDLKQTVGEYIVKIISPIREKLNLSEELFEA 343
                 6667257***************************8.799888642221114454..555566666666677999***************9999988887 PP

        Not3 149 ls 150
                 ++
  EPA06813.1 344 IK 345
                 76 PP

>> DUF4092  Domain of unknown function (DUF4092)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   3.2e-05      0.19      31      69 ..     243     281 ..     220     287 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.2e-05
     DUF4092  31 dsgqiqavieklwgatadaqregykkverfhvfhdstnf 69 
                   ++i+++i+k w  +a++q++   ++++  +fh+ ++f
  EPA06813.1 243 SDDEIRTKIKKAWCEEANIQNNPLLEISKHVIFHEFSEF 281
                 44789*****************************98887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 2050.91
//
Query:       EPA06814.1  [L=67]
Description: hypothetical protein BG20_I0052 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0069   17.0   1.4     0.0073   17.0   1.4    1.1  1  Multi_Drug_Res  Small Multidrug Resistance protein


Domain annotation for each model (and alignments):
>> Multi_Drug_Res  Small Multidrug Resistance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   1.4   4.1e-07    0.0073      32      79 ..       6      56 ..       1      65 [. 0.82

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.1e-07
                    --HHHHHHHHHHHHHHHHH---...----HHHHHHHHHHHHHHHHHHHHH- CS
  Multi_Drug_Res 32 sllvivgygisfllLskalksl...pvsvAYavwsGiGtvlivlvgillfg 79
                     l++i g++++++ L++ ++++    ++  Ya  +Gi ++++ +++++lfg
      EPA06814.1  6 KLTIIGGILLAVTYLIYNYHQTvhpGIGFNYAYVTGISMMIVFIASFILFG 56
                    567888999***999999988423258999********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       766  (0.0427241); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.47
# Mc/sec: 432.88
//
Query:       EPA06815.1  [L=515]
Description: ABC1 family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-23   82.3   0.0    1.1e-22   80.4   0.0    1.9  2  ABC1      ABC1 family
  ------ inclusion threshold ------
      0.029   14.3   0.0      0.058   13.3   0.0    1.6  1  APH       Phosphotransferase enzyme family
      0.064   12.6   0.4       0.12   11.7   0.4    1.5  1  Pkinase   Protein kinase domain
        0.1   12.7   0.0       0.28   11.3   0.0    1.7  2  CesT      Tir chaperone protein (CesT) family


Domain annotation for each model (and alignments):
>> ABC1  ABC1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.4   0.0   2.4e-26   1.1e-22       6     119 .]     105     217 ..     101     217 .. 0.91
   2 ?   -1.7   0.0      0.69   3.1e+03      47      67 ..     396     416 ..     385     450 .. 0.60

  Alignments for each domain:
  == domain 1  score: 80.4 bits;  conditional E-value: 2.4e-26
        ABC1   6 kleeiFaefdeePiAaASiaqVhrAklksgeeVavKvqrpgvkkriksDlellkllakllkkfl.kelrldleelvdefskslleEldferEAknaekf 103
                 +++e+F+++d +Pi  AS++qV+r++++ g+e++vKv+rpg++k +++Dl++lk ++ ++ +f+ ++lr + ++++ +f +++ eE+d++ E++n +k+
  EPA06815.1 105 PINETFDSIDTNPISGASLGQVYRGRIH-GQEIVVKVKRPGIEKIVDEDLKVLKKILPVALRFVdPNLRFSARAMLSQFIETIHEEMDYTIESSNLKKI 202
                 799**********************996.99************************9998776652677799**************************** PP

        ABC1 104 renfaklkevkvPkvy 119
                 ++++ k ++v +P+vy
  EPA06815.1 203 KHDMLKSNMV-IPSVY 217
                 ***9987765.67775 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.69
        ABC1  47 vkkriksDlellkllakllkk 67 
                 + k+ k D++ +k+l ++l++
  EPA06815.1 396 IYKTHKVDFKFVKVLKEVLEE 416
                 556666777777766666653 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.3e-05     0.058     147     187 ..     251     287 ..     213     312 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.3e-05
                 HHHHHHHHHHHHH--SSS-EEEE-SS-SGGGEEEC..TTEE CS
         APH 147 eleeqvlaalaallpgelptvllHgDlhpgNllvdpddgrv 187
                 +l   v   +   l+   +++l H D+hpgN+ v+ ddg++
  EPA06815.1 251 KLVIDVHKVFFTMLL---RHSLFHADPHPGNISVT-DDGKL 287
                 444445555555555...9****************.66776 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.4   2.7e-05      0.12      46     153 ..     193     303 ..     168     313 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.7e-05
                 HHHHHHHHHHSCTTB--...EEEEEEE.SSEEEEEEE--TTEBHHHHHH.HHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE CS
     Pkinase  46 lrEikilkklkhpnivr...lyevfee.kdelylvleyveggeladlle.rkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKi 139
                 + E + lkk+kh+ +     + +v+ + +++ +l +ey++g +++++   +++ ++ +++   +++++     l +++++H D  p Ni + ++g+l +
  EPA06815.1 193 TIESSNLKKIKHDMLKSnmvIPSVYDDySSKNVLTMEYIPGIKITNVDAlDEKGIDRQKLVIDVHKVFFT--MLLRHSLFHADPHPGNISVTDDGKLIL 289
                 556666666666554331102233333566778999****999888877555556666555555555544..4567889******************** PP

                 -SGTTSEESSSSCS CS
     Pkinase 140 tDFGlakelesssk 153
                  D+G++ +l+++++
  EPA06815.1 290 YDYGMVGRLDNETR 303
                 ********999875 PP

>> CesT  Tir chaperone protein (CesT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   6.1e-05      0.28      63     116 ..     263     315 ..     254     316 .. 0.84
   2 ?   -3.6   0.0       2.6   1.2e+04      18      45 ..     454     482 ..     451     489 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.1e-05
                 HHHHHHCHHSCTTT-EEEEETTTTEEEEEEEEEGCC--HHHHHHHHHHHHHHHH CS
        CesT  63 rlLeaNllgartaggalgldeesglllLwarlelesldeeaLeallealvalae 116
                  lL+++l++a++++g++++  ++g+l+L+   +  +ld+e+  +l++ ++al+e
  EPA06815.1 263 MLLRHSLFHADPHPGNISVT-DDGKLILYDYGMVGRLDNETRMRLIRLYLALVE 315
                 69******************.********9999999998876666666666665 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2.6
                 STTSEEEEEE.TTTEEEEEEEESTTEEEE CS
        CesT  18 dengvcsLsi.dddvllllleedsdeLll 45 
                 den +++L    + ++ll  +  s++++l
  EPA06815.1 454 DENRSIQLNTkPKSNVLLSGSILSSAIFL 482
                 78888888888888888877777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (515 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       720  (0.0401584); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.48
# Mc/sec: 3234.08
//
Query:       EPA06816.1  [L=275]
Description: CBS domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.1e-43  146.5   7.3    2.8e-11   43.7   0.1    4.1  4  CBS          CBS domain
  ------ inclusion threshold ------
      0.025   14.3   0.0      0.055   13.2   0.0    1.5  1  Sigma54_DBD  Sigma-54, DNA binding domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   0.1     2e-14   1.7e-10       3      51 ..       5      51 ..       3      56 .. 0.90
   2 !   23.2   0.0   7.6e-09   6.8e-05       5      55 ..      73     121 ..      65     123 .. 0.85
   3 !   40.6   0.1     3e-14   2.7e-10       3      54 ..     133     184 ..     131     187 .. 0.93
   4 !   43.7   0.1   3.1e-15   2.8e-11       1      56 [.     219     274 ..     219     275 .] 0.96

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 2e-14
                HHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHH CS
         CBS  3 dimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDl 51
                di+ ++++++  ++t++++l+++ e+++srl VV e+gk++Gi+t++D+
  EPA06816.1  5 DIC-KKPISILKNSTISDILKKLLENNLSRLIVV-ENGKPIGIITEKDV 51
                666.5666**************99*******999.9************7 PP

  == domain 2  score: 23.2 bits;  conditional E-value: 7.6e-09
                 SBSSCEEEETTSBHHHHHHHHHHHTSSEEEE.EETTTBEEEEEEHHHHHHHH CS
         CBS   5 mtrdvvtvppdttleealelmrekgvsrlPV.VdedgklvGivtlrDllral 55 
                 m r+++++  ++t e+ +e+m ekgvs+l + +   +++ Gi+t++Dl+++ 
  EPA06816.1  73 M-RPILFIQDNSTPEKSAEIMLEKGVSSLAIgT--KDEIDGIFTKTDLVKYY 121
                 3.6788***********************8844..555***********985 PP

  == domain 3  score: 40.6 bits;  conditional E-value: 3e-14
                 HHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEE.ETTTBEEEEEEHHHHHHH CS
         CBS   3 dimtrdvvtvppdttleealelmrekgvsrlPVV.dedgklvGivtlrDllra 54 
                 d+mt+++v+ +  ++l +++++m+e+++sr+ +V d ++k+vGi++ rDl+r 
  EPA06816.1 133 DFMTHEYVFTHTAAPLFKVVRKMIENKISRI-IVkDQNEKPVGIISFRDLFRI 184
                 99*****************************.99788889**********985 PP

  == domain 4  score: 43.7 bits;  conditional E-value: 3.1e-15
                 HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
         CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                 ++d+m++ +++++ d +l+ a +l+ e+++s+l V+d+++ +vGi++++D+l+a++
  EPA06816.1 219 ARDVMSKGIISIKFDKDLKNACKLILENNISGLAVLDGNNSIVGIISKTDILKAIK 274
                 58**********************88***************************985 PP

>> Sigma54_DBD  Sigma-54, DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   6.2e-06     0.055      61     111 ..     155     205 ..     149     214 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.2e-06
                  SXHHHHHHHHHHXEEEXSSXEEECSCCXXXCSSTSSBHHTHHHHCCTHHHH CS
  Sigma54_DBD  61 lhesTvSRvvsnkyiktprGvfelkafFsssvsseeggeasaeaikalikk 111
                  + e  +SR++ +   + p+G+++++ +F  s++  ++++ s  +i ++i+k
   EPA06816.1 155 MIENKISRIIVKDQNEKPVGIISFRDLFRISIELGSEEDDSGFTISEQIRK 205
                  67889*******************************9999*9999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1722.60
//
Query:       EPA06817.1  [L=206]
Description: transcriptional regulator, Sir2 family, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.6e-53  180.1   0.0    4.4e-53  179.8   0.0    1.1  1  SIR2          Sir2 family
  ------ inclusion threshold ------
      0.056   13.2   0.0        6.8    6.4   0.0    2.3  2  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain


Domain annotation for each model (and alignments):
>> SIR2  Sir2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.8   0.0   4.9e-57   4.4e-53       1     177 []      27     196 ..      27     196 .. 0.94

  Alignments for each domain:
  == domain 1  score: 179.8 bits;  conditional E-value: 4.9e-57
                 -GGGGGGGT---SSSTTSHHHHSCHHHHSSHHHHHHHHHHHHHHHHHHHHHHHCCTSS--HHHHHHHHHHHTTCEEEEEES-SSSHHHHTT-SSEEETT CS
        SIR2   1 GAGiStesGipdfRskeGlyaklakeelaspealfskkllveevfyniarellaeeaepnaaHkalkklekkgkllrliTQNiDgLekkaGskkvvelH 99 
                 GAGiS esGip+fR+k+Gl+++++  +la+ +a+ ++++lv+e +yn +r+ +  + epn  Hka+++lek    + ++TQNiDgL+++aGs+ v+elH
  EPA06817.1  27 GAGISQESGIPTFRGKDGLWKNHDVMQLATIDAFYDHPKLVWE-WYNERRKNIF-SSEPNLGHKAIAELEKFV-KVIVLTQNIDGLHQRAGSTDVLELH 122
                 9******************************************.*****99998.79*************988.67899******************** PP

                 EEEEEEEETTTSBEEECCGGHCHHHCCTT.B-TTTCCBEEEEE--CTSB-S.HHHHHHHHHHHH-SEEEEES--STSTT CS
        SIR2 100 GslakakcvkcekkldkeelqeeieaekvpecekcgkllkpdvvfFGealp.dklkkliekveeadlllviGtSlkVap 177
                 Gs+ +++c++c+ k +       +e +++p  +kcg++l+p+vv+FGe lp d ++++i +++++dl++v+GtSl V p
  EPA06817.1 123 GSIVTIRCTNCDFKGQI-----LTEFTEIPPLCKCGNILRPNVVWFGEPLPqDVWQQAIIHASRCDLMIVVGTSLVVSP 196
                 ************96665.....334455677899*****************999***********************98 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0   0.00076       6.8       2      25 ..      10      33 ..       9      40 .. 0.87
   2 ?    4.5   0.0     0.003        26      75      88 ..     179     192 ..     167     205 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.00076
                  HHHHHHHHH-SSEEEEE-CHHCHT CS
  TPP_enzyme_M  2 ekaaellkaakrpvilvGggvars 25
                  e +++ +k +k++v++ G g++++
    EPA06817.1 10 ESIIDKIKDSKKIVFVTGAGISQE 33
                  67899***************9976 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.003
                   HHH-SEEEEES-SS CS
  TPP_enzyme_M  75 leeaDlvlalGarf 88 
                   + ++Dl++++G+ +
    EPA06817.1 179 ASRCDLMIVVGTSL 192
                   578********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      637  (0.035529); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1357.40
//
Query:       EPA06818.1  [L=300]
Description: lactate/malate dehydrogenase, NAD binding domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-23   83.5   1.3    2.7e-23   82.6   1.3    1.4  1  Ldh_1_N          lactate/malate dehydrogenase, NAD binding do
    1.7e-21   76.9   0.4    4.2e-21   75.6   0.1    1.7  2  Ldh_1_C          lactate/malate dehydrogenase, alpha/beta C-t
    2.4e-06   27.2   0.3    1.2e-05   25.0   0.1    2.1  2  Glyco_hydro_4    Family 4 glycosyl hydrolase
     0.0033   17.5   1.5     0.0051   16.9   0.4    1.8  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
     0.0035   17.3   0.2      0.011   15.7   0.2    2.0  1  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
  ------ inclusion threshold ------
      0.011   16.3   0.3       0.04   14.5   0.2    2.1  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
      0.034   14.4   0.8        0.9    9.8   0.2    2.5  2  LPD3             Large polyvalent protein-associated domain 3
      0.079   13.2   0.1       0.25   11.6   0.1    2.0  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma


Domain annotation for each model (and alignments):
>> Ldh_1_N  lactate/malate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.6   1.3   1.2e-26   2.7e-23       3     141 .]       2     137 ..       1     137 [. 0.94

  Alignments for each domain:
  == domain 1  score: 82.6 bits;  conditional E-value: 1.2e-26
                 EEEETTTSHHHHHHHHHHHHTTSSSEEEEE-SSHHHHHHHHHHHHHCHCCSTS-EEEEESSGGGGTTESEEEE--S-SS-TTTTHHHHHHHHHHHHHHH CS
     Ldh_1_N   3 vavvGaaGgiGqslalllankkladelaLlDiakekleGvaldlshistflsvkvkvsekeeealkdadvvvitagvprkpGetRddLlkvNakIvkei 101
                 ++++G+ G++G ++a+l  ++ l d + +++ +k+k+ G+ald+s++    s  ++ + ++ + ++++++vvita+      ++R +++++ +k++kei
  EPA06818.1   2 ISIIGS-GKVGTAIAFLCITNSLDD-ILFVNRTKSKAIGEALDISNAIPANSNVTIHGTDDFSKISGSNIVVITASTGTY-LKSRTEMMDAQVKMIKEI 97 
                 89****.**************9988.99******************9888877777778****************98755.599*************** PP

                 HHHHHHHTTTSEEEE-SSSHHHHHHHHHHHHTS-GGGEEE CS
     Ldh_1_N 102 veaiakvapnaivlvvsNPvdiltevlkkasglpkkrvig 141
                  ++i+k++p+aivlvvsNP d+lt +++k +++++++vig
  EPA06818.1  98 SNKIKKYCPSAIVLVVSNPLDVLTFIFQKETQFSRNKVIG 137
                 **************************************98 PP

>> Ldh_1_C  lactate/malate dehydrogenase, alpha/beta C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.89     2e+03     137     155 ..      82     100 ..      34     109 .. 0.58
   2 !   75.6   0.1   1.9e-24   4.2e-21       2     161 ..     141     298 ..     140     300 .] 0.87

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.89
                 ------HHHHHHHHHHHHH CS
     Ldh_1_C 137 eilklndfeeekleksvke 155
                 +  ++ d + +++++  ++
  EPA06818.1  82 SRTEMMDAQVKMIKEISNK 100
                 3333444444444333333 PP

  == domain 2  score: 75.6 bits;  conditional E-value: 1.9e-24
                 HHHHHHHHHHHHHHHTS.-GGGEE--EEBSSST........ETTEEHHHHHTTSTTSTHHHHHHHHHHHHHHHHHHHHHHTTSSSS-HHHHHHHHHHHH CS
     Ldh_1_C   2 tLDivRaktflaekagv.tprsvkvtViGgHsg........vtiipllsqvkellklsekqleeliervqnggdevvkakkGagsatlsmAvAgakfve 91 
                 +LD+ R++++l+ek+g+ + +  ++ V+G+H++        v+i ++    + +  l++ +++++ +++qn   ++   k     +  ++A+   ++++
  EPA06818.1 141 SLDSSRFRYLLSEKFGIkQSQITDALVMGEHGDsmvpifsrVKINGK----NVSEMLNDSDKKTISTETQNYWRSLRLLK---TRSEFGIAKNTFDVIR 232
                 6****************666677**********88775555444444....55567889999999999999766665555...34899*********** PP

                 HHHTTHTEEEEEEEEEESCCCECCSSEEEEEEEEEEETTEEEEE-------HHHHHHHHHHHHHHHHHHH CS
     Ldh_1_C  92 allrdtkeilsagvyldgevglkdqeieyfsvPvvlgknGvekvleilklndfeeekleksvkeLkkeie 161
                 a++++ + +++a+++l+ge+g kd   + +++Pv ++knG+++++e +kln++e++ l++s++++++ i+
  EPA06818.1 233 AIIDNDELVIPASIVLNGEYGEKD---VALGIPVKINKNGIKEIIE-IKLNEQENKLLKISAQTIRNYIK 298
                 ************************...9******************.*******************9887 PP

>> Glyco_hydro_4  Family 4 glycosyl hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.39   8.7e+02      38      89 ..      31      83 ..       2      91 .. 0.57
   2 !   25.0   0.1   5.3e-09   1.2e-05     120     166 ..      90     138 ..      84     143 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.39
                   HHHHHHHHHHHHHHHH.HCTTTCEEEEESSHHHHHTT-SEEEE---TT.HHHHH CS
  Glyco_hydro_4 38 eerldaiqtlakklve.eagadlkieattdrkealkdadfVitairvG.lekar 89
                    ++ +ai +++++ +   a++++ i+ t+d  + ++  ++V++++  G ++k+r
     EPA06818.1 31 RTKSKAIGEALDISNAiPANSNVTIHGTDDFSK-ISGSNIVVITASTGtYLKSR 83
                   445555555555544314566677777766655.67888888888888644444 PP

  == domain 2  score: 25.0 bits;  conditional E-value: 5.3e-09
                    HHHHHHHHHHHHHHH-TTSEEEE-SSSHHHHHHHHHHHSTT..SEEEEE CS
  Glyco_hydro_4 120 tipvlleIakdieelcPdawvlnytNPaavvteallrlvpn..ikavgl 166
                    +++++ eI ++i+++cP a vl  +NP+ v+t +  + +++   k++g+
     EPA06818.1  90 QVKMIKEISNKIKKYCPSAIVLVVSNPLDVLTFIFQKETQFsrNKVIGI 138
                    799********************************99876511577887 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.4   2.3e-06    0.0051      15      99 ..       2      90 ..       1     102 [. 0.73
   2 ?   -1.8   0.0       1.3     3e+03      27      82 ..     189     244 ..     185     247 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.3e-06
                  EEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHH....HHHHHHH.T.ET-EEEEGCGHHHHHHT-SEEEE-SSSSS-SB-HHHHHCCH CS
  Shikimate_DH 15 vlliGaGemaelvakhLlakgvkkvvvaNRtlera....kelaeel.kgeeiealkleelkellaeadvvisataseepilekeeveeal 99
                  + +iG G++++ +a   +++++++++ +NRt ++a     ++ + +  + +++++  ++ +  ++ +++v++  ++ +++ ++ e+++a+
    EPA06818.1  2 ISIIGSGKVGTAIAFLCITNSLDDILFVNRTKSKAigeaLDISNAIpANSNVTIHGTDDFS-KISGSNIVVITASTGTYLKSRTEMMDAQ 90
                  679*****************************99733225667777333455555566655.6677777777667777777766666655 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.3
                   HHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE- CS
  Shikimate_DH  27 vakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisa 82 
                   v ++L ++  k +     ++ r  +l +  ++  i   +++ +++++++ ++vi a
    EPA06818.1 189 VSEMLNDSDKKTISTETQNYWRSLRLLKTRSEFGIAKNTFDVIRAIIDNDELVIPA 244
                   55556666666666666667777777777777777888888888888888888865 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.2     5e-06     0.011       2      79 ..       2      76 ..       1     141 [. 0.77

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5e-06
                    EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHHSSBTTTBTT----TTEEEES-HHHHHTT--EEEE---H CS
  NAD_Gly3P_dh_N  2 iavlGaGswGtalAkvlaenghevrlwvreeelieeineehenvkyLpgiklpenlvattdlaealkgadiivlvvPs 79
                    i+++G+G+ Gta+A ++  n  +  l+v++ +  ++i e+   ++ +p  + + +++ t+d+ + ++g++i+v+  ++
      EPA06818.1  2 ISIIGSGKVGTAIAFLCITNSLDDILFVNRTK-SKAIGEALDISNAIPA-NSNVTIHGTDDFSK-ISGSNIVVITAST 76
                    89*******************99889888765.5677777777777774.45556666666654.5667777766554 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.2   1.8e-05      0.04       2      50 ..       2      55 ..       1      92 [. 0.74
   2 ?   -1.8   0.0       2.1   4.8e+03      59      59 ..     166     166 ..     124     219 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.8e-05
                   EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC........-EE CS
  F420_oxidored  2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg........vkv 50
                   i iiG+G++g a+a  ++++     +i+++ +r+++ka   a +++        v++
     EPA06818.1  2 ISIIGSGKVGTAIAFLCITNS--LDDILFV-NRTKSKAIGEALDISnaipansnVTI 55
                   89******************9..99***99.88888887766666645555544444 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.1
                    H CS
  F420_oxidored  59 a 59 
                    +
     EPA06818.1 166 L 166
                    1 PP

>> LPD3  Large polyvalent protein-associated domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.086   1.9e+02      31      48 ..     181     198 ..     158     213 .. 0.86
   2 ?    9.8   0.2    0.0004       0.9      26      58 ..     257     286 ..     246     295 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.086
        LPD3  31 eieftrkgikkilsdkah 48 
                  +++++k+++++l+d+ +
  EPA06818.1 181 RVKINGKNVSEMLNDSDK 198
                 699**********96544 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0004
        LPD3  26 kdtgkeieftrkgikkilsdkahskneeklkav 58 
                  ++g+ ++++++gik+i+     + ne+ +k++
  EPA06818.1 257 VALGIPVKINKNGIKEIIE---IKLNEQENKLL 286
                 4699**************9...65555555554 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00011      0.25       1      61 [.       2      60 ..       2     108 .. 0.77
   2 ?   -1.9   0.0       1.7   3.7e+03     104     123 ..     203     222 ..     183     228 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                     EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHH CS
  Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyea 61
                     + iiG+G+vG a+a l+  ++    +i  + r+k+k+  +a ++++    +  +++   ++
       EPA06818.1  2 ISIIGSGKVGTAIAFLCITNSLD--DILFVNRTKSKAIGEALDISNAIPANSNVTIHGTDD 60
                     569****************9977..9**********7777666655555555555555555 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.7
                      GCCSCHCCSHHHHHTHHHHH CS
  Sacchrp_dh_NADP 104 eertnyalreavlklkekak 123
                       e +ny+ + ++lk ++++ 
       EPA06818.1 203 TETQNYWRSLRLLKTRSEFG 222
                      46689999999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       969  (0.0540465); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 1936.01
//
Query:       EPA06819.1  [L=48]
Description: hypothetical protein BG20_I0978 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 316.41
//
Query:       EPA06820.1  [L=434]
Description: amino acid permease [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.7e-50  169.6  61.1      2e-49  168.6  61.5    1.3  1  AA_permease_2   Amino acid permease
    5.3e-42  144.0  53.9    8.5e-42  143.3  53.9    1.3  1  AA_permease     Amino acid permease
    6.7e-06   25.1  23.9    6.7e-06   25.1  23.9    2.7  2  Spore_permease  Spore germination protein
  ------ inclusion threshold ------
       0.55   10.4   5.6       0.12   12.5   0.6    2.3  2  TMEM223         Transmembrane protein 223


Domain annotation for each model (and alignments):
>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.6  61.5   4.5e-53     2e-49       2     417 ..       9     412 ..       8     421 .. 0.84

  Alignments for each domain:
  == domain 1  score: 168.6 bits;  conditional E-value: 4.5e-53
  AA_permease_2   2 sllsafalvigsvigsgifvkn..laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaaf.gkkvaflsawfnwfayvpvlas 94 
                    +l+ +++  +g+++g+gi+v    +a+ +g a+++ +++++++  l  +l yaEls+ +p+   +y+++k+af ++++af+ +w++++  ++++a+
     EPA06820.1   9 GLFHLTMYGVGLILGAGIYVLIgeAAGFAGDAVWIAFVLGSIVA-LFAGLSYAELSAIFPKAAAEYTFVKNAFkNNFFAFIIGWLTVITSMITAAT 103
                    689999**************987566669999999999999998.78999***********************678999***************** PP

  AA_permease_2  95 ilsvaasyllnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgilkillpliiliilglitvdgggfsslstetdtffpngwpgv 190
                    ++  +++y+  +l+       +++++ ai+++ +++++n +gikes++ +++ +i+     li++i++g+ + d++  +          p+g +g+
     EPA06820.1 104 VALGFGGYFSEFLN-------IPIVISAILLIGILTIVNFIGIKESSWTNTVFTIIEAA-GLILIIVIGFTISDPDPVNY------FESPTGFTGI 185
                    ***********996.......478899*******************************6.7788999******9987762......23577***** PP

  AA_permease_2 191 llgllivlwsfdGfesaanvseevkk.kd.vpkaifigllivlvlyllvniaflgvvpddeianlsnlgsvaalffeavggkvvaiivvilialsl 284
                    + ++  ++++f+Gfe  anv+eev++ k+ +p+ai+++++i++ +y+lv++a++ +v+++ ++ +s  + +a++  + +g + ++ii++ ++ +++
     EPA06820.1 186 IIAFVLIFFAFIGFEDMANVAEEVRNpKKiIPRAIILSVIISGTIYVLVSLAVVRAVNWEDLSLSSA-P-LAEVAKRGLG-TQGQIIFSGIALFAI 278
                    ***********************8887655*********************************9776.3.3444444444.777777777777777 PP

  AA_permease_2 285 lgaintavigssrvlealardgvlPrffakvn.kfgspiraiiltaivslillllfllassaaynfllsvsslgliisyllliigalilrkkrphl 379
                       ++  +++ +r+++ +ard+ +P+ +akv+ k+++p++aii++++v+ i +   +++   ++ +++++++++++i ++++ ++++ilr+++p+ 
     EPA06820.1 279 TNTVLITLVAGARMIYGMARDRSFPNILAKVHsKTKTPWVAIITIMLVA-IGF---SFI--GDIVIVANITVFAVVITFGAINLSVIILRYTEPNI 368
                    77777778899*************************************9.544...444..389******************************** PP

  AA_permease_2 380 krpgkilvaiig.....alfllfll.valffppkgpatqssliy 417
                    +r+ +i+v+i       +++l++   +a+ f  ++  +++++i+
     EPA06820.1 369 ERKFRIPVNIGKfpvlpLFGLVISGyMAFQFEMEVMLVGFGIIV 412
                    99999999986544333222222221333344444445555544 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.3  53.9   1.9e-45   8.5e-42       1     393 [.      12     364 ..      12     421 .. 0.83

  Alignments for each domain:
  == domain 1  score: 143.3 bits;  conditional E-value: 1.9e-45
  AA_permease   1 hvlvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgp.elGfviGlnylfswitvlaleltaa 97 
                  h+++  +g + G+g++v +g +++ aG  ++++a++l+ +v ++++ls +e++ ++pk+++ yt++++  +   ++f iG++   + it ++ + t+a
   EPA06820.1  12 HLTMYGVGLILGAGIYVLIGEAAGFAGD-AVWIAFVLGSIVALFAGLSYAELSAIFPKAAAEYTFVKNAFKNnFFAFIIGWL---TVITSMITAATVA 105
                  899*************************.99*************************************9999799*******...3333333334444 PP

  AA_permease  98 siliqfwelvtdlpkawvtgavflvvlliinlvgvkvygeaefilalikiiaiiafiivgiillaggkpnkgagfrflgdngsifknnlppgfakeee 195
                    + ++ + +  +p + + +++++++l+i+n++g+k +  + +++++i    +i  i++g+ ++++ +p +      +           p g      
   EPA06820.1 106 LGFGGYFSEFLNIP-IVISAILLIGILTIVNFIGIKESSWTNTVFTIIEAAGLILIIVIGF-TISDPDPVNY-----FE---------SPTG------ 181
                  44444554455666.6666999**************9999999999999999999999994.6666666665.....22.........3344...... PP

  AA_permease 196 gafknfisvfvivvfaftGielvaiiagEvkdPeksiPkailqvviritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplin 293
                    f+++i++fv ++faf G+e  a++a+Ev++P+k iP+ai+  vi+ + +Yvl++l+++  v++ dl+l +     a++ +++ + +g  + + ++ 
   EPA06820.1 182 --FTGIIIAFVLIFFAFIGFEDMANVAEEVRNPKKIIPRAIILSVIISGTIYVLVSLAVVRAVNWEDLSLSS-----APLAEVAKRGLGTQG-QIIFS 271
                  ..*****************************************************************99999.....455666666666555.67777 PP

  AA_permease 294 aviltaalssansslysasRvlyslakdglaP.kvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisaliglivwlliilsylrf 390
                   + l a++++++  l+++ R++y +a+d+ +P   +k++sk + P++ai+  m+++  + ++     +    + ++ +i+ ++ +i++++i+ls + +
   EPA06820.1 272 GIALFAITNTVLITLVAGARMIYGMARDRSFPnILAKVHSKTKTPWVAIITIMLVAIGFSFI----GD----IVIVANITVFAVVITFGAINLSVIIL 361
                  7889999*************************7788999*************9999888744....44....45568999**************9999 PP

  AA_permease 391 Rka 393
                  R +
   EPA06820.1 362 RYT 364
                  976 PP

>> Spore_permease  Spore germination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1  23.9   1.5e-09   6.7e-06      12     246 ..      18     254 ..      10     288 .. 0.84
   2 ?   -2.6  13.0      0.43   1.9e+03      98     163 ..     300     365 ..     281     431 .. 0.73

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.5e-09
  Spore_permease  12 vsfqlGvgiltlprsvaeqatpdgWisvllagiiililvllmlkllkkfpektl.iellkkilg.kwLGsllsilfilyFlllaafelRefseli 104
                     v  +lG+gi +l + +a  a+   Wi+ +l+ i++l++ l + +l+  fp+    + ++k+ ++  + +++++ l ++  +++aa+++  f+  +
      EPA06820.1  18 VGLILGAGIYVLIGEAAGFAGDAVWIAFVLGSIVALFAGLSYAELSAIFPKAAAeYTFVKNAFKnNFFAFIIGWLTVITSMITAATVALGFGGYF 112
                     5789****************999***************************986548999999997788888888888888888888888887755 PP

  Spore_permease 105 qvflledtplwiiilllllvilYlvvkGieslareflfiivilliilllillfslklaeiknlrPv.lgngikpvlkslkttslsflgveillll 198
                     + fl  ++p++i  +ll+ +   + + Gi++ +  + ++++i  + l+li+++ + + +++ +      +g+  ++ ++  + ++f+g+e +  +
      EPA06820.1 113 SEFL--NIPIVISAILLIGILTIVNFIGIKESSWTNTVFTIIEAAGLILIIVIGFTISDPDPVNYFeSPTGFTGIIIAFVLIFFAFIGFEDMANV 205
                     4443..566666666666666666667***9999999999999999999999999999999887654679************************* PP

  Spore_permease 199 vpflkdkkkv.kkaallgvlistllyllttlivilvlsveqlkkatwpt 246
                      + ++++kk+  +a++l+v+is+ +y+l+ l v+ +   e l+ +  p+
      EPA06820.1 206 AEEVRNPKKIiPRAIILSVIISGTIYVLVSLAVVRAVNWEDLSLSSAPL 254
                     ******9996269****************99999888777776666555 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.43
  Spore_permease  98 Refseli.qvflledtplwiiilllllvilYlvvkGieslareflfiivilliilllillfslklae 163
                     R+f +++ +v + ++tp ++ii ++l+ i +  ++ i  +a  + +++v++++  + +++++l++ e
      EPA06820.1 300 RSFPNILaKVHSKTKTPWVAIITIMLVAIGFSFIGDIVIVAN-ITVFAVVITFGAINLSVIILRYTE 365
                     6666666256778899*999**99999999***********6.444444444444444444444444 PP

>> TMEM223  Transmembrane protein 223
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.6   2.7e-05      0.12      14     117 ..     270     377 ..     264     380 .. 0.89
   2 ?   -1.7   0.4      0.62   2.8e+03      66      81 ..     402     417 ..     394     424 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.7e-05
     TMEM223  14 frllglfaivqlifWsyl..aslafttlkdteveseekeeeelssnkkrvgltlicllvgvlilllgllfplRsvkkvvllkggkt..veivTyapfgk 108
                 f  + lfai+++++ + +  a + + + +d+++ +  +++++++++ +   +t++++++g+++++ +++++  +v  vv++ g+ +  v i  y+  ++
  EPA06820.1 270 FSGIALFAITNTVLITLVagARMIYGMARDRSFPNILAKVHSKTKTPWVAIITIMLVAIGFSFIGDIVIVANITVFAVVITFGAINlsVIILRYTEPNI 368
                 777899999999998888666788899999999999999999999999999*******************************99884577889999999 PP

     TMEM223 109 krsfevplk 117
                 +r+f++p++
  EPA06820.1 369 ERKFRIPVN 377
                 9****9986 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.62
     TMEM223  66 icllvgvlilllgllf 81 
                  ++lvg++i+++g++f
  EPA06820.1 402 EVMLVGFGIIVIGIMF 417
                 4567888888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1042  (0.0581181); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.77u 0.34s 00:00:01.11 Elapsed: 00:00:00.49
# Mc/sec: 2670.77
//
Query:       EPA06821.1  [L=85]
Description: transcriptional regulator, AsnC family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.1e-08   32.8   0.1    5.3e-08   32.7   0.1    1.1  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.1     3e-12   5.3e-08      13      75 .]      19      81 ..       6      81 .. 0.90

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 3e-12
                    HHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEEE CS
  AsnC_trans_reg 13 leefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivlet 75
                    + ++++ la+ +   e+  v G yd++lk  + d e l+ ++ +k++++  +++t t++v+e+
      EPA06821.1 19 IADIKRILANEEMSYEVQGVYGVYDIVLKLSSNDAEKLRSIITNKIRKIGKIQSTLTMMVIEE 81
                    6778888889999999********************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 588.41
//
Query:       EPA06822.1  [L=54]
Description: hypothetical protein BG20_I0977 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       136  (0.00758548); expected 358.6 (0.02)
Passed bias filter:                      127  (0.0070835); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 368.43
//
Query:       EPA06823.1  [L=122]
Description: hypothetical protein BG20_I1001 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-19   70.5   0.2    1.3e-18   67.4   0.2    1.9  1  UPF0020          Putative RNA methylase family UPF0020
    2.4e-11   43.8   0.0    1.3e-09   38.1   0.1    2.1  2  N6_N4_Mtase      DNA methylase
    5.4e-10   39.3   0.0    5.8e-10   39.2   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
    4.8e-09   36.8   0.0    5.6e-09   36.6   0.0    1.1  1  Methyltransf_25  Methyltransferase domain
    2.3e-06   27.4   0.0    2.7e-06   27.2   0.0    1.1  1  Cons_hypoth95    Conserved hypothetical protein 95
    8.9e-06   26.3   0.0      1e-05   26.1   0.0    1.1  1  Methyltransf_11  Methyltransferase domain
    5.4e-05   22.6   0.0      7e-05   22.2   0.0    1.2  1  N6_Mtase         N-6 DNA Methylase
    0.00011   21.8   0.0      0.015   14.7   0.0    2.1  2  AviRa            RRNA methyltransferase AviRa
    0.00013   21.6   0.0    0.00013   21.5   0.0    1.2  1  Methyltransf_5   MraW methylase family
    0.00028   20.5   0.0    0.00034   20.2   0.0    1.2  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    0.00068   19.1   0.0    0.00088   18.7   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
     0.0011   18.8   0.0     0.0011   18.7   0.0    1.1  1  Met_10           Met-10+ like-protein
     0.0011   18.5   0.0     0.0011   18.5   0.0    1.0  1  MTS              Methyltransferase small domain
     0.0027   17.1   0.0     0.0027   17.1   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
       0.01   15.6   0.0      0.011   15.4   0.0    1.3  1  MethyltransfD12  D12 class N6 adenine-specific DNA methyltran
  ------ inclusion threshold ------
      0.014   14.8   0.0      0.014   14.7   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
      0.042   14.6   0.0      0.051   14.3   0.0    1.2  1  Methyltransf_12  Methyltransferase domain


Domain annotation for each model (and alignments):
>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.4   0.2   1.2e-21   1.3e-18      20     154 ..       1     107 [.       1     118 [. 0.93

  Alignments for each domain:
  == domain 1  score: 67.4 bits;  conditional E-value: 1.2e-21
                 HHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--ST CS
     UPF0020  20 lvrlagwkpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklygsDldrrvvqgareNaekagvgdliefsqadaakLrlk 118
                 +++l g+k+ge+  DP+CG+Gt l+Ea  +g +++                          g+D+d+++ + ++eN+ + g + +i   + d+ +L+++
  EPA06823.1   1 MINLIGLKEGEVVCDPFCGTGTTLLEAESMGIHAI--------------------------GLDFDEKMFKISKENLDANGYNSKI--IKGDFSQLTRM 71 
                 899********************************..........................*******************999876..7889*****99 PP

                 TS---EEEE----------HHHHHHHHHHHHHHHHH CS
     UPF0020 119 egevdvivtnpPYGerlgskkalekLYseflrelkr 154
                  +e+d ivt++PYG + +s ++ e+L ++f  +l +
  EPA06823.1  72 IDEFDGIVTDLPYGTASKSSENPEELMKKFVATLPK 107
                 99****************************998876 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.1   1.2e-12   1.3e-09     187     231 .]       5      49 ..       1      49 [. 0.93
   2 ?    4.0   0.0     0.033        35       2      37 ..      76     107 ..      75     121 .. 0.72

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 1.2e-12
                  HHS-TT-EEEETT-TTTHHHHHHHHTT-EEEEEESSHHHHHHHHH CS
  N6_N4_Mtase 187 lstkkgdivlDpFaGSGtTavaakelgrkfiGieieeeyvelaek 231
                  + +k+g++v DpF+G+GtT+ +a+++g ++iG + +e+ ++++++
   EPA06823.1   5 IGLKEGEVVCDPFCGTGTTLLEAESMGIHAIGLDFDEKMFKISKE 49 
                  56899***********************************99885 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.033
                  EEEEE--SSSSSCS.....GCCGCCHHHHHHHHHHH CS
  N6_N4_Mtase   2 dlivtdpPYntgkdyendeqyeeedsyeeyleflek 37 
                  d ivtd PY+t ++     +++ e+ +++++  l k
   EPA06823.1  76 DGIVTDLPYGTASK----SSENPEELMKKFVATLPK 107
                  569*********99....566666666666655555 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   0.0   5.5e-13   5.8e-10       2      93 ..       8      97 ..       7     118 .. 0.80

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 5.5e-13
  Methyltransf_31  2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnevl....naladpdki 93
                     ++g +v+D+ CGtG+ ++e+   +  +++ +G+D++e++ + ++en++ +g+ n +  +gd+ +l      + fD i+++ +         +p++ 
       EPA06823.1  8 KEGEVVCDPFCGTGTTLLEAE-SM--GIHAIGLDFDEKMFKISKENLDANGY-NSKIIKGDFSQLTRM--IDEFDGIVTDLPYgtasKSSENPEEL 97
                     67889**************99.54..69************************.8**********8853..278******96655444444444444 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.0   5.3e-12   5.6e-09       1      71 [.      13      81 ..      13     107 .. 0.84

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 5.3e-12
                     EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEE CS
  Methyltransf_25  1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvss 71
                     v d  cGtG+++l++    g  + +g+D++e+m ++ +e+++++g+n ++++gd+++l    ++fD +v  
       EPA06823.1 13 VCDPFCGTGTTLLEAESM-G-IHAIGLDFDEKMFKISKENLDANGYNSKIIKGDFSQLTRMIDEFDGIVTD 81
                     67888**********999.5.**************************************9999****9983 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.0   2.5e-09   2.7e-06      42     136 ..      10      97 ..       2     119 .. 0.80

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 2.5e-09
                    C-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEEEE--SSSTTCH.HHHHHHH CS
  Cons_hypoth95  42 garvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdivflDPPyakellieevlell 136
                    g+ v D f+G+G+  lEA S g  +a+ ++ d++++ki kenl++ + ++   ++++ ++++l +      efd +  D Py +     e  e+l
     EPA06823.1  10 GEVVCDPFCGTGTTLLEAESMG-IHAIGLDFDEKMFKISKENLDANGYNS---KIIKGDFSQLTRM---IDEFDGIVTDLPYGTASKSSENPEEL 97 
                    66789*****************.578999******************774...6677777777676...468**********9876544444444 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   9.5e-09     1e-05       5      84 ..      18     101 ..      14     113 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 9.5e-09
                      -TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCT.SS-TT-EEEEEEES....-CCC-CCHHHHHHHH CS
  Methyltransf_11   5 cGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaekl.pfednsfDlvvsse....vlhhvedpekalkei 84 
                      cGtG  + + ++ g + +g+D++++m k++ke+   +g + +++++d+++l  + d  fD +v       +    e+pe+++k++
       EPA06823.1  18 CGTGTTLLEAESMGIHAIGLDFDEKMFKISKENLDANGYNSKIIKGDFSQLtRMID-EFDGIVTDLpygtASKSSENPEELMKKF 101
                      ***************************************99*********945665.9999998774443333336777777665 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   6.6e-08     7e-05      38     146 ..       1      95 [.       1     115 [. 0.74

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 6.6e-08
    N6_Mtase  38 ivellepksgesvyDpacGsggllvqaekvlkeedgktkelsiyGqeknettyrLakmNlllhgieykkvkirlgdtlekpkfekdkkfdvvvaNppfn 136
                 +++l+  k+ge+v Dp cG+g  l++ae++          ++  G++ +e+ ++++k Nl   g + k   i  gd  ++   ++  +fd +v+  p++
  EPA06823.1   1 MINLIGLKEGEVVCDPFCGTGTTLLEAESM---------GIHAIGLDFDEKMFKISKENLDANGYNSK---IIKGDF-SQLT-RMIDEFDGIVTDLPYG 85 
                 67889999*******************994.........57888***************977777766...777774.4333.34799*********** PP

    N6_Mtase 137 qkewkektle 146
                 ++  ++++ e
  EPA06823.1  86 TASKSSENPE 95 
                 9943222222 PP

>> AviRa  RRNA methyltransferase AviRa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.0    0.0098        10      57     100 ..      13      52 ..       4      59 .. 0.74
   2 !   14.7   0.0   1.4e-05     0.015     162     214 ..      70     117 ..      53     122 .] 0.66

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0098
       AviRa  57 lyDpCCGgayLltvlgllhgkkik.kvlasDvdeevlelakkNLs 100
                 + Dp CG++       ll ++++  + ++ D+de++ +++k+NL+
  EPA06823.1  13 VCDPFCGTGT-----TLLEAESMGiHAIGLDFDEKMFKISKENLD 52 
                 6799999773.....344444443245799*************96 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1.4e-05
       AviRa 162 eaekevdivitDlPYGelvswqgeseepvkqlleslaavldpeesvvaviadk 214
                  +  e d ++tDlPYG  ++ +++ e    +l+++  a+l p++  +a++++k
  EPA06823.1  70 RMIDEFDGIVTDLPYGTASKSSENPE----ELMKKFVATL-PKRKKLAIMCKK 117
                 34445899*********998777766....5666666666.555555555555 PP

>> Methyltransf_5  MraW methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   1.3e-07   0.00013      13     100 ..       2      82 ..       1     111 [. 0.89

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.3e-07
                     HHHT---TT-EEEES--TTSHHHHHHHTT--TT.EEEEEES-HHHHHHHTT.....---EEEEES-GGGHHHHHHHTTTT-EEEEEEE- CS
  Methyltransf_5  13 vellepkedgvyiDaTlGaggHsealLeqlsel.rligidrDksalarakerLkefekrltlvkgnfkelkealaeanvtkvdgillDL 100
                     ++l+  ke+ v +D   G+g   ++lLe+ s   ++ig+d D+++ +++ke+L +   + +++kg f++l+++++     ++dgi+ DL
      EPA06823.1   2 INLIGLKEGEVVCDPFCGTG---TTLLEAESMGiHAIGLDFDEKMFKISKENLDANGYNSKIIKGDFSQLTRMID-----EFDGIVTDL 82 
                     66777788888888888887...58999988888************************************99988.....679999998 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   3.2e-07   0.00034       2      94 ..      11      97 ..      10     119 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 3.2e-07
  Methyltransf_15  2 rvilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdlvflSpPwGGpsYkkqekfdl 94
                     +v+ D+f+G+G    +   ++ + i+++ +++  +++++N  + g ++ki  ++gd+ +l++ +   +  +d +++  P G  s + ++  +l
       EPA06823.1 11 EVVCDPFCGTGTTLLEAESMGIHAIGLDFDEKMFKISKENLDANGYNSKI--IKGDFSQLTRMID--E--FDGIVTDLPYGTASKSSENPEEL 97
                     5799**************999999*******************9999997..89****9998843..3..37788888888877776666555 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   8.4e-07   0.00088     160     232 ..       8      80 ..       3      82 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 8.4e-07
        PrmA 160 kegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellk....eekadviva 232
                 kege v D  +G+G   + a  +g  +++++D De   k++keN++ N+ ++k+ +  +++  +      ++d iv 
  EPA06823.1   8 KEGEVVCDPFCGTGTTLLEAESMGI-HAIGLDFDEKMFKISKENLDANGYNSKI-I--KGDFSQltrmIDEFDGIVT 80 
                 7889999999999999999999997.578***********************88.3..2333222223457888886 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   1.1e-06    0.0011      98     180 ..       7      86 ..       1     107 [. 0.89

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.1e-06
                 --TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---.TT-EEEEEE--TTTG CS
      Met_10  98 veegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgrevir.eqladrvvmnlpksa 180
                  +egevV+d f G G   + +     +   ++ d + + +k  ken+  N  ++++  i++D  +++r  + +d +v +lp+ +
  EPA06823.1   7 LKEGEVVCDPFCGTGTTLLEAES--MGIHAIGLDFDEKMFKISKENLDANGYNSKI--IKGDFSQLTRmIDEFDGIVTDLPYGT 86 
                 689************99988886..7788899***********************9..********998889999999988755 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.1e-06    0.0011      32     143 ..      10     119 ..       1     122 [] 0.80

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.1e-06
                 CSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTST.TS-EEEEEE---STTTCHCHHHHHHHHHHHHHHHE CS
         MTS  32 sgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeve.ekkfdlivsNPPfhagkatelavaeeliaeAkeaL 129
                  + v D  cG+G     l +es  ++   +d d +  +++kenl an+ + ++++ d  + +   ++fd iv+  P+ + ++ + +  eel+++  + L
  EPA06823.1  10 GEVVCDPFCGTGTT--LLEAESMGIHAIGLDFDEKMFKISKENLDANGYNSKIIKGDFSQLTRmIDEFDGIVTDLPYGTASK-SSENPEELMKKFVATL 105
                 45578889999975..45555666678999***************************988666469***********99998.5556678888888888 PP

                 EEEEEEEEEEETTS CS
         MTS 130 kegGeLliVanrkl 143
                  +  +L i  ++ l
  EPA06823.1 106 PKRKKLAIMCKKGL 119
                 88888888777666 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   2.5e-06    0.0027      57     132 ..       4      79 ..       1     108 [. 0.88

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.5e-06
                 TTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG---...--SEEE CS
        CMAS  57 klelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedlde...kvdrvv 132
                  ++lk+G+ + d  cG G+++ +a +  +++ +gl + ++  k +k+++d+ + +   ++   d+ +l     ++d +v
  EPA06823.1   4 LIGLKEGEVVCDPFCGTGTTLLEAESM-GIHAIGLDFDEKMFKISKENLDANGYN--SKIIKGDFSQLTRmidEFDGIV 79 
                 579******************998766.*************************65..5677888888877555788777 PP

>> MethyltransfD12  D12 class N6 adenine-specific DNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0     1e-05     0.011      20      62 ..       9      51 ..       3     110 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1e-05
                     --SEEEETT-TTSCCHHCS...SSCEEEEES-HHHHHHHHHHC CS
  MethyltransfD12 20 kgktfvepFaGggaVffeakkqgkkvlinDinedlinlykali 62
                      g+++++pF+G+g   +ea + g +++  D+ e+ + + k  +
       EPA06823.1  9 EGEVVCDPFCGTGTTLLEAESMGIHAIGLDFDEKMFKISKENL 51
                     5789***************99**********999999988544 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.4e-05     0.014      41     119 ..       3      77 ..       1     105 [. 0.80

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.4e-05
                      HH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEE CS
  Ubie_methyltran  41 klvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDv 119
                      +l + k+g+ v D  +Gtg     l+++     + ++lD++e+m+k++++ l  +g+   + ++++  +L    d fD 
       EPA06823.1   3 NLIGLKEGEVVCDPFCGTGTT---LLEAESMGIHAIGLDFDEKMFKISKENLDANGYN-SKIIKGDFSQLTRMIDEFDG 77 
                      56788999**********964...555555556889*****************99985.56788888888777777774 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   4.9e-05     0.051       5      47 ..      18      58 ..      18     105 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.9e-05
  Methyltransf_12  5 cGtGsllralleklpdieytgvDispsaiedakeklakrennn 47
                     cGtG++l + +    +i+ +g+D+++++++  ke l +++ n+
       EPA06823.1 18 CGTGTTLLEAESM--GIHAIGLDFDEKMFKISKENLDANGYNS 58
                     9******999999..**************88888888887633 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 848.63
//
Query:       EPA06824.1  [L=299]
Description: ribonuclease Z [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-15   57.1   0.0    1.2e-06   28.2   0.0    2.1  2  Lactamase_B_2  Beta-lactamase superfamily domain
    8.6e-08   32.4   0.0    5.2e-07   29.9   0.0    2.2  3  Lactamase_B    Metallo-beta-lactamase superfamily
    0.00034   20.2   0.0    0.00073   19.2   0.0    1.5  1  Lactamase_B_4  tRNase Z endonuclease


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0   4.6e-10   2.7e-06      34     116 ..      56     141 ..      32     156 .. 0.85
   2 !   28.2   0.0     2e-10   1.2e-06     132     201 .]     197     266 ..     183     266 .. 0.92

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 4.6e-10
                    EE-SS--HHHHGGGGCCCC...C--EE..EEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--C CS
  Lactamase_B_2  34 VllthaHyDHlaglltlre...lrpkk..lplyapkgvlavleanfvylaleeepavnvheldwgesfelgdggleitatparhksgr 116
                    +++th H DH+ gll l +   ++++   l++y+pkg+ + ++an++ l+++  ++v+++ ++ g+ f+ +    ++ a  a+h+   
     EPA06824.1  56 IFVTHLHGDHCVGLLGLLQtmtMQNRTepLEIYGPKGIEEFIAANIKILNFGLSFPVMITIVNEGKIFDSK--IYSVYACKANHSVIS 141
                    89****************99864444478*************************9********99999997..467999999998766 PP

  == domain 2  score: 28.2 bits;  conditional E-value: 2e-10
                    CTTEEEEEESS-S---HHHHHHHCT-SEEEEE-S-SSTTHHHH.HHT---STSHHHHCTTSSSSEEEEESB CS
  Lactamase_B_2 132 gggkrvyyigDtgyipeeigerlggadllllditayeddemir.hmgHltpeeaveaaadlgakrlvliHi 201
                    ++gk++  +gDt  ++ e+++ ++++d l++d t++e+ + ++ + +H+t ++a+ + + +++k l+l+H+
     EPA06824.1 197 RPGKKIGISGDTMPTK-ELEKFFEDCDYLVFDSTFLEESKERAeETYHSTAKQAAILGKNAKVKNLILTHF 266
                    689**********887.6688*****************997779**************************7 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.0   8.8e-11   5.2e-07       8      87 ..      21      95 ..      16     132 .. 0.87
   2 ?   -2.7   0.0      0.83     5e+03     141     157 ..     198     214 ..     196     219 .. 0.82
   3 ?   -0.8   0.0      0.22   1.3e+03      37      53 ..     250     266 ..     224     266 .. 0.80

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 8.8e-11
                 EEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHH CS
  Lactamase_B  8 syliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmeea 87
                 ++ +e dg+ +++D+G  t+ + ++      gl++++   +++THlH DH+ gl gl ++     + +++e + +++ e+
   EPA06824.1 21 CICLERDGEILMFDAGEATQISYLK-----SGLGWNKKMKIFVTHLHGDHCVGLLGLLQTMTMQNRTEPLEIYGPKGIEE 95
                 777899******************8.....6***************************9988888888888777776666 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.83
                  TTCCEEEECTTTSSHHC CS
  Lactamase_B 141 gggkvlftGDallaget 157
                  +g+k+ ++GD+ ++ e 
   EPA06824.1 198 PGKKIGISGDTMPTKEL 214
                  6889999****998765 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.22
                  HHTSGGGGEEEEE-SBS CS
  Lactamase_B  37 alglkpkdvdavilTHl 53 
                  a+  k  +v+ +ilTH+
   EPA06824.1 250 AILGKNAKVKNLILTHF 266
                  467788999*******6 PP

>> Lactamase_B_4  tRNase Z endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.2e-07   0.00073       9      56 ..      15      62 ..       8      68 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.2e-07
  Lactamase_B_4  9 Dtsg.PlllLqldskrYlfGkvgEgtQRavneqkvrlsklesiFLtgkv 56
                   + +g ++++L+ d +  +f + gE tQ    ++++  +k  +iF+t+ +
     EPA06824.1 15 ENRGlTCICLERDGEILMF-DAGEATQISYLKSGLGWNKKMKIFVTHLH 62
                   44566**************.**************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1919.20
//
Query:       EPA06825.1  [L=383]
Description: DnaJ domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.8e-12   44.8   0.1    1.1e-10   41.4   0.0    2.4  2  DnaJ      DnaJ domain


Domain annotation for each model (and alignments):
>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   0.0   6.3e-15   1.1e-10       3      55 ..       6      54 ..       4      62 .. 0.91
   2 ?    0.5   0.0     0.038   6.9e+02      19      42 ..     325     348 ..     316     368 .. 0.71

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 6.3e-15
                HHHHTSSTTG-HHHHHHHHHHHHHHHSTTTSCCHHHHHHHHHHHHHHHHHHTS CS
        DnaJ  3 YeiLgvskdasedeIkkaYrklalkyHPDknpkdpeaeekFkeineAyevLsd 55
                Y+iLg+++ ++e eI++a+r+lal+yH D+       +e+F +i++Aye L+ 
  EPA06825.1  6 YDILGITEGSTEIEIRNAFRRLALQYHSDRG----GENEQFIKIKQAYEDLKI 54
                *******************************....7779**********9975 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.038
                 HHHHHHHHHHSTTTSCCHHHHHHH CS
        DnaJ  19 kaYrklalkyHPDknpkdpeaeek 42 
                 k+ r+la ++ P kn+ +++a+  
  EPA06825.1 325 KKIRDLADEFVPNKNEYQKDATMV 348
                 66799999999****888877654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 2213.71
//
Query:       EPA06826.1  [L=108]
Description: nitrogen regulatory protein P-II [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-19   68.9   4.4    5.4e-19   68.7   4.4    1.1  1  P-II      Nitrogen regulatory protein P-II


Domain annotation for each model (and alignments):
>> P-II  Nitrogen regulatory protein P-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.7   4.4     3e-23   5.4e-19       1     101 [.       4     100 ..       4     101 .. 0.89

  Alignments for each domain:
  == domain 1  score: 68.7 bits;  conditional E-value: 3e-23
                 EEEEEEGGGHHHHHHHHHHTTGGCEEEEEEEEEESTCCEEEECTTEEEEEEEEEEEEEEEEEEGGGHHHHHHHHHHHH-SSSTTSEEEEEEEESEEEET CS
        P-II   1 ieaiirpekleevkeaLekagvkgltvtevkGrGkqkghtelyrgaeyevellpkvkleivvsdedvekvveaiikaaktgeiGDGkiFvlpveeviri 99 
                 ie+i+++e  ++v  a+++agv g+t+++ +G+G  +     + g++ e  + +  ++  vv+d+ v++vv ai+k+a+tge GDGkiFv+++ee + i
  EPA06826.1   4 IEVIVQSEVSKQVVRAIRNAGVGGVTLIQSLGQGAGE--RPEIGGHQIE--FNSTDVIITVVQDSMVDSVVSAIMKVAHTGEKGDGKIFVSNIEESYDI 98 
                 899*****************************99988..3335666555..55677777788************************************* PP

                 TT CS
        P-II 100 rt 101
                  t
  EPA06826.1  99 ST 100
                 99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 702.11
//
Query:       EPA06827.1  [L=228]
Description: hypothetical protein BG20_I0998 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1449.18
//
Query:       EPA06828.1  [L=165]
Description: dual specificity phosphatase, catalytic domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-16   60.7   0.0    1.5e-16   60.4   0.0    1.1  1  DSPc             Dual specificity phosphatase, catalytic doma
    1.7e-08   34.3   0.3    6.2e-08   32.5   0.0    1.7  2  Y_phosphatase    Protein-tyrosine phosphatase
      5e-07   30.0   0.0    7.5e-07   29.4   0.0    1.3  1  PTPlike_phytase  Inositol hexakisphosphate
     0.0016   18.1   0.0     0.0023   17.6   0.0    1.2  1  CDKN3            Cyclin-dependent kinase inhibitor 3 (CDKN3)
     0.0069   16.4   0.0     0.0087   16.0   0.0    1.2  1  Y_phosphatase3   Tyrosine phosphatase family
  ------ inclusion threshold ------
      0.028   14.0   0.0      0.032   13.8   0.0    1.2  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
      0.045   13.9   0.0      0.071   13.3   0.0    1.3  1  GDH_N            Glutamate dehydrogenase N terminal
       0.08   13.5   0.0       0.12   12.9   0.0    1.3  1  Rhodanese        Rhodanese-like domain
      0.099   12.2   0.0       0.17   11.4   0.0    1.4  1  Y_phosphatase2   Tyrosine phosphatase family


Domain annotation for each model (and alignments):
>> DSPc  Dual specificity phosphatase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.4   0.0   7.5e-20   1.5e-16      16     117 ..      47     145 ..      28     160 .. 0.81

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 7.5e-20
                 HHTCSEEEEESSSSSECECCTTTTSEEEEECCESSTTSCCGGGHHHHHHHHHHHHHTT-EEEEEESSSSSHHHHHHHHHHHHHHTSCHHHHHHHHHHHS CS
        DSPc  16 klgitlvinvtkevpnanalkkseieklripvedehetkiskyleeavefidkakqkgkkvlVHCqaGisRSatliiaYlmktknlslneayeflkerr 114
                 ++g+t ++ +t++     +   s i +l++p  d  ++   + ++ av+fi++  ++ ++v+VHC+aG+ R +t+ ++Y  k++++s+++a++ ++ +r
  EPA06828.1  47 NQGVTSIVTMTENAL--PDEWVSAIGYLHVPTPD-LTAPDMERIDTAVDFIHEKISNDQTVMVHCAAGMGRAGTILACYFVKYQKFSAKDAINKIRTER 142
                 445555555553333..23345899999***999.66666788******************************************************** PP

                 TT- CS
        DSPc 115 pai 117
                 p  
  EPA06828.1 143 PGS 145
                 653 PP

>> Y_phosphatase  Protein-tyrosine phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.39   7.8e+02      54      76 ..      37      59 ..      31      64 .. 0.79
   2 !   32.5   0.0   3.1e-11   6.2e-08     150     225 ..      85     151 ..      69     157 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.39
                   GHHHHHHHHHHTT--EEEEESBS CS
  Y_phosphatase 54 tvedFWrmvwqekvkvivmLtsl 76
                   t +d + +++++ v+ iv +t+ 
     EPA06828.1 37 TSSDEFDWIINQGVTSIVTMTEN 59
                   44555678999999999999975 PP

  == domain 2  score: 32.5 bits;  conditional E-value: 3.1e-11
                    SCCHHHHHHHHHHHHHHSTTSS-EEEECSSSSHHHHHHHHHHHHHHHHHHHSEEEHHHHHHHHHTTSTTSS-SHHH CS
  Y_phosphatase 150 esaksllklirkvekskeaksgpvvVhCsaGvgRtgtfvaldillqqleaeeevdvlqivkelrkqRpgmvqtleq 225
                    e+ + ++++i++  +    +++ v+VhC aG+gR+gt++a  ++       ++++ +++++++r++Rpg++q++ q
     EPA06828.1  85 ERIDTAVDFIHEKIS----NDQTVMVHCAAGMGRAGTILACYFVK-----YQKFSAKDAINKIRTERPGSIQSEVQ 151
                    445555566554444....4589**************98876653.....24577899**************9987 PP

>> PTPlike_phytase  Inositol hexakisphosphate
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   3.7e-10   7.5e-07      99     152 ..      68     122 ..      37     124 .. 0.89

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 3.7e-10
                      T-EEEEEEE-TTS---HHHHHHHHHHHHTS.-TT-EEEEE-SSSSHHHHHHHHHH CS
  PTPlike_phytase  99 slrYaRipitdekapeeedfdalvsilkea.pektalvfnCqmGrgRTTtamvia 152
                      ++ Y  +p +d +ap+ e +d+ v+++ e  ++++ ++++C +G gR  t ++++
       EPA06828.1  68 AIGYLHVPTPDLTAPDMERIDTAVDFIHEKiSNDQTVMVHCAAGMGRAGTILACY 122
                      577999************************999******************9997 PP

>> CDKN3  Cyclin-dependent kinase inhibitor 3 (CDKN3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.1e-06    0.0023     104     157 ..      72     125 ..      58     135 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.1e-06
                 EE----TTS---HHHHHHHHHHHHHHHHTT--EEEE-SSSSSHHHHHHHHHHHH CS
       CDKN3 104 hhhpiadggtpdiascleimeelatclknyrktlihcygglgrsclvaacllly 157
                  h p +d  +pd+      ++ +   + n +  ++hc  g+gr+  + ac ++ 
  EPA06828.1  72 LHVPTPDLTAPDMERIDTAVDFIHEKISNDQTVMVHCAAGMGRAGTILACYFVK 125
                 589*************999***************************9***8764 PP

>> Y_phosphatase3  Tyrosine phosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   4.4e-06    0.0087     110     139 ..      91     120 ..      52     125 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.4e-06
  Y_phosphatase3 110 yrkvfealadeepvlfHCtaGKDRTGvlaa 139
                     +  + e++ ++++v++HC+aG  R G + a
      EPA06828.1  91 VDFIHEKISNDQTVMVHCAAGMGRAGTILA 120
                     333445556655**************9987 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.6e-05     0.032      76     127 ..      66     114 ..      28     142 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.6e-05
                     C-SEEEE-----B-TTTTCB-THHHHHHHHHHHHHHHCEEEEEE-S---TTH CS
  UDPG_MGDP_dh_N  76 eadvifiaVgTPskkkgkaaDlkyvesaarsiaealkkgkvvvvkSTvpvgt 127
                      + + ++ V+TP  +   a+D++ + +a++ i e ++++++v+v     +g 
      EPA06828.1  66 VSAIGYLHVPTPDLT---APDMERIDTAVDFIHEKISNDQTVMVHCAAGMGR 114
                     56788999****999...99*********************99987666655 PP

>> GDH_N  Glutamate dehydrogenase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.6e-05     0.071      31      64 ..     127     160 ..     101     164 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.6e-05
       GDH_N  31 qavslepvfaalrkryPaarqsevqalaaafykr 64 
                 q +s +     +r   P + qsevq la  fy +
  EPA06828.1 127 QKFSAKDAINKIRTERPGSIQSEVQELAITFYEK 160
                 5666677777899*******************86 PP

>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   5.8e-05      0.12      35      83 ..      73     120 ..      66     148 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.8e-05
   Rhodanese  35 nvskdtlsrakkseapllelpeellelgidnkktvvvycdgggraaaa..a 83 
                 +v   ++++ + ++ +  ++  +++ ++i+n++tv v+c+ g++ a +  a
  EPA06828.1  73 HV---PTPDLTAPDMERIDTAVDFIHEKISNDQTVMVHCAAGMGRAGTilA 120
                 55...6777788888888888889999*****************4433332 PP

>> Y_phosphatase2  Tyrosine phosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   8.6e-05      0.17       4     125 ..      19     136 ..      17     164 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.6e-05
                     -TT-EE.EETTEEEESS--HH.HHHHHHHCT-SEEEE-SSS---HHHHHHHHHCT-EEEE-------GGG----HHHHHHHHHHHH-GGG-SEEE CS
  Y_phosphatase2   4 plnFsa.veselyrssypras.nfsflksLkLktiislspeeesqdelqfleeekiklyhiaiesnkeelveiksdllkkalklllnkenypvll 96 
                     p nFs  +e +l  s++p +s  f ++ +  + +i+ ++++  + + +       i ++h+  ++   +++e +++ +  + + + n   + v++
      EPA06828.1  19 PTNFSWlIEDKLAGSGMPTSSdEFDWIINQGVTSIVTMTENALPDEWVSA-----IGYLHVPTPDLTAPDMERIDTAVDFIHEKISN--DQTVMV 106
                     78888624558999999876427999999999999998888888876654.....88999988888887777777777766666655..568*** PP

                     E-SSSSSHHHHHHHHHH.HHTTB-HHHHHH CS
  Y_phosphatase2  97 hckrGkhrtglvigclR.klqkWslasiln 125
                     hc  G  r g++ +c   k qk s+  ++n
      EPA06828.1 107 HCAAGMGRAGTILACYFvKYQKFSAKDAIN 136
                     ***************766888888777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1075.75
//
Query:       EPA06829.1  [L=38]
Description: hypothetical protein BG20_I0975 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (38 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       874  (0.0487478); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.32s 00:00:00.73 Elapsed: 00:00:00.48
# Mc/sec: 240.20
//
Query:       EPA06830.1  [L=161]
Description: hypothetical protein BG20_I1000 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00057   20.0   0.1     0.0011   19.0   0.1    1.7  1  THUMP     THUMP domain


Domain annotation for each model (and alignments):
>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   6.4e-08    0.0011      77     136 ..      76     136 ..      14     143 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 6.4e-08
                 HHHHHCT-..EEEEEEEESSSTSSSHHHHHHHHHHHHHHCCTT-EE-SSS-SEEEEEEEETT CS
       THUMP  77 kkfeeeke..tFaVrvkrrgkhfeftsreinrevGkaivektglkVdlenPdivvrveiikd 136
                 ++fe  k+  tF  r+    ++ +f+  e++r  G++i +  ++ V+l nPdi++ + + ++
  EPA06830.1  76 ENFEVLKNakTFVCRIINLSSN-QFNIPELERSMGDMITKFSKAQVSLQNPDITIYLIFTNE 136
                 3444444466999999999999.*****************888************9877666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       746  (0.0416086); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1124.14
//
Query:       EPA06831.1  [L=110]
Description: hypothetical protein BG20_I0993 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.8e-05   23.4   0.0    6.1e-05   22.7   0.0    1.3  1  HTH_IclR      IclR helix-turn-helix domain
    0.00052   20.0   0.0    0.00073   19.5   0.0    1.2  1  HTH_20        Helix-turn-helix domain
    0.00064   19.6   0.0    0.00087   19.1   0.0    1.3  1  TrmB          Sugar-specific transcriptional regulator TrmB
     0.0082   15.9   0.0       0.01   15.6   0.0    1.1  1  DUF742        Protein of unknown function (DUF742)
  ------ inclusion threshold ------
      0.024   14.7   0.1      0.032   14.2   0.1    1.2  1  Hpr_kinase_N  HPr Serine kinase N terminus
      0.027   14.6   0.0      0.029   14.5   0.0    1.3  1  FUR           Ferric uptake regulator family
       0.03   14.2   0.0      0.049   13.5   0.0    1.3  1  HTH_5         Bacterial regulatory protein, arsR family
      0.063   13.5   0.1       0.19   12.0   0.0    1.7  2  DND1_DSRM     double strand RNA binding domain from DEAD END 
      0.077   12.6   0.0       0.18   11.4   0.0    1.7  1  HTH_24        Winged helix-turn-helix DNA-binding
      0.084   12.7   0.0        0.1   12.4   0.0    1.1  1  DUF2857       Protein of unknown function (DUF2857)


Domain annotation for each model (and alignments):
>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   3.4e-08   6.1e-05      20      48 ..      41      69 ..      31      70 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 3.4e-08
                BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
    HTH_IclR 20 tlselArrtglpkStvhRlLqtLvelGyv 48
                +  e++++t +p Stv+R LqtL+  +++
  EPA06831.1 41 SAMEISAETKIPISTVYRRLQTLHDNKLL 69
                567********************999887 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   4.1e-07   0.00073       1      53 [.      17      68 ..      17      71 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 4.1e-07
                HHHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTT CS
      HTH_20  1 dqiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagL 53
                d i+e+++++  r+il     +++ +a e+ ++  ++ +t++++L++L +  L
  EPA06831.1 17 DAILEVISDKYCRAILENS-MEKPKSAMEISAETKIPISTVYRRLQTLHDNKL 68
                6799**************9.****************************98776 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   4.9e-07   0.00087      20      51 ..      37      68 ..      29      87 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 4.9e-07
                HCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTS CS
        TrmB 20 lgpatadeiaeelgvprskvYevLrsLedkGl 51
                ++p++a ei+ e+++p s+vY+ L+ L d  l
  EPA06831.1 37 EKPKSAMEISAETKIPISTVYRRLQTLHDNKL 68
                68999**********************98755 PP

>> DUF742  Protein of unknown function (DUF742)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   5.7e-06      0.01      45      92 ..      28      76 ..      12      82 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.7e-06
      DUF742 45 hrailrLcre.plsVaelaAelklPvgvvrvLlsdLldaglltvrapvt 92
                +rail+   e p+s  e++Ae+k+P+++v   l  L+d  ll ++ +++
  EPA06831.1 28 CRAILENSMEkPKSAMEISAETKIPISTVYRRLQTLHDNKLLGISGSIS 76
                68888877777******************99999999999988777665 PP

>> Hpr_kinase_N  HPr Serine kinase N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   1.8e-05     0.032      63     112 ..       9      58 ..       7      67 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.8e-05
                   T-HHHHH..HHHHHHTT--S-EEEETTT---HHHHHHHHHH---EEEESS CS
  Hpr_kinase_N  63 klseeerkerleklfskkipciiltrgleppeellelaeeygvpllrtkl 112
                   k+++++rk+++ +++s k +  il +++e p+  +e+  e+++p+ +  +
    EPA06831.1   9 KIEDDSRKDAILEVISDKYCRAILENSMEKPKSAMEISAETKIPISTVYR 58 
                   78999****************************************87655 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.6e-05     0.029      35      70 ..      46      82 ..      15     103 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.6e-05
                HTTTT--HHHHHHHHHHHHHTTSEE.EEEETTSEEEE CS
         FUR 35 eedpeislaTVYrtLklleeaglvk.elefedgesry 70
                + + +i ++TVYr L++l++ +l+  + +++++ ++y
  EPA06831.1 46 SAETKIPISTVYRRLQTLHDNKLLGiSGSISEDGKKY 82
                567899**************99985123344333443 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.7e-05     0.049      13      42 ..      37      66 ..      30      69 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.7e-05
                TSSEEHHHHHHHHTS-HHHHHHHHHHHHHT CS
       HTH_5 13 egelcvcelaeelglsqstvShHLkkLrea 42
                e+++++ e+++e++++ stv + L  L++ 
  EPA06831.1 37 EKPKSAMEISAETKIPISTVYRRLQTLHDN 66
                799***********************9986 PP

>> DND1_DSRM  double strand RNA binding domain from DEAD END PROTEIN 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.7   3.1e+03      61      73 ..      36      48 ..      27      51 .. 0.76
   2 ?   12.0   0.0   0.00011      0.19      28      50 ..      76      98 ..      71     106 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.7
   DND1_DSRM 61 astkeeAkelaAe 73
                +++++ A e +Ae
  EPA06831.1 36 MEKPKSAMEISAE 48
                6778888888887 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00011
   DND1_DSRM 28 gpdgkllflYkVvipgietslkg 50
                + dgk++flYk +i++i+ts++g
  EPA06831.1 76 SEDGKKYFLYKSRIKAIATSFNG 98
                5799*****************98 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0    0.0001      0.18      22      44 ..      44      66 ..      41      69 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0001
      HTH_24 22 eLAerlglSpstvnrrlkrLeee 44
                e++ ++ +++stv rrl+ L ++
  EPA06831.1 44 EISAETKIPISTVYRRLQTLHDN 66
                8*****************99876 PP

>> DUF2857  Protein of unknown function (DUF2857)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   5.6e-05       0.1     117     174 ..       8      65 ..       3      66 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.6e-05
     DUF2857 117 RppaldeeeeaeiwraWqailgveeldstealdlmmsvaeeleisLtviWklvqewed 174
                 R+   d  ++a +     +++++ +++s+e  + +m+++ e++i+++++++ +q+++d
  EPA06831.1   8 RKIEDDSRKDAILEVISDKYCRAILENSMEKPKSAMEISAETKIPISTVYRRLQTLHD 65 
                 5554444444444444456667778899**************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 751.25
//
Query:       EPA06832.1  [L=178]
Description: hypothetical protein BG20_I0976 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1271.55
//
Query:       EPA06833.1  [L=352]
Description: radical SAM domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.5e-13   49.9   0.4    1.8e-12   48.0   0.0    2.1  2  Radical_SAM  Radical SAM superfamily
     0.0061   16.8   0.9      0.017   15.4   0.0    2.1  2  Fer4_12      4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.017   14.3   0.0      0.026   13.7   0.0    1.2  1  DUF3419      Protein of unknown function (DUF3419)
        3.6    7.1  15.1       0.83    9.2   0.2    3.7  4  zf-ribbon_3  zinc-ribbon domain
        5.5    7.2   9.9         16    5.7   0.9    3.5  4  zf-piccolo   Piccolo Zn-finger


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.0   0.0     5e-16   1.8e-12       3     167 .]      79     238 ..      77     238 .. 0.91
   2 ?   -1.0   0.1      0.55     2e+03       9      17 ..     324     332 ..     323     343 .. 0.87

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 5e-16
                  EESEESS--TTTSCCTT.HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHH CS
                  xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM   3 vtrgCnlrCsfCarpet.vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritvetngtlpdeeklerlle 99 
                   t gCn  C++C+++   +rr + g ++++ ++++ +  +     ++++  +  ep+   +f+++   +a+   +++ + +++ng+   +e ++ + e
   EPA06833.1  79 ATTGCNWLCKYCQNYDIsQRRKVEGVDMTPKQVVQTALDNG----ADGIAYTYNEPSIFIEFARDCGVIAHQ--KNLYNIFVSNGYDT-PESVKMMGE 169
                  689************9999******************8887....**************************9..7************8.********* PP

                  TT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET..EEEEEEEBTTTSHHHHHHHHHHH CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM 100 lgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikr..vvdrivglpGendeeleellell 167
                     d ++++ +   +  + +++ + ++++ v ++l  +r++      ++d iv   G n e  e+l +++
   EPA06833.1 170 FL-DSITVDFKGNAEPNFTRKFIGIPDPQPVFDTLLEIRDKTKIHveITDLIVPQVGDNLESAEKLCKFI 238
                  77.9999999998877555555599****************6555899*****99999999999998886 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.55
                  S--TTTSCC CS
                  xxxxxxxxx RF
  Radical_SAM   9 lrCsfCarp 17 
                  ++C+fC + 
   EPA06833.1 324 NKCKFCGNQ 332
                  79****985 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   4.8e-06     0.017       6     113 ..      74     176 ..      69     188 .. 0.68
   2 ?   -1.3   0.2      0.67   2.4e+03      18      36 ..     325     343 ..     318     348 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 4.8e-06
     Fer4_12   6 vrlslfvsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekdiwlytgytleelskkek 104
                 +++s+ ++gCn  Ck+C n ++ + ++ + ++ +  +++++ + ++  +g+ ++  EP+   +      ++ + k+ +   +i++++gy   e  k   
  EPA06833.1  74 KVFSIATTGCNWLCKYCQNYDISQRRKVEGVDMTP-KQVVQTALDNGADGIAYTYNEPSIFIEFARDCGVIAHQKNLY---NIFVSNGYDTPESVK-MM 167
                 4567889*************999888666665443.344444458889999999999999555444444444444433...589999988777664.36 PP

     Fer4_12 105 eellkeidv 113
                  e+l+ i v
  EPA06833.1 168 GEFLDSITV 176
                 666666655 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.67
     Fer4_12  18 sCkgCfnketwsfksgkef 36 
                 +Ck+C n+     k +k++
  EPA06833.1 325 KCKFCGNQIPIIGKLSKNY 343
                 8****99876666655555 PP

>> DUF3419  Protein of unknown function (DUF3419)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   7.3e-06     0.026      18      66 ..      59     112 ..      56     120 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.3e-06
     DUF3419  18 DprvdeeaLklepddrvlaItSaGdNaL.sYl....laspkrihaVDlNpaqna 66 
                 Dp + + +++ +p+++v++I+  G+N L +Y+     ++ +++  VD+ p q+ 
  EPA06833.1  59 DPIEKKPVIHYKPGSKVFSIATTGCNWLcKYCqnydISQRRKVEGVDMTPKQVV 112
                 666677788899**************997566444478999**********985 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.2      0.98   3.5e+03       2       8 ..      15      21 ..      14      22 .. 0.75
   2 ?   -0.4   0.4      0.24   8.4e+02      19      23 ..      87      91 ..      86      92 .. 0.83
   3 ?    9.2   0.2   0.00023      0.83       1      13 [.     296     309 ..     296     310 .. 0.81
   4 ?    7.3   0.4   0.00089       3.2      14      26 .]     321     333 ..     317     333 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.98
  zf-ribbon_3  2 tvrCPnC 8 
                 +vrC +C
   EPA06833.1 15 KVRCTAC 21
                 6889888 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.24
  zf-ribbon_3 19 CpyCG 23
                 C+yC+
   EPA06833.1 87 CKYCQ 91
                 ****7 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.00023
  zf-ribbon_3   1 stvrCPnCGa.pls 13 
                  ++++CP+C++ +++
   EPA06833.1 296 EHTYCPECKNiVIK 309
                  589*******6665 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.00089
  zf-ribbon_3  14 sddnvCpyCGtkl 26 
                  +d n+C+ CG ++
   EPA06833.1 321 DDKNKCKFCGNQI 333
                  789*******986 PP

>> zf-piccolo  Piccolo Zn-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.2      0.61   2.2e+03      20      28 ..      15      23 ..       4      32 .. 0.72
   2 ?    5.0   0.2    0.0073        26      45      55 ..      82      92 ..      74      96 .. 0.84
   3 ?    5.7   0.9    0.0044        16      17      39 ..     294     316 ..     287     332 .. 0.79
   4 ?   -1.2   0.2      0.63   2.3e+03      30      40 ..     325     334 ..     321     342 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.61
  zf-piccolo 20 yntCteCkk 28
                   Ct C +
  EPA06833.1 15 KVRCTACAR 23
                446999975 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0073
  zf-piccolo 45 kkeWlclnCQt 55
                + +Wlc  CQ 
  EPA06833.1 82 GCNWLCKYCQN 92
                669*******6 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.0044
  zf-piccolo  17 ppnyntCteCkkqvCnlCGFnpt 39 
                 p +++ C eCk+ v    GF+ +
  EPA06833.1 294 PLEHTYCPECKNIVIKRYGFDIE 316
                 568999**************875 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 0.63
  zf-piccolo  30 vCnlCGFnptp 40 
                  C  CG n  p
  EPA06833.1 325 KCKFCG-NQIP 334
                 477777.5545 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2312.55
//
Query:       EPA06834.1  [L=248]
Description: proliferating cell nuclear antigen [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.6e-20   70.9   0.1    1.4e-19   70.1   0.1    1.3  1  PCNA_N        Proliferating cell nuclear antigen, N-terminal 
    2.7e-18   66.4   0.6    1.1e-16   61.2   0.0    2.7  2  PCNA_C        Proliferating cell nuclear antigen, C-terminal 
      5e-07   29.0   0.1      0.012   14.6   0.0    2.2  2  Rad1          Repair protein Rad1/Rec1/Rad17
     0.0051   16.3   0.0     0.0062   16.0   0.0    1.1  1  Rad9          Rad9
  ------ inclusion threshold ------
       0.06   13.5   0.1       0.14   12.4   0.1    1.7  2  Receptor_2B4  Natural killer cell receptor 2B4


Domain annotation for each model (and alignments):
>> PCNA_N  Proliferating cell nuclear antigen, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.1   0.1   3.9e-23   1.4e-19       2     108 ..       3     108 ..       2     120 .. 0.89

  Alignments for each domain:
  == domain 1  score: 70.1 bits;  conditional E-value: 3.9e-23
                 EEEEESSHHHHHHHHHHHTTTCSEEEEEEETTEEEEEEE-TTSSEEEEEEEEGGGSSEEEESS-EEEEEEHHHHHHHHTTSTTTSEEEEEEETTSSEEE CS
      PCNA_N   2 learleqasllkklleaikdlvneanfdcddsGislqalDsshvaLvslelrsegfekyrCDrnlalgvnlnslskilkcannedsvtlkaedeadtla 100
                 +ea+ + +  lk ++ ai  lv+ea+f +  +Gi+ + +D shvaL+ ++  +++feky CD ++ +gv +  +sk++k a+++ds+ ++  +++  l 
  EPA06834.1   3 FEAKTSGSDDLKAIISAISTLVEEATFVATAEGITFRGMDPSHVALIDISWPNSAFEKYECDSDIKFGVRIDEFSKLIKRADKKDSIEISISEQNMLL- 100
                 8999999999*******************************************************************************988776555. PP

                 EEEEECTS CS
      PCNA_N 101 lvfesekk 108
                 +++ ++kk
  EPA06834.1 101 VTVGKNKK 108
                 33444444 PP

>> PCNA_C  Proliferating cell nuclear antigen, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.2     0.046   1.6e+02      20      46 ..      15      41 ..       6     116 .. 0.51
   2 !   61.2   0.0     3e-20   1.1e-16       3     127 ..     124     244 ..     122     245 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.046
                HHHHHHTTT-SEEEEEEETTEEEEEEE CS
      PCNA_C 20 ricrdlsqlsdsvvisvtkegvkfsas 46
                 i+  +s+l ++ +  +t eg+ f+  
  EPA06834.1 15 AIISAISTLVEEATFVATAEGITFRGM 41
                556666666666666666666666533 PP

  == domain 2  score: 61.2 bits;  conditional E-value: 3e-20
                 --SS-SEEEEEEHHHHHHHHHHHTTT-SEEEEEEETTEEEEEEEETTEEEEEEE--BEESSSGGGCBEEEESS-EEEEEEHHHHHHHGGGG.GC-SEEE CS
      PCNA_C   3 pdseydavvklpssefaricrdlsqlsdsvvisvtkegvkfsasGdiGsasivlkqvkdvdkeeeavklelkepvtltfalkYlaeftkat.sLservt 100
                 p + yd+ ++l+ss f +i  d++ +sd ++i  +     fs +Gd G+  i l+     ++ ee  +++ ke    t++l+Yl+ ++ka  + + ++t
  EPA06834.1 124 PKIPYDSKITLSSSRFDKILGDVQVVSDYLTIHTSDSKADFSGKGDSGEVVIDLE-----KDAEEIGEISSKEDSVGTYSLEYLNPVVKAVgTTAGQIT 217
                 7889******************************************998855443.....46789999**********************725789*** PP

                 EEEETTSEEEEEEEETTCEEEEEEE-B CS
      PCNA_C 101 lslssevPlvveykikdvgllayllak 127
                  ++ss  Pl +e+k++++g ++++la+
  EPA06834.1 218 CEFSSSKPLRIEFKVANIGRIHFYLAP 244
                 *************************98 PP

>> Rad1  Repair protein Rad1/Rec1/Rad17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   1.4e-05     0.052       1      67 [.       2      79 ..       2     111 .. 0.74
   2 !   14.6   0.0   3.5e-06     0.012     154     254 ..     117     210 ..      91     213 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.4e-05
        Rad1  1 vfsAtlsnvseLatlLksiafkd.kalvqissdGlkfi.vednrvlqaqafldkalFtsYtfenaqdd............e 67
                +f+A++s  + L  ++++i+    +a+  ++ +G++f   + ++v  +    +++ F++Y+ ++   d             
  EPA06834.1  2 TFEAKTSGSDDLKAIISAISTLVeEATFVATAEGITFRgMDPSHVALIDISWPNSAFEKYECDS---DikfgvridefskL 79
                699****************865439************835789999**************9933...12345555555441 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 3.5e-06
        Rad1 154 edldleldrqevvlkvilkselLhsalteLdatskklkilassekkapvfalsakgelgssevefpneksvlekfevsslsessessYkfallkkaaka 252
                 + +d +l +     k+ l s+ + ++l + + +s+ l+i +s++k+     +s+kg+ g++ +++ ++ + + ++  +  ++s+ + Y +++l+++ ka
  EPA06834.1 117 SATDTPLPKIPYDSKITLSSSRFDKILGDVQVVSDYLTIHTSDSKA----DFSGKGDSGEVVIDLEKDAEEIGEISSK--EDSVGT-YSLEYLNPVVKA 208
                 67888888889999*****************************744....8****************99999999888..555555.*******99999 PP

        Rad1 253 la 254
                 + 
  EPA06834.1 209 VG 210
                 85 PP

>> Rad9  Rad9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.7e-06    0.0062       4     247 ..      16     242 ..      13     245 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.7e-06
        Rad9   4 alqclsrigdelyleisedglelrtvnssrSayalvtlkksfFdkyekevseqirckilvKsvlsvfrslsakektvekvkisidekksrlivqllCkh 102
                 ++ ++s + +e  + ++ +g+++r ++ s+ a   +   +s F+ky  e +++i++ + +  + ++++ +     + + ++isi+e++      ll   
  EPA06834.1  16 IISAISTLVEEATFVATAEGITFRGMDPSHVALIDISWPNSAFEKY--ECDSDIKFGVRIDEFSKLIKRAD----KKDSIEISISEQNM-----LLVTV 103
                 6788999999999*********************************..78889999999999999997444....55788999976654.....55568 PP

        Rad9 103 gvkkthkisledseslkavfdkettpsklriksrvLsdllehfsssleeitielakervllksyeeeekdnkkalstelsideeeFeqyqlaedveitl 201
                 g  k++k+ l +s    + + k    sk++ +s  + ++l   +   + +ti+ +  +  +   ++++     +++ +l  d ee  +++ +ed   t+
  EPA06834.1 104 GKNKKYKMRLIESSATDTPLPKIPYDSKITLSSSRFDKILGDVQVVSDYLTIHTSDSKADF---SGKGDSG--EVVIDLEKDAEEIGEISSKEDSVGTY 197
                 999*************************************************999988654...4444333..67788888999999999999999999 PP

        Rad9 202 slkefkallvfaeslsaslslafdeaGkPllltikklslleakfil 247
                 sl  +  ++  + ++  +++++f+   kPl +++k  +   ++f l
  EPA06834.1 198 SLEYLNPVVKAVGTTAGQITCEFSSS-KPLRIEFKVANIGRIHFYL 242
                 99999999999999999999999865.8888888855555555555 PP

>> Receptor_2B4  Natural killer cell receptor 2B4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   3.8e-05      0.14      26      84 ..      32      89 ..       8     112 .. 0.81
   2 ?   -3.3   0.0       2.8     1e+04      78      92 ..     189     203 ..     185     212 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.8e-05
                  SSEEEEEEEEETSSSEEE.EEEEETTEEEESSTTHHHH.EEEETTTTEEEESS-SGGG-E CS
  Receptor_2B4 26 kdvsiewkkkeqshrkieqilkwendslkssnvsssdi.ygfevknlalsiksaklqdsG 84
                    + i ++ + +sh  + + + w n+  ++ + + sdi +g  +++++ +ik a ++ds 
    EPA06834.1 32 TAEGITFRGMDPSHVALID-ISWPNSAFEKYE-CDSDIkFGVRIDEFSKLIKRADKKDSI 89
                  5567778888888888774.69*******999.666644*******************95 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.8
                   -SGGG-EEEEEEEEE CS
  Receptor_2B4  78 aklqdsGlylleitn 92 
                   +k +  G y le  n
    EPA06834.1 189 SKEDSVGTYSLEYLN 203
                   455556788877654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 1744.06
//
Query:       EPA06835.1  [L=283]
Description: CBS domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.5e-43  145.5   8.9    3.3e-12   46.7   0.2    4.1  4  CBS           CBS domain
  ------ inclusion threshold ------
      0.012   15.5   0.4       0.62   10.0   0.0    2.9  3  LAMTOR5       Ragulator complex protein LAMTOR5
       0.04   14.2   1.3         11    6.4   0.0    3.5  3  IF3_N         Translation initiation factor IF-3, N-terminal 
       0.15   11.9   2.5        3.2    7.6   0.2    2.7  2  Peptidase_S7  Peptidase S7, Flavivirus NS3 serine protease
       0.28   11.5   6.3         24    5.3   0.0    4.2  3  UPF0113       UPF0113 PUA domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.1   1.1e-11   4.1e-08       6      55 ..       6      54 ..       2      56 .. 0.90
   2 !   28.7   0.1   3.8e-10   1.3e-06       2      53 ..      69     122 ..      68     125 .. 0.88
   3 !   39.9   0.0   1.2e-13   4.4e-10       1      51 [.     134     184 ..     134     189 .. 0.91
   4 !   46.7   0.2   9.1e-16   3.3e-12       1      55 [.     212     266 ..     212     267 .. 0.96

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 1.1e-11
                BSSCEEEETTSBHHHHHHHHHHHT.SSEEEEEETTTBEEEEEEHHHHHHHH CS
         CBS  6 trdvvtvppdttleealelmrekg.vsrlPVVdedgklvGivtlrDllral 55
                +++v+t++p+ ++ +al +m +++ v ++ VV   + +vGivt+rD+ r+l
  EPA06835.1  6 STPVITIKPELSIFDALLEM-QTKfVKHI-VVAVKNIPVGIVTERDINRFL 54
                79******************.8889****.7755889**********9998 PP

  == domain 2  score: 28.7 bits;  conditional E-value: 3.8e-10
                 HHHSBSSCEEEETT..SBHHHHHHHHHHHTSSEEEE.EETTTBEEEEEEHHHHHH CS
         CBS   2 gdimtrdvvtvppd..ttleealelmrekgvsrlPV.VdedgklvGivtlrDllr 53 
                 +++m ++v++++    +   +++ +m+  +++++ V V+++g+++Giv+++Dl +
  EPA06835.1  69 KHVMQKNVISITDGmeDHFVQCAARMETFKIGSV-VlVNDNGEIIGIVSRTDLTK 122
                 789******999999788********6555****.659**************976 PP

  == domain 3  score: 39.9 bits;  conditional E-value: 1.2e-13
                 HHHHSBSSCEEEETTSBHHHHHHHHHHHT.SSEEEEEETTTBEEEEEEHHHH CS
         CBS   1 Vgdimtrdvvtvppdttleealelmrekg.vsrlPVVdedgklvGivtlrDl 51 
                 V+++m++++vt++ +++l+ +  lm +k+ vsr+ V+de+g++vG+++   l
  EPA06835.1 134 VKQFMNKKIVTCRKNDSLKFVSSLM-NKNqVSRVIVTDENGNPVGLISTNTL 184
                 89***********************.7778****888**********97665 PP

  == domain 4  score: 46.7 bits;  conditional E-value: 9.1e-16
                 HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
         CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                 V+d+ t+++vtv+++++l+ a+ +m+++ ++++PV++++++lvGiv+++D++ra 
  EPA06835.1 212 VEDLLTDELVTVNEEDDLAIAASKMIKNQIGGIPVINSNHNLVGIVSKTDVVRAF 266
                 899**********************9999***********************985 PP

>> LAMTOR5  Ragulator complex protein LAMTOR5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       2.7   9.5e+03      61      69 ..       6      14 ..       4      20 .. 0.79
   2 ?    2.1   0.0      0.05   1.8e+02       1      43 [.      83     126 ..      83     129 .. 0.78
   3 ?   10.0   0.0   0.00017      0.62       7      32 ..     152     177 ..     146     183 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2.7
     LAMTOR5 61 eaPvitles 69
                ++Pvit++ 
  EPA06835.1  6 STPVITIKP 14
                589**9985 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.05
     LAMTOR5   1 mekqleevldevmskegvvGvlcaDeqGLcl..gsrGtlsnksag 43 
                 me ++ ++ ++ m++ ++  v++++++G  +   sr +l+++ a 
  EPA06835.1  83 MEDHFVQCAAR-METFKIGSVVLVNDNGEIIgiVSRTDLTKSYAS 126
                 78888887777.79999***********66633688888887776 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00017
     LAMTOR5   7 evldevmskegvvGvlcaDeqGLclg 32 
                 ++++ +m+k++v+ v+++De+G ++g
  EPA06835.1 152 KFVSSLMNKNQVSRVIVTDENGNPVG 177
                 78999*****************8876 PP

>> IF3_N  Translation initiation factor IF-3, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0031        11       9      27 ..     101     119 ..      95     125 .. 0.86
   2 ?    3.2   0.0     0.029     1e+02       7      27 ..     163     183 ..     158     188 .. 0.85
   3 ?    0.9   0.0      0.16   5.7e+02      10      30 ..     244     264 ..     237     268 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0031
                 EEEEE-SSS-EEEEEEHHH CS
       IF3_N   9 evrlvdedGeqlGvistre 27 
                  v lv+++Ge +G++s+ +
  EPA06835.1 101 SVVLVNDNGEIIGIVSRTD 119
                 799*************987 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.029
                 SSEEEEE-SSS-EEEEEEHHH CS
       IF3_N   7 arevrlvdedGeqlGvistre 27 
                 ++ v + de+G+ +G ist+ 
  EPA06835.1 163 VSRVIVTDENGNPVGLISTNT 183
                 57899999**********986 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.16
                 EEEE-SSS-EEEEEEHHHHHH CS
       IF3_N  10 vrlvdedGeqlGvistreAlr 30 
                 + +++++ + +G++s+ +++r
  EPA06835.1 244 IPVINSNHNLVGIVSKTDVVR 264
                 77999998889*****99987 PP

>> Peptidase_S7  Peptidase S7, Flavivirus NS3 serine protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.2   0.00089       3.2     101     126 ..     103     128 ..      98     131 .. 0.81
   2 ?    3.3   0.2     0.019        67      99     120 ..     243     264 ..     240     270 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00089
                   EEE-TTSXEEEECEEEEEXTTSXEEE CS
  Peptidase_S7 101 lvlnqnkqivgiYfatvevdkkeaev 126
                    ++n+n++i+gi + t+++++   ++
    EPA06835.1 103 VLVNDNGEIIGIVSRTDLTKSYASVF 128
                   358****************9766665 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.019
                   TSEEE-TTSXEEEECEEEEEXT CS
  Peptidase_S7  99 GSlvlnqnkqivgiYfatvevd 120
                   G +v+n+n + vgi + t++v 
    EPA06835.1 243 GIPVINSNHNLVGIVSKTDVVR 264
                   669*************999987 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.7     0.011        41      29      48 ..      96     114 ..      69     125 .. 0.61
   2 ?    5.3   0.0    0.0066        24      30      48 ..     160     178 ..     138     190 .. 0.83
   3 ?   -1.3   0.1      0.77   2.8e+03      32      48 ..     240     256 ..     230     261 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.011
     UPF0113  29 svkenqvvvVlnengeplGi 48 
                  +k  + vv++n nge++Gi
  EPA06835.1  96 TFK-IGSVVLVNDNGEIIGI 114
                 333.3345556888888886 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0066
     UPF0113  30 vkenqvvvVlnengeplGi 48 
                 +++  +v+V +eng+p+G+
  EPA06835.1 160 KNQVSRVIVTDENGNPVGL 178
                 455678***********97 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.77
     UPF0113  32 enqvvvVlnengeplGi 48 
                 + +++ V n n +++Gi
  EPA06835.1 240 QIGGIPVINSNHNLVGI 256
                 44567799999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1722.88
//
Query:       EPA06836.1  [L=99]
Description: 4Fe-4S binding domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-11   43.2  10.6    5.1e-07   29.3   0.7    2.3  2  Fer4      4Fe-4S binding domain
    6.9e-09   36.2   3.7    9.8e-09   35.7   3.7    1.2  1  Fer4_7    4Fe-4S dicluster domain
    3.5e-08   33.2   8.1     0.0013   18.7   0.6    2.2  2  Fer4_6    4Fe-4S binding domain
    4.5e-08   33.1   1.8    6.4e-08   32.6   1.8    1.2  1  Fer4_21   4Fe-4S dicluster domain
    4.4e-06   26.8   4.1    1.8e-05   24.8   4.2    1.8  2  Fer4_9    4Fe-4S dicluster domain
    1.5e-05   24.8   7.8      0.018   15.1   1.7    2.3  2  Fer4_2    4Fe-4S binding domain
    7.9e-05   23.1   4.2       0.12   12.9   0.5    2.3  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
    0.00014   21.9   8.3     0.0054   16.8   9.2    2.0  2  Fer4_10   4Fe-4S dicluster domain
    0.00025   21.3   6.9      0.081   13.5   2.0    2.2  2  Fer4_4    4Fe-4S binding domain
    0.00027   21.8   5.4      0.075   14.0   0.1    2.1  2  Fer4_16   4Fe-4S double cluster binding domain
     0.0013   19.5  11.2      0.097   13.7   3.6    2.3  2  Fer4_3    4Fe-4S binding domain
     0.0019   19.0   3.8        0.3   12.0   0.9    2.1  2  Fer4_22   4Fe-4S dicluster domain
     0.0052   17.2   5.8      0.048   14.1   5.8    2.0  1  Fer4_8    4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.031   14.8   6.7          1    9.9   6.8    2.1  1  Fer4_17   4Fe-4S dicluster domain
       0.08   13.7  10.7       0.51   11.1   2.1    2.8  2  Fer4_15   4Fe-4S single cluster domain
        0.7   10.1  10.3        1.8    8.8   3.1    2.1  2  Fer4_18   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   3.4   1.2e-06    0.0013       2      18 ..       8      24 ..       7      26 .. 0.90
   2 !   29.3   0.7   4.5e-10   5.1e-07       2      23 ..      47      68 ..      46      69 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.2e-06
                EEETTTSSS-THHHHHS CS
        Fer4  2 videekCigCGaCvevC 18
                 i e +CigC +Cve+C
  EPA06836.1  8 DISEQMCIGCALCVEIC 24
                58899************ PP

  == domain 2  score: 29.3 bits;  conditional E-value: 4.5e-10
                EEETTTSSS-THHHHHSTTTEE CS
        Fer4  2 videekCigCGaCvevCPvgAI 23
                v+ +e+Ci  GaC+ vCP+ AI
  EPA06836.1 47 VFYPERCISDGACIGVCPTKAI 68
                688******************9 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   3.7   8.7e-12   9.8e-09       2      52 .]      14      67 ..      13      67 .. 0.93

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 8.7e-12
      Fer4_7  2 CigCgaCvaaCp...vkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                CigC  Cv+ C     ++++++++e  k+ +  ++ pe+C++ gaC+ vCPt+a
  EPA06836.1 14 CIGCALCVEICTtlgPDVLRVKPVEGWKRGKAFVFYPERCISDGACIGVCPTKA 67
                ***********877789*******999999999*******************87 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   1.6   1.5e-06    0.0016       2      19 ..       7      24 ..       6      28 .. 0.90
   2 !   18.7   0.6   1.1e-06    0.0013       6      24 .]      50      68 ..      45      68 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.5e-06
      Fer4_6  2 veidpdkCigCgdCvrvC 19
                + i ++ CigC  Cv +C
  EPA06836.1  7 PDISEQMCIGCALCVEIC 24
                67899************* PP

  == domain 2  score: 18.7 bits;  conditional E-value: 1.1e-06
      Fer4_6  6 pdkCigCgdCvrvCPegai 24
                p++Ci+ g+C+ vCP++ai
  EPA06836.1 50 PERCISDGACIGVCPTKAI 68
                89***************98 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   1.8   5.7e-11   6.4e-08       3      57 ..       9      68 ..       7      71 .. 0.81

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 5.7e-11
     Fer4_21  3 idedkCigCgkCliaCedtshqaieidaktvl......kvvedeCvGCnlCssvCPvedci 57
                i e++CigC +C+  C + + + +++++ + +          ++C+    C+ vCP+ ++i
  EPA06836.1  9 ISEQMCIGCALCVEICTTLGPDVLRVKPVEGWkrgkafVFYPERCISDGACIGVCPT-KAI 68
                899*********************888776443333225569**************7.444 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   2.5    0.0001      0.11      34      48 ..      12      26 ..       4      28 .. 0.79
   2 !   24.8   4.2   1.6e-08   1.8e-05       2      51 .]      14      68 ..      13      68 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0001
      Fer4_9 34 eaCigCgaCveaCpk 48
                + CigC  Cve+C +
  EPA06836.1 12 QMCIGCALCVEICTT 26
                479999999999975 PP

  == domain 2  score: 24.8 bits;  conditional E-value: 1.6e-08
      Fer4_9  2 CtgCgaCveaC...pagvvvedaaerkarlraase..eaCigCgaCveaCpkgai 51
                C+gC  Cve C     +v + + +e+  r +a+    e+Ci+ gaC+ +Cp++ai
  EPA06836.1 14 CIGCALCVEICttlGPDVLRVKPVEGWKRGKAFVFypERCISDGACIGVCPTKAI 68
                ***********6665566677777777777665559999*************997 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   1.7   1.6e-05     0.018       5      22 .]       9      26 ..       5      26 .. 0.86
   2 !   13.2   0.5   6.5e-05     0.073       3      22 .]      46      65 ..      44      65 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.6e-05
      Fer4_2  5 vdtdrCigCgaCvsaCPa 22
                + +++CigC  Cv  C +
  EPA06836.1  9 ISEQMCIGCALCVEICTT 26
                5689************75 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 6.5e-05
      Fer4_2  3 vvvdtdrCigCgaCvsaCPa 22
                +v+ ++rCi+ gaC+ +CP+
  EPA06836.1 46 FVFYPERCISDGACIGVCPT 65
                78999***988********7 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.5   0.00011      0.12       4      17 ..      12      25 ..       9      39 .. 0.85
   2 !   11.7   0.2   0.00026      0.29       4      18 ..      51      65 ..      50      79 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
     Fer4_13  4 dtCiacgaCvelaP 17
                + Ci+c++Cve++ 
  EPA06836.1 12 QMCIGCALCVEICT 25
                67**********94 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00026
     Fer4_13  4 dtCiacgaCvelaPd 18
                ++Ci++gaC  ++P 
  EPA06836.1 51 ERCISDGACIGVCPT 65
                79************5 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   9.2   4.8e-06    0.0054       4      56 .]       9      64 ..       6      64 .. 0.82
   2 !   13.9   0.4   3.9e-05     0.044       5      23 ..      49      67 ..      45      93 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.8e-06
     Fer4_10  4 idddtCirCgkCvkaCPadl....tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                i ++ Ci+C+ Cv+ C ++l     +v+  +  ++++a    +e+C+  gaC+ +CP
  EPA06836.1  9 ISEQMCIGCALCVEIC-TTLgpdvLRVKPVEGWKRGKAFVFYPERCISDGACIGVCP 64
                67889***********.5569997666666666666666779**************9 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 3.9e-05
     Fer4_10  5 dddtCirCgkCvkaCPadl 23
                 +++Ci  g+C  +CP+++
  EPA06836.1 49 YPERCISDGACIGVCPTKA 67
                5799************955 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   2.0   7.2e-05     0.081       2      15 ..      12      25 ..      11      28 .. 0.90
   2 !   10.5   0.2   0.00063       0.7       1      16 [.      50      65 ..      50      72 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.2e-05
      Fer4_4  2 erCigCgsCvaaCP 15
                + CigC  Cv +C 
  EPA06836.1 12 QMCIGCALCVEICT 25
                68***********5 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00063
      Fer4_4  1 qerCigCgsCvaaCPq 16
                +erCi  g+C+ +CP+
  EPA06836.1 50 PERCISDGACIGVCPT 65
                69*************7 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   1.6    0.0014       1.6      53      65 ..      13      25 ..       5      27 .. 0.71
   2 !   14.0   0.1   6.7e-05     0.075       1      17 [.      52      68 ..      52      80 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0014
     Fer4_16 53 aitgCdiCqdvCP 65
                 ++gC+ C+++C 
  EPA06836.1 13 MCIGCALCVEICT 25
                4777888877774 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 6.7e-05
     Fer4_16  1 rCgtCgkCaevCPtnai 17
                rC++ g+C+ vCPt+ai
  EPA06836.1 52 RCISDGACIGVCPTKAI 68
                69999***********9 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   3.6   8.6e-05     0.097       1      12 [.      14      25 ..      14      28 .. 0.92
   2 !   10.6   0.9   0.00084      0.94       1      15 []      53      67 ..      52      67 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.6e-05
      Fer4_3  1 CtgCgaCvevCP 12
                C+gC +Cve C 
  EPA06836.1 14 CIGCALCVEICT 25
                ***********6 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00084
      Fer4_3  1 CtgCgaCvevCPvgA 15
                C+  gaC  vCP++A
  EPA06836.1 53 CISDGACIGVCPTKA 67
                55558********98 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.9   0.00026       0.3      77      93 ..       9      25 ..       4      27 .. 0.85
   2 !    8.0   0.1    0.0045         5       1      18 [.      52      69 ..      52      83 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00026
     Fer4_22 77 fgesgCvGCgRCieacp 93
                ++e++C+GC  C+e c+
  EPA06836.1  9 ISEQMCIGCALCVEICT 25
                6789************7 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0045
     Fer4_22  1 rClsCgaCtlvCptCsCf 18
                rC+s gaC  vCpt   f
  EPA06836.1 52 RCISDGACIGVCPTKAIF 69
                7*************7766 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   5.8   4.3e-05     0.048       4      64 ..      13      66 ..      11      67 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.3e-05
      Fer4_8  4 kCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64
                 Ci+C +C + C +l     + +  +g + + +    +       ++C + gaC  vCp++
  EPA06836.1 13 MCIGCALCVEICTTLGPDVLRVKPVEGWKRG-KAFVFY------PERCISDGACIGVCPTK 66
                6***********7776666666666666555.333333......799************97 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   6.8   0.00092         1       2      58 ..      14      65 ..      13      68 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00092
     Fer4_17  2 CiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPq 58
                Ci+C+ C++ C ++      + k+++      +++     + ++Ci+ g C  +CP 
  EPA06836.1 14 CIGCALCVEICTTLGPDVL-RVKPVEG----WKRGKAFVFYPERCISDGACIGVCPT 65
                *********8877655433.3344444....44444456899*************96 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   2.1   0.00046      0.51       6      20 ..      12      26 ..       8      48 .. 0.80
   2 ?    6.0   1.8     0.018        20       6      20 ..      51      65 ..      47      69 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00046
     Fer4_15  6 daCigcglCvaeape 20
                + Cigc+lCv+ +++
  EPA06836.1 12 QMCIGCALCVEICTT 26
                68**********954 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.018
     Fer4_15  6 daCigcglCvaeape 20
                ++Ci++g+C+ ++p+
  EPA06836.1 51 ERCISDGACIGVCPT 65
                79*******999985 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   3.1    0.0016       1.8      84      98 ..      13      27 ..       2      42 .. 0.74
   2 ?    6.1   0.7     0.011        12      60      74 ..      52      66 ..      42      70 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0016
     Fer4_18 84 eciscllcidacdkv 98
                 ci c+lc++ c+++
  EPA06836.1 13 MCIGCALCVEICTTL 27
                477777777777765 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.011
     Fer4_18 60 dcidcescvkvcPtg 74
                 ci+ ++c+ vcPt+
  EPA06836.1 52 RCISDGACIGVCPTK 66
                69999********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 584.30
//
Query:       EPA06837.1  [L=292]
Description: ribose-phosphate diphosphokinase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.9e-29  100.1   0.3      2e-28   98.7   0.1    1.8  2  Pribosyltran_N  N-terminal domain of ribose phosphate pyropho
    1.7e-19   69.9   2.2      2e-19   69.7   0.5    1.9  2  Pribosyltran    Phosphoribosyl transferase domain
    1.7e-14   54.3   1.6      1e-12   48.5   0.5    2.9  3  Pribosyl_synth  Phosphoribosyl synthetase-associated domain
    0.00013   21.5   0.1     0.0003   20.3   0.0    1.6  2  UPRTase         Uracil phosphoribosyltransferase
     0.0035   16.9   0.1     0.0072   15.9   0.1    1.5  1  PRTase_2        Phosphoribosyl transferase
      0.007   16.2   0.0      0.042   13.7   0.0    2.0  2  Asp_Glu_race    Asp/Glu/Hydantoin racemase
  ------ inclusion threshold ------
        2.8    8.2   6.2        2.8    8.2   3.5    2.4  2  Cu              Cupiennin


Domain annotation for each model (and alignments):
>> Pribosyltran_N  N-terminal domain of ribose phosphate pyrophosphokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.7   0.1   7.8e-32     2e-28       2     116 .]       5     119 ..       4     119 .. 0.97
   2 ?   -1.7   0.0         1   2.6e+03      33      57 ..     196     222 ..     171     245 .. 0.66

  Alignments for each domain:
  == domain 1  score: 98.7 bits;  conditional E-value: 7.8e-32
  Pribosyltran_N   2 kifagssskeLaekiakrlgvelgkakvsrfadgEikveieesvrgkdvfiiqslskpvndnlmelllmidalrrasakritaViPylgysrqdr 96 
                      +++gsss++La+k+ak+l  +l+k++++ f+dgE k++++e+ +++++++iqs+ +pv+++l++ l +i+ ++     ++++ViPy+gy+rqdr
      EPA06837.1   5 TVISGSSSEDLAKKVAKKLRANLIKSQLKIFPDGESKITLNEKPQKNKIIVIQSTYPPVDEKLIQTLAIISKAK-EYGTEVIVVIPYMGYARQDR 98 
                     589**********************************************************************9.6668999************* PP

  Pribosyltran_N  97 k.ksrepisaklvaklLeaaG 116
                     +  + e i++k++a+l++++G
      EPA06837.1  99 EfLPGEVITMKVIANLFKSVG 119
                     ******************998 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1
  Pribosyltran_N  33 adgEikveiee..svrgkdvfiiqsls 57 
                     ++g +k++  +  ++ g+d++++ ++ 
      EPA06837.1 196 KTGKVKIKSTNfdQIAGRDLILVDDMI 222
                     344444444435588888888887765 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.3   3.2e+03     102     121 ..     107     126 ..     105     129 .. 0.74
   2 !   69.7   0.5   7.7e-23     2e-19      19     144 ..     150     272 ..     140     283 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.3
                   HHHHHHHHHHCC-BSEEEEE CS
  Pribosyltran 102 TllaalelLkekgpeevria 121
                   T++ +++l k++g  +++++
    EPA06837.1 107 TMKVIANLFKSVGTSKIIVV 126
                   77888888888887777654 PP

  == domain 2  score: 69.7 bits;  conditional E-value: 7.7e-23
                   TEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE----TTSEEEEE-SEESSSHHHHHHHHHHHCC-B CS
  Pribosyltran  19 aaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrlledpagkkVliVDDildtGgTllaalelLkekgp 115
                   +a+++++ + k+++vv +++gG  +ak+ a+ L+v++ +++k++ r+ g+ +++ +      +   +ag+  ++VDD+++tGg++++a+e+Lk++++
    EPA06837.1 150 LAKYISKLKLKNPLVVSPDKGGKDRAKEFAKILNVEYIFLDKERNRKTGKVKIKST------NFDQIAGRDLILVDDMISTGGSIIKATEFLKKQKC 240
                   35556666999******************************************965......8899******************************* PP

                   SEEEEEEEE...E-HHHHHHHHHH-TTS.... CS
  Pribosyltran 116 eevriavlv...dkpateeevdknakrvfsls 144
                    +v +a+ +   ++ a  + +++++++++s++
    EPA06837.1 241 NRVFVACTHallRNDAENKIKKAGVTKIISTN 272
                   *******9987655555555666666666555 PP

>> Pribosyl_synth  Phosphoribosyl synthetase-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.048   1.2e+02     100     124 ..     109     133 ..      99     149 .. 0.74
   2 ?    0.2   0.0      0.25   6.5e+02       2      33 ..     159     190 ..     158     203 .. 0.80
   3 !   48.5   0.5   3.9e-16     1e-12      71     162 ..     200     283 ..     191     292 .] 0.86

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.048
                     HHHHHHHHHTT--EEEEEEEEE--- CS
  Pribosyl_synth 100 vaaaevlkerGaykiyvlathGlls 124
                        a+++k  G+ ki+v+  h ll 
      EPA06837.1 109 KVIANLFKSVGTSKIIVVDIHSLLG 133
                     4457788888888888888887775 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.25
                     GGGEEEEESSGGGHHHHHHHHHHTT-EEEEE- CS
  Pribosyl_synth   2 yrnavivakspgsakkatsyaerlrlglavih 33 
                      +n ++v+ + g  ++a+ +a+ l++    + 
      EPA06837.1 159 LKNPLVVSPDKGGKDRAKEFAKILNVEYIFLD 190
                     58999****************99987665555 PP

  == domain 3  score: 48.5 bits;  conditional E-value: 3.9e-16
                     ------EES--TTSEEEEEEEEE-S-HHHHHHHHHHHHTT--EEEEEEEEE---TTHHHHHHHSS--EEEEESSS--HHHHHT-TTEEEE-- CS
  Pribosyl_synth  71 ekppltvvGdvgGriaiivddliddvesfvaaaevlkerGaykiyvlathGllssdaprlleesaidevvvtntipheiqklrcskiktvdi 162
                      k   t    ++Gr  i+vdd+i    s+++a+e lk++   +++v +th ll +da ++++++ +++++ tntip +           vdi
      EPA06837.1 200 VKIKSTNFDQIAGRDLILVDDMISTGGSIIKATEFLKKQKCNRVFVACTHALLRNDAENKIKKAGVTKIISTNTIPGNTS--------LVDI 283
                     555556667899****************************************************************9874........3444 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.4   3.6e+03     138     158 ..     108     127 ..     107     145 .. 0.73
   2 !   20.3   0.0   1.2e-07    0.0003     100     158 ..     192     247 ..     169     270 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.4
     UPRTase 138 aaaiqlLkergvgeekIlvls 158
                 +++i  L +  vg++kI+v+ 
  EPA06837.1 108 MKVIANLFK-SVGTSKIIVVD 127
                 566777766.57888888876 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 1.2e-07
     UPRTase 100 qreeetlepveyynkLPkkiaertvlllDpviaTGgsaaaaiqlLkergvgeekIlvls 158
                 +r+ +t + ++  +++  +ia r  +l+D +i+TGgs+++a + Lk++ +  ++++v++
  EPA06837.1 192 ERNRKTGKVKIKSTNFD-QIAGRDLILVDDMISTGGSIIKATEFLKKQKC--NRVFVAC 247
                 45555555555555554.469999***********************665..5666654 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   2.8e-06    0.0072     121     169 ..     212     259 ..     198     274 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.8e-06
    PRTase_2 121 akelvLvDDEistGktalnliralqeklprkryvvvslvdwrseedeaa 169
                  + l+LvDD istG ++++  + l+++  ++ +v ++   +r+++ e++
  EPA06837.1 212 GRDLILVDDMISTGGSIIKATEFLKKQKCNRVFVACTHALLRNDA-ENK 259
                 478*********************999988887777766666665.333 PP

>> Asp_Glu_race  Asp/Glu/Hydantoin racemase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0       0.2     5e+02       3      38 ..       6      41 ..       5     125 .. 0.73
   2 !   13.7   0.0   1.6e-05     0.042     171     216 ..     227     272 ..     176     275 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.2
                  ECSCCCCHHHHHHHHHHBTTSSGGGS..EEEEE-CC CS
  Asp_Glu_race  3 gmgpeatlsvlrklveatpaesdqehlplivlndsa 38
                  ++++++++++ +k+ ++++a   + +l+++  + s+
    EPA06837.1  6 VISGSSSEDLAKKVAKKLRANLIKSQLKIFPDGESK 41
                  689999999999999999988877666666666555 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 1.6e-05
                   HHHHHHHHHHTTT-SEEEE-STTHHHHHHHHHHCC-TT.SEEEEHH CS
  Asp_Glu_race 171 ailkllerlaergadaviLGCTelplllekaealekeksvpvidpt 216
                    i+k+ e l+++++++v+++CT+  l  +++ +++k+   ++i+++
    EPA06837.1 227 SIIKATEFLKKQKCNRVFVACTHALLRNDAENKIKKAGVTKIISTN 272
                   5778888889*************99988888888777666666666 PP

>> Cu  Cupiennin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   3.5    0.0011       2.8       9      18 ..      15      25 ..      15      33 .. 0.76
   2 ?   -1.7   0.0       1.3   3.4e+03      17      23 ..     150     156 ..     141     157 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0011
          Cu  9 LAKKvAKtv.a 18
                LAKKvAK++ a
  EPA06837.1 15 LAKKVAKKLrA 25
                9*******952 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.3
          Cu  17 vakyiAk 23 
                 +akyi k
  EPA06837.1 150 LAKYISK 156
                 4899876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       678  (0.0378158); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 2002.84
//
Query:       EPA06838.1  [L=103]
Description: transcription factor S [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-19   70.0   5.9    1.1e-19   70.0   5.9    3.1  3  TFIIS_C         Transcription factor S-II (TFIIS)
     0.0004   20.3   9.4      0.014   15.4   1.7    2.5  2  DZR             Double zinc ribbon
    0.00058   19.7  15.8       0.21   11.5   5.9    3.6  3  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
     0.0072   16.2  15.0       0.65   10.0   0.4    4.1  3  zinc_ribbon_4   zinc-ribbon domain
  ------ inclusion threshold ------
      0.025   14.5   1.3      0.025   14.5   1.3    2.4  3  Prok-RING_1     Prokaryotic RING finger family 1
       0.08   12.9  15.3      0.076   13.0   3.2    3.4  3  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
      0.099   12.7   7.4       0.15   12.2   7.4    1.3  1  zf-RRPl_C4      Putative ribonucleoprotein zinc-finger pf C4 
       0.14   11.9  10.1       0.11   12.2   2.2    3.7  3  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
       0.17   11.6   0.0       0.17   11.6   0.0    2.9  3  Baculo_LEF5_C   Baculoviridae late expression factor 5 C-term
       0.25   11.9  15.5        2.3    8.8   0.6    4.0  4  zf-H2C2_2       Zinc-finger double domain
       0.25   11.3   9.5       0.79    9.7   1.2    2.7  2  C1_1            Phorbol esters/diacylglycerol binding domain 
        0.3   10.8  12.9       0.91    9.3   0.2    3.9  4  A2L_zn_ribbon   A2L zinc ribbon domain
       0.35   10.9  11.7    1.5e+02    2.4  11.7    2.8  1  zinc-ribbons_6  zinc-ribbons
       0.37   11.2  14.0        4.1    7.8   1.4    2.9  2  C1_2            C1 domain
       0.58    9.9  15.9         13    5.6   0.1    4.0  3  zinc_ribbon_2   zinc-ribbon domain
       0.79   10.2   7.6         19    5.8   0.8    3.1  3  Ribosomal_L44   Ribosomal protein L44
       0.99    9.9  10.9       0.18   12.2   6.6    2.0  1  DUF3795         Protein of unknown function (DUF3795)
        1.1    9.6  12.4        4.3    7.7   0.6    3.5  3  C1_4            TFIIH C1-like domain
        1.3    9.3  12.9        4.8    7.5   2.8    3.0  2  IBR             IBR domain, a half RING-finger domain
        1.7    8.4  12.1         13    5.7   3.4    3.9  3  Zn_Tnp_IS1      InsA N-terminal domain
        2.3    8.3  12.1        3.6    7.6   2.5    2.6  2  HypA            Hydrogenase/urease nickel incorporation, meta
        2.5    8.1  12.6       0.84    9.6   1.4    3.0  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
          6    6.4  17.5         33    4.1   5.9    4.1  3  zf-ribbon_3     zinc-ribbon domain
        7.8    7.3  16.9    7.8e+02    0.9  16.9    2.8  1  zinc_ribbon_15  zinc-ribbon family
        7.9    6.7  15.1        8.5    6.6   0.0    4.2  4  Zn-ribbon_8     Zinc ribbon domain
          8    6.9  11.3    1.6e+02    2.7  11.3    2.4  1  DnaJ_CXXCXGXG   DnaJ central domain
        8.3    5.8  15.0        5.5    6.4   3.4    3.6  3  zf-TFIIB        Transcription factor zinc-finger


Domain annotation for each model (and alignments):
>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.5      0.96   6.4e+02       2       7 ..       3       8 ..       2      10 .. 0.77
   2 ?    4.3   0.2     0.054        36       2       8 ..      19      25 ..      18      41 .. 0.83
   3 !   70.0   5.9   1.7e-22   1.1e-19       1      39 []      62     100 ..      62     100 .. 0.98

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.96
     TFIIS_C 2 kCpkCg 7
                Cp+C 
  EPA06838.1 3 FCPSCE 8
               599997 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.054
     TFIIS_C  2 kCpkCgs 8 
                +CpkC+ 
  EPA06838.1 19 QCPKCDY 25
                8***985 PP

  == domain 3  score: 70.0 bits;  conditional E-value: 1.7e-22
     TFIIS_C   1 akCpkCgsreayffqlQtRsaDEpmtvfykCtkCghrWr 39 
                 ++C+kCg++ea++++lQtRsaDEp+t fy+C kC ++Wr
  EPA06838.1  62 IECEKCGNDEAVWWMLQTRSADEPTTQFYRCSKCRYTWR 100
                 68************************************8 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   1.7   2.2e-05     0.014      13      37 ..       2      26 ..       1      35 [. 0.87
   2 !    9.2   1.1    0.0018       1.2      10      37 ..      59      98 ..      51     103 .] 0.76

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.2e-05
         DZR 13 rfCseCgtklkavaaedrCpsCgek 37
                +fC+ C  klk+  +  +Cp+C++ 
  EPA06838.1  2 KFCPSCEVKLKKGDSGLQCPKCDYV 26
                8**********9999*******987 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0018
         DZR 10 pdarfCseCgtk......lkavaa......edrCpsCgek 37
                  ++ C++Cg++      l+  +a       +rC++C + 
  EPA06838.1 59 TIKIECEKCGNDeavwwmLQTRSAdepttqFYRCSKCRYT 98
                55677*****998876665544448999999******986 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   5.9   0.00032      0.21       1      34 [.       1      30 [.       1      32 [. 0.78
   2 ?    3.9   0.3     0.073        49       4       9 ..      64      69 ..      53      74 .. 0.72
   3 !   10.4   2.5   0.00072      0.48       4      29 ..      64      97 ..      62      99 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00032
                    EEBESTTTSBEEEEECSCCCEEEESSSS-EEESS CS
  RNA_POL_M_15KD  1 lkFCpkCgNlLlpkedkegknfeCrqCgYeepad 34
                    +kFCp+C   L  k++++g  + C +C+Y+e ++
      EPA06838.1  1 MKFCPSCEVKL--KKGDSG--LQCPKCDYVEGKE 30
                    9******8554..666666..78*******9766 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.073
                    ESTTTS CS
  RNA_POL_M_15KD  4 CpkCgN 9 
                    C kCgN
      EPA06838.1 64 CEKCGN 69
                    555555 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00072
                    ESTTTS......BEEEEECSCCCE..EEESSSS- CS
  RNA_POL_M_15KD  4 CpkCgN......lLlpkedkegkn..feCrqCgY 29
                    C kCgN      +L  ++++e +   + C++C Y
      EPA06838.1 64 CEKCGNdeavwwMLQTRSADEPTTqfYRCSKCRY 97
                    99****999999********99999********9 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   3.9     0.047        31      18      33 ..      10      25 ..       3      26 .. 0.82
   2 ?    6.2   0.2     0.015       9.9      25      32 ..      61      68 ..      58      70 .. 0.62
   3 !   10.0   0.4   0.00098      0.65      27      36 .]      91     100 ..      84     100 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.047
  zinc_ribbon_4 18 klpakgvkvrCskCgh 33
                   kl+++ + ++C+kC  
     EPA06838.1 10 KLKKGDSGLQCPKCDY 25
                   788889999*****86 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.015
  zinc_ribbon_4 25 kvrCskCg 32
                   k+ C kCg
     EPA06838.1 61 KIECEKCG 68
                   55566665 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00098
  zinc_ribbon_4  27 rCskCghvFr 36 
                    rCskC+ ++r
     EPA06838.1  91 RCSKCRYTWR 100
                    9********7 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   1.3   3.7e-05     0.025       6      27 ..       3      24 ..       1      35 [. 0.92
   2 ?    0.0   0.2       1.2   8.3e+02       6      11 ..      63      68 ..      59      71 .. 0.61
   3 ?   -2.1   0.1       5.8   3.8e+03       7      11 ..      92      96 ..      89     100 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.7e-05
  Prok-RING_1  6 kCpvCgkelkeedDiVvCpeCg 27
                  Cp C+ +lk++d   +Cp+C 
   EPA06838.1  3 FCPSCEVKLKKGDSGLQCPKCD 24
                 6********************6 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.2
  Prok-RING_1  6 kCpvCg 11
                 +C+ Cg
   EPA06838.1 63 ECEKCG 68
                 555555 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 5.8
  Prok-RING_1  7 CpvCg 11
                 C+ C+
   EPA06838.1 92 CSKCR 96
                 66665 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.4       0.2   1.3e+02      21      27 ..       4      10 ..       2      14 .. 0.81
   2 ?    4.9   0.3      0.04        27      18      26 ..      17      25 ..      13      35 .. 0.80
   3 ?   13.0   3.2   0.00011     0.076      19      46 .]      62      98 ..      48      98 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.2
  Zn_Tnp_IS1595 21 CPhCgsr 27
                   CP C+++
     EPA06838.1  4 CPSCEVK 10
                   ****986 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.04
  Zn_Tnp_IS1595 18 gfvCPhCgs 26
                   g  CP+C +
     EPA06838.1 17 GLQCPKCDY 25
                   678****86 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 0.00011
  Zn_Tnp_IS1595 19 fvCPhCgsr..kayrikt.......rglfqCkeCrkq 46
                     C +Cg++    + ++t        + ++C++Cr++
     EPA06838.1 62 IECEKCGNDeaVWWMLQTrsadeptTQFYRCSKCRYT 98
                   56*******96667777799***************95 PP

>> zf-RRPl_C4  Putative ribonucleoprotein zinc-finger pf C4 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   7.4   0.00023      0.15       1      89 [.       1      98 [.       1     102 [. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00023
  zf-RRPl_C4  1 mkkCkyClskklknlnetvyCeaCeiyfkvknekqkvelvpike...........lekislrdkLCtkCkeknekekeircetfeeylkklklCkeCker 89
                mk C+ C   klk+ +  + C++C+ y + k++kq+ + v+ +e           +e++   ++ C+kC + +    ++++++ +e  ++   C++C+ +
  EPA06838.1  1 MKFCPSCE-VKLKKGDSGLQCPKCD-YVEGKETKQTKTVVEEQEsqfnvlteneaTETLPTIKIECEKCGNDEAVWWMLQTRSADEPTTQFYRCSKCRYT 98
                67788886.579999*********8.889899999999999998899999999988888888999*******999999*******************965 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   2.2   0.00017      0.11       4      29 ..       2      25 ..       1      27 [. 0.92
   2 ?    1.6   0.1      0.32   2.1e+02      22      29 ..      62      69 ..      58      71 .. 0.80
   3 ?    0.3   0.2      0.86   5.7e+02      23      28 ..      91      96 ..      90      98 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00017
  zf-NADH-PPase  4 rFCgrCGaptepaeggwarvCpaCgl 29
                   +FC+ C  ++++++g+ +++Cp C++
     EPA06838.1  2 KFCPSC--EVKLKKGDSGLQCPKCDY 25
                   699999..9***************97 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.32
  zf-NADH-PPase 22 rvCpaCgl 29
                     C+ Cg+
     EPA06838.1 62 IECEKCGN 69
                   579***97 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.86
  zf-NADH-PPase 23 vCpaCg 28
                   +C+ C+
     EPA06838.1 91 RCSKCR 96
                   577776 PP

>> Baculo_LEF5_C  Baculoviridae late expression factor 5 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.3       6.2   4.1e+03      37      41 ..      20      24 ..      19      25 .. 0.80
   2 ?    1.4   0.1      0.39   2.6e+02      36      41 ..      63      68 ..      57      69 .. 0.84
   3 ?   11.6   0.0   0.00025      0.17      23      40 ..      78      95 ..      70      97 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 6.2
  Baculo_LEF5_C 37 CskCg 41
                   C kC 
     EPA06838.1 20 CPKCD 24
                   99*96 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.39
  Baculo_LEF5_C 36 yCskCg 41
                    C kCg
     EPA06838.1 63 ECEKCG 68
                   6****9 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00025
  Baculo_LEF5_C 23 QnRagDEivsfvryCskC 40
                   Q+R+ DE       CskC
     EPA06838.1 78 QTRSADEPTTQFYRCSKC 95
                   *******8776666**** PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.6       1.1   7.3e+02      17      22 ..       4       9 ..       3      13 .. 0.78
   2 ?    8.8   0.6    0.0035       2.3      11      22 ..      14      25 ..       9      26 .. 0.79
   3 ?    3.4   0.1      0.17   1.1e+02      15      21 ..      62      68 ..      50      70 .. 0.82
   4 ?    7.6   0.4    0.0082       5.4      14      23 ..      89      98 ..      84      99 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 1.1
   zf-H2C2_2 17 CplCdk 22
                Cp+C  
  EPA06838.1  4 CPSCEV 9 
                ****75 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0035
   zf-H2C2_2 11 gekpyeCplCdk 22
                g++ ++Cp+Cd+
  EPA06838.1 14 GDSGLQCPKCDY 25
                56668******9 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.17
   zf-H2C2_2 15 yeCplCd 21
                 eC++C+
  EPA06838.1 62 IECEKCG 68
                89****7 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.0082
   zf-H2C2_2 14 pyeCplCdka 23
                +y C++C+++
  EPA06838.1 89 FYRCSKCRYT 98
                49******97 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   1.2    0.0012      0.79      12      36 ..       2      25 ..       1      27 [. 0.92
   2 ?    5.3   1.7     0.028        18      14      37 ..      64      98 ..      61     100 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0012
                -B-TTT-SB--SSSS-EEEETTT-- CS
        C1_1 12 tfCkhCgeflwgkekqglkCswCkl 36
                +fC  C+  l +k+  gl+C  C +
  EPA06838.1  2 KFCPSCEVKL-KKGDSGLQCPKCDY 25
                79********.9***********98 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.028
                -TTT-SB-...........-SSSS-EEEETTT--E CS
        C1_1 14 CkhCgefl...........wgkekqglkCswCkll 37
                C++Cg+              +  +q ++Cs C+++
  EPA06838.1 64 CEKCGNDEavwwmlqtrsaDEPTTQFYRCSKCRYT 98
                55555444445555555533367899******986 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.6       0.9     6e+02      23      28 ..       3       8 ..       2      10 .. 0.84
   2 ?    9.3   0.2    0.0014      0.91      19      31 ..      15      27 ..      11      29 .. 0.87
   3 ?    6.7   0.1    0.0091       6.1       4      16 ..      62      74 ..      60      83 .. 0.76
   4 ?    0.9   0.2      0.58   3.9e+02       5      10 ..      91      96 ..      86      98 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.9
  A2L_zn_ribbon 23 vCieCg 28
                   +C+ C+
     EPA06838.1  3 FCPSCE 8 
                   899997 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0014
  A2L_zn_ribbon 19 qgylvCieCgasf 31
                   +++l+C++C +++
     EPA06838.1 15 DSGLQCPKCDYVE 27
                   89*******9986 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0091
  A2L_zn_ribbon  4 kvCsvCggngiln 16
                   ++C++Cg++  ++
     EPA06838.1 62 IECEKCGNDEAVW 74
                   68******98777 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 0.58
  A2L_zn_ribbon  5 vCsvCg 10
                    Cs+C+
     EPA06838.1 91 RCSKCR 96
                   588885 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4  11.7      0.23   1.5e+02       3      24 ..       4      25 ..       2     103 .] 0.87

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.23
                    -SSS-S--EE-SSEEE-TTT-- CS
  zinc-ribbons_6  3 CpeCqqelekrgeqyhCeaCqe 24
                    Cp+C+ +l+k ++ ++C +C+ 
      EPA06838.1  4 CPSCEVKLKKGDSGLQCPKCDY 25
                    *********9999*******86 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   1.4    0.0061       4.1      19      41 ..       2      26 ..       1      27 [. 0.81
   2 ?    6.9   5.4     0.012       8.1      19      41 ..      62      98 ..      47     100 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0061
        C1_2 19 fnCsaCgrk.idgff.YsCseCdfs 41
                + C  C+ k  +g+    C++Cd++
  EPA06838.1  2 KFCPSCEVKlKKGDSgLQCPKCDYV 26
                7899*****7455557*******96 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.012
        C1_2 19 fnCsaCgrk..............idgff...YsCseCdfs 41
                 +C+ Cg++                      Y+Cs+C+++
  EPA06838.1 62 IECEKCGNDeavwwmlqtrsadeP---TtqfYRCSKCRYT 98
                566666666666666555433222...1445******997 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   6.4     0.057        38       1      19 [.       3      23 ..       3      29 .. 0.84
   2 ?    5.6   0.1      0.02        13       2       7 ..      64      69 ..      50      70 .. 0.78
   3 ?    4.0   0.3     0.067        44      14      21 ..      88      97 ..      84      98 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.057
  zinc_ribbon_2  1 fCpnCGaelqdnakF..CpyC 19
                   fCp+C  +l++++    Cp+C
     EPA06838.1  3 FCPSCEVKLKKGDSGlqCPKC 23
                   9********985554489999 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.02
  zinc_ribbon_2  2 CpnCGa 7 
                   C +CG+
     EPA06838.1 64 CEKCGN 69
                   555554 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.067
  zinc_ribbon_2 14 kF..CpyCGt 21
                   +F  C++C++
     EPA06838.1 88 QFyrCSKCRY 97
                   5666888875 PP

>> Ribosomal_L44  Ribosomal protein L44
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.8     0.029        19      48      73 ..      12      37 ..       6      38 .. 0.90
   2 ?    4.7   0.0     0.063        42      51      62 ..      59      70 ..      47      74 .. 0.87
   3 ?    2.7   0.2      0.27   1.8e+02      54      62 ..      90      98 ..      86     101 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.029
                   BB--EEEEETTT--EEE----BBS-- CS
  Ribosomal_L44 48 KKivlrleCteCkkkrlkalkRakkf 73
                   KK +  l+C +C + + k++k +k++
     EPA06838.1 12 KKGDSGLQCPKCDYVEGKETKQTKTV 37
                   888999***************99976 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.063
                   -EEEEETTT--E CS
  Ribosomal_L44 51 vlrleCteCkkk 62
                   ++++eC++C++ 
     EPA06838.1 59 TIKIECEKCGND 70
                   689******975 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.27
                   EEETTT--E CS
  Ribosomal_L44 54 leCteCkkk 62
                   ++C++C+++
     EPA06838.1 90 YRCSKCRYT 98
                   89****986 PP

>> DUF3795  Protein of unknown function (DUF3795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   6.6   0.00027      0.18       6      75 ..      17      95 ..      12     101 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00027
     DUF3795  6 GldCeeCeayeakekeekkkkkk..........eafeelllaleeikCeGCreeekkalaeeCkirkCakek.glefCaeC 75
                Gl+C +C+++e ke++++k+  +          e+ ++ +l + +i+Ce C ++e   ++   ++r+  + + ++  C +C
  EPA06838.1 17 GLQCPKCDYVEGKETKQTKTVVEeqesqfnvltENEATETLPTIKIECEKCGNDEAVWWML--QTRSADEPTtQFYRCSKC 95
                9**********99888877777689999*9998666667788899*******999987765..344333333256666666 PP

>> C1_4  TFIIH C1-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   2.1       2.1   1.4e+03      24      31 ..      16      23 ..       3      26 .. 0.46
   2 ?    7.4   0.1    0.0076         5       7      34 ..      43      70 ..      40      73 .. 0.88
   3 ?    7.7   0.6    0.0065       4.3      17      33 ..      81      97 ..      75      99 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 2.1
        C1_4 24 sryrCekC 31
                s  +C+kC
  EPA06838.1 16 SGLQCPKC 23
                33455555 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0076
        C1_4  7 kkfpklakkkkdeeltssryrCekCknd 34
                ++f+ l+++++ e+l ++  +CekC nd
  EPA06838.1 43 SQFNVLTENEATETLPTIKIECEKCGND 70
                57888999999999***********875 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0065
        C1_4 17 kdeeltssryrCekCkn 33
                + +e t+ +yrC kC+ 
  EPA06838.1 81 SADEPTTQFYRCSKCRY 97
                45678999*******85 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   2.8    0.0073       4.8      19      46 ..       2      25 ..       1      26 [. 0.82
   2 ?    5.3   7.1     0.035        23      19      46 ..      18      69 ..      10     102 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0073
         IBR 19 kwCprpdCeaiieksegcksvtCskCgf 46
                k Cp   Ce  ++ ++g + ++C+kC +
  EPA06838.1  2 KFCP--SCE--VKLKKGDSGLQCPKCDY 25
                79**..9**..77788877789****87 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.035
         IBR 19 kwCprpdCeaiieksegcks..........................vtCskCgf 46
                 +Cp  +C+++  k+ ++++                          ++C+kCg 
  EPA06838.1 18 LQCP--KCDYVEGKETKQTKtvveeqesqfnvlteneatetlptikIECEKCGN 69
                5799..9**77766666444578888899999999999******9977888875 PP

>> Zn_Tnp_IS1  InsA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.4      0.25   1.6e+02       8      12 ..       4       8 ..       3      10 .. 0.85
   2 ?    2.8   0.0      0.14        95       7      12 ..      19      24 ..      17      33 .. 0.80
   3 ?    5.7   3.4     0.019        13       3      35 .]      59      96 ..      57      96 .. 0.65

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.25
  Zn_Tnp_IS1  8 CPrCs 12
                CP+C+
  EPA06838.1  4 CPSCE 8 
                ****7 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.14
  Zn_Tnp_IS1  7 hCPrCs 12
                 CP+C 
  EPA06838.1 19 QCPKCD 24
                7****6 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.019
  Zn_Tnp_IS1  3 sVsihCPrCsstd.VyR..hGksta..gHeRfrCrdCk 35
                ++ i C +C  ++ V    + +s+     + +rC++C+
  EPA06838.1 59 TIKIECEKCGNDEaVWWmlQTRSADepTTQFYRCSKCR 96
                67888888888887764113344431135789*****8 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   2.5    0.0055       3.6      72     101 ..       3      32 ..       1      43 [. 0.72
   2 ?    4.7   3.7     0.046        30      65      93 ..      56      96 ..      26     102 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0055
                 EETTTS-EEECHHHHHS-TTTSSS-EEEEE CS
        HypA  72 rCreCgkefeleekalrCpkCgsadveivs 101
                  C +C+ + ++ ++ l+CpkC+  + + ++
  EPA06838.1   3 FCPSCEVKLKKGDSGLQCPKCDYVEGKETK 32 
                 5*****88886655899****976555444 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.046
                EEE--EEEETTTS-EEECHHHHH..............S-TTTS CS
        HypA 65 eevpvkvrCreCgkefeleekal..............rCpkCg 93
                +   +k++C++Cg++  +    +              rC kC 
  EPA06838.1 56 TLPTIKIECEKCGNDEAVWW--MlqtrsadepttqfyRCSKCR 96
                34557889999996654332..112345567788888888886 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   1.4    0.0013      0.84      30      55 ..       3      26 ..       2      31 .. 0.91
   2 ?    2.4   4.0      0.23   1.5e+02      30      56 ..      63      99 ..      32     101 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0013
  OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkCpnCgfe 55
                     C+ C  k+k+   +  ++Cp+C ++
      EPA06838.1  3 FCPSCEVKLKK--GDSGLQCPKCDYV 26
                    5**********..**********986 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.23
  OrfB_Zn_ribbon 30 tCseCgsknke..........alsgrtfkCpnCgfea 56
                    +C +Cg               +++++ ++C++C +++
      EPA06838.1 63 ECEKCGNDEAVwwmlqtrsadEPTTQFYRCSKCRYTW 99
                    6777777666666666667667778888999998876 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   5.9     0.049        33       2      22 ..       1      23 [.       1      26 [. 0.68
   2 ?    3.4   0.1      0.08        53       3      10 ..      62      69 ..      60      71 .. 0.73
   3 ?    2.4   0.6      0.16   1.1e+02       2       8 ..      89      95 ..      88      95 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.049
  zf-ribbon_3  2 tvrCPnCGaplssddn..vCpyC 22
                 +++CP+C  +l+++d+   Cp+C
   EPA06838.1  1 MKFCPSCEVKLKKGDSglQCPKC 23
                 68899998877888863346666 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.08
  zf-ribbon_3  3 vrCPnCGa 10
                 ++C +CG+
   EPA06838.1 62 IECEKCGN 69
                 67778875 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.16
  zf-ribbon_3  2 tvrCPnC 8 
                  +rC++C
   EPA06838.1 89 FYRCSKC 95
                 689**** PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9  16.9       1.2   7.8e+02      29      73 ..       9      69 ..       1     102 [. 0.87

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 1.2
  zinc_ribbon_15 29 fkwkkkkpylacskCkslleaskelgkeiekkesse................kkeCknCgk 73
                    +k+kk +  l+c kC ++ +++++++k++ ++++s+                k eC++Cg+
      EPA06838.1  9 VKLKKGDSGLQCPKCDYVEGKETKQTKTVVEEQESQfnvlteneatetlptiKIECEKCGN 69
                    57788999**************9999999988888899**************999999987 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.3      0.13        89      29      38 ..       4      13 ..       1      14 [. 0.76
   2 ?   -1.9   6.4       5.9   3.9e+03      26      32 ..      17      23 ..       4      29 .. 0.55
   3 ?    6.6   0.0     0.013       8.5       6      16 ..      62      72 ..      42      88 .. 0.70
   4 ?    2.9   0.9      0.19   1.2e+02       6      12 ..      90      96 ..      89     100 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.13
  Zn-ribbon_8 29 CPeCgsevrr 38
                 CP+C  ++++
   EPA06838.1  4 CPSCEVKLKK 13
                 ****877776 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5.9
  Zn-ribbon_8 26 ltaCPeC 32
                   +CP+C
   EPA06838.1 17 GLQCPKC 23
                 3457777 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.013
  Zn-ribbon_8  6 YrCeeCghefe 16
                  +Ce+Cg++  
   EPA06838.1 62 IECEKCGNDEA 72
                 46777776544 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.19
  Zn-ribbon_8  6 YrCeeCg 12
                 YrC +C 
   EPA06838.1 90 YRCSKCR 96
                 9*****7 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7  11.3      0.25   1.6e+02       1      65 [.       4      69 ..       4      98 .. 0.69

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.25
  DnaJ_CXXCXGXG  1 CkkCkGsgakkgkkktCktCkG.sGvvreeqktlgpfvqqsqstCpeCeGtGkvikekdkCkkCkG 65
                   C++C+ + +k ++  +C++C+  +G++++++kt+   ++++ +  +e e t ++ + k +C+kC +
     EPA06838.1  4 CPSCEVKLKKGDSGLQCPKCDYvEGKETKQTKTVVEEQESQFNVLTENEATETLPTIKIECEKCGN 69
                   99***99976666788****8514554444333222222222344444555554444667999965 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   3.4    0.0083       5.5       2      25 ..       4      23 ..       3      24 .. 0.92
   2 ?    5.4   0.6     0.017        12       1      13 [.      19      32 ..      19      40 .. 0.71
   3 ?    0.3   4.4      0.67   4.4e+02      17      26 ..      87      96 ..      63      99 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0083
    zf-TFIIB  2 CPkCqdeleeserggveidyCpqC 25
                CP+C + l++ ++g     +Cp+C
  EPA06838.1  4 CPSCEVKLKKGDSGL----QCPKC 23
                ************999....99999 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.017
    zf-TFIIB  1 kCPkCq.deleese 13
                +CPkC  +e +e++
  EPA06838.1 19 QCPKCDyVEGKETK 32
                7****845777766 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.67
    zf-TFIIB 17 veidyCpqCr 26
                 ++++C +Cr
  EPA06838.1 87 TQFYRCSKCR 96
                6789999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1281  (0.0714485); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                        39  (0.00217525); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 619.46
//
Query:       EPA06839.1  [L=39]
Description: hypothetical protein BG20_I0974 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); expected 358.6 (0.02)
Passed bias filter:                      167  (0.00931452); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.45
# Mc/sec: 259.33
//
Query:       EPA06840.1  [L=207]
Description: hypothetical protein BG20_I0984 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0094   15.5   0.1      0.012   15.1   0.1    1.1  1  Elong_Iki1     Elongator subunit Iki1
  ------ inclusion threshold ------
      0.055   12.9   0.0      0.069   12.6   0.0    1.1  1  Alpha_L_fucos  Alpha-L-fucosidase


Domain annotation for each model (and alignments):
>> Elong_Iki1  Elongator subunit Iki1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   1.4e-06     0.012      30     106 ..      41     121 ..      28     147 .. 0.56

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.4e-06
  Elong_Iki1  30 leelirrakssktkvifvsfetlkk........pkgvdvfieatersk.klkelakeiksalspkssekkkkalviiDslnplas......l 106
                 ++eli+   s k  vif+ f+   +         k+ +v i +   +k + k+++ ei++++s       +k+l++iDsln          +
  EPA06840.1  41 VNELIN---SYKFPVIFLDFDLHYSgyvvsemiKKNSNVEIYR--PNKtDWKQIILEIAKKISI------EKTLIVIDSLNGFYGmfdekeS 121
                 444443...4468999999996666334433444444444444..2221577777777777632......79*********55443443331 PP

>> Alpha_L_fucos  Alpha-L-fucosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   7.7e-06     0.069     201     271 ..      41     121 ..      15     137 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.7e-06
                    HHHHHHHSTTEEEEEES--SHH...............HHTTHHHHHHH..HHHHHHHSTT..-EEBGGG-B-TTSSBBEEBSS-- CS
  Alpha_L_fucos 201 lkelvtkYkpdilwfDgewekke..............eyynedwkseeelaklykelspgdevlvndrlgkkeaedyqtperglp 271
                    ++el+++Yk  ++++D++++ +                y  ++ ++++ + +++k++s +++++v d    + + +y +++++ +
     EPA06840.1  41 VNELINSYKFPVIFLDFDLHYSGyvvsemikknsnveIYRPNKTDWKQIILEIAKKISIEKTLIVID----SLNGFYGMFDEKES 121
                    79******************98888888888888887555666777787788888888888888888....33446777766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1318.30
//
Query:       EPA06841.1  [L=576]
Description: HAMP domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.3e-14   51.7   0.0    1.4e-13   51.0   0.0    1.4  1  HAMP           HAMP domain
      2e-12   47.4   0.2    4.1e-12   46.4   0.2    1.5  1  dCache_1       Cache domain
    1.1e-09   38.2   0.1      3e-09   36.8   0.0    1.7  2  Guanylate_cyc  Adenylate and Guanylate cyclase catalytic doma


Domain annotation for each model (and alignments):
>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0   0.0   2.4e-17   1.4e-13       2      52 ..     314     364 ..     313     365 .. 0.96

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 2.4e-17
                 HHHTTHHHHHHHHHHHHHHTTTBTSSTCCTTSSSHHHHHHHHHHHHHHHHH CS
        HAMP   2 larrilrPLrrLaraarriaaGdldtrlpvsgrDEiGeLarafNaMldrLr 52 
                 ++++i+rPL +L+ aa+++++Gd+++r  ++++DEiGeL +af+ M ++L+
  EPA06841.1 314 ISKTISRPLIKLKNAANQVSNGDFKVRTNITTKDEIGELSQAFDLMTEKLQ 364
                 7899*********************************************98 PP

>> dCache_1  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4   0.2   6.8e-16   4.1e-12       3     231 ..      32     267 ..      30     298 .. 0.76

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 6.8e-16
    dCache_1   3 ieeqaeeqllglaeqlanniedvldslenlaetlasnpslqdlleepnra....neasreslqallksilksnpdisgvylvdadGqviassdpssppn 97 
                 + ++a +qllg + + +n+++  ++s+  + + l+++p ++ l++e +++      ++r+s ++ + + +++ + + g+++ ++d ++i s+      +
  EPA06841.1  32 LTDSASNQLLGESSTRGNAVKLLFESRIEQNKILTNDPMIKILVTELDNTseheFDKIRDSKRRDFLTQVQAFQTLVGFSIGFEDVKIIGST------G 124
                 677899************************************99998888999988888888888888888888898888888888887643......3 PP

    dCache_1  98 leg.......tddpadrdwykealaggggkpvisdpyvdqtggkpvitiavpiyd....dsgkfiGvlaadldldnlqd.llsniklgetgyvfivdsd 184
                 ++         + + + +++++ l+    k+ i d+  ++t gk +i ++ pi+      + ++iGv++  ++ ++l++ l ++  lg+tg+v+iv+++
  EPA06841.1 125 KVFfslgkltDNSFLQDPLFQKGLQ----KS-IIDFEPSPT-GKKMIIVS-PIFAvdskKNDEPIGVIISRMRTESLDNiLTDKSGLGDTGEVYIVNER 216
                 3335533334445555555665555....55.789999999.98888777.**955566889*****************777799***********988 PP

    dCache_1 185 Gniiahpd.......kdllgknlrdelkaq..ealekalakiesgvssvklngeey 231
                  ++++ +        k+++     d+ + q    + k+ a+i     +v+++g++y
  EPA06841.1 217 FLMLSESRfinnaifKQKV-----DTVPVQkcFREGKDFAGIYKDYREVDIHGSSY 267
                 7777776544322222222.....44444466555555555666666666666655 PP

>> Guanylate_cyc  Adenylate and Guanylate cyclase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0      0.83     5e+03      42      65 ..     104     128 ..      98     136 .. 0.68
   2 !   36.8   0.0     5e-13     3e-09       7     179 ..     392     568 ..     388     572 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.83
  Guanylate_cyc  42 fdelldekk.vykvktiGdaymvvs 65 
                    f++l++     + vk+iG++  v +
     EPA06841.1 104 FQTLVGFSIgFEDVKIIGSTGKVFF 128
                    6666655443788999999866555 PP

  == domain 2  score: 36.8 bits;  conditional E-value: 5e-13
  Guanylate_cyc   7 devtilFadIvgftalssahspievvklLnelyarfdelldekkvykvktiGdaymvvsglp.eekaahaaklaelaLdmlealeevaves....k 97 
                    ++ ++   dI ++t++  + s  +  ++ +   +++ e++++ ++  vk iGda + ++ +   e++  ++k++++ L + e+ + + ++      
     EPA06841.1 392 EKYCVCMVDIMNSTKITYQLSESQTSEFYKIFLNSIAEIVRNFGGIVVKNIGDALLFYFPVInLEEELTLKKCLDCCLTLCESHDDIIKKLeeqkL 487
                    55678889************************************************9999875678899***********9987555544422225 PP

  Guanylate_cyc  98 eglkvrvGihtGpvvagviGakkprydvwGntvnlAsrmestgkagkiqvseetyellk.eeqfeltergevevkGkgklety 179
                    + ++ r+    G v +          d++G tvn  ++++ ++ a++  + ee y+ +k  +++ ++++ +  v+G ++   y
     EPA06841.1 488 PIFDYRISSTFGIVRIAKT-SISSVNDIFGSTVNRCAKINRLAPANRLILGEEFYDAAKnFDDYIFKKIADSTVPG-SDYSGY 568
                    77899*********99999.566677*********************************88999***********9.555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (576 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       990  (0.0552178); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.28s 00:00:00.95 Elapsed: 00:00:00.47
# Mc/sec: 3719.51
//
Query:       EPA06842.1  [L=383]
Description: aminotransferase, class V [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-68  230.6   0.0    3.3e-68  230.3   0.0    1.0  1  Aminotran_5      Aminotransferase class-V
    3.2e-07   29.8   0.0    4.8e-07   29.3   0.0    1.2  1  Aminotran_1_2    Aminotransferase class I and II
  ------ inclusion threshold ------
       0.07   13.4   0.1       0.14   12.4   0.1    1.5  1  YgbB             YgbB family
       0.12   12.0   0.6       0.31   10.7   0.6    1.7  1  EF-hand_1        EF hand
       0.24   10.7   0.0        1.1    8.5   0.0    1.8  1  Beta_elim_lyase  Beta-eliminating lyase


Domain annotation for each model (and alignments):
>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  230.3   0.0   9.2e-72   3.3e-68       1     369 [.      18     374 ..      18     376 .. 0.94

  Alignments for each domain:
  == domain 1  score: 230.3 bits;  conditional E-value: 9.2e-72
                  EEEBTTTS----HHHHHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEE..TT CS
  Aminotran_5   1 iyldsaAttqkpqeVldalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvt..ea 96 
                  iyl +a  +  p + ++a+++++ +yn  +  s+ +    + ++++++r+ + ++in +  ee+i t++tt++inlva++l  ++++  +i++   + 
   EPA06842.1  18 IYLNNASVSIMPLQSIEAMKDFLVSYNKMGPDSIDSK-PFIDEKLRNTRKVISKIINCQP-EEVILTQSTTDGINLVANGL--TFEKNSNIIIRgfSH 111
                  8*********************999999986666555.5599*****************7.********************..7*********74468 PP

                  SHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTTS.---HHHHTES CS
  Aminotran_5  97 ehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavghi.pidvkklgvD 193
                  ehhan+ pw +l+++   ++k +++d++g  + de+++ll+++tklva++h+   tG i pve+ig+l+ + + l+++D aq++g i ++dv+k+++D
   EPA06842.1 112 EHHANFYPWLRLKNK--TEIKNLSIDKNGFFNFDEFKTLLDKNTKLVAVSHALYNTGSILPVEKIGSLLEN-NSLFFIDTAQTIGCIgNFDVAKTKCD 206
                  ************965..99***********************************************88877.79**********98649********* PP

                  EEEEETTT.TTSSTT-EEEEEEHHHHHTS..SS.STTSEEEEETTEEEEHCTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHH CS
  Aminotran_5 194 flafsghK.llgPtGiGvlyvrkellekleplllggemveevsleettfaeapskfeaGTpnvagiiglgaaleyleeigleaiekhekelaeyller 290
                  f++f g K l+gP G+G+ y+ k+  e lepl +gge    ++  +  f++ p kf+ G  n +gi+gl+  ++yl ++g+e+i++++  l++ l+e+
   EPA06842.1 207 FMSFNGSKwLCGPMGTGLFYCNKKSHELLEPLTIGGESAMLYDNTNLAFKDIPDKFQTGFRNYVGIVGLESSVNYLLKFGMENIRTKNLLLSNLLREE 304
                  *************************************9999999999*************************************************** PP

                  HCTSTTEEEES.-B-CTCBSEEEEEETTCSHHHHHHHHHHTTEEEEEE-TTTHHHHHHTT.S-EEEEE--TTS-HHHHH CS
  Aminotran_5 291 lkslpgvrlygpdkaerrasivsfnfkgvhaedvatlLdeegIavrsGhhcaqplmkrlalegtvRaSlyiynteeevd 369
                  l++++++ lygp++a++r+sivsfn++g++++ ++  L++++I +   +            ++++RaS ++ nte e+ 
   EPA06842.1 305 LSKIKNIILYGPENAQERTSIVSFNLEGYDPQIIVEKLEKQNIVLAVREILE---------QKIIRASPHFFNTESEIL 374
                  *******************************************998755444.........899999999999999885 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.0   1.3e-10   4.8e-07      63     206 ..      72     207 ..      52     222 .. 0.84

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 1.3e-10
                    CHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSE.EEEEEBEET.TTTEE-HHHHHHHHTTHHCTTETEEEEEEES CS
  Aminotran_1_2  63 lklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilrlsgge.vvryplyse.edfhldlealeealkeapegnkktkvilves 156
                    ++ ++e +v++++ ++ +i++++  l++++ ++i++   +++++ n   + +++   +++  s  ++   ++++++++l++       tk+++v  
     EPA06842.1  72 INCQPE-EVILTQSTTDGINLVANGLTFEKNSNIIIRGFSHEHHANFYPWLRLKnKTEIKNLSIdKNGFFNFDEFKTLLDK------NTKLVAVSH 160
                    457899.77777776666666666666***********************999988888744446999*************......99******* PP

                    S-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHH.HGG CS
  Aminotran_1_2 157 phNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavat.ran 206
                    +  +tG++++ e++  l     ++n l f+D a  +++ g+ d+++t + +
     EPA06842.1 161 ALYNTGSILPVEKIGSL----LENNSLFFIDTAQTIGCIGNFDVAKTkCDF 207
                    *****************....557****************99988775444 PP

>> YgbB  YgbB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1     4e-05      0.14      53     144 ..       4      96 ..       2     107 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4e-05
                 T--SHHHHSTTTCGGCTTTCHHHHHH.HHHHHHHHTTEEEEEEEEEEECSSSTCGGGHHHHHHHHHHHHTS-GGGEEEEEEETTTSHHHHTTS CS
        YgbB  53 algdigelfpdtdpkykgadSaelLe.evlellkekgykivnvdvtiiaekpklapykeamrenlakllgleeeqvsvkattteklgfvGrge 144
                 + +di e fp++ + y +  S +++  +++e +k+  ++ +++    i +kp +++   + r+ ++k+++++ e+v ++  tt++++ v +g 
  EPA06842.1   4 TSKDISEDFPNSGKIYLNNASVSIMPlQSIEAMKDFLVSYNKMGPDSIDSKPFIDEKLRNTRKVISKIINCQPEEVILTQSTTDGINLVANGL 96 
                 57899999**9999999988888875388999999999999999999***************************************9998875 PP

>> EF-hand_1  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.6   8.5e-05      0.31      12      27 ..     135     150 ..     134     152 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 8.5e-05
                 TSSSEEEHHHHHHHHH CS
   EF-hand_1  12 DgdGkIdfeEfkellk 27 
                 D++G+ +f+Efk+ll 
  EPA06842.1 135 DKNGFFNFDEFKTLLD 150
                 9***********9985 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0   0.00029       1.1      60     213 ..      90     230 ..      57     282 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00029
                      HHHHHHHH--TTEEEEEETT-HHHHSSTTHHHHC.C--EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHH CS
  Beta_elim_lyase  60 nsillkillqrgeevivtepahihfdetgaiael.agvklrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelre 152
                      n ++  +  ++++++i++  +h h         l +  + ++l ++++G +++++++ ++++      ++kl+ +  +     G ++++e++  
       EPA06842.1  90 NLVANGLTFEKNSNIIIRGFSHEHHANFYPWLRLkNKTEIKNLSIDKNGFFNFDEFKTLLDK------NTKLVAVSHALYN-TGSILPVEKIGS 176
                      34444444477777777777777777775555555888889999999999999999999999......6889999999864.699999999888 PP

                      HHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHHHTTSSEEEEESSSTT--SS-.EEEEE-HH CS
  Beta_elim_lyase 153 vaaiakkygiplhlDgARfanaakslgeivkemfsyvDsvtmslkKdllanvG.gvlafrdd 213
                      +     +++  +++D A  +      + +v++    +D +++ ++K l+ ++G g+   +++
       EPA06842.1 177 LL----ENNSLFFIDTAQTIGCI--GNFDVAK--TKCDFMSFNGSKWLCGPMGtGLFYCNKK 230
                      76....57788888988666555..3333333..569****************666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2647.72
//
Query:       EPA06843.1  [L=154]
Description: universal stress family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.7e-28   97.6   0.3      1e-27   97.4   0.3    1.1  1  Usp       Universal stress protein family


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.4   0.3   5.7e-32     1e-27       1     140 [.       1     151 [.       1     152 [. 0.97

  Alignments for each domain:
  == domain 1  score: 97.4 bits;  conditional E-value: 5.7e-32
                 S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH.........HHHHHHCTTCEEEEEEEESS CS
         Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada.........akaaaeaggvkvevvveegd 90 
                 my +IlV+  g+++ +kAl++A++ ak++ a++illhv+++ + ++  ++  ++  +  ++ + ++e ++           + +++  +k  ++v+ g+
  EPA06843.1   1 MYNTILVPHAGTSAGDKALKHAIHAAKSSSAKIILLHVVEEIPRPPMFALSTSESMKLVKSFRNANEDLKkgmisemekRVKICNENNIKASITVTIGS 99 
                 9*****************************************************99999999999999999*******999****************** PP

                 HHHHHHHHHHHTTSSEEEEESCC.SSTTTTCS.SBHHHHHHHHHTSSEEEEE CS
         Usp  91 paeeilevaeeedadliVvGsrg.rsglsrll.lGSvseyvlrhapcpVlvV 140
                 +a+eil++ +++++dl+V+++r+ ++gl+ ll lGSvs+++++++ cpVl+V
  EPA06843.1 100 AADEILKIIKKQKVDLVVMAKRRkLKGLKSLLtLGSVSRKIVENTACPVLLV 151
                 *********************998999999777*****************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1078  (0.0601261); expected 358.6 (0.02)
Passed bias filter:                      587  (0.0327403); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 944.28
//
Query:       EPA06844.1  [L=317]
Description: putative K+-dependent Na+/Ca+ exchanger [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-45  154.1  40.5    5.1e-27   94.7  16.9    2.0  2  Na_Ca_ex  Sodium/calcium exchanger protein
  ------ inclusion threshold ------
       0.14   11.9   1.6         15    5.5   0.1    3.3  2  Flavi_M   Flavivirus envelope glycoprotein M
       0.15   12.0   0.1       0.15   12.0   0.1    3.8  4  FixQ      Cbb3-type cytochrome oxidase component FixQ


Domain annotation for each model (and alignments):
>> Na_Ca_ex  Sodium/calcium exchanger protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.6  15.6   7.7e-22   4.6e-18       3     150 ..       8     148 ..       6     149 .. 0.85
   2 !   94.7  16.9   8.5e-31   5.1e-27       3     149 ..     168     306 ..     166     307 .. 0.85

  Alignments for each domain:
  == domain 1  score: 65.6 bits;  conditional E-value: 7.7e-22
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHTHHHHHHHHHHBTTSSCECCH CS
    Na_Ca_ex   3 fvlfilslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaaltgevdlaignvlGsnifnlllviGlialigslkvdseslkl 101
                 ++l++++l++++ +a f ++s+e+++k  gi +  +G +++A ++s+pE+ +++++  t++v + +g ++Gsn+ n++l+ +l ++++++k+ +  ++ 
  EPA06844.1   8 IILLAVFLVILVKSAIFAINSIEKVTKRSGIGQLAAGFVIVAVATSVPEISVALFSTHTHNVGITLGDIFGSNVTNIGLIAALFLFLSPIKKIQVKTTK 106
                 6789999999999999999********9***********************************************************885433333344 PP

                 HH.HHHHHHHHHHHHHHHHTCHHHHHHTEEHHHHHHHHHHHHHHHHHHHH CS
    Na_Ca_ex 102 dl.gllllvallllllvlllllplfvpgrltvleglvllllYalylvlsl 150
                 +l +ll++++l+   l+lll+       + +++ g++ll+l+a++++++l
  EPA06844.1 107 SLfPLLITASLIP--LILLLV------QQGSKFIGIALLGLFAFFVYYML 148
                 4435544444433..445555......9*******************987 PP

  == domain 2  score: 94.7 bits;  conditional E-value: 8.5e-31
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHTHHHHHHHHHHBTTSSCECCH CS
    Na_Ca_ex   3 fvlfilslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaaltgevdlaignvlGsnifnlllviGlialigslkvdseslkl 101
                 ++lf+++++++ ++a+++v+sa++ia+ +gi++sv+G t++Alg+slpEl+++i+a+++   dlaig ++Gs+i n++lv+Gl++++++       +++
  EPA06844.1 168 LLLFFVGIAGVTLSAKMIVDSASSIAEFTGIKQSVIGATIIALGTSLPELTVDIVAIKRRLLDLAIGDIIGSCITNITLVLGLVLVLSP-------VEI 259
                 689***********************999**********************************************************66.......445 PP

                 HHHHHHHHHHHHHHHHHHT..CHHHHHHTEEHHHHHHHHHHHHHHHHHHH CS
    Na_Ca_ex 102 dlgllllvallllllvlll..llplfvpgrltvleglvllllYalylvls 149
                 ++g+l++++ ++++l ++l  l+     g++++++++vl+++Y+++l++ 
  EPA06844.1 260 NFGILSTLISFAIGLPVVLfvLIR---NGHIQKWQSMVLFAIYLIFLIMI 306
                 555554444444444433300333...5******************9875 PP

>> Flavi_M  Flavivirus envelope glycoprotein M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1    0.0024        15      45      71 ..      70      96 ..      63      98 .. 0.89
   2 ?    3.6   0.2     0.009        54      46      71 ..     231     256 ..     227     258 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0024
     Flavi_M 45 altlaylvGssitqkvvialllllvtP 71
                 +tl  + Gs++t  ++ia l l ++P
  EPA06844.1 70 GITLGDIFGSNVTNIGLIAALFLFLSP 96
                57888999*************999988 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.009
     Flavi_M  46 ltlaylvGssitqkvvialllllvtP 71 
                 l +  ++Gs it  +++  l+l+++P
  EPA06844.1 231 LAIGDIIGSCITNITLVLGLVLVLSP 256
                 788899***********999999988 PP

>> FixQ  Cbb3-type cytochrome oxidase component FixQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   1.0      0.61   3.7e+03      13      22 ..       9      18 ..       5      23 .. 0.51
   2 ?   12.0   0.1   2.6e-05      0.15      13      40 ..     131     158 ..     123     159 .. 0.87
   3 ?   -2.3   0.8      0.74   4.4e+03      15      24 ..     168     177 ..     168     182 .. 0.54
   4 ?   -1.7   2.6       0.5     3e+03      19      29 ..     293     303 ..     290     307 .. 0.53

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.61
        FixQ 13 wgllflvllf 22
                ++l ++++++
  EPA06844.1  9 ILLAVFLVIL 18
                3333333333 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 2.6e-05
        FixQ  13 wgllflvllfygvviyafrpgnrkdfed 40 
                 +  ++l++lf+  v+y++++++ +++e+
  EPA06844.1 131 FIGIALLGLFAFFVYYMLKSSKMQNHEQ 158
                 56689*****************999985 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 0.74
        FixQ  15 llflvllfyg 24 
                 ll++++  +g
  EPA06844.1 168 LLLFFVGIAG 177
                 4555555555 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 0.5
        FixQ  19 vllfygvviya 29 
                 ++lf++++i++
  EPA06844.1 293 MVLFAIYLIFL 303
                 45555555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1114  (0.062134); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2260.31
//
Query:       EPA06845.1  [L=140]
Description: universal stress family protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-30  105.4   0.0    4.2e-30  105.1   0.0    1.1  1  Usp       Universal stress protein family
  ------ inclusion threshold ------
      0.023   14.8   0.0      0.031   14.4   0.0    1.3  1  DUF3880   DUF based on E. rectale Gene description (DUF3880)


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.1   0.0   4.7e-34   4.2e-30       3     141 .]       5     140 .]       3     140 .] 0.89

  Alignments for each domain:
  == domain 1  score: 105.1 bits;  conditional E-value: 4.7e-34
                 SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTCEEEEEEEESSHHHHHHHHHHH CS
         Usp   3 krIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggvkvevvveegdpaeeilevaee 101
                 k+IlV++Dgs++s + l++A+e ak+ gae++  +v + +  +  ++  +++++e+++++ ++   +   ++a+ +g+  + ++ +g+ + ei+++a++
  EPA06845.1   5 KKILVPLDGSPNSNRGLDRAIEIAKEGGAEITGFYVFHLPLAAGIKY-TQKMKDEAQKKAIKAIGPA--MKRAQNAGALFKYKTGGGHTGSEIVKFAQK 100
                 8***********************************98776655555.5555555555555555555..48**************************** PP

                 TTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
         Usp 102 edadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                  ++d+iV+G+rg++g ++++lGS+s+yv++++++pVlvV+
  EPA06845.1 101 GKYDMIVIGARGMGGAKEAFLGSTSNYVMHKTKVPVLVVK 140
                 ***************************************8 PP

>> DUF3880  DUF based on E. rectale Gene description (DUF3880)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   3.4e-06     0.031      41      64 ..      40      63 ..      33     108 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.4e-06
     DUF3880 41 vyylPLAanverldpleaeaekee 64
                v++lPLAa ++  ++++ ea+k+ 
  EPA06845.1 40 VFHLPLAAGIKYTQKMKDEAQKKA 63
                9****************9997765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 878.50
//
Query:       EPA06846.1  [L=217]
Description: hypothetical protein BG20_I0980 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.4e-32  110.1   0.0    1.2e-31  109.8   0.0    1.1  1  Cyclase   Putative cyclase


Domain annotation for each model (and alignments):
>> Cyclase  Putative cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.8   0.0   6.5e-36   1.2e-31       1     135 [.       4     156 ..       4     157 .. 0.89

  Alignments for each domain:
  == domain 1  score: 109.8 bits;  conditional E-value: 6.5e-36
     Cyclase   1 idLshplsedtpvwp.dp...................islsehtGTHlDapgHfae..ktidelpleelvgpavvldvsakaaaedyeiitaedleaal 77 
                 idL++++s++tp++p +p                   + ls+htGTHlDap+Hf++   +++++ le+l+g+a+++ +++    +++  it++dl +++
  EPA06846.1   4 IDLTLTVSPSTPTFPgSPktqfilwstlkddgynlelLFLSSHTGTHLDAPYHFVKngIKVHQISLERLMGNAILIKIKKG---KNQ-AITKNDLITFE 98 
                 8*************65445678999999********999***************9976689*****************554...455.56*****9998 PP

     Cyclase  78 akqgveikpgdivlirTgwskrledkeky..rnpglseeaaewlaekgvkavGvDtlsvD 135
                 ++++ +i++ + ++++T+w+++l+ ++ y  +npgls++aa++l++k+v++vG+D +++D
  EPA06846.1  99 RNNN-NIPKHSSIIFHTEWQNYLN-RDFYfiDNPGLSQSAANYLVSKEVNLVGIDSPNID 156
                 8777.**************98854.4555799**************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1351.66
//
Query:       EPA06847.1  [L=329]
Description: copper binding protein, plastocyanin/azurin family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-07   31.6   0.0    3.9e-07   30.4   0.0    1.6  1  Copper-bind   Copper binding proteins, plastocyanin/azurin fa
  ------ inclusion threshold ------
      0.013   15.6   0.1       0.22   11.7   0.0    3.1  4  Cupredoxin_1  Cupredoxin-like domain
      0.026   14.8   0.3       0.08   13.2   0.0    1.9  2  DUF4064       Protein of unknown function (DUF4064)


Domain annotation for each model (and alignments):
>> Copper-bind  Copper binding proteins, plastocyanin/azurin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.0   6.6e-11   3.9e-07      12      99 .]      43     131 ..      37     131 .. 0.87

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 6.6e-11
                  SEEESSEEEEETTEEEEEEEESSSSBEEEEETTSSTTTGGGTTSCTTC...EEEEBSTTEEEEEEEESSEEEEEEETTTTTTTSEEEEEEE CS
  Copper-bind  12 lqFetkeitvkkgekvtfvnlavmgHNvvldkdgvpagvdkdkvkaed...etkliggGekdsvtfdeagtYkffCsPHaaagMkgkvtve 99 
                    ++++ ++v+ g++vt++n ++ gH v   + +   g  ++     d   +   + + e+ s tfd++g ++++Cs H    M+g ++v+
   EPA06847.1  43 VWYDPSVLSVDIGDTVTWINDDKEGHTVTSGESSGRFGWMNKDFGTPDglfDSDRFMPNESWSYTFDKSGLFSYYCSIHP--WMEGRIVVK 131
                  5699****************************888888766666666668855567788*********************..69***9996 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   3.6e-05      0.22      31     104 .]      44     130 ..       4     130 .. 0.84
   2 ?   -2.3   0.0      0.79   4.7e+03      29      47 ..     163     181 ..     153     193 .. 0.67
   3 ?   -1.6   0.0       0.5     3e+03      15      46 ..     256     289 ..     250     292 .. 0.67
   4 ?   -2.2   0.0      0.76   4.5e+03       3      20 ..     305     322 ..     303     329 .] 0.59

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.6e-05
  Cupredoxin_1  31 gfePskievkagekvklkiknkdktpeefesed.................lgeekvlapgktttitiaplkpGeYeftcdmhmdakGkliV 104
                    ++Ps++ v  g   ++++ n+dk+ ++++s +                 l  +   +p+++ + t+  +k G ++++c +h+ ++G ++V
    EPA06847.1  44 WYDPSVLSVDIGD--TVTWINDDKEGHTVTSGEssgrfgwmnkdfgtpdgLFDSDRFMPNESWSYTF--DKSGLFSYYCSIHPWMEGRIVV 130
                   699*********9..88999999999999998888899999999999999888899***********..**************99****98 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.79
  Cupredoxin_1  29 dggfePskievkagekvkl 47 
                   d + ePs+i+ +++ k+  
    EPA06847.1 163 DLTWEPSVIKTHEEVKFIY 181
                   3457888888887776654 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.5
  Cupredoxin_1  15 aaaaaektveitvkdg..gfePskievkagekvk 46 
                   ++aa +++++ +v d+  +++ ++i+vk  ++++
    EPA06847.1 256 TKAARTTEFSTVVYDNpdKISHEQIHVKPAQRLE 289
                   4566666666666655558888889988777665 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 0.76
  Cupredoxin_1   3 aalavllllsskaaaaae 20 
                   ++++++ ++++k ++++ 
    EPA06847.1 305 VFIVAIYWMKKKPKSSEP 322
                   667777777776665443 PP

>> DUF4064  Protein of unknown function (DUF4064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.2      0.46   2.7e+03      68      76 ..       7      15 ..       2      27 .. 0.51
   2 ?   13.2   0.0   1.3e-05      0.08      60      88 ..     291     319 ..     250     329 .] 0.72

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.46
     DUF4064 68 aliaivlgi 76
                 +i  +lg 
  EPA06847.1  7 IIIVVILGS 15
                222222222 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 1.3e-05
     DUF4064  60 llivlgvialiaivlgivgalllkknkkv 88 
                 +  +l+vi l  ++++iv+++++kk++k 
  EPA06847.1 291 YYELLTVIILAPAAVFIVAIYWMKKKPKS 319
                 4447899999*****************94 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2480.19
//
Query:       EPA06848.1  [L=47]
Description: hypothetical protein BG20_I2176, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.28s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 348.99
//
Query:       EPA06849.1  [L=258]
Description: hypothetical protein BG20_I2174 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-10   41.4   0.5      2e-10   40.8   0.5    1.3  1  Phage_integr_3  Archaeal phage integrase


Domain annotation for each model (and alignments):
>> Phage_integr_3  Archaeal phage integrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   0.5   1.1e-14     2e-10       7     157 ..     106     251 ..     100     254 .. 0.79

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 1.1e-14
                     HHHHHHHHHHHHH-HHHHHHHHHHHHH---HHHHHHHHHS..GGG-EEETTEEEEEEEE-SSS-EEEEEEESS---....--B--HHHHHHHHHT CS
  Phage_integr_3   7 eevrealeelkekseevelvykllvfsGiRLkevlklLreyDpekliveddiarYpialekgeKkafyiylptelakelerlelseeavkefeak 101
                      ++ + +e++++  e++++ +  ++ sG+R +e++  ++++D    i++++i   +i +++ +Kk+ ++y    l+ +++  ++s++   ++ + 
      EPA06849.1 106 VSIEKIVENIRKLPEKYQIFAMFVLVSGLRTSEAIDAFNNHD---KICHNGIL--EIFTDRNTKKTNAVYCHPFLHDKINF-KISNTGTYRNLNS 194
                     345555556666666799999999****************55...59999997..79*************99999988873.6776655544444 PP

                     -T..--GHHHHHHHHHHHHHTT--HHHHHHHTTSS-CCTTSCHHCHHHHHHHHHHHHH CS
  Phage_integr_3 102 kk..vkakyiRkwvatklaelgvpeevidFiqGrkpssvlekhYlnllvlAdeaYkkv 157
                     k    +++y+Rk ++t l+ ++++  +++F+qGrk    +++++l ++ + +++++k+
      EPA06849.1 195 KYlgCEIRYLRKLNYT-LIAMKIDGMMAQFMQGRKGDVSQRHYFLPMMSQNQKKWNKL 251
                     33579********998.56789*************98777777789999888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1096  (0.06113); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1928.65
//
Query:       EPA06850.1  [L=735]
Description: HYR domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.1e-11   42.3   0.6    7.1e-11   42.3   0.6    2.4  3  HYR           HYR domain
    2.2e-07   31.3   0.0    1.1e-06   28.9   0.0    2.3  1  Copper-bind   Copper binding proteins, plastocyanin/azurin fa
    7.6e-05   22.8   0.1    0.00035   20.7   0.0    2.2  2  Cupredoxin_1  Cupredoxin-like domain
    9.9e-05   22.3   4.2     0.0024   17.8   0.5    3.6  3  DUF5643       Family of unknown function (DUF5643)
    0.00049   20.4   0.6     0.0038   17.5   0.0    2.6  2  DUF4352       Domain of unknown function (DUF4352)
  ------ inclusion threshold ------
      0.083   12.8   0.1      0.083   12.8   0.1    3.5  4  DUF5067       Domain of unknown function (DUF5067)


Domain annotation for each model (and alignments):
>> HYR  HYR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       5.2   1.6e+04      11      39 ..      47      75 ..      45      82 .. 0.74
   2 ?   -3.3   0.0       3.9   1.2e+04      53      69 ..     210     227 ..     202     233 .. 0.74
   3 !   42.3   0.6   2.4e-14   7.1e-11       2      81 .]     295     373 ..     294     373 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 5.2
         HYR 11 pnnivrtvelgkstvevffteptakdnsg 39
                +++++++++ +k + ++++  ++ +d  +
  EPA06850.1 47 ISVKTKITNNDKERISIYYFYTVLDDDRH 75
                56678888899999999998888887766 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.9
         HYR  53 sFpvG.sttVtyvaeDes 69 
                  +++G  +tVt   +D +
  EPA06850.1 210 IMKIGkGSTVTWYNTDSA 227
                 567887788888888876 PP

  == domain 3  score: 42.3 bits;  conditional E-value: 2.4e-14
         HYR   2 DttpPtvkcpnnivrtvelgkstvevffteptakdnsgqaalvsrtaqpGdsFpvGsttVtyvaeDesgnea.sCkFtVtv 81 
                 D  pP++  p+ i+ ++  g+ + +v+f+  +++dn g +   + + ++G+ Fp+Gst+Vt  ++D sgn+a + +FtVtv
  EPA06850.1 295 DLVPPKILQPKDITEKAANGN-GIKVSFNVLAIDDNDG-NLIPTCNPSSGSLFPIGSTKVTCSVSDSSGNKAsPVTFTVTV 373
                 899*********999998875.799***********99.6666778999***********************99*****98 PP

>> Copper-bind  Copper binding proteins, plastocyanin/azurin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   3.8e-10   1.1e-06      13      98 ..     205     281 ..     195     282 .. 0.84

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 3.8e-10
                  EEESSEEEEETTEEEEEEEESSSSBEEEEET.TSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEESSEEEEEEETTTTTTTSEEEEEE CS
  Copper-bind  13 qFetkeitvkkgekvtfvnlavmgHNvvldk.dgvpagvdkdkvkaedetkliggGekdsvtfdeagtYkffCsPHaaagMkgkvtv 98 
                   ++++ +++ kg++vt+ n+++ +H v   + d+ p g  ++ +        + +G+++s++f+ +gtY +fC  H    M g+++v
   EPA06850.1 205 CYSPSIMKIGKGSTVTWYNTDSAAHTVTSGTpDKPPTGDFDSSL--------FMSGKSFSQKFSREGTYPYFCMVHP--WMTGTIVV 281
                  69999********************9988664666665544444........557**********************..69****98 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   1.2e-07   0.00035      29     104 .]     203     281 ..     177     281 .. 0.87
   2 ?   -2.6   0.1         2     6e+03      16      36 ..     619     639 ..     612     642 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.2e-07
  Cupredoxin_1  29 dggfePskievkagekvklkiknkdktpeefesed......lgeekvl.apgktttitiaplkpGeYeftcdmhmdakGkliV 104
                   +  ++Ps +++ +g   ++++ n+d+ +++++s         +++  l ++gk+++ ++    +G+Y+++c  h+ + G+++V
    EPA06850.1 203 SSCYSPSIMKIGKGS--TVTWYNTDSAAHTVTSGTpdkpptGDFDSSLfMSGKSFSQKF--SREGTYPYFCMVHPWMTGTIVV 281
                   4579**********9..99**************99999999888877736799999999..99************99*****9 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2
  Cupredoxin_1  16 aaaaektveitvkdggfePsk 36 
                   +++ + ++++t+k+ +++P++
    EPA06850.1 619 ESQTQGNIKVTLKKIEITPQH 639
                   456677799999998888876 PP

>> DUF5643  Family of unknown function (DUF5643)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1     0.065   1.9e+02      28      61 ..      60      94 ..      46     145 .. 0.63
   2 ?    1.1   0.0      0.12   3.7e+02      43      96 ..     317     374 ..     302     420 .. 0.66
   3 !   17.8   0.5   7.9e-07    0.0024       1      30 [.     612     641 ..     612     658 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.065
     DUF5643 28 strisysgdvenskeikek.sldfevvDdkGnele 61
                +++i+y ++v +++ ++e+   +++  +dkG+ ++
  EPA06850.1 60 RISIYYFYTVLDDDRHREFsTSNYFNLNDKGHTVS 94
                33444444444444444442222455555555544 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.12
     DUF5643  43 ikeksld.fevvDdkGnelegisgggsgtg....kkefeyeit.fepldenpksLtikPy 96 
                 ik   ++ + + D++Gn +    + +sg+     +++++++ +    ++  p + t++ +
  EPA06850.1 317 IKVS-FNvLAIDDNDGNLIP-TCNPSSGSLfpigSTKVTCSVSdSSGNKASPVTFTVTVQ 374
                 3333.553566688889988.677777777678777777777744444555555555443 PP

  == domain 3  score: 17.8 bits;  conditional E-value: 7.9e-07
     DUF5643   1 skvlkpnktveldgqkltvkkveitPlstr 30 
                 ++++++n+++++ ++k+t+kk+eitP  tr
  EPA06850.1 612 TTTINVNESQTQGNIKVTLKKIEITPQHTR 641
                 689********7777***********9998 PP

>> DUF4352  Domain of unknown function (DUF4352)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.3e-06    0.0038      39     114 ..      46     131 ..      30     140 .. 0.85
   2 ?   -0.5   0.1      0.48   1.4e+03       3      25 ..     617     638 ..     615     722 .. 0.54

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.3e-06
                 EEEEEEEEEE-SSS-EEEEGGGEEEEETTEEE-BEEESCCCCTTB..........--EEEE-TT-EEEEEEEEEESTT-CGEEEEE CS
     DUF4352  39 flivdvtvkNkgkealtvnssqfkLkdgdgkeydadlsasskadd..........lflgtlnpGkkvtGklvFdvpkgkkkleLey 114
                 +  v+ +++N++ke +++    + L d+  +e++++++   +++           + + +lnpG + ++k  F+vpk+  +++L +
  EPA06850.1  46 VISVKTKITNNDKERISIYYFYTVLDDDRHREFSTSNYFNLNDKGhtvseqqcpwESSIELNPGLSDDAKFCFEVPKENLTFTLHL 131
                 5678889***********99999998888777777777655554499*******999*********************98888875 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.48
                 TCEEECCTTEEEEEEEEEEEEEE CS
     DUF4352   3 vgetvkvgdlevtVnsveytksv 25 
                 v+e+ + g+++vt +++ +++++
  EPA06850.1 617 VNESQTQGNIKVTLKKI-EITPQ 638
                 55555555555555555.22222 PP

>> DUF5067  Domain of unknown function (DUF5067)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   2.8e-05     0.083      24      67 ..      27      69 ..      24     132 .. 0.84
   2 ?    1.1   0.0      0.12   3.6e+02      36      62 ..     353     382 ..     345     388 .. 0.79
   3 ?   -2.1   0.2       1.2   3.5e+03      31      72 ..     465     477 ..     445     502 .. 0.58
   4 ?   -1.6   0.1      0.83   2.5e+03      14      38 ..     614     637 ..     606     647 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.8e-05
                SSEEEEE---EEEEECCCTCEEEEEEEEEE-SS-TTBCHHHHHH CS
     DUF5067 24 ddftvkitkaevikdyegkpvlvvyyeftNnsdeeispssavsv 67
                ++++vki+kae i   e  +v+ v+ ++tNn +e is+ +++ v
  EPA06850.1 27 GNLDVKIEKAERI-WGEKADVISVKTKITNNDKERISIYYFYTV 69
                6889********8.246889*****************5555544 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.12
                 E...EECCCTCEEEEEEEEEE-SS-TTBCH CS
     DUF5067  36 i...kdyegkpvlvvyyeftNnsdeeisps 62 
                 +    d++g+++  v++++t  s +++ ps
  EPA06850.1 353 TcsvSDSSGNKASPVTFTVTVQSPKTEIPS 382
                 23358999************9999988876 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.2
                 ---EEEEECCCTCEEEEEEEEEE-SS-TTBCHHHHHHHEEEE CS
     DUF5067  31 tkaevikdyegkpvlvvyyeftNnsdeeispssavsvylkAy 72 
                 + +e++                             + + + +
  EPA06850.1 465 NTSETT-----------------------------QKTTEST 477
                 333333.............................1222222 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 0.83
                 EEEETTEEEESSEEEEE---EEEEE CS
     DUF5067  14 sskkkeeaeiddftvkitkaevikd 38 
                 +   +e+ + ++++v+++k+e++ +
  EPA06850.1 614 TINVNESQTQGNIKVTLKKIEIT-P 637
                 55556777789999999999984.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (735 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       695  (0.038764); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.76u 0.31s 00:00:01.07 Elapsed: 00:00:00.52
# Mc/sec: 4213.53
//
Query:       EPA06851.1  [L=77]
Description: hypothetical protein BG20_I2477, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.017   15.3   0.1      0.021   15.1   0.1    1.1  1  ATG16     Autophagy protein 16 (ATG16)


Domain annotation for each model (and alignments):
>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.1   1.1e-06     0.021     140     194 ..      18      72 ..       9      74 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.1e-06
       ATG16 140 kdreeelrekeklvqdlqDElsaLqlqlnqaEeklrklekENkeLveRWmkrkaq 194
                 ++++e+++ + +l   +q +++ Lq+q +++++ l kl++  ++L +R +  ++q
  EPA06851.1  18 EKLRETIKPQGALKPRIQTAVNKLQVQISKMDSMLGKLHERDAQLFQRVVTAMQQ 72 
                 56778888888888999************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1072  (0.0597914); expected 358.6 (0.02)
Passed bias filter:                      612  (0.0341346); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 516.30
//
Query:       EPA06852.1  [L=33]
Description: hypothetical protein BG20_I2476 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (33 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       109  (0.00607954); expected 358.6 (0.02)
Passed bias filter:                       89  (0.00496402); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 213.49
//
Query:       EPA06853.1  [L=253]
Description: putative glutamate racemase [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.5e-12   45.2   0.0    1.4e-11   44.7   0.0    1.2  1  Asp_Glu_race  Asp/Glu/Hydantoin racemase
  ------ inclusion threshold ------
      0.028   14.1   0.0      0.062   13.0   0.0    1.5  1  Redoxin       Redoxin
       0.17   10.7   0.0       0.25   10.1   0.0    1.2  1  LAX           Lymphocyte activation family X


Domain annotation for each model (and alignments):
>> Asp_Glu_race  Asp/Glu/Hydantoin racemase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7   0.0   2.3e-15   1.4e-11       3     222 ..       6     209 ..       4     210 .. 0.75

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 2.3e-15
                   EC.SCCCCHHHHHHHHHHBTTSSGGGS..EEEEE-CC.S-TCHHHHHCH.T..THH.HHHHHHHHHHC.TTESEEEE--CHHHHHHHHHHHH-SSEE CS
  Asp_Glu_race   3 gm.gpeatlsvlrklveatpaesdqehlplivlndsa.ipdrteaieeesgddpvl.klleaakkLek.agadaiviaCnTahavadelqkkikiPv 95 
                   ++ ++ ++lsv++ ++++++  +     ++i+++ds+ +p  +++i+       ++  +l+ +  L++  ++d+i++  nT +  +   + k  +Pv
    EPA06853.1   6 VFdSGLGSLSVIKPIQQEFK--C-----DIIYFADSKnFPYGKKSIK------EIKnITLHTITTLQNlFKPDLIIVGSNTLSLTLNSHS-KNIFPV 88 
                   67788888888888855554..4.....37******99997777772......2455888888888886799**********76666666.669999 PP

                   EECHHHHHHHHHH.HSS-EEEEEE-HHHHHCTH...HHHHHHHHGT.EE.E....T-CCCHHCCHCHHHH.TT-TTSH...HHHHHHHHHH.HHHTT CS
  Asp_Glu_race  96 lgiveataealka.tgvkkvglLgTrgtlksgl...yqkeleanqgiev.vvpseelqssvnqaiyeelk.aGevtee...arrailklle.rlaer 182
                   l      ++++k+ t+ k++++L+T+  +ks+l   y + ++   +i++ ++  + l+         el+ +G + +     +  i+k+l+ +l ++
    EPA06853.1  89 LP----PLNEAKKiTKSKSIAILATESIVKSKLlnrYSNLFKT-SNIKIfKINASPLV---------ELVeSGMFYSNpefCKIMIKKNLSsKLTKN 171
                   98....788888889****************985558888888.58866344444433.........4443454433332334444555553666** PP

                   T-SEEEE-STTHHHHHHHHHHCC-TT.SEEEEHHHHHHHH CS
  Asp_Glu_race 183 gadaviLGCTelplllekaealekeksvpvidptdilare 222
                   ++d v L  T+lp++l+ +e++ ++  + ++dp ++la++
    EPA06853.1 172 NVDIVTLSSTHLPFILKFLEEIFPN--IVFLDPSKLLAKK 209
                   ***********************96..9*********987 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     1e-05     0.062      52     104 ..     162     213 ..     152     227 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1e-05
                 HTHHHHHHCSTTTEEEEEESSSHHHHHHHHHTT-TSEEEE-TTSHHHHHTT-T CS
     Redoxin  52 eklaellkekgvdvvavvadndafvkefwgkeglkfpvlsDgsaaftkalGlr 104
                 ++l+ +l +++vd+v +++   +f  +f+++   +++v++D+s+ ++k+l+ +
  EPA06853.1 162 KNLSSKLTKNNVDIVTLSSTHLPFILKFLEEIF-PNIVFLDPSKLLAKKLKKK 213
                 7899999**********************9977.89999*********99866 PP

>> LAX  Lymphocyte activation family X
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   4.1e-05      0.25      58      92 ..      79     113 ..      67     132 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 4.1e-05
         LAX  58 rqraKNiYdllPrrQeelGRhqsrsiriFStEsLl 92 
                   ++KNi+ +lP   e +   +s+si i  tEs++
  EPA06853.1  79 NSHSKNIFPVLPPLNEAKKITKSKSIAILATESIV 113
                 5689*****************************76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       925  (0.0515924); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1526.88
//
Query:       EPA06854.1  [L=33]
Description: hypothetical protein BG20_I2428, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (33 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       181  (0.0100954); expected 358.6 (0.02)
Passed bias filter:                      130  (0.00725082); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.61
# Mc/sec: 163.48
//
Query:       EPA06855.1  [L=65]
Description: hypothetical protein BG20_I2426 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.048   13.9   0.1      0.053   13.8   0.1    1.0  1  DUF2072   Zn-ribbon containing protein


Domain annotation for each model (and alignments):
>> DUF2072  Zn-ribbon containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   2.9e-06     0.053      12      65 ..       5      61 ..       2      65 .] 0.74

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.9e-06
     DUF2072 12 edgskeilkGCpsCGgkkFlyvkeeekkedvseeke...elvaeaeeeieevldaee 65
                ++ sk+i++ C++CG   + ++k ++  +++   ++   + v++a+++++ v d ++
  EPA06855.1  5 HEVSKKIKSLCANCGHIEWNHIKTKNVINQEYPIQNpilQNVTNAKKKVKLVRDLKQ 61
                567899******************998887776666567777777777666544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       873  (0.0486921); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.20s 00:00:00.53 Elapsed: 00:00:00.35
# Mc/sec: 556.92
//
Query:       EPA06856.1  [L=157]
Description: hypothetical protein BG20_I2425 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0071   16.5   6.3         11    6.2   0.2    4.2  4  HNH       HNH endonuclease


Domain annotation for each model (and alignments):
>> HNH  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0     0.022     4e+02      13      29 ..       3      19 ..       2      22 .. 0.83
   2 !    6.2   0.2   0.00064        11      34      44 ..      40      50 ..      39      53 .. 0.83
   3 !    5.1   0.3    0.0014        26       1      27 [.      89     113 ..      89     127 .. 0.82
   4 !    4.1   0.1    0.0029        51      35      46 ..     137     148 ..     135     149 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.022
         HNH 13 alevdHiipisqggadd 29
                +l+ dH+  ++ +g+ +
  EPA06856.1  3 FLTLDHVRGRKAEGHST 19
                5899****999988765 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.00064
         HNH 34 qllCksCHnkk 44
                q lC++C+  k
  EPA06856.1 40 QVLCWNCNVLK 50
                78******877 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.0014
         HNH   1 CeyCgrkfhksealevdHiipisqgga 27 
                 C  Cg ++     l  dHi  ++ +g+
  EPA06856.1  89 CKCCGFNDILA--LGLDHISGKKTHGH 113
                 99*****8887..******99987555 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.0029
         HNH  35 llCksCHnkkhd 46 
                   C +C+ +k++
  EPA06856.1 137 VFCYNCNGAKGR 148
                 57*******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1065.09
//
Query:       EPA06857.1  [L=359]
Description: type I secretion target GGXGXDXXX repeat (2 copies), partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.5e-31  106.1  97.8      4e-10   39.5  12.3    5.9  6  HemolysinCabind  RTX calcium-binding nonapeptide repeat (4 co
    1.4e-07   32.1   2.0    1.4e-07   32.1   2.0    2.4  2  Big_9            Bacterial Ig domain
    2.5e-06   27.5   7.3    2.4e-05   24.4   7.3    2.9  1  Cu-binding_MopE  Putative metal-binding motif
    6.7e-06   26.0   0.2    6.7e-06   26.0   0.2    2.0  3  Cadherin_5       Cadherin-like domain
  ------ inclusion threshold ------
      0.026   14.3  13.8        1.7    8.5   6.6    2.6  2  Collagen         Collagen triple helix repeat (20 copies)


Domain annotation for each model (and alignments):
>> HemolysinCabind  RTX calcium-binding nonapeptide repeat (4 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.6   5.6e+03       7      14 ..     150     157 ..     145     161 .. 0.66
   2 !   34.8   8.3   3.2e-12   1.1e-08       1      34 [.     180     213 ..     180     215 .. 0.98
   3 !   39.5  12.3   1.1e-13     4e-10       4      36 .]     210     242 ..     208     242 .. 0.94
   4 !   32.3  18.1   1.9e-11   6.9e-08       1      36 []     234     269 ..     234     269 .. 0.97
   5 !   30.2  13.3   9.1e-11   3.3e-07       2      31 ..     262     291 ..     261     296 .. 0.94
   6 !   23.8  13.8     9e-09   3.2e-05       1      36 []     270     305 ..     270     305 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.6
  HemolysinCabind   7 DtlvGgaG 14 
                      Dt+  +aG
       EPA06857.1 150 DTISSTAG 157
                      77777666 PP

  == domain 2  score: 34.8 bits;  conditional E-value: 3.2e-12
  HemolysinCabind   1 yGgdGnDtlvGgaGnDtiyGgaGnDtlyGGaGnD 34 
                      +G+ GnD l+G++G+D i G aG+D ++G +GnD
       EPA06857.1 180 DGTPGNDNLQGTNGDDLIRGFAGDDKINGKKGND 213
                      69*******************************9 PP

  == domain 3  score: 39.5 bits;  conditional E-value: 1.1e-13
  HemolysinCabind   4 dGnDtlvGgaGnDtiyGgaGnDtlyGGaGnDtl 36 
                       GnD ++Gg+G+D i+Gg+GnDt++G +GnD +
       EPA06857.1 210 KGNDCIYGGSGDDKINGGSGNDTIFGEEGNDKI 242
                      6******************************65 PP

  == domain 4  score: 32.3 bits;  conditional E-value: 1.9e-11
  HemolysinCabind   1 yGgdGnDtlvGgaGnDtiyGgaGnDtlyGGaGnDtl 36 
                      +G +GnD ++G++G+D+i Gg+GnD ++G++G Dtl
       EPA06857.1 234 FGEEGNDKINGNNGDDYISGGDGNDKINGNNGIDTL 269
                      699*******************************98 PP

  == domain 5  score: 30.2 bits;  conditional E-value: 9.1e-11
  HemolysinCabind   2 GgdGnDtlvGgaGnDtiyGgaGnDtlyGGa 31 
                      G++G Dtl+G+aG Dti+Gg++nD+++GG 
       EPA06857.1 262 GNNGIDTLYGDAGKDTIHGGNDNDYINGGT 291
                      9***************************96 PP

  == domain 6  score: 23.8 bits;  conditional E-value: 9e-09
  HemolysinCabind   1 yGgdGnDtlvGgaGnDtiyGgaGnDtlyGGaGnDtl 36 
                      yG++G Dt++Gg+ nD+i+Gg   D  yGG+Gn+++
       EPA06857.1 270 YGDAGKDTIHGGNDNDYINGGTELDKCYGGNGNNVI 305
                      8********************************987 PP

>> Big_9  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   1.4       3.2   1.2e+04      22      40 ..      11      28 ..       4      45 .. 0.52
   2 !   32.1   2.0     4e-11   1.4e-07      16      88 ..      82     148 ..      61     150 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.2
       Big_9 22 vtvtedsvlandtdpdgda 40
                ++++ ds+     dpd d 
  EPA06857.1 11 ANLDNDSL-GDVCDPDADG 28
                44443333.3333333333 PP

  == domain 2  score: 32.1 bits;  conditional E-value: 4e-11
       Big_9  16 vavddsvtvtedsvlandtdpdgdaltvtsltvtlvtapanGtvtinadgtltytpnagfsgtdsftYtvsDg 88 
                 v+ ++++ v++ +vland   +    t+ts  + l +++ +  +  n+dg +t++p+ gf+gt++f+Y ++D 
  EPA06857.1  82 VIGNNQLVVPAPGVLANDLSQN----TITS--AILHSPAVHPELIWNGDGGFTFNPPVGFTGTYTFSYNATDQ 148
                 45556677778888***98654....3443..45789***********************************6 PP

>> Cu-binding_MopE  Putative metal-binding motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   7.3   6.8e-09   2.4e-05       1      30 []      42      72 ..      42      72 .. 0.93

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 6.8e-09
  Cu-binding_MopE  1 DCdDsdpaihPgatEvC.DgvDnnCdGvvDe 30
                     DC D +p i+Pg+ E + +gvD+nC + +De
       EPA06857.1 42 DCADDNPLIYPGQIEDPfNGVDDNCVNGTDE 72
                     9**************777*******888887 PP

>> Cadherin_5  Cadherin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.2       3.2   1.1e+04      53      73 ..      19      40 ..      11      42 .. 0.53
   2 !   26.0   0.2   1.9e-09   6.7e-06      31      92 ..      97     155 ..      71     162 .. 0.79
   3 ?   -3.1   0.5       2.3   8.1e+03      24      39 ..     305     321 ..     290     357 .. 0.55

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 3.2
  Cadherin_5 53 Gtvvd.ngdGtftftpeanynG 73
                G+v d ++dG+  +  ++n+ G
  EPA06857.1 19 GDVCDpDADGDGYISDASNFGG 40
                4444324555555555666655 PP

  == domain 2  score: 26.0 bits;  conditional E-value: 1.9e-09
  Cadherin_5  31 anasDvdgdtLsvssltadaenGtvvdngdGtftftpeanynGevtlsYtvsDgeggtttat 92 
                 an  D  ++t++ + l+  a + +++ ngdG ftf+p   ++G+ t+sY+ +D   +++ +t
  EPA06857.1  97 AN--DLSQNTITSAILHSPAVHPELIWNGDGGFTFNPPVGFTGTYTFSYNATDQYDTIS-ST 155
                 44..6667777777788889999******************************974433.33 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 2.3
  Cadherin_5  24 itaaqLLanasDvd.gd 39 
                 i++ ++L+++ D + g+
  EPA06857.1 305 IDECEILKKFDDDNeGE 321
                 55555555555544222 PP

>> Collagen  Collagen triple helix repeat (20 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   6.6   0.00047       1.7       4      55 ..     181     232 ..     179     239 .. 0.52
   2 ?    3.3  10.6      0.02        71      10      52 ..     226     271 ..     217     284 .. 0.35

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00047
                 XXXXXXXXXXXXXXX-----XXXXEEEE-TTSS-----------------BB CS
    Collagen   4 GepGepGppGppGkrGepGeaGekGekGpaGekGppGaaGkpGapGekGeaG 55 
                 G pG++  +G +G++  +G aG +  +G++G++   G  G++  +G +G++ 
  EPA06857.1 181 GTPGNDNLQGTNGDDLIRGFAGDDKINGKKGNDCIYGGSGDDKINGGSGNDT 232
                 5566666666666655555555555555555555555555555555555543 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.02
                 XXXXXXXXX-----XXXXEEEE-...TTSS---------------- CS
    Collagen  10 GppGppGkrGepGeaGekGekGp...aGekGppGaaGkpGapGekG 52 
                 G +G++   Ge+G++  +G++G+   +G +G++  +G++G +   G
  EPA06857.1 226 GGSGNDTIFGEEGNDKINGNNGDdyiSGGDGNDKINGNNGIDTLYG 271
                 2222222223333322222222200022222222222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 2224.88
//
Query:       EPA06858.1  [L=464]
Description: glycine--tRNA ligase, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-17   64.1   0.2    2.5e-17   62.8   0.2    1.7  1  HGTP_anticodon  Anticodon binding domain
    4.2e-12   46.4   0.8    5.7e-11   42.7   0.5    2.4  2  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
  ------ inclusion threshold ------
       0.14   12.2   0.7       0.66   10.1   0.2    2.3  2  zf-RRPl_C4      Putative ribonucleoprotein zinc-finger pf C4 
       0.18   11.2   0.8          6    6.3   0.1    2.6  2  zf-TFIIB        Transcription factor zinc-finger
       0.25   12.1   2.5       0.54   11.0   1.0    2.2  3  zinc_ribbon_15  zinc-ribbon family
       0.54   10.1   6.9        1.5    8.7   1.0    3.0  3  zinc_ribbon_5   zinc-ribbon domain
       0.71    9.8   3.9         16    5.5   0.4    2.8  2  zinc_ribbon_4   zinc-ribbon domain


Domain annotation for each model (and alignments):
>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.8   0.2   9.7e-21   2.5e-17       2      93 ..     371     459 ..     370     460 .. 0.90

  Alignments for each domain:
  == domain 1  score: 62.8 bits;  conditional E-value: 9.7e-21
                     EEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTCEEEEEETTHHHHHHHH CS
  HGTP_anticodon   2 vvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtreqervsldelveklke 93 
                     v v+ l +k+  l+e a++++ +L+++ +++ ld  ++ ig+++r+ d++g pfav+++++++e++tvt+r+rd+++qer++++e+ ++l +
      EPA06858.1 371 VGVLSLIKKDG-LKEKADEIYLQLKRK-YDAFLD-HSGAIGRRYRRLDEIGAPFAVTIDYQSMEDQTVTIRKRDSMSQERIKISEIDSILAK 459
                     67777777555.*************99.777776.89************************************************9888765 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.7   0.5   2.2e-14   5.7e-11       7     178 ..     132     347 ..     125     348 .. 0.66
   2 ?   -2.7   0.0       1.9     5e+03     119     119 ..     422     422 ..     352     455 .. 0.60

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 2.2e-14
                   TSEEEEE-SSSHHHHHHHHHHHEE...EBGGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGGHHHH..HHHHHHHHHHHHHHTT.SC CS
                   xxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxx RF
  tRNA-synt_2b   7 ndreyiLkPtneetfvelirdevl...rskrLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfhaeasldds..lrdlikaisriferlglef 98 
                   +++e +L+P+ ++ +   +        r k LPl ++q++  +R+E s  + LlR+reF q + ++f+ + +ldd+  + +++++i r+  +  +  
    EPA06858.1 132 EEEEAYLRPETCQSIFVDFPRL-YktmRGK-LPLGIAQVGKSFRNEISPRQSLLRLREFYQAEIEIFCNPTKLDDIekFTEIENTIIRVQTDSEIVA 226
                   67999*******9977555433.3111545.****************9556*******************999986225566666666655554433 PP

                   EEEEEEGTTSC.........................................BTTSEEEEEEEEETTTSEEEEEEEEEEEET.HHHHHTTE...EEE CS
                   xxxxxxxxxxx.........................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx...xxx RF
  tRNA-synt_2b  99 raiielmsaks.........................................adykdkkefeavsesltkgieigtiqklgt.rlserlga...tvl 150
                      ++     +                                         + ++   +fe+ +      +e++ ++ + +  ls+       ++ 
    EPA06858.1 227 MTCKKAV---EsgvvpnkfvayylailtefyektgiditksrfrklgdkekaFYAQVAFDFEVETT--IGWLELVACNYRSDyDLSSHATKskeKFE 318
                   3222222...13456677778888888888888888888888888888887333334456666555..34456666666655344444333355444 PP

                   CTTS.SEEEEEEEEEEEEHHHHHHHHHHH CS
                   xxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
  tRNA-synt_2b 151 denn.reksvimicaaigveRllsaileq 178
                    ++n  +  +++   ++g+ R l  ile+
    EPA06858.1 319 VMDNeDKVLPHVFEISMGIDRSLYTILEH 347
                   44441344688888888888888888886 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.9
                   E CS
                   x RF
  tRNA-synt_2b 119 e 119
                    
    EPA06858.1 422 A 422
                   2 PP

>> zf-RRPl_C4  Putative ribonucleoprotein zinc-finger pf C4 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.2   0.00026      0.66      18      68 ..      64     121 ..      47     144 .. 0.82
   2 ?   -0.9   0.0      0.68   1.7e+03      68     102 ..     211     246 ..     175     250 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00026
  zf-RRPl_C4  18 tvyCeaCeiyfkvknekqkvelvpike.......lekislrdkLCtkCkeknekekei 68 
                  + C +C++ f+ + +  ++++++i e        + i  +++ C kCk   e+ k++
  EPA06858.1  64 IIKCAKCKSTFRADRTIAEISKIEIPEsadlsefDNAILQNNIKCPKCKGDFESTKKF 121
                 467*********999999*******996777775455555677899999887776665 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.68
  zf-RRPl_C4  68 ircetfeeylkklklCkeCkervek.vlkndfvknf 102
                 i+ + ++ +     +  +Ck+ ve+ v+ n+fv ++
  EPA06858.1 211 IENTIIRVQTDSEIVAMTCKKAVESgVVPNKFVAYY 246
                 444444444444446667777776524556666666 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1     0.031        80       1      19 [.      66      88 ..      66      91 .. 0.78
   2 ?    6.3   0.1    0.0023         6       1      12 [.     107     118 ..     107     125 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.031
    zf-TFIIB  1 kCPkCqdele....eserggvei 19
                kC kC+++++    ++e +++ei
  EPA06858.1 66 KCAKCKSTFRadrtIAEISKIEI 88
                8******9997776666677765 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0023
    zf-TFIIB   1 kCPkCqdelees 12 
                 kCPkC+ ++e +
  EPA06858.1 107 KCPKCKGDFEST 118
                 799999888866 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   1.0   0.00021      0.54      35      80 ..      62     120 ..      58     123 .. 0.77
   2 ?    4.5   0.3     0.024        61       1      51 [.     106     151 ..     106     161 .. 0.75
   3 ?   -4.0   0.0         7   1.8e+04      30      45 ..     217     231 ..     208     236 .. 0.51

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00021
  zinc_ribbon_15  35 kpylacskCkslleaskelgkeiekkesse..............kkeCknCgkeveeefk 80 
                     +p+++c kCks++ a++ +  ei+k e  e              + +C++C+   e+  k
      EPA06858.1  62 DPIIKCAKCKSTFRADR-TIAEISKIEIPEsadlsefdnailqnNIKCPKCKGDFESTKK 120
                     799*************8.666666666666667888888888888888888877776655 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.024
  zinc_ribbon_15   1 ilCpkCgklskaelvkkkkvlklffipvfkwkkkkpylacskCkslleask 51 
                     i+CpkC+     ++  +kk+  +f + + + ++ ++yl  ++C+s++ +  
      EPA06858.1 106 IKCPKCK----GDFESTKKFNMMFKVGIGPEEE-EAYLRPETCQSIFVDFP 151
                     6799999....5666667777778888887777.99999999999987655 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 7
  zinc_ribbon_15  30 kwkkkkpylacskCks 45 
                     ++++++ ++   +Ck+
      EPA06858.1 217 RVQTDSEIV-AMTCKK 231
                     444433333.333444 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   1.0   0.00057       1.5       2      14 ..      64      76 ..      64      79 .. 0.68
   2 ?    3.4   0.1     0.025        63       3      12 ..     106     115 ..     102     118 .. 0.75
   3 ?   -2.7   0.0       2.1   5.3e+03      31      36 ..     143     148 ..     139     148 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00057
  zinc_ribbon_5  2 iirCpdCdtkFkl 14
                   ii+C +C+++F+ 
     EPA06858.1 64 IIKCAKCKSTFRA 76
                   6777777777764 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.025
  zinc_ribbon_5   3 irCpdCdtkF 12 
                    i+Cp+C+  F
     EPA06858.1 106 IKCPKCKGDF 115
                    7788887666 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 2.1
  zinc_ribbon_5  31 CaevFd 36 
                    C ++F+
     EPA06858.1 143 CQSIFV 148
                    888885 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.4    0.0063        16      26      36 .]      65      75 ..      64      78 .. 0.68
   2 ?    4.5   0.2     0.013        34       3       9 ..     106     112 ..     103     116 .. 0.59

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0063
  zinc_ribbon_4 26 vrCskCghvFr 36
                   ++C+kC+ +Fr
     EPA06858.1 65 IKCAKCKSTFR 75
                   56777776664 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.013
  zinc_ribbon_4   3 itCpsCk 9  
                    i Cp+Ck
     EPA06858.1 106 IKCPKCK 112
                    5566665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2939.59
//
Query:       EPA06859.1  [L=325]
Description: hypothetical protein BG20_I2478, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.046   13.4   0.2      0.096   12.4   0.2    1.5  1  DUF3172   Protein of unknown function (DUF3172)
      0.067   13.4   0.0       0.32   11.2   0.0    2.2  2  DUF1769   Protein of unknown function (DUF1769)
       0.27   11.2   1.0         14    5.7   0.1    2.4  2  PD40      WD40-like Beta Propeller Repeat


Domain annotation for each model (and alignments):
>> DUF3172  Protein of unknown function (DUF3172)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   1.6e-05     0.096       5      55 ..       7      57 ..       4      66 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.6e-05
     DUF3172  5 lailagvlvlGigiGvalsstanldpenvasreaidraaPnaelCvqyGas 55
                +ai  ++ ++ +g+G a+      d++ v+s+ ++ +++P +   +q+Ga 
  EPA06859.1  7 AAIAFSIAIVAVGVGFAFYHGNVQDNTPVVSAPVVTKTVPTTAPQAQFGAD 57
                688889******************************************996 PP

>> DUF1769  Protein of unknown function (DUF1769)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   5.4e-05      0.32       3      41 ..      51      91 ..      49      93 .. 0.91
   2 ?   -2.2   0.0      0.86   5.2e+03      19      40 ..     187     209 ..     178     211 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.4e-05
     DUF1769  3 dllfGndfdrpirdrlPpgf.saalkfak.fiDpglegDly 41
                + +fG d    ++++ P+ + +a++  ++   Dpg+ ++++
  EPA06859.1 51 QAQFGADIAAKVKQETPTKAlKAGWERITsATDPGVGHEAH 91
                568**********************99999******99875 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.86
     DUF1769  19 Ppgfsaalkfak.fiDpglegDl 40 
                 P+ + ++   ++ + Dpg+ +++
  EPA06859.1 187 PTSPTVMTGTIQsVQDPGVGHEA 209
                 77777777778877899998876 PP

>> PD40  WD40-like Beta Propeller Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1      0.01        60      14      22 ..     134     142 ..     124     142 .. 0.84
   2 ?    5.7   0.1    0.0024        14      16      23 ..     254     261 ..     253     262 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.01
                 EEE-TTSSE CS
        PD40  14 PsfSPDGkr 22 
                   ++PDGk+
  EPA06859.1 134 AIWTPDGKT 142
                 67*****97 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0024
                 E-TTSSEE CS
        PD40  16 fSPDGkrl 23 
                 ++PDGk++
  EPA06859.1 254 WTPDGKTI 261
                 *******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1913.20
//
Query:       EPA06860.1  [L=71]
Description: hypothetical protein BG20_I2402 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.32s 00:00:00.78 Elapsed: 00:00:00.50
# Mc/sec: 428.48
//
Query:       EPA06861.1  [L=154]
Description: hypothetical protein BG20_I2401 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.74    9.5   4.0        5.2    6.7   0.1    2.3  2  Tetraspanin  Tetraspanin family


Domain annotation for each model (and alignments):
>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1   0.00029       5.2      85     121 ..      13      48 ..       8      56 .. 0.75
   2 ?    3.8   0.7    0.0022        40       6      33 ..      57      85 ..      54     108 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.00029
                  XXXXXXXXXXXXXXXXX--HHH........HHHHHHH CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Tetraspanin  85 lllvlfllelaagilgfvfsdkargkvseiinnaiev 121
                  +  ++fl++++ ++++fv +++   ++s+++n+++ +
   EPA06861.1  13 MFSMVFLMLVTGALYLFVSTQE-IADASQEFNDNVGK 48 
                  5667888888877788887777.78888888888854 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.0022
                 XXXXXXXXXXXXXXXXXXXXXXX.XXX.. CS
                 xxxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
  Tetraspanin  6 fffnllfwligivllavGvwlrl.khaea 33
                 f+   +f  +g++ + +Gvw+++ kh+++
   EPA06861.1 57 FIETAFFAAVGAAYIPIGVWATIsKHTSK 85
                 6777899**************55444322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       759  (0.0423336); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1117.83
//
Query:       EPA06862.1  [L=112]
Description: hypothetical protein BG20_I2403 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      2e-06   27.6   0.2    2.8e-06   27.1   0.2    1.3  1  TrmB        Sugar-specific transcriptional regulator TrmB
    5.4e-05   22.7   1.1    0.00017   21.1   1.1    1.9  2  HTH_24      Winged helix-turn-helix DNA-binding
    7.9e-05   22.6   0.0    0.00012   22.1   0.0    1.3  1  HTH_20      Helix-turn-helix domain
    0.00072   19.3   0.0     0.0012   18.6   0.0    1.4  1  HTH_IclR    IclR helix-turn-helix domain
     0.0016   18.2   0.5     0.0024   17.7   0.5    1.3  1  HTH_5       Bacterial regulatory protein, arsR family
     0.0016   18.5   0.3     0.0035   17.5   0.1    1.6  1  DUF1492     Protein of unknown function (DUF1492)
     0.0032   17.4   0.9     0.0054   16.6   0.9    1.5  1  HTH_11      HTH domain
     0.0033   17.2   0.0      0.014   15.2   0.0    1.9  2  HTH_23      Homeodomain-like domain
     0.0084   16.0   0.0      0.012   15.5   0.0    1.2  1  MarR_2      MarR family
     0.0095   16.3   2.2      0.019   15.3   1.4    1.7  1  PriX        Primase X
  ------ inclusion threshold ------
      0.018   15.6   0.2      0.031   14.8   0.2    1.4  1  Mga         Mga helix-turn-helix domain
       0.03   13.8   0.0      0.055   13.0   0.0    1.5  1  Sigma70_r4  Sigma-70, region 4
      0.043   14.0   0.1       0.06   13.5   0.1    1.4  1  FUR         Ferric uptake regulator family
      0.076   12.8   0.0       0.14   12.0   0.0    1.5  1  HTH_8       Bacterial regulatory protein, Fis family
       0.12   12.4   0.3       0.17   11.9   0.3    1.3  1  HTH_Crp_2   Crp-like helix-turn-helix domain


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.2   2.3e-09   2.8e-06       9      58 ..      14      63 ..      11      82 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 2.3e-09
                HCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
        TrmB  9 yEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                  ++  laLl++ ++++++i+  l++p s++Y+ +++L d  l+++ k  
  EPA06862.1 14 EQSRSILALLSKSELNIQQISDTLNIPLSTAYRKVKKLDDLKLIKKTKVI 63
                5566679*************************************999865 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   1.1   1.4e-07   0.00017       2      48 .]      13      58 ..      12      58 .. 0.93
   2 ?   -1.7   0.0       1.8   2.2e+03      11      21 ..      83      93 ..      82      93 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.4e-07
      HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                de  r IL lL k + ++++++++ l++++st  r +k+L +  lIk
  EPA06862.1 13 DEQSRSILALLSK-SELNIQQISDTLNIPLSTAYRKVKKLDDLKLIK 58
                788999**99999.**************************9888886 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.8
      HTH_24 11 lLqknprisqr 21
                ++++++ +s++
  EPA06862.1 83 IIYRDGELSYK 93
                7999**99986 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   9.9e-08   0.00012       2      59 ..       6      62 ..       5      64 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 9.9e-08
                HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
      HTH_20  2 qiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvre 59
                +i++ ++++  r il++L ++ +l   ++ ++l ++ +t+++ +++L +  L++ +++
  EPA06862.1  6 DILDTITDEQSRSILALL-SKSELNIQQISDTLNIPLSTAYRKVKKLDDLKLIKKTKV 62
                58888999999*******.****************************99****99886 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0     1e-06    0.0012       7      50 ..       6      59 ..       4      61 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1e-06
                HHHCT-CTTBSS..........-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
    HTH_IclR  7 aiLdalaeapqe..........ltlselArrtglpkStvhRlLqtLvelGyveq 50
                +iLd ++ ++ +          l+++++++ + +p St++R ++ L  l+++++
  EPA06862.1  6 DILDTITDEQSRsilallskseLNIQQISDTLNIPLSTAYRKVKKLDDLKLIKK 59
                67777777777777777777779***********************99999986 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.5     2e-06    0.0024       5      47 .]      17      59 ..      13      59 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2e-06
                HHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
       HTH_5  5 lkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVek 47
                + IL lL+++el + ++++ l+++ st  +  kkL ++ L++k
  EPA06862.1 17 RSILALLSKSELNIQQISDTLNIPLSTAYRKVKKLDDLKLIKK 59
                579*******************************999988875 PP

>> DUF1492  Protein of unknown function (DUF1492)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   2.9e-06    0.0035      51      93 ..       7      49 ..       3      57 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.9e-06
     DUF1492 51 lidklensdsrsvLrmvyidkltvwqvidklnisrstyyrllr 93
                ++d++ + +srs+L +    +l+++q+ d lni  st yr+ +
  EPA06862.1  7 ILDTITDEQSRSILALLSKSELNIQQISDTLNIPLSTAYRKVK 49
                6899***********************************9876 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.9   4.5e-06    0.0054       3      42 ..      17      54 ..      15      75 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.5e-06
      HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeel 42
                ++il lL  +++ ++++++++ Ln+  +t +r +k+L +l
  EPA06862.1 17 RSILALL--SKSELNIQQISDTLNIPLSTAYRKVKKLDDL 54
                6899999..4444************************876 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.2e-05     0.014      10      37 ..      19      47 ..      14      55 .. 0.81
   2 ?   -0.5   0.0      0.95   1.1e+03      23      38 ..      62      78 ..      48      80 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.2e-05
      HTH_23 10 illllae.GlsvreIAreLgvsrrTvyrw 37
                il ll +  l++++I++ L+++ +T yr 
  EPA06862.1 19 ILALLSKsELNIQQISDTLNIPLSTAYRK 47
                5555555699*****************85 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.95
      HTH_23 23 IAreL.gvsrrTvyrwl 38
                + r L g +++ + +w+
  EPA06862.1 62 VIRTLeGLNESYYKNWI 78
                33444488888888887 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   9.7e-06     0.012       8      54 ..      17      60 ..       4      67 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 9.7e-06
                HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
      MarR_2  8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                + +La L  ++   l+++++ ++l+++ s++ r +k+L +  L+ ++
  EPA06862.1 17 RSILALLSKSE---LNIQQISDTLNIPLSTAYRKVKKLDDLKLIKKT 60
                34555555555...9*****************************886 PP

>> PriX  Primase X
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   1.4   1.6e-05     0.019      11      84 ..      10      82 ..       5      97 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.6e-05
                --SSTHHHHHHHTHHHHHHHTS---HHHHHHHHHHHH....TTSSSS---HHHHHHHHHHHHHHT-----HHHH CS
        PriX 11 glpDgRkrlilyvisrYLvnvkklseeealkklkeflksckkkknlskiyeswirsvikgvkekglkpislkkl 84
                 + D  +r il ++s+  +n++++s+   +  l+  +++ kk ++l+ i ++++   ++g  e  +k + ++ +
  EPA06862.1 10 TITDEQSRSILALLSKSELNIQQISDTLNI-PLSTAYRKVKKLDDLKLIKKTKVIRTLEGLNESYYKNWIYEVI 82
                689*********************987666.5777778*******************************99875 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.2   2.6e-05     0.031      24      56 ..      21      53 ..       7      63 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.6e-05
                HHHHHSEEEHHHHHHHCT--HHHHHHHHHHHHH CS
         Mga 24 flfeeeevsieelaqelyiSestlkrkikelnk 56
                 l+ + e++i++++++l i  st++rk+k+l  
  EPA06862.1 21 ALLSKSELNIQQISDTLNIPLSTAYRKVKKLDD 53
                467899************************975 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   4.6e-05     0.055       6      37 ..      13      44 ..       7      51 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.6e-05
                -HHHHHHHHHHHTTT--HHHHHHHHTS-HHHH CS
  Sigma70_r4  6 pererevlelrfgeglTleEIgerlgiSrerV 37
                +e+ r +l l    +l+ ++I+++l+i+++++
  EPA06862.1 13 DEQSRSILALLSKSELNIQQISDTLNIPLSTA 44
                477899999999*****************996 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1     5e-05      0.06      25      63 ..      24      62 ..       5      76 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5e-05
                EHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEE CS
         FUR 25 saeevykelkeedpeislaTVYrtLklleeaglvkelef 63
                s  e+  +  ++  +i l+T Yr +k l++++l+k++++
  EPA06862.1 24 SKSELNIQQISDTLNIPLSTAYRKVKKLDDLKLIKKTKV 62
                56667777778899*********************9886 PP

>> HTH_8  Bacterial regulatory protein, Fis family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00012      0.14      10      42 .]      19      51 ..      11      51 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
                HHHHHHHTTT-HHHHHHHHTS-HHHHHHHHHHT CS
       HTH_8 10 IeaALertgGnkskAArlLGisRrtLyrKLkkY 42
                I a L +++ n+++ ++ L+i  +t yrK kk+
  EPA06862.1 19 ILALLSKSELNIQQISDTLNIPLSTAYRKVKKL 51
                88899999***********************96 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.3   0.00014      0.17      21      66 ..      27      70 ..       7      72 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00014
                EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETEEEEES-HHHHH CS
   HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglisrgrririldleaLr 66
                 l+ +++++ l++  +t  r  ++L + +li++ +  +i+ le+L+
  EPA06862.1 27 ELNIQQISDTLNIPLSTAYRKVKKLDDLKLIKKTK--VIRTLEGLN 70
                56779***************************876..777788776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 774.30
//
Query:       EPA06863.1  [L=719]
Description: peptidase families S8 and S53 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.4e-18   65.0   0.1    1.2e-17   64.2   0.1    1.3  1  Peptidase_S8  Subtilase family


Domain annotation for each model (and alignments):
>> Peptidase_S8  Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.2   0.1   6.5e-22   1.2e-17      49     276 ..     285     537 ..     226     552 .. 0.82

  Alignments for each domain:
  == domain 1  score: 64.2 bits;  conditional E-value: 6.5e-22
                   S-TT-SC-SSS....HHHHHHHHHH-B..SSSSSB-SSTTSEEEEEE-SSTTSB-HH..HHHHHHHHHHHHCT-SEEEE-EESCETTCHHCHHHHHH CS
                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Peptidase_S8  49 tstnwarddngnsieHGthvAGiaaanapeegekngvapgakilsvkvldtsggsmetgteliraieeaaedkvdvinmslgestslpktgrsieal 145
                   + t + +ddng++  HGt +A +   +   e+      p  ki+s+k+ +++  s+    +++++i ++ +dk ++   s+g  + + + ++++e  
    EPA06863.1 285 YGTTNFDDDNGDDFGHGTPIACLSTFG---EER---REPISKIISYKIWSQDKPSDS-FLGILDGI-KKYKDKSRIFTSSIG--FPDAELEDVYE-- 369
                   344455666676778********9999...333...35778********99887774.47888776.56778**********..88888888775.. PP

                   HHHHHH.CCT-EEEEE--SS-T-HH...........EEE-TTCEECTTTSTTCEEEEEES..............TTSSB-TT--B-TT......... CS
                   xxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxx..............xxxxxxxxxxxxxxxx...xxxx RF
  Peptidase_S8 146 ainravnkkgvlvviSaGNngktgs...........slqagspvgtpstsknvitvgayt..............tegkiapfSsrGpssd...gklk 214
                    ++r ++++++ +v+SaGN ++++            ++ +  +v +p+++ ++i+vg++                eg+++p+S  G + +   + +k
    EPA06863.1 370 -LDRVIQRENIAFVCSAGNINPNQIeneirsgnsypNYLKKYQVMAPGNAISSIAVGSIAknnsmrgtplnsiaHEGDVSPYSCCGTKNEfifECIK 465
                   .9****999************9999999999**999999999999**************************************999998899999** PP

                   .-EEEE-S-.CCCCCCCCCHHHTTTHH.......EEEE-SHHHCHHHHHHHHHHHHHHHTT..--HHHHHHH CS
                   xxxxxxxxx.xxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxx RF
  Peptidase_S8 215 pdivapGgn.ivstwsrqsnnsaglss.......yqsmsGTSmAsPnaagaaAlllsalpk..ltpetvraa 276
                   pd v  G+n i++ +s  ++   g +s       y  + GTS++sP+ a+ +A +l ++ k   + et++a+
    EPA06863.1 466 PDFVEHGTNlIYEGASVTTQGINGITSytkngkvYSGFVGTSFSSPLLAKKFAEILAKYGKqiQNIETLKAI 537
                   *********85444433333333333355899*************************988766555666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (719 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.69u 0.32s 00:00:01.01 Elapsed: 00:00:00.50
# Mc/sec: 4328.36
//
Query:       EPA06864.1  [L=47]
Description: hypothetical protein BG20_I1442 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 306.19
//
Query:       EPA06865.1  [L=550]
Description: hypothetical protein BG20_I1440 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00053   20.2   0.0     0.0017   18.6   0.0    1.9  1  SH3_3            Bacterial SH3 domain
     0.0049   16.7   0.2       0.01   15.6   0.2    1.4  1  SH3_9            Variant SH3 domain
  ------ inclusion threshold ------
      0.021   15.1   0.0      0.054   13.7   0.0    1.7  1  UPF0102          Uncharacterised protein family UPF0102
      0.055   13.1   0.1       0.11   12.1   0.1    1.4  1  RE_Bpu10I        Bpu10I restriction endonuclease
      0.073   12.9   7.6      0.015   15.1   2.7    2.1  2  FACT-Spt16_Nlob  FACT complex subunit SPT16 N-terminal lobe d


Domain annotation for each model (and alignments):
>> SH3_3  Bacterial SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   4.7e-07    0.0017      16      50 ..      32      65 ..      25      69 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 4.7e-07
       SH3_3 16 igtlpyGekVevleetgggeWykvrtddgteGwvs 50
                +  l+++++V v++e+ gg Wy v td+g +G+v 
  EPA06865.1 32 LELLYFNSRVFVIGESSGG-WYYVITDKGNTGYVD 65
                556899************9.*************95 PP

>> SH3_9  Variant SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.2   2.9e-06      0.01      20      43 ..      40      64 ..      35      68 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.9e-06
       SH3_9 20 vitvieesedgWlegsl.tGrtGlv 43
                +++vi+es++gW++++  +G+tG+v
  EPA06865.1 40 RVFVIGESSGGWYYVITdKGNTGYV 64
                689*************77******8 PP

>> UPF0102  Uncharacterised protein family UPF0102
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.5e-05     0.054       1      47 [.     407     458 ..     407     485 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.5e-05
                 HHHHHHHHHHHTT-EEEEEEEEETT...EEEEEEE..TTEEEEEEEEE-... CS
     UPF0102   1 gEelaaeyLekkgyeilernwrcra...gEiDiia..tevlvfvEVKtRsse 47 
                 gE+la ++L ++g++il  + + +    g iDi+   + v+ f++ K+ +++
  EPA06865.1 407 GEKLATDFLAAEGHTILSFKPNIKGtnqGGIDIVTikDGVVNFIDNKALTRS 458
                 7****************665544333359*******988999*999984322 PP

>> RE_Bpu10I  Bpu10I restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1     3e-05      0.11      40     124 ..     422     516 ..     404     520 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3e-05
   RE_Bpu10I  40 slsFesslkelekkgelsirtkdq..DFa....igk..klylkasfdpdfkesvealevnlayvaaeCktnLDktmfqeasatae..dlklavPg 124
                  lsF++ +k ++++g   + +kd   +F+    +++  ++   +s  ++f+++++++ ++l  v a+ k  L+k ++q+a ++    + k av +
  EPA06865.1 422 ILSFKPNIKGTNQGGIDIVTIKDGvvNFIdnkaLTRsgNVSSVSSLTTNFQKNKDKVISELKSVLANAKSDLEKNVIQQALTAIDrgNFKKAVTN 516
                 578888899999999888888885335541111444556666788999*******************************9987651245666555 PP

>> FACT-Spt16_Nlob  FACT complex subunit SPT16 N-terminal lobe domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   2.7   4.2e-06     0.015      37     139 ..     277     375 ..     246     399 .. 0.78
   2 ?   -0.5   0.2      0.27   9.6e+02      16     114 ..     470     499 ..     456     543 .. 0.58

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.2e-06
                      S--TT----HHHHHHHHHHSS--SSEEEEEESSEEEEEEEHHHHHTTGGGCTSTT-..SSEEEEEEE-S-HHHHHHHHHHHHHHHHTTTSEEEE CS
  FACT-Spt16_Nlob  37 ksdeenpykKstalqtWLlGyefpdtlilltkkkiviltskkKaklLeplkekkeee.kvevellvreKdadenkknfeklieaikeagkkvGv 129
                      k +e+ p  K+  ++ W +Gy     ++ +++  + +++   K+  L ++  +++   k+e  +l +     + + +f+k+++a+k+++kk   
       EPA06865.1 277 KFKEDDPPLKKGHFHGWVIGYIVALIVTTFVTGGLALVAKFGKIAKLAKILRSTSFVkKLERVVL-K----VKTSGKFDKITDALKSKKKKFSS 365
                      5578899999999*************************************999965323333333.3....458999************99876 PP

                      -TT----SHH CS
  FACT-Spt16_Nlob 130 laKdkseGkf 139
                       +  ++++k+
       EPA06865.1 366 EPEINPQSKL 375
                      5555555555 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.27
                      HHHSHHHHHSTT-SEEEEEE-S--TT----HHHHHHHHHHSS--SSEEEEEESSEEEEEEEHHHHHTTGGGCTSTT-.SSEEEEEEE-S-HHHH CS
  FACT-Spt16_Nlob  16 awkeeeedkfssvdallvvlGksdeenpykKstalqtWLlGyefpdtlilltkkkiviltskkKaklLeplkekkeeekvevellvreKdaden 109
                      ++++++++ +s+++++l  +                                                                      +d +
       EPA06865.1 470 NFQKNKDKVISELKSVLANAK---------------------------------------------------------------------SDLE 494
                      444444444444444443333.....................................................................3333 PP

                      HHHHH CS
  FACT-Spt16_Nlob 110 kknfe 114
                      k+ ++
       EPA06865.1 495 KNVIQ 499
                      33333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (550 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       880  (0.0490825); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.34s 00:00:00.95 Elapsed: 00:00:00.48
# Mc/sec: 3465.92
//
Query:       EPA06866.1  [L=232]
Description: hypothetical protein BG20_I1449 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1581.23
//
Query:       EPA06867.1  [L=1090]
Description: hypothetical protein BG20_I1441 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.02   14.9   1.7        4.3    7.4   0.3    3.0  2  GvpG         Gas vesicle protein G
       0.02   14.9   1.9      0.038   14.0   1.9    1.3  1  Trypan_PARP  Procyclic acidic repetitive protein (PARP)
      0.061   12.3   1.0       0.16   10.9   1.0    1.7  1  DEC-1_N      DEC-1 protein, N-terminal region


Domain annotation for each model (and alignments):
>> GvpG  Gas vesicle protein G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1    0.0035        21      39      70 ..     115     146 ..     110     154 .. 0.86
   2 ?    7.4   0.3   0.00071       4.3      21      63 ..     774     818 ..     769     826 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0035
        GvpG  39 aLqqeLdaGeIdeeeFdrrEeelLdrLealer 70 
                 +L ++L + +I+  +  ++E+++L  +e+ + 
  EPA06867.1 115 SLRLRLSDDDITRMNLRKEEDQILGTIETTTF 146
                 68999**********************98774 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00071
        GvpG  21 eraeeqlddq.enlrkeLaaLqqeLda.GeIdeeeFdrrEeelLd 63 
                 +r+e+q++dq ++l+ e +aLq + d+  e ++e+F+rr e l +
  EPA06867.1 774 ARVERQVYDQrTQLQSEVSALQVATDKySEKTKEHFNRRTEILRL 818
                 5899999988357************97479999****99886644 PP

>> Trypan_PARP  Procyclic acidic repetitive protein (PARP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   1.9   6.3e-06     0.038      84     116 ..     187     219 ..     160     236 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.3e-06
  Trypan_PARP  84 eeepepepepepepepepepepepepepgaatl 116
                  e +p p p p p p p p p p p pep  a l
   EPA06867.1 187 EFSPSPSPSPSPSPSPSPSPSPSPSPEPYDADL 219
                  445666666777777777777777777766655 PP

>> DEC-1_N  DEC-1 protein, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   1.0   2.7e-05      0.16      86     142 ..     154     213 ..     131     244 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 2.7e-05
     DEC-1_N  86 llppmdlg.pqvGaalqsllplqsldgllGaa...apapalaaapppapapvpddpapapa 142
                  l   +++ + + + ++++ + + +dg+ G++   +p p ++ +p p+p+p+p  p+p p+
  EPA06867.1 154 TLGELSVDqSIISSCVAEMTAAKIIDGVTGDSdefSPSPSPSPSPSPSPSPSPS-PSPSPE 213
                 5566666645678899999***********988777777777777777777763.444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1090 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1228  (0.0684924); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.81u 0.28s 00:00:01.09 Elapsed: 00:00:00.45
# Mc/sec: 7333.71
//
Query:       EPA06868.1  [L=181]
Description: hypothetical protein BG20_I1448 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0043   16.8   0.1      0.011   15.6   0.1    1.7  1  UBA_3          Fungal ubiquitin-associated domain
  ------ inclusion threshold ------
       0.35   10.8   5.8       0.15   12.0   2.4    1.9  2  Endopep_inhib  IseA DL-endopeptidase inhibitor


Domain annotation for each model (and alignments):
>> UBA_3  Fungal ubiquitin-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   1.2e-06     0.011      18      52 ..     145     179 ..     134     180 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.2e-06
                 HHT--HHHHHHHHHHS--SS--SS--HHHHHHHHH CS
       UBA_3  18 sqGFekdkvievLkrLgiksldpednetankileE 52 
                 +  F +    ev+  L++k++   +ne+ ++ileE
  EPA06868.1 145 NSPFTTSLMDEVFHMLKYKKMPFSQNEQTQRILEE 179
                 55566666669***********************9 PP

>> Endopep_inhib  IseA DL-endopeptidase inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   2.4   1.7e-05      0.15       3      81 ..      38     115 ..      36     120 .. 0.90
   2 ?   -0.2   0.1     0.094   8.4e+02      63      82 ..     145     164 ..     117     166 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.7e-05
                    SS--HHHHHHHHHHHHHHHHHHHTTS-TT-S---EEEETTEEEEE--TTSSSHHHHHHHHTTTB-HHHHHHHHHTTT-E CS
  Endopep_inhib   3 knlsdkeakkLilnadelfwkilsgkspkkkeiksievkgkeYaklkddintkeklfnYLneyfTkeaiekiikdlkfk 81 
                    +nls+ ea+  i++++  +++  + + ++++    i++  ++Y+k+k+ ++++e  ++   + f +e + +ii+ +kf 
     EPA06868.1  38 GNLSETEALDFINSGELGYYEQTEQE-ITNNVKVPITITRTTYYKYKSFLESPEYQTKQVFKLFRDEYVTEIIQRFKFF 115
                    79*****************9999988.55576789999****************99999999************99996 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.094
                    TTTB-HHHHHHHHHTTT-EE CS
  Endopep_inhib  63 neyfTkeaiekiikdlkfke 82 
                    n+ fT +++++++ +lk+k+
     EPA06868.1 145 NSPFTTSLMDEVFHMLKYKK 164
                    77899999999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1297.41
//
Query:       EPA06869.1  [L=102]
Description: hypothetical protein BG20_I1444 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0042   16.8   0.0     0.0056   16.4   0.0    1.3  1  DUF5615   Domain of unknown function (DUF5615)


Domain annotation for each model (and alignments):
>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   3.1e-07    0.0056      18      59 ..      22      66 ..       3      80 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.1e-07
     DUF5615 18 reaghdvlhvrelg...legasDeeileyAkeedriivTkDkDFg 59
                 +++h+++ v +     ++g +De + +y++ +++ ++T D  F+
  EPA06869.1 22 LKPYHTIIKVGDNPeslKRGSPDEVVADYCNTNGCDLFTSDVGFY 66
                57788888888876332347*********************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 717.14
//
Query:       EPA06870.1  [L=428]
Description: site-specific recombinase, phage integrase family [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.9e-05   22.3   0.1     0.0075   16.1   0.0    3.3  2  Phage_integrase  Phage integrase family


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0      0.32   5.7e+03      41      68 ..      68      92 ..      67      96 .. 0.77
   2 !   16.1   0.0   4.2e-07    0.0075       4     158 ..     143     315 ..     140     328 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.32
                     TT-BGGGEECTTTEEEEEEEECSSSSEE CS
  Phage_integrase 41 lsLrvkdldlengvilvheregKgsker 68
                     ++L  kd dl+ +vi      +K+ k+r
       EPA06870.1 68 VELARKDTDLASNVIAT---YIKEDKKR 92
                     67899999999999998...66666655 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 4.2e-07
                      HHHHHHHHHHCCGCHHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEE...EEECSSSSEEEEECT.HHHHHHHHHHHHHH....CH CS
  Phage_integrase   4 tedeverllaaleeslkirdklllellyetGlRisEllsLrvkdldlengvilvh...eregKgskeravpls.eealellkellska....le 89 
                      t +e++++l+ +++   i+dk ++ l  + G+R       ++kd+ + +     +       +g  e + ++   ea++ l+++ ++      +
       EPA06870.1 143 TREEIQKMLEVAND---ITDKVIILLFSSGGFRLEAWDYFTWKDVIFFKDNNSYKggsLLIYRGDPESYFTFItPEACKTLEHYRENWkadiGR 233
                      67999999999999...*******************99******65544443333343223345555555554588888888888877655433 PP

                      CCTTTSBSSBET...TSSB--HHHHHHHHHHHHHHCT-S..........SC--TTHHHHHHHHHHHHHCTSHHHHHHHHT-S CS
  Phage_integrase  90 eaeksellfask...rgkplsrqtvrkafkraveeagie..........kpltpHtlRhsfataLleagvdlrvvqkllGHs 158
                        ++++ l+ s      ++l+++ vrk+++++v   g+           +    H +R++f t L +a vd    ++++GH+
       EPA06870.1 234 YPKPDDPLIKSIrypVIRRLNQKGVRKRINKVVSDIGLRpplppnkkrhEVQLDHGFRKYFNTMLRRAKVDYLDKEDMMGHK 315
                      3334444444446777899****************9999999999877655667***************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1568  (0.0874561); expected 358.6 (0.02)
Passed bias filter:                      804  (0.0448435); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.69u 0.32s 00:00:01.01 Elapsed: 00:00:00.52
# Mc/sec: 2498.24
//
Query:       EPA06871.1  [L=236]
Description: hypothetical protein BG20_I1445 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-08   34.7   0.0      4e-08   33.8   0.0    1.4  1  MUG113    Meiotically up-regulated gene 113
    5.2e-07   30.2   0.0    1.1e-06   29.2   0.0    1.5  1  T5orf172  T5orf172 domain


Domain annotation for each model (and alignments):
>> MUG113  Meiotically up-regulated gene 113
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.0   4.4e-12     4e-08       2      75 ..      86     150 ..      85     152 .. 0.91

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 4.4e-12
      MUG113   2 KIGrTnnverRlnelnrqcpskltllryyppsspnahrlErllhleLkdkrlrdekcdcEwFevpaeslkavir 75 
                 KIGr++nv +Rl++l+++++++l ll+  p     +  +E+  h+++ + r ++     EwF ++++  + vi 
  EPA06871.1  86 KIGRSKNVRKRLQNLKTGTSDDLYLLALEP----GSPTIEKIRHKQFVSDRRKG-----EWFVCTPKLFQHVIY 150
                 **********************99999887....668*****************.....******998888775 PP

>> T5orf172  T5orf172 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.0   1.2e-10   1.1e-06      13     102 ..      82     152 ..      60     153 .. 0.84

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 1.2e-10
    T5orf172  13 getillKIGrtsnvqrRlkelskyptkppselevvaekevrkvpnahrvErlihkeLadrryrvkcdcgkehrEwFevsleevdevvrri 102
                 g    +KIGr++nv++Rl++l+   t+ +++l ++a       p +  +E+  hk++ +   r        ++EwF ++++  ++v+  +
  EPA06871.1  82 GL--HMKIGRSKNVRKRLQNLK---TGTSDDLYLLAL-----EPGSPTIEKIRHKQFVS--DRR-------KGEWFVCTPKLFQHVIYTW 152
                 44..69****************...999999998665.....489**************..888.......8********9999998777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1577.82
//
Query:       EPA06872.1  [L=185]
Description: hypothetical protein BG20_I1446 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0011   18.6   0.1     0.0014   18.3   0.1    1.2  1  MmcB-like  DNA repair protein MmcB-like
  ------ inclusion threshold ------
      0.013   15.5   0.0      0.029   14.4   0.0    1.7  2  Hjc        Archaeal holliday junction resolvase (hjc)
      0.016   15.4   0.0      0.096   12.9   0.0    2.1  2  UPF0102    Uncharacterised protein family UPF0102
      0.026   14.1   0.6      0.074   12.6   0.1    2.0  2  AHJR-like  REase_AHJR-like
      0.058   13.9   0.3        0.1   13.1   0.1    1.8  1  NERD       Nuclease-related domain
      0.062   13.4   0.0       0.11   12.5   0.0    1.6  1  VRR_NUC    VRR-NUC domain


Domain annotation for each model (and alignments):
>> MmcB-like  DNA repair protein MmcB-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   4.7e-07    0.0014       8     117 ..      12     125 ..       5     150 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 4.7e-07
   MmcB-like   8 grqsetalairrgvlrllrelglaalpe..lsLasGr.raDl.valskkgeiwiieikssveDfrtDrkWpe.yrahcDrlffaveedvpleilPedvG 101
                  r  +  l i +  ++++++lg++a+p   + +a G   +Dl + l k++++++ie+kss +++   rk  +   ++ D ++ a++ + p+     ++G
  EPA06872.1  12 KRVGKYELDIIKDLQKYFSNLGYHAIPHarFDIAWGSiLSDLdLLLIKNDQLILIEVKSSKDNLSRARKQIDaIEDFVDEVYIATDYE-PKKWPSRKAG 109
                 566677889999999**********99723566888634566334556778999*********9877776652789********9987.6666667778 PP

   MmcB-like 102 liva.Daygaellreap 117
                  i++ D+y  +++re+ 
  EPA06872.1 110 RIIVrDNY-VNIIRESK 125
                 55551666.56778764 PP

>> Hjc  Archaeal holliday junction resolvase (hjc)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   9.7e-06     0.029      31      72 ..      53      93 ..      23     110 .. 0.79
   2 ?   -2.3   0.0       1.5   4.5e+03      65      65 ..     158     158 ..     121     177 .. 0.54

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 9.7e-06
                -SEEEEETTEEEEEEEEEESSSEEEEEHHHHHHHHHHHHHHT CS
         Hjc 31 pDviAirgdvvlviEvKsskkeriylkkeqvekllefarkag 72
                 D++ i++d +++iEvKssk +++   ++q++ + +f ++  
  EPA06872.1 53 LDLLLIKNDQLILIEVKSSK-DNLSRARKQIDAIEDFVDEVY 93
                69999**************9.778888999999999987653 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.5
                 H CS
         Hjc  65 l 65 
                 +
  EPA06872.1 158 T 158
                 2 PP

>> UPF0102  Uncharacterised protein family UPF0102
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.37   1.1e+03      17      32 ..       8      23 ..       5      31 .. 0.69
   2 ?   12.9   0.0   3.2e-05     0.096       7      57 ..      27      83 ..      23      88 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.37
                EEEEEEETTEEEEEEE CS
     UPF0102 17 lernwrcragEiDiia 32
                l+   r+   E+Dii 
  EPA06872.1  8 LKSTKRVGKYELDIIK 23
                5555566567****96 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 3.2e-05
                HHHHHTT-EEE.EEEEEETTE....EEEEEE..TTEEEEEEEEE-......------- CS
     UPF0102  7 eyLekkgyeil.ernwrcrag....EiDiia..tevlvfvEVKtRssekfgspaeavt 57
                +y+++ gy+ + + ++   +g    ++D+ +  +++l+ +EVK+  +++  +++++++
  EPA06872.1 27 KYFSNLGYHAIpHARFDIAWGsilsDLDLLLikNDQLILIEVKSS-KDNLSRARKQID 83
                56677777655477888888555559*******999********5.455556665555 PP

>> AHJR-like  REase_AHJR-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   2.5e-05     0.074       8      76 ..      17      86 ..      10      92 .. 0.70
   2 ?   -1.7   0.0      0.64   1.9e+03      80      99 ..     128     147 ..     111     175 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.5e-05
   AHJR-like  8 lererleslaeqyrekGyevllhPnredlP.dfLksYrpDliarkdeeaviiEvksrrs..saseqyLqela 76
                 e + +++l++ + + Gy+ + h   +      L+   +Dl+ +k+++ + iEvks++   s +++++ ++ 
  EPA06872.1 17 YELDIIKDLQKYFSNLGYHAIPHARFDIAWgSILS--DLDLLLIKNDQLILIEVKSSKDnlSRARKQIDAIE 86
                56677777777777778877777766644313444..58*****************9984455556666655 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.64
   AHJR-like  80 eqhpgWrfelvmtndedatv 99 
                 ++ p  + +lv+     + +
  EPA06872.1 128 NREPKLKTLLVLRKSSLNSL 147
                 44444444444444443333 PP

>> NERD  Nuclease-related domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   3.4e-05       0.1       7      56 ..      19      73 ..      13     151 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.4e-05
        NERD  7 ravakeLkelked.eylvlhdvrlrpg.tg...eiDhlvispkgifviEvKnwsG 56
                 ++ k L+++ ++ +y+ +   r++    +   ++D+l+i ++ +++iEvK+ + 
  EPA06872.1 19 LDIIKDLQKYFSNlGYHAIPHARFDIAwGSilsDLDLLLIKNDQLILIEVKSSKD 73
                5555556644223355555555553335124569*****************9654 PP

>> VRR_NUC  VRR-NUC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.8e-05      0.11      54      94 ..      48      88 ..      16      96 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.8e-05
                STS-SEEEEETTTTE..EEEEEEE-TT----H..HHHHHHHHH CS
     VRR_NUC 54 sGvPDLilwieeqkryvflliEvKgpgdrlsd..nQrkwldel 94
                s ++DL l++ ++++    liEvK+ +d ls   +Q + ++ +
  EPA06872.1 48 SILSDLDLLLIKNDQ--LILIEVKSSKDNLSRarKQIDAIEDF 88
                556788777777776..8************9622455555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       851  (0.047465); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1160.04
//
Query:       EPA06873.1  [L=229]
Description: methyltransferase domain protein [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-09   38.9   0.1    1.6e-09   38.3   0.1    1.3  1  Methyltransf_25  Methyltransferase domain
    4.4e-09   37.0   0.2    6.6e-09   36.4   0.2    1.3  1  Methyltransf_12  Methyltransferase domain
    4.2e-08   33.1   0.3    5.8e-08   32.7   0.3    1.2  1  Methyltransf_31  Methyltransferase domain
    5.6e-08   33.3   0.0      9e-08   32.7   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    6.1e-08   32.4   1.4     0.0076   15.7   0.0    2.6  3  CheR             CheR methyltransferase, SAM binding domain
    0.00014   21.7   0.0    0.00018   21.4   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    0.00092   19.2   0.5     0.0015   18.4   0.5    1.4  1  Methyltransf_18  Methyltransferase domain
     0.0012   18.3   0.3       0.01   15.3   0.2    2.3  3  Methyltransf_4   Putative methyltransferase
     0.0045   17.3   1.1      0.032   14.5   0.8    2.3  3  RnlB_antitoxin   Antitoxin to bacterial toxin RNase LS or Rnl
  ------ inclusion threshold ------
      0.011   15.7   0.1      0.021   14.8   0.1    1.4  1  Methyltransf_32  Methyltransferase domain
      0.043   13.9   0.2      0.078   13.1   0.2    1.5  1  FtsJ             FtsJ-like methyltransferase
      0.085   12.6   0.0       0.15   11.8   0.0    1.4  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3   0.1   1.1e-12   1.6e-09       1      97 []      38     132 ..      38     132 .. 0.90

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 1.1e-12
                      EEEET-TTSHHHHHHHCTS...T.SSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHHHHHHHHHHH CS
  Methyltransf_25   1 vLdlGcGtGrltlalakrl...g.kakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsdedlekalkeia 90 
                      ++d+Gc +G  ++++++ l   + ++  +g+Dis++ +++ar++++      +f++ ++ +++  +g+ D+v++s a  +++ + + +++++++
       EPA06873.1  38 IIDVGCSNGSAMKYAQTYLqqkNiESFTIGIDISKNVVDEARKNLD------QFINENVLNVDNCAGKADIVICSKAAIFVEGDVRCQIIRKCS 125
                      79*******9999888887653378889*****************4......8*********************9887778888899******* PP

                      HHEEEEE CS
  Methyltransf_25  91 rvLkpgG 97 
                      + Lk++G
       EPA06873.1 126 EFLKNDG 132
                      ****998 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.2   4.4e-12   6.6e-09       2      99 .]      40     134 ..      39     134 .. 0.87

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 4.4e-12
  Methyltransf_12   2 eiGcGtGsllrallekl....pdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhl.kdir.evldni 89 
                      ++Gc +Gs +++   +l    +++  +g+Dis+++++ a++ l + +n+n  +++++++         + D+v++s +   +  d+r ++++++
       EPA06873.1  40 DVGCSNGSAMKYAQTYLqqknIESFTIGIDISKNVVDEARKNLDQFINEN--VLNVDNCAG-------KADIVICSKAAIFVeGDVRcQIIRKC 124
                      9***********999999965666667********************866..555555552.......89******999999989999****** PP

  Methyltransf_12  90 rklLkpgGrl 99 
                       + Lk++G+l
       EPA06873.1 125 SEFLKNDGIL 134
                      ********86 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.3   3.9e-11   5.8e-08       2     110 ..      33     137 ..      32     175 .. 0.84

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 3.9e-11
  Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgp.kae..vvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnevl..naladp 90 
                      +k+ +++D+GC +G   + +   l + ++e   +GiDis++++  Ar+n++       +F  +++ + ++  +  k D++++  +         
       EPA06873.1  33 TKKFVIIDVGCSNGSAMKYAQTYLQQkNIEsfTIGIDISKNVVDEARKNLD-------QFINENVLNVDN--CAGKADIVICSKAAifVEGDVR 117
                      57789**********99998873333344566****************966.......899999999885..3489***999977767777788 PP

  Methyltransf_31  91 dkileeiervlkpggillie 110
                      ++i+++ ++ lk++gil+++
       EPA06873.1 118 CQIIRKCSEFLKNDGILITD 137
                      99*************99954 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.0     6e-11     9e-08       2      95 ..      40     135 ..      39     136 .. 0.89

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 6e-11
                      EET-TTSHHHHHHH....HTT...SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-..CCHHHHHHHHHH CS
  Methyltransf_11   2 dvGcGtGrlaeala....krg...arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhv..edpekalkeiaR 86 
                      dvGc +G+ +++ +    +     + ++g+D+sk++++ a+++  +      f+ +++ ++    ++ D+v++s +  +v  + + ++++++  
       EPA06873.1  40 DVGCSNGSAMKYAQtylqQ-KnieSFTIGIDISKNVVDEARKNLDQ------FINENVLNVDNCAGKADIVICSKAAIFVegDVRCQIIRKCSE 126
                      9************966641.257999**************999976......58999999988999**************9999********** PP

                      HEEEEEEEE CS
  Methyltransf_11  87 vLkpgGllv 95 
                       Lk++G+l+
       EPA06873.1 127 FLKNDGILI 135
                      *******98 PP

>> CheR  CheR methyltransferase, SAM binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   5.1e-06    0.0076       6      82 ..      12      80 ..       9      84 .. 0.81
   2 !   15.2   0.1   7.3e-06     0.011     121     172 ..      84     135 ..      80     138 .. 0.94
   3 ?   -2.2   0.0       1.6   2.4e+03     149     167 ..     171     189 ..     165     191 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5.1e-06
                TTTCHHHHHHHHCCH.HHHHHHHTSSSEEEEEES-TTTHHHHHHHHHHHCHSTTTSSS-EEEEEEESSCHHHHHHHH CS
        CheR  6 freakhfeelekevlepllakaknekrvriwsagcssGeEpYslAmllketlpkaaklkvkilAtDidlkvlekAka 82
                f + ++++ + +++le    ++++ k++ i  +gcs+G      Am  ++t+ ++++++   +++Di+++v+++A++
  EPA06873.1 12 FEDRYELTGIINYILE---YANNSTKKFVIIDVGCSNGS-----AMKYAQTYLQQKNIESFTIGIDISKNVVDEARK 80
                6777788888889995...23344599***********8.....7888888888888877888************97 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 7.3e-06
                 EEEE--TTT-SGGG--EEEEEE-SSGGGC-CHHHHHHHHHHHCCEEEEEEEE CS
        CheR 121 kFeklnllekksvlgklDvifcrnvliYfdeetqekvlerfaeklkpgglLl 172
                 +F + n+l+ ++  gk D+++c    i+ + +++ +++++ +e lk++g+L+
  EPA06873.1  84 QFINENVLNVDNCAGKADIVICSKAAIFVEGDVRCQIIRKCSEFLKNDGILI 135
                 688999**99***************************************997 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.6
                 C-CHHHHHHHHHHHCCEEE CS
        CheR 149 fdeetqekvlerfaeklkp 167
                 f++e ++++  rf++++k+
  EPA06873.1 171 FRKEYRRRIHTRFRKSMKK 189
                 8899999999999999986 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   1.2e-07   0.00018      12     133 ..      21     149 ..      10     186 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.2e-07
  Methyltransf_23  12 klerllpk...lraggrvLdiGcGtGillevlren..gf...svt.gvDlspeaveiae........kakkaqkdqfdeqeaaepqgkfdlIvl 88 
                       ++ +l++     ++  ++d+Gc  G+ +++++++  ++   s+t g+D+s + v++a+        +            + ++ +gk d++++
       EPA06873.1  21 IINYILEYannSTKKFVIIDVGCSNGSAMKYAQTYlqQKnieSFTiGIDISKNVVDEARknldqfinENV---------LNVDNCAGKADIVIC 105
                      455555443213344499**************55422444456667**********99764444443333.........45555669******* PP

  Methyltransf_23  89 revlehvp.d.ppellrqiatllkpgGylllseplaslkedrllldw 133
                      +     v+ d     +r+  + lk +G l+  +    + e+ +ll+w
       EPA06873.1 106 SKAAIFVEgDvRCQIIRKCSEFLKNDGILITDVD---CFEKTKLLEW 149
                      *999999986456999999999999998855443...5555555555 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.5     1e-06    0.0015      13      78 ..      33     102 ..      22     140 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1e-06
  Methyltransf_18  13 ekgsrvaDiGtDHg....ylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGlekl 78 
                      +k+ +++D+G+  g    y + yl ++++ +  i +Di+++ +++a++n+++   e+ ++v  + G + +
       EPA06873.1  33 TKKFVIIDVGCSNGsamkYAQTYLQQKNIESFTIGIDISKNVVDEARKNLDQFINENVLNVDNCAGKADI 102
                      556699******99777778999****************************9988888777777776555 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.2     7e-06      0.01       2      55 ..      35      92 ..      34     105 .. 0.78
   2 ?   -1.9   0.0       1.3     2e+03     100     121 ..     121     142 ..     117     150 .. 0.78
   3 ?   -0.4   0.0      0.47     7e+02     112     130 ..     188     206 ..     168     220 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 7e-06
                    -EEEEEET-TTSHHH....HHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEE CS
  Methyltransf_4  2 apvvleiGcGkGefl....valAkknPdknflGiEirvkvvakvlkkiealelkNlri 55
                    + v++++Gc +G+++      l +kn +   +Gi+i+++vv+++ k+ ++   +N++ 
      EPA06873.1 35 KFVIIDVGCSNGSAMkyaqTYLQQKNIESFTIGIDISKNVVDEARKNLDQFINENVLN 92
                    5689********98743334578999******************99998875555443 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.3
                     HHHHHHHEEEEEEEEEEESHHH CS
  Methyltransf_4 100 lkelarvLkkgGvlelaTDvee 121
                     + +  + Lk+ G+l +  D +e
      EPA06873.1 121 IRKCSEFLKNDGILITDVDCFE 142
                     5677889999999998888665 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.47
                     EEEEEESHHHHHHHHHHHH CS
  Methyltransf_4 112 vlelaTDveeyaeemlkvl 130
                         +TD   yae++l+  
      EPA06873.1 188 KKMYKTDAATYAEKILSAW 206
                     4456899999999888765 PP

>> RnlB_antitoxin  Antitoxin to bacterial toxin RNase LS or RnlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.8   2.1e-05     0.032      23      83 ..      28      89 ..      16      96 .. 0.77
   2 ?   -3.2   0.0       7.5   1.1e+04      68      83 ..     116     131 ..     107     137 .. 0.66
   3 ?   -0.0   0.0      0.75   1.1e+03      68      93 ..     179     204 ..     169     205 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.1e-05
  RnlB_antitoxin 23 LqkneakgevlfDlllsnGleenRFikldfdggkfnrnslkv..vskvdeelleasskflakn 83
                     ++n +k+ v++D+ +snG +  ++++++++++++   ++ +   ++v +e ++  ++f  +n
      EPA06873.1 28 YANNSTKKFVIIDVGCSNGSA-MKYAQTYLQQKNIESFTIGIdiSKNVVDEARKNLDQFINEN 89
                    467799**************9.9**********999877643214447777777777776666 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 7.5
  RnlB_antitoxin  68 vdeelleasskflakn 83 
                     v+ ++  + s+fl+++
      EPA06873.1 116 VRCQIIRKCSEFLKND 131
                     5556666777777766 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.75
  RnlB_antitoxin  68 vdeelleasskflaknpellensvLs 93 
                     + ++ ++ ++k+++++     + +Ls
      EPA06873.1 179 IHTRFRKSMKKMYKTDAATYAEKILS 204
                     77889999999999999888888887 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   1.4e-05     0.021       8      74 ..      17      85 ..      13     106 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.4e-05
  Methyltransf_32  8 rlaelvakllkelakesgaltvvDvGaGkgYLsfvlal..kekeyklkvvgidakeelvekaekraekl 74
                     +l  +++ +l+ ++++++++ ++DvG+ +g      +   ++k+ +   +gid+++++v++a+k  +++
       EPA06873.1 17 ELTGIINYILEYANNSTKKFVIIDVGCSNGSAMKYAQTylQQKNIESFTIGIDISKNVVDEARKNLDQF 85
                     577789999999999************9996655555565666789999************99876555 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.2   5.2e-05     0.078      23     103 ..      36     116 ..      13     157 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.2e-05
                 -EEEECT-TTSHHHHHHCCT.T....-SEEEEEESSSS...HHH.TTEEEECS-CCCSSHHHHHCHCHHHSSEEEEEE--S.-SS-CHH CS
        FtsJ  23 ktvvDlgaaPGgwsqvllqrlga...kgkvvavDlqpm...apl.pgvttiqgditdpetiekikealserkvdlvvsDga.pdvsgvh 103
                   ++D+g++ G+ ++++ + l++   ++  +++D+ ++   + + +  ++i+ ++++ ++           k+d+v++  a  +v+g  
  EPA06873.1  36 FVIIDVGCSNGSAMKYAQTYLQQkniESFTIGIDISKNvvdEARkNLDQFINENVLNVDNCA--------GKADIVICSKAaIFVEGDV 116
                 3499*************99997754559999***9888787555366677799999887765........3578888775435666654 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   9.7e-05      0.15      64     128 ..      24      92 ..      18     151 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.7e-05
                 HHHHHTT.--TT-EEEEES-TTSHHHHHHHHHHCTTC...EEEEEESBHHHHHHHHHHHHHCTTCSEEE CS
        PCMT  64 lalelle.lkkgarvLevGsGsGyltavlarlvgekg...rvvsierikelveeakrnlkkldlenviv 128
                 ++le+ +  +k+  +++vG+  G       +++++k      ++i+ +k++v+ea++nl +   env  
  EPA06873.1  24 YILEYANnSTKKFVIIDVGCSNGSAMKYAQTYLQQKNiesFTIGIDISKNVVDEARKNLDQFINENVLN 92 
                 5677776667777899****9998888888888877655579******************999988753 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       897  (0.0500307); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 1451.22
//
Query:       EPA06874.1  [L=404]
Description: eukaryotic DNA topoisomerase I, catalytic core, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.9e-70  236.1  11.2    2.9e-70  236.1  11.2    2.1  2  Topoisom_I    Eukaryotic DNA topoisomerase I, catalytic core
    7.1e-22   77.1   1.5    7.1e-22   77.1   1.5    3.5  5  Topo_C_assoc  C-terminal topoisomerase domain
    4.3e-17   62.3   0.4    4.3e-17   62.3   0.4    3.2  3  Topoisom_I_N  Eukaryotic DNA topoisomerase I, DNA binding fra
  ------ inclusion threshold ------
       0.12   11.9   4.9        0.1   12.1   1.2    2.3  2  MS_channel    Mechanosensitive ion channel
       0.28   11.4   3.1       0.47   10.7   1.1    2.2  2  DUF3135       Protein of unknown function (DUF3135)
        2.7    8.5   8.0        2.8    8.5   0.1    3.4  4  PhoU          PhoU domain


Domain annotation for each model (and alignments):
>> Topoisom_I  Eukaryotic DNA topoisomerase I, catalytic core
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  236.1  11.2   9.8e-74   2.9e-70       3     225 ..      65     286 ..      63     293 .. 0.96
   2 ?   -2.3   6.6      0.71   2.1e+03       6      33 ..     303     330 ..     296     344 .. 0.61

  Alignments for each domain:
  == domain 1  score: 236.1 bits;  conditional E-value: 9.8e-74
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-S-HHHHHHHHHHHHHHHH---------TTS-----GGG-BGGGEEE-TT.SEEEEEEE-GGG-EE CS
  Topoisom_I   3 klkgekdfkKYekarkLkkvvekiredykkklkskeilekqlatavylidklaLrvGnekeeeeadtvGccsLrvehvklsekektitldFlGKdsiry 101
                  lk+ +d++KYeka kL+k +eki+e++ k++k+k+ +  ++at++yli ++a+rvG+ek+ +eadtvG ++Lr eh++++++   i++dFlGKds+r+
  EPA06874.1  65 GLKQDRDKAKYEKAVKLSKEIEKIKERIVKDMKNKDPKISRIATVCYLIYRTAMRVGDEKDPDEADTVGATTLRKEHINITDD--AIEFDFLGKDSVRW 161
                 68*****************************************************************************8876..************** PP

                 EEEEE--H...HHHHHHHHHHTT--TTSBTTTT--HHHHHHHHTTTSTT--TTHHHHHHHHHHHHHHHHH..--------TTHHHHHHHHHHHHHHHHH CS
  Topoisom_I 102 fntvkvdk...qvyknlkifckkkkkgeevFdkintsklNkyLkelmegLsAKvFRTYnASitlqeqLkklekievdesnvaekikayneAnreVAilc 197
                 ++tvk +    q  +nlk+++++kk+++e+F++i+++++N+y +++++gL+AKvFRTY A++++++ Lk+    +v++++ +ek+ + + An e Ai+c
  EPA06874.1 162 QETVKAEGndkQFQENLKKLIQNKKPKDEIFEDITSRHVNAYYSSIVSGLTAKVFRTYLATTMVKNYLKEH--DNVKSKTPNEKLYHAKLANLEAAIMC 258
                 *****9755559999*******************************************************5..799999******************** PP

                 T-EE-XXXXXXXXXXXXXXXXXXXXXXX CS
  Topoisom_I 198 nhqrsvpkqheksmeklkkkiealkedi 225
                 nh+r++pk+ e+++e+ +++++++++d 
  EPA06874.1 259 NHKRTIPKTYEDTLENKRQTLKNISKDQ 286
                 **********************999986 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.71
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
  Topoisom_I   6 gekdfkKYekarkLkkvvekiredykkk 33 
                  + d +K +ka+k+k+  e+i+++ +k+
  EPA06874.1 303 AKTDAQKKNKAKKIKTLNEQIKKQKEKH 330
                 4556666666666666666666655544 PP

>> Topo_C_assoc  C-terminal topoisomerase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.6   4.9e+03      34      51 ..     224     246 ..     212     251 .. 0.53
   2 ?   -1.3   0.1      0.74   2.2e+03      39      57 ..     257     275 ..     250     293 .. 0.71
   3 ?   -2.5   0.4       1.7   5.2e+03       4      19 ..     298     313 ..     296     319 .. 0.58
   4 ?   -2.8   0.7       2.1   6.4e+03       2      16 ..     314     328 ..     310     330 .. 0.73
   5 !   77.1   1.5   2.4e-25   7.1e-22       1      68 [.     331     398 ..     331     399 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.6
  Topo_C_assoc  34 itvawckkhd.....vpiekiFs 51 
                   ++  + k+hd      p ek++ 
    EPA06874.1 224 MVKNYLKEHDnvkskTPNEKLYH 246
                   55555555542111145566665 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.74
  Topo_C_assoc  39 ckkhdvpiekiFsktlleK 57 
                   + +h+  i k +  tl +K
    EPA06874.1 257 MCNHKRTIPKTYEDTLENK 275
                   5567778899999999988 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 1.7
  Topo_C_assoc   4 ikklklqlkdkeenke 19 
                    ++++ + + +++nk 
    EPA06874.1 298 AESMEAKTDAQKKNKA 313
                   5566666666666654 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 2.1
  Topo_C_assoc   2 ekikklklqlkdkee 16 
                   +kik+l+ q+k+++e
    EPA06874.1 314 KKIKTLNEQIKKQKE 328
                   678888888877665 PP

  == domain 5  score: 77.1 bits;  conditional E-value: 2.4e-25
  Topo_C_assoc   1 kekikklklqlkdkeenkevaLgtSkinYlDPRitvawckkhdvpiekiFsktlleKfaWAmevdedf 68 
                   ke+++kl+lq++  e++k+++LgtS  nY+DPRi  aw+++++v++ek+++++l++Kf W+ + + ++
    EPA06874.1 331 KERVEKLQLQIDLSEKTKDYNLGTSLRNYIDPRIFKAWTDEVGVEWEKLYTAALQKKFLWVQNEKVSW 398
                   69***********************************************************9988777 PP

>> Topoisom_I_N  Eukaryotic DNA topoisomerase I, DNA binding fragment
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.3   0.4   1.4e-20   4.3e-17     150     213 .]       1      60 [.       1      60 [. 0.98
   2 ?   -1.1   0.3      0.37   1.1e+03      62      93 ..     172     204 ..     158     257 .. 0.57
   3 ?   -5.8  13.4         6   1.8e+04      70     121 ..     281     333 ..     223     349 .. 0.53

  Alignments for each domain:
  == domain 1  score: 62.3 bits;  conditional E-value: 1.4e-20
                   T-TTTT-EE----GGG-EEE--SSS-----STT---SEEE--TT---SEEEE-TTT--EEEEEE CS
  Topoisom_I_N 150 ehpktGklkkrvlpedvtiNigkdakvPeppaghkWkevvhdntvtwlaswkeningqvkyvmL 213
                   +hp +G++k r++++dvt+N+gk+akvPe     +W+++vhdn+++wla w++ ++++ kyv+L
    EPA06874.1   1 DHPLRGRWKPRITAKDVTLNLGKEAKVPEG----NWGKIVHDNDSMWLAGWTDYLTEKRKYVWL 60 
                   5****************************8....9***************************98 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.37
                   HHHHHHHHHHHHHTT-.---GGGEE-HHHHHHH CS
  Topoisom_I_N  62 knffkdfkkvlkekek.ikelekcdFskikeyl 93 
                   k f +++kk++++k+   + +e++  +++++y+
    EPA06874.1 172 KQFQENLKKLIQNKKPkDEIFEDITSRHVNAYY 204
                   445555555553333313334444444444443 PP

  == domain 3  score: -5.8 bits;  conditional E-value: 6
                   HHHHHTT-...---GGGEE-HHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHH CS
  Topoisom_I_N  70 kvlkekek...ikelekcdFskikeylekekekkkaltkeekkklkeekekleek 121
                   ++ k++      + l+k +  + k+  +++k++k ++ k   +++k++kek +e+
    EPA06874.1 281 NISKDQPWtktLEALKKAESMEAKT--DAQKKNKAKKIKTLNEQIKKQKEKHKER 333
                   2222222222234444544444444..4444444444444444555555554443 PP

>> MS_channel  Mechanosensitive ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1      0.11   3.1e+02     114     156 ..      56      98 ..      51     145 .. 0.74
   2 ?   12.1   1.2   3.4e-05       0.1      87     198 ..     230     367 ..     209     375 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.11
                 SEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-TTS-E CS
  MS_channel 114 gtrrikvsigvtyssdvkklekvleelkealkekpevlkdkel 156
                 +++++  + g++ + d  k ek+++  ke+ k k+++ kd++ 
  EPA06874.1  56 KYVWLADTAGLKQDRDKAKYEKAVKLSKEIEKIKERIVKDMKN 98 
                 5666666777888888889999999999998888888885543 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 3.4e-05
                 EETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-T..............................TS- CS
  MS_channel  87 rtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlk..............................dke 155
                 +++d+     Pn++l  ++ +Nl        +k++i  ty+     le+ +++lk++ k +p++++                              + +
  EPA06874.1 230 KEHDNVKSKTPNEKLYHAKLANLEA-AIMCNHKRTIPKTYEDT---LENKRQTLKNISKDQPWTKTlealkkaesmeaktdaqkknkakkiktlneQIK 324
                 5789999999***************.999**************...****************9999999999998888888888888888888877444 PP

                 EEEEEEEE-SSSEEEEEEEEEET...TTHHHHHHHHHHHHHHH CS
  MS_channel 156 llvvldefgdsslnfevrvfvktvvpeeylsvqseinlrikki 198
                  ++  ++   + l++++    kt +++  +s++++i  ri+k+
  EPA06874.1 325 KQKEKHKERVEKLQLQIDLSEKTKDYNLGTSLRNYIDPRIFKA 367
                 4444555555666666666666666777777777777777665 PP

>> DUF3135  Protein of unknown function (DUF3135)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1      0.55   1.6e+03       7      41 ..     278     314 ..     275     317 .. 0.80
   2 ?   10.7   1.1   0.00016      0.47      25      52 ..     317     344 ..     312     354 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.55
     DUF3135   7 eLvaLakedP..ealealrqelieelIesapeemqrr 41 
                 +L+++ k++P  ++leal++   +e+ ++a+++++++
  EPA06874.1 278 TLKNISKDQPwtKTLEALKKAESMEAKTDAQKKNKAK 314
                 577777777755689*****99999999998888765 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00016
     DUF3135  25 elieelIesapeemqrrLrglqfqiDmq 52 
                 +  +e I++ +e++++r ++lq qiD+ 
  EPA06874.1 317 KTLNEQIKKQKEKHKERVEKLQLQIDLS 344
                 566789********************86 PP

>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.1   0.00093       2.8      22      80 ..      70     122 ..      59     123 .. 0.77
   2 ?    0.4   0.0      0.32   9.5e+02      25      52 ..     176     203 ..     162     229 .. 0.72
   3 ?   -1.5   0.0       1.2   3.5e+03      43      64 ..     273     294 ..     266     301 .. 0.77
   4 ?    0.7   1.6      0.25   7.4e+02      23      68 ..     309     356 ..     289     361 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00093
                 T-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHHH CS
        PhoU  22 kdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERigD 80 
                 +d+   ++ +++ +ei+++ ++i    ++ +++++p+ +  r+++ +  i+r   R+gD
  EPA06874.1  70 RDKAKYEKAVKLSKEIEKIKERI----VKDMKNKDPKIS--RIATVCYLIYRTAMRVGD 122
                 45566688888888888886666....777888888865..89999************9 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.32
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
        PhoU  25 elarevierddeidrlekeierslleal 52 
                 e ++++i++ +  d+++++i+ ++++a+
  EPA06874.1 176 ENLKKLIQNKKPKDEIFEDITSRHVNAY 203
                 6677788888888888888888877776 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.2
                 HHHHHHHHHHHHHGG-SHHHHH CS
        PhoU  43 eiersllealakrqplaedlre 64 
                 e++r+ l+ ++k+qp+++ l++
  EPA06874.1 273 ENKRQTLKNISKDQPWTKTLEA 294
                 5678899999999999986665 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.25
                 -HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SH...HHHHHHHH CS
        PhoU  23 dtelarevierddeidrlekeiersllealakrqplae...dlrellsl 68 
                  ++ a+++  + ++i +  ++ +++ +e+l  +  l+e   d++  +sl
  EPA06874.1 309 KKNKAKKIKTLNEQIKKQKEKHKER-VEKLQLQIDLSEktkDYNLGTSL 356
                 2478888888888888888888888.66664433333333366666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3783  (0.210999); expected 358.6 (0.02)
Passed bias filter:                      707  (0.0394333); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.81u 0.36s 00:00:01.17 Elapsed: 00:00:00.52
# Mc/sec: 2319.88
//
Query:       EPA06875.1  [L=401]
Description: hypothetical protein BG20_I2202 [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2687.05
//
Query:       EPA06876.1  [L=68]
Description: hypothetical protein BG20_I2201, partial [Candidatus Nitrosoarchaeum limnia BG20]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0087   15.7   1.0     0.0093   15.6   1.0    1.0  1  Filament  Intermediate filament protein


Domain annotation for each model (and alignments):
>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   1.0   5.2e-07    0.0093     157     218 ..       6      67 ..       3      68 .] 0.93

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.2e-07
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-HHHH CS
    Filament 157 vevdaarkldLteilkeiraqyeelaeknreeaeewykskleelqeaaeknsealrsakeei 218
                 +  d++++++++e  +e+ + y++   kn +e+ + y++ +++++e+a++  e ++s+++ +
  EPA06876.1   6 IKHDDSKQIEVQELQNELESTYNNGSTKNPSEIFQKYSNEIKTIREKAKNVFEVVSSTRNTV 67 
                 67899*********************************************999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1577  (0.0879581); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 429.37
//
[ok]
